From f94144ea1b9604c06c9831c96311c94422b3179a Mon Sep 17 00:00:00 2001 From: ChayaSt Date: Wed, 1 Mar 2017 17:50:23 -0500 Subject: [PATCH 1/2] migrated from openmm --- charmm/README.md | 23 + charmm/charmm36.yaml | 192 + charmm/convert_charmm.py | 68 + charmm/ffxml/charmm36.xml | 107825 ++++++++++++ charmm/ffxml/water.xml | 39 + charmm/toppar/00toppar_file_format.txt | 299 + charmm/toppar/ace/acepar19.inp | 35 + charmm/toppar/ace/acepar22_prot.inp | 58 + charmm/toppar/ace/acepar27_na.inp | 53 + charmm/toppar/cheq/par_all30_cheq_prot.inp | 2625 + charmm/toppar/cheq/top_all30_cheq_prot.inp | 1662 + charmm/toppar/drude/00readme | 259 + charmm/toppar/drude/drude_aug15.doc | 1 + charmm/toppar/drude/drude_toppar_2015_7.tgz | Bin 0 -> 427170 bytes .../toppar/drude/drude_toppar_2015_7/00readme | 257 + .../drude/drude_toppar_2015_7/drude_aug15.doc | 1 + .../drude_toppar_2015_7/test/diff_svn.cmd | 7 + .../test/run_test_drude.cmd | 17 + .../test/test_drude_all.ene | 832 + .../test/test_drude_all_2013c.inp | 49 + .../test/test_drude_all_2013c.out | 126317 +++++++++++++++ .../test/test_drude_carbohydrate.str | 168 + .../test/test_drude_ions.str | 1249 + .../test/test_drude_lipid.str | 86 + .../test/test_drude_master_protein.str | 420 + .../test/test_drude_model.str | 233 + .../test/test_drude_nucleic_acids.str | 242 + .../test/test_drude_nucleic_acids_no_rna.str | 245 + .../drude_toppar_2015_7/toppar_defs_2013c.str | 20 + .../toppar_drude_carbohydrate_2013c.str | 5918 + .../toppar_drude_lipid_2013c.str | 1758 + .../toppar_drude_master_protein_2013c.str | 7183 + .../toppar_drude_model_2013c.str | 4563 + ...toppar_drude_nucleic_acid_2013c_no_rna.str | 2768 + charmm/toppar/drude/positive_drude/00readme | 9 + .../positive_drude/data/swm4_ion_bro.dat | 5 + .../positive_drude/data/swm4_ion_ces.dat | 5 + .../positive_drude/data/swm4_ion_cla.dat | 5 + .../positive_drude/data/swm4_ion_flu.dat | 5 + .../positive_drude/data/swm4_ion_iod.dat | 5 + .../positive_drude/data/swm4_ion_lit.dat | 5 + .../positive_drude/data/swm4_ion_pot.dat | 5 + .../positive_drude/data/swm4_ion_rub.dat | 5 + .../positive_drude/data/swm4_ion_sod.dat | 5 + .../positive_drude/data/swm4_ion_swm4.dat | 3 + .../positive_drude/positive_drude_test.inp | 144 + .../positive_drude_test_temp.inp | 157 + .../positive_drude_test_temp.out | 615 + .../toppar/drude/positive_drude/run_test.cmd | 14 + .../toppar_drude_positive_swm4_ions.str | 188 + charmm/toppar/gbsw/00readme | 2 + charmm/toppar/gbsw/par_all22_prot_gbsw.inp | 3287 + charmm/toppar/gbsw/radius_gbsw.str | 178 + charmm/toppar/metals/CHARMM_METAL.tgz | Bin 0 -> 1783214 bytes charmm/toppar/non_charmm/00readme | 72 + .../gromacs/charmm36-jul2014.ff.tgz | Bin 0 -> 311697 bytes charmm/toppar/non_charmm/par_amber_98.inp | 505 + .../toppar/non_charmm/par_amber_cornell.inp | 490 + charmm/toppar/non_charmm/par_bms_dec03.inp | 684 + charmm/toppar/non_charmm/par_opls_aa.inp | 2167 + charmm/toppar/non_charmm/par_opls_aam.inp | 2369 + charmm/toppar/non_charmm/par_opls_ligand.inp | 2365 + charmm/toppar/non_charmm/parm14sb_all.prm | 1594 + charmm/toppar/non_charmm/parm14sb_all.rtf | 4269 + .../toppar/non_charmm/top_amber_cornell.inp | 4050 + charmm/toppar/non_charmm/top_bms_dec03.inp | 1280 + charmm/toppar/non_charmm/top_opls_aa.inp | 1583 + charmm/toppar/non_charmm/top_opls_aam.inp | 1638 + .../non_charmm/toppar_chloroform_dh.str | 70 + .../non_charmm/toppar_water_ions_spc.str | 300 + .../non_charmm/toppar_water_ions_spc_e.str | 300 + .../toppar_water_ions_tip3p_pme_b.str | 295 + .../toppar_water_ions_tip3p_pme_f.str | 297 + .../non_charmm/toppar_water_ions_tip4p.str | 309 + .../toppar_water_ions_tip4p_2005.str | 306 + .../non_charmm/toppar_water_ions_tip4p_ew.str | 307 + .../non_charmm/toppar_water_ions_tip5p.str | 306 + .../non_charmm/toppar_water_ions_tip5p_ew.str | 306 + charmm/toppar/par_all22_prot.prm | 3125 + charmm/toppar/par_all35_ethers.prm | 254 + charmm/toppar/par_all36_carb.prm | 2628 + charmm/toppar/par_all36_cgenff.prm | 6570 + charmm/toppar/par_all36_lipid.prm | 532 + charmm/toppar/par_all36_na.prm | 1253 + charmm/toppar/par_all36_prot.prm | 3399 + charmm/toppar/par_hbond.inp | 88 + charmm/toppar/param19.inp | 438 + charmm/toppar/rush/par_rush_058.inp | 2219 + charmm/toppar/rush/par_rush_058_a.cmap | 925 + charmm/toppar/rush/top_rush_058.inp | 1810 + charmm/toppar/silicates/00README | 78 + charmm/toppar/silicates/code/cell.f | 40 + charmm/toppar/silicates/code/compile.txt | 3 + charmm/toppar/silicates/code/crystal.dat | 7 + charmm/toppar/silicates/code/crystal.f | 133 + charmm/toppar/silicates/code/input.xyz | 42 + charmm/toppar/silicates/code/patches.dat | 219 + charmm/toppar/silicates/code/patchfind.f | 668 + charmm/toppar/silicates/code/patchfind.x | Bin 0 -> 113019 bytes charmm/toppar/silicates/crystal.dat | 7 + charmm/toppar/silicates/crystal.img | 106 + charmm/toppar/silicates/image_patch.str | 94 + charmm/toppar/silicates/input.xyz | 42 + charmm/toppar/silicates/params.str | 75 + charmm/toppar/silicates/patches.dat | 256 + charmm/toppar/silicates/quartz_init.pdb | 85 + charmm/toppar/silicates/supp_mat_oct05.tar | Bin 0 -> 1372160 bytes charmm/toppar/silicates/test.inp | 252 + charmm/toppar/silicates/test.log | 2248 + charmm/toppar/silicates/test.out | 13316 ++ charmm/toppar/silicates/test_opt.crd | 1604 + charmm/toppar/silicates/test_opt.pdb | 1604 + charmm/toppar/silicates/test_opt.psf | 6169 + .../toppar/silicates/toppar/par_silicates.inp | 153 + .../toppar/silicates/toppar/top_silicates.inp | 371 + .../carb/.toppar_all36_carb_model.str.swp | Bin 0 -> 16384 bytes .../carb/toppar_all36_carb_glycolipid.str | 3692 + .../carb/toppar_all36_carb_glycopeptide.str | 485 + .../stream/carb/toppar_all36_carb_model.str | 2252 + .../lipid/toppar_all36_lipid_bacterial.str | 5474 + .../lipid/toppar_all36_lipid_cardiolipin.str | 14152 ++ .../lipid/toppar_all36_lipid_cholesterol.str | 1584 + .../lipid/toppar_all36_lipid_detergent.str | 2336 + .../lipid/toppar_all36_lipid_glycolipid.str | 380 + .../lipid/toppar_all36_lipid_inositol.str | 26045 +++ .../stream/lipid/toppar_all36_lipid_list.str | 66 + .../stream/lipid/toppar_all36_lipid_llo.str | 2148 + .../toppar_all36_lipid_miscellaneous.str | 17105 ++ .../stream/lipid/toppar_all36_lipid_model.str | 2392 + .../stream/lipid/toppar_all36_lipid_prot.str | 1191 + .../lipid/toppar_all36_lipid_sphingo.str | 6247 + .../stream/lipid/toppar_all36_lipid_yeast.str | 2516 + charmm/toppar/stream/misc/toppar_amines.str | 231 + .../stream/misc/toppar_dum_noble_gases.str | 62 + charmm/toppar/stream/misc/toppar_hbond.str | 38 + charmm/toppar/stream/misc/toppar_ions_won.str | 575 + .../stream/na/toppar_all36_na_model.str | 3438 + .../na/toppar_all36_na_modifications.str | 4959 + .../stream/na/toppar_all36_na_nad_ppi.str | 2602 + .../na/toppar_all36_na_reactive_rna.str | 1066 + .../.toppar_all36_prot_na_combined.str.swp | Bin 0 -> 16384 bytes .../prot/toppar_all36_prot_aldehydes.str | 242 + .../stream/prot/toppar_all36_prot_arg0.str | 446 + .../prot/toppar_all36_prot_d_aminoacids.str | 2541 + .../prot/toppar_all36_prot_fluoro_alkanes.str | 285 + .../stream/prot/toppar_all36_prot_heme.str | 602 + .../stream/prot/toppar_all36_prot_model.str | 2338 + .../prot/toppar_all36_prot_modify_res.str | 1575 + .../prot/toppar_all36_prot_na_combined.str | 1690 + .../prot/toppar_all36_prot_pyridines.str | 1166 + .../stream/prot/toppar_all36_prot_retinol.str | 1872 + .../tamdfff/par_all22_prot_tadcmap.ahbb4.inp | 4970 + .../toppar/tamdfff/par_tadmap.chi1.ahbb4.inp | 25518 +++ .../tamdfff/top_all22_prot_cmap.ahbb4.inp | 2232 + charmm/toppar/top_all22_prot.rtf | 1682 + charmm/toppar/top_all35_ethers.rtf | 1213 + charmm/toppar/top_all36_carb.rtf | 6028 + charmm/toppar/top_all36_cgenff.rtf | 30726 ++++ charmm/toppar/top_all36_lipid.rtf | 11768 ++ charmm/toppar/top_all36_na.rtf | 857 + charmm/toppar/top_all36_prot.rtf | 1777 + charmm/toppar/toph19.inp | 1319 + charmm/toppar/toppar_all.history | 872 + charmm/toppar/toppar_water_ions.str | 330 + 164 files changed, 549874 insertions(+) create mode 100644 charmm/README.md create mode 100644 charmm/charmm36.yaml create mode 100644 charmm/convert_charmm.py create mode 100644 charmm/ffxml/charmm36.xml create mode 100644 charmm/ffxml/water.xml create mode 100644 charmm/toppar/00toppar_file_format.txt create mode 100644 charmm/toppar/ace/acepar19.inp create mode 100644 charmm/toppar/ace/acepar22_prot.inp create mode 100644 charmm/toppar/ace/acepar27_na.inp create mode 100755 charmm/toppar/cheq/par_all30_cheq_prot.inp create mode 100755 charmm/toppar/cheq/top_all30_cheq_prot.inp create mode 100644 charmm/toppar/drude/00readme create mode 100644 charmm/toppar/drude/drude_aug15.doc create mode 100644 charmm/toppar/drude/drude_toppar_2015_7.tgz create mode 100644 charmm/toppar/drude/drude_toppar_2015_7/00readme create mode 100644 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create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_arg0.str create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_d_aminoacids.str create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_fluoro_alkanes.str create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_heme.str create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_model.str create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_modify_res.str create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_na_combined.str create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_pyridines.str create mode 100644 charmm/toppar/stream/prot/toppar_all36_prot_retinol.str create mode 100755 charmm/toppar/tamdfff/par_all22_prot_tadcmap.ahbb4.inp create mode 100755 charmm/toppar/tamdfff/par_tadmap.chi1.ahbb4.inp create mode 100755 charmm/toppar/tamdfff/top_all22_prot_cmap.ahbb4.inp create mode 100644 charmm/toppar/top_all22_prot.rtf create mode 100644 charmm/toppar/top_all35_ethers.rtf create mode 100644 charmm/toppar/top_all36_carb.rtf create mode 100644 charmm/toppar/top_all36_cgenff.rtf create mode 100644 charmm/toppar/top_all36_lipid.rtf create mode 100644 charmm/toppar/top_all36_na.rtf create mode 100644 charmm/toppar/top_all36_prot.rtf create mode 100644 charmm/toppar/toph19.inp create mode 100755 charmm/toppar/toppar_all.history create mode 100644 charmm/toppar/toppar_water_ions.str diff --git a/charmm/README.md b/charmm/README.md new file mode 100644 index 00000000..9bb21a21 --- /dev/null +++ b/charmm/README.md @@ -0,0 +1,23 @@ +This directory contains files and scripts needed to convert the CHARMM forcefield to ffxml files + +## Manifest +* ```toppar/``` - All files taken and unzipped from (http://mackerell.umaryland.edu/charmm_ff.html) Jan 2016. +* ```ffxml/``` - charmm36 ffxml +* ```charmm36.yaml``` - yaml file needed for convert_charmm.py script. Specifies files to include and exclude. +* ```convert_charmm.py``` - script to convert charmm top and par files to ffxml. + +### Dependencies +* ParmEd + +--- + +Notes on files that were excluded from conversion. + +There are two glycolipid stream files with duplicate dihedrals with different values. According to discussion with +Alex MacKerell, the carb glycolipid file should be used so the lipid glycolipid stream file was excluded. + +```toppar_all36_prot_aldehydes.str``` and ```toppar_all36_na_modifications.str``` have different values for the angle of +atom types O CD CT2. These files should not be used in the same system so both were excluded. A new atom type is needed +to correct this. If needed, CGenFF can be used for aldehydes or the user can convert these files at their own risk. + + diff --git a/charmm/charmm36.yaml b/charmm/charmm36.yaml new file mode 100644 index 00000000..a3c350b3 --- /dev/null +++ b/charmm/charmm36.yaml @@ -0,0 +1,192 @@ +# for CharMM36 --> OpenMM ffxml conversion +# Author: Chaya D. Stern, choderalab +# The include files structure is based on the file structure of unzipped toppar_c36_aug15.tgz +# excluded files include files that need to be excluded from the conversion because of duplicate parameters with different +# values. In addition, toppar_hbond.str and toppar_all36_lipid_list.str are not standard stream files. + +- sourcePackage: charmm36 + sourcePackageVersion: toppar_c36_aug15.tgz +- Source: + include: + - toppar/top_all36_carb.rtf + - toppar/par_all36_carb.prm + - toppar/top_all36_cgenff.rtf + - toppar/par_all36_cgenff.prm + - toppar/top_all36_lipid.rtf + - toppar/par_all36_lipid.prm + - toppar/top_all36_na.rtf + - toppar/par_all36_na.prm + - toppar/top_all36_prot.rtf + - toppar/par_all36_prot.prm + stream: + - toppar/toppar_water_ions.str + - toppar/stream/carb/*.str + - toppar/stream/lipid/*.str + - toppar/stream/prot/*.str + - toppar/stream/na/*.str + - toppar/stream/misc/*.str + exclude: + - toppar/stream/lipid/toppar_all36_lipid_list.str + - toppar/stream/lipid/toppar_all36_lipid_glycolipid.str + - toppar/stream/prot/toppar_all36_prot_aldehydes.str + - toppar/stream/na/toppar_all36_na_modifications.str + - toppar/stream/misc/toppar_hbond.str + References: + protein: + - >- + Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P. Mittal, J., Feig, M. and MacKerell, A.D., Jr. Optimization + of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and + sidechain chi1 and chi2 dihedral angles. JCTC, 8: 3257-3273, 2013, PMC3549273 + - >- + MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved treatment of the protein backbone in empirical + force fields," Journal of the American Chemical Society, 126: 698-699, 2004 + - >- + MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; + Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, C.; Michnick, S.; + Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, + J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular + modeling and dynamics Studies of proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. + - arginine: + - >- + Li, L., Vorobyov, I.V., MacKerell, Jr., A.D., Allen, T.W., "Is arginine charged in a membrane?" Biophysical + Journal, 94: L11-L13, 2008, PMCID: PMC2157258 + - fluoroalkanes: + - >- + Chen, I.-J., Yin, D. and MacKerell, Jr., A.D., "Combined Ab initio/Empirical Approach for Optimization of + Lennard-Jones Parameters for Polar-Neutral Compounds," Journal of Computational Chemistry, 2002, 23:199-213. + - phosphotyorosine: + - >- + Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. Structural Characterization of the + Phosphotyrosine Binding Region of a High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics + Simulation and Chemical Shift Calculations. Journal of the American Chemical Society, 1996, 118: 11265-11277. + - pyridines: + - >- + Yin, D., Ph.D. Thesis, "Parameterization for Empirical Force Field Calculations and A Theoretical Study of + Membrane Permeability of Pyridine Derivative," Department of Pharmaceutical Sciences, School of Pharmacy, + University of Maryland, 1997 + carbohydrates: + - pyranose monosaccharides: + - >- + Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M., Pastor, R.W., MacKerell, Jr., A.D. + "Additive empirical force field for hexopyranose monosaccharides," Journal of Computational Chemistry, 29: + 2543-2564, 2008. PMID: 18470966 + - linear sugars inositol sugar alcohols: + - >- + Hatcher, E., Guvench, O., and MacKerell, Jr., A.D., "CHARMM Additive All-Atom Force Field for Acyclic + Polyalcohols, Acyclic Carbohydrates and Inositol," Journal of Chemical Theory and Computation, 5: 1315-1327, + 2009, DOI: 10.1021/ct9000608. + - hexopyranose glycosidic linkages: + - >- + Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell, Jr., A. D. "Additive Empirical CHARMM + Force Field for glycosyl linked hexopyranoses," Journal of Chemical Theory and Computation, 5, 2353-2370, 2009, + DOI: 10.1021/ct900242e + - furanose monosaccharides: + - >- + Hatcher, E. R.; Guvench, O. and MacKerell, Jr., A.D. "CHARMM Additive All-Atom Force Field for + Aldopentofuranose Carbohydrates and Fructofuranose." Journal of Physical Chemistry B. 113:12466-76, 2009, + PMID: 19694450 + - glycosidic linkages involving furanoses: + - >- + Raman, E. P., Guvench, O., MacKerell, Jr., A.D., "CHARMM Additive All-Atom Force Field for Glycosidic Linkages + in Carbohydrates Involving Furanoses," Journal of Physical Chemistry B, 114: 12981-12994, 2010, PMID: 20845956 + - carbohydrate derivatives and glycosidic linkages for glycoproteins: + - >- + Guvench, O.; Mallajosyula, S. S.; Raman, E. P.; Hatcher, E. R.; Vanommeslaeghe, K.; Foster, T. J.; Jamison, + F. W. and MacKerell, Jr., A.D., "CHARMM additive all-atom force field for carbohydrate derivatives and its + utility in polysaccharide and carbohydrate-protein modeling," Journal of Chemical Theory and Computation 2011 + 7 (10), 3162-3180 + - O-glycan linkages: + - >- + Mallajosyula, S. S. and MacKerell, Jr., A.D., "Influence of Solvent and Intramolecular Hydrogen Bonding on the + Conformational Properties of O-Linked Glycopeptides," The Journal of Physical Chemistry B 2011 115 (38), + 11215-11229. + - phosphates and sulfates: + - >- + Mallajosyula, S. S.; Guvench, O; Hatcher E. R. and MacKerell, Jr., A.D., "CHARMM Additive All-Atom Force Field + for Phosphate and Sulfate Linked to Carbohydrates" Journal of Chemical Theory and Computation 2012 8 (2), + 759-776. + - glycolipids: + - >- + Kern, N. R., Lee, H. S., Wu, E. L., Park, S., Vanommeslaeghe, K., MacKerell, A. D., ... Im, W. (2014). Lipid- + Linked Oligosaccharides in Membrane Sample Conformations That Faciliate Binding to Oligosaccharyltransferase. + Biophysical Journal, 107(8), 1885-1895. + lipids: + - >- + Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O'Connor, Douglas J. Tobias, Carlos + Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of the CHARMM + All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843 + - PUFA modifications: + - >- + Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving the CHARMM Force Field for + Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B. 2012 ASAP http://dx.doi.org/10.1021/jp304056p + - atom nomenclature: + - >- + Sundaralingan, M., Ann. N.Y. Acad. Sci. USA, 195:324-355, 1972 + - bacterial: + - >- + Lim, J.B. and Klauda, J.B. Branching at the Iso- and Anteiso- Positions in Complex Chlamydia Membranes: A + Molecular Dynamics Study. Biochimica et Biophysica Acta (BBA) - Biomembranes 1808:323-331 (2011). + - >- + Pandit, K.R. and Klauda, J.B. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid + chain. Biochimica et Biophysica Acta (BBA) - Biomembranes 1818:1205-1210 (2012). + - cholesterol: + - >- + Lim, J.B., Rogaski, B. and Klauda, J.B.. "Update of the Cholesterol Force Field Parameters in CHARMM" 116: + 203-210 (2012). + - >- + Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. "Molecular Level Organization of Saturated and + Polyunsaturated Fatty Acids in a Phosphatidylcholine Bilayer Containing Cholesterol" Biochemistry, 43(49): + 15318-28, 2004 + - sphingomyelin: + - >- + Venable, R.M., B. Rogaski, H. Rui, A.D. MacKerell, Jr., R.W. Pastor, and J.B. Klauda. An Experimentally Validated + All-atom Force Field for Sphingomyelin. In prep. (2013). + nucleic acids: + - >- + Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D., "Impact of 2'-hydroxyl sampling on the + conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA," JCC, 32: + 1929-1943, 2011, PMC3082605 + - >- + Hart, K. Foloppe, N., Baker, C.M, Denning, E.J., Nilsson, L. and MacKerell Jr., A.D. "Optimization of the CHARMM + additive force field for DNA: Improved of the BI/BII conformational equilibrium," JCTC, 8:348-362, 2012, + PMC3285246 + - >- + Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for Nucleic Acids: 1) Parameter Optimization + Based on Small Molecule and Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104. + - >- + MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for Nucleic Acids: 2) Application to + Molecular Dynamics Simulations of DNA and RNA in Solution. JCC, 2000, 21: 105-120. + - atp adp nad+ nadh ppi: + - >- + Pavelites, J.J., Bash, P.A., Gao, J., and MacKerell, Jr., A.D. A Molecular Mechanics Force Field for NAD+, + NADH and the Pyrophosphate Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18: 221-239. + - reactive RNA: + - >- + Mayaan E, Moser A, MacKerell AD Jr, York DM. "CHARMM force field parameters for simulation of reactive + intermediates in native and thio-substituted ribozymes." J Comput Chem. 2007 Jan 30;28(2):495-507. + cgenff: + - >- + K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. + Vorobyov and A. D. Mackerell Jr., J. Comput. Chem. 2010, 31, 671-690. + - >- + W. Yu, X. He, K. Vanommeslaeghe, A. D. MacKerell Jr., J. Comput. Chem. 2012, 33, 2451-2468. + tip3p: + - >- + W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; M.L. Klein; "Comparison of simple potential functions for + simulating liquid water", J. Chem. Phys. 79 926-935 (1983). + ions: + - >- + Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for + Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063 + - zinc: + - >- + Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded + Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995) + - cations: + - >- + Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary + Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012. + amines: + - >- + Chen, I.-J., Yin, D. and MacKerell, Jr., A.D., "Combined Ab initio/Empirical Approach for Optimization of + Lennard-Jones Parameters for Polar-Neutral Compounds," Journal of Computational Chemistry, 2002, 23:199-213. \ No newline at end of file diff --git a/charmm/convert_charmm.py b/charmm/convert_charmm.py new file mode 100644 index 00000000..75cfcc84 --- /dev/null +++ b/charmm/convert_charmm.py @@ -0,0 +1,68 @@ +from parmed.charmm import CharmmParameterSet, CharmmPsfFile +from parmed import openmm +import glob +import yaml +from collections import OrderedDict +import hashlib +import os +import simtk.openmm.app as app +import simtk.openmm as mm +import simtk.unit as u + +data = yaml.safe_load(open('charmm36.yaml')) +source_pack = data[0]['sourcePackage'] +source_pack_ver = data[0]['sourcePackageVersion'] + +for entry in data[1:]: + charmm_references = entry['References'] + source_files = entry['Source'] + + +# files that should be excluded from conversion. +exclude_files = set(source_files['exclude']) + +# charmm36 main top and par files +charmm_files = source_files['include'] + +# add stream files +for files in source_files['stream']: + charmm_files.extend(glob.glob(files)) + +# exclude files from conversion +charmm_files = set(charmm_files) - exclude_files + +provenance = OrderedDict() +source = provenance['Source'] = [] +for fi in charmm_files: + source.append(OrderedDict()) + source[-1]['Source'] = fi + md5 = hashlib.md5() + with open(fi) as f: + md5.update(f.read()) + md5 = md5.hexdigest() + source[-1]['md5hash'] = md5 + source[-1]['sourcePackage'] = source_pack + source[-1]['sourcePackageVersion'] = source_pack_ver + +references = provenance['Reference'] = [] +for ff in charmm_references: + for cite in charmm_references[ff]: + references.append(OrderedDict()) + if type(cite) is dict: + for key in cite.keys(): + citation = cite[key] + references[-1]['Reference'] = citation + references[-1]['forcefield'] = ff + references[-1]['type'] = key + else: + citation = cite + references[-1]['Reference'] = citation + references[-1]['forcefield'] = ff + + +#generate recommended combination for charmm36 +params = CharmmParameterSet(*charmm_files) +params_omm = openmm.OpenMMParameterSet.from_parameterset(params) +params_omm.write('ffxml/charmm36.xml', provenance=provenance) + + diff --git a/charmm/ffxml/charmm36.xml b/charmm/ffxml/charmm36.xml new file mode 100644 index 00000000..12798757 --- /dev/null +++ b/charmm/ffxml/charmm36.xml @@ -0,0 +1,107825 @@ + + + 2016-03-22 + toppar/stream/prot/toppar_all36_prot_model.str + toppar/stream/prot/toppar_all36_prot_fluoro_alkanes.str + toppar/stream/misc/toppar_dum_noble_gases.str + toppar/stream/na/toppar_all36_na_model.str + toppar/stream/lipid/toppar_all36_lipid_cholesterol.str + toppar/top_all36_lipid.rtf + toppar/stream/prot/toppar_all36_prot_pyridines.str + toppar/par_all36_lipid.prm + toppar/stream/lipid/toppar_all36_lipid_llo.str + toppar/top_all36_na.rtf + toppar/stream/lipid/toppar_all36_lipid_cardiolipin.str + toppar/stream/carb/toppar_all36_carb_glycolipid.str + toppar/stream/lipid/toppar_all36_lipid_model.str + toppar/top_all36_prot.rtf + toppar/stream/lipid/toppar_all36_lipid_miscellaneous.str + toppar/stream/prot/toppar_all36_prot_d_aminoacids.str + toppar/top_all36_carb.rtf + toppar/stream/lipid/toppar_all36_lipid_bacterial.str + toppar/stream/lipid/toppar_all36_lipid_prot.str + toppar/stream/lipid/toppar_all36_lipid_inositol.str + toppar/stream/misc/toppar_ions_won.str + toppar/stream/carb/toppar_all36_carb_glycopeptide.str + toppar/stream/misc/toppar_amines.str + toppar/toppar_water_ions.str + toppar/stream/lipid/toppar_all36_lipid_sphingo.str + toppar/par_all36_carb.prm + toppar/stream/prot/toppar_all36_prot_retinol.str + toppar/par_all36_na.prm + toppar/top_all36_cgenff.rtf + toppar/stream/lipid/toppar_all36_lipid_yeast.str + toppar/stream/na/toppar_all36_na_nad_ppi.str + toppar/par_all36_prot.prm + toppar/stream/lipid/toppar_all36_lipid_detergent.str + toppar/stream/na/toppar_all36_na_reactive_rna.str + toppar/stream/prot/toppar_all36_prot_arg0.str + toppar/par_all36_cgenff.prm + toppar/stream/carb/toppar_all36_carb_model.str + toppar/stream/prot/toppar_all36_prot_heme.str + toppar/stream/prot/toppar_all36_prot_modify_res.str + toppar/stream/prot/toppar_all36_prot_na_combined.str + Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063 + ['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)'] + ['Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.'] + Chen, I.-J., Yin, D. and MacKerell, Jr., A.D., "Combined Ab initio/Empirical Approach for Optimization of Lennard-Jones Parameters for Polar-Neutral Compounds," Journal of Computational Chemistry, 2002, 23:199-213. + Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D., "Impact of 2'-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA," JCC, 32: 1929-1943, 2011, PMC3082605 + Hart, K. Foloppe, N., Baker, C.M, Denning, E.J., Nilsson, L. and MacKerell Jr., A.D. "Optimization of the CHARMM additive force field for DNA: Improved of the BI/BII conformational equilibrium," JCTC, 8:348-362, 2012, PMC3285246 + Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104. + MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA and RNA in Solution. JCC, 2000, 21: 105-120. + ['Pavelites, J.J., Bash, P.A., Gao, J., and MacKerell, Jr., A.D. A Molecular Mechanics Force Field for NAD+, NADH and the Pyrophosphate Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18: 221-239.'] + ['Mayaan E, Moser A, MacKerell AD Jr, York DM. "CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes." J Comput Chem. 2007 Jan 30;28(2):495-507.'] + ['Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M., Pastor, R.W., MacKerell, Jr., A.D. "Additive empirical force field for hexopyranose monosaccharides," Journal of Computational Chemistry, 29: 2543-2564, 2008. PMID: 18470966'] + ['Hatcher, E., Guvench, O., and MacKerell, Jr., A.D., "CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol," Journal of Chemical Theory and Computation, 5: 1315-1327, 2009, DOI: 10.1021/ct9000608.'] + ['Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell, Jr., A. D. "Additive Empirical CHARMM Force Field for glycosyl linked hexopyranoses," Journal of Chemical Theory and Computation, 5, 2353-2370, 2009, DOI: 10.1021/ct900242e'] + ['Hatcher, E. R.; Guvench, O. and MacKerell, Jr., A.D. "CHARMM Additive All-Atom Force Field for Aldopentofuranose Carbohydrates and Fructofuranose." Journal of Physical Chemistry B. 113:12466-76, 2009, PMID: 19694450'] + ['Raman, E. P., Guvench, O., MacKerell, Jr., A.D., "CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses," Journal of Physical Chemistry B, 114: 12981-12994, 2010, PMID: 20845956'] + ['Guvench, O.; Mallajosyula, S. S.; Raman, E. P.; Hatcher, E. R.; Vanommeslaeghe, K.; Foster, T. J.; Jamison, F. W. and MacKerell, Jr., A.D., "CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling," Journal of Chemical Theory and Computation 2011 7 (10), 3162-3180'] + ['Mallajosyula, S. S. and MacKerell, Jr., A.D., "Influence of Solvent and Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked Glycopeptides," The Journal of Physical Chemistry B 2011 115 (38), 11215-11229.'] + ['Mallajosyula, S. S.; Guvench, O; Hatcher E. R. and MacKerell, Jr., A.D., "CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates" Journal of Chemical Theory and Computation 2012 8 (2), 759-776.'] + ['Kern, N. R., Lee, H. S., Wu, E. L., Park, S., Vanommeslaeghe, K., MacKerell, A. D., ... Im, W. (2014). Lipid- Linked Oligosaccharides in Membrane Sample Conformations That Faciliate Binding to Oligosaccharyltransferase. Biophysical Journal, 107(8), 1885-1895.'] + K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov and A. D. Mackerell Jr., J. Comput. Chem. 2010, 31, 671-690. + W. Yu, X. He, K. Vanommeslaeghe, A. D. MacKerell Jr., J. Comput. Chem. 2012, 33, 2451-2468. + W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; M.L. Klein; "Comparison of simple potential functions for simulating liquid water", J. Chem. Phys. 79 926-935 (1983). + Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843 + ['Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B. 2012 ASAP http://dx.doi.org/10.1021/jp304056p'] + ['Sundaralingan, M., Ann. N.Y. Acad. Sci. USA, 195:324-355, 1972'] + ['Lim, J.B. and Klauda, J.B. Branching at the Iso- and Anteiso- Positions in Complex Chlamydia Membranes: A Molecular Dynamics Study. Biochimica et Biophysica Acta (BBA) - Biomembranes 1808:323-331 (2011).', 'Pandit, K.R. and Klauda, J.B. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. Biochimica et Biophysica Acta (BBA) - Biomembranes 1818:1205-1210 (2012).'] + ['Lim, J.B., Rogaski, B. and Klauda, J.B.. 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/charmm/ffxml/water.xml b/charmm/ffxml/water.xml new file mode 100644 index 00000000..9761fb7f --- /dev/null +++ b/charmm/ffxml/water.xml @@ -0,0 +1,39 @@ + + + 2016-02-19 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/charmm/toppar/00toppar_file_format.txt b/charmm/toppar/00toppar_file_format.txt new file mode 100644 index 00000000..5b7c2906 --- /dev/null +++ b/charmm/toppar/00toppar_file_format.txt @@ -0,0 +1,299 @@ + +Changes in the CHARMM toppar file format. +updated July 2015 + +As of July 2015 a new, additional version of the topology and +parameter files has been created in which the MASS numbers are all set +to -1. This coincides with changes in version 39 of CHARMM and onward +in which the MASS numbers are assigned as the new atom types are read. +This avoid problems with overlapping mass numbers, which has become an +issue as we have increased the number of atom types with CGenFF as +well as other aspects of the force field. As of July 2015 the default +version of the toppar files will contain the traditional MASS numbers +with a second version of the files included with "MASS -1". This will +allow for earlier versions of CHARMM to be used. As of July 2016 we +anticipate moving to "MASS -1" as the default for all the toppar +files. + +!July 2013 + +To facilitate the application of the CHARMM force field to +heterogeneous systems the toppar files have been converted to a +self-contained "stream" file format. This allows for each of the +individual sets of toppar files to be read in consequtively for +complex systems. For example, for a protein-inhibitor complex, the +protein topology and parameter files would be read followed by the +CGenFF topology and parameter files. To perform this the append and +flexible parameter reader are used, as shown below. Note that this +approach requires that the water and ion toppar files be read in +explicitly as they are no longer included in any of the parent toppar +files. To allow this approach the MASS numbers in each of the sets of +toppar files is unique as required to read them individually. The +range of MASS numbers in the individual files is given below. Note +that this file format has been tested on versions c34, c35 and c36 of +CHARMM; however it should work on version c32 and all subsequent +versions. + +Another significant change is in the terminal patching in the nucleic +acids. See the top_all36_na.rtf for details. + +Reordering of atoms in PC (choline) containing lipids as required for +new domain decomposition code in CHARMM + +Summary of toppar files + +toppar_water_ions.str: contains TIP3 water model and ion topology and +parameter information. This is now the only file that contains these +entities. + +Toplogy files +top_all22_prot.rtf all atom additive RTF for proteins, CHARMM22 with CMAP +top_all36_prot.rtf all atom additive RTF for proteins, CHARMM36 version, July 2012 +top_all36_na.rtf all atom additive RTF for nucleic acids, RNA/DNA updates +top_all35_ethers.rtf all atom additive RTF for ethers +top_all36_carb.rtf all atom additive RTF for carbohydrates +top_all36_cgenff.rtf all atom additive RTF for general molecules +top_all36_lipid.rtf all atom additive RTF for lipids +toph19.inp extended atom RTF for proteins + +Parameter files +par_all22_prot.prm all atom additive parameter for proteins, C22 with CMAP +par_all36_prot.prm all atom additive parameter for proteins, CHARMM36 version, July 2012 +par_all36_na.prm all atom additive parameter for nucleic acids, RNA/DNA updates +par_all35_ethers.prm all atom additive parameter for ethers +par_all36_carb.prm all atom additive parameter for carbohydrates +par_all36_cgenff.prm all atom additive parameter for general molecules +par_all36_lipid.prm all atom additive parameter for lipids +param19.inp extended atom parameters for proteins + +stream subdirecties: contain various molecules that have been +parametrized in the context of the CHARMM additive force fields. These +files require the specific "parent" toppar files be read prior to +reading these files. The dependencies are indicated in the individual +files. + +stream/prot + +toppar_all36_prot_aldehydes.str small molecule aldehydes +toppar_all36_prot_arg0.str neutral arginine model compounds and patches +toppar_all36_prot_d_amino_acids.str d-amino acids with the c36 protein force field +toppar_all36_prot_fluoro_alkanes.str optimized fluoroalkanes, requires + toppar_all22_prot_aliphatic_c27.str +toppar_all36_prot_heme.str heme, O2, CO, CO2 and related patches +toppar_all36_prot_model.str model compounds used in protein parameter + development as well as additional compounds +toppar_all36_prot_modify_res.str various modifed amino acid residues/patches + include posttranslational modifications (see na combined) +toppar_all36_prot_na_combined.str residues and patches, including phosphotyrosine, + serine and threonine that require both protein and + nucleic acid toppar parent files. +toppar_all36_prot_pyridines.str various substituted pyridines +toppar_all36_prot_retinol.str retinol, model compounds, Schiff's bases + +stream/na + +toppar_all36_na_modifications.str various chemical modifications of bases, backbone + and sugars (including carbocyclic sugars) +toppar_all36_na_model.str model compounds used in na parameter development + including individual bases etc. +toppar_all36_na_nad_ppi.str NAD, NADH, ADP, ATP and others. +toppar_all36_na_reactive_rna.str reactive species associated with phophate hydrolysis +toppar_all36_na_rna_modified.str modified RNA nucleotides (as in tRNA etc.) + +stream/lipid + +toppar_all36_lipid_bacterial.str various lipids found in bacteria +toppar_all36_lipid_cardiolipin.str cardiolipin +toppar_all36_lipid_cholesterol.str cholesterol; note that old cholesterol used on Anton +toppar_all36_lipid_detergent.str various detergents +toppar_all36_lipid_glycolipid.str various glycolipids +toppar_all36_lipid_inositol.str lipids contain various inositol analogs +toppar_all36_lipid_list.str list of required files for running test cases +toppar_all36_lipid_llo.str lipid linked oligosaccharides +toppar_all36_lipid_miscellaneous.str various lipids +toppar_all36_lipid_model.str model compounds used in lipid parameter development +toppar_all36_lipid_prot.str protein residues modified with lipids +toppar_all36_lipid_sphingo.str Ceramide/sphingomylein +toppar_all36_lipid_yeast.str various lipids in yeast + +stream/carb + +toppar_all36_carb_glycolipid.str model compounds for glycolipids + (some overlap with stream/lipid contents) +toppar_all36_carb_glycopeptide.str model compounds for glycoproteins +toppar_all36_carb_model.str model compounds using in carbohydrate parameter development + +stream/misc + +toppar_amines.str highly optimized neutral aliphatic amines +toppar_dum_noble_gases.str nobel gases and dummy atom +toppar_hbond.str stream file to estimate hydrogen bond interactions +toppar_ions_won.str extensive collection of ion parameters that covers + the majority of the periodic table. Caution: use + optimized ions in toppar_water_ions.str when possible. + +(D) Parameters for the polarizable force field based on a classical +Drude oscillator. As this force field is currently under development +such that the parameters have been placed in the "drude" subdirectory. +It is suggested that these be obtained from the MacKerell lab force +field web page. Also accessible via the CHARMM Gui. See the 00readme +for details and the approriate references. + +(E) Parameters for selected silicate and aluminosilicate surfaces have +been developed. These parameters are designed to be compatible with +the CHARMM22, 27 and 36 force fields allowing for biological +molecule-silicate surface interactions. As use of these parameters +requires creation of the surface, which entails creation of the +necessary patches, the parameters are included in the "silicates" +subdirectory. This directory also includes examples and code to +create the extended surfaces. See the 00readme file for more details. + +ref: Lopes, P.E.M., Murashov, V. Tazi, M. Demchuk, E. MacKerell, +A. D., Jr. "Development of an Empirical Force Field for +Silica. Application to the Quartz-Water Interface," Journal of +Physical Chemistry B, 110: 2782-2792, 2006. + +(F) Additional topology and parameter files from various sources are +included in subdirectories of the toppar directory. A description +follows: + +subdirectory non_charmm: Contains toppar files for AMBER, +Bristol-Myers Squibb (BMS) and OPLS force fields along with stream +files for a variety of water models. These files have been tested +to the extent that they may be considered reliable representations of +the original force fields, though potentially not exact +representations. These files are NOT maintained and, thus, use at +your own risk. See the 00readme files and note that AMBER requires a +special version of CHARMM as described in the 00readme file. + +tamdfff: An internal coordinate force field (ICFF) that was built +based on the CHARMM 22 protein force field. Specifically, it provides +a backbone covalent geometry suitable for torsion angle molecular +dynamics (TAMD) and the necessary CMAP cross-term corrections to +suppress distortions of the potential energy surface due to rigid +covalent geometry. Additional details can be found in tamd.doc. + +Ref. J. Chen, W. Im and C. L. Brooks III, J. Comp. Chem. 2005, 26, +1565-1578. + +rush: A simple implicit-solvent protein force-field that adds terms to +the bonded portion (bond + angle + dihe + impr + urey) of the all-atom +CHARMM22 force field to account for volume-exclusion (_R_epulsion), +the hydrophobic effect (_U_nburied _S_urface), and intra-molecular and +protein-solvent hydrogen-bonding (_H_ydrogen-bonding) (hence _R_ _U_ +_S_ _H_). Usage instructions are in doc/rush.doc + +gbsw: Optimized protein backbone parameters (par_all22_prot_gbsw.inp) +and atomic input radii (radius_gbsw.str) for a balanced GBSW implicit +solvent force field. The backbone phi/psi cross-term (CMAP) and the +atomic input radii have been re-optimized specifically to balance the +solvation and intramolecular interactions and to capture experimental +conformational equilibria of both helical peptides and +beta-hairpins. Additional information can be found in gbsw.doc. + +Ref. J. Chen, W. Im and C. L. Brooks III, J. Am. Chem. Soc. 128, +3728-36 (2006). + +ace: ACE2 solvation model developed by Michael Schaefer + +>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + +Example of command to read protein, nucleic acid and water/ions in a +CHARMM script + +* Generate and energy of molecules that require a combined +* Example to read protein, nucleic acid and water/ion toppar information +* + +set dir !set toppar directory + +set a @dir/top_all36_prot.rtf +set b @dir/par_all36_prot.prm +set c @dir/top_all36_na.rtf +set d @dir/par_all36_na.prm +set e @dir/toppar_water_ions.str + +! read the protein topology +read rtf card name @a + +! read the protein parameters +read para card flex name @b + +! append the nucleic acid topology +read rtf card append name @c + +! append the nucleic acid parameters +read para card flex append name @ + +! append water and ion toppar information +stream @e + +!remainder of charmm script....... + +stop + +>>>>>>>>>>>>>>>>>>>>>>>>>> +TOPPAR file MASS numbering + +Parent toppar files + +Water and ions: MASSes 1 to 20 +toppar_water_ions.str + +Proteins: MASSes 41 to 90 +top_all36_prot.rtf +par_all36_prot.prm + +Nucleic acids: MASSes 91 to 135 +top_all36_na.rtf +par_all36_na.prm + +Lipids: MASSes 136 to 170: 165-168 in toppar_all36_lipid_cer2.str +top_all36_lipid.rtf +par_all36_lipid.prm + +Carbohydrates: MASSes 171 to 230 +top_all36_carb.rtf +par_all36_carb.prm + +Ethers: MASSes 241 to 260 +top_all35_ethers.rtf +par_all35_ethers.prm + +CGenFF: MASSes 256 to 400 +top_all36_cgenff.rtf +par_all36_cgenff.prm + + +>>> Stream files subdirectory stream: Only those stream files that +contain novel atom types are listed below. + +toppar_all36_prot_aldehydes.str: MASSes 418 + +toppar_all36_na_modifications.str: MASSes 416 to 417, 469 to 483 + +toppar_all36_prot_pyridines.str: MASSes 419 to 424 + +toppar_all36_prot_retinol.str: MASSes 425 to 429 + +toppar_all36_prot_fluoro_alkanes.str: MASSes 430 to 437 + +toppar_all36_prot_d_amino_acids.str MASSes 438, 439 + +toppar_amines.str: MASSes 446 to 458 + +toppar_all36_na_nad_ppi.str: MASSes 459 to 465 + +toppar_all36_na_model.str: MASSes 466 to 468 + +toppar_all36_prot_na_combined.str: MASSes 484 to 485 + +toppar_all36_prot_heme.str: MASSes 486 to 494 + +toppar_dum_nobel_gases.str: MASSes 495 to 499 + +toppar_all36_prot_arg0.str MASSes 501 to 509 + +toppar_all36_na_reactive_rna.str MASSes 510 to 521 + +toppar_all36_lipid_cer2.str MASSes 165 to 168 diff --git a/charmm/toppar/ace/acepar19.inp b/charmm/toppar/ace/acepar19.inp new file mode 100644 index 00000000..dd5d3953 --- /dev/null +++ b/charmm/toppar/ace/acepar19.inp @@ -0,0 +1,35 @@ +* ACE2 parameter file (under construction, Jan 2002) +* >>>> for use with param19 <<<< +* Author: Michael Schaefer ! (schaefer@piaf.u-strasbg.fr) +* Reserved (4-letter) keywords: VOLU, SIGM, A012, RMIN, EQUI, END. +* The file MUST end with the END keyword. +* + +VOLUMES +! Effective Voronoi atom volumes, use with smoothing parameter alpha=1.3 +! Reference: M. Schaefer, C. Bartels, F. Leclerc, and M. Karplus, +! J. Comp. Chem. 22 (2001), 1857-1879. +H 0.0000 +HC 0.0000 +C 8.8950 +CH1E 12.4300 +CH2E 22.0330 +CH3E 34.0920 +CR1E 20.9790 +N 9.5580 +NR 16.5900 +NP 11.4950 +NH1 14.9440 +NH2 22.1290 +NH3 20.6410 +NC2 21.4010 +NH2P 16.3050 +O 22.3150 +OC 20.4850 +OH1 23.2660 +S 26.9630 +SH1E 34.1920 +SSO4 5.0260 +FE 10.7030 + +END diff --git a/charmm/toppar/ace/acepar22_prot.inp b/charmm/toppar/ace/acepar22_prot.inp new file mode 100644 index 00000000..ebc502ae --- /dev/null +++ b/charmm/toppar/ace/acepar22_prot.inp @@ -0,0 +1,58 @@ +* ACE2 parameter file (under construction, Jan 2002) +* >>>> for use with par_all22_prot <<<< +* Author: Michael Schaefer ! (schaefer@piaf.u-strasbg.fr) +* Reserved (4-letter) keywords: VOLU, SIGM, A012, RMIN, EQUI, END. +* The file MUST end with the END keyword. +* + +VOLUMES +! Effective Voronoi atom volumes, use with smoothing parameter alpha=1.3 +! Reference: M. Schaefer, C. Bartels, F. Leclerc, and M. Karplus, +! J. Comp. Chem. 22 (2001), 1857-1879. +H 0.0000 +HC 0.0000 +HA 0.0000 +HP 0.0000 +HB 0.0000 +HR1 0.0000 +HR3 0.0000 +HS 0.0000 +HT 0.0000 ! TIP3 +C 8.5590 +CA 21.2450 +CT1 12.3350 +CT2 21.9090 +CT3 34.1160 +CPH1 15.2480 +CPH2 17.8930 +CPT 10.4070 +CY 10.5050 +CP1 12.9160 +CP2 24.3960 +CP3 22.3300 +CC 9.2150 +CPA 10.7540 +CPB 11.1880 +CPM 19.9980 +CA3 10.2130 +N 9.4180 +NR1 18.0190 +NR2 17.8970 +NH1 14.7980 +NH2 25.0010 +NH3 24.5440 +NC2 24.5090 +NY 18.8470 +NP 17.6250 +NPH 11.5350 +NC2E 17.2860 +O 22.7090 +OC 21.6170 +OH1 24.4730 +OT 23.1570 ! TIP3, OT van der Waals volume +S 29.8490 +SM 26.3250 +SSO4 5.0260 ! SO4 sulfate S volume, from results on param19 +FE 10.4580 + +END diff --git a/charmm/toppar/ace/acepar27_na.inp b/charmm/toppar/ace/acepar27_na.inp new file mode 100644 index 00000000..f49c0263 --- /dev/null +++ b/charmm/toppar/ace/acepar27_na.inp @@ -0,0 +1,53 @@ +* ACE2 parameter file (under construction, Jan 2002) +* >>>> for use with par_all27_na <<<< +* Author: Michael Schaefer ! (schaefer@piaf.u-strasbg.fr) +* Reserved (4-letter) keywords: VOLU, SIGM, A012, RMIN, EQUI, END. +* The file MUST end with the END keyword. +* + +VOLUMES +! Effective Voronoi atom volumes, use with smoothing parameter alpha=1.1 +! Reference: M. Schaefer, C. Bartels, F. Leclerc, and M. Karplus, +! J. Comp. Chem. 22 (2001), 1857-1879. +HN1 0.0000 +HN2 0.0000 +HN3 0.0000 +HN5 0.0000 +HN7 0.0000 +HN8 0.0000 +HN9 0.0000 +CN1 8.3670 +CN1T 8.4060 +CN2 8.5500 +CN3 17.3170 +CN3T 9.8890 +CN4 17.1250 +CN5 8.9150 +CN5G 9.1600 +CN7 12.7100 +CN7B 12.2210 +CN8 20.2050 +CN8B 20.6310 +CN9 30.7750 +NN1 21.7910 +NN2 9.2230 +NN2B 9.2630 +NN2U 14.2200 +NN2G 14.0690 +NN3 13.9170 +NN3A 14.1390 +NN3G 16.3950 +NN4 16.7840 +NN3B 16.9620 +ON1 20.2730 +ON1C 20.3190 +ON2 15.7230 +ON3 19.4700 +ON5 20.8370 +ON6 16.4680 +ON6B 15.8860 +P 6.2230 +MG 7.0000 +SOD 10.6241 ! van der Waals volume + +END diff --git a/charmm/toppar/cheq/par_all30_cheq_prot.inp b/charmm/toppar/cheq/par_all30_cheq_prot.inp new file mode 100755 index 00000000..41b5ce35 --- /dev/null +++ b/charmm/toppar/cheq/par_all30_cheq_prot.inp @@ -0,0 +1,2625 @@ +*>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< +*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< +* + +!changes after 9/98 +! +!change alkene HA1 and HE2 to HE1 and HE2 +! +!version b5i for compatibility with topology +! +!all aliphatic carbons and hydrogens changed to Yin and MacKerell +!LJ parameters and corresponding internal terms + + +! references +! +!PROTEINS +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. +! +!PHOSPHOTYROSINE +! +!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. +!Structural Characterization of the Phosphotyrosine Binding Region of a +!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics +!Simulation and Chemical Shift Calculations. Journal of the American +!Chemical Society, 1996, 118: 11265-11277. +! +!IONS (see lipid and nucleic acid topology and parameter files for +!additional ions +! +!ZINC +! +!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) +! + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +!Heme to Sulfate (PSUL) link +SS FE 250.0 2.3200 !force constant a guess + !equilbrium bond length optimized to reproduce + !CSD survey values of + !2.341pm0.01 (mean, standard error) + !adm jr., 7/01 +C C 600.000 1.3350 ! ALLOW ARO HEM + ! Heme vinyl substituent (KK, from propene (JCS)) +CA CA 305.000 1.3750 ! ALLOW ARO + ! benzene, JES 8/25/89 +CE1 CE1 440.000 1.3400 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CE2 500.000 1.3420 ! + ! for propene, yin/adm jr., 12/95 +CE1 CT2 365.000 1.5020 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CT3 383.000 1.5040 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE2 510.000 1.3300 ! + ! for ethene, yin/adm jr., 12/95 +CP1 C 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CC 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CD 200.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 222.500 1.5270 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPB CE1 450.000 1.3800 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPA 299.800 1.4432 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB CPB 340.700 1.3464 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH1 CPH1 410.000 1.3600 ! ALLOW ARO + ! histidine, adm jr., 6/27/90 +CPM CPA 360.000 1.3716 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT CA 305.000 1.3680 ! ALLOW ARO + ! adm jr., 12/30/91, for jwk +CPT CPT 360.000 1.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT1 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT1 222.500 1.5000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT2 CA 230.000 1.4900 ! ALLOW ALI ARO + ! phe,tyr, JES 8/25/89 +CT2 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT2 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT3 CA 230.000 1.4900 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +CT3 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT3 CS 190.000 1.5310 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CT3 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 222.500 1.5280 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT3 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CY CA 350.000 1.3650 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CY CPT 350.000 1.4400 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 230.000 1.5100 ! ALLOW ARO + !JWK Kb from alkane freq.. b0 from TRP crystal +FE CM 258.000 1.9000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +FE CPM 0.000 3.3814 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +H CD 330.000 1.1100 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +!HA C 330.000 1.1000 ! ALLOW ARO HEM + ! Heme vinyl substituent (KK, from propene (JCS)) +!HA CA 340.000 1.0830 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA1 CC 317.130 1.1000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +HA1 C 317.130 1.1000 ! ALLOW POL ! ADDED SANDEEP +HA2 CP2 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA1 CPM 367.600 1.0900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA2 CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA1 CT1 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 322.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +!HA CY 330.000 1.0800 ! ALLOW ARO + ! JWK 05/14/91 new r0 from indole +HE1 CE1 360.500 1.1000 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 365.000 1.1000 ! + ! for ethene, yin/adm jr., 12/95 +HB1 CP1 330.000 1.0800 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT1 330.000 1.0800 ! ALLOW PEP ! ADDED SANDEEP + ! +!HB3 CT3 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HP CA 340.000 1.0800 ! ALLOW ARO + ! phe,tyr JES 8/25/89 +HP CY 350.000 1.0800 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HR1 CPH1 375.000 1.0830 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 340.000 1.0900 ! ALLOW ARO + ! his, adm jr., 6/28/29 +HR2 CPH2 333.000 1.0700 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR3 CPH1 365.000 1.0830 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HT HT 0.000 1.5139 ! ALLOW WAT + ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) +N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 320.000 1.4340 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 320.000 1.4550 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO + ! 403.0->463.0, 1.305->1.365 guanidinium (KK) +NC2 CT2 261.000 1.4900 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 261.000 1.4900 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NC2 HC 455.000 1.0000 ! ALLOW POL + ! 405.0->455.0 GUANIDINIUM (KK) +NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO + ! (DS) +NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +NH2 CT2 240.000 1.4550 + ! from NH2 CT3, neutral glycine, adm jr. +NH2 CT3 240.000 1.4550 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH2 H 480.000 1.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 HC 460.000 1.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT3 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 HC 403.000 1.0400 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 320.000 1.4850 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 320.000 1.5020 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP HC 460.000 1.0060 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NPH CPA 377.200 1.3757 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE 270.200 1.9580 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH2 400.000 1.3600 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 H 466.000 1.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 400.000 1.3200 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 FE 65.000 2.2000 ! ALLOW HEM + ! Heme (6-liganded): His ligand (KK 05/13/91) +NR3 CPH1 380.000 1.3700 ! ALLOW ARO + ! his, adm jr., 6/28/90 +NR3 CPH2 380.000 1.3200 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 H 453.000 1.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA 270.000 1.3700 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT 270.000 1.3750 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY H 465.000 0.9760 ! ALLOW ARO + ! indole JWK 08/28/89 +O C 620.000 1.2300 ! ALLOW PEP POL ARO + ! Peptide geometry, condensed phase (LK) +O CC 650.000 1.2300 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +OB CC 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid vibrations and geom. +OB CD 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 8/27/91, phenoxide +OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 7/23/91, acetic acid +OC CT2 450.000 1.3300 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 450.000 1.3300 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA 334.300 1.4110 ! ALLOW ARO ALC + ! MeOH, EMB 10/10/89, +OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC + ! adm jr. 5/02/91, acetic acid pure solvent +OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 H 545.000 0.9600 ! ALLOW ALC ARO + ! EMB 11/21/89 methanol vib fit +OM CM 1115.000 1.1280 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +OM FE 250.000 1.8000 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OM OM 600.000 1.2300 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OS CD 150.000 1.3340 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +OS CT3 340.000 1.4300 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OT HT 450.000 0.9572 ! ALLOW WAT + ! FROM TIP4P GEOM +OT LP 0.0 0.15 ! +S CT2 198.000 1.8180 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S CT3 240.000 1.8160 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S HS 275.000 1.3250 ! ALLOW SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +SM CT2 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM CT3 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM SM 173.000 2.0290 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SS CS 205.000 1.8360 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +!Heme to Sulfate (PSUL) link +CS SS FE 50.0 100.6 !force constant a guess + !equilibrium angle optimized to reproduce + !CSD survey values + !107.5pm0.6 (mean, standard error) + !adm jr., 7/01 +SS FE NPH 100.0 90.0 !force constant a guess + !adm jr., 7/01 +! +CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO + ! JES 8/25/89 +CE1 CE1 CT2 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CE1 CT3 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CT2 CT3 32.00 112.20 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT2 48.00 126.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT3 47.00 125.20 ! + ! for propene, yin/adm jr., 12/95 +CP1 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 C 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 100.000 114.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 100.000 111.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPA CPB CE1 70.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPA CPM CPA 94.200 125.1200 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPA NPH CPA 139.300 103.9000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB CE1 CE2 70.000 121.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB CE1 70.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB CPA 30.800 106.5100 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPM CPA CPB 61.600 124.0700 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT CA CA 60.000 118.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CPT CA 60.000 122.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT NY CA 110.000 108.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! from CT2 CT1 C, for lactams, adm jr. +CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CY CA 45.800 129.4000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 CY CPT 45.800 124.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! 107.5->120.0 to make planar Arg (KK) +CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/09/92, for ALA cter +CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! methylguanidinium, adm jr., 3/26/92 +CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 CT1 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +CY CT2 CT3 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +FE NPH CPA 96.150 128.0500 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO + ! his, adm jr. 8/13/90 acetamide geometry and vibrations +H NH2 H 23.000 120.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NY CA 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO + ! JES 8/25/89 phenol +H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +!HA C C 50.000 120.5000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK from propene (JCS)) +!HA C CPB 50.000 120.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +!HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK from propene (JCS)) +!HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +!HA CA CPT 41.000 122.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +!HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA2 CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA1 CPM CPA 12.700 117.4400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA1 CPM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +HA2 CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA2 CS HA2 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CS HA3 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA1 CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA1 CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA1 CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 HA1 35.500 109.00 5.40 1.80200 ! TEST for test cpd + ! based on HA CT2 HA +HA2 CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA2 CT2 CA 49.300 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +HA2 CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA2 CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA2 CT2 CE1 45.00 111.50 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HA2 CT2 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA2 CT2 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA2 CT2 CT1 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA2 CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 CY 33.430 109.5000 ! ALLOW ARO + ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA +HA2 CT2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA3 CT3 CA 49.300 107.5000 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +HA3 CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA3 CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA3 CT3 CE1 42.00 111.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HA3 CT3 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA3 CT3 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA3 CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA3 CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 HA3 35.500 108.40 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +!HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +!HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HE1 CE1 CE1 52.00 119.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HE1 CE1 CE2 42.00 118.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 40.00 116.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HE1 CE1 CT3 22.00 117.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CPB 50.000 120.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HE2 CE2 CE1 45.00 120.50 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE2 55.50 120.50 ! + ! for ethene, yin/adm jr., 12/95 +HE2 CE2 HE2 19.00 119.00 ! + ! for propene, yin/adm jr., 12/95 +HB1 CP1 C 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CC 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB2 CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! ADDED Sandeep +HB1 CT1 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB1 CT1 CT1 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CT2 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CT3 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB2 CT2 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB2 CT2 HB2 36.000 115.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT1 HB2 36.000 115.0000 ! ALLOW PEP ! ADDED SANDEEP + ! +HB2 CT1 C 50.000 109.5000 ! ALLOW PEP ! ADDED SANDEEP + ! +!HB CT3 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO + ! 35.3->49.0 GUANIDINIUM (KK) +HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI + ! 107.5->120.0 to make planar Arg (KK) +HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI + ! methylguanidinium, adm jr., 3/26/92 +HC NC2 HC 25.000 120.0000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH2 CT2 50.000 111.0000 ! ALLOW POL + ! from HC NH2 CT3, neutral glycine, adm jr. +HC NH2 CT3 50.000 111.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +HC NH2 HC 39.000 106.5000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 HC 44.000 109.5000 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP HC 51.000 107.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HT OT HT 55.000 104.5200 ! ALLOW WAT + ! TIP3P GEOMETRY, ADM JR. +N C CP1 20.000 112.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 C 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CC 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CP2 70.000 110.8000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 HB1 48.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 CP2 70.000 110.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 HA2 48.000 108.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO + ! changed from 60.0/120.3 for guanidinium (KK) +NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT2 HA2 51.500 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 HA3 51.500 107.5000 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C HA1 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! ADDED SANDEEP +HA1 C O 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! ADDED SANDEEP +NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 HB1 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 HB2 48.000 108.0000 ! ALLOW PEP ! ADDED SANDEEP + ! ALANINE DIPEPTIDE AB INITIO CALC's (LK) +NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/20/92, for asn,asp,gln,glu and cters +NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT1 CT2, for lactams, adm jr. +NH1 CT2 HA2 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT3 HA, for lactams, adm jr. +NH1 CT2 HB2 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT3 HA3 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! NMA crystal (JCS) +NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC HA1 44.000 111.00 50.00 1.98000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +NH2 CT2 HB2 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral glycine, adm jr. +NH2 CT2 CD 52.000 108.0000 + !from CT2 CT2 CD, neutral glycine, adm jr. +NH2 CT3 HA3 38.000 109.50 50.00 2.14000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP + ! new aliphatics, adm jr., 2/3/92 +NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! alanine (JCS) +NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + ! alanine (JCS) +NH3 CT2 HA2 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 HB2 51.500 107.5000 ! ALLOW ALI POL PEP + ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) +NH3 CT3 HA3 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 C 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 HA2 51.500 109.1500 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NPH CPA CPB 122.000 111.5400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM 88.000 124.3900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE CM 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NPH FE CPM 0.000 45.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +NPH FE NPH 14.390 90.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 FE CM 50.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR2 FE NPH 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +!NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +O C CP1 80.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C H 50.000 121.7000 ! ALLOW PEP POL ARO + ! acetaldehyde (JCS) +O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC HA1 44.000 122.0000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO + ! adm jr. 4/10/91, acetamide update +OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA CA 40.000 120.0000 ! ALLOW POL ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CT2 CT3 65.000 122.0000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT2 HA2 65.000 118.3000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 HA3 65.000 118.3000 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC + ! PARALLH19 WITH [122.3] (JES) +OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 HA1 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 HA2 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT3 HA3 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OM CM FE 35.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM FE NPH 5.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM OM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OS CT2 HA2 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +OS CT3 HA3 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 HA2 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +S CT3 HA3 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 HA2 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM CT3 HA3 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 55.000 118.0000 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA2 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA3 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +!Heme to Sulfate (PSUL) link +X FE SS X 0.0000 4 0.00 ! guess + !adm jr., 7/01 +X CS SS X 0.0000 3 0.20 ! guess + !from methanethiol, HS S CT3 HA + !adm jr., 7/01 + +C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 +CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c +CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c +CE1 CE1 CT3 HA3 0.0300 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 CT3 0.5000 1 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 CT3 1.3000 3 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 HA2 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT3 HA3 0.0500 3 180.00 ! + ! for propene, yin/adm jr., 12/95 +CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 +CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 +!CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT2 CT2 CT2 CT2 0.10 2 180.00 ! alkane, 4/98, adm jr. + ! lower butane gauche conformer +CT2 CT2 CT2 CT2 0.15 4 0.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT2 0.10 6 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.10 2 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.15 4 0.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.10 6 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! from CT2 CT1 NH1 C, for lactams, adm jr. +CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK +CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + !JWK +CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +CT3 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +!CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +!CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CT2 CT3 0.10 2 180.00 ! alkane, 4/98, adm jr., lower butane gauche conformer +CT3 CT2 CT2 CT3 0.15 4 0.00 ! alkane, 4/98, adm jr. +CT3 CT2 CT2 CT3 0.10 6 180.00 ! alkane, 4/98, adm jr. + ! +CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION + ! DTN 8/24/90 +CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from H NH1 CT2 CT3, for lactams, adm jr. +H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/20/89 +H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NY CA CY 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC + ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +!HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO + ! adm jr., 10/02/89 +!HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +!HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO + ! ADM JR., 10/02/89 +!HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! TRP (JES) +!HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +!HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK +!HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK +!HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +!HA CA NY H 1.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA1 CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL + ! adm jr. 4/10/91, acetamide update +HA1 C NH1 H 1.4000 2 180.00 ! ALLOW PEP POL ! ADDED SANDEEP +HA1 C NH1 CT3 1.4000 2 180.00 ! ALLOW PEP POL ! ADDED SANDEEP +HA2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA1 CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA2 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA2 CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA2 CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA2 CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA2 CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA2 CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA3 CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA3 CT3 CS HA2 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CS HA3 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA3 CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA3 CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA3 CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +!HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +!HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +!HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +!HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HE1 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +CT3 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +HE1 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 HA2 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE1 CE1 CT2 CT3 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT3 HA3 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE2 CE2 CE1 CT2 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +HE2 CE2 CE1 CPB 5.2000 2 180.00 ! + ! for vinyl, from butene, yin/adm jr., 12/95 +HB1 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! ADDED SANDEEP +HB2 CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! ADDED SANDEEP +NH1 C CT1 HB2 0.0000 1 0.00 ! ALLOW PEP ! ADDED SANDEEP +O C CT1 HB2 0.0000 1 0.00 ! ALLOW PEP ! ADDED SANDEEP + ! +!HB3 CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +!HB3 CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NH2 CT2 HB2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CD 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 HB1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 HA2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA NY H 0.4000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, his +HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, YES, 0.0 +HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 HA2 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 HA3 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 HA3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from NH1 C CT1 CT2, for lactams, adm jr. +NH1 C CT2 HA2 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT3 HA3 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO + ! adm jr. 3/24/92, for PRES GLYP +NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO + ! JWK +!NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +!NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB1 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP + ! from O C CT1 CT2, for lactams, adm jr. +O C CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT3 HA3 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 H 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB1 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 HB1 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +S CT2 CT2 HA2 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM CT2 CT2 HA2 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 HA2 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 HA3 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 HA3 0.1500 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +!X C C X 4.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO + ! 9.0->2.25 GUANIDINIUM (KK) +X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier +X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CE1 CE1 X 0.1500 1 0.00 + ! 2-butene, adm jr., 2/00 update +X CE1 CE1 X 8.5000 2 180.00 + ! 2-butene, adm jr., 2/00 update +X CE2 CE2 X 4.9000 2 180.00 ! + ! for ethene, yin/adm jr., 12/95 +X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP + ! changed to 0.0 RLD 5/19/92 +X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB CE1 X 3.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CT2 X 0.1900 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CT3 X 0.1525 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL + ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 +X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X FE CM X 0.0500 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X FE NPH X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +X FE OM X 0.0000 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB X X CE1 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +!HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK, from propene (JCS)) +HA1 CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +!HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO + ! Heme (6-liganded): substituents (KK 05/13/91) +!HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK, from propene (JCS)) +HE2 HE2 CE2 CE2 3.0 0 0.00 ! + ! for ethene, yin/adm jr., 12/95 +HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO + ! 5.75->40.0 GUANIDINIUM (KK) +NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +NH2 X X H 4.0000 0 0.0000 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO + !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf. +O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O HA1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! adm jr., 5/13/91, formamide geometry and vibrations +O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 HA1 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL + ! adm jr., 10/17/90, acetic acid vibrations +OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) + + + +cmap +C NH1 CT1 C NH1 CT1 C NH1 24 + 61.47387 61.70139 61.71619 61.44526 + 61.27102 61.56204 62.08615 62.16524 + 61.90445 61.10684 63.67618 60.03250 + 57.16239 56.56612 56.96806 57.58373 + 57.77730 57.94734 57.72137 57.57081 + 58.04843 58.74718 59.78054 60.71109 + + 61.51772 61.44986 61.16623 61.03657 + 61.31060 61.89634 62.38639 62.42802 + 62.30523 64.91323 62.23404 58.84987 + 57.10082 57.02325 57.25992 57.71560 + 57.92971 58.12840 58.17156 58.20515 + 58.67401 59.48252 60.38511 61.13752 + + 61.15978 61.01967 60.62431 60.84676 + 61.40239 62.05993 62.81529 62.68043 + 62.57471 63.76686 60.99156 58.36615 + 57.38187 57.23162 57.53077 57.81861 + 58.21912 58.42261 58.41346 58.54449 + 59.10557 59.93701 60.64304 61.02694 + + 60.69787 60.57855 60.83929 61.37866 + 62.11758 62.64843 63.20259 63.08541 + 63.01954 62.74712 60.07689 58.30659 + 57.64510 57.63221 57.76898 58.05211 + 58.34545 58.46437 58.52239 58.80421 + 59.35054 59.94672 60.43500 60.67312 + + 60.54867 60.98608 61.59870 62.30219 + 62.93774 63.29417 63.58453 63.68991 + 64.32059 62.33345 60.19324 58.99910 + 58.30978 58.07219 58.02410 58.26188 + 58.38723 58.53162 58.67693 59.09233 + 59.32216 59.90904 60.23699 60.40723 + + 61.05929 61.66412 62.34561 63.05387 + 63.63874 63.98711 64.16422 64.36331 + 64.44772 62.82568 61.10298 59.72838 + 59.03822 58.51756 58.36533 58.09103 + 58.02875 58.30040 58.57044 59.19206 + 59.72438 60.17861 60.40841 60.78954 + + 61.69004 62.00993 62.54891 63.24772 + 64.14706 64.70498 64.90720 65.89588 + 64.58312 62.99245 61.42216 60.10853 + 59.11974 58.29623 57.30506 56.87263 + 57.14502 57.61034 58.13547 59.21390 + 60.01268 60.44246 60.91453 61.30625 + + 61.09894 61.21216 61.69305 62.77380 + 63.84520 64.79207 65.26464 65.79291 + 64.13054 62.38497 61.07087 59.57062 + 58.27839 56.71559 55.60297 55.75801 + 56.27418 56.58290 57.37704 58.53107 + 59.62588 60.24514 60.75694 60.97561 + + 59.27758 59.61631 60.55050 62.02148 + 63.55231 64.75801 65.32814 64.77474 + 62.88591 61.39837 60.02485 58.46167 + 56.20943 54.42471 54.14552 54.49030 + 55.23829 55.83141 56.59478 57.71631 + 58.60667 59.26787 59.37430 59.33298 + + 57.50791 58.43596 60.17237 62.26223 + 63.92577 64.96242 64.97181 63.20068 + 61.30107 60.03491 58.40595 56.05410 + 53.71800 52.89809 53.02050 53.60809 + 54.37972 55.32934 56.39704 57.43302 + 57.51151 57.68616 57.51266 57.35748 + + 56.93335 58.67947 60.99270 64.12510 + 63.94698 63.80800 62.99679 61.49312 + 60.03053 58.68166 56.34164 53.48138 + 52.08961 51.55931 51.90286 52.85809 + 53.97922 55.69799 57.10073 57.01127 + 56.72910 56.36599 56.17659 56.26896 + + 57.56396 62.30184 60.76283 60.87524 + 61.41601 61.59481 61.19556 60.43814 + 59.00089 57.22468 53.96052 51.58809 + 50.70642 50.55113 51.25986 52.40447 + 54.53843 56.82446 56.96405 56.60812 + 56.05198 55.82737 55.76430 56.16303 + + 60.18910 58.62613 58.56484 59.16597 + 59.81934 60.22792 60.55097 59.85486 + 58.13923 54.93098 52.28222 50.74301 + 50.24900 49.96632 50.97516 53.10114 + 55.62558 56.33370 56.35719 56.12834 + 55.95804 55.98599 56.06412 57.22398 + + 57.64409 56.98276 57.43206 58.12714 + 58.89367 59.69459 60.12330 59.29861 + 56.36458 53.64626 51.80717 50.71794 + 50.09595 50.44231 52.07311 54.56792 + 55.45907 55.99206 56.41730 56.71119 + 56.78040 56.77700 60.27536 58.77082 + + 56.06609 56.30886 56.99556 57.83261 + 58.60435 59.43215 59.33521 57.46062 + 55.35086 53.65316 52.32488 51.17535 + 50.96685 51.60690 54.03597 54.93225 + 55.44818 56.33735 57.46476 58.10720 + 58.44918 58.60933 57.50697 56.56954 + + 55.99462 56.63149 57.50966 58.32630 + 58.83417 59.17148 58.26762 56.59435 + 55.23837 53.93459 52.56886 51.94172 + 51.89901 53.44577 54.81358 55.25808 + 56.03170 57.38521 58.69108 59.06368 + 58.19477 57.27346 56.37239 55.91753 + + 57.30341 58.00683 58.96676 59.28216 + 59.64417 59.11833 58.16829 56.83511 + 55.68108 54.43990 53.38400 52.94295 + 53.56521 54.88634 55.44714 55.97303 + 57.00137 58.37234 59.42213 58.77650 + 58.00881 57.26670 57.00983 57.07104 + + 58.79606 59.29415 59.80373 60.15234 + 60.14933 59.44031 58.27928 57.45339 + 56.36105 55.26146 54.41094 54.24221 + 55.06259 55.52055 55.94753 56.64659 + 57.75204 58.92621 59.42861 58.90505 + 58.44226 58.09904 58.04288 58.37179 + + 59.17509 59.40944 59.77456 60.06121 + 60.16856 59.70342 58.64291 57.61108 + 57.03921 56.15829 55.41410 55.51468 + 55.64945 55.74034 56.10624 56.94144 + 58.16029 59.46919 58.95131 58.69096 + 58.55689 58.48466 58.76499 59.05252 + + 58.78675 58.99953 59.36748 59.65199 + 59.68387 59.54378 59.14684 58.31679 + 57.85640 57.16164 56.34575 55.83635 + 55.61930 55.60463 56.08880 57.24199 + 59.43011 58.59266 58.23604 58.15226 + 58.17426 58.15233 58.40589 58.67079 + + 58.47036 59.02785 59.56295 59.70883 + 59.61892 59.49724 59.43284 59.18150 + 58.75838 57.64627 56.68551 55.99739 + 55.57653 55.57020 56.31232 59.29434 + 58.45342 57.95446 57.79877 57.80644 + 57.78060 57.61724 57.75469 58.06612 + + 58.97657 59.99158 60.49443 60.46804 + 60.11582 59.90927 59.91653 59.81750 + 59.22439 58.23575 57.24529 56.63986 + 56.05999 60.74996 58.65207 58.00089 + 57.95223 57.82322 57.80369 57.73741 + 57.43438 57.08295 57.30064 57.96956 + + 59.91168 61.17762 61.32354 61.17196 + 60.68997 60.50052 60.59876 60.58106 + 60.05134 59.30097 58.32664 64.24117 + 60.86166 57.87957 57.11211 57.50322 + 57.90352 57.95340 57.79178 57.43917 + 57.07478 57.11047 57.62888 58.82662 + + 60.92399 61.50504 61.73938 61.53258 + 61.10255 61.06271 61.41682 61.56841 + 61.12061 60.44049 59.22290 61.96949 + 58.20326 56.52957 56.84331 57.45674 + 57.83186 57.98960 57.31509 57.37459 + 57.32066 57.72211 58.61125 59.81687 + + 61.47374 61.70134 61.71572 61.44561 + 61.27047 61.56129 62.08499 62.16512 + 61.90407 61.10634 63.67618 60.03237 + 57.16235 56.56537 56.96714 57.57957 + 57.77707 57.96066 57.72130 57.57381 + 57.86317 58.62662 59.67696 60.65509 + + + + + + +C NH1 CT1 C NH1 CT1 C N 24 + 61.47387 61.70139 61.71619 61.44526 + 61.27102 61.56204 62.08615 62.16524 + 61.90445 61.10684 63.67618 60.03250 + 57.16239 56.56612 56.96806 57.58373 + 57.77730 57.94734 57.72137 57.57081 + 58.04843 58.74718 59.78054 60.71109 + + 61.51772 61.44986 61.16623 61.03657 + 61.31060 61.89634 62.38639 62.42802 + 62.30523 64.91323 62.23404 58.84987 + 57.10082 57.02325 57.25992 57.71560 + 57.92971 58.12840 58.17156 58.20515 + 58.67401 59.48252 60.38511 61.13752 + + 61.15978 61.01967 60.62431 60.84676 + 61.40239 62.05993 62.81529 62.68043 + 62.57471 63.76686 60.99156 58.36615 + 57.38187 57.23162 57.53077 57.81861 + 58.21912 58.42261 58.41346 58.54449 + 59.10557 59.93701 60.64304 61.02694 + + 60.69787 60.57855 60.83929 61.37866 + 62.11758 62.64843 63.20259 63.08541 + 63.01954 62.74712 60.07689 58.30659 + 57.64510 57.63221 57.76898 58.05211 + 58.34545 58.46437 58.52239 58.80421 + 59.35054 59.94672 60.43500 60.67312 + + 60.54867 60.98608 61.59870 62.30219 + 62.93774 63.29417 63.58453 63.68991 + 64.32059 62.33345 60.19324 58.99910 + 58.30978 58.07219 58.02410 58.26188 + 58.38723 58.53162 58.67693 59.09233 + 59.32216 59.90904 60.23699 60.40723 + + 61.05929 61.66412 62.34561 63.05387 + 63.63874 63.98711 64.16422 64.36331 + 64.44772 62.82568 61.10298 59.72838 + 59.03822 58.51756 58.36533 58.09103 + 58.02875 58.30040 58.57044 59.19206 + 59.72438 60.17861 60.40841 60.78954 + + 61.69004 62.00993 62.54891 63.24772 + 64.14706 64.70498 64.90720 65.89588 + 64.58312 62.99245 61.42216 60.10853 + 59.11974 58.29623 57.30506 56.87263 + 57.14502 57.61034 58.13547 59.21390 + 60.01268 60.44246 60.91453 61.30625 + + 61.09894 61.21216 61.69305 62.77380 + 63.84520 64.79207 65.26464 65.79291 + 64.13054 62.38497 61.07087 59.57062 + 58.27839 56.71559 55.60297 55.75801 + 56.27418 56.58290 57.37704 58.53107 + 59.62588 60.24514 60.75694 60.97561 + + 59.27758 59.61631 60.55050 62.02148 + 63.55231 64.75801 65.32814 64.77474 + 62.88591 61.39837 60.02485 58.46167 + 56.20943 54.42471 54.14552 54.49030 + 55.23829 55.83141 56.59478 57.71631 + 58.60667 59.26787 59.37430 59.33298 + + 57.50791 58.43596 60.17237 62.26223 + 63.92577 64.96242 64.97181 63.20068 + 61.30107 60.03491 58.40595 56.05410 + 53.71800 52.89809 53.02050 53.60809 + 54.37972 55.32934 56.39704 57.43302 + 57.51151 57.68616 57.51266 57.35748 + + 56.93335 58.67947 60.99270 64.12510 + 63.94698 63.80800 62.99679 61.49312 + 60.03053 58.68166 56.34164 53.48138 + 52.08961 51.55931 51.90286 52.85809 + 53.97922 55.69799 57.10073 57.01127 + 56.72910 56.36599 56.17659 56.26896 + + 57.56396 62.30184 60.76283 60.87524 + 61.41601 61.59481 61.19556 60.43814 + 59.00089 57.22468 53.96052 51.58809 + 50.70642 50.55113 51.25986 52.40447 + 54.53843 56.82446 56.96405 56.60812 + 56.05198 55.82737 55.76430 56.16303 + + 60.18910 58.62613 58.56484 59.16597 + 59.81934 60.22792 60.55097 59.85486 + 58.13923 54.93098 52.28222 50.74301 + 50.24900 49.96632 50.97516 53.10114 + 55.62558 56.33370 56.35719 56.12834 + 55.95804 55.98599 56.06412 57.22398 + + 57.64409 56.98276 57.43206 58.12714 + 58.89367 59.69459 60.12330 59.29861 + 56.36458 53.64626 51.80717 50.71794 + 50.09595 50.44231 52.07311 54.56792 + 55.45907 55.99206 56.41730 56.71119 + 56.78040 56.77700 60.27536 58.77082 + + 56.06609 56.30886 56.99556 57.83261 + 58.60435 59.43215 59.33521 57.46062 + 55.35086 53.65316 52.32488 51.17535 + 50.96685 51.60690 54.03597 54.93225 + 55.44818 56.33735 57.46476 58.10720 + 58.44918 58.60933 57.50697 56.56954 + + 55.99462 56.63149 57.50966 58.32630 + 58.83417 59.17148 58.26762 56.59435 + 55.23837 53.93459 52.56886 51.94172 + 51.89901 53.44577 54.81358 55.25808 + 56.03170 57.38521 58.69108 59.06368 + 58.19477 57.27346 56.37239 55.91753 + + 57.30341 58.00683 58.96676 59.28216 + 59.64417 59.11833 58.16829 56.83511 + 55.68108 54.43990 53.38400 52.94295 + 53.56521 54.88634 55.44714 55.97303 + 57.00137 58.37234 59.42213 58.77650 + 58.00881 57.26670 57.00983 57.07104 + + 58.79606 59.29415 59.80373 60.15234 + 60.14933 59.44031 58.27928 57.45339 + 56.36105 55.26146 54.41094 54.24221 + 55.06259 55.52055 55.94753 56.64659 + 57.75204 58.92621 59.42861 58.90505 + 58.44226 58.09904 58.04288 58.37179 + + 59.17509 59.40944 59.77456 60.06121 + 60.16856 59.70342 58.64291 57.61108 + 57.03921 56.15829 55.41410 55.51468 + 55.64945 55.74034 56.10624 56.94144 + 58.16029 59.46919 58.95131 58.69096 + 58.55689 58.48466 58.76499 59.05252 + + 58.78675 58.99953 59.36748 59.65199 + 59.68387 59.54378 59.14684 58.31679 + 57.85640 57.16164 56.34575 55.83635 + 55.61930 55.60463 56.08880 57.24199 + 59.43011 58.59266 58.23604 58.15226 + 58.17426 58.15233 58.40589 58.67079 + + 58.47036 59.02785 59.56295 59.70883 + 59.61892 59.49724 59.43284 59.18150 + 58.75838 57.64627 56.68551 55.99739 + 55.57653 55.57020 56.31232 59.29434 + 58.45342 57.95446 57.79877 57.80644 + 57.78060 57.61724 57.75469 58.06612 + + 58.97657 59.99158 60.49443 60.46804 + 60.11582 59.90927 59.91653 59.81750 + 59.22439 58.23575 57.24529 56.63986 + 56.05999 60.74996 58.65207 58.00089 + 57.95223 57.82322 57.80369 57.73741 + 57.43438 57.08295 57.30064 57.96956 + + 59.91168 61.17762 61.32354 61.17196 + 60.68997 60.50052 60.59876 60.58106 + 60.05134 59.30097 58.32664 64.24117 + 60.86166 57.87957 57.11211 57.50322 + 57.90352 57.95340 57.79178 57.43917 + 57.07478 57.11047 57.62888 58.82662 + + 60.92399 61.50504 61.73938 61.53258 + 61.10255 61.06271 61.41682 61.56841 + 61.12061 60.44049 59.22290 61.96949 + 58.20326 56.52957 56.84331 57.45674 + 57.83186 57.98960 57.31509 57.37459 + 57.32066 57.72211 58.61125 59.81687 + + 61.47374 61.70134 61.71572 61.44561 + 61.27047 61.56129 62.08499 62.16512 + 61.90407 61.10634 63.67618 60.03237 + 57.16235 56.56537 56.96714 57.57957 + 57.77707 57.96066 57.72130 57.57381 + 57.86317 58.62662 59.67696 60.65509 + + + + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 0.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO + ! NMA pure solvent, adm jr., 3/3/93 +CA 0.000000 -0.070000 1.950000 ! ALLOW ARO + ! benzene (JES) +CC 0.000000 -0.170000 1.800000 ! ALLOW PEP POL ARO + ! adm jr. 3/3/92, acetic acid heat of solvation +CD 0.000000 -0.200000 1.800000 ! ALLOW POL + ! adm jr. 3/19/92, acetate a.i. and dH of solvation +CE1 0.000000 -0.068000 2.090000 ! + ! for propene, yin/adm jr., 12/95 +CE2 0.000000 -0.064000 2.080000 ! + ! for ethene, yin/adm jr., 12/95 +CM 0.000000 -0.110000 2.100000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand carbon (KK 05/13/91) +CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH1 0.000000 -0.050000 2.200000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPH2 0.000000 -0.050000 2.200000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPM 0.000000 -0.090000 1.900000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT 0.000000 -0.300000 1.870000 0.000000 -0.090000 1.900000 ! ALLOW ARO + ! benzene (JES) +CS 0.000000 -0.110000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! isobutane pure solvent properties, adm jr, 2/3/92 +CT2 0.000000 -0.060000 2.010000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! Yin and MacKerell, adm jr., 5/30/02 +CT3 0.000000 -0.073000 2.020000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! Yin and MacKerell, adm jr., 5/30/02 +CY 0.000000 -0.350000 1.992400 ! ALLOW ARO + ! TRP, JWK 08/29/89 + +H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 +HA 0.000000 -0.022000 1.320000 ! + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HA1 0.000000 -0.020000 1.320000 ! + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HA2 0.000000 -0.032000 1.340000 ! + ! Yin and MacKerell, adm jr., 5/30/02 +HA3 0.000000 -0.023000 1.320000 ! + ! Yin and MacKerell, adm jr., 5/30/02 +HE1 0.000000 -0.031000 1.250000 ! + ! for propene, yin/adm jr., 12/95 +HE2 0.000000 -0.026000 1.260000 ! + ! for ethene, yin/adm jr., 12/95 +HB1 0.000000 -0.022000 1.320000 ! + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HB2 0.000000 -0.028000 1.340000 ! + ! Yin and MacKerell, adm jr., 5/30/02 +HC 0.000000 -0.016000 0.524500 ! ALLOW POL + ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 +HP 0.000000 -0.030000 1.308200 0.000000 -0.030000 1.358200 ! ALLOW ARO + ! JES 8/25/89 values from Jorgensen fit to hydration energy +HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS 0.000000 -0.120000 0.450000 ! ALLOW SUL + ! methanethiol pure solvent, adm jr., 6/22/92 +HT 0.000000 -0.046000 0.224500 ! ALLOW WAT + !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete +!HT 0.000000 -0.00000 0.2245000 +N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! JG 8/27/89; note: NH1 in ARG was changed to NC2. +NH1 0.000000 -0.300000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +NH2 0.000000 -0.150000 1.770000 ! ALLOW POL + ! adm jr. +NH3 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NP 0.000000 -0.200000 1.850000 ! ALLOW PRO + ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 +NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 0.000000 -0.350000 1.950000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR2 0.000000 -0.350000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NY 0.000000 -0.300000 1.900000 ! ALLOW ARO + ! trp, JWK +! +O 0.000000 -0.110000 1.900000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +OB 0.000000 -0.240000 1.950000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid carbonyl O +OC 0.000000 -0.240000 1.950000 ! ALLOW POL ION + ! JG 8/27/89 +OH1 0.000000 -0.377100 1.950000 ! ALLOW ALC ARO + ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) +OM 0.000000 -0.120000 1.700000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91) +OS 0.000000 -0.120000 1.800000 ! ALLOW ALC ARO + ! adm jr. 9/17/90, avoid O* wildcard +OT 0.000000 -0.286200 1.772900 ! ALLOW WAT + !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete +LP 0.0440 0.0000 0.8000 ! TIP4P lone pair +CAL 0.000000 -0.120000 1.710000 ! ALLOW ION + !Calcium (BP) +FE 0.010000 0.000000 0.650000 ! ALLOW HEM + ! Heme (6-liganded): Iron atom (KK 05/13/91) +S 0.000000 -0.470000 2.100000 ! ALLOW SUL ION + ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent +SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION + ! adm jr., 3/3/92, dimethyldisulphide pure solvent +SS 0.000000 -0.470000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +ZN 0.000000 -0.250000 1.090000 ! ALLOW ION + ! RHS March 18, 1990 +DUM 0.000000 -0.000000 0.000000 ! + ! dummy atom +HE 0.000000 -0.021270 1.4800 ! + ! helium, experimental pot. energy surface, adm jr., 12/95 +NE 0.000000 -0.086000 1.5300 + ! neon, semiempirical pot. energy surface, adm jr., 12/95 + + +NBFIX +!!OT OT -0.152073 3.5365 ! TIPS3P VDW INTERACTION +OT OT -0.28620 3.54586 ! TIPS4P VDW INTERACTION +HT HT 0.0 0.4490 +HT OT 0.0 1.9927 + + + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/cheq/top_all30_cheq_prot.inp b/charmm/toppar/cheq/top_all30_cheq_prot.inp new file mode 100755 index 00000000..711199df --- /dev/null +++ b/charmm/toppar/cheq/top_all30_cheq_prot.inp @@ -0,0 +1,1662 @@ +*CHARMM22 FLUC-Q Topology File for Proteins +* + 22 0 +MASS 1 H 1.00800 H ! polar H +MASS 2 HC 1.00800 H ! N-ter H +MASS 3 HA 1.00800 H ! nonpolar H +MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 5 HP 1.00800 H ! aromatic H +MASS 6 HR1 1.00800 H ! his he1, (+) his HG,HD2 +MASS 7 HR2 1.00800 H ! (+) his HE1 +MASS 8 HR3 1.00800 H ! neutral his HG, HD2 +MASS 9 HS 1.00800 H ! thiol hydrogen +MASS 10 HE1 1.00800 H ! for alkene; RHC=CR +MASS 11 HE2 1.00800 H ! for alkene; H2C=CR +MASS 12 HA1 1.00800 H ! aliphatic, bound to CT1 +MASS 13 HA2 1.00800 H ! aliphatic, bound to CT2 +MASS 14 HA3 1.00800 H ! aliphatic, bound to CT3 +MASS 15 HB1 1.00800 H ! aliphatic backbone H, to CT1 +MASS 16 HB2 1.00800 H ! aliphatic backbone H, to CT2 +MASS 20 C 12.01100 C ! carbonyl C, peptide backbone +MASS 21 CA 12.01100 C ! aromatic C +MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH +MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 +MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 +MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons +MASS 26 CPH2 12.01100 C ! his CE1 carbon +MASS 27 CPT 12.01100 C ! trp C between rings +MASS 28 CY 12.01100 C ! TRP C in pyrrole ring +MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) +MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) +MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) +MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 +MASS 34 CPA 12.01100 C ! heme alpha-C +MASS 35 CPB 12.01100 C ! heme beta-C +MASS 36 CPM 12.01100 C ! heme meso-C +MASS 37 CM 12.01100 C ! heme CO carbon +MASS 38 CS 12.01100 C ! thiolate carbon +MASS 39 CE1 12.01100 C ! for alkene; RHC=CR +MASS 40 CE2 12.01100 C ! for alkene; H2C=CR +MASS 50 N 14.00700 N ! proline N +MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen +MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen +MASS 53 NR3 14.00700 N ! charged his ring nitrogen +MASS 54 NH1 14.00700 N ! peptide nitrogen +MASS 55 NH2 14.00700 N ! amide nitrogen +MASS 56 NH3 14.00700 N ! ammonium nitrogen +MASS 57 NC2 14.00700 N ! guanidinium nitroogen +MASS 58 NY 14.00700 N ! TRP N in pyrrole ring +MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) +MASS 60 NPH 14.00700 N ! heme pyrrole N +MASS 70 O 15.99900 O ! carbonyl oxygen +MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid +MASS 72 OC 15.99900 O ! carboxylate oxygen +MASS 73 OH1 15.99900 O ! hydroxyl oxygen +MASS 74 OS 15.99940 O ! ester oxygen +MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN +MASS 76 OM 15.99900 O ! heme CO/O2 oxygen +MASS 81 S 32.06000 S ! sulphur +MASS 82 SM 32.06000 S ! sulfur C-S-S-C type +MASS 83 SS 32.06000 S ! thiolate sulfur +MASS 85 HE 4.00260 HE ! helium +MASS 86 NE 20.17970 NE ! neon +MASS 89 LP 0.000000 LP ! TIP4P +MASS 90 CAL 40.08000 CA ! calcium 2+ +MASS 91 ZN 65.37000 ZN ! zinc (II) cation +MASS 92 FE 55.84700 Fe ! heme iron 56 +MASS 99 DUM 0.00000 H ! dummy ATOM + + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DEFA FIRS none LAST none +AUTO ANGLES DIHE + + + +RESI ILE 0.0 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT1 -0.090 ECHH 306.79003 ECHA 98.44263 +ATOM HB HA1 0.090 ECHH 319.83594 ECHA 250.71406 +GROUP +ATOM CG2 CT3 -0.270 ECHH 319.64684 ECHA 120.17339 +ATOM HG21 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HG22 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HG23 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +GROUP +ATOM CG1 CT2 -0.180 ECHH 313.36138 ECHA 104.46972 +ATOM HG11 HA2 0.090 ECHH 318.27233 ECHA 250.71405 +ATOM HG12 HA2 0.090 ECHH 318.27233 ECHA 250.71405 +GROUP +ATOM CD CT3 -0.270 ECHH 319.64684 ECHA 120.17339 +ATOM HD1 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HD2 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HD3 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + + + + + +RESI ALA 0.0 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT3 -0.270 ECHH 319.64684 ECHA 120.17339 +ATOM HB1 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HB2 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HB3 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA N HN N CA +BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + + + +RESI LEU 0.0 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 313.36138 ECHA 104.46972 +ATOM HB1 HA2 0.090 ECHH 318.27233 ECHA 250.71405 +ATOM HB2 HA2 0.090 ECHH 318.27233 ECHA 250.71405 +GROUP +ATOM CG CT1 -0.090 ECHH 306.79003 ECHA 98.44263 +ATOM HG HA1 0.090 ECHH 319.83594 ECHA 250.71406 +GROUP +ATOM CD1 CT3 -0.270 ECHH 319.64684 ECHA 120.17339 +ATOM HD11 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HD12 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HD13 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +GROUP +ATOM CD2 CT3 -0.270 ECHH 319.64684 ECHA 120.17339 +ATOM HD21 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HD22 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HD23 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + + + + +RESI SER 0.0 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 0.050 ECHH 318.32246 ECHA 104.46972 +ATOM HB1 HA2 0.090 ECHH 313.80377 ECHA 250.71405 +ATOM HB2 HA2 0.090 ECHH 313.80377 ECHA 250.71405 +ATOM OG OH1 -0.660 ECHH 368.21306 ECHA 153.69934 +ATOM HG1 H 0.430 ECHH 257.82143 ECHA 258.63397 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + + + +RESI LYS 1.00 +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 313.36138 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +GROUP +ATOM CG CT2 -0.180 ECHH 313.36138 ECHA 104.46973 +ATOM HG1 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM HG2 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +GROUP +ATOM CD CT2 -0.180 ECHH 313.36138 ECHA 104.46973 +ATOM HD1 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM HD2 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +GROUP +ATOM CE CT2 0.210 ECHH 289.98519 ECHA 104.46973 +ATOM HE1 HA2 0.050 ECHH 289.23259 ECHA 250.71406 +ATOM HE2 HA2 0.050 ECHH 289.23259 ECHA 250.71406 +ATOM NZ NH3 -0.300 ECHH 252.73261 ECHA 129.95954 +ATOM HZ1 HC 0.330 ECHH 199.09579 ECHA 258.53102 +ATOM HZ2 HC 0.330 ECHH 199.09579 ECHA 258.53102 +ATOM HZ3 HC 0.330 ECHH 199.09579 ECHA 258.53102 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUBLE O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI CYS 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.110 ECHH 324.10774 ECHA 104.44482 +ATOM HB1 HA2 0.090 ECHH 316.22516 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 316.22516 ECHA 250.71406 +ATOM SG S -0.230 ECHH 358.52679 ECHA 121.70922 +ATOM HG1 HS 0.160 ECHH 292.64045 ECHA 236.71010 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + + +RESI GLN 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 316.60255 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 309.92563 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 309.92563 ECHA 250.71406 +GROUP +ATOM CG CT2 -0.180 ECHH 316.60255 ECHA 104.46972 +ATOM HG1 HA2 0.090 ECHH 309.92563 ECHA 250.71406 +ATOM HG2 HA2 0.090 ECHH 309.92563 ECHA 250.71406 +GROUP +ATOM CD CC 0.550 ECHH 329.95211 ECHA 107.22591 +ATOM OE1 O -0.550 ECHH 422.42521 ECHA 165.03958 +GROUP +ATOM NE2 NH2 -0.620 ECHH 325.52740 ECHA 129.95954 +ATOM HE21 H 0.320 ECHH 248.92062 ECHA 258.63396 +ATOM HE22 H 0.300 ECHH 248.92062 ECHA 258.63396 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD NE2 CG OE1 CD CG NE2 OE1 +IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + + + +RESI ASN 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 316.60255 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 309.92563 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 309.92563 ECHA 250.71406 +GROUP +ATOM CG CC 0.550 ECHH 329.95211 ECHA 107.22591 +ATOM OD1 O -0.550 ECHH 422.42521 ECHA 165.03958 +GROUP +ATOM ND2 NH2 -0.620 ECHH 325.52740 ECHA 129.95954 +ATOM HD21 H 0.320 ECHH 248.92062 ECHA 258.63396 +ATOM HD22 H 0.300 ECHH 248.92062 ECHA 258.63396 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +DOUBLE C O CG OD1 +IMPR N -C CA HN C CA +N O +IMPR CG ND2 CB OD1 CG CB ND2 OD1 +IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + + + + +RESI GLU -1.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 330.34515 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 329.33508 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 329.33508 ECHA 250.71406 +GROUP +ATOM CG CT2 -0.280 ECHH 330.34515 ECHA 104.46973 +ATOM HG1 HA2 0.090 ECHH 329.33508 ECHA 250.71406 +ATOM HG2 HA2 0.090 ECHH 329.33508 ECHA 250.71406 +ATOM CD CC 0.620 ECHH 373.01716 ECHA 107.22592 +ATOM OE1 OC -0.760 ECHH 464.94076 ECHA 165.03958 +ATOM OE2 OC -0.760 ECHH 464.94076 ECHA 165.03958 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +!IMPR OE1 CG OE2 CD +IMPR CD CG OE2 OE1 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + + + +RESI ASP -1.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.280 ECHH 330.34515 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 329.33508 ECHA 250.71405 +ATOM HB2 HA2 0.090 ECHH 329.33508 ECHA 250.71405 +ATOM CG CC 0.620 ECHH 373.01716 ECHA 107.22592 +ATOM OD1 OC -0.760 ECHH 464.94076 ECHA 165.03959 +ATOM OD2 OC -0.760 ECHH 464.94076 ECHA 165.03959 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +DOUBLE O C CG OD1 +IMPR N -C CA HN C CA +N O +!IMPR OD1 CB OD2 CG +IMPR CG CB OD2 OD1 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + + + + +RESI THR 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT1 0.140 ECHH 317.10600 ECHA 98.44263 +ATOM HB HA1 0.090 ECHH 324.32076 ECHA 250.71405 +ATOM OG1 OH1 -0.660 ECHH 373.91288 ECHA 153.69934 +ATOM HG1 H 0.430 ECHH 246.11112 ECHA 258.63396 +GROUP +ATOM CG2 CT3 -0.270 ECHH 319.64684 ECHA 120.17339 +ATOM HG21 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM HG22 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM HG23 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + + + + +RESI TRP 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 310.28712 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 316.75380 ECHA 250.71400 +ATOM HB2 HA2 0.090 ECHH 316.75380 ECHA 250.71400 +GROUP +ATOM CG CY -0.030 ECHH 323.36368 ECHA 77.81102 +ATOM CD1 CA 0.035 ECHH 332.37125 ECHA 112.74329 +ATOM HD1 HP 0.115 ECHH 319.45838 ECHA 227.07056 +ATOM NE1 NY -0.610 ECHH 302.88897 ECHA 109.15193 +ATOM HE1 H 0.380 ECHH 186.48607 ECHA 258.63396 +ATOM CE2 CPT 0.130 ECHH 320.67112 ECHA 95.60507 +ATOM CD2 CPT -0.020 ECHH 320.67112 ECHA 95.60507 +GROUP +ATOM CE3 CA -0.115 ECHH 332.37125 ECHA 112.74329 +ATOM HE3 HP 0.115 ECHH 319.45838 ECHA 227.07056 +GROUP +ATOM CZ3 CA -0.115 ECHH 332.37125 ECHA 112.74329 +ATOM HZ3 HP 0.115 ECHH 319.45838 ECHA 227.07056 +GROUP +ATOM CZ2 CA -0.115 ECHH 332.37125 ECHA 112.74329 +ATOM HZ2 HP 0.115 ECHH 319.45838 ECHA 227.07056 +GROUP +ATOM CH2 CA -0.115 ECHH 332.37125 ECHA 112.74329 +ATOM HH2 HP 0.115 ECHH 319.45838 ECHA 227.07056 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI MET 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 313.36138 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +GROUP +ATOM CG CT2 -0.140 ECHH 368.09633 ECHA 104.44482 +ATOM HG1 HA2 0.090 ECHH 372.00325 ECHA 250.71406 +ATOM HG2 HA2 0.090 ECHH 372.00325 ECHA 250.71406 +ATOM SD S -0.090 ECHH 405.91891 ECHA 121.70922 +ATOM CE CT3 -0.220 ECHH 327.72547 ECHA 120.17339 +ATOM HE1 HA3 0.090 ECHH 305.22896 ECHA 250.71406 +ATOM HE2 HA3 0.090 ECHH 305.22896 ECHA 250.71406 +ATOM HE3 HA3 0.090 ECHH 305.22896 ECHA 250.71406 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + + + + +RESI PHE 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 317.66960 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 312.42849 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 312.42849 ECHA 250.71406 +GROUP +ATOM CG CA 0.000 ECHH 332.41783 ECHA 112.74329 +GROUP +ATOM CD1 CA -0.115 ECHH 332.41783 ECHA 112.74329 +ATOM HD1 HP 0.115 ECHH 308.69580 ECHA 227.07056 +GROUP +ATOM CE1 CA -0.115 ECHH 332.41783 ECHA 112.74329 +ATOM HE1 HP 0.115 ECHH 308.69580 ECHA 227.07056 +GROUP +ATOM CZ CA -0.115 ECHH 332.41783 ECHA 112.74329 +ATOM HZ HP 0.115 ECHH 308.69580 ECHA 227.07056 +GROUP +ATOM CD2 CA -0.115 ECHH 332.41783 ECHA 112.74329 +ATOM HD2 HP 0.115 ECHH 308.69580 ECHA 227.07056 +GROUP +ATOM CE2 CA -0.115 ECHH 332.41783 ECHA 112.74329 +ATOM HE2 HP 0.115 ECHH 308.69580 ECHA 227.07056 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + + +RESI TYR 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 315.32573 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 318.09098 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 318.09098 ECHA 250.71406 +GROUP +ATOM CG CA 0.000 ECHH 325.09938 ECHA 112.74329 +GROUP +ATOM CD1 CA -0.115 ECHH 325.09938 ECHA 112.74329 +ATOM HD1 HP 0.115 ECHH 297.07676 ECHA 227.07056 +GROUP +ATOM CE1 CA -0.115 ECHH 325.09938 ECHA 112.74329 +ATOM HE1 HP 0.115 ECHH 297.07676 ECHA 227.07056 +GROUP +ATOM CZ CA 0.110 ECHH 325.09938 ECHA 112.74329 +ATOM OH OH1 -0.540 ECHH 364.84686 ECHA 153.69934 +ATOM HH H 0.430 ECHH 226.43012 ECHA 258.63397 +GROUP +ATOM CD2 CA -0.115 ECHH 325.09938 ECHA 112.74329 +ATOM HD2 HP 0.115 ECHH 297.07676 ECHA 227.07056 +GROUP +ATOM CE2 CA -0.115 ECHH 325.09938 ECHA 112.74329 +ATOM HE2 HP 0.115 ECHH 297.07676 ECHA 227.07056 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +DOUBLE O C CD1 CG CE1 CZ CE2 CD2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + + + + +RESI HSD 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.090 ECHH 329.81010 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 338.62251 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 338.62251 ECHA 250.71406 +ATOM ND1 NR1 -0.360 ECHH 338.34238 ECHA 126.12411 +ATOM HD1 H 0.320 ECHH 260.81817 ECHA 258.63396 +ATOM CG CPH1 -0.050 ECHH 349.68112 ECHA 121.34643 +GROUP +ATOM CE1 CPH2 0.250 ECHH 345.79126 ECHA 118.15622 +ATOM HE1 HR1 0.130 ECHH 314.08377 ECHA 265.58007 +ATOM NE2 NR2 -0.700 ECHH 396.72984 ECHA 123.47086 +ATOM CD2 CPH1 0.220 ECHH 349.68112 ECHA 121.34643 +ATOM HD2 HR3 0.100 ECHH 312.52715 ECHA 264.10651 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + + + + + +RESI VAL 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT1 -0.090 ECHH 306.79003 ECHA 98.44263 +ATOM HB HA1 0.090 ECHH 319.83594 ECHA 250.71406 +GROUP +ATOM CG1 CT3 -0.270 ECHH 319.64684 ECHA 120.17339 +ATOM HG11 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HG12 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +ATOM HG13 HA3 0.090 ECHH 315.55701 ECHA 250.71405 +GROUP +ATOM CG2 CT3 -0.270 ECHH 319.64684 ECHA 120.17339 +ATOM HG21 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM HG22 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM HG23 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + + + +RESI HSP 1.00 ! Protonated His +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.050 ECHH 308.73538 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 302.42841 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 302.42841 ECHA 250.71406 +ATOM CD2 CPH1 0.190 ECHH 297.35595 ECHA 121.34643 +ATOM HD2 HR1 0.130 ECHH 264.50951 ECHA 265.58007 +ATOM CG CPH1 0.190 ECHH 297.35595 ECHA 121.34643 +GROUP +ATOM NE2 NR3 -0.510 ECHH 279.32904 ECHA 123.47086 +ATOM HE2 H 0.440 ECHH 198.78874 ECHA 258.63397 +ATOM ND1 NR3 -0.510 ECHH 279.32904 ECHA 123.47086 +ATOM HD1 H 0.440 ECHH 198.78874 ECHA 258.63396 +ATOM CE1 CPH2 0.320 ECHH 274.19462 ECHA 118.15620 +ATOM HE1 HR2 0.180 ECHH 224.99361 ECHA 265.58090 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG NE2 CE1 +IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + + + +RESI HSE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.080 ECHH 329.81010 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 338.62251 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 338.62251 ECHA 250.71406 +ATOM ND1 NR2 -0.700 ECHH 396.72984 ECHA 123.47086 +ATOM CG CPH1 0.220 ECHH 349.68112 ECHA 121.34643 +ATOM CE1 CPH2 0.250 ECHH 345.79126 ECHA 118.15622 +ATOM HE1 HR1 0.130 ECHH 314.08377 ECHA 265.58007 +GROUP +ATOM NE2 NR1 -0.360 ECHH 338.34238 ECHA 126.12411 +ATOM HE2 H 0.320 ECHH 260.81817 ECHA 258.63396 +ATOM CD2 CPH1 -0.050 ECHH 349.68112 ECHA 121.34643 +ATOM HD2 HR3 0.090 ECHH 312.52715 ECHA 264.10651 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG CE1 ND1 +IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + + + + +RESI GLY 0.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 -0.020 ECHH 319.64684 ECHA 120.17339 +ATOM HA1 HB2 0.090 ECHH 266.05996 ECHA 250.71405 +ATOM HA2 HB2 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 + + +RESI ARG 1.00 +GROUP +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HN H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CA CT1 0.070 ECHH 319.64684 ECHA 120.17339 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71405 +GROUP +ATOM CB CT2 -0.180 ECHH 313.36138 ECHA 104.46973 +ATOM HB1 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +GROUP +ATOM CG CT2 -0.180 ECHH 313.36138 ECHA 104.46973 +ATOM HG1 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM HG2 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +GROUP +ATOM CD CT2 0.200 ECHH 313.36138 ECHA 104.46973 +ATOM HD1 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM HD2 HA2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM NE NC2 -0.700 ECHH 350.96041 ECHA 126.35324 +ATOM HE HC 0.440 ECHH 276.49391 ECHA 258.53102 +ATOM CZ C 0.640 ECHH 336.16817 ECHA 107.22592 +ATOM NH1 NC2 -0.800 ECHH 350.96041 ECHA 126.35324 +ATOM HH11 HC 0.460 ECHH 276.49391 ECHA 258.53102 +ATOM HH12 HC 0.460 ECHH 276.49391 ECHA 258.53102 +ATOM NH2 NC2 -0.800 ECHH 350.96041 ECHA 126.35324 +ATOM HH21 HC 0.460 ECHH 276.49391 ECHA 258.53102 +ATOM HH22 HC 0.460 ECHH 276.49391 ECHA 258.53102 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE O C CZ NH1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +IMPR CZ NH1 NH2 NE +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + + + +RESI PRO 0.00 +GROUP +ATOM N N -0.290 ECHH 344.16413 ECHA 115.86310 +ATOM CD CP3 0.000 ECHH 324.16415 ECHA 112.01937 +ATOM HD1 HA2 0.090 ECHH 317.70842 ECHA 250.71406 +ATOM HD2 HA2 0.090 ECHH 317.70842 ECHA 250.71406 +ATOM CA CP1 0.020 ECHH 321.66542 ECHA 98.00263 +ATOM HA HB1 0.090 ECHH 266.05996 ECHA 250.71406 +GROUP +ATOM CB CP2 -0.180 ECHH 327.80331 ECHA 114.15625 +ATOM HB1 HA2 0.090 ECHH 317.70842 ECHA 250.71406 +ATOM HB2 HA2 0.090 ECHH 317.70842 ECHA 250.71406 +GROUP +ATOM CG CP2 -0.180 ECHH 327.80331 ECHA 114.15625 +ATOM HG1 HA2 0.090 ECHH 317.70842 ECHA 250.71406 +ATOM HG2 HA2 0.090 ECHH 317.70842 ECHA 250.71406 +GROUP +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03958 +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +DOUBLE O C +IMPR N -C CA CD +IMPR C CA +N O +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 +PATCHING FIRS PROP + + +!RESI PRO 0.00 +!GROUP ! HD1 HD2 +!ATOM N N -0.29 ! | \ / +!ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02 +!ATOM HD1 HA2 0.09 ! | \ / +!ATOM HD2 HA2 0.09 ! | CG +!ATOM CA CP1 0.02 ! | / \ +!ATOM HA HB1 0.09 ! HA-CA--CB HG2 +!GROUP ! | / \ +!ATOM CB CP2 -0.18 ! | HB1 HB2 +!ATOM HB1 HA2 0.09 ! O=C +!ATOM HB2 HA2 0.09 ! | +!GROUP +!ATOM CG CP2 -0.18 +!ATOM HG1 HA2 0.09 +!ATOM HG2 HA2 0.09 +!GROUP +!ATOM C C 0.51 +!ATOM O O -0.51 +!BOND C CA C +N +!BOND N CA CA CB CB CG CG CD N CD +!BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +!DOUBLE O C +!IMPR N -C CA CD +!IMPR C CA +N O +!ACCEPTOR O C +!IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +!IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +!IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +!IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +!IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +!IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +!IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +!IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +!IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +!IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +!IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +!IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +!IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +!IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +!IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 + + + +PRES NTER 1.00 ! standard N-terminus +GROUP +ATOM N NH3 -0.300 ECHH 252.73261 ECHA 129.95954 +ATOM HT1 HC 0.330 ECHH 199.09579 ECHA 258.53102 +ATOM HT2 HC 0.330 ECHH 199.09579 ECHA 258.53102 +ATOM HT3 HC 0.330 ECHH 199.09579 ECHA 258.53102 +ATOM CA CT1 0.210 ECHH 317.10600 ECHA 98.44263 +ATOM HA HB1 0.100 ECHH 266.05996 ECHA 250.71405 +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + + + +PRES CTER -1.00 ! standard C-terminus +GROUP +ATOM C CC 0.340 ECHH 373.01716 ECHA 107.22592 +ATOM OT1 OC -0.670 ECHH 464.94076 ECHA 165.03958 +ATOM OT2 OC -0.670 ECHH 464.94076 ECHA 165.03958 +DELETE ATOM O +BOND C OT2 +DOUBLE C OT1 +!IMPR OT1 CA OT2 C +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES ACE 0.00 ! acetylated N-terminus +GROUP ! use in generate statement +ATOM CAY CT3 -0.270 ECHH 323.95532 ECHA 120.17339 +ATOM HY1 HA3 0.090 ECHH 302.47640 ECHA 250.71406 +ATOM HY2 HA3 0.090 ECHH 302.47640 ECHA 250.71406 +ATOM HY3 HA3 0.090 ECHH 302.47640 ECHA 250.71406 +GROUP +ATOM CY C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM OY O -0.510 ECHH 454.64172 ECHA 165.03959 + +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA HN +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + + +PRES CT3 0.00 ! N-Methylamide C-terminus +GROUP ! use in generate statement +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22592 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03959 +GROUP +ATOM NT NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM HNT H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CAT CT3 -0.110 ECHH 328.76012 ECHA 120.17339 +ATOM HT1 HA3 0.090 ECHH 310.47421 ECHA 250.71406 +ATOM HT2 HA3 0.090 ECHH 310.47421 ECHA 250.71406 +ATOM HT3 HA3 0.090 ECHH 310.47421 ECHA 250.71406 + +BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 +DIHE CA C NT CAT +IMPR NT C CAT HNT C CA NT O +DONOR HNT NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + + +PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. +GROUP ! use in a patch statement +ATOM 1CB CT2 -0.10 ECHH 324.10774 ECHA 104.44482 ! +ATOM 1SG SM -0.08 ECHH 358.52679 ECHA 121.70922 ! 2SG--2CB-- +GROUP ! / +ATOM 2SG SM -0.08 ECHH 358.52679 ECHA 121.70922 ! -1CB--1SG +ATOM 2CB CT2 -0.10 ECHH 324.10774 ECHA 104.44482 ! +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +ANGLE 1CB 1SG 2SG 1SG 2SG 2CB +DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG +DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG +DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA +DIHE 1CB 1SG 2SG 2CB +!DIHE 1CB 1SG 2SG 2CB +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + + + + +RESI TIP4 .000 ! TIPS4P WATER MODEL +GROUP +ATOM OH2 OT 0.000 ECHH 0.00000 ECHA 0.00000 +ATOM OM LP -0.888 ECHH 68.49000 ECHA 371.60000 +ATOM H1 HT 0.444 ECHH 0.00000 ECHA 353.00000 +ATOM H2 HT 0.444 ECHH 0.00000 ECHA 353.00000 +BOND OH2 H1 OH2 OM OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SH +THET H1 OH2 H2 +IC H1 OM *OH2 H2 0.9572 52.26 180.00 52.26 0.9572 +IC H2 H1 OH2 OM 0.0000 0.00 0.00 52.26 0.15 +PATC FIRS NONE LAST NONE + + + + +RESI SPCF .000 ! SPC WATER MODEL +GROUP +ATOM OH2 OT -0.820 ECHH 73.00000 ECHA 372.00000 +ATOM H1 HT 0.410 ECHH 0.00000 ECHA 396.00000 +ATOM H2 HT 0.410 ECHH 0.00000 ECHA 396.00000 +BOND OH2 H1 OH2 H2 H1 H2 +ANGLE H1 OH2 H2 +ACCE OH2 +PATC FIRS NONE LAST NONE + + +Resi ETHA 0.00 ! ethane, S. Fischer +Group +ATOM h11 ha3 0.090 ECHH 315.55702 ECHA 250.71406 +ATOM h12 ha3 0.090 ECHH 315.55702 ECHA 250.71406 +ATOM h13 ha3 0.090 ECHH 315.55702 ECHA 250.71406 +ATOM c1 ct3 -0.270 ECHH 319.64684 ECHA 120.17339 +Group +ATOM h21 ha3 0.090 ECHH 315.55702 ECHA 250.71406 +ATOM h22 ha3 0.090 ECHH 315.55702 ECHA 250.71406 +ATOM h23 ha3 0.090 ECHH 315.55702 ECHA 250.71406 +ATOM c2 ct3 -0.270 ECHH 319.64684 ECHA 120.17339 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 h21 c2 h22 c2 h23 +ic h11 c1 c2 h21 0.00 0.00 0.0 0.0 0.0 +ic h11 c1 c2 h22 0.00 0.00 120.0 0.0 0.0 +ic h11 c1 c2 h23 0.00 0.00 240.0 0.0 0.0 +ic h12 c1 c2 h23 0.00 0.00 120.0 0.0 0.0 +ic h13 c1 c2 h23 0.00 0.00 240.0 0.0 0.0 + + + +Resi PROP 0.00 ! propane, adm jr. +Group +ATOM h11 ha3 0.090 ECHH 315.55702 ECHA 250.71405 +ATOM h12 ha3 0.090 ECHH 315.55702 ECHA 250.71405 +ATOM h13 ha3 0.090 ECHH 315.55702 ECHA 250.71405 +ATOM c1 ct3 -0.270 ECHH 319.64684 ECHA 120.17339 +Group +ATOM c2 ct2 -0.180 ECHH 313.36136 ECHA 104.46972 +ATOM h21 ha2 0.090 ECHH 318.27230 ECHA 250.71405 +ATOM H22 ha2 0.090 ECHH 318.27230 ECHA 250.71405 +Group +ATOM h31 ha3 0.090 ECHH 315.55702 ECHA 250.71405 +ATOM h32 ha3 0.090 ECHH 315.55702 ECHA 250.71405 +ATOM h33 ha3 0.090 ECHH 315.55702 ECHA 250.71405 +ATOM c3 ct3 -0.270 ECHH 319.64684 ECHA 120.17339 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 h21 c2 h22 +bond c2 c3 c3 h31 c3 h32 c3 h33 +ic h11 c1 c2 c3 0.00 0.00 0.0 0.0 0.0 +ic h11 c1 c2 h21 0.00 0.00 120.0 0.0 0.0 +ic h11 c1 c2 h22 0.00 0.00 240.0 0.0 0.0 +ic c1 c2 c3 h31 0.00 0.00 0.0 0.0 0.0 +ic c1 c2 c3 h32 0.00 0.00 120.0 0.0 0.0 +ic c1 c2 c3 h33 0.00 0.00 240.0 0.0 0.0 +ic c3 c2 c1 h12 0.00 0.00 120.0 0.0 0.0 +ic c3 c2 c1 h13 0.00 0.00 120.0 0.0 0.0 + + + +RESI BUTA 0.00 +Group +ATOM h11 ha3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM h12 ha3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM h13 ha3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM c1 ct3 -0.270 ECHH 319.64684 ECHA 120.17339 +Group +ATOM h21 ha2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM h22 ha2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM c2 ct2 -0.180 ECHH 313.36138 ECHA 104.46973 +Group +ATOM h31 ha2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM h32 ha2 0.090 ECHH 318.27233 ECHA 250.71406 +ATOM c3 ct2 -0.180 ECHH 313.36138 ECHA 104.46973 +Group +ATOM h41 ha3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM h42 ha3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM h43 ha3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM c4 ct3 -0.270 ECHH 319.64684 ECHA 120.17339 +Bond h11 c1 h12 c1 h13 c1 c1 c2 +Bond h21 c2 h22 c2 c2 c3 +Bond h31 c3 h32 c3 c3 c4 +Bond h41 c4 h42 c4 h43 c4 +ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 +ic h11 c1 c2 h21 0.00 0.00 120.0 0.00 0.00 +ic h11 c1 c2 h22 0.00 0.00 240.0 0.00 0.00 +ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00 +ic h13 c1 c2 c3 0.00 0.00 240.0 0.00 0.00 +ic c1 c2 c3 c4 0.00 0.00 0.0 0.00 0.00 +ic c1 c2 c3 h31 0.00 0.00 120.0 0.00 0.00 +ic c1 c2 c3 h32 0.00 0.00 240.0 0.00 0.00 +ic h21 c2 c3 c4 0.00 0.00 120.0 0.00 0.00 +ic h22 c2 c3 c4 0.00 0.00 240.0 0.00 0.00 +ic c2 c3 c4 h41 0.00 0.00 0.0 0.00 0.00 +ic c2 c3 c4 h42 0.00 0.00 120.0 0.00 0.00 +ic c2 c3 c4 h43 0.00 0.00 240.0 0.00 0.00 +ic h31 c3 c4 h43 0.00 0.00 120.0 0.00 0.00 +ic h32 c3 c4 h43 0.00 0.00 240.0 0.00 0.00 + + + +RESI MEOH 0.00 ! methanol, adm jr. +GROUP ! order of ATOMs to match that used in ab initio +ATOM CB CT3 -0.040 ECHH 319.61609 ECHA 120.17339 +ATOM OG OH1 -0.660 ECHH 370.09577 ECHA 153.69934 +ATOM HG1 H 0.430 ECHH 263.77048 ECHA 258.63396 +ATOM HB1 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM HB2 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +ATOM HB3 HA3 0.090 ECHH 315.55701 ECHA 250.71406 +BOND CB OG OG HG1 +BOND CB HB1 CB HB2 CB HB3 +DONO HG1 OG +ACCE OG +! only for analysis +IC HG1 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HG1 OG CB HB2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HG1 OG CB HB3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG CB HB1 HB2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HG1 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 + + + + +RESI NMA 0.00 ! N-methylacetamide, Louis Kuchnir +GROUP +ATOM CL CT3 -0.270 ECHH 386.40888 ECHA 120.17339 +ATOM HL1 HA3 0.090 ECHH 376.34117 ECHA 250.71406 +ATOM HL2 HA3 0.090 ECHH 376.34117 ECHA 250.71406 +ATOM HL3 HA3 0.090 ECHH 376.34117 ECHA 250.71406 +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22591 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03959 +ATOM N NH1 -0.470 ECHH 341.31244 ECHA 129.95954 +ATOM H H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CR CT3 -0.110 ECHH 372.66416 ECHA 120.17339 +ATOM HR1 HA3 0.090 ECHH 389.32283 ECHA 250.71406 +ATOM HR2 HA3 0.090 ECHH 389.32283 ECHA 250.71406 +ATOM HR3 HA3 0.090 ECHH 389.32283 ECHA 250.71406 +BOND HL1 CL HL2 CL HL3 CL +BOND CL C C N N CR +BOND N H +BOND HR1 CR HR2 CR HR3 CR +DOUBLE C O +! multiple dihedrals (check) +DIHE CL C N CR +IMPR N C CR H +IMPR C CL N O + +ic o c n h 1.2233 122.84 180. 119.23 0.9933 ! variable 1 +ic h n c cl 0.9933 119.23 0. 116.25 1.5118 ! variable 8 +ic o c n cr 1.2233 122.84 0. 122.57 1.4488 ! variable 8 +ic n c cl hl1 1.3418 116.25 180. 109.3 1.109 ! variable 2 +ic n c cl hl2 1.3418 116.25 60. 109.3 1.109 ! variable 3 +ic n c cl hl3 1.3418 116.25 300. 109.3 1.109 ! variable 4 +ic c n cr hr1 1.3418 122.57 180. 110.7 1.113 ! variable 5 +ic c n cr hr2 1.3418 122.57 60. 110.7 1.113 ! variable 6 +ic c n cr hr3 1.3418 122.57 300. 110.7 1.113 ! variable 7 + + +RESI MAS 0.00 ! methylacetate +GROUP ! +ATOM C1 CT3 -0.170 ECHH 309.51727 ECHA 120.15679 +ATOM C CD 0.630 ECHH 319.22256 ECHA 107.19935 +ATOM OM OS -0.340 ECHH 357.88524 ECHA 153.61134 +ATOM C2 CT3 -0.140 ECHH 309.51727 ECHA 120.15679 +ATOM O OB -0.520 ECHH 401.02666 ECHA 164.94993 +ATOM H11 HA3 0.090 ECHH 291.69898 ECHA 250.64764 +ATOM H12 HA3 0.090 ECHH 291.69898 ECHA 250.64764 +ATOM H13 HA3 0.090 ECHH 291.69898 ECHA 250.64764 +ATOM H21 HA3 0.090 ECHH 291.69898 ECHA 250.64764 +ATOM H22 HA3 0.090 ECHH 291.69898 ECHA 250.64764 +ATOM H23 HA3 0.090 ECHH 291.69898 ECHA 250.64764 + +BOND C1 C C OM OM C2 +DOUBLE C O +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IMPR C C1 OM O +! internal coordinates from experiment for heavy ATOMs +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 + + + +RESI FORM 0.00 ! formamide, adm jr. +GROUP +ATOM HA HA1 0.080 ECHH 323.88327 ECHA 250.71406 +ATOM C CC 0.420 ECHH 354.45672 ECHA 107.22592 +ATOM N NH2 -0.690 ECHH 343.48907 ECHA 129.95954 +ATOM Hc H 0.350 ECHH 268.09520 ECHA 258.63396 +ATOM Ht H 0.350 ECHH 268.09520 ECHA 258.63396 +ATOM O O -0.510 ECHH 439.29594 ECHA 165.03959 + +BOND C HA C N N Hc N Ht +DOUBLE C O +!BOND O DUM +IMPR C HA N O c n ha o +! GAS PHASE GEOMETRY +!IC DUM O C N 1.00 90.0 0. 124.70 1.352 +IC O C N HC 1.2190 124.70 0. 118.50 1.0016 ! variable 1 +IC HC N C HA 1.0016 118.50 180. 112.70 1.0980 ! variable 2 +IC O C N HT 1.2190 124.70 180. 120.00 1.0015 ! variable 3 + + + +RESI ACEH 0.00 ! acetic acid, ADM jr. +GROUP +ATOM C2 CT3 -0.300 ECHH 315.45540 ECHA 120.15679 +ATOM C1 CD 0.750 ECHH 325.03867 ECHA 107.19935 +ATOM H21 HA3 0.090 ECHH 299.55521 ECHA 250.64764 +ATOM H22 HA3 0.090 ECHH 299.55521 ECHA 250.64764 +ATOM H23 HA3 0.090 ECHH 299.55521 ECHA 250.64764 +ATOM O2 OB -0.550 ECHH 402.85345 ECHA 164.94993 +ATOM O1 OH1 -0.610 ECHH 350.93400 ECHA 153.61134 +ATOM HO1 H 0.440 ECHH 236.96905 ECHA 258.63397 +BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23 +DOUBLE C1 O2 +IMPR C1 C2 O1 O2 +DONO BLNK HO1 ! O1 +ACCE O1 +ACCE O2 +IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 +IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 + + + +RESI NMF 0.00 ! N-methylformamide,SAPATEL +GROUP +ATOM HL HA1 0.090 ECHH 323.88327 ECHA 250.71406 +ATOM C C 0.510 ECHH 360.67099 ECHA 107.22591 +ATOM O O -0.510 ECHH 454.64172 ECHA 165.03959 +ATOM N NH1 -0.510 ECHH 341.31244 ECHA 129.95954 +ATOM H H 0.310 ECHH 263.18689 ECHA 258.63397 +ATOM CR CT3 -0.160 ECHH 372.66416 ECHA 120.17339 +ATOM HR1 HA3 0.090 ECHH 389.32283 ECHA 250.71406 +ATOM HR2 HA3 0.090 ECHH 389.32283 ECHA 250.71406 +ATOM HR3 HA3 0.090 ECHH 389.32283 ECHA 250.71406 +BOND HL C +BOND C N N CR +BOND N H +BOND HR1 CR HR2 CR HR3 CR +DOUBLE C O +! multiple dihedrals (check) +DIHE O C N CR +IMPR N C CR H +IMPR C H N O + diff --git a/charmm/toppar/drude/00readme b/charmm/toppar/drude/00readme new file mode 100644 index 00000000..3b41871b --- /dev/null +++ b/charmm/toppar/drude/00readme @@ -0,0 +1,259 @@ +* $Id: 00readme 34 2015-08-04 21:09:45Z alex $ + +Toppar files for polarizable model based on the classical Drude +oscillator. + +August 2015 release +adm jr. + +Included are the toppar stream files to perform calculations with the +classical Drude oscillator polarizable force field. Each stream file +includes both the topology and parameters for that class of compounds. +In ALL cases the master file, toppar_drude_master_protein_2013c.str, +must initally be streamed, followed by any additional files that are +required. The master file contains the water model, all ions and the +proteins. + +See the test subdirectory for test cases. + +drude_may13b.doc contains the CHARMM Drude documentation + +Note: This is a force field in development and the coverage is limited. For +example, at this time only the lipids DPPC and DMPC are available. + +toppar_drude_master_protein_2013c.str: master file with water, ions +and protein. Must be read first in all cases. + +toppar_drude_carbohydrate_2013c.str: carbohydrates including polyols, +hexapyranoses and furanoses. No glycosidic linkages are currently +available. + +toppar_drude_lipid_2013c.str: lipids (DPPC and DMPC only) + +toppar_drude_model_2013c.str: model compounds used for development of +the majority of the nonbond parameters. Note that model compounds +specific for the indvidual classes molecules are included in the +respective toppar stream files. + +toppar_drude_nucleic_acid_2013c.str: DNA only + +NOTE: These parameters are developmental and may change in future +release of the Drude polarizabile force field. + +References + +Water + +SWM4-NDP, negative Drude (this will be the default model): Lamoureux, +G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D., +Jr., A polarizable model of water for molecular dynamics simulations +of biomolecules, Chemical Physics Letters, 2006, 418: 245-249. + +SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander +D. MacKerell, Jr. "Six-site Polarizable Model of Water Based on the +Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508, +2013 + +Proteins + +Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and +MacKerell, A.D., Jr., “Polarizable Force Field for Peptides and +Proteins based on the Classical Drude Oscillator,” Journal of +Chemical Theory and Computation, 9: 5430–5449, 2013 DOI: +10.1021/ct400781b, NIHMS53671 + +Atomic ions + +Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I., +Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating +Monovalent and Divalent Ions in Aqueous Solution Using a Drude +Polarizable Force Field, “Journal of Chemical Theory and Computation, +6: 774–786, 2010 + +Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B., +“Simulation study of ion pairing in concentrated aqueous salt +solutions with a polarizable force field,” Faraday Discussions, 160, +135–149, 2013, PMC3695446 + +Lipids + +Chowdhary, J., Harder, E., Lopes, P.E.M., MacKerell, Jr., A.D, and +Roux, B., “A Polarizable Model for Phosphatidylcholine-Containing +Biological Membranes,” Journal of Physical Chemistry, B.,117: +9142-9160, 2013. + +Nucleic Acids + +Savelyev, A. and MacKerell, A.D., Jr., “All-Atom Polarizable Force +Field for DNA Based on the Classical Drude Oscillator Model,” Journal +of Computational Chemistry, 35: 1219-1239, 2014, DOI: 10.1002/jcc.23611 + +Parameters for Monovaletn Ions-DNA Interactions +Savelyev, A. and MacKerell, A.D., Jr., “Balancing the Interactions of Ions, +Water, and DNA in the Drude Polarizable Force Field,” Journal +of Physical Chemistry B, 118: 6742−6757, 2014, DOI: 10.1021/jp503469s + +Savelyev, A. and MacKerell, A.D., Jr., “Competition among Li+, Na+, K+, and Rb+ +Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 +and Drude Polarizable Force Fields,” Journal of Physical Chemistry B, 119: 4428−4440, 2015, +DOI: 10.1021/acs.jpcb.5b00683 + +Carbohydrates + +Hexapyranoses: Note that revisions to the hexapyranoses are ongoing + +Patel, D.S., He, X., and MacKerell, A.D., Jr., +“Polarizable Empirical Force Field for Hexopyranose Monosaccharides +based on the Classical Drude Oscillator,” Journal of Physical +Chemistry B., ASAP article, 2014, 10.1021/jp412696m, NIHMSID #566721 + +polyalcohols + +He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., “Polarizable +Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical +Drude Oscillator,” Biopolymers, 99: 724-738 2013, DOI: +10.1002/bip.22286 + +furanoses + +Jana, M. and MacKerell, A.D., Jr., “CHARMM Drude Polarizable Force +Field for Aldopentofuranoses and Methyl-aldopentofuranosides,” Journal +of Physical Chemistry B, 119: 7846-7859, 2015, doi: +10.1021/acs.jpcb.5b01767, PMC4483154 + +Review + +Lopes, P.E.M., B. Roux, R., MacKerell, A.D., Jr. “Molecular modeling +and dynamics studies with explicit inclusion of electronic +polarizability. Theory and applications.” Theoretical Chemistry +Accounts, 124:11-28, 2009, PMC2888514 + +General method + +Anisimov, V.M., Lamoureux, G., Vorobyov, I.V., Huang, N., +Roux, B. and MacKerell, A.D., Jr. :Determination of Electrostatic +Parameters for a Polarizable Force Field Based on the Classical Drude +Oscillator," Journal of Chemical Theory and Computing, 1:153-168, +2005. + +Water model (see POSTIVE DRUDE REFERENCES below) + +SWM4-NDP, negative Drude (this will be the default model): Lamoureux, +G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D., +Jr., A polarizable model of water for molecular dynamics simulations +of biomolecules, Chemical Physics Letters, 2006, 418: 245-249. + +SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander +D. MacKerell, Jr. "Six-site Polarizable Model of Water Based on the +Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508, +2013 + +Alkanes: + +Igor V. Vorobyov, Victor M. Anisimov and Alexander D. MacKerell, +Jr. "Polarizable Empirical Force Field for Alkanes Based on the +Classical Drude Oscillator Model," Journal of Physical Chemistry B, +109: 18988-18999, 2005. + +Anisotropic polarizability model: + +Harder, E., Anisimov, V.M., Vorobyov, I.V., Lopes, P.E., Noskov, S., +MacKerell, A.D., Jr. and Roux, B. Atomic Level Anisotropy in the +Electrostatic Modeling of Lone Pairs for a Polarizable Force Field +based on the Classical Drude Oscillator, Journal of Chemical Theory +and Computation, 2: 1587-1597, 2006 + +Ethers: + +Vorobyov, I.V., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., +Pastor, R.W. and MacKerell, A.D., Jr., Additive and Classical Drude +Polarizable Force Fields for Linear and Cyclic Ethers, Journal of +Chemical Theory and Computation, 3: 1120-1133, 2007. + +Baker, C. and MacKerell, Jr. A.D., “Polarizability Rescaling and +atom-based Thole Scaling in the CHARMM Drude Polarizable Force Field +for Ethers” Journal of Molecular Modeling, 16: 567-576, 2010, +PMC2818097 + +Sulfur containing compounds + +Zhu, X. and MacKerell, A.D., Jr. “Polarizable Empirical Force Field +for Sulfur-Containing Compounds Based on the Classical Drude +Oscillator Model,” Journal of Computational Chemistry, 12: 2330-2341, +2010. PMC2923574 + +Alcohols: + +Anisimov, V.M., Vorobyov, I.V., Roux, B., and MacKerell, A.D., Jr. +Polarizable empirical force field for the primary and secondary +alcohol series based on the classical Drude model. Journal of Chemical +Theory and Computation, 3, 1927-1946, 2007. + +Amides: + +Harder, E., Anisimov, V.M., Whitfield, T., MacKerell, A.D., Jr., Roux, +B. "Understanding the Dielectric Properties of Liquid Amides from a +Polarizable Force Field," Journal of Physical Chemistry, +112:3509-3521. 2008, PMID: 18302362 + +Amide model used in 2013 protein FF + +Lin, B., Lopes, P.E.M., Roux, B., and MacKerell, A.D., Jr., +“Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide +Solutions Modeled by the CHARMM Additive and Drude Polarizable Force +Fields,” Journal of Chemical Physics, 139: 084509, 2013, PMC3772949 + +Aromatics: + +Lopes, P., Lamoureux, G., Roux, B., MacKerell, A.D., Jr., "Polarizable +Empirical Force Field for Aromatic Compounds Based on the Classical +Drude Oscillator," Journal of Physical Chemistry, B. 111:2873-2885, +2007 + +Heterocycles + +Lopes, P.E.M., Lamoureux, G., MacKerell, A.D., Jr., “Polarizable +Empirical Force Field for Nitrogen-containing Heteroaromatic Compounds +Based on the Classical Drude Oscillator” Journal of Computational +Chemistry, 30: 1821-1838, 2009, PMC251901 + +Nucleic Acid Bases + +Baker, C.M., Anisimov, V.M., and MacKerell, A.D., Jr., “Development of +CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the +Classical Drude Oscillator Model,” Journal of Physical Chemistry, +B. 115; 580–596, 2011, PMC3166616 + +Polyalcohols + +He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., “Polarizable +Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical +Drude Oscillator,” Biopolymers, 99: 724-738 2013, DOI: +10.1002/bip.22286 + +Atomic Ions + +Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I., +Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating +Monovalent and Divalent Ions in Aqueous Solution Using a Drude +Polarizable Force Field, “Journal of Chemical Theory and Computation, +6: 774–786, 2010 + +Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B., +“Simulation study of ion pairing in concentrated aqueous salt +solutions with a polarizable force field,” Faraday Discussions, 160, +135–149, 2013,PMC3695446 + +POSTIVE DRUDE REFERENCES + +SWM4-DP, positive Drude (works with ions of Lamoureux and Roux): +Lamoureux, G., MacKerell, A.D., Jr., Roux, B. "A simple polarizable +model of water based on classical Drude oscillators," Journal of +Chemical Physics, 119: 5185-5197, 2003 + +Ions + +Lamoureux, G.; Roux, B. Absolute Hydration Free Energy Scale for +Alkali and Halide Ions Established from Simulations with a Polarizable +Force Field, J. Phys. Chem. B 2006, 110, 3308 + diff --git a/charmm/toppar/drude/drude_aug15.doc b/charmm/toppar/drude/drude_aug15.doc new file mode 100644 index 00000000..b20a8dbc --- /dev/null +++ b/charmm/toppar/drude/drude_aug15.doc @@ -0,0 +1 @@ +CHARMM Element doc/drude.doc $Revision: 1.1.1.1 $ File: DRUDE, Node: Top, Next: Syntax, Up: (chmdoc/commands.doc) Polarizable Drude Oscillator Format by Benoit Roux (roux@uchicago.edu) and Guillaume Lamoureux (Guillaume.Lamoureux@umontreal.ca) and Alex MacKerell Jr. (alex@outerbanks.umaryland.edu) Classical drude particles are generated for all atoms for which polarizabilities (ie. via the ALPHA keyword) are specified in the RTF file. This allows for the drudes to be generated automatically when a molecule is generated in CHARMM (only the heavy atoms carry a polarizability in the current force field but the code is general and allows assigning a polarizability to any atom including hydrogens). In addition, code has been developed to allow for inclusion of atom-based Thole scale factors, atom-based anisotropic polarizabilities and the addition of lone pairs to selected atoms at the RTF level. These capabilities allow for all the information for the polarizable Drude force field to be included in the RTF and parameter files. This implementation replaces the old "Drude Oscillator Command" and "ANISOTROPY keyword" (see below) used to generate the Drude polarizable model prior to July 2007. For each atom with a specified polarizability, a "Drude oscillator" is created by attaching to the atom an additional particle (using a fictitious chemical bond of length zero and of force constant 'KDRUDE = k/2'). Each Drude particle is given a mass and a charge, taken from the mass and the charge of its atom (so that the total mass and charge are conserved for the "atom-Drude" pair). As a whole, each "atom-Drude" pair carries a total charge 'q', unchanged From the partial charge the non-polarizable atom had prior to calling the DRUDE command during system generation. The "atom-Drude" pair forms a dipole 'q*d', where 'q' is the charge on the Drude particle and 'd' is the displacement vector going from the atom to its Drude particle. Any external electrostatic field 'E' creates a net displacement 'd = q*E/k', and thus the "atom-Drude" pair behaves as a point charge 'q' with a polarizability 'alpha = q**2/k'. The polarizabilities (in Angst**3) are specified with the ALPHA command in the RTF, along with the THOLE factors (see below), and converted into charges 'q', assuming a force constant 'k = 2*KDRUDE', where KDRUDE is specified in the parameter file (see below); a value of 500 should always be used. See J. Chem. Phys. 119, 3025-3039 (2003) for more details. In the Drude treatment of polarization the force constant of the spring between the atom-Drude pair is a diagonal rank-2 tensor with components KDRUDE. This leads to an isotropic atomic polarizability, 'alpha = alpha_{11} = alpha_{22} = alpha_{33} = q**2/k'. The ANISOTROPY command, which is typically included in the RTF, modifies the components of the Drude force constant tensor allowing for anisotropic atomic polarizabilites. See J. Chem. Theory Comput. 2, 1587-1597 (2006) for more details. The bonded lists are modified so that, if the "real" atoms are in a 1-2, 1-3, or 1-4 relationship, their corresponding Drude particles will also be in a 1-2, 1-3, or 1-4 relationship, respectively. For a single atom (charges in parenthesis): DRUDE A --------> A~DA For a diatomic molecule: A1 DRUDE A1~DA1 | --------> | A2 A2~DA2 1-2 pairs: A1-A2, A1-DA2, DA1-A2, DA1-DA2 For a triatomic molecule: A1 A1~DA1 \ DRUDE \ A2 --------> A2~DA2 / / A3 A3~DA3 1-2 pairs: A1-A2, A1-DA2, DA1-A2, DA1-DA2, A2-A3, A2-DA3, DA2-A3, DA2-DA3 1-3 pairs: A1-A3, A1-DA3, DA1-A3, DA1-DA3 Thus, the bonded interactions are modified to allow 1-2 and 1-3 screened dipole-dipole interactions, as proposed by Thole [see Chem.Phys. 59, 341 (1981)]. If two atoms were not "seeing" each others in the non-polarizable force field, their dipoles (and only their dipoles, not their net partial charges) will "see" each others in the polarizable force field. The screening function strength is modulated by a parameter "a" that has been generalized to depend on the atom type associated with the interacting pair of Drude oscillators and are then generated via a standard arithmetic combination rule (a = a_i + a_j). These variable atomic THOLE parameters "a_i" are specified in the RTF through the THOLE keyword. * Menu: * Description:: Description of new DRUDE model RTF Description of new DRUDE model RTF 1) Items in RTF file A) The AUTOGENERATE command now includes a flag for the drude particles. This should be specified at the beginning of the RTF. AUTO ANGLES DIHE DRUDE B) MASS statements must be included for Drude particle types. MASS 104 DRUD 0.00000 DD ! drude particle The default drude type is DRUD. However, alternate drude types may be specified. These additional drude types must be i) specified with MASS statements, ii) the ATOMs to which they are applied must include a "TYPE drudetype" statement and iii) the NONBond parameters must be specified. For example, to include a special drude type on water the following would be needed in the RTF i) MASS 153 DOH2 0.00000 DD ! water Drude ii) ATOM OH2 ODW 0.00000 ALPHA -0.97825258 TYPE DOH2 iii) (NONBOND section) D* 0.0 -0.0000 0.0000 ! Wildcard for Drudes and dummy atom iv) (via NBFIX) MAGD DOH2 -0.01000 3.10000 Term iv) is an NBFIX that allows for the interactions between, for example, magnesium and the water drude to be treated with a special LJ term. Indeed, the motivation for additional drude types are such special terms may be applied in special cases. Note that NBFIX terms have been used between select real atoms in the Drude force field to improve the free energies of hydration. See J. Chem. Theory Comput. 6. 1181-1198 (2010) for more details. C) ALPHA and THOLE parameters are set in the RTF after the charge. The presence of the "ALPHA" keyword flags that atom as being polarizable and a drude particle is created and assigned to it when calling the GENERATE command. An atom based Thole scale factor may also be specified via the "THOLE" keyword. If the THOLE term is missing, a default value of 1.3 is assigned to that atom. This corresponds to a parameter a = a_i + a_j = 2.6 which is the THOLE parameter in the old Drude command syntax. ATOM C C 0.630 ALPHA -1.104 THOLE 1.073 Note that a negative sign on alpha leads to the charge on the Drude particle to be negative. This convention was chosen because the Drudes are meant to represent electronic degrees of freedom of the system. D) Specific drude types for a polarizable atom may be specified as follows using the "TYPE" keyword. See 1A) above, sections i to iv for more details. ATOM C C 0.630 ALPHA -1.104 TYPE DC E) Lone pairs may now be set directly in the RTF using a syntax similar to the standard lonepair command (lonepair.doc). All options for the generation of lonepairs (FIXed, CENTer, COLOcate etc.) as specified in the lonepair documentation may be used although the atom selection specification is simplified as shown in the following example. LONEPAIR relative LPA O C CL distance 0.3 angle 91.0 dihe 0.0 LONEPAIR relative LPB O C N distance 0.3 angle 91.0 dihe 0.0 F) Atom based anisotropic polarizabilities may be assigned to selected atoms via the ANISOTROPY keyword in the RTF. The anisotropic polarizability tensor is defined as ALPHA_iso (the isotropic polarizability) times a tensor A whith trace{A}=3. The tensor A is diagonal in the local reference frame and is completely specified by {A11, A22, A33}. The first atom selects the atom on which the polarizability is to be made anisotropic. The second atom along with the first defines the "11" direction of the {A} tensor and the 3rd and 4th atom selections define the "22" direction of the tensor, with the anisotropy defined by fractional polarizability components. Accordingly, only the 11 and 22 direction are needed since the trace of the {A} tensor is set to 3. An example follows ANISOTROPY O C CA N A11 0.6968 A22 1.2194 In the code, the variables A11 and A22 are read into the variables A11ANIS(IPT) and A22ANIS(IPT). We define the components of the tensor relative to the isotropic drude, so ALPHA11+ALPHA22+ALPHA33 = 3*ALPHA_iso. The factors A11 and A22 (and A33) represent the factors modifying the components of the isotropic polarizability tensor q**2/KDRUDE. For example, setting A11=A22=1 would keep the Drude completely isotropic. By virtue of the trace we know that A11+A22+A33=3, so we only need to set two of these terms. Thus A33 = THREE-A11ANIS(IPT)-A22ANIS(IPT). This sets the relative magnitude of the polarizability tensor in all 3 directions. Once the polarizability along a given direction is known, we need to get the harmonic force constant in this direction. As the polarizability in a given direction is defined as QDRUDE**2/K_direction, the 3 harmonic force constants are thus K11(NANISO) = ONE/A11ANIS(IPT) K22(NANISO) = ONE/A22ANIS(IPT) K33(NANISO) = ONE/A33 Now, in principle this would mean that you have to calculate the forces from 3 different springs (K11, K22, K33) in 3 different directions. But since we know the overall trace which is related to the isotropic polarizability, we are going to re-write this so that there are only 2 springs with force constants KPAR in the parallel and KPERP in the perpendicular direction, and add an isotropic KDRUDE spring on top of that. 2) Items in the Parameter file A) The KDRUDE force constant for all the atoms is set by a wildcard in the bond parameters. The term must be included for all drude types included in the model. The wildcard terms can be overwritten by putting chemical type specific bond parameters following the wild card term. Note that 500.00 is the default force constant and should not be changed. DRUD X 500.000 0.0000 DRUD O 487.740 0.0000 B) NONBOND parameters must be included for all drude types. In addition, NBFIX terms for the drudes may be included as needed (see 1A above). C) A pair-specific Thole shielding can be introduced in the parameter file for any nonbond pair (following a syntax similar to NBFIX) using the keyword THOLe. This feature was introduced to permit accurate models of divalent cations with polarizable atoms. The TCUT assigns a radius within which all Thole interaction are calculated between the specificed atoms. The 'aij' typically is assigned by the user. A default value 1.2 can also be used. THOLE TCUT 5.0 MAXNBTHOLE 50000 CL SODD @aij 3) Command Line Items A) A "DRUDE" flag must be included with the GENErate command to specify the inclusion of drudes on the molecule. The drude mass is set in this command using the DMASS keyword followed by the mass in AMU; a value of 0.4 is highly suggested. generate NMA first none last none setup warn DRUDE DMASS 0.4 An additional command that may be included with the generate command is the HYPErpolarizability term. This command invokes a higher exponent half-wall potential on the Drude particles to minimize the potential for polarization catastrophe. In the HYPEpolarzation command HORD is the order of the exponent, KHYP is the force constant and RHYP represent atom-Drude distance at which the hypepolarization term is invoked. An example of the command follows. Note that if DrudeHardWall, as described in the following section, use of HYPErpolarization is not required. Experience with several systems suggest that the DrudeHardWall feature is a more effective way than HYPER to generate stable simulations with a 1 fs timesteps. generate NMA first none last none setup warn DRUDE DMASS 0.4 HYPE HORD 4 KHYP 40000 RHYP 0.2 B) DrudeHardWall command When the Drude particles move far away from the nucleus (eg. > 0.2 Ang.), simulations become unstable and polarization catastrophe may occur. Introducing hard wall constraints on the length of Drude-nuclei bonds is a way to avoid such instability. In each MD step, the length of Drude bonds are checked and compared with "L_WALL". When the length of a Drude bond is larger than "L_WALL", the relative velocities along bond vector are flipped and scaled down according to the temperature of the drude bond. In addition, the displacement relative to "L_WALL" is flipped and scaled down according to new velocities along the bond vector to make sure the Drude bond is not longer than "L_WALL". DrudeHardWall L_WALL real Example: DrudeHardWall L_WALL 0.2 ! set the hard wall at 0.2 Angstrom DrudeHardWall L_WALL 0.0 ! turn off the hard wall when L_WALL equals 0.0 Description of Extended PSF format for CHARMM and NAMD The PSF has been extended for the Drude model. The default format is for CHARMM and the XPLOR format is for NAMD. The PSF following generation of the Drude model explicitly provides the THOLE, ALPHA, lone pair and anisotropic polarization information for CHARMM/NAMD PSF reader. * Menu: * Syntax:: Syntax of the DRUDE command * Description:: Description of the DRUDE command * Toppar:: Effect on the topology and parameters * Warnings:: To be aware of when using the DRUDE command * Examples:: Usage examples of the DRUDE command File: DRUDE, Node: Syntax, Previous: Top, Next: Description, Up: Top Syntax of the DRUDE command DRUDe RESEt GENErate { generate-spec } DRUDe [DMASS real] [KDRUde real] [HYPE] { hype-spec } generate-spec::= [see struct.doc] File: DRUDE, Node: Description, Previous: Syntax, Next: Toppar, Up: Top Description of the DRUDE command ------------------------------------------------------------------- Keyword Default Purpose ------------------------------------------------------------------- RESET Deactivates the Drude particles. After a reset, the user should delete all Drude particles. DMASS 0.0 Mass of the Drude oscillators (in amu). The default zero value causes the masses to be read from the topology file. Any nonzero value will override the topology file. A value of 0.4 is suggested. KDRUDE 0.0 Force constant of the atom-Drude bonds (in kcal/mol/Angst**2). The default zero value causes the bond force constants to be read from the parameter file. Any nonzero value will override the parameter file. A value of 500. is suggested. VTHOLE Uses variable thole parameters for dipole-dipole interactions. This term is set by default and is only used in the fitcharge routine. ALPHA 0.0 Atomic polarizability specificed in the parameter file. Zero indicates no polarizability on that atom. THOLE 2.6 The screening factor for dipole-dipole interactions between atoms excluded from the non-bonded interactions. To have no dipole-dipole interactions between these bonded atoms, use THOLE = 0. THOLE is specified in the parameter file. SHAPE 1 Specifies the shape of the dipole-dipole screening function. Only 1 option is currently available. HYPE Off Specify the inclusion of hyperpolarization term on the Drude oscillators to minimize potential of polarization catastophe hype-spec::= [HORD int] [KHYP int] [RHYP real] (XXXXX defaults have not been set for the following, may be a good idea XXXXXX) HORD xx Order of the exponent the hyperpolarization. Typically 4. KHYP xx Force constant. Typically 40,000. RHYP xx Atom-Drude distance of the flat-well potential. The hyperpolarization is not activited until the atom-Drude distance is greater than RHYP. Typically 0.2 Angst. ------------------------------------------------------------------- 1) KDRUDE KDRUDE is the force constant (in kcal/mol/Angst**2) for the bond between each atom and its Drude particle the user wishes to use. It overrides any bond constant found in the parameter file. The default value for KDRUDE is 500 kcal/mol/Angst**2. This should NOT be changed! The atomic polarizabilities (in Angst**3) may be read from the WMAIN array: alpha = abs(WMAIN) The charge on every Drude particle is computed using the following formula: q = sqrt( 2*KDRUDE * alpha / CCELEC ) * sign(WMAIN) The charges are given the signs of the WMAIN values. As long as KDRUDE is large enough, the Drude particles will stay very close to their atoms, and the sign of 'q' is irrelevant. However, as the Drude represents the electronic degrees of freedom, the sign of alpha is set to a negative value, thereby yielding a negative charge on the Drude particles. ------------------------------------------------------------------- 2) THOLE, SHAPE For 1-2 and 1-3 atoms only. All other interactions are regular Coulombic. See THOLE keyword in the parameter file to perform Thole scaling between nonbonded atoms. The THOLE parameter is a dimensionless factor that specifies the extent of the smearing of the charge 'q' on the Drude oscillators and of a contribution '-q' on the "real" atom. The default value of THOLE is 2.6, that is, the 1-2 and 1-3 dipole-dipole interactions are turned on by default. To turn the interactions off, set THOLE to zero. The default constant THOLE of 2.6 can be replaced by variable thole by specifying an atom specific Thole value in the topology file. The THOLE parameter between oscillators I and J is given by THOLE = THOLEI + THOLEJ. Values of THOLEI may also be given in the WCOMP array for all Drude oscillator containing atoms prior to the DRUDE command. Because the dipole are explicitly made of two charges, the screened dipole-dipole interaction between two polarizable atoms (that is, two "atom-Drude" pairs) is actually the sum of the following four screened charge-charge interactions: ('q1' on Drude 1) - ('q2' on Drude 2) ('q1' on Drude 1) - ('-q2' on atom 2) ('-q1' on atom 1) - ('q2' on Drude 2) ('-q1' on atom 1) - ('-q2' on atom 2) The screened charge-charge interaction has the form: U(r12) = CCELEC * q1*q2 * S(u12)/r12 where 'u12' is the normalized distance: u12 = r12 * THOLE / (alpha1*alpha2)**(1/6) 'S' is a screening function defined by the SHAPE parameter: SHAPE Screening function Charge distributions 1 S(u) = 1 - (1+u/2)*exp(-u) Slater-Delta 2 S(u) = erf(u) Gaussian The default value of SHAPE is 1, which is also the only shape currently implemented. SHAPE=2 is reserved for Gaussian-Gaussian distributions. Two "atom-Drude" pairs have dipole-dipole interactions if the following conditions are met: 1. The THOLE parameter is nonzero. 2. In the non-polarizable force field, the two atoms were in the nonbonded exclusion list. To see if all the desired atoms have dipole-dipole interactions, use PRNLEV > 7. Each call to the energy will print the atom numbers, polarizabilities and Drude particles's charges of each interacting pair. The energy from the dipole-dipole interactions is added to the ELEC energy term, and "SKIP ELEC" will skip the Thole interactions as well. File: DRUDE, Node: Toppar, Previous: Description, Next: Warnings, Up: Top Effect on the topology and parameters ------------------------------------------------------------------- 1) New atoms The Drude particles are inserted immediately after their corresponding atoms in the PSF and coordinate file. For an atom type 'CA1', the DRUDE command will assign the atom type 'DCA1' for the Drude particle. Since no regular atoms have names starting with a 'D', the Drude oscillators can be selected with "SELECT TYPE D* END". ------------------------------------------------------------------- 2) Masses The masses for the selected atoms are modified so that the total mass of the atom-Drude pair corresponds to the atomic mass. Try "SCALAR MASS SHOW" before and after calling the DRUDE command. ------------------------------------------------------------------- 3) Charges The charges for the selected atoms are modified so that the total charge of the atom-Drude pair corresponds to the atomic partial charge. Try "SCALAR CHARGE SHOW" before and after calling the DRUDE command. ------------------------------------------------------------------- 4) Bonded interactions In addition to the atom-Drude bonds, zero force bonds are created between the atom-Drude pairs to maintain the same 1-2, 1-3, and 1-4 relationships that existed prior to the DRUDE call. For example, for two bonded atoms A1 and A2, with Drude particles DA1 and DA2, DA1 DA2 | | A1 ----- A2 zero force bonds are created between DA1 and DA2, between DA1 and A2, and between A1 and DA2, so that any particle of the A1-DA1 pair is 1-2 bonded to any particle of the A2-DA2 pair. Since the force constants of these fictitious bonds are zero, the computational overhead is minimal. ------------------------------------------------------------------- 5) Non-bonded interactions Whether the Drude particles have Lennard-Jones parameters or not, the Lennard-Jones parameters of the selected atoms are kept unchanged. Since the polarizable force field is built from the same "ingredients" as the non-polarizable force field, all the NBONDS options can be used as before (notably the PMEWALD method). File: DRUDE, Node: Warnings, Previous: Toppar, Next: Examples, Up: Top Issues to be aware of when using the DRUDE command ------------------------------------------------------------------- 1) Once all molecules in the system have been generated and any patching performed, invoke the following commands to create the drude and lone pair coordinates and set up the needed arrays. COOR SDRUDE COOR SHAKE ------------------------------------------------------------------- 2) The preferred call to SHAKE is: COOR COPY COMP SHAKE BONH PARAM TOLERANCE 10E-9 - NOFAST - SELECT .NOT. TYPE D* END - SELECT .NOT. TYPE D* END ------------------------------------------------------------------- 3) Always delete all the Drude particles after a RESET Treat this sequence of commands a single command: DRUDE RESET DELETE ATOMS SELECT TYPE D* END The "DRUDE RESET" command puts back the mass and the charge of the Drude particles on the heavy atoms, and erases the distinction between a Drude particle and a regular atom. Note to fully clear all the relevant arrays to allow for a new molecule to be generated all the following commands must be performed. SHAKE OFF DRUDE RESET LONE CLEAR DELETE ATOM SELE ALL END ------------------------------------------------------------------- 4) DMASS and KDRUDE are overriding the toppar files Any nonzero value for DMASS and KDRUDE specified by the user in a GENErate statement overrides the values from the topology and parameter files. ------------------------------------------------------------------- 5) Syntax and Description of the DrudeHardWall command DrudeHardWall L_WALL real Example: DrudeHardWall L_WALL 0.2 ! set the hard wall at 0.2 Angstrom DrudeHardWall L_WALL 0.0 ! turn off the hard wall when L_WALL equals 0.0 When the Drudes move too far away from the nucleus, the simulations become unstable leading to polarization catastrophe. To avoid this instability and "hard wall constraint" on the length of Drude-nuclei bonds is introduced. In each MD step, the length of Drude bonds are checked and compared with "L_WALL". When the length of Drude bond is larger than "L_WALL", the relative velocities along the bond vector are reversed and scaled down according to the temperature of the Drude bond. In addition, the displacement relative to "L_WALL" is reversed and scaled down according to new the velocities along the bond vector to make sure the Drude bond is not longer than "L_WALL". File: DRUDE, Node: Examples, Previous: Warnings, Next: Top, Up: Top Usage examples of the DRUDE command ------------------------------------------------------------------- 1) Polarizable benzene (see test/c30test/drude_benzene.inp) After reading the standard, non-polarizable topology and parameter files, a standard benzene molecule is generated: READ SEQUENCE BENZ 1 GENERATE BENZ SETUP FIRST NONE LAST NONE DRUDE DMASS 0.4 Obtain the benzene coordinates using IC build or reading in the coordinates. READ COOR CARD.... Then generate drude and lone pair coordinates. COOR SDRUDE COOR SHAKE The structure is minimized: MINI SD STEP 0.001 NSTEP 1000 NPRINT 100 Since benzene is a nonpolar molecule, the Drude particles are not significantly moved from their heavy atoms. To find the induced atomic dipoles for a given structure, one should use "CONS FIX SELECT .NOT. TYPE D* END" before calling MINI. The molecular polarizability is obtained using the VIBRAN command with the DIPOLES keyword: VIBRAN DIAGONALIZE PRINT NORMAL VECTORS DIPOLES SELECT ALL END END The total polarizability is an anisotropic tensor similar to the experimental results for benzene [J.Chem.Phys. 95, 5873 (1991)]. The strong anisotropy comes from the 1-2 and 1-3 dipole-dipole interactions. Deactivating these interactions by using THOLE=0 leads to the polarizability tensor being almost isotropic. ------------------------------------------------------------------- 2) SWM4-NDP water (see test/c30test/swm4.inp) See J. Chem. Phys. 119, 5185-5197 (2003) and Chem. Phys. Lett. 418, 245-249 (2005) for a complete description of the model. After reading the topology and parameter files, the model is built as following: READ SEQUENCE SWM4 ... GENERATE WAT SETUP NOANGLE NODIHEDRAL DRUDE DMASS 0.4 READ COOR CARD ... Then generate drude and lone pair coordinates. COOR SDRUDE COOR SHAKE SHAKE the waters COOR COPY COMP SHAKE BONH PARAM TOLERANCE 1.0E-9 - NOFAST - SELECT ( SEGID WAT .AND. .NOT. TYPE D* ) END - SELECT ( SEGID WAT .AND. .NOT. TYPE D* ) END ------------------------------------------------------------------- 3) Protein, with disulfide patches, SWM4-NDP water and ions Note that for complex systems it is suggested that the system initially be equilibrated using the additive force field, with the final coordinates used to initiate the Drude simulations. Tools to perform this may be found on the CHARMM Gui or in the MacKerell web site. ! Read protein open read card unit 10 name protein.crd read sequence coor unit 10 generate PROA setup warn first NTER last CTER DRUDE DMASS 0.4 ! NOTE: the DRUDE statement after 'patch' is not necessary ! Disulfide bonds patch disu2 PROA 26 PROA 84 setup warn DRUDE DMASS 0.4 autogenerate angles dihedrals patch disu2 PROA 40 PROA 95 setup warn DRUDE DMASS 0.4 autogenerate angles dihedrals patch disu2 PROA 58 PROA 110 setup warn DRUDE DMASS 0.4 autogenerate angles dihedrals patch disu2 PROA 65 PROA 72 setup warn DRUDE DMASS 0.4 autogenerate angles dihedrals ! Read xtal waters open read card unit 10 name xtal_water.crd read sequence coor unit 10 generate WATA setup warn noangle nodihedral DRUDE DMASS 0.4 read coor card unit 10 resid ! Read solvent waters open read card unit 10 name solv_water.crd read sequence coor unit 10 generate SOLV setup warn noangle nodihedral DRUDE DMASS 0.4 read coor card unit 10 resid ! Read IONS open read card unit 10 name ions.crd read sequence coor unit 10 generate CL setup warn noangle nodihedral DRUDE DMASS 0.4 read coor card unit 10 resid COOR SDRUDE COOR SHAKE ! cell parameters SET BOXTYPE = RECT SET XTLTYPE = CUBIC SET A = 62.75993 SET B = 62.75993 SET C = 62.75993 SET ALPHA = 90.0 SET BETA = 90.0 SET GAMMA = 90.0 SET XCEN = 0 SET YCEN = 0 SET ZCEN = 0 ! ! Setup PBC (Periodic Boundary Condition) ! CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma crystal build noper 0 cutoff @3 !Image centering by residue IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele resname SWM4 end IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele ( segid pot .or. segid cl ) end ! ! Nonbonded Options ! set 3 16.0 ! cutim set 4 16.0 ! cutnb set 5 10.0 ! ctonnb set 6 12.0 ! ctofnb set 7 switch set 8 atom set 9 vatom set 10 vswitch !Note use of vswitch set kap 0.34 ! epsilon for the PME set ord 6 ! spline order for PME ! fftx dimensions should correspond to 1 A or less; must ! be power of 2, 3 or 5 set fftx 64 set ffty 64 set fftz 64 !invoke drudehardwall to avoid polarization catastrophe. DrudeHardWall L_WALL 0.2 update inbfrq -1 imgfrq -1 ihbfrq 0 - ewald pmewald kappa @kap fftx @fftx ffty @ffty fftz @fftz order @ord - @7 @8 @9 @10 cutimg @3 cutnb @4 ctofnb @6 ctonnb @5 energy !minimize only the Drudes cons harm force 100000.0 sele .not. type D* end mini SD nstep 50 cons harm force 0.0 sele .not. type D* end coor copy comp SHAKE bonh param tolerance 1.0e-9 - nofast - select ( .not. (type D*)) end - select ( .not. (type D*)) end noreset !minimize full system mini SD nstep 50 ! with proper equilibration, Hyperpolarization and/or Hardwall ! 1 fs timestep should be possible set timestep 0.0005 !0.001 set nstep 200000 set seed 21320 set ii 0 set jj 1 open read unit 11 card name @tmp/hsd12.psf@psfid.@ii.res open write unit 12 card name @tmp/hsd12.psf@psfid.@jj.res open write unit 13 file name @tmp/hsd12.psf@psfid.@jj.dcd ! Set up temperature control for NVT simulation !scf THER 2 TAU 0.005 TREF 0.00 SELECT TYPE D* END - TPCONTROL NTHER 4 CMDAMP 10.0 NSTEP 20 - THER 1 TAU 0.1 TREF @temp SELECT .NOT. (resname swm4 .or. TYPE D* ) END - THER 2 TAU 0.1 TREF @temp SELECT resname swm4 .and. .NOT. TYPE D* END - THER 3 TAU 0.005 TREF 1.00 SELECT TYPE D* .and. .not. resname swm4 END - THER 4 TAU 0.005 TREF 1.00 SELECT resname swm4 .and. TYPE D* END !- ! BARO BTAU 0.1 PREF 1.00 DSCY !Activate BARO for NPT simulation ! Setup and run the Thermodynamic Integration loop using Langevine ! Dynamics. 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zzxc7$0>1PMN0mc!8f#+I%hy{6LiuK50JA{t{{_JWKKo+S0;Z>PCg^w1%k^Ab+Wj(P zx;tb2ew*_DeqZS*L;AqJzJL)w;thq$C{%s`=aG3bUuGLY=W_KR;wh<3YVTTP_%eQ9 zgI@&T83eTv%jv!BxB`k)L z-56;DqC+0^OP8sX?GkKfqzmdzm6i$vE%r?kW<+FDp|;I$OF6`G$?qE^%$KvuLB%{` z)hhXwNroLKVi|PHLB$eM4xu0_vx{4~_#%eO_@xwHsWdMmAFHotMJ(?X%C9p&6u!+T zzi{cmUsE0npH^wkZ=WS14I@^=>5tjt&)JUywti>WK;;HRgKQ}Ji4y7W8m{EP+FnG$ z!h)v!u5=>YYwz|dWh=9d(rV;kxAtm8n7$N6zxI;kTWJY?Aqp2gpUug$sIj zdUZYt?na;Pcy$35R{VB(B7Y~8?akZ!<S7x1>1#}{J5;D3mO`Q?`lPg#v#HbM43 zln;!F8y1lBs6qW2b40wjz>t?k5WmJGQ^aRu4!_1c5r2@RC}Z_&OkVMFNChu~!yIYB zg~-w zPW!-aDAy~2!SBAO(m0n1i-?~^&YmBShpPcs;-Gx?Kk*PwG)TpSc=Kk$RO!u||7-uV z|JncSfA&B7pZ(ANXaBSR+5hZ+_CNcd{m=eq|Fi$u|LlMEKl`8k&;I9Ce*QO`00c7t GNLT A~DA For a diatomic molecule: A1 DRUDE A1~DA1 | --------> | A2 A2~DA2 1-2 pairs: A1-A2, A1-DA2, DA1-A2, DA1-DA2 For a triatomic molecule: A1 A1~DA1 \ DRUDE \ A2 --------> A2~DA2 / / A3 A3~DA3 1-2 pairs: A1-A2, A1-DA2, DA1-A2, DA1-DA2, A2-A3, A2-DA3, DA2-A3, DA2-DA3 1-3 pairs: A1-A3, A1-DA3, DA1-A3, DA1-DA3 Thus, the bonded interactions are modified to allow 1-2 and 1-3 screened dipole-dipole interactions, as proposed by Thole [see Chem.Phys. 59, 341 (1981)]. If two atoms were not "seeing" each others in the non-polarizable force field, their dipoles (and only their dipoles, not their net partial charges) will "see" each others in the polarizable force field. The screening function strength is modulated by a parameter "a" that has been generalized to depend on the atom type associated with the interacting pair of Drude oscillators and are then generated via a standard arithmetic combination rule (a = a_i + a_j). These variable atomic THOLE parameters "a_i" are specified in the RTF through the THOLE keyword. * Menu: * Description:: Description of new DRUDE model RTF Description of new DRUDE model RTF 1) Items in RTF file A) The AUTOGENERATE command now includes a flag for the drude particles. This should be specified at the beginning of the RTF. AUTO ANGLES DIHE DRUDE B) MASS statements must be included for Drude particle types. MASS 104 DRUD 0.00000 DD ! drude particle The default drude type is DRUD. However, alternate drude types may be specified. These additional drude types must be i) specified with MASS statements, ii) the ATOMs to which they are applied must include a "TYPE drudetype" statement and iii) the NONBond parameters must be specified. For example, to include a special drude type on water the following would be needed in the RTF i) MASS 153 DOH2 0.00000 DD ! water Drude ii) ATOM OH2 ODW 0.00000 ALPHA -0.97825258 TYPE DOH2 iii) (NONBOND section) D* 0.0 -0.0000 0.0000 ! Wildcard for Drudes and dummy atom iv) (via NBFIX) MAGD DOH2 -0.01000 3.10000 Term iv) is an NBFIX that allows for the interactions between, for example, magnesium and the water drude to be treated with a special LJ term. Indeed, the motivation for additional drude types are such special terms may be applied in special cases. Note that NBFIX terms have been used between select real atoms in the Drude force field to improve the free energies of hydration. See J. Chem. Theory Comput. 6. 1181-1198 (2010) for more details. C) ALPHA and THOLE parameters are set in the RTF after the charge. The presence of the "ALPHA" keyword flags that atom as being polarizable and a drude particle is created and assigned to it when calling the GENERATE command. An atom based Thole scale factor may also be specified via the "THOLE" keyword. If the THOLE term is missing, a default value of 1.3 is assigned to that atom. This corresponds to a parameter a = a_i + a_j = 2.6 which is the THOLE parameter in the old Drude command syntax. ATOM C C 0.630 ALPHA -1.104 THOLE 1.073 Note that a negative sign on alpha leads to the charge on the Drude particle to be negative. This convention was chosen because the Drudes are meant to represent electronic degrees of freedom of the system. D) Specific drude types for a polarizable atom may be specified as follows using the "TYPE" keyword. See 1A) above, sections i to iv for more details. ATOM C C 0.630 ALPHA -1.104 TYPE DC E) Lone pairs may now be set directly in the RTF using a syntax similar to the standard lonepair command (lonepair.doc). All options for the generation of lonepairs (FIXed, CENTer, COLOcate etc.) as specified in the lonepair documentation may be used although the atom selection specification is simplified as shown in the following example. LONEPAIR relative LPA O C CL distance 0.3 angle 91.0 dihe 0.0 LONEPAIR relative LPB O C N distance 0.3 angle 91.0 dihe 0.0 F) Atom based anisotropic polarizabilities may be assigned to selected atoms via the ANISOTROPY keyword in the RTF. The anisotropic polarizability tensor is defined as ALPHA_iso (the isotropic polarizability) times a tensor A whith trace{A}=3. The tensor A is diagonal in the local reference frame and is completely specified by {A11, A22, A33}. The first atom selects the atom on which the polarizability is to be made anisotropic. The second atom along with the first defines the "11" direction of the {A} tensor and the 3rd and 4th atom selections define the "22" direction of the tensor, with the anisotropy defined by fractional polarizability components. Accordingly, only the 11 and 22 direction are needed since the trace of the {A} tensor is set to 3. An example follows ANISOTROPY O C CA N A11 0.6968 A22 1.2194 In the code, the variables A11 and A22 are read into the variables A11ANIS(IPT) and A22ANIS(IPT). We define the components of the tensor relative to the isotropic drude, so ALPHA11+ALPHA22+ALPHA33 = 3*ALPHA_iso. The factors A11 and A22 (and A33) represent the factors modifying the components of the isotropic polarizability tensor q**2/KDRUDE. For example, setting A11=A22=1 would keep the Drude completely isotropic. By virtue of the trace we know that A11+A22+A33=3, so we only need to set two of these terms. Thus A33 = THREE-A11ANIS(IPT)-A22ANIS(IPT). This sets the relative magnitude of the polarizability tensor in all 3 directions. Once the polarizability along a given direction is known, we need to get the harmonic force constant in this direction. As the polarizability in a given direction is defined as QDRUDE**2/K_direction, the 3 harmonic force constants are thus K11(NANISO) = ONE/A11ANIS(IPT) K22(NANISO) = ONE/A22ANIS(IPT) K33(NANISO) = ONE/A33 Now, in principle this would mean that you have to calculate the forces from 3 different springs (K11, K22, K33) in 3 different directions. But since we know the overall trace which is related to the isotropic polarizability, we are going to re-write this so that there are only 2 springs with force constants KPAR in the parallel and KPERP in the perpendicular direction, and add an isotropic KDRUDE spring on top of that. 2) Items in the Parameter file A) The KDRUDE force constant for all the atoms is set by a wildcard in the bond parameters. The term must be included for all drude types included in the model. The wildcard terms can be overwritten by putting chemical type specific bond parameters following the wild card term. Note that 500.00 is the default force constant and should not be changed. DRUD X 500.000 0.0000 DRUD O 487.740 0.0000 B) NONBOND parameters must be included for all drude types. In addition, NBFIX terms for the drudes may be included as needed (see 1A above). C) A pair-specific Thole shielding can be introduced in the parameter file for any nonbond pair (following a syntax similar to NBFIX) using the keyword THOLe. This feature was introduced to permit accurate models of divalent cations with polarizable atoms. The TCUT assigns a radius within which all Thole interaction are calculated between the specificed atoms. The 'aij' typically is assigned by the user. A default value 1.2 can also be used. THOLE TCUT 5.0 MAXNBTHOLE 50000 CL SODD @aij 3) Command Line Items A) A "DRUDE" flag must be included with the GENErate command to specify the inclusion of drudes on the molecule. The drude mass is set in this command using the DMASS keyword followed by the mass in AMU; a value of 0.4 is highly suggested. generate NMA first none last none setup warn DRUDE DMASS 0.4 An additional command that may be included with the generate command is the HYPErpolarizability term. This command invokes a higher exponent half-wall potential on the Drude particles to minimize the potential for polarization catastrophe. In the HYPEpolarzation command HORD is the order of the exponent, KHYP is the force constant and RHYP represent atom-Drude distance at which the hypepolarization term is invoked. An example of the command follows. Note that if DrudeHardWall, as described in the following section, use of HYPErpolarization is not required. Experience with several systems suggest that the DrudeHardWall feature is a more effective way than HYPER to generate stable simulations with a 1 fs timesteps. generate NMA first none last none setup warn DRUDE DMASS 0.4 HYPE HORD 4 KHYP 40000 RHYP 0.2 B) DrudeHardWall command When the Drude particles move far away from the nucleus (eg. > 0.2 Ang.), simulations become unstable and polarization catastrophe may occur. Introducing hard wall constraints on the length of Drude-nuclei bonds is a way to avoid such instability. In each MD step, the length of Drude bonds are checked and compared with "L_WALL". When the length of a Drude bond is larger than "L_WALL", the relative velocities along bond vector are flipped and scaled down according to the temperature of the drude bond. In addition, the displacement relative to "L_WALL" is flipped and scaled down according to new velocities along the bond vector to make sure the Drude bond is not longer than "L_WALL". DrudeHardWall L_WALL real Example: DrudeHardWall L_WALL 0.2 ! set the hard wall at 0.2 Angstrom DrudeHardWall L_WALL 0.0 ! turn off the hard wall when L_WALL equals 0.0 Description of Extended PSF format for CHARMM and NAMD The PSF has been extended for the Drude model. The default format is for CHARMM and the XPLOR format is for NAMD. The PSF following generation of the Drude model explicitly provides the THOLE, ALPHA, lone pair and anisotropic polarization information for CHARMM/NAMD PSF reader. * Menu: * Syntax:: Syntax of the DRUDE command * Description:: Description of the DRUDE command * Toppar:: Effect on the topology and parameters * Warnings:: To be aware of when using the DRUDE command * Examples:: Usage examples of the DRUDE command File: DRUDE, Node: Syntax, Previous: Top, Next: Description, Up: Top Syntax of the DRUDE command DRUDe RESEt GENErate { generate-spec } DRUDe [DMASS real] [KDRUde real] [HYPE] { hype-spec } generate-spec::= [see struct.doc] File: DRUDE, Node: Description, Previous: Syntax, Next: Toppar, Up: Top Description of the DRUDE command ------------------------------------------------------------------- Keyword Default Purpose ------------------------------------------------------------------- RESET Deactivates the Drude particles. After a reset, the user should delete all Drude particles. DMASS 0.0 Mass of the Drude oscillators (in amu). The default zero value causes the masses to be read from the topology file. Any nonzero value will override the topology file. A value of 0.4 is suggested. KDRUDE 0.0 Force constant of the atom-Drude bonds (in kcal/mol/Angst**2). The default zero value causes the bond force constants to be read from the parameter file. Any nonzero value will override the parameter file. A value of 500. is suggested. VTHOLE Uses variable thole parameters for dipole-dipole interactions. This term is set by default and is only used in the fitcharge routine. ALPHA 0.0 Atomic polarizability specificed in the parameter file. Zero indicates no polarizability on that atom. THOLE 2.6 The screening factor for dipole-dipole interactions between atoms excluded from the non-bonded interactions. To have no dipole-dipole interactions between these bonded atoms, use THOLE = 0. THOLE is specified in the parameter file. SHAPE 1 Specifies the shape of the dipole-dipole screening function. Only 1 option is currently available. HYPE Off Specify the inclusion of hyperpolarization term on the Drude oscillators to minimize potential of polarization catastophe hype-spec::= [HORD int] [KHYP int] [RHYP real] (XXXXX defaults have not been set for the following, may be a good idea XXXXXX) HORD xx Order of the exponent the hyperpolarization. Typically 4. KHYP xx Force constant. Typically 40,000. RHYP xx Atom-Drude distance of the flat-well potential. The hyperpolarization is not activited until the atom-Drude distance is greater than RHYP. Typically 0.2 Angst. ------------------------------------------------------------------- 1) KDRUDE KDRUDE is the force constant (in kcal/mol/Angst**2) for the bond between each atom and its Drude particle the user wishes to use. It overrides any bond constant found in the parameter file. The default value for KDRUDE is 500 kcal/mol/Angst**2. This should NOT be changed! The atomic polarizabilities (in Angst**3) may be read from the WMAIN array: alpha = abs(WMAIN) The charge on every Drude particle is computed using the following formula: q = sqrt( 2*KDRUDE * alpha / CCELEC ) * sign(WMAIN) The charges are given the signs of the WMAIN values. As long as KDRUDE is large enough, the Drude particles will stay very close to their atoms, and the sign of 'q' is irrelevant. However, as the Drude represents the electronic degrees of freedom, the sign of alpha is set to a negative value, thereby yielding a negative charge on the Drude particles. ------------------------------------------------------------------- 2) THOLE, SHAPE For 1-2 and 1-3 atoms only. All other interactions are regular Coulombic. See THOLE keyword in the parameter file to perform Thole scaling between nonbonded atoms. The THOLE parameter is a dimensionless factor that specifies the extent of the smearing of the charge 'q' on the Drude oscillators and of a contribution '-q' on the "real" atom. The default value of THOLE is 2.6, that is, the 1-2 and 1-3 dipole-dipole interactions are turned on by default. To turn the interactions off, set THOLE to zero. The default constant THOLE of 2.6 can be replaced by variable thole by specifying an atom specific Thole value in the topology file. The THOLE parameter between oscillators I and J is given by THOLE = THOLEI + THOLEJ. Values of THOLEI may also be given in the WCOMP array for all Drude oscillator containing atoms prior to the DRUDE command. Because the dipole are explicitly made of two charges, the screened dipole-dipole interaction between two polarizable atoms (that is, two "atom-Drude" pairs) is actually the sum of the following four screened charge-charge interactions: ('q1' on Drude 1) - ('q2' on Drude 2) ('q1' on Drude 1) - ('-q2' on atom 2) ('-q1' on atom 1) - ('q2' on Drude 2) ('-q1' on atom 1) - ('-q2' on atom 2) The screened charge-charge interaction has the form: U(r12) = CCELEC * q1*q2 * S(u12)/r12 where 'u12' is the normalized distance: u12 = r12 * THOLE / (alpha1*alpha2)**(1/6) 'S' is a screening function defined by the SHAPE parameter: SHAPE Screening function Charge distributions 1 S(u) = 1 - (1+u/2)*exp(-u) Slater-Delta 2 S(u) = erf(u) Gaussian The default value of SHAPE is 1, which is also the only shape currently implemented. SHAPE=2 is reserved for Gaussian-Gaussian distributions. Two "atom-Drude" pairs have dipole-dipole interactions if the following conditions are met: 1. The THOLE parameter is nonzero. 2. In the non-polarizable force field, the two atoms were in the nonbonded exclusion list. To see if all the desired atoms have dipole-dipole interactions, use PRNLEV > 7. Each call to the energy will print the atom numbers, polarizabilities and Drude particles's charges of each interacting pair. The energy from the dipole-dipole interactions is added to the ELEC energy term, and "SKIP ELEC" will skip the Thole interactions as well. File: DRUDE, Node: Toppar, Previous: Description, Next: Warnings, Up: Top Effect on the topology and parameters ------------------------------------------------------------------- 1) New atoms The Drude particles are inserted immediately after their corresponding atoms in the PSF and coordinate file. For an atom type 'CA1', the DRUDE command will assign the atom type 'DCA1' for the Drude particle. Since no regular atoms have names starting with a 'D', the Drude oscillators can be selected with "SELECT TYPE D* END". ------------------------------------------------------------------- 2) Masses The masses for the selected atoms are modified so that the total mass of the atom-Drude pair corresponds to the atomic mass. Try "SCALAR MASS SHOW" before and after calling the DRUDE command. ------------------------------------------------------------------- 3) Charges The charges for the selected atoms are modified so that the total charge of the atom-Drude pair corresponds to the atomic partial charge. Try "SCALAR CHARGE SHOW" before and after calling the DRUDE command. ------------------------------------------------------------------- 4) Bonded interactions In addition to the atom-Drude bonds, zero force bonds are created between the atom-Drude pairs to maintain the same 1-2, 1-3, and 1-4 relationships that existed prior to the DRUDE call. For example, for two bonded atoms A1 and A2, with Drude particles DA1 and DA2, DA1 DA2 | | A1 ----- A2 zero force bonds are created between DA1 and DA2, between DA1 and A2, and between A1 and DA2, so that any particle of the A1-DA1 pair is 1-2 bonded to any particle of the A2-DA2 pair. Since the force constants of these fictitious bonds are zero, the computational overhead is minimal. ------------------------------------------------------------------- 5) Non-bonded interactions Whether the Drude particles have Lennard-Jones parameters or not, the Lennard-Jones parameters of the selected atoms are kept unchanged. Since the polarizable force field is built from the same "ingredients" as the non-polarizable force field, all the NBONDS options can be used as before (notably the PMEWALD method). File: DRUDE, Node: Warnings, Previous: Toppar, Next: Examples, Up: Top Issues to be aware of when using the DRUDE command ------------------------------------------------------------------- 1) Once all molecules in the system have been generated and any patching performed, invoke the following commands to create the drude and lone pair coordinates and set up the needed arrays. COOR SDRUDE COOR SHAKE ------------------------------------------------------------------- 2) The preferred call to SHAKE is: COOR COPY COMP SHAKE BONH PARAM TOLERANCE 10E-9 - NOFAST - SELECT .NOT. TYPE D* END - SELECT .NOT. TYPE D* END ------------------------------------------------------------------- 3) Always delete all the Drude particles after a RESET Treat this sequence of commands a single command: DRUDE RESET DELETE ATOMS SELECT TYPE D* END The "DRUDE RESET" command puts back the mass and the charge of the Drude particles on the heavy atoms, and erases the distinction between a Drude particle and a regular atom. Note to fully clear all the relevant arrays to allow for a new molecule to be generated all the following commands must be performed. SHAKE OFF DRUDE RESET LONE CLEAR DELETE ATOM SELE ALL END ------------------------------------------------------------------- 4) DMASS and KDRUDE are overriding the toppar files Any nonzero value for DMASS and KDRUDE specified by the user in a GENErate statement overrides the values from the topology and parameter files. ------------------------------------------------------------------- 5) Syntax and Description of the DrudeHardWall command DrudeHardWall L_WALL real Example: DrudeHardWall L_WALL 0.2 ! set the hard wall at 0.2 Angstrom DrudeHardWall L_WALL 0.0 ! turn off the hard wall when L_WALL equals 0.0 When the Drudes move too far away from the nucleus, the simulations become unstable leading to polarization catastrophe. To avoid this instability and "hard wall constraint" on the length of Drude-nuclei bonds is introduced. In each MD step, the length of Drude bonds are checked and compared with "L_WALL". When the length of Drude bond is larger than "L_WALL", the relative velocities along the bond vector are reversed and scaled down according to the temperature of the Drude bond. In addition, the displacement relative to "L_WALL" is reversed and scaled down according to new the velocities along the bond vector to make sure the Drude bond is not longer than "L_WALL". File: DRUDE, Node: Examples, Previous: Warnings, Next: Top, Up: Top Usage examples of the DRUDE command ------------------------------------------------------------------- 1) Polarizable benzene (see test/c30test/drude_benzene.inp) After reading the standard, non-polarizable topology and parameter files, a standard benzene molecule is generated: READ SEQUENCE BENZ 1 GENERATE BENZ SETUP FIRST NONE LAST NONE DRUDE DMASS 0.4 Obtain the benzene coordinates using IC build or reading in the coordinates. READ COOR CARD.... Then generate drude and lone pair coordinates. COOR SDRUDE COOR SHAKE The structure is minimized: MINI SD STEP 0.001 NSTEP 1000 NPRINT 100 Since benzene is a nonpolar molecule, the Drude particles are not significantly moved from their heavy atoms. To find the induced atomic dipoles for a given structure, one should use "CONS FIX SELECT .NOT. TYPE D* END" before calling MINI. The molecular polarizability is obtained using the VIBRAN command with the DIPOLES keyword: VIBRAN DIAGONALIZE PRINT NORMAL VECTORS DIPOLES SELECT ALL END END The total polarizability is an anisotropic tensor similar to the experimental results for benzene [J.Chem.Phys. 95, 5873 (1991)]. The strong anisotropy comes from the 1-2 and 1-3 dipole-dipole interactions. Deactivating these interactions by using THOLE=0 leads to the polarizability tensor being almost isotropic. ------------------------------------------------------------------- 2) SWM4-NDP water (see test/c30test/swm4.inp) See J. Chem. Phys. 119, 5185-5197 (2003) and Chem. Phys. Lett. 418, 245-249 (2005) for a complete description of the model. After reading the topology and parameter files, the model is built as following: READ SEQUENCE SWM4 ... GENERATE WAT SETUP NOANGLE NODIHEDRAL DRUDE DMASS 0.4 READ COOR CARD ... Then generate drude and lone pair coordinates. COOR SDRUDE COOR SHAKE SHAKE the waters COOR COPY COMP SHAKE BONH PARAM TOLERANCE 1.0E-9 - NOFAST - SELECT ( SEGID WAT .AND. .NOT. TYPE D* ) END - SELECT ( SEGID WAT .AND. .NOT. TYPE D* ) END ------------------------------------------------------------------- 3) Protein, with disulfide patches, SWM4-NDP water and ions Note that for complex systems it is suggested that the system initially be equilibrated using the additive force field, with the final coordinates used to initiate the Drude simulations. Tools to perform this may be found on the CHARMM Gui or in the MacKerell web site. ! Read protein open read card unit 10 name protein.crd read sequence coor unit 10 generate PROA setup warn first NTER last CTER DRUDE DMASS 0.4 ! NOTE: the DRUDE statement after 'patch' is not necessary ! Disulfide bonds patch disu2 PROA 26 PROA 84 setup warn DRUDE DMASS 0.4 autogenerate angles dihedrals patch disu2 PROA 40 PROA 95 setup warn DRUDE DMASS 0.4 autogenerate angles dihedrals patch disu2 PROA 58 PROA 110 setup warn DRUDE DMASS 0.4 autogenerate angles dihedrals patch disu2 PROA 65 PROA 72 setup warn DRUDE DMASS 0.4 autogenerate angles dihedrals ! Read xtal waters open read card unit 10 name xtal_water.crd read sequence coor unit 10 generate WATA setup warn noangle nodihedral DRUDE DMASS 0.4 read coor card unit 10 resid ! Read solvent waters open read card unit 10 name solv_water.crd read sequence coor unit 10 generate SOLV setup warn noangle nodihedral DRUDE DMASS 0.4 read coor card unit 10 resid ! Read IONS open read card unit 10 name ions.crd read sequence coor unit 10 generate CL setup warn noangle nodihedral DRUDE DMASS 0.4 read coor card unit 10 resid COOR SDRUDE COOR SHAKE ! cell parameters SET BOXTYPE = RECT SET XTLTYPE = CUBIC SET A = 62.75993 SET B = 62.75993 SET C = 62.75993 SET ALPHA = 90.0 SET BETA = 90.0 SET GAMMA = 90.0 SET XCEN = 0 SET YCEN = 0 SET ZCEN = 0 ! ! Setup PBC (Periodic Boundary Condition) ! CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma crystal build noper 0 cutoff @3 !Image centering by residue IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele resname SWM4 end IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele ( segid pot .or. segid cl ) end ! ! Nonbonded Options ! set 3 16.0 ! cutim set 4 16.0 ! cutnb set 5 10.0 ! ctonnb set 6 12.0 ! ctofnb set 7 switch set 8 atom set 9 vatom set 10 vswitch !Note use of vswitch set kap 0.34 ! epsilon for the PME set ord 6 ! spline order for PME ! fftx dimensions should correspond to 1 A or less; must ! be power of 2, 3 or 5 set fftx 64 set ffty 64 set fftz 64 !invoke drudehardwall to avoid polarization catastrophe. DrudeHardWall L_WALL 0.2 update inbfrq -1 imgfrq -1 ihbfrq 0 - ewald pmewald kappa @kap fftx @fftx ffty @ffty fftz @fftz order @ord - @7 @8 @9 @10 cutimg @3 cutnb @4 ctofnb @6 ctonnb @5 energy !minimize only the Drudes cons harm force 100000.0 sele .not. type D* end mini SD nstep 50 cons harm force 0.0 sele .not. type D* end coor copy comp SHAKE bonh param tolerance 1.0e-9 - nofast - select ( .not. (type D*)) end - select ( .not. (type D*)) end noreset !minimize full system mini SD nstep 50 ! with proper equilibration, Hyperpolarization and/or Hardwall ! 1 fs timestep should be possible set timestep 0.0005 !0.001 set nstep 200000 set seed 21320 set ii 0 set jj 1 open read unit 11 card name @tmp/hsd12.psf@psfid.@ii.res open write unit 12 card name @tmp/hsd12.psf@psfid.@jj.res open write unit 13 file name @tmp/hsd12.psf@psfid.@jj.dcd ! Set up temperature control for NVT simulation !scf THER 2 TAU 0.005 TREF 0.00 SELECT TYPE D* END - TPCONTROL NTHER 4 CMDAMP 10.0 NSTEP 20 - THER 1 TAU 0.1 TREF @temp SELECT .NOT. (resname swm4 .or. TYPE D* ) END - THER 2 TAU 0.1 TREF @temp SELECT resname swm4 .and. .NOT. TYPE D* END - THER 3 TAU 0.005 TREF 1.00 SELECT TYPE D* .and. .not. resname swm4 END - THER 4 TAU 0.005 TREF 1.00 SELECT resname swm4 .and. TYPE D* END !- ! BARO BTAU 0.1 PREF 1.00 DSCY !Activate BARO for NPT simulation ! Setup and run the Thermodynamic Integration loop using Langevine ! Dynamics. DYNAMICS vv2 start nstep @nstep timestp @timestep - ntrfrq @nstep iprfrq -1 - nprint 1000 iseed @seed - iasvel 1 firstt @temp finalt @temp - inbfrq -1 imgfrq -1 ihbfrq 0 ilbfrq 0 - iunread 11 - iunwrite 12 - iuncrd 13 nsavcrd 2000 Details of the command to perform molecular dynamics for the polarizable Drude mdoel is explained in *note vv2:(chmdoc/vv2.doc). \ No newline at end of file diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/diff_svn.cmd b/charmm/toppar/drude/drude_toppar_2015_7/test/diff_svn.cmd new file mode 100644 index 00000000..2da36361 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/diff_svn.cmd @@ -0,0 +1,7 @@ +diff test_drude_all.inp /raid/alex/param/drude/toppar/test/test_drude_all.inp +diff test_drude_carbohydrate.str /raid/alex/param/drude/toppar/test/test_drude_carbohydrate.str +diff test_drude_ions.str /raid/alex/param/drude/toppar/test/test_drude_ions.str +diff test_drude_lipid.str /raid/alex/param/drude/toppar/test/test_drude_lipid.str +diff test_drude_master_protein.str /raid/alex/param/drude/toppar/test/test_drude_master_protein.str +diff test_drude_model.str /raid/alex/param/drude/toppar/test/test_drude_model.str +diff test_drude_nucleic_acids.str /raid/alex/param/drude/toppar/test/test_drude_nucleic_acids.str diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/run_test_drude.cmd b/charmm/toppar/drude/drude_toppar_2015_7/test/run_test_drude.cmd new file mode 100755 index 00000000..63f0c2a1 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/run_test_drude.cmd @@ -0,0 +1,17 @@ +#!/bin/csh -f +# run charmm test cases + +#charmm executable +setenv charmm /home/alex/charmm/code/c39b2/exec/gnu/charmm + +setenv outdir . + +#mkdir -p $outdir + +$charmm mindr:0 mini:0 < test_drude_all_2013c.inp > $outdir/test_drude_all_2013c.out + +#grep for crashed jobs +grep '! I I I I I !' $outdir/*.out +grep '\ XXX /' $outdir/*.out +grep 'CHECK THOSE INPUTS, ACE' $outdir/*.out + diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all.ene b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all.ene new file mode 100644 index 00000000..ba535523 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all.ene @@ -0,0 +1,832 @@ +$ID: TEST_DRUDE_ALL.INP 28 2015-07-29 23:54:15Z ALEX $ +RESIDUE NAMES AND ENERGIES +SWM4 STARTING E: 0 +SWM4 DIPOLE: 1.85 +LI STARTING E: 0 +LI DIPOLE: 0 +SOD STARTING E: 0 +SOD DIPOLE: 0 +POT STARTING E: 0 +POT DIPOLE: 0 +RB STARTING E: 0 +RB DIPOLE: 0 +CS STARTING E: 0 +CS DIPOLE: 0 +F STARTING E: 0 +F DIPOLE: 0 +CLA STARTING E: 0 +CLA DIPOLE: 0 +BR STARTING E: 0 +BR DIPOLE: 0 +I STARTING E: 0 +I DIPOLE: 0 +ZN STARTING E: 0 +ZN DIPOLE: 0 +MAG STARTING E: 0 +MAG DIPOLE: 0 +CAL STARTING E: 0 +CAL DIPOLE: 0 +SR STARTING E: 0 +SR DIPOLE: 0 +BA STARTING E: 0 +BA DIPOLE: 0 +HE STARTING E: 0 +HE DIPOLE: 0 +NE STARTING E: 0 +NE DIPOLE: 0 +HE1 STARTING E: 0 +HE1 DIPOLE: 0 +NE1 STARTING E: 0 +NE1 DIPOLE: 0 +ALAD STARTING E: 393.328 +ALAD DIPOLE: 5.81322 +GNTE-GLY-ALA-GLY-CTEG STARTING E: 149.651 +GNTE-GLY-ALA-GLY-CTEG DIPOLE: 45.9636 +GNTE-GLY-ALA-GLY-CNEG STARTING E: 138.642 +GNTE-GLY-ALA-GLY-CNEG DIPOLE: 23.8917 +GNTE-GLY-ALA-GLY-CT1G STARTING E: 491.081 +GNTE-GLY-ALA-GLY-CT1G DIPOLE: 24.2005 +GNTE-GLY-ALA-GLY-CT2G STARTING E: 107.624 +GNTE-GLY-ALA-GLY-CT2G DIPOLE: 27.1995 +GNTE-GLY-ALA-GLY-CT3 STARTING E: 132.058 +GNTE-GLY-ALA-GLY-CT3 DIPOLE: 24.4386 +ACE-GLY-ALA-GLY-CTEG STARTING E: 250.199 +ACE-GLY-ALA-GLY-CTEG DIPOLE: 27.5843 +ACE-GLY-ALA-GLY-CNEG STARTING E: 204.518 +ACE-GLY-ALA-GLY-CNEG DIPOLE: 4.42297 +ACE-GLY-ALA-GLY-CT1G STARTING E: 558.292 +ACE-GLY-ALA-GLY-CT1G DIPOLE: 4.32038 +ACE-GLY-ALA-GLY-CT2G STARTING E: 170.834 +ACE-GLY-ALA-GLY-CT2G DIPOLE: 5.84158 +ACE-GLY-ALA-GLY-CT3 STARTING E: 199.218 +ACE-GLY-ALA-GLY-CT3 DIPOLE: 6.12543 +PROP-PRO-ALA-PRO-CTEP STARTING E: 1254.94 +PROP-PRO-ALA-PRO-CTEP DIPOLE: 44.8736 +PROP-PRO-ALA-PRO-CT3 STARTING E: 1320.42 +PROP-PRO-ALA-PRO-CT3 DIPOLE: 21.1107 +ACP-PRO-ALA-PRO-CTEP STARTING E: 1356.72 +ACP-PRO-ALA-PRO-CTEP DIPOLE: 26.9672 +ACP-PRO-ALA-PRO-CT3 STARTING E: 1389.51 +ACP-PRO-ALA-PRO-CT3 DIPOLE: 8.93072 +NTER-ALA-ALA-ALA-CTER STARTING E: 137.135 +NTER-ALA-ALA-ALA-CTER DIPOLE: 50.6467 +NTER-ALA-ALA-ALA-CNEU STARTING E: 154.861 +NTER-ALA-ALA-ALA-CNEU DIPOLE: 24.2375 +NTER-ALA-ALA-ALA-CT1 STARTING E: 391.728 +NTER-ALA-ALA-ALA-CT1 DIPOLE: 24.2744 +NTER-ALA-ALA-ALA-CT2 STARTING E: 134.746 +NTER-ALA-ALA-ALA-CT2 DIPOLE: 28.3646 +NTER-ALA-ALA-ALA-CT3 STARTING E: 191.676 +NTER-ALA-ALA-ALA-CT3 DIPOLE: 25.7356 +ACE-ALA-ALA-ALA-CTER STARTING E: 239.943 +ACE-ALA-ALA-ALA-CTER DIPOLE: 31.5543 +ACE-ALA-ALA-ALA-CNEU STARTING E: 226.219 +ACE-ALA-ALA-ALA-CNEU DIPOLE: 4.90742 +ACE-ALA-ALA-ALA-CT1 STARTING E: 464.417 +ACE-ALA-ALA-ALA-CT1 DIPOLE: 4.86066 +ACE-ALA-ALA-ALA-CT2 STARTING E: 203.112 +ACE-ALA-ALA-ALA-CT2 DIPOLE: 6.23519 +ACE-ALA-ALA-ALA-CT3 STARTING E: 263.431 +ACE-ALA-ALA-ALA-CT3 DIPOLE: 6.85564 +NTER-ARG-ALA-ARG-CTER STARTING E: -204.755 +NTER-ARG-ALA-ARG-CTER DIPOLE: 52.2314 +NTER-ARG-ALA-ARG-CNEU STARTING E: -106.926 +NTER-ARG-ALA-ARG-CNEU DIPOLE: 28.0609 +NTER-ARG-ALA-ARG-CT1 STARTING E: 133.221 +NTER-ARG-ALA-ARG-CT1 DIPOLE: 29.5997 +NTER-ARG-ALA-ARG-CT2 STARTING E: -124.479 +NTER-ARG-ALA-ARG-CT2 DIPOLE: 28.1053 +NTER-ARG-ALA-ARG-CT3 STARTING E: -17.133 +NTER-ARG-ALA-ARG-CT3 DIPOLE: 31.898 +ACE-ARG-ALA-ARG-CTER STARTING E: -171.744 +ACE-ARG-ALA-ARG-CTER DIPOLE: 55.0977 +ACE-ARG-ALA-ARG-CNEU STARTING E: -106.169 +ACE-ARG-ALA-ARG-CNEU DIPOLE: 46.3311 +ACE-ARG-ALA-ARG-CT1 STARTING E: 135.315 +ACE-ARG-ALA-ARG-CT1 DIPOLE: 46.4042 +ACE-ARG-ALA-ARG-CT2 STARTING E: -127.131 +ACE-ARG-ALA-ARG-CT2 DIPOLE: 42.3828 +ACE-ARG-ALA-ARG-CT3 STARTING E: -15.8228 +ACE-ARG-ALA-ARG-CT3 DIPOLE: 48.2871 +NTER-ASN-ALA-ASN-CTER STARTING E: 63.4993 +NTER-ASN-ALA-ASN-CTER DIPOLE: 47.622 +NTER-ASN-ALA-ASN-CNEU STARTING E: 112.834 +NTER-ASN-ALA-ASN-CNEU DIPOLE: 26.0879 +NTER-ASN-ALA-ASN-CT1 STARTING E: 387.566 +NTER-ASN-ALA-ASN-CT1 DIPOLE: 25.8831 +NTER-ASN-ALA-ASN-CT2 STARTING E: 73.7288 +NTER-ASN-ALA-ASN-CT2 DIPOLE: 31.225 +NTER-ASN-ALA-ASN-CT3 STARTING E: 1400.09 +NTER-ASN-ALA-ASN-CT3 DIPOLE: 25.7456 +ACE-ASN-ALA-ASN-CTER STARTING E: 193.831 +ACE-ASN-ALA-ASN-CTER DIPOLE: 26.669 +ACE-ASN-ALA-ASN-CNEU STARTING E: 210.21 +ACE-ASN-ALA-ASN-CNEU DIPOLE: 3.21936 +ACE-ASN-ALA-ASN-CT1 STARTING E: 486.278 +ACE-ASN-ALA-ASN-CT1 DIPOLE: 4.74871 +ACE-ASN-ALA-ASN-CT2 STARTING E: 167.328 +ACE-ASN-ALA-ASN-CT2 DIPOLE: 6.85671 +ACE-ASN-ALA-ASN-CT3 STARTING E: 1498.15 +ACE-ASN-ALA-ASN-CT3 DIPOLE: 3.1159 +NTER-ASP-ALA-ASP-CTER STARTING E: 266.829 +NTER-ASP-ALA-ASP-CTER DIPOLE: 61.3582 +NTER-ASP-ALA-ASP-CNEU STARTING E: 172.634 +NTER-ASP-ALA-ASP-CNEU DIPOLE: 43.2213 +NTER-ASP-ALA-ASP-CT1 STARTING E: 442.911 +NTER-ASP-ALA-ASP-CT1 DIPOLE: 41.6172 +NTER-ASP-ALA-ASP-CT2 STARTING E: 154.705 +NTER-ASP-ALA-ASP-CT2 DIPOLE: 49.353 +NTER-ASP-ALA-ASP-CT3 STARTING E: 968.707 +NTER-ASP-ALA-ASP-CT3 DIPOLE: 40.0613 +ACE-ASP-ALA-ASP-CTER STARTING E: 501.261 +ACE-ASP-ALA-ASP-CTER DIPOLE: 46.3854 +ACE-ASP-ALA-ASP-CNEU STARTING E: 374.23 +ACE-ASP-ALA-ASP-CNEU DIPOLE: 27.4595 +ACE-ASP-ALA-ASP-CT1 STARTING E: 645.843 +ACE-ASP-ALA-ASP-CT1 DIPOLE: 26.6526 +ACE-ASP-ALA-ASP-CT2 STARTING E: 352.582 +ACE-ASP-ALA-ASP-CT2 DIPOLE: 33.4572 +ACE-ASP-ALA-ASP-CT3 STARTING E: 1170.96 +ACE-ASP-ALA-ASP-CT3 DIPOLE: 23.6576 +NTER-CYS-ALA-CYS-CTER STARTING E: 161.729 +NTER-CYS-ALA-CYS-CTER DIPOLE: 51.3309 +NTER-CYS-ALA-CYS-CNEU STARTING E: 162.933 +NTER-CYS-ALA-CYS-CNEU DIPOLE: 26.7795 +NTER-CYS-ALA-CYS-CT1 STARTING E: 405.786 +NTER-CYS-ALA-CYS-CT1 DIPOLE: 26.6973 +NTER-CYS-ALA-CYS-CT2 STARTING E: 165.008 +NTER-CYS-ALA-CYS-CT2 DIPOLE: 31.6938 +NTER-CYS-ALA-CYS-CT3 STARTING E: 226.053 +NTER-CYS-ALA-CYS-CT3 DIPOLE: 27.2807 +ACE-CYS-ALA-CYS-CTER STARTING E: 274.738 +ACE-CYS-ALA-CYS-CTER DIPOLE: 32.5968 +ACE-CYS-ALA-CYS-CNEU 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109.115 +NTER-GLUP-ALA-GLUP-CNEU DIPOLE: 28.8938 +NTER-GLUP-ALA-GLUP-CT1 STARTING E: 347.994 +NTER-GLUP-ALA-GLUP-CT1 DIPOLE: 28.4487 +NTER-GLUP-ALA-GLUP-CT2 STARTING E: 101.443 +NTER-GLUP-ALA-GLUP-CT2 DIPOLE: 34.1593 +NTER-GLUP-ALA-GLUP-CT3 STARTING E: 164.838 +NTER-GLUP-ALA-GLUP-CT3 DIPOLE: 28.5664 +ACE-GLUP-ALA-GLUP-CTER STARTING E: 206.982 +ACE-GLUP-ALA-GLUP-CTER DIPOLE: 32.0521 +ACE-GLUP-ALA-GLUP-CNEU STARTING E: 189.788 +ACE-GLUP-ALA-GLUP-CNEU DIPOLE: 4.65398 +ACE-GLUP-ALA-GLUP-CT1 STARTING E: 430.004 +ACE-GLUP-ALA-GLUP-CT1 DIPOLE: 3.78024 +ACE-GLUP-ALA-GLUP-CT2 STARTING E: 178.486 +ACE-GLUP-ALA-GLUP-CT2 DIPOLE: 9.17446 +ACE-GLUP-ALA-GLUP-CT3 STARTING E: 246.142 +ACE-GLUP-ALA-GLUP-CT3 DIPOLE: 5.06077 +DEET STARTING E: -2.05008 +DEET DIPOLE: 1.4482 +DME STARTING E: 8.06268 +DME DIPOLE: 1.224935E-05 +DMET STARTING E: 2.40973 +DMET DIPOLE: 1.32035 +MEET STARTING E: -0.177244 +MEET DIPOLE: 1.39611 +THF STARTING E: 11.9164 +THF DIPOLE: 1.82422 +TF2M STARTING E: 5.59411 +TF2M DIPOLE: 1.84506 +THP STARTING E: 12.0068 +THP DIPOLE: 1.79954 +MPET STARTING E: 5.18211 +MPET DIPOLE: 1.31471 +MBET STARTING E: 5.2206 +MBET DIPOLE: 1.37439 +EPET STARTING E: 3.57723 +EPET DIPOLE: 1.36896 +ETHA STARTING E: 4.46839 +ETHA DIPOLE: 5.376752E-16 +PROP1 STARTING E: 3.72893 +PROP1 DIPOLE: 0.114828 +IBUT STARTING E: -4.17502 +IBUT DIPOLE: 0.179806 +BUTA STARTING E: 4.53681 +BUTA DIPOLE: 1.438076E-05 +PENT STARTING E: 4.90412 +PENT DIPOLE: 0.11456 +HEXA STARTING E: 5.5024 +HEXA DIPOLE: 1.330135E-04 +HEPT STARTING E: 6.10777 +HEPT DIPOLE: 0.113976 +CPEN STARTING E: 10.6744 +CPEN DIPOLE: 1.162E-02 +CHEX STARTING E: 4.80197 +CHEX DIPOLE: 9.553956E-05 +MEOH STARTING E: 11.6558 +MEOH DIPOLE: 1.8385 +ETOH STARTING E: 3.02316 +ETOH DIPOLE: 1.93715 +PRO1 STARTING E: 8.23186 +PRO1 DIPOLE: 1.94115 +BUO1 STARTING E: 8.30368 +BUO1 DIPOLE: 1.94072 +PRO2 STARTING E: -9.39499 +PRO2 DIPOLE: 2.00051 +BUO2 STARTING E: 3.30713 +BUO2 DIPOLE: 2.00544 +BENZ STARTING E: 27.709 +BENZ DIPOLE: 2.086737E-15 +TOLU STARTING E: 23.6932 +TOLU DIPOLE: 0.696379 +ACEM STARTING E: -74.6041 +ACEM DIPOLE: 4.58697 +NMA STARTING E: 14.1422 +NMA DIPOLE: 4.52355 +DMA STARTING E: 43.1415 +DMA DIPOLE: 5.424 +PYR STARTING E: 23.3567 +PYR DIPOLE: 2.40619 +PYRM STARTING E: -14.5299 +PYRM DIPOLE: 2.20442 +PYRR STARTING E: -4.22645 +PYRR DIPOLE: 1.97233 +IMID STARTING E: 0.36357 +IMID DIPOLE: 3.99453 +INDO STARTING E: 4.78505 +INDO DIPOLE: 3.08253 +PUR1 STARTING E: 64.7356 +PUR1 DIPOLE: 6.95806 +PUR0 STARTING E: 33.6396 +PUR0 DIPOLE: 7.58988 +4MIM STARTING E: -1.15743 +4MIM DIPOLE: 5.24964 +MIND STARTING E: 14.8585 +MIND DIPOLE: 2.74025 +MAS STARTING E: -5.07241 +MAS DIPOLE: 3.05252 +ACEH STARTING E: -61.9662 +ACEH DIPOLE: 1.95975 +IMIM STARTING E: 45.4438 +IMIM DIPOLE: 1.5401 +GUAN STARTING E: -302.104 +GUAN DIPOLE: 8.529451E-16 +MGUAN STARTING E: -188.721 +MGUAN DIPOLE: 1.45252 +PHEN STARTING E: 23.5005 +PHEN DIPOLE: 1.85856 +MESH STARTING E: 2.58433 +MESH DIPOLE: 1.5163 +ETSH STARTING E: -3.45143 +ETSH DIPOLE: 1.6034 +PRSH STARTING E: 4.82504 +PRSH DIPOLE: 1.60117 +BUSH STARTING E: 3.44281 +BUSH DIPOLE: 1.60877 +DMDS STARTING E: -3.00568 +DMDS DIPOLE: 2.12697 +DMS STARTING E: -2.13589 +DMS DIPOLE: 1.87332 +EMS STARTING E: 0.444552 +EMS DIPOLE: 1.74012 +NC4 STARTING E: -63.3239 +NC4 DIPOLE: 4.077328E-05 +NH5 STARTING E: 36.847 +NH5 DIPOLE: 5.32215 +NC5 STARTING E: -28.804 +NC5 DIPOLE: 2.47005 +ACET STARTING E: 6.6207 +ACET DIPOLE: 4.71119 +ETAM STARTING E: 389.977 +ETAM DIPOLE: 5.04135 +NEOP STARTING E: 0.532291 +NEOP DIPOLE: 7.527714E-04 +BU2M STARTING E: -1.15638 +BU2M DIPOLE: 0.319337 +BU22M STARTING E: -13.8979 +BU22M DIPOLE: 0.146489 +BU23M STARTING E: -0.278212 +BU23M DIPOLE: 0.360997 +CPNM STARTING E: 11.9078 +CPNM DIPOLE: 0.185211 +CHXM STARTING E: 2.8007 +CHXM DIPOLE: 8.656568E-02 +DIOX STARTING E: 11.7832 +DIOX DIPOLE: 1.047568E-03 +CRES STARTING E: 7.63022 +CRES DIPOLE: 1.45246 +B3MO1 STARTING E: 1.88684 +B3MO1 DIPOLE: 1.90334 +CPO1 STARTING E: 14.8124 +CPO1 DIPOLE: 1.46546 +BGUAN STARTING E: -204.292 +BGUAN DIPOLE: 10.4975 +CHOL STARTING E: -38.562 +CHOL DIPOLE: 3.14469 +DECA STARTING E: 276.241 +DECA DIPOLE: 0.623959 +PEND STARTING E: 413.295 +PEND DIPOLE: 0.532265 +OCTD STARTING E: 495.527 +OCTD DIPOLE: 0.719398 +DMP STARTING E: 8.08042 +DMP DIPOLE: 10.5292 +EAS STARTING E: -17.3982 +EAS DIPOLE: 2.64169 +MPRO STARTING E: 5764.86 +MPRO DIPOLE: 0.478598 +MBU STARTING E: 5825.53 +MBU DIPOLE: 0.539284 +PE STARTING E: 13.2174 +PE DIPOLE: 21.7995 +PC STARTING E: -72.3985 +PC DIPOLE: 21.8727 +DMPC STARTING E: -66.5147 +DMPC DIPOLE: 20.7383 +DPPC STARTING E: -64.8058 +DPPC DIPOLE: 20.7074 +EGLY STARTING E: 11.3805 +EGLY DIPOLE: 2.955946E-02 +MGLYOL STARTING E: 30.3457 +MGLYOL DIPOLE: 3.10932 +MERYOL STARTING E: 47.4629 +MERYOL DIPOLE: 1.37679 +DTHROL STARTING E: 60.5735 +DTHROL DIPOLE: 3.55712 +LTHROL STARTING E: 54.49 +LTHROL DIPOLE: 2.5749 +MRIBOL STARTING E: 58.8337 +MRIBOL DIPOLE: 1.90975 +DARAOL STARTING E: 67.0514 +DARAOL DIPOLE: 2.06249 +LARAOL STARTING E: 65.6502 +LARAOL DIPOLE: 2.68966 +MXYLOL STARTING E: 55.2362 +MXYLOL DIPOLE: 3.79856 +MALLOL STARTING E: 96.21 +MALLOL DIPOLE: 0.257725 +DALTOL STARTING E: 84.938 +DALTOL DIPOLE: 2.2748 +LALTOL STARTING E: 85.6548 +LALTOL DIPOLE: 4.28497 +DGLUOL STARTING E: 87.4061 +DGLUOL DIPOLE: 2.60053 +LGLUOL STARTING E: 77.3389 +LGLUOL DIPOLE: 4.17707 +DMANOL STARTING E: 79.6652 +DMANOL DIPOLE: 2.50423 +LMANOL STARTING E: 81.868 +LMANOL DIPOLE: 2.36638 +DGULOL STARTING E: 86.8292 +DGULOL DIPOLE: 2.1709 +LGULOL STARTING E: 80.9309 +LGULOL DIPOLE: 4.25533 +DIDIOL STARTING E: 82.654 +DIDIOL DIPOLE: 4.61759 +LIDIOL STARTING E: 89.0257 +LIDIOL DIPOLE: 4.83329 +MGALOL STARTING E: 81.1929 +MGALOL DIPOLE: 2.49589 +AGLC STARTING E: 69.9881 +AGLC DIPOLE: 1.9083 +BGLC STARTING E: 77.1925 +BGLC DIPOLE: 4.60939 +AALT STARTING E: 79.8576 +AALT DIPOLE: 2.06797 +BALT STARTING E: 81.716 +BALT DIPOLE: 1.98299 +AALL STARTING E: 71.3537 +AALL DIPOLE: 1.37558 +BALL STARTING E: 72.4944 +BALL DIPOLE: 2.57648 +AGAL STARTING E: 70.3536 +AGAL DIPOLE: 3.5746 +BGAL STARTING E: 72.2666 +BGAL DIPOLE: 3.17083 +AGUL STARTING E: 71.6569 +AGUL DIPOLE: 2.21848 +BGUL STARTING E: 78.6373 +BGUL DIPOLE: 3.74185 +AIDO STARTING E: 75.2863 +AIDO DIPOLE: 2.58842 +BIDO STARTING E: 73.3832 +BIDO DIPOLE: 1.69759 +AMAN STARTING E: 71.0426 +AMAN DIPOLE: 3.6713 +BMAN STARTING E: 65.8046 +BMAN DIPOLE: 1.85383 +ATAL STARTING E: 63.7363 +ATAL DIPOLE: 3.78067 +BTAL STARTING E: 65.532 +BTAL DIPOLE: 2.50432 +ARIB STARTING E: 63.6956 +ARIB DIPOLE: 3.0411 +BRIB STARTING E: 66.6048 +BRIB DIPOLE: 3.47125 +AARB STARTING E: 62.7882 +AARB DIPOLE: 2.2774 +BARB STARTING E: 65.5355 +BARB DIPOLE: 3.59391 +AXYF STARTING E: 61.5117 +AXYF DIPOLE: 2.03073 +BXYF STARTING E: 63.6041 +BXYF DIPOLE: 2.75359 +ALYF STARTING E: 63.1022 +ALYF DIPOLE: 2.57136 +BLYF STARTING E: 67.1736 +BLYF DIPOLE: 2.3652 +ADEO STARTING E: 30.8019 +ADEO DIPOLE: 2.01832 +BDEO STARTING E: 33.219 +BDEO DIPOLE: 2.32787 +ADE STARTING E: 177.602 +ADE DIPOLE: 7.88425 +CYT STARTING E: -6.19746 +CYT DIPOLE: 10.8714 +THY STARTING E: -6.9521 +THY DIPOLE: 6.9301 +GUA STARTING E: -10.0026 +GUA DIPOLE: 5.68634 +ADEB STARTING E: 97.0078 +ADEB DIPOLE: 5.05199 +MADE STARTING E: 114.471 +MADE DIPOLE: 5.19035 +CYTB STARTING E: -88.1639 +CYTB DIPOLE: 7.85701 +MCYT STARTING E: -63.901 +MCYT DIPOLE: 7.76883 +THYB STARTING E: -81.1611 +THYB DIPOLE: 5.93698 +MTHY STARTING E: -47.5 +MTHY DIPOLE: 6.49948 +GUAB STARTING E: -92.1229 +GUAB DIPOLE: 8.2167 +URAB STARTING E: -97.1626 +URAB DIPOLE: 4.58894 +T3PS STARTING E: 196.755 +T3PS DIPOLE: 18.2111 +T3PM STARTING E: 1.07209 +T3PM DIPOLE: 14.2466 +DMPN STARTING E: -5.02073 +DMPN DIPOLE: 8.19331 +BDEONA STARTING E: 21.7766 +BDEONA DIPOLE: 4.19099 +BDEONA STARTING E: 649.152 +OLIGOMER_DNA STARTING E: 649.152 +LI ENERGY: 45.2495 +POT ENERGY: 43.5516 +SOD ENERGY: 44.729 +RB ENERGY: 46.3099 +CS ENERGY: 52.6004 +F ENERGY: 234.841 +CLA ENERGY: 256.045 +BR ENERGY: 273.975 +I ENERGY: 335.114 +ZN ENERGY: -49.5825 +MAG ENERGY: -48.4701 +CAL ENERGY: -48.7952 +SR ENERGY: -50.346 +BA ENERGY: -49.7742 diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all_2013c.inp b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all_2013c.inp new file mode 100644 index 00000000..e6c6eaa9 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all_2013c.inp @@ -0,0 +1,49 @@ +* $Id: test_drude_all.inp 28 2015-07-29 23:54:15Z alex $ +* Master test case for drude +* + +! OPTIONAL variables to be set from the command-line: +! pdbdir : directory to write structures to. No structures written if not set. +! mindr : set to 1 to minimize drude particles. +! mini : set to 1 to minimize structures. + +set testcases 6 +set test1 test_drude_master_protein.str +set test2 test_drude_model.str +set test3 test_drude_lipid.str +set test4 test_drude_carbohydrate.str +set test5 test_drude_nucleic_acids_no_rna.str +set test6 test_drude_ions.str + +ioformat extend + +set toppar .. +stream @toppar/toppar_defs_2013c.str + +!Not using ENVI because lowercase strings still cannot be set from the cmdline +if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + system "`echo mkdir @PDBDIR | awk '{print tolower($0)}'`" + endif +if @?mini eq 0 set mini 0 +if @mini eq 0 then + if @?mindr eq 0 set mindr 0 + if @mindr eq 0 then + set ins + else + set ins _mindr + endif + else + set mindr 1 + set ins _mini + endif + +open unit 90 write form name test_drude_all@ins.ene +echu 90 +echo $Id: test_drude_all.inp 28 2015-07-29 23:54:15Z alex $ +echo residue names and energies + +set testcasei 1 +label loop_tests +stream @test@@testcasei +incr testcasei +if @testcasei le @testcases goto loop_tests diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all_2013c.out b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all_2013c.out new file mode 100644 index 00000000..736541aa --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_all_2013c.out @@ -0,0 +1,126317 @@ + Parameter: MINDR <- "0" + Parameter: MINI <- "0" +1 + Chemistry at HARvard Macromolecular Mechanics + (CHARMM) - Developmental Version 39b2 February 15, 2015 + SVN revision 367 + Copyright(c) 1984-2014 President and Fellows of Harvard College + All Rights Reserved + Current operating system: Linux-2.6.32-5-amd64(x86_64)@ocracoke + Created on 8/4/15 at 16:43:06 by user: alex + + Maximum number of ATOMS: 360720, and RESidues: 120240 + RDTITL> * $ID: TEST_DRUDE_ALL.INP 28 2015-07-29 23:54:15Z ALEX $ + RDTITL> * MASTER TEST CASE FOR DRUDE + RDTITL> * + + CHARMM> + + CHARMM> ! OPTIONAL variables to be set from the command-line: + CHARMM> ! pdbdir : directory to write structures to. No structures written if not set. + CHARMM> ! mindr : set to 1 to minimize drude particles. + CHARMM> ! mini : set to 1 to minimize structures. + CHARMM> + + CHARMM> set testcases 6 + Parameter: TESTCASES <- "6" + + CHARMM> set test1 test_drude_master_protein.str + Parameter: TEST1 <- "TEST_DRUDE_MASTER_PROTEIN.STR" + + CHARMM> set test2 test_drude_model.str + Parameter: TEST2 <- "TEST_DRUDE_MODEL.STR" + + CHARMM> set test3 test_drude_lipid.str + Parameter: TEST3 <- "TEST_DRUDE_LIPID.STR" + + CHARMM> set test4 test_drude_carbohydrate.str + Parameter: TEST4 <- "TEST_DRUDE_CARBOHYDRATE.STR" + + CHARMM> set test5 test_drude_nucleic_acids_no_rna.str + Parameter: TEST5 <- "TEST_DRUDE_NUCLEIC_ACIDS_NO_RNA.STR" + + CHARMM> set test6 test_drude_ions.str + Parameter: TEST6 <- "TEST_DRUDE_IONS.STR" + + CHARMM> + + CHARMM> ioformat extend + MISCOM> Expanded I/O format is used. + + CHARMM> + + CHARMM> set toppar .. + Parameter: TOPPAR <- ".." + + CHARMM> stream @toppar/toppar_defs_2013c.str + Parameter: TOPPAR -> ".." + VOPEN> Attempting to open::../toppar_defs_2013c.str:: + OPNLGU> Unit 99 opened for READONLY access to ../toppar_defs_2013c.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * $ID: TOPPAR_DEFS.STR 26 2015-07-27 18:26:03Z ALEX $ + RDTITL> * STREAMS ALL DRUDE STREAM FILES + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> ! Requires the variable "toppar" + CHARMM> + + CHARMM> set streamfiles 5 + Parameter: STREAMFILES <- "5" + + CHARMM> set str1 toppar_drude_master_protein_2013c.str + Parameter: STR1 <- "TOPPAR_DRUDE_MASTER_PROTEIN_2013C.STR" + + CHARMM> set str2 toppar_drude_lipid_2013c.str + Parameter: STR2 <- "TOPPAR_DRUDE_LIPID_2013C.STR" + + CHARMM> set str3 toppar_drude_carbohydrate_2013c.str + Parameter: STR3 <- "TOPPAR_DRUDE_CARBOHYDRATE_2013C.STR" + + CHARMM> set str4 toppar_drude_model_2013c.str + Parameter: STR4 <- "TOPPAR_DRUDE_MODEL_2013C.STR" + + CHARMM> set str5 toppar_drude_nucleic_acid_2013c_no_rna.str + Parameter: STR5 <- "TOPPAR_DRUDE_NUCLEIC_ACID_2013C_NO_RNA.STR" + + CHARMM> + + CHARMM> set i 1 + Parameter: I <- "1" + + CHARMM> label loop_streams + + CHARMM> stream @toppar/@str@@i + Parameter: I -> "1" + Parameter: TOPPAR -> ".." + Parameter: STR1 -> "TOPPAR_DRUDE_MASTER_PROTEIN_2013C.STR" + VOPEN> Attempting to open::../toppar_drude_master_protein_2013c.str:: + OPNLGU> Unit 98 opened for READONLY access to ../toppar_drude_master_protein_2013c.str + + INPUT STREAM SWITCHING TO UNIT 98 + RDTITL> * $ID: TOPPAR_DRUDE_MASTER_PROTEIN.STR 33 2015-08-04 14:44:59Z ALEX $ + RDTITL> * DRUDE MASTER TOPOLOGY AND PARAMETER STREAM FILE + RDTITL> * INCLUDES WATER, IONS AND 2013 PROTEIN FF RELEASE + RDTITL> * OCTOBER 2013 + RDTITL> * IONS UPDATED, JUNE 2014 + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> ioformat extended + MISCOM> Expanded I/O format is used. + + CHARMM> + + CHARMM> !This file must be streamed prior to additional Drude FF toppar stream files + CHARMM> !and it includes parameters for the model compounds (toppar_drude_model*.str) + CHARMM> + + CHARMM> !references + CHARMM> ! + CHARMM> !Proteins + CHARMM> !Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and + CHARMM> !MacKerell, A.D., Jr., “Polarizable Force Field for Peptides and + CHARMM> !Proteins based on the Classical Drude Oscillator,” Journal of + CHARMM> !Chemical Theory and Computation, 9: 5430–5449, 2013 DOI: + CHARMM> !10.1021/ct400781b, NIHMS53671 + CHARMM> ! + CHARMM> !water + CHARMM> !SWM4-NDP, negative Drude (this will be the default model): Lamoureux, + CHARMM> !G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D., + CHARMM> !Jr., A polarizable model of water for molecular dynamics simulations + CHARMM> !of biomolecules, Chemical Physics Letters, 2006, 418: 245-249. + CHARMM> ! + CHARMM> !SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander + CHARMM> !D. MacKerell, Jr. "Six-site Polarizable Model of Water Based on the + CHARMM> !Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508, + CHARMM> !2013 + CHARMM> + + CHARMM> !atomic ions + CHARMM> !Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I., + CHARMM> !Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating + CHARMM> !Monovalent and Divalent Ions in Aqueous Solution Using a Drude + CHARMM> !Polarizable Force Field, “Journal of Chemical Theory and Computation, + CHARMM> !6: 774–786, 2010 + CHARMM> ! + CHARMM> !Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B., + CHARMM> !“Simulation study of ion pairing in concentrated aqueous salt + CHARMM> !solutions with a polarizable force field,” Faraday Discussions, 160, + CHARMM> !135–149, 2013, PMC3695446 + CHARMM> + + CHARMM> + + CHARMM> ! note use of D for second character to indicate Drude + CHARMM> ! polarizable FF (be careful of Cadmium: use CDM) + CHARMM> + + CHARMM> ! Parameter labeling after ! + CHARMM> ! RESName, generic compound name of model compound followed by additional comments + CHARMM> ! for example ! BENZ, benzene, based on crystal survey data + CHARMM> + + CHARMM> !Formatting information + CHARMM> !RTF section: please use the following format for future residues, including the spacing + CHARMM> !(and please clean a few up of the residues not in this format if you so desire....) + CHARMM> + + CHARMM> !RESI ALA 0.000 + CHARMM> !ATOM N ND2A2 -0.427 ALPHA -1.056 THOLE 0.711 + CHARMM> !BOND A1 A2 A3 A4 A5 A6 A7 A8 + CHARMM> !IMPR A1 A2 A3 A4 + CHARMM> !CMAP A1 A2 A3 A4 A1 A2 A3 A4 + CHARMM> !LONEPAIR relative A1 A2 A3 A4 distance 0.30 angle 91.00 dihe 180.00 + CHARMM> !ANISOTROPY A1 A2 A3 A4 A11 0.6968 A22 1.2194 + CHARMM> !IC A1 A2 A3 A4 1.3474 124.31 180.00 114.26 0.9979 + CHARMM> + + CHARMM> !parameter section + CHARMM> !bond + CHARMM> !CD32E OD30A 360.00 1.415 ! comment + CHARMM> !angles + CHARMM> !HDA1A CD31A CD31A 34.50 110.10 ! comment + CHARMM> !HDA1A CD31A CD31A 34.50 110.10 22.53 2.1790 ! comment + CHARMM> !dihedrals + CHARMM> !CD2O1A ND2A2 CD31C CD2O2A 0.000 3 180.00 ! comment + CHARMM> !impropers + CHARMM> !CD2O1A CD31A ND2A2 OD2C1A 120.000 0 0.00 ! comment + CHARMM> !nonbond (LJ) + CHARMM> !HDW 0.0 -0.0000 0.0000 ! comment + CHARMM> !nbfix + CHARMM> !CD30A ODW -0.00500 4.04699 ! comment + CHARMM> + + CHARMM> !ioformat extended + CHARMM> + + CHARMM> read rtf card !append + MAINIO> Residue topology file being read from unit 98. + RDTITL> * TOPOLOGY FOR DRUDE WATER, IONS AND PROTEINS + RDTITL> * + + DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA + Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000 + + CHARMM> + + CHARMM> read para card !append + + PARAMETER FILE BEING READ FROM UNIT 98 + RDTITL> * DRUDE POLARIZABLE FF PARAMETERS + RDTITL> * + + PARRDR> WARNING: wild card for drude X + 218 1 224 HDP1A DRUD 500.0000 0.0000 24977 + 219 2 224 HDP1B DRUD 500.0000 0.0000 24978 + 220 3 224 HDA1A DRUD 500.0000 0.0000 24979 + 221 4 224 HDA1C DRUD 500.0000 0.0000 24980 + 222 5 224 HDA1R5 DRUD 500.0000 0.0000 24981 + 223 6 224 HDA2A DRUD 500.0000 0.0000 24982 + 224 7 224 HDA2C DRUD 500.0000 0.0000 24983 + 225 8 224 HDA2E DRUD 500.0000 0.0000 24984 + 226 9 224 HDA2R5 DRUD 500.0000 0.0000 24985 + 227 10 224 HDA3A DRUD 500.0000 0.0000 24986 + 228 11 224 HDA3B DRUD 500.0000 0.0000 24987 + 229 12 224 HDA3C DRUD 500.0000 0.0000 24988 + 230 13 224 HDR5A DRUD 500.0000 0.0000 24989 + 231 14 224 HDR5B DRUD 500.0000 0.0000 24990 + 232 15 224 HDR5C DRUD 500.0000 0.0000 24991 + 233 16 224 HDR5D DRUD 500.0000 0.0000 24992 + 234 17 224 HDR5E DRUD 500.0000 0.0000 24993 + 235 18 224 HDR6A DRUD 500.0000 0.0000 24994 + 236 19 224 HDR6B DRUD 500.0000 0.0000 24995 + 237 20 224 HDR6C DRUD 500.0000 0.0000 24996 + 238 41 224 CD2O1A DRUD 500.0000 0.0000 25017 + 239 42 224 CD2O2A DRUD 500.0000 0.0000 25018 + 240 43 224 CD2O3A DRUD 500.0000 0.0000 25019 + 241 44 224 CD2O3B DRUD 500.0000 0.0000 25020 + 242 45 224 CD2R5A DRUD 500.0000 0.0000 25021 + 243 46 224 CD2R5B DRUD 500.0000 0.0000 25022 + 244 47 224 CD2R5C DRUD 500.0000 0.0000 25023 + 245 48 224 CD2R5D DRUD 500.0000 0.0000 25024 + 246 49 224 CD2R5E DRUD 500.0000 0.0000 25025 + 247 50 224 CD2R6A DRUD 500.0000 0.0000 25026 + 248 51 224 CD2R6B DRUD 500.0000 0.0000 25027 + 249 52 224 CD2R6C DRUD 500.0000 0.0000 25028 + 250 53 224 CD2R6D DRUD 500.0000 0.0000 25029 + 251 54 224 CD2R6F DRUD 500.0000 0.0000 25030 + 252 55 224 CD2R6H DRUD 500.0000 0.0000 25031 + 253 60 224 CD2N1A DRUD 500.0000 0.0000 25036 + 254 61 224 CD30A DRUD 500.0000 0.0000 25037 + 255 62 224 CD31A DRUD 500.0000 0.0000 25038 + 256 63 224 CD31C DRUD 500.0000 0.0000 25039 + 257 64 224 CD31FA DRUD 500.0000 0.0000 25040 + 258 65 224 CD31FB DRUD 500.0000 0.0000 25041 + 259 66 224 CD31FC DRUD 500.0000 0.0000 25042 + 260 67 224 CD31G DRUD 500.0000 0.0000 25043 + 261 68 224 CD315A DRUD 500.0000 0.0000 25044 + 262 69 224 CD315B DRUD 500.0000 0.0000 25045 + 263 70 224 CD316A DRUD 500.0000 0.0000 25046 + 264 71 224 CD32A DRUD 500.0000 0.0000 25047 + 265 72 224 CD32AL DRUD 500.0000 0.0000 25048 + 266 73 224 CD32B DRUD 500.0000 0.0000 25049 + 267 74 224 CD32C DRUD 500.0000 0.0000 25050 + 268 75 224 CD32E DRUD 500.0000 0.0000 25051 + 269 76 224 CD32F DRUD 500.0000 0.0000 25052 + 270 77 224 CD325A DRUD 500.0000 0.0000 25053 + 271 78 224 CD325B DRUD 500.0000 0.0000 25054 + 272 79 224 CD326A DRUD 500.0000 0.0000 25055 + 273 80 224 CD326B DRUD 500.0000 0.0000 25056 + 274 81 224 CD33A DRUD 500.0000 0.0000 25057 + 275 82 224 CD33B DRUD 500.0000 0.0000 25058 + 276 83 224 CD33C DRUD 500.0000 0.0000 25059 + 277 84 224 CD33D DRUD 500.0000 0.0000 25060 + 278 85 224 CD33E DRUD 500.0000 0.0000 25061 + 279 86 224 CD31HA DRUD 500.0000 0.0000 25062 + 280 87 224 CD31HB DRUD 500.0000 0.0000 25063 + 281 88 224 CD31HC DRUD 500.0000 0.0000 25064 + 282 131 224 ND2A1 DRUD 500.0000 0.0000 25107 + 283 132 224 ND2A2 DRUD 500.0000 0.0000 25108 + 284 133 224 ND2A3 DRUD 500.0000 0.0000 25109 + 285 134 224 ND2B1 DRUD 500.0000 0.0000 25110 + 286 135 224 ND2R5A DRUD 500.0000 0.0000 25111 + 287 136 224 ND2R5B DRUD 500.0000 0.0000 25112 + 288 137 224 ND2R5C DRUD 500.0000 0.0000 25113 + 289 138 224 ND2R5D DRUD 500.0000 0.0000 25114 + 290 139 224 ND2R5E DRUD 500.0000 0.0000 25115 + 291 140 224 ND2R5F DRUD 500.0000 0.0000 25116 + 292 141 224 ND2R6A DRUD 500.0000 0.0000 25117 + 293 142 224 ND2R6B DRUD 500.0000 0.0000 25118 + 294 143 224 ND2R6C DRUD 500.0000 0.0000 25119 + 295 144 224 ND2R6D DRUD 500.0000 0.0000 25120 + 296 145 224 ND2P1A DRUD 500.0000 0.0000 25121 + 297 146 224 ND3P2A DRUD 500.0000 0.0000 25122 + 298 147 224 ND3P3A DRUD 500.0000 0.0000 25123 + 299 148 224 ND3A3 DRUD 500.0000 0.0000 25124 + 300 171 224 OD2C1A DRUD 500.0000 0.0000 25147 + 301 172 224 OD2C1B DRUD 500.0000 0.0000 25148 + 302 173 224 OD2C2A DRUD 500.0000 0.0000 25149 + 303 174 224 OD2C2B DRUD 500.0000 0.0000 25150 + 304 175 224 OD2C2C DRUD 500.0000 0.0000 25151 + 305 176 224 OD2C3A DRUD 500.0000 0.0000 25152 + 306 177 224 OD2C3B DRUD 500.0000 0.0000 25153 + 307 178 224 OD30A DRUD 500.0000 0.0000 25154 + 308 179 224 OD30B DRUD 500.0000 0.0000 25155 + 309 180 224 OD30BN DRUD 500.0000 0.0000 25156 + 310 181 224 OD30C DRUD 500.0000 0.0000 25157 + 311 182 224 OD30CL DRUD 500.0000 0.0000 25158 + 312 183 224 OD30D DRUD 500.0000 0.0000 25159 + 313 184 224 OD305A DRUD 500.0000 0.0000 25160 + 314 185 224 OD306A DRUD 500.0000 0.0000 25161 + 315 186 224 OD31A DRUD 500.0000 0.0000 25162 + 316 187 224 OD31B DRUD 500.0000 0.0000 25163 + 317 188 224 OD31C DRUD 500.0000 0.0000 25164 + 318 189 224 OD31E DRUD 500.0000 0.0000 25165 + 319 190 224 OD31F DRUD 500.0000 0.0000 25166 + 320 211 224 PD1A DRUD 500.0000 0.0000 25187 + 321 212 224 PD1AN DRUD 500.0000 0.0000 25188 + 322 221 224 DUM DRUD 500.0000 0.0000 25197 + 323 222 224 XED DRUD 500.0000 0.0000 25198 + 324 223 224 NED DRUD 500.0000 0.0000 25199 + 325 224 224 DRUD DRUD 500.0000 0.0000 25200 + 326 226 224 SD31A DRUD 500.0000 0.0000 25649 + 327 227 224 SD31B DRUD 500.0000 0.0000 25875 + 328 228 224 SD30A DRUD 500.0000 0.0000 26102 + 329 229 224 SD30B DRUD 500.0000 0.0000 26330 + 330 231 224 LPD DRUD 500.0000 0.0000 26789 + 331 232 224 LPDW DRUD 500.0000 0.0000 27020 + 332 233 224 LPDO1 DRUD 500.0000 0.0000 27252 + 333 234 224 LPDNA1 DRUD 500.0000 0.0000 27485 + 334 241 224 ODW DRUD 500.0000 0.0000 29144 + 335 242 224 ODW6 DRUD 500.0000 0.0000 29385 + 336 243 224 HDW DRUD 500.0000 0.0000 29627 + 337 244 224 DOH2 DRUD 500.0000 0.0000 29870 + 338 251 224 LID DRUD 500.0000 0.0000 31599 + 339 252 224 POTD DRUD 500.0000 0.0000 31850 + 340 253 224 SODD DRUD 500.0000 0.0000 32102 + 341 254 224 RBD DRUD 500.0000 0.0000 32355 + 342 255 224 CSD DRUD 500.0000 0.0000 32609 + 343 256 224 FAD DRUD 500.0000 0.0000 32864 + 344 257 224 CLAD DRUD 500.0000 0.0000 33120 + 345 258 224 BRAD DRUD 500.0000 0.0000 33377 + 346 259 224 IAD DRUD 500.0000 0.0000 33635 + 347 271 224 MAGD DRUD 500.0000 0.0000 36809 + 348 272 224 CALD DRUD 500.0000 0.0000 37080 + 349 273 224 SRD DRUD 500.0000 0.0000 37352 + 350 274 224 BAD DRUD 500.0000 0.0000 37625 + 351 275 224 ZND DRUD 500.0000 0.0000 37899 + + THOLE CUTOFF 5.000 + MAXNBTHOLE -5000 + Pair-specific Thole: 1 ODW BAD 1.4586900000000000 241 274 + Pair-specific Thole: 2 ODW CALD 1.5087699999999999 241 272 + Pair-specific Thole: 3 ODW MAGD 1.5156700000000001 241 271 + Pair-specific Thole: 4 ODW SRD 1.2379199999999999 241 273 + Pair-specific Thole: 5 ODW ZND 2.1477300000000001 241 275 + Pair-specific Thole: 6 CALD OD2C1A 1.3200000000000001 272 171 + Pair-specific Thole: 7 CALD OD31A 1.0500000000000000 272 186 + Pair-specific Thole: 8 CLAD ND2A2 2.8599999999999999 257 132 + Pair-specific Thole: 9 SODD OD31A 1.8200000000000001 253 186 + Pair-specific Thole: 10 POTD OD2C1A 2.1899999999999999 252 171 + Pair-specific Thole: 11 POTD OD2C2A 0.22000000000000000 252 173 + Pair-specific Thole: 12 CD32C OD2C2C 1.4500000000000000 74 175 + PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. + + CHARMM> + + VCLOSE: Closing unit 98 with status "KEEP" + + RETURNING TO INPUT STREAM 99 + + CHARMM> incr i + Parameter: I <- "2" + + CHARMM> if @i le @streamfiles goto loop_streams + Parameter: I -> "2" + Parameter: STREAMFILES -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> stream @toppar/@str@@i + Parameter: I -> "2" + Parameter: TOPPAR -> ".." + Parameter: STR2 -> "TOPPAR_DRUDE_LIPID_2013C.STR" + VOPEN> Attempting to open::../toppar_drude_lipid_2013c.str:: + OPNLGU> Unit 98 opened for READONLY access to ../toppar_drude_lipid_2013c.str + + INPUT STREAM SWITCHING TO UNIT 98 + RDTITL> * $ID: TOPPAR_DRUDE_LIPID.STR 33 2015-08-04 14:44:59Z ALEX $ + RDTITL> * DRUDE TOPOLOGY AND PARAMETER STREAM FILE + RDTITL> * LIPIDS + RDTITL> * OCTOBER 2013 + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> !requires toppar_drude_master*.str + CHARMM> + + CHARMM> ioformat extended + MISCOM> Expanded I/O format is used. + + CHARMM> + + CHARMM> !lipids + CHARMM> + + CHARMM> !references + CHARMM> !Chowdhary, J., Harder, E., Lopes, P.E.M., MacKerell, Jr., A.D, and + CHARMM> !Roux, B., “A Polarizable Model for Phosphatidylcholine-Containing + CHARMM> !Biological Membranes,” Journal of Physical Chemistry, B.,117: + CHARMM> !9142-9160, 2013. + CHARMM> + + CHARMM> read rtf card append + MAINIO> Residue topology file being read from unit 98. + RDTITL> * TOPOLOGY FOR DRUDE LIPIDS + RDTITL> * + + DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA + Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000 + + CHARMM> + + CHARMM> read para card append + + PARAMETER FILE BEING READ FROM UNIT 98 + RDTITL> * DRUDE POLARIZABLE FF PARAMETERS + RDTITL> * + PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. + + VCLOSE: Closing unit 98 with status "KEEP" + + RETURNING TO INPUT STREAM 99 + + CHARMM> incr i + Parameter: I <- "3" + + CHARMM> if @i le @streamfiles goto loop_streams + Parameter: I -> "3" + Parameter: STREAMFILES -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> stream @toppar/@str@@i + Parameter: I -> "3" + Parameter: TOPPAR -> ".." + Parameter: STR3 -> "TOPPAR_DRUDE_CARBOHYDRATE_2013C.STR" + VOPEN> Attempting to open::../toppar_drude_carbohydrate_2013c.str:: + OPNLGU> Unit 98 opened for READONLY access to ../toppar_drude_carbohydrate_2013c.str + + INPUT STREAM SWITCHING TO UNIT 98 + RDTITL> * $ID: TOPPAR_DRUDE_CARBOHYDRATE.STR 25 2015-07-24 16:15:55Z ALEX $ + RDTITL> * DRUDE TOPOLOGY AND PARAMETER STREAM FILE FOR CARBOHYDRATES + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> !OD31F to OD31E, but OD31E parameters maintained + CHARMM> !requires toppar_drude_master*.str + CHARMM> + + CHARMM> !carbohydrates + CHARMM> + + CHARMM> !references + CHARMM> ! + CHARMM> !Patel, D.S., He, X., and MacKerell, A.D., Jr., + CHARMM> !“Polarizable Empirical Force Field for Hexopyranose Monosaccharides + CHARMM> !based on the Classical Drude Oscillator,” Journal of Physical + CHARMM> !Chemistry B., ASAP article, 2014, 10.1021/jp412696m, NIHMSID #566721 + CHARMM> ! + CHARMM> !polyalcohols + CHARMM> ! + CHARMM> !He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., “Polarizable + CHARMM> !Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical + CHARMM> !Drude Oscillator,” Biopolymers, 99: 724-738 2013, DOI: + CHARMM> !10.1002/bip.22286 + CHARMM> ! + CHARMM> !furanoses + CHARMM> ! + CHARMM> !Jana, M. and MacKerell, A.D., Jr., “CHARMM Drude Polarizable Force + CHARMM> !Field for Aldopentofuranoses and Methyl-aldopentofuranosides,” Journal + CHARMM> !of Physical Chemistry B, 119: 7846-7859, 2015, doi: + CHARMM> !10.1021/acs.jpcb.5b01767, PMC4483154 + CHARMM> ! + CHARMM> + + CHARMM> read rtf card append + MAINIO> Residue topology file being read from unit 98. + RDTITL> * DRUDE CARBOHYDRATES + RDTITL> * + + DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA + Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000 + + CHARMM> + + CHARMM> read para card append + + PARAMETER FILE BEING READ FROM UNIT 98 + RDTITL> * DRUDE POLARIZABLE FF PARAMETERS + RDTITL> * + PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. + + CHARMM> + + VCLOSE: Closing unit 98 with status "KEEP" + + RETURNING TO INPUT STREAM 99 + + CHARMM> incr i + Parameter: I <- "4" + + CHARMM> if @i le @streamfiles goto loop_streams + Parameter: I -> "4" + Parameter: STREAMFILES -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> stream @toppar/@str@@i + Parameter: I -> "4" + Parameter: TOPPAR -> ".." + Parameter: STR4 -> "TOPPAR_DRUDE_MODEL_2013C.STR" + VOPEN> Attempting to open::../toppar_drude_model_2013c.str:: + OPNLGU> Unit 98 opened for READONLY access to ../toppar_drude_model_2013c.str + + INPUT STREAM SWITCHING TO UNIT 98 + RDTITL> * $ID: TOPPAR_DRUDE_MODEL.STR 29 2015-07-29 23:57:18Z ALEX $ + RDTITL> * DRUDE TOPOLOGY AND PARAMETER STREAM FILE + RDTITL> * SMALL MOLECULE MODEL COMPOUNDS + RDTITL> * OCTOBER 2013 + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> !requires toppar_drude_master*.str + CHARMM> + + CHARMM> !model compounds + CHARMM> + + CHARMM> !references + CHARMM> !Alkanes + CHARMM> !Igor V. Vorobyov, Victor M. Anisimov and Alexander D. MacKerell, + CHARMM> !Jr. "Polarizable Empirical Force Field for Alkanes Based on the + CHARMM> !Classical Drude Oscillator Model," Journal of Physical Chemistry B, + CHARMM> !109: 18988-18999, 2005. + CHARMM> ! + CHARMM> !Anisotropic polarizability model + CHARMM> !Harder, E., Anisimov, V.M., Vorobyov, I.V., Lopes, P.E., Noskov, S., + CHARMM> !MacKerell, A.D., Jr. and Roux, B. Atomic Level Anisotropy in the + CHARMM> !Electrostatic Modeling of Lone Pairs for a Polarizable Force Field + CHARMM> !based on the Classical Drude Oscillator, Journal of Chemical Theory + CHARMM> !and Computation, 2: 1587-1597, 2006 + CHARMM> ! + CHARMM> !Ethers + CHARMM> ! + CHARMM> !Vorobyov, I.V., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., + CHARMM> !Pastor, R.W. and MacKerell, A.D., Jr., Additive and Classical Drude + CHARMM> !Polarizable Force Fields for Linear and Cyclic Ethers, Journal of + CHARMM> !Chemical Theory and Computation, 3: 1120-1133, 2007. + CHARMM> ! + CHARMM> !Baker, C. and MacKerell, Jr. A.D., “Polarizability Rescaling and + CHARMM> !atom-based Thole Scaling in the CHARMM Drude Polarizable Force Field + CHARMM> !for Ethers” Journal of Molecular Modeling, 16: 567-576, 2010, + CHARMM> !PMC2818097 + CHARMM> + + CHARMM> !Sulfur containing compounds + CHARMM> !Zhu, X. and MacKerell, A.D., Jr. “Polarizable Empirical Force Field + CHARMM> !for Sulfur-Containing Compounds Based on the Classical Drude + CHARMM> !Oscillator Model,” Journal of Computational Chemistry, 12: 2330-2341, + CHARMM> !2010. PMC2923574 + CHARMM> ! + CHARMM> !Alcohols + CHARMM> !Anisimov, V.M., Vorobyov, I.V., Roux, B., and MacKerell, A.D., Jr. + CHARMM> !Polarizable empirical force field for the primary and secondary + CHARMM> !alcohol series based on the classical Drude model. Journal of Chemical + CHARMM> !Theory and Computation, 3, 1927-1946, 2007. + CHARMM> + + CHARMM> !Amides + CHARMM> !Harder, E., Anisimov, V.M., Whitfield, T., MacKerell, A.D., Jr., Roux, + CHARMM> !B. "Understanding the Dielectric Properties of Liquid Amides from a + CHARMM> !Polarizable Force Field," Journal of Physical Chemistry, + CHARMM> !112:3509-3521. 2008, PMID: 18302362 + CHARMM> ! + CHARMM> !Final amide model used on 2013 protein FF + CHARMM> !Lin, B., Lopes, P.E.M., Roux, B., and MacKerell, A.D., Jr., + CHARMM> !“Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide + CHARMM> !Solutions Modeled by the CHARMM Additive and Drude Polarizable Force + CHARMM> !Fields,” Journal of Chemical Physics, 139: 084509, 2013, PMC3772949 + CHARMM> ! + CHARMM> !Aromatics + CHARMM> !Lopes, P., Lamoureux, G., Roux, B., MacKerell, A.D., Jr., "Polarizable + CHARMM> !Empirical Force Field for Aromatic Compounds Based on the Classical + CHARMM> !Drude Oscillator," Journal of Physical Chemistry, B. 111:2873-2885, + CHARMM> !2007 + CHARMM> ! + CHARMM> !Heterocycles + CHARMM> !Lopes, P.E.M., Lamoureux, G., MacKerell, A.D., Jr., “Polarizable + CHARMM> !Empirical Force Field for Nitrogen-containing Heteroaromatic Compounds + CHARMM> !Based on the Classical Drude Oscillator” Journal of Computational + CHARMM> !Chemistry, 30: 1821-1838, 2009, PMC251901 + CHARMM> ! + CHARMM> !Nucleic Acid Bases + CHARMM> !Baker, C.M., Anisimov, V.M., and MacKerell, A.D., Jr., “Development of + CHARMM> !CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the + CHARMM> !Classical Drude Oscillator Model,” Journal of Physical Chemistry, + CHARMM> !B. 115; 580–596, 2011, PMC3166616 + CHARMM> + + CHARMM> read rtf card append + MAINIO> Residue topology file being read from unit 98. + RDTITL> * TOPOLOGY FOR DRUDE MODEL COMPOUNDS + RDTITL> * + + DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA + Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000 + + CHARMM> + + CHARMM> read para card append + + PARAMETER FILE BEING READ FROM UNIT 98 + RDTITL> * DRUDE POLARIZABLE FF PARAMETERS + RDTITL> * + PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. + + VCLOSE: Closing unit 98 with status "KEEP" + + RETURNING TO INPUT STREAM 99 + + CHARMM> incr i + Parameter: I <- "5" + + CHARMM> if @i le @streamfiles goto loop_streams + Parameter: I -> "5" + Parameter: STREAMFILES -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> stream @toppar/@str@@i + Parameter: I -> "5" + Parameter: TOPPAR -> ".." + Parameter: STR5 -> "TOPPAR_DRUDE_NUCLEIC_ACID_2013C_NO_RNA.STR" + VOPEN> Attempting to open::../toppar_drude_nucleic_acid_2013c_no_rna.str:: + OPNLGU> Unit 98 opened for READONLY access to ../toppar_drude_nucleic_acid_2013c_no_rna.str + + INPUT STREAM SWITCHING TO UNIT 98 + RDTITL> * $ID: TOPPAR_DRUDE_NUCLEIC_ACID.STR 33 2015-08-04 14:44:59Z ALEX $ + RDTITL> * DRUDE TOPOLOGY AND PARAMETER STREAM FILE + RDTITL> * NUCLEIC ACIDS + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> !cannot be used with RNA + CHARMM> + + CHARMM> !contains March 2014 DNA parameters with subsequently refined ion-nucleic acid parameters + CHARMM> + + CHARMM> !requires toppar_drude_master*.str + CHARMM> + + CHARMM> !nucleic acids + CHARMM> + + CHARMM> !references + CHARMM> ! + CHARMM> !Savelyev, A. and MacKerell, A.D., Jr., “All-Atom Polarizable Force + CHARMM> !Field for DNA Based on the Classical Drude Oscillator Model,” Journal + CHARMM> !of Computational Chemistry, 35: 1219-1239, 2014, DOI: 10.1002/jcc.23611 + CHARMM> ! + CHARMM> !Parameters for Monovaletn Ions-DNA Interactions + CHARMM> !Savelyev, A. and MacKerell, A.D., Jr., “Balancing the Interactions of Ions, + CHARMM> !Water, and DNA in the Drude Polarizable Force Field,” Journal + CHARMM> !of Physical Chemistry B, 118: 6742−6757, 2014, DOI: 10.1021/jp503469s + CHARMM> ! + CHARMM> !Savelyev, A. and MacKerell, A.D., Jr., “Competition among Li+, Na+, K+, and Rb+ + CHARMM> !Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 + CHARMM> !and Drude Polarizable Force Fields,” Journal of Physical Chemistry B, 119: 4428−4440, 2015, + CHARMM> !DOI: 10.1021/acs.jpcb.5b00683 + CHARMM> ! + CHARMM> + + CHARMM> read rtf card append + MAINIO> Residue topology file being read from unit 98. + RDTITL> * TOPOLOGY FOR DRUDE NUCLEIC ACIDS + RDTITL> * + + DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA + Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000 + + CHARMM> + + CHARMM> read para card append + + PARAMETER FILE BEING READ FROM UNIT 98 + RDTITL> * DRUDE POLARIZABLE FF PARAMETERS + RDTITL> * + THOLE CUTOFF 5.000 + MAXNBTHOLE -5000 + PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. + + VCLOSE: Closing unit 98 with status "KEEP" + + RETURNING TO INPUT STREAM 99 + + CHARMM> incr i + Parameter: I <- "6" + + CHARMM> if @i le @streamfiles goto loop_streams + Parameter: I -> "6" + Parameter: STREAMFILES -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> return + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> + + CHARMM> !Not using ENVI because lowercase strings still cannot be set from the cmdline + CHARMM> if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> if @?mini eq 0 set mini 0 + Comparing "1" and "0". + IF test evaluated as false. Skipping command + + CHARMM> if @mini eq 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> if @?mindr eq 0 set mindr 0 + Comparing "1" and "0". + IF test evaluated as false. Skipping command + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> set ins + Parameter: INS <- "" + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> + + CHARMM> open unit 90 write form name test_drude_all@ins.ene + Parameter: INS -> "" + VOPEN> Attempting to open::test_drude_all.ene:: + OPNLGU> Unit 90 opened for WRITE access to test_drude_all.ene + + CHARMM> echu 90 + + CHARMM> echo $Id: test_drude_all.inp 28 2015-07-29 23:54:15Z alex $ + + CHARMM> echo residue names and energies + + CHARMM> + + CHARMM> set testcasei 1 + Parameter: TESTCASEI <- "1" + + CHARMM> label loop_tests + + CHARMM> stream @test@@testcasei + Parameter: TESTCASEI -> "1" + Parameter: TEST1 -> "TEST_DRUDE_MASTER_PROTEIN.STR" + VOPEN> Attempting to open::test_drude_master_protein.str:: + OPNLGU> Unit 99 opened for READONLY access to test_drude_master_protein.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * $ID: TEST_DRUDE_MASTER_PROTEIN.STR 30 2015-07-30 13:50:30Z ALEX $ + RDTITL> * TEST CASE, DRUDE MASTER_PROTEIN TOPPAR FILE + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> ! goto skip_to_ions_noble + CHARMM> ! goto skip_to_master_prot_model + CHARMM> ! goto skip_to_monopept + CHARMM> + + CHARMM> set boml 0 ! set to -1 if the series contains 3-membered rings + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> set nres 1 ! skip swm6 water due to bug + Parameter: NRES <- "1" + + CHARMM> set resi1 swm4 + Parameter: RESI1 <- "SWM4" + + CHARMM> ! set resi2 swm6 + CHARMM> set seed1 1 H1 1 OH2 1 H2 + Parameter: SEED1 <- "1 H1 1 OH2 1 H2" + + CHARMM> ! set seed2 1 H1 1 OH2 1 H2 + CHARMM> + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> label loop_master_water + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "1" + Parameter: RESI1 -> "SWM4" + Parameter: RESIDUE <- "SWM4" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "SWM4" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue noangle nodihedral first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SWM4" + Drude polarizability will be setup for SEGID: SWM4 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SWM4. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 5 Number of groups = 1 + Number of bonds = 5 Number of angles = 1 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 1 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 1 + Number of true-bonds = 5 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 1 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "1" + Parameter: SEED1 -> "1 H1 1 OH2 1 H2" + + CHARMM> ic build + **** WARNING **** 1 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 10 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + Allocate space for 5000 Thole shielding pairs + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 10 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "SWM4" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 0.00000000 0.00000000 + 0.64536246 0.38745470 + 0.84605627 + + Transpose of the rotation matrix + 0.790796 0.612079 0.000000 + -0.612079 0.790796 0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.78434 0.22334 0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 1.000000 ANGLE IS 37.74 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 5 atoms have been selected out of 5 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.000000 1.850000 0.000000 1.850000 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "SWM4" + RDCMND substituted energy or value "?RDIP" to "1.85" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 5 Number of groups = 1 + Number of bonds = 5 Number of angles = 1 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 1 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 2 + + CHARMM> delete atom sele all end + SELRPN> 5 atoms have been selected out of 5 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 5 bonds deleted + DELTIC: 1 angles deleted + DELTIC: 1 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "2" + + CHARMM> if count le @nres goto loop_master_water + Parameter: NRES -> "1" + Comparing "2" and "1". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + CHARMM> label skip_to_ions_noble + + CHARMM> + + CHARMM> set boml 0 ! set to -1 if the series contains 3-membered rings + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> set nres 18 + Parameter: NRES <- "18" + + CHARMM> + + CHARMM> set resi1 li + Parameter: RESI1 <- "LI" + + CHARMM> set resi2 sod + Parameter: RESI2 <- "SOD" + + CHARMM> set resi3 pot + Parameter: RESI3 <- "POT" + + CHARMM> set resi4 rb + Parameter: RESI4 <- "RB" + + CHARMM> set resi5 cs + Parameter: RESI5 <- "CS" + + CHARMM> set resi6 f + Parameter: RESI6 <- "F" + + CHARMM> set resi7 cla + Parameter: RESI7 <- "CLA" + + CHARMM> set resi8 br + Parameter: RESI8 <- "BR" + + CHARMM> set resi9 i + Parameter: RESI9 <- "I" + + CHARMM> set resi10 zn + Parameter: RESI10 <- "ZN" + + CHARMM> set resi11 mag + Parameter: RESI11 <- "MAG" + + CHARMM> set resi12 cal + Parameter: RESI12 <- "CAL" + + CHARMM> set resi13 sr + Parameter: RESI13 <- "SR" + + CHARMM> set resi14 ba + Parameter: RESI14 <- "BA" + + CHARMM> set resi15 he + Parameter: RESI15 <- "HE" + + CHARMM> set resi16 ne + Parameter: RESI16 <- "NE" + + CHARMM> set resi17 he1 + Parameter: RESI17 <- "HE1" + + CHARMM> set resi18 ne1 + Parameter: RESI18 <- "NE1" + + CHARMM> + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> label loop_master_ions_noble + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "1" + Parameter: RESI1 -> "LI" + Parameter: RESIDUE <- "LI" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "LI" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LI" + Drude polarizability will be setup for SEGID: LI mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LI. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "LI" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "LI" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "2" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "2" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "2" + Parameter: RESI2 -> "SOD" + Parameter: RESIDUE <- "SOD" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "SOD" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SOD" + Drude polarizability will be setup for SEGID: SOD mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SOD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "SOD" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "SOD" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "3" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "3" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "3" + Parameter: RESI3 -> "POT" + Parameter: RESIDUE <- "POT" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "POT" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "POT" + Drude polarizability will be setup for SEGID: POT mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is POT. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "POT" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "POT" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "4" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "4" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "4" + Parameter: RESI4 -> "RB" + Parameter: RESIDUE <- "RB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "RB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "RB" + Drude polarizability will be setup for SEGID: RB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is RB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "RB" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "RB" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "5" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "5" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "5" + Parameter: RESI5 -> "CS" + Parameter: RESIDUE <- "CS" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CS" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CS" + Drude polarizability will be setup for SEGID: CS mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CS" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CS" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "6" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "6" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "6" + Parameter: RESI6 -> "F" + Parameter: RESIDUE <- "F" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "F" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "F" + Drude polarizability will be setup for SEGID: F mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is F. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "F" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "F" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "7" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "7" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "7" + Parameter: RESI7 -> "CLA" + Parameter: RESIDUE <- "CLA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CLA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CLA" + Drude polarizability will be setup for SEGID: CLA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CLA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CLA" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CLA" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "8" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "8" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "8" + Parameter: RESI8 -> "BR" + Parameter: RESIDUE <- "BR" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BR" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BR" + Drude polarizability will be setup for SEGID: BR mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BR" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BR" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "9" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "9" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "9" + Parameter: RESI9 -> "I" + Parameter: RESIDUE <- "I" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "I" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "I" + Drude polarizability will be setup for SEGID: I mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is I. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "I" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "I" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "10" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "10" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "10" + Parameter: RESI10 -> "ZN" + Parameter: RESIDUE <- "ZN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ZN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ZN" + Drude polarizability will be setup for SEGID: ZN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ZN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ZN" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ZN" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "11" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "11" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "11" + Parameter: RESI11 -> "MAG" + Parameter: RESIDUE <- "MAG" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MAG" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MAG" + Drude polarizability will be setup for SEGID: MAG mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MAG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MAG" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MAG" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "12" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "12" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "12" + Parameter: RESI12 -> "CAL" + Parameter: RESIDUE <- "CAL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CAL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CAL" + Drude polarizability will be setup for SEGID: CAL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CAL" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CAL" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "13" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "13" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "13" + Parameter: RESI13 -> "SR" + Parameter: RESIDUE <- "SR" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "SR" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SR" + Drude polarizability will be setup for SEGID: SR mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "SR" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "SR" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "14" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "14" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "14" + Parameter: RESI14 -> "BA" + Parameter: RESIDUE <- "BA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BA" + Drude polarizability will be setup for SEGID: BA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BA" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BA" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "15" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "15" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "15" + Parameter: RESI15 -> "HE" + Parameter: RESIDUE <- "HE" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "HE" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HE" + Drude polarizability will be setup for SEGID: HE mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "HE" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "HE" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "16" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "16" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "16" + Parameter: RESI16 -> "NE" + Parameter: RESIDUE <- "NE" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "NE" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "NE" + Drude polarizability will be setup for SEGID: NE mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is NE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "NE" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "NE" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "17" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "17" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "17" + Parameter: RESI17 -> "HE1" + Parameter: RESIDUE <- "HE1" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "HE1" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HE1" + Drude polarizability will be setup for SEGID: HE1 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HE1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "HE1" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "HE1" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "18" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "18" and "18". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "18" + Parameter: RESI18 -> "NE1" + Parameter: RESIDUE <- "NE1" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "NE1" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "NE1" + Drude polarizability will be setup for SEGID: NE1 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is NE1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 1 + Number of true-bonds = 1 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 1 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 1 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 51 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 0 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "NE1" + RDCMND substituted energy or value "?ENER" to "0" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + **WARNING** ALL SELECTED COORDINATES UNDEFINED + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> coor dipole oxyz select all end + SELRPN> 2 atoms have been selected out of 2 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 0.000000 0.000000 0.000000 + + **** WARNING **** FOR THIS OPERATION, THERE WERE 2 MISSING COORDINATES + + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "NE1" + RDCMND substituted energy or value "?RDIP" to "0" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 2 Number of groups = 1 + Number of bonds = 1 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 1 + + CHARMM> delete atom sele all end + SELRPN> 2 atoms have been selected out of 2 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 1 bonds deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "19" + + CHARMM> if count le @nres goto loop_master_ions_noble + Parameter: NRES -> "18" + Comparing "19" and "18". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + CHARMM> label skip_to_master_prot_model + + CHARMM> + + CHARMM> set boml 0 ! set to -1 if the series contains 3-membered rings + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> set nres 1 + Parameter: NRES <- "1" + + CHARMM> + + CHARMM> set resi1 alad + Parameter: RESI1 <- "ALAD" + + CHARMM> set seed1 1 N 1 CA 1 C + Parameter: SEED1 <- "1 N 1 CA 1 C" + + CHARMM> + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> label loop_master_prot_model + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "1" + Parameter: RESI1 -> "ALAD" + Parameter: RESIDUE <- "ALAD" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ALAD" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALAD" + Drude polarizability will be setup for SEGID: ALAD mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALAD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 36 Number of groups = 1 + Number of bonds = 35 Number of angles = 36 + Number of dihedrals = 41 Number of impropers = 4 + Number of cross-terms = 1 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 10 + Number of true-bonds = 35 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "1" + Parameter: SEED1 -> "1 N 1 CA 1 C" + + CHARMM> ic build + **** WARNING **** 14 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 189 exclusions and 123 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 2593 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 441 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 441 atom pairs and 312 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 2593 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 441 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 393.32820 0.00000 140.23908 +ENER INTERN> 0.00000 36.27241 149.26112 18.98284 19.90658 +ENER CROSS> -2.72987 0.00000 0.00000 0.00000 +ENER EXTERN> 194.12036 -22.48523 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ALAD" + RDCMND substituted energy or value "?ENER" to "393.328" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 50.38237581 27.73931746 -24.37104825 + 63.63574594 24.89002182 + 88.35857387 + + Transpose of the rotation matrix + 0.892241 0.409547 -0.190202 + -0.174863 0.701716 0.690665 + 0.416327 -0.582981 0.697714 + CENTER OF ATOMS BEFORE TRANSLATION 0.92243 0.83354 0.58430 + AXIS OF ROTATION IS 0.834109 0.397215 0.382729 ANGLE IS 49.77 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 36 atoms have been selected out of 36 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -5.083446 -2.571258 -1.157893 5.813219 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ALAD" + RDCMND substituted energy or value "?RDIP" to "5.81322" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 36 Number of groups = 1 + Number of bonds = 35 Number of angles = 36 + Number of dihedrals = 41 Number of impropers = 4 + Number of cross-terms = 1 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 14 + + CHARMM> delete atom sele all end + SELRPN> 36 atoms have been selected out of 36 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 35 bonds deleted + DELTIC: 36 angles deleted + DELTIC: 41 dihedrals deleted + DELTIC: 4 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "2" + + CHARMM> if count le @nres goto loop_master_prot_model + Parameter: NRES -> "1" + Comparing "2" and "1". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + CHARMM> label skip_to_monopept + + CHARMM> + + CHARMM> set boml 0 + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> !20 AA + 2 (His -> (HSD,HDE,HSP)) + 1 (patchable) + CHARMM> set naa 25 + Parameter: NAA <- "25" + + CHARMM> set patched 25 ! 23 and higher are patched AA + Parameter: PATCHED <- "25" + + CHARMM> set aa1 GLY + Parameter: AA1 <- "GLY" + + CHARMM> set aa2 PRO + Parameter: AA2 <- "PRO" + + CHARMM> set aa3 ALA + Parameter: AA3 <- "ALA" + + CHARMM> set aa4 ARG + Parameter: AA4 <- "ARG" + + CHARMM> set aa5 ASN + Parameter: AA5 <- "ASN" + + CHARMM> set aa6 ASP + Parameter: AA6 <- "ASP" + + CHARMM> set aa7 CYS + Parameter: AA7 <- "CYS" + + CHARMM> set aa8 GLN + Parameter: AA8 <- "GLN" + + CHARMM> set aa9 GLU + Parameter: AA9 <- "GLU" + + CHARMM> set aa10 HSD + Parameter: AA10 <- "HSD" + + CHARMM> set aa11 HSE + Parameter: AA11 <- "HSE" + + CHARMM> set aa12 HSP + Parameter: AA12 <- "HSP" + + CHARMM> set aa13 ILE + Parameter: AA13 <- "ILE" + + CHARMM> set aa14 LEU + Parameter: AA14 <- "LEU" + + CHARMM> set aa15 LYS + Parameter: AA15 <- "LYS" + + CHARMM> set aa16 MET + Parameter: AA16 <- "MET" + + CHARMM> set aa17 PHE + Parameter: AA17 <- "PHE" + + CHARMM> set aa18 SER + Parameter: AA18 <- "SER" + + CHARMM> set aa19 TRP + Parameter: AA19 <- "TRP" + + CHARMM> set aa20 THR + Parameter: AA20 <- "THR" + + CHARMM> set aa21 TYR + Parameter: AA21 <- "TYR" + + CHARMM> set aa22 VAL + Parameter: AA22 <- "VAL" + + CHARMM> set aa23 HSD + Parameter: AA23 <- "HSD" + + CHARMM> set pa23 HS2 + Parameter: PA23 <- "HS2" + + CHARMM> set aa24 ASP + Parameter: AA24 <- "ASP" + + CHARMM> set pa24 ASPP + Parameter: PA24 <- "ASPP" + + CHARMM> set aa25 GLU + Parameter: AA25 <- "GLU" + + CHARMM> set pa25 GLUP + Parameter: PA25 <- "GLUP" + + CHARMM> ! the following patches are not yet created + CHARMM> !set aa26 LYS + CHARMM> !set pa26 LSN + CHARMM> !set aa27 CYS + CHARMM> !set pa27 CYSM + CHARMM> !set aa28 CYS + CHARMM> !set pa28 CSSM + CHARMM> !set aa29 ARG + CHARMM> !set pa29 RNE + CHARMM> !set aa30 ARG + CHARMM> !set pa30 RNH + CHARMM> + + CHARMM> set npn 2 + Parameter: NPN <- "2" + + CHARMM> set pn1 NTER + Parameter: PN1 <- "NTER" + + CHARMM> set pn2 ACE + Parameter: PN2 <- "ACE" + + CHARMM> + + CHARMM> set npc 5 + Parameter: NPC <- "5" + + CHARMM> set pc1 CTER + Parameter: PC1 <- "CTER" + + CHARMM> set pc2 CNEU + Parameter: PC2 <- "CNEU" + + CHARMM> set pc3 CT1 + Parameter: PC3 <- "CT1" + + CHARMM> set pc4 CT2 + Parameter: PC4 <- "CT2" + + CHARMM> set pc5 CT3 + Parameter: PC5 <- "CT3" + + CHARMM> + + CHARMM> set special 2 ! 1 and 2 should be treated special when termini + Parameter: SPECIAL <- "2" + + CHARMM> set s1npn 2 + Parameter: S1NPN <- "2" + + CHARMM> set s1pn1 GNTE + Parameter: S1PN1 <- "GNTE" + + CHARMM> set s1pn2 ACE + Parameter: S1PN2 <- "ACE" + + CHARMM> + + CHARMM> set s1npc 5 + Parameter: S1NPC <- "5" + + CHARMM> set s1pc1 CTEG + Parameter: S1PC1 <- "CTEG" + + CHARMM> set s1pc2 CNEG + Parameter: S1PC2 <- "CNEG" + + CHARMM> set s1pc3 CT1G + Parameter: S1PC3 <- "CT1G" + + CHARMM> set s1pc4 CT2G + Parameter: S1PC4 <- "CT2G" + + CHARMM> set s1pc5 CT3 + Parameter: S1PC5 <- "CT3" + + CHARMM> + + CHARMM> set s2npn 2 + Parameter: S2NPN <- "2" + + CHARMM> set s2pn1 PROP + Parameter: S2PN1 <- "PROP" + + CHARMM> set s2pn2 ACP + Parameter: S2PN2 <- "ACP" + + CHARMM> + + CHARMM> set s2npc 2 + Parameter: S2NPC <- "2" + + CHARMM> set s2pc1 CTEP + Parameter: S2PC1 <- "CTEP" + + CHARMM> set s2pc2 CT3 + Parameter: S2PC2 <- "CT3" + + CHARMM> + + CHARMM> set countaa 1 + Parameter: COUNTAA <- "1" + + CHARMM> label loop_aa + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "1" + Parameter: AA1 -> "GLY" + Parameter: RESIDUE <- "GLY" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "1" + Parameter: SPECIAL -> "2" + Comparing "1" and "2". + IF test evaluated as true. Performing command + + CHARMM> set varp s@countaa + Parameter: COUNTAA -> "1" + Parameter: VARP <- "S1" + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "S1" + Parameter: S1NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "S1" + Parameter: S1NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "GLY" + Parameter: PATCH <- "GLY" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "S1" + Parameter: S1PN1 -> "GNTE" + Parameter: FIRST <- "GNTE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "S1" + Parameter: S1PC1 -> "CTEG" + Parameter: LAST <- "CTEG" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "GNTE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CTEG" + Parameter: NAM <- "GNTE-GLY-ALA-GLY-CTEG" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * GNTE-GLY-ALA-GLY-CTEG + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "GNTE" + Parameter: LAST -> "CTEG" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'GNTE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTEG' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 14 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 49 Number of groups = 4 + Number of bonds = 48 Number of angles = 45 + Number of dihedrals = 56 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 14 + Number of true-bonds = 48 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 22 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 432 + : Ran out of space. RESIZING + with mode 5 found 278 exclusions and 176 interactions(1-4) + found 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 4803 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 898 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 898 atom pairs and 454 atom exclusions. + There are 0 group pairs and 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 4803 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 898 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 149.65086 243.67734 39.44185 +ENER INTERN> 16.15009 32.94764 5.40255 13.51231 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 50.79711 33.12115 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CTEG" + RDCMND substituted energy or value "?ENER" to "149.651" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 15.17206014 4.77603798 -6.57137065 + 225.77666147 239.38230275 + 397.84526102 + + Transpose of the rotation matrix + 0.818024 0.575165 -0.004770 + -0.565771 0.806103 0.173496 + 0.103634 -0.139225 0.984823 + CENTER OF ATOMS BEFORE TRANSLATION 4.37182 3.02847 0.12346 + AXIS OF ROTATION IS 0.263240 0.091252 0.960405 ANGLE IS 36.44 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -45.813625 -3.654045 0.642633 45.963608 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CTEG" + RDCMND substituted energy or value "?RDIP" to "45.9636" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 49 Number of groups = 4 + Number of bonds = 48 Number of angles = 45 + Number of dihedrals = 56 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 22 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 48 bonds deleted + DELTIC: 45 angles deleted + DELTIC: 56 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "S1" + Parameter: S1PC2 -> "CNEG" + Parameter: LAST <- "CNEG" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "GNTE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CNEG" + Parameter: NAM <- "GNTE-GLY-ALA-GLY-CNEG" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * GNTE-GLY-ALA-GLY-CNEG + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "GNTE" + Parameter: LAST -> "CNEG" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'GNTE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEG' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 14 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 50 Number of groups = 4 + Number of bonds = 49 Number of angles = 46 + Number of dihedrals = 58 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 14 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 22 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 451 451 441 + : Ran out of space. RESIZING + with mode 5 found 284 exclusions and 182 interactions(1-4) + found 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 5001 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 941 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 941 atom pairs and 466 atom exclusions. + There are 0 group pairs and 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 5001 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 941 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 138.64237 11.00850 32.02056 +ENER INTERN> 15.82730 27.26627 28.10774 21.63009 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 18.26158 29.82940 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CNEG" + RDCMND substituted energy or value "?ENER" to "138.642" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 15.40075362 4.10215564 -7.28352017 + 251.50158839 267.09485873 + 424.80197822 + + Transpose of the rotation matrix + 0.808916 0.587896 -0.005766 + -0.578249 0.797337 0.172861 + 0.106222 -0.136496 0.984929 + CENTER OF ATOMS BEFORE TRANSLATION 4.48954 3.13986 0.12099 + AXIS OF ROTATION IS 0.255315 0.092424 0.962430 ANGLE IS 37.29 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -23.788031 -2.220204 -0.118858 23.891711 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CNEG" + RDCMND substituted energy or value "?RDIP" to "23.8917" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 50 Number of groups = 4 + Number of bonds = 49 Number of angles = 46 + Number of dihedrals = 58 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 22 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 46 angles deleted + DELTIC: 58 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "S1" + Parameter: S1PC3 -> "CT1G" + Parameter: LAST <- "CT1G" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "GNTE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CT1G" + Parameter: NAM <- "GNTE-GLY-ALA-GLY-CT1G" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * GNTE-GLY-ALA-GLY-CT1G + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "GNTE" + Parameter: LAST -> "CT1G" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'GNTE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1G' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 15 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 54 Number of groups = 4 + Number of bonds = 53 Number of angles = 52 + Number of dihedrals = 61 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 15 + Number of true-bonds = 53 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 23 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 491 491 477 + : Ran out of space. RESIZING + with mode 5 found 312 exclusions and 194 interactions(1-4) + found 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 5833 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1119 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1119 atom pairs and 506 atom exclusions. + There are 0 group pairs and 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 5833 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1119 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 491.08054 -352.43817 285.40976 +ENER INTERN> 15.82730 27.28226 5.89778 21.29031 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 362.72189 60.34101 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CT1G" + RDCMND substituted energy or value "?ENER" to "491.081" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 17.10014870 2.02200551 -9.36266897 + 332.30830661 346.31937533 + 506.18457094 + + Transpose of the rotation matrix + 0.788530 0.614943 -0.008086 + -0.606352 0.779577 0.156833 + 0.102747 -0.118765 0.987592 + CENTER OF ATOMS BEFORE TRANSLATION 4.83322 3.48371 0.11203 + AXIS OF ROTATION IS 0.219268 0.088180 0.971672 ANGLE IS 38.94 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 54 atoms have been selected out of 54 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.184755 -0.777309 -0.399248 24.200537 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CT1G" + RDCMND substituted energy or value "?RDIP" to "24.2005" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 54 Number of groups = 4 + Number of bonds = 53 Number of angles = 52 + Number of dihedrals = 61 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 23 + + CHARMM> delete atom sele all end + SELRPN> 54 atoms have been selected out of 54 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 53 bonds deleted + DELTIC: 52 angles deleted + DELTIC: 61 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "S1" + Parameter: S1PC4 -> "CT2G" + Parameter: LAST <- "CT2G" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "GNTE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CT2G" + Parameter: NAM <- "GNTE-GLY-ALA-GLY-CT2G" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * GNTE-GLY-ALA-GLY-CT2G + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "GNTE" + Parameter: LAST -> "CT2G" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'GNTE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2G' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 14 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 49 Number of groups = 4 + Number of bonds = 48 Number of angles = 48 + Number of dihedrals = 60 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 14 + Number of true-bonds = 48 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 20 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 436 436 432 + : Ran out of space. RESIZING + with mode 5 found 266 exclusions and 180 interactions(1-4) + found 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 5833 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 910 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 910 atom pairs and 446 atom exclusions. + There are 0 group pairs and 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 5833 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 910 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 107.62366 383.45688 29.31988 +ENER INTERN> 17.36986 28.17920 6.67888 5.51487 0.00000 +ENER CROSS> -10.83000 0.00000 0.00000 0.00000 +ENER EXTERN> 25.89905 34.81181 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CT2G" + RDCMND substituted energy or value "?ENER" to "107.624" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 15.17206014 4.57434587 -6.42022767 + 237.69312067 240.56171334 + 391.26367399 + + Transpose of the rotation matrix + 0.807520 0.589823 -0.004506 + -0.582223 0.798292 0.154099 + 0.094488 -0.121815 0.988045 + CENTER OF ATOMS BEFORE TRANSLATION 4.34683 3.06181 0.12346 + AXIS OF ROTATION IS 0.228378 0.081939 0.970118 ANGLE IS 37.16 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -27.116962 1.957211 -0.809012 27.199537 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CT2G" + RDCMND substituted energy or value "?RDIP" to "27.1995" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 49 Number of groups = 4 + Number of bonds = 48 Number of angles = 48 + Number of dihedrals = 60 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 20 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 48 bonds deleted + DELTIC: 48 angles deleted + DELTIC: 60 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "S1" + Parameter: S1PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "GNTE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CT3" + Parameter: NAM <- "GNTE-GLY-ALA-GLY-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * GNTE-GLY-ALA-GLY-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "GNTE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'GNTE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 15 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 53 Number of groups = 4 + Number of bonds = 52 Number of angles = 54 + Number of dihedrals = 66 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 15 + Number of true-bonds = 52 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 472 472 468 + : Ran out of space. RESIZING + with mode 5 found 287 exclusions and 195 interactions(1-4) + found 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 5833 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1091 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1091 atom pairs and 482 atom exclusions. + There are 0 group pairs and 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 5833 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1091 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 132.05826 -24.43460 29.12519 +ENER INTERN> 17.36986 40.72592 8.98234 7.39198 0.00000 +ENER CROSS> -5.49000 0.00000 0.00000 0.00000 +ENER EXTERN> 25.16891 37.90925 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CT3" + RDCMND substituted energy or value "?ENER" to "132.058" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 16.42699268 2.32655522 -9.10736738 + 328.80224661 344.59787910 + 509.08094455 + + Transpose of the rotation matrix + 0.791563 0.611040 -0.007628 + -0.602838 0.782860 0.154004 + 0.100074 -0.117305 0.988041 + CENTER OF ATOMS BEFORE TRANSLATION 4.79102 3.43337 0.11414 + AXIS OF ROTATION IS 0.217311 0.086266 0.972283 ANGLE IS 38.63 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 53 atoms have been selected out of 53 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.123114 -3.913401 0.088941 24.438642 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "GNTE-GLY-ALA-GLY-CT3" + RDCMND substituted energy or value "?RDIP" to "24.4386" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 53 Number of groups = 4 + Number of bonds = 52 Number of angles = 54 + Number of dihedrals = 66 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 53 atoms have been selected out of 53 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 52 bonds deleted + DELTIC: 54 angles deleted + DELTIC: 66 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "S1" + Parameter: S1PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "S1" + Parameter: S1PC1 -> "CTEG" + Parameter: LAST <- "CTEG" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CTEG" + Parameter: NAM <- "ACE-GLY-ALA-GLY-CTEG" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLY-ALA-GLY-CTEG + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTEG" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTEG' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 17 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 58 Number of groups = 5 + Number of bonds = 57 Number of angles = 51 + Number of dihedrals = 63 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 17 + Number of true-bonds = 57 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 27 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 516 516 513 + : Ran out of space. RESIZING + with mode 5 found 332 exclusions and 212 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 6729 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1321 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1321 atom pairs and 544 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 6729 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1321 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 250.19943 -118.14117 50.24392 +ENER INTERN> 16.35166 31.71418 91.16797 15.34783 0.00000 +ENER CROSS> -9.79000 0.00000 0.00000 0.00000 +ENER EXTERN> 83.53062 21.87717 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLY-ALA-GLY-CTEG" + RDCMND substituted energy or value "?ENER" to "250.199" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 31.09883579 -15.26358534 -56.74791738 + 264.18895424 339.00956336 + 651.68939346 + + Transpose of the rotation matrix + 0.863541 0.499541 -0.068956 + -0.455723 0.831608 0.317405 + 0.215901 -0.242667 0.945780 + CENTER OF ATOMS BEFORE TRANSLATION 3.48435 2.68544 0.32411 + AXIS OF ROTATION IS 0.489832 0.249133 0.835462 ANGLE IS 34.87 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 58 atoms have been selected out of 58 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -26.818318 -6.110688 -2.080997 27.584294 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLY-ALA-GLY-CTEG" + RDCMND substituted energy or value "?RDIP" to "27.5843" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 58 Number of groups = 5 + Number of bonds = 57 Number of angles = 51 + Number of dihedrals = 63 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 27 + + CHARMM> delete atom sele all end + SELRPN> 58 atoms have been selected out of 58 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 57 bonds deleted + DELTIC: 51 angles deleted + DELTIC: 63 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "S1" + Parameter: S1PC2 -> "CNEG" + Parameter: LAST <- "CNEG" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CNEG" + Parameter: NAM <- "ACE-GLY-ALA-GLY-CNEG" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLY-ALA-GLY-CNEG + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEG" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEG' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 17 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 58 Number of angles = 52 + Number of dihedrals = 65 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 17 + Number of true-bonds = 58 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 27 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 541 541 522 + : Ran out of space. RESIZING + with mode 5 found 338 exclusions and 218 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 6963 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1373 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1373 atom pairs and 556 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 6963 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1373 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 204.51762 45.68181 46.24478 +ENER INTERN> 16.02886 26.03281 113.87316 23.46560 0.00000 +ENER CROSS> -9.79000 0.00000 0.00000 0.00000 +ENER EXTERN> 50.99806 -16.09087 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLY-ALA-GLY-CNEG" + RDCMND substituted energy or value "?ENER" to "204.518" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 31.41586119 -17.14748851 -58.90606537 + 293.88050891 373.96534094 + 689.79618357 + + Transpose of the rotation matrix + 0.855419 0.513624 -0.066699 + -0.469653 0.823510 0.318209 + 0.218367 -0.240876 0.945671 + CENTER OF ATOMS BEFORE TRANSLATION 3.59915 2.78566 0.31862 + AXIS OF ROTATION IS 0.479293 0.244382 0.842944 ANGLE IS 35.68 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 59 atoms have been selected out of 59 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.317035 -3.562734 -2.601750 4.422973 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLY-ALA-GLY-CNEG" + RDCMND substituted energy or value "?RDIP" to "4.42297" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 58 Number of angles = 52 + Number of dihedrals = 65 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 27 + + CHARMM> delete atom sele all end + SELRPN> 59 atoms have been selected out of 59 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 58 bonds deleted + DELTIC: 52 angles deleted + DELTIC: 65 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "S1" + Parameter: S1PC3 -> "CT1G" + Parameter: LAST <- "CT1G" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CT1G" + Parameter: NAM <- "ACE-GLY-ALA-GLY-CT1G" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLY-ALA-GLY-CT1G + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1G" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1G' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 63 Number of groups = 5 + Number of bonds = 62 Number of angles = 58 + Number of dihedrals = 68 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 18 + Number of true-bonds = 62 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 560 560 558 + : Ran out of space. RESIZING + with mode 5 found 366 exclusions and 230 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 7939 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1587 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1587 atom pairs and 596 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 7939 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1587 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 558.29214 -353.77452 268.27226 +ENER INTERN> 16.02886 26.04880 91.66320 23.12583 0.00000 +ENER CROSS> -9.79000 0.00000 0.00000 0.00000 +ENER EXTERN> 395.45745 15.75801 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLY-ALA-GLY-CT1G" + RDCMND substituted energy or value "?ENER" to "558.292" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 33.44133248 -23.11074479 -65.50662271 + 388.38780207 476.92212049 + 806.01070281 + + Transpose of the rotation matrix + 0.835911 0.545366 -0.061881 + -0.505825 0.809215 0.298851 + 0.213058 -0.218512 0.952291 + CENTER OF ATOMS BEFORE TRANSLATION 3.95027 3.10287 0.29839 + AXIS OF ROTATION IS 0.429905 0.228461 0.873492 ANGLE IS 36.99 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 63 atoms have been selected out of 63 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 2.094321 -2.422765 -2.899950 4.320379 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLY-ALA-GLY-CT1G" + RDCMND substituted energy or value "?RDIP" to "4.32038" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 63 Number of groups = 5 + Number of bonds = 62 Number of angles = 58 + Number of dihedrals = 68 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 63 atoms have been selected out of 63 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 62 bonds deleted + DELTIC: 58 angles deleted + DELTIC: 68 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "S1" + Parameter: S1PC4 -> "CT2G" + Parameter: LAST <- "CT2G" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CT2G" + Parameter: NAM <- "ACE-GLY-ALA-GLY-CT2G" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLY-ALA-GLY-CT2G + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2G" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2G' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 17 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 58 Number of groups = 5 + Number of bonds = 57 Number of angles = 54 + Number of dihedrals = 67 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 17 + Number of true-bonds = 57 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 526 526 513 + : Ran out of space. RESIZING + with mode 5 found 320 exclusions and 216 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 7939 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1333 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1333 atom pairs and 536 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 7939 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1333 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 170.83397 387.45817 44.47804 +ENER INTERN> 17.57142 26.94574 92.44430 7.35038 0.00000 +ENER CROSS> -18.34000 0.00000 0.00000 0.00000 +ENER EXTERN> 58.63498 -13.77285 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLY-ALA-GLY-CT2G" + RDCMND substituted energy or value "?ENER" to "170.834" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 31.09883579 -15.79307473 -56.35113138 + 277.23463592 341.21251958 + 642.93963879 + + Transpose of the rotation matrix + 0.856673 0.511262 -0.068718 + -0.473076 0.831739 0.290531 + 0.205693 -0.216381 0.954395 + CENTER OF ATOMS BEFORE TRANSLATION 3.46324 2.71361 0.32411 + AXIS OF ROTATION IS 0.444389 0.240566 0.862929 ANGLE IS 34.77 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 58 atoms have been selected out of 58 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -4.134216 0.129213 -4.124999 5.841580 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLY-ALA-GLY-CT2G" + RDCMND substituted energy or value "?RDIP" to "5.84158" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 58 Number of groups = 5 + Number of bonds = 57 Number of angles = 54 + Number of dihedrals = 67 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 58 atoms have been selected out of 58 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 57 bonds deleted + DELTIC: 54 angles deleted + DELTIC: 67 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "S1" + Parameter: S1PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLY" + Parameter: PATCH -> "GLY" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-GLY-ALA-GLY-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLY-ALA-GLY-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLY" + Parameter: RESIDUE -> "GLY" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLY ALA GLY + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLY" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: GLY mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLY . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 61 Number of angles = 60 + Number of dihedrals = 73 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 18 + Number of true-bonds = 61 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "1" + Parameter: PATCHED -> "25" + Comparing "1" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 26 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 551 551 549 + : Ran out of space. RESIZING + with mode 5 found 341 exclusions and 231 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 7939 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1550 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1550 atom pairs and 572 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 7939 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1550 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 199.21758 -28.38361 43.40073 +ENER INTERN> 17.57142 39.49245 94.74776 9.22749 0.00000 +ENER CROSS> -13.00000 0.00000 0.00000 0.00000 +ENER EXTERN> 57.90422 -6.72577 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLY-ALA-GLY-CT3" + RDCMND substituted energy or value "?ENER" to "199.218" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 32.69049051 -22.18628446 -64.56073905 + 382.68883579 471.61590290 + 804.11513614 + + Transpose of the rotation matrix + 0.837984 0.542257 -0.061158 + -0.503888 0.811931 0.294730 + 0.209475 -0.216162 0.953622 + CENTER OF ATOMS BEFORE TRANSLATION 3.89995 3.05370 0.30320 + AXIS OF ROTATION IS 0.427427 0.226420 0.875237 ANGLE IS 36.70 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 62 atoms have been selected out of 62 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 2.106958 -5.397229 -1.987853 6.125432 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLY-ALA-GLY-CT3" + RDCMND substituted energy or value "?RDIP" to "6.12543" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 61 Number of angles = 60 + Number of dihedrals = 73 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 26 + + CHARMM> delete atom sele all end + SELRPN> 62 atoms have been selected out of 62 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 61 bonds deleted + DELTIC: 60 angles deleted + DELTIC: 73 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "2" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "2" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "2" + Parameter: AA2 -> "PRO" + Parameter: RESIDUE <- "PRO" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "2" + Parameter: SPECIAL -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> set varp s@countaa + Parameter: COUNTAA -> "2" + Parameter: VARP <- "S2" + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "S2" + Parameter: S2NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "S2" + Parameter: S2NPC -> "2" + Parameter: MAXCT <- "2" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "2" + Parameter: PATCHED -> "25" + Comparing "2" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "PRO" + Parameter: PATCH <- "PRO" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "S2" + Parameter: S2PN1 -> "PROP" + Parameter: FIRST <- "PROP" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "S2" + Parameter: S2PC1 -> "CTEP" + Parameter: LAST <- "CTEP" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "PROP" + Parameter: PATCH -> "PRO" + Parameter: PATCH -> "PRO" + Parameter: LAST -> "CTEP" + Parameter: NAM <- "PROP-PRO-ALA-PRO-CTEP" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PROP-PRO-ALA-PRO-CTEP + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PRO" + Parameter: RESIDUE -> "PRO" + + RESIDUE SEQUENCE -- 3 RESIDUES + PRO ALA PRO + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PRO" + Parameter: FIRST -> "PROP" + Parameter: LAST -> "CTEP" + Drude polarizability will be setup for SEGID: PRO mass of Drudes particles = 0.4000 + THE PATCH 'PROP' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTEP' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PRO . + ATOMS "N " "-C " "CA " "CD " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PRO . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PRO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 69 Number of groups = 4 + Number of bonds = 70 Number of angles = 81 + Number of dihedrals = 125 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 70 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "2" + Parameter: PATCHED -> "25" + Comparing "2" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 636 636 630 + : Ran out of space. RESIZING + with mode 5 found 428 exclusions and 308 interactions(1-4) + found 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 9523 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1918 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1918 atom pairs and 736 atom exclusions. + There are 0 group pairs and 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 9523 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1918 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1254.94291 -1055.72533 1188.67911 +ENER INTERN> 20.76266 49.42850 19.90174 55.17013 0.02570 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 1070.22132 41.71285 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "PROP-PRO-ALA-PRO-CTEP" + RDCMND substituted energy or value "?ENER" to "1254.94" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 99.94372745 79.18932652 139.71731367 + 318.97295449 348.97965868 + 699.78756458 + + Transpose of the rotation matrix + 0.844931 0.500657 0.188239 + -0.496530 0.865030 -0.071983 + -0.198871 -0.032646 0.979482 + CENTER OF ATOMS BEFORE TRANSLATION 4.38080 2.43320 0.05361 + AXIS OF ROTATION IS -0.036749 -0.361645 0.931591 ANGLE IS 32.36 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 69 atoms have been selected out of 69 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -44.094222 7.809902 -2.888021 44.873552 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "PROP-PRO-ALA-PRO-CTEP" + RDCMND substituted energy or value "?RDIP" to "44.8736" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 69 Number of groups = 4 + Number of bonds = 70 Number of angles = 81 + Number of dihedrals = 125 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 69 atoms have been selected out of 69 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 70 bonds deleted + DELTIC: 81 angles deleted + DELTIC: 125 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "S2" + Parameter: S2PC2 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "PROP" + Parameter: PATCH -> "PRO" + Parameter: PATCH -> "PRO" + Parameter: LAST -> "CT3" + Parameter: NAM <- "PROP-PRO-ALA-PRO-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PROP-PRO-ALA-PRO-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PRO" + Parameter: RESIDUE -> "PRO" + + RESIDUE SEQUENCE -- 3 RESIDUES + PRO ALA PRO + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PRO" + Parameter: FIRST -> "PROP" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: PRO mass of Drudes particles = 0.4000 + THE PATCH 'PROP' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PRO . + ATOMS "N " "-C " "CA " "CD " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PRO . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PRO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 4 + Number of bonds = 74 Number of angles = 90 + Number of dihedrals = 135 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 21 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "2" + Parameter: PATCHED -> "25" + Comparing "2" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 27 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 679 679 666 + : Ran out of space. RESIZING + with mode 5 found 437 exclusions and 325 interactions(1-4) + found 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 10659 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2191 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2191 atom pairs and 762 atom exclusions. + There are 0 group pairs and 5 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 10659 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2191 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1320.41784 -65.47493 1134.15360 +ENER INTERN> 28.55446 55.96704 41.43626 64.84992 0.02570 +ENER CROSS> 0.38633 0.00000 0.00000 0.00000 +ENER EXTERN> 1070.19669 59.00143 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "PROP-PRO-ALA-PRO-CT3" + RDCMND substituted energy or value "?ENER" to "1320.42" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 124.13388292 86.69064469 198.90929116 + 324.44097137 375.59192091 + 878.98523907 + + Transpose of the rotation matrix + 0.873352 0.437838 0.213434 + -0.402755 0.895559 -0.189111 + -0.273942 0.079199 0.958480 + CENTER OF ATOMS BEFORE TRANSLATION 4.76308 2.48982 0.17416 + AXIS OF ROTATION IS -0.266173 -0.483494 0.833898 ANGLE IS 30.27 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 73 atoms have been selected out of 73 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -21.038761 -1.549233 -0.795596 21.110721 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "PROP-PRO-ALA-PRO-CT3" + RDCMND substituted energy or value "?RDIP" to "21.1107" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 4 + Number of bonds = 74 Number of angles = 90 + Number of dihedrals = 135 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 27 + + CHARMM> delete atom sele all end + SELRPN> 73 atoms have been selected out of 73 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 135 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "S2" + Parameter: S2PN2 -> "ACP" + Parameter: FIRST <- "ACP" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "S2" + Parameter: S2PC1 -> "CTEP" + Parameter: LAST <- "CTEP" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACP" + Parameter: PATCH -> "PRO" + Parameter: PATCH -> "PRO" + Parameter: LAST -> "CTEP" + Parameter: NAM <- "ACP-PRO-ALA-PRO-CTEP" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACP-PRO-ALA-PRO-CTEP + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PRO" + Parameter: RESIDUE -> "PRO" + + RESIDUE SEQUENCE -- 3 RESIDUES + PRO ALA PRO + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PRO" + Parameter: FIRST -> "ACP" + Parameter: LAST -> "CTEP" + Drude polarizability will be setup for SEGID: PRO mass of Drudes particles = 0.4000 + THE PATCH 'ACP' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTEP' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACP . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IC NOT FOUND FOR RESIDUE 1 ACP . + ATOMS "A1 " "A2 " "A3 " "A4 " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PRO . + ATOMS "N " "-C " "CA " "CD " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PRO . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PRO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 5 + Number of bonds = 79 Number of angles = 87 + Number of dihedrals = 129 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 23 + Number of true-bonds = 79 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "2" + Parameter: PATCHED -> "25" + Comparing "2" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 718 718 711 + : Ran out of space. RESIZING + with mode 5 found 482 exclusions and 350 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 12169 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2521 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2521 atom pairs and 832 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 12169 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2521 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1356.72468 -36.30684 1125.95918 +ENER INTERN> 19.35417 53.00450 35.45383 81.01052 0.02570 +ENER CROSS> 0.10552 0.00000 0.00000 0.00000 +ENER EXTERN> 1113.35111 54.41933 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACP-PRO-ALA-PRO-CTEP" + RDCMND substituted energy or value "?ENER" to "1356.72" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 128.32189135 50.07408483 66.54776617 + 351.83883204 437.35618893 + 941.34020357 + + Transpose of the rotation matrix + 0.879720 0.469055 0.077968 + -0.366010 0.563329 0.740740 + 0.303526 -0.680182 0.667252 + CENTER OF ATOMS BEFORE TRANSLATION 3.75556 2.20023 0.26477 + AXIS OF ROTATION IS 0.854176 0.135593 0.501993 ANGLE IS 56.28 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 78 atoms have been selected out of 78 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -23.261508 -4.132653 -13.002058 26.967204 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACP-PRO-ALA-PRO-CTEP" + RDCMND substituted energy or value "?RDIP" to "26.9672" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 5 + Number of bonds = 79 Number of angles = 87 + Number of dihedrals = 129 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 78 atoms have been selected out of 78 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 79 bonds deleted + DELTIC: 87 angles deleted + DELTIC: 129 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 1 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "S2" + Parameter: S2PC2 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACP" + Parameter: PATCH -> "PRO" + Parameter: PATCH -> "PRO" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACP-PRO-ALA-PRO-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACP-PRO-ALA-PRO-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PRO" + Parameter: RESIDUE -> "PRO" + + RESIDUE SEQUENCE -- 3 RESIDUES + PRO ALA PRO + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PRO" + Parameter: FIRST -> "ACP" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: PRO mass of Drudes particles = 0.4000 + THE PATCH 'ACP' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACP . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IC NOT FOUND FOR RESIDUE 1 ACP . + ATOMS "A1 " "A2 " "A3 " "A4 " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PRO . + ATOMS "N " "-C " "CA " "CD " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PRO . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PRO . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PRO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 5 + Number of bonds = 83 Number of angles = 96 + Number of dihedrals = 139 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 24 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "2" + Parameter: PATCHED -> "25" + Comparing "2" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 761 761 747 + : Ran out of space. RESIZING + with mode 5 found 491 exclusions and 367 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2830 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2830 atom pairs and 858 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2830 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1389.50967 -32.78500 1079.32148 +ENER INTERN> 27.14598 59.54304 56.98834 90.69031 0.02570 +ENER CROSS> 2.77184 0.00000 0.00000 0.00000 +ENER EXTERN> 1113.32899 39.01547 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACP-PRO-ALA-PRO-CT3" + RDCMND substituted energy or value "?ENER" to "1389.51" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 149.26315921 58.56282781 125.23523832 + 359.37087236 473.33830825 + 1156.39003522 + + Transpose of the rotation matrix + 0.901087 0.419306 0.110564 + -0.426355 0.903205 0.049419 + -0.079140 -0.091670 0.992640 + CENTER OF ATOMS BEFORE TRANSLATION 4.12638 2.26200 0.36178 + AXIS OF ROTATION IS 0.160677 -0.216043 0.963072 ANGLE IS 26.04 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 82 atoms have been selected out of 82 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 4.329962 -1.068541 -7.737398 8.930716 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACP-PRO-ALA-PRO-CT3" + RDCMND substituted energy or value "?RDIP" to "8.93072" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 5 + Number of bonds = 83 Number of angles = 96 + Number of dihedrals = 139 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 82 atoms have been selected out of 82 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 139 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "3" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "3" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "3" + Parameter: AA3 -> "ALA" + Parameter: RESIDUE <- "ALA" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "3" + Parameter: SPECIAL -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "ALA" + Parameter: PATCH <- "ALA" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-ALA-ALA-ALA-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ALA-ALA-ALA-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 16 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 57 Number of groups = 6 + Number of bonds = 56 Number of angles = 57 + Number of dihedrals = 74 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 16 + Number of true-bonds = 56 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 508 508 504 + : Ran out of space. RESIZING + with mode 5 found 324 exclusions and 226 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1272 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1272 atom pairs and 550 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1272 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 137.13473 1252.37494 34.06020 +ENER INTERN> 21.59150 52.16461 21.86533 19.67084 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 14.88694 9.23551 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ALA-ALA-ALA-CTER" + RDCMND substituted energy or value "?ENER" to "137.135" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 34.34536811 26.56987614 -11.43812960 + 233.40118229 267.21456289 + 578.08561569 + + Transpose of the rotation matrix + 0.877977 0.478687 0.003882 + -0.440101 0.803961 0.399948 + 0.188329 -0.352854 0.916530 + CENTER OF ATOMS BEFORE TRANSLATION 4.89496 2.37632 -0.10619 + AXIS OF ROTATION IS 0.626270 0.153445 0.764356 ANGLE IS 36.94 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 57 atoms have been selected out of 57 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -50.461491 -3.975660 1.710333 50.646749 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ALA-ALA-ALA-CTER" + RDCMND substituted energy or value "?RDIP" to "50.6467" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 57 Number of groups = 6 + Number of bonds = 56 Number of angles = 57 + Number of dihedrals = 74 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 57 atoms have been selected out of 57 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 56 bonds deleted + DELTIC: 57 angles deleted + DELTIC: 74 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-ALA-ALA-ALA-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ALA-ALA-ALA-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 16 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 58 Number of groups = 6 + Number of bonds = 57 Number of angles = 58 + Number of dihedrals = 76 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 16 + Number of true-bonds = 57 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 523 523 513 + : Ran out of space. RESIZING + with mode 5 found 330 exclusions and 232 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1323 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1323 atom pairs and 562 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1323 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 154.86105 -17.72632 30.10202 +ENER INTERN> 21.64901 49.73160 31.22456 12.95073 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 14.47433 27.11083 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ALA-ALA-ALA-CNEU" + RDCMND substituted energy or value "?ENER" to "154.861" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 34.57020502 26.82317422 -10.83516223 + 238.94670550 282.30182777 + 609.52762512 + + Transpose of the rotation matrix + 0.879879 0.475177 0.004416 + -0.435889 0.803358 0.405731 + 0.189247 -0.358919 0.913982 + CENTER OF ATOMS BEFORE TRANSLATION 4.99458 2.41817 -0.10436 + AXIS OF ROTATION IS 0.635250 0.153552 0.756888 ANGLE IS 37.00 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 58 atoms have been selected out of 58 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.222779 -0.526461 0.660229 24.237493 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ALA-ALA-ALA-CNEU" + RDCMND substituted energy or value "?RDIP" to "24.2375" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 58 Number of groups = 6 + Number of bonds = 57 Number of angles = 58 + Number of dihedrals = 76 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 58 atoms have been selected out of 58 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 57 bonds deleted + DELTIC: 58 angles deleted + DELTIC: 76 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-ALA-ALA-ALA-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ALA-ALA-ALA-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 17 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 62 Number of groups = 6 + Number of bonds = 61 Number of angles = 64 + Number of dihedrals = 79 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 17 + Number of true-bonds = 61 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 560 560 549 + : Ran out of space. RESIZING + with mode 5 found 358 exclusions and 244 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1533 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1533 atom pairs and 602 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1533 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 391.72761 -236.86655 167.71688 +ENER INTERN> 21.64901 49.59174 11.36575 12.55295 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 242.27517 56.57299 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ALA-ALA-ALA-CT1" + RDCMND substituted energy or value "?ENER" to "391.728" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 36.25613179 28.40083648 -8.68283843 + 301.32973817 364.99576450 + 724.55654523 + + Transpose of the rotation matrix + 0.866327 0.499422 0.007413 + -0.461327 0.794382 0.395139 + 0.191452 -0.345740 0.918591 + CENTER OF ATOMS BEFORE TRANSLATION 5.35018 2.67883 -0.09762 + AXIS OF ROTATION IS 0.603757 0.149977 0.782933 ANGLE IS 37.85 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 62 atoms have been selected out of 62 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.267018 0.552620 0.230854 24.274408 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ALA-ALA-ALA-CT1" + RDCMND substituted energy or value "?RDIP" to "24.2744" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 62 Number of groups = 6 + Number of bonds = 61 Number of angles = 64 + Number of dihedrals = 79 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 62 atoms have been selected out of 62 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 61 bonds deleted + DELTIC: 64 angles deleted + DELTIC: 79 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-ALA-ALA-ALA-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ALA-ALA-ALA-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 16 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 57 Number of groups = 6 + Number of bonds = 56 Number of angles = 60 + Number of dihedrals = 78 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 16 + Number of true-bonds = 56 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 22 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 514 514 504 + : Ran out of space. RESIZING + with mode 5 found 312 exclusions and 228 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1284 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1284 atom pairs and 540 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1284 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 134.74563 256.98198 27.76055 +ENER INTERN> 29.30964 47.21545 10.40628 15.16293 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 18.95572 24.15560 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ALA-ALA-ALA-CT2" + RDCMND substituted energy or value "?ENER" to "134.746" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 34.34536811 26.62466332 -11.66118824 + 237.37980332 262.48823991 + 565.28928111 + + Transpose of the rotation matrix + 0.874478 0.485049 0.004016 + -0.449186 0.806641 0.384137 + 0.183086 -0.337724 0.923267 + CENTER OF ATOMS BEFORE TRANSLATION 4.85811 2.38537 -0.10619 + AXIS OF ROTATION IS 0.604508 0.149959 0.782357 ANGLE IS 36.66 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 57 atoms have been selected out of 57 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -28.203281 2.919811 -0.776248 28.364642 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ALA-ALA-ALA-CT2" + RDCMND substituted energy or value "?RDIP" to "28.3646" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 57 Number of groups = 6 + Number of bonds = 56 Number of angles = 60 + Number of dihedrals = 78 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 22 + + CHARMM> delete atom sele all end + SELRPN> 57 atoms have been selected out of 57 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 56 bonds deleted + DELTIC: 60 angles deleted + DELTIC: 78 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-ALA-ALA-ALA-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ALA-ALA-ALA-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 17 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 61 Number of groups = 6 + Number of bonds = 60 Number of angles = 66 + Number of dihedrals = 84 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 17 + Number of true-bonds = 60 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 23 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 545 545 540 + : Ran out of space. RESIZING + with mode 5 found 333 exclusions and 243 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1497 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1497 atom pairs and 576 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1497 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 191.67647 -56.93084 32.02151 +ENER INTERN> 29.30964 60.08700 43.51501 11.88658 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 17.19972 34.23852 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ALA-ALA-ALA-CT3" + RDCMND substituted energy or value "?ENER" to "191.676" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 35.58607663 27.84254738 -8.74106154 + 277.82685573 350.46984939 + 745.99397841 + + Transpose of the rotation matrix + 0.881765 0.471650 0.006042 + -0.435856 0.809816 0.392720 + 0.180334 -0.348920 0.919638 + CENTER OF ATOMS BEFORE TRANSLATION 5.34056 2.58659 -0.09922 + AXIS OF ROTATION IS 0.625912 0.147095 0.765896 ANGLE IS 36.33 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 61 atoms have been selected out of 61 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -25.503098 -2.989275 1.724855 25.735557 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ALA-ALA-ALA-CT3" + RDCMND substituted energy or value "?RDIP" to "25.7356" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 61 Number of groups = 6 + Number of bonds = 60 Number of angles = 66 + Number of dihedrals = 84 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 23 + + CHARMM> delete atom sele all end + SELRPN> 61 atoms have been selected out of 61 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 60 bonds deleted + DELTIC: 66 angles deleted + DELTIC: 84 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-ALA-ALA-ALA-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ALA-ALA-ALA-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 19 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 66 Number of groups = 7 + Number of bonds = 65 Number of angles = 63 + Number of dihedrals = 81 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 19 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 29 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 586 586 585 + : Ran out of space. RESIZING + with mode 5 found 378 exclusions and 262 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1767 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1767 atom pairs and 640 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1767 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 239.94310 -48.26662 44.03724 +ENER INTERN> 21.40772 48.26309 107.46768 22.84460 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 44.54695 0.74306 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ALA-ALA-ALA-CTER" + RDCMND substituted energy or value "?ENER" to "239.943" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 57.04801290 8.68164668 -82.43743162 + 251.82233169 341.36271118 + 871.75971879 + + Transpose of the rotation matrix + 0.913222 0.400697 -0.073937 + -0.315793 0.810690 0.493008 + 0.257487 -0.426877 0.866877 + CENTER OF ATOMS BEFORE TRANSLATION 4.06629 2.17189 0.11546 + AXIS OF ROTATION IS 0.758866 0.273410 0.591074 ANGLE IS 37.31 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 66 atoms have been selected out of 66 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -29.963129 -9.859992 -0.814145 31.554261 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ALA-ALA-ALA-CTER" + RDCMND substituted energy or value "?RDIP" to "31.5543" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 66 Number of groups = 7 + Number of bonds = 65 Number of angles = 63 + Number of dihedrals = 81 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 29 + + CHARMM> delete atom sele all end + SELRPN> 66 atoms have been selected out of 66 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 63 angles deleted + DELTIC: 81 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-ALA-ALA-ALA-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ALA-ALA-ALA-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 19 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 67 Number of groups = 7 + Number of bonds = 66 Number of angles = 64 + Number of dihedrals = 83 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 19 + Number of true-bonds = 66 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 29 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 602 602 594 + : Ran out of space. RESIZING + with mode 5 found 384 exclusions and 268 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1827 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1827 atom pairs and 652 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1827 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 226.21878 13.72432 42.09732 +ENER INTERN> 21.46523 45.83007 116.82691 16.12449 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 44.13610 -12.83402 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ALA-ALA-ALA-CNEU" + RDCMND substituted energy or value "?ENER" to "226.219" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 57.27490131 8.38231965 -83.18887077 + 258.40028430 359.79429734 + 913.38866318 + + Transpose of the rotation matrix + 0.913530 0.400493 -0.071191 + -0.314825 0.806949 0.499718 + 0.257581 -0.434094 0.863258 + CENTER OF ATOMS BEFORE TRANSLATION 4.16490 2.21117 0.11374 + AXIS OF ROTATION IS 0.764553 0.269180 0.585662 ANGLE IS 37.64 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 67 atoms have been selected out of 67 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.366470 -4.518703 -1.878781 4.907423 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ALA-ALA-ALA-CNEU" + RDCMND substituted energy or value "?RDIP" to "4.90742" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 67 Number of groups = 7 + Number of bonds = 66 Number of angles = 64 + Number of dihedrals = 83 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 29 + + CHARMM> delete atom sele all end + SELRPN> 67 atoms have been selected out of 67 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 66 bonds deleted + DELTIC: 64 angles deleted + DELTIC: 83 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-ALA-ALA-ALA-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ALA-ALA-ALA-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 71 Number of groups = 7 + Number of bonds = 70 Number of angles = 70 + Number of dihedrals = 86 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 20 + Number of true-bonds = 70 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 650 650 630 + : Ran out of space. RESIZING + with mode 5 found 412 exclusions and 280 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2073 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2073 atom pairs and 692 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2073 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 464.41705 -238.19827 160.85370 +ENER INTERN> 21.46523 45.69021 96.96809 15.72670 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 271.93620 17.96061 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ALA-ALA-ALA-CT1" + RDCMND substituted energy or value "?ENER" to "464.417" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 58.96890933 6.55888847 -85.91144618 + 327.79277579 460.82463705 + 1066.53314526 + + Transpose of the rotation matrix + 0.900806 0.429992 -0.060463 + -0.348565 0.799101 0.489836 + 0.258942 -0.420172 0.869715 + CENTER OF ATOMS BEFORE TRANSLATION 4.52216 2.45045 0.10733 + AXIS OF ROTATION IS 0.734191 0.257695 0.628137 ANGLE IS 38.30 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 71 atoms have been selected out of 71 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.234389 -3.673544 -2.266841 4.860657 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ALA-ALA-ALA-CT1" + RDCMND substituted energy or value "?RDIP" to "4.86066" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 71 Number of groups = 7 + Number of bonds = 70 Number of angles = 70 + Number of dihedrals = 86 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 71 atoms have been selected out of 71 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 70 bonds deleted + DELTIC: 70 angles deleted + DELTIC: 86 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-ALA-ALA-ALA-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ALA-ALA-ALA-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 19 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 66 Number of groups = 7 + Number of bonds = 65 Number of angles = 66 + Number of dihedrals = 85 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 19 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 27 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 604 604 585 + : Ran out of space. RESIZING + with mode 5 found 366 exclusions and 264 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1779 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1779 atom pairs and 630 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1779 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 203.11188 261.30517 40.45948 +ENER INTERN> 29.12587 43.31393 96.00863 18.33668 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 48.61710 -18.78033 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ALA-ALA-ALA-CT2" + RDCMND substituted energy or value "?ENER" to "203.112" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 57.04801290 8.62207342 -82.19488707 + 256.01254592 336.63190864 + 855.49248739 + + Transpose of the rotation matrix + 0.911254 0.404997 -0.074789 + -0.323881 0.816880 0.477292 + 0.254395 -0.410711 0.875557 + CENTER OF ATOMS BEFORE TRANSLATION 4.03446 2.17971 0.11546 + AXIS OF ROTATION IS 0.743060 0.275453 0.609908 ANGLE IS 36.69 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 66 atoms have been selected out of 66 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -4.547444 -1.810405 -3.862737 6.235186 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ALA-ALA-ALA-CT2" + RDCMND substituted energy or value "?RDIP" to "6.23519" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 66 Number of groups = 7 + Number of bonds = 65 Number of angles = 66 + Number of dihedrals = 85 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 27 + + CHARMM> delete atom sele all end + SELRPN> 66 atoms have been selected out of 66 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 66 angles deleted + DELTIC: 85 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ALA" + Parameter: PATCH -> "ALA" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-ALA-ALA-ALA-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ALA-ALA-ALA-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ALA" + Parameter: RESIDUE -> "ALA" + + RESIDUE SEQUENCE -- 3 RESIDUES + ALA ALA ALA + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALA" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ALA mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ALA . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 70 Number of groups = 7 + Number of bonds = 69 Number of angles = 72 + Number of dihedrals = 91 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 69 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "3" + Parameter: PATCHED -> "25" + Comparing "3" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 624 624 621 + : Ran out of space. RESIZING + with mode 5 found 387 exclusions and 279 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2028 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2028 atom pairs and 666 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 13449 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2028 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 263.43130 -60.31942 42.69898 +ENER INTERN> 29.12587 56.18547 129.11736 15.06034 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 46.86083 -5.30857 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ALA-ALA-ALA-CT3" + RDCMND substituted energy or value "?ENER" to "263.431" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 58.29685602 7.19628869 -85.75742332 + 301.69697097 441.25249270 + 1086.29027542 + + Transpose of the rotation matrix + 0.911431 0.406886 -0.061129 + -0.327195 0.806825 0.491911 + 0.249473 -0.428342 0.868497 + CENTER OF ATOMS BEFORE TRANSLATION 4.50195 2.36680 0.10887 + AXIS OF ROTATION IS 0.755878 0.255123 0.602960 ANGLE IS 37.50 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 70 atoms have been selected out of 70 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 1.056217 -6.747020 -0.601656 6.855645 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ALA-ALA-ALA-CT3" + RDCMND substituted energy or value "?RDIP" to "6.85564" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 70 Number of groups = 7 + Number of bonds = 69 Number of angles = 72 + Number of dihedrals = 91 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 70 atoms have been selected out of 70 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 69 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 91 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "4" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "4" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "4" + Parameter: AA4 -> "ARG" + Parameter: RESIDUE <- "ARG" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "4" + Parameter: SPECIAL -> "2" + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "ARG" + Parameter: PATCH <- "ARG" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-ARG-ALA-ARG-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ARG-ALA-ARG-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 10 + Number of bonds = 96 Number of angles = 105 + Number of dihedrals = 146 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 12 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 28 + Number of true-bonds = 96 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 871 871 864 + : Ran out of space. RESIZING + with mode 5 found 536 exclusions and 380 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 18819 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4120 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4120 atom pairs and 916 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 18819 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4120 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -204.75547 468.18677 36.52359 +ENER INTERN> 34.52370 54.15639 24.42499 38.97604 0.01490 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 36.55287 -391.12436 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ARG-ALA-ARG-CTER" + RDCMND substituted energy or value "?ENER" to "-204.755" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 274.33133925 216.73878643 -322.83199158 + 678.31899882 338.51834726 + 1412.92839860 + + Transpose of the rotation matrix + 0.934966 0.305907 -0.179610 + -0.176194 0.839911 0.513328 + 0.307886 -0.448298 0.839187 + CENTER OF ATOMS BEFORE TRANSLATION 6.30784 1.73242 -1.26746 + AXIS OF ROTATION IS 0.814236 0.412777 0.408209 ANGLE IS 36.19 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : -20.685122 -47.909915 2.210137 52.231398 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ARG-ALA-ARG-CTER" + RDCMND substituted energy or value "?RDIP" to "52.2314" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 10 + Number of bonds = 96 Number of angles = 105 + Number of dihedrals = 146 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 12 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 96 bonds deleted + DELTIC: 105 angles deleted + DELTIC: 146 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 12 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-ARG-ALA-ARG-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ARG-ALA-ARG-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 10 + Number of bonds = 97 Number of angles = 106 + Number of dihedrals = 148 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 12 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 28 + Number of true-bonds = 97 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 875 875 873 + : Ran out of space. RESIZING + with mode 5 found 542 exclusions and 386 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 19209 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4211 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4211 atom pairs and 928 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 19209 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4211 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -106.92610 -97.82937 32.83976 +ENER INTERN> 34.41875 50.47103 33.62221 30.14430 0.01490 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 34.81390 -288.13119 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ARG-ALA-ARG-CNEU" + RDCMND substituted energy or value "?ENER" to "-106.926" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 276.13516149 222.05215227 -318.28496777 + 696.29612336 354.69259991 + 1424.09735339 + + Transpose of the rotation matrix + 0.931383 0.322296 -0.169267 + -0.193969 0.832821 0.518445 + 0.308062 -0.450039 0.838190 + CENTER OF ATOMS BEFORE TRANSLATION 6.34482 1.77564 -1.25453 + AXIS OF ROTATION IS 0.809227 0.398837 0.431371 ANGLE IS 36.76 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 98 atoms have been selected out of 98 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -5.855098 -27.442874 0.136717 28.060866 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ARG-ALA-ARG-CNEU" + RDCMND substituted energy or value "?RDIP" to "28.0609" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 10 + Number of bonds = 97 Number of angles = 106 + Number of dihedrals = 148 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 12 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 98 atoms have been selected out of 98 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 97 bonds deleted + DELTIC: 106 angles deleted + DELTIC: 148 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 12 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-ARG-ALA-ARG-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ARG-ALA-ARG-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 102 Number of groups = 10 + Number of bonds = 101 Number of angles = 112 + Number of dihedrals = 151 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 12 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 29 + Number of true-bonds = 101 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 926 926 909 + : Ran out of space. RESIZING + with mode 5 found 570 exclusions and 398 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 20809 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4581 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4581 atom pairs and 968 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 20809 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4581 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 133.22133 -240.14743 128.71868 +ENER INTERN> 34.41875 50.33117 14.00001 30.96253 0.01490 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 267.28191 -261.50794 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ARG-ALA-ARG-CT1" + RDCMND substituted energy or value "?ENER" to "133.221" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 283.82882642 249.92006419 -303.37130308 + 825.75185682 422.83178850 + 1462.46537164 + + Transpose of the rotation matrix + 0.905571 0.405990 -0.122933 + -0.288947 0.802548 0.521945 + 0.310564 -0.437137 0.844074 + CENTER OF ATOMS BEFORE TRANSLATION 6.46613 2.00231 -1.20533 + AXIS OF ROTATION IS 0.760435 0.343710 0.551001 ANGLE IS 39.10 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 102 atoms have been selected out of 102 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -9.613019 -27.991194 -0.477183 29.599743 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ARG-ALA-ARG-CT1" + RDCMND substituted energy or value "?RDIP" to "29.5997" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 102 Number of groups = 10 + Number of bonds = 101 Number of angles = 112 + Number of dihedrals = 151 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 12 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 102 atoms have been selected out of 102 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 101 bonds deleted + DELTIC: 112 angles deleted + DELTIC: 151 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 12 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-ARG-ALA-ARG-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ARG-ALA-ARG-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 10 + Number of bonds = 96 Number of angles = 108 + Number of dihedrals = 150 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 12 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 28 + Number of true-bonds = 96 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 868 868 864 + : Ran out of space. RESIZING + with mode 5 found 524 exclusions and 382 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 20809 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4132 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4132 atom pairs and 906 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 20809 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4132 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -124.47905 257.70038 31.73525 +ENER INTERN> 40.93748 48.12695 13.06906 35.08076 0.01490 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 40.00417 -291.25237 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ARG-ALA-ARG-CT2" + RDCMND substituted energy or value "?ENER" to "-124.479" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 274.33133925 216.84688431 -325.57145563 + 679.89314901 329.23297101 + 1409.39511359 + + Transpose of the rotation matrix + 0.936423 0.298685 -0.184116 + -0.169651 0.844752 0.507556 + 0.307132 -0.444052 0.841717 + CENTER OF ATOMS BEFORE TRANSLATION 6.28556 1.73330 -1.26746 + AXIS OF ROTATION IS 0.814138 0.420281 0.400679 ANGLE IS 35.76 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -9.706128 -26.326584 -1.616247 28.105341 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ARG-ALA-ARG-CT2" + RDCMND substituted energy or value "?RDIP" to "28.1053" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 10 + Number of bonds = 96 Number of angles = 108 + Number of dihedrals = 150 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 12 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 96 bonds deleted + DELTIC: 108 angles deleted + DELTIC: 150 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 12 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-ARG-ALA-ARG-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ARG-ALA-ARG-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 101 Number of groups = 10 + Number of bonds = 100 Number of angles = 114 + Number of dihedrals = 156 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 29 + Number of true-bonds = 100 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 903 903 900 + : Ran out of space. RESIZING + with mode 5 found 545 exclusions and 397 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 20809 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4505 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4505 atom pairs and 942 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 20809 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4505 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -17.13296 -107.34609 41.89788 +ENER INTERN> 40.93748 60.99849 48.20805 34.54928 0.01490 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 75.48646 -272.76763 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ARG-ALA-ARG-CT3" + RDCMND substituted energy or value "?ENER" to "-17.133" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 281.70125021 242.06985674 -301.08943161 + 788.57005407 427.33494642 + 1484.55799467 + + Transpose of the rotation matrix + 0.912032 0.390218 -0.126207 + -0.270882 0.804215 0.529019 + 0.307931 -0.448295 0.839172 + CENTER OF ATOMS BEFORE TRANSLATION 6.48469 1.93846 -1.21727 + AXIS OF ROTATION IS 0.777344 0.345308 0.525831 ANGLE IS 38.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 101 atoms have been selected out of 101 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -9.502952 -30.414172 1.467435 31.897983 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ARG-ALA-ARG-CT3" + RDCMND substituted energy or value "?RDIP" to "31.898" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 101 Number of groups = 10 + Number of bonds = 100 Number of angles = 114 + Number of dihedrals = 156 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 101 atoms have been selected out of 101 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 100 bonds deleted + DELTIC: 114 angles deleted + DELTIC: 156 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 13 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-ARG-ALA-ARG-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ARG-ALA-ARG-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 31 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 106 Number of groups = 11 + Number of bonds = 105 Number of angles = 111 + Number of dihedrals = 153 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 31 + Number of true-bonds = 105 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 946 946 945 + : Ran out of space. RESIZING + with mode 5 found 590 exclusions and 416 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 22473 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4975 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4975 atom pairs and 1006 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 22473 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4975 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -171.74376 154.61080 42.87427 +ENER INTERN> 34.22039 50.73729 110.06803 42.55354 0.01490 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 70.03967 -474.04758 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ARG-ALA-ARG-CTER" + RDCMND substituted energy or value "?ENER" to "-171.744" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 340.45563888 198.16176680 -488.95281703 + 685.29511277 394.61171964 + 1881.57075322 + + Transpose of the rotation matrix + 0.944006 0.230172 -0.236375 + -0.084186 0.860776 0.501974 + 0.319006 -0.453967 0.831955 + CENTER OF ATOMS BEFORE TRANSLATION 5.67191 1.65980 -1.03085 + AXIS OF ROTATION IS 0.831696 0.483197 0.273500 ANGLE IS 35.08 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 106 atoms have been selected out of 106 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : 17.819289 -52.133868 0.536455 55.097686 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ARG-ALA-ARG-CTER" + RDCMND substituted energy or value "?RDIP" to "55.0977" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 106 Number of groups = 11 + Number of bonds = 105 Number of angles = 111 + Number of dihedrals = 153 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 106 atoms have been selected out of 106 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 105 bonds deleted + DELTIC: 111 angles deleted + DELTIC: 153 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 13 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-ARG-ALA-ARG-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ARG-ALA-ARG-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 31 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 107 Number of groups = 11 + Number of bonds = 106 Number of angles = 112 + Number of dihedrals = 155 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 31 + Number of true-bonds = 106 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 958 958 954 + : Ran out of space. RESIZING + with mode 5 found 596 exclusions and 422 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 22899 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5075 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5075 atom pairs and 1018 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 22899 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5075 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -106.16912 -65.57464 40.41900 +ENER INTERN> 34.11544 47.05193 119.26525 33.72180 0.01490 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 68.30282 -403.31127 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ARG-ALA-ARG-CNEU" + RDCMND substituted energy or value "?ENER" to "-106.169" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 341.72212400 202.56115099 -484.60199499 + 703.90223892 413.77383961 + 1897.71833812 + + Transpose of the rotation matrix + 0.942751 0.242384 -0.229064 + -0.097075 0.856558 0.506838 + 0.319056 -0.455586 0.831051 + CENTER OF ATOMS BEFORE TRANSLATION 5.71173 1.70007 -1.02122 + AXIS OF ROTATION IS 0.830811 0.473163 0.293037 ANGLE IS 35.39 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 107 atoms have been selected out of 107 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 34.188239 -31.221995 -1.709774 46.331113 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ARG-ALA-ARG-CNEU" + RDCMND substituted energy or value "?RDIP" to "46.3311" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 107 Number of groups = 11 + Number of bonds = 106 Number of angles = 112 + Number of dihedrals = 155 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 107 atoms have been selected out of 107 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 106 bonds deleted + DELTIC: 112 angles deleted + DELTIC: 155 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 13 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-ARG-ALA-ARG-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ARG-ALA-ARG-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 32 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 111 Number of groups = 11 + Number of bonds = 110 Number of angles = 118 + Number of dihedrals = 158 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 32 + Number of true-bonds = 110 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 991 991 990 + : Ran out of space. RESIZING + with mode 5 found 624 exclusions and 434 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5481 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5481 atom pairs and 1058 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5481 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 135.31533 -241.48445 126.75464 +ENER INTERN> 34.11544 46.91207 99.64305 34.54003 0.01490 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 300.76994 -375.35011 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ARG-ALA-ARG-CT1" + RDCMND substituted energy or value "?ENER" to "135.315" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 347.38853722 225.61905637 -469.92876884 + 837.17366230 497.33631455 + 1952.85559206 + + Transpose of the rotation matrix + 0.931908 0.304028 -0.197775 + -0.167135 0.843917 0.509775 + 0.321892 -0.442008 0.837266 + CENTER OF ATOMS BEFORE TRANSLATION 5.84601 1.91108 -0.98442 + AXIS OF ROTATION IS 0.804996 0.439523 0.398499 ANGLE IS 36.24 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 111 atoms have been selected out of 111 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 31.767743 -33.745597 -2.322667 46.404199 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ARG-ALA-ARG-CT1" + RDCMND substituted energy or value "?RDIP" to "46.4042" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 111 Number of groups = 11 + Number of bonds = 110 Number of angles = 118 + Number of dihedrals = 158 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 111 atoms have been selected out of 111 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 110 bonds deleted + DELTIC: 118 angles deleted + DELTIC: 158 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 13 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-ARG-ALA-ARG-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ARG-ALA-ARG-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 31 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 106 Number of groups = 11 + Number of bonds = 105 Number of angles = 114 + Number of dihedrals = 157 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 31 + Number of true-bonds = 105 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 949 949 945 + : Ran out of space. RESIZING + with mode 5 found 578 exclusions and 418 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4987 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4987 atom pairs and 996 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4987 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -127.13143 262.44676 39.48454 +ENER INTERN> 40.63418 44.70785 98.71209 38.65826 0.01490 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 73.49254 -409.84125 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ARG-ALA-ARG-CT2" + RDCMND substituted energy or value "?ENER" to "-127.131" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 340.45563888 198.24968518 -491.18088339 + 686.88165615 385.22346197 + 1875.29260318 + + Transpose of the rotation matrix + 0.944441 0.225203 -0.239404 + -0.080250 0.864333 0.496476 + 0.318733 -0.449680 0.834384 + CENTER OF ATOMS BEFORE TRANSLATION 5.65152 1.66061 -1.03085 + AXIS OF ROTATION IS 0.829824 0.489513 0.267897 ANGLE IS 34.76 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 106 atoms have been selected out of 106 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 29.810189 -29.912522 -3.591403 42.382832 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ARG-ALA-ARG-CT2" + RDCMND substituted energy or value "?RDIP" to "42.3828" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 106 Number of groups = 11 + Number of bonds = 105 Number of angles = 114 + Number of dihedrals = 157 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 13 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 106 atoms have been selected out of 106 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 105 bonds deleted + DELTIC: 114 angles deleted + DELTIC: 157 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 13 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ARG" + Parameter: PATCH -> "ARG" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-ARG-ALA-ARG-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ARG-ALA-ARG-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ARG" + Parameter: RESIDUE -> "ARG" + + RESIDUE SEQUENCE -- 3 RESIDUES + ARG ALA ARG + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARG" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ARG mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ARG . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 32 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARG. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 110 Number of groups = 11 + Number of bonds = 109 Number of angles = 120 + Number of dihedrals = 163 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 14 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 32 + Number of true-bonds = 109 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "4" + Parameter: PATCHED -> "25" + Comparing "4" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 987 987 981 + : Ran out of space. RESIZING + with mode 5 found 599 exclusions and 433 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5396 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5396 atom pairs and 1032 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5396 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -15.82282 -111.30861 47.41580 +ENER INTERN> 40.63418 57.57939 133.85109 38.12678 0.01490 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 108.97467 -387.39383 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ARG-ALA-ARG-CT3" + RDCMND substituted energy or value "?ENER" to "-15.8228" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 345.75027694 219.12214272 -468.68261393 + 798.82975518 497.90965434 + 1976.90908047 + + Transpose of the rotation matrix + 0.934957 0.294354 -0.198019 + -0.155125 0.841196 0.518001 + 0.319049 -0.453591 0.832143 + CENTER OF ATOMS BEFORE TRANSLATION 5.85742 1.85162 -0.99337 + AXIS OF ROTATION IS 0.817249 0.434929 0.378076 ANGLE IS 36.47 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 110 atoms have been selected out of 110 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 32.031801 -36.131530 -0.342655 48.287070 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ARG-ALA-ARG-CT3" + RDCMND substituted energy or value "?RDIP" to "48.2871" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 110 Number of groups = 11 + Number of bonds = 109 Number of angles = 120 + Number of dihedrals = 163 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 14 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 110 atoms have been selected out of 110 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 109 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 163 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 14 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "5" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "5" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "5" + Parameter: AA5 -> "ASN" + Parameter: RESIDUE <- "ASN" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "5" + Parameter: SPECIAL -> "2" + Comparing "5" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "ASN" + Parameter: PATCH <- "ASN" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-ASN-ALA-ASN-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASN-ALA-ASN-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 69 + Number of dihedrals = 94 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 22 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 669 669 666 + : Ran out of space. RESIZING + with mode 5 found 434 exclusions and 308 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2341 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2341 atom pairs and 742 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2341 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 63.49935 -79.32217 66.92554 +ENER INTERN> 29.92174 46.61946 22.37955 35.47100 0.01414 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 148.34550 -216.97204 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASN-ALA-ASN-CTER" + RDCMND substituted energy or value "?ENER" to "63.4993" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 69.34607835 52.53543006 -59.23815026 + 488.89087245 393.92314623 + 719.29928300 + + Transpose of the rotation matrix + 0.801061 0.598342 -0.016944 + -0.533760 0.726838 0.432211 + 0.270926 -0.337184 0.901613 + CENTER OF ATOMS BEFORE TRANSLATION 4.99741 2.72169 -0.36929 + AXIS OF ROTATION IS 0.550060 0.205805 0.809369 ANGLE IS 44.38 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 75 atoms have been selected out of 75 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -47.236715 -0.243776 6.040474 47.621991 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASN-ALA-ASN-CTER" + RDCMND substituted energy or value "?RDIP" to "47.622" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 69 + Number of dihedrals = 94 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 75 atoms have been selected out of 75 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 69 angles deleted + DELTIC: 94 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-ASN-ALA-ASN-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASN-ALA-ASN-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 76 Number of groups = 6 + Number of bonds = 75 Number of angles = 70 + Number of dihedrals = 96 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 75 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 682 682 675 + : Ran out of space. RESIZING + with mode 5 found 440 exclusions and 314 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2410 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2410 atom pairs and 754 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2410 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 112.83354 -49.33419 66.32527 +ENER INTERN> 29.83426 41.49771 31.59571 26.59265 0.01414 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 149.73845 -164.15938 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASN-ALA-ASN-CNEU" + RDCMND substituted energy or value "?ENER" to "112.834" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 69.69441432 54.02500326 -57.69123878 + 505.85895162 411.64521994 + 734.98702257 + + Transpose of the rotation matrix + 0.796956 0.603883 -0.013650 + -0.539069 0.721251 0.434973 + 0.272518 -0.339296 0.900340 + CENTER OF ATOMS BEFORE TRANSLATION 5.05326 2.77547 -0.36443 + AXIS OF ROTATION IS 0.549179 0.202975 0.810681 ANGLE IS 44.82 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 76 atoms have been selected out of 76 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.073885 9.250441 3.931085 26.087852 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASN-ALA-ASN-CNEU" + RDCMND substituted energy or value "?RDIP" to "26.0879" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 76 Number of groups = 6 + Number of bonds = 75 Number of angles = 70 + Number of dihedrals = 96 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 76 atoms have been selected out of 76 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 75 bonds deleted + DELTIC: 70 angles deleted + DELTIC: 96 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-ASN-ALA-ASN-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASN-ALA-ASN-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 80 Number of groups = 6 + Number of bonds = 79 Number of angles = 76 + Number of dihedrals = 99 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 23 + Number of true-bonds = 79 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 718 718 711 + : Ran out of space. RESIZING + with mode 5 found 468 exclusions and 326 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2692 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2692 atom pairs and 794 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2692 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 387.56643 -274.73289 164.55824 +ENER INTERN> 29.83426 41.35786 11.94774 27.53553 0.01414 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 415.53837 -136.38148 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASN-ALA-ASN-CT1" + RDCMND substituted energy or value "?ENER" to "387.566" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 71.84426683 61.67033495 -52.92150200 + 622.56535653 483.44372119 + 781.83109788 + + Transpose of the rotation matrix + 0.762429 0.647072 -0.000396 + -0.588267 0.693394 0.416110 + 0.269528 -0.317021 0.909314 + CENTER OF ATOMS BEFORE TRANSLATION 5.22548 3.05151 -0.34621 + AXIS OF ROTATION IS 0.501580 0.184671 0.845171 ANGLE IS 46.96 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 80 atoms have been selected out of 80 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -23.154923 11.013853 3.532278 25.883052 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASN-ALA-ASN-CT1" + RDCMND substituted energy or value "?RDIP" to "25.8831" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 80 Number of groups = 6 + Number of bonds = 79 Number of angles = 76 + Number of dihedrals = 99 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 80 atoms have been selected out of 80 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 79 bonds deleted + DELTIC: 76 angles deleted + DELTIC: 99 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-ASN-ALA-ASN-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASN-ALA-ASN-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 72 + Number of dihedrals = 98 Number of impropers = 10 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 673 673 666 + : Ran out of space. RESIZING + with mode 5 found 422 exclusions and 310 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2353 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2353 atom pairs and 732 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2353 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 73.72880 313.83764 63.17739 +ENER INTERN> 36.47680 39.75017 11.01450 29.03360 0.01414 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 141.57245 -173.67287 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASN-ALA-ASN-CT2" + RDCMND substituted energy or value "?ENER" to "73.7288" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 69.34607835 52.43738527 -60.03090571 + 487.72669619 385.40400046 + 713.04074190 + + Transpose of the rotation matrix + 0.801091 0.598274 -0.017921 + -0.535735 0.730059 0.424265 + 0.266911 -0.330274 0.905361 + CENTER OF ATOMS BEFORE TRANSLATION 4.96879 2.71815 -0.36929 + AXIS OF ROTATION IS 0.542226 0.204686 0.814920 ANGLE IS 44.09 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 75 atoms have been selected out of 75 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -28.989157 11.233802 2.904165 31.225050 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASN-ALA-ASN-CT2" + RDCMND substituted energy or value "?RDIP" to "31.225" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 72 + Number of dihedrals = 98 Number of impropers = 10 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 75 atoms have been selected out of 75 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 98 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-ASN-ALA-ASN-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASN-ALA-ASN-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 6 + Number of bonds = 78 Number of angles = 78 + Number of dihedrals = 104 Number of impropers = 10 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 23 + Number of true-bonds = 78 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 704 704 702 + : Ran out of space. RESIZING + with mode 5 found 443 exclusions and 325 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2638 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2638 atom pairs and 768 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2638 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1400.08902 -1326.36022 1267.32285 +ENER INTERN> 36.47680 52.62172 45.92653 28.60231 0.01414 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 1394.51045 -153.50294 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASN-ALA-ASN-CT3" + RDCMND substituted energy or value "?ENER" to "1400.09" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 71.06252044 59.79661794 -52.34108093 + 596.54544764 488.42521405 + 806.61254136 + + Transpose of the rotation matrix + 0.778031 0.628220 -0.002794 + -0.567282 0.704458 0.426533 + 0.269925 -0.330271 0.904467 + CENTER OF ATOMS BEFORE TRANSLATION 5.24643 2.98385 -0.35059 + AXIS OF ROTATION IS 0.525210 0.189263 0.829659 ANGLE IS 46.09 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 79 atoms have been selected out of 79 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.104446 7.515460 5.033019 25.745636 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASN-ALA-ASN-CT3" + RDCMND substituted energy or value "?RDIP" to "25.7456" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 6 + Number of bonds = 78 Number of angles = 78 + Number of dihedrals = 104 Number of impropers = 10 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 79 atoms have been selected out of 79 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 78 bonds deleted + DELTIC: 78 angles deleted + DELTIC: 104 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-ASN-ALA-ASN-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASN-ALA-ASN-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 75 + Number of dihedrals = 101 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 25 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 751 751 747 + : Ran out of space. RESIZING + with mode 5 found 488 exclusions and 344 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2998 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2998 atom pairs and 832 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2998 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 193.83103 1206.25799 67.03837 +ENER INTERN> 29.50901 44.91295 108.05730 38.65842 0.01414 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 189.18431 -211.17511 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASN-ALA-ASN-CTER" + RDCMND substituted energy or value "?ENER" to "193.831" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 100.17283404 25.59560729 -147.23781841 + 517.18276261 488.85065595 + 1032.77529299 + + Transpose of the rotation matrix + 0.856822 0.507442 -0.091425 + -0.413635 0.782331 0.465687 + 0.307834 -0.361195 0.880214 + CENTER OF ATOMS BEFORE TRANSLATION 4.33534 2.52406 -0.16695 + AXIS OF ROTATION IS 0.635776 0.306984 0.708202 ANGLE IS 40.56 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -25.109781 -8.224158 3.619414 26.669046 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASN-ALA-ASN-CTER" + RDCMND substituted energy or value "?RDIP" to "26.669" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 75 + Number of dihedrals = 101 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 75 angles deleted + DELTIC: 101 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-ASN-ALA-ASN-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASN-ALA-ASN-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 7 + Number of bonds = 84 Number of angles = 76 + Number of dihedrals = 103 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 25 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 763 763 756 + : Ran out of space. RESIZING + with mode 5 found 494 exclusions and 350 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3076 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3076 atom pairs and 844 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3076 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 210.20992 -16.37889 66.90749 +ENER INTERN> 29.42153 39.79121 117.27346 29.78008 0.01414 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 190.57976 -191.32026 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASN-ALA-ASN-CNEU" + RDCMND substituted energy or value "?ENER" to "210.21" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 100.41413294 26.30256183 -146.42828087 + 535.80929750 510.22955807 + 1054.47586871 + + Transpose of the rotation matrix + 0.853018 0.514541 -0.087227 + -0.420614 0.776766 0.468740 + 0.308941 -0.363155 0.879019 + CENTER OF ATOMS BEFORE TRANSLATION 4.39306 2.57447 -0.16498 + AXIS OF ROTATION IS 0.633667 0.301767 0.712322 ANGLE IS 41.03 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 85 atoms have been selected out of 85 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.322825 2.948844 1.250749 3.219359 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASN-ALA-ASN-CNEU" + RDCMND substituted energy or value "?RDIP" to "3.21936" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 7 + Number of bonds = 84 Number of angles = 76 + Number of dihedrals = 103 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 85 atoms have been selected out of 85 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 76 angles deleted + DELTIC: 103 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-ASN-ALA-ASN-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASN-ALA-ASN-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 7 + Number of bonds = 88 Number of angles = 82 + Number of dihedrals = 106 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 26 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 808 808 792 + : Ran out of space. RESIZING + with mode 5 found 522 exclusions and 362 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3394 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3394 atom pairs and 884 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3394 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 486.27785 -276.06793 158.39224 +ENER INTERN> 29.42153 39.65135 97.62550 30.72296 0.01414 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 456.37865 -162.20628 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASN-ALA-ASN-CT1" + RDCMND substituted energy or value "?ENER" to "486.278" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 102.16329272 29.90880748 -143.84136293 + 661.76484033 599.48825380 + 1120.59859960 + + Transpose of the rotation matrix + 0.825054 0.560593 -0.070864 + -0.474441 0.755394 0.451980 + 0.306907 -0.339288 0.889209 + CENTER OF ATOMS BEFORE TRANSLATION 4.57753 2.83163 -0.15757 + AXIS OF ROTATION IS 0.583313 0.278488 0.763014 ANGLE IS 42.71 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 89 atoms have been selected out of 89 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.242676 4.097471 0.855213 4.748711 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASN-ALA-ASN-CT1" + RDCMND substituted energy or value "?RDIP" to "4.74871" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 7 + Number of bonds = 88 Number of angles = 82 + Number of dihedrals = 106 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 89 atoms have been selected out of 89 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 82 angles deleted + DELTIC: 106 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-ASN-ALA-ASN-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASN-ALA-ASN-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 78 + Number of dihedrals = 105 Number of impropers = 12 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 25 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 754 754 747 + : Ran out of space. RESIZING + with mode 5 found 476 exclusions and 346 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3010 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3010 atom pairs and 822 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3010 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 167.32817 318.94968 64.07500 +ENER INTERN> 36.06407 38.04366 96.69225 32.22103 0.01414 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 182.41303 -204.61002 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASN-ALA-ASN-CT2" + RDCMND substituted energy or value "?ENER" to "167.328" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 100.17283404 25.55128372 -147.59620309 + 515.91374702 479.73229227 + 1023.68077456 + + Transpose of the rotation matrix + 0.857219 0.506508 -0.092873 + -0.414845 0.786103 0.458198 + 0.305089 -0.354248 0.883985 + CENTER OF ATOMS BEFORE TRANSLATION 4.30978 2.52090 -0.16695 + AXIS OF ROTATION IS 0.629192 0.308199 0.713534 ANGLE IS 40.21 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -5.252437 4.407125 -0.060669 6.856714 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASN-ALA-ASN-CT2" + RDCMND substituted energy or value "?RDIP" to "6.85671" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 78 + Number of dihedrals = 105 Number of impropers = 12 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 78 angles deleted + DELTIC: 105 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASN" + Parameter: PATCH -> "ASN" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-ASN-ALA-ASN-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASN-ALA-ASN-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASN" + Parameter: RESIDUE -> "ASN" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASN ALA ASN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ASN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 7 + Number of bonds = 87 Number of angles = 84 + Number of dihedrals = 111 Number of impropers = 12 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 26 + Number of true-bonds = 87 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "5" + Parameter: PATCHED -> "25" + Comparing "5" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 785 785 783 + : Ran out of space. RESIZING + with mode 5 found 497 exclusions and 361 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3331 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3331 atom pairs and 858 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3331 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1498.14787 -1330.81970 1207.67974 +ENER INTERN> 36.06407 50.91521 131.60429 31.78974 0.01414 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 1435.35099 -179.98057 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASN-ALA-ASN-CT3" + RDCMND substituted energy or value "?ENER" to "1498.15" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 101.47781450 29.02208749 -143.68079285 + 633.35603030 601.18011368 + 1147.12877278 + + Transpose of the rotation matrix + 0.835487 0.544788 -0.071884 + -0.455808 0.760130 0.463078 + 0.306920 -0.354131 0.883397 + CENTER OF ATOMS BEFORE TRANSLATION 4.58898 2.76839 -0.15936 + AXIS OF ROTATION IS 0.607005 0.281367 0.743221 ANGLE IS 42.31 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 1.697640 0.845755 2.472157 3.115902 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASN-ALA-ASN-CT3" + RDCMND substituted energy or value "?RDIP" to "3.1159" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 7 + Number of bonds = 87 Number of angles = 84 + Number of dihedrals = 111 Number of impropers = 12 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 87 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 111 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 8 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "6" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "6" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "6" + Parameter: AA6 -> "ASP" + Parameter: RESIDUE <- "ASP" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "6" + Parameter: SPECIAL -> "2" + Comparing "6" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "ASP" + Parameter: PATCH <- "ASP" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 63 + Number of dihedrals = 86 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 22 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 675 675 666 + : Ran out of space. RESIZING + with mode 5 found 458 exclusions and 300 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2317 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2317 atom pairs and 758 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2317 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 266.82884 1231.31903 48.31176 +ENER INTERN> 21.41378 47.20830 30.31909 39.02720 1.31251 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 117.26004 12.56792 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CTER" + RDCMND substituted energy or value "?ENER" to "266.829" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 67.50785654 53.86357363 -58.45932962 + 476.28204005 383.25312473 + 728.22870694 + + Transpose of the rotation matrix + 0.810860 0.584996 -0.016935 + -0.524880 0.739724 0.421081 + 0.258858 -0.332549 0.906865 + CENTER OF ATOMS BEFORE TRANSLATION 5.03087 2.62226 -0.36885 + AXIS OF ROTATION IS 0.550250 0.201365 0.810356 ANGLE IS 43.22 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 75 atoms have been selected out of 75 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -59.385458 15.430948 0.296101 61.358246 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CTER" + RDCMND substituted energy or value "?RDIP" to "61.3582" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 63 + Number of dihedrals = 86 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 75 atoms have been selected out of 75 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 63 angles deleted + DELTIC: 86 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 76 Number of groups = 6 + Number of bonds = 75 Number of angles = 64 + Number of dihedrals = 88 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 22 + Number of true-bonds = 75 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 679 679 675 + : Ran out of space. RESIZING + with mode 5 found 464 exclusions and 306 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2386 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2386 atom pairs and 770 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2386 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 172.63443 94.19441 46.58760 +ENER INTERN> 21.39535 42.66099 39.60347 30.17041 1.31251 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 116.99820 -77.22650 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CNEU" + RDCMND substituted energy or value "?ENER" to "172.634" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 67.85587356 55.33109879 -56.87719364 + 492.76745151 401.21907585 + 744.81584134 + + Transpose of the rotation matrix + 0.806796 0.590674 -0.013591 + -0.530381 0.734195 0.423857 + 0.260339 -0.334758 0.905627 + CENTER OF ATOMS BEFORE TRANSLATION 5.08807 2.67531 -0.36400 + AXIS OF ROTATION IS 0.549303 0.198349 0.811741 ANGLE IS 43.67 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 76 atoms have been selected out of 76 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -35.109986 25.146936 -1.732490 43.221303 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CNEU" + RDCMND substituted energy or value "?RDIP" to "43.2213" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 76 Number of groups = 6 + Number of bonds = 75 Number of angles = 64 + Number of dihedrals = 88 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 76 atoms have been selected out of 76 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 75 bonds deleted + DELTIC: 64 angles deleted + DELTIC: 88 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 80 Number of groups = 6 + Number of bonds = 79 Number of angles = 70 + Number of dihedrals = 91 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 23 + Number of true-bonds = 79 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 716 716 711 + : Ran out of space. RESIZING + with mode 5 found 492 exclusions and 318 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2668 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2668 atom pairs and 810 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2668 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 442.91106 -270.27663 159.38130 +ENER INTERN> 21.39535 42.52113 19.85445 31.05569 1.31251 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 371.55376 -42.50183 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT1" + RDCMND substituted energy or value "?ENER" to "442.911" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 70.00453004 62.91977342 -51.91521447 + 608.06145784 475.52583597 + 795.45607263 + + Transpose of the rotation matrix + 0.772445 0.635081 -0.000128 + -0.580218 0.705797 0.406445 + 0.258215 -0.313882 0.913675 + CENTER OF ATOMS BEFORE TRANSLATION 5.26743 2.94963 -0.34580 + AXIS OF ROTATION IS 0.501563 0.179884 0.846213 ANGLE IS 45.90 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 80 atoms have been selected out of 80 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -30.190080 28.564778 -2.144693 41.617150 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT1" + RDCMND substituted energy or value "?RDIP" to "41.6172" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 80 Number of groups = 6 + Number of bonds = 79 Number of angles = 70 + Number of dihedrals = 91 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 80 atoms have been selected out of 80 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 79 bonds deleted + DELTIC: 70 angles deleted + DELTIC: 91 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 66 + Number of dihedrals = 90 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 22 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 676 676 666 + : Ran out of space. RESIZING + with mode 5 found 446 exclusions and 302 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2329 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2329 atom pairs and 748 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2329 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 154.70496 288.20610 47.22765 +ENER INTERN> 28.52477 40.50323 18.90583 34.90544 1.31251 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 113.74868 -72.73550 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT2" + RDCMND substituted energy or value "?ENER" to "154.705" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 67.50785654 53.78820793 -59.25361031 + 475.57095333 374.75163963 + 721.54469253 + + Transpose of the rotation matrix + 0.810794 0.585058 -0.017902 + -0.526815 0.742725 0.413311 + 0.255108 -0.325679 0.910414 + CENTER OF ATOMS BEFORE TRANSLATION 5.00216 2.61954 -0.36885 + AXIS OF ROTATION IS 0.542306 0.200347 0.815945 ANGLE IS 42.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 75 atoms have been selected out of 75 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -41.098760 27.193290 -2.670741 49.352973 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT2" + RDCMND substituted energy or value "?RDIP" to "49.353" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 66 + Number of dihedrals = 90 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 75 atoms have been selected out of 75 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 66 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 6 + Number of bonds = 78 Number of angles = 72 + Number of dihedrals = 96 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 23 + Number of true-bonds = 78 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 711 711 702 + : Ran out of space. RESIZING + with mode 5 found 467 exclusions and 317 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2614 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2614 atom pairs and 784 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2614 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 968.70737 -814.00242 765.31706 +ENER INTERN> 28.52477 53.37478 52.94173 34.42695 1.31251 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 918.61134 -115.92471 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT3" + RDCMND substituted energy or value "?ENER" to "968.707" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 69.22307130 61.01065578 -51.38476888 + 581.11312032 479.21587110 + 820.44319945 + + Transpose of the rotation matrix + 0.788249 0.615350 -0.002631 + -0.558647 0.717394 0.416244 + 0.258023 -0.326635 0.909249 + CENTER OF ATOMS BEFORE TRANSLATION 5.28661 2.88062 -0.35018 + AXIS OF ROTATION IS 0.525547 0.184399 0.830540 ANGLE IS 44.97 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 79 atoms have been selected out of 79 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -31.918304 24.203280 -0.577594 40.061334 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT3" + RDCMND substituted energy or value "?RDIP" to "40.0613" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 6 + Number of bonds = 78 Number of angles = 72 + Number of dihedrals = 96 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 79 atoms have been selected out of 79 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 78 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 96 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 69 + Number of dihedrals = 93 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -3.00000 + Number of Drudes = 25 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 43 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 754 754 747 + : Ran out of space. RESIZING + with mode 5 found 512 exclusions and 336 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2974 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2974 atom pairs and 848 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2974 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 501.26065 467.44672 51.84572 +ENER INTERN> 20.96488 45.28541 115.99139 42.98579 1.31251 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 156.85806 123.19262 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CTER" + RDCMND substituted energy or value "?ENER" to "501.261" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 98.32132437 28.43874165 -146.94496679 + 501.70594984 473.71287366 + 1045.03698987 + + Transpose of the rotation matrix + 0.865711 0.492029 -0.091932 + -0.402734 0.793762 0.455794 + 0.297236 -0.357561 0.885325 + CENTER OF ATOMS BEFORE TRANSLATION 4.36521 2.43528 -0.16656 + AXIS OF ROTATION IS 0.640298 0.306365 0.704385 ANGLE IS 39.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -3.000000 + DIPOLE MOMENT (DEBYES) : -45.711155 7.417549 -2.660720 46.385441 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CTER" + RDCMND substituted energy or value "?RDIP" to "46.3854" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 69 + Number of dihedrals = 93 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 43 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 69 angles deleted + DELTIC: 93 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 7 + Number of bonds = 84 Number of angles = 70 + Number of dihedrals = 95 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 25 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 43 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 758 758 756 + : Ran out of space. RESIZING + with mode 5 found 518 exclusions and 342 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3052 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3052 atom pairs and 860 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3052 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 374.23035 127.03030 50.91007 +ENER INTERN> 20.94645 40.73810 125.27576 34.12900 1.31251 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 156.59866 0.55987 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CNEU" + RDCMND substituted energy or value "?ENER" to "374.23" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 98.56249442 29.13311606 -146.11997732 + 519.73848699 495.28154253 + 1067.80690997 + + Transpose of the rotation matrix + 0.861962 0.499339 -0.087648 + -0.409949 0.788219 0.458968 + 0.298267 -0.359682 0.884119 + CENTER OF ATOMS BEFORE TRANSLATION 4.42418 2.48491 -0.16460 + AXIS OF ROTATION IS 0.638107 0.300806 0.708756 ANGLE IS 39.90 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 85 atoms have been selected out of 85 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -19.175913 19.024321 -4.938121 27.459524 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CNEU" + RDCMND substituted energy or value "?RDIP" to "27.4595" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 7 + Number of bonds = 84 Number of angles = 70 + Number of dihedrals = 95 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 43 + + CHARMM> delete atom sele all end + SELRPN> 85 atoms have been selected out of 85 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 70 angles deleted + DELTIC: 95 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 7 + Number of bonds = 88 Number of angles = 76 + Number of dihedrals = 98 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 26 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 44 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 798 798 792 + : Ran out of space. RESIZING + with mode 5 found 546 exclusions and 354 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3370 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3370 atom pairs and 900 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3370 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 645.84301 -271.61266 153.52082 +ENER INTERN> 20.94645 40.59825 105.52674 35.01427 1.31251 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 411.15321 36.62157 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT1" + RDCMND substituted energy or value "?ENER" to "645.843" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 100.31116778 32.70261335 -143.44683664 + 643.76073200 586.99288848 + 1138.58747750 + + Transpose of the rotation matrix + 0.834337 0.546672 -0.070940 + -0.464462 0.766441 0.443669 + 0.296913 -0.337220 0.893378 + CENTER OF ATOMS BEFORE TRANSLATION 4.61525 2.74005 -0.15720 + AXIS OF ROTATION IS 0.587368 0.276692 0.760553 ANGLE IS 41.66 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 89 atoms have been selected out of 89 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -13.368242 22.427785 -5.352040 26.652575 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT1" + RDCMND substituted energy or value "?RDIP" to "26.6526" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 7 + Number of bonds = 88 Number of angles = 76 + Number of dihedrals = 98 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 44 + + CHARMM> delete atom sele all end + SELRPN> 89 atoms have been selected out of 89 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 76 angles deleted + DELTIC: 98 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 9 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 72 + Number of dihedrals = 97 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 25 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 752 752 747 + : Ran out of space. RESIZING + with mode 5 found 500 exclusions and 338 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2986 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2986 atom pairs and 838 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2986 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 352.58158 293.26143 51.32093 +ENER INTERN> 28.07587 38.58034 104.57812 38.86403 1.31251 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 153.34844 1.33227 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT2" + RDCMND substituted energy or value "?ENER" to "352.582" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 98.32132437 28.40471015 -147.30362539 + 500.91851426 464.67337050 + 1035.49274809 + + Transpose of the rotation matrix + 0.866057 0.491145 -0.093395 + -0.403876 0.797426 0.448327 + 0.294669 -0.350556 0.888977 + CENTER OF ATOMS BEFORE TRANSLATION 4.33958 2.43285 -0.16656 + AXIS OF ROTATION IS 0.633581 0.307768 0.709827 ANGLE IS 39.08 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -25.846223 20.324845 -6.185197 33.457185 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT2" + RDCMND substituted energy or value "?RDIP" to "33.4572" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 72 + Number of dihedrals = 97 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 97 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 7 + Number of bonds = 87 Number of angles = 78 + Number of dihedrals = 103 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 26 + Number of true-bonds = 87 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "6" + Parameter: PATCHED -> "25" + Comparing "6" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 791 791 783 + : Ran out of space. RESIZING + with mode 5 found 521 exclusions and 353 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3307 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3307 atom pairs and 874 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3307 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1170.96419 -818.38261 727.57528 +ENER INTERN> 28.07587 51.45189 138.61403 38.38554 1.31251 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 958.21104 -37.47668 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT3" + RDCMND substituted energy or value "?ENER" to "1170.96" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 99.62580702 31.80252668 -143.30969425 + 614.49529681 587.25902360 + 1165.14570859 + + Transpose of the rotation matrix + 0.844812 0.530189 -0.072052 + -0.445439 0.771505 0.454274 + 0.296440 -0.351682 0.887943 + CENTER OF ATOMS BEFORE TRANSLATION 4.62505 2.67571 -0.15898 + AXIS OF ROTATION IS 0.611486 0.279578 0.740217 ANGLE IS 41.22 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -14.580445 18.267604 -3.658721 23.657577 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT3" + RDCMND substituted energy or value "?RDIP" to "23.6576" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 7 + Number of bonds = 87 Number of angles = 78 + Number of dihedrals = 103 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 87 bonds deleted + DELTIC: 78 angles deleted + DELTIC: 103 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "7" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "7" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "7" + Parameter: AA7 -> "CYS" + Parameter: RESIDUE <- "CYS" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "7" + Parameter: SPECIAL -> "2" + Comparing "7" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "CYS" + Parameter: PATCH <- "CYS" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-CYS-ALA-CYS-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-CYS-ALA-CYS-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 65 Number of groups = 6 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 80 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 18 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 584 584 576 + : Ran out of space. RESIZING + with mode 5 found 384 exclusions and 264 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1696 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1696 atom pairs and 648 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1696 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 161.72853 1009.23566 32.07834 +ENER INTERN> 20.91934 41.58899 21.62232 31.62785 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 33.07567 15.17436 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-CYS-ALA-CYS-CTER" + RDCMND substituted energy or value "?ENER" to "161.729" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 51.56918334 37.20787526 -43.74377058 + 414.91466491 338.16590084 + 569.17869437 + + Transpose of the rotation matrix + 0.782420 0.622593 -0.014046 + -0.559102 0.712206 0.424462 + 0.274270 -0.324254 0.905337 + CENTER OF ATOMS BEFORE TRANSLATION 4.65671 2.85455 -0.28224 + AXIS OF ROTATION IS 0.524193 0.201856 0.827331 ANGLE IS 45.57 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 65 atoms have been selected out of 65 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -50.973986 -6.042776 0.012311 51.330912 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-CYS-ALA-CYS-CTER" + RDCMND substituted energy or value "?RDIP" to "51.3309" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 65 Number of groups = 6 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 80 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 65 atoms have been selected out of 65 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 64 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 80 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-CYS-ALA-CYS-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-CYS-ALA-CYS-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 66 Number of groups = 6 + Number of bonds = 65 Number of angles = 60 + Number of dihedrals = 82 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 18 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 588 588 585 + : Ran out of space. RESIZING + with mode 5 found 390 exclusions and 270 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1755 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1755 atom pairs and 660 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1755 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 162.93307 -1.20454 27.82349 +ENER INTERN> 20.79032 36.46714 30.79587 22.76089 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 31.05135 23.34750 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-CYS-ALA-CYS-CNEU" + RDCMND substituted energy or value "?ENER" to "162.933" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 51.86139240 38.31831570 -42.47244117 + 431.11263478 356.76179208 + 587.68789692 + + Transpose of the rotation matrix + 0.779700 0.626055 -0.011091 + -0.562063 0.707590 0.428256 + 0.275959 -0.327677 0.903590 + CENTER OF ATOMS BEFORE TRANSLATION 4.72601 2.91508 -0.27797 + AXIS OF ROTATION IS 0.525987 0.199733 0.826707 ANGLE IS 45.94 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 66 atoms have been selected out of 66 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -26.700218 1.372924 -1.534742 26.779507 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-CYS-ALA-CYS-CNEU" + RDCMND substituted energy or value "?RDIP" to "26.7795" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 66 Number of groups = 6 + Number of bonds = 65 Number of angles = 60 + Number of dihedrals = 82 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 66 atoms have been selected out of 66 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 60 angles deleted + DELTIC: 82 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-CYS-ALA-CYS-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-CYS-ALA-CYS-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 19 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 70 Number of groups = 6 + Number of bonds = 69 Number of angles = 66 + Number of dihedrals = 85 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 19 + Number of true-bonds = 69 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 31 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 624 624 621 + : Ran out of space. RESIZING + with mode 5 found 418 exclusions and 282 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1997 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1997 atom pairs and 700 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1997 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 405.78608 -242.85301 159.71069 +ENER INTERN> 20.79032 36.32728 11.20930 23.67417 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 260.68269 55.38231 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-CYS-ALA-CYS-CT1" + RDCMND substituted energy or value "?ENER" to "405.786" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 53.79796711 44.00207994 -38.53042481 + 542.86294084 433.19288429 + 642.77979465 + + Transpose of the rotation matrix + 0.746490 0.665396 0.000529 + -0.606499 0.680088 0.411873 + 0.273699 -0.307780 0.911241 + CENTER OF ATOMS BEFORE TRANSLATION 4.94088 3.22490 -0.26208 + AXIS OF ROTATION IS 0.484065 0.183744 0.855523 ANGLE IS 48.02 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 70 atoms have been selected out of 70 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -26.407102 3.307416 -2.114962 26.697324 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-CYS-ALA-CYS-CT1" + RDCMND substituted energy or value "?RDIP" to "26.6973" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 70 Number of groups = 6 + Number of bonds = 69 Number of angles = 66 + Number of dihedrals = 85 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 70 atoms have been selected out of 70 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 69 bonds deleted + DELTIC: 66 angles deleted + DELTIC: 85 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-CYS-ALA-CYS-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-CYS-ALA-CYS-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 65 Number of groups = 6 + Number of bonds = 64 Number of angles = 62 + Number of dihedrals = 84 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 18 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 586 586 576 + : Ran out of space. RESIZING + with mode 5 found 372 exclusions and 266 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1708 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1708 atom pairs and 638 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1708 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 165.00824 240.77783 29.19575 +ENER INTERN> 27.13805 34.68660 10.28766 26.71643 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 45.50093 31.13858 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-CYS-ALA-CYS-CT2" + RDCMND substituted energy or value "?ENER" to "165.008" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 51.56918334 37.13315278 -44.34968627 + 413.80449169 329.75607994 + 561.49845431 + + Transpose of the rotation matrix + 0.781246 0.624048 -0.014822 + -0.562953 0.714623 0.415209 + 0.269703 -0.316036 0.909605 + CENTER OF ATOMS BEFORE TRANSLATION 4.62368 2.85048 -0.28224 + AXIS OF ROTATION IS 0.513912 0.199961 0.834212 ANGLE IS 45.35 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 65 atoms have been selected out of 65 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -31.365408 3.655663 -2.709885 31.693787 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-CYS-ALA-CYS-CT2" + RDCMND substituted energy or value "?RDIP" to "31.6938" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 65 Number of groups = 6 + Number of bonds = 64 Number of angles = 62 + Number of dihedrals = 84 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 65 atoms have been selected out of 65 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 64 bonds deleted + DELTIC: 62 angles deleted + DELTIC: 84 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-CYS-ALA-CYS-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-CYS-ALA-CYS-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 19 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 69 Number of groups = 6 + Number of bonds = 68 Number of angles = 68 + Number of dihedrals = 90 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 19 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 29 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 616 616 612 + : Ran out of space. RESIZING + with mode 5 found 393 exclusions and 281 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1953 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1953 atom pairs and 674 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1953 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 226.05275 -61.04451 34.99296 +ENER INTERN> 27.13805 47.55814 45.74301 26.26027 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 48.80412 35.10916 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-CYS-ALA-CYS-CT3" + RDCMND substituted energy or value "?ENER" to "226.053" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 53.06791631 42.61594397 -38.16294111 + 518.19713768 436.51585318 + 668.39599282 + + Transpose of the rotation matrix + 0.764778 0.644291 -0.001759 + -0.584292 0.694705 0.419509 + 0.271508 -0.319804 0.907749 + CENTER OF ATOMS BEFORE TRANSLATION 4.96091 3.14934 -0.26588 + AXIS OF ROTATION IS 0.506489 0.187210 0.841678 ANGLE IS 46.87 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 69 atoms have been selected out of 69 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -27.273572 -0.378180 -0.495795 27.280699 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-CYS-ALA-CYS-CT3" + RDCMND substituted energy or value "?RDIP" to "27.2807" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 69 Number of groups = 6 + Number of bonds = 68 Number of angles = 68 + Number of dihedrals = 90 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 29 + + CHARMM> delete atom sele all end + SELRPN> 69 atoms have been selected out of 69 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 68 bonds deleted + DELTIC: 68 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-CYS-ALA-CYS-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-CYS-ALA-CYS-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 7 + Number of bonds = 73 Number of angles = 65 + Number of dihedrals = 87 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 21 + Number of true-bonds = 73 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 658 658 657 + : Ran out of space. RESIZING + with mode 5 found 438 exclusions and 300 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2263 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2263 atom pairs and 738 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2263 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 274.73836 -48.68561 42.55732 +ENER INTERN> 20.58581 39.67225 107.27631 35.22243 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 72.41345 4.89811 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-CYS-ALA-CYS-CTER" + RDCMND substituted energy or value "?ENER" to "274.738" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.39190291 10.09906787 -121.11830768 + 446.77769705 432.77282775 + 845.30962292 + + Transpose of the rotation matrix + 0.842312 0.531101 -0.091878 + -0.434531 0.769984 0.467234 + 0.318893 -0.353633 0.879347 + CENTER OF ATOMS BEFORE TRANSLATION 3.94660 2.61406 -0.06314 + AXIS OF ROTATION IS 0.616132 0.308319 0.724790 ANGLE IS 41.77 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 74 atoms have been selected out of 74 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -29.323305 -14.063030 -2.220051 32.596836 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-CYS-ALA-CYS-CTER" + RDCMND substituted energy or value "?RDIP" to "32.5968" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 7 + Number of bonds = 73 Number of angles = 65 + Number of dihedrals = 87 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 74 atoms have been selected out of 74 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 73 bonds deleted + DELTIC: 65 angles deleted + DELTIC: 87 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-CYS-ALA-CYS-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-CYS-ALA-CYS-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 7 + Number of bonds = 74 Number of angles = 66 + Number of dihedrals = 89 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 678 678 666 + : Ran out of space. RESIZING + with mode 5 found 444 exclusions and 306 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2331 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2331 atom pairs and 750 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2331 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 243.04887 31.68949 40.43341 +ENER INTERN> 20.45679 34.55040 116.44986 26.35546 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 70.39160 -19.82525 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-CYS-ALA-CYS-CNEU" + RDCMND substituted energy or value "?ENER" to "243.049" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.60959233 10.36293233 -120.78912660 + 464.95764611 455.45471396 + 870.76342261 + + Transpose of the rotation matrix + 0.839027 0.537017 -0.087450 + -0.440009 0.764246 0.471508 + 0.320041 -0.357129 0.877515 + CENTER OF ATOMS BEFORE TRANSLATION 4.01705 2.67053 -0.06230 + AXIS OF ROTATION IS 0.616386 0.303115 0.726766 ANGLE IS 42.24 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 75 atoms have been selected out of 75 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -2.219428 -4.711159 -3.986508 6.558439 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-CYS-ALA-CYS-CNEU" + RDCMND substituted energy or value "?RDIP" to "6.55844" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 7 + Number of bonds = 74 Number of angles = 66 + Number of dihedrals = 89 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 75 atoms have been selected out of 75 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 66 angles deleted + DELTIC: 89 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-CYS-ALA-CYS-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-CYS-ALA-CYS-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 7 + Number of bonds = 78 Number of angles = 72 + Number of dihedrals = 92 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 22 + Number of true-bonds = 78 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 703 703 702 + : Ran out of space. RESIZING + with mode 5 found 472 exclusions and 318 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2609 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2609 atom pairs and 790 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2609 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 487.23518 -244.18631 153.99164 +ENER INTERN> 20.45679 34.41055 96.86330 27.26875 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 300.02191 13.54389 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-CYS-ALA-CYS-CT1" + RDCMND substituted energy or value "?ENER" to "487.235" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 81.26950784 11.70347937 -119.73178118 + 587.77070540 551.16385574 + 948.37941335 + + Transpose of the rotation matrix + 0.810404 0.581569 -0.070870 + -0.491909 0.741140 0.456877 + 0.318230 -0.335394 0.886702 + CENTER OF ATOMS BEFORE TRANSLATION 4.24334 2.95743 -0.05915 + AXIS OF ROTATION IS 0.570076 0.279975 0.772417 ANGLE IS 44.02 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 79 atoms have been selected out of 79 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.627216 -3.339405 -4.560983 5.687494 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-CYS-ALA-CYS-CT1" + RDCMND substituted energy or value "?RDIP" to "5.68749" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 7 + Number of bonds = 78 Number of angles = 72 + Number of dihedrals = 92 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 79 atoms have been selected out of 79 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 78 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 92 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-CYS-ALA-CYS-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-CYS-ALA-CYS-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 7 + Number of bonds = 73 Number of angles = 68 + Number of dihedrals = 91 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 73 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 676 676 657 + : Ran out of space. RESIZING + with mode 5 found 426 exclusions and 302 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2275 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2275 atom pairs and 728 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2275 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 241.37484 245.86034 41.07960 +ENER INTERN> 26.80452 32.76986 95.94165 30.31100 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 84.84046 -15.78265 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-CYS-ALA-CYS-CT2" + RDCMND substituted energy or value "?ENER" to "241.375" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.39190291 10.08235128 -121.25386050 + 445.54031368 423.65977398 + 834.58908952 + + Transpose of the rotation matrix + 0.842062 0.531234 -0.093392 + -0.437282 0.773726 0.458403 + 0.315779 -0.345165 0.883824 + CENTER OF ATOMS BEFORE TRANSLATION 3.91759 2.61048 -0.06314 + AXIS OF ROTATION IS 0.607238 0.309202 0.731885 ANGLE IS 41.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 74 atoms have been selected out of 74 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -7.653352 -3.058003 -5.474448 9.894178 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-CYS-ALA-CYS-CT2" + RDCMND substituted energy or value "?RDIP" to "9.89418" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 7 + Number of bonds = 73 Number of angles = 68 + Number of dihedrals = 91 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 74 atoms have been selected out of 74 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 73 bonds deleted + DELTIC: 68 angles deleted + DELTIC: 91 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "CYS" + Parameter: PATCH -> "CYS" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-CYS-ALA-CYS-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-CYS-ALA-CYS-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "CYS" + Parameter: RESIDUE -> "CYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + CYS ALA CYS + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: CYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 CYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 7 + Number of bonds = 77 Number of angles = 74 + Number of dihedrals = 97 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 22 + Number of true-bonds = 77 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "7" + Parameter: PATCHED -> "25" + Comparing "7" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 696 696 693 + : Ran out of space. RESIZING + with mode 5 found 447 exclusions and 317 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2556 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2556 atom pairs and 764 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2556 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 306.84315 -65.46831 44.55791 +ENER INTERN> 26.80452 45.64141 131.39700 29.85484 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 88.14360 -7.38822 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-CYS-ALA-CYS-CT3" + RDCMND substituted energy or value "?ENER" to "306.843" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 80.60559619 11.37515491 -119.69077082 + 560.25332897 550.97706551 + 975.45892341 + + Transpose of the rotation matrix + 0.822913 0.563614 -0.071791 + -0.471799 0.748262 0.466379 + 0.316576 -0.349918 0.881667 + CENTER OF ATOMS BEFORE TRANSLATION 4.25212 2.88716 -0.05990 + AXIS OF ROTATION IS 0.593886 0.282552 0.753302 ANGLE IS 43.41 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 78 atoms have been selected out of 78 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -1.166401 -6.693140 -2.821563 7.356618 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-CYS-ALA-CYS-CT3" + RDCMND substituted energy or value "?RDIP" to "7.35662" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 7 + Number of bonds = 77 Number of angles = 74 + Number of dihedrals = 97 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 78 atoms have been selected out of 78 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 77 bonds deleted + DELTIC: 74 angles deleted + DELTIC: 97 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "8" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "8" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "8" + Parameter: AA8 -> "GLN" + Parameter: RESIDUE <- "GLN" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "8" + Parameter: SPECIAL -> "2" + Comparing "8" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "GLN" + Parameter: PATCH <- "GLN" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-GLN-ALA-GLN-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLN-ALA-GLN-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 81 + Number of dihedrals = 112 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 24 + Number of true-bonds = 82 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 745 745 738 + : Ran out of space. RESIZING + with mode 5 found 478 exclusions and 340 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2925 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2925 atom pairs and 818 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2925 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 39.25423 267.58891 34.09529 +ENER INTERN> 29.71742 47.56750 22.51274 35.71951 0.00420 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 34.19204 -128.17917 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLN-ALA-GLN-CTER" + RDCMND substituted energy or value "?ENER" to "39.2542" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 167.21713638 125.33402453 -134.87234266 + 585.71073479 407.81744600 + 861.57077473 + + Transpose of the rotation matrix + 0.816581 0.575953 -0.038395 + -0.452470 0.679972 0.576983 + 0.358423 -0.453780 0.815853 + CENTER OF ATOMS BEFORE TRANSLATION 5.23250 2.32587 -0.88124 + AXIS OF ROTATION IS 0.683000 0.262938 0.681450 ANGLE IS 48.99 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -54.701085 -5.014553 0.102442 54.930546 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLN-ALA-GLN-CTER" + RDCMND substituted energy or value "?RDIP" to "54.9305" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 81 + Number of dihedrals = 112 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 82 bonds deleted + DELTIC: 81 angles deleted + DELTIC: 112 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-GLN-ALA-GLN-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLN-ALA-GLN-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 8 + Number of bonds = 83 Number of angles = 82 + Number of dihedrals = 114 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 24 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 748 748 747 + : Ran out of space. RESIZING + with mode 5 found 484 exclusions and 346 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3002 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3002 atom pairs and 830 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3002 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 51.03813 -11.78389 30.40510 +ENER INTERN> 29.56740 42.57367 31.66438 26.85479 0.00420 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 32.48821 -109.83453 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLN-ALA-GLN-CNEU" + RDCMND substituted energy or value "?ENER" to "51.0381" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 168.19823090 129.10828244 -131.27325997 + 604.71550168 426.20048885 + 876.39920013 + + Transpose of the rotation matrix + 0.810605 0.584810 -0.030283 + -0.462480 0.671050 0.579485 + 0.359211 -0.455728 0.814420 + CENTER OF ATOMS BEFORE TRANSLATION 5.28171 2.37747 -0.87075 + AXIS OF ROTATION IS 0.679623 0.255705 0.687552 ANGLE IS 49.61 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -31.457490 7.579042 -2.298112 32.439125 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLN-ALA-GLN-CNEU" + RDCMND substituted energy or value "?RDIP" to "32.4391" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 8 + Number of bonds = 83 Number of angles = 82 + Number of dihedrals = 114 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 82 angles deleted + DELTIC: 114 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-GLN-ALA-GLN-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLN-ALA-GLN-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 8 + Number of bonds = 87 Number of angles = 88 + Number of dihedrals = 117 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 25 + Number of true-bonds = 87 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 784 784 783 + : Ran out of space. RESIZING + with mode 5 found 512 exclusions and 358 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3316 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3316 atom pairs and 870 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3316 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 289.52262 -238.48450 140.88724 +ENER INTERN> 29.56740 42.43381 12.10902 27.76275 0.00420 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 262.05795 -82.13252 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLN-ALA-GLN-CT1" + RDCMND substituted energy or value "?ENER" to "289.523" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 172.73836751 148.36748791 -120.01313683 + 733.75775158 500.62536473 + 921.93121195 + + Transpose of the rotation matrix + 0.769392 0.638773 0.002092 + -0.527024 0.632935 0.567132 + 0.360945 -0.437450 0.823624 + CENTER OF ATOMS BEFORE TRANSLATION 5.43566 2.64078 -0.83117 + AXIS OF ROTATION IS 0.635729 0.227093 0.737751 ANGLE IS 52.20 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -30.230842 10.269700 -3.008887 32.069050 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLN-ALA-GLN-CT1" + RDCMND substituted energy or value "?RDIP" to "32.069" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 8 + Number of bonds = 87 Number of angles = 88 + Number of dihedrals = 117 Number of impropers = 9 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 87 bonds deleted + DELTIC: 88 angles deleted + DELTIC: 117 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-GLN-ALA-GLN-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLN-ALA-GLN-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 84 + Number of dihedrals = 116 Number of impropers = 10 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 24 + Number of true-bonds = 82 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 740 740 738 + : Ran out of space. RESIZING + with mode 5 found 466 exclusions and 342 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2937 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2937 atom pairs and 808 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2937 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 51.07162 238.45100 30.86615 +ENER INTERN> 35.76555 40.74317 11.19354 32.25899 0.00420 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 45.81444 -104.24828 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLN-ALA-GLN-CT2" + RDCMND substituted energy or value "?ENER" to "51.0716" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 167.21713638 125.15992745 -136.77055080 + 584.92800465 398.69833981 + 855.81244117 + + Transpose of the rotation matrix + 0.817318 0.574738 -0.040839 + -0.452839 0.684560 0.571239 + 0.356270 -0.448390 0.819767 + CENTER OF ATOMS BEFORE TRANSLATION 5.20655 2.32349 -0.88124 + AXIS OF ROTATION IS 0.679262 0.264548 0.684557 ANGLE IS 48.64 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -36.443397 9.089525 -3.851421 37.756775 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLN-ALA-GLN-CT2" + RDCMND substituted energy or value "?RDIP" to "37.7568" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 84 + Number of dihedrals = 116 Number of impropers = 10 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 82 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 116 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-GLN-ALA-GLN-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLN-ALA-GLN-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 8 + Number of bonds = 86 Number of angles = 90 + Number of dihedrals = 122 Number of impropers = 10 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 25 + Number of true-bonds = 86 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 780 780 774 + : Ran out of space. RESIZING + with mode 5 found 487 exclusions and 357 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3254 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3254 atom pairs and 844 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3254 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 110.05791 -58.98629 34.29288 +ENER INTERN> 35.76555 53.61471 46.92838 31.79812 0.00420 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 47.43115 -100.92419 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLN-ALA-GLN-CT3" + RDCMND substituted energy or value "?ENER" to "110.058" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 171.37921541 143.50405666 -118.59306642 + 703.08955621 505.76002388 + 946.32652858 + + Transpose of the rotation matrix + 0.785845 0.618412 -0.003793 + -0.503885 0.643841 0.575820 + 0.358536 -0.450594 0.817568 + CENTER OF ATOMS BEFORE TRANSLATION 5.45507 2.57429 -0.84072 + AXIS OF ROTATION IS 0.656508 0.231750 0.717836 ANGLE IS 51.42 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 87 atoms have been selected out of 87 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -31.302998 6.800046 -0.863041 32.044706 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLN-ALA-GLN-CT3" + RDCMND substituted energy or value "?RDIP" to "32.0447" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 8 + Number of bonds = 86 Number of angles = 90 + Number of dihedrals = 122 Number of impropers = 10 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 87 atoms have been selected out of 87 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 86 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 122 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-GLN-ALA-GLN-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLN-ALA-GLN-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 87 + Number of dihedrals = 119 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 27 + Number of true-bonds = 91 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 827 827 819 + : Ran out of space. RESIZING + with mode 5 found 532 exclusions and 376 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3654 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3654 atom pairs and 908 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3654 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 149.61068 -39.55276 40.58796 +ENER INTERN> 29.32523 45.40671 108.18306 46.48919 0.00420 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 72.58300 -147.05072 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLN-ALA-GLN-CTER" + RDCMND substituted energy or value "?ENER" to "149.611" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 216.17161932 98.14948062 -254.11919398 + 603.70376832 486.60647067 + 1202.28822182 + + Transpose of the rotation matrix + 0.876359 0.461363 -0.138347 + -0.307594 0.757103 0.576352 + 0.370650 -0.462536 0.805406 + CENTER OF ATOMS BEFORE TRANSLATION 4.60500 2.18415 -0.64641 + AXIS OF ROTATION IS 0.747874 0.366416 0.553556 ANGLE IS 43.99 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -30.507303 -17.697697 -1.890309 35.319645 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLN-ALA-GLN-CTER" + RDCMND substituted energy or value "?RDIP" to "35.3196" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 87 + Number of dihedrals = 119 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 91 bonds deleted + DELTIC: 87 angles deleted + DELTIC: 119 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-GLN-ALA-GLN-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLN-ALA-GLN-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 9 + Number of bonds = 92 Number of angles = 88 + Number of dihedrals = 121 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 27 + Number of true-bonds = 92 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 831 831 828 + : Ran out of space. RESIZING + with mode 5 found 538 exclusions and 382 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3740 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3740 atom pairs and 920 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3740 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 128.55616 21.05451 38.34196 +ENER INTERN> 29.17522 40.41288 117.33470 37.62447 0.00420 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 70.88160 -161.54692 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLN-ALA-GLN-CNEU" + RDCMND substituted energy or value "?ENER" to "128.556" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 216.79872776 101.01184052 -251.07484385 + 623.96544181 508.36827739 + 1222.65740408 + + Transpose of the rotation matrix + 0.871962 0.472030 -0.129884 + -0.319305 0.749431 0.579997 + 0.371116 -0.464263 0.804197 + CENTER OF ATOMS BEFORE TRANSLATION 4.65619 2.23228 -0.63946 + AXIS OF ROTATION IS 0.744441 0.357157 0.564134 ANGLE IS 44.54 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 93 atoms have been selected out of 93 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -6.247021 -2.795463 -4.460528 8.169222 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLN-ALA-GLN-CNEU" + RDCMND substituted energy or value "?RDIP" to "8.16922" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 9 + Number of bonds = 92 Number of angles = 88 + Number of dihedrals = 121 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 93 atoms have been selected out of 93 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 92 bonds deleted + DELTIC: 88 angles deleted + DELTIC: 121 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-GLN-ALA-GLN-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLN-ALA-GLN-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 9 + Number of bonds = 96 Number of angles = 94 + Number of dihedrals = 124 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 28 + Number of true-bonds = 96 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 866 866 864 + : Ran out of space. RESIZING + with mode 5 found 566 exclusions and 394 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4090 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4090 atom pairs and 960 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4090 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 368.37920 -239.82304 137.19170 +ENER INTERN> 29.17522 40.27302 97.77935 38.53243 0.00420 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 300.45034 -132.50536 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLN-ALA-GLN-CT1" + RDCMND substituted energy or value "?ENER" to "368.379" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 220.01208785 115.57394073 -241.23512741 + 760.10578297 599.25457874 + 1286.13271423 + + Transpose of the rotation matrix + 0.842328 0.530261 -0.096476 + -0.388605 0.721559 0.573009 + 0.373457 -0.445170 0.813851 + CENTER OF ATOMS BEFORE TRANSLATION 4.82165 2.47714 -0.61309 + AXIS OF ROTATION IS 0.702303 0.324142 0.633800 ANGLE IS 46.46 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -4.620682 -1.099513 -5.176462 7.025339 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLN-ALA-GLN-CT1" + RDCMND substituted energy or value "?RDIP" to "7.02534" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 9 + Number of bonds = 96 Number of angles = 94 + Number of dihedrals = 124 Number of impropers = 11 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 96 bonds deleted + DELTIC: 94 angles deleted + DELTIC: 124 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-GLN-ALA-GLN-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLN-ALA-GLN-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 90 + Number of dihedrals = 123 Number of impropers = 12 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 27 + Number of true-bonds = 91 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 830 830 819 + : Ran out of space. RESIZING + with mode 5 found 520 exclusions and 378 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3666 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3666 atom pairs and 898 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3666 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 124.88674 243.49246 38.52870 +ENER INTERN> 35.37337 38.58238 96.86387 43.02867 0.00420 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 84.20714 -159.66288 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLN-ALA-GLN-CT2" + RDCMND substituted energy or value "?ENER" to "124.887" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 216.17161932 98.02177639 -255.51157348 + 602.86508647 477.05862139 + 1193.83205523 + + Transpose of the rotation matrix + 0.877182 0.458916 -0.141240 + -0.306626 0.761743 0.570727 + 0.369504 -0.457323 0.808902 + CENTER OF ATOMS BEFORE TRANSLATION 4.58159 2.18200 -0.64641 + AXIS OF ROTATION IS 0.745081 0.370162 0.554828 ANGLE IS 43.62 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -11.737649 -1.845772 -6.183080 13.394393 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLN-ALA-GLN-CT2" + RDCMND substituted energy or value "?RDIP" to "13.3944" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 90 + Number of dihedrals = 123 Number of impropers = 12 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 91 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 123 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLN" + Parameter: PATCH -> "GLN" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-GLN-ALA-GLN-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLN-ALA-GLN-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLN" + Parameter: RESIDUE -> "GLN" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLN ALA GLN + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLN" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: GLN mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLN . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 9 + Number of bonds = 95 Number of angles = 96 + Number of dihedrals = 129 Number of impropers = 12 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 28 + Number of true-bonds = 95 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "8" + Parameter: PATCHED -> "25" + Comparing "8" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 861 861 855 + : Ran out of space. RESIZING + with mode 5 found 541 exclusions and 393 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4019 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4019 atom pairs and 934 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4019 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 188.23259 -63.34585 41.01550 +ENER INTERN> 35.37337 51.45392 132.59870 42.56780 0.00420 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 85.82378 -151.97917 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLN-ALA-GLN-CT3" + RDCMND substituted energy or value "?ENER" to "188.233" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 218.97192476 111.88901444 -240.56912842 + 727.53365062 600.96755806 + 1312.24602248 + + Transpose of the rotation matrix + 0.852146 0.513773 -0.099425 + -0.369222 0.724927 0.581512 + 0.370841 -0.458823 0.807439 + CENTER OF ATOMS BEFORE TRANSLATION 4.83285 2.41518 -0.61948 + AXIS OF ROTATION IS 0.720801 0.325826 0.611787 ANGLE IS 46.19 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 96 atoms have been selected out of 96 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -5.108595 -4.280859 -2.991761 7.305760 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLN-ALA-GLN-CT3" + RDCMND substituted energy or value "?RDIP" to "7.30576" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 9 + Number of bonds = 95 Number of angles = 96 + Number of dihedrals = 129 Number of impropers = 12 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 96 atoms have been selected out of 96 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 95 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 129 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 8 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "9" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "9" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "9" + Parameter: AA9 -> "GLU" + Parameter: RESIDUE <- "GLU" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "9" + Parameter: SPECIAL -> "2" + Comparing "9" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "GLU" + Parameter: PATCH <- "GLU" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-GLU-ALA-GLU-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLU-ALA-GLU-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 75 + Number of dihedrals = 104 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 24 + Number of true-bonds = 82 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 740 740 738 + : Ran out of space. RESIZING + with mode 5 found 502 exclusions and 332 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2901 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2901 atom pairs and 834 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2901 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 240.93901 -52.70642 35.30815 +ENER INTERN> 20.96304 50.44571 29.53722 37.64054 0.01205 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 35.86191 68.75854 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLU-ALA-GLU-CTER" + RDCMND substituted energy or value "?ENER" to "240.939" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 156.97117468 119.29576754 -136.86063858 + 563.51741604 398.96171140 + 888.49153917 + + Transpose of the rotation matrix + 0.834299 0.549169 -0.048567 + -0.432805 0.706985 0.559332 + 0.341504 -0.445630 0.827520 + CENTER OF ATOMS BEFORE TRANSLATION 5.33476 2.28389 -0.85689 + AXIS OF ROTATION IS 0.689175 0.267500 0.673411 ANGLE IS 46.81 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -57.993671 24.346521 5.675657 63.152451 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLU-ALA-GLU-CTER" + RDCMND substituted energy or value "?RDIP" to "63.1525" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 75 + Number of dihedrals = 104 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 82 bonds deleted + DELTIC: 75 angles deleted + DELTIC: 104 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-GLU-ALA-GLU-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLU-ALA-GLU-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 8 + Number of bonds = 83 Number of angles = 76 + Number of dihedrals = 106 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 24 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 748 748 747 + : Ran out of space. RESIZING + with mode 5 found 508 exclusions and 338 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2978 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2978 atom pairs and 846 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2978 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 161.36324 79.57576 33.27333 +ENER INTERN> 20.84747 45.60614 38.72390 28.77563 0.01205 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 34.19342 -4.51538 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLU-ALA-GLU-CNEU" + RDCMND substituted energy or value "?ENER" to "161.363" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 157.91045271 122.86129752 -133.31913892 + 581.43483154 417.12441318 + 903.77190539 + + Transpose of the rotation matrix + 0.828560 0.558434 -0.040496 + -0.443155 0.698284 0.562151 + 0.342202 -0.447830 0.826043 + CENTER OF ATOMS BEFORE TRANSLATION 5.38456 2.33403 -0.84669 + AXIS OF ROTATION IS 0.685667 0.259810 0.679970 ANGLE IS 47.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -34.047488 37.519671 3.420456 50.780475 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLU-ALA-GLU-CNEU" + RDCMND substituted energy or value "?RDIP" to "50.7805" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 8 + Number of bonds = 83 Number of angles = 76 + Number of dihedrals = 106 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 76 angles deleted + DELTIC: 106 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-GLU-ALA-GLU-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLU-ALA-GLU-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 8 + Number of bonds = 87 Number of angles = 82 + Number of dihedrals = 109 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 25 + Number of true-bonds = 87 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 784 784 783 + : Ran out of space. RESIZING + with mode 5 found 536 exclusions and 350 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3292 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3292 atom pairs and 886 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3292 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 404.83167 -243.46842 145.67364 +ENER INTERN> 20.84747 45.46629 19.11739 29.68585 0.01205 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 264.39967 27.58294 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLU-ALA-GLU-CT1" + RDCMND substituted energy or value "?ENER" to "404.832" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 162.29282712 141.26346050 -122.05604510 + 706.10123305 492.33615830 + 951.82104413 + + Transpose of the rotation matrix + 0.788963 0.614388 -0.008097 + -0.509220 0.661173 0.550950 + 0.343850 -0.430556 0.834499 + CENTER OF ATOMS BEFORE TRANSLATION 5.54292 2.59277 -0.80820 + AXIS OF ROTATION IS 0.640302 0.229599 0.733006 ANGLE IS 50.04 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -27.895435 41.328876 2.977603 49.950950 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLU-ALA-GLU-CT1" + RDCMND substituted energy or value "?RDIP" to "49.951" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 8 + Number of bonds = 87 Number of angles = 82 + Number of dihedrals = 109 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 87 bonds deleted + DELTIC: 82 angles deleted + DELTIC: 109 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-GLU-ALA-GLU-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLU-ALA-GLU-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 78 + Number of dihedrals = 108 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 24 + Number of true-bonds = 82 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 740 740 738 + : Ran out of space. RESIZING + with mode 5 found 490 exclusions and 334 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2913 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2913 atom pairs and 824 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2913 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 156.27981 248.55186 34.02006 +ENER INTERN> 27.29083 43.75412 18.19116 30.43781 0.01205 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 45.15358 1.90026 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLU-ALA-GLU-CT2" + RDCMND substituted energy or value "?ENER" to "156.28" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 156.97117468 119.18518681 -138.71084568 + 563.30600744 390.00825400 + 882.53126692 + + Transpose of the rotation matrix + 0.835095 0.547730 -0.051074 + -0.432886 0.711600 0.553385 + 0.339450 -0.440019 0.831358 + CENTER OF ATOMS BEFORE TRANSLATION 5.30875 2.28234 -0.85689 + AXIS OF ROTATION IS 0.685356 0.269425 0.676534 ANGLE IS 46.45 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -40.412784 38.828774 2.039618 56.080539 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLU-ALA-GLU-CT2" + RDCMND substituted energy or value "?RDIP" to "56.0805" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 78 + Number of dihedrals = 108 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 82 bonds deleted + DELTIC: 78 angles deleted + DELTIC: 108 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-GLU-ALA-GLU-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLU-ALA-GLU-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 8 + Number of bonds = 86 Number of angles = 84 + Number of dihedrals = 114 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 25 + Number of true-bonds = 86 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 777 777 774 + : Ran out of space. RESIZING + with mode 5 found 511 exclusions and 349 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3230 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3230 atom pairs and 860 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3230 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 217.12880 -60.84899 38.25008 +ENER INTERN> 27.29083 56.62566 53.46919 29.97787 0.01205 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 56.52117 -2.20797 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLU-ALA-GLU-CT3" + RDCMND substituted energy or value "?ENER" to "217.129" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 160.97175556 136.48514644 -120.75968208 + 675.05004508 496.20738726 + 976.23284416 + + Transpose of the rotation matrix + 0.804590 0.593675 -0.013633 + -0.485947 0.671438 0.559488 + 0.341308 -0.443533 0.828726 + CENTER OF ATOMS BEFORE TRANSLATION 5.56115 2.52558 -0.81749 + AXIS OF ROTATION IS 0.661715 0.234163 0.712250 ANGLE IS 49.28 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 87 atoms have been selected out of 87 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -29.923493 37.365892 4.974446 48.128686 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLU-ALA-GLU-CT3" + RDCMND substituted energy or value "?RDIP" to "48.1287" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 8 + Number of bonds = 86 Number of angles = 84 + Number of dihedrals = 114 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 87 atoms have been selected out of 87 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 86 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 114 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-GLU-ALA-GLU-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLU-ALA-GLU-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 81 + Number of dihedrals = 111 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -3.00000 + Number of Drudes = 27 + Number of true-bonds = 91 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 45 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 830 830 819 + : Ran out of space. RESIZING + with mode 5 found 556 exclusions and 368 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3630 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3630 atom pairs and 924 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3630 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 443.11722 -225.98842 40.82538 +ENER INTERN> 20.59349 48.00256 115.17922 49.02866 0.01205 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 72.54476 143.08647 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLU-ALA-GLU-CTER" + RDCMND substituted energy or value "?ENER" to "443.117" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 204.98133635 93.20746543 -256.81230568 + 580.53724452 476.73261192 + 1239.94588385 + + Transpose of the rotation matrix + 0.887615 0.437926 -0.142691 + -0.292393 0.775130 0.560071 + 0.355873 -0.455405 0.816064 + CENTER OF ATOMS BEFORE TRANSLATION 4.69726 2.14628 -0.62444 + AXIS OF ROTATION IS 0.754147 0.370260 0.542374 ANGLE IS 42.32 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -3.000000 + DIPOLE MOMENT (DEBYES) : -44.434888 13.717877 3.251792 46.617739 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLU-ALA-GLU-CTER" + RDCMND substituted energy or value "?RDIP" to "46.6177" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 81 + Number of dihedrals = 111 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 45 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 91 bonds deleted + DELTIC: 81 angles deleted + DELTIC: 111 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-GLU-ALA-GLU-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLU-ALA-GLU-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 9 + Number of bonds = 92 Number of angles = 82 + Number of dihedrals = 113 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 27 + Number of true-bonds = 92 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 45 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 834 834 828 + : Ran out of space. RESIZING + with mode 5 found 562 exclusions and 374 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3716 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3716 atom pairs and 936 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3716 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 330.86539 112.25183 39.77642 +ENER INTERN> 20.47793 43.16299 124.36590 40.16376 0.01205 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 70.87862 37.13414 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLU-ALA-GLU-CNEU" + RDCMND substituted energy or value "?ENER" to "330.865" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 205.58082905 95.89381745 -253.83469046 + 599.64041532 498.22758135 + 1260.92416186 + + Transpose of the rotation matrix + 0.883600 0.448482 -0.134593 + -0.303849 0.767885 0.563940 + 0.356269 -0.457401 0.814774 + CENTER OF ATOMS BEFORE TRANSLATION 4.74909 2.19304 -0.61773 + AXIS OF ROTATION IS 0.750888 0.360880 0.553112 ANGLE IS 42.85 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 93 atoms have been selected out of 93 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -19.326794 29.204453 0.822491 35.030008 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLU-ALA-GLU-CNEU" + RDCMND substituted energy or value "?RDIP" to "35.03" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 9 + Number of bonds = 92 Number of angles = 82 + Number of dihedrals = 113 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 45 + + CHARMM> delete atom sele all end + SELRPN> 93 atoms have been selected out of 93 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 92 bonds deleted + DELTIC: 82 angles deleted + DELTIC: 113 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-GLU-ALA-GLU-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLU-ALA-GLU-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 9 + Number of bonds = 96 Number of angles = 88 + Number of dihedrals = 116 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 28 + Number of true-bonds = 96 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 46 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 865 865 864 + : Ran out of space. RESIZING + with mode 5 found 590 exclusions and 386 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4066 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4066 atom pairs and 976 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4066 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 575.67062 -244.80523 141.21560 +ENER INTERN> 20.47793 43.02314 104.75940 41.07397 0.01205 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 301.08390 70.57023 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLU-ALA-GLU-CT1" + RDCMND substituted energy or value "?ENER" to "575.671" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 208.68942015 109.71300520 -244.07560745 + 731.08533244 589.87373306 + 1327.70808854 + + Transpose of the rotation matrix + 0.856122 0.506517 -0.102448 + -0.372240 0.741951 0.557626 + 0.358458 -0.439260 0.823746 + CENTER OF ATOMS BEFORE TRANSLATION 4.91896 2.43359 -0.59226 + AXIS OF ROTATION IS 0.708737 0.327682 0.624753 ANGLE IS 44.69 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -12.901034 32.894555 0.389837 35.336107 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLU-ALA-GLU-CT1" + RDCMND substituted energy or value "?RDIP" to "35.3361" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 9 + Number of bonds = 96 Number of angles = 88 + Number of dihedrals = 116 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 46 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 96 bonds deleted + DELTIC: 88 angles deleted + DELTIC: 116 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 9 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-GLU-ALA-GLU-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLU-ALA-GLU-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 84 + Number of dihedrals = 115 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 27 + Number of true-bonds = 91 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 43 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 830 830 819 + : Ran out of space. RESIZING + with mode 5 found 544 exclusions and 370 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3642 atom pairs and 914 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 322.15282 253.51780 40.21369 +ENER INTERN> 26.92128 41.31097 103.83316 41.82594 0.01205 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 81.83812 39.92130 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLU-ALA-GLU-CT2" + RDCMND substituted energy or value "?ENER" to "322.153" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 204.98133635 93.12688183 -258.16060889 + 580.29033682 467.40006882 + 1231.23809395 + + Transpose of the rotation matrix + 0.888362 0.435487 -0.145481 + -0.291456 0.779688 0.554202 + 0.354778 -0.449931 0.819570 + CENTER OF ATOMS BEFORE TRANSLATION 4.67379 2.14487 -0.62444 + AXIS OF ROTATION IS 0.751156 0.374225 0.543801 ANGLE IS 41.94 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -26.206815 29.736561 -0.751869 39.643732 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLU-ALA-GLU-CT2" + RDCMND substituted energy or value "?RDIP" to "39.6437" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 84 + Number of dihedrals = 115 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 43 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 91 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 115 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLU" + Parameter: PATCH -> "GLU" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-GLU-ALA-GLU-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLU-ALA-GLU-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 9 + Number of bonds = 95 Number of angles = 90 + Number of dihedrals = 121 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 28 + Number of true-bonds = 95 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "9" + Parameter: PATCHED -> "25" + Comparing "9" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 44 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 856 856 855 + : Ran out of space. RESIZING + with mode 5 found 565 exclusions and 385 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3995 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3995 atom pairs and 950 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3995 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 387.26216 -65.10934 43.51376 +ENER INTERN> 26.92128 54.18251 139.11119 41.36600 0.01205 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 93.20561 40.07351 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLU-ALA-GLU-CT3" + RDCMND substituted energy or value "?ENER" to "387.262" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 207.67463081 106.11990872 -243.50003142 + 698.16510985 590.20460402 + 1353.72874784 + + Transpose of the rotation matrix + 0.865327 0.490062 -0.105109 + -0.353037 0.744819 0.566223 + 0.355772 -0.452861 0.817523 + CENTER OF ATOMS BEFORE TRANSLATION 4.92898 2.37104 -0.59843 + AXIS OF ROTATION IS 0.727591 0.329052 0.601944 ANGLE IS 44.45 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 96 atoms have been selected out of 96 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -14.144290 29.080672 2.414061 32.427983 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLU-ALA-GLU-CT3" + RDCMND substituted energy or value "?RDIP" to "32.428" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 9 + Number of bonds = 95 Number of angles = 90 + Number of dihedrals = 121 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 44 + + CHARMM> delete atom sele all end + SELRPN> 96 atoms have been selected out of 96 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 95 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 121 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "10" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "10" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "10" + Parameter: AA10 -> "HSD" + Parameter: RESIDUE <- "HSD" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "10" + Parameter: SPECIAL -> "2" + Comparing "10" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "HSD" + Parameter: PATCH <- "HSD" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 83 + Number of dihedrals = 118 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 26 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 762 762 756 + : Ran out of space. RESIZING + with mode 5 found 502 exclusions and 324 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2901 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2901 atom pairs and 826 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2901 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 216.77863 170.48353 32.96312 +ENER INTERN> 20.29512 40.69502 22.43026 37.89697 0.00184 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 75.69502 22.04439 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CTER" + RDCMND substituted energy or value "?ENER" to "216.779" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 61.67539275 30.93571237 -79.45655448 + 547.37941911 427.12908499 + 951.48620513 + + Transpose of the rotation matrix + 0.845755 0.531783 -0.043657 + -0.501121 0.819753 0.277277 + 0.183239 -0.212631 0.959798 + CENTER OF ATOMS BEFORE TRANSLATION 5.54480 2.55756 -0.43726 + AXIS OF ROTATION IS 0.420343 0.194677 0.886235 ANGLE IS 35.64 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -58.106085 -10.082679 1.642658 58.997253 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CTER" + RDCMND substituted energy or value "?RDIP" to "58.9973" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 83 + Number of dihedrals = 118 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 83 angles deleted + DELTIC: 118 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 6 + Number of bonds = 85 Number of angles = 84 + Number of dihedrals = 120 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 26 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 770 770 765 + : Ran out of space. RESIZING + with mode 5 found 508 exclusions and 330 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2978 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2978 atom pairs and 838 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2978 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 217.22891 -0.45028 29.48561 +ENER INTERN> 20.13184 35.58179 31.56809 29.04265 0.00184 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 70.34289 32.83981 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CNEU" + RDCMND substituted energy or value "?ENER" to "217.229" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 62.07807181 32.64621973 -77.74571251 + 563.26222840 443.37557057 + 964.97130465 + + Transpose of the rotation matrix + 0.841301 0.539074 -0.040152 + -0.508318 0.814196 0.280531 + 0.183918 -0.215601 0.959005 + CENTER OF ATOMS BEFORE TRANSLATION 5.59194 2.60469 -0.43206 + AXIS OF ROTATION IS 0.420302 0.189823 0.887307 ANGLE IS 36.17 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -36.976351 2.259328 1.328915 37.069140 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CNEU" + RDCMND substituted energy or value "?RDIP" to "37.0691" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 6 + Number of bonds = 85 Number of angles = 84 + Number of dihedrals = 120 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 120 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 6 + Number of bonds = 89 Number of angles = 90 + Number of dihedrals = 123 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 27 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 805 805 801 + : Ran out of space. RESIZING + with mode 5 found 536 exclusions and 342 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3292 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3292 atom pairs and 878 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3292 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 465.38849 -248.15959 139.51568 +ENER INTERN> 20.13184 35.44193 12.03253 29.92292 0.00184 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 307.04143 63.09600 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT1" + RDCMND substituted energy or value "?ENER" to "465.388" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 64.43600461 41.62488666 -72.36353449 + 677.31551517 510.66600364 + 1007.31747606 + + Transpose of the rotation matrix + 0.809345 0.586759 -0.025956 + -0.558126 0.782109 0.277130 + 0.182909 -0.209807 0.960482 + CENTER OF ATOMS BEFORE TRANSLATION 5.74023 2.85209 -0.41242 + AXIS OF ROTATION IS 0.385985 0.165563 0.907527 ANGLE IS 39.11 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -36.167280 4.955830 1.026996 36.519681 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT1" + RDCMND substituted energy or value "?RDIP" to "36.5197" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 6 + Number of bonds = 89 Number of angles = 90 + Number of dihedrals = 123 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 123 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 86 + Number of dihedrals = 122 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 26 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 758 758 756 + : Ran out of space. RESIZING + with mode 5 found 490 exclusions and 326 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2913 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2913 atom pairs and 816 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2913 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 207.59526 257.79324 29.37139 +ENER INTERN> 26.23525 33.82957 11.12086 32.72070 0.00184 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 75.60602 38.54102 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT2" + RDCMND substituted energy or value "?ENER" to "207.595" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 61.67539275 30.87862496 -80.40065789 + 547.22211102 418.75110305 + 946.48872878 + + Transpose of the rotation matrix + 0.846596 0.530339 -0.044894 + -0.500377 0.821829 0.272431 + 0.181376 -0.208175 0.961127 + CENTER OF ATOMS BEFORE TRANSLATION 5.51878 2.55599 -0.43726 + AXIS OF ROTATION IS 0.414477 0.195136 0.888893 ANGLE IS 35.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -41.948994 4.112879 0.430937 42.152337 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT2" + RDCMND substituted energy or value "?RDIP" to "42.1523" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 86 + Number of dihedrals = 122 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 86 angles deleted + DELTIC: 122 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 6 + Number of bonds = 88 Number of angles = 92 + Number of dihedrals = 128 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 27 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 795 795 792 + : Ran out of space. RESIZING + with mode 5 found 511 exclusions and 341 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3230 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3230 atom pairs and 852 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3230 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 323.23141 -115.63615 47.07735 +ENER INTERN> 26.23525 46.70112 47.03407 32.23739 0.00184 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 135.26155 40.32019 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT3" + RDCMND substituted energy or value "?ENER" to "323.231" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 63.60359137 39.28738446 -71.61372452 + 649.05550414 515.36546491 + 1031.01269592 + + Transpose of the rotation matrix + 0.821548 0.569476 -0.027475 + -0.540306 0.793040 0.281350 + 0.182011 -0.216297 0.959212 + CENTER OF ATOMS BEFORE TRANSLATION 5.76089 2.78768 -0.41716 + AXIS OF ROTATION IS 0.403227 0.169740 0.899220 ANGLE IS 38.10 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 87 atoms have been selected out of 87 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -36.976633 1.009628 2.107301 37.050390 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT3" + RDCMND substituted energy or value "?RDIP" to "37.0504" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 6 + Number of bonds = 88 Number of angles = 92 + Number of dihedrals = 128 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 87 atoms have been selected out of 87 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 92 angles deleted + DELTIC: 128 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 89 + Number of dihedrals = 125 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 29 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 840 840 837 + : Ran out of space. RESIZING + with mode 5 found 556 exclusions and 360 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3630 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3630 atom pairs and 916 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3630 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 323.44646 -0.21505 39.31714 +ENER INTERN> 19.94442 38.13739 108.08595 44.41999 0.00184 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 112.83892 5.34795 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CTER" + RDCMND substituted energy or value "?ENER" to "323.446" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 94.92337109 5.29298881 -180.54104298 + 571.25922354 522.24642862 + 1325.52563456 + + Transpose of the rotation matrix + 0.888629 0.446589 -0.104387 + -0.395522 0.861463 0.318504 + 0.232166 -0.241744 0.942156 + CENTER OF ATOMS BEFORE TRANSLATION 4.88674 2.39317 -0.24587 + AXIS OF ROTATION IS 0.525574 0.315724 0.789994 ANGLE IS 32.21 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -32.703785 -18.374294 -1.180854 37.530609 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CTER" + RDCMND substituted energy or value "?RDIP" to "37.5306" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 89 + Number of dihedrals = 125 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 89 angles deleted + DELTIC: 125 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 7 + Number of bonds = 94 Number of angles = 90 + Number of dihedrals = 127 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 29 + Number of true-bonds = 94 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 848 848 846 + : Ran out of space. RESIZING + with mode 5 found 562 exclusions and 366 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3716 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3716 atom pairs and 928 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3716 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 291.22979 32.21667 37.22880 +ENER INTERN> 19.78114 33.02416 117.22378 35.56566 0.00184 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 107.48913 -16.52593 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CNEU" + RDCMND substituted energy or value "?ENER" to "291.23" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 95.19692690 6.29588314 -179.41789054 + 588.47445602 541.83912911 + 1344.61257926 + + Transpose of the rotation matrix + 0.885184 0.454200 -0.100757 + -0.402821 0.856588 0.322479 + 0.232777 -0.244866 0.941199 + CENTER OF ATOMS BEFORE TRANSLATION 4.93640 2.43751 -0.24322 + AXIS OF ROTATION IS 0.525047 0.308668 0.793127 ANGLE IS 32.70 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 93 atoms have been selected out of 93 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -9.504739 -4.834480 -1.879174 10.827906 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CNEU" + RDCMND substituted energy or value "?RDIP" to "10.8279" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 7 + Number of bonds = 94 Number of angles = 90 + Number of dihedrals = 127 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 93 atoms have been selected out of 93 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 127 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 7 + Number of bonds = 98 Number of angles = 96 + Number of dihedrals = 130 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 30 + Number of true-bonds = 98 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 883 883 882 + : Ran out of space. RESIZING + with mode 5 found 590 exclusions and 378 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4066 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4066 atom pairs and 968 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4066 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 540.72618 -249.49639 135.91278 +ENER INTERN> 19.78114 32.88431 97.68821 36.44594 0.00184 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 344.18670 15.06803 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT1" + RDCMND substituted energy or value "?ENER" to "540.726" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 97.06897392 11.52859904 -175.76320017 + 710.11387443 625.62426078 + 1405.19068099 + + Transpose of the rotation matrix + 0.861635 0.500144 -0.086258 + -0.451544 0.833034 0.319628 + 0.231716 -0.236454 0.943609 + CENTER OF ATOMS BEFORE TRANSLATION 5.09797 2.66885 -0.23319 + AXIS OF ROTATION IS 0.484734 0.277176 0.829582 ANGLE IS 35.00 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -7.986433 -3.025748 -2.216808 8.823407 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT1" + RDCMND substituted energy or value "?RDIP" to "8.82341" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 7 + Number of bonds = 98 Number of angles = 96 + Number of dihedrals = 130 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 98 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 130 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 92 + Number of dihedrals = 129 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 29 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 841 841 837 + : Ran out of space. RESIZING + with mode 5 found 544 exclusions and 362 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3642 atom pairs and 906 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 277.97535 262.75083 37.00217 +ENER INTERN> 25.88454 31.27195 96.77655 39.24371 0.00184 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 112.75161 -14.44485 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT2" + RDCMND substituted energy or value "?ENER" to "277.975" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 94.92337109 5.26088952 -181.07189654 + 571.05901142 513.42792983 + 1317.69203030 + + Transpose of the rotation matrix + 0.889314 0.444912 -0.105711 + -0.394995 0.863833 0.312685 + 0.230434 -0.236320 0.943956 + CENTER OF ATOMS BEFORE TRANSLATION 4.86328 2.39176 -0.24587 + AXIS OF ROTATION IS 0.518797 0.317650 0.793693 ANGLE IS 31.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -14.995116 -3.319680 -3.090358 15.666017 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT2" + RDCMND substituted energy or value "?RDIP" to "15.666" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 92 + Number of dihedrals = 129 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 92 angles deleted + DELTIC: 129 dihedrals deleted + DELTIC: 14 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 7 + Number of bonds = 97 Number of angles = 98 + Number of dihedrals = 135 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 30 + Number of true-bonds = 97 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "10" + Parameter: PATCHED -> "25" + Comparing "10" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 875 875 873 + : Ran out of space. RESIZING + with mode 5 found 565 exclusions and 377 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3995 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3995 atom pairs and 942 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3995 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 397.86157 -119.88622 51.00163 +ENER INTERN> 25.88454 44.14349 132.68976 38.76040 0.00184 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 172.40705 -8.41552 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT3" + RDCMND substituted energy or value "?ENER" to "397.862" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 96.35366010 10.16514633 -175.49102133 + 679.77881898 626.89040567 + 1430.80546854 + + Transpose of the rotation matrix + 0.869494 0.486271 -0.086720 + -0.436465 0.838578 0.326015 + 0.231253 -0.245618 0.941379 + CENTER OF ATOMS BEFORE TRANSLATION 5.11000 2.60857 -0.23562 + AXIS OF ROTATION IS 0.505393 0.281127 0.815810 ANGLE IS 34.44 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 96 atoms have been selected out of 96 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -8.407280 -6.682247 -0.977918 10.783836 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT3" + RDCMND substituted energy or value "?RDIP" to "10.7838" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 7 + Number of bonds = 97 Number of angles = 98 + Number of dihedrals = 135 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 96 atoms have been selected out of 96 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 97 bonds deleted + DELTIC: 98 angles deleted + DELTIC: 135 dihedrals deleted + DELTIC: 14 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "11" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "11" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "11" + Parameter: AA11 -> "HSE" + Parameter: RESIDUE <- "HSE" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "11" + Parameter: SPECIAL -> "2" + Comparing "11" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "HSE" + Parameter: PATCH <- "HSE" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-HSE-ALA-HSE-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSE-ALA-HSE-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 83 + Number of dihedrals = 118 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 26 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 762 762 756 + : Ran out of space. RESIZING + with mode 5 found 504 exclusions and 328 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2899 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2899 atom pairs and 832 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2899 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 118.54535 279.31622 29.71263 +ENER INTERN> 20.12146 40.49898 23.26134 39.06056 0.00013 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 36.91971 -39.03684 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSE-ALA-HSE-CTER" + RDCMND substituted energy or value "?ENER" to "118.545" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 70.37919169 36.84367103 -94.10707672 + 546.58250915 410.82595913 + 958.63714303 + + Transpose of the rotation matrix + 0.852198 0.520499 -0.053290 + -0.482540 0.821228 0.304532 + 0.202272 -0.233807 0.951010 + CENTER OF ATOMS BEFORE TRANSLATION 5.54237 2.49992 -0.48649 + AXIS OF ROTATION IS 0.461417 0.219046 0.859717 ANGLE IS 35.69 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -40.533649 -7.038553 -6.115371 41.592255 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSE-ALA-HSE-CTER" + RDCMND substituted energy or value "?RDIP" to "41.5923" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 83 + Number of dihedrals = 118 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 83 angles deleted + DELTIC: 118 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-HSE-ALA-HSE-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSE-ALA-HSE-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 6 + Number of bonds = 85 Number of angles = 84 + Number of dihedrals = 120 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 26 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 770 770 765 + : Ran out of space. RESIZING + with mode 5 found 510 exclusions and 334 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2976 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2976 atom pairs and 844 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2976 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 131.38784 -12.84250 25.92538 +ENER INTERN> 19.95818 35.43474 32.39911 30.22651 0.00013 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 34.13419 -18.48500 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSE-ALA-HSE-CNEU" + RDCMND substituted energy or value "?ENER" to "131.388" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 70.82680414 38.77716111 -92.22135740 + 562.98259260 427.14333246 + 971.81653444 + + Transpose of the rotation matrix + 0.847304 0.528830 -0.049136 + -0.490814 0.815011 0.307992 + 0.202921 -0.236846 0.950119 + CENTER OF ATOMS BEFORE TRANSLATION 5.58907 2.54781 -0.48070 + AXIS OF ROTATION IS 0.460463 0.213023 0.861740 ANGLE IS 36.27 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -19.628816 5.796461 -6.567616 21.494719 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSE-ALA-HSE-CNEU" + RDCMND substituted energy or value "?RDIP" to "21.4947" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 6 + Number of bonds = 85 Number of angles = 84 + Number of dihedrals = 120 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 120 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-HSE-ALA-HSE-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSE-ALA-HSE-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 6 + Number of bonds = 89 Number of angles = 90 + Number of dihedrals = 123 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 27 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 805 805 801 + : Ran out of space. RESIZING + with mode 5 found 538 exclusions and 346 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3290 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3290 atom pairs and 884 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3290 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 374.37170 -242.98386 138.27912 +ENER INTERN> 19.95818 35.29488 12.86354 31.04897 0.00013 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 264.43125 13.05475 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSE-ALA-HSE-CT1" + RDCMND substituted energy or value "?ENER" to "374.372" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 73.35425840 48.86639506 -86.33486869 + 679.29297676 493.95800911 + 1012.80741271 + + Transpose of the rotation matrix + 0.813558 0.580584 -0.032320 + -0.545297 0.781051 0.304319 + 0.201927 -0.229957 0.952022 + CENTER OF ATOMS BEFORE TRANSLATION 5.73485 2.79767 -0.45885 + AXIS OF ROTATION IS 0.421340 0.184731 0.887889 ANGLE IS 39.35 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -18.597681 7.607608 -6.839607 21.225684 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSE-ALA-HSE-CT1" + RDCMND substituted energy or value "?RDIP" to "21.2257" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 6 + Number of bonds = 89 Number of angles = 90 + Number of dihedrals = 123 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 123 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-HSE-ALA-HSE-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSE-ALA-HSE-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 86 + Number of dihedrals = 122 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 26 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 758 758 756 + : Ran out of space. RESIZING + with mode 5 found 492 exclusions and 330 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2911 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2911 atom pairs and 822 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2911 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 127.03164 247.34006 26.87282 +ENER INTERN> 26.06159 33.57221 11.95092 33.90589 0.00013 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 46.95193 -14.95102 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSE-ALA-HSE-CT2" + RDCMND substituted energy or value "?ENER" to "127.032" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 70.37919169 36.76714550 -95.15660173 + 546.21228070 402.35733793 + 953.79421501 + + Transpose of the rotation matrix + 0.853290 0.518550 -0.054787 + -0.481376 0.823762 0.299489 + 0.200432 -0.229178 0.952525 + CENTER OF ATOMS BEFORE TRANSLATION 5.51638 2.49803 -0.48649 + AXIS OF ROTATION IS 0.455938 0.220108 0.862365 ANGLE IS 35.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.697084 7.706410 -7.478570 26.930721 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSE-ALA-HSE-CT2" + RDCMND substituted energy or value "?RDIP" to "26.9307" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 86 + Number of dihedrals = 122 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 86 angles deleted + DELTIC: 122 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-HSE-ALA-HSE-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSE-ALA-HSE-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 6 + Number of bonds = 88 Number of angles = 92 + Number of dihedrals = 128 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 27 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 795 795 792 + : Ran out of space. RESIZING + with mode 5 found 513 exclusions and 345 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3228 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3228 atom pairs and 858 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3228 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 194.74944 -67.71780 31.97753 +ENER INTERN> 26.06159 46.44375 47.86413 33.37864 0.00013 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 56.91515 -11.35395 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSE-ALA-HSE-CT3" + RDCMND substituted energy or value "?ENER" to "194.749" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 72.48092618 46.26992187 -85.47394080 + 651.00283056 499.25903945 + 1036.42247796 + + Transpose of the rotation matrix + 0.825724 0.563047 -0.034044 + -0.527042 0.791614 0.309152 + 0.201016 -0.237332 0.950403 + CENTER OF ATOMS BEFORE TRANSLATION 5.75618 2.73337 -0.46412 + AXIS OF ROTATION IS 0.440056 0.189282 0.877794 ANGLE IS 38.38 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 87 atoms have been selected out of 87 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -19.436530 3.993869 -5.751559 20.659384 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSE-ALA-HSE-CT3" + RDCMND substituted energy or value "?RDIP" to "20.6594" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 6 + Number of bonds = 88 Number of angles = 92 + Number of dihedrals = 128 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 87 atoms have been selected out of 87 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 92 angles deleted + DELTIC: 128 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-HSE-ALA-HSE-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSE-ALA-HSE-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 89 + Number of dihedrals = 125 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 29 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 840 840 837 + : Ran out of space. RESIZING + with mode 5 found 558 exclusions and 364 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3628 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3628 atom pairs and 922 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3628 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 241.53496 -46.78552 37.61772 +ENER INTERN> 19.79301 38.36566 108.91280 45.57396 0.00013 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 75.49461 -41.27521 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSE-ALA-HSE-CTER" + RDCMND substituted energy or value "?ENER" to "241.535" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 105.21092374 11.46799035 -197.84084111 + 568.91633835 502.76309283 + 1332.41179326 + + Transpose of the rotation matrix + 0.893699 0.433727 -0.114816 + -0.375542 0.863158 0.337530 + 0.245500 -0.258532 0.934286 + CENTER OF ATOMS BEFORE TRANSLATION 4.88456 2.34117 -0.29028 + AXIS OF ROTATION IS 0.558254 0.337463 0.757939 ANGLE IS 32.27 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -15.373026 -13.761554 -8.564050 22.339499 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSE-ALA-HSE-CTER" + RDCMND substituted energy or value "?RDIP" to "22.3395" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 89 + Number of dihedrals = 125 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 89 angles deleted + DELTIC: 125 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-HSE-ALA-HSE-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSE-ALA-HSE-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 7 + Number of bonds = 94 Number of angles = 90 + Number of dihedrals = 127 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 29 + Number of true-bonds = 94 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 848 848 846 + : Ran out of space. RESIZING + with mode 5 found 564 exclusions and 370 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3714 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3714 atom pairs and 934 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3714 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 221.56874 19.96622 35.51165 +ENER INTERN> 19.62973 33.30141 118.05056 36.73991 0.00013 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 72.71149 -53.53449 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSE-ALA-HSE-CNEU" + RDCMND substituted energy or value "?ENER" to "221.569" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 105.50803494 12.66859064 -196.52546795 + 586.62332612 522.43544741 + 1351.14251620 + + Transpose of the rotation matrix + 0.890077 0.442164 -0.110696 + -0.383699 0.857924 0.341676 + 0.246045 -0.261644 0.933276 + CENTER OF ATOMS BEFORE TRANSLATION 4.93381 2.38613 -0.28716 + AXIS OF ROTATION IS 0.556982 0.329342 0.762433 ANGLE IS 32.79 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 93 atoms have been selected out of 93 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 7.520368 0.269001 -9.371602 12.018953 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSE-ALA-HSE-CNEU" + RDCMND substituted energy or value "?RDIP" to "12.019" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 7 + Number of bonds = 94 Number of angles = 90 + Number of dihedrals = 127 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 93 atoms have been selected out of 93 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 127 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-HSE-ALA-HSE-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSE-ALA-HSE-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 7 + Number of bonds = 98 Number of angles = 96 + Number of dihedrals = 130 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 30 + Number of true-bonds = 98 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 883 883 882 + : Ran out of space. RESIZING + with mode 5 found 592 exclusions and 382 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4064 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4064 atom pairs and 974 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4064 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 465.89182 -244.32309 134.94876 +ENER INTERN> 19.62973 33.16155 98.51500 37.56237 0.00013 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 303.00757 -20.65452 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSE-ALA-HSE-CT1" + RDCMND substituted energy or value "?ENER" to "465.892" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 107.46944676 18.90030046 -192.27189043 + 710.36048384 605.75621155 + 1410.07266633 + + Transpose of the rotation matrix + 0.865930 0.491195 -0.094299 + -0.435985 0.833676 0.338970 + 0.245115 -0.252412 0.936059 + CENTER OF ATOMS BEFORE TRANSLATION 5.09309 2.61948 -0.27532 + AXIS OF ROTATION IS 0.513838 0.294909 0.805605 ANGLE IS 35.13 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 9.282938 1.236859 -9.647621 13.445421 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSE-ALA-HSE-CT1" + RDCMND substituted energy or value "?RDIP" to "13.4454" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 7 + Number of bonds = 98 Number of angles = 96 + Number of dihedrals = 130 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 98 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 130 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-HSE-ALA-HSE-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSE-ALA-HSE-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 92 + Number of dihedrals = 129 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 29 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 841 841 837 + : Ran out of space. RESIZING + with mode 5 found 546 exclusions and 366 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3640 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3640 atom pairs and 912 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3640 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 213.52759 252.36423 35.99119 +ENER INTERN> 25.73313 31.43888 97.60237 40.41929 0.00013 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 85.52856 -53.68477 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSE-ALA-HSE-CT2" + RDCMND substituted energy or value "?ENER" to "213.528" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 105.21092374 11.42232934 -198.46706837 + 568.49619581 493.84891839 + 1324.73609887 + + Transpose of the rotation matrix + 0.894513 0.431640 -0.116336 + -0.374643 0.865800 0.331713 + 0.243904 -0.253137 0.936180 + CENTER OF ATOMS BEFORE TRANSLATION 4.86111 2.33946 -0.29028 + AXIS OF ROTATION IS 0.552159 0.340105 0.761216 ANGLE IS 31.98 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.940403 1.866430 -10.553778 10.891784 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSE-ALA-HSE-CT2" + RDCMND substituted energy or value "?RDIP" to "10.8918" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 92 + Number of dihedrals = 129 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 92 angles deleted + DELTIC: 129 dihedrals deleted + DELTIC: 14 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSE" + Parameter: PATCH -> "HSE" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-HSE-ALA-HSE-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSE-ALA-HSE-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSE" + Parameter: RESIDUE -> "HSE" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSE ALA HSE + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 2 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: HSE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 7 + Number of bonds = 97 Number of angles = 98 + Number of dihedrals = 135 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 30 + Number of true-bonds = 97 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "11" + Parameter: PATCHED -> "25" + Comparing "11" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 875 875 873 + : Ran out of space. RESIZING + with mode 5 found 567 exclusions and 381 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3993 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3993 atom pairs and 948 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3993 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 285.58072 -72.05313 39.49570 +ENER INTERN> 25.73313 44.31043 133.51558 39.89204 0.00013 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 95.49171 -45.75229 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSE-ALA-HSE-CT3" + RDCMND substituted energy or value "?ENER" to "285.581" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 106.73248990 17.29447481 -191.93440252 + 680.05745296 607.63683249 + 1435.68097525 + + Transpose of the rotation matrix + 0.873571 0.477378 -0.094785 + -0.420806 0.838691 0.345717 + 0.244533 -0.262122 0.933539 + CENTER OF ATOMS BEFORE TRANSLATION 5.10573 2.55935 -0.27818 + AXIS OF ROTATION IS 0.534895 0.298598 0.790396 ANGLE IS 34.62 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 96 atoms have been selected out of 96 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 8.840564 -2.207654 -8.447075 12.425071 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSE-ALA-HSE-CT3" + RDCMND substituted energy or value "?RDIP" to "12.4251" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 7 + Number of bonds = 97 Number of angles = 98 + Number of dihedrals = 135 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 96 atoms have been selected out of 96 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 97 bonds deleted + DELTIC: 98 angles deleted + DELTIC: 135 dihedrals deleted + DELTIC: 14 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "12" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "12" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "12" + Parameter: AA12 -> "HSP" + Parameter: RESIDUE <- "HSP" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "12" + Parameter: SPECIAL -> "2" + Comparing "12" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "HSP" + Parameter: PATCH <- "HSP" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-HSP-ALA-HSP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSP-ALA-HSP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 87 + Number of dihedrals = 126 Number of impropers = 13 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 26 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 762 762 756 + : Ran out of space. RESIZING + with mode 5 found 490 exclusions and 330 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2913 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2913 atom pairs and 820 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2913 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 316.93368 -31.35296 44.74385 +ENER INTERN> 21.38329 42.95116 23.74157 39.43900 0.00895 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 98.59997 93.08975 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSP-ALA-HSP-CTER" + RDCMND substituted energy or value "?ENER" to "316.934" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 56.47754786 30.89018936 -66.04629272 + 440.62806217 375.85986835 + 1034.87129679 + + Transpose of the rotation matrix + 0.900349 0.433359 -0.039647 + -0.410949 0.876673 0.250130 + 0.143154 -0.208912 0.967400 + CENTER OF ATOMS BEFORE TRANSLATION 5.80545 2.18058 -0.38385 + AXIS OF ROTATION IS 0.469243 0.186863 0.863072 ANGLE IS 29.28 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : -34.089426 -29.082493 1.182525 44.824979 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSP-ALA-HSP-CTER" + RDCMND substituted energy or value "?RDIP" to "44.825" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 87 + Number of dihedrals = 126 Number of impropers = 13 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 87 angles deleted + DELTIC: 126 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-HSP-ALA-HSP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSP-ALA-HSP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 6 + Number of bonds = 85 Number of angles = 88 + Number of dihedrals = 128 Number of impropers = 13 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 26 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 770 770 765 + : Ran out of space. RESIZING + with mode 5 found 496 exclusions and 336 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2990 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2990 atom pairs and 832 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2990 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 442.59778 -125.66410 41.59573 +ENER INTERN> 21.27641 39.23580 32.93683 30.63635 0.00895 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 95.50046 225.28298 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSP-ALA-HSP-CNEU" + RDCMND substituted energy or value "?ENER" to "442.598" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 56.83688908 32.15251683 -64.37046665 + 451.62777337 391.52030547 + 1052.49523897 + + Transpose of the rotation matrix + 0.897211 0.440079 -0.036632 + -0.417631 0.872544 0.253477 + 0.143513 -0.212124 0.966647 + CENTER OF ATOMS BEFORE TRANSLATION 5.85805 2.22020 -0.37928 + AXIS OF ROTATION IS 0.469156 0.181521 0.864258 ANGLE IS 29.75 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -13.490071 -17.639066 1.009580 22.229213 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSP-ALA-HSP-CNEU" + RDCMND substituted energy or value "?RDIP" to "22.2292" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 6 + Number of bonds = 85 Number of angles = 88 + Number of dihedrals = 128 Number of impropers = 13 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 88 angles deleted + DELTIC: 128 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-HSP-ALA-HSP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSP-ALA-HSP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 6 + Number of bonds = 89 Number of angles = 94 + Number of dihedrals = 131 Number of impropers = 13 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 27 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 805 805 801 + : Ran out of space. RESIZING + with mode 5 found 524 exclusions and 348 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3304 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3304 atom pairs and 872 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3304 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 685.65184 -243.05406 141.39771 +ENER INTERN> 21.27641 39.09595 13.31748 31.37476 0.00895 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 329.14107 253.71722 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSP-ALA-HSP-CT1" + RDCMND substituted energy or value "?ENER" to "685.652" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 59.03132004 39.26404876 -58.57948113 + 544.85573161 465.89008629 + 1115.05327324 + + Transpose of the rotation matrix + 0.872769 0.487531 -0.024269 + -0.466659 0.847924 0.251506 + 0.143195 -0.208181 0.967551 + CENTER OF ATOMS BEFORE TRANSLATION 6.03982 2.44341 -0.36204 + AXIS OF ROTATION IS 0.428692 0.156172 0.889850 ANGLE IS 32.42 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -16.334050 -17.470082 0.773055 23.929115 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSP-ALA-HSP-CT1" + RDCMND substituted energy or value "?RDIP" to "23.9291" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 6 + Number of bonds = 89 Number of angles = 94 + Number of dihedrals = 131 Number of impropers = 13 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 94 angles deleted + DELTIC: 131 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-HSP-ALA-HSP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSP-ALA-HSP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 90 + Number of dihedrals = 130 Number of impropers = 14 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 26 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 758 758 756 + : Ran out of space. RESIZING + with mode 5 found 478 exclusions and 332 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2925 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2925 atom pairs and 810 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2925 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 414.12080 271.53104 39.83345 +ENER INTERN> 27.78143 37.04568 12.38737 33.91752 0.00895 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 97.47051 215.96935 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSP-ALA-HSP-CT2" + RDCMND substituted energy or value "?ENER" to "414.121" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 56.47754786 30.98849421 -66.87073980 + 443.32457953 368.51880296 + 1027.87727504 + + Transpose of the rotation matrix + 0.900711 0.432512 -0.040672 + -0.410665 0.878254 0.244997 + 0.141684 -0.203969 0.968670 + CENTER OF ATOMS BEFORE TRANSLATION 5.77958 2.18366 -0.38385 + AXIS OF ROTATION IS 0.461659 0.187511 0.867013 ANGLE IS 29.09 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -17.284107 -15.127755 0.070313 22.969420 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSP-ALA-HSP-CT2" + RDCMND substituted energy or value "?RDIP" to "22.9694" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 90 + Number of dihedrals = 130 Number of impropers = 14 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 130 dihedrals deleted + DELTIC: 14 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-HSP-ALA-HSP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSP-ALA-HSP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 6 + Number of bonds = 88 Number of angles = 96 + Number of dihedrals = 136 Number of impropers = 14 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 27 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 795 795 792 + : Ran out of space. RESIZING + with mode 5 found 499 exclusions and 347 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3242 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3242 atom pairs and 846 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3242 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 535.08045 -120.95964 50.76191 +ENER INTERN> 27.78143 49.91723 47.55162 33.32625 0.00895 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 137.95771 243.09726 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSP-ALA-HSP-CT3" + RDCMND substituted energy or value "?ENER" to "535.08" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 58.23837275 37.08005111 -58.23402473 + 515.04507071 462.32863306 + 1138.44808246 + + Transpose of the rotation matrix + 0.883255 0.468190 -0.025679 + -0.447063 0.857384 0.255005 + 0.141407 -0.213754 0.966599 + CENTER OF ATOMS BEFORE TRANSLATION 6.05066 2.37486 -0.36620 + AXIS OF ROTATION IS 0.449953 0.160383 0.878533 ANGLE IS 31.39 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 87 atoms have been selected out of 87 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -16.659638 -20.365293 1.630419 26.361847 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSP-ALA-HSP-CT3" + RDCMND substituted energy or value "?RDIP" to "26.3618" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 6 + Number of bonds = 88 Number of angles = 96 + Number of dihedrals = 136 Number of impropers = 14 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 87 atoms have been selected out of 87 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 136 dihedrals deleted + DELTIC: 14 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-HSP-ALA-HSP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSP-ALA-HSP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 93 + Number of dihedrals = 133 Number of impropers = 15 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 29 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 840 840 837 + : Ran out of space. RESIZING + with mode 5 found 544 exclusions and 366 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3642 atom pairs and 910 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 335.06293 200.01752 49.49882 +ENER INTERN> 21.09800 38.69594 109.38185 45.74335 0.00895 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 130.36414 -4.89929 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSP-ALA-HSP-CTER" + RDCMND substituted energy or value "?ENER" to "335.063" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 88.05158036 11.80160712 -168.24106872 + 455.37432094 453.14540428 + 1437.93564355 + + Transpose of the rotation matrix + 0.928779 0.357279 -0.098597 + -0.314837 0.900897 0.298768 + 0.195569 -0.246448 0.949219 + CENTER OF ATOMS BEFORE TRANSLATION 5.12190 2.05307 -0.19768 + AXIS OF ROTATION IS 0.596467 0.321818 0.735296 ANGLE IS 27.20 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -0.099601 -35.192438 -0.737373 35.200303 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSP-ALA-HSP-CTER" + RDCMND substituted energy or value "?RDIP" to "35.2003" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 93 + Number of dihedrals = 133 Number of impropers = 15 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 93 angles deleted + DELTIC: 133 dihedrals deleted + DELTIC: 15 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-HSP-ALA-HSP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSP-ALA-HSP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 7 + Number of bonds = 94 Number of angles = 94 + Number of dihedrals = 135 Number of impropers = 15 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 29 + Number of true-bonds = 94 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 848 848 846 + : Ran out of space. RESIZING + with mode 5 found 550 exclusions and 372 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3728 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3728 atom pairs and 922 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3728 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 428.72817 -93.66524 47.38118 +ENER INTERN> 20.99112 34.98059 118.57710 36.94070 0.00895 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 127.26663 95.29309 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSP-ALA-HSP-CNEU" + RDCMND substituted energy or value "?ENER" to "428.728" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 88.30399173 12.47737951 -167.24336838 + 467.24251971 471.71690068 + 1462.01982318 + + Transpose of the rotation matrix + 0.926492 0.364017 -0.095420 + -0.321284 0.897175 0.303074 + 0.195932 -0.250139 0.948178 + CENTER OF ATOMS BEFORE TRANSLATION 5.17676 2.09022 -0.19555 + AXIS OF ROTATION IS 0.596348 0.314069 0.738735 ANGLE IS 27.63 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 93 atoms have been selected out of 93 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 22.954438 -22.767516 -1.249643 32.354716 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSP-ALA-HSP-CNEU" + RDCMND substituted energy or value "?RDIP" to "32.3547" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 7 + Number of bonds = 94 Number of angles = 94 + Number of dihedrals = 135 Number of impropers = 15 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 93 atoms have been selected out of 93 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 94 angles deleted + DELTIC: 135 dihedrals deleted + DELTIC: 15 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-HSP-ALA-HSP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSP-ALA-HSP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 7 + Number of bonds = 98 Number of angles = 100 + Number of dihedrals = 138 Number of impropers = 15 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 30 + Number of true-bonds = 98 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 883 883 882 + : Ran out of space. RESIZING + with mode 5 found 578 exclusions and 384 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4078 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4078 atom pairs and 962 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4078 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 673.12288 -244.39471 138.05043 +ENER INTERN> 20.99112 34.84073 98.95776 37.67911 0.00895 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 360.90641 125.06881 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSP-ALA-HSP-CT1" + RDCMND substituted energy or value "?ENER" to "673.123" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 90.09582068 16.25765517 -163.73349652 + 565.83767264 561.58156880 + 1547.52409208 + + Transpose of the rotation matrix + 0.909279 0.407929 -0.082499 + -0.367348 0.879820 0.301615 + 0.195622 -0.243947 0.949854 + CENTER OF ATOMS BEFORE TRANSLATION 5.36976 2.29809 -0.18749 + AXIS OF ROTATION IS 0.552217 0.281514 0.784733 ANGLE IS 29.60 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 21.174282 -23.798746 -1.503353 31.890290 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSP-ALA-HSP-CT1" + RDCMND substituted energy or value "?RDIP" to "31.8903" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 7 + Number of bonds = 98 Number of angles = 100 + Number of dihedrals = 138 Number of impropers = 15 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 98 bonds deleted + DELTIC: 100 angles deleted + DELTIC: 138 dihedrals deleted + DELTIC: 15 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-HSP-ALA-HSP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSP-ALA-HSP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 96 + Number of dihedrals = 137 Number of impropers = 16 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 29 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 841 841 837 + : Ran out of space. RESIZING + with mode 5 found 532 exclusions and 368 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3654 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3654 atom pairs and 900 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3654 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 396.99659 276.12629 45.86953 +ENER INTERN> 27.49613 32.79047 98.02765 40.22186 0.00895 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 129.23619 82.72535 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSP-ALA-HSP-CT2" + RDCMND substituted energy or value "?ENER" to "396.997" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 88.05158036 11.85223263 -168.66564659 + 458.13622729 445.70487755 + 1428.01073462 + + Transpose of the rotation matrix + 0.929042 0.356282 -0.099723 + -0.314948 0.903030 0.292139 + 0.194136 -0.240002 0.951163 + CENTER OF ATOMS BEFORE TRANSLATION 5.09856 2.05585 -0.19768 + AXIS OF ROTATION IS 0.587624 0.324498 0.741215 ANGLE IS 26.92 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 18.593784 -20.407480 -2.564202 27.726687 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSP-ALA-HSP-CT2" + RDCMND substituted energy or value "?RDIP" to "27.7267" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 96 + Number of dihedrals = 137 Number of impropers = 16 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 7 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 137 dihedrals deleted + DELTIC: 16 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 7 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSP" + Parameter: PATCH -> "HSP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-HSP-ALA-HSP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSP-ALA-HSP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSP" + Parameter: RESIDUE -> "HSP" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSP ALA HSP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 2 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: HSP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 7 + Number of bonds = 97 Number of angles = 102 + Number of dihedrals = 143 Number of impropers = 16 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 30 + Number of true-bonds = 97 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "12" + Parameter: PATCHED -> "25" + Comparing "12" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 875 875 873 + : Ran out of space. RESIZING + with mode 5 found 553 exclusions and 383 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4007 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4007 atom pairs and 936 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4007 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 521.70594 -124.70934 54.80506 +ENER INTERN> 27.49613 45.66201 133.19190 39.63060 0.00895 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 169.72318 113.60317 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSP-ALA-HSP-CT3" + RDCMND substituted energy or value "?ENER" to "521.706" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 89.39993467 15.10031730 -163.68172417 + 534.29252694 554.01634318 + 1571.74358043 + + Transpose of the rotation matrix + 0.915992 0.392514 -0.083019 + -0.351081 0.884367 0.307632 + 0.194169 -0.252642 0.947877 + CENTER OF ATOMS BEFORE TRANSLATION 5.37261 2.23445 -0.18944 + AXIS OF ROTATION IS 0.576753 0.285342 0.765465 ANGLE IS 29.06 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 96 atoms have been selected out of 96 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 21.031169 -26.415042 -0.487434 33.768360 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSP-ALA-HSP-CT3" + RDCMND substituted energy or value "?RDIP" to "33.7684" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 7 + Number of bonds = 97 Number of angles = 102 + Number of dihedrals = 143 Number of impropers = 16 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 96 atoms have been selected out of 96 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 97 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 143 dihedrals deleted + DELTIC: 16 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 8 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "13" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "13" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "13" + Parameter: AA13 -> "ILE" + Parameter: RESIDUE <- "ILE" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "13" + Parameter: SPECIAL -> "2" + Comparing "13" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "ILE" + Parameter: PATCH <- "ILE" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-ILE-ALA-ILE-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ILE-ALA-ILE-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 12 + Number of bonds = 80 Number of angles = 93 + Number of dihedrals = 128 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 22 + Number of true-bonds = 80 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 731 731 720 + : Ran out of space. RESIZING + with mode 5 found 458 exclusions and 340 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2782 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2782 atom pairs and 798 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2782 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 187.36826 334.33767 28.10046 +ENER INTERN> 22.08066 43.39681 22.45949 30.33173 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 42.21391 29.16567 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ILE-ALA-ILE-CTER" + RDCMND substituted energy or value "?ENER" to "187.368" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 131.93796977 78.65547676 -73.32546932 + 541.98197361 422.00426393 + 781.56692268 + + Transpose of the rotation matrix + 0.798631 0.601709 -0.011596 + -0.497011 0.670289 0.551084 + 0.339365 -0.434349 0.834369 + CENTER OF ATOMS BEFORE TRANSLATION 4.91211 2.53845 -0.74249 + AXIS OF ROTATION IS 0.649572 0.231344 0.724248 ANGLE IS 49.33 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 81 atoms have been selected out of 81 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -48.230203 -6.424545 3.364563 48.772406 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ILE-ALA-ILE-CTER" + RDCMND substituted energy or value "?RDIP" to "48.7724" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 12 + Number of bonds = 80 Number of angles = 93 + Number of dihedrals = 128 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 81 atoms have been selected out of 81 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 80 bonds deleted + DELTIC: 93 angles deleted + DELTIC: 128 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-ILE-ALA-ILE-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ILE-ALA-ILE-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 12 + Number of bonds = 81 Number of angles = 94 + Number of dihedrals = 130 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 81 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 737 737 729 + : Ran out of space. RESIZING + with mode 5 found 464 exclusions and 346 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2857 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2857 atom pairs and 810 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2857 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 197.55510 -10.18684 24.14872 +ENER INTERN> 21.94017 38.69649 31.62060 21.51125 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 40.29925 45.76734 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ILE-ALA-ILE-CNEU" + RDCMND substituted energy or value "?ENER" to "197.555" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 132.69629493 81.74321840 -70.10622442 + 559.94942180 440.90165680 + 798.52592369 + + Transpose of the rotation matrix + 0.794510 0.607221 -0.006044 + -0.502736 0.663315 0.554319 + 0.340603 -0.437374 0.832282 + CENTER OF ATOMS BEFORE TRANSLATION 4.96563 2.58979 -0.73344 + AXIS OF ROTATION IS 0.648897 0.226822 0.726281 ANGLE IS 49.83 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 82 atoms have been selected out of 82 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.052149 3.665226 1.408056 24.370523 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ILE-ALA-ILE-CNEU" + RDCMND substituted energy or value "?RDIP" to "24.3705" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 12 + Number of bonds = 81 Number of angles = 94 + Number of dihedrals = 130 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 82 atoms have been selected out of 82 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 81 bonds deleted + DELTIC: 94 angles deleted + DELTIC: 130 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-ILE-ALA-ILE-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ILE-ALA-ILE-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 12 + Number of bonds = 85 Number of angles = 100 + Number of dihedrals = 133 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 23 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 31 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 768 768 765 + : Ran out of space. RESIZING + with mode 5 found 492 exclusions and 358 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3163 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3163 atom pairs and 850 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3163 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 438.75167 -241.19658 138.10981 +ENER INTERN> 21.94017 38.55663 12.05108 22.29420 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 272.61694 73.57265 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ILE-ALA-ILE-CT1" + RDCMND substituted energy or value "?ENER" to "438.752" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 136.39310523 97.57106126 -59.98938176 + 682.96057223 518.47764997 + 850.16219633 + + Transpose of the rotation matrix + 0.760145 0.649572 0.015385 + -0.554028 0.635603 0.537644 + 0.339460 -0.417211 0.843032 + CENTER OF ATOMS BEFORE TRANSLATION 5.13385 2.85297 -0.69932 + AXIS OF ROTATION IS 0.608123 0.206395 0.766543 ANGLE IS 51.73 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 86 atoms have been selected out of 86 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -23.332856 5.436708 0.736714 23.969204 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ILE-ALA-ILE-CT1" + RDCMND substituted energy or value "?RDIP" to "23.9692" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 12 + Number of bonds = 85 Number of angles = 100 + Number of dihedrals = 133 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 86 atoms have been selected out of 86 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 100 angles deleted + DELTIC: 133 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-ILE-ALA-ILE-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ILE-ALA-ILE-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 12 + Number of bonds = 80 Number of angles = 96 + Number of dihedrals = 132 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 80 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 721 721 720 + : Ran out of space. RESIZING + with mode 5 found 446 exclusions and 342 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2794 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2794 atom pairs and 788 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2794 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 190.83293 247.91874 24.54137 +ENER INTERN> 28.20620 36.64046 11.13025 23.05256 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 51.77097 50.49250 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ILE-ALA-ILE-CT2" + RDCMND substituted energy or value "?ENER" to "190.833" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 131.93796977 78.48563866 -74.92251632 + 541.01817060 413.13942285 + 774.69940272 + + Transpose of the rotation matrix + 0.798466 0.601896 -0.013170 + -0.499609 0.674662 0.543343 + 0.335921 -0.427261 0.839407 + CENTER OF ATOMS BEFORE TRANSLATION 4.88555 2.53563 -0.74249 + AXIS OF ROTATION IS 0.643187 0.231331 0.729929 ANGLE IS 48.98 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 81 atoms have been selected out of 81 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -28.896583 5.592829 -0.032082 29.432861 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ILE-ALA-ILE-CT2" + RDCMND substituted energy or value "?RDIP" to "29.4329" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 12 + Number of bonds = 80 Number of angles = 96 + Number of dihedrals = 132 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 81 atoms have been selected out of 81 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 80 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 132 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-ILE-ALA-ILE-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ILE-ALA-ILE-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 12 + Number of bonds = 84 Number of angles = 102 + Number of dihedrals = 138 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 23 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 29 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 761 761 756 + : Ran out of space. RESIZING + with mode 5 found 467 exclusions and 357 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3103 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3103 atom pairs and 824 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3103 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 276.57184 -85.73891 36.77234 +ENER INTERN> 28.20620 49.51200 46.73792 22.49635 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 79.12192 55.05745 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ILE-ALA-ILE-CT3" + RDCMND substituted energy or value "?ENER" to "276.572" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 135.23793081 93.62356917 -58.94452041 + 654.51609682 522.41565606 + 875.36950273 + + Transpose of the rotation matrix + 0.775999 0.630630 0.011429 + -0.532532 0.645362 0.547647 + 0.337987 -0.431060 0.836631 + CENTER OF ATOMS BEFORE TRANSLATION 5.15122 2.78733 -0.70755 + AXIS OF ROTATION IS 0.629468 0.210030 0.748102 ANGLE IS 51.02 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 85 atoms have been selected out of 85 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.234499 2.156179 2.773957 24.487852 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ILE-ALA-ILE-CT3" + RDCMND substituted energy or value "?RDIP" to "24.4879" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 12 + Number of bonds = 84 Number of angles = 102 + Number of dihedrals = 138 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 29 + + CHARMM> delete atom sele all end + SELRPN> 85 atoms have been selected out of 85 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 138 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-ILE-ALA-ILE-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ILE-ALA-ILE-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 13 + Number of bonds = 89 Number of angles = 99 + Number of dihedrals = 135 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 25 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 809 809 801 + : Ran out of space. RESIZING + with mode 5 found 512 exclusions and 376 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3493 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3493 atom pairs and 888 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3493 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 304.41128 -27.83944 36.85496 +ENER INTERN> 21.79128 41.52584 108.11747 39.45626 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 80.91183 17.93858 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ILE-ALA-ILE-CTER" + RDCMND substituted energy or value "?ENER" to "304.411" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 175.53998759 49.27266090 -179.19236113 + 565.28915109 507.34511088 + 1089.01706473 + + Transpose of the rotation matrix + 0.855654 0.507022 -0.103851 + -0.364187 0.732429 0.575253 + 0.367729 -0.454396 0.811357 + CENTER OF ATOMS BEFORE TRANSLATION 4.30270 2.37232 -0.51632 + AXIS OF ROTATION IS 0.720621 0.330045 0.609734 ANGLE IS 45.60 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -25.347003 -16.780596 0.837153 30.409863 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ILE-ALA-ILE-CTER" + RDCMND substituted energy or value "?RDIP" to "30.4099" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 13 + Number of bonds = 89 Number of angles = 99 + Number of dihedrals = 135 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 99 angles deleted + DELTIC: 135 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-ILE-ALA-ILE-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ILE-ALA-ILE-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 91 Number of groups = 13 + Number of bonds = 90 Number of angles = 100 + Number of dihedrals = 137 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 25 + Number of true-bonds = 90 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 815 815 810 + : Ran out of space. RESIZING + with mode 5 found 518 exclusions and 382 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3577 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3577 atom pairs and 900 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3577 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 281.72760 22.68367 34.77029 +ENER INTERN> 21.65079 36.82552 117.27859 30.63577 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 78.99963 1.66729 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ILE-ALA-ILE-CNEU" + RDCMND substituted energy or value "?ENER" to "281.728" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 176.01739719 51.50728653 -176.63982294 + 584.68871607 529.62348949 + 1111.65750224 + + Transpose of the rotation matrix + 0.851904 0.514602 -0.097180 + -0.372162 0.725440 0.578992 + 0.368449 -0.457079 0.809521 + CENTER OF ATOMS BEFORE TRANSLATION 4.35763 2.42041 -0.51064 + AXIS OF ROTATION IS 0.718973 0.323120 0.615363 ANGLE IS 46.10 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 91 atoms have been selected out of 91 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.484290 -4.639382 -1.393819 4.868381 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ILE-ALA-ILE-CNEU" + RDCMND substituted energy or value "?RDIP" to "4.86838" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 91 Number of groups = 13 + Number of bonds = 90 Number of angles = 100 + Number of dihedrals = 137 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 91 atoms have been selected out of 91 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 90 bonds deleted + DELTIC: 100 angles deleted + DELTIC: 137 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-ILE-ALA-ILE-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ILE-ALA-ILE-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 95 Number of groups = 13 + Number of bonds = 94 Number of angles = 106 + Number of dihedrals = 140 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 26 + Number of true-bonds = 94 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 857 857 846 + : Ran out of space. RESIZING + with mode 5 found 546 exclusions and 394 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3919 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3919 atom pairs and 940 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3919 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 524.26101 -242.53341 134.89265 +ENER INTERN> 21.65079 36.68567 97.70906 31.41873 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 311.31631 30.81044 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ILE-ALA-ILE-CT1" + RDCMND substituted energy or value "?ENER" to "524.261" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 178.66168320 62.90951110 -168.37397680 + 715.71860489 623.48359871 + 1181.79156390 + + Transpose of the rotation matrix + 0.823985 0.562064 -0.071638 + -0.430327 0.703024 0.566195 + 0.368601 -0.435708 0.821153 + CENTER OF ATOMS BEFORE TRANSLATION 4.53551 2.66578 -0.48914 + AXIS OF ROTATION IS 0.678192 0.298000 0.671753 ANGLE IS 47.62 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 95 atoms have been selected out of 95 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 2.016998 -3.527528 -2.094364 4.571443 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ILE-ALA-ILE-CT1" + RDCMND substituted energy or value "?RDIP" to "4.57144" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 95 Number of groups = 13 + Number of bonds = 94 Number of angles = 106 + Number of dihedrals = 140 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 95 atoms have been selected out of 95 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 106 angles deleted + DELTIC: 140 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-ILE-ALA-ILE-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ILE-ALA-ILE-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 13 + Number of bonds = 89 Number of angles = 102 + Number of dihedrals = 139 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 25 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 804 804 801 + : Ran out of space. RESIZING + with mode 5 found 500 exclusions and 378 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3505 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3505 atom pairs and 878 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3505 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 271.28014 252.98087 34.83413 +ENER INTERN> 27.91683 34.76949 96.78823 32.17708 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 90.47065 2.66786 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ILE-ALA-ILE-CT2" + RDCMND substituted energy or value "?ENER" to "271.28" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 175.53998759 49.15455799 -180.30292410 + 564.24941057 497.98414375 + 1079.53367309 + + Transpose of the rotation matrix + 0.855963 0.506044 -0.106049 + -0.365464 0.737258 0.568231 + 0.365735 -0.447628 0.816007 + CENTER OF ATOMS BEFORE TRANSLATION 4.27880 2.36978 -0.51632 + AXIS OF ROTATION IS 0.715806 0.332434 0.614092 ANGLE IS 45.20 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -4.954220 -3.293756 -3.082488 6.700362 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ILE-ALA-ILE-CT2" + RDCMND substituted energy or value "?RDIP" to "6.70036" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 13 + Number of bonds = 89 Number of angles = 102 + Number of dihedrals = 139 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 139 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ILE" + Parameter: PATCH -> "ILE" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-ILE-ALA-ILE-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ILE-ALA-ILE-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ILE" + Parameter: RESIDUE -> "ILE" + + RESIDUE SEQUENCE -- 3 RESIDUES + ILE ALA ILE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ILE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ILE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ILE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ILE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 13 + Number of bonds = 93 Number of angles = 108 + Number of dihedrals = 145 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 26 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "13" + Parameter: PATCHED -> "25" + Comparing "13" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 839 839 837 + : Ran out of space. RESIZING + with mode 5 found 521 exclusions and 393 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3850 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3850 atom pairs and 914 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3850 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 361.40930 -90.12916 43.51641 +ENER INTERN> 27.91683 47.64104 132.39590 31.62088 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 117.82154 11.62313 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ILE-ALA-ILE-CT3" + RDCMND substituted energy or value "?ENER" to "361.409" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 177.75950882 60.05897072 -167.93974724 + 685.16292495 624.20478451 + 1208.42548158 + + Transpose of the rotation matrix + 0.834632 0.545832 -0.073868 + -0.410890 0.706305 0.576457 + 0.366823 -0.450778 0.813782 + CENTER OF ATOMS BEFORE TRANSLATION 4.54486 2.60444 -0.49435 + AXIS OF ROTATION IS 0.698180 0.299524 0.650254 ANGLE IS 47.36 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 94 atoms have been selected out of 94 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 1.511878 -6.562346 0.040598 6.734375 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ILE-ALA-ILE-CT3" + RDCMND substituted energy or value "?RDIP" to "6.73438" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 13 + Number of bonds = 93 Number of angles = 108 + Number of dihedrals = 145 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 94 atoms have been selected out of 94 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 108 angles deleted + DELTIC: 145 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "14" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "14" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "14" + Parameter: AA14 -> "LEU" + Parameter: RESIDUE <- "LEU" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "14" + Parameter: SPECIAL -> "2" + Comparing "14" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "LEU" + Parameter: PATCH <- "LEU" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-LEU-ALA-LEU-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LEU-ALA-LEU-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 12 + Number of bonds = 80 Number of angles = 93 + Number of dihedrals = 128 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 22 + Number of true-bonds = 80 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 727 727 720 + : Ran out of space. RESIZING + with mode 5 found 458 exclusions and 336 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2782 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2782 atom pairs and 794 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2782 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 21075.07135 -20713.66204 16527.11250 +ENER INTERN> 20.24058 42.88718 22.56044 26.52579 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 20960.43985 4.69749 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LEU-ALA-LEU-CTER" + RDCMND substituted energy or value "?ENER" to "21075.1" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 111.94399962 67.61336270 -101.38387205 + 556.85962731 439.11806292 + 789.52754601 + + Transpose of the rotation matrix + 0.794897 0.605491 -0.038986 + -0.495025 0.684347 0.535369 + 0.350841 -0.406264 0.843718 + CENTER OF ATOMS BEFORE TRANSLATION 5.13538 2.69778 -0.65749 + AXIS OF ROTATION IS 0.627787 0.259898 0.733714 ANGLE IS 48.59 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 81 atoms have been selected out of 81 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -47.731195 -6.916968 2.234320 48.281504 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LEU-ALA-LEU-CTER" + RDCMND substituted energy or value "?RDIP" to "48.2815" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 12 + Number of bonds = 80 Number of angles = 93 + Number of dihedrals = 128 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 81 atoms have been selected out of 81 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 80 bonds deleted + DELTIC: 93 angles deleted + DELTIC: 128 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-LEU-ALA-LEU-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LEU-ALA-LEU-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 12 + Number of bonds = 81 Number of angles = 94 + Number of dihedrals = 130 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 81 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 733 733 729 + : Ran out of space. RESIZING + with mode 5 found 464 exclusions and 342 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2857 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2857 atom pairs and 806 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2857 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 22562.28480 -1487.21345 16942.92711 +ENER INTERN> 20.09438 37.85730 31.71599 17.65377 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 22433.33125 23.91211 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LEU-ALA-LEU-CNEU" + RDCMND substituted energy or value "?ENER" to "22562.3" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 112.58477911 70.26994925 -98.70559490 + 573.85772928 456.40152021 + 804.24263611 + + Transpose of the rotation matrix + 0.790985 0.610917 -0.033525 + -0.500497 0.677590 0.538864 + 0.351917 -0.409454 0.841726 + CENTER OF ATOMS BEFORE TRANSLATION 5.18567 2.74766 -0.64947 + AXIS OF ROTATION IS 0.627610 0.255091 0.735550 ANGLE IS 49.07 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 82 atoms have been selected out of 82 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -25.002815 3.437918 0.560336 25.244287 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LEU-ALA-LEU-CNEU" + RDCMND substituted energy or value "?RDIP" to "25.2443" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 12 + Number of bonds = 81 Number of angles = 94 + Number of dihedrals = 130 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 82 atoms have been selected out of 82 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 81 bonds deleted + DELTIC: 94 angles deleted + DELTIC: 130 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-LEU-ALA-LEU-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LEU-ALA-LEU-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 12 + Number of bonds = 85 Number of angles = 100 + Number of dihedrals = 133 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 23 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 31 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 775 775 765 + : Ran out of space. RESIZING + with mode 5 found 492 exclusions and 354 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3163 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3163 atom pairs and 846 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3163 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 32949.05092 -10386.76612 22655.43019 +ENER INTERN> 20.09438 37.71744 12.15497 18.58133 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 32809.43633 53.34647 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LEU-ALA-LEU-CT1" + RDCMND substituted energy or value "?ENER" to "32949.1" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 115.83874293 83.97720877 -90.42954172 + 691.54185619 526.45018561 + 848.57428228 + + Transpose of the rotation matrix + 0.758291 0.651812 -0.011659 + -0.549551 0.648741 0.526430 + 0.350697 -0.392780 0.850138 + CENTER OF ATOMS BEFORE TRANSLATION 5.34107 3.00504 -0.61927 + AXIS OF ROTATION IS 0.590949 0.232954 0.772342 ANGLE IS 51.05 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 86 atoms have been selected out of 86 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.229022 5.266838 -0.044415 24.794900 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LEU-ALA-LEU-CT1" + RDCMND substituted energy or value "?RDIP" to "24.7949" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 12 + Number of bonds = 85 Number of angles = 100 + Number of dihedrals = 133 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 86 atoms have been selected out of 86 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 100 angles deleted + DELTIC: 133 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-LEU-ALA-LEU-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LEU-ALA-LEU-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 12 + Number of bonds = 80 Number of angles = 96 + Number of dihedrals = 132 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 80 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 722 722 720 + : Ran out of space. RESIZING + with mode 5 found 446 exclusions and 338 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2794 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2794 atom pairs and 784 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2794 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 18082.98967 14866.06125 15881.78771 +ENER INTERN> 26.31966 36.02608 11.23829 20.22515 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 17972.37814 27.26235 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LEU-ALA-LEU-CT2" + RDCMND substituted energy or value "?ENER" to "18083" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 111.94399962 67.45038521 -102.79669774 + 555.81612800 430.59914974 + 783.79752617 + + Transpose of the rotation matrix + 0.794999 0.605244 -0.040698 + -0.497109 0.688473 0.528098 + 0.347648 -0.399606 0.848207 + CENTER OF ATOMS BEFORE TRANSLATION 5.10886 2.69472 -0.65749 + AXIS OF ROTATION IS 0.621707 0.260253 0.738748 ANGLE IS 48.25 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 81 atoms have been selected out of 81 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -29.868202 5.297302 -0.957477 30.349426 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LEU-ALA-LEU-CT2" + RDCMND substituted energy or value "?RDIP" to "30.3494" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 12 + Number of bonds = 80 Number of angles = 96 + Number of dihedrals = 132 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 81 atoms have been selected out of 81 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 80 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 132 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-LEU-ALA-LEU-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LEU-ALA-LEU-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 12 + Number of bonds = 84 Number of angles = 102 + Number of dihedrals = 138 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 23 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 29 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 757 757 756 + : Ran out of space. RESIZING + with mode 5 found 467 exclusions and 353 interactions(1-4) + found 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3103 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3103 atom pairs and 820 atom exclusions. + There are 0 group pairs and 27 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3103 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 58197.97292 -40114.98325 45887.07381 +ENER INTERN> 26.31966 48.89762 46.92223 19.78032 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 58028.90810 31.70499 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LEU-ALA-LEU-CT3" + RDCMND substituted energy or value "?ENER" to "58198" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 114.79037266 80.58352733 -89.33875465 + 664.83051650 531.81064022 + 872.99781170 + + Transpose of the rotation matrix + 0.772992 0.634238 -0.015004 + -0.529663 0.658196 0.535010 + 0.349199 -0.405612 0.844712 + CENTER OF ATOMS BEFORE TRANSLATION 5.36155 2.94132 -0.62655 + AXIS OF ROTATION IS 0.610732 0.236472 0.755703 ANGLE IS 50.36 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 85 atoms have been selected out of 85 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -25.127775 1.955214 1.928772 25.277422 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LEU-ALA-LEU-CT3" + RDCMND substituted energy or value "?RDIP" to "25.2774" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 12 + Number of bonds = 84 Number of angles = 102 + Number of dihedrals = 138 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 29 + + CHARMM> delete atom sele all end + SELRPN> 85 atoms have been selected out of 85 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 138 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-LEU-ALA-LEU-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LEU-ALA-LEU-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 13 + Number of bonds = 89 Number of angles = 99 + Number of dihedrals = 135 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 25 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 805 805 801 + : Ran out of space. RESIZING + with mode 5 found 512 exclusions and 372 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3493 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3493 atom pairs and 884 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3493 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 21193.37124 37004.60168 15788.20016 +ENER INTERN> 19.86867 40.90127 108.23191 30.86655 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 20999.61415 -0.78131 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LEU-ALA-LEU-CTER" + RDCMND substituted energy or value "?ENER" to "21193.4" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 152.49017148 36.56508276 -206.99178449 + 584.66056425 535.61652714 + 1119.42425783 + + Transpose of the rotation matrix + 0.851536 0.510461 -0.119654 + -0.373474 0.750743 0.544888 + 0.367973 -0.419304 0.829928 + CENTER OF ATOMS BEFORE TRANSLATION 4.50365 2.51572 -0.43982 + AXIS OF ROTATION IS 0.690687 0.349305 0.633196 ANGLE IS 44.27 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -23.656316 -16.423268 0.434877 28.801634 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LEU-ALA-LEU-CTER" + RDCMND substituted energy or value "?RDIP" to "28.8016" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 13 + Number of bonds = 89 Number of angles = 99 + Number of dihedrals = 135 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 99 angles deleted + DELTIC: 135 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-LEU-ALA-LEU-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LEU-ALA-LEU-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 91 Number of groups = 13 + Number of bonds = 90 Number of angles = 100 + Number of dihedrals = 137 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 25 + Number of true-bonds = 90 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 811 811 810 + : Ran out of space. RESIZING + with mode 5 found 518 exclusions and 378 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3577 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3577 atom pairs and 896 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3577 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 22647.66098 -1454.28974 16194.98247 +ENER INTERN> 19.72247 35.87139 117.38747 21.99452 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 22472.50803 -14.49289 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LEU-ALA-LEU-CNEU" + RDCMND substituted energy or value "?ENER" to "22647.7" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 152.89524153 38.42352692 -204.92321345 + 603.18468313 556.33225096 + 1139.70755155 + + Transpose of the rotation matrix + 0.848127 0.517448 -0.113702 + -0.380530 0.744306 0.548823 + 0.368616 -0.422205 0.828170 + CENTER OF ATOMS BEFORE TRANSLATION 4.55591 2.56267 -0.43499 + AXIS OF ROTATION IS 0.689750 0.342605 0.637861 ANGLE IS 44.74 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 91 atoms have been selected out of 91 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.900948 -4.275031 -1.444300 4.601478 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LEU-ALA-LEU-CNEU" + RDCMND substituted energy or value "?RDIP" to "4.60148" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 91 Number of groups = 13 + Number of bonds = 90 Number of angles = 100 + Number of dihedrals = 137 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 91 atoms have been selected out of 91 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 90 bonds deleted + DELTIC: 100 angles deleted + DELTIC: 137 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-LEU-ALA-LEU-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LEU-ALA-LEU-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 95 Number of groups = 13 + Number of bonds = 94 Number of angles = 106 + Number of dihedrals = 140 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 26 + Number of true-bonds = 94 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 853 853 846 + : Ran out of space. RESIZING + with mode 5 found 546 exclusions and 390 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3919 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3919 atom pairs and 936 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3919 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 33035.76448 -10388.10350 21703.05090 +ENER INTERN> 19.72247 35.73153 97.82645 22.92208 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 32848.61209 16.27987 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LEU-ALA-LEU-CT1" + RDCMND substituted energy or value "?ENER" to "33035.8" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 155.26539872 47.95472069 -198.30509373 + 729.38454597 642.87418124 + 1201.87957982 + + Transpose of the rotation matrix + 0.822363 0.561750 -0.090307 + -0.433742 0.721693 0.539468 + 0.368220 -0.404469 0.837149 + CENTER OF ATOMS BEFORE TRANSLATION 4.72310 2.80345 -0.41667 + AXIS OF ROTATION IS 0.652581 0.316998 0.688223 ANGLE IS 46.32 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 95 atoms have been selected out of 95 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.455773 -3.142489 -2.063854 4.490607 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LEU-ALA-LEU-CT1" + RDCMND substituted energy or value "?RDIP" to "4.49061" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 95 Number of groups = 13 + Number of bonds = 94 Number of angles = 106 + Number of dihedrals = 140 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 95 atoms have been selected out of 95 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 106 angles deleted + DELTIC: 140 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-LEU-ALA-LEU-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LEU-ALA-LEU-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 13 + Number of bonds = 89 Number of angles = 102 + Number of dihedrals = 139 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 25 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 807 807 801 + : Ran out of space. RESIZING + with mode 5 found 500 exclusions and 374 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3505 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3505 atom pairs and 874 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3505 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 18164.61616 14871.14832 15189.49092 +ENER INTERN> 25.94775 34.04016 96.90976 24.56590 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 18011.55420 -14.89161 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LEU-ALA-LEU-CT2" + RDCMND substituted energy or value "?ENER" to "18164.6" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 152.49017148 36.45606170 -207.93687054 + 583.52688141 526.55045674 + 1110.98498445 + + Transpose of the rotation matrix + 0.851913 0.509346 -0.121699 + -0.374522 0.755012 0.538228 + 0.366028 -0.412945 0.833966 + CENTER OF ATOMS BEFORE TRANSLATION 4.47977 2.51296 -0.43982 + AXIS OF ROTATION IS 0.685766 0.351636 0.637241 ANGLE IS 43.91 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -4.544247 -2.934393 -3.139763 6.254515 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LEU-ALA-LEU-CT2" + RDCMND substituted energy or value "?RDIP" to "6.25451" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 13 + Number of bonds = 89 Number of angles = 102 + Number of dihedrals = 139 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 139 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LEU" + Parameter: PATCH -> "LEU" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-LEU-ALA-LEU-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LEU-ALA-LEU-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LEU" + Parameter: RESIDUE -> "LEU" + + RESIDUE SEQUENCE -- 3 RESIDUES + LEU ALA LEU + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LEU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: LEU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LEU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 13 + Number of bonds = 93 Number of angles = 108 + Number of dihedrals = 145 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 26 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "14" + Parameter: PATCHED -> "25" + Comparing "14" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 840 840 837 + : Ran out of space. RESIZING + with mode 5 found 521 exclusions and 389 interactions(1-4) + found 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3850 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3850 atom pairs and 910 atom exclusions. + There are 0 group pairs and 29 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3850 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 58284.02229 -40119.40612 43980.34917 +ENER INTERN> 25.94775 46.91171 132.59371 24.12107 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 58068.08411 -6.02606 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LEU-ALA-LEU-CT3" + RDCMND substituted energy or value "?ENER" to "58284" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 154.42956935 45.58895026 -197.83220936 + 700.45813251 645.06998534 + 1228.09516249 + + Transpose of the rotation matrix + 0.832065 0.547009 -0.091914 + -0.416146 0.725184 0.548572 + 0.366728 -0.418198 0.831036 + CENTER OF ATOMS BEFORE TRANSLATION 4.73505 2.74369 -0.42110 + AXIS OF ROTATION IS 0.671519 0.318573 0.669009 ANGLE IS 46.04 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 94 atoms have been selected out of 94 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.966419 -6.244714 -0.046190 6.547166 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LEU-ALA-LEU-CT3" + RDCMND substituted energy or value "?RDIP" to "6.54717" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 13 + Number of bonds = 93 Number of angles = 108 + Number of dihedrals = 145 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 94 atoms have been selected out of 94 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 108 angles deleted + DELTIC: 145 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "15" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "15" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "15" + Parameter: AA15 -> "LYS" + Parameter: RESIDUE <- "LYS" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "15" + Parameter: SPECIAL -> "2" + Comparing "15" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "LYS" + Parameter: PATCH <- "LYS" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-LYS-ALA-LYS-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LYS-ALA-LYS-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 12 + Number of bonds = 88 Number of angles = 105 + Number of dihedrals = 146 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 24 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 798 798 792 + : Ran out of space. RESIZING + with mode 5 found 500 exclusions and 356 interactions(1-4) + found 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3416 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3416 atom pairs and 856 atom exclusions. + There are 0 group pairs and 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3416 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 275.45908 58008.56320 30.43486 +ENER INTERN> 23.44748 41.15155 22.90635 33.20530 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 34.86159 122.16682 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LYS-ALA-LYS-CTER" + RDCMND substituted energy or value "?ENER" to "275.459" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 215.32968229 150.74667900 -238.59787066 + 629.07008588 376.86795347 + 1108.01358856 + + Transpose of the rotation matrix + 0.885425 0.446577 -0.128809 + -0.317732 0.783847 0.533507 + 0.339219 -0.431454 0.835929 + CENTER OF ATOMS BEFORE TRANSLATION 5.78070 2.13052 -1.05531 + AXIS OF ROTATION IS 0.732722 0.355386 0.580361 ANGLE IS 41.18 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 89 atoms have been selected out of 89 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : -21.784811 -51.656126 0.182027 56.062166 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LYS-ALA-LYS-CTER" + RDCMND substituted energy or value "?RDIP" to "56.0622" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 12 + Number of bonds = 88 Number of angles = 105 + Number of dihedrals = 146 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 89 atoms have been selected out of 89 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 105 angles deleted + DELTIC: 146 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 8 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-LYS-ALA-LYS-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LYS-ALA-LYS-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 12 + Number of bonds = 89 Number of angles = 106 + Number of dihedrals = 148 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 24 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 806 806 801 + : Ran out of space. RESIZING + with mode 5 found 506 exclusions and 362 interactions(1-4) + found 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3499 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3499 atom pairs and 868 atom exclusions. + There are 0 group pairs and 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3499 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 368.97862 -93.51954 25.38380 +ENER INTERN> 23.30413 36.29918 32.06469 24.34662 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 32.96771 222.27629 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LYS-ALA-LYS-CNEU" + RDCMND substituted energy or value "?ENER" to "368.979" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 216.64474776 155.21999674 -234.65027996 + 647.61777809 393.68680659 + 1120.17370445 + + Transpose of the rotation matrix + 0.879321 0.461376 -0.118010 + -0.333932 0.774023 0.537938 + 0.339534 -0.433613 0.834683 + CENTER OF ATOMS BEFORE TRANSLATION 5.82273 2.17815 -1.04359 + AXIS OF ROTATION IS 0.727031 0.342389 0.595144 ANGLE IS 41.93 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -3.753588 -34.837160 -1.681412 35.079114 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LYS-ALA-LYS-CNEU" + RDCMND substituted energy or value "?RDIP" to "35.0791" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 12 + Number of bonds = 89 Number of angles = 106 + Number of dihedrals = 148 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 106 angles deleted + DELTIC: 148 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 8 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-LYS-ALA-LYS-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LYS-ALA-LYS-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 12 + Number of bonds = 93 Number of angles = 112 + Number of dihedrals = 151 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 25 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 841 841 837 + : Ran out of space. RESIZING + with mode 5 found 534 exclusions and 374 interactions(1-4) + found 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3837 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3837 atom pairs and 908 atom exclusions. + There are 0 group pairs and 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3837 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 608.21491 -239.23629 132.03680 +ENER INTERN> 23.30413 36.15932 12.49942 25.23801 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 264.15133 249.14271 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LYS-ALA-LYS-CT1" + RDCMND substituted energy or value "?ENER" to "608.215" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 222.46084213 178.30978548 -222.22614781 + 776.40065482 461.94744146 + 1158.87427973 + + Transpose of the rotation matrix + 0.839949 0.537797 -0.072531 + -0.421886 0.731210 0.536046 + 0.341319 -0.419651 0.841067 + CENTER OF ATOMS BEFORE TRANSLATION 5.95501 2.42399 -0.99918 + AXIS OF ROTATION IS 0.674832 0.292227 0.677647 ANGLE IS 45.08 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 94 atoms have been selected out of 94 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -8.723643 -35.332680 -2.417696 36.473901 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LYS-ALA-LYS-CT1" + RDCMND substituted energy or value "?RDIP" to "36.4739" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 12 + Number of bonds = 93 Number of angles = 112 + Number of dihedrals = 151 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 94 atoms have been selected out of 94 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 112 angles deleted + DELTIC: 151 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 8 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-LYS-ALA-LYS-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LYS-ALA-LYS-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 12 + Number of bonds = 88 Number of angles = 108 + Number of dihedrals = 150 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 24 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 793 793 792 + : Ran out of space. RESIZING + with mode 5 found 488 exclusions and 358 interactions(1-4) + found 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3428 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3428 atom pairs and 846 atom exclusions. + There are 0 group pairs and 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3428 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 359.47220 248.74272 24.79062 +ENER INTERN> 29.54978 34.41791 11.58150 29.44727 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 43.35490 221.58083 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LYS-ALA-LYS-CT2" + RDCMND substituted energy or value "?ENER" to "359.472" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 215.32968229 150.63555504 -240.87786841 + 629.02926468 367.76432332 + 1103.78847226 + + Transpose of the rotation matrix + 0.887363 0.441488 -0.132948 + -0.313605 0.789292 0.527892 + 0.337992 -0.426738 0.838842 + CENTER OF ATOMS BEFORE TRANSLATION 5.75643 2.12934 -1.05531 + AXIS OF ROTATION IS 0.731465 0.360848 0.578574 ANGLE IS 40.73 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 89 atoms have been selected out of 89 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -7.216823 -33.318303 -3.460460 34.266115 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LYS-ALA-LYS-CT2" + RDCMND substituted energy or value "?RDIP" to "34.2661" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 12 + Number of bonds = 88 Number of angles = 108 + Number of dihedrals = 150 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 8 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 89 atoms have been selected out of 89 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 108 angles deleted + DELTIC: 150 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 8 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-LYS-ALA-LYS-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-LYS-ALA-LYS-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 12 + Number of bonds = 92 Number of angles = 114 + Number of dihedrals = 156 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 3.00000 + Number of Drudes = 25 + Number of true-bonds = 92 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 31 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 831 831 828 + : Ran out of space. RESIZING + with mode 5 found 509 exclusions and 373 interactions(1-4) + found 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3769 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3769 atom pairs and 882 atom exclusions. + There are 0 group pairs and 26 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3769 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 447.07716 -87.60496 33.68185 +ENER INTERN> 29.54978 47.28946 47.22730 28.97317 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 62.59767 235.99978 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-LYS-ALA-LYS-CT3" + RDCMND substituted energy or value "?ENER" to "447.077" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 220.79138047 172.25343299 -220.27672424 + 743.68201900 467.88668062 + 1181.93979073 + + Transpose of the rotation matrix + 0.851682 0.518271 -0.077674 + -0.399769 0.738349 0.543162 + 0.338856 -0.431550 0.836027 + CENTER OF ATOMS BEFORE TRANSLATION 5.97577 2.35951 -1.00992 + AXIS OF ROTATION IS 0.695097 0.297040 0.654682 ANGLE IS 44.52 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 93 atoms have been selected out of 93 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 3.000000 + DIPOLE MOMENT (DEBYES) : -8.385921 -37.764245 -0.388828 38.686083 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-LYS-ALA-LYS-CT3" + RDCMND substituted energy or value "?RDIP" to "38.6861" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 12 + Number of bonds = 92 Number of angles = 114 + Number of dihedrals = 156 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 93 atoms have been selected out of 93 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 92 bonds deleted + DELTIC: 114 angles deleted + DELTIC: 156 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 9 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-LYS-ALA-LYS-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LYS-ALA-LYS-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 13 + Number of bonds = 97 Number of angles = 111 + Number of dihedrals = 153 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 27 + Number of true-bonds = 97 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 876 876 873 + : Ran out of space. RESIZING + with mode 5 found 554 exclusions and 392 interactions(1-4) + found 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4199 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4199 atom pairs and 946 atom exclusions. + There are 0 group pairs and 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4199 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 318.57932 128.49783 39.21923 +ENER INTERN> 23.04841 38.73741 108.58217 36.79844 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 71.98537 44.75752 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LYS-ALA-LYS-CTER" + RDCMND substituted energy or value "?ENER" to "318.579" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 271.67314544 125.42410599 -379.33684972 + 642.86193122 451.53232968 + 1510.88762822 + + Transpose of the rotation matrix + 0.916012 0.345658 -0.203576 + -0.197184 0.829913 0.521884 + 0.349344 -0.437909 0.828369 + CENTER OF ATOMS BEFORE TRANSLATION 5.14127 2.01542 -0.81887 + AXIS OF ROTATION IS 0.778086 0.448241 0.440071 ANGLE IS 38.08 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 98 atoms have been selected out of 98 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : 16.696224 -57.740097 -1.159364 60.116777 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LYS-ALA-LYS-CTER" + RDCMND substituted energy or value "?RDIP" to "60.1168" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 13 + Number of bonds = 97 Number of angles = 111 + Number of dihedrals = 153 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 98 atoms have been selected out of 98 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 97 bonds deleted + DELTIC: 111 angles deleted + DELTIC: 153 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 9 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-LYS-ALA-LYS-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LYS-ALA-LYS-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 99 Number of groups = 13 + Number of bonds = 98 Number of angles = 112 + Number of dihedrals = 155 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 27 + Number of true-bonds = 98 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 884 884 882 + : Ran out of space. RESIZING + with mode 5 found 560 exclusions and 398 interactions(1-4) + found 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4291 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4291 atom pairs and 958 atom exclusions. + There are 0 group pairs and 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4291 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 379.42279 -60.84346 36.25269 +ENER INTERN> 22.90506 33.88504 117.74051 27.93975 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 70.09383 112.18859 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LYS-ALA-LYS-CNEU" + RDCMND substituted energy or value "?ENER" to "379.423" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 272.55068138 128.99204428 -375.75225237 + 662.41814014 471.58465152 + 1528.25561910 + + Transpose of the rotation matrix + 0.912970 0.358340 -0.195138 + -0.210591 0.823448 0.526864 + 0.349482 -0.439916 0.827246 + CENTER OF ATOMS BEFORE TRANSLATION 5.18594 2.05988 -0.81060 + AXIS OF ROTATION IS 0.775297 0.436752 0.456247 ANGLE IS 38.57 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 99 atoms have been selected out of 99 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 35.958709 -39.819260 -3.194841 53.747644 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LYS-ALA-LYS-CNEU" + RDCMND substituted energy or value "?RDIP" to "53.7476" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 99 Number of groups = 13 + Number of bonds = 98 Number of angles = 112 + Number of dihedrals = 155 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 99 atoms have been selected out of 99 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 98 bonds deleted + DELTIC: 112 angles deleted + DELTIC: 155 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 9 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-LYS-ALA-LYS-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LYS-ALA-LYS-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 103 Number of groups = 13 + Number of bonds = 102 Number of angles = 118 + Number of dihedrals = 158 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 28 + Number of true-bonds = 102 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 919 919 918 + : Ran out of space. RESIZING + with mode 5 found 588 exclusions and 410 interactions(1-4) + found 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4665 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4665 atom pairs and 998 atom exclusions. + There are 0 group pairs and 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4665 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 619.99823 -240.57544 129.82279 +ENER INTERN> 22.90506 33.74519 98.17524 28.83114 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 301.27648 140.39512 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LYS-ALA-LYS-CT1" + RDCMND substituted energy or value "?ENER" to "619.998" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 276.72208944 147.36519872 -364.07982943 + 797.00525227 555.95946054 + 1583.88007006 + + Transpose of the rotation matrix + 0.891800 0.423072 -0.160320 + -0.284693 0.800159 0.527915 + 0.351627 -0.425153 0.834028 + CENTER OF ATOMS BEFORE TRANSLATION 5.33139 2.28883 -0.77912 + AXIS OF ROTATION IS 0.737206 0.395995 0.547462 ANGLE IS 40.27 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 103 atoms have been selected out of 103 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 32.363499 -42.571242 -3.931567 53.620555 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LYS-ALA-LYS-CT1" + RDCMND substituted energy or value "?RDIP" to "53.6206" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 103 Number of groups = 13 + Number of bonds = 102 Number of angles = 118 + Number of dihedrals = 158 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 103 atoms have been selected out of 103 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 102 bonds deleted + DELTIC: 118 angles deleted + DELTIC: 158 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 9 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-LYS-ALA-LYS-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LYS-ALA-LYS-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 13 + Number of bonds = 97 Number of angles = 114 + Number of dihedrals = 157 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 27 + Number of true-bonds = 97 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 877 877 873 + : Ran out of space. RESIZING + with mode 5 found 542 exclusions and 394 interactions(1-4) + found 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4211 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4211 atom pairs and 936 atom exclusions. + There are 0 group pairs and 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4211 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 366.29725 253.70098 35.72585 +ENER INTERN> 29.15071 32.00378 97.25733 33.04040 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 80.48037 107.87466 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LYS-ALA-LYS-CT2" + RDCMND substituted energy or value "?ENER" to "366.297" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 271.67314544 125.33787896 -381.10602205 + 642.79688001 442.11291447 + 1503.90436561 + + Transpose of the rotation matrix + 0.916905 0.341342 -0.206811 + -0.194099 0.834161 0.516238 + 0.348727 -0.433199 0.831100 + CENTER OF ATOMS BEFORE TRANSLATION 5.11923 2.01434 -0.81887 + AXIS OF ROTATION IS 0.776053 0.454087 0.437660 ANGLE IS 37.71 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 98 atoms have been selected out of 98 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 31.898916 -38.235056 -5.082728 50.052917 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LYS-ALA-LYS-CT2" + RDCMND substituted energy or value "?RDIP" to "50.0529" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 13 + Number of bonds = 97 Number of angles = 114 + Number of dihedrals = 157 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 9 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 98 atoms have been selected out of 98 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 97 bonds deleted + DELTIC: 114 angles deleted + DELTIC: 157 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 9 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "LYS" + Parameter: PATCH -> "LYS" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-LYS-ALA-LYS-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-LYS-ALA-LYS-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "LYS" + Parameter: RESIDUE -> "LYS" + + RESIDUE SEQUENCE -- 3 RESIDUES + LYS ALA LYS + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 2 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LYS" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: LYS mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LYS . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LYS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 102 Number of groups = 13 + Number of bonds = 101 Number of angles = 120 + Number of dihedrals = 163 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 10 + Number of NB exclusions = 0 Total charge = 2.00000 + Number of Drudes = 28 + Number of true-bonds = 101 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "15" + Parameter: PATCHED -> "25" + Comparing "15" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 911 911 909 + : Ran out of space. RESIZING + with mode 5 found 563 exclusions and 409 interactions(1-4) + found 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4588 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4588 atom pairs and 972 atom exclusions. + There are 0 group pairs and 28 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4588 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 458.14850 -91.85125 41.76702 +ENER INTERN> 29.15071 44.87532 132.90312 32.56631 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 99.72304 126.54000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-LYS-ALA-LYS-CT3" + RDCMND substituted energy or value "?ENER" to "458.148" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 275.44873816 142.54077416 -363.05180736 + 762.66530375 558.28964663 + 1608.98751174 + + Transpose of the rotation matrix + 0.897704 0.409838 -0.161742 + -0.268867 0.800382 0.535816 + 0.349053 -0.437517 0.828698 + CENTER OF ATOMS BEFORE TRANSLATION 5.34420 2.22871 -0.78676 + AXIS OF ROTATION IS 0.753429 0.395392 0.525366 ANGLE IS 40.24 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 102 atoms have been selected out of 102 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 2.000000 + DIPOLE MOMENT (DEBYES) : 32.806032 -44.810344 -1.872767 55.567166 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-LYS-ALA-LYS-CT3" + RDCMND substituted energy or value "?RDIP" to "55.5672" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 102 Number of groups = 13 + Number of bonds = 101 Number of angles = 120 + Number of dihedrals = 163 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 10 + Number of NB exclusions = 0 Total charge = 2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 102 atoms have been selected out of 102 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 101 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 163 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 10 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "16" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "16" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "16" + Parameter: AA16 -> "MET" + Parameter: RESIDUE <- "MET" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "16" + Parameter: SPECIAL -> "2" + Comparing "16" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "MET" + Parameter: PATCH <- "MET" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-MET-ALA-MET-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-MET-ALA-MET-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 MET . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 8 + Number of bonds = 80 Number of angles = 83 + Number of dihedrals = 104 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 22 + Number of true-bonds = 80 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 722 722 720 + : Ran out of space. RESIZING + with mode 5 found 484 exclusions and 312 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2756 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2756 atom pairs and 796 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2756 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 152.82461 305.32389 28.68653 +ENER INTERN> 20.83345 41.56032 22.33213 32.45545 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 34.08558 3.83768 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-MET-ALA-MET-CTER" + RDCMND substituted energy or value "?ENER" to "152.825" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 134.17558230 93.88426246 -156.29794823 + 565.16884966 383.98235379 + 917.54008278 + + Transpose of the rotation matrix + 0.847233 0.525129 -0.080219 + -0.423550 0.758909 0.494633 + 0.320625 -0.385093 0.865392 + CENTER OF ATOMS BEFORE TRANSLATION 5.40950 2.44417 -0.76072 + AXIS OF ROTATION IS 0.649499 0.295941 0.700407 ANGLE IS 42.63 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 81 atoms have been selected out of 81 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -44.723445 -9.344273 4.134889 45.875912 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-MET-ALA-MET-CTER" + RDCMND substituted energy or value "?RDIP" to "45.8759" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 8 + Number of bonds = 80 Number of angles = 83 + Number of dihedrals = 104 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 81 atoms have been selected out of 81 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 80 bonds deleted + DELTIC: 83 angles deleted + DELTIC: 104 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-MET-ALA-MET-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-MET-ALA-MET-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 MET . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 8 + Number of bonds = 81 Number of angles = 84 + Number of dihedrals = 106 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 81 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 730 730 729 + : Ran out of space. RESIZING + with mode 5 found 490 exclusions and 318 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2831 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2831 atom pairs and 808 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2831 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 170.47181 -17.64720 24.52689 +ENER INTERN> 20.69774 36.54238 31.49853 23.58529 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 32.29102 28.13684 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-MET-ALA-MET-CNEU" + RDCMND substituted energy or value "?ENER" to "170.472" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 134.96098249 97.07762637 -153.34356878 + 583.45712443 401.15065348 + 930.74774630 + + Transpose of the rotation matrix + 0.841030 0.536143 -0.072246 + -0.435278 0.749930 0.498135 + 0.321251 -0.387500 0.864084 + CENTER OF ATOMS BEFORE TRANSLATION 5.45745 2.49600 -0.75145 + AXIS OF ROTATION IS 0.645427 0.286770 0.707945 ANGLE IS 43.32 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 82 atoms have been selected out of 82 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -23.471494 4.785416 2.400052 24.074291 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-MET-ALA-MET-CNEU" + RDCMND substituted energy or value "?RDIP" to "24.0743" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 8 + Number of bonds = 81 Number of angles = 84 + Number of dihedrals = 106 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 82 atoms have been selected out of 82 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 81 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 106 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-MET-ALA-MET-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-MET-ALA-MET-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 MET . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 8 + Number of bonds = 85 Number of angles = 90 + Number of dihedrals = 109 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 23 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 768 768 765 + : Ran out of space. RESIZING + with mode 5 found 518 exclusions and 330 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3137 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3137 atom pairs and 848 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3137 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 411.18139 -240.70958 141.63645 +ENER INTERN> 20.69774 36.40252 11.92191 24.50854 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 262.48406 57.44662 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-MET-ALA-MET-CT1" + RDCMND substituted energy or value "?ENER" to "411.181" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 138.75979638 113.42281999 -144.23941586 + 708.42114588 469.76765819 + 970.97538513 + + Transpose of the rotation matrix + 0.800331 0.598225 -0.039970 + -0.505989 0.709687 0.490225 + 0.321631 -0.372117 0.870679 + CENTER OF ATOMS BEFORE TRANSLATION 5.60520 2.76126 -0.71650 + AXIS OF ROTATION IS 0.595970 0.249905 0.763130 ANGLE IS 46.34 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 86 atoms have been selected out of 86 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -22.496495 7.040463 1.877695 23.647117 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-MET-ALA-MET-CT1" + RDCMND substituted energy or value "?RDIP" to "23.6471" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 8 + Number of bonds = 85 Number of angles = 90 + Number of dihedrals = 109 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 86 atoms have been selected out of 86 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 109 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-MET-ALA-MET-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-MET-ALA-MET-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 MET . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 8 + Number of bonds = 80 Number of angles = 86 + Number of dihedrals = 108 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 80 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 723 723 720 + : Ran out of space. RESIZING + with mode 5 found 472 exclusions and 314 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2768 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2768 atom pairs and 786 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2768 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 166.16972 245.01167 25.05201 +ENER INTERN> 26.99778 34.71652 11.00209 28.72804 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 45.39154 29.79374 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-MET-ALA-MET-CT2" + RDCMND substituted energy or value "?ENER" to "166.17" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 134.17558230 93.72339580 -157.93555912 + 564.31527291 375.10844714 + 912.64601086 + + Transpose of the rotation matrix + 0.848708 0.522303 -0.083033 + -0.422059 0.763522 0.488774 + 0.318685 -0.379782 0.868450 + CENTER OF ATOMS BEFORE TRANSLATION 5.38293 2.44156 -0.76072 + AXIS OF ROTATION IS 0.646023 0.298794 0.702407 ANGLE IS 42.24 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 81 atoms have been selected out of 81 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -28.584526 6.045835 1.001102 29.234046 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-MET-ALA-MET-CT2" + RDCMND substituted energy or value "?RDIP" to "29.234" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 81 Number of groups = 8 + Number of bonds = 80 Number of angles = 86 + Number of dihedrals = 108 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 81 atoms have been selected out of 81 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 80 bonds deleted + DELTIC: 86 angles deleted + DELTIC: 108 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-MET-ALA-MET-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-MET-ALA-MET-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 MET . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 8 + Number of bonds = 84 Number of angles = 92 + Number of dihedrals = 114 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 23 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 757 757 756 + : Ran out of space. RESIZING + with mode 5 found 493 exclusions and 329 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3077 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3077 atom pairs and 822 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3077 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 236.45801 -70.28829 31.85733 +ENER INTERN> 26.99778 47.58807 46.54626 28.27930 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 53.60560 38.00101 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-MET-ALA-MET-CT3" + RDCMND substituted energy or value "?ENER" to "236.458" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 137.58002109 109.31869767 -142.86592515 + 679.11243367 476.02757839 + 994.68491652 + + Transpose of the rotation matrix + 0.814363 0.578676 -0.044123 + -0.484203 0.719387 0.498026 + 0.319937 -0.384209 0.866039 + CENTER OF ATOMS BEFORE TRANSLATION 5.62749 2.69465 -0.72493 + AXIS OF ROTATION IS 0.617599 0.254856 0.744057 ANGLE IS 45.58 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 85 atoms have been selected out of 85 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -23.259519 3.648124 3.675142 23.828988 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-MET-ALA-MET-CT3" + RDCMND substituted energy or value "?RDIP" to "23.829" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 8 + Number of bonds = 84 Number of angles = 92 + Number of dihedrals = 114 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 85 atoms have been selected out of 85 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 92 angles deleted + DELTIC: 114 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-MET-ALA-MET-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-MET-ALA-MET-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 9 + Number of bonds = 89 Number of angles = 89 + Number of dihedrals = 111 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 25 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 802 802 801 + : Ran out of space. RESIZING + with mode 5 found 538 exclusions and 348 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3467 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3467 atom pairs and 886 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3467 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 268.71995 -32.26194 37.44299 +ENER INTERN> 20.45126 39.48202 107.99371 36.04983 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 72.73492 -2.66178 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-MET-ALA-MET-CTER" + RDCMND substituted energy or value "?ENER" to "268.72" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 178.44838089 65.99721988 -272.25068176 + 586.01064392 470.98279592 + 1276.09902760 + + Transpose of the rotation matrix + 0.891370 0.425360 -0.156618 + -0.301294 0.814147 0.496373 + 0.338647 -0.395264 0.853864 + CENTER OF ATOMS BEFORE TRANSLATION 4.75036 2.28747 -0.53273 + AXIS OF ROTATION IS 0.711983 0.395475 0.580241 ANGLE IS 38.77 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -19.622153 -17.339603 2.144641 26.273374 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-MET-ALA-MET-CTER" + RDCMND substituted energy or value "?RDIP" to "26.2734" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 9 + Number of bonds = 89 Number of angles = 89 + Number of dihedrals = 111 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 89 angles deleted + DELTIC: 111 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-MET-ALA-MET-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-MET-ALA-MET-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 91 Number of groups = 9 + Number of bonds = 90 Number of angles = 90 + Number of dihedrals = 113 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 25 + Number of true-bonds = 90 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 811 811 810 + : Ran out of space. RESIZING + with mode 5 found 544 exclusions and 354 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3551 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3551 atom pairs and 898 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3551 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 253.51171 15.20824 35.24075 +ENER INTERN> 20.31554 34.46409 117.16011 27.17967 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 70.94280 -11.22050 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-MET-ALA-MET-CNEU" + RDCMND substituted energy or value "?ENER" to "253.512" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 178.94281655 68.31879298 -269.83194766 + 605.66220906 491.65306158 + 1294.88105521 + + Transpose of the rotation matrix + 0.887300 0.436327 -0.149389 + -0.312655 0.807215 0.500650 + 0.339036 -0.397520 0.852662 + CENTER OF ATOMS BEFORE TRANSLATION 4.80080 2.33589 -0.52687 + AXIS OF ROTATION IS 0.708684 0.385382 0.590971 ANGLE IS 39.32 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 91 atoms have been selected out of 91 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 3.169554 -1.692249 0.207618 3.599011 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-MET-ALA-MET-CNEU" + RDCMND substituted energy or value "?RDIP" to "3.59901" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 91 Number of groups = 9 + Number of bonds = 90 Number of angles = 90 + Number of dihedrals = 113 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 91 atoms have been selected out of 91 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 90 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 113 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-MET-ALA-MET-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-MET-ALA-MET-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 MET . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 95 Number of groups = 9 + Number of bonds = 94 Number of angles = 96 + Number of dihedrals = 116 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 26 + Number of true-bonds = 94 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 848 848 846 + : Ran out of space. RESIZING + with mode 5 found 572 exclusions and 366 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3893 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3893 atom pairs and 938 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3893 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 495.55880 -242.04709 137.97822 +ENER INTERN> 20.31554 34.32423 97.58349 28.10292 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 301.13483 19.42780 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-MET-ALA-MET-CT1" + RDCMND substituted energy or value "?ENER" to "495.559" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 181.65162236 80.15531796 -262.09351357 + 738.29509077 577.29003320 + 1352.92333115 + + Transpose of the rotation matrix + 0.860393 0.495146 -0.120640 + -0.379776 0.780795 0.496115 + 0.339844 -0.381038 0.859835 + CENTER OF ATOMS BEFORE TRANSLATION 4.96220 2.58276 -0.50469 + AXIS OF ROTATION IS 0.663647 0.348399 0.661959 ANGLE IS 41.37 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 95 atoms have been selected out of 95 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 4.738036 -0.625388 -0.304514 4.788823 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-MET-ALA-MET-CT1" + RDCMND substituted energy or value "?RDIP" to "4.78882" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 95 Number of groups = 9 + Number of bonds = 94 Number of angles = 96 + Number of dihedrals = 116 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 95 atoms have been selected out of 95 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 116 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-MET-ALA-MET-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-MET-ALA-MET-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 9 + Number of bonds = 89 Number of angles = 92 + Number of dihedrals = 115 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 25 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 802 802 801 + : Ran out of space. RESIZING + with mode 5 found 526 exclusions and 350 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3479 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3479 atom pairs and 876 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3479 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 245.49371 250.06510 35.40748 +ENER INTERN> 26.61558 32.63823 96.66367 32.32242 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 84.04262 -13.27881 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-MET-ALA-MET-CT2" + RDCMND substituted energy or value "?ENER" to "245.494" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 178.44838089 65.88456662 -273.39748375 + 585.09084780 461.63272976 + 1268.37279088 + + Transpose of the rotation matrix + 0.892345 0.422325 -0.159255 + -0.299754 0.818301 0.490440 + 0.337444 -0.389904 0.856800 + CENTER OF ATOMS BEFORE TRANSLATION 4.72644 2.28512 -0.53273 + AXIS OF ROTATION IS 0.708686 0.399847 0.581281 ANGLE IS 38.40 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.410124 -0.742005 -1.358084 2.864203 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-MET-ALA-MET-CT2" + RDCMND substituted energy or value "?RDIP" to "2.8642" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 9 + Number of bonds = 89 Number of angles = 92 + Number of dihedrals = 115 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 92 angles deleted + DELTIC: 115 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "MET" + Parameter: PATCH -> "MET" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-MET-ALA-MET-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-MET-ALA-MET-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "MET" + Parameter: RESIDUE -> "MET" + + RESIDUE SEQUENCE -- 3 RESIDUES + MET ALA MET + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MET" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: MET mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 MET . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 MET . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 MET . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 9 + Number of bonds = 93 Number of angles = 98 + Number of dihedrals = 121 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 26 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "16" + Parameter: PATCHED -> "25" + Comparing "16" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 842 842 837 + : Ran out of space. RESIZING + with mode 5 found 547 exclusions and 365 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3824 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3824 atom pairs and 912 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3824 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 320.15923 -74.66552 39.93096 +ENER INTERN> 26.61558 45.50977 132.20783 31.87368 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 92.25662 -0.69425 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-MET-ALA-MET-CT3" + RDCMND substituted energy or value "?ENER" to "320.159" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 180.73383282 77.17661124 -261.45508880 + 706.94769614 580.08466977 + 1378.68150143 + + Transpose of the rotation matrix + 0.868543 0.480324 -0.122155 + -0.362398 0.783626 0.504577 + 0.338085 -0.393978 0.854681 + CENTER OF ATOMS BEFORE TRANSLATION 4.97552 2.52064 -0.51006 + AXIS OF ROTATION IS 0.683277 0.349975 0.640820 ANGLE IS 41.11 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 94 atoms have been selected out of 94 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 4.444013 -3.783500 1.530670 6.033827 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-MET-ALA-MET-CT3" + RDCMND substituted energy or value "?RDIP" to "6.03383" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 9 + Number of bonds = 93 Number of angles = 98 + Number of dihedrals = 121 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 94 atoms have been selected out of 94 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 98 angles deleted + DELTIC: 121 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "17" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "17" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "17" + Parameter: AA17 -> "PHE" + Parameter: RESIDUE <- "PHE" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "17" + Parameter: SPECIAL -> "2" + Comparing "17" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "PHE" + Parameter: PATCH <- "PHE" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-PHE-ALA-PHE-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-PHE-ALA-PHE-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 6 + Number of bonds = 90 Number of angles = 93 + Number of dihedrals = 134 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 28 + Number of true-bonds = 90 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 817 817 810 + : Ran out of space. RESIZING + with mode 5 found 520 exclusions and 364 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3396 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3396 atom pairs and 884 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3396 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 219.93696 100.22227 29.62213 +ENER INTERN> 23.64182 41.29579 22.19857 30.34577 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 102.36922 2.36580 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-PHE-ALA-PHE-CTER" + RDCMND substituted energy or value "?ENER" to "219.937" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 76.70815977 21.34494758 -100.26661147 + 636.55167026 472.04033743 + 1078.15325987 + + Transpose of the rotation matrix + 0.844443 0.532696 -0.056130 + -0.505391 0.827080 0.246005 + 0.177470 -0.179370 0.967642 + CENTER OF ATOMS BEFORE TRANSLATION 5.73426 2.58759 -0.50444 + AXIS OF ROTATION IS 0.371207 0.203853 0.905897 ANGLE IS 34.96 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 89 atoms have been selected out of 89 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -48.587127 -10.745061 -0.724190 49.766351 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-PHE-ALA-PHE-CTER" + RDCMND substituted energy or value "?RDIP" to "49.7664" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 6 + Number of bonds = 90 Number of angles = 93 + Number of dihedrals = 134 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 89 atoms have been selected out of 89 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 90 bonds deleted + DELTIC: 93 angles deleted + DELTIC: 134 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-PHE-ALA-PHE-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-PHE-ALA-PHE-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 6 + Number of bonds = 91 Number of angles = 94 + Number of dihedrals = 136 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 28 + Number of true-bonds = 91 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 823 823 819 + : Ran out of space. RESIZING + with mode 5 found 526 exclusions and 370 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3479 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3479 atom pairs and 896 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3479 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 232.95257 -13.01560 25.74838 +ENER INTERN> 23.53881 36.46001 31.39788 21.49195 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 98.27901 24.06491 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-PHE-ALA-PHE-CNEU" + RDCMND substituted energy or value "?ENER" to "232.953" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 77.17354898 23.40964658 -98.47422001 + 653.94654340 487.40321781 + 1088.85493456 + + Transpose of the rotation matrix + 0.839671 0.540544 -0.052592 + -0.513053 0.821255 0.249635 + 0.178130 -0.182629 0.966911 + CENTER OF ATOMS BEFORE TRANSLATION 5.77418 2.63358 -0.49884 + AXIS OF ROTATION IS 0.372013 0.198562 0.906741 ANGLE IS 35.52 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -28.712424 3.051800 -0.509607 28.878651 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-PHE-ALA-PHE-CNEU" + RDCMND substituted energy or value "?RDIP" to "28.8787" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 6 + Number of bonds = 91 Number of angles = 94 + Number of dihedrals = 136 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 91 bonds deleted + DELTIC: 94 angles deleted + DELTIC: 136 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-PHE-ALA-PHE-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-PHE-ALA-PHE-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 6 + Number of bonds = 95 Number of angles = 100 + Number of dihedrals = 139 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 29 + Number of true-bonds = 95 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 865 865 855 + : Ran out of space. RESIZING + with mode 5 found 554 exclusions and 382 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3817 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3817 atom pairs and 936 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3817 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 475.10152 -242.14896 132.04012 +ENER INTERN> 23.53881 36.32015 11.77282 22.36717 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 331.08187 52.30070 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-PHE-ALA-PHE-CT1" + RDCMND substituted energy or value "?ENER" to "475.102" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.77172049 34.10057214 -93.04625433 + 774.78766262 547.81854343 + 1121.51543251 + + Transpose of the rotation matrix + 0.807782 0.588247 -0.038131 + -0.562028 0.788059 0.251174 + 0.177801 -0.181463 0.967191 + CENTER OF ATOMS BEFORE TRANSLATION 5.89509 2.87171 -0.47761 + AXIS OF ROTATION IS 0.346728 0.173054 0.921863 ANGLE IS 38.60 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 94 atoms have been selected out of 94 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -27.778072 5.309309 -0.739864 28.290589 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-PHE-ALA-PHE-CT1" + RDCMND substituted energy or value "?RDIP" to "28.2906" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 6 + Number of bonds = 95 Number of angles = 100 + Number of dihedrals = 139 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 94 atoms have been selected out of 94 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 95 bonds deleted + DELTIC: 100 angles deleted + DELTIC: 139 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-PHE-ALA-PHE-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-PHE-ALA-PHE-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 6 + Number of bonds = 90 Number of angles = 96 + Number of dihedrals = 138 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 28 + Number of true-bonds = 90 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 816 816 810 + : Ran out of space. RESIZING + with mode 5 found 508 exclusions and 366 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3408 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3408 atom pairs and 874 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3408 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 223.92955 251.17197 26.29886 +ENER INTERN> 30.07127 34.49372 10.84280 24.82391 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 108.56110 25.59675 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-PHE-ALA-PHE-CT2" + RDCMND substituted energy or value "?ENER" to "223.93" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 76.70815977 21.23467549 -101.35216166 + 635.69328702 463.49063268 + 1074.71911147 + + Transpose of the rotation matrix + 0.845743 0.530486 -0.057465 + -0.503706 0.829270 0.242058 + 0.176063 -0.175773 0.968558 + CENTER OF ATOMS BEFORE TRANSLATION 5.71008 2.58513 -0.50444 + AXIS OF ROTATION IS 0.366650 0.204922 0.907510 ANGLE IS 34.74 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 89 atoms have been selected out of 89 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -33.823521 4.786371 -1.338294 34.186707 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-PHE-ALA-PHE-CT2" + RDCMND substituted energy or value "?RDIP" to "34.1867" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 6 + Number of bonds = 90 Number of angles = 96 + Number of dihedrals = 138 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 89 atoms have been selected out of 89 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 90 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 138 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-PHE-ALA-PHE-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-PHE-ALA-PHE-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 6 + Number of bonds = 94 Number of angles = 102 + Number of dihedrals = 144 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 29 + Number of true-bonds = 94 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 847 847 846 + : Ran out of space. RESIZING + with mode 5 found 529 exclusions and 381 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3749 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3749 atom pairs and 910 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3749 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 305.30612 -81.37657 35.57738 +ENER INTERN> 30.07127 47.36526 45.95655 24.33832 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 137.62322 24.51149 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-PHE-ALA-PHE-CT3" + RDCMND substituted energy or value "?ENER" to "305.306" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 78.88078856 31.41402997 -91.98231578 + 746.57391664 555.70326399 + 1143.97757853 + + Transpose of the rotation matrix + 0.818395 0.573314 -0.039257 + -0.546767 0.797881 0.253834 + 0.176849 -0.186272 0.966451 + CENTER OF ATOMS BEFORE TRANSLATION 5.91878 2.81187 -0.48274 + AXIS OF ROTATION IS 0.359948 0.176746 0.916078 ANGLE IS 37.69 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 93 atoms have been selected out of 93 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -28.484714 1.540823 0.199184 28.527053 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-PHE-ALA-PHE-CT3" + RDCMND substituted energy or value "?RDIP" to "28.5271" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 6 + Number of bonds = 94 Number of angles = 102 + Number of dihedrals = 144 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 93 atoms have been selected out of 93 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 144 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-PHE-ALA-PHE-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-PHE-ALA-PHE-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 31 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 7 + Number of bonds = 99 Number of angles = 99 + Number of dihedrals = 141 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 31 + Number of true-bonds = 99 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 895 895 891 + : Ran out of space. RESIZING + with mode 5 found 574 exclusions and 400 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4179 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4179 atom pairs and 974 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4179 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 341.89884 -36.59273 35.93910 +ENER INTERN> 23.24466 39.18142 107.88456 37.77617 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 141.04513 -1.90310 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-PHE-ALA-PHE-CTER" + RDCMND substituted energy or value "?ENER" to "341.899" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 112.34789616 -5.89429939 -208.88781728 + 661.41582867 572.06652645 + 1475.75883581 + + Transpose of the rotation matrix + 0.886441 0.449132 -0.111820 + -0.404858 0.869503 0.282940 + 0.224305 -0.205538 0.952597 + CENTER OF ATOMS BEFORE TRANSLATION 5.09910 2.43051 -0.31859 + AXIS OF ROTATION IS 0.469844 0.323303 0.821414 ANGLE IS 31.32 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 98 atoms have been selected out of 98 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -22.127403 -18.213678 -3.312788 28.850209 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-PHE-ALA-PHE-CTER" + RDCMND substituted energy or value "?RDIP" to "28.8502" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 7 + Number of bonds = 99 Number of angles = 99 + Number of dihedrals = 141 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 98 atoms have been selected out of 98 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 99 bonds deleted + DELTIC: 99 angles deleted + DELTIC: 141 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-PHE-ALA-PHE-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-PHE-ALA-PHE-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 31 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 99 Number of groups = 7 + Number of bonds = 100 Number of angles = 100 + Number of dihedrals = 143 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 31 + Number of true-bonds = 100 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 901 901 900 + : Ran out of space. RESIZING + with mode 5 found 580 exclusions and 406 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4271 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4271 atom pairs and 986 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4271 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 322.08311 19.81573 33.57581 +ENER INTERN> 23.14165 34.34564 117.08388 28.92235 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 136.95736 -13.03775 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-PHE-ALA-PHE-CNEU" + RDCMND substituted energy or value "?ENER" to "322.083" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 112.66212769 -4.53941559 -207.55431748 + 680.13963479 590.70431640 + 1491.39126768 + + Transpose of the rotation matrix + 0.882878 0.456925 -0.108379 + -0.412245 0.864648 0.287120 + 0.224902 -0.208813 0.951744 + CENTER OF ATOMS BEFORE TRANSLATION 5.14181 2.47390 -0.31537 + AXIS OF ROTATION IS 0.470193 0.315983 0.824059 ANGLE IS 31.83 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 99 atoms have been selected out of 99 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.435554 -3.402247 -3.546032 4.933491 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-PHE-ALA-PHE-CNEU" + RDCMND substituted energy or value "?RDIP" to "4.93349" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 99 Number of groups = 7 + Number of bonds = 100 Number of angles = 100 + Number of dihedrals = 143 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 99 atoms have been selected out of 99 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 100 bonds deleted + DELTIC: 100 angles deleted + DELTIC: 143 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-PHE-ALA-PHE-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-PHE-ALA-PHE-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 32 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 103 Number of groups = 7 + Number of bonds = 104 Number of angles = 106 + Number of dihedrals = 146 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 32 + Number of true-bonds = 104 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 943 943 936 + : Ran out of space. RESIZING + with mode 5 found 608 exclusions and 418 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4645 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4645 atom pairs and 1026 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4645 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 565.56781 -243.48470 129.07605 +ENER INTERN> 23.14165 34.20578 97.45882 29.79756 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 369.75921 16.53479 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-PHE-ALA-PHE-CT1" + RDCMND substituted energy or value "?ENER" to "565.568" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 114.68969760 2.43945920 -203.34256118 + 808.41540754 667.09411774 + 1539.52485365 + + Transpose of the rotation matrix + 0.859835 0.501743 -0.094539 + -0.458718 0.840456 0.288463 + 0.224190 -0.204664 0.952812 + CENTER OF ATOMS BEFORE TRANSLATION 5.27670 2.69743 -0.30313 + AXIS OF ROTATION IS 0.438055 0.283133 0.853196 ANGLE IS 34.25 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 103 atoms have been selected out of 103 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.098160 -2.006756 -3.801239 4.436490 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-PHE-ALA-PHE-CT1" + RDCMND substituted energy or value "?RDIP" to "4.43649" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 103 Number of groups = 7 + Number of bonds = 104 Number of angles = 106 + Number of dihedrals = 146 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 103 atoms have been selected out of 103 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 104 bonds deleted + DELTIC: 106 angles deleted + DELTIC: 146 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-PHE-ALA-PHE-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-PHE-ALA-PHE-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 31 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 7 + Number of bonds = 99 Number of angles = 102 + Number of dihedrals = 145 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 31 + Number of true-bonds = 99 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 894 894 891 + : Ran out of space. RESIZING + with mode 5 found 562 exclusions and 402 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4191 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4191 atom pairs and 964 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4191 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 309.34820 256.21961 33.82555 +ENER INTERN> 29.67411 32.37935 96.52880 32.25431 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 147.23875 -15.21712 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-PHE-ALA-PHE-CT2" + RDCMND substituted energy or value "?ENER" to "309.348" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 112.34789616 -5.96394448 -209.57342354 + 660.48881756 563.04042002 + 1469.59574356 + + Transpose of the rotation matrix + 0.887383 0.446940 -0.113123 + -0.403592 0.871681 0.278004 + 0.222858 -0.201040 0.953896 + CENTER OF ATOMS BEFORE TRANSLATION 5.07714 2.42828 -0.31859 + AXIS OF ROTATION IS 0.464027 0.325448 0.823870 ANGLE IS 31.08 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 98 atoms have been selected out of 98 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -6.001935 -1.954636 -4.654723 7.842849 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-PHE-ALA-PHE-CT2" + RDCMND substituted energy or value "?RDIP" to "7.84285" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 7 + Number of bonds = 99 Number of angles = 102 + Number of dihedrals = 145 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 98 atoms have been selected out of 98 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 99 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 145 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "PHE" + Parameter: PATCH -> "PHE" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-PHE-ALA-PHE-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-PHE-ALA-PHE-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "PHE" + Parameter: RESIDUE -> "PHE" + + RESIDUE SEQUENCE -- 3 RESIDUES + PHE ALA PHE + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHE" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: PHE mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 32 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 102 Number of groups = 7 + Number of bonds = 103 Number of angles = 108 + Number of dihedrals = 151 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 32 + Number of true-bonds = 103 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "17" + Parameter: PATCHED -> "25" + Comparing "17" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 930 930 927 + : Ran out of space. RESIZING + with mode 5 found 583 exclusions and 417 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4568 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4568 atom pairs and 1000 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4568 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 395.09679 -85.74859 40.86023 +ENER INTERN> 29.67411 45.25090 131.64254 31.76872 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 176.30081 -11.93028 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-PHE-ALA-PHE-CT3" + RDCMND substituted energy or value "?ENER" to "395.097" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 113.93654234 0.68263010 -202.85722552 + 778.24153730 671.77112167 + 1564.35793604 + + Transpose of the rotation matrix + 0.866595 0.489940 -0.094721 + -0.445972 0.845565 0.293476 + 0.223879 -0.212082 0.951262 + CENTER OF ATOMS BEFORE TRANSLATION 5.29225 2.64116 -0.30610 + AXIS OF ROTATION IS 0.455286 0.286919 0.842847 ANGLE IS 33.73 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 102 atoms have been selected out of 102 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.784722 -5.586159 -2.723569 6.264087 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-PHE-ALA-PHE-CT3" + RDCMND substituted energy or value "?RDIP" to "6.26409" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 102 Number of groups = 7 + Number of bonds = 103 Number of angles = 108 + Number of dihedrals = 151 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 102 atoms have been selected out of 102 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 103 bonds deleted + DELTIC: 108 angles deleted + DELTIC: 151 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "18" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "18" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "18" + Parameter: AA18 -> "SER" + Parameter: RESIDUE <- "SER" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "18" + Parameter: SPECIAL -> "2" + Comparing "18" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "SER" + Parameter: PATCH <- "SER" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-SER-ALA-SER-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-SER-ALA-SER-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 SER . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 65 Number of groups = 6 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 80 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 18 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 584 584 576 + : Ran out of space. RESIZING + with mode 5 found 384 exclusions and 264 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1696 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1696 atom pairs and 648 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1696 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 194.39843 200.69836 31.47956 +ENER INTERN> 20.03103 40.52929 22.57161 34.98198 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 29.90988 48.65463 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-SER-ALA-SER-CTER" + RDCMND substituted energy or value "?ENER" to "194.398" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 44.96789976 34.66171574 -37.56710315 + 403.66844761 337.08633001 + 562.68517317 + + Transpose of the rotation matrix + 0.784502 0.620043 -0.010170 + -0.563947 0.720155 0.404153 + 0.257917 -0.311324 0.914635 + CENTER OF ATOMS BEFORE TRANSLATION 4.64316 2.82434 -0.24915 + AXIS OF ROTATION IS 0.507748 0.190252 0.840236 ANGLE IS 44.79 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 65 atoms have been selected out of 65 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -50.776647 -7.846819 -0.215917 51.379831 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-SER-ALA-SER-CTER" + RDCMND substituted energy or value "?RDIP" to "51.3798" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 65 Number of groups = 6 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 80 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 65 atoms have been selected out of 65 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 64 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 80 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-SER-ALA-SER-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-SER-ALA-SER-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 SER . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 66 Number of groups = 6 + Number of bonds = 65 Number of angles = 60 + Number of dihedrals = 82 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 18 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 588 588 585 + : Ran out of space. RESIZING + with mode 5 found 390 exclusions and 270 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1755 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1755 atom pairs and 660 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1755 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 195.23341 -0.83498 27.61583 +ENER INTERN> 19.86775 35.18287 31.70940 26.17186 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 27.98395 56.59758 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-SER-ALA-SER-CNEU" + RDCMND substituted energy or value "?ENER" to "195.233" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 45.24278878 35.62856549 -36.42903660 + 419.42844371 355.71123775 + 581.79078942 + + Transpose of the rotation matrix + 0.782134 0.623064 -0.007672 + -0.566416 0.716047 0.407983 + 0.259693 -0.314751 0.912957 + CENTER OF ATOMS BEFORE TRANSLATION 4.71343 2.88405 -0.24537 + AXIS OF ROTATION IS 0.509943 0.188647 0.839268 ANGLE IS 45.12 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 66 atoms have been selected out of 66 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -26.394070 -0.767375 -1.712300 26.460683 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-SER-ALA-SER-CNEU" + RDCMND substituted energy or value "?RDIP" to "26.4607" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 66 Number of groups = 6 + Number of bonds = 65 Number of angles = 60 + Number of dihedrals = 82 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 66 atoms have been selected out of 66 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 60 angles deleted + DELTIC: 82 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-SER-ALA-SER-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-SER-ALA-SER-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 SER . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 19 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 70 Number of groups = 6 + Number of bonds = 69 Number of angles = 66 + Number of dihedrals = 85 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 19 + Number of true-bonds = 69 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 31 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 624 624 621 + : Ran out of space. RESIZING + with mode 5 found 418 exclusions and 282 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1997 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1997 atom pairs and 700 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1997 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 433.21210 -237.97869 159.57778 +ENER INTERN> 19.86775 35.04302 12.17383 26.92585 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 256.80560 84.67605 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-SER-ALA-SER-CT1" + RDCMND substituted energy or value "?ENER" to "433.212" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 47.11503190 40.60270058 -32.87728257 + 529.28868817 433.04933292 + 639.10264804 + + Transpose of the rotation matrix + 0.750171 0.661240 0.002244 + -0.609177 0.689777 0.391294 + 0.257191 -0.294904 0.920263 + CENTER OF ATOMS BEFORE TRANSLATION 4.93275 3.19120 -0.23135 + AXIS OF ROTATION IS 0.468002 0.173880 0.866452 ANGLE IS 47.15 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 70 atoms have been selected out of 70 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -26.212862 1.120580 -2.304593 26.337824 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-SER-ALA-SER-CT1" + RDCMND substituted energy or value "?RDIP" to "26.3378" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 70 Number of groups = 6 + Number of bonds = 69 Number of angles = 66 + Number of dihedrals = 85 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 70 atoms have been selected out of 70 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 69 bonds deleted + DELTIC: 66 angles deleted + DELTIC: 85 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-SER-ALA-SER-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-SER-ALA-SER-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 SER . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 65 Number of groups = 6 + Number of bonds = 64 Number of angles = 62 + Number of dihedrals = 84 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 18 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 586 586 576 + : Ran out of space. RESIZING + with mode 5 found 372 exclusions and 266 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1708 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1708 atom pairs and 638 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1708 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 195.36500 237.84710 28.74936 +ENER INTERN> 25.97116 33.44372 11.26178 26.58079 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 43.73487 64.83269 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-SER-ALA-SER-CT2" + RDCMND substituted energy or value "?ENER" to "195.365" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 44.96789976 34.60089247 -38.10257819 + 402.72421705 328.75715548 + 554.73102031 + + Transpose of the rotation matrix + 0.783161 0.621725 -0.010798 + -0.567943 0.722269 0.394674 + 0.253177 -0.302961 0.918758 + CENTER OF ATOMS BEFORE TRANSLATION 4.61009 2.82059 -0.24915 + AXIS OF ROTATION IS 0.496831 0.187994 0.847241 ANGLE IS 44.59 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 65 atoms have been selected out of 65 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -31.032637 1.606551 -2.856952 31.205252 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-SER-ALA-SER-CT2" + RDCMND substituted energy or value "?RDIP" to "31.2053" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 65 Number of groups = 6 + Number of bonds = 64 Number of angles = 62 + Number of dihedrals = 84 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 65 atoms have been selected out of 65 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 64 bonds deleted + DELTIC: 62 angles deleted + DELTIC: 84 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-SER-ALA-SER-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-SER-ALA-SER-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 SER . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 19 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 69 Number of groups = 6 + Number of bonds = 68 Number of angles = 68 + Number of dihedrals = 90 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 19 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 29 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 616 616 612 + : Ran out of space. RESIZING + with mode 5 found 393 exclusions and 281 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1953 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1953 atom pairs and 674 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1953 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 240.73059 -45.36559 33.00468 +ENER INTERN> 25.97116 46.31527 47.17499 26.00318 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 39.06058 60.76542 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-SER-ALA-SER-CT3" + RDCMND substituted energy or value "?ENER" to "240.731" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 46.40036474 39.37832113 -32.57038304 + 504.66650480 435.74666670 + 664.84341583 + + Transpose of the rotation matrix + 0.768358 0.640020 0.000181 + -0.586994 0.704586 0.398745 + 0.255078 -0.306485 0.917062 + CENTER OF ATOMS BEFORE TRANSLATION 4.95170 3.11559 -0.23470 + AXIS OF ROTATION IS 0.490419 0.177256 0.853270 ANGLE IS 45.97 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 69 atoms have been selected out of 69 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -27.033744 -2.592144 -0.748675 27.168052 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-SER-ALA-SER-CT3" + RDCMND substituted energy or value "?RDIP" to "27.1681" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 69 Number of groups = 6 + Number of bonds = 68 Number of angles = 68 + Number of dihedrals = 90 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 29 + + CHARMM> delete atom sele all end + SELRPN> 69 atoms have been selected out of 69 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 68 bonds deleted + DELTIC: 68 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-SER-ALA-SER-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-SER-ALA-SER-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 7 + Number of bonds = 73 Number of angles = 65 + Number of dihedrals = 87 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 21 + Number of true-bonds = 73 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 658 658 657 + : Ran out of space. RESIZING + with mode 5 found 438 exclusions and 300 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2263 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2263 atom pairs and 738 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2263 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 306.46752 -65.73693 42.31303 +ENER INTERN> 19.84853 38.65130 108.20333 38.88852 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 69.81457 36.39126 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-SER-ALA-SER-CTER" + RDCMND substituted energy or value "?ENER" to "306.468" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 71.85662216 8.49258764 -113.22460575 + 434.59421212 430.09027869 + 837.56655891 + + Transpose of the rotation matrix + 0.843964 0.529303 -0.086965 + -0.439251 0.775021 0.454313 + 0.307869 -0.345225 0.886587 + CENTER OF ATOMS BEFORE TRANSLATION 3.93470 2.58752 -0.03407 + AXIS OF ROTATION IS 0.607307 0.299905 0.735687 ANGLE IS 41.17 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 74 atoms have been selected out of 74 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -29.048711 -15.743317 -2.343297 33.123567 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-SER-ALA-SER-CTER" + RDCMND substituted energy or value "?RDIP" to "33.1236" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 7 + Number of bonds = 73 Number of angles = 65 + Number of dihedrals = 87 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 74 atoms have been selected out of 74 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 73 bonds deleted + DELTIC: 65 angles deleted + DELTIC: 87 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-SER-ALA-SER-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-SER-ALA-SER-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 7 + Number of bonds = 74 Number of angles = 66 + Number of dihedrals = 89 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 21 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 678 678 666 + : Ran out of space. RESIZING + with mode 5 found 444 exclusions and 306 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2331 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2331 atom pairs and 750 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2331 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 274.38398 32.08354 40.47700 +ENER INTERN> 19.68525 33.30488 117.34112 30.07840 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 67.89113 11.41321 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-SER-ALA-SER-CNEU" + RDCMND substituted energy or value "?ENER" to "274.384" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 72.07152324 8.63301296 -113.04486756 + 452.27922042 452.75209056 + 863.69076086 + + Transpose of the rotation matrix + 0.840888 0.534819 -0.082918 + -0.444266 0.769615 0.458607 + 0.309087 -0.348799 0.884762 + CENTER OF ATOMS BEFORE TRANSLATION 4.00599 2.64322 -0.03362 + AXIS OF ROTATION IS 0.607884 0.295135 0.737138 ANGLE IS 41.61 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 75 atoms have been selected out of 75 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.795610 -6.743038 -4.064983 8.075696 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-SER-ALA-SER-CNEU" + RDCMND substituted energy or value "?RDIP" to "8.0757" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 7 + Number of bonds = 74 Number of angles = 66 + Number of dihedrals = 89 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 75 atoms have been selected out of 75 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 66 angles deleted + DELTIC: 89 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-SER-ALA-SER-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-SER-ALA-SER-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 SER . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 7 + Number of bonds = 78 Number of angles = 72 + Number of dihedrals = 92 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 22 + Number of true-bonds = 78 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 703 703 702 + : Ran out of space. RESIZING + with mode 5 found 472 exclusions and 318 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2609 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2609 atom pairs and 790 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2609 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 513.69839 -239.31441 153.91062 +ENER INTERN> 19.68525 33.16503 97.80555 30.83239 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 296.71175 40.82842 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-SER-ALA-SER-CT1" + RDCMND substituted energy or value "?ENER" to "513.698" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 73.72099128 9.34994788 -112.46458390 + 572.94358588 549.22474476 + 943.90878763 + + Transpose of the rotation matrix + 0.813000 0.578312 -0.067725 + -0.494719 0.747413 0.443427 + 0.307058 -0.327002 0.893748 + CENTER OF ATOMS BEFORE TRANSLATION 4.23614 2.92757 -0.03192 + AXIS OF ROTATION IS 0.561085 0.272945 0.781463 ANGLE IS 43.36 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 79 atoms have been selected out of 79 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.297173 -5.397398 -4.662198 7.138369 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-SER-ALA-SER-CT1" + RDCMND substituted energy or value "?RDIP" to "7.13837" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 7 + Number of bonds = 78 Number of angles = 72 + Number of dihedrals = 92 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 79 atoms have been selected out of 79 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 78 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 92 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-SER-ALA-SER-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-SER-ALA-SER-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 7 + Number of bonds = 73 Number of angles = 68 + Number of dihedrals = 91 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 73 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 676 676 657 + : Ran out of space. RESIZING + with mode 5 found 426 exclusions and 302 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2275 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2275 atom pairs and 728 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2275 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 270.76419 242.93419 40.96950 +ENER INTERN> 25.78866 31.56573 96.89350 30.48732 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 83.64133 15.89765 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-SER-ALA-SER-CT2" + RDCMND substituted energy or value "?ENER" to "270.764" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 71.85662216 8.48426985 -113.29783373 + 433.53446359 421.08014328 + 826.57574814 + + Transpose of the rotation matrix + 0.843607 0.529643 -0.088351 + -0.442215 0.778617 0.445199 + 0.304588 -0.336503 0.891063 + CENTER OF ATOMS BEFORE TRANSLATION 3.90565 2.58422 -0.03407 + AXIS OF ROTATION IS 0.597788 0.300490 0.743206 ANGLE IS 40.83 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 74 atoms have been selected out of 74 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -7.204256 -5.010270 -5.550669 10.383354 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-SER-ALA-SER-CT2" + RDCMND substituted energy or value "?RDIP" to "10.3834" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 7 + Number of bonds = 73 Number of angles = 68 + Number of dihedrals = 91 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 74 atoms have been selected out of 74 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 73 bonds deleted + DELTIC: 68 angles deleted + DELTIC: 91 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "SER" + Parameter: PATCH -> "SER" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-SER-ALA-SER-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-SER-ALA-SER-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "SER" + Parameter: RESIDUE -> "SER" + + RESIDUE SEQUENCE -- 3 RESIDUES + SER ALA SER + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "SER" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: SER mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 SER . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SER. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 7 + Number of bonds = 77 Number of angles = 74 + Number of dihedrals = 97 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 22 + Number of true-bonds = 77 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "18" + Parameter: PATCHED -> "25" + Comparing "18" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 696 696 693 + : Ran out of space. RESIZING + with mode 5 found 447 exclusions and 317 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2556 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2556 atom pairs and 764 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2556 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 320.55605 -49.79185 43.34688 +ENER INTERN> 25.78866 44.43728 132.80671 29.90972 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 78.96699 16.25669 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-SER-ALA-SER-CT3" + RDCMND substituted energy or value "?ENER" to "320.556" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 73.05959104 9.17279947 -112.44483388 + 545.51072099 548.39319043 + 971.00607292 + + Transpose of the rotation matrix + 0.825512 0.560208 -0.068535 + -0.474595 0.754759 0.452879 + 0.305434 -0.341331 0.888934 + CENTER OF ATOMS BEFORE TRANSLATION 4.24397 2.85731 -0.03232 + AXIS OF ROTATION IS 0.585270 0.275586 0.762569 ANGLE IS 42.73 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 78 atoms have been selected out of 78 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.813207 -8.765673 -2.954104 9.285745 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-SER-ALA-SER-CT3" + RDCMND substituted energy or value "?RDIP" to "9.28575" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 7 + Number of bonds = 77 Number of angles = 74 + Number of dihedrals = 97 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 78 atoms have been selected out of 78 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 77 bonds deleted + DELTIC: 74 angles deleted + DELTIC: 97 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "19" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "19" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "19" + Parameter: AA19 -> "TRP" + Parameter: RESIDUE <- "TRP" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "19" + Parameter: SPECIAL -> "2" + Comparing "19" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "TRP" + Parameter: PATCH <- "TRP" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-TRP-ALA-TRP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TRP-ALA-TRP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 34 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 103 Number of groups = 6 + Number of bonds = 106 Number of angles = 111 + Number of dihedrals = 166 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 34 + Number of true-bonds = 106 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 962 962 954 + : Ran out of space. RESIZING + with mode 5 found 626 exclusions and 436 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4627 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4627 atom pairs and 1062 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4627 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 193.34955 127.20650 27.95310 +ENER INTERN> 24.86087 51.37041 23.19416 37.48649 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 69.42990 -10.71229 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TRP-ALA-TRP-CTER" + RDCMND substituted energy or value "?ENER" to "193.35" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 77.67258436 -12.33149185 -51.34968650 + 865.81820722 412.78780728 + 1407.33469530 + + Transpose of the rotation matrix + 0.879645 0.474497 -0.032827 + -0.473929 0.880240 0.023837 + 0.040206 -0.005411 0.999177 + CENTER OF ATOMS BEFORE TRANSLATION 6.24288 1.82992 -0.31903 + AXIS OF ROTATION IS 0.030733 0.076741 0.996577 ANGLE IS 28.41 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 103 atoms have been selected out of 103 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -43.996867 -8.836797 -3.831488 45.038801 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TRP-ALA-TRP-CTER" + RDCMND substituted energy or value "?RDIP" to "45.0388" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 103 Number of groups = 6 + Number of bonds = 106 Number of angles = 111 + Number of dihedrals = 166 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 103 atoms have been selected out of 103 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 106 bonds deleted + DELTIC: 111 angles deleted + DELTIC: 166 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-TRP-ALA-TRP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TRP-ALA-TRP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 34 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 104 Number of groups = 6 + Number of bonds = 107 Number of angles = 112 + Number of dihedrals = 168 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 34 + Number of true-bonds = 107 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 966 966 963 + : Ran out of space. RESIZING + with mode 5 found 632 exclusions and 442 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4724 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4724 atom pairs and 1074 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4724 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 206.10290 -12.75335 24.74894 +ENER INTERN> 24.73186 46.59823 32.36696 28.63634 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 65.88438 10.16513 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TRP-ALA-TRP-CNEU" + RDCMND substituted energy or value "?ENER" to "206.103" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 77.98713902 -10.88886132 -50.28935338 + 886.82994208 428.76703064 + 1416.51184146 + + Transpose of the rotation matrix + 0.873161 0.486436 -0.031160 + -0.485793 0.873682 0.026165 + 0.039951 -0.007709 0.999172 + CENTER OF ATOMS BEFORE TRANSLATION 6.27515 1.87382 -0.31596 + AXIS OF ROTATION IS 0.034727 0.072904 0.996734 ANGLE IS 29.19 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 104 atoms have been selected out of 104 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -24.535457 8.573065 -2.067630 26.072230 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TRP-ALA-TRP-CNEU" + RDCMND substituted energy or value "?RDIP" to "26.0722" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 104 Number of groups = 6 + Number of bonds = 107 Number of angles = 112 + Number of dihedrals = 168 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 104 atoms have been selected out of 104 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 107 bonds deleted + DELTIC: 112 angles deleted + DELTIC: 168 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-TRP-ALA-TRP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TRP-ALA-TRP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 35 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 108 Number of groups = 6 + Number of bonds = 111 Number of angles = 118 + Number of dihedrals = 171 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 35 + Number of true-bonds = 111 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 43 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1013 1013 999 + : Ran out of space. RESIZING + with mode 5 found 660 exclusions and 454 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5118 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5118 atom pairs and 1114 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5118 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 449.80652 -243.70362 122.90333 +ENER INTERN> 24.73186 46.45838 12.78039 29.50434 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 298.23488 40.37667 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TRP-ALA-TRP-CT1" + RDCMND substituted energy or value "?ENER" to "449.807" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 80.01684488 -3.50705272 -46.99827543 + 1029.50711070 491.42176467 + 1446.36285281 + + Transpose of the rotation matrix + 0.833848 0.551459 -0.024294 + -0.550505 0.834024 0.036718 + 0.040511 -0.017243 0.999030 + CENTER OF ATOMS BEFORE TRANSLATION 6.37531 2.09847 -0.30426 + AXIS OF ROTATION IS 0.048826 0.058637 0.997085 ANGLE IS 33.55 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 108 atoms have been selected out of 108 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -22.956357 10.917872 -2.093916 25.506445 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TRP-ALA-TRP-CT1" + RDCMND substituted energy or value "?RDIP" to "25.5064" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 108 Number of groups = 6 + Number of bonds = 111 Number of angles = 118 + Number of dihedrals = 171 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 43 + + CHARMM> delete atom sele all end + SELRPN> 108 atoms have been selected out of 108 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 111 bonds deleted + DELTIC: 118 angles deleted + DELTIC: 171 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-TRP-ALA-TRP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TRP-ALA-TRP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 34 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 103 Number of groups = 6 + Number of bonds = 106 Number of angles = 114 + Number of dihedrals = 170 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 34 + Number of true-bonds = 106 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 960 960 954 + : Ran out of space. RESIZING + with mode 5 found 614 exclusions and 438 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4639 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4639 atom pairs and 1052 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4639 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 195.78872 254.01780 24.77356 +ENER INTERN> 31.07958 44.64586 11.85698 32.50603 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 74.35102 11.80925 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TRP-ALA-TRP-CT2" + RDCMND substituted energy or value "?ENER" to "195.789" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 77.67258436 -12.35943011 -52.03919325 + 865.87206801 403.08921394 + 1404.96391411 + + Transpose of the rotation matrix + 0.881733 0.470560 -0.033476 + -0.469993 0.882353 0.023646 + 0.040665 -0.005115 0.999160 + CENTER OF ATOMS BEFORE TRANSLATION 6.22190 1.82907 -0.31903 + AXIS OF ROTATION IS 0.030470 0.078547 0.996445 ANGLE IS 28.16 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 103 atoms have been selected out of 103 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -29.840197 10.336223 -2.307634 31.663860 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TRP-ALA-TRP-CT2" + RDCMND substituted energy or value "?RDIP" to "31.6639" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 103 Number of groups = 6 + Number of bonds = 106 Number of angles = 114 + Number of dihedrals = 170 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 103 atoms have been selected out of 103 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 106 bonds deleted + DELTIC: 114 angles deleted + DELTIC: 170 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-TRP-ALA-TRP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TRP-ALA-TRP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 35 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 107 Number of groups = 6 + Number of bonds = 110 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 35 + Number of true-bonds = 110 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 992 992 990 + : Ran out of space. RESIZING + with mode 5 found 635 exclusions and 453 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5036 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5036 atom pairs and 1088 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 24643 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5036 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 280.45153 -84.66281 32.41389 +ENER INTERN> 31.07958 57.51740 47.31233 32.01345 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 101.17272 15.91604 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TRP-ALA-TRP-CT3" + RDCMND substituted energy or value "?ENER" to "280.452" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.26303921 -5.45607195 -46.29239123 + 992.57850811 500.19561579 + 1467.76559530 + + Transpose of the rotation matrix + 0.845280 0.533754 -0.024648 + -0.532916 0.845502 0.033550 + 0.038747 -0.015223 0.999133 + CENTER OF ATOMS BEFORE TRANSLATION 6.39679 2.03915 -0.30710 + AXIS OF ROTATION IS 0.045596 0.059266 0.997200 ANGLE IS 32.33 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 107 atoms have been selected out of 107 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -23.848081 7.068684 -1.946278 24.949655 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TRP-ALA-TRP-CT3" + RDCMND substituted energy or value "?RDIP" to "24.9497" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 107 Number of groups = 6 + Number of bonds = 110 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 107 atoms have been selected out of 107 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 110 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-TRP-ALA-TRP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TRP-ALA-TRP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 37 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 112 Number of groups = 7 + Number of bonds = 115 Number of angles = 117 + Number of dihedrals = 173 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 37 + Number of true-bonds = 115 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 47 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1040 1040 1035 + : Ran out of space. RESIZING + with mode 5 found 680 exclusions and 472 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 25089 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5536 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5536 atom pairs and 1152 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 25089 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5536 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 311.90897 -31.45745 34.24359 +ENER INTERN> 24.46545 48.78068 108.86448 45.03014 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 105.68377 -15.58555 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TRP-ALA-TRP-CTER" + RDCMND substituted energy or value "?ENER" to "311.909" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 107.80871263 -25.77547573 -158.54171735 + 874.28327825 474.67502642 + 1870.25481870 + + Transpose of the rotation matrix + 0.926198 0.368548 -0.079565 + -0.364739 0.929267 0.058551 + 0.095516 -0.025209 0.995109 + CENTER OF ATOMS BEFORE TRANSLATION 5.64624 1.75335 -0.17131 + AXIS OF ROTATION IS 0.110424 0.230813 0.966712 ANGLE IS 22.29 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 112 atoms have been selected out of 112 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -16.278952 -17.786387 -7.395186 25.220005 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TRP-ALA-TRP-CTER" + RDCMND substituted energy or value "?RDIP" to "25.22" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 112 Number of groups = 7 + Number of bonds = 115 Number of angles = 117 + Number of dihedrals = 173 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 47 + + CHARMM> delete atom sele all end + SELRPN> 112 atoms have been selected out of 112 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 115 bonds deleted + DELTIC: 117 angles deleted + DELTIC: 173 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-TRP-ALA-TRP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TRP-ALA-TRP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 37 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 113 Number of groups = 7 + Number of bonds = 116 Number of angles = 118 + Number of dihedrals = 175 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 37 + Number of true-bonds = 116 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 47 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1049 1049 1044 + : Ran out of space. RESIZING + with mode 5 found 686 exclusions and 478 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 25539 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5642 atom pairs and 1164 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 25539 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 292.06687 19.84211 32.29969 +ENER INTERN> 24.33644 44.00851 118.03727 36.17999 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 102.14055 -27.30589 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TRP-ALA-TRP-CNEU" + RDCMND substituted energy or value "?ENER" to "292.067" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 108.05155497 -24.98722600 -157.87060437 + 896.00975485 493.66600338 + 1883.76253087 + + Transpose of the rotation matrix + 0.921905 0.379520 -0.077813 + -0.375487 0.924769 0.061742 + 0.095392 -0.027702 0.995054 + CENTER OF ATOMS BEFORE TRANSLATION 5.68122 1.79444 -0.16979 + AXIS OF ROTATION IS 0.114706 0.222124 0.968248 ANGLE IS 22.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 113 atoms have been selected out of 113 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 3.924536 0.849074 -6.059370 7.269035 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TRP-ALA-TRP-CNEU" + RDCMND substituted energy or value "?RDIP" to "7.26903" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 113 Number of groups = 7 + Number of bonds = 116 Number of angles = 118 + Number of dihedrals = 175 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 47 + + CHARMM> delete atom sele all end + SELRPN> 113 atoms have been selected out of 113 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 116 bonds deleted + DELTIC: 118 angles deleted + DELTIC: 175 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-TRP-ALA-TRP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TRP-ALA-TRP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 38 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 117 Number of groups = 7 + Number of bonds = 120 Number of angles = 124 + Number of dihedrals = 178 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 38 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 48 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1080 + : Ran out of space. RESIZING + with mode 5 found 714 exclusions and 490 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6072 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 6072 atom pairs and 1204 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6072 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 537.10759 -245.04073 120.87207 +ENER INTERN> 24.33644 43.86865 98.45070 37.04800 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 334.49010 4.24371 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TRP-ALA-TRP-CT1" + RDCMND substituted energy or value "?ENER" to "537.108" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 109.80810594 -20.95653582 -155.70720499 + 1042.85073046 571.43625011 + 1927.46918542 + + Transpose of the rotation matrix + 0.896623 0.437138 -0.070558 + -0.432331 0.898685 0.073861 + 0.095696 -0.035721 0.994769 + CENTER OF ATOMS BEFORE TRANSLATION 5.79398 2.00452 -0.16399 + AXIS OF ROTATION IS 0.122853 0.186388 0.974765 ANGLE IS 26.49 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 117 atoms have been selected out of 117 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 5.640877 1.947803 -6.059917 8.505059 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TRP-ALA-TRP-CT1" + RDCMND substituted energy or value "?RDIP" to "8.50506" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 117 Number of groups = 7 + Number of bonds = 120 Number of angles = 124 + Number of dihedrals = 178 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 48 + + CHARMM> delete atom sele all end + SELRPN> 117 atoms have been selected out of 117 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 120 bonds deleted + DELTIC: 124 angles deleted + DELTIC: 178 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-TRP-ALA-TRP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TRP-ALA-TRP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 37 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 112 Number of groups = 7 + Number of bonds = 115 Number of angles = 120 + Number of dihedrals = 177 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 37 + Number of true-bonds = 115 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 45 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1038 1038 1035 + : Ran out of space. RESIZING + with mode 5 found 668 exclusions and 474 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5548 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5548 atom pairs and 1142 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5548 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 278.16687 258.94072 32.18304 +ENER INTERN> 30.68416 42.05613 97.52729 40.04968 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 110.60655 -29.24695 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TRP-ALA-TRP-CT2" + RDCMND substituted energy or value "?ENER" to "278.167" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 107.80871263 -25.79047777 -158.91196259 + 874.32373528 464.75885690 + 1865.30866600 + + Transpose of the rotation matrix + 0.927624 0.364792 -0.080255 + -0.361094 0.930780 0.057091 + 0.095525 -0.023979 0.995138 + CENTER OF ATOMS BEFORE TRANSLATION 5.62695 1.75257 -0.17131 + AXIS OF ROTATION IS 0.107913 0.233982 0.966233 ANGLE IS 22.06 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 112 atoms have been selected out of 112 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.759001 2.396258 -6.592383 7.231573 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TRP-ALA-TRP-CT2" + RDCMND substituted energy or value "?RDIP" to "7.23157" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 112 Number of groups = 7 + Number of bonds = 115 Number of angles = 120 + Number of dihedrals = 177 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 45 + + CHARMM> delete atom sele all end + SELRPN> 112 atoms have been selected out of 112 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 115 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 177 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TRP" + Parameter: PATCH -> "TRP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-TRP-ALA-TRP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TRP-ALA-TRP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TRP" + Parameter: RESIDUE -> "TRP" + + RESIDUE SEQUENCE -- 3 RESIDUES + TRP ALA TRP + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TRP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: TRP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TRP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 38 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TRP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 116 Number of groups = 7 + Number of bonds = 119 Number of angles = 126 + Number of dihedrals = 183 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 38 + Number of true-bonds = 119 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "19" + Parameter: PATCHED -> "25" + Comparing "19" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 46 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1075 1075 1071 + : Ran out of space. RESIZING + with mode 5 found 689 exclusions and 489 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5981 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5981 atom pairs and 1178 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5981 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 367.03172 -88.86484 37.96903 +ENER INTERN> 30.68416 54.92768 132.98265 39.55710 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 137.42815 -20.93802 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TRP-ALA-TRP-CT3" + RDCMND substituted energy or value "?ENER" to "367.032" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 109.12061379 -22.02179545 -155.42317547 + 1004.73965756 576.64102171 + 1951.23036413 + + Transpose of the rotation matrix + 0.902678 0.424518 -0.070408 + -0.419829 0.904713 0.072377 + 0.094424 -0.035774 0.994889 + CENTER OF ATOMS BEFORE TRANSLATION 5.80878 1.94900 -0.16540 + AXIS OF ROTATION IS 0.124734 0.190105 0.973808 ANGLE IS 25.69 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 116 atoms have been selected out of 116 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 5.333749 -1.690693 -5.814171 8.069195 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TRP-ALA-TRP-CT3" + RDCMND substituted energy or value "?RDIP" to "8.06919" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 116 Number of groups = 7 + Number of bonds = 119 Number of angles = 126 + Number of dihedrals = 183 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 46 + + CHARMM> delete atom sele all end + SELRPN> 116 atoms have been selected out of 116 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 119 bonds deleted + DELTIC: 126 angles deleted + DELTIC: 183 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "20" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "20" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "20" + Parameter: AA20 -> "THR" + Parameter: RESIDUE <- "THR" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "20" + Parameter: SPECIAL -> "2" + Comparing "20" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "THR" + Parameter: PATCH <- "THR" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-THR-ALA-THR-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-THR-ALA-THR-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 THR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 8 + Number of bonds = 72 Number of angles = 71 + Number of dihedrals = 98 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 20 + Number of true-bonds = 72 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 653 653 648 + : Ran out of space. RESIZING + with mode 5 found 434 exclusions and 318 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2194 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2194 atom pairs and 752 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2194 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 187.80417 179.22754 30.53033 +ENER INTERN> 21.83449 44.13493 22.70963 38.51776 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 27.88872 34.99864 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-THR-ALA-THR-CTER" + RDCMND substituted energy or value "?ENER" to "187.804" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 96.76243072 51.09086781 -36.30332967 + 451.56160045 391.86193190 + 640.84469387 + + Transpose of the rotation matrix + 0.785558 0.618777 0.003631 + -0.509447 0.643407 0.571395 + 0.351230 -0.450714 0.820667 + CENTER OF ATOMS BEFORE TRANSLATION 4.65637 2.70877 -0.53877 + AXIS OF ROTATION IS 0.654550 0.222600 0.722505 ANGLE IS 51.33 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 73 atoms have been selected out of 73 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -50.812887 -7.210254 1.448672 51.342341 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-THR-ALA-THR-CTER" + RDCMND substituted energy or value "?RDIP" to "51.3423" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 8 + Number of bonds = 72 Number of angles = 71 + Number of dihedrals = 98 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 73 atoms have been selected out of 73 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 72 bonds deleted + DELTIC: 71 angles deleted + DELTIC: 98 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-THR-ALA-THR-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-THR-ALA-THR-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 THR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 8 + Number of bonds = 73 Number of angles = 72 + Number of dihedrals = 100 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 20 + Number of true-bonds = 73 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 659 659 657 + : Ran out of space. RESIZING + with mode 5 found 440 exclusions and 324 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2261 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2261 atom pairs and 764 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2261 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 188.32479 -0.52062 27.07373 +ENER INTERN> 21.66743 39.27147 31.84396 33.50206 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 26.09366 38.22620 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-THR-ALA-THR-CNEU" + RDCMND substituted energy or value "?ENER" to "188.325" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 97.26253249 53.21658828 -33.81803327 + 467.79712347 410.96513439 + 660.34849536 + + Transpose of the rotation matrix + 0.783247 0.621667 0.007419 + -0.511491 0.637560 0.576102 + 0.353414 -0.455025 0.817344 + CENTER OF ATOMS BEFORE TRANSLATION 4.71956 2.76282 -0.53149 + AXIS OF ROTATION IS 0.656492 0.220286 0.721452 ANGLE IS 51.75 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 74 atoms have been selected out of 74 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -25.986711 0.224916 -0.611052 25.994867 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-THR-ALA-THR-CNEU" + RDCMND substituted energy or value "?RDIP" to "25.9949" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 8 + Number of bonds = 73 Number of angles = 72 + Number of dihedrals = 100 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 74 atoms have been selected out of 74 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 73 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 100 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-THR-ALA-THR-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-THR-ALA-THR-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 THR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 8 + Number of bonds = 77 Number of angles = 78 + Number of dihedrals = 103 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 21 + Number of true-bonds = 77 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 701 701 693 + : Ran out of space. RESIZING + with mode 5 found 468 exclusions and 336 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2535 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2535 atom pairs and 804 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2535 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 426.64419 -238.31939 149.92360 +ENER INTERN> 21.66743 39.13162 12.31404 34.15998 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 254.81833 66.83279 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-THR-ALA-THR-CT1" + RDCMND substituted energy or value "?ENER" to "426.644" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 99.97967122 64.20437951 -25.95333265 + 581.33057891 491.10361160 + 719.79517958 + + Transpose of the rotation matrix + 0.753737 0.656821 0.021593 + -0.556298 0.620199 0.553069 + 0.349875 -0.428881 0.832856 + CENTER OF ATOMS BEFORE TRANSLATION 4.91953 3.04219 -0.50423 + AXIS OF ROTATION IS 0.615688 0.205834 0.760632 ANGLE IS 52.89 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 78 atoms have been selected out of 78 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -25.608964 1.894662 -1.426985 25.718575 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-THR-ALA-THR-CT1" + RDCMND substituted energy or value "?RDIP" to "25.7186" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 8 + Number of bonds = 77 Number of angles = 78 + Number of dihedrals = 103 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 78 atoms have been selected out of 78 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 77 bonds deleted + DELTIC: 78 angles deleted + DELTIC: 103 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-THR-ALA-THR-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-THR-ALA-THR-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 THR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 8 + Number of bonds = 72 Number of angles = 74 + Number of dihedrals = 102 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 20 + Number of true-bonds = 72 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 655 655 648 + : Ran out of space. RESIZING + with mode 5 found 422 exclusions and 320 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2206 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2206 atom pairs and 742 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2206 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 189.61602 237.02817 27.66456 +ENER INTERN> 27.74383 37.24015 11.39923 33.91535 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 41.25971 48.51774 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-THR-ALA-THR-CT2" + RDCMND substituted energy or value "?ENER" to "189.616" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 96.76243072 50.97187818 -37.46262216 + 450.74844398 383.37638228 + 632.73773768 + + Transpose of the rotation matrix + 0.784382 0.620272 0.002660 + -0.515251 0.649175 0.559543 + 0.345342 -0.440266 0.828797 + CENTER OF ATOMS BEFORE TRANSLATION 4.62690 2.70574 -0.53877 + AXIS OF ROTATION IS 0.644507 0.220904 0.731992 ANGLE IS 50.86 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 73 atoms have been selected out of 73 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -30.664677 2.398299 -2.157446 30.833891 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-THR-ALA-THR-CT2" + RDCMND substituted energy or value "?RDIP" to "30.8339" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 8 + Number of bonds = 72 Number of angles = 74 + Number of dihedrals = 102 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 73 atoms have been selected out of 73 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 72 bonds deleted + DELTIC: 74 angles deleted + DELTIC: 102 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-THR-ALA-THR-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-THR-ALA-THR-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 THR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 77 Number of groups = 8 + Number of bonds = 76 Number of angles = 80 + Number of dihedrals = 108 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 21 + Number of true-bonds = 76 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 31 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 688 688 684 + : Ran out of space. RESIZING + with mode 5 found 443 exclusions and 335 interactions(1-4) + found 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2483 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2483 atom pairs and 778 atom exclusions. + There are 0 group pairs and 13 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2483 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 237.72549 -48.10947 32.12454 +ENER INTERN> 27.74383 50.11170 47.36348 33.26931 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 37.11615 46.68102 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-THR-ALA-THR-CT3" + RDCMND substituted energy or value "?ENER" to "237.725" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 99.06175323 61.46125301 -25.32759528 + 555.19451189 493.28132410 + 745.65603276 + + Transpose of the rotation matrix + 0.770333 0.637369 0.018653 + -0.534200 0.629117 0.564661 + 0.348162 -0.444941 0.825112 + CENTER OF ATOMS BEFORE TRANSLATION 4.93544 2.97244 -0.51078 + AXIS OF ROTATION IS 0.638471 0.208381 0.740899 ANGLE IS 52.25 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 77 atoms have been selected out of 77 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -26.475321 -1.406615 0.758672 26.523513 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-THR-ALA-THR-CT3" + RDCMND substituted energy or value "?RDIP" to "26.5235" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 77 Number of groups = 8 + Number of bonds = 76 Number of angles = 80 + Number of dihedrals = 108 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 77 atoms have been selected out of 77 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 76 bonds deleted + DELTIC: 80 angles deleted + DELTIC: 108 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-THR-ALA-THR-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-THR-ALA-THR-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 9 + Number of bonds = 81 Number of angles = 77 + Number of dihedrals = 105 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 23 + Number of true-bonds = 81 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 731 731 729 + : Ran out of space. RESIZING + with mode 5 found 488 exclusions and 354 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2833 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2833 atom pairs and 842 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2833 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 297.72721 -60.00172 41.03109 +ENER INTERN> 21.73561 42.13550 108.32770 44.58342 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 67.22601 19.04898 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-THR-ALA-THR-CTER" + RDCMND substituted energy or value "?ENER" to "297.727" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 132.86423245 21.94132304 -126.79588165 + 479.39295310 480.87685037 + 920.58448623 + + Transpose of the rotation matrix + 0.842354 0.531996 -0.086142 + -0.379272 0.698747 0.606552 + 0.382875 -0.478260 0.790363 + CENTER OF ATOMS BEFORE TRANSLATION 4.01558 2.50773 -0.31289 + AXIS OF ROTATION IS 0.726900 0.314274 0.610613 ANGLE IS 48.26 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 82 atoms have been selected out of 82 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -28.887532 -16.871741 -0.709649 33.461153 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-THR-ALA-THR-CTER" + RDCMND substituted energy or value "?RDIP" to "33.4612" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 9 + Number of bonds = 81 Number of angles = 77 + Number of dihedrals = 105 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 82 atoms have been selected out of 82 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 81 bonds deleted + DELTIC: 77 angles deleted + DELTIC: 105 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-THR-ALA-THR-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-THR-ALA-THR-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 9 + Number of bonds = 82 Number of angles = 78 + Number of dihedrals = 107 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 23 + Number of true-bonds = 82 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 748 748 738 + : Ran out of space. RESIZING + with mode 5 found 494 exclusions and 360 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2909 atom pairs and 854 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 265.37736 32.34985 39.36508 +ENER INTERN> 21.56855 37.27205 117.46203 39.56772 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 65.43340 -10.59638 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-THR-ALA-THR-CNEU" + RDCMND substituted energy or value "?ENER" to "265.377" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 133.17470664 23.23980474 -125.15233008 + 497.28056307 503.59548062 + 946.44665454 + + Transpose of the rotation matrix + 0.839551 0.537256 -0.080680 + -0.384263 0.692212 0.610888 + 0.384051 -0.481869 0.787596 + CENTER OF ATOMS BEFORE TRANSLATION 4.07964 2.55834 -0.30912 + AXIS OF ROTATION IS 0.727005 0.309183 0.613082 ANGLE IS 48.72 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.729792 -7.421059 -3.059049 8.211095 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-THR-ALA-THR-CNEU" + RDCMND substituted energy or value "?RDIP" to "8.21109" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 9 + Number of bonds = 82 Number of angles = 78 + Number of dihedrals = 107 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 82 bonds deleted + DELTIC: 78 angles deleted + DELTIC: 107 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-THR-ALA-THR-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-THR-ALA-THR-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 THR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 9 + Number of bonds = 86 Number of angles = 84 + Number of dihedrals = 110 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 24 + Number of true-bonds = 86 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 779 779 774 + : Ran out of space. RESIZING + with mode 5 found 522 exclusions and 372 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3219 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3219 atom pairs and 894 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3219 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 505.03246 -239.65510 145.66825 +ENER INTERN> 21.56855 37.13219 97.93211 40.22564 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 294.15705 19.34692 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-THR-ALA-THR-CT1" + RDCMND substituted energy or value "?ENER" to "505.032" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 135.18452295 29.90734101 -119.79770195 + 620.10499630 601.03026037 + 1026.82325596 + + Transpose of the rotation matrix + 0.813668 0.578184 -0.060397 + -0.437480 0.677431 0.591353 + 0.382825 -0.454743 0.804148 + CENTER OF ATOMS BEFORE TRANSLATION 4.28834 2.81822 -0.29490 + AXIS OF ROTATION IS 0.686450 0.290843 0.666481 ANGLE IS 49.64 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 87 atoms have been selected out of 87 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.238196 -6.194373 -3.922777 7.335883 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-THR-ALA-THR-CT1" + RDCMND substituted energy or value "?RDIP" to "7.33588" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 9 + Number of bonds = 86 Number of angles = 84 + Number of dihedrals = 110 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 87 atoms have been selected out of 87 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 86 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 110 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-THR-ALA-THR-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-THR-ALA-THR-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 9 + Number of bonds = 81 Number of angles = 80 + Number of dihedrals = 109 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 23 + Number of true-bonds = 81 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 733 733 729 + : Ran out of space. RESIZING + with mode 5 found 476 exclusions and 356 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2845 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2845 atom pairs and 832 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2845 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 262.94138 242.09108 39.53960 +ENER INTERN> 27.64494 35.24073 97.01729 39.98102 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 80.59875 -4.03135 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-THR-ALA-THR-CT2" + RDCMND substituted energy or value "?ENER" to "262.941" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 132.86423245 21.87222019 -127.46913708 + 478.49107149 471.81791943 + 909.72683465 + + Transpose of the rotation matrix + 0.842009 0.532252 -0.087915 + -0.383186 0.704803 0.597010 + 0.379723 -0.469000 0.797402 + CENTER OF ATOMS BEFORE TRANSLATION 3.98934 2.50504 -0.31289 + AXIS OF ROTATION IS 0.719835 0.315778 0.618160 ANGLE IS 47.77 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 82 atoms have been selected out of 82 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -7.096482 -5.907146 -4.891425 10.448946 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-THR-ALA-THR-CT2" + RDCMND substituted energy or value "?RDIP" to "10.4489" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 9 + Number of bonds = 81 Number of angles = 80 + Number of dihedrals = 109 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 82 atoms have been selected out of 82 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 81 bonds deleted + DELTIC: 80 angles deleted + DELTIC: 109 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "THR" + Parameter: PATCH -> "THR" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-THR-ALA-THR-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-THR-ALA-THR-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "THR" + Parameter: RESIDUE -> "THR" + + RESIDUE SEQUENCE -- 3 RESIDUES + THR ALA THR + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: THR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 THR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 THR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 THR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 9 + Number of bonds = 85 Number of angles = 86 + Number of dihedrals = 115 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 24 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "20" + Parameter: PATCHED -> "25" + Comparing "20" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 766 766 765 + : Ran out of space. RESIZING + with mode 5 found 497 exclusions and 371 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3158 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3158 atom pairs and 868 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3158 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 315.44475 -52.50337 42.18229 +ENER INTERN> 27.64494 48.11227 132.98155 39.33497 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 76.45513 -1.47411 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-THR-ALA-THR-CT3" + RDCMND substituted energy or value "?ENER" to "315.445" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 134.43617437 28.23832578 -119.62052791 + 591.52374211 599.90438439 + 1053.84759638 + + Transpose of the rotation matrix + 0.825366 0.561181 -0.062026 + -0.416692 0.679588 0.603762 + 0.380971 -0.472479 0.794748 + CENTER OF ATOMS BEFORE TRANSLATION 4.29525 2.75317 -0.29833 + AXIS OF ROTATION IS 0.707996 0.291422 0.643285 ANGLE IS 49.47 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 86 atoms have been selected out of 86 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.797452 -9.219914 -1.618121 9.394736 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-THR-ALA-THR-CT3" + RDCMND substituted energy or value "?RDIP" to "9.39474" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 9 + Number of bonds = 85 Number of angles = 86 + Number of dihedrals = 115 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 86 atoms have been selected out of 86 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 86 angles deleted + DELTIC: 115 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "21" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "21" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "21" + Parameter: AA21 -> "TYR" + Parameter: RESIDUE <- "TYR" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "21" + Parameter: SPECIAL -> "2" + Comparing "21" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "TYR" + Parameter: PATCH <- "TYR" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-TYR-ALA-TYR-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TYR-ALA-TYR-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 6 + Number of bonds = 98 Number of angles = 95 + Number of dihedrals = 138 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 30 + Number of true-bonds = 98 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 883 883 882 + : Ran out of space. RESIZING + with mode 5 found 580 exclusions and 408 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4076 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4076 atom pairs and 988 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4076 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 204.89553 110.54922 30.02561 +ENER INTERN> 23.74826 41.03854 22.41068 30.65617 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 108.69813 -19.37624 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TYR-ALA-TYR-CTER" + RDCMND substituted energy or value "?ENER" to "204.896" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.47165658 22.38011405 -124.27167091 + 690.96806282 529.07774533 + 1349.20316936 + + Transpose of the rotation matrix + 0.874354 0.481267 -0.062356 + -0.457254 0.860053 0.226338 + 0.162558 -0.169387 0.972051 + CENTER OF ATOMS BEFORE TRANSLATION 6.17887 2.54285 -0.55735 + AXIS OF ROTATION IS 0.379383 0.215626 0.899763 ANGLE IS 31.44 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -45.161541 -12.151263 -2.332457 46.825830 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TYR-ALA-TYR-CTER" + RDCMND substituted energy or value "?RDIP" to "46.8258" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 6 + Number of bonds = 98 Number of angles = 95 + Number of dihedrals = 138 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 98 bonds deleted + DELTIC: 95 angles deleted + DELTIC: 138 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-TYR-ALA-TYR-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TYR-ALA-TYR-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 6 + Number of bonds = 99 Number of angles = 96 + Number of dihedrals = 140 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 30 + Number of true-bonds = 99 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 903 903 891 + : Ran out of space. RESIZING + with mode 5 found 586 exclusions and 414 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4167 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4167 atom pairs and 1000 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4167 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 220.10775 -15.21222 26.04973 +ENER INTERN> 23.64816 36.21938 31.61304 21.79817 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 104.38013 4.72887 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TYR-ALA-TYR-CNEU" + RDCMND substituted energy or value "?ENER" to "220.108" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.99288241 24.63908123 -122.49706119 + 707.99917064 542.80704011 + 1357.39907084 + + Transpose of the rotation matrix + 0.870216 0.489073 -0.059433 + -0.464858 0.855052 0.229767 + 0.163191 -0.172319 0.971429 + CENTER OF ATOMS BEFORE TRANSLATION 6.21170 2.58463 -0.55166 + AXIS OF ROTATION IS 0.379729 0.210246 0.900890 ANGLE IS 31.97 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 98 atoms have been selected out of 98 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -27.703214 3.541522 -2.071101 28.005355 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TYR-ALA-TYR-CNEU" + RDCMND substituted energy or value "?RDIP" to "28.0054" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 6 + Number of bonds = 99 Number of angles = 96 + Number of dihedrals = 140 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 98 atoms have been selected out of 98 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 99 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 140 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-TYR-ALA-TYR-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TYR-ALA-TYR-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 31 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 102 Number of groups = 6 + Number of bonds = 103 Number of angles = 102 + Number of dihedrals = 143 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 31 + Number of true-bonds = 103 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 43 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 934 934 927 + : Ran out of space. RESIZING + with mode 5 found 614 exclusions and 426 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4537 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4537 atom pairs and 1040 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4537 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 462.27686 -242.16911 129.33537 +ENER INTERN> 23.64816 36.07953 11.98369 22.68585 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 337.64491 32.51473 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TYR-ALA-TYR-CT1" + RDCMND substituted energy or value "?ENER" to "462.277" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 82.80765114 36.43962057 -117.21092141 + 827.98150563 595.65274469 + 1383.02136860 + + Transpose of the rotation matrix + 0.844163 0.534004 -0.047213 + -0.510702 0.827845 0.232070 + 0.163011 -0.171793 0.971553 + CENTER OF ATOMS BEFORE TRANSLATION 6.30947 2.80291 -0.53003 + AXIS OF ROTATION IS 0.354387 0.184470 0.916723 ANGLE IS 34.74 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 102 atoms have been selected out of 102 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -26.648354 5.625470 -2.284253 27.331273 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TYR-ALA-TYR-CT1" + RDCMND substituted energy or value "?RDIP" to "27.3313" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 102 Number of groups = 6 + Number of bonds = 103 Number of angles = 102 + Number of dihedrals = 143 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 43 + + CHARMM> delete atom sele all end + SELRPN> 102 atoms have been selected out of 102 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 103 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 143 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-TYR-ALA-TYR-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TYR-ALA-TYR-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 6 + Number of bonds = 98 Number of angles = 98 + Number of dihedrals = 142 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 30 + Number of true-bonds = 98 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 892 892 882 + : Ran out of space. RESIZING + with mode 5 found 568 exclusions and 410 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4088 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4088 atom pairs and 978 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4088 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 209.13252 253.14434 26.45259 +ENER INTERN> 30.20122 34.26435 11.05318 25.13089 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 113.95886 4.98402 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TYR-ALA-TYR-CT2" + RDCMND substituted energy or value "?ENER" to "209.133" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.47165658 22.27524365 -125.47268449 + 690.34826661 520.63489691 + 1347.40456097 + + Transpose of the rotation matrix + 0.875894 0.478298 -0.063565 + -0.454697 0.862299 0.222917 + 0.161433 -0.166349 0.972763 + CENTER OF ATOMS BEFORE TRANSLATION 6.15666 2.54091 -0.55735 + AXIS OF ROTATION IS 0.375855 0.217247 0.900853 ANGLE IS 31.19 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -32.964878 5.073116 -2.827707 33.472610 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TYR-ALA-TYR-CT2" + RDCMND substituted energy or value "?RDIP" to "33.4726" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 6 + Number of bonds = 98 Number of angles = 98 + Number of dihedrals = 142 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 98 bonds deleted + DELTIC: 98 angles deleted + DELTIC: 142 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-TYR-ALA-TYR-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-TYR-ALA-TYR-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 31 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 101 Number of groups = 6 + Number of bonds = 102 Number of angles = 104 + Number of dihedrals = 148 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 31 + Number of true-bonds = 102 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 927 927 918 + : Ran out of space. RESIZING + with mode 5 found 589 exclusions and 425 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4461 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4461 atom pairs and 1014 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4461 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 293.52017 -84.38765 35.80480 +ENER INTERN> 30.20122 47.13590 46.12906 24.65466 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 146.37448 3.58485 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-TYR-ALA-TYR-CT3" + RDCMND substituted energy or value "?ENER" to "293.52" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 81.86356955 33.42894945 -115.85919364 + 799.25570690 605.14304539 + 1403.82045939 + + Transpose of the rotation matrix + 0.851230 0.522617 -0.047737 + -0.498974 0.834176 0.234894 + 0.162581 -0.176129 0.970848 + CENTER OF ATOMS BEFORE TRANSLATION 6.33448 2.74722 -0.53528 + AXIS OF ROTATION IS 0.366631 0.187603 0.911256 ANGLE IS 34.09 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 101 atoms have been selected out of 101 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -27.202320 1.949138 -1.428459 27.309446 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-TYR-ALA-TYR-CT3" + RDCMND substituted energy or value "?RDIP" to "27.3094" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 101 Number of groups = 6 + Number of bonds = 102 Number of angles = 104 + Number of dihedrals = 148 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 101 atoms have been selected out of 101 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 102 bonds deleted + DELTIC: 104 angles deleted + DELTIC: 148 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-TYR-ALA-TYR-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TYR-ALA-TYR-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 33 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 106 Number of groups = 7 + Number of bonds = 107 Number of angles = 101 + Number of dihedrals = 145 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 33 + Number of true-bonds = 107 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 47 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 975 975 963 + : Ran out of space. RESIZING + with mode 5 found 634 exclusions and 444 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4931 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4931 atom pairs and 1078 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4931 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 330.13861 -36.61844 36.42406 +ENER INTERN> 23.34174 38.87710 108.09450 38.08763 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 146.96649 -19.89885 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TYR-ALA-TYR-CTER" + RDCMND substituted energy or value "?ENER" to "330.139" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 117.15358003 -5.05523301 -244.38372963 + 714.77070926 633.39289484 + 1802.07166595 + + Transpose of the rotation matrix + 0.905636 0.409099 -0.111631 + -0.370945 0.891828 0.258928 + 0.205482 -0.193085 0.959424 + CENTER OF ATOMS BEFORE TRANSLATION 5.55389 2.40142 -0.38104 + AXIS OF ROTATION IS 0.472970 0.331815 0.816209 ANGLE IS 28.54 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 106 atoms have been selected out of 106 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -16.792475 -18.482012 -5.011754 25.469387 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TYR-ALA-TYR-CTER" + RDCMND substituted energy or value "?RDIP" to "25.4694" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 106 Number of groups = 7 + Number of bonds = 107 Number of angles = 101 + Number of dihedrals = 145 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 47 + + CHARMM> delete atom sele all end + SELRPN> 106 atoms have been selected out of 106 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 107 bonds deleted + DELTIC: 101 angles deleted + DELTIC: 145 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-TYR-ALA-TYR-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TYR-ALA-TYR-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 33 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 107 Number of groups = 7 + Number of bonds = 108 Number of angles = 102 + Number of dihedrals = 147 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 33 + Number of true-bonds = 108 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 47 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 981 981 972 + : Ran out of space. RESIZING + with mode 5 found 640 exclusions and 450 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5031 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5031 atom pairs and 1090 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5031 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 312.55681 17.58180 33.96171 +ENER INTERN> 23.24164 34.05795 117.29686 29.22963 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 142.65090 -28.59017 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TYR-ALA-TYR-CNEU" + RDCMND substituted energy or value "?ENER" to "312.557" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 117.51116728 -3.45615248 -242.93354286 + 732.98344869 650.20700985 + 1814.64670245 + + Transpose of the rotation matrix + 0.902685 0.416285 -0.108933 + -0.377770 0.887882 0.262591 + 0.206033 -0.195886 0.958738 + CENTER OF ATOMS BEFORE TRANSLATION 5.58980 2.44101 -0.37747 + AXIS OF ROTATION IS 0.472901 0.324874 0.819037 ANGLE IS 29.00 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 107 atoms have been selected out of 107 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 2.493710 -2.192287 -5.258804 6.219303 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TYR-ALA-TYR-CNEU" + RDCMND substituted energy or value "?RDIP" to "6.2193" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 107 Number of groups = 7 + Number of bonds = 108 Number of angles = 102 + Number of dihedrals = 147 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 47 + + CHARMM> delete atom sele all end + SELRPN> 107 atoms have been selected out of 107 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 108 bonds deleted + DELTIC: 102 angles deleted + DELTIC: 147 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-TYR-ALA-TYR-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TYR-ALA-TYR-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 34 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 111 Number of groups = 7 + Number of bonds = 112 Number of angles = 108 + Number of dihedrals = 150 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 34 + Number of true-bonds = 112 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 48 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1012 1012 1008 + : Ran out of space. RESIZING + with mode 5 found 668 exclusions and 462 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5437 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5437 atom pairs and 1130 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5437 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 556.06258 -243.50577 126.75532 +ENER INTERN> 23.24164 33.91809 97.66751 30.11731 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 375.91469 0.53334 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TYR-ALA-TYR-CT1" + RDCMND substituted energy or value "?ENER" to "556.063" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 119.70575436 4.85410962 -238.39937654 + 859.60402843 718.30126995 + 1853.79702131 + + Transpose of the rotation matrix + 0.884421 0.456307 -0.097899 + -0.419073 0.868824 0.263671 + 0.205372 -0.192169 0.959632 + CENTER OF ATOMS BEFORE TRANSLATION 5.70206 2.64676 -0.36387 + AXIS OF ROTATION IS 0.441492 0.293725 0.847827 ANGLE IS 31.08 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 111 atoms have been selected out of 111 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 4.050058 -0.862515 -5.486712 6.873929 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TYR-ALA-TYR-CT1" + RDCMND substituted energy or value "?RDIP" to "6.87393" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 111 Number of groups = 7 + Number of bonds = 112 Number of angles = 108 + Number of dihedrals = 150 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 48 + + CHARMM> delete atom sele all end + SELRPN> 111 atoms have been selected out of 111 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 112 bonds deleted + DELTIC: 108 angles deleted + DELTIC: 150 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-TYR-ALA-TYR-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TYR-ALA-TYR-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 33 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 106 Number of groups = 7 + Number of bonds = 107 Number of angles = 104 + Number of dihedrals = 149 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 33 + Number of true-bonds = 107 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 45 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 970 970 963 + : Ran out of space. RESIZING + with mode 5 found 622 exclusions and 446 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4943 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4943 atom pairs and 1068 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4943 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 297.89112 258.17146 34.11389 +ENER INTERN> 29.79470 32.10292 96.73699 32.56235 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 152.22894 -32.02480 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TYR-ALA-TYR-CT2" + RDCMND substituted energy or value "?ENER" to "297.891" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 117.15358003 -5.12692824 -245.20480935 + 714.09772208 624.52804809 + 1797.58364908 + + Transpose of the rotation matrix + 0.906634 0.406585 -0.112706 + -0.369177 0.893799 0.254621 + 0.204261 -0.189240 0.960451 + CENTER OF ATOMS BEFORE TRANSLATION 5.53357 2.39965 -0.38104 + AXIS OF ROTATION IS 0.468055 0.334245 0.818049 ANGLE IS 28.30 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 106 atoms have been selected out of 106 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -3.137946 -0.848298 -6.274982 7.066945 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TYR-ALA-TYR-CT2" + RDCMND substituted energy or value "?RDIP" to "7.06694" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 106 Number of groups = 7 + Number of bonds = 107 Number of angles = 104 + Number of dihedrals = 149 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 45 + + CHARMM> delete atom sele all end + SELRPN> 106 atoms have been selected out of 106 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 107 bonds deleted + DELTIC: 104 angles deleted + DELTIC: 149 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "TYR" + Parameter: PATCH -> "TYR" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-TYR-ALA-TYR-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-TYR-ALA-TYR-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "TYR" + Parameter: RESIDUE -> "TYR" + + RESIDUE SEQUENCE -- 3 RESIDUES + TYR ALA TYR + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 2 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TYR" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: TYR mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 TYR . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 34 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 110 Number of groups = 7 + Number of bonds = 111 Number of angles = 110 + Number of dihedrals = 155 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 34 + Number of true-bonds = 111 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "21" + Parameter: PATCHED -> "25" + Comparing "21" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 46 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1005 1005 999 + : Ran out of space. RESIZING + with mode 5 found 643 exclusions and 461 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5352 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 5352 atom pairs and 1104 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 5352 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 386.62148 -88.73036 41.22034 +ENER INTERN> 29.79470 44.97446 131.81288 32.08612 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 184.64450 -29.08118 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-TYR-ALA-TYR-CT3" + RDCMND substituted energy or value "?ENER" to "386.621" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 118.91177907 2.73157002 -237.69517243 + 829.10682639 724.63479278 + 1877.32464416 + + Transpose of the rotation matrix + 0.888957 0.447439 -0.097744 + -0.409310 0.871914 0.268757 + 0.205477 -0.198906 0.958236 + CENTER OF ATOMS BEFORE TRANSLATION 5.71949 2.59421 -0.36718 + AXIS OF ROTATION IS 0.457555 0.296667 0.838232 ANGLE IS 30.73 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 110 atoms have been selected out of 110 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 3.844196 -4.459285 -4.502994 7.412153 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-TYR-ALA-TYR-CT3" + RDCMND substituted energy or value "?RDIP" to "7.41215" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 110 Number of groups = 7 + Number of bonds = 111 Number of angles = 110 + Number of dihedrals = 155 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 46 + + CHARMM> delete atom sele all end + SELRPN> 110 atoms have been selected out of 110 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 111 bonds deleted + DELTIC: 110 angles deleted + DELTIC: 155 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "22" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "22" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "22" + Parameter: AA22 -> "VAL" + Parameter: RESIDUE <- "VAL" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "22" + Parameter: SPECIAL -> "2" + Comparing "22" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "VAL" + Parameter: PATCH <- "VAL" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-VAL-ALA-VAL-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-VAL-ALA-VAL-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 10 + Number of bonds = 72 Number of angles = 81 + Number of dihedrals = 110 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 20 + Number of true-bonds = 72 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 653 653 648 + : Ran out of space. RESIZING + with mode 5 found 414 exclusions and 306 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2214 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2214 atom pairs and 720 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2214 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 327.60283 59.01864 95.03478 +ENER INTERN> 21.77263 42.62727 22.49612 26.30795 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 191.90812 24.77075 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-VAL-ALA-VAL-CTER" + RDCMND substituted energy or value "?ENER" to "327.603" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 59.43345216 56.48272948 -38.59541497 + 526.07957367 400.37875668 + 643.87568322 + + Transpose of the rotation matrix + 0.756331 0.654136 0.008338 + -0.599378 0.687800 0.409484 + 0.262123 -0.314703 0.912279 + CENTER OF ATOMS BEFORE TRANSLATION 4.63124 2.54747 -0.37297 + AXIS OF ROTATION IS 0.492730 0.172673 0.852878 ANGLE IS 47.30 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 73 atoms have been selected out of 73 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -48.202937 -3.986146 1.510467 48.391053 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-VAL-ALA-VAL-CTER" + RDCMND substituted energy or value "?RDIP" to "48.3911" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 10 + Number of bonds = 72 Number of angles = 81 + Number of dihedrals = 110 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 73 atoms have been selected out of 73 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 72 bonds deleted + DELTIC: 81 angles deleted + DELTIC: 110 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-VAL-ALA-VAL-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-VAL-ALA-VAL-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 10 + Number of bonds = 73 Number of angles = 82 + Number of dihedrals = 112 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 20 + Number of true-bonds = 73 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 659 659 657 + : Ran out of space. RESIZING + with mode 5 found 420 exclusions and 312 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2281 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2281 atom pairs and 732 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2281 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 337.02079 -9.41795 93.19017 +ENER INTERN> 21.62262 37.14614 31.64767 17.46296 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 189.72362 41.69777 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-VAL-ALA-VAL-CNEU" + RDCMND substituted energy or value "?ENER" to "337.021" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 59.78443602 58.07703901 -36.92192272 + 545.09612251 420.39326642 + 662.17797757 + + Transpose of the rotation matrix + 0.753690 0.657143 0.010674 + -0.602016 0.683765 0.412362 + 0.263682 -0.317219 0.910957 + CENTER OF ATOMS BEFORE TRANSLATION 4.69271 2.60603 -0.36793 + AXIS OF ROTATION IS 0.493933 0.171288 0.852461 ANGLE IS 47.61 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 74 atoms have been selected out of 74 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -22.670911 3.596555 -0.142720 22.954864 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-VAL-ALA-VAL-CNEU" + RDCMND substituted energy or value "?RDIP" to "22.9549" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 74 Number of groups = 10 + Number of bonds = 73 Number of angles = 82 + Number of dihedrals = 112 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 74 atoms have been selected out of 74 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 73 bonds deleted + DELTIC: 82 angles deleted + DELTIC: 112 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-VAL-ALA-VAL-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-VAL-ALA-VAL-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 10 + Number of bonds = 77 Number of angles = 88 + Number of dihedrals = 115 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 21 + Number of true-bonds = 77 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 29 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 701 701 693 + : Ran out of space. RESIZING + with mode 5 found 448 exclusions and 324 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2555 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2555 atom pairs and 772 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2555 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 577.40597 -240.38519 169.45871 +ENER INTERN> 21.62262 37.00629 12.09231 18.31704 0.00000 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 421.05843 69.58929 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-VAL-ALA-VAL-CT1" + RDCMND substituted energy or value "?ENER" to "577.406" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 61.94333847 66.11033533 -31.71950595 + 671.59271996 501.29668054 + 716.63682949 + + Transpose of the rotation matrix + 0.721687 0.691926 0.020144 + -0.640898 0.656902 0.397153 + 0.261568 -0.299530 0.917531 + CENTER OF ATOMS BEFORE TRANSLATION 4.88378 2.90108 -0.34906 + AXIS OF ROTATION IS 0.457388 0.158500 0.875028 ANGLE IS 49.60 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 78 atoms have been selected out of 78 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -22.166119 5.177000 -0.642054 22.771701 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-VAL-ALA-VAL-CT1" + RDCMND substituted energy or value "?RDIP" to "22.7717" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 78 Number of groups = 10 + Number of bonds = 77 Number of angles = 88 + Number of dihedrals = 115 Number of impropers = 5 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 29 + + CHARMM> delete atom sele all end + SELRPN> 78 atoms have been selected out of 78 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 77 bonds deleted + DELTIC: 88 angles deleted + DELTIC: 115 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-VAL-ALA-VAL-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-VAL-ALA-VAL-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 10 + Number of bonds = 72 Number of angles = 84 + Number of dihedrals = 114 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 20 + Number of true-bonds = 72 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 26 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 655 655 648 + : Ran out of space. RESIZING + with mode 5 found 402 exclusions and 308 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2226 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2226 atom pairs and 710 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2226 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 334.43660 242.96937 92.97642 +ENER INTERN> 27.82077 35.47428 11.17663 19.14630 0.00000 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 203.89792 47.38070 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-VAL-ALA-VAL-CT2" + RDCMND substituted energy or value "?ENER" to "334.437" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 59.43345216 56.37490946 -39.39493833 + 524.61216833 391.27727328 + 636.30783214 + + Transpose of the rotation matrix + 0.754943 0.655743 0.007886 + -0.602878 0.689248 0.401840 + 0.258068 -0.308121 0.915676 + CENTER OF ATOMS BEFORE TRANSLATION 4.60188 2.54351 -0.37297 + AXIS OF ROTATION IS 0.484104 0.170592 0.858220 ANGLE IS 47.16 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 73 atoms have been selected out of 73 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -27.312780 6.104740 -1.203972 28.012592 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-VAL-ALA-VAL-CT2" + RDCMND substituted energy or value "?RDIP" to "28.0126" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 73 Number of groups = 10 + Number of bonds = 72 Number of angles = 84 + Number of dihedrals = 114 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 26 + + CHARMM> delete atom sele all end + SELRPN> 73 atoms have been selected out of 73 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 72 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 114 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-VAL-ALA-VAL-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-VAL-ALA-VAL-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 21 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 77 Number of groups = 10 + Number of bonds = 76 Number of angles = 90 + Number of dihedrals = 120 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 21 + Number of true-bonds = 76 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 27 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 688 688 684 + : Ran out of space. RESIZING + with mode 5 found 423 exclusions and 323 interactions(1-4) + found 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2503 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2503 atom pairs and 746 atom exclusions. + There are 0 group pairs and 19 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2503 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 407.60502 -73.16842 93.16788 +ENER INTERN> 27.82077 48.34582 46.91146 18.64274 0.00000 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 219.67517 50.76906 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-VAL-ALA-VAL-CT3" + RDCMND substituted energy or value "?ENER" to "407.605" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 61.15954218 64.16415178 -31.22677210 + 643.72595828 505.35951111 + 742.31127936 + + Transpose of the rotation matrix + 0.739722 0.672683 0.017600 + -0.620503 0.671756 0.404623 + 0.260360 -0.310229 0.914314 + CENTER OF ATOMS BEFORE TRANSLATION 4.90188 2.82960 -0.35360 + AXIS OF ROTATION IS 0.477388 0.162119 0.863607 ANGLE IS 48.48 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 77 atoms have been selected out of 77 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -23.151631 1.626815 0.865600 23.224853 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-VAL-ALA-VAL-CT3" + RDCMND substituted energy or value "?RDIP" to "23.2249" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 77 Number of groups = 10 + Number of bonds = 76 Number of angles = 90 + Number of dihedrals = 120 Number of impropers = 6 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 27 + + CHARMM> delete atom sele all end + SELRPN> 77 atoms have been selected out of 77 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 76 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 120 dihedrals deleted + DELTIC: 6 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-VAL-ALA-VAL-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-VAL-ALA-VAL-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 11 + Number of bonds = 81 Number of angles = 87 + Number of dihedrals = 117 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 23 + Number of true-bonds = 81 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 731 731 729 + : Ran out of space. RESIZING + with mode 5 found 468 exclusions and 342 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2853 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2853 atom pairs and 810 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2853 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 439.45348 -31.84846 94.28817 +ENER INTERN> 21.55276 41.01395 108.09056 29.06889 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 231.68039 13.37693 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-VAL-ALA-VAL-CTER" + RDCMND substituted energy or value "?ENER" to "439.453" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 90.28787402 32.21166631 -120.95152809 + 549.38519126 481.51227267 + 921.26969930 + + Transpose of the rotation matrix + 0.826274 0.558876 -0.070215 + -0.471249 0.754177 0.457321 + 0.308540 -0.344783 0.886526 + CENTER OF ATOMS BEFORE TRANSLATION 3.99321 2.36414 -0.16529 + AXIS OF ROTATION IS 0.590040 0.278618 0.757776 ANGLE IS 42.82 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 82 atoms have been selected out of 82 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -27.327767 -13.940876 -0.768319 30.687867 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-VAL-ALA-VAL-CTER" + RDCMND substituted energy or value "?RDIP" to "30.6879" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 11 + Number of bonds = 81 Number of angles = 87 + Number of dihedrals = 117 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 82 atoms have been selected out of 82 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 81 bonds deleted + DELTIC: 87 angles deleted + DELTIC: 117 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-VAL-ALA-VAL-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-VAL-ALA-VAL-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 11 + Number of bonds = 82 Number of angles = 88 + Number of dihedrals = 119 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 23 + Number of true-bonds = 82 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 33 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 748 748 738 + : Ran out of space. RESIZING + with mode 5 found 474 exclusions and 348 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2929 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2929 atom pairs and 822 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2929 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 415.87157 23.58191 92.90812 +ENER INTERN> 21.40275 35.53282 117.24211 20.22389 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 229.49843 -2.69843 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-VAL-ALA-VAL-CNEU" + RDCMND substituted energy or value "?ENER" to "415.872" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 90.52862115 32.94920129 -120.10459724 + 570.03210893 505.22642724 + 945.73860442 + + Transpose of the rotation matrix + 0.822649 0.564684 -0.066188 + -0.476884 0.748710 0.460451 + 0.309565 -0.347225 0.885214 + CENTER OF ATOMS BEFORE TRANSLATION 4.05570 2.41856 -0.16330 + AXIS OF ROTATION IS 0.589310 0.274163 0.759966 ANGLE IS 43.26 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.384882 -4.214339 -2.686217 5.012439 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-VAL-ALA-VAL-CNEU" + RDCMND substituted energy or value "?RDIP" to "5.01244" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 11 + Number of bonds = 82 Number of angles = 88 + Number of dihedrals = 119 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 33 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 82 bonds deleted + DELTIC: 88 angles deleted + DELTIC: 119 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-VAL-ALA-VAL-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-VAL-ALA-VAL-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 11 + Number of bonds = 86 Number of angles = 94 + Number of dihedrals = 122 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 24 + Number of true-bonds = 86 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 779 779 774 + : Ran out of space. RESIZING + with mode 5 found 502 exclusions and 360 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3239 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3239 atom pairs and 862 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3239 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 657.59225 -241.72069 164.00754 +ENER INTERN> 21.40275 35.39297 97.68676 21.07797 0.00000 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 460.83219 26.52962 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-VAL-ALA-VAL-CT1" + RDCMND substituted energy or value "?ENER" to "657.592" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 92.27555845 36.65135617 -117.38575213 + 705.59734870 603.69211903 + 1020.15551936 + + Transpose of the rotation matrix + 0.792710 0.607493 -0.050634 + -0.525806 0.723412 0.447440 + 0.308446 -0.328066 0.892879 + CENTER OF ATOMS BEFORE TRANSLATION 4.25629 2.69170 -0.15579 + AXIS OF ROTATION IS 0.546360 0.252979 0.798431 ANGLE IS 45.21 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 87 atoms have been selected out of 87 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 2.016499 -3.066251 -3.214073 4.878364 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-VAL-ALA-VAL-CT1" + RDCMND substituted energy or value "?RDIP" to "4.87836" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 11 + Number of bonds = 86 Number of angles = 94 + Number of dihedrals = 122 Number of impropers = 7 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 87 atoms have been selected out of 87 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 86 bonds deleted + DELTIC: 94 angles deleted + DELTIC: 122 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-VAL-ALA-VAL-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-VAL-ALA-VAL-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 11 + Number of bonds = 81 Number of angles = 90 + Number of dihedrals = 121 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 23 + Number of true-bonds = 81 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 31 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 733 733 729 + : Ran out of space. RESIZING + with mode 5 found 456 exclusions and 344 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2865 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2865 atom pairs and 800 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2865 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 409.49412 248.09813 92.68634 +ENER INTERN> 27.60090 33.86096 96.77107 21.90724 0.00000 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 243.67198 -0.80803 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-VAL-ALA-VAL-CT2" + RDCMND substituted energy or value "?ENER" to "409.494" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 90.28787402 32.16388384 -121.30585186 + 547.81191662 471.83428085 + 910.97330513 + + Transpose of the rotation matrix + 0.826027 0.559082 -0.071462 + -0.473413 0.757016 0.450340 + 0.305875 -0.338162 0.889993 + CENTER OF ATOMS BEFORE TRANSLATION 3.96707 2.36062 -0.16529 + AXIS OF ROTATION IS 0.582851 0.278923 0.763208 ANGLE IS 42.56 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 82 atoms have been selected out of 82 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -5.023911 -2.393649 -4.072967 6.896252 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-VAL-ALA-VAL-CT2" + RDCMND substituted energy or value "?RDIP" to "6.89625" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 82 Number of groups = 11 + Number of bonds = 81 Number of angles = 90 + Number of dihedrals = 121 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 82 atoms have been selected out of 82 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 81 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 121 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "VAL" + Parameter: PATCH -> "VAL" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-VAL-ALA-VAL-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-VAL-ALA-VAL-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "VAL" + Parameter: RESIDUE -> "VAL" + + RESIDUE SEQUENCE -- 3 RESIDUES + VAL ALA VAL + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "VAL" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: VAL mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 VAL . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is VAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 11 + Number of bonds = 85 Number of angles = 96 + Number of dihedrals = 127 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 24 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "22" + Parameter: PATCHED -> "25" + Comparing "22" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 32 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 766 766 765 + : Ran out of space. RESIZING + with mode 5 found 477 exclusions and 359 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3178 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3178 atom pairs and 836 atom exclusions. + There are 0 group pairs and 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3178 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 487.14483 -77.65071 92.99955 +ENER INTERN> 27.60090 46.73250 132.50591 21.40367 0.00000 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 259.44920 7.06265 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-VAL-ALA-VAL-CT3" + RDCMND substituted energy or value "?ENER" to "487.145" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 91.59063708 35.75092514 -117.26502923 + 675.39584960 604.41292573 + 1047.20342546 + + Transpose of the rotation matrix + 0.805662 0.590072 -0.052195 + -0.506552 0.731937 0.455712 + 0.307107 -0.340711 0.888595 + CENTER OF ATOMS BEFORE TRANSLATION 4.26520 2.62527 -0.15760 + AXIS OF ROTATION IS 0.568009 0.256254 0.782112 ANGLE IS 44.51 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 86 atoms have been selected out of 86 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 1.412451 -6.350686 -1.548554 6.687619 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-VAL-ALA-VAL-CT3" + RDCMND substituted energy or value "?RDIP" to "6.68762" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 11 + Number of bonds = 85 Number of angles = 96 + Number of dihedrals = 127 Number of impropers = 8 + Number of cross-terms = 3 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 32 + + CHARMM> delete atom sele all end + SELRPN> 86 atoms have been selected out of 86 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 127 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "23" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "23" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "23" + Parameter: AA23 -> "HSD" + Parameter: RESIDUE <- "HSD" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "23" + Parameter: SPECIAL -> "2" + Comparing "23" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "HSD" + Parameter: PATCH <- "HSD" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 83 + Number of dihedrals = 118 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 26 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 762 762 756 + : Ran out of space. RESIZING + with mode 5 found 502 exclusions and 324 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2901 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2901 atom pairs and 826 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2901 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 216.77863 270.36620 32.96312 +ENER INTERN> 20.29512 40.69502 22.43026 37.89697 0.00184 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 75.69502 22.04439 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CTER" + RDCMND substituted energy or value "?ENER" to "216.779" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 61.67539275 30.93571237 -79.45655448 + 547.37941911 427.12908499 + 951.48620513 + + Transpose of the rotation matrix + 0.845755 0.531783 -0.043657 + -0.501121 0.819753 0.277277 + 0.183239 -0.212631 0.959798 + CENTER OF ATOMS BEFORE TRANSLATION 5.54480 2.55756 -0.43726 + AXIS OF ROTATION IS 0.420343 0.194677 0.886235 ANGLE IS 35.64 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -58.106085 -10.082679 1.642658 58.997253 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CTER" + RDCMND substituted energy or value "?RDIP" to "58.9973" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 83 + Number of dihedrals = 118 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 83 angles deleted + DELTIC: 118 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 6 + Number of bonds = 85 Number of angles = 84 + Number of dihedrals = 120 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 26 + Number of true-bonds = 85 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 770 770 765 + : Ran out of space. RESIZING + with mode 5 found 508 exclusions and 330 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2978 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2978 atom pairs and 838 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2978 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 217.22891 -0.45028 29.48561 +ENER INTERN> 20.13184 35.58179 31.56809 29.04265 0.00184 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 70.34289 32.83981 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CNEU" + RDCMND substituted energy or value "?ENER" to "217.229" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 62.07807181 32.64621973 -77.74571251 + 563.26222840 443.37557057 + 964.97130465 + + Transpose of the rotation matrix + 0.841301 0.539074 -0.040152 + -0.508318 0.814196 0.280531 + 0.183918 -0.215601 0.959005 + CENTER OF ATOMS BEFORE TRANSLATION 5.59194 2.60469 -0.43206 + AXIS OF ROTATION IS 0.420302 0.189823 0.887307 ANGLE IS 36.17 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -36.976351 2.259328 1.328915 37.069140 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CNEU" + RDCMND substituted energy or value "?RDIP" to "37.0691" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 6 + Number of bonds = 85 Number of angles = 84 + Number of dihedrals = 120 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 4 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 120 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 4 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 6 + Number of bonds = 89 Number of angles = 90 + Number of dihedrals = 123 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 27 + Number of true-bonds = 89 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 805 805 801 + : Ran out of space. RESIZING + with mode 5 found 536 exclusions and 342 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3292 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3292 atom pairs and 878 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3292 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 465.38849 -248.15959 139.51568 +ENER INTERN> 20.13184 35.44193 12.03253 29.92292 0.00184 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 307.04143 63.09600 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT1" + RDCMND substituted energy or value "?ENER" to "465.388" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 64.43600461 41.62488666 -72.36353449 + 677.31551517 510.66600364 + 1007.31747606 + + Transpose of the rotation matrix + 0.809345 0.586759 -0.025956 + -0.558126 0.782109 0.277130 + 0.182909 -0.209807 0.960482 + CENTER OF ATOMS BEFORE TRANSLATION 5.74023 2.85209 -0.41242 + AXIS OF ROTATION IS 0.385985 0.165563 0.907527 ANGLE IS 39.11 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -36.167280 4.955830 1.026996 36.519681 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT1" + RDCMND substituted energy or value "?RDIP" to "36.5197" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 6 + Number of bonds = 89 Number of angles = 90 + Number of dihedrals = 123 Number of impropers = 11 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 123 dihedrals deleted + DELTIC: 11 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 86 + Number of dihedrals = 122 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 26 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 34 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 758 758 756 + : Ran out of space. RESIZING + with mode 5 found 490 exclusions and 326 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2913 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2913 atom pairs and 816 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2913 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 207.59526 257.79324 29.37139 +ENER INTERN> 26.23525 33.82957 11.12086 32.72070 0.00184 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 75.60602 38.54102 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT2" + RDCMND substituted energy or value "?ENER" to "207.595" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 61.67539275 30.87862496 -80.40065789 + 547.22211102 418.75110305 + 946.48872878 + + Transpose of the rotation matrix + 0.846596 0.530339 -0.044894 + -0.500377 0.821829 0.272431 + 0.181376 -0.208175 0.961127 + CENTER OF ATOMS BEFORE TRANSLATION 5.51878 2.55599 -0.43726 + AXIS OF ROTATION IS 0.414477 0.195136 0.888893 ANGLE IS 35.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 83 atoms have been selected out of 83 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -41.948994 4.112879 0.430937 42.152337 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT2" + RDCMND substituted energy or value "?RDIP" to "42.1523" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 6 + Number of bonds = 84 Number of angles = 86 + Number of dihedrals = 122 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 34 + + CHARMM> delete atom sele all end + SELRPN> 83 atoms have been selected out of 83 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 86 angles deleted + DELTIC: 122 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-HSD-ALA-HSD-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-HSD-ALA-HSD-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 6 + Number of bonds = 88 Number of angles = 92 + Number of dihedrals = 128 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 27 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 8 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 35 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 795 795 792 + : Ran out of space. RESIZING + with mode 5 found 511 exclusions and 341 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3230 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3230 atom pairs and 852 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3230 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 323.23141 -115.63615 47.07735 +ENER INTERN> 26.23525 46.70112 47.03407 32.23739 0.00184 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 135.26155 40.32019 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT3" + RDCMND substituted energy or value "?ENER" to "323.231" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 63.60359137 39.28738446 -71.61372452 + 649.05550414 515.36546491 + 1031.01269592 + + Transpose of the rotation matrix + 0.821548 0.569476 -0.027475 + -0.540306 0.793040 0.281350 + 0.182011 -0.216297 0.959212 + CENTER OF ATOMS BEFORE TRANSLATION 5.76089 2.78768 -0.41716 + AXIS OF ROTATION IS 0.403227 0.169740 0.899220 ANGLE IS 38.10 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 87 atoms have been selected out of 87 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -36.976633 1.009628 2.107301 37.050390 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-HSD-ALA-HSD-CT3" + RDCMND substituted energy or value "?RDIP" to "37.0504" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 6 + Number of bonds = 88 Number of angles = 92 + Number of dihedrals = 128 Number of impropers = 12 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 35 + + CHARMM> delete atom sele all end + SELRPN> 87 atoms have been selected out of 87 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 92 angles deleted + DELTIC: 128 dihedrals deleted + DELTIC: 12 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 89 + Number of dihedrals = 125 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 29 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 840 840 837 + : Ran out of space. RESIZING + with mode 5 found 556 exclusions and 360 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3630 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3630 atom pairs and 916 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3630 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 323.44646 -0.21505 39.31714 +ENER INTERN> 19.94442 38.13739 108.08595 44.41999 0.00184 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 112.83892 5.34795 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CTER" + RDCMND substituted energy or value "?ENER" to "323.446" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 94.92337109 5.29298881 -180.54104298 + 571.25922354 522.24642862 + 1325.52563456 + + Transpose of the rotation matrix + 0.888629 0.446589 -0.104387 + -0.395522 0.861463 0.318504 + 0.232166 -0.241744 0.942156 + CENTER OF ATOMS BEFORE TRANSLATION 4.88674 2.39317 -0.24587 + AXIS OF ROTATION IS 0.525574 0.315724 0.789994 ANGLE IS 32.21 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -32.703785 -18.374294 -1.180854 37.530609 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CTER" + RDCMND substituted energy or value "?RDIP" to "37.5306" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 89 + Number of dihedrals = 125 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 89 angles deleted + DELTIC: 125 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 7 + Number of bonds = 94 Number of angles = 90 + Number of dihedrals = 127 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 29 + Number of true-bonds = 94 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 848 848 846 + : Ran out of space. RESIZING + with mode 5 found 562 exclusions and 366 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3716 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3716 atom pairs and 928 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3716 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 291.22979 32.21667 37.22880 +ENER INTERN> 19.78114 33.02416 117.22378 35.56566 0.00184 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 107.48913 -16.52593 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CNEU" + RDCMND substituted energy or value "?ENER" to "291.23" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 95.19692690 6.29588314 -179.41789054 + 588.47445602 541.83912911 + 1344.61257926 + + Transpose of the rotation matrix + 0.885184 0.454200 -0.100757 + -0.402821 0.856588 0.322479 + 0.232777 -0.244866 0.941199 + CENTER OF ATOMS BEFORE TRANSLATION 4.93640 2.43751 -0.24322 + AXIS OF ROTATION IS 0.525047 0.308668 0.793127 ANGLE IS 32.70 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 93 atoms have been selected out of 93 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -9.504739 -4.834480 -1.879174 10.827906 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CNEU" + RDCMND substituted energy or value "?RDIP" to "10.8279" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 7 + Number of bonds = 94 Number of angles = 90 + Number of dihedrals = 127 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 5 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 93 atoms have been selected out of 93 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 127 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 7 + Number of bonds = 98 Number of angles = 96 + Number of dihedrals = 130 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 30 + Number of true-bonds = 98 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 883 883 882 + : Ran out of space. RESIZING + with mode 5 found 590 exclusions and 378 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4066 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4066 atom pairs and 968 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4066 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 540.72618 -249.49639 135.91278 +ENER INTERN> 19.78114 32.88431 97.68821 36.44594 0.00184 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 344.18670 15.06803 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT1" + RDCMND substituted energy or value "?ENER" to "540.726" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 97.06897392 11.52859904 -175.76320017 + 710.11387443 625.62426078 + 1405.19068099 + + Transpose of the rotation matrix + 0.861635 0.500144 -0.086258 + -0.451544 0.833034 0.319628 + 0.231716 -0.236454 0.943609 + CENTER OF ATOMS BEFORE TRANSLATION 5.09797 2.66885 -0.23319 + AXIS OF ROTATION IS 0.484734 0.277176 0.829582 ANGLE IS 35.00 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 97 atoms have been selected out of 97 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -7.986433 -3.025748 -2.216808 8.823407 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT1" + RDCMND substituted energy or value "?RDIP" to "8.82341" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 7 + Number of bonds = 98 Number of angles = 96 + Number of dihedrals = 130 Number of impropers = 13 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 97 atoms have been selected out of 97 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 98 bonds deleted + DELTIC: 96 angles deleted + DELTIC: 130 dihedrals deleted + DELTIC: 13 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 29 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 92 + Number of dihedrals = 129 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 29 + Number of true-bonds = 93 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 841 841 837 + : Ran out of space. RESIZING + with mode 5 found 544 exclusions and 362 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3642 atom pairs and 906 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3642 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 277.97535 262.75083 37.00217 +ENER INTERN> 25.88454 31.27195 96.77655 39.24371 0.00184 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 112.75161 -14.44485 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT2" + RDCMND substituted energy or value "?ENER" to "277.975" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 94.92337109 5.26088952 -181.07189654 + 571.05901142 513.42792983 + 1317.69203030 + + Transpose of the rotation matrix + 0.889314 0.444912 -0.105711 + -0.394995 0.863833 0.312685 + 0.230434 -0.236320 0.943956 + CENTER OF ATOMS BEFORE TRANSLATION 4.86328 2.39176 -0.24587 + AXIS OF ROTATION IS 0.518797 0.317650 0.793693 ANGLE IS 31.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 92 atoms have been selected out of 92 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -14.995116 -3.319680 -3.090358 15.666017 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT2" + RDCMND substituted energy or value "?RDIP" to "15.666" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 7 + Number of bonds = 93 Number of angles = 92 + Number of dihedrals = 129 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 92 atoms have been selected out of 92 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 92 angles deleted + DELTIC: 129 dihedrals deleted + DELTIC: 14 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "HSD" + Parameter: PATCH -> "HSD" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-HSD-ALA-HSD-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-HSD-ALA-HSD-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "HSD" + Parameter: RESIDUE -> "HSD" + + RESIDUE SEQUENCE -- 3 RESIDUES + HSD ALA HSD + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 2 HSE - 0 HSP - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HSD" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: HSD mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 HSD . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 30 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HSD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 7 + Number of bonds = 97 Number of angles = 98 + Number of dihedrals = 135 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 30 + Number of true-bonds = 97 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "23" + Parameter: PATCHED -> "25" + Comparing "23" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 875 875 873 + : Ran out of space. RESIZING + with mode 5 found 565 exclusions and 377 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3995 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3995 atom pairs and 942 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3995 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 397.86157 -119.88622 51.00163 +ENER INTERN> 25.88454 44.14349 132.68976 38.76040 0.00184 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 172.40705 -8.41552 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT3" + RDCMND substituted energy or value "?ENER" to "397.862" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 96.35366010 10.16514633 -175.49102133 + 679.77881898 626.89040567 + 1430.80546854 + + Transpose of the rotation matrix + 0.869494 0.486271 -0.086720 + -0.436465 0.838578 0.326015 + 0.231253 -0.245618 0.941379 + CENTER OF ATOMS BEFORE TRANSLATION 5.11000 2.60857 -0.23562 + AXIS OF ROTATION IS 0.505393 0.281127 0.815810 ANGLE IS 34.44 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 96 atoms have been selected out of 96 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -8.407280 -6.682247 -0.977918 10.783836 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-HSD-ALA-HSD-CT3" + RDCMND substituted energy or value "?RDIP" to "10.7838" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 7 + Number of bonds = 97 Number of angles = 98 + Number of dihedrals = 135 Number of impropers = 14 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 96 atoms have been selected out of 96 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 97 bonds deleted + DELTIC: 98 angles deleted + DELTIC: 135 dihedrals deleted + DELTIC: 14 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "24" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "24" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "24" + Parameter: AA24 -> "ASP" + Parameter: RESIDUE <- "ASP" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "24" + Parameter: SPECIAL -> "2" + Comparing "24" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set patch @residue ! for variable "nam" below + Parameter: RESIDUE -> "ASP" + Parameter: PATCH <- "ASP" + + CHARMM> endif + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 63 + Number of dihedrals = 86 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 22 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 675 675 666 + : Ran out of space. RESIZING + with mode 5 found 458 exclusions and 300 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2317 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2317 atom pairs and 758 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2317 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 266.82884 131.03274 48.31176 +ENER INTERN> 21.41378 47.20830 30.31909 39.02720 1.31251 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 117.26004 12.56792 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CTER" + RDCMND substituted energy or value "?ENER" to "266.829" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 67.50785654 53.86357363 -58.45932962 + 476.28204005 383.25312473 + 728.22870694 + + Transpose of the rotation matrix + 0.810860 0.584996 -0.016935 + -0.524880 0.739724 0.421081 + 0.258858 -0.332549 0.906865 + CENTER OF ATOMS BEFORE TRANSLATION 5.03087 2.62226 -0.36885 + AXIS OF ROTATION IS 0.550250 0.201365 0.810356 ANGLE IS 43.22 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 75 atoms have been selected out of 75 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -59.385458 15.430948 0.296101 61.358246 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CTER" + RDCMND substituted energy or value "?RDIP" to "61.3582" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 63 + Number of dihedrals = 86 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 75 atoms have been selected out of 75 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 63 angles deleted + DELTIC: 86 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 76 Number of groups = 6 + Number of bonds = 75 Number of angles = 64 + Number of dihedrals = 88 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 22 + Number of true-bonds = 75 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 679 679 675 + : Ran out of space. RESIZING + with mode 5 found 464 exclusions and 306 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2386 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2386 atom pairs and 770 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2386 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 172.63443 94.19441 46.58760 +ENER INTERN> 21.39535 42.66099 39.60347 30.17041 1.31251 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 116.99820 -77.22650 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CNEU" + RDCMND substituted energy or value "?ENER" to "172.634" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 67.85587356 55.33109879 -56.87719364 + 492.76745151 401.21907585 + 744.81584134 + + Transpose of the rotation matrix + 0.806796 0.590674 -0.013591 + -0.530381 0.734195 0.423857 + 0.260339 -0.334758 0.905627 + CENTER OF ATOMS BEFORE TRANSLATION 5.08807 2.67531 -0.36400 + AXIS OF ROTATION IS 0.549303 0.198349 0.811741 ANGLE IS 43.67 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 76 atoms have been selected out of 76 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -35.109986 25.146936 -1.732490 43.221303 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CNEU" + RDCMND substituted energy or value "?RDIP" to "43.2213" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 76 Number of groups = 6 + Number of bonds = 75 Number of angles = 64 + Number of dihedrals = 88 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 76 atoms have been selected out of 76 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 75 bonds deleted + DELTIC: 64 angles deleted + DELTIC: 88 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 80 Number of groups = 6 + Number of bonds = 79 Number of angles = 70 + Number of dihedrals = 91 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 23 + Number of true-bonds = 79 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 716 716 711 + : Ran out of space. RESIZING + with mode 5 found 492 exclusions and 318 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2668 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2668 atom pairs and 810 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2668 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 442.91106 -270.27663 159.38130 +ENER INTERN> 21.39535 42.52113 19.85445 31.05569 1.31251 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 371.55376 -42.50183 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT1" + RDCMND substituted energy or value "?ENER" to "442.911" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 70.00453004 62.91977342 -51.91521447 + 608.06145784 475.52583597 + 795.45607263 + + Transpose of the rotation matrix + 0.772445 0.635081 -0.000128 + -0.580218 0.705797 0.406445 + 0.258215 -0.313882 0.913675 + CENTER OF ATOMS BEFORE TRANSLATION 5.26743 2.94963 -0.34580 + AXIS OF ROTATION IS 0.501563 0.179884 0.846213 ANGLE IS 45.90 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 80 atoms have been selected out of 80 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -30.190080 28.564778 -2.144693 41.617150 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT1" + RDCMND substituted energy or value "?RDIP" to "41.6172" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 80 Number of groups = 6 + Number of bonds = 79 Number of angles = 70 + Number of dihedrals = 91 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 80 atoms have been selected out of 80 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 79 bonds deleted + DELTIC: 70 angles deleted + DELTIC: 91 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 22 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 66 + Number of dihedrals = 90 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 22 + Number of true-bonds = 74 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 36 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 676 676 666 + : Ran out of space. RESIZING + with mode 5 found 446 exclusions and 302 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2329 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2329 atom pairs and 748 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2329 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 154.70496 288.20610 47.22765 +ENER INTERN> 28.52477 40.50323 18.90583 34.90544 1.31251 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 113.74868 -72.73550 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT2" + RDCMND substituted energy or value "?ENER" to "154.705" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 67.50785654 53.78820793 -59.25361031 + 475.57095333 374.75163963 + 721.54469253 + + Transpose of the rotation matrix + 0.810794 0.585058 -0.017902 + -0.526815 0.742725 0.413311 + 0.255108 -0.325679 0.910414 + CENTER OF ATOMS BEFORE TRANSLATION 5.00216 2.61954 -0.36885 + AXIS OF ROTATION IS 0.542306 0.200347 0.815945 ANGLE IS 42.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 75 atoms have been selected out of 75 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -41.098760 27.193290 -2.670741 49.352973 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT2" + RDCMND substituted energy or value "?RDIP" to "49.353" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 75 Number of groups = 6 + Number of bonds = 74 Number of angles = 66 + Number of dihedrals = 90 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 36 + + CHARMM> delete atom sele all end + SELRPN> 75 atoms have been selected out of 75 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 74 bonds deleted + DELTIC: 66 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 2 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-ASP-ALA-ASP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-ASP-ALA-ASP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 23 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 6 + Number of bonds = 78 Number of angles = 72 + Number of dihedrals = 96 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 23 + Number of true-bonds = 78 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 37 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 711 711 702 + : Ran out of space. RESIZING + with mode 5 found 467 exclusions and 317 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2614 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2614 atom pairs and 784 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2614 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 968.70737 -814.00242 765.31706 +ENER INTERN> 28.52477 53.37478 52.94173 34.42695 1.31251 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 918.61134 -115.92471 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT3" + RDCMND substituted energy or value "?ENER" to "968.707" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 69.22307130 61.01065578 -51.38476888 + 581.11312032 479.21587110 + 820.44319945 + + Transpose of the rotation matrix + 0.788249 0.615350 -0.002631 + -0.558647 0.717394 0.416244 + 0.258023 -0.326635 0.909249 + CENTER OF ATOMS BEFORE TRANSLATION 5.28661 2.88062 -0.35018 + AXIS OF ROTATION IS 0.525547 0.184399 0.830540 ANGLE IS 44.97 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 79 atoms have been selected out of 79 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -31.918304 24.203280 -0.577594 40.061334 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-ASP-ALA-ASP-CT3" + RDCMND substituted energy or value "?RDIP" to "40.0613" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 79 Number of groups = 6 + Number of bonds = 78 Number of angles = 72 + Number of dihedrals = 96 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 37 + + CHARMM> delete atom sele all end + SELRPN> 79 atoms have been selected out of 79 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 78 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 96 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 69 + Number of dihedrals = 93 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -3.00000 + Number of Drudes = 25 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 43 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 754 754 747 + : Ran out of space. RESIZING + with mode 5 found 512 exclusions and 336 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2974 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2974 atom pairs and 848 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2974 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 501.26065 467.44672 51.84572 +ENER INTERN> 20.96488 45.28541 115.99139 42.98579 1.31251 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 156.85806 123.19262 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CTER" + RDCMND substituted energy or value "?ENER" to "501.261" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 98.32132437 28.43874165 -146.94496679 + 501.70594984 473.71287366 + 1045.03698987 + + Transpose of the rotation matrix + 0.865711 0.492029 -0.091932 + -0.402734 0.793762 0.455794 + 0.297236 -0.357561 0.885325 + CENTER OF ATOMS BEFORE TRANSLATION 4.36521 2.43528 -0.16656 + AXIS OF ROTATION IS 0.640298 0.306365 0.704385 ANGLE IS 39.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -3.000000 + DIPOLE MOMENT (DEBYES) : -45.711155 7.417549 -2.660720 46.385441 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CTER" + RDCMND substituted energy or value "?RDIP" to "46.3854" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 69 + Number of dihedrals = 93 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -3.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 43 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 69 angles deleted + DELTIC: 93 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 7 + Number of bonds = 84 Number of angles = 70 + Number of dihedrals = 95 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 25 + Number of true-bonds = 84 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 43 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 758 758 756 + : Ran out of space. RESIZING + with mode 5 found 518 exclusions and 342 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3052 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3052 atom pairs and 860 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3052 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 374.23035 127.03030 50.91007 +ENER INTERN> 20.94645 40.73810 125.27576 34.12900 1.31251 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 156.59866 0.55987 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CNEU" + RDCMND substituted energy or value "?ENER" to "374.23" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 98.56249442 29.13311606 -146.11997732 + 519.73848699 495.28154253 + 1067.80690997 + + Transpose of the rotation matrix + 0.861962 0.499339 -0.087648 + -0.409949 0.788219 0.458968 + 0.298267 -0.359682 0.884119 + CENTER OF ATOMS BEFORE TRANSLATION 4.42418 2.48491 -0.16460 + AXIS OF ROTATION IS 0.638107 0.300806 0.708756 ANGLE IS 39.90 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 85 atoms have been selected out of 85 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -19.175913 19.024321 -4.938121 27.459524 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CNEU" + RDCMND substituted energy or value "?RDIP" to "27.4595" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 7 + Number of bonds = 84 Number of angles = 70 + Number of dihedrals = 95 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 43 + + CHARMM> delete atom sele all end + SELRPN> 85 atoms have been selected out of 85 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 70 angles deleted + DELTIC: 95 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 7 + Number of bonds = 88 Number of angles = 76 + Number of dihedrals = 98 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 26 + Number of true-bonds = 88 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 44 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 798 798 792 + : Ran out of space. RESIZING + with mode 5 found 546 exclusions and 354 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3370 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3370 atom pairs and 900 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3370 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 645.84301 -271.61266 153.52082 +ENER INTERN> 20.94645 40.59825 105.52674 35.01427 1.31251 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 411.15321 36.62157 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT1" + RDCMND substituted energy or value "?ENER" to "645.843" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 100.31116778 32.70261335 -143.44683664 + 643.76073200 586.99288848 + 1138.58747750 + + Transpose of the rotation matrix + 0.834337 0.546672 -0.070940 + -0.464462 0.766441 0.443669 + 0.296913 -0.337220 0.893378 + CENTER OF ATOMS BEFORE TRANSLATION 4.61525 2.74005 -0.15720 + AXIS OF ROTATION IS 0.587368 0.276692 0.760553 ANGLE IS 41.66 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 89 atoms have been selected out of 89 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -13.368242 22.427785 -5.352040 26.652575 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT1" + RDCMND substituted energy or value "?RDIP" to "26.6526" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 7 + Number of bonds = 88 Number of angles = 76 + Number of dihedrals = 98 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 44 + + CHARMM> delete atom sele all end + SELRPN> 89 atoms have been selected out of 89 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 76 angles deleted + DELTIC: 98 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 9 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 72 + Number of dihedrals = 97 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 25 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 752 752 747 + : Ran out of space. RESIZING + with mode 5 found 500 exclusions and 338 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2986 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2986 atom pairs and 838 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2986 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 352.58158 293.26143 51.32093 +ENER INTERN> 28.07587 38.58034 104.57812 38.86403 1.31251 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 153.34844 1.33227 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT2" + RDCMND substituted energy or value "?ENER" to "352.582" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 98.32132437 28.40471015 -147.30362539 + 500.91851426 464.67337050 + 1035.49274809 + + Transpose of the rotation matrix + 0.866057 0.491145 -0.093395 + -0.403876 0.797426 0.448327 + 0.294669 -0.350556 0.888977 + CENTER OF ATOMS BEFORE TRANSLATION 4.33958 2.43285 -0.16656 + AXIS OF ROTATION IS 0.633581 0.307768 0.709827 ANGLE IS 39.08 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 84 atoms have been selected out of 84 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -25.846223 20.324845 -6.185197 33.457185 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT2" + RDCMND substituted energy or value "?RDIP" to "33.4572" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 7 + Number of bonds = 83 Number of angles = 72 + Number of dihedrals = 97 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 84 atoms have been selected out of 84 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 83 bonds deleted + DELTIC: 72 angles deleted + DELTIC: 97 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 3 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "ASP" + Parameter: PATCH -> "ASP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-ASP-ALA-ASP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-ASP-ALA-ASP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "ASP" + Parameter: RESIDUE -> "ASP" + + RESIDUE SEQUENCE -- 3 RESIDUES + ASP ALA ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 2 GLU - 0 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ASP" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: ASP mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 ASP . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 26 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ASP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 7 + Number of bonds = 87 Number of angles = 78 + Number of dihedrals = 103 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 26 + Number of true-bonds = 87 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "24" + Parameter: PATCHED -> "25" + Comparing "24" and "25". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 42 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 791 791 783 + : Ran out of space. RESIZING + with mode 5 found 521 exclusions and 353 interactions(1-4) + found 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3307 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3307 atom pairs and 874 atom exclusions. + There are 0 group pairs and 11 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3307 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1170.96419 -818.38261 727.57528 +ENER INTERN> 28.07587 51.45189 138.61403 38.38554 1.31251 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 958.21104 -37.47668 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT3" + RDCMND substituted energy or value "?ENER" to "1170.96" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 99.62580702 31.80252668 -143.30969425 + 614.49529681 587.25902360 + 1165.14570859 + + Transpose of the rotation matrix + 0.844812 0.530189 -0.072052 + -0.445439 0.771505 0.454274 + 0.296440 -0.351682 0.887943 + CENTER OF ATOMS BEFORE TRANSLATION 4.62505 2.67571 -0.15898 + AXIS OF ROTATION IS 0.611486 0.279578 0.740217 ANGLE IS 41.22 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 88 atoms have been selected out of 88 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -2.000000 + DIPOLE MOMENT (DEBYES) : -14.580445 18.267604 -3.658721 23.657577 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-ASP-ALA-ASP-CT3" + RDCMND substituted energy or value "?RDIP" to "23.6576" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 7 + Number of bonds = 87 Number of angles = 78 + Number of dihedrals = 103 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 42 + + CHARMM> delete atom sele all end + SELRPN> 88 atoms have been selected out of 88 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 87 bonds deleted + DELTIC: 78 angles deleted + DELTIC: 103 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "25" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @aa@@countaa + Parameter: COUNTAA -> "25" + Parameter: AA25 -> "GLU" + Parameter: RESIDUE <- "GLU" + + CHARMM> if @countaa le @special then + Parameter: COUNTAA -> "25" + Parameter: SPECIAL -> "2" + Comparing "25" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> set varp + Parameter: VARP <- "" + + CHARMM> endif + + CHARMM> set maxnt @@@{varp}npn + Parameter: VARP -> "" + Parameter: NPN -> "2" + Parameter: MAXNT <- "2" + + CHARMM> set maxct @@@{varp}npc + Parameter: VARP -> "" + Parameter: NPC -> "5" + Parameter: MAXCT <- "5" + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> set patch @pa@@countaa + Parameter: COUNTAA -> "25" + Parameter: PA25 -> "GLUP" + Parameter: PATCH <- "GLUP" + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> + + CHARMM> set countnt 1 + Parameter: COUNTNT <- "1" + + CHARMM> label loop_nt + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "1" + Parameter: VARP -> "" + Parameter: PN1 -> "NTER" + Parameter: FIRST <- "NTER" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "NTER-GLUP-ALA-GLUP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLUP-ALA-GLUP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 75 + Number of dihedrals = 104 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 24 + Number of true-bonds = 82 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 8 + Number of bonds = 83 Number of angles = 75 + Number of dihedrals = 104 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 24 + Number of true-bonds = 82 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 9 + Number of bonds = 84 Number of angles = 75 + Number of dihedrals = 104 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 28 + Number of true-bonds = 83 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 757 757 756 + : Ran out of space. RESIZING + with mode 5 found 514 exclusions and 344 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3056 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3056 atom pairs and 858 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3056 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 93.63325 1077.33094 34.62906 +ENER INTERN> 26.21906 52.48634 42.87620 30.78151 0.01443 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 30.61792 -87.08222 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CTER" + RDCMND substituted energy or value "?ENER" to "93.6333" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 177.13466002 133.90406684 -146.28427891 + 586.69007343 407.46290494 + 911.10008547 + + Transpose of the rotation matrix + 0.832455 0.552073 -0.047260 + -0.428259 0.695181 0.577337 + 0.351586 -0.460367 0.815137 + CENTER OF ATOMS BEFORE TRANSLATION 5.36847 2.22798 -0.93245 + AXIS OF ROTATION IS 0.700104 0.269088 0.661397 ANGLE IS 47.83 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 85 atoms have been selected out of 85 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -51.021805 -6.530188 1.801789 51.469549 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CTER" + RDCMND substituted energy or value "?RDIP" to "51.4695" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 9 + Number of bonds = 84 Number of angles = 75 + Number of dihedrals = 104 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 85 atoms have been selected out of 85 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 75 angles deleted + DELTIC: 104 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "NTER-GLUP-ALA-GLUP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLUP-ALA-GLUP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 8 + Number of bonds = 83 Number of angles = 76 + Number of dihedrals = 106 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 24 + Number of true-bonds = 83 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 8 + Number of bonds = 84 Number of angles = 76 + Number of dihedrals = 106 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 24 + Number of true-bonds = 83 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 9 + Number of bonds = 85 Number of angles = 76 + Number of dihedrals = 106 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 28 + Number of true-bonds = 84 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 40 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 766 766 765 + : Ran out of space. RESIZING + with mode 5 found 520 exclusions and 350 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3135 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3135 atom pairs and 870 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3135 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 109.11508 -15.48182 30.88607 +ENER INTERN> 26.10350 47.64677 52.06289 21.91661 0.01443 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 29.02524 -65.37436 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CNEU" + RDCMND substituted energy or value "?ENER" to "109.115" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 178.20776799 137.83661376 -142.46048152 + 605.08096096 425.71951720 + 926.10776675 + + Transpose of the rotation matrix + 0.826480 0.561639 -0.038632 + -0.439141 0.686112 0.580004 + 0.352259 -0.462397 0.813697 + CENTER OF ATOMS BEFORE TRANSLATION 5.41671 2.27759 -0.92161 + AXIS OF ROTATION IS 0.696335 0.261119 0.668532 ANGLE IS 48.46 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 86 atoms have been selected out of 86 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -28.098868 6.708960 -0.540945 28.893756 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CNEU" + RDCMND substituted energy or value "?RDIP" to "28.8938" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 86 Number of groups = 9 + Number of bonds = 85 Number of angles = 76 + Number of dihedrals = 106 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 40 + + CHARMM> delete atom sele all end + SELRPN> 86 atoms have been selected out of 86 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 85 bonds deleted + DELTIC: 76 angles deleted + DELTIC: 106 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "NTER-GLUP-ALA-GLUP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLUP-ALA-GLUP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 8 + Number of bonds = 87 Number of angles = 82 + Number of dihedrals = 109 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 25 + Number of true-bonds = 87 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 8 + Number of bonds = 88 Number of angles = 82 + Number of dihedrals = 109 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 25 + Number of true-bonds = 87 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 9 + Number of bonds = 89 Number of angles = 82 + Number of dihedrals = 109 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 29 + Number of true-bonds = 88 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 41 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 802 802 801 + : Ran out of space. RESIZING + with mode 5 found 548 exclusions and 362 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3457 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3457 atom pairs and 910 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3457 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 347.99397 -238.87889 143.05707 +ENER INTERN> 26.10350 47.50692 32.45638 22.82682 0.01443 +ENER CROSS> -2.28000 0.00000 0.00000 0.00000 +ENER EXTERN> 258.44889 -37.08296 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CT1" + RDCMND substituted energy or value "?ENER" to "347.994" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 183.09938636 158.08701293 -130.30109561 + 732.34608912 501.05641784 + 973.35360409 + + Transpose of the rotation matrix + 0.785917 0.618319 -0.003930 + -0.506766 0.647743 0.568873 + 0.354291 -0.445096 0.822416 + CENTER OF ATOMS BEFORE TRANSLATION 5.57012 2.53309 -0.88065 + AXIS OF ROTATION IS 0.651498 0.230165 0.722893 ANGLE IS 51.09 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 90 atoms have been selected out of 90 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -26.898767 9.183450 -1.203900 28.448705 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CT1" + RDCMND substituted energy or value "?RDIP" to "28.4487" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 90 Number of groups = 9 + Number of bonds = 89 Number of angles = 82 + Number of dihedrals = 109 Number of impropers = 7 + Number of cross-terms = 1 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 41 + + CHARMM> delete atom sele all end + SELRPN> 90 atoms have been selected out of 90 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 89 bonds deleted + DELTIC: 82 angles deleted + DELTIC: 109 dihedrals deleted + DELTIC: 7 improper dihedrals deleted + DELTIC: 1 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "NTER-GLUP-ALA-GLUP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLUP-ALA-GLUP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 24 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 83 Number of groups = 8 + Number of bonds = 82 Number of angles = 78 + Number of dihedrals = 108 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 24 + Number of true-bonds = 82 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 84 Number of groups = 8 + Number of bonds = 83 Number of angles = 78 + Number of dihedrals = 108 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 24 + Number of true-bonds = 82 Number of zero-bonds = 1 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 9 + Number of bonds = 84 Number of angles = 78 + Number of dihedrals = 108 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 28 + Number of true-bonds = 83 Number of zero-bonds = 1 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 38 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 757 757 756 + : Ran out of space. RESIZING + with mode 5 found 502 exclusions and 346 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3068 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3068 atom pairs and 848 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3068 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 101.44259 246.55138 30.94339 +ENER INTERN> 32.54685 45.79474 31.53015 23.57878 0.01443 +ENER CROSS> -10.46000 0.00000 0.00000 0.00000 +ENER EXTERN> 40.78683 -62.34919 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CT2" + RDCMND substituted energy or value "?ENER" to "101.443" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 177.13466002 133.78373548 -148.29763099 + 586.46423752 398.39313926 + 905.28667155 + + Transpose of the rotation matrix + 0.833320 0.550532 -0.049916 + -0.428166 0.699929 0.571641 + 0.349644 -0.454988 0.818984 + CENTER OF ATOMS BEFORE TRANSLATION 5.34306 2.22646 -0.93245 + AXIS OF ROTATION IS 0.696686 0.271147 0.664159 ANGLE IS 47.46 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 85 atoms have been selected out of 85 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -33.087786 8.212950 -2.146323 34.159345 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CT2" + RDCMND substituted energy or value "?RDIP" to "34.1593" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 85 Number of groups = 9 + Number of bonds = 84 Number of angles = 78 + Number of dihedrals = 108 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 38 + + CHARMM> delete atom sele all end + SELRPN> 85 atoms have been selected out of 85 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 84 bonds deleted + DELTIC: 78 angles deleted + DELTIC: 108 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "NTER" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "NTER-GLUP-ALA-GLUP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * NTER-GLUP-ALA-GLUP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "NTER" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "HN " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "HN " "N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 25 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 87 Number of groups = 8 + Number of bonds = 86 Number of angles = 84 + Number of dihedrals = 114 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 25 + Number of true-bonds = 86 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 88 Number of groups = 8 + Number of bonds = 87 Number of angles = 84 + Number of dihedrals = 114 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 25 + Number of true-bonds = 86 Number of zero-bonds = 1 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 9 + Number of bonds = 88 Number of angles = 84 + Number of dihedrals = 114 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 29 + Number of true-bonds = 87 Number of zero-bonds = 1 + Number of aniso. terms = 7 Number of lone-pairs = 14 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 39 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 801 801 792 + : Ran out of space. RESIZING + with mode 5 found 523 exclusions and 361 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3393 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3393 atom pairs and 884 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3393 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 164.83791 -63.39532 35.12049 +ENER INTERN> 32.54685 58.66629 66.80818 23.11885 0.01443 +ENER CROSS> -4.56000 0.00000 0.00000 0.00000 +ENER EXTERN> 43.43503 -55.19171 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CT3" + RDCMND substituted energy or value "?ENER" to "164.838" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 181.65476493 152.82858974 -128.86467022 + 700.59468490 505.18337995 + 997.67805899 + + Transpose of the rotation matrix + 0.801752 0.597572 -0.010042 + -0.483264 0.658089 0.577386 + 0.351638 -0.458067 0.816410 + CENTER OF ATOMS BEFORE TRANSLATION 5.58825 2.46675 -0.89054 + AXIS OF ROTATION IS 0.672431 0.234878 0.701904 ANGLE IS 50.35 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 89 atoms have been selected out of 89 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -27.952490 5.818804 0.914950 28.566367 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "NTER-GLUP-ALA-GLUP-CT3" + RDCMND substituted energy or value "?RDIP" to "28.5664" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 89 Number of groups = 9 + Number of bonds = 88 Number of angles = 84 + Number of dihedrals = 114 Number of impropers = 8 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 39 + + CHARMM> delete atom sele all end + SELRPN> 89 atoms have been selected out of 89 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 88 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 114 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "2" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set first @@@{varp}pn@@countnt + Parameter: COUNTNT -> "2" + Parameter: VARP -> "" + Parameter: PN2 -> "ACE" + Parameter: FIRST <- "ACE" + + CHARMM> + + CHARMM> set countct 1 + Parameter: COUNTCT <- "1" + + CHARMM> label loop_ct + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "1" + Parameter: VARP -> "" + Parameter: PC1 -> "CTER" + Parameter: LAST <- "CTER" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CTER" + Parameter: NAM <- "ACE-GLUP-ALA-GLUP-CTER" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLUP-ALA-GLUP-CTER + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CTER" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 81 + Number of dihedrals = 111 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -3.00000 + Number of Drudes = 27 + Number of true-bonds = 91 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 9 + Number of bonds = 92 Number of angles = 81 + Number of dihedrals = 111 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 27 + Number of true-bonds = 91 Number of zero-bonds = 1 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 10 + Number of bonds = 93 Number of angles = 81 + Number of dihedrals = 111 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 31 + Number of true-bonds = 92 Number of zero-bonds = 1 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 45 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 844 844 837 + : Ran out of space. RESIZING + with mode 5 found 568 exclusions and 380 interactions(1-4) + found 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3803 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3803 atom pairs and 948 atom exclusions. + There are 0 group pairs and 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3803 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 206.98218 -42.14427 40.85309 +ENER INTERN> 25.84951 50.04319 128.51821 42.16964 0.01443 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 67.34410 -101.62691 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CTER" + RDCMND substituted energy or value "?ENER" to "206.982" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 228.21927868 108.00380689 -271.20565584 + 602.49207535 482.81047482 + 1266.93391559 + + Transpose of the rotation matrix + 0.887830 0.436179 -0.146645 + -0.282398 0.768050 0.574762 + 0.363330 -0.468879 0.805074 + CENTER OF ATOMS BEFORE TRANSLATION 4.74130 2.09864 -0.69771 + AXIS OF ROTATION IS 0.764083 0.373369 0.526093 ANGLE IS 43.07 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 94 atoms have been selected out of 94 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -26.141938 -18.545048 -0.128771 32.052087 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CTER" + RDCMND substituted energy or value "?RDIP" to "32.0521" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 10 + Number of bonds = 93 Number of angles = 81 + Number of dihedrals = 111 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 45 + + CHARMM> delete atom sele all end + SELRPN> 94 atoms have been selected out of 94 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 81 angles deleted + DELTIC: 111 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "2" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "2" + Parameter: VARP -> "" + Parameter: PC2 -> "CNEU" + Parameter: LAST <- "CNEU" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CNEU" + Parameter: NAM <- "ACE-GLUP-ALA-GLUP-CNEU" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLUP-ALA-GLUP-CNEU + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CNEU" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 9 + Number of bonds = 92 Number of angles = 82 + Number of dihedrals = 113 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 27 + Number of true-bonds = 92 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 9 + Number of bonds = 93 Number of angles = 82 + Number of dihedrals = 113 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 27 + Number of true-bonds = 92 Number of zero-bonds = 1 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 95 Number of groups = 10 + Number of bonds = 94 Number of angles = 82 + Number of dihedrals = 113 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 31 + Number of true-bonds = 93 Number of zero-bonds = 1 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 45 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 848 848 846 + : Ran out of space. RESIZING + with mode 5 found 574 exclusions and 386 interactions(1-4) + found 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3891 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3891 atom pairs and 960 atom exclusions. + There are 0 group pairs and 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3891 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 189.78793 17.19424 38.56993 +ENER INTERN> 25.73395 45.20362 137.70489 33.30474 0.01443 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 65.75377 -112.59746 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CNEU" + RDCMND substituted energy or value "?ENER" to "189.788" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 228.91471335 111.03893544 -267.90830289 + 622.01171890 504.34581369 + 1287.49928608 + + Transpose of the rotation matrix + 0.883746 0.447149 -0.138028 + -0.294467 0.760593 0.578608 + 0.363707 -0.470698 0.803842 + CENTER OF ATOMS BEFORE TRANSLATION 4.79157 2.14492 -0.69037 + AXIS OF ROTATION IS 0.760691 0.363731 0.537632 ANGLE IS 43.61 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 95 atoms have been selected out of 95 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.301549 -3.064688 -2.640085 4.653976 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CNEU" + RDCMND substituted energy or value "?RDIP" to "4.65398" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 95 Number of groups = 10 + Number of bonds = 94 Number of angles = 82 + Number of dihedrals = 113 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 45 + + CHARMM> delete atom sele all end + SELRPN> 95 atoms have been selected out of 95 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 94 bonds deleted + DELTIC: 82 angles deleted + DELTIC: 113 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 7 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "3" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "3" + Parameter: VARP -> "" + Parameter: PC3 -> "CT1" + Parameter: LAST <- "CT1" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CT1" + Parameter: NAM <- "ACE-GLUP-ALA-GLUP-CT1" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLUP-ALA-GLUP-CT1 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT1" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT1' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "DO " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "O " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOA " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "LPOB " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "O " "C " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 9 + Number of bonds = 96 Number of angles = 88 + Number of dihedrals = 116 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 28 + Number of true-bonds = 96 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 9 + Number of bonds = 97 Number of angles = 88 + Number of dihedrals = 116 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 28 + Number of true-bonds = 96 Number of zero-bonds = 1 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 99 Number of groups = 10 + Number of bonds = 98 Number of angles = 88 + Number of dihedrals = 116 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 32 + Number of true-bonds = 97 Number of zero-bonds = 1 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 46 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 883 883 882 + : Ran out of space. RESIZING + with mode 5 found 602 exclusions and 398 interactions(1-4) + found 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4249 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4249 atom pairs and 1000 atom exclusions. + There are 0 group pairs and 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4249 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 430.00364 -240.21570 139.05489 +ENER INTERN> 25.73395 45.06377 118.09839 34.21495 0.01443 +ENER CROSS> -5.33000 0.00000 0.00000 0.00000 +ENER EXTERN> 295.17644 -82.96828 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CT1" + RDCMND substituted energy or value "?ENER" to "430.004" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 232.38929686 126.62406259 -257.10474121 + 755.73368319 595.87381056 + 1353.00317485 + + Transpose of the rotation matrix + 0.855966 0.506535 -0.103654 + -0.364897 0.733868 0.572965 + 0.366295 -0.452615 0.812999 + CENTER OF ATOMS BEFORE TRANSLATION 4.95630 2.38255 -0.66247 + AXIS OF ROTATION IS 0.719451 0.329672 0.611315 ANGLE IS 45.46 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 99 atoms have been selected out of 99 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.725198 -1.686870 -3.304356 3.780240 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CT1" + RDCMND substituted energy or value "?RDIP" to "3.78024" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 99 Number of groups = 10 + Number of bonds = 98 Number of angles = 88 + Number of dihedrals = 116 Number of impropers = 9 + Number of cross-terms = 2 + Number of HB acceptors = 9 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 46 + + CHARMM> delete atom sele all end + SELRPN> 99 atoms have been selected out of 99 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 98 bonds deleted + DELTIC: 88 angles deleted + DELTIC: 116 dihedrals deleted + DELTIC: 9 improper dihedrals deleted + DELTIC: 2 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 9 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "4" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "4" + Parameter: VARP -> "" + Parameter: PC4 -> "CT2" + Parameter: LAST <- "CT2" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CT2" + Parameter: NAM <- "ACE-GLUP-ALA-GLUP-CT2" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLUP-ALA-GLUP-CT2 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT2" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT2' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT1 " "NT " WERE REQUESTED. + ** WARNING ** DONOR NOT FOUND FOR RESIDUE 3 CT2 . + ATOMS "HT2 " "NT " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 27 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 92 Number of groups = 9 + Number of bonds = 91 Number of angles = 84 + Number of dihedrals = 115 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 27 + Number of true-bonds = 91 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 93 Number of groups = 9 + Number of bonds = 92 Number of angles = 84 + Number of dihedrals = 115 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 27 + Number of true-bonds = 91 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 10 + Number of bonds = 93 Number of angles = 84 + Number of dihedrals = 115 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 31 + Number of true-bonds = 92 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 43 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 843 843 837 + : Ran out of space. RESIZING + with mode 5 found 556 exclusions and 382 interactions(1-4) + found 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3815 atom pairs and 938 atom exclusions. + There are 0 group pairs and 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 178.48631 251.51733 38.46831 +ENER INTERN> 32.17730 43.35159 117.17215 34.96691 0.01443 +ENER CROSS> -13.51000 0.00000 0.00000 0.00000 +ENER EXTERN> 77.51470 -113.20078 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CT2" + RDCMND substituted energy or value "?ENER" to "178.486" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 228.21927868 107.91376799 -272.71216257 + 602.23287698 473.38082500 + 1258.41738094 + + Transpose of the rotation matrix + 0.888628 0.433539 -0.149614 + -0.281161 0.772697 0.569112 + 0.362339 -0.463663 0.808534 + CENTER OF ATOMS BEFORE TRANSLATION 4.71833 2.09727 -0.69771 + AXIS OF ROTATION IS 0.761472 0.377466 0.526953 ANGLE IS 42.70 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 94 atoms have been selected out of 94 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -7.775764 -2.068559 -4.407861 9.174458 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CT2" + RDCMND substituted energy or value "?RDIP" to "9.17446" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 94 Number of groups = 10 + Number of bonds = 93 Number of angles = 84 + Number of dihedrals = 115 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 43 + + CHARMM> delete atom sele all end + SELRPN> 94 atoms have been selected out of 94 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 93 bonds deleted + DELTIC: 84 angles deleted + DELTIC: 115 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 5 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "5" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set last @@@{varp}pc@@countct + Parameter: COUNTCT -> "5" + Parameter: VARP -> "" + Parameter: PC5 -> "CT3" + Parameter: LAST <- "CT3" + + CHARMM> + + CHARMM> set nam @{first}-@{patch}-ala-@{patch}-@last + Parameter: FIRST -> "ACE" + Parameter: PATCH -> "GLUP" + Parameter: PATCH -> "GLUP" + Parameter: LAST -> "CT3" + Parameter: NAM <- "ACE-GLUP-ALA-GLUP-CT3" + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ACE-GLUP-ALA-GLUP-CT3 + RDTITL> * + + SEQRDR> 3 + + SEQRDR> @RESIDUE ALA @RESIDUE + Parameter: RESIDUE -> "GLU" + Parameter: RESIDUE -> "GLU" + + RESIDUE SEQUENCE -- 3 RESIDUES + GLU ALA GLU + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 0 GLU - 2 LYS - 0 TYR - 0 + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first @first last @last setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GLU" + Parameter: FIRST -> "ACE" + Parameter: LAST -> "CT3" + Drude polarizability will be setup for SEGID: GLU mass of Drudes particles = 0.4000 + THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 ACE . + ATOMS "CY " "N " "CA " "C " + ATOMS "N " "CA " "C " "NT " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "N " "-C " "CA " "HN " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "+N " WERE REQUESTED. + ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "C " "CA " "+N " "O " WERE REQUESTED. + ** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 GLU . + ATOMS "-C " "N " "CA " "C " + ATOMS "N " "CA " "C " "+N " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 28 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 96 Number of groups = 9 + Number of bonds = 95 Number of angles = 90 + Number of dihedrals = 121 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 28 + Number of true-bonds = 95 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + CHARMM> if @countaa ge @patched then + Parameter: COUNTAA -> "25" + Parameter: PATCHED -> "25" + Comparing "25" and "25". + IF test evaluated as true. Performing command + + CHARMM> patch @patch @residue 1 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 1 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 1 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 1 HE2 ADDED. + ATOM GLU GLU 1 LPP1 ADDED. + ATOM GLU GLU 1 LPP2 ADDED. + ATOM GLU GLU 1 LPP3 ADDED. + ATOM GLU GLU 1 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 97 Number of groups = 9 + Number of bonds = 96 Number of angles = 90 + Number of dihedrals = 121 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 28 + Number of true-bonds = 95 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch @patch @residue 3 setup warn drude dmass 0.4 !show + Parameter: PATCH -> "GLUP" + Parameter: RESIDUE -> "GLU" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GLU 3 GLU LP1A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP1B AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2A AND ALL REFERENCES TO IT DELETED. + ATOM GLU 3 GLU LP2B AND ALL REFERENCES TO IT DELETED. + ATOM GLU GLU 3 HE2 ADDED. + ATOM GLU GLU 3 LPP1 ADDED. + ATOM GLU GLU 3 LPP2 ADDED. + ATOM GLU GLU 3 LPP3 ADDED. + ATOM GLU GLU 3 LPP4 ADDED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 4 lonepair atoms deleted + 2 anisotropic terms deleted + DELTIC: 4 bonds deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 10 + Number of bonds = 97 Number of angles = 90 + Number of dihedrals = 121 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 32 + Number of true-bonds = 96 Number of zero-bonds = 1 + Number of aniso. terms = 8 Number of lone-pairs = 16 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> endif + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed 1 N 1 CA 1 C + + CHARMM> ic build + **** WARNING **** 44 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 881 881 873 + : Ran out of space. RESIZING + with mode 5 found 577 exclusions and 397 interactions(1-4) + found 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4176 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 4176 atom pairs and 974 atom exclusions. + There are 0 group pairs and 17 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 4176 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 246.14198 -67.65567 41.53697 +ENER INTERN> 32.17730 56.22314 152.45018 34.50697 0.01443 +ENER CROSS> -7.61000 0.00000 0.00000 0.00000 +ENER EXTERN> 80.16280 -101.78285 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @nam starting E: ?ener + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CT3" + RDCMND substituted energy or value "?ENER" to "246.142" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 231.28557705 122.57165343 -256.43607292 + 722.19940262 596.48142421 + 1378.95006976 + + Transpose of the rotation matrix + 0.865125 0.490090 -0.106631 + -0.345629 0.736602 0.581341 + 0.363454 -0.466078 0.806643 + CENTER OF ATOMS BEFORE TRANSLATION 4.96649 2.32076 -0.66923 + AXIS OF ROTATION IS 0.737602 0.331038 0.588521 ANGLE IS 45.24 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 98 atoms have been selected out of 98 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.205071 -4.778582 -1.150816 5.060772 + + CHARMM> echo @nam dipole: ?rdip + Parameter: NAM -> "ACE-GLUP-ALA-GLUP-CT3" + RDCMND substituted energy or value "?RDIP" to "5.06077" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 3 + Number of atoms = 98 Number of groups = 10 + Number of bonds = 97 Number of angles = 90 + Number of dihedrals = 121 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 8 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 44 + + CHARMM> delete atom sele all end + SELRPN> 98 atoms have been selected out of 98 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 97 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 121 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 6 donors deleted + DELTIC: 8 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr countct + Parameter: COUNTCT <- "6" + + CHARMM> if countct le @maxct goto loop_ct + Parameter: MAXCT -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countnt + Parameter: COUNTNT <- "3" + + CHARMM> if countnt le @maxnt goto loop_nt + Parameter: MAXNT -> "2" + Comparing "3" and "2". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> incr countaa + Parameter: COUNTAA <- "26" + + CHARMM> if countaa le @naa goto loop_aa + Parameter: NAA -> "25" + Comparing "26" and "25". + IF test evaluated as false. Skipping command + + CHARMM> + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> incr testcasei + Parameter: TESTCASEI <- "2" + + CHARMM> if @testcasei le @testcases goto loop_tests + Parameter: TESTCASEI -> "2" + Parameter: TESTCASES -> "6" + Comparing "2" and "6". + IF test evaluated as true. Performing command + + CHARMM> stream @test@@testcasei + Parameter: TESTCASEI -> "2" + Parameter: TEST2 -> "TEST_DRUDE_MODEL.STR" + VOPEN> Attempting to open::test_drude_model.str:: + OPNLGU> Unit 99 opened for READONLY access to test_drude_model.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * $ID: TEST_DRUDE_MODEL.STR 28 2015-07-29 23:54:15Z ALEX $ + RDTITL> * TEST CASE, DRUDE MODEL COMPOUNDS ("model") TOPPAR FILE + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> set boml 0 ! set to -1 if the series contains 3-membered rings + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> set nres 72 + Parameter: NRES <- "72" + + CHARMM> + + CHARMM> !ethers + CHARMM> set resi1 DEET + Parameter: RESI1 <- "DEET" + + CHARMM> set resi2 DME + Parameter: RESI2 <- "DME" + + CHARMM> set resi3 DMET + Parameter: RESI3 <- "DMET" + + CHARMM> set resi4 MEET + Parameter: RESI4 <- "MEET" + + CHARMM> set resi5 THF + Parameter: RESI5 <- "THF" + + CHARMM> set resi6 TF2M + Parameter: RESI6 <- "TF2M" + + CHARMM> set resi7 THP + Parameter: RESI7 <- "THP" + + CHARMM> set resi8 MPET + Parameter: RESI8 <- "MPET" + + CHARMM> set resi9 MBET + Parameter: RESI9 <- "MBET" + + CHARMM> set resi10 EPET + Parameter: RESI10 <- "EPET" + + CHARMM> !alkanes + CHARMM> set resi11 ETHA + Parameter: RESI11 <- "ETHA" + + CHARMM> set resi12 PROP1 + Parameter: RESI12 <- "PROP1" + + CHARMM> set resi13 IBUT + Parameter: RESI13 <- "IBUT" + + CHARMM> set resi14 BUTA + Parameter: RESI14 <- "BUTA" + + CHARMM> set resi15 PENT + Parameter: RESI15 <- "PENT" + + CHARMM> set resi16 HEXA + Parameter: RESI16 <- "HEXA" + + CHARMM> set resi17 HEPT + Parameter: RESI17 <- "HEPT" + + CHARMM> set resi18 CPEN + Parameter: RESI18 <- "CPEN" + + CHARMM> set resi19 CHEX + Parameter: RESI19 <- "CHEX" + + CHARMM> set resi20 MEOH + Parameter: RESI20 <- "MEOH" + + CHARMM> set resi21 ETOH + Parameter: RESI21 <- "ETOH" + + CHARMM> set resi22 PRO1 + Parameter: RESI22 <- "PRO1" + + CHARMM> set resi23 BUO1 + Parameter: RESI23 <- "BUO1" + + CHARMM> set resi24 PRO2 + Parameter: RESI24 <- "PRO2" + + CHARMM> set resi25 BUO2 + Parameter: RESI25 <- "BUO2" + + CHARMM> !aromatics + CHARMM> set resi26 BENZ + Parameter: RESI26 <- "BENZ" + + CHARMM> set resi27 TOLU + Parameter: RESI27 <- "TOLU" + + CHARMM> !amides + CHARMM> set resi28 ACEM + Parameter: RESI28 <- "ACEM" + + CHARMM> set resi29 NMA + Parameter: RESI29 <- "NMA" + + CHARMM> set resi30 DMA + Parameter: RESI30 <- "DMA" + + CHARMM> !heterocycles + CHARMM> set resi31 PYR + Parameter: RESI31 <- "PYR" + + CHARMM> set resi32 PYRM + Parameter: RESI32 <- "PYRM" + + CHARMM> set resi33 PYRR + Parameter: RESI33 <- "PYRR" + + CHARMM> set resi34 IMID + Parameter: RESI34 <- "IMID" + + CHARMM> set resi35 INDO + Parameter: RESI35 <- "INDO" + + CHARMM> set resi36 PUR1 + Parameter: RESI36 <- "PUR1" + + CHARMM> set resi37 PUR0 + Parameter: RESI37 <- "PUR0" + + CHARMM> set resi38 4MIM + Parameter: RESI38 <- "4MIM" + + CHARMM> set resi39 MIND + Parameter: RESI39 <- "MIND" + + CHARMM> !misc + CHARMM> set resi40 MAS + Parameter: RESI40 <- "MAS" + + CHARMM> set resi41 ACEH + Parameter: RESI41 <- "ACEH" + + CHARMM> !charged + CHARMM> set resi42 IMIM + Parameter: RESI42 <- "IMIM" + + CHARMM> set resi43 GUAN + Parameter: RESI43 <- "GUAN" + + CHARMM> set resi44 MGUAN + Parameter: RESI44 <- "MGUAN" + + CHARMM> set resi45 PHEN + Parameter: RESI45 <- "PHEN" + + CHARMM> !sulfur containing + CHARMM> set resi46 MESH + Parameter: RESI46 <- "MESH" + + CHARMM> set resi47 ETSH + Parameter: RESI47 <- "ETSH" + + CHARMM> set resi48 PRSH + Parameter: RESI48 <- "PRSH" + + CHARMM> set resi49 BUSH + Parameter: RESI49 <- "BUSH" + + CHARMM> set resi50 DMDS + Parameter: RESI50 <- "DMDS" + + CHARMM> set resi51 DMS + Parameter: RESI51 <- "DMS" + + CHARMM> set resi52 EMS + Parameter: RESI52 <- "EMS" + + CHARMM> !lipid model compounds + CHARMM> set resi53 NC4 + Parameter: RESI53 <- "NC4" + + CHARMM> set resi54 NH5 + Parameter: RESI54 <- "NH5" + + CHARMM> set resi55 NC5 + Parameter: RESI55 <- "NC5" + + CHARMM> set resi56 ACET + Parameter: RESI56 <- "ACET" + + CHARMM> set resi57 ETAM + Parameter: RESI57 <- "ETAM" + + CHARMM> set resi58 NEOP + Parameter: RESI58 <- "NEOP" + + CHARMM> set resi59 BU2M + Parameter: RESI59 <- "BU2M" + + CHARMM> set resi60 BU22M + Parameter: RESI60 <- "BU22M" + + CHARMM> set resi61 BU23M + Parameter: RESI61 <- "BU23M" + + CHARMM> set resi62 CPNM + Parameter: RESI62 <- "CPNM" + + CHARMM> set resi63 CHXM + Parameter: RESI63 <- "CHXM" + + CHARMM> set resi64 DIOX + Parameter: RESI64 <- "DIOX" + + CHARMM> set resi65 CRES + Parameter: RESI65 <- "CRES" + + CHARMM> set resi66 B3MO1 + Parameter: RESI66 <- "B3MO1" + + CHARMM> set resi67 CPO1 + Parameter: RESI67 <- "CPO1" + + CHARMM> set resi68 BGUAN + Parameter: RESI68 <- "BGUAN" + + CHARMM> set resi69 CHOL + Parameter: RESI69 <- "CHOL" + + CHARMM> !misc alkanes + CHARMM> set resi70 DECA + Parameter: RESI70 <- "DECA" + + CHARMM> set resi71 PEND + Parameter: RESI71 <- "PEND" + + CHARMM> set resi72 OCTD + Parameter: RESI72 <- "OCTD" + + CHARMM> + + CHARMM> set seed1 1 C1 1 C2 1 O3 + Parameter: SEED1 <- "1 C1 1 C2 1 O3" + + CHARMM> set seed2 1 C1 1 O2 1 C3 + Parameter: SEED2 <- "1 C1 1 O2 1 C3" + + CHARMM> set seed3 1 C1 1 O2 1 C3 + Parameter: SEED3 <- "1 C1 1 O2 1 C3" + + CHARMM> set seed4 1 C1 1 C2 1 O3 + Parameter: SEED4 <- "1 C1 1 C2 1 O3" + + CHARMM> set seed5 1 O1 1 C1 1 C2 + Parameter: SEED5 <- "1 O1 1 C1 1 C2" + + CHARMM> set seed6 1 O1 1 C1 1 C2 + Parameter: SEED6 <- "1 O1 1 C1 1 C2" + + CHARMM> set seed7 1 O1 1 C1 1 C2 + Parameter: SEED7 <- "1 O1 1 C1 1 C2" + + CHARMM> set seed8 1 C1 1 O2 1 C3 + Parameter: SEED8 <- "1 C1 1 O2 1 C3" + + CHARMM> set seed9 1 C1 1 O2 1 C3 + Parameter: SEED9 <- "1 C1 1 O2 1 C3" + + CHARMM> set seed10 1 C1 1 C2 1 O3 + Parameter: SEED10 <- "1 C1 1 C2 1 O3" + + CHARMM> set seed11 1 H11 1 C1 1 C2 + Parameter: SEED11 <- "1 H11 1 C1 1 C2" + + CHARMM> set seed12 1 C1 1 C2 1 C3 + Parameter: SEED12 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed13 1 C1 1 CT 1 C2 + Parameter: SEED13 <- "1 C1 1 CT 1 C2" + + CHARMM> set seed14 1 C1 1 C2 1 C3 + Parameter: SEED14 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed15 1 C1 1 C2 1 C3 + Parameter: SEED15 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed16 1 C1 1 C2 1 C3 + Parameter: SEED16 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed17 1 C1 1 C2 1 C3 + Parameter: SEED17 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed18 1 C1 1 C2 1 C3 + Parameter: SEED18 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed19 1 C1 1 C2 1 C3 + Parameter: SEED19 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed20 1 HO1 1 O1 1 C1 + Parameter: SEED20 <- "1 HO1 1 O1 1 C1" + + CHARMM> set seed21 1 HO1 1 O1 1 C1 + Parameter: SEED21 <- "1 HO1 1 O1 1 C1" + + CHARMM> set seed22 1 HO1 1 O1 1 C1 + Parameter: SEED22 <- "1 HO1 1 O1 1 C1" + + CHARMM> set seed23 1 HO1 1 O1 1 C1 + Parameter: SEED23 <- "1 HO1 1 O1 1 C1" + + CHARMM> set seed24 1 HO2 1 O2 1 C2 + Parameter: SEED24 <- "1 HO2 1 O2 1 C2" + + CHARMM> set seed25 1 HO2 1 O2 1 C2 + Parameter: SEED25 <- "1 HO2 1 O2 1 C2" + + CHARMM> set seed26 1 CG 1 CD1 1 CE1 + Parameter: SEED26 <- "1 CG 1 CD1 1 CE1" + + CHARMM> set seed27 1 CG 1 CD1 1 CE1 + Parameter: SEED27 <- "1 CG 1 CD1 1 CE1" + + CHARMM> set seed28 1 N 1 C 1 CL + Parameter: SEED28 <- "1 N 1 C 1 CL" + + CHARMM> set seed29 1 N 1 C 1 CL + Parameter: SEED29 <- "1 N 1 C 1 CL" + + CHARMM> set seed30 1 N 1 C 1 CL + Parameter: SEED30 <- "1 N 1 C 1 CL" + + CHARMM> set seed31 1 CG 1 CD1 1 CE1 + Parameter: SEED31 <- "1 CG 1 CD1 1 CE1" + + CHARMM> set seed32 1 C4 1 C5 1 C6 + Parameter: SEED32 <- "1 C4 1 C5 1 C6" + + CHARMM> set seed33 1 N5 1 C1 1 C2 + Parameter: SEED33 <- "1 N5 1 C1 1 C2" + + CHARMM> set seed34 1 ND1 1 CG 1 CD2 + Parameter: SEED34 <- "1 ND1 1 CG 1 CD2" + + CHARMM> set seed35 1 CG 1 CD1 1 NE1 + Parameter: SEED35 <- "1 CG 1 CD1 1 NE1" + + CHARMM> set seed36 1 C6 1 C5 1 C4 + Parameter: SEED36 <- "1 C6 1 C5 1 C4" + + CHARMM> set seed37 1 C6 1 C5 1 C4 + Parameter: SEED37 <- "1 C6 1 C5 1 C4" + + CHARMM> set seed38 1 ND1 1 CG 1 CB + Parameter: SEED38 <- "1 ND1 1 CG 1 CB" + + CHARMM> set seed39 1 CG 1 CD1 1 NE1 + Parameter: SEED39 <- "1 CG 1 CD1 1 NE1" + + CHARMM> set seed40 1 C1 1 C 1 OM + Parameter: SEED40 <- "1 C1 1 C 1 OM" + + CHARMM> set seed41 1 O2 1 C2 1 C1 + Parameter: SEED41 <- "1 O2 1 C2 1 C1" + + CHARMM> set seed42 1 CG 1 CD2 1 NE2 + Parameter: SEED42 <- "1 CG 1 CD2 1 NE2" + + CHARMM> set seed43 1 N1 1 C 1 N2 + Parameter: SEED43 <- "1 N1 1 C 1 N2" + + CHARMM> set seed44 1 N1 1 C 1 N2 + Parameter: SEED44 <- "1 N1 1 C 1 N2" + + CHARMM> set seed45 1 CG 1 CD1 1 CE1 + Parameter: SEED45 <- "1 CG 1 CD1 1 CE1" + + CHARMM> set seed46 1 HS1 1 S1 1 C1 + Parameter: SEED46 <- "1 HS1 1 S1 1 C1" + + CHARMM> set seed47 1 HS1 1 S1 1 C1 + Parameter: SEED47 <- "1 HS1 1 S1 1 C1" + + CHARMM> set seed48 1 HS1 1 S1 1 C1 + Parameter: SEED48 <- "1 HS1 1 S1 1 C1" + + CHARMM> set seed49 1 HS1 1 S1 1 C1 + Parameter: SEED49 <- "1 HS1 1 S1 1 C1" + + CHARMM> set seed50 1 H11 1 C1 1 S1 + Parameter: SEED50 <- "1 H11 1 C1 1 S1" + + CHARMM> set seed51 1 H21 1 C2 1 S1 + Parameter: SEED51 <- "1 H21 1 C2 1 S1" + + CHARMM> set seed52 1 H31 1 C3 1 C2 + Parameter: SEED52 <- "1 H31 1 C3 1 C2" + + CHARMM> set seed53 1 C1 1 N 1 C2 + Parameter: SEED53 <- "1 C1 1 N 1 C2" + + CHARMM> set seed54 1 HN4 1 N 1 C1 + Parameter: SEED54 <- "1 HN4 1 N 1 C1" + + CHARMM> set seed55 1 C4 1 N 1 C1 + Parameter: SEED55 <- "1 C4 1 N 1 C1" + + CHARMM> set seed56 1 O1 1 C2 1 C1 + Parameter: SEED56 <- "1 O1 1 C2 1 C1" + + CHARMM> set seed57 1 N 1 C1 1 C5 + Parameter: SEED57 <- "1 N 1 C1 1 C5" + + CHARMM> set seed58 1 C2 1 CT 1 C1 + Parameter: SEED58 <- "1 C2 1 CT 1 C1" + + CHARMM> set seed59 1 C1 1 CT 1 C2 + Parameter: SEED59 <- "1 C1 1 CT 1 C2" + + CHARMM> set seed60 1 C4 1 CT 1 C1 + Parameter: SEED60 <- "1 C4 1 CT 1 C1" + + CHARMM> set seed61 1 C1 1 CT 1 C2 + Parameter: SEED61 <- "1 C1 1 CT 1 C2" + + CHARMM> set seed62 1 C1 1 C2 1 C3 + Parameter: SEED62 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed63 1 C1 1 C2 1 C3 + Parameter: SEED63 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed64 1 O1 1 C1 1 C2 + Parameter: SEED64 <- "1 O1 1 C1 1 C2" + + CHARMM> set seed65 1 CG 1 CD1 1 CE1 + Parameter: SEED65 <- "1 CG 1 CD1 1 CE1" + + CHARMM> set seed66 1 C1 1 C2 1 C3 + Parameter: SEED66 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed67 1 C1 1 C2 1 C3 + Parameter: SEED67 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed68 1 CA 1 CB 1 CG + Parameter: SEED68 <- "1 CA 1 CB 1 CG" + + CHARMM> set seed69 1 C4 1 N 1 C1 + Parameter: SEED69 <- "1 C4 1 N 1 C1" + + CHARMM> set seed70 1 C1 1 C2 1 C3 + Parameter: SEED70 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed71 1 C1 1 C2 1 C3 + Parameter: SEED71 <- "1 C1 1 C2 1 C3" + + CHARMM> set seed72 1 C1 1 C2 1 C3 + Parameter: SEED72 <- "1 C1 1 C2 1 C3" + + CHARMM> + + CHARMM> label loop_model1 + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "1" + Parameter: RESI1 -> "DEET" + Parameter: RESIDUE <- "DEET" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DEET" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DEET" + Drude polarizability will be setup for SEGID: DEET mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DEET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 23 Number of groups = 1 + Number of bonds = 22 Number of angles = 25 + Number of dihedrals = 24 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 22 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "1" + Parameter: SEED1 -> "1 C1 1 C2 1 O3" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 134 exclusions and 58 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 119 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 119 atom pairs and 192 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 119 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -2.05008 248.19206 2.97000 +ENER INTERN> 0.01439 0.23080 0.00704 0.00113 0.00000 +ENER EXTERN> -0.15482 -2.14862 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DEET" + RDCMND substituted energy or value "?ENER" to "-2.05008" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 6.72842942 -0.00000000 0.00000000 + 35.01763919 32.32286788 + 57.07567843 + + Transpose of the rotation matrix + 0.813306 0.581837 -0.000000 + -0.581837 0.813306 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.18374 1.09887 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 35.58 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 23 atoms have been selected out of 23 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000072 -1.448202 -0.000000 1.448202 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DEET" + RDCMND substituted energy or value "?RDIP" to "1.4482" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 23 Number of groups = 1 + Number of bonds = 22 Number of angles = 25 + Number of dihedrals = 24 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 23 atoms have been selected out of 23 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 22 bonds deleted + DELTIC: 25 angles deleted + DELTIC: 24 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "2" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "2" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "2" + Parameter: RESI2 -> "DME" + Parameter: RESIDUE <- "DME" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DME" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DME" + Drude polarizability will be setup for SEGID: DME mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DME. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 27 Number of angles = 26 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 27 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 6 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "2" + Parameter: SEED2 -> "1 C1 1 O2 1 C3" + + CHARMM> ic build + **** WARNING **** 12 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 244 244 243 + : Ran out of space. RESIZING + with mode 5 found 182 exclusions and 77 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 196 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 196 atom pairs and 259 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 196 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 8.06268 -10.11276 5.76416 +ENER INTERN> 0.68668 1.53756 0.08359 3.93719 0.00000 +ENER EXTERN> 0.32049 1.49717 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DME" + RDCMND substituted energy or value "?ENER" to "8.06268" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 6.78299066 -0.00007630 -0.00007913 + 37.33865631 50.06254781 + 108.03681561 + + Transpose of the rotation matrix + 0.887919 0.459999 -0.000001 + -0.459999 0.887919 -0.000007 + -0.000002 0.000006 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.69056 1.26042 -0.00000 + AXIS OF ROTATION IS -0.000014 -0.000002 1.000000 ANGLE IS 27.39 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 28 atoms have been selected out of 28 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.000008 -0.000009 -0.000001 0.000012 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DME" + RDCMND substituted energy or value "?RDIP" to "1.224935E-05" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 27 Number of angles = 26 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 12 + + CHARMM> delete atom sele all end + SELRPN> 28 atoms have been selected out of 28 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 27 bonds deleted + DELTIC: 26 angles deleted + DELTIC: 21 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "3" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "3" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "3" + Parameter: RESI3 -> "DMET" + Parameter: RESIDUE <- "DMET" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DMET" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DMET" + Drude polarizability will be setup for SEGID: DMET mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 3 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DMET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 14 Number of angles = 13 + Number of dihedrals = 6 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 3 + Number of true-bonds = 14 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "3" + Parameter: SEED3 -> "1 C1 1 O2 1 C3" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 84 exclusions and 12 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 21 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 21 atom pairs and 96 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 21 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 2.40973 5.65295 6.18500 +ENER INTERN> 0.44458 0.61608 0.00931 0.00075 0.00000 +ENER EXTERN> 0.22347 1.11553 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DMET" + RDCMND substituted energy or value "?ENER" to "2.40973" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 3.39970728 -0.00020924 -0.00030473 + 9.96232453 6.55341255 + 15.00669095 + + Transpose of the rotation matrix + 0.824373 0.566047 -0.000023 + -0.566047 0.824373 -0.000000 + 0.000019 0.000013 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.07319 0.49868 -0.00000 + AXIS OF ROTATION IS -0.000011 0.000037 1.000000 ANGLE IS 34.48 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 15 atoms have been selected out of 15 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 1.320355 0.000000 1.320355 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DMET" + RDCMND substituted energy or value "?RDIP" to "1.32035" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 14 Number of angles = 13 + Number of dihedrals = 6 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 15 atoms have been selected out of 15 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 14 bonds deleted + DELTIC: 13 angles deleted + DELTIC: 6 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "4" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "4" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "4" + Parameter: RESI4 -> "MEET" + Parameter: RESIDUE <- "MEET" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MEET" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MEET" + Drude polarizability will be setup for SEGID: MEET mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MEET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 19 Number of groups = 1 + Number of bonds = 18 Number of angles = 19 + Number of dihedrals = 15 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 4 + Number of true-bonds = 18 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "4" + Parameter: SEED4 -> "1 C1 1 C2 1 O3" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 109 exclusions and 35 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 62 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 62 atom pairs and 144 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 62 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -0.17724 2.58698 4.05894 +ENER INTERN> 0.01176 0.16309 0.00396 0.00068 0.00000 +ENER EXTERN> 0.08741 -0.44414 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MEET" + RDCMND substituted energy or value "?ENER" to "-0.177244" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 5.11322965 -0.00000000 -0.00000000 + 14.04323958 14.00902414 + 38.77575282 + + Transpose of the rotation matrix + 0.911532 0.411228 -0.000000 + -0.411228 0.911532 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.79111 0.65897 -0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 1.000000 ANGLE IS 24.28 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 19 atoms have been selected out of 19 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.273093 -1.369144 0.000000 1.396114 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MEET" + RDCMND substituted energy or value "?RDIP" to "1.39611" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 19 Number of groups = 1 + Number of bonds = 18 Number of angles = 19 + Number of dihedrals = 15 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 19 atoms have been selected out of 19 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 18 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 15 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "5" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "5" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "5" + Parameter: RESI5 -> "THF" + Parameter: RESIDUE <- "THF" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "THF" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THF" + Drude polarizability will be setup for SEGID: THF mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THF. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 21 Number of groups = 1 + Number of bonds = 21 Number of angles = 25 + Number of dihedrals = 33 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 21 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "5" + Parameter: SEED5 -> "1 O1 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 192 192 189 + : Ran out of space. RESIZING + with mode 5 found 142 exclusions and 56 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 68 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 68 atom pairs and 198 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 68 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 11.91644 -12.09369 6.00258 +ENER INTERN> 0.19542 3.88052 1.02780 7.30986 0.00000 +ENER EXTERN> -0.68946 0.19230 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "THF" + RDCMND substituted energy or value "?ENER" to "11.9164" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 8.94114843 4.46957704 -1.62812460 + 22.35280230 -0.08818752 + 23.94289704 + + Transpose of the rotation matrix + 0.810311 -0.535130 -0.238812 + 0.578635 0.795078 0.181748 + 0.092615 -0.285458 0.953906 + CENTER OF ATOMS BEFORE TRANSLATION 0.69901 0.96078 0.21965 + AXIS OF ROTATION IS 0.373038 0.264626 -0.889278 ANGLE IS 38.77 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 21 atoms have been selected out of 21 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.000249 1.824216 0.000038 1.824216 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "THF" + RDCMND substituted energy or value "?RDIP" to "1.82422" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 21 Number of groups = 1 + Number of bonds = 21 Number of angles = 25 + Number of dihedrals = 33 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 21 atoms have been selected out of 21 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 21 bonds deleted + DELTIC: 25 angles deleted + DELTIC: 33 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "6" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "6" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "6" + Parameter: RESI6 -> "TF2M" + Parameter: RESIDUE <- "TF2M" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "TF2M" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TF2M" + Drude polarizability will be setup for SEGID: TF2M mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TF2M. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 25 Number of angles = 31 + Number of dihedrals = 42 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 25 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "6" + Parameter: SEED6 -> "1 O1 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 227 227 225 + : Ran out of space. RESIZING + with mode 5 found 168 exclusions and 86 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 132 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 132 atom pairs and 254 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 132 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 5.59411 6.32233 6.53911 +ENER INTERN> 0.66349 4.14160 0.93421 7.63961 0.00000 +ENER EXTERN> -0.87350 -6.91130 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "TF2M" + RDCMND substituted energy or value "?ENER" to "5.59411" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 15.91950067 -7.73229601 7.75588548 + 37.77886972 -9.14464734 + 31.28713300 + + Transpose of the rotation matrix + 0.567426 -0.758279 0.320998 + 0.769191 0.627256 0.122046 + -0.293893 0.177657 0.939183 + CENTER OF ATOMS BEFORE TRANSLATION 0.89654 0.67343 0.24793 + AXIS OF ROTATION IS -0.033754 -0.373221 -0.927128 ANGLE IS 55.46 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 25 atoms have been selected out of 25 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.590081 1.718288 -0.321750 1.845056 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "TF2M" + RDCMND substituted energy or value "?RDIP" to "1.84506" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 25 Number of angles = 31 + Number of dihedrals = 42 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 25 atoms have been selected out of 25 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 25 bonds deleted + DELTIC: 31 angles deleted + DELTIC: 42 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "7" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "7" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "7" + Parameter: RESI7 -> "THP" + Parameter: RESIDUE <- "THP" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "THP" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THP" + Drude polarizability will be setup for SEGID: THP mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 25 Number of angles = 31 + Number of dihedrals = 42 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 25 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "7" + Parameter: SEED7 -> "1 O1 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 226 226 225 + : Ran out of space. RESIZING + with mode 5 found 164 exclusions and 86 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 136 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 136 atom pairs and 250 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 136 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 12.00685 -6.41274 7.57620 +ENER INTERN> 0.72061 0.93169 0.27857 9.37750 0.00000 +ENER EXTERN> -0.19903 0.89751 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "THP" + RDCMND substituted energy or value "?ENER" to "12.0068" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 18.26851073 9.38406672 -7.46658310 + 30.54000886 4.07042277 + 32.35126558 + + Transpose of the rotation matrix + 0.438818 0.855826 0.273863 + -0.825445 0.263493 0.499212 + 0.355077 -0.445122 0.822063 + CENTER OF ATOMS BEFORE TRANSLATION 0.70364 1.02275 0.61156 + AXIS OF ROTATION IS 0.489283 0.042079 0.871109 ANGLE IS 74.80 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 25 atoms have been selected out of 25 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.546465 -0.006900 0.920191 1.799543 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "THP" + RDCMND substituted energy or value "?RDIP" to "1.79954" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 25 Number of angles = 31 + Number of dihedrals = 42 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 25 atoms have been selected out of 25 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 25 bonds deleted + DELTIC: 31 angles deleted + DELTIC: 42 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "8" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "8" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "8" + Parameter: RESI8 -> "MPET" + Parameter: RESIDUE <- "MPET" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MPET" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MPET" + Drude polarizability will be setup for SEGID: MPET mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MPET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 23 Number of groups = 1 + Number of bonds = 22 Number of angles = 25 + Number of dihedrals = 24 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 22 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "8" + Parameter: SEED8 -> "1 C1 1 O2 1 C3" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 131 exclusions and 54 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 122 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 122 atom pairs and 185 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 122 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 5.18211 6.82474 5.96946 +ENER INTERN> 0.75945 0.85083 0.17039 1.69048 0.00000 +ENER EXTERN> -0.04227 1.75323 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MPET" + RDCMND substituted energy or value "?ENER" to "5.18211" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 6.49676091 -0.00010569 -0.00019594 + 31.02952581 32.22355179 + 62.71238663 + + Transpose of the rotation matrix + 0.848876 0.528592 -0.000003 + -0.528592 0.848876 0.000003 + 0.000004 -0.000001 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.11091 1.04938 0.00000 + AXIS OF ROTATION IS 0.000004 0.000007 1.000000 ANGLE IS 31.91 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 23 atoms have been selected out of 23 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.067290 1.312984 0.000001 1.314707 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MPET" + RDCMND substituted energy or value "?RDIP" to "1.31471" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 23 Number of groups = 1 + Number of bonds = 22 Number of angles = 25 + Number of dihedrals = 24 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 23 atoms have been selected out of 23 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 22 bonds deleted + DELTIC: 25 angles deleted + DELTIC: 24 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "9" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "9" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "9" + Parameter: RESI9 -> "MBET" + Parameter: RESIDUE <- "MBET" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MBET" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MBET" + Drude polarizability will be setup for SEGID: MBET mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MBET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 27 Number of groups = 1 + Number of bonds = 26 Number of angles = 31 + Number of dihedrals = 33 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 26 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "9" + Parameter: SEED9 -> "1 C1 1 O2 1 C3" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 153 exclusions and 70 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 198 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 198 atom pairs and 223 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 198 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 5.22060 -0.03849 5.86510 +ENER INTERN> 0.85104 0.91732 0.21879 2.09706 0.00000 +ENER EXTERN> -0.24231 1.37869 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MBET" + RDCMND substituted energy or value "?ENER" to "5.2206" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 8.04138212 -0.00013795 -0.00045305 + 39.50592238 51.51327529 + 115.09732109 + + Transpose of the rotation matrix + 0.892065 0.451907 -0.000004 + -0.451907 0.892065 0.000015 + 0.000010 -0.000012 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.69291 1.26126 0.00001 + AXIS OF ROTATION IS 0.000030 0.000015 1.000000 ANGLE IS 26.87 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 27 atoms have been selected out of 27 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.187001 1.361613 0.000032 1.374394 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MBET" + RDCMND substituted energy or value "?RDIP" to "1.37439" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 27 Number of groups = 1 + Number of bonds = 26 Number of angles = 31 + Number of dihedrals = 33 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 27 atoms have been selected out of 27 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 26 bonds deleted + DELTIC: 31 angles deleted + DELTIC: 33 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "10" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "10" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "10" + Parameter: RESI10 -> "EPET" + Parameter: RESIDUE <- "EPET" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "EPET" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "EPET" + Drude polarizability will be setup for SEGID: EPET mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is EPET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 27 Number of groups = 3 + Number of bonds = 26 Number of angles = 31 + Number of dihedrals = 33 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 26 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "10" + Parameter: SEED10 -> "1 C1 1 C2 1 O3" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 156 exclusions and 77 interactions(1-4) + found 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 195 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 195 atom pairs and 233 atom exclusions. + There are 0 group pairs and 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 195 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 3.57723 1.64336 5.99191 +ENER INTERN> 0.97962 0.93632 0.23662 1.69108 0.00000 +ENER EXTERN> -0.22480 -0.04160 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "EPET" + RDCMND substituted energy or value "?ENER" to "3.57723" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 8.05015885 0.00000000 0.00000000 + 53.22948052 56.14769941 + 94.47345057 + + Transpose of the rotation matrix + 0.819989 0.572380 0.000000 + -0.572380 0.819989 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.62890 1.45564 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 34.92 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 27 atoms have been selected out of 27 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.077052 -1.366794 -0.000000 1.368964 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "EPET" + RDCMND substituted energy or value "?RDIP" to "1.36896" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 27 Number of groups = 3 + Number of bonds = 26 Number of angles = 31 + Number of dihedrals = 33 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 27 atoms have been selected out of 27 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 26 bonds deleted + DELTIC: 31 angles deleted + DELTIC: 33 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "11" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "11" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "11" + Parameter: RESI11 -> "ETHA" + Parameter: RESIDUE <- "ETHA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ETHA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ETHA" + Drude polarizability will be setup for SEGID: ETHA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 2 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ETHA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 10 Number of groups = 2 + Number of bonds = 9 Number of angles = 12 + Number of dihedrals = 9 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 2 + Number of true-bonds = 9 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "11" + Parameter: SEED11 -> "1 H11 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 2 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 36 exclusions and 9 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 9 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 9 atom pairs and 45 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 9 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 4.46839 -0.89116 5.79144 +ENER INTERN> 0.61552 0.11086 0.04542 -0.00000 0.00000 +ENER EXTERN> -0.16819 3.86479 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ETHA" + RDCMND substituted energy or value "?ENER" to "4.46839" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 3.11724965 0.00000000 0.00000000 + 9.42765859 2.44511252 + 4.06466451 + + Transpose of the rotation matrix + 0.361299 0.932450 0.000000 + -0.704634 0.273027 0.654940 + 0.610699 -0.236629 0.755681 + CENTER OF ATOMS BEFORE TRANSLATION 1.36889 0.71151 -0.00000 + AXIS OF ROTATION IS 0.454510 0.311326 0.834564 ANGLE IS 78.76 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 10 atoms have been selected out of 10 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 -0.000000 -0.000000 0.000000 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ETHA" + RDCMND substituted energy or value "?RDIP" to "5.376752E-16" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 10 Number of groups = 2 + Number of bonds = 9 Number of angles = 12 + Number of dihedrals = 9 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 2 + + CHARMM> delete atom sele all end + SELRPN> 10 atoms have been selected out of 10 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 9 bonds deleted + DELTIC: 12 angles deleted + DELTIC: 9 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "12" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "12" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "12" + Parameter: RESI12 -> "PROP1" + Parameter: RESIDUE <- "PROP1" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PROP1" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PROP1" + Drude polarizability will be setup for SEGID: PROP1 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 3 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROP1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 3 + Number of bonds = 13 Number of angles = 18 + Number of dihedrals = 18 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 3 + Number of true-bonds = 13 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "12" + Parameter: SEED12 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 3 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 58 exclusions and 24 interactions(1-4) + found 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 33 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 33 atom pairs and 82 atom exclusions. + There are 0 group pairs and 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 33 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 3.72893 0.73946 6.64714 +ENER INTERN> 0.67777 0.17530 0.10815 0.00879 0.00000 +ENER EXTERN> -0.26209 3.02101 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PROP1" + RDCMND substituted energy or value "?ENER" to "3.72893" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 4.66442407 0.00000000 0.00000000 + 12.25475549 6.95000960 + 17.98015782 + + Transpose of the rotation matrix + 0.830920 0.556392 0.000000 + -0.556392 0.830920 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.18786 0.50497 -0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 1.000000 ANGLE IS 33.81 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 14 atoms have been selected out of 14 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.000131 -0.114828 -0.000000 0.114828 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PROP1" + RDCMND substituted energy or value "?RDIP" to "0.114828" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 3 + Number of bonds = 13 Number of angles = 18 + Number of dihedrals = 18 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 3 + + CHARMM> delete atom sele all end + SELRPN> 14 atoms have been selected out of 14 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 13 bonds deleted + DELTIC: 18 angles deleted + DELTIC: 18 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "13" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "13" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "13" + Parameter: RESI13 -> "IBUT" + Parameter: RESIDUE <- "IBUT" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "IBUT" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "IBUT" + Drude polarizability will be setup for SEGID: IBUT mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is IBUT. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 4 + Number of bonds = 17 Number of angles = 24 + Number of dihedrals = 27 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "13" + Parameter: SEED13 -> "1 C1 1 CT 1 C2" + + CHARMM> ic build + **** WARNING **** 4 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 81 exclusions and 45 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 72 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 72 atom pairs and 126 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 72 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -4.17502 7.90394 9.55540 +ENER INTERN> 0.86906 0.29791 0.20899 0.01177 0.00000 +ENER EXTERN> -0.24991 -5.31284 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "IBUT" + RDCMND substituted energy or value "?ENER" to "-4.17502" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 12.15983823 6.28626664 -4.33266490 + 20.49119757 2.32651532 + 22.26036395 + + Transpose of the rotation matrix + 0.000007 0.881020 0.473079 + 0.950721 0.146671 -0.273160 + -0.310046 0.449769 -0.837603 + CENTER OF ATOMS BEFORE TRANSLATION 1.40419 0.17836 -0.33216 + AXIS OF ROTATION IS -0.676856 -0.733217 -0.065260 ANGLE IS 147.72 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.000043 -0.000050 -0.179806 0.179806 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "IBUT" + RDCMND substituted energy or value "?RDIP" to "0.179806" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 4 + Number of bonds = 17 Number of angles = 24 + Number of dihedrals = 27 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 4 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 24 angles deleted + DELTIC: 27 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "14" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "14" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "14" + Parameter: RESI14 -> "BUTA" + Parameter: RESIDUE <- "BUTA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BUTA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BUTA" + Drude polarizability will be setup for SEGID: BUTA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BUTA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 4 + Number of bonds = 17 Number of angles = 24 + Number of dihedrals = 27 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "14" + Parameter: SEED14 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 4 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 80 exclusions and 40 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 73 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 73 atom pairs and 120 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 73 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 4.53681 -8.71183 7.50696 +ENER INTERN> 0.77659 0.39828 0.17121 0.55077 0.00000 +ENER EXTERN> -0.43155 3.07153 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BUTA" + RDCMND substituted energy or value "?ENER" to "4.53681" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 6.20815247 0.00004359 0.00005648 + 16.26271842 14.93446560 + 43.14801127 + + Transpose of the rotation matrix + 0.913512 0.406811 0.000002 + -0.406811 0.913512 0.000005 + 0.000001 -0.000005 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.82336 0.70323 -0.00000 + AXIS OF ROTATION IS 0.000012 -0.000001 1.000000 ANGLE IS 24.00 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.000005 -0.000011 -0.000007 0.000014 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BUTA" + RDCMND substituted energy or value "?RDIP" to "1.438076E-05" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 4 + Number of bonds = 17 Number of angles = 24 + Number of dihedrals = 27 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 4 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 24 angles deleted + DELTIC: 27 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "15" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "15" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "15" + Parameter: RESI15 -> "PENT" + Parameter: RESIDUE <- "PENT" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PENT" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PENT" + Drude polarizability will be setup for SEGID: PENT mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PENT. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 5 + Number of bonds = 21 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 5 + Number of true-bonds = 21 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "15" + Parameter: SEED15 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 102 exclusions and 56 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 129 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 129 atom pairs and 158 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 129 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 4.90412 -0.36730 6.75788 +ENER INTERN> 0.87007 0.51061 0.23493 0.82768 0.00000 +ENER EXTERN> -0.63401 3.09484 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PENT" + RDCMND substituted energy or value "?ENER" to "4.90412" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 7.75550262 -0.00000000 0.00000000 + 36.73525372 35.18114322 + 65.60640407 + + Transpose of the rotation matrix + 0.830544 0.556953 -0.000000 + -0.556953 0.830544 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.28521 1.15873 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 33.85 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.000014 -0.114560 0.000000 0.114560 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PENT" + RDCMND substituted energy or value "?RDIP" to "0.11456" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 5 + Number of bonds = 21 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 21 bonds deleted + DELTIC: 30 angles deleted + DELTIC: 36 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "16" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "16" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "16" + Parameter: RESI16 -> "HEXA" + Parameter: RESIDUE <- "HEXA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "HEXA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HEXA" + Drude polarizability will be setup for SEGID: HEXA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HEXA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 6 + Number of bonds = 25 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 6 + Number of true-bonds = 25 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "16" + Parameter: SEED16 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 124 exclusions and 72 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 201 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 201 atom pairs and 196 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 201 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 5.50240 -0.59828 6.54395 +ENER INTERN> 0.96734 0.61331 0.29438 1.36089 0.00000 +ENER EXTERN> -0.84330 3.10978 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "HEXA" + RDCMND substituted energy or value "?ENER" to "5.5024" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 9.29852497 0.00000000 0.00000000 + 47.51368265 56.97357397 + 116.34628502 + + Transpose of the rotation matrix + 0.870936 0.491397 0.000000 + -0.491397 0.870936 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.88283 1.41248 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 29.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 26 atoms have been selected out of 26 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.000068 -0.000114 -0.000000 0.000133 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "HEXA" + RDCMND substituted energy or value "?RDIP" to "1.330135E-04" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 6 + Number of bonds = 25 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 26 atoms have been selected out of 26 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 25 bonds deleted + DELTIC: 36 angles deleted + DELTIC: 45 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "17" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "17" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "17" + Parameter: RESI17 -> "HEPT" + Parameter: RESIDUE <- "HEPT" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "HEPT" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "HEPT" + Drude polarizability will be setup for SEGID: HEPT mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 7 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is HEPT. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 30 Number of groups = 7 + Number of bonds = 29 Number of angles = 42 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 7 + Number of true-bonds = 29 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "17" + Parameter: SEED17 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 146 exclusions and 88 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 289 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 289 atom pairs and 234 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 289 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 6.10777 -0.60537 6.35642 +ENER INTERN> 1.06419 0.72304 0.35402 1.89405 0.00000 +ENER EXTERN> -1.05557 3.12804 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "HEPT" + RDCMND substituted energy or value "?ENER" to "6.10777" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 10.84422186 0.00000000 0.00000000 + 83.45575236 96.60686883 + 162.50668278 + + Transpose of the rotation matrix + 0.830262 0.557374 0.000000 + -0.557374 0.830262 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 3.36184 1.84350 0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 1.000000 ANGLE IS 33.87 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 30 atoms have been selected out of 30 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.000095 -0.113976 0.000000 0.113976 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "HEPT" + RDCMND substituted energy or value "?RDIP" to "0.113976" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 30 Number of groups = 7 + Number of bonds = 29 Number of angles = 42 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 30 atoms have been selected out of 30 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 29 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "18" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "18" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "18" + Parameter: RESI18 -> "CPEN" + Parameter: RESIDUE <- "CPEN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CPEN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CPEN" + Drude polarizability will be setup for SEGID: CPEN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CPEN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 20 Number of groups = 5 + Number of bonds = 20 Number of angles = 30 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 20 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "18" + Parameter: SEED18 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 110 exclusions and 60 interactions(1-4) + found 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 80 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 80 atom pairs and 170 atom exclusions. + There are 0 group pairs and 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 80 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 10.67437 -4.56660 5.56000 +ENER INTERN> 1.47420 0.90081 1.27181 7.84314 0.00000 +ENER EXTERN> -0.85740 0.04182 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CPEN" + RDCMND substituted energy or value "?ENER" to "10.6744" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 9.02779266 -1.17922706 -1.56194233 + 26.12053485 -0.10713414 + 26.05957659 + + Transpose of the rotation matrix + 0.856585 0.503597 -0.112484 + -0.508032 0.861241 -0.012932 + 0.090364 0.068222 0.993569 + CENTER OF ATOMS BEFORE TRANSLATION 0.76641 1.03560 0.00001 + AXIS OF ROTATION IS -0.078413 0.195997 0.977464 ANGLE IS 31.16 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 20 atoms have been selected out of 20 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.001306 -0.011546 0.000019 0.011620 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CPEN" + RDCMND substituted energy or value "?RDIP" to "1.162E-02" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 20 Number of groups = 5 + Number of bonds = 20 Number of angles = 30 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 20 atoms have been selected out of 20 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 20 bonds deleted + DELTIC: 30 angles deleted + DELTIC: 45 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "19" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "19" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "19" + Parameter: RESI19 -> "CHEX" + Parameter: RESIDUE <- "CHEX" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CHEX" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CHEX" + Drude polarizability will be setup for SEGID: CHEX mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CHEX. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 6 + Number of bonds = 24 Number of angles = 36 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 6 + Number of true-bonds = 24 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "19" + Parameter: SEED19 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 132 exclusions and 84 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 144 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 144 atom pairs and 216 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 144 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 4.80197 5.87241 5.18057 +ENER INTERN> 0.65548 1.08611 0.31824 2.86379 0.00000 +ENER EXTERN> -0.53767 0.41602 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CHEX" + RDCMND substituted energy or value "?ENER" to "4.80197" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 19.14911442 -10.04082343 6.87846314 + 32.90834123 3.62895187 + 35.71343359 + + Transpose of the rotation matrix + 0.557049 0.800590 -0.220797 + -0.772702 0.402209 -0.491079 + -0.304346 0.444166 0.842668 + CENTER OF ATOMS BEFORE TRANSLATION 0.76478 1.11616 -0.58831 + AXIS OF ROTATION IS -0.510452 -0.045601 0.858696 ANGLE IS 66.36 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 24 atoms have been selected out of 24 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.000017 -0.000052 0.000078 0.000096 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CHEX" + RDCMND substituted energy or value "?RDIP" to "9.553956E-05" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 6 + Number of bonds = 24 Number of angles = 36 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 24 atoms have been selected out of 24 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 24 bonds deleted + DELTIC: 36 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "20" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "20" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "20" + Parameter: RESI20 -> "MEOH" + Parameter: RESIDUE <- "MEOH" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MEOH" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MEOH" + Drude polarizability will be setup for SEGID: MEOH mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 2 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MEOH. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 10 Number of groups = 1 + Number of bonds = 9 Number of angles = 7 + Number of dihedrals = 3 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 2 + Number of true-bonds = 9 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "20" + Parameter: SEED20 -> "1 HO1 1 O1 1 C1" + + CHARMM> ic build + **** WARNING **** 4 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 42 exclusions and 3 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3 atom pairs and 45 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 11.65577 -6.85380 0.01837 +ENER INTERN> 0.01375 0.12195 0.00169 0.00007 0.00000 +ENER EXTERN> -0.01364 11.53196 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MEOH" + RDCMND substituted energy or value "?ENER" to "11.6558" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.86267964 0.00000000 -0.00000000 + 6.93873726 2.42228698 + 3.49360919 + + Transpose of the rotation matrix + 0.458511 0.888689 0.000000 + -0.888689 0.458511 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.12092 0.76474 0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 1.000000 ANGLE IS 62.71 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 10 atoms have been selected out of 10 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.606489 1.735582 -0.000000 1.838497 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MEOH" + RDCMND substituted energy or value "?RDIP" to "1.8385" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 10 Number of groups = 1 + Number of bonds = 9 Number of angles = 7 + Number of dihedrals = 3 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 4 + + CHARMM> delete atom sele all end + SELRPN> 10 atoms have been selected out of 10 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 9 bonds deleted + DELTIC: 7 angles deleted + DELTIC: 3 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "21" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "21" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "21" + Parameter: RESI21 -> "ETOH" + Parameter: RESIDUE <- "ETOH" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ETOH" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ETOH" + Drude polarizability will be setup for SEGID: ETOH mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 3 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ETOH. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 1 + Number of bonds = 13 Number of angles = 13 + Number of dihedrals = 12 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 3 + Number of true-bonds = 13 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "21" + Parameter: SEED21 -> "1 HO1 1 O1 1 C1" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 66 exclusions and 22 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 25 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 25 atom pairs and 88 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 25 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 3.02316 8.63262 6.70086 +ENER INTERN> 0.00000 0.28863 0.11098 0.84847 0.00000 +ENER EXTERN> -0.14144 1.91652 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ETOH" + RDCMND substituted energy or value "?ENER" to "3.02316" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 3.42184390 0.00000000 0.00000000 + 10.61033974 7.19657418 + 16.71677988 + + Transpose of the rotation matrix + 0.833836 0.552013 0.000000 + -0.552013 0.833836 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.72325 1.01184 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 33.51 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 14 atoms have been selected out of 14 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.391484 1.897179 0.000000 1.937149 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ETOH" + RDCMND substituted energy or value "?RDIP" to "1.93715" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 1 + Number of bonds = 13 Number of angles = 13 + Number of dihedrals = 12 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 14 atoms have been selected out of 14 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 13 bonds deleted + DELTIC: 13 angles deleted + DELTIC: 12 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "22" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "22" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "22" + Parameter: RESI22 -> "PRO1" + Parameter: RESIDUE <- "PRO1" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PRO1" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PRO1" + Drude polarizability will be setup for SEGID: PRO1 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PRO1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 3 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "22" + Parameter: SEED22 -> "1 HO1 1 O1 1 C1" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 88 exclusions and 40 interactions(1-4) + found 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 65 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 65 atom pairs and 128 atom exclusions. + There are 0 group pairs and 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 65 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 8.23186 -5.20870 6.45879 +ENER INTERN> 0.00000 0.54391 0.23232 2.57628 0.00000 +ENER EXTERN> -0.28239 5.16174 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PRO1" + RDCMND substituted energy or value "?ENER" to "8.23186" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 5.05466176 -0.00000000 0.00000000 + 27.88665781 19.74047916 + 27.96085791 + + Transpose of the rotation matrix + 0.707771 0.706442 -0.000000 + -0.706442 0.707771 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.11901 1.53634 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 44.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.017203 1.941079 0.000000 1.941155 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PRO1" + RDCMND substituted energy or value "?RDIP" to "1.94115" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 3 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 21 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "23" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "23" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "23" + Parameter: RESI23 -> "BUO1" + Parameter: RESIDUE <- "BUO1" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BUO1" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BUO1" + Drude polarizability will be setup for SEGID: BUO1 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BUO1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 4 + Number of bonds = 21 Number of angles = 25 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 5 + Number of true-bonds = 21 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "23" + Parameter: SEED23 -> "1 HO1 1 O1 1 C1" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 110 exclusions and 56 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 121 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 121 atom pairs and 166 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 121 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 8.30368 -0.07183 4.71986 +ENER INTERN> 0.00000 0.69744 0.30892 2.97696 0.00000 +ENER EXTERN> -0.47534 4.79570 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BUO1" + RDCMND substituted energy or value "?ENER" to "8.30368" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 6.68747962 0.00000000 0.00000000 + 39.51465566 37.12899245 + 59.45553064 + + Transpose of the rotation matrix + 0.793520 0.608545 0.000000 + -0.608545 0.793520 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.67799 1.85629 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 37.48 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.215575 1.928708 0.000000 1.940718 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BUO1" + RDCMND substituted energy or value "?RDIP" to "1.94072" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 4 + Number of bonds = 21 Number of angles = 25 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 21 bonds deleted + DELTIC: 25 angles deleted + DELTIC: 30 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "24" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "24" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "24" + Parameter: RESI24 -> "PRO2" + Parameter: RESIDUE <- "PRO2" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PRO2" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PRO2" + Drude polarizability will be setup for SEGID: PRO2 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PRO2. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 3 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "24" + Parameter: SEED24 -> "1 HO2 1 O2 1 C2" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 91 exclusions and 47 interactions(1-4) + found 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 62 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 62 atom pairs and 138 atom exclusions. + There are 0 group pairs and 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 62 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -9.39499 17.69868 9.74846 +ENER INTERN> 0.00000 0.70076 0.11020 3.42575 0.00000 +ENER EXTERN> -0.08496 -13.54675 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PRO2" + RDCMND substituted energy or value "?ENER" to "-9.39499" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 21.44616897 -0.00000000 -0.00000000 + 14.83905463 8.42958254 + 14.05367468 + + Transpose of the rotation matrix + 0.690458 0.723372 -0.000000 + 0.000000 0.000000 1.000000 + 0.723372 -0.690458 -0.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.73007 1.23575 0.00000 + AXIS OF ROTATION IS 0.855538 0.366097 0.366097 ANGLE IS 98.90 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.044707 -0.000000 -2.000009 2.000509 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PRO2" + RDCMND substituted energy or value "?RDIP" to "2.00051" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 3 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 21 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "25" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "25" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "25" + Parameter: RESI25 -> "BUO2" + Parameter: RESIDUE <- "BUO2" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BUO2" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BUO2" + Drude polarizability will be setup for SEGID: BUO2 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BUO2. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 4 + Number of bonds = 21 Number of angles = 25 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 21 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "25" + Parameter: SEED25 -> "1 HO2 1 O2 1 C2" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 113 exclusions and 66 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 118 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 118 atom pairs and 179 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 118 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 3.30713 -12.70212 9.52090 +ENER INTERN> 0.00000 1.38254 0.20683 4.60361 0.00000 +ENER EXTERN> 4.05868 -6.94454 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BUO2" + RDCMND substituted energy or value "?ENER" to "3.30713" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 28.16717939 -9.47509983 -4.71761219 + 32.42530835 16.64369489 + 19.83133790 + + Transpose of the rotation matrix + 0.494700 0.745080 -0.447357 + 0.328804 0.316029 0.889951 + 0.804462 -0.587352 -0.088646 + CENTER OF ATOMS BEFORE TRANSLATION 1.94047 1.65894 -0.22748 + AXIS OF ROTATION IS 0.745888 0.632042 0.210177 ANGLE IS 97.99 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.311394 -0.059414 -1.980223 2.005437 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BUO2" + RDCMND substituted energy or value "?RDIP" to "2.00544" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 4 + Number of bonds = 21 Number of angles = 25 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 21 bonds deleted + DELTIC: 25 angles deleted + DELTIC: 30 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "26" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "26" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "26" + Parameter: RESI26 -> "BENZ" + Parameter: RESIDUE <- "BENZ" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BENZ" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BENZ" + Drude polarizability will be setup for SEGID: BENZ mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BENZ. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 18 Number of angles = 18 + Number of dihedrals = 24 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 18 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "26" + Parameter: SEED26 -> "1 CG 1 CD1 1 CE1" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 90 exclusions and 42 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 63 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 63 atom pairs and 132 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 63 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 27.70896 -24.40183 17.43698 +ENER INTERN> 0.00000 0.00000 0.37159 0.00000 0.00000 +ENER EXTERN> 25.63331 1.70406 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BENZ" + RDCMND substituted energy or value "?ENER" to "27.709" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 -0.00000000 0.00000000 + 29.42482500 0.00000000 + 29.42482500 + + Transpose of the rotation matrix + 0.991386 0.130969 -0.000000 + -0.130969 0.991386 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.68750 1.19078 0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 1.000000 ANGLE IS 7.53 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.000000 -0.000000 -0.000000 0.000000 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BENZ" + RDCMND substituted energy or value "?RDIP" to "2.086737E-15" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 18 Number of angles = 18 + Number of dihedrals = 24 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 18 bonds deleted + DELTIC: 18 angles deleted + DELTIC: 24 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "27" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "27" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "27" + Parameter: RESI27 -> "TOLU" + Parameter: RESIDUE <- "TOLU" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "TOLU" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "TOLU" + Drude polarizability will be setup for SEGID: TOLU mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 7 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is TOLU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 1 + Number of bonds = 22 Number of angles = 24 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 7 + Number of true-bonds = 22 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "27" + Parameter: SEED27 -> "1 CG 1 CD1 1 CE1" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 112 exclusions and 60 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 119 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 119 atom pairs and 172 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 119 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 23.69317 4.01578 15.73357 +ENER INTERN> 0.00000 0.70146 0.35472 0.00000 0.00000 +ENER EXTERN> 26.60470 -3.96771 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "TOLU" + RDCMND substituted energy or value "?ENER" to "23.6932" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.66701041 -0.00000000 -0.00000000 + 56.06757755 13.77327056 + 38.60924757 + + Transpose of the rotation matrix + 0.482017 0.876162 -0.000000 + -0.876162 0.482017 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.40282 0.67310 0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 1.000000 ANGLE IS 61.18 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.696006 0.022817 -0.000000 0.696379 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "TOLU" + RDCMND substituted energy or value "?RDIP" to "0.696379" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 1 + Number of bonds = 22 Number of angles = 24 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 22 bonds deleted + DELTIC: 24 angles deleted + DELTIC: 30 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "28" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "28" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "28" + Parameter: RESI28 -> "ACEM" + Parameter: RESIDUE <- "ACEM" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ACEM" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ACEM" + Drude polarizability will be setup for SEGID: ACEM mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ACEM. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 14 Number of angles = 12 + Number of dihedrals = 10 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 4 + Number of true-bonds = 14 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "28" + Parameter: SEED28 -> "1 N 1 C 1 CL" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 69 exclusions and 30 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 36 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 36 atom pairs and 99 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 36 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -74.60414 98.29731 33.56317 +ENER INTERN> 0.00000 0.84503 15.98182 1.85400 0.00000 +ENER EXTERN> 12.64708 -105.93207 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ACEM" + RDCMND substituted energy or value "?ENER" to "-74.6041" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.67714224 -0.00000000 0.00000000 + 12.90850671 -0.03270479 + 16.57839147 + + Transpose of the rotation matrix + 0.999960 -0.008911 0.000000 + 0.008911 0.999960 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.31203 0.15816 0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 -1.000000 ANGLE IS 0.51 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 15 atoms have been selected out of 15 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.746236 2.646883 -0.000000 4.586968 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ACEM" + RDCMND substituted energy or value "?RDIP" to "4.58697" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 14 Number of angles = 12 + Number of dihedrals = 10 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 15 atoms have been selected out of 15 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 14 bonds deleted + DELTIC: 12 angles deleted + DELTIC: 10 dihedrals deleted + DELTIC: 2 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "29" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "29" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "29" + Parameter: RESI29 -> "NMA" + Parameter: RESIDUE <- "NMA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "NMA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "NMA" + Drude polarizability will be setup for SEGID: NMA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is NMA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 19 Number of groups = 1 + Number of bonds = 18 Number of angles = 18 + Number of dihedrals = 16 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 5 + Number of true-bonds = 18 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "29" + Parameter: SEED29 -> "1 N 1 C 1 CL" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 90 exclusions and 45 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 81 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 81 atom pairs and 135 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 81 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 14.14216 -88.74630 29.99539 +ENER INTERN> 15.96346 21.20063 20.44798 2.34000 0.00000 +ENER EXTERN> 3.02708 -48.83699 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "NMA" + RDCMND substituted energy or value "?ENER" to "14.1422" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 3.13398979 0.00000000 0.00000000 + 29.89939659 15.53944628 + 34.01211415 + + Transpose of the rotation matrix + 0.752060 0.659095 0.000000 + -0.659095 0.752060 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.88127 -0.13266 -0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 41.23 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 19 atoms have been selected out of 19 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -1.528653 4.257435 -0.000000 4.523553 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "NMA" + RDCMND substituted energy or value "?RDIP" to "4.52355" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 19 Number of groups = 1 + Number of bonds = 18 Number of angles = 18 + Number of dihedrals = 16 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 19 atoms have been selected out of 19 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 18 bonds deleted + DELTIC: 18 angles deleted + DELTIC: 16 dihedrals deleted + DELTIC: 2 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "30" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "30" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "30" + Parameter: RESI30 -> "DMA" + Parameter: RESIDUE <- "DMA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DMA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DMA" + Drude polarizability will be setup for SEGID: DMA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DMA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 23 Number of groups = 1 + Number of bonds = 22 Number of angles = 24 + Number of dihedrals = 22 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 22 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "30" + Parameter: SEED30 -> "1 N 1 C 1 CL" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 112 exclusions and 66 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 141 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 141 atom pairs and 178 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 141 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 43.14147 -28.99931 30.58625 +ENER INTERN> 0.00000 1.03612 15.98643 8.38000 0.00000 +ENER EXTERN> 37.19632 -19.45741 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DMA" + RDCMND substituted energy or value "?ENER" to "43.1415" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 4.96749511 0.00000000 -0.00000000 + 33.95128825 1.74845193 + 42.93208625 + + Transpose of the rotation matrix + 0.982815 0.184592 0.000000 + -0.184592 0.982815 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.53274 0.09861 0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 1.000000 ANGLE IS 10.64 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 23 atoms have been selected out of 23 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -4.394866 3.178832 -0.000000 5.424004 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DMA" + RDCMND substituted energy or value "?RDIP" to "5.424" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 23 Number of groups = 1 + Number of bonds = 22 Number of angles = 24 + Number of dihedrals = 22 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 23 atoms have been selected out of 23 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 22 bonds deleted + DELTIC: 24 angles deleted + DELTIC: 22 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "31" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "31" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "31" + Parameter: RESI31 -> "PYR" + Parameter: RESIDUE <- "PYR" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PYR" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PYR" + Drude polarizability will be setup for SEGID: PYR mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PYR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 18 Number of angles = 16 + Number of dihedrals = 20 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 6 + Number of true-bonds = 18 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 1 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "31" + Parameter: SEED31 -> "1 CG 1 CD1 1 CE1" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 96 exclusions and 40 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 57 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 57 atom pairs and 136 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 57 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 23.35675 19.78472 8.40715 +ENER INTERN> 2.65276 2.32595 0.24066 -0.00000 0.00000 +ENER EXTERN> 17.22785 0.90952 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PYR" + RDCMND substituted energy or value "?ENER" to "23.3567" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 0.00000002 0.00000001 + 28.20326455 -0.59971604 + 28.86630401 + + Transpose of the rotation matrix + 0.861335 -0.508038 -0.000000 + 0.508038 0.861335 0.000000 + -0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.70682 1.19888 0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 -1.000000 ANGLE IS 30.53 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.000255 -2.406187 -0.000000 2.406188 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PYR" + RDCMND substituted energy or value "?RDIP" to "2.40619" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 18 Number of angles = 16 + Number of dihedrals = 20 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 18 bonds deleted + DELTIC: 16 angles deleted + DELTIC: 20 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "32" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "32" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "32" + Parameter: RESI32 -> "PYRM" + Parameter: RESIDUE <- "PYRM" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PYRM" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PYRM" + Drude polarizability will be setup for SEGID: PYRM mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PYRM. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 18 Number of angles = 14 + Number of dihedrals = 16 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 6 + Number of true-bonds = 18 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "32" + Parameter: SEED32 -> "1 C4 1 C5 1 C6" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 103 exclusions and 36 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 50 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 50 atom pairs and 139 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 50 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -14.52993 37.88668 15.81600 +ENER INTERN> 1.99326 4.15127 0.71844 0.00000 0.00000 +ENER EXTERN> 21.24165 -42.63455 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PYRM" + RDCMND substituted energy or value "?ENER" to "-14.5299" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 0.00000002 0.00000003 + 26.20721708 -0.36831227 + 25.84119179 + + Transpose of the rotation matrix + 0.526788 -0.849996 -0.000000 + 0.849996 0.526788 0.000000 + -0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.68922 1.14981 0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 -1.000000 ANGLE IS 58.21 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 2.204420 0.001756 -0.000000 2.204421 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PYRM" + RDCMND substituted energy or value "?RDIP" to "2.20442" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 18 Number of angles = 14 + Number of dihedrals = 16 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 18 bonds deleted + DELTIC: 14 angles deleted + DELTIC: 16 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "33" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "33" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "33" + Parameter: RESI33 -> "PYRR" + Parameter: RESIDUE <- "PYRR" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PYRR" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PYRR" + Drude polarizability will be setup for SEGID: PYRR mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PYRR. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 15 Number of angles = 15 + Number of dihedrals = 20 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 15 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "33" + Parameter: SEED33 -> "1 N5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 75 exclusions and 25 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 30 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 30 atom pairs and 100 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 30 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -4.22645 -10.30348 8.75298 +ENER INTERN> 0.08602 0.69586 0.21243 0.00000 0.00000 +ENER EXTERN> -0.59140 -4.62935 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PYRR" + RDCMND substituted energy or value "?ENER" to "-4.22645" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 0.00000000 0.00000000 + 19.57807140 -0.21452670 + 19.72228821 + + Transpose of the rotation matrix + 0.811976 -0.583690 -0.000000 + 0.583690 0.811976 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.68631 0.95739 0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 -1.000000 ANGLE IS 35.71 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 15 atoms have been selected out of 15 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.002440 -1.972332 0.000000 1.972334 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PYRR" + RDCMND substituted energy or value "?RDIP" to "1.97233" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 15 Number of angles = 15 + Number of dihedrals = 20 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 15 atoms have been selected out of 15 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 15 bonds deleted + DELTIC: 15 angles deleted + DELTIC: 20 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "34" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "34" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "34" + Parameter: RESI34 -> "IMID" + Parameter: RESIDUE <- "IMID" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "IMID" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "IMID" + Drude polarizability will be setup for SEGID: IMID mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is IMID. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 15 Number of angles = 13 + Number of dihedrals = 16 Number of impropers = 8 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 15 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 1 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "34" + Parameter: SEED34 -> "1 ND1 1 CG 1 CD2" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 81 exclusions and 21 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 24 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 24 atom pairs and 102 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 24 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.36357 -4.59002 8.82064 +ENER INTERN> 0.01205 0.09760 0.07397 0.00000 0.00000 +ENER EXTERN> -0.52693 0.70688 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "IMID" + RDCMND substituted energy or value "?ENER" to "0.36357" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 -0.00000002 0.00000000 + 16.70017672 -0.13659090 + 18.56694062 + + Transpose of the rotation matrix + 0.997362 -0.072590 0.000000 + 0.072590 0.997362 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.67256 0.90725 -0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 -1.000000 ANGLE IS 4.16 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 15 atoms have been selected out of 15 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.939873 -3.882389 0.000000 3.994534 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "IMID" + RDCMND substituted energy or value "?RDIP" to "3.99453" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 15 Number of angles = 13 + Number of dihedrals = 16 Number of impropers = 8 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 15 atoms have been selected out of 15 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 15 bonds deleted + DELTIC: 13 angles deleted + DELTIC: 16 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "35" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "35" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "35" + Parameter: RESI35 -> "INDO" + Parameter: RESIDUE <- "INDO" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "INDO" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "INDO" + Drude polarizability will be setup for SEGID: INDO mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is INDO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 26 Number of angles = 27 + Number of dihedrals = 40 Number of impropers = 10 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 9 + Number of true-bonds = 26 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "35" + Parameter: SEED35 -> "1 CG 1 CD1 1 NE1" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 143 exclusions and 77 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 157 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 157 atom pairs and 220 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 157 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 4.78505 -4.42148 6.64135 +ENER INTERN> 1.38567 3.23905 0.72348 0.00000 0.00000 +ENER EXTERN> 10.37723 -10.94037 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "INDO" + RDCMND substituted energy or value "?ENER" to "4.78505" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 0.00000000 -0.00000000 + 71.22513429 -20.65820043 + 55.75565565 + + Transpose of the rotation matrix + 0.569806 -0.821779 -0.000000 + 0.821779 0.569806 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION -0.02337 2.00146 0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 -1.000000 ANGLE IS 55.26 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 25 atoms have been selected out of 25 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.044073 2.307322 0.000000 3.082527 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "INDO" + RDCMND substituted energy or value "?RDIP" to "3.08253" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 26 Number of angles = 27 + Number of dihedrals = 40 Number of impropers = 10 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 25 atoms have been selected out of 25 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 26 bonds deleted + DELTIC: 27 angles deleted + DELTIC: 40 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 1 donors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "36" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "36" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "36" + Parameter: RESI36 -> "PUR1" + Parameter: RESIDUE <- "PUR1" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PUR1" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PUR1" + Drude polarizability will be setup for SEGID: PUR1 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PUR1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 26 Number of angles = 21 + Number of dihedrals = 28 Number of impropers = 8 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 9 + Number of true-bonds = 26 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "36" + Parameter: SEED36 -> "1 C6 1 C5 1 C4" + + CHARMM> ic build + **** WARNING **** 12 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 236 236 234 + : Ran out of space. RESIZING + with mode 5 found 165 exclusions and 72 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 135 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 135 atom pairs and 237 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 135 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 64.73557 -59.95052 14.20084 +ENER INTERN> 4.09734 45.17834 2.47879 -0.00000 0.00000 +ENER EXTERN> 10.35918 2.62193 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PUR1" + RDCMND substituted energy or value "?ENER" to "64.7356" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 0.00000001 0.00000000 + 46.14447193 -17.51125204 + 63.74189135 + + Transpose of the rotation matrix + 0.851167 -0.524895 -0.000000 + 0.524895 0.851167 0.000000 + -0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.51660 0.71386 -0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 -1.000000 ANGLE IS 31.66 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 25 atoms have been selected out of 25 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.627468 -6.442900 0.000000 6.958056 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PUR1" + RDCMND substituted energy or value "?RDIP" to "6.95806" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 26 Number of angles = 21 + Number of dihedrals = 28 Number of impropers = 8 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 12 + + CHARMM> delete atom sele all end + SELRPN> 25 atoms have been selected out of 25 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 26 bonds deleted + DELTIC: 21 angles deleted + DELTIC: 28 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "37" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "37" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "37" + Parameter: RESI37 -> "PUR0" + Parameter: RESIDUE <- "PUR0" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PUR0" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PUR0" + Drude polarizability will be setup for SEGID: PUR0 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PUR0. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 26 Number of angles = 21 + Number of dihedrals = 28 Number of impropers = 8 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 9 + Number of true-bonds = 26 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 3 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "37" + Parameter: SEED37 -> "1 C6 1 C5 1 C4" + + CHARMM> ic build + **** WARNING **** 12 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 237 237 234 + : Ran out of space. RESIZING + with mode 5 found 164 exclusions and 76 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 136 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 136 atom pairs and 240 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 136 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 33.63958 31.09599 13.53930 +ENER INTERN> 4.69975 41.09259 3.62451 0.00000 0.00000 +ENER EXTERN> 9.79206 -25.56933 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PUR0" + RDCMND substituted energy or value "?ENER" to "33.6396" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 -0.00000001 0.00000004 + 44.87328724 -16.49067441 + 64.35748641 + + Transpose of the rotation matrix + 0.868515 -0.495663 0.000000 + 0.495663 0.868515 0.000000 + -0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.49587 0.75688 0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 -1.000000 ANGLE IS 29.71 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 25 atoms have been selected out of 25 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 6.832362 3.305305 -0.000000 7.589875 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PUR0" + RDCMND substituted energy or value "?RDIP" to "7.58988" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 25 Number of groups = 1 + Number of bonds = 26 Number of angles = 21 + Number of dihedrals = 28 Number of impropers = 8 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 12 + + CHARMM> delete atom sele all end + SELRPN> 25 atoms have been selected out of 25 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 26 bonds deleted + DELTIC: 21 angles deleted + DELTIC: 28 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "38" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "38" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "38" + Parameter: RESI38 -> "4MIM" + Parameter: RESIDUE <- "4MIM" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "4MIM" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "4MIM" + Drude polarizability will be setup for SEGID: 4MIM mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is 4MIM. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 19 Number of groups = 1 + Number of bonds = 19 Number of angles = 19 + Number of dihedrals = 22 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 19 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 1 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "38" + Parameter: SEED38 -> "1 ND1 1 CG 1 CB" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 103 exclusions and 40 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 68 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 68 atom pairs and 143 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 68 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -1.15743 34.79701 8.53926 +ENER INTERN> 0.03508 0.12067 0.04107 0.00000 0.00000 +ENER EXTERN> -0.54210 -0.81215 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "4MIM" + RDCMND substituted energy or value "?ENER" to "-1.15743" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.63121813 -0.00000002 -0.00000000 + 36.57790283 13.17738984 + 29.51286373 + + Transpose of the rotation matrix + 0.608715 0.793389 -0.000000 + -0.793389 0.608715 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.03835 -0.38449 0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 1.000000 ANGLE IS 52.50 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 19 atoms have been selected out of 19 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 4.366967 2.913473 -0.000000 5.249640 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "4MIM" + RDCMND substituted energy or value "?RDIP" to "5.24964" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 19 Number of groups = 1 + Number of bonds = 19 Number of angles = 19 + Number of dihedrals = 22 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 19 atoms have been selected out of 19 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 19 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 22 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "39" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "39" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "39" + Parameter: RESI39 -> "MIND" + Parameter: RESIDUE <- "MIND" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MIND" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MIND" + Drude polarizability will be setup for SEGID: MIND mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MIND. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 29 Number of groups = 1 + Number of bonds = 30 Number of angles = 33 + Number of dihedrals = 46 Number of impropers = 8 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 10 + Number of true-bonds = 30 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "39" + Parameter: SEED39 -> "1 CG 1 CD1 1 NE1" + + CHARMM> ic build + **** WARNING **** 10 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 165 exclusions and 96 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 241 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 241 atom pairs and 261 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 241 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 14.85854 -16.01597 13.72053 +ENER INTERN> 1.47234 8.04520 0.92017 0.00000 0.00000 +ENER EXTERN> 10.18067 -5.75984 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MIND" + RDCMND substituted energy or value "?ENER" to "14.8585" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.65285456 -0.00000000 0.00000000 + 111.64806320 -8.94177889 + 62.11076489 + + Transpose of the rotation matrix + 0.172361 -0.985034 0.000000 + 0.985034 0.172361 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION -0.21657 1.48263 -0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 -1.000000 ANGLE IS 80.07 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 29 atoms have been selected out of 29 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 1.331750 2.394869 -0.000000 2.740247 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MIND" + RDCMND substituted energy or value "?RDIP" to "2.74025" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 29 Number of groups = 1 + Number of bonds = 30 Number of angles = 33 + Number of dihedrals = 46 Number of impropers = 8 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 10 + + CHARMM> delete atom sele all end + SELRPN> 29 atoms have been selected out of 29 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 30 bonds deleted + DELTIC: 33 angles deleted + DELTIC: 46 dihedrals deleted + DELTIC: 8 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "40" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "40" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "40" + Parameter: RESI40 -> "MAS" + Parameter: RESIDUE <- "MAS" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MAS" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MAS" + Drude polarizability will be setup for SEGID: MAS mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MAS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 20 Number of groups = 1 + Number of bonds = 19 Number of angles = 16 + Number of dihedrals = 11 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 19 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "40" + Parameter: SEED40 -> "1 C1 1 C 1 OM" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 115 exclusions and 42 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 75 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 75 atom pairs and 157 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 75 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -5.07241 19.93095 17.72977 +ENER INTERN> 1.08043 1.40773 1.08560 1.65786 0.00000 +ENER EXTERN> 7.25366 -17.55770 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MAS" + RDCMND substituted energy or value "?ENER" to "-5.07241" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 3.38539631 0.00000000 0.00000000 + 20.70062990 11.90264157 + 38.12769066 + + Transpose of the rotation matrix + 0.891824 0.452383 0.000000 + -0.452383 0.891824 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.83554 0.42477 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 26.90 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 20 atoms have been selected out of 20 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.138126 2.178597 -0.000000 3.052518 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MAS" + RDCMND substituted energy or value "?RDIP" to "3.05252" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 20 Number of groups = 1 + Number of bonds = 19 Number of angles = 16 + Number of dihedrals = 11 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 20 atoms have been selected out of 20 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 19 bonds deleted + DELTIC: 16 angles deleted + DELTIC: 11 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "41" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "41" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "41" + Parameter: RESI41 -> "ACEH" + Parameter: RESIDUE <- "ACEH" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ACEH" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ACEH" + Drude polarizability will be setup for SEGID: ACEH mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ACEH. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 16 Number of groups = 1 + Number of bonds = 15 Number of angles = 10 + Number of dihedrals = 8 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 4 + Number of true-bonds = 15 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "41" + Parameter: SEED41 -> "1 O2 1 C2 1 C1" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 87 exclusions and 30 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 33 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 33 atom pairs and 117 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 33 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -61.96618 56.89377 20.81237 +ENER INTERN> 0.76515 1.03148 10.63930 0.00000 0.00000 +ENER EXTERN> 0.31519 -74.71730 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ACEH" + RDCMND substituted energy or value "?ENER" to "-61.9662" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.85893212 0.00000000 -0.00000000 + 19.68968082 2.51269763 + 13.69390296 + + Transpose of the rotation matrix + 0.341760 0.939787 0.000000 + -0.939787 0.341760 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.41656 0.02832 -0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 1.000000 ANGLE IS 70.02 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 16 atoms have been selected out of 16 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.848411 -1.766585 0.000000 1.959751 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ACEH" + RDCMND substituted energy or value "?RDIP" to "1.95975" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 16 Number of groups = 1 + Number of bonds = 15 Number of angles = 10 + Number of dihedrals = 8 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 16 atoms have been selected out of 16 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 15 bonds deleted + DELTIC: 10 angles deleted + DELTIC: 8 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "42" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "42" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "42" + Parameter: RESI42 -> "IMIM" + Parameter: RESIDUE <- "IMIM" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "IMIM" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "IMIM" + Drude polarizability will be setup for SEGID: IMIM mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is IMIM. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 15 Number of angles = 15 + Number of dihedrals = 20 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 5 + Number of true-bonds = 15 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "42" + Parameter: SEED42 -> "1 CG 1 CD2 1 NE2" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 75 exclusions and 25 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 30 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 30 atom pairs and 100 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 30 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 45.44381 -107.40999 15.80966 +ENER INTERN> 0.60607 1.23462 0.39255 -0.00000 0.00000 +ENER EXTERN> -0.15825 43.36881 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "IMIM" + RDCMND substituted energy or value "?ENER" to "45.4438" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 -0.00000000 0.00000000 + 19.53428430 -0.32153414 + 18.60891747 + + Transpose of the rotation matrix + 0.299014 -0.954249 0.000000 + 0.954249 0.299014 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.65580 0.96044 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 -1.000000 ANGLE IS 72.60 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 15 atoms have been selected out of 15 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -1.476195 0.439029 0.000000 1.540097 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "IMIM" + RDCMND substituted energy or value "?RDIP" to "1.5401" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 15 Number of angles = 15 + Number of dihedrals = 20 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 15 atoms have been selected out of 15 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 15 bonds deleted + DELTIC: 15 angles deleted + DELTIC: 20 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 2 donors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "43" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "43" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "43" + Parameter: RESI43 -> "GUAN" + Parameter: RESIDUE <- "GUAN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "GUAN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GUAN" + Drude polarizability will be setup for SEGID: GUAN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GUAN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 1 + Number of bonds = 13 Number of angles = 12 + Number of dihedrals = 12 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 4 + Number of true-bonds = 13 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "43" + Parameter: SEED43 -> "1 N1 1 C 1 N2" + + CHARMM> ic build + **** WARNING **** 4 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 55 exclusions and 24 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 36 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 36 atom pairs and 79 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 36 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -302.10407 347.54787 37.51939 +ENER INTERN> 5.43561 0.84695 0.49704 0.00000 0.00000 +ENER EXTERN> -0.51189 -308.37178 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "GUAN" + RDCMND substituted energy or value "?ENER" to "-302.104" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 -0.00000000 0.00000000 + 17.93360587 0.00000000 + 17.93360587 + + Transpose of the rotation matrix + 0.133930 -0.990991 0.000000 + 0.990991 0.133930 0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.34020 -0.00000 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 -1.000000 ANGLE IS 82.30 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 14 atoms have been selected out of 14 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 -0.000000 0.000000 0.000000 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "GUAN" + RDCMND substituted energy or value "?RDIP" to "8.529451E-16" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 1 + Number of bonds = 13 Number of angles = 12 + Number of dihedrals = 12 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 4 + + CHARMM> delete atom sele all end + SELRPN> 14 atoms have been selected out of 14 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 13 bonds deleted + DELTIC: 12 angles deleted + DELTIC: 12 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "44" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "44" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "44" + Parameter: RESI44 -> "MGUAN" + Parameter: RESIDUE <- "MGUAN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MGUAN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MGUAN" + Drude polarizability will be setup for SEGID: MGUAN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MGUAN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 17 Number of angles = 18 + Number of dihedrals = 18 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 5 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "44" + Parameter: SEED44 -> "1 N1 1 C 1 N2" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 76 exclusions and 37 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 77 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 77 atom pairs and 113 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 77 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -188.72075 -113.38331 29.85510 +ENER INTERN> 3.16991 1.16875 0.15308 0.64000 0.00000 +ENER EXTERN> -0.37876 -193.47372 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MGUAN" + RDCMND substituted energy or value "?ENER" to "-188.721" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.66584513 -0.00000000 -0.00000000 + 25.07591370 -10.16130190 + 38.53217569 + + Transpose of the rotation matrix + 0.880931 -0.473244 0.000000 + 0.473244 0.880931 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.91535 -0.27962 0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 -1.000000 ANGLE IS 28.25 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -1.441471 0.178824 0.000000 1.452521 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MGUAN" + RDCMND substituted energy or value "?RDIP" to "1.45252" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 17 Number of angles = 18 + Number of dihedrals = 18 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 18 angles deleted + DELTIC: 18 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "45" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "45" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "45" + Parameter: RESI45 -> "PHEN" + Parameter: RESIDUE <- "PHEN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PHEN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PHEN" + Drude polarizability will be setup for SEGID: PHEN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 7 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PHEN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 1 + Number of bonds = 22 Number of angles = 19 + Number of dihedrals = 26 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 7 + Number of true-bonds = 22 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "45" + Parameter: SEED45 -> "1 CG 1 CD1 1 CE1" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 120 exclusions and 64 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 111 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 111 atom pairs and 184 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 111 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 23.50048 -212.22124 18.50238 +ENER INTERN> 0.00000 0.00000 0.35163 0.00000 0.00000 +ENER EXTERN> 25.19158 -2.04272 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PHEN" + RDCMND substituted energy or value "?ENER" to "23.5005" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.21375568 0.00000000 0.00000000 + 53.63856728 11.23120000 + 35.38453137 + + Transpose of the rotation matrix + 0.429731 0.902957 0.000000 + -0.902957 0.429731 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.92522 1.68449 0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 1.000000 ANGLE IS 64.55 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 1.163998 1.448913 -0.000000 1.858558 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PHEN" + RDCMND substituted energy or value "?RDIP" to "1.85856" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 1 + Number of bonds = 22 Number of angles = 19 + Number of dihedrals = 26 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 22 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 26 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "46" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "46" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "46" + Parameter: RESI46 -> "MESH" + Parameter: RESIDUE <- "MESH" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MESH" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MESH" + Drude polarizability will be setup for SEGID: MESH mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 2 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MESH. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 10 Number of groups = 1 + Number of bonds = 9 Number of angles = 7 + Number of dihedrals = 3 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 2 + Number of true-bonds = 9 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "46" + Parameter: SEED46 -> "1 HS1 1 S1 1 C1" + + CHARMM> ic build + **** WARNING **** 4 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 42 exclusions and 3 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 3 atom pairs and 45 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 3 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 2.58433 20.91615 0.01231 +ENER INTERN> 0.00082 0.06587 0.00156 0.00001 0.00000 +ENER EXTERN> -0.00541 2.52149 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MESH" + RDCMND substituted energy or value "?ENER" to "2.58433" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 2.87504461 0.00000000 -0.00000000 + 10.77694173 2.12807150 + 3.76483488 + + Transpose of the rotation matrix + 0.269395 0.963030 0.000000 + -0.963030 0.269395 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.36183 0.99432 0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 1.000000 ANGLE IS 74.37 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 10 atoms have been selected out of 10 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.932782 1.195439 0.000000 1.516297 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MESH" + RDCMND substituted energy or value "?RDIP" to "1.5163" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 10 Number of groups = 1 + Number of bonds = 9 Number of angles = 7 + Number of dihedrals = 3 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 4 + + CHARMM> delete atom sele all end + SELRPN> 10 atoms have been selected out of 10 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 9 bonds deleted + DELTIC: 7 angles deleted + DELTIC: 3 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "47" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "47" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "47" + Parameter: RESI47 -> "ETSH" + Parameter: RESIDUE <- "ETSH" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ETSH" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ETSH" + Drude polarizability will be setup for SEGID: ETSH mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 3 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ETSH. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 1 + Number of bonds = 13 Number of angles = 13 + Number of dihedrals = 12 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 3 + Number of true-bonds = 13 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "47" + Parameter: SEED47 -> "1 HS1 1 S1 1 C1" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 66 exclusions and 22 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 25 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 25 atom pairs and 88 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 25 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -3.45143 6.03577 3.74129 +ENER INTERN> 0.00077 0.02255 0.00455 1.03524 0.00000 +ENER EXTERN> -0.21761 -4.29693 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ETSH" + RDCMND substituted energy or value "?ENER" to "-3.45143" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 4.34230746 0.00000000 0.00000000 + 17.37587346 9.56197874 + 15.65110157 + + Transpose of the rotation matrix + 0.674602 0.738182 0.000000 + -0.738182 0.674602 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.93172 1.38007 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 47.58 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 14 atoms have been selected out of 14 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.531829 1.512634 0.000000 1.603404 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ETSH" + RDCMND substituted energy or value "?RDIP" to "1.6034" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 1 + Number of bonds = 13 Number of angles = 13 + Number of dihedrals = 12 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 14 atoms have been selected out of 14 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 13 bonds deleted + DELTIC: 13 angles deleted + DELTIC: 12 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "48" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "48" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "48" + Parameter: RESI48 -> "PRSH" + Parameter: RESIDUE <- "PRSH" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PRSH" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PRSH" + Drude polarizability will be setup for SEGID: PRSH mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PRSH. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 3 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "48" + Parameter: SEED48 -> "1 HS1 1 S1 1 C1" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 88 exclusions and 40 interactions(1-4) + found 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 65 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 65 atom pairs and 128 atom exclusions. + There are 0 group pairs and 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 65 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 4.82504 -8.27647 3.51289 +ENER INTERN> 0.01166 0.12578 0.03122 3.00906 0.00000 +ENER EXTERN> -0.35309 2.00040 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PRSH" + RDCMND substituted energy or value "?ENER" to "4.82504" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 5.95704334 0.00000000 0.00000000 + 41.39129238 20.86820402 + 22.67426134 + + Transpose of the rotation matrix + 0.543510 0.839403 0.000000 + -0.839403 0.543510 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.22681 2.00039 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 57.08 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.774923 1.401160 0.000000 1.601173 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PRSH" + RDCMND substituted energy or value "?RDIP" to "1.60117" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 3 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 21 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "49" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "49" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "49" + Parameter: RESI49 -> "BUSH" + Parameter: RESIDUE <- "BUSH" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BUSH" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BUSH" + Drude polarizability will be setup for SEGID: BUSH mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BUSH. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 4 + Number of bonds = 21 Number of angles = 25 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 5 + Number of true-bonds = 21 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "49" + Parameter: SEED49 -> "1 HS1 1 S1 1 C1" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 110 exclusions and 56 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 121 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 121 atom pairs and 166 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 121 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 3.44281 1.38223 3.26646 +ENER INTERN> 0.01873 0.19555 0.03368 3.40515 0.00000 +ENER EXTERN> -0.58966 0.37935 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BUSH" + RDCMND substituted energy or value "?ENER" to "3.44281" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 7.57456010 0.00000000 0.00000000 + 61.00442183 41.66999736 + 47.99331589 + + Transpose of the rotation matrix + 0.650288 0.759688 0.000000 + -0.759688 0.650288 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 2.72645 2.42956 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 49.44 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.582476 1.499621 0.000000 1.608770 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BUSH" + RDCMND substituted energy or value "?RDIP" to "1.60877" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 4 + Number of bonds = 21 Number of angles = 25 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 21 bonds deleted + DELTIC: 25 angles deleted + DELTIC: 30 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "50" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "50" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "50" + Parameter: RESI50 -> "DMDS" + Parameter: RESIDUE <- "DMDS" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DMDS" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DMDS" + Drude polarizability will be setup for SEGID: DMDS mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DMDS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 17 Number of angles = 14 + Number of dihedrals = 7 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "50" + Parameter: SEED50 -> "1 H11 1 C1 1 S1" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 104 exclusions and 28 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 49 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 49 atom pairs and 132 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 49 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -3.00568 6.44849 6.52140 +ENER INTERN> 0.00277 0.18231 0.00548 1.68413 0.00000 +ENER EXTERN> -0.59941 -4.28096 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DMDS" + RDCMND substituted energy or value "?ENER" to "-3.00568" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 36.99368927 15.52069813 6.65072266 + 23.59913491 2.96093268 + 10.06079059 + + Transpose of the rotation matrix + 0.183687 0.534943 0.824679 + -0.223503 0.839708 -0.494910 + -0.957239 -0.093410 0.273805 + CENTER OF ATOMS BEFORE TRANSLATION 1.48482 1.45262 1.23149 + AXIS OF ROTATION IS -0.203004 -0.900962 0.383481 ANGLE IS 81.45 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.000000 -2.126966 0.000000 2.126966 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DMDS" + RDCMND substituted energy or value "?RDIP" to "2.12697" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 1 + Number of bonds = 17 Number of angles = 14 + Number of dihedrals = 7 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 14 angles deleted + DELTIC: 7 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "51" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "51" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "51" + Parameter: RESI51 -> "DMS" + Parameter: RESIDUE <- "DMS" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DMS" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DMS" + Drude polarizability will be setup for SEGID: DMS mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 3 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DMS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 1 + Number of bonds = 13 Number of angles = 13 + Number of dihedrals = 6 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 3 + Number of true-bonds = 13 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "51" + Parameter: SEED51 -> "1 H21 1 C2 1 S1" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 70 exclusions and 12 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 21 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 21 atom pairs and 82 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 21 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -2.13589 -0.86980 6.42181 +ENER INTERN> 0.00058 0.08667 0.00219 0.00003 0.00000 +ENER EXTERN> -0.09175 -2.13362 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DMS" + RDCMND substituted energy or value "?ENER" to "-2.13589" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 12.16882652 8.46560222 -1.90095629 + 18.55694950 -0.14494582 + 5.34446041 + + Transpose of the rotation matrix + 0.062982 -0.817935 -0.571852 + 0.575955 0.497734 -0.648488 + 0.815052 -0.288518 0.502442 + CENTER OF ATOMS BEFORE TRANSLATION 1.17501 1.21474 0.61514 + AXIS OF ROTATION IS -0.180075 0.693798 -0.697293 ANGLE IS 88.19 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 14 atoms have been selected out of 14 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.000000 -1.873323 0.000000 1.873323 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DMS" + RDCMND substituted energy or value "?RDIP" to "1.87332" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 1 + Number of bonds = 13 Number of angles = 13 + Number of dihedrals = 6 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 14 atoms have been selected out of 14 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 13 bonds deleted + DELTIC: 13 angles deleted + DELTIC: 6 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "52" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "52" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "52" + Parameter: RESI52 -> "EMS" + Parameter: RESIDUE <- "EMS" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "EMS" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "EMS" + Drude polarizability will be setup for SEGID: EMS mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is EMS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 2 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 15 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "52" + Parameter: SEED52 -> "1 H31 1 C3 1 C2" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 94 exclusions and 32 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 59 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 59 atom pairs and 126 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 59 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.44455 -2.58044 4.64240 +ENER INTERN> 0.00510 0.23076 0.01733 0.63261 0.00000 +ENER EXTERN> -0.32967 -0.11158 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "EMS" + RDCMND substituted energy or value "?ENER" to "0.444552" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 33.20555026 10.70558493 5.38907297 + 19.75724326 2.76328106 + 8.60095133 + + Transpose of the rotation matrix + 0.187692 0.474024 0.860275 + -0.028202 0.878080 -0.477682 + -0.981823 0.065396 0.178177 + CENTER OF ATOMS BEFORE TRANSLATION 1.51725 1.26048 1.06951 + AXIS OF ROTATION IS -0.273582 -0.927978 0.253002 ANGLE IS 82.99 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.639773 -0.992538 -1.278108 1.740116 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "EMS" + RDCMND substituted energy or value "?RDIP" to "1.74012" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 2 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 15 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 15 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "53" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "53" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "53" + Parameter: RESI53 -> "NC4" + Parameter: RESIDUE <- "NC4" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "NC4" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "NC4" + Drude polarizability will be setup for SEGID: NC4 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is NC4. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 1 + Number of bonds = 21 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 5 + Number of true-bonds = 21 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "53" + Parameter: SEED53 -> "1 C1 1 N 1 C2" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 105 exclusions and 72 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 126 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 126 atom pairs and 177 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 126 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -63.32392 63.76847 24.77368 +ENER INTERN> 0.19959 0.00254 0.17986 0.00000 0.00000 +ENER EXTERN> -0.86322 -62.84269 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "NC4" + RDCMND substituted energy or value "?ENER" to "-63.3239" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 23.84137502 0.00000000 0.00000000 + 23.84137502 0.00000000 + 23.84057877 + + Transpose of the rotation matrix + 0.000000 0.036251 0.999343 + 0.000000 0.999343 -0.036251 + -1.000000 0.000000 -0.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.49478 0.00000 0.00000 + AXIS OF ROTATION IS -0.018126 -0.999671 0.018126 ANGLE IS 90.02 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : 0.000000 -0.000000 -0.000041 0.000041 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "NC4" + RDCMND substituted energy or value "?RDIP" to "4.077328E-05" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 1 + Number of bonds = 21 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 21 bonds deleted + DELTIC: 30 angles deleted + DELTIC: 36 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "54" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "54" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "54" + Parameter: RESI54 -> "NH5" + Parameter: RESIDUE <- "NH5" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "NH5" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "NH5" + Drude polarizability will be setup for SEGID: NH5 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 3 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is NH5. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 2 + Number of bonds = 13 Number of angles = 18 + Number of dihedrals = 18 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 3 + Number of true-bonds = 13 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "54" + Parameter: SEED54 -> "1 HN4 1 N 1 C1" + + CHARMM> ic build + **** WARNING **** 3 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 58 exclusions and 24 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 33 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 33 atom pairs and 82 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 33 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 36.84698 -100.17090 21.94203 +ENER INTERN> 0.83808 1.19384 0.29068 0.01905 0.00000 +ENER EXTERN> -0.32708 34.83241 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "NH5" + RDCMND substituted energy or value "?ENER" to "36.847" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 4.52525923 0.00000000 0.00000000 + 11.71135361 6.61372812 + 17.36541197 + + Transpose of the rotation matrix + 0.834580 0.550887 0.000000 + -0.550887 0.834580 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.91334 0.90216 0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 1.000000 ANGLE IS 33.43 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 14 atoms have been selected out of 14 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -5.318799 -0.188885 -0.000000 5.322152 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "NH5" + RDCMND substituted energy or value "?RDIP" to "5.32215" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 14 Number of groups = 2 + Number of bonds = 13 Number of angles = 18 + Number of dihedrals = 18 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 3 + + CHARMM> delete atom sele all end + SELRPN> 14 atoms have been selected out of 14 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 13 bonds deleted + DELTIC: 18 angles deleted + DELTIC: 18 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "55" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "55" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "55" + Parameter: RESI55 -> "NC5" + Parameter: RESIDUE <- "NC5" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "NC5" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "NC5" + Drude polarizability will be setup for SEGID: NC5 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is NC5. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 2 + Number of bonds = 25 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 6 + Number of true-bonds = 25 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "55" + Parameter: SEED55 -> "1 C4 1 N 1 C1" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 127 exclusions and 90 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 198 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 198 atom pairs and 217 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 198 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -28.80404 65.65102 19.77503 +ENER INTERN> 0.94488 1.03849 0.49372 0.12351 0.00000 +ENER EXTERN> -1.27092 -30.13373 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "NC5" + RDCMND substituted energy or value "?ENER" to "-28.804" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 25.30941778 0.00000000 -0.00000000 + 36.43887837 13.53832045 + 42.33128067 + + Transpose of the rotation matrix + 0.778666 0.627438 -0.000000 + -0.627438 0.778666 0.000000 + 0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.83674 0.27031 0.00000 + AXIS OF ROTATION IS 0.000000 0.000000 1.000000 ANGLE IS 38.86 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 26 atoms have been selected out of 26 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -2.451140 0.305030 -0.000000 2.470046 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "NC5" + RDCMND substituted energy or value "?RDIP" to "2.47005" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 2 + Number of bonds = 25 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 26 atoms have been selected out of 26 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 25 bonds deleted + DELTIC: 36 angles deleted + DELTIC: 45 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "56" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "56" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "56" + Parameter: RESI56 -> "ACET" + Parameter: RESIDUE <- "ACET" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ACET" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ACET" + Drude polarizability will be setup for SEGID: ACET mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ACET. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 14 Number of angles = 9 + Number of dihedrals = 6 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 4 + Number of true-bonds = 14 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "56" + Parameter: SEED56 -> "1 O1 1 C2 1 C1" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 81 exclusions and 24 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 24 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 24 atom pairs and 105 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 24 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 6.62070 -35.42475 12.21712 +ENER INTERN> 0.03272 1.18920 4.01952 2.52000 0.00000 +ENER EXTERN> 0.90236 -2.04309 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ACET" + RDCMND substituted energy or value "?ENER" to "6.6207" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.62804435 -0.00000000 0.00000000 + 16.94123634 2.37559041 + 13.62833360 + + Transpose of the rotation matrix + 0.462621 0.886556 -0.000000 + -0.886556 0.462621 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.36851 0.22339 0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 1.000000 ANGLE IS 62.44 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 15 atoms have been selected out of 15 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : 4.710740 -0.065202 -0.000000 4.711191 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ACET" + RDCMND substituted energy or value "?RDIP" to "4.71119" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 15 Number of groups = 1 + Number of bonds = 14 Number of angles = 9 + Number of dihedrals = 6 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 15 atoms have been selected out of 15 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 14 bonds deleted + DELTIC: 9 angles deleted + DELTIC: 6 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "57" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "57" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "57" + Parameter: RESI57 -> "ETAM" + Parameter: RESIDUE <- "ETAM" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ETAM" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ETAM" + Drude polarizability will be setup for SEGID: ETAM mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ETAM. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 2 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "57" + Parameter: SEED57 -> "1 N 1 C1 1 C5" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 88 exclusions and 40 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 65 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 65 atom pairs and 128 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 65 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 389.97717 -383.35647 503.62179 +ENER INTERN> 1.18308 67.91004 52.55161 3.27593 0.00000 +ENER EXTERN> 226.59779 38.45873 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ETAM" + RDCMND substituted energy or value "?ENER" to "389.977" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 7.94918858 5.03165792 1.60430637 + 18.97295510 10.37204886 + 18.99384724 + + Transpose of the rotation matrix + 0.675548 0.707570 0.207317 + -0.673412 0.477603 0.564280 + 0.300252 -0.520808 0.799129 + CENTER OF ATOMS BEFORE TRANSLATION 1.29619 1.00604 0.28541 + AXIS OF ROTATION IS 0.616969 0.052842 0.785211 ANGLE IS 61.57 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -4.965029 0.085757 -0.869668 5.041348 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ETAM" + RDCMND substituted energy or value "?RDIP" to "5.04135" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 2 + Number of bonds = 17 Number of angles = 19 + Number of dihedrals = 21 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 21 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "58" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "58" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "58" + Parameter: RESI58 -> "NEOP" + Parameter: RESIDUE <- "NEOP" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "NEOP" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "NEOP" + Drude polarizability will be setup for SEGID: NEOP mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is NEOP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 5 + Number of bonds = 21 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 5 + Number of true-bonds = 21 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "58" + Parameter: SEED58 -> "1 C2 1 CT 1 C1" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 105 exclusions and 72 interactions(1-4) + found 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 126 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 126 atom pairs and 177 atom exclusions. + There are 0 group pairs and 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 126 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 0.53229 389.44488 12.52422 +ENER INTERN> 0.00313 2.01157 0.13733 14.39904 0.00000 +ENER EXTERN> 7.17713 -23.19591 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "NEOP" + RDCMND substituted energy or value "?ENER" to "0.532291" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 25.44129114 0.00579342 0.00324067 + 25.42776363 -0.00828724 + 25.42553471 + + Transpose of the rotation matrix + 0.012312 0.340983 0.939989 + -0.705256 0.669369 -0.233578 + -0.708846 -0.660057 0.248721 + CENTER OF ATOMS BEFORE TRANSLATION 1.53710 -0.00029 -0.00017 + AXIS OF ROTATION IS 0.213369 -0.824917 0.523437 ANGLE IS 91.99 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.000117 0.000725 0.000166 0.000753 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "NEOP" + RDCMND substituted energy or value "?RDIP" to "7.527714E-04" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 5 + Number of bonds = 21 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 21 bonds deleted + DELTIC: 30 angles deleted + DELTIC: 36 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "59" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "59" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "59" + Parameter: RESI59 -> "BU2M" + Parameter: RESIDUE <- "BU2M" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BU2M" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BU2M" + Drude polarizability will be setup for SEGID: BU2M mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 5 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BU2M. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 5 + Number of bonds = 21 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 5 + Number of true-bonds = 21 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "59" + Parameter: SEED59 -> "1 C1 1 CT 1 C2" + + CHARMM> ic build + **** WARNING **** 5 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 103 exclusions and 62 interactions(1-4) + found 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 128 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 128 atom pairs and 165 atom exclusions. + There are 0 group pairs and 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 128 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -1.15638 1.68867 6.52844 +ENER INTERN> 0.04504 0.62369 0.11571 1.03983 0.00000 +ENER EXTERN> -0.24194 -2.73871 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BU2M" + RDCMND substituted energy or value "?ENER" to "-1.15638" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 34.49812736 -10.27664509 7.25689722 + 23.55909527 1.36619395 + 24.52347428 + + Transpose of the rotation matrix + 0.308494 -0.437009 0.844899 + 0.816789 0.576936 0.000179 + -0.487531 0.690049 0.534926 + CENTER OF ATOMS BEFORE TRANSLATION 1.47374 0.09297 0.78787 + AXIS OF ROTATION IS -0.352816 -0.681436 -0.641222 ANGLE IS 77.87 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 22 atoms have been selected out of 22 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.050634 -0.000585 -0.315296 0.319337 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BU2M" + RDCMND substituted energy or value "?RDIP" to "0.319337" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 22 Number of groups = 5 + Number of bonds = 21 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 5 + + CHARMM> delete atom sele all end + SELRPN> 22 atoms have been selected out of 22 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 21 bonds deleted + DELTIC: 30 angles deleted + DELTIC: 36 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "60" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "60" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "60" + Parameter: RESI60 -> "BU22M" + Parameter: RESIDUE <- "BU22M" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BU22M" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BU22M" + Drude polarizability will be setup for SEGID: BU22M mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BU22M. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 6 + Number of bonds = 25 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 6 + Number of true-bonds = 25 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "60" + Parameter: SEED60 -> "1 C4 1 CT 1 C1" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 127 exclusions and 90 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 198 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 198 atom pairs and 217 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 198 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -13.89789 12.74152 10.16694 +ENER INTERN> 0.04829 2.42204 0.19990 1.50749 0.00000 +ENER EXTERN> 0.07364 -18.14925 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BU22M" + RDCMND substituted energy or value "?ENER" to "-13.8979" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 33.67972238 3.75490982 -11.44796523 + 29.10395163 -6.43230564 + 47.02506265 + + Transpose of the rotation matrix + 0.834671 -0.269763 -0.480158 + 0.550733 0.402340 0.731311 + -0.004094 -0.874843 0.484389 + CENTER OF ATOMS BEFORE TRANSLATION 1.18927 0.12308 0.21924 + AXIS OF ROTATION IS 0.861041 0.255213 -0.439858 ANGLE IS 68.86 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 26 atoms have been selected out of 26 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.018328 -0.145334 0.001003 0.146489 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BU22M" + RDCMND substituted energy or value "?RDIP" to "0.146489" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 6 + Number of bonds = 25 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 26 atoms have been selected out of 26 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 25 bonds deleted + DELTIC: 36 angles deleted + DELTIC: 45 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "61" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "61" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "61" + Parameter: RESI61 -> "BU23M" + Parameter: RESIDUE <- "BU23M" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BU23M" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BU23M" + Drude polarizability will be setup for SEGID: BU23M mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BU23M. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 6 + Number of bonds = 25 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 25 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "61" + Parameter: SEED61 -> "1 C1 1 CT 1 C2" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 126 exclusions and 85 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 199 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 199 atom pairs and 211 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 199 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -0.27821 -13.61968 6.68876 +ENER INTERN> 0.26753 1.34841 0.18991 2.14050 0.00000 +ENER EXTERN> 1.66992 -5.89448 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BU23M" + RDCMND substituted energy or value "?ENER" to "-0.278212" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 35.96842560 -11.40775531 7.94815044 + 48.12870609 0.38089205 + 26.61190630 + + Transpose of the rotation matrix + 0.137845 -0.829802 0.540765 + 0.619136 0.498349 0.606893 + -0.773091 0.251150 0.582455 + CENTER OF ATOMS BEFORE TRANSLATION 1.51611 -0.25821 0.84464 + AXIS OF ROTATION IS 0.178944 -0.660889 -0.728838 ANGLE IS 83.72 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 26 atoms have been selected out of 26 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.016085 0.012198 -0.360432 0.360997 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BU23M" + RDCMND substituted energy or value "?RDIP" to "0.360997" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 6 + Number of bonds = 25 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 26 atoms have been selected out of 26 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 25 bonds deleted + DELTIC: 36 angles deleted + DELTIC: 45 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "62" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "62" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "62" + Parameter: RESI62 -> "CPNM" + Parameter: RESIDUE <- "CPNM" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CPNM" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CPNM" + Drude polarizability will be setup for SEGID: CPNM mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CPNM. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 6 + Number of bonds = 24 Number of angles = 36 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 6 + Number of true-bonds = 24 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "62" + Parameter: SEED62 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 6 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 133 exclusions and 83 interactions(1-4) + found 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 143 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 143 atom pairs and 216 atom exclusions. + There are 0 group pairs and 15 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 143 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 11.90780 -12.18601 3.85545 +ENER INTERN> 0.06159 1.15020 1.07303 11.85195 0.00000 +ENER EXTERN> -0.64281 -1.58616 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CPNM" + RDCMND substituted energy or value "?ENER" to "11.9078" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 14.66499690 -9.35434219 -7.45498431 + 45.85857181 12.02761869 + 36.39248043 + + Transpose of the rotation matrix + 0.548987 0.791331 -0.269088 + -0.813203 0.580091 0.046847 + 0.193167 0.193105 0.961976 + CENTER OF ATOMS BEFORE TRANSLATION 0.54291 0.66031 0.20770 + AXIS OF ROTATION IS -0.087256 0.275778 0.957253 ANGLE IS 56.94 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 24 atoms have been selected out of 24 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.169364 -0.016725 0.073071 0.185211 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CPNM" + RDCMND substituted energy or value "?RDIP" to "0.185211" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 6 + Number of bonds = 24 Number of angles = 36 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 6 + + CHARMM> delete atom sele all end + SELRPN> 24 atoms have been selected out of 24 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 24 bonds deleted + DELTIC: 36 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "63" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "63" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "63" + Parameter: RESI63 -> "CHXM" + Parameter: RESIDUE <- "CHXM" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CHXM" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CHXM" + Drude polarizability will be setup for SEGID: CHXM mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 7 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CHXM. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 7 + Number of bonds = 28 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 7 + Number of true-bonds = 28 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "63" + Parameter: SEED63 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 259 259 252 + : Ran out of space. RESIZING + with mode 5 found 155 exclusions and 107 interactions(1-4) + found 20 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 223 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 223 atom pairs and 262 atom exclusions. + There are 0 group pairs and 20 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 223 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 2.80070 9.10710 3.52573 +ENER INTERN> 0.09893 0.94160 0.14133 4.30873 0.00000 +ENER EXTERN> -0.71675 -1.97314 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CHXM" + RDCMND substituted energy or value "?ENER" to "2.8007" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 36.85138006 -15.94096833 -4.79949244 + 37.42937048 7.27596617 + 46.14936563 + + Transpose of the rotation matrix + 0.560102 0.608237 -0.562435 + -0.825180 0.349610 -0.443678 + -0.073229 0.712616 0.697722 + CENTER OF ATOMS BEFORE TRANSLATION 0.57285 1.04524 -0.24170 + AXIS OF ROTATION IS -0.606811 0.256730 0.752243 ANGLE IS 72.32 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 28 atoms have been selected out of 28 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.068700 0.000113 0.052668 0.086566 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CHXM" + RDCMND substituted energy or value "?RDIP" to "8.656568E-02" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 7 + Number of bonds = 28 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 28 atoms have been selected out of 28 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 28 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "64" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "64" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "64" + Parameter: RESI64 -> "DIOX" + Parameter: RESIDUE <- "DIOX" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DIOX" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DIOX" + Drude polarizability will be setup for SEGID: DIOX mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DIOX. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 1 + Number of bonds = 26 Number of angles = 26 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 26 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 6 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "64" + Parameter: SEED64 -> "1 O1 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 12 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 235 235 234 + : Ran out of space. RESIZING + with mode 5 found 196 exclusions and 97 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 129 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 129 atom pairs and 293 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 129 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 11.78315 -8.98246 6.91205 +ENER INTERN> 0.05227 0.10594 0.00108 7.82186 0.00000 +ENER EXTERN> 0.43006 3.37195 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DIOX" + RDCMND substituted energy or value "?ENER" to "11.7832" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 15.23225456 8.48774546 -7.30914844 + 30.00441983 3.41508681 + 30.88619218 + + Transpose of the rotation matrix + 0.479798 0.854192 0.200373 + -0.809431 0.342820 0.476756 + 0.338550 -0.390935 0.855894 + CENTER OF ATOMS BEFORE TRANSLATION 0.74512 1.09072 0.54963 + AXIS OF ROTATION IS 0.461197 0.073444 0.884253 ANGLE IS 70.17 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 26 atoms have been selected out of 26 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.000943 -0.000358 0.000281 0.001048 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DIOX" + RDCMND substituted energy or value "?RDIP" to "1.047568E-03" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 1 + Number of bonds = 26 Number of angles = 26 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 12 + + CHARMM> delete atom sele all end + SELRPN> 26 atoms have been selected out of 26 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 26 bonds deleted + DELTIC: 26 angles deleted + DELTIC: 30 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "65" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "65" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "65" + Parameter: RESI65 -> "CRES" + Parameter: RESIDUE <- "CRES" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CRES" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CRES" + Drude polarizability will be setup for SEGID: CRES mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 8 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CRES. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 1 + Number of bonds = 26 Number of angles = 25 + Number of dihedrals = 32 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 8 + Number of true-bonds = 26 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "65" + Parameter: SEED65 -> "1 CG 1 CD1 1 CE1" + + CHARMM> ic build + **** WARNING **** 10 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 142 exclusions and 82 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 183 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 183 atom pairs and 224 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 183 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 7.63022 4.15294 13.64048 +ENER INTERN> 2.69030 0.43900 0.24486 0.00013 0.00000 +ENER EXTERN> 17.91709 -13.66116 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CRES" + RDCMND substituted energy or value "?ENER" to "7.63022" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.86845750 0.03163881 -0.01943787 + 93.49533911 32.04621240 + 49.69135549 + + Transpose of the rotation matrix + 0.466767 0.884380 0.000174 + -0.884380 0.466767 0.001034 + 0.000833 -0.000637 0.999999 + CENTER OF ATOMS BEFORE TRANSLATION 0.66802 1.20659 0.00112 + AXIS OF ROTATION IS 0.000945 0.000373 0.999999 ANGLE IS 62.18 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 26 atoms have been selected out of 26 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.338885 1.412374 0.002121 1.452463 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CRES" + RDCMND substituted energy or value "?RDIP" to "1.45246" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 1 + Number of bonds = 26 Number of angles = 25 + Number of dihedrals = 32 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 10 + + CHARMM> delete atom sele all end + SELRPN> 26 atoms have been selected out of 26 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 26 bonds deleted + DELTIC: 25 angles deleted + DELTIC: 32 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "66" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "66" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "66" + Parameter: RESI66 -> "B3MO1" + Parameter: RESIDUE <- "B3MO1" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "B3MO1" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "B3MO1" + Drude polarizability will be setup for SEGID: B3MO1 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is B3MO1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 5 + Number of bonds = 25 Number of angles = 31 + Number of dihedrals = 39 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 25 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "66" + Parameter: SEED66 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 133 exclusions and 78 interactions(1-4) + found 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 192 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 192 atom pairs and 211 atom exclusions. + There are 0 group pairs and 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 192 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1.88684 5.74338 4.71460 +ENER INTERN> 0.04370 0.76627 0.09958 3.64773 0.00000 +ENER EXTERN> -0.23422 -2.43621 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "B3MO1" + RDCMND substituted energy or value "?ENER" to "1.88684" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 15.48843595 -11.08696624 -1.90648587 + 47.80008532 35.08696056 + 69.59262145 + + Transpose of the rotation matrix + 0.794729 0.598517 -0.100914 + -0.551228 0.642109 -0.532770 + -0.254074 0.479034 0.840222 + CENTER OF ATOMS BEFORE TRANSLATION 1.42676 0.62976 -0.20197 + AXIS OF ROTATION IS -0.657360 -0.099507 0.746979 ANGLE IS 50.32 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 26 atoms have been selected out of 26 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.150849 1.656380 0.925394 1.903340 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "B3MO1" + RDCMND substituted energy or value "?RDIP" to "1.90334" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 5 + Number of bonds = 25 Number of angles = 31 + Number of dihedrals = 39 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 26 atoms have been selected out of 26 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 25 bonds deleted + DELTIC: 31 angles deleted + DELTIC: 39 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "67" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "67" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "67" + Parameter: RESI67 -> "CPO1" + Parameter: RESIDUE <- "CPO1" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CPO1" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CPO1" + Drude polarizability will be setup for SEGID: CPO1 mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CPO1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 5 + Number of bonds = 24 Number of angles = 31 + Number of dihedrals = 48 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 24 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "67" + Parameter: SEED67 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 217 217 216 + : Ran out of space. RESIZING + with mode 5 found 143 exclusions and 89 interactions(1-4) + found 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 133 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 133 atom pairs and 232 atom exclusions. + There are 0 group pairs and 10 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 133 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 14.81244 -12.92560 9.36250 +ENER INTERN> 0.06247 1.23549 1.21416 13.64183 0.00000 +ENER EXTERN> -0.92990 -0.41161 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CPO1" + RDCMND substituted energy or value "?ENER" to "14.8124" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 12.64508005 0.98337653 -6.37375326 + 45.02064899 12.37313901 + 31.83328999 + + Transpose of the rotation matrix + 0.524990 0.848784 -0.062857 + -0.773266 0.506527 0.381432 + 0.355592 -0.151643 0.922257 + CENTER OF ATOMS BEFORE TRANSLATION 0.57622 0.60022 0.37117 + AXIS OF ROTATION IS 0.303240 0.238035 0.922705 ANGLE IS 61.52 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 24 atoms have been selected out of 24 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.068393 0.000670 1.003042 1.465455 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CPO1" + RDCMND substituted energy or value "?RDIP" to "1.46546" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 5 + Number of bonds = 24 Number of angles = 31 + Number of dihedrals = 48 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 24 atoms have been selected out of 24 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 24 bonds deleted + DELTIC: 31 angles deleted + DELTIC: 48 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "68" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "68" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "68" + Parameter: RESI68 -> "BGUAN" + Parameter: RESIDUE <- "BGUAN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BGUAN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BGUAN" + Drude polarizability will be setup for SEGID: BGUAN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 8 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BGUAN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 30 Number of groups = 4 + Number of bonds = 29 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 8 + Number of true-bonds = 29 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "68" + Parameter: SEED68 -> "1 CA 1 CB 1 CG" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 142 exclusions and 84 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 293 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 293 atom pairs and 226 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 293 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -204.29213 219.10457 26.43233 +ENER INTERN> 3.49603 2.01253 0.25366 3.44974 0.00000 +ENER EXTERN> -0.91248 -212.59161 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BGUAN" + RDCMND substituted energy or value "?ENER" to "-204.292" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 6.50077454 0.03563890 0.07520606 + 79.36230564 83.72816662 + 166.58678843 + + Transpose of the rotation matrix + 0.854975 0.518668 0.000393 + -0.518668 0.854976 -0.000387 + -0.000536 0.000127 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 3.39180 1.72518 0.00088 + AXIS OF ROTATION IS -0.000495 -0.000895 0.999999 ANGLE IS 31.24 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 30 atoms have been selected out of 30 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : 10.495033 -0.229629 0.000186 10.497545 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BGUAN" + RDCMND substituted energy or value "?RDIP" to "10.4975" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 30 Number of groups = 4 + Number of bonds = 29 Number of angles = 36 + Number of dihedrals = 45 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 30 atoms have been selected out of 30 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 29 bonds deleted + DELTIC: 36 angles deleted + DELTIC: 45 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "69" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "69" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "69" + Parameter: RESI69 -> "CHOL" + Parameter: RESIDUE <- "CHOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CHOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CHOL" + Drude polarizability will be setup for SEGID: CHOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 7 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CHOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 30 Number of groups = 2 + Number of bonds = 29 Number of angles = 37 + Number of dihedrals = 48 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 7 + Number of true-bonds = 29 Number of zero-bonds = 0 + Number of aniso. terms = 1 Number of lone-pairs = 2 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "69" + Parameter: SEED69 -> "1 C4 1 N 1 C1" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 262 262 261 + : Ran out of space. RESIZING + with mode 5 found 157 exclusions and 106 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 278 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 278 atom pairs and 263 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 278 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -38.56200 -165.73013 21.08291 +ENER INTERN> 1.15231 1.55575 0.57513 6.87864 0.00000 +ENER EXTERN> 0.72296 -49.44680 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CHOL" + RDCMND substituted energy or value "?ENER" to "-38.562" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 27.14080838 1.96345299 -0.71272425 + 38.77897111 19.80981550 + 67.26865912 + + Transpose of the rotation matrix + 0.889778 0.456363 0.005208 + -0.375836 0.726204 0.575652 + 0.258925 -0.514160 0.817678 + CENTER OF ATOMS BEFORE TRANSLATION 2.18418 0.36331 0.01010 + AXIS OF ROTATION IS 0.781510 0.181941 0.596774 ANGLE IS 44.21 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 30 atoms have been selected out of 30 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 1.000000 + DIPOLE MOMENT (DEBYES) : -2.881340 1.241316 0.214750 3.144695 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CHOL" + RDCMND substituted energy or value "?RDIP" to "3.14469" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 30 Number of groups = 2 + Number of bonds = 29 Number of angles = 37 + Number of dihedrals = 48 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 30 atoms have been selected out of 30 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 29 bonds deleted + DELTIC: 37 angles deleted + DELTIC: 48 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "70" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "70" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "70" + Parameter: RESI70 -> "DECA" + Parameter: RESIDUE <- "DECA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DECA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DECA" + Drude polarizability will be setup for SEGID: DECA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DECA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 10 + Number of bonds = 41 Number of angles = 60 + Number of dihedrals = 81 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "70" + Parameter: SEED70 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 10 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 212 exclusions and 136 interactions(1-4) + found 24 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 649 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 649 atom pairs and 348 atom exclusions. + There are 0 group pairs and 24 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 649 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 276.24091 -314.80291 23.12849 +ENER INTERN> 0.00000 202.46292 52.97160 17.25126 0.00000 +ENER EXTERN> 0.59578 2.95935 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DECA" + RDCMND substituted energy or value "?ENER" to "276.241" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 10.74364404 -7.27521631 -1.80277177 + 185.74949989 265.40682231 + 480.40997565 + + Transpose of the rotation matrix + 0.861717 0.507320 -0.008378 + -0.492308 0.831995 -0.255768 + -0.122786 0.224525 0.966702 + CENTER OF ATOMS BEFORE TRANSLATION 5.12709 2.72446 0.04922 + AXIS OF ROTATION IS -0.430790 -0.102616 0.896599 ANGLE IS 33.88 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 42 atoms have been selected out of 42 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.209649 -0.144815 0.569562 0.623959 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DECA" + RDCMND substituted energy or value "?RDIP" to "0.623959" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 10 + Number of bonds = 41 Number of angles = 60 + Number of dihedrals = 81 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 10 + + CHARMM> delete atom sele all end + SELRPN> 42 atoms have been selected out of 42 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 60 angles deleted + DELTIC: 81 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "71" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "71" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "71" + Parameter: RESI71 -> "PEND" + Parameter: RESIDUE <- "PEND" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PEND" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PEND" + Drude polarizability will be setup for SEGID: PEND mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 15 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PEND. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 15 + Number of bonds = 61 Number of angles = 90 + Number of dihedrals = 126 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 15 + Number of true-bonds = 61 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "71" + Parameter: SEED71 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 15 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 322 exclusions and 216 interactions(1-4) + found 39 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1569 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1569 atom pairs and 538 atom exclusions. + There are 0 group pairs and 39 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1569 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 413.29493 -137.05402 23.13654 +ENER INTERN> 0.00000 297.77303 84.02103 27.86475 0.00000 +ENER EXTERN> 0.82546 2.81065 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PEND" + RDCMND substituted energy or value "?ENER" to "413.295" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 16.27057716 -17.25272724 -11.60877712 + 599.01806493 893.84059822 + 1486.22869250 + + Transpose of the rotation matrix + 0.849810 0.527005 -0.009365 + -0.510217 0.818019 -0.265563 + -0.132293 0.230456 0.964048 + CENTER OF ATOMS BEFORE TRANSLATION 7.82963 4.44152 0.01683 + AXIS OF ROTATION IS -0.428979 -0.106314 0.897036 ANGLE IS 35.32 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 62 atoms have been selected out of 62 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.337721 -0.218571 0.348537 0.532265 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PEND" + RDCMND substituted energy or value "?RDIP" to "0.532265" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 15 + Number of bonds = 61 Number of angles = 90 + Number of dihedrals = 126 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 15 + + CHARMM> delete atom sele all end + SELRPN> 62 atoms have been selected out of 62 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 61 bonds deleted + DELTIC: 90 angles deleted + DELTIC: 126 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "72" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "72" and "72". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "72" + Parameter: RESI72 -> "OCTD" + Parameter: RESIDUE <- "OCTD" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "OCTD" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "OCTD" + Drude polarizability will be setup for SEGID: OCTD mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is OCTD. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 74 Number of groups = 18 + Number of bonds = 73 Number of angles = 108 + Number of dihedrals = 153 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 18 + Number of true-bonds = 73 Number of zero-bonds = 0 + Number of aniso. terms = 0 Number of lone-pairs = 0 + + CHARMM> + + CHARMM> !temporary + CHARMM> !if @count ge 70 then + CHARMM> !IC GENERATE + CHARMM> !endif + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "72" + Parameter: SEED72 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 18 COORDINATES ARE STILL UNDEFINED + + CHARMM> !ic print + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> !coor print + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 388 exclusions and 264 interactions(1-4) + found 48 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2313 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 2313 atom pairs and 652 atom exclusions. + There are 0 group pairs and 48 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 2313 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 495.52726 -82.23233 23.13884 +ENER INTERN> 0.00000 354.95910 102.65069 34.23285 0.00000 +ENER EXTERN> 0.96288 2.72174 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "OCTD" + RDCMND substituted energy or value "?ENER" to "495.527" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 19.49601205 -14.54672680 -3.58426131 + 978.93842096 1517.19850611 + 2541.38167594 + + Transpose of the rotation matrix + 0.853744 0.520684 -0.003085 + -0.501616 0.820860 -0.273076 + -0.139654 0.234684 0.961988 + CENTER OF ATOMS BEFORE TRANSLATION 9.48061 5.42373 0.02794 + AXIS OF ROTATION IS -0.441686 -0.118798 0.889270 ANGLE IS 35.09 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 74 atoms have been selected out of 74 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.415641 -0.156651 0.565895 0.719398 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "OCTD" + RDCMND substituted energy or value "?RDIP" to "0.719398" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 74 Number of groups = 18 + Number of bonds = 73 Number of angles = 108 + Number of dihedrals = 153 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 18 + + CHARMM> delete atom sele all end + SELRPN> 74 atoms have been selected out of 74 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 73 bonds deleted + DELTIC: 108 angles deleted + DELTIC: 153 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "73" + + CHARMM> if count le @nres goto loop_model1 + Parameter: NRES -> "72" + Comparing "73" and "72". + IF test evaluated as false. Skipping command + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> incr testcasei + Parameter: TESTCASEI <- "3" + + CHARMM> if @testcasei le @testcases goto loop_tests + Parameter: TESTCASEI -> "3" + Parameter: TESTCASES -> "6" + Comparing "3" and "6". + IF test evaluated as true. Performing command + + CHARMM> stream @test@@testcasei + Parameter: TESTCASEI -> "3" + Parameter: TEST3 -> "TEST_DRUDE_LIPID.STR" + VOPEN> Attempting to open::test_drude_lipid.str:: + OPNLGU> Unit 99 opened for READONLY access to test_drude_lipid.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * $ID: TEST_DRUDE_LIPID.STR 28 2015-07-29 23:54:15Z ALEX $ + RDTITL> * TEST CASE, DRUDE LIPID TOPPAR FILE + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> set boml 0 ! set to -1 if the series contains 3-membered rings + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> set nres 8 + Parameter: NRES <- "8" + + CHARMM> set resi1 dmp + Parameter: RESI1 <- "DMP" + + CHARMM> set resi2 eas + Parameter: RESI2 <- "EAS" + + CHARMM> set resi3 mpro + Parameter: RESI3 <- "MPRO" + + CHARMM> set resi4 mbu + Parameter: RESI4 <- "MBU" + + CHARMM> set resi5 pe + Parameter: RESI5 <- "PE" + + CHARMM> set resi6 pc + Parameter: RESI6 <- "PC" + + CHARMM> set resi7 dmpc + Parameter: RESI7 <- "DMPC" + + CHARMM> set resi8 dppc + Parameter: RESI8 <- "DPPC" + + CHARMM> set seed1 1 O11 1 P 1 O12 + Parameter: SEED1 <- "1 O11 1 P 1 O12" + + CHARMM> set seed2 1 C2 1 OM 1 C + Parameter: SEED2 <- "1 C2 1 OM 1 C" + + CHARMM> set seed3 1 C2 1 OM 1 C + Parameter: SEED3 <- "1 C2 1 OM 1 C" + + CHARMM> set seed4 1 C2 1 OM 1 C + Parameter: SEED4 <- "1 C2 1 OM 1 C" + + CHARMM> set seed5 1 HN1 1 N 1 C1 + Parameter: SEED5 <- "1 HN1 1 N 1 C1" + + CHARMM> set seed6 1 C4 1 N 1 C1 + Parameter: SEED6 <- "1 C4 1 N 1 C1" + + CHARMM> set seed7 1 C15 1 N 1 C12 + Parameter: SEED7 <- "1 C15 1 N 1 C12" + + CHARMM> set seed8 1 C15 1 N 1 C12 + Parameter: SEED8 <- "1 C15 1 N 1 C12" + + CHARMM> + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> label loop_lipid1 + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "1" + Parameter: RESI1 -> "DMP" + Parameter: RESIDUE <- "DMP" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DMP" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DMP" + Drude polarizability will be setup for SEGID: DMP mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 7 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DMP. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 20 Number of groups = 1 + Number of bonds = 19 Number of angles = 20 + Number of dihedrals = 12 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 7 + Number of true-bonds = 19 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "1" + Parameter: SEED1 -> "1 O11 1 P 1 O12" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 93 exclusions and 36 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 97 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 97 atom pairs and 129 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 97 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 8.08042 487.44683 35.02595 +ENER INTERN> 0.21668 0.98368 0.00076 84.65068 0.00000 +ENER EXTERN> 8.09972 -85.87109 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DMP" + RDCMND substituted energy or value "?ENER" to "8.08042" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 28.06866372 13.44404993 16.82290468 + 27.05665391 4.94614215 + 29.28376479 + + Transpose of the rotation matrix + 0.584313 0.467105 0.663620 + -0.624248 0.781226 -0.000239 + -0.518550 -0.414124 0.748069 + CENTER OF ATOMS BEFORE TRANSLATION 0.98747 0.74645 -0.00022 + AXIS OF ROTATION IS 0.249135 -0.711599 0.656932 ANGLE IS 56.16 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 20 atoms have been selected out of 20 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -0.000730 10.529234 0.001375 10.529235 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DMP" + RDCMND substituted energy or value "?RDIP" to "10.5292" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 20 Number of groups = 1 + Number of bonds = 19 Number of angles = 20 + Number of dihedrals = 12 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 20 atoms have been selected out of 20 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 19 bonds deleted + DELTIC: 20 angles deleted + DELTIC: 12 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "2" + + CHARMM> if count le @nres goto loop_lipid1 + Parameter: NRES -> "8" + Comparing "2" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "2" + Parameter: RESI2 -> "EAS" + Parameter: RESIDUE <- "EAS" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "EAS" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "EAS" + Drude polarizability will be setup for SEGID: EAS mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is EAS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 1 + Number of bonds = 23 Number of angles = 22 + Number of dihedrals = 20 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 6 + Number of true-bonds = 23 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "2" + Parameter: SEED2 -> "1 C2 1 OM 1 C" + + CHARMM> ic build + **** WARNING **** 10 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 139 exclusions and 62 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 137 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 137 atom pairs and 201 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 137 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -17.39822 25.47864 14.94666 +ENER INTERN> 0.03570 1.02594 1.00651 9.99011 0.00000 +ENER EXTERN> 1.81057 -31.26705 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "EAS" + RDCMND substituted energy or value "?ENER" to "-17.3982" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 5.11291913 -0.00000000 -0.00000000 + 42.46427148 29.35024661 + 57.66995821 + + Transpose of the rotation matrix + 0.790810 0.612061 -0.000000 + -0.612061 0.790810 0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.25138 0.39590 -0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 1.000000 ANGLE IS 37.74 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 24 atoms have been selected out of 24 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -2.267010 -1.356168 -0.000000 2.641690 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "EAS" + RDCMND substituted energy or value "?RDIP" to "2.64169" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 1 + Number of bonds = 23 Number of angles = 22 + Number of dihedrals = 20 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 10 + + CHARMM> delete atom sele all end + SELRPN> 24 atoms have been selected out of 24 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 23 bonds deleted + DELTIC: 22 angles deleted + DELTIC: 20 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "3" + + CHARMM> if count le @nres goto loop_lipid1 + Parameter: NRES -> "8" + Comparing "3" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "3" + Parameter: RESI3 -> "MPRO" + Parameter: RESIDUE <- "MPRO" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MPRO" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MPRO" + Drude polarizability will be setup for SEGID: MPRO mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MPRO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 1 + Number of bonds = 23 Number of angles = 22 + Number of dihedrals = 20 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 6 + Number of true-bonds = 23 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "3" + Parameter: SEED3 -> "1 C2 1 OM 1 C" + + CHARMM> ic build + **** WARNING **** 10 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 137 exclusions and 62 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 139 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 139 atom pairs and 199 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 139 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 5764.86173 -5782.25995 511.29921 +ENER INTERN> 5556.19237 70.86200 122.24914 8.64615 0.00088 +ENER EXTERN> 2.01319 4.89799 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MPRO" + RDCMND substituted energy or value "?ENER" to "5764.86" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 4.77339353 1.11377204 2.43595707 + 37.30997491 17.23919393 + 68.14850001 + + Transpose of the rotation matrix + 0.912218 0.407975 0.037599 + -0.408294 0.912850 0.000891 + -0.033959 -0.016164 0.999293 + CENTER OF ATOMS BEFORE TRANSLATION 2.35741 1.23551 -0.01452 + AXIS OF ROTATION IS 0.020810 -0.087311 0.995964 ANGLE IS 24.19 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 24 atoms have been selected out of 24 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.266503 0.292246 -0.269489 0.478598 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MPRO" + RDCMND substituted energy or value "?RDIP" to "0.478598" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 1 + Number of bonds = 23 Number of angles = 22 + Number of dihedrals = 20 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 10 + + CHARMM> delete atom sele all end + SELRPN> 24 atoms have been selected out of 24 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 23 bonds deleted + DELTIC: 22 angles deleted + DELTIC: 20 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "4" + + CHARMM> if count le @nres goto loop_lipid1 + Parameter: NRES -> "8" + Comparing "4" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "4" + Parameter: RESI4 -> "MBU" + Parameter: RESIDUE <- "MBU" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MBU" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MBU" + Drude polarizability will be setup for SEGID: MBU mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 7 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MBU. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 27 Number of angles = 28 + Number of dihedrals = 29 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 7 + Number of true-bonds = 27 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "4" + Parameter: SEED4 -> "1 C2 1 OM 1 C" + + CHARMM> ic build + **** WARNING **** 11 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 159 exclusions and 78 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 219 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 219 atom pairs and 237 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 219 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 5825.53375 -60.67202 468.63568 +ENER INTERN> 5594.85519 71.34828 138.17598 16.18938 0.00088 +ENER EXTERN> 3.62026 1.34378 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MBU" + RDCMND substituted energy or value "?ENER" to "5825.53" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 6.42968224 1.25392302 3.54551886 + 39.40924640 22.62725138 + 111.58443024 + + Transpose of the rotation matrix + 0.960484 0.276306 0.033562 + -0.276724 0.960912 0.008453 + -0.029915 -0.017406 0.999401 + CENTER OF ATOMS BEFORE TRANSLATION 2.86461 1.29429 -0.00115 + AXIS OF ROTATION IS 0.046403 -0.113910 0.992407 ANGLE IS 16.18 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 28 atoms have been selected out of 28 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.291019 0.362947 -0.272771 0.539284 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MBU" + RDCMND substituted energy or value "?RDIP" to "0.539284" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 27 Number of angles = 28 + Number of dihedrals = 29 Number of impropers = 1 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 11 + + CHARMM> delete atom sele all end + SELRPN> 28 atoms have been selected out of 28 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 27 bonds deleted + DELTIC: 28 angles deleted + DELTIC: 29 dihedrals deleted + DELTIC: 1 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "5" + + CHARMM> if count le @nres goto loop_lipid1 + Parameter: NRES -> "8" + Comparing "5" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "5" + Parameter: RESI5 -> "PE" + Parameter: RESIDUE <- "PE" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PE" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PE" + Drude polarizability will be setup for SEGID: PE mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 2 + Number of bonds = 27 Number of angles = 32 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 9 + Number of true-bonds = 27 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "5" + Parameter: SEED5 -> "1 HN1 1 N 1 C1" + + CHARMM> ic build + **** WARNING **** 9 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 137 exclusions and 66 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 241 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 241 atom pairs and 203 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 241 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 13.21745 5812.31630 35.82983 +ENER INTERN> 2.48250 6.05940 0.36454 123.28104 0.00000 +ENER EXTERN> 0.04925 -119.01928 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PE" + RDCMND substituted energy or value "?ENER" to "13.2174" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 77.19656153 -46.08001774 34.33960218 + 72.29245299 -18.17800684 + 34.18301289 + + Transpose of the rotation matrix + 0.351147 -0.618801 0.702695 + 0.508214 0.756277 0.412024 + -0.786393 0.212438 0.580048 + CENTER OF ATOMS BEFORE TRANSLATION 0.43839 2.12816 -1.94457 + AXIS OF ROTATION IS 0.106268 -0.792856 -0.600072 ANGLE IS 69.90 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 28 atoms have been selected out of 28 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 18.745999 10.955343 1.946075 21.799524 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PE" + RDCMND substituted energy or value "?RDIP" to "21.7995" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 2 + Number of bonds = 27 Number of angles = 32 + Number of dihedrals = 30 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 9 + + CHARMM> delete atom sele all end + SELRPN> 28 atoms have been selected out of 28 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 27 bonds deleted + DELTIC: 32 angles deleted + DELTIC: 30 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "6" + + CHARMM> if count le @nres goto loop_lipid1 + Parameter: NRES -> "8" + Comparing "6" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "6" + Parameter: RESI6 -> "PC" + Parameter: RESIDUE <- "PC" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "PC" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "PC" + Drude polarizability will be setup for SEGID: PC mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PC. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 40 Number of groups = 2 + Number of bonds = 39 Number of angles = 50 + Number of dihedrals = 57 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 39 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "6" + Parameter: SEED6 -> "1 C4 1 N 1 C1" + + CHARMM> ic build + **** WARNING **** 12 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 206 exclusions and 132 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 574 atom pairs and 338 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 27379 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -72.39848 85.61593 33.30104 +ENER INTERN> 2.74698 9.50759 1.91258 146.46908 0.00000 +ENER EXTERN> 2.59406 -235.62877 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "PC" + RDCMND substituted energy or value "?ENER" to "-72.3985" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 129.73440013 -94.18220308 34.53299289 + 147.65424739 -24.98483384 + 50.11547963 + + Transpose of the rotation matrix + 0.212454 -0.716611 0.664329 + 0.626682 0.621549 0.470050 + -0.749756 0.316459 0.581137 + CENTER OF ATOMS BEFORE TRANSLATION 1.16366 1.31800 -1.36100 + AXIS OF ROTATION IS 0.078506 -0.722784 -0.686600 ANGLE IS 78.02 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 40 atoms have been selected out of 40 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 18.271481 11.872681 1.899726 21.872735 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "PC" + RDCMND substituted energy or value "?RDIP" to "21.8727" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 40 Number of groups = 2 + Number of bonds = 39 Number of angles = 50 + Number of dihedrals = 57 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 12 + + CHARMM> delete atom sele all end + SELRPN> 40 atoms have been selected out of 40 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 39 bonds deleted + DELTIC: 50 angles deleted + DELTIC: 57 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "7" + + CHARMM> if count le @nres goto loop_lipid1 + Parameter: NRES -> "8" + Comparing "7" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "7" + Parameter: RESI7 -> "DMPC" + Parameter: RESIDUE <- "DMPC" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DMPC" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DMPC" + Drude polarizability will be setup for SEGID: DMPC mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 46 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DMPC. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 172 Number of groups = 28 + Number of bonds = 171 Number of angles = 226 + Number of dihedrals = 313 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 46 + Number of true-bonds = 171 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 8 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "7" + Parameter: SEED7 -> "1 C15 1 N 1 C12" + + CHARMM> ic build + **** WARNING **** 54 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1546 1546 1539 + : Ran out of space. RESIZING + with mode 5 found 987 exclusions and 686 interactions(1-4) + found 70 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 59169 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 13719 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 13719 atom pairs and 1673 atom exclusions. + There are 0 group pairs and 70 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 59169 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 13719 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -66.51471 -5.88377 20.54906 +ENER INTERN> 2.24574 10.30737 2.94154 176.05568 0.01134 +ENER EXTERN> 13.67352 -271.74989 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DMPC" + RDCMND substituted energy or value "?ENER" to "-66.5147" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 3507.46316791 -2466.07477320 -3284.38251136 + 7036.31680663 838.99881440 + 3894.33815156 + + Transpose of the rotation matrix + 0.433277 0.719629 -0.542592 + -0.651103 0.666203 0.363646 + 0.623166 0.195724 0.757203 + CENTER OF ATOMS BEFORE TRANSLATION 5.85210 9.10109 -6.68269 + AXIS OF ROTATION IS 0.092916 0.645051 0.758470 ANGLE IS 64.64 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 172 atoms have been selected out of 172 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -19.654016 6.609711 -0.330116 20.738312 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DMPC" + RDCMND substituted energy or value "?RDIP" to "20.7383" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 172 Number of groups = 28 + Number of bonds = 171 Number of angles = 226 + Number of dihedrals = 313 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 54 + + CHARMM> delete atom sele all end + SELRPN> 172 atoms have been selected out of 172 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 171 bonds deleted + DELTIC: 226 angles deleted + DELTIC: 313 dihedrals deleted + DELTIC: 2 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "8" + + CHARMM> if count le @nres goto loop_lipid1 + Parameter: NRES -> "8" + Comparing "8" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "8" + Parameter: RESI8 -> "DPPC" + Parameter: RESIDUE <- "DPPC" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DPPC" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DPPC" + Drude polarizability will be setup for SEGID: DPPC mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 50 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DPPC. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 188 Number of groups = 32 + Number of bonds = 187 Number of angles = 250 + Number of dihedrals = 349 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 50 + Number of true-bonds = 187 Number of zero-bonds = 0 + Number of aniso. terms = 8 Number of lone-pairs = 8 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "8" + Parameter: SEED8 -> "1 C15 1 N 1 C12" + + CHARMM> ic build + **** WARNING **** 58 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1698 1698 1683 + : Ran out of space. RESIZING + with mode 5 found 1075 exclusions and 750 interactions(1-4) + found 82 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 16503 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 16503 atom pairs and 1825 atom exclusions. + There are 0 group pairs and 82 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 16503 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -64.80583 -1.70888 19.60575 +ENER INTERN> 2.28901 10.72580 2.98062 178.16529 0.01270 +ENER EXTERN> 12.67345 -271.65269 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DPPC" + RDCMND substituted energy or value "?ENER" to "-64.8058" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 4725.97288931 -2897.49391426 -4323.26148331 + 9490.86688446 1004.14617966 + 4669.28780339 + + Transpose of the rotation matrix + 0.408362 0.742869 -0.530459 + -0.624345 0.651238 0.431373 + 0.665908 0.155034 0.729747 + CENTER OF ATOMS BEFORE TRANSLATION 6.05520 10.22279 -6.99871 + AXIS OF ROTATION IS 0.150377 0.651033 0.744004 ANGLE IS 66.75 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 188 atoms have been selected out of 188 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -19.374688 7.255822 -0.878116 20.707404 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DPPC" + RDCMND substituted energy or value "?RDIP" to "20.7074" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 188 Number of groups = 32 + Number of bonds = 187 Number of angles = 250 + Number of dihedrals = 349 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 58 + + CHARMM> delete atom sele all end + SELRPN> 188 atoms have been selected out of 188 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 187 bonds deleted + DELTIC: 250 angles deleted + DELTIC: 349 dihedrals deleted + DELTIC: 2 improper dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "9" + + CHARMM> if count le @nres goto loop_lipid1 + Parameter: NRES -> "8" + Comparing "9" and "8". + IF test evaluated as false. Skipping command + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> incr testcasei + Parameter: TESTCASEI <- "4" + + CHARMM> if @testcasei le @testcases goto loop_tests + Parameter: TESTCASEI -> "4" + Parameter: TESTCASES -> "6" + Comparing "4" and "6". + IF test evaluated as true. Performing command + + CHARMM> stream @test@@testcasei + Parameter: TESTCASEI -> "4" + Parameter: TEST4 -> "TEST_DRUDE_CARBOHYDRATE.STR" + VOPEN> Attempting to open::test_drude_carbohydrate.str:: + OPNLGU> Unit 99 opened for READONLY access to test_drude_carbohydrate.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * $ID: TEST_DRUDE_CARBOHYDRATE.STR 28 2015-07-29 23:54:15Z ALEX $ + RDTITL> * TEST CASE, DRUDE CARBOHYDRATE TOPPAR FILE + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> set boml 0 ! set to -1 if the series contains 3-membered rings + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> set nres 47 + Parameter: NRES <- "47" + + CHARMM> + + CHARMM> !polyols + CHARMM> set resi1 egly + Parameter: RESI1 <- "EGLY" + + CHARMM> set seed1 1 O1 1 C1 1 C2 + Parameter: SEED1 <- "1 O1 1 C1 1 C2" + + CHARMM> set resi2 mglyol + Parameter: RESI2 <- "MGLYOL" + + CHARMM> set seed2 1 C1 1 C2 1 C3 + Parameter: SEED2 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi3 meryol + Parameter: RESI3 <- "MERYOL" + + CHARMM> set seed3 1 C1 1 C2 1 C3 + Parameter: SEED3 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi4 dthrol + Parameter: RESI4 <- "DTHROL" + + CHARMM> set seed4 1 C1 1 C2 1 C3 + Parameter: SEED4 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi5 lthrol + Parameter: RESI5 <- "LTHROL" + + CHARMM> set seed5 1 C1 1 C2 1 C3 + Parameter: SEED5 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi6 mribol + Parameter: RESI6 <- "MRIBOL" + + CHARMM> set seed6 1 C1 1 C2 1 C3 + Parameter: SEED6 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi7 daraol + Parameter: RESI7 <- "DARAOL" + + CHARMM> set seed7 1 C1 1 C2 1 C3 + Parameter: SEED7 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi8 laraol + Parameter: RESI8 <- "LARAOL" + + CHARMM> set seed8 1 C1 1 C2 1 C3 + Parameter: SEED8 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi9 mxylol + Parameter: RESI9 <- "MXYLOL" + + CHARMM> set seed9 1 C1 1 C2 1 C3 + Parameter: SEED9 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi10 mallol + Parameter: RESI10 <- "MALLOL" + + CHARMM> set seed10 1 C1 1 C2 1 C3 + Parameter: SEED10 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi11 daltol + Parameter: RESI11 <- "DALTOL" + + CHARMM> set seed11 1 C1 1 C2 1 C3 + Parameter: SEED11 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi12 laltol + Parameter: RESI12 <- "LALTOL" + + CHARMM> set seed12 1 C1 1 C2 1 C3 + Parameter: SEED12 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi13 dgluol + Parameter: RESI13 <- "DGLUOL" + + CHARMM> set seed13 1 C1 1 C2 1 C3 + Parameter: SEED13 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi14 lgluol + Parameter: RESI14 <- "LGLUOL" + + CHARMM> set seed15 1 C1 1 C2 1 C3 + Parameter: SEED15 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi15 dmanol + Parameter: RESI15 <- "DMANOL" + + CHARMM> set seed15 1 C1 1 C2 1 C3 + Parameter: SEED15 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi16 lmanol + Parameter: RESI16 <- "LMANOL" + + CHARMM> set seed16 1 C1 1 C2 1 C3 + Parameter: SEED16 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi17 dgulol + Parameter: RESI17 <- "DGULOL" + + CHARMM> set seed17 1 C1 1 C2 1 C3 + Parameter: SEED17 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi18 lgulol + Parameter: RESI18 <- "LGULOL" + + CHARMM> set seed18 1 C1 1 C2 1 C3 + Parameter: SEED18 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi19 didiol + Parameter: RESI19 <- "DIDIOL" + + CHARMM> set seed19 1 C1 1 C2 1 C3 + Parameter: SEED19 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi20 lidiol + Parameter: RESI20 <- "LIDIOL" + + CHARMM> set seed20 1 C1 1 C2 1 C3 + Parameter: SEED20 <- "1 C1 1 C2 1 C3" + + CHARMM> set resi21 mgalol + Parameter: RESI21 <- "MGALOL" + + CHARMM> set seed21 1 C1 1 C2 1 C3 + Parameter: SEED21 <- "1 C1 1 C2 1 C3" + + CHARMM> !hexapyranoses + CHARMM> set resi22 aglc + Parameter: RESI22 <- "AGLC" + + CHARMM> set seed22 1 O5 1 C1 1 C2 + Parameter: SEED22 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi23 bglc + Parameter: RESI23 <- "BGLC" + + CHARMM> set seed23 1 O5 1 C1 1 C2 + Parameter: SEED23 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi24 aalt + Parameter: RESI24 <- "AALT" + + CHARMM> set seed24 1 O5 1 C1 1 C2 + Parameter: SEED24 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi25 balt + Parameter: RESI25 <- "BALT" + + CHARMM> set seed25 1 O5 1 C1 1 C2 + Parameter: SEED25 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi26 aall + Parameter: RESI26 <- "AALL" + + CHARMM> set seed26 1 O5 1 C1 1 C2 + Parameter: SEED26 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi27 ball + Parameter: RESI27 <- "BALL" + + CHARMM> set seed27 1 O5 1 C1 1 C2 + Parameter: SEED27 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi28 agal + Parameter: RESI28 <- "AGAL" + + CHARMM> set seed28 1 O5 1 C1 1 C2 + Parameter: SEED28 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi29 bgal + Parameter: RESI29 <- "BGAL" + + CHARMM> set seed29 1 O5 1 C1 1 C2 + Parameter: SEED29 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi30 agul + Parameter: RESI30 <- "AGUL" + + CHARMM> set seed30 1 O5 1 C1 1 C2 + Parameter: SEED30 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi31 bgul + Parameter: RESI31 <- "BGUL" + + CHARMM> set seed31 1 O5 1 C1 1 C2 + Parameter: SEED31 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi32 aido + Parameter: RESI32 <- "AIDO" + + CHARMM> set seed32 1 O5 1 C1 1 C2 + Parameter: SEED32 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi33 bido + Parameter: RESI33 <- "BIDO" + + CHARMM> set seed33 1 O5 1 C1 1 C2 + Parameter: SEED33 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi34 aman + Parameter: RESI34 <- "AMAN" + + CHARMM> set seed34 1 O5 1 C1 1 C2 + Parameter: SEED34 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi35 bman + Parameter: RESI35 <- "BMAN" + + CHARMM> set seed35 1 O5 1 C1 1 C2 + Parameter: SEED35 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi36 atal + Parameter: RESI36 <- "ATAL" + + CHARMM> set seed36 1 O5 1 C1 1 C2 + Parameter: SEED36 <- "1 O5 1 C1 1 C2" + + CHARMM> set resi37 btal + Parameter: RESI37 <- "BTAL" + + CHARMM> set seed37 1 O5 1 C1 1 C2 + Parameter: SEED37 <- "1 O5 1 C1 1 C2" + + CHARMM> !furanoses + CHARMM> set resi38 ARIB + Parameter: RESI38 <- "ARIB" + + CHARMM> set seed38 1 C4 1 O4 1 C1 + Parameter: SEED38 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi39 BRIB + Parameter: RESI39 <- "BRIB" + + CHARMM> set seed39 1 C4 1 O4 1 C1 + Parameter: SEED39 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi40 AARB + Parameter: RESI40 <- "AARB" + + CHARMM> set seed40 1 C4 1 O4 1 C1 + Parameter: SEED40 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi41 BARB + Parameter: RESI41 <- "BARB" + + CHARMM> set seed41 1 C4 1 O4 1 C1 + Parameter: SEED41 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi42 AXYF + Parameter: RESI42 <- "AXYF" + + CHARMM> set seed42 1 C4 1 O4 1 C1 + Parameter: SEED42 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi43 BXYF + Parameter: RESI43 <- "BXYF" + + CHARMM> set seed43 1 C4 1 O4 1 C1 + Parameter: SEED43 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi44 ALYF + Parameter: RESI44 <- "ALYF" + + CHARMM> set seed44 1 C4 1 O4 1 C1 + Parameter: SEED44 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi45 BLYF + Parameter: RESI45 <- "BLYF" + + CHARMM> set seed45 1 C4 1 O4 1 C1 + Parameter: SEED45 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi46 ADEO + Parameter: RESI46 <- "ADEO" + + CHARMM> set seed46 1 C4 1 O4 1 C1 + Parameter: SEED46 <- "1 C4 1 O4 1 C1" + + CHARMM> set resi47 BDEO + Parameter: RESI47 <- "BDEO" + + CHARMM> set seed47 1 C4 1 O4 1 C1 + Parameter: SEED47 <- "1 C4 1 O4 1 C1" + + CHARMM> + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> label loop_carb1 + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "1" + Parameter: RESI1 -> "EGLY" + Parameter: RESIDUE <- "EGLY" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "EGLY" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "EGLY" + Drude polarizability will be setup for SEGID: EGLY mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 4 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is EGLY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 2 + Number of bonds = 17 Number of angles = 14 + Number of dihedrals = 15 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 4 + Number of true-bonds = 17 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "1" + Parameter: SEED1 -> "1 O1 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 8 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 96 exclusions and 44 interactions(1-4) + found 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 57 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 57 atom pairs and 140 atom exclusions. + There are 0 group pairs and 1 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 57 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 11.38048 -76.18631 8.45988 +ENER INTERN> 0.00000 0.21327 0.39426 3.38171 0.00000 +ENER EXTERN> -0.07905 7.47028 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "EGLY" + RDCMND substituted energy or value "?ENER" to "11.3805" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 3.51053781 0.00000000 0.00000000 + 17.06754486 16.54128132 + 32.81172673 + + Transpose of the rotation matrix + 0.845495 0.533983 0.000000 + -0.533983 0.845495 -0.000000 + -0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 1.69798 0.70268 0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 1.000000 ANGLE IS 32.27 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 18 atoms have been selected out of 18 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.029548 -0.000822 -0.000000 0.029559 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "EGLY" + RDCMND substituted energy or value "?RDIP" to "2.955946E-02" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 18 Number of groups = 2 + Number of bonds = 17 Number of angles = 14 + Number of dihedrals = 15 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 8 + + CHARMM> delete atom sele all end + SELRPN> 18 atoms have been selected out of 18 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 17 bonds deleted + DELTIC: 14 angles deleted + DELTIC: 15 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "2" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "2" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "2" + Parameter: RESI2 -> "MGLYOL" + Parameter: RESIDUE <- "MGLYOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MGLYOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MGLYOL" + Drude polarizability will be setup for SEGID: MGLYOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 6 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MGLYOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 3 + Number of bonds = 25 Number of angles = 21 + Number of dihedrals = 27 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 6 + Number of true-bonds = 25 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 6 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "2" + Parameter: SEED2 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 12 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 227 227 225 + : Ran out of space. RESIZING + with mode 5 found 151 exclusions and 97 interactions(1-4) + found 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 174 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 174 atom pairs and 248 atom exclusions. + There are 0 group pairs and 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 174 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 30.34571 -18.96523 20.29017 +ENER INTERN> 3.43757 9.42675 0.47078 9.80011 0.00000 +ENER EXTERN> 0.98482 6.22568 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MGLYOL" + RDCMND substituted energy or value "?ENER" to "30.3457" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 11.26048542 5.49132209 -3.52511751 + 42.54742936 29.05213508 + 51.26193942 + + Transpose of the rotation matrix + 0.756639 0.653679 0.014182 + -0.559865 0.636541 0.530441 + 0.337710 -0.409292 0.847603 + CENTER OF ATOMS BEFORE TRANSLATION 1.45195 0.25120 -0.26106 + AXIS OF ROTATION IS 0.599096 0.206255 0.773655 ANGLE IS 51.66 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 26 atoms have been selected out of 26 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 3.004254 0.437284 -0.671652 3.109321 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MGLYOL" + RDCMND substituted energy or value "?RDIP" to "3.10932" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 26 Number of groups = 3 + Number of bonds = 25 Number of angles = 21 + Number of dihedrals = 27 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 12 + + CHARMM> delete atom sele all end + SELRPN> 26 atoms have been selected out of 26 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 25 bonds deleted + DELTIC: 21 angles deleted + DELTIC: 27 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "3" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "3" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "3" + Parameter: RESI3 -> "MERYOL" + Parameter: RESIDUE <- "MERYOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MERYOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MERYOL" + Drude polarizability will be setup for SEGID: MERYOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 8 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MERYOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 34 Number of groups = 4 + Number of bonds = 33 Number of angles = 28 + Number of dihedrals = 39 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 8 + Number of true-bonds = 33 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "3" + Parameter: SEED3 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 16 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 310 310 297 + : Ran out of space. RESIZING + with mode 5 found 206 exclusions and 151 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 355 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 355 atom pairs and 357 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 355 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 47.46288 -17.11717 20.15688 +ENER INTERN> 10.53030 5.32051 0.73719 21.22479 0.00000 +ENER EXTERN> 0.13779 9.51230 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MERYOL" + RDCMND substituted energy or value "?ENER" to "47.4629" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 33.89994764 -16.06663741 -21.97529013 + 38.48800014 10.21964973 + 91.33423071 + + Transpose of the rotation matrix + 0.908751 0.232666 -0.346465 + -0.383161 0.794166 -0.471686 + 0.165405 0.561397 0.810848 + CENTER OF ATOMS BEFORE TRANSLATION 1.83648 0.86834 -0.09320 + AXIS OF ROTATION IS -0.790361 0.391607 0.471140 ANGLE IS 40.81 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 34 atoms have been selected out of 34 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.287760 -0.466855 -0.138784 1.376786 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MERYOL" + RDCMND substituted energy or value "?RDIP" to "1.37679" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 34 Number of groups = 4 + Number of bonds = 33 Number of angles = 28 + Number of dihedrals = 39 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 16 + + CHARMM> delete atom sele all end + SELRPN> 34 atoms have been selected out of 34 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 33 bonds deleted + DELTIC: 28 angles deleted + DELTIC: 39 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "4" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "4" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "4" + Parameter: RESI4 -> "DTHROL" + Parameter: RESIDUE <- "DTHROL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DTHROL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DTHROL" + Drude polarizability will be setup for SEGID: DTHROL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 8 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DTHROL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 34 Number of groups = 4 + Number of bonds = 33 Number of angles = 28 + Number of dihedrals = 39 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 8 + Number of true-bonds = 33 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "4" + Parameter: SEED4 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 16 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 310 310 297 + : Ran out of space. RESIZING + with mode 5 found 206 exclusions and 151 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 355 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 355 atom pairs and 357 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 355 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 60.57348 -13.11060 25.21690 +ENER INTERN> 12.62035 12.87516 1.71747 22.34135 0.00000 +ENER EXTERN> 0.24053 10.77863 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DTHROL" + RDCMND substituted energy or value "?ENER" to "60.5735" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 30.64769476 3.19845276 6.13904923 + 40.46662748 10.69188162 + 93.24530599 + + Transpose of the rotation matrix + 0.975835 0.193690 0.101141 + -0.211497 0.953558 0.214466 + -0.054904 -0.230675 0.971481 + CENTER OF ATOMS BEFORE TRANSLATION 1.86895 0.78854 -0.08611 + AXIS OF ROTATION IS 0.715852 -0.250944 0.651600 ANGLE IS 18.11 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 34 atoms have been selected out of 34 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.396313 -3.229959 -0.520331 3.557116 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DTHROL" + RDCMND substituted energy or value "?RDIP" to "3.55712" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 34 Number of groups = 4 + Number of bonds = 33 Number of angles = 28 + Number of dihedrals = 39 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 16 + + CHARMM> delete atom sele all end + SELRPN> 34 atoms have been selected out of 34 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 33 bonds deleted + DELTIC: 28 angles deleted + DELTIC: 39 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "5" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "5" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "5" + Parameter: RESI5 -> "LTHROL" + Parameter: RESIDUE <- "LTHROL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "LTHROL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LTHROL" + Drude polarizability will be setup for SEGID: LTHROL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 8 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LTHROL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 34 Number of groups = 4 + Number of bonds = 33 Number of angles = 28 + Number of dihedrals = 39 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 8 + Number of true-bonds = 33 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 8 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "5" + Parameter: SEED5 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 16 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 310 310 297 + : Ran out of space. RESIZING + with mode 5 found 206 exclusions and 151 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 355 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 355 atom pairs and 357 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 355 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 54.48996 6.08351 23.68814 +ENER INTERN> 11.12942 10.42380 1.01284 20.91762 0.00000 +ENER EXTERN> -0.65677 11.66306 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "LTHROL" + RDCMND substituted energy or value "?ENER" to "54.49" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 33.35206487 -2.56753716 -1.81166699 + 43.30308415 15.86182326 + 88.52963384 + + Transpose of the rotation matrix + 0.952341 0.302200 -0.041487 + -0.299382 0.899945 -0.316970 + -0.058453 0.314284 0.947528 + CENTER OF ATOMS BEFORE TRANSLATION 1.87045 0.80661 -0.00635 + AXIS OF ROTATION IS -0.723779 -0.019452 0.689757 ANGLE IS 25.85 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 34 atoms have been selected out of 34 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.494557 -2.435853 0.672426 2.574903 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "LTHROL" + RDCMND substituted energy or value "?RDIP" to "2.5749" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 34 Number of groups = 4 + Number of bonds = 33 Number of angles = 28 + Number of dihedrals = 39 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 16 + + CHARMM> delete atom sele all end + SELRPN> 34 atoms have been selected out of 34 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 33 bonds deleted + DELTIC: 28 angles deleted + DELTIC: 39 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "6" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "6" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "6" + Parameter: RESI6 -> "MRIBOL" + Parameter: RESIDUE <- "MRIBOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MRIBOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MRIBOL" + Drude polarizability will be setup for SEGID: MRIBOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MRIBOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 5 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "6" + Parameter: SEED6 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 20 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 371 371 369 + : Ran out of space. RESIZING + with mode 5 found 261 exclusions and 205 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 600 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 600 atom pairs and 466 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 600 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 58.83375 -4.34378 23.08087 +ENER INTERN> 8.15068 10.02103 0.77995 27.74312 0.00000 +ENER EXTERN> 2.01945 10.11953 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MRIBOL" + RDCMND substituted energy or value "?ENER" to "58.8337" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 33.59780854 11.27789328 19.82200970 + 56.66668752 27.40693441 + 189.49230793 + + Transpose of the rotation matrix + 0.971197 0.199085 0.130928 + -0.229986 0.926907 0.296563 + -0.062316 -0.318133 0.945996 + CENTER OF ATOMS BEFORE TRANSLATION 2.47598 0.90518 -0.14556 + AXIS OF ROTATION IS 0.794034 -0.249623 0.554254 ANGLE IS 22.77 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 42 atoms have been selected out of 42 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.055760 -0.481768 1.516715 1.909753 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MRIBOL" + RDCMND substituted energy or value "?RDIP" to "1.90975" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 5 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 20 + + CHARMM> delete atom sele all end + SELRPN> 42 atoms have been selected out of 42 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 51 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "7" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "7" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "7" + Parameter: RESI7 -> "DARAOL" + Parameter: RESIDUE <- "DARAOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DARAOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DARAOL" + Drude polarizability will be setup for SEGID: DARAOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DARAOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 5 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "7" + Parameter: SEED7 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 20 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 371 371 369 + : Ran out of space. RESIZING + with mode 5 found 261 exclusions and 205 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 600 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 600 atom pairs and 466 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 600 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 67.05144 -8.21769 23.28044 +ENER INTERN> 10.15812 11.96041 0.93826 31.16905 0.00000 +ENER EXTERN> 0.44466 12.38094 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DARAOL" + RDCMND substituted energy or value "?ENER" to "67.0514" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 44.82024164 11.51960091 9.59559027 + 79.85833409 49.53105788 + 129.14973237 + + Transpose of the rotation matrix + 0.841178 0.527014 0.121142 + -0.515536 0.713942 0.473823 + 0.163223 -0.461023 0.872248 + CENTER OF ATOMS BEFORE TRANSLATION 2.27670 1.24899 0.15660 + AXIS OF ROTATION IS 0.667301 0.030037 0.744182 ANGLE IS 44.46 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 42 atoms have been selected out of 42 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.890819 1.847094 -0.220339 2.062490 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DARAOL" + RDCMND substituted energy or value "?RDIP" to "2.06249" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 5 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 20 + + CHARMM> delete atom sele all end + SELRPN> 42 atoms have been selected out of 42 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 51 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "8" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "8" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "8" + Parameter: RESI8 -> "LARAOL" + Parameter: RESIDUE <- "LARAOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "LARAOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LARAOL" + Drude polarizability will be setup for SEGID: LARAOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LARAOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 5 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "8" + Parameter: SEED8 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 20 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 371 371 369 + : Ran out of space. RESIZING + with mode 5 found 261 exclusions and 205 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 600 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 600 atom pairs and 466 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 600 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 65.65018 1.40126 24.63053 +ENER INTERN> 10.39428 11.51993 0.52331 30.39965 0.00000 +ENER EXTERN> 0.56016 12.25284 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "LARAOL" + RDCMND substituted energy or value "?ENER" to "65.6502" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 56.53116183 -19.01972556 -15.35792993 + 87.89989769 49.87938492 + 110.58092003 + + Transpose of the rotation matrix + 0.752763 0.615447 -0.233608 + -0.530187 0.356473 -0.769304 + -0.390191 0.702960 0.594642 + CENTER OF ATOMS BEFORE TRANSLATION 2.11207 1.29585 -0.29749 + AXIS OF ROTATION IS -0.786446 -0.083643 0.611969 ANGLE IS 69.39 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 42 atoms have been selected out of 42 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.877744 1.255487 2.210792 2.689663 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "LARAOL" + RDCMND substituted energy or value "?RDIP" to "2.68966" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 5 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 20 + + CHARMM> delete atom sele all end + SELRPN> 42 atoms have been selected out of 42 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 51 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "9" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "9" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "9" + Parameter: RESI9 -> "MXYLOL" + Parameter: RESIDUE <- "MXYLOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MXYLOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MXYLOL" + Drude polarizability will be setup for SEGID: MXYLOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MXYLOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 5 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "9" + Parameter: SEED9 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 20 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 371 371 369 + : Ran out of space. RESIZING + with mode 5 found 261 exclusions and 205 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 600 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 600 atom pairs and 466 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 600 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 55.23620 10.41397 20.28594 +ENER INTERN> 10.90269 5.81065 0.55926 26.70586 0.00000 +ENER EXTERN> 0.36252 10.89522 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MXYLOL" + RDCMND substituted energy or value "?ENER" to "55.2362" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 61.01773659 9.91238230 43.88721462 + 84.74413300 73.02920048 + 151.29165943 + + Transpose of the rotation matrix + 0.821678 0.499419 0.274637 + -0.104659 0.605878 -0.788644 + -0.560260 0.619268 0.550105 + CENTER OF ATOMS BEFORE TRANSLATION 2.33478 0.84606 0.19014 + AXIS OF ROTATION IS -0.806939 -0.478518 0.346224 ANGLE IS 60.74 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 42 atoms have been selected out of 42 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.528506 1.406509 0.019946 3.798555 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MXYLOL" + RDCMND substituted energy or value "?RDIP" to "3.79856" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 42 Number of groups = 5 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 20 + + CHARMM> delete atom sele all end + SELRPN> 42 atoms have been selected out of 42 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 51 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "10" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "10" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "10" + Parameter: RESI10 -> "MALLOL" + Parameter: RESIDUE <- "MALLOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MALLOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MALLOL" + Drude polarizability will be setup for SEGID: MALLOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MALLOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "10" + Parameter: SEED10 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 96.21000 -40.97380 21.37838 +ENER INTERN> 11.25005 8.24365 0.77773 38.69216 0.00000 +ENER EXTERN> 9.23497 28.01144 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MALLOL" + RDCMND substituted energy or value "?ENER" to "96.21" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 43.47827780 -29.17188294 2.92332582 + 159.44354306 149.75212444 + 231.61922157 + + Transpose of the rotation matrix + 0.781973 0.621173 -0.051595 + -0.463521 0.524170 -0.714418 + -0.416733 0.582571 0.697814 + CENTER OF ATOMS BEFORE TRANSLATION 2.82694 1.48098 0.00414 + AXIS OF ROTATION IS -0.749809 -0.211092 0.627078 ANGLE IS 59.87 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.112252 0.084073 0.216225 0.257725 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MALLOL" + RDCMND substituted energy or value "?RDIP" to "0.257725" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "11" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "11" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "11" + Parameter: RESI11 -> "DALTOL" + Parameter: RESIDUE <- "DALTOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DALTOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DALTOL" + Drude polarizability will be setup for SEGID: DALTOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DALTOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "11" + Parameter: SEED11 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 84.93801 11.27200 20.80008 +ENER INTERN> 11.25005 8.24365 0.77773 37.14975 0.00000 +ENER EXTERN> 6.57136 20.94545 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DALTOL" + RDCMND substituted energy or value "?ENER" to "84.938" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 38.97847359 -6.00375077 12.24946438 + 165.87241302 151.28600754 + 231.61922157 + + Transpose of the rotation matrix + 0.778897 0.626883 0.018359 + -0.476709 0.610821 -0.632176 + -0.407515 0.483648 0.774607 + CENTER OF ATOMS BEFORE TRANSLATION 2.82694 1.45273 -0.21048 + AXIS OF ROTATION IS -0.686178 -0.261892 0.678655 ANGLE IS 54.40 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.248907 -1.900264 -0.062815 2.274800 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DALTOL" + RDCMND substituted energy or value "?RDIP" to "2.2748" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "12" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "12" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "12" + Parameter: RESI12 -> "LALTOL" + Parameter: RESIDUE <- "LALTOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "LALTOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LALTOL" + Drude polarizability will be setup for SEGID: LALTOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LALTOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "12" + Parameter: SEED12 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 85.65482 -0.71681 21.65936 +ENER INTERN> 11.25005 8.24365 0.77773 36.92310 0.00000 +ENER EXTERN> 6.78569 21.67459 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "LALTOL" + RDCMND substituted energy or value "?ENER" to "85.6548" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 34.36617223 6.67862547 -14.70717509 + 163.96997742 144.67841334 + 233.99426341 + + Transpose of the rotation matrix + 0.786363 0.617308 -0.023729 + -0.522753 0.685398 0.506911 + 0.329184 -0.386212 0.861672 + CENTER OF ATOMS BEFORE TRANSLATION 2.77504 1.47071 0.21110 + AXIS OF ROTATION IS 0.599161 0.236755 0.764822 ANGLE IS 48.19 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.554684 1.218667 -2.059144 4.284974 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "LALTOL" + RDCMND substituted energy or value "?RDIP" to "4.28497" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "13" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "13" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "13" + Parameter: RESI13 -> "DGLUOL" + Parameter: RESIDUE <- "DGLUOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DGLUOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DGLUOL" + Drude polarizability will be setup for SEGID: DGLUOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DGLUOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "13" + Parameter: SEED13 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 87.40612 -1.75130 23.92555 +ENER INTERN> 11.25005 8.24365 0.77773 35.83987 0.00000 +ENER EXTERN> 6.32543 24.96939 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DGLUOL" + RDCMND substituted energy or value "?ENER" to "87.4061" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 38.84561748 -22.82570451 -10.03100715 + 159.85001634 148.48233531 + 235.55235858 + + Transpose of the rotation matrix + 0.786044 0.614212 -0.069844 + -0.527219 0.607108 -0.594525 + -0.322762 0.504146 0.801038 + CENTER OF ATOMS BEFORE TRANSLATION 2.79954 1.49064 0.21414 + AXIS OF ROTATION IS -0.684811 -0.157646 0.711464 ANGLE IS 53.34 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.038402 2.347946 0.414283 2.600530 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DGLUOL" + RDCMND substituted energy or value "?RDIP" to "2.60053" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "14" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "14" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "14" + Parameter: RESI14 -> "LGLUOL" + Parameter: RESIDUE <- "LGLUOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "LGLUOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LGLUOL" + Drude polarizability will be setup for SEGID: LGLUOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LGLUOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "14" + Parameter: SEED14 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 77.33892 10.06720 22.88434 +ENER INTERN> 11.25005 8.24365 0.77773 35.55051 0.00000 +ENER EXTERN> 6.21715 15.29982 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "LGLUOL" + RDCMND substituted energy or value "?ENER" to "77.3389" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 34.37003519 23.07174570 7.05741058 + 169.91683532 147.46296253 + 230.12824953 + + Transpose of the rotation matrix + 0.771284 0.633348 0.063182 + -0.577652 0.654841 0.487341 + 0.267282 -0.412376 0.870923 + CENTER OF ATOMS BEFORE TRANSLATION 2.80245 1.43281 -0.21352 + AXIS OF ROTATION IS 0.590990 0.134066 0.795460 ANGLE IS 49.57 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.686710 -0.668883 1.846261 4.177070 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "LGLUOL" + RDCMND substituted energy or value "?RDIP" to "4.17707" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "15" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "15" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "15" + Parameter: RESI15 -> "DMANOL" + Parameter: RESIDUE <- "DMANOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DMANOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DMANOL" + Drude polarizability will be setup for SEGID: DMANOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DMANOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "15" + Parameter: SEED15 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 79.66524 -2.32633 20.71720 +ENER INTERN> 11.25005 8.24365 0.77773 37.08837 0.00000 +ENER EXTERN> 2.62839 19.67705 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DMANOL" + RDCMND substituted energy or value "?ENER" to "79.6652" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 38.85277803 0.74267664 -0.99893349 + 166.30617449 149.97751703 + 235.55235858 + + Transpose of the rotation matrix + 0.782606 0.622516 -0.001011 + -0.616008 0.774657 0.142969 + 0.089784 -0.111266 0.989727 + CENTER OF ATOMS BEFORE TRANSLATION 2.79954 1.46239 -0.00049 + AXIS OF ROTATION IS 0.200563 0.071627 0.977059 ANGLE IS 39.33 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.470028 0.412355 -0.008381 2.504225 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DMANOL" + RDCMND substituted energy or value "?RDIP" to "2.50423" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "16" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "16" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "16" + Parameter: RESI16 -> "LMANOL" + Parameter: RESIDUE <- "LMANOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "LMANOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LMANOL" + Drude polarizability will be setup for SEGID: LMANOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LMANOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "16" + Parameter: SEED16 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 81.86798 -2.20273 21.06185 +ENER INTERN> 11.25005 8.24365 0.77773 37.09292 0.00000 +ENER EXTERN> 2.55697 21.94665 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "LMANOL" + RDCMND substituted energy or value "?ENER" to "81.868" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 38.93503907 0.12174783 -2.00586929 + 163.54425262 145.96367381 + 230.12824953 + + Transpose of the rotation matrix + 0.781789 0.623525 -0.004851 + -0.615101 0.772456 0.157996 + 0.102262 -0.120536 0.987428 + CENTER OF ATOMS BEFORE TRANSLATION 2.80245 1.46105 0.00110 + AXIS OF ROTATION IS 0.218617 0.084072 0.972182 ANGLE IS 39.57 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.358573 0.188460 -0.037330 2.366385 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "LMANOL" + RDCMND substituted energy or value "?RDIP" to "2.36638" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "17" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "17" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "17" + Parameter: RESI17 -> "DGULOL" + Parameter: RESIDUE <- "DGULOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DGULOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DGULOL" + Drude polarizability will be setup for SEGID: DGULOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DGULOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "17" + Parameter: SEED17 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 86.82924 -4.96127 23.57280 +ENER INTERN> 11.25005 8.24365 0.77773 35.92342 0.00000 +ENER EXTERN> 7.27877 23.35561 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DGULOL" + RDCMND substituted energy or value "?ENER" to "86.8292" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 38.98168713 -22.15614820 -10.14402475 + 161.78700832 148.21792596 + 231.67206663 + + Transpose of the rotation matrix + 0.780581 0.621168 -0.069592 + -0.534479 0.605592 -0.589568 + -0.324076 0.497401 0.804715 + CENTER OF ATOMS BEFORE TRANSLATION 2.82744 1.45235 -0.20645 + AXIS OF ROTATION IS -0.676483 -0.158380 0.719226 ANGLE IS 53.46 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.304412 -1.704909 -0.323442 2.170903 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DGULOL" + RDCMND substituted energy or value "?RDIP" to "2.1709" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "18" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "18" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "18" + Parameter: RESI18 -> "LGULOL" + Parameter: RESIDUE <- "LGULOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "LGULOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LGULOL" + Drude polarizability will be setup for SEGID: LGULOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LGULOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "18" + Parameter: SEED18 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 80.93092 5.89832 23.14672 +ENER INTERN> 11.25005 8.24365 0.77773 35.62982 0.00000 +ENER EXTERN> 7.36196 17.66770 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "LGULOL" + RDCMND substituted energy or value "?ENER" to "80.9309" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 34.53117656 22.82667919 7.68619323 + 168.05467462 147.74796314 + 233.93879971 + + Transpose of the rotation matrix + 0.776985 0.626307 0.063512 + -0.573472 0.662583 0.481781 + 0.259661 -0.410759 0.873987 + CENTER OF ATOMS BEFORE TRANSLATION 2.77454 1.47110 0.20707 + AXIS OF ROTATION IS 0.591804 0.130058 0.795521 ANGLE IS 48.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.607960 1.650680 -1.538081 4.255328 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "LGULOL" + RDCMND substituted energy or value "?RDIP" to "4.25533" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "19" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "19" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "19" + Parameter: RESI19 -> "DIDIOL" + Parameter: RESIDUE <- "DIDIOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DIDIOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DIDIOL" + Drude polarizability will be setup for SEGID: DIDIOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DIDIOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "19" + Parameter: SEED19 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 82.65404 -1.72312 24.66825 +ENER INTERN> 11.25005 8.24365 0.77773 34.38102 0.00000 +ENER EXTERN> 10.90049 17.10110 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DIDIOL" + RDCMND substituted energy or value "?ENER" to "82.654" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 29.96203616 0.40731071 -0.81252314 + 168.13500535 149.75251488 + 231.67206663 + + Transpose of the rotation matrix + 0.777022 0.629472 -0.001161 + -0.628674 0.776127 0.048940 + 0.031707 -0.037298 0.998801 + CENTER OF ATOMS BEFORE TRANSLATION 2.82744 1.42410 -0.42108 + AXIS OF ROTATION IS 0.068360 0.026054 0.997320 ANGLE IS 39.11 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.658584 -3.179871 2.035320 4.617594 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DIDIOL" + RDCMND substituted energy or value "?RDIP" to "4.61759" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "20" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "20" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "20" + Parameter: RESI20 -> "LIDIOL" + Parameter: RESIDUE <- "LIDIOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "LIDIOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "LIDIOL" + Drude polarizability will be setup for SEGID: LIDIOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is LIDIOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "20" + Parameter: SEED20 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 89.02565 -6.37161 25.37601 +ENER INTERN> 11.25005 8.24365 0.77773 34.38133 0.00000 +ENER EXTERN> 11.02053 23.35236 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "LIDIOL" + RDCMND substituted energy or value "?ENER" to "89.0257" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 30.06936893 -1.12824094 -1.07765869 + 161.57393080 146.28808163 + 233.93879971 + + Transpose of the rotation matrix + 0.787422 0.616396 -0.004849 + -0.616400 0.787323 -0.013183 + -0.004308 0.013369 0.999901 + CENTER OF ATOMS BEFORE TRANSLATION 2.77454 1.49934 0.42169 + AXIS OF ROTATION IS -0.021533 0.000439 0.999768 ANGLE IS 38.06 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.223144 3.904051 -1.782321 4.833286 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "LIDIOL" + RDCMND substituted energy or value "?RDIP" to "4.83329" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "21" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "21" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "21" + Parameter: RESI21 -> "MGALOL" + Parameter: RESIDUE <- "MGALOL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MGALOL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MGALOL" + Drude polarizability will be setup for SEGID: MGALOL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MGALOL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "21" + Parameter: SEED21 -> "1 C1 1 C2 1 C3" + + CHARMM> ic build + **** WARNING **** 24 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 444 444 441 + : Ran out of space. RESIZING + with mode 5 found 316 exclusions and 259 interactions(1-4) + found 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 909 atom pairs and 575 atom exclusions. + There are 0 group pairs and 12 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 909 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 81.19290 7.83275 22.68270 +ENER INTERN> 11.25005 8.24365 0.77773 35.75361 0.00000 +ENER EXTERN> 3.22832 21.93955 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MGALOL" + RDCMND substituted energy or value "?ENER" to "81.1929" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 38.77139160 -15.40762181 -23.39215012 + 162.22114197 146.90866619 + 235.60657314 + + Transpose of the rotation matrix + 0.785443 0.612565 -0.088558 + -0.590618 0.784580 0.188691 + 0.185067 -0.095902 0.978035 + CENTER OF ATOMS BEFORE TRANSLATION 2.80004 1.46201 0.00354 + AXIS OF ROTATION IS 0.224744 0.216082 0.950157 ANGLE IS 39.28 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 50 atoms have been selected out of 50 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.430110 0.245318 -0.513681 2.495893 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MGALOL" + RDCMND substituted energy or value "?RDIP" to "2.49589" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 50 Number of groups = 6 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 63 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 24 + + CHARMM> delete atom sele all end + SELRPN> 50 atoms have been selected out of 50 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 63 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "22" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "22" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "22" + Parameter: RESI22 -> "AGLC" + Parameter: RESIDUE <- "AGLC" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AGLC" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AGLC" + Drude polarizability will be setup for SEGID: AGLC mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AGLC. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "22" + Parameter: SEED22 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 69.98813 11.20477 17.27651 +ENER INTERN> 5.72769 12.27955 1.84035 33.83102 0.00000 +ENER EXTERN> 2.80225 13.50727 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AGLC" + RDCMND substituted energy or value "?ENER" to "69.9881" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 36.05185923 15.04290946 -27.65098482 + 109.24822700 35.06917032 + 171.08726591 + + Transpose of the rotation matrix + 0.917161 0.377272 -0.128383 + -0.318188 0.887211 0.334086 + 0.239944 -0.265560 0.933758 + CENTER OF ATOMS BEFORE TRANSLATION 0.54319 1.16955 0.77634 + AXIS OF ROTATION IS 0.606073 0.372274 0.702914 ANGLE IS 29.65 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.884844 -1.041281 -1.332056 1.908295 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AGLC" + RDCMND substituted energy or value "?RDIP" to "1.9083" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "23" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "23" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "23" + Parameter: RESI23 -> "BGLC" + Parameter: RESIDUE <- "BGLC" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BGLC" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BGLC" + Drude polarizability will be setup for SEGID: BGLC mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BGLC. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "23" + Parameter: SEED23 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 77.19254 -7.20440 19.24271 +ENER INTERN> 6.45072 16.51758 1.24101 34.74726 0.00000 +ENER EXTERN> 0.89168 17.34428 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BGLC" + RDCMND substituted energy or value "?ENER" to "77.1925" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 57.91910314 36.16450509 -46.00830077 + 108.38097933 44.44993781 + 173.56623672 + + Transpose of the rotation matrix + 0.911657 0.357628 -0.202444 + -0.187177 0.799911 0.570181 + 0.365850 -0.481917 0.796185 + CENTER OF ATOMS BEFORE TRANSLATION 0.55645 1.15324 0.64158 + AXIS OF ROTATION IS 0.800664 0.432481 0.414606 ANGLE IS 41.07 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 3.786447 1.741970 -1.968472 4.609395 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BGLC" + RDCMND substituted energy or value "?RDIP" to "4.60939" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "24" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "24" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "24" + Parameter: RESI24 -> "AALT" + Parameter: RESIDUE <- "AALT" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AALT" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AALT" + Drude polarizability will be setup for SEGID: AALT mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AALT. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "24" + Parameter: SEED24 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 79.85756 -2.66502 18.10232 +ENER INTERN> 7.26281 12.18506 1.34872 37.10452 0.00000 +ENER EXTERN> 2.86194 19.09450 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AALT" + RDCMND substituted energy or value "?ENER" to "79.8576" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 58.30811280 12.10192742 -20.74151000 + 93.66404421 22.56549169 + 141.77059302 + + Transpose of the rotation matrix + 0.933020 0.320729 -0.163116 + -0.225392 0.874304 0.429874 + 0.280486 -0.364316 0.888033 + CENTER OF ATOMS BEFORE TRANSLATION 0.40784 1.11262 0.71572 + AXIS OF ROTATION IS 0.748514 0.418089 0.514712 ANGLE IS 32.04 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.484607 0.730365 -1.873020 2.067965 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AALT" + RDCMND substituted energy or value "?RDIP" to "2.06797" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "25" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "25" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "25" + Parameter: RESI25 -> "BALT" + Parameter: RESIDUE <- "BALT" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BALT" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BALT" + Drude polarizability will be setup for SEGID: BALT mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BALT. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "25" + Parameter: SEED25 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 81.71604 -1.85848 22.03159 +ENER INTERN> 9.73807 16.51753 1.91788 34.96706 0.00000 +ENER EXTERN> 2.49956 16.07593 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BALT" + RDCMND substituted energy or value "?ENER" to "81.716" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 91.35896928 28.10591698 -21.90993633 + 74.01213500 33.51040606 + 138.87475544 + + Transpose of the rotation matrix + 0.929272 0.323903 -0.177597 + -0.041886 0.570069 0.820529 + 0.367014 -0.755055 0.543316 + CENTER OF ATOMS BEFORE TRANSLATION 0.42430 0.88632 0.73045 + AXIS OF ROTATION IS 0.923169 0.319100 0.214324 ANGLE IS 58.58 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.834285 0.400122 0.638411 1.982995 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BALT" + RDCMND substituted energy or value "?RDIP" to "1.98299" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "26" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "26" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "26" + Parameter: RESI26 -> "AALL" + Parameter: RESIDUE <- "AALL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AALL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AALL" + Drude polarizability will be setup for SEGID: AALL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AALL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "26" + Parameter: SEED26 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 71.35365 10.36238 18.27775 +ENER INTERN> 5.04244 14.21469 2.07966 36.19523 0.00000 +ENER EXTERN> 3.31047 10.51117 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AALL" + RDCMND substituted energy or value "?ENER" to "71.3537" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 54.96985306 21.57473790 -33.07853475 + 69.00236079 -0.23555008 + 171.96129225 + + Transpose of the rotation matrix + 0.963644 -0.052509 -0.261980 + 0.177963 0.857495 0.482733 + 0.199299 -0.511806 0.835664 + CENTER OF ATOMS BEFORE TRANSLATION 0.55125 1.15887 1.05948 + AXIS OF ROTATION IS 0.887768 0.411758 -0.205729 ANGLE IS 34.07 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.257496 -0.004497 -0.557594 1.375583 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AALL" + RDCMND substituted energy or value "?RDIP" to "1.37558" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "27" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "27" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "27" + Parameter: RESI27 -> "BALL" + Parameter: RESIDUE <- "BALL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BALL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BALL" + Drude polarizability will be setup for SEGID: BALL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BALL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "27" + Parameter: SEED27 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 72.49440 -1.14075 22.45108 +ENER INTERN> 9.73246 12.07886 1.34535 35.48547 0.00000 +ENER EXTERN> 3.15199 10.70028 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BALL" + RDCMND substituted energy or value "?ENER" to "72.4944" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 93.87258567 36.25782095 -58.46995855 + 58.75275919 12.47376937 + 158.44535462 + + Transpose of the rotation matrix + 0.850645 -0.061775 -0.522099 + 0.409698 0.700228 0.584661 + 0.329471 -0.711242 0.620954 + CENTER OF ATOMS BEFORE TRANSLATION 0.50831 0.95744 0.97214 + AXIS OF ROTATION IS 0.799571 0.525418 -0.290898 ANGLE IS 54.13 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.474938 0.715803 0.023627 2.576480 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BALL" + RDCMND substituted energy or value "?RDIP" to "2.57648" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "28" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "28" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "28" + Parameter: RESI28 -> "AGAL" + Parameter: RESIDUE <- "AGAL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AGAL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AGAL" + Drude polarizability will be setup for SEGID: AGAL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AGAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "28" + Parameter: SEED28 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 70.35360 2.14080 20.97242 +ENER INTERN> 4.84674 13.75139 1.95662 33.03390 0.00000 +ENER EXTERN> 2.35648 14.40847 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AGAL" + RDCMND substituted energy or value "?ENER" to "70.3536" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 28.00969685 -4.84585655 -5.03179794 + 100.35990008 8.02124090 + 173.76473794 + + Transpose of the rotation matrix + 0.993282 0.109424 -0.037651 + -0.111526 0.991997 -0.059187 + 0.030873 0.062988 0.997537 + CENTER OF ATOMS BEFORE TRANSLATION 0.42181 1.34278 0.48555 + AXIS OF ROTATION IS -0.467007 0.261929 0.844570 ANGLE IS 7.52 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.977178 -0.653675 1.867312 3.574596 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AGAL" + RDCMND substituted energy or value "?RDIP" to "3.5746" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "29" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "29" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "29" + Parameter: RESI29 -> "BGAL" + Parameter: RESIDUE <- "BGAL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BGAL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BGAL" + Drude polarizability will be setup for SEGID: BGAL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BGAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "29" + Parameter: SEED29 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 72.26661 -1.91302 20.27019 +ENER INTERN> 9.31566 8.95071 1.52539 35.43945 0.00000 +ENER EXTERN> 5.79134 11.24408 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BGAL" + RDCMND substituted energy or value "?ENER" to "72.2666" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 40.53191027 19.25249649 -10.09523121 + 87.40039946 9.82019044 + 165.63877824 + + Transpose of the rotation matrix + 0.992298 0.106785 -0.062787 + -0.078132 0.932840 0.351717 + 0.096129 -0.344102 0.933998 + CENTER OF ATOMS BEFORE TRANSLATION 0.56758 1.36850 0.25142 + AXIS OF ROTATION IS 0.943738 0.215538 0.250802 ANGLE IS 21.63 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.636047 1.569443 0.801408 3.170828 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BGAL" + RDCMND substituted energy or value "?RDIP" to "3.17083" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "30" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "30" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "30" + Parameter: RESI30 -> "AGUL" + Parameter: RESIDUE <- "AGUL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AGUL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AGUL" + Drude polarizability will be setup for SEGID: AGUL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AGUL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "30" + Parameter: SEED30 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 71.65692 0.60970 20.01636 +ENER INTERN> 8.36884 10.69236 1.52142 32.94678 0.00000 +ENER EXTERN> 0.93783 17.18968 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AGUL" + RDCMND substituted energy or value "?ENER" to "71.6569" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 43.03162800 -0.72121263 -5.64004219 + 76.59345656 23.20555708 + 178.56540478 + + Transpose of the rotation matrix + 0.976530 0.211596 -0.040202 + -0.211067 0.977323 0.017015 + 0.042891 -0.008130 0.999047 + CENTER OF ATOMS BEFORE TRANSLATION 0.58250 1.02329 0.72688 + AXIS OF ROTATION IS 0.058276 0.192575 0.979550 ANGLE IS 12.46 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.127404 1.897773 0.221519 2.218480 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AGUL" + RDCMND substituted energy or value "?RDIP" to "2.21848" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "31" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "31" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "31" + Parameter: RESI31 -> "BGUL" + Parameter: RESIDUE <- "BGUL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BGUL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BGUL" + Drude polarizability will be setup for SEGID: BGUL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BGUL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "31" + Parameter: SEED31 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 78.63727 -6.98036 20.68030 +ENER INTERN> 10.08628 10.39292 1.07460 36.81017 0.00000 +ENER EXTERN> 1.38918 18.88413 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BGUL" + RDCMND substituted energy or value "?ENER" to "78.6373" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 57.52300219 16.95575232 -22.51013890 + 77.04030511 26.56663722 + 173.68318612 + + Transpose of the rotation matrix + 0.965137 0.218905 -0.143498 + -0.099934 0.814877 0.570954 + 0.241918 -0.536709 0.808344 + CENTER OF ATOMS BEFORE TRANSLATION 0.55381 0.99637 0.55063 + AXIS OF ROTATION IS 0.911380 0.317118 0.262340 ANGLE IS 37.42 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.125252 3.001661 -0.689012 3.741845 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BGUL" + RDCMND substituted energy or value "?RDIP" to "3.74185" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "32" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "32" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "32" + Parameter: RESI32 -> "AIDO" + Parameter: RESIDUE <- "AIDO" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AIDO" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AIDO" + Drude polarizability will be setup for SEGID: AIDO mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AIDO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "32" + Parameter: SEED32 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 75.28626 3.35101 20.78033 +ENER INTERN> 7.49093 10.96892 2.32174 36.61561 0.00000 +ENER EXTERN> 3.65491 14.23417 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AIDO" + RDCMND substituted energy or value "?ENER" to "75.2863" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 56.00248562 -12.18817252 -11.95626869 + 87.28023049 23.17247230 + 135.57459089 + + Transpose of the rotation matrix + 0.907990 0.383162 -0.169532 + -0.415232 0.876976 -0.241857 + 0.056005 0.289999 0.955387 + CENTER OF ATOMS BEFORE TRANSLATION 0.32050 0.98621 0.65103 + AXIS OF ROTATION IS -0.539693 0.228860 0.810157 ANGLE IS 29.52 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.116571 -0.659919 -2.240024 2.588423 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AIDO" + RDCMND substituted energy or value "?RDIP" to "2.58842" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "33" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "33" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "33" + Parameter: RESI33 -> "BIDO" + Parameter: RESIDUE <- "BIDO" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BIDO" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BIDO" + Drude polarizability will be setup for SEGID: BIDO mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BIDO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "33" + Parameter: SEED33 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 73.38320 1.90307 22.00822 +ENER INTERN> 8.33745 9.90618 1.15460 35.91072 0.00000 +ENER EXTERN> 2.87802 15.19622 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BIDO" + RDCMND substituted energy or value "?ENER" to "73.3832" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 67.81248117 12.01274020 -21.75718735 + 82.87376446 23.37212194 + 145.32367169 + + Transpose of the rotation matrix + 0.943482 0.267785 -0.195275 + -0.107925 0.805329 0.582922 + 0.313358 -0.528901 0.788714 + CENTER OF ATOMS BEFORE TRANSLATION 0.44307 1.02155 0.49042 + AXIS OF ROTATION IS 0.869245 0.397659 0.293737 ANGLE IS 39.76 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 1.688223 -0.022963 0.176563 1.697586 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BIDO" + RDCMND substituted energy or value "?RDIP" to "1.69759" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "34" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "34" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "34" + Parameter: RESI34 -> "AMAN" + Parameter: RESIDUE <- "AMAN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AMAN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AMAN" + Drude polarizability will be setup for SEGID: AMAN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AMAN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "34" + Parameter: SEED34 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 71.04265 2.34055 18.36400 +ENER INTERN> 6.19488 8.55137 1.76366 34.19974 0.00000 +ENER EXTERN> 4.06092 16.27207 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AMAN" + RDCMND substituted energy or value "?ENER" to "71.0426" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 53.12266229 8.55893053 -28.15189642 + 115.59836471 36.59693341 + 129.25895818 + + Transpose of the rotation matrix + 0.790761 0.591485 -0.157613 + -0.476787 0.756640 0.447403 + 0.383888 -0.278642 0.880334 + CENTER OF ATOMS BEFORE TRANSLATION 0.34944 1.16911 0.71485 + AXIS OF ROTATION IS 0.518396 0.386631 0.762746 ANGLE IS 44.45 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.815783 -1.159755 -2.050557 3.671301 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AMAN" + RDCMND substituted energy or value "?RDIP" to "3.6713" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "35" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "35" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "35" + Parameter: RESI35 -> "BMAN" + Parameter: RESIDUE <- "BMAN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BMAN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BMAN" + Drude polarizability will be setup for SEGID: BMAN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BMAN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "35" + Parameter: SEED35 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 65.80457 5.23808 16.99560 +ENER INTERN> 3.50854 12.11806 1.13710 36.01699 0.00000 +ENER EXTERN> 0.94700 12.07689 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BMAN" + RDCMND substituted energy or value "?ENER" to "65.8046" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 79.16234215 32.50290489 -39.43648201 + 106.60179807 41.79771759 + 126.62053863 + + Transpose of the rotation matrix + 0.833539 0.517085 -0.194515 + -0.252901 0.670168 0.697794 + 0.491177 -0.532445 0.689382 + CENTER OF ATOMS BEFORE TRANSLATION 0.34210 1.06961 0.60910 + AXIS OF ROTATION IS 0.766427 0.427179 0.479694 ANGLE IS 53.38 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 0.696714 -1.629999 -0.542581 1.853834 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BMAN" + RDCMND substituted energy or value "?RDIP" to "1.85383" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "36" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "36" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "36" + Parameter: RESI36 -> "ATAL" + Parameter: RESIDUE <- "ATAL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ATAL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ATAL" + Drude polarizability will be setup for SEGID: ATAL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ATAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "36" + Parameter: SEED36 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 63.73626 2.06830 20.21585 +ENER INTERN> 4.75873 9.86651 1.49042 32.58036 0.00000 +ENER EXTERN> 4.61157 10.42868 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ATAL" + RDCMND substituted energy or value "?ENER" to "63.7363" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 41.19604791 -5.78724350 2.27175557 + 96.18507627 9.51341807 + 138.58756950 + + Transpose of the rotation matrix + 0.978075 0.208002 0.010239 + -0.205530 0.972041 -0.113550 + -0.033572 0.108956 0.993480 + CENTER OF ATOMS BEFORE TRANSLATION 0.39863 1.39579 0.32456 + AXIS OF ROTATION IS -0.471778 -0.092892 0.876811 ANGLE IS 13.64 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.017513 -2.259165 0.290231 3.780667 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ATAL" + RDCMND substituted energy or value "?RDIP" to "3.78067" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "37" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "37" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "37" + Parameter: RESI37 -> "BTAL" + Parameter: RESIDUE <- "BTAL" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BTAL" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BTAL" + Drude polarizability will be setup for SEGID: BTAL mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 12 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BTAL. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 12 + Number of true-bonds = 49 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "37" + Parameter: SEED37 -> "1 O5 1 C1 1 C2" + + CHARMM> ic build + **** WARNING **** 25 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 450 450 441 + : Ran out of space. RESIZING + with mode 5 found 361 exclusions and 305 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 815 atom pairs and 666 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 815 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 65.53204 -1.79578 17.45177 +ENER INTERN> 7.90795 11.75144 1.78283 30.27280 0.00000 +ENER EXTERN> 2.32166 11.49535 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BTAL" + RDCMND substituted energy or value "?ENER" to "65.532" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 51.35774454 19.04279253 -12.73816757 + 94.62829705 11.54129955 + 142.86295915 + + Transpose of the rotation matrix + 0.978404 0.183872 -0.094429 + -0.134428 0.913052 0.385053 + 0.157019 -0.364043 0.918051 + CENTER OF ATOMS BEFORE TRANSLATION 0.41133 1.43283 0.22503 + AXIS OF ROTATION IS 0.879353 0.295171 0.373647 ANGLE IS 25.21 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 49 atoms have been selected out of 49 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.413589 0.349176 0.569452 2.504319 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BTAL" + RDCMND substituted energy or value "?RDIP" to "2.50432" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 49 Number of groups = 5 + Number of bonds = 49 Number of angles = 42 + Number of dihedrals = 66 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 25 + + CHARMM> delete atom sele all end + SELRPN> 49 atoms have been selected out of 49 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 49 bonds deleted + DELTIC: 42 angles deleted + DELTIC: 66 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "38" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "38" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "38" + Parameter: RESI38 -> "ARIB" + Parameter: RESIDUE <- "ARIB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ARIB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ARIB" + Drude polarizability will be setup for SEGID: ARIB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ARIB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "38" + Parameter: SEED38 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 377 377 369 + : Ran out of space. RESIZING + with mode 5 found 306 exclusions and 237 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 514 atom pairs and 543 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 63.69556 1.83648 13.27344 +ENER INTERN> 1.83548 9.47599 0.36239 41.91597 0.00000 +ENER EXTERN> 0.02376 10.08197 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ARIB" + RDCMND substituted energy or value "?ENER" to "63.6956" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 30.12578139 -4.66007255 16.13404004 + 104.65213855 37.10257121 + 88.50949161 + + Transpose of the rotation matrix + 0.636204 0.768884 0.063730 + -0.690773 0.604462 -0.396810 + -0.343623 0.208429 0.915686 + CENTER OF ATOMS BEFORE TRANSLATION 0.15859 0.85559 -0.22868 + AXIS OF ROTATION IS -0.370897 -0.249631 0.894494 ANGLE IS 54.68 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 41 atoms have been selected out of 41 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.351055 -1.520653 1.186782 3.041102 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ARIB" + RDCMND substituted energy or value "?RDIP" to "3.0411" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 41 atoms have been selected out of 41 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "39" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "39" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "39" + Parameter: RESI39 -> "BRIB" + Parameter: RESIDUE <- "BRIB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BRIB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BRIB" + Drude polarizability will be setup for SEGID: BRIB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BRIB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "39" + Parameter: SEED39 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 377 377 369 + : Ran out of space. RESIZING + with mode 5 found 306 exclusions and 237 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 514 atom pairs and 543 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 66.60483 -2.90928 12.60844 +ENER INTERN> 1.83548 9.47599 0.36239 44.88279 0.00000 +ENER EXTERN> -0.57260 10.62078 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BRIB" + RDCMND substituted energy or value "?ENER" to "66.6048" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 16.71085211 -12.24329591 0.51603542 + 101.88839642 37.37773092 + 116.06370962 + + Transpose of the rotation matrix + 0.764235 0.642401 -0.057145 + -0.641520 0.748086 -0.169761 + -0.066305 0.166397 0.983827 + CENTER OF ATOMS BEFORE TRANSLATION 0.30023 0.81213 -0.43434 + AXIS OF ROTATION IS -0.253278 -0.006902 0.967369 ANGLE IS 41.58 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 41 atoms have been selected out of 41 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.431148 0.392568 0.350303 3.471254 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BRIB" + RDCMND substituted energy or value "?RDIP" to "3.47125" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 41 atoms have been selected out of 41 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "40" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "40" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "40" + Parameter: RESI40 -> "AARB" + Parameter: RESIDUE <- "AARB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AARB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AARB" + Drude polarizability will be setup for SEGID: AARB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AARB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "40" + Parameter: SEED40 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 377 377 369 + : Ran out of space. RESIZING + with mode 5 found 306 exclusions and 237 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 514 atom pairs and 543 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 62.78822 3.81661 12.66073 +ENER INTERN> 1.52800 7.34795 0.68670 45.14520 0.00000 +ENER EXTERN> -0.79618 8.87655 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AARB" + RDCMND substituted energy or value "?ENER" to "62.7882" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 31.92671162 -10.70579422 22.85332388 + 100.86428762 41.94787582 + 101.78759507 + + Transpose of the rotation matrix + 0.724595 0.684232 0.082396 + -0.567917 0.660553 -0.491059 + -0.390425 0.309025 0.867221 + CENTER OF ATOMS BEFORE TRANSLATION 0.23421 0.81516 -0.30001 + AXIS OF ROTATION IS -0.513089 -0.303217 0.802994 ANGLE IS 51.23 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 41 atoms have been selected out of 41 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.938082 -1.016489 0.630188 2.277400 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AARB" + RDCMND substituted energy or value "?RDIP" to "2.2774" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 41 atoms have been selected out of 41 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "41" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "41" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "41" + Parameter: RESI41 -> "BARB" + Parameter: RESIDUE <- "BARB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BARB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BARB" + Drude polarizability will be setup for SEGID: BARB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BARB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "41" + Parameter: SEED41 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 377 377 369 + : Ran out of space. RESIZING + with mode 5 found 306 exclusions and 237 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 514 atom pairs and 543 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 65.53547 -2.74725 13.34155 +ENER INTERN> 1.52800 7.34795 0.68670 45.74948 0.00000 +ENER EXTERN> 0.55783 9.66551 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BARB" + RDCMND substituted energy or value "?ENER" to "65.5355" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 20.86111321 -18.29790878 -2.15724500 + 99.94143399 41.97889028 + 109.68682497 + + Transpose of the rotation matrix + 0.731964 0.672613 -0.108725 + -0.674952 0.693999 -0.250611 + -0.093109 0.256822 0.961963 + CENTER OF ATOMS BEFORE TRANSLATION 0.27336 0.80193 -0.55081 + AXIS OF ROTATION IS -0.352379 0.010844 0.935795 ANGLE IS 46.06 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 41 atoms have been selected out of 41 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.230449 1.302718 0.885036 3.593906 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BARB" + RDCMND substituted energy or value "?RDIP" to "3.59391" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 41 atoms have been selected out of 41 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "42" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "42" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "42" + Parameter: RESI42 -> "AXYF" + Parameter: RESIDUE <- "AXYF" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "AXYF" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "AXYF" + Drude polarizability will be setup for SEGID: AXYF mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is AXYF. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "42" + Parameter: SEED42 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 377 377 369 + : Ran out of space. RESIZING + with mode 5 found 306 exclusions and 237 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 514 atom pairs and 543 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 61.51170 4.02377 14.14338 +ENER INTERN> 1.49751 6.34426 0.94260 44.12620 0.00000 +ENER EXTERN> 0.06457 8.53656 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "AXYF" + RDCMND substituted energy or value "?ENER" to "61.5117" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 51.34007244 25.02617094 34.86087532 + 76.49699402 36.01101221 + 94.46309569 + + Transpose of the rotation matrix + 0.718168 0.551088 0.424896 + -0.577121 0.812848 -0.078800 + -0.388802 -0.188625 0.901806 + CENTER OF ATOMS BEFORE TRANSLATION 0.39022 0.77128 -0.14122 + AXIS OF ROTATION IS 0.078707 -0.583147 0.808545 ANGLE IS 44.24 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 41 atoms have been selected out of 41 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.974282 -1.600029 0.783939 2.030733 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "AXYF" + RDCMND substituted energy or value "?RDIP" to "2.03073" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 41 atoms have been selected out of 41 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "43" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "43" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "43" + Parameter: RESI43 -> "BXYF" + Parameter: RESIDUE <- "BXYF" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BXYF" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BXYF" + Drude polarizability will be setup for SEGID: BXYF mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BXYF. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "43" + Parameter: SEED43 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 377 377 369 + : Ran out of space. RESIZING + with mode 5 found 306 exclusions and 237 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 514 atom pairs and 543 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 63.60408 -2.09238 13.05474 +ENER INTERN> 1.49751 6.34426 0.94260 45.80831 0.00000 +ENER EXTERN> -0.55289 9.56429 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BXYF" + RDCMND substituted energy or value "?ENER" to "63.6041" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 50.48928872 17.91402149 10.58020224 + 77.53548970 36.61020214 + 82.46978981 + + Transpose of the rotation matrix + 0.689689 0.672141 0.269361 + -0.604469 0.329609 0.725242 + 0.398681 -0.663012 0.633616 + CENTER OF ATOMS BEFORE TRANSLATION 0.33070 0.79202 -0.38387 + AXIS OF ROTATION IS 0.734361 0.068408 0.675303 ANGLE IS 70.95 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 41 atoms have been selected out of 41 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.918348 1.757782 0.901326 2.753587 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BXYF" + RDCMND substituted energy or value "?RDIP" to "2.75359" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 41 atoms have been selected out of 41 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "44" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "44" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "44" + Parameter: RESI44 -> "ALYF" + Parameter: RESIDUE <- "ALYF" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ALYF" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ALYF" + Drude polarizability will be setup for SEGID: ALYF mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ALYF. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "44" + Parameter: SEED44 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 377 377 369 + : Ran out of space. RESIZING + with mode 5 found 306 exclusions and 237 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 514 atom pairs and 543 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 63.10218 0.50190 14.02645 +ENER INTERN> 1.61736 8.50552 0.72991 42.47279 0.00000 +ENER EXTERN> 0.17822 9.59839 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ALYF" + RDCMND substituted energy or value "?ENER" to "63.1022" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 55.14634662 -14.68047630 13.58732759 + 93.25045137 50.18551339 + 78.77898484 + + Transpose of the rotation matrix + 0.650249 0.759194 -0.028299 + -0.415655 0.324334 -0.849729 + -0.635931 0.564297 0.526460 + CENTER OF ATOMS BEFORE TRANSLATION 0.43513 0.67878 -0.45115 + AXIS OF ROTATION IS -0.730302 -0.313823 0.606774 ANGLE IS 75.49 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 41 atoms have been selected out of 41 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -1.236519 -2.022218 -0.996764 2.571358 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ALYF" + RDCMND substituted energy or value "?RDIP" to "2.57136" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 41 atoms have been selected out of 41 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "45" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "45" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "45" + Parameter: RESI45 -> "BLYF" + Parameter: RESIDUE <- "BLYF" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BLYF" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BLYF" + Drude polarizability will be setup for SEGID: BLYF mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BLYF. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 41 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "45" + Parameter: SEED45 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 21 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 377 377 369 + : Ran out of space. RESIZING + with mode 5 found 306 exclusions and 237 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 514 atom pairs and 543 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 514 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 67.17361 -4.07143 15.82897 +ENER INTERN> 1.61736 8.50552 0.72991 43.33196 0.00000 +ENER EXTERN> 1.54549 11.44338 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BLYF" + RDCMND substituted energy or value "?ENER" to "67.1736" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 39.78702052 -24.20423862 -7.41688901 + 91.68325781 50.83101491 + 90.02476575 + + Transpose of the rotation matrix + 0.669441 0.713061 -0.208309 + -0.658292 0.439484 -0.611151 + -0.344239 0.546258 0.763611 + CENTER OF ATOMS BEFORE TRANSLATION 0.49699 0.65896 -0.69860 + AXIS OF ROTATION IS -0.643136 -0.075532 0.762018 ANGLE IS 64.13 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 41 atoms have been selected out of 41 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.299843 -0.168711 0.525787 2.365205 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BLYF" + RDCMND substituted energy or value "?RDIP" to "2.3652" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 41 Number of groups = 4 + Number of bonds = 41 Number of angles = 35 + Number of dihedrals = 54 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 21 + + CHARMM> delete atom sele all end + SELRPN> 41 atoms have been selected out of 41 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 41 bonds deleted + DELTIC: 35 angles deleted + DELTIC: 54 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "46" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "46" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "46" + Parameter: RESI46 -> "ADEO" + Parameter: RESIDUE <- "ADEO" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ADEO" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ADEO" + Drude polarizability will be setup for SEGID: ADEO mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ADEO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 37 Number of groups = 4 + Number of bonds = 37 Number of angles = 34 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 9 + Number of true-bonds = 37 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 9 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "46" + Parameter: SEED46 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 18 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 338 338 333 + : Ran out of space. RESIZING + with mode 5 found 273 exclusions and 181 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 393 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 393 atom pairs and 454 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 393 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 30.80192 36.37169 11.76370 +ENER INTERN> 1.16341 6.28008 0.83975 33.81527 0.00000 +ENER EXTERN> -0.46003 -10.83656 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ADEO" + RDCMND substituted energy or value "?ENER" to "30.8019" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 25.31014850 3.37408492 25.42128527 + 69.88666897 35.05783036 + 96.89916772 + + Transpose of the rotation matrix + 0.821324 0.524465 0.224419 + -0.439134 0.832372 -0.338110 + -0.364126 0.179148 0.913957 + CENTER OF ATOMS BEFORE TRANSLATION 0.16636 0.54101 -0.16303 + AXIS OF ROTATION IS -0.416485 -0.473884 0.775870 ANGLE IS 38.39 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 37 atoms have been selected out of 37 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -0.706008 -1.889048 0.081635 2.018320 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ADEO" + RDCMND substituted energy or value "?RDIP" to "2.01832" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 37 Number of groups = 4 + Number of bonds = 37 Number of angles = 34 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 18 + + CHARMM> delete atom sele all end + SELRPN> 37 atoms have been selected out of 37 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 37 bonds deleted + DELTIC: 34 angles deleted + DELTIC: 51 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "47" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "47" and "47". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "47" + Parameter: RESI47 -> "BDEO" + Parameter: RESIDUE <- "BDEO" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BDEO" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BDEO" + Drude polarizability will be setup for SEGID: BDEO mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BDEO. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 37 Number of groups = 4 + Number of bonds = 37 Number of angles = 34 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 9 + Number of true-bonds = 37 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 9 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "47" + Parameter: SEED47 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 18 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 338 338 333 + : Ran out of space. RESIZING + with mode 5 found 273 exclusions and 181 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 393 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 393 atom pairs and 454 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 393 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 33.21903 -2.41711 12.41480 +ENER INTERN> 1.16341 6.28008 0.83975 36.30098 0.00000 +ENER EXTERN> -0.58461 -10.78057 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BDEO" + RDCMND substituted energy or value "?ENER" to "33.219" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 16.23847189 -7.29382929 0.13171513 + 68.33985015 35.64849322 + 106.95085941 + + Transpose of the rotation matrix + 0.857380 0.513661 -0.032424 + -0.509661 0.838548 -0.192570 + -0.071727 0.181631 0.980747 + CENTER OF ATOMS BEFORE TRANSLATION 0.22134 0.52244 -0.44461 + AXIS OF ROTATION IS -0.343209 -0.036047 0.938567 ANGLE IS 33.04 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 37 atoms have been selected out of 37 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -2.304955 -0.077721 0.316391 2.327867 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BDEO" + RDCMND substituted energy or value "?RDIP" to "2.32787" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 37 Number of groups = 4 + Number of bonds = 37 Number of angles = 34 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 18 + + CHARMM> delete atom sele all end + SELRPN> 37 atoms have been selected out of 37 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 37 bonds deleted + DELTIC: 34 angles deleted + DELTIC: 51 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "48" + + CHARMM> if count le @nres goto loop_carb1 + Parameter: NRES -> "47" + Comparing "48" and "47". + IF test evaluated as false. Skipping command + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> incr testcasei + Parameter: TESTCASEI <- "5" + + CHARMM> if @testcasei le @testcases goto loop_tests + Parameter: TESTCASEI -> "5" + Parameter: TESTCASES -> "6" + Comparing "5" and "6". + IF test evaluated as true. Performing command + + CHARMM> stream @test@@testcasei + Parameter: TESTCASEI -> "5" + Parameter: TEST5 -> "TEST_DRUDE_NUCLEIC_ACIDS_NO_RNA.STR" + VOPEN> Attempting to open::test_drude_nucleic_acids_no_rna.str:: + OPNLGU> Unit 99 opened for READONLY access to test_drude_nucleic_acids_no_rna.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * $ID: TEST_DRUDE_NUCLEIC_ACIDS.STR 28 2015-07-29 23:54:15Z ALEX $ + RDTITL> * TEST CASE, DRUDE CARBOHYDRATE TOPPAR FILE + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> set boml 0 ! set to -1 if the series contains 3-membered rings + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> !loop for nucleotides + CHARMM> set nres 4 + Parameter: NRES <- "4" + + CHARMM> set resi1 ade + Parameter: RESI1 <- "ADE" + + CHARMM> set resi2 cyt + Parameter: RESI2 <- "CYT" + + CHARMM> set resi3 thy + Parameter: RESI3 <- "THY" + + CHARMM> set resi4 gua + Parameter: RESI4 <- "GUA" + + CHARMM> + + CHARMM> set seed1 1 c5' 1 c4' 1 c3' + Parameter: SEED1 <- "1 C5' 1 C4' 1 C3'" + + CHARMM> set seed2 1 c5' 1 c4' 1 c3' + Parameter: SEED2 <- "1 C5' 1 C4' 1 C3'" + + CHARMM> set seed3 1 c5' 1 c4' 1 c3' + Parameter: SEED3 <- "1 C5' 1 C4' 1 C3'" + + CHARMM> set seed4 1 c5' 1 c4' 1 c3' + Parameter: SEED4 <- "1 C5' 1 C4' 1 C3'" + + CHARMM> + + CHARMM> + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> label loop_na1 + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "1" + Parameter: RESI1 -> "ADE" + Parameter: RESIDUE <- "ADE" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ADE" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first 5ter last 3ter setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ADE" + Drude polarizability will be setup for SEGID: ADE mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 19 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ADE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 63 Number of groups = 5 + Number of bonds = 65 Number of angles = 58 + Number of dihedrals = 89 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 19 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> patch deox @residue 1 setup warn + Parameter: RESIDUE -> "ADE" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM ADE 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM ADE 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM ADE 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM ADE 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 61 Number of angles = 54 + Number of dihedrals = 80 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 19 + Number of true-bonds = 65 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> autogenerate angles dihedrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 61 Number of angles = 57 + Number of dihedrals = 86 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 61 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 10 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "1" + Parameter: SEED1 -> "1 C5' 1 C4' 1 C3'" + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 555 555 549 + : Ran out of space. RESIZING + with mode 5 found 424 exclusions and 295 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1287 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1287 atom pairs and 719 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1287 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 177.60159 -144.38256 70.71814 +ENER INTERN> 69.28330 30.52523 44.34878 22.24122 0.00000 +ENER EXTERN> 72.84704 -61.64398 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ADE" + RDCMND substituted energy or value "?ENER" to "177.602" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 422.36740694 151.19044426 -41.55385346 + 104.12810246 -31.81440355 + 115.63226835 + + Transpose of the rotation matrix + 0.133712 -0.371455 -0.918772 + -0.970512 0.138548 -0.197257 + 0.200566 0.918055 -0.341977 + CENTER OF ATOMS BEFORE TRANSLATION 1.99454 -0.20823 -2.75972 + AXIS OF ROTATION IS -0.659993 0.662376 0.354496 ANGLE IS 122.33 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 59 atoms have been selected out of 59 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -1.788448 7.231629 2.581925 7.884246 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ADE" + RDCMND substituted energy or value "?RDIP" to "7.88425" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 61 Number of angles = 57 + Number of dihedrals = 86 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 59 atoms have been selected out of 59 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 61 bonds deleted + DELTIC: 57 angles deleted + DELTIC: 86 dihedrals deleted + DELTIC: 2 improper dihedrals deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "2" + + CHARMM> if count le @nres goto loop_na1 + Parameter: NRES -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "2" + Parameter: RESI2 -> "CYT" + Parameter: RESIDUE <- "CYT" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CYT" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first 5ter last 3ter setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYT" + Drude polarizability will be setup for SEGID: CYT mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 17 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYT. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 60 Number of angles = 53 + Number of dihedrals = 81 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 17 + Number of true-bonds = 60 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 12 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> patch deox @residue 1 setup warn + Parameter: RESIDUE -> "CYT" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM CYT 1 CYT O2' AND ALL REFERENCES TO IT DELETED. + ATOM CYT 1 CYT LPHA AND ALL REFERENCES TO IT DELETED. + ATOM CYT 1 CYT LPHB AND ALL REFERENCES TO IT DELETED. + ATOM CYT 1 CYT DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 55 Number of groups = 5 + Number of bonds = 56 Number of angles = 49 + Number of dihedrals = 72 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 17 + Number of true-bonds = 60 Number of zero-bonds = -4 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> autogenerate angles dihedrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 55 Number of groups = 5 + Number of bonds = 56 Number of angles = 52 + Number of dihedrals = 78 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 18 + Number of true-bonds = 56 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 10 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "2" + Parameter: SEED2 -> "1 C5' 1 C4' 1 C3'" + + CHARMM> ic build + **** WARNING **** 26 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 517 517 504 + : Ran out of space. RESIZING + with mode 5 found 383 exclusions and 273 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1102 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1102 atom pairs and 656 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1102 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -6.19746 183.79905 30.32575 +ENER INTERN> 20.53098 11.97469 1.87382 17.71135 0.00000 +ENER EXTERN> 14.80198 -73.09028 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CYT" + RDCMND substituted energy or value "?ENER" to "-6.19746" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 329.41211100 75.45149995 20.46215888 + 63.35849521 -7.89515282 + 108.08395078 + + Transpose of the rotation matrix + 0.073235 0.251471 0.965090 + -0.978883 0.203310 0.021305 + -0.190854 -0.946270 0.261050 + CENTER OF ATOMS BEFORE TRANSLATION 1.68431 0.14076 -2.39929 + AXIS OF ROTATION IS 0.497261 -0.594068 0.632309 ANGLE IS 103.37 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 55 atoms have been selected out of 55 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -0.598407 10.148220 -3.852617 10.871389 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CYT" + RDCMND substituted energy or value "?RDIP" to "10.8714" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 55 Number of groups = 5 + Number of bonds = 56 Number of angles = 52 + Number of dihedrals = 78 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 5 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 26 + + CHARMM> delete atom sele all end + SELRPN> 55 atoms have been selected out of 55 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 56 bonds deleted + DELTIC: 52 angles deleted + DELTIC: 78 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 4 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "3" + + CHARMM> if count le @nres goto loop_na1 + Parameter: NRES -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "3" + Parameter: RESI3 -> "THY" + Parameter: RESIDUE <- "THY" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "THY" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first 5ter last 3ter setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THY" + Drude polarizability will be setup for SEGID: THY mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THY . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THY . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THY . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THY . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THY . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THY . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 THY . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 THY . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 18 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 63 Number of groups = 5 + Number of bonds = 64 Number of angles = 58 + Number of dihedrals = 87 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 18 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> patch deox @residue 1 setup warn + Parameter: RESIDUE -> "THY" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM THY 1 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM THY 1 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM THY 1 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM THY 1 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 60 Number of angles = 54 + Number of dihedrals = 78 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 18 + Number of true-bonds = 64 Number of zero-bonds = -4 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> autogenerate angles dihedrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 60 Number of angles = 57 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 19 + Number of true-bonds = 60 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "3" + Parameter: SEED3 -> "1 C5' 1 C4' 1 C3'" + + CHARMM> ic build + **** WARNING **** 28 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 558 558 540 + : Ran out of space. RESIZING + with mode 5 found 403 exclusions and 301 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1308 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1308 atom pairs and 704 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1308 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -6.95210 0.75464 32.58623 +ENER INTERN> 23.47286 14.14422 1.87654 25.18138 0.00003 +ENER EXTERN> 11.90619 -83.53330 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "THY" + RDCMND substituted energy or value "?ENER" to "-6.9521" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 358.25621873 62.37218656 48.41177820 + 71.11999987 -21.07856355 + 137.81368150 + + Transpose of the rotation matrix + 0.177985 0.183653 0.966744 + -0.924261 0.368383 0.100181 + -0.337733 -0.911354 0.235309 + CENTER OF ATOMS BEFORE TRANSLATION 1.48894 0.22896 -2.59125 + AXIS OF ROTATION IS 0.508808 -0.656159 0.557287 ANGLE IS 96.27 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 59 atoms have been selected out of 59 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 4.183139 5.365902 -1.317071 6.930096 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "THY" + RDCMND substituted energy or value "?RDIP" to "6.9301" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 59 Number of groups = 5 + Number of bonds = 60 Number of angles = 57 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 5 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 28 + + CHARMM> delete atom sele all end + SELRPN> 59 atoms have been selected out of 59 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 60 bonds deleted + DELTIC: 57 angles deleted + DELTIC: 84 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 3 donors deleted + DELTIC: 5 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "4" + + CHARMM> if count le @nres goto loop_na1 + Parameter: NRES -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "4" + Parameter: RESI4 -> "GUA" + Parameter: RESIDUE <- "GUA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "GUA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first 5ter last 3ter setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GUA" + Drude polarizability will be setup for SEGID: GUA mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GUA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> patch deox @residue 1 setup warn + Parameter: RESIDUE -> "GUA" + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM GUA 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM GUA 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM GUA 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM GUA 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> autogenerate angles dihedrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "4" + Parameter: SEED4 -> "1 C5' 1 C4' 1 C3'" + + CHARMM> ic build + **** WARNING **** 30 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 579 579 576 + : Ran out of space. RESIZING + with mode 5 found 441 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1450 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1450 atom pairs and 760 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1450 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -10.00257 3.05048 27.89030 +ENER INTERN> 22.39519 17.32529 3.76924 22.24003 0.00000 +ENER EXTERN> 7.22930 -82.96162 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "GUA" + RDCMND substituted energy or value "?ENER" to "-10.0026" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 434.77214025 178.02078282 -75.25552336 + 140.63160061 -72.91573891 + 160.25385550 + + Transpose of the rotation matrix + 0.251344 -0.428148 -0.868053 + -0.907795 0.206834 -0.364867 + 0.335760 0.879721 -0.336684 + CENTER OF ATOMS BEFORE TRANSLATION 2.21376 -0.39123 -2.86699 + AXIS OF ROTATION IS -0.692698 0.670003 0.266956 ANGLE IS 116.06 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 62 atoms have been selected out of 62 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -2.364537 -4.986690 -1.369790 5.686337 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "GUA" + RDCMND substituted energy or value "?RDIP" to "5.68634" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 30 + + CHARMM> delete atom sele all end + SELRPN> 62 atoms have been selected out of 62 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 64 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "5" + + CHARMM> if count le @nres goto loop_na1 + Parameter: NRES -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> ! various NA model compounds + CHARMM> set nres 12 + Parameter: NRES <- "12" + + CHARMM> !set nres 13 + CHARMM> set resi1 adeb + Parameter: RESI1 <- "ADEB" + + CHARMM> set resi2 made + Parameter: RESI2 <- "MADE" + + CHARMM> set resi3 cytb + Parameter: RESI3 <- "CYTB" + + CHARMM> set resi4 mcyt + Parameter: RESI4 <- "MCYT" + + CHARMM> set resi5 thyb + Parameter: RESI5 <- "THYB" + + CHARMM> set resi6 mthy + Parameter: RESI6 <- "MTHY" + + CHARMM> set resi7 guab + Parameter: RESI7 <- "GUAB" + + CHARMM> set resi8 urab + Parameter: RESI8 <- "URAB" + + CHARMM> set resi9 t3ps + Parameter: RESI9 <- "T3PS" + + CHARMM> set resi10 t3pm + Parameter: RESI10 <- "T3PM" + + CHARMM> set resi11 dmpn + Parameter: RESI11 <- "DMPN" + + CHARMM> !set resi12 bribna ! RNA doesn't run + CHARMM> !set resi13 bdeona + CHARMM> !set resi12 bribna + CHARMM> set resi12 bdeona + Parameter: RESI12 <- "BDEONA" + + CHARMM> + + CHARMM> set seed1 1 c4 1 n9 1 C8 + Parameter: SEED1 <- "1 C4 1 N9 1 C8" + + CHARMM> set seed2 1 c4 1 n9 1 C8 + Parameter: SEED2 <- "1 C4 1 N9 1 C8" + + CHARMM> set seed3 1 c2 1 n1 1 C6 + Parameter: SEED3 <- "1 C2 1 N1 1 C6" + + CHARMM> set seed4 1 c2 1 n1 1 C6 + Parameter: SEED4 <- "1 C2 1 N1 1 C6" + + CHARMM> set seed5 1 c2 1 n1 1 C6 + Parameter: SEED5 <- "1 C2 1 N1 1 C6" + + CHARMM> set seed6 1 c2 1 n1 1 C6 + Parameter: SEED6 <- "1 C2 1 N1 1 C6" + + CHARMM> set seed7 1 c4 1 n9 1 C8 + Parameter: SEED7 <- "1 C4 1 N9 1 C8" + + CHARMM> set seed8 1 c2 1 n1 1 C6 + Parameter: SEED8 <- "1 C2 1 N1 1 C6" + + CHARMM> set seed9 1 c4A 1 O4A 1 C1A + Parameter: SEED9 <- "1 C4A 1 O4A 1 C1A" + + CHARMM> set seed10 1 c4' 1 O4' 1 C1' + Parameter: SEED10 <- "1 C4' 1 O4' 1 C1'" + + CHARMM> set seed11 1 o11 1 p 1 o12 + Parameter: SEED11 <- "1 O11 1 P 1 O12" + + CHARMM> set seed12 1 c4 1 o4 1 c1 + Parameter: SEED12 <- "1 C4 1 O4 1 C1" + + CHARMM> set seed13 1 c4 1 o4 1 c1 + Parameter: SEED13 <- "1 C4 1 O4 1 C1" + + CHARMM> + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> label loop_na2 + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "1" + Parameter: RESI1 -> "ADEB" + Parameter: RESIDUE <- "ADEB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "ADEB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "ADEB" + Drude polarizability will be setup for SEGID: ADEB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is ADEB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 29 Number of angles = 24 + Number of dihedrals = 32 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 10 + Number of true-bonds = 29 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 3 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "1" + Parameter: SEED1 -> "1 C4 1 N9 1 C8" + + CHARMM> ic build + **** WARNING **** 13 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 264 264 261 + : Ran out of space. RESIZING + with mode 5 found 181 exclusions and 93 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 197 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 197 atom pairs and 274 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 197 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 97.00782 -107.01039 93.11806 +ENER INTERN> 53.24156 21.66453 42.91574 -0.00000 0.00000 +ENER EXTERN> 71.23198 -92.04601 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "ADEB" + RDCMND substituted energy or value "?ENER" to "97.0078" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 -0.00000004 0.00000001 + 55.55863755 -6.05461339 + 76.53936116 + + Transpose of the rotation matrix + 0.965944 -0.258750 0.000000 + 0.258750 0.965944 -0.000000 + -0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION -0.57419 0.88807 -0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 -1.000000 ANGLE IS 15.00 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 28 atoms have been selected out of 28 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.831801 4.183721 0.000000 5.051991 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "ADEB" + RDCMND substituted energy or value "?RDIP" to "5.05199" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 29 Number of angles = 24 + Number of dihedrals = 32 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 13 + + CHARMM> delete atom sele all end + SELRPN> 28 atoms have been selected out of 28 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 29 bonds deleted + DELTIC: 24 angles deleted + DELTIC: 32 dihedrals deleted + DELTIC: 2 improper dihedrals deleted + DELTIC: 2 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "2" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "2" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "2" + Parameter: RESI2 -> "MADE" + Parameter: RESIDUE <- "MADE" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MADE" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MADE" + Drude polarizability will be setup for SEGID: MADE mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 11 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MADE. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 32 Number of groups = 1 + Number of bonds = 33 Number of angles = 30 + Number of dihedrals = 38 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 11 + Number of true-bonds = 33 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 3 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "2" + Parameter: SEED2 -> "1 C4 1 N9 1 C8" + + CHARMM> ic build + **** WARNING **** 14 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 299 299 297 + : Ran out of space. RESIZING + with mode 5 found 203 exclusions and 114 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 293 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 293 atom pairs and 317 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 293 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 114.47102 -17.46321 86.29666 +ENER INTERN> 53.03907 22.00729 42.87168 -0.00000 0.00000 +ENER EXTERN> 71.30591 -74.75293 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MADE" + RDCMND substituted energy or value "?ENER" to "114.471" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.69321461 -0.00000004 0.00000001 + 74.74003752 -29.83483973 + 110.28192822 + + Transpose of the rotation matrix + 0.869408 -0.494094 0.000000 + 0.494094 0.869408 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION -0.19095 0.59897 -0.00000 + AXIS OF ROTATION IS -0.000000 -0.000000 -1.000000 ANGLE IS 29.61 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 32 atoms have been selected out of 32 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : 2.927865 4.285707 0.000000 5.190345 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MADE" + RDCMND substituted energy or value "?RDIP" to "5.19035" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 32 Number of groups = 1 + Number of bonds = 33 Number of angles = 30 + Number of dihedrals = 38 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 3 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 14 + + CHARMM> delete atom sele all end + SELRPN> 32 atoms have been selected out of 32 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 33 bonds deleted + DELTIC: 30 angles deleted + DELTIC: 38 dihedrals deleted + DELTIC: 2 improper dihedrals deleted + DELTIC: 2 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "3" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "3" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "3" + Parameter: RESI3 -> "CYTB" + Parameter: RESIDUE <- "CYTB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "CYTB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "CYTB" + Drude polarizability will be setup for SEGID: CYTB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 8 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is CYTB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 1 + Number of bonds = 24 Number of angles = 19 + Number of dihedrals = 24 Number of impropers = 4 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 8 + Number of true-bonds = 24 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 3 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "3" + Parameter: SEED3 -> "1 C2 1 N1 1 C6" + + CHARMM> ic build + **** WARNING **** 11 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 140 exclusions and 70 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 136 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 136 atom pairs and 210 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 136 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -88.16389 202.63491 22.67213 +ENER INTERN> 2.94944 3.89033 0.00131 -0.00000 0.00000 +ENER EXTERN> 8.05772 -103.06269 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "CYTB" + RDCMND substituted energy or value "?ENER" to "-88.1639" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 0.00000000 0.00000001 + 67.09200065 -1.70808776 + 37.71605703 + + Transpose of the rotation matrix + 0.057853 -0.998325 0.000000 + 0.998325 0.057853 0.000000 + -0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.37318 1.20215 -0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 -1.000000 ANGLE IS 86.68 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 24 atoms have been selected out of 24 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -5.767536 5.335549 0.000000 7.857006 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "CYTB" + RDCMND substituted energy or value "?RDIP" to "7.85701" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 1 + Number of bonds = 24 Number of angles = 19 + Number of dihedrals = 24 Number of impropers = 4 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 11 + + CHARMM> delete atom sele all end + SELRPN> 24 atoms have been selected out of 24 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 24 bonds deleted + DELTIC: 19 angles deleted + DELTIC: 24 dihedrals deleted + DELTIC: 4 improper dihedrals deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "4" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "4" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "4" + Parameter: RESI4 -> "MCYT" + Parameter: RESIDUE <- "MCYT" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MCYT" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MCYT" + Drude polarizability will be setup for SEGID: MCYT mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MCYT. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 28 Number of angles = 25 + Number of dihedrals = 30 Number of impropers = 4 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 9 + Number of true-bonds = 28 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 3 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "4" + Parameter: SEED4 -> "1 C2 1 N1 1 C6" + + CHARMM> ic build + **** WARNING **** 12 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 253 253 252 + : Ran out of space. RESIZING + with mode 5 found 162 exclusions and 92 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 216 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 216 atom pairs and 254 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 216 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -63.90105 -24.26284 32.10691 +ENER INTERN> 3.85040 4.17636 0.19111 -0.00000 0.00000 +ENER EXTERN> 18.56121 -90.68013 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MCYT" + RDCMND substituted energy or value "?ENER" to "-63.901" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.74312132 -0.00000000 0.00000002 + 92.58423727 -18.88091107 + 50.12631667 + + Transpose of the rotation matrix + 0.355512 -0.934672 0.000000 + 0.934672 0.355512 0.000000 + -0.000000 -0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.62762 0.81804 -0.00000 + AXIS OF ROTATION IS 0.000000 -0.000000 -1.000000 ANGLE IS 69.18 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 28 atoms have been selected out of 28 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.081636 7.131491 0.000000 7.768825 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MCYT" + RDCMND substituted energy or value "?RDIP" to "7.76883" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 28 Number of angles = 25 + Number of dihedrals = 30 Number of impropers = 4 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 2 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 12 + + CHARMM> delete atom sele all end + SELRPN> 28 atoms have been selected out of 28 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 28 bonds deleted + DELTIC: 25 angles deleted + DELTIC: 30 dihedrals deleted + DELTIC: 4 improper dihedrals deleted + DELTIC: 2 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "5" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "5" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "5" + Parameter: RESI5 -> "THYB" + Parameter: RESIDUE <- "THYB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "THYB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "THYB" + Drude polarizability will be setup for SEGID: THYB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is THYB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 28 Number of angles = 24 + Number of dihedrals = 30 Number of impropers = 4 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 9 + Number of true-bonds = 28 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "5" + Parameter: SEED5 -> "1 C2 1 N1 1 C6" + + CHARMM> ic build + **** WARNING **** 13 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 253 253 252 + : Ran out of space. RESIZING + with mode 5 found 160 exclusions and 99 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 218 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 218 atom pairs and 259 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 218 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -81.16106 17.26001 30.37213 +ENER INTERN> 4.73626 6.60534 0.00306 2.76038 0.00003 +ENER EXTERN> 4.39442 -99.66054 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "THYB" + RDCMND substituted energy or value "?ENER" to "-81.1611" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 1.60597741 0.10168424 0.09933096 + 89.04602142 18.76374187 + 55.00978719 + + Transpose of the rotation matrix + 0.405086 0.914277 0.001391 + -0.914277 0.405088 -0.001101 + -0.001570 -0.000826 0.999998 + CENTER OF ATOMS BEFORE TRANSLATION 0.67957 1.59866 0.00356 + AXIS OF ROTATION IS -0.000150 -0.001619 0.999999 ANGLE IS 66.10 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 28 atoms have been selected out of 28 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : 0.375937 -5.925024 0.022415 5.936981 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "THYB" + RDCMND substituted energy or value "?RDIP" to "5.93698" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 28 Number of groups = 1 + Number of bonds = 28 Number of angles = 24 + Number of dihedrals = 30 Number of impropers = 4 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 13 + + CHARMM> delete atom sele all end + SELRPN> 28 atoms have been selected out of 28 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 28 bonds deleted + DELTIC: 24 angles deleted + DELTIC: 30 dihedrals deleted + DELTIC: 4 improper dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "6" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "6" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "6" + Parameter: RESI6 -> "MTHY" + Parameter: RESIDUE <- "MTHY" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "MTHY" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "MTHY" + Drude polarizability will be setup for SEGID: MTHY mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 10 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is MTHY. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 32 Number of groups = 1 + Number of bonds = 32 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 4 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 10 + Number of true-bonds = 32 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "6" + Parameter: SEED6 -> "1 C2 1 N1 1 C6" + + CHARMM> ic build + **** WARNING **** 14 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 289 289 288 + : Ran out of space. RESIZING + with mode 5 found 182 exclusions and 120 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 314 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 314 atom pairs and 302 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 314 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -47.50003 -33.66103 36.42999 +ENER INTERN> 6.96105 8.56828 0.07181 2.76036 0.00003 +ENER EXTERN> 13.39911 -79.26066 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "MTHY" + RDCMND substituted energy or value "?ENER" to "-47.5" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 3.34914522 0.14015668 0.06818214 + 124.62276064 0.11428790 + 61.04749971 + + Transpose of the rotation matrix + 0.001799 0.999998 0.001157 + -0.999998 0.001800 -0.001177 + -0.001179 -0.001155 0.999999 + CENTER OF ATOMS BEFORE TRANSLATION 0.82913 1.22102 0.00311 + AXIS OF ROTATION IS -0.000011 -0.001168 0.999999 ANGLE IS 89.90 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 32 atoms have been selected out of 32 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -2.635251 -5.941221 0.025291 6.499484 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "MTHY" + RDCMND substituted energy or value "?RDIP" to "6.49948" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 32 Number of groups = 1 + Number of bonds = 32 Number of angles = 30 + Number of dihedrals = 36 Number of impropers = 4 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 14 + + CHARMM> delete atom sele all end + SELRPN> 32 atoms have been selected out of 32 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 32 bonds deleted + DELTIC: 30 angles deleted + DELTIC: 36 dihedrals deleted + DELTIC: 4 improper dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "7" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "7" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "7" + Parameter: RESI7 -> "GUAB" + Parameter: RESIDUE <- "GUAB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "GUAB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "GUAB" + Drude polarizability will be setup for SEGID: GUAB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 11 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is GUAB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 31 Number of groups = 1 + Number of bonds = 32 Number of angles = 26 + Number of dihedrals = 36 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 11 + Number of true-bonds = 32 Number of zero-bonds = 0 + Number of aniso. terms = 3 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "7" + Parameter: SEED7 -> "1 C4 1 N9 1 C8" + + CHARMM> ic build + **** WARNING **** 15 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 294 294 288 + : Ran out of space. RESIZING + with mode 5 found 198 exclusions and 117 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 267 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 267 atom pairs and 315 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 267 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -92.12292 44.62289 24.18966 +ENER INTERN> 4.85395 8.46346 1.89423 0.00000 0.00000 +ENER EXTERN> 5.22047 -112.55502 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "GUAB" + RDCMND substituted energy or value "?ENER" to "-92.1229" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 -0.00000004 -0.00000002 + 77.37999615 19.75370457 + 103.31389267 + + Transpose of the rotation matrix + 0.879989 0.474994 -0.000000 + -0.474994 0.879989 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION -0.89983 0.52644 0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 1.000000 ANGLE IS 28.36 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 31 atoms have been selected out of 31 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -4.509542 -6.868639 -0.000000 8.216701 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "GUAB" + RDCMND substituted energy or value "?RDIP" to "8.2167" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 31 Number of groups = 1 + Number of bonds = 32 Number of angles = 26 + Number of dihedrals = 36 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 3 Number of HB donors = 3 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 15 + + CHARMM> delete atom sele all end + SELRPN> 31 atoms have been selected out of 31 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 32 bonds deleted + DELTIC: 26 angles deleted + DELTIC: 36 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 3 donors deleted + DELTIC: 3 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "8" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "8" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "8" + Parameter: RESI8 -> "URAB" + Parameter: RESIDUE <- "URAB" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "URAB" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "URAB" + Drude polarizability will be setup for SEGID: URAB mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 8 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is URAB. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 1 + Number of bonds = 24 Number of angles = 18 + Number of dihedrals = 24 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 8 + Number of true-bonds = 24 Number of zero-bonds = 0 + Number of aniso. terms = 2 Number of lone-pairs = 4 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "8" + Parameter: SEED8 -> "1 C2 1 N1 1 C6" + + CHARMM> ic build + **** WARNING **** 12 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 138 exclusions and 78 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 138 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 138 atom pairs and 216 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 138 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -97.16257 5.03965 27.12192 +ENER INTERN> 2.20193 4.31936 0.00000 0.00000 0.00000 +ENER EXTERN> 3.92548 -107.60934 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "URAB" + RDCMND substituted energy or value "?ENER" to "-97.1626" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00000000 -0.00000000 0.00000000 + 62.86081494 0.14033382 + 38.36646335 + + Transpose of the rotation matrix + 0.005729 0.999984 0.000000 + -0.999984 0.005729 -0.000000 + 0.000000 0.000000 1.000000 + CENTER OF ATOMS BEFORE TRANSLATION 0.38591 1.20864 -0.00000 + AXIS OF ROTATION IS -0.000000 0.000000 1.000000 ANGLE IS 89.67 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 24 atoms have been selected out of 24 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -0.000000 + DIPOLE MOMENT (DEBYES) : -2.040337 -4.110403 0.000000 4.588942 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "URAB" + RDCMND substituted energy or value "?RDIP" to "4.58894" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 24 Number of groups = 1 + Number of bonds = 24 Number of angles = 18 + Number of dihedrals = 24 Number of impropers = 2 + Number of cross-terms = 0 + Number of HB acceptors = 2 Number of HB donors = 1 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 12 + + CHARMM> delete atom sele all end + SELRPN> 24 atoms have been selected out of 24 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 24 bonds deleted + DELTIC: 18 angles deleted + DELTIC: 24 dihedrals deleted + DELTIC: 2 improper dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 2 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "9" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "9" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "9" + Parameter: RESI9 -> "T3PS" + Parameter: RESIDUE <- "T3PS" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "T3PS" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "T3PS" + Drude polarizability will be setup for SEGID: T3PS mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 16 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is T3PS. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 54 Number of groups = 6 + Number of bonds = 55 Number of angles = 64 + Number of dihedrals = 87 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 16 + Number of true-bonds = 55 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 6 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "9" + Parameter: SEED9 -> "1 C4A 1 O4A 1 C1A" + + CHARMM> ic build + **** WARNING **** 22 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 499 499 495 + : Ran out of space. RESIZING + with mode 5 found 376 exclusions and 203 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1055 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 1055 atom pairs and 579 atom exclusions. + There are 0 group pairs and 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1055 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 196.75493 -293.91750 60.08536 +ENER INTERN> 156.89153 29.62032 2.06443 35.60340 0.00000 +ENER EXTERN> -0.30943 -27.11533 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "T3PS" + RDCMND substituted energy or value "?ENER" to "196.755" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 147.94623283 210.47850057 12.87108609 + 440.67919480 10.91530844 + 106.28325351 + + Transpose of the rotation matrix + 0.035125 0.885515 0.463282 + -0.995103 0.073845 -0.065701 + -0.092390 -0.458705 0.883772 + CENTER OF ATOMS BEFORE TRANSLATION 0.21542 3.86701 1.51667 + AXIS OF ROTATION IS 0.196504 -0.277838 0.940315 ANGLE IS 90.21 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 54 atoms have been selected out of 54 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : 5.975199 -17.199125 -0.362594 18.211106 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "T3PS" + RDCMND substituted energy or value "?RDIP" to "18.2111" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 54 Number of groups = 6 + Number of bonds = 55 Number of angles = 64 + Number of dihedrals = 87 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 22 + + CHARMM> delete atom sele all end + SELRPN> 54 atoms have been selected out of 54 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 55 bonds deleted + DELTIC: 64 angles deleted + DELTIC: 87 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "10" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "10" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "10" + Parameter: RESI10 -> "T3PM" + Parameter: RESIDUE <- "T3PM" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "T3PM" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "T3PM" + Drude polarizability will be setup for SEGID: T3PM mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 11 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is T3PM. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 35 Number of groups = 3 + Number of bonds = 35 Number of angles = 39 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 11 + Number of true-bonds = 35 Number of zero-bonds = 0 + Number of aniso. terms = 5 Number of lone-pairs = 3 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "10" + Parameter: SEED10 -> "1 C4' 1 O4' 1 C1'" + + CHARMM> ic build + **** WARNING **** 14 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 319 319 315 + : Ran out of space. RESIZING + with mode 5 found 222 exclusions and 107 interactions(1-4) + found 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 373 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 373 atom pairs and 329 atom exclusions. + There are 0 group pairs and 3 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 373 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1.07209 195.68284 27.09836 +ENER INTERN> 1.45521 14.49061 1.55442 16.35232 0.00000 +ENER EXTERN> 1.12299 -33.90346 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "T3PM" + RDCMND substituted energy or value "?ENER" to "1.07209" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 120.33856953 29.37686018 -6.50543517 + 35.85213209 -1.20393133 + 53.52723760 + + Transpose of the rotation matrix + 0.085450 -0.297448 -0.950906 + 0.995888 0.054321 0.072500 + 0.030089 -0.953191 0.300867 + CENTER OF ATOMS BEFORE TRANSLATION 0.63134 1.28222 1.69743 + AXIS OF ROTATION IS 0.534163 0.510886 -0.673547 ANGLE IS 106.24 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 35 atoms have been selected out of 35 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : 10.956798 9.092318 -0.493791 14.246596 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "T3PM" + RDCMND substituted energy or value "?RDIP" to "14.2466" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 35 Number of groups = 3 + Number of bonds = 35 Number of angles = 39 + Number of dihedrals = 45 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 14 + + CHARMM> delete atom sele all end + SELRPN> 35 atoms have been selected out of 35 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 35 bonds deleted + DELTIC: 39 angles deleted + DELTIC: 45 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "11" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "11" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "11" + Parameter: RESI11 -> "DMPN" + Parameter: RESIDUE <- "DMPN" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "DMPN" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "DMPN" + Drude polarizability will be setup for SEGID: DMPN mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 7 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DMPN. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 20 Number of groups = 1 + Number of bonds = 19 Number of angles = 20 + Number of dihedrals = 12 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 7 + Number of true-bonds = 19 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 0 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "11" + Parameter: SEED11 -> "1 O11 1 P 1 O12" + + CHARMM> ic build + **** WARNING **** 7 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 93 exclusions and 36 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 97 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 97 atom pairs and 129 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 97 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -5.02073 6.09282 32.34830 +ENER INTERN> 0.21668 4.74356 0.00076 24.70545 0.00000 +ENER EXTERN> 2.95688 -37.64407 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "DMPN" + RDCMND substituted energy or value "?ENER" to "-5.02073" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 28.06866372 13.44404993 16.82290468 + 27.05665391 4.94614215 + 29.28376479 + + Transpose of the rotation matrix + 0.584313 0.467105 0.663620 + -0.624248 0.781226 -0.000239 + -0.518550 -0.414124 0.748069 + CENTER OF ATOMS BEFORE TRANSLATION 0.98747 0.74645 -0.00022 + AXIS OF ROTATION IS 0.249135 -0.711599 0.656932 ANGLE IS 56.16 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 20 atoms have been selected out of 20 + THE TOTAL CHARGE OF SELECTED ATOMS IS: -1.000000 + DIPOLE MOMENT (DEBYES) : -0.000715 8.193310 0.001167 8.193310 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "DMPN" + RDCMND substituted energy or value "?RDIP" to "8.19331" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 20 Number of groups = 1 + Number of bonds = 19 Number of angles = 20 + Number of dihedrals = 12 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 7 + + CHARMM> delete atom sele all end + SELRPN> 20 atoms have been selected out of 20 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 19 bonds deleted + DELTIC: 20 angles deleted + DELTIC: 12 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "12" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "12" and "12". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> set residue @resi@@count + Parameter: COUNT -> "12" + Parameter: RESI12 -> "BDEONA" + Parameter: RESIDUE <- "BDEONA" + + CHARMM> read sequence @residue 1 + Parameter: RESIDUE -> "BDEONA" + + CHARMM> + + CHARMM> bomlev @boml + Parameter: BOML -> "0" + + CHARMM> generate @residue first none last none setup warn drude dmass 0.4 !show + Parameter: RESIDUE -> "BDEONA" + Drude polarizability will be setup for SEGID: BDEONA mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 9 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is BDEONA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 37 Number of groups = 4 + Number of bonds = 37 Number of angles = 34 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 9 + Number of true-bonds = 37 Number of zero-bonds = 0 + Number of aniso. terms = 4 Number of lone-pairs = 9 + + CHARMM> bomlev 0 + + CHARMM> + + CHARMM> ic param + + CHARMM> ic seed @seed@@count + Parameter: COUNT -> "12" + Parameter: SEED12 -> "1 C4 1 O4 1 C1" + + CHARMM> ic build + **** WARNING **** 18 COORDINATES ARE STILL UNDEFINED + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 338 338 333 + : Ran out of space. RESIZING + with mode 5 found 273 exclusions and 181 interactions(1-4) + found 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 393 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> if @mindr eq 0 then + Parameter: MINDR -> "0" + Comparing "0" and "0". + IF test evaluated as true. Performing command + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 393 atom pairs and 454 atom exclusions. + There are 0 group pairs and 6 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 70689 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 393 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 21.77658 -26.79731 15.18274 +ENER INTERN> 1.57384 5.86933 1.40951 24.26294 0.00000 +ENER EXTERN> -0.11756 -11.22148 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> else + Skip commands until next ENDIF + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BDEONA" + RDCMND substituted energy or value "?ENER" to "21.7766" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if @mini ne 0 then + Parameter: MINI -> "0" + Comparing "0" and "0". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor orient + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 16.23847189 -7.29382929 0.13171513 + 68.33985015 35.64849322 + 106.95085941 + + Transpose of the rotation matrix + 0.857380 0.513661 -0.032424 + -0.509661 0.838548 -0.192570 + -0.071727 0.181631 0.980747 + CENTER OF ATOMS BEFORE TRANSLATION 0.22134 0.52244 -0.44461 + AXIS OF ROTATION IS -0.343209 -0.036047 0.938567 ANGLE IS 33.04 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor dipole oxyz select all end + SELRPN> 37 atoms have been selected out of 37 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT (DEBYES) : -3.826223 -1.591916 0.624671 4.190990 + + CHARMM> echo @residue dipole: ?rdip + Parameter: RESIDUE -> "BDEONA" + RDCMND substituted energy or value "?RDIP" to "4.19099" + + CHARMM> !! Check molecular polarizability + CHARMM> !VIBRAN + CHARMM> !diag dscf fini step 0.001 + CHARMM> !END + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 37 Number of groups = 4 + Number of bonds = 37 Number of angles = 34 + Number of dihedrals = 51 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 18 + + CHARMM> delete atom sele all end + SELRPN> 37 atoms have been selected out of 37 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 1 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 37 bonds deleted + DELTIC: 34 angles deleted + DELTIC: 51 dihedrals deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr count + Parameter: COUNT <- "13" + + CHARMM> if count le @nres goto loop_na2 + Parameter: NRES -> "12" + Comparing "13" and "12". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> + + CHARMM> !oligonucleotides, RNA not yet tested + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * 1BNA, STRAND 1 + RDTITL> * + + SEQRDR> 12 + + SEQRDR> cyt gua cyt gua ade ade thy thy cyt gua cyt gua + + RESIDUE SEQUENCE -- 12 RESIDUES + CYT GUA CYT GUA ADE ADE THY THY CYT GUA CYT GUA + + CHARMM> + + CHARMM> generate a first 5ter last 3ter setup warn drude dmass 0.4 !show + Drude polarizability will be setup for SEGID: A mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 CYT . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 12 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 255 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is A. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 752 Number of groups = 57 + Number of bonds = 781 Number of angles = 750 + Number of dihedrals = 1114 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 100 Number of HB donors = 38 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 255 + Number of true-bonds = 781 Number of zero-bonds = 0 + Number of aniso. terms = 100 Number of lone-pairs = 106 + + CHARMM> + + CHARMM> ! patch for deoxy + CHARMM> patch deox a 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 1 CYT O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 1 CYT LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 1 CYT LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 1 CYT DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 748 Number of groups = 57 + Number of bonds = 777 Number of angles = 746 + Number of dihedrals = 1105 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 99 Number of HB donors = 37 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 255 + Number of true-bonds = 781 Number of zero-bonds = -4 + Number of aniso. terms = 99 Number of lone-pairs = 104 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 2 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 2 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 2 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 2 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 744 Number of groups = 57 + Number of bonds = 773 Number of angles = 742 + Number of dihedrals = 1096 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 98 Number of HB donors = 36 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 256 + Number of true-bonds = 777 Number of zero-bonds = -4 + Number of aniso. terms = 98 Number of lone-pairs = 102 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 3 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 3 CYT O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 3 CYT LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 3 CYT LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 3 CYT DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 740 Number of groups = 57 + Number of bonds = 769 Number of angles = 738 + Number of dihedrals = 1087 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 97 Number of HB donors = 35 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 257 + Number of true-bonds = 773 Number of zero-bonds = -4 + Number of aniso. terms = 97 Number of lone-pairs = 100 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 4 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 4 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 4 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 4 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 4 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 736 Number of groups = 57 + Number of bonds = 765 Number of angles = 734 + Number of dihedrals = 1078 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 96 Number of HB donors = 34 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 258 + Number of true-bonds = 769 Number of zero-bonds = -4 + Number of aniso. terms = 96 Number of lone-pairs = 98 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 5 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 5 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 5 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 5 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 5 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 732 Number of groups = 57 + Number of bonds = 761 Number of angles = 730 + Number of dihedrals = 1069 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 95 Number of HB donors = 33 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 259 + Number of true-bonds = 765 Number of zero-bonds = -4 + Number of aniso. terms = 95 Number of lone-pairs = 96 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 6 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 6 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 6 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 6 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 6 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 728 Number of groups = 57 + Number of bonds = 757 Number of angles = 726 + Number of dihedrals = 1060 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 94 Number of HB donors = 32 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 260 + Number of true-bonds = 761 Number of zero-bonds = -4 + Number of aniso. terms = 94 Number of lone-pairs = 94 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 7 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 7 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 7 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 7 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 7 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 724 Number of groups = 57 + Number of bonds = 753 Number of angles = 722 + Number of dihedrals = 1051 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 93 Number of HB donors = 32 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 261 + Number of true-bonds = 757 Number of zero-bonds = -4 + Number of aniso. terms = 93 Number of lone-pairs = 92 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 8 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 8 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 8 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 8 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 8 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 720 Number of groups = 57 + Number of bonds = 749 Number of angles = 718 + Number of dihedrals = 1042 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 92 Number of HB donors = 32 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 262 + Number of true-bonds = 753 Number of zero-bonds = -4 + Number of aniso. terms = 92 Number of lone-pairs = 90 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 9 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 9 CYT O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 9 CYT LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 9 CYT LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 9 CYT DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 716 Number of groups = 57 + Number of bonds = 745 Number of angles = 714 + Number of dihedrals = 1033 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 91 Number of HB donors = 31 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 263 + Number of true-bonds = 749 Number of zero-bonds = -4 + Number of aniso. terms = 91 Number of lone-pairs = 88 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 10 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 10 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 10 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 10 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 10 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 712 Number of groups = 57 + Number of bonds = 741 Number of angles = 710 + Number of dihedrals = 1024 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 90 Number of HB donors = 30 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 264 + Number of true-bonds = 745 Number of zero-bonds = -4 + Number of aniso. terms = 90 Number of lone-pairs = 86 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 11 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 11 CYT O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 11 CYT LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 11 CYT LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 11 CYT DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 708 Number of groups = 57 + Number of bonds = 737 Number of angles = 706 + Number of dihedrals = 1015 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 89 Number of HB donors = 29 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 265 + Number of true-bonds = 741 Number of zero-bonds = -4 + Number of aniso. terms = 89 Number of lone-pairs = 84 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox a 12 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM A 12 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM A 12 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM A 12 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM A 12 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 704 Number of groups = 57 + Number of bonds = 733 Number of angles = 702 + Number of dihedrals = 1006 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 88 Number of HB donors = 28 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 266 + Number of true-bonds = 737 Number of zero-bonds = -4 + Number of aniso. terms = 88 Number of lone-pairs = 82 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> autogenerate angles dihedrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 704 Number of groups = 57 + Number of bonds = 733 Number of angles = 738 + Number of dihedrals = 1078 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 88 Number of HB donors = 28 + Number of NB exclusions = 0 Total charge = -11.00000 + Number of Drudes = 267 + Number of true-bonds = 733 Number of zero-bonds = 0 + Number of aniso. terms = 88 Number of lone-pairs = 82 + + CHARMM> + + CHARMM> ic para + + CHARMM> ic seed 1 C5' 1 C4' 1 C3' + + CHARMM> ic build + **** WARNING **** 325 COORDINATES ARE STILL UNDEFINED + + CHARMM> + + CHARMM> coor sdrude + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> coor print + + COORDINATE FILE MODULE + TITLE> * $ID: TEST_DRUDE_ALL.INP 28 2015-07-29 23:54:15Z ALEX $ + TITLE> * MASTER TEST CASE FOR DRUDE + TITLE> * + 704 EXT + 1 1 CYT H5T -1.4336255804 0.6575674293 -1.1389401969 A 1 0.0000000000 + 2 1 CYT O5' -0.4648085703 0.6815132066 -1.1804154998 A 1 0.0000000000 + 3 1 CYT DO5' -0.4648085703 0.6815132066 -1.1804154998 A 1 0.0000000000 + 4 1 CYT C5' 0.0000000000 0.0000000000 0.0000000000 A 1 0.0000000000 + 5 1 CYT DC5' 0.0000000000 0.0000000000 0.0000000000 A 1 0.0000000000 + 6 1 CYT H5' -0.2820545856 -1.0745271547 -0.0125540686 A 1 0.0000000000 + 7 1 CYT H5'' -0.2820545856 0.5481357197 0.9242907787 A 1 0.0000000000 + 8 1 CYT LP5A -0.4980126118 1.0238755213 -1.1157197727 A 1 0.0000000000 + 9 1 CYT LP5B -0.4980126118 0.4543039061 -1.4445620981 A 1 0.0000000000 + 10 1 CYT N1 2.1648554673 -0.1529178883 -3.3490717991 A 1 0.0000000000 + 11 1 CYT DN1 2.1648554673 -0.1529178883 -3.3490717991 A 1 0.0000000000 + 12 1 CYT C6 1.0302004405 0.5296686041 -3.6763784602 A 1 0.0000000000 + 13 1 CYT DC6 1.0302004405 0.5296686041 -3.6763784602 A 1 0.0000000000 + 14 1 CYT H6 0.6013362472 1.1624016052 -2.9134076527 A 1 0.0000000000 + 15 1 CYT C2 2.7743820643 -0.9815933180 -4.2663968504 A 1 0.0000000000 + 16 1 CYT DC2 2.7743820643 -0.9815933180 -4.2663968504 A 1 0.0000000000 + 17 1 CYT O2 3.8024244708 -1.5882743484 -3.9419959598 A 1 0.0000000000 + 18 1 CYT DO2 3.8024244708 -1.5882743484 -3.9419959598 A 1 0.0000000000 + 19 1 CYT LP2A 3.9157685741 -1.7833610239 -4.2095670780 A 1 0.0000000000 + 20 1 CYT LP2B 3.8880519502 -1.5106072307 -3.6116389505 A 1 0.0000000000 + 21 1 CYT N3 2.2273710116 -1.1075117542 -5.5007628640 A 1 0.0000000000 + 22 1 CYT DN3 2.2273710116 -1.1075117542 -5.5007628640 A 1 0.0000000000 + 23 1 CYT LP3 2.3738798024 -1.3152036639 -5.7413854833 A 1 0.0000000000 + 24 1 CYT C4 1.1174599986 -0.4352774321 -5.8102052002 A 1 0.0000000000 + 25 1 CYT DC4 1.1174599986 -0.4352774321 -5.8102052002 A 1 0.0000000000 + 26 1 CYT N4 0.5968940815 -0.5757198546 -7.0336658870 A 1 0.0000000000 + 27 1 CYT DN4 0.5968940815 -0.5757198546 -7.0336658870 A 1 0.0000000000 + 28 1 CYT H41 1.0571325666 -1.1872289933 -7.6927084577 A 1 0.0000000000 + 29 1 CYT H42 -0.2425668157 -0.0796397511 -7.2969336840 A 1 0.0000000000 + 30 1 CYT C5 0.4823826963 0.4129337870 -4.8903956354 A 1 0.0000000000 + 31 1 CYT DC5 0.4823826963 0.4129337870 -4.8903956354 A 1 0.0000000000 + 32 1 CYT H5 -0.4151426357 0.9422441125 -5.1744358751 A 1 0.0000000000 + 33 1 CYT C4' 1.5280000000 0.0000000000 0.0000000000 A 1 0.0000000000 + 34 1 CYT DC4' 1.5280000000 0.0000000000 0.0000000000 A 1 0.0000000000 + 35 1 CYT H4' 1.9223792379 -0.5841549819 0.8445282552 A 1 0.0000000000 + 36 1 CYT O4' 2.0077260724 -0.6292226946 -1.2236721522 A 1 0.0000000000 + 37 1 CYT DO4' 2.0077260724 -0.6292226946 -1.2236721522 A 1 0.0000000000 + 38 1 CYT LPRA 1.7173792175 -0.6553625944 -1.4173611025 A 1 0.0000000000 + 39 1 CYT LPRB 2.2735941540 -0.8270268007 -1.1110324665 A 1 0.0000000000 + 40 1 CYT LPX 2.0179505217 -0.5356843417 -1.1898189813 A 1 0.0000000000 + 41 1 CYT C1' 2.6353660821 0.0947449509 -1.9576009803 A 1 0.0000000000 + 42 1 CYT DC1' 2.6353660821 0.0947449509 -1.9576009803 A 1 0.0000000000 + 43 1 CYT H1' 3.6798680499 -0.2327942716 -1.8492787900 A 1 0.0000000000 + 44 1 CYT C2' 2.4537820544 1.5370555862 -1.4964098245 A 1 0.0000000000 + 45 1 CYT DC2' 2.4537820544 1.5370555862 -1.4964098245 A 1 0.0000000000 + 46 1 CYT H2'' 1.5729875190 1.9495528387 -2.0102648655 A 1 0.0000000000 + 47 1 CYT H2' 3.3958309942 2.0739476954 -1.6815871939 A 1 0.0000000000 + 48 1 CYT C3' 2.1958276598 1.3632058600 0.0000000000 A 1 0.0000000000 + 49 1 CYT DC3' 2.1958276598 1.3632058600 0.0000000000 A 1 0.0000000000 + 50 1 CYT H3' 1.5032053044 2.1494580709 0.3347861013 A 1 0.0000000000 + 51 1 CYT O3' 3.3464683640 1.4713423082 0.8271287194 A 1 0.0000000000 + 52 1 CYT DO3' 3.3464683640 1.4713423082 0.8271287194 A 1 0.0000000000 + 53 2 GUA P 4.4515136773 2.5754544515 0.4805291801 A 2 0.0000000000 + 54 2 GUA DP 4.4515136773 2.5754544515 0.4805291801 A 2 0.0000000000 + 55 2 GUA O1P 3.8496947225 3.6301449796 -0.3658949898 A 2 0.0000000000 + 56 2 GUA DO1P 3.8496947225 3.6301449796 -0.3658949898 A 2 0.0000000000 + 57 2 GUA O2P 5.0954202192 3.0425811269 1.7286770257 A 2 0.0000000000 + 58 2 GUA DO2P 5.0954202192 3.0425811269 1.7286770257 A 2 0.0000000000 + 59 2 GUA O5' 5.4945769966 1.7214088966 -0.3804849094 A 2 0.0000000000 + 60 2 GUA DO5' 5.4945769966 1.7214088966 -0.3804849094 A 2 0.0000000000 + 61 2 GUA C5' 5.9141299062 0.4334002262 0.1082860298 A 2 0.0000000000 + 62 2 GUA DC5' 5.9141299062 0.4334002262 0.1082860298 A 2 0.0000000000 + 63 2 GUA H5' 5.3341922308 -0.3642842099 -0.4032731878 A 2 0.0000000000 + 64 2 GUA H5'' 5.9065160396 0.4378554165 1.2192510068 A 2 0.0000000000 + 65 2 GUA N9 7.5311512169 1.8277386039 -3.2561158623 A 2 0.0000000000 + 66 2 GUA DN9 7.5311512169 1.8277386039 -3.2561158623 A 2 0.0000000000 + 67 2 GUA C4 7.7721362811 1.5687103575 -4.5882350223 A 2 0.0000000000 + 68 2 GUA DC4 7.7721362811 1.5687103575 -4.5882350223 A 2 0.0000000000 + 69 2 GUA N3 8.6678210502 0.6770868175 -5.0768875137 A 2 0.0000000000 + 70 2 GUA DN3 8.6678210502 0.6770868175 -5.0768875137 A 2 0.0000000000 + 71 2 GUA LP3 8.8762375212 0.4745358920 -4.8818600869 A 2 0.0000000000 + 72 2 GUA C2 8.6681244554 0.6556405127 -6.4037141655 A 2 0.0000000000 + 73 2 GUA DC2 8.6681244554 0.6556405127 -6.4037141655 A 2 0.0000000000 + 74 2 GUA N1 7.8568503051 1.4437198862 -7.1856285816 A 2 0.0000000000 + 75 2 GUA DN1 7.8568503051 1.4437198862 -7.1856285816 A 2 0.0000000000 + 76 2 GUA H1 7.9413560835 1.3440486131 -8.2073058353 A 2 0.0000000000 + 77 2 GUA N2 9.4974570669 -0.1730947517 -7.0546260496 A 2 0.0000000000 + 78 2 GUA DN2 9.4974570669 -0.1730947517 -7.0546260496 A 2 0.0000000000 + 79 2 GUA H21 9.5890408018 -0.2794081192 -8.0548309723 A 2 0.0000000000 + 80 2 GUA H22 10.0947752211 -0.7534030331 -6.4831776082 A 2 0.0000000000 + 81 2 GUA C6 6.9316201494 2.3644627941 -6.6991816096 A 2 0.0000000000 + 82 2 GUA DC6 6.9316201494 2.3644627941 -6.6991816096 A 2 0.0000000000 + 83 2 GUA O6 6.2454072667 3.0290217128 -7.4882280742 A 2 0.0000000000 + 84 2 GUA DO6 6.2454072667 3.0290217128 -7.4882280742 A 2 0.0000000000 + 85 2 GUA LP6A 6.0320309279 3.2424012151 -7.3109155647 A 2 0.0000000000 + 86 2 GUA LP6B 6.3261855104 2.9440560730 -7.8180093887 A 2 0.0000000000 + 87 2 GUA C5 6.9217010825 2.3967701046 -5.2862364752 A 2 0.0000000000 + 88 2 GUA DC5 6.9217010825 2.3967701046 -5.2862364752 A 2 0.0000000000 + 89 2 GUA N7 6.1571272534 3.1651313929 -4.4139607998 A 2 0.0000000000 + 90 2 GUA DN7 6.1571272534 3.1651313929 -4.4139607998 A 2 0.0000000000 + 91 2 GUA LP7 5.9119596027 3.4060015169 -4.4801000953 A 2 0.0000000000 + 92 2 GUA C8 6.5535503204 2.7928422052 -3.2287749440 A 2 0.0000000000 + 93 2 GUA DC8 6.5535503204 2.7928422052 -3.2287749440 A 2 0.0000000000 + 94 2 GUA H8 6.1689025293 3.1873904686 -2.2883081745 A 2 0.0000000000 + 95 2 GUA C4' 7.3584756348 0.1776782887 -0.2747644981 A 2 0.0000000000 + 96 2 GUA DC4' 7.3584756348 0.1776782887 -0.2747644981 A 2 0.0000000000 + 97 2 GUA H4' 7.6707149792 -0.8355775099 0.0181847781 A 2 0.0000000000 + 98 2 GUA O4' 7.4946476842 0.2714928877 -1.7225517180 A 2 0.0000000000 + 99 2 GUA DO4' 7.4946476842 0.2714928877 -1.7225517180 A 2 0.0000000000 + 100 2 GUA LPRA 7.1877762202 0.4079084863 -1.8211452728 A 2 0.0000000000 + 101 2 GUA LPRB 7.7054030368 0.0026425335 -1.7987204018 A 2 0.0000000000 + 102 2 GUA LPX 7.5347940713 0.3268090765 -1.6495559176 A 2 0.0000000000 + 103 2 GUA C1' 8.2153032940 1.1706452843 -2.1076070619 A 2 0.0000000000 + 104 2 GUA DC1' 8.2153032940 1.1706452843 -2.1076070619 A 2 0.0000000000 + 105 2 GUA H1' 9.1311854489 0.6662330075 -2.4492620538 A 2 0.0000000000 + 106 2 GUA C2' 8.5004474544 2.1130399171 -0.9429117481 A 2 0.0000000000 + 107 2 GUA DC2' 8.5004474544 2.1130399171 -0.9429117481 A 2 0.0000000000 + 108 2 GUA H2'' 7.7158878707 2.8839470593 -0.9299333977 A 2 0.0000000000 + 109 2 GUA H2' 9.5262789277 2.4933415689 -1.0571065034 A 2 0.0000000000 + 110 2 GUA C3' 8.3831406145 1.1776573207 0.2601281779 A 2 0.0000000000 + 111 2 GUA DC3' 8.3831406145 1.1776573207 0.2601281779 A 2 0.0000000000 + 112 2 GUA H3' 7.9828733044 1.7448405425 1.1134096517 A 2 0.0000000000 + 113 2 GUA O3' 9.6075429684 0.6081591988 0.7032085373 A 2 0.0000000000 + 114 2 GUA DO3' 9.6075429684 0.6081591988 0.7032085373 A 2 0.0000000000 + 115 3 CYT P 10.9282728191 1.5114755111 0.7067172807 A 3 0.0000000000 + 116 3 CYT DP 10.9282728191 1.5114755111 0.7067172807 A 3 0.0000000000 + 117 3 CYT O1P 10.5498316926 2.9424800985 0.7062433103 A 3 0.0000000000 + 118 3 CYT DO1P 10.5498316926 2.9424800985 0.7062433103 A 3 0.0000000000 + 119 3 CYT O2P 11.8201661037 1.0829284704 1.8074306006 A 3 0.0000000000 + 120 3 CYT DO2P 11.8201661037 1.0829284704 1.8074306006 A 3 0.0000000000 + 121 3 CYT O5' 11.5811698337 1.1248308745 -0.7014558526 A 3 0.0000000000 + 122 3 CYT DO5' 11.5811698337 1.1248308745 -0.7014558526 A 3 0.0000000000 + 123 3 CYT C5' 11.6783484864 -0.2644381317 -1.0680291029 A 3 0.0000000000 + 124 3 CYT DC5' 11.6783484864 -0.2644381317 -1.0680291029 A 3 0.0000000000 + 125 3 CYT H5' 10.8420840079 -0.5272584205 -1.7506038005 A 3 0.0000000000 + 126 3 CYT H5'' 11.8038229964 -0.8815906406 -0.1527696162 A 3 0.0000000000 + 127 3 CYT N1 13.2127545251 2.4782224780 -3.5205411555 A 3 0.0000000000 + 128 3 CYT DN1 13.2127545251 2.4782224780 -3.5205411555 A 3 0.0000000000 + 129 3 CYT C6 12.6280488181 3.1797549397 -2.5073938605 A 3 0.0000000000 + 130 3 CYT DC6 12.6280488181 3.1797549397 -2.5073938605 A 3 0.0000000000 + 131 3 CYT H6 12.6609440373 2.7379999071 -1.5224215788 A 3 0.0000000000 + 132 3 CYT C2 13.2138365242 2.9728862248 -4.8070159888 A 3 0.0000000000 + 133 3 CYT DC2 13.2138365242 2.9728862248 -4.8070159888 A 3 0.0000000000 + 134 3 CYT O2 13.7515771770 2.3150679829 -5.7060594532 A 3 0.0000000000 + 135 3 CYT DO2 13.7515771770 2.3150679829 -5.7060594532 A 3 0.0000000000 + 136 3 CYT LP2A 13.7240057669 2.4843790921 -6.0111390586 A 3 0.0000000000 + 137 3 CYT LP2B 13.8832251389 2.0184400082 -5.5749844414 A 3 0.0000000000 + 138 3 CYT N3 12.6236833670 4.1693950513 -5.0495482121 A 3 0.0000000000 + 139 3 CYT DN3 12.6236833670 4.1693950513 -5.0495482121 A 3 0.0000000000 + 140 3 CYT LP3 12.6181793876 4.3043435126 -5.3724392448 A 3 0.0000000000 + 141 3 CYT C4 12.0548001277 4.8470770068 -4.0512120827 A 3 0.0000000000 + 142 3 CYT DC4 12.0548001277 4.8470770068 -4.0512120827 A 3 0.0000000000 + 143 3 CYT N4 11.4792128775 6.0246228817 -4.3151325820 A 3 0.0000000000 + 144 3 CYT DN4 11.4792128775 6.0246228817 -4.3151325820 A 3 0.0000000000 + 145 3 CYT H41 11.4896529920 6.3713379598 -5.2636997428 A 3 0.0000000000 + 146 3 CYT H42 11.0405795558 6.5604764155 -3.5799035025 A 3 0.0000000000 + 147 3 CYT C5 12.0433733492 4.3603537825 -2.7352314524 A 3 0.0000000000 + 148 3 CYT DC5 12.0433733492 4.3603537825 -2.7352314524 A 3 0.0000000000 + 149 3 CYT H5 11.5736665542 4.9353146228 -1.9508874214 A 3 0.0000000000 + 150 3 CYT C4' 12.9375409929 -0.5010361023 -1.8784065655 A 3 0.0000000000 + 151 3 CYT DC4' 12.9375409929 -0.5010361023 -1.8784065655 A 3 0.0000000000 + 152 3 CYT H4' 12.9861798176 -1.5396808520 -2.2373652661 A 3 0.0000000000 + 153 3 CYT O4' 12.9221818965 0.3627401848 -3.0518998394 A 3 0.0000000000 + 154 3 CYT DO4' 12.9221818965 0.3627401848 -3.0518998394 A 3 0.0000000000 + 155 3 CYT LPRA 12.6563159360 0.5803679202 -2.9851655914 A 3 0.0000000000 + 156 3 CYT LPRB 13.0387359793 0.1517479244 -3.3056662907 A 3 0.0000000000 + 157 3 CYT LPX 12.9845474286 0.3599686375 -2.9737790423 A 3 0.0000000000 + 158 3 CYT C1' 13.8147906371 1.1861660457 -3.0880473917 A 3 0.0000000000 + 159 3 CYT DC1' 13.8147906371 1.1861660457 -3.0880473917 A 3 0.0000000000 + 160 3 CYT H1' 14.5058122323 0.8137959598 -3.8586508397 A 3 0.0000000000 + 161 3 CYT C2' 14.4879837721 1.2503972454 -1.7210743247 A 3 0.0000000000 + 162 3 CYT DC2' 14.4879837721 1.2503972454 -1.7210743247 A 3 0.0000000000 + 163 3 CYT H2'' 13.9577453500 2.0008271948 -1.1163412374 A 3 0.0000000000 + 164 3 CYT H2' 15.5582239154 1.4497964184 -1.8786370281 A 3 0.0000000000 + 165 3 CYT C3' 14.2568768662 -0.1621978910 -1.1851908126 A 3 0.0000000000 + 166 3 CYT DC3' 14.2568768662 -0.1621978910 -1.1851908126 A 3 0.0000000000 + 167 3 CYT H3' 14.1352135796 -0.1123529066 -0.0930765685 A 3 0.0000000000 + 168 3 CYT O3' 15.3164979606 -1.0787956275 -1.4236466067 A 3 0.0000000000 + 169 3 CYT DO3' 15.3164979606 -1.0787956275 -1.4236466067 A 3 0.0000000000 + 170 4 GUA P 16.8279695892 -0.5707783295 -1.2906355140 A 4 0.0000000000 + 171 4 GUA DP 16.8279695892 -0.5707783295 -1.2906355140 A 4 0.0000000000 + 172 4 GUA O1P 16.8677599524 0.6541464175 -0.4605944720 A 4 0.0000000000 + 173 4 GUA DO1P 16.8677599524 0.6541464175 -0.4605944720 A 4 0.0000000000 + 174 4 GUA O2P 17.6880668108 -1.6851704751 -0.8334058942 A 4 0.0000000000 + 175 4 GUA DO2P 17.6880668108 -1.6851704751 -0.8334058942 A 4 0.0000000000 + 176 4 GUA O5' 17.1751662810 -0.2060908702 -2.8089166718 A 4 0.0000000000 + 177 4 GUA DO5' 17.1751662810 -0.2060908702 -2.8089166718 A 4 0.0000000000 + 178 4 GUA C5' 16.8356454040 -1.1441991547 -3.8474572009 A 4 0.0000000000 + 179 4 GUA DC5' 16.8356454040 -1.1441991547 -3.8474572009 A 4 0.0000000000 + 180 4 GUA H5' 15.8845869237 -0.8341479429 -4.3308587039 A 4 0.0000000000 + 181 4 GUA H5'' 16.8908280571 -2.1784667657 -3.4455039904 A 4 0.0000000000 + 182 4 GUA N9 18.7728778097 2.1943567582 -4.8370594167 A 4 0.0000000000 + 183 4 GUA DN9 18.7728778097 2.1943567582 -4.8370594167 A 4 0.0000000000 + 184 4 GUA C4 18.7586652105 3.3163026336 -5.6375257462 A 4 0.0000000000 + 185 4 GUA DC4 18.7586652105 3.3163026336 -5.6375257462 A 4 0.0000000000 + 186 4 GUA N3 18.9824060110 3.3443050998 -6.9736323723 A 4 0.0000000000 + 187 4 GUA DN3 18.9824060110 3.3443050998 -6.9736323723 A 4 0.0000000000 + 188 4 GUA LP3 19.0536018611 3.0642634745 -7.1711363951 A 4 0.0000000000 + 189 4 GUA C2 18.9002616947 4.5756900454 -7.4613540419 A 4 0.0000000000 + 190 4 GUA DC2 18.9002616947 4.5756900454 -7.4613540419 A 4 0.0000000000 + 191 4 GUA N1 18.6217169330 5.6868929681 -6.7009160889 A 4 0.0000000000 + 192 4 GUA DN1 18.6217169330 5.6868929681 -6.7009160889 A 4 0.0000000000 + 193 4 GUA H1 18.5823649496 6.5950396588 -7.1852930182 A 4 0.0000000000 + 194 4 GUA N2 19.0951283003 4.7858227410 -8.7713739868 A 4 0.0000000000 + 195 4 GUA DN2 19.0951283003 4.7858227410 -8.7713739868 A 4 0.0000000000 + 196 4 GUA H21 19.0591144483 5.6706764794 -9.2570043650 A 4 0.0000000000 + 197 4 GUA H22 19.2999493316 3.9716230446 -9.3328249638 A 4 0.0000000000 + 198 4 GUA C6 18.3894600784 5.6749750673 -5.3274665204 A 4 0.0000000000 + 199 4 GUA DC6 18.3894600784 5.6749750673 -5.3274665204 A 4 0.0000000000 + 200 4 GUA O6 18.1459419306 6.7333793124 -4.7311441533 A 4 0.0000000000 + 201 4 GUA DO6 18.1459419306 6.7333793124 -4.7311441533 A 4 0.0000000000 + 202 4 GUA LP6A 18.0964152512 6.6701803230 -4.3904786344 A 4 0.0000000000 + 203 4 GUA LP6B 18.1484131796 7.0010955740 -4.9565812759 A 4 0.0000000000 + 204 4 GUA C5 18.4742145084 4.3682255287 -4.7956973665 A 4 0.0000000000 + 205 4 GUA DC5 18.4742145084 4.3682255287 -4.7956973665 A 4 0.0000000000 + 206 4 GUA N7 18.3114332082 3.9218603359 -3.4879980791 A 4 0.0000000000 + 207 4 GUA DN7 18.3114332082 3.9218603359 -3.4879980791 A 4 0.0000000000 + 208 4 GUA LP7 18.2378022261 4.0997320824 -3.1956966588 A 4 0.0000000000 + 209 4 GUA C8 18.4973148944 2.6334523526 -3.5646066126 A 4 0.0000000000 + 210 4 GUA DC8 18.4973148944 2.6334523526 -3.5646066126 A 4 0.0000000000 + 211 4 GUA H8 18.4465105694 1.9432852647 -2.7224734216 A 4 0.0000000000 + 212 4 GUA C4' 17.8732131349 -1.0947832021 -4.9516615604 A 4 0.0000000000 + 213 4 GUA DC4' 17.8732131349 -1.0947832021 -4.9516615604 A 4 0.0000000000 + 214 4 GUA H4' 17.5864538358 -1.7445427322 -5.7916506422 A 4 0.0000000000 + 215 4 GUA O4' 17.9613857190 0.2655598988 -5.4665635736 A 4 0.0000000000 + 216 4 GUA DO4' 17.9613857190 0.2655598988 -5.4665635736 A 4 0.0000000000 + 217 4 GUA LPRA 17.7768770114 0.4495793413 -5.2329113071 A 4 0.0000000000 + 218 4 GUA LPRB 17.9833613278 0.2168323078 -5.8124576245 A 4 0.0000000000 + 219 4 GUA LPX 18.0292735746 0.2090503402 -5.4196817131 A 4 0.0000000000 + 220 4 GUA C1' 19.0379245903 0.8031911587 -5.2989215592 A 4 0.0000000000 + 221 4 GUA DC1' 19.0379245903 0.8031911587 -5.2989215592 A 4 0.0000000000 + 222 4 GUA H1' 19.5008938885 0.8160394811 -6.2966661906 A 4 0.0000000000 + 223 4 GUA C2' 19.8590514488 -0.0236551736 -4.3150486838 A 4 0.0000000000 + 224 4 GUA DC2' 19.8590514488 -0.0236551736 -4.3150486838 A 4 0.0000000000 + 225 4 GUA H2'' 19.6354177724 0.3359294169 -3.2998211719 A 4 0.0000000000 + 226 4 GUA H2' 20.9158515149 0.0457885031 -4.6122879746 A 4 0.0000000000 + 227 4 GUA C3' 19.3070399314 -1.4306126786 -4.5425578568 A 4 0.0000000000 + 228 4 GUA DC3' 19.3070399314 -1.4306126786 -4.5425578568 A 4 0.0000000000 + 229 4 GUA H3' 19.3343248702 -1.9811522555 -3.5906325938 A 4 0.0000000000 + 230 4 GUA O3' 20.0318891154 -2.2193747793 -5.4765050978 A 4 0.0000000000 + 231 4 GUA DO3' 20.0318891154 -2.2193747793 -5.4765050978 A 4 0.0000000000 + 232 5 ADE P 21.6298074157 -2.1367074818 -5.4884731241 A 5 0.0000000000 + 233 5 ADE DP 21.6298074157 -2.1367074818 -5.4884731241 A 5 0.0000000000 + 234 5 ADE O1P 22.1086903701 -1.6145231914 -4.1888629045 A 5 0.0000000000 + 235 5 ADE DO1P 22.1086903701 -1.6145231914 -4.1888629045 A 5 0.0000000000 + 236 5 ADE O2P 22.1915535584 -3.4417910120 -5.9030744509 A 5 0.0000000000 + 237 5 ADE DO2P 22.1915535584 -3.4417910120 -5.9030744509 A 5 0.0000000000 + 238 5 ADE O5' 21.8829471384 -1.0493257395 -6.6340041744 A 5 0.0000000000 + 239 5 ADE DO5' 21.8829471384 -1.0493257395 -6.6340041744 A 5 0.0000000000 + 240 5 ADE C5' 21.1740770879 -1.1715440154 -7.8815834122 A 5 0.0000000000 + 241 5 ADE DC5' 21.1740770879 -1.1715440154 -7.8815834122 A 5 0.0000000000 + 242 5 ADE H5' 20.2975139791 -0.4889398081 -7.8784830286 A 5 0.0000000000 + 243 5 ADE H5'' 20.9848304513 -2.2449060110 -8.0969917150 A 5 0.0000000000 + 244 5 ADE N9 23.8367672177 1.7639956311 -7.4682726580 A 5 0.0000000000 + 245 5 ADE DN9 23.8367672177 1.7639956311 -7.4682726580 A 5 0.0000000000 + 246 5 ADE C4 24.0424164022 3.1247060787 -7.5449954095 A 5 0.0000000000 + 247 5 ADE DC4 24.0424164022 3.1247060787 -7.5449954095 A 5 0.0000000000 + 248 5 ADE N3 24.1108774189 3.8794292065 -8.6525468031 A 5 0.0000000000 + 249 5 ADE DN3 24.1108774189 3.8794292065 -8.6525468031 A 5 0.0000000000 + 250 5 ADE LP3 24.0939418812 3.8665585703 -9.0018998255 A 5 0.0000000000 + 251 5 ADE C2 24.2587318258 4.6947397380 -8.1232356160 A 5 0.0000000000 + 252 5 ADE DC2 24.2587318258 4.6947397380 -8.1232356160 A 5 0.0000000000 + 253 5 ADE H2 24.3661984093 5.5689272143 -8.7482533675 A 5 0.0000000000 + 254 5 ADE N1 24.4278974400 5.5101206636 -7.0964829968 A 5 0.0000000000 + 255 5 ADE DN1 24.4278974400 5.5101206636 -7.0964829968 A 5 0.0000000000 + 256 5 ADE LP1 24.4795762603 5.8549983571 -7.1262936679 A 5 0.0000000000 + 257 5 ADE C6 24.3781774380 4.8648460894 -5.9437329609 A 5 0.0000000000 + 258 5 ADE DC6 24.3781774380 4.8648460894 -5.9437329609 A 5 0.0000000000 + 259 5 ADE N6 24.5269436551 5.5097405435 -4.7820321579 A 5 0.0000000000 + 260 5 ADE DN6 24.5269436551 5.5097405435 -4.7820321579 A 5 0.0000000000 + 261 5 ADE H61 24.6797952305 6.5080550818 -4.7922536305 A 5 0.0000000000 + 262 5 ADE H62 24.4830592092 4.9837933137 -3.9208970541 A 5 0.0000000000 + 263 5 ADE C5 24.1646714925 3.5563831924 -6.2378486838 A 5 0.0000000000 + 264 5 ADE DC5 24.1646714925 3.5563831924 -6.2378486838 A 5 0.0000000000 + 265 5 ADE N7 24.0393000628 2.4946591827 -5.3584860802 A 5 0.0000000000 + 266 5 ADE DN7 24.0393000628 2.4946591827 -5.3584860802 A 5 0.0000000000 + 267 5 ADE LP7 24.0535368593 2.4898634741 -5.0088086363 A 5 0.0000000000 + 268 5 ADE C8 23.8464953538 1.4559512736 -6.1364682289 A 5 0.0000000000 + 269 5 ADE DC8 23.8464953538 1.4559512736 -6.1364682289 A 5 0.0000000000 + 270 5 ADE H8 23.7042281889 0.4325835273 -5.7892240645 A 5 0.0000000000 + 271 5 ADE C4' 22.0457487733 -0.6882116240 -9.0238768388 A 5 0.0000000000 + 272 5 ADE DC4' 22.0457487733 -0.6882116240 -9.0238768388 A 5 0.0000000000 + 273 5 ADE H4' 21.4913259899 -0.6965956956 -9.9739005672 A 5 0.0000000000 + 274 5 ADE O4' 22.4494446406 0.6887218147 -8.7698772480 A 5 0.0000000000 + 275 5 ADE DO4' 22.4494446406 0.6887218147 -8.7698772480 A 5 0.0000000000 + 276 5 ADE LPRA 22.3527987113 0.7382942481 -8.4371579395 A 5 0.0000000000 + 277 5 ADE LPRB 22.4158110843 0.8391601613 -9.0841018297 A 5 0.0000000000 + 278 5 ADE LPX 22.5038606025 0.6051800434 -8.7776022427 A 5 0.0000000000 + 279 5 ADE C1' 23.6453720752 0.8493866065 -8.6283443763 A 5 0.0000000000 + 280 5 ADE DC1' 23.6453720752 0.8493866065 -8.6283443763 A 5 0.0000000000 + 281 5 ADE H1' 23.9719715989 1.3403710890 -9.5569277000 A 5 0.0000000000 + 282 5 ADE C2' 24.3127740557 -0.5107455046 -8.4535723916 A 5 0.0000000000 + 283 5 ADE DC2' 24.3127740557 -0.5107455046 -8.4535723916 A 5 0.0000000000 + 284 5 ADE H2'' 24.3204750793 -0.7497750505 -7.3798845550 A 5 0.0000000000 + 285 5 ADE H2' 25.3038766351 -0.4662462887 -8.9286886900 A 5 0.0000000000 + 286 5 ADE C3' 23.3662560375 -1.4315605726 -9.2231240868 A 5 0.0000000000 + 287 5 ADE DC3' 23.3662560375 -1.4315605726 -9.2231240868 A 5 0.0000000000 + 288 5 ADE H3' 23.3508680000 -2.4157592001 -8.7320881716 A 5 0.0000000000 + 289 5 ADE O3' 23.7256143867 -1.6707339364 -10.5771798903 A 5 0.0000000000 + 290 5 ADE DO3' 23.7256143867 -1.6707339364 -10.5771798903 A 5 0.0000000000 + 291 6 ADE P 25.2697207296 -1.8665136250 -10.9482943271 A 6 0.0000000000 + 292 6 ADE DP 25.2697207296 -1.8665136250 -10.9482943271 A 6 0.0000000000 + 293 6 ADE O1P 26.0258861868 -2.2513764981 -9.7354108166 A 6 0.0000000000 + 294 6 ADE DO1P 26.0258861868 -2.2513764981 -9.7354108166 A 6 0.0000000000 + 295 6 ADE O2P 25.3906807190 -2.7878034374 -12.1003749547 A 6 0.0000000000 + 296 6 ADE DO2P 25.3906807190 -2.7878034374 -12.1003749547 A 6 0.0000000000 + 297 6 ADE O5' 25.6795763936 -0.3857305074 -11.3932885444 A 6 0.0000000000 + 298 6 ADE DO5' 25.6795763936 -0.3857305074 -11.3932885444 A 6 0.0000000000 + 299 6 ADE C5' 24.8223640768 0.3332441549 -12.3000136895 A 6 0.0000000000 + 300 6 ADE DC5' 24.8223640768 0.3332441549 -12.3000136895 A 6 0.0000000000 + 301 6 ADE H5' 24.1785941668 1.0330934486 -11.7254771205 A 6 0.0000000000 + 302 6 ADE H5'' 24.3162381298 -0.3849274715 -12.9800041606 A 6 0.0000000000 + 303 6 ADE N9 28.2294912253 2.0339693166 -11.1264907707 A 6 0.0000000000 + 304 6 ADE DN9 28.2294912253 2.0339693166 -11.1264907707 A 6 0.0000000000 + 305 6 ADE C4 28.7970721134 3.1460394802 -10.5426562251 A 6 0.0000000000 + 306 6 ADE DC4 28.7970721134 3.1460394802 -10.5426562251 A 6 0.0000000000 + 307 6 ADE N3 28.9423937174 4.3668581660 -11.0806593551 A 6 0.0000000000 + 308 6 ADE DN3 28.9423937174 4.3668581660 -11.0806593551 A 6 0.0000000000 + 309 6 ADE LP3 28.8813117066 4.5548838356 -11.3694764867 A 6 0.0000000000 + 310 6 ADE C2 29.3740302750 4.7069216524 -10.2653010116 A 6 0.0000000000 + 311 6 ADE DC2 29.3740302750 4.7069216524 -10.2653010116 A 6 0.0000000000 + 312 6 ADE H2 29.6470479232 5.7478896776 -10.3561136444 A 6 0.0000000000 + 313 6 ADE N1 29.8848622994 4.7649203103 -9.0473639037 A 6 0.0000000000 + 314 6 ADE DN1 29.8848622994 4.7649203103 -9.0473639037 A 6 0.0000000000 + 315 6 ADE LP1 30.0270684976 5.0526575079 -8.9077762886 A 6 0.0000000000 + 316 6 ADE C6 29.7933692513 3.6044168274 -8.4208300353 A 6 0.0000000000 + 317 6 ADE DC6 29.7933692513 3.6044168274 -8.4208300353 A 6 0.0000000000 + 318 6 ADE N6 30.2530343342 3.4519986891 -7.1746174841 A 6 0.0000000000 + 319 6 ADE DN6 30.2530343342 3.4519986891 -7.1746174841 A 6 0.0000000000 + 320 6 ADE H61 30.6767837608 4.2417659095 -6.7089951467 A 6 0.0000000000 + 321 6 ADE H62 30.1659768370 2.5505894081 -6.7274236779 A 6 0.0000000000 + 322 6 ADE C5 29.1890335414 2.7436945482 -9.2799572132 A 6 0.0000000000 + 323 6 ADE DC5 29.1890335414 2.7436945482 -9.2799572132 A 6 0.0000000000 + 324 6 ADE N7 28.8765854378 1.4112055110 -9.0723431360 A 6 0.0000000000 + 325 6 ADE DN7 28.8765854378 1.4112055110 -9.0723431360 A 6 0.0000000000 + 326 6 ADE LP7 28.9301915501 1.2091225776 -8.7916495793 A 6 0.0000000000 + 327 6 ADE C8 28.3101857149 1.0367412915 -10.1949792757 A 6 0.0000000000 + 328 6 ADE DC8 28.3101857149 1.0367412915 -10.1949792757 A 6 0.0000000000 + 329 6 ADE H8 27.9293968410 0.0361600975 -10.3997647921 A 6 0.0000000000 + 330 6 ADE C4' 25.6528844782 1.2178776924 -13.2088125491 A 6 0.0000000000 + 331 6 ADE DC4' 25.6528844782 1.2178776924 -13.2088125491 A 6 0.0000000000 + 332 6 ADE H4' 25.0098861457 1.8365344604 -13.8520986035 A 6 0.0000000000 + 333 6 ADE O4' 26.4528313139 2.1245230847 -12.3954792640 A 6 0.0000000000 + 334 6 ADE DO4' 26.4528313139 2.1245230847 -12.3954792640 A 6 0.0000000000 + 335 6 ADE LPRA 26.4140010371 1.9947424039 -12.0727577362 A 6 0.0000000000 + 336 6 ADE LPRB 26.4256924122 2.4281716738 -12.5674124323 A 6 0.0000000000 + 337 6 ADE LPX 26.4803857388 2.0519008339 -12.4584615025 A 6 0.0000000000 + 338 6 ADE C1' 27.6539377444 1.9738750372 -12.4990923254 A 6 0.0000000000 + 339 6 ADE DC1' 27.6539377444 1.9738750372 -12.4990923254 A 6 0.0000000000 + 340 6 ADE H1' 27.9925825352 2.8369993457 -13.0909843204 A 6 0.0000000000 + 341 6 ADE C2' 27.9299088306 0.6601063166 -13.2228199803 A 6 0.0000000000 + 342 6 ADE DC2' 27.9299088306 0.6601063166 -13.2228199803 A 6 0.0000000000 + 343 6 ADE H2'' 27.9974347046 -0.1362708398 -12.4670265687 A 6 0.0000000000 + 344 6 ADE H2' 28.8303879654 0.7950494958 -13.8400133585 A 6 0.0000000000 + 345 6 ADE C3' 26.6794049179 0.5036936361 -14.0875636405 A 6 0.0000000000 + 346 6 ADE DC3' 26.6794049179 0.5036936361 -14.0875636405 A 6 0.0000000000 + 347 6 ADE H3' 26.4474755036 -0.5670278012 -14.1863783685 A 6 0.0000000000 + 348 6 ADE O3' 26.7946049135 1.0072223416 -15.4115716630 A 6 0.0000000000 + 349 6 ADE DO3' 26.7946049135 1.0072223416 -15.4115716630 A 6 0.0000000000 + 350 7 THY P 28.1670275072 0.7957381270 -16.2065878020 A 7 0.0000000000 + 351 7 THY DP 28.1670275072 0.7957381270 -16.2065878020 A 7 0.0000000000 + 352 7 THY O1P 28.9233103814 -0.3231290828 -15.6006468633 A 7 0.0000000000 + 353 7 THY DO1P 28.9233103814 -0.3231290828 -15.6006468633 A 7 0.0000000000 + 354 7 THY O2P 27.8881420140 0.6730613682 -17.6549901303 A 7 0.0000000000 + 355 7 THY DO2P 27.8881420140 0.6730613682 -17.6549901303 A 7 0.0000000000 + 356 7 THY O5' 28.9191750962 2.1769669703 -15.9146956187 A 7 0.0000000000 + 357 7 THY DO5' 28.9191750962 2.1769669703 -15.9146956187 A 7 0.0000000000 + 358 7 THY C5' 28.1963407326 3.4124846247 -16.0724759042 A 7 0.0000000000 + 359 7 THY DC5' 28.1963407326 3.4124846247 -16.0724759042 A 7 0.0000000000 + 360 7 THY H5' 27.8468152806 3.7670967991 -15.0792975898 A 7 0.0000000000 + 361 7 THY H5'' 27.4327135058 3.2960219126 -16.8709938409 A 7 0.0000000000 + 362 7 THY N1 32.0590447496 3.5611100456 -15.0983954969 A 7 0.0000000000 + 363 7 THY DN1 32.0590447496 3.5611100456 -15.0983954969 A 7 0.0000000000 + 364 7 THY C6 31.7152562024 2.2356627660 -15.1531230383 A 7 0.0000000000 + 365 7 THY DC6 31.7152562024 2.2356627660 -15.1531230383 A 7 0.0000000000 + 366 7 THY H6 30.9835709351 1.9531588435 -15.8955704798 A 7 0.0000000000 + 367 7 THY C2 32.9807633925 4.0415093711 -14.1932092611 A 7 0.0000000000 + 368 7 THY DC2 32.9807633925 4.0415093711 -14.1932092611 A 7 0.0000000000 + 369 7 THY O2 33.2977358202 5.2170369443 -14.1310142870 A 7 0.0000000000 + 370 7 THY DO2 33.2977358202 5.2170369443 -14.1310142870 A 7 0.0000000000 + 371 7 THY LP2A 33.5355102099 5.2637045949 -13.8784564323 A 7 0.0000000000 + 372 7 THY LP2B 33.1219839484 5.4012766354 -14.3711538627 A 7 0.0000000000 + 373 7 THY N3 33.5312702346 3.0957361144 -13.3503303530 A 7 0.0000000000 + 374 7 THY DN3 33.5312702346 3.0957361144 -13.3503303530 A 7 0.0000000000 + 375 7 THY H3 34.2641241415 3.4509350465 -12.6258589115 A 7 0.0000000000 + 376 7 THY C4 33.2455514321 1.7462419641 -13.3345014479 A 7 0.0000000000 + 377 7 THY DC4 33.2455514321 1.7462419641 -13.3345014479 A 7 0.0000000000 + 378 7 THY O4 33.8036362390 0.9962488867 -12.5310084347 A 7 0.0000000000 + 379 7 THY DO4 33.8036362390 0.9962488867 -12.5310084347 A 7 0.0000000000 + 380 7 THY LP4A 33.6906749292 0.6679572553 -12.5753293919 A 7 0.0000000000 + 381 7 THY LP4B 34.0248942418 1.1788983103 -12.3305487523 A 7 0.0000000000 + 382 7 THY C5 32.2667344377 1.3381769354 -14.3197100676 A 7 0.0000000000 + 383 7 THY DC5 32.2667344377 1.3381769354 -14.3197100676 A 7 0.0000000000 + 384 7 THY C5M 31.8977596668 -0.1147796417 -14.3723864733 A 7 0.0000000000 + 385 7 THY DC5M 31.8977596668 -0.1147796417 -14.3723864733 A 7 0.0000000000 + 386 7 THY H51 31.1441170312 -0.2390452747 -15.1791713456 A 7 0.0000000000 + 387 7 THY H52 31.4152924355 -0.3572540822 -13.4014320374 A 7 0.0000000000 + 388 7 THY H53 32.6909227163 -0.8678453434 -14.5675925841 A 7 0.0000000000 + 389 7 THY C4' 29.1275743584 4.4988548131 -16.5733349142 A 7 0.0000000000 + 390 7 THY DC4' 29.1275743584 4.4988548131 -16.5733349142 A 7 0.0000000000 + 391 7 THY H4' 28.6119375899 5.4693564286 -16.6207199043 A 7 0.0000000000 + 392 7 THY O4' 30.2396516191 4.6439828903 -15.6429297081 A 7 0.0000000000 + 393 7 THY DO4' 30.2396516191 4.6439828903 -15.6429297081 A 7 0.0000000000 + 394 7 THY LPRA 30.2045374158 4.3645574280 -15.4351115093 A 7 0.0000000000 + 395 7 THY LPRB 30.2784092872 4.9911475398 -15.6211455570 A 7 0.0000000000 + 396 7 THY LPX 30.2381297935 4.6156891569 -15.7388314740 A 7 0.0000000000 + 397 7 THY C1' 31.3295729133 4.3771879217 -16.1087399432 A 7 0.0000000000 + 398 7 THY DC1' 31.3295729133 4.3771879217 -16.1087399432 A 7 0.0000000000 + 399 7 THY H1' 31.8236669441 5.3516382049 -16.2364808307 A 7 0.0000000000 + 400 7 THY C2' 31.1392500717 3.6701436750 -17.4465723913 A 7 0.0000000000 + 401 7 THY DC2' 31.1392500717 3.6701436750 -17.4465723913 A 7 0.0000000000 + 402 7 THY H2'' 31.0702026270 2.5895530472 -17.2527777952 A 7 0.0000000000 + 403 7 THY H2' 31.9618809471 3.9732927664 -18.1109360501 A 7 0.0000000000 + 404 7 THY C3' 29.8017450068 4.2383868425 -17.9200557216 A 7 0.0000000000 + 405 7 THY DC3' 29.8017450068 4.2383868425 -17.9200557216 A 7 0.0000000000 + 406 7 THY H3' 29.2694913043 3.4642740337 -18.4922928713 A 7 0.0000000000 + 407 7 THY O3' 29.8956938272 5.3687522204 -18.7763600901 A 7 0.0000000000 + 408 7 THY DO3' 29.8956938272 5.3687522204 -18.7763600901 A 7 0.0000000000 + 409 8 THY P 31.0499847101 5.4108393328 -19.8836817428 A 8 0.0000000000 + 410 8 THY DP 31.0499847101 5.4108393328 -19.8836817428 A 8 0.0000000000 + 411 8 THY O1P 31.5291710676 4.0363709140 -20.1523991418 A 8 0.0000000000 + 412 8 THY DO1P 31.5291710676 4.0363709140 -20.1523991418 A 8 0.0000000000 + 413 8 THY O2P 30.5785380227 6.1693561608 -21.0639724919 A 8 0.0000000000 + 414 8 THY DO2P 30.5785380227 6.1693561608 -21.0639724919 A 8 0.0000000000 + 415 8 THY O5' 32.1876000068 6.2409747967 -19.1251128874 A 8 0.0000000000 + 416 8 THY DO5' 32.1876000068 6.2409747967 -19.1251128874 A 8 0.0000000000 + 417 8 THY C5' 31.8259599335 7.4534934106 -18.4374333995 A 8 0.0000000000 + 418 8 THY DC5' 31.8259599335 7.4534934106 -18.4374333995 A 8 0.0000000000 + 419 8 THY H5' 31.7097186928 7.2440117202 -17.3525710140 A 8 0.0000000000 + 420 8 THY H5'' 30.9713350756 7.9349353659 -18.9591143326 A 8 0.0000000000 + 421 8 THY N1 35.6629595722 6.3770823114 -18.5383164849 A 8 0.0000000000 + 422 8 THY DN1 35.6629595722 6.3770823114 -18.5383164849 A 8 0.0000000000 + 423 8 THY C6 34.9580782430 5.3905206352 -19.1769357228 A 8 0.0000000000 + 424 8 THY DC6 34.9580782430 5.3905206352 -19.1769357228 A 8 0.0000000000 + 425 8 THY H6 34.0940625493 5.7004878695 -19.7459675274 A 8 0.0000000000 + 426 8 THY C2 36.7826585427 6.1044709299 -17.7822290958 A 8 0.0000000000 + 427 8 THY DC2 36.7826585427 6.1044709299 -17.7822290958 A 8 0.0000000000 + 428 8 THY O2 37.4209268970 6.9697607909 -17.2076929575 A 8 0.0000000000 + 429 8 THY DO2 37.4209268970 6.9697607909 -17.2076929575 A 8 0.0000000000 + 430 8 THY LP2A 37.6904106248 6.8260970264 -17.0366980944 A 8 0.0000000000 + 431 8 THY LP2B 37.2766126029 7.2833200181 -17.2656066482 A 8 0.0000000000 + 432 8 THY N3 37.1422687217 4.7724599331 -17.7157692311 A 8 0.0000000000 + 433 8 THY DN3 37.1422687217 4.7724599331 -17.7157692311 A 8 0.0000000000 + 434 8 THY H3 38.0256107073 4.5313304786 -17.1244456964 A 8 0.0000000000 + 435 8 THY C4 36.4943343522 3.7170903203 -18.3235490292 A 8 0.0000000000 + 436 8 THY DC4 36.4943343522 3.7170903203 -18.3235490292 A 8 0.0000000000 + 437 8 THY O4 36.9112830536 2.5646698024 -18.1907709421 A 8 0.0000000000 + 438 8 THY DO4 36.9112830536 2.5646698024 -18.1907709421 A 8 0.0000000000 + 439 8 THY LP4A 36.7065583202 2.3422321199 -18.3671491180 A 8 0.0000000000 + 440 8 THY LP4B 37.1969134734 2.5632705090 -17.9885005655 A 8 0.0000000000 + 441 8 THY C5 35.3310046172 4.1028164417 -19.0936886838 A 8 0.0000000000 + 442 8 THY DC5 35.3310046172 4.1028164417 -19.0936886838 A 8 0.0000000000 + 443 8 THY C5M 34.5666926725 3.0159199084 -19.7897369415 A 8 0.0000000000 + 444 8 THY DC5M 34.5666926725 3.0159199084 -19.7897369415 A 8 0.0000000000 + 445 8 THY H51 33.7184188081 3.4939767734 -20.3247267403 A 8 0.0000000000 + 446 8 THY H52 34.1540959457 2.3569532673 -18.9961073636 A 8 0.0000000000 + 447 8 THY H53 35.0885534886 2.3805444492 -20.5369185221 A 8 0.0000000000 + 448 8 THY C4' 32.9578726017 8.4581093238 -18.5256183113 A 8 0.0000000000 + 449 8 THY DC4' 32.9578726017 8.4581093238 -18.5256183113 A 8 0.0000000000 + 450 8 THY H4' 32.7325495842 9.3588853892 -17.9358454585 A 8 0.0000000000 + 451 8 THY O4' 34.1681073225 7.8672970600 -17.9691071888 A 8 0.0000000000 + 452 8 THY DO4' 34.1681073225 7.8672970600 -17.9691071888 A 8 0.0000000000 + 453 8 THY LPRA 34.0810636538 7.5301903334 -17.9332958132 A 8 0.0000000000 + 454 8 THY LPRB 34.3047492012 8.1301800475 -17.7827700431 A 8 0.0000000000 + 455 8 THY LPX 34.1473908275 7.8982993021 -18.0618955923 A 8 0.0000000000 + 456 8 THY C1' 35.0767345610 7.7278405017 -18.7634846607 A 8 0.0000000000 + 457 8 THY DC1' 35.0767345610 7.7278405017 -18.7634846607 A 8 0.0000000000 + 458 8 THY H1' 35.8050118506 8.5064891041 -18.4927106895 A 8 0.0000000000 + 459 8 THY C2' 34.5392422412 7.9354724483 -20.1755473331 A 8 0.0000000000 + 460 8 THY DC2' 34.5392422412 7.9354724483 -20.1755473331 A 8 0.0000000000 + 461 8 THY H2'' 34.1940405068 6.9620409057 -20.5540533363 A 8 0.0000000000 + 462 8 THY H2' 35.3291864557 8.4146124193 -20.7725507051 A 8 0.0000000000 + 463 8 THY C3' 33.3679149638 8.8871537796 -19.9340900633 A 8 0.0000000000 + 464 8 THY DC3' 33.3679149638 8.8871537796 -19.9340900633 A 8 0.0000000000 + 465 8 THY H3' 32.5764948972 8.6693859902 -20.6663683356 A 8 0.0000000000 + 466 8 THY O3' 33.6723606960 10.2677139976 -20.0796088617 A 8 0.0000000000 + 467 8 THY DO3' 33.6723606960 10.2677139976 -20.0796088617 A 8 0.0000000000 + 468 9 CYT P 34.6528190065 10.7271576098 -21.2577145780 A 9 0.0000000000 + 469 9 CYT DP 34.6528190065 10.7271576098 -21.2577145780 A 9 0.0000000000 + 470 9 CYT O1P 34.6929725372 9.6818262605 -22.3049309377 A 9 0.0000000000 + 471 9 CYT DO1P 34.6929725372 9.6818262605 -22.3049309377 A 9 0.0000000000 + 472 9 CYT O2P 34.2762046730 12.0828546223 -21.7170001801 A 9 0.0000000000 + 473 9 CYT DO2P 34.2762046730 12.0828546223 -21.7170001801 A 9 0.0000000000 + 474 9 CYT O5' 36.0587156142 10.7839263189 -20.4968254915 A 9 0.0000000000 + 475 9 CYT DO5' 36.0587156142 10.7839263189 -20.4968254915 A 9 0.0000000000 + 476 9 CYT C5' 36.1348222101 11.4434719151 -19.2188992797 A 9 0.0000000000 + 477 9 CYT DC5' 36.1348222101 11.4434719151 -19.2188992797 A 9 0.0000000000 + 478 9 CYT H5' 36.0938540946 10.6857138027 -18.4074528818 A 9 0.0000000000 + 479 9 CYT H5'' 35.3935601815 12.2702741407 -19.1835484011 A 9 0.0000000000 + 480 9 CYT N1 39.4773414254 9.9795466379 -20.8238580197 A 9 0.0000000000 + 481 9 CYT DN1 39.4773414254 9.9795466379 -20.8238580197 A 9 0.0000000000 + 482 9 CYT C6 38.4757590392 9.6273600671 -21.6801835087 A 9 0.0000000000 + 483 9 CYT DC6 38.4757590392 9.6273600671 -21.6801835087 A 9 0.0000000000 + 484 9 CYT H6 37.6576113227 10.3236633724 -21.7906191053 A 9 0.0000000000 + 485 9 CYT C2 40.5573221603 9.1461846784 -20.6267277416 A 9 0.0000000000 + 486 9 CYT DC2 40.5573221603 9.1461846784 -20.6267277416 A 9 0.0000000000 + 487 9 CYT O2 41.4509895421 9.4913292693 -19.8441660366 A 9 0.0000000000 + 488 9 CYT DO2 41.4509895421 9.4913292693 -19.8441660366 A 9 0.0000000000 + 489 9 CYT LP2A 41.6999005680 9.2456352890 -19.8308330247 A 9 0.0000000000 + 490 9 CYT LP2B 41.3750426004 9.8038239624 -19.7060388170 A 9 0.0000000000 + 491 9 CYT N3 40.6081855741 7.9693513784 -21.2984511201 A 9 0.0000000000 + 492 9 CYT DN3 40.6081855741 7.9693513784 -21.2984511201 A 9 0.0000000000 + 493 9 CYT LP3 40.8777545904 7.7502105730 -21.2559087544 A 9 0.0000000000 + 494 9 CYT C4 39.6231274198 7.6348789585 -22.1335227536 A 9 0.0000000000 + 495 9 CYT DC4 39.6231274198 7.6348789585 -22.1335227536 A 9 0.0000000000 + 496 9 CYT N4 39.6957099399 6.4693192291 -22.7844999382 A 9 0.0000000000 + 497 9 CYT DN4 39.6957099399 6.4693192291 -22.7844999382 A 9 0.0000000000 + 498 9 CYT H41 40.4945157929 5.8715047156 -22.6275699643 A 9 0.0000000000 + 499 9 CYT H42 38.9651686408 6.1890079058 -23.4231195216 A 9 0.0000000000 + 500 9 CYT C5 38.5157068872 8.4695287213 -22.3475662656 A 9 0.0000000000 + 501 9 CYT DC5 38.5157068872 8.4695287213 -22.3475662656 A 9 0.0000000000 + 502 9 CYT H5 37.7359053878 8.1674315708 -23.0309745866 A 9 0.0000000000 + 503 9 CYT C4' 37.4838932935 12.1168540199 -19.0613564200 A 9 0.0000000000 + 504 9 CYT DC4' 37.4838932935 12.1168540199 -19.0613564200 A 9 0.0000000000 + 505 9 CYT H4' 37.5910599601 12.5553413435 -18.0582391923 A 9 0.0000000000 + 506 9 CYT O4' 38.5374770677 11.1218441059 -19.2141580626 A 9 0.0000000000 + 507 9 CYT DO4' 38.5374770677 11.1218441059 -19.2141580626 A 9 0.0000000000 + 508 9 CYT LPRA 38.3644620778 10.8430161773 -19.3358987688 A 9 0.0000000000 + 509 9 CYT LPRB 38.7632690328 11.2077105447 -18.9608895427 A 9 0.0000000000 + 510 9 CYT LPX 38.5154328458 11.2024414849 -19.2690954341 A 9 0.0000000000 + 511 9 CYT C1' 39.2701232387 11.3002359957 -20.1667823745 A 9 0.0000000000 + 512 9 CYT DC1' 39.2701232387 11.3002359957 -20.1667823745 A 9 0.0000000000 + 513 9 CYT H1' 40.2138929452 11.6574126280 -19.7289198455 A 9 0.0000000000 + 514 9 CYT C2' 38.6490152498 12.3499724939 -21.0823194631 A 9 0.0000000000 + 515 9 CYT DC2' 38.6490152498 12.3499724939 -21.0823194631 A 9 0.0000000000 + 516 9 CYT H2'' 38.0029638932 11.8304922972 -21.8053394973 A 9 0.0000000000 + 517 9 CYT H2' 39.4650326983 12.9396726301 -21.5254551905 A 9 0.0000000000 + 518 9 CYT C3' 37.8279114582 13.1843564558 -20.0996707326 A 9 0.0000000000 + 519 9 CYT DC3' 37.8279114582 13.1843564558 -20.0996707326 A 9 0.0000000000 + 520 9 CYT H3' 36.9263012774 13.5512195610 -20.6120285607 A 9 0.0000000000 + 521 9 CYT O3' 38.4870313166 14.3343836866 -19.5870228801 A 9 0.0000000000 + 522 9 CYT DO3' 38.4870313166 14.3343836866 -19.5870228801 A 9 0.0000000000 + 523 10 GUA P 39.4102739761 15.2013404251 -20.5649436413 A 10 0.0000000000 + 524 10 GUA DP 39.4102739761 15.2013404251 -20.5649436413 A 10 0.0000000000 + 525 10 GUA O1P 39.0321046967 14.9329569025 -21.9706286419 A 10 0.0000000000 + 526 10 GUA DO1P 39.0321046967 14.9329569025 -21.9706286419 A 10 0.0000000000 + 527 10 GUA O2P 39.3764334126 16.6217654685 -20.1502829096 A 10 0.0000000000 + 528 10 GUA DO2P 39.3764334126 16.6217654685 -20.1502829096 A 10 0.0000000000 + 529 10 GUA O5' 40.8556551743 14.5842048479 -20.2670560266 A 10 0.0000000000 + 530 10 GUA DO5' 40.8556551743 14.5842048479 -20.2670560266 A 10 0.0000000000 + 531 10 GUA C5' 41.2639495583 14.3908511453 -18.8996504351 A 10 0.0000000000 + 532 10 GUA DC5' 41.2639495583 14.3908511453 -18.8996504351 A 10 0.0000000000 + 533 10 GUA H5' 41.1089283755 13.3287278738 -18.6129736325 A 10 0.0000000000 + 534 10 GUA H5'' 40.7932496435 15.1667925510 -18.2588091714 A 10 0.0000000000 + 535 10 GUA N9 43.8469642688 13.5376305897 -21.8113831170 A 10 0.0000000000 + 536 10 GUA DN9 43.8469642688 13.5376305897 -21.8113831170 A 10 0.0000000000 + 537 10 GUA C4 44.6647000810 12.5681103686 -22.3508732212 A 10 0.0000000000 + 538 10 GUA DC4 44.6647000810 12.5681103686 -22.3508732212 A 10 0.0000000000 + 539 10 GUA N3 45.8306777328 12.1248313417 -21.8216995068 A 10 0.0000000000 + 540 10 GUA DN3 45.8306777328 12.1248313417 -21.8216995068 A 10 0.0000000000 + 541 10 GUA LP3 45.9723837996 12.2403178459 -21.5232329962 A 10 0.0000000000 + 542 10 GUA C2 46.3880013603 11.1851867038 -22.5749506791 A 10 0.0000000000 + 543 10 GUA DC2 46.3880013603 11.1851867038 -22.5749506791 A 10 0.0000000000 + 544 10 GUA N1 45.8459553694 10.7195318488 -23.7496747743 A 10 0.0000000000 + 545 10 GUA DN1 45.8459553694 10.7195318488 -23.7496747743 A 10 0.0000000000 + 546 10 GUA H1 46.3655059256 9.9868424856 -24.2537913447 A 10 0.0000000000 + 547 10 GUA N2 47.5509160114 10.6342042883 -22.1976856633 A 10 0.0000000000 + 548 10 GUA DN2 47.5509160114 10.6342042883 -22.1976856633 A 10 0.0000000000 + 549 10 GUA H21 48.0690453955 9.9159525105 -22.6832331119 A 10 0.0000000000 + 550 10 GUA H22 47.9517944916 10.9740409500 -21.3351849459 A 10 0.0000000000 + 551 10 GUA C6 44.6492088789 11.1644563557 -24.3067106983 A 10 0.0000000000 + 552 10 GUA DC6 44.6492088789 11.1644563557 -24.3067106983 A 10 0.0000000000 + 553 10 GUA O6 44.2443159379 10.6801745929 -25.3728504080 A 10 0.0000000000 + 554 10 GUA DO6 44.2443159379 10.6801745929 -25.3728504080 A 10 0.0000000000 + 555 10 GUA LP6A 43.9409819198 10.8289044796 -25.4643266031 A 10 0.0000000000 + 556 10 GUA LP6B 44.4694117968 10.4378661086 -25.4873862220 A 10 0.0000000000 + 557 10 GUA C5 44.0454177838 12.1661309017 -23.5132117882 A 10 0.0000000000 + 558 10 GUA DC5 44.0454177838 12.1661309017 -23.5132117882 A 10 0.0000000000 + 559 10 GUA N7 42.8590449832 12.8668453216 -23.7064368980 A 10 0.0000000000 + 560 10 GUA DN7 42.8590449832 12.8668453216 -23.7064368980 A 10 0.0000000000 + 561 10 GUA LP7 42.6238073371 12.8466224211 -23.9648054026 A 10 0.0000000000 + 562 10 GUA C8 42.7867686988 13.6631176260 -22.6763191591 A 10 0.0000000000 + 563 10 GUA DC8 42.7867686988 13.6631176260 -22.6763191591 A 10 0.0000000000 + 564 10 GUA H8 41.9793337887 14.3708790351 -22.4886421656 A 10 0.0000000000 + 565 10 GUA C4' 42.7563162404 14.6213197148 -18.7655537365 A 10 0.0000000000 + 566 10 GUA DC4' 42.7563162404 14.6213197148 -18.7655537365 A 10 0.0000000000 + 567 10 GUA H4' 43.0998262488 14.3972763517 -17.7448650251 A 10 0.0000000000 + 568 10 GUA O4' 43.4636105487 13.7220090467 -19.6679987064 A 10 0.0000000000 + 569 10 GUA DO4' 43.4636105487 13.7220090467 -19.6679987064 A 10 0.0000000000 + 570 10 GUA LPRA 43.2063481494 13.5931748476 -19.8672919754 A 10 0.0000000000 + 571 10 GUA LPRB 43.7327302795 13.6117664306 -19.4732652064 A 10 0.0000000000 + 572 10 GUA LPX 43.4586579032 13.8218681674 -19.6660941532 A 10 0.0000000000 + 573 10 GUA C1' 44.0988002401 14.2765281904 -20.5427156510 A 10 0.0000000000 + 574 10 GUA DC1' 44.0988002401 14.2765281904 -20.5427156510 A 10 0.0000000000 + 575 10 GUA H1' 45.1497224202 14.1619032270 -20.2387030048 A 10 0.0000000000 + 576 10 GUA C2' 43.6924161610 15.7454654735 -20.5975357967 A 10 0.0000000000 + 577 10 GUA DC2' 43.6924161610 15.7454654735 -20.5975357967 A 10 0.0000000000 + 578 10 GUA H2'' 42.8459792341 15.8378761581 -21.2939586525 A 10 0.0000000000 + 579 10 GUA H2' 44.5824197583 16.3342998486 -20.8643085007 A 10 0.0000000000 + 580 10 GUA C3' 43.2598816664 16.0106145553 -19.1557950310 A 10 0.0000000000 + 581 10 GUA DC3' 43.2598816664 16.0106145553 -19.1557950310 A 10 0.0000000000 + 582 10 GUA H3' 42.4428988852 16.7471764316 -19.1597620963 A 10 0.0000000000 + 583 10 GUA O3' 44.2703014242 16.5452872473 -18.3114097721 A 10 0.0000000000 + 584 10 GUA DO3' 44.2703014242 16.5452872473 -18.3114097721 A 10 0.0000000000 + 585 11 CYT P 45.2767481950 17.6403802295 -18.9014574547 A 11 0.0000000000 + 586 11 CYT DP 45.2767481950 17.6403802295 -18.9014574547 A 11 0.0000000000 + 587 11 CYT O1P 44.6749966731 18.2735296504 -20.0964507420 A 11 0.0000000000 + 588 11 CYT DO1P 44.6749966731 18.2735296504 -20.0964507420 A 11 0.0000000000 + 589 11 CYT O2P 45.6910221596 18.5661530112 -17.8234881374 A 11 0.0000000000 + 590 11 CYT DO2P 45.6910221596 18.5661530112 -17.8234881374 A 11 0.0000000000 + 591 11 CYT O5' 46.5163908938 16.7291603272 -19.3392752581 A 11 0.0000000000 + 592 11 CYT DO5' 46.5163908938 16.7291603272 -19.3392752581 A 11 0.0000000000 + 593 11 CYT C5' 47.0131175044 15.7378039978 -18.4203828200 A 11 0.0000000000 + 594 11 CYT DC5' 47.0131175044 15.7378039978 -18.4203828200 A 11 0.0000000000 + 595 11 CYT H5' 46.6021653900 14.7418487475 -18.6915147049 A 11 0.0000000000 + 596 11 CYT H5'' 46.8576198050 16.0878225988 -17.3774885567 A 11 0.0000000000 + 597 11 CYT N1 48.8926413894 16.2407777408 -21.8997235418 A 11 0.0000000000 + 598 11 CYT DN1 48.8926413894 16.2407777408 -21.8997235418 A 11 0.0000000000 + 599 11 CYT C6 47.8199937311 17.0824550379 -21.9384834260 A 11 0.0000000000 + 600 11 CYT DC6 47.8199937311 17.0824550379 -21.9384834260 A 11 0.0000000000 + 601 11 CYT H6 47.5205486258 17.5383462208 -21.0063375907 A 11 0.0000000000 + 602 11 CYT C2 49.3381974102 15.6187937956 -23.0461644231 A 11 0.0000000000 + 603 11 CYT DC2 49.3381974102 15.6187937956 -23.0461644231 A 11 0.0000000000 + 604 11 CYT O2 50.3133872745 14.8605275632 -22.9813103606 A 11 0.0000000000 + 605 11 CYT DO2 50.3133872745 14.8605275632 -22.9813103606 A 11 0.0000000000 + 606 11 CYT LP2A 50.3846473787 14.7297975858 -23.2980621096 A 11 0.0000000000 + 607 11 CYT LP2B 50.4308694532 14.8444995553 -22.6520064878 A 11 0.0000000000 + 608 11 CYT N3 48.6924005240 15.8572952099 -24.2144107400 A 11 0.0000000000 + 609 11 CYT DN3 48.6924005240 15.8572952099 -24.2144107400 A 11 0.0000000000 + 610 11 CYT LP3 48.7970904883 15.7046645526 -24.5114694780 A 11 0.0000000000 + 611 11 CYT C4 47.6444267649 16.6822841945 -24.2408715723 A 11 0.0000000000 + 612 11 CYT DC4 47.6444267649 16.6822841945 -24.2408715723 A 11 0.0000000000 + 613 11 CYT N4 47.0240214965 16.9016779611 -25.4047154957 A 11 0.0000000000 + 614 11 CYT DN4 47.0240214965 16.9016779611 -25.4047154957 A 11 0.0000000000 + 615 11 CYT H41 47.3644667730 16.4372547320 -26.2344793645 A 11 0.0000000000 + 616 11 CYT H42 46.2279123321 17.5211023476 -25.4559368578 A 11 0.0000000000 + 617 11 CYT C5 47.1758942815 17.3247525928 -23.0847804180 A 11 0.0000000000 + 618 11 CYT DC5 47.1758942815 17.3247525928 -23.0847804180 A 11 0.0000000000 + 619 11 CYT H5 46.3244129735 17.9866236288 -23.1422809724 A 11 0.0000000000 + 620 11 CYT C4' 48.5153031693 15.5979400832 -18.5691521491 A 11 0.0000000000 + 621 11 CYT DC4' 48.5153031693 15.5979400832 -18.5691521491 A 11 0.0000000000 + 622 11 CYT H4' 48.9006866794 14.7867499390 -17.9339749296 A 11 0.0000000000 + 623 11 CYT O4' 48.8307327496 15.2544127808 -19.9497045793 A 11 0.0000000000 + 624 11 CYT DO4' 48.8307327496 15.2544127808 -19.9497045793 A 11 0.0000000000 + 625 11 CYT LPRA 48.5259954388 15.3048868887 -20.1142874942 A 11 0.0000000000 + 626 11 CYT LPRB 49.0793327191 15.0105538434 -19.9146207687 A 11 0.0000000000 + 627 11 CYT LPX 48.8541805503 15.3351869831 -19.8956145719 A 11 0.0000000000 + 628 11 CYT C1' 49.4875343695 16.0868616182 -20.5427709526 A 11 0.0000000000 + 629 11 CYT DC1' 49.4875343695 16.0868616182 -20.5427709526 A 11 0.0000000000 + 630 11 CYT H1' 50.4926915347 15.6463842152 -20.6178624352 A 11 0.0000000000 + 631 11 CYT C2' 49.5048843919 17.3777001140 -19.7307580436 A 11 0.0000000000 + 632 11 CYT DC2' 49.5048843919 17.3777001140 -19.7307580436 A 11 0.0000000000 + 633 11 CYT H2'' 48.6418903016 17.9853825238 -20.0405374633 A 11 0.0000000000 + 634 11 CYT H2' 50.4860073534 17.8546029750 -19.8720428463 A 11 0.0000000000 + 635 11 CYT C3' 49.3376125037 16.8584897571 -18.3030160218 A 11 0.0000000000 + 636 11 CYT DC3' 49.3376125037 16.8584897571 -18.3030160218 A 11 0.0000000000 + 637 11 CYT H3' 48.7648679662 17.5960162909 -17.7216226036 A 11 0.0000000000 + 638 11 CYT O3' 50.5498102378 16.6489860001 -17.5913319139 A 11 0.0000000000 + 639 11 CYT DO3' 50.5498102378 16.6489860001 -17.5913319139 A 11 0.0000000000 + 640 12 GUA P 51.7452663288 17.6979291604 -17.7671812554 A 12 0.0000000000 + 641 12 GUA DP 51.7452663288 17.6979291604 -17.7671812554 A 12 0.0000000000 + 642 12 GUA O1P 51.2076877604 18.9821411318 -18.2699743890 A 12 0.0000000000 + 643 12 GUA DO1P 51.2076877604 18.9821411318 -18.2699743890 A 12 0.0000000000 + 644 12 GUA O2P 52.5265710855 17.7754544980 -16.5124905727 A 12 0.0000000000 + 645 12 GUA DO2P 52.5265710855 17.7754544980 -16.5124905727 A 12 0.0000000000 + 646 12 GUA O5' 52.6195387171 16.9947897815 -18.9073404393 A 12 0.0000000000 + 647 12 GUA DO5' 52.6195387171 16.9947897815 -18.9073404393 A 12 0.0000000000 + 648 12 GUA C5' 52.9241524400 15.5923123506 -18.7883633581 A 12 0.0000000000 + 649 12 GUA DC5' 52.9241524400 15.5923123506 -18.7883633581 A 12 0.0000000000 + 650 12 GUA H5' 52.2218638521 15.0055310979 -19.4182835917 A 12 0.0000000000 + 651 12 GUA H5'' 52.9973667108 15.3185384608 -17.7141154687 A 12 0.0000000000 + 652 12 GUA N9 54.4419170268 17.6309266656 -21.8573338461 A 12 0.0000000000 + 653 12 GUA DN9 54.4419170268 17.6309266656 -21.8573338461 A 12 0.0000000000 + 654 12 GUA C4 54.5550316412 17.6933567053 -23.2295650453 A 12 0.0000000000 + 655 12 GUA DC4 54.5550316412 17.6933567053 -23.2295650453 A 12 0.0000000000 + 656 12 GUA N3 55.3058946301 16.8741691189 -24.0049110778 A 12 0.0000000000 + 657 12 GUA DN3 55.3058946301 16.8741691189 -24.0049110778 A 12 0.0000000000 + 658 12 GUA LP3 55.5034736826 16.6108255300 -23.8861143095 A 12 0.0000000000 + 659 12 GUA C2 55.2079118284 17.1864100063 -25.2909258518 A 12 0.0000000000 + 660 12 GUA DC2 55.2079118284 17.1864100063 -25.2909258518 A 12 0.0000000000 + 661 12 GUA N1 54.4371378104 18.2168523804 -25.7754059100 A 12 0.0000000000 + 662 12 GUA DN1 54.4371378104 18.2168523804 -25.7754059100 A 12 0.0000000000 + 663 12 GUA H1 54.4357402826 18.3693775673 -26.7940491813 A 12 0.0000000000 + 664 12 GUA N2 55.8884554798 16.4746581152 -26.2011733918 A 12 0.0000000000 + 665 12 GUA DN2 55.8884554798 16.4746581152 -26.2011733918 A 12 0.0000000000 + 666 12 GUA H21 55.8948674134 16.6147420250 -27.2013910607 A 12 0.0000000000 + 667 12 GUA H22 56.4556396091 15.7169744747 -25.8485862898 A 12 0.0000000000 + 668 12 GUA C6 53.6601496874 19.0673786218 -24.9922433666 A 12 0.0000000000 + 669 12 GUA DC6 53.6601496874 19.0673786218 -24.9922433666 A 12 0.0000000000 + 670 12 GUA O6 52.9987401063 19.9690483408 -25.5257694520 A 12 0.0000000000 + 671 12 GUA DO6 52.9987401063 19.9690483408 -25.5257694520 A 12 0.0000000000 + 672 12 GUA LP6A 52.8243739490 20.1498543803 -25.2820367720 A 12 0.0000000000 + 673 12 GUA LP6B 53.0453009531 19.9624734916 -25.8725962948 A 12 0.0000000000 + 674 12 GUA C5 53.7560600503 18.7448812087 -23.6195260891 A 12 0.0000000000 + 675 12 GUA DC5 53.7560600503 18.7448812087 -23.6195260891 A 12 0.0000000000 + 676 12 GUA N7 53.1488122090 19.3369363896 -22.5165583718 A 12 0.0000000000 + 677 12 GUA DN7 53.1488122090 19.3369363896 -22.5165583718 A 12 0.0000000000 + 678 12 GUA LP7 52.9284834984 19.6082536558 -22.4980597138 A 12 0.0000000000 + 679 12 GUA C8 53.5849141495 18.6442318943 -21.5014763161 A 12 0.0000000000 + 680 12 GUA DC8 53.5849141495 18.6442318943 -21.5014763161 A 12 0.0000000000 + 681 12 GUA H8 53.3165604602 18.8239185831 -20.4604196455 A 12 0.0000000000 + 682 12 GUA C4' 54.2985955813 15.3087626305 -19.3617407273 A 12 0.0000000000 + 683 12 GUA DC4' 54.2985955813 15.3087626305 -19.3617407273 A 12 0.0000000000 + 684 12 GUA H4' 54.5139625491 14.2300742678 -19.3547775809 A 12 0.0000000000 + 685 12 GUA O4' 54.3396086374 15.7498859567 -20.7499626045 A 12 0.0000000000 + 686 12 GUA DO4' 54.3396086374 15.7498859567 -20.7499626045 A 12 0.0000000000 + 687 12 GUA LPRA 54.0439194139 15.9343871521 -20.7820124414 A 12 0.0000000000 + 688 12 GUA LPRB 54.5123779446 15.4904904603 -20.9092257292 A 12 0.0000000000 + 689 12 GUA LPX 54.3909506076 15.7811682834 -20.6700537931 A 12 0.0000000000 + 690 12 GUA C1' 55.1280996049 16.6464426859 -20.9748074027 A 12 0.0000000000 + 691 12 GUA DC1' 55.1280996049 16.6464426859 -20.9748074027 A 12 0.0000000000 + 692 12 GUA H1' 55.9536134167 16.1616230500 -21.5165424553 A 12 0.0000000000 + 693 12 GUA C2' 55.6019121655 17.2359754351 -19.6504649979 A 12 0.0000000000 + 694 12 GUA DC2' 55.6019121655 17.2359754351 -19.6504649979 A 12 0.0000000000 + 695 12 GUA H2'' 54.9130774256 18.0479471999 -19.3744060291 A 12 0.0000000000 + 696 12 GUA H2' 56.6533802518 17.5364467496 -19.7693424668 A 12 0.0000000000 + 697 12 GUA C3' 55.4662417101 16.0435900986 -18.7039887452 A 12 0.0000000000 + 698 12 GUA DC3' 55.4662417101 16.0435900986 -18.7039887452 A 12 0.0000000000 + 699 12 GUA H3' 55.1957383273 16.4129458595 -17.7037866447 A 12 0.0000000000 + 700 12 GUA O3' 56.6467518741 15.2706800825 -18.5342380461 A 12 0.0000000000 + 701 12 GUA DO3' 56.6467518741 15.2706800825 -18.5342380461 A 12 0.0000000000 + 702 12 GUA H3T 57.3148503161 15.8327607381 -18.1116155096 A 12 0.0000000000 + 703 12 GUA LP3A 56.6377180729 15.1043772561 -18.2264040642 A 12 0.0000000000 + 704 12 GUA LP3B 56.8494378842 15.2977560535 -18.8182895785 A 12 0.0000000000 + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 6601 6601 6597 + : Ran out of space. RESIZING + with mode 5 found 4983 exclusions and 3483 interactions(1-4) + found 132 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 242473 ATOM PAIRS WERE FOUND FOR ATOM LIST + 22 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> cons harm force 100000. sele .not. type D* end + SELRPN> 461 atoms have been selected out of 704 + CSTRAN: Harmonic Restraints + ABSOlute type as set number 1. Number of selected atoms: 461 + Reference coordinates set to main coordinates. + Mass weighting will NOT be used for new restraints. + The force constant of 100000.00000 will be used. + An exponent of 2 will be used. + The XYZ scale factors are: 1.00000 1.00000 1.00000 + A total of 461 atoms are restrained. + + CHARMM> mini ABNR nstep 200 nprint 20 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 242473 atom pairs and 8466 atom exclusions. + There are 0 group pairs and 132 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 242473 ATOM PAIRS WERE FOUND FOR ATOM LIST + 22 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + + ABNER> An energy minimization has been requested. + + EIGRNG = 0.0005000 MINDIM = 5 + NPRINT = 20 NSTEP = 200 + PSTRCT = 0.0000000 SDSTP = 0.0200000 + STPLIM = 1.0000000 STRICT = 0.1000000 + TOLFUN = 0.0000000 TOLGRD = 0.0000000 + TOLITR = 100 TOLSTP = 0.0000000 + FMEM = 0.0000000 +MINI MIN: Cycle ENERgy Delta-E GRMS Step-size +MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +MINI EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +MINI> 0 1008.16767 -986.39109 42.04403 0.00000 +MINI INTERN> 348.11591 276.72277 115.28040 330.54303 0.00005 +MINI EXTERN> 305.35243 -367.84692 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 20 699.75666 308.41101 24.99441 0.00325 +MINI INTERN> 731.41207 276.28175 114.56912 330.54883 0.00006 +MINI EXTERN> 302.86181 -1061.21689 0.00000 0.00000 0.00000 +MINI CONSTR> 5.29991 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 40 672.18676 27.56990 14.17064 0.00236 +MINI INTERN> 747.68212 275.99297 114.47286 330.51575 0.00006 +MINI EXTERN> 302.11533 -1103.08839 0.00000 0.00000 0.00000 +MINI CONSTR> 4.49607 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 60 663.82729 8.35947 47.59687 0.00431 +MINI INTERN> 855.62402 275.88431 114.51348 330.51084 0.00006 +MINI EXTERN> 302.57299 -1221.64190 0.00000 0.00000 0.00000 +MINI CONSTR> 6.36350 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 80 658.10904 5.71824 7.57676 0.00074 +MINI INTERN> 865.91277 275.94639 114.47803 330.50618 0.00006 +MINI EXTERN> 302.35112 -1235.22973 0.00000 0.00000 0.00000 +MINI CONSTR> 4.14422 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 100 654.70609 3.40295 11.40579 0.00077 +MINI INTERN> 981.12611 276.00677 114.47778 330.50662 0.00005 +MINI EXTERN> 302.34903 -1353.87142 0.00000 0.00000 0.00000 +MINI CONSTR> 4.11115 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 120 653.55491 1.15118 4.76587 0.00043 +MINI INTERN> 1014.71520 275.96290 114.47924 330.50661 0.00006 +MINI EXTERN> 302.37291 -1388.63997 0.00000 0.00000 0.00000 +MINI CONSTR> 4.15796 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 140 653.49215 0.06276 0.59272 0.00005 +MINI INTERN> 994.74516 275.96962 114.47923 330.50680 0.00006 +MINI EXTERN> 302.36330 -1368.67969 0.00000 0.00000 0.00000 +MINI CONSTR> 4.10767 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 160 653.32350 0.16865 0.94990 0.00008 +MINI INTERN> 1022.06036 275.96869 114.47822 330.50648 0.00006 +MINI EXTERN> 302.36826 -1396.15902 0.00000 0.00000 0.00000 +MINI CONSTR> 4.10046 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 180 653.25401 0.06948 1.11225 0.00013 +MINI INTERN> 1026.72644 275.97634 114.48360 330.50650 0.00006 +MINI EXTERN> 302.38471 -1400.87547 0.00000 0.00000 0.00000 +MINI CONSTR> 4.05183 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 200 653.22620 0.02782 0.25340 0.00003 +MINI INTERN> 1023.22188 275.97010 114.48191 330.50656 0.00006 +MINI EXTERN> 302.38635 -1397.41437 0.00000 0.00000 0.00000 +MINI CONSTR> 4.07371 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + ABNER> Minimization exiting with number of steps limit ( 200) exceeded. + +ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size +ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ABNR EXTERN: VDWaals ELEC HBONds ASP USER +ABNR CONSTR: HARMonic CDIHedral CIC RESDistance NOE + ---------- --------- --------- --------- --------- --------- +ABNR> 200 653.22620 0.02782 0.25340 0.00004 +ABNR INTERN> 1023.22188 275.97010 114.48191 330.50656 0.00006 +ABNR EXTERN> 302.38635 -1397.41437 0.00000 0.00000 0.00000 +ABNR CONSTR> 4.07371 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> cons harm clear + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 242473 atom pairs and 8466 atom exclusions. + There are 0 group pairs and 132 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 242473 ATOM PAIRS WERE FOUND FOR ATOM LIST + 22 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 649.15249 4.07371 33.61530 +ENER INTERN> 1023.22188 275.97010 114.48191 330.50656 0.00006 +ENER EXTERN> 302.38635 -1397.41437 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "BDEONA" + RDCMND substituted energy or value "?ENER" to "649.152" + + CHARMM> + + CHARMM> set residue oligomer_dna + Parameter: RESIDUE <- "OLIGOMER_DNA" + + CHARMM> + + CHARMM> echo @residue starting E: ?ener + Parameter: RESIDUE -> "OLIGOMER_DNA" + RDCMND substituted energy or value "?ENER" to "649.152" + + CHARMM> + + CHARMM> if @?pdbdir eq 1 then + Comparing "0" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> !write data to check + CHARMM> !write title unit 90 + CHARMM> !* @residue @enetmp minimized E: ?ener ?rdip + CHARMM> !* + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 12 + Number of atoms = 704 Number of groups = 57 + Number of bonds = 733 Number of angles = 738 + Number of dihedrals = 1078 Number of impropers = 34 + Number of cross-terms = 0 + Number of HB acceptors = 88 Number of HB donors = 28 + Number of NB exclusions = 0 Total charge = -11.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 325 + + CHARMM> delete atom sele all end + SELRPN> 704 atoms have been selected out of 704 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 12 residues deleted. + + Message from MAPIC: 1 segments deleted. + DELTIC: 733 bonds deleted + DELTIC: 738 angles deleted + DELTIC: 1078 dihedrals deleted + DELTIC: 34 improper dihedrals deleted + DELTIC: 28 donors deleted + DELTIC: 88 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> incr testcasei + Parameter: TESTCASEI <- "6" + + CHARMM> if @testcasei le @testcases goto loop_tests + Parameter: TESTCASEI -> "6" + Parameter: TESTCASES -> "6" + Comparing "6" and "6". + IF test evaluated as true. Performing command + + CHARMM> stream @test@@testcasei + Parameter: TESTCASEI -> "6" + Parameter: TEST6 -> "TEST_DRUDE_IONS.STR" + VOPEN> Attempting to open::test_drude_ions.str:: + OPNLGU> Unit 99 opened for READONLY access to test_drude_ions.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * $ID: TEST_DRUDE_IONS.STR 23 2014-08-12 22:20:19Z ALEX $ + RDTITL> * TEST CASE, DRUDE IONS IN SEVERAL TOPPAR STREAM FILES + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> set boml 0 ! set to -1 if the series contains 3-membered rings + Parameter: BOML <- "0" + + CHARMM> + + CHARMM> ! 1) amino acid - ion pairs + CHARMM> set ion = 1 + Parameter: ION <- "1" + + CHARMM> + + CHARMM> label ionloop_aa + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> set molec LI + Parameter: MOLEC <- "LI" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "1" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "1" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "1" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "1" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "1" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "1" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "1" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "1" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "1" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "1" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "LI" + + RESIDUE SEQUENCE -- 1 RESIDUES + LI + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "1" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "1" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "1" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "1" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "1" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "1" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "1" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "1" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "1" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "1" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 45.24954 603.90295 12.50777 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 49.98690 -273.74260 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "LI" + RDCMND substituted energy or value "?ENER" to "45.2495" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "2" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "2" + Comparing "2" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> set molec POT + Parameter: MOLEC <- "POT" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "2" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "2" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "2" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "2" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "2" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "2" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "2" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "2" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "2" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "2" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "POT" + + RESIDUE SEQUENCE -- 1 RESIDUES + POT + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "2" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "2" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "2" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "2" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "2" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "2" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "2" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "2" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "2" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "2" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 43.55165 1.69790 12.35834 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 49.61307 -275.06666 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "POT" + RDCMND substituted energy or value "?ENER" to "43.5516" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "3" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "3" + Comparing "3" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> set molec SOD + Parameter: MOLEC <- "SOD" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "3" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "3" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "3" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "3" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "3" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "3" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "3" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "3" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "3" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "3" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "SOD" + + RESIDUE SEQUENCE -- 1 RESIDUES + SOD + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "3" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "3" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "3" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "3" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "3" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "3" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "3" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "3" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "3" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "3" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 44.72904 -1.17739 12.39942 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 49.92952 -274.20573 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "SOD" + RDCMND substituted energy or value "?ENER" to "44.729" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "4" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "4" + Comparing "4" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> set molec RB + Parameter: MOLEC <- "RB" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "4" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "4" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "4" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "4" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "4" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "4" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "4" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "4" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "4" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "4" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "RB" + + RESIDUE SEQUENCE -- 1 RESIDUES + RB + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "4" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "4" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "4" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "4" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "4" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "4" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "4" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "4" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "4" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "4" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 46.30986 -1.58082 12.29024 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 53.16002 -275.85540 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "RB" + RDCMND substituted energy or value "?ENER" to "46.3099" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "5" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "5" + Comparing "5" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "5" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "5" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "5" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "5" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> set molec CS + Parameter: MOLEC <- "CS" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "5" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "5" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "5" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "5" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "5" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "5" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "5" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "5" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "5" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "CS" + + RESIDUE SEQUENCE -- 1 RESIDUES + CS + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "5" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "5" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "5" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "5" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "5" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "5" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "5" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "5" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "5" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "5" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "5" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "5" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "5" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 52.60039 -6.29053 12.49074 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 60.22984 -276.63469 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "CS" + RDCMND substituted energy or value "?ENER" to "52.6004" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "6" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "6" + Comparing "6" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "6" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "6" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "6" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "6" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "6" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "6" and "6". + IF test evaluated as true. Performing command + + CHARMM> set molec F + Parameter: MOLEC <- "F" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "6" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "6" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "6" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "6" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "6" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "6" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "6" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "6" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "F" + + RESIDUE SEQUENCE -- 1 RESIDUES + F + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "6" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "6" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "6" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "6" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "6" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "6" and "6". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "6" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "6" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "6" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "6" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "6" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "6" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "6" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "6" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 234.84100 -182.24061 25.22384 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 55.17187 -89.33612 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "F" + RDCMND substituted energy or value "?ENER" to "234.841" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "7" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "7" + Comparing "7" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "7" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "7" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "7" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "7" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "7" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "7" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "7" and "7". + IF test evaluated as true. Performing command + + CHARMM> set molec CLA + Parameter: MOLEC <- "CLA" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "7" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "7" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "7" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "7" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "7" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "7" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "7" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "CLA" + + RESIDUE SEQUENCE -- 1 RESIDUES + CLA + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "7" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "7" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "7" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "7" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "7" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "7" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "7" and "7". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "7" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "7" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "7" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "7" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "7" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "7" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "7" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 256.04521 -21.20421 25.21069 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 77.89690 -90.85693 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "CLA" + RDCMND substituted energy or value "?ENER" to "256.045" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "8" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "8" + Comparing "8" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "8" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "8" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "8" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "8" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "8" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "8" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "8" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "8" and "8". + IF test evaluated as true. Performing command + + CHARMM> set molec BR + Parameter: MOLEC <- "BR" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "8" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "8" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "8" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "8" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "8" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "8" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "BR" + + RESIDUE SEQUENCE -- 1 RESIDUES + BR + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "8" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "8" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "8" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "8" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "8" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "8" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "8" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "8" and "8". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "8" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "8" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "8" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "8" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "8" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "8" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 273.97492 -17.92971 26.64067 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 96.34591 -91.37624 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "BR" + RDCMND substituted energy or value "?ENER" to "273.975" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "9" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "9" + Comparing "9" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "9" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "9" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "9" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "9" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "9" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "9" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "9" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "9" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "9" and "9". + IF test evaluated as true. Performing command + + CHARMM> set molec I + Parameter: MOLEC <- "I" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "9" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "9" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "9" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "9" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "9" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "I" + + RESIDUE SEQUENCE -- 1 RESIDUES + I + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "9" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "9" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "9" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "9" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "9" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "9" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "9" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "9" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "9" and "9". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "9" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "9" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "9" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "9" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "9" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 335.11442 -61.13950 38.20350 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 158.40921 -92.30003 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "I" + RDCMND substituted energy or value "?ENER" to "335.114" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -2.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "10" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "10" + Comparing "10" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "10" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "10" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "10" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "10" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "10" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "10" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "10" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "10" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "10" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "10" and "10". + IF test evaluated as true. Performing command + + CHARMM> set molec ZN + Parameter: MOLEC <- "ZN" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "10" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "10" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "10" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "10" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "ZN" + + RESIDUE SEQUENCE -- 1 RESIDUES + ZN + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "10" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "10" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "10" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "10" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "10" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "10" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "10" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "10" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "10" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "10" and "10". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "10" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "10" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "10" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "10" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -49.58252 384.69694 17.41589 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 49.59090 -368.17866 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "ZN" + RDCMND substituted energy or value "?ENER" to "-49.5825" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "11" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "11" + Comparing "11" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "11" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "11" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "11" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "11" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "11" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "11" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "11" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "11" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "11" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "11" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "11" and "11". + IF test evaluated as true. Performing command + + CHARMM> set molec MAG + Parameter: MOLEC <- "MAG" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "11" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "11" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "11" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "MAG" + + RESIDUE SEQUENCE -- 1 RESIDUES + MAG + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "11" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "11" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "11" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "11" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "11" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "11" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "11" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "11" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "11" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "11" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "11" and "11". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "11" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "11" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "11" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -48.47013 -1.11239 17.29773 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 49.90595 -367.38133 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "MAG" + RDCMND substituted energy or value "?ENER" to "-48.4701" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "12" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "12" + Comparing "12" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "12" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "12" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "12" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "12" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "12" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "12" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "12" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "12" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "12" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "12" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "12" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "12" and "12". + IF test evaluated as true. Performing command + + CHARMM> set molec CAL + Parameter: MOLEC <- "CAL" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "12" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "12" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "CAL" + + RESIDUE SEQUENCE -- 1 RESIDUES + CAL + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "12" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "12" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "12" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "12" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "12" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "12" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "12" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "12" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "12" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "12" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "12" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "12" and "12". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "12" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "12" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -48.79517 0.32504 16.99804 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 48.40260 -366.20301 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "CAL" + RDCMND substituted energy or value "?ENER" to "-48.7952" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "13" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "13" + Comparing "13" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "13" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "13" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "13" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "13" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "13" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "13" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "13" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "13" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "13" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "13" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "13" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "13" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "13" and "13". + IF test evaluated as true. Performing command + + CHARMM> set molec SR + Parameter: MOLEC <- "SR" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "13" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "SR" + + RESIDUE SEQUENCE -- 1 RESIDUES + SR + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "13" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "13" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "13" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "13" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "13" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "13" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "13" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "13" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "13" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "13" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "13" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "13" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "13" and "13". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "13" and "14". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -50.34605 1.55088 17.56510 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 49.43391 -368.78520 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "SR" + RDCMND substituted energy or value "?ENER" to "-50.346" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "14" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "14" + Comparing "14" and "14". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "14" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "14" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "14" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "14" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "14" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "14" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "14" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "14" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "14" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "14" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "14" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "14" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "14" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "14" and "14". + IF test evaluated as true. Performing command + + CHARMM> set molec BA + Parameter: MOLEC <- "BA" + + CHARMM> endif + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * PEPTIDE FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 5 + + SEQRDR> val gly tyr gly asp + + RESIDUE SEQUENCE -- 5 RESIDUES + VAL GLY TYR GLY ASP + ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 2 TITRATABLE GROUPS + THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF + HIS - 0 HSD - 0 HSE - 0 HSP - 0 ASP - 1 GLU - 0 LYS - 0 TYR - 1 + + CHARMM> + + CHARMM> gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: PROA mass of Drudes particles = 0.4000 + THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 36 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is PROA. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 5 + Number of atoms = 120 Number of groups = 10 + Number of bonds = 120 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 36 + Number of true-bonds = 120 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> !write coor pdb name temp.pdb + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "BA" + + RESIDUE SEQUENCE -- 1 RESIDUES + BA + + CHARMM> + + CHARMM> gene ION setup first none last none DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 37 + Number of true-bonds = 121 Number of zero-bonds = 0 + Number of aniso. terms = 9 Number of lone-pairs = 18 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "14" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "14" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "14" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "14" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 5 then + Comparing "14" and "5". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 6 then + Comparing "14" and "6". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 7 then + Comparing "14" and "7". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 8 then + Comparing "14" and "8". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 9 then + Comparing "14" and "9". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 10 then + Comparing "14" and "10". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 11 then + Comparing "14" and "11". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 12 then + Comparing "14" and "12". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 13 then + Comparing "14" and "13". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 14 then + Comparing "14" and "14". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1091 1091 1089 + : Ran out of space. RESIZING + with mode 5 found 717 exclusions and 502 interactions(1-4) + found 16 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6664 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER CROSS: CMAPs PMF1D PMF2D PRIMO +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -49.77418 -0.57187 17.75414 +ENER INTERN> 164.79752 40.37234 19.19440 57.75194 7.57256 +ENER CROSS> -20.68352 0.00000 0.00000 0.00000 +ENER EXTERN> 50.67959 -369.45901 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> echo @molec energy: ?ener + Parameter: MOLEC -> "BA" + RDCMND substituted energy or value "?ENER" to "-49.7742" + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 6 + Number of atoms = 122 Number of groups = 11 + Number of bonds = 121 Number of angles = 115 + Number of dihedrals = 162 Number of impropers = 10 + Number of cross-terms = 3 + Number of HB acceptors = 6 Number of HB donors = 4 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 55 + + CHARMM> delete atom sele all end + SELRPN> 122 atoms have been selected out of 122 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 6 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 121 bonds deleted + DELTIC: 115 angles deleted + DELTIC: 162 dihedrals deleted + DELTIC: 10 improper dihedrals deleted + DELTIC: 3 crossterm maps deleted + DELTIC: 4 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "15" + + CHARMM> if @ion .le. 14 goto ionloop_aa + Parameter: ION -> "15" + Comparing "15" and "14". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !2) nucleic acid - ions pairs + CHARMM> ! + CHARMM> !Note multiple loops + CHARMM> ! + CHARMM> + + CHARMM> set ion = 1 + Parameter: ION <- "1" + + CHARMM> + + CHARMM> ! at_od2c2c + CHARMM> + + CHARMM> label ionloop_na1 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> set molec LI + Parameter: MOLEC <- "LI" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 2 + + SEQRDR> ade thy + + RESIDUE SEQUENCE -- 2 RESIDUES + ADE THY + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 40 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 126 Number of groups = 10 + Number of bonds = 130 Number of angles = 122 + Number of dihedrals = 182 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 15 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = 0 + Number of aniso. terms = 15 Number of lone-pairs = 21 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 122 Number of groups = 10 + Number of bonds = 126 Number of angles = 118 + Number of dihedrals = 173 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 14 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = -4 + Number of aniso. terms = 14 Number of lone-pairs = 19 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox dna1 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 2 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 114 + Number of dihedrals = 164 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 41 + Number of true-bonds = 126 Number of zero-bonds = -4 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 42 + Number of true-bonds = 122 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "LI" + + RESIDUE SEQUENCE -- 1 RESIDUES + LI + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 43 + Number of true-bonds = 123 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1137 1137 1107 + : Ran out of space. RESIZING + with mode 5 found 831 exclusions and 589 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6309 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 96729.29154 -96779.06572 93436.23353 +ENER INTERN> 214.65562 30.25504 4.50577 51.72939 0.00004 +ENER EXTERN> 97383.76023 -955.61453 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 56 + + CHARMM> delete atom sele all end + SELRPN> 120 atoms have been selected out of 120 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 123 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 13 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "2" + + CHARMM> if @ion .le. 4 goto ionloop_na1 + Parameter: ION -> "2" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> set molec SOD + Parameter: MOLEC <- "SOD" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 2 + + SEQRDR> ade thy + + RESIDUE SEQUENCE -- 2 RESIDUES + ADE THY + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 40 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 126 Number of groups = 10 + Number of bonds = 130 Number of angles = 122 + Number of dihedrals = 182 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 15 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = 0 + Number of aniso. terms = 15 Number of lone-pairs = 21 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 122 Number of groups = 10 + Number of bonds = 126 Number of angles = 118 + Number of dihedrals = 173 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 14 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = -4 + Number of aniso. terms = 14 Number of lone-pairs = 19 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox dna1 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 2 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 114 + Number of dihedrals = 164 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 41 + Number of true-bonds = 126 Number of zero-bonds = -4 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 42 + Number of true-bonds = 122 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "SOD" + + RESIDUE SEQUENCE -- 1 RESIDUES + SOD + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 43 + Number of true-bonds = 123 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1137 1137 1107 + : Ran out of space. RESIZING + with mode 5 found 831 exclusions and 589 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6309 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 389598.56581-292869.27427 375461.71073 +ENER INTERN> 214.65562 30.25504 4.50577 51.72939 0.00004 +ENER EXTERN> 390313.23405 -1015.81409 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 56 + + CHARMM> delete atom sele all end + SELRPN> 120 atoms have been selected out of 120 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 123 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 13 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "3" + + CHARMM> if @ion .le. 4 goto ionloop_na1 + Parameter: ION -> "3" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> set molec POT + Parameter: MOLEC <- "POT" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 2 + + SEQRDR> ade thy + + RESIDUE SEQUENCE -- 2 RESIDUES + ADE THY + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 40 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 126 Number of groups = 10 + Number of bonds = 130 Number of angles = 122 + Number of dihedrals = 182 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 15 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = 0 + Number of aniso. terms = 15 Number of lone-pairs = 21 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 122 Number of groups = 10 + Number of bonds = 126 Number of angles = 118 + Number of dihedrals = 173 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 14 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = -4 + Number of aniso. terms = 14 Number of lone-pairs = 19 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox dna1 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 2 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 114 + Number of dihedrals = 164 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 41 + Number of true-bonds = 126 Number of zero-bonds = -4 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 42 + Number of true-bonds = 122 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "POT" + + RESIDUE SEQUENCE -- 1 RESIDUES + POT + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 43 + Number of true-bonds = 123 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1137 1137 1107 + : Ran out of space. RESIZING + with mode 5 found 831 exclusions and 589 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6309 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1759503.9208-1369905.3549 1731729.0012 +ENER INTERN> 214.65562 30.25504 4.50577 51.72939 0.00004 +ENER EXTERN> 1760361.1719 -1158.3970 0.0000 0.0000 0.0000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 56 + + CHARMM> delete atom sele all end + SELRPN> 120 atoms have been selected out of 120 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 123 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 13 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "4" + + CHARMM> if @ion .le. 4 goto ionloop_na1 + Parameter: ION -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> set molec RB + Parameter: MOLEC <- "RB" + + CHARMM> endif + + CHARMM> + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 2 + + SEQRDR> ade thy + + RESIDUE SEQUENCE -- 2 RESIDUES + ADE THY + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 40 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 126 Number of groups = 10 + Number of bonds = 130 Number of angles = 122 + Number of dihedrals = 182 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 15 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = 0 + Number of aniso. terms = 15 Number of lone-pairs = 21 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 122 Number of groups = 10 + Number of bonds = 126 Number of angles = 118 + Number of dihedrals = 173 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 14 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = -4 + Number of aniso. terms = 14 Number of lone-pairs = 19 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox dna1 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 2 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 114 + Number of dihedrals = 164 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 41 + Number of true-bonds = 126 Number of zero-bonds = -4 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 42 + Number of true-bonds = 122 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "RB" + + RESIDUE SEQUENCE -- 1 RESIDUES + RB + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 43 + Number of true-bonds = 123 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1137 1137 1107 + : Ran out of space. RESIZING + with mode 5 found 831 exclusions and 589 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6309 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 3383535.8850-1624031.9642 3328959.1722 +ENER INTERN> 214.65562 30.25504 4.50577 51.72939 0.00004 +ENER EXTERN> 3384464.9862 -1230.2471 0.0000 0.0000 0.0000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 56 + + CHARMM> delete atom sele all end + SELRPN> 120 atoms have been selected out of 120 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 123 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 13 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "5" + + CHARMM> if @ion .le. 4 goto ionloop_na1 + Parameter: ION -> "5" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !at_od30bn + CHARMM> + + CHARMM> set ion = 1 + Parameter: ION <- "1" + + CHARMM> + + CHARMM> label ionloop_na2 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> set molec LI + Parameter: MOLEC <- "LI" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 2 + + SEQRDR> ade thy + + RESIDUE SEQUENCE -- 2 RESIDUES + ADE THY + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 40 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 126 Number of groups = 10 + Number of bonds = 130 Number of angles = 122 + Number of dihedrals = 182 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 15 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = 0 + Number of aniso. terms = 15 Number of lone-pairs = 21 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 122 Number of groups = 10 + Number of bonds = 126 Number of angles = 118 + Number of dihedrals = 173 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 14 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = -4 + Number of aniso. terms = 14 Number of lone-pairs = 19 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox dna1 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 2 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 114 + Number of dihedrals = 164 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 41 + Number of true-bonds = 126 Number of zero-bonds = -4 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 42 + Number of true-bonds = 122 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "LI" + + RESIDUE SEQUENCE -- 1 RESIDUES + LI + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 43 + Number of true-bonds = 123 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1137 1137 1107 + : Ran out of space. RESIZING + with mode 5 found 831 exclusions and 589 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6309 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 8023.4567 3375512.4283 7733.4767 +ENER INTERN> 136.53543 30.23814 4.50577 51.72942 0.00004 +ENER EXTERN> 8558.92442 -758.47656 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 56 + + CHARMM> delete atom sele all end + SELRPN> 120 atoms have been selected out of 120 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 123 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 13 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "2" + + CHARMM> if @ion .le. 4 goto ionloop_na2 + Parameter: ION -> "2" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> set molec SOD + Parameter: MOLEC <- "SOD" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 2 + + SEQRDR> ade thy + + RESIDUE SEQUENCE -- 2 RESIDUES + ADE THY + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 40 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 126 Number of groups = 10 + Number of bonds = 130 Number of angles = 122 + Number of dihedrals = 182 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 15 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = 0 + Number of aniso. terms = 15 Number of lone-pairs = 21 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 122 Number of groups = 10 + Number of bonds = 126 Number of angles = 118 + Number of dihedrals = 173 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 14 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = -4 + Number of aniso. terms = 14 Number of lone-pairs = 19 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox dna1 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 2 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 114 + Number of dihedrals = 164 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 41 + Number of true-bonds = 126 Number of zero-bonds = -4 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 42 + Number of true-bonds = 122 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "SOD" + + RESIDUE SEQUENCE -- 1 RESIDUES + SOD + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 43 + Number of true-bonds = 123 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1137 1137 1107 + : Ran out of space. RESIZING + with mode 5 found 831 exclusions and 589 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6309 ATOM PAIRS WERE FOUND FOR ATOM LIST + 3 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 33496.38861 -25472.93195 30940.70756 +ENER INTERN> 136.53543 30.23814 4.50577 51.72942 0.00004 +ENER EXTERN> 34044.07614 -770.69633 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 56 + + CHARMM> delete atom sele all end + SELRPN> 120 atoms have been selected out of 120 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 123 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 13 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "3" + + CHARMM> if @ion .le. 4 goto ionloop_na2 + Parameter: ION -> "3" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> set molec POT + Parameter: MOLEC <- "POT" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 2 + + SEQRDR> ade thy + + RESIDUE SEQUENCE -- 2 RESIDUES + ADE THY + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 40 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 126 Number of groups = 10 + Number of bonds = 130 Number of angles = 122 + Number of dihedrals = 182 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 15 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = 0 + Number of aniso. terms = 15 Number of lone-pairs = 21 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 122 Number of groups = 10 + Number of bonds = 126 Number of angles = 118 + Number of dihedrals = 173 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 14 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = -4 + Number of aniso. terms = 14 Number of lone-pairs = 19 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox dna1 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 2 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 114 + Number of dihedrals = 164 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 41 + Number of true-bonds = 126 Number of zero-bonds = -4 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 42 + Number of true-bonds = 122 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "POT" + + RESIDUE SEQUENCE -- 1 RESIDUES + POT + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 43 + Number of true-bonds = 123 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1137 1137 1107 + : Ran out of space. RESIZING + with mode 5 found 831 exclusions and 589 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6309 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 88230.44527 -54734.05666 79910.05420 +ENER INTERN> 136.53543 30.23814 4.50577 51.72942 0.00004 +ENER EXTERN> 88807.09349 -799.65700 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 56 + + CHARMM> delete atom sele all end + SELRPN> 120 atoms have been selected out of 120 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 123 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 13 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "4" + + CHARMM> if @ion .le. 4 goto ionloop_na2 + Parameter: ION -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> set molec RB + Parameter: MOLEC <- "RB" + + CHARMM> endif + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 2 + + SEQRDR> ade thy + + RESIDUE SEQUENCE -- 2 RESIDUES + ADE THY + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 ADE . + ATOMS "O2P " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 2 THY . + ATOMS "O3' " "+P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 40 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 126 Number of groups = 10 + Number of bonds = 130 Number of angles = 122 + Number of dihedrals = 182 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 15 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = 0 + Number of aniso. terms = 15 Number of lone-pairs = 21 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 ADE O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 ADE DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 122 Number of groups = 10 + Number of bonds = 126 Number of angles = 118 + Number of dihedrals = 173 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 14 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 40 + Number of true-bonds = 130 Number of zero-bonds = -4 + Number of aniso. terms = 14 Number of lone-pairs = 19 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> patch deox dna1 2 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 2 THY O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 2 THY DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 114 + Number of dihedrals = 164 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 41 + Number of true-bonds = 126 Number of zero-bonds = -4 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 2 + Number of atoms = 118 Number of groups = 10 + Number of bonds = 122 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 42 + Number of true-bonds = 122 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "RB" + + RESIDUE SEQUENCE -- 1 RESIDUES + RB + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 43 + Number of true-bonds = 123 Number of zero-bonds = 0 + Number of aniso. terms = 13 Number of lone-pairs = 17 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 1137 1137 1107 + : Ran out of space. RESIZING + with mode 5 found 831 exclusions and 589 interactions(1-4) + found 21 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 6309 ATOM PAIRS WERE FOUND FOR ATOM LIST + 2 SPECIFIC THOLE SHIELDING PAIRS FOUND + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 172506.24561 -84275.80034 155852.87729 +ENER INTERN> 136.53543 30.23814 4.50577 51.72942 0.00004 +ENER EXTERN> 173097.48491 -814.24809 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 3 + Number of atoms = 120 Number of groups = 11 + Number of bonds = 123 Number of angles = 120 + Number of dihedrals = 176 Number of impropers = 5 + Number of cross-terms = 0 + Number of HB acceptors = 13 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 56 + + CHARMM> delete atom sele all end + SELRPN> 120 atoms have been selected out of 120 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 3 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 123 bonds deleted + DELTIC: 120 angles deleted + DELTIC: 176 dihedrals deleted + DELTIC: 5 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 13 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "5" + + CHARMM> if @ion .le. 4 goto ionloop_na2 + Parameter: ION -> "5" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !gua_nd2b1 + CHARMM> + + CHARMM> set ion = 1 + Parameter: ION <- "1" + + CHARMM> + + CHARMM> label ionloop_na3 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> set molec LI + Parameter: MOLEC <- "LI" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "LI" + + RESIDUE SEQUENCE -- 1 RESIDUES + LI + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 308520.32637-136014.08076 413809.92717 +ENER INTERN> 122.68856 12.23415 2.57080 20.11493 0.00039 +ENER EXTERN> 309050.51769 -687.80015 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "2" + + CHARMM> if @ion .le. 4 goto ionloop_na3 + Parameter: ION -> "2" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> set molec SOD + Parameter: MOLEC <- "SOD" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "SOD" + + RESIDUE SEQUENCE -- 1 RESIDUES + SOD + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 568611.69240-260091.36603 761799.83677 +ENER INTERN> 122.68856 12.23415 2.57080 20.11493 0.00039 +ENER EXTERN> 569177.06744 -722.98387 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "3" + + CHARMM> if @ion .le. 4 goto ionloop_na3 + Parameter: ION -> "3" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> set molec POT + Parameter: MOLEC <- "POT" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "POT" + + RESIDUE SEQUENCE -- 1 RESIDUES + POT + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1286711.4677 -718099.7753 1721886.7397 +ENER INTERN> 122.68856 12.23415 2.57080 20.11493 0.00039 +ENER EXTERN> 1287360.1755 -806.3167 0.0000 0.0000 0.0000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "4" + + CHARMM> if @ion .le. 4 goto ionloop_na3 + Parameter: ION -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> set molec RB + Parameter: MOLEC <- "RB" + + CHARMM> endif + + CHARMM> + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "RB" + + RESIDUE SEQUENCE -- 1 RESIDUES + RB + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1787216.9323 -500505.4646 2390152.4928 +ENER INTERN> 122.68856 12.23415 2.57080 20.11493 0.00039 +ENER EXTERN> 1787907.6330 -848.3095 0.0000 0.0000 0.0000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "5" + + CHARMM> if @ion .le. 4 goto ionloop_na3 + Parameter: ION -> "5" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !gua_nd2r6b + CHARMM> + + CHARMM> set ion = 1 + Parameter: ION <- "1" + + CHARMM> + + CHARMM> label ionloop_na4 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> set molec LI + Parameter: MOLEC <- "LI" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "LI" + + RESIDUE SEQUENCE -- 1 RESIDUES + LI + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 254591.9006 1532625.0317 342825.5667 +ENER INTERN> 156.32988 12.23631 2.57080 20.11479 0.00018 +ENER EXTERN> 254946.13570 -545.48705 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "2" + + CHARMM> if @ion .le. 4 goto ionloop_na4 + Parameter: ION -> "2" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> set molec SOD + Parameter: MOLEC <- "SOD" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "SOD" + + RESIDUE SEQUENCE -- 1 RESIDUES + SOD + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 493253.58974-238661.68913 665124.18234 +ENER INTERN> 156.32988 12.23631 2.57080 20.11479 0.00018 +ENER EXTERN> 493654.43155 -592.09376 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "3" + + CHARMM> if @ion .le. 4 goto ionloop_na4 + Parameter: ION -> "3" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> set molec POT + Parameter: MOLEC <- "POT" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "POT" + + RESIDUE SEQUENCE -- 1 RESIDUES + POT + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1149182.5123 -655928.9225 1558533.4868 +ENER INTERN> 156.32988 12.23631 2.57080 20.11479 0.00018 +ENER EXTERN> 1149693.7423 -702.4820 0.0000 0.0000 0.0000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "4" + + CHARMM> if @ion .le. 4 goto ionloop_na4 + Parameter: ION -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> set molec RB + Parameter: MOLEC <- "RB" + + CHARMM> endif + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "RB" + + RESIDUE SEQUENCE -- 1 RESIDUES + RB + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1754239.5932 -605057.0810 2387000.3643 +ENER INTERN> 156.32988 12.23631 2.57080 20.11479 0.00018 +ENER EXTERN> 1754806.4498 -758.1085 0.0000 0.0000 0.0000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "5" + + CHARMM> if @ion .le. 4 goto ionloop_na4 + Parameter: ION -> "5" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !gua_nd2r6c + CHARMM> + + CHARMM> set ion = 1 + Parameter: ION <- "1" + + CHARMM> + + CHARMM> label ionloop_na5 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> set molec LI + Parameter: MOLEC <- "LI" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "LI" + + RESIDUE SEQUENCE -- 1 RESIDUES + LI + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "1" and "1". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "1" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "1" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "1" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 282627.7236 1471611.8696 380232.2521 +ENER INTERN> 121.26562 12.23547 2.57080 20.11456 0.00017 +ENER EXTERN> 283118.70411 -647.16711 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "2" + + CHARMM> if @ion .le. 4 goto ionloop_na5 + Parameter: ION -> "2" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> set molec SOD + Parameter: MOLEC <- "SOD" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "SOD" + + RESIDUE SEQUENCE -- 1 RESIDUES + SOD + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "2" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "2" and "2". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "2" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "2" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 309965.14130 -27337.41769 416587.65696 +ENER INTERN> 121.26562 12.23547 2.57080 20.11456 0.00017 +ENER EXTERN> 310482.47715 -673.52245 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "3" + + CHARMM> if @ion .le. 4 goto ionloop_na5 + Parameter: ION -> "3" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> set molec POT + Parameter: MOLEC <- "POT" + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "POT" + + RESIDUE SEQUENCE -- 1 RESIDUES + POT + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "3" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "3" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "3" and "3". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "3" and "4". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 856858.2589 -546893.1176 1149621.1834 +ENER INTERN> 121.26562 12.23547 2.57080 20.11456 0.00017 +ENER EXTERN> 857438.01754 -735.94521 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "4" + + CHARMM> if @ion .le. 4 goto ionloop_na5 + Parameter: ION -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> set molec RB + Parameter: MOLEC <- "RB" + + CHARMM> endif + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * SSDNA FOR INTERACTIONS WITH IONS + RDTITL> * + + SEQRDR> 1 + + SEQRDR> gua + + RESIDUE SEQUENCE -- 1 RESIDUES + GUA + + CHARMM> + + CHARMM> generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + Drude polarizability will be setup for SEGID: DNA1 mass of Drudes particles = 0.4000 + THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE + THE PATCH '3TER' WILL BE USED FOR THE LAST RESIDUE + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "DP " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "DO1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "DO2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O5' " "P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O1P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "P " "O2P " WERE REQUESTED. + ** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O3' " "+P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O1P " "P " WERE REQUESTED. + ** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 GUA . + ATOMS "O2P " "P " WERE REQUESTED. + + MKDRUDE generate list and setup for drude polarizability + + All okay for 20 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is DNA1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 66 Number of groups = 5 + Number of bonds = 68 Number of angles = 60 + Number of dihedrals = 93 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 7 Number of HB donors = 6 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = 0 + Number of aniso. terms = 7 Number of lone-pairs = 13 + + CHARMM> + + CHARMM> patch deox dna1 1 setup warn + Drude polarizability will be setup mass of Drudes particles = 0.4000 + ATOM DNA1 1 GUA O2' AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHA AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA LPHB AND ALL REFERENCES TO IT DELETED. + ATOM DNA1 1 GUA DO2' AND ALL REFERENCES TO IT DELETED. + + Message from MAPIC: Atom numbers are changed. + LONEPRD: 2 lonepair atoms deleted + 1 anisotropic terms deleted + DELTIC: 5 bonds deleted + DELTIC: 4 angles deleted + DELTIC: 9 dihedrals deleted + DELTIC: 1 donors deleted + DELTIC: 1 acceptors deleted + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 56 + Number of dihedrals = 84 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 20 + Number of true-bonds = 68 Number of zero-bonds = -4 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + MKDRUDE generate list and setup for drude polarizability + + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + + CHARMM> + + CHARMM> AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 62 Number of groups = 5 + Number of bonds = 64 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = -0.00000 + Number of Drudes = 21 + Number of true-bonds = 64 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + DRUDE + + CHARMM> + + CHARMM> read coor pdb + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> PEPTIDE FOR INTERACTIONS WITH IONS + TITLE> * + + CHARMM> + + CHARMM> read sequence card + MAINIO> Sequence information being read from unit 99. + RDTITL> * ION + RDTITL> * + + SEQRDR> 1 + + SEQRDR> @molec + Parameter: MOLEC -> "RB" + + RESIDUE SEQUENCE -- 1 RESIDUES + RB + + CHARMM> + + CHARMM> gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + Number of Drudes = 22 + Number of true-bonds = 65 Number of zero-bonds = 0 + Number of aniso. terms = 6 Number of lone-pairs = 11 + + CHARMM> + + CHARMM> if ion eq 1 then + Comparing "4" and "1". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 2 then + Comparing "4" and "2". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 3 then + Comparing "4" and "3". + IF test evaluated as false. Skip to ELSE or ENDIF + + CHARMM> + + CHARMM> if ion eq 4 then + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> read coor pdb resid + read CHARMM-pdb format + SPATIAL COORDINATES BEING READ FROM UNIT 99 + TITLE> LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS + TITLE> DATE: 7/18/14 0: 9:19 CREATED BY USER: HUE + TITLE> * + + CHARMM> endif + + CHARMM> + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch + BYGRoup NOEXtnd NOEWald + CUTNB =999.000 CTEXNB =999.000 CTONNB =995.000 CTOFNB =997.000 + CGONNB = 0.000 CGOFNB = 10.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + 606 606 585 + : Ran out of space. RESIZING + with mode 5 found 442 exclusions and 319 interactions(1-4) + found 9 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 991233 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 1574 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 1189856.1584 -332997.8995 1594942.4135 +ENER INTERN> 121.26562 12.23547 2.57080 20.11456 0.00017 +ENER EXTERN> 1190467.3729 -767.4011 0.0000 0.0000 0.0000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> shake off + SHKCOM> SHAKE constraints removed. + + CHARMM> drude reset + DRUDE> Drude particles ready to be deleted + + Call: DELETE ATOMS SELECT TYPE D* END + + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 64 Number of groups = 6 + Number of bonds = 65 Number of angles = 59 + Number of dihedrals = 90 Number of impropers = 3 + Number of cross-terms = 0 + Number of HB acceptors = 6 Number of HB donors = 5 + Number of NB exclusions = 0 Total charge = 1.00000 + + CHARMM> lone clear +LONEPR: Lone-pair facility is cleared + ***** WARNING ***** Number of atoms with zero mass that are no longer lonepairs: 31 + + CHARMM> delete atom sele all end + SELRPN> 64 atoms have been selected out of 64 + + Message from MAPIC: Atom numbers are changed. + + Message from MAPIC: 2 residues deleted. + + Message from MAPIC: 2 segments deleted. + DELTIC: 65 bonds deleted + DELTIC: 59 angles deleted + DELTIC: 90 dihedrals deleted + DELTIC: 3 improper dihedrals deleted + DELTIC: 5 donors deleted + DELTIC: 6 acceptors deleted + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 0 Number of residues = 0 + Number of atoms = 0 Number of groups = 0 + Number of bonds = 0 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> incr ion by 1 + Parameter: ION <- "5" + + CHARMM> if @ion .le. 4 goto ionloop_na5 + Parameter: ION -> "5" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> incr testcasei + Parameter: TESTCASEI <- "7" + + CHARMM> if @testcasei le @testcases goto loop_tests + Parameter: TESTCASEI -> "7" + Parameter: TESTCASES -> "6" + Comparing "7" and "6". + IF test evaluated as false. Skipping command + + VCLOSE: Closing unit 90 with status "KEEP" +$$$$$$ New timer profile $$$$$ + Shake Setup 0.00 Other: 0.00 + Shake time 0.02 Other: 0.00 + List time 0.12 Other: 0.00 + Electrostatic & VDW 4.63 Other: 0.00 + Nonbond force 4.86 Other: 0.23 + Bond energy 0.01 Other: 0.00 + Angle energy 0.03 Other: 0.00 + Dihedral energy 0.05 Other: 0.00 + Restraints energy 0.00 Other: 0.00 + INTRNL energy 0.11 Other: 0.02 + Energy time 5.00 Other: 0.03 + Total time 7.52 Other: 2.38 + + NORMAL TERMINATION BY END OF FILE + NO WARNINGS WERE ISSUED + + $$$$$ JOB ACCOUNTING INFORMATION $$$$$ + ELAPSED TIME: 7.55 SECONDS + CPU TIME: 7.09 SECONDS diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_carbohydrate.str b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_carbohydrate.str new file mode 100644 index 00000000..d5bda602 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_carbohydrate.str @@ -0,0 +1,168 @@ +* $Id: test_drude_carbohydrate.str 28 2015-07-29 23:54:15Z alex $ +* Test case, Drude carbohydrate toppar file +* + +set boml 0 ! set to -1 if the series contains 3-membered rings + +set nres 47 + +!polyols +set resi1 egly +set seed1 1 O1 1 C1 1 C2 +set resi2 mglyol +set seed2 1 C1 1 C2 1 C3 +set resi3 meryol +set seed3 1 C1 1 C2 1 C3 +set resi4 dthrol +set seed4 1 C1 1 C2 1 C3 +set resi5 lthrol +set seed5 1 C1 1 C2 1 C3 +set resi6 mribol +set seed6 1 C1 1 C2 1 C3 +set resi7 daraol +set seed7 1 C1 1 C2 1 C3 +set resi8 laraol +set seed8 1 C1 1 C2 1 C3 +set resi9 mxylol +set seed9 1 C1 1 C2 1 C3 +set resi10 mallol +set seed10 1 C1 1 C2 1 C3 +set resi11 daltol +set seed11 1 C1 1 C2 1 C3 +set resi12 laltol +set seed12 1 C1 1 C2 1 C3 +set resi13 dgluol +set seed13 1 C1 1 C2 1 C3 +set resi14 lgluol +set seed15 1 C1 1 C2 1 C3 +set resi15 dmanol +set seed15 1 C1 1 C2 1 C3 +set resi16 lmanol +set seed16 1 C1 1 C2 1 C3 +set resi17 dgulol +set seed17 1 C1 1 C2 1 C3 +set resi18 lgulol +set seed18 1 C1 1 C2 1 C3 +set resi19 didiol +set seed19 1 C1 1 C2 1 C3 +set resi20 lidiol +set seed20 1 C1 1 C2 1 C3 +set resi21 mgalol +set seed21 1 C1 1 C2 1 C3 +!hexapyranoses +set resi22 aglc +set seed22 1 O5 1 C1 1 C2 +set resi23 bglc +set seed23 1 O5 1 C1 1 C2 +set resi24 aalt +set seed24 1 O5 1 C1 1 C2 +set resi25 balt +set seed25 1 O5 1 C1 1 C2 +set resi26 aall +set seed26 1 O5 1 C1 1 C2 +set resi27 ball +set seed27 1 O5 1 C1 1 C2 +set resi28 agal +set seed28 1 O5 1 C1 1 C2 +set resi29 bgal +set seed29 1 O5 1 C1 1 C2 +set resi30 agul +set seed30 1 O5 1 C1 1 C2 +set resi31 bgul +set seed31 1 O5 1 C1 1 C2 +set resi32 aido +set seed32 1 O5 1 C1 1 C2 +set resi33 bido +set seed33 1 O5 1 C1 1 C2 +set resi34 aman +set seed34 1 O5 1 C1 1 C2 +set resi35 bman +set seed35 1 O5 1 C1 1 C2 +set resi36 atal +set seed36 1 O5 1 C1 1 C2 +set resi37 btal +set seed37 1 O5 1 C1 1 C2 +!furanoses +set resi38 ARIB +set seed38 1 C4 1 O4 1 C1 +set resi39 BRIB +set seed39 1 C4 1 O4 1 C1 +set resi40 AARB +set seed40 1 C4 1 O4 1 C1 +set resi41 BARB +set seed41 1 C4 1 O4 1 C1 +set resi42 AXYF +set seed42 1 C4 1 O4 1 C1 +set resi43 BXYF +set seed43 1 C4 1 O4 1 C1 +set resi44 ALYF +set seed44 1 C4 1 O4 1 C1 +set resi45 BLYF +set seed45 1 C4 1 O4 1 C1 +set resi46 ADEO +set seed46 1 C4 1 O4 1 C1 +set resi47 BDEO +set seed47 1 C4 1 O4 1 C1 + +set count 1 +label loop_carb1 + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first none last none setup warn drude dmass 0.4 !show +bomlev 0 + +ic param +ic seed @seed@@count +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_carb1 diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_ions.str b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_ions.str new file mode 100644 index 00000000..d796aa89 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_ions.str @@ -0,0 +1,1249 @@ +* $Id: test_drude_ions.str 23 2014-08-12 22:20:19Z alex $ +* Test case, Drude ions in several toppar stream files +* + +set boml 0 ! set to -1 if the series contains 3-membered rings + +! 1) amino acid - ion pairs +set ion = 1 + +label ionloop_aa + +if ion eq 1 then + set molec LI +endif + +if ion eq 2 then + set molec POT +endif + +if ion eq 3 then + set molec SOD +endif + +if ion eq 4 then + set molec RB +endif + +if ion eq 5 then + set molec CS +endif + +if ion eq 6 then + set molec F +endif + +if ion eq 7 then + set molec CLA +endif + +if ion eq 8 then + set molec BR +endif + +if ion eq 9 then + set molec I +endif + +if ion eq 10 then + set molec ZN +endif + +if ion eq 11 then + set molec MAG +endif + +if ion eq 12 then + set molec CAL +endif + +if ion eq 13 then + set molec SR +endif + +if ion eq 14 then + set molec BA +endif + +read sequence card +* peptide for interactions with ions +* +5 +val gly tyr gly asp + +gene PROA setup first NTER last CTER DRUDE DMASS 0.4 + +!write coor pdb name temp.pdb + +read coor pdb +REMARK peptide for interactions with ions +ATOM 1 N VAL 1 -4.600 2.198 7.058 1.00 0.00 PROA +ATOM 2 DN VAL 1 -4.609 2.196 6.942 1.00 0.00 PROA +ATOM 3 HT1 VAL 1 -4.555 1.264 7.477 1.00 0.00 PROA +ATOM 4 HT2 VAL 1 -4.651 2.206 6.034 1.00 0.00 PROA +ATOM 5 HT3 VAL 1 -5.415 2.638 7.494 1.00 0.00 PROA +ATOM 6 CA VAL 1 -3.424 2.965 7.600 1.00 0.00 PROA +ATOM 7 DCA VAL 1 -3.403 2.973 7.597 1.00 0.00 PROA +ATOM 8 HA VAL 1 -2.600 2.637 6.980 1.00 0.00 PROA +ATOM 9 C VAL 1 -3.244 2.455 9.046 1.00 0.00 PROA +ATOM 10 DC VAL 1 -3.275 2.430 8.986 1.00 0.00 PROA +ATOM 11 O VAL 1 -2.091 2.303 9.512 1.00 0.00 PROA +ATOM 12 DO VAL 1 -2.095 2.289 9.491 1.00 0.00 PROA +ATOM 13 LPOA VAL 1 -1.969 2.396 9.254 1.00 0.00 PROA +ATOM 14 LPOB VAL 1 -2.204 2.209 9.774 1.00 0.00 PROA +ATOM 15 CB VAL 1 -3.656 4.447 7.376 1.00 0.00 PROA +ATOM 16 DCB VAL 1 -3.694 4.401 7.293 1.00 0.00 PROA +ATOM 17 HB VAL 1 -3.844 4.621 6.286 1.00 0.00 PROA +ATOM 18 CG1 VAL 1 -4.871 4.978 8.160 1.00 0.00 PROA +ATOM 19 DCG1 VAL 1 -4.843 4.951 8.090 1.00 0.00 PROA +ATOM 20 HG11 VAL 1 -4.712 4.850 9.252 1.00 0.00 PROA +ATOM 21 HG12 VAL 1 -5.008 6.066 7.978 1.00 0.00 PROA +ATOM 22 HG13 VAL 1 -5.814 4.466 7.881 1.00 0.00 PROA +ATOM 23 CG2 VAL 1 -2.388 5.237 7.743 1.00 0.00 PROA +ATOM 24 DCG2 VAL 1 -2.443 5.207 7.779 1.00 0.00 PROA +ATOM 25 HG21 VAL 1 -2.552 6.325 7.572 1.00 0.00 PROA +ATOM 26 HG22 VAL 1 -2.133 5.085 8.815 1.00 0.00 PROA +ATOM 27 HG23 VAL 1 -1.526 4.919 7.117 1.00 0.00 PROA +ATOM 28 N GLY 2 -4.393 2.033 9.663 1.00 0.00 PROA +ATOM 29 DN GLY 2 -4.429 2.027 9.507 1.00 0.00 PROA +ATOM 30 HN GLY 2 -5.106 2.733 9.917 1.00 0.00 PROA +ATOM 31 CA GLY 2 -4.400 0.819 10.446 1.00 0.00 PROA +ATOM 32 DCA GLY 2 -4.409 0.825 10.439 1.00 0.00 PROA +ATOM 33 HA1 GLY 2 -3.923 0.002 9.859 1.00 0.00 PROA +ATOM 34 HA2 GLY 2 -5.450 0.511 10.638 1.00 0.00 PROA +ATOM 35 C GLY 2 -3.689 1.075 11.743 1.00 0.00 PROA +ATOM 36 DC GLY 2 -3.675 1.072 11.703 1.00 0.00 PROA +ATOM 37 O GLY 2 -2.909 0.156 12.141 1.00 0.00 PROA +ATOM 38 DO GLY 2 -2.878 0.170 12.146 1.00 0.00 PROA +ATOM 39 LPOA GLY 2 -2.974 -0.011 11.900 1.00 0.00 PROA +ATOM 40 LPOB GLY 2 -2.838 0.315 12.385 1.00 0.00 PROA +ATOM 41 N TYR 3 -3.908 2.248 12.305 1.00 0.00 PROA +ATOM 42 DN TYR 3 -3.857 2.255 12.184 1.00 0.00 PROA +ATOM 43 HN TYR 3 -4.904 2.503 12.513 1.00 0.00 PROA +ATOM 44 CA TYR 3 -2.872 2.730 13.210 1.00 0.00 PROA +ATOM 45 DCA TYR 3 -2.843 2.727 13.235 1.00 0.00 PROA +ATOM 46 HA TYR 3 -1.916 2.621 12.647 1.00 0.00 PROA +ATOM 47 C TYR 3 -2.808 1.881 14.491 1.00 0.00 PROA +ATOM 48 DC TYR 3 -2.758 1.875 14.461 1.00 0.00 PROA +ATOM 49 O TYR 3 -1.737 1.821 15.112 1.00 0.00 PROA +ATOM 50 DO TYR 3 -1.703 1.778 15.080 1.00 0.00 PROA +ATOM 51 LPOA TYR 3 -1.605 2.002 14.912 1.00 0.00 PROA +ATOM 52 LPOB TYR 3 -1.860 1.640 15.317 1.00 0.00 PROA +ATOM 53 CB TYR 3 -2.995 4.207 13.650 1.00 0.00 PROA +ATOM 54 DCB TYR 3 -2.981 4.239 13.566 1.00 0.00 PROA +ATOM 55 HB1 TYR 3 -3.920 4.336 14.257 1.00 0.00 PROA +ATOM 56 HB2 TYR 3 -2.142 4.462 14.316 1.00 0.00 PROA +ATOM 57 CG TYR 3 -3.020 5.220 12.540 1.00 0.00 PROA +ATOM 58 DCG TYR 3 -2.976 5.267 12.491 1.00 0.00 PROA +ATOM 59 CD1 TYR 3 -4.252 5.771 12.121 1.00 0.00 PROA +ATOM 60 DCD1 TYR 3 -4.217 5.745 12.111 1.00 0.00 PROA +ATOM 61 HD1 TYR 3 -5.169 5.410 12.564 1.00 0.00 PROA +ATOM 62 CD2 TYR 3 -1.815 5.734 11.994 1.00 0.00 PROA +ATOM 63 DCD2 TYR 3 -1.786 5.748 11.973 1.00 0.00 PROA +ATOM 64 HD2 TYR 3 -0.882 5.325 12.343 1.00 0.00 PROA +ATOM 65 CE1 TYR 3 -4.289 6.840 11.201 1.00 0.00 PROA +ATOM 66 DCE1 TYR 3 -4.273 6.849 11.168 1.00 0.00 PROA +ATOM 67 HE1 TYR 3 -5.228 7.284 10.909 1.00 0.00 PROA +ATOM 68 CE2 TYR 3 -1.843 6.802 11.065 1.00 0.00 PROA +ATOM 69 DCE2 TYR 3 -1.810 6.878 10.986 1.00 0.00 PROA +ATOM 70 HE2 TYR 3 -0.926 7.196 10.668 1.00 0.00 PROA +ATOM 71 CZ TYR 3 -3.087 7.343 10.681 1.00 0.00 PROA +ATOM 72 DCZ TYR 3 -3.073 7.352 10.660 1.00 0.00 PROA +ATOM 73 OH TYR 3 -3.112 8.372 9.732 1.00 0.00 PROA +ATOM 74 DOH TYR 3 -3.122 8.361 9.725 1.00 0.00 PROA +ATOM 75 HH TYR 3 -2.210 8.686 9.624 1.00 0.00 PROA +ATOM 76 LP1A TYR 3 -3.072 8.244 9.408 1.00 0.00 PROA +ATOM 77 LP1B TYR 3 -3.168 8.681 9.885 1.00 0.00 PROA +ATOM 78 N GLY 4 -3.863 1.093 14.769 1.00 0.00 PROA +ATOM 79 DN GLY 4 -3.734 1.075 14.703 1.00 0.00 PROA +ATOM 80 HN GLY 4 -4.797 1.426 14.435 1.00 0.00 PROA +ATOM 81 CA GLY 4 -3.890 0.093 15.807 1.00 0.00 PROA +ATOM 82 DCA GLY 4 -3.905 0.074 15.805 1.00 0.00 PROA +ATOM 83 HA1 GLY 4 -2.919 0.027 16.347 1.00 0.00 PROA +ATOM 84 HA2 GLY 4 -4.060 -0.901 15.339 1.00 0.00 PROA +ATOM 85 C GLY 4 -5.038 0.414 16.735 1.00 0.00 PROA +ATOM 86 DC GLY 4 -5.000 0.419 16.712 1.00 0.00 PROA +ATOM 87 O GLY 4 -4.839 0.178 17.950 1.00 0.00 PROA +ATOM 88 DO GLY 4 -4.839 0.178 17.939 1.00 0.00 PROA +ATOM 89 LPOA GLY 4 -4.562 0.079 17.891 1.00 0.00 PROA +ATOM 90 LPOB GLY 4 -5.114 0.275 18.019 1.00 0.00 PROA +ATOM 91 N ASP 5 -6.092 0.960 16.186 1.00 0.00 PROA +ATOM 92 DN ASP 5 -5.958 0.997 16.146 1.00 0.00 PROA +ATOM 93 HN ASP 5 -6.325 0.642 15.238 1.00 0.00 PROA +ATOM 94 CA ASP 5 -7.012 1.902 16.800 1.00 0.00 PROA +ATOM 95 DCA ASP 5 -7.057 1.942 16.832 1.00 0.00 PROA +ATOM 96 HA ASP 5 -6.654 2.026 17.846 1.00 0.00 PROA +ATOM 97 C ASP 5 -8.528 1.413 16.746 1.00 0.00 PROA +ATOM 98 DC ASP 5 -8.497 1.391 16.752 1.00 0.00 PROA +ATOM 99 CB ASP 5 -6.814 3.289 16.116 1.00 0.00 PROA +ATOM 100 DCB ASP 5 -6.679 3.298 15.964 1.00 0.00 PROA +ATOM 101 HB1 ASP 5 -7.629 3.948 16.494 1.00 0.00 PROA +ATOM 102 HB2 ASP 5 -5.926 3.702 16.655 1.00 0.00 PROA +ATOM 103 CG ASP 5 -6.550 3.523 14.613 1.00 0.00 PROA +ATOM 104 DCG ASP 5 -6.516 3.451 14.487 1.00 0.00 PROA +ATOM 105 OD1 ASP 5 -6.640 4.730 14.229 1.00 0.00 PROA +ATOM 106 DOD1 ASP 5 -6.630 4.723 14.235 1.00 0.00 PROA +ATOM 107 OD2 ASP 5 -6.135 2.575 13.875 1.00 0.00 PROA +ATOM 108 DOD2 ASP 5 -6.036 2.511 13.819 1.00 0.00 PROA +ATOM 109 LP1A ASP 5 -6.722 4.936 14.500 1.00 0.00 PROA +ATOM 110 LP1B ASP 5 -6.575 4.751 13.886 1.00 0.00 PROA +ATOM 111 LP2A ASP 5 -6.098 2.283 14.064 1.00 0.00 PROA +ATOM 112 LP2B ASP 5 -6.094 2.689 13.546 1.00 0.00 PROA +ATOM 113 OT1 ASP 5 -9.361 2.260 17.176 1.00 0.00 PROA +ATOM 114 DOT1 ASP 5 -9.357 2.247 17.161 1.00 0.00 PROA +ATOM 115 OT2 ASP 5 -8.783 0.245 16.310 1.00 0.00 PROA +ATOM 116 DOT2 ASP 5 -8.779 0.241 16.306 1.00 0.00 PROA +ATOM 117 LPT1 ASP 5 -9.685 2.128 17.160 1.00 0.00 PROA +ATOM 118 LPT2 ASP 5 -9.195 2.552 17.274 1.00 0.00 PROA +ATOM 119 LPT3 ASP 5 -9.128 0.184 16.324 1.00 0.00 PROA +ATOM 120 LPT4 ASP 5 -8.487 0.086 16.213 1.00 0.00 PROA +END + +read sequence card +* ion +* +1 +@molec + +gene ION setup first none last none DRUDE DMASS 0.4 + +if ion eq 1 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 LI LI 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DLI LI 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 2 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 POT POT 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DPOT POT 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 3 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 SOD SOD 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DSOD SOD 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 4 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 RB RB 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DRB RB 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 5 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 CS CS 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DCS CS 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 6 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 F F 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DF F 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 7 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 CLA CLA 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DCLA CLA 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 8 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 BR BR 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DBR BR 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 9 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 I I 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DI I 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 10 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 ZN ZN 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DZN ZN 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 11 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 MAG MAG 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DMAG MAG 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 12 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 CAL CAL 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DCAL CAL 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 13 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 SR SR 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DSR SR 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + +if ion eq 14 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF AMINO ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 1 BA BA 1 -0.164 0.175 13.644 1.00 0.00 ION +ATOM 2 DBA BA 1 -0.126 0.157 13.626 1.00 0.00 ION +END +endif + + coor shake + energy + +echo @molec energy: ?ener + + shake off + drude reset + lone clear + delete atom sele all end + +incr ion by 1 +if @ion .le. 14 goto ionloop_aa + +!2) nucleic acid - ions pairs +! +!Note multiple loops +! + +set ion = 1 + +! at_od2c2c + +label ionloop_na1 + +if ion eq 1 then + set molec LI +endif + +if ion eq 2 then + set molec SOD +endif + +if ion eq 3 then + set molec POT +endif + +if ion eq 4 then + set molec RB +endif + + +read sequence card +* ssdna for interactions with ions +* +2 +ade thy + +generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + +patch deox dna1 1 setup warn +patch deox dna1 2 setup warn + +AUTOGENERATE ANGLES DIHEDRALS + +read coor pdb +REMARK peptide for interactions with ions +ATOM 1 H5T ADE 1 0.733 -8.612 -1.330 1.00 0.00 DNA1 +ATOM 2 O5' ADE 1 0.427 -7.826 -1.788 1.00 0.00 DNA1 +ATOM 3 DO5' ADE 1 0.410 -7.824 -1.779 1.00 0.00 DNA1 +ATOM 4 C5' ADE 1 1.443 -7.510 -2.756 1.00 0.00 DNA1 +ATOM 5 DC5' ADE 1 1.438 -7.502 -2.751 1.00 0.00 DNA1 +ATOM 6 H5' ADE 1 1.059 -6.719 -3.435 1.00 0.00 DNA1 +ATOM 7 H5'' ADE 1 1.675 -8.423 -3.345 1.00 0.00 DNA1 +ATOM 8 LP5A ADE 1 0.492 -7.659 -1.487 1.00 0.00 DNA1 +ATOM 9 LP5B ADE 1 0.187 -8.037 -1.931 1.00 0.00 DNA1 +ATOM 10 N9 ADE 1 1.098 -4.468 -0.370 1.00 0.00 DNA1 +ATOM 11 DN9 ADE 1 1.105 -4.465 -0.368 1.00 0.00 DNA1 +ATOM 12 C4 ADE 1 1.091 -3.102 -0.262 1.00 0.00 DNA1 +ATOM 13 DC4 ADE 1 1.102 -3.130 -0.258 1.00 0.00 DNA1 +ATOM 14 N3 ADE 1 2.168 -2.292 -0.209 1.00 0.00 DNA1 +ATOM 15 DN3 ADE 1 2.151 -2.297 -0.202 1.00 0.00 DNA1 +ATOM 16 LP3 ADE 1 2.502 -2.396 -0.221 1.00 0.00 DNA1 +ATOM 17 C2 ADE 1 1.802 -1.033 -0.105 1.00 0.00 DNA1 +ATOM 18 DC2 ADE 1 1.819 -1.030 -0.103 1.00 0.00 DNA1 +ATOM 19 H2 ADE 1 2.617 -0.311 -0.056 1.00 0.00 DNA1 +ATOM 20 N1 ADE 1 0.575 -0.516 -0.051 1.00 0.00 DNA1 +ATOM 21 DN1 ADE 1 0.531 -0.535 -0.051 1.00 0.00 DNA1 +ATOM 22 LP1 ADE 1 0.531 -0.170 -0.023 1.00 0.00 DNA1 +ATOM 23 C6 ADE 1 -0.482 -1.346 -0.105 1.00 0.00 DNA1 +ATOM 24 DC6 ADE 1 -0.497 -1.337 -0.107 1.00 0.00 DNA1 +ATOM 25 N6 ADE 1 -1.719 -0.832 -0.051 1.00 0.00 DNA1 +ATOM 26 DN6 ADE 1 -1.708 -0.825 -0.054 1.00 0.00 DNA1 +ATOM 27 H61 ADE 1 -2.530 -1.416 -0.089 1.00 0.00 DNA1 +ATOM 28 H62 ADE 1 -1.873 0.153 0.029 1.00 0.00 DNA1 +ATOM 29 C5 ADE 1 -0.219 -2.721 -0.217 1.00 0.00 DNA1 +ATOM 30 DC5 ADE 1 -0.223 -2.686 -0.217 1.00 0.00 DNA1 +ATOM 31 N7 ADE 1 -1.050 -3.830 -0.296 1.00 0.00 DNA1 +ATOM 32 DN7 ADE 1 -1.064 -3.854 -0.301 1.00 0.00 DNA1 +ATOM 33 LP7 ADE 1 -1.399 -3.853 -0.294 1.00 0.00 DNA1 +ATOM 34 C8 ADE 1 -0.229 -4.831 -0.385 1.00 0.00 DNA1 +ATOM 35 DC8 ADE 1 -0.244 -4.822 -0.376 1.00 0.00 DNA1 +ATOM 36 H8 ADE 1 -0.534 -5.874 -0.465 1.00 0.00 DNA1 +ATOM 37 C4' ADE 1 2.695 -7.020 -2.053 1.00 0.00 DNA1 +ATOM 38 DC4' ADE 1 2.684 -7.036 -2.010 1.00 0.00 DNA1 +ATOM 39 H4' ADE 1 3.593 -7.149 -2.693 1.00 0.00 DNA1 +ATOM 40 O4' ADE 1 2.477 -5.630 -1.823 1.00 0.00 DNA1 +ATOM 41 DO4' ADE 1 2.473 -5.632 -1.825 1.00 0.00 DNA1 +ATOM 42 LPRA ADE 1 2.149 -5.593 -1.939 1.00 0.00 DNA1 +ATOM 43 LPRB ADE 1 2.798 -5.501 -1.879 1.00 0.00 DNA1 +ATOM 44 LPX ADE 1 2.480 -5.699 -1.751 1.00 0.00 DNA1 +ATOM 45 C1' ADE 1 2.308 -5.333 -0.452 1.00 0.00 DNA1 +ATOM 46 DC1' ADE 1 2.316 -5.363 -0.445 1.00 0.00 DNA1 +ATOM 47 H1' ADE 1 3.214 -4.806 -0.084 1.00 0.00 DNA1 +ATOM 48 C2' ADE 1 2.148 -6.679 0.247 1.00 0.00 DNA1 +ATOM 49 DC2' ADE 1 2.203 -6.695 0.256 1.00 0.00 DNA1 +ATOM 50 H2'' ADE 1 1.082 -6.985 0.301 1.00 0.00 DNA1 +ATOM 51 H2' ADE 1 2.569 -6.656 1.275 1.00 0.00 DNA1 +ATOM 52 C3' ADE 1 2.950 -7.607 -0.665 1.00 0.00 DNA1 +ATOM 53 DC3' ADE 1 2.937 -7.606 -0.702 1.00 0.00 DNA1 +ATOM 54 H3' ADE 1 2.579 -8.652 -0.616 1.00 0.00 DNA1 +ATOM 55 O3' ADE 1 4.324 -7.545 -0.307 1.00 0.00 DNA1 +ATOM 56 DO3' ADE 1 4.352 -7.537 -0.197 1.00 0.00 DNA1 +ATOM 57 P THY 2 4.728 -7.626 1.238 1.00 0.00 DNA1 +ATOM 58 DP THY 2 4.732 -7.863 1.551 1.00 0.00 DNA1 +ATOM 59 O1P THY 2 6.009 -8.356 1.380 1.00 0.00 DNA1 +ATOM 60 DO1P THY 2 5.861 -8.344 1.473 1.00 0.00 DNA1 +ATOM 61 O2P THY 2 3.592 -8.164 2.021 1.00 0.00 DNA1 +ATOM 62 DO2P THY 2 3.891 -8.201 2.072 1.00 0.00 DNA1 +ATOM 63 O5' THY 2 4.945 -6.081 1.592 1.00 0.00 DNA1 +ATOM 64 DO5' THY 2 4.915 -6.179 1.579 1.00 0.00 DNA1 +ATOM 65 C5' THY 2 5.582 -5.227 0.624 1.00 0.00 DNA1 +ATOM 66 DC5' THY 2 5.575 -5.199 0.645 1.00 0.00 DNA1 +ATOM 67 H5' THY 2 4.811 -4.810 -0.059 1.00 0.00 DNA1 +ATOM 68 H5'' THY 2 6.308 -5.824 0.032 1.00 0.00 DNA1 +ATOM 69 N1 THY 2 3.515 -2.969 3.010 1.00 0.00 DNA1 +ATOM 70 DN1 THY 2 3.495 -2.965 3.014 1.00 0.00 DNA1 +ATOM 71 C6 THY 2 2.818 -4.148 2.980 1.00 0.00 DNA1 +ATOM 72 DC6 THY 2 2.825 -4.215 2.983 1.00 0.00 DNA1 +ATOM 73 H6 THY 2 3.425 -5.049 2.894 1.00 0.00 DNA1 +ATOM 74 C2 THY 2 2.884 -1.752 3.115 1.00 0.00 DNA1 +ATOM 75 DC2 THY 2 2.904 -1.746 3.122 1.00 0.00 DNA1 +ATOM 76 O2 THY 2 3.489 -0.694 3.143 1.00 0.00 DNA1 +ATOM 77 DO2 THY 2 3.475 -0.701 3.146 1.00 0.00 DNA1 +ATOM 78 LP2A THY 2 3.263 -0.428 3.171 1.00 0.00 DNA1 +ATOM 79 LP2B THY 2 3.833 -0.752 3.120 1.00 0.00 DNA1 +ATOM 80 N3 THY 2 1.506 -1.802 3.189 1.00 0.00 DNA1 +ATOM 81 DN3 THY 2 1.518 -1.818 3.190 1.00 0.00 DNA1 +ATOM 82 H3 THY 2 1.029 -0.916 3.267 1.00 0.00 DNA1 +ATOM 83 C4 THY 2 0.726 -2.941 3.166 1.00 0.00 DNA1 +ATOM 84 DC4 THY 2 0.716 -2.970 3.165 1.00 0.00 DNA1 +ATOM 85 O4 THY 2 -0.502 -2.859 3.239 1.00 0.00 DNA1 +ATOM 86 DO4 THY 2 -0.472 -2.838 3.239 1.00 0.00 DNA1 +ATOM 87 LP4A THY 2 -0.644 -3.179 3.228 1.00 0.00 DNA1 +ATOM 88 LP4B THY 2 -0.598 -2.523 3.264 1.00 0.00 DNA1 +ATOM 89 C5 THY 2 1.477 -4.168 3.053 1.00 0.00 DNA1 +ATOM 90 DC5 THY 2 1.484 -4.132 3.052 1.00 0.00 DNA1 +ATOM 91 C5M THY 2 0.707 -5.455 3.022 1.00 0.00 DNA1 +ATOM 92 DC5M THY 2 0.737 -5.489 3.011 1.00 0.00 DNA1 +ATOM 93 H51 THY 2 1.400 -6.317 3.116 1.00 0.00 DNA1 +ATOM 94 H52 THY 2 0.158 -5.544 2.060 1.00 0.00 DNA1 +ATOM 95 H53 THY 2 -0.013 -5.485 3.867 1.00 0.00 DNA1 +ATOM 96 C4' THY 2 6.306 -4.095 1.327 1.00 0.00 DNA1 +ATOM 97 DC4' THY 2 6.299 -4.110 1.357 1.00 0.00 DNA1 +ATOM 98 H4' THY 2 7.108 -3.671 0.688 1.00 0.00 DNA1 +ATOM 99 O4' THY 2 5.313 -3.099 1.557 1.00 0.00 DNA1 +ATOM 100 DO4' THY 2 5.301 -3.098 1.566 1.00 0.00 DNA1 +ATOM 101 LPRA THY 2 5.026 -3.262 1.441 1.00 0.00 DNA1 +ATOM 102 LPRB THY 2 5.497 -2.806 1.501 1.00 0.00 DNA1 +ATOM 103 LPX THY 2 5.356 -3.153 1.629 1.00 0.00 DNA1 +ATOM 104 C1' THY 2 5.002 -2.958 2.928 1.00 0.00 DNA1 +ATOM 105 DC1' THY 2 5.018 -2.996 2.923 1.00 0.00 DNA1 +ATOM 106 H1' THY 2 5.425 -2.000 3.296 1.00 0.00 DNA1 +ATOM 107 C2' THY 2 5.664 -4.141 3.627 1.00 0.00 DNA1 +ATOM 108 DC2' THY 2 5.656 -4.132 3.616 1.00 0.00 DNA1 +ATOM 109 H2'' THY 2 4.981 -5.015 3.681 1.00 0.00 DNA1 +ATOM 110 H2' THY 2 5.991 -3.875 4.655 1.00 0.00 DNA1 +ATOM 111 C3' THY 2 6.858 -4.420 2.715 1.00 0.00 DNA1 +ATOM 112 DC3' THY 2 6.864 -4.418 2.723 1.00 0.00 DNA1 +ATOM 113 H3' THY 2 7.172 -5.484 2.764 1.00 0.00 DNA1 +ATOM 114 O3' THY 2 7.933 -3.562 3.073 1.00 0.00 DNA1 +ATOM 115 DO3' THY 2 7.928 -3.566 3.078 1.00 0.00 DNA1 +ATOM 116 H3T THY 2 7.621 -2.654 3.075 1.00 0.00 DNA1 +ATOM 117 LP3A THY 2 7.944 -3.523 3.421 1.00 0.00 DNA1 +ATOM 118 LP3B THY 2 8.110 -3.465 2.787 1.00 0.00 DNA1 +END + +read sequence card +* ion +* +1 +@molec + +gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + + +if ion eq 1 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 LI LI 1 4.792 -8.165 2.022 1.00 0.00 ION +ATOM 64 DLI LI 1 4.890 -8.255 2.223 1.00 0.00 ION +END +endif + + + +if ion eq 2 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 SOD SOD 1 4.792 -8.165 2.022 1.00 0.00 ION +ATOM 64 DSOD SOD 1 4.890 -8.255 2.223 1.00 0.00 ION +END +endif + +if ion eq 3 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 POT POT 1 4.792 -8.165 2.022 1.00 0.00 ION +ATOM 64 DPOT POT 1 4.890 -8.255 2.223 1.00 0.00 ION +END +endif + +if ion eq 4 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 RB RB 1 4.792 -8.165 2.022 1.00 0.00 ION +ATOM 64 DRB RB 1 4.890 -8.255 2.223 1.00 0.00 ION +END +endif + + coor shake + energy + + shake off + drude reset + lone clear + delete atom sele all end + +incr ion by 1 +if @ion .le. 4 goto ionloop_na1 + +!at_od30bn + +set ion = 1 + +label ionloop_na2 + +if ion eq 1 then + set molec LI +endif + +if ion eq 2 then + set molec SOD +endif + +if ion eq 3 then + set molec POT +endif + +if ion eq 4 then + set molec RB +endif + +read sequence card +* ssdna for interactions with ions +* +2 +ade thy + +generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + +patch deox dna1 1 setup warn +patch deox dna1 2 setup warn + +AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + +read coor pdb +REMARK peptide for interactions with ions +ATOM 1 H5T ADE 1 0.733 -8.612 -1.330 1.00 0.00 DNA1 +ATOM 2 O5' ADE 1 0.427 -7.826 -1.788 1.00 0.00 DNA1 +ATOM 3 DO5' ADE 1 0.411 -7.822 -1.783 1.00 0.00 DNA1 +ATOM 4 C5' ADE 1 1.443 -7.510 -2.756 1.00 0.00 DNA1 +ATOM 5 DC5' ADE 1 1.438 -7.501 -2.752 1.00 0.00 DNA1 +ATOM 6 H5' ADE 1 1.059 -6.719 -3.435 1.00 0.00 DNA1 +ATOM 7 H5'' ADE 1 1.675 -8.423 -3.345 1.00 0.00 DNA1 +ATOM 8 LP5A ADE 1 0.492 -7.659 -1.487 1.00 0.00 DNA1 +ATOM 9 LP5B ADE 1 0.187 -8.037 -1.931 1.00 0.00 DNA1 +ATOM 10 N9 ADE 1 1.098 -4.468 -0.370 1.00 0.00 DNA1 +ATOM 11 DN9 ADE 1 1.110 -4.461 -0.367 1.00 0.00 DNA1 +ATOM 12 C4 ADE 1 1.091 -3.102 -0.262 1.00 0.00 DNA1 +ATOM 13 DC4 ADE 1 1.108 -3.123 -0.257 1.00 0.00 DNA1 +ATOM 14 N3 ADE 1 2.168 -2.292 -0.209 1.00 0.00 DNA1 +ATOM 15 DN3 ADE 1 2.159 -2.295 -0.200 1.00 0.00 DNA1 +ATOM 16 LP3 ADE 1 2.502 -2.396 -0.221 1.00 0.00 DNA1 +ATOM 17 C2 ADE 1 1.802 -1.033 -0.105 1.00 0.00 DNA1 +ATOM 18 DC2 ADE 1 1.821 -1.033 -0.102 1.00 0.00 DNA1 +ATOM 19 H2 ADE 1 2.617 -0.311 -0.056 1.00 0.00 DNA1 +ATOM 20 N1 ADE 1 0.575 -0.516 -0.051 1.00 0.00 DNA1 +ATOM 21 DN1 ADE 1 0.537 -0.532 -0.050 1.00 0.00 DNA1 +ATOM 22 LP1 ADE 1 0.531 -0.170 -0.023 1.00 0.00 DNA1 +ATOM 23 C6 ADE 1 -0.482 -1.346 -0.105 1.00 0.00 DNA1 +ATOM 24 DC6 ADE 1 -0.495 -1.338 -0.106 1.00 0.00 DNA1 +ATOM 25 N6 ADE 1 -1.719 -0.832 -0.051 1.00 0.00 DNA1 +ATOM 26 DN6 ADE 1 -1.707 -0.825 -0.054 1.00 0.00 DNA1 +ATOM 27 H61 ADE 1 -2.530 -1.416 -0.089 1.00 0.00 DNA1 +ATOM 28 H62 ADE 1 -1.873 0.153 0.029 1.00 0.00 DNA1 +ATOM 29 C5 ADE 1 -0.219 -2.721 -0.217 1.00 0.00 DNA1 +ATOM 30 DC5 ADE 1 -0.225 -2.684 -0.216 1.00 0.00 DNA1 +ATOM 31 N7 ADE 1 -1.050 -3.830 -0.296 1.00 0.00 DNA1 +ATOM 32 DN7 ADE 1 -1.069 -3.850 -0.300 1.00 0.00 DNA1 +ATOM 33 LP7 ADE 1 -1.399 -3.853 -0.294 1.00 0.00 DNA1 +ATOM 34 C8 ADE 1 -0.229 -4.831 -0.385 1.00 0.00 DNA1 +ATOM 35 DC8 ADE 1 -0.248 -4.825 -0.378 1.00 0.00 DNA1 +ATOM 36 H8 ADE 1 -0.534 -5.874 -0.465 1.00 0.00 DNA1 +ATOM 37 C4' ADE 1 2.695 -7.020 -2.053 1.00 0.00 DNA1 +ATOM 38 DC4' ADE 1 2.685 -7.028 -2.017 1.00 0.00 DNA1 +ATOM 39 H4' ADE 1 3.593 -7.149 -2.693 1.00 0.00 DNA1 +ATOM 40 O4' ADE 1 2.477 -5.630 -1.823 1.00 0.00 DNA1 +ATOM 41 DO4' ADE 1 2.475 -5.630 -1.821 1.00 0.00 DNA1 +ATOM 42 LPRA ADE 1 2.149 -5.593 -1.939 1.00 0.00 DNA1 +ATOM 43 LPRB ADE 1 2.798 -5.501 -1.879 1.00 0.00 DNA1 +ATOM 44 LPX ADE 1 2.480 -5.699 -1.751 1.00 0.00 DNA1 +ATOM 45 C1' ADE 1 2.308 -5.333 -0.452 1.00 0.00 DNA1 +ATOM 46 DC1' ADE 1 2.325 -5.351 -0.445 1.00 0.00 DNA1 +ATOM 47 H1' ADE 1 3.214 -4.806 -0.084 1.00 0.00 DNA1 +ATOM 48 C2' ADE 1 2.148 -6.679 0.247 1.00 0.00 DNA1 +ATOM 49 DC2' ADE 1 2.188 -6.667 0.241 1.00 0.00 DNA1 +ATOM 50 H2'' ADE 1 1.082 -6.985 0.301 1.00 0.00 DNA1 +ATOM 51 H2' ADE 1 2.569 -6.656 1.275 1.00 0.00 DNA1 +ATOM 52 C3' ADE 1 2.950 -7.607 -0.665 1.00 0.00 DNA1 +ATOM 53 DC3' ADE 1 2.927 -7.587 -0.724 1.00 0.00 DNA1 +ATOM 54 H3' ADE 1 2.579 -8.652 -0.616 1.00 0.00 DNA1 +ATOM 55 O3' ADE 1 4.324 -7.545 -0.307 1.00 0.00 DNA1 +ATOM 56 DO3' ADE 1 4.356 -7.509 -0.253 1.00 0.00 DNA1 +ATOM 57 P THY 2 4.728 -7.626 1.239 1.00 0.00 DNA1 +ATOM 58 DP THY 2 4.816 -7.518 1.270 1.00 0.00 DNA1 +ATOM 59 O1P THY 2 6.009 -8.356 1.380 1.00 0.00 DNA1 +ATOM 60 DO1P THY 2 6.000 -8.236 1.391 1.00 0.00 DNA1 +ATOM 61 O2P THY 2 3.592 -8.164 2.021 1.00 0.00 DNA1 +ATOM 62 DO2P THY 2 3.630 -8.118 2.014 1.00 0.00 DNA1 +ATOM 63 O5' THY 2 4.945 -6.081 1.592 1.00 0.00 DNA1 +ATOM 64 DO5' THY 2 5.292 -6.192 1.610 1.00 0.00 DNA1 +ATOM 65 C5' THY 2 5.582 -5.227 0.624 1.00 0.00 DNA1 +ATOM 66 DC5' THY 2 5.647 -5.328 0.784 1.00 0.00 DNA1 +ATOM 67 H5' THY 2 4.811 -4.810 -0.059 1.00 0.00 DNA1 +ATOM 68 H5'' THY 2 6.308 -5.824 0.032 1.00 0.00 DNA1 +ATOM 69 N1 THY 2 3.515 -2.969 3.010 1.00 0.00 DNA1 +ATOM 70 DN1 THY 2 3.511 -2.972 3.013 1.00 0.00 DNA1 +ATOM 71 C6 THY 2 2.818 -4.148 2.980 1.00 0.00 DNA1 +ATOM 72 DC6 THY 2 2.841 -4.207 2.982 1.00 0.00 DNA1 +ATOM 73 H6 THY 2 3.425 -5.049 2.894 1.00 0.00 DNA1 +ATOM 74 C2 THY 2 2.884 -1.752 3.115 1.00 0.00 DNA1 +ATOM 75 DC2 THY 2 2.905 -1.745 3.124 1.00 0.00 DNA1 +ATOM 76 O2 THY 2 3.489 -0.694 3.143 1.00 0.00 DNA1 +ATOM 77 DO2 THY 2 3.476 -0.708 3.147 1.00 0.00 DNA1 +ATOM 78 LP2A THY 2 3.263 -0.428 3.171 1.00 0.00 DNA1 +ATOM 79 LP2B THY 2 3.833 -0.752 3.120 1.00 0.00 DNA1 +ATOM 80 N3 THY 2 1.506 -1.802 3.189 1.00 0.00 DNA1 +ATOM 81 DN3 THY 2 1.517 -1.816 3.192 1.00 0.00 DNA1 +ATOM 82 H3 THY 2 1.029 -0.916 3.267 1.00 0.00 DNA1 +ATOM 83 C4 THY 2 0.726 -2.941 3.166 1.00 0.00 DNA1 +ATOM 84 DC4 THY 2 0.716 -2.964 3.167 1.00 0.00 DNA1 +ATOM 85 O4 THY 2 -0.502 -2.859 3.239 1.00 0.00 DNA1 +ATOM 86 DO4 THY 2 -0.467 -2.841 3.240 1.00 0.00 DNA1 +ATOM 87 LP4A THY 2 -0.644 -3.179 3.228 1.00 0.00 DNA1 +ATOM 88 LP4B THY 2 -0.598 -2.523 3.264 1.00 0.00 DNA1 +ATOM 89 C5 THY 2 1.477 -4.168 3.053 1.00 0.00 DNA1 +ATOM 90 DC5 THY 2 1.489 -4.136 3.054 1.00 0.00 DNA1 +ATOM 91 C5M THY 2 0.707 -5.455 3.022 1.00 0.00 DNA1 +ATOM 92 DC5M THY 2 0.736 -5.479 3.015 1.00 0.00 DNA1 +ATOM 93 H51 THY 2 1.400 -6.317 3.116 1.00 0.00 DNA1 +ATOM 94 H52 THY 2 0.158 -5.544 2.060 1.00 0.00 DNA1 +ATOM 95 H53 THY 2 -0.013 -5.485 3.867 1.00 0.00 DNA1 +ATOM 96 C4' THY 2 6.306 -4.095 1.327 1.00 0.00 DNA1 +ATOM 97 DC4' THY 2 6.290 -4.185 1.371 1.00 0.00 DNA1 +ATOM 98 H4' THY 2 7.108 -3.671 0.688 1.00 0.00 DNA1 +ATOM 99 O4' THY 2 5.313 -3.099 1.557 1.00 0.00 DNA1 +ATOM 100 DO4' THY 2 5.311 -3.122 1.572 1.00 0.00 DNA1 +ATOM 101 LPRA THY 2 5.026 -3.262 1.441 1.00 0.00 DNA1 +ATOM 102 LPRB THY 2 5.497 -2.806 1.501 1.00 0.00 DNA1 +ATOM 103 LPX THY 2 5.356 -3.153 1.629 1.00 0.00 DNA1 +ATOM 104 C1' THY 2 5.002 -2.958 2.928 1.00 0.00 DNA1 +ATOM 105 DC1' THY 2 5.031 -3.016 2.915 1.00 0.00 DNA1 +ATOM 106 H1' THY 2 5.425 -2.000 3.296 1.00 0.00 DNA1 +ATOM 107 C2' THY 2 5.664 -4.141 3.627 1.00 0.00 DNA1 +ATOM 108 DC2' THY 2 5.667 -4.157 3.583 1.00 0.00 DNA1 +ATOM 109 H2'' THY 2 4.981 -5.015 3.681 1.00 0.00 DNA1 +ATOM 110 H2' THY 2 5.991 -3.875 4.655 1.00 0.00 DNA1 +ATOM 111 C3' THY 2 6.858 -4.420 2.715 1.00 0.00 DNA1 +ATOM 112 DC3' THY 2 6.840 -4.459 2.694 1.00 0.00 DNA1 +ATOM 113 H3' THY 2 7.172 -5.484 2.764 1.00 0.00 DNA1 +ATOM 114 O3' THY 2 7.933 -3.562 3.073 1.00 0.00 DNA1 +ATOM 115 DO3' THY 2 7.915 -3.581 3.069 1.00 0.00 DNA1 +ATOM 116 H3T THY 2 7.621 -2.654 3.075 1.00 0.00 DNA1 +ATOM 117 LP3A THY 2 7.944 -3.523 3.421 1.00 0.00 DNA1 +ATOM 118 LP3B THY 2 8.110 -3.465 2.787 1.00 0.00 DNA1 +END + +read sequence card +* ion +* +1 +@molec + +gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + +if ion eq 1 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 LI LI 1 5.945 -6.381 1.592 1.00 0.00 ION +ATOM 64 DLI LI 1 5.988 -6.387 1.581 1.00 0.00 ION +END +endif + +if ion eq 2 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 SOD SOD 1 5.945 -6.381 1.592 1.00 0.00 ION +ATOM 64 DSOD SOD 1 5.988 -6.387 1.581 1.00 0.00 ION +END +endif + +if ion eq 3 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 POT POT 1 5.945 -6.381 1.592 1.00 0.00 ION +ATOM 64 DPOT POT 1 5.988 -6.387 1.581 1.00 0.00 ION +END +endif + +if ion eq 4 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 RB RB 1 5.945 -6.381 1.592 1.00 0.00 ION +ATOM 64 DRB RB 1 5.988 -6.387 1.581 1.00 0.00 ION +END +endif + + coor shake + energy + + shake off + drude reset + lone clear + delete atom sele all end + +incr ion by 1 +if @ion .le. 4 goto ionloop_na2 + +!gua_nd2b1 + +set ion = 1 + +label ionloop_na3 + +if ion eq 1 then + set molec LI +endif + +if ion eq 2 then + set molec SOD +endif + +if ion eq 3 then + set molec POT +endif + +if ion eq 4 then + set molec RB +endif + + +read sequence card +* ssdna for interactions with ions +* +1 +gua + +generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + +patch deox dna1 1 setup warn + +AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + +read coor pdb +REMARK peptide for interactions with ions +ATOM 1 H5T GUA 1 -0.377 -7.979 -2.289 1.00 0.00 DNA1 +ATOM 2 O5' GUA 1 0.427 -7.826 -1.788 1.00 0.00 DNA1 +ATOM 3 DO5' GUA 1 0.424 -7.822 -1.778 1.00 0.00 DNA1 +ATOM 4 C5' GUA 1 1.443 -7.510 -2.756 1.00 0.00 DNA1 +ATOM 5 DC5' GUA 1 1.441 -7.500 -2.748 1.00 0.00 DNA1 +ATOM 6 H5' GUA 1 1.059 -6.719 -3.435 1.00 0.00 DNA1 +ATOM 7 H5'' GUA 1 1.675 -8.423 -3.345 1.00 0.00 DNA1 +ATOM 8 LP5A GUA 1 0.422 -8.171 -1.728 1.00 0.00 DNA1 +ATOM 9 LP5B GUA 1 0.270 -7.533 -1.679 1.00 0.00 DNA1 +ATOM 10 N9 GUA 1 1.098 -4.468 -0.370 1.00 0.00 DNA1 +ATOM 11 DN9 GUA 1 1.111 -4.448 -0.371 1.00 0.00 DNA1 +ATOM 12 C4 GUA 1 1.101 -3.094 -0.261 1.00 0.00 DNA1 +ATOM 13 DC4 GUA 1 1.122 -3.092 -0.265 1.00 0.00 DNA1 +ATOM 14 N3 GUA 1 2.214 -2.317 -0.212 1.00 0.00 DNA1 +ATOM 15 DN3 GUA 1 2.242 -2.231 -0.225 1.00 0.00 DNA1 +ATOM 16 LP3 GUA 1 2.542 -2.438 -0.225 1.00 0.00 DNA1 +ATOM 17 C2 GUA 1 1.921 -1.023 -0.106 1.00 0.00 DNA1 +ATOM 18 DC2 GUA 1 2.031 -0.936 -0.192 1.00 0.00 DNA1 +ATOM 19 N1 GUA 1 0.628 -0.540 -0.053 1.00 0.00 DNA1 +ATOM 20 DN1 GUA 1 0.744 -0.523 -0.083 1.00 0.00 DNA1 +ATOM 21 H1 GUA 1 0.489 0.456 0.028 1.00 0.00 DNA1 +ATOM 22 N2 GUA 1 2.891 -0.108 -0.040 1.00 0.00 DNA1 +ATOM 23 DN2 GUA 1 2.875 -0.110 -0.449 1.00 0.00 DNA1 +ATOM 24 H21 GUA 1 3.856 -0.367 -0.073 1.00 0.00 DNA1 +ATOM 25 H22 GUA 1 2.685 0.867 0.037 1.00 0.00 DNA1 +ATOM 26 C6 GUA 1 -0.532 -1.326 -0.103 1.00 0.00 DNA1 +ATOM 27 DC6 GUA 1 -0.525 -1.318 -0.109 1.00 0.00 DNA1 +ATOM 28 O6 GUA 1 -1.635 -0.790 -0.047 1.00 0.00 DNA1 +ATOM 29 DO6 GUA 1 -1.600 -0.774 -0.049 1.00 0.00 DNA1 +ATOM 30 LP6A GUA 1 -1.887 -1.032 -0.064 1.00 0.00 DNA1 +ATOM 31 LP6B GUA 1 -1.598 -0.443 -0.020 1.00 0.00 DNA1 +ATOM 32 C5 GUA 1 -0.218 -2.705 -0.216 1.00 0.00 DNA1 +ATOM 33 DC5 GUA 1 -0.167 -2.659 -0.218 1.00 0.00 DNA1 +ATOM 34 N7 GUA 1 -1.059 -3.814 -0.295 1.00 0.00 DNA1 +ATOM 35 DN7 GUA 1 -1.053 -3.820 -0.296 1.00 0.00 DNA1 +ATOM 36 LP7 GUA 1 -1.408 -3.834 -0.293 1.00 0.00 DNA1 +ATOM 37 C8 GUA 1 -0.232 -4.827 -0.384 1.00 0.00 DNA1 +ATOM 38 DC8 GUA 1 -0.239 -4.813 -0.380 1.00 0.00 DNA1 +ATOM 39 H8 GUA 1 -0.543 -5.869 -0.463 1.00 0.00 DNA1 +ATOM 40 C4' GUA 1 2.695 -7.020 -2.053 1.00 0.00 DNA1 +ATOM 41 DC4' GUA 1 2.680 -7.012 -2.031 1.00 0.00 DNA1 +ATOM 42 H4' GUA 1 3.593 -7.149 -2.693 1.00 0.00 DNA1 +ATOM 43 O4' GUA 1 2.477 -5.630 -1.823 1.00 0.00 DNA1 +ATOM 44 DO4' GUA 1 2.472 -5.620 -1.827 1.00 0.00 DNA1 +ATOM 45 LPRA GUA 1 2.149 -5.593 -1.939 1.00 0.00 DNA1 +ATOM 46 LPRB GUA 1 2.798 -5.501 -1.879 1.00 0.00 DNA1 +ATOM 47 LPX GUA 1 2.480 -5.699 -1.751 1.00 0.00 DNA1 +ATOM 48 C1' GUA 1 2.308 -5.333 -0.452 1.00 0.00 DNA1 +ATOM 49 DC1' GUA 1 2.304 -5.325 -0.454 1.00 0.00 DNA1 +ATOM 50 H1' GUA 1 3.214 -4.806 -0.084 1.00 0.00 DNA1 +ATOM 51 C2' GUA 1 2.148 -6.679 0.247 1.00 0.00 DNA1 +ATOM 52 DC2' GUA 1 2.177 -6.675 0.254 1.00 0.00 DNA1 +ATOM 53 H2'' GUA 1 1.082 -6.985 0.301 1.00 0.00 DNA1 +ATOM 54 H2' GUA 1 2.569 -6.656 1.275 1.00 0.00 DNA1 +ATOM 55 C3' GUA 1 2.950 -7.607 -0.665 1.00 0.00 DNA1 +ATOM 56 DC3' GUA 1 2.956 -7.594 -0.666 1.00 0.00 DNA1 +ATOM 57 H3' GUA 1 2.579 -8.652 -0.616 1.00 0.00 DNA1 +ATOM 58 O3' GUA 1 4.324 -7.545 -0.307 1.00 0.00 DNA1 +ATOM 59 DO3' GUA 1 4.320 -7.535 -0.302 1.00 0.00 DNA1 +ATOM 60 H3T GUA 1 4.402 -7.620 0.647 1.00 0.00 DNA1 +ATOM 61 LP3A GUA 1 4.463 -7.866 -0.310 1.00 0.00 DNA1 +ATOM 62 LP3B GUA 1 4.419 -7.212 -0.255 1.00 0.00 DNA1 +END + +read sequence card +* ion +* +1 +@molec + +gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + + +if ion eq 1 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 LI LI 1 2.891 -0.108 -1.045 1.00 0.00 ION +ATOM 64 DLI LI 1 2.891 -0.105 -1.121 1.00 0.00 ION +END +endif + + + +if ion eq 2 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 SOD SOD 1 2.891 -0.108 -1.045 1.00 0.00 ION +ATOM 64 DSOD SOD 1 2.891 -0.105 -1.121 1.00 0.00 ION +END +endif + +if ion eq 3 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 POT POT 1 2.891 -0.108 -1.045 1.00 0.00 ION +ATOM 64 DPOT POT 1 2.891 -0.105 -1.121 1.00 0.00 ION +END +endif + +if ion eq 4 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 RB RB 1 2.891 -0.108 -1.045 1.00 0.00 ION +ATOM 64 DRB RB 1 2.891 -0.105 -1.121 1.00 0.00 ION +END +endif + + coor shake + energy + + shake off + drude reset + lone clear + delete atom sele all end + +incr ion by 1 +if @ion .le. 4 goto ionloop_na3 + +!gua_nd2r6b + +set ion = 1 + +label ionloop_na4 + +if ion eq 1 then + set molec LI +endif + +if ion eq 2 then + set molec SOD +endif + +if ion eq 3 then + set molec POT +endif + +if ion eq 4 then + set molec RB +endif + +read sequence card +* ssdna for interactions with ions +* +1 +gua + +generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + +patch deox dna1 1 setup warn + +AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + +read coor pdb +REMARK peptide for interactions with ions +ATOM 1 H5T GUA 1 -0.377 -7.979 -2.289 1.00 0.00 DNA1 +ATOM 2 O5' GUA 1 0.427 -7.826 -1.788 1.00 0.00 DNA1 +ATOM 3 DO5' GUA 1 0.425 -7.817 -1.773 1.00 0.00 DNA1 +ATOM 4 C5' GUA 1 1.443 -7.510 -2.756 1.00 0.00 DNA1 +ATOM 5 DC5' GUA 1 1.442 -7.496 -2.743 1.00 0.00 DNA1 +ATOM 6 H5' GUA 1 1.059 -6.719 -3.435 1.00 0.00 DNA1 +ATOM 7 H5'' GUA 1 1.675 -8.423 -3.345 1.00 0.00 DNA1 +ATOM 8 LP5A GUA 1 0.422 -8.171 -1.728 1.00 0.00 DNA1 +ATOM 9 LP5B GUA 1 0.270 -7.533 -1.679 1.00 0.00 DNA1 +ATOM 10 N9 GUA 1 1.098 -4.468 -0.370 1.00 0.00 DNA1 +ATOM 11 DN9 GUA 1 1.117 -4.410 -0.370 1.00 0.00 DNA1 +ATOM 12 C4 GUA 1 1.101 -3.094 -0.261 1.00 0.00 DNA1 +ATOM 13 DC4 GUA 1 1.255 -3.037 -0.331 1.00 0.00 DNA1 +ATOM 14 N3 GUA 1 2.214 -2.317 -0.210 1.00 0.00 DNA1 +ATOM 15 DN3 GUA 1 2.234 -2.326 -0.556 1.00 0.00 DNA1 +ATOM 16 LP3 GUA 1 2.542 -2.438 -0.222 1.00 0.00 DNA1 +ATOM 17 C2 GUA 1 1.921 -1.023 -0.106 1.00 0.00 DNA1 +ATOM 18 DC2 GUA 1 1.976 -1.167 -0.167 1.00 0.00 DNA1 +ATOM 19 N1 GUA 1 0.628 -0.540 -0.053 1.00 0.00 DNA1 +ATOM 20 DN1 GUA 1 0.733 -0.583 -0.070 1.00 0.00 DNA1 +ATOM 21 H1 GUA 1 0.489 0.456 0.028 1.00 0.00 DNA1 +ATOM 22 N2 GUA 1 2.891 -0.108 -0.043 1.00 0.00 DNA1 +ATOM 23 DN2 GUA 1 2.832 -0.176 -0.060 1.00 0.00 DNA1 +ATOM 24 H21 GUA 1 3.856 -0.367 -0.073 1.00 0.00 DNA1 +ATOM 25 H22 GUA 1 2.685 0.867 0.037 1.00 0.00 DNA1 +ATOM 26 C6 GUA 1 -0.532 -1.326 -0.103 1.00 0.00 DNA1 +ATOM 27 DC6 GUA 1 -0.529 -1.343 -0.103 1.00 0.00 DNA1 +ATOM 28 O6 GUA 1 -1.635 -0.790 -0.047 1.00 0.00 DNA1 +ATOM 29 DO6 GUA 1 -1.592 -0.779 -0.046 1.00 0.00 DNA1 +ATOM 30 LP6A GUA 1 -1.887 -1.032 -0.064 1.00 0.00 DNA1 +ATOM 31 LP6B GUA 1 -1.598 -0.443 -0.020 1.00 0.00 DNA1 +ATOM 32 C5 GUA 1 -0.218 -2.705 -0.216 1.00 0.00 DNA1 +ATOM 33 DC5 GUA 1 -0.101 -2.675 -0.215 1.00 0.00 DNA1 +ATOM 34 N7 GUA 1 -1.059 -3.814 -0.295 1.00 0.00 DNA1 +ATOM 35 DN7 GUA 1 -1.036 -3.806 -0.292 1.00 0.00 DNA1 +ATOM 36 LP7 GUA 1 -1.408 -3.834 -0.293 1.00 0.00 DNA1 +ATOM 37 C8 GUA 1 -0.232 -4.827 -0.384 1.00 0.00 DNA1 +ATOM 38 DC8 GUA 1 -0.226 -4.793 -0.375 1.00 0.00 DNA1 +ATOM 39 H8 GUA 1 -0.543 -5.869 -0.463 1.00 0.00 DNA1 +ATOM 40 C4' GUA 1 2.695 -7.020 -2.053 1.00 0.00 DNA1 +ATOM 41 DC4' GUA 1 2.673 -7.002 -2.022 1.00 0.00 DNA1 +ATOM 42 H4' GUA 1 3.593 -7.149 -2.693 1.00 0.00 DNA1 +ATOM 43 O4' GUA 1 2.477 -5.630 -1.823 1.00 0.00 DNA1 +ATOM 44 DO4' GUA 1 2.468 -5.608 -1.824 1.00 0.00 DNA1 +ATOM 45 LPRA GUA 1 2.149 -5.593 -1.939 1.00 0.00 DNA1 +ATOM 46 LPRB GUA 1 2.798 -5.501 -1.879 1.00 0.00 DNA1 +ATOM 47 LPX GUA 1 2.480 -5.699 -1.751 1.00 0.00 DNA1 +ATOM 48 C1' GUA 1 2.308 -5.333 -0.452 1.00 0.00 DNA1 +ATOM 49 DC1' GUA 1 2.291 -5.297 -0.455 1.00 0.00 DNA1 +ATOM 50 H1' GUA 1 3.214 -4.806 -0.084 1.00 0.00 DNA1 +ATOM 51 C2' GUA 1 2.148 -6.679 0.247 1.00 0.00 DNA1 +ATOM 52 DC2' GUA 1 2.177 -6.660 0.252 1.00 0.00 DNA1 +ATOM 53 H2'' GUA 1 1.082 -6.985 0.301 1.00 0.00 DNA1 +ATOM 54 H2' GUA 1 2.569 -6.656 1.275 1.00 0.00 DNA1 +ATOM 55 C3' GUA 1 2.950 -7.607 -0.665 1.00 0.00 DNA1 +ATOM 56 DC3' GUA 1 2.953 -7.589 -0.667 1.00 0.00 DNA1 +ATOM 57 H3' GUA 1 2.579 -8.652 -0.616 1.00 0.00 DNA1 +ATOM 58 O3' GUA 1 4.324 -7.545 -0.307 1.00 0.00 DNA1 +ATOM 59 DO3' GUA 1 4.315 -7.532 -0.302 1.00 0.00 DNA1 +ATOM 60 H3T GUA 1 4.402 -7.620 0.647 1.00 0.00 DNA1 +ATOM 61 LP3A GUA 1 4.463 -7.866 -0.310 1.00 0.00 DNA1 +ATOM 62 LP3B GUA 1 4.419 -7.212 -0.255 1.00 0.00 DNA1 +END + +read sequence card +* ion +* +1 +@molec + +gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + +if ion eq 1 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 LI LI 1 2.214 -2.317 -1.213 1.00 0.00 ION +ATOM 64 DLI LI 1 2.184 -2.308 -1.411 1.00 0.00 ION +END +endif + +if ion eq 2 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 SOD SOD 1 2.214 -2.317 -1.213 1.00 0.00 ION +ATOM 64 DSOD SOD 1 2.184 -2.308 -1.411 1.00 0.00 ION +END +endif + +if ion eq 3 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 POT POT 1 2.214 -2.317 -1.213 1.00 0.00 ION +ATOM 64 DPOT POT 1 2.184 -2.308 -1.411 1.00 0.00 ION +END +endif + +if ion eq 4 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 RB RB 1 2.214 -2.317 -1.213 1.00 0.00 ION +ATOM 64 DRB RB 1 2.184 -2.308 -1.411 1.00 0.00 ION +END +endif + + coor shake + energy + + shake off + drude reset + lone clear + delete atom sele all end + +incr ion by 1 +if @ion .le. 4 goto ionloop_na4 + +!gua_nd2r6c + +set ion = 1 + +label ionloop_na5 + +if ion eq 1 then + set molec LI +endif + +if ion eq 2 then + set molec SOD +endif + +if ion eq 3 then + set molec POT +endif + +if ion eq 4 then + set molec RB +endif + +read sequence card +* ssdna for interactions with ions +* +1 +gua + +generate DNA1 first 5TER last 3TER setup warn drude dmass 0.4 + +patch deox dna1 1 setup warn + +AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + +read coor pdb +REMARK peptide for interactions with ions +ATOM 1 H5T GUA 1 -0.377 -7.979 -2.289 1.00 0.00 DNA1 +ATOM 2 O5' GUA 1 0.427 -7.826 -1.788 1.00 0.00 DNA1 +ATOM 3 DO5' GUA 1 0.422 -7.820 -1.777 1.00 0.00 DNA1 +ATOM 4 C5' GUA 1 1.443 -7.510 -2.756 1.00 0.00 DNA1 +ATOM 5 DC5' GUA 1 1.439 -7.499 -2.747 1.00 0.00 DNA1 +ATOM 6 H5' GUA 1 1.059 -6.719 -3.435 1.00 0.00 DNA1 +ATOM 7 H5'' GUA 1 1.675 -8.423 -3.345 1.00 0.00 DNA1 +ATOM 8 LP5A GUA 1 0.422 -8.171 -1.728 1.00 0.00 DNA1 +ATOM 9 LP5B GUA 1 0.270 -7.533 -1.679 1.00 0.00 DNA1 +ATOM 10 N9 GUA 1 1.098 -4.468 -0.370 1.00 0.00 DNA1 +ATOM 11 DN9 GUA 1 1.102 -4.440 -0.372 1.00 0.00 DNA1 +ATOM 12 C4 GUA 1 1.101 -3.094 -0.261 1.00 0.00 DNA1 +ATOM 13 DC4 GUA 1 1.094 -3.066 -0.274 1.00 0.00 DNA1 +ATOM 14 N3 GUA 1 2.214 -2.317 -0.212 1.00 0.00 DNA1 +ATOM 15 DN3 GUA 1 2.195 -2.242 -0.223 1.00 0.00 DNA1 +ATOM 16 LP3 GUA 1 2.542 -2.438 -0.225 1.00 0.00 DNA1 +ATOM 17 C2 GUA 1 1.921 -1.023 -0.106 1.00 0.00 DNA1 +ATOM 18 DC2 GUA 1 1.821 -0.980 -0.188 1.00 0.00 DNA1 +ATOM 19 N1 GUA 1 0.628 -0.540 -0.052 1.00 0.00 DNA1 +ATOM 20 DN1 GUA 1 0.650 -0.538 -0.439 1.00 0.00 DNA1 +ATOM 21 H1 GUA 1 0.489 0.456 0.028 1.00 0.00 DNA1 +ATOM 22 N2 GUA 1 2.891 -0.108 -0.043 1.00 0.00 DNA1 +ATOM 23 DN2 GUA 1 2.800 -0.126 -0.071 1.00 0.00 DNA1 +ATOM 24 H21 GUA 1 3.856 -0.367 -0.073 1.00 0.00 DNA1 +ATOM 25 H22 GUA 1 2.685 0.867 0.037 1.00 0.00 DNA1 +ATOM 26 C6 GUA 1 -0.532 -1.326 -0.103 1.00 0.00 DNA1 +ATOM 27 DC6 GUA 1 -0.457 -1.262 -0.175 1.00 0.00 DNA1 +ATOM 28 O6 GUA 1 -1.635 -0.790 -0.047 1.00 0.00 DNA1 +ATOM 29 DO6 GUA 1 -1.567 -0.771 -0.065 1.00 0.00 DNA1 +ATOM 30 LP6A GUA 1 -1.887 -1.032 -0.064 1.00 0.00 DNA1 +ATOM 31 LP6B GUA 1 -1.598 -0.443 -0.020 1.00 0.00 DNA1 +ATOM 32 C5 GUA 1 -0.218 -2.705 -0.216 1.00 0.00 DNA1 +ATOM 33 DC5 GUA 1 -0.162 -2.601 -0.239 1.00 0.00 DNA1 +ATOM 34 N7 GUA 1 -1.059 -3.814 -0.295 1.00 0.00 DNA1 +ATOM 35 DN7 GUA 1 -1.050 -3.806 -0.299 1.00 0.00 DNA1 +ATOM 36 LP7 GUA 1 -1.408 -3.834 -0.293 1.00 0.00 DNA1 +ATOM 37 C8 GUA 1 -0.232 -4.827 -0.384 1.00 0.00 DNA1 +ATOM 38 DC8 GUA 1 -0.243 -4.801 -0.381 1.00 0.00 DNA1 +ATOM 39 H8 GUA 1 -0.543 -5.869 -0.463 1.00 0.00 DNA1 +ATOM 40 C4' GUA 1 2.695 -7.020 -2.053 1.00 0.00 DNA1 +ATOM 41 DC4' GUA 1 2.676 -7.012 -2.030 1.00 0.00 DNA1 +ATOM 42 H4' GUA 1 3.593 -7.149 -2.693 1.00 0.00 DNA1 +ATOM 43 O4' GUA 1 2.477 -5.630 -1.823 1.00 0.00 DNA1 +ATOM 44 DO4' GUA 1 2.468 -5.620 -1.827 1.00 0.00 DNA1 +ATOM 45 LPRA GUA 1 2.149 -5.593 -1.939 1.00 0.00 DNA1 +ATOM 46 LPRB GUA 1 2.798 -5.501 -1.879 1.00 0.00 DNA1 +ATOM 47 LPX GUA 1 2.480 -5.699 -1.751 1.00 0.00 DNA1 +ATOM 48 C1' GUA 1 2.308 -5.333 -0.452 1.00 0.00 DNA1 +ATOM 49 DC1' GUA 1 2.296 -5.325 -0.455 1.00 0.00 DNA1 +ATOM 50 H1' GUA 1 3.214 -4.806 -0.084 1.00 0.00 DNA1 +ATOM 51 C2' GUA 1 2.148 -6.679 0.247 1.00 0.00 DNA1 +ATOM 52 DC2' GUA 1 2.173 -6.674 0.254 1.00 0.00 DNA1 +ATOM 53 H2'' GUA 1 1.082 -6.985 0.301 1.00 0.00 DNA1 +ATOM 54 H2' GUA 1 2.569 -6.656 1.275 1.00 0.00 DNA1 +ATOM 55 C3' GUA 1 2.950 -7.607 -0.665 1.00 0.00 DNA1 +ATOM 56 DC3' GUA 1 2.954 -7.594 -0.666 1.00 0.00 DNA1 +ATOM 57 H3' GUA 1 2.579 -8.652 -0.616 1.00 0.00 DNA1 +ATOM 58 O3' GUA 1 4.324 -7.545 -0.307 1.00 0.00 DNA1 +ATOM 59 DO3' GUA 1 4.318 -7.536 -0.302 1.00 0.00 DNA1 +ATOM 60 H3T GUA 1 4.402 -7.620 0.647 1.00 0.00 DNA1 +ATOM 61 LP3A GUA 1 4.463 -7.866 -0.310 1.00 0.00 DNA1 +ATOM 62 LP3B GUA 1 4.419 -7.212 -0.255 1.00 0.00 DNA1 +END + +read sequence card +* ion +* +1 +@molec + +gene ION setup first none last none NOANGLE NODIHEDRAL DRUDE DMASS 0.4 + +if ion eq 1 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 LI LI 1 0.628 -0.540 -1.054 1.00 0.00 ION +ATOM 64 DLI LI 1 0.638 -0.536 -1.115 1.00 0.00 ION +END +endif + +if ion eq 2 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATION PAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 SOD SOD 1 0.628 -0.540 -1.054 1.00 0.00 ION +ATOM 64 DSOD SOD 1 0.638 -0.536 -1.115 1.00 0.00 ION +END +endif + +if ion eq 3 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 POT POT 1 0.628 -0.540 -1.054 1.00 0.00 ION +ATOM 64 DPOT POT 1 0.638 -0.536 -1.115 1.00 0.00 ION +END +endif + +if ion eq 4 then +read coor pdb resid +REMARK LOOP FOR CALCULATE SINGLE POINT ENERGY OF NUCLEIC ACID - CATIONPAIRS +REMARK DATE: 7/18/14 0: 9:19 CREATED BY USER: hue +ATOM 63 RB RB 1 0.628 -0.540 -1.054 1.00 0.00 ION +ATOM 64 DRB RB 1 0.638 -0.536 -1.115 1.00 0.00 ION +END +endif + + coor shake + energy + + shake off + drude reset + lone clear + delete atom sele all end + +incr ion by 1 +if @ion .le. 4 goto ionloop_na5 diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_lipid.str b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_lipid.str new file mode 100644 index 00000000..0d356bd5 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_lipid.str @@ -0,0 +1,86 @@ +* $Id: test_drude_lipid.str 28 2015-07-29 23:54:15Z alex $ +* Test case, Drude lipid toppar file +* + +set boml 0 ! set to -1 if the series contains 3-membered rings + +set nres 8 +set resi1 dmp +set resi2 eas +set resi3 mpro +set resi4 mbu +set resi5 pe +set resi6 pc +set resi7 dmpc +set resi8 dppc +set seed1 1 O11 1 P 1 O12 +set seed2 1 C2 1 OM 1 C +set seed3 1 C2 1 OM 1 C +set seed4 1 C2 1 OM 1 C +set seed5 1 HN1 1 N 1 C1 +set seed6 1 C4 1 N 1 C1 +set seed7 1 C15 1 N 1 C12 +set seed8 1 C15 1 N 1 C12 + +set count 1 +label loop_lipid1 + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first none last none setup warn drude dmass 0.4 !show +bomlev 0 + +ic param +ic seed @seed@@count +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_lipid1 diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_master_protein.str b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_master_protein.str new file mode 100644 index 00000000..17391f98 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_master_protein.str @@ -0,0 +1,420 @@ +* $Id: test_drude_master_protein.str 30 2015-07-30 13:50:30Z alex $ +* Test case, Drude master_protein toppar file +* + +! goto skip_to_ions_noble +! goto skip_to_master_prot_model +! goto skip_to_monopept + +set boml 0 ! set to -1 if the series contains 3-membered rings + +set nres 1 ! skip swm6 water due to bug +set resi1 swm4 +! set resi2 swm6 +set seed1 1 H1 1 OH2 1 H2 +! set seed2 1 H1 1 OH2 1 H2 + +set count 1 +label loop_master_water + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue noangle nodihedral first none last none setup warn drude dmass 0.4 !show +bomlev 0 + +ic param +ic seed @seed@@count +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_master_water + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +label skip_to_ions_noble + +set boml 0 ! set to -1 if the series contains 3-membered rings + +set nres 18 + +set resi1 li +set resi2 sod +set resi3 pot +set resi4 rb +set resi5 cs +set resi6 f +set resi7 cla +set resi8 br +set resi9 i +set resi10 zn +set resi11 mag +set resi12 cal +set resi13 sr +set resi14 ba +set resi15 he +set resi16 ne +set resi17 he1 +set resi18 ne1 + +set count 1 +label loop_master_ions_noble + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first none last none setup warn drude dmass 0.4 !show +bomlev 0 + +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_master_ions_noble + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +label skip_to_master_prot_model + +set boml 0 ! set to -1 if the series contains 3-membered rings + +set nres 1 + +set resi1 alad +set seed1 1 N 1 CA 1 C + +set count 1 +label loop_master_prot_model + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first none last none setup warn drude dmass 0.4 !show +bomlev 0 + +ic param +ic seed @seed@@count +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_master_prot_model + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +label skip_to_monopept + +set boml 0 + +!20 AA + 2 (His -> (HSD,HDE,HSP)) + 1 (patchable) +set naa 25 +set patched 25 ! 23 and higher are patched AA +set aa1 GLY +set aa2 PRO +set aa3 ALA +set aa4 ARG +set aa5 ASN +set aa6 ASP +set aa7 CYS +set aa8 GLN +set aa9 GLU +set aa10 HSD +set aa11 HSE +set aa12 HSP +set aa13 ILE +set aa14 LEU +set aa15 LYS +set aa16 MET +set aa17 PHE +set aa18 SER +set aa19 TRP +set aa20 THR +set aa21 TYR +set aa22 VAL +set aa23 HSD +set pa23 HS2 +set aa24 ASP +set pa24 ASPP +set aa25 GLU +set pa25 GLUP +! the following patches are not yet created +!set aa26 LYS +!set pa26 LSN +!set aa27 CYS +!set pa27 CYSM +!set aa28 CYS +!set pa28 CSSM +!set aa29 ARG +!set pa29 RNE +!set aa30 ARG +!set pa30 RNH + +set npn 2 +set pn1 NTER +set pn2 ACE + +set npc 5 +set pc1 CTER +set pc2 CNEU +set pc3 CT1 +set pc4 CT2 +set pc5 CT3 + +set special 2 ! 1 and 2 should be treated special when termini +set s1npn 2 +set s1pn1 GNTE +set s1pn2 ACE + +set s1npc 5 +set s1pc1 CTEG +set s1pc2 CNEG +set s1pc3 CT1G +set s1pc4 CT2G +set s1pc5 CT3 + +set s2npn 2 +set s2pn1 PROP +set s2pn2 ACP + +set s2npc 2 +set s2pc1 CTEP +set s2pc2 CT3 + +set countaa 1 +label loop_aa + +set residue @aa@@countaa +if @countaa le @special then + set varp s@countaa + else + set varp + endif +set maxnt @@@{varp}npn +set maxct @@@{varp}npc +if @countaa ge @patched then + set patch @pa@@countaa + else + set patch @residue ! for variable "nam" below + endif + +set countnt 1 +label loop_nt + +set first @@@{varp}pn@@countnt + +set countct 1 +label loop_ct + +set last @@@{varp}pc@@countct + +set nam @{first}-@{patch}-ala-@{patch}-@last + +read sequence card +* @nam +* +3 +@RESIDUE ALA @RESIDUE + +bomlev @boml +generate @residue first @first last @last setup warn drude dmass 0.4 !show +if @countaa ge @patched then + patch @patch @residue 1 setup warn drude dmass 0.4 !show + patch @patch @residue 3 setup warn drude dmass 0.4 !show + endif +bomlev 0 + +ic param +ic seed 1 N 1 CA 1 C +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @nam starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@nam.psf + write coor pdb name @pdbdir/@nam_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + write coor pdb name error.pdb + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @nam minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@nam_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @nam dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr countct +if countct le @maxct goto loop_ct + +incr countnt +if countnt le @maxnt goto loop_nt + +incr countaa +if countaa le @naa goto loop_aa + diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_model.str b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_model.str new file mode 100644 index 00000000..b0730594 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_model.str @@ -0,0 +1,233 @@ +* $Id: test_drude_model.str 28 2015-07-29 23:54:15Z alex $ +* Test case, Drude model compounds ("model") toppar file +* + +set boml 0 ! set to -1 if the series contains 3-membered rings + +set count 1 +set nres 72 + +!ethers +set resi1 DEET +set resi2 DME +set resi3 DMET +set resi4 MEET +set resi5 THF +set resi6 TF2M +set resi7 THP +set resi8 MPET +set resi9 MBET +set resi10 EPET +!alkanes +set resi11 ETHA +set resi12 PROP1 +set resi13 IBUT +set resi14 BUTA +set resi15 PENT +set resi16 HEXA +set resi17 HEPT +set resi18 CPEN +set resi19 CHEX +set resi20 MEOH +set resi21 ETOH +set resi22 PRO1 +set resi23 BUO1 +set resi24 PRO2 +set resi25 BUO2 +!aromatics +set resi26 BENZ +set resi27 TOLU +!amides +set resi28 ACEM +set resi29 NMA +set resi30 DMA +!heterocycles +set resi31 PYR +set resi32 PYRM +set resi33 PYRR +set resi34 IMID +set resi35 INDO +set resi36 PUR1 +set resi37 PUR0 +set resi38 4MIM +set resi39 MIND +!misc +set resi40 MAS +set resi41 ACEH +!charged +set resi42 IMIM +set resi43 GUAN +set resi44 MGUAN +set resi45 PHEN +!sulfur containing +set resi46 MESH +set resi47 ETSH +set resi48 PRSH +set resi49 BUSH +set resi50 DMDS +set resi51 DMS +set resi52 EMS +!lipid model compounds +set resi53 NC4 +set resi54 NH5 +set resi55 NC5 +set resi56 ACET +set resi57 ETAM +set resi58 NEOP +set resi59 BU2M +set resi60 BU22M +set resi61 BU23M +set resi62 CPNM +set resi63 CHXM +set resi64 DIOX +set resi65 CRES +set resi66 B3MO1 +set resi67 CPO1 +set resi68 BGUAN +set resi69 CHOL +!misc alkanes +set resi70 DECA +set resi71 PEND +set resi72 OCTD + +set seed1 1 C1 1 C2 1 O3 +set seed2 1 C1 1 O2 1 C3 +set seed3 1 C1 1 O2 1 C3 +set seed4 1 C1 1 C2 1 O3 +set seed5 1 O1 1 C1 1 C2 +set seed6 1 O1 1 C1 1 C2 +set seed7 1 O1 1 C1 1 C2 +set seed8 1 C1 1 O2 1 C3 +set seed9 1 C1 1 O2 1 C3 +set seed10 1 C1 1 C2 1 O3 +set seed11 1 H11 1 C1 1 C2 +set seed12 1 C1 1 C2 1 C3 +set seed13 1 C1 1 CT 1 C2 +set seed14 1 C1 1 C2 1 C3 +set seed15 1 C1 1 C2 1 C3 +set seed16 1 C1 1 C2 1 C3 +set seed17 1 C1 1 C2 1 C3 +set seed18 1 C1 1 C2 1 C3 +set seed19 1 C1 1 C2 1 C3 +set seed20 1 HO1 1 O1 1 C1 +set seed21 1 HO1 1 O1 1 C1 +set seed22 1 HO1 1 O1 1 C1 +set seed23 1 HO1 1 O1 1 C1 +set seed24 1 HO2 1 O2 1 C2 +set seed25 1 HO2 1 O2 1 C2 +set seed26 1 CG 1 CD1 1 CE1 +set seed27 1 CG 1 CD1 1 CE1 +set seed28 1 N 1 C 1 CL +set seed29 1 N 1 C 1 CL +set seed30 1 N 1 C 1 CL +set seed31 1 CG 1 CD1 1 CE1 +set seed32 1 C4 1 C5 1 C6 +set seed33 1 N5 1 C1 1 C2 +set seed34 1 ND1 1 CG 1 CD2 +set seed35 1 CG 1 CD1 1 NE1 +set seed36 1 C6 1 C5 1 C4 +set seed37 1 C6 1 C5 1 C4 +set seed38 1 ND1 1 CG 1 CB +set seed39 1 CG 1 CD1 1 NE1 +set seed40 1 C1 1 C 1 OM +set seed41 1 O2 1 C2 1 C1 +set seed42 1 CG 1 CD2 1 NE2 +set seed43 1 N1 1 C 1 N2 +set seed44 1 N1 1 C 1 N2 +set seed45 1 CG 1 CD1 1 CE1 +set seed46 1 HS1 1 S1 1 C1 +set seed47 1 HS1 1 S1 1 C1 +set seed48 1 HS1 1 S1 1 C1 +set seed49 1 HS1 1 S1 1 C1 +set seed50 1 H11 1 C1 1 S1 +set seed51 1 H21 1 C2 1 S1 +set seed52 1 H31 1 C3 1 C2 +set seed53 1 C1 1 N 1 C2 +set seed54 1 HN4 1 N 1 C1 +set seed55 1 C4 1 N 1 C1 +set seed56 1 O1 1 C2 1 C1 +set seed57 1 N 1 C1 1 C5 +set seed58 1 C2 1 CT 1 C1 +set seed59 1 C1 1 CT 1 C2 +set seed60 1 C4 1 CT 1 C1 +set seed61 1 C1 1 CT 1 C2 +set seed62 1 C1 1 C2 1 C3 +set seed63 1 C1 1 C2 1 C3 +set seed64 1 O1 1 C1 1 C2 +set seed65 1 CG 1 CD1 1 CE1 +set seed66 1 C1 1 C2 1 C3 +set seed67 1 C1 1 C2 1 C3 +set seed68 1 CA 1 CB 1 CG +set seed69 1 C4 1 N 1 C1 +set seed70 1 C1 1 C2 1 C3 +set seed71 1 C1 1 C2 1 C3 +set seed72 1 C1 1 C2 1 C3 + +label loop_model1 + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first none last none setup warn drude dmass 0.4 !show + +!temporary +!if @count ge 70 then +!IC GENERATE +!endif + +ic param +ic seed @seed@@count +ic build +!ic print +coor sdrude +coor shake +!coor print +bomlev 0 + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_model1 diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_nucleic_acids.str b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_nucleic_acids.str new file mode 100644 index 00000000..b78178ee --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_nucleic_acids.str @@ -0,0 +1,242 @@ +* $Id: test_drude_nucleic_acids.str 28 2015-07-29 23:54:15Z alex $ +* Test case, Drude carbohydrate toppar file +* + +set boml 0 ! set to -1 if the series contains 3-membered rings + +!loop for nucleotides +set nres 4 +set resi1 ade +set resi2 cyt +set resi3 thy +set resi4 gua + +set seed1 1 c5' 1 c4' 1 c3' +set seed2 1 c5' 1 c4' 1 c3' +set seed3 1 c5' 1 c4' 1 c3' +set seed4 1 c5' 1 c4' 1 c3' + + +set count 1 +label loop_na1 + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first 5ter last 3ter setup warn drude dmass 0.4 !show +bomlev 0 + +patch deox @residue 1 setup warn + +autogenerate angles dihedrals + +ic param +ic seed @seed@@count +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_na1 + +! various NA model compounds +set nres 13 +set resi1 adeb +set resi2 made +set resi3 cytb +set resi4 mcyt +set resi5 thyb +set resi6 mthy +set resi7 guab +set resi8 urab +set resi9 t3ps +set resi10 t3pm +set resi11 dmpn +set resi12 bribna +set resi13 bdeona + +set seed1 1 c4 1 n9 1 C8 +set seed2 1 c4 1 n9 1 C8 +set seed3 1 c2 1 n1 1 C6 +set seed4 1 c2 1 n1 1 C6 +set seed5 1 c2 1 n1 1 C6 +set seed6 1 c2 1 n1 1 C6 +set seed7 1 c4 1 n9 1 C8 +set seed8 1 c2 1 n1 1 C6 +set seed9 1 c4A 1 O4A 1 C1A +set seed10 1 c4' 1 O4' 1 C1' +set seed11 1 o11 1 p 1 o12 +set seed12 1 c4 1 o4 1 c1 +set seed13 1 c4 1 o4 1 c1 + +set count 1 +label loop_na2 + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first none last none setup warn drude dmass 0.4 !show +bomlev 0 + +ic param +ic seed @seed@@count +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_na2 + + +!oligonucleotides, RNA not yet tested + +read sequence card +* 1bna, strand 1 +* +12 +cyt gua cyt gua ade ade thy thy cyt gua cyt gua + +generate a first 5ter last 3ter setup warn drude dmass 0.4 !show + +! patch for deoxy +patch deox a 1 setup warn +patch deox a 2 setup warn +patch deox a 3 setup warn +patch deox a 4 setup warn +patch deox a 5 setup warn +patch deox a 6 setup warn +patch deox a 7 setup warn +patch deox a 8 setup warn +patch deox a 9 setup warn +patch deox a 10 setup warn +patch deox a 11 setup warn +patch deox a 12 setup warn + +autogenerate angles dihedrals + +ic para +ic seed 1 C5' 1 C4' 1 C3' +ic build + +coor sdrude +coor shake +coor print + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +cons harm force 100000. sele .not. type D* end +mini ABNR nstep 200 nprint 20 +cons harm clear +energy + +echo @residue starting E: ?ener + +set residue oligomer_dna + +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb +endif + +!write data to check +!write title unit 90 +!* @residue @enetmp minimized E: ?ener ?rdip +!* + +shake off +drude reset +lone clear +delete atom sele all end + diff --git a/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_nucleic_acids_no_rna.str b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_nucleic_acids_no_rna.str new file mode 100644 index 00000000..b7c6cfa4 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/test/test_drude_nucleic_acids_no_rna.str @@ -0,0 +1,245 @@ +* $Id: test_drude_nucleic_acids.str 28 2015-07-29 23:54:15Z alex $ +* Test case, Drude carbohydrate toppar file +* + +set boml 0 ! set to -1 if the series contains 3-membered rings + +!loop for nucleotides +set nres 4 +set resi1 ade +set resi2 cyt +set resi3 thy +set resi4 gua + +set seed1 1 c5' 1 c4' 1 c3' +set seed2 1 c5' 1 c4' 1 c3' +set seed3 1 c5' 1 c4' 1 c3' +set seed4 1 c5' 1 c4' 1 c3' + + +set count 1 +label loop_na1 + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first 5ter last 3ter setup warn drude dmass 0.4 !show +bomlev 0 + +patch deox @residue 1 setup warn + +autogenerate angles dihedrals + +ic param +ic seed @seed@@count +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_na1 + +! various NA model compounds +set nres 12 +!set nres 13 +set resi1 adeb +set resi2 made +set resi3 cytb +set resi4 mcyt +set resi5 thyb +set resi6 mthy +set resi7 guab +set resi8 urab +set resi9 t3ps +set resi10 t3pm +set resi11 dmpn +!set resi12 bribna ! RNA doesn't run +!set resi13 bdeona +!set resi12 bribna +set resi12 bdeona + +set seed1 1 c4 1 n9 1 C8 +set seed2 1 c4 1 n9 1 C8 +set seed3 1 c2 1 n1 1 C6 +set seed4 1 c2 1 n1 1 C6 +set seed5 1 c2 1 n1 1 C6 +set seed6 1 c2 1 n1 1 C6 +set seed7 1 c4 1 n9 1 C8 +set seed8 1 c2 1 n1 1 C6 +set seed9 1 c4A 1 O4A 1 C1A +set seed10 1 c4' 1 O4' 1 C1' +set seed11 1 o11 1 p 1 o12 +set seed12 1 c4 1 o4 1 c1 +set seed13 1 c4 1 o4 1 c1 + +set count 1 +label loop_na2 + +set residue @resi@@count +read sequence @residue 1 + +bomlev @boml +generate @residue first none last none setup warn drude dmass 0.4 !show +bomlev 0 + +ic param +ic seed @seed@@count +ic build +coor sdrude +coor shake + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +if @mindr eq 0 then + energy + else + cons harm force 100000. sele .not. type D* end + mini ABNR nstep 200 nprint 20 + cons harm clear + endif +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb + endif + +if @mini ne 0 then + mini sd nstep 1000 tolgrd 0.0001 nprint 100 + if ?grms gt 0.0001 mini abnr nstep 1000 tolgrd 0.0001 + if ?grms gt 0.0001 then + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + echu + echo FATAL ERROR: MINIMIZATION NOT CONVERGED + stop + endif + echo @residue minimized E: ?ener + if @?pdbdir eq 1 then ! cannot use 1-line syntax because substitution will fail + write coor pdb name @pdbdir/@residue_min.pdb + endif + endif + +coor orient +coor dipole oxyz select all end +echo @residue dipole: ?rdip +!! Check molecular polarizability +!VIBRAN +!diag dscf fini step 0.001 +!END + +shake off +drude reset +lone clear +delete atom sele all end + +incr count +if count le @nres goto loop_na2 + + +!oligonucleotides, RNA not yet tested + +read sequence card +* 1bna, strand 1 +* +12 +cyt gua cyt gua ade ade thy thy cyt gua cyt gua + +generate a first 5ter last 3ter setup warn drude dmass 0.4 !show + +! patch for deoxy +patch deox a 1 setup warn +patch deox a 2 setup warn +patch deox a 3 setup warn +patch deox a 4 setup warn +patch deox a 5 setup warn +patch deox a 6 setup warn +patch deox a 7 setup warn +patch deox a 8 setup warn +patch deox a 9 setup warn +patch deox a 10 setup warn +patch deox a 11 setup warn +patch deox a 12 setup warn + +autogenerate angles dihedrals + +ic para +ic seed 1 C5' 1 C4' 1 C3' +ic build + +coor sdrude +coor shake +coor print + +update inbfrq -1 ihbfrq 0 switch atom vatom vswitch cutnb 999.0 ctofnb 997.0 ctonnb 995.0 + +cons harm force 100000. sele .not. type D* end +mini ABNR nstep 200 nprint 20 +cons harm clear +energy + +echo @residue starting E: ?ener + +set residue oligomer_dna + +echo @residue starting E: ?ener + +if @?pdbdir eq 1 then + write psf card name @pdbdir/@residue.psf + write coor pdb name @pdbdir/@residue_start.pdb +endif + +!write data to check +!write title unit 90 +!* @residue @enetmp minimized E: ?ener ?rdip +!* + +shake off +drude reset +lone clear +delete atom sele all end + diff --git a/charmm/toppar/drude/drude_toppar_2015_7/toppar_defs_2013c.str b/charmm/toppar/drude/drude_toppar_2015_7/toppar_defs_2013c.str new file mode 100644 index 00000000..210f8dc5 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/toppar_defs_2013c.str @@ -0,0 +1,20 @@ +* $Id: toppar_defs.str 26 2015-07-27 18:26:03Z alex $ +* Streams all drude stream files +* + +! Requires the variable "toppar" + +set streamfiles 5 +set str1 toppar_drude_master_protein_2013c.str +set str2 toppar_drude_lipid_2013c.str +set str3 toppar_drude_carbohydrate_2013c.str +set str4 toppar_drude_model_2013c.str +set str5 toppar_drude_nucleic_acid_2013c_no_rna.str + +set i 1 +label loop_streams +stream @toppar/@str@@i +incr i +if @i le @streamfiles goto loop_streams + +return diff --git a/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_carbohydrate_2013c.str b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_carbohydrate_2013c.str new file mode 100644 index 00000000..b98c3f23 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_carbohydrate_2013c.str @@ -0,0 +1,5918 @@ +* $Id: toppar_drude_carbohydrate.str 25 2015-07-24 16:15:55Z alex $ +* DRUDE topology and parameter stream file for carbohydrates +* + +!OD31F to OD31E, but OD31E parameters maintained +!requires toppar_drude_master*.str + +!carbohydrates + +!references +! +!Patel, D.S., He, X., and MacKerell, A.D., Jr., +!“Polarizable Empirical Force Field for Hexopyranose Monosaccharides +!based on the Classical Drude Oscillator,” Journal of Physical +!Chemistry B., ASAP article, 2014, 10.1021/jp412696m, NIHMSID #566721 +! +!polyalcohols +! +!He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., “Polarizable +!Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical +!Drude Oscillator,” Biopolymers, 99: 724-738 2013, DOI: +!10.1002/bip.22286 +! +!furanoses +! +!Jana, M. and MacKerell, A.D., Jr., “CHARMM Drude Polarizable Force +!Field for Aldopentofuranoses and Methyl-aldopentofuranosides,” Journal +!of Physical Chemistry B, 119: 7846-7859, 2015, doi: +!10.1021/acs.jpcb.5b01767, PMC4483154 +! + +read rtf card append +* Drude carbohydrates +* +38 + +DEFA FIRS NONE LAST NONE +AUTOGENERATE ANGLES DIHEDRALS DRUDE + +!ioformat extended + +!polyols +RESI EGLY 0.000 ! ethylene glycol, xhe +! +! H21 H11 +! \ / +! H22--C2--C1--H11 +! / \ +! HO2--2O O1--HO1 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H21 HDA2A 0.070 +ATOM H22 HDA2A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 + +BOND C1 C2 C1 O1 C2 O2 +BOND C1 H11 C1 H12 O1 HO1 +BOND C2 H21 C2 H22 O2 HO2 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +IC HO1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC O2 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O2 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 O2 HO2 0.0000 0.00 180.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI MGLYOL 0.000 ! Meso-GLYcerOL, glycerol, xhe +! +! HO2 +! | +! H11 O2 H31 +! | | | +! HO1--O1--C1--C2--C3--O3--HO3 +! | | | +! H12 H2 H32 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H31 HDA2A 0.070 +ATOM H32 HDA2A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 + +BOND C1 C2 C2 C3 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H31 C3 H32 O3 HO3 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 O3 1.5614 104.35 -179.21 109.84 1.3948 +IC O1 C2 *C1 H11 1.4314 107.79 134.95 116.24 1.0888 +IC O1 C2 *C1 H12 1.4314 107.79 -110.15 104.20 1.0930 +IC C2 C1 O1 HO1 1.5614 107.79 -44.46 96.37 1.0016 +IC O1 C1 C2 C3 1.4314 107.79 -179.55 104.35 1.5671 +IC C3 C1 *C2 O2 1.5671 104.35 -114.63 106.58 1.4526 +IC O2 C1 *C2 H2 1.4526 106.58 -127.27 107.70 1.0874 +IC C1 C2 O2 HO2 1.5614 106.58 -179.25 99.24 0.9726 +IC O3 C2 *C3 H31 1.3948 109.84 -124.08 111.99 1.1041 +IC H31 C2 *C3 H32 1.1041 111.99 -118.34 109.12 1.1120 +IC C2 C3 O3 HO3 1.5671 109.84 168.92 113.91 1.0009 +PATCH FIRST NONE LAST NONE + +RESI MERYOL 0.000 ! Meso-ERYthritOL (mertitol) +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! H3-C3-O3-HO3 +! | +! H41-C4-H42 +! | +! O4-HO4 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H41 HDA2A 0.070 +ATOM H42 HDA2A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H41 C4 H42 O4 HO4 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6259 108.86 -172.77 113.90 1.5743 +IC O1 C2 *C1 H11 1.4014 112.12 115.55 103.98 1.1662 +IC O1 C2 *C1 H12 1.4014 112.12 -120.90 108.56 1.1365 +IC C2 C1 O1 HO1 1.6259 112.12 -83.41 109.87 0.9573 +IC O1 C1 C2 C3 1.4014 112.12 -40.11 108.86 1.5519 +IC C3 C1 *C2 O2 1.5519 108.86 120.00 117.26 1.4093 +IC O2 C1 *C2 H2 1.4093 117.26 125.89 103.86 1.0853 +IC C1 C2 O2 HO2 1.6259 117.26 161.24 110.44 0.9565 +IC C4 C2 *C3 O3 1.5743 113.90 122.82 112.99 1.4151 +IC O3 C2 *C3 H3 1.4151 112.99 119.44 108.28 1.0882 +IC C2 C3 O3 HO3 1.5519 112.99 59.23 107.97 0.9870 +IC C2 C3 C4 O4 1.5519 113.90 64.75 112.09 1.4267 +IC O4 C3 *C4 H41 1.4267 112.09 -125.03 113.11 1.1073 +IC H41 C3 *C4 H42 1.1073 113.11 -120.20 111.82 1.1551 +IC C3 C4 O4 HO4 1.5743 112.09 41.58 105.29 0.9507 +PATCH FIRST NONE LAST NONE + +RESI DTHROL 0.000 ! D-THReitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! H3-C3-O3-HO3 +! | +! H41-C4-H42 +! | +! O4-HO4 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H41 HDA2A 0.070 +ATOM H42 HDA2A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H41 C4 H42 O4 HO4 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6133 109.49 -179.64 112.66 1.6033 +IC O1 C2 *C1 H11 1.4339 111.79 116.55 111.17 1.1673 +IC O1 C2 *C1 H12 1.4339 111.79 -133.85 118.71 1.1020 +IC C2 C1 O1 HO1 1.6133 111.79 74.41 100.55 0.9809 +IC O1 C1 C2 C3 1.4339 111.79 -36.33 109.49 1.5493 +IC C3 C1 *C2 O2 1.5493 109.49 -123.45 111.59 1.4118 +IC O2 C1 *C2 H2 1.4118 111.59 -107.72 103.84 1.1268 +IC C1 C2 O2 HO2 1.6133 111.59 -49.02 104.62 0.9492 +IC C4 C2 *C3 O3 1.6033 112.66 116.79 110.78 1.4657 +IC O3 C2 *C3 H3 1.4657 110.78 123.28 108.04 1.1153 +IC C2 C3 O3 HO3 1.5493 110.78 -45.76 93.49 0.9392 +IC C2 C3 C4 O4 1.5493 112.66 -71.77 113.16 1.3868 +IC O4 C3 *C4 H41 1.3868 113.16 -124.93 107.98 1.1179 +IC H41 C3 *C4 H42 1.1179 107.98 -112.45 102.71 1.1552 +IC C3 C4 O4 HO4 1.6033 113.16 61.41 112.22 0.9955 +PATCH FIRST NONE LAST NONE + +RESI LTHROL 0.000 ! L-THReitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! HO3-O3-C3-H3 +! | +! H41-C4-H42 +! | +! O4-HO4 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H41 HDA2A 0.070 +ATOM H42 HDA2A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H41 C4 H42 O4 HO4 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6051 108.42 -178.14 117.74 1.4808 +IC O1 C2 *C1 H11 1.3860 112.31 116.93 101.78 1.0899 +IC O1 C2 *C1 H12 1.3860 112.31 -117.34 102.31 1.1502 +IC C2 C1 O1 HO1 1.6051 112.31 -79.47 99.92 0.9436 +IC O1 C1 C2 C3 1.3860 112.31 59.93 108.42 1.6250 +IC C3 C1 *C2 O2 1.6250 108.42 126.18 114.04 1.4167 +IC O2 C1 *C2 H2 1.4167 114.04 127.02 110.02 1.1273 +IC C1 C2 O2 HO2 1.6051 114.04 58.65 114.59 0.9324 +IC C4 C2 *C3 O3 1.4808 117.74 -120.55 109.09 1.4175 +IC O3 C2 *C3 H3 1.4175 109.09 -120.37 108.92 1.1156 +IC C2 C3 O3 HO3 1.6250 109.09 59.06 103.30 0.9300 +IC C2 C3 C4 O4 1.6250 117.74 62.09 112.92 1.4559 +IC O4 C3 *C4 H42 1.4559 112.92 114.71 113.36 1.1171 +IC H42 C3 *C4 H41 1.1171 113.36 120.10 117.05 1.0813 +IC C3 C4 O4 HO4 1.4808 112.92 -64.44 109.22 0.9634 +PATCH FIRST NONE LAST NONE + +RESI MRIBOL 0.000 ! Meso-RIBitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! HO3-O3-C3-H3 +! | +! HO4-O4-C4-H4 +! | +! H51-C5-H52 +! | +! O5-HO5 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H51 HDA2A 0.070 +ATOM H52 HDA2A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H51 C5 H52 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5589 110.56 -163.15 113.22 1.6303 +IC O1 C2 *C1 H11 1.4222 116.80 124.61 105.66 1.1281 +IC O1 C2 *C1 H12 1.4222 116.80 -117.60 105.48 1.1051 +IC C2 C1 O1 HO1 1.5589 116.80 -164.04 112.13 0.9841 +IC O1 C1 C2 C3 1.4222 116.80 66.64 110.56 1.5250 +IC C3 C1 *C2 O2 1.5250 110.56 -113.04 103.83 1.4235 +IC O2 C1 *C2 H2 1.4235 103.83 -118.87 113.85 1.0963 +IC C1 C2 O2 HO2 1.5589 103.83 20.73 96.42 0.9656 +IC C4 C2 *C3 O3 1.6303 113.22 -126.84 108.09 1.4090 +IC O3 C2 *C3 H3 1.4090 108.09 -113.93 107.34 1.1051 +IC C2 C3 O3 HO3 1.5250 108.09 174.85 107.58 0.9853 +IC C2 C3 C4 C5 1.5250 113.22 -55.42 109.40 1.5351 +IC C5 C3 *C4 O4 1.5351 109.40 -125.27 107.97 1.4431 +IC O4 C3 *C4 H4 1.4431 107.97 -115.10 109.87 1.1304 +IC C3 C4 O4 HO4 1.6303 107.97 164.00 99.47 0.9714 +IC C3 C4 C5 O5 1.6303 109.40 177.89 110.44 1.4060 +IC O5 C4 *C5 H51 1.4060 110.44 -120.82 110.24 1.1278 +IC H51 C4 *C5 H52 1.1278 110.24 -118.19 116.45 1.1298 +IC C4 C5 O5 HO5 1.5351 110.44 -149.39 107.20 0.9880 +PATCH FIRST NONE LAST NONE + +RESI DARAOL 0.000 ! D-ARAbitOL (same as lyxitol) +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! H3-C3-O3-HO3 +! | +! H4-C4-O4-HO4 +! | +! H51-C5-H52 +! | +! O5-HO5 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H51 HDA2A 0.070 +ATOM H52 HDA2A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H51 C5 H52 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6056 112.65 173.24 109.58 1.5414 +IC O1 C2 *C1 H11 1.3851 114.18 118.96 103.71 1.1026 +IC O1 C2 *C1 H12 1.3851 114.18 -120.67 108.43 1.0860 +IC C2 C1 O1 HO1 1.6056 114.18 -73.78 112.70 1.0086 +IC O1 C1 C2 C3 1.3851 114.18 -47.65 112.65 1.5013 +IC C3 C1 *C2 O2 1.5013 112.65 -123.92 110.69 1.4462 +IC O2 C1 *C2 H2 1.4462 110.69 -125.35 104.98 1.1102 +IC C1 C2 O2 HO2 1.6056 110.69 69.62 100.22 0.9866 +IC C4 C2 *C3 O3 1.5414 109.58 126.30 111.67 1.4412 +IC O3 C2 *C3 H3 1.4412 111.67 115.35 108.34 1.1263 +IC C2 C3 O3 HO3 1.5013 111.67 76.22 94.88 0.9539 +IC C2 C3 C4 C5 1.5013 109.58 170.70 112.68 1.5413 +IC C5 C3 *C4 O4 1.5413 112.68 123.00 105.68 1.4531 +IC O4 C3 *C4 H4 1.4531 105.68 114.88 109.48 1.1137 +IC C3 C4 O4 HO4 1.5414 105.68 -118.03 102.41 0.9501 +IC C3 C4 C5 O5 1.5414 112.68 65.14 110.15 1.4606 +IC O5 C4 *C5 H51 1.4606 110.15 -131.01 117.80 1.0534 +IC H51 C4 *C5 H52 1.0534 117.80 -114.28 114.07 1.1820 +IC C4 C5 O5 HO5 1.5413 110.15 -62.35 106.12 0.9490 +PATCH FIRST NONE LAST NONE + +RESI LARAOL 0.000 ! L-ARAbitOL (same as lyxitol) +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! HO3-O3-C3-H3 +! | +! HO4-O4-C4-H4 +! | +! H51-C5-H52 +! | +! O5-HO5 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H51 HDA2A 0.070 +ATOM H52 HDA2A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H51 C5 H52 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5163 110.17 -159.68 111.55 1.5270 +IC O1 C2 *C1 H11 1.4216 114.98 124.75 113.88 1.1363 +IC O1 C2 *C1 H12 1.4216 114.98 -117.51 109.99 1.1097 +IC C2 C1 O1 HO1 1.5163 114.98 78.09 105.93 0.9211 +IC O1 C1 C2 C3 1.4216 114.98 56.30 110.17 1.5404 +IC C3 C1 *C2 O2 1.5404 110.17 128.22 116.71 1.4565 +IC O2 C1 *C2 H2 1.4565 116.71 116.82 102.32 1.1457 +IC C1 C2 O2 HO2 1.5163 116.71 -80.57 96.32 0.9470 +IC C4 C2 *C3 O3 1.5270 111.55 -126.83 106.30 1.4622 +IC O3 C2 *C3 H3 1.4622 106.30 -117.91 108.12 1.1110 +IC C2 C3 O3 HO3 1.5404 106.30 -77.10 112.46 0.9927 +IC C2 C3 C4 C5 1.5404 111.55 -174.48 110.50 1.5672 +IC C5 C3 *C4 O4 1.5672 110.50 -127.64 113.29 1.4485 +IC O4 C3 *C4 H4 1.4485 113.29 -114.25 108.64 1.0962 +IC C3 C4 O4 HO4 1.5270 113.29 110.84 102.74 0.9758 +IC C3 C4 C5 O5 1.5270 110.50 -77.67 107.30 1.4592 +IC O5 C4 *C5 H52 1.4592 107.30 129.47 106.02 1.1807 +IC H52 C4 *C5 H51 1.1807 106.02 119.78 106.58 1.0953 +IC C4 C5 O5 HO5 1.5672 107.30 78.68 108.32 0.9484 +PATCH FIRST NONE LAST NONE + +RESI MXYLOL 0.000 ! Meso-XYLitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! H3-C3-O3-HO3 +! | +! HO4-O4-C4-H4 +! | +! H51-C5-H52 +! | +! O5-HO5 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H51 HDA2A 0.070 +ATOM H52 HDA2A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H51 C5 H52 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5323 110.65 166.89 113.05 1.5788 +IC O1 C2 *C1 H11 1.4361 108.54 115.14 108.79 1.0730 +IC O1 C2 *C1 H12 1.4361 108.54 -124.47 109.06 1.1440 +IC C2 C1 O1 HO1 1.5323 108.54 -164.41 109.20 0.9440 +IC O1 C1 C2 C3 1.4361 108.54 -169.12 110.65 1.5607 +IC C3 C1 *C2 O2 1.5607 110.65 -123.52 110.46 1.4429 +IC O2 C1 *C2 H2 1.4429 110.46 -115.49 104.71 1.1635 +IC C1 C2 O2 HO2 1.5323 110.46 -48.09 111.45 0.9664 +IC C4 C2 *C3 O3 1.5788 113.05 130.70 109.20 1.4492 +IC O3 C2 *C3 H3 1.4492 109.20 111.37 108.76 1.1324 +IC C2 C3 O3 HO3 1.5607 109.20 -48.82 103.09 1.0049 +IC C2 C3 C4 C5 1.5607 113.05 -77.67 110.05 1.5698 +IC C5 C3 *C4 O4 1.5698 110.05 -119.84 110.05 1.4236 +IC O4 C3 *C4 H4 1.4236 110.05 -118.04 111.71 1.1318 +IC C3 C4 O4 HO4 1.5788 110.05 -33.69 112.14 0.9528 +IC C3 C4 C5 O5 1.5788 110.05 -177.74 113.29 1.4361 +IC O5 C4 *C5 H51 1.4361 113.29 -114.53 106.11 1.1050 +IC H51 C4 *C5 H52 1.1050 106.11 -122.72 106.53 1.1383 +IC C4 C5 O5 HO5 1.5698 113.29 32.43 104.43 1.0021 +PATCH FIRST NONE LAST NONE + +RESI MALLOL 0.000 ! Meso-ALLitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! H3-C3-O3-HO3 +! | +! H4-C4-O4-HO4 +! | +! H5-C5-O5-HO5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI DALTOL 0.000 ! D-ALTritOL (same as talitol) +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! H3-C3-O3-HO3 +! | +! H4-C4-O4-HO4 +! | +! H5-C5-O5-HO5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI LALTOL 0.000 ! L-ALTritOL (same as talitol) +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! HO3-O3-C3-H3 +! | +! HO4-O4-C4-H4 +! | +! HO5-O5-C5-H5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI DGLUOL 0.000 ! D-GLUcitOL (sorbitol) +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! HO3-O3-C3-H3 +! | +! H4-C4-O4-HO4 +! | +! H5-C5-O5-HO5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI LGLUOL 0.000 ! L-GLUcitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! H3-C3-O3-HO3 +! | +! HO4-O4-C4-H4 +! | +! HO5-O5-C5-H5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI DMANOL 0.000 ! D-MANnitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! HO3-O3-C3-H3 +! | +! H4-C4-O4-HO4 +! | +! H5-C5-O5-HO5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI LMANOL 0.000 ! L-MANnitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! H3-C3-O3-HO3 +! | +! HO4-O4-C4-H4 +! | +! HO5-O5-C5-H5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI DGULOL 0.000 ! D-GULitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! H3-C3-O3-HO3 +! | +! HO4-O4-C4-H4 +! | +! H5-C5-O5-HO5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI LGULOL 0.000 ! L-GULitOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! HO3-O3-C3-H3 +! | +! H4-C4-O4-HO4 +! | +! HO5-O5-C5-H5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI DIDIOL 0.000 ! D-IDItOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! HO2-O2-C2-H2 +! | +! H3-C3-O3-HO3 +! | +! HO4-O4-C4-H4 +! | +! H5-C5-O5-HO5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI LIDIOL 0.000 ! L-IDItOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! HO3-O3-C3-H3 +! | +! H4-C4-O4-HO4 +! | +! HO5-O5-C5-H5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE + +RESI MGALOL 0.000 ! Meso-GALacticOL +! O1-HO1 +! | +! H11-C1-H12 +! | +! H2-C2-O2-HO2 +! | +! HO3-O3-C3-H3 +! | +! HO4-O4-C4-H4 +! | +! H5-C5-O5-HO5 +! | +! H61-C6-H62 +! | +! O6-HO6 +! +GROUP +ATOM C1 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H11 HDA2A 0.070 +ATOM H12 HDA2A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO1 HDP1A 0.320 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 +GROUP +ATOM C2 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C5 CD31G 0.010 ALPHA -1.650 THOLE 0.700 +ATOM H5 HDA1A 0.070 +ATOM O5 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO5 HDP1A 0.320 +ATOM LP5A LPD -0.200 +ATOM LP5B LPD -0.200 +GROUP +ATOM C6 CD32F -0.060 ALPHA -1.650 THOLE 0.700 +ATOM H61 HDA2A 0.070 +ATOM H62 HDA2A 0.070 +ATOM O6 OD31E 0.000 ALPHA -1.000 THOLE 1.000 +ATOM HO6 HDP1A 0.320 +ATOM LP6A LPD -0.200 +ATOM LP6B LPD -0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 O2 C2 H2 O2 HO2 +BOND C3 O3 C3 H3 O3 HO3 +BOND C4 O4 C4 H4 O4 HO4 +BOND C5 O5 C5 H5 O5 HO5 +BOND C6 O6 C6 H61 C6 H62 O6 HO6 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATCH FIRST NONE LAST NONE +!polyols + +!hexopyranoses +!!! dpatel !!! +!!! *mingjun* refitted alpha and thole with transferred charge parameters for group +!!! HO1-O1-C1-H1-O5-C5-H5 from furanose +RESI AGLC 0.000 ! 4C1 alpha-D-glucose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! H4 / \ H1 +! \ / HO3 \ / +! C4 | C1 +! / \ O3 H2 / \ +! HO4-O4 \| | / O1-HO1 +! C3---C2 +! | | +! H3 O2-HO2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4077 108.33 -123.34 103.67 1.1200 +IC O1 O5 *C1 C2 1.4077 108.39 -119.83 112.62 1.5516 +IC O2 C3 *C2 H2 1.4293 114.98 -108.39 100.80 1.0662 +IC O2 C1 *C2 C3 1.4293 117.26 -138.07 113.63 1.4880 +IC O3 C4 *C3 H3 1.4122 110.86 120.36 107.49 1.1219 +IC O3 C2 *C3 C4 1.4122 109.00 121.20 109.13 1.5315 +IC O4 C5 *C4 H4 1.4206 109.25 -124.20 109.65 1.1311 +IC O4 C3 *C4 C5 1.4206 103.58 -118.81 114.40 1.5087 +IC C6 O5 *C5 H5 1.4718 112.19 113.05 108.36 1.1212 +IC C6 C4 *C5 O5 1.4718 112.04 128.71 113.93 1.4175 +IC O6 H62 *C6 H61 1.3851 111.30 -112.76 100.96 1.1590 +IC O6 C5 *C6 H62 1.3851 110.28 -128.49 116.95 1.1067 +IC O5 C1 C2 C3 1.4351 112.62 51.83 113.63 1.4880 +IC C1 C2 C3 C4 1.5516 113.63 -48.48 109.13 1.5315 +IC C2 C3 C4 C5 1.4880 109.13 47.85 114.40 1.5087 +IC C3 C4 C5 O5 1.5315 114.40 -49.84 113.93 1.4175 +IC C4 C5 O5 C1 1.5087 113.93 51.43 114.13 1.4351 +IC C5 O5 C1 C2 1.4175 114.13 -51.82 112.62 1.5516 +IC C4 C5 C6 O6 1.5087 112.04 -173.06 110.28 1.3851 +IC O5 C1 O1 HO1 1.4351 108.39 47.62 101.41 0.9789 +IC C1 C2 O2 HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC C2 C3 O3 HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC C3 C4 O4 HO4 1.5315 103.58 55.55 110.36 0.9685 +IC C5 C6 O6 HO6 1.4718 110.28 -101.06 108.67 0.9667 +PATCH FIRST NONE LAST NONE + + +RESI BGLC 0.000 ! 4C1 beta-D-glucose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! H4 / \ O1-HO1 +! \ / HO3 \ / +! C4 | C1 +! / \ O3 H2 / \ +! HO4-O4 \| | / H1 +! C3---C2 +! | | +! H3 O2-HO2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3899 110.90 120.10 104.58 1.0836 +IC O1 O5 *C1 C2 1.3899 108.62 122.10 110.88 1.5316 +IC O2 C3 *C2 H2 1.4594 108.12 -118.78 111.06 1.1375 +IC O2 C1 *C2 C3 1.4594 115.65 -125.60 113.28 1.4983 +IC O3 C4 *C3 H3 1.4071 113.48 122.06 103.39 1.0895 +IC O3 C2 *C3 C4 1.4071 108.48 124.18 109.26 1.5497 +IC O4 C5 *C4 H4 1.3940 111.12 -110.35 108.66 1.0857 +IC O4 C3 *C4 C5 1.3940 112.77 -129.39 115.62 1.5530 +IC C6 O5 *C5 H5 1.5597 111.17 120.85 110.98 1.1092 +IC C6 C4 *C5 O5 1.5597 109.90 122.92 110.30 1.4512 +IC O6 H62 *C6 H61 1.4589 116.11 -112.93 103.57 1.1467 +IC O6 C5 *C6 H62 1.4589 109.41 -135.95 118.22 1.0853 +IC O5 C1 C2 C3 1.4620 110.88 57.82 113.28 1.4983 +IC C1 C2 C3 C4 1.5316 113.28 -48.40 109.26 1.5497 +IC C2 C3 C4 C5 1.4983 109.26 45.07 115.62 1.5530 +IC C3 C4 C5 O5 1.5497 115.62 -49.19 110.30 1.4512 +IC C4 C5 O5 C1 1.5530 110.30 56.36 112.12 1.4620 +IC C5 O5 C1 C2 1.4512 112.12 -61.39 110.88 1.5316 +IC C4 C5 C6 O6 1.5530 109.90 -177.46 109.41 1.4589 +IC O5 C1 O1 HO1 1.4620 108.62 72.25 106.48 0.9328 +IC C1 C2 O2 HO2 1.5316 115.65 135.41 116.81 0.9527 +IC C2 C3 O3 HO3 1.4983 108.48 -71.46 120.86 0.9441 +IC C3 C4 O4 HO4 1.5497 112.77 47.45 109.31 0.9911 +IC C5 C6 O6 HO6 1.5597 109.41 -54.60 118.82 0.95210 +PATCH FIRST NONE LAST NONE + + +RESI AALT 0.000 ! 4C1 alpha-D-altrose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! H4 / \ H1 +! \ / HO2 \ / +! C4 | C1 +! / \ H3 O2 / \ +! HO4-O4 \| | / O1-HO1 +! C3---C2 +! | | +! HO3-O3 H2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4059 109.84 -116.86 107.03 1.0749 +IC O1 O5 *C1 C2 1.4059 106.65 -124.27 118.28 1.5314 +IC O2 C3 *C2 H2 1.4540 106.08 123.94 116.41 1.0734 +IC O2 C1 *C2 C3 1.4540 108.11 116.16 111.37 1.4724 +IC O3 C4 *C3 H3 1.4262 116.38 -115.23 108.33 1.1702 +IC O3 C2 *C3 C4 1.4262 108.86 -129.67 111.42 1.4998 +IC O4 C5 *C4 H4 1.4250 108.92 -122.02 114.73 1.1508 +IC O4 C3 *C4 C5 1.4250 103.39 -116.89 111.54 1.4873 +IC C6 O5 *C5 H5 1.5191 108.29 117.76 108.02 1.1275 +IC C6 C4 *C5 O5 1.5191 112.49 120.64 109.76 1.4455 +IC O6 H62 *C6 H61 1.3863 101.25 -112.12 102.65 1.1299 +IC O6 C5 *C6 H62 1.3863 110.53 -110.40 108.93 1.1288 +IC O5 C1 C2 C3 1.4181 118.28 41.70 111.37 1.4724 +IC C1 C2 C3 C4 1.5314 111.37 -43.82 111.42 1.4998 +IC C2 C3 C4 C5 1.4724 111.42 56.21 111.54 1.4873 +IC C3 C4 C5 O5 1.4998 111.54 -61.84 109.76 1.4455 +IC C4 C5 O5 C1 1.4873 109.76 56.28 111.65 1.4181 +IC C5 O5 C1 C2 1.4455 111.65 -47.85 118.28 1.5314 +IC C4 C5 C6 O6 1.4873 112.49 178.99 110.53 1.3863 +IC O5 C1 O1 HO1 1.4181 106.65 56.46 100.91 0.9422 +IC C1 C2 O2 HO2 1.5314 108.11 -153.83 113.21 1.0131 +IC C2 C3 O3 HO3 1.4724 108.86 164.64 101.47 0.9893 +IC C3 C4 O4 HO4 1.4998 103.39 -131.59 111.45 0.9477 +IC C5 C6 O6 HO6 1.5191 110.53 -85.80 108.22 0.9698 +PATCH FIRST NONE LAST NONE + + +RESI BALT 0.000 ! 4C1 beta-D-altrose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! H4 / \ O1-HO1 +! \ / HO2 \ / +! C4 | C1 +! / \ H3 O2 / \ +! HO4-O4 \| | / H1 +! C3---C2 +! | | +! HO3-O3 H2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4318 113.28 122.84 113.44 1.1912 +IC O1 O5 *C1 C2 1.4318 98.01 118.50 110.22 1.4937 +IC O2 C3 *C2 H2 1.4452 105.69 112.57 107.58 1.1287 +IC O2 C1 *C2 C3 1.4452 118.30 118.45 106.22 1.4707 +IC O3 C4 *C3 H3 1.4161 116.67 -116.77 107.70 1.1602 +IC O3 C2 *C3 C4 1.4161 109.34 -129.39 110.06 1.5310 +IC O4 C5 *C4 H4 1.4041 109.84 -121.00 103.00 1.1380 +IC O4 C3 *C4 C5 1.4041 106.00 -121.86 115.49 1.5108 +IC C6 O5 *C5 H5 1.4772 112.24 122.31 107.27 1.0848 +IC C6 C4 *C5 O5 1.4772 110.66 124.06 109.24 1.4004 +IC O6 H62 *C6 H61 1.4160 113.83 -126.41 115.87 1.1685 +IC O6 C5 *C6 H62 1.4160 108.88 -122.00 104.54 1.1002 +IC O5 C1 C2 C3 1.4644 110.22 65.02 106.22 1.4707 +IC C1 C2 C3 C4 1.4937 106.22 -56.25 110.06 1.5310 +IC C2 C3 C4 C5 1.4707 110.06 49.69 115.49 1.5108 +IC C3 C4 C5 O5 1.5310 115.49 -46.27 109.24 1.4004 +IC C4 C5 O5 C1 1.5108 109.24 53.35 112.97 1.4644 +IC C5 O5 C1 C2 1.4004 112.97 -65.99 110.22 1.4937 +IC C4 C5 C6 O6 1.5108 110.66 -172.71 108.88 1.4160 +IC O5 C1 O1 HO1 1.4644 98.01 -48.09 108.23 0.9538 +IC C1 C2 O2 HO2 1.4937 118.30 -74.78 103.83 0.9777 +IC C2 C3 O3 HO3 1.4707 109.34 106.07 116.48 0.9998 +IC C3 C4 O4 HO4 1.5310 106.00 -43.64 106.03 0.9690 +IC C5 C6 O6 HO6 1.4772 108.88 -129.43 110.69 0.9739 +PATCH FIRST NONE LAST NONE + + +RESI AALL 0.000 ! 4C1 alpha-D-allose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! H4 / \ H1 +! \ / \ / +! C4 C1 +! / \ H3 H2 / \ +! HO4-O4 \| | / O1-HO1 +! C3---C2 +! | | +! HO3-O3 O2-HO2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4098 110.83 -123.55 103.31 1.1208 +IC O1 O5 *C1 C2 1.4098 109.08 -122.35 110.92 1.5564 +IC O2 C3 *C2 H2 1.4479 114.09 -105.38 102.92 1.0648 +IC O2 C1 *C2 C3 1.4479 116.87 -135.18 112.80 1.4510 +IC O3 C4 *C3 H3 1.4756 113.82 -112.82 103.37 1.1328 +IC O3 C2 *C3 C4 1.4756 109.58 -126.87 111.42 1.5452 +IC O4 C5 *C4 H4 1.4147 111.32 -125.80 108.92 1.1328 +IC O4 C3 *C4 C5 1.4147 105.29 -121.63 112.88 1.5179 +IC C6 O5 *C5 H5 1.4813 111.46 111.89 106.04 1.1158 +IC C6 C4 *C5 O5 1.4813 113.62 129.33 114.16 1.4217 +IC O6 H62 *C6 H61 1.4254 104.77 -121.62 104.03 1.1216 +IC O6 C5 *C6 H62 1.4254 111.38 -121.22 118.00 1.1175 +IC O5 C1 C2 C3 1.4402 110.92 54.57 112.80 1.4510 +IC C1 C2 C3 C4 1.5564 112.80 -50.62 111.42 1.5452 +IC C2 C3 C4 C5 1.4510 111.42 46.53 112.88 1.5179 +IC C3 C4 C5 O5 1.5452 112.88 -46.19 114.16 1.4217 +IC C4 C5 O5 C1 1.5179 114.16 51.39 114.72 1.4402 +IC C5 O5 C1 C2 1.4217 114.72 -54.00 110.92 1.5564 +IC C4 C5 C6 O6 1.5179 113.62 -59.78 111.38 1.4254 +IC O5 C1 O1 HO1 1.4402 109.08 58.48 102.60 0.9806 +IC C1 C2 O2 HO2 1.5564 116.87 -119.27 106.08 0.9438 +IC C2 C3 O3 HO3 1.4510 109.58 -29.18 102.05 0.9525 +IC C3 C4 O4 HO4 1.5452 105.29 -22.81 109.42 0.9570 +IC C5 C6 O6 HO6 1.4813 111.38 63.12 111.98 0.9972 +PATCH FIRST NONE LAST NONE + + +RESI BALL 0.000 ! 4C1 beta-D-allose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! H4 / \ O1-HO1 +! \ / \ / +! C4 C1 +! / \ H3 H2 / \ +! HO4-O4 \| | / H1 +! C3---C2 +! | | +! HO3-O3 O2-HO2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4195 111.04 124.25 111.51 1.1174 +IC O1 O5 *C1 C2 1.4195 102.62 117.00 107.12 1.4947 +IC O2 C3 *C2 H2 1.4041 113.70 -121.08 106.92 1.2090 +IC O2 C1 *C2 C3 1.4041 113.52 -125.56 106.07 1.5053 +IC O3 C4 *C3 H3 1.3756 114.59 -114.99 112.58 1.0991 +IC O3 C2 *C3 C4 1.3756 110.80 -130.25 113.12 1.4926 +IC O4 C5 *C4 H4 1.4086 116.22 -115.71 106.93 1.0762 +IC O4 C3 *C4 C5 1.4086 108.71 -128.79 110.69 1.5002 +IC C6 O5 *C5 H5 1.4986 113.17 117.77 109.71 1.1598 +IC C6 C4 *C5 O5 1.4986 111.00 125.30 108.99 1.4520 +IC O6 H62 *C6 H61 1.3973 108.34 -115.37 109.69 1.0887 +IC O6 C5 *C6 H62 1.3973 111.64 -118.40 107.03 1.1034 +IC O5 C1 C2 C3 1.3963 107.12 63.98 106.07 1.5053 +IC C1 C2 C3 C4 1.4947 106.07 -56.87 113.12 1.4926 +IC C2 C3 C4 C5 1.5053 113.12 50.62 110.69 1.5002 +IC C3 C4 C5 O5 1.4926 110.69 -49.08 108.99 1.4520 +IC C4 C5 O5 C1 1.5002 108.99 61.15 112.84 1.3963 +IC C5 O5 C1 C2 1.4520 112.84 -69.50 107.12 1.4947 +IC C4 C5 C6 O6 1.5002 111.00 -67.09 111.64 1.3973 +IC O5 C1 O1 HO1 1.3963 102.62 -59.81 110.50 0.9588 +IC C1 C2 O2 HO2 1.4947 113.52 75.20 110.55 0.9684 +IC C2 C3 O3 HO3 1.5053 110.80 54.33 102.92 0.9436 +IC C3 C4 O4 HO4 1.4926 108.71 -37.98 105.06 0.9792 +IC C5 C6 O6 HO6 1.4986 111.64 43.65 106.81 0.9783 +PATCH FIRST NONE LAST NONE + + +RESI AGAL 0.000 ! 4C1 alpha-D-galactose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! HO4-O4 / \ H1 +! \ / HO3 \ / +! C4 | C1 +! / \ O3 H2 / \ +! H4 \| | / O1-HO1 +! C3---C2 +! | | +! H3 O2-HO2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3865 108.93 -123.99 104.38 1.1081 +IC O1 O5 *C1 C2 1.3865 108.96 -118.67 108.85 1.5226 +IC O2 C3 *C2 H2 1.4411 111.34 -110.11 102.47 1.1187 +IC O2 C1 *C2 C3 1.4411 115.23 -135.16 118.19 1.4969 +IC O3 C4 *C3 H3 1.4266 109.02 118.09 104.61 1.1300 +IC O3 C2 *C3 C4 1.4266 116.32 123.96 109.32 1.5156 +IC O4 C5 *C4 H4 1.4233 107.75 119.05 111.86 1.0818 +IC O4 C3 *C4 C5 1.4233 111.62 121.16 112.36 1.4931 +IC C6 O5 *C5 H5 1.5325 113.82 109.66 108.87 1.1501 +IC C6 C4 *C5 O5 1.5325 115.44 135.15 114.56 1.4252 +IC O6 H62 *C6 H61 1.4421 111.00 -121.63 104.24 1.1078 +IC O6 C5 *C6 H62 1.4421 112.98 -123.79 108.85 1.1420 +IC O5 C1 C2 C3 1.4134 108.85 48.90 118.19 1.4969 +IC C1 C2 C3 C4 1.5226 118.19 -46.22 109.32 1.5156 +IC C2 C3 C4 C5 1.4969 109.32 44.65 112.36 1.4931 +IC C3 C4 C5 O5 1.5156 112.36 -50.65 114.56 1.4252 +IC C4 C5 O5 C1 1.4931 114.56 55.65 115.64 1.4134 +IC C5 O5 C1 C2 1.4252 115.64 -51.39 108.85 1.5226 +IC C4 C5 C6 O6 1.4931 115.44 65.25 112.98 1.4421 +IC O5 C1 O1 HO1 1.4134 108.96 63.08 109.87 0.9758 +IC C1 C2 O2 HO2 1.5226 115.23 -42.41 115.36 0.9113 +IC C2 C3 O3 HO3 1.4969 116.32 -21.70 115.24 0.9926 +IC C3 C4 O4 HO4 1.5156 111.62 -23.31 104.57 0.9949 +IC C5 C6 O6 HO6 1.5325 112.98 -45.14 110.63 0.9762 +PATC FIRS NONE LAST NONE + + +RESI BGAL 0.000 ! 4C1 beta-D-galactose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! HO4-O4 / \ O1-HO1 +! \ / HO3 \ / +! C4 | C1 +! / \ O3 H2 / \ +! H4 \| | / H1 +! C3---C2 +! | | +! H3 O2-HO2 +! +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3474 106.42 116.51 115.09 1.1438 +IC O1 O5 *C1 C2 1.3474 104.56 115.77 113.93 1.5410 +IC O2 C3 *C2 H2 1.4631 108.10 -121.28 108.50 1.1329 +IC O2 C1 *C2 C3 1.4631 114.38 -122.04 110.23 1.4726 +IC O3 C4 *C3 H3 1.4614 112.11 123.20 113.19 1.1731 +IC O3 C2 *C3 C4 1.4614 110.41 123.80 109.34 1.5276 +IC O4 C5 *C4 H4 1.4408 117.10 124.69 105.11 1.1036 +IC O4 C3 *C4 C5 1.4408 108.63 126.45 105.69 1.5707 +IC C6 O5 *C5 H5 1.5525 105.55 121.59 108.44 1.0948 +IC C6 C4 *C5 O5 1.5525 109.96 114.62 107.87 1.4748 +IC O6 H62 *C6 H61 1.4039 115.08 -121.25 107.51 1.1562 +IC O6 C5 *C6 H62 1.4039 111.39 -123.55 102.46 1.1003 +IC O5 C1 C2 C3 1.3914 113.93 52.67 110.23 1.4726 +IC C1 C2 C3 C4 1.5410 110.23 -56.55 109.34 1.5276 +IC C2 C3 C4 C5 1.4726 109.34 62.95 105.69 1.5707 +IC C3 C4 C5 O5 1.5276 105.69 -63.57 107.87 1.4748 +IC C4 C5 O5 C1 1.5707 107.87 61.04 112.05 1.3914 +IC C5 O5 C1 C2 1.4748 112.05 -55.18 113.93 1.5410 +IC C4 C5 C6 O6 1.5707 109.96 47.46 111.39 1.4039 +IC O5 C1 O1 HO1 1.3914 104.56 47.03 104.25 0.9837 +IC C1 C2 O2 HO2 1.5410 114.38 86.78 105.57 0.9458 +IC C2 C3 O3 HO3 1.4726 110.41 -41.42 104.34 0.9789 +IC C3 C4 O4 HO4 1.5276 108.63 -53.94 107.01 0.9519 +IC C5 C6 O6 HO6 1.5525 111.39 -11.52 102.88 0.9548 +PATCH FIRST NONE LAST NONE + + +RESI AGUL 0.000 ! 4C1 alpha-D-gulose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! HO4-O4 / \ H1 +! \ / \ / +! C4 C1 +! / \ H3 H2 / \ +! H4 \| | / OH1-H1 +! C3---C2 +! | | +! HO3-O3 O2-HO2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3730 109.13 -114.32 110.17 1.0759 +IC O1 O5 *C1 C2 1.3730 110.11 -124.26 115.65 1.5446 +IC O2 C3 *C2 H2 1.4253 116.11 -117.13 110.47 1.1056 +IC O2 C1 *C2 C3 1.4253 116.42 -134.99 110.24 1.4821 +IC O3 C4 *C3 H3 1.4366 112.23 -118.25 111.07 1.1689 +IC O3 C2 *C3 C4 1.4366 110.15 -125.94 112.38 1.4818 +IC O4 C5 *C4 H4 1.4291 112.18 115.14 108.47 1.1681 +IC O4 C3 *C4 C5 1.4291 107.17 123.89 112.71 1.4952 +IC C6 O5 *C5 H5 1.5584 110.62 116.21 108.29 1.1257 +IC C6 C4 *C5 O5 1.5584 110.85 124.27 112.26 1.4186 +IC O6 H62 *C6 H61 1.3799 102.93 -113.47 106.66 1.1307 +IC O6 C5 *C6 H62 1.3799 111.99 -112.02 106.89 1.1210 +IC O5 C1 C2 C3 1.4591 115.65 47.62 110.24 1.4821 +IC C1 C2 C3 C4 1.5446 110.24 -46.69 112.38 1.4818 +IC C2 C3 C4 C5 1.4821 112.38 52.71 112.71 1.4952 +IC C3 C4 C5 O5 1.4818 112.71 -57.13 112.26 1.4186 +IC C4 C5 O5 C1 1.4952 112.26 55.40 110.94 1.4591 +IC C5 O5 C1 C2 1.4186 110.94 -52.14 115.65 1.5446 +IC C4 C5 C6 O6 1.4952 110.85 -166.43 111.99 1.3799 +IC O5 C1 O1 HO1 1.4591 110.11 -74.56 109.17 0.9540 +IC C1 C2 O2 HO2 1.5446 116.42 -66.49 108.06 0.9292 +IC C2 C3 O3 HO3 1.4821 110.15 105.79 106.12 0.9949 +IC C3 C4 O4 HO4 1.4818 107.17 79.28 112.61 0.9495 +IC C5 C6 O6 HO6 1.5584 111.99 -91.22 109.74 0.9787 +PATC FIRS NONE LAST NONE + +RESI BGUL 0.000 ! 4C1 beta-D-gulose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! HO4-O4 / \ O1-HO1 +! \ / \ / +! C4 C1 +! / \ H3 H2 / \ +! H4 \| | / H1 +! C3---C2 +! | | +! HO3-O3 O2-HO2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3825 109.34 125.34 110.63 1.1765 +IC O1 O5 *C1 C2 1.3825 105.20 119.53 113.55 1.5176 +IC O2 C3 *C2 H2 1.4360 113.17 -113.77 111.02 1.1213 +IC O2 C1 *C2 C3 1.4360 116.61 -130.62 110.04 1.5067 +IC O3 C4 *C3 H3 1.4253 112.90 -120.39 107.67 1.1673 +IC O3 C2 *C3 C4 1.4253 109.69 -125.40 110.93 1.5032 +IC O4 C5 *C4 H4 1.3908 113.46 123.34 110.19 1.1566 +IC O4 C3 *C4 C5 1.3908 108.13 124.77 110.57 1.4791 +IC C6 O5 *C5 H5 1.5276 112.58 118.28 105.66 1.1232 +IC C6 C4 *C5 O5 1.5276 110.58 124.45 109.25 1.4518 +IC O6 H62 *C6 H61 1.3660 102.24 -115.00 103.17 1.1275 +IC O6 C5 *C6 H62 1.3660 111.24 -112.09 109.18 1.1265 +IC O5 C1 C2 C3 1.4490 113.55 50.27 110.04 1.5067 +IC C1 C2 C3 C4 1.5176 110.04 -50.09 110.93 1.5032 +IC C2 C3 C4 C5 1.5067 110.93 57.08 110.57 1.4791 +IC C3 C4 C5 O5 1.5032 110.57 -61.38 109.25 1.4518 +IC C4 C5 O5 C1 1.4791 109.25 60.60 111.35 1.4490 +IC C5 O5 C1 C2 1.4518 111.35 -56.04 113.55 1.5176 +IC C4 C5 C6 O6 1.4791 110.58 -176.59 111.24 1.3660 +IC O5 C1 O1 HO1 1.4490 105.20 171.60 108.75 0.9716 +IC C1 C2 O2 HO2 1.5176 116.61 -127.96 107.98 0.9472 +IC C2 C3 O3 HO3 1.5067 109.69 130.39 105.07 1.0055 +IC C3 C4 O4 HO4 1.5032 108.13 82.45 111.30 0.9602 +IC C5 C6 O6 HO6 1.5276 111.24 -97.14 109.20 0.9823 +PATCH FIRST NONE LAST NONE + + +RESI AIDO 0.000 ! 4C1 alpha-D-idose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! HO4-O4 / \ H1 +! \ / HO2 \ / +! C4 | C1 +! / \ H3 O2 / \ +! H4 \| | / O1-HO1 +! C3---C2 +! | | +! HO3-O3 H2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4030 110.70 -118.01 108.88 1.1054 +IC O1 O5 *C1 C2 1.4030 109.49 -123.53 112.49 1.5064 +IC O2 C3 *C2 H2 1.4727 106.55 115.47 118.67 1.1042 +IC O2 C1 *C2 C3 1.4727 114.02 119.04 109.20 1.5200 +IC O3 C4 *C3 H3 1.3943 115.01 -112.29 105.01 1.1238 +IC O3 C2 *C3 C4 1.3943 110.14 -129.45 112.14 1.4804 +IC O4 C5 *C4 H4 1.3892 107.94 119.64 111.65 1.0936 +IC O4 C3 *C4 C5 1.3892 112.33 120.17 109.88 1.5085 +IC C6 O5 *C5 H5 1.4888 112.14 120.03 112.38 1.1256 +IC C6 C4 *C5 O5 1.4888 110.66 126.55 112.81 1.4342 +IC O6 H62 *C6 H61 1.4374 107.23 -124.60 117.65 1.1136 +IC O6 C5 *C6 H62 1.4374 109.49 -113.02 101.29 1.1194 +IC O5 C1 C2 C3 1.3559 112.49 54.93 109.20 1.5200 +IC C1 C2 C3 C4 1.5064 109.20 -52.86 112.14 1.4804 +IC C2 C3 C4 C5 1.5200 112.14 51.12 109.88 1.5085 +IC C3 C4 C5 O5 1.4804 109.88 -50.48 112.81 1.4342 +IC C4 C5 O5 C1 1.5085 112.81 54.91 114.73 1.3559 +IC C5 O5 C1 C2 1.4342 114.73 -57.05 112.49 1.5064 +IC C4 C5 C6 O6 1.5085 110.66 -162.82 109.49 1.4374 +IC O5 C1 O1 HO1 1.3559 109.49 56.20 106.74 0.9610 +IC C1 C2 O2 HO2 1.5064 114.02 -149.77 114.21 1.0133 +IC C2 C3 O3 HO3 1.5200 110.14 -41.24 109.63 0.9224 +IC C3 C4 O4 HO4 1.4804 112.33 55.76 112.56 0.9964 +IC C5 C6 O6 HO6 1.4888 109.49 -121.61 102.80 0.9533 +PATCH FIRST NONE LAST NONE + + +RESI BIDO 0.000 ! 4C1 beta-D-idose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! HO4-O4 / \ O1-HO1 +! \ / HO2 \ / +! C4 | C1 +! / \ H3 O2 / \ +! H4 \| | / H1 +! C3---C2 +! | | +! HO3-O3 H2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3628 112.08 120.79 108.00 1.1750 +IC O1 O5 *C1 C2 1.3628 106.67 125.22 115.43 1.5202 +IC O2 C3 *C2 H2 1.4093 107.12 113.85 108.43 1.1113 +IC O2 C1 *C2 C3 1.4093 114.99 119.35 107.74 1.5055 +IC O3 C4 *C3 H3 1.4194 112.06 -119.21 105.92 1.1298 +IC O3 C2 *C3 C4 1.4194 109.82 -123.13 109.02 1.5258 +IC O4 C5 *C4 H4 1.3936 112.11 114.28 108.15 1.0879 +IC O4 C3 *C4 C5 1.3936 107.61 126.57 116.15 1.4852 +IC C6 O5 *C5 H5 1.4598 110.36 116.44 107.74 1.1268 +IC C6 C4 *C5 O5 1.4598 114.14 127.04 112.82 1.4371 +IC O6 H62 *C6 H61 1.3728 112.75 -114.37 102.31 1.1593 +IC O6 C5 *C6 H62 1.3728 111.22 -129.49 114.76 1.1023 +IC O5 C1 C2 C3 1.4409 115.43 58.58 107.74 1.5055 +IC C1 C2 C3 C4 1.5202 107.74 -52.96 109.02 1.5258 +IC C2 C3 C4 C5 1.5055 109.02 51.16 116.15 1.4852 +IC C3 C4 C5 O5 1.5258 116.15 -47.54 112.82 1.4371 +IC C4 C5 O5 C1 1.4852 112.82 47.40 112.38 1.4409 +IC C5 O5 C1 C2 1.4371 112.38 -55.49 115.43 1.5202 +IC C4 C5 C6 O6 1.4852 114.14 -162.57 111.22 1.3728 +IC O5 C1 O1 HO1 1.4409 106.67 -44.97 112.65 0.9677 +IC C1 C2 O2 HO2 1.5202 114.99 -80.74 113.28 0.9808 +IC C2 C3 O3 HO3 1.5055 109.82 106.91 109.96 0.9958 +IC C3 C4 O4 HO4 1.5258 107.61 51.84 98.03 0.9995 +IC C5 C6 O6 HO6 1.4598 111.22 -138.12 110.40 0.9879 +PATCH FIRST NONE LAST NONE + + +RESI AMAN 0.000 ! 4C1 alpha-D-mannose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! H4 / \ H1 +! \ / HO3 HO2 \ / +! C4 | | C1 +! / \ O3 O2 / \ +! HO4-O4 \| | / O1-HO1 +! C3---C2 +! | | +! H3 H2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3975 110.50 -118.09 109.89 1.1050 +IC O1 O5 *C1 C2 1.3975 108.93 -123.71 113.70 1.4876 +IC O2 C3 *C2 H2 1.4750 107.62 114.46 115.21 1.1022 +IC O2 C1 *C2 C3 1.4750 114.83 120.80 109.00 1.5586 +IC O3 C4 *C3 H3 1.4261 109.30 119.59 108.95 1.1150 +IC O3 C2 *C3 C4 1.4261 109.19 118.55 107.65 1.5049 +IC O4 C5 *C4 H4 1.3887 107.72 -127.19 110.85 1.1254 +IC O4 C3 *C4 C5 1.3887 108.42 -117.81 110.46 1.5035 +IC C6 O5 *C5 H5 1.4825 112.02 117.79 109.03 1.1288 +IC C6 C4 *C5 O5 1.4825 112.70 127.52 112.13 1.4375 +IC O6 H62 *C6 H61 1.4292 107.96 -123.56 113.24 1.1140 +IC O6 C5 *C6 H62 1.4292 109.39 -114.45 102.63 1.1098 +IC O5 C1 C2 C3 1.3632 113.70 56.64 109.00 1.5586 +IC C1 C2 C3 C4 1.4876 109.00 -56.11 107.65 1.5049 +IC C2 C3 C4 C5 1.5586 107.65 55.76 110.46 1.5035 +IC C3 C4 C5 O5 1.5049 110.46 -54.16 112.13 1.4375 +IC C4 C5 O5 C1 1.5035 112.13 53.40 114.61 1.3632 +IC C5 O5 C1 C2 1.4375 114.61 -55.52 113.70 1.4876 +IC C4 C5 C6 O6 1.5035 112.70 -173.75 109.39 1.4292 +IC O5 C1 O1 HO1 1.3632 108.93 53.42 107.62 0.9615 +IC C1 C2 O2 HO2 1.4876 114.83 -137.09 114.41 1.0113 +IC C2 C3 O3 HO3 1.5586 109.19 60.11 113.74 0.9944 +IC C3 C4 O4 HO4 1.5049 108.42 42.16 103.57 0.9552 +IC C5 C6 O6 HO6 1.4825 109.39 -84.75 103.86 0.9396 +PATCH FIRST NONE LAST NONE + + +RESI BMAN 0.000 ! 4C1 beta-D-mannose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! H4 / \ O1-HO1 +! \ / HO3 HO2 \ / +! C4 | | C1 +! / \ O3 O2 / \ +! HO4-O4 \| | / H1 +! C3---C2 +! | | +! H3 H2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4147 114.01 123.87 115.47 1.1241 +IC O1 O5 *C1 C2 1.4147 102.76 121.94 110.36 1.5194 +IC O2 C3 *C2 H2 1.4714 110.16 123.24 108.47 1.1051 +IC O2 C1 *C2 C3 1.4714 114.57 122.69 107.36 1.5071 +IC O3 C4 *C3 H3 1.3878 111.68 114.99 113.62 1.1108 +IC O3 C2 *C3 C4 1.3878 109.74 124.46 111.76 1.5071 +IC O4 C5 *C4 H4 1.3992 108.74 -119.41 104.60 1.1086 +IC O4 C3 *C4 C5 1.3992 114.29 -123.16 110.67 1.5450 +IC C6 O5 *C5 H5 1.5345 108.55 116.69 108.96 1.0801 +IC C6 C4 *C5 O5 1.5345 111.73 122.98 113.28 1.4134 +IC O6 H62 *C6 H61 1.4228 107.34 -116.56 114.05 1.1041 +IC O6 C5 *C6 H62 1.4228 116.50 -120.25 107.28 1.1156 +IC O5 C1 C2 C3 1.4381 110.36 63.05 107.36 1.5071 +IC C1 C2 C3 C4 1.5194 107.36 -55.99 111.76 1.5071 +IC C2 C3 C4 C5 1.5071 111.76 49.25 110.67 1.5450 +IC C3 C4 C5 O5 1.5071 110.67 -49.18 113.28 1.4134 +IC C4 C5 O5 C1 1.5450 113.28 56.65 110.70 1.4381 +IC C5 O5 C1 C2 1.4134 110.70 -64.29 110.36 1.5194 +IC C4 C5 C6 O6 1.5450 111.73 -168.80 116.50 1.4228 +IC O5 C1 O1 HO1 1.4381 102.76 -14.89 110.00 0.9891 +IC C1 C2 O2 HO2 1.5194 114.57 -31.81 104.69 0.9864 +IC C2 C3 O3 HO3 1.5071 109.74 46.67 101.47 0.9688 +IC C3 C4 O4 HO4 1.5071 114.29 42.72 117.62 0.9726 +IC C5 C6 O6 HO6 1.5345 116.50 -62.83 105.97 0.9733 +PATCH FIRST NONE LAST NONE + + +RESI ATAL 0.000 ! 4C1 alpha-D-talose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! HO4-O4 / \ H1 +! \ / HO3 HO2 \ / +! C4 | | C1 +! / \ O3 O2 / \ +! H4 \| | / O1-HO1 +! C3---C2 +! | | +! H3 H2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4221 107.55 -121.04 103.18 1.1260 +IC O1 O5 *C1 C2 1.4221 108.10 -120.96 116.21 1.5424 +IC O2 C3 *C2 H2 1.4492 108.99 111.12 111.71 1.1130 +IC O2 C1 *C2 C3 1.4492 110.19 121.38 111.84 1.4843 +IC O3 C4 *C3 H3 1.4110 114.05 118.54 103.93 1.1185 +IC O3 C2 *C3 C4 1.4110 111.20 126.43 108.81 1.5416 +IC O4 C5 *C4 H4 1.3621 111.29 117.93 107.00 1.0823 +IC O4 C3 *C4 C5 1.3621 110.03 125.60 113.70 1.5072 +IC C6 O5 *C5 H5 1.5017 109.27 111.35 106.33 1.1114 +IC C6 C4 *C5 O5 1.5017 116.34 129.67 115.09 1.4356 +IC O6 H62 *C6 H61 1.4386 106.14 -124.99 106.59 1.1207 +IC O6 C5 *C6 H62 1.4386 110.98 -119.80 114.03 1.1369 +IC O5 C1 C2 C3 1.4303 116.21 51.66 111.84 1.4843 +IC C1 C2 C3 C4 1.5424 111.84 -50.94 108.81 1.5416 +IC C2 C3 C4 C5 1.4843 108.81 51.41 113.70 1.5072 +IC C3 C4 C5 O5 1.5416 113.70 -49.51 115.09 1.4356 +IC C4 C5 O5 C1 1.5072 115.09 46.15 113.29 1.4303 +IC C5 O5 C1 C2 1.4356 113.29 -47.30 116.21 1.5424 +IC C4 C5 C6 O6 1.5072 116.34 63.06 110.98 1.4386 +IC O5 C1 O1 HO1 1.4303 108.10 62.34 103.18 0.9787 +IC C1 C2 O2 HO2 1.5424 110.19 97.32 103.39 0.9815 +IC C2 C3 O3 HO3 1.4843 111.20 60.87 105.69 0.9861 +IC C3 C4 O4 HO4 1.5416 110.03 150.82 103.42 0.9772 +IC C5 C6 O6 HO6 1.5017 110.98 78.75 112.42 0.9516 +PATC FIRS NONE LAST NONE + + +RESI BTAL 0.000 ! 4C1 beta-D-talose +!RING * 6 C1 C2 C3 C4 C5 O5 +! +! O6-HO6 +! | +! H61-C6-H62 +! | +! H5-C5---O5 +! HO4-O4 / \ O1-HO1 +! \ / HO3 HO2 \ / +! C4 | | C1 +! / \ O3 O2 / \ +! H4 \| | / H1 +! C3---C2 +! | | +! H3 H2 +! +GROUP +ATOM C1 CD31HA 0.124 ALPHA -0.614 THOLE 2.458 !In MGLYOL: ALPHA -1.650 THOLE 0.70 !In CPO1: ALPHA -1.000 THOLE 1.3 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -0.873 THOLE 0.468 !In MGLYOL: ALPHA -1.000 THOLE 1.0 +ATOM HO1 HDP1A 0.333 +ATOM C5 CD31HC 0.112 ALPHA -0.604 THOLE 0.351 !In THP: ALPHA -1.696 THOLE 0.316 +ATOM H5 HDA2E 0.069 +ATOM O5 OD306A 0.000 ALPHA -0.717 THOLE 0.491 !In THP: ALPHA -0.530 THOLE 2.046 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP5A LPD -0.152 +ATOM LP5B LPD -0.152 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability +GROUP +ATOM C2 CD31HB 0.010 ALPHA -0.761 THOLE 0.215 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.541 THOLE 0.329 +ATOM HO2 HDP1A 0.320 +ATOM LP2A LPD -0.200 +ATOM LP2B LPD -0.200 +GROUP +ATOM C3 CD31HB 0.010 ALPHA -0.701 THOLE 2.483 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.212 THOLE 2.329 +ATOM HO3 HDP1A 0.320 +ATOM LP3A LPD -0.200 +ATOM LP3B LPD -0.200 +GROUP +ATOM C4 CD31HB 0.010 ALPHA -1.020 THOLE 0.275 +ATOM H4 HDA1A 0.070 +ATOM O4 OD31E 0.000 ALPHA -0.699 THOLE 2.464 +ATOM HO4 HDP1A 0.320 +ATOM LP4A LPD -0.200 +ATOM LP4B LPD -0.200 +GROUP +ATOM C6 CD32A -0.060 ALPHA -0.226 THOLE 0.250 ! In ETOH: ALPHA -1.000 THOLE 1.3 +ATOM H61 HDA2A 0.080 +ATOM H62 HDA2A 0.080 +ATOM O6 OD31A 0.000 ALPHA -0.343 THOLE 0.260 ! In ETOH: ALPHA -1.028 THOLE 1.3 +ATOM HO6 HDP1A 0.360 +ATOM LP6A LPD -0.230 +ATOM LP6B LPD -0.230 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B +BOND O5 LP5A O5 LP5B O5 LPX5 +BOND O6 LP6A O6 LP6B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP4A O4 C4 HO4 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP4B O4 C4 HO4 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O4 C4 LP4A LP4B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP5A O5 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP6A O6 C6 HO6 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP6B O6 C6 HO6 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O6 C6 LP6A LP6B A11 0.8108 A22 1.2162 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3889 106.87 117.83 101.80 1.1309 +IC O1 O5 *C1 C2 1.3889 112.84 124.25 116.58 1.5618 +IC O2 C3 *C2 H2 1.4489 109.20 113.88 114.91 1.1114 +IC O2 C1 *C2 C3 1.4489 112.96 121.77 109.28 1.5591 +IC O3 C4 *C3 H3 1.4529 113.77 116.04 109.93 1.1125 +IC O3 C2 *C3 C4 1.4529 112.93 125.64 106.60 1.5550 +IC O4 C5 *C4 H4 1.4470 115.26 126.65 112.14 1.0859 +IC O4 C3 *C4 C5 1.4470 108.47 129.11 113.03 1.6431 +IC C6 O5 *C5 H5 1.5283 109.17 120.52 109.23 1.1154 +IC C6 C4 *C5 O5 1.5283 113.70 121.95 108.88 1.4584 +IC O6 H62 *C6 H61 1.4345 107.01 -118.66 112.81 1.1184 +IC O6 C5 *C6 H62 1.4345 113.18 -117.75 107.19 1.0553 +IC O5 C1 C2 C3 1.4104 116.58 57.36 109.28 1.5591 +IC C1 C2 C3 C4 1.5618 109.28 -53.96 106.60 1.5550 +IC C2 C3 C4 C5 1.5591 106.60 55.67 113.03 1.6431 +IC C3 C4 C5 O5 1.5550 113.03 -54.67 108.88 1.4584 +IC C4 C5 O5 C1 1.6431 108.88 52.47 113.48 1.4104 +IC C5 O5 C1 C2 1.4584 113.48 -57.26 116.58 1.5618 +IC C4 C5 C6 O6 1.6431 113.70 53.91 113.18 1.4345 +IC O5 C1 O1 HO1 1.4104 112.84 72.22 102.95 0.9977 +IC C1 C2 O2 HO2 1.5618 112.96 75.45 111.93 0.9813 +IC C2 C3 O3 HO3 1.5591 112.93 50.13 113.60 0.9452 +IC C3 C4 O4 HO4 1.5550 108.47 171.51 110.20 0.9652 +IC C5 C6 O6 HO6 1.5283 113.18 80.67 113.04 0.9869 +PATCH FIRST NONE LAST NONE +!hexopyranoses + +!furanoses, rima +RESI ARIB 0.000 ! alpha-Ribose +!RING * 5 C1 C2 C3 C4 O4 +! +! HO5--O5 +! \ O4 +! H51--C5 / \ H1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / O1--HO1 +! C3----C2 +! / \ / \ +! HO3--O3 H3 O2 H2 +! | +! HO2 +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from glycerol +ATOM C2 CD31FB -0.006 ALPHA -1.438 THOLE 1.015 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.940 THOLE 0.670 +ATOM HO2 HDP1A 0.322 +ATOM LP2A LPD -0.193 +ATOM LP2B LPD -0.193 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4343 107.06 -43.51 102.91 1.5564 +IC O4 C1 C2 C3 1.4227 102.91 29.68 103.27 1.5615 +IC C1 C2 C3 C4 1.5564 103.27 -6.90 103.97 1.5386 +IC C3 O4 *C4 C5 1.5386 104.85 125.17 112.30 1.5446 +IC C3 O4 *C4 H4 1.5386 104.85 -116.42 106.12 1.1143 +IC O4 C4 C5 O5 1.4343 112.30 -178.59 110.88 1.4293 +IC C4 C5 O5 HO5 1.5446 110.88 -86.85 110.49 0.9639 +IC O5 C4 *C5 H51 1.4293 110.88 119.78 108.95 1.1027 +IC O5 C4 *C5 H52 1.4293 110.88 -122.02 109.96 1.1020 +IC C2 O4 *C1 O1 1.5564 102.91 122.54 109.76 1.4025 +IC O4 C1 O1 HO1 1.4227 109.76 66.79 107.33 0.9584 +IC C2 O4 *C1 H1 1.5564 102.91 -117.68 108.69 1.1117 +IC C3 C1 *C2 H2 1.5615 103.27 -113.35 106.87 1.1124 +IC C3 C1 *C2 O2 1.5615 103.27 127.46 116.16 1.4278 +IC C1 C2 O2 HO2 1.5564 116.16 -81.77 106.00 0.9665 +IC C2 C4 *C3 O3 1.5615 103.97 -125.04 111.07 1.4263 +IC C2 C4 *C3 H3 1.5615 103.97 115.28 109.94 1.1126 +IC C4 C3 O3 HO3 1.5386 111.07 -77.15 108.40 0.9644 +IC C2 C4 *C3 H4 1.5615 103.97 -95.69 28.61 2.1867 + +RESI BRIB 0.000 ! beta-Ribose +!RING * 5 C1 C2 C3 C4 O4 +! +! HO5--O5 +! \ O4 +! H51--C5 / \ O1--HO1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / H1 +! C3----C2 +! / \ / \ +! HO3--O3 H3 O2 H2 +! | +! HO2 +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from glycerol +ATOM C2 CD31FB -0.006 ALPHA -1.438 THOLE 1.015 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.940 THOLE 0.670 +ATOM HO2 HDP1A 0.322 +ATOM LP2A LPD -0.193 +ATOM LP2B LPD -0.193 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4343 107.06 -43.51 102.91 1.5564 +IC O4 C1 C2 C3 1.4227 102.91 29.68 103.27 1.5615 +IC C1 C2 C3 C4 1.5564 103.27 -6.90 103.97 1.5386 +IC C3 O4 *C4 C5 1.5386 104.85 125.17 112.30 1.5446 +IC C3 O4 *C4 H4 1.5386 104.85 -116.42 106.12 1.1143 +IC O4 C4 C5 O5 1.4343 112.30 -178.59 110.88 1.4293 +IC C4 C5 O5 HO5 1.5446 110.88 -86.85 110.49 0.9639 +IC O5 C4 *C5 H51 1.4293 110.88 119.78 108.95 1.1027 +IC O5 C4 *C5 H52 1.4293 110.88 -122.02 109.96 1.1020 +IC C2 O4 *C1 O1 1.5564 102.91 -122.54 109.76 1.4025 +IC O4 C1 O1 HO1 1.4227 109.76 66.79 107.33 0.9584 +IC C2 O4 *C1 H1 1.5564 102.91 117.68 108.69 1.1117 +IC C3 C1 *C2 H2 1.5615 103.27 -113.35 106.87 1.1124 +IC C3 C1 *C2 O2 1.5615 103.27 127.46 116.16 1.4278 +IC C1 C2 O2 HO2 1.5564 116.16 -81.77 106.00 0.9665 +IC C2 C4 *C3 O3 1.5615 103.97 -125.04 111.07 1.4263 +IC C2 C4 *C3 H3 1.5615 103.97 115.28 109.94 1.1126 +IC C4 C3 O3 HO3 1.5386 111.07 -77.15 108.40 0.9644 +IC C2 C4 *C3 H4 1.5615 103.97 -95.69 28.61 2.1867 + +RESI AARB 0.000 ! alpha-Arabinose +!RING * 5 C1 C2 C3 C4 O4 +! HO5--O5 +! \ O4 +! H51--C5 / \ H1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / O1--HO1 +! C3----C2 +! / \ / \ +! HO3--O3 H3 H2 O2 +! | +! HO2 +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from glycerol +ATOM C2 CD31FB -0.006 ALPHA -1.438 THOLE 1.015 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.940 THOLE 0.670 +ATOM HO2 HDP1A 0.322 +ATOM LP2A LPD -0.193 +ATOM LP2B LPD -0.193 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4319 108.67 -17.05 106.71 1.5578 +IC O4 C1 C2 C3 1.4302 106.71 -10.12 102.15 1.5355 +IC C1 C2 C3 C4 1.5578 102.15 31.25 101.91 1.5267 +IC C3 O4 *C4 C5 1.5267 102.62 124.20 112.49 1.5454 +IC C3 O4 *C4 H4 1.5267 102.62 -115.89 106.69 1.1135 +IC O4 C4 C5 O5 1.4319 112.49 -179.23 111.10 1.4305 +IC C4 C5 O5 HO5 1.5454 111.10 -93.06 110.47 0.9646 +IC O5 C4 *C5 H51 1.4305 111.10 119.95 108.87 1.1029 +IC O5 C4 *C5 H52 1.4305 111.10 -122.01 109.82 1.1021 +IC C2 O4 *C1 O1 1.5578 106.71 122.01 110.02 1.3992 +IC O4 C1 O1 HO1 1.4302 110.02 65.19 106.88 0.9590 +IC C2 O4 *C1 H1 1.5578 106.71 -118.66 107.16 1.1129 +IC C3 C1 *C2 H2 1.5355 102.15 115.71 109.19 1.1138 +IC C3 C1 *C2 O2 1.5355 102.15 -121.95 114.37 1.4285 +IC C1 C2 O2 HO2 1.5578 114.37 -171.75 108.32 0.9638 +IC C2 C4 *C3 O3 1.5355 101.91 -122.00 112.32 1.4206 +IC C2 C4 *C3 H3 1.5355 101.91 116.42 109.37 1.1143 +IC C4 C3 O3 HO3 1.5267 112.32 -53.24 107.21 0.9692 +IC C2 C4 *C3 H4 1.5355 101.91 -71.04 28.67 2.1783 +! +RESI BARB 0.000 ! beta-Arabinose +!RING * 5 C1 C2 C3 C4 O4 +! +! HO5--O5 +! \ O4 +! H51--C5 / \ O1--HO1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / H1 +! C3----C2 +! / \ / \ +! HO3--O3 H3 H2 O2 +! | +! HO2 +! +! +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from glycerol +ATOM C2 CD31FB -0.006 ALPHA -1.438 THOLE 1.015 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.940 THOLE 0.670 +ATOM HO2 HDP1A 0.322 +ATOM LP2A LPD -0.193 +ATOM LP2B LPD -0.193 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4319 108.67 -17.05 106.71 1.5578 +IC O4 C1 C2 C3 1.4302 106.71 -10.12 102.15 1.5355 +IC C1 C2 C3 C4 1.5578 102.15 31.25 101.91 1.5267 +IC C3 O4 *C4 C5 1.5267 102.62 124.20 112.49 1.5454 +IC C3 O4 *C4 H4 1.5267 102.62 -115.89 106.69 1.1135 +IC O4 C4 C5 O5 1.4319 112.49 -179.23 111.10 1.4305 +IC C4 C5 O5 HO5 1.5454 111.10 -93.06 110.47 0.9646 +IC O5 C4 *C5 H51 1.4305 111.10 119.95 108.87 1.1029 +IC O5 C4 *C5 H52 1.4305 111.10 -122.01 109.82 1.1021 +IC C2 O4 *C1 O1 1.5578 106.71 -122.01 110.02 1.3992 +IC O4 C1 O1 HO1 1.4302 110.02 65.19 106.88 0.9590 +IC C2 O4 *C1 H1 1.5578 106.71 118.66 107.16 1.1129 +IC C3 C1 *C2 H2 1.5355 102.15 115.71 109.19 1.1138 +IC C3 C1 *C2 O2 1.5355 102.15 -121.95 114.37 1.4285 +IC C1 C2 O2 HO2 1.5578 114.37 -171.75 108.32 0.9638 +IC C2 C4 *C3 O3 1.5355 101.91 -122.00 112.32 1.4206 +IC C2 C4 *C3 H3 1.5355 101.91 116.42 109.37 1.1143 +IC C4 C3 O3 HO3 1.5267 112.32 -53.24 107.21 0.9692 +IC C2 C4 *C3 H4 1.5355 101.91 -71.04 28.67 2.1783 + +RESI AXYF 0.000 ! alpha-Xylofuranose +!RING * 5 C1 C2 C3 C4 O4 +! HO5--O5 +! \ O4 +! H51--C5 / \ H1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / O1--HO1 +! C3----C2 +! / \ / \ +! H3 O3 O2 H2 +! | | +! HO3 HO2 +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from glycerol +ATOM C2 CD31FB -0.006 ALPHA -1.438 THOLE 1.015 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.940 THOLE 0.670 +ATOM HO2 HDP1A 0.322 +ATOM LP2A LPD -0.193 +ATOM LP2B LPD -0.193 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4368 109.21 7.17 106.92 1.5609 +IC O4 C1 C2 C3 1.4288 106.92 -29.31 100.61 1.5256 +IC C1 C2 C3 C4 1.5609 100.61 38.33 101.22 1.5366 +IC C3 O4 *C4 C5 1.5366 105.95 126.07 111.10 1.5466 +IC C3 O4 *C4 H4 1.5366 105.95 -115.62 106.41 1.1129 +IC O4 C4 C5 O5 1.4368 111.10 -170.12 111.17 1.4292 +IC C4 C5 O5 HO5 1.5466 111.17 -86.81 110.69 0.9637 +IC O5 C4 *C5 H51 1.4292 111.17 119.44 108.73 1.1031 +IC O5 C4 *C5 H52 1.4292 111.17 -122.76 110.12 1.1017 +IC C2 O4 *C1 O1 1.5609 106.92 123.12 110.19 1.4024 +IC O4 C1 O1 HO1 1.4288 110.19 60.16 106.38 0.9603 +IC C2 O4 *C1 H1 1.5609 106.92 -117.24 106.84 1.1130 +IC C3 C1 *C2 H2 1.5256 100.61 -119.80 111.22 1.1086 +IC C3 C1 *C2 O2 1.5256 100.61 116.99 113.84 1.4299 +IC C1 C2 O2 HO2 1.5609 113.84 25.15 106.11 0.9678 +IC C2 C4 *C3 O3 1.5256 101.22 116.82 111.32 1.4223 +IC C2 C4 *C3 H3 1.5256 101.22 -120.45 112.39 1.1104 +IC C4 C3 O3 HO3 1.5366 111.32 68.17 107.50 0.9664 +IC C2 C4 *C3 H4 1.5256 101.22 -77.82 29.09 2.1676 + +RESI BXYF 0.000 ! beta-Xylofuranose +!RING * 5 C1 C2 C3 C4 O4 +! HO5--O5 +! \ O4 +! H51--C5 / \ O1--HO1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / H1 +! C3----C2 +! / \ / \ +! H3 O3 O2 H2 +! | | +! HO3 HO2 +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from glycerol +ATOM C2 CD31FB -0.006 ALPHA -1.438 THOLE 1.015 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.940 THOLE 0.670 +ATOM HO2 HDP1A 0.322 +ATOM LP2A LPD -0.193 +ATOM LP2B LPD -0.193 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4368 109.21 7.17 106.92 1.5609 +IC O4 C1 C2 C3 1.4288 106.92 -29.31 100.61 1.5256 +IC C1 C2 C3 C4 1.5609 100.61 38.33 101.22 1.5366 +IC C3 O4 *C4 C5 1.5366 105.95 126.07 111.10 1.5466 +IC C3 O4 *C4 H4 1.5366 105.95 -115.62 106.41 1.1129 +IC O4 C4 C5 O5 1.4368 111.10 -170.12 111.17 1.4292 +IC C4 C5 O5 HO5 1.5466 111.17 -86.81 110.69 0.9637 +IC O5 C4 *C5 H51 1.4292 111.17 119.44 108.73 1.1031 +IC O5 C4 *C5 H52 1.4292 111.17 -122.76 110.12 1.1017 +IC C2 O4 *C1 O1 1.5609 106.92 -123.12 110.19 1.4024 +IC O4 C1 O1 HO1 1.4288 110.19 60.16 106.38 0.9603 +IC C2 O4 *C1 H1 1.5609 106.92 117.24 106.84 1.1130 +IC C3 C1 *C2 H2 1.5256 100.61 -119.80 111.22 1.1086 +IC C3 C1 *C2 O2 1.5256 100.61 116.99 113.84 1.4299 +IC C1 C2 O2 HO2 1.5609 113.84 25.15 106.11 0.9678 +IC C2 C4 *C3 O3 1.5256 101.22 116.82 111.32 1.4223 +IC C2 C4 *C3 H3 1.5256 101.22 -120.45 112.39 1.1104 +IC C4 C3 O3 HO3 1.5366 111.32 68.17 107.50 0.9664 +IC C2 C4 *C3 H4 1.5256 101.22 -77.82 29.09 2.1676 + +RESI ALYF 0.000 ! alpha-lyxofuranose +!RING * 5 C1 C2 C3 C4 O4 +! HO5--O5 +! \ O4 +! H51--C5 / \ H1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / O1--HO1 +! C3----C2 +! / \ / \ +! H3 O3 H2 O2 +! | | +! HO3 HO2 +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from glycerol +ATOM C2 CD31FB -0.006 ALPHA -1.438 THOLE 1.015 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.940 THOLE 0.670 +ATOM HO2 HDP1A 0.322 +ATOM LP2A LPD -0.193 +ATOM LP2B LPD -0.193 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4315 107.76 -22.45 106.42 1.5606 +IC O4 C1 C2 C3 1.4298 106.42 -6.06 102.41 1.5494 +IC C1 C2 C3 C4 1.5606 102.41 29.67 101.01 1.5315 +IC C3 O4 *C4 C5 1.5315 102.23 127.07 113.37 1.5469 +IC C3 O4 *C4 H4 1.5315 102.23 -114.55 106.16 1.1145 +IC O4 C4 C5 O5 1.4315 113.37 172.78 110.88 1.4279 +IC C4 C5 O5 HO5 1.5469 110.88 -89.23 111.11 0.9627 +IC O5 C4 *C5 H51 1.4279 110.88 120.67 109.96 1.1012 +IC O5 C4 *C5 H52 1.4279 110.88 -120.92 109.55 1.1021 +IC C2 O4 *C1 O1 1.5606 106.42 121.62 109.95 1.3992 +IC O4 C1 O1 HO1 1.4298 109.95 66.51 107.28 0.9594 +IC C2 O4 *C1 H1 1.5606 106.42 -119.08 107.39 1.1123 +IC C3 C1 *C2 H2 1.5494 102.41 115.35 109.45 1.1122 +IC C3 C1 *C2 O2 1.5494 102.41 -123.37 114.05 1.4282 +IC C1 C2 O2 HO2 1.5606 114.05 104.03 106.69 0.9675 +IC C2 C4 *C3 O3 1.5494 101.01 118.58 111.21 1.4279 +IC C2 C4 *C3 H3 1.5494 101.01 -119.18 112.30 1.1095 +IC C4 C3 O3 HO3 1.5315 111.21 -32.26 108.53 0.9635 +IC C2 C4 *C3 H4 1.5494 101.01 -68.34 28.96 2.1721 + +RESI BLYF 0.000 ! beta-lyxofuranose +!RING * 5 C1 C2 C3 C4 O4 +! HO5--O5 +! \ O4 +! H51--C5 / \ O1--HO1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / H1 +! C3----C2 +! / \ / \ +! H3 O3 H2 O2 +! | | +! HO3 HO2 +! +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from glycerol +ATOM C2 CD31FB -0.006 ALPHA -1.438 THOLE 1.015 +ATOM H2 HDA1A 0.070 +ATOM O2 OD31E 0.000 ALPHA -0.940 THOLE 0.670 +ATOM HO2 HDP1A 0.322 +ATOM LP2A LPD -0.193 +ATOM LP2B LPD -0.193 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4315 107.76 -22.45 106.42 1.5606 +IC O4 C1 C2 C3 1.4298 106.42 -6.06 102.41 1.5494 +IC C1 C2 C3 C4 1.5606 102.41 29.67 101.01 1.5315 +IC C3 O4 *C4 C5 1.5315 102.23 127.07 113.37 1.5469 +IC C3 O4 *C4 H4 1.5315 102.23 -114.55 106.16 1.1145 +IC O4 C4 C5 O5 1.4315 113.37 172.78 110.88 1.4279 +IC C4 C5 O5 HO5 1.5469 110.88 -89.23 111.11 0.9627 +IC O5 C4 *C5 H51 1.4279 110.88 120.67 109.96 1.1012 +IC O5 C4 *C5 H52 1.4279 110.88 -120.92 109.55 1.1021 +IC C2 O4 *C1 O1 1.5606 106.42 -121.62 109.95 1.3992 +IC O4 C1 O1 HO1 1.4298 109.95 66.51 107.28 0.9594 +IC C2 O4 *C1 H1 1.5606 106.42 119.08 107.39 1.1123 +IC C3 C1 *C2 H2 1.5494 102.41 115.35 109.45 1.1122 +IC C3 C1 *C2 O2 1.5494 102.41 -123.37 114.05 1.4282 +IC C1 C2 O2 HO2 1.5606 114.05 104.03 106.69 0.9675 +IC C2 C4 *C3 O3 1.5494 101.01 118.58 111.21 1.4279 +IC C2 C4 *C3 H3 1.5494 101.01 -119.18 112.30 1.1095 +IC C4 C3 O3 HO3 1.5315 111.21 -32.26 108.53 0.9635 +IC C2 C4 *C3 H4 1.5494 101.01 -68.34 28.96 2.1721 + +RESI ADEO 0.000 ! alpha-Deoxy-Ribose +!RING * 5 C1 C2 C3 C4 O4 +! +! HO5--O5 +! \ O4 +! H51--C5 / \ H1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / O1--HO1 +! C3----C2 +! / \ / \ +! HO3--O3 H3 H21 H22 +! +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from THF +ATOM C2 CD325B -0.142 ALPHA -1.617 THOLE 1.103! ALPHA @ALPHA1 THOLE @THOLE1 !ALPHA -1.617 THOLE 1.103 +ATOM H21 HDA2R5 0.071 +ATOM H22 HDA2R5 0.071 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H21 C2 H22 C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 O4 C4 C5 C5 H51 +BOND C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4309 108.67 -19.01 106.25 1.5278 +IC O4 C1 C2 C3 1.4258 106.25 -8.82 103.23 1.5178 +IC C1 C2 C3 C4 1.5278 103.23 31.05 101.83 1.5232 +IC C3 O4 *C4 C5 1.5232 101.44 124.05 113.01 1.5448 +IC C3 O4 *C4 H4 1.5232 101.44 -115.42 106.74 1.1134 +IC O4 C4 C5 O5 1.4309 113.01 -178.27 111.12 1.4304 +IC C4 C5 O5 HO5 1.5448 111.12 -87.73 110.40 0.9643 +IC O4 C4 *C5 H51 2.4824 32.04 59.71 109.84 1.1020 +IC O4 C4 *C5 H52 2.4824 32.04 -58.37 108.86 1.1027 +IC C2 O4 *C1 O1 1.5278 106.25 119.87 110.66 1.3905 +IC O4 C1 O1 HO1 1.4258 110.66 60.11 106.63 0.9584 +IC C2 O4 *C1 H1 1.5278 106.25 -119.86 107.45 1.1137 +IC C3 C1 *C2 H21 1.5178 103.23 118.42 111.24 1.1030 +IC C3 C1 *C2 H22 1.5178 103.23 -122.05 112.95 1.0962 +IC C2 C4 *C3 O3 1.5178 101.83 -120.07 112.49 1.4116 +IC C4 C3 O3 HO3 1.5232 112.49 -53.93 107.21 0.9673 +IC C2 C4 *C3 H3 1.5178 101.83 117.41 109.93 1.1144 + +RESI BDEO 0.000 ! beta-Deoxy-Ribose +!RING * 5 C1 C2 C3 C4 O4 +! +! HO5--O5 +! \ O4 +! H51--C5 / \ O1--HO1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / H1 +! C3----C2 +! / \ / \ +! HO3--O3 H3 H21 H22 +! +! +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.684 THOLE 2.074 +ATOM C1 CD31FA 0.124 ALPHA -1.022 THOLE 0.462 +ATOM H1 HDA1A 0.070 +ATOM O1 OD31E 0.000 ALPHA -1.176 THOLE 1.559 +ATOM HO1 HDP1A 0.333 +ATOM C4 CD31FC 0.112 ALPHA -1.014 THOLE 0.820 +ATOM H4 HDA2E 0.069 +ATOM LP1A LPD -0.202 +ATOM LP1B LPD -0.202 +ATOM LP4A LPD -0.152 +ATOM LP4B LPD -0.152 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +GROUP ! taken from ETOH +ATOM C5 CD32A -0.086 ALPHA -1.805 THOLE 0.353 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -0.732 THOLE 1.027 +ATOM HO5 HDP1A 0.328 +ATOM LP5A LPD -0.201 +ATOM LP5B LPD -0.201 +GROUP ! taken from THF +ATOM C2 CD325B -0.142 ALPHA -1.617 THOLE 1.103! ALPHA @ALPHA1 THOLE @THOLE1 !ALPHA -1.617 THOLE 1.103 +ATOM H21 HDA2R5 0.071 +ATOM H22 HDA2R5 0.071 +GROUP ! taken from glycerol +ATOM C3 CD31FB -0.006 ALPHA -1.127 THOLE 1.340 +ATOM H3 HDA1A 0.070 +ATOM O3 OD31E 0.000 ALPHA -0.881 THOLE 0.328 +ATOM HO3 HDP1A 0.322 +ATOM LP3A LPD -0.193 +ATOM LP3B LPD -0.193 +! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H21 C2 H22 C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 O4 C4 C5 C5 H51 +BOND C5 H52 C5 O5 O5 HO5 +BOND O1 LP1A O1 LP1B +BOND O3 LP3A O3 LP3B +BOND O4 LP4A O4 LP4B O4 LPX4 +BOND O5 LP5A O5 LP5B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 + +LONEPAIR bisector LP4A O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP4B O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX4 O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4 LPX4 LP4A LP4B A11 0.8889 A22 1.2222 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4309 108.67 -19.01 106.25 1.5278 +IC O4 C1 C2 C3 1.4258 106.25 -8.82 103.23 1.5178 +IC C1 C2 C3 C4 1.5278 103.23 31.05 101.83 1.5232 +IC C3 O4 *C4 C5 1.5232 101.44 124.05 113.01 1.5448 +IC C3 O4 *C4 H4 1.5232 101.44 -115.42 106.74 1.1134 +IC O4 C4 C5 O5 1.4309 113.01 -178.27 111.12 1.4304 +IC C4 C5 O5 HO5 1.5448 111.12 -87.73 110.40 0.9643 +IC O4 C4 *C5 H51 2.4824 32.04 59.71 109.84 1.1020 +IC O4 C4 *C5 H52 2.4824 32.04 -58.37 108.86 1.1027 +IC C2 O4 *C1 O1 1.5278 106.25 -119.87 110.66 1.3905 +IC O4 C1 O1 HO1 1.4258 110.66 60.11 106.63 0.9584 +IC C2 O4 *C1 H1 1.5278 106.25 119.86 107.45 1.1137 +IC C3 C1 *C2 H21 1.5178 103.23 118.42 111.24 1.1030 +IC C3 C1 *C2 H22 1.5178 103.23 -122.05 112.95 1.0962 +IC C2 C4 *C3 O3 1.5178 101.83 -120.07 112.49 1.4116 +IC C4 C3 O3 HO3 1.5232 112.49 -53.93 107.21 0.9673 +IC C2 C4 *C3 H3 1.5178 101.83 117.41 109.93 1.1144 + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! O-alkyl patches for furanose ! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +PRES FOMA 0.000 ! adding alpha O-methyl to C1 on aldopentose +dele atom HO1 +dele atom LP1A +dele atom LP1B +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.505 THOLE 0.807 +ATOM C1 CD31FA 0.152 ALPHA -1.000 THOLE 0.487 +ATOM H1 HDA1A 0.070 +ATOM O1 OD30A 0.000 ALPHA -0.503 THOLE 0.443 +ATOM CM CD33E -0.053 ALPHA -1.038 THOLE 0.667 +ATOM HM1 HDA3A 0.069 +ATOM HM2 HDA3A 0.069 +ATOM HM3 HDA3A 0.069 +ATOM C4 CD31FC 0.131 ALPHA -1.029 THOLE 0.909 +ATOM H4 HDA2E 0.069 +ATOM LPMA LPD -0.121 +ATOM LPMB LPD -0.121 +ATOM LP4A LPD -0.167 +ATOM LP4B LPD -0.167 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +ATOM LPX1 LPD 0.000 !dummy for anisotropic polarizability +BOND O1 CM +BOND CM HM1 CM HM2 CM HM3 +BOND O1 LPMA O1 LPMB O1 LPX1 + +LONEPAIR bisector LPMA O1 C1 CM distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPMB O1 C1 CM distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX1 O1 C1 CM distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O1 LPX1 LPMA LPMB A11 0.8889 A22 1.2222 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O4 C1 O1 CM 1.4477 109.89 66.08 108.74 1.4244 +IC C1 O1 CM HM1 1.4355 108.74 59.11 111.44 1.0883 +IC HM1 O1 *CM HM2 1.0883 111.44 119.69 113.64 1.0586 +IC HM3 O1 *CM HM2 1.1131 110.64 -122.99 113.64 1.0586 + +PRES FOMB 0.000 ! adding beta O-methyl to C1 on aldopentose +dele atom HO1 +dele atom LP1A +dele atom LP1B +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.505 THOLE 0.807 +ATOM C1 CD31FA 0.152 ALPHA -1.000 THOLE 0.487 +ATOM H1 HDA1A 0.070 +ATOM O1 OD30A 0.000 ALPHA -0.503 THOLE 0.443 +ATOM CM CD33E -0.053 ALPHA -1.038 THOLE 0.667 +ATOM HM1 HDA3A 0.069 +ATOM HM2 HDA3A 0.069 +ATOM HM3 HDA3A 0.069 +ATOM C4 CD31FC 0.131 ALPHA -1.029 THOLE 0.909 +ATOM H4 HDA2E 0.069 +ATOM LPMA LPD -0.121 +ATOM LPMB LPD -0.121 +ATOM LP4A LPD -0.167 +ATOM LP4B LPD -0.167 +ATOM LPX4 LPD 0.000 !dummy for anisotropic polarizability +ATOM LPX1 LPD 0.000 !dummy for anisotropic polarizability +BOND O1 CM +BOND CM HM1 CM HM2 CM HM3 +BOND O1 LPMA O1 LPMB O1 LPX1 + +LONEPAIR bisector LPMA O1 C1 CM distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPMB O1 C1 CM distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX1 O1 C1 CM distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O1 LPX1 LPMA LPMB A11 0.8889 A22 1.2222 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O4 C1 O1 CM 1.4138 114.30 -66.36 108.55 1.4077 +IC C1 O1 CM HM1 1.4353 108.55 41.11 109.39 1.0734 +IC HM1 O1 *CM HM2 1.0734 109.39 129.90 119.45 1.0441 +IC HM3 O1 *CM HM2 1.1148 107.24 -121.74 119.45 1.0441 +!furanoses, rima + +end + +read para card append +* Drude polarizable FF parameters +* + +BONDS +!atom type Kb b0 +!============================================ +! +!polyols +OD31E CD32F 320.0 1.425 ! ethylene glycol, glycerol, xhe, polyols +OD31E CD31G 350.0 1.430 ! glycerol, xhe, polyols +CD32F CD32F 222.5 1.500 ! ethylene glycol, xhe +CD32F CD31G 222.5 1.510 ! glycerol, xhe, polyols +CD31G CD31G 222.5 1.510 ! xhe, polyols +CD32F HDA2A 309.0 1.080 ! ethylene glycol, glycerol, xhe, polyols +CD31G HDA1A 309.0 1.080 ! glycerol, xhe, polyols +!OD31E LPD 0.00 0.000 ! ethylene glycol, glycerol, xhe +!CD32F LPD 0.00 0.000 ! ethylene glycol, glycerol, xhe +!CD31G LPD 0.00 0.000 ! glycerol, xhe +!polyols +!hexopyranoses +CD31HB OD306A 280.0 1.430 +CD31HB CD31HB 222.5 1.520 ! +CD31HB CD31HC 222.5 1.520 +CD31HC CD32A 222.5 1.510 +OD31E CD31HA 350.0 1.400 ! hexopyranose, dpatel +CD31HA OD306A 280.0 1.430 ! +CD31HA CD31HB 222.5 1.520 ! +CD31HA HDA1A 309.0 1.093 ! glycerol, xhe +!CD31HA LPD 0.00 0.000 ! glycerol, xhe +OD306A CD31HC 280.0 1.415 ! Hexopyranose, dpatel +CD31HC HDA2E 309.0 1.111 ! from, THP, tetrahydropyran, viv, dpatel +CD31HB HDA1A 309.0 1.093 ! from, CD31G HDA1A, glycerol, xhe +!CD31HC LPD 0.00 0.000 ! DMP, dpatel +CD31HB OD31E 350.0 1.440 ! from, OD31E CD31G, glycerol, xhe +OD31E HDP1A 536.5 0.970 ! Old parameters from xibing, all carb vaildated with this set. dpatel +OD31E LPD 0.00 0.000 ! +!hexopyranoses +!furanoses, rima +OD305A CD31FA 280.0 1.430 ! dpatel +CD31FC OD305A 280.0 1.415 ! Hexopyranose, dpatel +CD31FA HDA1A 309.0 1.093 ! glycerol, xhe +OD31E CD31FA 350.0 1.400 ! hexopyranose, dpatel +CD31FA CD31FB 222.5 1.520 ! +CD31FB HDA1A 309.0 1.093 ! from, CD31G HDA1A, glycerol, xhe +CD31FB OD31E 350.0 1.440 ! from, OD31E CD31G, glycerol, xhe +CD31FB CD31FB 222.5 1.520 ! +CD31FB CD31FC 222.5 1.520 +CD31FC HDA2E 307.0 1.100 ! THF, THF neutron diffr, viv +CD31FC CD32A 222.5 1.510 +CD31FA CD325B 222.5 1.520 ! for deoxy +CD325B CD31FB 222.5 1.520 ! for deoxy +OD30A CD31FA 280.0 1.430 ! for OME +!furanoses, rima + +ANGLES +!atom types Ktheta Theta0 Kub S0 +!================================================== +!polyols +CD31G OD31E HDP1A 59.00 108.00 ! glycerol, xhe +CD32F OD31E HDP1A 49.00 107.30 ! ethylene glycol, glycerol, xh +OD31E CD31G CD32F 59.30 111.00 ! glycerol, xhe +OD31E CD32F CD31G 66.00 111.00 ! glycerol, xhe +OD31E CD32F CD32F 66.00 111.00 ! ethylene glycol, xhe +OD31E CD31G CD31G 66.00 111.00 !!! MERYOL +OD31E CD32F HDA2A 54.00 110.50 ! ethylene glycol, glycerol, xhe +OD31E CD31G HDA1A 47.00 110.50 ! glycerol, xhe +CD32F CD31G CD31G 58.35 113.50 11.16 2.561 !!! MERYOL +CD32F CD31G CD32F 58.35 113.50 11.16 2.561 ! glycerol, xhe +CD31G CD31G CD31G 58.35 113.50 11.16 2.561 !!! MRIBOL ! CD32F CD31G CD31G +CD32F CD32F HDA2A 26.50 110.10 22.53 2.179 ! ethylene glycol, xhe +CD31G CD32F HDA2A 26.50 110.10 22.53 2.179 ! glycerol, xhe +CD32F CD31G HDA1A 34.50 110.10 22.53 2.179 ! glycerol, xhe +CD31G CD31G HDA1A 34.50 110.10 22.53 2.179 !!! MERYOL +HDA2A CD32F HDA2A 35.50 109.00 5.40 1.802 ! ethylene glycol, glycerol, xhe +!polyols +!hexapyranoses +HDA1A CD31HB OD306A 45.00 109.50 ! from, THP, OD306A CD326B HDA2E +OD31E CD31HB OD306A 85.00 111.50 ! +OD306A CD31HB CD31HB 45.00 111.50 ! from, THP, OD306A CD326B CD326B +HDA2E CD31HC CD31HB 26.50 110.10 22.53 2.179 ! from, CHXM, CD326A CD316A HDA1A +HDA2E CD31HC CD32A 34.50 110.10 22.53 2.179 ! from, CHXM, CD33A CD316A HDA1A +OD306A CD31HC CD31HB 45.00 111.50 ! from, THP, OD306A CD326B CD326B +OD306A CD31HC CD32A 75.00 106.50 ! +CD31HB CD31HC CD32A 58.35 112.00 11.16 2.561 ! from, cyclohexane,CD326B CD326B CD326B +CD31HB OD306A CD31HC 95.00 109.70 ! from, THP, CD326B OD306A CD326B +CD31HB CD31HB HDA1A 34.50 110.10 22.53 2.179 ! from, cyclohexane, CD326B CD326B HDA2E +CD31HB CD31HB OD31E 65.30 109.00 ! from, glycerol, OD31E CD31HB CD32F , before molvib 65.0 +CD31HB CD31HB CD31HB 58.35 112.00 11.16 2.561 ! from, cyclohexane,CD326B CD326B CD326B +CD31HC CD31HB CD31HB 58.35 112.00 11.16 2.561 ! from, cyclohexane,CD326B CD326B CD326B +CD31HC CD31HB HDA1A 26.50 110.10 22.53 2.179 ! from, CHXM, CD316A CD326A HDA2A +CD31HC CD31HB OD31E 65.30 109.00 ! from, glycerol, OD31E CD31HB CD32F +CD31HC CD32A HDA2A 34.60 110.10 22.53 2.179 ! from, CD33A CD32A HDA2A +CD31HC CD32A OD31A 63.00 111.00 ! from, ETOH, OD31A CD32A CD33A, before molvib 66.0 +OD306A CD31HC HDA2E 45.00 109.50 ! from, OD306A CD326B HDA2E, THP, sng +CD31HA CD31HB CD31HB 58.35 112.00 11.16 2.561 ! from, cyclohexane,CD326B CD326B CD326B +CD31HA OD306A CD31HC 95.00 109.70 ! from, THP, CD326B OD306A CD326B +CD31HA CD31HB OD31E 65.30 109.00 ! from, glycerol, OD31E CD31HB CD32F, before molvib 65.0 +CD31HA OD31E HDP1A 59.00 108.00 ! glycerol, xhe 59.0 before molvib +CD31HA CD31HB HDA1A 34.50 110.10 22.53 2.179 ! from, cyclohexane, CD326B CD326B HDA2E +CD31HB CD31HA HDA1A 34.50 110.10 22.53 2.179 ! from, cyclohexane, CD326B CD326B HDA2E +OD31E CD31HA HDA1A 47.00 110.50 ! glycerol, xhe +HDA1A CD31HA OD306A 45.00 109.50 ! from, THP, OD306A CD326B HDA2E +OD31E CD31HA OD306A 90.00 111.50 ! +CD31HB CD31HA OD31E 65.30 109.00 ! from, glycerol, OD31E CD31HB CD32F +OD306A CD31HA CD31HB 45.00 111.50 ! from, THP, OD306A CD326B CD326B +HDA1A CD31HB OD31E 47.00 110.50 ! from, OD31E CD31G HDA1A, glycerol, xhe +CD31HB OD31E HDP1A 59.00 108.00 ! from, CD31G OD31E HDP1A, glycerol, xhe +!hexapyranoses +!furanoses, rima +CD31FA OD305A CD31FC 95.00 111.00 ! THF, CD325B OD305A CD325B +OD305A CD31FA HDA1A 70.00 107.30 ! THF, viv 10/21/05, OD305A CD325B HDA2R5 +OD305A CD31FA OD31E 90.00 111.50 ! from dpatel, OD306A CD31FA OD31E +OD305A CD31FA CD31FB 45.00 111.10 ! THF, viv 10/21/05, OD305A CD325B CD325B +OD305A CD31FC HDA2E 70.00 107.30 ! THF, viv 10/21/05, OD305A CD325B HDA2R5 +OD305A CD31FC CD32A 75.00 106.50 ! from dpatel, OD306A CD31FC CD32A +OD305A CD31FC CD31FB 45.00 111.50 ! THF, viv 10/21/05, OD305A CD325B CD325B +OD31E CD31FA HDA1A 47.00 110.50 ! glycerol, xhe +CD31FB CD31FA HDA1A 35.00 111.40 22.53 2.179 ! ! CPEN 10/17/05 viv +CD31FA CD31FB HDA1A 35.00 111.40 22.53 2.179 ! ! CPEN 10/17/05 viv +CD31FA OD31E HDP1A 59.00 108.00 ! glycerol, xhe 59.0 before molvib +CD31FB OD31E HDP1A 59.00 108.00 ! from, CD31G OD31E HDP1A, glycerol, xhe +HDA1A CD31FB OD31E 47.00 110.50 ! from, OD31E CD31G HDA1A, glycerol, xhe +CD31FB CD31FB OD31E 65.30 109.00 ! from, glycerol, OD31E CD31FB CD32F , before molvib 65.0 +CD31FC CD32A HDA2A 34.60 110.10 22.53 2.179 ! from, CD33A CD32A HDA2A +CD31FB CD31FB HDA1A 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +CD31FC CD31FB OD31E 65.30 109.00 ! from, glycerol, OD31E CD31FB CD32F +CD31FC CD31FB HDA1A 35.00 111.40 22.53 2.179 ! CPNM 10/17/05 cmb +CD31FC CD31FB CD31FB 58.00 109.50 11.16 2.561 ! THF, CSD/NDB survey, viv +CD31FC CD32A OD31A 63.00 111.00 ! from, ETOH, OD31A CD32A CD33A, before molvib 66.0 +HDA2E CD31FC CD32A 34.50 110.10 22.53 2.179 ! CPNM, cmb +CD31FA CD31FB CD31FB 58.00 109.50 11.16 2.561 ! THF, CSD/NDB survey, viv +CD31FA CD31FB OD31E 65.30 109.00 ! from, glycerol, OD31E CD31FB CD32F, before molvib 65.0 +CD32A CD31FC CD31FB 58.00 109.50 11.16 2.561 ! THF, CSD/NDB survey, viv +HDA2E CD31FC CD31FB 35.00 111.40 22.53 2.179 ! CPNM 01/10, cmb +CD31FB CD31FA OD31E 65.30 109.00 ! from, glycerol, OD31E CD31FB CD32F +!for deoxy +OD305A CD31FA CD325B 45.00 111.10 ! THF, viv 10/21/05, OD305A CD325B CD325B +HDA1A CD31FA CD325B 35.00 111.40 22.53 2.179 ! ! CPEN 10/17/05 viv +OD31E CD31FA CD325B 65.30 109.00 ! from, glycerol, OD31E CD31HB CD32F +CD31FA CD325B HDA2R5 35.00 111.40 22.53 2.179 ! ! CPEN 10/17/05 viv +CD31FB CD325B HDA2R5 35.00 111.40 22.53 2.179 ! ! CPEN 10/17/05 vi +CD31FA CD325B CD31FB 58.00 109.50 11.16 2.561 ! THF, CSD/NDB survey, viv +CD31FC CD31FB CD325B 58.00 109.50 11.16 2.561 ! THF, CSD/NDB survey, viv +CD325B CD31FB HDA1A 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +CD325B CD31FB OD31E 65.30 109.00 ! from, glycerol, OD31E CD31HB CD32F , before molvib 65.0 +!for OME +OD305A CD31FA OD30A 90.00 111.50 ! from dpatel, OD306A CD31HA OD31E +HDA1A CD31FA OD30A 47.00 110.50 ! glycerol, xhe +OD30A CD31FA CD31FB 65.30 109.00 ! from, glycerol, OD31E CD31HB CD32F, before molvib 65.0 +CD31FA OD30A CD33E 95.00 109.70 ! DME dimethylether,viv +!furanoses, rima + +DIHEDRALS +!atom types Kchi n delta +!================================================= +! +!Please follow these conventions when fitting dihedral parameters +!1) use positive force constants in all cases (switch the phase...) +! (vary phase during fitting and keep force constants positive) +!2) maintain the phase at 0 or 180 if possiple. perform initial +! fitting with this contraint and, if necessary, only then +! vary the phases during fitting. note that if the phases +! are NOT 0 or 180 the parameters are NOT transferable across +! stereoisomers +!3) refit with only individual multiplicities of 1 through 6 +!4) maintain the number of significant figures used below +! +!polyols +HDP1A OD31E CD32F HDA2A 0.200 3 0.00 ! ethylene glycol, glycerol, xhe +HDP1A OD31E CD31G HDA1A 0.200 3 0.00 ! glycerol, xhe +OD31E CD32F CD32F HDA2A 0.200 3 0.00 ! ethylene glycol, xhe +OD31E CD31G CD32F HDA2A 0.200 3 0.00 ! glycerol, xhe +OD31E CD32F CD31G HDA1A 0.200 3 0.00 ! glycerol, xhe +OD31E CD31G CD31G HDA1A 0.200 3 0.00 ! +HDA2A CD32F CD32F HDA2A 0.200 3 0.00 ! ethylene glycol, xhe +HDA2A CD32F CD31G HDA1A 0.200 3 0.00 ! glycerol, xhe +HDA1A CD31G CD31G HDA1A 0.200 3 0.00 ! +HDA2A CD32F CD31G CD32F 0.200 3 0.00 ! glycerol, xhe +HDA2A CD32F CD31G CD31G 0.200 3 0.00 ! +HDA1A CD31G CD31G CD32F 0.200 3 0.00 ! +HDA1A CD31G CD31G CD31G 0.200 3 0.00 ! +!!! *** EGLY dihedral fit begin +CD32F CD31G CD31G CD32F 1.5480 1 180.00 ! +CD32F CD31G CD31G CD32F 0.3290 2 180.00 ! +CD32F CD31G CD31G CD32F 0.0960 3 180.00 ! +CD31G CD31G CD31G CD32F 1.5480 1 180.00 ! RMSE = 1.22424 +CD31G CD31G CD31G CD32F 0.3290 2 180.00 ! RMSE = 1.22424 +CD31G CD31G CD31G CD32F 0.0960 3 180.00 ! RMSE = 1.22424 +CD31G CD31G CD31G CD31G 1.5480 1 180.00 ! RMSE = 1.22424 +CD31G CD31G CD31G CD31G 0.3290 2 180.00 ! RMSE = 1.22424 +CD31G CD31G CD31G CD31G 0.0960 3 180.00 ! RMSE = 1.22424 +CD32F CD31G CD31G OD31E 0.3100 1 0.00 ! RMSE = 1.22424 +CD32F CD31G CD31G OD31E 0.1370 2 0.00 ! RMSE = 1.22424 +CD32F CD31G CD31G OD31E 0.1130 3 0.00 ! RMSE = 1.22424 +CD31G CD31G CD31G OD31E 0.3100 1 0.00 ! RMSE = 1.22424 +CD31G CD31G CD31G OD31E 0.1370 2 0.00 ! RMSE = 1.22424 +CD31G CD31G CD31G OD31E 0.1130 3 0.00 ! RMSE = 1.22424 +CD31G CD31G CD32F OD31E 0.3100 1 0.00 ! RMSE = 1.22424 +CD31G CD31G CD32F OD31E 0.1370 2 0.00 ! RMSE = 1.22424 +CD31G CD31G CD32F OD31E 0.1130 3 0.00 ! RMSE = 1.22424 +CD32F CD31G CD32F OD31E 0.3100 1 0.00 ! RMSE = 1.22424 +CD32F CD31G CD32F OD31E 0.1370 2 0.00 ! RMSE = 1.22424 +CD32F CD31G CD32F OD31E 0.1130 3 0.00 ! RMSE = 1.22424 +OD31E CD31G CD32F OD31E 1.3050 1 180.00 ! RMSE = 1.22424 +OD31E CD31G CD32F OD31E 0.3760 2 180.00 ! RMSE = 1.22424 +OD31E CD31G CD32F OD31E 0.4130 3 180.00 ! RMSE = 1.22424 +OD31E CD31G CD31G OD31E 1.3050 1 180.00 ! RMSE = 1.22424 +OD31E CD31G CD31G OD31E 0.3760 2 180.00 ! RMSE = 1.22424 +OD31E CD31G CD31G OD31E 0.4130 3 180.00 ! RMSE = 1.22424 +! +OD31E CD32F CD32F OD31E 0.0500 1 180.00 ! 2 +OD31E CD32F CD32F OD31E 0.9530 2 0.00 ! 2 +OD31E CD32F CD32F OD31E 0.0500 3 0.00 ! 2 +CD32F CD32F OD31E HDP1A 0.7080 1 0.00 ! 1 +CD32F CD32F OD31E HDP1A 0.3430 2 0.00 ! 1 +CD32F CD32F OD31E HDP1A 0.1000 3 0.00 ! 1 +! +CD32F CD31G OD31E HDP1A 0.5750 1 0.00 ! RMSE = 1.22424 +CD32F CD31G OD31E HDP1A 0.4780 2 0.00 ! RMSE = 1.22424 +CD32F CD31G OD31E HDP1A 0.2480 3 0.00 ! RMSE = 1.22424 +CD31G CD32F OD31E HDP1A 0.5750 1 0.00 ! RMSE = 1.22424 +CD31G CD32F OD31E HDP1A 0.4780 2 0.00 ! RMSE = 1.22424 +CD31G CD32F OD31E HDP1A 0.2480 3 0.00 ! RMSE = 1.22424 +CD31G CD31G OD31E HDP1A 0.5750 1 0.00 ! RMSE = 1.22424 +CD31G CD31G OD31E HDP1A 0.4780 2 0.00 ! RMSE = 1.22424 +CD31G CD31G OD31E HDP1A 0.2480 3 0.00 ! RMSE = 1.22424 +!!! *** EGLY dihedral fit end +!polyols +!hexapyranoses +!!!!!!!!!!!!! dpatel !!!!!!!!!! +!!! *** refitted dihedrals (mingjun) +OD306A CD31HA OD31E HDP1A 1.0065 1 0.00 ! RMSE = 0.539327 +OD306A CD31HA OD31E HDP1A 1.1013 2 0.00 ! RMSE = 0.539327 +OD306A CD31HA OD31E HDP1A 0.0961 3 0.00 ! RMSE = 0.539327 +CD31HB CD31HA OD31E HDP1A 0.3808 1 0.00 ! RMSE = 0.539327 +CD31HB CD31HA OD31E HDP1A 0.1353 2 0.00 ! RMSE = 0.539327 +CD31HB CD31HA OD31E HDP1A 0.4168 3 0.00 ! RMSE = 0.539327 +CD31HA CD31HB OD31E HDP1A 0.1322 1 180.00 ! RMSE = 0.539327 +CD31HA CD31HB OD31E HDP1A 0.4382 2 0.00 ! RMSE = 0.539327 +CD31HA CD31HB OD31E HDP1A 0.1432 3 0.00 ! RMSE = 0.539327 +CD31HB CD31HB OD31E HDP1A 0.2872 1 0.00 ! RMSE = 0.539327 +CD31HB CD31HB OD31E HDP1A 0.3264 2 0.00 ! RMSE = 0.539327 +CD31HB CD31HB OD31E HDP1A 0.3594 3 0.00 ! RMSE = 0.539327 +CD31HC CD31HB OD31E HDP1A 0.2781 1 0.00 ! RMSE = 0.539327 +CD31HC CD31HB OD31E HDP1A 0.4546 2 0.00 ! RMSE = 0.539327 +CD31HC CD31HB OD31E HDP1A 0.2708 3 0.00 ! RMSE = 0.539327 +CD31HC CD32A OD31A HDP1A 0.6350 1 0.00 ! RMSE = 0.539327 +CD31HC CD32A OD31A HDP1A 0.7179 2 0.00 ! RMSE = 0.539327 +CD31HC CD32A OD31A HDP1A 0.1598 3 0.00 ! RMSE = 0.539327 +OD306A CD31HC CD32A OD31A 1.0264 1 180.00 ! RMSE = 0.539327 +OD306A CD31HC CD32A OD31A 0.3973 2 0.00 ! RMSE = 0.539327 +OD306A CD31HC CD32A OD31A 0.1981 3 0.00 ! RMSE = 0.539327 +CD31HB CD31HC CD32A OD31A 0.2058 1 180.00 ! RMSE = 0.539327 +CD31HB CD31HC CD32A OD31A 0.0209 2 0.00 ! RMSE = 0.539327 +CD31HB CD31HC CD32A OD31A 0.4122 3 180.00 ! RMSE = 0.539327 +CD32A CD31HC OD306A CD31HA 0.2333 1 180.00 ! RMSE = 0.539327 +CD32A CD31HC OD306A CD31HA 0.0349 2 180.00 ! RMSE = 0.539327 +CD32A CD31HC OD306A CD31HA 0.4837 3 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HC CD32A 0.5360 1 180.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HC CD32A 0.2545 2 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HC CD32A 0.0179 3 180.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HC CD32A 2.1817 1 0.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HC CD32A 0.7026 2 180.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HC CD32A 0.1379 3 180.00 ! RMSE = 0.539327 +CD31HC CD31HB CD31HB OD31E 0.1170 1 0.00 ! RMSE = 0.539327 +CD31HC CD31HB CD31HB OD31E 0.0383 2 180.00 ! RMSE = 0.539327 +CD31HC CD31HB CD31HB OD31E 0.1833 3 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HB CD31HC 0.1176 1 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HB CD31HC 0.0709 2 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HB CD31HC 0.1653 3 180.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HB CD31HC 0.5234 4 180.00 ! RMSE = 0.539327 +CD31HB CD31HA OD306A CD31HC 0.1797 1 180.00 ! RMSE = 0.539327 +CD31HB CD31HA OD306A CD31HC 0.1258 2 180.00 ! RMSE = 0.539327 +CD31HB CD31HA OD306A CD31HC 0.0998 3 0.00 ! RMSE = 0.539327 +CD31HB CD31HA OD306A CD31HC 0.0578 4 0.00 ! RMSE = 0.539327 +OD31E CD31HA OD306A CD31HC 0.9550 1 180.00 ! RMSE = 0.539327 +OD31E CD31HA OD306A CD31HC 0.0754 2 180.00 ! RMSE = 0.539327 +OD31E CD31HA OD306A CD31HC 0.1739 3 180.00 ! RMSE = 0.539327 +CD31HA CD31HB CD31HB CD31HB 0.1784 1 180.00 ! RMSE = 0.539327 +CD31HA CD31HB CD31HB CD31HB 0.1098 2 180.00 ! RMSE = 0.539327 +CD31HA CD31HB CD31HB CD31HB 0.0477 3 180.00 ! RMSE = 0.539327 +CD31HA CD31HB CD31HB CD31HB 0.3427 4 180.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HB OD31E 0.0869 1 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HB OD31E 0.1657 2 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HB OD31E 0.1376 3 180.00 ! RMSE = 0.539327 +CD31HB CD31HC OD306A CD31HA 0.3266 1 180.00 ! RMSE = 0.539327 +CD31HB CD31HC OD306A CD31HA 0.1677 2 180.00 ! RMSE = 0.539327 +CD31HB CD31HC OD306A CD31HA 0.3044 3 0.00 ! RMSE = 0.539327 +CD31HB CD31HC OD306A CD31HA 0.1069 4 0.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HC OD306A 0.0820 1 180.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HC OD306A 0.2759 2 0.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HC OD306A 0.2809 3 180.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HB OD31E 0.8137 1 180.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HB OD31E 0.0174 2 180.00 ! RMSE = 0.539327 +OD31E CD31HB CD31HB OD31E 0.1812 3 0.00 ! RMSE = 0.539327 +CD31HA CD31HB CD31HB OD31E 0.1237 1 0.00 ! RMSE = 0.539327 +CD31HA CD31HB CD31HB OD31E 0.0026 2 180.00 ! RMSE = 0.539327 +CD31HA CD31HB CD31HB OD31E 0.7974 3 180.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HC OD306A 0.1399 1 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HC OD306A 0.0360 2 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HC OD306A 0.0352 3 0.00 ! RMSE = 0.539327 +CD31HB CD31HB CD31HC OD306A 0.7279 4 0.00 ! RMSE = 0.539327 +OD306A CD31HA CD31HB CD31HB 0.1692 1 180.00 ! RMSE = 0.539327 +OD306A CD31HA CD31HB CD31HB 0.1246 2 180.00 ! RMSE = 0.539327 +OD306A CD31HA CD31HB CD31HB 0.0499 3 180.00 ! RMSE = 0.539327 +OD306A CD31HA CD31HB CD31HB 0.1359 4 180.00 ! RMSE = 0.539327 +OD31E CD31HA CD31HB CD31HB 0.2706 1 180.00 ! RMSE = 0.539327 +OD31E CD31HA CD31HB CD31HB 0.4590 2 180.00 ! RMSE = 0.539327 +OD31E CD31HA CD31HB CD31HB 0.1841 3 180.00 ! RMSE = 0.539327 +OD306A CD31HA CD31HB OD31E 0.1607 1 180.00 ! RMSE = 0.539327 +OD306A CD31HA CD31HB OD31E 0.0714 2 180.00 ! RMSE = 0.539327 +OD306A CD31HA CD31HB OD31E 0.0468 3 0.00 ! RMSE = 0.539327 +OD31E CD31HA CD31HB OD31E 0.5324 1 180.00 ! RMSE = 0.539327 +OD31E CD31HA CD31HB OD31E 0.2932 2 0.00 ! RMSE = 0.539327 +OD31E CD31HA CD31HB OD31E 0.0387 3 0.00 ! RMSE = 0.539327 +!parameters involved non-hydroxyl hydrogen from model compounds +CD31HC CD31HB CD31HB HDA1A 0.190 3 0.00 ! from, THP, viv +HDA2E CD31HC CD31HB CD31HB 0.190 3 0.00 ! from, THP, viv +HDA2E CD31HC CD31HB HDA1A 0.190 3 0.00 ! from, THP, viv +HDA2E CD31HC CD31HB OD31E 0.270 1 0.00 ! from, ethylene glycol, xhe +HDA2E CD31HC CD31HB OD31E 0.050 2 0.00 ! from, ethylene glycol, xhe +HDA2E CD31HC CD31HB OD31E 0.120 3 0.00 ! from, ethylene glycol, xhe +HDA2E CD31HC CD32A HDA2A 0.190 3 0.00 ! from, ethylene glycol, xhe +HDA2E CD31HC CD32A OD31A 0.175 3 0.00 ! from, ETOH, ethanol +OD306A CD31HC CD31HB HDA1A 0.190 3 0.00 ! from, THP, viv +OD306A CD31HC CD32A HDA2A 0.190 3 0.00 ! from, DEET, diethylether alex +CD31HB CD31HC CD32A HDA2A 0.190 3 0.00 ! from, THP, viv +HDA1A CD31HB CD31HC CD32A 0.190 3 0.00 ! from, THP, viv +CD31HB OD306A CD31HC HDA2E 0.284 3 0.00 ! from, DMET, viv +CD31HB CD31HB CD31HB HDA1A 0.190 3 0.00 ! from, THP, viv +HDA1A CD31HB OD306A CD31HC 0.284 3 0.00 ! from, DMET, viv +HDA1A CD31HB CD31HB HDA1A 0.190 3 0.00 ! from, THP, viv +OD31E CD31HB CD31HB HDA1A 0.270 1 0.00 ! from, ethylene glycol, xhe +OD31E CD31HB CD31HB HDA1A 0.050 2 0.00 ! from, ethylene glycol, xhe +OD31E CD31HB CD31HB HDA1A 0.120 3 0.00 ! from, ethylene glycol, xhe +!after change in anomeric carbon atom type +CD31HA CD31HB CD31HB HDA1A 0.190 3 0.00 ! from, THP, viv +CD31HA OD306A CD31HC HDA2E 0.284 3 0.00 ! from, DMET, viv +HDP1A OD31E CD31HA HDA1A 0.060 1 0.00 ! glycerol, xhe +HDP1A OD31E CD31HA HDA1A 0.060 2 0.00 ! glycerol, xhe +HDP1A OD31E CD31HA HDA1A 0.000 3 0.00 ! glycerol, xhe +HDA1A CD31HA CD31HB HDA1A 0.190 3 0.00 ! from, THP, viv +OD31E CD31HB CD31HA HDA1A 0.270 1 0.00 ! from, ethylene glycol, xhe +OD31E CD31HB CD31HA HDA1A 0.050 2 0.00 ! from, ethylene glycol, xhe +OD31E CD31HB CD31HA HDA1A 0.120 3 0.00 ! from, ethylene glycol, xhe +CD31HB CD31HB CD31HA HDA1A 0.190 3 0.00 ! from, THP, viv +HDA1A CD31HA OD306A CD31HC 0.284 3 0.00 ! from, DMET, viv +OD31E CD31HA CD31HB HDA1A 0.270 1 0.00 ! from, ethylene glycol, xhe +OD31E CD31HA CD31HB HDA1A 0.050 2 0.00 ! from, ethylene glycol, xhe +OD31E CD31HA CD31HB HDA1A 0.120 3 0.00 ! from, ethylene glycol, xhe +OD306A CD31HA CD31HB HDA1A 0.190 3 0.00 ! from, THP, viv +HDA1A CD31HB OD31E HDP1A 0.060 1 0.00 ! glycerol, xhe +HDA1A CD31HB OD31E HDP1A 0.060 2 0.00 ! glycerol, xhe +HDA1A CD31HB OD31E HDP1A 0.000 3 0.00 ! glycerol, xhe +!hexapyranoses +!furanoses, rima +OD305A CD31FA CD31FB HDA1A 0.190 3 0.00 ! THF viv +OD305A CD31FC CD32A HDA2A 0.200 3 0.00 ! TF2M, cmb +OD305A CD31FC CD31FB HDA1A 0.190 3 0.00 ! THF viv +CD31FA OD305A CD31FC HDA2E 0.300 3 0.00 ! THF, viv +HDA1A CD31FA OD305A CD31FC 0.300 3 0.00 ! THF, viv +CD31FA CD31FB CD31FB HDA1A 0.190 3 0.00 ! THF, viv +HDP1A OD31E CD31FA HDA1A 0.060 1 0.00 ! glycerol, xhe +HDP1A OD31E CD31FA HDA1A 0.060 2 0.00 ! glycerol, xhe +HDP1A OD31E CD31FA HDA1A 0.000 3 0.00 ! glycerol, xhe +HDA1A CD31FA CD31FB HDA1A 0.190 3 0.00 ! THF, viv +OD31E CD31FB CD31FA HDA1A 0.270 1 0.00 ! from, ethylene glycol, xhe +OD31E CD31FB CD31FA HDA1A 0.050 2 0.00 ! from, ethylene glycol, xhe +OD31E CD31FB CD31FA HDA1A 0.120 3 0.00 ! from, ethylene glycol, xhe +CD31FB CD31FB CD31FA HDA1A 0.190 3 0.00 ! THF, viv +OD31E CD31FA CD31FB HDA1A 0.270 1 0.00 ! from, ethylene glycol, xhe +OD31E CD31FA CD31FB HDA1A 0.050 2 0.00 ! from, ethylene glycol, xhe +OD31E CD31FA CD31FB HDA1A 0.120 3 0.00 ! from, ethylene glycol, xhe +CD31FC CD31FB CD31FB HDA1A 0.190 3 0.00 ! THF, viv +HDA2E CD31FC CD32A HDA2A 0.190 3 0.00 ! from, ethylene glycol, xhe +HDA2E CD31FC CD32A OD31A 0.175 3 0.00 ! from, ETOH, ethanol +HDA2E CD31FC CD31FB CD31FB 0.190 3 0.00 ! THF, viv +HDA2E CD31FC CD31FB HDA1A 0.190 3 0.00 ! THF, viv +HDA2E CD31FC CD31FB OD31E 0.270 1 0.00 ! from, ethylene glycol, xhe +HDA2E CD31FC CD31FB OD31E 0.050 2 0.00 ! from, ethylene glycol, xhe +HDA2E CD31FC CD31FB OD31E 0.120 3 0.00 ! from, ethylene glycol, xhe +CD31FB CD31FB CD31FC CD32A 0.410 3 180.00 ! CPNM, cmb +HDA1A CD31FB CD31FC CD32A 0.190 3 0.00 ! THF, viv +CD31FB CD31FC CD32A HDA2A 0.190 3 0.00 ! THF, viv +HDA1A CD31FB OD31E HDP1A 0.060 1 0.00 ! glycerol, xhe +HDA1A CD31FB OD31E HDP1A 0.060 2 0.00 ! glycerol, xhe +HDA1A CD31FB OD31E HDP1A 0.000 3 0.00 ! glycerol, xhe +HDA1A CD31FB CD31FB HDA1A 0.190 3 0.00 ! THF, viv +OD31E CD31FB CD31FB HDA1A 0.270 1 0.00 ! from, ethylene glycol, xhe +OD31E CD31FB CD31FB HDA1A 0.050 2 0.00 ! from, ethylene glycol, xhe +OD31E CD31FB CD31FB HDA1A 0.120 3 0.00 ! from, ethylene glycol, xhe +!fitdih furanoses +CD31FA CD31FB CD31FB CD31FC 1.0392 1 0.00 ! RMSE = 0.593558 !all_ft_0.001b_123.prm +CD31FA CD31FB CD31FB CD31FC 0.9303 2 0.00 ! RMSE = 0.593558 +CD31FA CD31FB CD31FB CD31FC 0.7483 3 0.00 ! RMSE = 0.593558 +CD31FA CD31FB CD31FB OD31E 0.2742 1 0.00 ! RMSE = 0.593558 +CD31FA CD31FB CD31FB OD31E 0.0453 2 0.00 ! RMSE = 0.593558 +CD31FA CD31FB CD31FB OD31E 0.5903 3 180.00 ! RMSE = 0.593558 +CD31FA CD31FB OD31E HDP1A 0.2611 1 0.00 ! RMSE = 0.593558 +CD31FA CD31FB OD31E HDP1A 0.5154 2 0.00 ! RMSE = 0.593558 +CD31FA CD31FB OD31E HDP1A 0.1830 3 0.00 ! RMSE = 0.593558 +CD31FB CD31FC OD305A CD31FA 0.6882 1 0.00 ! RMSE = 0.593558 +CD31FB CD31FC OD305A CD31FA 0.7079 2 0.00 ! RMSE = 0.593558 +CD31FB CD31FC OD305A CD31FA 0.7433 3 0.00 ! RMSE = 0.593558 +CD32A CD31FC OD305A CD31FA 0.9269 1 180.00 ! RMSE = 0.593558 +CD32A CD31FC OD305A CD31FA 0.5245 2 0.00 ! RMSE = 0.593558 +CD32A CD31FC OD305A CD31FA 0.2728 3 0.00 ! RMSE = 0.593558 +CD31FB CD31FA OD31E HDP1A 0.3772 1 0.00 ! RMSE = 0.593558 +CD31FB CD31FA OD31E HDP1A 0.4430 2 0.00 ! RMSE = 0.593558 +CD31FB CD31FA OD31E HDP1A 0.1763 3 180.00 ! RMSE = 0.593558 +CD31FB CD31FB CD31FC OD305A 0.5081 1 0.00 ! RMSE = 0.593558 +CD31FB CD31FB CD31FC OD305A 0.4468 2 0.00 ! RMSE = 0.593558 +CD31FB CD31FB CD31FC OD305A 0.3245 3 0.00 ! RMSE = 0.593558 +CD31FB CD31FB OD31E HDP1A 0.4056 1 0.00 ! RMSE = 0.593558 +CD31FB CD31FB OD31E HDP1A 0.4316 2 0.00 ! RMSE = 0.593558 +CD31FB CD31FB OD31E HDP1A 0.2648 3 0.00 ! RMSE = 0.593558 +OD31E CD31FA CD31FB CD31FB 0.1215 1 0.00 ! RMSE = 0.593558 +OD31E CD31FA CD31FB CD31FB 0.6332 2 180.00 ! RMSE = 0.593558 +OD31E CD31FA CD31FB CD31FB 0.3012 3 180.00 ! RMSE = 0.593558 +OD305A CD31FA CD31FB CD31FB 0.4187 1 0.00 ! RMSE = 0.593558 +OD305A CD31FA CD31FB CD31FB 0.2784 2 0.00 ! RMSE = 0.593558 +OD305A CD31FA CD31FB CD31FB 0.0200 3 0.00 ! RMSE = 0.593558 +CD31FB CD31FC CD32A OD31A 0.5003 1 180.00 ! RMSE = 0.593558 +CD31FB CD31FC CD32A OD31A 0.2096 2 0.00 ! RMSE = 0.593558 +CD31FB CD31FC CD32A OD31A 0.0681 3 0.00 ! RMSE = 0.593558 +CD31FC CD31FB CD31FB OD31E 0.3659 1 180.00 ! RMSE = 0.593558 +CD31FC CD31FB CD31FB OD31E 0.2749 2 0.00 ! RMSE = 0.593558 +CD31FC CD31FB CD31FB OD31E 0.8934 3 0.00 ! RMSE = 0.593558 +CD31FC CD31FB OD31E HDP1A 0.3741 1 0.00 ! RMSE = 0.593558 +CD31FC CD31FB OD31E HDP1A 0.0242 2 0.00 ! RMSE = 0.593558 +CD31FC CD31FB OD31E HDP1A 0.1025 3 0.00 ! RMSE = 0.593558 +CD31FC CD32A OD31A HDP1A 0.3581 1 0.00 ! RMSE = 0.593558 +CD31FC CD32A OD31A HDP1A 0.4874 2 0.00 ! RMSE = 0.593558 +CD31FC CD32A OD31A HDP1A 0.1880 3 0.00 ! RMSE = 0.593558 +CD31FB CD31FA OD305A CD31FC 0.8201 1 0.00 ! RMSE = 0.593558 +CD31FB CD31FA OD305A CD31FC 0.5947 2 0.00 ! RMSE = 0.593558 +CD31FB CD31FA OD305A CD31FC 0.2261 3 0.00 ! RMSE = 0.593558 +OD31E CD31FA OD305A CD31FC 1.1409 1 180.00 ! RMSE = 0.593558 +OD31E CD31FA OD305A CD31FC 1.0488 2 0.00 ! RMSE = 0.593558 +OD31E CD31FA OD305A CD31FC 0.3135 3 0.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FC CD32A 0.1541 1 0.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FC CD32A 0.3485 2 180.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FC CD32A 0.0817 3 0.00 ! RMSE = 0.593558 +OD31E CD31FA CD31FB OD31E 0.2182 1 180.00 ! RMSE = 0.593558 +OD31E CD31FA CD31FB OD31E 0.1501 2 180.00 ! RMSE = 0.593558 +OD31E CD31FA CD31FB OD31E 0.0060 3 0.00 ! RMSE = 0.593558 +OD305A CD31FA CD31FB OD31E 0.4388 1 0.00 ! RMSE = 0.593558 +OD305A CD31FA CD31FB OD31E 0.4009 2 180.00 ! RMSE = 0.593558 +OD305A CD31FA CD31FB OD31E 0.3834 3 0.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FB OD31E 0.4307 1 180.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FB OD31E 0.6208 2 180.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FB OD31E 0.4495 3 180.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FC OD305A 0.7740 1 180.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FC OD305A 0.0201 2 0.00 ! RMSE = 0.593558 +OD31E CD31FB CD31FC OD305A 0.5125 3 0.00 ! RMSE = 0.593558 +OD305A CD31FA OD31E HDP1A 0.7166 1 0.00 ! RMSE = 0.593558 +OD305A CD31FA OD31E HDP1A 1.0359 2 0.00 ! RMSE = 0.593558 +OD305A CD31FA OD31E HDP1A 0.6708 3 0.00 ! RMSE = 0.593558 +OD305A CD31FC CD32A OD31A 0.9708 1 180.00 ! RMSE = 0.593558 +OD305A CD31FC CD32A OD31A 0.7860 2 0.00 ! RMSE = 0.593558 +OD305A CD31FC CD32A OD31A 0.0222 3 180.00 ! RMSE = 0.593558 +!for deoxy sugar, trans param +OD305A CD31FA CD325B HDA2R5 0.190 3 0.00 ! THF viv +CD31FA CD325B CD31FB CD31FC 1.0392 1 0.00 ! RMSE = 0.593558 +CD31FA CD325B CD31FB CD31FC 0.9303 2 0.00 ! RMSE = 0.593558 +CD31FA CD325B CD31FB CD31FC 0.7483 3 0.00 ! RMSE = 0.593558 +CD31FA CD325B CD31FB HDA1A 0.190 3 0.00 ! THF, viv +HDA1A CD31FA CD325B HDA2R5 0.190 3 0.00 ! THF, viv +HDA1A CD31FA CD325B CD31FB 0.190 3 0.00 ! THF, viv +OD31E CD31FA CD325B HDA2R5 0.270 1 0.00 ! from, ethylene glycol, xhe +OD31E CD31FA CD325B HDA2R5 0.050 2 0.00 ! from, ethylene glycol, xhe +OD31E CD31FA CD325B HDA2R5 0.120 3 0.00 ! from, ethylene glycol, xhe +CD31FC CD31FB CD325B HDA2R5 0.190 3 0.00 ! THF, viv +HDA2E CD31FC CD31FB CD325B 0.190 3 0.00 ! THF, viv +CD32A CD31FC CD31FB CD325B 0.410 3 180.00 ! CPNM, cmb +HDA2R5 CD325B CD31FB HDA1A 0.190 3 0.00 ! THF, viv +HDA2R5 CD325B CD31FB OD31E 0.270 1 0.00 ! from, ethylene glycol, xhe +HDA2R5 CD325B CD31FB OD31E 0.050 2 0.00 ! from, ethylene glycol, xh +HDA2R5 CD325B CD31FB OD31E 0.120 3 0.00 ! from, ethylene glycol, xhe +!fitdih deoxy +OD31E CD31FB CD325B CD31FA 1.6826 1 0.00 ! RMSE = 0.826767 !adbd_ft_0.01b_123.prm +OD31E CD31FB CD325B CD31FA 0.3708 2 180.00 ! RMSE = 0.826767 +OD31E CD31FB CD325B CD31FA 1.0478 3 180.00 ! RMSE = 0.826767 +CD325B CD31FA OD31E HDP1A 0.5210 1 0.00 ! RMSE = 0.826767 +CD325B CD31FA OD31E HDP1A 0.2497 2 0.00 ! RMSE = 0.826767 +CD325B CD31FA OD31E HDP1A 0.2382 3 0.00 ! RMSE = 0.826767 +CD325B CD31FB CD31FC OD305A 0.4277 1 180.00 ! RMSE = 0.826767 +CD325B CD31FB CD31FC OD305A 0.3937 2 180.00 ! RMSE = 0.826767 +CD325B CD31FB CD31FC OD305A 0.3030 3 180.00 ! RMSE = 0.826767 +CD325B CD31FB OD31E HDP1A 0.9384 1 0.00 ! RMSE = 0.826767 +CD325B CD31FB OD31E HDP1A 0.0104 2 0.00 ! RMSE = 0.826767 +CD325B CD31FB OD31E HDP1A 0.2568 3 0.00 ! RMSE = 0.826767 +OD31E CD31FA CD325B CD31FB 0.2311 1 0.00 ! RMSE = 0.826767 +OD31E CD31FA CD325B CD31FB 0.3468 2 180.00 ! RMSE = 0.826767 +OD31E CD31FA CD325B CD31FB 0.0532 3 0.00 ! RMSE = 0.826767 +OD305A CD31FA CD325B CD31FB 0.2237 1 0.00 ! RMSE = 0.826767 +OD305A CD31FA CD325B CD31FB 0.1834 2 0.00 ! RMSE = 0.826767 +OD305A CD31FA CD325B CD31FB 0.1093 3 0.00 ! RMSE = 0.826767 +CD325B CD31FA OD305A CD31FC 0.3531 1 0.00 ! RMSE = 0.826767 +CD325B CD31FA OD305A CD31FC 0.1220 2 0.00 ! RMSE = 0.826767 +CD325B CD31FA OD305A CD31FC 0.2640 3 180.00 ! RMSE = 0.826767 +!FOR OME +CD31FA OD30A CD33E HDA3A 0.000 3 0.00 ! DME, viv +HDA1A CD31FA OD30A CD33E 0.000 3 0.00 ! DME, viv +OD30A CD31FA CD31FB HDA1A 0.000 3 0.00 ! from, ethylene glycol, xhe +OD30A CD31FA CD31FB CD31FB 1.3664 1 0.00 ! RMSE = 1.21693 +OD30A CD31FA CD31FB CD31FB 1.0474 2 0.00 ! RMSE = 1.21693 +OD30A CD31FA CD31FB CD31FB 1.8077 3 180.00 ! RMSE = 1.21693 +CD31FB CD31FA OD30A CD33E 1.3198 1 180.00 ! RMSE = 1.21693 +CD31FB CD31FA OD30A CD33E 0.5302 2 180.00 ! RMSE = 1.21693 +CD31FB CD31FA OD30A CD33E 0.0701 3 0.00 ! RMSE = 1.21693 +OD30A CD31FA CD31FB OD31E 0.2039 1 180.00 ! RMSE = 1.21693 +OD30A CD31FA CD31FB OD31E 1.6691 2 180.00 ! RMSE = 1.21693 +OD30A CD31FA CD31FB OD31E 1.6110 3 0.00 ! RMSE = 1.21693 +OD30A CD31FA OD305A CD31FC 0.8447 1 0.00 ! RMSE = 1.21693 +OD30A CD31FA OD305A CD31FC 1.8332 2 0.00 ! RMSE = 1.21693 +OD30A CD31FA OD305A CD31FC 0.6738 3 0.00 ! RMSE = 1.21693 +OD305A CD31FA OD30A CD33E 0.4818 1 180.00 ! RMSE = 1.21693 +OD305A CD31FA OD30A CD33E 1.2301 2 0.00 ! RMSE = 1.21693 +OD305A CD31FA OD30A CD33E 1.0062 3 0.00 ! RMSE = 1.21693 +!furanoses, rima + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! + +NONBONDED nbxmod 5 atom vatom cdiel vdistance switch vswitch - +cutnb 16.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +NBFIX +! +OD31A ODW -0.17790 3.52190 ! DPatel, check-120 for ETOH +OD31E ODW -0.17990 3.48690 ! DPatel, check-5; under validation, mingjun; best hydration free energy +!OD31E ODW -0.20530 3.44690 ! DPatel, check-12; under validation, mingjun; best diffusion constant + +END + diff --git a/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_lipid_2013c.str b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_lipid_2013c.str new file mode 100644 index 00000000..739afd2d --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_lipid_2013c.str @@ -0,0 +1,1758 @@ +* $Id: toppar_drude_lipid.str 33 2015-08-04 14:44:59Z alex $ +* DRUDE topology and parameter stream file +* Lipids +* October 2013 +* + +!requires toppar_drude_master*.str + +ioformat extended + +!lipids + +!references +!Chowdhary, J., Harder, E., Lopes, P.E.M., MacKerell, Jr., A.D, and +!Roux, B., “A Polarizable Model for Phosphatidylcholine-Containing +!Biological Membranes,” Journal of Physical Chemistry, B.,117: +!9142-9160, 2013. + +read rtf card append +* Topology for Drude lipids +* +38 + +DEFA FIRS NONE LAST NONE +AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + +!! Lipids +!Atom nomenclature is based on that of Sundaralingan, M., +!Ann. N.Y. Acad. Sci. USA, 195:324-355, 1972 + +RESI EAS 0.000 ! ethylacetate, atom naming consistent with MAS +! +GROUP +ATOM C CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! H33 +ATOM OM OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! | +ATOM O OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! H31-C3-H32 +ATOM C1 CD33C -0.275 ALPHA -1.993 THOLE 0.410 ! | +ATOM H11 HDA3A 0.069 ! H21-C2-H22 +ATOM H12 HDA3A 0.069 ! \ +ATOM H13 HDA3A 0.069 ! OM +ATOM C2 CD32C 0.086 ALPHA -1.797 THOLE 0.410 ! / +ATOM H21 HDA2A 0.116 ! O=C +ATOM H22 HDA2A 0.116 ! | +ATOM C3 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! H11-C1-H12 +ATOM H31 HDA3A 0.059 ! | +ATOM H32 HDA3A 0.059 ! H13 +ATOM H33 HDA3A 0.059 ! +ATOM LP1A LPD -0.349 ! +ATOM LP1B LPD -0.258 ! +ATOM LPMA LPD -0.170 +ATOM LPMB LPD -0.170 + +BOND C1 C C OM C O OM C2 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 C3 +BOND C3 H31 C3 H32 C3 H33 +BOND O LP1A O LP1B +BOND OM LPMA OM LPMB + +IMPR O C1 OM C + +!carbonyl O LP positions and anisotropic polarizability from NMA +LONEPAIR relative LP1A O C C1 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1B O C C1 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LP1A LP1B A11 0.6968 A22 1.2194 + +!ether O LP positions and anisotropic polarizability from MeOH +LONEPAIR relative LPMA OM C C2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPMB OM C C2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OM C LPMA LPMB A11 0.8108 A22 1.2162 + +IC C2 OM C C1 1.4420 113.44 -180.00 109.83 1.5046 +IC C OM C2 C3 1.3413 113.44 -180.00 107.87 1.5290 +IC O OM *C C1 1.2022 124.56 -180.00 109.83 1.5046 +IC OM C C1 H11 1.3413 109.83 180.00 110.49 1.1109 +IC H11 C *C1 H12 1.1109 110.49 119.96 109.94 1.1103 +IC H11 C *C1 H13 1.1109 110.49 -119.96 109.94 1.1103 +IC C3 OM *C2 H21 1.5290 107.87 119.98 110.33 1.1144 +IC C3 OM *C2 H22 1.5290 107.87 -119.98 110.33 1.1144 +IC OM C2 C3 H31 1.4420 107.87 -180.00 110.47 1.1107 +IC H31 C2 *C3 H32 1.1107 110.47 120.05 110.43 1.1113 +IC H31 C2 *C3 H33 1.1107 110.47 -120.05 110.43 1.1113 + +RESI MPRO 0.000 ! methylpropionate, atom names consistent with MAS +! +GROUP ! H23 +ATOM C CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! | +ATOM OM OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! H21-C2-H22 +ATOM O OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! \ +ATOM C2 CD33D -0.030 ALPHA -1.797 THOLE 0.410 ! OM +ATOM H21 HDA3A 0.116 ! / +ATOM H22 HDA3A 0.116 ! O=C +ATOM H23 HDA3A 0.116 ! | +ATOM C1 CD32C -0.206 ALPHA -1.993 THOLE 0.410 ! H11-C1-H12 +ATOM H11 HDA2A 0.069 ! | +ATOM H12 HDA2A 0.069 ! H31-C3-H32 +ATOM C3 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! | +ATOM H31 HDA3A 0.059 ! H33 +ATOM H32 HDA3A 0.059 ! +ATOM H33 HDA3A 0.059 ! +ATOM LP1A LPD -0.349 ! +ATOM LP1B LPD -0.258 ! +ATOM LPMA LPD -0.170 ! +ATOM LPMB LPD -0.170 ! + +BOND C1 C C OM C O OM C2 +BOND C1 H11 C1 H12 C1 C3 C2 H23 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 C3 H33 +BOND O LP1A O LP1B +BOND OM LPMA OM LPMB + +IMPR O C1 OM C + +!LP positions and anisotropic polarizability from NMA +LONEPAIR relative LP1A O C C1 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1B O C C1 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LP1A LP1B A11 0.6968 A22 1.2194 + +!LP positions and anisotropic polarizability from MeOH +LONEPAIR relative LPMA OM C C2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPMB OM C C2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OM C LPMA LPMB A11 0.8108 A22 1.2162 + +IC C2 OM C C1 1.4469 122.96 178.85 109.19 1.5224 +IC OM C C1 C3 1.3452 109.19 -179.20 111.90 1.5391 +IC C1 OM *C O 1.5224 109.19 179.62 125.11 1.2034 +IC C OM C2 H21 1.3452 122.96 94.60 110.01 1.1119 +IC H21 OM *C2 H22 1.1119 110.01 -120.55 111.55 1.1132 +IC H21 OM *C2 H23 1.1119 110.01 -94.09 68.64 5.2649 +IC C3 C *C1 H11 1.5391 111.90 121.09 108.59 1.1111 +IC H11 C *C1 H12 1.1111 108.59 117.79 108.58 1.1111 +IC C C1 C3 H31 1.5224 111.90 179.89 110.31 1.1111 +IC H31 C1 *C3 H32 1.1111 110.31 119.85 110.66 1.1113 +IC H31 C1 *C3 H33 1.1111 110.31 -119.85 110.65 1.1113 + +RESI MBU 0.000 ! methylbutyrate +! +GROUP ! H23 +ATOM C CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! | +ATOM OM OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! H21-C2-H22 +ATOM O OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! \ +ATOM C2 CD33D -0.030 ALPHA -1.797 THOLE 0.410 ! OM +ATOM H21 HDA3A 0.116 ! / +ATOM H22 HDA3A 0.116 ! O=C +ATOM H23 HDA3A 0.116 ! | +ATOM C1 CD32C -0.206 ALPHA -1.993 THOLE 0.410 ! H11-C1-H12 +ATOM H11 HDA2A 0.069 ! | +ATOM H12 HDA2A 0.069 ! H31-C3-H32 +ATOM C3 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H31 HDA2A 0.078 ! H41-C4-H42 +ATOM H32 HDA2A 0.078 ! | +ATOM C4 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! H43 +ATOM H41 HDA3A 0.059 ! +ATOM H42 HDA3A 0.059 ! +ATOM H43 HDA3A 0.059 ! +ATOM LP1A LPD -0.349 ! +ATOM LP1B LPD -0.258 ! +ATOM LPMA LPD -0.170 ! +ATOM LPMB LPD -0.170 ! + +BOND C1 C C OM C O OM C2 +BOND C1 C3 C3 C4 +BOND C1 H11 C1 H12 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 +BOND C4 H41 C4 H42 C4 H43 +BOND O LP1A O LP1B +BOND OM LPMA OM LPMB + +IMPR O C1 OM C + +!LP positions and anisotropic polarizability from NMA +LONEPAIR relative LP1A O C C1 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1B O C C1 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LP1A LP1B A11 0.6968 A22 1.2194 + +!LP positions and anisotropic polarizability from MeOH +LONEPAIR relative LPMA OM C C2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPMB OM C C2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OM C LPMA LPMB A11 0.8108 A22 1.2162 + +!redo with IC generate +! internal coordinates from experiment for heavy atoms +IC C2 OM C C1 1.4469 122.96 178.85 109.19 1.5224 +IC OM C C1 C3 1.3452 109.19 -179.20 111.90 1.5391 +IC C1 OM *C O 1.5224 109.19 179.62 125.11 1.2034 +IC C OM C2 H21 1.3452 122.96 94.60 110.01 1.1119 +IC H21 OM *C2 H22 1.1119 110.01 -120.55 111.55 1.1132 +IC H21 OM *C2 H23 1.1119 110.01 -94.09 68.64 5.2649 +IC C3 C *C1 H11 1.5391 111.90 121.09 108.59 1.1111 +IC H11 C *C1 H12 1.1111 108.59 117.79 108.58 1.1111 +IC C C1 C3 C4 1.5224 111.90 179.89 110.31 1.1111 +IC C4 C1 *C3 H31 1.1111 110.31 119.85 110.66 1.1113 +IC C4 C1 *C3 H32 1.1111 110.31 -119.85 110.65 1.1113 +IC C1 C3 C4 H41 1.5224 111.90 179.89 110.31 1.1111 +IC H41 C3 *C4 H42 1.1111 110.31 119.85 110.66 1.1113 +IC H41 C3 *C4 H43 1.1111 110.31 -119.85 110.65 1.1113 + +RESI DMP -1.000 ! Dimethylphosphate +! +! lipid specific, differs from nucleic acid DMPN +! +! H11 +! | +! H13- C1-H12 +! \ +! O13 O11 +! \\ / +! (-) P1 +! // \ +! O14 O12 +! / +! H23-C2-H22 +! | +! H21 +! +GROUP +ATOM P PD1A 1.191 ALPHA -0.974 THOLE 2.098 +ATOM O13 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 +ATOM O14 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 +ATOM O11 OD30B -0.470 ALPHA -0.901 THOLE 0.181 +ATOM O12 OD30B -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C1 CD33C 0.1725 ALPHA -1.642 THOLE 0.862 +ATOM H11 HDA3A 0.026 +ATOM H12 HDA3A 0.026 +ATOM H13 HDA3A 0.026 +ATOM C2 CD33C 0.1725 ALPHA -1.642 THOLE 0.862 +ATOM H21 HDA3A 0.026 +ATOM H22 HDA3A 0.026 +ATOM H23 HDA3A 0.026 + +BOND P O11 P O12 P O13 P O14 +BOND O11 C1 O12 C2 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 + +ANISOTROPY O11 O13 O12 O14 A11 1.0000 A22 0.6000 +ANISOTROPY O12 O14 O11 O13 A11 1.0000 A22 0.6000 +ANISOTROPY O13 P O11 O12 A11 0.6000 A22 1.0000 +ANISOTROPY O14 P O12 O11 A11 0.6000 A22 1.0000 + +IC O11 P O12 C2 1.5837 102.73 72.47 116.87 1.4386 +IC O12 P O11 C1 1.5843 102.73 72.47 116.85 1.4394 +IC O13 P O11 C1 1.4910 107.70 -41.57 116.85 1.4394 +IC O14 P O12 C2 1.4906 107.67 -41.56 116.87 1.4386 +IC H11 C1 O11 P 1.1128 110.79 -42.95 116.85 1.5837 +IC H12 C1 O11 P 1.1118 109.92 77.01 116.85 1.5837 +IC H13 C1 O11 P 1.1095 109.84 -163.26 116.85 1.5837 +IC H21 C2 O12 P 1.1125 110.79 -42.95 116.87 1.5843 +IC H22 C2 O12 P 1.1123 109.91 77.00 116.87 1.5843 +IC H23 C2 O12 P 1.1094 109.84 -163.30 116.87 1.5843 +IC O12 O11 *P O13 1.5843 102.73 -114.04 107.70 1.4910 +IC O12 O11 *P O14 1.5843 102.73 113.68 108.15 1.4906 +IC P O11 C1 H11 1.5837 116.85 -42.95 110.79 1.1128 +IC H11 O11 *C1 H12 1.1128 110.79 119.96 109.92 1.1118 +IC H11 O11 *C1 H13 1.1128 110.79 -120.31 109.84 1.1095 +IC P O12 C2 H21 1.5843 116.87 -42.95 110.79 1.1125 +IC H21 O12 *C2 H22 1.1125 110.79 119.95 109.91 1.1123 +IC H21 O12 *C2 H23 1.1125 110.79 -120.35 109.84 1.1094 +patch first none last none + +RESI PE 0.000 ! phosphatidylethanolamine +GROUP ! HN2 +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 ! | +ATOM C1 CD32AL 0.043 ALPHA -1.256 THOLE 0.895 ! HN1---N---HN3 (+) +ATOM HN1 HDP1B 0.340 ! | +ATOM HN2 HDP1B 0.340 ! | +ATOM HN3 HDP1B 0.340 ! | +ATOM H11 HDA2C 0.143 ! H12---C1---H11 +ATOM H12 HDA2C 0.143 ! | +GROUP ! | +ATOM C5 CD32AL 0.1985 ALPHA -1.642 THOLE 0.862 ! | +ATOM H51 HDA2A 0.026 ! H52---C5---H51 +ATOM H52 HDA2A 0.026 ! | +ATOM P1 PD1A 1.191 ALPHA -0.974 THOLE 2.098 ! (-) O3 O1 +ATOM O3 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! \ / +ATOM O4 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! P1 (+) +ATOM O1 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! / \ +ATOM O2 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! (-) O4 O2 +ATOM C6 CD33A 0.1725 ALPHA -1.642 THOLE 0.862 ! | +ATOM H61 HDA3A 0.026 ! H63-C6-H62 +ATOM H62 HDA3A 0.026 ! | +ATOM H63 HDA3A 0.026 ! H61 + +BOND N C1 N HN1 N HN2 N HN3 +BOND C1 H11 C1 H12 C1 C5 +BOND C5 H51 C5 H52 +BOND P1 O1 +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C5 O2 C6 +BOND C6 H61 C6 H62 C6 H63 + +ANISOTROPY O1 O3 O2 O4 A11 1.0000 A22 0.6000 +ANISOTROPY O2 O4 O1 O3 A11 1.0000 A22 0.6000 +ANISOTROPY O3 P1 O1 O2 A11 0.6000 A22 1.0000 +ANISOTROPY O4 P1 O2 O1 A11 0.6000 A22 1.0000 + +! from crd snapshot of DMPC lipid +IC HN1 N C1 C5 1.0200 114.21 -69.91 118.00 1.5484 ! via dmpc snapshot (alpha6) +IC C5 C1 N HN2 1.5484 118.00 51.44 109.96 1.0200 ! via dmpc snapshot (alpha6) +IC C5 C1 N HN3 1.5484 118.00 168.71 110.33 1.0200 ! via dmpc snapshot (alpha6) +IC HN1 N C1 H11 1.0200 109.96 170.00 105.69 1.0800 +IC HN2 N C1 H12 1.0200 110.33 170.00 107.40 1.0800 +IC N C1 C5 H51 1.5691 118.00 -72.28 107.58 1.1110 +IC N C1 C5 H52 1.5691 118.00 173.53 110.91 1.1110 +IC N C1 C5 O1 1.5691 118.00 51.35 114.45 1.4136 ! dmpc snapshot (alpha5) +IC C1 C5 O1 P1 1.5484 114.45 -125.77 126.65 1.5528 ! dmpc snapshot (alpha4) +IC C5 O1 P1 O2 1.4136 126.65 -79.26 105.72 1.5948 ! dmpc snapshot (alpha3) +IC O3 P1 O1 C5 1.4635 108.40 164.76 126.65 1.4136 ! dmpc snapshot (alpha3) +IC O4 P1 O1 C5 1.4948 108.72 34.37 126.65 1.4136 ! dmpc snapshot (alpha3) +IC O1 P1 O2 C6 1.5528 105.72 -39.76 120.14 1.4507 ! dmpc snapshot (alpha2) +IC H61 C6 O2 P1 1.1110 109.78 -17.52 120.14 1.5948 +IC H62 C6 O2 P1 1.1110 110.89 -131.34 120.14 1.5948 +IC H63 C6 O2 P1 1.1000 110.00 107.02 120.14 1.5948 ! approximate geo for IC build (E.H) + +RESI PC 0.000 ! phosphatidylcholine +GROUP +ATOM N ND3P2A 0.688 ALPHA -0.829 THOLE 0.793 ! +ATOM C1 CD32AL -0.166 ALPHA -1.393 THOLE 1.099 ! | +ATOM C2 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! -C3- +ATOM C3 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | +ATOM C4 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | | | +ATOM H11 HDA2C 0.122 ! -C2---N---C4- (+) +ATOM H12 HDA2C 0.122 ! | | | +ATOM H21 HDA3C 0.122 ! | +ATOM H22 HDA3C 0.122 ! -C1- +ATOM H23 HDA3C 0.122 ! | +ATOM H31 HDA3C 0.122 ! | +ATOM H32 HDA3C 0.122 ! | +ATOM H33 HDA3C 0.122 ! | +ATOM H41 HDA3C 0.122 ! | +ATOM H42 HDA3C 0.122 ! | +ATOM H43 HDA3C 0.122 ! | +GROUP ! | +ATOM C5 CD32AL 0.1985 ALPHA -1.642 THOLE 0.862 ! | +ATOM H51 HDA2A 0.026 ! H52---C5---H51 +ATOM H52 HDA2A 0.026 ! | +ATOM P1 PD1A 1.191 ALPHA -0.974 THOLE 2.098 ! (-) O3 O1 +ATOM O3 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! \ / +ATOM O4 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! P1 (+) +ATOM O1 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! / \ +ATOM O2 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! (-) O4 O2 +ATOM C6 CD33A 0.1725 ALPHA -1.642 THOLE 0.862 ! | +ATOM H61 HDA3A 0.026 ! H63-C6-H62 +ATOM H62 HDA3A 0.026 ! | +ATOM H63 HDA3A 0.026 ! H61 + +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C5 O2 C6 +BOND C6 H61 C6 H62 C6 H63 + +ANISOTROPY O1 O3 O2 O4 A11 1.0000 A22 0.6000 +ANISOTROPY O2 O4 O1 O3 A11 1.0000 A22 0.6000 +ANISOTROPY O3 P1 O1 O2 A11 0.6000 A22 1.0000 +ANISOTROPY O4 P1 O2 O1 A11 0.6000 A22 1.0000 + +! from crd snapshot of DMPC lipid +IC C4 N C1 C5 1.5287 114.21 -69.91 118.00 1.5484 ! dmpc snapshot (alpha6) +IC C5 C1 N C2 1.5484 118.00 51.44 109.96 1.5245 ! dmpc snapshot (alpha6) +IC C5 C1 N C3 1.5484 118.00 168.71 110.33 1.4813 ! dmpc snapshot (alpha6) +IC C2 N C1 H11 1.5245 109.96 -72.71 105.69 1.0800 +IC C3 N C1 H12 1.4813 110.33 -64.78 107.40 1.0800 +IC C1 N C2 H21 1.5691 109.96 -177.49 105.79 1.0800 +IC C3 N C2 H22 1.4813 106.57 -59.07 111.14 1.0800 +IC C4 N C2 H23 1.5287 107.82 61.96 105.88 1.0800 +IC C1 N C3 H31 1.5691 110.33 -38.84 109.46 1.0800 +IC C2 N C3 H32 1.5245 106.57 -38.04 112.72 1.0800 +IC C4 N C3 H33 1.5287 107.63 -47.68 111.09 1.0800 +IC C1 N C4 H41 1.5691 114.21 82.27 104.85 1.0800 +IC C2 N C4 H42 1.5245 107.82 -162.05 102.16 1.0800 +IC C3 N C4 H43 1.4813 107.63 -41.86 106.62 1.0800 +IC N C1 C5 H51 1.5691 118.00 -72.28 107.58 1.1110 +IC N C1 C5 H52 1.5691 118.00 173.53 110.91 1.1110 +IC N C1 C5 O1 1.5691 118.00 51.35 114.45 1.4136 ! dmpc snapshot (alpha5) +IC C1 C5 O1 P1 1.5484 114.45 -125.77 126.65 1.5528 ! dmpc snapshot (alpha4) +IC C5 O1 P1 O2 1.4136 126.65 -79.26 105.72 1.5948 ! dmpc snapshot (alpha3) +IC O3 P1 O1 C5 1.4635 108.40 164.76 126.65 1.4136 ! dmpc snapshot (alpha3) +IC O4 P1 O1 C5 1.4948 108.72 34.37 126.65 1.4136 ! dmpc snapshot (alpha3) +IC O1 P1 O2 C6 1.5528 105.72 -39.76 120.14 1.4507 ! dmpc snapshot (alpha2) +IC H61 C6 O2 P1 1.1110 109.78 -17.52 120.14 1.5948 +IC H62 C6 O2 P1 1.1110 110.89 -131.34 120.14 1.5948 +IC H63 C6 O2 P1 1.1000 110.00 107.02 120.14 1.5948 ! approximate geo for IC build (E.H) + +RESI GLYC 0.000 ! Model compound for glycerol headgroup the + ! aliphatic tail linker region +GROUP ! +ATOM C3 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! +ATOM H31 HDA3A 0.059 ! +ATOM H32 HDA3A 0.059 ! +ATOM H33 HDA3A 0.059 ! +GROUP ! +ATOM C1 CD32C 0.086 ALPHA -1.797 THOLE 0.410 ! H12 H21 H33 +ATOM H11 HDA2A 0.116 ! | | | +ATOM H12 HDA2A 0.116 ! H11--C1--C2--C3--H31 +ATOM O4 OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! / | | +ATOM C5 CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! O4 O8 H32 +ATOM O6 OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! / \ +ATOM C7 CD33C -0.275 ALPHA -1.993 THOLE 0.410 ! O6=C5 C9=O10 +ATOM H71 HDA3A 0.069 ! / \ +ATOM H72 HDA3A 0.069 ! H71-C7-H73 H113-C11-H111 +ATOM H73 HDA3A 0.069 ! | | +ATOM LP4A LPD -0.170 ! H72 H112 +ATOM LP4B LPD -0.170 ! +ATOM LP6A LPD -0.349 +ATOM LP6B LPD -0.258 +GROUP +ATOM C2 CD31C 0.202 ALPHA -1.797 THOLE 0.410 ! +ATOM H21 HDA1A 0.116 ! +ATOM O8 OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! +ATOM C9 CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! +ATOM O10 OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! +ATOM C11 CD33C -0.275 ALPHA -1.993 THOLE 0.410 ! +ATOM H111 HDA3A 0.069 ! +ATOM H112 HDA3A 0.069 ! +ATOM H113 HDA3A 0.069 ! +ATOM LP8A LPD -0.170 ! +ATOM LP8B LPD -0.170 ! +ATOM LP1A LPD -0.349 +ATOM LP1B LPD -0.258 + +BOND C1 C2 C2 C3 +BOND C1 O4 O4 C5 C5 C7 C5 O6 +BOND C2 O8 O8 C9 C9 C11 C9 O10 +BOND C1 H11 C1 H12 +BOND C2 H21 +BOND C3 H31 C3 H32 C3 H33 +BOND C7 H71 C7 H72 C7 H73 +BOND C11 H111 C11 H112 C11 H113 +BOND O4 LP4A O4 LP4B +BOND O6 LP6A O6 LP6B +BOND O8 LP8A O8 LP8B +BOND O10 LP1A O10 LP1B + +IMPR O6 C7 O4 C5 O10 C11 O8 C9 + +!ether O LP positions and anisotropic polarizability from MeOH +LONEPAIR relative LP4A O4 C5 C1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP4B O4 C5 C1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY O4 C5 LP4A LP4B A11 0.8108 A22 1.2162 + +!carbonyl O LP positions and anisotropic polarizability from NMA +LONEPAIR relative LP6A O6 C5 C7 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP6B O6 C5 C7 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O6 C5 LP6A LP6B A11 0.6968 A22 1.2194 + +!ether O LP positions and anisotropic polarizability from MeOH +LONEPAIR relative LP8A O8 C9 C2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP8B O8 C9 C2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY O8 C9 LP8A LP8B A11 0.8108 A22 1.2162 + +!carbonyl O LP positions and anisotropic polarizability from NMA +LONEPAIR relative LP1A O10 C9 C11 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1B O10 C9 C11 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O10 C9 LP1A LP1B A11 0.6968 A22 1.2194 + +! dmpc snapshot (E.H.) (beta2* and gamma2* definition unconventional) +IC O8 C2 C1 O4 1.4433 108.96 67.26 112.00 1.4482 ! crystal table (theta4) +IC C1 C3 *C2 O8 1.5416 111.86 117.87 104.73 1.4433 +IC C1 C3 *C2 H21 1.5416 111.86 -120.45 111.42 1.1131 +IC C3 C2 C1 O4 1.5260 111.86 -177.43 112.00 1.4482 ! crystal table (theta3)**start at diff angle +IC O4 C2 *C1 H11 1.4482 112.00 -119.53 108.04 1.1122 +IC O4 C2 *C1 H12 1.4482 112.00 125.00 109.59 1.1124 +IC C2 C1 O4 C5 1.5416 112.00 89.28 115.78 1.3407 ! dmpc snapshot (gamma1) +IC C1 O4 C5 O6 1.4482 115.78 -0.39 124.47 1.2022 ! crystal table (gamma2*) +IC O6 O4 *C5 C7 1.2022 124.47 -179.51 109.80 1.5034 +IC O4 C5 C7 H71 1.3407 109.80 63.08 109.67 1.1111 +IC H71 C5 *C7 H72 1.1111 109.67 -120.08 110.14 1.1101 +IC H71 C5 *C7 H73 1.1111 109.67 119.72 110.52 1.1108 ! approximate geo +IC C3 C2 O8 C9 1.5260 104.73 140.03 118.41 1.3347 ! dmpc snapshot (beta1)**start at diff angle +IC C2 O8 C9 O10 1.4433 118.41 0.49 125.22 1.2016 ! crystal table (beta2*)**start at diff angle +IC O10 O8 *C9 C11 1.2016 125.22 179.82 109.49 1.5064 +IC O8 C9 C11 H111 1.3347 109.49 59.03 109.95 1.1102 +IC H111 C9 *C11 H112 1.1102 109.95 -120.13 109.88 1.1102 +IC H111 C9 *C11 H113 1.1102 109.95 119.96 110.46 1.1108 ! approximate geo +IC H31 C3 C2 C1 1.1115 110.41 -178.97 111.86 1.5416 +IC H31 C2 *C3 H32 1.1115 110.41 120.08 110.68 1.1112 +IC H31 C2 *C3 H33 1.1115 110.41 -119.74 110.41 1.1108 ! approximate geo + +RESI GLYP -1.000 ! Model compound for glycerol headgroup the + ! aliphatic tail linker region, phosphorylated +GROUP ! +ATOM P1 PD1A 1.191 ALPHA -0.974 THOLE 2.098 +ATOM OP3 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 +ATOM OP4 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! HP11 +ATOM OP1 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! | +ATOM OP2 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! HP13-CP1-HP12 + ! \ +ATOM CP1 CD33A 0.1725 ALPHA -1.642 THOLE 0.862 ! (-)OP3 OP1 +ATOM HP11 HDA3A 0.026 ! \ / +ATOM HP12 HDA3A 0.026 ! P1 (+) +ATOM HP13 HDA3A 0.026 ! / \ + ! (-)OP4 OP2 +ATOM C3 CD32AL 0.1985 ALPHA -1.642 THOLE 0.862 ! \ +ATOM H31 HDA2A 0.026 ! \ +ATOM H32 HDA2A 0.026 ! \ +GROUP ! | +ATOM C1 CD32C 0.086 ALPHA -1.797 THOLE 0.410 ! H12 H21 | +ATOM H11 HDA2A 0.116 ! | | | +ATOM H12 HDA2A 0.116 ! H11--C1--C2--C3--H31 +ATOM O4 OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! / | | +ATOM C5 CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! O4 O8 H32 +ATOM O6 OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! / \ +ATOM C7 CD33C -0.275 ALPHA -1.993 THOLE 0.410 ! O6=C5 C9=O10 +ATOM H71 HDA3A 0.069 ! / \ +ATOM H72 HDA3A 0.069 ! H71-C7-H73 H113-C11-H111 +ATOM H73 HDA3A 0.069 ! | | +ATOM LP4A LPD -0.170 ! H72 H112 +ATOM LP4B LPD -0.170 ! +ATOM LP6A LPD -0.349 +ATOM LP6B LPD -0.258 +GROUP ! +ATOM C2 CD31C 0.202 ALPHA -1.797 THOLE 0.410 ! +ATOM H21 HDA1A 0.116 ! +ATOM O8 OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! +ATOM C9 CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! +ATOM O10 OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! +ATOM C11 CD33C -0.275 ALPHA -1.993 THOLE 0.410 ! +ATOM H111 HDA3A 0.069 ! +ATOM H112 HDA3A 0.069 ! +ATOM H113 HDA3A 0.069 ! +ATOM LP8A LPD -0.170 ! +ATOM LP8B LPD -0.170 ! +ATOM LP1A LPD -0.349 +ATOM LP1B LPD -0.258 + +BOND P1 OP1 P1 OP2 P1 OP3 P1 OP4 OP1 CP1 +BOND CP1 HP11 CP1 HP12 CP1 HP13 OP2 C3 +BOND C1 C2 C2 C3 +BOND C1 O4 O4 C5 C5 C7 C5 O6 +BOND C2 O8 O8 C9 C9 C11 C9 O10 +BOND C1 H11 C1 H12 C2 H21 C3 H31 C3 H32 +BOND C7 H71 C7 H72 C7 H73 +BOND C11 H111 C11 H112 C11 H113 +BOND LP4A O4 LP4B O4 +BOND LP6A O6 LP6B O6 +BOND LP8A O8 LP8B O8 +BOND LP1A O10 LP1B O10 + +IMPR O6 C7 O4 C5 O10 C11 O8 C9 + +!ether O LP positions and anisotropic polarizability from MeOH +LONEPAIR relative LP4A O4 C5 C1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP4B O4 C5 C1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY O4 C5 LP4A LP4B A11 0.8108 A22 1.2162 + +!carbonyl O LP positions and anisotropic polarizability from NMA +LONEPAIR relative LP6A O6 C5 C7 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP6B O6 C5 C7 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O6 C5 LP6A LP6B A11 0.6968 A22 1.2194 + +!ether O LP positions and anisotropic polarizability from MeOH +LONEPAIR relative LP8A O8 C9 C2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP8B O8 C9 C2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY O8 C9 LP8A LP8B A11 0.8108 A22 1.2162 + +!carbonyl O LP positions and anisotropic polarizability from NMA +LONEPAIR relative LP1A O10 C9 C11 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1B O10 C9 C11 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O10 C9 LP1A LP1B A11 0.6968 A22 1.2194 + +ANISOTROPY OP1 OP3 OP2 OP4 A11 1.0000 A22 0.6000 +ANISOTROPY OP2 OP4 OP1 OP3 A11 1.0000 A22 0.6000 +ANISOTROPY OP3 P1 OP1 OP2 A11 0.6000 A22 1.0000 +ANISOTROPY OP4 P1 OP2 OP1 A11 0.6000 A22 1.0000 + +! edited dmpc snapshot (E.H.) (beta2* and gamma2* definition unconventional) +IC CP1 OP1 P1 OP2 1.4186 112.33 -78.53 103.34 1.5770 ! crystal data (alpha3) +IC OP1 OP2 *P1 OP3 1.5812 103.34 -115.61 107.34 1.4868 +IC OP1 OP2 *P1 OP4 1.5812 103.34 114.59 106.97 1.4890 +IC P1 OP1 CP1 HP11 1.5812 112.33 44.89 112.05 1.1131 ! approximate geo +IC HP11 OP1 *CP1 HP12 1.1131 112.05 118.82 108.95 1.1108 +IC HP11 OP1 *CP1 HP13 1.1131 112.05 -123.08 110.83 1.1122 +IC OP1 P1 OP2 C3 1.5812 103.34 -63.74 113.53 1.4211 ! crystal data (alpha2) +IC P1 OP2 C3 C2 1.5770 113.53 -118.59 110.80 1.5411 ! dmpc snapshot (alpha1) +IC C2 OP2 *C3 H31 1.5411 110.80 -117.79 107.25 1.1126 +IC C2 OP2 *C3 H32 1.5411 110.80 124.94 114.26 1.1129 +IC OP2 C3 C2 C1 1.4211 110.80 66.66 113.75 1.5413 ! dmpc snapshot (theta1) +IC C1 C3 *C2 O8 1.5413 113.75 120.93 106.41 1.4493 +IC C1 C3 *C2 H21 1.5413 113.75 -118.94 106.83 1.1155 +IC C3 C2 C1 O4 1.5411 113.75 177.67 111.80 1.4509 ! crystal table (theta3) +IC O4 C2 *C1 H11 1.4509 111.80 -120.29 108.58 1.1124 +IC O4 C2 *C1 H12 1.4509 111.80 124.04 109.30 1.1138 +IC C2 C1 O4 C5 1.5413 111.80 93.38 117.70 1.3380 ! dmpc snapshot (gamma1) +IC C1 O4 C5 O6 1.4509 117.70 -1.20 125.29 1.2005 ! crystal table (gamma2*) +IC O6 O4 *C5 C7 1.2005 125.29 -179.32 109.42 1.5078 +IC O4 C5 C7 H71 1.3380 109.42 63.59 109.44 1.1106 +IC H71 C5 *C7 H72 1.1106 109.44 -120.01 109.93 1.1097 +IC H71 C5 *C7 H73 1.1106 109.44 119.76 110.38 1.1102 ! approximate geo +IC C3 C2 O8 C9 1.5411 106.41 137.58 118.77 1.3280 ! dmpc snapshot (beta1) +IC C2 O8 C9 O10 1.4493 118.77 -0.90 125.92 1.2021 ! crystal table (beta2*) +IC O10 O8 *C9 C11 1.2021 125.92 179.92 109.19 1.5092 +IC O8 C9 C11 H111 1.3280 109.19 59.28 109.75 1.1100 +IC H111 C9 *C11 H112 1.1100 109.75 -119.89 109.63 1.1101 +IC H111 C9 *C11 H113 1.1100 109.75 120.11 110.45 1.1101 ! approximate geo + +RESI DMPC 0.000 ! 1,2 dimiristoyl-SN-glycero-3-Phosphorylcholine +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N ND3P2A 0.688 ALPHA -0.829 THOLE 0.793 ! | +ATOM C13 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! H15A-C15-H15C +ATOM H13A HDA3C 0.122 ! | +ATOM H13B HDA3C 0.122 ! H13B | H14A +ATOM H13C HDA3C 0.122 ! | | | +ATOM C14 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! H13A-C13--N--C14-H14B (+) +ATOM H14A HDA3C 0.122 ! | | | +ATOM H14B HDA3C 0.122 ! H13C | H14C +ATOM H14C HDA3C 0.122 ! | +ATOM C15 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | +ATOM H15A HDA3C 0.122 ! | alpha6 +ATOM H15B HDA3C 0.122 ! | +ATOM H15C HDA3C 0.122 ! | +ATOM C12 CD32AL -0.166 ALPHA -1.393 THOLE 1.099 ! H12A--C12---H12B +ATOM H12A HDA2C 0.122 ! | +ATOM H12B HDA2C 0.122 ! | +GROUP ! alpha5 +ATOM C11 CD32AL 0.1985 ALPHA -1.642 THOLE 0.862 ! | +ATOM H11A HDA2A 0.026 ! H11A--C11---H11B +ATOM H11B HDA2A 0.026 ! | alpha4 +ATOM P PD1A 1.191 ALPHA -0.974 THOLE 2.098 ! (-) O13 O12 +ATOM O13 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! \ / alpha3 +ATOM O14 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! P (+) +ATOM O11 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! / \ alpha2 +ATOM O12 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! (-) O14 O11 +ATOM C1 CD32AL 0.1985 ALPHA -1.642 THOLE 0.862 ! | alpha1 +ATOM HA HDA2A 0.026 ! HA---C1---HB +ATOM HB HDA2A 0.026 ! | theta1 +GROUP ! \ +ATOM C2 CD31C 0.202 ALPHA -1.797 THOLE 0.410 ! HS---C2- - - - - - - +ATOM HS HDA1A 0.116 ! | beta1 | +ATOM O21 OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! O22 O21 theta3 +ATOM C21 CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! \\ / beta2 | +ATOM O22 OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! C21 +ATOM C22 CD32C -0.206 ALPHA -1.993 THOLE 0.410 ! | beta3 | +ATOM H2R HDA2A 0.069 ! H2R---C22---H2S +ATOM H2S HDA2A 0.069 ! | | +ATOM LP1A LPD -0.349 ! +ATOM LP1B LPD -0.258 ! | | +ATOM LPMA LPD -0.170 ! +ATOM LPMB LPD -0.170 ! | | +GROUP ! beta4 +ATOM C3 CD32C 0.086 ALPHA -1.797 THOLE 0.410 ! | | +ATOM HX HDA2A 0.116 ! HX---C3---HY +ATOM HY HDA2A 0.116 ! | | gamma1 +ATOM O31 OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! O32 O31 +ATOM C31 CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! | \\ / gamma2 +ATOM O32 OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! C31 +ATOM C32 CD32C -0.206 ALPHA -1.993 THOLE 0.410 ! | | gamma3 +ATOM H2X HDA2A 0.069 ! H2X---C32---H2Y +ATOM H2Y HDA2A 0.069 ! | | +ATOM LP1C LPD -0.349 ! +ATOM LP1D LPD -0.258 ! | | +ATOM LPMC LPD -0.170 ! +ATOM LPMD LPD -0.170 ! | | +GROUP ! gamma4 +ATOM C23 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H3R HDA2A 0.078 ! H3R ---C23---H3S +ATOM H3S HDA2A 0.078 ! | | +GROUP ! +ATOM C24 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H4R HDA2A 0.078 ! H4R ---C24---H4S | +ATOM H4S HDA2A 0.078 ! | +GROUP ! +ATOM C25 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H5R HDA2A 0.078 ! H5R ---C25---H5S +ATOM H5S HDA2A 0.078 ! | | +GROUP ! +ATOM C26 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H6R HDA2A 0.078 ! H6R ---C26---H6S | +ATOM H6S HDA2A 0.078 ! | +GROUP ! +ATOM C27 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H7R HDA2A 0.078 ! H7R ---C27---H7S +ATOM H7S HDA2A 0.078 ! | | +GROUP ! +ATOM C28 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H8R HDA2A 0.078 ! H8R ---C28---H8S | +ATOM H8S HDA2A 0.078 ! | +GROUP ! +ATOM C29 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H9R HDA2A 0.078 ! H9R ---C29---H9S +ATOM H9S HDA2A 0.078 ! | | +GROUP ! +ATOM C210 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H10R HDA2A 0.078 ! H10R--C210--H10S | +ATOM H10S HDA2A 0.078 ! | +GROUP ! +ATOM C211 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H11R HDA2A 0.078 ! H11R--C211--H11S +ATOM H11S HDA2A 0.078 ! | | +GROUP ! +ATOM C212 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H12R HDA2A 0.078 ! H12R--C212--H12S | +ATOM H12S HDA2A 0.078 ! | +GROUP ! +ATOM C213 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H13R HDA2A 0.078 ! H13R--C213--H13S +ATOM H13S HDA2A 0.078 ! | | +GROUP ! +GROUP ! | +ATOM C214 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! | +ATOM H14R HDA3A 0.059 ! H14R--C214--H14S | +ATOM H14S HDA3A 0.059 ! | +ATOM H14T HDA3A 0.059 ! H14T | +GROUP ! +ATOM C33 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H3X HDA2A 0.078 ! H3X ---C33---H3Y +ATOM H3Y HDA2A 0.078 ! | +GROUP ! +ATOM C34 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H4X HDA2A 0.078 ! H4X ---C34---H4Y +ATOM H4Y HDA2A 0.078 ! | +GROUP ! +ATOM C35 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H5X HDA2A 0.078 ! H5X ---C35---H5Y +ATOM H5Y HDA2A 0.078 ! | +GROUP ! +ATOM C36 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H6X HDA2A 0.078 ! H6X ---C36---H6Y +ATOM H6Y HDA2A 0.078 ! | +GROUP ! +ATOM C37 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H7X HDA2A 0.078 ! H7X ---C37---H7Y +ATOM H7Y HDA2A 0.078 ! | +GROUP ! +ATOM C38 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H8X HDA2A 0.078 ! H8X ---C38---H8Y +ATOM H8Y HDA2A 0.078 ! | +GROUP ! +ATOM C39 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H9X HDA2A 0.078 ! H9X ---C39---H9Y +ATOM H9Y HDA2A 0.078 ! | +GROUP ! +ATOM C310 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H10X HDA2A 0.078 ! H10X--C310--H10Y +ATOM H10Y HDA2A 0.078 ! | +GROUP ! +ATOM C311 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H11X HDA2A 0.078 ! H11X--C311--H11Y +ATOM H11Y HDA2A 0.078 ! | +GROUP ! +ATOM C312 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H12X HDA2A 0.078 ! H12X--C312--H12Y +ATOM H12Y HDA2A 0.078 ! | +GROUP ! +ATOM C313 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H13X HDA2A 0.078 ! H13X--C313--H13Y +ATOM H13Y HDA2A 0.078 ! | +GROUP ! +ATOM C314 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! | +ATOM H14X HDA3A 0.059 ! H14X--C314--H14Y +ATOM H14Y HDA3A 0.059 ! | +ATOM H14Z HDA3A 0.059 ! H14Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +BOND C21 O22 +BOND LP1A O22 LP1B O22 +BOND LPMA O21 LPMB O21 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +BOND C31 O32 +BOND LP1C O32 LP1D O32 +BOND LPMC O31 LPMD O31 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +LONEPAIR relative LP1A O22 C21 C22 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1B O22 C21 C22 distance 0.30 angle 91.0 dihe 180.0 +LONEPAIR relative LP1C O32 C31 C32 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1D O32 C31 C32 distance 0.30 angle 91.0 dihe 180.0 +LONEPAIR relative LPMA O21 C21 C2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPMB O21 C21 C2 distance 0.35 angle 110.9 dihe 269.0 +LONEPAIR relative LPMC O31 C31 C3 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPMD O31 C31 C3 distance 0.35 angle 110.9 dihe 269.0 + +ANISOTROPY O22 C21 LP1A LP1B A11 0.6968 A22 1.2194 +ANISOTROPY O32 C31 LP1C LP1D A11 0.6968 A22 1.2194 +ANISOTROPY O21 C21 LPMA LPMB A11 0.8108 A22 1.2162 +ANISOTROPY O31 C31 LPMC LPMD A11 0.8108 A22 1.2162 + +ANISOTROPY O12 O13 O11 O14 A11 1.0000 A22 0.6000 +ANISOTROPY O11 O14 O12 O13 A11 1.0000 A22 0.6000 +ANISOTROPY O13 P O12 O11 A11 0.6000 A22 1.0000 +ANISOTROPY O14 P O11 O12 A11 0.6000 A22 1.0000 + +!IC table from IC generate, minimized geometry +IC C15 N C12 C11 1.4976 109.72 180.00 116.86 1.5415 +IC C13 C12 *N C14 1.4955 110.64 -119.74 108.01 1.5030 +IC C13 C12 *N C15 1.4955 110.64 122.73 109.72 1.4976 +IC C12 N C13 H13A 1.5224 110.64 -177.67 111.18 1.0813 +IC H13A N *C13 H13B 1.0813 111.18 119.03 109.35 1.0870 +IC H13A N *C13 H13C 1.0813 111.18 -122.04 111.32 1.0813 +IC C12 N C14 H14A 1.5224 108.01 56.08 111.03 1.0952 +IC H14A N *C14 H14B 1.0952 111.03 123.93 113.88 1.0740 +IC H14A N *C14 H14C 1.0952 111.03 -112.36 110.24 1.0938 +IC C12 N C15 H15A 1.5224 109.72 176.74 110.89 1.0821 +IC H15A N *C15 H15B 1.0821 110.89 121.45 111.48 1.0812 +IC H15A N *C15 H15C 1.0821 110.89 -118.76 109.68 1.0875 +IC C13 N C12 C11 1.4955 110.64 57.27 116.86 1.5415 +IC C11 N *C12 H12A 1.5415 116.86 -126.38 111.91 1.0785 +IC H12A N *C12 H12B 1.0785 111.91 -116.30 108.18 1.0972 +IC N C12 C11 O12 1.5224 116.86 127.42 108.31 1.4234 +IC O12 C12 *C11 H11A 1.4234 108.31 -123.13 113.24 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.24 -118.65 109.16 1.1130 +IC C12 C11 O12 P 1.5415 108.31 -67.88 118.40 1.5875 +IC C11 O12 P O11 1.4234 118.40 -166.94 104.13 1.5782 +IC O11 O12 *P O13 1.5782 104.13 117.91 108.15 1.4793 +IC O11 O12 *P O14 1.5782 104.13 -117.27 106.75 1.4823 +IC O12 P O11 C1 1.5875 104.13 177.32 118.17 1.4318 +IC P O11 C1 C2 1.5782 118.17 167.65 110.87 1.5511 +IC C2 O11 *C1 HA 1.5511 110.87 -119.11 111.42 1.1172 +IC HA O11 *C1 HB 1.1172 111.42 -120.82 110.01 1.1145 +IC O11 C1 C2 C3 1.4318 110.87 177.69 110.63 1.5578 +IC C3 C1 *C2 O21 1.5578 110.63 120.78 108.07 1.4415 !defines S chirality +IC C3 C1 *C2 HS 1.5578 110.63 -118.30 106.69 1.1168 !defines S chirality +IC C1 C2 O21 C21 1.5511 108.07 147.89 115.06 1.3179 +IC C2 O21 C21 C22 1.4415 115.06 179.61 108.77 1.5289 +IC C22 O21 *C21 O22 1.5289 108.77 -179.08 126.52 1.2183 +IC O21 C21 C22 C23 1.3179 108.77 -173.00 112.01 1.5450 +IC C23 C21 *C22 H2R 1.5450 112.01 -121.50 107.73 1.1091 +IC H2R C21 *C22 H2S 1.1091 107.73 -117.24 107.85 1.1091 +IC C1 C2 C3 O31 1.5511 110.63 175.48 112.70 1.4436 +IC O31 C2 *C3 HX 1.4436 112.70 -118.48 106.61 1.1129 +IC HX C2 *C3 HY 1.1129 106.61 -115.12 109.44 1.1145 +IC C2 C3 O31 C31 1.5578 112.70 87.10 115.14 1.3313 +IC C3 O31 C31 C32 1.4436 115.14 -172.45 108.40 1.5287 +IC C32 O31 *C31 O32 1.5287 108.40 -178.98 125.63 1.2169 +IC O31 C31 C32 C33 1.3313 108.40 -169.89 113.40 1.5448 +IC C33 C31 *C32 H2X 1.5448 113.40 -121.09 107.19 1.1104 +IC H2X C31 *C32 H2Y 1.1104 107.19 -116.85 108.01 1.1089 +IC C21 C22 C23 C24 1.5289 112.01 177.45 112.54 1.5336 +IC C24 C22 *C23 H3R 1.5336 112.54 -120.79 109.48 1.1146 +IC H3R C22 *C23 H3S 1.1146 109.48 -117.62 109.70 1.1144 +IC C22 C23 C24 C25 1.5450 112.54 -177.78 112.24 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.24 -121.51 109.37 1.1130 +IC H4R C23 *C24 H4S 1.1130 109.37 -117.64 109.09 1.1133 +IC C23 C24 C25 C26 1.5336 112.24 178.33 112.83 1.5342 +IC C26 C24 *C25 H5R 1.5342 112.83 -121.07 108.90 1.1136 +IC H5R C24 *C25 H5S 1.1136 108.90 -117.22 109.21 1.1132 +IC C24 C25 C26 C27 1.5346 112.83 -177.92 112.39 1.5344 +IC C27 C25 *C26 H6R 1.5344 112.39 -121.57 109.28 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.28 -117.51 109.01 1.1133 +IC C25 C26 C27 C28 1.5342 112.39 178.43 112.74 1.5342 +IC C28 C26 *C27 H7R 1.5342 112.74 -121.06 108.92 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.92 -117.29 109.22 1.1131 +IC C26 C27 C28 C29 1.5344 112.74 -178.17 112.46 1.5345 +IC C29 C27 *C28 H8R 1.5345 112.46 -121.56 109.25 1.1130 +IC H8R C27 *C28 H8S 1.1130 109.25 -117.46 109.01 1.1133 +IC C27 C28 C29 C210 1.5342 112.46 178.92 112.68 1.5343 +IC C210 C28 *C29 H9R 1.5343 112.68 -121.11 108.98 1.1135 +IC H9R C28 *C29 H9S 1.1135 108.98 -117.36 109.19 1.1131 +IC C28 C29 C210 C211 1.5345 112.68 -178.62 112.55 1.5345 +IC C211 C29 *C210 H10R 1.5345 112.55 -121.48 109.19 1.1130 +IC H10R C29 *C210 H10S 1.1130 109.19 -117.42 109.05 1.1132 +IC C29 C210 C211 C212 1.5343 112.55 179.33 112.62 1.5345 +IC C212 C210 *C211 H11R 1.5345 112.62 -121.19 109.03 1.1133 +IC H11R C210 *C211 H11S 1.1133 109.03 -117.37 109.14 1.1131 +IC C210 C211 C212 C213 1.5345 112.62 -179.30 112.67 1.5338 +IC C213 C211 *C212 H12R 1.5338 112.67 -121.40 109.15 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.15 -117.41 109.09 1.1133 +IC C211 C212 C213 C214 1.5345 112.67 179.80 113.26 1.5308 +IC C214 C212 *C213 H13R 1.5308 113.26 -121.66 108.77 1.1142 +IC H13R C212 *C213 H13S 1.1142 108.77 -116.66 108.78 1.1140 +IC C212 C213 C214 H14R 1.5338 113.26 -59.87 110.43 1.1113 +IC H14R C213 *C214 H14S 1.1113 110.43 119.85 110.46 1.1113 +IC H14R C213 *C214 H14T 1.1113 110.43 -120.04 110.62 1.1112 +IC C31 C32 C33 C34 1.5287 113.40 179.64 111.32 1.5341 +IC C34 C32 *C33 H3X 1.5341 111.32 -120.86 109.71 1.1137 +IC H3X C32 *C33 H3Y 1.1137 109.71 -118.09 109.81 1.1143 +IC C32 C33 C34 C35 1.5448 111.32 -176.82 113.37 1.5345 +IC C35 C33 *C34 H4X 1.5345 113.37 -121.80 109.05 1.1135 +IC H4X C33 *C34 H4Y 1.1135 109.05 -117.12 108.83 1.1136 +IC C33 C34 C35 C36 1.5341 113.37 178.26 111.94 1.5348 +IC C36 C34 *C35 H5X 1.5348 111.94 -120.83 109.02 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.02 -117.61 109.44 1.1129 +IC C34 C35 C36 C37 1.5345 111.94 -176.79 113.19 1.5342 +IC C37 C35 *C36 H6X 1.5342 113.19 -121.90 109.15 1.1132 +IC H6X C35 *C36 H6Y 1.1132 109.15 -117.14 108.76 1.1136 +IC C35 C36 C37 C38 1.5348 113.19 177.72 112.13 1.5346 +IC C38 C36 *C37 H7X 1.5346 112.13 -120.80 109.00 1.1133 +IC H7X C36 *C37 H7Y 1.1133 109.00 -117.59 109.40 1.1128 +IC C36 C37 C38 C39 1.5342 112.13 -177.62 112.99 1.5342 +IC C39 C37 *C38 H8X 1.5342 112.99 -121.75 109.20 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.20 -117.24 108.86 1.1136 +IC C37 C38 C39 C310 1.5346 112.99 178.21 112.22 1.5344 +IC C310 C38 *C39 H9X 1.5344 112.22 -120.97 109.07 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.07 -117.54 109.30 1.1130 +IC C38 C39 C310 C311 1.5342 112.22 -178.81 112.83 1.5339 +IC C311 C39 *C310 H10X 1.5339 112.83 -121.55 109.12 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.12 -117.29 108.97 1.1134 +IC C39 C310 C311 C312 1.5344 112.83 179.12 112.41 1.5346 +IC C312 C310 *C311 H11X 1.5346 112.41 -121.13 109.11 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.11 -117.49 109.19 1.1130 +IC C310 C311 C312 C313 1.5339 112.41 -179.72 112.68 1.5336 +IC C313 C311 *C312 H12X 1.5336 112.68 -121.39 109.14 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.14 -117.34 109.09 1.1133 +IC C311 C312 C313 C314 1.5346 112.68 179.81 113.29 1.5308 +IC C314 C312 *C313 H13X 1.5308 113.29 -121.66 108.73 1.1141 +IC H13X C312 *C313 H13Y 1.1141 108.73 -116.66 108.73 1.1141 +IC C312 C313 C314 H14X 1.5336 113.29 -59.97 110.46 1.1113 +IC H14X C313 *C314 H14Y 1.1113 110.46 119.87 110.46 1.1113 +IC H14X C313 *C314 H14Z 1.1113 110.46 -120.06 110.59 1.1112 + +RESI DPPC 0.000 ! +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N ND3P2A 0.688 ALPHA -0.829 THOLE 0.793 ! | +ATOM C13 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! H15A-C15-H15C +ATOM H13A HDA3C 0.122 ! | +ATOM H13B HDA3C 0.122 ! H13B | H14A +ATOM H13C HDA3C 0.122 ! | | | +ATOM C14 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! H13A-C13--N--C14-H14B (+) +ATOM H14A HDA3C 0.122 ! | | | +ATOM H14B HDA3C 0.122 ! H13C | H14C +ATOM H14C HDA3C 0.122 ! | +ATOM C15 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | +ATOM H15A HDA3C 0.122 ! | alpha6 +ATOM H15B HDA3C 0.122 ! | +ATOM H15C HDA3C 0.122 ! | +ATOM C12 CD32AL -0.166 ALPHA -1.393 THOLE 1.099 ! H12A--C12---H12B +ATOM H12A HDA2C 0.122 ! | +ATOM H12B HDA2C 0.122 ! | +GROUP ! alpha5 +ATOM C11 CD32AL 0.1985 ALPHA -1.642 THOLE 0.862 ! | +ATOM H11A HDA2A 0.026 ! H11A--C11---H11B +ATOM H11B HDA2A 0.026 ! | alpha4 +ATOM P PD1A 1.191 ALPHA -0.974 THOLE 2.098 ! (-) O13 O12 +ATOM O13 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! \ / alpha3 +ATOM O14 OD2C2B -0.876 ALPHA -0.931 THOLE 1.083 ! P (+) +ATOM O11 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! / \ alpha2 +ATOM O12 OD30B -0.470 ALPHA -0.901 THOLE 0.181 ! (-) O14 O11 +ATOM C1 CD32AL 0.1985 ALPHA -1.642 THOLE 0.862 ! | alpha1 +ATOM HA HDA2A 0.026 ! HA---C1---HB +ATOM HB HDA2A 0.026 ! | theta1 +GROUP ! | +ATOM C2 CD31C 0.202 ALPHA -1.797 THOLE 0.410 ! HS---C2- - - - - - +ATOM HS HDA1A 0.116 ! | beta1 | +ATOM O21 OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! O22 O21 theta3 +ATOM C21 CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! \\ / beta2 | +ATOM O22 OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! C21 +ATOM C22 CD32C -0.206 ALPHA -1.993 THOLE 0.410 ! | beta3 | +ATOM H2R HDA2A 0.069 ! H2R---C22---H2S +ATOM H2S HDA2A 0.069 ! | | +ATOM LP1A LPD -0.349 ! +ATOM LP1B LPD -0.258 ! | | +ATOM LPMA LPD -0.170 ! +ATOM LPMB LPD -0.170 ! | | +GROUP ! beta4 +ATOM C3 CD32C 0.086 ALPHA -1.797 THOLE 0.410 ! | | +ATOM HX HDA2A 0.116 ! HX---C3---HY +ATOM HY HDA2A 0.116 ! | | gamma1 +ATOM O31 OD30CL 0.000 ALPHA -0.732 THOLE 0.601 ! O32 O31 +ATOM C31 CD2O3B 0.697 ALPHA -1.370 THOLE 1.747 ! | \\ / gamma2 +ATOM O32 OD2C3B 0.000 ALPHA -0.904 THOLE 0.565 ! C31 +ATOM C32 CD32C -0.206 ALPHA -1.993 THOLE 0.410 ! | | gamma3 +ATOM H2X HDA2A 0.069 ! H2X---C32---H2Y +ATOM H2Y HDA2A 0.069 ! | | +ATOM LP1C LPD -0.349 ! +ATOM LP1D LPD -0.258 ! | | +ATOM LPMC LPD -0.170 ! +ATOM LPMD LPD -0.170 ! | | +GROUP ! gamma4 +ATOM C23 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H3R HDA2A 0.078 ! H3R ---C23---H3S +ATOM H3S HDA2A 0.078 ! | | +GROUP ! +ATOM C24 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H4R HDA2A 0.078 ! H4R ---C24---H4S | +ATOM H4S HDA2A 0.078 ! | +GROUP ! +ATOM C25 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H5R HDA2A 0.078 ! H5R ---C25---H5S +ATOM H5S HDA2A 0.078 ! | | +GROUP ! +ATOM C26 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H6R HDA2A 0.078 ! H6R ---C26---H6S | +ATOM H6S HDA2A 0.078 ! | +GROUP ! +ATOM C27 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H7R HDA2A 0.078 ! H7R ---C27---H7S +ATOM H7S HDA2A 0.078 ! | | +GROUP ! +ATOM C28 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! +ATOM H8R HDA2A 0.078 ! H8R ---C28---H8S | +ATOM H8S HDA2A 0.078 ! | +GROUP ! +ATOM C29 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H9R HDA2A 0.078 ! H9R ---C29---H9S +ATOM H9S HDA2A 0.078 ! | | +GROUP ! +ATOM C210 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H10R HDA2A 0.078 ! H10R--C210--H10S | +ATOM H10S HDA2A 0.078 ! | +GROUP ! +ATOM C211 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H11R HDA2A 0.078 ! H11R--C211--H11S +ATOM H11S HDA2A 0.078 ! | | +GROUP ! +ATOM C212 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H12R HDA2A 0.078 ! H12R--C212--H12S | +ATOM H12S HDA2A 0.078 ! | +GROUP ! +ATOM C213 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | | +ATOM H13R HDA2A 0.078 ! H13R--C213--H13S +ATOM H13S HDA2A 0.078 ! | | +GROUP ! +ATOM C214 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H14R HDA2A 0.078 ! H14R--C214--H14S | +ATOM H14S HDA2A 0.078 ! | +GROUP ! +ATOM C215 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H15R HDA2A 0.078 ! H15R--C215--H15S | +ATOM H15S HDA2A 0.078 ! | +GROUP ! | +ATOM C216 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! | +ATOM H16R HDA3A 0.059 ! H16R--C216--H16S | +ATOM H16S HDA3A 0.059 ! | +ATOM H16T HDA3A 0.059 ! H16T | +GROUP ! +ATOM C33 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H3X HDA2A 0.078 ! H3X ---C33---H3Y +ATOM H3Y HDA2A 0.078 ! | +GROUP ! +ATOM C34 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H4X HDA2A 0.078 ! H4X ---C34---H4Y +ATOM H4Y HDA2A 0.078 ! | +GROUP ! +ATOM C35 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H5X HDA2A 0.078 ! H5X ---C35---H5Y +ATOM H5Y HDA2A 0.078 ! | +GROUP ! +ATOM C36 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H6X HDA2A 0.078 ! H6X ---C36---H6Y +ATOM H6Y HDA2A 0.078 ! | +GROUP ! +ATOM C37 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H7X HDA2A 0.078 ! H7X ---C37---H7Y +ATOM H7Y HDA2A 0.078 ! | +GROUP ! +ATOM C38 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H8X HDA2A 0.078 ! H8X ---C38---H8Y +ATOM H8Y HDA2A 0.078 ! | +GROUP ! +ATOM C39 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H9X HDA2A 0.078 ! H9X ---C39---H9Y +ATOM H9Y HDA2A 0.078 ! | +GROUP ! +ATOM C310 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H10X HDA2A 0.078 ! H10X--C310--H10Y +ATOM H10Y HDA2A 0.078 ! | +GROUP ! +ATOM C311 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H11X HDA2A 0.078 ! H11X--C311--H11Y +ATOM H11Y HDA2A 0.078 ! | +GROUP ! +ATOM C312 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H12X HDA2A 0.078 ! H12X--C312--H12Y +ATOM H12Y HDA2A 0.078 ! | +GROUP ! +ATOM C313 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H13X HDA2A 0.078 ! H13X--C313--H13Y +ATOM H13Y HDA2A 0.078 ! | +GROUP ! +ATOM C314 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H14X HDA2A 0.078 ! H14X--C314--H14Y +ATOM H14Y HDA2A 0.078 ! | +GROUP ! +ATOM C315 CD32AL -0.156 ALPHA -1.660 THOLE 1.300 ! | +ATOM H15X HDA2A 0.078 ! H15X--C315--H15Y +ATOM H15Y HDA2A 0.078 ! | +GROUP ! +ATOM C316 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! | +ATOM H16X HDA3A 0.059 ! H16X--C316--H16Y +ATOM H16Y HDA3A 0.059 ! | +ATOM H16Z HDA3A 0.059 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +BOND C21 O22 +BOND LP1A O22 LP1B O22 +BOND LPMA O21 LPMB O21 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +BOND C31 O32 +BOND LP1C O32 LP1D O32 +BOND LPMC O31 LPMD O31 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +LONEPAIR relative LP1A O22 C21 C22 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1B O22 C21 C22 distance 0.30 angle 91.0 dihe 180.0 +LONEPAIR relative LP1C O32 C31 C32 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1D O32 C31 C32 distance 0.30 angle 91.0 dihe 180.0 +LONEPAIR relative LPMA O21 C21 C2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPMB O21 C21 C2 distance 0.35 angle 110.9 dihe 269.0 +LONEPAIR relative LPMC O31 C31 C3 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPMD O31 C31 C3 distance 0.35 angle 110.9 dihe 269.0 + +ANISOTROPY O22 C21 LP1A LP1B A11 0.6968 A22 1.2194 +ANISOTROPY O32 C31 LP1C LP1D A11 0.6968 A22 1.2194 +ANISOTROPY O21 C21 LPMA LPMB A11 0.8108 A22 1.2162 +ANISOTROPY O31 C31 LPMC LPMD A11 0.8108 A22 1.2162 + +ANISOTROPY O12 O13 O11 O14 A11 1.0000 A22 0.6000 +ANISOTROPY O11 O14 O12 O13 A11 1.0000 A22 0.6000 +ANISOTROPY O13 P O12 O11 A11 0.6000 A22 1.0000 +ANISOTROPY O14 P O11 O12 A11 0.6000 A22 1.0000 + +!IC table from IC generate, minimized geometry +IC C15 N C12 C11 1.4975 109.67 -179.96 116.86 1.5411 +IC C13 C12 *N C14 1.4954 110.61 -119.72 108.04 1.5030 +IC C13 C12 *N C15 1.4954 110.61 122.74 109.67 1.4975 +IC C12 N C13 H13A 1.5222 110.61 -177.62 111.18 1.0811 +IC H13A N *C13 H13B 1.0811 111.18 119.00 109.33 1.0870 +IC H13A N *C13 H13C 1.0811 111.18 -122.05 111.32 1.0813 +IC C12 N C14 H14A 1.5222 108.04 55.75 111.02 1.0953 +IC H14A N *C14 H14B 1.0953 111.02 123.86 113.88 1.0740 +IC H14A N *C14 H14C 1.0953 111.02 -112.40 110.25 1.0937 +IC C12 N C15 H15A 1.5222 109.67 176.85 110.89 1.0820 +IC H15A N *C15 H15B 1.0820 110.89 121.48 111.48 1.0813 +IC H15A N *C15 H15C 1.0820 110.89 -118.74 109.66 1.0876 +IC C13 N C12 C11 1.4954 110.61 57.30 116.86 1.5411 +IC C11 N *C12 H12A 1.5411 116.86 -126.39 111.90 1.0787 +IC H12A N *C12 H12B 1.0787 111.90 -116.29 108.17 1.0973 +IC N C12 C11 O12 1.5222 116.86 127.40 108.21 1.4230 +IC O12 C12 *C11 H11A 1.4230 108.21 -123.09 113.27 1.1137 +IC H11A C12 *C11 H11B 1.1137 113.27 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5411 108.21 -68.07 118.42 1.5874 +IC C11 O12 P O11 1.4230 118.42 -166.83 104.01 1.5775 +IC O11 O12 *P O13 1.5775 104.01 117.90 108.15 1.4792 +IC O11 O12 *P O14 1.5775 104.01 -117.24 106.77 1.4822 +IC O12 P O11 C1 1.5874 104.01 178.48 118.38 1.4312 +IC P O11 C1 C2 1.5775 118.38 167.50 110.65 1.5505 +IC C2 O11 *C1 HA 1.5505 110.65 -119.12 111.48 1.1171 +IC HA O11 *C1 HB 1.1171 111.48 -120.88 110.00 1.1145 +IC O11 C1 C2 C3 1.4312 110.65 176.57 110.77 1.5573 +IC C3 C1 *C2 O21 1.5573 110.77 120.75 108.04 1.4418 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.77 -118.27 106.63 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5505 108.04 147.09 115.01 1.3179 +IC C2 O21 C21 C22 1.4418 115.01 179.22 108.80 1.5292 +IC C22 O21 *C21 O22 1.5292 108.80 -178.84 126.50 1.2187 +IC O21 C21 C22 C23 1.3179 108.80 -177.42 111.91 1.5450 +IC C23 C21 *C22 H2R 1.5450 111.91 -121.60 107.88 1.1091 +IC H2R C21 *C22 H2S 1.1091 107.88 -117.29 107.69 1.1091 +IC C1 C2 C3 O31 1.5505 110.77 174.77 112.55 1.4433 +IC O31 C2 *C3 HX 1.4433 112.55 -118.38 106.64 1.1128 +IC HX C2 *C3 HY 1.1128 106.64 -115.20 109.46 1.1144 +IC C2 C3 O31 C31 1.5573 112.55 88.07 115.30 1.3310 +IC C3 O31 C31 C32 1.4433 115.30 -172.19 108.29 1.5287 +IC C32 O31 *C31 O32 1.5287 108.29 -179.12 125.69 1.2167 +IC O31 C31 C32 C33 1.3310 108.29 -167.41 113.60 1.5449 +IC C33 C31 *C32 H2X 1.5449 113.60 -121.15 107.11 1.1105 +IC H2X C31 *C32 H2Y 1.1105 107.11 -116.79 108.04 1.1091 +IC C21 C22 C23 C24 1.5292 111.91 176.40 112.78 1.5339 +IC C24 C22 *C23 H3R 1.5339 112.78 -120.84 109.53 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.53 -117.51 109.55 1.1144 +IC C22 C23 C24 C25 1.5450 112.78 -179.42 112.02 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.02 -121.40 109.42 1.1129 +IC H4R C23 *C24 H4S 1.1129 109.42 -117.70 109.09 1.1132 +IC C23 C24 C25 C26 1.5339 112.02 177.20 113.15 1.5345 +IC C26 C24 *C25 H5R 1.5345 113.15 -121.11 108.85 1.1137 +IC H5R C24 *C25 H5S 1.1137 108.85 -117.08 109.10 1.1133 +IC C24 C25 C26 C27 1.5348 113.15 -179.00 112.16 1.5349 +IC C27 C25 *C26 H6R 1.5349 112.16 -121.50 109.37 1.1128 +IC H6R C25 *C26 H6S 1.1128 109.37 -117.60 108.99 1.1133 +IC C25 C26 C27 C28 1.5345 112.16 177.46 113.03 1.5345 +IC C28 C26 *C27 H7R 1.5345 113.03 -121.07 108.86 1.1136 +IC H7R C26 *C27 H7S 1.1136 108.86 -117.16 109.14 1.1132 +IC C26 C27 C28 C29 1.5349 113.03 -178.73 112.29 1.5348 +IC C29 C27 *C28 H8R 1.5348 112.29 -121.53 109.34 1.1129 +IC H8R C27 *C28 H8S 1.1129 109.34 -117.54 108.99 1.1133 +IC C27 C28 C29 C210 1.5345 112.29 177.77 112.89 1.5345 +IC C210 C28 *C29 H9R 1.5345 112.89 -121.06 108.89 1.1135 +IC H9R C28 *C29 H9S 1.1135 108.89 -117.23 109.16 1.1131 +IC C28 C29 C210 C211 1.5348 112.89 -178.85 112.40 1.5348 +IC C211 C29 *C210 H10R 1.5348 112.40 -121.51 109.29 1.1130 +IC H10R C29 *C210 H10S 1.1130 109.29 -117.49 109.00 1.1133 +IC C29 C210 C211 C212 1.5345 112.40 178.16 112.78 1.5345 +IC C212 C210 *C211 H11R 1.5345 112.78 -121.11 108.96 1.1135 +IC H11R C210 *C211 H11S 1.1135 108.96 -117.30 109.16 1.1131 +IC C210 C211 C212 C213 1.5348 112.78 -179.23 112.49 1.5347 +IC C213 C211 *C212 H12R 1.5347 112.49 -121.45 109.24 1.1130 +IC H12R C211 *C212 H12S 1.1130 109.24 -117.45 109.03 1.1133 +IC C211 C212 C213 C214 1.5345 112.49 178.82 112.71 1.5347 +IC C214 C212 *C213 H13R 1.5347 112.71 -121.19 109.01 1.1133 +IC H13R C212 *C213 H13S 1.1133 109.01 -117.33 109.14 1.1131 +IC C212 C213 C214 C215 1.5347 112.71 -179.59 112.61 1.5341 +IC C215 C213 *C214 H14R 1.5341 112.61 -121.38 109.18 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.18 -117.39 109.09 1.1133 +IC C213 C214 C215 C216 1.5347 112.61 179.60 113.33 1.5309 +IC C216 C214 *C215 H15R 1.5309 113.33 -121.65 108.72 1.1142 +IC H15R C214 *C215 H15S 1.1142 108.72 -116.62 108.76 1.1141 +IC C214 C215 C216 H16R 1.5341 113.33 -59.94 110.45 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.45 119.88 110.47 1.1113 +IC H16R C215 *C216 H16T 1.1113 110.45 -120.04 110.63 1.1112 +IC C31 C32 C33 C34 1.5287 113.60 179.68 111.12 1.5341 +IC C34 C32 *C33 H3X 1.5341 111.12 -120.80 109.72 1.1137 +IC H3X C32 *C33 H3Y 1.1137 109.72 -118.17 109.87 1.1142 +IC C32 C33 C34 C35 1.5449 111.12 -176.44 113.54 1.5344 +IC C35 C33 *C34 H4X 1.5344 113.54 -121.87 109.02 1.1135 +IC H4X C33 *C34 H4Y 1.1135 109.02 -117.04 108.81 1.1137 +IC C33 C34 C35 C36 1.5341 113.54 178.53 111.77 1.5349 +IC C36 C34 *C35 H5X 1.5349 111.77 -120.78 109.03 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.03 -117.69 109.50 1.1128 +IC C34 C35 C36 C37 1.5344 111.77 -176.24 113.37 1.5344 +IC C37 C35 *C36 H6X 1.5344 113.37 -122.00 109.13 1.1132 +IC H6X C35 *C36 H6Y 1.1132 109.13 -117.05 108.69 1.1137 +IC C35 C36 C37 C38 1.5349 113.37 177.81 111.98 1.5349 +IC C38 C36 *C37 H7X 1.5349 111.98 -120.73 108.96 1.1133 +IC H7X C36 *C37 H7Y 1.1133 108.96 -117.64 109.48 1.1127 +IC C36 C37 C38 C39 1.5344 111.98 -176.74 113.17 1.5344 +IC C39 C37 *C38 H8X 1.5344 113.17 -121.93 109.18 1.1131 +IC H8X C37 *C38 H8Y 1.1131 109.18 -117.13 108.74 1.1137 +IC C37 C38 C39 C310 1.5349 113.17 177.75 112.16 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.16 -120.81 108.99 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.99 -117.58 109.40 1.1128 +IC C38 C39 C310 C311 1.5344 112.16 -177.62 113.02 1.5345 +IC C311 C39 *C310 H10X 1.5345 113.02 -121.78 109.17 1.1131 +IC H10X C39 *C310 H10Y 1.1131 109.17 -117.21 108.84 1.1136 +IC C39 C310 C311 C312 1.5348 113.02 178.36 112.30 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.30 -120.94 109.01 1.1133 +IC H11X C310 *C311 H11Y 1.1133 109.01 -117.52 109.31 1.1129 +IC C310 C311 C312 C313 1.5345 112.30 -178.23 112.89 1.5345 +IC C313 C311 *C312 H12X 1.5345 112.89 -121.63 109.15 1.1131 +IC H12X C311 *C312 H12Y 1.1131 109.15 -117.28 108.93 1.1135 +IC C311 C312 C313 C314 1.5348 112.89 178.95 112.43 1.5350 +IC C314 C312 *C313 H13X 1.5350 112.43 -121.07 109.04 1.1133 +IC H13X C312 *C313 H13Y 1.1133 109.04 -117.48 109.23 1.1130 +IC C312 C313 C314 C315 1.5345 112.43 -178.86 112.82 1.5338 +IC C315 C313 *C314 H14X 1.5338 112.82 -121.48 109.14 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.14 -117.32 109.05 1.1133 +IC C313 C314 C315 C316 1.5350 112.82 179.62 113.25 1.5310 +IC C316 C314 *C315 H15X 1.5310 113.25 -121.59 108.75 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.75 -116.70 108.80 1.1140 +IC C314 C315 C316 H16X 1.5338 113.25 -59.74 110.45 1.1114 +IC H16X C315 *C316 H16Y 1.1114 110.45 119.85 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1114 110.45 -120.06 110.62 1.1112 + +end + +read para card append +* Drude polarizable FF parameters +* + +!All new model compound parameters should be included in the +!toppar_drude_master_protein stream file to avoid +!conflicts being generated + +BONDS +!atom type Kb b0 +!============================================ +! +!from master file, for lipids, these parameters are idenical to parameters in the master file based +!on the following atom type equivalencies +!CD32A to CD32AL +!CD2O3A to CD2O3B +!OD2C3A to OC2C3B +!OD30C to OD30CL +CD32AL CD32AL 222.50 1.530 ! alkanes, 3/92 +CD32AL CD32C 222.50 1.530 ! alkane +CD32AL CD33A 222.50 1.528 ! alkanes, 3/92 +CD32AL HDA2A 309.00 1.111 ! alkanes, 4/98 +CD32AL LPD 0.00 0.000 ! +CD32AL HDA2C 300.00 1.080 ! GLYP, NC4, qm, EH 2007 +CD31C CD32AL 222.50 1.528 ! 3/92 %PEML oct09 alterado em nov09 +CD32C CD2O3B 200.00 1.510 ! MAS, csd, EH 2007, ACEH +CD33C CD2O3B 133.00 1.510 ! ACEH, PEML +ND3P2A CD32AL 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P3A CD32AL 215.00 1.510 ! NC1, qm, EH 2007, ammonium cations +OD30B CD32AL 335.00 1.420 ! DMP, csd, EH/IV 2007 +OD31B CD32AL 396.00 1.425 ! ETOH, ethanol +OD30CL CD2O3B 150.00 1.330 ! MAS, csd, EH 2007, PEML 2009 *** changed FC to match vibr. spectra *** +OD30CL CD32C 340.00 1.440 ! MAS, csd, EH 2007 +OD30CL CD33D 340.00 1.440 ! MAS, csd, EH 2007 +OD30CL CD31C 340.00 1.440 ! MAS, csd, EH 2007 +OD30CL LPD 0.00 0.000 ! MAS +OD2C3B CD2O3B 730.00 1.200 ! MAS, csd, EH 2007, PEML 2009 *** b0 should be 1.220 based on MP2/6-31g*, confirm +OD2C3B LPD 0.00 0.000 ! MAS +!end of identical parameters + +ANGLES +!atom types Ktheta Theta0 Kub S0 +!================================================== +! +!from master file, for lipids, these parameters are idenical to parameters in the master file based +!on the following atom type equivalencies +!CD32A to CD32AL +!CD2O3A to CD2O3B +!OD2C3A to OC2C3B +!OD30C to OD30CL +OD2C3B CD2O3B OD30CL 90.00 123.00 160.00 2.2576 ! MAS, csd, EH 2007 +OD2C3B CD2O3B CD32C 70.00 126.00 20.00 2.4420 ! MAS, csd, EH 2007 +OD2C3B CD2O3B CD33C 70.00 126.00 20.00 2.4420 ! MAS, csd, EH 2007 +OD30CL CD2O3B CD32C 55.00 111.00 20.00 2.3260 ! MAS, csd, EH 2007 +OD30CL CD2O3B CD33C 55.00 111.00 20.00 2.3260 ! MAS, csd, EH 2007 +CD32AL CD31C CD32C 58.35 113.50 11.16 2.5610 ! GLYC, Lipid, alkane +CD32AL CD31C HDA1A 34.50 110.10 22.53 2.1790 ! GLYC, Lipid, alkane +ND3P2A CD31C CD32AL 67.70 113.00 ! CHOL, qm EH 2007, ammonium cations +OD30C CD31C CD32AL 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30CL CD31C HDA1A 60.00 109.50 ! EAS, Lipid, charmm27 +OD30CL CD31C CD32AL 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30CL CD31C CD32C 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30CL CD32C CD31C 40.00 110.00 +CD32AL CD32C HDA2A 26.50 110.10 22.53 2.1790 ! MBU, alkane +OD30CL CD32C HDA2A 60.00 109.50 ! MAS, charmm27 +OD30CL CD32C CD33A 40.00 110.00 ! EAS, EH 2007 +CD2O3B CD32C HDA2A 33.00 109.50 30.00 2.1630 ! MPO, charmm27 +CD2O3B CD32C CD33A 52.00 108.00 ! MPO, alkane +ND3P3A CD32C CD32AL 67.70 113.00 ! ETAM, qm EH 2007, ammonium cations +CD2O3B CD32C CD32AL 52.00 108.00 ! MBU, alkane +CD32AL CD32AL CD32AL 58.35 113.60 11.16 2.561 ! alkane, 3/92 +CD32AL CD32AL CD32C 58.35 113.60 11.16 2.5610 ! GLYC, Lipid, alkane +CD32AL CD32AL CD33A 58.00 115.00 8.00 2.561 ! alkane, 3/92 +CD32AL CD32AL HDA2A 26.50 110.10 22.53 2.179 ! alkane, 4/98 +CD32AL CD32AL HDA2C 26.50 110.10 22.53 2.179 ! LYS, alkane, 4/98 +CD31C CD32AL HDA2A 34.60 110.10 22.53 2.1790 ! MBU, alkane +CD32C CD32AL HDA2A 34.60 110.10 22.53 2.1790 ! MBU, alkane +CD32C CD32AL CD33A 58.00 115.00 8.00 2.5610 ! MBU, alkane +CD33A CD32AL HDA2A 34.60 110.10 22.53 2.179 ! alkane, 4/98 +CD33A CD32AL HDA2C 26.50 110.10 22.53 2.1790 ! NC5, alkane, ammonium cations +HDA2A CD32AL HDA2A 35.50 109.00 5.40 1.802 ! alkane, 3/92 +HDA2C CD32AL HDA2C 24.00 109.50 28.00 1.7670 ! NC4, charmm27 +ND3P2A CD32AL CD32AL 67.70 113.00 ! CHOL, qm EH 2007, ammonium cations +ND3P2A CD32AL CD33A 67.70 113.00 ! NC5, qm EH 2007, ammonium cations +ND3P2A CD32AL HDA2C 40.00 109.50 27.00 2.1300 ! NC4, charmm27, ammonium cations +ND3P3A CD32AL CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD32AL CD32AL 67.70 113.00 ! ETAM, qm EH 2007, ammonium cations +ND3P3A CD32AL CD33A 67.70 113.00 ! NH5, qm EH 2007, ammonium cations +ND3P3A CD32AL HDA2A 40.00 109.50 27.00 2.1300 ! NC1, charmm27 +ND3P3A CD32AL HDA2C 40.00 109.50 27.00 2.1300 ! NC1, charmm27 +OD30B CD32AL CD31C 75.70 110.10 ! DMP, Lipid, charmm27, need work** +OD30B CD32AL HDA2A 60.00 109.50 ! DMP, charmm27 +OD30B CD32AL CD32AL 75.70 110.10 ! DMP, Lipid, charmm27, need work** +CD32AL CD33A HDA3A 34.60 111.50 22.53 2.179 ! alkane, 4/98 +CD2O3B CD33C HDA3A 33.00 109.50 30.00 2.1630 ! MAS, charmm27 +OD30CL CD33D HDA3A 60.00 109.50 ! MAS, charmm27 +CD32AL ND3P2A CD33A 60.00 109.50 26.00 2.4660 ! NC4, qm, EH 2007, ammonium cations +CD32AL ND3P3A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +PD1A OD30B CD32AL 40.00 112.50 ! DMP, csd, EH/IV 2007**better molvib fit +CD2O3B OD30CL CD31C 15.00 100.00 10.00 2.0151 ! MAS, csd, EH 2007 PEML 2009 **gives CSD/vibr spectra +CD2O3B OD30CL CD32C 15.00 100.00 10.00 2.0151 ! MAS, csd, EH 2007 PEML 2009 **gives CSD/vibr spectra +CD2O3B OD30CL CD33D 15.00 100.00 10.00 2.0151 ! MAS, csd, EH 2007 PEML 2009 **gives CSD/vibr spectra +!end of identical parameters + +DIHEDRALS +!atom types Kchi n delta +!================================================= +! +!Please follow these conventions when fitting dihedral parameters +!1) use positive force constants in all cases (switch the phase...) +! (vary phase during fitting and keep force constants positive) +!2) maintain the phase at 0 or 180 if possiple. perform initial +! fitting with this contraint and, if necessary, only then +! vary the phases during fitting. note that if the phases +! are NOT 0 or 180 the parameters are NOT transferable across +! stereoisomers +!3) refit with only individual multiplicities of 1 through 6 +!4) maintain the number of significant figures used below +! +!HDP1A ND2A1 CD2O1A OD2C1A 2.000 2 180.00 ! comment +!from master file, for lipids, these parameters are idenical to parameters in the master file based +!on the following atom type equivalencies +!CD32A to CD32AL +!CD2O3A to CD2O3B +!OD2C3A to OC2C3B +!OD30C to OD30CL +OD30CL CD2O3B CD31C HDA1A 0.200 3 180.00 ! CT1, MAS +OD30CL CD2O3B CD33C HDA3A 0.000 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +OD30CL CD2O3B CD32C HDA2A 0.000 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +OD2C3B CD2O3B CD32C HDA2A 0.000 3 180.00 ! MAS, PEML 2009 +OD2C3B CD2O3B CD33C HDA3A 0.000 3 180.00 ! MAS, PEML 2009 +OD2C3B CD2O3B OD30CL CD33D 0.229 1 0.00 ! lipids +OD2C3B CD2O3B OD30CL CD33D 3.567 2 180.00 ! lipids +OD2C3B CD2O3B OD30CL CD33D 0.049 3 180.00 ! lipids +OD2C3B CD2O3B OD30CL CD33D 0.040 6 180.00 ! lipids +CD32C CD31C CD32AL HDA2A 0.190 3 0.00 ! GLYC, alkane +HDA1A CD31C CD32AL HDA2A 0.200 3 0.00 ! GLN, IBUT, isobutane, 3/92 +OD30CL CD31C CD32AL HDA2A 0.190 3 0.00 ! EAS/Lipid-H, charmm27 +CD32AL CD31C CD32C HDA2A 0.200 3 0.00 ! GLYC, alkane, lipid +HDA1A CD31C CD32C OD30CL 0.200 3 0.00 ! EAS/Lipid-H, charmm27 +OD30CL CD31C CD32C HDA2A 0.190 3 0.00 ! EAS/Lipid-H, charmm27 +CD32AL CD32AL CD32AL HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +CD32AL CD32AL CD32AL CD32C 0.083 2 0.00 ! Lipid, alkane +CD32AL CD32AL CD32AL CD32C 0.139 3 180.00 ! Lipid, alkane +CD32AL CD32AL CD32AL CD32C 0.078 4 0.00 ! Lipid, alkane +CD32AL CD32AL CD32AL CD32C 0.136 5 0.00 ! Lipid, alkane +CD32C CD32AL CD32AL HDA2A 0.160 3 0.00 ! Lipid-H, alkane, ester +CD33A CD32AL CD32AL HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +HDA2A CD32AL CD32AL HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +HDA2A CD32AL CD32AL HDA2C 0.190 3 0.00 ! LYS +ND3P2A CD32AL CD32AL HDA2A 0.190 3 0.00 ! CHOL, charmm27, ammonium cation +ND3P3A CD32AL CD32AL HDA2A 0.190 3 0.00 ! ETAM, charmm27, ammonium cation +ND3P3A CD32AL CD32AL OD30B 1.000 1 180.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32AL CD32AL OD30B 0.500 2 0.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32AL CD32AL OD30B 0.500 3 0.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +OD30B CD32AL CD32AL HDA2C 0.190 3 0.00 ! CHOL, charmm27, ammonium cation +CD32AL CD32AL CD33A HDA3A 0.140 3 0.00 ! BUTA, butane, 10/07, va +HDA2A CD32AL CD33A HDA3A 0.145 3 0.00 ! PROP, propane, butane, 10/07, va +CD32C CD32AL CD33A HDA3A 0.160 3 0.00 ! MBU, alkane, ester +CD32AL CD32AL CD32C CD2O3B 0.350 1 0.00 ! MBU, EH 2007, ester +CD32AL CD32AL CD32C HDA2A 0.190 3 0.00 ! alkane, ester +CD33A CD32AL CD32C HDA2A 0.190 3 0.00 ! alkane, ester +HDA2A CD32AL CD32C HDA2A 0.190 3 0.00 ! alkane, ester +HDA2A CD32AL CD32C CD2O3B 0.200 3 0.00 ! alkane, ester +OD30CL CD32C CD33A HDA3A 0.000 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +CD2O3B CD32C CD33A HDA3A 0.200 3 0.00 ! alkane, ester +CD32AL ND3P2A CD33A HDA3C 0.230 3 0.00 ! NC4, charmm27 , ammonium cation +CD33A ND3P2A CD32AL HDA2C 0.260 3 0.00 ! NC4, charmm27, ammonium cation +HDP1B ND3P3A CD32AL CD33A 0.320 3 0.00 ! ETAM, qm, EH 2007, ammonium cation +HDP1B ND3P3A CD32AL HDA2C 0.100 3 0.00 ! ETAM, charmm27, ammonium cation +CD2O3B OD30CL CD32C HDA2A 0.200 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +CD2O3B OD30CL CD33D HDA3A 0.200 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +CD33D OD30CL CD2O3B CD32C 2.500 2 180.00 ! CT1, MAS +!end of identical parameters +! +!start DPPC +CD32AL OD30B PD1A OD2C2B 0.000 1 0.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD2C2B 1.669 2 0.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD2C2B 0.634 3 180.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD2C2B 1.430 4 180.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD2C2B 1.037 5 0.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD2C2B 0.192 6 0.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD30B 3.797 1 180.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD30B 0.000 2 0.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD30B 0.477 3 180.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD30B 0.755 4 0.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD30B 1.712 5 0.00 ! MODIFIED BY JC +CD32AL OD30B PD1A OD30B 0.000 6 0.00 ! MODIFIED BY JC +CD33A OD30B PD1A OD2C2B 14.079 1 180.00 ! MODIFIED BY JC +CD33A OD30B PD1A OD2C2B 5.853 2 180.00 ! MODIFIED BY JC +CD33A OD30B PD1A OD2C2B 2.667 3 180.00 ! MODIFIED BY JC +CD33A OD30B PD1A OD2C2B 0.064 4 180.00 ! MODIFIED BY JC +CD33A OD30B PD1A OD2C2B 2.679 5 180.00 ! MODIFIED BY JC +CD33A OD30B PD1A OD2C2B 0.000 6 180.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33A 12.797 1 180.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33A 8.757 2 180.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33A 4.875 3 0.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33A 0.006 4 180.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33A 4.882 5 180.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33A 0.008 6 0.00 ! MODIFIED BY JC +CD33C OD30B PD1A OD2C2B 1.156 1 0.00 ! MODIFIED BY JC +CD33C OD30B PD1A OD2C2B 7.183 2 180.00 ! MODIFIED BY JC +CD33C OD30B PD1A OD2C2B 2.246 3 180.00 ! MODIFIED BY JC +CD33C OD30B PD1A OD2C2B 0.115 4 180.00 ! MODIFIED BY JC +CD33C OD30B PD1A OD2C2B 1.396 5 0.00 ! MODIFIED BY JC +CD33C OD30B PD1A OD2C2B 0.442 6 180.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33C 0.672 1 0.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33C 8.699 2 180.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33C 4.295 3 0.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33C 0.358 4 0.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33C 2.897 5 0.00 ! MODIFIED BY JC +OD30B PD1A OD30B CD33C 0.616 6 0.00 ! MODIFIED BY JC +CD32AL CD32AL OD30B PD1A 1.256 1 180.00 ! MODIFIED BY JC +CD32AL CD32AL OD30B PD1A 3.317 2 0.00 ! MODIFIED BY JC +CD32AL CD32AL OD30B PD1A 0.000 3 0.00 ! MODIFIED BY JC +CD32AL CD32AL OD30B PD1A 0.663 4 180.00 ! MODIFIED BY JC +CD32AL CD32AL OD30B PD1A 2.218 5 0.00 ! MODIFIED BY JC +CD32AL CD32AL OD30B PD1A 1.838 6 0.00 ! MODIFIED BY JC +PD1A OD30B CD32AL CD31C 4.563 1 180.00 ! MODIFIED BY JC +PD1A OD30B CD32AL CD31C 2.274 2 180.00 ! MODIFIED BY JC +PD1A OD30B CD32AL CD31C 0.017 3 180.00 ! MODIFIED BY JC +PD1A OD30B CD32AL CD31C 0.000 4 180.00 ! MODIFIED BY JC +PD1A OD30B CD32AL CD31C 0.615 5 180.00 ! MODIFIED BY JC +PD1A OD30B CD32AL CD31C 1.078 6 180.00 ! MODIFIED BY JC +HDA1A CD31C CD32AL OD30B 0.200 3 0.00 ! Lipid, charmm27 +OD30B CD32AL CD31C CD32C 5.284 1 180.00 ! MODIFIED BY JC +OD30B CD32AL CD31C CD32C 0.000 2 0.00 ! MODIFIED BY JC +OD30B CD32AL CD31C CD32C 0.000 3 180.00 ! MODIFIED BY JC +OD30B CD32AL CD31C CD32C 0.000 4 0.00 ! MODIFIED BY JC +OD30B CD32AL CD31C CD32C 0.000 5 0.00 ! MODIFIED BY JC +OD30B CD32AL CD31C CD32C 0.713 6 0.00 ! MODIFIED BY JC +OD30B CD32AL CD31C OD30CL 3.747 1 180.00 ! MODIFIED BY JC +OD30B CD32AL CD31C OD30CL 0.167 2 0.00 ! MODIFIED BY JC +OD30B CD32AL CD31C OD30CL 0.320 3 180.00 ! MODIFIED BY JC +OD30B CD32AL CD31C OD30CL 0.917 4 0.00 ! MODIFIED BY JC +OD30B CD32AL CD31C OD30CL 1.017 5 180.00 ! MODIFIED BY JC +OD30B CD32AL CD31C OD30CL 0.000 6 180.00 ! MODIFIED BY JC +PD1A OD30B CD32AL HDA2A 0.000 3 0.00 ! DMP, charmm27 +HDP1A OD30B CD32AL CD32AL 0.140 3 0.00 ! CHOL, charmm27, not necessary for lipid, ammonium cation +HDP1A OD30B CD32AL HDA2A 0.140 3 0.00 ! CHOL, charmm27, not necessary for lipid, ammonium cation +PD1A OD30B CD33A HDA3A 0.000 3 0.00 ! DMP, charmm27 +PD1A OD30B CD33C HDA3A 0.000 3 0.00 ! DMP, cmb, 06/09 +CD31C OD30CL CD2O3B OD2C3B 0.219 1 180.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B OD2C3B 3.424 2 180.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B OD2C3B 2.427 3 0.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B OD2C3B 0.224 4 0.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B OD2C3B 1.143 5 0.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B OD2C3B 0.587 6 180.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B CD32C 2.500 2 180.00 ! MAS, EH 2007 +CD31C OD30CL CD2O3B CD33C 0.485 1 180.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B CD33C 2.552 2 180.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B CD33C 2.803 3 0.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B CD33C 0.000 4 180.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B CD33C 1.377 5 0.00 ! MODIFIED BY JC +CD31C OD30CL CD2O3B CD33C 0.000 6 0.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B OD2C3B 0.017 1 180.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B OD2C3B 3.011 2 180.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B OD2C3B 0.486 3 180.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B OD2C3B 0.073 4 180.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B OD2C3B 0.823 5 180.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B OD2C3B 0.251 6 0.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B CD32C 2.500 2 180.00 ! MAS, EH 2007 +CD32C OD30CL CD2O3B CD33C 1.810 1 180.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B CD33C 2.929 2 180.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B CD33C 0.048 3 0.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B CD33C 0.000 4 0.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B CD33C 0.781 5 180.00 ! MODIFIED BY JC +CD32C OD30CL CD2O3B CD33C 0.000 6 0.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B OD2C3B 0.229 1 0.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B OD2C3B 3.567 2 180.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B OD2C3B 0.049 3 180.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B OD2C3B 0.040 6 180.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B CD31C 2.500 2 180.00 ! CT1, MAS +CD33C OD30CL CD2O3B CD32C 1.872 1 0.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B CD32C 3.045 2 180.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B CD32C 0.748 3 0.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B CD32C 0.217 4 0.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B CD32C 0.000 5 0.00 ! MODIFIED BY JC +CD33C OD30CL CD2O3B CD32C 0.048 6 180.00 ! MODIFIED BY JC +CD33C CD2O3B OD30CL CD33C 0.340 1 180.00 ! MODIFIED BY JC +CD33C CD2O3B OD30CL CD33C 3.517 2 180.00 ! MODIFIED BY JC +CD33C CD2O3B OD30CL CD33C 0.300 3 0.00 ! MODIFIED BY JC +CD33C CD2O3B OD30CL CD33C 0.226 4 180.00 ! MODIFIED BY JC +CD33C CD2O3B OD30CL CD33C 0.162 5 0.00 ! MODIFIED BY JC +CD33C CD2O3B OD30CL CD33C 0.000 6 0.00 ! MODIFIED BY JC +! Lipid-b1 +!from toppar_drude_master_sep09f_rimp2_vtz.str,newtorfit +CD33A CD31C OD30CL CD2O3B 2.133 1 180.00 ! MODIFIED BY JC +CD33A CD31C OD30CL CD2O3B 0.022 2 0.00 ! MODIFIED BY JC +CD33A CD31C OD30CL CD2O3B 0.090 3 0.00 ! MODIFIED BY JC +CD33A CD31C OD30CL CD2O3B 0.000 4 0.00 ! MODIFIED BY JC +CD33A CD31C OD30CL CD2O3B 0.177 5 0.00 ! MODIFIED BY JC +CD33A CD31C OD30CL CD2O3B 0.000 6 0.00 ! MODIFIED BY JC +CD32AL CD31C OD30CL CD2O3B 0.921 1 180.00 ! MODIFIED BY JC +CD32AL CD31C OD30CL CD2O3B 0.911 2 0.00 ! MODIFIED BY JC +CD32AL CD31C OD30CL CD2O3B 0.000 3 0.00 ! MODIFIED BY JC +CD32AL CD31C OD30CL CD2O3B 0.000 4 0.00 ! MODIFIED BY JC +CD32AL CD31C OD30CL CD2O3B 0.000 5 180.00 ! MODIFIED BY JC +CD32AL CD31C OD30CL CD2O3B 0.701 6 180.00 ! MODIFIED BY JC +CD32C CD31C OD30CL CD2O3B 1.029 1 180.00 ! MODIFIED BY JC +CD32C CD31C OD30CL CD2O3B 0.676 2 0.00 ! MODIFIED BY JC +CD32C CD31C OD30CL CD2O3B 0.000 3 0.00 ! MODIFIED BY JC +CD32C CD31C OD30CL CD2O3B 0.251 4 180.00 ! MODIFIED BY JC +CD32C CD31C OD30CL CD2O3B 0.249 5 0.00 ! MODIFIED BY JC +CD32C CD31C OD30CL CD2O3B 0.000 6 180.00 ! MODIFIED BY JC +CD2O3B OD30CL CD31C HDA1A 0.200 3 180.00 ! MAS, PEML 2009 +CD2O3B OD30CL CD31C HDA2A 0.200 3 180.00 ! IPRA from MAS, PEML 2009 +! Lipid-g1 +!from toppar_drude_master_sep09f_rimp2_vtz.str,newtorfit +CD31C CD32C OD30CL CD2O3B 0.000 1 0.00 ! MODIFIED BY JC +CD31C CD32C OD30CL CD2O3B 1.344 2 0.00 ! MODIFIED BY JC +CD31C CD32C OD30CL CD2O3B 0.293 3 180.00 ! MODIFIED BY JC +CD31C CD32C OD30CL CD2O3B 0.000 4 180.00 ! MODIFIED BY JC +CD31C CD32C OD30CL CD2O3B 0.414 5 0.00 ! MODIFIED BY JC +CD31C CD32C OD30CL CD2O3B 0.000 6 180.00 ! MODIFIED BY JC +!!!! Lipid-t3/t4 +OD30CL CD31C CD32C OD30CL 1.973 1 180.00 ! MODIFIED BY JC +OD30CL CD31C CD32C OD30CL 0.216 2 0.00 ! MODIFIED BY JC +OD30CL CD31C CD32C OD30CL 2.668 3 180.00 ! MODIFIED BY JC +OD30CL CD31C CD32C OD30CL 0.680 4 180.00 ! MODIFIED BY JC +OD30CL CD31C CD32C OD30CL 0.169 5 180.00 ! MODIFIED BY JC +OD30CL CD31C CD32C OD30CL 0.321 6 180.00 ! MODIFIED BY JC +CD33A CD31C CD32C OD30CL 1.154 1 180.00 ! MODIFIED BY JC +CD33A CD31C CD32C OD30CL 1.522 2 180.00 ! MODIFIED BY JC +CD33A CD31C CD32C OD30CL 1.886 3 0.00 ! MODIFIED BY JC +CD33A CD31C CD32C OD30CL 0.127 4 0.00 ! MODIFIED BY JC +CD33A CD31C CD32C OD30CL 0.000 5 0.00 ! MODIFIED BY JC +CD33A CD31C CD32C OD30CL 0.000 6 180.00 ! MODIFIED BY JC +CD32AL CD31C CD32C OD30CL 0.000 1 0.00 ! MODIFIED BY JC +CD32AL CD31C CD32C OD30CL 0.000 2 180.00 ! MODIFIED BY JC +CD32AL CD31C CD32C OD30CL 2.404 3 0.00 ! MODIFIED BY JC +CD32AL CD31C CD32C OD30CL 0.256 4 0.00 ! MODIFIED BY JC +CD32AL CD31C CD32C OD30CL 0.000 5 0.00 ! MODIFIED BY JC +CD32AL CD31C CD32C OD30CL 0.026 6 0.00 ! MODIFIED BY JC +!end DPPC + +!new-dihe-terms 2013-oct-11 Hui +CD32AL CD32AL ND3P2A CD33A 0.000 6 180.00 ! JC-v2-1, PC headgroup +CD32AL CD32AL ND3P2A CD33A 0.333 3 0.00 ! JC-v2-1 +CD32AL CD32AL ND3P2A CD33A 0.462 5 180.00 ! JC-v2-1 +CD32AL CD32AL ND3P2A CD33A 1.053 2 180.00 ! JC-v2-1 +CD32AL CD32AL ND3P2A CD33A 3.568 4 0.00 ! JC-v2-1 +CD32AL CD32AL ND3P2A CD33A 3.965 1 180.00 ! JC-v2-1 +HDP1B ND3P3A CD32AL CD32AL 0.000 2 0.00 ! JC-v2-2, PE headgroup +HDP1B ND3P3A CD32AL CD32AL 0.047 6 0.00 ! JC-v2-2 +HDP1B ND3P3A CD32AL CD32AL 0.276 3 0.00 ! JC-v2-2 +HDP1B ND3P3A CD32AL CD32AL 0.305 1 180.00 ! JC-v2-2 +HDP1B ND3P3A CD32AL CD32AL 0.934 4 180.00 ! JC-v2-2 +HDP1B ND3P3A CD32AL CD32AL 1.670 5 0.00 ! JC-v2-2 +CD33A CD32C OD30CL CD2O3B 0.106 5 180.00 ! JC-v2-3: EAS, ester to glycerol +CD33A CD32C OD30CL CD2O3B 0.119 6 180.00 ! JC-v2-3 +CD33A CD32C OD30CL CD2O3B 0.231 2 0.00 ! JC-v2-3 +CD33A CD32C OD30CL CD2O3B 0.278 4 0.00 ! JC-v2-3 +CD33A CD32C OD30CL CD2O3B 0.425 3 0.00 ! JC-v2-3 +CD33A CD32C OD30CL CD2O3B 1.138 1 180.00 ! JC-v2-3 +CD32AL CD32C CD2O3B OD2C3B 0.031 2 0.00 ! JC-v2-9: ester to aliphatic tail +CD32AL CD32C CD2O3B OD2C3B 0.387 1 180.00 ! JC-v2-9 +CD32AL CD32C CD2O3B OD2C3B 0.839 6 0.00 ! JC-v2-9 +CD32AL CD32C CD2O3B OD2C3B 0.916 4 0.00 ! JC-v2-9 +CD32AL CD32C CD2O3B OD2C3B 1.748 3 0.00 ! JC-v2-9 +CD32AL CD32C CD2O3B OD2C3B 3.501 5 180.00 ! JC-v2-9 +CD33A CD32C CD2O3B OD2C3B 0.000 4 0.00 ! JC-v2-10: ester to aliphatic tail, MPRO +CD33A CD32C CD2O3B OD2C3B 0.000 6 0.00 ! JC-v2-10 +CD33A CD32C CD2O3B OD2C3B 0.142 1 180.00 ! JC-v2-10 +CD33A CD32C CD2O3B OD2C3B 0.271 2 180.00 ! JC-v2-10 +CD33A CD32C CD2O3B OD2C3B 1.017 3 0.00 ! JC-v2-10 +CD33A CD32C CD2O3B OD2C3B 2.891 5 180.00 ! JC-v2-10 +OD30CL CD2O3B CD32C CD32AL 0.218 1 180.00 ! JC-v2-11: ester to aliphatic tail +OD30CL CD2O3B CD32C CD32AL 0.303 2 180.00 ! JC-v2-11 +OD30CL CD2O3B CD32C CD32AL 0.720 6 180.00 ! JC-v2-11 +OD30CL CD2O3B CD32C CD32AL 0.983 4 180.00 ! JC-v2-11 +OD30CL CD2O3B CD32C CD32AL 1.647 3 0.00 ! JC-v2-11 +OD30CL CD2O3B CD32C CD32AL 3.430 5 180.00 ! JC-v2-11 +OD30CL CD2O3B CD32C CD33A 0.000 4 0.00 ! JC-v2-12: ester to aliphatic tail, MPRO +OD30CL CD2O3B CD32C CD33A 0.012 6 180.00 ! JC-v2-12 +OD30CL CD2O3B CD32C CD33A 0.086 1 180.00 ! JC-v2-12 +OD30CL CD2O3B CD32C CD33A 0.154 2 180.00 ! JC-v2-12 +OD30CL CD2O3B CD32C CD33A 1.008 3 0.00 ! JC-v2-12 +OD30CL CD2O3B CD32C CD33A 2.828 5 180.00 ! JC-v2-12 +ND3P2A CD32AL CD32AL OD30B 0.000 1 0.00 ! JC-v2-16: PC +ND3P2A CD32AL CD32AL OD30B 0.000 3 180.00 ! JC-v2-16 +ND3P2A CD32AL CD32AL OD30B 0.000 4 0.00 ! JC-v2-16 +ND3P2A CD32AL CD32AL OD30B 0.031 5 0.00 ! JC-v2-16 +ND3P2A CD32AL CD32AL OD30B 0.646 6 0.00 ! JC-v2-16 +ND3P2A CD32AL CD32AL OD30B 3.887 2 0.00 ! JC-v2-16 +CD33A CD32AL CD32C CD2O3B 0.000 1 180.00 ! JC-v2-21: MBU +CD33A CD32AL CD32C CD2O3B 0.071 2 0.00 ! JC-v2-21 +CD33A CD32AL CD32C CD2O3B 0.451 3 180.00 ! JC-v2-21 +CD33A CD32AL CD32C CD2O3B 0.000 4 180.00 ! JC-v2-21 +CD33A CD32AL CD32C CD2O3B 0.025 5 0.00 ! JC-v2-21 +CD33A CD32AL CD32C CD2O3B 0.064 6 180.00 ! JC-v2-21 +!aliphatic chain +CD33A CD32AL CD32AL CD32AL 0.093 1 0.00 ! JC-v2-20, aliphatic chain, identical to master file +CD33A CD32AL CD32AL CD32AL 0.143 2 0.00 ! JC-v2-20 +CD33A CD32AL CD32AL CD32AL 0.055 4 0.00 ! JC-v2-20 +CD33A CD32AL CD32AL CD32AL 0.102 5 0.00 ! JC-v2-20 +!only 2,3 fold terms differ from master file +CD32AL CD32AL CD32AL CD32AL 0.073 1 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 JC-v2-22, aliphatic chain +CD32AL CD32AL CD32AL CD32AL 0.104 2 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 JC-v2-22 +CD32AL CD32AL CD32AL CD32AL 0.058 3 180.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 JC-v2-22 +CD32AL CD32AL CD32AL CD32AL 0.098 4 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 JC-v2-22 +CD32AL CD32AL CD32AL CD32AL 0.046 5 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 JC-v2-22 +!end new-dihe terms + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +OD2C3B CD33A OD30CL CD2O3B 85.000 0 0.00 ! MAS +OD2C3B CD32AL OD30CL CD2O3B 85.000 0 0.00 ! MAS +OD2C3B CD33C OD30CL CD2O3B 85.000 0 0.00 ! MAS +OD2C3B CD33D OD30CL CD2O3B 85.000 0 0.00 ! MAS +OD2C3B CD32C OD30CL CD2O3B 85.000 0 0.00 ! MAS +OD2C3B CD31C OD30CL CD2O3B 85.000 0 0.00 ! MAS, CT1 + +NONBONDED nbxmod 5 atom vatom cdiel vdistance switch vswitch - +cutnb 16.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +NBFIX + +end diff --git a/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_master_protein_2013c.str b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_master_protein_2013c.str new file mode 100644 index 00000000..26e7017d --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_master_protein_2013c.str @@ -0,0 +1,7183 @@ +* $Id: toppar_drude_master_protein.str 33 2015-08-04 14:44:59Z alex $ +* DRUDE master topology and parameter stream file +* Includes water, ions and 2013 protein FF release +* October 2013 +* Ions updated, June 2014 +* + +ioformat extended + +!This file must be streamed prior to additional Drude FF toppar stream files +!and it includes parameters for the model compounds (toppar_drude_model*.str) + +!references +! +!Proteins +!Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and +!MacKerell, A.D., Jr., “Polarizable Force Field for Peptides and +!Proteins based on the Classical Drude Oscillator,” Journal of +!Chemical Theory and Computation, 9: 5430–5449, 2013 DOI: +!10.1021/ct400781b, NIHMS53671 +! +!water +!SWM4-NDP, negative Drude (this will be the default model): Lamoureux, +!G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D., +!Jr., A polarizable model of water for molecular dynamics simulations +!of biomolecules, Chemical Physics Letters, 2006, 418: 245-249. +! +!SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander +!D. MacKerell, Jr. "Six-site Polarizable Model of Water Based on the +!Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508, +!2013 + +!atomic ions +!Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I., +!Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating +!Monovalent and Divalent Ions in Aqueous Solution Using a Drude +!Polarizable Force Field, “Journal of Chemical Theory and Computation, +!6: 774–786, 2010 +! +!Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B., +!“Simulation study of ion pairing in concentrated aqueous salt +!solutions with a polarizable force field,” Faraday Discussions, 160, +!135–149, 2013, PMC3695446 + + +! note use of D for second character to indicate Drude +! polarizable FF (be careful of Cadmium: use CDM) + +! Parameter labeling after ! +! RESName, generic compound name of model compound followed by additional comments +! for example ! BENZ, benzene, based on crystal survey data + +!Formatting information +!RTF section: please use the following format for future residues, including the spacing +!(and please clean a few up of the residues not in this format if you so desire....) + +!RESI ALA 0.000 +!ATOM N ND2A2 -0.427 ALPHA -1.056 THOLE 0.711 +!BOND A1 A2 A3 A4 A5 A6 A7 A8 +!IMPR A1 A2 A3 A4 +!CMAP A1 A2 A3 A4 A1 A2 A3 A4 +!LONEPAIR relative A1 A2 A3 A4 distance 0.30 angle 91.00 dihe 180.00 +!ANISOTROPY A1 A2 A3 A4 A11 0.6968 A22 1.2194 +!IC A1 A2 A3 A4 1.3474 124.31 180.00 114.26 0.9979 + +!parameter section +!bond +!CD32E OD30A 360.00 1.415 ! comment +!angles +!HDA1A CD31A CD31A 34.50 110.10 ! comment +!HDA1A CD31A CD31A 34.50 110.10 22.53 2.1790 ! comment +!dihedrals +!CD2O1A ND2A2 CD31C CD2O2A 0.000 3 180.00 ! comment +!impropers +!CD2O1A CD31A ND2A2 OD2C1A 120.000 0 0.00 ! comment +!nonbond (LJ) +!HDW 0.0 -0.0000 0.0000 ! comment +!nbfix +!CD30A ODW -0.00500 4.04699 ! comment + +!ioformat extended + +read rtf card !append +* Topology for drude water, ions and proteins +* +38 + +MASS 1 HDP1A 1.00800 H ! polar H, general +MASS 2 HDP1B 1.00800 H ! polar H, ammonium cations +MASS 3 HDA1A 1.00800 H ! aliphatic, H, methyl (-CH), general +MASS 4 HDA1C 1.00800 H ! aliphatic, H, methyl (-CH), special case for ammonium cations +MASS 5 HDA1R5 1.00800 H ! aliphatic, H, methyl (-CH), 5-membered ring +MASS 6 HDA2A 1.00800 H ! aliphatic, H, methyl (-CH2), general +MASS 7 HDA2C 1.00800 H ! aliphatic, H, methyl (-CH2), special case for ammonium cations +MASS 8 HDA2E 1.00800 H ! aliphatic, H, methyl (-CH2), ethers +MASS 9 HDA2R5 1.00800 H ! aliphatic, H, methyl (-CH2), 5-membered ring +MASS 10 HDA3A 1.00800 H ! aliphatic, H, methyl (-CH3), general +MASS 11 HDA3B 1.00800 H ! aliphatic, H, methyl (-CH3), special case for methanol +MASS 12 HDA3C 1.00800 H ! aliphatic, H, methyl (-CH3), special case for ammonium cations +MASS 13 HDR5A 1.00800 H ! 5-membered ring, HG and HD2 in imidazole +MASS 14 HDR5B 1.00800 H ! 5-membered ring, HE1 in imidazole +MASS 15 HDR5C 1.00800 H ! 5-membered ring, H on carbon adjacent to N in pyrrole +MASS 16 HDR5D 1.00800 H ! 5-membered ring, HG and HD2 in imidazolium +MASS 17 HDR5E 1.00800 H ! 5-membered ring, HE1 in imidazolium +MASS 18 HDR6A 1.00800 H ! aromatic H, 6-membered ring, general +MASS 19 HDR6B 1.00800 H ! aromatic H, 6-membered ring, adjacent to N (pyridine) +MASS 20 HDR6C 1.00800 H ! aromatic H, 6-membered ring, between 2 N's (pyrimidine) + +MASS 41 CD2O1A 12.01100 C ! carbonyl C, neutral (amide) +MASS 42 CD2O2A 12.01100 C ! carboxylate C, anionic +MASS 43 CD2O3A 12.01100 C ! carboxylate C, neutral (esters, acids) +MASS 44 CD2O3B 12.01100 C ! ester carbonyl C, for lipids +MASS 45 CD2R5A 12.01100 C ! 5-membered ring, CG and CD2 in imidazole +MASS 46 CD2R5B 12.01100 C ! 5-membered ring, CE1 in imidazole +MASS 47 CD2R5C 12.01100 C ! 5-membered ring, pyrole, adjacent to N +MASS 48 CD2R5D 12.01100 C ! 5-membered ring, CG and CD2 in imidizolium +MASS 49 CD2R5E 12.01100 C ! 5-membered ring, CE1 in imidizolium +MASS 50 CD2R6A 12.01100 C ! aromatic C, 6-membered ring +MASS 51 CD2R6B 12.01100 C ! aromatic C, 6-membered ring, adjacent to N (pyridine) +MASS 52 CD2R6C 12.01100 C ! aromatic C, 6-membered ring, between 2 heteroatoms (pyrimidine) +MASS 53 CD2R6D 12.01100 C ! aromatic C, 6-membered ring, bridging far from N (indole) +MASS 54 CD2R6F 12.01100 C ! aromatic C, 6-membered ring, bridging adjacent to N7 (purine) +MASS 55 CD2R6H 12.01100 C ! aromatic C, 6-membered ring, cytosine cmb 01/09 +MASS 60 CD2N1A 12.01100 C ! guanidinium C (EH) +MASS 61 CD30A 12.01100 C ! aliphatic sp3 C, 0 hydrogens +MASS 62 CD31A 12.01100 C ! aliphatic sp3 C, 1 hydrogen +MASS 63 CD31C 12.01100 C ! aliphatic sp3 C, 1 hydrogen, special case for carbons adjacent to esters/amides +MASS 64 CD31FA 12.01100 C ! aliphatic sp3 C, 1 hydrogen, furanoses, anomeric C1 +MASS 65 CD31FB 12.01100 C ! aliphatic sp3 C, 1 hydrogen, furanoses, C2,C3 +MASS 66 CD31FC 12.01100 C ! aliphatic sp3 C, 1 hydrogen, furanoses, C4 +MASS 67 CD31G 12.01100 C ! aliphatic sp3 C, 1 hydrogen, glycerol, xhe +MASS 68 CD315A 12.01100 C ! aliphatic sp3 C, 1 hydrogen, ether, 5-memberd ring, CPNM +MASS 69 CD315B 12.01100 C ! aliphatic sp3 C, 1 hydrogen, ether, 5-memberd ring, TF2M +MASS 70 CD316A 12.01100 C ! aliphatic sp3 C, 1 hydrogens, 6-membered ring +MASS 71 CD32A 12.01100 C ! aliphatic sp3 C, 2 hydrogens +MASS 72 CD32AL 12.01100 C ! aliphatic sp3 C, 2 hydrogens, for lipids +MASS 73 CD32B 12.01100 C ! added for GLU, from CD32A +MASS 74 CD32C 12.01100 C ! aliphatic sp3 C, 2 hydrogens, special case for carbons adjacent to esters/amides (see +MASS 75 CD32E 12.01100 C ! aliphatic sp3 C, 2 hydrogens, ether, for CH2 adjacent to O in linear ethers +MASS 76 CD32F 12.01100 C ! aliphatic sp3 C, 2 hydrogens, ethylene glycol, glycerol, xhe +MASS 77 CD325A 12.01100 C ! aliphatic sp3 C, 2 hydrogens, 5-membered ring +MASS 78 CD325B 12.01100 C ! aliphatic sp3 C, 2 hydrogens, ether, 5-membered ring, THF +MASS 79 CD326A 12.01100 C ! aliphatic sp3 C, 2 hydrogens, 6-membered ring +MASS 80 CD326B 12.01100 C ! aliphatic sp3 C, 2 hydrogens, ether, 6-membered ring, THP +MASS 81 CD33A 12.01100 C ! aliphatic sp3 C, 3 hydrogens +MASS 82 CD33B 12.01100 C ! aliphatic sp3 C, 3 hydrogens: special case for methanol +MASS 83 CD33C 12.01100 C ! aliphatic sp3 C, 3 hydrogens: special case for carbons adjacent to esters/amides (see +MASS 84 CD33D 12.01100 C ! aliphatic sp3 C, 3 hydrogens: special methyl C for esters (MAS), neutral acids (ACEH) +MASS 85 CD33E 12.01100 C ! aliphatic sp3 C, 3 hydrogens: special case for CH3 adjacent to a O in linear ethers +MASS 86 CD31HA 12.01100 C ! anomeric carbon, Hexopyranose, dpatel +MASS 87 CD31HB 12.01100 C ! aliphatic sp3 C, 1 hydrogens, 6-membered ring, Hexopyranose +MASS 88 CD31HC 12.01100 C ! aliphatic sp3 C, 1 hydrogens, ether, 6-membered ring, Hexopyranose 1 + +MASS 131 ND2A1 14.00700 N ! amide, primary (ACEM) +MASS 132 ND2A2 14.00700 N ! amide, secondary (NMA, peptide bond) +MASS 133 ND2A3 14.00700 N ! amide, tertiary (DMA) +MASS 134 ND2B1 14.00700 N ! amine, primary (NA bases) +MASS 135 ND2R5A 14.00700 N ! neutral his protonated ring nitrogen +MASS 136 ND2R5B 14.00700 N ! neutral his unprotonated ring nitrogen +MASS 137 ND2R5C 14.00700 N ! positive his protonated ring nitrogen +MASS 138 ND2R5D 14.00700 N ! aromatic N, 5-membered, purine bases +MASS 139 ND2R5E 14.00700 N ! neutral unprotonated ring nitrogen from Gua/Ade +MASS 140 ND2R5F 14.00700 N ! N1 in THY, alexey +MASS 141 ND2R6A 14.00700 N ! aromatic N, 6-membered ring (pyridine) +MASS 142 ND2R6B 14.00700 N ! aromatic N, 6-membered ring (pyrimidine, N-C-N connectivity) +MASS 143 ND2R6C 14.00700 N ! aromatic N, 6-membered ring: protonated: NA bases +MASS 144 ND2R6D 14.00700 N ! N9 in GUA, alexey +MASS 145 ND2P1A 14.00700 N ! protonated sp2 nitrogen: guanidinium (EH) +MASS 146 ND3P2A 14.00700 N ! protonated sp3 nitrogen, 0, 1 or 3 hydrogens +MASS 147 ND3P3A 14.00700 N ! protonated sp3 nitrogen, 3 or 4 hydrogens (includes ammonia) +MASS 148 ND3A3 14.00700 N ! imino nitrogen as in proline + +MASS 171 OD2C1A 15.99940 O ! carbonyl O, neutral (acetone, NMA, acetamide) +MASS 172 OD2C1B 15.99940 O ! carbonyl O, neutral (NA bases) +MASS 173 OD2C2A 15.99940 O ! carboxylate O, anionic (acetate) +MASS 174 OD2C2B 15.99940 O ! carboxylate O, anionic (phosphate), lipids +MASS 175 OD2C2C 15.99940 O ! carboxylate O, anionic (phosphate), nucleic acids +MASS 176 OD2C3A 15.99940 O ! carboxylate O, neutral (esters) +MASS 177 OD2C3B 15.99940 O ! carbonyl O for esters, for lipids +MASS 178 OD30A 15.99940 O ! ether oxygen +MASS 179 OD30B 15.99940 O ! ester oxygen (phosphate), lipid +MASS 180 OD30BN 15.99940 O ! ester oxygen (phosphate), nucleic acid +MASS 181 OD30C 15.99940 O ! ester oxygen (esters) +MASS 182 OD30CL 15.99940 O ! ester oxygen (esters), for lipids +MASS 183 OD30D 15.99900 O ! hydroxyl oxygen in acids +MASS 184 OD305A 15.99940 O ! ether oxygen, 5-membered ring (tetrahydrofuran) +MASS 185 OD306A 15.99940 O ! ether oxygen, 6-membered ring (tetrahydropyran) +MASS 186 OD31A 15.99900 O ! hydroxyl oxygen +MASS 187 OD31B 15.99900 O ! hydroxyl oxygen, special case for long, primary alcohols +MASS 188 OD31C 15.99900 O ! hydroxyl oxygen, phenol +MASS 189 OD31E 15.99900 O ! hydroxyl oxygen, ethylene glycol, glycerol, xhe +MASS 190 OD31F 15.99900 O ! hydroxyl oxygen, Carbohydrates, dpatel +! phosphorous +MASS 211 PD1A 30.974000 P ! phosphorus, (DMP) +MASS 212 PD1AN 30.974000 P ! phosphorus, (DMP), nucleic acids +! Rare gases, dummy atom, lone pair +MASS 221 DUM 0.00000 H ! dummy atom +MASS 222 XED 4.00260 He ! helium +MASS 223 NED 20.17970 Ne ! neon +MASS 224 DRUD 0.00000 H ! drude particle +! Sulfurs +MASS 226 SD31A 32.06000 S ! MESH +MASS 227 SD31B 32.06000 S ! ETSH +MASS 228 SD30A 32.06000 S ! EMS, DMS +MASS 229 SD30B 32.06000 S ! DMDS +! Lone pairs +MASS 231 LPD 0.00000 H ! general lone pair without LJ parameters, NBFIX or NBTHOLE +MASS 232 LPDW 0.00000 H ! lone pair for water: Note overlap of SWM4 and SWM6 LPs +MASS 233 LPDO1 0.00000 H ! lone pair, amide carbonyl oxygen, based on NMA +MASS 234 LPDNA1 0.00000 H ! lone pair, general nucleic acid +! SWM4 and SWM6 polarizable water models +MASS 241 ODW 15.99940 O ! water oxygen, SWM4 +MASS 242 ODW6 15.99940 O ! water oxygen, SWM6 +MASS 243 HDW 1.00800 H ! water hydrogen +MASS 244 DOH2 0.00000 H ! water Drude +!! Monovalent ions +MASS 251 LID 6.94120 Li ! Lithium +MASS 252 POTD 39.10200 K ! Potassium +MASS 253 SODD 23.00000 Na ! Sodium +MASS 254 RBD 85.46783 Rb ! Rubidium +MASS 255 CSD 132.90545 Cs ! Caesium +MASS 256 FAD 18.99840 F ! Fluoride +MASS 257 CLAD 35.45320 CL ! Chloride +MASS 258 BRAD 79.90410 Br ! Bromide +MASS 259 IAD 126.90447 I ! Iodide +! Divalent ions +MASS 271 MAGD 24.30000 Mg ! Magnesium +MASS 272 CALD 40.08000 CA ! calcium +MASS 273 SRD 87.62000 Sr ! Strontium +MASS 274 BAD 137.33000 Ba ! Barium +MASS 275 ZND 65.38400 Zn ! Zinc + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA + +!DEFA FIRS NTER LAST CTER +!reset default patches +DEFA FIRS NONE LAST NONE +AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE + +! SWM4-NDP water +RESI SWM4 0.000 +GROUP +ATOM OH2 ODW 0.00000 TYPE DOH2 ALPHA -0.97825258 THOLE 1.3 +ATOM OM LPDW -1.11466 +ATOM H1 HDW 0.55733 +ATOM H2 HDW 0.55733 +BOND OH2 H1 +BOND OH2 H2 +BOND OH2 OM +BOND H1 H2 ! for SHAKE +ANGLE H1 OH2 H2 +ACCEPTOR OH2 +LONEPAIR bisector OM OH2 H1 H2 distance 0.24034492 angle 0.0 dihe 0.0 +IC H1 OH2 H2 H1 0.9572 104.52 0.00 37.74 1.5139 +IC H1 OM *OH2 H2 0.9572 52.26 180.00 52.26 0.9572 +IC H2 H1 OH2 OM 1.5139 37.74 0.01 52.26 0.24034492 +PATCH FIRST NONE LAST NONE + +! SWM6-NDP water +RESI SWM6 0.0000 ! +GROUP ! OL1 H1 +ATOM OH2 ODW6 0.2880 TYPE DOH2 ALPHA -0.88 THOLE 1.3 ! \ / +ATOM OL1 LPDW -0.1080 ! DOH2~OH2-OM +ATOM OL2 LPDW -0.1080 ! / \ +ATOM H1 HDW 0.5307 ! OL2 H2 +ATOM H2 HDW 0.5307 ! +ATOM OM LPDW -1.1334 ! +BOND OH2 H1 +BOND OH2 H2 +BOND OH2 OL1 +BOND OH2 OL2 +BOND OH2 OM +BOND H1 H2 ! for SHAKE +ANGLE H1 OH2 H2 +ACCEPTOR OH2 +LONEPAIR bisector OL1 OH2 H1 H2 distance 0.315 angle 129.451 dihe 90.0 +LONEPAIR bisector OL2 OH2 H1 H2 distance 0.315 angle 129.451 dihe 270.0 +LONEPAIR bisector OM OH2 H1 H2 distance 0.247 angle 0.000 dihe 0.0 +IC H1 OH2 H2 H1 0.9572 104.520 0.000 37.740 1.5139 +IC H2 H1 OH2 OL1 1.5139 37.740 123.054 112.888 0.3150 +IC H1 H2 OH2 OL2 1.5139 37.740 123.054 112.888 0.3150 +IC H1 OL1 *OH2 H2 0.9572 112.888 118.270 112.888 0.9572 +IC H2 OL2 *OH2 H1 0.9572 112.888 118.270 112.888 0.9572 +IC H2 H1 OH2 OM 1.5139 37.740 0.000 52.260 0.2470 +PATCH FIRST NONE LAST NONE + +!! Monovalent Ions + +RESI LI 1.000 ! Lithium Ion +GROUP +ATOM LI LID 1.000 ALPHA -0.032 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.000 ! Potassium Ion +GROUP +ATOM POT POTD 1.000 ALPHA -0.830 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.000 ! Sodium Ion +GROUP +ATOM SOD SODD 1.000 ALPHA -0.157 +PATCHING FIRST NONE LAST NONE + +RESI RB 1.000 ! Rubidium Ion +GROUP +ATOM RB RBD 1.000 ALPHA -1.370 +PATCHING FIRST NONE LAST NONE + +RESI CS 1.000 ! Caesium Ion +GROUP +ATOM CS CSD 1.000 ALPHA -2.360 +PATCHING FIRST NONE LAST NONE + +RESI F -1.000 ! Fluoride Ion +GROUP +ATOM F FAD -1.000 ALPHA -1.786 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.000 ! Chloride Ion +GROUP +ATOM CLA CLAD -1.000 ALPHA -3.969 +PATCHING FIRST NONE LAST NONE + +RESI BR -1.000 ! Bromide Ion +GROUP +ATOM BR BRAD -1.000 ALPHA -5.262 +PATCHING FIRST NONE LAST NONE + +RESI I -1.000 ! Iodide Ion +GROUP +ATOM I IAD -1.000 ALPHA -7.439 +PATCHING FIRST NONE LAST NONE + +!! Divalent Ions +! Yu et al. JCTC 2010, 6, 774-786 +RESI ZN 2.000 ! Zinc Ion +GROUP +ATOM ZN ZND 2.000 ALPHA -0.420 +PATCHING FIRST NONE LAST NONE +! +RESI MAG 2.000 ! Magnesium Ion +GROUP +ATOM MAG MAGD 2.000 ALPHA -0.075 +PATCHING FIRST NONE LAST NONE +! +RESI CAL 2.000 ! Calcium Ion +GROUP +ATOM CAL CALD 2.000 ALPHA -0.490 +PATCHING FIRST NONE LAST NONE +! +RESI SR 2.000 ! Strontium Ion +GROUP +ATOM SR SRD 2.000 ALPHA -0.870 +PATCHING FIRST NONE LAST NONE +! +RESI BA 2.000 ! Barium Ion +GROUP +ATOM BA BAD 2.000 ALPHA -1.560 +PATCHING FIRST NONE LAST NONE +! + +!! Dummy atom and rare gases +RESI DUM 0.000 ! DUMMY ATOM +GROUP +ATOM DUM DUM 0.000 +PATCHING FIRST NONE LAST NONE + +RESI HE 0.000 ! helium +GROUP +ATOM HE XED 0.000 ALPHA -0.205 +PATCHING FIRST NONE LAST NONE + +RESI NE 0.000 ! neon +GROUP +ATOM NE NED 0.000 ALPHA -0.396 +PATCHING FIRST NONE LAST NONE + +RESI HE1 0.000 ! helium +GROUP +ATOM HE01 XED 0.000 ALPHA -0.205 +PATCHING FIRST NONE LAST NONE + +RESI NE1 0.000 ! neon +GROUP +ATOM NE01 NED 0.000 ALPHA -0.396 +PATCHING FIRST NONE LAST NONE + +RESI ALAD 0.000 ! Alanine dipeptide +! +! HY1 OY O HT1 +! \ || HN HA || HNT / +! \ || | | || | / +! HY2--CAY--CY---N---CA--C----NT---CAT--HT2 +! / | \ +! / HB1--CB--HB3 \ +! HY3 | HT3 +! HB2 +! +GROUP +ATOM CAY CD33C -0.102 ALPHA -1.894 THOLE 2.122 +ATOM HY1 HDA3A 0.048 +ATOM HY2 HDA3A 0.048 +ATOM HY3 HDA3A 0.048 +ATOM CY CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM OY OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPY1 LPDO1 -0.312 +ATOM LPY2 LPDO1 -0.227 +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM CB CD33A -0.099 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA3A 0.033 +ATOM HB2 HDA3A 0.033 +ATOM HB3 HDA3A 0.033 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +ATOM NT ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HNT HDP1A 0.272 +ATOM CAT CD33C -0.055 ALPHA -1.639 THOLE 2.122 +ATOM HTC1 HDA3A 0.055 +ATOM HTC2 HDA3A 0.055 +ATOM HTC3 HDA3A 0.055 + +BOND CAY CY CY N N CA +BOND CA C C NT NT CAT +BOND CY OY C O +BOND N HN NT HNT +BOND CA HA CA CB CB HB1 CB HB2 CB HB3 +BOND CAY HY1 CAY HY2 CAY HY3 +BOND CAT HTC1 CAT HTC2 CAT HTC3 +BOND OY LPY1 OY LPY2 +BOND O LPOA O LPOB + +IMPR CY CAY N OY N CY CA HN +IMPR C CA NT O NT C CAT HNT + +!2D correction surface +CMAP CY N CA C N CA C NT + +LONEPAIR relative LPY1 OY CY CAY distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPY2 OY CY CAY distance 0.30 angle 91.0 dihe 180.0 +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OY CY LPY1 LPY2 A11 0.82322 A22 1.14332 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +IC CY N CA C 0.00 0.00 -86.00 0.00 0.00 !phi C7eq=-86,C7ax=76 +IC N CA C NT 0.00 0.00 79.00 0.00 0.00 !psi C7eq= 79,C7ax=-55 +IC CAY CY N CA 0.00 0.00 180.00 0.00 0.00 !omega left +IC CA C NT CAT 0.00 0.00 180.00 0.00 0.00 !omega right +IC N CAY *CY OY 0.00 0.00 144.00 0.00 0.00 +IC CA CY *N HN 0.00 0.00 180.00 0.00 0.00 +IC NT CA *C O 0.00 0.00 120.00 0.00 0.00 +IC CAT C *NT HNT 0.00 0.00 180.00 0.00 0.00 +IC C N *CA CB 0.00 0.00 -120.00 0.00 0.00 !define L sugar +IC C N *CA HA 0.00 0.00 120.00 0.00 0.00 ! +IC N CA CB HB1 0.00 0.00 180.00 0.00 0.00 +IC HB1 CA *CB HB2 0.00 0.00 120.00 0.00 0.00 +IC HB1 CA *CB HB3 0.00 0.00 -120.00 0.00 0.00 +IC N CY CAY HY1 0.00 0.00 180.00 0.00 0.00 +IC HY1 CY *CAY HY2 0.00 0.00 120.00 0.00 0.00 +IC HY1 CY *CAY HY3 0.00 0.00 -120.00 0.00 0.00 +IC C NT CAT HTC1 0.00 0.00 180.00 0.00 0.00 +IC HTC1 NT *CAT HTC2 0.00 0.00 120.00 0.00 0.00 +IC HTC1 NT *CAT HTC3 0.00 0.00 -120.00 0.00 0.00 +patch first none last none + +RESI ALA 0.000 +! +! | +! HN-N +! | HB1 +! | / +! HA-CA--CB-HB2 +! | \ +! | HB3 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD33A -0.099 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA3A 0.033 +ATOM HB2 HDA3A 0.033 +ATOM HB3 HDA3A 0.033 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 CB HB3 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 !phi, -60. for a-helix +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 !psi, -45. for a-helix +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +RESI ARG 1.000 ! arginine +! +! | HH11 +! HN-N | +! | HB1 HG1 HD1 HE NH1-HH12 +! | | | | | //(+) +! HA-CA--CB--CG--CD--NE--CZ +! | | | | \ +! | HB2 HG2 HD2 NH2-HH22 +! O=C | +! | HH21 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM HG1 HDA2A 0.078 +ATOM HG2 HDA2A 0.078 +GROUP +ATOM CD CD32A 0.227 ALPHA -1.788 THOLE 0.342 +ATOM HD1 HDA2A 0.078 +ATOM HD2 HDA2A 0.078 +ATOM NE ND2P1A -0.748 ALPHA -1.550 THOLE 1.538 +ATOM HE HDP1B 0.378 +ATOM CZ CD2N1A 1.129 ALPHA -1.096 THOLE 0.262 +ATOM NH1 ND2P1A -0.809 ALPHA -1.403 THOLE 1.538 +ATOM HH11 HDP1B 0.369 +ATOM HH12 HDP1B 0.369 +ATOM NH2 ND2P1A -0.809 ALPHA -1.403 THOLE 1.538 +ATOM HH21 HDP1B 0.369 +ATOM HH22 HDP1B 0.369 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD HD1 CD HD2 +BOND CD NE NE HE NE CZ +BOND CZ NH1 NH1 HH11 NH1 HH12 +BOND CZ NH2 NH2 HH21 NH2 HH22 +BOND O LPOA O LPOB + +IMPR CZ NH1 NH2 NE +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +RESI ASN 0.000 +! +! | +! HN-N +! | HB1 OD1 HD21 (cis to OD1) +! | | || / +! HA-CA--CB--CG--ND2 +! | | \ +! | HB2 HD22 (trans to OD1) +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32C -0.302 ALPHA -1.417 THOLE 1.130 +ATOM HB1 HDA2A 0.082 +ATOM HB2 HDA2A 0.082 +ATOM CG CD2O1A 0.906 ALPHA -1.583 THOLE 1.095 +ATOM OD1 OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM ND2 ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HD21 HDP1A 0.303 +ATOM HD22 HDP1A 0.351 +ATOM LPDA LPD -0.411 +ATOM LPDB LPD -0.264 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG OD1 +BOND CG ND2 ND2 HD21 ND2 HD22 +BOND O LPOA O LPOB +BOND OD1 LPDA OD1 LPDB + +IMPR CG CB ND2 OD1 ND2 HD21 HD22 CG +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LPDA OD1 CG CB distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPDB OD1 CG CB distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OD1 CG LPDA LPDB A11 0.88 A22 1.32 + +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +RESI ASP -1.000 +! +! | +! HN-N +! | HB1 OD1 +! | | // +! HA-CA--CB--CG +! | | \ +! | HB2 OD2(-) +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.190 ALPHA -2.528 THOLE 1.414 ! charge adjusted +ATOM HB1 HDA2A 0.004 +ATOM HB2 HDA2A 0.004 +ATOM CG CD2O2A 0.708 ALPHA -1.016 THOLE 0.899 +ATOM OD1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OD2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LP1A LPD -0.383 +ATOM LP1B LPD -0.383 +ATOM LP2A LPD -0.383 +ATOM LP2B LPD -0.383 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG OD1 CG OD2 +BOND O LPOA O LPOB +BOND OD1 LP1A OD1 LP1B +BOND OD2 LP2A OD2 LP2B + +IMPH OD1 CB OD2 CG +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LP1A OD1 CG CB distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP1B OD1 CG CB distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2A OD2 CG CB distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP2B OD2 CG CB distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OD1 CG LP1A LP1B A11 0.7229 A22 1.265 +ANISOTROPY OD2 CG LP2A LP2B A11 0.7229 A22 1.265 + +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +RESI CYS 0.000 ! cystiene +! +! | +! HN-N +! | HB1 +! | | +! HA-CA--CB--SG +! | | \ +! | HB2 HG1 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A 0.106 ALPHA -1.273 THOLE 0.716 +ATOM HB1 HDA2A 0.013 +ATOM HB2 HDA2A 0.013 +ATOM SG SD31B 0.050 ALPHA -2.180 THOLE 1.612 +ATOM HG1 HDP1A 0.148 +ATOM LPGA LPD -0.165 +ATOM LPGB LPD -0.165 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB SG SG HG1 +BOND SG LPGA SG LPGB +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +LONEPAIR relative LPGA SG CB HG1 distance 0.75 angle 95.0 dihe 100.0 +LONEPAIR relative LPGB SG CB HG1 distance 0.75 angle 95.0 dihe 260.0 +ANISOTROPY SG CB LPGA LPGB A11 0.8800 A22 1.3200 + +DONOR HN N +DONOR HG1 SG +ACCEPTOR SG +ACCEPTOR O C +!C22 IC table +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +RESI GLN 0.000 +! +! | +! HN-N +! | HB1 HG1 OE1 HE21 (cis to OE1) +! | | | || / +! HA-CA--CB--CG--CD--NE2 +! | | | \ +! | HB2 HG2 HE22 (trans to OE1) +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32C -0.302 ALPHA -1.417 THOLE 1.130 +ATOM HG1 HDA2A 0.082 +ATOM HG2 HDA2A 0.082 +ATOM CD CD2O1A 0.906 ALPHA -1.583 THOLE 1.095 +ATOM OE1 OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM NE2 ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HE21 HDP1A 0.303 +ATOM HE22 HDP1A 0.351 +ATOM LPEA LPD -0.411 +ATOM LPEB LPD -0.264 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD OE1 +BOND CD NE2 NE2 HE21 NE2 HE22 +BOND O LPOA O LPOB +BOND OE1 LPEA OE1 LPEB + +IMPR CD CG NE2 OE1 NE2 HE21 HE22 CD +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LPEA OE1 CD CG distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPEB OE1 CD CG distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OE1 CD LPEA LPEB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +RESI GLU -1.000 ! glutamate +! +! | +! HN-N +! | HB1 HG1 OE1 +! | | | // +! HA-CA--CB--CG--CD +! | | | \ +! | HB2 HG2 OE2(-) +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32B -0.066 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32A -0.190 ALPHA -2.528 THOLE 1.414 +ATOM HG1 HDA2A 0.004 +ATOM HG2 HDA2A 0.004 +ATOM CD CD2O2A 0.708 ALPHA -1.016 THOLE 0.899 +ATOM OE1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OE2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LP1A LPD -0.383 +ATOM LP1B LPD -0.383 +ATOM LP2A LPD -0.383 +ATOM LP2B LPD -0.383 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD OE1 CD OE2 +BOND O LPOA O LPOB +BOND OE1 LP1A OE1 LP1B +BOND OE2 LP2A OE2 LP2B + +IMPH OE1 CG OE2 CD +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LP1A OE1 CD CG distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP1B OE1 CD CG distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2A OE2 CD CG distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP2B OE2 CD CG distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OE1 CD LP1A LP1B A11 0.7229 A22 1.265 +ANISOTROPY OE2 CD LP2A LP2B A11 0.7229 A22 1.265 + +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI GLY 0.000 +! +! | +! N-H +! | +! | +! HA1-CA-HA2 +! | +! | +! C=O +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C 0.186 ALPHA -0.960 THOLE 1.078 +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 + +BOND N CA CA C C +N +BOND N HN C O +BOND CA HA1 CA HA2 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 +PATCHING FIRS GNTE + +RESI HSD 0.000 ! neutral HIS, proton on ND1 +! +! | HD1 HE1 +! HN-N | / +! | HB1 ND1--CE1 +! | | / || +! HA-CA--CB--CG || +! | | \\ || +! | HB2 CD2--NE2 +! O=C | +! | HD2 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A 0.017 ALPHA -1.739 THOLE 0.399 !charge adjusted +ATOM HB1 HDA2A 0.078 +ATOM HB2 HDA2A 0.078 +ATOM ND1 ND2R5A -0.040 ALPHA -1.522 THOLE 1.114 +ATOM HD1 HDP1A 0.256 +ATOM CG CD2R5A -0.252 ALPHA -1.272 THOLE 1.190 +ATOM CE1 CD2R5B 0.064 ALPHA -1.493 THOLE 1.297 +ATOM HE1 HDR5B -0.018 +ATOM NE2 ND2R5B 0.000 ALPHA -1.146 THOLE 0.816 +ATOM LPE2 LPD -0.365 +ATOM CD2 CD2R5A 0.141 ALPHA -1.515 THOLE 1.190 +ATOM HD2 HDR5A 0.041 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG ND1 ND1 CE1 CE1 NE2 +BOND NE2 CD2 CD2 CG +BOND ND1 HD1 CE1 HE1 CD2 HD2 +BOND O LPOA O LPOB +BOND NE2 LPE2 + +IMPH ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +LONEPAIR bisector LPE2 NE2 CE1 CD2 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY NE2 LPE2 CE1 CD2 A11 0.808 A22 1.384 + +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +!C22 IC table +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +RESI HSE 0.000 ! neutral HIS, proton on NE2, see patch HS2 below +! +! | HE1 +! HN-N / +! | HB1 ND1--CE1 +! | | / || +! HA-CA--CB--CG || +! | | \\ || +! | HB2 CD2--NE2 +! O=C | \ +! | HD2 HE2 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A 0.017 ALPHA -1.739 THOLE 0.399 !charge adjusted +ATOM HB1 HDA2A 0.078 +ATOM HB2 HDA2A 0.078 +ATOM ND1 ND2R5B 0.000 ALPHA -1.146 THOLE 0.816 +ATOM LPD1 LPD -0.365 +ATOM NE2 ND2R5A -0.040 ALPHA -1.522 THOLE 1.114 +ATOM HE2 HDP1A 0.256 +ATOM CG CD2R5A -0.252 ALPHA -1.272 THOLE 1.190 +ATOM CE1 CD2R5B 0.064 ALPHA -1.493 THOLE 1.297 +ATOM HE1 HDR5B -0.018 +ATOM CD2 CD2R5A 0.141 ALPHA -1.515 THOLE 1.190 +ATOM HD2 HDR5A 0.041 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG ND1 ND1 CE1 CE1 NE2 +BOND NE2 CD2 CD2 CG +BOND NE2 HE2 CE1 HE1 CD2 HD2 +BOND O LPOA O LPOB +BOND ND1 LPD1 + +IMPH NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +LONEPAIR bisector LPD1 ND1 CE1 CG distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY ND1 LPD1 CE1 CG A11 0.808 A22 1.384 + +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C + +!C22 IC table +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +RESI HSP 1.000 ! protonated HIS +! +! | HD1 HE1 +! HN-N \ / +! | HB1 ND1--CE1 +! | | / || +! HA-CA--CB--CG || +! | | \\ || +! | HB2 CD2--NE2 +! O=C | \ +! | HD2 HE2 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +!electrostatic terms need to be refit to methylimidazolium +ATOM CB CD32A 0.017 ALPHA -1.739 THOLE 0.399 !from HSE/HSD +ATOM HB1 HDA2A 0.078 !from HSD/HSE +ATOM HB2 HDA2A 0.078 !from HSD/HSE +ATOM ND1 ND2R5C -0.171 ALPHA -1.260 THOLE 1.194 +ATOM HD1 HDP1A 0.340 +ATOM NE2 ND2R5C -0.171 ALPHA -1.260 THOLE 1.194 +ATOM HE2 HDP1A 0.340 +ATOM CG CD2R5D -0.012 ALPHA -1.522 THOLE 1.196 +ATOM CE1 CD2R5E 0.170 ALPHA -1.500 THOLE 1.317 +ATOM HE1 HDR5E 0.170 +ATOM CD2 CD2R5D -0.012 ALPHA -1.522 THOLE 1.196 +ATOM HD2 HDR5D 0.173 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG ND1 ND1 CE1 CE1 NE2 +BOND NE2 CD2 CD2 CG +BOND ND1 HD1 CE1 HE1 CD2 HD2 NE2 HE2 +BOND O LPOA O LPOB + +!impropers need to be checked +IMPR ND1 CE1 CG HD1 NE2 CE1 CD2 HE2 +IMPR CE1 ND1 NE2 HE1 CD2 CG NE2 HD2 !CG CD2 ND1 CB is this needed: check with methylimidazolium +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C + +!C22 IC table +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +RESI ILE 0.000 !nomenclature of CD changed to CD1 to conform to PDB standard +! +! | HG21 HG22 +! HN-N | / +! | CG2--HG23 +! | / +! HA-CA--CB-HB HD11 +! | \ / +! | CG1--CD1--HD12 +! O=C / \ \ +! | HG11 HG12 HD13 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD31A -0.095 ALPHA -1.302 THOLE 1.3 +ATOM HB HDA1A 0.095 +GROUP +ATOM CG2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HG21 HDA3A 0.059 +ATOM HG22 HDA3A 0.059 +ATOM HG23 HDA3A 0.059 +GROUP +ATOM CG1 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM HG11 HDA2A 0.078 +ATOM HG12 HDA2A 0.078 +GROUP +ATOM CD1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HD11 HDA3A 0.059 +ATOM HD12 HDA3A 0.059 +ATOM HD13 HDA3A 0.059 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB +BOND CB CG1 CG1 HG11 CG1 HG12 +BOND CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 +BOND CG1 CD1 CD1 HD11 CD1 HD12 CD1 HD13 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD1 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD1 CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD1 CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD1 HD11 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD11 CG1 *CD1 HD12 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD11 CG1 *CD1 HD13 1.1115 110.3100 -119.7000 111.0200 1.1103 + +RESI LEU 0.000 +! +! | HD11 HD12 +! HN-N | / +! | HB1 CD1--HD13 +! | | / +! HA-CA--CB--CG-HG +! | | \ +! | HB2 CD2--HD23 +! O=C | \ +! | HD21 HD22 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD31A -0.095 ALPHA -1.302 THOLE 1.3 +ATOM HG HDA1A 0.095 +GROUP +ATOM CD1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HD11 HDA3A 0.059 +ATOM HD12 HDA3A 0.059 +ATOM HD13 HDA3A 0.059 +GROUP +ATOM CD2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HD21 HDA3A 0.059 +ATOM HD22 HDA3A 0.059 +ATOM HD23 HDA3A 0.059 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG +BOND CG CD1 CD1 HD11 CD1 HD12 CD1 HD13 +BOND CG CD2 CD2 HD21 CD2 HD22 CD2 HD23 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +RESI LYS 1.000 ! lysine +! +! | +! HN-N +! | HB1 HG1 HD1 HE1 HZ1 +! | | | | | / +! HA-CA--CB--CG--CD--CE--NZ--HZ2 +! | | | | | \ +! | HB2 HG2 HD2 HE2 HZ3 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM HG1 HDA2A 0.078 +ATOM HG2 HDA2A 0.078 +GROUP +ATOM CD CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM HD1 HDA2A 0.078 +ATOM HD2 HDA2A 0.078 +GROUP +ATOM CE CD32A 0.043 ALPHA -1.656 THOLE 0.895 +ATOM HE1 HDA2C 0.143 +ATOM HE2 HDA2C 0.143 +ATOM NZ ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HZ1 HDP1B 0.340 +ATOM HZ2 HDP1B 0.340 +ATOM HZ3 HDP1B 0.340 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD HD1 CD HD2 +BOND CD CE CE HE1 CE HE2 +BOND CE NZ NZ HZ1 NZ HZ2 NZ HZ3 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI MET 0.000 ! methionine +! +! | +! HN-N +! | HB1 HG1 HE1 +! | | | | +! HA-CA--CB--CG--SD--CE--HE3 +! | | | | +! | HB2 HG2 HE2 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32A -0.041 ALPHA -1.300 THOLE 1.646 +ATOM HG1 HDA2A 0.082 +ATOM HG2 HDA2A 0.082 +ATOM SD SD30A 0.000 ALPHA -2.051 THOLE 1.543 +ATOM CE CD33A -0.161 ALPHA -1.587 THOLE 1.542 +ATOM HE1 HDA3A 0.082 +ATOM HE2 HDA3A 0.082 +ATOM HE3 HDA3A 0.082 +ATOM LP1A LPD -0.104 +ATOM LP1B LPD -0.104 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG SD +BOND SD CE CE HE1 CE HE2 CE HE3 +BOND O LPOA O LPOB +BOND SD LP1A SD LP1B + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR bisector LP1A SD CE CG distance 0.70 angle 95.0 dihe 100.0 +LONEPAIR bisector LP1B SD CG CE distance 0.70 angle 95.0 dihe 100.0 +ANISOTROPY SD CE LP1A LP1B A11 0.7808 A22 1.3662 + +DONOR HN N +ACCEPTOR SD +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +RESI PHE 0.000 +! +! | HD1 HE1 +! HN-N | | +! | HB1 CD1--CE1 +! | | // \\ +! HA-CA--CB--CG CZ--HZ +! | | \ __ / +! | HB2 CD2--CE2 +! O=C | | +! | HD2 HE2 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.150 ALPHA -1.608 THOLE 0.438 +ATOM HB1 HDA2A 0.079 +ATOM HB2 HDA2A 0.079 +ATOM CG CD2R6A 0.037 ALPHA -1.550 THOLE 1.262 +ATOM CD1 CD2R6A -0.087 ALPHA -1.604 THOLE 1.262 +ATOM HD1 HDR6A 0.099 +ATOM CD2 CD2R6A -0.087 ALPHA -1.604 THOLE 1.262 +ATOM HD2 HDR6A 0.099 +ATOM CE1 CD2R6A -0.114 ALPHA -1.606 THOLE 1.262 +ATOM HE1 HDR6A 0.096 +ATOM CE2 CD2R6A -0.114 ALPHA -1.606 THOLE 1.262 +ATOM HE2 HDR6A 0.096 +ATOM CZ CD2R6A -0.133 ALPHA -1.610 THOLE 1.262 +ATOM HZ HDR6A 0.100 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG CD1 CD1 CE1 CE1 CZ +BOND CG CD2 CD2 CE2 CE2 CZ +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +RESI PRO 0.000 ! Proline +! +! +! HD1 HD2 +! | \ / +! N---CD HG1 +! | \ / +! | CG +! | / \ +! HA-CA--CB HG2 +! | / \ +! | HB1 HB2 +! O=C +! | +! +GROUP +ATOM N ND3A3 -0.203 ALPHA -1.113 THOLE 2.078 +ATOM CA CD31C -0.047 ALPHA -1.807 THOLE 0.622 +ATOM HA HDA1A 0.016 +ATOM CD CD32A -0.033 ALPHA -1.442 THOLE 0.626 +ATOM HD1 HDA2A 0.092 +ATOM HD2 HDA2A 0.092 +ATOM CB CD32A -0.115 ALPHA -1.378 THOLE 0.483 +ATOM HB1 HDA2A 0.136 +ATOM HB2 HDA2A 0.136 +ATOM CG CD32A -0.414 ALPHA -2.066 THOLE 0.644 +ATOM HG1 HDA2A 0.142 +ATOM HG2 HDA2A 0.142 +ATOM C CD2O1A 0.595 ALPHA -0.829 THOLE 1.512 +ATOM O OD2C1A 0.000 ALPHA -0.540 THOLE 1.282 +ATOM LPOA LPDO1 -0.314 +ATOM LPOB LPDO1 -0.225 + +BOND N CA CA C C +N CA HA +BOND C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD HD1 CD HD2 +BOND CD N +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA CD +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +ACCEPTOR O C +!C22 IC Table +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 +PATCHING FIRS PROP + +RESI SER 0.000 +! +! | +! HN-N +! | HB1 +! | | +! HA-CA--CB--OG +! | | \ +! | HB2 HG1 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM HB1 HDA2A 0.080 +ATOM HB2 HDA2A 0.080 +ATOM OG OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HG1 HDP1A 0.360 +ATOM LPGA LPD -0.230 +ATOM LPGB LPD -0.230 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB OG OG HG1 +BOND O LPOA O LPOB +BOND OG LPGA OG LPGB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LPGA OG CB HG1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPGB OG CB HG1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OG CB LPGA LPGB A11 0.8108 A22 1.2162 + +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +!C22 IC table +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +RESI THR 0.000 +! +! | +! HN-N +! | OG1--HG1 +! | / +! HA-CA--CB-HB +! | \ +! | CG2--HG21 +! O=C / \ +! | HG21 HG22 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD31A 0.000 ALPHA -1.000 THOLE 1.3 +ATOM HB HDA1A 0.100 +ATOM OG1 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HG1 HDP1A 0.360 +ATOM LPGA LPD -0.230 +ATOM LPGB LPD -0.230 +GROUP +ATOM CG2 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM HG21 HDA3A 0.060 +ATOM HG22 HDA3A 0.060 +ATOM HG23 HDA3A 0.060 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB +BOND CB OG1 OG1 HG1 +BOND CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 +BOND O LPOA O LPOB +BOND OG1 LPGA OG1 LPGB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LPGA OG1 CB HG1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPGB OG1 CB HG1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OG1 CB LPGA LPGB A11 0.8108 A22 1.2162 + +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +!C22 IC table +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +RESI TRP 0.000 +! +! | HE3 +! HN-N | +! | HB1 CE3 +! | | / \\ +! HA-CA--CB---CG-----CD2 CZ3-HZ3 +! | | || || | +! | HB2 CD1 CE2 CH2-HH2 +! O=C / \ / \ // +! | HD1 NE1 CZ2 +! | | +! HE1 HZ2 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.046 ALPHA -2.044 THOLE 1.346 !adjusted to neutralize group +ATOM HB1 HDA2A 0.045 +ATOM HB2 HDA2A 0.045 +ATOM CG CD2R5C -0.098 ALPHA -1.269 THOLE 1.346 +ATOM CD1 CD2R5A 0.059 ALPHA -1.612 THOLE 1.265 +ATOM HD1 HDR5A 0.083 +ATOM NE1 ND2R5A -0.276 ALPHA -1.380 THOLE 1.146 +ATOM HE1 HDP1A 0.294 +ATOM CE2 CD2R6D 0.053 ALPHA -1.267 THOLE 1.009 +ATOM CD2 CD2R6D -0.099 ALPHA -1.266 THOLE 1.344 +ATOM CE3 CD2R6A -0.034 ALPHA -1.622 THOLE 1.300 +ATOM HE3 HDR6A 0.094 +ATOM CZ3 CD2R6A -0.154 ALPHA -1.617 THOLE 1.300 +ATOM HZ3 HDR6A 0.087 +ATOM CZ2 CD2R6A -0.115 ALPHA -1.611 THOLE 1.300 +ATOM HZ2 HDR6A 0.110 +ATOM CH2 CD2R6A -0.188 ALPHA -1.621 THOLE 1.300 +ATOM HH2 HDR6A 0.140 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG CD1 CD1 NE1 NE1 CE2 +BOND CE2 CD2 CD2 CG CD2 CE3 CE3 CZ3 +BOND CZ3 CH2 CH2 CZ2 CZ2 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 CZ3 HZ3 +BOND CH2 HH2 CZ2 HZ2 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI TYR 0.000 +! +! | HD1 HE1 +! HN-N | | +! | HB1 CD1--CE1 +! | | // \\ +! HA-CA--CB--CG CZ--OH +! | | \ __ / \ +! | HB2 CD2--CE2 HH +! O=C | | +! | HD2 HE2 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.192 ALPHA -1.802 THOLE 0.148 +ATOM HB1 HDA2A 0.075 +ATOM HB2 HDA2A 0.075 +ATOM CG CD2R6A 0.086 ALPHA -1.418 THOLE 1.270 +ATOM CD1 CD2R6A -0.202 ALPHA -1.427 THOLE 1.270 +ATOM HD1 HDR6A 0.118 +ATOM CD2 CD2R6A -0.202 ALPHA -1.427 THOLE 1.270 +ATOM HD2 HDR6A 0.118 +ATOM CE1 CD2R6A -0.136 ALPHA -1.444 THOLE 1.270 +ATOM HE1 HDR6A 0.123 +ATOM CE2 CD2R6A -0.136 ALPHA -1.444 THOLE 1.270 +ATOM HE2 HDR6A 0.123 +ATOM CZ CD2R6A 0.297 ALPHA -1.174 THOLE 1.270 +ATOM OH OD31C 0.000 ALPHA -0.683 THOLE 0.601 +ATOM HH HDP1A 0.319 +ATOM LP1A LPD -0.233 +ATOM LP1B LPD -0.233 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG CD1 CD1 CE1 CE1 CZ +BOND CG CD2 CD2 CE2 CE2 CZ +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH OH HH +BOND O LPOA O LPOB +BOND OH LP1A OH LP1B + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LP1A OH CZ HH distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP1B OH CZ HH distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OH CZ LP1A LP1B A11 0.8108 A22 1.2162 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +RESI VAL 0.000 +! +! | HG11 HG12 +! HN-N | / +! | CG1--HG13 +! | / +! HA-CA--CB-HB +! | \ +! | CG2--HG21 +! O=C | \ +! | HG21 HG22 +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD31A -0.074 ALPHA -1.914 THOLE 0.593 +ATOM HB HDA1A 0.074 +GROUP +ATOM CG1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HG11 HDA3A 0.059 +ATOM HG12 HDA3A 0.059 +ATOM HG13 HDA3A 0.059 +GROUP +ATOM CG2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HG21 HDA3A 0.059 +ATOM HG22 HDA3A 0.059 +ATOM HG23 HDA3A 0.059 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB +BOND CB CG1 CG1 HG11 CG1 HG12 CG1 HG13 +BOND CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +PRES NTER 1.000 ! N-terminus in polypeptide +! +! HT1 +! (+) / +! --CA---N--HT2 +! | \ +! HA HT3 +! +DELETE ATOM HN +! +GROUP ! use in generate statement +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HT1 HDP1B 0.340 +ATOM HT2 HDP1B 0.340 +ATOM HT3 HDP1B 0.340 +ATOM CA CD31C 0.388 ALPHA -0.960 THOLE 1.078 ! charge adjusted to yield unit charge +ATOM HA HDA1C -0.017 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 + +BOND N HT1 N HT2 N HT3 + +IC C CA N HT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT1 CA *N HT3 0.0000 0.0000 -120.0000 0.0000 0.0000 + +PRES NTES 1.000 ! N-terminus in single amino acid +! Note: with CT3 use NTER +! +! HT1 +! (+) / +! --CA---N--HT2 +! | \ +! HA HT3 +! +DELETE ATOM HN +! +GROUP ! use in generate statement +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HT1 HDP1B 0.340 +ATOM HT2 HDP1B 0.340 +ATOM HT3 HDP1B 0.340 +ATOM CA CD31C 0.186 ALPHA -1.656 THOLE 0.895 ! charge adjusted to yield unit charge +ATOM HA HDA1C 0.143 ! charge adjusted to yield unit charge + +BOND N HT1 N HT2 N HT3 + +IC C CA N HT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT1 CA *N HT3 0.0000 0.0000 -120.0000 0.0000 0.0000 + +PRES GNTE 1.000 ! Glycine N-terminus (formally GLYP) in polypeptide +! +! HA1 HT1 +! |(+)/ +! --CA--N--HT2 +! | \ +! HA2 HT3 +! +DELETE ATOM HN +! +GROUP ! use in generate statement +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HT1 HDP1B 0.340 +ATOM HT2 HDP1B 0.340 +ATOM HT3 HDP1B 0.340 +ATOM CA CD32C 0.085 ALPHA -1.656 THOLE 0.895 !charge adjusted to yield neutral charge +ATOM HA1 HDA2C 0.143 +ATOM HA2 HDA2C 0.143 +ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPOA LPDO1 -0.312 +ATOM LPOB LPDO1 -0.227 + +BOND N HT1 N HT2 N HT3 + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES GNTS 1.000 ! Glycine N-terminus in single amino acid +! +! HA1 HT1 +! |(+)/ +! --CA--N--HT2 +! | \ +! HA2 HT3 +! +DELETE ATOM HN +! +GROUP ! use in generate statement +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HT1 HDP1B 0.340 +ATOM HT2 HDP1B 0.340 +ATOM HT3 HDP1B 0.340 +ATOM CA CD32C 0.043 ALPHA -1.656 THOLE 0.895 +ATOM HA1 HDA2C 0.143 +ATOM HA2 HDA2C 0.143 + +BOND N HT1 N HT2 N HT3 + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +!optimization required +PRES PROP 1.000 ! Proline N-Terminal !yields unit charge +! +! HA +! | +! -CA HT1 +! / \ / +! N(+) +! / \ +! -CD HT2 +! | \ +! +GROUP ! use in generate statement +ATOM N ND3P2A -0.070 ALPHA -1.479 THOLE 0.111 +ATOM HT1 HDP1B 0.266 +ATOM HT2 HDP1B 0.266 +ATOM CD CD32A 0.119 ALPHA -1.578 THOLE 1.429 +ATOM HD1 HDA2C 0.104 +ATOM HD2 HDA2C 0.104 +ATOM CA CD31C 0.114 ALPHA -1.578 THOLE 1.429 !correction from 0.165 to obtain unit charge +ATOM HA HDA1C 0.104 +ATOM C CD2O1A 0.528 ALPHA -1.342 THOLE 0.887 +ATOM O OD2C1A 0.000 ALPHA -0.682 THOLE 1.905 +ATOM LPOA LPDO1 -0.371 +ATOM LPOB LPDO1 -0.215 +ATOM CB CD32A -0.116 ALPHA -1.710 THOLE 1.295 +ATOM HB1 HDA2A 0.084 +ATOM HB2 HDA2A 0.084 +ATOM CG CD32A -0.143 ALPHA -2.049 THOLE 1.295 +ATOM HG1 HDA2A 0.071 +ATOM HG2 HDA2A 0.071 + +BOND HT1 N HT2 N + +DONOR HT1 N +DONOR HT2 N +IC HT1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES ACE 0.000 ! acetylated N-terminus in di- and polypeptides + ! use in generate statement +! +! HY1 HY2 HY3 +! \ | / +! CAY +! | +! CY=OY +! | +! +GROUP + +ATOM CAY CD33C -0.102 ALPHA -1.894 THOLE 2.122 +ATOM HY1 HDA3A 0.048 +ATOM HY2 HDA3A 0.048 +ATOM HY3 HDA3A 0.048 +ATOM CY CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM OY OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPY1 LPDO1 -0.312 +ATOM LPY2 LPDO1 -0.227 + +BOND N CY CAY CY CY OY +BOND CAY HY1 CAY HY2 CAY HY3 +BOND OY LPY1 OY LPY2 + +IMPR CY CAY N OY N CY CA HN +CMAP CY N CA C N CA C +N +CMAP CY N CA C N CA C NT !for dipeptide + +LONEPAIR relative LPY1 OY CY CAY distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPY2 OY CY CAY distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OY CY LPY1 LPY2 A11 0.82322 A22 1.14332 + +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACP 0.000 ! acetylated N-terminus for proline + ! use in generate statement +! +!this patch is directly from ACE. It is anticipated that different electrostatic +!terms will be required for the imino proton in Proline +! +! +! HY1 HY2 HY3 +! \ | / +! CAY +! | +! CY=OY +! | +GROUP +ATOM CAY CD33C -0.102 ALPHA -1.894 THOLE 2.122 +ATOM HY1 HDA3A 0.048 +ATOM HY2 HDA3A 0.048 +ATOM HY3 HDA3A 0.048 +ATOM CY CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM OY OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPY1 LPDO1 -0.312 +ATOM LPY2 LPDO1 -0.227 + +BOND N CY CAY CY CY OY +BOND CAY HY1 CAY HY2 CAY HY3 +BOND OY LPY1 OY LPY2 + +IMPR CY CAY N OY N CY CA CD +CMAP CY N CA C N CA C +N +CMAP CY N CA C N CA C NT !for dipeptide + +LONEPAIR relative LPY1 OY CY CAY distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPY2 OY CY CAY distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OY CY LPY1 LPY2 A11 0.82322 A22 1.14332 + +ACCEPTOR OY CY +IC A1 A2 A3 A4 1.3474 124.31 180.00 114.26 0.9979 +IC CY N CA C 0.0000 0.00 -60.00 0.00 0.0000 +IC CY CA *N CD 0.0000 0.00 180.00 0.00 0.0000 +IC CAY CY N CA 0.0000 0.00 180.00 0.00 0.0000 +IC N CAY *CY OY 0.0000 0.00 180.00 0.00 0.0000 +IC OY CY CAY HY1 0.0000 0.00 180.00 0.00 0.0000 +IC HY1 CY *CAY HY2 0.0000 0.00 120.00 0.00 0.0000 +IC HY1 CY *CAY HY3 0.0000 0.00 -120.00 0.00 0.0000 + +!correct once neutral amine electrostatic terms are available +!PRES NNEU 0.000 ! neutral N-terminus; charges from LSN +! ! use in generate statement +!! HT1 +!! / +!! --CA--N--HT2 +!! | +!! HA +!! +!DELETE ATOM HN +!GROUP +!ATOM N NH2 -0.960 +!ATOM HT1 H 0.340 +!ATOM HT2 H 0.340 +!ATOM CA CT1 0.190 +!ATOM HA HB 0.090 +!BOND N HT1 N HT2 +!DONOR HT1 N +!DONOR HT2 N +!IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CTER -1.000 ! C-terminus for polypeptide +! +! OT2(-) +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O2A 0.484 ALPHA -1.016 THOLE 0.899 !charge adjusted to yield -1 total charge for COO atoms +ATOM OT1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OT2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LPT1 LPD -0.383 +ATOM LPT2 LPD -0.383 +ATOM LPT3 LPD -0.383 +ATOM LPT4 LPD -0.383 + +BOND C OT1 C OT2 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPH C OT1 OT2 CA + +LONEPAIR relative LPT1 OT1 C OT2 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LPT3 OT2 C OT1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT4 OT2 C OT1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.7229 A22 1.265 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.7229 A22 1.265 + +IC N CA C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CTEG -1.000 ! C-terminus for polypeptide terminating with a glycine +! +! OT2(-) +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C -0.038 ALPHA -0.960 THOLE 1.078 !charge adjusted to yield -1 total charge +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O2A 0.708 ALPHA -1.016 THOLE 0.899 !charge adjusted to yield -1 total charge for COO atoms +ATOM OT1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OT2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LPT1 LPD -0.383 +ATOM LPT2 LPD -0.383 +ATOM LPT3 LPD -0.383 +ATOM LPT4 LPD -0.383 + +BOND C OT1 C OT2 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPH C OT1 OT2 CA + +LONEPAIR relative LPT1 OT1 C OT2 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LPT3 OT2 C OT1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT4 OT2 C OT1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.7229 A22 1.265 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.7229 A22 1.265 + +IC N CA C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CTEP -1.000 ! C-terminus for polypeptide terminated with proline +! +! OT2(-) +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND3A3 -0.239 ALPHA -1.400 THOLE 0.754 +ATOM CA CD31C -0.141 ALPHA -1.500 THOLE 0.432 +ATOM HA HDA1A -0.014 +ATOM CD CD32A 0.017 ALPHA -1.500 THOLE 1.100 +ATOM HD1 HDA2A 0.072 +ATOM HD2 HDA2A 0.072 +ATOM CB CD32A -0.116 ALPHA -1.710 THOLE 1.295 +ATOM HB1 HDA2A 0.084 +ATOM HB2 HDA2A 0.084 +ATOM CG CD32A -0.143 ALPHA -2.049 THOLE 1.295 +ATOM HG1 HDA2A 0.071 +ATOM HG2 HDA2A 0.071 +ATOM C CD2O2A 0.708 ALPHA -1.016 THOLE 0.899 !charge adjusted to yield -1 total charge for COO atoms +ATOM OT1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OT2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LPT1 LPD -0.383 +ATOM LPT2 LPD -0.383 +ATOM LPT3 LPD -0.383 +ATOM LPT4 LPD -0.383 + +BOND C OT1 C OT2 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPH C OT1 OT2 CA + +LONEPAIR relative LPT1 OT1 C OT2 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LPT3 OT2 C OT1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT4 OT2 C OT1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.7229 A22 1.265 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.7229 A22 1.265 + +IC N CA C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CTES -1.000 ! C-terminus for single amino acid +! Note: with ACE use CTER +! +! OT2(-) +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM C CD2O2A 0.526 ALPHA -1.016 THOLE 0.899 !charge adjusted to yield -1 total charge for COO atoms +ATOM OT1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OT2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LPT1 LPD -0.383 +ATOM LPT2 LPD -0.383 +ATOM LPT3 LPD -0.383 +ATOM LPT4 LPD -0.383 + +BOND C OT1 C OT2 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPH C OT1 OT2 CA + +LONEPAIR relative LPT1 OT1 C OT2 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LPT3 OT2 C OT1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT4 OT2 C OT1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.7229 A22 1.265 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.7229 A22 1.265 + +IC N CA C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CNEU 0.000 ! protonated C-terminus for polypeptide +! +! OT2-HT +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.103 ALPHA -0.960 THOLE 1.078 !charge adjusted from 0.858 to yield 0 total charge for COOH atoms +ATOM HA HDA1A -0.017 +ATOM C CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM OT1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OT2 OD30D 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HT HDP1A 0.374 +ATOM LPT1 LPD -0.319 +ATOM LPT2 LPD -0.319 +ATOM LPT3 LPD -0.285 +ATOM LPT4 LPD -0.285 + +BOND C OT1 C OT2 OT2 HT +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPH OT1 CA OT2 C + +!standard carbonyl +LONEPAIR relative LPT1 OT1 C OT2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPT3 OT2 C HT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C HT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +IC N CA C OT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC OT1 CAN *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 !dummy IC for building dipeptides *DELETE* +IC CA C OT2 HT 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CNEG 0.000 ! protonated C-terminus for polypeptide with terminal glycine + ! Yes, the patch name is not ideal; the total charge is zero +! +! OT2-HT +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C 0.120 ALPHA -0.960 THOLE 1.078 !charge adjusted to yield 0 total charge for COOH atoms +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM OT1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OT2 OD30D 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HT HDP1A 0.374 +ATOM LPT1 LPD -0.319 +ATOM LPT2 LPD -0.319 +ATOM LPT3 LPD -0.285 +ATOM LPT4 LPD -0.285 + +BOND C OT1 C OT2 OT2 HT +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPH OT1 CA OT2 C + +!standard carbonyl +LONEPAIR relative LPT1 OT1 C OT2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPT3 OT2 C HT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C HT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +IC N CA C OT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 HT 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CNES 0.000 ! protonated C-terminus for single amino acid +! Note: with ACE use CNEU +! +! OT2-HT +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM C CD2O3A 0.834 ALPHA -1.207 THOLE 0.708 !charge adjusted from 0.858 to yield 0 total charge for COOH atoms +ATOM OT1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OT2 OD30D 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HT HDP1A 0.374 +ATOM LPT1 LPD -0.319 +ATOM LPT2 LPD -0.319 +ATOM LPT3 LPD -0.285 +ATOM LPT4 LPD -0.285 + +BOND C OT1 C OT2 OT2 HT +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPH OT1 CA OT2 C + +!standard carbonyl +LONEPAIR relative LPT1 OT1 C OT2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPT3 OT2 C HT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C HT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +IC N CA C OT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC OT1 CAN *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 !dummy IC for building dipeptides *DELETE* +IC CA C OT2 HT 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT1 0.000 ! methylated C-terminus from methyl acetate + ! total charge to neutralize C-terminal peptide bond + ! use in generate statement +! +! OT1 +! // +! -CA--C HT1 +! | \ / +! HA OT2--CT--HT2 +! \ +! HT3 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.059 ALPHA -0.960 THOLE 1.078 !charge adjusted to achieve neutral system +ATOM HA HDA1A -0.017 +ATOM C CD2O3A 0.697 ALPHA -1.370 THOLE 1.747 +ATOM OT1 OD2C3A 0.000 ALPHA -0.904 THOLE 0.565 +ATOM OT2 OD30C 0.000 ALPHA -0.732 THOLE 0.601 +ATOM CT CD33D -0.030 ALPHA -1.797 THOLE 0.410 +ATOM HT1 HDA3A 0.116 +ATOM HT2 HDA3A 0.116 +ATOM HT3 HDA3A 0.116 +ATOM LPT1 LPD -0.349 +ATOM LPT2 LPD -0.258 +ATOM LPT3 LPD -0.170 +ATOM LPT4 LPD -0.170 + +BOND C OT1 C OT2 OT2 CT +BOND CT HT1 CT HT2 CT HT3 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR C OT2 CA OT1 + +!LP positions and anisotropic polarizability from MAS +LONEPAIR relative LPT1 OT1 C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!LP positions and anisotropic polarizability from MAS +LONEPAIR relative LPT3 OT2 C CT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C CT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 + +PRES CT1G 0.000 ! methylated C-terminus from methyl acetate, for C-terminal GLY + ! total charge to neutralize C-terminal peptide bond + ! use in generate statement +! +! OT1 +! // +! -CA--C HT1 +! | \ / +! HA OT2--CT--HT2 +! \ +! HT3 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C 0.076 ALPHA -0.960 THOLE 1.078 !charge adjusted to achieve neutral system +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O3A 0.697 ALPHA -1.370 THOLE 1.747 +ATOM OT1 OD2C3A 0.000 ALPHA -0.904 THOLE 0.565 +ATOM OT2 OD30C 0.000 ALPHA -0.732 THOLE 0.601 +ATOM CT CD33D -0.030 ALPHA -1.797 THOLE 0.410 +ATOM HT1 HDA3A 0.116 +ATOM HT2 HDA3A 0.116 +ATOM HT3 HDA3A 0.116 +ATOM LPT1 LPD -0.349 +ATOM LPT2 LPD -0.258 +ATOM LPT3 LPD -0.170 +ATOM LPT4 LPD -0.170 + +BOND C OT1 C OT2 OT2 CT +BOND CT HT1 CT HT2 CT HT3 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR C OT2 CA OT1 + +!LP positions and anisotropic polarizability from MAS +LONEPAIR relative LPT1 OT1 C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!LP positions and anisotropic polarizability from MAS +LONEPAIR relative LPT3 OT2 C CT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C CT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 + +PRES CT2 0.000 ! amidated C-terminus for polypeptide +! ! use in generate statement +! | +! O=C +! | +! NT +! / \ +! HTC1 HTC2 (HTC1 is cis to O) +! +! +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.726 ALPHA -1.583 THOLE 1.095 !charge adjusted to yield neutral charge +ATOM O OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM NT ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HTC1 HDP1A 0.303 +ATOM HTC2 HDP1A 0.351 +ATOM LPOA LPDO1 -0.411 +ATOM LPOB LPDO1 -0.264 + +BOND C NT NT HTC1 NT HTC2 + +IMPR C CA NT O NT HTC1 HTC2 C +CMAP -C N CA C N CA C NT + +DONOR HT1 NT +DONOR HT2 NT + +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HTC1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HTC1 C *NT HTC2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT2G 0.000 ! amidated C-terminus for polypeptide terminating with a glycine +! ! use in generate statement +! | +! O=C +! | +! NT +! / \ +! HTC1 HTC2 (HTC1 is cis to O) +! +! +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C 0.090 ALPHA -0.960 THOLE 1.078 +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O1A 0.822 ALPHA -1.583 THOLE 1.095 !charge adjusted to yield neutral charge +ATOM O OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM NT ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HTC1 HDP1A 0.303 +ATOM HTC2 HDP1A 0.351 +ATOM LPOA LPDO1 -0.411 +ATOM LPOB LPDO1 -0.264 + +BOND C NT NT HTC1 NT HTC2 + +IMPR C CA NT O NT HTC1 HTC2 C +CMAP -C N CA C N CA C NT + +DONOR HTC1 NT +DONOR HTC2 NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HTC1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HTC1 C *NT HTC2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT2S 0.000 ! amidated C-terminus for single amino acid +! ! use in generate statement +! | ! HTC1/HTC2 nomenclature to avoid conflict with NTER in single amino acids +! O=C +! | +! NT +! / \ +! HTC1 HTC2 (HTC1 is cis to O) +! +! +ATOM C CD2O1A 0.768 ALPHA -1.583 THOLE 1.095 !charge adjusted to yield neutral charge +ATOM O OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM NT ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HTC1 HDP1A 0.303 +ATOM HTC2 HDP1A 0.351 +ATOM LPOA LPDO1 -0.411 +ATOM LPOB LPDO1 -0.264 + +BOND C NT NT HTC1 NT HTC2 + +IMPR C CA NT O NT HTC1 HTC2 C +CMAP -C N CA C N CA C NT + +DONOR HTC1 NT +DONOR HTC2 NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HTC1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HTC1 C *NT HTC2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT3 0.000 ! N-Methylamide C-terminus +! ! use in generate statement +! | ! NOT compatible with PRES NTER for single amino acid due to non-unit charge +! C=O +! | +! NT-HNT +! | +! HTC1-CAT-HTC3 +! | +! HTC2 +! +ATOM NT ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HNT HDP1A 0.272 +ATOM CAT CD33C -0.055 ALPHA -1.639 THOLE 2.122 +ATOM HTC1 HDA3A 0.055 +ATOM HTC2 HDA3A 0.055 +ATOM HTC3 HDA3A 0.055 + +BOND C NT NT HNT NT CAT +BOND CAT HTC1 CAT HTC2 CAT HTC3 + +IMPR C CA NT O NT C CAT HNT +CMAP -C N CA C N CA C NT + +DONOR HNT NT +IC N CA C NT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HTC1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC HTC1 NT *CAT HTC2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HTC1 NT *CAT HTC3 0.0000 0.0000 -120.0000 0.0000 0.0000 + +PRES DISU 0.000 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. +! +! 2SG--2CB-- +! / +! -1CB--1SG +! +DELETE ATOM 1HG1 +DELETE ATOM 1LPGA +DELETE ATOM 1LPGB +DELETE ATOM 2HG1 +DELETE ATOM 2LPGA +DELETE ATOM 2LPGB +ATOM 1CB CD32A -0.070 ALPHA -1.888 THOLE 1.067 +ATOM 1HB1 HDA2A 0.087 +ATOM 1HB2 HDA2A 0.087 +ATOM 1SG SD30B 0.000 ALPHA -2.686 THOLE 1.082 +ATOM 1LPSA LPD -0.052 +ATOM 1LPSB LPD -0.052 +ATOM 2CB CD32A -0.070 ALPHA -1.888 THOLE 1.067 +ATOM 2HB1 HDA2A 0.087 +ATOM 2HB2 HDA2A 0.087 +ATOM 2SG SD30B 0.000 ALPHA -2.686 THOLE 1.082 +ATOM 2LPSA LPD -0.052 +ATOM 2LPSB LPD -0.052 + +BOND 1SG 2SG +BOND 1SG 1LPSA 1SG 1LPSB +BOND 2SG 2LPSA 2SG 2LPSB + +LONEPAIR bisector 1LPSA 1SG 1CB 2SG distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector 1LPSB 1SG 2SG 1CB distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector 2LPSA 2SG 2CB 1SG distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector 2LPSB 2SG 1SG 2CB distance 0.90 angle 110.0 dihe 90.0 +ANISOTROPY 1SG 1CB 1LPSA 1LPSB A11 0.9208 A22 1.0102 +ANISOTROPY 2SG 2CB 2LPSA 2LPSB A11 0.9208 A22 1.0102 + +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES ASPP 0.000 ! patch for protonated aspartic acid, proton on od2 + ! via acetic acid, use in a patch statementand + ! follow with AUTOgenerate ANGLes DIHEdrals command +! +! HB1 OD1 +! | // +! -CB--CG +! | \ +! HB2 OD2-HD2 +! +DELETE ATOM LP1A +DELETE ATOM LP1B +DELETE ATOM LP2A +DELETE ATOM LP2B +! +GROUP +ATOM CB CD32C -0.208 ALPHA -2.114 THOLE 0.750 !charge adjusted +ATOM HB1 HDA2A 0.092 +ATOM HB2 HDA2A 0.092 +ATOM CG CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM OD1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OD2 OD30D 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HD2 HDP1A 0.374 +ATOM LPP1 LPD -0.319 +ATOM LPP2 LPD -0.319 +ATOM LPP3 LPD -0.285 +ATOM LPP4 LPD -0.285 + +BOND OD2 HD2 +BOND OD1 LPP1 OD1 LPP2 +BOND OD2 LPP3 OD2 LPP4 + +!standard carbonyl +LONEPAIR relative LPP1 OD1 CG OD2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPP2 OD1 CG OD2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OD1 CG LPP1 LPP2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPP3 OD2 CG HD2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPP4 OD2 CG HD2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OD2 CG LPP3 LPP4 A11 0.8108 A22 1.2162 + +DONOR HD2 OD2 +IC OD1 CG OD2 HD2 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES GLUP 0.000 ! patch for protonated glutamic acid, proton on oe2 + ! via acetic acid, use in a patch statementand + ! follow with AUTOgenerate ANGLes DIHEdrals command +! +! HG1 OE1 +! | // +! -CG--CD +! | \ +! HG2 OE2-HE2 +! +DELETE ATOM LP1A +DELETE ATOM LP1B +DELETE ATOM LP2A +DELETE ATOM LP2B +! +GROUP +ATOM CG CD32C -0.208 ALPHA -2.114 THOLE 0.750 !charge adjusted +ATOM HG1 HDA2A 0.092 +ATOM HG2 HDA2A 0.092 +ATOM CD CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM OE1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OE2 OD30D 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HE2 HDP1A 0.374 +ATOM LPP1 LPD -0.319 +ATOM LPP2 LPD -0.319 +ATOM LPP3 LPD -0.285 +ATOM LPP4 LPD -0.285 + +BOND OE2 HE2 +BOND OE1 LPP1 OE1 LPP2 +BOND OE2 LPP3 OE2 LPP4 + +!standard carbonyl +LONEPAIR relative LPP1 OE1 CD OE2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPP2 OE1 CD OE2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OE1 CD LPP1 LPP2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPP3 OE2 CD HE2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPP4 OE2 CD HE2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OE2 CD LPP3 LPP4 A11 0.8108 A22 1.2162 + +DONOR HE2 OE2 +IC OE1 CD OE2 HE2 0.0000 0.0000 0.0000 0.0000 0.0000 + +!to be completed when neutral methylamine is optimized +!see NNEU above +!PRES LSN 0.000 ! patch for neutral lysine based on methylamine +! ! use in a patch statement +! ! follow with AUTOgenerate ANGLes DIHEdrals command +!DELETE ATOM HZ3 +!GROUP +!ATOM CE CT2 0.13 +!ATOM HE1 HA 0.075 +!ATOM HE2 HA 0.075 +!ATOM NZ NH2 -0.96 +!ATOM HZ1 HC 0.34 +!ATOM HZ2 HC 0.34 + +PRES LINK 0.000 ! linkage for cyclic peptide, may also be used for joining images + ! Note that the following number is required to include the CMAP + ! terms for the residues surrounding the link + ! 1 refers to residue 1 position from the C terminus (residue n-1) + ! 2 refers to the C terminus (residue n) which is a glycine + ! 3 refers to the N terminus (usually residue 1) + ! 4 refers to the N terminus plus 1 (usually residue 2) + ! use in a patch statement, perform initial + ! generation using first NONE last NONE + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 2C 3N +IMPR 3N 2C 3CA 3HN 2C 2CA 3N 2O + +CMAP 1C 2N 2CA 2C 2N 2CA 2C 3N +CMAP 2C 3N 3CA 3C 3N 3CA 3C 4N + +IC 2N 2CA 2C 3N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 3N 2CA *2C 2O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2CA 2C 3N 3CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2C 3N 3CA 3C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2C 3CA *3N 3HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 (convert HSD to HSE) + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +! HE1 +! / +! HB1 ND1--CE1 +! | / | +! -CB--CG | +! | \ | +! HB2 CD2--NE2 +! | \ +! HD2 HE2 +! +DELETE ATOM HD1 +DELETE ATOM LPE2 +DELETE ACCE NE2 + +GROUP +ATOM CB CD32A 0.017 ALPHA -1.739 THOLE 0.399 !charge adjusted +ATOM HB1 HDA2A 0.078 +ATOM HB2 HDA2A 0.078 +ATOM ND1 ND2R5B 0.000 ALPHA -1.146 THOLE 0.816 +ATOM LPD1 LPD -0.365 +ATOM NE2 ND2R5A -0.040 ALPHA -1.522 THOLE 1.114 +ATOM HE2 HDP1A 0.256 +ATOM CG CD2R5A -0.252 ALPHA -1.272 THOLE 1.190 +ATOM CE1 CD2R5B 0.064 ALPHA -1.493 THOLE 1.297 +ATOM HE1 HDR5B -0.018 +ATOM CD2 CD2R5A 0.141 ALPHA -1.515 THOLE 1.190 +ATOM HD2 HDR5A 0.041 + +BOND NE2 HE2 +BOND ND1 LPD1 + +IMPH NE2 CD2 CE1 HE2 + +LONEPAIR bisector LPD1 ND1 CE1 CG distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY ND1 LPD1 CE1 CG A11 0.808 A22 1.384 + +DONOR HE2 NE2 +ACCEP ND1 + +IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 + + +end + +read para card !append +* Drude polarizable FF parameters +* + +BONDS +!atom type Kb b0 +!============================================ +! +ND2A1 CD2O1A 420.00 1.350 ! ACEM, acetamide +ND2A1 CD2R6B 360.00 1.362 ! CTY, va +ND2A1 CD2R6C 360.00 1.369 ! ADE, cmb +ND2A1 HDP1A 480.00 1.025 ! ACEM, acetamide +ND2A2 CD2O1A 376.20 1.285 ! NMA, N-methylacetamide %PEML jan13 +ND2A2 CD31C 307.90 1.445 ! ALAD, alanine dipeptide %PEML jan13 +ND2A2 CD32C 338.00 1.425 ! GLYD, glycine dipeptide %PEML jan13 +ND2A2 CD33C 330.80 1.461 ! NMA, N-methylacetamide %PEML jan13 +ND2A2 HDP1A 459.30 1.030 ! NMA, N-methylacetamide %PEML jan13 +ND2A2 HDP1B 459.30 1.030 ! NMA, N-methylacetamide %PEML jan13 +ND2A3 CD2O1A 370.00 1.310 ! DMA, N,N-dimethylacetamide +ND2A3 CD33C 330.00 1.450 ! DMA, N,N-dimethylacetamide +ND3A3 HDP1A 440.00 1.025 ! PRLD, pyrrolidine, PEML % CHECK THESE ?? +ND2B1 CD2R6B 360.00 1.362 ! NA bases, cmb 04/10 +ND2B1 CD2R6C 360.00 1.369 ! NA bases, cmb 04/10 +ND2B1 HDP1A 480.00 1.025 ! NA bases, cmb 04/10 +ND2P1A CD2N1A 463.00 1.400 ! GUAN, geo opt (EH) +ND2P1A CD32A 285.30 1.488 ! GUAN, from GEOM OPT (PEML) +ND2P1A CD33A 285.30 1.488 ! GUAN, from GEOM OPT (PEML) +ND2P1A HDP1B 455.00 1.010 ! GUAN, geo opt (EH) +ND2R5A CD2R5A 400.00 1.380 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5A CD2R5B 400.00 1.360 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5A CD2R6D 279.90 1.415 ! INDO, indole +ND2R5A CD2R6F 428.02 1.381 ! PUR0/1, purine +ND2R5A HDP1A 466.00 1.000 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5B CD2R5A 400.00 1.380 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5B CD2R5B 400.00 1.320 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5B CD2R6F 428.02 1.381 ! PUR0/1, purine +ND2R5C CD2R5D 400.00 1.375 ! IMIM, geo opt (EH) +ND2R5C CD2R5E 400.00 1.350 ! IMIM, geo opt (EH) +ND2R5C HDP1A 466.00 1.000 ! IMIM, first guess (EH) +ND2R5D CD2R5B 400.00 1.370 ! ADE, cmb 04/10 +ND2R5D CD2R6F 350.00 1.370 ! ADE, cmb 04/10 +ND2R5D CD32A 400.00 1.456 ! Et-Gua, cmb 04/10 +ND2R5D CD33A 400.00 1.456 ! ADE, cmb 04/10 +ND2R5D HDP1A 466.00 1.000 ! ADE, IMID, imidazole, geom + freq, peml 2006 +ND2R5E CD2R5B 400.00 1.320 ! GUA/ADE, cmb 04/10 +ND2R5E CD2R6F 428.02 1.381 ! GUA/ADE, cmb 04/10 +ND2R6A CD2R6B 407.80 1.334 ! PYR, pyridine, geom + freq, peml 2005 +ND2R6B CD2O1A 360.00 1.330 ! CYT, va +ND2R6B CD2R6B 350.10 1.312 ! PYRM, pyrimidine, geom + freq, peml 2006 +ND2R6B CD2R6C 423.40 1.322 ! PYRM, pyrimidine, geom + freq, peml 2006 +ND2R6B CD2R6F 420.00 1.332 ! PUR0/1, purine +ND2R6B CD2R6H 420.00 1.332 ! CYT, cmb 04/10 +ND2R6B HDP1A 474.00 1.010 ! CYT +ND2R6C CD33A 400.00 1.456 ! CYT, cmb 04/10 +ND2R6C CD2O1A 340.00 1.370 ! THY, va +ND2R6C CD2R6C 400.00 1.392 ! GUA, cmb 04/10 +ND2R6C CD2R6H 420.00 1.332 ! CYT, cmb 04/10 +ND2R6C HDP1A 474.00 1.023 ! THY, cmb 04/10 +ND3A3 CD2O1A 479.10 1.364 ! 450.00 1.340 ! PRO +ND3A3 CD31C 233.52 1.437 ! 180.70 1.510 ! PRO +ND3A3 CD32A 215.01 1.461 ! 180.70 1.510 ! PRO +ND3A3 CD32C 180.70 1.510 ! PRLD, pyrrolidine, PEML +ND3P2A CD31A 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P2A CD31C 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P2A CD32A 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P2A CD33A 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P3A CD31A 180.70 1.510 ! NTER, NC1, qm, EH 2007, From ND3P3A CD33A %% +ND3P3A CD31C 180.70 1.510 ! NTER, NC1, qm, EH 2007, From ND3P3A CD33A %% +ND3P3A CD32A 215.00 1.510 ! NC1, qm, EH 2007, ammonium cations +ND3P3A CD32C 215.00 1.510 ! NC1, qm, EH 2007, ammonium cations +ND3P3A CD33A 215.00 1.510 ! NC1, qm, EH 2007, ammonium cations +ND3P2A HDP1B 440.00 1.025 ! NH4, NMA, need work** +ND3P3A HDP1B 440.00 1.025 ! NH4, NMA, need work** +OD2C1A CD2O1A 673.70 1.245 ! NMA, N-methylacetamide %PEML jan13 +OD2C2A CD2O2A 527.00 1.250 ! ACET, CTER, PEML +OD2C1B CD2O1A 623.00 1.239 ! NA bases, cmb 04/10 +OD2C2B PD1A 525.00 1.500 ! DMP, cmb, 06/09 +OD2C2C PD1AN 525.00 1.500 ! DMP, nucleic acid +OD2C3A CD2O3A 730.00 1.200 ! MAS, csd, EH 2007, PEML 2009 *** b0 should be 1.220 based on MP2/6-31g*, confirm +OD305A CD315B 350.00 1.425 ! TF2M, cmb +OD305A CD325B 350.00 1.425 ! THF, CSD/NDB survey, viv +OD306A CD326B 360.00 1.415 ! THP, tetrahydropyran, viv +OD30A CD32E 360.00 1.415 ! DEET, diethylether, alex +OD30A CD33E 360.00 1.415 ! DEET, diethylether, alex +OD30B PD1A 240.00 1.600 ! DMP, cmb, 06/09 +OD30BN PD1AN 240.00 1.600 ! DMP, nucleic acid +OD30B CD32A 335.00 1.420 ! DMP, csd, EH/IV 2007 +OD30B CD33A 335.00 1.420 ! DMP, csd, EH/IV 2007 +OD30B CD33C 335.00 1.440 ! DMP, cmb, 06/09 +OD30BN CD33C 335.00 1.440 ! DMP, nucleic acid +OD30B HDP1A 536.50 0.970 ! CHOL, MEOH, not necessary for lipid +OD30C CD2O3A 150.00 1.330 ! MAS, csd, EH 2007, PEML 2009 *** changed FC to match vibr. spectra *** +OD30C CD31C 340.00 1.440 ! MAS, csd, EH 2007 +OD30C CD32C 340.00 1.440 ! MAS, csd, EH 2007 +OD30C CD33C 340.00 1.440 ! MAS, csd, EH 2007 +OD30C CD33D 340.00 1.440 ! MAS, csd, EH 2007 +OD30D CD2O3A 205.50 1.269 ! ACEH, PEML +OD30D HDP1A 480.40 0.969 ! ACEH, PEML +OD31A CD31A 350.00 1.440 ! PRO2, 2-propanol +OD31A CD315A 350.00 1.440 ! CPO1, cyclopropanol +OD31A CD32A 396.00 1.425 ! ETOH, ethanol +OD31A CD33B 430.00 1.425 ! MEOH, methanol +OD31A HDP1A 536.50 0.970 ! MEOH, methanol +OD31B CD32A 396.00 1.425 ! ETOH, ethanol +OD31B HDP1A 536.50 0.970 ! PRO1, 1-propanol +OD31C CD2R6A 334.30 1.411 ! PHEN, phenol +OD31C HDP1A 545.00 0.960 ! PHEN, phenol +ODW HDW 450.00 0.9572 ! SWM4, SWM4-NDP water, Guillaume 2005 +ODW DOH2 500.00 0.000 ! SWM4, SWM4-NDP water, Guillaume 2005 +HDW HDW 0.00 1.5139 ! SWM4 and SWM6 water models +ODW6 HDW 450.0 0.9572 ! SWM6-NDP water +ODW6 DOH2 500.0 0.0000 ! SWM6-NDP water +SD30A CD32A 228.00 1.806 ! EMS +SD30A CD33A 230.00 1.795 ! EMS +SD30B SD30B 155.50 2.036 ! DMDS +SD30B CD32A 204.10 1.806 ! DMDS, Disulfide patch +SD30B CD33A 204.10 1.806 ! DMDS +SD31A CD33A 218.00 1.811 ! MESH +SD31A HDP1A 283.00 1.3497 ! MESH +SD31B CD32A 220.00 1.810 ! ETSH +SD31B HDP1A 283.00 1.3497 ! ETSH, from 1.3497 +CD2O1A CD2R6A 302.00 1.390 ! THY, va +CD2O1A CD2R6F 302.00 1.360 ! GUA, cmb 04/10 +CD2O1A CD31A 299.30 1.467 ! CT2, ALAD, alanine dipeptide ??? CHECK THIS +CD2O1A CD31C 195.90 1.340 ! NMA, N-methylacetamide %PEML jan13 +CD2O1A CD32A 350.00 1.525 ! GLYP, GLYD, glycine dipeptide +CD2O1A CD32C 350.00 1.430 ! GLYD, PEML oct09 alterado em nov09 +CD2O1A CD33C 106.1 1.153 ! NMA, N-methylacetamide %PEML jan13 +CD2O2A CD31A 114.50 1.561 ! NTER/ACET, PEML +CD2O2A CD31C 90.00 1.560 ! CTER, PEML +CD2O2A CD32A 110.00 1.535 ! ACET, PEML +CD2O2A CD32C 90.00 1.560 ! CTER, PEML +CD2O2A CD33A 110.00 1.535 ! ACET, PEML +CD2O3A CD31A 282.20 1.505 ! ACEH/CNEU PEML +CD2O3A CD31C 108.00 1.509 ! CNEU, PEML +CD2O3A CD32C 200.00 1.510 ! MAS, csd, EH 2007, ACEH +CD2O3A CD33C 133.00 1.510 ! ACEH, PEML +CD2R5A CD2R5A 410.00 1.360 ! IMID, imidazole, geom + freq, peml 2006 +CD2R5A CD2R5C 322.60 1.397 ! PYRR, pyrrole CY CA 350.000 1.3650 ! ALLOW ARO +CD2R5A CD32A 229.60 1.500 ! 4MIM, 4-methyl-imidazole +CD2R5A CD33A 229.60 1.500 ! 4MIM, 4-methyl-imidazole +CD2R5A HDR5A 365.00 1.083 ! IMID, imidazole, geom + freq, peml 2006 +CD2R5B HDR5B 340.00 1.090 ! IMID, imidazole, geom + freq, peml 2006 +CD2R5C CD2R5C 322.90 1.430 ! PYRR, pyrrole CY CPT 350.000 1.4400 ! ALLOW ARO +CD2R5C CD2R6D 407.60 1.420 ! INDO, indole +CD2R5C CD32A 229.63 1.500 ! INDM, methyl-indole, Trp +CD2R5C CD33A 229.63 1.500 ! INDM, methyl-indole +CD2R5C HDR5C 370.20 1.080 ! PYRR, pyrrole HA CY 330.000 1.0800 ! ALLOW ARO +CD2R5D CD2R5D 410.00 1.360 ! IMIM +CD2R5D CD32A 229.60 1.500 ! 4MIM, 4-methyl-imidazole +CD2R5D HDR5D 365.00 1.083 ! IMIM +CD2R5E HDR5E 340.00 1.090 ! IMIM +CD2R6A CD2R6A 305.00 1.375 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6A CD2R6B 361.10 1.378 ! PYR, pyridine, geom + freq, peml 2005 +CD2R6A CD2R6D 315.00 1.382 ! INDO, indole +CD2R6A CD2R6H 460.00 1.280 ! CYT, cmb 04/10 +CD2R6A CD32A 230.00 1.490 ! PHE/TOLU +CD2R6A CD33A 230.00 1.490 ! TOLU, toluene, geom + freq, peml 2005 +CD2R6A HDR6A 340.00 1.080 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6B CD2R6F 295.82 1.398 ! PUR0/1, purine +CD2R6B HDR6B 340.00 1.080 ! PYR, pyridine, geom + freq, peml 2005 +CD2R6C CD2R6F 360.00 1.358 ! ADE, cmb 04/10 +CD2R6C HDR6C 320.00 1.080 ! PYRM, pyrimidine, geom + freq, peml 2006 +CD2R6D CD2R6D 198.20 1.400 ! INDO, indole +CD2R6F CD2R6F 331.89 1.469 ! PUR0/1, purine +CD2R6H HDR6B 340.00 1.080 ! CYT, cmb 04/10 +CD30A CD32A 222.50 1.538 ! alkanes, 10/98 +CD30A CD33A 222.50 1.538 ! NEOP, neopentane, 10/98 +CD315B CD325B 195.00 1.518 ! TF2M, cmb +CD315B CD33A 222.50 1.528 ! TF2M, 2-methyl-THF,viv; mod cmb +CD315A CD33A 222.50 1.528 ! CPNM, 2-methyl-THF,viv; mod cmb +CD315B HDA1R5 307.00 1.100 ! TF2M, cmb +CD315A HDA1R5 307.00 1.100 ! CPNM, cmb by analogy +CD31A CD31A 222.50 1.500 ! alkanes, 3/92 +CD31A CD31C 222.50 1.500 ! 3/92 +CD31A CD32A 222.50 1.538 ! alkanes, 3/92 +CD31A CD33A 225.00 1.538 ! va, 9/07 +CD31A HDA1A 309.00 1.111 ! IBUT, isobutane, alkanes, 4/98 +CD31A HDA1C 300.00 1.080 ! NTER, NC4, qm, EH 2007, From CD33A HDA3C +CD31C HDA1C 300.00 1.080 ! NTER, NC4, qm, EH 2007, From CD33A HDA3C +CD31C CD31C 222.50 1.500 ! alkane +CD31C CD32A 222.50 1.528 ! 3/92 %PEML oct09 alterado em nov09 +CD31C CD32B 222.50 1.528 ! GLU, from CD31C CD32A +CD31C CD32C 222.50 1.528 ! 3/92 ??? CHECK THIS +CD31C CD33A 180.40 1.541 ! 3/92 %PEML jan13 +CD31C CD33C 222.50 1.528 ! alkane ??? CHECK THIS +CD31C HDA1A 309.00 1.111 ! alkanes, 4/98 +CD325A CD325A 195.00 1.548 ! CPEN, cyclopentane, viv +CD315A CD325A 195.00 1.548 ! CPNM, from CPEN, cmb +CD325A HDA2R5 307.00 1.116 ! CPEN, cyclopentane, viv +CD325B CD325B 195.00 1.518 ! THF, CSD/NDB survey, viv +CD325B HDA2R5 307.00 1.100 ! THF, THF neutron diffr, viv +CD316A CD326A 222.50 1.530 ! CHXM, from alkanes CD32A, cmb 12/09 +CD316A HDA1A 309.00 1.111 ! CHXM, from alkanes CD32A, cmb 12/09 +CD316A CD33A 225.00 1.538 ! CHXM, from va, 9/07. cmb 12/09 +CD326A CD326A 222.50 1.530 ! CHEX, from alkanes CD32A, cmb 9/09 +CD326A HDA2A 309.00 1.111 ! CHEX, from alkanes CD32A, cmb 9/09 +CD326B CD326B 222.50 1.530 ! THP, tetrahydropyran, viv +CD326B HDA2E 309.00 1.111 ! THP, tetrahydropyran, viv +CD32A CD32A 222.50 1.530 ! alkanes, 3/92 +CD32A CD32B 222.50 1.530 ! GLU, from CD32A CD32A +CD32B CD32C 222.50 1.530 ! GLUP, from CD32A CD32A +CD32A CD32C 222.50 1.530 ! alkane +CD32A CD32E 222.50 1.530 ! ethers +CD32A CD33A 222.50 1.528 ! alkanes, 3/92 +CD32A CD33C 222.50 1.528 ! alkane +CD32A HDA2A 309.00 1.111 ! alkanes, 4/98 +CD32B HDA2A 309.00 1.111 ! GLU, from CD32A HDA2A +CD32A HDA2C 300.00 1.080 ! GLYP, NC4, qm, EH 2007 +CD32C HDA2C 300.00 1.080 ! GLYP, NC4, qm, EH 2007 +CD32C CD32C 222.50 1.530 ! alkane +CD32C CD33A 222.50 1.528 ! alkane +CD32C CD33C 222.50 1.528 ! alkane +CD32C HDA2A 309.00 1.111 ! 4/98 +CD32E CD32E 222.50 1.530 ! ethers +CD32E CD33A 222.50 1.528 ! ethers +CD32E HDA2E 309.00 1.111 ! ethers, cmb +CD33A CD33A 222.50 1.530 ! alkanes, 3/92 +CD33A HDA3A 322.00 1.111 ! alkanes, 4/98 +CD33A HDA3C 300.00 1.080 ! NC4, qm, EH 2007, ammonium cations +CD33B HDA3B 322.00 1.111 ! alkanes, 4/98, MEOH, methanol special case +CD33C CD33C 222.50 1.530 ! alkane +CD33C HDA3A 322.00 1.111 ! 4/98 +CD33D HDA3A 322.00 1.111 ! 4/98 +CD33E HDA3A 322.00 1.111 ! ethers +X DRUD 500.00 0.000 ! +! +ODW LPDW 0.00 0.24034492 ! SWM4, SWM4-NDP water, Guillaume 2005 +DOH2 LPDW 500.00 0.000 ! SWM4 and SWM6 water models +ODW6 LPDW 0.00 0.000 ! SWM6-NDP water +HDP1A LPD 0.00 0.000 ! ACEH, PEML +CD2O1A LPD 0.00 0.000 ! NMA +CD2O2A LPD 0.00 0.000 ! Acetate +CD2O3A LPD 0.00 0.000 ! MAS +CD2R5A LPD 0.00 0.000 ! IMID +CD2R5B LPD 0.00 0.000 ! IMID +CD2R6A LPD 0.00 0.000 ! PHEN +CD2R6B LPD 0.00 0.000 ! PYR +CD2R6C LPD 0.00 0.000 ! PYRM +CD2R6F LPD 0.00 0.000 ! PUR0/1 +CD2R6H LPD 0.00 0.000 ! CYT,THY,URA, cmb 04/10 +CD315B LPD 0.00 0.000 ! TF2M +CD31A LPD 0.00 0.000 ! PRO2 +CD31C LPD 0.00 0.000 ! MAS +CD325B LPD 0.00 0.000 ! THF +CD326B LPD 0.00 0.000 ! DMP +CD32A LPD 0.00 0.000 ! DEET +CD32C LPD 0.00 0.000 ! MAS +CD32E LPD 0.00 0.000 ! DEET +CD33A LPD 0.00 0.000 ! DMP +CD33B LPD 0.00 0.000 ! MEOH +CD33C LPD 0.00 0.000 ! MAS +CD33E LPD 0.00 0.000 ! DMP +ND2R5B LPD 0.00 0.000 ! IMID +ND2R5B LPDNA1 0.00 0.000 ! Purine +ND2R5E LPDNA1 0.00 0.000 ! GUA/ADE, cmb 04/10 +ND2R6A LPDNA1 0.00 0.000 ! PYR +ND2R6B LPDNA1 0.00 0.000 ! PYRM +OD2C1A LPD 0.00 0.000 ! NMA +OD2C1A LPDO1 0.00 0.000 ! NMA, special LP +OD2C2A LPD 0.00 0.000 ! Acetate, DMP +OD2C1B LPDNA1 0.00 0.000 ! NA bases, cmb 04/10 +OD2C3A LPD 0.00 0.000 ! MAS +OD305A LPD 0.00 0.000 ! THF +OD306A LPD 0.00 0.000 ! THP +OD30A LPD 0.00 0.000 ! DEET +OD30B LPD 0.00 0.000 ! DMP +OD30C LPD 0.00 0.000 ! MAS +OD30D LPD 0.00 0.000 ! ACEH, PEML +OD31A LPD 0.00 0.000 ! ETOH +OD31B LPD 0.00 0.000 ! PRO1 +OD31C LPD 0.00 0.000 ! PHEN +SD30A LPD 0.00 0.000 ! EMS, DMS +SD30B LPD 0.00 0.000 ! DMDS +SD31A LPD 0.00 0.000 ! MESH +SD31B LPD 0.00 0.000 ! ETSH +PD1A LPD 0.00 0.000 ! DMP +PD1AN LPD 0.00 0.000 ! DMP, nucleic acid + +ANGLES +!atom types Ktheta Theta0 Kub S0 +!================================================== +CD2O1A ND2A1 HDP1A 50.00 123.50 ! ACEM +HDP1A ND2A1 HDP1A 24.00 113.00 ! ACEM +CD2O1A ND2A2 CD31C 40.90 116.10 ! ALAD % +CD2O1A ND2A2 CD32C 80.20 121.00 ! GLYD +CD2O1A ND2A2 CD33C 97.70 120.77 ! NMA+ALAD % +CD2O1A ND2A2 HDP1A 45.60 120.26 ! NMA+ALAD % +CD31C ND2A2 HDP1A 72.20 123.64 ! ALAD % +CD32C ND2A2 HDP1A 64.50 119.00 ! GLYD +CD33C ND2A2 HDP1A 48.00 118.97 ! NMA+ALAD % +CD2O1A ND2A3 CD33C 10.00 119.20 ! DMA +CD33C ND2A3 CD33C 40.00 121.60 ! DMA +CD32C ND3A3 HDP1A 64.50 119.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ?? +CD2N1A ND2P1A CD32A 62.30 120.00 ! ARG, c22 +CD2N1A ND2P1A CD33A 62.39 120.00 ! GUAN, c22 +CD2N1A ND2P1A HDP1B 49.00 124.00 ! GUAN, geo opt (EH) +CD32A ND2P1A HDP1B 40.40 120.00 ! ARG, c22 +CD33A ND2P1A HDP1B 40.40 120.00 ! GUAN, c22 +HDP1B ND2P1A HDP1B 25.00 114.00 ! GUAN, geo opt (EH) +CD2R5A ND2R5A CD2R5A 119.08 106.00 ! PYRR, pyrrole +CD2R5A ND2R5A CD2R5B 130.00 107.50 ! IMID, imidazole +CD2R5A ND2R5A CD2R6D 81.40 108.60 ! INDO, indole +CD2R5A ND2R5A HDP1A 30.00 125.50 20.00 2.1500 ! IMID, imidazole +CD2R5B ND2R5A CD2R6F 137.46 109.60 ! PUR0/1, purine +CD2R5B ND2R5A HDP1A 30.00 127.00 20.00 2.1400 ! IMID, imidazole +CD2R6D ND2R5A HDP1A 12.80 125.90 ! INDO, indole +CD2R6F ND2R5A HDP1A 37.59 125.50 28.70 2.2021 ! PUR0/1, purine +CD2R5A ND2R5B CD2R5B 130.00 104.00 ! IMID, imidazole +CD2R5B ND2R5B CD2R6F 127.91 103.00 ! PUR0/1, purine +CD2R5B ND2R5D CD32A 17.00 127.80 ! Et-Gua, cmb 04/10 +CD2R5A ND2R5C HDP1A 25.00 126.00 15.00 2.1300 ! IMID, imidazole +CD2R5B ND2R5C HDP1A 25.00 126.00 15.00 2.0900 ! IMID, imidazole +CD2R5D ND2R5C CD2R5E 130.00 111.00 ! IMIM, geo opt (EH) +CD2R5D ND2R5C HDP1A 30.000 125.50 20.00 2.1500 ! IMIM +CD2R5E ND2R5C HDP1A 30.000 127.00 20.00 2.1400 ! IMIM +CD2R5B ND2R5D HDP1A 30.00 127.00 20.00 2.1400 ! ADE/IMID, imidazole +CD2R6F ND2R5D HDP1A 28.00 126.00 ! ADE, cmb 04/10 +CD2R6F ND2R5D CD32A 17.00 125.90 ! Et-Gua, cmb 04/10 +CD2R6B ND2R6A CD2R6B 19.60 100.00 54.20 2.2850 ! PYR, pyridine +CD2O1A ND2R6B CD2R6H 100.00 118.00 ! CYT, cmb 04/10 +CD2O1A ND2R6C CD33A 60.00 115.40 ! CYT, +CD2O1A ND2R6B HDP1A 37.00 121.20 ! CYT, +CD2R6B ND2R6B CD2R6C 27.50 110.00 66.70 2.2000 ! PYRM, pyrimidine +CD2R6C ND2R6B CD2R6F 26.30 121.10 75.00 2.3797 ! PUR0/1, purine (for model cmpds?) +CD2R6H ND2R6C CD33A 60.00 120.50 ! CYT, cmb 04/10 +CD2R6H ND2R6C HDP1A 37.00 114.70 ! CYT, cmb 04/10 +CD2R6C ND2R6C HDP1A 45.00 115.60 ! GUA, cmb 04/10 +CD2O1A ND3A3 CD31C 35.00 111.00 ! PRO +CD2O1A ND3A3 CD32A 35.00 111.00 ! PRO +CD31C ND3A3 CD32A 50.00 111.00 ! PRO +CD32C ND3A3 CD32C 50.00 111.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ?? +CD32A ND3P2A CD31C 60.00 109.50 26.00 2.4660 ! NC4, qm, EH 2007, ammonium cations, +CD32A ND3P2A CD33A 60.00 109.50 26.00 2.4660 ! NC4, qm, EH 2007, ammonium cations +CD33A ND3P2A CD33A 60.00 109.50 26.00 2.4660 ! NC4, qm, EH 2007, ammonium cations +CD31A ND3P2A HDP1B 28.80 113.10 11.30 1.983 ! NTER, PEML +CD31C ND3P2A HDP1B 28.80 113.10 11.30 1.983 ! NTER, PEML +CD32A ND3P2A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +CD32C ND3P2A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +CD33A ND3P2A HDP1B 33.00 109.50 4.00 2.0560 ! NC1, charmm27 (etam), ammonium cations +HDP1B ND3P2A HDP1B 41.00 109.50 ! NH4, charmm27, ammonium cations +CD31A ND3P3A HDP1B 28.80 113.10 11.30 1.983 ! NTER, PEML +CD31C ND3P3A HDP1B 28.80 113.10 11.30 1.983 ! NTER, PEML +CD32A ND3P3A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +CD32C ND3P3A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +CD33A ND3P3A HDP1B 33.00 109.50 4.00 2.0560 ! NC1, charmm27 (etam), ammonium cations +HDP1B ND3P3A HDP1B 41.00 109.50 ! NH4, charmm27, ammonium cations +CD315B OD305A CD325B 95.00 111.00 ! TF2M 02/09, cmb +CD325B OD305A CD325B 95.00 111.00 ! THF, viv 10/21/05 +CD326B OD306A CD326B 95.00 109.70 ! THP, viv +CD32A OD30A CD32A 95.00 109.70 ! DEET, diethylether, alex +CD32A OD30A CD33A 95.00 109.70 ! DEET, diethylether, alex +CD32E OD30A CD32E 95.00 109.70 ! DEET, diethylether, alex +CD32E OD30A CD33E 95.00 109.70 ! DEET, diethylether, alex +CD33A OD30A CD33A 95.00 109.70 ! DME dimethylether,viv +CD33E OD30A CD33E 95.00 109.70 ! DME dimethylether,viv +PD1A OD30B CD32A 40.00 112.50 ! DMP, csd, EH/IV 2007**better molvib fit +PD1A OD30B CD33A 40.00 112.50 ! DMP, csd, EH/IV 2007**better molvib fit +PD1A OD30B CD33C 40.00 120.50 ! DMP, cmb, 06/09 +PD1AN OD30BN CD32A 40.00 112.50 ! DMP, csd, nucleic acids +PD1AN OD30BN CD33A 40.00 112.50 ! DMP, csd, nucleic acids +PD1AN OD30BN CD33C 40.00 120.50 ! DMP, cmb, nucleic acids +CD2O3A OD30C CD31C 15.00 100.00 10.00 2.0151 ! MAS, csd, EH 2007 PEML 2009 **gives CSD/vibr spectra +CD2O3A OD30C CD32C 15.00 100.00 10.00 2.0151 ! MAS, csd, EH 2007 PEML 2009 **gives CSD/vibr spectra +CD2O3A OD30C CD33C 15.00 100.00 10.00 2.0151 ! MAS, csd, EH 2007 PEML 2009 **gives CSD/vibr spectra +CD2O3A OD30C CD33D 15.00 100.00 10.00 2.0151 ! MAS, csd, EH 2007 PEML 2009 **gives CSD/vibr spectra +CD2O3A OD30D HDP1A 58.90 110.20 15.10 2.3770 ! ACEH, PEML +CD2R6A OD31A HDP1A 65.00 108.00 ! PHE, Phenol +CD31A OD31A HDP1A 59.00 108.00 ! PRO2, 2-propanol +CD315A OD31A HDP1A 59.00 108.00 ! CPO1, cyclohexanol +CD32A OD31A HDP1A 49.00 106.00 ! ETOH, ethanol +CD33B OD31A HDP1A 58.20 106.00 ! MEOH, methanol +CD32A OD31B HDP1A 49.00 106.00 ! PRO1, 1-propanol +CD2R6A OD31C HDP1A 65.00 108.00 ! PHEN, Phenol +HDW ODW HDW 55.000 104.52 ! SWM4-NDP water Guillaume 2005 +HDW ODW6 HDW 55.000 104.52 ! SWM6-NDP water model +CD32A SD30A CD33A 21.00 97.10 ! EMS +CD33A SD30A CD33A 21.00 97.10 ! DMS +SD30B SD30B CD32A 60.00 104.25 ! DMDS, Disulfide patch +SD30B SD30B CD33A 60.00 104.25 ! DMDS +CD33A SD31A HDP1A 40.00 96.10 ! MESH +CD32A SD31B HDP1A 45.80 96.48 ! ETSH +OD2C2B PD1A OD2C2B 60.00 116.00 ! DMP, csd, EH/IV 2007 +OD2C2B PD1A OD30B 80.00 107.00 ! DMP, csd, EH/IV 2007**better molvib fit +OD30B PD1A OD30B 90.00 104.00 ! DMP, csd, EH/IV 2007 +ND2P1A CD2N1A ND2P1A 52.00 120.00 90.00 2.3642 ! GUAN, geo opt (EH) +ND2A1 CD2O1A OD2C1A 85.00 125.00 ! ACEM +ND2A1 CD2O1A CD31C 62.37 110.66 ! CT2 +ND2A1 CD2O1A CD32C 40.00 114.00 ! ASN, Acetamide +ND2A1 CD2O1A CD33C 40.00 114.00 ! ACEM +ND2A2 CD2O1A OD2C1A 89.70 130.90 ! NMA+ALAD % important for N-C=O +ND2A2 CD2O1A CD31A 62.37 110.66 ! NTER-(X)n-CNEU +ND2A2 CD2O1A CD31C 74.80 102.10 174.4 2.6308 ! ALAD % important for Ca-C-N (dCT-C-N) +ND2A2 CD2O1A CD32A 62.37 110.66 ! NTER-(X)n-CNEU +ND2A2 CD2O1A CD32C 92.10 114.70 179.80 2.4290 ! GLYD % +ND2A2 CD2O1A CD33C 51.50 109.82 84.40 2.9072 ! NMA+ALAD % important for Ca-C-N +ND2A3 CD2O1A OD2C1A 70.00 123.00 ! DMA +ND2A3 CD2O1A CD33C 70.00 115.00 ! DMA +ND2R6B CD2O1A ND2R6B 50.00 113.00 ! CYT, va +ND3A3 CD2O1A CD31C 63.37 108.69 ! 62.00 110.00 ! PRO, uncommented, zhu +ND3A3 CD2O1A CD32A 63.37 108.69 ! 62.00 110.00 ! PRO, uncommented, zhu +ND3A3 CD2O1A CD32C 63.37 108.69 ! 62.00 110.00 ! PRO, uncommented, zhu +ND3A3 CD2O1A CD33C 63.37 108.69 ! 62.00 110.00 ! PRO +ND3A3 CD2O1A OD2C1A 66.19 129.68 ! 62.00 110.00 ! PRO +OD2C1A CD2O1A CD31A 69.30 111.80 ! NTER-(X)n-CNEU +OD2C1A CD2O1A CD31C 96.00 127.00 107.6 2.4358 ! ALAD % important for Ca-C=O (dC=O) +OD2C1A CD2O1A CD32A 69.30 111.80 ! NTER-(X)n-CNEU +OD2C1A CD2O1A CD32C 110.40 116.20 180.10 2.4180 ! GLYD ??? CHECK +OD2C1A CD2O1A CD33C 59.20 116.10 81.70 2.4774 ! NMA+ALAD % important for Ca-C=O (dC=O) +OD2C2A CD2O2A OD2C2A 83.70 127.90 128.80 2.3790 ! ACET, PEML +OD2C2A CD2O2A CD31A 40.00 109.30 ! NTER, PEML +OD2C2A CD2O2A CD31C 48.90 123.00 29.90 2.2930 ! CTER, PEML, ACET +OD2C2A CD2O2A CD32A 48.90 123.00 29.90 2.2930 ! CTER, PEML, ACET +OD2C2A CD2O2A CD32C 40.00 109.30 ! NTER, PEML, terminal Gly +OD2C2A CD2O2A CD33A 23.80 123.00 34.90 2.3910 ! ACET, PEML +OD2C3A CD2O3A OD30C 90.00 123.00 160.00 2.2576 ! MAS, csd, EH 2007 +OD2C3A CD2O3A OD30D 98.80 117.50 178.30 2.4240 ! ACEH, PEML +OD2C3A CD2O3A CD31A 80.00 121.00 39.90 2.412 ! NTER, PEML +OD2C3A CD2O3A CD31C 50.50 123.20 33.10 2.226 ! CNEU +OD2C3A CD2O3A CD32C 70.00 126.00 20.00 2.4420 ! MAS, csd, EH 2007 +OD2C3A CD2O3A CD33C 70.00 126.00 20.00 2.4420 ! MAS, csd, EH 2007 +OD30C CD2O3A CD31C 55.00 111.00 20.00 2.3260 ! MAS, csd, EH 2007 +OD30C CD2O3A CD32C 55.00 111.00 20.00 2.3260 ! MAS, csd, EH 2007 +OD30C CD2O3A CD33C 55.00 111.00 20.00 2.3260 ! MAS, csd, EH 2007 +OD30D CD2O3A CD31A 65.00 107.30 26.80 2.253 ! NTER, PEML +OD30D CD2O3A CD31C 46.20 115.70 36.00 2.126 ! CNEU +OD30D CD2O3A CD32C 46.20 115.70 36.00 2.126 ! CNEU +OD30D CD2O3A CD33C 48.50 113.40 26.80 2.3370 ! ACEH, PEML +ND2R5A CD2R5A CD2R5A 130.00 106.00 ! IMID, imidazole +ND2R5A CD2R5A CD2R5C 100.02 106.00 28.00 2.2400 ! PYRR, pyrrole +ND2R5A CD2R5A CD32A 45.80 124.00 ! HSD, 4MIM, 4-methyl-imidazole +ND2R5A CD2R5A CD33A 45.80 124.00 ! 4MIM, 4-methyl-imidazole +ND2R5A CD2R5A HDR5A 25.00 124.00 20.00 2.1400 ! IMID, imidazole +ND2R5B CD2R5A CD2R5A 130.00 110.00 ! IMID, imidazole +ND2R5B CD2R5A CD32A 45.800 120.00 ! HSE, c22 +ND2R5B CD2R5A HDR5A 25.00 120.00 20.00 2.1400 ! IMID, imidazole +ND2R5C CD2R5A CD32A 45.800 122.00 ! HSP, c22 +CD2R5A CD2R5A CD32A 45.80 130.00 ! HSD, 4MIM, 4-methyl-imidazole +CD2R5A CD2R5A CD33A 45.80 130.00 ! 4MIM, 4-methyl-imidazole +CD2R5A CD2R5A HDR5A 25.00 130.00 20.00 2.2000 ! IMID, imidazole +CD2R5A CD2R5A HDR5B 22.00 130.00 15.00 2.2150 ! IMID, imidazole +CD2R5C CD2R5A HDR5A 18.63 125.00 28.00 2.1730 ! PYRR, pyrrole +ND2R5A CD2R5B ND2R5B 130.00 112.50 ! IMID, imidazole +ND2R5A CD2R5B HDR5B 25.00 122.50 20.00 2.1400 ! IMID, imidazole +ND2R5B CD2R5B HDR5B 25.00 125.00 20.00 2.1200 ! IMID, imidazole +ND2R5D CD2R5B HDR5B 25.00 122.50 20.00 2.1400 ! ADE/IMID, imidazole +ND2R5E CD2R5B HDR5B 25.00 125.00 20.00 2.1200 ! ADE, 04/10 +CD2R5A CD2R5C CD2R5C 80.00 106.40 27.90 2.2610 ! PYRR, pyrrole +CD2R5A CD2R5C CD2R6D 81.90 106.10 22.50 2.2163 ! INDO, indole +CD2R5A CD2R5C CD32A 45.80 122.30 ! INDM, methyl-indole, Trp +CD2R5A CD2R5C CD33A 45.80 122.30 ! INDM, methyl-indole +CD2R5A CD2R5C HDR5C 12.72 126.40 28.00 2.2150 ! PYRR, pyrrole +CD2R5C CD2R5C HDR5C 23.80 126.40 28.00 2.2150 ! PYRR, pyrrole +CD2R6D CD2R5C CD32A 45.80 122.30 ! INDM, methyl-indole, Trp +CD2R6D CD2R5C CD33A 45.80 122.30 ! INDM, methyl-indole +CD2R6D CD2R5C HDR5C 1.70 124.70 8.39 2.3781 ! INDO, indole +ND2R5C CD2R5D CD2R5D 130.00 105.50 ! IMIM, geo opt (EH) +ND2R5C CD2R5D CD32A 45.80 124.00 ! HSP, 4MIM, 4-methyl-imidazole +ND2R5C CD2R5D HDR5D 25.00 124.00 20.00 2.1400 ! IMIM, from IMID (EH) +CD2R5D CD2R5D CD32A 45.80 130.00 ! HSP, 4MIM, 4-methyl-imidazole +CD2R5D CD2R5D HDR5D 25.000 130.00 20.00 2.2000 ! IMIM +ND2R5C CD2R5E ND2R5C 130.00 107.75 ! IMIM, geo opt (EH) +ND2R5C CD2R5E HDR5E 25.00 125.00 20.00 2.1200 ! IMIM, from IMID (EH) +OD31A CD2R6A CD2R6A 45.20 120.00 ! PHE, Phenol +OD31C CD2R6A CD2R6A 45.20 120.00 ! PHEN, Phenol +CD2O1A CD2R6A CD33A 38.00 118.70 ! THY +CD2O1A CD2R6A HDR6A 30.00 120.30 ! URA +CD2R6A CD2R6A CD2R6A 40.00 120.00 35.00 2.4162 ! BENZ, benzene +CD2R6A CD2R6A CD2R6B 46.10 120.00 29.80 2.4480 ! PYR, pyridine +CD2R6A CD2R6A CD2R6D 143.50 123.80 ! INDO, indole +CD2R6A CD2R6A CD32A 45.80 122.30 ! PHE/TOLU +CD2R6A CD2R6A CD33A 45.80 122.30 ! TOLU, toluene +CD2R6A CD2R6A HDR6A 30.00 120.00 22.00 2.1525 ! BENZ, benzene +CD2R6B CD2R6A CD2R6B 60.20 128.00 33.20 2.4400 ! PYRM, pyrimidine +CD2R6B CD2R6A HDR6A 26.00 120.00 21.00 2.1525 ! PYR, pyridine +CD2R6D CD2R6A HDR6A 43.50 122.60 19.90 2.0833 ! INDO, indole +CD2R6H CD2R6A CD33A 38.00 124.60 ! THY, cmb +CD2R6H CD2R6A HDR6A 30.00 117.50 ! CYT, cmb +ND2R6A CD2R6B CD2R6A 27.40 119.20 ! PYR, pyridine +ND2R6A CD2R6B HDR6B 25.90 112.00 32.20 2.0500 ! PYR, pyridine +ND2R6B CD2R6B CD2R6A 44.30 121.00 ! nucleic acids, from 125.00 ! PYRM, pyrimidine +ND2R6B CD2R6B CD2R6F 23.16 123.30 ! PUR0/1, purine +ND2R6B CD2R6B HDR6B 28.40 112.00 23.90 2.0500 ! PYRM, pyrimidine +CD2R6A CD2R6B HDR6B 43.40 120.00 18.60 2.1525 ! PYR, pyridine +CD2R6F CD2R6B HDR6B 13.06 105.10 27.60 2.1019 ! PUR0/1, purine +ND2R5D CD32A HDA2A 33.43 107.00 ! Et-Gua, cmb 04/10 +ND2R5D CD32A CD33A 43.43 107.00 ! Et-Gua, cmb 04/10 +ND2R6B CD2R6C ND2R6B 17.00 141.00 ! nucleic acids, from 135.00 ! PYRM, pyrimidine +ND2R6B CD2R6C HDR6C 28.40 112.00 23.90 2.0500 ! PYRM, pyrimidine +ND2R5A CD2R6D CD2R6A 132.10 130.90 ! INDO, indole +ND2R5A CD2R6D CD2R6D 31.40 105.50 ! INDO, indole +CD2R5C CD2R6D CD2R6A 144.30 130.90 ! INDO, indole +CD2R5C CD2R6D CD2R6D 81.90 106.10 22.59 2.2163 ! INDO, indole +CD2R6A CD2R6D CD2R6D 50.10 126.50 ! INDO, indole +ND2R5A CD2R6F ND2R6B 130.00 110.00 ! PUR0, purine tautomer B +ND2R5A CD2R6F CD2R6B 130.00 110.00 ! PUR1, purine tautomer A +ND2R5A CD2R6F CD2R6F 111.40 96.00 ! PUR0/1, purine +ND2R5B CD2R6F ND2R6B 130.00 110.00 ! PUR1, purine tautomer A +ND2R5E CD2R6F ND2R6B 130.00 110.00 ! ADE, cmb 04/10 +ND2R5B CD2R6F CD2R6B 130.00 110.00 ! PUR0, purine tautomer B +ND2R5E CD2R6F CD2R6B 130.00 110.00 ! ADE, cmb 04/10 +ND2R5B CD2R6F CD2R6F 99.82 101.50 ! PUR0/1, purine +ND2R6B CD2R6F CD2R6F 29.82 120.50 ! nucleic acids, from 100.50 ! PUR0/1, purine (model compounds) +CD2R5B CD2R6F CD2R6F 58.07 117.30 9.20 2.3476 ! PUR0/1, purine +CD2R6B CD2R6F CD2R6F 79.82 109.20 4.50 2.2904 ! PUR0/1, purine +ND2R6B CD2R6H CD2R6A 10.00 115.00 ! CYT, cmb +ND2R6C CD2R6H HDR6B 30.00 116.00 ! CYT, cmb 04/10 +CD2R6A CD2R6H HDR6B 30.00 122.00 ! CYT, cmb +CD32A CD30A CD32A 58.35 113.50 11.16 2.561 ! glycerol ? need check +CD33A CD30A CD33A 53.35 114.00 8.00 2.561 ! alkane 3/2/92 ? need check +CD33A CD30A CD32A 53.35 114.00 8.00 2.561 ! alkane 3/2/92 ? need check +OD305A CD315B CD325B 45.00 111.10 ! TF2M 02/09, cmb +OD305A CD315B CD33A 45.00 111.50 ! TF2M, viv; cmb +OD305A CD315B HDA1R5 70.00 107.30 ! TF2M 02/09, cmb +CD325B CD315B CD325B 58.00 109.50 11.16 2.561 ! TF2M 02/09, cmb +CD325B CD315B CD33A 53.35 114.00 8.00 2.561 ! TF2M, cmb +CD325A CD315A CD33A 53.35 114.00 8.00 2.561 ! CPNM, cmb +CD325A CD315A OD31A 53.35 114.00 8.00 2.561 ! CPO1, cmb +CD325B CD315B HDA1R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +CD325A CD315A HDA1R5 35.00 111.40 22.53 2.179 ! CPNM 01/10, cmb +CD33A CD315B HDA1R5 34.50 110.10 22.53 2.179 ! TF2M, cmb +CD33A CD315A HDA1R5 34.50 110.10 22.53 2.179 ! CPNM, cmb +OD31A CD315A HDA1R5 34.50 110.10 22.53 2.179 ! CPO1, cmb need test +ND3P2A CD31A CD2O1A 78.50 97.50 ! NTER, PEML +ND3P2A CD31C CD2O1A 78.50 97.50 ! NTER, PEML +ND3P2A CD31A CD2O2A 55.10 104.40 ! NTER, PEML +ND3P2A CD31A CD2O3A 71.90 103.10 ! NTER, PEML +ND3P2A CD31A CD31A 67.80 113.80 ! NTER, PEML +ND3P2A CD31A CD32A 67.80 113.80 ! NTER, PEML +ND3P2A CD31A CD33A 67.80 113.80 ! NTER, PEML +ND3P2A CD31A HDA1C 31.10 106.30 34.90 2.048 ! NTER, PEML +ND3P3A CD31A CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD31C CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD31A CD2O2A 55.10 104.40 ! NTER, PEML +ND3P3A CD31C CD2O2A 55.10 104.40 ! NTER, PEML +ND3P3A CD32C CD2O2A 55.10 104.40 ! NTER, PEML +ND3P3A CD31A CD2O3A 71.90 103.10 ! NTER, PEML +ND3P3A CD31C CD2O3A 71.90 103.10 ! NTER, PEML +ND3P3A CD31A CD31A 67.80 113.80 ! NTER, PEML +ND3P3A CD31C CD31A 67.80 113.80 ! NTER, PEML +ND3P3A CD31A CD32A 67.80 113.80 ! NTER, PEML +ND3P3A CD31C CD32A 67.80 113.80 ! NTER, PEML +ND3P3A CD31C CD32B 67.80 113.80 ! NTER, PEML by analogy GLU, NTER +ND3P3A CD31C CD32C 67.80 113.80 ! NTER, PEML by analogy ASN, NTER +ND3P3A CD31A CD33A 67.80 113.80 ! NTER, PEML +ND3P3A CD31C CD33A 67.80 113.80 ! NTER, PEML +ND3P3A CD31A HDA1C 31.10 106.30 34.90 2.048 ! NTER, PEML +ND3P3A CD31C HDA1C 31.10 106.30 34.90 2.048 ! NTER, PEML +OD31A CD31A CD31A 66.00 113.10 ! THR/PRO2, NTER +OD31A CD31A CD31C 66.00 113.10 ! THR/PRO2 +OD31A CD31A CD32A 59.30 113.10 ! BUO2, 2-butanol +OD31A CD31A CD33A 66.00 113.10 ! PRO2, 2-propanol +OD31A CD31A HDA1A 47.00 104.00 ! PRO2, 2-propanol +CD2O1A CD31A CD31A 42.50 111.30 ! c22, NTER-(X)n-CNEU +CD2O1A CD31A CD32A 42.50 111.30 ! NTER-(X)n-CNEU +CD2O1A CD31A CD33A 42.50 111.30 ! FOR NTER-(X)n-CNEU +CD2O1A CD31A HDA1C 48.90 111.90 ! NTER-(X)n-CNEU +CD2O1A CD31C HDA1C 48.90 111.90 ! NTER-(X)n-CNEU +CD2O2A CD31A CD31A 22.20 116.30 ! NTEZ, PEML +CD2O2A CD31A CD32A 22.20 116.30 ! NTEZ, PEML +CD2O2A CD31A CD33A 22.20 116.30 ! NTER, PEML +CD2O2A CD31A HDA1C 35.30 113.10 39.10 2.257 ! NTER, PEML +CD2O2A CD31C HDA1C 35.30 113.10 39.10 2.257 ! NTER, PEML +CD2O2A CD31C HDA2C 35.30 113.10 39.10 2.257 ! NTER, PEML +CD2O3A CD31A CD31A 55.90 107.50 ! NTER, PEML +CD2O3A CD31A CD32A 55.90 107.50 ! NTER, PEML +CD2O3A CD31A CD33A 25.50 108.20 ! CNEU +CD2O3A CD31A HDA1C 22.90 119.20 10.90 2.121 ! CNEU +CD2O3A CD31C HDA1C 22.90 119.20 10.90 2.121 ! CNEU +CD31A CD31A CD31A 53.35 111.00 8.00 2.561 ! alkane, 3/92 +CD31A CD31A CD32A 58.35 113.50 11.16 2.561 ! glycerol +CD31A CD31A CD33A 53.35 108.50 8.00 2.561 ! alkane, 3/92 +CD31A CD31A HDA1A 34.50 110.10 22.53 2.179 ! alkane, 3/92 +CD31A CD31A HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD31A CD31C HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD31C CD31A CD32A 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31C CD31A CD33A 53.35 108.50 8.00 2.561 ! special case for amides, based on alkane, 3/92 +CD31C CD31A HDA1A 34.50 110.10 22.53 2.179 ! alkane, 3/92 +CD32A CD31A CD32A 58.35 113.50 11.16 2.561 ! glycerol +CD32A CD31A CD33A 53.35 114.00 8.00 2.561 ! alkane 3/2/92 +CD32A CD31A HDA1A 34.50 110.10 22.53 2.179 ! alkane, 3/92 +CD32A CD31A HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD32A CD31C HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD32B CD31C HDA1C 34.50 110.10 22.53 2.179 ! NTER, PEML by analogy GLU, CTER +CD32C CD31C HDA1C 34.50 110.10 22.53 2.179 ! NTER, PEML by analogy ASN, CTER +CD32C CD31A HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD33A CD31A CD33A 55.00 112.00 8.00 2.561 ! IBUT +CD33A CD31A HDA1A 34.50 110.10 22.53 2.179 ! IBUT, isobutane, alkane, 3/92 +CD33A CD31A HDA1C 70.10 116.50 32.50 1.9232 ! ALAD % +CD33A CD31C HDA1C 70.40 117.82 53.70 2.0946 ! ALAD % +ND2A2 CD31C CD2O1A 55.70 103.68 ! ALAD, tau % important for N-Ca-C +ND2A2 CD31C CD2O2A 40.40 112.20 ! CTER, PEML +ND2A2 CD31C CD2O3A 54.60 100.50 ! CT1 +ND2A2 CD31C CD31A 60.60 116.50 ! ALAD % important for N-Ca-Cb 60.60 113.50 ! ALAD +ND2A2 CD31C CD32A 70.00 113.50 ! GLN, c22 % +ND2A2 CD31C CD32B 70.00 113.50 ! GLU, from ND2A2 CD31C CD32A % CHECK THESE +ND2A2 CD31C CD32C 70.00 113.50 ! ASN, c22 % +ND2A2 CD31C CD33A 71.70 118.00 ! ALAD % important for N-Ca-Cb +ND2A2 CD31C HDA1A 34.80 107.70 ! ALAD % +ND3A3 CD31C CD2O1A 20.42 94.79 ! 40.00 112.00 ! PRO +ND3A3 CD31C CD2O2A 20.42 94.79 ! 40.00 112.00 ! PRO +ND3A3 CD31C CD32A 87.40 110.04 ! 70.00 113.00 ! PRO +ND3A3 CD32C CD32A 70.00 113.50 ! PRLD, pyrrolidine, PEML % CHECK THESE ??? +ND3A3 CD31C HDA1A 69.62 109.54 ! 50.00 111.00 ! PRO +OD30C CD31C CD32A 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30C CD31C CD32C 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30C CD31C CD33A 40.00 110.00 ! EAS, EH 2007 +OD30C CD31C HDA1A 60.00 109.50 ! EAS, Lipid, charmm27 +CD2O1A CD31C CD31A 42.50 111.30 ! ILE, c22 +CD2O1A CD31C CD31C 42.50 111.30 ! ILE, c22 +CD2O1A CD31C CD32A 42.50 111.30 ! LEU/GLN/GLU, c22 +CD2O1A CD31C CD32B 42.50 111.30 ! GLU, from CD2O1A CD31C CD32A +CD2O1A CD31C CD32C 42.50 111.30 ! LEU, c22 +CD2O1A CD31C CD33A 56.90 111.23 ! ALAD % +CD2O1A CD31C HDA1A 27.40 110.87 ! ALAD % important for C-Ca-Ha 58.60 109.90 ! ALAD +CD2O2A CD31C CD31A 30.60 120.70 ! CTER, PEML, Val +CD2O2A CD31C CD32A 30.60 120.70 ! CTER, PEML, Asp +CD2O2A CD31C CD32B 30.60 120.70 ! CTER, PEML, Glu +CD2O2A CD31C CD32C 30.60 120.70 ! CTER, PEML, Asn +CD2O2A CD31C CD33A 30.60 120.70 ! CTER, PEML +CD2O2A CD31C HDA1A 29.70 118.90 5.10 2.137 ! CTER, PEML, ACET +CD2O3A CD31C CD31A 55.90 107.50 ! NTER, PEML +CD2O3A CD31C CD32A 55.90 107.50 ! CNEU +CD2O3A CD31C CD33A 25.50 108.20 ! CNEU +CD2O3A CD31C HDA1A 22.90 119.20 10.90 2.121 ! CNEU +CD31A CD31C HDA1A 34.50 110.10 22.53 2.179 ! special case for amides, based on alkane, 3/92 +CD32A CD31C CD32C 58.35 113.50 11.16 2.5610 ! GLYC, Lipid, alkane +CD32A CD31C HDA1A 34.50 110.10 22.53 2.1790 ! GLYC, Lipid, alkane +CD32B CD31C HDA1A 34.50 110.10 22.53 2.1790 ! GLU, from CD32A CD31C HDA1A +CD32C CD31C CD33A 58.35 113.50 11.16 2.5610 ! GLYC, Lipid, alkane +CD32C CD31C HDA1A 34.50 110.10 22.53 2.1790 ! GlYC, Lipid, alkane ??? CHECK THIS AGAINST VALUES BELOW +CD33A CD31C HDA1A 70.40 117.82 53.70 2.0946 ! ALAD % +CD325A CD325A CD325A 58.00 106.00 11.16 2.561 ! CPEN 10/17/05 viv +CD325A CD315A CD325A 58.00 106.00 11.16 2.561 ! CPNM 10/17/05 cmb +CD325A CD325A HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +CD315A CD325A HDA2R5 35.00 111.40 22.53 2.179 ! CPNM 10/17/05 cmb +HDA2R5 CD325A HDA2R5 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv +CD315A CD325A CD325A 58.00 109.50 11.16 2.561 ! CPNM 01/10, cmb +CD315A CD33A HDA3A 33.43 110.10 22.53 2.179 ! CPNM, viv; cmb +OD305A CD325B CD325B 45.00 111.10 ! THF, viv 10/21/05 +OD305A CD325B HDA2R5 70.00 107.30 ! THF, viv 10/21/05 +CD315B CD325B CD325B 58.00 109.50 11.16 2.561 ! TF2M 02/09, cmb +CD315B CD325B HDA2R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +CD325B CD325B CD325B 58.00 109.50 11.16 2.561 ! THF, CSD/NDB survey, viv +CD325B CD325B HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +HDA2R5 CD325B HDA2R5 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv +CD326A CD326A CD326A 58.35 113.60 11.16 2.561 ! CHEX, from alkane CD32A, 9/09, cmb +CD326A CD316A CD33A 53.35 114.00 8.00 2.561 ! CHXM, from alkane 3/2/92, cmb 12/09 +CD316A CD33A HDA3A 33.43 110.10 22.53 2.179 ! CHXM, from alkane, 4/98, 12/09, cmb +CD33A CD316A HDA1A 34.50 110.10 22.53 2.179 ! CHXM, from, IBUT, 3/92, 12/09, cmb +CD326A CD316A CD326A 58.35 113.60 11.16 2.561 ! CHXM, from alkane CD32A, 12/09, cmb +CD316A CD326A CD326A 58.35 113.60 11.16 2.561 ! CHXM, from alkane CD32A, 12/09, cmb +CD326A CD316A HDA1A 26.50 110.10 22.53 2.179 ! CHXM, from alkane CD32A, 12/09, cmb +CD316A CD326A HDA2A 26.50 110.10 22.53 2.179 ! CHXM, from alkane CD32A, 9/09, cmb +CD326A CD326A HDA2A 26.50 110.10 22.53 2.179 ! CHEX, from alkane CD32A, 9/09, cmb +HDA2A CD326A HDA2A 35.50 109.00 5.40 1.802 ! CHEX, from alkane CD32A, 9/09, cmb +OD306A CD326B CD326B 45.00 111.50 ! THP, viv +OD306A CD326B HDA2E 45.00 109.50 ! THP, sng +CD326B CD326B CD326B 58.35 112.00 11.16 2.561 ! cyclohexane, sng +CD326B CD326B HDA2E 34.50 110.10 22.53 2.179 ! cyclohexane, sng +HDA2E CD326B HDA2E 35.50 109.00 5.40 1.802 ! THP viv +ND2P1A CD32A CD32A 74.70 116.10 ! ARG, from GEOM OPT of GUAN (PEML) +ND2P1A CD32A HDA2A 51.50 107.50 ! ARG, c22 +ND3A3 CD32A CD32A 70.00 113.00 ! PRO +ND3A3 CD32A HDA2A 50.00 111.00 ! PRO +ND3P2A CD31C CD32A 67.70 113.00 ! CHOL, qm EH 2007, ammonium cations +ND3P2A CD32A CD32A 67.70 113.00 ! CHOL, qm EH 2007, ammonium cations +ND3P2A CD32A CD33A 67.70 113.00 ! NC5, qm EH 2007, ammonium cations +ND3P2A CD31C HDA1C 40.00 109.50 27.00 2.1300 ! NC4, charmm27, ammonium cations +ND3P2A CD32A HDA2C 40.00 109.50 27.00 2.1300 ! NC4, charmm27, ammonium cations +ND3P3A CD32A CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD32C CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD32A CD32A 67.70 113.00 ! ETAM, qm EH 2007, ammonium cations +ND3P3A CD32C CD32A 67.70 113.00 ! ETAM, qm EH 2007, ammonium cations +ND3P3A CD32A CD33A 67.70 113.00 ! NH5, qm EH 2007, ammonium cations +ND3P3A CD32A HDA2A 40.00 109.50 27.00 2.1300 ! NC1, charmm27 +ND3P3A CD32A HDA2C 40.00 109.50 27.00 2.1300 ! NC1, charmm27 +ND3P3A CD32C HDA2C 40.00 109.50 27.00 2.1300 ! NC1, charmm27 +OD30A CD32A CD32A 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32A CD33A 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32A HDA2A 60.00 109.50 ! DMP, dimethylphosphate, alex +OD30B CD32A CD31C 75.70 110.10 ! DMP, Lipid, charmm27, need work** +OD30B CD32A CD32A 75.70 110.10 ! DMP, Lipid, charmm27, need work** +OD30B CD32A HDA2A 60.00 109.50 ! DMP, charmm27 +OD31A CD32A CD31C 66.00 112.50 ! SER/PRO1 +OD31A CD32A CD32A 66.00 112.50 ! ETAM +OD31A CD32A CD33A 66.00 112.50 ! ETOH, ethanol +OD31A CD32A HDA2A 54.00 111.50 ! ETOH, ethanol +OD31B CD32A CD32A 66.00 112.50 ! PRO1, 1-propanol +OD31B CD32A HDA2A 54.00 111.50 ! PRO1, 1-propanol +SD30A CD32A CD32A 65.00 113.20 ! EMS, Met +SD30A CD32A CD33A 65.00 113.20 ! EMS +SD30A CD32A HDA2A 30.10 109.80 ! EMS +SD30B CD32A CD31C 58.00 112.50 ! DMDS, c22, Disulfide patch +SD30B CD32A HDA2A 42.70 108.30 ! DMDS, Disulfide patch +SD31B CD32A CD31C 43.00 113.20 ! PRSH +SD31B CD32A CD32A 43.00 113.20 ! PRSH +SD31B CD32A CD33A 43.00 113.20 ! ETSH +SD31B CD32A HDA2A 46.10 106.30 ! ETSH +CD2O1A CD32A HDA2C 48.90 111.90 ! NTER-(X)n-CNEU +CD2O1A CD32C HDA2C 48.90 111.90 ! NTER-(X)n-CNEU +CD2O2A CD32A CD31C 22.20 116.30 ! NTEZ, PEML +CD2O2A CD32A CD32A 30.60 120.70 ! CTER, PEML, Glu +CD2O2A CD32A CD32B 30.60 120.70 ! GLU, from CD2O2A CD32A CD32B +CD2O2A CD32A HDA2A 29.70 118.90 5.10 2.137 ! CTER, PEML, Asp +CD2R5A CD32A CD31C 58.35 113.00 ! HSD, c22 +CD2R5A CD32A HDA2A 33.43 109.50 ! HSD, 4MIM, 4-methyl-imidazole +CD2R5C CD32A CD31C 58.35 113.00 ! TRP, c22 +CD2R5C CD32A HDA2A 49.30 107.50 ! INDM, methyl-indole, Trp +CD2R5D CD32A CD31C 58.35 113.00 ! HSP, c22 +CD2R5D CD32A HDA2A 33.43 109.50 ! HSP, 4MIM, 4-methyl-imidazole +CD2R6A CD32A CD31C 51.80 107.50 ! PHE, c22 +CD2R6A CD32A HDA2A 49.30 107.50 ! PHE/TOLU +CD30A CD32A CD32A 58.35 113.50 11.16 2.561 ! glycerol ? need check +CD30A CD32A CD33A 58.35 113.50 11.16 2.561 ! glycerol ? need check +CD30A CD32A HDA2A 26.50 110.10 22.53 2.179 ! alkane, 4/98 ? need check +CD31A CD32A CD31A 58.35 113.50 11.16 2.561 ! glycerol +CD31A CD32A CD31C 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31A CD32A CD32A 58.35 113.50 11.16 2.561 ! glycerol +CD31A CD32A CD32C 58.35 113.50 11.16 2.561 ! NTER +CD31A CD32A CD33A 58.35 113.50 11.16 2.561 ! glycerol +CD31A CD32A HDA2A 26.50 110.10 22.53 2.179 ! alkane, 4/98 +CD31C CD32A CD32A 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31C CD32B CD32A 58.35 113.50 11.16 2.561 ! GLU, from CD31C CD32A CD32A +CD31C CD32B CD32C 58.35 113.50 11.16 2.561 ! GLUP, from CD31C CD32A CD32A +CD31C CD32A CD32C 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31C CD32A CD33A 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31C CD32A HDA2A 34.60 110.10 22.53 2.1790 ! MBU, alkane +CD31C CD32B HDA2A 34.60 110.10 22.53 2.1790 ! GLU, from CD31C CD32A HDA2A +CD32A CD32A CD32A 58.35 113.60 11.16 2.561 ! alkane, 3/92 +CD32A CD32A CD32C 58.35 113.60 11.16 2.5610 ! GLYC, Lipid, alkane +CD32A CD32A CD32E 58.35 113.60 11.16 2.561 ! ethers +CD32A CD32A CD33A 58.00 115.00 8.00 2.561 ! alkane, 3/92 +CD32A CD32A HDA2A 26.50 110.10 22.53 2.179 ! alkane, 4/98 +CD32A CD32B HDA2A 26.50 110.10 22.53 2.179 ! GLU, from CD32A CD32A HDA2A +CD32B CD32A HDA2A 26.50 110.10 22.53 2.179 ! GLU, from CD32A CD32A HDA2A +CD32B CD32C HDA2A 26.50 110.10 22.53 2.179 ! GLUP, from CD32A CD32A HDA2A +CD32A CD32A HDA2C 26.50 110.10 22.53 2.179 ! LYS, alkane, 4/98 +CD32C CD32A CD33A 58.00 115.00 8.00 2.5610 ! MBU, alkane +CD32C CD32A HDA2A 34.60 110.10 22.53 2.1790 ! MBU, alkane +CD32C CD32B HDA2A 34.60 110.10 22.53 2.1790 ! MBU, alkane, GLUP +CD32E CD32A CD33A 58.00 115.00 8.00 2.561 ! ethers +CD32E CD32A HDA2A 26.50 110.10 22.53 2.179 ! ether +CD33A CD32A CD33A 53.35 114.00 8.00 2.561 ! alkane 3/92 +CD33A CD32A HDA2A 34.60 110.10 22.53 2.179 ! alkane, 4/98 +CD33A CD32A HDA2C 26.50 110.10 22.53 2.1790 ! NC5, alkane, ammonium cations +HDA2A CD32A HDA2A 35.50 109.00 5.40 1.802 ! alkane, 3/92 +HDA2A CD32B HDA2A 35.50 109.00 5.40 1.802 ! GLU, from HDA2A CD32A HDA2A +HDA2C CD32A HDA2C 24.00 109.50 28.00 1.7670 ! NC4, charmm27 +HDA2C CD32C HDA2C 24.00 109.50 28.00 1.7670 ! NC4, charmm27 +ND2A2 CD32C CD2O1A 58.55 100.46 ! GLYD, tau, needs to be checked +ND2A2 CD32C CD2O2A 40.40 112.20 ! CTER, terminal Gly +ND2A2 CD32C CD2O3A 54.60 100.50 ! CNEU +ND2A2 CD32C HDA2A 42.50 111.30 ! GLYD +ND3A3 CD32C HDA2A 42.50 111.30 ! PRLD, pyrrolidine, PEML +OD30C CD32C CD31C 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30C CD32C CD33A 40.00 110.00 ! EAS, EH 2007 +OD30C CD32C HDA2A 60.00 109.50 ! MAS, charmm27 +CD2O1A CD32C CD31C 42.50 111.30 ! ASN, c22 +CD2O1A CD32C CD32A 42.50 111.30 ! GLN, c22 +CD2O1A CD32C HDA2A 42.50 111.30 ! GLYD +CD2O2A CD32C HDA2A 29.70 118.90 5.10 2.137 ! CTER, PEML, ACET, terminal Gly +CD2O3A CD32C CD31C 52.00 108.00 ! MBU, alkane, ASPP +CD2O3A CD31C CD32B 52.00 108.00 ! PEML by analogy GLU, CNEU +CD2O3A CD31C CD32C 52.00 108.00 ! PEML by analogy ASN, CNEU +CD2O3A CD32C CD32B 52.00 108.00 ! MBU, alkane, GLUP +CD2O3A CD32C CD32A 52.00 108.00 ! MBU, alkane +CD2O3A CD32C CD33A 52.00 108.00 ! MPO, alkane +CD2O3A CD32C HDA2A 33.00 109.50 30.00 2.1630 ! MPO, charmm27 +CD31C CD32C HDA2A 26.50 110.10 22.53 2.1790 ! GLYC, Lipid, alkane +CD32A CD32C HDA2A 26.50 110.10 22.53 2.1790 ! MBU, alkane +CD33A CD32C HDA2A 34.60 110.10 22.53 2.1790 ! MPO, alkane +HDA2A CD32C HDA2A 35.50 109.00 5.40 1.8020 ! MPO, alkane +OD30A CD32E CD32A 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32E CD32E 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32E CD33A 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32E HDA2E 60.00 109.50 ! DMP, ethers +CD32A CD32E HDA2E 26.50 110.10 22.53 2.179 ! ether +CD32E CD32E HDA2E 26.50 110.10 22.53 2.179 ! ether +CD33A CD32E HDA2E 34.60 110.10 22.53 2.179 ! ether +HDA2E CD32E HDA2E 35.50 109.00 5.40 1.802 ! ethers +ND2P1A CD33A HDA3A 51.50 107.50 ! GUAN, c22 +ND2R5D CD33A HDA3A 33.43 107.00 ! ADE, cmb 04/10 +ND2R6C CD33A HDA3A 33.43 104.00 ! CYT, cmb 04/10 +ND3P2A CD33A HDA3C 40.00 109.50 27.00 2.1300 ! NC4, charmm27, ammonium cations +ND3P3A CD33A HDA3C 40.00 109.50 27.00 2.1300 ! NC1, charmm27, ammonium cations +OD30A CD33A HDA3A 60.00 109.50 ! DMP, dimethylphosphate, alex +OD30B CD33A HDA3A 60.00 109.50 ! DMP, charmm27 +SD30A CD33A HDA3A 41.30 109.00 ! EMS +SD30B CD33A HDA3A 42.70 108.30 ! DMDS +SD31A CD33A HDA3A 40.00 108.69 ! MESH +CD2O2A CD33A HDA3A 27.70 107.50 25.30 2.1670 ! ACET, PEML +CD2R5A CD33A HDA3A 33.43 109.50 ! 4MIM, 4-methyl-imidazole +CD2R5C CD33A HDA3A 49.30 107.50 ! INDM, methyl-indole +CD2R6A CD33A HDA3A 49.30 107.50 ! TOLU, toluene +CD30A CD33A HDA3A 33.43 110.10 22.53 2.179 ! alkane, 4/98 ? need check +CD315B CD33A HDA3A 33.43 110.10 22.53 2.179 ! TF2M, viv; cmb +CD31A CD33A HDA3A 33.43 110.10 22.53 2.179 ! alkane, 4/98 +CD31C CD33A HDA3A 34.60 110.10 22.53 2.1790 ! MPO, alkane +CD32A CD33A HDA3A 34.60 111.50 22.53 2.179 ! alkane, 4/98 +CD32C CD33A HDA3A 34.60 110.10 22.53 2.1790 ! MPO, alkane +CD32E CD33A HDA3A 34.60 111.50 22.53 2.179 ! ether +CD33A CD33A HDA3A 37.50 110.10 22.53 2.179 ! alkane, 4/98 +HDA3A CD33A HDA3A 35.50 108.40 5.40 1.802 ! alkane, 3/92 +HDA3C CD33A HDA3C 24.00 109.50 28.00 1.7670 ! NC4, charmm27, ammonium cations +OD31A CD33B HDA3B 61.00 108.89 ! MEOH, methanol +HDA3B CD33B HDA3B 35.50 108.40 5.40 1.802 ! alkane, 3/92, special for MEOH, methanol +ND2A2 CD33C HDA3A 85.60 126.43 ! NMA+ALAD % +ND2A3 CD33C HDA3A 51.50 109.50 ! DMA % +OD30B CD33C HDA3A 60.00 109.50 ! DMP, cmb, 06/09 +OD30BN CD33C HDA3A 60.00 109.50 ! DMP, nucleic acids +OD30C CD33C HDA3A 60.00 109.50 ! MAS, charmm27 +CD2O1A CD33C HDA3A 49.00 107.87 ! NMA+ALAD % +CD2O3A CD33C HDA3A 33.00 109.50 30.00 2.1630 ! MAS, charmm27 +HDA3A CD33C HDA3A 35.50 108.40 5.40 1.8020 ! MAS, alkane +OD30C CD33D HDA3A 60.00 109.50 ! MAS, charmm27 +HDA3A CD33D HDA3A 35.50 108.40 5.40 1.8020 ! MAS, alkane +OD30A CD33E HDA3A 60.00 109.50 ! DMP, ethers +HDA3A CD33E HDA3A 35.50 108.40 5.40 1.802 ! ethers +CD2R6A CD32A CD31A 51.80 107.50 ! PHE, c22 !!PEML added to allow NTER patch on TYR + +DIHEDRALS +!atom types Kchi n delta +!================================================= +! +!Please follow these conventions when fitting torsion parameters +!1) use positive force constants in all cases (switch the phase...) +! (vary phase during fitting and keep force constants positive) +!2) maintain the phase at 0 or 180 if possiple. perform initial +! fitting with this contraint and, if necessary, only then +! vary the phases during fitting. note that if the phases +! are NOT 0 or 180 the parameters are NOT transferable across +! stereoisomers +!3) refit with only individual multiplicities of 1 through 6 +!4) maintain the number of significant figures used below +! +HDP1A ND2A1 CD2O1A OD2C1A 2.000 2 180.00 ! ACEM +HDP1A ND2A1 CD2O1A CD31C 2.000 2 180.00 ! CT2/ACEM +HDP1A ND2A1 CD2O1A CD32C 2.000 2 180.00 ! ASN, acem +HDP1A ND2A1 CD2O1A CD33C 2.000 2 180.00 ! ACEM +HDP1A ND2B1 CD2R6C ND2R6C 1.400 2 180.00 ! GUA, cmb 04/10 +CD31C ND2A2 CD2O1A OD2C1A 6.390 2 180.00 ! ALAD omega left % +CD31C ND2A2 CD2O1A OD2C1A 0.680 3 0.00 ! ALAD omega left % +CD31C ND2A2 CD2O1A CD31A 1.700 1 0.00 ! NTER, from NMA +CD31C ND2A2 CD2O1A CD31A 2.000 2 180.00 ! NTER, from NMA +CD31C ND2A2 CD2O1A CD31C 0.820 1 0.00 ! ALAD omega +CD31C ND2A2 CD2O1A CD31C 3.000 2 180.00 ! ALAD omega +CD31C ND2A2 CD2O1A CD32C 0.820 1 0.00 ! GLYD omega right +CD31C ND2A2 CD2O1A CD32C 3.000 2 180.00 ! GLYD omega right +CD31C ND2A2 CD2O1A CD33C 0.010 1 0.00 ! ALAD acetylated N-terminus omega left % +CD31C ND2A2 CD2O1A CD33C 1.880 2 180.00 ! ALAD acetylated N-terminus omega left % +CD31C ND2A2 CD2O1A CD33C 0.480 3 0.00 ! ALAD acetylated N-terminus omega left % +CD31C ND2A2 CD2O1A CD33C 0.530 4 0.00 ! ALAD acetylated N-terminus omega left % +CD32C ND2A2 CD2O1A OD2C1A 0.820 1 180.00 ! GLYD omega right +CD32C ND2A2 CD2O1A OD2C1A 3.000 2 180.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD31C 0.820 1 0.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD31C 3.000 2 180.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD32A 1.000 1 0.00 ! GLYD +CD32C ND2A2 CD2O1A CD32A 2.500 2 180.00 ! GLYD +CD32C ND2A2 CD2O1A CD32C 0.820 1 0.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD32C 3.000 2 180.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD33A 1.000 1 0.00 ! GLYD/NMA +CD32C ND2A2 CD2O1A CD33A 2.500 2 180.00 ! GLYD/NMA +CD32C ND2A2 CD2O1A CD33C 0.820 1 0.00 ! GLYD acetylated N-terminus omega left +CD32C ND2A2 CD2O1A CD33C 3.000 2 180.00 ! GLYD acetylated N-terminus omega left +CD33C ND2A2 CD2O1A OD2C1A 0.820 1 180.00 ! NMA/ALAD N-acetyl C-terminus omega right % +CD33C ND2A2 CD2O1A OD2C1A 3.000 2 180.00 ! NMA/ALAD N-acetyl C-terminus omega right % +CD33C ND2A2 CD2O1A CD31A 2.000 2 180.00 ! NTER, from NMA +CD33C ND2A2 CD2O1A CD31C 0.670 1 0.00 ! ALAD N-acetyl C-terminus omega right % +CD33C ND2A2 CD2O1A CD31C 3.460 2 180.00 ! ALAD N-acetyl C-terminus omega right % +CD33C ND2A2 CD2O1A CD32A 1.000 1 0.00 ! GLYD/NMA +CD33C ND2A2 CD2O1A CD32A 2.500 2 180.00 ! GLYD/NMA +CD33C ND2A2 CD2O1A CD32C 0.820 1 0.00 ! GLYD omega right +CD33C ND2A2 CD2O1A CD32C 3.000 2 180.00 ! GLYD omega right +CD33C ND2A2 CD2O1A CD33C 0.820 1 0.00 ! NMA % +CD33C ND2A2 CD2O1A CD33C 3.000 2 180.00 ! NMA +HDP1A ND2A2 CD2O1A OD2C1A 0.000 2 180.00 ! ALAD peptide bond omega right +HDP1A ND2A2 CD2O1A CD31A 3.900 2 180.00 ! NTER +HDP1A ND2A2 CD2O1A CD31C 0.000 2 180.00 ! ALAD omega right +HDP1A ND2A2 CD2O1A CD32A 3.900 2 180.00 ! GLYP/NTER +HDP1A ND2A2 CD2O1A CD32C 0.000 2 180.00 ! GLYD omega right +HDP1A ND2A2 CD2O1A CD33C 0.000 2 180.00 ! NMA/acetylated N-terminus +CD2O1A ND2A2 CD31C CD2O1A 0.000 3 180.00 ! ALAD, phi, cmap +CD2O1A ND2A2 CD31C CD2O2A 4.000 1 0.00 ! CTER, PEML, pseudo-phi from ACE-CTER % +CD2O1A ND2A2 CD31C CD2O2A 2.500 2 180.00 ! CTER, PEML, pseudo-phi from ACE-CTER %k +CD2O1A ND2A2 CD31C CD2O3A 0.300 1 0.00 ! CNEU, PEML pseudo-phi +CD2O1A ND2A2 CD31C CD2O3A 0.000 2 180.00 ! CNEU, PEML pseudo-phi +CD2O1A ND2A2 CD31C CD31A 1.800 1 0.00 ! ILE/VAL, c22 +CD2O1A ND2A2 CD31C CD32A 1.800 1 0.00 ! GLN, c22 +CD2O1A ND2A2 CD31C CD32B 1.800 1 0.00 ! GLU, from CD2O1A ND2A2 CD31C CD32A +CD2O1A ND2A2 CD31C CD32C 1.800 1 0.00 ! ASN, c22 +CD2O1A ND2A2 CD31C CD33A 0.000 1 0.00 ! ALAD, phi, cmap +CD2O1A ND2A2 CD31C HDA1A 0.200 3 0.00 ! ALAD, phi, cmap +HDP1A ND2A2 CD31C CD2O1A 0.000 1 0.00 ! ALAD, phi, cmap +HDP1A ND2A2 CD31C CD2O2A 2.500 3 0.00 ! CTER PEML +HDP1A ND2A2 CD31C CD2O3A 0.000 3 0.00 ! CNEU, PEML pseudo-phi +HDP1A ND2A2 CD31C CD31A 0.200 3 0.00 ! ILE/VAL, alkanes +HDP1A ND2A2 CD31C CD32A 0.200 3 0.00 ! GLN, c22 +HDP1A ND2A2 CD31C CD32B 0.200 3 0.00 ! GLU, from HDP1A ND2A2 CD31C CD32A +HDP1A ND2A2 CD31C CD32C 0.000 1 0.00 ! ASN, c22 +HDP1A ND2A2 CD31C CD33A 0.000 1 0.00 ! ALAD, phi, cmap +HDP1A ND2A2 CD31C HDA1A 0.160 3 0.00 ! ALAD, phi, cmap +CD2O1A ND2A2 CD32C CD2O1A 0.000 3 180.00 ! GLYD, phi, cmap +CD2O1A ND2A2 CD32C CD2O2A 3.000 1 0.00 ! CTER, PEML, GLY +CD2O1A ND2A2 CD32C CD2O2A 2.000 2 180.00 ! CTER, PEML, GLY +CD2O1A ND2A2 CD32C CD2O3A 3.500 1 0.00 ! CNEU, PEML, gly +CD2O1A ND2A2 CD32C HDA2A 0.200 3 0.00 ! GLYD +HDP1A ND2A2 CD32C CD2O1A 0.000 1 0.00 ! GLYD, phi, cmap +HDP1A ND2A2 CD32C CD2O2A 2.500 3 0.00 ! CTER PEML, GLY +HDP1A ND2A2 CD32C CD2O3A 2.500 3 0.00 ! GLYP/CTER PEML +HDP1A ND2A2 CD32C HDA2A 0.160 3 0.00 ! GLYD, phi, cmap +CD2O1A ND2A2 CD33C HDA3A 0.200 3 0.00 ! NMA +HDP1A ND2A2 CD33C HDA3A 0.160 3 0.00 ! NMA +HDP1A ND3A3 CD32C HDA2A 0.160 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ?? +CD33C ND2A3 CD2O1A OD2C1A 2.000 2 180.00 ! DMA, N,N-dimethylacetamide +CD33C ND2A3 CD2O1A CD33C 1.700 1 0.00 ! DMA, N,N-dimethylacetamide +CD33C ND2A3 CD2O1A CD33C 2.000 2 180.00 ! DMA, N,N-dimethylacetamide +CD2O1A ND2A3 CD33C HDA3A 0.000 3 0.00 ! DMA, N,N-dimethylacetamide +CD33C ND2A3 CD33C HDA3A 0.300 3 0.00 ! DMA, N,N-dimethylacetamide +CD32A ND2P1A CD2N1A ND2P1A 0.170 1 180.00 ! ARG, chi5 QM PES fit (PEML) +CD32A ND2P1A CD2N1A ND2P1A 2.210 2 180.00 ! ARG, chi5 QM PES fit (PEML) +CD32A ND2P1A CD2N1A ND2P1A 0.150 5 180.00 ! ARG, chi5 QM PES fit (PEML) +CD33A ND2P1A CD2N1A ND2P1A 0.170 1 180.00 ! ARG, chi5 QM PES fit (PEML) +CD33A ND2P1A CD2N1A ND2P1A 2.210 2 180.00 ! ARG, chi5 QM PES fit (PEML) +CD33A ND2P1A CD2N1A ND2P1A 0.150 5 180.00 ! ARG, chi5 QM PES fit (PEML) +HDP1B ND2P1A CD2N1A ND2P1A 1.900 2 180.00 ! ARG, c22 In c22 it is the same as [CD33A ND2P1A CD2N1] +CD2N1A ND2P1A CD32A CD32A 1.500 1 0.00 ! ARG, chi4 QM PES fit (PEML) +CD2N1A ND2P1A CD32A CD32A 0.440 2 0.00 ! ARG, chi4 QM PES fit (PEML) +CD2N1A ND2P1A CD32A CD32A 0.080 3 0.00 ! ARG, chi4 QM PES fit (PEML) +CD2N1A ND2P1A CD32A HDA2A 0.000 3 0.00 ! ARG, c22 +HDP1B ND2P1A CD32A CD32A 0.000 3 0.00 ! ARG, c22 +HDP1B ND2P1A CD32A HDA2A 0.000 3 0.00 ! ARG, c22 +CD2N1A ND2P1A CD33A HDA3A 0.000 3 0.00 ! ARG, c22 +HDP1B ND2P1A CD33A HDA3A 0.000 3 0.00 ! ARG, c22 +CD2R5A ND2R5A CD2R5A CD2R5C 14.400 2 180.00 ! PYRR, pyrrole +CD2R5A ND2R5A CD2R5A HDR5A 2.600 2 180.00 ! PYRR, pyrrole +CD2R5B ND2R5A CD2R5A CD2R5A 14.000 2 180.00 ! IMID, imidazole +CD2R5B ND2R5A CD2R5A CD32A 3.000 2 180.00 ! HSD/4MIM, 4-methyl-imidazole +CD2R5B ND2R5A CD2R5A CD33A 3.000 2 180.00 ! 4MIM, 4-methyl-imidazole +CD2R5B ND2R5A CD2R5A HDR5A 3.000 2 180.00 ! IMID, imidazole +CD2R6D ND2R5A CD2R5A CD2R5C 9.520 2 180.00 ! INDO, indole +CD2R6D ND2R5A CD2R5A HDR5A 0.810 2 180.00 ! INDO, indole +HDP1A ND2R5A CD2R5A CD2R5A 1.100 2 180.00 ! IMID, imidazole +HDP1A ND2R5A CD2R5A CD2R5C 1.300 2 180.00 ! PYRR, pyrrole +HDP1A ND2R5A CD2R5A CD32A 1.000 2 180.00 ! HSD/4MIM, 4-methyl-imidazole +HDP1A ND2R5A CD2R5A CD33A 1.000 2 180.00 ! 4MIM, 4-methyl-imidazole +HDP1A ND2R5A CD2R5A HDR5A 0.000 2 180.00 ! IMID, imidazole +CD2R5A ND2R5A CD2R5B ND2R5B 14.000 2 180.00 ! IMID, imidazole +CD2R5A ND2R5A CD2R5B HDR5B 3.000 2 180.00 ! IMID, imidazole +CD2R6F ND2R5A CD2R5B ND2R5B 12.000 2 180.00 ! PUR0/1, purine, imidazole ring +CD2R6F ND2R5A CD2R5B HDR5B 4.700 2 180.00 ! PUR0/1, purine, imidazole ring +HDP1A ND2R5A CD2R5B ND2R5B 1.100 2 180.00 ! IMID, imidazole +HDP1A ND2R5A CD2R5B HDR5B 0.900 2 180.00 ! IMID, imidazole +CD2R5A ND2R5A CD2R6D CD2R6A 2.040 2 180.00 ! INDO, indole +CD2R5A ND2R5A CD2R6D CD2R6D 8.260 2 180.00 ! INDO, indole +HDP1A ND2R5A CD2R6D CD2R6A 0.250 2 180.00 ! INDO, indole +HDP1A ND2R5A CD2R6D CD2R6D 0.250 2 180.00 ! INDO, indole +CD2R5B ND2R5A CD2R6F ND2R6B 7.600 2 180.00 ! PUR1, purine, butterfly mode +CD2R5B ND2R5A CD2R6F CD2R6B 2.000 2 180.00 ! PUR1, purine, tautomer A, imidazole ring +CD2R5B ND2R5A CD2R6F CD2R6F 6.200 2 180.00 ! PUR0/1, purine, imidazole ring +HDP1A ND2R5A CD2R6F ND2R6B 1.000 2 180.00 ! PUR0, purine, tautomer B, imidazole ring +HDP1A ND2R5A CD2R6F CD2R6B 1.000 2 180.00 ! PUR1, purine, tautomer A, imidazole ring +HDP1A ND2R5A CD2R6F CD2R6F 2.700 2 180.00 ! PUR0/1, purine +CD2R5B ND2R5B CD2R5A CD2R5A 14.000 2 180.00 ! IMID, imidazole +CD2R5B ND2R5B CD2R5A CD32A 3.000 2 180.00 ! HSE, c22 +CD2R5B ND2R5B CD2R5A HDR5A 3.000 2 180.00 ! IMID, imidazole +CD2R5A ND2R5B CD2R5B ND2R5A 14.000 2 180.00 ! IMID, imidazole +CD2R5A ND2R5B CD2R5B HDR5B 3.000 2 180.00 ! IMID, imidazole +CD2R6F ND2R5B CD2R5B ND2R5A 11.500 2 180.00 ! PUR0/1, purine, imidazole ring +CD2R6F ND2R5B CD2R5B HDR5B 4.700 2 180.00 ! PUR0/1, purine, imidazole ring +CD2R6F ND2R5E CD2R5B ND2R5D 14.000 2 180.00 ! ADE, cmb 04/10 +CD2R6F ND2R5E CD2R5B HDR5B 4.700 2 180.00 ! ADE, cmb 04/10 +CD2R5B ND2R5B CD2R6F ND2R6B 7.600 2 180.00 ! PUR0, purine, butterfly mode +CD2R5B ND2R5B CD2R6F CD2R6B 2.000 2 180.00 ! PUR0, purine, tautomer B, imidazole ring +CD2R5B ND2R5B CD2R6F CD2R6F 6.700 2 180.00 ! PUR1, purine, butterfly mode +CD2R5B ND2R5E CD2R6F CD2O1A 2.000 2 180.00 ! GUA, cmb 04/10 +CD2R5B ND2R5E CD2R6F CD2R6C 2.000 2 180.00 ! ADE, cmb 04/10 +CD2R5B ND2R5E CD2R6F CD2R6F 6.700 2 180.00 ! ADE, cmb 04/10 +CD2R5E ND2R5C CD2R5D CD2R5D 14.000 2 180.00 ! IMIM, from IMID (EH) +CD2R5E ND2R5C CD2R5D CD32A 2.500 2 180.00 ! HSP, c22 +CD2R5E ND2R5C CD2R5D HDR5D 3.000 2 180.00 ! IMIM, from IMID (EH) +HDP1A ND2R5C CD2R5D CD2R5D 1.100 2 180.00 ! IMIM, from IMID (EH) +HDP1A ND2R5C CD2R5D CD32A 3.000 2 180.00 ! HSP, c22 +HDP1A ND2R5C CD2R5D HDR5D 0.000 2 180.00 ! IMIM, from IMID (EH) +CD2R5D ND2R5C CD2R5E ND2R5C 14.000 2 180.00 ! IMIM, from IMID (EH) +CD2R5D ND2R5C CD2R5E HDR5E 3.000 2 180.00 ! IMIM, from IMID (EH) +HDP1A ND2R5C CD2R5E ND2R5C 1.100 2 180.00 ! IMIM, from IMID (EH) +HDP1A ND2R5C CD2R5E HDR5E 0.900 2 180.00 ! IMIM, from IMID (EH) +CD2R6F ND2R5D CD2R5B ND2R5E 6.000 2 180.00 ! ADE, cmb 04/10 +CD2R6F ND2R5D CD2R5B HDR5B 3.500 2 180.00 ! ADE, va H8, cmb 04/10 +CD33A ND2R5D CD2R5B ND2R5E 1.000 2 180.00 ! ADE, cmb 04/10 +CD33A ND2R5D CD2R5B HDR5B 1.000 2 180.00 ! ADE, cmb 04/10 +HDP1A ND2R5D CD2R5B ND2R5B 1.000 2 180.00 ! IMID, imidazole +HDP1A ND2R5D CD2R5B ND2R5E 1.000 2 180.00 ! ADE, cmb 04/10 +HDP1A ND2R5D CD2R5B HDR5B 1.000 2 180.00 ! ADE, IMID, imidazole +CD2R5B ND2R5D CD2R6F ND2R6B 2.000 2 180.00 ! ADE, cmb 04/10 +CD2R5B ND2R5D CD2R6F CD2R6F 6.000 2 180.00 ! ADE, cmb 04/10 +CD33A ND2R5D CD2R6F ND2R6B 1.000 2 180.00 ! ADE, cmb +CD33A ND2R5D CD2R6F CD2R6F 1.000 2 180.00 ! ADE, cmb +HDP1A ND2R5D CD2R6F ND2R6B 1.500 2 180.00 ! ADE, cmb 04/10 +HDP1A ND2R5D CD2R6F CD2R6F 1.200 2 180.00 ! ADE, cmb 04/10 +CD2R5B ND2R5D CD33A HDA3A 0.000 3 0.00 ! ADE, cmb 04/10 +CD2R6F ND2R5D CD33A HDA3A 0.000 3 0.00 ! ADE, cmb +CD2R6B ND2R6A CD2R6B CD2R6A 2.200 2 180.00 ! PYR, pyridine +CD2R6B ND2R6A CD2R6B HDR6B 4.300 2 180.00 ! PYR, pyridine +CD2R6B ND2R6B CD2O1A ND2R6B 0.600 2 180.00 ! CYT, c27 +CD2R6B ND2R6B CD2O1A ND2R6C 0.600 2 180.00 ! CYT, cmb 04/10 +CD2R6B ND2R6B CD2O1A OD2C1B 1.600 2 180.00 ! CYT, cmb 04/10 +CD2R6H ND2R6B CD2O1A ND2R6B 0.600 2 180.00 ! CYT, cmb 04/10 +CD2R6H ND2R6C CD2O1A ND2R6B 0.600 2 180.00 ! CYT, cmb 04/10 +CD2R6H ND2R6B CD2O1A ND2R6C 1.500 2 180.00 ! THY, cmb +CD2R6H ND2R6C CD2O1A ND2R6C 1.500 2 180.00 ! THY, cmb 04/10 +CD2R6H ND2R6C CD2O1A OD2C1B 1.600 2 180.00 ! CYT, cmb 04/10 +CD33A ND2R6C CD2O1A ND2R6B 0.900 2 180.00 ! CYT, cmb 04/10 +CD33A ND2R6C CD2O1A ND2R6C 0.700 2 180.00 ! THY, cmb 04/10 +CD33A ND2R6C CD2O1A OD2C1B 0.900 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2R6B CD2O1A ND2R6B 3.000 2 180.00 ! CYT, c27 +HDP1A ND2R6B CD2O1A ND2R6C 1.600 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6B CD2O1A OD2C1B 3.000 2 180.00 ! CYT, c27 +CD2O1A ND2R6B CD2R6B ND2B1 2.000 2 180.00 ! CYT, cmb 04/10 +CD2O1A ND2R6B CD2R6B CD2R6A 0.600 2 180.00 ! CYT, c27 +CD2R6C ND2R6B CD2R6B CD2R6A 2.000 2 180.00 ! PYRM, pyrimidine +CD2R6C ND2R6B CD2R6B CD2R6F 7.800 2 180.00 ! PUR0/1, purine +CD2R6C ND2R6B CD2R6B HDR6B 10.740 2 180.00 ! PYRM, pyrimidine +CD2R6B ND2R6B CD2R6C ND2R6B 4.520 2 180.00 ! PYRM, pyrimidine +CD2R6B ND2R6B CD2R6C HDR6C 8.150 2 180.00 ! PYRM, pyrimidine +CD2R6C ND2R6B CD2R6C ND2B1 4.000 2 180.00 ! ADE, N6, cmb 04/10 +CD2R6C ND2R6B CD2R6C ND2R6B 1.800 2 180.00 ! ADE +CD2R6C ND2R6B CD2R6C CD2R6F 10.000 2 180.00 ! ADE, cmb 04/10 +CD2R6C ND2R6B CD2R6C HDR6C 6.000 2 180.00 ! ADE, va H2 +CD2R6F ND2R6B CD2R6C ND2R6B 0.100 2 180.00 ! PUR0/1, purine +CD2R6F ND2R6B CD2R6C HDR6C 6.500 2 180.00 ! PUR0/1, purine +CD2R6F ND2R6B CD2R6C ND2B1 4.000 2 180.00 ! GUA, cmb 04/10 +CD2R6F ND2R6B CD2R6C ND2R6C 2.000 2 180.00 ! GUA, cmb 04/10 +CD2R6C ND2R6B CD2R6F ND2R5A 7.600 2 180.00 ! PUR1, purine, butterfly mode +CD2R6C ND2R6B CD2R6F ND2R5B 7.600 2 180.00 ! PUR0, purine, butterfly mode +CD2R6C ND2R6B CD2R6F CD2R6F 7.800 2 180.00 ! PUR0/1, purine +CD2R6C ND2R6B CD2R6F ND2R5D 2.000 2 180.00 ! ADE, butterfly motion, cmb 04/10 +CD2O1A ND2R6C CD2R6H CD2R6A 0.600 2 180.00 ! CYT, cmb 04/10 +CD2O1A ND2R6C CD2R6H HDR6B 3.600 2 180.00 ! CYT, cmb 04/10 +CD33A ND2R6C CD2R6H CD2R6A 1.000 2 180.00 ! CYT, cmb 04/10 +CD33A ND2R6C CD2R6H HDR6B 1.000 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2R6C CD2R6H CD2R6A 1.600 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2R6C CD2R6H HDR6B 1.500 2 180.00 ! CYT, cmb 04/10 +CD2O1A ND2R6C CD33A HDA3A 0.000 3 0.00 ! CYT, cmb 04/10 +CD2R6H ND2R6C CD33A HDA3A 0.000 3 0.00 ! CYT, cmb 04/10 +CD2O1A ND2R6C CD2O1A ND2R6B 1.500 2 180.00 ! THY, cmb 04/10 +CD2O1A ND2R6C CD2O1A ND2R6C 1.500 2 180.00 ! THY, cmb 04/10 +CD2O1A ND2R6C CD2O1A OD2C1B 0.900 2 180.00 ! THY, cmb 04/10 +CD2O1A ND2R6C CD2O1A CD2R6A 0.900 2 180.00 ! THY, cmb 04/10 +CD2R6C ND2R6C CD2O1A OD2C1B 8.000 2 180.00 ! GUA, cmb 04/10 +CD2R6C ND2R6C CD2O1A CD2R6F 0.200 2 180.00 ! GUA, cmb 04/10 +HDP1A ND2R6C CD2O1A ND2R6B 3.800 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6C CD2O1A ND2R6C 3.800 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6C CD2O1A OD2C1B 0.000 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6C CD2O1A CD2R6A 4.800 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6C CD2O1A CD2R6F 3.600 2 180.00 ! GUA, cmb 04/10 +CD2O1A ND2R6C CD2R6C ND2B1 4.000 2 180.00 ! GUA, cmb 04/10 +CD2O1A ND2R6C CD2R6C ND2R6B 0.200 2 180.00 ! GUA, cmb 04/10 +HDP1A ND2R6C CD2R6C ND2B1 0.000 2 180.00 ! GUA, cmb 04/10 +HDP1A ND2R6C CD2R6C ND2R6B 3.600 2 180.00 ! GUA, cmb 04/10 +CD31C ND3A3 CD2O1A OD2C1A 2.500 2 180.00 ! PRO +CD31C ND3A3 CD2O1A CD31C 2.500 2 180.00 ! PRO +CD31C ND3A3 CD2O1A CD32C 2.500 2 180.00 ! PRO +CD31C ND3A3 CD2O1A CD32A 2.500 2 180.00 ! PRO +CD31C ND3A3 CD2O1A CD33C 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A OD2C1A 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A CD31C 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A CD32A 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A CD32C 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A CD33C 2.500 2 180.00 ! PRO +CD2O1A ND3A3 CD31C CD2O1A 0.300 1 0.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD2O1A 0.200 2 0.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD2O1A 2.600 3 0.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD2O2A 0.200 3 0.00 ! PRO, CTER +CD2O1A ND3A3 CD31C CD32A 0.300 1 180.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD32A 0.700 2 180.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD32A 0.700 3 0.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C HDA1A 0.200 3 0.00 ! PRO +CD32A ND3A3 CD31C CD2O1A 1.800 1 0.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD2O1A 1.200 2 0.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD2O1A 0.500 3 180.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD2O2A 0.200 3 0.00 ! PRO, CTER +CD32A ND3A3 CD31C CD32A 0.500 1 180.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD32A 1.700 2 180.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD32A 1.600 3 0.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C HDA1A 0.200 3 0.00 ! PRO +CD2O1A ND3A3 CD32A CD32A 2.400 1 180.00 ! PRO FIT PES PEML CHI4 +CD2O1A ND3A3 CD32A CD32A 1.000 2 0.00 ! PRO FIT PES PEML CHI4 +CD2O1A ND3A3 CD32A CD32A 0.700 3 180.00 ! PRO FIT PES PEML CHI4 +CD2O1A ND3A3 CD32A HDA2A 0.200 3 0.00 ! PRO FIXED PES PEML CHI4 +CD31C ND3A3 CD32A CD32A 0.600 1 180.0 ! PRO FIT PES PEML CHI4 +CD31C ND3A3 CD32A CD32A 0.900 2 180.0 ! PRO FIT PES PEML CHI4 +CD31C ND3A3 CD32A CD32A 1.000 3 0.0 ! PRO FIT PES PEML CHI4 +CD31C ND3A3 CD32A HDA2A 0.200 3 0.00 ! PRO FIXED PES PEML CHI4 +CD32C ND3A3 CD32C CD32A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +ND3A3 CD32C CD32A CD32A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +HDP1A ND3A3 CD31C CD32A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +CD32C CD32A CD32A CD32C 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +CD32C ND3A3 CD32C HDA2A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +ND3A3 CD32C CD32A HDA2A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +HDP1A ND3A3 CD32C CD32A 0.000 1 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +CD32A ND3P2A CD31C CD32A 0.260 3 0.00 ! N-terminal PRO +CD32A ND3P2A CD31C HDA1C 0.200 3 0.00 ! N-terminal PRO +CD32A ND3P2A CD31C CD2O1A 0.260 3 0.00 ! N-terminal PRO +CD33A ND3P2A CD32A CD32A 0.260 3 0.00 ! NC5/CHOL, qm, EH 2007, ammonium cation, to lipids +CD33A ND3P2A CD32A CD33A 0.260 3 0.00 ! NC5/CHOL, qm, EH 2007, ammonium cation +HDA2C CD32A ND3P2A CD31C 0.260 3 0.00 ! N-terminal PRO +CD31C ND3P2A CD32A CD32A 0.260 3 0.00 ! N-terminal PRO +HDA1C CD31C CD32A HDA2A 0.200 3 0.00 ! N-terminal PRO +HDA1C CD31C CD31A CD32A 0.200 3 0.00 ! PEML by analogy ILE +HDA1C CD31C CD32A CD31A 0.200 3 0.00 ! PEML by analogy LEU +HDA1C CD31C CD32A CD32A 0.200 3 0.00 ! N-terminal PRO +HDA1C CD31C CD32B CD32A 0.200 3 0.00 ! PEML by analogy GLU +HDA1C CD31C CD32B CD32C 0.200 3 0.00 ! alex by analogy GLUP +CD33A ND3P2A CD32A HDA2C 0.260 3 0.00 ! NC4, charmm27, ammonium cation +CD32A ND3P2A CD33A HDA3C 0.230 3 0.00 ! NC4, charmm27 , ammonium cation +CD33A ND3P2A CD33A HDA3C 0.230 3 0.00 ! NC4, charmm27, ammonium cation +HDP1B ND3P2A CD31A CD2O1A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 +HDP1B ND3P2A CD31C CD2O1A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 +HDP1B ND3P2A CD31A CD2O2A 0.320 3 0.00 ! NTER, zwitterionic dipeptide %% +HDP1B ND3P2A CD31A CD2O3A 0.320 3 0.00 ! CNEU/NTER, CNEU %% +HDP1B ND3P2A CD31C CD2O3A 0.320 3 0.00 ! CNEU/NTER, CNEU %% +HDP1B ND3P2A CD31A CD31A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P2A CD31A CD32A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P2A CD31C CD32A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P2A CD31A CD33A 0.320 3 0.00 ! CNEU/NTER, NTER-CT3 ETAM, qm, EH 2007 %% +HDP1B ND3P2A CD31A HDA1C 0.100 3 0.00 ! CNEU/NTER, ETAM, qm, EH 2007 %% +HDP1B ND3P2A CD31C HDA1C 0.100 3 0.00 ! CNEU/NTER, ETAM, qm, EH 2007 %% +HDP1B ND3P2A CD32A CD2O1A 0.320 3 0.00 ! NTER, ETAM, gly +HDP1B ND3P2A CD32C CD2O1A 0.320 3 0.00 ! NTER, ETAM, gly +HDP1B ND3P2A CD32A CD32A 0.320 3 0.00 ! ETAM, qm, EH 2007, ammonium cation, for lipids +HDP1B ND3P2A CD32A CD33A 0.320 3 0.00 ! ETAM, qm, EH 2007, ammonium cation +HDP1B ND3P2A CD32A HDA2C 0.100 3 0.00 ! ETAM, charmm27, gly +HDP1B ND3P2A CD32C HDA2C 0.100 3 0.00 ! ETAM, charmm27, gly +HDP1B ND3P2A CD33A HDA3C 0.100 3 0.00 ! NC1, charmm27 (etam), not necessary for lipid, NH4+ +HDP1B ND3P3A CD31A CD2O1A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 +HDP1B ND3P3A CD31C CD2O1A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 +HDP1B ND3P3A CD31A CD2O2A 0.320 3 0.00 ! NTER, zwitterionic dipeptide %% +HDP1B ND3P3A CD31C CD2O2A 0.320 3 0.00 ! NTER, zwitterionic dipeptide %% +HDP1B ND3P3A CD32C CD2O2A 0.320 3 0.00 ! NTER, zwitterionic dipeptide %% +HDP1B ND3P3A CD31A CD2O3A 0.320 3 0.00 ! CNEU/NTER, CNEU %% +HDP1B ND3P3A CD31C CD2O3A 0.320 3 0.00 ! CNEU/NTER, CNEU %% +HDP1B ND3P3A CD31A CD31A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P3A CD31C CD31A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P3A CD31A CD32A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P3A CD31C CD32A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P3A CD31C CD32B 0.320 3 0.00 ! PEML by analogy, GLU, NTER +HDP1B ND3P3A CD31C CD32C 0.320 3 0.00 ! PEML by analogy, ASN, NTER +HDP1B ND3P3A CD31A CD33A 0.320 3 0.00 ! CNEU/NTER, NTER-CT3 ETAM, qm, EH 2007 %% +HDP1B ND3P3A CD31C CD33A 0.320 3 0.00 ! CNEU/NTER, NTER-CT3 ETAM, qm, EH 2007 %% +HDP1B ND3P3A CD31A HDA1C 0.100 3 0.00 ! CNEU/NTER, ETAM, qm, EH 2007 %% +HDP1B ND3P3A CD31C HDA1C 0.100 3 0.00 ! CNEU/NTER, ETAM, qm, EH 2007 %% +HDP1B ND3P3A CD32A CD2O1A 0.320 3 0.00 ! NTER, ETAM, gly +HDP1B ND3P3A CD32C CD2O1A 0.320 3 0.00 ! NTER, ETAM, gly +HDP1B ND3P3A CD32A CD32A 0.320 3 0.00 ! ETAM, qm, EH 2007, ammonium cation, +HDP1B ND3P3A CD32A CD33A 0.320 3 0.00 ! ETAM, qm, EH 2007, ammonium cation +HDP1B ND3P3A CD32A HDA2C 0.100 3 0.00 ! ETAM, charmm27, ammonium cation +HDP1B ND3P3A CD32C HDA2C 0.100 3 0.00 ! ETAM, charmm27, gly +HDP1B ND3P3A CD33A HDA3C 0.100 3 0.00 ! NC1, charmm27 (etam), not necessary for lipid, ammonium cat( +CD325B OD305A CD315B CD325B 0.500 3 0.00 ! TF2M, cmb +CD325B OD305A CD315B CD33A 0.300 3 0.00 ! TF2M, cmb +CD325B OD305A CD315B HDA1R5 0.300 3 0.00 ! TF2M, cmb +CD315B OD305A CD325B CD325B 0.500 3 0.00 ! TF2M, cmb +CD315B OD305A CD325B HDA2R5 0.300 3 0.00 ! TF2M, cmb +CD325B OD305A CD325B CD325B 0.500 3 0.00 ! THF, viv +CD325B OD305A CD325B HDA2R5 0.300 3 0.00 ! THF, viv +CD326B OD306A CD326B CD326B 0.52702 1 180.00 ! THP, sng 1/06 +CD326B OD306A CD326B CD326B 0.68297 2 0.00 ! THP, sng 1/06 +CD326B OD306A CD326B CD326B 0.20977 3 180.00 ! THP, sng 1/06 +CD326B OD306A CD326B CD326B 0.15037 4 0.00 ! THP, sng 1/06 +CD326B OD306A CD326B HDA2E 0.284 3 0.00 ! DMET, viv +CD32A OD30A CD32A CD32A 0.570 1 0.00 ! DMOE, ATM +CD32A OD30A CD32A CD32A 0.290 2 0.00 ! DMOE, ATM +CD32A OD30A CD32A CD32A 0.430 3 0.00 ! DMOE, ATM +CD32A OD30A CD32A CD33A 0.400 1 0.00 ! DEET, ATM +CD32A OD30A CD32A CD33A 0.490 3 0.00 ! DEET +CD32A OD30A CD32A HDA2A 0.284 3 0.00 ! DEET, alex +CD33A OD30A CD32A CD32A 0.570 1 0.00 ! DMOE, 1,2-dimethoxyethane (DMOE), 2/12/05, ATM +CD33A OD30A CD32A CD32A 0.290 2 0.00 ! DMOE, ATM +CD33A OD30A CD32A CD32A 0.430 3 0.00 ! DMOE, ATM +CD33A OD30A CD32A CD33A 0.400 1 0.00 ! MEE, viv +CD33A OD30A CD32A CD33A 0.490 3 0.00 ! MEE, viv +CD33A OD30A CD32A HDA2A 0.284 3 0.00 ! DEET, alex +CD32E OD30A CD32E CD32A 0.570 1 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32A 0.290 2 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32A 0.430 3 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32E 0.570 1 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32E 0.290 2 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32E 0.430 3 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD33A 0.400 1 0.00 ! DEET, ATM +CD32E OD30A CD32E CD33A 0.490 3 0.00 ! DEET +CD32E OD30A CD32E HDA2E 0.284 3 0.00 ! DEET, alex +CD33E OD30A CD32E CD32A 0.570 1 0.00 ! DMOE, +CD33E OD30A CD32E CD32A 0.290 2 0.00 ! DMOE, ATM +CD33E OD30A CD32E CD32A 0.430 3 0.00 ! DMOE, ATM +CD33E OD30A CD32E CD32E 0.570 1 0.00 ! DMOE, +CD33E OD30A CD32E CD32E 0.290 2 0.00 ! DMOE, ATM +CD33E OD30A CD32E CD32E 0.430 3 0.00 ! DMOE, ATM +CD33E OD30A CD32E CD33A 0.400 1 0.00 ! MEE, viv +CD33E OD30A CD32E CD33A 0.490 3 0.00 ! MEE, viv +CD33E OD30A CD32E HDA2E 0.284 3 0.00 ! DEET, alex +CD32A OD30A CD33A HDA3A 0.284 3 0.00 ! DEET, alex +CD33A OD30A CD33A HDA3A 0.284 3 0.00 ! DME, viv +CD32E OD30A CD33E HDA3A 0.284 3 0.00 ! DEET, alex +CD33E OD30A CD33E HDA3A 0.284 3 0.00 ! DME, viv +HDA1A CD31C CD32C HDA2A 0.200 3 0.00 ! Lipid, alkane +CD32A CD32A CD32A CD32C 0.083 2 0.00 ! Lipid, alkane +CD32A CD32A CD32A CD32C 0.139 3 180.00 ! Lipid, alkane +CD32A CD32A CD32A CD32C 0.078 4 0.00 ! Lipid, alkane +CD32A CD32A CD32A CD32C 0.136 5 0.00 ! Lipid, alkane +CD33A CD31C CD32C HDA2A 0.200 3 0.00 ! GLYC, alkane, lipid +CD32A CD31C CD32C HDA2A 0.200 3 0.00 ! GLYC, alkane, lipid +CD32C CD31C CD32A HDA2A 0.190 3 0.00 ! GLYC, alkane +CD32C CD31C CD33A HDA3A 0.190 3 0.00 ! GLYC, alkane, lipid +CD32C CD32A CD32A HDA2A 0.160 3 0.00 ! Lipid-H, alkane, ester +HDA1A CD31C CD32C OD30C 0.200 3 0.00 ! EAS/Lipid-H, charmm27 +OD30C CD31C CD32C HDA2A 0.190 3 0.00 ! EAS/Lipid-H, charmm27 +CD2O3A OD30C CD32C CD33A 1.250 1 180.00 ! EAS, EH 2007 +CD2O3A OD30C CD32C CD33A 0.500 3 180.00 ! EAS, EH 2007 +CD2O3A OD30C CD32C HDA2A 0.200 3 180.00 ! MAS, PEML 2009 +CD2O3A OD30C CD33C HDA3A 0.200 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +CD2O3A OD30C CD33D HDA3A 0.200 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +HDP1A OD30D CD2O3A OD2C3A 1.110 2 180.00 ! ACEH, PEML +HDP1A OD30D CD2O3A CD31A 3.800 2 180.00 ! CNEU/ACEH, PEML +HDP1A OD30D CD2O3A CD31C 3.800 2 180.00 ! CNEU/ACEH, PEML +HDP1A OD30D CD2O3A CD32C 3.800 2 180.00 ! FROM ACEH, PEML, gly +HDP1A OD30D CD2O3A CD33C 3.760 2 180.00 ! ACEH, PEML +HDP1A OD31A CD2R6A CD2R6A 0.990 2 180.00 ! PHEN, phenol +HDP1A OD31A CD31A CD32A 1.660 1 0.00 ! BUO2, 2-butanol +HDP1A OD31A CD31A CD32A 0.120 2 0.00 ! BUO2, 2-butanol +HDP1A OD31A CD31A CD32A 0.340 3 0.00 ! BUO2, 2-butanol +HDP1A OD31A CD315A CD325A 1.660 1 0.00 ! CPO1, from BUO2, 2-butanol, cmb needs test +HDP1A OD31A CD315A CD325A 0.120 2 0.00 ! CPO1, from BUO2, 2-butanol, cmb needs test +HDP1A OD31A CD315A CD325A 0.340 3 0.00 ! CPO1, from BUO2, 2-butanol, cmb needs test +HDP1A OD31A CD31A CD33A 1.660 1 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A CD33A 0.120 2 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A CD33A 0.340 3 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A HDA1A 0.060 1 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A HDA1A 0.060 2 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A HDA1A 0.000 3 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD315A HDA1R5 0.060 1 0.00 ! CPO1, from PRO2, 2-propanol, needs test +HDP1A OD31A CD315A HDA1R5 0.060 2 0.00 ! CPO1, from PRO2, 2-propanol, needs test +HDP1A OD31A CD315A HDA1R5 0.000 3 0.00 ! CPO1, from PRO2, 2-propanol, needs test +HDP1A OD31A CD32A CD32A 1.250 1 0.00 ! ETAM, from ethanol +HDP1A OD31A CD32A CD32A 0.350 2 0.00 ! ETAM +HDP1A OD31A CD32A CD32A 0.360 3 0.00 ! ETAM +HDP1A OD31A CD32A CD33A 1.250 1 0.00 ! ETOH, ethanol +HDP1A OD31A CD32A CD33A 0.350 2 0.00 ! ETOH, ethanol +HDP1A OD31A CD32A CD33A 0.360 3 0.00 ! ETOH, ethanol +HDP1A OD31A CD32A HDA2A 0.140 2 0.00 ! ETOH, ethanol +HDP1A OD31A CD32A HDA2A 0.130 3 0.00 ! ETOH, ethanol +HDP1A OD31A CD33B HDA3B 0.179 3 0.00 ! MEOH, methanol +HDP1A OD31B CD32A CD32A 1.050 1 0.00 ! PRO1, 1-propanol +HDP1A OD31B CD32A CD32A 0.370 2 0.00 ! PRO1, 1-propanol +HDP1A OD31B CD32A CD32A 0.340 3 0.00 ! PRO1, 1-propanol +HDP1A OD31B CD32A HDA2A 0.140 2 0.00 ! PRO1, 1-propanol +HDP1A OD31B CD32A HDA2A 0.130 3 0.00 ! PRO1, 1-propanol +HDP1A OD31C CD2R6A CD2R6A 0.990 2 180.00 ! PHEN, phenol +CD33A SD30A CD32A CD32A 0.2577 1 0.00 ! MET/EMS, chi3, sig fig,! +CD33A SD30A CD32A CD32A 0.4111 2 0.00 ! MET/EMS, chi3 +CD33A SD30A CD32A CD32A 0.5999 3 0.00 ! MET/EMS, chi3 +CD33A SD30A CD32A CD33A 0.2577 1 0.00 ! EMS +CD33A SD30A CD32A CD33A 0.4111 2 0.00 ! EMS +CD33A SD30A CD32A CD33A 0.5999 3 0.00 ! EMS +CD33A SD30A CD32A HDA2A 0.2800 3 0.00 ! EMS +CD32A SD30A CD33A HDA3A 0.2800 3 0.00 ! EMS +CD33A SD30A CD33A HDA3A 0.2800 3 0.00 ! DMS +CD32A SD30B SD30B CD32A 0.8123 1 0.00 ! DISU/DMDS +CD32A SD30B SD30B CD32A 3.8234 2 0.00 ! DISU/DMDS +CD32A SD30B SD30B CD32A 1.0123 3 0.00 ! DISU/DMDS +CD33A SD30B SD30B CD33A 0.8123 1 0.00 ! DMDS +CD33A SD30B SD30B CD33A 3.8234 2 0.00 ! DMDS +CD33A SD30B SD30B CD33A 1.0123 3 0.00 ! DMDS +SD30B SD30B CD32A CD31C 0.200 3 0.00 ! DISU, chi2, c22 +SD30B SD30B CD32A HDA2A 0.2777 3 0.00 ! DISU/DMDS +SD30B SD30B CD33A HDA3A 0.2777 3 0.00 ! DMDs +HDP1A SD31A CD33A HDA3A 0.203 3 0.00 ! MESH +HDP1A SD31B CD32A CD32A 0.280 1 180.00 ! PRSH +HDP1A SD31B CD32A CD32A 0.255 2 0.00 ! PRSH +HDP1A SD31B CD32A CD32A 0.365 3 0.00 ! PRSH +HDP1A SD31B CD32A CD33A 0.240 1 180.00 ! ETSH +HDP1A SD31B CD32A CD33A 0.200 2 0.00 ! ETSH +HDP1A SD31B CD32A CD33A 0.420 3 0.00 ! ETSH +HDP1A SD31B CD32A HDA2A 0.140 2 0.00 ! ETSH +HDP1A SD31B CD32A HDA2A 0.130 3 0.00 ! ETSH +ND2R6C CD2O1A CD2R6A CD2R6H 1.800 2 180.00 ! THY, cmb 04/10 +ND2R6C CD2O1A CD2R6A CD33A 1.000 2 180.00 ! THY, cmb 04/10 +ND2R6C CD2O1A CD2R6A HDR6A 1.000 2 180.00 ! URA +OD2C1B CD2O1A CD2R6A CD2R6H 1.000 2 180.00 ! THY, cmb 04/10 +OD2C1B CD2O1A CD2R6A CD33A 1.000 2 180.00 ! THY, cmb 04/10 +OD2C1B CD2O1A CD2R6A HDR6A 6.000 2 180.00 ! URA +ND2R6C CD2O1A CD2R6F ND2R5E 2.000 2 180.00 ! GUA, cmb 04/10 +ND2R6C CD2O1A CD2R6F CD2R6F 0.200 2 180.00 ! GUA, cmb 04/10 +OD2C1B CD2O1A CD2R6F ND2R5E 0.000 2 180.00 ! GUA, cmb 04/10 +OD2C1B CD2O1A CD2R6F CD2R6F 8.000 2 180.00 ! GUA, cmb 04/10 +ND2A1 CD2O1A CD31A ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A1 CD2O1A CD31A ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND2A1 CD2O1A CD31C ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A1 CD2O1A CD31C ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31A ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31A ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31C ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31C ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND3A3 CD2O1A CD31C ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A3 CD2O1A CD31C ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31A CD31A 0.000 3 0.00 ! NTER +ND2A2 CD2O1A CD31A CD32A 0.000 3 0.00 ! NTER +ND2A2 CD2O1A CD31A CD33A 0.000 3 0.00 ! NTER +ND2A2 CD2O1A CD31A HDA1C 0.000 3 180.00 ! NTER +ND2A2 CD2O1A CD31C HDA1C 0.000 3 180.00 ! N-terminal PRO +OD2C1A CD2O1A CD31A ND3P3A 0.300 1 0.00 ! NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31A ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31C ND3P3A 0.300 1 0.00 ! NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31C ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31A ND3P2A 0.000 3 0.00 ! NTER-CT3 PRO +OD2C1A CD2O1A CD31C ND3P2A 0.000 3 0.00 ! NTER-CT3 PRO +OD2C1A CD2O1A CD31A CD31A 0.000 1 0.00 ! NTER +OD2C1A CD2O1A CD31A CD32A 0.000 1 0.00 ! NTER +OD2C1A CD2O1A CD31A CD33A 0.000 1 0.00 ! NTER +OD2C1A CD2O1A CD31A HDA1C 0.000 3 180.00 ! NTER +OD2C1A CD2O1A CD31C HDA1C 0.000 3 180.00 ! NTER +ND2A1 CD2O1A CD31C ND2A2 0.000 1 0.00 ! CT2, guess +ND2A1 CD2O1A CD31C CD33A 0.000 1 0.00 ! CT2, guess +ND2A1 CD2O1A CD31C CD32C 0.000 1 0.00 ! PEML by analogy, ASN CT2 +ND2A1 CD2O1A CD31C HDA1A 0.200 3 0.00 ! CT2, alkanes +ND2A1 CD2O1A CD31C HDA1C 0.200 3 0.00 ! CT2, alkanes +ND2A2 CD2O1A CD31C ND2A2 0.000 3 180.00 ! ALAD, psi, cmap +ND2A2 CD2O1A CD31C ND3A3 0.200 3 0.00 ! PRO +ND2A2 CD2O1A CD31C CD31A 0.000 1 0.00 ! ILE/VAL, c22 +ND2A2 CD2O1A CD31C CD32A 0.000 1 0.00 ! GLN, c22 +ND2A2 CD2O1A CD31C CD32B 0.000 1 0.00 ! GLU, from ND2A2 CD2O1A CD31C CD32A +ND2A2 CD2O1A CD31C CD32C 0.000 1 0.00 ! ASN, c22 +ND2A2 CD2O1A CD31C CD33A 0.000 1 0.00 ! ALAD, will effect psi +ND2A2 CD2O1A CD31C HDA1A 0.200 3 0.00 ! ALAD +ND3A3 CD2O1A CD31C ND2A2 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD32C ND2A2 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C ND3A3 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C CD31A 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C CD32A 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C CD32C 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C CD33A 0.200 3 0.00 ! PRO, adjacent to NTER +ND3A3 CD2O1A CD31C HDA1A 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C HDA1C 0.200 3 0.00 ! PRO +OD2C1A CD2O1A CD31C ND2A2 0.000 1 0.00 ! ALAD, psi, cmap +OD2C1A CD2O1A CD31C ND3A3 0.200 3 0.00 ! PRO +OD2C1A CD2O1A CD31C CD31A 1.400 1 0.00 ! ILE/VAL, c22 +OD2C1A CD2O1A CD31C CD32A 1.400 1 0.00 ! GLN, c22 +OD2C1A CD2O1A CD31C CD32B 1.400 1 0.00 ! GLU, from OD2C1A CD2O1A CD31C CD32A +OD2C1A CD2O1A CD31C CD32C 1.400 1 0.00 ! ASN, c22 +OD2C1A CD2O1A CD31C CD33A 3.920 1 0.00 ! ALAD, will effect psi +OD2C1A CD2O1A CD31C HDA1A 0.230 3 0.00 ! ALAD +ND2A2 CD2O1A CD32A ND3P3A 0.000 1 0.00 ! NTER, gly +ND2A2 CD2O1A CD32C ND3P3A 0.000 1 0.00 ! NTER, gly +ND2A2 CD2O1A CD31C ND3P2A 0.000 1 0.00 ! NTER, gly +ND2A2 CD2O1A CD32A HDA2C 0.200 3 0.00 ! GLYD +ND2A2 CD2O1A CD32C HDA2C 0.200 3 0.00 ! GLYD +ND3A3 CD2O1A CD32A ND3P3A 0.200 3 0.00 ! PRO, adjacent to NTER +ND3A3 CD2O1A CD32C ND3P3A 0.200 3 0.00 ! PRO, adjacent to NTER +ND3A3 CD2O1A CD32A HDA2C 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD32C HDA2C 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD32C HDA2A 0.200 3 0.00 ! PRO +OD2C1A CD2O1A CD32A ND3P3A 0.000 1 0.00 ! NTER, gly +OD2C1A CD2O1A CD32C ND3P3A 0.000 1 0.00 ! NTER, gly +OD2C1A CD2O1A CD32A HDA2C 0.230 3 0.00 ! GLYD +OD2C1A CD2O1A CD32C HDA2C 0.230 3 0.00 ! GLYD +ND2A1 CD2O1A CD32C ND2A2 0.000 1 0.00 ! CT2, guess, gly +ND2A1 CD2O1A CD32C CD32A 0.000 1 0.00 ! GLN, c22, chi3 +ND2A1 CD2O1A CD32C HDA2A 0.000 1 0.00 ! ASN, c22 +ND2A2 CD2O1A CD32C ND2A2 0.000 3 180.00 ! GLYD, psi, cmap +ND2A2 CD2O1A CD32C HDA2A 0.200 3 0.00 ! GLYD +OD2C1A CD2O1A CD32C ND2A2 0.000 3 180.00 ! GLYD, psi, cmap +OD2C1A CD2O1A CD32C CD32A 1.400 1 0.00 ! GLN, c22, chi3 +OD2C1A CD2O1A CD32C HDA2A 0.230 3 0.00 ! GLYD +ND2A1 CD2O1A CD33C HDA3A 0.079 3 180.00 ! ACEM +ND2A2 CD2O1A CD33C HDA3A 0.200 3 0.00 ! NMA +ND2A3 CD2O1A CD33C HDA3A 0.000 3 180.00 ! DMA, N,N-dimethylacetamide +ND3A3 CD2O1A CD33C HDA3A 0.200 3 0.00 ! PRO +OD2C1A CD2O1A CD33C HDA3A 0.230 3 0.00 ! NMA +OD2C2A CD2O2A CD31A ND3P3A 0.900 2 180.00 ! NTER, zwitterionic dipeptide also NTER-CT3 %% +OD2C2A CD2O2A CD31C ND3P3A 0.900 2 180.00 ! NTER, zwitterionic dipeptide also NTER-CT3 %% +OD2C2A CD2O2A CD32C ND3P3A 0.900 2 180.00 ! NTER, zwitterionic dipeptide also NTER-CT3 %% +OD2C2A CD2O2A CD31A CD31A 0.000 1 0.00 ! CTER +OD2C2A CD2O2A CD31A CD32A 0.000 1 0.00 ! CTER +OD2C2A CD2O2A CD31A CD33A 0.000 1 0.00 ! NTER, +OD2C2A CD2O2A CD31A HDA1C 0.000 3 180.00 ! NTER +OD2C2A CD2O2A CD31C ND2A2 3.000 1 0.00 ! CTER, PEML, pseudo-psi from ACE-CTER % +OD2C2A CD2O2A CD31C ND2A2 2.000 2 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER % +OD2C2A CD2O2A CD31C ND3A3 0.200 3 0.00 ! PRO, CTER +OD2C2A CD2O2A CD31C CD31A 0.000 1 0.00 ! CTER, PEML, Val/Ile +OD2C2A CD2O2A CD31C CD31A 0.000 2 180.00 ! CTER, PEML, Val/Ile +OD2C2A CD2O2A CD31C CD32A 0.000 1 0.00 ! CTER, PEML, Leu +OD2C2A CD2O2A CD31C CD32A 0.000 2 180.00 ! CTER, PEML, Leu +OD2C2A CD2O2A CD31C CD32B 0.000 1 0.00 ! CTER, Glu +OD2C2A CD2O2A CD31C CD32B 0.000 2 180.00 ! CTER, Glu, *CONFIRM* +OD2C2A CD2O2A CD31C CD32C 0.000 1 0.00 ! CTER, PEML, Leu +OD2C2A CD2O2A CD31C CD32C 0.000 2 180.00 ! CTER, PEML, Leu *CONFIRM* +OD2C2A CD2O2A CD31C CD33A 0.000 1 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER +OD2C2A CD2O2A CD31C CD33A 0.000 2 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER +OD2C2A CD2O2A CD31C HDA1A 0.000 1 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER +OD2C2A CD2O2A CD31C HDA1C 0.000 1 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER +OD2C2A CD2O2A CD32A CD32A 0.200 3 0.00 ! GLU, c22, chi3, old +OD2C2A CD2O2A CD32A CD32B 0.200 3 0.00 ! GLU, c22, chi3 +OD2C2A CD2O2A CD32A HDA2A 0.420 3 180.00 ! ASP, ACET, PEML +OD2C2A CD2O2A CD32C ND2A2 1.500 1 0.00 ! CTER, PEML, Gly +OD2C2A CD2O2A CD32C ND2A2 1.000 2 180.00 ! CTER, PEML, Gly +OD2C2A CD2O2A CD32C HDA2A 0.000 1 180.00 ! CTER, PEML, GLY +OD2C2A CD2O2A CD32C HDA2C 0.000 1 180.00 ! CTER, PEML, GLY +OD2C2A CD2O2A CD33A HDA3A 0.420 3 180.00 ! ASP, ACET, PEML +OD2C3A CD2O3A CD31A ND3P3A 0.000 1 0.00 ! CNEU/NTER +OD2C3A CD2O3A CD31C ND3P3A 0.000 1 0.00 ! CNEU/NTER +OD2C3A CD2O3A CD31A CD31A 0.900 2 180.00 ! CNEU/NTER +OD2C3A CD2O3A CD31A CD32A 0.900 2 180.00 ! CNEU/NTER +OD2C3A CD2O3A CD31A CD33A 0.400 1 0.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31A CD33A 1.400 2 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31A HDA1C 0.000 1 0.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C HDA1C 0.000 1 0.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD31A ND3P3A 0.000 1 0.00 ! CNEU/NTER +OD30D CD2O3A CD31C ND3P3A 0.000 1 0.00 ! CNEU/NTER +OD30D CD2O3A CD31A CD31A 1.500 2 0.00 ! CNEU/NTER +OD30D CD2O3A CD31A CD32A 1.500 2 0.00 ! CNEU/NTER +OD30D CD2O3A CD31A CD33A 0.400 1 180.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD31A CD33A 1.400 2 180.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD31A HDA1C 0.200 3 180.00 ! CNEU +OD30D CD2O3A CD31C HDA1C 0.200 3 180.00 ! CNEU +OD2C3A CD2O3A CD31C ND2A2 0.000 1 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C ND2A2 2.800 2 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C CD31A 0.900 2 180.00 ! CNEU/NTER +OD2C3A CD2O3A CD31C CD32A 0.900 2 180.00 ! CNEU/NTER +OD2C3A CD2O3A CD31C CD32B 0.900 2 180.00 ! PEML by analogy GLU, CNEU +OD2C3A CD2O3A CD31C CD32C 0.900 2 180.00 ! PEML by analogy ASN, CNEU +OD2C3A CD2O3A CD31C CD33A 0.400 1 0.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C CD33A 1.400 2 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C HDA1A 0.000 1 0.00 ! CNEU, PEML pseudo-psi +OD30C CD2O3A CD31C ND2A2 0.200 3 0.00 ! CT1, c22 +OD30C CD2O3A CD31C CD31A 0.300 1 0.00 ! CT1, PEML by analogy ILE, CT1 +OD30C CD2O3A CD31C CD31A 0.300 2 180.00 ! CT1, PEML by analogy ILE, CT1 +OD30C CD2O3A CD31C CD32A 0.300 1 0.00 ! CT1, PEML by analogy with OD30C CD2O3A CD31C CD33A +OD30C CD2O3A CD31C CD32A 0.300 2 180.00 ! CT1, PEML by analogy with OD30C CD2O3A CD31C CD33A +OD30C CD2O3A CD31C CD32B 0.300 1 0.00 ! CT1, PEML by analogy GLU, CT1 +OD30C CD2O3A CD31C CD32B 0.300 2 180.00 ! CT1, PEML by analogy GLU, CT1 +OD30C CD2O3A CD31C CD32C 0.300 1 0.00 ! CT1, PEML by analogy ASN, CT1 +OD30C CD2O3A CD31C CD32C 0.300 2 180.00 ! CT1, PEML by analogy ASN, CT1 +OD30C CD2O3A CD31C CD33A 0.300 1 0.00 ! CT1, MPO, EH 2007 +OD30C CD2O3A CD31C CD33A 0.300 2 180.00 ! CT1, MPO, EH 2007 +OD30C CD2O3A CD31C HDA1A 0.200 3 180.00 ! CT1, MAS +OD30D CD2O3A CD31C ND2A2 0.000 1 0.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD31C ND2A2 2.800 2 180.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD31C CD31A 1.500 2 0.00 ! CNEU/NTER +OD30D CD2O3A CD31C CD32A 1.500 2 0.00 ! CNEU/NTER +OD30D CD2O3A CD31C CD32B 1.500 2 0.00 ! PEML by analogy GLU, CNEU +OD30D CD2O3A CD31C CD32C 1.500 2 0.00 ! PEML by analogy ASN, CNEU +OD30D CD2O3A CD31C CD33A 0.400 1 180.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD31C CD33A 1.400 2 180.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD31C HDA1A 0.000 1 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD32C ND2A2 5.160 1 0.00 ! CNEU, PEML, gly +OD2C3A CD2O3A CD32C ND2A2 0.000 2 180.00 ! CNEU, PEML, gly +OD2C3A CD2O3A CD32C CD31C 0.200 3 0.00 ! ASPP, c22, chi2 +OD2C3A CD2O3A CD32C CD32B 0.200 3 0.00 ! GLUP, c22, chi2 +OD2C3A CD2O3A CD32C CD32A 0.100 4 0.00 ! MPO, EH 2007, ester +OD2C3A CD2O3A CD32C CD33A 0.100 4 0.00 ! MPO, EH 2007, ester +OD2C3A CD2O3A CD32C HDA2A 0.000 3 180.00 ! MAS, PEML 2009 +OD30C CD2O3A CD32C ND2A2 0.200 3 0.00 ! CT1, c22, gly +OD30C CD2O3A CD32C CD32A 0.300 1 0.00 ! MPO, EH 2007, ester +OD30C CD2O3A CD32C CD32A 0.300 2 180.00 ! MPO, EH 2007, ester +OD30C CD2O3A CD32C CD33A 0.300 1 0.00 ! MPO, EH 2007, ester +OD30C CD2O3A CD32C CD33A 0.300 2 180.00 ! MPO, EH 2007, ester +OD30C CD2O3A CD32C HDA2A 0.000 3 180.00 ! MAS, PEML 2009 +OD30D CD2O3A CD32C ND2A2 2.830 1 0.00 ! CNEU, PEML, gly +OD30D CD2O3A CD32C CD31C 0.100 1 180.00 ! ASPP/CNEU, PEML pseudo-psi +OD30D CD2O3A CD32C CD31C 0.160 2 180.00 ! ASPP/CNEU, PEML pseudo-psi +OD30D CD2O3A CD32C CD32A 0.100 1 180.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD32C CD32A 0.160 2 180.00 ! CNEU, PEML pseudo-psi +OD30D CD2O3A CD32C CD32B 0.100 1 180.00 ! GLUP, PEML pseudo-psi +OD30D CD2O3A CD32C CD32B 0.160 2 180.00 ! GLUP, PEML pseudo-psi +OD30D CD2O3A CD32C HDA2A 0.200 3 180.00 ! CNEU, gly +OD2C3A CD2O3A CD33C HDA3A 0.000 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +OD30C CD2O3A CD33C HDA3A 0.000 3 180.00 ! MAS, PEML 2009 +OD30D CD2O3A CD33C HDA3A 0.000 6 180.00 ! ACEH, PEML +ND2R5A CD2R5A CD2R5A ND2R5B 14.000 2 180.00 ! IMID, imidazole +ND2R5A CD2R5A CD2R5A CD32A 3.000 2 180.00 ! HSE, c22 +ND2R5A CD2R5A CD2R5A HDR5A 3.000 2 180.00 ! IMID, imidazole +ND2R5B CD2R5A CD2R5A CD32A 3.000 2 180.00 ! HSD/4MIM, 4-methyl-imidazole +ND2R5B CD2R5A CD2R5A CD33A 3.000 2 180.00 ! 4MIM, 4-methyl-imidazole +ND2R5B CD2R5A CD2R5A HDR5A 3.000 2 180.00 ! IMID, imidazole +CD32A CD2R5A CD2R5A HDR5A 2.000 2 180.00 ! HSD/4MIM, 4-methyl-imidazole +CD33A CD2R5A CD2R5A HDR5A 2.000 2 180.00 ! 4MIM, 4-methyl-imidazole +HDR5A CD2R5A CD2R5A HDR5A 2.000 2 180.00 ! IMID, imidazole +ND2R5A CD2R5A CD2R5C CD2R5C 7.800 2 180.00 ! PYRR, pyrrole +ND2R5A CD2R5A CD2R5C CD2R6D 8.190 2 180.00 ! INDO, indole +ND2R5A CD2R5A CD2R5C CD32A 3.000 2 180.00 ! TRP/INDM, methyl-indole +ND2R5A CD2R5A CD2R5C CD33A 3.000 2 180.00 ! INDM, methyl-indole +ND2R5A CD2R5A CD2R5C HDR5C 1.100 2 180.00 ! PYRR, pyrrole +HDR5A CD2R5A CD2R5C CD2R5C 3.400 2 180.00 ! PYRR, pyrrole +HDR5A CD2R5A CD2R5C CD2R6D 0.810 2 180.00 ! INDO, indole +HDR5A CD2R5A CD2R5C CD32A 4.200 2 180.00 ! TRP/INDM, methyl-indole +HDR5A CD2R5A CD2R5C CD33A 4.200 2 180.00 ! INDM, methyl-indole +HDR5A CD2R5A CD2R5C HDR5C 0.280 2 180.00 ! PYRR, pyrrole +ND2R5A CD2R5A CD32A HDA2A 0.190 3 0.00 ! HSD/4MIM, 4-methyl-imidazole +ND2R5B CD2R5A CD32A HDA2A 0.190 3 0.00 ! HSE, 4MIM, 4-methyl-imidazole +CD2R5A CD2R5A CD32A HDA2A 0.000 3 0.00 ! HSD/4MIM, 4-methyl-imidazole +ND2R5A CD2R5A CD33A HDA3A 0.190 3 0.00 ! 4MIM, 4-methyl-imidazole +CD2R5A CD2R5A CD33A HDA3A 0.000 3 0.00 ! 4MIM, 4-methyl-imidazole +CD2R5A CD2R5C CD2R5C CD2R5A 10.900 2 180.00 ! PYRR, pyrrole +CD2R5A CD2R5C CD2R5C HDR5C 3.900 2 180.00 ! PYRR, pyrrole +HDR5C CD2R5C CD2R5C HDR5C 0.700 2 180.00 ! PYRR, pyrrole +CD2R5A CD2R5C CD2R6D CD2R6A 6.610 2 180.00 ! INDO, indole +CD2R5A CD2R5C CD2R6D CD2R6D 6.340 2 180.00 ! INDO, indole +CD32A CD2R5C CD2R6D CD2R6A 3.100 2 180.00 ! TRP/INDM, methyl-indole +CD32A CD2R5C CD2R6D CD2R6D 3.100 2 180.00 ! TRP/INDM, methyl-indole +CD33A CD2R5C CD2R6D CD2R6A 3.100 2 180.00 ! INDM, methyl-indole +CD33A CD2R5C CD2R6D CD2R6D 3.100 2 180.00 ! INDM, methyl-indole +HDR5C CD2R5C CD2R6D CD2R6A 0.150 2 180.00 ! INDO, indole +HDR5C CD2R5C CD2R6D CD2R6D 0.150 2 180.00 ! INDO, indole +CD2R5A CD2R5C CD32A HDA2A 0.000 3 0.00 ! TRP/INDM, methyl-indole +CD2R6D CD2R5C CD32A HDA2A 0.000 3 0.00 ! TRP/INDM, methyl-indole +CD2R5A CD2R5C CD33A HDA3A 0.000 3 0.00 ! INDM, methyl-indole +CD2R6D CD2R5C CD33A HDA3A 0.000 3 0.00 ! INDM, methyl-indole +ND2R5C CD2R5D CD2R5D ND2R5C 14.000 2 180.00 ! IMIM, from IMID (EH) +ND2R5C CD2R5D CD2R5D CD32A 2.500 2 180.00 ! HSP, c22 +ND2R5C CD2R5D CD2R5D HDR5D 3.000 2 180.00 ! IMIM, from IMID (EH) +CD32A CD2R5D CD2R5D HDR5D 2.000 2 180.00 ! HSP/4MIM, 4-methyl-imidazole +HDR5D CD2R5D CD2R5D HDR5D 2.000 2 180.00 ! IMIM, from IMID (EH) +ND2R5C CD2R5D CD32A HDA2A 0.190 3 0.00 ! HSP, c22 +CD2R5D CD2R5D CD32A HDA2A 0.000 3 0.00 ! HSP/4MIM, 4-methyl-imidazole +OD31A CD2R6A CD2R6A CD2R6A 3.100 2 180.00 ! PHEN, phenol +OD31A CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! PHEN, phenol +OD31C CD2R6A CD2R6A CD2R6A 3.100 2 180.00 ! PHEN, phenol +OD31C CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! PHEN, phenol +CD2R6A CD2R6A CD2R6A CD2R6A 2.800 2 180.00 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6A CD2R6A CD2R6A CD2R6B 5.350 2 180.00 ! PYR, pyridine +CD2R6A CD2R6A CD2R6A CD2R6D 1.590 2 180.00 ! INDO, indole +CD2R6A CD2R6A CD2R6A CD32A 3.100 2 180.00 ! PHE/TOLU +CD2R6A CD2R6A CD2R6A CD33A 3.100 2 180.00 ! TOLU, toluene, geom + freq, peml 2005 +CD2R6A CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6B CD2R6A CD2R6A HDR6A 3.600 2 180.00 ! PYR, pyridine +CD2R6D CD2R6A CD2R6A HDR6A 1.200 2 180.00 ! INDO, indole +CD32A CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! PHE/TOLU +CD33A CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! TOLU, toluene, geom + freq, peml 2005 +HDR6A CD2R6A CD2R6A HDR6A 2.400 2 180.00 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6A CD2R6A CD2R6B ND2R6A 0.860 2 180.00 ! PYR, pyridine +CD2R6A CD2R6A CD2R6B CD2R6A 4.400 2 180.00 ! PYR, pyridine +CD2R6A CD2R6A CD2R6B HDR6B 5.400 2 180.00 ! PYR, pyridine +CD2R6B CD2R6A CD2R6B ND2R6B 0.810 2 180.00 ! PYRM, pyrimidine +CD2R6B CD2R6A CD2R6B HDR6B 1.380 2 180.00 ! PYRM, pyrimidine +CD2R6H CD2R6A CD2R6B ND2B1 2.000 2 180.00 ! CYT, cmb 04/10 +CD2R6H CD2R6A CD2R6B ND2R6B 0.800 2 180.00 ! CTT/PYRM, pyrimidine, cmb +HDR6A CD2R6A CD2R6B ND2B1 2.000 2 180.00 ! CYT, cmb 04/10 +HDR6A CD2R6A CD2R6B ND2R6A 1.200 2 180.00 ! PYR, pyridine +HDR6A CD2R6A CD2R6B ND2R6B 3.420 2 180.00 ! PYRM, pyrimidine +HDR6A CD2R6A CD2R6B HDR6B 2.400 2 180.00 ! PYR, pyridine +CD2R6A CD2R6A CD2R6D ND2R5A 1.930 2 180.00 ! INDO, indole +CD2R6A CD2R6A CD2R6D CD2R5C 1.680 2 180.00 ! INDO, indole +CD2R6A CD2R6A CD2R6D CD2R6D 1.340 2 180.00 ! INDO, indole +HDR6A CD2R6A CD2R6D ND2R5A 0.920 2 180.00 ! INDO, indole +HDR6A CD2R6A CD2R6D CD2R5C 0.440 2 180.00 ! INDO, indole +HDR6A CD2R6A CD2R6D CD2R6D 0.920 2 180.00 ! INDO, indole +HDR6A CD2R6A CD2R6F ND2R6B 2.800 2 180.00 ! CYT/PYRM, pyrimidine, cmb +CD2O1A CD2R6A CD2R6H ND2R6B 3.000 2 180.00 ! THY, cmb 04/10 +CD2O1A CD2R6A CD2R6H ND2R6C 3.000 2 180.00 ! THY, cmb 04/10 +CD2O1A CD2R6A CD2R6H HDR6B 1.000 2 180.00 ! THY, cmb 04/10 +CD2R6B CD2R6A CD2R6H ND2R6B 0.800 2 180.00 ! CYT/PYRM, pyrimidine, cmb +CD2R6B CD2R6A CD2R6H ND2R6C 0.800 2 180.00 ! CYT, cmb 04/10 +CD2R6B CD2R6A CD2R6H HDR6B 4.200 2 180.00 ! CYT/PYRM, pyrimidine, cmb +CD33A CD2R6A CD2R6H ND2R6B 5.600 2 180.00 ! THY, cmb +CD33A CD2R6A CD2R6H ND2R6C 5.600 2 180.00 ! THY, cmb 04/10 +CD33A CD2R6A CD2R6H HDR6B 1.000 2 180.00 ! THY, cmb 04/10 +HDR6A CD2R6A CD2R6H ND2R6B 2.800 2 180.00 ! CYT/PYRM, pyrimidine, cmb +HDR6A CD2R6A CD2R6H ND2R6C 2.800 2 180.00 ! CYT, cmb 04/10 +HDR6A CD2R6A CD2R6H HDR6B 2.400 2 180.00 ! CYT/PYR, pyridine, cmb +CD2R6A CD2R6A CD32A HDA2A 0.000 6 0.00 ! PHE/TOLU +CD2O1A CD2R6A CD33A HDA3A 0.460 3 0.00 ! THY +CD2R6A CD2R6A CD33A HDA3A 0.000 6 0.00 ! TOLU, toluene, geom + freq, peml 2005 +CD2R6H CD2R6A CD33A HDA3A 0.460 3 0.00 ! THY, cmb 04/10 +HDR6A CD2R6A CD33A HDA3A 0.000 6 0.00 ! TOLU, toluene, geom + freq, peml 2005 +ND2R6B CD2R6B CD2R6F ND2R5A 7.600 2 180.00 ! PUR0, purine, butterfly mode +ND2R6B CD2R6B CD2R6F ND2R5B 7.600 2 180.00 ! PUR1, purine, butterfly mode +ND2R6B CD2R6B CD2R6F CD2R6F 0.100 2 180.00 ! PUR0/1, purine +HDR6B CD2R6B CD2R6F ND2R5A 2.000 2 180.00 ! PUR1, purine, tautomer A, imidazole ring +HDR6B CD2R6B CD2R6F ND2R5B 2.000 2 180.00 ! PUR0, purine, tautomer B, imidazole ring +HDR6B CD2R6B CD2R6F CD2R6F 0.100 2 180.00 ! PUR0/1, purine, imidazole ring +ND2B1 CD2R6C CD2R6F ND2R5E 0.000 2 180.00 ! ADE, cmb 04/10 +ND2B1 CD2R6C CD2R6F CD2R6F 4.000 2 180.00 ! ADE, cmb 04/10 +ND2R6B CD2R6C CD2R6F ND2R5E 2.000 2 180.00 ! ADE, butterfly motion, cmb 04/10 +ND2R6B CD2R6C CD2R6F CD2R6F 1.800 2 180.00 ! ADE, cmb 04/10 +ND2R5A CD2R6D CD2R6D CD2R5C 8.500 2 180.00 ! INDO, indole +ND2R5A CD2R6D CD2R6D CD2R6A 1.610 2 180.00 ! INDO, indole +CD2R5C CD2R6D CD2R6D CD2R6A 1.760 2 180.00 ! INDO, indole +CD2R6A CD2R6D CD2R6D CD2R6A 3.460 2 180.00 ! INDO, indole +ND2R5A CD2R6F CD2R6F ND2R5B 5.100 2 180.00 ! PUR0/1, purine, imidazole ring +ND2R5A CD2R6F CD2R6F ND2R6B 12.500 2 180.00 ! PUR0, purine, butterfly mode +ND2R5A CD2R6F CD2R6F CD2R6B 12.500 2 180.00 ! PUR1, purine, butterfly mode +ND2R5B CD2R6F CD2R6F ND2R6B 12.500 2 180.00 ! PUR1, purine, butterfly mode +ND2R5B CD2R6F CD2R6F CD2R6B 12.500 2 180.00 ! PUR0, purine, butterfly mode +ND2R5E CD2R6F CD2R6F ND2R6B 12.500 2 180.00 ! GUA, cmb 04/10 +ND2R6B CD2R6F CD2R6F CD2R6B 0.100 2 180.00 ! PUR0/1, purine +ND2R5E CD2R6F CD2R6F ND2R5D 14.000 2 180.00 ! ADE, cmb 04/10 +ND2R5D CD2R6F CD2R6F CD2O1A 0.000 2 180.00 ! GUA, cmb 04/10 +ND2R5D CD2R6F CD2R6F CD2R6C 3.000 2 180.00 ! ADE, va A; butterfly motion, cmb 04/10 +ND2R6B CD2R6F CD2R6F CD2O1A 2.000 2 180.00 ! GUA, cmb 04/10 +ND2R6B CD2R6F CD2R6F CD2R6C 2.000 2 180.00 ! ADE, cmb 04/10 +CD32A ND2R5D CD2R6F ND2R6B 1.000 2 180.00 ! va; Et-Gua +CD32A ND2R5D CD2R6F CD2R6F 1.000 2 180.00 ! va; Et-Gua +CD32A ND2R5D CD2R5B ND2R5E 1.000 2 180.00 ! va; Et-Gua +CD32A ND2R5D CD2R5B HDR5B 1.000 2 180.00 ! va; Et-Gua +CD33A CD32A ND2R5D CD2R6F 1.000 3 0.00 ! va; Et-Gua +HDA2A CD32A ND2R5D CD2R6F 0.000 3 0.00 ! va; Et-Gua +HDA2A CD32A ND2R5D CD2R5B 0.000 3 0.00 ! va; Et-Gua +CD33A CD32A ND2R5D CD2R5B 1.000 3 0.00 ! va; Et-Gua +ND2R5D CD32A CD33A HDA3A 0.160 3 0.00 ! va; Et-Gua +CD31A CD30A CD32A HDA2A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD32A CD30A CD32A HDA2A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD32A CD30A CD32A HDA3A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD33A CD30A CD32A HDA2A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD31A CD30A CD33A HDA3A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD32A CD30A CD33A HDA3A 0.200 3 0.00 ! NEOP, nopentane, alkane, 3/92 - cmb, needs test +CD33A CD30A CD33A HDA3A 0.200 3 0.00 ! NEOP, nopentane, alkane, 3/92 +CD33A CD315B CD315B CD33A 0.200 3 0.00 ! THF, cmb +OD305A CD315B CD325B CD325B 0.000 3 0.00 ! TF2M, cmb +OD305A CD315B CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +CD325B CD315B CD325B CD325B 0.410 3 180.00 ! TF2M, cmb +CD325B CD315B CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +CD33A CD315B CD325B CD325B 0.200 3 0.00 ! TF2M, cmb +CD33A CD315B CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +HDA1R5 CD315B CD325B CD325B 0.200 3 0.00 ! TF2M, cmb +HDA1R5 CD315B CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +OD305A CD315B CD33A HDA3A 0.200 3 0.00 ! TF2M, cmb +CD325B CD315B CD33A HDA3A 0.200 3 0.00 ! TF2M, cmb +CD325A CD315A CD33A HDA3A 0.200 3 0.00 ! CPNM, cmb +HDA1R5 CD315B CD33A HDA3A 0.200 3 0.00 ! TF2M, cmb +HDA1R5 CD315A CD33A HDA3A 0.200 3 0.00 ! CPNM, cmb +ND3P3A CD31C CD31A CD33A 0.550 1 180.00 ! ILE/VAL, chi1, Xiao, NTER +ND3P3A CD31C CD31A CD33A 0.230 2 0.00 ! ILE/VAL, chi1, Xiao, NTER +ND3P3A CD31C CD31A CD33A 0.540 3 0.00 ! ILE/VAL, chi1, Xiao, NTER +ND3P3A CD31A CD31A HDA1A 0.000 1 0.00 ! NTER +ND3P3A CD31C CD31A HDA1A 0.000 1 0.00 ! NTER +OD31A CD31A CD31A CD2O1A 0.200 3 0.00 ! THR, c22, chi1, WHAT IS THIS? +OD31A CD31A CD31A HDA1C 0.075 3 0.00 ! THR/BUO2, NTER +CD2O1A CD31A CD31A HDA1A 0.200 3 0.00 ! NTER +CD2O2A CD31A CD31A CD33A 0.200 3 0.00 ! CTER +CD2O2A CD31A CD31A HDA1A 0.200 3 0.00 ! CTER +CD2O3A CD31A CD31A CD33A 0.200 3 0.00 ! CNEU +CD2O3A CD31A CD31A HDA1A 0.200 3 0.00 ! CNEU +CD31A CD31A CD31A HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD32A CD31A CD31A HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD33A CD31A CD31A HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD33A CD31A CD31A HDA1C 0.200 3 0.00 ! NTER +CD33A CD31A CD31C HDA1C 0.200 3 0.00 ! NTER +HDA1A CD31A CD31A HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD31A HDA1C 0.200 3 0.00 ! NTER +HDA1A CD31A CD31C HDA1C 0.200 3 0.00 ! NTER +OD31A CD31A CD31C HDA1A 0.075 3 0.00 ! THR/BUO2 +CD31A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER +OD31A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER - Thr, jing +CD31A CD32A CD31C CD2O2A 0.200 3 0.00 ! CTER, zhu +CD31A CD31A CD31C CD2O3A 0.200 3 0.00 ! CNEU +CD32A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER +CD32A CD31A CD31C CD2O3A 0.200 3 0.00 ! CNEU +CD32A CD31A CD31C HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +CD33A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER, VAL +CD33A CD31A CD31C CD2O3A 0.200 3 0.00 ! CNEU +CD33A CD31A CD31C HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +HDA1A CD31A CD31C ND2A2 0.200 3 0.00 ! ILE/VAL, alkanes +HDA1A CD31A CD31C CD2O1A 0.200 3 0.00 ! ILE/VAL, alkanes +HDA1A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER +HDA1A CD31A CD31C CD2O3A 0.200 3 0.00 ! CNEU +HDA1A CD31A CD31C HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +ND3P2A CD31A CD32A HDA2A 0.000 1 0.00 ! NTER +ND3P2A CD31C CD32A HDA2A 0.000 1 0.00 ! NTER +ND3P3A CD31A CD32A HDA2A 0.000 1 0.00 ! NTER +ND3P3A CD31C CD32A HDA2A 0.000 1 0.00 ! NTER +ND3P3A CD31C CD32B HDA2A 0.000 1 0.00 ! NTER, PEML by analogy for GLU +ND3P3A CD31C CD32C HDA2A 0.000 1 0.00 ! NTER, PEML by analogy for ASN +ND3P3A CD31C CD32A CD32C 0.200 3 0.00 ! NTER +ND3P3A CD31C CD32A CD2R5A 0.200 3 0.00 ! NTER, PEML by analogy for HSD +ND3P3A CD31C CD32A CD2R5C 0.200 3 0.00 ! NTER, PEML by analogy for TRP +ND3P3A CD31C CD32A CD2R5D 0.200 3 0.00 ! NTER, PEML by analogy for HSP +ND3P3A CD31C CD32A CD2R6A 0.200 3 0.00 ! NTER, PEML by analogy for PHE +ND3P3A CD31C CD31A CD32A 0.200 3 0.00 ! NTER, PEML by analogy for ILE +ND3P3A CD31C CD32A CD31A 0.200 3 0.00 ! NTER, PEML by analogy for LEU +ND3P3A CD31C CD32B CD32A 0.200 3 0.00 ! NTER, PEML by analogy for GLU +ND3P3A CD31C CD32B CD32C 0.200 3 0.00 ! NTER, alex by analogy for GLUP +ND3P3A CD31C CD32A CD2O2A 0.200 3 0.00 ! NTER - ASP, jing +OD31A CD31A CD32A CD33A 0.200 1 0.00 ! BUO2, 2-butanol +OD31A CD31A CD32A CD33A 0.410 2 0.00 ! BUO2, 2-butanol +OD31A CD31A CD32A CD33A 0.400 3 0.00 ! BUO2, 2-butanol +OD31A CD31A CD32A CD32A 0.200 1 0.00 ! PEO2, 2-pentanol, cmb - needs test +OD31A CD31A CD32A CD32A 0.410 2 0.00 ! PEO2, 2-pentanol, cmb - needs test +OD31A CD31A CD32A CD32A 0.400 3 0.00 ! PEO2, 2-pentanol, cmb - needs test +OD31A CD31A CD32A HDA2A 0.075 3 0.00 ! BUO2, 2-butanol +CD2O1A CD31A CD32A HDA2A 0.200 3 0.00 ! NTER +CD2O2A CD31A CD32A CD32C 0.200 3 0.00 ! CTER +CD2O2A CD31C CD32A CD32C 0.200 3 0.00 ! GLUP +CD2O3A CD31C CD32B CD32C 0.200 3 0.00 ! GLUP +CD2O2A CD31A CD32A HDA2A 0.200 3 0.00 ! CTER +CD2O3A CD31A CD32A CD32C 0.200 3 0.00 ! CNEU +CD2O3A CD31C CD32A CD32C 0.200 3 0.00 ! GLUP +CD2O3A CD31C CD32A CD2R5C 0.200 3 0.00 ! PEML by analogy TRP +CD2O3A CD31A CD32A HDA2A 0.200 3 0.00 ! CNEU +CD31A CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD31C CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +CD32A CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD33A CD31A CD31A CD33A 0.126 2 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD31A CD33A 0.084 3 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD31A CD33A 0.144 4 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD31A CD33A 0.200 5 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD32A 0.126 2 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD32A 0.084 3 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD32A 0.144 4 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD32A 0.200 5 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD33A 0.126 2 0.00 ! alkane, Igor 3/26/2005 +CD33A CD31A CD32A CD33A 0.084 3 0.00 ! alkane, Igor 3/26/2005 +CD33A CD31A CD32A CD33A 0.144 4 0.00 ! alkane, Igor 3/26/2005 +CD33A CD31A CD32A CD33A 0.200 5 0.00 ! alkane, Igor 3/26/2005 +CD33A CD30A CD32A CD33A 0.126 2 0.00 ! cmb, from alkane, Igor 3/26/2005 - needs test +CD33A CD30A CD32A CD33A 0.084 3 0.00 ! cmb, from alkane, Igor 3/26/2005 - needs test +CD33A CD30A CD32A CD33A 0.144 4 0.00 ! cmb, from alkane, Igor 3/26/2005 - needs test +CD33A CD30A CD32A CD33A 0.200 5 0.00 ! cmb, from alkane, Igor 3/26/2005 - needs test +CD33A CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD32A CD31A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD32A CD31C 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +HDA1A CD31A CD32A CD32A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD32A CD33A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1C CD31A CD32A CD32A 0.200 3 0.00 ! NTER +HDA1C CD31A CD32A CD32C 0.200 3 0.00 ! NTER +HDA1C CD31C CD32A CD32C 0.200 3 0.00 ! NTER +HDA1C CD31C CD32A CD2R5A 0.200 3 0.00 ! NTER, PEML by analogy HSD +HDA1C CD31C CD32A CD2R5C 0.200 3 0.00 ! NTER, PEML by analogy TRP +HDA1C CD31C CD32A CD2R5D 0.200 3 0.00 ! NTER, PEML by analogy HSP +HDA1C CD31C CD32A CD2R6A 0.200 3 0.00 ! NTER, PEML by analogy PHE +HDA1C CD31C CD32A CD2O2A 0.200 3 0.00 ! NTER - ASP, jing +HDA1C CD31A CD32A HDA2A 0.200 3 0.00 ! NTER +ND3P3A CD31A CD33A HDA3A 0.000 1 0.00 ! CNEU/NTER, NTER-CT3 %% +ND3P3A CD31C CD33A HDA3A 0.000 1 0.00 ! CNEU/NTER, NTER-CT3 %% +OD31A CD31A CD33A HDA3A 0.075 3 0.00 ! PRO2, 2-propanol +CD2O1A CD31A CD33A HDA3A 0.200 3 0.00 ! NTER, IBUT, isobutane, 3/92 +CD2O2A CD31A CD33A HDA3A 0.200 3 0.00 ! CTER, zwitterionic amino acid +CD2O3A CD31A CD33A HDA3A 0.200 3 0.00 ! CNEU +CD31A CD31A CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD31C CD31A CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +CD32A CD31A CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD33A CD31A CD33A HDA3A 0.150 3 0.00 ! IBUT, isobutane, 10/07, va +HDA1A CD31A CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD316A CD33A HDA3A 0.200 3 0.00 ! CHXM, from IBUT, 3/92, cmb 12/09 +HDA1C CD31A CD33A HDA3A 0.200 3 0.00 ! CNEU/NTER, IBUT, isobutane, 3/92 *DELETE* +HDA1C CD31C CD33A HDA3A 0.200 3 0.00 ! CNEU/NTER, IBUT, isobutane, 3/92 *DELETE* +ND2A2 CD31C CD32A SD30B 0.200 3 0.00 ! DISU, chi1, c22 +ND2A2 CD31C CD32A HDA2A 0.200 3 0.00 ! GLN, alkanes +ND2A2 CD31C CD32B HDA2A 0.200 3 0.00 ! GLU, from ND2A2 CD31C CD32A HDA2A +ND3A3 CD31C CD32A CD32A 0.800 1 0.00 ! PRO FIT PES PEML CHI1 +ND3A3 CD31C CD32A CD32A 2.800 2 0.00 ! PRO FIT PES PEML CHI1 +ND3A3 CD31C CD32A CD32A 1.100 3 0.00 ! PRO FIT PES PEML CHI1 +ND3A3 CD31C CD32A HDA2A 0.200 3 0.00 ! PRO +OD30C CD31C CD32A HDA2A 0.190 3 0.00 ! EAS/Lipid-H, charmm27 +CD2O1A CD31C CD32A SD30B 0.200 3 0.00 ! DISU, chi1, c22 +CD2O1A CD31C CD32A HDA2A 0.200 3 0.00 ! GLN, alkanes +CD2O1A CD31C CD32B HDA2A 0.200 3 0.00 ! GLU, from CD2O1A CD31C CD32A HDA2A +CD2O2A CD31C CD32A SD31B 0.200 3 0.00 ! CTER, terminal Cys +CD2O3A CD31C CD32A SD31B 0.200 3 0.00 ! PEML by analogy CYS, CNEU +CD2O2A CD31C CD32A CD2R5C 0.200 3 0.00 ! TRP/CTER, PEML +CD2O2A CD31C CD32A CD2R5D 0.200 3 0.00 ! CTER, PEML, HSE +CD2O2A CD31C CD32A CD2R5A 0.200 3 0.00 ! CTER, PEML, HSD +CD2O3A CD31C CD32A CD2R5A 0.200 3 0.00 ! CNEU, PEML, HSD +CD2O3A CD31C CD32A CD2R5D 0.200 3 0.00 ! CNEU, PEML, HSP +CD2O2A CD31C CD32A CD32A 0.200 3 0.00 ! CTER +CD2O3A CD31C CD32A CD31A 0.200 3 0.00 ! CNEU, PEML by analogy LEU +CD2O3A CD31C CD32A CD32A 0.200 3 0.00 ! CNEU, PEML by analogy with CD2O2A CD31C CD32A CD32A +CD2O3A CD31C CD32B CD32A 0.200 3 0.00 ! CNEU, PEML by analogy GLU +CD2O2A CD31C CD32B CD32A 0.200 3 0.00 ! CTER, Glu +CD2O2A CD31C CD32B CD32C 0.200 3 0.00 ! CTER, GLUP +CD2O2A CD31C CD32A HDA2A 0.200 3 0.00 ! CTER +CD2O2A CD31C CD32B HDA2A 0.200 3 0.00 ! CTER, Glu +CD2O3A CD31C CD32A HDA2A 0.200 3 0.00 ! CNEU +HDA1A CD31C CD32A OD31A 0.270 1 0.00 ! SER/PRO1, 1-propanol +HDA1A CD31C CD32A OD31A 0.050 2 0.00 ! SER/PRO1, 1-propanol +HDA1A CD31C CD32A OD31A 0.120 3 0.00 ! SER/PRO1, 1-propanol +HDA1A CD31C CD32A SD30B 0.190 3 0.00 ! DISU, c22 +HDA1A CD31C CD32A SD31B 0.120 3 0.00 ! CYS/PRSH +HDA1C CD31C CD32A SD31B 0.120 3 0.00 ! PEML by analogy CYS, CTER +HDA1A CD31C CD32A CD2O2A 0.200 3 0.00 ! ASP, c22 +HDA1A CD31C CD32A CD2R5A 0.190 3 0.00 ! HSD, alkanes +HDA1A CD31C CD32A CD2R5C 0.200 3 0.00 ! TRP, alkanes +HDA1A CD31C CD32A CD2R5D 0.190 3 0.00 ! HSP, alkanes +HDA1A CD31C CD32A CD2R6A 0.040 3 0.00 ! PHE, c22 +HDA1A CD31C CD32A CD31A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +HDA1A CD31C CD32A CD32A 0.190 3 0.00 ! LYS +HDA1A CD31C CD32B CD32A 0.190 3 0.00 ! GLU, from HDA1A CD31C CD32A CD32A +HDA1A CD31C CD32B CD32C 0.190 3 0.00 ! GLUP, from HDA1A CD31C CD32A CD32A +HDA1A CD31C CD32A CD32C 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +HDA1A CD31C CD32A HDA2A 0.200 3 0.00 ! GLN, IBUT, isobutane, 3/92 +HDA1A CD31C CD32B HDA2A 0.200 3 0.00 ! GLU, from HDA1A CD31C CD32A HDA2A +ND2A2 CD31C CD32C CD2O3A 0.200 3 0.00 ! ASPP, c22, chi1 +ND2A2 CD31C CD32C HDA2A 0.200 3 0.00 ! ASN, alkanes +CD2O1A CD31C CD32C CD2O3A 0.200 3 0.00 ! GLUP, c22, chi1 +CD2O1A CD32C CD31C CD2O3A 0.200 3 0.00 ! PEML by analogy ASN, CNEU +CD2O1A CD31C CD32C HDA2A 0.200 3 0.00 ! ASN, alkanes +CD2O2A CD31C CD32C CD2O1A 0.200 3 0.00 ! CTER, ASN +CD2O2A CD31C CD32A CD2O2A 0.200 3 0.00 ! PEML by analogy CTER, ASP +CD2O2A CD31C CD32A CD2R6A 0.200 3 0.00 ! PEML by analogy CTER, PHE +CD2O3A CD31C CD32A CD2O2A 0.200 3 0.00 ! PEML by analogy CNEU, ASP +CD2O2A CD31C CD32C HDA2A 0.200 3 0.00 ! CTER +HDA1A CD31C CD32C CD2O1A 0.200 3 0.00 ! ASN, alkanes +HDA1A CD31C CD32C CD2O3A 0.200 3 0.00 ! ASPP/GLUP, c22 +HDA2A CD32B CD31C CD2O3A 0.200 3 0.00 ! PEML by analogy GLU, CNEU +HDA2A CD32C CD31C CD2O3A 0.200 3 0.00 ! PEML by analogy ASN, CNEU +ND2A2 CD31C CD33A HDA3A 0.040 3 0.00 ! ALAD +OD30C CD31C CD33A HDA3A 0.160 3 0.00 ! EAS, charmm27 +CD2O1A CD31C CD33A HDA3A 0.870 3 0.00 ! ALAD +CD2O2A CD31C CD33A HDA3A 0.200 3 0.00 ! CTER +CD2O3A CD31C CD33A HDA3A 0.200 3 0.00 ! CNEU +HDA1A CD31C CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +CD325A CD325A CD325A CD325A 0.410 3 180.00 ! CPEN, cyclopentane, viv 10/4/05 +CD325A CD315A CD325A CD325A 0.410 3 180.00 ! CPNM, cmb +CD315A CD325A CD325A CD325A 0.410 3 180.00 ! CPNM, cmb +CD325A CD325A CD325A CD33A 0.160 3 0.00 ! CPEN, viv +CD325A CD325A CD315A CD33A 0.160 3 0.00 ! CPNM, cmb +CD325A CD325A CD315A OD31A 0.160 3 0.00 ! CPO1, cmb, needs test +CD325A CD325A CD325A HDA2R5 0.160 3 0.00 ! CPEN, viv +CD325A CD325A CD315A HDA1R5 0.160 3 0.00 ! CPNM, cmb +CD315A CD325A CD325A HDA2R5 0.160 3 0.00 ! CPNM, cmb +CD325A CD315A CD325A HDA2R5 0.160 3 0.00 ! CPNM, cmb +CD33A CD325A CD325A CD33A 0.160 3 0.00 ! CPEN, cyclopentane, viv +CD33A CD315A CD325A HDA2R5 0.160 3 0.00 ! CPNM, cmb +OD31A CD315A CD325A HDA2R5 0.160 3 0.00 ! CPO1, cmb +CD33A CD325A CD325A HDA2R5 0.160 3 0.00 ! CPEN, viv +HDA2R5 CD325A CD325A HDA2R5 0.160 3 0.00 ! CPEN, viv +HDA1R5 CD315A CD325A HDA2R5 0.160 3 0.00 ! CPNM, cmb +OD305A CD325B CD325B CD325B 0.000 3 0.00 ! THF, viv +OD305A CD325B CD325B HDA2R5 0.190 3 0.00 ! THF viv +CD315B CD325B CD325B CD325B 0.410 3 180.00 ! TF2M, cmb +CD315B CD325B CD325B HDA2R5 0.190 3 0.00 ! TF2M, cmb +CD325B CD325B CD325B CD325B 0.410 3 180.00 ! THF, viv +CD325B CD325B CD325B HDA2R5 0.190 3 0.00 ! THF, viv +HDA2R5 CD325B CD325B HDA2R5 0.190 3 0.00 ! THF, viv +CD316A CD326A CD326A CD326A 0.073 1 0.00 ! CHXM, from CD32A, 9/09, cmb +CD316A CD326A CD326A CD326A 0.043 2 0.00 ! CHXM, from CD32A, 9/09, cmb +CD316A CD326A CD326A CD326A 0.119 3 180.00 ! CHXM, from CD32A, 9/09, cmb +CD316A CD326A CD326A CD326A 0.098 4 0.00 ! CHXM, from CD32A, 9/09, cmb +CD316A CD326A CD326A CD326A 0.046 5 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.073 1 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.043 2 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.119 3 180.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.098 4 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.046 5 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.073 1 0.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.043 2 0.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.119 3 180.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.098 4 0.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.046 5 0.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.073 1 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.043 2 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.119 3 180.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.098 4 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.046 5 0.00 ! CHXM, from CD32A, 9/09, cmb +CD33A CD316A CD326A HDA2A 0.190 3 0.00 ! CHXM, from CD32A, 12/09, cmb +CD326A CD326A CD316A HDA1A 0.190 3 0.00 ! CHXM, from CD32A, 12/09, cmb +CD316A CD326A CD326A HDA2A 0.190 3 0.00 ! CHXM, from CD32A, 12/09, cmb +CD326A CD316A CD326A HDA2A 0.190 3 0.00 ! CHXM, from CD32A, 12/09, cmb +CD326A CD326A CD326A HDA2A 0.190 3 0.00 ! CHEX, from CD32A, 9/09, cmb +HDA1A CD316A CD326A HDA2A 0.190 3 0.00 ! CHXM, from CD32A, 9/09, cmb +HDA2A CD326A CD326A HDA2A 0.190 3 0.00 ! CHEX, from CD32A, 9/09, cmb +OD306A CD326B CD326B CD326B 0.19225 1 180.00 ! THP, sng 1/06 +OD306A CD326B CD326B CD326B 1.00000 2 180.00 ! THP, sng 1/06 +OD306A CD326B CD326B CD326B 0.59457 3 0.00 ! THP, sng 1/06 +OD306A CD326B CD326B CD326B 0.07862 4 180.00 ! THP, sng 1/06 +OD306A CD326B CD326B OD306A 0.19225 1 180.00 ! DIOX, from THP, sng 1/06, cmb - needs test +OD306A CD326B CD326B OD306A 1.00000 2 180.00 ! DIOX, from THP, sng 1/06, cmb - needs test +OD306A CD326B CD326B OD306A 0.59457 3 0.00 ! DIOX, from THP, sng 1/06, cmb - needs test +OD306A CD326B CD326B OD306A 0.07862 4 180.00 ! DIOX, from THP, sng 1/06, cmb - needs test +OD306A CD326B CD326B HDA2E 0.190 3 0.00 ! THP, viv +CD326B CD326B CD326B CD326B 0.498 2 0.00 ! THP, sng cyclohexane 2/06 +CD326B CD326B CD326B CD326B 0.59844 3 180.00 ! THP, sng cyclohexane 2/06 +CD326B CD326B CD326B CD326B 0.41746 4 0.00 ! THP, sng cyclohexane 2/06 +CD326B CD326B CD326B CD326B 0.24829 5 180.00 ! THP, sng cyclohexane 2/06 +CD326B CD326B CD326B CD33A 0.190 3 0.00 ! THP, viv +CD326B CD326B CD326B HDA2E 0.190 3 0.00 ! THP, viv +CD33A CD326B CD326B CD33A 0.190 3 0.00 ! THP, tetrahydropyran, viv +CD33A CD326B CD326B HDA2E 0.190 3 0.00 ! THP, viv +HDA2E CD326B CD326B HDA2E 0.190 3 0.00 ! THP, viv +OD306A CD326B CD33A HDA3A 0.160 3 0.00 ! Methyl-THP, viv +CD326B CD326B CD33A HDA3A 0.160 3 0.00 ! Methyl-THP, viv +HDA2E CD326B CD33A HDA3A 0.160 3 0.00 ! Methyl-THP, viv +ND2P1A CD32A CD32A CD32A 0.550 2 0.00 ! ARG, chi3 QM PES fit (PEML) +ND2P1A CD32A CD32A CD32A 0.310 3 0.00 ! ARG, chi3 QM PES fit (PEML) +ND2P1A CD32A CD32A CD32A 0.210 4 0.00 ! ARG, chi3 QM PES fit (PEML) +ND2P1A CD32A CD32A HDA2A 0.190 3 0.00 ! ARG, c22 +ND3A3 CD32A CD32A CD32A 2.100 1 0.00 ! PRO FIT PES PEML CHI3 +ND3A3 CD32A CD32A CD32A 0.800 2 0.00 ! PRO FIT PES PEML CHI3 +ND3A3 CD32A CD32A CD32A 0.600 3 0.00 ! PRO FIT PES PEML CHI3 +ND3A3 CD32A CD32A HDA2A 0.200 3 0.00 ! PRO +ND3P3A CD32A CD32A OD30B 1.000 1 180.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32A CD32A OD30B 0.500 2 0.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32A CD32A OD30B 0.500 3 0.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32A CD32A OD31A 1.000 1 180.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32A CD32A OD31A 0.500 2 0.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32A CD32A OD31A 0.500 3 0.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +!!!! fitting here +ND3P2A CD32A CD32A OD30B 2.750 1 0.00 ! Lipid-a5 (oct. 09 EH) +ND3P2A CD32A CD32A OD30B 0.750 2 0.00 ! Lipid-a5 (oct. 09 EH) +ND3P2A CD32A CD32A OD30B 0.000 3 0.00 ! Lipid-a5 (oct. 09 EH) +ND3P2A CD32A CD32A OD31A 2.750 1 0.00 ! CHOL, Lipid-a5 (oct. 09 EH) +ND3P2A CD32A CD32A OD31A 0.750 2 0.00 ! CHOL, Lipid-a5 (oct. 09 EH) +ND3P2A CD32A CD32A OD31A 0.000 3 0.00 ! CHOL, Lipid-a5 (oct. 09 EH) +!!!!!! +ND3P2A CD32A CD32A HDA2A 0.190 3 0.00 ! CHOL, charmm27, ammonium cation +ND3P3A CD32A CD32A HDA2A 0.190 3 0.00 ! ETAM, charmm27, ammonium cation +ND3P3A CD32A CD32A CD32A 0.200 3 0.00 ! LYS, chi4 +ND3P2A CD31C CD32A CD32A 0.200 3 0.00 ! LYS, chi4 +ND3P2A CD32A CD32A CD32A 0.200 3 0.00 ! LYS, chi4 +OD30A CD32A CD32A OD30A 0.3681 1 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 1.2036 2 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 0.1171 3 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 0.1612 4 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 0.0340 5 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 0.0225 6 0.00 ! DMOE, viv +OD30A CD32A CD32A CD32A 0.160 1 180.00 ! MPE, ATM +OD30A CD32A CD32A CD32A 0.390 2 0.00 ! MPE, ATM +OD30A CD32A CD32A CD33A 0.160 1 180.00 ! MPE, methylpropylether, 2/12/05, ATM +OD30A CD32A CD32A CD33A 0.390 2 0.00 ! MPE, ATM +OD30A CD32A CD32A HDA2A 0.190 3 0.00 ! DEET, diethylether alex +OD30B CD32A CD32A HDA2C 0.190 3 0.00 ! CHOL, charmm27, ammonium cation +OD31B CD32A CD32A CD32A 0.200 1 0.00 ! BUO1, 1-butanol +OD31B CD32A CD32A CD32A 0.410 2 0.00 ! BUO1, 1-butanol +OD31B CD32A CD32A CD32A 0.400 3 0.00 ! BUO1, 1-butanol +OD31B CD32A CD32A CD31A 0.200 1 0.00 ! B3MO1 from BUO1, cmb needs test +OD31B CD32A CD32A CD31A 0.410 2 0.00 ! B3MO1 from BUO1, cmb needs test +OD31B CD32A CD32A CD31A 0.400 3 0.00 ! B3MO1 from BUO1, cmb needs test +OD31B CD32A CD32A CD33A 0.200 1 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A CD33A 0.410 2 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A CD33A 0.400 3 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A HDA2A 0.270 1 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A HDA2A 0.050 2 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A HDA2A 0.120 3 0.00 ! PRO1, 1-propanol +SD30A CD32A CD32A HDA2A 0.139 3 0.00 ! MET/EMS +SD31B CD32A CD32A CD32A 0.580 1 0.00 ! BUSH +SD31B CD32A CD32A CD32A 0.450 2 0.00 ! BUSH +SD31B CD32A CD32A CD32A 0.200 3 0.00 ! BUSH +SD31B CD32A CD32A CD33A 0.580 1 0.00 ! PRSH +SD31B CD32A CD32A CD33A 0.450 2 0.00 ! PRSH +SD31B CD32A CD32A CD33A 0.200 3 0.00 ! PRSH +SD31B CD32A CD32A HDA2A 0.270 1 0.00 ! PRSH +SD31B CD32A CD32A HDA2A 0.050 2 0.00 ! PRSH +SD31B CD32A CD32A HDA2A 0.120 3 0.00 ! PRSH +CD2O2A CD32A CD32B HDA2A 0.200 3 0.00 ! GLU, c22 +CD30A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +CD31A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +CD32A CD32A CD31C ND3P3A 0.341 1 0.00 ! LYS, NTER, chi1, updated 05/13, jing +CD32A CD32A CD31C ND3P3A 0.622 2 0.00 ! LYS, NTER, chi1 +CD32A CD32A CD31C ND3P3A 1.577 3 0.00 ! LYS, NTER, chi1 +CD31C CD32A CD32A HDA2A 0.190 3 0.00 ! LYS +CD31C CD32B CD32A HDA2A 0.190 3 0.00 ! GLU, from CD31C CD32A CD32A HDA2A +CD31C CD32B CD32C HDA2A 0.190 3 0.00 ! GLUP, from CD31C CD32A CD32A HDA2A +CD32A CD32A CD32A CD32A 0.073 1 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD32A 0.043 2 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD32A 0.119 3 180.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD32A 0.098 4 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD32A 0.046 5 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD33A 0.093 1 0.00 ! PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD33A 0.143 2 0.00 ! PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD33A 0.055 4 0.00 ! PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD33A 0.102 5 0.00 ! PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD31A CD32A CD32A CD33A 0.093 1 0.00 ! from PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, +CD31A CD32A CD32A CD33A 0.143 2 0.00 ! from PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, +CD31A CD32A CD32A CD33A 0.055 4 0.00 ! from PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, +CD31A CD32A CD32A CD33A 0.102 5 0.00 ! from PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, +CD32A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +CD32A CD32A CD32A HDA2C 0.190 3 0.00 ! LYS +CD32E CD32A CD32A CD33A 0.093 1 0.00 ! ethers/DEET +CD32E CD32A CD32A CD33A 0.143 2 0.00 ! ethers/DEET +CD32E CD32A CD32A CD33A 0.055 4 0.00 ! ethers/DEET +CD32E CD32A CD32A CD33A 0.102 5 0.00 ! ethers/DEET +CD32E CD32A CD32A HDA2A 0.190 3 0.00 ! ethers/DEET +CD33A CD32A CD32A CD33A 0.150 1 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A CD33A 0.170 2 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A CD33A 0.114 3 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A CD33A 0.094 4 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A CD33A 0.070 5 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +HDA2A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +HDA2A CD32B CD32A HDA2A 0.190 3 0.00 ! GLU, from HDA2A CD32A CD32A HDA2A +HDA2A CD32A CD32A HDA2C 0.190 3 0.00 ! LYS +CD31A CD32A CD32C HDA2A 0.190 3 0.00 ! alkane, ester +CD31C CD32B CD32C CD2O3A 0.200 3 0.00 ! GLUP, c22, chi2 +CD31C CD32A CD32C HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell ADDED FOR ALAD +CD32A CD32A CD32C CD2O3A 0.350 1 0.00 ! MBU, EH 2007, ester +CD32A CD32A CD32C HDA2A 0.190 3 0.00 ! alkane, ester +CD33A CD32A CD32C CD2O3A 0.350 1 0.00 ! MBU, EH 2007, ester +CD33A CD32A CD32C HDA2A 0.190 3 0.00 ! alkane, ester +HDA2A CD32A CD32C CD2O1A 0.200 3 0.00 ! GLN, alkanes +HDA1C CD31C CD32C CD2O1A 0.200 3 0.00 ! PEML by analogy ASN, CTER +HDA2A CD32A CD32C CD2O3A 0.200 3 0.00 ! alkane, ester +HDA2A CD32B CD32C CD2O3A 0.200 3 0.00 ! GLUP, alkane, ester +HDA2A CD32A CD32C HDA2A 0.190 3 0.00 ! alkane, ester +HDA2A CD32B CD32C HDA2A 0.190 3 0.00 ! GLUP, alkane, ester +HDA1C CD31C CD32B HDA2A 0.190 3 0.00 ! PEML by analogy GLU, CTER +HDA1C CD31C CD32C HDA2A 0.190 3 0.00 ! PEML by analogy ASN, CTER +CD32A CD32A CD32E OD30A 0.160 1 180.00 ! MPE, ATM +CD32A CD32A CD32E OD30A 0.390 2 0.00 ! MPE, ATM +CD32A CD32A CD32E HDA2E 0.190 3 0.00 ! ethers/DEET +CD33A CD32A CD32E OD30A 0.160 1 180.00 ! MPE, methylpropylether, 2/12/05, ATM +CD33A CD32A CD32E OD30A 0.390 2 0.00 ! MPE, ATM +CD33A CD32A CD32E HDA2E 0.190 3 0.00 ! ethers/DEET +HDA2A CD32A CD32E OD30A 0.190 3 0.00 ! DEET, diethylether alex +HDA2A CD32A CD32E HDA2E 0.190 3 0.00 ! ethers/DEET +ND3P2A CD32A CD33A HDA3A 0.160 3 0.00 ! NC5, charmm27, ammonium cation +ND3P3A CD32A CD33A HDA3A 0.160 3 0.00 ! NH5, charmm27, ammonium cation +OD30A CD32A CD33A HDA3A 0.160 3 0.00 ! DEET, alex +OD31A CD32A CD32A HDA2C 0.175 3 0.00 ! ETAM, from ethanol +OD31A CD32A CD33A HDA3A 0.175 3 0.00 ! ETOH, ethanol +SD30A CD32A CD33A HDA3A 0.1388 3 0.00 ! EMS +SD31B CD32A CD33A HDA3A 0.175 3 0.00 ! ETSH +CD30A CD32A CD33A HDA3A 0.160 3 0.00 ! PROP, propane, 4/98, yin and mackerell +CD31A CD32A CD33A HDA3A 0.160 3 0.00 ! PROP, propane, 4/98, yin and mackerell +CD31C CD32A CD33A HDA3A 0.160 3 0.00 ! PROP, propane, 4/98, yin and mackerell ADDED FOR ALAD +CD32A CD32A CD33A HDA3A 0.140 3 0.00 ! BUTA, butane, 10/07, va +CD326A CD316A CD33A HDA3A 0.140 3 0.00 ! CHXM, from BUTA, butane, 10/07, va, cmb 12/09 +CD32C CD32A CD33A HDA3A 0.160 3 0.00 ! MBU, alkane, ester +CD32E CD32A CD33A HDA3A 0.140 3 0.00 ! ethers/DEET +CD33A CD32A CD33A HDA3A 0.185 3 0.00 ! PROP, propane, 10/07, va +HDA2A CD32A CD33A HDA3A 0.145 3 0.00 ! PROP, propane, butane, 10/07, va +HDA2C CD32A CD33A HDA3A 0.160 3 0.00 ! NC5, charmm27, ammonium cation +OD30C CD32C CD33A HDA3A 0.160 3 0.00 ! EAS, charmm27 +CD2O3A CD32C CD33A HDA3A 0.200 3 0.00 ! alkane, ester +HDA2A CD32C CD33A HDA3A 0.160 3 0.00 ! alkane, ester +OD30A CD32E CD32E OD30A 0.3681 1 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 1.2036 2 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 0.1171 3 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 0.1612 4 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 0.0340 5 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 0.0225 6 0.00 ! DMOE, viv +OD30A CD32E CD32E HDA2E 0.190 3 0.00 ! DEET, diethylether alex +HDA2E CD32E CD32E HDA2E 0.190 3 0.00 ! ethers/DEET +OD30A CD32E CD33A HDA3A 0.160 3 0.00 ! DEET, alex +HDA2E CD32E CD33A HDA3A 0.145 3 0.00 ! ethers/DEET +HDA3A CD33A CD33A HDA3A 0.144 3 0.00 ! ETHA, ethane, 10/07, va +!!! FOR TYR-NTER +HDA1C CD31A CD32A CD2R6A 0.040 3 0.00 ! PHE, c22 +CD2R6A CD32A CD31A CD2O2A 0.040 3 0.00 ! TO ALLOW NTER-TYR-CTER +!!! FOR PHE-CNEU +CD2R6A CD32A CD31C CD2O3A 0.040 3 0.00 ! PHE, c22, chi1 +! Protein chi1/2 fitting +! Variable cutoff based on QM and weighted for alphaR and EXT +! Shared terms were fitted simultaneously +! Manually adjust to reproduce chi1, chi2 distribution from pdb survey data, jing +! Group-fitted side-chain for lys/arg/met +CD2O1A CD31C CD32A CD32A 3.624 1 180.00 +CD2O1A CD31C CD32A CD32A 0.359 2 0.00 +CD2O1A CD31C CD32A CD32A 1.347 3 180.00 +CD32A CD32A CD31C ND2A2 0.341 1 0.00 +CD32A CD32A CD31C ND2A2 0.622 2 0.00 +CD32A CD32A CD31C ND2A2 1.577 3 0.00 +CD31C CD32A CD32A CD32A 0.494 1 180.00 +CD31C CD32A CD32A CD32A 0.740 2 180.00 +CD31C CD32A CD32A CD32A 0.319 3 180.00 +CD31C CD32A CD32A SD30A 0.179 1 180.00 +CD31C CD32A CD32A SD30A 0.034 2 180.00 +CD31C CD32A CD32A SD30A 0.288 3 180.00 +! Group-fitted side-chain for asn +CD31C CD32C CD2O1A ND2A1 1.206 1 0.00 +CD31C CD32C CD2O1A ND2A1 2.892 2 180.00 +CD31C CD32C CD2O1A ND2A1 0.102 3 180.00 +CD31C CD32C CD2O1A OD2C1A 2.320 1 0.00 +CD31C CD32C CD2O1A OD2C1A 1.288 2 0.00 +CD31C CD32C CD2O1A OD2C1A 0.494 3 180.00 +CD2O1A CD31C CD32C CD2O1A 2.996 1 180.00 +CD2O1A CD31C CD32C CD2O1A 0.168 2 0.00 +CD2O1A CD31C CD32C CD2O1A 0.186 3 180.00 +CD2O1A CD32C CD31C ND2A2 1.432 1 0.00 +CD2O1A CD32C CD31C ND2A2 1.356 2 180.00 +CD2O1A CD32C CD31C ND2A2 0.038 3 180.00 +! Group-fitted side-chain for asp +CD31C CD32A CD2O2A OD2C2A 1.386 1 180.00 +CD31C CD32A CD2O2A OD2C2A 0.968 2 180.00 +CD31C CD32A CD2O2A OD2C2A 0.870 3 0.00 +CD2O1A CD31C CD32A CD2O2A 4.200 1 180.00 +CD2O1A CD31C CD32A CD2O2A 0.376 2 0.00 +CD2O1A CD31C CD32A CD2O2A 1.002 3 180.00 +CD2O2A CD32A CD31C ND2A2 0.196 1 180.00 +CD2O2A CD32A CD31C ND2A2 0.948 2 180.00 +CD2O2A CD32A CD31C ND2A2 0.472 3 0.00 +! Fitted cys side-chain +CD31C CD32A SD31B HDP1A 0.318 1 180.00 +CD31C CD32A SD31B HDP1A 0.638 2 0.00 +CD31C CD32A SD31B HDP1A 0.422 3 0.00 +CD2O1A CD31C CD32A SD31B 0.182 1 0.00 +CD2O1A CD31C CD32A SD31B 0.284 2 180.00 +CD2O1A CD31C CD32A SD31B 1.424 3 180.00 +ND2A2 CD31C CD32A SD31B 0.562 1 180.00 +ND2A2 CD31C CD32A SD31B 0.192 2 180.00 +ND2A2 CD31C CD32A SD31B 1.696 3 0.00 +! Group-fitted side-chain for gln +CD2O1A CD32C CD32A CD31C 0.396 1 0.00 +CD2O1A CD32C CD32A CD31C 0.364 2 180.00 +CD2O1A CD32C CD32A CD31C 0.457 3 180.00 +CD2O1A CD31C CD32A CD32C 2.864 1 0.00 +CD2O1A CD31C CD32A CD32C 0.145 2 0.00 +CD2O1A CD31C CD32A CD32C 0.338 3 180.00 +CD32C CD32A CD31C ND2A2 3.174 1 180.00 +CD32C CD32A CD31C ND2A2 0.414 2 0.00 +CD32C CD32A CD31C ND2A2 0.545 3 0.00 +! Group-fitted side-chain for glu +CD2O2A CD32A CD32B CD31C 1.000 1 0.00 +CD2O2A CD32A CD32B CD31C 3.486 2 180.00 +CD2O2A CD32A CD32B CD31C 0.676 3 180.00 +CD2O1A CD31C CD32B CD32A 0.542 1 0.00 +CD2O1A CD31C CD32B CD32A 0.198 2 180.00 +CD2O1A CD31C CD32B CD32A 0.074 3 180.00 +CD2O1A CD31C CD32B CD32C 0.542 1 0.00 !Terminal patc +CD2O1A CD31C CD32B CD32C 0.198 2 180.00 +CD2O1A CD31C CD32B CD32C 0.074 3 180.00 +CD32A CD32B CD31C ND2A2 2.958 1 180.00 +CD32A CD32B CD31C ND2A2 0.804 2 0.00 +CD32A CD32B CD31C ND2A2 0.136 3 180.00 +CD32C CD32B CD31C ND2A2 2.958 1 180.00 ! GLUP +CD32C CD32B CD31C ND2A2 0.804 2 0.00 ! GLUP +CD32C CD32B CD31C ND2A2 0.136 3 180.00 ! GLUP +! Group-fitted side-chain for hsd/hse +CD2R5A CD2R5A CD32A CD31C 1.796 1 0.00 +CD2R5A CD2R5A CD32A CD31C 0.240 2 180.00 +CD2R5A CD2R5A CD32A CD31C 0.070 3 0.00 +CD31C CD32A CD2R5A ND2R5A 1.508 1 0.00 +CD31C CD32A CD2R5A ND2R5A 0.658 2 0.00 +CD31C CD32A CD2R5A ND2R5A 0.146 3 0.00 +CD31C CD32A CD2R5A ND2R5B 2.730 1 0.00 +CD31C CD32A CD2R5A ND2R5B 1.142 2 0.00 +CD31C CD32A CD2R5A ND2R5B 0.030 3 180.00 +CD2O1A CD31C CD32A CD2R5A 0.748 1 180.00 +CD2O1A CD31C CD32A CD2R5A 0.340 2 180.00 +CD2O1A CD31C CD32A CD2R5A 1.192 3 180.00 +CD2R5A CD32A CD31C ND2A2 1.464 1 180.00 +CD2R5A CD32A CD31C ND2A2 0.320 2 180.00 +CD2R5A CD32A CD31C ND2A2 1.134 3 0.00 +! Group-fitted side-chain for hsp +CD2R5D CD2R5D CD32A CD31C 1.236 1 180.00 +CD2R5D CD2R5D CD32A CD31C 0.350 2 180.00 +CD2R5D CD2R5D CD32A CD31C 0.158 3 0.00 +CD31C CD32A CD2R5D ND2R5C 2.938 1 180.00 +CD31C CD32A CD2R5D ND2R5C 0.284 2 0.00 +CD31C CD32A CD2R5D ND2R5C 0.260 3 0.00 +CD2O1A CD31C CD32A CD2R5D 1.096 1 180.00 +CD2O1A CD31C CD32A CD2R5D 0.296 2 0.00 +CD2O1A CD31C CD32A CD2R5D 1.128 3 180.00 +CD2R5D CD32A CD31C ND2A2 1.360 1 180.00 +CD2R5D CD32A CD31C ND2A2 0.354 2 180.00 +CD2R5D CD32A CD31C ND2A2 1.160 3 0.00 +! Group-fitted side-chain for ile/val +CD31C CD31A CD32A CD33A 0.372 1 0.00 +CD31C CD31A CD32A CD33A 1.028 2 180.00 +CD31C CD31A CD32A CD33A 0.042 3 0.00 +CD2O1A CD31C CD31A CD32A 0.488 1 180.00 +CD2O1A CD31C CD31A CD32A 0.124 2 180.00 +CD2O1A CD31C CD31A CD32A 0.010 3 180.00 +CD32A CD31A CD31C ND2A2 1.042 1 180.00 +CD32A CD31A CD31C ND2A2 1.660 2 0.00 +CD32A CD31A CD31C ND2A2 0.214 3 0.00 +! Fitted leu side-chain +CD31C CD32A CD31A CD33A 0.202 1 180.00 +CD31C CD32A CD31A CD33A 0.266 2 180.00 +CD31C CD32A CD31A CD33A 0.088 3 0.00 +CD2O1A CD31C CD32A CD31A 1.786 1 180.00 +CD2O1A CD31C CD32A CD31A 0.062 2 0.00 +CD2O1A CD31C CD32A CD31A 0.604 3 180.00 +CD31A CD32A CD31C ND2A2 0.116 1 180.00 +CD31A CD32A CD31C ND2A2 0.258 2 0.00 +CD31A CD32A CD31C ND2A2 0.516 3 0.00 +! Group-fitted side-chain for phe/tyr +CD2R6A CD2R6A CD32A CD31C 0.330 1 0.00 +CD2R6A CD2R6A CD32A CD31C 0.036 2 0.00 +CD2R6A CD2R6A CD32A CD31C 0.100 3 180.00 +CD2O1A CD31C CD32A CD2R6A 1.666 1 180.00 +CD2O1A CD31C CD32A CD2R6A 0.414 2 180.00 +CD2O1A CD31C CD32A CD2R6A 0.726 3 180.00 +CD2R6A CD32A CD31C ND2A2 1.924 1 180.00 +CD2R6A CD32A CD31C ND2A2 0.572 2 180.00 +CD2R6A CD32A CD31C ND2A2 0.652 3 0.00 +! Fitted ser side-chain +CD31C CD32A OD31A HDP1A 0.248 1 0.00 +CD31C CD32A OD31A HDP1A 0.554 2 0.00 +CD31C CD32A OD31A HDP1A 0.380 3 0.00 +CD2O1A CD31C CD32A OD31A 0.834 1 0.00 +CD2O1A CD31C CD32A OD31A 0.664 2 0.00 +CD2O1A CD31C CD32A OD31A 1.064 3 180.00 +ND2A2 CD31C CD32A OD31A 0.662 1 180.00 +ND2A2 CD31C CD32A OD31A 0.534 2 180.00 +ND2A2 CD31C CD32A OD31A 1.256 3 0.00 +! Group-fitted side-chain for thr/val +CD31C CD31A OD31A HDP1A 0.510 1 0.00 +CD31C CD31A OD31A HDP1A 0.210 2 0.00 +CD31C CD31A OD31A HDP1A 0.290 3 0.00 +CD2O1A CD31C CD31A OD31A 0.770 1 0.00 +CD2O1A CD31C CD31A OD31A 0.590 2 180.00 +CD2O1A CD31C CD31A OD31A 0.530 3 180.00 +ND2A2 CD31C CD31A OD31A 1.452 1 180.00 +ND2A2 CD31C CD31A OD31A 0.480 2 0.00 +ND2A2 CD31C CD31A OD31A 1.040 3 0.00 +! Fitted trp side-chain +CD2R5A CD2R5C CD32A CD31C 0.928 1 0.00 +CD2R5A CD2R5C CD32A CD31C 0.380 2 0.00 +CD2R5A CD2R5C CD32A CD31C 0.868 3 180.00 +CD2R6D CD2R5C CD32A CD31C 0.942 1 0.00 +CD2R6D CD2R5C CD32A CD31C 0.262 2 180.00 +CD2R6D CD2R5C CD32A CD31C 0.244 3 180.00 +CD2O1A CD31C CD32A CD2R5C 2.076 1 180.00 +CD2O1A CD31C CD32A CD2R5C 0.886 2 0.00 +CD2O1A CD31C CD32A CD2R5C 0.992 3 180.00 +CD2R5C CD32A CD31C ND2A2 1.976 1 180.00 +CD2R5C CD32A CD31C ND2A2 0.196 2 180.00 +CD2R5C CD32A CD31C ND2A2 0.978 3 0.00 +! Fitted val side-chain +CD2O1A CD31C CD31A CD33A 0.220 1 180.00 +CD2O1A CD31C CD31A CD33A 0.220 2 180.00 +CD2O1A CD31C CD31A CD33A 0.098 3 180.00 +CD33A CD31A CD31C ND2A2 0.170 1 0.00 +CD33A CD31A CD31C ND2A2 0.326 2 0.00 +CD33A CD31A CD31C ND2A2 0.432 3 0.00 + +CD2O1A CD32C CD31C ND3P3A 1.432 1 0.00 ! PEML by analogy ASN NTER +CD2O1A CD32C CD31C ND3P3A 1.356 2 180.00 ! PEML by analogy ASN NTER +CD2O1A CD32C CD31C ND3P3A 0.038 3 180.00 ! PEML by analogy ASN NTER +ND3P3A CD31C CD32A SD31B 0.562 1 180.00 ! PEML by analogy CYS NTER +ND3P3A CD31C CD32A SD31B 0.192 2 180.00 ! PEML by analogy CYS NTER +ND3P3A CD31C CD32A SD31B 1.696 3 0.00 ! PEML by analogy CYS NTER +CD2O2A CD31C CD32A OD31A 0.834 1 0.00 ! PEML by analogy SER +CD2O2A CD31C CD32A OD31A 0.664 2 0.00 ! PEML by analogy SER +CD2O2A CD31C CD32A OD31A 1.064 3 180.00 ! PEML by analogy SER +CD2O3A CD31C CD32A OD31A 0.834 1 0.00 ! PEML by analogy SER +CD2O3A CD31C CD32A OD31A 0.664 2 0.00 ! PEML by analogy SER +CD2O3A CD31C CD32A OD31A 1.064 3 180.00 ! PEML by analogy SER +CD2O3A CD31C CD31A OD31A 0.834 1 0.00 ! PEML by analogy THR +CD2O3A CD31C CD31A OD31A 0.664 2 0.00 ! PEML by analogy THR +CD2O3A CD31C CD31A OD31A 1.064 3 180.00 ! PEML by analogy THR +CD2O2A CD31C CD32A SD30B 0.834 1 0.00 ! alex by analogy CYS +CD2O2A CD31C CD32A SD30B 0.664 2 0.00 ! alex by analogy CYS +CD2O2A CD31C CD32A SD30B 1.064 3 180.00 ! alex by analogy CYS +! FROM ANALOGY ABOVE - PEML: VERIFY !!! +ND3A3 CD2O1A CD31C CD32B 0.200 3 0.00 ! PRO +HDA1C CD31C CD32A OD31A 0.270 1 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD32A OD31A 0.050 2 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD32A OD31A 0.120 3 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD31A OD31A 0.270 1 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD31A OD31A 0.050 2 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD31A OD31A 0.120 3 0.00 ! SER/PRO1, 1-propanol +ND3P3A CD31C CD32A OD31A 0.500 2 0.00 ! FROM ANALOGY ABOVE - PEML: VERIFY !!!!!!!!!!!!!!!!!!!!!!!!! +ND3P3A CD31C CD32A OD31A 0.500 3 0.00 ! Discovered when doing protein tests using Xiao's proteins +ND3P3A CD31C CD31A OD31A 0.500 2 0.00 ! PEML: Appeared on Crambin xtal simulations: THR-NTER +ND3P3A CD31C CD31A OD31A 0.500 3 0.00 ! PEML: Appeared on Crambin xtal simulations: THR-NTER +CD31A CD31C CD2O1A ND2A1 0.000 1 0.00 ! PRES CT2, guess +CD32A CD31C CD2O1A ND2A1 0.000 1 0.00 ! PRES CT2, guess +CD32B CD31C CD2O1A ND2A1 0.000 1 0.00 ! PRES CT2, guess +! CT1 +CD33D OD30C CD2O3A CD31C 2.500 2 180.00 ! CT1, MAS +CD33D OD30C CD2O3A CD32C 2.500 2 180.00 ! CT1, MAS +CD33D OD30C CD2O3A CD33C 2.500 2 180.00 ! CT1, MAS +CD33D OD30C CD2O3A OD2C3A 0.229 1 0.00 ! lipids +CD33D OD30C CD2O3A OD2C3A 3.567 2 180.00 ! lipids +CD33D OD30C CD2O3A OD2C3A 0.049 3 180.00 ! lipids +CD33D OD30C CD2O3A OD2C3A 0.040 6 180.00 ! lipids + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +OD2C3A CD32C OD30D CD2O3A 85.000 0 0.00 ! ACEH/CTP, PEML +CD2O1A CD32A ND2A2 OD2C1A 100.000 0 0.00 ! NMA/GLY +CD2O1A CD31C ND3A3 OD2C1A 0. 0 0. ! Pro +CD2O1A CD32C ND3A3 OD2C1A 0. 0 0. ! Pro +ND3A3 CD2O1A CD31C CD32A 0. 0 0. ! Pro +CD2O1A CD31C ND2A1 OD2C1A 120.000 0 0.00 ! NTER +CD2O1A CD31A ND2A2 OD2C1A 120.000 0 0.00 ! NTER +CD2O1A CD32A ND3A3 OD2C1A 120.000 0 0.00 ! NTER +CD2O1A CD33C ND3A3 OD2C1A 120.000 0 0.00 ! NTER +OD2C2A CD31A OD2C2A CD2O2A 71.000 0 0.00 ! CTER +OD2C2A CD32A OD2C2A CD2O2A 71.000 0 0.00 ! ASP/GLU +OD2C2A CD33A OD2C2A CD2O2A 71.000 0 0.00 ! ACET +OD2C2A CD31C OD2C2A CD2O2A 71.000 0 0.00 ! CTER +OD2C2A CD32C OD2C2A CD2O2A 71.000 0 0.00 ! CTER, Gly +OD2C3A CD31C OD30D CD2O3A 85.000 0 0.00 ! ACEH/CTP, PEML +OD2C3A CD31A OD30D CD2O3A 85.000 0 0.00 ! ACEH/CTP, PEML +CD2O1A CD32C ND2A1 OD2C1A 90.000 0 0.00 ! ACEM/ASN +CD2O1A CD31C ND2A2 OD2C1A 37.200 0 0.00 ! ALAD, alanine dipeptide % +CD2O1A CD32C ND2A2 OD2C1A 100.000 0 0.00 ! NMA/GLY +CD2O1A CD33C ND2A2 OD2C1A 89.400 0 0.00 ! NMA/GLY +OD2C1A ND2A1 CD33C CD2O1A 90.000 0 0.00 ! ACEM, acetamide +ND2A1 HDP1A HDP1A CD2O1A 4.000 0 0.00 ! ACEM, acetamide +OD2C1A ND2A3 CD33C CD2O1A 60.000 0 0.00 ! DMA, N,N-dimethylacetamide +ND2A2 CD2O1A CD31C HDP1A 30.700 0 0.00 ! ALAD, alanine dipeptide +ND2A2 CD2O1A CD32C HDP1A 40.000 0 0.00 ! GLYD +ND2A2 CD2O1A CD33C HDP1A 35.600 0 0.00 ! NMA +CD2O2A OD2C2A OD2C2A CD33A 71.000 0 0.00 ! acetate +CD2O2A OD2C2A OD2C2A CD32A 71.000 0 0.00 ! acetate +CD2O2A OD2C2A OD2C2A CD32C 71.000 0 0.00 ! acetate +CD2O2A OD2C2A OD2C2A CD31A 71.000 0 0.00 ! acetate, CTER +CD2O2A OD2C2A OD2C2A CD31C 71.000 0 0.00 ! acetate, CTER +ND2R5A CD2R5A CD2R5B HDP1A 0.450 0 0.00 ! IMID, imidazole +ND2R5A CD2R5B CD2R5A HDP1A 0.450 0 0.00 ! IMID, imidazole +CD2R5A CD2R5A ND2R5B HDR5A 0.500 0 0.00 ! IMID, imidazole +CD2R5A ND2R5B CD2R5A HDR5A 0.500 0 0.00 ! IMID, imidazole +CD2R5B ND2R5A ND2R5B HDR5B 0.500 0 0.00 ! IMID, imidazole +CD2R5B ND2R5B ND2R5A HDR5B 0.500 0 0.00 ! IMID, imidazole +CD2R5A CD2R5A ND2R5A HDR5A 0.500 0 0.00 ! IMID, imidazole +CD2R5A ND2R5A CD2R5A HDR5A 0.500 0 0.00 ! IMID, imidazole +ND2R5C CD2R5E CD2R5D HDP1A 0.450 0 0.00 ! IMIM, from IMID (EH) +CD2R5D CD2R5D ND2R5C HDR5D 0.500 0 0.00 ! IMIM, from IMID (EH) +CD2R5E ND2R5C ND2R5C HDR5E 0.500 0 0.00 ! IMIM, from IMID (EH) +CD2N1A ND2P1A ND2P1A ND2P1A 40.000 0 0.00 ! GUAN, c22 +HDR5A ND2R5A CD2R5C CD2R5A 0.450 0 0.00 ! Pyrrole +HDR5A CD2R5C ND2R5A CD2R5A 0.450 0 0.00 ! Pyrrole +HDP1A CD2R5A CD2R5A ND2R5A 0.450 0 0.00 ! Pyrrole +HDR5C CD2R5A CD2R5C CD2R5C 0.450 0 0.00 ! Pyrrole +HDR5C CD2R5C CD2R5A CD2R5C 0.450 0 0.00 ! Pyrrole +HDP1A CD2R5A CD2R6D ND2R5A 0.450 0 0.00 ! INDO, indole +HDP1A CD2R6D CD2R5A ND2R5A 0.450 0 0.00 ! INDO, indole +CD2R6A CD2R6A CD2R6D HDR6A 0.450 0 0.00 ! INDO, indole +HDR6A CD2R6A CD2R6D CD2R6A 0.450 0 0.00 ! INDO, indole +HDR5C CD2R6D CD2R5A CD2R5C 0.450 0 0.00 ! INDO, indole +HDR5C CD2R5A CD2R6D CD2R5C 0.450 0 0.00 ! INDO, indole +ND2R5A CD2R6F CD2R5B HDP1A 0.450 0 0.00 ! PUR0/1, purine +ND2R5A CD2R5B CD2R6F HDP1A 0.450 0 0.00 ! PUR0/1, purine +CD2R6F CD2R6F CD2R6B ND2R5A 20.000 0 0.00 ! PUR1, purine +CD2R6F CD2R6B CD2R6F ND2R5A 20.000 0 0.00 ! PUR1, purine +CD2R6F CD2R6F ND2R6B ND2R5B 10.000 0 0.00 ! PUR1, purine +CD2R6F ND2R6B CD2R6F ND2R5B 10.000 0 0.00 ! PUR1, purine +CD2R6F CD2R6F CD2R6B ND2R5B 20.000 0 0.00 ! PUR0, purine +CD2R6F CD2R6B CD2R6F ND2R5B 20.000 0 0.00 ! PUR0, purine +CD2R6F CD2R6F ND2R6B ND2R5A 10.000 0 0.00 ! PUR0, purine +CD2R6F ND2R6B CD2R6F ND2R5A 10.000 0 0.00 ! PUR0, purine +CD2O1A ND2R6B ND2R6B OD2C1B 80.000 0 0.00 ! CYT, cmb 04/10 +CD2O1A ND2R6C ND2R6C OD2C1B 80.000 0 0.00 ! CYT, cmb 04/10 +CD2O1A ND2R6C ND2R6B OD2C1B 80.000 0 0.00 ! CYT, cmb 04/10 +CD2R6B ND2R6B CD2R6A ND2B1 60.000 0 0.00 ! CYT, cmb 04/10 +!ND2B1 CD2R6B HDP1A HDP1A 6.000 0 0.00 ! CYT, cmb 04/10 +ND2R6B CD2R6H CD2O1A HDP1A 1.000 0 0.00 ! Cytosine, mod cmb +ND2R6C CD2R6H CD2O1A HDP1A 1.000 0 0.00 ! CYT, cmb 04/10 +ND2R6C CD2R6H CD2O1A CD33A 14.000 0 0.00 ! CYT, cmb 04/10 +CD2O1A ND2R6B ND2R6C OD2C1B 110.000 0 0.00 ! THY, cmb 04/10 +CD2O1A ND2R6C CD2R6A OD2C1B 90.000 0 0.00 ! THY, cmb 04/10 +CD2R6A CD2O1A CD2R6H CD33A 14.000 0 0.00 ! THY, cmb 04/10 +!ND2B1 CD2R6C HDP1A HDP1A 6.000 0 0.00 ! ADE, cmb 04/10 +!CD2R6C ND2R6B CD2R6F ND2B1 40.000 0 0.00 ! ADE, cmb 04/10 +CD2R6C ND2R6B ND2R6C ND2B1 40.000 0 0.00 ! GUA, cmb 04/10 +CD2O1A ND2R6C CD2R6F OD2C1B 90.000 0 0.00 ! GUA, cmb 04/10 +ND2B1 HDP1A CD2R6C HDP1A 6.000 0 0.00 ! GUA, cmb 04/10 +OD2C3A CD33A OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD32A OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD33C OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD33D OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD32C OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD31C OD30C CD2O3A 85.000 0 0.00 ! MAS, CT1 +CD2O3A OD30D CD33C OD2C3A 85.000 0 0.00 ! ACEH, PEML +CD2O3A OD30D CD33D OD2C3A 85.000 0 0.00 ! ACEH, PEML + +CMAP + +! CMAP pure dipeptide cmap +! alanine-based map, rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ level +! transfer to following 2 CMAP surfaces for +! residue adjacent to Pro and C-terminal CT2 patch + +!rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ +CD2O1A ND2A2 CD31C CD2O1A ND2A2 CD31C CD2O1A ND2A2 24 + +! insertion 1 +! alanine map, pure RIMP2 MP2-CBS dipeptide +! CD2O1A ND2A2 CD31C CD2O1A ND2A2 CD31C CD2O1A ND2A2 24 + +!-180 + -2.28 -1.63 -0.73 0.48 2.78 + 3.87 4.34 3.47 3.08 -0.19 + 0.42 -4.22 -8.18 -8.82 -7.96 + -5.97 -3.54 -1.63 -0.62 -0.24 + -2.15 -3.13 -3.02 -2.75 + +!-165 + -1.83 -1.36 -0.59 0.57 2.87 + 3.95 4.30 3.30 3.08 0.00 + -0.94 -5.51 -7.90 -8.21 -7.24 + -5.26 -2.99 -1.25 -0.29 0.15 + -1.62 -2.47 -2.32 -2.13 + +!-150 + -2.07 -1.67 -0.90 0.29 2.60 + 3.61 3.74 2.74 2.69 2.06 + -2.54 -6.39 -7.93 -8.08 -7.02 + -5.03 -2.86 -1.26 -0.38 0.09 + -1.63 -2.45 -2.34 -2.24 + +!-135 + -2.61 -2.10 -1.22 0.02 2.29 + 3.07 2.98 2.06 2.30 0.39 + -4.04 -7.04 -8.35 -8.36 -7.17 + -5.15 -3.10 -1.70 -1.86 -1.35 + -2.07 -2.94 -2.88 -2.81 + +!-120 + -2.96 -2.33 -1.41 -0.26 1.81 + 2.38 2.30 1.58 2.84 -0.93 + -4.92 -7.44 -8.56 -8.38 -7.03 + -5.06 -3.32 -3.14 -2.26 -1.68 + -2.40 -3.34 -3.33 -3.25 + +!-105 + -2.84 -2.27 -1.50 -0.52 1.43 + 2.01 2.08 1.63 2.27 -1.45 + -4.95 -7.17 -8.02 -7.54 -6.08 + -4.60 -4.32 -3.26 -2.23 -1.52 + -2.23 -3.20 -3.23 -3.15 + +!-90 + -2.48 -2.08 -1.48 -0.61 1.35 + 2.06 2.37 2.21 1.18 -2.35 + -5.43 -7.30 -7.73 -6.90 -5.94 + -5.07 -4.08 -3.02 -1.96 -1.09 + -1.71 -2.67 -2.71 -2.66 + +!-75 + -2.40 -2.20 -1.73 -0.84 1.26 + 2.18 2.77 2.69 0.18 -3.07 + -5.74 -7.10 -7.07 -6.70 -6.51 + -5.06 -4.22 -3.11 -1.96 -0.98 + -1.43 -2.32 -2.37 -2.41 + +!-60 + -3.05 -2.95 -2.38 -1.29 1.00 + 2.11 2.93 2.32 -0.14 -2.96 + -5.02 -5.94 -6.32 -6.85 -7.10 + -5.78 -4.80 -3.47 -2.21 -1.22 + -1.71 -2.65 -2.76 -2.91 + +!-45 + -4.06 -3.74 -2.81 -1.50 0.83 + 2.14 2.78 1.46 -0.78 -2.98 + -4.57 -5.77 -7.06 -8.05 -8.36 + -6.81 -5.38 -3.72 -2.35 -1.58 + -2.43 -3.63 -3.81 -3.95 + +!-30 + -4.71 -3.96 1.96 -0.46 0.68 + 1.58 1.56 0.46 -1.27 -3.02 + -4.82 -6.96 -8.77 -9.85 -9.86 + -7.62 -5.59 -3.56 -2.30 -2.09 + -3.46 -4.77 -4.84 -4.86 + +!-15 + -3.80 -2.59 -2.10 -1.15 -0.11 + 0.62 0.78 0.07 -1.38 -3.34 + -6.27 -8.99 -10.94 -11.69 -10.87 + -7.75 -5.17 -3.17 -2.82 -3.10 + -4.47 -4.55 -4.47 -4.32 + +!0 + -1.98 -1.95 -1.69 -1.02 -0.23 + 0.57 1.01 0.35 -1.35 -4.76 + -8.25 -10.95 -12.38 -12.00 -10.21 + -7.70 -5.53 -5.03 -4.78 -4.90 + -4.93 -4.86 -4.80 -4.51 + +!15 + -1.87 -1.78 -1.46 -0.82 0.15 + 1.35 1.89 0.81 -2.28 -5.94 + -9.06 -10.89 -11.14 -10.14 -8.29 + -6.43 -6.05 -5.54 -5.10 -4.87 + -4.80 -4.92 -3.50 -2.34 + +!30 + -1.99 -1.66 -1.16 -0.30 1.03 + 2.31 2.29 0.41 -2.60 -5.73 + -8.04 -9.04 -8.94 -8.03 -6.82 + -6.64 -6.26 -5.33 -4.42 -4.03 + -4.10 -3.73 -3.17 -2.48 + +!45 + -1.47 -0.97 -0.27 0.79 2.12 + 2.93 2.38 0.47 -2.15 -4.71 + -6.44 -7.21 -7.24 -6.87 -6.96 + -6.97 -5.99 -4.43 -3.26 -3.13 + -3.38 -3.21 -2.71 -2.07 + +!60 + -0.25 0.29 1.09 2.15 3.24 + 3.67 2.88 1.09 -1.20 -3.43 + -5.02 -5.96 -6.48 -7.10 -7.72 + -7.17 -5.47 -3.60 -2.55 -2.50 + -2.42 -2.06 -1.49 -0.83 + +!75 + 0.80 1.27 2.04 3.05 4.02 + 4.35 3.55 1.89 -0.22 -2.37 + -4.16 -5.59 -6.95 -8.28 -8.47 + -7.22 -5.06 -3.08 -2.03 -1.84 + -1.45 -0.94 -0.33 0.31 + +!90 + 1.19 1.56 2.24 3.16 4.09 + 4.55 3.85 2.29 0.25 -2.03 + -4.24 -6.36 -8.35 -9.35 -8.91 + -7.14 -4.65 -2.71 -2.11 -1.63 + -1.06 -0.48 0.13 0.75 + +!105 + 0.85 1.19 1.79 2.64 3.51 + 4.11 3.80 2.33 0.23 -2.34 + -5.16 -7.82 -9.64 -10.17 -9.27 + -6.93 -4.13 -2.99 -2.44 -1.78 + -1.18 -0.66 -0.14 0.40 + +!120 + -0.37 0.20 0.92 1.80 2.66 + 3.32 3.41 2.32 0.06 -3.09 + -6.49 -9.23 -10.81 -11.03 -9.68 + -5.28 -4.68 -3.78 -2.83 -2.05 + -1.57 -1.37 -1.23 -0.91 + +!135 + -1.88 -0.97 0.01 1.08 2.05 + 2.79 3.06 2.18 -0.27 -3.82 + -7.43 -10.18 -11.71 -6.87 -8.35 + -7.60 -5.99 -4.34 -3.02 -2.25 + -2.17 -2.47 -2.69 -2.53 + +!150 + -2.62 -1.65 -0.49 0.79 1.97 + 2.87 3.26 2.46 -0.06 -3.69 + -7.26 -9.94 -6.98 -10.30 -10.58 + -8.88 -6.48 -4.32 -2.93 -2.53 + -2.75 -3.16 -3.41 -3.25 + +!165 + -3.17 -2.34 -1.27 0.04 2.34 + 3.37 3.84 3.06 0.59 -2.91 + -6.27 -4.76 -8.94 -11.30 -10.73 + -8.74 -6.35 -4.48 -3.63 -3.61 + -3.72 -3.93 -3.99 -3.74 + + +! for C-terminal CT2 patch +!rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ +CD2O1A ND2A2 CD31C CD2O1A ND2A2 CD31C CD2O1A ND2A1 24 + +! insertion 2 +! alanine map, pure RIMP2 MP2-CBS dipeptide +! 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glycine map +! for GLY with amidated C-terminus (CT2G) +! rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ +CD2O1A ND2A2 CD32C CD2O1A ND2A2 CD32C CD2O1A ND2A1 24 + +!-180 + -3.21 -2.92 -2.05 -0.77 0.55 + 1.52 1.80 0.96 -1.13 -3.98 + -6.62 -8.29 -8.55 -5.43 -6.62 + -3.98 -1.13 0.97 1.80 1.52 + 0.55 -0.77 -2.05 -2.92 + +!-165 + -3.53 -3.47 -2.68 -1.34 0.14 + 1.30 1.68 0.82 -1.26 -3.99 + -6.43 -7.78 -6.37 -3.25 -6.93 + -4.19 -1.30 0.83 1.72 1.57 + 0.72 -0.54 -1.89 -2.97 + +!-150 + -4.34 -4.35 -3.48 -1.96 -0.29 + 0.95 1.18 0.19 -1.70 -4.11 + -6.13 -6.51 -4.46 -9.33 -7.42 + -4.60 -1.69 0.44 1.37 1.31 + 0.52 -0.78 -2.27 -3.57 + +!-135 + -5.18 -5.15 -4.15 -2.51 -0.86 + 0.16 0.22 -0.61 -2.20 -4.14 + -5.51 -10.04 -10.61 -9.83 -7.81 + -4.94 -2.06 -0.05 0.88 0.90 + 0.12 -1.25 -2.88 -4.33 + +!-120 + -5.65 -5.58 -4.60 -3.07 -1.60 + -0.68 -0.52 -1.14 -2.38 -3.88 + -8.55 -10.35 -10.74 -9.79 -7.63 + -4.79 -2.16 -0.37 0.59 0.67 + -0.11 -1.55 -3.27 -4.79 + +!-105 + -5.73 -5.75 -4.91 -3.54 -2.15 + -1.18 -0.87 -1.23 -2.18 -5.66 + -8.60 -10.12 -10.25 -9.03 -6.77 + -4.31 -2.14 -0.49 0.56 0.73 + -0.06 -1.53 -3.28 -4.83 + +!-90 + -5.82 -6.00 -5.33 -4.05 -2.63 + -1.52 -0.98 -1.04 -2.79 -5.90 + -8.38 -9.56 -9.29 -7.75 -5.88 + -4.01 -2.15 -0.54 0.52 0.76 + 0.01 -1.48 -3.25 -4.83 + +!-75 + -6.39 -6.76 -6.25 -4.98 -3.41 + -2.04 -1.14 -0.92 -3.22 -6.01 + -8.05 -8.72 -7.99 -6.86 -5.75 + -4.34 -2.67 -1.01 0.11 0.40 + -0.30 -1.80 -3.61 -5.26 + +!-60 + -7.51 -8.03 -7.49 -5.97 -4.14 + -2.56 -1.41 -1.71 -3.72 -6.05 + -7.50 -7.70 -7.38 -7.20 -6.64 + -5.42 -3.61 -1.72 -0.46 -0.20 + -1.02 -2.63 -4.50 -6.23 + +!-45 + -8.62 -8.95 -8.00 -6.17 -4.42 + -2.94 -1.96 -2.58 -4.28 -6.00 + -6.97 -7.46 -8.20 -8.57 -8.13 + -6.72 -4.48 -2.23 -0.84 -0.76 + -1.89 -3.73 -5.62 -7.34 + +!-30 + -9.06 -8.81 -7.33 -4.52 0.14 + -3.58 -2.91 -3.41 -4.68 -5.96 + -7.09 -8.71 -10.04 -10.50 -9.82 + -7.86 -5.05 -2.42 -1.09 -1.44 + -2.92 -4.74 -6.50 -8.09 + +!-15 + -8.59 -6.27 -1.91 -5.03 -4.72 + -3.75 -3.33 -3.71 -4.80 -6.22 + -8.64 -10.90 -12.29 -12.45 -11.12 + -8.41 -5.15 -2.57 -1.93 -2.55 + -3.90 -5.42 -6.99 -8.29 + +!0 + -4.39 -7.37 -7.10 -5.76 -4.47 + -3.46 -2.95 -3.43 -4.72 -7.64 + -10.64 -12.82 -13.69 -12.82 -10.64 + -7.64 -4.72 -3.43 -2.95 -3.46 + -4.47 -5.76 -7.11 -7.37 + +!15 + -8.59 -8.29 -6.99 -5.42 -3.90 + -2.55 -1.93 -2.57 -5.15 -8.41 + -11.12 -12.45 -12.29 -10.90 -8.64 + -6.22 -4.80 -3.71 -3.33 -3.75 + -4.72 -5.03 -1.91 -6.27 + +!30 + -9.06 -8.09 -6.50 -4.74 -2.92 + -1.44 -1.09 -2.42 -5.05 -7.86 + -9.82 -10.50 -10.04 -8.71 -7.09 + -5.96 -4.68 -3.41 -2.91 -3.58 + -0.02 -4.52 -7.33 -8.81 + +!45 + -8.62 -7.34 -5.62 -3.73 -1.89 + -0.76 -0.84 -2.23 -4.48 -6.72 + -8.13 -8.57 -8.20 -7.46 -6.97 + -6.00 -4.28 -2.58 -1.96 -2.94 + -4.42 -6.17 -8.00 -8.95 + +!60 + -7.51 -6.23 -4.50 -2.63 -1.02 + -0.20 -0.46 -1.72 -3.61 -5.42 + -6.64 -7.20 -7.38 -7.70 -7.50 + -6.05 -3.72 -1.71 -1.41 -2.56 + -4.14 -5.97 -7.49 -8.03 + +!75 + -6.39 -5.26 -3.61 -1.80 -0.30 + 0.40 0.11 -1.01 -2.67 -4.34 + -5.75 -6.86 -7.99 -8.72 -8.05 + -6.01 -3.22 -0.92 -1.14 -2.04 + -3.41 -4.98 -6.25 -6.76 + +!90 + -5.83 -4.83 -3.25 -1.48 0.01 + 0.76 0.52 -0.54 -2.15 -4.01 + -5.88 -7.75 -9.29 -9.56 -8.38 + -5.90 -2.79 -1.04 -0.98 -1.52 + -2.63 -4.05 -5.33 -6.00 + +!105 + -5.73 -4.83 -3.28 -1.53 -0.06 + 0.73 0.56 -0.49 -2.14 -4.31 + -6.77 -9.03 -10.25 -10.12 -8.60 + -5.66 -2.18 -1.23 -0.87 -1.18 + -2.15 -3.54 -4.91 -5.75 + +!120 + -5.65 -4.79 -3.27 -1.55 -0.11 + 0.67 0.59 -0.37 -2.16 -4.79 + -7.63 -9.79 -10.74 -10.35 -8.55 + -3.88 -2.38 -1.14 -0.52 -0.68 + -1.60 -3.07 -4.60 -5.58 + +!135 + -5.19 -4.33 -2.88 -1.25 0.12 + 0.90 0.88 -0.05 -2.06 -4.94 + -7.81 -9.83 -10.61 -10.04 -5.51 + -4.14 -2.20 -0.61 0.22 0.16 + -0.86 -2.51 -4.15 -5.15 + +!150 + -4.34 -3.57 -2.27 -0.78 0.52 + 1.31 1.37 0.44 -1.69 -4.60 + -7.42 -9.33 -4.46 -6.51 -6.13 + -4.11 -1.70 0.19 1.18 0.95 + -0.29 -1.96 -3.48 -4.35 + +!165 + -3.53 -2.97 -1.89 -0.54 0.72 + 1.57 1.72 0.83 -1.30 -4.19 + -6.93 -3.25 -6.37 -7.78 -6.43 + -3.99 -1.26 0.82 1.68 1.30 + 0.14 -1.34 -2.68 -3.47 + + +! glycine map +! for GLY adjacent to N-terminal PRO +! rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ +CD2O1A ND2A2 CD32C CD2O1A ND2A2 CD32C CD2O1A ND3A3 24 + +!-180 + -3.21 -2.92 -2.05 -0.77 0.55 + 1.52 1.80 0.96 -1.13 -3.98 + -6.62 -8.29 -8.55 -5.43 -6.62 + -3.98 -1.13 0.97 1.80 1.52 + 0.55 -0.77 -2.05 -2.92 + +!-165 + -3.53 -3.47 -2.68 -1.34 0.14 + 1.30 1.68 0.82 -1.26 -3.99 + -6.43 -7.78 -6.37 -3.25 -6.93 + -4.19 -1.30 0.83 1.72 1.57 + 0.72 -0.54 -1.89 -2.97 + +!-150 + -4.34 -4.35 -3.48 -1.96 -0.29 + 0.95 1.18 0.19 -1.70 -4.11 + -6.13 -6.51 -4.46 -9.33 -7.42 + -4.60 -1.69 0.44 1.37 1.31 + 0.52 -0.78 -2.27 -3.57 + +!-135 + -5.18 -5.15 -4.15 -2.51 -0.86 + 0.16 0.22 -0.61 -2.20 -4.14 + -5.51 -10.04 -10.61 -9.83 -7.81 + -4.94 -2.06 -0.05 0.88 0.90 + 0.12 -1.25 -2.88 -4.33 + +!-120 + -5.65 -5.58 -4.60 -3.07 -1.60 + -0.68 -0.52 -1.14 -2.38 -3.88 + -8.55 -10.35 -10.74 -9.79 -7.63 + -4.79 -2.16 -0.37 0.59 0.67 + -0.11 -1.55 -3.27 -4.79 + +!-105 + -5.73 -5.75 -4.91 -3.54 -2.15 + -1.18 -0.87 -1.23 -2.18 -5.66 + -8.60 -10.12 -10.25 -9.03 -6.77 + -4.31 -2.14 -0.49 0.56 0.73 + -0.06 -1.53 -3.28 -4.83 + +!-90 + -5.82 -6.00 -5.33 -4.05 -2.63 + -1.52 -0.98 -1.04 -2.79 -5.90 + -8.38 -9.56 -9.29 -7.75 -5.88 + -4.01 -2.15 -0.54 0.52 0.76 + 0.01 -1.48 -3.25 -4.83 + +!-75 + -6.39 -6.76 -6.25 -4.98 -3.41 + -2.04 -1.14 -0.92 -3.22 -6.01 + -8.05 -8.72 -7.99 -6.86 -5.75 + -4.34 -2.67 -1.01 0.11 0.40 + -0.30 -1.80 -3.61 -5.26 + +!-60 + -7.51 -8.03 -7.49 -5.97 -4.14 + -2.56 -1.41 -1.71 -3.72 -6.05 + -7.50 -7.70 -7.38 -7.20 -6.64 + -5.42 -3.61 -1.72 -0.46 -0.20 + -1.02 -2.63 -4.50 -6.23 + +!-45 + -8.62 -8.95 -8.00 -6.17 -4.42 + -2.94 -1.96 -2.58 -4.28 -6.00 + -6.97 -7.46 -8.20 -8.57 -8.13 + -6.72 -4.48 -2.23 -0.84 -0.76 + -1.89 -3.73 -5.62 -7.34 + +!-30 + -9.06 -8.81 -7.33 -4.52 0.14 + -3.58 -2.91 -3.41 -4.68 -5.96 + -7.09 -8.71 -10.04 -10.50 -9.82 + -7.86 -5.05 -2.42 -1.09 -1.44 + -2.92 -4.74 -6.50 -8.09 + +!-15 + -8.59 -6.27 -1.91 -5.03 -4.72 + -3.75 -3.33 -3.71 -4.80 -6.22 + -8.64 -10.90 -12.29 -12.45 -11.12 + -8.41 -5.15 -2.57 -1.93 -2.55 + -3.90 -5.42 -6.99 -8.29 + +!0 + -4.39 -7.37 -7.10 -5.76 -4.47 + -3.46 -2.95 -3.43 -4.72 -7.64 + -10.64 -12.82 -13.69 -12.82 -10.64 + -7.64 -4.72 -3.43 -2.95 -3.46 + -4.47 -5.76 -7.11 -7.37 + +!15 + -8.59 -8.29 -6.99 -5.42 -3.90 + -2.55 -1.93 -2.57 -5.15 -8.41 + -11.12 -12.45 -12.29 -10.90 -8.64 + -6.22 -4.80 -3.71 -3.33 -3.75 + -4.72 -5.03 -1.91 -6.27 + +!30 + -9.06 -8.09 -6.50 -4.74 -2.92 + -1.44 -1.09 -2.42 -5.05 -7.86 + -9.82 -10.50 -10.04 -8.71 -7.09 + -5.96 -4.68 -3.41 -2.91 -3.58 + -0.02 -4.52 -7.33 -8.81 + +!45 + -8.62 -7.34 -5.62 -3.73 -1.89 + -0.76 -0.84 -2.23 -4.48 -6.72 + -8.13 -8.57 -8.20 -7.46 -6.97 + -6.00 -4.28 -2.58 -1.96 -2.94 + -4.42 -6.17 -8.00 -8.95 + +!60 + -7.51 -6.23 -4.50 -2.63 -1.02 + -0.20 -0.46 -1.72 -3.61 -5.42 + -6.64 -7.20 -7.38 -7.70 -7.50 + -6.05 -3.72 -1.71 -1.41 -2.56 + -4.14 -5.97 -7.49 -8.03 + +!75 + -6.39 -5.26 -3.61 -1.80 -0.30 + 0.40 0.11 -1.01 -2.67 -4.34 + -5.75 -6.86 -7.99 -8.72 -8.05 + -6.01 -3.22 -0.92 -1.14 -2.04 + -3.41 -4.98 -6.25 -6.76 + +!90 + -5.83 -4.83 -3.25 -1.48 0.01 + 0.76 0.52 -0.54 -2.15 -4.01 + -5.88 -7.75 -9.29 -9.56 -8.38 + -5.90 -2.79 -1.04 -0.98 -1.52 + -2.63 -4.05 -5.33 -6.00 + +!105 + -5.73 -4.83 -3.28 -1.53 -0.06 + 0.73 0.56 -0.49 -2.14 -4.31 + -6.77 -9.03 -10.25 -10.12 -8.60 + -5.66 -2.18 -1.23 -0.87 -1.18 + -2.15 -3.54 -4.91 -5.75 + +!120 + -5.65 -4.79 -3.27 -1.55 -0.11 + 0.67 0.59 -0.37 -2.16 -4.79 + -7.63 -9.79 -10.74 -10.35 -8.55 + -3.88 -2.38 -1.14 -0.52 -0.68 + -1.60 -3.07 -4.60 -5.58 + +!135 + -5.19 -4.33 -2.88 -1.25 0.12 + 0.90 0.88 -0.05 -2.06 -4.94 + -7.81 -9.83 -10.61 -10.04 -5.51 + -4.14 -2.20 -0.61 0.22 0.16 + -0.86 -2.51 -4.15 -5.15 + +!150 + -4.34 -3.57 -2.27 -0.78 0.52 + 1.31 1.37 0.44 -1.69 -4.60 + -7.42 -9.33 -4.46 -6.51 -6.13 + -4.11 -1.70 0.19 1.18 0.95 + -0.29 -1.96 -3.48 -4.35 + +!165 + -3.53 -2.97 -1.89 -0.54 0.72 + 1.57 1.72 0.83 -1.30 -4.19 + -6.93 -3.25 -6.37 -7.78 -6.43 + -3.99 -1.26 0.82 1.68 1.30 + 0.14 -1.34 -2.68 -3.47 + +! 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Hydrogens +HDW 0.0 -0.0000 0.0000 ! SWM4-NDP water, GL, 2005, also for SWM6-NDP +HDA1A 0.0 -0.0200 1.3400 ! IBUT, isobutane, exp. dHvap/MV, VA, 10/07 +HDA2A 0.0 -0.0210 1.3400 ! PROP, propane, exp. dHvap/MV, VA, 10/07 +HDA2E 0.0 -0.0350 1.3400 ! THP, cmb 11/08 +HDA1R5 0.0 -0.0450 1.3400 ! TF2M, cmb. From JPCB 109, 18988. +HDA2R5 0.0 -0.0350 1.3000 ! CPEN, cyclopentane, MD sim., 8/06 viv +HDA3A 0.0 -0.0240 1.3400 ! ETHA, ethane, yin and mackerell, 4/98 +HDA3B 0.0 -0.0350 1.3400 ! special methyl H for MEOH, methanol +HDP1A 0.0 -0.0100 0.4000 ! -0.01 0.9 ! ethanol 1,4-term ! polar hydrogen, adm jr. and va +HDP1B 0.0 -0.0750 0.5500 ! GUAN and NC1, EH +HDA1C 0.0 -0.0460 0.9250 ! NC4, EH 2007 +HDA2C 0.0 -0.0460 0.9250 ! NC4, EH 2007 +HDA3C 0.0 -0.0460 0.9250 ! NC4, EH 2007 +HDR5A 0.0 -0.0550 1.2500 ! IMID, imidazole (HG, HD1 atoms), PYRR on C removed from N +HDR5B 0.0 -0.0870 1.1030 ! IMID, imidazole (HE2 polar H atom on C between two Ns) +HDR5C 0.0 -0.0360 1.1800 ! PYRR, pyrrole, on C adjacent to N +! +HDR5D 0.0 -0.0350 0.7000 ! TESTING FOR IMIM +HDR5E 0.0 -0.1000 0.5500 ! TESTING FOR IMIM +! +HDR6A 0.0 -0.0300 1.0500 ! BENZ, benzene (standard aromatic) +HDR6B 0.0 -0.0700 0.8000 ! PYR, pyridine (on carbon adjacent to N) +HDR6C 0.0 -0.0700 0.8000 ! PYRM, pyrimidine (on carbon between 2 Ns) + +!! Carbons +CD2O1A 0.0 -0.0500 1.7750 ! NMA, N-methylacetamide +CD2O2A 0.0 -0.2300 1.8000 ! anionic C=O carbon, ACET DMP +CD2O3A 0.0 -0.0920 1.6500 ! 0.0 -0.13 2.2 ! MAS, ACEH PEML +CD2O3B 0.0 -0.0300 1.7750 ! from CD2O3A for lipids +CD2N1A 0.0 -0.0750 1.9000 ! GUAN, EH +CD2R5A 0.0 -0.0950 2.0700 !intermediate to CD2R6A and CD2R5B, -0.132 2.074 ! IMID, imidazole, CG,CD2 +CD2R5B 0.0 -0.0930 1.9800 ! IMID, imidazole, CE1 +CD2R5C 0.0 -0.0500 2.0900 ! too big (balance with its H) PYRR, pyrrole +CD2R5D 0.0 -0.0500 1.8000 ! TESTING FOR IMIM +CD2R5E 0.0 -0.1000 1.8500 ! TESTING FOR IMIM +! +CD2R6A 0.0 -0.0690 2.0900 ! BENZ, benzene +CD2R6B 0.0 -0.0940 2.0000 ! PYR, pyridine (adjacent to N) +CD2R6C 0.0 -0.1120 2.0000 ! PYRM, pyrimidine (between 2 Ns) +CD2R6D 0.0 -0.0380 1.9000 ! INDO, indole: 5,6 membered ring bisector C +CD2R6F 0.0 -0.0380 1.9000 ! PUR0/1, purine: 5,6 membered ring bisector C +CD2R6H 0.0 -0.1400 1.8000 ! CYT/THY/URA, cmb 04/11 +! +CD30A 0.0 -0.0200 2.2000 0.0 -0.01 1.9 ! NEOP, neopentane, by analogy from CD31A, needs work +CD31A 0.0 -0.0220 2.2000 0.0 -0.01 1.9 ! IBUT, isobutane, dHvap/MV, VA, 10/07 +CD31FA 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! from, glycerol, furanoses, anomeric C1 +CD31FB 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! from, glycerol, furanoses, C2,C3 +CD31FC 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! from THF, furanoses, C4 +!!CD31AL 0.0 -0.0220 2.2000 0.0 -0.01 1.9 ! IBUT, isobutane, dHvap/MV, VA, 10/07, for lipids +CD32A 0.0 -0.0560 2.1000 0.0 -0.01 1.9 ! PROP, propane, VA, 10/07 +CD32AL 0.0 -0.0560 2.1000 0.0 -0.01 1.9 ! PROP, propane, VA, 10/07, for lipids +CD32B 0.0 -0.0560 2.1000 0.0 -0.01 1.9 ! for GLU, from CD32A +CD32E 0.0 -0.0540 2.0200 0.0 -0.01 1.9 ! DMET, ethers, cmb 11/08 +CD32F 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! ethylene glycol, xhe +CD31G 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! glycerol, xhe +CD31HA 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! from, glycerol, xhe, anomeric Carbon, dpatel +CD31HB 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! from, glycerol, xhe +CD31HC 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! from, THP, tetrahydropyran, viv, Hexopyranose, dpatel +CD315A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! CPNM, cmb, from JPCB 109, 18988 +CD325A 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, viv +CD326A 0.0 -0.0560 2.1000 0.0 -0.01 1.9 ! CHEX, from CD32A, 9/09, cmb +CD316A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! CHXM, cmb, from JPCB 109, 18988 +CD315B 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! TF2M, cmb, from JPCB 109, 18988 +CD325B 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! THF, tetrahydrofuran, from CPEN, viv +CD326B 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! THP, tetrahydropyran, viv +CD33A 0.0 -0.0780 2.0400 0.0 -0.01 1.9 ! ETHA, ethane, 4/98, yin, adm jr. +CD33B 0.0 -0.1100 2.0400 0.0 -0.01 1.9 ! special methyl C for MEOH, methanol +CD31C 0.0 -0.0320 1.8000 0.0 -0.01 1.9 ! NMA/MAS/ACEH PEML +CD32C 0.0 -0.0560 1.8100 0.0 -0.01 1.9 ! NMA/MAS/ACEH PEML +CD33C 0.0 -0.078 1.9400 ! special methyl C for amides +CD33D 0.0 -0.0780 1.9400 ! special methyl C for MAS, CT1, lipid conflict +CD33E 0.0 -0.1040 2.0000 0.0 -0.01 1.9 ! DMET, ethers, cmb 11/08 + +!! Nitrogens +ND2A1 0.0 -0.1600 1.8500 ! ACEM, acetamide +ND2A2 0.0 -0.2000 1.8300 ! NMA, N-methylacetamide +ND2A3 0.0 -0.2500 1.9600 ! DMA +ND2B1 0.0 -0.1600 1.8200 ! NA bases, cmb 04/10 +ND2R5A 0.0 -0.0870 1.8610 ! IMID, imidazole (N-H donor) +ND2R5B 0.0 -0.0690 1.9560 ! IMID, imidazole (N acceptor) +ND2R5C 0.0 -0.1050 1.8500 ! IMIM, imidazolium, EH +ND2R5D 0.0 -0.2300 1.9800 ! GUA/ADE 5-member ring, cmb 04/10 +ND2R5E 0.0 -0.0690 1.7360 ! NA bases, cmb 04/10 +ND2R5F 0.0 -0.2300 1.9800 ! N9 in GUA +ND2R6A 0.0 -0.0650 1.9800 ! PYR, pyridine (N acceptor) +ND2R6B 0.0 -0.1000 1.9000 ! PYRM, pyrimidine (N acceptor) +ND2R6C 0.0 -0.1250 1.7000 ! GUAB, guanine (N donor), cmb 04/10 +ND2R6D 0.0 -0.1050 1.8500 ! N1 in THY +ND2P1A 0.0 -0.0750 1.8000 ! GUAN, EH +ND3P2A 0.0 -0.2000 1.7400 ! protonated sp3 N, 0-2 hydrogens, NC4, EH 2007 +ND3P3A 0.0 -0.2000 1.7400 ! protonated sp3 N, 3-4 hydrogens, NH4, EH 2007 +ND3A3 0.0 -0.2000 1.8000 ! imino N + +!! Oxygens +ODW 0.0 -0.21094325 1.78692899 ! SWM4, SWM4-NDP water, GL, 2005 +ODW6 0.0 -0.1620 1.7950 ! SWM6-NDP water +OD2C1A 0.0 -0.2000 1.7800 ! NMA, N-methylacetamide (ACEM) +OD2C2A 0.0 -0.2000 1.9100 ! ACET, EH +OD2C1B 0.0 -0.2000 1.8500 ! Carbonyl O, NA bases, cmb 04/10 +OD2C2B 0.0 -0.1900 1.9700 ! DMP, cmb, 06/09, lipids +OD2C2C 0.0 -0.0700 1.8650 ! DMP, nucleic acids +OD2C3A 0.0 -0.1600 1.8800 ! ! 0.0 -0.18 1.35 ! MAS,ACEH EML +OD2C3B 0.0 -0.1800 1.7500 ! from OD2C3B for lipids ! MAS,ACEH EML JC-v2-24 +! +OD30A 0.0 -0.0600 1.7400 ! linear ethers 11/18/08 cmb +OD30B 0.0 -0.1700 1.7700 ! DMP, cmb, 06/09, lipids +OD30BN 0.0 -0.0200 1.7500 ! DMP, nucleic acids +OD30C 0.0 -0.1720 1.7000 ! Of the MAS/ACEH series OD30C and OD30D is the only different parameter.( +OD30CL 0.0 -0.1220 1.7500 ! from OD30CL for lipids *** Comment: of the MAS/ACEH series OD30C and OD30D is the only different parameter. JC-v2-25 +OD30D 0.0 -0.1720 1.7100 ! ACEH, PEML Jan2012 +OD305A 0.0 -0.0800 1.7200 ! THF, tetrahydrofuran, drude+lp,H2O int.+ cond phase 11/18/08 cmb +OD306A 0.0 -0.0800 1.7400 ! THP, tetrahydropyran, drude+lp,H2O int.+ cond phase 11/18/08 cmb +OD31A 0.0 -0.1500 1.7650 ! alcohols, va +OD31B 0.0 -0.1500 1.7400 ! alcohols, va, long chain primary alcohols +OD31C 0.0 -0.2500 1.5500 ! Phenol, p-Cresol +OD31E 0.0 -0.2000 1.7000 ! ethylene glycol, xhe +OD31F 0.0 -0.2000 1.7000 ! carbohydrates + +!! Sulfurs +SD31A 0.0 -0.4300 2.0500 ! MESH +SD31B 0.0 -0.4200 2.0200 ! ETSH, PRSH +SD30A 0.0 -0.3100 2.0500 ! EMS +SD30B 0.0 -0.3200 2.0000 ! DMDS + +!! Phosphorous +PD1A 0.0 -0.2700 1.9000 ! DMP, cmb 06/09, lipids +PD1AN 0.0 -0.3200 1.9000 ! DMP, nucleic acids + +!! Monovalent Ions +!Yu et al., JCTC, 6, 774-786, 2010 +LID 0.0 -0.03000 1.1000000 ! Li +SODD 0.0 -0.03151 1.4616800 ! Na +POTD 0.0 -0.1419265 1.6866521 ! K +RBD 0.0 -0.2730669 1.7855083 ! Rb +CSD 0.0 -0.2766036 2.0238218 ! Cs +FAD 0.0 -0.0026181 2.4622406 ! Flouride +CLAD 0.0 -0.0719737 2.4811139 ! Cloride +BRAD 0.0 -0.0823440 2.6262883 ! Bromide +IAD 0.0 -0.2084343 2.7579694 ! Iodide + +!! Divalent Ions. +! Require the use of Thole parameters that need to be transmitted to USERB and USERE. +! Yu et al. JCTC 6, 774-786, 2010 +ZND 0.0 -0.2500 0.9349678 ! Zn +MAGD 0.0 -0.0500 1.1264156 ! Mg +CALD 0.0 -0.2100 1.2708552 ! Ca +SRD 0.0 -0.3400 1.3059400 ! Sr +BAD 0.0 -0.6000 1.5717385 ! Ba + +D* 0.0 -0.0000 0.0000 ! Wildcard for Drudes and dummy atom + +!Do NOT put atom types with all zero values as the last LJ parameter due to a bug in CHARMM +LPD 0.0 -0.0000 0.0000 ! General Lone pair; no NBFIX terms +LPDW 0.0 -0.0000 0.0000 ! Lone pairs on water: Note overlap of SWM4 and SWM6 LPs +LPDO1 0.0 -0.0000 0.0000 ! Lone pairs on OD2C1A in NMA, peptide bond +LPDNA1 0.0 -0.0000 0.0000 ! General Nucleic Acid Lone pairs + +!! Rare gas parameters +XED 0.0 -0.02127 1.4800 ! HE, helium, experimental pot. energy surface, adm jr., 12/95 +NED 0.0 -0.08600 1.5300 ! NE, neon, semiempirical pot. energy surface, adm jr., 12/95 + +NBFIX +! In column 1 place the water or ion (positive before negative) atom type +! For non water/ion terms place in alphabetical order +ODW CD2O3A -0.11528 3.48690 ! MAS, PEML +ODW CD2O3B -0.03235 3.55798 ! for lipids, truncated +ODW CD2R6B -0.14080 3.85690 ! PYR, pyridine, PEML +ODW CD2R6C -0.15090 3.83690 ! PYRM, pyrimidine, PEML +ODW OD2C1A -0.20540 3.60690 ! NMA, PEML +ODW OD2C3A -0.22964 3.76690 ! MAS, PEML +ODW OD2C3B -0.27942 3.62321 ! for lipids, truncated +ODW OD30C -0.14000 3.58690 ! MAS, PEML +ODW OD30CL -0.16583 3.53691 ! MAS, PEML JC-v2-28, truncated +ODW OD305A -0.14990 3.54690 ! THF, 01/12 xhe +ODW OD306A -0.14990 3.58690 ! THP, 01/12 xhe +ODW ND2A2 -0.20540 3.63690 ! NMA, PEML +ODW ND2P1A -0.14156 3.51693 ! guanidinium LJ, PEML +ODW ND2R6B -0.14520 3.73690 ! PYR, pyridine, PEML +ODW ND2R6B -0.14520 3.73690 ! PYRM, pyrimidine, PEML +ODW SD30B -0.26981 3.78693 ! DMDS, Xiao +ODW SD30A -0.26572 3.82693 ! EMS, Xiao + +! Ions +LID CLAD -0.04647 3.80000 ! Savelyev-2015 +LID OD2C2C -0.04582 3.13500 ! nucleic acids, Savelyev-2015 +LID OD30BN -0.02449 3.02000 ! nucleic acids, Savelyev-2015 +LID ND2B1 -0.06928 3.60000 ! nucleic acids, Savelyev-2015 +LID ND2R6B -0.05477 3.60000 ! nucleic acids, Savelyev-2015 +LID ND2R6C -0.06123 3.60000 ! nucleic acids, Savelyev-2015 + +!SODD OD2C1A -0.09000 2.88000 ! protein backbone/amide, Hui-2015 +SODD LPDO1 -0.06000 2.77000 ! protein backbone/amide, Hui-2015 +SODD OD31A -0.06000 3.07000 ! ethanol, ser, thr, Hui-2015 +SODD CLAD -0.04762 4.09000 ! Savelyev-2014 +SODD OD2C2C -0.04696 3.49668 ! nucleic acids, Savelyev-2014 +SODD OD30BN -0.02510 3.38168 ! nucleic acids, Savelyev-2014 +SODD ND2B1 -0.07100 3.78000 ! nucleic acids, Savelyev-2014 +SODD ND2R6B -0.05600 3.79000 ! nucleic acids, Savelyev-2014 +SODD ND2R6C -0.06276 3.62000 ! nucleic acids, Savelyev-2014 + +POTD CLAD -0.10107 4.21000 ! Savelyev-2015 +POTD ND2B1 -0.15060 3.80000 ! nucleic acids, Savelyev-2015 +POTD ND2R6B -0.11913 3.80000 ! nucleic acids, Savelyev-2015 +POTD ND2R6C -0.13319 3.70000 ! nucleic acids, Savelyev-2015 +POTD OD2C1A -0.18000 3.21000 ! protein backbone/amide, Hui-2015 +POTD LPDO1 -0.07000 3.02000 ! protein backbone/amide, Hui-2015 +POTD OD31A -0.15000 3.34000 ! ethanol, ser, thr, Hui-2015 +POTD OD2C2A -0.07000 3.52000 ! glu, asp, Hui-2015 + +RBD CLAD -0.14019 4.27000 ! Savelyev-2015 +RBD ND2B1 -0.20902 3.80000 ! nucleic acids, Savelyev-2015 +RBD ND2R6B -0.16524 3.82000 ! nucleic acids, Savelyev-2015 +RBD ND2R6C -0.18475 3.70000 ! nucleic acids, Savelyev-2015 + +!for chloride +CALD OD2C1A -0.22000 2.85000 ! protein backbone/amide, Hui-2015 +CALD LPDO1 -0.37000 2.50000 ! protein backbone/amide, Hui-2015 +CALD OD31A -0.10000 3.28000 ! ethanol, ser, thr, Hui-2015 +CALD OD2C2A -0.11000 3.51500 ! glu, asp, Hui-2015 +CLAD ND2A2 -0.08000 4.65000 ! protein/backbone, Hui-2015 +CLAD HDP1A -0.00100 3.54000 ! protein/backbone, Hui-2015 +CLAD OD31A -0.10390 4.05000 ! ethanol, ser, thr, Hui-2015 +!for chloride, nucleic acids +CLAD ND2B1 -0.07000 4.31000 +CLAD ND2R5E -0.07000 4.31000 +CLAD ND2R5F -0.07000 4.31000 +CLAD ND2R5D -0.07000 4.31000 +CLAD ND2R6C -0.07000 4.31000 +CLAD ND2R6B -0.07000 4.31000 +CLAD ND2R6D -0.07000 4.31000 + +!lone pair - acceptor +LPDNA1 LID -0.09000 2.60000 ! nucleic acid bases +LPDNA1 SODD -0.09000 2.92000 ! nucleic acid bases +LPDNA1 POTD -0.09000 3.37000 ! nucleic acid bases +LPDNA1 RBD -0.09000 3.57000 ! nucleic acid bases + +!Parameters for screening term required for divalent ions +THOLE TCUT 5.0 MAXNBTHOLE 5000 +!command for NAMD is "drudeNbtholeCut 5" +ODW BAD 1.45869 +ODW CALD 1.50877 +ODW MAGD 1.51567 +ODW SRD 1.23792 +ODW ZND 2.14773 +! ions with OD2C1A , NMA protein backbone (from ion-NMA interaction) +CALD OD2C1A 1.32000 ! protein backbone/amide, Hui-2015 +CALD OD31A 1.05000 ! ethanol, ser, thr, Hui-2015 +CLAD ND2A2 2.86000 ! protein backbone/amide, Hui-2015 +!SODD OD2C1A 1.04000 ! protein backbone/amide, Hui-2015, in progress +SODD OD31A 1.82000 ! ethanol, ser, thr, Hui-2015 +POTD OD2C1A 2.19000 ! protein backbone/amide, Hui-2015 +POTD OD2C2A 0.22000 ! protein, glu, asp, Hui-2015 +! nucleic acids +CD32C OD2C2C 1.45000 !-1.642 -0.931 !phosphate anionic O to C5' special 1,4 term + +END + diff --git a/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_model_2013c.str b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_model_2013c.str new file mode 100644 index 00000000..fb5d8ecf --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_model_2013c.str @@ -0,0 +1,4563 @@ +* $Id: toppar_drude_model.str 29 2015-07-29 23:57:18Z alex $ +* DRUDE topology and parameter stream file +* Small molecule model compounds +* October 2013 +* + +!requires toppar_drude_master*.str + +!model compounds + +!references +!Alkanes +!Igor V. Vorobyov, Victor M. Anisimov and Alexander D. MacKerell, +!Jr. "Polarizable Empirical Force Field for Alkanes Based on the +!Classical Drude Oscillator Model," Journal of Physical Chemistry B, +!109: 18988-18999, 2005. +! +!Anisotropic polarizability model +!Harder, E., Anisimov, V.M., Vorobyov, I.V., Lopes, P.E., Noskov, S., +!MacKerell, A.D., Jr. and Roux, B. Atomic Level Anisotropy in the +!Electrostatic Modeling of Lone Pairs for a Polarizable Force Field +!based on the Classical Drude Oscillator, Journal of Chemical Theory +!and Computation, 2: 1587-1597, 2006 +! +!Ethers +! +!Vorobyov, I.V., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., +!Pastor, R.W. and MacKerell, A.D., Jr., Additive and Classical Drude +!Polarizable Force Fields for Linear and Cyclic Ethers, Journal of +!Chemical Theory and Computation, 3: 1120-1133, 2007. +! +!Baker, C. and MacKerell, Jr. A.D., “Polarizability Rescaling and +!atom-based Thole Scaling in the CHARMM Drude Polarizable Force Field +!for Ethers” Journal of Molecular Modeling, 16: 567-576, 2010, +!PMC2818097 + +!Sulfur containing compounds +!Zhu, X. and MacKerell, A.D., Jr. “Polarizable Empirical Force Field +!for Sulfur-Containing Compounds Based on the Classical Drude +!Oscillator Model,” Journal of Computational Chemistry, 12: 2330-2341, +!2010. PMC2923574 +! +!Alcohols +!Anisimov, V.M., Vorobyov, I.V., Roux, B., and MacKerell, A.D., Jr. +!Polarizable empirical force field for the primary and secondary +!alcohol series based on the classical Drude model. Journal of Chemical +!Theory and Computation, 3, 1927-1946, 2007. + +!Amides +!Harder, E., Anisimov, V.M., Whitfield, T., MacKerell, A.D., Jr., Roux, +!B. "Understanding the Dielectric Properties of Liquid Amides from a +!Polarizable Force Field," Journal of Physical Chemistry, +!112:3509-3521. 2008, PMID: 18302362 +! +!Final amide model used on 2013 protein FF +!Lin, B., Lopes, P.E.M., Roux, B., and MacKerell, A.D., Jr., +!“Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide +!Solutions Modeled by the CHARMM Additive and Drude Polarizable Force +!Fields,” Journal of Chemical Physics, 139: 084509, 2013, PMC3772949 +! +!Aromatics +!Lopes, P., Lamoureux, G., Roux, B., MacKerell, A.D., Jr., "Polarizable +!Empirical Force Field for Aromatic Compounds Based on the Classical +!Drude Oscillator," Journal of Physical Chemistry, B. 111:2873-2885, +!2007 +! +!Heterocycles +!Lopes, P.E.M., Lamoureux, G., MacKerell, A.D., Jr., “Polarizable +!Empirical Force Field for Nitrogen-containing Heteroaromatic Compounds +!Based on the Classical Drude Oscillator” Journal of Computational +!Chemistry, 30: 1821-1838, 2009, PMC251901 +! +!Nucleic Acid Bases +!Baker, C.M., Anisimov, V.M., and MacKerell, A.D., Jr., “Development of +!CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the +!Classical Drude Oscillator Model,” Journal of Physical Chemistry, +!B. 115; 580–596, 2011, PMC3166616 + +read rtf card append +* Topology for drude model compounds +* +38 + +DEFA FIRS NONE LAST NONE +AUTOGENERATE ANGLES DIHEDRALS DRUDE + +!!alkanes + +Resi ETHA 0.000 ! ethane +! +! H1 H4 +! \ / +! H2-C1--C2-H5 +! / \ +! H3 H6 +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H21 HDA3A 0.059 +ATOM H22 HDA3A 0.059 +ATOM H23 HDA3A 0.059 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 h21 c2 h22 c2 h23 +! IC for ETHA staggered conformer MP2/6-31G* optimized +IC H11 C1 C2 H21 1.0932 111.18 180.00 111.18 1.0932 +IC H11 C1 C2 H22 1.0932 111.18 -60.00 111.18 1.0932 +IC H11 C1 C2 H23 1.0932 111.18 60.00 111.18 1.0932 +IC H12 C1 C2 H23 1.0932 111.18 180.00 111.18 1.0932 +IC H13 C1 C2 H23 1.0932 111.18 -60.00 111.18 1.0932 +IC C1 C2 H21 BLNK 1.5261 111.18 0.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI PROP1 0.000 ! propane, renamed from PROP +! +! H11 H21 H31 +! \ | / +! H12-C1--C2--C3-H32 +! / | \ +! H13 H22 H33 +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H21 HDA2A 0.078 +ATOM H22 HDA2A 0.078 +GROUP +ATOM C3 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H31 HDA3A 0.059 +ATOM H32 HDA3A 0.059 +ATOM H33 HDA3A 0.059 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 h21 c2 h22 +bond c2 c3 c3 h31 c3 h32 c3 h33 +! IC for PROP staggered conformer MP2/6-31G* optimized +IC C1 C2 C3 H31 1.5260 112.39 59.77 110.82 1.0946 +IC C1 C2 C3 H32 1.5260 112.39 180.00 111.49 1.0938 +IC C1 C2 C3 H33 1.5260 112.39 -59.77 110.82 1.0946 +IC H11 C1 C2 C3 1.0946 110.82 -59.77 112.39 1.5260 +IC H11 C1 C2 H21 1.0946 110.82 62.14 109.48 1.0960 +IC H11 C1 C2 H22 1.0946 110.82 178.32 109.48 1.0960 +IC C3 C2 C1 H12 1.5260 112.39 59.77 110.82 1.0946 +IC C3 C2 C1 H13 1.5260 112.39 180.00 111.49 1.0938 +PATCH FIRST NONE LAST NONE + +Resi BUTA 0.000 ! butane +! +! H11 H21 H31 H41 +! \ | | / +! H12-C1--C2--C3--C4-H42 +! / | | \ +! H13 H22 H33 H43 +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM H21 HDA2A 0.078 +ATOM H22 HDA2A 0.078 +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +GROUP +ATOM H31 HDA2A 0.078 +ATOM H32 HDA2A 0.078 +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +GROUP +ATOM C4 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H41 HDA3A 0.059 +ATOM H42 HDA3A 0.059 +ATOM H43 HDA3A 0.059 +Bond h11 c1 h12 c1 h13 c1 c1 c2 +Bond h21 c2 h22 c2 c2 c3 +Bond h31 c3 h32 c3 c3 c4 +Bond h41 c4 h42 c4 h43 c4 +! IC for BUTA trans conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5263 112.90 180.00 112.90 1.5263 +IC C1 C2 C3 H31 1.5263 112.90 57.85 109.11 1.0973 +IC C1 C2 C3 H32 1.5263 112.90 -57.85 109.11 1.0973 +IC C2 C3 C4 H41 1.5268 112.90 -59.80 110.84 1.0944 +IC C2 C3 C4 H42 1.5268 112.90 59.80 110.84 1.0944 +IC C2 C3 C4 H43 1.5268 112.90 180.00 111.48 1.0940 +IC H11 C1 C2 C3 1.0944 110.84 59.80 112.90 1.5268 +IC H11 C1 C2 H21 1.0944 110.84 -178.34 109.62 1.0973 +IC H11 C1 C2 H22 1.0944 110.84 -62.06 109.62 1.0973 +IC H12 C1 C2 C3 1.0940 111.48 -180.00 112.90 1.5268 +IC H13 C1 C2 C3 1.0944 110.84 -59.80 112.90 1.5268 +IC H21 C2 C3 C4 1.0973 109.11 57.85 112.90 1.5263 +IC H22 C2 C3 C4 1.0973 109.11 -57.85 112.90 1.5263 +IC H31 C3 C4 H43 1.0973 109.62 -58.14 111.48 1.0940 +IC H32 C3 C4 H43 1.0973 109.62 58.14 111.48 1.0940 +PATCH FIRST NONE LAST NONE + +Resi PENT 0.000 ! pentane +! +! H11 H21 H31 H41 H51 +! \ | | | / +! H12-C1--C2--C3--C4--C5-H52 +! / | | | \ +! H13 H22 H33 H42 H53 +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H21 HDA2A 0.078 +ATOM H22 HDA2A 0.078 +GROUP +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H31 HDA2A 0.078 +ATOM H32 HDA2A 0.078 +GROUP +ATOM C4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H41 HDA2A 0.078 +ATOM H42 HDA2A 0.078 +GROUP +ATOM C5 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H51 HDA3A 0.059 +ATOM H52 HDA3A 0.059 +ATOM H53 HDA3A 0.059 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C5 H53 +! IC for PENT tt conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5264 112.83 180.00 113.35 1.5266 +IC C2 C3 C4 C5 1.5266 113.35 180.00 112.83 1.5264 +IC C3 C4 C5 H51 1.5266 112.83 180.00 111.50 1.0940 +IC H11 C1 C2 C3 1.0940 111.50 180.00 112.83 1.5266 +IC H11 C2 *C1 H12 1.0940 111.50 120.20 110.82 1.0945 +IC H11 C2 *C1 H13 1.0940 111.50 -120.20 110.82 1.0945 +IC C1 C3 *C2 H21 1.5264 112.83 122.12 109.12 1.0973 +IC C1 C3 *C2 H22 1.5264 112.83 -122.12 109.12 1.0973 +IC C2 C4 *C3 H31 1.5266 113.35 122.09 109.25 1.0986 +IC C2 C4 *C3 H32 1.5266 113.35 -122.09 109.25 1.0986 +IC C3 C5 *C4 H41 1.5266 112.83 121.83 109.63 1.0973 +IC C3 C5 *C4 H42 1.5266 112.83 -121.83 109.63 1.0973 +IC C4 H51 *C5 H52 1.5264 111.50 121.91 107.89 1.0945 +IC C4 H51 *C5 H53 1.5264 111.50 -121.91 107.89 1.0945 +patc firs none last none + +Resi HEXA 0.000 ! hexane +! +! H11 H21 H31 H41 H51 H61 +! \ | | | | / +! H12-C1--C2--C3--C4--C5--C6-H62 +! / | | | | \ +! H13 H22 H33 H42 H52 H63 +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H21 HDA2A 0.078 +ATOM H22 HDA2A 0.078 +GROUP +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H31 HDA2A 0.078 +ATOM H32 HDA2A 0.078 +GROUP +ATOM C4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H41 HDA2A 0.078 +ATOM H42 HDA2A 0.078 +GROUP +ATOM C5 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H51 HDA2A 0.078 +ATOM H52 HDA2A 0.078 +GROUP +ATOM C6 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H61 HDA3A 0.059 +ATOM H62 HDA3A 0.059 +ATOM H63 HDA3A 0.059 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C6 H61 C6 H62 C6 H63 +! IC for HEXA ttt conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5263 112.85 180.00 113.27 1.5274 +IC C2 C3 C4 C5 1.5267 113.27 180.00 113.27 1.5267 +IC C3 C4 C5 C6 1.5274 113.27 180.00 112.85 1.5263 +IC C4 C5 C6 H61 1.5267 112.85 180.00 111.48 1.0941 +IC H11 C1 C2 C3 1.0941 111.48 180.00 112.85 1.5267 +IC H11 C2 *C1 H12 1.0941 111.48 120.20 110.84 1.0945 +IC H11 C2 *C1 H13 1.0941 111.48 -120.20 110.84 1.0945 +IC C3 C1 *C2 H21 1.5267 112.85 121.86 109.61 1.0973 +IC C3 C1 *C2 H22 1.5267 112.85 -121.86 109.61 1.0973 +IC C4 C2 *C3 H31 1.5274 113.27 122.07 109.25 1.0985 +IC C4 C2 *C3 H32 1.5274 113.27 -122.07 109.25 1.0985 +IC C5 C3 *C4 H41 1.5267 113.27 -122.06 109.28 1.0985 +IC C5 C3 *C4 H42 1.5267 113.27 122.06 109.28 1.0985 +IC C6 C4 *C5 H51 1.5263 112.85 122.12 109.14 1.0973 +IC C6 C4 *C5 H52 1.5263 112.85 -122.12 109.14 1.0973 +IC H61 C5 *C6 H62 1.0941 111.48 120.20 110.84 1.0945 +IC H61 C5 *C6 H63 1.0941 111.48 -120.20 110.84 1.0945 +patc firs none last none + +Resi HEPT 0.000 ! heptane +! +! H11 H21 H31 H41 H71 +! \ | | | / +! H12-C1--C2--C3--C4....C7-H72 +! / | | | \ +! H13 H22 H33 H42 H73 +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H21 HDA2A 0.078 +ATOM H22 HDA2A 0.078 +GROUP +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H31 HDA2A 0.078 +ATOM H32 HDA2A 0.078 +GROUP +ATOM C4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H41 HDA2A 0.078 +ATOM H42 HDA2A 0.078 +GROUP +ATOM C5 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H51 HDA2A 0.078 +ATOM H52 HDA2A 0.078 +GROUP +ATOM C6 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H61 HDA2A 0.078 +ATOM H62 HDA2A 0.078 +GROUP +ATOM C7 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H71 HDA3A 0.059 +ATOM H72 HDA3A 0.059 +ATOM H73 HDA3A 0.059 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +Bond C6 C7 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C6 H61 C6 H62 C7 H71 C7 H72 +Bond C7 H73 +! IC for HEPT tttt conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5265 112.82 180.00 113.31 1.5271 +IC C2 C3 C4 C5 1.5270 113.31 180.00 113.24 1.5271 +IC C3 C4 C5 C6 1.5271 113.24 180.00 113.32 1.5270 +IC C4 C5 C6 C7 1.5271 113.32 180.00 112.81 1.5264 +IC C5 C6 C7 H71 1.5270 112.81 59.80 110.84 1.0945 +IC H11 C1 C2 C3 1.0940 111.50 180.00 112.82 1.5270 +IC H11 C2 *C1 H12 1.0940 111.50 120.20 110.84 1.0945 +IC H11 C2 *C1 H13 1.0940 111.50 -120.20 110.84 1.0945 +IC C3 C1 *C2 H21 1.5270 112.82 121.84 109.62 1.0973 +IC C3 C1 *C2 H22 1.5270 112.82 -121.84 109.62 1.0973 +IC C4 C2 *C3 H31 1.5271 113.31 122.09 109.23 1.0986 +IC C4 C2 *C3 H32 1.5271 113.31 -122.09 109.23 1.0986 +IC C5 C3 *C4 H41 1.5271 113.24 -122.06 109.27 1.0985 +IC C5 C3 *C4 H42 1.5271 113.24 122.06 109.27 1.0985 +IC C6 C4 *C5 H51 1.5270 113.32 122.06 109.29 1.0986 +IC C6 C4 *C5 H52 1.5270 113.32 -122.06 109.29 1.0986 +IC C7 C5 *C6 H61 1.5264 112.81 122.11 109.13 1.0973 +IC C7 C5 *C6 H62 1.5264 112.81 -122.11 109.13 1.0973 +IC H71 C6 *C7 H72 1.0945 110.84 120.20 111.51 1.0940 +IC H71 C6 *C7 H73 1.0945 110.84 -119.60 110.84 1.0945 +patc firs none last none + +Resi OCT 0.000 ! octane +! +! H11 H21 H31 H41 H81 +! \ | | | / +! H12-C1--C2--C3--C4....C8-H82 +! / | | | \ +! H13 H22 H33 H42 H83 +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H21 HDA2A 0.078 +ATOM H22 HDA2A 0.078 +GROUP +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H31 HDA2A 0.078 +ATOM H32 HDA2A 0.078 +GROUP +ATOM C4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H41 HDA2A 0.078 +ATOM H42 HDA2A 0.078 +GROUP +ATOM C5 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H51 HDA2A 0.078 +ATOM H52 HDA2A 0.078 +GROUP +ATOM C6 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H61 HDA2A 0.078 +ATOM H62 HDA2A 0.078 +GROUP +ATOM C7 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H71 HDA2A 0.078 +ATOM H72 HDA2A 0.078 +GROUP +ATOM C8 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H81 HDA3A 0.059 +ATOM H82 HDA3A 0.059 +ATOM H83 HDA3A 0.059 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +Bond C6 C7 C7 C8 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C6 H61 C6 H62 C7 H71 C7 H72 +Bond C8 H81 C8 H82 C8 H83 + +patc firs none last none + +Resi OCT2 0.000 ! octane +! +! H11 H21 H31 H41 H81 +! \ | | | / +! H12-C1--C2--C3--C4....C8-H82 +! / | | | \ +! H13 H22 H33 H42 H83 +! +! half-octane for crystal calculations (see xtloct1.inp) +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H21 HDA2A 0.078 +ATOM H22 HDA2A 0.078 +GROUP +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H31 HDA2A 0.078 +ATOM H32 HDA2A 0.078 +GROUP +ATOM C4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H41 HDA2A 0.078 +ATOM H42 HDA2A 0.078 + +Bond C1 C2 C2 C3 C3 C4 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 H41 0.0000 0.00 60.00 0.00 0.0000 +IC C2 C3 C4 H42 0.0000 0.00 -60.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +RESI DECA 0.000 ! decane +! +! H1A H2A H3A H4A H10A +! \ | | | / +! H1B-C1--C2--C3--C4...--C10-H10B +! / | | | \ +! H1C H2B H3B H4B H10C +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H1A HDA3A 0.059 +ATOM H1B HDA3A 0.059 +ATOM H1C HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H2A HDA2A 0.078 +ATOM H2B HDA2A 0.078 +GROUP +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H3A HDA2A 0.078 +ATOM H3B HDA2A 0.078 +GROUP +ATOM C4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H4A HDA2A 0.078 +ATOM H4B HDA2A 0.078 +GROUP +ATOM C5 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H5A HDA2A 0.078 +ATOM H5B HDA2A 0.078 +GROUP +ATOM C6 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H6A HDA2A 0.078 +ATOM H6B HDA2A 0.078 +GROUP +ATOM C7 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H7A HDA2A 0.078 +ATOM H7B HDA2A 0.078 +GROUP +ATOM C8 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H8A HDA2A 0.078 +ATOM H8B HDA2A 0.078 +GROUP +ATOM C9 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H9A HDA2A 0.078 +ATOM H9B HDA2A 0.078 +GROUP +ATOM C10 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H10A HDA3A 0.059 +ATOM H10B HDA3A 0.059 +ATOM H10C HDA3A 0.059 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C5 C6 C6 C7 C7 C8 C8 C9 C9 C10 +Bond C1 H1A C1 H1B C1 H1C C2 H2A C2 H2B +Bond C3 H3A C3 H3B C4 H4A C4 H4B +Bond C5 H5A C5 H5B C6 H6A C6 H6B +Bond C7 H7A C7 H7B C8 H8A C8 H8B +Bond C9 H9A C9 H9B C10 H10A C10 H10B C10 H10C +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 H1A 0.0000 0.00 180.00 0.00 0.0000 +IC H1A C2 *C1 H1B 0.0000 0.00 90.00 0.00 0.0000 +IC H1A C2 *C1 H1C 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2A 0.0000 0.00 90.00 0.00 0.0000 +IC C3 C1 *C2 H2B 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3A 0.0000 0.00 90.00 0.00 0.0000 +IC C4 C2 *C3 H3B 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4A 0.0000 0.00 90.00 0.00 0.0000 +IC C5 C3 *C4 H4B 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5A 0.0000 0.00 90.00 0.00 0.0000 +IC C6 C4 *C5 H5B 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6A 0.0000 0.00 90.00 0.00 0.0000 +IC C7 C5 *C6 H6B 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7A 0.0000 0.00 90.00 0.00 0.0000 +IC C8 C6 *C7 H7B 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8A 0.0000 0.00 90.00 0.00 0.0000 +IC C9 C7 *C8 H8B 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 H9A 0.0000 0.00 90.00 0.00 0.0000 +IC C10 C8 *C9 H9B 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 H10A 0.0000 0.00 180.00 0.00 0.0000 +IC H10A C9 *C10 H10B 0.0000 0.00 90.00 0.00 0.0000 +IC H10A C9 *C10 H10C 0.0000 0.00 180.00 0.00 0.0000 +patc firs none last none + +RESI PEND 0.000 ! pentadecane +! +! H1A H2A H3A H4A H15A +! \ | | | / +! H1B-C1--C2--C3--C4..--C15-H15B +! / | | | \ +! H1C H2B H3B H4B H15C +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H1A HDA3A 0.059 +ATOM H1B HDA3A 0.059 +ATOM H1C HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H2A HDA2A 0.078 +ATOM H2B HDA2A 0.078 +GROUP +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H3A HDA2A 0.078 +ATOM H3B HDA2A 0.078 +GROUP +ATOM C4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H4A HDA2A 0.078 +ATOM H4B HDA2A 0.078 +GROUP +ATOM C5 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H5A HDA2A 0.078 +ATOM H5B HDA2A 0.078 +GROUP +ATOM C6 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H6A HDA2A 0.078 +ATOM H6B HDA2A 0.078 +GROUP +ATOM C7 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H7A HDA2A 0.078 +ATOM H7B HDA2A 0.078 +GROUP +ATOM C8 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H8A HDA2A 0.078 +ATOM H8B HDA2A 0.078 +GROUP +ATOM C9 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H9A HDA2A 0.078 +ATOM H9B HDA2A 0.078 +GROUP +ATOM C10 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H10A HDA2A 0.078 +ATOM H10B HDA2A 0.078 +GROUP +ATOM C11 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H11A HDA2A 0.078 +ATOM H11B HDA2A 0.078 +GROUP +ATOM C12 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H12A HDA2A 0.078 +ATOM H12B HDA2A 0.078 +GROUP +ATOM C13 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H13A HDA2A 0.078 +ATOM H13B HDA2A 0.078 +GROUP +ATOM C14 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H14A HDA2A 0.078 +ATOM H14B HDA2A 0.078 +GROUP +ATOM C15 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H15A HDA3A 0.059 +ATOM H15B HDA3A 0.059 +ATOM H15C HDA3A 0.059 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C5 C6 C6 C7 C7 C8 C8 C9 C9 C10 +Bond C10 C11 C11 C12 C12 C13 C13 C14 C14 C15 +Bond C1 H1A C1 H1B C1 H1C C2 H2A C2 H2B +Bond C3 H3A C3 H3B C4 H4A C4 H4B +Bond C5 H5A C5 H5B C6 H6A C6 H6B +Bond C7 H7A C7 H7B C8 H8A C8 H8B +Bond C9 H9A C9 H9B C10 H10A C10 H10B +Bond C11 H11A C11 H11B C12 H12A C12 H12B +Bond C13 H13A C13 H13B +Bond C14 H14A C14 H14B C15 H15A C15 H15B C15 H15C +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 H1A 0.0000 0.00 180.00 0.00 0.0000 +IC H1A C2 *C1 H1B 0.0000 0.00 90.00 0.00 0.0000 +IC H1A C2 *C1 H1C 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2A 0.0000 0.00 90.00 0.00 0.0000 +IC C3 C1 *C2 H2B 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3A 0.0000 0.00 90.00 0.00 0.0000 +IC C4 C2 *C3 H3B 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4A 0.0000 0.00 90.00 0.00 0.0000 +IC C5 C3 *C4 H4B 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5A 0.0000 0.00 90.00 0.00 0.0000 +IC C6 C4 *C5 H5B 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6A 0.0000 0.00 90.00 0.00 0.0000 +IC C7 C5 *C6 H6B 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7A 0.0000 0.00 90.00 0.00 0.0000 +IC C8 C6 *C7 H7B 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8A 0.0000 0.00 90.00 0.00 0.0000 +IC C9 C7 *C8 H8B 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 H9A 0.0000 0.00 90.00 0.00 0.0000 +IC C10 C8 *C9 H9B 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H10A 0.0000 0.00 90.00 0.00 0.0000 +IC C11 C9 *C10 H10B 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H11A 0.0000 0.00 90.00 0.00 0.0000 +IC C12 C10 *C11 H11B 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H12A 0.0000 0.00 90.00 0.00 0.0000 +IC C13 C11 *C12 H12B 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 H13A 0.0000 0.00 90.00 0.00 0.0000 +IC C14 C12 *C13 H13B 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H14A 0.0000 0.00 90.00 0.00 0.0000 +IC C15 C13 *C14 H14B 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 H15A 0.0000 0.00 180.00 0.00 0.0000 +IC H15A C14 *C15 H15B 0.0000 0.00 90.00 0.00 0.0000 +IC H15A C14 *C15 H15C 0.0000 0.00 180.00 0.00 0.0000 +patc firs none last none + +RESI OCTD 0.000 ! octadecane +! +! H1A H2A H3A H4A H18A +! \ | | | / +! H1B-C1--C2--C3--C4..--C18-H18B +! / | | | \ +! H1C H2C H3B H4B H18C +! +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H1A HDA3A 0.059 +ATOM H1B HDA3A 0.059 +ATOM H1C HDA3A 0.059 +GROUP +ATOM C2 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H2A HDA2A 0.078 +ATOM H2B HDA2A 0.078 +GROUP +ATOM C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H3A HDA2A 0.078 +ATOM H3B HDA2A 0.078 +GROUP +ATOM C4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H4A HDA2A 0.078 +ATOM H4B HDA2A 0.078 +GROUP +ATOM C5 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H5A HDA2A 0.078 +ATOM H5B HDA2A 0.078 +GROUP +ATOM C6 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H6A HDA2A 0.078 +ATOM H6B HDA2A 0.078 +GROUP +ATOM C7 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H7A HDA2A 0.078 +ATOM H7B HDA2A 0.078 +GROUP +ATOM C8 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H8A HDA2A 0.078 +ATOM H8B HDA2A 0.078 +GROUP +ATOM C9 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H9A HDA2A 0.078 +ATOM H9B HDA2A 0.078 +GROUP +ATOM C10 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H10A HDA2A 0.078 +ATOM H10B HDA2A 0.078 +GROUP +ATOM C11 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H11A HDA2A 0.078 +ATOM H11B HDA2A 0.078 +GROUP +ATOM C12 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H12A HDA2A 0.078 +ATOM H12B HDA2A 0.078 +GROUP +ATOM C13 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H13A HDA2A 0.078 +ATOM H13B HDA2A 0.078 +GROUP +ATOM C14 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H14A HDA2A 0.078 +ATOM H14B HDA2A 0.078 +GROUP +ATOM C15 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H15A HDA2A 0.078 +ATOM H15B HDA2A 0.078 +GROUP +ATOM C16 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H16A HDA2A 0.078 +ATOM H16B HDA2A 0.078 +GROUP +ATOM C17 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H17A HDA2A 0.078 +ATOM H17B HDA2A 0.078 +GROUP +ATOM C18 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H18A HDA3A 0.059 +ATOM H18B HDA3A 0.059 +ATOM H18C HDA3A 0.059 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C5 C6 C6 C7 C7 C8 C8 C9 C9 C10 +Bond C10 C11 C11 C12 C12 C13 C13 C14 C14 C15 +Bond C15 C16 C16 C17 C17 C18 +Bond C1 H1A C1 H1B C1 H1C C2 H2A C2 H2B +Bond C3 H3A C3 H3B C4 H4A C4 H4B +Bond C5 H5A C5 H5B C6 H6A C6 H6B +Bond C7 H7A C7 H7B C8 H8A C8 H8B +Bond C9 H9A C9 H9B C10 H10A C10 H10B +Bond C11 H11A C11 H11B C12 H12A C12 H12B +Bond C13 H13A C13 H13B C14 H14A C14 H14B +Bond C15 H15A C15 H15B C16 H16A C16 H16B +Bond C17 H17A C17 H17B C18 H18A C18 H18B C18 H18C +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 H1A 0.0000 0.00 180.00 0.00 0.0000 +IC H1A C2 *C1 H1B 0.0000 0.00 90.00 0.00 0.0000 +IC H1A C2 *C1 H1C 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2A 0.0000 0.00 90.00 0.00 0.0000 +IC C3 C1 *C2 H2B 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3A 0.0000 0.00 90.00 0.00 0.0000 +IC C4 C2 *C3 H3B 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4A 0.0000 0.00 90.00 0.00 0.0000 +IC C5 C3 *C4 H4B 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5A 0.0000 0.00 90.00 0.00 0.0000 +IC C6 C4 *C5 H5B 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6A 0.0000 0.00 90.00 0.00 0.0000 +IC C7 C5 *C6 H6B 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7A 0.0000 0.00 90.00 0.00 0.0000 +IC C8 C6 *C7 H7B 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8A 0.0000 0.00 90.00 0.00 0.0000 +IC C9 C7 *C8 H8B 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 H9A 0.0000 0.00 90.00 0.00 0.0000 +IC C10 C8 *C9 H9B 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H10A 0.0000 0.00 90.00 0.00 0.0000 +IC C11 C9 *C10 H10B 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H11A 0.0000 0.00 90.00 0.00 0.0000 +IC C12 C10 *C11 H11B 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H12A 0.0000 0.00 90.00 0.00 0.0000 +IC C13 C11 *C12 H12B 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 H13A 0.0000 0.00 90.00 0.00 0.0000 +IC C14 C12 *C13 H13B 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H14A 0.0000 0.00 90.00 0.00 0.0000 +IC C15 C13 *C14 H14B 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 C16 0.0000 0.00 180.00 0.00 0.0000 +IC C16 C14 *C15 H15A 0.0000 0.00 90.00 0.00 0.0000 +IC C16 C14 *C15 H15B 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C15 C16 C17 0.0000 0.00 180.00 0.00 0.0000 +IC C17 C15 *C16 H16A 0.0000 0.00 90.00 0.00 0.0000 +IC C17 C15 *C16 H16B 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C16 C17 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C18 C16 *C17 H17A 0.0000 0.00 90.00 0.00 0.0000 +IC C18 C16 *C17 H17B 0.0000 0.00 180.00 0.00 0.0000 +IC C16 C17 C18 H18A 0.0000 0.00 180.00 0.00 0.0000 +IC H18A C17 *C18 H18B 0.0000 0.00 90.00 0.00 0.0000 +IC H18A C17 *C18 H18C 0.0000 0.00 180.00 0.00 0.0000 +patc firs none last none + +!! Branched alkanes + +RESI IBUT 0.000 ! Isobutane +! +! H12 +! | +! H11-C1-H13 +! | +! CT-HT +! / \ +! / \ +! H21-C2 C3-H31 +! / | | \ +! H22 H23 H33 H32 +! +! +GROUP +ATOM CT CD31A -0.095 ALPHA -1.302 THOLE 1.3 +ATOM HT HDA1A 0.095 +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H21 HDA3A 0.059 +ATOM H22 HDA3A 0.059 +ATOM H23 HDA3A 0.059 +GROUP +atom C3 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H31 HDA3A 0.059 +atom H32 HDA3A 0.059 +atom H33 HDA3A 0.059 +Bond ct c1 ct c2 ct c3 ct ht +Bond c1 h11 c1 h12 c1 h13 +Bond c2 h21 c2 h22 c2 h23 +Bond c3 h31 c3 h32 c3 h33 +!! IC for IBUT staggered conformer MP2/6-31G* optimized +IC C1 CT C2 H21 1.5272 110.84 178.49 111.23 1.0946 +IC C2 CT C1 H11 1.5272 110.84 -57.98 111.23 1.0946 +IC C1 CT C3 H31 1.5272 110.84 -57.98 111.23 1.0946 +IC C2 C1 *CT C3 1.5272 110.84 -123.53 110.84 1.5272 +IC C2 C1 *CT HT 1.5272 110.84 118.24 108.06 1.0986 +IC H11 CT *C1 H12 1.0946 111.23 119.74 110.37 1.0958 +IC H11 CT *C1 H13 1.0946 111.23 -120.51 111.23 1.0946 +IC H21 CT *C2 H22 1.0946 111.23 119.74 110.37 1.0958 +IC H21 CT *C2 H23 1.0946 111.23 -120.51 111.23 1.0946 +IC H31 CT *C3 H32 1.0946 111.23 119.74 110.37 1.0958 +IC H31 CT *C3 H33 1.0946 111.23 -120.51 111.23 1.0946 +patc firs none last none + +RESI NEOP 0.000 ! Neopentane +! +! H11 H12 H13 +! \ | / +! C1 +! H43 | H21 +! \ | / +! H42-C4--CT--C2-H22 +! / | \ +! H41 | H23 +! C3 +! / | \ +! H31 H32 H33 +! +GROUP +atom CT CD30A 0.000 ALPHA -1.302 THOLE 1.3 +GROUP +ATOM c1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM h11 HDA3A 0.059 +ATOM h12 HDA3A 0.059 +ATOM h13 HDA3A 0.059 +GROUP +ATOM c2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM h21 HDA3A 0.059 +ATOM h22 HDA3A 0.059 +ATOM h23 HDA3A 0.059 +GROUP +atom c3 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM h31 HDA3A 0.059 +atom h32 HDA3A 0.059 +atom h33 HDA3A 0.059 +GROUP +atom c4 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM h41 HDA3A 0.059 +atom h42 HDA3A 0.059 +atom h43 HDA3A 0.059 + +Bond ct c1 ct c2 ct c3 ct c4 +Bond c1 h11 c1 h12 c1 h13 +Bond c2 h21 c2 h22 c2 h23 +Bond c3 h31 c3 h32 c3 h33 +Bond c4 h41 c4 h42 c4 h43 +IC C2 CT C1 H11 1.5369 109.47 120.10 110.32 1.1102 +IC C2 C1 *CT C3 1.5369 109.48 120.00 109.47 1.5385 +IC C2 C1 *CT C4 1.5369 109.48 -120.02 109.47 1.5379 +IC C1 C2 *CT C4 1.5369 109.48 -120.02 109.47 1.5379 +IC H11 CT *C1 H12 1.1102 110.32 120.04 110.32 1.1098 +IC H11 CT *C1 H13 1.1102 110.32 -119.96 110.31 1.1108 +IC C3 CT C2 H21 1.5369 109.47 120.00 110.33 1.1101 +IC H21 CT *C2 H22 1.1101 110.33 120.02 110.33 1.1103 +IC H21 CT *C2 H23 1.1101 110.33 -120.00 110.32 1.1106 +IC C4 CT C3 H31 1.5369 109.47 120.62 110.30 1.1103 +IC H31 CT *C3 H32 1.1103 110.30 119.99 110.30 1.1101 +IC H31 CT *C3 H33 1.1103 110.30 -120.00 110.30 1.1100 +IC C2 CT C4 H41 1.5369 109.47 120.00 110.31 1.1102 +IC H41 CT *C4 H42 1.1102 110.31 -120.02 110.30 1.1100 +IC H41 CT *C4 H43 1.1102 110.31 119.99 110.31 1.1104 +patc firs none last none + +RESI BU2M 0.000 ! 2-methyl butane CMB 11/10 from JCTC, 6, 1181. +! +! H12 +! | +! H11-C1-H13 H41 +! | / +! CT-HT C4-H42 +! / \ / \ +! / \ / H43 +! H21-C2 C3 +! / | | \ +! H22 H23 H31 H32 +! +! +GROUP +ATOM CT CD31A -0.095 ALPHA -1.302 THOLE 1.3 +ATOM HT HDA1A 0.095 +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H21 HDA3A 0.059 +ATOM H22 HDA3A 0.059 +ATOM H23 HDA3A 0.059 +GROUP +atom C3 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM H31 HDA2A 0.078 +atom H32 HDA2A 0.078 +GROUP +atom H41 HDA3A 0.059 +atom H42 HDA3A 0.059 +atom H43 HDA3A 0.059 +atom C4 CD33A -0.177 ALPHA -2.051 THOLE 1.3 + +Bond ct c1 ct c2 ct c3 ct ht +Bond c1 h11 c1 h12 c1 h13 +Bond c2 h21 c2 h22 c2 h23 +Bond c3 h31 c3 h32 c3 c4 +Bond h41 c4 h42 c4 h43 c4 +IC C1 CT C2 H21 1.5394 109.54 -59.27 110.21 1.1109 +IC C2 CT C1 H11 1.5399 109.54 -60.45 110.74 1.1095 +IC C1 CT C3 H31 1.5394 112.65 59.70 108.18 1.1133 +IC C1 C2 C3 H32 2.5153 60.69 157.16 89.71 1.1132 +IC C2 C3 C4 H41 2.5697 96.91 -150.49 110.68 1.1107 +IC C2 C3 C4 H42 2.5697 96.91 -30.82 111.46 1.1099 +IC C2 C3 C4 H43 2.5697 96.91 89.91 111.43 1.1106 +IC H21 C2 C3 C4 1.1109 143.75 -134.89 96.91 1.5320 +IC H22 C2 C3 C4 1.1098 94.61 -5.00 96.91 1.5320 +IC H31 C3 C4 H43 1.1133 108.85 -61.23 111.43 1.1106 +IC H32 C3 C4 H43 1.1132 108.84 -178.03 111.43 1.1106 +IC C2 C1 *CT C3 1.5399 109.54 126.22 112.65 1.5479 +IC C2 C1 *CT HT 1.5399 109.54 -116.35 107.42 1.1175 +IC H11 CT *C1 H12 1.1095 110.74 119.73 110.21 1.1117 +IC H11 CT *C1 H13 1.1095 110.74 -120.44 110.40 1.1103 +IC H21 CT *C2 H22 1.1109 110.21 119.73 110.70 1.1098 +IC H21 CT *C2 H23 1.1109 110.21 -119.89 110.39 1.1101 +IC H31 CT *C3 H32 1.1133 108.18 116.09 108.19 1.1132 +IC C1 C3 *CT C2 1.5394 112.65 124.53 112.65 1.5399 +IC C1 C3 *CT HT 1.5394 112.65 -117.75 106.88 1.1175 +IC C3 CT C1 H11 1.5479 112.65 65.78 110.74 1.1095 +IC H11 CT *C1 H12 1.1095 110.74 119.73 110.21 1.1117 +IC H11 CT *C1 H13 1.1095 110.74 -120.44 110.40 1.1103 +IC C3 CT C2 H21 1.5479 112.65 174.50 110.21 1.1109 +IC H21 CT *C2 H22 1.1109 110.21 119.73 110.70 1.1098 +IC H21 CT *C2 H23 1.1109 110.21 -119.89 110.39 1.1101 +IC C4 CT *C3 H31 1.5320 115.09 121.96 108.18 1.1133 +IC H31 CT *C3 H32 1.1133 108.18 116.09 108.19 1.1132 +IC CT C3 C4 H41 1.5479 115.09 179.97 110.68 1.1107 +IC H41 C3 *C4 H42 1.1107 110.68 119.67 111.46 1.1099 +IC H41 C3 *C4 H43 1.1107 110.68 -119.60 111.43 1.1106 +patc firs none last none + +RESI BU22M 0.000 ! 2,2-dimethylbutan CMB 11/10 from JCTC, 6, 1181. +! +! H11 H12 H13 +! \ | / +! C1 +! H53 H42 | H21 +! \ | | / +! H52--C5--C4--CT--C2-H22 +! / | | \ +! H51 H41 | H23 +! C3 +! / | \ +! H31 H32 H33 +! +GROUP +atom CT CD30A 0.000 ALPHA -1.302 THOLE 1.3 +GROUP +ATOM c1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM h11 HDA3A 0.059 +ATOM h12 HDA3A 0.059 +ATOM h13 HDA3A 0.059 +GROUP +ATOM c2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM h21 HDA3A 0.059 +ATOM h22 HDA3A 0.059 +ATOM h23 HDA3A 0.059 +GROUP +atom c3 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM h31 HDA3A 0.059 +atom h32 HDA3A 0.059 +atom h33 HDA3A 0.059 +GROUP +atom c4 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM h41 HDA2A 0.078 +atom h42 HDA2A 0.078 +GROUP +atom c5 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM h51 HDA3A 0.059 +atom h52 HDA3A 0.059 +atom h53 HDA3A 0.059 + +Bond ct c1 ct c2 ct c3 ct c4 +Bond c1 h11 c1 h12 c1 h13 +Bond c2 h21 c2 h22 c2 h23 +Bond c3 h31 c3 h32 c3 h33 +Bond c4 h41 c4 h42 c4 c5 +Bond c5 h51 c5 h52 c5 h53 + +IC C1 C4 *CT C2 1.5388 110.90 -119.33 108.50 1.5391 +IC C1 C4 *CT C3 1.5388 110.90 121.35 110.89 1.5392 +IC C4 CT C1 H11 1.5504 110.90 -175.66 110.10 1.1104 +IC H11 CT *C1 H12 1.1104 110.10 119.71 110.31 1.1106 +IC H11 CT *C1 H13 1.1104 110.10 -119.70 110.97 1.1093 +IC C4 CT C2 H21 1.5504 108.50 60.05 110.34 1.1101 +IC H21 CT *C2 H22 1.1101 110.34 119.95 110.28 1.1098 +IC H21 CT *C2 H23 1.1101 110.34 -120.10 110.34 1.1101 +IC C4 CT C3 H31 1.5504 110.89 -64.65 110.96 1.1090 +IC H31 CT *C3 H32 1.1090 110.96 120.62 110.31 1.1102 +IC H31 CT *C3 H33 1.1090 110.96 -119.68 110.07 1.1107 +IC C2 CT C4 C5 0.0244 38.32 180.00 115.97 1.5336 +IC C5 CT *C4 H41 1.5336 115.97 -122.17 107.85 1.1128 +IC H41 CT *C4 H42 1.1128 107.85 -115.67 107.84 1.1127 +IC CT C4 C5 H51 1.5504 115.97 -60.55 111.58 1.1100 +IC H51 C4 *C5 H52 1.1100 111.58 -119.44 110.52 1.1109 +IC H51 C4 *C5 H53 1.1100 111.58 121.07 111.60 1.1097 +patc firs none last none + +RESI BU23M 0.000 ! 2,3-dimethyl butane CMB 11/10 from JCTC, 6, 1181. +! +! H12 +! | +! H11-C1-H13 H41 +! | / +! CT-HT C4-H42 +! / \ / \ +! / \ / H43 +! H21-C2 C3 H51 +! / | | \ / +! H22 H23 H31 C5-H52 +! | +! H53 +GROUP +ATOM CT CD31A -0.095 ALPHA -1.302 THOLE 1.3 +ATOM HT HDA1A 0.095 +GROUP +ATOM C1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 +GROUP +ATOM C2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H21 HDA3A 0.059 +ATOM H22 HDA3A 0.059 +ATOM H23 HDA3A 0.059 +GROUP +atom C3 CD31A -0.095 ALPHA -1.302 THOLE 1.3 +ATOM H31 HDA1A 0.095 +GROUP +atom H41 HDA3A 0.059 +atom H42 HDA3A 0.059 +atom H43 HDA3A 0.059 +atom C4 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +GROUP +atom H51 HDA3A 0.059 +atom H52 HDA3A 0.059 +atom H53 HDA3A 0.059 +atom C5 CD33A -0.177 ALPHA -2.051 THOLE 1.3 + +Bond ct c1 ct c2 ct c3 ct ht +Bond c1 h11 c1 h12 c1 h13 +Bond c2 h21 c2 h22 c2 h23 +Bond c3 h31 c3 c5 c3 c4 +Bond h41 c4 h42 c4 h43 c4 +Bond h51 c5 h52 c5 h53 c5 + +IC C1 CT C2 H21 1.5443 110.08 178.98 110.44 1.1105 +IC C2 CT C1 H11 1.5429 110.08 -60.99 111.19 1.1089 +IC C1 CT C3 H31 1.5443 113.69 177.35 107.25 1.1167 +IC C2 C3 C4 H41 2.5063 146.38 49.76 110.44 1.1103 +IC C2 C3 C4 H42 2.5063 146.38 -71.21 111.26 1.1092 +IC C2 C3 C4 H43 2.5063 146.38 169.32 109.84 1.1109 +IC H21 C2 C3 C4 1.1105 87.92 -125.55 146.38 1.5421 +IC H22 C2 C3 C4 1.1097 95.00 125.83 146.38 1.5421 +IC H31 C3 C4 H43 1.1167 107.76 55.63 109.84 1.1109 +IC C2 C1 *CT C3 1.5429 110.08 122.90 113.69 1.5315 +IC C2 C1 *CT HT 1.5429 110.08 -117.65 107.85 1.1155 +IC H11 CT *C1 H12 1.1089 111.19 118.95 109.51 1.1108 +IC H11 CT *C1 H13 1.1089 111.19 -121.87 111.46 1.1086 +IC H21 CT *C2 H22 1.1105 110.44 -120.78 111.17 1.1097 +IC H21 CT *C2 H23 1.1105 110.44 119.63 109.99 1.1102 +IC C1 C3 *CT C2 1.5443 113.69 123.37 109.22 1.5429 +IC C1 C3 *CT HT 1.5443 113.69 -119.49 107.79 1.1155 +IC C3 CT C1 H11 1.5315 113.69 61.90 111.19 1.1089 +IC H11 CT *C1 H12 1.1089 111.19 118.95 109.51 1.1108 +IC H11 CT *C1 H13 1.1089 111.19 -121.87 111.46 1.1086 +IC C3 CT C2 H21 1.5315 109.22 53.50 110.44 1.1105 +IC H21 CT *C2 H22 1.1105 110.44 -120.78 111.17 1.1097 +IC H21 CT *C2 H23 1.1105 110.44 119.63 109.99 1.1102 +IC C5 CT *C3 C4 1.5430 112.46 124.89 110.93 1.5421 +IC C5 CT *C3 H31 1.5430 112.46 -117.67 107.25 1.1167 +IC CT C3 C4 H41 1.5315 110.93 53.20 110.44 1.1103 +IC H41 C3 *C4 H42 1.1103 110.44 -120.97 111.26 1.1092 +IC H41 C3 *C4 H43 1.1103 110.44 119.56 109.84 1.1109 +IC CT C3 C5 H51 1.5315 112.46 68.70 110.51 1.1098 +IC H51 C3 *C5 H52 1.1098 110.51 -120.00 110.51 1.1098 +IC H51 C3 *C5 H53 1.1098 110.51 120.00 110.51 1.1098 +patc firs none last none + +!! cyclic alkanes + +RESI CPEN 0.000 ! cyclopentane +! +! H3A H4A +! | | +! H3B-C3---C4-H4B +! | | +! H2A-C2 C5-H5A +! /\ /\ +! H2B \ / H5B +! C1 +! / \ +! H1A H1B +! +GROUP +ATOM C1 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H1A HDA2R5 0.0265 +ATOM H1B HDA2R5 0.0265 +GROUP +ATOM C2 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H2A HDA2R5 0.0265 +ATOM H2B HDA2R5 0.0265 +GROUP +ATOM C3 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H3A HDA2R5 0.0265 +ATOM H3B HDA2R5 0.0265 +GROUP +ATOM C4 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H4A HDA2R5 0.0265 +ATOM H4B HDA2R5 0.0265 +GROUP +ATOM C5 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H5A HDA2R5 0.0265 +ATOM H5B HDA2R5 0.0265 + +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C1 +!! IC for CPEN C2 conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5485 105.88 -13.32 105.00 1.5334 +IC H1A C1 C2 C3 1.0958 110.05 104.06 105.88 1.5485 +IC C5 C2 *C1 H1A 1.5334 105.00 117.38 110.05 1.0958 +IC H1A C2 *C1 H1B 1.0958 110.05 119.30 112.68 1.0944 +IC C3 C1 *C2 H2A 1.5485 105.88 -120.88 110.89 1.0943 +IC H2A C1 *C2 H2B 1.0943 110.89 -118.52 111.32 1.0943 +IC C4 C2 *C3 H3A 1.5334 105.00 -123.32 112.68 1.0944 +IC H3A C2 *C3 H3B 1.0944 112.68 -119.30 110.05 1.0958 +IC C5 C3 *C4 H4A 1.5288 102.87 -116.68 110.22 1.0972 +IC H4A C3 *C4 H4B 1.0972 110.22 -120.38 113.00 1.0949 +IC C4 C1 *C5 H5A 1.5288 102.87 122.95 113.00 1.0949 +IC C4 C1 *C5 H5B 1.5288 102.87 -116.68 110.22 1.0972 +patc firs none last none + +RESI CHEX 0.000 ! cyclohexane +! +! H4A H4B +! \ / +! C4 +! H3A / \ H5A +! \/ \/ +! H3B-C3 C5-H5B +! | | +! | | +! H2A-C2 C6-H6A +! /\ /\ +! H2B \ / H6B +! C1 +! / \ +! H1A H1B +! +GROUP +ATOM C1 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H1A HDA2A 0.040 +ATOM H1B HDA2A 0.040 +GROUP +ATOM C2 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H2A HDA2A 0.040 +ATOM H2B HDA2A 0.040 +GROUP +ATOM C3 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H3A HDA2A 0.040 +ATOM H3B HDA2A 0.040 +GROUP +ATOM C4 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H4A HDA2A 0.040 +ATOM H4B HDA2A 0.040 +GROUP +ATOM C5 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H5A HDA2A 0.040 +ATOM H5B HDA2A 0.040 +GROUP +ATOM C6 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H6A HDA2A 0.040 +ATOM H6B HDA2A 0.040 + +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C6 +BOND C6 H6A C6 H6B C6 C1 +!! IC for CHEX chair conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5294 111.17 -55.59 111.17 1.5294 +IC C2 C3 C4 C5 1.5294 111.17 55.59 111.17 1.5294 +IC C6 C1 C2 C3 1.5294 111.17 55.59 111.17 1.5294 +IC C2 C6 *C1 H1A 1.5294 111.17 -122.75 110.33 1.0967 +IC H1A C6 *C1 H1B 1.0967 110.33 -116.87 109.11 1.0988 +IC C3 C1 *C2 H2A 1.5294 111.17 -120.39 109.11 1.0988 +IC H2A C1 *C2 H2B 1.0988 109.11 -116.87 110.33 1.0967 +IC C4 C2 *C3 H3A 1.5294 111.17 -122.75 110.34 1.0967 +IC H3A C2 *C3 H3B 1.0967 110.34 -116.87 109.11 1.0988 +IC C5 C3 *C4 H4A 1.5294 111.17 -120.39 109.11 1.0988 +IC H4A C3 *C4 H4B 1.0988 109.11 -116.87 110.33 1.0967 +IC C6 C4 *C5 H5A 1.5294 111.17 -122.75 110.33 1.0967 +IC H5A C4 *C5 H5B 1.0967 110.33 -116.87 109.11 1.0988 +IC C5 C1 *C6 H6A 1.5294 111.17 120.39 109.11 1.0988 +IC C5 C1 *C6 H6B 1.5294 111.17 -122.75 110.33 1.0967 +patc firs none last none + +RESI CPNM 0.000 ! methylcyclopentane CMB 11/10 from JCTC, 6, 1181. +! +! H3A H4A +! | | +! H3B-C3---C4-H4B +! | | +! H2A-C2 C5-H5A +! /\ /\ +! H2B \ / H5B +! C1 +! / \ +! H1A C6-H6C +! / \ +! H6A H6B +! +GROUP +ATOM C1 CD315A -0.0265 ALPHA -1.395 THOLE 1.3 +ATOM H1A HDA1R5 0.0265 +GROUP +ATOM C2 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H2A HDA2R5 0.0265 +ATOM H2B HDA2R5 0.0265 +GROUP +ATOM C3 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H3A HDA2R5 0.0265 +ATOM H3B HDA2R5 0.0265 +GROUP +ATOM C4 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H4A HDA2R5 0.0265 +ATOM H4B HDA2R5 0.0265 +GROUP +ATOM C5 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H5A HDA2R5 0.0265 +ATOM H5B HDA2R5 0.0265 +GROUP +ATOM C6 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H6A HDA3A 0.059 +ATOM H6B HDA3A 0.059 +ATOM H6C HDA3A 0.059 + +BOND C1 H1A C1 C6 C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C1 +BOND C6 H6A C6 H6B C6 H6C +IC C1 C2 C3 C4 1.5574 108.15 -11.11 105.05 1.5464 +IC H1A C1 C2 C3 1.1032 108.34 101.69 108.15 1.5522 +IC C5 C2 *C1 H1A 1.5490 103.18 114.74 108.34 1.1032 +IC H1A C2 *C1 C6 1.1032 108.34 121.23 114.02 1.5292 +IC C3 C1 *C2 H2A 1.5522 108.15 -121.62 110.32 1.1132 +IC H2A C1 *C2 H2B 1.1132 110.32 -117.67 110.89 1.1134 +IC C4 C2 *C3 H3A 1.5464 105.05 -122.53 112.49 1.1111 +IC H3A C2 *C3 H3B 1.1111 112.49 -119.26 109.78 1.1145 +IC C5 C3 *C4 H4A 1.5416 103.09 -117.59 110.26 1.1145 +IC H4A C3 *C4 H4B 1.1145 110.26 -120.27 112.77 1.1108 +IC C4 C1 *C5 H5A 1.5416 105.24 122.77 112.34 1.1113 +IC C4 C1 *C5 H5B 1.5416 105.24 -118.12 109.92 1.1152 +IC C5 C2 *C1 C6 1.5490 103.18 -124.03 114.02 1.5292 +IC C6 C2 *C1 H1A 1.5292 114.02 -121.23 108.34 1.1032 +IC C3 C1 *C2 H2A 1.5522 108.15 -121.62 110.32 1.1132 +IC H2A C1 *C2 H2B 1.1132 110.32 -117.67 110.89 1.1134 +IC C1 C2 C3 C4 1.5574 108.15 -11.11 105.05 1.5464 +IC C4 C2 *C3 H3A 1.5464 105.05 -122.53 112.49 1.1111 +IC H3A C2 *C3 H3B 1.1111 112.49 -119.26 109.78 1.1145 +IC C5 C3 *C4 H4A 1.5416 103.09 -117.59 110.26 1.1145 +IC H4A C3 *C4 H4B 1.1145 110.26 -120.27 112.77 1.1108 +IC C4 C1 *C5 H5A 1.5416 105.24 122.77 112.34 1.1113 +IC C4 C1 *C5 H5B 1.5416 105.24 -118.12 109.92 1.1152 +IC C2 C1 C6 H6A 1.5574 114.87 120.30 110.38 1.1111 +IC H6A C1 *C6 H6B 1.1111 110.38 119.97 110.38 1.1109 +IC H6A C1 *C6 H6C 1.1111 110.38 -119.97 110.39 1.1110 +patc firs none last none + +RESI CHXM 0.000 ! methylcyclohexane CMB 11/10 from JCTC, 6, 1181. +! +! H4A H4B +! \ / +! C4 +! H3A / \ H5A +! \/ \/ +! H3B-C3 C5-H5B +! | | +! | | +! H2A-C2 C6-H6A +! /\ /\ +! H2B \ / H6B +! C1 +! / \ +! H1A C7-H7A +! /\ +! H7C H7B +GROUP +ATOM C1 CD316A -0.040 ALPHA -1.359 THOLE 1.3 +ATOM H1A HDA1A 0.040 +GROUP +ATOM C2 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H2A HDA2A 0.040 +ATOM H2B HDA2A 0.040 +GROUP +ATOM C3 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H3A HDA2A 0.040 +ATOM H3B HDA2A 0.040 +GROUP +ATOM C4 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H4A HDA2A 0.040 +ATOM H4B HDA2A 0.040 +GROUP +ATOM C5 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H5A HDA2A 0.040 +ATOM H5B HDA2A 0.040 +GROUP +ATOM C6 CD326A -0.080 ALPHA -1.359 THOLE 1.3 +ATOM H6A HDA2A 0.040 +ATOM H6B HDA2A 0.040 +GROUP +ATOM C7 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM H7A HDA3A 0.059 +ATOM H7B HDA3A 0.059 +ATOM H7C HDA3A 0.059 + +BOND C1 H1A C1 C7 C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C6 +BOND C6 H6A C6 H6B C6 C1 +BOND C7 H7A C7 H7B C7 H7C +IC C1 C2 C3 C4 1.5400 113.04 -52.80 112.09 1.5350 +IC C2 C3 C4 C5 1.5370 112.09 52.83 112.00 1.5352 +IC C6 C1 C2 C3 1.5398 111.21 51.76 113.04 1.5370 +IC C2 C6 *C1 H1A 1.5400 111.21 -116.71 107.10 1.1166 +IC C3 C1 *C2 H2A 1.5370 113.04 -119.39 108.07 1.1135 +IC H2A C1 *C2 H2B 1.1135 108.07 -117.41 109.81 1.1110 +IC C4 C2 *C3 H3A 1.5350 112.09 -122.02 109.62 1.1117 +IC H3A C2 *C3 H3B 1.1117 109.62 -117.76 108.84 1.1126 +IC C5 C3 *C4 H4A 1.5352 112.00 -119.74 108.51 1.1134 +IC H4A C3 *C4 H4B 1.1134 108.51 -117.92 109.85 1.1113 +IC C6 C4 *C5 H5A 1.5371 112.09 -121.99 109.66 1.1117 +IC H5A C4 *C5 H5B 1.1117 109.66 -117.68 108.65 1.1125 +IC C5 C1 *C6 H6A 1.5371 113.05 119.38 108.07 1.1135 +IC C5 C1 *C6 H6B 1.5371 113.05 -123.20 109.82 1.1109 +IC C2 C6 *C1 C7 1.5400 111.21 126.65 112.23 1.5425 +IC C7 C6 *C1 H1A 1.5425 112.23 116.64 107.10 1.1166 +IC C6 C1 C2 C3 1.5398 111.21 51.76 113.04 1.5370 +IC C3 C1 *C2 H2A 1.5370 113.04 -119.39 108.07 1.1135 +IC H2A C1 *C2 H2B 1.1135 108.07 -117.41 109.81 1.1110 +IC C1 C2 C3 C4 1.5400 113.04 -52.80 112.09 1.5350 +IC C4 C2 *C3 H3A 1.5350 112.09 -122.02 109.62 1.1117 +IC H3A C2 *C3 H3B 1.1117 109.62 -117.76 108.84 1.1126 +IC C2 C3 C4 C5 1.5370 112.09 52.83 112.00 1.5352 +IC C5 C3 *C4 H4A 1.5352 112.00 -119.74 108.51 1.1134 +IC H4A C3 *C4 H4B 1.1134 108.51 -117.92 109.85 1.1113 +IC C6 C4 *C5 H5A 1.5371 112.09 -121.99 109.66 1.1117 +IC H5A C4 *C5 H5B 1.1117 109.66 -117.68 108.65 1.1125 +IC C5 C1 *C6 H6A 1.5371 113.05 119.38 108.07 1.1135 +IC C5 C1 *C6 H6B 1.5371 113.05 -123.20 109.82 1.1109 +IC C6 C1 C7 H7A 1.5398 112.23 176.79 110.20 1.1104 +IC H7A C1 *C7 H7B 1.1104 110.20 120.15 110.93 1.1095 +IC H7A C1 *C7 H7C 1.1104 110.20 -119.71 110.19 1.1105 +patc firs none last none + +!!amides + +RESI ACEM 0.000 ! acetamide +! +! the amide charges listed below are used in asparagine and glutamine +! +! HL1 Ht (trans to O) +! \ / +! HL2--CL--C---N +! / || \ +! HL3 O Hc (cis to O) +! + +GROUP +ATOM CL CD33C -0.384 ALPHA -1.417 THOLE 1.130 +ATOM C CD2O1A 0.906 ALPHA -1.583 THOLE 1.095 +ATOM N ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HC HDP1A 0.303 +ATOM HT HDP1A 0.351 +ATOM O OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM HL1 HDA3A 0.082 +ATOM HL2 HDA3A 0.082 +ATOM HL3 HDA3A 0.082 +ATOM LPA LPDO1 -0.411 +ATOM LPB LPDO1 -0.264 + +BOND C N N Hc N Ht C O +BOND C CL CL HL1 CL HL2 CL HL3 +BOND O LPA O LPB + +IMPR C CL N O +IMPR N HC HT C + +!from NMA +LONEPAIR relative LPA O C CL distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPB O C CL distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPA LPB A11 0.82322 A22 1.14332 + +IC N C CL HL1 0.0000 0.00 180.00 0.00 0.0000 +IC HL1 CL C O 0.0000 0.00 0.00 0.00 0.0000 +IC CL C N HC 0.0000 0.00 180.00 0.00 0.0000 +IC HC C *N HT 0.0000 0.00 180.00 0.00 0.0000 +IC HL1 C *CL HL2 0.0000 0.00 120.00 0.00 0.0000 +IC HL1 C *CL HL3 0.0000 0.00 -120.00 0.00 0.0000 + +RESI NMA 0.000 ! N-methylacetamide +! +! Hl1 H +! \ / +! Hl2--CL--C---N +! / || \ +! Hl3 O Cc--Hc3 (typically cis to O) +! / \ +! Hc1 Hc2 +! +GROUP +ATOM CL CD33C -0.249 ALPHA -1.584 THOLE 0.330 +ATOM HL1 HDA3A 0.050 +ATOM HL2 HDA3A 0.050 +ATOM HL3 HDA3A 0.050 +ATOM C CD2O1A 0.784 ALPHA -1.748 THOLE 1.517 +ATOM O OD2C1A 0.035 ALPHA -1.032 THOLE 0.915 +ATOM N ND2A2 -0.585 ALPHA -1.544 THOLE 0.438 +ATOM H HDP1A 0.297 +ATOM CC CD33C 0.119 ALPHA -1.229 THOLE 0.738 +ATOM HC1 HDA3A 0.041 +ATOM HC2 HDA3A 0.041 +ATOM HC3 HDA3A 0.041 +ATOM LPA LPDO1 -0.418 +ATOM LPB LPDO1 -0.256 + +BOND HL1 CL HL2 CL HL3 CL +BOND CL C C N N CC +BOND C O N H +BOND HC1 CC HC2 CC HC3 CC +BOND O LPA O LPB + +IMPR C CL N O N C CC H + +LONEPAIR relative LPA O C CL distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPB O C CL distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPA LPB A11 0.82322 A22 1.14332 + +IC N C CL HL1 1.3400 115.20 180.00 114.23 1.1110 +IC HL1 CL C O 1.1110 114.23 0.00 120.38 1.2390 +IC CL C N CC 1.5250 115.20 180.00 118.74 1.4430 +IC CC C *N H 1.4430 118.74 180.00 123.50 1.0250 +IC HL1 C *CL HL2 1.1110 114.23 120.00 114.23 1.1110 +IC HL1 C *CL HL3 1.1110 114.23 -120.00 114.23 1.1110 +IC C N CC HC1 1.3400 118.74 180.00 111.88 1.1110 +IC HC1 N *CC HC2 1.1110 111.88 120.00 111.88 1.1110 +IC HC1 N *CC HC3 1.1110 111.88 -120.00 111.88 1.1110 + +RESI DMA 0.000 ! N,N-dimethylacetamide +! +! Ht1 Ht2 +! \ / +! Hl1 Ct--Ht3 (trans to O) +! \ / +! Hl2--CL--C---N +! / || \ +! Hl3 O Cc--Hc3 (cis to O) +! / \ +! Hc1 Hc2 +! +GROUP +ATOM CL CD33C -0.214 ALPHA -2.405 THOLE 0.812 +ATOM HL1 HDA3A 0.043 +ATOM HL2 HDA3A 0.043 +ATOM HL3 HDA3A 0.043 +ATOM C CD2O1A 0.596 ALPHA -1.520 THOLE 1.010 +ATOM O OD2C1A -0.010 ALPHA -1.243 THOLE 1.248 +ATOM N ND2A3 -0.340 ALPHA -1.439 THOLE 1.319 +ATOM CT CD33C 0.070 ALPHA -2.037 THOLE 0.812 +ATOM HT1 HDA3A 0.058 +ATOM HT2 HDA3A 0.058 +ATOM HT3 HDA3A 0.058 +ATOM CC CD33C 0.037 ALPHA -1.898 THOLE 0.812 +ATOM HC1 HDA3A 0.054 +ATOM HC2 HDA3A 0.054 +ATOM HC3 HDA3A 0.054 +ATOM LPA LPDO1 -0.318 +ATOM LPB LPDO1 -0.286 + +BOND CL C C O C N N CT N CC +BOND HL1 CL HL2 CL HL3 CL +BOND HC1 CC HC2 CC HC3 CC +BOND HT1 CT HT2 CT HT3 CT +BOND O LPA O LPB + +IMPR C CL N O + +!from NMA +LONEPAIR relative LPA O C CL distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPB O C CL distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPA LPB A11 0.82322 A22 1.14332 + +IC N C CL HL1 0.0000 0.00 180.00 0.00 0.0000 +IC HL1 CL C O 0.0000 0.00 0.00 0.00 0.0000 +IC CL C N CT 0.0000 0.00 180.00 0.00 0.0000 +IC CT C *N CC 0.0000 0.00 180.00 0.00 0.0000 +IC HL1 C *CL HL2 0.0000 0.00 120.00 0.00 0.0000 +IC HL1 C *CL HL3 0.0000 0.00 -120.00 0.00 0.0000 +IC C N CT HT1 0.0000 0.00 180.00 0.00 0.0000 +IC HT1 N *CT HT2 0.0000 0.00 120.00 0.00 0.0000 +IC HT1 N *CT HT3 0.0000 0.00 -120.00 0.00 0.0000 +IC C N CC HC1 0.0000 0.00 180.00 0.00 0.0000 +IC HC1 N *CC HC2 0.0000 0.00 120.00 0.00 0.0000 +IC HC1 N *CC HC3 0.0000 0.00 -120.00 0.00 0.0000 + +!! Cyclic ethers, December 2006 + +RESI THF 0.000 ! Tetrahydrofuran +! +! H2A H3A +! | | +! H2B-C2---C3-H3B +! | | +! | | +! H1A-C1 C4-H4A +! /\ /\ +! H1B \ / H4B +! O1 +! +GROUP +ATOM O1 OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM C1 CD325B 0.039 ALPHA -1.562 THOLE 1.103 +ATOM H1A HDA2R5 0.055 +ATOM H1B HDA2R5 0.055 +ATOM C2 CD325B -0.141 ALPHA -1.617 THOLE 1.103 +ATOM H2A HDA2R5 0.072 +ATOM H2B HDA2R5 0.072 +ATOM C3 CD325B -0.141 ALPHA -1.617 THOLE 1.103 +ATOM H3A HDA2R5 0.072 +ATOM H3B HDA2R5 0.072 +ATOM C4 CD325B 0.039 ALPHA -1.562 THOLE 1.103 +ATOM H4A HDA2R5 0.055 +ATOM H4B HDA2R5 0.055 +ATOM LP1A LPD -0.152 +ATOM LP1B LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND O1 C1 C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 O1 +BOND O1 LP1A O1 LP1B O1 LPX + +LONEPAIR bisector LP1A O1 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP1B O1 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O1 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O1 LPX LP1A LP1B A11 0.8889 A22 1.2222 + +!! IC for THF C2 conformer MP2/6-31G* optimized +IC O1 C1 C2 C3 1.4368 106.09 32.94 101.18 1.5273 +IC C1 C2 C3 C4 1.5252 101.18 -39.14 101.18 1.5252 +IC C2 C3 C4 O1 1.5273 101.18 32.94 106.09 1.4368 +IC C3 C4 O1 C1 1.5252 106.09 -12.88 109.31 1.4368 +IC C4 O1 C1 C2 1.4368 109.31 -12.88 106.09 1.5252 +IC O1 C2 *C1 H1A 1.4368 106.09 118.91 113.61 1.0945 +IC O1 C2 *C1 H1B 1.4368 106.09 -118.66 111.00 1.0989 +IC C1 C3 *C2 H2A 1.5252 101.18 116.76 110.18 1.0949 +IC C1 C3 *C2 H2B 1.5252 101.18 -121.33 113.76 1.0935 +IC C2 C4 *C3 H3A 1.5273 101.18 121.95 112.88 1.0935 +IC C2 C4 *C3 H3B 1.5273 101.18 -116.64 110.35 1.0949 +IC C3 O1 *C4 H4A 1.5252 106.09 119.76 109.32 1.0989 +IC C3 O1 *C4 H4B 1.5252 106.09 -122.32 108.34 1.0945 +patc firs none last none + +RESI TF2M 0.000 ! 2-methyl-THF +! +! H2A H3A +! | | +! H2B-C2---C3-H3B +! | | +! | | +! H1A-C1 C4-H4A +! /\ /\ +! H5A-C5 \ / H4B +! /\ O1 +! H5B H5C +! +GROUP +ATOM O1 OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM C1 CD315B 0.094 ALPHA -1.562 THOLE 1.103 +ATOM H1A HDA1R5 0.055 +ATOM C2 CD325B -0.141 ALPHA -1.617 THOLE 1.103 +ATOM H2A HDA2R5 0.072 +ATOM H2B HDA2R5 0.072 +ATOM C3 CD325B -0.141 ALPHA -1.617 THOLE 1.103 +ATOM H3A HDA2R5 0.072 +ATOM H3B HDA2R5 0.072 +ATOM C4 CD325B 0.039 ALPHA -1.562 THOLE 1.103 +ATOM H4A HDA2R5 0.055 +ATOM H4B HDA2R5 0.055 +ATOM C5 CD33A -0.150 ALPHA -1.887 THOLE 0.456 +ATOM H5A HDA3A 0.050 +ATOM H5B HDA3A 0.050 +ATOM H5C HDA3A 0.050 +ATOM LP1A LPD -0.152 +ATOM LP1B LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND O1 C1 C1 H1A C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 O1 +BOND C1 C5 C5 H5A C5 H5B C5 H5C +BOND O1 LP1A O1 LP1B O1 LPX + +LONEPAIR bisector LP1A O1 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP1B O1 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O1 C1 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O1 LPX LP1A LP1B A11 0.8889 A22 1.2222 + +!! IC for TF2M C2 conformer MP2/6-31G* optimized +IC O1 C1 C2 C3 1.4443 106.24 14.28 103.29 1.5304 +IC C4 O1 C1 C2 1.4284 108.41 12.12 106.24 1.5435 +IC O1 C1 C5 H5A 1.4443 107.53 53.68 110.10 1.0928 +IC C2 O1 *C1 C5 1.5435 106.24 122.57 107.53 1.5167 +IC C2 O1 *C1 H1A 1.5435 106.24 -118.83 108.34 1.0993 +IC C3 C1 *C2 H2A 1.5304 103.29 122.32 112.09 1.0941 +IC H2A C1 *C2 H2B 1.0941 112.09 120.11 110.49 1.0949 +IC C4 C2 *C3 H3A 1.5208 100.72 115.91 110.89 1.0944 +IC H3A C2 *C3 H3B 1.0944 110.89 122.35 113.36 1.0940 +IC C3 O1 *C4 H4A 1.5208 104.28 -122.07 107.42 1.0931 +IC C3 O1 *C4 H4B 1.5208 104.28 119.33 110.91 1.1016 +IC H5A C1 *C5 H5B 1.0928 110.10 120.29 110.81 1.0947 +IC H5A C1 *C5 H5C 1.0928 110.10 -119.30 109.89 1.0938 +patc firs none last none + +RESI THP 0.000 ! Tetrahydro-2H-Pyran +! +! H3A H3B +! \ / +! C3 +! H2A / \ H4A +! \/ \/ +! H2B-C2 C4-H4B +! | | +! | | +! H1A-C1 C5-H5A +! /\ /\ +! H1B \ / H5B +! O1 +! +GROUP +ATOM O1 OD306A 0.000 ALPHA -0.530 THOLE 2.046 +ATOM C1 CD326B -0.016 ALPHA -1.696 THOLE 0.316 +ATOM H1A HDA2E 0.069 +ATOM H1B HDA2E 0.069 +ATOM C2 CD326B -0.148 ALPHA -1.427 THOLE 0.316 +ATOM H2A HDA2E 0.081 +ATOM H2B HDA2E 0.081 +ATOM C3 CD326B -0.158 ALPHA -1.698 THOLE 0.316 +ATOM H3A HDA2E 0.080 +ATOM H3B HDA2E 0.080 +ATOM C4 CD326B -0.148 ALPHA -1.427 THOLE 0.316 +ATOM H4A HDA2E 0.081 +ATOM H4B HDA2E 0.081 +ATOM C5 CD326B -0.016 ALPHA -1.696 THOLE 0.316 +ATOM H5A HDA2E 0.069 +ATOM H5B HDA2E 0.069 +ATOM LP1A LPD -0.137 +ATOM LP1B LPD -0.137 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND O1 C1 C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 O1 +BOND O1 LP1A O1 LP1B O1 LPX + +LONEPAIR bisector LP1A O1 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP1B O1 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O1 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O1 LPX LP1A LP1B A11 0.8889 A22 1.2222 + +!! IC for THP chair conformer MP2/6-31G* optimized +IC O1 C1 C2 C3 1.4266 111.33 57.16 109.96 1.5293 +IC C1 C2 C3 C4 1.5230 109.96 -52.34 109.87 1.5293 +IC C5 O1 C1 C2 1.4266 110.87 -61.89 111.33 1.5230 +IC C2 O1 *C1 H1A 1.5230 111.33 -121.53 105.76 1.0934 +IC H1A O1 *C1 H1B 1.0934 105.76 -116.45 109.72 1.1033 +IC C3 C1 *C2 H2A 1.5293 109.96 122.65 109.93 1.0971 +IC H2A C1 *C2 H2B 1.0971 109.93 117.29 108.46 1.0963 +IC C4 C2 *C3 H3A 1.5293 109.87 -122.83 110.84 1.0956 +IC H3A C2 *C3 H3B 1.0956 110.84 -117.43 109.20 1.0986 +IC C5 C3 *C4 H4A 1.5230 109.96 -119.25 109.78 1.0963 +IC H4A C3 *C4 H4B 1.0963 109.78 -118.81 111.12 1.0971 +IC C4 O1 *C5 H5A 1.5230 111.33 121.53 105.76 1.0934 +IC C4 O1 *C5 H5B 1.5230 111.33 -122.02 109.72 1.1033 +patc firs none last none + +RESI DIOX 0.000 ! 1,4-Dioxane, added by cmb +! +! O3 +! H2A / \ H4A +! \/ \/ +! H2B-C2 C4-H4B +! | | +! | | +! H1A-C1 C5-H5A +! /\ /\ +! H1B \ / H5B +! O1 +! +GROUP +ATOM O1 OD306A 0.000 ALPHA -0.530 THOLE 2.046 +ATOM C1 CD326B -0.001 ALPHA -1.696 THOLE 0.316 +ATOM H1A HDA2E 0.069 +ATOM H1B HDA2E 0.069 +ATOM C2 CD326B -0.001 ALPHA -1.696 THOLE 0.316 +ATOM H2A HDA2E 0.069 +ATOM H2B HDA2E 0.069 +ATOM O3 OD306A 0.000 ALPHA -0.530 THOLE 2.046 +ATOM C4 CD326B -0.001 ALPHA -1.696 THOLE 0.316 +ATOM H4A HDA2E 0.069 +ATOM H4B HDA2E 0.069 +ATOM C5 CD326B -0.001 ALPHA -1.696 THOLE 0.316 +ATOM H5A HDA2E 0.069 +ATOM H5B HDA2E 0.069 +ATOM LP1A LPD -0.137 +ATOM LP1B LPD -0.137 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM LP2A LPD -0.137 +ATOM LP2B LPD -0.137 +ATOM LPX2 LPD 0.000 !dummy for anisotropic polarizability +BOND O1 C1 C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 O3 +BOND O3 LP2A O3 LP2B O3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 O1 +BOND O1 LP1A O1 LP1B +BOND O1 LPX +BOND O3 LPX2 +LONEPAIR bisector LP1A O1 C1 C5 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP1B O1 C1 C5 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O1 C1 C5 distance 0.10 angle 0.0 dihe 0.0 +LONEPAIR bisector LP2A O3 C4 C2 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2B O3 C4 C2 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX2 O3 C4 C2 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O1 LPX LP1A LP1B A11 0.8889 A22 1.2222 +ANISOTROPY O3 LPX2 LP2A LP2B A11 0.8889 A22 1.2222 +IC O1 C1 C2 O3 1.4202 111.44 56.32 111.44 1.4190 +IC C5 O1 C1 C2 1.4193 110.26 -55.66 111.44 1.5370 +IC C2 O1 *C1 H1A 1.5370 111.44 -121.24 109.03 1.1109 +IC H1A O1 *C1 H1B 1.1109 109.03 -117.81 109.15 1.1123 +IC H2A C1 *C2 H2B 1.1111 109.66 118.31 109.39 1.1121 +IC C5 O3 *C4 H4A 1.5370 111.44 -120.93 109.16 1.1123 +IC H4A O3 *C4 H4B 1.1123 109.16 -117.82 109.06 1.1110 +IC C4 O1 *C5 H5A 1.5370 111.45 121.21 109.03 1.1112 +IC C4 O1 *C5 H5B 1.5370 111.45 -120.97 109.19 1.1122 +IC C5 O1 C1 C2 1.4193 110.26 -55.66 111.44 1.5370 +IC C2 O1 *C1 H1A 1.5370 111.44 -121.24 109.03 1.1109 +IC H1A O1 *C1 H1B 1.1109 109.03 -117.81 109.15 1.1123 +IC O1 C1 C2 O3 1.4202 111.44 56.32 111.44 1.4190 +IC O3 C1 *C2 H2A 1.4190 111.44 120.86 109.66 1.1111 +IC H2A C1 *C2 H2B 1.1111 109.66 118.31 109.39 1.1121 +IC C1 C2 O3 C4 1.5370 111.44 -55.68 110.31 1.4194 +IC C5 O3 *C4 H4A 1.5370 111.44 -120.93 109.16 1.1123 +IC H4A O3 *C4 H4B 1.1123 109.16 -117.82 109.06 1.1110 +IC C4 O1 *C5 H5A 1.5370 111.45 121.21 109.03 1.1112 +IC C4 O1 *C5 H5B 1.5370 111.45 -120.97 109.19 1.1122 +patc firs none last none + +!! Acyclic ethers + +RESI DMET 0.000 ! Dimethylether +! +! H11 H31 +! | | +! H13 - C1 - O2 - C3 - H33 +! | | +! H12 H32 +! +GROUP +ATOM C1 CD33E -0.037 ALPHA -1.798 THOLE 1.074 +ATOM H11 HDA3A 0.051 +ATOM H12 HDA3A 0.051 +ATOM H13 HDA3A 0.051 +ATOM O2 OD30A 0.000 ALPHA -0.705 THOLE 1.312 +ATOM C3 CD33E -0.037 ALPHA -1.798 THOLE 1.074 +ATOM H31 HDA3A 0.051 +ATOM H32 HDA3A 0.051 +ATOM H33 HDA3A 0.051 +ATOM LP2A LPD -0.116 +ATOM LP2B LPD -0.116 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND C1 O2 O2 C3 +BOND C1 H11 C1 H12 C1 H13 +BOND C3 H31 C3 H32 C3 H33 +BOND O2 LP2A O2 LP2B O2 LPX + +LONEPAIR bisector LP2A O2 C1 C3 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2B O2 C1 C3 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O2 C1 C3 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O2 LPX LP2A LP2B A11 0.8889 A22 1.2222 + +!! IC for DMET staggered (C2v) conformer MP2/6-31G* optimized +IC C1 O2 C3 H31 1.4156 111.05 -60.70 111.47 1.0993 +IC H11 C1 O2 C3 1.0993 111.47 -60.70 111.05 1.4156 +IC H11 O2 *C1 H12 1.0993 111.47 -119.30 106.89 1.0906 +IC H11 O2 *C1 H13 1.0993 111.47 121.39 111.47 1.0993 +IC H31 O2 *C3 H32 1.0993 111.47 -119.30 106.89 1.0906 +IC H31 O2 *C3 H33 1.0993 111.47 121.39 111.47 1.0993 +patc firs none last none + +RESI MEET 0.000 ! Methylethylether +! +! H1A H2A H4A +! | | | +! H1C - C1 - C2 - O3 - C4 - H4C +! | | | +! H1B H2B H4B +! +GROUP +ATOM C1 CD33A -0.150 ALPHA -1.887 THOLE 0.456 +ATOM H11 HDA3A 0.050 +ATOM H12 HDA3A 0.050 +ATOM H13 HDA3A 0.050 +ATOM C2 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H21 HDA2E 0.060 +ATOM H22 HDA2E 0.060 +ATOM O3 OD30A 0.000 ALPHA -0.705 THOLE 1.312 +ATOM C4 CD33E -0.037 ALPHA -1.798 THOLE 1.074 +ATOM H41 HDA3A 0.051 +ATOM H42 HDA3A 0.051 +ATOM H43 HDA3A 0.051 +ATOM LP3A LPD -0.116 +ATOM LP3B LPD -0.116 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND C1 C2 C2 O3 O3 C4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 C4 H43 +BOND O3 LP3A O3 LP3B O3 LPX + +LONEPAIR bisector LP3A O3 C2 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP3B O3 C2 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O3 C2 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O3 LPX LP3A LP3B A11 0.8889 A22 1.2222 + +!! IC for MEET trans (t) conformer MP2/6-31G* optimized +IC C1 C2 O3 C4 1.5296 110.11 -180.00 111.05 1.4190 +IC C2 O3 C4 H41 1.4183 111.05 60.36 110.32 1.1113 +IC H11 C1 C2 O3 1.1106 110.47 180.00 110.11 1.4183 +IC H11 C2 *C1 H12 1.1106 110.47 120.09 110.34 1.1111 +IC H11 C2 *C1 H13 1.1106 110.47 -120.09 110.34 1.1111 +IC O3 C1 *C2 H21 1.4183 110.11 -120.56 109.50 1.1125 +IC O3 C1 *C2 H22 1.4183 110.11 120.56 109.50 1.1125 +IC H41 O3 *C4 H42 1.1113 110.32 -120.72 110.32 1.1113 +IC H41 O3 *C4 H43 1.1113 110.32 119.64 109.66 1.1110 +patc firs none last none + +RESI DEET 0.000 ! Diethylether +! +! H1A H2A H4A H5A +! | | | | +! H1C - C1 - C2 - O3 - C4 - C5 - H5C +! | | | | +! H1B H2B H4B H5B +! +GROUP +ATOM C1 CD33A -0.150 ALPHA -1.887 THOLE 0.456 +ATOM H11 HDA3A 0.050 +ATOM H12 HDA3A 0.050 +ATOM H13 HDA3A 0.050 +ATOM C2 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H21 HDA2E 0.060 +ATOM H22 HDA2E 0.060 +ATOM O3 OD30A 0.000 ALPHA -0.704 THOLE 1.312 +ATOM C4 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H41 HDA2E 0.060 +ATOM H42 HDA2E 0.060 +ATOM C5 CD33A -0.150 ALPHA -1.887 THOLE 0.456 +ATOM H51 HDA3A 0.050 +ATOM H52 HDA3A 0.050 +ATOM H53 HDA3A 0.050 +ATOM LP3A LPD -0.116 +ATOM LP3B LPD -0.116 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND C1 C2 C2 O3 O3 C4 C4 C5 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 +BOND C5 H51 C5 H52 C5 H53 +BOND O3 LP3A O3 LP3B O3 LPX + +LONEPAIR bisector LP3A O3 C2 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP3B O3 C2 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O3 C2 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O3 LPX LP3A LP3B A11 0.8889 A22 1.2222 + +!! IC for DEET tt conformer MP2/6-31G* optimized +IC C1 C2 O3 C4 1.5296 110.07 180.00 111.30 1.4188 +IC C2 O3 C4 C5 1.4188 111.30 180.00 110.07 1.5296 +IC H11 C1 C2 O3 1.1107 110.48 -180.00 110.07 1.4188 +IC O3 C4 C5 H51 1.4188 110.07 180.00 110.48 1.1107 +IC H11 C2 *C1 H12 1.1107 110.48 120.09 110.35 1.1111 +IC H11 C2 *C1 H13 1.1107 110.48 -120.09 110.35 1.1111 +IC O3 C1 *C2 H21 1.4188 110.07 120.56 109.49 1.1125 +IC O3 C1 *C2 H22 1.4188 110.07 -120.56 109.49 1.1125 +IC C5 O3 *C4 H41 1.5296 110.07 120.48 109.62 1.1125 +IC C5 O3 *C4 H42 1.5296 110.07 -120.48 109.62 1.1125 +IC H51 C4 *C5 H52 1.1107 110.48 120.09 110.35 1.1111 +IC H51 C4 *C5 H53 1.1107 110.48 -120.09 110.35 1.1111 +patc firs none last none + +RESI DME 0.000 ! Dimethoxyethane +! +! H12 H11 +! \ / +! H13-C1 H31 H32 H61 H62 +! \ \ / \ / +! O2--C3 C6-H63 +! \ / +! H41-C4--O5 +! / +! H42 +! +GROUP +ATOM C1 CD33E -0.037 ALPHA -1.798 THOLE 1.074 +ATOM H11 HDA3A 0.051 +ATOM H12 HDA3A 0.051 +ATOM H13 HDA3A 0.051 +ATOM O2 OD30A 0.000 ALPHA -0.705 THOLE 1.312 +ATOM C3 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H31 HDA2E 0.060 +ATOM H32 HDA2E 0.060 +ATOM C4 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H41 HDA2E 0.060 +ATOM H42 HDA2E 0.060 +ATOM O5 OD30A 0.000 ALPHA -0.705 THOLE 1.312 +ATOM C6 CD33E -0.037 ALPHA -1.798 THOLE 1.074 +ATOM H61 HDA3A 0.051 +ATOM H62 HDA3A 0.051 +ATOM H63 HDA3A 0.051 +ATOM LP2A LPD -0.116 +ATOM LP2B LPD -0.116 +ATOM LPX2 LPD 0.000 !dummy for anisotropic polarizability +ATOM LP5A LPD -0.116 +ATOM LP5B LPD -0.116 +ATOM LPX5 LPD 0.000 !dummy for anisotropic polarizability + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 O2 O2 C3 +BOND C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 +BOND C4 O5 O5 C6 +BOND C6 H61 C6 H62 C6 H63 +BOND O2 LP2A O2 LP2B O2 LPX2 +BOND O5 LP5A O5 LP5B O5 LPX5 + +LONEPAIR bisector LP2A O2 C1 C3 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2B O2 C1 C3 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX2 O2 C1 C3 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O2 LPX2 LP2A LP2B A11 0.8889 A22 1.2222 + +LONEPAIR bisector LP5A O5 C4 C6 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP5B O5 C4 C6 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX5 O5 C4 C6 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O5 LPX5 LP5A LP5B A11 0.8889 A22 1.2222 + +!! IC for DME ttt conformer MP2/6-31G(d) opt. +IC C1 O2 C3 C4 1.4177 111.45 -180.00 106.95 1.5133 +IC H11 C1 O2 C3 1.0906 106.80 180.00 111.45 1.4180 +IC O2 C3 C4 O5 1.4180 106.95 180.00 106.95 1.4180 +IC C3 C4 O5 C6 1.5133 106.95 -180.00 111.45 1.4177 +IC C4 O5 C6 H61 1.4180 111.45 180.00 106.80 1.0906 +IC H11 O2 *C1 H12 1.0906 106.80 119.29 111.35 1.0986 +IC H11 O2 *C1 H13 1.0906 106.80 -119.29 111.35 1.0986 +IC C4 O2 *C3 H31 1.5133 106.95 -119.86 111.19 1.1001 +IC H31 O2 *C3 H32 1.1001 111.19 -120.27 111.19 1.1001 +IC O5 C3 *C4 H41 1.4180 106.95 -120.75 109.80 1.1001 +IC H41 C3 *C4 H42 1.1001 109.80 -118.49 109.80 1.1001 +IC H61 O5 *C6 H62 1.0906 106.80 119.29 111.35 1.0986 +IC H61 O5 *C6 H63 1.0906 106.80 -119.29 111.35 1.0986 +patc firs none last none + +RESI MPET 0.000 ! Methyl Propyl Ether +! +! H11 H31 H41 H51 +! | | | | +! H11 - C1 - O2 - C3 - C4 - C5 - H53 +! | | | | +! H12 H32 H42 H52 +! +GROUP +ATOM C1 CD33E -0.037 ALPHA -1.798 THOLE 1.074 +ATOM H11 HDA3A 0.051 +ATOM H12 HDA3A 0.051 +ATOM H13 HDA3A 0.051 +ATOM O2 OD30A 0.000 ALPHA -0.705 THOLE 1.312 +ATOM C3 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H31 HDA2E 0.060 +ATOM H32 HDA2E 0.060 +ATOM C4 CD32A -0.120 ALPHA -1.696 THOLE 0.918 +ATOM H41 HDA2A 0.060 +ATOM H42 HDA2A 0.060 +ATOM C5 CD33A -0.150 ALPHA -1.887 THOLE 0.456 +ATOM H51 HDA3A 0.050 +ATOM H52 HDA3A 0.050 +ATOM H53 HDA3A 0.050 +ATOM LP2A LPD -0.116 +ATOM LP2B LPD -0.116 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND C1 H11 C1 H12 C1 H13 C1 O2 +BOND O2 C3 C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 C4 C5 +BOND C5 H51 C5 H52 C5 H53 +BOND O2 LP2A O2 LP2B O2 LPX + +LONEPAIR bisector LP2A O2 C1 C3 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2B O2 C1 C3 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O2 C1 C3 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O2 LPX LP2A LP2B A11 0.8889 A22 1.2222 + +!! IC for MPET tt conformer MP2/6-31G(d) opt. +IC C1 O2 C3 C4 1.4167 111.53 180.00 108.22 1.5159 +IC O2 C3 C4 C5 1.4196 108.22 180.00 112.12 1.5264 +IC H11 C1 O2 C3 1.0991 111.47 -60.71 111.53 1.4196 +IC C3 C4 C5 H51 1.5159 112.12 60.05 111.12 1.0944 +IC H11 O2 *C1 H12 1.0991 111.47 -119.29 106.86 1.0908 +IC H11 O2 *C1 H13 1.0991 111.47 121.42 111.47 1.0991 +IC C4 O2 *C3 H31 1.5159 108.22 -120.91 110.25 1.1031 +IC H31 O2 *C3 H32 1.1031 110.25 -118.17 110.25 1.1031 +IC C5 C3 *C4 H41 1.5264 112.12 -122.18 108.33 1.0947 +IC H41 C3 *C4 H42 1.0947 108.33 -115.64 108.33 1.0947 +IC H51 C4 *C5 H52 1.0944 111.12 -120.11 111.12 1.0944 +IC H51 C4 *C5 H53 1.0944 111.12 119.95 111.05 1.0931 +patc firs none last none + +RESI MBET 0.000 ! Methyl Butyl Ether +! +! H11 H31 H41 H51 H6A +! | | | | | +! H11 - C1 - O2 - C3 - C4 - C5 - C6 - H6C +! | | | | | +! H12 H32 H42 H52 H6B +! +GROUP +ATOM C1 CD33E -0.037 ALPHA -1.798 THOLE 1.074 +ATOM H11 HDA3A 0.051 +ATOM H12 HDA3A 0.051 +ATOM H13 HDA3A 0.051 +ATOM O2 OD30A 0.000 ALPHA -0.705 THOLE 1.312 +ATOM C3 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H31 HDA2E 0.060 +ATOM H32 HDA2E 0.060 +ATOM C4 CD32A -0.120 ALPHA -1.696 THOLE 0.918 +ATOM H41 HDA2A 0.060 +ATOM H42 HDA2A 0.060 +ATOM C5 CD32A -0.120 ALPHA -1.696 THOLE 0.918 +ATOM H51 HDA2A 0.060 +ATOM H52 HDA2A 0.060 +ATOM C6 CD33A -0.150 ALPHA -1.887 THOLE 0.456 +ATOM H61 HDA3A 0.050 +ATOM H62 HDA3A 0.050 +ATOM H63 HDA3A 0.050 +ATOM LP2A LPD -0.116 +ATOM LP2B LPD -0.116 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND C1 H11 C1 H12 C1 H13 C1 O2 +BOND O2 C3 C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 C4 C5 +BOND C5 H51 C5 H52 C5 C6 +BOND C6 H61 C6 H62 C6 H63 +BOND O2 LP2A O2 LP2B O2 LPX + +LONEPAIR bisector LP2A O2 C1 C3 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2B O2 C1 C3 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O2 C1 C3 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O2 LPX LP2A LP2B A11 0.8889 A22 1.2222 + +!! IC for MBET ttt conformer MP2/6-31G(d) opt. +IC C1 O2 C3 C4 1.4167 111.49 -180.00 108.17 1.5161 +IC H11 C1 O2 C3 1.0908 106.86 -180.00 111.49 1.4201 +IC O2 C3 C4 C5 1.4201 108.17 -180.00 112.65 1.5270 +IC C3 C4 C5 C6 1.5161 112.65 -180.00 112.43 1.5265 +IC C4 C5 C6 H61 1.5270 112.43 -59.80 110.80 1.0942 +IC H11 O2 *C1 H12 1.0908 106.86 -119.29 111.47 1.0991 +IC H11 O2 *C1 H13 1.0908 106.86 119.29 111.47 1.0992 +IC C4 O2 *C3 H31 1.5161 108.17 -120.93 110.21 1.1030 +IC H31 O2 *C3 H32 1.1030 110.21 -118.13 110.21 1.1030 +IC C5 C3 *C4 H41 1.5270 112.65 -122.13 108.47 1.0960 +IC H41 C3 *C4 H42 1.0960 108.47 -115.75 108.47 1.0960 +IC C6 C4 *C5 H51 1.5265 112.43 -121.91 109.41 1.0972 +IC H51 C4 *C5 H52 1.0972 109.41 -116.18 109.41 1.0972 +IC H61 C5 *C6 H62 1.0942 110.80 -120.20 111.41 1.0938 +IC H61 C5 *C6 H63 1.0942 110.80 119.61 110.80 1.0942 +patc firs none last none + +RESI EPET 0.000 ! Ethyl Propyl Ether +! +! H11 H21 H41 H51 H61 +! | | | | | +! H13 - C1 - C2 - O3 - C4 - C5 - C6 - H63 +! | | | | | +! H12 H22 H42 H52 H62 +! +GROUP +ATOM C1 CD33A -0.150 ALPHA -1.887 THOLE 0.456 +ATOM H11 HDA3A 0.050 +ATOM H12 HDA3A 0.050 +ATOM H13 HDA3A 0.050 +ATOM C2 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H21 HDA2E 0.060 +ATOM H22 HDA2E 0.060 +ATOM O3 OD30A 0.000 ALPHA -0.704 THOLE 1.312 +ATOM C4 CD32E -0.004 ALPHA -1.696 THOLE 0.918 +ATOM H41 HDA2E 0.060 +ATOM H42 HDA2E 0.060 +GROUP +ATOM C5 CD32A -0.120 ALPHA -1.696 THOLE 0.918 +ATOM H51 HDA2A 0.060 +ATOM H52 HDA2A 0.060 +GROUP +ATOM C6 CD33A -0.150 ALPHA -1.887 THOLE 0.456 +ATOM H61 HDA3A 0.050 +ATOM H62 HDA3A 0.050 +ATOM H63 HDA3A 0.050 +ATOM LP3A LPD -0.116 +ATOM LP3B LPD -0.116 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability + +BOND C1 C2 C2 O3 O3 C4 +BOND C4 C5 C5 C6 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 +BOND C5 H51 C5 H52 +BOND C6 H61 C6 H62 C6 H63 +BOND O3 LP3A O3 LP3B O3 LPX + +LONEPAIR bisector LP3A O3 C2 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP3B O3 C2 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O3 C2 C4 distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O3 LPX LP3A LP3B A11 0.8889 A22 1.2222 + +!! IC for EPET ttt conformer MP2/6-31G(d) opt. +IC C1 C2 O3 C4 1.5140 107.70 180.00 112.04 1.4204 +IC H11 C1 C2 O3 1.0938 110.62 180.00 107.70 1.4216 +IC C2 O3 C4 C5 1.4216 112.04 180.00 108.18 1.5162 +IC O3 C4 C5 C6 1.4204 108.18 180.00 112.13 1.5264 +IC C4 C5 C6 H61 1.5162 112.13 -60.05 111.11 1.0944 +IC H11 C2 *C1 H12 1.0938 110.62 -120.23 110.08 1.0920 +IC H11 C2 *C1 H13 1.0938 110.62 120.23 110.08 1.0920 +IC O3 C1 *C2 H21 1.4216 107.70 120.47 110.86 1.1015 +IC O3 C1 *C2 H22 1.4216 107.70 -120.47 110.86 1.1015 +IC C5 O3 *C4 H41 1.5162 108.18 -120.89 110.26 1.1029 +IC C5 O3 *C4 H42 1.5162 108.18 120.89 110.26 1.1029 +IC C6 C4 *C5 H51 1.5264 112.13 -122.18 108.33 1.0948 +IC C6 C4 *C5 H52 1.5264 112.13 122.18 108.33 1.0948 +IC H61 C5 *C6 H62 1.0944 111.11 -119.95 111.06 1.0931 +IC H61 C5 *C6 H63 1.0944 111.11 120.10 111.11 1.0944 +patc firs none last none + +! Sulfur containing model compounds +RESI MESH 0.000 ! methanethiol +! +! H1A +! \ +! H1B--C1--S1 +! / \ +! H1C HS1 +! +GROUP +ATOM H11 HDA3A 0.060 +ATOM H12 HDA3A 0.060 +ATOM H13 HDA3A 0.060 +ATOM C1 CD33A -0.095 ALPHA -1.397 THOLE 1.330 +ATOM S1 SD31A 0.195 ALPHA -2.157 THOLE 1.118 +ATOM HS1 HDP1A 0.120 +ATOM LP1A LPD -0.200 +ATOM LP1B LPD -0.200 + +BOND C1 S1 S1 HS1 +BOND C1 H11 C1 H12 C1 H13 +BOND S1 LP1A S1 LP1B + +LONEPAIR relative LP1A S1 C1 HS1 distance 0.8 angle 95.0 dihe 100.0 +LONEPAIR relative LP1B S1 C1 HS1 distance 0.8 angle 95.0 dihe 260.0 +ANISOTROPY S1 C1 LP1A LP1B A11 0.8800 A22 1.3200 + +IC HS1 S1 C1 H11 1.3505 96.77 -180.00 109.54 1.1110 +IC HS1 H11 *C1 S1 2.3848 143.76 0.00 109.54 1.8127 +IC H11 S1 *C1 H12 1.1110 109.54 119.90 109.75 1.1109 +IC H11 S1 *C1 H13 1.1110 109.54 -119.90 109.75 1.1109 + +RESI ETSH 0.000 ! ethanethiol +! +! H21 H11 H12 +! \ \ / +! H22--C2--C1 +! / \ +! H23 S1--HS1 +! +GROUP +ATOM C1 CD32A 0.106 ALPHA -1.273 THOLE 0.716 +ATOM S1 SD31B 0.050 ALPHA -2.180 THOLE 1.612 +ATOM HS1 HDP1A 0.148 +ATOM H11 HDA2A 0.013 +ATOM H12 HDA2A 0.013 +ATOM C2 CD33A -0.180 ALPHA -1.435 THOLE 1.496 +ATOM H21 HDA3A 0.060 +ATOM H22 HDA3A 0.060 +ATOM H23 HDA3A 0.060 +ATOM LP1A LPD -0.165 +ATOM LP1B LPD -0.165 + +BOND C1 C2 C1 S1 C1 H11 C1 H12 S1 HS1 +BOND C2 H21 C2 H22 C2 H23 +BOND S1 LP1A S1 LP1B + +LONEPAIR relative LP1A S1 C1 HS1 distance 0.75 angle 95.0 dihe 100.0 +LONEPAIR relative LP1B S1 C1 HS1 distance 0.75 angle 95.0 dihe 260.0 +ANISOTROPY S1 C1 LP1A LP1B A11 0.8800 A22 1.3200 + +IC HS1 S1 C1 C2 1.3496 96.50 180.00 113.24 1.5264 +IC C2 S1 *C1 H11 1.5264 113.24 121.62 106.59 1.1111 +IC C2 S1 *C1 H12 1.5264 113.24 -121.62 106.59 1.1111 +IC S1 C1 C2 H21 1.8093 113.24 180.00 110.86 1.1105 +IC H21 C1 *C2 H22 1.1105 110.86 119.94 111.04 1.1111 +IC H21 C1 *C2 H23 1.1105 110.86 -119.94 111.04 1.1111 + +RESI PRSH 0.000 ! propanethiol +! +! H31 H11 H12 +! \ \ / +! H32--C3--C2--C1 +! / / \ \ +! H33 H21 H22 S1--HS1 +! +GROUP +ATOM C1 CD32A 0.106 ALPHA -1.273 THOLE 0.716 +ATOM S1 SD31B 0.050 ALPHA -2.180 THOLE 1.612 +ATOM HS1 HDP1A 0.148 +ATOM H11 HDA2A 0.013 +ATOM H12 HDA2A 0.013 +GROUP +ATOM C2 CD32A -0.120 ALPHA -1.162 THOLE 1.496 +ATOM H21 HDA2A 0.060 +ATOM H22 HDA2A 0.060 +GROUP +ATOM C3 CD33A -0.180 ALPHA -1.435 THOLE 2.156 +ATOM H31 HDA3A 0.060 +ATOM H32 HDA3A 0.060 +ATOM H33 HDA3A 0.060 +ATOM LP1A LPD -0.165 +ATOM LP1B LPD -0.165 + +BOND C1 C2 C1 S1 C1 H11 C1 H12 S1 HS1 +BOND C2 H21 C2 H22 C2 C3 +BOND C3 H31 C3 H32 C3 H33 +BOND S1 LP1A S1 LP1B + +LONEPAIR relative LP1A S1 C1 HS1 distance 0.75 angle 95.0 dihe 100.0 +LONEPAIR relative LP1B S1 C1 HS1 distance 0.75 angle 95.0 dihe 260.0 +ANISOTROPY S1 C1 LP1A LP1B A11 0.8800 A22 1.3200 + +IC HS1 S1 C1 C2 1.3497 96.51 180.00 113.70 1.5344 +IC S1 C1 C2 C3 1.8107 113.70 -180.00 114.10 1.5317 +IC C2 S1 *C1 H11 1.5344 113.70 121.68 106.53 1.1108 +IC C2 S1 *C1 H12 1.5344 113.70 -121.68 106.53 1.1108 +IC C3 C1 *C2 H21 1.5317 114.10 121.56 108.63 1.1136 +IC C3 C1 *C2 H22 1.5317 114.10 -121.56 108.63 1.1136 +IC C1 C2 C3 H31 1.5344 114.10 180.00 110.95 1.1110 +IC H31 C2 *C3 H32 1.1110 110.95 119.96 111.01 1.1110 +IC H31 C2 *C3 H33 1.1110 110.95 -119.96 111.01 1.1110 + +RESI BUSH 0.000 ! butylthiol +! +! H41 H31 H32 H11 H12 +! \ \ / \ / +! H42--C4--C3--C2--C1 +! / / \ \ +! H43 H21 H22 S1--HS1 +! +GROUP +ATOM C1 CD32A 0.106 ALPHA -1.273 THOLE 0.716 +ATOM S1 SD31B 0.050 ALPHA -2.180 THOLE 1.612 +ATOM HS1 HDP1A 0.148 +ATOM H11 HDA2A 0.013 +ATOM H12 HDA2A 0.013 +GROUP +ATOM C2 CD32A -0.120 ALPHA -1.162 THOLE 1.496 +ATOM H21 HDA2A 0.060 +ATOM H22 HDA2A 0.060 + +GROUP +ATOM C3 CD32A -0.120 ALPHA -1.162 THOLE 1.496 +ATOM H31 HDA2A 0.060 +ATOM H32 HDA2A 0.060 +GROUP +ATOM C4 CD33A -0.180 ALPHA -1.435 THOLE 2.156 +ATOM H41 HDA3A 0.060 +ATOM H42 HDA3A 0.060 +ATOM H43 HDA3A 0.060 +ATOM LP1A LPD -0.165 +ATOM LP1B LPD -0.165 + +BOND C1 C2 C1 S1 C1 H11 C1 H12 S1 HS1 +BOND C2 H21 C2 H22 C2 C3 +BOND C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 C4 H43 +BOND S1 LP1A S1 LP1B + +LONEPAIR relative LP1A S1 C1 HS1 distance 0.75 angle 95.0 dihe 100.0 +LONEPAIR relative LP1B S1 C1 HS1 distance 0.75 angle 95.0 dihe 260.0 +ANISOTROPY S1 C1 LP1A LP1B A11 0.8800 A22 1.3200 + +IC HS1 S1 C1 C2 1.3497 96.53 180.00 113.62 1.5336 +IC S1 C1 C2 C3 1.8105 113.62 180.00 113.14 1.5365 +IC C1 C2 C3 C4 1.5336 113.14 180.00 113.60 1.5291 +IC C2 S1 *C1 H11 1.5336 113.62 121.68 106.53 1.1108 +IC C2 S1 *C1 H12 1.5336 113.62 -121.68 106.53 1.1108 +IC C3 C1 *C2 H21 1.5365 113.14 121.14 109.04 1.1129 +IC C3 C1 *C2 H22 1.5365 113.14 -121.14 109.04 1.1129 +IC C4 C2 *C3 H31 1.5291 113.60 121.56 108.74 1.1135 +IC C4 C2 *C3 H32 1.5291 113.60 -121.56 108.74 1.1135 +IC C2 C3 C4 H41 1.5365 113.60 -180.00 111.04 1.1109 +IC H41 C3 *C4 H42 1.1109 111.04 120.03 110.98 1.1110 +IC H41 C3 *C4 H43 1.1109 111.04 -120.03 110.98 1.1110 + +RESI DMS 0.000 ! dimethylsulfide +! +! H21 H22 +! \ / +!H23--C2 H11 +! \ / +! S1--C1-H12 +! \ +! H13 +group +ATOM H21 HDA3A 0.087 +ATOM H22 HDA3A 0.087 +ATOM H23 HDA3A 0.087 +ATOM C2 CD33A -0.157 ALPHA -1.587 THOLE 1.542 +ATOM S1 SD30A 0.000 ALPHA -2.051 THOLE 1.543 +ATOM C1 CD33A -0.157 ALPHA -1.587 THOLE 1.542 +ATOM H11 HDA3A 0.087 +ATOM H12 HDA3A 0.087 +ATOM H13 HDA3A 0.087 +ATOM LP1A LPD -0.104 +ATOM LP1B LPD -0.104 + +BOND C2 H21 C2 H22 C2 H23 +BOND C2 S1 S1 C1 +BOND C1 H11 C1 H12 C1 H13 +BOND S1 LP1A S1 LP1B + +LONEPAIR bisector LP1A S1 C1 C2 distance 0.70 angle 95.0 dihe 100.0 +LONEPAIR bisector LP1B S1 C2 C1 distance 0.70 angle 95.0 dihe 100.0 +ANISOTROPY S1 C1 LP1A LP1B A11 0.7808 A22 1.3662 + +IC H21 C2 S1 C1 1.1107 109.90 60.15 96.78 1.7940 +IC H22 C2 S1 C1 1.1109 109.60 180.00 96.78 1.7940 +IC H23 C2 S1 C1 1.1107 109.90 -60.15 96.78 1.7940 +IC C2 S1 C1 H11 1.7940 96.78 60.15 109.90 1.1107 +IC C2 S1 C1 H12 1.7940 96.78 -180.00 109.60 1.1109 +IC C2 S1 C1 H13 1.7940 96.78 -60.15 109.90 1.1107 + +patch first none last none + +RESI EMS 0.000 ! ethylmethylsulfide +! +! H31 H21 H22 +! \ \ / +!H32-C3--C2 H11 +! / \ / +! H33 S1--C1-H12 +! \ +! H13 +GROUP +ATOM H31 HDA3A 0.060 +ATOM H32 HDA3A 0.060 +ATOM H33 HDA3A 0.060 +ATOM C3 CD33A -0.180 ALPHA -1.435 THOLE 1.542 +GROUP +ATOM H21 HDA2A 0.082 +ATOM H22 HDA2A 0.082 +ATOM C2 CD32A -0.041 ALPHA -1.300 THOLE 1.646 +ATOM S1 SD30A 0.000 ALPHA -2.051 THOLE 1.543 +ATOM C1 CD33A -0.161 ALPHA -1.587 THOLE 1.542 +ATOM H11 HDA3A 0.082 +ATOM H12 HDA3A 0.082 +ATOM H13 HDA3A 0.082 +ATOM LP1A LPD -0.104 +ATOM LP1B LPD -0.104 + +BOND C3 H31 C3 H32 C3 H33 +BOND C3 C2 C2 H21 C2 H22 +BOND C2 S1 S1 C1 +BOND C1 H11 C1 H12 C1 H13 +BOND S1 LP1A S1 LP1B + +LONEPAIR bisector LP1A S1 C1 C2 distance 0.70 angle 95.0 dihe 100.0 +LONEPAIR bisector LP1B S1 C2 C1 distance 0.70 angle 95.0 dihe 100.0 +ANISOTROPY S1 C1 LP1A LP1B A11 0.7808 A22 1.3662 + +IC H31 C3 C2 S1 1.1112 111.01 57.32 113.39 1.8083 +IC H32 C3 C2 S1 1.1108 110.82 177.04 113.39 1.8083 +IC H33 C3 C2 S1 1.1102 111.51 -63.04 113.39 1.8083 +IC H31 C3 C2 H21 1.1112 111.01 179.47 109.90 1.1118 +IC H32 C3 C2 H21 1.1108 110.82 -60.81 109.90 1.1118 +IC H33 C3 C2 H21 1.1102 111.51 59.11 109.90 1.1118 +IC H31 C3 C2 H22 1.1112 111.01 -62.61 109.01 1.1126 +IC H32 C3 C2 H22 1.1108 110.82 57.11 109.01 1.1126 +IC H33 C3 C2 H22 1.1102 111.51 177.03 109.01 1.1126 +IC C3 C2 S1 C1 1.5311 113.39 71.33 100.75 1.7963 +IC H21 C2 S1 C1 1.1118 108.91 -51.37 100.75 1.7963 +IC H22 C2 S1 C1 1.1126 107.67 -167.98 100.75 1.7963 +IC C2 S1 C1 H11 1.8083 100.75 56.77 109.93 1.1107 +IC C2 S1 C1 H12 1.8083 100.75 176.53 109.51 1.1109 +IC C2 S1 C1 H13 1.8083 100.75 -63.77 110.17 1.1104 +patch first none last none + +RESI DMDS 0.000 ! dimethyldisulfide +! +! H11 +! \ +! H12-C1 +! / \ +! H13 S1--S2 H21 +! \ / +! C2-H22 +! \ +! H23 +GROUP +ATOM H11 HDA3A 0.087 ! +ATOM H12 HDA3A 0.087 ! +ATOM H13 HDA3A 0.087 ! +ATOM C1 CD33A -0.157 ALPHA -1.888 THOLE 1.067 +ATOM S1 SD30B 0.000 ALPHA -2.686 THOLE 1.082 +ATOM S2 SD30B 0.000 ALPHA -2.683 THOLE 1.082 +ATOM C2 CD33A -0.157 ALPHA -1.887 THOLE 1.067 +ATOM H21 HDA3A 0.087 ! +ATOM H22 HDA3A 0.087 ! +ATOM H23 HDA3A 0.087 ! +ATOM LP1A LPD -0.052 ! +ATOM LP1B LPD -0.052 ! +ATOM LP2A LPD -0.052 ! +ATOM LP2B LPD -0.052 ! + +BOND H11 C1 H12 C1 H13 C1 C1 S1 +BOND S1 S2 S2 C2 C2 H21 C2 H22 +BOND C2 H23 +BOND S1 LP1A S1 LP1B +BOND S2 LP2A S2 LP2B + +LONEPAIR bisector LP1A S1 C1 S2 distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector LP1B S1 S2 C1 distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2A S2 C2 S1 distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2B S2 S1 C2 distance 0.90 angle 110.0 dihe 90.0 + +ANISOTROPY S1 C1 LP1A LP1B A11 0.9208 A22 1.0102 +ANISOTROPY S2 C2 LP2A LP2B A11 0.9208 A22 1.0102 + +IC H11 C1 S1 S2 1.1107 109.22 59.46 103.94 2.0325 +IC H12 C1 S1 S2 1.1104 109.33 179.40 103.94 2.0325 +IC H13 C1 S1 S2 1.1103 109.43 -60.47 103.94 2.0325 +IC C1 S1 S2 C2 1.8052 103.94 84.34 103.94 1.8052 +IC S1 S2 C2 H21 2.0325 103.94 59.46 109.22 1.1107 +IC S1 S2 C2 H22 2.0325 103.94 179.40 109.33 1.1104 +IC S1 S2 C2 H23 2.0325 103.94 -60.47 109.43 1.1103 + +!! Aromatics + +RESI BENZ 0.000 ! benzene +! +! HD1 HE1 +! | | +! CD1--CE1 +! / \ +! HG--CG CZ--HZ +! \ / +! CD2--CE2 +! | | +! HD2 HE2 +! +GROUP +ATOM CG CD2R6A -0.1106 ALPHA -1.615 THOLE 1.195 +ATOM HG HDR6A 0.1106 +ATOM CD1 CD2R6A -0.1106 ALPHA -1.615 THOLE 1.195 +ATOM HD1 HDR6A 0.1106 +ATOM CD2 CD2R6A -0.1106 ALPHA -1.615 THOLE 1.195 +ATOM HD2 HDR6A 0.1106 +ATOM CE1 CD2R6A -0.1106 ALPHA -1.615 THOLE 1.195 +ATOM HE1 HDR6A 0.1106 +ATOM CE2 CD2R6A -0.1106 ALPHA -1.615 THOLE 1.195 +ATOM HE2 HDR6A 0.1106 +ATOM CZ CD2R6A -0.1106 ALPHA -1.615 THOLE 1.195 +ATOM HZ HDR6A 0.1106 +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 +PATCHING FIRST NONE LAST NONE + +RESI TOLU 0.000 ! toluene +! +! HD1 HE1 +! | | +! HB1 CD1--CE1 +! \ / \ +! HB2-CB--CG CZ--HZ +! / \ / +! HB3 CD2--CE2 +! | | +! HD2 HE2 +! +GROUP +ATOM CB CD33A -0.229 ALPHA -1.608 THOLE 0.438 +ATOM HB1 HDA3A 0.079 +ATOM HB2 HDA3A 0.079 +ATOM HB3 HDA3A 0.079 +ATOM CG CD2R6A 0.037 ALPHA -1.550 THOLE 1.262 +ATOM CD1 CD2R6A -0.087 ALPHA -1.604 THOLE 1.262 +ATOM HD1 HDR6A 0.099 +ATOM CD2 CD2R6A -0.087 ALPHA -1.604 THOLE 1.262 +ATOM HD2 HDR6A 0.099 +ATOM CE1 CD2R6A -0.114 ALPHA -1.606 THOLE 1.262 +ATOM HE1 HDR6A 0.096 +ATOM CE2 CD2R6A -0.114 ALPHA -1.606 THOLE 1.262 +ATOM HE2 HDR6A 0.096 +ATOM CZ CD2R6A -0.133 ALPHA -1.610 THOLE 1.262 +ATOM HZ HDR6A 0.100 +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 CG CB +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +BOND CB HB1 CB HB2 CB HB3 +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG CB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG HB1 *CB HB2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CG HB1 *CB HB3 0.0000 0.0000 -120.0000 0.0000 0.0000 +PATCHING FIRST NONE LAST NONE + +RESI PHEN 0.000 ! Phenol +! +! HD1 HE1 +! | | +! CD1--CE1 HH +! / \ / +! HG--CG CZ--OH +! \ / +! CD2--CE2 +! | | +! HD2 HE2 +! +GROUP +ATOM CG CD2R6A -0.165 ALPHA -1.3993 THOLE 1.254 +ATOM HG HDR6A 0.1188 +ATOM CD1 CD2R6A -0.2453 ALPHA -1.3594 THOLE 1.254 +ATOM HD1 HDR6A 0.1518 +ATOM CD2 CD2R6A -0.2453 ALPHA -1.3594 THOLE 1.254 +ATOM HD2 HDR6A 0.1518 +ATOM CE1 CD2R6A -0.0935 ALPHA -1.3447 THOLE 1.254 +ATOM HE1 HDR6A 0.1210 +ATOM CE2 CD2R6A -0.0935 ALPHA -1.3447 THOLE 1.254 +ATOM HE2 HDR6A 0.1210 +ATOM CZ CD2R6A 0.2794 ALPHA -1.0906 THOLE 1.254 +ATOM OH OD31C 0.000 ALPHA -0.6286 THOLE 0.672 +ATOM HH HDP1A 0.3476 +ATOM LP1A LPD -0.2244 +ATOM LP1B LPD -0.2244 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH OH HH +BOND OH LP1A OH LP1B + +LONEPAIR relative LP1A OH CZ HH distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP1B OH CZ HH distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OH CZ LP1A LP1B A11 0.8108 A22 1.2162 + +IC CG CD1 CE1 CZ 0.0000 0.00 0.00 0.00 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CE1 *CZ OH 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CZ OH HH 0.0000 0.00 180.00 0.00 0.0000 + +RESI CRES 0.000 ! p-Cresol +! +! HD1 HE1 +! | | +! HB1 CD1--CE1 HZ +! \ / \ / +! HB2-CB--CG CZ--OZ +! / \ / +! HB3 CD2--CE2 +! | | +! HD2 HE2 +! +GROUP +ATOM CB CD33A -0.267 ALPHA -1.802 THOLE 0.148 +ATOM HB1 HDA3A 0.075 +ATOM HB2 HDA3A 0.075 +ATOM HB3 HDA3A 0.075 +ATOM CG CD2R6A 0.086 ALPHA -1.418 THOLE 1.270 +ATOM CD1 CD2R6A -0.202 ALPHA -1.427 THOLE 1.270 +ATOM HD1 HDR6A 0.118 +ATOM CD2 CD2R6A -0.202 ALPHA -1.427 THOLE 1.270 +ATOM HD2 HDR6A 0.118 +ATOM CE1 CD2R6A -0.136 ALPHA -1.444 THOLE 1.270 +ATOM HE1 HDR6A 0.123 +ATOM CE2 CD2R6A -0.136 ALPHA -1.444 THOLE 1.270 +ATOM HE2 HDR6A 0.123 +ATOM CZ CD2R6A 0.297 ALPHA -1.174 THOLE 1.270 +ATOM OZ OD31C 0.000 ALPHA -0.683 THOLE 0.601 +ATOM HZ HDP1A 0.319 +ATOM LP1A LPD -0.233 +ATOM LP1B LPD -0.233 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG CB CD1 HD1 CD2 HD2 CE1 HE1 +BOND CB HB1 CB HB2 CB HB3 +BOND CE2 HE2 CZ OZ OZ HZ +BOND OZ LP1A OZ LP1B + +LONEPAIR relative LP1A OZ CZ HZ distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP1B OZ CZ HZ distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OZ CZ LP1A LP1B A11 0.8108 A22 1.2162 + +IC HB1 CG *CB HB2 1.1114 108.67 -119.56 108.81 1.1116 +IC HB1 CG *CB HB3 1.1114 108.67 120.27 110.46 1.1119 +IC HB1 CB CG CD2 1.1114 108.67 -116.17 121.13 1.4147 +IC CD2 CB *CG CD1 1.4147 121.13 179.86 119.50 1.4130 +IC CB CG CD1 CE1 1.4946 119.50 -179.98 120.36 1.4154 +IC CE1 CG *CD1 HD1 1.4154 120.36 -179.97 119.44 1.0789 +IC CB CG CD2 CE2 1.4946 121.13 179.97 120.38 1.4155 +IC CE2 CG *CD2 HD2 1.4155 120.38 179.97 119.13 1.0787 +IC CG CD1 CE1 CZ 1.4130 120.36 0.05 119.84 1.4095 +IC CZ CD1 *CE1 HE1 1.4095 119.84 180.00 121.14 1.0776 +IC CZ CD2 *CE2 HE2 1.4085 119.80 180.00 120.16 1.0771 +IC CE2 CE1 *CZ OZ 1.4085 120.26 179.98 120.19 1.4047 +IC CE1 CZ OZ HZ 1.4095 120.19 -179.94 106.64 0.9683 + +!! heterocycles, 6-membered + +RESI PYR 0.000 ! pyridine +! +! HD1 HE1 +! | | +! CD1--CE1 +! / \ +! HG--CG NZ: +! \ / +! CD2--CE2 +! | | +! HD2 HE2 +! +GROUP +ATOM CG CD2R6A -0.132 ALPHA -1.595 THOLE 1.312 +ATOM HG HDR6A 0.207 +ATOM CD1 CD2R6A -0.175 ALPHA -1.618 THOLE 1.312 +ATOM HD1 HDR6A 0.074 +ATOM CD2 CD2R6A -0.175 ALPHA -1.618 THOLE 1.312 +ATOM HD2 HDR6A 0.074 +ATOM CE1 CD2R6B 0.194 ALPHA -1.629 THOLE 0.988 +ATOM HE1 HDR6B 0.052 +ATOM CE2 CD2R6B 0.194 ALPHA -1.629 THOLE 0.988 +ATOM HE2 HDR6B 0.052 +ATOM NZ ND2R6A 0.000 ALPHA -1.018 THOLE 1.057 +ATOM LP1 LPDNA1 -0.365 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND NZ LP1 + +LONEPAIR bisector LP1 NZ CE1 CE2 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY NZ LP1 CE1 CE2 A11 1.1611 A22 0.6778 + +IC CG CD1 CE1 NZ 1.4118 118.47 0.00 123.61 1.3678 +IC CD1 CE1 NZ CE2 1.4130 123.61 0.00 116.89 1.3678 +IC CE1 NZ CE2 CD2 1.3678 116.89 0.00 123.61 1.4130 +IC CD1 CD2 *CG HG 1.4118 118.95 180.00 120.52 1.0808 +IC CE1 CG *CD1 HD1 1.4130 118.47 180.00 121.03 1.0778 +IC CE2 CG *CD2 HD2 1.4130 118.47 180.00 121.03 1.0778 +IC NZ CD1 *CE1 HE1 1.3678 123.61 180.00 121.66 1.0778 +IC NZ CD2 *CE2 HE2 1.3678 123.61 180.00 121.66 1.0778 +IC NZ CE1 CD1 CG 1.3678 123.61 0.00 118.47 1.4118 +IC CE2 NZ CE1 CD1 1.3678 116.89 0.00 123.61 1.4130 +IC CD1 CE1 NZ CE2 1.4130 123.61 0.00 116.89 1.3678 + +PATCHING FIRST NONE LAST NONE + +RESI PYRM 0.000 ! pyrimidine, NA based numbering +! +! H6 +! | .. +! C6---N1 +! / \ +! H5--C5 C2--H2 +! \ / +! C4---N3 +! | .. +! HD2 +! +GROUP +ATOM C5 CD2R6A -0.468 ALPHA -1.641 THOLE 1.057 +ATOM H5 HDR6A 0.153 +ATOM C6 CD2R6B 0.263 ALPHA -1.618 THOLE 1.169 +ATOM H6 HDR6B 0.115 +ATOM C4 CD2R6B 0.263 ALPHA -1.618 THOLE 1.169 +ATOM H4 HDR6B 0.115 +ATOM N1 ND2R6B 0.000 ALPHA -1.024 THOLE 1.089 ! fitchg -0.8724 +ATOM LP1 LPDNA1 -0.465 +ATOM N3 ND2R6B 0.000 ALPHA -1.024 THOLE 1.089 ! fitchg -0.8724 +ATOM LP3 LPDNA1 -0.465 +ATOM C2 CD2R6C 0.432 ALPHA -1.629 THOLE 0.761 +ATOM H2 HDR6C 0.057 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 +BOND C2 H2 C4 H4 C5 H5 C6 H6 +BOND N1 LP1 N3 LP3 + +LONEPAIR bisector LP1 N1 C6 C2 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP3 N3 C4 C2 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY N1 LP1 C6 C2 A11 1.2376 A22 0.6648 +ANISOTROPY N3 LP3 C4 C2 A11 1.2376 A22 0.6648 + +IC C6 C4 *C5 H5 1.4028 116.35 180.00 121.83 1.0765 +IC C4 C5 C6 N1 1.4028 116.35 0.00 123.05 1.3455 +IC N1 C5 *C6 H6 1.3455 123.05 180.00 121.97 1.0819 +IC C6 C5 C4 N3 1.4028 116.35 0.00 123.05 1.3455 +IC N3 C5 *C4 H4 1.3455 123.05 180.00 121.97 1.0819 +IC C5 C6 N1 C2 1.4028 123.05 0.00 114.23 1.3518 +IC N3 N1 *C2 H2 1.3518 129.10 180.00 115.45 1.0795 + +PATCHING FIRST NONE LAST NONE + +!! heterocycles, 5-membered + +RESI IMID 0.000 ! Imidazole +! +! HD1 HE1 +! | / +! ND1--CE1 +! / || +! HG-CG || +! \\ || +! CD2--NE2 +! | : +! HD2 +! + +GROUP +ATOM CG CD2R5A -0.343 ALPHA -1.632 THOLE 0.949 +ATOM HG HDR5A 0.215 +ATOM CD2 CD2R5A 0.037 ALPHA -1.626 THOLE 0.949 +ATOM HD2 HDR5A 0.091 +ATOM ND1 ND2R5A -0.053 ALPHA -1.393 THOLE 0.670 +ATOM HD1 HDP1A 0.244 +ATOM CE1 CD2R5B 0.040 ALPHA -1.632 THOLE 1.568 +ATOM HE1 HDR5B 0.107 +ATOM NE2 ND2R5B 0.000 ALPHA -1.044 THOLE 0.788 +ATOM LP1 LPD -0.338 + +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG HG NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 +BOND NE2 LP1 + +IMPH ND1 CG CE1 HD1 ND1 CE1 CG HD1 +IMPH CD2 CG NE2 HD2 CD2 NE2 CG HD2 +IMPH CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 +IMPH CG CD2 ND1 HG CG ND1 CD2 HG + +LONEPAIR bisector LP1 NE2 CE1 CD2 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY NE2 LP1 CE1 CD2 A11 0.808 A22 1.384 + +IC CD2 ND1 *CG HG 1.3595 105.92 180.00 124.82 1.0814 +IC ND1 CG CD2 NE2 1.3788 105.92 0.00 110.41 1.3819 +IC NE2 CG *CD2 HD2 1.3819 110.41 180.00 129.91 1.0837 +IC HG CG ND1 CE1 1.0814 124.82 180.00 106.63 1.3566 +IC CE1 CG *ND1 HD1 1.3566 106.63 180.00 126.70 1.0020 +IC NE2 ND1 *CE1 HE1 1.3179 112.19 180.00 123.17 1.0889 + +PATCHING FIRST NONE LAST NONE + +RESI PYRR 0.000 ! pyrrole +! H2 H1 +! \ ____ / +! C2----C1 +! | \ +! | N5--H5 +! |____ / +! C3----C4 +! / \ +! H3 H4 +! +GROUP +ATOM C1 CD2R5A -0.004 ALPHA -1.618 THOLE 0.190 +ATOM HP1 HDR5A 0.084 +ATOM C2 CD2R5C -0.202 ALPHA -1.621 THOLE 1.018 +ATOM HP2 HDR5C 0.112 +ATOM C3 CD2R5C -0.202 ALPHA -1.621 THOLE 1.018 +ATOM HP3 HDR5C 0.112 +ATOM C4 CD2R5A -0.004 ALPHA -1.618 THOLE 0.190 +ATOM HP4 HDR5A 0.084 +ATOM N5 ND2R5A -0.273 ALPHA -1.378 THOLE 1.648 +ATOM HP5 HDP1A 0.293 + +BOND C1 HP1 C1 C2 C2 HP2 C2 C3 C3 HP3 +BOND C3 C4 C4 HP4 C4 N5 N5 HP5 N5 C1 + +IC C2 N5 *C1 HP1 1.3890 108.34 180.00 125.54 1.0793 +IC N5 C1 C2 C3 1.3818 108.34 0.00 107.30 1.4201 +IC C3 C1 *C2 HP2 1.4201 107.30 180.00 126.71 1.0795 +IC C1 C2 C3 C4 1.3890 107.30 0.00 107.30 1.3890 +IC C4 C2 *C3 HP3 1.3890 107.30 180.00 125.99 1.0795 +IC N5 C3 *C4 HP4 1.3818 108.34 180.00 126.12 1.0793 +IC C4 C1 *N5 HP5 1.3818 108.73 180.00 125.64 0.9999 + +PATCHING FIRST NONE LAST NONE + +RESI INDO 0.000 ! indole +! HE3 +! | +! HG CE3 +! \ / \\ +! CG-----CD2 CZ3-HZ3 +! || || | +! CD1 CE2 CH2-HH2 +! / \ / \ // +! HD1 NE1 CZ2 +! | | +! HE1 HZ2 +GROUP +ATOM CD2 CD2R6D -0.177 ALPHA -1.121 THOLE 1.344 +ATOM CE2 CD2R6D 0.033 ALPHA -1.253 THOLE 1.009 +ATOM CZ2 CD2R6A -0.069 ALPHA -1.616 THOLE 1.300 +ATOM CH2 CD2R6A -0.086 ALPHA -1.619 THOLE 1.300 +ATOM CZ3 CD2R6A -0.162 ALPHA -1.618 THOLE 1.300 +ATOM CE3 CD2R6A -0.028 ALPHA -1.618 THOLE 1.300 +ATOM CG CD2R5C -0.140 ALPHA -1.620 THOLE 1.346 +ATOM CD1 CD2R5A 0.055 ALPHA -1.618 THOLE 1.265 +ATOM NE1 ND2R5A -0.207 ALPHA -1.384 THOLE 1.146 +ATOM HZ2 HDR6A 0.035 +ATOM HH2 HDR6A 0.122 +ATOM HZ3 HDR6A 0.076 +ATOM HE3 HDR6A 0.076 +ATOM HG HDR5C 0.102 +ATOM HD1 HDR5A 0.047 +ATOM HE1 HDP1A 0.323 + +BOND CG HG CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND CZ3 CH2 CD2 CE3 NE1 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 +BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 +BOND CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 + +IMPH HZ2 CH2 CE2 CZ2 HZ2 CE2 CH2 CZ2 +IMPH HE3 CD2 CZ3 CE3 HE3 CZ3 CD2 CE3 +IMPH HG CD2 CD1 CG HG CD1 CD2 CG +IMPH HD1 CG NE1 CD1 HD1 NE1 CG CD1 +IMPH HE1 CE2 CD1 NE1 HE1 CD1 CE2 NE1 + +DONOR HE1 NE1 + +IC CG CD1 NE1 CE2 1.3980 108.50 0.00 109.08 1.4036 +IC CD1 CG CD2 CE2 1.3980 107.62 0.00 107.55 1.4113 +IC CD2 CG CD1 NE1 1.4197 107.62 0.00 108.50 1.3812 +IC CE2 CG *CD2 CE3 1.4113 107.55 -180.00 132.39 1.3997 +IC CE2 CD2 CE3 CZ3 1.4113 120.06 0.00 119.84 1.4067 +IC CD2 CE3 CZ3 CH2 1.3997 119.84 0.00 120.02 1.4157 +IC CE3 CZ3 CH2 CZ2 1.4067 120.02 0.00 119.90 1.4061 +IC CZ3 CD2 *CE3 HE3 1.4067 119.84 -180.00 120.80 1.0765 +IC CH2 CE3 *CZ3 HZ3 1.4157 120.02 -180.00 119.94 1.0789 +IC CZ2 CZ3 *CH2 HH2 1.4061 119.90 -180.00 119.98 1.0789 +IC CE2 CH2 *CZ2 HZ2 1.3987 119.78 -180.00 119.32 1.0760 +IC CD1 CE2 *NE1 HE1 1.3812 109.08 -180.00 125.06 0.9970 +IC CG NE1 *CD1 HD1 1.3980 108.50 -180.00 125.45 1.0783 +IC CD1 CD2 *CG HG 1.3980 107.62 -180.00 127.51 1.0830 + +PATCHING FIRST NONE LAST NONE + +RESI PUR0 0.000 ! purine +! +! H6 +! | +! C6 +! // \ +! N1 C5--N7\ +! | || C8-H8 +! C2 C4--N9// +! / \\ / | +! H2 N3 H9 +! +GROUP +ATOM N1 ND2R6B 0.000 ALPHA -1.01745 THOLE 0.916 +ATOM LP1 LPDNA1 -0.477 +ATOM C2 CD2R6C 0.173 ALPHA -1.6439 THOLE 1.309 +ATOM H2 HDR6C 0.087 +ATOM N3 ND2R6B 0.000 ALPHA -0.9911 THOLE 0.916 +ATOM LP2 LPDNA1 -0.463 +ATOM C4 CD2R6F 0.218 ALPHA -1.28945 THOLE 1.170 +ATOM C5 CD2R6F 0.051 ALPHA -1.26395 THOLE 1.271 +ATOM C6 CD2R6B 0.150 ALPHA -1.3498 THOLE 1.244 +ATOM H6 HDR6B 0.092 +ATOM N7 ND2R5B 0.000 ALPHA -1.02765 THOLE 1.065 +ATOM LP3 LPDNA1 -0.345 +ATOM C8 CD2R5B 0.085 ALPHA -1.3175 THOLE 1.122 +ATOM H8 HDR5B 0.140 +ATOM N9 ND2R5A -0.119 ALPHA -1.3991 THOLE 1.176 +ATOM H9 HDP1A 0.408 + +BOND N1 C2 C2 H2 C2 N3 N3 C4 +BOND C4 C5 C5 C6 C6 H6 C4 N9 +BOND N9 C8 N9 H9 C8 N7 C8 H8 +BOND N7 C5 C6 N1 +BOND N1 LP1 N3 LP2 N7 LP3 + +IMPR N9 C4 C8 H9 N9 C8 C4 H9 +IMPR C8 N9 N7 H8 C8 N7 N9 H8 +IMPR C5 C4 C6 N7 C5 C6 C4 N7 +IMPR C4 C5 N3 N9 C4 N3 C5 N9 + +LONEPAIR bisector LP1 N1 C6 C2 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP2 N3 C4 C2 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY N1 LP1 C6 C2 A11 1.2376 A22 0.6648 +ANISOTROPY N3 LP3 C4 C2 A11 1.2376 A22 0.6648 +LONEPAIR bisector LP3 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY N7 LP3 C5 C8 A11 0.808 A22 1.384 + +IC C6 C4 *C5 N9 1.4024 117.26 -180.00 36.89 2.1921 +IC C6 C5 C4 N3 1.4024 117.26 0.00 127.63 1.3432 +IC N3 C5 *C4 N7 1.3432 127.63 180.00 33.08 2.3210 +IC C5 C4 N3 C2 1.4024 127.63 -0.00 108.84 1.3779 +IC C4 N3 C2 N1 1.3432 108.84 -0.00 130.05 1.3571 +IC N1 N3 *C2 H2 1.3571 130.05 -180.00 114.85 1.0797 +IC C6 C5 N9 C8 1.4024 154.14 180.00 68.13 1.3846 +IC C8 C5 *N9 H9 1.3846 68.13 -180.00 161.86 0.9996 +IC N1 C5 *C6 H6 1.3507 118.75 180.00 120.74 1.0732 +IC N7 N9 *C8 H8 1.3508 114.15 -180.00 122.64 1.0892 + +PATCHING FIRST NONE LAST NONE + +RESI PUR1 0.000 ! purine 7H +! +! H6 +! | +! C6 H9 +! // \ | +! N1 C5--N9\ +! | || C8-H8 +! C2 C4--N7// +! / \\ / +! H2 N3 +! +GROUP +ATOM C5 CD2R6F -0.066 ALPHA -1.269 THOLE 1.271 +ATOM C4 CD2R6F 0.360 ALPHA -1.034 THOLE 1.170 +ATOM N3 ND2R6B 0.000 ALPHA -1.027 THOLE 0.916 +ATOM LP2 LPDNA1 -0.352 +ATOM C2 CD2R6C 0.123 ALPHA -1.500 THOLE 1.309 +ATOM N1 ND2R6B 0.000 ALPHA -0.999 THOLE 0.916 +ATOM LP1 LPDNA1 -0.338 +ATOM C6 CD2R6B 0.188 ALPHA -1.629 THOLE 1.244 +ATOM N9 ND2R5A -0.208 ALPHA -1.140 THOLE 1.176 +ATOM C8 CD2R5B -0.134 ALPHA -1.524 THOLE 1.122 +ATOM N7 ND2R5B 0.000 ALPHA -0.993 THOLE 1.065 +ATOM LP3 LPDNA1 -0.265 +ATOM H2 HDR6C 0.069 +ATOM H6 HDR6B 0.132 +ATOM H9 HDP1A 0.346 +ATOM H8 HDR5B 0.145 + +BOND N1 C2 C2 H2 C2 N3 N3 C4 +BOND C4 C5 C5 C6 C6 H6 C5 N9 +BOND N9 C8 N9 H9 C8 N7 C8 H8 +BOND N7 C4 C6 N1 +BOND N1 LP1 N3 LP2 N7 LP3 + +IMPR N9 C5 C8 H9 N9 C8 C5 H9 +IMPR C8 N9 N7 H8 C8 N7 N9 H8 +IMPR C5 C4 C6 N9 C5 C6 C4 N9 +IMPR C4 C5 N3 N7 C4 N3 C5 N7 + +LONEPAIR bisector LP1 N1 C6 C2 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP2 N3 C4 C2 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP3 N7 C4 C8 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY N1 LP1 C6 C2 A11 1.2376 A22 0.6648 +ANISOTROPY N3 LP3 C4 C2 A11 1.2376 A22 0.6648 +ANISOTROPY N7 LP3 C4 C8 A11 0.808 A22 1.384 + +IC C6 C4 *C5 N9 1.3952 120.97 180.00 107.18 1.3707 +IC C6 C5 C4 N3 1.3952 120.97 0.00 122.76 1.3555 +IC N3 C5 *C4 N7 1.3555 122.76 180.00 110.59 1.3797 +IC C5 C4 N3 C2 1.4089 122.76 0.00 111.18 1.3711 +IC C4 N3 C2 N1 1.3555 111.18 0.00 130.13 1.3567 +IC N1 N3 *C2 H2 1.3567 130.13 180.00 114.73 1.0796 +IC C6 C5 N9 C8 1.3952 131.84 180.00 104.85 1.3833 +IC C8 C5 *N9 H9 1.3833 104.85 180.00 127.90 1.0052 +IC N1 C5 *C6 H6 1.3451 117.65 180.00 122.26 1.0729 +IC N7 N9 *C8 H8 1.3540 114.25 180.00 122.89 1.0899 + +PATCHING FIRST NONE LAST NONE + +RESI 4MIM 0.000 ! 4-methylimidazole +! HD1 HE1 +! | / +! HB1 ND1--CE1 +! | / || +! HB2-CB-CG || +! | \\ || +! HB3 CD2--NE2 +! | +! HD2 +! +GROUP +ATOM CG CD2R5A -0.252 ALPHA -1.272 THOLE 1.190 +ATOM CB CD33A -0.061 ALPHA -1.739 THOLE 0.399 +ATOM HB1 HDA3A 0.078 +ATOM HB2 HDA3A 0.078 +ATOM HB3 HDA3A 0.078 +ATOM ND1 ND2R5A -0.040 ALPHA -1.522 THOLE 1.114 +ATOM HD1 HDP1A 0.256 +ATOM CD2 CD2R5A 0.141 ALPHA -1.515 THOLE 1.190 +ATOM HD2 HDR5A 0.041 +ATOM CE1 CD2R5B 0.064 ALPHA -1.493 THOLE 1.297 +ATOM HE1 HDR5B -0.018 +ATOM NE2 ND2R5B 0.000 ALPHA -1.146 THOLE 0.816 +ATOM LP1 LPD -0.365 + +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG CB +BOND NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 +BOND CB HB1 CB HB2 CB HB3 +BOND NE2 LP1 + +IMPH ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 + +LONEPAIR bisector LP1 NE2 CE1 CD2 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY NE2 LP1 CE1 CD2 A11 0.808 A22 1.384 + +IC CD2 ND1 *CG CB 1.3651 105.36 180.00 123.93 1.5057 +IC ND1 CG CB HB1 1.3802 123.93 180.00 111.01 1.1120 +IC HB1 CG *CB HB2 1.1120 111.01 120.05 110.14 1.1113 +IC HB1 CG *CB HB3 1.1120 111.01 -120.05 110.14 1.1113 +IC CB CG ND1 CE1 1.5057 123.93 180.00 107.01 1.3564 +IC CE1 CG *ND1 HD1 1.3564 107.01 180.00 126.62 1.0002 +IC CB CG CD2 NE2 1.5057 130.71 180.00 110.73 1.3846 +IC NE2 CG *CD2 HD2 1.3846 110.73 180.00 129.85 1.0817 +IC NE2 ND1 *CE1 HE1 1.3179 112.29 180.00 122.48 1.0888 + +PATCHING FIRST NONE LAST NONE + +RESI MIND 0.000 ! Methylindole +! +! HB3 HE3 +! | | +! HB1-CB-HB2 CE3 +! \ / \\ +! CG-----CD2 CZ3-HZ3 +! || || | +! CD1 CE2 CH2-HH2 +! / \ / \ // +! HD1 NE1 CZ2 +! | | +! HE1 HZ2 +! +GROUP +ATOM CG CD2R5C -0.098 ALPHA -1.269 THOLE 1.346 +ATOM CB CD33A -0.091 ALPHA -2.044 THOLE 1.346 +ATOM HB1 HDA3A 0.045 +ATOM HB2 HDA3A 0.045 +ATOM HB3 HDA3A 0.045 +ATOM CD2 CD2R6D -0.099 ALPHA -1.266 THOLE 1.344 +ATOM CD1 CD2R5A 0.059 ALPHA -1.612 THOLE 1.265 +ATOM HD1 HDR5A 0.083 +ATOM NE1 ND2R5A -0.276 ALPHA -1.380 THOLE 1.146 +ATOM HE1 HDP1A 0.294 +ATOM CE2 CD2R6D 0.053 ALPHA -1.267 THOLE 1.009 +ATOM CE3 CD2R6A -0.034 ALPHA -1.622 THOLE 1.300 +ATOM HE3 HDR6A 0.094 +ATOM CZ2 CD2R6A -0.115 ALPHA -1.611 THOLE 1.300 +ATOM HZ2 HDR6A 0.110 +ATOM CZ3 CD2R6A -0.154 ALPHA -1.617 THOLE 1.300 +ATOM HZ3 HDR6A 0.087 +ATOM CH2 CD2R6A -0.188 ALPHA -1.621 THOLE 1.300 +ATOM HH2 HDR6A 0.140 + +BOND CG CB CD2 CG NE1 CD1 +BOND CB HB1 CB HB2 CB HB3 +BOND CZ2 CE2 +BOND CZ3 CH2 CD2 CE3 NE1 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 +BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 +BOND CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 + +IMPH HZ2 CH2 CE2 CZ2 HZ2 CE2 CH2 CZ2 +IMPH HE3 CD2 CZ3 CE3 HE3 CZ3 CD2 CE3 +IMPH HD1 CG NE1 CD1 HD1 NE1 CG CD1 +IMPH HE1 CE2 CD1 NE1 HE1 CD1 CE2 NE1 + +IC CG CD1 NE1 CE2 1.3987 107.97 0.00 108.47 1.4312 +IC CD1 CG CD2 CE2 1.3987 109.62 0.00 105.10 1.4084 +IC CD2 CG CD1 NE1 1.4439 109.62 0.00 107.97 1.3792 +IC CE2 CG *CD2 CE3 1.4084 105.10 180.00 129.43 1.3853 +IC CE2 CD2 CE3 CZ3 1.4084 125.47 0.00 114.38 1.4053 +IC CD2 CE3 CZ3 CH2 1.3853 114.38 0.00 121.97 1.4121 +IC CE3 CZ3 CH2 CZ2 1.4053 121.97 0.00 121.76 1.4101 +IC CZ3 CD2 *CE3 HE3 1.4053 114.38 180.00 123.59 1.0769 +IC CH2 CE3 *CZ3 HZ3 1.4121 121.97 180.00 118.92 1.0805 +IC CZ2 CZ3 *CH2 HH2 1.4101 121.76 180.00 118.96 1.0806 +IC CE2 CH2 *CZ2 HZ2 1.3932 116.99 180.00 120.75 1.0770 +IC CD1 CE2 *NE1 HE1 1.3792 108.47 180.00 124.81 0.9980 +IC CG NE1 *CD1 HD1 1.3987 107.97 180.00 125.93 1.0785 +IC CD1 CD2 *CG CB 1.3987 109.62 180.00 124.76 1.5077 +IC CD2 CG CB HB1 1.4439 124.76 180.00 110.11 1.1115 +IC HB1 CG *CB HB2 1.1115 110.11 -120.25 108.65 1.1107 +IC HB1 CG *CB HB3 1.1115 110.11 120.25 108.65 1.1107 +IC NE1 CG *CD1 HD1 1.3792 107.97 180.00 126.10 1.0785 +IC CE2 CD1 *NE1 HE1 1.4312 108.47 180.00 126.71 0.9980 +IC CG CD2 CE3 CZ3 1.4439 129.43 180.00 114.38 1.4053 +IC CD2 NE1 *CE2 CZ2 1.4084 108.84 180.00 131.73 1.3932 +IC NE1 CE2 CZ2 CH2 1.4312 131.73 180.00 116.99 1.4101 + +PATCHING FIRST NONE LAST NONE + +RESI PRLD 0.000 ! Pyrrolidine, PEML ** FULL POLARIZABILITY ** +! +! HN HD1 HD2 +! \ \ / +! N---CD HG1 +! | \ / +! HA1 | CG +! \ | / \ +! CA--CB HG2 +! / / \ +! HA2 HB1 HB2 +! +! +GROUP +ATOM CA CD32C 0.201 ALPHA -2.010 THOLE 0.365 +ATOM HA1 HDA2A 0.037 +ATOM HA2 HDA2A 0.037 +ATOM CB CD32A -0.103 ALPHA -1.651 THOLE 1.365 +ATOM HB1 HDA2A 0.016 +ATOM HB2 HDA2A 0.016 +ATOM CG CD32A -0.102 ALPHA -1.650 THOLE 1.365 +ATOM HG1 HDA2A 0.016 +ATOM HG2 HDA2A 0.016 +ATOM CD CD32C 0.203 ALPHA -2.008 THOLE 0.365 +ATOM HD1 HDA2A 0.036 +ATOM HD2 HDA2A 0.036 +ATOM N ND3A3 -0.782 ALPHA -1.505 THOLE 0.202 +ATOM HN HDP1A 0.373 + +BOND N CA CA HA1 CA HA2 CA CB +BOND CB HB1 CB HB2 CB CG +BOND CG HG1 CG HG2 CG CD +BOND CD HD1 CD HD2 CD N N HN + +patc firs none last none + +!!alcohols +RESI MEOH 0.000 ! methanol +! +! H1A +! \ +! H1B--C1--O1 +! / \ +! H1C HO1 +! +GROUP +ATOM C1 CD33B -0.140 ALPHA -1.000 THOLE 1.3 +ATOM O1 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO1 HDP1A 0.360 +ATOM H1A HDA3B 0.080 +ATOM H1B HDA3B 0.080 +ATOM H1C HDA3B 0.080 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 + +BOND C1 O1 O1 HO1 +BOND C1 H1A C1 H1B C1 H1C +BOND O1 LP1A O1 LP1B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +IC HO1 O1 C1 H1A 0.9724 107.62 -180.00 109.46 1.1124 +IC HO1 H1A *C1 O1 1.9573 137.73 0.00 109.46 1.4296 +IC H1A O1 *C1 H1B 1.1124 109.46 119.63 110.08 1.1122 +IC H1A O1 *C1 H1C 1.1124 109.46 -119.63 110.08 1.1122 + +RESI ETOH 0.000 ! ethanol +! +! H2A H1A H1B +! \ \ / +! H2B--C2--C1 +! / \ +! H2C O1--HO1 +! +GROUP +ATOM C1 CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM O1 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO1 HDP1A 0.360 +ATOM H1A HDA2A 0.080 +ATOM H1B HDA2A 0.080 +ATOM C2 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H2A HDA3A 0.060 +ATOM H2B HDA3A 0.060 +ATOM H2C HDA3A 0.060 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 + +BOND C1 C2 C1 O1 C1 H1A C1 H1B O1 HO1 +BOND C2 H2A C2 H2B C2 H2C +BOND O1 LP1A O1 LP1B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +IC HO1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H1A 0.0000 0.00 120.00 0.00 0.0000 +IC C2 O1 *C1 H1B 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C2 H2A 0.0000 0.00 180.00 0.00 0.0000 +IC H2A C1 *C2 H2B 0.0000 0.00 120.00 0.00 0.0000 +IC H2A C1 *C2 H2C 0.0000 0.00 -120.00 0.00 0.0000 + +RESI PRO1 0.000 ! 1-propanol +! +! H3A H2A H1A H1B +! \ \ \ / +! H3B--C3--C2--C1 +! / / \ +! H3C H2B O1--HO1 +! +GROUP +ATOM C1 CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM O1 OD31B 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO1 HDP1A 0.360 +ATOM H1A HDA2A 0.080 +ATOM H1B HDA2A 0.080 +GROUP +ATOM C2 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H2A HDA2A 0.060 +ATOM H2B HDA2A 0.060 +GROUP +ATOM C3 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H3A HDA3A 0.060 +ATOM H3B HDA3A 0.060 +ATOM H3C HDA3A 0.060 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 + +BOND C1 C2 C1 O1 C1 H1A C1 H1B O1 HO1 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 H3C +BOND O1 LP1A O1 LP1B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +IC HO1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC O1 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H1A 0.0000 0.00 120.00 0.00 0.0000 +IC C2 O1 *C1 H1B 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H2A 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H2B 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 C3 H3A 0.0000 0.00 180.00 0.00 0.0000 +IC H3A C2 *C3 H3B 0.0000 0.00 120.00 0.00 0.0000 +IC H3A C2 *C3 H3C 0.0000 0.00 -120.00 0.00 0.0000 + +RESI BUO1 0.000 ! 1-butanol +! +! H4A H3A H2A H1A H1B +! \ \ \ \ / +! H4B--C4--C3--C2--C1 +! / / / \ +! H4C H3B H2B O1--HO1 +! +GROUP +ATOM C1 CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM O1 OD31B 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO1 HDP1A 0.360 +ATOM H1A HDA2A 0.080 +ATOM H1B HDA2A 0.080 +GROUP +ATOM C2 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H2A HDA2A 0.060 +ATOM H2B HDA2A 0.060 +GROUP +ATOM C3 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H3A HDA2A 0.060 +ATOM H3B HDA2A 0.060 +GROUP +ATOM C4 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H4A HDA3A 0.060 +ATOM H4B HDA3A 0.060 +ATOM H4C HDA3A 0.060 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 + +BOND C1 C2 C1 O1 C1 H1A C1 H1B O1 HO1 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 H4C +BOND O1 LP1A O1 LP1B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +IC HO1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC O1 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H1A 0.0000 0.00 120.00 0.00 0.0000 +IC C2 O1 *C1 H1B 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H2A 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H2B 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H3A 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C4 H4A 0.0000 0.00 180.00 0.00 0.0000 +IC H4A C3 *C4 H4B 0.0000 0.00 120.00 0.00 0.0000 +IC H4A C3 *C4 H4C 0.0000 0.00 -120.00 0.00 0.0000 + +RESI PRO2 0.000 ! 2-propanol +! +! H1B H1C H3C H3B +! \ / \ / +! H1A--C1 C3--H3A +! \ / +! C2 +! / \ +! O2 H2A +! | +! HO2 +! +GROUP +ATOM C2 CD31A 0.000 ALPHA -1.000 THOLE 1.3 +ATOM O2 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO2 HDP1A 0.360 +ATOM H2A HDA1A 0.100 +GROUP +ATOM C1 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H1A HDA3A 0.060 +ATOM H1B HDA3A 0.060 +ATOM H1C HDA3A 0.060 +GROUP +ATOM C3 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H3A HDA3A 0.060 +ATOM H3B HDA3A 0.060 +ATOM H3C HDA3A 0.060 +ATOM LP2A LPD -0.230 +ATOM LP2B LPD -0.230 + +BOND C1 C2 C2 C3 C2 O2 C2 H2A O2 HO2 +BOND C1 H1A C1 H1B C1 H1C C3 H3A C3 H3B C3 H3C +BOND O2 LP2A O2 LP2B + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +IC HO2 O2 C2 H2A 0.0000 0.00 0.00 0.00 0.0000 +IC H2A O2 *C2 C1 0.0000 0.00 120.00 0.00 0.0000 +IC H2A O2 *C2 C3 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 C2 C1 H1A 0.0000 0.00 180.00 0.00 0.0000 +IC H1A C2 *C1 H1B 0.0000 0.00 120.00 0.00 0.0000 +IC H1A C2 *C1 H1C 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 C2 C3 H3A 0.0000 0.00 180.00 0.00 0.0000 +IC H3A C2 *C3 H3B 0.0000 0.00 120.00 0.00 0.0000 +IC H3A C2 *C3 H3C 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI BUO2 0.000 ! 2-butanol +! +! H1B H1C H3A H3B H4A +! \ / \ / / +! H1A--C1 C3---C4--H4B +! \ / \ +! C2 H4C +! / \ +! O2 H2A +! | +! HO2 +! +GROUP +ATOM C2 CD31A 0.000 ALPHA -1.000 THOLE 1.3 +ATOM O2 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO2 HDP1A 0.360 +ATOM H2A HDA1A 0.100 +GROUP +ATOM C1 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H1A HDA3A 0.060 +ATOM H1B HDA3A 0.060 +ATOM H1C HDA3A 0.060 +GROUP +ATOM C3 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H3A HDA2A 0.060 +ATOM H3B HDA2A 0.060 +GROUP +ATOM C4 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H4A HDA3A 0.060 +ATOM H4B HDA3A 0.060 +ATOM H4C HDA3A 0.060 +ATOM LP2A LPD -0.230 +ATOM LP2B LPD -0.230 + +BOND C1 C2 C2 C3 C2 O2 C2 H2A O2 HO2 +BOND C1 H1A C1 H1B C1 H1C C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 H4C +BOND O2 LP2A O2 LP2B + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +IC HO2 O2 C2 H2A 0.0000 0.00 0.00 0.00 0.0000 +IC H2A O2 *C2 C1 0.0000 0.00 120.00 0.00 0.0000 +IC H2A O2 *C2 C3 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC O2 C2 C1 H1A 0.0000 0.00 180.00 0.00 0.0000 +IC H1A C2 *C1 H1B 0.0000 0.00 120.00 0.00 0.0000 +IC H1A C2 *C1 H1C 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H3A 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C4 H4A 0.0000 0.00 180.00 0.00 0.0000 +IC H4A C3 *C4 H4B 0.0000 0.00 120.00 0.00 0.0000 +IC H4A C3 *C4 H4C 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +Resi PEO1 0.000 ! pentan-1-ol CMB 11/10 from JCTC, 6, 1181 +! +!HO1-O1 H2A H3A H4A H5A +! \ | | | / +! H1A-C1--C2--C3--C4--C5-H5B +! / | | | \ +! H1B H2B H3B H4B H5C +! +GROUP +ATOM C1 CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM O1 OD31B 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO1 HDP1A 0.360 +ATOM H1A HDA2A 0.080 +ATOM H1B HDA2A 0.080 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 +GROUP +ATOM C2 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H2A HDA2A 0.060 +ATOM H2B HDA2A 0.060 +GROUP +ATOM C3 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H3A HDA2A 0.060 +ATOM H3B HDA2A 0.060 +GROUP +ATOM C4 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H4A HDA2A 0.060 +ATOM H4B HDA2A 0.060 +GROUP +ATOM C5 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H5A HDA3A 0.060 +ATOM H5B HDA3A 0.060 +ATOM H5C HDA3A 0.060 + +BOND C1 C2 C1 O1 C1 H1A C1 H1B O1 HO1 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 H5C +BOND O1 LP1A O1 LP1B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +IC HO1 O1 C1 C2 0.9706 107.33 -179.95 110.76 1.5347 +IC O1 C1 C2 C3 1.4278 110.76 -179.64 112.90 1.5375 +IC C1 C2 C3 C4 1.5347 112.90 176.65 113.83 1.5378 +IC C2 C3 C4 C5 1.5375 113.83 64.67 114.72 1.5313 +IC O1 C2 *C1 H1A 1.4278 110.76 121.80 108.23 1.1140 +IC O1 C2 *C1 H1B 1.4278 110.76 -121.81 108.17 1.1141 +IC C2 C1 O1 HO1 1.5347 110.76 -179.95 107.33 0.9706 +IC C3 C1 *C2 H2A 1.5375 112.90 -121.60 108.78 1.1125 +IC H2A C1 *C2 H2B 1.1125 108.78 -117.43 108.94 1.1129 +IC C1 C2 C3 C4 1.5347 112.90 176.65 113.83 1.5378 +IC C4 C2 *C3 H3A 1.5378 113.83 -120.69 108.47 1.1129 +IC H3A C2 *C3 H3B 1.1129 108.47 -117.23 109.19 1.1127 +IC C2 C3 C4 C5 1.5375 113.83 64.67 114.72 1.5313 +IC C5 C3 *C4 H4A 1.5313 114.72 121.18 108.10 1.1138 +IC H4A C3 *C4 H4B 1.1138 108.10 116.33 108.76 1.1129 +IC C3 C4 C5 H5A 1.5378 114.72 176.54 110.86 1.1108 +IC H5A C4 *C5 H5B 1.1108 110.86 119.84 111.39 1.1104 +IC H5A C4 *C5 H5C 1.1108 110.86 -119.86 110.96 1.1110 +patc firs none last none + +Resi HXO1 0.000 ! hexan-1-ol CMB 11/10 from JCTC, 6, 1181. +! +!HO1-O1 H2A H3A H4A H5A H6A +! \ | | | | / +! H1A-C1--C2--C3--C4--C5--C6-H6B +! / | | | | \ +! H1B H2B H3B H4B H5B H6B +! +GROUP +ATOM C1 CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM O1 OD31B 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO1 HDP1A 0.360 +ATOM H1A HDA2A 0.080 +ATOM H1B HDA2A 0.080 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 +GROUP +ATOM C2 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H2A HDA2A 0.060 +ATOM H2B HDA2A 0.060 +GROUP +ATOM C3 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H3A HDA2A 0.060 +ATOM H3B HDA2A 0.060 +GROUP +ATOM C4 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H4A HDA2A 0.060 +ATOM H4B HDA2A 0.060 +GROUP +ATOM C5 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H5A HDA2A 0.060 +ATOM H5B HDA2A 0.060 +GROUP +ATOM C6 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H6A HDA3A 0.060 +ATOM H6B HDA3A 0.060 +ATOM H6C HDA3A 0.060 + +BOND C1 C2 C1 O1 C1 H1A C1 H1B O1 HO1 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C6 +BOND C6 H6A C6 H6B C6 H6C +BOND O1 LP1A O1 LP1B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +IC HO1 O1 C1 C2 0.9705 107.34 -180.00 110.77 1.5352 +IC O1 C1 C2 C3 1.4277 110.77 -179.72 112.88 1.5372 +IC C1 C2 C3 C4 1.5352 112.88 175.65 114.03 1.5392 +IC C2 C3 C4 C5 1.5372 114.03 61.90 115.15 1.5390 +IC C3 C4 C5 C6 1.5392 115.15 60.72 114.85 1.5307 +IC O1 C2 *C1 H1A 1.4277 110.77 121.81 108.21 1.1141 +IC O1 C2 *C1 H1B 1.4277 110.77 -121.82 108.16 1.1139 +IC C2 C1 O1 HO1 1.5352 110.77 -180.00 107.34 0.9705 +IC C3 C1 *C2 H2A 1.5372 112.88 -121.57 108.71 1.1125 +IC H2A C1 *C2 H2B 1.1125 108.71 -117.41 108.90 1.1130 +IC C1 C2 C3 C4 1.5352 112.88 175.65 114.03 1.5392 +IC C4 C2 *C3 H3A 1.5392 114.03 -120.34 108.33 1.1137 +IC H3A C2 *C3 H3B 1.1137 108.33 -116.74 109.21 1.1117 +IC C2 C3 C4 C5 1.5372 114.03 61.90 115.15 1.5390 +IC C5 C3 *C4 H4A 1.5390 115.15 121.55 108.46 1.1135 +IC H4A C3 *C4 H4B 1.1135 108.46 116.56 108.52 1.1131 +IC C3 C4 C5 C6 1.5392 115.15 60.72 114.85 1.5307 +IC C6 C4 *C5 H5A 1.5307 114.85 121.04 107.86 1.1143 +IC H5A C4 *C5 H5B 1.1143 107.86 115.98 109.28 1.1126 +IC C4 C5 C6 H6A 1.5390 114.85 56.14 110.99 1.1108 +IC H6A C5 *C6 H6B 1.1108 110.99 119.88 110.85 1.1111 +IC H6A C5 *C6 H6C 1.1108 110.99 -120.36 111.33 1.1105 +patc firs none last none + +Resi PEO2 0.000 ! pentan-2-ol CMB 11/10 from JCTC, 6, 1181. +! +! H1A H2A H3A H4A H5A +! \ | | | / +! H1B-C1--C2--C3--C4--C5-H5B +! / | | | \ +! H1C O2 H3B H4B H5C +! / +! HO2 +GROUP +ATOM C2 CD31A 0.000 ALPHA -1.000 THOLE 1.3 +ATOM O2 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO2 HDP1A 0.360 +ATOM H2A HDA1A 0.100 +ATOM LP2A LPD -0.230 +ATOM LP2B LPD -0.230 +GROUP +ATOM C1 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H1A HDA3A 0.060 +ATOM H1B HDA3A 0.060 +ATOM H1C HDA3A 0.060 +GROUP +ATOM C3 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H3A HDA2A 0.060 +ATOM H3B HDA2A 0.060 +GROUP +ATOM C4 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H4A HDA2A 0.060 +ATOM H4B HDA2A 0.060 +GROUP +ATOM C5 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H5A HDA3A 0.060 +ATOM H5B HDA3A 0.060 +ATOM H5C HDA3A 0.060 + +BOND C1 C2 C2 C3 C2 O2 C2 H2A O2 HO2 +BOND C1 H1A C1 H1B C1 H1C C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 H5C +BOND O2 LP2A O2 LP2B + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 + +IC HO2 O2 C2 H2A 0.9694 106.75 175.76 103.78 1.1153 +IC H2A O2 *C2 C1 1.1153 103.78 116.25 109.87 1.5336 +IC H2A O2 *C2 C3 1.1153 103.78 -117.63 112.70 1.5431 +IC O2 C2 C3 C4 1.4338 112.70 68.89 115.42 1.5411 +IC O2 C2 C1 H1A 1.4338 109.87 66.13 110.56 1.1106 +IC C1 C2 C3 C4 1.5336 112.35 -166.34 115.42 1.5411 +IC C2 C3 C4 C5 1.5431 115.42 -74.50 115.64 1.5312 +IC H1A C1 C2 C3 1.1106 110.56 -60.19 112.35 1.5431 +IC H1A C2 *C1 H1B 1.1106 110.56 -120.20 110.47 1.1114 +IC H1A C2 *C1 H1C 1.1106 110.56 120.01 110.33 1.1106 +IC C1 C3 *C2 H2A 1.5336 112.35 120.64 108.88 1.1153 +IC C2 C4 *C3 H3A 1.5431 115.42 -119.02 107.11 1.1143 +IC C2 C4 *C3 H3B 1.5431 115.42 124.77 109.70 1.1108 +IC C3 C5 *C4 H4A 1.5411 115.64 -123.39 109.40 1.1125 +IC C3 C5 *C4 H4B 1.5411 115.64 120.30 107.80 1.1146 +IC O2 C3 *C2 C1 1.4338 112.70 124.77 112.35 1.5336 +IC C1 C3 *C2 H2A 1.5336 112.35 120.64 108.88 1.1153 +IC C3 C2 O2 HO2 1.5431 112.70 58.13 106.75 0.9694 +IC C3 C2 C1 H1A 1.5431 112.35 -60.19 110.56 1.1106 +IC H1A C2 *C1 H1B 1.1106 110.56 -120.20 110.47 1.1114 +IC H1A C2 *C1 H1C 1.1106 110.56 120.01 110.33 1.1106 +IC C4 C2 *C3 H3A 1.5411 115.42 119.08 107.01 1.1143 +IC H3A C2 *C3 H3B 1.1143 107.01 116.25 109.89 1.1108 +IC C2 C3 C4 C5 1.5431 115.42 -74.50 115.64 1.5312 +IC C5 C3 *C4 H4A 1.5312 115.64 123.64 108.91 1.1125 +IC H4A C3 *C4 H4B 1.1125 108.91 115.90 107.50 1.1146 +IC C3 C4 C5 H5A 1.5411 115.64 -54.53 111.05 1.1105 +IC H5A C4 *C5 H5B 1.1105 111.05 -119.99 110.86 1.1107 +IC H5A C4 *C5 H5C 1.1105 111.05 120.40 111.33 1.1104 +patc firs none last none + +RESI B3MO1 0.000 ! 3-methylbutan-1-ol CMB 11/10 JCTC, 6, 1181. +! +! H4A H3A H2A H1A H1B +! \ \ \ \ / +! H4B--C4--C3--C2--C1 +! / | \ \ +! H4C C5 H1A O1--HO1 +! / | \ +! H5A H5B H5C +GROUP +ATOM C1 CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM O1 OD31B 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO1 HDP1A 0.360 +ATOM H1A HDA2A 0.080 +ATOM H1B HDA2A 0.080 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 +GROUP +ATOM C2 CD32A -0.120 ALPHA -1.200 THOLE 1.3 +ATOM H2A HDA2A 0.060 +ATOM H2B HDA2A 0.060 +GROUP +ATOM C3 CD31A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM H3A HDA1A 0.060 +GROUP +ATOM C4 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H4A HDA3A 0.060 +ATOM H4B HDA3A 0.060 +ATOM H4C HDA3A 0.060 +GROUP +ATOM C5 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM H5A HDA3A 0.060 +ATOM H5B HDA3A 0.060 +ATOM H5C HDA3A 0.060 + +BOND C1 C2 C1 O1 C1 H1A C1 H1B O1 HO1 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 C5 C3 C4 +BOND C4 H4A C4 H4B C4 H4C +BOND C5 H5A C5 H5B C5 H5C +BOND O1 LP1A O1 LP1B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +IC HO1 O1 C1 C2 0.9707 107.32 -179.78 110.66 1.5361 +IC O1 C1 C2 C3 1.4279 110.66 -175.81 114.54 1.5466 +IC C1 C2 C3 C4 1.5361 114.54 177.13 111.06 1.5392 +IC C2 O1 *C1 H1A 1.5361 110.66 -119.91 110.85 1.1141 +IC C2 O1 *C1 H1B 1.5361 110.66 120.68 110.56 1.1128 +IC C3 C1 *C2 H2A 1.5466 114.54 -121.88 108.95 1.1123 +IC C3 C1 *C2 H2B 1.5466 114.54 120.96 108.63 1.1131 +IC C4 C2 *C3 H3A 1.5392 111.06 -117.56 107.63 1.1155 +IC C2 C3 C4 H4A 1.5466 111.06 -177.36 110.44 1.1103 +IC H4A C3 *C4 H4B 1.1103 110.44 120.02 110.35 1.1107 +IC H4A C3 *C4 H4C 1.1103 110.44 -120.05 110.28 1.1107 +IC O1 C2 *C1 H1A 1.4279 110.66 121.55 108.09 1.1141 +IC O1 C2 *C1 H1B 1.4279 110.66 -121.69 108.85 1.1128 +IC C2 C1 O1 HO1 1.5361 110.66 -179.78 107.32 0.9707 +IC C3 C1 *C2 H2A 1.5466 114.54 -121.88 108.95 1.1123 +IC H2A C1 *C2 H2B 1.1123 108.95 -117.16 108.63 1.1131 +IC C1 C2 C3 C5 1.5361 114.54 -59.45 113.28 1.5408 +IC C5 C2 *C3 C4 1.5408 113.28 -123.42 111.06 1.5392 +IC C5 C2 *C3 H3A 1.5408 113.28 119.02 107.63 1.1155 +IC C2 C3 C4 H4A 1.5466 111.06 -177.36 110.44 1.1103 +IC H4A C3 *C4 H4B 1.1103 110.44 120.02 110.35 1.1107 +IC H4A C3 *C4 H4C 1.1103 110.44 -120.05 110.28 1.1107 +IC C2 C3 C5 H5A 1.5466 113.28 -177.61 110.14 1.1105 +IC H5A C3 *C5 H5B 1.1105 110.14 -119.74 111.08 1.1094 +IC H5A C3 *C5 H5C 1.1105 110.14 119.65 110.20 1.1106 +PATCH FIRST NONE LAST NONE + +RESI CPO1 0.000 ! cyclopentanol CMB 11/10 from JCTC, 6, 1181. +! +! H3A H4A +! | | +! H3B-C3---C4-H4B +! | | +! H2A-C2 C5-H5A +! /\ /\ +! H2B \ / H5B +! C1 +! / \ +! H1A O1-HO1 +! +GROUP +ATOM C1 CD315A 0.000 ALPHA -1.000 THOLE 1.3 +ATOM H1A HDA1R5 0.100 +ATOM O1 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO1 HDP1A 0.360 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 +GROUP +ATOM C2 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H2A HDA2R5 0.0265 +ATOM H2B HDA2R5 0.0265 +GROUP +ATOM C3 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H3A HDA2R5 0.0265 +ATOM H3B HDA2R5 0.0265 +GROUP +ATOM C4 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H4A HDA2R5 0.0265 +ATOM H4B HDA2R5 0.0265 +GROUP +ATOM C5 CD325A -0.0530 ALPHA -1.395 THOLE 1.3 +ATOM H5A HDA2R5 0.0265 +ATOM H5B HDA2R5 0.0265 + +BOND C1 H1A C1 O1 C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C1 +BOND O1 HO1 +BOND O1 LP1A O1 LP1B + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 + +IC C1 C2 C3 C4 1.5474 106.19 23.34 105.70 1.5545 +IC H1A C1 C2 C3 1.1085 108.39 76.95 106.19 1.5487 +IC C5 C2 *C1 H1A 1.5470 101.31 113.94 108.39 1.1085 +IC C3 C1 *C2 H2A 1.5487 106.19 -123.14 112.39 1.1113 +IC H2A C1 *C2 H2B 1.1113 112.39 -118.75 109.83 1.1158 +IC C4 C2 *C3 H3A 1.5545 105.70 -118.92 110.49 1.1141 +IC H3A C2 *C3 H3B 1.1141 110.49 -119.00 111.62 1.1117 +IC C5 C3 *C4 H4A 1.5487 105.71 -119.27 109.96 1.1143 +IC H4A C3 *C4 H4B 1.1143 109.96 -118.92 112.07 1.1119 +IC C4 C1 *C5 H5A 1.5487 106.19 123.13 112.39 1.1117 +IC C4 C1 *C5 H5B 1.5487 106.19 -118.13 109.86 1.1157 +IC C5 C2 *C1 O1 1.5470 101.31 -123.03 114.08 1.4442 +IC O1 C2 *C1 H1A 1.4442 114.08 -123.02 108.39 1.1085 +IC C2 C1 O1 HO1 1.5474 114.08 57.91 107.26 0.9701 +IC C3 C1 *C2 H2A 1.5487 106.19 -123.14 112.39 1.1113 +IC H2A C1 *C2 H2B 1.1113 112.39 -118.75 109.83 1.1158 +IC C1 C2 C3 C4 1.5474 106.19 23.34 105.70 1.5545 +IC C4 C2 *C3 H3A 1.5545 105.70 -118.92 110.49 1.1141 +IC H3A C2 *C3 H3B 1.1141 110.49 -119.00 111.62 1.1117 +IC C5 C3 *C4 H4A 1.5487 105.71 -119.27 109.96 1.1143 +IC H4A C3 *C4 H4B 1.1143 109.96 -118.92 112.07 1.1119 +IC C4 C1 *C5 H5A 1.5487 106.19 123.13 112.39 1.1117 +IC C4 C1 *C5 H5B 1.5487 106.19 -118.13 109.86 1.1157 +patc firs none last none + +!molecular ions +RESI NH4 1.000 ! ammonium HN3 +GROUP ! | +ATOM N ND3P3A -0.692 ALPHA -1.400 ! | +ATOM HN1 HDP1B 0.423 ! HN2------N------HN4 (+) +ATOM HN2 HDP1B 0.423 ! | +ATOM HN3 HDP1B 0.423 ! | +ATOM HN4 HDP1B 0.423 ! HN1 + +BOND N HN1 N HN2 N HN3 N HN4 + +RESI NC1 1.000 ! methylammonium +GROUP ! HN3 +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 ! | +ATOM C1 CD33A -0.100 ALPHA -1.656 THOLE 0.895 ! | +ATOM HN2 HDP1B 0.340 ! HN2------N------HN4 (+) +ATOM HN3 HDP1B 0.340 ! | +ATOM HN4 HDP1B 0.340 ! | +ATOM H11 HDA3C 0.143 ! H11-C1-H13 +ATOM H12 HDA3C 0.143 ! | +ATOM H13 HDA3C 0.143 ! H12 + +BOND N C1 N HN2 N HN3 N HN4 +BOND C1 H11 C1 H12 C1 H13 + +RESI NC2 1.000 ! dimethylammonium +GROUP ! +ATOM N ND3P2A -0.070 ALPHA -1.479 THOLE 0.111 ! HN3 +ATOM C1 CD33A -0.043 ALPHA -1.578 THOLE 1.429 ! H23 | +ATOM C2 CD33A -0.043 ALPHA -1.578 THOLE 1.429 ! | | +ATOM HN3 HDP1B 0.266 ! H22-C2------N------HN4 (+) +ATOM HN4 HDP1B 0.266 ! | | +ATOM H11 HDA3C 0.104 ! H21 | +ATOM H12 HDA3C 0.104 ! H11-C1-H13 +ATOM H13 HDA3C 0.104 ! | +ATOM H21 HDA3C 0.104 ! H12 +ATOM H22 HDA3C 0.104 +ATOM H23 HDA3C 0.104 + +BOND N C1 N C2 N HN3 N HN4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 + +RESI NC3 1.000 ! trimethylammonium +GROUP ! H32 +ATOM N ND3P2A 0.219 ALPHA -0.661 THOLE 0.803 ! | +ATOM C1 CD33A -0.107 ALPHA -1.527 THOLE 2.113 ! H31-C3-H33 +ATOM C2 CD33A -0.107 ALPHA -1.527 THOLE 2.113 ! H23 | +ATOM C3 CD33A -0.107 ALPHA -1.527 THOLE 2.113 ! | | +ATOM HN4 HDP1B 0.202 ! H22-C2------N------HN4 (+) +ATOM H11 HDA3C 0.100 ! | | +ATOM H12 HDA3C 0.100 ! H21 | +ATOM H13 HDA3C 0.100 ! H11-C1-H13 +ATOM H21 HDA3C 0.100 ! | +ATOM H22 HDA3C 0.100 ! H12 +ATOM H23 HDA3C 0.100 +ATOM H31 HDA3C 0.100 +ATOM H32 HDA3C 0.100 +ATOM H33 HDA3C 0.100 + +BOND N C1 N C2 N C3 N HN4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 + +RESI NC4 1.000 ! tetramethylammonium +GROUP ! +ATOM N ND3P2A 0.688 ALPHA -0.829 THOLE 0.793 ! H32 +ATOM C1 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | +ATOM C2 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! H31-C3-H33 +ATOM C3 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! H23 | H41 +ATOM C4 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | | | +ATOM H11 HDA3C 0.122 ! H22-C2------N------C4-H42 (+) +ATOM H12 HDA3C 0.122 ! | | | +ATOM H13 HDA3C 0.122 ! H21 | H43 +ATOM H21 HDA3C 0.122 ! H11-C1-H13 +ATOM H22 HDA3C 0.122 ! | +ATOM H23 HDA3C 0.122 ! H12 +ATOM H31 HDA3C 0.122 +ATOM H32 HDA3C 0.122 +ATOM H33 HDA3C 0.122 +ATOM H41 HDA3C 0.122 +ATOM H42 HDA3C 0.122 +ATOM H43 HDA3C 0.122 + +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 + +IC C1 N C2 H21 1.4948 109.47 -180.00 109.38 1.0795 +IC C2 C1 *N C3 1.4948 109.47 120.00 109.47 1.4948 +IC C2 C1 *N C4 1.4948 109.47 -120.00 109.47 1.4948 +IC C2 N C1 H11 1.4948 109.47 -180.00 109.38 1.0795 +IC H11 N *C1 H12 1.0795 109.38 120.00 109.38 1.0795 +IC H11 N *C1 H13 1.0795 109.38 -120.00 109.38 1.0795 +IC H21 N *C2 H22 1.0795 109.38 120.00 109.38 1.0795 +IC H21 N *C2 H23 1.0795 109.38 -120.00 109.38 1.0795 +IC C1 N C3 H31 1.4948 109.47 180.00 109.38 1.0795 +IC H31 N *C3 H32 1.0795 109.38 120.00 109.38 1.0795 +IC H31 N *C3 H33 1.0795 109.38 -120.00 109.38 1.0795 +IC C1 N C4 H41 1.4948 109.47 -180.00 109.38 1.0795 +IC H41 N *C4 H42 1.0795 109.38 120.00 109.38 1.0795 +IC H41 N *C4 H43 1.0795 109.38 -120.00 109.38 1.0795 + +RESI NH5 1.000 ! methylammonium ethyl analog +GROUP +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM C1 CD32A 0.043 ALPHA -1.256 THOLE 0.895 +ATOM HN2 HDP1B 0.340 +ATOM HN3 HDP1B 0.340 +ATOM HN4 HDP1B 0.340 ! | +ATOM H11 HDA2C 0.143 ! ---N--- (+) +ATOM H12 HDA2C 0.143 ! | +GROUP ! C1 +ATOM C5 CD33A -0.177 ALPHA -2.051 THOLE 1.300 ! | +ATOM H51 HDA3A 0.059 ! C5 +ATOM H52 HDA3A 0.059 +ATOM H53 HDA3A 0.059 + +BOND N C1 N HN2 N HN3 N HN4 +BOND C1 H11 C1 H12 C1 C5 +BOND C5 H51 C5 H52 C5 H53 + +! MP2/6-36+G* structure +IC HN4 N C1 C5 1.03 111.00 180.00 110.00 1.5217 +IC C5 C1 N HN2 1.5217 110.00 -61.05 111.00 1.03 +IC C5 C1 N HN3 1.5217 110.00 61.05 111.00 1.03 +IC HN4 N C1 H11 1.03 111.00 57.27 105.76 1.0809 +IC HN4 N C1 H12 1.03 111.00 -57.27 105.76 1.0809 +IC N C1 C5 H51 1.5176 110.00 180.00 107.05 1.0836 +IC N C1 C5 H52 1.5176 110.00 62.29 112.00 1.0820 +IC N C1 C5 H53 1.5176 110.00 -62.29 112.00 1.0820 + + +RESI NC5 1.000 ! tetramethylammonium ethyl analog +GROUP +ATOM N ND3P2A 0.688 ALPHA -0.829 THOLE 0.793 ! +ATOM C1 CD32A -0.166 ALPHA -1.393 THOLE 1.099 ! | +ATOM C2 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! -C3- +ATOM C3 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | +ATOM C4 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | | | +ATOM H11 HDA2C 0.122 ! -C2---N---C4- (+) +ATOM H12 HDA2C 0.122 ! | | | +ATOM H21 HDA3C 0.122 ! | +ATOM H22 HDA3C 0.122 ! -C1- +ATOM H23 HDA3C 0.122 ! | +ATOM H31 HDA3C 0.122 ! | +ATOM H32 HDA3C 0.122 ! -C5- +ATOM H33 HDA3C 0.122 ! | +ATOM H41 HDA3C 0.122 +ATOM H42 HDA3C 0.122 +ATOM H43 HDA3C 0.122 +GROUP +ATOM C5 CD33A -0.177 ALPHA -2.051 THOLE 1.300 +ATOM H51 HDA3A 0.059 +ATOM H52 HDA3A 0.059 +ATOM H53 HDA3A 0.059 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 C5 H53 +! ab-initio HF/6-31G* structure +IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217 +IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950 +IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950 +IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809 +IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809 +IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795 +IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773 +IC C1 N C2 H23 1.5176 111.12 -54.79 109.07 1.0797 +IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795 +IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773 +IC C1 N C3 H33 1.5176 111.12 54.79 109.07 1.0797 +IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793 +IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793 +IC C1 N C4 H43 1.5176 107.80 -60.03 109.12 1.0793 +IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820 + +RESI CHOL 1.000 ! choline, based on tetramethylammonium(NC4) and ethanol(ETOH) +GROUP +ATOM N ND3P2A 0.688 ALPHA -0.829 THOLE 0.793 ! +ATOM C1 CD32A -0.166 ALPHA -1.393 THOLE 1.099 ! | +ATOM C2 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! -C3- +ATOM C3 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | +ATOM C4 CD33A -0.288 ALPHA -1.793 THOLE 1.099 ! | | | +ATOM H11 HDA2C 0.122 ! -C2---N---C4- (+) +ATOM H12 HDA2C 0.122 ! | | | +ATOM H21 HDA3C 0.122 ! | +ATOM H22 HDA3C 0.122 ! -C1- +ATOM H23 HDA3C 0.122 ! | +ATOM H31 HDA3C 0.122 ! | +ATOM H32 HDA3C 0.122 ! | +ATOM H33 HDA3C 0.122 ! | +ATOM H41 HDA3C 0.122 ! | +ATOM H42 HDA3C 0.122 ! | +ATOM H43 HDA3C 0.122 ! | +GROUP ! | +ATOM C5 CD32A -0.060 ALPHA -1.000 THOLE 1.300 ! OH1 +ATOM H51 HDA2A 0.080 ! \ +ATOM H52 HDA2A 0.080 ! HO1 +ATOM OH1 OD31A 0.000 ALPHA -1.028 THOLE 1.300 +ATOM HO1 HDP1A 0.360 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 + +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND C5 OH1 OH1 HO1 +BOND OH1 LP1A OH1 LP1B + +LONEPAIR relative LP1A OH1 C5 HO1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP1B OH1 C5 HO1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OH1 C5 LP1A LP1B A11 0.8108 A22 1.2162 + +! ab-initio HF/6-31G* geometry of gauche conformer +IC C4 N C1 C5 1.4964 107.76 161.60 116.58 1.5208 +IC C5 C1 N C2 1.5208 116.58 -80.13 111.04 1.5031 +IC C5 C1 N C3 1.5208 116.58 42.05 111.71 1.4945 +IC N C1 C5 OH1 1.5158 116.58 56.02 109.57 1.3947 +IC C1 C5 OH1 HO1 1.5208 109.57 169.05 110.84 0.9491 +IC C2 N C1 H11 1.5031 111.04 158.76 106.72 1.0813 +IC C3 N C1 H12 1.4945 111.71 165.25 106.14 1.0802 +IC C1 N C2 H21 1.5158 111.04 -179.38 108.21 1.0796 +IC C3 N C2 H22 1.4945 109.20 -63.85 109.22 1.0746 +IC C4 N C2 H23 1.4964 108.15 57.69 108.56 1.0794 +IC C1 N C3 H31 1.5158 111.71 173.42 108.53 1.0794 +IC C2 N C3 H32 1.5031 109.20 177.22 109.23 1.0800 +IC C4 N C3 H33 1.4964 108.88 174.14 109.12 1.0773 +IC C1 N C4 H41 1.5158 107.76 175.04 109.01 1.0793 +IC C2 N C4 H42 1.5031 108.15 -64.86 109.05 1.0796 +IC C3 N C4 H43 1.4945 108.88 56.40 109.30 1.0794 +IC N C1 C5 H51 1.5158 116.58 176.61 105.66 1.0855 +IC N C1 C5 H52 1.5158 116.58 -67.32 110.89 1.0847 + +RESI GUAN 1.000 ! guanidinium +GROUP +ATOM C CD2N1A 1.315 ALPHA -1.159 THOLE 0.521 ! H11 H12 +ATOM N1 ND2P1A -0.903 ALPHA -1.407 THOLE 1.553 ! \ / +ATOM H11 HDP1B 0.399 ! N1 +ATOM H12 HDP1B 0.399 ! | +ATOM N2 ND2P1A -0.903 ALPHA -1.407 THOLE 1.553 ! C +ATOM H21 HDP1B 0.399 ! / \ +ATOM H22 HDP1B 0.399 ! H21-N2 N3-H31 +ATOM N3 ND2P1A -0.903 ALPHA -1.407 THOLE 1.553 ! | | +ATOM H31 HDP1B 0.399 ! H22 H32 +ATOM H32 HDP1B 0.399 ! + +BOND C N1 C N2 C N3 +BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 H32 +IMPH C N2 N1 N3 + +IC N1 C N2 H21 1.3402 120.00 0.00 121.39 0.9969 +IC N2 N1 *C N3 1.3402 120.00 180.00 120.00 1.3402 +IC N2 C *N1 H11 2.3212 30.00 0.00 121.39 0.9969 +IC N2 C *N1 H12 2.3212 30.00 -180.00 121.39 0.9969 +IC N1 C *N2 H22 2.3212 30.00 180.00 121.39 0.9969 +IC N1 C *N3 H31 2.3212 30.00 0.00 121.39 0.9969 +IC N1 C *N3 H32 2.3212 30.00 -180.00 121.39 0.9969 +patc firs none last none + +RESI MGUAN 1.000 ! methylguanidinium +GROUP +ATOM C CD2N1A 1.129 ALPHA -1.096 THOLE 0.262 ! H11 H12 +ATOM N1 ND2P1A -0.809 ALPHA -1.403 THOLE 1.538 ! \ / +ATOM H11 HDP1B 0.369 ! N1 +ATOM H12 HDP1B 0.369 ! | +ATOM N2 ND2P1A -0.809 ALPHA -1.403 THOLE 1.538 ! C +ATOM H21 HDP1B 0.369 ! / \ +ATOM H22 HDP1B 0.369 ! H21-N2 N3-H31 +ATOM N3 ND2P1A -0.748 ALPHA -1.550 THOLE 1.538 ! | | +ATOM H31 HDP1B 0.378 ! H22 HC2-C2-HC1 +ATOM C2 CD33A 0.149 ALPHA -1.788 THOLE 0.342 ! | +ATOM HC1 HDA3A 0.078 ! HC3 +ATOM HC2 HDA3A 0.078 +ATOM HC3 HDA3A 0.078 + +BOND C N1 C N2 C N3 +BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 C2 +BOND C2 HC1 C2 HC2 C2 HC3 +IMPH C N2 N1 N3 + +IC N1 C N2 H21 1.3523 118.93 0.00 121.59 0.9999 +IC N2 N1 *C N3 1.3507 118.93 180.00 119.60 1.3613 +IC N2 C *N1 H11 2.3282 30.52 0.00 121.77 1.0000 +IC N2 C *N1 H12 2.3282 30.52 -180.00 122.27 0.9997 +IC N1 C *N2 H22 2.3282 30.55 180.00 122.39 0.9983 +IC N1 C *N3 H31 2.3453 30.09 0.00 118.52 1.0023 +IC N1 C *N3 C2 2.3453 30.09 180.00 121.90 1.5024 +IC C N3 C2 HC1 1.3613 121.90 -180.00 109.19 1.1142 +IC HC1 N3 *C2 HC2 1.1142 109.19 119.25 110.12 1.1140 +IC HC1 N3 *C2 HC3 1.1142 109.19 -119.25 110.12 1.1140 +patc firs none last none + +RESI BGUAN 1.000 ! butylguanidinium +! +! HH11 +! | +! HA2 HB1 HG1 HD1 HE NH1-HH12 +! | | | | | //(+) +! HA1-CA--CB--CG--CD--NE--CZ +! | | | | \ +! HA3 HB2 HG2 HD2 NH2-HH22 +! | +! HH21 +! +ATOM CA CD33A -0.177 ALPHA -2.051 THOLE 1.300 +ATOM HA1 HDA3A 0.059 +ATOM HA2 HDA3A 0.059 +ATOM HA3 HDA3A 0.059 +GROUP +ATOM CB CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM HB1 HDA2A 0.078 +ATOM HB2 HDA2A 0.078 +GROUP +ATOM CG CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM HG1 HDA2A 0.078 +ATOM HG2 HDA2A 0.078 +GROUP !symmetrized charges etc. +ATOM CD CD32A 0.227 ALPHA -1.788 THOLE 0.342 +ATOM HD1 HDA2A 0.078 +ATOM HD2 HDA2A 0.078 +ATOM NE ND2P1A -0.748 ALPHA -1.550 THOLE 1.538 +ATOM HE HDP1B 0.378 +ATOM CZ CD2N1A 1.129 ALPHA -1.096 THOLE 0.262 +ATOM NH1 ND2P1A -0.809 ALPHA -1.403 THOLE 1.538 +ATOM HH11 HDP1B 0.369 +ATOM HH12 HDP1B 0.369 +ATOM NH2 ND2P1A -0.809 ALPHA -1.403 THOLE 1.538 +ATOM HH21 HDP1B 0.369 +ATOM HH22 HDP1B 0.369 + +BOND CA HA1 CA HA2 CA HA3 +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD HD1 CD HD2 +BOND CD NE NE HE NE CZ +BOND CZ NH1 NH1 HH11 NH1 HH12 +BOND CZ NH2 NH2 HH21 NH2 HH22 +IMPR CZ NH1 NH2 NE + +IC HA1 CB *CA HA2 1.1115 111.35 -120.39 111.35 1.1115 +IC HA1 CB *CA HA3 1.1115 111.35 119.80 111.01 1.1120 +IC HA1 CA CB CG 1.1115 111.35 60.19 113.54 1.5340 +IC CG CA *CB HB1 1.5340 113.54 121.73 108.64 1.1144 +IC HB1 CA *CB HB2 1.1144 108.64 116.54 108.64 1.1144 +IC CA CB CG CD 1.5284 113.54 179.99 113.70 1.5155 +IC CD CB *CG HG1 1.5155 113.70 121.87 108.03 1.1143 +IC HG1 CB *CG HG2 1.1143 108.03 116.26 108.03 1.1143 +IC CB CG CD NE 1.5340 113.70 -180.00 109.94 1.4731 +IC NE CG *CD HD1 1.4731 109.94 120.14 109.50 1.1156 +IC HD1 CG *CD HD2 1.1156 109.50 119.73 109.51 1.1156 +IC CG CD NE CZ 1.5155 109.94 179.93 122.37 1.3548 +IC CZ CD *NE HE 1.3548 122.37 -179.96 116.74 0.9990 +IC CD NE CZ NH1 1.4731 122.37 -179.97 119.66 1.3525 +IC NH1 NE *CZ NH2 1.3525 119.66 180.00 121.52 1.3514 +IC NE CZ NH1 HH11 1.3548 119.66 180.00 121.92 0.9993 +IC HH11 CZ *NH1 HH12 0.9993 121.92 -180.00 121.75 0.9994 +IC NE CZ NH2 HH21 1.3548 121.52 180.00 121.56 0.9995 +IC HH21 CZ *NH2 HH22 0.9995 121.56 -179.98 122.17 0.9983 + +RESI IMIM 1.000 ! Imidazolium, EH +GROUP +ATOM CG CD2R5D -0.012 ALPHA -1.522 THOLE 1.196 ! HD1 HE1 +ATOM HG HDR5D 0.173 ! | / +ATOM CD2 CD2R5D -0.012 ALPHA -1.522 THOLE 1.196 ! ND1--CE1 +ATOM HD2 HDR5D 0.173 ! / | +ATOM ND1 ND2R5C -0.171 ALPHA -1.260 THOLE 1.194 ! HG-CG | +ATOM HD1 HDP1A 0.340 ! \ | +ATOM NE2 ND2R5C -0.171 ALPHA -1.260 THOLE 1.194 ! CD2--NE2 +ATOM HE2 HDP1A 0.340 ! | \ +ATOM CE1 CD2R5E 0.170 ALPHA -1.500 THOLE 1.317 ! HD2 HE2 +ATOM HE1 HDR5E 0.170 + +BOND NE2 CD2 ND1 CG CD2 CG CE1 ND1 +BOND NE2 CE1 CG HG +BOND ND1 HD1 CD2 HD2 CE1 HE1 NE2 HE2 + +!impropers need to be checked +IMPR ND1 CE1 CG HD1 NE2 CE1 CD2 HE2 +IMPR CE1 ND1 NE2 HE1 CG CD2 ND1 HG CD2 CG NE2 HD2 + +DONO HD1 ND1 +DONO HE2 NE2 +IC CG CD2 NE2 CE1 0.0000 0.00 0.00 0.00 0.0000 +IC CD2 NE2 CE1 ND1 0.0000 0.00 0.00 0.00 0.0000 +IC CD2 ND1 *CG HG 0.0000 0.00 180.00 0.00 0.0000 +IC NE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CD2 *NE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC NE2 ND1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 + + +RESI ACET -1.000 ! acetate, Harder, Sep 09 +! +! H1 O1 +! \ // +! H2--C1--C2 (-1) +! / \ +! H3 O2 +! +GROUP +ATOM C1 CD33A -0.194 ALPHA -2.528 THOLE 1.414 +ATOM H1 HDA3A 0.004 +ATOM H2 HDA3A 0.004 +ATOM H3 HDA3A 0.004 +ATOM C2 CD2O2A 0.708 ALPHA -1.016 THOLE 0.899 +ATOM O1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM O2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LP1A LPD -0.383 +ATOM LP1B LPD -0.383 +ATOM LP2A LPD -0.383 +ATOM LP2B LPD -0.383 + +BOND C1 C2 C2 O1 C2 O2 +BOND C1 H1 C1 H2 C1 H3 +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B + +IMPH O1 C1 O2 C2 + +LONEPAIR relative LP1A O1 C2 C1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP1B O1 C2 C1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY O1 C2 LP1A LP1B A11 0.7229 A22 1.265 +LONEPAIR relative LP2A O2 C2 C1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP2B O2 C2 C1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.7229 A22 1.265 + +IC O1 C2 C1 H1 1.2543 118.04 180.00 111.57 1.1108 +IC O1 O2 *C2 C1 1.2543 122.88 180.00 119.08 1.5229 +IC H1 C2 *C1 H2 1.1108 111.57 120.15 110.12 1.1112 +IC H1 C2 *C1 H3 1.1108 111.57 -120.15 110.12 1.1112 +IC H1 C1 C2 O2 1.1108 111.57 0.00 119.08 1.2536 + +RESI ACEH 0.000 ! acetic acid +! +! H1 O2 +! \ // +! H2-C1--C2 +! / \ +! H3 O1-HO1 + +GROUP +ATOM C1 CD33C -0.300 ALPHA -2.114 THOLE 0.750 +ATOM H1 HDA3A 0.092 +ATOM H2 HDA3A 0.092 +ATOM H3 HDA3A 0.092 +ATOM C2 CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM O2 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM LP2A LPD -0.319 +ATOM LP2B LPD -0.319 +ATOM O1 OD30D 0.000 ALPHA -1.280 THOLE 1.124 +ATOM LP1A LPD -0.285 +ATOM LP1B LPD -0.285 +ATOM HO1 HDP1A 0.374 + +BOND C2 O1 O1 HO1 C2 O2 +BOND C1 C2 C1 H1 C1 H2 C1 H3 +BOND O2 LP2A O2 LP2B +BOND O1 LP1A O1 LP1B + +IMPR O2 C1 O1 C2 !analogous to acetate + +!LP positions and anistropic polarization from NMA +LONEPAIR relative LP2A O2 C2 O1 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP2B O2 C2 O1 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O2 C2 LP2A LP2B A11 0.6968 A22 1.2194 +!LP positions and anistropic polarization from MeOH +LONEPAIR relative LP1A O1 C2 HO1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP1B O1 C2 HO1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY O1 C2 LP1A LP1B A11 0.8108 A22 1.2162 + +IC O2 C2 C1 H1 1.2000 126.00 0.00 109.50 1.1110 +IC HO1 O1 C2 O2 0.9700 110.00 0.00 123.00 1.2000 +IC HO1 O1 C2 C1 0.9700 110.00 180.00 111.00 1.5100 +IC O1 C2 C1 H1 1.3300 111.00 180.00 109.50 1.1110 +IC O1 C2 C1 H2 1.3300 111.00 60.00 109.50 1.1110 +IC O1 C2 C1 H3 1.3300 111.00 -60.00 109.50 1.1110 + +!!esters + +RESI MAS 0.000 ! methylacetate +! +GROUP +ATOM C1 CD33C -0.275 ALPHA -1.993 THOLE 0.410 ! H22 +ATOM C CD2O3A 0.697 ALPHA -1.370 THOLE 1.747 ! | +ATOM OM OD30C 0.000 ALPHA -0.732 THOLE 0.601 ! H21-C2-H23 +ATOM C2 CD33D -0.030 ALPHA -1.797 THOLE 0.410 ! \ +ATOM O OD2C3A 0.000 ALPHA -0.904 THOLE 0.565 ! OM +ATOM H11 HDA3A 0.069 ! / +ATOM H12 HDA3A 0.069 ! O=C +ATOM H13 HDA3A 0.069 ! | +ATOM H21 HDA3A 0.116 ! H11-C1-H13 +ATOM H22 HDA3A 0.116 ! | +ATOM H23 HDA3A 0.116 ! H12 +ATOM LP1A LPD -0.349 ! +ATOM LP1B LPD -0.258 ! +ATOM LPMA LPD -0.170 +ATOM LPMB LPD -0.170 + +BOND C1 C C OM C O OM C2 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND O LP1A O LP1B +BOND OM LPMA OM LPMB + +IMPR O C1 OM C + +!LP positions and anisotropic polarizability from NMA +LONEPAIR relative LP1A O C C1 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LP1B O C C1 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LP1A LP1B A11 0.6968 A22 1.2194 + +!LP positions and anisotropic polarizability from MeOH +LONEPAIR relative LPMA OM C C2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPMB OM C C2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OM C LPMA LPMB A11 0.8108 A22 1.2162 + +! internal coordinates from experiment for heavy atoms +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 + + +RESI ETAM 1.000 ! ethanolamine, based on methylammonium (NC1) and ethanol (ETOH) +! +GROUP +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 ! HN2 +ATOM HN1 HDP1B 0.340 ! | +ATOM HN2 HDP1B 0.340 ! (+) HN1-N-HN3 +ATOM HN3 HDP1B 0.340 ! | +ATOM C1 CD32A 0.043 ALPHA -1.656 THOLE 0.895 ! H12-C1-H11 +ATOM H11 HDA2C 0.143 ! | +ATOM H12 HDA2C 0.143 ! H51-C5-H52 +GROUP ! | +ATOM C5 CD32A -0.060 ALPHA -1.000 THOLE 1.300 ! OH1 +ATOM H51 HDA2A 0.080 ! \ +ATOM H52 HDA2A 0.080 ! HO1 +ATOM OH1 OD31A 0.000 ALPHA -1.028 THOLE 1.300 +ATOM HO1 HDP1A 0.360 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 + +BOND N HN1 N HN2 N HN3 N C1 +BOND C1 H11 C1 H12 C1 C5 +BOND C5 H51 C5 H52 +BOND C5 OH1 OH1 HO1 +BOND OH1 LP1A OH1 LP1B + +!from MeOH +LONEPAIR relative LP1A OH1 C5 HO1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP1B OH1 C5 HO1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OH1 C5 LP1A LP1B A11 0.8108 A22 1.2162 + +! HF/6-31G* OPTIMIZED STRUCTURE: +IC N C1 C5 OH1 1.5084 107.86 48.44 104.92 1.3987 +IC C1 C5 OH1 HO1 1.5191 104.92 173.19 111.99 0.9495 +IC HN1 N C1 C5 1.0145 108.35 -49.03 107.86 1.5191 +IC HN2 N C1 C5 1.0107 112.05 69.23 107.86 1.5191 +IC HN3 N C1 C5 1.0102 112.39 -169.37 107.86 1.5191 +IC HN2 N C1 H11 1.5031 111.04 158.76 106.72 1.0813 +IC HN3 N C1 H12 1.4945 111.71 165.25 106.14 1.0802 +IC N C1 C5 H51 1.5158 116.58 176.61 105.66 1.0855 +IC N C1 C5 H52 1.5158 116.58 -67.32 110.89 1.0847 + +end + +read para card append +* Drude polarizable FF parameters +* + +!All new model compound parameters should be included in the +!toppar_drude_master_protein stream file to avoid +!conflicts being generated + +BONDS +!atom type Kb b0 +!============================================ +! + +ANGLES +!atom types Ktheta Theta0 Kub S0 +!================================================== +! + +DIHEDRALS +!atom types Kchi n delta +!================================================= +! +!Please follow these conventions when fitting dihedral parameters +!1) use positive force constants in all cases (switch the phase...) +! (vary phase during fitting and keep force constants positive) +!2) maintain the phase at 0 or 180 if possiple. perform initial +! fitting with this contraint and, if necessary, only then +! vary the phases during fitting. note that if the phases +! are NOT 0 or 180 the parameters are NOT transferable across +! stereoisomers +!3) refit with only individual multiplicities of 1 through 6 +!4) maintain the number of significant figures used below +! +!HDP1A ND2A1 CD2O1A OD2C1A 2.000 2 180.00 ! comment +! + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! + +NONBONDED nbxmod 5 atom vatom cdiel vdistance switch vswitch - +cutnb 16.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +NBFIX + +end diff --git a/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_nucleic_acid_2013c_no_rna.str b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_nucleic_acid_2013c_no_rna.str new file mode 100644 index 00000000..d0ba7436 --- /dev/null +++ b/charmm/toppar/drude/drude_toppar_2015_7/toppar_drude_nucleic_acid_2013c_no_rna.str @@ -0,0 +1,2768 @@ +* $Id: toppar_drude_nucleic_acid.str 33 2015-08-04 14:44:59Z alex $ +* DRUDE topology and parameter stream file +* Nucleic acids +* + +!cannot be used with RNA + +!contains March 2014 DNA parameters with subsequently refined ion-nucleic acid parameters + +!requires toppar_drude_master*.str + +!nucleic acids + +!references +! +!Savelyev, A. and MacKerell, A.D., Jr., “All-Atom Polarizable Force +!Field for DNA Based on the Classical Drude Oscillator Model,” Journal +!of Computational Chemistry, 35: 1219-1239, 2014, DOI: 10.1002/jcc.23611 +! +!Parameters for Monovaletn Ions-DNA Interactions +!Savelyev, A. and MacKerell, A.D., Jr., “Balancing the Interactions of Ions, +!Water, and DNA in the Drude Polarizable Force Field,” Journal +!of Physical Chemistry B, 118: 6742−6757, 2014, DOI: 10.1021/jp503469s +! +!Savelyev, A. and MacKerell, A.D., Jr., “Competition among Li+, Na+, K+, and Rb+ +!Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 +!and Drude Polarizable Force Fields,” Journal of Physical Chemistry B, 119: 4428−4440, 2015, +!DOI: 10.1021/acs.jpcb.5b00683 +! + +read rtf card append +* Topology for Drude nucleic acids +* +38 + +! +DECL +P +DECL +O1P +DECL +O2P +DECL +O5' +DECL -O3' + +DEFA FIRS 5TER LAST 3TER +AUTOGENERATE ANGLES DIHEDRALS DRUDE + +RESI CYT -1.000 ! Cytosine +! +! H42 H41 +! \ / +! N4 +! | +! C4 +! / \\ +! H5-C5 N3 +! || | +! H6-C6 C2 +! \ / \\ +! N1 O2 +! / +! O1P H5' H4' O4' / +! | | \ / \ / +! -P-O5'-C5'----C4' C1'-H1' +! | | \ / +! O2P H5'' C3'-C2'-H2'' +! / \ \ +! O3' H3' O2'-H2' +!GROUP +ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP +ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862 +ATOM H5' HDA2A 0.026 +ATOM H5'' HDA2A 0.026 +GROUP !!NA base +ATOM N1 ND2R6C -0.042 ALPHA -1.110 THOLE 1.016 +ATOM C6 CD2R6H -0.132 ALPHA -1.748 THOLE 1.515 +ATOM H6 HDR6B 0.251 +ATOM C2 CD2O1A 0.410 ALPHA -1.577 THOLE 1.652 +ATOM O2 OD2C1B 0.000 ALPHA -0.672 THOLE 0.795 +ATOM LP2A LPDNA1 -0.191 +ATOM LP2B LPDNA1 -0.221 +ATOM N3 ND2R6B 0.000 ALPHA -0.500 THOLE 0.935 +ATOM LP3 LPDNA1 -0.523 +ATOM C4 CD2R6B 0.584 ALPHA -1.147 THOLE 1.310 +ATOM N4 ND2B1 -0.688 ALPHA -1.621 THOLE 0.552 +ATOM H41 HDP1A 0.346 +ATOM H42 HDP1A 0.346 +ATOM C5 CD2R6A -0.268 ALPHA -1.852 THOLE 1.143 +ATOM H5 HDR6A 0.128 +GROUP !! THF +ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H4' HDA1R5 0.055 +ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM LPRA LPD -0.152 +ATOM LPRB LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H1' HDA1R5 0.055 +GROUP !! EtOH +ATOM C2' CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge +ATOM H2'' HDA1R5 0.080 +ATOM O2' OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM H2' HDP1A 0.360 +ATOM LPHA LPD -0.230 +ATOM LPHB LPD -0.230 +GROUP +ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e +ATOM H3' HDA1R5 0.026 +ATOM O3' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 +BOND C2 O2 C4 N4 N4 H41 N4 H42 C5 H5 C6 H6 +BOND LP2A O2 LP2B O2 +BOND LP3 N3 + +BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2' +BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1' +BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P O3' +P +BOND O4' LPRA O4' LPRB +BOND O4' LPX +BOND O2' LPHA O2' LPHB + +IMPR C2 N1 N3 O2 C4 N3 C5 N4 +IMPR N4 C4 H41 H42 + +! Base lone pairs +LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99 +! O4' Lone pairs +LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0 +! O2' Lone pairs +LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0 +!Anisotropies +! Base anisotropies +ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM +!O4' Anisotropy +ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222 +!O2' anisotropy +ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162 +!Phosphate Anisotropy +ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000 +ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000 +ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000 +ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000 +DONO H42 N4 +DONO H2' O2' +DONO H41 N4 +ACCE O2 C2 +ACCE N3 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +RESI THY -1.000 ! Thymine +! +! H51 O4 +! | || +! H52-C5M C4 H3 +! | \ / \ / +! H53 C5 N3 +! || | +! H6-C6 C2 +! \ / \\ +! N1 O2 +! / +! O1P H5' H4' O4' / +! | | \ / \ / +! -P-O5'-C5'----C4' C1'-H1' +! | | \ / +! O2P H5'' C3'-C2'-H2'' +! / \ \ +! O3' H3' O2'-H2' +! +GROUP +ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP +ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862 +ATOM H5' HDA2A 0.026 +ATOM H5'' HDA2A 0.026 +GROUP +ATOM N1 ND2R6D -0.157 ALPHA -0.986 THOLE 1.309 +ATOM C6 CD2R6H 0.139 ALPHA -1.537 THOLE 0.991 !!!CB +ATOM H6 HDR6B 0.282 +ATOM C2 CD2O1A 0.510 ALPHA -0.982 THOLE 1.702 +ATOM O2 OD2C1B 0.000 ALPHA -0.580 THOLE 2.069 +ATOM LP2A LPDNA1 -0.155 +ATOM LP2B LPDNA1 -0.232 +ATOM N3 ND2R6C -0.520 ALPHA -0.760 THOLE 1.252 +ATOM H3 HDP1A 0.297 +ATOM C4 CD2O1A 0.465 ALPHA -1.010 THOLE 0.844 +ATOM O4 OD2C1B 0.000 ALPHA -1.562 THOLE 2.043 +ATOM LP4A LPDNA1 -0.272 +ATOM LP4B LPDNA1 -0.152 +ATOM C5 CD2R6A -0.200 ALPHA -1.203 THOLE 1.423 +ATOM C5M CD33A -0.146 ALPHA -1.536 THOLE 0.535 +ATOM H51 HDA3A 0.047 +ATOM H52 HDA3A 0.047 +ATOM H53 HDA3A 0.047 +GROUP !! THF +ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H4' HDA1R5 0.055 +ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM LPRA LPD -0.152 +ATOM LPRB LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H1' HDA1R5 0.055 +GROUP !! EtOH +ATOM C2' CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge +ATOM H2'' HDA1R5 0.080 +ATOM O2' OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM H2' HDP1A 0.360 +ATOM LPHA LPD -0.230 +ATOM LPHB LPD -0.230 +GROUP +ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e +ATOM H3' HDA1R5 0.026 +ATOM O3' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 +BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 C5M +BOND C5M H51 C5M H52 C5M H53 C6 H6 +BOND LP2A O2 LP2B O2 +BOND LP4A O4 LP4B O4 + +BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2' +BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1' +BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P O3' +P +BOND O4' LPRA O4' LPRB +BOND O4' LPX +BOND O2' LPHA O2' LPHB + +IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M + +! Base lone pairs +LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0 +! O4' Lone pairs +LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0 +! O2' Lone pairs +LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0 +!Anisotropies +! Base anisotropies +ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA +!O4' Anisotropy +ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222 +!O2' anisotropy +ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162 +!Phosphate Anisotropy +ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000 +ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000 +ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000 +ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 + +RESI URA -1.000 ! Uracil +! +! O4 +! || +! C4 H3 +! / \ / +! H5-C5 N3 +! || | +! H6-C6 C2 +! \ / \\ +! N1 O2 +! / +! O1P H5' H4' O4' / +! | | \ / \ / +! -P-O5'-C5'----C4' C1'-H1' +! | | \ / +! O2P H5'' C3'-C2'-H2'' +! / \ \ +! O3' H3' O2'-H2' +! +GROUP +ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP +ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862 +ATOM H5' HDA2A 0.026 +ATOM H5'' HDA2A 0.026 +GROUP +ATOM N1 ND2R6C -0.240 ALPHA -1.192 THOLE 1.639 +ATOM C6 CD2R6H 0.095 ALPHA -0.500 THOLE 0.544 !!!CB +ATOM H6 HDR6B 0.341 +ATOM C2 CD2O1A 0.636 ALPHA -1.072 THOLE 1.120 +ATOM O2 OD2C1B 0.000 ALPHA -0.799 THOLE 1.076 +ATOM LP2A LPDNA1 -0.126 +ATOM LP2B LPDNA1 -0.229 +ATOM N3 ND2R6C -0.593 ALPHA -1.631 THOLE 1.574 +ATOM H3 HDP1A 0.317 +ATOM C4 CD2O1A 0.557 ALPHA -1.072 THOLE 1.079 +ATOM O4 OD2C1B 0.000 ALPHA -0.657 THOLE 1.156 +ATOM LP4A LPDNA1 -0.254 +ATOM LP4B LPDNA1 -0.192 +ATOM C5 CD2R6A -0.321 ALPHA -1.949 THOLE 1.307 +ATOM H5 HDR6A 0.009 +GROUP !! THF +ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H4' HDA1R5 0.055 +ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM LPRA LPD -0.152 +ATOM LPRB LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H1' HDA1R5 0.055 +GROUP !! EtOH +ATOM C2' CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge +ATOM H2'' HDA1R5 0.080 +ATOM O2' OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM H2' HDP1A 0.360 +ATOM LPHA LPD -0.230 +ATOM LPHB LPD -0.230 +GROUP +ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e +ATOM H3' HDA1R5 0.026 +ATOM O3' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 +BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 H5 +BOND C6 H6 +BOND LP2A O2 LP2B O2 +BOND LP4A O4 LP4B O4 + +BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2' +BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1' +BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P O3' +P +BOND O4' LPRA O4' LPRB +BOND O4' LPX +BOND O2' LPHA O2' LPHB + +IMPR C2 N1 N3 O2 C4 N3 C5 O4 + +! Base lone pairs +LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0 +! O4' Lone pairs +LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0 +! O2' Lone pairs +LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0 +!Anisotropies +! Base anisotropies +ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA +!O4' Anisotropy +ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222 +!O2' anisotropy +ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162 +!Phosphate Anisotropy +ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000 +ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000 +ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000 +ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000 + +DONO H3 N3 +DONO H2' O2' +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 +IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 +IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 +IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 +IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 +IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 +IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 +IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + + +RESI ADE -1.000 ! Adenine +! +! H61 H62 +! \ / +! N6 +! | +! C6 +! // \ +! N1 C5--N7\\ +! | || C8-H8 +! C2 C4--N9/ +! / \\ / \ +! H2 N3 \ +! \ +! / +! O1P H5' H4' O4' / +! | | \ / \ / +! -P-O5'-C5'----C4' C1'-H1' +! | | \ / +! O2P H5'' C3'-C2'-H2'' +! / \ \ +! O3' H3' O2'-H2' +! +GROUP +ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP +ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862 +ATOM H5' HDA2A 0.026 +ATOM H5'' HDA2A 0.026 +GROUP +ATOM N9 ND2R5D 0.051 ALPHA -0.685 THOLE 1.031 +ATOM C4 CD2R6F 0.245 ALPHA -1.039 THOLE 1.051 !!!CB +ATOM N3 ND2R6B 0.000 ALPHA -1.596 THOLE 0.144 +ATOM LP3 LPDNA1 -0.554 +ATOM C2 CD2R6C 0.233 ALPHA -1.128 THOLE 1.029 +ATOM H2 HDR6C 0.176 +ATOM N1 ND2R6B 0.000 ALPHA -1.513 THOLE 1.232 +ATOM LP1 LPDNA1 -0.464 +ATOM C6 CD2R6C 0.404 ALPHA -1.452 THOLE 0.595 +ATOM N6 ND2B1 -0.766 ALPHA -1.337 THOLE 0.344 +ATOM H61 HDP1A 0.373 +ATOM H62 HDP1A 0.373 +ATOM C5 CD2R6F -0.107 ALPHA -1.236 THOLE 1.927 !!!CB +ATOM N7 ND2R5E 0.000 ALPHA -1.468 THOLE 0.546 +ATOM LP7 LPDNA1 -0.176 +ATOM C8 CD2R5B 0.047 ALPHA -1.358 THOLE 1.901 +ATOM H8 HDR5B 0.165 +GROUP !! THF +ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H4' HDA1R5 0.055 +ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM LPRA LPD -0.152 +ATOM LPRB LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H1' HDA1R5 0.055 +GROUP !! EtOH +ATOM C2' CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge +ATOM H2'' HDA1R5 0.080 +ATOM O2' OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM H2' HDP1A 0.360 +ATOM LPHA LPD -0.230 +ATOM LPHB LPD -0.230 +GROUP +ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e +ATOM H3' HDA1R5 0.026 +ATOM O3' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 + +BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 +BOND C6 C5 C5 C4 N9 C8 C8 N7 N7 C5 +BOND C8 H8 C6 N6 N6 H61 N6 H62 C2 H2 +BOND LP1 N1 +BOND LP3 N3 +BOND LP7 N7 + +BOND N9 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2' +BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1' +BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P O3' +P +BOND O4' LPRA O4' LPRB +BOND O4' LPX +BOND O2' LPHA O2' LPHB + +! Base lone pairs +LONEPAIR bisector LP1 N1 C2 C6 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99 +! O4' Lone pairs +LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0 +! O2' Lone pairs +LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0 +!Anisotropies +! Base anisotropies +ANISOTROPY N1 LP1 C6 C2 A11 0.808 A22 1.384 !based on PYRM +ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM +ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID +!O4' Anisotropy +ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222 +!O2' anisotropy +ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162 +!Phosphate Anisotropy +ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000 +ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000 +ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000 +ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000 + +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +RESI GUA -1.000 ! Guanine +! +! O6 +! || +! C6 +! / \ +! H1-N1 C5--N7\\ +! | || C8-H8 +! C2 C4--N9/ +! / \\ / \ +! H21-N2 N3 \ +! | \ +! H22 \ +! \ +! / +! O1P H5' H4' O4' / +! | | \ / \ / +! -P-O5'-C5'----C4' C1'-H1' +! | | \ / +! O2P H5'' C3'-C2'-H2'' +! / \ \ +! O3' H3' O2'-H2' +! | +GROUP +ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP +ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862 +ATOM H5' HDA2A 0.026 +ATOM H5'' HDA2A 0.026 +GROUP +ATOM N9 ND2R5D 0.191 ALPHA -0.878 THOLE 0.928 +ATOM C4 CD2R6F 0.208 ALPHA -1.268 THOLE 1.244 !!!CB +ATOM N3 ND2R6B 0.000 ALPHA -0.773 THOLE 1.245 +ATOM LP3 LPDNA1 -0.413 +ATOM C2 CD2R6C 0.559 ALPHA -1.109 THOLE 1.461 +ATOM N1 ND2R6C -0.337 ALPHA -1.572 THOLE 0.152 +ATOM H1 HDP1A 0.287 +ATOM N2 ND2B1 -0.702 ALPHA -1.408 THOLE 0.529 +ATOM H21 HDP1A 0.327 +ATOM H22 HDP1A 0.327 +ATOM C6 CD2O1A 0.244 ALPHA -0.948 THOLE 1.751 +ATOM O6 OD2C1B 0.000 ALPHA -0.607 THOLE 1.168 +ATOM LP6A LPDNA1 -0.250 +ATOM LP6B LPDNA1 -0.177 +ATOM C5 CD2R6F -0.011 ALPHA -1.779 THOLE 1.396 !!!CB +ATOM N7 ND2R5E 0.000 ALPHA -0.657 THOLE 1.284 +ATOM LP7 LPDNA1 -0.316 +ATOM C8 CD2R5B -0.102 ALPHA -1.418 THOLE 0.886 +ATOM H8 HDR5B 0.165 +GROUP !! THF +ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H4' HDA1R5 0.055 +ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM LPRA LPD -0.152 +ATOM LPRB LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H1' HDA1R5 0.055 +GROUP !! EtOH +ATOM C2' CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge +ATOM H2'' HDA1R5 0.080 +ATOM O2' OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM H2' HDP1A 0.360 +ATOM LPHA LPD -0.230 +ATOM LPHB LPD -0.230 +GROUP +ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e +ATOM H3' HDA1R5 0.026 +ATOM O3' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 + +BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 C6 C5 +BOND C5 C4 N9 C8 C8 N7 C5 N7 C8 H8 C6 O6 +BOND N1 H1 C2 N2 N2 H21 N2 H22 +BOND LP3 N3 +BOND LP7 N7 +BOND LP6A O6 LP6B O6 + +BOND N9 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2' +BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1' +BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P O3' +P +BOND O4' LPRA O4' LPRB +BOND O4' LPX +BOND O2' LPHA O2' LPHB + +IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 + +! Base lone pairs +LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR relative LP6A O6 C6 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP6B O6 C6 C5 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99 +! O4' Lone pairs +LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0 +! O2' Lone pairs +LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0 +!Anisotropies +! Base anisotropies +ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM +ANISOTROPY O6 C6 C5 N1 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID +!O4' Anisotropy +ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222 +!O2' anisotropy +ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162 +!Phosphate Anisotropy +ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000 +ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000 +ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000 +ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000 + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +DONO H2' O2' +ACCE O6 C6 +ACCE N3 +ACCE N7 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +! Chi and sugar-phosphate backbone in B-DNA ike conformation +IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + + +PRES 5TER 0.000 ! 5-terminal HYDROXYL patch, from MeOH +! +! Base +! H5T1 H4' O4' / +! | \ / \ / +! H5T-O5T-C5T----C4' C1'-H1' +! | \ / +! H5T2 C3'-C2D-H2D +! / \ \ +! O3' H3' H2Da +! | +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P +DELETE ATOM DP +DELETE ATOM DO1P +DELETE ATOM DO2P +DELETE ATOM DO5' +DELETE ATOM DC5' +GROUP +ATOM H5T HDP1A 0.360 +ATOM O5' OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM C5' CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM H5' HDA2A 0.080 +ATOM H5'' HDA2A 0.080 +ATOM LP5A LPD -0.230 +ATOM LP5B LPD -0.230 + +BOND O5' H5T +BOND O5' LP5A O5' LP5B + +LONEPAIR relative LP5A O5' C5' H5T distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5' C5' H5T distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O5' C5' LP5A LP5B A11 0.8108 A22 1.2162 + +DONO H5T O5' + +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +PRES 3TER -0.100 ! 3-terminal HYDROXYL patch, from MeOH +! +! \ +! C3T- +! / \ +! O3T H3' +! | +! H3T +GROUP +ATOM C3' CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge +ATOM H3' HDA1R5 0.080 +ATOM O3' OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM H3T HDP1A 0.260 +ATOM LP3A LPD -0.230 +ATOM LP3B LPD -0.230 + +BOND O3' H3T +BOND O3' LP3A O3' LP3B + +LONEPAIR relative LP3A O3' C3' H3T distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3' C3' H3T distance 0.35 angle 110.0 dihe 269.0 +ANISOTROPY O3' C3' LP3A LP3B A11 0.8108 A22 1.2162 + +DONO H3T O3' + +IC H3T O3' C3' C4' 0.0000 0.00 -180.00 0.00 0.0000 + + + +PRES DEOX 0.000 ! Patch to make DEOXYribose from default ribose bases + +DELETE ATOM O2' +DELETE ATOM LPHA +DELETE ATOM LPHB +DELETE ATOM DO2' + +GROUP +ATOM C2' CD325B -0.144 ALPHA -1.617 THOLE 1.103 !neutralize group charge +ATOM H2' HDA2R5 0.072 +ATOM H2'' HDA2R5 0.072 + +BOND C2' H2' + +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +!nucleic acid model compounds + +RESI CYTB 0.000 ! Cytosine base +! +! H42 H41 +! \ / +! N4 +! | +! C4 +! / \\ +! H5-C5 N3 +! || | +! H6-C6 C2 +! \ / \\ +! N1 O2 +! | +! H1 +! +ATOM N1 ND2R6C -0.244 ALPHA -1.110 THOLE 1.016 +ATOM C6 CD2R6H -0.132 ALPHA -1.748 THOLE 1.515 !!!CB +ATOM H6 HDR6B 0.251 +ATOM C2 CD2O1A 0.410 ALPHA -1.577 THOLE 1.652 +ATOM O2 OD2C1B 0.000 ALPHA -0.672 THOLE 0.795 +ATOM LP2A LPDNA1 -0.191 +ATOM LP2B LPDNA1 -0.221 +ATOM N3 ND2R6B 0.000 ALPHA -0.500 THOLE 0.935 +ATOM LP3 LPDNA1 -0.523 +ATOM C4 CD2R6B 0.584 ALPHA -1.147 THOLE 1.310 +ATOM N4 ND2B1 -0.688 ALPHA -1.621 THOLE 0.552 +ATOM H41 HDP1A 0.346 +ATOM H42 HDP1A 0.346 +ATOM C5 CD2R6A -0.268 ALPHA -1.852 THOLE 1.143 +ATOM H5 HDR6A 0.128 +ATOM H1 HDP1A 0.202 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 +BOND C2 O2 C4 N4 N4 H41 N4 H42 C5 H5 C6 H6 N1 H1 +BOND LP2A O2 LP2B O2 +BOND LP3 N3 + +IMPR C2 N1 N3 O2 C4 N3 C5 N4 +IMPR N4 C4 H41 H42 N1 C6 C2 H1 + +LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM + +DONO H42 N4 +DONO H41 N4 +ACCE O2 C2 +ACCE N3 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC H1 N1 C2 N3 0.0 0.0 180.0 0.0 0.0 + +RESI MCYT 0.000 ! 1-Me-Cytosine, va ; MOLVIB atom ordering; modified cmb 04/10 +! +! H42 H41 +! \ / +! N4 +! | +! C4 +! / \\ +! H5-C5 N3 +! || | +! H6-C6 C2 +! \ / \\ +! N1 O2 +! | +! C1 H11,H12,H13 +! +GROUP +ATOM N1 ND2R6C -0.244 ALPHA -1.110 THOLE 1.016 +ATOM C6 CD2R6H -0.132 ALPHA -1.748 THOLE 1.515 !!!CB +ATOM H6 HDR6B 0.251 +ATOM C2 CD2O1A 0.410 ALPHA -1.577 THOLE 1.652 +ATOM O2 OD2C1B 0.000 ALPHA -0.672 THOLE 0.795 +ATOM LP2A LPDNA1 -0.191 +ATOM LP2B LPDNA1 -0.221 +ATOM N3 ND2R6B 0.000 ALPHA -0.500 THOLE 0.935 +ATOM LP3 LPDNA1 -0.523 +ATOM C4 CD2R6B 0.584 ALPHA -1.147 THOLE 1.310 +ATOM N4 ND2B1 -0.688 ALPHA -1.621 THOLE 0.552 +ATOM H41 HDP1A 0.346 +ATOM H42 HDP1A 0.346 +ATOM C5 CD2R6A -0.268 ALPHA -1.852 THOLE 1.143 +ATOM H5 HDR6A 0.128 +ATOM C1 CD33A -0.146 ALPHA -1.324 THOLE 0.477 +ATOM H11 HDA3A 0.116 +ATOM H12 HDA3A 0.116 +ATOM H13 HDA3A 0.116 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 +BOND C2 O2 C4 N4 N4 H41 N4 H42 C5 H5 C6 H6 +BOND N1 C1 C1 H11 C1 H12 C1 H13 +BOND LP2A O2 LP2B O2 +BOND LP3 N3 +IMPR C2 N1 N3 O2 C4 N3 C5 N4 +IMPR N4 C4 H41 H42 N1 C6 C2 C1 + +LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM + +DONO H42 N4 +DONO H41 N4 +ACCE O2 C2 +ACCE N3 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C2 C6 *N1 C1 0.0 0.0 180.0 0.0 0.0 +IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0 +IC H11 N1 *C1 H13 0.0 0.0 -120.0 0.0 0.0 + + +PRES CYTM 0.202 ! Me-CYT patch onto CYTB +! use as "LAST CYTM" in generate statement or as "PRES CYTM" in patch statement +DELE ATOM H1 +ATOM C1 CD33A -0.146 ALPHA -1.324 THOLE 0.477 +ATOM H11 HDA3A 0.116 +ATOM H12 HDA3A 0.116 +ATOM H13 HDA3A 0.116 + +BOND N1 C1 C1 H11 C1 H12 C1 H13 + +IMPR N1 C6 C2 C1 + +IC C2 C6 *N1 C1 0.0 0.0 180.0 0.0 0.0 +IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0 +IC H11 N1 *C1 H13 0.0 0.0 240.0 0.0 0.0 + +RESI THYB 0.000 ! Thymine base, modified cmb 04/10 +! +! H51 O4 +! | || +! H52-C5M C4 H3 +! | \ / \ / +! H53 C5 N3 +! || | +! H6-C6 C2 +! \ / \\ +! N1 O2 +! | +! H1 +! +GROUP +ATOM N1 ND2R6C -0.397 ALPHA -0.986 THOLE 1.309 +ATOM C6 CD2R6H 0.139 ALPHA -1.537 THOLE 0.991 !!!CB +ATOM H6 HDR6B 0.282 +ATOM C2 CD2O1A 0.510 ALPHA -0.982 THOLE 1.702 +ATOM O2 OD2C1B 0.000 ALPHA -0.580 THOLE 2.069 +ATOM LP2A LPDNA1 -0.155 +ATOM LP2B LPDNA1 -0.232 +ATOM N3 ND2R6C -0.520 ALPHA -0.760 THOLE 1.252 +ATOM H3 HDP1A 0.297 +ATOM C4 CD2O1A 0.465 ALPHA -1.010 THOLE 0.844 +ATOM O4 OD2C1B 0.000 ALPHA -1.562 THOLE 2.043 +ATOM LP4A LPDNA1 -0.272 +ATOM LP4B LPDNA1 -0.152 +ATOM C5 CD2R6A -0.200 ALPHA -1.203 THOLE 1.423 +ATOM C5M CD33A -0.146 ALPHA -1.536 THOLE 0.535 +ATOM H51 HDA3A 0.047 +ATOM H52 HDA3A 0.047 +ATOM H53 HDA3A 0.047 +ATOM H1 HDP1A 0.240 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 +BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 C5M +BOND C5M H51 C5M H52 C5M H53 C6 H6 N1 H1 +BOND LP2A O2 LP2B O2 +BOND LP4A O4 LP4B O4 + +IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M +IMPR N1 C6 C2 H1 + +LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +IC C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 + +RESI MTHY 0.000 ! 1-Me-Thymin, va ; MOLVIB atom ordering; modified cmb 04/10 +! +! H51 O4 +! | || +! H52-C5M C4 H3 +! | \ / \ / +! H53 C5 N3 +! || | +! H6-C6 C2 +! \ / \\ +! N1 O2 +! | +! C1 H11,H12,H13 +! +GROUP +ATOM N1 ND2R6C -0.397 ALPHA -0.986 THOLE 1.309 +ATOM C6 CD2R6H 0.139 ALPHA -1.537 THOLE 0.991 !!!CB +ATOM H6 HDR6B 0.282 +ATOM C2 CD2O1A 0.510 ALPHA -0.982 THOLE 1.702 +ATOM O2 OD2C1B 0.000 ALPHA -0.580 THOLE 2.069 +ATOM LP2A LPDNA1 -0.155 +ATOM LP2B LPDNA1 -0.232 +ATOM N3 ND2R6C -0.520 ALPHA -0.760 THOLE 1.252 +ATOM H3 HDP1A 0.297 +ATOM C4 CD2O1A 0.465 ALPHA -1.010 THOLE 0.844 +ATOM O4 OD2C1B 0.000 ALPHA -1.562 THOLE 2.043 +ATOM LP4A LPDNA1 -0.272 +ATOM LP4B LPDNA1 -0.152 +ATOM C5 CD2R6A -0.200 ALPHA -1.203 THOLE 1.423 +ATOM C5M CD33A -0.146 ALPHA -1.536 THOLE 0.535 +ATOM H51 HDA3A 0.047 +ATOM H52 HDA3A 0.047 +ATOM H53 HDA3A 0.047 +ATOM C1 CD33A -0.018 ALPHA -1.250 THOLE 0.436 +ATOM H11 HDA3A 0.086 +ATOM H12 HDA3A 0.086 +ATOM H13 HDA3A 0.086 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 +BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 C5M +BOND C5M H51 C5M H52 C5M H53 C6 H6 N1 C1 +BOND C1 H11 C1 H12 C1 H13 +BOND LP2A O2 LP2B O2 +BOND LP4A O4 LP4B O4 + +IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M +IMPR N1 C6 C2 C1 + +LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +IC C2 C6 *N1 C1 0.0 0.0 180.0 0.0 0.0 +IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0 +IC H11 N1 *C1 H13 0.0 0.0 -120.0 0.0 0.0 + + +PRES THYM 0.240 ! Me-THY patch with THYB +! use as "LAST THYM" in generate statement or as "PRES THYM" in patch statement +DELE ATOM H1 +ATOM C1 CD33A -0.018 ALPHA -1.250 THOLE 0.436 +ATOM H11 HDA3A 0.086 +ATOM H12 HDA3A 0.086 +ATOM H13 HDA3A 0.086 + +BOND N1 C1 C1 H11 C1 H12 C1 H13 + +IC C5 C6 N1 C1 0.0 0.0 180.0 0.0 0.0 +IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0 +IC H11 N1 *C1 H13 0.0 0.0 240.0 0.0 0.0 + +RESI URAB 0.000 ! Uracil base; modified cmb 04/10 +! +! O4 +! || +! C4 H3 +! / \ / +! H5-C5 N3 +! || | +! H6-C6 C2 +! \ / \\ +! N1 O2 +! | +! H1 +! +GROUP +ATOM N1 ND2R6C -0.239 ALPHA -1.192 THOLE 1.639 +ATOM C6 CD2R6H 0.095 ALPHA -0.500 THOLE 0.544 !!!CB +ATOM H6 HDR6B 0.341 +ATOM C2 CD2O1A 0.636 ALPHA -1.072 THOLE 1.120 +ATOM O2 OD2C1B 0.000 ALPHA -0.799 THOLE 1.076 +ATOM LP2A LPDNA1 -0.126 +ATOM LP2B LPDNA1 -0.229 +ATOM N3 ND2R6C -0.593 ALPHA -1.631 THOLE 1.574 +ATOM H3 HDP1A 0.317 +ATOM C4 CD2O1A 0.557 ALPHA -1.072 THOLE 1.079 +ATOM O4 OD2C1B 0.000 ALPHA -0.657 THOLE 1.156 +ATOM LP4A LPDNA1 -0.254 +ATOM LP4B LPDNA1 -0.192 +ATOM C5 CD2R6A -0.321 ALPHA -1.949 THOLE 1.307 +ATOM H5 HDR6A 0.009 +ATOM H1 HDP1A -0.001 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 +BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 H5 +BOND C6 H6 N1 H1 +BOND LP2A O2 LP2B O2 +BOND LP4A O4 LP4B O4 + +IMPR C2 N1 N3 O2 C4 N3 C5 O4 + +LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 +IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 +IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 +IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 +IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 +IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 + +PRES URAM -0.001 ! Me-URA patch with URAB +! use as "LAST URAM" in generate statement or as "PRES URAM" in patch statement +DELE ATOM H1 +ATOM C1 CD33A -0.364 ALPHA -1.863 THOLE 0.686 +ATOM H11 HDA3A 0.121 +ATOM H12 HDA3A 0.121 +ATOM H13 HDA3A 0.121 + +BOND N1 C1 C1 H11 C1 H12 C1 H13 + +IC C5 C6 N1 C1 0.0 0.0 180.0 0.0 0.0 +IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0 +IC H11 N1 *C1 H13 0.0 0.0 240.0 0.0 0.0 + +RESI ADEB 0.000 ! Adenine base; modified cmb 04/10 +! +! H61 H62 +! \ / +! N6 +! | +! C6 +! // \ +! N1 C5--N7\\ +! | || C8-H8 +! C2 C4--N9/ +! / \\ / \ +! H2 N3 H9 +! +GROUP +ATOM N9 ND2R5D -0.230 ALPHA -0.685 THOLE 1.031 +ATOM C4 CD2R6F 0.245 ALPHA -1.039 THOLE 1.051 !!!CB +ATOM N3 ND2R6B 0.000 ALPHA -1.596 THOLE 0.144 +ATOM LP3 LPDNA1 -0.554 +ATOM C2 CD2R6C 0.233 ALPHA -1.128 THOLE 1.029 +ATOM H2 HDR6C 0.176 +ATOM N1 ND2R6B 0.000 ALPHA -1.513 THOLE 1.232 +ATOM LP1 LPDNA1 -0.464 +ATOM C6 CD2R6C 0.404 ALPHA -1.452 THOLE 0.595 +ATOM N6 ND2B1 -0.766 ALPHA -1.337 THOLE 0.344 +ATOM H61 HDP1A 0.373 +ATOM H62 HDP1A 0.373 +ATOM C5 CD2R6F -0.107 ALPHA -1.236 THOLE 1.927 !!!CB +ATOM N7 ND2R5E 0.000 ALPHA -1.468 THOLE 0.546 +ATOM LP7 LPDNA1 -0.176 +ATOM C8 CD2R5B 0.047 ALPHA -1.358 THOLE 1.901 +ATOM H8 HDR5B 0.165 +ATOM H9 HDP1A 0.281 + +BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 +BOND C6 C5 C5 C4 N9 C8 C8 N7 N7 C5 +BOND C8 H8 C6 N6 N6 H61 N6 H62 C2 H2 N9 H9 +BOND LP1 N1 LP3 N3 LP7 N7 + +LONEPAIR bisector LP1 N1 C2 C6 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY N1 LP1 C6 C2 A11 0.808 A22 1.384 !based on PYRM +ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM +ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID + +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +DONO H61 N6 +DONO H62 N6 +ACCE N3 +ACCE N7 +ACCE N1 + +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0 + +RESI MADE 0.000 ! 9-Me-Adenine; MOLVIB atom ordering; modified cmb 04/10 +! +! H61 H62 +! \ / +! N6 +! | +! C6 +! // \ +! N1 C5--N7\\ +! | || C8-H8 +! C2 C4--N9/ +! / \\ / \ +! H2 N3 C9 H91,H92,H93 +! +GROUP +ATOM N9 ND2R5D -0.230 ALPHA -0.685 THOLE 1.031 +ATOM C4 CD2R6F 0.245 ALPHA -1.039 THOLE 1.051 !!!CB +ATOM N3 ND2R6B 0.000 ALPHA -1.596 THOLE 0.144 +ATOM LP3 LPDNA1 -0.554 +ATOM C2 CD2R6C 0.233 ALPHA -1.128 THOLE 1.029 +ATOM H2 HDR6C 0.176 +ATOM N1 ND2R6B 0.000 ALPHA -1.513 THOLE 1.232 +ATOM LP1 LPDNA1 -0.464 +ATOM C6 CD2R6C 0.404 ALPHA -1.452 THOLE 0.595 +ATOM N6 ND2B1 -0.766 ALPHA -1.337 THOLE 0.344 +ATOM H61 HDP1A 0.373 +ATOM H62 HDP1A 0.373 +ATOM C5 CD2R6F -0.107 ALPHA -1.236 THOLE 1.927 !!!CB +ATOM N7 ND2R5E 0.000 ALPHA -1.468 THOLE 0.546 +ATOM LP7 LPDNA1 -0.176 +ATOM C8 CD2R5B 0.047 ALPHA -1.358 THOLE 1.901 +ATOM H8 HDR5B 0.165 +ATOM C9 CD33A -0.175 ALPHA -1.403 THOLE 0.403 +ATOM H91 HDA3A 0.152 +ATOM H92 HDA3A 0.152 +ATOM H93 HDA3A 0.152 + +BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 +BOND C6 C5 C5 C4 N9 C8 C8 N7 N7 C5 +BOND C8 H8 C6 N6 N6 H61 N6 H62 C2 H2 +BOND N9 C9 C9 H91 C9 H92 C9 H93 +!DOUB N1 C6 C2 N3 C4 C5 N7 C8 +BOND LP1 N1 +BOND LP3 N3 +BOND LP7 N7 + +LONEPAIR bisector LP1 N1 C2 C6 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY N1 LP1 C6 C2 A11 0.808 A22 1.384 !based on PYRM +ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM +ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID + +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +DONO H61 N6 +DONO H62 N6 +ACCE N3 +ACCE N7 +ACCE N1 + +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0 +IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 +IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0 +IC H91 N9 *C9 H93 0.0 0.0 -120.0 0.0 0.0 + + +PRES ADEM 0.281 ! Me-ADE patch with ADEB +! use as "LAST ADEM" in generate statement or as "PRES ADEM" in patch statement +DELE ATOM H9 +ATOM C9 CD33A -0.175 ALPHA -1.403 THOLE 0.403 +ATOM H91 HDA3A 0.152 +ATOM H92 HDA3A 0.152 +ATOM H93 HDA3A 0.152 + +BOND N9 C9 C9 H91 C9 H92 C9 H93 + +IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0 +IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 +IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0 +IC H91 N9 *C9 H93 0.0 0.0 -120.0 0.0 0.0 + +RESI GUAB 0.000 ! Guanine base +! +! O6 +! || +! C6 +! / \ +! H1-N1 C5--N7\\ +! | || C8-H8 +! C2 C4--N9/ +! / \\ / \ +! H21-N2 N3 H9 +! | +! H22 +GROUP +ATOM N9 ND2R5D -0.025 ALPHA -0.878 THOLE 0.928 +ATOM C4 CD2R6F 0.208 ALPHA -1.268 THOLE 1.244 !!!CB +ATOM N3 ND2R6B 0.000 ALPHA -0.773 THOLE 1.245 +ATOM LP3 LPDNA1 -0.413 +ATOM C2 CD2R6C 0.559 ALPHA -1.109 THOLE 1.461 +ATOM N1 ND2R6C -0.337 ALPHA -1.572 THOLE 0.152 +ATOM H1 HDP1A 0.287 +ATOM N2 ND2B1 -0.702 ALPHA -1.408 THOLE 0.529 +ATOM H21 HDP1A 0.327 +ATOM H22 HDP1A 0.327 +ATOM C6 CD2O1A 0.244 ALPHA -0.948 THOLE 1.751 +ATOM O6 OD2C1B 0.000 ALPHA -0.607 THOLE 1.168 +ATOM LP6A LPDNA1 -0.250 +ATOM LP6B LPDNA1 -0.177 +ATOM C5 CD2R6F -0.011 ALPHA -1.779 THOLE 1.396 !!!CB +ATOM N7 ND2R5E 0.000 ALPHA -0.657 THOLE 1.284 +ATOM LP7 LPDNA1 -0.316 +ATOM C8 CD2R5B -0.102 ALPHA -1.418 THOLE 0.886 +ATOM H8 HDR5B 0.165 +ATOM H9 HDP1A 0.216 + +BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 C6 C5 +BOND C5 C4 N9 C8 C8 N7 C5 N7 C8 H8 C6 O6 +BOND N1 H1 C2 N2 N2 H21 N2 H22 N9 H9 +BOND LP3 N3 LP7 N7 +BOND LP6A O6 LP6B O6 + +IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 + +LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99 +LONEPAIR relative LP6A O6 C6 N1 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP6B O6 C6 C5 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM +ANISOTROPY O6 C6 C5 N1 A11 0.6968 A22 1.2194 !based on NMA +ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +ACCE O6 C6 +ACCE N3 +ACCE N7 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0 + +PRES GUAM 0.216 ! Me-GUA patch with GUAB +! use as "LAST GUAM" in generate statement or as "PRES GUAM" in patch statement +DELE ATOM H9 +ATOM C9 CD33A -0.264 ALPHA -1.793 THOLE 0.571 +ATOM H91 HDA3A 0.160 +ATOM H92 HDA3A 0.160 +ATOM H93 HDA3A 0.160 + +BOND N9 C9 C9 H91 C9 H92 C9 H93 + +IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0 +IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 +IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0 +IC H91 N9 *C9 H93 0.0 0.0 -120.0 0.0 0.0 + +PRES GUAE 0.216 ! Ethyl-GUA patch with GUAB +! use as "LAST GUAE" in generate statement or as "PRES GUAE" in patch statement +DELE ATOM H9 +ATOM C9 CD32A -0.104 ALPHA -1.162 THOLE 0.571 +ATOM H91 HDA2A 0.160 +ATOM H92 HDA2A 0.160 +GROUP +ATOM C10 CD33A -0.177 ALPHA -1.436 THOLE 1.3 +ATOM H11 HDA3A 0.059 +ATOM H12 HDA3A 0.059 +ATOM H13 HDA3A 0.059 + +BOND N9 C9 C9 H91 C9 H92 C9 C10 +BOND C10 H11 C10 H12 C10 H13 + +IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0 +IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 +IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0 +IC H91 N9 *C9 C10 0.0 0.0 -120.0 0.0 0.0 +IC C10 C9 C10 H11 0.0 0.0 180.0 0.0 0.0 +IC H11 C9 *C10 H12 0.0 0.0 120.0 0.0 0.0 +IC H11 C9 *C10 H13 0.0 0.0 -120.0 0.0 0.0 + +! backbone model compounds + +RESI T3PS -1.000 ! 3-phosphate-tetrahydrofuran (phosphate -1) + ! capped with a furan +! +! H41a O41 H11a +! \ / \ / +! H42a--C4a C11--H12a +! | | +! H31a--C3a--C2a--H21a +! / \ +! O3a H22a +! | +! O1P==P==O2P +! | +! O5b (-1) H4b1 O4b H1b1 +! \ \ / \ / +! C5b-------C4b C1b-H1b2 +! / \ | | +! H5b1 H5b2 C3b----C2b-H2b2 +! / | \ +! H3b1 H3b2 H2b1 +! +! +GROUP +ATOM O4A OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM LP1 LPD -0.152 +ATOM LP2 LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1A CD315A 0.092 ALPHA -1.562 THOLE 1.103 ! neutralize group charge !+ 0.05e +ATOM H11A HDA2R5 0.055 +ATOM H12A HDA2R5 0.055 +ATOM C4A CD315B 0.092 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H41A HDA2R5 0.055 +ATOM H42A HDA2R5 0.055 +GROUP +ATOM C2A CD325B -0.144 ALPHA -1.617 THOLE 1.103 ! neutralize group charge +ATOM H21A HDA2R5 0.072 +ATOM H22A HDA2R5 0.072 +GROUP +ATOM C3A CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e +ATOM H31A HDA1R5 0.026 +ATOM O3A OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 +ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O5B OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C5B CD32C 0.1985 ALPHA -1.642 THOLE 0.862 +ATOM H5B1 HDA2A 0.026 +ATOM H5B2 HDA2A 0.026 +GROUP +ATOM O4B OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM LPA LPD -0.152 +ATOM LPB LPD -0.152 +ATOM LPX2 LPD 0.000 !dummy for anisotropic polarizability +ATOM C4B CD315B 0.097 ALPHA -1.562 THOLE 1.103 ! neutralize group charge +ATOM H4B1 HDA1R5 0.055 +ATOM C1B CD315A 0.042 ALPHA -1.562 THOLE 1.103 +ATOM H1B1 HDA2R5 0.055 +ATOM H1B2 HDA2R5 0.055 +GROUP +ATOM C2B CD325B -0.144 ALPHA -1.617 THOLE 1.103 ! neutralize group charge +ATOM H2B1 HDA2R5 0.072 +ATOM H2B2 HDA2R5 0.072 +GROUP +ATOM C3B CD315B -0.144 ALPHA -1.617 THOLE 1.103 ! neutralize group charge +ATOM H3B1 HDA2R5 0.072 +ATOM H3B2 HDA2R5 0.072 + +BOND C1A O4A C1A C2A C2A C3A C3A C4A C4A O4A C3A O3A +BOND C1A H11A C1A H12A C2A H21A C2A H22A C3A H31A C4A H41A +BOND C4A H42A O3A P P O1P P O2P P O5B O5B C5B +BOND C5B H5B1 C5B H5B2 C5B C4B C4B O4B O4B C1B C1B C2B +BOND C2B C3B C3B C4B C4B H4B1 C1B H1B1 C1B H1B2 C2B H2B1 +BOND C2B H2B2 C3B H3B1 C3B H3B2 + +BOND O4A LP1 O4A LP2 O4A LPX +BOND O4B LPA O4B LPB O4B LPX2 + +! O4A Lone pairs +LONEPAIR bisector LP1 O4A C1A C4A distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2 O4A C1A C4A distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4A C1A C4A distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4A LPX LP1 LP2 A11 0.8889 A22 1.2222 +! O4B Lone pairs +LONEPAIR bisector LPA O4B C1B C4B distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPB O4B C1B C4B distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX2 O4B C1B C4B distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4B LPX2 LPA LPB A11 0.8889 A22 1.2222 + +ANISOTROPY O5B O1P O3A O2P A11 1.0000 A22 0.6000 +ANISOTROPY O3A O2P O5B O1P A11 1.0000 A22 0.6000 +ANISOTROPY O1P P O5B O3A A11 0.6000 A22 1.0000 +ANISOTROPY O2P P O3A O5B A11 0.6000 A22 1.0000 + +IC C4a O4a C1a C2a 1.4055 108.09 -21.00 106.18 1.5457 !0.0 for c3aendo (north) pucker +IC O4a C1a C2a C3a 1.4127 106.18 30.00 103.11 1.5346 ! +IC C1a C2a C3a C4a 1.5457 103.11 -30.00 100.86 1.5211 !0.0 for o4aendo barrier +IC C2a C3a C4a O4a 1.5346 100.86 20.00 103.15 1.4055 +IC C3a C4a O4a C1a 1.5211 103.15 0.00 108.09 1.4127 +IC C2a O4a *C1a H11a 0.0000 0.00 120.00 0.00 0.0000 +IC C2a O4a *C1a H12a 0.0000 0.00 -120.00 0.00 0.0000 +IC C3a C1a *C2a H22a 0.0000 0.00 120.00 0.00 0.0000 +IC C3a C1a *C2a H21a 0.0000 0.00 -120.00 0.00 0.0000 +IC C1a C2a O2T H2T 0.0000 0.00 180.00 0.00 0.0000 +IC C2a C4a *C3a O3a 0.0000 0.00 -120.00 0.00 0.0000 +IC C2a C4a *C3a H31a 0.0000 0.00 120.00 0.00 0.0000 +IC O4a C3a *C4a H41a 0.0000 0.00 120.00 0.00 0.0000 +IC O4a C3a *C4a H42a 0.0000 0.00 -120.00 0.00 0.0000 +IC C4a C3a O3a P 0.0000 000.00 -164.29 000.00 0.0000 !epsilon bi:-164.29,bii:-92.78 +IC C3a O3a P O5b 0.0000 000.00 -89.68 000.00 0.0000 !zeta bi:-89.68,bii:159.19 +IC O5b O3a *P O1P 0.0000 000.00 -115.82 000.00 0.0000 +IC O5b O3a *P O2P 0.0000 000.00 115.90 000.00 0.0000 +IC O3a P O5b C5b 0.0000 000.00 -46.90 000.00 0.0000 !alpha+1:A:291, B:298 +IC P O5B C5B C4B 0.0000 0.00 180.00 0.00 0.0000 !beta+1:A:175, B:168 +IC H5b1 C5b O5b P 0.0000 000.00 180.00 000.00 0.0000 +IC H5b2 C5b O5b P 0.0000 000.00 60.00 000.00 0.0000 +IC O3a P O5B C5B 0.0000 0.00 180.00 0.00 0.0000 +IC C4B O5B *C5B H5B1 0.0000 0.00 120.00 0.00 0.0000 +IC C4B O5B *C5B H5B2 0.0000 0.00 -120.00 0.00 0.0000 +IC O5B C5B C4B C3B 0.0000 0.00 180.00 0.00 0.0000 !gamma+1,A:57, B:51 +IC C5B C4B C3B C2B 0.0000 0.00 -108.00 0.00 0.0000 !-155:c3aendo(north) -108:c2aendo(south) +IC C4B C3B C2B C1B 0.0000 0.00 -40.00 0.00 0.0000 !40:c3aendo(north) -40:c2aendo(south) +IC C3B C2B C1B O4B 0.0000 0.00 40.00 0.00 0.0000 !-40:c3aendo(north) 40:c2aendo(south) +!following IC is used to define C3'endo in surfaces, but commented due to redundancy +!IC C4B O4B C1B C2B 0.0000 0.00 25.00 0.00 0.0000 !0.0: c3aendo(north) 25:c2aendo(south) +IC O4B C3B *C4B H4B1 0.0000 0.00 120.00 0.00 0.0000 +IC C2B O4B *C1B H1B1 0.0000 0.00 120.00 0.00 0.0000 +IC C2B O4B *C1B H1B2 0.0000 0.00 -120.00 0.00 0.0000 +IC C3B C1B *C2B H2B1 0.0000 0.00 -120.00 0.00 0.0000 +IC C3B C1B *C2B H2B2 0.0000 0.00 120.00 0.00 0.0000 +IC C2B C4B *C3B H3B1 0.0000 0.00 120.00 0.00 0.0000 +IC C2B C4B *C3B H3B2 0.0000 0.00 -120.00 0.00 0.0000 + +PATC FIRS NONE LAST NONE + +RESI T3PM -1.000 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1) + ! capped with a methyl group. This is to investigate the differences + ! between BI and BII forms of DNA +! +! H41' O4' H11' +! \ / \ / +! H42'--C4' C1'--H12' +! | | +! H31'--C3'--C2'--H21' +! / \ +! O3' H22' +! | +! O1P==P==O2P +! | +! O3T (-1) +! \ +! C3T--H3T3 +! / \ +! H3T1 H3T2 +! +GROUP +ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545 +ATOM LP1 LPD -0.152 +ATOM LP2 LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1' CD315A 0.092 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H11' HDA2R5 0.055 +ATOM H12' HDA2R5 0.055 +ATOM C4' CD315B 0.092 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e +ATOM H41' HDA2R5 0.055 +ATOM H42' HDA2R5 0.055 +GROUP +ATOM C2' CD325B -0.144 ALPHA -1.617 THOLE 1.103 +ATOM H21' HDA2R5 0.072 +ATOM H22' HDA2R5 0.072 +GROUP +ATOM C3' CD315B -0.0755 ALPHA -1.617 THOLE 1.103 ! -0.3e +ATOM H31' HDA1R5 0.026 +ATOM O3' OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 +ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O3T OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C3T CD32C 0.1725 ALPHA -1.642 THOLE 0.862 +ATOM H3T1 HDA2A 0.026 +ATOM H3T2 HDA2A 0.026 +ATOM H3T3 HDA2A 0.026 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T C3T +BOND C3T H3T1 C3T H3T2 C3T H3T3 +BOND O4' LP1 O4' LP2 O4' LPX + +! O4' Lone pairs +LONEPAIR bisector LP1 O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LP2 O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0 +ANISOTROPY O4' LPX LP1 LP2 A11 0.8889 A22 1.2222 + +ANISOTROPY O3T O1P O3' O2P A11 1.0000 A22 0.6000 +ANISOTROPY O3' O2P O3T O1P A11 1.0000 A22 0.6000 +ANISOTROPY O1P P O3T O3' A11 0.6000 A22 1.0000 +ANISOTROPY O2P P O3' O3T A11 0.6000 A22 1.0000 + +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000 +IC C3' O3' P O3T 0.0000 000.00 -95.22 000.00 0.0000 +IC O3T O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 +IC O3T O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000 +IC C3T O3T P O3' 0.0000 000.00 -46.90 000.00 0.0000 +IC H3T1 C3T O3T P 0.0000 000.00 180.00 000.00 0.0000 +IC H3T2 C3T O3T P 0.0000 000.00 60.00 000.00 0.0000 +IC H3T3 C3T O3T P 0.0000 000.00 -60.00 000.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI DMPN -1.000 ! Dimethylphosphate, nucleic acids +! +! nucleic acid specific, differs from lipid DMP +! +! H11 +! | +! H13- C1-H12 +! \ +! O13 O11 +! \\ / +! (-) P1 +! // \ +! O14 O12 +! / +! H23-C2-H22 +! | +! H21 +! +GROUP +ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 +ATOM O13 OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O14 OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e +ATOM O11 OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM O12 OD30BN -0.470 ALPHA -0.901 THOLE 0.181 +ATOM C1 CD33C 0.0725 ALPHA -1.642 THOLE 0.862 ! -0.1e +ATOM H11 HDA3A 0.026 +ATOM H12 HDA3A 0.026 +ATOM H13 HDA3A 0.026 +ATOM C2 CD33C 0.0725 ALPHA -1.642 THOLE 0.862 ! -0.1e +ATOM H21 HDA3A 0.026 +ATOM H22 HDA3A 0.026 +ATOM H23 HDA3A 0.026 + +BOND P O11 P O12 P O13 P O14 +BOND O11 C1 O12 C2 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 + +ANISOTROPY O11 O13 O12 O14 A11 1.0000 A22 0.6000 +ANISOTROPY O12 O14 O11 O13 A11 1.0000 A22 0.6000 +ANISOTROPY O13 P O11 O12 A11 0.6000 A22 1.0000 +ANISOTROPY O14 P O12 O11 A11 0.6000 A22 1.0000 + +IC O11 P O12 C2 1.5837 102.73 72.47 116.87 1.4386 +IC O12 P O11 C1 1.5843 102.73 72.47 116.85 1.4394 +IC O13 P O11 C1 1.4910 107.70 -41.57 116.85 1.4394 +IC O14 P O12 C2 1.4906 107.67 -41.56 116.87 1.4386 +IC H11 C1 O11 P 1.1128 110.79 -42.95 116.85 1.5837 +IC H12 C1 O11 P 1.1118 109.92 77.01 116.85 1.5837 +IC H13 C1 O11 P 1.1095 109.84 -163.26 116.85 1.5837 +IC H21 C2 O12 P 1.1125 110.79 -42.95 116.87 1.5843 +IC H22 C2 O12 P 1.1123 109.91 77.00 116.87 1.5843 +IC H23 C2 O12 P 1.1094 109.84 -163.30 116.87 1.5843 +IC O12 O11 *P O13 1.5843 102.73 -114.04 107.70 1.4910 +IC O12 O11 *P O14 1.5843 102.73 113.68 108.15 1.4906 +IC P O11 C1 H11 1.5837 116.85 -42.95 110.79 1.1128 +IC H11 O11 *C1 H12 1.1128 110.79 119.96 109.92 1.1118 +IC H11 O11 *C1 H13 1.1128 110.79 -120.31 109.84 1.1095 +IC P O12 C2 H21 1.5843 116.87 -42.95 110.79 1.1125 +IC H21 O12 *C2 H22 1.1125 110.79 119.95 109.91 1.1123 +IC H21 O12 *C2 H23 1.1125 110.79 -120.35 109.84 1.1094 +patch first none last none + +RESI BRIBNA 0.000 ! beta-Ribose +! +! HO5--O5 +! \ O4 +! H51--C5 / \ O1--HO1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / H1 +! C3----C2 +! / \ / \ +! O3 H3 O2 H2 +! | | +! HO3 HO2 +! +! + +GROUP +ATOM O4 OD305A 0.000 ALPHA -0.618 THOLE 1.545 ! from THF +ATOM LPRA LPD -0.152 +ATOM LPRB LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1 CD315A 0.144 ALPHA -1.562 THOLE 1.103 +ATOM H1 HDA1R5 0.055 ! from THF +ATOM O1 OD31A 0.000 ALPHA -1.028 THOLE 1.3 ! from EtOH +ATOM HO1 HDP1A 0.360 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 +ATOM C4 CD315B 0.150 ALPHA -1.562 THOLE 1.103 +ATOM H4 HDA1R5 0.055 ! from THF +GROUP +ATOM C5 CD32A -0.060 ALPHA -1.000 THOLE 1.3 +ATOM H51 HDA2A 0.080 +ATOM H52 HDA2A 0.080 +ATOM O5 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM LP5A LPD -0.230 +ATOM LP5B LPD -0.230 +ATOM HO5 HDP1A 0.360 +GROUP +ATOM C2 CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge +ATOM H2 HDA1R5 0.080 +ATOM O2 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO2 HDP1A 0.360 +ATOM LP2A LPD -0.230 +ATOM LP2B LPD -0.230 +GROUP +ATOM C3 CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge +ATOM H3 HDA1R5 0.080 +ATOM O3 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HO3 HDP1A 0.360 +ATOM LP3A LPD -0.230 +ATOM LP3B LPD -0.230 + +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 + +BOND O4 LPRA O4 LPRB O4 LPX +BOND O1 LP1A O1 LP1B +BOND O2 LP2A O2 LP2B +BOND O3 LP3A O3 LP3B +BOND O5 LP5A O5 LP5B + +LONEPAIR bisector LPRA O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPRB O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 + +LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 + +ANISOTROPY O4 LPX LPRA LPRB A11 0.8889 A22 1.2222 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from crystal geometry* +IC C4 O4 C1 C2 1.4440 110.08 18.97 105.48 1.5227 +IC O4 C1 C2 C3 1.4297 105.48 -35.29 101.04 1.5223 +IC C1 C2 C3 C4 1.5227 101.04 37.68 102.70 1.5258 +IC C3 O4 *C4 C5 1.5258 105.50 121.77 111.20 1.4950 +IC C3 O4 *C4 H4 1.5258 105.50 -118.83 108.63 0.9263 +IC O4 C4 C5 O5 1.4440 111.20 64.86 111.55 1.4236 +IC C4 C5 O5 HO5 1.4950 111.55 -127.57 107.69 0.8505 +IC O5 C4 *C5 H51 1.4236 111.55 -124.94 108.14 0.9881 +IC O5 C4 *C5 H52 1.4236 111.55 119.60 108.76 0.9311 +IC C2 O4 *C1 O1 1.5227 105.48 -116.55 111.30 1.3905 +IC O4 C1 O1 HO1 1.4227 109.76 66.79 107.33 0.9584 +IC C2 O4 *C1 H1 1.5227 105.48 122.60 106.81 0.9349 +IC C3 C1 *C2 H2 1.5223 101.04 -123.72 113.32 0.9736 +IC C3 C1 *C2 O2 1.5223 101.04 114.67 111.40 1.4145 +IC C1 C2 O2 HO2 1.5227 111.40 80.30 105.08 0.8475 +IC C2 C4 *C3 O3 1.5223 102.70 -122.33 110.28 1.4117 +IC C2 C4 *C3 H3 1.5223 102.70 114.19 111.24 0.9813 +IC C4 C3 O3 HO3 1.5258 110.28 -141.24 107.85 0.8418 +IC C2 C4 *C3 H4 1.5223 102.70 -89.81 25.03 2.0467 + + +RESI BDEONA 0.000 ! beta-Deoxy-Ribose ! Updtaed C3, C5, H51, H52, H3, O1, O3, O5 as in DNA +! +! HO5--O5 +! \ O4 +! H51--C5 / \ O1--HO1 +! / \ / \ / +! H52 C4 C1 +! / \ / \ +! H4 \ / H1 +! C3----C2 +! / \ / \ +! O3 H3 H21 H22 +! | +! HO3 +! +ATOM O4 OD305A 0.000 ALPHA -0.618 THOLE 1.545 ! from THF +ATOM LPRA LPD -0.152 +ATOM LPRB LPD -0.152 +ATOM LPX LPD 0.000 !dummy for anisotropic polarizability +ATOM C1 CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! from THF, neutralize group charge +ATOM H1 HDA1R5 0.055 ! from THF +ATOM O1 OD31A 0.000 ALPHA -0.901 THOLE 0.18 +ATOM LP1A LPD -0.230 +ATOM LP1B LPD -0.230 +ATOM HO1 HDP1A 0.360 +ATOM C4 CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! from THF +ATOM H4 HDA1R5 0.055 ! from THF +GROUP +ATOM C5 CD32A 0.1975 ALPHA -1.642 THOLE 0.862 +ATOM H51 HDA2A 0.026 +ATOM H52 HDA2A 0.026 +ATOM O5 OD31A 0.000 ALPHA -0.901 THOLE 0.181 +ATOM LP5A LPD -0.230 +ATOM LP5B LPD -0.230 +ATOM HO5 HDP1A 0.360 +GROUP +ATOM C2 CD325B -0.144 ALPHA -1.617 THOLE 1.103 +ATOM H21 HDA2R5 0.072 +ATOM H22 HDA2R5 0.072 +GROUP +ATOM C3 CD315B -0.0755 ALPHA -1.642 THOLE 0.862 +ATOM H3 HDA1R5 0.026 +ATOM O3 OD31A 0.000 ALPHA -0.901 THOLE 0.18 +ATOM LP3A LPD -0.230 +ATOM LP3B LPD -0.230 +ATOM HO3 HDP1A 0.360 + +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H21 C2 H22 C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 O4 C4 C5 C5 H51 +BOND C5 H52 C5 O5 O5 HO5 +BOND O4 LPRA O4 LPRB O4 LPX +BOND O1 LP1A O1 LP1B +BOND O3 LP3A O3 LP3B +BOND O5 LP5A O5 LP5B + +LONEPAIR bisector LPRA O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0 +LONEPAIR bisector LPRB O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0 +LONEPAIR bisector LPX O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0 + +LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0 + +LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0 + +LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0 +LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0 + +ANISOTROPY O4 LPX LPRA LPRB A11 0.8889 A22 1.2222 +ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162 +ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162 +ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162 + +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4309 108.67 -19.01 106.25 1.5278 +IC O4 C1 C2 C3 1.4258 106.25 -8.82 103.23 1.5178 +IC C1 C2 C3 C4 1.5278 103.23 31.05 101.83 1.5232 +IC C3 O4 *C4 C5 1.5232 101.44 124.05 113.01 1.5448 +IC C3 O4 *C4 H4 1.5232 101.44 -115.42 106.74 1.1134 +IC O4 C4 C5 O5 1.4309 113.01 -178.27 111.12 1.4304 +IC C4 C5 O5 HO5 1.5448 111.12 -87.73 110.40 0.9643 +IC O4 C4 *C5 H51 2.4824 32.04 59.71 109.84 1.1020 +IC O4 C4 *C5 H52 2.4824 32.04 -58.37 108.86 1.1027 +IC C2 O4 *C1 O1 1.5278 106.25 -119.87 110.66 1.3905 +IC O4 C1 O1 HO1 1.4258 110.66 60.11 106.63 0.9584 +IC C2 O4 *C1 H1 1.5278 106.25 119.86 107.45 1.1137 +IC C3 C1 *C2 H21 1.5178 103.23 118.42 111.24 1.1030 +IC C3 C1 *C2 H22 1.5178 103.23 -122.05 112.95 1.0962 +IC C2 C4 *C3 O3 1.5178 101.83 -120.07 112.49 1.4116 +IC C4 C3 O3 HO3 1.5232 112.49 -53.93 107.21 0.9673 +IC C2 C4 *C3 H3 1.5178 101.83 117.41 109.93 1.1144 + +end + +read para card append +* Drude polarizable FF parameters +* + +BONDS +!atom type Kb b0 +!============================================ + +!!! indicates commented by alex +!!! CD325B HDA1R5 307.00 1.100 ! TF2M, cmb BRIB +!!! CD325B OD31A 350.00 1.440 ! C2'-O2', from PRO2 OD31A-CD31A BRIB +! NEW GUA (N9 is ND9G) +ND2R5F CD2R5B 400.00 1.370 ! Gua +ND2R5F CD2R6F 350.00 1.370 ! Gua +ND2R5F CD315B 220.00 1.456 ! N9-C1' purine glycosidic linkage +! NEW THY (N1 is ND1T) +ND2R6D CD2O1A 340.00 1.370 ! THY +ND2R6D CD2R6H 420.00 1.332 ! THY +ND2R6D CD315B 220.00 1.456 ! N1-C1' pyrimidine glycosidic linkage, from additive +!!additional nucleic acid parameters: watch for conflicts with carbohydrates +CD315B CD315B 195.00 1.518 ! C1'-C2', from THF CD325B-CD325B +CD315B OD31A 350.00 1.440 ! C2'-O2', from PRO2 OD31A-CD31A +CD315B OD30BN 335.00 1.440 ! C3'-O3', from DMP OD30B-CD33C +CD315B CD32C 222.50 1.528 ! C4'-C5', from TF2M CD315B-CD33A +CD315B CD32A 222.50 1.528 ! C4'-C5', from TF2M CD315B-CD33A +CD32C OD30BN 335.00 1.440 ! C5'-O5', from DMP OD30B-CD33C +! C1' is CD315A +ND2R6C CD315A 220.00 1.456 ! N1-C1' pyrimidine glycosidic linkage, from additive +ND2R5D CD315A 220.00 1.456 ! N9-C1' purine glycosidic linkage +ND2R6D CD315A 220.00 1.456 ! N1-C1' pyrimidine glycosidic linkage, from additive +OD305A CD315A 350.00 1.425 ! TF2M, cmb +CD315A CD325B 195.00 1.518 ! TF2M, cmb +CD315A CD315B 195.00 1.518 ! TF2M, cmb +CD315B HDA2R5 307.00 1.100 ! for T3PS +CD315A HDA2R5 307.00 1.100 ! for T3PS + +ANGLES +!atom types Ktheta Theta0 Kub S0 +!================================================== +! C1' is CD315A +!T3PS +OD305A CD315A HDA2R5 70.00 107.30 ! THF, viv 10/21/05 +HDA2R5 CD315A HDA2R5 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv +CD325B CD315A HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +CD315B CD315A HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +!!CYT +CD2R6H ND2R6C CD315A 45.00 115.90 ! CYT +CD2O1A ND2R6C CD315A 45.00 120.00 ! CYT +ND2R6C CD315A CD315B 110.00 113.70 ! CYT +ND2R6C CD315A HDA1R5 43.00 111.00 ! CYT +!!GUA +CD2R6F ND2R5D CD315A 45.00 126.50 ! GUA +CD2R5B ND2R5D CD315A 45.00 126.30 ! GUA +ND2R5D CD315A CD315B 110.00 111.00 ! GUA +ND2R5D CD315A HDA1R5 43.00 111.00 ! GUA +! Glycosidic linkage +ND2R6C CD315A OD305A 110.00 108.00 +ND2R6C CD315A CD325B 110.00 111.70 +ND2R5D CD315A OD305A 110.00 108.00 +ND2R5D CD315A CD325B 110.00 111.50 +! Repeating for new type of N1 in THY +CD2R6H ND2R6D CD315A 45.00 115.90 ! THY +CD2O1A ND2R6D CD315A 45.00 120.00 ! THY +ND2R6D CD315A HDA1R5 43.00 111.00 ! THY +ND2R6D CD315A OD305A 110.00 108.00 ! THY +ND2R6D CD315A CD325B 110.00 111.70 ! THY +ND2R6D CD315A CD315B 110.00 111.70 ! THY +! Sugar group +CD315A OD305A CD315B 95.00 111.00 +OD305A CD315A CD325B 45.00 111.10 +CD315A CD325B CD315B 58.00 109.50 11.16 2.561 +CD315A CD315B OD31A 115.00 109.70 !RNA +OD305A CD315A CD315B 45.00 111.10 !RNA +CD315A CD315B CD315B 58.00 109.50 11.16 2.561 !RNA +! Hydrogens +OD305A CD315A HDA1R5 70.00 107.30 ! TF2M 02/09, cmb +CD325B CD315A HDA1R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +CD315A CD325B HDA2R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +CD315A CD315B HDA1R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +CD315B CD315A HDA1R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +CD315A CD315B HDA2R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +!! End of C1' CD315A !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!NH-2 Bases ADE/GUA/CYT!!!!!!!!!!! +CD2R6C ND2B1 HDP1A 45.00 121.50 ! ADE, va !pyramidal 45.0 115.5 ! planar 45.0 120.0, cmb 04/10 +HDP1A ND2B1 HDP1A 24.00 117.00 ! NA bases, cmb 04/10 +CD2R6B ND2B1 HDP1A 40.00 121.50 ! CYT, va !pyramidal 40.0 115.5 ! planar 40.0 120.0, cmb 04/10 +ND2B1 CD2R6B ND2R6B 81.00 122.30 ! CYT, cmb 04/10 ! N3-C4-N4 +ND2B1 CD2R6B CD2R6A 81.00 120.00 ! CYT, cmb 04/10 ! C5-C4-N4 +OD2C1B CD2O1A CD2R6A 93.00 122.60 ! THY, cmb 04/10 ! C5-C4-O4 +ND2R6B CD2O1A OD2C1B 130.00 125.00 ! CYT, cmb 04/10 ! O2-C2-N3 +CD2O1A ND2R6C HDP1A 40.50 114.00 ! THY, cmb 04/10 ! C2/C4-N3 +CD2O1A ND2R6C CD2O1A 40.00 132.00 ! THY, cmb 04/10 ! C2-N3-C4 +CD2O1A ND2R6B CD2R6B 50.00 120.00 ! CYT, va ! C2-N3-C4 +CD2O1A ND2R6C CD2R6H 100.00 119.00 ! THY/CYT, cmb 04/10 ! C2-N1-C6 +ND2R6C CD2O1A ND2R6C 50.00 120.00 ! THY, cmb 04/10 ! N1-C2-N3 +ND2R6B CD2O1A ND2R6C 50.00 126.00 ! CYT, cmb 04/10 ! N1-C2-N3 +ND2R6C CD2O1A CD2R6A 70.00 118.00 ! THY, cmb 04/10 ! N3-C4-C5 +CD2O1A CD2R6A CD2R6H 100.00 118.70 ! THY, cmb 04/10 ! C4-C5-C6 +CD2R6B CD2R6A CD2R6H 50.00 117.00 ! CYT, cmb ! C4-C5-C6 +ND2R6C CD2R6H CD2R6A 10.00 114.00 ! THY/CYT, cmb 04/10 ! N1-C6-C5 +ND2B1 CD2R6C ND2R6C 95.00 116.40 ! GUA, cmb 04/10 ! N1-C2-N2 +ND2B1 CD2R6C ND2R6B 45.00 127.00 ! ADE/GUA, cmb 04/10 ! N3-C2-N2/N1-C6-N6 +ND2B1 CD2R6C CD2R6F 45.00 123.00 ! ADE, cmb 04/10 ! N6-C6-C51) +ND2R6C CD2O1A OD2C1B 70.00 124.40 ! THY, cmb 04/10 ! N1-C6-O6) +OD2C1B CD2O1A CD2R6F 50.00 125.70 ! GUA, cmb 04/10 ! C5-C6-O6) +ND2R5D CD2R6F ND2R6B 100.00 118.00 ! ADE/GUA, cmb 04/10 ! N3-C4-N9 +ND2R5E CD2R6F CD2R6C 100.00 128.00 ! ADE, bridgeC5, cmb 04/10 ! N7-C5-C6 +ND2R5E CD2R6F CD2O1A 125.00 129.00 ! GUA, cmb 04/10 ! N7-C5-C6 +CD2R5B ND2R5D CD33A 17.00 125.80 ! ADE, cmb 04/10 ! C8-N9-C9 +CD2R6F ND2R5D CD33A 17.00 127.90 ! ADE, cmb 04/10 ! C4-N9-C9 +CD2R5B ND2R5E CD2R6F 127.91 103.00 ! ADE, cmb 04/10 +CD2R5B ND2R5D CD2R6F 100.00 106.30 ! ADE, cmb 04/10 ! C8-N9-C4 +ND2R5E CD2R6F CD2R6F 99.82 116.50 ! ADE, cmb 04/10 ! C4-C5-N7 +ND2R5D CD2R6F CD2R6F 100.00 105.00 ! ADE, cmb 04/10 ! C5-C4-N9 +ND2R5E CD2R5B ND2R5D 130.00 109.50 ! ADE, cmb 04/10 ! N7-C8-N9 +ND2R6B CD2R6C ND2R6C 70.00 130.20 ! GUA, cmb 04/10 ! N3-C2-N1 +CD2R6C ND2R6B CD2R6C 90.00 111.80 ! ADE, cmb ! C2-N1-C6 +CD2O1A ND2R6C CD2R6C 70.00 123.10 ! GUA, cmb 04/10 ! C2-N1-C6 +ND2R6B CD2R6C CD2R6F 60.00 106.70 ! ADE, cmb 04/10 ! N1-C6-C5 +ND2R6C CD2O1A CD2R6F 70.00 107.80 ! GUA, cmb 04/10 ! N1-C6-C5 +CD2R6C CD2R6F CD2R6F 60.00 121.00 ! ADE, cmb 04/10 ! C6-C5-C4 +CD2O1A CD2R6F CD2R6F 70.00 120.00 ! GUA, cmb 04/10 ! C6-C5-C4 +! Repeating for new type of N9 in GUA +ND2R5F CD2R5B HDR5B 25.00 122.50 20.00 2.1400 ! GUA +CD2R6F ND2R5F CD315B 45.00 126.50 ! GUA +CD2R5B ND2R5F CD315B 45.00 126.30 ! GUA +ND2R5F CD315B HDA1R5 43.00 111.00 ! GUA +ND2R5F CD315B CD315B 110.00 111.00 ! GUA +ND2R5F CD315B CD325B 110.00 111.00 ! GUA +CD2R5B ND2R5F CD2R6F 100.00 106.30 ! GUA +ND2R5F CD2R6F ND2R6B 100.00 118.00 ! GUA +ND2R5F CD2R6F CD2R6F 100.00 105.00 ! GUA +ND2R5E CD2R5B ND2R5F 130.00 109.50 ! GUA +ND2R5F CD315B OD305A 110.00 108.00 ! GUA +! Repeating for new type of N1 in THY +CD2O1A ND2R6D CD2R6H 100.00 119.00 ! THY +CD2R6H ND2R6D CD315B 45.00 115.90 ! THY +CD2O1A ND2R6D CD315B 45.00 120.00 ! THY +ND2R6D CD315B HDA1R5 43.00 111.00 ! THY +ND2R6D CD315B OD305A 110.00 108.00 ! THY +ND2R6D CD315B CD325B 110.00 111.70 ! THY +ND2R6D CD2R6H HDR6B 30.00 116.00 ! THY +ND2R6D CD2R6H CD2R6A 10.00 114.00 ! THY +ND2R6D CD2O1A OD2C1B 70.00 124.40 ! THY +ND2R6D CD2O1A ND2R6C 50.00 120.00 ! THY +ND2R6D CD315B CD315B 110.00 113.70 ! THY +OD305A CD315A OD31A 45.00 116.50 ! for BRIB +!! Everywhere +OD305A CD325B CD315B 45.00 111.10 ! O4'-C1'-C2', from THF +CD315B CD315B HDA1R5 35.00 111.40 ! C1'-C2'-H2'', from TF2M +CD315B OD31A HDP1A 59.00 108.00 ! C2'-O2'-H2', from PRO2 !RNA +CD315B CD315B CD315B 58.00 109.50 11.16 2.561 ! C1'-C2'-C3', from THF +HDA1R5 CD315B OD30BN 34.50 110.10 22.53 2.179 ! H3'-C3'-O3', from TF2M +HDA1R5 CD315B OD31A 34.50 110.10 22.53 2.179 ! H2''-C2'-O2', from TF2M !RNA +CD325B CD315B CD32C 53.35 114.00 8.00 2.561 ! C3'-C4'-C5', from TF2M +HDA1R5 CD315B CD32C 34.50 110.10 22.53 2.179 ! H4'-C4'-C5', from TF2M +CD315B CD32C HDA2A 33.43 110.10 22.53 2.179 ! C4'-C5'-H5'', from TF2M +CD315B CD32A HDA2A 33.43 110.10 22.53 2.179 ! C4'-C5'-H5'', from TF2M +HDA2A CD32C OD30BN 60.00 109.50 ! H5'-C5'-O5', from DMP +!!CYT +CD2R6H ND2R6C CD315B 45.00 115.90 ! CYT +CD2O1A ND2R6C CD315B 45.00 120.00 ! CYT +ND2R6C CD315B CD315B 110.00 113.70 ! CYT +ND2R6C CD315B HDA1R5 43.00 111.00 ! CYT +!!GUA +CD2R6F ND2R5D CD315B 45.00 126.50 ! GUA +CD2R5B ND2R5D CD315B 45.00 126.30 ! GUA +ND2R5D CD315B CD315B 110.00 111.00 ! GUA +ND2R5D CD315B HDA1R5 43.00 111.00 ! GUA +!!5TER +CD32A CD315B HDA1R5 34.50 110.10 22.53 2.179 ! C5T-C4'-H4', from TF2M +! Sugar group +CD325B CD315B HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +CD315B CD325B CD315B 58.00 109.50 11.16 2.561 +CD325B CD315B CD315B 58.00 109.50 11.16 2.561 +OD305A CD315B CD315B 45.00 111.10 +CD315B OD305A CD315B 95.00 111.00 +OD305A CD315B CD32C 90.00 109.20 +OD305A CD315B CD32A 90.00 109.20 +CD315B CD315B CD32C 45.00 111.00 +CD315B CD315B CD32A 45.00 111.00 +CD325B CD315B OD30BN 115.00 109.70 +CD325B CD315A OD31A 115.00 109.70 ! for BDEO +CD325B CD315B OD31A 115.00 109.70 !3TER +CD315B CD315B OD30BN 115.00 109.70 !RNA +CD315B CD315B OD31A 115.00 109.70 !RNA +CD315B CD315A OD31A 115.00 109.70 ! for BRIB +! Backbone +CD315B CD32C OD30BN 70.00 108.40 +OD31A CD32A CD315B 70.00 108.40 +OD30BN PD1AN OD30BN 90.00 107.50 +CD32C OD30BN PD1AN 40.00 124.50 +CD315B OD30BN PD1AN 40.00 114.50 +! Phosphate group +OD2C2C PD1AN OD2C2C 120.00 125.00 +OD2C2C PD1AN OD30BN 98.90 113.00 +! Glycosidic linkage +ND2R6C CD315B OD305A 110.00 108.00 +ND2R6C CD315B CD325B 110.00 111.70 +ND2R5D CD315B OD305A 110.00 108.00 +ND2R5D CD315B CD325B 110.00 111.50 +OD305A CD315B HDA2R5 70.00 107.30 +HDA2R5 CD315B HDA2R5 38.50 106.80 5.40 1.802 +CD315B CD315B HDA2R5 35.00 111.40 22.53 2.179 + +DIHEDRALS +!atom types Kchi n delta +!================================================= +! +!Please follow these conventions when fitting dihedral parameters +!1) use positive force constants in all cases (switch the phase...) +! (vary phase during fitting and keep force constants positive) +!2) maintain the phase at 0 or 180 if possiple. perform initial +! fitting with this contraint and, if necessary, only then +! vary the phases during fitting. note that if the phases +! are NOT 0 or 180 the parameters are NOT transferable across +! stereoisomers +!3) refit with only individual multiplicities of 1 through 6 +!4) maintain the number of significant figures used below +! +! ND3A3 CD2O1A CD31C CD32B 0.200 3 0.00 ! comment +! +! C1' is CD315A +!T3PS +HDA2R5 CD315A CD325B HDA2R5 0.190 3 0.00 ! THF, viv +CD315B OD305A CD315A HDA2R5 0.300 3 0.00 ! TF2M, cmb +CD315B CD325B CD315A HDA2R5 0.190 3 0.00 ! TF2M, cmb +CD315A OD305A CD315B HDA2R5 0.300 3 0.00 ! TF2M, cmb +CD315A CD325B CD315B HDA2R5 0.190 3 0.00 ! TF2M, cmb +! Involving N1/N9 (not Chi) +ND2R6C CD315A CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' !RNA +HDA2R5 CD325B CD315A ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1 +HDA1R5 CD325B CD315A ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1 +CD2O1A ND2R6C CD315A HDA1R5 0.000 3 0.00 ! C2-N1-C1'-H1' +CD2R6H ND2R6C CD315A HDA1R5 0.195 3 0.00 ! C6-N1-C1'-H1' +ND2R6C CD315A OD305A CD315B 0.000 3 0.00 ! N1-C1a-O4a-C4a +ND2R6C CD315A CD325B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a +!!! ND2R5D CD315A CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' ! RNA +HDA2R5 CD325B CD315A ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9 +HDA1R5 CD325B CD315A ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9 +CD2R6F ND2R5D CD315A HDA1R5 0.000 3 0.00 ! C4-N9-C1'-H1' +CD2R5B ND2R5D CD315A HDA1R5 0.195 3 0.00 ! C8-N9-C1'-H1' +ND2R5D CD315A CD325B CD315B 0.000 3 0.00 ! N9-C1a-C2D-C3a +ND2R5D CD315A OD305A CD315B 0.000 3 0.00 ! N9-C1a-O4a-C4a +ND2R6C CD315A CD315B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' !RNA +HDA2R5 CD315B CD315A ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1 +HDA1R5 CD315B CD315A ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1 + +ND2R6C CD315A CD315B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a !RNA +ND2R5D CD315A CD315B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' !RNA +HDA2R5 CD315B CD315A ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9 +HDA1R5 CD315B CD315A ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9 +ND2R5D CD315A CD315B CD315B 0.000 3 0.00 ! N9-C1a-C2D-C3a !RNA +ND2R6D CD315A CD315B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a !RNA +ND2R6D CD315A CD325B HDA2R5 0.000 3 0.00 ! N1-C1a-C2D-H2D +CD2O1A ND2R6D CD315A HDA1R5 0.000 3 0.00 ! C2-N1-C1a-H1a, from C27 +CD2R6H ND2R6D CD315A HDA1R5 0.195 3 0.00 ! C6-N1-C1a-H1a +ND2R6D CD315A OD305A CD315B 0.000 3 0.00 ! N1-C1a-O4a-C4a +ND2R6D CD315A CD325B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a +CD2R6A CD2R6H ND2R6D CD315A 11.000 2 180.00 ! C5-C6-N1-C1', from C27 +HDR6B CD2R6H ND2R6D CD315A 0.300 2 180.00 ! H6-C6-N1-C1', from C27 +OD2C1B CD2O1A ND2R6D CD315A 11.000 2 180.00 ! O2-C2-N1-C1', from C27 +ND2R6B CD2O1A ND2R6D CD315A 11.000 2 180.00 ! N3-C2-N1-C1', from C27 +ND2R6D CD2O1A ND2R6D CD315A 11.000 2 180.00 ! N3-C2-N1-C1' +ND2R6C CD2O1A ND2R6D CD315A 11.000 2 180.00 ! N3-C2-N1-C1' +! Chi Adenine/Guanine +!O4'-C1'-N9-C4, ADE +OD305A CD315A ND2R5D CD2R6F 1.302 1 -64.20 +OD305A CD315A ND2R5D CD2R6F 1.989 2 -30.10 +OD305A CD315A ND2R5D CD2R6F 0.948 3 2.12 +OD305A CD315A ND2R5D CD2R6F 0.035 4 -122.90 +!O4'-C1'-N9-C4, GUA +OD305A CD315A ND2R5F CD2R6F 1.302 1 -64.20 +OD305A CD315A ND2R5F CD2R6F 1.989 2 -30.10 +OD305A CD315A ND2R5F CD2R6F 0.948 3 2.12 +OD305A CD315A ND2R5F CD2R6F 0.035 4 -122.90 +!O4'-C1'-N9-C8 +CD2R5B ND2R5F CD315A OD305A 1.400 1 0.00 ! GUA +CD2R5B ND2R5D CD315A OD305A 1.500 1 0.00 ! ADE +!C2'-C1'-N9-C4 +CD2R6F ND2R5F CD315A CD325B 0.000 3 0.00 ! GUA +CD2R6F ND2R5D CD315A CD325B 1.200 1 0.00 ! ADE +CD2R6F ND2R5F CD315A CD315B 0.000 3 0.00 ! GUA +CD2R6F ND2R5D CD315A CD315B 1.200 1 0.00 ! ADE +!C2'-C1'-N9-C8 +CD2R5B ND2R5D CD315A CD325B 0.000 3 180.00 ! ADE +CD2R5B ND2R5F CD315A CD325B 0.000 3 180.00 ! GUA +CD2R5B ND2R5D CD315A CD315B 0.000 3 180.00 ! ADE +CD2R5B ND2R5F CD315A CD315B 0.000 3 180.00 ! GUA +! Chi Cytosine/Thymine +!O4'-C1'-N1-C2, CYT +CD2O1A ND2R6C CD315A OD305A 0.000 3 0.00 +!O4'-C1'-N1-C2, THY +OD305A CD315A ND2R6D CD2O1A 1.174 1 -79.32 +OD305A CD315A ND2R6D CD2O1A 1.960 2 -48.12 +OD305A CD315A ND2R6D CD2O1A 1.112 3 -26.88 +OD305A CD315A ND2R6D CD2O1A 0.051 4 205.92 +!O4'-C1'-N1-C6 +CD2R6H ND2R6C CD315A OD305A 0.350 1 0.00 ! CYT +CD2R6H ND2R6D CD315A OD305A 1.900 1 0.00 ! THY +!C2'-C1'-N1-C2 +CD2O1A ND2R6C CD315A CD325B 0.800 3 -20.00 ! CYT +CD2O1A ND2R6D CD315A CD325B 0.150 3 -20.00 ! THY +CD2O1A ND2R6C CD315A CD315B 0.800 3 -20.00 ! CYT +CD2O1A ND2R6D CD315A CD315B 0.150 3 -20.00 ! THY +!C2'-C1'-N1-C6 +CD2R6H ND2R6C CD315A CD325B 0.000 3 180.00 ! CYT +CD2R6H ND2R6D CD315A CD325B 0.000 3 180.00 ! THY +CD2R6H ND2R6C CD315A CD315B 0.000 3 180.00 ! CYT +CD2R6H ND2R6D CD315A CD315B 0.000 3 180.00 ! THY +! End of Chi's !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!dihedrals that include both base and sugar atoms (but not glycosidic linkage) +! Cyt +CD2R6A CD2R6H ND2R6C CD315A 11.000 2 180.00 ! C5-C6-N1-C1', from C27 +HDR6B CD2R6H ND2R6C CD315A 0.300 2 180.00 ! H6-C6-N1-C1', from C27 +OD2C1B CD2O1A ND2R6C CD315A 11.000 2 180.00 ! O2-C2-N1-C1', from C27 +ND2R6B CD2O1A ND2R6C CD315A 11.000 2 180.00 ! N3-C2-N1-C1', from C27 +! Thy +ND2R6C CD2O1A ND2R6C CD315A 11.000 2 180.00 ! N3-C2-N1-C1' +! Gua +ND2R6B CD2R6F ND2R5D CD315A 11.000 2 180.00 ! N3-C4-N9-C1' +CD2R6F CD2R6F ND2R5D CD315A 11.000 2 180.00 ! C5-C4-N9-C1', from C27 +ND2R5E CD2R5B ND2R5D CD315A 11.000 2 180.00 ! N7-C8-N9-C1', from C27 +HDR5B CD2R5B ND2R5D CD315A 0.300 2 180.00 ! H8-C8-N9-C1', from C27 +!Hydrogens +HDA1R5 CD325B CD315A OD305A 0.195 3 180.00 ! H3'-C3'-C4'-O4' +HDA1R5 CD325B CD315A HDA1R5 0.200 3 0.00 ! H3'-C3'-C4'-H4' +OD305A CD315A OD31A HDP1A 0.200 3 0.00 ! HO1-O1-C1-O4 +HDA1R5 CD315A OD305A CD315B 0.000 3 0.00 ! H1'-C1'-O4'-C4' +HDA1R5 CD315A CD325B CD315B 0.195 3 0.00 ! H1'-C1'-C2'-C3' +HDA1R5 CD315A CD325B HDA2R5 0.195 3 0.00 ! TF2M, cmb +HDA1R5 CD315B CD315A OD305A 0.195 3 180.00 ! H3'-C3'-C4'-O4' +HDA1R5 CD315B CD315A HDA1R5 0.200 3 0.00 ! H3'-C3'-C4'-H4' +HDA1R5 CD315A CD315B CD315B 0.195 3 0.00 ! H1'-C1'-C2'-C3' !RNA + +! Exocyclic groups +CD315A OD305A CD315B CD32C 0.300 3 0.00 ! C5'-C4'-O4'-C1' +CD315A CD325B CD315B OD30BN 0.200 3 0.00 ! C1'-C2'-C3'-O3' +CD315A OD305A CD315B CD32A 0.300 3 0.00 ! C5'-C4'-O4'-C1' +CD315A CD325B CD315B OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3' +CD315A CD315B CD315B OD30BN 0.200 3 0.00 ! C1'-C2'-C3'-O3' +CD315A CD315B CD315B OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3' +CD315B CD315B CD315A OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3', for BRIB +CD315B CD315B CD315B CD32C 0.200 3 0.00 ! C5'-C4'-C3'-C2' +CD315B CD315B CD315B CD32A 0.200 3 0.00 ! C5'-C4'-C3'-C2' +HDA1R5 CD315B OD305A CD315A 0.000 3 0.00 ! H4'-C4'-O4'-C1' +OD305A CD315A CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +HDA1R5 CD315B CD325B CD315A 0.195 3 0.00 ! H3'-C3'-C2'-C1' +! Hydroxyl group in RNA +CD315B OD305A CD315A OD31A 0.000 3 180.00 ! O1-C1-O4-C4, for BRIB +!conflict with DNA; used for 3TER in DNA. May need new atom type +!3TER patch; conflict with RNA 2'OH +CD315B CD315B OD31A HDP1A 0.200 1 0.00 ! 3TER patch, conflict +CD315B CD325B OD31A HDP1A 0.200 1 0.00 ! DNA 3TER patch +!CD315B CD315B OD31A HDP1A 1.660 1 0.00 ! PRO2 !RNA 2'OH +!CD315B CD315B OD31A HDP1A 0.120 2 0.00 ! PRO2 !RNA 2'OH +!CD315B CD315B OD31A HDP1A 0.340 3 0.00 ! PRO2 !RNA 2'OH +! +CD315B CD315B CD315B OD31A 0.000 3 0.00 ! O2'-C2'-C3'-C4' !RNA +HDA1R5 CD315A CD315B OD31A 0.000 3 0.00 ! H1'-C1'-C2'-O2' !RNA +OD305A CD315A CD315B OD31A 0.000 3 0.00 ! O2'-C2'-C1'-O4' !RNA +HDA1R5 CD315B CD315B CD315A 0.195 3 0.00 ! H3'-C3'-C2'-C1' !RNA +OD31A CD315B CD315B OD31A 0.000 3 180.00 ! O2-C2-C1-O1, for BRIB +OD31A CD315B CD315A OD31A 0.000 3 180.00 ! O2'-C2'-C1'-O1, for BRIB +!! End of C1' is CD315A!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! Repeating torsions for GUA (N9 is ND9G) +ND2R5F CD315B CD325B HDA2R5 0.000 3 0.00 ! N9-C1a-C2D-H2D +CD2R6F ND2R5F CD315B HDA1R5 0.000 3 0.00 ! C4-N9-C1a-H1a +CD2R5B ND2R5F CD315B HDA1R5 0.195 3 0.00 ! C8-N9-C1a-H1a +CD2R6F ND2R5E CD2R5B ND2R5F 14.000 2 180.00 ! ADE, cmb 04/10 +CD2R6F ND2R5F CD2R5B ND2R5E 6.000 2 180.00 ! ADE, cmb 04/10 +CD2R6F ND2R5F CD2R5B HDR5B 3.500 2 180.00 ! ADE, va H8, cmb 04/10 +CD33A ND2R5F CD2R5B ND2R5E 1.000 2 180.00 ! ADE, cmb 04/10 +CD33A ND2R5F CD2R5B HDR5B 1.000 2 180.00 ! ADE, cmb 04/10 +HDP1A ND2R5F CD2R5B ND2R5B 1.000 2 180.00 ! IMID, imidazole +HDP1A ND2R5F CD2R5B ND2R5E 1.000 2 180.00 ! ADE, cmb 04/10 +HDP1A ND2R5F CD2R5B HDR5B 1.000 2 180.00 ! ADE, IMID, imidazole +CD2R5B ND2R5F CD2R6F ND2R6B 2.000 2 180.00 ! ADE, cmb 04/10 +CD2R5B ND2R5F CD2R6F CD2R6F 6.000 2 180.00 ! ADE, cmb 04/10 +CD33A ND2R5F CD2R6F ND2R6B 1.000 2 180.00 ! ADE, cmb +CD33A ND2R5F CD2R6F CD2R6F 1.000 2 180.00 ! ADE, cmb +HDP1A ND2R5F CD2R6F ND2R6B 1.500 2 180.00 ! ADE, cmb 04/10 +HDP1A ND2R5F CD2R6F CD2R6F 1.200 2 180.00 ! ADE, cmb 04/10 +CD2R5B ND2R5F CD33A HDA3A 0.000 3 0.00 ! ADE, cmb 04/10 +CD2R6F ND2R5F CD33A HDA3A 0.000 3 0.00 ! ADE, cmb +CD2R6C ND2R6B CD2R6F ND2R5F 2.000 2 180.00 ! ADE, butterfly motion, cmb 04/10 +ND2R5E CD2R6F CD2R6F ND2R5F 14.000 2 180.00 ! ADE, cmb 04/10 +ND2R5F CD2R6F CD2R6F CD2O1A 0.000 2 180.00 ! GUA, cmb 04/10 +ND2R5F CD2R6F CD2R6F CD2R6C 3.000 2 180.00 ! ADE, va A; butterfly motion, cmb 04/10 +CD32A ND2R5F CD2R6F ND2R6B 1.000 2 180.00 ! va; Et-Gua +CD32A ND2R5F CD2R6F CD2R6F 1.000 2 180.00 ! va; Et-Gua +CD32A ND2R5F CD2R5B ND2R5E 1.000 2 180.00 ! va; Et-Gua +CD32A ND2R5F CD2R5B HDR5B 1.000 2 180.00 ! va; Et-Gua +CD33A CD32A ND2R5F CD2R6F 1.000 3 0.00 ! va; Et-Gua +HDA2A CD32A ND2R5F CD2R6F 0.000 3 0.00 ! va; Et-Gua +HDA2A CD32A ND2R5F CD2R5B 0.000 3 0.00 ! va; Et-Gua +CD33A CD32A ND2R5F CD2R5B 1.000 3 0.00 ! va; Et-Gua +ND2R5F CD32A CD33A HDA3A 0.160 3 0.00 ! va; Et-Gua +ND2R5F CD315B CD325B CD315B 0.000 3 0.00 ! N9-C1a-C2D-C3a +ND2R5F CD315B OD305A CD315B 0.000 3 0.00 ! N9-C1a-O4a-C4a +ND2R6B CD2R6F ND2R5F CD315B 11.000 2 180.00 ! N3-C4-N9-C1' +CD2R6F CD2R6F ND2R5F CD315B 11.000 2 180.00 ! C5-C4-N9-C1', from C27 +ND2R5F CD315B CD315B HDA1R5 0.000 3 0.00 ! N9-C1'-C2'-H2'' +ND2R5F CD315B CD315B OD31A 0.000 3 0.00 ! N9-C1'-C2'-O2' +ND2R5F CD315B CD325B OD31A 0.000 3 0.00 ! N9-C1'-C2'-O2' ! RNA +ND2R5F CD315B CD315B CD315B 0.000 3 0.00 ! N9-C1'-C2'-C3' +ND2R5E CD2R5B ND2R5F CD315B 11.000 2 180.00 ! N7-C8-N9-C1', from C27 +HDR5B CD2R5B ND2R5F CD315B 0.300 2 180.00 ! H8-C8-N9-C1', from C27 +! Repeating torsions for THY (N1 is ND1T) +ND2R6D CD315B CD325B HDA2R5 0.000 3 0.00 ! N1-C1a-C2D-H2D +CD2O1A ND2R6D CD315B HDA1R5 0.000 3 0.00 ! C2-N1-C1a-H1a, from C27 +CD2R6H ND2R6D CD315B HDA1R5 0.195 3 0.00 ! C6-N1-C1a-H1a +HDP1A ND2B1 CD2R6C ND2R6D 1.400 2 180.00 ! GUA, cmb 04/10 +CD2R6B ND2R6B CD2O1A ND2R6D 0.600 2 180.00 ! CYT, cmb 04/10 +CD2R6H ND2R6D CD2O1A ND2R6B 0.600 2 180.00 ! CYT, cmb 04/10 +CD2R6H ND2R6B CD2O1A ND2R6D 1.500 2 180.00 ! THY, cmb +CD2R6H ND2R6D CD2O1A ND2R6D 1.500 2 180.00 ! THY, cmb 04/10 +CD2R6H ND2R6D CD2O1A OD2C1B 1.600 2 180.00 ! CYT, cmb 04/10 +CD33A ND2R6D CD2O1A ND2R6B 0.900 2 180.00 ! CYT, cmb 04/10 +CD33A ND2R6D CD2O1A ND2R6D 0.700 2 180.00 ! THY, cmb 04/10 +CD33A ND2R6D CD2O1A OD2C1B 0.900 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2R6B CD2O1A ND2R6D 1.600 2 180.00 ! THY, cmb 04/10 +CD2R6F ND2R6B CD2R6C ND2R6D 2.000 2 180.00 ! GUA, cmb 04/10 +CD2O1A ND2R6D CD2R6H CD2R6A 0.600 2 180.00 ! CYT, cmb 04/10 +CD2O1A ND2R6D CD2R6H HDR6B 3.600 2 180.00 ! CYT, cmb 04/10 +CD33A ND2R6D CD2R6H CD2R6A 1.000 2 180.00 ! CYT, cmb 04/10 +CD33A ND2R6D CD2R6H HDR6B 1.000 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2R6D CD2R6H CD2R6A 1.600 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2R6D CD2R6H HDR6B 1.500 2 180.00 ! CYT, cmb 04/10 +CD2O1A ND2R6D CD33A HDA3A 0.000 3 0.00 ! CYT, cmb 04/10 +CD2R6H ND2R6D CD33A HDA3A 0.000 3 0.00 ! CYT, cmb 04/10 +CD2O1A ND2R6D CD2O1A ND2R6B 1.500 2 180.00 ! THY, cmb 04/10 +CD2O1A ND2R6D CD2O1A ND2R6D 1.500 2 180.00 ! THY, cmb 04/10 +CD2O1A ND2R6D CD2O1A OD2C1B 0.900 2 180.00 ! THY, cmb 04/10 +CD2O1A ND2R6D CD2O1A CD2R6A 0.900 2 180.00 ! THY, cmb 04/10 +CD2R6C ND2R6D CD2O1A OD2C1B 8.000 2 180.00 ! GUA, cmb 04/10 +CD2R6C ND2R6D CD2O1A CD2R6F 0.200 2 180.00 ! GUA, cmb 04/10 +HDP1A ND2R6D CD2O1A ND2R6B 3.800 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6D CD2O1A ND2R6D 3.800 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6D CD2O1A OD2C1B 0.000 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6D CD2O1A CD2R6A 4.800 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6D CD2O1A CD2R6F 3.600 2 180.00 ! GUA, cmb 04/10 +CD2O1A ND2R6D CD2R6C ND2B1 4.000 2 180.00 ! GUA, cmb 04/10 +CD2O1A ND2R6D CD2R6C ND2R6B 0.200 2 180.00 ! GUA, cmb 04/10 +HDP1A ND2R6D CD2R6C ND2B1 0.000 2 180.00 ! GUA, cmb 04/10 +HDP1A ND2R6D CD2R6C ND2R6B 3.600 2 180.00 ! GUA, cmb 04/10 +ND2R6D CD2O1A CD2R6A CD2R6H 1.800 2 180.00 ! THY, cmb 04/10 +ND2R6D CD2O1A CD2R6A CD33A 1.000 2 180.00 ! THY, cmb 04/10 +ND2R6D CD2O1A CD2R6A HDR6A 1.000 2 180.00 ! URA +ND2R6D CD2O1A CD2R6F ND2R5E 2.000 2 180.00 ! GUA, cmb 04/10 +ND2R6D CD2O1A CD2R6F CD2R6F 0.200 2 180.00 ! GUA, cmb 04/10 +CD2O1A CD2R6A CD2R6H ND2R6D 3.000 2 180.00 ! THY, cmb 04/10 +CD2R6B CD2R6A CD2R6H ND2R6D 0.800 2 180.00 ! CYT, cmb 04/10 +CD33A CD2R6A CD2R6H ND2R6D 5.600 2 180.00 ! THY, cmb 04/10 +HDR6A CD2R6A CD2R6H ND2R6D 2.800 2 180.00 ! CYT, cmb 04/10 +ND2R6D CD315B OD305A CD315B 0.000 3 0.00 ! N1-C1a-O4a-C4a +ND2R6D CD315B CD325B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a +CD2R6A CD2R6H ND2R6D CD315B 11.000 2 180.00 ! C5-C6-N1-C1', from C27 +HDR6B CD2R6H ND2R6D CD315B 0.300 2 180.00 ! H6-C6-N1-C1', from C27 +ND2R6D CD315B CD315B HDA1R5 0.000 3 0.00 ! N1-C1'-C2'-H2'' +ND2R6D CD315B CD315B OD31A 0.000 3 0.00 ! N1-C1'-C2'-O2' +ND2R6D CD315B CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' ! RNA +ND2R6C CD315B CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' ! RNA +ND2R5D CD315B CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' ! RNA +ND2R6D CD315B CD315B CD315B 0.000 3 0.00 ! N1-C1'-C2'-C3' +OD2C1B CD2O1A ND2R6D CD315B 11.000 2 180.00 ! O2-C2-N1-C1', from C27 +ND2R6B CD2O1A ND2R6D CD315B 11.000 2 180.00 ! N3-C2-N1-C1', from C27 +ND2R6D CD2O1A ND2R6D CD315B 11.000 2 180.00 ! N3-C2-N1-C1' +CD2O1A ND2R6C CD2O1A ND2R6D 1.500 2 180.00 ! THY, cmb 04/10 +HDP1A ND2R6C CD2O1A ND2R6D 3.800 2 180.00 ! THY, cmb 04/10 +CD2R6H ND2R6D CD2O1A ND2R6C 1.500 2 180.00 ! THY, cmb 04/10 +ND2R6C CD2O1A ND2R6D CD315B 11.000 2 180.00 ! N3-C2-N1-C1' +! Torsions involving Hydrogens +HDA2R5 CD325B CD315B OD30BN 0.195 3 0.00 ! H2'-C2'-C3'-O3' +HDA1R5 CD325B CD315B OD30BN 0.195 3 0.00 ! H2'-C2'-C3'-O3' +HDA2R5 CD325B CD315B OD31A 0.195 3 0.00 ! H2'-C2'-C3'-O3T +HDA2R5 CD325B CD315A OD31A 0.195 3 0.00 ! H2'-C2'-C3'-O3T, for BDEO +HDA2R5 CD325B CD315B CD315B 0.195 3 0.00 ! H2'-C2'-C3'-C4' +HDA2R5 CD325B CD315B ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9 +HDA1R5 CD325B CD315B ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9 +HDA2R5 CD325B CD315B ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1 +HDA1R5 CD325B CD315B ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1 +HDA1R5 CD315B OD305A CD315B 0.000 3 0.00 ! H1'-C1'-O4'-C4' +HDA1R5 CD315B CD325B CD315B 0.195 3 0.00 ! H1'-C1'-C2'-C3' +CD2R6F ND2R5D CD315B HDA1R5 0.000 3 0.00 ! C4-N9-C1'-H1' +CD2R5B ND2R5D CD315B HDA1R5 0.195 3 0.00 ! C8-N9-C1'-H1' +CD2O1A ND2R6C CD315B HDA1R5 0.000 3 0.00 ! C2-N1-C1'-H1' +CD2R6H ND2R6C CD315B HDA1R5 0.195 3 0.00 ! C6-N1-C1'-H1' +HDA1R5 CD315B CD315B CD32C 0.195 3 0.00 ! H3'-C3'-C4'-C5' +HDA1R5 CD315B CD315B OD305A 0.195 3 180.00 ! H3'-C3'-C4'-O4' +HDA1R5 CD315B CD315B HDA1R5 0.195 3 0.00 ! H3'-C3'-C4'-H4' +HDA1R5 CD315B CD315B OD30BN 0.195 3 0.00 ! H4'-C4'-C3'-O3' +CD325B CD315B CD315B HDA1R5 0.000 3 0.00 ! H4'-C4'-C3'-C2' +HDA1R5 CD315B CD315B HDA2R5 0.200 3 0.00 ! TF2M, cmb +HDA2R5 CD315B CD315B OD30BN 0.200 3 0.00 ! H2D-C2D-C3a-O3a, from TF2M +CD325B CD315B CD315B HDA2R5 0.200 3 0.00 ! TF2M, cmb +CD315B OD305A CD315B HDA2R5 0.300 3 0.00 ! TF2M, cmb +OD305A CD315B CD315B HDA2R5 0.200 3 0.00 ! TF2M, cmb +CD315B CD325B CD315B HDA2R5 0.190 3 0.00 ! TF2M, cmb +HDA2R5 CD315B CD325B HDA2R5 0.190 3 0.00 ! THF, viv +HDA2R5 CD325B CD315B CD32C 0.200 3 0.00 ! H3'-C3'-C4'-C5', from TF2M +HDA2R5 CD315B CD315B CD32C 0.200 3 0.00 ! H3'-C3'-C4'-C5', from TF2M +CD32A CD315B CD315B HDA1R5 0.200 3 0.00 ! C5T-C4a-C3a-H3a, from TF2M +CD315B CD315B CD315B HDA1R5 0.200 3 0.00 ! C2a-C3a-C4a-H4a, from THF +HDA1R5 CD315B CD315B OD31A 0.200 3 0.00 ! H1a-C1a-C2a-O2a, from TF2M +HDA1R5 CD315B CD315A OD31A 0.200 3 0.00 ! H1a-C1a-C2a-O2a, from TF2M, fro BRIB +OD31A CD32A CD315B HDA1R5 0.270 1 0.00 ! O5T-C5T-C4a-H4a, from PRO1 +HDA2A CD32A CD315B HDA1R5 0.200 3 0.00 ! H5T1-C5T-C4a-H4a, from TF2M +HDA2A CD32A CD315B OD305A 0.200 3 0.00 ! H5T1-C5T-C4a-O4a, from TF2M +HDP1A ND2B1 CD2R6B ND2R6B 1.300 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2B1 CD2R6B CD2R6A 1.300 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2B1 CD2R6C ND2R6B 1.000 2 180.00 ! ADE +HDP1A ND2B1 CD2R6C CD2R6F 1.000 2 180.00 ! ADE, cmb 04/10 +! +ND2R5D CD315B CD325B CD315B 0.000 3 0.00 ! N9-C1a-C2D-C3a +ND2R5D CD315B OD305A CD315B 0.000 3 0.00 ! N9-C1a-O4a-C4a +ND2R6C CD315B OD305A CD315B 0.000 3 0.00 ! N1-C1a-O4a-C4a +ND2R6C CD315B CD325B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a +HDA2A CD32C OD30BN PD1AN 0.000 3 0.00 +CD315B CD315B CD32C HDA2A 0.200 3 0.00 +CD325B CD315B CD32C HDA2A 0.200 3 0.00 +HDA1R5 CD315B CD32C HDA2A 0.200 3 0.00 +HDA1R5 CD315B CD32C OD30BN 0.200 3 0.00 +OD305A CD315B CD32C HDA2A 0.195 1 0.00 +HDA1R5 CD315B OD30BN PD1AN 0.000 3 0.00 +!Sugar +CD315B OD305A CD315A CD325B 0.250 3 0.00 ! C2'-C1'-O4'-C4' ! nu_0 +CD315B CD325B CD315A OD305A 0.250 6 0.00 ! C3'-C2'-C1'-O4' ! nu_1 +CD315A CD325B CD315B CD315B 0.250 3 0.00 ! C1'-C2'-C3'-C4' ! nu_2 +CD325B CD315B CD315B OD305A 0.200 4 0.00 ! C2'-C3'-C4'-O4' ! nu_3 +CD325B CD315B CD315B OD305A 0.060 5 180.00 ! C2'-C3'-C4'-O4' ! nu_3 +CD325B CD315B CD315B OD305A 0.060 6 180.00 ! C2'-C3'-C4'-O4' ! nu_3 +CD315A OD305A CD315B CD315B 0.200 6 180.00 ! C1'-O4'-C4'-C3' ! nu_4 +CD315B OD305A CD315A CD315B 0.250 3 0.00 ! C2'-C1'-O4'-C4' ! nu_0 !RNA +CD315B CD315B CD315A OD305A 0.250 6 0.00 ! C3'-C2'-C1'-O4' ! nu_1 !RNA +CD315A CD315B CD315B CD315B 0.250 3 0.00 ! C1'-C2'-C3'-C4' ! nu_2 !RNA +CD315B CD315B CD315B OD305A 0.200 4 0.00 ! C2'-C3'-C4'-O4' ! nu_3 !RNA +CD315B CD315B CD315B OD305A 0.060 5 180.00 ! C2'-C3'-C4'-O4' ! nu_3 !RNA +CD315B CD315B CD315B OD305A 0.060 6 180.00 ! C2'-C3'-C4'-O4' ! nu_3 !RNA + +!Sugar torsions +!!! CD315B OD305A CD315B CD325B 0.250 3 0.00 ! C2'-C1'-O4'-C4' ! nu_0 +!!! CD315B CD325B CD315B OD305A 0.250 6 0.00 ! C3'-C2'-C1'-O4' ! nu_1 +!!! CD315B CD325B CD315B CD315B 0.250 3 0.00 ! C1'-C2'-C3'-C4' ! nu_2 +!!! CD315B OD305A CD315B CD315B 0.200 6 180.00 ! C1'-O4'-C4'-C3' ! nu_4 +! Exocyclic torsions +CD315B OD305A CD315B CD32C 0.300 3 0.00 ! C5'-C4'-O4'-C1' +CD325B CD315B CD315B CD32C 0.200 3 0.00 ! C5'-C4'-C3'-C2' +CD315B CD325B CD315B OD30BN 0.200 3 0.00 ! C1'-C2'-C3'-O3' +OD30BN CD315B CD315B OD305A 0.200 3 0.00 ! O4'-C4'-C3'-O3' +CD315B OD305A CD315B CD32A 0.300 3 0.00 ! C5'-C4'-O4'-C1' +CD325B CD315B CD315B CD32A 0.200 3 0.00 ! C5'-C4'-C3'-C2' +CD315B CD325B CD315B OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3' +OD31A CD315B CD315B OD305A 0.200 3 0.00 ! O4'-C4'-C3'-O3' !RNA +CD315B CD325B CD315A OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3', for BDEO +!!! OD31A CD325B CD315B OD30BN 0.200 3 0.00 ! O2'-C2'-C3'-O3', RNA + +!! DNA Backbone parameters !! +!DMPN specific, differs from lipid DMP +CD33C OD30BN PD1AN OD2C2C 1.090 1 180.00 ! DMP +CD33C OD30BN PD1AN OD2C2C 1.730 2 0.00 ! DMP +CD33C OD30BN PD1AN OD2C2C 0.610 3 180.00 ! DMP +CD33C OD30BN PD1AN OD30BN 2.140 1 180.00 ! DMP +CD33C OD30BN PD1AN OD30BN 3.000 2 0.00 ! DMP +CD33C OD30BN PD1AN OD30BN 1.760 3 0.00 ! DMP +PD1AN OD30BN CD33C HDA3A 0.000 3 0.00 ! DMP, nucleic acids +! Alpha +CD32C OD30BN PD1AN OD30BN 0.727 1 -132.18 +CD32C OD30BN PD1AN OD30BN 1.274 2 -5.54 +CD32C OD30BN PD1AN OD30BN 0.568 3 -37.37 +CD32C OD30BN PD1AN OD30BN 0.267 4 -19.84 +!Alpha_2: O1P-P-O5'-C5' +CD32C OD30BN PD1AN OD2C2C 0.100 3 0.00 +!Beta +CD315B CD32C OD30BN PD1AN 0.800 1 220.00 +HDP1A OD31A CD32A CD315B 0.800 1 220.00 !TER +HDP1A OD31A CD315A CD315B 0.800 1 220.00 !TER, for BRIB +! Gamma +CD315B CD315B CD32C OD30BN 3.131 1 142.51 +CD315B CD315B CD32C OD30BN 0.951 2 -132.16 +CD315B CD315B CD32C OD30BN 1.158 3 -81.35 +CD315B CD315B CD32C OD30BN 0.000 4 0.00 +CD315B CD315B CD32C OD30BN 0.543 5 -153.61 +CD315B CD315B CD32C OD30BN 0.000 6 0.00 +!Gamma 5TER +OD31A CD32A CD315B CD315B 3.131 1 142.51 +OD31A CD32A CD315B CD315B 0.951 2 -132.16 +OD31A CD32A CD315B CD315B 1.158 3 -81.35 +OD31A CD32A CD315B CD315B 0.000 4 0.00 +OD31A CD32A CD315B CD315B 0.543 5 -153.61 +OD31A CD32A CD315B CD315B 0.000 6 0.00 +!Gamma_2: O4'-C4'-C5'-O5' +OD305A CD315B CD32C OD30BN 3.400 1 180.00 +OD31A CD32A CD315B OD305A 3.400 1 180.00 +!Delta +OD30BN CD315B CD315B CD32C 0.200 3 0.00 +OD31A CD315B CD315B CD32C 0.200 3 0.00 +OD30BN CD315B CD315B CD32A 0.200 3 0.00 +OD31A CD315B CD315B CD32A 0.200 3 0.00 !RNA +!Epsilon +CD315B CD315B OD30BN PD1AN 1.200 1 180.00 !RNA; note the conflict of the P-O3'-C3'-C4' +CD315B CD315B OD30BN PD1AN 0.400 2 0.00 ! and P-O3'-C3'-C2' terms in RNA +CD315B CD315B OD30BN PD1AN 0.000 3 180.00 ! May require a new RNA atom type +CD315B CD315B OD30BN PD1AN 0.200 4 -10.00 +CD315B CD315B OD30BN PD1AN 0.500 5 10.00 +!Epsilon_2: C2'-C3'-O3'-P/H3T +CD325B CD315A OD31A HDP1A 2.100 1 180.00 ! for BDEO +CD325B CD315B OD31A HDP1A 2.100 1 180.00 ! for BDEO +CD325B CD315B OD30BN PD1AN 2.100 1 180.00 +HDA1R5 CD315B OD31A HDP1A 0.000 1 0.00 !RNA +!Zeta +CD315B OD30BN PD1AN OD30BN 0.717 1 39.87 +CD315B OD30BN PD1AN OD30BN 0.533 2 2.71 +CD315B OD30BN PD1AN OD30BN 0.120 3 149.03 +CD315B OD30BN PD1AN OD30BN 0.027 4 -58.52 +CD315B OD30BN PD1AN OD2C2C 0.100 3 0.00 ! Zeta_2: C3'-O3'-P-O1P +!! End of DNA backbone torsions !! +! Chi Adenine/Guanine +!O4'-C1'-N9-C4, ADE +OD305A CD315B ND2R5D CD2R6F 1.302 1 -64.20 +OD305A CD315B ND2R5D CD2R6F 1.989 2 -30.10 +OD305A CD315B ND2R5D CD2R6F 0.948 3 2.12 +OD305A CD315B ND2R5D CD2R6F 0.035 4 -122.90 +!O4'-C1'-N9-C4, GUA +OD305A CD315B ND2R5F CD2R6F 1.302 1 -64.20 +OD305A CD315B ND2R5F CD2R6F 1.989 2 -30.10 +OD305A CD315B ND2R5F CD2R6F 0.948 3 2.12 +OD305A CD315B ND2R5F CD2R6F 0.035 4 -122.90 +!O4'-C1'-N9-C8 +CD2R5B ND2R5F CD315B OD305A 1.400 1 0.00 ! GUA +CD2R5B ND2R5D CD315B OD305A 1.500 1 0.00 ! ADE +!C2'-C1'-N9-C4 +CD2R6F ND2R5F CD315B CD325B 0.000 3 0.00 ! GUA +CD2R6F ND2R5D CD315B CD325B 1.200 1 0.00 ! ADE +!C2'-C1'-N9-C8 +CD2R5B ND2R5D CD315B CD325B 0.000 3 180.00 ! ADE +CD2R5B ND2R5F CD315B CD325B 0.000 3 180.00 ! GUA +! Chi Cytosine/Thymine +!O4'-C1'-N1-C2, CYT +CD2O1A ND2R6C CD315B OD305A 0.000 3 0.00 +!O4'-C1'-N1-C2, THY +OD305A CD315B ND2R6D CD2O1A 1.174 1 -79.32 +OD305A CD315B ND2R6D CD2O1A 1.960 2 -48.12 +OD305A CD315B ND2R6D CD2O1A 1.112 3 -26.88 +OD305A CD315B ND2R6D CD2O1A 0.051 4 205.92 +!O4'-C1'-N1-C6 +CD2R6H ND2R6C CD315B OD305A 0.350 1 0.00 ! CYT +CD2R6H ND2R6D CD315B OD305A 1.900 1 0.00 ! THY +!C2'-C1'-N1-C2 +CD2O1A ND2R6C CD315B CD325B 0.800 3 -20.00 ! CYT +CD2O1A ND2R6D CD315B CD325B 0.150 3 -20.00 ! THY +!C2'-C1'-N1-C6 +CD2R6H ND2R6C CD315B CD325B 0.000 3 180.00 ! CYT +CD2R6H ND2R6D CD315B CD325B 0.000 3 180.00 ! THY +! End of Chi's !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +CD315B CD315B CD315B OD30BN 0.300 3 0.00 ! C1'-C2'-C3'-O3', from TF2M +OD31A CD315B CD315B OD30BN 0.200 3 0.00 ! O2'-C2'-C3'-O3', from THF +HDA1R5 CD315B CD325B OD305A 0.200 3 0.00 ! H3'-C3'-C4'-O4', from THF +!dihedrals that include both base and sugar atoms (but not glycosidic linkage) +!! Cyt +CD2R6A CD2R6H ND2R6C CD315B 11.000 2 180.00 ! C5-C6-N1-C1', from C27 +HDR6B CD2R6H ND2R6C CD315B 0.300 2 180.00 ! H6-C6-N1-C1', from C27 +ND2R6C CD315B CD315B HDA1R5 0.000 3 0.00 ! N1-C1'-C2'-H2'' +ND2R6C CD315B CD315B OD31A 0.000 3 0.00 ! N1-C1'-C2'-O2' !RNA +ND2R6C CD315B CD315B CD315B 0.000 3 0.00 ! N1-C1'-C2'-C3' +OD2C1B CD2O1A ND2R6C CD315B 11.000 2 180.00 ! O2-C2-N1-C1', from C27 +ND2R6B CD2O1A ND2R6C CD315B 11.000 2 180.00 ! N3-C2-N1-C1', from C27 +!! Thy +ND2R6C CD2O1A ND2R6C CD315B 11.000 2 180.00 ! N3-C2-N1-C1' +!! Gua +ND2R6B CD2R6F ND2R5D CD315B 11.000 2 180.00 ! N3-C4-N9-C1' +CD2R6F CD2R6F ND2R5D CD315B 11.000 2 180.00 ! C5-C4-N9-C1', from C27 +CD2R6F ND2R5D CD315B CD315B 0.000 3 0.00 ! C4-N9-C1'-C2' +ND2R5D CD315B CD315B HDA1R5 0.000 3 0.00 ! N9-C1'-C2'-H2'' +ND2R5D CD315B CD315B OD31A 0.000 3 0.00 ! N9-C1'-C2'-O2' !RNA +ND2R5D CD315B CD315B CD315B 0.000 3 0.00 ! N9-C1'-C2'-C3' +ND2R5E CD2R5B ND2R5D CD315B 11.000 2 180.00 ! N7-C8-N9-C1', from C27 +HDR5B CD2R5B ND2R5D CD315B 0.300 2 180.00 ! H8-C8-N9-C1', from C27 +CD2R5B ND2R5D CD315B CD315B 0.000 3 180.00 ! C8-N9-C1'-C2' +!! 5TER +HDA2A CD32A CD315B CD315B 0.200 3 0.00 ! H5T1-C5T-C4'-C3', from TF2M + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +CD2O1A ND2R6D ND2R6C OD2C1B 80.000 0 0.00 ! CYT, cmb 04/10 +ND2B1 CD2R6B HDP1A HDP1A 12.000 0 0.00 ! CYT, cmb 04/10 +ND2B1 CD2R6C HDP1A HDP1A 12.000 0 0.00 ! ADE, cmb 04/10 +CD2R6C ND2R6B CD2R6F ND2B1 60.000 0 0.00 ! ADE, cmb 04/10 + + +NONBONDED nbxmod 5 atom vatom cdiel vdistance switch vswitch - +cutnb 16.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +NBFIX + +!Parameters for screening term required for divalent ions +THOLE TCUT 5.0 MAXNBTHOLE 5000 + +END diff --git a/charmm/toppar/drude/positive_drude/00readme b/charmm/toppar/drude/positive_drude/00readme new file mode 100644 index 00000000..2b2c6b22 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/00readme @@ -0,0 +1,9 @@ + +Temporary test case for the postitive drude models is +positive_drude_test_temp.inp due to bug related to "drude reset" and +"dele atom" that only effects energies etc. following deletion of all +atoms and drudes and generation of new atoms with drudes. To run the +test case edit run_test.cmd to point to the charmm executable and then +source run_test.cmd. Files in the data subdirectory will have the +energies for each complex. + diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_bro.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_bro.dat new file mode 100644 index 00000000..eb29163b --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_bro.dat @@ -0,0 +1,5 @@ + BRO + EINITIAL = 31.9154 + UMIN = -14.1419 + DMIN = 3.18837 + MU = 2.66317 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_ces.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_ces.dat new file mode 100644 index 00000000..5d5e9bc7 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_ces.dat @@ -0,0 +1,5 @@ + CES + EINITIAL = -10.2471 + UMIN = -14.17 + DMIN = 2.99737 + MU = 2.60754 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_cla.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_cla.dat new file mode 100644 index 00000000..2592a312 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_cla.dat @@ -0,0 +1,5 @@ + CLA + EINITIAL = 24.8241 + UMIN = -16.2467 + DMIN = 3.01716 + MU = 2.75749 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_flu.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_flu.dat new file mode 100644 index 00000000..fc24fd3e --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_flu.dat @@ -0,0 +1,5 @@ + FLU + EINITIAL = 16.23 + UMIN = -6.102769E+07 + DMIN = 1.90061 + MU = 7.20789 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_iod.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_iod.dat new file mode 100644 index 00000000..3caeac35 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_iod.dat @@ -0,0 +1,5 @@ + IOD + EINITIAL = 51.6207 + UMIN = -11.6237 + DMIN = 3.45474 + MU = 2.54601 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_lit.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_lit.dat new file mode 100644 index 00000000..fd443e81 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_lit.dat @@ -0,0 +1,5 @@ + LIT + EINITIAL = -14.2786 + UMIN = -33.9486 + DMIN = 1.94319 + MU = 3.33777 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_pot.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_pot.dat new file mode 100644 index 00000000..7165dda0 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_pot.dat @@ -0,0 +1,5 @@ + POT + EINITIAL = -13.8 + UMIN = -18.578 + DMIN = 2.60958 + MU = 2.79562 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_rub.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_rub.dat new file mode 100644 index 00000000..4a2d057f --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_rub.dat @@ -0,0 +1,5 @@ + RUB + EINITIAL = -12.9731 + UMIN = -16.4737 + DMIN = 2.78181 + MU = 2.70421 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_sod.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_sod.dat new file mode 100644 index 00000000..539c9b86 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_sod.dat @@ -0,0 +1,5 @@ + SOD + EINITIAL = -14.2663 + UMIN = -24.9862 + DMIN = 2.24663 + MU = 3.04009 diff --git a/charmm/toppar/drude/positive_drude/data/swm4_ion_swm4.dat b/charmm/toppar/drude/positive_drude/data/swm4_ion_swm4.dat new file mode 100644 index 00000000..0092b3b9 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/data/swm4_ion_swm4.dat @@ -0,0 +1,3 @@ + SWM4-NDP PENTAMER + EINITIAL = -1.0885 + UMIN = -1.20197 diff --git a/charmm/toppar/drude/positive_drude/positive_drude_test.inp b/charmm/toppar/drude/positive_drude/positive_drude_test.inp new file mode 100644 index 00000000..3d1b08e4 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/positive_drude_test.inp @@ -0,0 +1,144 @@ +* test ions with swm4 water +* + +set toppardir . + +stream @toppardir/toppar_drude_positive_swm4_ions.str + +!data file +open unit 33 write form name swm4_ion.dat + +!test water model alone + +!! Generate water residues + +read sequence SWM4 5 +generate BULK setup noangle nodihedral drude dmass 0.4 + +read coor card +* water coordinated +* + 15 + 1 1 SWM4 OH2 7.38263 0.89233 -4.71643 BULK 1 -2.47655 + 2 1 SWM4 H1 7.30586 0.03258 -4.30272 BULK 1 -2.60884 + 3 1 SWM4 H2 7.54089 1.49503 -3.98984 BULK 1 -3.13461 + 4 2 SWM4 OH2 -6.20797 4.45953 0.73205 BULK 2 0.94227 + 5 2 SWM4 H1 -5.29193 4.71233 0.84693 BULK 2 1.64723 + 6 2 SWM4 H2 -6.68689 5.00122 1.35929 BULK 2 0.17114 + 7 3 SWM4 OH2 6.06969 6.29872 6.92235 BULK 3 2.53526 + 8 3 SWM4 H1 6.72984 6.67673 7.50333 BULK 3 3.25850 + 9 3 SWM4 H2 5.35053 6.05270 7.50417 BULK 3 2.71730 + 10 4 SWM4 OH2 0.22109 -4.53529 -5.63924 BULK 4 -0.75622 + 11 4 SWM4 H1 0.41942 -4.34638 -6.55642 BULK 4 -0.30566 + 12 4 SWM4 H2 -0.71907 -4.71479 -5.62906 BULK 4 -0.12645 + 13 5 SWM4 OH2 -5.19509 1.26039 -1.16892 BULK 5 1.07017 + 14 5 SWM4 H1 -5.93523 1.34878 -0.56841 BULK 5 0.70060 + 15 5 SWM4 H2 -5.53474 1.55603 -2.01359 BULK 5 1.11651 + +!========================================================= +! DRUDE and LONE PAIR SETUP +!--------------------------------------------------------- +coor sdrude +coor shake + +SHAKE bonh param tolerance 1.0e-9 - + nofast - + select ( .not. type D* ) end - + select ( .not. type D* ) end + +coor print + +update inbfrq -1 ihbfrq 0 atom switch vatom vfswitch cutnb 99.0 ctofnb 89.0 ctonnb 79.0 + +! Minimize positions of Drude particles +! constrain position of regular atoms +!cons fix select .not. type D* end +energy +set einit ?ener +mini SD nstep 10 nprint 1 +cons fix select none end +energy + +write title unit 33 +* SWM4-NDP pentamer +* Einitial = @einit +* Umin = ?ENER +* + +drude reset +delete atom sele all end + +!! Monomer + ion + +set count 1 + +label ion_loop + +if count eq 1 set iontype LIT +if count eq 2 set iontype SOD +if count eq 3 set iontype POT +if count eq 4 set iontype RUB +if count eq 5 set iontype CES +if count eq 6 set iontype FLU +if count eq 7 set iontype CLA +if count eq 8 set iontype BRO +if count eq 9 set iontype IOD + +read sequence SWM4 1 +generate SOLV setup noangle nodihedral drude dmass 0.4 +read sequence @IONTYPE 1 +generate ION setup first none last none drude dmass 0.4 + +read coor card +* SWM4 +* + 4 + 1 1 SWM4 OH2 1.25163 -0.00023 0.27019 + 2 1 SWM4 OM 1.37619 -0.00008 0.06798 + 3 1 SWM4 H1 1.55899 0.75708 -0.22804 + 4 1 SWM4 H2 1.55883 -0.75682 -0.22925 + +coor orient select type O* end +coor set xdir -3.0 select type @IONTYPE end +coor init sele type D* end + +coor print +coor sdrude +coor print +print psf +bomlev -1 +coor shake +coor print +coor stat + +update inbfrq -1 ihbfrq 0 atom switch vatom vfswitch cutnb 99.0 ctofnb 89.0 ctonnb 79.0 + +!================================================== +! Water-ion interaction +!-------------------------------------------------- + +energy +set einit ?ener +mini SD step 0.01 nstep 5000 nprint 1000 +coor orient select type O* .or. type @IONTYPE end + +energy ! ?ENER +quick 1 6 ! ?DIST +coor dipole select segid SOLV end ! ?RDIP + +write title unit 33 +* @IONTYPE +* Einitial = @einit +* Umin = ?ENER +* Dmin = ?DIST +* mu = ?RDIP +* + +drude reset +delete atom select all end + +calc count = @count + 1 + +if count le 9 goto ion_loop + +stop diff --git a/charmm/toppar/drude/positive_drude/positive_drude_test_temp.inp b/charmm/toppar/drude/positive_drude/positive_drude_test_temp.inp new file mode 100644 index 00000000..d533f6aa --- /dev/null +++ b/charmm/toppar/drude/positive_drude/positive_drude_test_temp.inp @@ -0,0 +1,157 @@ +* test ions with swm4 water +* + +!set id1 swm4 + +set toppardir . + +stream @toppardir/toppar_drude_positive_swm4_ions.str + +!data file +open unit 33 write form name data/swm4_ion_@id1.dat + +!test water model alone + +if id1 eq swm4 then + +!! Generate water residues + +read sequence SWM4 5 +generate BULK setup noangle nodihedral drude dmass 0.4 + +read coor card +* water coordinated +* + 15 + 1 1 SWM4 OH2 7.38263 0.89233 -4.71643 BULK 1 -2.47655 + 2 1 SWM4 H1 7.30586 0.03258 -4.30272 BULK 1 -2.60884 + 3 1 SWM4 H2 7.54089 1.49503 -3.98984 BULK 1 -3.13461 + 4 2 SWM4 OH2 -6.20797 4.45953 0.73205 BULK 2 0.94227 + 5 2 SWM4 H1 -5.29193 4.71233 0.84693 BULK 2 1.64723 + 6 2 SWM4 H2 -6.68689 5.00122 1.35929 BULK 2 0.17114 + 7 3 SWM4 OH2 6.06969 6.29872 6.92235 BULK 3 2.53526 + 8 3 SWM4 H1 6.72984 6.67673 7.50333 BULK 3 3.25850 + 9 3 SWM4 H2 5.35053 6.05270 7.50417 BULK 3 2.71730 + 10 4 SWM4 OH2 0.22109 -4.53529 -5.63924 BULK 4 -0.75622 + 11 4 SWM4 H1 0.41942 -4.34638 -6.55642 BULK 4 -0.30566 + 12 4 SWM4 H2 -0.71907 -4.71479 -5.62906 BULK 4 -0.12645 + 13 5 SWM4 OH2 -5.19509 1.26039 -1.16892 BULK 5 1.07017 + 14 5 SWM4 H1 -5.93523 1.34878 -0.56841 BULK 5 0.70060 + 15 5 SWM4 H2 -5.53474 1.55603 -2.01359 BULK 5 1.11651 + +!========================================================= +! DRUDE and LONE PAIR SETUP +!--------------------------------------------------------- +coor sdrude +coor shake + +SHAKE bonh param tolerance 1.0e-9 - + nofast - + select ( .not. type D* ) end - + select ( .not. type D* ) end + +coor print + +update inbfrq -1 ihbfrq 0 atom switch vatom vfswitch cutnb 99.0 ctofnb 89.0 ctonnb 79.0 + +! Minimize positions of Drude particles +! constrain position of regular atoms +!cons fix select .not. type D* end +energy +set einit ?ener +mini SD nstep 10 nprint 1 +cons fix select none end +energy + +write title unit 33 +* SWM4-NDP pentamer +* Einitial = @einit +* Umin = ?ENER +* + +drude reset +delete atom sele all end + +stop +endif !if swm4 + +!! Monomer + ion + +!set count 1 +!label ion_loop + +if count eq 1 set iontype LIT +if count eq 2 set iontype SOD +if count eq 3 set iontype POT +if count eq 4 set iontype RUB +if count eq 5 set iontype CES +if count eq 6 set iontype FLU +if count eq 7 set iontype CLA +if count eq 8 set iontype BRO +if count eq 9 set iontype IOD + +read sequence SWM4 1 +generate SOLV setup noangle nodihedral drude dmass 0.4 +read sequence @IONTYPE 1 +generate ION setup first none last none drude dmass 0.4 + +read coor card +* SWM4 +* + 4 + 1 1 SWM4 OH2 1.25163 -0.00023 0.27019 + 2 1 SWM4 OM 1.37619 -0.00008 0.06798 + 3 1 SWM4 H1 1.55899 0.75708 -0.22804 + 4 1 SWM4 H2 1.55883 -0.75682 -0.22925 + +coor orient select type O* end +coor set xdir -3.0 select type @IONTYPE end + +coor print +coor sdrude +coor print +print psf +bomlev -1 +coor shake +coor print +coor stat + +!SHAKE bonh param tolerance 1.0e-9 - +! nofast - +! select ( segid SOLV .and. .not. type D* ) end - +! select ( segid SOLV .and. .not. type D* ) end + + +update inbfrq -1 ihbfrq 0 atom switch vatom vfswitch cutnb 99.0 ctofnb 89.0 ctonnb 79.0 + +!================================================== +! Water-ion interaction +!-------------------------------------------------- + +energy +set einit ?ener +mini SD step 0.01 nstep 5000 nprint 1000 +coor orient select type O* .or. type @IONTYPE end + +energy ! ?ENER +quick 1 6 ! ?DIST +coor dipole select segid SOLV end ! ?RDIP + +write title unit 33 +* @IONTYPE +* Einitial = @einit +* Umin = ?ENER +* Dmin = ?DIST +* mu = ?RDIP +* + +stop + +drude reset +delete atom select all end + +calc count = @count + 1 + +if count le 9 goto ion_loop + +stop diff --git a/charmm/toppar/drude/positive_drude/positive_drude_test_temp.out b/charmm/toppar/drude/positive_drude/positive_drude_test_temp.out new file mode 100644 index 00000000..9cafe5e8 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/positive_drude_test_temp.out @@ -0,0 +1,615 @@ + Processing passed argument "count:9" + Parameter: count <- "9" + Processing passed argument "id1:iod" + Parameter: id1 <- "iod" +1 + Chemistry at HARvard Macromolecular Mechanics + (CHARMM) - Developmental Version 35a1 August 15, 2007 + Copyright(c) 1984-2001 President and Fellows of Harvard College + All Rights Reserved + Current operating system: Linux-2.6.17-10-generic(i686)@nihiwatu + Created on 8/ 6/ 7 at 16:30:14 by user: alex + + Maximum number of ATOMS: 60120, and RESidues: 20040 + Current HEAP size: 10240000, and STACK size: 10000000 + + Processing passed argument "count:9" + Parameter: COUNT <- "9" + Processing passed argument "id1:iod" + Parameter: ID1 <- "IOD" + RDTITL> * TEST IONS WITH SWM4 WATER + RDTITL> * + + CHARMM> + + CHARMM> !set id1 swm4 + CHARMM> + + CHARMM> set toppardir . + Parameter: TOPPARDIR <- "." + + CHARMM> + + CHARMM> stream @toppardir/toppar_drude_positive_swm4_ions.str + Parameter: TOPPARDIR -> "." + VOPEN> Attempting to open::./toppar_drude_positive_swm4_ions.str:: + OPNLGU> Unit 99 opened for READONLY access to /raid/alex/param/polarizable/toppar/toppar_aug07/drude/positive_drude/./toppar_drude_positive_swm4_ions.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * STREAM FILE THAT INCLUDES BOTH THE TOPOLOGY + RDTITL> * AND PARAMETER INFORMATION FOR THE SWM4-DP + RDTITL> * POLARIZABLE WATER MODEL WITH A + RDTITL> * POSITIVE DRUDE CHARGE + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> !scale polarizabilities for negative ions + CHARMM> calc AlphaFLU = 2.467 * 0.724 ! from Hattig98 +Evaluating: 2.467*0.724 + Parameter: ALPHAFLU <- "1.78611" + + CHARMM> calc AlphaCLA = 5.482 * 0.724 ! from Hattig98 +Evaluating: 5.482*0.724 + Parameter: ALPHACLA <- "3.96897" + + CHARMM> calc AlphaBRO = 7.268 * 0.724 ! from Hattig98 +Evaluating: 7.268*0.724 + Parameter: ALPHABRO <- "5.26203" + + CHARMM> calc AlphaIOD = 10.275 * 0.724 ! from Hattig98 +Evaluating: 10.275*0.724 + Parameter: ALPHAIOD <- "7.4391" + + CHARMM> + + CHARMM> read rtf card + MAINIO> Residue topology file being read from unit 99. + RDTITL> * SWM4-DP AND ION TOPOLOGY + RDTITL> * POSITIVE DRUDE MODEL + RDTITL> * + + DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA + Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000 + + CHARMM> + + CHARMM> read param card + + PARAMETER FILE BEING READ FROM UNIT 99 + RDTITL> * REQUIRED PARAMETERS FOR POSITIVE DRUDE SWM4 AND IONS + RDTITL> * + WARNING from DECODF -- Zero length string being converted to 0. + + PARRDR> WARNING: wild card for drude X + 5 100 40 DRUD OWP 500.0000 0.0000 4990 + 6 100 42 DRUD LP 500.0000 0.0000 4992 + 7 100 43 DRUD DOH2 500.0000 0.0000 4993 + 8 100 60 DRUD LIT 500.0000 0.0000 5010 + 9 100 61 DRUD SOD 500.0000 0.0000 5011 + 10 100 62 DRUD POT 500.0000 0.0000 5012 + 11 100 63 DRUD RUB 500.0000 0.0000 5013 + 12 100 64 DRUD CES 500.0000 0.0000 5014 + 13 100 65 DRUD FLU 500.0000 0.0000 5015 + 14 100 66 DRUD CLA 500.0000 0.0000 5016 + 15 100 67 DRUD BRO 500.0000 0.0000 5017 + 16 100 68 DRUD IOD 500.0000 0.0000 5018 + 17 100 100 DRUD DRUD 500.0000 0.0000 5050 + + PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. + + CHARMM> + + CHARMM> return + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> + + CHARMM> !data file + CHARMM> open unit 33 write form name data/swm4_ion_@id1.dat + Parameter: ID1 -> "IOD" + VOPEN> Attempting to open::data/swm4_ion_iod.dat:: + OPNLGU> Unit 33 opened for WRITE access to /raid/alex/param/polarizable/toppar/toppar_aug07/drude/positive_drude/data/swm4_ion_iod.dat + + CHARMM> + + CHARMM> !test water model alone + CHARMM> + + CHARMM> if id1 eq swm4 then + Comparing "IOD" and "SWM4". + IF test evaluated as false. Skip to ELSE or ENDIF + **** Warning **** The following extraneous characters + were found while command processing in MISCOM + !IF SWM4 + + CHARMM> + + CHARMM> !! Monomer + ion + CHARMM> + + CHARMM> !set count 1 + CHARMM> !label ion_loop + CHARMM> + + CHARMM> if count eq 1 set iontype LIT + Comparing "9" and "1". + IF test evaluated as false. Skipping command + + CHARMM> if count eq 2 set iontype SOD + Comparing "9" and "2". + IF test evaluated as false. Skipping command + + CHARMM> if count eq 3 set iontype POT + Comparing "9" and "3". + IF test evaluated as false. Skipping command + + CHARMM> if count eq 4 set iontype RUB + Comparing "9" and "4". + IF test evaluated as false. Skipping command + + CHARMM> if count eq 5 set iontype CES + Comparing "9" and "5". + IF test evaluated as false. Skipping command + + CHARMM> if count eq 6 set iontype FLU + Comparing "9" and "6". + IF test evaluated as false. Skipping command + + CHARMM> if count eq 7 set iontype CLA + Comparing "9" and "7". + IF test evaluated as false. Skipping command + + CHARMM> if count eq 8 set iontype BRO + Comparing "9" and "8". + IF test evaluated as false. Skipping command + + CHARMM> if count eq 9 set iontype IOD + Comparing "9" and "9". + IF test evaluated as true. Performing command + Parameter: IONTYPE <- "IOD" + + CHARMM> + + CHARMM> read sequence SWM4 1 + + CHARMM> generate SOLV setup noangle nodihedral drude dmass 0.4 + Drude polarizability will be setup for SEGID: SOLV mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 1 has been generated. Its identifier is SOLV. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 5 Number of groups = 1 + Number of bonds = 5 Number of angles = 1 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 1 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + Number of Drudes = 1 + Number of true-bonds = 5 Number of zero-bonds = 0 + + CHARMM> read sequence @IONTYPE 1 + Parameter: IONTYPE -> "IOD" + + CHARMM> generate ION setup first none last none drude dmass 0.4 + Drude polarizability will be setup for SEGID: ION mass of Drudes particles = 0.4000 + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + + MKDRUDE generate list and setup for drude polarizability + + All okay for 1 added Drude particles + + GENPSF> Segment 2 has been generated. Its identifier is ION. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 7 Number of groups = 2 + Number of bonds = 6 Number of angles = 1 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 1 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = -1.00000 + Number of Drudes = 2 + Number of true-bonds = 6 Number of zero-bonds = 0 + + CHARMM> + + CHARMM> read coor card + SPATIAL COORDINATES BEING READ FROM UNIT 5 + RDTITL> * SWM4 + RDTITL> * + ** WARNING ** After reading, there are no coordinates for selected atom: 2 1 SWM4 DOH2 + ** WARNING ** After reading, there are no coordinates for selected atom: 6 2 IOD IOD + ** WARNING ** After reading, there are no coordinates for selected atom: 7 2 IOD DIOD + + ** A total of 3 selected atoms have no coordinates + *** LEVEL 2 WARNING *** BOMLEV IS 0 + + CHARMM> + + CHARMM> coor orient select type O* end + SELRPN> 2 atoms have been selected out of 7 + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.02044444 -0.00001517 -0.01259364 + 0.00000001 0.00000934 + 0.00775760 + + Transpose of the rotation matrix + 0.524473 0.000632 -0.851427 + -0.595998 0.714416 -0.366601 + 0.608042 0.699721 0.375069 + CENTER OF ATOMS BEFORE TRANSLATION 1.31391 -0.00015 0.16908 + AXIS OF ROTATION IS -0.560210 0.766756 0.313449 ANGLE IS 72.12 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> coor set xdir -3.0 select type @IONTYPE end + Parameter: IONTYPE -> "IOD" + SELRPN> 1 atoms have been selected out of 7 + SELECTED COORDINATES SET IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor print + + COORDINATE FILE MODULE + TITLE> * TEST IONS WITH SWM4 WATER + TITLE> * + 7 + 1 1 SWM4 OH2 -0.11875 0.00000 0.00000 SOLV 1 0.00000 + 2 1 SWM4 DOH2****************************** SOLV 1 0.00000 + 3 1 SWM4 OM 0.11875 0.00000 0.00000 SOLV 1 0.00000 + 4 1 SWM4 H1 0.46714 0.54050 0.52992 SOLV 1 0.00000 + 5 1 SWM4 H2 0.46713 -0.54052 -0.52994 SOLV 1 0.00000 + 6 2 IOD IOD -3.00000 0.00000 0.00000 ION 1 0.00000 + 7 2 IOD DIOD****************************** ION 1 0.00000 + + CHARMM> coor sdrude + + CHARMM> coor print + + COORDINATE FILE MODULE + TITLE> * TEST IONS WITH SWM4 WATER + TITLE> * + 7 + 1 1 SWM4 OH2 -0.11875 0.00000 0.00000 SOLV 1 0.00000 + 2 1 SWM4 DOH2 -0.11875 0.00000 0.00000 SOLV 1 0.00000 + 3 1 SWM4 OM 0.11875 0.00000 0.00000 SOLV 1 0.00000 + 4 1 SWM4 H1 0.46714 0.54050 0.52992 SOLV 1 0.00000 + 5 1 SWM4 H2 0.46713 -0.54052 -0.52994 SOLV 1 0.00000 + 6 2 IOD IOD -3.00000 0.00000 0.00000 ION 1 0.00000 + 7 2 IOD DIOD -3.00000 0.00000 0.00000 ION 1 0.00000 + + CHARMM> print psf + + PSF FILE MODULE + CONTROL ARRAY : 18 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 +* TEST IONS WITH SWM4 WATER +* DATE: 8/ 6/ 7 16:30:14 CREATED BY USER: alex +* + + NATOM NBOND NTHETA NPHI NIMPHI NNB NDON NACC NRES NSEG NGRP NST2 + 7 6 1 0 0 0 0 1 2 2 2 0 + + + PARTITION OF SEGMENTS - NICTOT ARRAY AND SEGMENT IDENTIFIERS : + SEGMENT NUMBER ID NRES NATOM NBOND NTHETA NPHI NIMPHI NNB NDON NACC TYPE + 1 SOLV 1 + 2 ION 2 + + ATOM CHARACTERISTICS : + ATOM TYPE CHARGE ATOM CODE COUNT OF MOVEMENT FLAG MASS + EXCLUSIONS + + RESIDUE 1 1 SWM4 TO 5 + GROUP 1 TYPE 1 MOVE 0 TO 5 + 1 OH2 -1.7718 40 0 0 15.5994 + 2 DOH2 1.7718 43 0 0 0.400000 + 3 OM -1.1074 42 0 -1 0.00000 + 4 H1 0.5537 41 0 0 1.00800 + 5 H2 0.5537 41 0 0 1.00800 + RESIDUE 2 1 IOD TO 7 + GROUP 2 TYPE 2 MOVE 0 TO 7 + 6 IOD -5.7331 68 0 0 126.504 + 7 DIOD 4.7331 100 0 0 0.400000 + + BOND ARRAY (BY COLUMNS) : + 1 1 1 1 1 4 6 + 2 4 5 3 5 7 + + THETA ARRAY (BY COLUMNS) : + 1 4 + 1 + 5 + + PHI ARRAY (BY COLUMNS) : + + IMPROPER TORSION ARRAY (BY COLUMNS) : + + CROSSTERM TORSION ARRAY (BY COLUMNS) : + + HYDROGEN DONOR ARRAYS : + + HYDROGEN ACCEPTOR ARRAYS : + 1 1 + 0 + + NON-BONDED EXCLUSION ARRAY : + + LONEPAIR ARRAYS: NUMLP,NUMLPH= 1 4 + 1 3 1 F -0.238080 0.00000 0.00000 + 1 3 1 4 5 + + CHARMM> bomlev -1 + + CHARMM> coor shake + SELECTED COORDINATES CONSTRAINED IN THE MAIN SET. + + + CHARMM> coor print + + COORDINATE FILE MODULE + TITLE> * TEST IONS WITH SWM4 WATER + TITLE> * DATE: 8/ 6/ 7 16:30:14 CREATED BY USER: alex + TITLE> * + 7 + 1 1 SWM4 OH2 -0.11875 0.00000 0.00000 SOLV 1 0.00000 + 2 1 SWM4 DOH2 -0.11875 0.00000 0.00000 SOLV 1 0.00000 + 3 1 SWM4 OM 0.11933 0.00000 0.00000 SOLV 1 0.00000 + 4 1 SWM4 H1 0.46714 0.54050 0.52992 SOLV 1 0.00000 + 5 1 SWM4 H2 0.46713 -0.54052 -0.52994 SOLV 1 0.00000 + 6 2 IOD IOD -3.00000 0.00000 0.00000 ION 1 0.00000 + 7 2 IOD DIOD -3.00000 0.00000 0.00000 ION 1 0.00000 + + CHARMM> coor stat + STATISTICS FOR 7 SELECTED ATOMS: + XMIN = -3.000000 XMAX = 0.467139 XAVE = -0.740556 + YMIN = -0.540516 YMAX = 0.540500 YAVE = -0.000003 + ZMIN = -0.529935 ZMAX = 0.529923 ZAVE = -0.000002 + WMIN = 0.000000 WMAX = 0.000000 WAVE = 0.000000 + + CHARMM> + + CHARMM> !SHAKE bonh param tolerance 1.0e-9 - + CHARMM> ! nofast - + CHARMM> ! select ( segid SOLV .and. .not. type D* ) end - + CHARMM> ! select ( segid SOLV .and. .not. type D* ) end + CHARMM> + + CHARMM> + + CHARMM> update inbfrq -1 ihbfrq 0 atom switch vatom vfswitch cutnb 99.0 ctofnb 89.0 ctonnb 79.0 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VFSWIt + BYGRoup NOEXtnd NOEWald + CUTNB = 99.000 CTEXNB =999.000 CTONNB = 79.000 CTOFNB = 89.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 11 exclusions and 0 interactions(1-4) + found 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 99 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 10 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + CHARMM> + + CHARMM> !================================================== + CHARMM> ! Water-ion interaction + CHARMM> !-------------------------------------------------- + CHARMM> + + CHARMM> energy + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VFSWIt + BYGRoup NOEXtnd NOEWald + CUTNB = 99.000 CTEXNB =999.000 CTONNB = 79.000 CTOFNB = 89.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 10 atom pairs and 11 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 99 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 10 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 51.62070 0.00000 85.63411 +ENER EXTERN> 37.35395 14.26675 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> set einit ?ener + RDCMND substituted energy or value "?ENER" to "51.6207" + Parameter: EINIT <- "51.6207" + + CHARMM> mini SD step 0.01 nstep 5000 nprint 1000 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VFSWIt + BYGRoup NOEXtnd NOEWald + CUTNB = 99.000 CTEXNB =999.000 CTONNB = 79.000 CTOFNB = 89.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 10 atom pairs and 11 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 99 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 10 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + + + + STEEPD> An energy minimization has been requested. + + NSTEP = 5000 NPRINT = 1000 + STEP = 0.0100000 TOLFUN = 0.0000000 + TOLGRD = 0.0000000 TOLSTP = 0.0000000 + +MINI MIN: Cycle ENERgy Delta-E GRMS Step-size +MINI EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +MINI> 0 51.62070 0.00000 85.63411 0.01000 +MINI EXTERN> 37.35395 14.26675 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 1000 3.32544 48.29526 3.40701 0.00217 +MINI INTERN> 0.21269 0.02073 0.00000 0.00000 0.00000 +MINI EXTERN> -0.12442 3.21644 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 2000 -7.10627 10.43171 1.16192 0.00113 +MINI INTERN> 0.56108 0.39741 0.00000 0.00000 0.00000 +MINI EXTERN> -0.18061 -7.88416 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 3000 -10.94942 3.84315 0.84662 0.00059 +MINI INTERN> 2.55463 1.56045 0.00000 0.00000 0.00000 +MINI EXTERN> 2.23266 -17.29716 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 4000 -11.62373 0.67431 0.00023 0.00000 +MINI INTERN> 3.41558 0.71975 0.00000 0.00000 0.00000 +MINI EXTERN> 2.98553 -18.74459 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 5000 -11.62373 0.00000 0.00000 0.00000 +MINI INTERN> 3.41567 0.71956 0.00000 0.00000 0.00000 +MINI EXTERN> 2.98555 -18.74452 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + STEEPD> Minimization exiting with number of steps limit ( 5000) exceeded. + +STPD MIN: Cycle ENERgy Delta-E GRMS Step-size +STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +STPD EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +STPD> 5000 -11.62373 0.00000 0.00000 0.00000 +STPD INTERN> 3.41567 0.71956 0.00000 0.00000 0.00000 +STPD EXTERN> 2.98555 -18.74452 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> coor orient select type O* .or. type @IONTYPE end + Parameter: IONTYPE -> "IOD" + SELRPN> 3 atoms have been selected out of 7 + + ORIENT THE COORDINATES TO ALIGN WITH AXIS + + MOMENTS + 0.00527900 0.00536175 -0.00002284 + 0.01725951 0.29829144 + 7.53290685 + + Transpose of the rotation matrix + 0.999216 0.039596 0.000025 + -0.028225 0.711809 0.701806 + 0.027771 -0.701256 0.712368 + CENTER OF ATOMS BEFORE TRANSLATION -0.75821 -0.05370 -0.05776 + AXIS OF ROTATION IS 0.998639 0.019748 0.048272 ANGLE IS 44.63 + + ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. + + + CHARMM> + + CHARMM> energy ! ?ENER + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec SWITch VATOm VFSWIt + BYGRoup NOEXtnd NOEWald + CUTNB = 99.000 CTEXNB =999.000 CTONNB = 79.000 CTOFNB = 89.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 10 atom pairs and 11 atom exclusions. + There are 0 group pairs and 0 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 99 ATOM PAIRS AND 0 GROUP PAIRS + + General atom nonbond list generation found: + 10 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +ENER> 0 -11.62373 0.00000 0.00000 +ENER INTERN> 3.41567 0.71956 0.00000 0.00000 0.00000 +ENER EXTERN> 2.98555 -18.74452 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> quick 1 6 ! ?DIST + QUICKA: Atom 1 SOLV 1 SWM4 OH2 is at: 1.21399 -0.07108 0.00000 + QUICKA: Atom 6 ION 1 IOD IOD is at: -2.24010 -0.00409 0.00000 + QUICKA: The distance is: 3.45474 + + + + CHARMM> coor dipole select segid SOLV end ! ?RDIP + SELRPN> 5 atoms have been selected out of 7 + THE TOTAL CHARGE OF SELECTED ATOMS IS: 0.000000 + DIPOLE MOMENT ABOUT CENTER OF GEOMETRY (DEBYES) : -2.176480 1.321015 0.000000 2.546006 + + CHARMM> + + CHARMM> write title unit 33 + RDTITL> * IOD + RDTITL> * EINITIAL = 51.6207 + RDTITL> * UMIN = -11.6237 + RDTITL> * DMIN = 3.45474 + RDTITL> * MU = 2.54601 + RDTITL> * + + CHARMM> + + CHARMM> stop + VCLOSE: Closing unit 33 with status "KEEP" +$$$$$$ New timer profile $$$$$ + Shake time 0.01 Other: 0.00 + List time 0.00 Other: 0.00 + Electrostatic & VDW 0.02 Other: 0.00 + Nonbond force 0.04 Other: 0.03 + Bond energy 0.01 Other: 0.00 + Angle energy 0.01 Other: 0.00 + Dihedral energy 0.01 Other: 0.00 + Restraints energy 0.01 Other: 0.00 + INTRNL energy 0.07 Other: 0.03 + Energy time 0.13 Other: 0.02 + Total time 0.21 Other: 0.06 + + NORMAL TERMINATION BY NORMAL STOP + MAXIMUM STACK SPACE USED IS 47512 + STACK CURRENTLY IN USE IS 0 + MOST SEVERE WARNING WAS AT LEVEL 2 + HEAP PRINTOUT- HEAP SIZE 10240000 + SPACE CURRENTLY IN USE IS 0 + MAXIMUM SPACE USED IS 5032 + FREE LIST + PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 + + $$$$$ JOB ACCOUNTING INFORMATION $$$$$ + ELAPSED TIME: 0.21 SECONDS + CPU TIME: 0.00 SECONDS diff --git a/charmm/toppar/drude/positive_drude/run_test.cmd b/charmm/toppar/drude/positive_drude/run_test.cmd new file mode 100644 index 00000000..18cd5b36 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/run_test.cmd @@ -0,0 +1,14 @@ +# simple script to run water and the different water-ion pairs individually due to a shake error that is being corrected for c35a2. + +alias charmm='/raid/lopes/charmm-raid3/c34a2j-pre-release-of-c34b1/c34a2j-fix/exec/gnu/charmm' + +charmm count:0 id1:swm4 < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:1 id1:lit < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:2 id1:sod < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:3 id1:pot < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:4 id1:rub < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:5 id1:ces < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:6 id1:flu < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:7 id1:cla < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:8 id1:bro < positive_drude_test_temp.inp > positive_drude_test_temp.out +charmm count:9 id1:iod < positive_drude_test_temp.inp > positive_drude_test_temp.out diff --git a/charmm/toppar/drude/positive_drude/toppar_drude_positive_swm4_ions.str b/charmm/toppar/drude/positive_drude/toppar_drude_positive_swm4_ions.str new file mode 100644 index 00000000..af73ef01 --- /dev/null +++ b/charmm/toppar/drude/positive_drude/toppar_drude_positive_swm4_ions.str @@ -0,0 +1,188 @@ +* Stream file that includes both the topology +* and parameter information for the SWM4-DP +* polarizable water model with a +* positive Drude charge +* + +!scale polarizabilities for negative ions +calc AlphaFLU = 2.467 * 0.724 ! from Hattig98 +calc AlphaCLA = 5.482 * 0.724 ! from Hattig98 +calc AlphaBRO = 7.268 * 0.724 ! from Hattig98 +calc AlphaIOD = 10.275 * 0.724 ! from Hattig98 + +read rtf card +* SWM4-DP and ION topology +* positive Drude model +* +32 1 + +!postive Drude +MASS 40 OWP 15.99940 ! water oxygen +MASS 41 HWP 1.00800 ! water hydrogen +MASS 42 LP 0.00000 ! water M site +MASS 43 DOH2 0.00000 ! Drude for oxygen +!ions of Lamoureux and Roux +MASS 60 LIT 6.94100 ! Lithium Ion +MASS 61 SOD 22.98977 ! Sodium Ion +MASS 62 POT 39.10200 ! Potassium Ion +MASS 63 RUB 85.46780 ! Rubidium Ion +MASS 64 CES 132.90540 ! Cesium Ion +MASS 65 FLU 18.99840 ! Fluoride Ion +MASS 66 CLA 35.45300 ! Chloride Ion +MASS 67 BRO 79.90400 ! Bromide Ion +MASS 68 IOD 126.90450 ! Iodine Ion +MASS 100 DRUD 0.00000 ! Drude wildcard + +DEFA FIRS NONE LAST NONE +AUTO ANGLES DIHE DRUDE !note use of DRUDE + +RESI SWM4 0.000 +GROUP +ATOM OH2 OWP 0.00000 TYPE DOH2 ALPHA 1.04252 THOLE 1.3 +ATOM OM LP -1.10740 +ATOM H1 HWP 0.55370 +ATOM H2 HWP 0.55370 +BOND OH2 H1 +BOND OH2 H2 +BOND OH2 OM +BOND H1 H2 ! for SHAKE +ANGLE H1 OH2 H2 +ACCEPTOR OH2 +LONEPAIR bisector OM OH2 H1 H2 distance 0.23808 angle 0.0 dihe 0.0 +IC H1 OH2 H2 H1 0.9572 104.52 0.00 37.74 1.5139 +IC H1 OM *OH2 H2 0.9572 52.26 180.00 52.26 0.9572 +IC H2 H1 OH2 OM 1.5139 37.74 0.01 52.26 0.23808 +PATCH FIRST NONE LAST NONE + +!* Ions of Lamoureux and Roux. To be used with +!* SWM4-DP model with POSITIVE Drude +!* + +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 ALPHA 0.0320 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 ALPHA 0.1570 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 ALPHA 0.8300 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 ALPHA 1.3700 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 ALPHA 2.3600 +PATCHING FIRST NONE LAST NONE + +RESI FLU -1.00 ! Fluoride Ion +GROUP +ATOM FLU FLU -1.00 ALPHA @AlphaFLU +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 ALPHA @AlphaCLA +PATCHING FIRST NONE LAST NONE + +RESI BRO -1.00 ! Bromide Ion +GROUP +ATOM BRO BRO -1.00 ALPHA @AlphaBRO +PATCHING FIRST NONE LAST NONE + +RESI IOD -1.00 ! Iodine Ion +GROUP +ATOM IOD IOD -1.00 ALPHA @AlphaIOD +PATCHING FIRST NONE LAST NONE + +END + +read param card +* Required parameters for positive Drude SWM4 and ions +* + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +!SWM4-DP parameters (positive Drude model) +OWP HWP 450.000 0.9572 +HWP HWP 0.000 1.5139 +OWP LP 0.000 0.238080 +OWP DOH2 500.000 0.000 + +!ion Drude parameters, wildcard +DRUD X 500.000 + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +! SWM4-DP parameters (positive Drude model) +HWP OWP HWP 55.000 104.52 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + +NONBONDED nbxmod 5 atom cdiel switch vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +! SWM4-DP, positive Drude +OWP 0.000000 -0.20568356 1.78488412 +HWP 0.000000 -0.000 0.000 +LP 0.000000 -0.000 0.000 +DOH2 0.0 -0.0 0.000 ! Drude + +!ions of Lamoureux and Roux +LIT 0.0 -0.003000 1.370000 ! lithium +SOD 0.0 -0.031510 1.450000 ! sodium +POT 0.0 -0.182900 1.645000 ! potassium +RUB 0.0 -0.351900 1.750000 ! rubidium +CES 0.0 -0.357600 1.980000 ! cesium +FLU 0.0 -0.010000 2.260000 ! fluoride +CLA 0.0 -0.076580 2.460000 ! chloride +BRO 0.0 -0.108200 2.570000 ! bromide +IOD 0.0 -0.159100 2.760000 ! iodine +DRUD 0.0 -0.00 0.00 ! Drude wildcard + +end + +return diff --git a/charmm/toppar/gbsw/00readme b/charmm/toppar/gbsw/00readme new file mode 100644 index 00000000..f340ac5d --- /dev/null +++ b/charmm/toppar/gbsw/00readme @@ -0,0 +1,2 @@ + +Files yet to be tested with c36 protein parameters diff --git a/charmm/toppar/gbsw/par_all22_prot_gbsw.inp b/charmm/toppar/gbsw/par_all22_prot_gbsw.inp new file mode 100755 index 00000000..28a96ce5 --- /dev/null +++ b/charmm/toppar/gbsw/par_all22_prot_gbsw.inp @@ -0,0 +1,3287 @@ +*>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<< +*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< +*>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<< +* All comments to ADM jr. via the CHARMM web site: www.charmm.org +* parameter set discussion forum +* + +! references +! +!PROTEINS +! +!MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the +!treatment of backbone energetics in protein force fields: limitations +!of gas-phase quantum mechanics in reproducing protein conformational +!distributions in molecular dynamics simulations, Journal of +!Computational Chemistry, 25: 1400-1415, 2004. +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. +! +!IONS (see lipid and nucleic acid topology and parameter files for +!additional ions +! +!ZINC +! +!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) +! + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +!Carbon Dioxide +CST OST 937.96 1.1600 ! JES +!Heme to Sulfate (PSUL) link +SS FE 250.0 2.3200 !force constant a guess + !equilbrium bond length optimized to reproduce + !CSD survey values of + !2.341pm0.01 (mean, standard error) + !adm jr., 7/01 +C C 600.000 1.3350 ! ALLOW ARO HEM + ! Heme vinyl substituent (KK, from propene (JCS)) +CA CA 305.000 1.3750 ! ALLOW ARO + ! benzene, JES 8/25/89 +CE1 CE1 440.000 1.3400 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CE2 500.000 1.3420 ! + ! for propene, yin/adm jr., 12/95 +CE1 CT2 365.000 1.5020 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CT3 383.000 1.5040 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE2 510.000 1.3300 ! + ! for ethene, yin/adm jr., 12/95 +CP1 C 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CC 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CD 200.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 222.500 1.5270 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPB CE1 450.000 1.3800 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPA 299.800 1.4432 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB CPB 340.700 1.3464 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH1 CPH1 410.000 1.3600 ! ALLOW ARO + ! histidine, adm jr., 6/27/90 +CPM CPA 360.000 1.3716 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT CA 305.000 1.3680 ! ALLOW ARO + ! adm jr., 12/30/91, for jwk +CPT CPT 360.000 1.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT1 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT1 222.500 1.5000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT2 CA 230.000 1.4900 ! ALLOW ALI ARO + ! phe,tyr, JES 8/25/89 +CT2 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT2 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT3 CA 230.000 1.4900 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +CT3 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT3 CS 190.000 1.5310 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CT3 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 222.500 1.5280 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT3 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CY CA 350.000 1.3650 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CY CPT 350.000 1.4400 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 230.000 1.5100 ! ALLOW ARO + !JWK Kb from alkane freq.. b0 from TRP crystal +FE CM 258.000 1.9000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +FE CPM 0.000 3.3814 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +H CD 330.000 1.1100 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +!HA C 330.000 1.1000 ! ALLOW ARO HEM + ! Heme vinyl substituent (KK, from propene (JCS)) +HA CA 340.000 1.0830 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA CC 317.130 1.1000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +HA CP2 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CPM 367.600 1.0900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT1 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 322.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CY 330.000 1.0800 ! ALLOW ARO + ! JWK 05/14/91 new r0 from indole +HE1 CE1 360.500 1.1000 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 365.000 1.1000 ! + ! for ethene, yin/adm jr., 12/95 +HB CP1 330.000 1.0800 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HP CA 340.000 1.0800 ! ALLOW ARO + ! phe,tyr JES 8/25/89 +HP CY 350.000 1.0800 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HR1 CPH1 375.000 1.0830 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 340.000 1.0900 ! ALLOW ARO + ! his, adm jr., 6/28/29 +HR2 CPH2 333.000 1.0700 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR3 CPH1 365.000 1.0830 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HT HT 0.000 1.5139 ! ALLOW WAT + ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) +N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 320.000 1.4340 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 320.000 1.4550 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO + ! 403.0->463.0, 1.305->1.365 guanidinium (KK) +NC2 CT2 261.000 1.4900 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 261.000 1.4900 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NC2 HC 455.000 1.0000 ! ALLOW POL + ! 405.0->455.0 GUANIDINIUM (KK) +NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO + ! (DS) +NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +NH2 CT2 240.000 1.4550 + ! from NH2 CT3, neutral glycine, adm jr. +NH2 CT3 240.000 1.4550 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH2 H 480.000 1.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 HC 460.000 1.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT3 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 HC 403.000 1.0400 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 320.000 1.4850 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 320.000 1.5020 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP HC 460.000 1.0060 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NPH CPA 377.200 1.3757 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE 270.200 1.9580 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH2 400.000 1.3600 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 H 466.000 1.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 400.000 1.3200 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 FE 65.000 2.2000 ! ALLOW HEM + ! Heme (6-liganded): His ligand (KK 05/13/91) +NR3 CPH1 380.000 1.3700 ! ALLOW ARO + ! his, adm jr., 6/28/90 +NR3 CPH2 380.000 1.3200 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 H 453.000 1.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA 270.000 1.3700 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT 270.000 1.3750 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY H 465.000 0.9760 ! ALLOW ARO + ! indole JWK 08/28/89 +O C 620.000 1.2300 ! ALLOW PEP POL ARO + ! Peptide geometry, condensed phase (LK) +O CC 650.000 1.2300 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +OB CC 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid vibrations and geom. +OB CD 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 8/27/91, phenoxide +OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 7/23/91, acetic acid +OC CT2 450.000 1.3300 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 450.000 1.3300 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA 334.300 1.4110 ! ALLOW ARO ALC + ! MeOH, EMB 10/10/89, +OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC + ! adm jr. 5/02/91, acetic acid pure solvent +OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 H 545.000 0.9600 ! ALLOW ALC ARO + ! EMB 11/21/89 methanol vib fit +OM CM 1115.000 1.1280 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +OM FE 250.000 1.8000 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OM OM 600.000 1.2300 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OS CD 150.000 1.3340 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +OS CT3 340.000 1.4300 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OT HT 450.000 0.9572 ! ALLOW WAT + ! FROM TIPS3P GEOM +S CT2 198.000 1.8180 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S CT3 240.000 1.8160 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S HS 275.000 1.3250 ! ALLOW SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +SM CT2 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM CT3 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM SM 173.000 2.0290 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SS CS 205.000 1.8360 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +!Carbon Dioxide, JES +OST CST OST 3000.00 180.0000 ! CO2, JES +!Heme to Sulfate (PSUL) link +CS SS FE 50.0 100.6 !force constant a guess + !equilibrium angle optimized to reproduce + !CSD survey values + !107.5pm0.6 (mean, standard error) + !adm jr., 7/01 +SS FE NPH 100.0 90.0 !force constant a guess + !adm jr., 7/01 +! +CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO + ! JES 8/25/89 +CE1 CE1 CT2 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CE1 CT3 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CT2 CT3 32.00 112.20 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT2 48.00 126.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT3 47.00 125.20 ! + ! for propene, yin/adm jr., 12/95 +CP1 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 C 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 100.000 114.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 100.000 111.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPA CPB CE1 70.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPA CPM CPA 94.200 125.1200 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPA NPH CPA 139.300 103.9000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB CE1 CE2 70.000 121.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB CE1 70.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB CPA 30.800 106.5100 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPM CPA CPB 61.600 124.0700 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT CA CA 60.000 118.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CPT CA 60.000 122.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT NY CA 110.000 108.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! from CT2 CT1 C, for lactams, adm jr. +CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CY CA 45.800 129.4000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 CY CPT 45.800 124.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! 107.5->120.0 to make planar Arg (KK) +CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/09/92, for ALA cter +CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! methylguanidinium, adm jr., 3/26/92 +CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 CT1 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +CY CT2 CT3 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +FE NPH CPA 96.150 128.0500 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO + ! his, adm jr. 8/13/90 acetamide geometry and vibrations +H NH2 H 23.000 120.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NY CA 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO + ! JES 8/25/89 phenol +H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +!HA C C 50.000 120.5000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK from propene (JCS)) +!HA C CPB 50.000 120.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +!HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK from propene (JCS)) +HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA CA CPT 41.000 122.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CPM CPA 12.700 117.4400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CPM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd + ! based on HA CT2 HA +HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT2 CE1 45.00 111.50 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HA CT2 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 CY 33.430 109.5000 ! ALLOW ARO + ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA +HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT3 CE1 42.00 111.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HA CT3 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HE1 CE1 CE1 52.00 119.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HE1 CE1 CE2 42.00 118.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 40.00 116.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HE1 CE1 CT3 22.00 117.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CPB 50.000 120.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HE2 CE2 CE1 45.00 120.50 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE2 55.50 120.50 ! + ! for ethene, yin/adm jr., 12/95 +HE2 CE2 HE2 19.00 119.00 ! + ! for propene, yin/adm jr., 12/95 +HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB CT1 CT1 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CT2 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CT3 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB CT2 HB 36.000 115.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO + ! 35.3->49.0 GUANIDINIUM (KK) +HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI + ! 107.5->120.0 to make planar Arg (KK) +HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI + ! methylguanidinium, adm jr., 3/26/92 +HC NC2 HC 25.000 120.0000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH2 CT2 50.000 111.0000 ! ALLOW POL + ! from HC NH2 CT3, neutral glycine, adm jr. +HC NH2 CT3 50.000 111.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +HC NH2 HC 39.000 106.5000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 HC 44.000 109.5000 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP HC 51.000 107.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HT OT HT 55.000 104.5200 ! ALLOW WAT + ! TIP3P GEOMETRY, ADM JR. +N C CP1 20.000 112.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 C 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CC 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CP2 70.000 110.8000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 CP2 70.000 110.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO + ! changed from 60.0/120.3 for guanidinium (KK) +NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/20/92, for asn,asp,gln,glu and cters +NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT1 CT2, for lactams, adm jr. +NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT3 HA, for lactams, adm jr. +NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! NMA crystal (JCS) +NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +NH2 CT2 HA 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral lysine +NH2 CT2 HB 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral glycine, adm jr. +NH2 CT2 CD 52.000 108.0000 + !from CT2 CT2 CD, neutral glycine, adm jr. +NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + !from NH3 CT2 CT2, neutral lysine +NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP + ! new aliphatics, adm jr., 2/3/92 +NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! alanine (JCS) +NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + ! alanine (JCS) +NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP + ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) +NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 C 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NPH CPA CPB 122.000 111.5400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM 88.000 124.3900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE CM 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NPH FE CPM 0.000 45.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +NPH FE NPH 14.390 90.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 FE CM 50.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR2 FE NPH 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +O C CP1 80.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C H 50.000 121.7000 ! ALLOW PEP POL ARO + ! acetaldehyde (JCS) +O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC HA 44.000 122.0000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO + ! adm jr. 4/10/91, acetamide update +OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA CA 40.000 120.0000 ! ALLOW POL ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CT2 CT3 65.000 122.0000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT2 HA 65.000 118.3000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 HA 65.000 118.3000 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC + ! PARALLH19 WITH [122.3] (JES) +OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OM CM FE 35.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM FE NPH 5.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM OM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 55.000 118.0000 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +!Heme to Sulfate (PSUL) link +X FE SS X 0.0000 4 0.00 ! guess + !adm jr., 7/01 +X CS SS X 0.0000 3 0.20 ! guess + !from methanethiol, HS S CT3 HA + !adm jr., 7/01 + +C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 +CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c +CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c +CE1 CE1 CT3 HA 0.0300 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 CT3 0.5000 1 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 CT3 1.3000 3 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 HA 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT3 HA 0.0500 3 180.00 ! + ! for propene, yin/adm jr., 12/95 +CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 +CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 +CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! from CT2 CT1 NH1 C, for lactams, adm jr. +CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK +CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + !JWK +CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +CT3 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION + ! DTN 8/24/90 +CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from H NH1 CT2 CT3, for lactams, adm jr. +H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/20/89 +H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NY CA CY 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC + ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO + ! adm jr., 10/02/89 +HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO + ! ADM JR., 10/02/89 +HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! TRP (JES) +HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK +HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK +HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA NY H 1.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL + ! adm jr. 4/10/91, acetamide update +HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HE1 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +CT3 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +HE1 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 HA 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE1 CE1 CT2 CT3 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT3 HA 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE2 CE2 CE1 CT2 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +HE2 CE2 CE1 CPB 5.2000 2 180.00 ! + ! for vinyl, from butene, yin/adm jr., 12/95 +HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NH2 CT2 CT2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral lysine +HC NH2 CT2 HA 0.1100 3 0.00 + !from X CT3 NH2 X, neutral lysine +HC NH2 CT2 HB 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CD 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA NY H 0.4000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, his +HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, YES, 0.0 +HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from NH1 C CT1 CT2, for lactams, adm jr. +NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO + ! adm jr. 3/24/92, for PRES GLYP +NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO + ! JWK +NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP + ! from O C CT1 CT2, for lactams, adm jr. +O C CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT3 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 H 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +!X C C X 4.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO + ! 9.0->2.25 GUANIDINIUM (KK) +X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier +X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CE1 CE1 X 0.1500 1 0.00 + ! 2-butene, adm jr., 2/00 update +X CE1 CE1 X 8.5000 2 180.00 + ! 2-butene, adm jr., 2/00 update +X CE2 CE2 X 4.9000 2 180.00 ! + ! for ethene, yin/adm jr., 12/95 +X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP + ! changed to 0.0 RLD 5/19/92 +X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB CE1 X 3.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI + ! rotation barrier in Ethane (SF) +X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL + ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 +X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X FE CM X 0.0500 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X FE NPH X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +X FE NR2 X 0.0500 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): from param19.inp +X FE OM X 0.0000 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB X X CE1 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +!HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK, from propene (JCS)) +HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +!HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO + ! Heme (6-liganded): substituents (KK 05/13/91) +!HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK, from propene (JCS)) +HE2 HE2 CE2 CE2 3.0 0 0.00 ! + ! for ethene, yin/adm jr., 12/95 +HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO + ! 5.75->40.0 GUANIDINIUM (KK) +NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +NH2 X X H 4.0000 0 0.0000 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO + !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf. +O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! adm jr., 5/13/91, formamide geometry and vibrations +O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL + ! adm jr., 10/17/90, acetic acid vibrations +OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) + +CMAP +! 2D grid correction data. The following surfaces are the correction +! to the CHARMM22 phi, psi alanine, proline and glycine dipeptide surfaces. +! Use of CMAP requires generation with the topology file containing the +! CMAP specifications along with version 31 or later of CHARMM. Note that +! use of "skip CMAP" yields the charmm22 energy surfaces. +! +! references +!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Accurate Treatment of +!Protein Backbone Conformational Energetics in Empirical Force Fields, Submitted +!for publication. + +!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Improved Treatment of the +!Protein Backbone in Empirical Force Fields, Journal of the American Chemical +!Society, In Press. + + +! alanine map +! +! NOTE: CMAP for GBSW with re-optimized radii set given in "radius_gbsw.str" +! new map = QM_CMAP with stablization of beta/extended region +! Ref: J. Chen, W. Im and C. L. Brooks III (2005), JACS submitted. + +C NH1 CT1 C NH1 CT1 C NH1 24 + + -0.5147 0.2687 0.4713 0.7510 1.6210 ! -180 + 2.1954 2.0644 1.7648 0.7559 -0.7135 + 0.9761 -2.4755 -5.4557 -5.8964 -5.3059 + -3.9756 -3.0886 -3.2842 -3.1771 -3.1461 + -2.8354 -2.5742 -2.4120 -1.3386 + + -0.7221 0.2912 0.5770 0.8723 1.3990 ! -165 + 1.9616 2.3338 1.9041 0.5615 0.5184 + -0.1163 -3.5754 -5.2845 -5.1603 -4.1960 + -3.2762 -2.7153 -2.3062 -2.1018 -2.2103 + -2.0183 -2.0511 -1.9837 -1.5645 + + -0.7150 -0.0193 0.6243 1.0472 1.6539 ! -150 + 2.1914 2.2964 1.9605 0.8249 2.0383 + -1.1515 -3.7486 -4.6583 -4.5319 -3.7964 + -2.5721 -1.7272 -1.4614 -1.2829 -1.6207 + -1.6410 -1.8418 -1.7637 -1.4311 + + -0.3558 0.4355 0.9774 1.3780 1.9295 ! -135 + 2.3934 2.4358 2.1630 1.7615 1.1901 + -1.5186 -3.3089 -3.7761 -3.4053 -2.7684 + -1.8360 -0.9579 -0.4782 -0.7186 -1.1856 + -1.7183 -1.7567 -1.2875 -0.7441 + + 0.4324 0.9592 1.5090 1.8411 2.6990 ! -120 + 2.8093 2.6143 2.4817 2.6947 0.6824 + -1.3983 -2.5618 -2.7451 -2.4947 -1.8083 + -0.8555 -0.0873 -0.0610 -0.4836 -1.0666 + -1.4320 -1.3649 -0.6913 0.0024 + + 0.7674 1.2867 1.8180 2.0655 2.3706 ! -105 + 2.8974 2.7303 2.8788 2.5420 0.5452 + -1.0921 -1.6944 -2.0123 -1.6024 -0.6564 + -0.3062 -0.1224 -0.0553 -0.2757 -0.5784 + -0.7579 -0.7092 -0.1116 0.3843 + + 0.6560 1.4432 1.5895 2.0462 2.4515 ! -90 + 2.8192 3.0529 3.8737 2.4207 0.4491 + -0.7916 -1.3830 -1.3389 -0.9874 -0.7683 + -0.4944 -0.2324 -0.1918 -0.4625 -0.2353 + -0.2869 -0.1065 0.0993 0.3032 + + -0.0032 0.4491 1.1809 1.9430 2.8141 ! -75 + 3.1758 3.5553 3.8873 2.1013 0.1091 + -1.0322 -1.3820 -0.6739 -0.8174 -0.8270 + -0.1118 0.0537 -0.2036 -0.3078 -0.5710 + -0.6361 -0.2338 -0.0943 -0.3998 + + -1.4533 -0.2700 0.7170 2.1686 3.2082 ! -60 + 3.8669 4.2511 3.3481 1.2975 -0.4875 + -1.1799 -0.6843 -0.8537 -1.1588 -0.3476 + 0.1148 0.2428 -0.1776 -0.6299 -1.3749 + -1.6769 -1.6734 -1.6666 -1.7188 + + -2.6967 -0.9219 1.3474 3.2113 4.3760 ! -45 + 4.8649 4.3552 2.4365 0.4085 -0.2908 + -0.4360 -0.5012 -0.8222 -0.6072 0.0579 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-3.153350 -2.780320 +-1.715700 -0.534910 0.258100 0.329180 -0.126160 +-0.940260 -1.319240 -0.990850 -0.896700 + +! glycine before proline map: use glycine map +C NH1 CT2 C NH1 CT2 C N 24 + +!-180 +-0.549160 -0.535500 -0.588110 -0.754620 -0.679290 +-0.038150 0.298460 0.326040 -0.375610 -1.704360 +-3.061280 -3.956460 -3.576280 -1.038930 2.012450 +-1.714610 -0.377660 0.317310 0.294580 -0.042920 +-0.676620 -0.744600 -0.586590 -0.554770 + +!-165 +-0.709450 -0.896700 -0.990850 -1.319240 -0.940260 +-0.126160 0.329180 0.258100 -0.534910 -1.715700 +-2.780320 -3.153350 -1.636020 1.822690 -2.675640 +-1.810120 -0.410680 0.180860 0.196710 -0.000430 +-0.271890 -0.462500 -0.348750 -0.477660 + +!-150 +-1.224850 -1.482430 -1.665900 -1.656770 -1.119780 +-1.642540 -0.054220 -0.290670 -0.887080 -1.626260 +-2.165440 -1.546500 0.753400 -2.949180 -2.225630 +-1.664160 -0.628990 0.000490 0.033160 -0.092820 +-0.339050 -0.563330 -0.794980 -0.710760 + +!-135 +-1.787640 -2.117750 -2.143020 -1.803720 -1.567160 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+-2.793280 -2.412680 -1.959970 -1.401500 -0.950190 +-0.540540 -0.467320 -0.633810 -0.893140 -1.695490 +-2.776760 -4.255190 -4.662850 -4.448210 -3.332800 +-2.567680 -1.195390 -1.681850 -1.951490 -2.266680 +-2.626630 -3.013710 -3.178150 -3.079570 + +!120 +-2.330190 -1.914850 -1.601800 -1.068330 -0.661220 +-0.297950 -0.173830 -0.158900 -0.553910 -1.455320 +-2.394430 -3.215190 -3.975820 -3.783210 -3.014390 +-0.975570 -1.358170 -1.289220 -1.435540 -1.705860 +-1.970070 -2.364070 -2.596140 -2.593790 + +!135 +-1.796120 -1.465530 -1.267450 -0.880610 -0.288370 +-0.055650 0.100910 -0.207560 -0.758950 -1.718060 +-2.220710 -2.435890 -4.372310 0.338010 -1.062570 +-1.337360 -1.020630 -0.851590 -0.801350 -0.886880 +-1.567160 -1.803720 -2.143020 -2.117750 + +!150 +-1.263610 -0.710760 -0.794980 -0.563330 -0.339050 +-0.092820 0.033160 0.000490 -0.628990 -1.664160 +-2.225630 -2.949180 0.753400 -1.546500 -2.165440 +-1.626260 -0.887080 -0.290670 -0.054220 -1.642540 +-1.119780 -1.656770 -1.665900 -1.482430 + +!165 +-0.684660 -0.477660 -0.348750 -0.462500 -0.271890 +-0.000430 0.196710 0.180860 -0.410680 -1.810120 +-2.675640 1.822690 -1.636020 -3.153350 -2.780320 +-1.715700 -0.534910 0.258100 0.329180 -0.126160 +-0.940260 -1.319240 -0.990850 -0.896700 + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!carbons +C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO + ! NMA pure solvent, adm jr., 3/3/93 +CA 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! benzene (JES) +CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO + ! adm jr. 3/3/92, acetic acid heat of solvation +CD 0.000000 -0.070000 2.000000 ! ALLOW POL + ! adm jr. 3/19/92, acetate a.i. and dH of solvation +CE1 0.000000 -0.068000 2.090000 ! + ! for propene, yin/adm jr., 12/95 +CE2 0.000000 -0.064000 2.080000 ! + ! for ethene, yin/adm jr., 12/95 +CM 0.000000 -0.110000 2.100000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand carbon (KK 05/13/91) +CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO + ! benzene (JES) +CS 0.000000 -0.110000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +CST 0.000000 -0.058000 1.563000 ! + ! carbon dioxide, JES +CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! isobutane pure solvent properties, adm jr, 2/3/92 +CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! propane pure solvent properties, adm jr, 2/3/92 +CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +CY 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! TRP, JWK 08/29/89 +!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str) +CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! from CT1x: needs work +CT1x 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92: needs work +CT2x 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CT3x 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +! hydrogens +H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 +HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HE1 0.000000 -0.031000 1.250000 ! + ! for propene, yin/adm jr., 12/95 +HE2 0.000000 -0.026000 1.260000 ! + ! for ethene, yin/adm jr., 12/95 +HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HC 0.000000 -0.046000 0.224500 ! ALLOW POL + ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 +HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO + ! JES 8/25/89 values from Jorgensen fit to hydration energy +HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS 0.000000 -0.100000 0.450000 ! ALLOW SUL + ! methanethiol pure solvent, adm jr., 6/22/92 +HT 0.000000 -0.046000 0.224500 ! ALLOW WAT + !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete +!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str) +HA1 0.0 -0.022 1.3200 ! alkane, 3/92 +HA2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98 +HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98 +!nitrogens +N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! JG 8/27/89; note: NH1 in ARG was changed to NC2. +NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +NH2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NH3 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NP 0.000000 -0.200000 1.850000 ! ALLOW PRO + ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 +NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NY 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! trp, JWK +! oxygens +O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid carbonyl O +OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) +OM 0.000000 -0.120000 1.700000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91) +OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 9/17/90, avoid O* wildcard +OST 0.000000 -0.165000 1.692000 ! + ! carbon dioxide, JES +OT 0.000000 -0.152100 1.768200 ! ALLOW WAT + !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete +! sulfurs +S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION + ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent +SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION + ! adm jr., 3/3/92, dimethyldisulphide pure solvent +SS 0.000000 -0.470000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +! ions and miscellaneous types +SOD 0.0 -0.0469 1.36375 ! sodium + ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol +POT 0.0 -0.0870 1.76375 ! potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CLA 0.0 -0.150 2.27 ! chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +!CAL 0.000000 -0.120000 1.710000 ! Calcium (BP) in proteins prior + ! to 2003; not recommended due to need for NBFIX terms +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +CES 0.0 -0.1900 2.100 + ! Cesium, so far untested. +ZN 0.000000 -0.250000 1.090000 ! ALLOW ION + ! RHS March 18, 1990 +FE 0.010000 0.000000 0.650000 ! ALLOW HEM + ! Heme (6-liganded): Iron atom (KK 05/13/91) +HE 0.000000 -0.021270 1.4800 ! + ! helium, experimental pot. energy surface, adm jr., 12/95 +NE 0.000000 -0.086000 1.5300 + ! neon, semiempirical pot. energy surface, adm jr., 12/95 +CLAL 0.000000 -0.030000 1.908200 ! chlorine from Jorgensen/BOSS + ! for choroacetaldehyde +DUM 0.000000 -0.000000 0.000000 ! + ! dummy atom +!pyridine series LJ parametes (see toppar_pyridines.str) +CAP 0.000000 -0.070000 1.992400 ! +FA 0.000000 -0.12000 1.700000 + ! from 1,3-difluorobenzene pure solvent +CN 0.000000 -0.200000 1.750000 ! cyanopyridine +NC 0.000000 -0.600000 1.850000 ! cyanopyridine +OCA 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! 3acp +COA 0.000000 -0.110000 2.000000 ! 3acp +!fluorinated alkanes LJ parameters (see toppar_fluoro_alkanes.str) +CF1 0.000000 -0.060000 1.900000 +CF2 0.000000 -0.042000 2.050000 +CF3 0.000000 -0.020000 2.300000 +HF1 0.000000 -0.028000 1.3200 +HF2 0.000000 -0.030000 1.3000 +F1 0.0 -0.135 1.63 +F2 0.0 -0.105 1.63 +F3 0.0 -0.097 1.60 +!protein model compounds (see toppar_all22_prot_model.str) +C3 0.000000 -0.020000 2.275000 ! cyclopropane, JMW and CBP 4/04 +!retinol model compounds +CC1A 0.0 -0.0680 2.0900 ! +CC1B 0.0 -0.0680 2.0900 ! +CC2 0.0 -0.0640 2.0800 ! +NS1 0.000000 -0.200000 1.850000 !N for deprotonated Schiff's base +NS2 0.000000 -0.200000 1.850000 !N for protonated Schiff's base + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/gbsw/radius_gbsw.str b/charmm/toppar/gbsw/radius_gbsw.str new file mode 100755 index 00000000..8b698a57 --- /dev/null +++ b/charmm/toppar/gbsw/radius_gbsw.str @@ -0,0 +1,178 @@ +* Atomic radius derived from solvent electrostatic charge distribution +* Tested with free energy perturbation with explicit solvent +* Authors: Mafalda Nina, Dmitrii Belogv, and Benoit Roux +* University of Montreal, June 1996. +* M. Nina and B. Roux. Atomic Radii for Continuum Electrostatics Calculations based on +* Molecular Dynamics Free Energy Simulations. J. Phys. Chem. B 101: 5239-5248 (1997). +* + +! UPDATES: +! -------- +! 1. PMF guided optimization of input radii for charged residues (2005) +! ref: J. Chen, W. Im and C. L. Brooks III, JACS (submitted). +! +! +! GLU and ASP modified December 1st, 1998 by Mafalda Nina +! +! Protonated histidine HSP has been included, January 1999 by Mafalda Nina +! dG_elec = -68.15 kcal/mol (MD/FES) or -68.10 kcal/mol (PBEQ) +! +! TEA and ions added by Benoit Roux, January 1999. +! +! sodium added by Benoit Roux, November 2000 + +scalar wmain set 1.3 select type ZN end + +! Set to zero all H radii +scalar wmain set 0.0 sele chem H* end + +! Set heavy atoms to average default values +scalar wmain set 2.3 sele chem C* end +scalar wmain set 1.8 sele chem O* end +scalar wmain set 2.3 sele chem N* end +scalar wmain set 2.3 sele chem S* end + +!Patches CT3 N-Methylamide C-terminus +! ACE acetylated N-terminus (ACP for PRO) +scalar wmain set 2.06 sele (type CAY .or. type CAT) end +scalar wmain set 2.04 sele type CY end +scalar wmain set 1.52 sele type OY end +scalar wmain set 2.23 sele type NT end +scalar wmain set 1.40 sele type OT* end ! for COO- terminus + +!Backbone +scalar wmain set 2.04 sele type C end + ! for peptide bond +scalar wmain set 1.52 sele type O end + ! for peptide bond +scalar wmain set 2.23 sele type N end + ! for peptide bond +scalar wmain set 2.86 sele type CA end + ! for all CA except GLY +scalar wmain set 2.38 sele (resnam GLY .and. type CA) end + ! for GLY only + +!Hydrogens +scalar wmain set 0.00 sele type H* end + ! for all hydrogens + +!Carbons +scalar wmain set 2.67 sele type CB end + ! for all residues +scalar wmain set 2.46 sele type CG* end + ! for ARG, GLN, ILE, LYS, MET, PHE, THR, TRP, VAL, HSP, HSD +scalar wmain set 2.77 sele resnam GLU .and. type CG end + ! for GLU only +scalar wmain set 2.44 sele type CD* end + ! for ARG, ILE, LEU, LYS +scalar wmain set 1.98 sele (resnam GLN .and. type CD) .or. (resnam ASN .and. type CG) .or. - + (resnam GLU .and. type CD) .or. (resnam ASP .and. type CG) end + ! for ASP, GLU, ASN, GLN +scalar wmain set 1.98 sele (resnam PRO .and. (type CB .or. type CG .or. type CD)) end + ! for PRO only +scalar wmain set 2.00 sele (resnam TYR .and. (type CE* .or. type CD* .or. - + type CZ)) .or. (resnam PHE .and. (type CE* .or. - + type CD* .or. type CZ)) end + ! for TYR, PHE rings +scalar wmain set 1.78 sele (resnam TRP .and. (type CE* .or. type CD* .or. - + type CZ* .or. type CH2)) end + ! for TRP ring only +scalar wmain set 2.10 sele type CE end + ! for MET only +scalar wmain set 2.80 sele (resnam ARG .and. type CZ) .or. (resnam LYS .and. type CE) end + ! for ARG, LYS +scalar wmain set 1.98 select (( resnam HSD .or. resnam HSP .or. resn HIS ) .and. type CE1) - + .or. (( resnam HSD .or. resnam HSP .or. resn HIS ) .and. type CD2) end + ! for neutral HSD and protonated HSP + +!Oxygens +scalar wmain set 1.40 sele (resnam GLU .or. resnam ASP) .and. (type OE* .or. type OD*) end + ! for GLU, ASP +scalar wmain set 1.42 sele (resnam ASN .or. resnam GLN) .and. (type OE* .or. type OD*) end + ! for ASN, GLN +scalar wmain set 1.64 sele type OG* end + ! for SER, THR +scalar wmain set 1.85 sele (resnam TYR .and. type OH) end + ! for TYR only +scalar wmain set 2.2 select resname TIP3 .and. type OH2 end + ! for explicit water molecules + +!Nitrogens +scalar wmain set 1.80 sele ( resn HSD .or. resn HIS ) .and. (type NE2 .or. type ND1) end + ! for neutral HSD (HIS is HSD) +scalar wmain set 2.30 sele resnam HSP .and. (type NE2 .or. type ND1) end + ! for protonated HSP +scalar wmain set 2.13 sele resnam ARG .and. (type NH* .or. type NE) .or. - + (resnam LYS .and. type NZ) end + ! for ARG, LYS +scalar wmain set 2.15 sele (resnam GLN .and. type NE2) .or. (resnam ASN .and. type ND2) end + ! for GLN, ASN +scalar wmain set 2.40 sele resnam TRP .and. type NE1 end + ! for TRP + +!Sulphur +scalar wmain set 2.00 sele type S* end + ! for MET, CYS + +!Ions +scalar wmain set 2.035 select resname POT end + !potassium ion K+ + +scalar wmain set 2.035 select resname CLA end + !chloride ion Cl- + +scalar wmain set 1.66 select resname SOD end + !sodium ion Na+ + +scalar wmain set 2.15 sele resnam TEA .and. type N end +scalar wmain set 2.30 sele ( type C1 .or. type C2 .or. type C3 .or. type C4 ) .and. resnam TEA end +scalar wmain set 2.30 sele ( type C5 .or. type C6 .or. type C7 .or. type C8 ) .and. resnam TEA end + ! Tetramethylamonium (TEA) + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!! PMF guided optimization of input radii for charged residues !! +!! !! +!! J. Chen, W. Im and C. L. Brooks III, JACS (submitted) !! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!! NOTE: should be used only with GBSW; +!! NOTE: for optimal accuracy in peptide and protein conformational equilibrium, +!! the modified CMAP in "~toppar/gbsw/par_all22_prot_gbsw.inp" should be used. +!! + +! ASP and GLU (no change) + +! LYS: +scalar wmain set 1.8 select resn LYS .and. type NZ end + +! ARG: +scalar wmain set 1.7 select resn ARG .and. ( type NH* .or. type NE ) end +scalar wmain set 2.2 select resn ARG .and. type CZ end + +! GLN and ASN +scalar wmain set 1.6 select resn GLN .and. type OE1 end +scalar wmain set 1.6 select resn ASN .and. type OD1 end +scalar wmain set 2.0 select resn GLN .and. type NE2 end +scalar wmain set 2.0 select resn ASN .and. type ND2 end + +! HSD and HSP: hnd(1.8->1.9), hpnd/hpne(2.3->1.9) +scalar wmain set 1.9 select resn HSD .and. type ND1 end +scalar wmain set 1.9 select resn HSP .and. type ND1 end +scalar wmain set 1.9 select resn HSP .and. type NE2 end + +! TRP: NE (2.4->1.8), C*(1.78->2.0) +scalar wmain set 1.85 select resn TRP .and. type NE1 end +scalar wmain set 2.0 select resn TRP - + .and. 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z&*?cmr|0yXp3`%BPS5E%J*VgNoSxHjdQQ*jIX$Q6^qij4lh5-%hDCOx0Pu4Fhi(@G literal 0 HcmV?d00001 diff --git a/charmm/toppar/non_charmm/00readme b/charmm/toppar/non_charmm/00readme new file mode 100644 index 00000000..397b033b --- /dev/null +++ b/charmm/toppar/non_charmm/00readme @@ -0,0 +1,72 @@ + +This directory contains topology and parameter files that are +compatible with CHARMM but are not part of the CHARMM force field +development efforts. The parameters have been approved by the +original developers, or individuals closely associated with those +developers. However, they have not been exhaustively tested in the +context of CHARMM and are not supported. Please carefully read the +header sections of the respective files to obtain information on their +proper use along with the appropriate references. + +BMS nucleic acid force field + +par_bms_dec03.prm +top_bms_dec03.rtf + +AMBER Cornell 94 force field for proteins and nucleic acids and the +1998 variant of the nucleic acid parameters. Requires CHARMM compiled +with AMBER keyword in pref.dat. Note that such versions of CHARMM can +NOT be used with the CHARMM force field. + +top_amber_cornell.inp +par_amber_cornell.inp +par_amber_98.inp + +parm14sb_all.rtf, parm14sb_all.prm: added July 2015 + +Additional versions of CHARMM compatible AMBER files may be obtained +from Jeff Klauda's website: + +http://www.glue.umd.edu/~jbklauda/research/download.html +or +http://terpconnect.umd.edu/~jbklauda/research/download.html + +OPLS AA protein force field along with ligand parameters. Requires +CHARMM compiled with OPLS keyword in pref.dat. + +top_opls_aa.inp +par_opls_aa.inp +par_opls_ligand.inp + +top_opls_aam.inp +par_opls_aam.inp: added July 2015 + +Version of Amber FF99SB* from Robert Best (not +tested). e_corr_ff99sb.pdf contains the energy correction that +converts the FFSB99 backbone potential to FFSB99* + +charmm_ff99sbstar.tgz + +Stream files containing various water models. Note that the water +atom types are the same as in the TIP3P model such that the following +files can NOT be used simultaneously with the TIP3P model in the +default toppar_water_ions.str file. This can be overcome by changing +the water atom types in the following files. + +Caution: The models with LPs fail with late versions of C36 +(post-fortran 90 conversion) and early versions of C37 + +toppar_water_ions_spc.str +toppar_water_ions_spc_e.str +toppar_water_ions_tip3p_pme_b.str +toppar_water_ions_tip3p_pme_f.str +toppar_water_ions_tip4p.str +toppar_water_ions_tip4p_2005.str +toppar_water_ions_tip4p_ew.str +toppar_water_ions_tip5p.str +toppar_water_ions_tip5p_ew.str + +GROMACS + +A full representation of the charmm36 FFs is in the gromacs +subdirectory. 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OPLS +H1 0.0 -0.0157 1.3870 0.0 -0.00785 1.3870 ! Veenstra JCC,8,(1992),963 +H2 0.0 -0.0157 1.2870 0.0 -0.00785 1.2870 ! Veenstra JCC,8,(1992),963 +H3 0.0 -0.0157 1.1870 0.0 -0.00785 1.1870 ! Veenstra JCC,8,(1992),963 +HP 0.0 -0.0157 1.1000 0.0 -0.00785 1.1000 ! Veenstra JCC,8,(1992),963 +HA 0.0 -0.0150 1.4590 0.0 -0.0075 1.4590 ! Spellmeyer +H4 0.0 -0.0150 1.4090 0.0 -0.0075 1.4090 ! Spellmeyer, 1 e- withdr. nghbr +H5 0.0 -0.0150 1.3590 0.0 -0.0075 1.3590 ! Spellmeyer, 2 e- withdr. nghbr +HW 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! TIP3P water model +!HT 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! TIP3P water model, charmm name +O 0.0 -0.2100 1.6612 0.0 -0.1050 1.6612 ! OPLS +O2 0.0 -0.2100 1.6612 0.0 -0.1050 1.6612 ! OPLS +OW 0.0 -0.1520 1.7683 0.0 -0.0760 1.7683 ! TIP3P water model +!OT 0.0 -0.1520 1.7683 0.0 -0.0760 1.7683 ! TIP3P water model, charmm name +OH 0.0 -0.2104 1.7210 0.0 -0.1052 1.7210 ! OPLS +OS 0.0 -0.1700 1.6837 0.0 -0.0850 1.6837 ! OPLS ether +CT 0.0 -0.1094 1.9080 0.0 -0.0547 1.9080 ! Spellmeyer +CA 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! Spellmeyer +C 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CM 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! Spellmeyer +CS 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CB 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CC 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CN 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CK 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CQ 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CW 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CV 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CR 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CX 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CY 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CD 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +N* 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS +NS 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! niu +S 0.0 -0.2500 2.0000 0.0 -0.1250 2.0000 ! Cornell CH3SH & CH3SCH3 FEP's +SH 0.0 -0.2500 2.0000 0.0 -0.1250 2.0000 ! Cornell CH3SH & CH3SCH3 FEP's +P 0.0 -0.2000 2.1000 0.0 -0.1000 2.1000 ! JCC,7,(1986),230; +IM 0.0 -0.1 2.47 0.0 -0.05 2.47 ! Cl- Smith, JCP 1994,100:5,3757 +Li 0.0 -0.0183 1.1370 0.0 -0.00915 1.1370 ! Li+ Aqvist JPC 1990,94,8021. (adapted) +!IP 0.0 -0.00277 1.8680 0.0 -0.001385 1.8680 ! Na+ Aqvist JPC 1990,94,8021. (adapted) +SOD 0.0 -0.00277 1.8680 0.0 -0.001385 1.8680 ! niu +K 0.0 -0.000328 2.6580 0.0 -0.000164 2.6580 ! K+ Aqvist JPC 1990,94,8021. (adapted) +Rb 0.0 -0.00017 2.9560 0.0 -0.000085 2.9560 ! Rb+ Aqvist JPC 1990,94,8021. (adapted) +I 0.0 -0.40 2.35 0.0 -0.20 2.35 ! JCC,7,(1986),230; +F 0.0 -0.061 1.75 0.0 -0.0305 1.75 ! Gough JCC 13,(1992),963. +IB 0.0 -0.1 5.0 0.0 -0.05 5.0 ! solvated ion, vacuum apprx + +END + diff --git a/charmm/toppar/non_charmm/par_amber_cornell.inp b/charmm/toppar/non_charmm/par_amber_cornell.inp new file mode 100644 index 00000000..506860b7 --- /dev/null +++ b/charmm/toppar/non_charmm/par_amber_cornell.inp @@ -0,0 +1,490 @@ +* AMBER Cornell et al. (parm94) force field conversion +* See: JACS (1995) 117, 5179-5197. +* nucleic acid part converted by tec3, march 1997 +* protein part converted by tec3, feb 1999 +* + +! +! This is a hand-conversion of the Cornell et. al. force field +! parm94.dat file (except for the torsion which were converted via +! a perl script). All the atom type names are the same except where +! otherwise noted. +! +! Any problems? Let me know... +! cheatham@helix.nih.gov, cheatham@cgl.ucsf.edu +! +! note: types N* remaned to NS +! C* renamed to CS +! +! note: the HO and HW nonbonded parameters, although zero in +! Cornell et al. should not have a 0.0 vdw radius in CHARMM +! to avoid difficulties with the 0.0/0.0 in the FAST OFF +! van der Waal code... +! +! note: the default nonbonded options chosen here are to match AMBER. +! It is not recommended that users actually run with GROUP based +! truncation and a switch unless really trying to match AMBER. +! Better would be ATOM based FSHIFT VSHIFT, however note that this +! does modify the energies (and effectively the parameters). +! + +BONDS +OW HW 553.0 0.9572 ! TIP3P water +HW HW 553.0 1.5136 ! TIP3P water +C CA 469.0 1.409 ! JCC,7,(1986),230; TYR +C CB 447.0 1.419 ! JCC,7,(1986),230; GUA +C CM 410.0 1.444 ! JCC,7,(1986),230; THY,URA +C CT 317.0 1.522 ! JCC,7,(1986),230; AA +C NS 424.0 1.383 ! JCC,7,(1986),230; CYT,URA +C NA 418.0 1.388 ! JCC,7,(1986),230; GUA.URA +C NC 457.0 1.358 ! JCC,7,(1986),230; CYT +C O 570.0 1.229 ! JCC,7,(1986),230; AA,CYT,GUA,THY,URA +C O2 656.0 1.250 ! JCC,7,(1986),230; GLU,ASP +C OH 450.0 1.364 ! JCC,7,(1986),230; TYR +CA CA 469.0 1.400 ! JCC,7,(1986),230; BENZENE,PHE,TRP,TYR +CA CB 469.0 1.404 ! JCC,7,(1986),230; ADE,TRP +CA CM 427.0 1.433 ! JCC,7,(1986),230; CYT +CA CT 317.0 1.510 ! JCC,7,(1986),230; PHE,TYR +CA HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR +CA H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; no assigned +CA N2 481.0 1.340 ! JCC,7,(1986),230; ARG,CYT,GUA +CA NA 427.0 1.381 ! JCC,7,(1986),230; GUA +CA NC 483.0 1.339 ! JCC,7,(1986),230; ADE,CYT,GUA +CB CB 520.0 1.370 ! JCC,7,(1986),230; ADE,GUA +CB NS 436.0 1.374 ! JCC,7,(1986),230; ADE,GUA +CB NB 414.0 1.391 ! JCC,7,(1986),230; ADE,GUA +CB NC 461.0 1.354 ! JCC,7,(1986),230; ADE,GUA +CK H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA +CK NS 440.0 1.371 ! JCC,7,(1986),230; ADE,GUA +CK NB 529.0 1.304 ! JCC,7,(1986),230; ADE,GUA +CM CM 549.0 1.350 ! JCC,7,(1986),230; CYT,THY,URA +CM CT 317.0 1.510 ! JCC,7,(1986),230; THY +CM HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +CM H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +CM H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; not assigned +CM NS 448.0 1.365 ! JCC,7,(1986),230; CYT,THY,URA +CQ H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE +CQ NC 502.0 1.324 ! JCC,7,(1986),230; ADE +CT CT 310.0 1.526 ! JCC,7,(1986),230; AA, SUGARS +CT HC 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, SUGARS +CT H1 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, RIBOSE +CT H2 340.0 1.090 ! changed from 331 bsd on NMA nmodes; SUGARS +CT H3 340.0 1.090 ! changed from 331 bsd on NMA nmodes; not assigned +CT HP 340.0 1.090 ! changed from 331; AA lysine, methyl ammonium cation +CT NS 337.0 1.475 ! JCC,7,(1986),230; ADE,CYT,GUA,THY,URA +CT N2 337.0 1.463 ! JCC,7,(1986),230; ARG +CT OH 320.0 1.410 ! JCC,7,(1986),230; SUGARS +CT OS 320.0 1.410 ! JCC,7,(1986),230; NUCLEIC ACIDS +H N2 434.0 1.010 ! JCC,7,(1986),230; ADE,CYT,GUA,ARG +H NS 434.0 1.010 ! for plain unmethylated bases ADE,CYT,GUA,ARG +H NA 434.0 1.010 ! JCC,7,(1986),230; GUA,URA,HIS +HO OH 553.0 0.960 ! JCC,7,(1986),230; SUGARS,SER,TYR +HO OS 553.0 0.960 ! JCC,7,(1986),230; NUCLEOTIDE ENDS +O2 P 525.0 1.480 ! JCC,7,(1986),230; NA PHOSPHATES +OH P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES +OS P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES +CS HC 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes, not needed AA +C N 490.0 1.335 ! JCC,7,(1986),230; AA +CS CB 388.0 1.459 ! JCC,7,(1986),230; TRP +CS CT 317.0 1.495 ! JCC,7,(1986),230; TRP +CS CW 546.0 1.352 ! JCC,7,(1986),230; TRP +CA CN 469.0 1.400 ! JCC,7,(1986),230; TRP +CB CN 447.0 1.419 ! JCC,7,(1986),230; TRP +CC CT 317.0 1.504 ! JCC,7,(1986),230; HIS +CC CV 512.0 1.375 ! JCC,7,(1986),230; HIS(delta) +CC CW 518.0 1.371 ! JCC,7,(1986),230; HIS(epsilon) +CC NA 422.0 1.385 ! JCC,7,(1986),230; HIS +CC NB 410.0 1.394 ! JCC,7,(1986),230; HIS +CN NA 428.0 1.380 ! JCC,7,(1986),230; TRP +CR H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS +CR NA 477.0 1.343 ! JCC,7,(1986),230; HIS +CR NB 488.0 1.335 ! JCC,7,(1986),230; HIS +CT N 337.0 1.449 ! JCC,7,(1986),230; AA +CT N3 367.0 1.471 ! JCC,7,(1986),230; LYS +CT S 227.0 1.810 ! changed from 222.0 based on dimethylS nmodes +CT SH 237.0 1.810 ! changed from 222.0 based on methanethiol nmodes +CV H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; HIS +CV NB 410.0 1.394 ! JCC,7,(1986),230; HIS +CW H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) +CW NA 427.0 1.381 ! JCC,7,(1986),230; HIS,TRP +H N 434.0 1.010 ! JCC,7,(1986),230; AA +H N3 434.0 1.010 ! JCC,7,(1986),230; LYS +HS SH 274.0 1.336 ! JCC,7,(1986),230; CYS +S S 166.0 2.038 ! JCC,7,(1986),230; CYX (SCHERAGA) +CT F 367.0 1.380 ! JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 + +THETAS +HW OW HW 100. 104.52 ! TIP3P water +HW HW OW 0. 127.74 ! (found in crystallographic water with 3 bonds) +CB C NA 70.0 111.30 ! NA +CB C O 80.0 128.80 ! +CM C NA 70.0 114.10 ! +CM C O 80.0 125.30 ! +CT C O 80.0 120.40 ! +CT C O2 70.0 117.00 ! +CT C OH 70.0 117.00 ! +NS C NA 70.0 115.40 ! +NS C NC 70.0 118.60 ! +NS C O 80.0 120.90 ! +NA C O 80.0 120.60 ! +NC C O 80.0 122.50 ! +CT C N 70.0 116.60 ! AA general +N C O 80.0 122.90 ! AA general +O C O 80.0 126.00 ! AA COO terminal residues +O2 C O2 80.0 126.00 ! AA GLU (SCH JPC 79,2379) +O C OH 80.0 126.00 ! +CA C CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA tyr +CA C OH 70.0 120.00 ! AA tyr +C CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes +CA CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes +CA CA CB 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes +CA CA CT 70.0 120.00 ! +CA CA HA 35.0 120.00 ! +CA CA H4 35.0 120.00 ! +CB CA HA 35.0 120.00 ! +CB CA H4 35.0 120.00 ! +CB CA N2 70.0 123.50 ! +CB CA NC 70.0 117.30 ! +CM CA N2 70.0 120.10 ! +CM CA NC 70.0 121.50 ! +N2 CA NA 70.0 116.00 ! +N2 CA NC 70.0 119.30 ! +NA CA NC 70.0 123.30 ! +C CA HA 35.0 120.00 ! AA tyr +N2 CA N2 70.0 120.00 ! AA arg +CN CA HA 35.0 120.00 ! AA trp +CA CA CN 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +C CB CB 63.0 119.20 ! changed from 85.0 bsd on C6H6 nmodes; NA gua +C CB NB 70.0 130.00 ! +CA CB CB 63.0 117.30 ! changed from 85.0 bsd on C6H6 nmodes; NA ade +CA CB NB 70.0 132.40 ! +CB CB NS 70.0 106.20 ! +CB CB NB 70.0 110.40 ! +CB CB NC 70.0 127.70 ! +NS CB NC 70.0 126.20 ! +CS CB CA 63.0 134.90 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +CS CB CN 63.0 108.80 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +CA CB CN 63.0 116.20 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +H5 CK NS 35.0 123.05 ! +H5 CK NB 35.0 123.05 ! +NS CK NB 70.0 113.90 ! +C CM CM 63.0 120.70 ! changed from 85.0 bsd on C6H6 nmodes; NA thy +C CM CT 70.0 119.70 ! +C CM HA 35.0 119.70 ! +C CM H4 35.0 119.70 ! +CA CM CM 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt +CA CM HA 35.0 123.30 ! +CA CM H4 35.0 123.30 ! +CM CM CT 70.0 119.70 ! +CM CM HA 35.0 119.70 ! +CM CM H4 35.0 119.70 ! +CM CM NS 70.0 121.20 ! +H4 CM NS 35.0 119.10 ! +H5 CQ NC 35.0 115.45 ! +NC CQ NC 70.0 129.10 ! +CM CT HC 50.0 109.50 ! changed based on NMA nmodes +CT CT CT 40.0 109.50 ! +CT CT HC 50.0 109.50 ! changed based on NMA nmodes +CT CT H1 50.0 109.50 ! changed based on NMA nmodes +CT CT H2 50.0 109.50 ! changed based on NMA nmodes +CT CT HP 50.0 109.50 ! changed based on NMA nmodes +CT CT NS 50.0 109.50 ! +CT CT OH 50.0 109.50 ! +CT CT OS 50.0 109.50 ! +HC CT HC 35.0 109.50 ! +H1 CT H1 35.0 109.50 ! +HP CT HP 35.0 109.50 ! AA lys, ch3nh4+ +H2 CT NS 50.0 109.50 ! changed based on NMA nmodes +H1 CT NS 50.0 109.50 ! changed based on NMA nmodes +H1 CT OH 50.0 109.50 ! changed based on NMA nmodes +H1 CT OS 50.0 109.50 ! changed based on NMA nmodes +H2 CT OS 50.0 109.50 ! changed based on NMA nmodes +NS CT OS 50.0 109.50 ! +H1 CT N 50.0 109.50 ! AA general changed based on NMA nmodes +C CT H1 50.0 109.50 ! AA general changed based on NMA nmodes +C CT HP 50.0 109.50 ! AA zwitterion changed based on NMA nmodes +H1 CT S 50.0 109.50 ! AA cys changed based on NMA nmodes +H1 CT SH 50.0 109.50 ! AA cyx changed based on NMA nmodes +CT CT S 50.0 114.70 ! AA cyx (SCHERAGA JPC 79,1428) +CT CT SH 50.0 108.60 ! AA cys +H2 CT H2 35.0 109.50 ! AA lys +H1 CT N2 50.0 109.50 ! AA arg changed based on NMA nmodes +HP CT N3 50.0 109.50 ! AA lys, ch3nh3+, changed based on NMA nmodes +CA CT CT 63.0 114.00 ! AA phe tyr (SCH JPC 79,2379) +C CT HC 50.0 109.50 ! AA gln changed based on NMA nmodes +C CT N 63.0 110.10 ! AA general +CT CT N2 80.0 111.20 ! AA arg (JCP 76, 1439) +CT CT N 80.0 109.70 ! AA ala, general (JACS 94, 2657) +C CT CT 63.0 111.10 ! AA general +CA CT HC 50.0 109.50 ! AA tyr changed based on NMA nmodes +CT CT N3 80.0 111.20 ! AA lys (JCP 76, 1439) +CC CT CT 63.0 113.10 ! AA his +CC CT HC 50.0 109.50 ! AA his changed based on NMA nmodes +C CT N3 80.0 111.20 ! AA amino terminal residues +CS CT CT 63.0 115.60 ! AA trp +CS CT HC 50.0 109.50 ! AA trp changed based on NMA nmodes +CT CC NA 70.0 120.00 ! AA his +CT CC CV 70.0 120.00 ! AA his +CT CC NB 70.0 120.00 ! AA his +CV CC NA 70.0 120.00 ! AA his +CW CC NA 70.0 120.00 ! AA his +CW CC NB 70.0 120.00 ! AA his +CT CC CW 70.0 120.00 ! AA his +H5 CR NA 35.0 120.00 ! AA his +H5 CR NB 35.0 120.00 ! AA his +NA CR NA 70.0 120.00 ! AA his +NA CR NB 70.0 120.00 ! AA his +CC CV H4 35.0 120.00 ! AA his +CC CV NB 70.0 120.00 ! AA his +H4 CV NB 35.0 120.00 ! AA his +CC CW H4 35.0 120.00 ! AA his +CC CW NA 70.0 120.00 ! AA his +H4 CW NA 35.0 120.00 ! AA his +CS CW H4 35.0 120.00 ! AA trp +CS CW NA 70.0 108.70 ! AA trp +CT CS CW 70.0 125.00 ! AA trp +CB CS CT 70.0 128.60 ! AA trp +CB CS CW 63.0 106.40 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +CA CN NA 70.0 132.80 ! AA trp +CB CN NA 70.0 104.40 ! AA trp +CA CN CB 63.0 122.70 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +C N CT 50.0 121.90 ! AA general +C N H 30.0 120.00 ! AA general, gln, asn,changed based on NMA nmodes +CT N H 30.0 118.04 ! AA general, changed based on NMA nmodes +CT N CT 50.0 118.00 ! AA pro (DETAR JACS 99,1232) +H N H 35.0 120.00 ! ade,cyt,gua,gln,asn ** +C NS CM 70.0 121.60 ! +C NS CT 70.0 117.60 ! +C NS H 30.0 119.20 ! changed based on NMA nmodes +CB NS CK 70.0 105.40 ! +CB NS CT 70.0 125.80 ! +CB NS H 30.0 125.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes +CK NS CT 70.0 128.80 ! +CK NS H 30.0 128.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes +CM NS CT 70.0 121.20 ! +CM NS H 30.0 121.20 ! for unmethylated n.a. bases,chngd bsd NMA nmodes +CA N2 H 35.0 120.00 ! +H N2 H 35.0 120.00 ! +CT N2 H 35.0 118.40 ! AA arg +CA N2 CT 50.0 123.20 ! AA arg +CT N3 H 50.0 109.50 ! AA lys, changed based on NMA nmodes +CT N3 CT 50.0 109.50 ! AA pro/nt +H N3 H 35.0 109.50 ! AA lys, AA(end) +C NA C 70.0 126.40 ! +C NA CA 70.0 125.20 ! +C NA H 30.0 116.80 ! changed based on NMA nmodes +CA NA H 30.0 118.00 ! changed based on NMA nmodes +CC NA CR 70.0 120.00 ! AA his +CC NA H 30.0 120.00 ! AA his, changed based on NMA nmodes +CR NA CW 70.0 120.00 ! AA his +CR NA H 30.0 120.00 ! AA his, changed based on NMA nmodes +CW NA H 30.0 120.00 ! AA his, changed based on NMA nmodes +CN NA CW 70.0 111.60 ! AA trp +CN NA H 30.0 123.10 ! AA trp, changed based on NMA nmodes +CB NB CK 70.0 103.80 ! +CC NB CR 70.0 117.00 ! AA his +CR NB CV 70.0 117.00 ! AA his +C NC CA 70.0 120.50 ! +CA NC CB 70.0 112.20 ! +CA NC CQ 70.0 118.60 ! +CB NC CQ 70.0 111.00 ! +C OH HO 35.0 113.00 ! +CT OH HO 55.0 108.50 ! +HO OH P 45.0 108.50 ! +CT OS CT 60.0 109.50 ! +CT OS P 100.0 120.50 ! +P OS P 100.0 120.50 ! +O2 P OH 45.0 108.23 ! +O2 P O2 140.0 119.90 ! +O2 P OS 100.0 108.23 ! +OH P OS 45.0 102.60 ! +OS P OS 45.0 102.60 ! +CT S CT 62.0 98.90 ! AA met +CT S S 68.0 103.70 ! AA cyx (SCHERAGA JPC 79,1428) +CT SH HS 43.0 96.00 ! changed from 44.0 based on methanethiol nmodes +HS SH HS 35.0 92.07 ! AA cys +F CT F 77.0 109.10 ! JCC,13,(1992),963; +F CT H1 35.0 109.50 ! JCC,13,(1992),963; + +PHI +X C CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6 +X C CB X 3.00000000 2 180.0 ! intrpol.bsd.on C6H6 +X C CM X 2.17500000 2 180.0 ! intrpol.bsd.on C6H6 +X C NS X 1.45000000 2 180.0 ! JCC,7,(1986),230 +X C NA X 1.35000000 2 180.0 ! JCC,7,(1986),230 +X C NC X 4.00000000 2 180.0 ! JCC,7,(1986),230 +X C OH X 0.90000000 2 180.0 ! JCC,7,(1986),230 +X C CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 +X CA CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6 +X CA CB X 3.50000000 2 180.0 ! intrpol.bsd.on C6H6 +X CA CM X 2.55000000 2 180.0 ! intrpol.bsd.on C6H6 +X CA CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 +X CA N2 X 2.40000000 2 180.0 ! reinterpolated 93' +X CA NA X 1.50000000 2 180.0 ! JCC,7,(1986),230 +X CA NC X 4.80000000 2 180.0 ! JCC,7,(1986),230 +X CB CB X 5.45000000 2 180.0 ! intrpol.bsd.on C6H6 +X CB NS X 1.65000000 2 180.0 ! JCC,7,(1986),230 +X CB NB X 2.55000000 2 180.0 ! JCC,7,(1986),230 +X CB NC X 4.15000000 2 180.0 ! JCC,7,(1986),230 +X CK NS X 1.70000000 2 180.0 ! JCC,7,(1986),230 +X CK NB X 10.00000000 2 180.0 ! JCC,7,(1986),230 +X CM CM X 6.65000000 2 180.0 ! intrpol.bsd.on C6H6 +X CM CT X 0.00000000 3 0.0 ! JCC,7,(1986),230 +X CM NS X 1.85000000 2 180.0 ! JCC,7,(1986),230 +X CQ NC X 6.80000000 2 180.0 ! JCC,7,(1986),230 +X CT CT X 0.15555556 3 0.0 ! JCC,7,(1986),230 +X CT N X 0.00000000 2 0.0 ! JCC,7,(1986),230 +X CT NS X 0.00000000 2 0.0 ! JCC,7,(1986),230 +X CT N2 X 0.00000000 3 0.0 ! JCC,7,(1986),230 +X CT OH X 0.16666667 3 0.0 ! JCC,7,(1986),230 +X CT OS X 0.38333333 3 0.0 ! JCC,7,(1986),230 +X OH P X 0.25000000 3 0.0 ! JCC,7,(1986),230 +X OS P X 0.25000000 3 0.0 ! JCC,7,(1986),230 +X C N X 2.50000000 2 180.0 ! AA|check Wendy?&NMA +X CT N3 X 0.15555556 3 0.0 ! JCC,7,(1986),230 +X CT S X 0.33333333 3 0.0 ! JCC,7,(1986),230 +X CT SH X 0.25000000 3 0.0 ! JCC,7,(1986),230 +X CS CB X 1.67500000 2 180.0 ! intrpol.bsd.onC6H6aa +X CS CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 +X CS CW X 6.52500000 2 180.0 ! intrpol.bsd.on C6H6 +X CA CN X 3.62500000 2 180.0 ! reinterpolated 93' +X CB CN X 3.00000000 2 180.0 ! reinterpolated 93' +X CC CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 +X CC CV X 5.15000000 2 180.0 ! intrpol.bsd.on C6H6 +X CC CW X 5.37500000 2 180.0 ! intrpol.bsd.on C6H6 +X CC NA X 1.40000000 2 180.0 ! JCC,7,(1986),230 +X CC NB X 2.40000000 2 180.0 ! JCC,7,(1986),230 +X CN NA X 1.52500000 2 180.0 ! reinterpolated 93' +X CR NA X 2.32500000 2 180.0 ! JCC,7,(1986),230 +X CR NB X 5.00000000 2 180.0 ! JCC,7,(1986),230 +X CV NB X 2.40000000 2 180.0 ! JCC,7,(1986),230 +X CW NA X 1.50000000 2 180.0 ! JCC,7,(1986),230 +CT CT OS CT 0.38300000 3 0.0 ! +CT CT OS CT 0.10000000 2 180.0 ! +C N CT C 0.20000000 2 180.0 ! +N CT C N 0.40000000 4 180.0 ! +N CT C N 1.35000000 2 180.0 ! +N CT C N 0.75000000 1 180.0 ! +CT CT N C 0.50000000 4 180.0 ! +CT CT N C 0.15000000 3 180.0 ! +CT CT N C 0.53000000 1 0.0 ! +CT CT C N 0.10000000 4 0.0 ! +CT CT C N 0.07000000 2 0.0 ! +H N C O 2.50000000 2 180.0 ! JCC,7,(1986),230 +H N C O 2.00000000 1 0.0 ! J.C.cistrans-NMA DE +CT S S CT 3.50000000 2 0.0 ! JCC,7,(1986),230 +CT S S CT 0.60000000 3 0.0 ! JCC,7,(1986),230 +OS CT CT OS 0.14400000 3 0.0 ! JCC,7,(1986),230 +OS CT CT OS 1.00000000 2 0.0 ! pucker anal (93') +OS CT CT OH 0.14400000 3 0.0 ! JCC,7,(1986),230 +OS CT CT OH 1.00000000 2 0.0 ! pucker anal (93') +OH CT CT OH 0.14400000 3 0.0 ! JCC,7,(1986),230 +OH CT CT OH 1.00000000 2 0.0 ! check glicolWC? puc +OH P OS CT 0.25000000 3 0.0 ! JCC,7,(1986),230 +OH P OS CT 1.20000000 2 0.0 ! gg> ene.631g*/mp2 +OS P OS CT 0.25000000 3 0.0 ! JCC,7,(1986),230 +OS P OS CT 1.20000000 2 0.0 ! gg> ene.631g*/mp2 +OS CT NS CK 0.50000000 2 180.0 ! sugar frag calc (PC) +OS CT NS CK 2.50000000 1 0.0 ! sugar frag calc (PC) +OS CT NS CM 0.50000000 2 180.0 ! sugar frag calc (PC) +OS CT NS CM 2.50000000 1 0.0 ! sugar frag calc (PC) + +IMPHI +X X C O 10.50000000 2 180.0 ! JCC,7,(1986),230 +X O2 C O2 10.50000000 2 180.0 ! JCC,7,(1986),230 +X X N H 1.00000000 2 180.0 ! JCC,7,(1986),230 +X X N2 H 1.00000000 2 180.0 ! JCC,7,(1986),230 +X X NA H 1.00000000 2 180.0 ! JCC,7,(1986),230 +X N2 CA N2 10.50000000 2 180.0 ! JCC,7,(1986),230 +X CT N CT 1.00000000 2 180.0 ! JCC,7,(1986),230 +X X CA HA 1.10000000 2 180.0 ! bsd.on C6H6 nmodes +X X CW H4 1.10000000 2 180.0 ! +X X CR H5 1.10000000 2 180.0 ! +X X CV H4 1.10000000 2 180.0 ! +X X CQ H5 1.10000000 2 180.0 ! +X X CK H5 1.10000000 2 180.0 ! +X X CM H4 1.10000000 2 180.0 ! +X X CM HA 1.10000000 2 180.0 ! +X X CA H4 1.10000000 2 180.0 ! bsd.on C6H6 nmodes +X X CA H5 1.10000000 2 180.0 ! bsd.on C6H6 nmodes +CK CB NS CT 1.00000000 2 180.0 ! +CM C NS CT 1.00000000 2 180.0 ! dac guess, 9/94 +CM C CM CT 1.10000000 2 180.0 ! +CT O C OH 10.50000000 2 180.0 ! +NA CV CC CT 1.10000000 2 180.0 ! +NB CW CC CT 1.10000000 2 180.0 ! +NA CW CC CT 1.10000000 2 180.0 ! +CW CB CS CT 1.10000000 2 180.0 ! +CA CA CA CT 1.10000000 2 180.0 ! +C CM CM CT 1.10000000 2 180.0 ! dac guess, 9/94 +NC CM CA N2 1.10000000 2 180.0 ! dac guess, 9/94 +CB NC CA N2 1.10000000 2 180.0 ! dac, 10/94 +NA NC CA N2 1.10000000 2 180.0 ! dac, 10/94 +CA CA C OH 1.10000000 2 180.0 ! + +! +! Note: the HO and HW parameters, although zero in Cornell et al. +! should not have a 0.0 vdw radius in CHARMM to avoid difficulties +! with the 0.0/0.0 in the FAST OFF van der Waal code... +! +! NOTE: the defaults chosen here are to match AMBER. It is not +! recommended that users actually run with GROUP based truncation +! and a switch. Better would be ATOM based FSHIFT VSHIFT +NONBONDED NBXMOD 5 GROUP SWITCH CDIEL - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 0.83333333 WMIN 1.4 +! Emin Rmin/2 Emin/2 Rmin (for 1-4's) +! (kcal/mol) (A) +H 0.0 -0.0157 0.6000 0.0 -0.00785 0.6000 ! Ferguson base pair geom. +HO 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! OPLS, JACS,110,(1988),1657 +HS 0.0 -0.0157 0.6000 0.0 -0.00785 0.6000 ! W. Cornell CH3SH --> CH3OH FEP +HC 0.0 -0.0157 1.4870 0.0 -0.00785 1.4870 ! OPLS +H1 0.0 -0.0157 1.3870 0.0 -0.00785 1.3870 ! Veenstra JCC,8,(1992),963 +H2 0.0 -0.0157 1.2870 0.0 -0.00785 1.2870 ! Veenstra JCC,8,(1992),963 +H3 0.0 -0.0157 1.1870 0.0 -0.00785 1.1870 ! Veenstra JCC,8,(1992),963 +HP 0.0 -0.0157 1.1000 0.0 -0.00785 1.1000 ! Veenstra JCC,8,(1992),963 +HA 0.0 -0.0150 1.4590 0.0 -0.0075 1.4590 ! Spellmeyer +H4 0.0 -0.0150 1.4090 0.0 -0.0075 1.4090 ! Spellmeyer, 1 e- withdr. nghbr +H5 0.0 -0.0150 1.3590 0.0 -0.0075 1.3590 ! Spellmeyer, 2 e- withdr. nghbr +HW 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! TIP3P water model +O 0.0 -0.2100 1.6612 0.0 -0.1050 1.6612 ! OPLS +O2 0.0 -0.2100 1.6612 0.0 -0.1050 1.6612 ! OPLS +OW 0.0 -0.1520 1.7683 0.0 -0.0760 1.7683 ! TIP3P water model +OH 0.0 -0.2104 1.7210 0.0 -0.1052 1.7210 ! OPLS +OS 0.0 -0.1700 1.6837 0.0 -0.0850 1.6837 ! OPLS ether +CT 0.0 -0.1094 1.9080 0.0 -0.0547 1.9080 ! Spellmeyer +CA 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! Spellmeyer +C 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CM 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! Spellmeyer +CS 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CB 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CC 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CN 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CK 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CQ 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CW 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CV 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CR 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CX 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CY 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +CD 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS +N* 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS +S 0.0 -0.2500 2.0000 0.0 -0.1250 2.0000 ! Cornell CH3SH & CH3SCH3 FEP's +SH 0.0 -0.2500 2.0000 0.0 -0.1250 2.0000 ! Cornell CH3SH & CH3SCH3 FEP's +P 0.0 -0.2000 2.1000 0.0 -0.1000 2.1000 ! JCC,7,(1986),230; +IM 0.0 -0.1 2.47 0.0 -0.05 2.47 ! Cl- Smith, JCP 1994,100:5,3757 +Li 0.0 -0.0183 1.1370 0.0 -0.00915 1.1370 ! Li+ Aqvist JPC 1990,94,8021. (adapted) +IP 0.0 -0.00277 1.8680 0.0 -0.001385 1.8680 ! Na+ Aqvist JPC 1990,94,8021. (adapted) +K 0.0 -0.000328 2.6580 0.0 -0.000164 2.6580 ! K+ Aqvist JPC 1990,94,8021. (adapted) +Rb 0.0 -0.00017 2.9560 0.0 -0.000085 2.9560 ! Rb+ Aqvist JPC 1990,94,8021. (adapted) +I 0.0 -0.40 2.35 0.0 -0.20 2.35 ! JCC,7,(1986),230; +F 0.0 -0.061 1.75 0.0 -0.0305 1.75 ! Gough JCC 13,(1992),963. +IB 0.0 -0.1 5.0 0.0 -0.05 5.0 ! solvated ion, vacuum apprx + +END + + + + + + + diff --git a/charmm/toppar/non_charmm/par_bms_dec03.inp b/charmm/toppar/non_charmm/par_bms_dec03.inp new file mode 100644 index 00000000..c3280626 --- /dev/null +++ b/charmm/toppar/non_charmm/par_bms_dec03.inp @@ -0,0 +1,684 @@ +* \\\\\\\ All-Hydrogen Nucleic Acid Topology File //////// +* \\\\\\\\\\\\\\\\\\ Developmental /////////////////////// +* David R. Langley +* Version 1.00, August 1995 +* Version 1.05, June 1999 +* Version 1.10, November 2000 +* Version 1.15, April 2003 +*.................................................................. +*.................................................................. +* David R. Langley, Molecular Dynamic Simulations of Environment +* and Sequence Dependent DNA Conformations: The Development of +* the BMS Nucleic Acid Force Field and Comparison with Experimental +* Results. J. Biomol. Struct. Dyn., 1998, 16, 487-509. +*.................................................................. +*.................................................................. +* Parameters for 2'-deoxy-6-thioguanine (patch residue id: TG) were added 11-22-00. +* - +* The modeified TIPS3P WATER MODEL with 5% reduced charges (residue id: T95) +* provides stable (4M NaCl) A-DNA simulations by balancing the +* Na-H2O, Cl-H2O, DNA-Na, DNA-Cl, DNA-H2O interactions. +* + +BONDS ! FORCE EQUI +CK CF 302.0 1.425 !U,T, par_a4 JWK 9/30/91 +CK CB 302.0 1.360 !G, JWK, adm jr., 7/24/91 +CK NSP 302.0 1.400 !C,U, JWK, adm jr., 7/24/91 +CK NAG 340.0 1.410 !G, par_a4 JWK 9/30/91 +CK NAT 340.0 1.410 !U, par_a4 JWK 9/30/91 +CK NC 400.0 1.358 !C, par_a6 JWK 9/30/91 +CK OK 620.0 1.235 !U,A,G par_a4 adm jr., 10/2/91 +CK OKC 620.0 1.245 !C, adm jr., 10/2/91 +CK OKG 620.0 1.235 !G, DRL +CK S 523.0 1.664 !TG, DRL, B3LYP/6-31+G** (1.664A) +CA CF 302.0 1.420 !C, JWK, adm jr., 7/24/91 +CA CB 302.0 1.360 !A, JWK, adm jr., 10/2/91 +CA NAN 400.0 1.365 !C,A,G JWK, adm jr., 10/2/91 +CA NAG 400.0 1.400 !G, JWK, adm jr., 7/24/91 +CA NC 400.0 1.340 !C, par_a6 JWK 9/30/91 +CA NCA 320.0 1.340 !A, par_a8 JWK 9/30/91 +CF CF 560.0 1.335 !C, par_a4 JWK 9/30/91 +CF CTT 230.0 1.480 !T, par_51, adm jr., 7/24/91 +CF HAR 350.0 1.09 !C,U, JWK +CF NSP 302.0 1.365 !C,U, JWK, adm jr., 7/24/91 +CE HAR 380.0 1.09 !G,A, JWK par_a7 9/30/91 +CE NS 300.0 1.365 !G,A, JWK, adm jr., 7/24/91 +CE NAG 350.0 1.365 !Inosine, adm jr., 2/94 +CE NCA 310.0 1.310 !A, JWK, par_a7 9/30/91 +CE NB 400.0 1.308 !G,A, JWK par_a8 9/30/91 +CE NBG 400.0 1.308 !G, DRL +CB CB 320.0 1.370 !G,A, JWK par_a8 9/30/91 +CB NS 302.0 1.408 !G,A, JWK, adm jr., 7/24/91 +CB NCA 350.0 1.336 !A, JWK par_a8 9/30/91 +CB NB 350.0 1.360 !G,A, JWK, par_a8 9/30/91 +CB NBG 350.0 1.360 !G, DRL +HNA NAN 488.0 1.00 !A,C,G, JWK, adm jr., 7/24/91 +HB NS 474.0 1.01 !C,U, JWK +HB NSP 474.0 1.01 !C,U, JWK +HB NAG 471.0 1.01 !G, JWK, par_a12 9/30/91 +HB NAT 474.0 1.01 !U, JWK, adm jr., 7/24/91 +! +!for RNA +CK NSR 302.0 1.400 !DRL +CF NSR 302.0 1.365 !DRL +CE NSR 300.0 1.365 !DRL +CB NSR 302.0 1.408 !DRL +HB NSR 474.0 1.01 !DRL +CTT NAG 400.0 1.46 !DRL for 1methylguanine +CF CT5 230.0 1.480 !PSU, DRL +! +OS P 270.0 1.60 !DMP, ADM Jr. +OCP P 580.0 1.48 !DMP, ADM Jr. +OHP P 237.0 1.58 !MP_1, ADM Jr. +HOP OHP 545.0 0.960 !MP_1, ADM Jr. +CT5 NS 300.0 1.48 !DRL/quanta +CT5 NSR 300.0 1.48 !DRL/quanta +CT5 NSP 300.0 1.48 !DRL/quanta +CTT NS 400.0 1.46 !DRL/quanta +CTT NSR 400.0 1.46 !DRL/quanta +CTT NSP 400.0 1.46 !DRL/quanta +HAT CTT 340.0 1.09 !DRL/quanta +CTT CTT 268.0 1.529 !DRL/quanta +CTT CT5 268.0 1.529 !DRL/quanta +CTT OS 393.0 1.42 !DRL/quanta +CTT OH 375.0 1.405 !DRL/quanta +HA5 CT5 340.0 1.09 !DRL/quanta +CT5 CT5 320.0 1.5483 !DRL !MP2 1.5483A +CT5 OE 340.0 1.4415 !DRL !MP2 1.4415A +CT5 OS 393.0 1.42 !DRL/quanta +CT5 OH 375.0 1.405 !DRL/quanta +HO OH 505.0 0.948 !DRL/quanta +!TIPS3P +HT HT 0.0 1.5139 !TIPS3P (for SHAKE w/PARM) +HT OT 450.0 0.9572 !TIPS3P +!AMBER TIP3P water +HW HW 553.0 1.5136 ! TIP3P water +OW HW 553.0 0.9572 ! TIP3P water +!ethanol and trifloroethanol +CT CT 268.0 1.529 !quanta +HA CT 340.0 1.09 !quanta +CT OT 375.0 1.405 !quanta +HO OT 505.0 0.948 !quanta +CF3 CT 208.0 1.52 !quanta +CF3 XF 275.0 1.32 !quanta + +THETAS ! FORCE EQUI +CF CK NAT 67.0 113.4 !U,T, JWK, adm jr., 7/24/91 +CF CK OK 100.0 124.7 !U,T, par_a3 JWK 9/30/91 +CB CK NAG 67.0 109.4 !G, JWK, adm jr., 7/24/91 +!!!CB CK OK 100.0 125.6 !G, par_a3 adm jr., 10/2/91 +CB CK OKG 100.0 125.6 !G, DRL +CB CK S 100.0 128.26 ! 80.0 128.8 !TG, DRL, B3LYP/6-31+G** (130.26) +NSP CK NAT 67.0 114.6 !U,T, JWK, adm jr., 7/24/91 +NSP CK NC 70.0 116.4 !C, JWK, adm jr., 7/24/91 +NSP CK OK 100.0 123.5 !C,U,G par_a3 JWK 9/30/91 +NSP CK OKC 100.0 121.5 !C, adm jr., 10/2/91 +!!!NAG CK OK 100.0 125.0 !G, par_a4 adm jr., 10/2/91 +NAG CK OKG 100.0 125.0 !G, DRL +NAG CK S 100.0 121.45 ! 80.0 120.6 !TG, DRL, B3LYP/6-31+G** (119.45) +NAT CK OK 100.0 121.9 !U, par_a3 JWK 9/30/91 +NC CK OKC 100.0 122.1 !C, par_a3 JWK 9/30/91 +CF CA NAN 70.0 117.9 !C, JWK, adm jr., 7/24/91 +CF CA NC 70.0 119.8 !C, JWK, adm jr., 7/24/91 +CB CA NAN 70.0 119.1 !A, adm jr., 6/7/92 +CB CA NCA 80.0 112.6 !A, JWK par_a9 9/30/91 +NAN CA NAG 70.0 114.8 20. 2.30 !G, JWK, adm jr., 7/24/91 +NAN CA NC 70.0 122.3 !C, JWK, adm jr., 7/24/91 +NAN CA NCA 70.0 128.3 !A, adm jr., 6/7/92 +NAG CA NCA 70.0 122.9 !G, JWK par_49, par_a11 9/30/91 +CK CF CF 125.0 118.0 !U,T, JWK, adm jr., 7/24/91 +CK CF CTT 70.0 118.3 !T, JWK, adm jr., 7/24/91 +CK CF HAR 30.0 120.0 !C,U, JWK, adm jr., 7/24/91 +CA CF CF 125.0 119.3 !C, JWK, adm jr., 7/24/91 +CA CF HAR 30.0 118.7 !C, JWK, adm jr., 7/24/91 +CF CF CTT 70.0 123.7 !T, JWK, adm jr., 7/24/91 +CF CF HAR 30.0 122.0 !C,U, JWK, adm jr., 7/24/91 +CF CF NSP 125.0 124.2 !C,U, JWK, adm jr., 7/24/91 +HAR CF NSP 30.0 113.8 !C,U, JWK, adm jr., 7/24/91 +HAR CE NS 40.0 119.0 !G,A, JWK, par_a9 9/30/91 +HAR CE NCA 35.0 114.75 !A, JWK, par_a9 9/30/91 +HAR CE NAG 35.0 114.75 !Inosine, adm jr., 2/94 +HAR CE NB 40.0 126.7 !G,A, JWK, par_a9 9/30/91 +HAR CE NBG 40.0 126.7 !G, DRL +NS CE NB 100.0 114.3 !G,A, JWK, par_a9 9/30/91 +NS CE NBG 100.0 114.3 !G, DRL +NCA CE NCA 80.0 130.5 !A, JWK, par_a9 9/30/91 +CK CB CB 125.0 119.5 !G, JWK, adm jr., 7/24/91 +!!!CK CB NB 125.0 128.8 !G, JWK, adm jr., 7/24/91 +CK CB NBG 125.0 128.8 !G, DRL +CA CB CB 100.0 119.7 !A, JWK, par_a7 9/30/91 +CA CB NB 120.0 128.6 !A, JWK, par_a9 9/30/91 +CB CB NS 100.0 105.1 !G,A, JWK, par_a9 9/30/91 +CB CB NCA 100.0 127.5 !A, JWK, par_a7 9/30/91 +CB CB NB 100.0 111.7 !G,A, JWK, par_a7 9/30/91 +CB CB NBG 100.0 111.7 !G, DRL +NS CB NCA 140.0 127.4 !A, JWK, par_a9 9/30/91 +CA NAN HNA 40.0 120.0 ! par_a6 JWK 9/30/91 +HNA NAN HNA 32.0 120.0 ! par_a5 JWK 9/30/91 +CK NSP CT5 70.0 128.4 !from CN4 NN2 CN7, adm jr., 7/24/91 +CK NSP CF 125.0 120.6 !C,U, JWK +CK NSP CTT 70.0 117.7 !1-M-T XTAL, adm jr., 7/24/91 +CK NSP HB 40.5 122.0 !C,U JWK, adm jr., 7/24/91 +CF NSP CT5 70.0 121.7 !from CN3 NN2 CN7, adm jr., 7/24/91 +CF NSP CTT 70.0 121.7 !1-M-T XTAL, adm jr., 7/24/91 +CF NSP HB 32.0 117.4 !C,U, JWK, adm jr., 7/24/91 +CE NS CB 110.0 105.6 !G,A, JWK, par_a9 9/30/91 +CE NS CT5 70.0 128.4 !from CN4 NN2 CN7, adm jr., 7/24/91 +CE NS CTT 70.0 128.4 !9-M-ADE, adm jr., 7/24/91 +CE NS HB 30.0 125.0 !G,A, JWK, par_a9 9/30/91 +CB NS CT5 70.0 126.0 !from CN5 NN2 CN7, adm jr., 7/24/91 +CB NS CTT 70.0 126.0 !9-M-ADE, adm jr., 7/24/91 +CB NS HB 30.0 129.4 !G,A, JWK, par_a9 9/30/91 +CK NAG CA 125.0 128.7 !G, JWK, adm jr., 7/24/91 +CK NAG CE 125.0 129.7 !Inosine, adm jr., 2/94 +CK NAG HB 40.5 114.3 !G, adm jr., 7/24/91 +CA NAG HB 40.5 117.0 !G par_49, adm jr., 7/24/91 +CE NAG HB 40.5 116.0 !Inosine, adm jr., 2/94 +CK NAT CK 90.0 129.2 !U,T, par_a4 JWK 9/30/91 +CK NAT HB 40.5 115.4 !T,U, JWK, adm jr., 7/24/91 +CK NC CA 70.0 119.7 !C, JWK, adm jr., 7/24/91 +CA NCA CB 90.0 112.0 !G, JWK, par_a11 9/30/91 +CA NCA CE 90.0 119.9 !A, JWK, par_a9 9/30/91 +CE NCA CB 90.0 110.3 !A, JWK, par_a9 9/30/91 +CE NB CB 110.0 103.3 !G,A, JWK, par_a9 9/30/91 +CE NBG CB 110.0 103.3 !G, DRL +CF CTT HAT 33.43 110.1 22.53 2.179 ! Alkanes, sacred +! +CT5 OS P 20.0 120.0 35.0 2.33 !DMP, ADM JR. +CTT OS P 20.0 120.0 35.0 2.33 !DMP, ADM Jr. +P OS P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 +HOP OHP P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. +! +OS P OS 45.0 102.6 !DRL/amber4.1 +OS P OCP 100.0 108.23 !DRL/amber4.1 +OCP P OCP 140.0 119.9 !DRL/amber4.1 +! +OS P OHP 48.1 108.0 !MP_1, ADM Jr. | +OCP P OHP 98.9 108.23 !MP_1, ADM Jr. |DRL untested +OHP P OHP 98.9 104.0 !MP_0, ADM Jr. | +! +OE CT5 NS 70.0 108.0 !ADM Jr. +HA5 CT5 NS 43.0 111.0 !ADM Jr. +CT5 CT5 NS 70.0 113.7 !ADM Jr. +OE CT5 NSP 70.0 108.0 !ADM Jr. +HA5 CT5 NSP 43.0 111.0 !ADM Jr. +CT5 CT5 NSP 70.0 113.7 !ADM Jr. +! +HAT CTT HAT 33.0 107.8 !quanta !MP2 108.075 +HAT CTT CTT 37.5 110.7 !quanta +HAT CTT CT5 37.5 110.7 !quanta !MP2 111.425 +CTT CT5 CT5 38.35 112.7 !DRL !MP2 102.9 +CTT CT5 HA5 37.5 110.7 !quanta +CTT CT5 OE 57.0 110.0 !quanta !MP2 107.6 +HAT CTT OS 59.0 108.25 !quanta +CTT CTT OS 80.0 109.47 !quanta +CT5 CTT OS 80.0 109.47 !quanta +HAT CTT OH 55.0 108.0 !quanta +CT5 CTT OH 45.0 110.5 !quanta +HO OH CTT 59.0 106.7 !quanta +HA5 CT5 HA5 33.0 107.8 !quanta !MP2 108.075 +HA5 CT5 CT5 37.5 110.7 !quanta !MP2 111.425 +CT5 CT5 CT5 38.35 112.7 !DRL +HA5 CT5 OE 55.5 109.47 !quanta !MP2 109.3 +CT5 CT5 OE 37.0 112.0 !DRL +CT5 OE CT5 33.0 108.0 !DRL +HA5 CT5 OS 59.0 108.25 !quanta +CT5 CT5 OS 80.0 109.47 !quanta +HA5 CT5 OH 55.0 108.0 !quanta +CT5 CT5 OH 45.0 110.5 !quanta +HO OH CT5 59.0 106.7 !quanta +! +!RNA +NSR CK NAT 67.0 114.6 !DRL +NSR CK NC 70.0 116.4 !DRL +NSR CK OK 100.0 123.5 !DRL +NSR CK OKC 100.0 121.5 !DRL +CF CF NSR 125.0 124.2 !DRL +HAR CF NSR 30.0 113.8 !DRL +HAR CE NSR 40.0 119.0 !DRL +NSR CE NB 100.0 114.3 !DRL +NSR CE NBG 100.0 114.3 !DRL +CB CB NSR 100.0 105.1 !DRL +NSR CB NCA 140.0 127.4 !DRL +CK NSR CT5 70.0 128.4 !DRL +CK NSR CF 125.0 120.6 !DRL +CK NSR CTT 70.0 117.7 !DRL +CK NSR HB 40.5 122.0 !DRL +CF NSR CT5 70.0 121.7 !DRL +CF NSR CTT 70.0 121.7 !DRL +CF NSR HB 32.0 117.4 !DRL +CE NSR CB 110.0 105.6 !DRL +CE NSR CT5 70.0 128.4 !DRL +CE NSR CTT 70.0 128.4 !DRL +CE NSR HB 30.0 125.0 !DRL +CB NSR CT5 70.0 126.0 !DRL +CB NSR CTT 70.0 126.0 !DRL +CB NSR HB 30.0 129.4 !DRL +OE CT5 NSR 70.0 108.0 !DRL +HA5 CT5 NSR 43.0 111.0 !DRL +CT5 CT5 NSR 70.0 113.7 !DRL +CK NAG CTT 40.5 114.3 !G, DRL for 1-methylguanine +CA NAG CTT 40.5 117.0 !G, DRL for 1-methylguanine +HAT CTT NAG 43.0 111.0 !G, DRL for 1-methylguanine +CF CF CT5 70.0 123.7 !PSU, DRL +CK CF CT5 70.0 118.3 !PSU, DRL +OE CT5 CF 70.0 108.0 !PSU, DRL +HA5 CT5 CF 43.0 111.0 !PSU, DRL +CT5 CT5 CF 70.0 113.7 !PSU, DRL +!TIPS3P +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY +!AMBER TIP3P water +HW OW HW 100. 104.52 ! TIP3P water +HW HW OW 0. 127.74 ! (found in crystallographic water with 3 bonds) +!ethanol and trifloroethanol +HA CT CT 37.5 110.7 !quanta +HA CT HA 33.0 107.8 !quanta +CT CT OT 45.0 110.5 !quanta +HA CT OT 55.0 108.0 !quanta +HO OT CT 59.0 106.7 !quanta +CT CF3 XF 75.0 115.0 !quanta +XF CF3 XF 110.0 112.3 !quanta +CF3 CT OT 57.0 103.0 !quanta +HA CT CF3 37.5 109.47 !quanta + +PHI ! FORCE PERIOD PHASE + X CTT CTT X 0.15 3 0.0 +! + X CT5 CT5 X 0.15 3 0.0 !cyclohexane + X CT5 OE X 0.27 3 0.0 !THF + CT5 CT5 OE CT5 0.27 3 0.0 ! + CT5 CT5 OE CT5 -0.025 4 0.0 ! + CT5 CT5 CT5 OE -0.10 2 0.0 ! +! +! X-angle between BASES and RIBOSE + X NS CT5 X 0.0 3 0.0 !chi for ADE and GUA + CB NS CT5 CT5 0.1 4 0.0 + CB NS CT5 CT5 1.5 1 0.0 + CB NS CT5 OE -0.30 4 0.0 +! + X NSP CT5 X 0.0 3 0.0 !chi for THY, CYT, URA + CK NSP CT5 CT5 1.3 1 0.0 + CK NSP CT5 OE 0.2 1 0.0 + CK NSP CT5 OE -0.65 4 0.0 +! + +X CF CT5 X 0.15 3 0.0 !chi test for PSU + +! +!Special terms for controling relative minimum energy for ribose. +! CT5 CT5 CT5 NS -0.4 1 0.0 !-0.3 1 0.0 favors C2'-endo +! CT5 CT5 CT5 NSP -0.4 1 0.0 !-0.5 1 0.0 favors C3'-endo +! +!Special terms for controling energy barrier between minimum +! CT5 CT5 CT5 NS -0.5 4 0.0 !-0.3 4 0.0 !The second term if used +! CT5 CT5 CT5 NSP -0.5 4 0.0 !-0.3 4 0.0 !lowers barrier between +! OH CT5 CT5 CTT 3.80 1 0.0 ! 3.46 1 0.0 !C2'-endo and C3'-endo. +! OS CT5 CT5 CTT 3.80 1 0.0 ! 3.46 1 0.0 ! +! +!!Special Terms must be adjusted below to avoid errors!! +!!when using versions of CHARMM newer than version 23.x.!! +! + CT5 OE CT5 NS -0.5 3 0.0 !v0 + CT5 OE CT5 NSP -0.5 3 0.0 +! + CT5 CT5 CT5 NS -0.3 6 0.0 !v1 + CT5 CT5 CT5 NS -0.5 4 0.0 + CT5 CT5 CT5 NS -0.4 1 0.0 + CT5 CT5 CT5 NSP -0.3 6 0.0 + CT5 CT5 CT5 NSP -0.5 4 0.0 + CT5 CT5 CT5 NSP -0.4 1 0.0 +! + CT5 CT5 CT5 OH 0.1 3 0.0 !v2 + CT5 CT5 CT5 OS 0.1 3 0.0 +! + CT5 CT5 CT5 CTT 0.20 1 0.0 !v3' + CT5 CT5 CT5 CTT 0.18 3 0.0 + OE CT5 CT5 OH 0.10 1 0.0 !v3 + OE CT5 CT5 OH 0.39 2 0.0 + OE CT5 CT5 OH 0.24 3 0.0 + OE CT5 CT5 OS 0.10 1 0.0 + OE CT5 CT5 OS 0.39 2 0.0 + OE CT5 CT5 OS 0.24 3 0.0 + OH CT5 CT5 CTT -0.80 4 0.0 !v3 delta + OH CT5 CT5 CTT -0.50 3 0.0 + OH CT5 CT5 CTT 3.80 1 0.0 + OS CT5 CT5 CTT -0.80 4 0.0 + OS CT5 CT5 CTT -0.50 3 0.0 + OS CT5 CT5 CTT 3.80 1 0.0 +! + CT5 OE CT5 CTT 0.95 1 0.0 !v4 + CT5 OE CT5 CTT 0.16 3 0.0 +! + X CTT OS X -0.10 3 0.0 !beta dimethylphosphate + CT5 CTT OS P 0.10 3 0.0 ! C4'-C5'-O5'-P + X CT5 OS X -0.10 3 0.0 !epsilon C4'-C3'-O3'-P + CT5 CT5 OS P 0.10 3 0.0 ! +! + X CT5 CTT X 0.28 3 0.0 !gamma + OE CT5 CTT OH 1.00 2 0.0 + OE CT5 CTT OH 0.15 3 0.0 + OE CT5 CTT OS 1.00 2 0.0 + OE CT5 CTT OS 0.15 3 0.0 +! + X CTT OH X 0.25 3 0.0 !5'-hydroxyl of ribose + HAT CTT OH HO 0.05 3 0.0 + CT5 CTT OH HO 0.35 1 0.0 + CT5 CTT OH HO 0.35 3 0.0 +! + X CT5 OH X 0.25 3 0.0 !3'-hydroxyl of ribose + HA5 CT5 OH HO 0.05 3 0.0 + CT5 CT5 OH HO 0.35 1 0.0 + CT5 CT5 OH HO 0.35 3 0.0 +! +! RNA May Need More Work +! + X NSR CT5 X 0.0 3 0.0 + CK NSR CT5 OE -0.4 4 0.0 + CB NSR CT5 OE 0.2 2 0.0 +! + CT5 CT5 CT5 NSR 0.1 6 0.0 + CT5 CT5 CT5 NSR 0.7 2 0.0 +! + OH CT5 CT5 NSR 0.1 6 0.0 + OH CT5 CT5 NSR 1.3 1 0.0 +! + + CT5 CT5 CT5 CF 0.1 6 0.0 !PSU, DRL + CT5 CT5 CT5 CF 0.7 2 0.0 !PSU, DRL +! + OH CT5 CT5 CF 0.1 6 0.0 !PSU, DRL + OH CT5 CT5 CF 1.3 1 0.0 !PSU, DRL +! +! PHOSPHATE + X OS P X 0.25 3 0.0 !DRL/MP2/6-31+G* + CT5 OS P OS 0.23 3 0.0 !DRL/MP2/6-31+G* + CT5 OS P OS 1.10 2 0.0 !DRL/MP2/6-31+G* + CT5 OS P OS -0.10 1 0.0 !DRL/MP2/6-31+G* + CTT OS P OS 0.23 3 0.0 !DRL/MP2/6-31+G* + CTT OS P OS 1.10 2 0.0 !DRL/MP2/6-31+G* + CTT OS P OS -0.10 1 0.0 !DRL/MP2/6-31+G* +! + X OH P X 0.25 3 0.0 ! + CT5 OS P OHP 0.23 3 0.0 ! + CT5 OS P OHP 1.10 2 0.0 ! + CT5 OS P OHP -0.10 1 0.0 ! + CTT OS P OHP 0.23 3 0.0 ! + CTT OS P OHP 1.10 2 0.0 ! + CTT OS P OHP -0.10 1 0.0 ! +! +! BASES +! Uracil +NSP CF CF CK 4.0 2 180.0 ! par_31 +NSR CF CF CK 4.0 2 180.0 !DRL +CF CF CK NAT 3.0 2 180.0 ! par_a1 JWK 9/30/91 +CF CK NSP CK 3.5 2 180.0 ! PAR_32 +CF CK NSR CK 3.5 2 180.0 !DRL +CK NAT CK NSP 3.5 2 180.0 ! PAR_32 +CK NAT CK NSR 3.5 2 180.0 !DRL +CK NSP CF CF 3.5 2 180.0 ! PAR_32 +CK NSR CF CF 3.5 2 180.0 !DRL +NAT CK NSP CF 3.0 2 180.0 ! par_a1 JWK 9/30/91 +NAT CK NSR CF 3.0 2 180.0 !DRL +HAR CF CF HAR 3.0 2 180.0 ! par_34 +HAR CF CK OK 4.0 2 180.0 ! par_a1 JWK 9/30/91 +OK CK NSP HB 3.0 2 180.0 ! par_a1 JWK 9/30/91 +OK CK NSR HB 3.0 2 180.0 !DRL +!!!OK CK NAG HB 3.0 2 180.0 ! PAR_36, adm jr., 7/24/91 +OKG CK NAG HB 3.0 2 180.0 !G, DRL +OK CK NAT HB 2.5 2 180.0 ! par_a2 JWK 9/30/91 +HB NSP CF HAR 1.8 2 180.0 ! PAR_36 +HB NSR CF HAR 1.8 2 180.0 !DRL +NSP CK NAT HB 1.8 2 180.0 ! par_a2 JWK 9/30/91 +NSR CK NAT HB 1.8 2 180.0 !DRL +CF CK NAT HB 1.8 2 180.0 ! par_a2 JWK 9/30/91 +!Thymine +NSP CK CF CTT 3.00 3 0.0 ! par_51 +NSR CK CF CTT 3.00 3 0.0 !DRL +NSP CF CF CTT 3.00 3 0.0 ! par_51 +NSR CF CF CTT 3.00 3 0.0 !DRL +CK CF CTT HAT 0.00 3 0.0 ! par_51, adm jr. 8/1/91 +CF CF CTT HAT 0.00 3 0.0 ! par_51, adm jr. 8/1/91 +! Cytosine +NSP CF CF CA 4.0 2 180.0 ! par_7 +NSR CF CF CA 4.0 2 180.0 !DRL +CF CF CA NC 4.0 2 180.0 ! par_39 +CF CA NC CK 4.5 2 180.0 ! par_13 +CA NC CK NSP 4.5 2 180.0 ! par_13 +CA NC CK NSR 4.5 2 180.0 !DRL +NC CK NSP CF 3.5 2 180.0 ! par_39 +NC CK NSR CF 3.5 2 180.0 !DRL +NC CA NAN HNA 2.0 2 180.0 ! par_40 +CF CA NAN HNA 2.0 2 180.0 ! par_40 +NAN CA CF HAR 2.0 2 180.0 ! par_39 +OKC CK NSP HB 3.0 2 180.0 ! par_a1 adm jr., 10/2/91 +OKC CK NSR HB 3.0 2 180.0 !DRL +X CA NC X 1.0 2 180.0 ! par_41 +! 5-methylcytosine +! Adenine +NCA CA CB CB 6.0 2 180.0 ! par_24 par_a7 9/30/91 +CB CA NCA CE 6.0 2 180.0 ! par_24 par_a7 9/30/91 +NB CE NS CB 10.0 2 180.0 ! par_47 par_a7 9/30/91 +NBG CE NS CB 10.0 2 180.0 !DRL +NB CE NSR CB 10.0 2 180.0 !DRL +NBG CE NSR CB 10.0 2 180.0 !DRL +NCA CE NCA CB 6.0 2 180.0 ! par_24 par_a7 9/30/91 +NCA CE NCA CA 8.0 2 180.0 ! par_43 par_a7 9/30/91 +NS CE NB CB 8.0 2 180.0 ! par_25 par_a7 9/30/91 +NS CE NBG CB 8.0 2 180.0 !DRL +NSR CE NB CB 8.0 2 180.0 !DRL +NSR CE NBG CB 8.0 2 180.0 !DRL +CA CB CB NCA 6.0 2 180.0 ! par_24 par_a7 9/30/91 +NB CB CB NS 8.0 2 180.0 ! par_25 par_a7 9/30/91 +NBG CB CB NS 8.0 2 180.0 !DRL +NB CB CB NSR 8.0 2 180.0 !DRL +NBG CB CB NSR 8.0 2 180.0 !DRL +CB CB NS CE 10.0 2 180.0 ! par_47 par_a7 9/30/91 +CB CB NSR CE 10.0 2 180.0 !DRL +CB CB NCA CE 6.0 2 180.0 ! par_24 par_a7 9/30/91 +CB CB NB CE 8.0 2 180.0 ! par_25 par_a7 9/30/91 +CB CB NBG CE 8.0 2 180.0 !DRL +CB CA NAN HNA 2.5 2 180.0 ! par_26 par_a10 9/30/91 +HB NS CE HAR 1.5 2 180.0 ! par_44 par_a7 9/30/91 +HB NSR CE HAR 1.5 2 180.0 !DRL +NCA CA NAN HNA 2.5 2 180.0 ! par_40 par_a10 9/30/91 +! Butterfly motion +NCA CB CB NB 20.0 2 180.0 !A, par_24 par_a7 9/30/91 +NCA CB CB NBG 20.0 2 180.0 !G, DRL +CA CB CB NS 20.0 2 180.0 !A, par_24 +CA CB CB NSR 20.0 2 180.0 !DRL +! Guanine +NAG CK CB CB 6.0 2 180.0 ! par_49 +CB CK NAG CA 6.0 2 180.0 ! par_49 +CK NAG CA NCA 6.0 2 180.0 ! par_49 +NAG CA NCA CB 6.0 2 180.0 ! par_49 +CA NCA CB CB 6.0 2 180.0 ! par_49 +CK CB CB NCA 6.0 2 180.0 ! par_49 +NAG CA NAN HNA 2.0 2 180.0 ! par_49 +! Butterfly motion +CK CB CB NS 20.0 2 180.0 ! par_49 +CK CB CB NSR 20.0 2 180.0 !DRL +! inosine, adm jr., 2/94 +HAR CE NAG HB 1.5 2 180.0 +HAR CE NAG CK 1.5 2 180.0 +! Wild cards for inosine +! Wild cards for uracil, thymine and cytosine +X CK NC X 1.0 2 180.0 ! par_39 +X CK NSP X 0.9 2 180.0 ! par_36 +X CK NSR X 0.9 2 180.0 !DRL +X CK NAG X 0.9 2 180.0 ! par_36 +X CK NAT X 0.9 2 180.0 ! par_36 +X CF NSP X 1.0 2 180.0 ! par_36 +X CF NSR X 1.0 2 180.0 !DRL +X CF CF X 1.0 2 180.0 ! par_36 +X CK CF X 1.0 2 180.0 ! par_36 +X CA CF X 0.8 2 180.0 ! par_39 +! Wild cards for adenine and guanine +X CK CB X 1.0 2 180.0 ! par_49 +X CA NAG X 1.0 2 180.0 ! par_49 +X CA CB X 1.0 2 180.0 ! par_41 +X CE NS X 1.5 2 180.0 ! par_44 +X CE NSR X 1.5 2 180.0 !DRL +X CE NCA X 3.5 2 180.0 ! par_47 par_a7 9/30/91 +X CE NB X 1.0 2 180.0 ! par_41 +X CE NBG X 1.0 2 180.0 !DRL +X CB CB X 0.0 2 180.0 ! par_20 +X CB NS X 1.5 2 180.0 ! par_44 +X CB NSR X 1.5 2 180.0 !DRL +X CB NCA X 1.0 2 180.0 ! par_41 par_a7 9/30/91 +X CB NB X 1.0 2 180.0 ! par_41 +X CB NBG X 1.0 2 180.0 !DRL +X CA NCA X 1.0 2 180.0 ! par_41 par_a7 9/30/91 +! MISC. +CK NSP CTT HAT 0.19 3 0.0 ! 1-M-THY +CK NSR CTT HAT 0.19 3 0.0 !DRL +CF NSP CTT HAT 0.00 3 0.0 ! 1-M-THY +CF NSR CTT HAT 0.00 3 0.0 !DRL +CE NS CTT HAT 0.00 3 0.0 ! 9-M-ADE +CE NSR CTT HAT 0.00 3 0.0 !DRL +CB NS CTT HAT 0.19 3 0.0 ! 9-M-ADE +CB NSR CTT HAT 0.19 3 0.0 !DRL +CA NAG CTT HAT 0.19 3 0.0 !DRL for 1-methylguanine +CK NAG CTT HAT 0.19 3 0.0 !DRL for 1-methylguanine +!ethanol and trifloroethanol + CT CT OT HO 0.35 1 0.0 !quanta + CT CT OT HO 0.35 3 0.0 !quanta + HA CT OT HO 0.05 3 0.0 !quanta + X CT CT X 0.15 3 0.0 !quanta + X CT OT X 0.25 3 0.0 !quanta + X CF3 CT X 0.12 3 0.0 !quanta + +IMPHI ! FORCE PERIOD PHASE +HB CE CB NS 7.0 0 0.0 !A, JWK par_42 +HB CE CB NSR 7.0 0 0.0 !DRL +HB CK CK NAT 4.0 0 0.0 !U, JWK par_35 +HB X X NS 0.3 0 0.0 !C,U, JWK par_15 +HB X X NSP 0.3 0 0.0 !C,U, JWK par_15 +HB X X NSR 0.3 0 0.0 !DRL +HB X X NAG 0.3 0 0.0 !G, JWK par_15 +HB CE CK NAG 0.8 0 0.0 !Inosine, adm jr., 2/94 +HNA X X NAN 2.0 0 0.0 !C, JWK par_40 +HAR CK CF CF 18.0 0 0.0 ! JWK par_37 +HAR X X CF 15.0 0 0.0 !C, JWK par_37 +CK X X OK 70.0 0 0.0 !U, JWK par_32 +CK X X OKC 70.0 0 0.0 !C, par_32, adm jr., 10/2/91 +CK X X OKG 70.0 0 0.0 !G, DRL +CK X X S 70.0 0 0.0 !TG, DRL, B3LYP/6-31+G** +CA X X NAN 90.0 0 0.0 !C, JWK par_15 +HAR X X CE 20.0 0 0.0 !A, JWK par_42 +CTT X X CF 20.0 0 0.0 !T par_51 +CTT X X NAG 20.0 0 0.0 !G, DRL for 1-methylguanine +NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VSWITCH - + CUTNB 13.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 +! Emin Rmin/2 +! (kcal/mol) (A) +HNA 0.0 -0.0460 0.2245 +HB 0.0 -0.0460 0.2245 +HOP 0.0 -0.0460 0.2245 +HO 0.0 -0.0460 0.2245 +HAR 0.0 -0.0420 1.320 +HA5 0.1 -0.0420 1.330 +HAT 0.1 -0.0420 1.330 +! +NAN 0.0 -0.20 1.85 +NS 0.0 -0.20 1.85 +NSP 0.0 -0.20 1.85 +NSR 0.0 -0.20 1.85 +NAG 0.0 -0.20 1.85 +NAT 0.0 -0.20 1.85 +NC 0.0 -0.20 1.85 +NCA 0.0 -0.20 1.85 +NB 0.0 -0.20 1.85 +NBG 0.0 -0.20 1.85 !DRL +! +OK 0.0 -0.1200 1.70 +OKC 0.0 -0.1200 1.70 +OKG 0.0 -0.1200 1.70 !DRL +OS 0.84 -0.1591 1.600 0.84 -0.20 1.36 +OCP 0.0 -0.2100 1.6612 !amber4.1 +OHP 0.0 -0.1521 1.77 +OH 0.84 -0.1521 1.550 0.84 -0.20 1.48 +OE 0.84 -0.1591 1.600 0.84 -0.20 1.36 +! +!TIP3P water model, J. Chem. Phys., 79, 926, 1983. +! As in OPLS and AMBER +OW 0.0 -0.1521 1.76825 !OPLS TIP3P water model +HW 0.0 -0.0000 0.0000 !OPLS TIP3P water model +! +!OW 0.0 -0.1520 1.7683 !AMBER TIP3P water model +!HW 0.0 -0.0000 0.0000 !AMBER TIP3P water model +! +OT 0.0 -0.1521 1.7682 !CHARMM TIP3P +HT 0.0 -0.0460 0.2245 !CHARMM TIP3P +! +CK 0.0 -0.14 1.800 +CA 0.0 -0.14 1.800 +CF 0.0 -0.18 1.800 +CE 0.0 -0.12 1.800 +CB 0.0 -0.12 1.800 +CT5 1.65 -0.0903 1.800 1.65 -0.1 1.75 !quanta +CTT 1.65 -0.0903 1.800 1.65 -0.1 1.75 !quanta +! +S 0.00 -0.2500 2.0000 0.00 -0.1250 2.0000 !W. Cornell CH3SH and CH3SCH3 FEP's +P 0.0 -0.2000 2.100 !amber4.1 +! +!ethanol and trifloroethanol +CT 1.65 -0.0903 1.800 1.65 -0.1 1.75 !quanta +CF3 1.65 -0.0903 1.800 1.65 -0.1 1.75 !quanta +HA 0.1 -0.0420 1.330 !quanta +XF 0.32 -0.1000 1.700 0.32 -0.15 1.55 !quanta +! +!Ions +! +K 0.00 -0.000328 2.6580 !K+ Aqvist JPC 1990,94,8021. (adapted) +MG 0.0 -0.001 1.65 !Blaise Prodhom + +!SOD 0.0 -1.607 0.9485 !Na+ JACS 106, 903 (1984) oplsaa +!XCl 0.0 -0.11779 2.20862 !Cl- JACS 106, 903 (1984) oplsaa +! +!SOD 0.0 -0.002772 1.665222 !Na+ Aqvist's cation/oplsaa +!SOD 0.0 -0.00277 1.8680 !Na+ Aqvist JPC 1990,94,8021. (AMBER4.1) +!SOD 0.0 -0.1000 1.532 !from Benoit Roux, CHARMM22 +!XCL 0.00 -0.1 2.47 0.00 -0.05 2.47 !Smith & Dang, JCP 1994,100:5,3757, AMBER +! +!SOD 0.0 -0.0469 1.36375 !Na+ D. Beglovd and B. Roux, dA=-100.8 kcal/mol +!XCL 0.0 -0.150 2.27 !Cl- D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol +! +! the SOD and XCL prameters below are being tested to do away with the NBFIX terms required when using Benoit Roux Na+ (SOD). + SOD 0.0 -0.3100 1.163 !Na+ DRL !Na-OH2 -25.6814@2.2365(RHF/6-31G**++) or -25.6807@2.23678(RHF/CSDZ**++) + !free energy of solvation for Na+ = -101.41859 + 0.32836 = -101.09023 kcal/mol + XCL 0.0 -0.090 2.50 !Cl- DRL !Cl-OH2 -12.3925@2.3828((RHF/6-31G**++) or -12.3985@2.3794(RHF/CSDZ**++) + !free energy of solvation for CL- = -72.78375 + 3.16320 = -69.62055 kcal/mol +! +!Noble Gases +! +HE 0.0 -0.000414175 1.575 !DRL -0.0.000414175kcal/mol at 3.15A He<->He, HF/6-31+G** +NE 0.0 -0.0441795 1.64009 !DRL -0.0441795kcal/mol at 3.280A Ne<->Ne, UHF/6-31+G** +AR 0.0 -0.0240273 2.285639 !DRL +! +DUM 0.0 -0.000 1.00 !dummy atom + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +! +! Only use these with Benoit Roux Na+ (SOD) +!SOD OT -0.5831 2.6880 ! from Benoit Roux +!SOD OKG -2.0000 2.4500 ! DRL Use with Benoit Roux Na+ +!SOD NBG -2.0 2.5500 ! DRL Use with Benoit Roux Na+ +!ethanol and trifloroethanol +CT HO -0.15 3.00 !quanta +HA HO -0.05 3.10 !quanta +! +! Note: HAEX AND AAEX SHOULD BE SET TO 4 AND 2 FOR HBONDS TO +! BE ANALYZED. +! +HBOND AEXP 4 REXP 6 HAEX 0 AAEX 0 NOACCEPTORS HBNOEXCLUSIONS ALL - + CUTHB 0.5 CTOFHB 5.0 CTONHB 4.0 CUTHA 90.0 CTOFHA 90.0 CTONHA 90.0 +! +H* N* -0.0 2.0 +H* O* -0.0 2.0 +N* N* -0.0 3.0 +N* O* -0.0 2.9 +O* N* -0.0 2.85 +O* O* -0.0 2.75 +END diff --git a/charmm/toppar/non_charmm/par_opls_aa.inp b/charmm/toppar/non_charmm/par_opls_aa.inp new file mode 100644 index 00000000..f3ba5cc0 --- /dev/null +++ b/charmm/toppar/non_charmm/par_opls_aa.inp @@ -0,0 +1,2167 @@ +* Parameter File for OPLS for proteins * +* + +!README for CHARMM topology/parameter files for OPLS-AA (opls.rtf, opls.prm) +!** reference for OPLS-AA for proteins: +!** Jorgensen, W.L. et al., J. Am. Chem. Soc. 118:11225-11236 (1996) +!and see additional reference below +! +!Proper usage of these files requires CHARMM software version c28b1 or greater. +!If you are presently using c28b1, please check that you have the latest release, +!as not all of the pertinant code was included in the initial release, but was +!included in a later bugfix. Compilation of CHARMM requires that the OPLS +!keyword be included in pref.dat at compile time. The relevant code has added +!the ability to combine Lennard-Jones radii with a geometric average, and use +!V2-Fourier terms for improper dihedrals. The CHARMM program compiled with the +!OPLS option in pref.dat can still use all other previously released topology and +!parameter files (CHARMM22, CHARMM19, etc.). +! +!Atom and residue names in the OPLS-AA topology file agree with that in CHARMM22. +!Consequently, any CHARMM script that reads CHARMM22 topology and parameter files +!can be converted to using OPLS-AA by adjusting the appropriate file OPEN +!statements. The atom types have the OPLS atom type embedded within them for +!easy cross-reference. For example, type H140 in opls.rtf and opls.prm is +!type 140 the OPLS-AA parameter files available from Prof. Jorgensen. +! +!The topology and parameter files here include only the protein portion of the +!OPLS-AA force field. User-defined topology and parameter files are required for +!other functionalities. +! +!While the OPLS-AA topology and parameter files are compatible with all +!functionality within CHARMM that is also compatible with CHARMM22, minimizations +!and simulations with a distance-dependent dielectric (RDIE) is not recommended +!as collapse of atoms with hydrogens on heteroatoms is possible, causing +!unreasonable structures and energies. Also, there is no current +!optimzied parameter set for the linearized form of the Generalized Born equation +!as currently implemented in CHARMM. +! +!Any questions, email priced@scripps.edu +! +!**** These files were created in the laboratory of: +!**** Prof. C.L. Brooks III +!**** Dept. of Mol. Biol. +!**** The Scripps Research Institute +! +!**** OPLS-AA is developed in the laboratory of: +!**** Prof. W.L. Jorgensen +!**** Dept. of Chemistry +!**** Yale University +!Additional References +! +!OPLS All-Atom Model for Amines: Resolution of the Amine Hydration +!Problem. R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc., 121, +!4827-4836 (1999). +! +!Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro +!Compounds with the OPLS-AA Force Field. M. L. P. Price, D. Ostrovsky, +!and W. L. Jorgensen, J. Comput. Chem., 22, 1340-1352 (2001). +! +!Evaluation and Reparameterization of the OPLS-AA Force Field for +!Proteins via Comparison with Accurate Quantum Chemical Calculations on +!Peptides. G. Kaminski, R. A. Friesner, J. Tirado-Rives and W. L. +!Jorgensen, J. Phys. Chem. B, 105, 6474-6487 (2001). +! +!Perfluoroalkanes: Conformational Analysis and Liquid-State Properties +!from Ab Initio and Monte Carlo Calculations. E. K. Watkins and +!W. L. Jorgensen, J. Phys. Chem. A, 105, 4118-4125 (2001). +! +!Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic +!Charges.Blagovif, M. U.; Jorgensen, W. L., J. Comput. Chem. 2004, 25, +!0000-0000. Submitted. +! +!A five-site model for liquid water and the reproduction of the density +!anomaly by rigid, non-polarizable models. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 112, 8910-8922 (2000). +! +!Diffusion constant of the TIP5P model of liquid water. M. W. Mahoney +!and W. L. Jorgensen, J. Chem. Phys., 114, 363-366 (2001). +! +!Rapid Estimation of Electronic Degrees of Freedom in Monte Carlo +!Calculations for Polarizable Models of Liquid Water. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 114, 9337-9349 (2001). +! +!Quantum, intramolecular flexibility, and polarizability effects on the +!reproduction of the density anomaly of liquid water by simple +!potential functions. M. W. Mahoney and W. L. Jorgensen, +!J. Chem. Phys., 115, 10758-10768 (2001). +! + +BOND +OT HT 450.0 0.9572 +HT HT 0.0 1.5139 +S203 S203 166.0 2.038 +!! below are automatically generated by pepz2rtf +C135 C136 268.00 1.529 +C135 C137 268.00 1.529 +C135 C158 268.00 1.529 +C135 C224 268.00 1.529 +C135 C235 317.00 1.522 +C135 C283 268.00 1.529 +C135 C293 268.00 1.529 +C135 H140 340.00 1.090 +C136 C136 268.00 1.529 +C136 C137 268.00 1.529 +C136 C210 268.00 1.529 +C136 C224 268.00 1.529 +C136 C235 317.00 1.522 +C136 C245 268.00 1.529 +C136 C246 268.00 1.529 +C136 C267 317.00 1.522 +C136 C274 268.00 1.529 +C136 C283 268.00 1.529 +C136 C285 268.00 1.529 +C136 C292 268.00 1.529 +C136 C293 268.00 1.529 +C136 C295 268.00 1.529 +C136 C296 268.00 1.529 +C136 C308 268.00 1.529 +C136 C500 317.00 1.495 +C136 H140 340.00 1.090 +C137 C224 268.00 1.529 +C137 C283 268.00 1.529 +C137 C293 268.00 1.529 +C137 H140 340.00 1.090 +C145 C145 469.00 1.400 +C145 C149 317.00 1.510 +C145 C166 469.00 1.400 +C145 C501 469.00 1.404 +C145 C502 469.00 1.400 +C145 H146 367.00 1.080 +C149 C224 268.00 1.529 +C149 C283 268.00 1.529 +C149 C293 268.00 1.529 +C149 H140 340.00 1.090 +C157 C224 268.00 1.529 +C157 C283 268.00 1.529 +C157 C293 268.00 1.529 +C157 H140 340.00 1.090 +C157 O154 320.00 1.410 +C158 C224 268.00 1.529 +C158 C283 268.00 1.529 +C158 C293 268.00 1.529 +C158 H140 340.00 1.090 +C158 O154 320.00 1.410 +C166 O167 450.00 1.364 +C206 C224 268.00 1.529 +C206 C283 268.00 1.529 +C206 C293 268.00 1.529 +C206 H140 340.00 1.090 +C206 S200 222.00 1.810 +C209 H140 340.00 1.090 +C209 S202 222.00 1.810 +C210 H140 340.00 1.090 +C210 S202 222.00 1.810 +C214 C224 268.00 1.529 +C214 C283 268.00 1.529 +C214 C293 268.00 1.529 +C214 H140 340.00 1.090 +C214 S203 222.00 1.810 +C223 C235 317.00 1.522 +C223 H140 340.00 1.090 +C223 N238 337.00 1.449 +C224 C235 317.00 1.522 +C224 C274 268.00 1.529 +C224 C505 268.00 1.529 +C224 H140 340.00 1.090 +C224 N238 337.00 1.449 +C235 C246 317.00 1.522 +C235 C292 317.00 1.522 +C235 C293 317.00 1.522 +C235 C295 317.00 1.522 +C235 N237 490.00 1.335 +C235 N238 490.00 1.335 +C235 N239 490.00 1.335 +C235 O236 570.00 1.229 +C242 H140 340.00 1.090 +C242 N238 337.00 1.449 +C245 H140 340.00 1.090 +C245 N239 337.00 1.449 +C246 H140 340.00 1.090 +C246 N239 337.00 1.449 +C267 O268 450.00 1.364 +C267 O269 570.00 1.229 +C271 C274 317.00 1.522 +C271 C283 317.00 1.522 +C271 C284 317.00 1.522 +C271 C285 317.00 1.522 +C271 O272 656.00 1.250 +C274 C283 268.00 1.529 +C274 C293 268.00 1.529 +C274 H140 340.00 1.090 +C283 C505 268.00 1.529 +C283 H140 340.00 1.090 +C283 N238 337.00 1.449 +C284 H140 340.00 1.090 +C284 N238 337.00 1.449 +C285 H140 340.00 1.090 +C285 N239 337.00 1.449 +C292 H140 340.00 1.090 +C292 N287 367.00 1.471 +C293 C505 268.00 1.529 +C293 H140 340.00 1.090 +C293 N287 367.00 1.471 +C295 H140 340.00 1.090 +C295 N309 367.00 1.471 +C296 H140 340.00 1.090 +C296 N309 367.00 1.471 +C302 N300 481.00 1.340 +C302 N303 481.00 1.340 +C307 C308 268.00 1.529 +C307 H140 340.00 1.090 +C307 N303 337.00 1.463 +C308 H140 340.00 1.090 +C500 C501 388.00 1.459 +C500 C514 546.00 1.352 +C501 C502 447.00 1.419 +C502 N503 428.00 1.380 +C505 C507 317.00 1.504 +C505 C508 317.00 1.504 +C505 C510 317.00 1.504 +C505 H140 340.00 1.090 +C506 H146 367.00 1.080 +C506 N503 477.00 1.343 +C506 N511 488.00 1.335 +C507 C508 520.00 1.370 +C507 H146 367.00 1.080 +C507 N511 410.00 1.394 +C508 H146 367.00 1.080 +C508 N503 427.00 1.381 +C509 H146 367.00 1.080 +C509 N512 477.00 1.343 +C510 C510 520.00 1.370 +C510 H146 367.00 1.080 +C510 N512 427.00 1.381 +C514 H146 367.00 1.080 +C514 N503 427.00 1.381 +H155 O154 553.00 0.945 +H168 O167 553.00 0.945 +H204 S200 274.00 1.336 +H240 N237 434.00 1.010 +H241 N238 434.00 1.010 +H270 O268 553.00 0.945 +H290 N287 434.00 1.010 +H301 N300 434.00 1.010 +H304 N303 434.00 1.010 +H310 N309 434.00 1.010 +H504 N503 434.00 1.010 +H513 N512 434.00 1.010 +ANGLE +HT OT HT 55.0 104.52 +H140 C135 H140 33.0 107.8 +H140 C136 H140 33.0 107.8 +H140 C149 H140 33.0 107.8 +H140 C157 H140 33.0 107.8 +H140 C206 H140 33.0 107.8 +H140 C209 H140 33.0 107.8 +H140 C210 H140 33.0 107.8 +H140 C214 H140 33.0 107.8 +H140 C223 H140 33.0 107.8 +H140 C242 H140 33.0 107.8 +H140 C245 H140 33.0 107.8 +H140 C274 H140 33.0 107.8 +H140 C284 H140 33.0 107.8 +H140 C292 H140 33.0 107.8 +H140 C296 H140 33.0 107.8 +H140 C307 H140 33.0 107.8 +H140 C308 H140 33.0 107.8 +H140 C505 H140 33.0 107.8 +H290 N287 H290 35.0 109.5 +H310 N309 H310 35.0 109.5 +!! below are automatically generated with pepz2rtf +C135 C136 C137 58.35 112.70 +C135 C136 H140 37.50 110.70 +C135 C137 C135 58.35 112.70 +C135 C137 C136 58.35 112.70 +C135 C137 C224 58.35 112.70 +C135 C137 C283 58.35 112.70 +C135 C137 C293 58.35 112.70 +C135 C137 H140 37.50 110.70 +C135 C158 C224 58.35 112.70 +C135 C158 C283 58.35 112.70 +C135 C158 C293 58.35 112.70 +C135 C158 H140 37.50 110.70 +C135 C158 O154 50.00 109.50 +C135 C224 C235 63.00 111.10 +C135 C224 H140 37.50 110.70 +C135 C224 N238 80.00 109.70 +C135 C235 N238 70.00 116.60 +C135 C235 N239 70.00 116.60 +C135 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/dev/null +++ b/charmm/toppar/non_charmm/par_opls_aam.inp @@ -0,0 +1,2369 @@ +* Parameter File for OPLS-AA/M for proteins * +* + +!README for CHARMM topology/parameter files for OPLS-AA (opls.rtf, opls.prm) +!** reference for OPLS-AA for proteins: +!** Jorgensen, W.L. et al., J. Am. Chem. Soc. 118:11225-11236 (1996) +!** reference for OPLS-AA/M: +!** Robertson, M.J. et al., J. Chem. Theory Comput., (2015) +!and see additional reference below +! +!PLEASE ENSURE USE OF PROPER LJ COMBINING RULES AND 1-4 SCALING TO ENSURE +!PROPER IMPLEMENTATION OF THE OPLS-AA/M FORCE FIELD +! +!Proper usage of these files requires CHARMM software version c28b1 or greater. +!If you are presently using c28b1, please check that you have the latest release, +!as not all of the pertinant code was included in the initial release, but was +!included in a later bugfix. Compilation of CHARMM requires that the OPLS +!keyword be included in pref.dat at compile time. The relevant code has added +!the ability to combine Lennard-Jones radii with a geometric average, and use +!V2-Fourier terms for improper dihedrals. The CHARMM program compiled with the +!OPLS option in pref.dat can still use all other previously released topology and +!parameter files (CHARMM22, CHARMM19, etc.). +! +!Atom and residue names in the OPLS-AA topology file agree with that in CHARMM22. +!Consequently, any CHARMM script that reads CHARMM22 topology and parameter files +!can be converted to using OPLS-AA by adjusting the appropriate file OPEN +!statements. The atom types have the OPLS atom type embedded within them for +!easy cross-reference. For example, type H140 in opls.rtf and opls.prm is +!type 140 the OPLS-AA parameter files available from Prof. Jorgensen. +! +!The topology and parameter files here include only the protein portion of the +!OPLS-AA force field. User-defined topology and parameter files are required for +!other functionalities. +! +!While the OPLS-AA topology and parameter files are compatible with all +!functionality within CHARMM that is also compatible with CHARMM22, minimizations +!and simulations with a distance-dependent dielectric (RDIE) is not recommended +!as collapse of atoms with hydrogens on heteroatoms is possible, causing +!unreasonable structures and energies. Also, there is no current +!optimzied parameter set for the linearized form of the Generalized Born equation +!as currently implemented in CHARMM. +! +!Any questions, email michael.robertson@yale.edu +! +!**** These files were created in the laboratory of: +!**** Prof. C.L. Brooks III +!**** Dept. of Mol. Biol. +!**** The Scripps Research Institute +! +!**** OPLS-AA is developed in the laboratory of: +!**** Prof. W.L. Jorgensen +!**** Dept. of Chemistry +!**** Yale University +!**** The original file was modified to OPLS-AA/M by +!**** M.J.R. in the lab of Prof. W.L. Jorgensen 2014-2015 +!**** To support standard amino acids and Cter/Nter patches +!**** Please carefully check over all submission scripts and +!**** ensure your choices of parameters are appropriate for any +!**** non-standard systems +! +!Additional References +! +!OPLS All-Atom Model for Amines: Resolution of the Amine Hydration +!Problem. R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc., 121, +!4827-4836 (1999). +! +!Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro +!Compounds with the OPLS-AA Force Field. M. L. P. Price, D. Ostrovsky, +!and W. L. Jorgensen, J. Comput. Chem., 22, 1340-1352 (2001). +! +!Evaluation and Reparameterization of the OPLS-AA Force Field for +!Proteins via Comparison with Accurate Quantum Chemical Calculations on +!Peptides. G. Kaminski, R. A. Friesner, J. Tirado-Rives and W. L. +!Jorgensen, J. Phys. Chem. B, 105, 6474-6487 (2001). +! +!Perfluoroalkanes: Conformational Analysis and Liquid-State Properties +!from Ab Initio and Monte Carlo Calculations. E. K. Watkins and +!W. L. Jorgensen, J. Phys. Chem. A, 105, 4118-4125 (2001). +! +!Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic +!Charges.Blagovif, M. U.; Jorgensen, W. L., J. Comput. Chem. 2004, 25, +!0000-0000. Submitted. +! +!A five-site model for liquid water and the reproduction of the density +!anomaly by rigid, non-polarizable models. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 112, 8910-8922 (2000). +! +!Diffusion constant of the TIP5P model of liquid water. M. W. Mahoney +!and W. L. Jorgensen, J. Chem. Phys., 114, 363-366 (2001). +! +!Rapid Estimation of Electronic Degrees of Freedom in Monte Carlo +!Calculations for Polarizable Models of Liquid Water. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 114, 9337-9349 (2001). +! +!Quantum, intramolecular flexibility, and polarizability effects on the +!reproduction of the density anomaly of liquid water by simple +!potential functions. M. W. Mahoney and W. L. Jorgensen, +!J. Chem. Phys., 115, 10758-10768 (2001). +! +!Improved Peptide and Protein Torsional Energetics with the OPLS-AA +!Force Field M. J. Robertson, J. Tirado-Rives and W. L. Jorgensen, +!J. Chem. Theory. Comput. (2015) + +BOND +OT HT 450.0 0.9572 +HT HT 0.0 1.5139 +S203 S203 166.0 2.038 +!! below are automatically generated by pepz2rtf +C135 C136 268.00 1.529 +C135 C137 268.00 1.529 +C135 C158 268.00 1.529 +C135 C224 268.00 1.529 +C135 C235 317.00 1.522 +C135 C283 268.00 1.529 +C135 C293 268.00 1.529 +C135 H140 340.00 1.090 +C136 C136 268.00 1.529 +C136 C137 268.00 1.529 +C136 C210 268.00 1.529 +C136 C224 268.00 1.529 +C136 C235 317.00 1.522 +C136 C245 268.00 1.529 +C136 C246 268.00 1.529 +C136 C267 317.00 1.522 +C136 C274 268.00 1.529 +C136 C283 268.00 1.529 +C136 C285 268.00 1.529 +C136 C292 268.00 1.529 +C136 C293 268.00 1.529 +C136 C295 268.00 1.529 +C136 C296 268.00 1.529 +C136 C308 268.00 1.529 +C136 C500 317.00 1.495 +C136 H140 340.00 1.090 +C137 C224 268.00 1.529 +C137 C283 268.00 1.529 +C137 C293 268.00 1.529 +C137 H140 340.00 1.090 +C145 C145 469.00 1.400 +C145 C149 317.00 1.510 +C145 C166 469.00 1.400 +C145 C501 469.00 1.404 +C145 C502 469.00 1.400 +C145 H146 367.00 1.080 +C149 C224 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C224 H140 37.50 110.70 +C135 C224 N238 80.00 109.70 +C135 C235 N238 70.00 116.60 +C135 C235 N239 70.00 116.60 +C135 C235 O236 80.00 120.40 +C135 C283 C271 63.00 111.10 +C135 C283 H140 37.50 110.70 +C135 C283 N238 80.00 109.70 +C135 C293 C235 63.00 111.10 +C135 C293 H140 37.50 110.70 +C135 C293 N287 80.00 111.20 +C136 C135 H140 37.50 110.70 +C136 C136 C136 58.35 112.70 +C136 C136 C224 58.35 112.70 +C136 C136 C235 63.00 111.10 +C136 C136 C245 58.35 112.70 +C136 C136 C246 58.35 112.70 +C136 C136 C267 63.00 111.10 +C136 C136 C283 58.35 112.70 +C136 C136 C285 58.35 112.70 +C136 C136 C292 58.35 112.70 +C136 C136 C293 58.35 112.70 +C136 C136 C295 58.35 112.70 +C136 C136 C296 58.35 112.70 +C136 C136 H140 37.50 110.70 +C136 C137 C224 58.35 112.70 +C136 C137 C283 58.35 112.70 +C136 C137 C293 58.35 112.70 +C136 C137 H140 37.50 110.70 +C136 C210 H140 37.50 110.70 +C136 C210 S202 50.00 114.70 +C136 C224 C235 63.00 111.10 +C136 C224 H140 37.50 110.70 +C136 C224 N238 80.00 109.70 +C136 C235 N237 70.00 116.60 +C136 C235 O236 80.00 120.40 +C136 C245 H140 37.50 110.70 +C136 C245 N239 80.00 109.70 +C136 C246 C235 63.00 111.10 +C136 C246 H140 37.50 110.70 +C136 C246 N239 80.00 109.70 +C136 C267 O268 70.00 108.00 +C136 C267 O269 80.00 120.40 +C136 C274 C271 63.00 111.10 +C136 C274 H140 37.50 110.70 +C136 C283 C271 63.00 111.10 +C136 C283 H140 37.50 110.70 +C136 C283 N238 80.00 109.70 +C136 C285 C271 63.00 111.10 +C136 C285 H140 37.50 110.70 +C136 C285 N239 80.00 109.70 +C136 C292 H140 37.50 110.70 +C136 C292 N287 80.00 111.20 +C136 C293 C235 63.00 111.10 +C136 C293 H140 37.50 110.70 +C136 C293 N287 80.00 111.20 +C136 C295 C235 63.00 111.10 +C136 C295 H140 37.50 110.70 +C136 C295 N309 80.00 111.20 +C136 C296 H140 37.50 110.70 +C136 C296 N309 80.00 111.20 +C136 C308 C307 58.35 112.70 +C136 C308 H140 37.50 110.70 +C136 C500 C501 70.00 128.60 +C136 C500 C514 70.00 125.00 +C137 C135 H140 37.50 110.70 +C137 C136 C224 58.35 112.70 +C137 C136 C283 58.35 112.70 +C137 C136 C293 58.35 112.70 +C137 C136 H140 37.50 110.70 +C137 C224 C235 63.00 111.10 +C137 C224 H140 37.50 110.70 +C137 C224 N238 80.00 109.70 +C137 C283 C271 63.00 111.10 +C137 C283 H140 37.50 110.70 +C137 C283 N238 80.00 109.70 +C137 C293 C235 63.00 111.10 +C137 C293 H140 37.50 110.70 +C137 C293 N287 80.00 111.20 +C145 C145 C145 63.00 120.00 +C145 C145 C149 70.00 120.00 +C145 C145 C166 63.00 120.00 +C145 C145 C501 63.00 120.00 +C145 C145 C502 85.00 120.00 +C145 C145 H146 35.00 120.00 +C145 C149 C224 63.00 114.00 +C145 C149 C283 63.00 114.00 +C145 C149 C293 63.00 114.00 +C145 C149 H140 35.00 109.50 +C145 C166 C145 63.00 120.00 +C145 C166 O167 70.00 120.00 +C145 C501 C500 85.00 134.90 +C145 C501 C502 85.00 116.20 +C145 C502 C501 85.00 122.70 +C145 C502 N503 70.00 132.80 +C149 C224 C235 63.00 111.10 +C149 C224 H140 37.50 110.70 +C149 C224 N238 80.00 109.70 +C149 C283 C271 63.00 111.10 +C149 C283 H140 37.50 110.70 +C149 C283 N238 80.00 109.70 +C149 C293 C235 63.00 111.10 +C149 C293 H140 37.50 110.70 +C149 C293 N287 80.00 111.20 +C157 C224 C235 63.00 111.10 +C157 C224 H140 37.50 110.70 +C157 C224 N238 80.00 109.70 +C157 C283 C271 63.00 111.10 +C157 C283 H140 37.50 110.70 +C157 C283 N238 80.00 109.70 +C157 C293 C235 63.00 111.10 +C157 C293 H140 37.50 110.70 +C157 C293 N287 80.00 111.20 +C157 O154 H155 55.00 108.50 +C158 C135 H140 37.50 110.70 +C158 C224 C235 63.00 111.10 +C158 C224 H140 37.50 110.70 +C158 C224 N238 80.00 109.70 +C158 C283 C271 63.00 111.10 +C158 C283 H140 37.50 110.70 +C158 C283 N238 80.00 109.70 +C158 C293 C235 63.00 111.10 +C158 C293 H140 37.50 110.70 +C158 C293 N287 80.00 111.20 +C158 O154 H155 55.00 108.50 +C166 C145 H146 35.00 120.00 +C166 O167 H168 35.00 113.00 +C206 C224 C235 63.00 111.10 +C206 C224 H140 37.50 110.70 +C206 C224 N238 80.00 109.70 +C206 C283 C271 63.00 111.10 +C206 C283 H140 37.50 110.70 +C206 C283 N238 80.00 109.70 +C206 C293 C235 63.00 111.10 +C206 C293 H140 37.50 110.70 +C206 C293 N287 80.00 111.20 +C206 S200 H204 44.00 96.00 +C209 S202 C210 62.00 98.90 +C210 C136 C224 58.35 112.70 +C210 C136 C283 58.35 112.70 +C210 C136 C293 58.35 112.70 +C210 C136 H140 37.50 110.70 +C214 C224 C235 63.00 111.10 +C214 C224 H140 37.50 110.70 +C214 C224 N238 80.00 109.70 +C214 C283 C271 63.00 111.10 +C214 C283 H140 37.50 110.70 +C214 C283 N238 80.00 109.70 +C214 C293 C235 63.00 111.10 +C214 C293 H140 37.50 110.70 +C214 C293 N287 80.00 111.20 +C214 S203 S203 68.00 103.70 +C223 C235 N238 70.00 116.60 +C223 C235 N239 70.00 116.60 +C223 C235 O236 80.00 120.40 +C223 N238 C235 50.00 121.90 +C223 N238 H241 38.00 118.40 +C224 C135 H140 37.50 110.70 +C224 C136 C235 63.00 111.10 +C224 C136 C267 63.00 111.10 +C224 C136 C274 58.35 112.70 +C224 C136 C308 58.35 112.70 +C224 C136 C500 63.00 115.60 +C224 C136 H140 37.50 110.70 +C224 C137 H140 37.50 110.70 +C224 C149 H140 37.50 110.70 +C224 C157 H140 37.50 110.70 +C224 C157 O154 50.00 109.50 +C224 C158 H140 37.50 110.70 +C224 C158 O154 50.00 109.50 +C224 C206 H140 37.50 110.70 +C224 C206 S200 50.00 108.60 +C224 C214 H140 37.50 110.70 +C224 C214 S203 50.00 114.70 +C224 C235 N238 70.00 116.60 +C224 C235 N239 70.00 116.60 +C224 C235 O236 80.00 120.40 +C223 C267 O268 70.00 108.00 ! protonated C-terminal Gly, adm jr. +C224 C267 O268 70.00 108.00 +C223 C267 O269 80.00 120.40 ! protonated C-terminal Gly, adm jr. +C224 C267 O269 80.00 120.40 +C224 C274 C271 63.00 111.10 +C224 C274 H140 37.50 110.70 +C224 C505 C507 63.00 114.00 +C224 C505 C508 63.00 114.00 +C224 C505 C510 63.00 114.00 +C224 C505 H140 37.50 110.70 +C224 N238 C235 50.00 121.90 +C224 N238 H241 38.00 118.40 +C235 C135 H140 35.00 109.50 +C235 C136 C283 63.00 111.10 +C235 C136 C293 63.00 111.10 +C235 C136 H140 35.00 109.50 +C235 C223 H140 35.00 109.50 +C235 C223 N238 63.00 110.10 +C235 C224 C274 63.00 111.10 +C235 C224 C505 63.00 111.10 +C235 C224 H140 35.00 109.50 +C235 C224 N238 63.00 110.10 +C235 C246 H140 35.00 109.50 +C235 C246 N239 63.00 110.10 +C235 C292 H140 35.00 109.50 +C235 C292 N287 80.00 111.20 +C235 C293 C274 63.00 111.10 +C235 C293 C505 63.00 111.10 +C235 C293 H140 35.00 109.50 +C235 C293 N287 80.00 111.20 +C235 C295 H140 35.00 109.50 +C235 C295 N309 80.00 111.20 +C235 N237 H240 35.00 119.80 +C235 N238 C242 50.00 121.90 +C235 N238 C283 50.00 121.90 +C235 N238 C284 50.00 121.90 +C235 N238 H241 35.00 119.80 +C235 N239 C245 50.00 121.90 +C235 N239 C246 50.00 121.90 +C235 N239 C285 50.00 121.90 +C242 N238 H241 38.00 118.40 +C245 C136 H140 37.50 110.70 +C245 N238 C285 50.00 118.00 +C245 N239 C246 50.00 118.00 +C245 N239 C285 50.00 118.00 +C246 C136 H140 37.50 110.70 +C246 C235 N238 70.00 116.60 +C246 C235 N239 70.00 116.60 +C246 C235 O236 80.00 120.40 +C267 C136 C283 63.00 111.10 +C267 C136 C293 63.00 111.10 +C267 C136 H140 35.00 109.50 +C267 C223 H140 35.00 109.50 !protonated C-terminal Gly, adm jr. +C267 C224 H140 35.00 109.50 +C267 C223 N238 63.00 110.10 !protonated C-terminal Gly, adm jr. +C267 C224 N238 63.00 110.10 +C267 O268 H270 35.00 113.00 +C271 C274 C283 63.00 111.10 +C271 C274 C293 63.00 111.10 +C271 C274 H140 35.00 109.50 +C271 C283 C274 63.00 111.10 +C271 C283 C505 63.00 111.10 +C271 C283 H140 35.00 109.50 +C271 C283 N238 63.00 110.10 +C271 C284 H140 35.00 109.50 +C271 C284 N238 63.00 110.10 +C271 C285 H140 35.00 109.50 +C271 C285 N239 63.00 110.10 +C274 C136 C283 58.35 112.70 +C274 C136 C293 58.35 112.70 +C274 C136 H140 37.50 110.70 +C274 C224 H140 37.50 110.70 +C274 C224 N238 80.00 109.70 +C274 C271 O272 70.00 117.00 +C274 C283 H140 37.50 110.70 +C274 C283 N238 80.00 109.70 +C274 C293 H140 37.50 110.70 +C274 C293 N287 80.00 111.20 +C283 C135 H140 37.50 110.70 +C283 C136 C308 58.35 112.70 +C283 C136 C500 63.00 115.60 +C283 C136 H140 37.50 110.70 +C283 C137 H140 37.50 110.70 +C283 C149 H140 37.50 110.70 +C283 C157 H140 37.50 110.70 +C283 C157 O154 50.00 109.50 +C283 C158 H140 37.50 110.70 +C283 C158 O154 50.00 109.50 +C283 C206 H140 37.50 110.70 +C283 C206 S200 50.00 108.60 +C283 C214 H140 37.50 110.70 +C283 C214 S203 50.00 114.70 +C283 C271 O272 70.00 117.00 +C283 C274 H140 37.50 110.70 +C283 C505 C507 63.00 114.00 +C283 C505 C508 63.00 114.00 +C283 C505 C510 63.00 114.00 +C283 C505 H140 37.50 110.70 +C283 N238 H241 38.00 118.40 +C284 C271 O272 70.00 117.00 +C284 N238 H241 38.00 118.40 +C285 C136 H140 37.50 110.70 +C285 C271 O272 70.00 117.00 +C292 C136 H140 37.50 110.70 +C292 C235 N238 70.00 116.60 +C292 C235 N239 70.00 116.60 +C292 C235 O236 80.00 120.40 +C292 N287 H290 35.00 109.50 +C293 C135 H140 37.50 110.70 +C293 C136 C308 58.35 112.70 +C293 C136 C500 63.00 115.60 +C293 C136 H140 37.50 110.70 +C293 C137 H140 37.50 110.70 +C293 C149 H140 37.50 110.70 +C293 C157 H140 37.50 110.70 +C293 C157 O154 50.00 109.50 +C293 C158 H140 37.50 110.70 +C293 C158 O154 50.00 109.50 +C293 C206 H140 37.50 110.70 +C293 C206 S200 50.00 108.60 +C293 C214 H140 37.50 110.70 +C293 C214 S203 50.00 114.70 +C293 C235 N238 70.00 116.60 +C293 C235 N239 70.00 116.60 +C293 C235 O236 80.00 120.40 +C293 C274 H140 37.50 110.70 +C293 C505 C507 63.00 114.00 +C293 C505 C508 63.00 114.00 +C293 C505 C510 63.00 114.00 +C293 C505 H140 37.50 110.70 +C293 N287 H290 35.00 109.50 +C295 C136 H140 37.50 110.70 +C295 C235 N238 70.00 116.60 +C295 C235 N239 70.00 116.60 +C295 C235 O236 80.00 120.40 +C295 N309 C296 50.00 113.00 +C295 N309 H310 35.00 109.50 +C296 C136 H140 37.50 110.70 +C296 N309 H310 35.00 109.50 +C302 N300 H301 35.00 120.00 +C302 N303 C307 50.00 123.20 +C302 N303 H304 35.00 120.00 +C307 C308 H140 37.50 110.70 +C307 N303 H304 35.00 118.40 +C308 C136 H140 37.50 110.70 +C308 C307 H140 37.50 110.70 +C308 C307 N303 80.00 111.20 +C500 C136 H140 35.00 109.50 +C500 C501 C502 85.00 108.80 +C500 C514 H146 35.00 120.00 +C500 C514 N503 70.00 108.70 +C501 C145 H146 35.00 120.00 +C501 C500 C514 85.00 106.40 +C501 C502 N503 70.00 104.40 +C502 C145 H146 35.00 120.00 +C502 N503 C514 70.00 111.60 +C502 N503 H504 35.00 123.10 +C505 C224 H140 37.50 110.70 +C505 C224 N238 80.00 109.70 +C505 C283 H140 37.50 110.70 +C505 C283 N238 80.00 109.70 +C505 C293 H140 37.50 110.70 +C505 C293 N287 80.00 111.20 +C505 C507 C508 70.00 130.70 +C505 C507 N511 70.00 124.50 +C505 C508 C507 70.00 130.70 +C505 C508 N503 70.00 121.60 +C505 C510 C510 70.00 130.70 +C505 C510 N512 70.00 121.60 +C506 N503 C508 70.00 109.80 +C506 N503 H504 35.00 124.00 +C506 N511 C507 70.00 110.00 +C507 C505 H140 35.00 109.50 +C507 C508 H146 35.00 130.70 +C507 C508 N503 70.00 106.30 +C508 C505 H140 35.00 109.50 +C508 C507 H146 35.00 128.20 +C508 C507 N511 70.00 111.00 +C508 N503 H504 35.00 124.00 +C509 N512 C510 70.00 109.80 +C509 N512 H513 35.00 124.00 +C510 C505 H140 35.00 109.50 +C510 C510 H146 35.00 130.70 +C510 C510 N512 70.00 106.30 +C510 N512 H513 35.00 124.00 +C514 N503 H504 35.00 124.00 +H140 C157 O154 35.00 109.50 +H140 C158 O154 35.00 109.50 +H140 C206 S200 35.00 109.50 +H140 C209 S202 35.00 109.50 +H140 C210 S202 35.00 109.50 +H140 C214 S203 35.00 109.50 +H140 C223 N238 35.00 109.50 +H140 C224 N238 35.00 109.50 +H140 C242 N238 35.00 109.50 +H140 C245 N239 35.00 109.50 +H140 C246 N239 35.00 109.50 +H140 C283 N238 35.00 109.50 +H140 C284 N238 35.00 109.50 +H140 C285 N239 35.00 109.50 +H140 C292 N287 35.00 109.50 +H140 C293 N287 35.00 109.50 +H140 C295 N309 35.00 109.50 +H140 C296 N309 35.00 109.50 +H140 C307 N303 35.00 109.50 +H146 C506 N503 35.00 120.00 +H146 C506 N511 35.00 120.00 +H146 C507 N511 35.00 120.00 +H146 C508 N503 35.00 121.60 +H146 C509 N512 35.00 120.00 +H146 C510 N512 35.00 120.00 +H146 C514 N503 35.00 121.60 +H240 N237 H240 35.00 120.00 +H301 N300 H301 35.00 120.00 +N237 C235 O236 80.00 122.90 +N238 C235 O236 80.00 122.90 +N239 C235 O236 80.00 122.90 +N300 C302 N300 70.00 120.00 +N300 C302 N303 70.00 120.00 +N503 C506 N511 70.00 120.00 +N512 C509 N512 70.00 120.00 +O268 C267 O269 80.00 121.00 +O272 C271 O272 80.00 126.00 +DIHEDRAL +X C145 C145 X 3.6250 2 180.0 +X C145 C166 X 3.6250 2 180.0 +X C145 C501 X 3.5000 2 180.0 +X C145 C502 X 3.6250 2 180.0 +X C302 N300 X 1.9500 2 180.0 +X C500 C501 X 1.6750 2 180.0 +X C500 C514 X 6.5250 2 180.0 +X C501 C502 X 3.0000 2 180.0 +X C502 N503 X 1.5250 2 180.0 +X C506 N503 X 2.3250 2 180.0 +X C506 N511 X 5.0000 2 180.0 +X C507 C508 X 5.3750 2 180.0 +X C507 N511 X 2.4000 2 180.0 +X C509 N512 X 2.3250 2 180.0 +X C510 C510 X 5.3750 2 180.0 +X C514 N503 X 1.5000 2 180.0 +C135 C136 C137 C135 0.6500 1 0.0 +C135 C136 C137 C135 -0.1000 2 180.0 +C135 C136 C137 C135 0.1000 3 0.0 +C135 C136 C137 C224 0.6500 1 0.0 +C135 C136 C137 C224 -0.1000 2 180.0 +C135 C136 C137 C224 0.1000 3 0.0 +C135 C136 C137 C283 0.6500 1 0.0 +C135 C136 C137 C283 -0.1000 2 180.0 +C135 C136 C137 C283 0.1000 3 0.0 +C135 C136 C137 C293 0.6500 1 0.0 +C135 C136 C137 C293 -0.1000 2 180.0 +C135 C136 C137 C293 0.1000 3 0.0 +C135 C136 C137 H140 0.1500 3 0.0 +C135 C137 C135 H140 0.1500 3 0.0 +C135 C137 C136 C224 0.6500 1 0.0 +C135 C137 C136 C224 -0.1000 2 180.0 +C135 C137 C136 C224 0.1000 3 0.0 +C135 C137 C136 C283 0.6500 1 0.0 +C135 C137 C136 C283 -0.1000 2 180.0 +C135 C137 C136 C283 0.1000 3 0.0 +C135 C137 C136 C293 0.6500 1 0.0 +C135 C137 C136 C293 -0.1000 2 180.0 +C135 C137 C136 C293 0.1000 3 0.0 +C135 C137 C136 H140 0.1500 3 0.0 +C135 C137 C224 C235 -0.7110 1 0.0 +C135 C137 C224 C235 0.5340 2 180.0 +C135 C137 C224 C235 0.0000 3 0.0 +C135 C137 C224 H140 0.1500 3 0.0 +C135 C137 C224 N238 1.4970 1 0.0 +C135 C137 C224 N238 0.1260 2 180.0 +C135 C137 C224 N238 0.1500 3 0.0 +C135 C137 C283 C271 -0.7110 1 0.0 +C135 C137 C283 C271 0.5340 2 180.0 +C135 C137 C283 C271 0.0000 3 0.0 +C135 C137 C283 H140 0.1500 3 0.0 +C135 C137 C283 N238 1.4970 1 0.0 +C135 C137 C283 N238 0.1260 2 180.0 +C135 C137 C283 N238 0.1500 3 0.0 +C135 C137 C293 C235 -0.7110 1 0.0 +C135 C137 C293 C235 0.5340 2 180.0 +C135 C137 C293 C235 0.0000 3 0.0 +C135 C137 C293 H140 0.1500 3 0.0 +C135 C137 C293 N287 1.4970 1 0.0 +C135 C137 C293 N287 0.1260 2 180.0 +C135 C137 C293 N287 0.1500 3 0.0 +C135 C158 C224 C235 -0.7110 1 0.0 +C135 C158 C224 C235 0.5340 2 180.0 +C135 C158 C224 C235 0.0000 3 0.0 +C135 C158 C224 H140 0.1500 3 0.0 +C135 C158 C224 N238 1.4970 1 0.0 +C135 C158 C224 N238 0.1260 2 180.0 +C135 C158 C224 N238 0.1500 3 0.0 +C135 C158 C283 C271 -0.7110 1 0.0 +C135 C158 C283 C271 0.5340 2 180.0 +C135 C158 C283 C271 0.0000 3 0.0 +C135 C158 C283 H140 0.1500 3 0.0 +C135 C158 C283 N238 1.4970 1 0.0 +C135 C158 C283 N238 0.1260 2 180.0 +C135 C158 C283 N238 0.1500 3 0.0 +C135 C158 C293 C235 -0.7110 1 0.0 +C135 C158 C293 C235 0.5340 2 180.0 +C135 C158 C293 C235 0.0000 3 0.0 +C135 C158 C293 H140 0.1500 3 0.0 +C135 C158 C293 N287 1.4970 1 0.0 +C135 C158 C293 N287 0.1260 2 180.0 +C135 C158 C293 N287 0.1500 3 0.0 +C135 C158 O154 H155 -0.1780 1 0.0 +C135 C158 O154 H155 -0.0870 2 180.0 +C135 C158 O154 H155 0.2460 3 0.0 +C135 C224 C235 N238 0.8895 1 0.0 +C135 C224 C235 N238 0.2095 2 180.0 +C135 C224 C235 N238 -0.0550 3 0.0 +C135 C224 C235 N239 0.8895 1 0.0 +C135 C224 C235 N239 0.2095 2 180.0 +C135 C224 C235 N239 -0.0550 3 0.0 +C135 C224 C235 O236 0.0000 1 0.0 +C135 C224 C267 O268 0.5000 1 0.0 +C135 C224 C267 O268 0.2730 2 180.0 +C135 C224 C267 O268 0.2250 3 0.0 +C135 C224 C267 O269 0.2730 2 180.0 +C135 C224 N238 C235 -0.3410 1 0.0 +C135 C224 N238 C235 0.0650 2 180.0 +C135 C224 N238 C235 0.1690 3 0.0 +C135 C224 N238 H241 0.0000 1 0.0 +C135 C235 N238 C223 1.1500 1 0.0 +C135 C235 N238 C223 3.0445 2 180.0 +C135 C235 N238 C224 1.1500 1 0.0 +C135 C235 N238 C224 3.0445 2 180.0 +C135 C235 N238 H241 2.4500 2 180.0 +C135 C235 N239 C245 1.1500 1 0.0 +C135 C235 N239 C245 3.0445 2 180.0 +C135 C235 N239 C246 1.1500 1 0.0 +C135 C235 N239 C246 3.0445 2 180.0 +C135 C283 C271 O272 0.4100 2 180.0 +C135 C283 N238 C235 -0.3410 1 0.0 +C135 C283 N238 C235 0.0650 2 180.0 +C135 C283 N238 C235 0.1690 3 0.0 +C135 C283 N238 H241 0.0000 1 0.0 +C135 C293 C235 N238 0.8895 1 0.0 +C135 C293 C235 N238 0.2095 2 180.0 +C135 C293 C235 N238 -0.0550 3 0.0 +C135 C293 C235 N239 0.8895 1 0.0 +C135 C293 C235 N239 0.2095 2 180.0 +C135 C293 C235 N239 -0.0550 3 0.0 +C135 C293 C235 O236 0.0000 1 0.0 +C135 C293 N287 H290 0.1735 3 0.0 +C136 C136 C136 C224 0.6500 1 0.0 +C136 C136 C136 C224 -0.1000 2 180.0 +C136 C136 C136 C224 0.1000 3 0.0 +! protonated Glu, adm jr. +C267 C136 C136 C224 0.6500 1 0.0 +C267 C136 C136 C224 -0.1000 2 180.0 +C267 C136 C136 C224 0.1000 3 0.0 +! +C136 C136 C136 C283 0.6500 1 0.0 +C136 C136 C136 C283 -0.1000 2 180.0 +C136 C136 C136 C283 0.1000 3 0.0 +C136 C136 C136 C292 0.6500 1 0.0 +C136 C136 C136 C292 -0.1000 2 180.0 +C136 C136 C136 C292 0.1000 3 0.0 +C136 C136 C136 C293 0.6500 1 0.0 +C136 C136 C136 C293 -0.1000 2 180.0 +C136 C136 C136 C293 0.1000 3 0.0 +C136 C136 C136 H140 0.1500 3 0.0 +! protonated Glu, adm jr. +C267 C136 C136 H140 0.1500 3 0.0 +! +C136 C136 C224 C235 -1.1790 1 0.0 +C136 C136 C224 C235 0.4555 2 180.0 +C136 C136 C224 C235 0.0000 3 0.0 +C136 C136 C224 H140 0.1500 3 0.0 +C136 C136 C224 N238 0.4420 1 0.0 +C136 C136 C224 N238 0.4485 2 180.0 +C136 C136 C224 N238 0.4400 3 0.0 +C136 C136 C235 N237 1.4220 1 0.0 +C136 C136 C235 N237 -0.1805 2 180.0 +C136 C136 C235 N237 -0.1625 3 0.0 +C136 C136 C235 O236 0.2030 1 0.0 +C136 C136 C235 O236 0.6520 2 180.0 +C136 C136 C235 O236 0.0695 3 0.0 +C136 C136 C245 H140 0.1500 3 0.0 +C136 C136 C245 N239 0.4225 1 0.0 +C136 C136 C245 N239 -0.4810 2 180.0 +C136 C136 C245 N239 0.3565 3 0.0 +C136 C136 C246 C235 -0.8755 1 0.0 +C136 C136 C246 C235 0.8030 2 180.0 +C136 C136 C246 C235 0.0000 3 0.0 +C136 C136 C246 H140 0.1500 3 0.0 +C136 C136 C246 N239 0.7860 1 0.0 +C136 C136 C246 N239 0.0795 2 180.0 +C136 C136 C246 N239 0.1000 3 0.0 +C136 C136 C267 O268 0.5000 1 0.0 +C136 C136 C267 O268 0.2730 2 180.0 +C136 C136 C267 O268 0.2250 3 0.0 +C136 C136 C267 O269 0.2730 2 180.0 +C136 C136 C283 C271 -1.1790 1 0.0 +C136 C136 C283 C271 0.4555 2 180.0 +C136 C136 C283 C271 0.0000 3 0.0 +C136 C136 C283 H140 0.1500 3 0.0 +C136 C136 C283 N238 0.4420 1 0.0 +C136 C136 C283 N238 0.4485 2 180.0 +C136 C136 C283 N238 0.4400 3 0.0 +C136 C136 C285 C271 -0.8755 1 0.0 +C136 C136 C285 C271 0.8030 2 180.0 +C136 C136 C285 C271 0.0000 3 0.0 +C136 C136 C285 H140 0.1500 3 0.0 +C136 C136 C285 N239 0.7860 1 0.0 +C136 C136 C285 N239 0.0795 2 180.0 +C136 C136 C285 N239 0.1000 3 0.0 +C136 C136 C292 H140 0.1500 3 0.0 +C136 C136 C292 N287 1.3660 1 0.0 +C136 C136 C292 N287 -0.1145 2 180.0 +C136 C136 C292 N287 0.2425 3 0.0 +C136 C136 C293 C235 -1.1790 1 0.0 +C136 C136 C293 C235 0.4555 2 180.0 +C136 C136 C293 C235 0.0000 3 0.0 +C136 C136 C293 H140 0.1500 3 0.0 +C136 C136 C293 N287 0.4420 1 0.0 +C136 C136 C293 N287 0.4485 2 180.0 +C136 C136 C293 N287 0.4400 3 0.0 +C136 C136 C295 C235 -0.8755 1 0.0 +C136 C136 C295 C235 0.8030 2 180.0 +C136 C136 C295 C235 0.0000 3 0.0 +C136 C136 C295 H140 0.1500 3 0.0 +C136 C136 C295 N309 1.3660 1 0.0 +C136 C136 C295 N309 -0.1145 2 180.0 +C136 C136 C295 N309 0.2425 3 0.0 +C136 C136 C296 H140 0.1500 3 0.0 +C136 C136 C296 N309 1.3660 1 0.0 +C136 C136 C296 N309 -0.1145 2 180.0 +C136 C136 C296 N309 0.2425 3 0.0 +C136 C137 C135 H140 0.1500 3 0.0 +C136 C137 C224 C235 -0.7110 1 0.0 +C136 C137 C224 C235 0.5340 2 180.0 +C136 C137 C224 C235 0.0000 3 0.0 +C136 C137 C224 H140 0.1500 3 0.0 +C136 C137 C224 N238 1.4970 1 0.0 +C136 C137 C224 N238 0.1260 2 180.0 +C136 C137 C224 N238 0.1500 3 0.0 +C136 C137 C283 C271 -0.7110 1 0.0 +C136 C137 C283 C271 0.5340 2 180.0 +C136 C137 C283 C271 0.0000 3 0.0 +C136 C137 C283 H140 0.1500 3 0.0 +C136 C137 C283 N238 1.4970 1 0.0 +C136 C137 C283 N238 0.1260 2 180.0 +C136 C137 C283 N238 0.1500 3 0.0 +C136 C137 C293 C235 -0.7110 1 0.0 +C136 C137 C293 C235 0.5340 2 180.0 +C136 C137 C293 C235 0.0000 3 0.0 +C136 C137 C293 H140 0.1500 3 0.0 +C136 C137 C293 N287 1.4970 1 0.0 +C136 C137 C293 N287 0.1260 2 180.0 +C136 C137 C293 N287 0.1500 3 0.0 +C136 C210 S202 C209 0.4625 1 0.0 +C136 C210 S202 C209 -0.2880 2 180.0 +C136 C210 S202 C209 0.3385 3 0.0 +C136 C224 C235 N238 0.8895 1 0.0 +C136 C224 C235 N238 0.2095 2 180.0 +C136 C224 C235 N238 -0.0550 3 0.0 +C136 C224 C235 N239 0.8895 1 0.0 +C136 C224 C235 N239 0.2095 2 180.0 +C136 C224 C235 N239 -0.0550 3 0.0 +C136 C224 C235 O236 0.0000 1 0.0 +C136 C224 N238 C235 -0.3410 1 0.0 +C136 C224 N238 C235 0.0650 2 180.0 +C136 C224 N238 C235 0.1690 3 0.0 +C136 C224 N238 H241 0.0000 1 0.0 +C136 C235 N237 H240 2.4500 2 180.0 +C136 C245 N239 C235 -0.3410 1 0.0 +C136 C245 N239 C235 0.0650 2 180.0 +C136 C245 N239 C235 0.1690 3 0.0 +C136 C245 N239 C246 1.4295 1 0.0 +C136 C245 N239 C246 1.0290 2 180.0 +C136 C245 N239 C246 -5.6330 3 0.0 +C136 C245 N239 C285 1.4295 1 0.0 +C136 C245 N239 C285 1.0290 2 180.0 +C136 C245 N239 C285 -5.6330 3 0.0 +C136 C246 C235 N238 2.5145 1 0.0 +C136 C246 C235 N238 0.3595 2 180.0 +C136 C246 C235 N238 1.1200 3 0.0 +C136 C246 C235 N239 2.5145 1 0.0 +C136 C246 C235 N239 0.3595 2 180.0 +C136 C246 C235 N239 1.1200 3 0.0 +C136 C246 C235 O236 0.0000 1 0.0 +C136 C246 N239 C235 -0.3410 1 0.0 +C136 C246 N239 C235 0.0650 2 180.0 +C136 C246 N239 C235 0.1690 3 0.0 +C136 C246 N239 C245 2.3765 1 0.0 +C136 C246 N239 C245 -0.3670 2 180.0 +C136 C267 O268 H270 0.7500 1 0.0 +C136 C267 O268 H270 2.7500 2 180.0 +C136 C274 C271 O272 0.2730 2 180.0 +C136 C283 C271 O272 0.4100 2 180.0 +C136 C283 N238 C235 -0.3410 1 0.0 +C136 C283 N238 C235 0.0650 2 180.0 +C136 C283 N238 C235 0.1690 3 0.0 +C136 C283 N238 H241 0.0000 1 0.0 +C136 C285 C271 O272 0.4100 2 180.0 +C136 C285 N239 C235 -0.3410 1 0.0 +C136 C285 N239 C235 0.0650 2 180.0 +C136 C285 N239 C235 0.1690 3 0.0 +C136 C285 N239 C245 2.3765 1 0.0 +C136 C285 N239 C245 -0.3670 2 180.0 +C136 C292 N287 H290 0.1735 3 0.0 +C136 C293 C235 N238 0.8895 1 0.0 +C136 C293 C235 N238 0.2095 2 180.0 +C136 C293 C235 N238 -0.0550 3 0.0 +C136 C293 C235 N239 0.8895 1 0.0 +C136 C293 C235 N239 0.2095 2 180.0 +C136 C293 C235 N239 -0.0550 3 0.0 +C136 C293 C235 O236 0.0000 1 0.0 +C136 C293 N287 H290 0.1735 3 0.0 +C136 C295 C235 N238 2.5145 1 0.0 +C136 C295 C235 N238 0.3595 2 180.0 +C136 C295 C235 N238 1.1200 3 0.0 +C136 C295 C235 N239 2.5145 1 0.0 +C136 C295 C235 N239 0.3595 2 180.0 +C136 C295 C235 N239 1.1200 3 0.0 +C136 C295 C235 O236 0.0000 1 0.0 +C136 C295 N309 C296 0.71895 1 0.0 +C136 C295 N309 C296 -0.0619 2 180.0 +C136 C295 N309 C296 0.13195 3 0.0 +C136 C295 N309 H310 0.1735 3 0.0 +C136 C296 N309 C295 0.71895 1 0.0 +C136 C296 N309 C295 -0.0619 2 180.0 +C136 C296 N309 C295 0.13195 3 0.0 +C136 C296 N309 H310 0.1735 3 0.0 +C136 C308 C307 H140 0.1500 3 0.0 +C136 C308 C307 N303 1.3660 1 0.0 +C136 C308 C307 N303 -0.1145 2 180.0 +C136 C308 C307 N303 0.2425 3 0.0 +C137 C136 C135 H140 0.1500 3 0.0 +C137 C136 C224 C235 -0.8755 1 0.0 +C137 C136 C224 C235 0.8030 2 180.0 +C137 C136 C224 C235 0.0000 3 0.0 +C137 C136 C224 H140 0.1500 3 0.0 +C137 C136 C224 N238 0.7860 1 0.0 +C137 C136 C224 N238 0.0795 2 180.0 +C137 C136 C224 N238 0.1000 3 0.0 +C137 C136 C283 C271 -0.8755 1 0.0 +C137 C136 C283 C271 0.8030 2 180.0 +C137 C136 C283 C271 0.0000 3 0.0 +C137 C136 C283 H140 0.1500 3 0.0 +C137 C136 C283 N238 0.7860 1 0.0 +C137 C136 C283 N238 0.0795 2 180.0 +C137 C136 C283 N238 0.1000 3 0.0 +C137 C136 C293 C235 -0.8755 1 0.0 +C137 C136 C293 C235 0.8030 2 180.0 +C137 C136 C293 C235 0.0000 3 0.0 +C137 C136 C293 H140 0.1500 3 0.0 +C137 C136 C293 N287 0.7860 1 0.0 +C137 C136 C293 N287 0.0795 2 180.0 +C137 C136 C293 N287 0.1000 3 0.0 +C137 C224 C235 N238 0.8895 1 0.0 +C137 C224 C235 N238 0.2095 2 180.0 +C137 C224 C235 N238 -0.0550 3 0.0 +C137 C224 C235 N239 0.8895 1 0.0 +C137 C224 C235 N239 0.2095 2 180.0 +C137 C224 C235 N239 -0.0550 3 0.0 +C137 C224 C235 O236 0.0000 1 0.0 +C137 C224 N238 C235 -0.3410 1 0.0 +C137 C224 N238 C235 0.0650 2 180.0 +C137 C224 N238 C235 0.1690 3 0.0 +C137 C224 N238 H241 0.0000 1 0.0 +C137 C283 C271 O272 0.4100 2 180.0 +C137 C283 N238 C235 -0.3410 1 0.0 +C137 C283 N238 C235 0.0650 2 180.0 +C137 C283 N238 C235 0.1690 3 0.0 +C137 C283 N238 H241 0.0000 1 0.0 +C137 C293 C235 N238 0.8895 1 0.0 +C137 C293 C235 N238 0.2095 2 180.0 +C137 C293 C235 N238 -0.0550 3 0.0 +C137 C293 C235 N239 0.8895 1 0.0 +C137 C293 C235 N239 0.2095 2 180.0 +C137 C293 C235 N239 -0.0550 3 0.0 +C137 C293 C235 O236 0.0000 1 0.0 +C137 C293 N287 H290 0.1735 3 0.0 +C145 C145 C149 C224 0.0000 1 0.0 +C145 C145 C149 C283 0.0000 1 0.0 +C145 C145 C149 C293 0.0000 1 0.0 +C145 C145 C149 H140 0.0000 1 0.0 +C145 C149 C224 C235 -0.7030 1 0.0 +C145 C149 C224 C235 0.8885 2 180.0 +C145 C149 C224 C235 0.0000 3 0.0 +C145 C149 C224 H140 0.2310 3 0.0 +C145 C149 C224 N238 0.8560 1 0.0 +C145 C149 C224 N238 0.3625 2 180.0 +C145 C149 C224 N238 0.1830 3 0.0 +C145 C149 C283 C271 -0.7030 1 0.0 +C145 C149 C283 C271 0.8885 2 180.0 +C145 C149 C283 C271 0.0000 3 0.0 +C145 C149 C283 H140 0.2310 3 0.0 +C145 C149 C283 N238 0.8560 1 0.0 +C145 C149 C283 N238 0.3625 2 180.0 +C145 C149 C283 N238 0.1830 3 0.0 +C145 C149 C293 C235 -0.7030 1 0.0 +C145 C149 C293 C235 0.8885 2 180.0 +C145 C149 C293 C235 0.0000 3 0.0 +C145 C149 C293 H140 0.2310 3 0.0 +C145 C149 C293 N287 0.8560 1 0.0 +C145 C149 C293 N287 0.3625 2 180.0 +C145 C149 C293 N287 0.1830 3 0.0 +C145 C166 C145 H146 3.6250 2 180.0 +C145 C166 O167 H168 0.8410 2 180.0 +C145 C501 C500 C514 1.6750 2 180.0 +C145 C502 C501 C500 3.0000 2 180.0 +C149 C224 C235 N238 0.8895 1 0.0 +C149 C224 C235 N238 0.2095 2 180.0 +C149 C224 C235 N238 -0.0550 3 0.0 +C149 C224 C235 N239 0.8895 1 0.0 +C149 C224 C235 N239 0.2095 2 180.0 +C149 C224 C235 N239 -0.0550 3 0.0 +C149 C224 C235 O236 0.0000 1 0.0 +C149 C224 N238 C235 -0.3410 1 0.0 +C149 C224 N238 C235 0.0650 2 180.0 +C149 C224 N238 C235 0.1690 3 0.0 +C149 C224 N238 H241 0.0000 1 0.0 +C149 C283 C271 O272 0.4100 2 180.0 +C149 C283 N238 C235 -0.3410 1 0.0 +C149 C283 N238 C235 0.0650 2 180.0 +C149 C283 N238 C235 0.1690 3 0.0 +C149 C283 N238 H241 0.0000 1 0.0 +C149 C293 C235 N238 0.8895 1 0.0 +C149 C293 C235 N238 0.2095 2 180.0 +C149 C293 C235 N238 -0.0550 3 0.0 +C149 C293 C235 N239 0.8895 1 0.0 +C149 C293 C235 N239 0.2095 2 180.0 +C149 C293 C235 N239 -0.0550 3 0.0 +C149 C293 C235 O236 0.0000 1 0.0 +C149 C293 N287 H290 0.1735 3 0.0 +C157 C224 C235 N238 0.8895 1 0.0 +C157 C224 C235 N238 0.2095 2 180.0 +C157 C224 C235 N238 -0.0550 3 0.0 +C157 C224 C235 N239 0.8895 1 0.0 +C157 C224 C235 N239 0.2095 2 180.0 +C157 C224 C235 N239 -0.0550 3 0.0 +C157 C224 C235 O236 0.0000 1 0.0 +C157 C224 N238 C235 -0.3410 1 0.0 +C157 C224 N238 C235 0.0650 2 180.0 +C157 C224 N238 C235 0.1690 3 0.0 +C157 C224 N238 H241 0.0000 1 0.0 +C157 C283 C271 O272 0.4100 2 180.0 +C157 C283 N238 C235 -0.3410 1 0.0 +C157 C283 N238 C235 0.0650 2 180.0 +C157 C283 N238 C235 0.1690 3 0.0 +C157 C283 N238 H241 0.0000 1 0.0 +C157 C293 C235 N238 0.8895 1 0.0 +C157 C293 C235 N238 0.2095 2 180.0 +C157 C293 C235 N238 -0.0550 3 0.0 +! repeated, adm jr. +!C157 C293 C235 N238 0.8895 1 0.0 +!C157 C293 C235 N238 0.2095 2 180.0 +!C157 C293 C235 N238 -0.0550 3 0.0 +! +C157 C293 C235 O236 0.0000 1 0.0 +C157 C293 N287 H290 0.1735 3 0.0 +C158 C224 C235 N238 0.8895 1 0.0 +C158 C224 C235 N238 0.2095 2 180.0 +C158 C224 C235 N238 -0.0550 3 0.0 +C158 C224 C235 N239 0.8895 1 0.0 +C158 C224 C235 N239 0.2095 2 180.0 +C158 C224 C235 N239 -0.0550 3 0.0 +C158 C224 C235 O236 0.0000 1 0.0 +C158 C224 N238 C235 -0.3410 1 0.0 +C158 C224 N238 C235 0.0650 2 180.0 +C158 C224 N238 C235 0.1690 3 0.0 +C158 C224 N238 H241 0.0000 1 0.0 +C158 C283 C271 O272 0.4100 2 180.0 +C158 C283 N238 C235 -0.3410 1 0.0 +C158 C283 N238 C235 0.0650 2 180.0 +C158 C283 N238 C235 0.1690 3 0.0 +C158 C283 N238 H241 0.0000 1 0.0 +C158 C293 C235 N238 0.8895 1 0.0 +C158 C293 C235 N238 0.2095 2 180.0 +C158 C293 C235 N238 -0.0550 3 0.0 +C158 C293 C235 N239 0.8895 1 0.0 +C158 C293 C235 N239 0.2095 2 180.0 +C158 C293 C235 N239 -0.0550 3 0.0 +C158 C293 C235 O236 0.0000 1 0.0 +C158 C293 N287 H290 0.1735 3 0.0 +C206 C224 C235 N238 0.8895 1 0.0 +C206 C224 C235 N238 0.2095 2 180.0 +C206 C224 C235 N238 -0.0550 3 0.0 +C206 C224 C235 N239 0.8895 1 0.0 +C206 C224 C235 N239 0.2095 2 180.0 +C206 C224 C235 N239 -0.0550 3 0.0 +C206 C224 C235 O236 0.0000 1 0.0 +C206 C224 N238 C235 -0.3410 1 0.0 +C206 C224 N238 C235 0.0650 2 180.0 +C206 C224 N238 C235 0.1690 3 0.0 +C206 C224 N238 H241 0.0000 1 0.0 +C206 C283 C271 O272 0.4100 2 180.0 +C206 C283 N238 C235 -0.3410 1 0.0 +C206 C283 N238 C235 0.0650 2 180.0 +C206 C283 N238 C235 0.1690 3 0.0 +C206 C283 N238 H241 0.0000 1 0.0 +C206 C293 C235 N238 0.8895 1 0.0 +C206 C293 C235 N238 0.2095 2 180.0 +C206 C293 C235 N238 -0.0550 3 0.0 +C206 C293 C235 N239 0.8895 1 0.0 +C206 C293 C235 N239 0.2095 2 180.0 +C206 C293 C235 N239 -0.0550 3 0.0 +C206 C293 C235 O236 0.0000 1 0.0 +C206 C293 N287 H290 0.1735 3 0.0 +C209 S202 C210 H140 0.3235 3 0.0 +C210 C136 C224 C235 -0.4555 1 0.0 +C210 C136 C224 C235 0.3495 2 180.0 +C210 C136 C224 C235 0.0000 3 0.0 +C210 C136 C224 H140 0.1500 3 0.0 +C210 C136 C224 N238 0.1070 1 0.0 +C210 C136 C224 N238 0.2705 2 180.0 +C210 C136 C224 N238 0.1960 3 0.0 +C210 C136 C283 C271 -0.4555 1 0.0 +C210 C136 C283 C271 0.3495 2 180.0 +C210 C136 C283 C271 0.0000 3 0.0 +C210 C136 C283 H140 0.1500 3 0.0 +C210 C136 C283 N238 0.1070 1 0.0 +C210 C136 C283 N238 0.2705 2 180.0 +C210 C136 C283 N238 0.1960 3 0.0 +C210 C136 C293 C235 -0.4555 1 0.0 +C210 C136 C293 C235 0.3495 2 180.0 +C210 C136 C293 C235 0.0000 3 0.0 +C210 C136 C293 H140 0.1500 3 0.0 +C210 C136 C293 N287 0.1070 1 0.0 +C210 C136 C293 N287 0.2705 2 180.0 +C210 C136 C293 N287 0.1960 3 0.0 +C210 S202 C209 H140 0.3235 3 0.0 +C214 C224 C235 N238 0.8895 1 0.0 +C214 C224 C235 N238 0.2095 2 180.0 +C214 C224 C235 N238 -0.0550 3 0.0 +C214 C224 C235 N239 0.8895 1 0.0 +C214 C224 C235 N239 0.2095 2 180.0 +C214 C224 C235 N239 -0.0550 3 0.0 +C214 C224 C235 O236 0.0000 1 0.0 +C214 C224 N238 C235 -0.3410 1 0.0 +C214 C224 N238 C235 0.0650 2 180.0 +C214 C224 N238 C235 0.1690 3 0.0 +C214 C224 N238 H241 0.0000 1 0.0 +C214 C283 C271 O272 0.4100 2 180.0 +C214 C283 N238 C235 -0.3410 1 0.0 +C214 C283 N238 C235 0.0650 2 180.0 +C214 C283 N238 C235 0.1690 3 0.0 +C214 C283 N238 H241 0.0000 1 0.0 +C214 C293 C235 N238 0.8895 1 0.0 +C214 C293 C235 N238 0.2095 2 180.0 +C214 C293 C235 N238 -0.0550 3 0.0 +C214 C293 C235 N239 0.8895 1 0.0 +C214 C293 C235 N239 0.2095 2 180.0 +C214 C293 C235 N239 -0.0550 3 0.0 +C214 C293 C235 O236 0.0000 1 0.0 +C214 C293 N287 H290 0.1735 3 0.0 +C214 S203 S203 C214 -3.7070 2 180.0 +C214 S203 S203 C214 0.8525 3 0.0 +C223 C235 N238 C223 1.1500 1 0.0 +C223 C235 N238 C223 3.0445 2 180.0 +C223 C235 N238 C224 1.1500 1 0.0 +C223 C235 N238 C224 3.0445 2 180.0 +C223 C235 N238 C242 1.1500 1 0.0 +C223 C235 N238 C242 3.0445 2 180.0 +C223 C235 N238 C283 1.1500 1 0.0 +C223 C235 N238 C283 3.0445 2 180.0 +! N-terminal Pro (Pres prop), adm jr. +C295 C235 N238 C283 1.1500 1 0.0 +C295 C235 N238 C283 3.0445 2 180.0 +! +C223 C235 N238 C284 1.1500 1 0.0 +C223 C235 N238 C284 3.0445 2 180.0 +C223 C235 N238 H241 2.4500 2 180.0 +C223 C235 N239 C245 1.1500 1 0.0 +C223 C235 N239 C245 3.0445 2 180.0 +C223 C235 N239 C246 1.1500 1 0.0 +C223 C235 N239 C246 3.0445 2 180.0 +C223 C235 N239 C285 1.1500 1 0.0 +C223 C235 N239 C285 3.0445 2 180.0 +C223 N238 C235 C224 1.1500 1 0.0 +C223 N238 C235 C224 3.0445 2 180.0 +C223 N238 C235 C246 1.1500 1 0.0 +C223 N238 C235 C246 3.0445 2 180.0 +C223 N238 C235 C292 1.1500 1 0.0 +C223 N238 C235 C292 3.0445 2 180.0 +C223 N238 C235 C293 1.1500 1 0.0 +C223 N238 C235 C293 3.0445 2 180.0 +C223 N238 C235 C295 1.1500 1 0.0 +C223 N238 C235 C295 3.0445 2 180.0 +C223 N238 C235 O236 3.0445 2 180.0 +C224 C136 C136 C235 -0.6335 1 0.0 +C224 C136 C136 C235 0.2395 2 180.0 +C224 C136 C136 C235 -0.2430 3 0.0 +C224 C136 C136 H140 0.1500 3 0.0 +C224 C136 C137 H140 0.1500 3 0.0 +C224 C136 C210 H140 0.1500 3 0.0 +C224 C136 C210 S202 -0.7825 1 0.0 +C224 C136 C210 S202 -0.0045 2 180.0 +C224 C136 C210 S202 -0.2250 3 0.0 +C224 C136 C235 N237 0.7470 1 0.0 +C224 C136 C235 N237 -0.2555 2 180.0 +C224 C136 C235 N237 0.0625 3 0.0 +C224 C136 C235 O236 0.8280 1 0.0 +C224 C136 C235 O236 0.6520 2 180.0 +C224 C136 C235 O236 0.2195 3 0.0 +C224 C136 C267 O268 0.5000 1 0.0 +C224 C136 C267 O268 0.2730 2 180.0 +C224 C136 C267 O268 0.2250 3 0.0 +C224 C136 C267 O269 0.2730 2 180.0 +C224 C136 C274 C271 -0.4425 1 0.0 +C224 C136 C274 C271 0.5125 2 180.0 +C224 C136 C274 C271 -0.6465 3 0.0 +C224 C136 C274 H140 0.1500 3 0.0 +C224 C136 C308 C307 0.6500 1 0.0 +C224 C136 C308 C307 -0.1000 2 180.0 +C224 C136 C308 C307 0.1000 3 0.0 +C224 C136 C308 H140 0.1500 3 0.0 +C224 C136 C500 C501 0.0000 1 0.0 +C224 C136 C500 C514 -0.3570 1 0.0 +C224 C137 C135 H140 0.1500 3 0.0 +C224 C137 C136 H140 0.1500 3 0.0 +C224 C157 O154 H155 -0.1780 1 0.0 +C224 C157 O154 H155 -0.0870 2 180.0 +C224 C157 O154 H155 0.2460 3 0.0 +C224 C158 C135 H140 0.1500 3 0.0 +C224 C158 O154 H155 -0.1780 1 0.0 +C224 C158 O154 H155 -0.0870 2 180.0 +C224 C158 O154 H155 0.2460 3 0.0 +C224 C206 S200 H204 -0.3795 1 0.0 +C224 C206 S200 H204 -0.1410 2 180.0 +C224 C206 S200 H204 0.3400 3 0.0 +C224 C214 S203 S203 0.9705 1 0.0 +C224 C214 S203 S203 -0.4180 2 180.0 +C224 C214 S203 S203 0.4675 3 0.0 +C224 C235 N238 C224 1.1500 1 0.0 +C224 C235 N238 C224 3.0445 2 180.0 +C224 C235 N238 C242 1.1500 1 0.0 +C224 C235 N238 C242 3.0445 2 180.0 +C224 C235 N238 C283 1.1500 1 0.0 +C224 C235 N238 C283 3.0445 2 180.0 +C224 C235 N238 C284 1.1500 1 0.0 +C224 C235 N238 C284 3.0445 2 180.0 +C224 C235 N238 H241 2.4500 2 180.0 +C224 C235 N239 C245 1.1500 1 0.0 +C224 C235 N239 C245 3.0445 2 180.0 +C224 C235 N239 C246 1.1500 1 0.0 +C224 C235 N239 C246 3.0445 2 180.0 +C224 C235 N239 C285 1.1500 1 0.0 +C224 C235 N239 C285 3.0445 2 180.0 +! protonated C-terminal Gly, adm jr. +C223 C267 O268 H270 0.7500 1 0.0 +C223 C267 O268 H270 2.7500 2 180.0 +! +C224 C267 O268 H270 0.7500 1 0.0 +C224 C267 O268 H270 2.7500 2 180.0 +C224 C274 C271 O272 1.2500 1 0.0 +C224 C274 C271 O272 0.5000 2 180.0 +C224 C274 C271 O272 0.6750 3 0.0 +C224 C505 C507 C508 0.0000 1 0.0 +C224 C505 C507 N511 -0.2800 1 0.0 +C224 C505 C507 N511 -0.3700 2 180.0 +C224 C505 C507 N511 0.1745 3 0.0 +C224 C505 C508 C507 0.0000 1 0.0 +C224 C505 C508 N503 -0.2800 1 0.0 +C224 C505 C508 N503 -0.3700 2 180.0 +C224 C505 C508 N503 0.1745 3 0.0 +C224 C505 C510 C510 0.0000 1 0.0 +C224 C505 C510 N512 -1.9950 1 0.0 +C224 C505 C510 N512 0.8400 2 180.0 +C224 C505 C510 N512 0.1450 3 0.0 +C224 N238 C235 C246 1.1500 1 0.0 +C224 N238 C235 C246 3.0445 2 180.0 +C224 N238 C235 C292 1.1500 1 0.0 +C224 N238 C235 C292 3.0445 2 180.0 +C224 N238 C235 C293 1.1500 1 0.0 +C224 N238 C235 C293 3.0445 2 180.0 +C224 N238 C235 C295 1.1500 1 0.0 +C224 N238 C235 C295 3.0445 2 180.0 +C224 N238 C235 O236 3.0445 2 180.0 +C235 C136 C136 C283 -0.6335 1 0.0 +C235 C136 C136 C283 0.2395 2 180.0 +C235 C136 C136 C283 -0.2430 3 0.0 +C235 C136 C136 C293 -0.6335 1 0.0 +C235 C136 C136 C293 0.2395 2 180.0 +C235 C136 C136 C293 -0.2430 3 0.0 +C235 C136 C136 H140 -0.0500 3 0.0 +C235 C136 C224 C235 0.2990 1 0.0 +C235 C136 C224 C235 0.7790 2 180.0 +C235 C136 C224 C235 0.1275 3 0.0 +C235 C136 C224 H140 0.1500 3 0.0 +C235 C136 C224 N238 -2.7505 1 0.0 +C235 C136 C224 N238 0.7635 2 180.0 +C235 C136 C224 N238 0.0000 3 0.0 +C235 C136 C283 C271 0.2990 1 0.0 +C235 C136 C283 C271 0.7790 2 180.0 +C235 C136 C283 C271 0.1275 3 0.0 +C235 C136 C283 H140 0.1500 3 0.0 +C235 C136 C283 N238 -2.7505 1 0.0 +C235 C136 C283 N238 0.7635 2 180.0 +C235 C136 C283 N238 0.0000 3 0.0 +C235 C136 C293 C235 0.2990 1 0.0 +C235 C136 C293 C235 0.7790 2 180.0 +C235 C136 C293 C235 0.1275 3 0.0 +C235 C136 C293 H140 0.1500 3 0.0 +C235 C136 C293 N287 -2.7505 1 0.0 +C235 C136 C293 N287 0.7635 2 180.0 +C235 C136 C293 N287 0.0000 3 0.0 +C235 C223 N238 C235 -1.2555 1 0.0 +C235 C223 N238 C235 0.1050 2 180.0 +C235 C223 N238 C235 -0.1000 3 0.0 +C235 C223 N238 H241 0.0000 1 0.0 +C235 C224 C135 H140 -0.0380 3 0.0 +C235 C224 C136 C267 0.2990 1 0.0 +C235 C224 C136 C267 0.7790 2 180.0 +C235 C224 C136 C267 0.1275 3 0.0 +C235 C224 C136 C274 -0.8820 1 0.0 +C235 C224 C136 C274 0.3500 2 180.0 +C235 C224 C136 C274 0.0000 3 0.0 +C235 C224 C136 C308 -0.9855 1 0.0 +C235 C224 C136 C308 0.3850 2 180.0 +C235 C224 C136 C308 0.0000 3 0.0 +C235 C224 C136 C500 -0.2530 1 0.0 +C235 C224 C136 C500 0.4875 2 180.0 +C235 C224 C136 C500 0.0000 3 0.0 +C235 C224 C136 H140 -0.0380 3 0.0 +C235 C224 C137 H140 -0.0380 3 0.0 +C235 C224 C149 H140 -0.0380 3 0.0 +C235 C224 C157 H140 -0.0380 3 0.0 +C235 C224 C157 O154 -2.8965 1 0.0 +C235 C224 C157 O154 0.2025 2 180.0 +C235 C224 C157 O154 0.0000 3 0.0 +C235 C224 C158 H140 -0.0380 3 0.0 +C235 C224 C158 O154 -2.8965 1 0.0 +C235 C224 C158 O154 0.2025 2 180.0 +C235 C224 C158 O154 0.0000 3 0.0 +C235 C224 C206 H140 -0.0380 3 0.0 +C235 C224 C206 S200 -1.6615 1 0.0 +C235 C224 C206 S200 0.2645 2 180.0 +C235 C224 C206 S200 0.0000 3 0.0 +C235 C224 C214 H140 -0.0380 3 0.0 +C235 C224 C214 S203 -1.6615 1 0.0 +C235 C224 C214 S203 0.2645 2 180.0 +C235 C224 C214 S203 0.0000 3 0.0 +C235 C224 C274 C271 0.7715 1 0.0 +C235 C224 C274 C271 0.3480 2 180.0 +C235 C224 C274 C271 0.0000 3 0.0 +C235 C224 C274 H140 -0.0380 3 0.0 +C235 C224 C505 C507 -0.6410 1 0.0 +C235 C224 C505 C507 0.8225 2 180.0 +C235 C224 C505 C507 -0.0085 3 0.0 +C235 C224 C505 C508 -0.6410 1 0.0 +C235 C224 C505 C508 0.8225 2 180.0 +C235 C224 C505 C508 -0.0085 3 0.0 +C235 C224 C505 C510 -0.8540 1 0.0 +C235 C224 C505 C510 0.7580 2 180.0 +C235 C224 C505 C510 -0.2510 3 0.0 +C235 C224 C505 H140 -0.0380 3 0.0 +C235 C224 N238 C235 -1.2555 1 0.0 +C235 C224 N238 C235 0.1050 2 180.0 +C235 C224 N238 C235 -0.1000 3 0.0 +C235 C224 N238 H241 0.0000 1 0.0 +! protonated C-terminal Gly, adm jr. +C235 N238 C223 C267 -1.2555 1 0.0 +C235 N238 C223 C267 0.1050 2 180.0 +C235 N238 C223 C267 -0.1000 3 0.0 !note, in the original par file N238 was N248, which i think is a mistake, adm jr. +! +C235 N238 C224 C267 -1.2555 1 0.0 +C235 N238 C224 C267 0.1050 2 180.0 +C235 N238 C224 C267 -0.1000 3 0.0 !note, in the original par file N238 was N248, which i think is a mistake, adm jr. +C235 C246 C136 H140 -0.0380 3 0.0 +C235 C246 N239 C235 -1.2555 1 0.0 +C235 C246 N239 C235 0.1050 2 180.0 +C235 C246 N239 C235 -0.1000 3 0.0 +C235 C246 N239 C245 -0.8685 1 0.0 +C235 C246 N239 C245 0.6255 2 180.0 +C235 C246 N239 C245 -1.7505 3 0.0 +C235 C292 N287 H290 0.1735 3 0.0 +C235 C293 C135 H140 -0.0380 3 0.0 +C235 C293 C136 C274 -0.8820 1 0.0 +C235 C293 C136 C274 0.3500 2 180.0 +C235 C293 C136 C274 0.0000 3 0.0 +C235 C293 C136 C308 -0.9855 1 0.0 +C235 C293 C136 C308 0.3850 2 180.0 +C235 C293 C136 C308 0.0000 3 0.0 +C235 C293 C136 C500 -0.2530 1 0.0 +C235 C293 C136 C500 0.4875 2 180.0 +C235 C293 C136 C500 0.0000 3 0.0 +C235 C293 C136 H140 -0.0380 3 0.0 +C235 C293 C137 H140 -0.0380 3 0.0 +C235 C293 C149 H140 -0.0380 3 0.0 +C235 C293 C157 H140 -0.0380 3 0.0 +C235 C293 C157 O154 -2.8965 1 0.0 +C235 C293 C157 O154 0.2025 2 180.0 +C235 C293 C157 O154 0.0000 3 0.0 +C235 C293 C158 H140 -0.0380 3 0.0 +C235 C293 C158 O154 -2.8965 1 0.0 +C235 C293 C158 O154 0.2025 2 180.0 +C235 C293 C158 O154 0.0000 3 0.0 +C235 C293 C206 H140 -0.0380 3 0.0 +C235 C293 C206 S200 -1.6615 1 0.0 +C235 C293 C206 S200 0.2645 2 180.0 +C235 C293 C206 S200 0.0000 3 0.0 +C235 C293 C214 H140 -0.0380 3 0.0 +C235 C293 C214 S203 -1.6615 1 0.0 +C235 C293 C214 S203 0.2645 2 180.0 +C235 C293 C214 S203 0.0000 3 0.0 +C235 C293 C274 C271 0.7715 1 0.0 +C235 C293 C274 C271 0.3480 2 180.0 +C235 C293 C274 C271 0.0000 3 0.0 +C235 C293 C274 H140 -0.0380 3 0.0 +C235 C293 C505 C507 -0.6410 1 0.0 +C235 C293 C505 C507 0.8225 2 180.0 +C235 C293 C505 C507 -0.0085 3 0.0 +C235 C293 C505 C508 -0.6410 1 0.0 +C235 C293 C505 C508 0.8225 2 180.0 +C235 C293 C505 C508 -0.0085 3 0.0 +C235 C293 C505 C510 -0.8540 1 0.0 +C235 C293 C505 C510 0.7580 2 180.0 +C235 C293 C505 C510 -0.2510 3 0.0 +C235 C293 C505 H140 -0.0380 3 0.0 +C235 C293 N287 H290 0.1735 3 0.0 +C235 C295 C136 H140 -0.0380 3 0.0 +C235 C295 N309 C296 0.71895 1 0.0 +C235 C295 N309 C296 -0.0619 2 180.0 +C235 C295 N309 C296 0.13195 3 0.0 +C235 C295 N309 H310 0.1735 3 0.0 +C235 N238 C223 H140 0.0000 1 0.0 +C235 N238 C224 C274 -0.3410 1 0.0 +C235 N238 C224 C274 0.0650 2 180.0 +C235 N238 C224 C274 0.1690 3 0.0 +C235 N238 C224 C505 -0.3410 1 0.0 +C235 N238 C224 C505 0.0650 2 180.0 +C235 N238 C224 C505 0.1690 3 0.0 +C235 N238 C224 H140 0.0000 1 0.0 +C235 N238 C242 H140 0.0000 1 0.0 +C235 N238 C283 C271 -1.2555 1 0.0 +C235 N238 C283 C271 0.1050 2 180.0 +C235 N238 C283 C271 -0.1000 3 0.0 +C235 N238 C283 C274 -0.3410 1 0.0 +C235 N238 C283 C274 0.0650 2 180.0 +C235 N238 C283 C274 0.1690 3 0.0 +C235 N238 C283 C505 -0.3410 1 0.0 +C235 N238 C283 C505 0.0650 2 180.0 +C235 N238 C283 C505 0.1690 3 0.0 +C235 N238 C283 H140 0.0000 1 0.0 +C235 N238 C284 C271 -1.2555 1 0.0 +C235 N238 C284 C271 0.1050 2 180.0 +C235 N238 C284 C271 -0.1000 3 0.0 +C235 N238 C284 H140 0.0000 1 0.0 +C235 N239 C245 H140 0.0000 1 0.0 +C235 N239 C246 H140 0.0000 1 0.0 +C235 N239 C285 C271 -1.2555 1 0.0 +C235 N239 C285 C271 0.1050 2 180.0 +C235 N239 C285 C271 -0.1000 3 0.0 +C235 N239 C285 H140 0.0000 1 0.0 +C242 N238 C235 C246 1.1500 1 0.0 +C242 N238 C235 C246 3.0445 2 180.0 +C242 N238 C235 O236 3.0445 2 180.0 +C245 C136 C136 C246 0.6500 1 0.0 +C245 C136 C136 C246 -0.1000 2 180.0 +C245 C136 C136 C246 0.1000 3 0.0 +C245 C136 C136 C285 0.6500 1 0.0 +C245 C136 C136 C285 -0.1000 2 180.0 +C245 C136 C136 C285 0.1000 3 0.0 +C245 C136 C136 H140 0.1500 3 0.0 +C245 N239 C235 C246 1.1500 1 0.0 +C245 N239 C235 C246 3.0445 2 180.0 +C245 N239 C235 C292 1.1500 1 0.0 +C245 N239 C235 C292 3.0445 2 180.0 +C245 N239 C235 C293 1.1500 1 0.0 +C245 N239 C235 C293 3.0445 2 180.0 +C245 N239 C235 C295 1.1500 1 0.0 +C245 N239 C235 C295 3.0445 2 180.0 +C245 N239 C235 O236 3.0445 2 180.0 +C245 N239 C246 H140 0.0000 1 0.0 +C245 N239 C285 C271 -0.8685 1 0.0 +C245 N239 C285 C271 0.6255 2 180.0 +C245 N239 C285 C271 -1.7505 3 0.0 +C245 N239 C285 H140 0.0000 1 0.0 +C246 C136 C136 H140 0.1500 3 0.0 +C246 C235 N238 C283 1.1500 1 0.0 +C246 C235 N238 C283 3.0445 2 180.0 +C246 C235 N238 C284 1.1500 1 0.0 +C246 C235 N238 C284 3.0445 2 180.0 +C246 C235 N238 H241 2.4500 2 180.0 +C246 C235 N239 C246 1.1500 1 0.0 +C246 C235 N239 C246 3.0445 2 180.0 +C246 C235 N239 C285 1.1500 1 0.0 +C246 C235 N239 C285 3.0445 2 180.0 +C246 N239 C235 C292 1.1500 1 0.0 +C246 N239 C235 C292 3.0445 2 180.0 +C246 N239 C235 C293 1.1500 1 0.0 +C246 N239 C235 C293 3.0445 2 180.0 +C246 N239 C235 C295 1.1500 1 0.0 +C246 N239 C235 C295 3.0445 2 180.0 +C246 N239 C235 O236 3.0445 2 180.0 +C246 N239 C245 H140 0.0000 1 0.0 +C267 C136 C224 H140 -0.0380 3 0.0 +C267 C136 C224 N238 -2.7505 1 0.0 +C267 C136 C224 N238 0.7635 2 180.0 +C267 C136 C224 N238 0.0000 3 0.0 +C267 C224 C135 H140 0.0370 3 0.0 +! protonated C-terminal Gly, adm jr. +C267 C223 N238 H241 0.0000 1 0.0 +! +C267 C224 N238 H241 0.0000 1 0.0 +C271 C274 C136 C283 -0.4425 1 0.0 +C271 C274 C136 C283 0.5125 2 180.0 +C271 C274 C136 C283 -0.6465 3 0.0 +C271 C274 C136 C293 -0.4425 1 0.0 +C271 C274 C136 C293 0.5125 2 180.0 +C271 C274 C136 C293 -0.6465 3 0.0 +C271 C274 C136 H140 -0.1125 3 0.0 +C271 C274 C224 H140 0.1500 3 0.0 +C271 C274 C224 N238 -3.9450 1 0.0 +C271 C274 C224 N238 0.3310 2 180.0 +C271 C274 C224 N238 0.4985 3 0.0 +C271 C274 C283 C271 0.7715 1 0.0 +C271 C274 C283 C271 0.3480 2 180.0 +C271 C274 C283 C271 0.0000 3 0.0 +C271 C274 C283 H140 0.1500 3 0.0 +C271 C274 C283 N238 -3.9450 1 0.0 +C271 C274 C283 N238 0.3310 2 180.0 +C271 C274 C283 N238 0.4985 3 0.0 +C271 C274 C293 H140 0.1500 3 0.0 +C271 C274 C293 N287 -3.9450 1 0.0 +C271 C274 C293 N287 0.3310 2 180.0 +C271 C274 C293 N287 0.4985 3 0.0 +C271 C283 C135 H140 -0.0380 3 0.0 +C271 C283 C136 C274 -0.8820 1 0.0 +C271 C283 C136 C274 0.3500 2 180.0 +C271 C283 C136 C274 0.0000 3 0.0 +C271 C283 C136 C308 -0.9855 1 0.0 +C271 C283 C136 C308 0.3850 2 180.0 +C271 C283 C136 C308 0.0000 3 0.0 +C271 C283 C136 C500 -0.2530 1 0.0 +C271 C283 C136 C500 0.4875 2 180.0 +C271 C283 C136 C500 0.0000 3 0.0 +C271 C283 C136 H140 -0.0380 3 0.0 +C271 C283 C137 H140 -0.0380 3 0.0 +C271 C283 C149 H140 -0.0380 3 0.0 +C271 C283 C157 H140 -0.0380 3 0.0 +C271 C283 C157 O154 -2.8965 1 0.0 +C271 C283 C157 O154 0.2025 2 180.0 +C271 C283 C157 O154 0.0000 3 0.0 +C271 C283 C158 H140 -0.0380 3 0.0 +C271 C283 C158 O154 -2.8965 1 0.0 +C271 C283 C158 O154 0.2025 2 180.0 +C271 C283 C158 O154 0.0000 3 0.0 +C271 C283 C206 H140 -0.0380 3 0.0 +C271 C283 C206 S200 -1.6615 1 0.0 +C271 C283 C206 S200 0.2645 2 180.0 +C271 C283 C206 S200 0.0000 3 0.0 +C271 C283 C214 H140 -0.0380 3 0.0 +C271 C283 C214 S203 -1.6615 1 0.0 +C271 C283 C214 S203 0.2645 2 180.0 +C271 C283 C214 S203 0.0000 3 0.0 +C271 C283 C274 H140 -0.0380 3 0.0 +C271 C283 C505 C507 -0.6410 1 0.0 +C271 C283 C505 C507 0.8225 2 180.0 +C271 C283 C505 C507 -0.0085 3 0.0 +C271 C283 C505 C508 -0.6410 1 0.0 +C271 C283 C505 C508 0.8225 2 180.0 +C271 C283 C505 C508 -0.0085 3 0.0 +C271 C283 C505 C510 -0.8540 1 0.0 +C271 C283 C505 C510 0.7580 2 180.0 +C271 C283 C505 C510 -0.2510 3 0.0 +C271 C283 C505 H140 -0.0380 3 0.0 +C271 C283 N238 H241 0.0000 1 0.0 +C271 C284 N238 H241 0.0000 1 0.0 +C271 C285 C136 H140 -0.0380 3 0.0 +C274 C136 C224 H140 0.1500 3 0.0 +C274 C136 C224 N238 0.9935 1 0.0 +C274 C136 C224 N238 0.2285 2 180.0 +C274 C136 C224 N238 0.4100 3 0.0 +C274 C136 C283 H140 0.1500 3 0.0 +C274 C136 C283 N238 0.9935 1 0.0 +C274 C136 C283 N238 0.2285 2 180.0 +C274 C136 C283 N238 0.4100 3 0.0 +C274 C136 C293 H140 0.1500 3 0.0 +C274 C136 C293 N287 0.9935 1 0.0 +C274 C136 C293 N287 0.2285 2 180.0 +C274 C136 C293 N287 0.4100 3 0.0 +C274 C224 C235 N238 0.8895 1 0.0 +C274 C224 C235 N238 0.2095 2 180.0 +C274 C224 C235 N238 -0.0550 3 0.0 +C274 C224 C235 N239 0.8895 1 0.0 +C274 C224 C235 N239 0.2095 2 180.0 +C274 C224 C235 N239 -0.0550 3 0.0 +C274 C224 C235 O236 0.0000 1 0.0 +C274 C224 N238 H241 0.0000 1 0.0 +C274 C283 C271 O272 0.4100 2 180.0 +C274 C283 N238 H241 0.0000 1 0.0 +C274 C293 C235 N238 0.8895 1 0.0 +C274 C293 C235 N238 0.2095 2 180.0 +C274 C293 C235 N238 -0.0550 3 0.0 +C274 C293 C235 N239 0.8895 1 0.0 +C274 C293 C235 N239 0.2095 2 180.0 +C274 C293 C235 N239 -0.0550 3 0.0 +C274 C293 C235 O236 0.0000 1 0.0 +C274 C293 N287 H290 0.1735 3 0.0 +C283 C136 C136 H140 0.1500 3 0.0 +C283 C136 C137 H140 0.1500 3 0.0 +C283 C136 C210 H140 0.1500 3 0.0 +C283 C136 C210 S202 -0.7825 1 0.0 +C283 C136 C210 S202 -0.0045 2 180.0 +C283 C136 C210 S202 -0.2250 3 0.0 +C283 C136 C235 N237 0.7470 1 0.0 +C283 C136 C235 N237 -0.2555 2 180.0 +C283 C136 C235 N237 0.0625 3 0.0 +C283 C136 C235 O236 0.8280 1 0.0 +C283 C136 C235 O236 0.6520 2 180.0 +C283 C136 C235 O236 0.2195 3 0.0 +C283 C136 C267 O268 0.5000 1 0.0 +C283 C136 C267 O268 0.2730 2 180.0 +C283 C136 C267 O268 0.2250 3 0.0 +C283 C136 C267 O269 0.2730 2 180.0 +C283 C136 C274 H140 0.1500 3 0.0 +C283 C136 C308 C307 0.6500 1 0.0 +C283 C136 C308 C307 -0.1000 2 180.0 +C283 C136 C308 C307 0.1000 3 0.0 +C283 C136 C308 H140 0.1500 3 0.0 +C283 C136 C500 C501 0.0000 1 0.0 +C283 C136 C500 C514 -0.3570 1 0.0 +C283 C137 C135 H140 0.1500 3 0.0 +C283 C137 C136 H140 0.1500 3 0.0 +C283 C157 O154 H155 -0.1780 1 0.0 +C283 C157 O154 H155 -0.0870 2 180.0 +C283 C157 O154 H155 0.2460 3 0.0 +C283 C158 C135 H140 0.1500 3 0.0 +C283 C158 O154 H155 -0.1780 1 0.0 +C283 C158 O154 H155 -0.0870 2 180.0 +C283 C158 O154 H155 0.2460 3 0.0 +C283 C206 S200 H204 -0.3795 1 0.0 +C283 C206 S200 H204 -0.1410 2 180.0 +C283 C206 S200 H204 0.3400 3 0.0 +C283 C214 S203 S203 0.9705 1 0.0 +C283 C214 S203 S203 -0.4180 2 180.0 +C283 C214 S203 S203 0.4675 3 0.0 +C283 C274 C271 O272 1.2500 1 0.0 +C283 C274 C271 O272 0.5000 2 180.0 +C283 C274 C271 O272 0.6750 3 0.0 +C283 C505 C507 C508 0.0000 1 0.0 +C283 C505 C507 N511 -0.2800 1 0.0 +C283 C505 C507 N511 -0.3700 2 180.0 +C283 C505 C507 N511 0.1745 3 0.0 +C283 C505 C508 C507 0.0000 1 0.0 +C283 C505 C508 N503 -0.2800 1 0.0 +C283 C505 C508 N503 -0.3700 2 180.0 +C283 C505 C508 N503 0.1745 3 0.0 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0.6500 1 0.0 +C293 C136 C308 C307 -0.1000 2 180.0 +C293 C136 C308 C307 0.1000 3 0.0 +C293 C136 C308 H140 0.1500 3 0.0 +C293 C136 C500 C501 0.0000 1 0.0 +C293 C136 C500 C514 -0.3570 1 0.0 +C293 C137 C135 H140 0.1500 3 0.0 +C293 C137 C136 H140 0.1500 3 0.0 +C293 C157 O154 H155 -0.1780 1 0.0 +C293 C157 O154 H155 -0.0870 2 180.0 +C293 C157 O154 H155 0.2460 3 0.0 +C293 C158 C135 H140 0.1500 3 0.0 +C293 C158 O154 H155 -0.1780 1 0.0 +C293 C158 O154 H155 -0.0870 2 180.0 +C293 C158 O154 H155 0.2460 3 0.0 +C293 C206 S200 H204 -0.3795 1 0.0 +C293 C206 S200 H204 -0.1410 2 180.0 +C293 C206 S200 H204 0.3400 3 0.0 +C293 C214 S203 S203 0.9705 1 0.0 +C293 C214 S203 S203 -0.4180 2 180.0 +C293 C214 S203 S203 0.4675 3 0.0 +C293 C235 N238 H241 2.4500 2 180.0 +C293 C274 C271 O272 1.2500 1 0.0 +C293 C274 C271 O272 0.5000 2 180.0 +C293 C274 C271 O272 0.6750 3 0.0 +C293 C505 C507 C508 0.0000 1 0.0 +C293 C505 C507 N511 -0.2800 1 0.0 +C293 C505 C507 N511 -0.3700 2 180.0 +C293 C505 C507 N511 0.1745 3 0.0 +C293 C505 C508 C507 0.0000 1 0.0 +C293 C505 C508 N503 -0.2800 1 0.0 +C293 C505 C508 N503 -0.3700 2 180.0 +C293 C505 C508 N503 0.1745 3 0.0 +C293 C505 C510 C510 0.0000 1 0.0 +C293 C505 C510 N512 -1.9950 1 0.0 +C293 C505 C510 N512 0.8400 2 180.0 +C293 C505 C510 N512 0.1450 3 0.0 +C295 C136 C136 C296 0.6500 1 0.0 +C295 C136 C136 C296 -0.1000 2 180.0 +C295 C136 C136 C296 0.1000 3 0.0 +C295 C136 C136 H140 0.1500 3 0.0 +C295 C235 N238 H241 2.4500 2 180.0 +C295 N309 C296 H140 0.15085 3 0.0 +C296 C136 C136 H140 0.1500 3 0.0 +C296 N309 C295 H140 0.15085 3 0.0 +C302 N303 C307 C308 0.9145 1 0.0 +C302 N303 C307 C308 0.1215 2 180.0 +C302 N303 C307 C308 -0.2490 3 0.0 +C302 N303 C307 H140 0.0885 3 0.0 +C307 C308 C136 H140 0.1500 3 0.0 +C307 N303 C302 N300 3.9680 2 180.0 +C308 C136 C224 H140 0.1500 3 0.0 +C308 C136 C224 N238 0.0515 1 0.0 +C308 C136 C224 N238 0.3265 2 180.0 +C308 C136 C224 N238 0.2815 3 0.0 +C308 C136 C283 H140 0.1500 3 0.0 +C308 C136 C283 N238 0.0515 1 0.0 +C308 C136 C283 N238 0.3265 2 180.0 +C308 C136 C283 N238 0.2815 3 0.0 +C308 C136 C293 H140 0.1500 3 0.0 +C308 C136 C293 N287 0.0515 1 0.0 +C308 C136 C293 N287 0.3265 2 180.0 +C308 C136 C293 N287 0.2815 3 0.0 +C308 C307 N303 H304 -0.0950 1 0.0 +C308 C307 N303 H304 -0.2085 2 180.0 +C308 C307 N303 H304 0.2090 3 0.0 +C500 C136 C224 H140 0.2310 3 0.0 +C500 C136 C224 N238 -0.2940 1 0.0 +C500 C136 C224 N238 0.5100 2 180.0 +C500 C136 C224 N238 0.3325 3 0.0 +C500 C136 C283 H140 0.2310 3 0.0 +C500 C136 C283 N238 -0.2940 1 0.0 +C500 C136 C283 N238 0.5100 2 180.0 +C500 C136 C283 N238 0.3325 3 0.0 +C500 C136 C293 H140 0.2310 3 0.0 +C500 C136 C293 N287 -0.2940 1 0.0 +C500 C136 C293 N287 0.5100 2 180.0 +C500 C136 C293 N287 0.3325 3 0.0 +C500 C501 C145 H146 3.5000 2 180.0 +C501 C500 C136 H140 0.0000 1 0.0 +C501 C502 C145 H146 3.6250 2 180.0 +C502 C501 C145 H146 3.5000 2 180.0 +C502 C501 C500 C514 1.6750 2 180.0 +C502 N503 C514 H146 1.5000 2 180.0 +C505 C224 C235 N238 0.8895 1 0.0 +C505 C224 C235 N238 0.2095 2 180.0 +C505 C224 C235 N238 -0.0550 3 0.0 +C505 C224 C235 N239 0.8895 1 0.0 +C505 C224 C235 N239 0.2095 2 180.0 +C505 C224 C235 N239 -0.0550 3 0.0 +C505 C224 C235 O236 0.0000 1 0.0 +C505 C224 N238 H241 0.0000 1 0.0 +C505 C283 C271 O272 0.4100 2 180.0 +C505 C283 N238 H241 0.0000 1 0.0 +C505 C293 C235 N238 0.8895 1 0.0 +C505 C293 C235 N238 0.2095 2 180.0 +C505 C293 C235 N238 -0.0550 3 0.0 +C505 C293 C235 O236 0.0000 1 0.0 +C505 C293 N287 H290 0.1735 3 0.0 +C505 C508 C507 H146 5.3750 2 180.0 +C505 C508 C507 N511 5.3750 2 180.0 +C505 C508 N503 C506 1.4000 2 180.0 +C505 C508 N503 H504 1.4000 2 180.0 +C505 C510 N512 C509 1.4000 2 180.0 +C505 C510 N512 H513 1.4000 2 180.0 +C506 N503 C508 C507 1.4000 2 180.0 +C506 N503 C508 H146 2.5000 2 180.0 +C506 N511 C507 C508 2.4000 2 180.0 +C506 N511 C507 H146 2.4000 2 180.0 +C507 C505 C224 H140 0.2310 3 0.0 +C507 C505 C224 N238 -0.2710 1 0.0 +C507 C505 C224 N238 0.2175 2 180.0 +C507 C505 C224 N238 0.0000 3 0.0 +C507 C505 C283 H140 0.2310 3 0.0 +C507 C505 C283 N238 -0.2710 1 0.0 +C507 C505 C283 N238 0.2175 2 180.0 +C507 C505 C283 N238 0.0000 3 0.0 +C507 C505 C293 H140 0.2310 3 0.0 +C507 C505 C293 N287 -0.2710 1 0.0 +C507 C505 C293 N287 0.2175 2 180.0 +C507 C505 C293 N287 0.0000 3 0.0 +C507 C508 C505 H140 0.0000 1 0.0 +C507 C508 N503 H504 1.4000 2 180.0 +C507 N511 C506 H146 5.0000 2 180.0 +C507 N511 C506 N503 5.0000 2 180.0 +C508 C505 C224 H140 0.2310 3 0.0 +C508 C505 C224 N238 -0.2710 1 0.0 +C508 C505 C224 N238 0.2175 2 180.0 +C508 C505 C224 N238 0.0000 3 0.0 +C508 C505 C283 H140 0.2310 3 0.0 +C508 C505 C283 N238 -0.2710 1 0.0 +C508 C505 C283 N238 0.2175 2 180.0 +C508 C505 C283 N238 0.0000 3 0.0 +C508 C505 C293 H140 0.2310 3 0.0 +C508 C505 C293 N287 -0.2710 1 0.0 +C508 C505 C293 N287 0.2175 2 180.0 +C508 C505 C293 N287 0.0000 3 0.0 +C508 C507 C505 H140 0.0000 1 0.0 +C508 N503 C506 H146 2.3250 2 180.0 +C508 N503 C506 N511 2.3250 2 180.0 +C509 N512 C510 C510 1.4000 2 180.0 +C509 N512 C510 H146 2.5000 2 180.0 +C510 C505 C224 H140 0.2310 3 0.0 +C510 C505 C224 N238 -1.5190 1 0.0 +C510 C505 C224 N238 0.2095 2 180.0 +C510 C505 C224 N238 0.0000 3 0.0 +C510 C505 C283 H140 0.2310 3 0.0 +C510 C505 C283 N238 -1.5190 1 0.0 +C510 C505 C283 N238 0.2095 2 180.0 +C510 C505 C283 N238 0.0000 3 0.0 +C510 C505 C293 H140 0.2310 3 0.0 +C510 C505 C293 N287 -1.5190 1 0.0 +C510 C505 C293 N287 0.2095 2 180.0 +C510 C505 C293 N287 0.0000 3 0.0 +C510 C510 C505 H140 0.0000 1 0.0 +C510 C510 N512 H513 1.4000 2 180.0 +C510 N512 C509 H146 2.3250 2 180.0 +C510 N512 C509 N512 2.3250 2 180.0 +C514 C500 C136 H140 -0.2400 3 0.0 +H140 C135 C136 H140 0.1500 3 0.0 +H140 C135 C137 H140 0.1500 3 0.0 +H140 C135 C158 H140 0.1500 3 0.0 +H140 C135 C158 O154 0.2340 3 0.0 +H140 C135 C224 H140 0.1500 3 0.0 +H140 C135 C224 N238 0.2320 3 0.0 +H140 C135 C235 N238 0.0000 1 0.0 +H140 C135 C235 N239 0.0000 1 0.0 +H140 C135 C235 O236 0.0000 1 0.0 +H140 C135 C283 H140 0.1500 3 0.0 +H140 C135 C283 N238 0.2320 3 0.0 +H140 C135 C293 H140 0.1500 3 0.0 +H140 C135 C293 N287 0.2320 3 0.0 +H140 C136 C136 H140 0.1500 3 0.0 +H140 C136 C137 H140 0.1500 3 0.0 +H140 C136 C210 H140 0.1500 3 0.0 +H140 C136 C210 S202 0.2260 3 0.0 +H140 C136 C224 H140 0.1500 3 0.0 +H140 C136 C224 N238 0.2320 3 0.0 +H140 C136 C235 N237 0.0000 1 0.0 +H140 C136 C235 O236 0.0000 1 0.0 +H140 C136 C245 H140 0.1500 3 0.0 +H140 C136 C245 N239 0.2320 3 0.0 +H140 C136 C246 H140 0.1500 3 0.0 +H140 C136 C246 N239 0.2320 3 0.0 +H140 C136 C267 O268 0.0000 1 0.0 +H140 C136 C267 O269 0.0000 1 0.0 +H140 C136 C274 H140 0.1500 3 0.0 +H140 C136 C283 H140 0.1500 3 0.0 +H140 C136 C283 N238 0.2320 3 0.0 +H140 C136 C285 H140 0.1500 3 0.0 +H140 C136 C285 N239 0.2320 3 0.0 +H140 C136 C292 H140 0.1500 3 0.0 +H140 C136 C292 N287 0.1920 3 0.0 +H140 C136 C293 H140 0.1500 3 0.0 +H140 C136 C293 N287 0.2320 3 0.0 +H140 C136 C295 H140 0.1500 3 0.0 +H140 C136 C295 N309 0.1920 3 0.0 +H140 C136 C296 H140 0.1500 3 0.0 +H140 C136 C296 N309 0.1920 3 0.0 +H140 C136 C308 H140 0.1500 3 0.0 +H140 C137 C224 H140 0.1500 3 0.0 +H140 C137 C224 N238 0.2320 3 0.0 +H140 C137 C283 H140 0.1500 3 0.0 +H140 C137 C283 N238 0.2320 3 0.0 +H140 C137 C293 H140 0.1500 3 0.0 +H140 C137 C293 N287 0.2320 3 0.0 +H140 C149 C224 H140 0.1500 3 0.0 +H140 C149 C224 N238 0.2320 3 0.0 +H140 C149 C283 H140 0.1500 3 0.0 +H140 C149 C283 N238 0.2320 3 0.0 +H140 C149 C293 H140 0.1500 3 0.0 +H140 C149 C293 N287 0.2320 3 0.0 +H140 C157 C224 H140 0.1500 3 0.0 +H140 C157 C224 N238 0.2320 3 0.0 +H140 C157 C283 H140 0.1500 3 0.0 +H140 C157 C283 N238 0.2320 3 0.0 +H140 C157 C293 H140 0.1500 3 0.0 +H140 C157 C293 N287 0.2320 3 0.0 +H140 C157 O154 H155 0.1762 3 0.0 +H140 C158 C224 H140 0.1500 3 0.0 +H140 C158 C224 N238 0.2320 3 0.0 +H140 C158 C283 H140 0.1500 3 0.0 +H140 C158 C283 N238 0.2320 3 0.0 +H140 C158 C293 H140 0.1500 3 0.0 +H140 C158 C293 N287 0.2320 3 0.0 +H140 C158 O154 H155 0.1762 3 0.0 +H140 C206 C224 H140 0.1500 3 0.0 +H140 C206 C224 N238 0.2320 3 0.0 +H140 C206 C283 H140 0.1500 3 0.0 +H140 C206 C283 N238 0.2320 3 0.0 +H140 C206 C293 H140 0.1500 3 0.0 +H140 C206 C293 N287 0.2320 3 0.0 +H140 C206 S200 H204 0.2400 3 0.0 +H140 C214 C224 H140 0.1500 3 0.0 +H140 C214 C224 N238 0.2320 3 0.0 +H140 C214 C283 H140 0.1500 3 0.0 +H140 C214 C283 N238 0.2320 3 0.0 +H140 C214 C293 H140 0.1500 3 0.0 +H140 C214 C293 N287 0.2320 3 0.0 +H140 C214 S203 S203 0.2790 3 0.0 +H140 C223 C235 N238 0.0000 1 0.0 +H140 C223 C235 N239 0.0000 1 0.0 +H140 C223 C235 O236 0.0000 1 0.0 +H140 C223 N238 H241 0.0000 1 0.0 +H140 C224 C157 O154 0.2340 3 0.0 +H140 C224 C158 O154 0.2340 3 0.0 +H140 C224 C206 S200 0.2260 3 0.0 +H140 C224 C214 S203 0.2260 3 0.0 +H140 C224 C235 N238 0.0000 1 0.0 +H140 C224 C235 N239 0.0000 1 0.0 +H140 C224 C235 O236 0.0000 1 0.0 +! protonated C-terminal Gly, adm jr. +H140 C223 C267 O268 0.0000 1 0.0 +H140 C223 C267 O269 0.0000 1 0.0 +! +H140 C224 C267 O268 0.0000 1 0.0 +H140 C224 C267 O269 0.0000 1 0.0 +H140 C224 C274 H140 0.1500 3 0.0 +H140 C224 C505 H140 0.1500 3 0.0 +H140 C224 N238 H241 0.0000 1 0.0 +H140 C242 N238 H241 0.0000 1 0.0 +H140 C246 C235 N238 0.0000 1 0.0 +H140 C246 C235 N239 0.0000 1 0.0 +H140 C246 C235 O236 0.0000 1 0.0 +H140 C274 C224 N238 0.2320 3 0.0 +H140 C274 C271 O272 0.0000 1 0.0 +H140 C274 C283 H140 0.1500 3 0.0 +H140 C274 C283 N238 0.2320 3 0.0 +H140 C274 C293 H140 0.1500 3 0.0 +H140 C274 C293 N287 0.2320 3 0.0 +H140 C283 C157 O154 0.2340 3 0.0 +H140 C283 C158 O154 0.2340 3 0.0 +H140 C283 C206 S200 0.2260 3 0.0 +H140 C283 C214 S203 0.2260 3 0.0 +H140 C283 C271 O272 0.0000 1 0.0 +H140 C283 C505 H140 0.1500 3 0.0 +H140 C283 N238 H241 0.0000 1 0.0 +H140 C284 C271 O272 0.0000 1 0.0 +H140 C284 N238 H241 0.0000 1 0.0 +H140 C285 C271 O272 0.0000 1 0.0 +H140 C292 C235 N238 0.0000 1 0.0 +H140 C292 C235 O236 0.0000 1 0.0 +H140 C292 N287 H290 0.1305 3 0.0 +H140 C293 C157 O154 0.2340 3 0.0 +H140 C293 C158 O154 0.2340 3 0.0 +H140 C293 C206 S200 0.2260 3 0.0 +H140 C293 C214 S203 0.2260 3 0.0 +H140 C293 C235 N238 0.0000 1 0.0 +H140 C293 C235 N239 0.0000 1 0.0 +H140 C293 C235 O236 0.0000 1 0.0 +H140 C293 C505 H140 0.1500 3 0.0 +H140 C293 N287 H290 0.1305 3 0.0 +H140 C295 C235 N238 0.0000 1 0.0 +H140 C295 C235 N239 0.0000 1 0.0 +H140 C295 C235 O236 0.0000 1 0.0 +H140 C295 N309 H310 0.1305 3 0.0 +H140 C296 N309 H310 0.1920 3 0.0 +H140 C307 C308 H140 0.1500 3 0.0 +H140 C307 N303 H304 0.0000 1 0.0 +H140 C308 C307 N303 -0.2910 3 0.0 +H140 C505 C224 N238 0.2320 3 0.0 +H140 C505 C283 N238 0.2320 3 0.0 +H140 C505 C293 N287 0.2320 3 0.0 +H140 C505 C507 N511 0.2095 3 0.0 +H140 C505 C508 N503 0.2095 3 0.0 +H140 C505 C510 N512 0.2095 3 0.0 +H146 C508 C507 N511 5.3750 2 180.0 +H146 C508 N503 H504 2.5000 2 180.0 +H146 C510 N512 H513 2.5000 2 180.0 +H240 N237 C235 O236 2.4500 2 180.0 +H241 N238 C235 O236 2.4500 2 180.0 +H270 O268 C267 O269 2.7500 2 180.0 +H301 N300 C302 N300 1.9500 2 180.0 +H301 N300 C302 N303 1.9500 2 180.0 +H304 N303 C302 N300 1.9500 2 180.0 +H504 N503 C506 N511 2.3250 2 180.0 +H513 N512 C509 N512 2.3250 2 180.0 +N238 C223 C235 N238 0.9050 1 0.0 +N238 C223 C235 N238 1.0775 2 180.0 +N238 C223 C235 N238 -0.2350 3 0.0 +N238 C223 C235 N239 0.9050 1 0.0 +N238 C223 C235 N239 1.0775 2 180.0 +N238 C223 C235 N239 -0.2350 3 0.0 +N238 C223 C235 O236 0.0000 1 0.0 +N238 C224 C157 O154 3.1290 1 0.0 +N238 C224 C157 O154 -0.5185 2 180.0 +N238 C224 C157 O154 0.6835 3 0.0 +N238 C224 C158 O154 3.1290 1 0.0 +N238 C224 C158 O154 -0.5185 2 180.0 +N238 C224 C158 O154 0.6835 3 0.0 +N238 C224 C206 S200 1.0275 1 0.0 +N238 C224 C206 S200 0.2645 2 180.0 +N238 C224 C206 S200 0.2720 3 0.0 +N238 C224 C214 S203 1.0275 1 0.0 +N238 C224 C214 S203 0.2645 2 180.0 +N238 C224 C214 S203 0.2720 3 0.0 +N238 C224 C235 N238 0.9050 1 0.0 +N238 C224 C235 N238 1.0775 2 180.0 +N238 C224 C235 N238 -0.2350 3 0.0 +N238 C224 C235 N239 0.9050 1 0.0 +N238 C224 C235 N239 1.0775 2 180.0 +N238 C224 C235 N239 -0.2350 3 0.0 +N238 C224 C235 O236 0.0000 1 0.0 +! protonated C-terminal Gly, adm jr. +N238 C223 C267 O268 2.6300 1 0.0 +N238 C223 C267 O268 0.4100 2 180.0 +N238 C223 C267 O268 0.0000 3 0.0 +! +N238 C224 C267 O268 2.6300 1 0.0 +N238 C224 C267 O268 0.4100 2 180.0 +N238 C224 C267 O268 0.0000 3 0.0 +! protonated C-terminal Gly, adm jr. +N238 C223 C267 O269 0.0000 1 0.0 +! +N238 C224 C267 O269 0.0000 1 0.0 +N238 C235 C246 N239 -0.4700 1 0.0 +N238 C235 C246 N239 1.3775 2 180.0 +N238 C235 C246 N239 -1.3350 3 0.0 +N238 C235 C292 N287 0.9050 1 0.0 +N238 C235 C292 N287 1.0775 2 180.0 +N238 C235 C292 N287 -0.2350 3 0.0 +N238 C235 C293 N287 0.9050 1 0.0 +N238 C235 C293 N287 1.0775 2 180.0 +N238 C235 C293 N287 -0.2350 3 0.0 +N238 C235 C295 N309 -0.4700 1 0.0 +N238 C235 C295 N309 1.3775 2 180.0 +N238 C235 C295 N309 -1.3350 3 0.0 +N238 C283 C157 O154 3.1290 1 0.0 +N238 C283 C157 O154 -0.5185 2 180.0 +N238 C283 C157 O154 0.6835 3 0.0 +N238 C283 C158 O154 3.1290 1 0.0 +N238 C283 C158 O154 -0.5185 2 180.0 +N238 C283 C158 O154 0.6835 3 0.0 +N238 C283 C206 S200 1.0275 1 0.0 +N238 C283 C206 S200 0.2645 2 180.0 +N238 C283 C206 S200 0.2720 3 0.0 +N238 C283 C214 S203 1.0275 1 0.0 +N238 C283 C214 S203 0.2645 2 180.0 +N238 C283 C214 S203 0.2720 3 0.0 +N238 C283 C271 O272 0.4100 2 180.0 +N238 C284 C271 O272 0.4100 2 180.0 +N239 C235 C246 N239 -0.4700 1 0.0 +N239 C235 C246 N239 1.3775 2 180.0 +N239 C235 C246 N239 -1.3350 3 0.0 +N239 C235 C293 N287 0.9050 1 0.0 +N239 C235 C293 N287 1.0775 2 180.0 +N239 C235 C293 N287 -0.2350 3 0.0 +N239 C235 C295 N309 -0.4700 1 0.0 +N239 C235 C295 N309 1.3775 2 180.0 +N239 C235 C295 N309 -1.3350 3 0.0 +N239 C246 C235 O236 0.0000 1 0.0 +N239 C285 C271 O272 0.4100 2 180.0 +N287 C292 C235 O236 0.0000 1 0.0 +N287 C293 C157 O154 3.1290 1 0.0 +N287 C293 C157 O154 -0.5185 2 180.0 +N287 C293 C157 O154 0.6835 3 0.0 +N287 C293 C158 O154 3.1290 1 0.0 +N287 C293 C158 O154 -0.5185 2 180.0 +N287 C293 C158 O154 0.6835 3 0.0 +N287 C293 C206 S200 1.0275 1 0.0 +N287 C293 C206 S200 0.2645 2 180.0 +N287 C293 C206 S200 0.2720 3 0.0 +N287 C293 C214 S203 1.0275 1 0.0 +N287 C293 C214 S203 0.2645 2 180.0 +N287 C293 C214 S203 0.2720 3 0.0 +N287 C293 C235 O236 0.0000 1 0.0 +N309 C295 C235 O236 0.0000 1 0.0 +N503 C508 C507 N511 5.3750 2 180.0 +C267 C136 C293 N287 -2.7505 1 0.0 +C267 C136 C293 N287 0.7635 2 180.0 +C267 C136 C293 N287 0.0000 3 0.0 +C235 C293 C136 C267 0.2990 1 0.0 +C235 C293 C136 C267 0.7790 2 180.0 +C235 C293 C136 C267 0.1275 3 0.0 +C267 C136 C283 N238 -2.7505 1 0.0 +C267 C136 C283 N238 0.7635 2 180.0 +C267 C136 C283 N238 0.0000 3 0.0 +C267 C136 C283 C271 0.2990 1 0.0 +C267 C136 C283 C271 0.7790 2 180.0 +C267 C136 C283 C271 0.1275 3 0.0 +IMPROPER +C136 C500 C501 C514 1.1000 2 180.0 +C136 C500 C514 C501 1.1000 2 180.0 +C145 C502 C501 N503 1.1000 2 180.0 +C145 C502 N503 C501 1.1000 2 180.0 +C149 C145 C145 C145 1.1000 2 180.0 +C245 N238 C235 C285 2.5000 2 180.0 +C245 N238 C285 C235 2.5000 2 180.0 +C245 N239 C235 C246 2.5000 2 180.0 +C245 N239 C235 C285 2.5000 2 180.0 +C245 N239 C246 C235 2.5000 2 180.0 +C245 N239 C285 C235 2.5000 2 180.0 +C502 C501 C145 C500 1.1000 2 180.0 +C502 C501 C500 C145 1.1000 2 180.0 +C505 C507 C508 N511 1.1000 2 180.0 +C505 C507 N511 C508 1.1000 2 180.0 +C505 C508 C507 N503 1.1000 2 180.0 +C505 C508 N503 C507 1.1000 2 180.0 +C505 C510 C510 N512 1.1000 2 180.0 +C505 C510 N512 C510 1.1000 2 180.0 +H146 C145 C145 C145 1.1000 2 180.0 +H146 C145 C166 C145 1.1000 2 180.0 +H146 C145 C145 C166 1.1000 2 180.0 +H146 C145 C145 C501 1.1000 2 180.0 +H146 C145 C501 C145 1.1000 2 180.0 +H146 C145 C145 C502 1.1000 2 180.0 +H146 C145 C502 C145 1.1000 2 180.0 +H146 C506 N503 N511 1.1000 2 180.0 +H146 C506 N511 N503 1.1000 2 180.0 +H146 C507 C508 N511 1.1000 2 180.0 +H146 C507 N511 C508 1.1000 2 180.0 +H146 C508 C507 N503 1.1000 2 180.0 +H146 C508 N503 C507 1.1000 2 180.0 +H146 C509 N512 N512 1.1000 2 180.0 +H146 C510 C510 N512 1.1000 2 180.0 +H146 C510 N512 C510 1.1000 2 180.0 +H146 C514 C500 N503 1.1000 2 180.0 +H146 C514 N503 C500 1.1000 2 180.0 +H240 N237 C235 H240 2.5000 2 180.0 +H240 N237 H240 C235 2.5000 2 180.0 +H241 N238 C223 C235 2.5000 2 180.0 +H241 N238 C224 C235 2.5000 2 180.0 +H241 N238 C235 C223 2.5000 2 180.0 +H241 N238 C235 C224 2.5000 2 180.0 +H241 N238 C235 C242 2.5000 2 180.0 +H241 N238 C235 C283 2.5000 2 180.0 +H241 N238 C235 C284 2.5000 2 180.0 +H241 N238 C242 C235 2.5000 2 180.0 +H241 N238 C283 C235 2.5000 2 180.0 +H241 N238 C284 C235 2.5000 2 180.0 +H301 N300 C302 H301 2.5000 2 180.0 +H301 N300 H301 C302 2.5000 2 180.0 +H304 N303 C302 C307 2.5000 2 180.0 +H304 N303 C307 C302 2.5000 2 180.0 +H504 N503 C502 C514 2.5000 2 180.0 +H504 N503 C506 C508 2.5000 2 180.0 +H504 N503 C508 C506 2.5000 2 180.0 +H504 N503 C514 C502 2.5000 2 180.0 +H513 N512 C509 C510 2.5000 2 180.0 +H513 N512 C510 C509 2.5000 2 180.0 +N300 C302 N300 N303 10.5000 2 180.0 +N300 C302 N303 N300 10.5000 2 180.0 +O167 C166 C145 C145 1.1000 2 180.0 +O236 C235 C135 N239 10.5 2 180.0 +O236 C235 C135 N238 10.5000 2 180.0 +O236 C235 C136 N237 10.5000 2 180.0 +O236 C235 C223 N238 10.5000 2 180.0 +O236 C235 C223 N239 10.5000 2 180.0 +O236 C235 C224 N238 10.5000 2 180.0 +O236 C235 C224 N239 10.5000 2 180.0 +O236 C235 C246 N238 10.5000 2 180.0 +O236 C235 C246 N239 10.5000 2 180.0 +O236 C235 C292 N238 10.5000 2 180.0 +O236 C235 C293 N238 10.5000 2 180.0 +O236 C235 C293 N239 10.5000 2 180.0 +O236 C235 C295 N238 10.5000 2 180.0 +O236 C235 C295 N239 10.5000 2 180.0 +O236 C235 N237 C136 10.5000 2 180.0 +O236 C235 N238 C135 10.5000 2 180.0 +O236 C235 N238 C223 10.5000 2 180.0 +O236 C235 N238 C224 10.5000 2 180.0 +O236 C235 N238 C246 10.5000 2 180.0 +O236 C235 N238 C292 10.5000 2 180.0 +O236 C235 N238 C293 10.5000 2 180.0 +O236 C235 N238 C295 10.5000 2 180.0 +O236 C235 N239 C135 10.5000 2 180.0 +O236 C235 N239 C223 10.5000 2 180.0 +O236 C235 N239 C224 10.5000 2 180.0 +O236 C235 N239 C246 10.5000 2 180.0 +O236 C235 N239 C293 10.5000 2 180.0 +O236 C235 N239 C295 10.5000 2 180.0 +O269 C267 C136 O268 10.5000 2 180.0 +O269 C267 O268 C136 10.5000 2 180.0 +O269 C267 C224 O268 10.5000 2 180.0 +O269 C267 O268 C224 10.5000 2 180.0 +O272 C271 C274 O272 10.5000 2 180.0 +O272 C271 C283 O272 10.5000 2 180.0 +O272 C271 C284 O272 10.5000 2 180.0 +O272 C271 C285 O272 10.5000 2 180.0 +O272 C271 O272 C274 10.5000 2 180.0 +O272 C271 O272 C283 10.5000 2 180.0 +O272 C271 O272 C284 10.5000 2 180.0 +O272 C271 O272 C285 10.5000 2 180.0 +O268 C267 C136 O269 10.5 2 180.0 +! Neutral C termini, adm jr +O268 C267 C223 O269 10.5 2 180.0 ! Gly +O268 C267 C224 O269 10.5 2 180.0 +! + +NONBONDED nbxmod 5 atom cdiel switch vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 11.5 eps 1.0 e14fac 0.5 wmin 1.5 - +geom !assigns use of OPLS combining rules + +C135 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C136 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C137 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C145 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C149 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C157 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C158 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C166 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C206 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C209 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C210 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C214 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C223 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C224 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C235 0.00 -0.105000 2.1046163 0.00 -0.052500 2.1046163 +C242 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C245 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C246 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C267 0.00 -0.105000 2.1046163 0.00 -0.052500 2.1046163 +C271 0.00 -0.105000 2.1046163 0.00 -0.052500 2.1046163 +C274 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C283 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C284 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C285 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C292 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C293 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C295 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C296 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C302 0.00 -0.050000 1.2627698 0.00 -0.025000 1.2627698 +C307 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C308 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C500 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C501 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C502 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C505 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C506 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C507 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C508 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C509 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C510 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C514 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +H140 0.00 -0.030000 1.4030776 0.00 -0.015000 1.4030776 +H146 0.00 -0.030000 1.3581791 0.00 -0.015000 1.3581791 +H155 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H168 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H204 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H240 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H241 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H270 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H290 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H301 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H304 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H310 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H504 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H513 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +N237 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N238 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N239 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N287 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N300 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N303 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N309 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N503 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N511 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N512 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +O154 0.00 -0.170000 1.7510408 0.00 -0.085000 1.7510408 +O167 0.00 -0.170000 1.7229792 0.00 -0.085000 1.7229792 +O236 0.00 -0.210000 1.6612438 0.00 -0.105000 1.6612438 +O268 0.00 -0.170000 1.6836931 0.00 -0.085000 1.6836931 +O269 0.00 -0.210000 1.6612438 0.00 -0.105000 1.6612438 +O272 0.00 -0.210000 1.6612438 0.00 -0.105000 1.6612438 +S200 0.00 -0.425000 2.0204317 0.00 -0.212500 2.0204317 +S202 0.00 -0.355000 2.0204317 0.00 -0.177500 2.0204317 +S203 0.00 -0.355000 2.0204317 0.00 -0.177500 2.0204317 +OT 0.00 -0.152100 1.768200 0.00 -0.152100 1.768200 +HT 0.00 -0.046000 0.224500 0.00 -0.046000 0.22450 +SOD 0.00 -0.000500 2.9969737 0.00 -0.000500 2.9969737 +CLA 0.00 -0.710000 2.2561487 0.00 -0.710000 2.2561487 + +HBOND CUTHB 0.5 + + +END diff --git a/charmm/toppar/non_charmm/par_opls_ligand.inp b/charmm/toppar/non_charmm/par_opls_ligand.inp new file mode 100644 index 00000000..433020db --- /dev/null +++ b/charmm/toppar/non_charmm/par_opls_ligand.inp @@ -0,0 +1,2365 @@ +* Parameter File for OPLS for proteins * +* + +!README for CHARMM topology/parameter files for OPLS-AA (opls.rtf, opls.prm) +!** reference for OPLS-AA for proteins: +!** Jorgensen, W.L. et al., J. Am. Chem. Soc. 118:11225-11236 (1996) +!and see additional reference below +! +!Proper usage of these files requires CHARMM software version c28b1 or greater. +!If you are presently using c28b1, please check that you have the latest release, +!as not all of the pertinant code was included in the initial release, but was +!included in a later bugfix. Compilation of CHARMM requires that the OPLS +!keyword be included in pref.dat at compile time. The relevant code has added +!the ability to combine Lennard-Jones radii with a geometric average, and use +!V2-Fourier terms for improper dihedrals. The CHARMM program compiled with the +!OPLS option in pref.dat can still use all other previously released topology and +!parameter files (CHARMM22, CHARMM19, etc.). +! +!Atom and residue names in the OPLS-AA topology file agree with that in CHARMM22. +!Consequently, any CHARMM script that reads CHARMM22 topology and parameter files +!can be converted to using OPLS-AA by adjusting the appropriate file OPEN +!statements. The atom types have the OPLS atom type embedded within them for +!easy cross-reference. For example, type H140 in opls.rtf and opls.prm is +!type 140 the OPLS-AA parameter files available from Prof. Jorgensen. +! +!The topology and parameter files here include only the protein portion of the +!OPLS-AA force field. User-defined topology and parameter files are required for +!other functionalities. +! +!While the OPLS-AA topology and parameter files are compatible with all +!functionality within CHARMM that is also compatible with CHARMM22, minimizations +!and simulations with a distance-dependent dielectric (RDIE) is not recommended +!as collapse of atoms with hydrogens on heteroatoms is possible, causing +!unreasonable structures and energies. Also, there is no current +!optimzied parameter set for the linearized form of the Generalized Born equation +!as currently implemented in CHARMM. +! +!Any questions, email priced@scripps.edu +! +!**** These files were created in the laboratory of: +!**** Prof. C.L. Brooks III +!**** Dept. of Mol. Biol. +!**** The Scripps Research Institute +! +!**** OPLS-AA is developed in the laboratory of: +!**** Prof. W.L. Jorgensen +!**** Dept. of Chemistry +!**** Yale University +! +!Additional References +! +!OPLS All-Atom Model for Amines: Resolution of the Amine Hydration +!Problem. R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc., 121, +!4827-4836 (1999). +! +!Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro +!Compounds with the OPLS-AA Force Field. M. L. P. Price, D. Ostrovsky, +!and W. L. Jorgensen, J. Comput. Chem., 22, 1340-1352 (2001). +! +!Evaluation and Reparameterization of the OPLS-AA Force Field for +!Proteins via Comparison with Accurate Quantum Chemical Calculations on +!Peptides. G. Kaminski, R. A. Friesner, J. Tirado-Rives and W. L. +!Jorgensen, J. Phys. Chem. B, 105, 6474-6487 (2001). +! +!Perfluoroalkanes: Conformational Analysis and Liquid-State Properties +!from Ab Initio and Monte Carlo Calculations. E. K. Watkins and +!W. L. Jorgensen, J. Phys. Chem. A, 105, 4118-4125 (2001). +! +!Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic +!Charges.Blagovif, M. U.; Jorgensen, W. L., J. Comput. Chem. 2004, 25, +!0000-0000. Submitted. +! +!A five-site model for liquid water and the reproduction of the density +!anomaly by rigid, non-polarizable models. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 112, 8910-8922 (2000). +! +!Diffusion constant of the TIP5P model of liquid water. M. W. Mahoney +!and W. L. Jorgensen, J. Chem. Phys., 114, 363-366 (2001). +! +!Rapid Estimation of Electronic Degrees of Freedom in Monte Carlo +!Calculations for Polarizable Models of Liquid Water. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 114, 9337-9349 (2001). +! +!Quantum, intramolecular flexibility, and polarizability effects on the +!reproduction of the density anomaly of liquid water by simple +!potential functions. M. W. Mahoney and W. L. Jorgensen, +!J. Chem. Phys., 115, 10758-10768 (2001). +! + +BOND +!ligand +C145 C148 317.00 1.510 +C246 C149 268.00 1.529 +C246 C158 268.00 1.529 +C158 C158 268.00 1.529 +C247 O248 570.00 1.229 +C247 N239 490.00 1.335 +N239 C149 337.00 1.449 +C145 C729 469.00 1.400 +C145 C221 469.00 1.400 +C145 C199 469.00 1.400 +C145 C263 469.00 1.400 +C145 C735 469.00 1.400 +C221 C218 317.00 1.510 +C145 C149 317.00 1.510 +C218 H140 340.00 1.090 +C148 H140 340.00 1.090 +C218 O154 320.00 1.410 +C199 O179 450.00 1.364 +O179 C181 320.00 1.410 +C181 H185 340.00 1.090 +C735 S734 250.00 1.740 +S734 H204 274.00 1.336 +C263 Cl 300.00 1.725 +C729 Br 300.00 1.870 +!water +OT HT 450.0 0.9572 +HT HT 0.0 1.5139 +S203 S203 166.0 2.038 +!! below are automatically generated by pepz2rtf +C135 C136 268.00 1.529 +C135 C137 268.00 1.529 +C135 C158 268.00 1.529 +C135 C224 268.00 1.529 +C135 C235 317.00 1.522 +C135 C283 268.00 1.529 +C135 C293 268.00 1.529 +C135 H140 340.00 1.090 +C136 C136 268.00 1.529 +C136 C137 268.00 1.529 +C136 C210 268.00 1.529 +C136 C224 268.00 1.529 +C136 C235 317.00 1.522 +C136 C245 268.00 1.529 +C136 C246 268.00 1.529 +C136 C267 317.00 1.522 +C136 C274 268.00 1.529 +C136 C283 268.00 1.529 +C136 C285 268.00 1.529 +C136 C292 268.00 1.529 +C136 C293 268.00 1.529 +C136 C295 268.00 1.529 +C136 C296 268.00 1.529 +C136 C308 268.00 1.529 +C136 C500 317.00 1.495 +C136 H140 340.00 1.090 +C137 C224 268.00 1.529 +C137 C283 268.00 1.529 +C137 C293 268.00 1.529 +C137 H140 340.00 1.090 +C145 C145 469.00 1.400 +C145 C149 317.00 1.510 +C145 C166 469.00 1.400 +C145 C501 469.00 1.404 +C145 C502 469.00 1.400 +C145 H146 367.00 1.080 +C149 C224 268.00 1.529 +C149 C283 268.00 1.529 +C149 C293 268.00 1.529 +C149 H140 340.00 1.090 +C157 C224 268.00 1.529 +C157 C283 268.00 1.529 +C157 C293 268.00 1.529 +C157 H140 340.00 1.090 +C157 O154 320.00 1.410 +C158 C224 268.00 1.529 +C158 C283 268.00 1.529 +C158 C293 268.00 1.529 +C158 H140 340.00 1.090 +C158 O154 320.00 1.410 +C166 O167 450.00 1.364 +C206 C224 268.00 1.529 +C206 C283 268.00 1.529 +C206 C293 268.00 1.529 +C206 H140 340.00 1.090 +C206 S200 222.00 1.810 +C209 H140 340.00 1.090 +C209 S202 222.00 1.810 +C210 H140 340.00 1.090 +C210 S202 222.00 1.810 +C214 C224 268.00 1.529 +C214 C283 268.00 1.529 +C214 C293 268.00 1.529 +C214 H140 340.00 1.090 +C214 S203 222.00 1.810 +C223 C235 317.00 1.522 +C223 H140 340.00 1.090 +C223 N238 337.00 1.449 +C224 C235 317.00 1.522 +C224 C274 268.00 1.529 +C224 C505 268.00 1.529 +C224 H140 340.00 1.090 +C224 N238 337.00 1.449 +C235 C246 317.00 1.522 +C235 C292 317.00 1.522 +C235 C293 317.00 1.522 +C235 C295 317.00 1.522 +C235 N237 490.00 1.335 +C235 N238 490.00 1.335 +C235 N239 490.00 1.335 +C235 O236 570.00 1.229 +C242 H140 340.00 1.090 +C242 N238 337.00 1.449 +C245 H140 340.00 1.090 +C245 N239 337.00 1.449 +C246 H140 340.00 1.090 +C246 N239 337.00 1.449 +C267 O268 450.00 1.364 +C267 O269 570.00 1.229 +C271 C274 317.00 1.522 +C271 C283 317.00 1.522 +C271 C284 317.00 1.522 +C271 C285 317.00 1.522 +C271 O272 656.00 1.250 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367.00 1.080 +C509 N512 477.00 1.343 +C510 C510 520.00 1.370 +C510 H146 367.00 1.080 +C510 N512 427.00 1.381 +C514 H146 367.00 1.080 +C514 N503 427.00 1.381 +H155 O154 553.00 0.945 +H168 O167 553.00 0.945 +H204 S200 274.00 1.336 +H240 N237 434.00 1.010 +H241 N238 434.00 1.010 +H270 O268 553.00 0.945 +H290 N287 434.00 1.010 +H301 N300 434.00 1.010 +H304 N303 434.00 1.010 +H310 N309 434.00 1.010 +H504 N503 434.00 1.010 +H513 N512 434.00 1.010 +ANGLE +!ligand +C145 C145 C221 63.00 120.00 +C145 C145 C199 63.00 120.00 +C145 C145 C263 63.00 120.00 +C145 C145 C729 63.00 120.00 +C145 C145 C735 63.00 120.00 +C145 C221 C145 63.00 120.00 +C145 C199 C145 63.00 120.00 +C145 C263 C145 63.00 120.00 +C145 C729 C145 63.00 120.00 +C145 C735 C145 63.00 120.00 +H146 C145 C199 35.00 120.00 +H146 C145 C221 35.00 120.00 +H146 C145 C263 35.00 120.00 +H146 C145 C729 35.00 120.00 +H146 C145 C735 35.00 120.00 +C145 C199 O179 70.00 120.00 +C145 C221 C218 70.00 120.00 +C145 C145 C148 70.00 120.00 +C145 C735 S734 70.00 120.00 +C145 C263 Cl 75.00 120.00 +C145 C729 Br 75.00 120.00 +H140 C218 H140 33.00 107.80 +H140 C148 H140 33.00 107.80 +H185 C181 H185 33.00 107.80 +H140 C246 C158 37.50 110.70 +H140 C246 C149 37.50 110.70 +H140 C158 C246 37.50 110.70 +H140 C158 C158 37.50 110.70 +C145 C148 H140 35.00 109.50 +O248 C247 N239 80.00 122.90 +N239 C247 N239 70.00 114.20 +C247 N239 C246 50.00 121.90 +C247 N239 C149 50.00 121.90 +C149 N239 C246 50.00 118.00 +N239 C246 C158 80.00 109.70 +N239 C246 C149 80.00 109.70 +C149 C246 C158 58.35 112.70 +N239 C149 C145 63.00 114.00 +N239 C149 H140 35.00 109.50 +C246 C158 C158 58.35 112.70 +C246 C158 O154 50.00 109.50 +C246 C149 C145 63.00 114.00 +C246 C149 H140 37.50 110.70 +C221 C218 H140 35.00 109.50 +O154 C218 H140 35.00 109.50 +C221 C218 O154 50.00 109.50 +C218 O154 H155 55.00 108.50 +C199 O179 C181 75.00 111.00 +O179 C181 H185 35.00 109.50 +C158 C158 O154 50.00 109.50 +C735 S734 H204 50.00 96.00 +!water +HT OT HT 55.0 104.52 +H140 C135 H140 33.0 107.8 +H140 C136 H140 33.0 107.8 +H140 C149 H140 33.0 107.8 +H140 C157 H140 33.0 107.8 +H140 C206 H140 33.0 107.8 +H140 C209 H140 33.0 107.8 +H140 C210 H140 33.0 107.8 +H140 C214 H140 33.0 107.8 +H140 C223 H140 33.0 107.8 +H140 C242 H140 33.0 107.8 +H140 C245 H140 33.0 107.8 +H140 C274 H140 33.0 107.8 +H140 C284 H140 33.0 107.8 +H140 C292 H140 33.0 107.8 +H140 C296 H140 33.0 107.8 +H140 C307 H140 33.0 107.8 +H140 C308 H140 33.0 107.8 +H140 C505 H140 33.0 107.8 +H290 N287 H290 35.0 109.5 +H310 N309 H310 35.0 109.5 +!! below are automatically generated with pepz2rtf +C135 C136 C137 58.35 112.70 +C135 C136 H140 37.50 110.70 +C135 C137 C135 58.35 112.70 +C135 C137 C136 58.35 112.70 +C135 C137 C224 58.35 112.70 +C135 C137 C283 58.35 112.70 +C135 C137 C293 58.35 112.70 +C135 C137 H140 37.50 110.70 +C135 C158 C224 58.35 112.70 +C135 C158 C283 58.35 112.70 +C135 C158 C293 58.35 112.70 +C135 C158 H140 37.50 110.70 +C135 C158 O154 50.00 109.50 +C135 C224 C235 63.00 111.10 +C135 C224 H140 37.50 110.70 +C135 C224 N238 80.00 109.70 +C135 C235 N238 70.00 116.60 +C135 C235 N239 70.00 116.60 +C135 C235 O236 80.00 120.40 +C135 C283 C271 63.00 111.10 +C135 C283 H140 37.50 110.70 +C135 C283 N238 80.00 109.70 +C135 C293 C235 63.00 111.10 +C135 C293 H140 37.50 110.70 +C135 C293 N287 80.00 111.20 +C136 C135 H140 37.50 110.70 +C136 C136 C136 58.35 112.70 +C136 C136 C224 58.35 112.70 +C136 C136 C235 63.00 111.10 +C136 C136 C245 58.35 112.70 +C136 C136 C246 58.35 112.70 +C136 C136 C267 63.00 111.10 +C136 C136 C283 58.35 112.70 +C136 C136 C285 58.35 112.70 +C136 C136 C292 58.35 112.70 +C136 C136 C293 58.35 112.70 +C136 C136 C295 58.35 112.70 +C136 C136 C296 58.35 112.70 +C136 C136 H140 37.50 110.70 +C136 C137 C224 58.35 112.70 +C136 C137 C283 58.35 112.70 +C136 C137 C293 58.35 112.70 +C136 C137 H140 37.50 110.70 +C136 C210 H140 37.50 110.70 +C136 C210 S202 50.00 114.70 +C136 C224 C235 63.00 111.10 +C136 C224 H140 37.50 110.70 +C136 C224 N238 80.00 109.70 +C136 C235 N237 70.00 116.60 +C136 C235 O236 80.00 120.40 +C136 C245 H140 37.50 110.70 +C136 C245 N239 80.00 109.70 +C136 C246 C235 63.00 111.10 +C136 C246 H140 37.50 110.70 +C136 C246 N239 80.00 109.70 +C136 C267 O268 70.00 108.00 +C136 C267 O269 80.00 120.40 +C136 C274 C271 63.00 111.10 +C136 C274 H140 37.50 110.70 +C136 C283 C271 63.00 111.10 +C136 C283 H140 37.50 110.70 +C136 C283 N238 80.00 109.70 +C136 C285 C271 63.00 111.10 +C136 C285 H140 37.50 110.70 +C136 C285 N239 80.00 109.70 +C136 C292 H140 37.50 110.70 +C136 C292 N287 80.00 111.20 +C136 C293 C235 63.00 111.10 +C136 C293 H140 37.50 110.70 +C136 C293 N287 80.00 111.20 +C136 C295 C235 63.00 111.10 +C136 C295 H140 37.50 110.70 +C136 C295 N309 80.00 111.20 +C136 C296 H140 37.50 110.70 +C136 C296 N309 80.00 111.20 +C136 C308 C307 58.35 112.70 +C136 C308 H140 37.50 110.70 +C136 C500 C501 70.00 128.60 +C136 C500 C514 70.00 125.00 +C137 C135 H140 37.50 110.70 +C137 C136 C224 58.35 112.70 +C137 C136 C283 58.35 112.70 +C137 C136 C293 58.35 112.70 +C137 C136 H140 37.50 110.70 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C235 63.00 111.10 +C157 C224 H140 37.50 110.70 +C157 C224 N238 80.00 109.70 +C157 C283 C271 63.00 111.10 +C157 C283 H140 37.50 110.70 +C157 C283 N238 80.00 109.70 +C157 C293 C235 63.00 111.10 +C157 C293 H140 37.50 110.70 +C157 C293 N287 80.00 111.20 +C157 O154 H155 55.00 108.50 +C158 C135 H140 37.50 110.70 +C158 C224 C235 63.00 111.10 +C158 C224 H140 37.50 110.70 +C158 C224 N238 80.00 109.70 +C158 C283 C271 63.00 111.10 +C158 C283 H140 37.50 110.70 +C158 C283 N238 80.00 109.70 +C158 C293 C235 63.00 111.10 +C158 C293 H140 37.50 110.70 +C158 C293 N287 80.00 111.20 +C158 O154 H155 55.00 108.50 +C166 C145 H146 35.00 120.00 +C166 O167 H168 35.00 113.00 +C206 C224 C235 63.00 111.10 +C206 C224 H140 37.50 110.70 +C206 C224 N238 80.00 109.70 +C206 C283 C271 63.00 111.10 +C206 C283 H140 37.50 110.70 +C206 C283 N238 80.00 109.70 +C206 C293 C235 63.00 111.10 +C206 C293 H140 37.50 110.70 +C206 C293 N287 80.00 111.20 +C206 S200 H204 44.00 96.00 +C209 S202 C210 62.00 98.90 +C210 C136 C224 58.35 112.70 +C210 C136 C283 58.35 112.70 +C210 C136 C293 58.35 112.70 +C210 C136 H140 37.50 110.70 +C214 C224 C235 63.00 111.10 +C214 C224 H140 37.50 110.70 +C214 C224 N238 80.00 109.70 +C214 C283 C271 63.00 111.10 +C214 C283 H140 37.50 110.70 +C214 C283 N238 80.00 109.70 +C214 C293 C235 63.00 111.10 +C214 C293 H140 37.50 110.70 +C214 C293 N287 80.00 111.20 +C214 S203 S203 68.00 103.70 +C223 C235 N238 70.00 116.60 +C223 C235 N239 70.00 116.60 +C223 C235 O236 80.00 120.40 +C223 N238 C235 50.00 121.90 +C223 N238 H241 38.00 118.40 +C224 C135 H140 37.50 110.70 +C224 C136 C235 63.00 111.10 +C224 C136 C267 63.00 111.10 +C224 C136 C274 58.35 112.70 +C224 C136 C308 58.35 112.70 +C224 C136 C500 63.00 115.60 +C224 C136 H140 37.50 110.70 +C224 C137 H140 37.50 110.70 +C224 C149 H140 37.50 110.70 +C224 C157 H140 37.50 110.70 +C224 C157 O154 50.00 109.50 +C224 C158 H140 37.50 110.70 +C224 C158 O154 50.00 109.50 +C224 C206 H140 37.50 110.70 +C224 C206 S200 50.00 108.60 +C224 C214 H140 37.50 110.70 +C224 C214 S203 50.00 114.70 +C224 C235 N238 70.00 116.60 +C224 C235 N239 70.00 116.60 +C224 C235 O236 80.00 120.40 +C224 C274 C271 63.00 111.10 +C224 C274 H140 37.50 110.70 +C224 C505 C507 63.00 114.00 +C224 C505 C508 63.00 114.00 +C224 C505 C510 63.00 114.00 +C224 C505 H140 37.50 110.70 +C224 N238 C235 50.00 121.90 +C224 N238 H241 38.00 118.40 +C235 C135 H140 35.00 109.50 +C235 C136 C283 63.00 111.10 +C235 C136 C293 63.00 111.10 +C235 C136 H140 35.00 109.50 +C235 C223 H140 35.00 109.50 +C235 C223 N238 63.00 110.10 +C235 C224 C274 63.00 111.10 +C235 C224 C505 63.00 111.10 +C235 C224 H140 35.00 109.50 +C235 C224 N238 63.00 110.10 +C235 C246 H140 35.00 109.50 +C235 C246 N239 63.00 110.10 +C235 C292 H140 35.00 109.50 +C235 C292 N287 80.00 111.20 +C235 C293 C274 63.00 111.10 +C235 C293 C505 63.00 111.10 +C235 C293 H140 35.00 109.50 +C235 C293 N287 80.00 111.20 +C235 C295 H140 35.00 109.50 +C235 C295 N309 80.00 111.20 +C235 N237 H240 35.00 119.80 +C235 N238 C242 50.00 121.90 +C235 N238 C283 50.00 121.90 +C235 N238 C284 50.00 121.90 +C235 N238 H241 35.00 119.80 +C235 N239 C245 50.00 121.90 +C235 N239 C246 50.00 121.90 +C235 N239 C285 50.00 121.90 +C242 N238 H241 38.00 118.40 +C245 C136 H140 37.50 110.70 +C245 N238 C285 50.00 118.00 +C245 N239 C246 50.00 118.00 +C245 N239 C285 50.00 118.00 +C246 C136 H140 37.50 110.70 +C246 C235 N238 70.00 116.60 +C246 C235 N239 70.00 116.60 +C246 C235 O236 80.00 120.40 +C267 C136 C283 63.00 111.10 +C267 C136 C293 63.00 111.10 +C267 C136 H140 35.00 109.50 +C267 O268 H270 35.00 113.00 +C271 C274 C283 63.00 111.10 +C271 C274 C293 63.00 111.10 +C271 C274 H140 35.00 109.50 +C271 C283 C274 63.00 111.10 +C271 C283 C505 63.00 111.10 +C271 C283 H140 35.00 109.50 +C271 C283 N238 63.00 110.10 +C271 C284 H140 35.00 109.50 +C271 C284 N238 63.00 110.10 +C271 C285 H140 35.00 109.50 +C271 C285 N239 63.00 110.10 +C274 C136 C283 58.35 112.70 +C274 C136 C293 58.35 112.70 +C274 C136 H140 37.50 110.70 +C274 C224 H140 37.50 110.70 +C274 C224 N238 80.00 109.70 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H290 35.00 109.50 +C293 C135 H140 37.50 110.70 +C293 C136 C308 58.35 112.70 +C293 C136 C500 63.00 115.60 +C293 C136 H140 37.50 110.70 +C293 C137 H140 37.50 110.70 +C293 C149 H140 37.50 110.70 +C293 C157 H140 37.50 110.70 +C293 C157 O154 50.00 109.50 +C293 C158 H140 37.50 110.70 +C293 C158 O154 50.00 109.50 +C293 C206 H140 37.50 110.70 +C293 C206 S200 50.00 108.60 +C293 C214 H140 37.50 110.70 +C293 C214 S203 50.00 114.70 +C293 C235 N238 70.00 116.60 +C293 C235 N239 70.00 116.60 +C293 C235 O236 80.00 120.40 +C293 C274 H140 37.50 110.70 +C293 C505 C507 63.00 114.00 +C293 C505 C508 63.00 114.00 +C293 C505 C510 63.00 114.00 +C293 C505 H140 37.50 110.70 +C293 N287 H290 35.00 109.50 +C295 C136 H140 37.50 110.70 +C295 C235 N238 70.00 116.60 +C295 C235 N239 70.00 116.60 +C295 C235 O236 80.00 120.40 +C295 N309 C296 50.00 113.00 +C295 N309 H310 35.00 109.50 +C296 C136 H140 37.50 110.70 +C296 N309 H310 35.00 109.50 +C302 N300 H301 35.00 120.00 +C302 N303 C307 50.00 123.20 +C302 N303 H304 35.00 120.00 +C307 C308 H140 37.50 110.70 +C307 N303 H304 35.00 118.40 +C308 C136 H140 37.50 110.70 +C308 C307 H140 37.50 110.70 +C308 C307 N303 80.00 111.20 +C500 C136 H140 35.00 109.50 +C500 C501 C502 85.00 108.80 +C500 C514 H146 35.00 120.00 +C500 C514 N503 70.00 108.70 +C501 C145 H146 35.00 120.00 +C501 C500 C514 85.00 106.40 +C501 C502 N503 70.00 104.40 +C502 C145 H146 35.00 120.00 +C502 N503 C514 70.00 111.60 +C502 N503 H504 35.00 123.10 +C505 C224 H140 37.50 110.70 +C505 C224 N238 80.00 109.70 +C505 C283 H140 37.50 110.70 +C505 C283 N238 80.00 109.70 +C505 C293 H140 37.50 110.70 +C505 C293 N287 80.00 111.20 +C505 C507 C508 70.00 130.70 +C505 C507 N511 70.00 124.50 +C505 C508 C507 70.00 130.70 +C505 C508 N503 70.00 121.60 +C505 C510 C510 70.00 130.70 +C505 C510 N512 70.00 121.60 +C506 N503 C508 70.00 109.80 +C506 N503 H504 35.00 120.00 +C506 N511 C507 70.00 110.00 +C507 C505 H140 35.00 109.50 +C507 C508 H146 35.00 130.70 +C507 C508 N503 70.00 106.30 +C508 C505 H140 35.00 109.50 +C508 C507 H146 35.00 128.20 +C508 C507 N511 70.00 111.00 +C508 N503 H504 35.00 120.00 +C509 N512 C510 70.00 109.80 +C509 N512 H513 35.00 120.00 +C510 C505 H140 35.00 109.50 +C510 C510 H146 35.00 130.70 +C510 C510 N512 70.00 106.30 +C510 N512 H513 35.00 120.00 +C514 N503 H504 35.00 120.00 +H140 C157 O154 35.00 109.50 +H140 C158 O154 35.00 109.50 +H140 C206 S200 35.00 109.50 +H140 C209 S202 35.00 109.50 +H140 C210 S202 35.00 109.50 +H140 C214 S203 35.00 109.50 +H140 C223 N238 35.00 109.50 +H140 C224 N238 35.00 109.50 +H140 C242 N238 35.00 109.50 +H140 C245 N239 35.00 109.50 +H140 C246 N239 35.00 109.50 +H140 C283 N238 35.00 109.50 +H140 C284 N238 35.00 109.50 +H140 C285 N239 35.00 109.50 +H140 C292 N287 35.00 109.50 +H140 C293 N287 35.00 109.50 +H140 C295 N309 35.00 109.50 +H140 C296 N309 35.00 109.50 +H140 C307 N303 35.00 109.50 +H146 C506 N503 35.00 120.00 +H146 C506 N511 35.00 120.00 +H146 C507 N511 35.00 120.00 +H146 C508 N503 35.00 121.60 +H146 C509 N512 35.00 120.00 +H146 C510 N512 35.00 120.00 +H146 C514 N503 35.00 121.60 +H240 N237 H240 35.00 120.00 +H301 N300 H301 35.00 120.00 +N237 C235 O236 80.00 122.90 +N238 C235 O236 80.00 122.90 +N239 C235 O236 80.00 122.90 +N300 C302 N300 70.00 120.00 +N300 C302 N303 70.00 120.00 +N503 C506 N511 70.00 120.00 +N512 C509 N512 70.00 120.00 +O268 C267 O269 80.00 121.00 +O272 C271 O272 80.00 126.00 +DIHEDRAL +! ligand +X C145 C199 X 3.6250 2 180.0 +X C145 C221 X 3.6250 2 180.0 +X C145 C263 X 3.6250 2 180.0 +X C145 C729 X 3.6250 2 180.0 +X C145 C735 X 3.6250 2 180.0 +! end ligand +X C145 C145 X 3.6250 2 180.0 +X C145 C166 X 3.6250 2 180.0 +X C145 C501 X 3.5000 2 180.0 +X C145 C502 X 3.6250 2 180.0 +X C302 N300 X 1.9500 2 180.0 +X C500 C501 X 1.6750 2 180.0 +X C500 C514 X 6.5250 2 180.0 +X C501 C502 X 3.0000 2 180.0 +X C502 N503 X 1.5250 2 180.0 +X C506 N503 X 2.3250 2 180.0 +X C506 N511 X 5.0000 2 180.0 +X C507 C508 X 5.3750 2 180.0 +X C507 N511 X 2.4000 2 180.0 +X C509 N512 X 2.3250 2 180.0 +X C510 C510 X 5.3750 2 180.0 +X C514 N503 X 1.5000 2 180.0 +! ligand +C246 C158 C158 H140 0.1500 3 0.0 +C246 C158 C158 C246 0.6500 1 0.0 +C246 C158 C158 C246 -0.0250 2 180.0 +C246 C158 C158 C246 0.1000 3 0.0 +C246 C158 C158 O154 0.8555 1 0.0 +C246 C158 C158 O154 -0.2500 2 180.0 +C246 C158 C158 O154 0.3315 3 0.0 +C246 C158 O154 H155 -0.1780 1 0.0 +C246 C158 O154 H155 0.0870 2 180.0 +C246 C158 O154 H155 0.2460 3 0.0 +C246 C149 C145 C145 0.0000 1 0.0 +H140 C246 C158 H140 0.1500 3 0.0 +H140 C246 C158 C158 0.1500 3 0.0 +H140 C246 C158 O154 0.2340 3 0.0 +H140 C246 C149 H140 0.1500 3 0.0 +H140 C246 N239 C149 0.0000 1 0.0 +C158 C246 C149 H140 0.1500 3 0.0 +C158 C246 C149 C145 0.6500 1 0.0 +C158 C246 C149 C145 -0.0250 2 180.0 +C158 C246 C149 C145 0.1000 3 0.0 +C158 C158 C246 C149 0.6500 1 0.0 +C158 C158 C246 C149 -0.0250 2 180.0 +C158 C158 C246 C149 0.1000 3 0.0 +C158 C158 O154 H155 -0.1780 1 0.0 +C158 C158 O154 H155 0.0870 2 180.0 +C158 C158 O154 H155 0.2460 3 0.0 +H140 C158 C246 C149 0.1500 3 0.0 +H140 C158 C158 H140 0.1500 3 0.0 +H140 C158 C158 O154 0.2340 3 0.0 +H140 C246 C149 C145 0.2310 3 0.0 +C149 C246 C158 O154 0.8555 1 0.0 +C149 C246 C158 O154 -0.2500 2 180.0 +C149 C246 C158 O154 0.3315 3 0.0 +H140 C218 O154 H155 0.2250 3 0.0 +O154 C158 C158 O154 4.2540 1 0.0 +O248 C247 N239 C149 3.0445 2 180.0 +O248 C247 N239 C246 3.0445 2 180.0 +N239 C247 N239 C149 1.1500 1 0.0 +N239 C247 N239 C149 3.0445 2 180.0 +N239 C247 N239 C246 1.1500 1 0.0 +N239 C247 N239 C246 3.0445 2 180.0 +C247 N239 C246 C149 0.2310 2 180.0 +C247 N239 C246 C158 0.2310 2 180.0 +C247 N239 C246 H140 0.0000 1 0.0 +C247 N239 C149 C145 -0.6980 1 0.0 +C247 N239 C149 C145 -0.2135 2 180.0 +C247 N239 C149 H140 0.0000 1 0.0 +C246 N239 C149 C145 0.0000 1 0.0 +C246 N239 C149 H140 0.0000 1 0.0 +C149 N239 C246 C149 0.0000 1 0.0 +C149 N239 C246 C158 0.0000 1 0.0 +N239 C246 C149 C145 0.9820 1 0.0 +N239 C246 C149 C145 0.3295 3 0.0 +N239 C246 C149 H140 0.2320 3 0.0 +N239 C246 C158 C158 1.9640 1 0.0 +N239 C246 C158 C158 0.6590 3 0.0 +! N -CT-CT-OH approximated with N -CT-CT-CT +N239 C246 C158 O154 1.9640 1 0.0 +N239 C246 C158 O154 0.6590 3 0.0 +N239 C246 C158 H140 0.2320 3 0.0 +N239 C149 C145 C145 0.0000 1 0.0 +C145 C221 C218 H140 0.0000 1 0.0 +C145 C221 C218 O154 0.0000 1 0.0 +C221 C218 O154 H155 -0.4500 1 0.0 +C145 C199 O179 C181 1.5000 2 180.0 +C199 O179 C181 H185 0.3800 3 0.0 +C145 C735 S734 H204 0.5500 2 180.0 +C145 C145 C148 H140 0.0000 1 0.0 +! end ligand +C135 C136 C137 C135 0.6500 1 0.0 +C135 C136 C137 C135 -0.0250 2 180.0 +C135 C136 C137 C135 0.1000 3 0.0 +C135 C136 C137 C224 0.6500 1 0.0 +C135 C136 C137 C224 -0.0250 2 180.0 +C135 C136 C137 C224 0.1000 3 0.0 +C135 C136 C137 C283 0.6500 1 0.0 +C135 C136 C137 C283 -0.0250 2 180.0 +C135 C136 C137 C283 0.1000 3 0.0 +C135 C136 C137 C293 0.6500 1 0.0 +C135 C136 C137 C293 -0.0250 2 180.0 +C135 C136 C137 C293 0.1000 3 0.0 +C135 C136 C137 H140 0.1500 3 0.0 +C135 C137 C135 H140 0.1500 3 0.0 +C135 C137 C136 C224 0.6500 1 0.0 +C135 C137 C136 C224 -0.0250 2 180.0 +C135 C137 C136 C224 0.1000 3 0.0 +C135 C137 C136 C283 0.6500 1 0.0 +C135 C137 C136 C283 -0.0250 2 180.0 +C135 C137 C136 C283 0.1000 3 0.0 +C135 C137 C136 C293 0.6500 1 0.0 +C135 C137 C136 C293 -0.0250 2 180.0 +C135 C137 C136 C293 0.1000 3 0.0 +C135 C137 C136 H140 0.1500 3 0.0 +C135 C137 C224 C235 -0.8485 1 0.0 +C135 C137 C224 C235 -0.2280 2 180.0 +C135 C137 C224 C235 0.2925 3 0.0 +C135 C137 C224 H140 0.1500 3 0.0 +C135 C137 C224 N238 0.4225 1 0.0 +C135 C137 C224 N238 -0.4810 2 180.0 +C135 C137 C224 N238 0.3565 3 0.0 +C135 C137 C283 C271 -0.8485 1 0.0 +C135 C137 C283 C271 -0.2280 2 180.0 +C135 C137 C283 C271 0.2925 3 0.0 +C135 C137 C283 H140 0.1500 3 0.0 +C135 C137 C283 N238 0.4225 1 0.0 +C135 C137 C283 N238 -0.4810 2 180.0 +C135 C137 C283 N238 0.3565 3 0.0 +C135 C137 C293 C235 -0.8485 1 0.0 +C135 C137 C293 C235 -0.2280 2 180.0 +C135 C137 C293 C235 0.2925 3 0.0 +C135 C137 C293 H140 0.1500 3 0.0 +C135 C137 C293 N287 0.4225 1 0.0 +C135 C137 C293 N287 -0.4810 2 180.0 +C135 C137 C293 N287 0.3565 3 0.0 +C135 C158 C224 C235 -0.8485 1 0.0 +C135 C158 C224 C235 -0.2280 2 180.0 +C135 C158 C224 C235 0.2925 3 0.0 +C135 C158 C224 H140 0.1500 3 0.0 +C135 C158 C224 N238 0.4225 1 0.0 +C135 C158 C224 N238 -0.4810 2 180.0 +C135 C158 C224 N238 0.3565 3 0.0 +C135 C158 C283 C271 -0.8485 1 0.0 +C135 C158 C283 C271 -0.2280 2 180.0 +C135 C158 C283 C271 0.2925 3 0.0 +C135 C158 C283 H140 0.1500 3 0.0 +C135 C158 C283 N238 0.4225 1 0.0 +C135 C158 C283 N238 -0.4810 2 180.0 +C135 C158 C283 N238 0.3565 3 0.0 +C135 C158 C293 C235 -0.8485 1 0.0 +C135 C158 C293 C235 -0.2280 2 180.0 +C135 C158 C293 C235 0.2925 3 0.0 +C135 C158 C293 H140 0.1500 3 0.0 +C135 C158 C293 N287 0.4225 1 0.0 +C135 C158 C293 N287 -0.4810 2 180.0 +C135 C158 C293 N287 0.3565 3 0.0 +C135 C158 O154 H155 -0.1780 1 0.0 +C135 C158 O154 H155 -0.0870 2 180.0 +C135 C158 O154 H155 0.2460 3 0.0 +C135 C224 C235 N238 0.5865 1 0.0 +C135 C224 C235 N238 0.0945 2 180.0 +C135 C224 C235 N238 -0.6000 3 0.0 +C135 C224 C235 N239 0.2310 2 180.0 +C135 C224 C235 O236 0.0000 1 0.0 +C135 C224 N238 C235 0.2310 2 180.0 +C135 C224 N238 H241 0.0000 1 0.0 +C135 C235 N238 C223 1.1500 1 0.0 +C135 C235 N238 C223 3.0445 2 180.0 +C135 C235 N238 C224 1.1500 1 0.0 +C135 C235 N238 C224 3.0445 2 180.0 +C135 C235 N238 H241 2.4500 2 180.0 +C135 C235 N239 C245 1.1500 1 0.0 +C135 C235 N239 C245 3.0445 2 180.0 +C135 C235 N239 C246 1.1500 1 0.0 +C135 C235 N239 C246 3.0445 2 180.0 +C135 C283 C271 O272 0.4100 2 180.0 +C135 C283 N238 C235 0.2310 2 180.0 +C135 C283 N238 H241 0.0000 1 0.0 +C135 C293 C235 N238 0.5865 1 0.0 +C135 C293 C235 N238 0.0945 2 180.0 +C135 C293 C235 N238 -0.6000 3 0.0 +C135 C293 C235 N239 0.5865 1 0.0 +C135 C293 C235 N239 0.0945 2 180.0 +C135 C293 C235 N239 -0.6000 3 0.0 +C135 C293 C235 O236 0.0000 1 0.0 +C135 C293 N287 H290 0.1735 3 0.0 +C136 C136 C136 C224 0.6500 1 0.0 +C136 C136 C136 C224 -0.0250 2 180.0 +C136 C136 C136 C224 0.1000 3 0.0 +C136 C136 C136 C283 0.6500 1 0.0 +C136 C136 C136 C283 -0.0250 2 180.0 +C136 C136 C136 C283 0.1000 3 0.0 +C136 C136 C136 C292 0.6500 1 0.0 +C136 C136 C136 C292 -0.0250 2 180.0 +C136 C136 C136 C292 0.1000 3 0.0 +C136 C136 C136 C293 0.6500 1 0.0 +C136 C136 C136 C293 -0.0250 2 180.0 +C136 C136 C136 C293 0.1000 3 0.0 +C136 C136 C136 H140 0.1500 3 0.0 +C136 C136 C224 C235 -0.8485 1 0.0 +C136 C136 C224 C235 -0.2280 2 180.0 +C136 C136 C224 C235 0.2925 3 0.0 +C136 C136 C224 H140 0.1500 3 0.0 +C136 C136 C224 N238 0.4225 1 0.0 +C136 C136 C224 N238 -0.4810 2 180.0 +C136 C136 C224 N238 0.3565 3 0.0 +C136 C136 C235 N237 1.6250 1 0.0 +C136 C136 C235 N237 -0.2010 2 180.0 +C136 C136 C235 N237 -0.0680 3 0.0 +C136 C136 C235 O236 0.5830 2 180.0 +C136 C136 C245 H140 0.1500 3 0.0 +C136 C136 C245 N239 0.4225 1 0.0 +C136 C136 C245 N239 -0.4810 2 180.0 +C136 C136 C245 N239 0.3565 3 0.0 +C136 C136 C246 C235 -0.8485 1 0.0 +C136 C136 C246 C235 -0.2280 2 180.0 +C136 C136 C246 C235 0.2925 3 0.0 +C136 C136 C246 H140 0.1500 3 0.0 +C136 C136 C246 N239 0.4225 1 0.0 +C136 C136 C246 N239 -0.4810 2 180.0 +C136 C136 C246 N239 0.3565 3 0.0 +C136 C136 C267 O268 0.5000 1 0.0 +C136 C136 C267 O268 0.2730 2 180.0 +C136 C136 C267 O268 0.2250 3 0.0 +C136 C136 C267 O269 0.2730 2 180.0 +C136 C136 C283 C271 -0.8485 1 0.0 +C136 C136 C283 C271 -0.2280 2 180.0 +C136 C136 C283 C271 0.2925 3 0.0 +C136 C136 C283 H140 0.1500 3 0.0 +C136 C136 C283 N238 0.4225 1 0.0 +C136 C136 C283 N238 -0.4810 2 180.0 +C136 C136 C283 N238 0.3565 3 0.0 +C136 C136 C285 C271 -0.8485 1 0.0 +C136 C136 C285 C271 -0.2280 2 180.0 +C136 C136 C285 C271 0.2925 3 0.0 +C136 C136 C285 H140 0.1500 3 0.0 +C136 C136 C285 N239 0.4225 1 0.0 +C136 C136 C285 N239 -0.4810 2 180.0 +C136 C136 C285 N239 0.3565 3 0.0 +C136 C136 C292 H140 0.1500 3 0.0 +C136 C136 C292 N287 1.3660 1 0.0 +C136 C136 C292 N287 -0.1145 2 180.0 +C136 C136 C292 N287 0.2425 3 0.0 +C136 C136 C293 C235 -0.8485 1 0.0 +C136 C136 C293 C235 -0.2280 2 180.0 +C136 C136 C293 C235 0.2925 3 0.0 +C136 C136 C293 H140 0.1500 3 0.0 +C136 C136 C293 N287 0.4225 1 0.0 +C136 C136 C293 N287 -0.4810 2 180.0 +C136 C136 C293 N287 0.3565 3 0.0 +C136 C136 C295 C235 -0.8485 1 0.0 +C136 C136 C295 C235 -0.2280 2 180.0 +C136 C136 C295 C235 0.2925 3 0.0 +C136 C136 C295 H140 0.1500 3 0.0 +C136 C136 C295 N309 1.3660 1 0.0 +C136 C136 C295 N309 -0.1145 2 180.0 +C136 C136 C295 N309 0.2425 3 0.0 +C136 C136 C296 H140 0.1500 3 0.0 +C136 C136 C296 N309 1.3660 1 0.0 +C136 C136 C296 N309 -0.1145 2 180.0 +C136 C136 C296 N309 0.2425 3 0.0 +C136 C137 C135 H140 0.1500 3 0.0 +C136 C137 C224 C235 -0.8485 1 0.0 +C136 C137 C224 C235 -0.2280 2 180.0 +C136 C137 C224 C235 0.2925 3 0.0 +C136 C137 C224 H140 0.1500 3 0.0 +C136 C137 C224 N238 0.4225 1 0.0 +C136 C137 C224 N238 -0.4810 2 180.0 +C136 C137 C224 N238 0.3565 3 0.0 +C136 C137 C283 C271 -0.8485 1 0.0 +C136 C137 C283 C271 -0.2280 2 180.0 +C136 C137 C283 C271 0.2925 3 0.0 +C136 C137 C283 H140 0.1500 3 0.0 +C136 C137 C283 N238 0.4225 1 0.0 +C136 C137 C283 N238 -0.4810 2 180.0 +C136 C137 C283 N238 0.3565 3 0.0 +C136 C137 C293 C235 -0.8485 1 0.0 +C136 C137 C293 C235 -0.2280 2 180.0 +C136 C137 C293 C235 0.2925 3 0.0 +C136 C137 C293 H140 0.1500 3 0.0 +C136 C137 C293 N287 0.4225 1 0.0 +C136 C137 C293 N287 -0.4810 2 180.0 +C136 C137 C293 N287 0.3565 3 0.0 +C136 C210 S202 C209 0.4625 1 0.0 +C136 C210 S202 C209 -0.2880 2 180.0 +C136 C210 S202 C209 0.3385 3 0.0 +C136 C224 C235 N238 0.5865 1 0.0 +C136 C224 C235 N238 0.0945 2 180.0 +C136 C224 C235 N238 -0.6000 3 0.0 +C136 C224 C235 N239 0.2310 2 180.0 +C136 C224 C235 O236 0.0000 1 0.0 +C136 C224 N238 C235 0.2310 2 180.0 +C136 C224 N238 H241 0.0000 1 0.0 +C136 C235 N237 H240 2.4500 2 180.0 +C136 C245 N239 C235 0.2310 2 180.0 +C136 C245 N239 C246 1.4295 1 0.0 +C136 C245 N239 C246 1.0290 2 180.0 +C136 C245 N239 C246 -5.6330 3 0.0 +C136 C245 N239 C285 1.4295 1 0.0 +C136 C245 N239 C285 1.0290 2 180.0 +C136 C245 N239 C285 -5.6330 3 0.0 +C136 C246 C235 N238 0.5865 1 0.0 +C136 C246 C235 N238 0.0945 2 180.0 +C136 C246 C235 N238 -0.6000 3 0.0 +C136 C246 C235 N239 0.2310 2 180.0 +C136 C246 C235 O236 0.0000 1 0.0 +C136 C246 N239 C235 0.2310 2 180.0 +C136 C246 N239 C245 2.3765 1 0.0 +C136 C246 N239 C245 -0.3670 2 180.0 +C136 C267 O268 H270 0.7500 1 0.0 +C136 C267 O268 H270 2.7500 2 180.0 +C136 C274 C271 O272 0.2730 2 180.0 +C136 C283 C271 O272 0.4100 2 180.0 +C136 C283 N238 C235 0.2310 2 180.0 +C136 C283 N238 H241 0.0000 1 0.0 +C136 C285 C271 O272 0.4100 2 180.0 +C136 C285 N239 C235 0.2310 2 180.0 +C136 C285 N239 C245 2.3765 1 0.0 +C136 C285 N239 C245 -0.3670 2 180.0 +C136 C292 N287 H290 0.1735 3 0.0 +C136 C293 C235 N238 0.5865 1 0.0 +C136 C293 C235 N238 0.0945 2 180.0 +C136 C293 C235 N238 -0.6000 3 0.0 +C136 C293 C235 N239 0.5865 1 0.0 +C136 C293 C235 N239 0.0945 2 180.0 +C136 C293 C235 N239 -0.6000 3 0.0 +C136 C293 C235 O236 0.0000 1 0.0 +C136 C293 N287 H290 0.1735 3 0.0 +C136 C295 C235 N238 0.5865 1 0.0 +C136 C295 C235 N238 0.0945 2 180.0 +C136 C295 C235 N238 -0.6000 3 0.0 +C136 C295 C235 N239 0.5865 1 0.0 +C136 C295 C235 N239 0.0945 2 180.0 +C136 C295 C235 N239 -0.6000 3 0.0 +C136 C295 C235 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N238 C246 10.5000 2 180.0 +O236 C235 N238 C292 10.5000 2 180.0 +O236 C235 N238 C293 10.5000 2 180.0 +O236 C235 N238 C295 10.5000 2 180.0 +O236 C235 N239 C135 10.5000 2 180.0 +O236 C235 N239 C223 10.5000 2 180.0 +O236 C235 N239 C224 10.5000 2 180.0 +O236 C235 N239 C246 10.5000 2 180.0 +O236 C235 N239 C293 10.5000 2 180.0 +O236 C235 N239 C295 10.5000 2 180.0 +O269 C267 C136 O268 10.5000 2 180.0 +O269 C267 O268 C136 10.5000 2 180.0 +O272 C271 C274 O272 10.5000 2 180.0 +O272 C271 C283 O272 10.5000 2 180.0 +O272 C271 C284 O272 10.5000 2 180.0 +O272 C271 C285 O272 10.5000 2 180.0 +O272 C271 O272 C274 10.5000 2 180.0 +O272 C271 O272 C283 10.5000 2 180.0 +O272 C271 O272 C284 10.5000 2 180.0 +O272 C271 O272 C285 10.5000 2 180.0 +O268 C267 C136 O269 10.5 2 180.0 +O268 C267 O269 C136 10.5 2 180.0 + +NONBONDED nbxmod 5 atom cdiel switch vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 11.5 eps 1.0 e14fac 0.5 wmin 1.5 - +geom !assigns use of OPLS combining rules + +! ligand +C148 0.00 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1.9643086 +C145 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C149 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C157 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C158 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C166 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C206 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C209 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C210 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C214 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C223 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C224 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C235 0.00 -0.105000 2.1046163 0.00 -0.052500 2.1046163 +C242 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C245 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C246 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C267 0.00 -0.105000 2.1046163 0.00 -0.052500 2.1046163 +C271 0.00 -0.105000 2.1046163 0.00 -0.052500 2.1046163 +C274 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C283 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C284 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C285 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C292 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C293 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C295 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C296 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C302 0.00 -0.050000 1.2627698 0.00 -0.025000 1.2627698 +C307 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C308 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C500 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C501 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C502 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C505 0.00 -0.066000 1.9643086 0.00 -0.033000 1.9643086 +C506 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C507 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C508 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C509 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C510 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +C514 0.00 -0.070000 1.9923701 0.00 -0.035000 1.9923701 +H140 0.00 -0.030000 1.4030776 0.00 -0.015000 1.4030776 +H146 0.00 -0.030000 1.3581791 0.00 -0.015000 1.3581791 +H155 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H168 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H204 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H240 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H241 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H270 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H290 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H301 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H304 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H310 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H504 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +H513 0.00 0.000000 0.0000000 0.00 0.000000 0.0000000 +N237 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N238 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N239 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N287 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N300 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N303 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N309 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N503 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N511 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +N512 0.00 -0.170000 1.8240008 0.00 -0.085000 1.8240008 +O154 0.00 -0.170000 1.7510408 0.00 -0.085000 1.7510408 +O167 0.00 -0.170000 1.7229792 0.00 -0.085000 1.7229792 +O236 0.00 -0.210000 1.6612438 0.00 -0.105000 1.6612438 +O268 0.00 -0.170000 1.6836931 0.00 -0.085000 1.6836931 +O269 0.00 -0.210000 1.6612438 0.00 -0.105000 1.6612438 +O272 0.00 -0.210000 1.6612438 0.00 -0.105000 1.6612438 +S200 0.00 -0.250000 1.9923701 0.00 -0.125000 1.9923701 +S202 0.00 -0.250000 1.9923701 0.00 -0.125000 1.9923701 +S203 0.00 -0.250000 1.9923701 0.00 -0.125000 1.9923701 +OT 0.00 -0.152100 1.7682000 0.00 -0.152100 1.7682000 +!HT 0.00 -0.046000 0.224500 0.00 -0.046000 0.22450 +HT 0.00 0.000000 0.2245000 0.00 0.000000 0.224500 + +HBOND CUTHB 0.5 + +END + + diff --git a/charmm/toppar/non_charmm/parm14sb_all.prm b/charmm/toppar/non_charmm/parm14sb_all.prm new file mode 100644 index 00000000..29419f83 --- /dev/null +++ b/charmm/toppar/non_charmm/parm14sb_all.prm @@ -0,0 +1,1594 @@ +* AMBER ff14SB force field conversion +* See: http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00255 +* J. Chem. Theory Comput., DOI: 10.1021/acs.jctc.5b00255 +* + +! +! This is a semi-automatic conversion of the AMBER parm14SB force field, which +! is comprised of two following files: +! $AMBERHOME/dat/leap/parm/parm10.dat +! $AMBERHOME/dat/leap/parm/frcmod.ff14SB +! according to the description in $AMBERHOME/dat/leap/cmd/leaprc.ff14SB +! +! Converted by Dr. Xibing He, Florida State University, in July 2015 +! Email: +! +! Years ago Dr. Jeff Klauda (Univ. of Maryland, College Park) converted the +! AMBER99 & AMBER99SB force-field files to CHARMM format: +! http://terpconnect.umd.edu/~jbklauda/research/download.html +! His work was taken as reference to this conversion work. +! +! All the atom type names are the same except where otherwise noted. +! Note: type N* renamed to NG +! type C* renamed to CG +! In Dr. Klauda's conversion files of AMBER99, types N* is renamed to NS, and +! type C* renamed to CS. But in AMBER14SB, atom type CS already exists. +! +! The VDW parameter of SOD (Na+), POT (K+) and CLA (Cl-) are copied from +! Dr. Cheatham's & Dr. Klauda's files. They cannot be found in parm10.dat or +! frcmod.ff14SB under the AMBER directory $AmberTools15/dat/leap/parm/, but +! still can be found in parm99.dat, and the parameters agree with those in +! Dr. Cheatham's & Dr. Klauda's files. +! +! The following remarks are copied from Dr. Klauda's conversion file of ff99SB: +! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! note: the HO and HW nonbonded parameters, although zero in +! Cornell et al. should not have a 0.0 vdw radius in CHARMM +! to avoid difficulties with the 0.0/0.0 in the FAST OFF +! van der Waal code... +! +! note: the default nonbonded options chosen here are to match AMBER. +! It is not recommended that users actually run with GROUP based +! truncation and a switch unless really trying to match AMBER. +! Better would be ATOM based FSHIFT VSHIFT, however note that this +! does modify the energies (and effectively the parameters). +! +! Also note that long-range interactions are handeled differently between +! AMBER and CHARMM. To avoid differences when comparing energies and +! forces the the cuttoffs were set to be large in the individule +! comparison input files, i.e. 80 Angs. +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! +! + +ATOMS +MASS 1 C 12.01 ! sp2 C carbonyl group +MASS 2 CA 12.01 ! sp2 C pure aromatic (benzene) +MASS 3 CB 12.01 ! sp2 aromatic C, 5&6 membered ring junction +MASS 4 CC 12.01 ! sp2 aromatic C, 5 memb. ring HIS +MASS 5 CD 12.01 ! sp2 C atom in the middle of: C=CD-CD=C +MASS 6 CI 12.01 ! parmbsc0 +MASS 7 CK 12.01 ! sp2 C 5 memb.ring in purines (dA,dG) +MASS 8 CP 12.01 ! sp2 C 5 memb.ring in purines (G) +MASS 9 CM 12.01 ! sp2 C pyrimidines in pos. 5 & 6 (dT,dC) +MASS 10 CS 12.01 ! sp2 C pyrimidines in pos. 5 & 6 (U) +MASS 11 CN 12.01 ! sp2 C aromatic 5&6 memb.ring junct.(TRP) +MASS 12 CQ 12.01 ! sp2 C in 5 mem.ring of purines between 2 N +MASS 13 CR 12.01 ! sp2 arom as CQ but in HIS +MASS 14 CT 12.01 ! sp3 aliphatic C +MASS 15 CV 12.01 ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +MASS 16 CW 12.01 ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +MASS 17 CG 12.01 ! sp2 arom. 5 memb.ring w/1 subst. (TRP) +MASS 18 CX 12.01 ! protein C-alpha (new to ff10) +MASS 19 CY 12.01 ! nitrile C (Howard et al.JCC,16,243,1995) +MASS 20 CZ 12.01 ! sp C (Howard et al.JCC,16,243,1995) +MASS 21 C5 12.01 ! sp2 C 5 memb.ring in purines (A) +MASS 22 C4 12.01 ! sp2 C pyrimidines in pos. 5 & 6 (C) +MASS 23 CO 12.01 ! sp2 C carboxylate group +MASS 24 2C 12.01 ! sp3 aliphatic C with two (duo) heavy atoms +MASS 25 3C 12.01 ! sp3 aliphatic C with three (tres) heavy atoms +MASS 26 C8 12.01 ! sp3 aliphatic C basic AA side chain +MASS 27 C0 40.08 ! calcium +MASS 28 H 1.008 ! H bonded to nitrogen atoms +MASS 29 HC 1.008 ! H aliph. bond. to C without electrwd.group +MASS 30 H1 1.008 ! H aliph. bond. to C with 1 electrwd. group +MASS 31 H2 1.008 ! H aliph. bond. to C with 2 electrwd.groups +MASS 32 H3 1.008 ! H aliph. bond. to C with 3 eletrwd.groups +MASS 33 HA 1.008 ! H arom. bond. to C without elctrwd. groups +MASS 34 H4 1.008 ! H arom. bond. to C with 1 electrwd. group +MASS 35 H5 1.008 ! H arom.at C with 2 elctrwd. gr,+HCOO group +MASS 36 HO 1.008 ! hydroxyl group +MASS 37 HS 1.008 ! hydrogen bonded to sulphur (pol?) +MASS 38 HW 1.008 ! H in TIP3P water +MASS 39 HP 1.008 ! H bonded to C next to positively charged gr +MASS 40 HZ 1.008 ! H bond sp C (Howard et al.JCC,16,243,1995) +MASS 41 F 19.00 ! fluorine (not fluoride!) +MASS 42 Cl 35.45 ! chlorine (Applequist) (not chloride!) +MASS 43 Br 79.90 ! bromine (Applequist) (not bromide!) +MASS 44 I 126.9 ! iodine (Applequist) (not iodide!) +MASS 45 MG 24.305 ! magnesium +MASS 46 N 14.01 ! sp2 nitrogen in amide groups +MASS 47 NA 14.01 ! sp2 N in 5 memb.ring w/H atom (HIS) +MASS 48 NB 14.01 ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +MASS 49 NC 14.01 ! sp2 N in 6 memb.ring w/LP (ADE,GUA) +MASS 50 N2 14.01 ! sp2 N in amino groups +MASS 51 N3 14.01 ! sp3 N for charged amino groups (Lys, etc) +MASS 52 NT 14.01 ! sp3 N for amino groups amino groups +MASS 53 NG 14.01 ! sp2 N +MASS 54 NY 14.01 ! nitrile N (Howard et al.JCC,16,243,1995) +MASS 55 O 16.00 ! carbonyl group oxygen +MASS 56 O2 16.00 ! carboxyl and phosphate group oxygen +MASS 57 OW 16.00 ! oxygen in TIP3P water +MASS 58 OH 16.00 ! oxygen in hydroxyl group +MASS 59 OS 16.00 ! ether and ester oxygen +MASS 60 OP 16.00 ! 2- phosphate oxygen +MASS 61 P 30.97 ! phosphate,pol:JACS,112,8543,90,K.J.Miller +MASS 62 S 32.06 ! S in disulfide linkage,pol:JPC,102,2399,98 +MASS 63 SH 32.06 ! S in cystine +!MASS 64 CU 63.55 ! copper +!MASS 65 FE 55.00 ! iron +MASS 66 Zn 65.4 ! Zn2+ +MASS 67 EP 0.00 ! extra point +MASS 68 SOD 22.99 ! Na+ +MASS 69 POT 39.10 ! K+ +MASS 70 CLA 35.45 ! Cl- + +BONDS +OW HW 553.0 0.9572 ! TIP3P water +HW HW 553.0 1.5136 ! TIP3P water +C C 310.0 1.525 ! Junmei et al, 1999 +C CA 469.0 1.409 ! JCC,7,(1986),230; (not used any more in TYR) +C CB 447.0 1.419 ! JCC,7,(1986),230; GUA +C CM 410.0 1.444 ! JCC,7,(1986),230; THY,URA +C CS 410.0 1.444 ! JCC,7,(1986),230; THY,URA +C CT 317.0 1.522 ! JCC,7,(1986),230; AA +C CX 317.0 1.522 ! JCC,7,(1986),230; AA (was C-CT) +C N 490.0 1.335 ! JCC,7,(1986),230; AA +C NG 424.0 1.383 ! JCC,7,(1986),230; CYT,URA +C NA 418.0 1.388 ! JCC,7,(1986),230; GUA.URA +C NC 457.0 1.358 ! JCC,7,(1986),230; CYT +C O 570.0 1.229 ! JCC,7,(1986),230; AA,CYT,GUA,THY,URA +C O2 656.0 1.250 ! JCC,7,(1986),230; GLU,ASP +C OH 450.0 1.364 ! JCC,7,(1986),230; (not used any more for TYR) +C OS 450.0 1.323 ! Junmei et al, 1999 +C H4 367.0 1.080 ! Junmei et al, 1999 +C H5 367.0 1.080 ! Junmei et al, 1999 +CA CA 469.0 1.400 ! JCC,7,(1986),230; BENZENE,PHE,TRP,TYR +CA CB 469.0 1.404 ! JCC,7,(1986),230; ADE,TRP +CA CM 427.0 1.433 ! JCC,7,(1986),230; CYT +CA CS 427.0 1.433 ! JCC,7,(1986),230; CYT +CA CN 469.0 1.400 ! JCC,7,(1986),230; TRP +CA CT 317.0 1.510 ! JCC,7,(1986),230; PHE,TYR +CA HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR +CA H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; no assigned +CA N2 481.0 1.340 ! JCC,7,(1986),230; ARG,CYT,GUA +CA NA 427.0 1.381 ! JCC,7,(1986),230; GUA +CA NC 483.0 1.339 ! JCC,7,(1986),230; ADE,CYT,GUA +CA OH 450.0 1.364 ! substituted for C-OH in tyr +CB CB 520.0 1.370 ! JCC,7,(1986),230; ADE,GUA +CB NG 436.0 1.374 ! JCC,7,(1986),230; ADE,GUA +CB NB 414.0 1.391 ! JCC,7,(1986),230; ADE,GUA +CB NC 461.0 1.354 ! JCC,7,(1986),230; ADE,GUA +CD HA 367.0 1.080 ! Junmei et al, 1999 +CD CD 469.0 1.400 ! Junmei et al, 1999 +CD CM 549.0 1.350 ! Junmei et al, 1999 +CD CS 549.0 1.350 ! Junmei et al, 1999 +CD CT 317.0 1.510 ! Junmei et al, 1999 +CK H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA +CK NG 440.0 1.371 ! JCC,7,(1986),230; ADE,GUA +CK NB 529.0 1.304 ! JCC,7,(1986),230; ADE,GUA +CP H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA +CP NG 440.0 1.371 ! JCC,7,(1986),230; ADE,GUA +CP NB 529.0 1.304 ! JCC,7,(1986),230; ADE,GUA +CM CM 549.0 1.350 ! JCC,7,(1986),230; CYT,THY,URA +CM CT 317.0 1.510 ! JCC,7,(1986),230; THY +CM HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +CM H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +CM H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; not assigned +CM NG 448.0 1.365 ! JCC,7,(1986),230; CYT,THY,URA +CM OS 480.0 1.240 ! Junmei et al, 1999 +CS CS 549.0 1.350 ! JCC,7,(1986),230; CYT,THY,URA +CS CT 317.0 1.510 ! JCC,7,(1986),230; THY +CS HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +CS H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +CS H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; not assigned +CS NG 448.0 1.365 ! JCC,7,(1986),230; CYT,THY,URA +CS OS 480.0 1.240 ! Junmei et al, 1999 +CQ H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE +CQ NC 502.0 1.324 ! JCC,7,(1986),230; ADE +CT CT 310.0 1.526 ! JCC,7,(1986),230; AA, SUGARS +CX CT 310.0 1.526 ! JCC,7,(1986),230; AA, SUGARS (was CT-CT) +CT HC 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, SUGARS +CT H1 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, RIBOSE +CX H1 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, RIBOSE (was CT-H1) +CT H2 340.0 1.090 ! changed from 331 bsd on NMA nmodes; SUGARS +CT H3 340.0 1.090 ! changed from 331 bsd on NMA nmodes; not assigned +CT HP 340.0 1.090 ! changed from 331; AA-lysine, methyl ammonium cation +CX HP 340.0 1.090 ! changed from 331; AA-lysine, methyl ammonium cation (was CT-HP) +CT NG 337.0 1.475 ! JCC,7,(1986),230; ADE,CYT,GUA,THY,URA +CT N2 337.0 1.463 ! JCC,7,(1986),230; ARG +CT OH 320.0 1.410 ! JCC,7,(1986),230; SUGARS +CT OS 320.0 1.410 ! JCC,7,(1986),230; NUCLEIC ACIDS +CG HC 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes, not needed AA +CG CB 388.0 1.459 ! JCC,7,(1986),230; TRP +CG CT 317.0 1.495 ! JCC,7,(1986),230; TRP +CG CW 546.0 1.352 ! JCC,7,(1986),230; TRP +CB CN 447.0 1.419 ! JCC,7,(1986),230; TRP +CC CT 317.0 1.504 ! JCC,7,(1986),230; HIS +CC CV 512.0 1.375 ! JCC,7,(1986),230; HIS(delta) +CC CW 518.0 1.371 ! JCC,7,(1986),230; HIS(epsilon) +CC NA 422.0 1.385 ! JCC,7,(1986),230; HIS +CC NB 410.0 1.394 ! JCC,7,(1986),230; HIS +CN NA 428.0 1.380 ! JCC,7,(1986),230; TRP +CR H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS +CR NA 477.0 1.343 ! JCC,7,(1986),230; HIS +CR NB 488.0 1.335 ! JCC,7,(1986),230; HIS +CT N 337.0 1.449 ! JCC,7,(1986),230; AA +CX N 337.0 1.449 ! JCC,7,(1986),230; AA (was CT-N) +CT N3 367.0 1.471 ! JCC,7,(1986),230; LYS +CX N3 367.0 1.471 ! JCC,7,(1986),230; LYS (was CT-N3) +CT NT 367.0 1.471 ! for neutral amines +CT S 227.0 1.810 ! changed from 222.0 based on dimethylS nmodes +CT SH 237.0 1.810 ! changed from 222.0 based on methanethiol nmodes +CT CY 400.0 1.458 ! Howard et al JCC.16,243,1995 +CT CZ 400.0 1.459 ! Howard et al JCC,16,243,1995 +CV H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; HIS +CV NB 410.0 1.394 ! JCC,7,(1986),230; HIS +CW H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) +CW NA 427.0 1.381 ! JCC,7,(1986),230; HIS,TRP +CY NY 600.0 1.150 ! Howard et al JCC,16,243,1995 +CZ CZ 600.0 1.206 ! Howard et al JCC,16,243,1995 +CZ HZ 400.0 1.056 ! Howard et al JCC,16,243,1995 +OP P 525.0 1.480 ! JCC,7,(1986),230; NA PHOSPHATES +O2 P 525.0 1.480 ! JCC,7,(1986),230; NA PHOSPHATES +OH P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES +OS P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES +NA P 250.0 1.840 ! phosphohistidine +H N2 434.0 1.010 ! JCC,7,(1986),230; ADE,CYT,GUA,ARG +H NG 434.0 1.010 ! for plain unmethylated bases ADE,CYT,GUA,ARG +H NA 434.0 1.010 ! JCC,7,(1986),230; GUA,URA,HIS +H N 434.0 1.010 ! JCC,7,(1986),230; AA +H N3 434.0 1.010 ! JCC,7,(1986),230; LYS +H NT 434.0 1.010 ! for neutral amines +HO OH 553.0 0.960 ! JCC,7,(1986),230; SUGARS,SER,TYR +HO OS 553.0 0.960 ! JCC,7,(1986),230; NUCLEOTIDE ENDS +HS SH 274.0 1.336 ! JCC,7,(1986),230; CYS +S S 166.0 2.038 ! JCC,7,(1986),230; CYX (SCHERAGA) +F CT 367.0 1.380 ! JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 +Cl CT 232.0 1.766 ! 6-31g* opt +Br CT 159.0 1.944 ! Junmei et al,99 +I CT 148.0 2.166 ! Junmei et al,99 +F CA 386.0 1.359 ! Junmei et al,99 +Cl CA 193.0 1.727 ! Junmei et al,99 +I CA 171.0 2.075 ! Junmei et al,99 +Br CA 172.0 1.890 ! Junmei et al,99 +EP O 600.0 0.200 ! or 0.35 +EP OH 600.0 0.200 ! or 0.35 +EP OS 600.0 0.200 ! or 0.35 +EP N3 600.0 0.200 ! or 0.35 +EP NT 600.0 0.200 ! or 0.35 +EP NB 600.0 0.200 ! or 0.35 histidines, nucleic acids +EP NC 600.0 0.200 ! or 0.35 nucleic acids +EP S 600.0 0.700 ! cys,cyx,met +EP SH 600.0 0.700 ! cys,cyx +CI H1 340.0 1.090 ! parmbsc0 +CI CT 310.0 1.526 ! parmbsc0 +OS CI 320.0 1.410 ! parmbsc0 +OH CI 320.0 1.410 ! parmbsc0 +C5 H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA +C5 NG 440.0 1.371 ! JCC,7,(1986),230; ADE,GUA +C5 NB 529.0 1.304 ! JCC,7,(1986),230; ADE,GUA +C C4 410.0 1.444 ! JCC,7,(1986),230; THY,URA +CA C4 427.0 1.433 ! JCC,7,(1986),230; CYT +C4 C4 549.0 1.350 ! JCC,7,(1986),230; CYT,THY,URA +C4 CT 317.0 1.510 ! JCC,7,(1986),230; THY +C4 HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +C4 H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +C4 NG 448.0 1.365 ! JCC,7,(1986),230; CYT,THY,URA +C 2C 317.0 1.5220 ! +CG 2C 317.0 1.4950 ! +C8 C8 310.0 1.5260 ! +C8 CX 310.0 1.5260 ! +C8 H1 340.0 1.0900 ! +C8 HC 340.0 1.0900 ! +C8 HP 340.0 1.0900 ! +C8 N2 337.0 1.4630 ! +C8 N3 367.0 1.4710 ! +CA 2C 317.0 1.5100 ! +CC 2C 317.0 1.5040 ! +CO O2 656.0 1.2500 ! +CO 2C 317.0 1.5220 ! +CT 2C 310.0 1.5260 ! +CT 3C 310.0 1.5260 ! +CX 2C 310.0 1.5260 ! +CX 3C 310.0 1.5260 ! +H1 2C 340.0 1.0900 ! +H1 3C 340.0 1.0900 ! +HC 2C 340.0 1.0900 ! +HC 3C 340.0 1.0900 ! +OH 2C 320.0 1.4100 ! +OH 3C 320.0 1.4100 ! +S 2C 227.0 1.8100 ! +SH 2C 237.0 1.8100 ! +2C 2C 310.0 1.5260 ! +2C 3C 310.0 1.5260 ! + +THETAS +HW OW HW 100. 104.52 ! TIP3P water +HW HW OW 0. 127.74 ! (found in crystallographic water with 3 bonds) +C C O 80.0 120.00 ! Junmei et al, 1999 acrolein +C C OH 80.0 120.00 ! Junmei et al, 1999 +CA C CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA +CA C OH 70.0 120.00 ! AA (not used in tyr) +CA C OS 70.0 120.00 ! phosphotyrosine +CC NA P 76.7 125.10 ! phosphohistidine +CR NA P 76.7 125.10 ! phosphohistidine +NA P OP 42.9 102.38 ! phosphohistidine +CB C NA 70.0 111.30 ! NA +CB C O 80.0 128.80 ! +CM C NA 70.0 114.10 ! +CM C O 80.0 125.30 ! +CS C NA 70.0 114.10 ! +CS C O 80.0 125.30 ! +CT C O 80.0 120.40 ! +CX C O 80.0 120.40 ! (was CT-C-O) +CT C O2 70.0 117.00 ! +CX C O2 70.0 117.00 ! (was CT-C -O2) +CT C N 70.0 116.60 ! AA general +CX C N 70.0 116.60 ! AA general (was CT-C-N) +CT C CT 63.0 117.00 ! Junmei et al, 1999 +CT C OS 80.0 115.00 ! Junmei et al, 1999 +CT C OH 80.0 110.00 ! Junmei et al, 1999 +CX C OH 80.0 110.00 ! Junmei et al, 1999 (was CT-C-OH) +NG C NA 70.0 115.40 ! +NG C NC 70.0 118.60 ! +NG C O 80.0 120.90 ! +NA C O 80.0 120.60 ! +NC C O 80.0 122.50 ! +N C O 80.0 122.90 ! AA general +O C O 80.0 126.00 ! AA COO- terminal residues +O C OH 80.0 120.00 ! (check with Junmei for: theta0:120.0?) +O C OS 80.0 125.00 ! Junmei et al, 1999 +O2 C O2 80.0 126.00 ! AA GLU (SCH JPC 79,2379) +H4 C C 50.0 120.00 ! Junmei et al, 1999 +H4 C CM 50.0 115.00 ! Junmei et al, 1999 +H4 C CS 50.0 115.00 ! Junmei et al, 1999 +H4 C CT 50.0 115.00 ! Junmei et al, 1999 +H4 C O 50.0 120.00 ! Junmei et al, 1999 +H4 C OH 50.0 120.00 ! Junmei et al, 1999 +H5 C N 50.0 120.00 ! Junmei et al, 1999 +H5 C O 50.0 119.00 ! Junmei et al, 1999 +H5 C OH 50.0 107.00 ! Junmei et al, 1999 +H5 C OS 50.0 107.00 ! Junmei et al, 1999 +C CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes +C CA HA 50.0 120.00 ! AA (not used in tyr) +CA CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes +CA CA CB 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes +CA CA CT 70.0 120.00 ! +CA CA HA 50.0 120.00 ! +CA CA H4 50.0 120.00 ! +CA CA OH 70.0 120.00 ! replacement in tyr +CA CA CN 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +CB CA HA 50.0 120.00 ! +CB CA H4 50.0 120.00 ! +CB CA N2 70.0 123.50 ! +CB CA NC 70.0 117.30 ! +CM CA N2 70.0 120.10 ! +CM CA NC 70.0 121.50 ! +CS CA N2 70.0 120.10 ! +CS CA NC 70.0 121.50 ! +CN CA HA 50.0 120.00 ! AA trp +NA CA NC 70.0 123.30 ! +N2 CA NA 70.0 116.00 ! +N2 CA NC 70.0 119.30 ! +N2 CA N2 70.0 120.00 ! AA arg +F CA CA 70.0 121.00 ! Junmei et al,99 +Cl CA CA 70.0 118.80 ! Junmei et al,99 +Br CA CA 70.0 118.80 ! Junmei et al,99 +I CA CA 70.0 118.80 ! Junmei et al,99 +C CB CB 63.0 119.20 ! changed from 85.0 bsd on C6H6 nmodes; NA gua +C CB NB 70.0 130.00 ! +CA CB CB 63.0 117.30 ! changed from 85.0 bsd on C6H6 nmodes; NA ade +CA CB NB 70.0 132.40 ! +CB CB NG 70.0 106.20 ! +CB CB NB 70.0 110.40 ! +CB CB NC 70.0 127.70 ! +CG CB CA 63.0 134.90 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +CG CB CN 63.0 108.80 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +CA CB CN 63.0 116.20 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +NG CB NC 70.0 126.20 ! +CD CD CM 63.0 120.00 ! Junmei et al, 1999 +CD CD CS 63.0 120.00 ! Junmei et al, 1999 +CD CD CT 70.0 120.00 ! Junmei et al, 1999 +CM CD CT 70.0 120.00 ! Junmei et al, 1999 +CS CD CT 70.0 120.00 ! Junmei et al, 1999 +HA CD HA 35.0 119.00 ! Junmei et al, 1999 +HA CD CD 50.0 120.00 ! Junmei et al, 1999 +HA CD CM 50.0 120.00 ! Junmei et al, 1999 +HA CD CS 50.0 120.00 ! Junmei et al, 1999 +H5 CK NG 50.0 123.05 ! +H5 CK NB 50.0 123.05 ! +NG CK NB 70.0 113.90 ! +H5 CP NG 50.0 123.05 ! +H5 CP NB 50.0 123.05 ! +NG CP NB 70.0 113.90 ! +C CM CM 63.0 120.70 ! changed from 85.0 bsd on C6H6 nmodes; NA thy +C CM CT 70.0 119.70 ! +C CM HA 50.0 119.70 ! +C CM H4 50.0 119.70 ! +CA CM CM 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt +CA CM HA 50.0 123.30 ! +CA CM H4 50.0 123.30 ! +CM CM CT 70.0 119.70 ! +CM CM HA 50.0 119.70 ! +CM CM H4 50.0 119.70 ! +CM CM NG 70.0 121.20 ! +CM CM OS 80.0 125.00 ! Junmei et al, 1999 +H4 CM NG 50.0 119.10 ! +H4 CM OS 50.0 113.00 ! Junmei et al, 1999 +HA CM HA 35.0 120.00 ! Junmei et al, 1999 +HA CM CD 50.0 120.00 ! Junmei et al, 1999 +HA CM CT 50.0 120.00 ! Junmei et al, 1999 +C CS CS 63.0 120.70 ! changed from 85.0 bsd on C6H6 nmodes; NA thy +C CS CT 70.0 119.70 ! +C CS HA 50.0 119.70 ! +C CS H4 50.0 119.70 ! +CA CS CS 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt +CA CS HA 50.0 123.30 ! +CA CS H4 50.0 123.30 ! +CM CS CT 70.0 119.70 ! +CS CS HA 50.0 119.70 ! +CS CS H4 50.0 119.70 ! +CS CS NG 70.0 121.20 ! +CS CS OS 80.0 125.00 ! Junmei et al, 1999 +H4 CS NG 50.0 119.10 ! +H4 CS OS 50.0 113.00 ! Junmei et al, 1999 +HA CS HA 35.0 120.00 ! Junmei et al, 1999 +HA CS CD 50.0 120.00 ! Junmei et al, 1999 +HA CS CT 50.0 120.00 ! Junmei et al, 1999 +NC CQ NC 70.0 129.10 ! +H5 CQ NC 50.0 115.45 ! +H1 CT H1 35.0 109.50 ! +H1 CX H1 35.0 109.50 ! (was H1-CT-H1) +H1 CT NG 50.0 109.50 ! changed based on NMA nmodes +H1 CT OH 50.0 109.50 ! changed based on NMA nmodes +H1 CT OS 50.0 109.50 ! changed based on NMA nmodes +H1 CT CM 50.0 109.50 ! Junmei et al, 1999 +H1 CT CS 50.0 109.50 ! Junmei et al, 1999 +H1 CT CY 50.0 110.00 ! Junmei et al, 1999 +H1 CT CZ 50.0 110.00 ! Junmei et al, 1999 +H1 CT N 50.0 109.50 ! AA general changed based on NMA nmodes +H1 CX N 50.0 109.50 ! AA general (was H1-CT-N) +H1 CT S 50.0 109.50 ! AA cys changed based on NMA nmodes +H1 CT SH 50.0 109.50 ! AA cyx changed based on NMA nmodes +H1 CT N2 50.0 109.50 ! AA arg changed based on NMA nmodes +H1 CT NT 50.0 109.50 ! neutral amines +H2 CT H2 35.0 109.50 ! AA lys +H2 CT NG 50.0 109.50 ! changed based on NMA nmodes +H2 CT OS 50.0 109.50 ! changed based on NMA nmodes +HP CT HP 35.0 109.50 ! AA lys, ch3nh4+ +HP CX HP 35.0 109.50 ! AA lys, ch3nh4+ (was HP-CT-HP) +HP CT N3 50.0 109.50 ! AA lys, ch3nh3+, changed based on NMA nmodes +HP CX N3 50.0 109.50 ! AA lys, ch3nh3+, changed based on NMA nmodes (was HP-CT-N3) +HC CT HC 35.0 109.50 ! +HC CT CM 50.0 109.50 ! changed based on NMA nmodes +HC CT CS 50.0 109.50 ! changed based on NMA nmodes +HC CT CD 50.0 109.50 ! Junmei et al, 1999 +HC CT CZ 50.0 110.00 ! Junmei et al, 1999 +C CT H1 50.0 109.50 ! AA general changed based on NMA nmodes +C CX H1 50.0 109.50 ! AA general (was C-CT-H1) +C CT HP 50.0 109.50 ! AA zwitterion changed based on NMA nmodes +C CX HP 50.0 109.50 ! AA zwitterion changed based on NMA nmodes (was C -CT-HP) +C CT HC 50.0 109.50 ! AA gln changed based on NMA nmodes +C CT N 63.0 110.10 ! AA general +C CX N 63.0 110.10 ! AA general (was C-CT-N) +C CT N3 80.0 111.20 ! AA amino terminal residues +C CX N3 80.0 111.20 ! AA amino terminal residues (was C -CT-N3) +C CT CT 63.0 111.10 ! AA general +C CT CX 63.0 111.10 ! AA general (was C -CT-CT) +C CX CT 63.0 111.10 ! AA general (was C-CT-CT) +C CT OS 60.0 109.50 ! Junmei et al, 1999 +CA CT HC 50.0 109.50 ! AA tyr changed based on NMA nmodes +CC CT CT 63.0 113.10 ! AA his +CC CT CX 63.0 113.10 ! AA his (was CC-CT-CT) +CC CT HC 50.0 109.50 ! AA his changed based on NMA nmodes +CM CT CT 63.0 111.00 ! Junmei et al, 1999 (last change: Mar24,99) +CM CT OS 50.0 109.50 ! Junmei et al, 1999 +CS CT CT 63.0 111.00 ! Junmei et al, 1999 (last change: Mar24,99) +CS CT OS 50.0 109.50 ! Junmei et al, 1999 +CT CT CT 40.0 109.50 ! +CT CT CX 40.0 109.50 ! (was CT-CT-CT) +CT CT HC 50.0 109.50 ! changed based on NMA nmodes +CX CT HC 50.0 109.50 ! changed based on NMA nmodes (was CT-CT-HC) +CT CT H1 50.0 109.50 ! changed based on NMA nmodes +CT CX H1 50.0 109.50 ! changed based on NMA nmodes (was CT-CT-H1) +CX CT H1 50.0 109.50 ! changed based on NMA nmodes (was CT-CT-H1) +CT CT H2 50.0 109.50 ! changed based on NMA nmodes +CT CT HP 50.0 109.50 ! changed based on NMA nmodes +CT CX HP 50.0 109.50 ! changed based on NMA nmodes (was CT-CT-HP) +CT CT NG 50.0 109.50 ! +CT CT OH 50.0 109.50 ! +CX CT OH 50.0 109.50 ! (was CT-CT-OH) +CT CT OS 50.0 109.50 ! +CT CT S 50.0 114.70 ! AA cyx (SCHERAGA JPC 79,1428) +CX CT S 50.0 114.70 ! AA cyx (SCHERAGA JPC 79,1428) (was CT-CT-S ) +CT CT SH 50.0 108.60 ! AA cys +CX CT SH 50.0 108.60 ! AA cys (was CT-CT-SH) +CT CT CA 63.0 114.00 ! AA phe tyr (SCH JPC 79,2379) +CX CT CA 63.0 114.00 ! AA phe tyr (SCH JPC 79,2379) (was CT-CT-CA) +CT CT N2 80.0 111.20 ! AA arg (JCP 76, 1439) +CT CT N 80.0 109.70 ! AA ala, general (JACS 94, 2657) +CT CX N 80.0 109.70 ! AA ala, general (was CT-CT-N) +CT CT N3 80.0 111.20 ! AA lys (JCP 76, 1439) +CT CX N3 80.0 111.20 ! AA lys (JCP 76, 1439) (was CT-CT-N3) +CT CT NT 80.0 111.20 ! neutral amines +CT CT CY 63.0 110.00 ! Junmei et al, 1999 +CT CT CZ 63.0 110.00 ! Junmei et al, 1999 +CG CT CT 63.0 115.60 ! AA trp +CG CT CX 63.0 115.60 ! AA trp (was C*-CT-CT) +CG CT HC 50.0 109.50 ! AA trp changed based on NMA nmodes +OS CT OS 160.0 101.00 ! Junmei et al, 1999 +OS CT CY 50.0 110.00 ! Junmei et al, 1999 +OS CT CZ 50.0 110.00 ! Junmei et al, 1999 +OS CT NG 50.0 109.50 ! +F CT F 77.0 109.10 ! JCC,13,(1992),963; +F CT H1 50.0 109.50 ! JCC,13,(1992),963; +F CT CT 50.0 109.00 ! +F CT H2 50.0 109.50 ! +Cl CT CT 50.0 108.50 ! (6-31g* opt value) +Cl CT H1 50.0 108.50 ! (6-31g* opt value) +Br CT CT 50.0 108.00 ! Junmei et al 99 +Br CT H1 50.0 106.50 ! Junmei et al 99 +I CT CT 50.0 106.00 ! Junmei et al,99 +CT CC NA 70.0 120.00 ! AA his +CT CC CV 70.0 120.00 ! AA his +CT CC NB 70.0 120.00 ! AA his +CV CC NA 70.0 120.00 ! AA his +CW CC NA 70.0 120.00 ! AA his +CW CC NB 70.0 120.00 ! AA his +CT CC CW 70.0 120.00 ! AA his +H5 CR NA 50.0 120.00 ! AA his +H5 CR NB 50.0 120.00 ! AA his +NA CR NA 70.0 120.00 ! AA his +NA CR NB 70.0 120.00 ! AA his +CC CV H4 50.0 120.00 ! AA his +CC CV NB 70.0 120.00 ! AA his +H4 CV NB 50.0 120.00 ! AA his +CC CW H4 50.0 120.00 ! AA his +CC CW NA 70.0 120.00 ! AA his +CG CW H4 50.0 120.00 ! AA trp +CG CW NA 70.0 108.70 ! AA trp +H4 CW NA 50.0 120.00 ! AA his +CB CG CT 70.0 128.60 ! AA trp +CB CG CW 63.0 106.40 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +CT CG CW 70.0 125.00 ! AA trp +CA CN CB 63.0 122.70 ! changed from 85.0 bsd on C6H6 nmodes; AA trp +CA CN NA 70.0 132.80 ! AA trp +CB CN NA 70.0 104.40 ! AA trp +CT CY NY 80.0 180.00 ! Junmei et al, 1999 +CT CZ CZ 80.0 180.00 ! Junmei et al, 1999 +CZ CZ HZ 50.0 180.00 ! Junmei et al, 1999 +C N CT 50.0 121.90 ! AA general +C N CX 50.0 121.90 ! AA general (was C-N-CT) +C N H 50.0 120.00 ! AA general, gln, asn,changed based on NMA nmodes +CT N H 50.0 118.04 ! AA general, changed based on NMA nmodes +CX N H 50.0 118.04 ! AA general, (was CT-N-H) +CT N CT 50.0 118.00 ! AA pro (DETAR JACS 99,1232) +CT N CX 50.0 118.00 ! AA pro (DETAR JACS 99,1232) (was CT-N -CT) +H N H 35.0 120.00 ! ade,cyt,gua,gln,asn ** +C NG CM 70.0 121.60 ! +C NG CS 70.0 121.60 ! +C NG CT 70.0 117.60 ! +C NG H 50.0 119.20 ! changed based on NMA nmodes +CB NG CK 70.0 105.40 ! +CB NG CP 70.0 105.40 ! +CB NG CT 70.0 125.80 ! +CB NG H 50.0 125.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes +CK NG CT 70.0 128.80 ! +CK NG H 50.0 128.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes +CP NG CT 70.0 128.80 ! +CP NG H 50.0 128.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes +CM NG CT 70.0 121.20 ! +CM NG H 50.0 121.20 ! for unmethylated n.a. bases,chngd bsd NMA nmodes +CS NG CT 70.0 121.20 ! +CS NG H 50.0 121.20 ! for unmethylated n.a. bases,chngd bsd NMA nmodes +CA N2 H 50.0 120.00 ! +CA N2 CT 50.0 123.20 ! AA arg +CT N2 H 50.0 118.40 ! AA arg +H N2 H 35.0 120.00 ! +CT N3 H 50.0 109.50 ! AA lys, changed based on NMA nmodes +CX N3 H 50.0 109.50 ! AA lys, changed based on NMA nmodes (was CT-N3-H ) +CT N3 CT 50.0 109.50 ! AA pro/nt +CT N3 CX 50.0 109.50 ! AA pro/nt (was CT-N3-CT) +H N3 H 35.0 109.50 ! AA lys, AA(end) +CT NT H 50.0 109.50 ! neutral amines +CT NT CT 50.0 109.50 ! neutral amines +H NT H 35.0 109.50 ! neutral amines +C NA C 70.0 126.40 ! +C NA CA 70.0 125.20 ! +C NA H 50.0 116.80 ! changed based on NMA nmodes +CA NA H 50.0 118.00 ! changed based on NMA nmodes +CC NA CR 70.0 120.00 ! AA his +CC NA H 50.0 120.00 ! AA his, changed based on NMA nmodes +CR NA CW 70.0 120.00 ! AA his +CR NA H 50.0 120.00 ! AA his, changed based on NMA nmodes +CW NA H 50.0 120.00 ! AA his, changed based on NMA nmodes +CN NA CW 70.0 111.60 ! AA trp +CN NA H 50.0 123.10 ! AA trp, changed based on NMA nmodes +CB NB CK 70.0 103.80 ! +CB NB CP 70.0 103.80 ! +CC NB CR 70.0 117.00 ! AA his +CR NB CV 70.0 117.00 ! AA his +C NC CA 70.0 120.50 ! +CA NC CB 70.0 112.20 ! +CA NC CQ 70.0 118.60 ! +CB NC CQ 70.0 111.00 ! +C OH HO 50.0 113.00 ! (not used in tyr anymore) +CA OH HO 50.0 113.00 ! replacement in tyr +CT OH HO 55.0 108.50 ! +HO OH P 45.0 108.50 ! +C OS CT 60.0 117.00 ! Junmei et al, 1999 +CM OS CT 60.0 117.00 ! Junmei et al, 1999 +CS OS CT 60.0 117.00 ! Junmei et al, 1999 +CT OS CT 60.0 109.50 ! +CT OS P 100.0 120.50 ! +C OS P 100.0 120.50 ! phosphotyrosine +P OS P 100.0 120.50 ! +O2 P OH 45.0 108.23 ! +O2 P O2 140.0 119.90 ! +OP P OP 140.0 119.90 ! +OP P OS 100.0 108.23 ! +O2 P OS 100.0 108.23 ! +OH P OS 45.0 102.60 ! +OS P OS 45.0 102.60 ! +CT S CT 62.0 98.90 ! AA met +CT S S 68.0 103.70 ! AA cyx (SCHERAGA JPC 79,1428) +CT SH HS 43.0 96.00 ! changed from 44.0 based on methanethiol nmodes +HS SH HS 35.0 92.07 ! AA cys +CB NB EP 150.0 126.0 ! NA +CC NB EP 150.0 126.0 ! his,NA +CK NB EP 150.0 126.0 ! NA +CP NB EP 150.0 126.0 ! NA +CR NB EP 150.0 126.0 ! his,NA +CV NB EP 150.0 126.0 ! his,NA +C NC EP 150.0 120.0 ! NA +CA NC EP 150.0 120.0 ! NA +CB NC EP 150.0 120.0 ! NA +CQ NC EP 150.0 120.0 ! NA +CT N3 EP 150.0 109.5 ! in neutral lysine +H N3 EP 150.0 109.5 ! in neutral lysine +CT NT EP 150.0 109.5 ! +H NT EP 150.0 109.5 ! +C O EP 150.0 120.0 ! +EP O EP 150.0 120.0 ! +C OH EP 150.0 120.0 ! +CT OH EP 150.0 109.5 ! +HO OH EP 150.0 109.5 ! +EP OH EP 150.0 109.5 ! +C OS EP 150.0 109.5 ! +CM OS EP 150.0 109.5 ! methyl vinyl ether +CS OS EP 150.0 109.5 ! methyl vinyl ether +CT OS EP 150.0 109.5 ! +EP OS EP 150.0 109.5 ! +CT S EP 150.0 90.0 ! cys,cyx,met +CT SH EP 150.0 90.0 ! cys,cyx,met +P OS EP 150.0 109.5 ! NA +EP S EP 150.0 180.0 ! cys,cyx,met +EP SH EP 150.0 180.0 ! cys,cyx,met +HS SH EP 150.0 90.0 ! cys +H1 CI CT 50.0 109.50 ! parmbsc0 +H1 CI H1 35.0 109.50 ! parmbsc0 +CI CT H1 50.0 109.50 ! parmbsc0 +CI CT OS 50.0 109.50 ! parmbsc0 +CI CT CT 40.0 109.50 ! parmbsc0 +OS CI H1 50.0 109.50 ! parmbsc0 +OS CI CT 50.0 109.50 ! parmbsc0 +P OS CI 100.0 120.50 ! parmbsc0 +OH CI H1 50.0 109.50 ! parmbsc0 +OH CI CT 50.0 109.50 ! parmbsc0 +HO OH CI 55.0 108.50 ! parmbsc0 +H5 C5 NG 50.0 123.05 ! +H5 C5 NB 50.0 123.05 ! +NG C5 NB 70.0 113.90 ! +CB NG C5 70.0 105.40 ! +C5 NG CT 70.0 128.80 ! +CB NB C5 70.0 103.80 ! +C4 C NA 70.0 114.10 ! +C4 C O 80.0 125.30 ! +C4 CA N2 70.0 120.10 ! +C4 CA NC 70.0 121.50 ! +C C4 C4 63.0 120.70 ! changed from 85.0 bsd on C6H6 nmodes; NA thy +C C4 CT 70.0 119.70 ! +C C4 HA 50.0 119.70 ! +C C4 H4 50.0 119.70 ! +CA C4 C4 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt +CA C4 HA 50.0 123.30 ! +CA C4 H4 50.0 123.30 ! +C4 C4 CT 70.0 119.70 ! +C4 C4 HA 50.0 119.70 ! +C4 C4 H4 50.0 119.70 ! +C4 C4 NG 70.0 121.20 ! +H4 C4 NG 50.0 119.10 ! +H1 CT C4 50.0 109.50 ! Junmei et al, 1999 +HC CT C4 50.0 109.50 ! changed based on NMA nmodes +C NG C4 70.0 121.60 ! +C4 NG CT 70.0 121.20 ! +EP S S 150.0 96.70 ! AA cyx (dac, from parm91 LP-S-S) +N C 2C 70.0 116.60 ! +O C 2C 80.0 120.40 ! +OH C 2C 80.0 110.00 ! +CB CG 2C 70.0 128.60 ! +CW CG 2C 70.0 125.00 ! +C8 C8 C8 40.0 109.50 ! +C8 C8 CX 40.0 109.50 ! +C8 C8 H1 50.0 109.50 ! +C8 C8 HC 50.0 109.50 ! +C8 C8 HP 50.0 109.50 ! +C8 C8 N2 80.0 111.20 ! +C8 C8 N3 80.0 111.20 ! +CX C8 HC 50.0 109.50 ! +H1 C8 H1 35.0 109.50 ! +H1 C8 N2 50.0 109.50 ! +HC C8 HC 35.0 109.50 ! +HP C8 HP 35.0 109.50 ! +HP C8 N3 50.0 109.50 ! +CA CA 2C 70.0 120.00 ! +CV CC 2C 70.0 120.00 ! +CW CC 2C 70.0 120.00 ! +NA CC 2C 70.0 120.00 ! +NB CC 2C 70.0 120.00 ! +O2 CO O2 80.0 126.00 ! +O2 CO 2C 70.0 117.00 ! +HC CT 2C 50.0 109.50 ! +HC CT 3C 50.0 109.50 ! +C CX C8 63.0 111.10 ! +C CX 2C 63.0 111.10 ! +C CX 3C 63.0 111.10 ! +C8 CX H1 50.0 109.50 ! +C8 CX N 80.0 109.70 ! +C8 CX N3 80.0 111.20 ! +H1 CX 2C 50.0 109.50 ! +H1 CX 3C 50.0 109.50 ! +HP CX C8 50.0 109.50 ! changed based on NMA nmodes (was CT-CT-HP) +HP CX CG 50.0 109.50 ! changed based on NMA nmodes (was CT-CT-HP) +HP CX 2C 50.0 109.50 ! changed based on NMA nmodes (was CT-CT-HP) +HP CX 3C 50.0 109.50 ! changed based on NMA nmodes (was CT-CT-HP) +N CX 2C 80.0 109.70 ! +N CX 3C 80.0 109.70 ! +N3 CX 2C 80.0 111.20 ! +N3 CX 3C 80.0 111.20 ! +C8 N2 CA 50.0 123.20 ! +C8 N2 H 50.0 118.40 ! +C8 N3 H 50.0 109.50 ! +HO OH 2C 55.0 108.50 ! +HO OH 3C 55.0 108.50 ! +CT S 2C 62.0 98.90 ! +2C S S 68.0 103.70 ! +HS SH 2C 43.0 96.00 ! +C 2C CX 63.0 111.10 ! +C 2C HC 50.0 109.50 ! +C 2C 2C 63.0 111.10 ! +CG 2C CX 63.0 115.60 ! +CG 2C HC 50.0 109.50 ! +CA 2C CX 63.0 114.00 ! +CA 2C HC 50.0 109.50 ! +CC 2C CX 63.0 113.10 ! +CC 2C HC 50.0 109.50 ! +CO 2C CX 63.0 111.10 ! +CO 2C HC 50.0 109.50 ! +CO 2C 2C 63.0 111.10 ! +CT 2C HC 50.0 109.50 ! +CT 2C 3C 40.0 109.50 ! +CX 2C H1 50.0 109.50 ! +CX 2C HC 50.0 109.50 ! +CX 2C OH 50.0 109.50 ! +CX 2C S 50.0 114.70 ! +CX 2C SH 50.0 108.60 ! +CX 2C 2C 40.0 109.50 ! +CX 2C 3C 40.0 109.50 ! +H1 2C H1 35.0 109.50 ! +H1 2C OH 50.0 109.50 ! +H1 2C S 50.0 109.50 ! +H1 2C SH 50.0 109.50 ! +H1 2C 2C 50.0 109.50 ! +HC 2C HC 35.0 109.50 ! +HC 2C 2C 50.0 109.50 ! +HC 2C 3C 50.0 109.50 ! +S 2C 2C 50.0 114.70 ! +CT 3C CT 40.0 109.50 ! +CT 3C CX 40.0 109.50 ! +CT 3C H1 50.0 109.50 ! +CT 3C HC 50.0 109.50 ! +CT 3C OH 50.0 109.50 ! +CT 3C 2C 40.0 109.50 ! +CX 3C H1 50.0 109.50 ! +CX 3C HC 50.0 109.50 ! +CX 3C OH 50.0 109.50 ! +CX 3C 2C 40.0 109.50 ! +H1 3C OH 50.0 109.50 ! +HC 3C 2C 50.0 109.50 ! + +PHI +X C C X 3.62500000 2 180.0 ! Junmei et al, 1999 +X C CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6 +X C CB X 3.00000000 2 180.0 ! intrpol.bsd.on C6H6 +X C CM X 2.17500000 2 180.0 ! intrpol.bsd.on C6H6 +X C CS X 2.17500000 2 180.0 ! intrpol.bsd.on C6H6 +X C CT X 0.00000000 2 0.000 ! JCC,7,(1986),230 +X C CX X 0.00000000 2 0.000 ! JCC,7,(1986),230 (was X -C -CT-X ) +X C N X 2.50000000 2 180.0 ! AA,NMA +X C NG X 1.45000000 2 180.0 ! JCC,7,(1986),230 +X C NA X 1.35000000 2 180.0 ! JCC,7,(1986),230 +X C NC X 4.00000000 2 180.0 ! JCC,7,(1986),230 +X C O X 2.80000000 2 180.0 ! Junmei et al, 1999 +X C OH X 2.30000000 2 180.0 ! Junmei et al, 1999 +X C OS X 2.70000000 2 180.0 ! Junmei et al, 1999 +X CA CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6 +X CA CB X 3.50000000 2 180.0 ! intrpol.bsd.on C6H6 +X CA CM X 2.55000000 2 180.0 ! intrpol.bsd.on C6H6 +X CA CS X 2.55000000 2 180.0 ! intrpol.bsd.on C6H6 +X CA CN X 3.62500000 2 180.0 ! reinterpolated 93' +X CA CT X 0.00000000 2 0.000 ! JCC,7,(1986),230 +X CA N2 X 2.40000000 2 180.0 ! reinterpolated 93' +X CA NA X 1.50000000 2 180.0 ! JCC,7,(1986),230 +X CA NC X 4.80000000 2 180.0 ! JCC,7,(1986),230 +X CA OH X 0.90000000 2 180.0 ! Junmei et al, 99 +X CB CB X 5.45000000 2 180.0 ! intrpol.bsd.on C6H6 +X CB CN X 3.00000000 2 180.0 ! reinterpolated 93' +X CB NG X 1.65000000 2 180.0 ! JCC,7,(1986),230 +X CB NB X 2.55000000 2 180.0 ! JCC,7,(1986),230 +X CB NC X 4.15000000 2 180.0 ! JCC,7,(1986),230 +X CC CT X 0.00000000 2 0.000 ! JCC,7,(1986),230 +X CC CV X 5.15000000 2 180.0 ! intrpol.bsd.on C6H6 +X CC CW X 5.37500000 2 180.0 ! intrpol.bsd.on C6H6 +X CC NA X 1.40000000 2 180.0 ! JCC,7,(1986),230 +X CC NB X 2.40000000 2 180.0 ! JCC,7,(1986),230 +X CD CD X 1.00000000 2 180.0 ! Junmei et al, 1999 +X CD CT X 0.00000000 2 0.000 ! Junmei et al, 1999 +X CD CM X 6.65000000 2 180.0 ! Junmei et al, 1999 +X CD CS X 6.65000000 2 180.0 ! Junmei et al, 1999 +X CK NG X 1.70000000 2 180.0 ! JCC,7,(1986),230 +X CK NB X 10.0000000 2 180.0 ! JCC,7,(1986),230 +X CP NG X 1.70000000 2 180.0 ! JCC,7,(1986),230 +X CP NB X 10.0000000 2 180.0 ! JCC,7,(1986),230 +X CM CM X 6.65000000 2 180.0 ! intrpol.bsd.on C6H6 +X CM CT X 0.00000000 3 0.000 ! JCC,7,(1986),230 +X CM NG X 1.85000000 2 180.0 ! JCC,7,(1986),230 +X CM OS X 1.05000000 2 180.0 ! Junmei et al, 1999 +X CS CS X 6.65000000 2 180.0 ! intrpol.bsd.on C6H6 +X CS CT X 0.00000000 3 0.000 ! JCC,7,(1986),230 +X CS NG X 1.85000000 2 180.0 ! JCC,7,(1986),230 +X CS OS X 1.05000000 2 180.0 ! Junmei et al, 1999 +X CN NA X 1.52500000 2 180.0 ! reinterpolated 93' +X CQ NC X 6.80000000 2 180.0 ! JCC,7,(1986),230 +X CT CT X 0.15555556 3 0.000 ! JCC,7,(1986),230 +X CT CX X 0.15555556 3 0.000 ! JCC,7,(1986),230 (was X -CT-CT-X ) +X CT CY X 0.00000000 1 0.000 ! Junmei et al, 1999 +X CT CZ X 0.00000000 1 0.000 ! Junmei et al, 1999 +X CT N X 0.00000000 2 0.000 ! JCC,7,(1986),230 +X CX N X 0.00000000 2 0.000 ! JCC,7,(1986),230 (was X -CT-N -X ) +X CT NG X 0.00000000 2 0.000 ! JCC,7,(1986),230 +X CT N2 X 0.00000000 3 0.000 ! JCC,7,(1986),230 +X CT NT X 0.30000000 3 0.000 ! Junmei et al, 1999 +X CT N3 X 0.15555556 3 0.000 ! JCC,7,(1986),230 +X CX N3 X 0.15555556 3 0.000 ! JCC,7,(1986),230 (was X -CT-N3-X ) +X CT OH X 0.16666667 3 0.000 ! JCC,7,(1986),230 +X CT OS X 0.38333333 3 0.000 ! JCC,7,(1986),230 +X CT S X 0.33333333 3 0.000 ! JCC,7,(1986),230 +X CT SH X 0.25000000 3 0.000 ! JCC,7,(1986),230 +X CG CB X 1.67500000 2 180.0 ! intrpol.bsd.onC6H6aa +X CG CT X 0.00000000 2 0.000 ! JCC,7,(1986),230 +X CG CW X 6.52500000 2 180.0 ! intrpol.bsd.on C6H6 +X CR NA X 2.32500000 2 180.0 ! JCC,7,(1986),230 +X CR NB X 5.00000000 2 180.0 ! JCC,7,(1986),230 +X CV NB X 2.40000000 2 180.0 ! JCC,7,(1986),230 +X CW NA X 1.50000000 2 180.0 ! JCC,7,(1986),230 +X OH P X 0.25000000 3 0.000 ! JCC,7,(1986),230 +X OS P X 0.25000000 3 0.000 ! JCC,7,(1986),230 +X CI OS X 0.38333333 3 0.000 ! +X CI OH X 0.16666667 3 0.000 ! +X CI CT X 0.15555556 3 0.000 ! +X C5 NG X 1.70000000 2 180.0 ! JCC,7,(1986),230 +X C5 NB X 10.0000000 2 180.0 ! JCC,7,(1986),230 +X C C4 X 2.17500000 2 180.0 ! intrpol.bsd.on C6H6 +X CA C4 X 2.55000000 2 180.0 ! intrpol.bsd.on C6H6 +X C4 C4 X 6.65000000 2 180.0 ! intrpol.bsd.on C6H6 +X C4 CT X 0.00000000 3 0.000 ! JCC,7,(1986),230 +X C4 NG X 1.85000000 2 180.0 ! JCC,7,(1986),230 +CT OS CT CI 0.38300000 3 0.000 ! +CT OS CT CI 0.10000000 2 180.0 ! +H1 CI CT OS 0.25000000 1 0.000 ! +H1 CI CT OH 0.25000000 1 0.000 ! +H1 CT CI OS 0.25000000 1 0.000 ! +H1 CT CI OH 0.25000000 1 0.000 ! +CI CT CT CT 0.18000000 3 0.000 ! +CI CT CT CT 0.25000000 2 180.0 ! +CI CT CT CT 0.20000000 1 180.0 ! +OP P OS CA 0.00000000 1 180.0 ! phosphotyrosine +CC NA P OP 0.24000000 3 0.000 ! phosphohistidine +CR NA P OP 0.00000000 3 0.000 ! phosphohistidine +OS P OS CI 0.18518100 1 31.79508 ! alfa +OS P OS CI 1.25653100 2 351.95960 ! alfa +OS P OS CI 0.35485800 3 357.24748 ! alfa +OH P OS CI 0.18518100 1 31.79508 ! alfa +OH P OS CI 1.25653100 2 351.95960 ! alfa +OH P OS CI 0.35485800 3 357.24748 ! alfa +CT CT CI OS 1.17804000 1 190.97653 ! gamma +CT CT CI OS 0.09210200 2 295.63279 ! gamma +CT CT CI OS 0.96283000 3 348.09535 ! gamma +CT CT CI OH 1.17804000 1 190.97653 ! gamma +CT CT CI OH 0.09210200 2 295.63279 ! gamma +CT CT CI OH 0.96283000 3 348.09535 ! gamma +HC CT C4 C4 0.38000000 3 180.0 ! Junmei et al, 1999 +HC CT C4 C4 1.15000000 1 0.000 ! Junmei et al, 1999 +C4 C4 C O 2.17500000 2 180.0 ! Junmei et al, 1999 +C4 C4 C O 0.30000000 3 0.000 ! Junmei et al, 1999 +OS CT NG C5 0.96561000 1 68.7902 ! ol3 chi ade +OS CT NG C5 1.07403000 2 15.6360 ! ol3 chi ade +OS CT NG C5 0.45754000 3 171.5787 ! ol3 chi ade +OS CT NG C5 0.30917000 4 19.0921 ! ol3 chi ade +OS CT NG CP 0.70510000 1 74.7558 ! ol3 chi gua +OS CT NG CP 1.06546000 2 6.2286 ! ol3 chi gua +OS CT NG CP 0.44273000 3 168.6503 ! ol3 chi gua +OS CT NG CP 0.25602000 4 3.9746 ! ol3 chi gua +OS CT NG C4 1.22506000 1 146.9892 ! ol3 chi cyt +OS CT NG C4 1.63459000 2 16.4766 ! ol3 chi cyt +OS CT NG C4 0.93747000 3 185.8774 ! ol3 chi cyt +OS CT NG C4 0.31033000 4 32.1590 ! ol3 chi cyt +OS CT NG CS 1.02514000 1 149.8583 ! ol3 chi ura +OS CT NG CS 1.74876000 2 16.7648 ! ol3 chi ura +OS CT NG CS 0.58150000 3 179.3474 ! ol3 chi ura +OS CT NG CS 0.35148000 4 16.0016 ! ol3 chi ura +C N CX C 0.00000000 4 0.000 ! four amplitudes and +C N CX C 0.42000000 3 0.000 ! phases for phi +C N CX C 0.27000000 2 0.000 ! +C N CX C 0.00000000 1 0.000 ! +N CX C N 0.00000000 4 0.000 ! four amplitudes and +N CX C N 0.55000000 3 180.0 ! phases for psi +N CX C N 1.58000000 2 180.0 ! +N CX C N 0.45000000 1 180.0 ! +CT CT N C 0.00000000 4 0.000 ! four amplitudes and +CT CT N C 0.40000000 3 0.000 ! phases for phi' +CT CT N C 2.00000000 2 0.000 ! +CT CT N C 2.00000000 1 0.000 ! +!CT CX N C 0.00000000 4 0.000 ! four amplitudes and +!CT CX N C 0.40000000 3 0.000 ! phases for phi' +!CT CX N C 2.00000000 2 0.000 ! +!CT CX N C 2.00000000 1 0.000 ! +CT CT C N 0.00000000 4 0.000 ! four amplitudes and +CT CT C N 0.40000000 3 0.000 ! phases for psi' +CT CT C N 0.20000000 2 0.000 ! +CT CT C N 0.20000000 1 0.000 ! +!CT CX C N 0.00000000 4 0.000 ! four amplitudes and +!CT CX C N 0.40000000 3 0.000 ! phases for psi' +!CT CX C N 0.20000000 2 0.000 ! +!CT CX C N 0.20000000 1 0.000 ! +CX CT C N 0.00000000 4 0.000 ! four amplitudes and +CX CT C N 0.40000000 3 0.000 ! phases for psi' +CX CT C N 0.20000000 2 0.000 ! +CX CT C N 0.20000000 1 0.000 ! +H N C O 2.50000000 2 180.0 ! JCC,7,(1986),230 +H N C O 2.00000000 1 0.000 ! J.C.cistrans-NMA DE +CT S S CT 3.50000000 2 0.000 ! JCC,7,(1986),230 +CT S S CT 0.60000000 3 0.000 ! JCC,7,(1986),230 +OH P OS CT 0.25000000 3 0.000 ! JCC,7,(1986),230 +OH P OS CT 1.20000000 2 0.000 ! gg> ene.631g*/mp2 +OS P OS CT 0.25000000 3 0.000 ! JCC,7,(1986),230 +OS P OS CT 1.20000000 2 0.000 ! gg> ene.631g*/mp2 +H1 CT C O 0.80000000 1 0.000 ! Junmei et al, 1999 +H1 CT C O 0.00000000 2 0.000 ! Explicit of wild card X-C-CT-X +H1 CT C O 0.08000000 3 180.0 ! Junmei et al, 1999 +H1 CX C O 0.80000000 1 0.000 ! Junmei et al, 1999 (was H1-CT-C -O ) +H1 CX C O 0.00000000 2 0.000 ! Explicit of wild card X-C-CT-X +H1 CX C O 0.08000000 3 180.0 ! Junmei et al, 1999 (was H1-CT-C -O ) +HC CT C O 0.80000000 1 0.000 ! Junmei et al, 1999 +HC CT C O 0.00000000 2 0.000 ! Explicit of wild card X-C-CT-X +HC CT C O 0.08000000 3 180.0 ! Junmei et al, 1999 +HC CT CT HC 0.15000000 3 0.000 ! Junmei et al, 1999 +HC CT CT CT 0.16000000 3 0.000 ! Junmei et al, 1999 +HC CT CT CX 0.16000000 3 0.000 ! Junmei et al, 1999 (was HC-CT-CT-CT) +HC CT CM CM 0.38000000 3 180.0 ! Junmei et al, 1999 +HC CT CM CM 1.15000000 1 0.000 ! Junmei et al, 1999 +HC CT CS CS 0.38000000 3 180.0 ! Junmei et al, 1999 +HC CT CS CS 1.15000000 1 0.000 ! Junmei et al, 1999 +HO OH CT CT 0.16000000 3 0.000 ! Junmei et al, 1999 +HO OH CT CT 0.25000000 1 0.000 ! Junmei et al, 1999 +HO OH CT CX 0.16000000 3 0.000 ! Junmei et al, 1999 (was HO-OH-CT-CT) +HO OH CT CX 0.25000000 1 0.000 ! Junmei et al, 1999 (was HO-OH-CT-CT) +HO OH C O 2.30000000 2 180.0 ! Junmei et al, 1999 +HO OH C O 1.90000000 1 0.000 ! Junmei et al, 1999 +CM CM C O 2.17500000 2 180.0 ! Junmei et al, 1999 +CM CM C O 0.30000000 3 0.000 ! Junmei et al, 1999 +CT CM CM CT 6.65000000 2 180.0 ! Junmei et al, 1999 +CT CM CM CT 1.90000000 1 180.0 ! Junmei et al, 1999 +CS CS C O 2.17500000 2 180.0 ! Junmei et al, 1999 +CS CS C O 0.30000000 3 0.000 ! Junmei et al, 1999 +CT CS CS CT 6.65000000 2 180.0 ! Junmei et al, 1999 +CT CS CS CT 1.90000000 1 180.0 ! Junmei et al, 1999 +CT CT CT CT 0.18000000 3 0.000 ! Junmei et al, 1999 +CT CT CT CT 0.25000000 2 180.0 ! Junmei et al, 1999 +CT CT CT CT 0.20000000 1 180.0 ! Junmei et al, 1999 +CX CT CT CT 0.18000000 3 0.000 ! Junmei et al, 1999 (was CT-CT-CT-CT) +CX CT CT CT 0.25000000 2 180.0 ! Junmei et al, 1999 (was CT-CT-CT-CT) +CX CT CT CT 0.20000000 1 180.0 ! Junmei et al, 1999 (was CT-CT-CT-CT) +CT CT NT CT 0.30000000 3 0.000 ! Junmei et al, 1999 +CT CT NT CT 0.48000000 2 180.0 ! Junmei et al, 1999 +CT CT OS CT 0.38300000 3 0.000 ! +CT CT OS CT 0.10000000 2 180.0 ! +CT CT OS C 0.38300000 3 0.000 ! Junmei et al, 1999 +CT CT OS C 0.80000000 1 180.0 ! Junmei et al, 1999 +CT OS CT OS 0.10000000 3 0.000 ! Junmei et al, 1999 +CT OS CT OS 0.85000000 2 180.0 ! Junmei et al, 1999 +CT OS CT OS 1.35000000 1 180.0 ! Junmei et al, 1999 +CT OS CT NG 0.38300000 3 0.000 ! parm98.dat, TC,PC,PAK +CT OS CT NG 0.65000000 2 0.000 ! Piotr et al. +CT CZ CZ HZ 0.00000000 1 0.000 ! Junmei et al, 1999 +O C OS CT 2.70000000 2 180.0 ! Junmei et al, 1999 +O C OS CT 1.40000000 1 180.0 ! Junmei et al, 1999 +OS CT NG CK 0.00000000 2 0.000 ! parm98, TC,PC,PAK +OS CT NG CK 2.50000000 1 0.000 ! parm98, TC,PC,PAK +OS CT NG CM 0.00000000 2 0.000 ! parm98, TC,PC,PAK +OS CT NG CM 2.50000000 1 0.000 ! parm98, TC,PC,PAK +OS CT CT OS 0.14400000 3 0.000 ! parm98, TC,PC,PAK +OS CT CT OS 1.17500000 2 0.000 ! Piotr et al. +OS CT CT OH 0.14400000 3 0.000 ! parm98, TC,PC,PAK +OS CT CT OH 1.17500000 2 0.000 ! parm98, TC,PC,PAK +OH CT CT OH 0.14400000 3 0.000 ! parm98, TC,PC,PAK +OH CT CT OH 1.17500000 2 0.000 ! parm98, TC,PC,PAK +F CT CT F 0.00000000 3 0.000 ! JCC,7,(1986),230 +F CT CT F 1.20000000 1 180.0 ! Junmei et al, 1999 +Cl CT CT Cl 0.00000000 3 0.000 ! JCC,7,(1986),230 +Cl CT CT Cl 0.45000000 1 180.0 ! Junmei et al, 1999 +Br CT CT Br 0.00000000 3 0.000 ! JCC,7,(1986),230 +Br CT CT Br 0.00000000 1 180.0 ! Junmei et al, 1999 +H1 CT CT OS 0.00000000 3 0.000 ! JCC,7,(1986),230 +H1 CT CT OS 0.25000000 1 0.000 ! Junmei et al, 1999 +H1 CT CT OH 0.00000000 3 0.000 ! JCC,7,(1986),230 +H1 CT CT OH 0.25000000 1 0.000 ! Junmei et al, 1999 +H1 CX CT OH 0.00000000 3 0.000 ! JCC,7,(1986),230 (was H1-CT-CT-OH) +H1 CX CT OH 0.25000000 1 0.000 ! Junmei et al, 1999 (was H1-CT-CT-OH) +H1 CT CT F 0.00000000 3 0.000 ! JCC,7,(1986),230 +H1 CT CT F 0.19000000 1 0.000 ! Junmei et al, 1999 +H1 CT CT Cl 0.00000000 3 0.000 ! JCC,7,(1986),230 +H1 CT CT Cl 0.25000000 1 0.000 ! Junmei et al, 1999 +H1 CT CT Br 0.00000000 3 0.000 ! JCC,7,(1986),230 +H1 CT CT Br 0.55000000 1 0.000 ! Junmei et al, 1999 +HC CT CT OS 0.00000000 3 0.000 ! JCC,7,(1986),230 +HC CT CT OS 0.25000000 1 0.000 ! Junmei et al, 1999 +HC CT CT OH 0.00000000 3 0.000 ! JCC,7,(1986),230 +HC CT CT OH 0.25000000 1 0.000 ! Junmei et al, 1999 +HC CT CT F 0.00000000 3 0.000 ! JCC,7,(1986),230 +HC CT CT F 0.19000000 1 0.000 ! Junmei et al, 1999 +HC CT CT Cl 0.00000000 3 0.000 ! JCC,7,(1986),230 +HC CT CT Cl 0.25000000 1 0.000 ! Junmei et al, 1999 +HC CT CT Br 0.00000000 3 0.000 ! JCC,7,(1986),230 +HC CT CT Br 0.55000000 1 0.000 ! Junmei et al, 1999 +H1 CT NT EP 0.00000000 3 0.000 ! +CT CT NT EP 0.00000000 3 0.000 ! +CT C N EP 0.00000000 2 180.000 ! +O C N EP 0.00000000 2 180.000 ! +H1 CT OH EP 0.00000000 3 0.000 ! +CT CT OH EP 0.00000000 3 0.000 ! +H1 CT OS EP 0.00000000 3 0.000 ! +H2 CT OS EP 0.00000000 3 0.000 ! +CT CT OS EP 0.00000000 3 0.000 ! +CM CM OS EP 0.00000000 2 180.000 ! +HA CM OS EP 0.00000000 2 180.000 ! +H4 CM OS EP 0.00000000 2 180.000 ! +CS CS OS EP 0.00000000 2 180.000 ! +HA CS OS EP 0.00000000 2 180.000 ! +H4 CS OS EP 0.00000000 2 180.000 ! +N CT CT OH 0.00000000 1 0.000 ! HYP +N CT CT OH 1.49000000 2 0.000 ! HYP (JCC 26:1612,2005) +N CT CT OH 0.15600000 3 0.000 ! HYP +N CT CT OH 0.00000000 4 0.000 ! HYP +EP S S CT 0.00000000 3 0.000 ! cyx (dac) +EP S S EP 0.00000000 3 0.000 ! cyx (dac) +C8 CX N C 0.00000000 4 0.000 ! phi' +C8 CX N C 0.80000000 3 0.000 ! +C8 CX N C 1.80000000 2 0.000 ! +C8 CX N C 2.00000000 1 0.000 ! +CT CX N C 0.00000000 4 0.000 ! +CT CX N C 0.80000000 3 0.000 ! +CT CX N C 1.80000000 2 0.000 ! +CT CX N C 2.00000000 1 0.000 ! +2C CX N C 0.00000000 4 0.000 ! +2C CX N C 0.80000000 3 0.000 ! +2C CX N C 1.80000000 2 0.000 ! +2C CX N C 2.00000000 1 0.000 ! +3C CX N C 0.00000000 4 0.000 ! +3C CX N C 0.80000000 3 0.000 ! +3C CX N C 1.80000000 2 0.000 ! +3C CX N C 2.00000000 1 0.000 ! +N C CX C8 0.00000000 4 0.000 ! psi' +N C CX C8 0.40000000 3 0.000 ! +N C CX C8 0.20000000 2 0.000 ! +N C CX C8 0.20000000 1 0.000 ! +N C CX CT 0.00000000 4 0.000 ! +N C CX CT 0.40000000 3 0.000 ! +N C CX CT 0.20000000 2 0.000 ! +N C CX CT 0.20000000 1 0.000 ! +N C CX 2C 0.00000000 4 0.000 ! +N C CX 2C 0.40000000 3 0.000 ! +N C CX 2C 0.20000000 2 0.000 ! +N C CX 2C 0.20000000 1 0.000 ! +N C CX 3C 0.00000000 4 0.000 ! +N C CX 3C 0.40000000 3 0.000 ! +N C CX 3C 0.20000000 2 0.000 ! +N C CX 3C 0.20000000 1 0.000 ! +N C 2C HC 0.00000000 2 0.000 ! JCC,7,(1986),230 (X -C -CT-X ) +O C 2C HC 0.08000000 3 180.0 ! Junmei et al, 1999 (HC-CT-C -O ) +O C 2C HC 0.00000000 2 0.000 ! +O C 2C HC 0.80000000 1 0.000 ! +OH C 2C HC 0.00000000 2 0.000 ! +CB CG 2C HC 0.00000000 2 0.000 ! JCC,7,(1986),230 (X -C*-CT-X ) +CW CG 2C HC 0.00000000 2 0.000 ! +X C8 C8 X 0.15555556 3 0.000 ! JCC,7,(1986),230 (X -CT-CT-X ) +C8 C8 C8 HC 0.16000000 3 0.000 ! Junmei et al, 1999 (was HC-CT-CT-CT) +CX C8 C8 HC 0.16000000 3 0.000 ! +HC C8 C8 HC 0.15000000 3 0.000 ! Junmei et al, 1999 (HC-CT-CT-HC) +X C8 CX X 0.15555556 3 0.000 ! +X C8 N2 X 0.00000000 3 0.000 ! JCC,7,(1986),230 (X -CT-N2-X ) +X C8 N3 X 0.15555556 3 0.000 ! JCC,7,(1986),230 (was X -CT-N3-X ) +X CA 2C X 0.00000000 2 0.000 ! JCC,7,(1986),230 (was X -CA-CT-X ) +2C CC CV H4 5.15000000 2 180.0 ! +2C CC CV NB 5.15000000 2 180.0 ! +2C CC CW H4 5.37500000 2 180.0 ! +2C CC CW NA 5.37500000 2 180.0 ! +2C CC NA CR 1.40000000 2 180.0 ! +2C CC NA H 1.40000000 2 180.0 ! +2C CC NB CR 2.40000000 2 180.0 ! +CV CC 2C HC 0.00000000 2 0.000 ! +CW CC 2C HC 0.00000000 2 0.000 ! +NA CC 2C HC 0.00000000 2 0.000 ! +NB CC 2C HC 0.00000000 2 0.000 ! +O2 CO 2C HC 0.00000000 2 0.000 ! +H1 CT S 2C 0.33333333 3 0.000 ! +HC CT 2C HC 0.15000000 3 0.000 ! +HC CT 2C 3C 0.16000000 3 0.000 ! +HC CT 3C CT 0.16000000 3 0.000 ! +HC CT 3C CX 0.16000000 3 0.000 ! +HC CT 3C H1 0.15555556 3 0.000 ! +HC CT 3C HC 0.15000000 3 0.000 ! +HC CT 3C OH 0.00000000 3 0.000 ! +HC CT 3C OH 0.25000000 1 0.000 ! +HC CT 3C 2C 0.16000000 3 0.000 ! +X CX 2C X 0.15555556 3 0.000 ! +H1 CX 2C OH 0.00000000 3 0.000 ! +H1 CX 2C OH 0.25000000 1 0.000 ! +X CX 3C X 0.15555556 3 0.000 ! +H1 CX 3C OH 0.00000000 3 0.000 ! +H1 CX 3C OH 0.25000000 1 0.000 ! +HO OH 2C H1 0.16666667 3 0.000 ! JCC,7,(1986),230 +HO OH 3C H1 0.16666667 3 0.000 ! +EP S S 2C 0.00000000 3 0.000 ! cyx (dac) +X S 2C X 0.33333333 3 0.000 ! JCC,7,(1986),230 (X -CT-S -X ) +X SH 2C X 0.25000000 3 0.000 ! JCC,7,(1986),230 (X -CT-SH-X ) +X 2C 2C X 0.15555556 3 0.000 ! +CX 2C 2C HC 0.16000000 3 0.000 ! Junmei et al, 1999 +HC 2C 2C HC 0.15000000 3 0.000 ! Junmei et al, 1999 +CT 2C 3C HC 0.16000000 3 0.000 ! Junmei et al, 1999 +CX 2C 3C HC 0.16000000 3 0.000 ! +HC 2C 3C CT 0.16000000 3 0.000 ! +HC 2C 3C CX 0.16000000 3 0.000 ! +HC 2C 3C HC 0.15000000 3 0.000 ! +C CX C8 C8 0.15555556 3 0.000 ! Arg Lys +N CX C8 C8 0.15555556 3 0.000 ! +N3 CX C8 C8 0.15555556 3 0.000 ! +CX C8 C8 C8 0.18000000 3 0.000 ! +CX C8 C8 C8 0.25000000 2 180.0 ! +CX C8 C8 C8 0.20000000 1 180.0 ! +C8 C8 C8 N2 0.15555556 3 0.000 ! +C8 C8 N2 CA 0.00000000 1 0.000 ! +C8 C8 C8 C8 0.18000000 3 0.000 ! +C8 C8 C8 C8 0.25000000 2 180.0 ! +C8 C8 C8 C8 0.20000000 1 180.0 ! +C8 C8 C8 N3 0.15555556 3 0.000 ! +C8 N2 CA N2 0.00000000 4 0.000 ! Arg Lys copied +C8 N2 CA N2 2.40000000 2 180.0 ! +H N2 CA N2 0.00000000 4 0.000 ! +H N2 CA N2 2.40000000 2 180.0 ! +C8 C8 N3 H 0.15555556 3 0.000 ! +C CX 2C SH 0.07500000 4 0.000 ! C +C CX 2C SH 0.25100000 3 0.000 ! +C CX 2C SH 0.33700000 2 180.0 ! +C CX 2C SH 0.26900000 1 180.0 ! +N CX 2C SH 0.03300000 4 0.000 ! +N CX 2C SH 0.25100000 3 0.000 ! +N CX 2C SH 0.48600000 2 180.0 ! +N CX 2C SH 0.15400000 1 0.000 ! +N3 CX 2C SH 0.03300000 4 0.000 ! +N3 CX 2C SH 0.25100000 3 0.000 ! +N3 CX 2C SH 0.48600000 2 180.0 ! +N3 CX 2C SH 0.15400000 1 0.000 ! +CX 2C SH HS 0.03000000 4 0.000 ! +CX 2C SH HS 0.25200000 3 0.000 ! +CX 2C SH HS 0.61200000 2 0.000 ! +CX 2C SH HS 0.09200000 1 0.000 ! +C CX 2C CO 0.15400000 4 0.000 ! D +C CX 2C CO 0.05800000 3 0.000 ! +C CX 2C CO 0.45900000 2 180.0 ! +C CX 2C CO 0.42400000 1 0.000 ! +N CX 2C CO 0.08900000 4 0.000 ! +N CX 2C CO 0.05800000 3 0.000 ! +N CX 2C CO 0.64700000 2 180.0 ! +N CX 2C CO 2.15400000 1 180.0 ! +N3 CX 2C CO 0.08900000 4 0.000 ! +N3 CX 2C CO 0.05800000 3 0.000 ! +N3 CX 2C CO 0.64700000 2 180.0 ! +N3 CX 2C CO 2.15400000 1 180.0 ! +CX 2C CO O2 0.03100000 4 180.0 ! +CX 2C CO O2 0.00000000 3 0.000 ! +CX 2C CO O2 0.76900000 2 180.0 ! +CX 2C CO O2 0.00000000 1 0.000 ! +C CX 2C C 0.10700000 4 0.000 ! DhN +C CX 2C C 0.03300000 3 0.000 ! +C CX 2C C 0.30300000 2 180.0 ! +C CX 2C C 1.04600000 1 0.000 ! +N CX 2C C 0.05900000 4 0.000 ! +N CX 2C C 0.03300000 3 0.000 ! +N CX 2C C 0.29700000 2 180.0 ! +N CX 2C C 0.68800000 1 180.0 ! +N3 CX 2C C 0.05900000 4 0.000 ! +N3 CX 2C C 0.03300000 3 0.000 ! +N3 CX 2C C 0.29700000 2 180.0 ! +N3 CX 2C C 0.68800000 1 180.0 ! +CX 2C C O 0.00000000 1 0.000 ! +CX 2C C OH 0.19900000 4 180.0 ! +CX 2C C OH 0.00800000 3 0.000 ! +CX 2C C OH 0.57500000 2 180.0 ! +CX 2C C OH 1.19900000 1 180.0 ! +2C C OH HO 0.11300000 4 0.000 ! +2C C OH HO 0.47900000 3 0.000 ! +2C C OH HO 2.70600000 2 180.0 ! +2C C OH HO 0.44800000 1 180.0 ! +CX 2C C N 0.00800000 4 0.000 ! +CX 2C C N 0.30100000 3 180.0 ! +CX 2C C N 0.48500000 2 180.0 ! +CX 2C C N 0.82800000 1 180.0 ! +C CX CT CC 0.02500000 4 0.000 ! Hie,dp +C CX CT CC 0.21900000 3 0.000 ! +C CX CT CC 0.24400000 2 180.0 ! +C CX CT CC 0.14300000 1 180.0 ! +N CX CT CC 0.08900000 4 0.000 ! +N CX CT CC 0.21900000 3 0.000 ! +N CX CT CC 0.22100000 2 180.0 ! +N CX CT CC 0.30600000 1 180.0 ! +N3 CX CT CC 0.08900000 4 0.000 ! +N3 CX CT CC 0.21900000 3 0.000 ! +N3 CX CT CC 0.22100000 2 180.0 ! +N3 CX CT CC 0.30600000 1 180.0 ! +CX CT CC NA 0.03700000 4 180.0 ! +CX CT CC NA 0.68600000 3 0.000 ! +CX CT CC NA 0.39200000 2 180.0 ! +CX CT CC NA 0.16000000 1 180.0 ! +CX CT CC CV 0.01000000 4 180.0 ! +CX CT CC CV 0.12200000 3 180.0 ! +CX CT CC CV 0.75000000 2 0.000 ! +CX CT CC CV 0.67400000 1 180.0 ! +CX CT CC NB 0.04700000 4 180.0 ! +CX CT CC NB 0.74000000 3 0.000 ! +CX CT CC NB 0.20400000 2 0.000 ! +CX CT CC NB 0.69000000 1 0.000 ! +C CX 3C CT 0.11200000 4 0.000 ! ITV +C CX 3C CT 0.14800000 3 0.000 ! +C CX 3C CT 0.28900000 2 180.0 ! +C CX 3C CT 0.40600000 1 180.0 ! +C CX 3C 2C 0.11500000 4 0.000 ! +C CX 3C 2C 0.11300000 3 0.000 ! +C CX 3C 2C 0.73500000 2 180.0 ! +C CX 3C 2C 0.16200000 1 0.000 ! +N CX 3C CT 0.00100000 4 180.0 ! +N CX 3C CT 0.14800000 3 0.000 ! +N CX 3C CT 0.21600000 2 180.0 ! +N CX 3C CT 0.33700000 1 0.000 ! +N CX 3C 2C 0.09700000 4 180.0 ! +N CX 3C 2C 0.11300000 3 0.000 ! +N CX 3C 2C 0.14400000 2 180.0 ! +N CX 3C 2C 0.31000000 1 0.000 ! +N3 CX 3C CT 0.00100000 4 180.0 ! +N3 CX 3C CT 0.14800000 3 0.000 ! +N3 CX 3C CT 0.21600000 2 180.0 ! +N3 CX 3C CT 0.33700000 1 0.000 ! +N3 CX 3C 2C 0.09700000 4 180.0 ! +N3 CX 3C 2C 0.11300000 3 0.000 ! +N3 CX 3C 2C 0.14400000 2 180.0 ! +N3 CX 3C 2C 0.31000000 1 0.000 ! +CX 3C 2C CT 0.23000000 4 0.000 ! +CX 3C 2C CT 0.10700000 3 0.000 ! +CX 3C 2C CT 0.05300000 2 0.000 ! +CX 3C 2C CT 0.44700000 1 0.000 ! +CT 3C 2C CT 0.22400000 4 0.000 ! +CT 3C 2C CT 0.10700000 3 0.000 ! +CT 3C 2C CT 0.07700000 2 180.0 ! +CT 3C 2C CT 0.20200000 1 0.000 ! +C CX 3C OH 0.15600000 4 0.000 ! +C CX 3C OH 0.31500000 3 0.000 ! +C CX 3C OH 0.11900000 2 180.0 ! +C CX 3C OH 0.69700000 1 180.0 ! +N CX 3C OH 0.09500000 4 0.000 ! +N CX 3C OH 0.31500000 3 0.000 ! +N CX 3C OH 0.00600000 2 0.000 ! +N CX 3C OH 0.67400000 1 0.000 ! +N3 CX 3C OH 0.09500000 4 0.000 ! +N3 CX 3C OH 0.31500000 3 0.000 ! +N3 CX 3C OH 0.00600000 2 0.000 ! +N3 CX 3C OH 0.67400000 1 0.000 ! +CX 3C OH HO 0.01300000 4 0.000 ! +CX 3C OH HO 0.23600000 3 0.000 ! +CX 3C OH HO 0.25100000 2 0.000 ! +CX 3C OH HO 0.00600000 1 180.0 ! +CT 3C OH HO 0.04800000 4 0.000 ! +CT 3C OH HO 0.23600000 3 0.000 ! +CT 3C OH HO 0.07900000 2 180.0 ! +CT 3C OH HO 0.64300000 1 0.000 ! +C CX 2C 3C 0.19000000 4 0.000 ! L +C CX 2C 3C 0.14400000 3 0.000 ! +C CX 2C 3C 0.62000000 2 180.0 ! +C CX 2C 3C 0.70600000 1 0.000 ! +N CX 2C 3C 0.07300000 4 0.000 ! +N CX 2C 3C 0.14400000 3 0.000 ! +N CX 2C 3C 0.25900000 2 180.0 ! +N CX 2C 3C 0.09800000 1 0.000 ! +N3 CX 2C 3C 0.07300000 4 0.000 ! +N3 CX 2C 3C 0.14400000 3 0.000 ! +N3 CX 2C 3C 0.25900000 2 180.0 ! +N3 CX 2C 3C 0.09800000 1 0.000 ! +CX 2C 3C CT 0.17900000 4 0.000 ! +CX 2C 3C CT 0.14200000 3 0.000 ! +CX 2C 3C CT 0.02700000 2 180.0 ! +CX 2C 3C CT 0.37900000 1 0.000 ! +C CX 2C OH 0.12900000 4 0.000 ! S +C CX 2C OH 0.40100000 3 0.000 ! +C CX 2C OH 0.21800000 2 180.0 ! +C CX 2C OH 0.66100000 1 180.0 ! +N CX 2C OH 0.16000000 4 0.000 ! +N CX 2C OH 0.40100000 3 0.000 ! +N CX 2C OH 0.24600000 2 180.0 ! +N CX 2C OH 0.66600000 1 0.000 ! +N3 CX 2C OH 0.16000000 4 0.000 ! +N3 CX 2C OH 0.40100000 3 0.000 ! +N3 CX 2C OH 0.24600000 2 180.0 ! +N3 CX 2C OH 0.66600000 1 0.000 ! +CX 2C OH HO 0.00700000 4 0.000 ! +CX 2C OH HO 0.26700000 3 0.000 ! +CX 2C OH HO 0.44400000 2 0.000 ! +CX 2C OH HO 0.21100000 1 0.000 ! +C CX CT CG 0.07400000 4 0.000 ! W_CB +C CX CT CG 0.23400000 3 0.000 ! +C CX CT CG 0.35300000 2 180.0 ! +C CX CT CG 0.01700000 1 180.0 ! +N CX CT CG 0.03100000 4 0.000 ! +N CX CT CG 0.23400000 3 0.000 ! +N CX CT CG 0.31300000 2 180.0 ! +N CX CT CG 0.07900000 1 0.000 ! +N3 CX CT CG 0.03100000 4 0.000 ! +N3 CX CT CG 0.23400000 3 0.000 ! +N3 CX CT CG 0.31300000 2 180.0 ! +N3 CX CT CG 0.07900000 1 0.000 ! +CX CT CG CB 0.09500000 4 180.0 ! +CX CT CG CB 0.81900000 3 0.000 ! +CX CT CG CB 0.40800000 2 0.000 ! +CX CT CG CB 0.36500000 1 0.000 ! +CX CT CG CW 0.00000000 4 0.000 ! +CX CT CG CW 0.00000000 3 0.000 ! +CX CT CG CW 0.00000000 2 0.000 ! +CX CT CG CW 0.00000000 1 0.000 ! +C CX CT CA 0.01200000 4 180.0 ! FY +C CX CT CA 0.19200000 3 0.000 ! +C CX CT CA 0.46900000 2 180.0 ! +C CX CT CA 0.05500000 1 0.000 ! +N CX CT CA 0.00700000 4 180.0 ! +N CX CT CA 0.19200000 3 0.000 ! +N CX CT CA 0.29000000 2 180.0 ! +N CX CT CA 0.01200000 1 180.0 ! +N3 CX CT CA 0.00700000 4 180.0 ! +N3 CX CT CA 0.19200000 3 0.000 ! +N3 CX CT CA 0.29000000 2 180.0 ! +N3 CX CT CA 0.01200000 1 180.0 ! +CX CT CA CA 0.04800000 4 180.0 ! +CX CT CA CA 0.00000000 3 0.000 ! +CX CT CA CA 0.06900000 2 180.0 ! +CX CT CA CA 0.00000000 1 0.000 ! +CA C OH HO 0.06500000 4 0.000 ! +CA C OH HO 0.00000000 3 0.000 ! +CA C OH HO 0.88300000 2 180.0 ! +CA C OH HO 0.00000000 1 0.000 ! +C CX 2C 2C 0.14500000 4 0.000 ! Glh Gln Glu Met +C CX 2C 2C 0.14400000 3 0.000 ! +C CX 2C 2C 0.39300000 2 180.0 ! +C CX 2C 2C 0.42100000 1 180.0 ! +N CX 2C 2C 0.07800000 4 0.000 ! +N CX 2C 2C 0.14400000 3 0.000 ! +N CX 2C 2C 0.18400000 2 180.0 ! +N CX 2C 2C 0.10000000 1 180.0 ! +N3 CX 2C 2C 0.07800000 4 0.000 ! +N3 CX 2C 2C 0.14400000 3 0.000 ! +N3 CX 2C 2C 0.18400000 2 180.0 ! +N3 CX 2C 2C 0.10000000 1 180.0 ! +CX 2C 2C C 0.13800000 4 0.000 ! +CX 2C 2C C 0.41200000 3 180.0 ! +CX 2C 2C C 0.08300000 2 0.000 ! +CX 2C 2C C 0.19600000 1 180.0 ! +2C 2C C O 0.00000000 1 0.000 ! +2C 2C C OH 0.06600000 4 180.0 ! +2C 2C C OH 0.02500000 3 180.0 ! +2C 2C C OH 1.10400000 2 180.0 ! +2C 2C C OH 0.82400000 1 180.0 ! +2C 2C C N 0.04200000 4 0.000 ! +2C 2C C N 0.08500000 3 180.0 ! +2C 2C C N 0.84500000 2 180.0 ! +2C 2C C N 0.60900000 1 180.0 ! +CX 2C 2C CO 0.05600000 4 180.0 ! +CX 2C 2C CO 0.60800000 3 180.0 ! +CX 2C 2C CO 0.22200000 2 180.0 ! +CX 2C 2C CO 1.36700000 1 180.0 ! +2C 2C CO O2 0.06400000 4 0.000 ! +2C 2C CO O2 0.39000000 2 180.0 ! +CX 2C 2C S 0.02800000 4 0.000 ! +CX 2C 2C S 0.01600000 3 0.000 ! +CX 2C 2C S 0.24500000 2 0.000 ! +CX 2C 2C S 0.41700000 1 0.000 ! +2C 2C S CT 0.05700000 4 0.000 ! +2C 2C S CT 0.41400000 3 0.000 ! +2C 2C S CT 0.44200000 2 0.000 ! +2C 2C S CT 0.24700000 1 180.0 ! +C CX 2C S 0.27800000 4 0.000 ! C-C +C CX 2C S 0.32300000 3 0.000 ! +C CX 2C S 0.39400000 2 180.0 ! +C CX 2C S 0.60200000 1 0.000 ! +N CX 2C S 0.06400000 4 0.000 ! +N CX 2C S 0.32300000 3 0.000 ! +N CX 2C S 0.02100000 2 180.0 ! +N CX 2C S 0.46900000 1 0.000 ! +N3 CX 2C S 0.06400000 4 0.000 ! +N3 CX 2C S 0.32300000 3 0.000 ! +N3 CX 2C S 0.02100000 2 180.0 ! +N3 CX 2C S 0.46900000 1 0.000 ! +CX 2C S S 0.13500000 4 180.0 ! +CX 2C S S 0.30200000 3 0.000 ! +CX 2C S S 0.66600000 2 0.000 ! +CX 2C S S 0.05600000 1 0.000 ! +2C S S 2C 0.37900000 4 0.000 ! +2C S S 2C 0.68200000 3 0.000 ! +2C S S 2C 4.48000000 2 0.000 ! +2C S S 2C 0.42000000 1 0.000 ! + +IMPHI +X X C O 10.5 2 180.0 ! JCC,7,(1986),230 +X O2 C O2 10.5 2 180.0 ! JCC,7,(1986),230 +X X N H 1.0 2 180.0 ! JCC,7,(1986),230 +X X N2 H 1.0 2 180.0 ! JCC,7,(1986),230 +X X NA H 1.0 2 180.0 ! JCC,7,(1986),230 +X N2 CA N2 10.5 2 180.0 ! JCC,7,(1986),230 +X CT N CT 1.0 2 180.0 ! JCC,7,(1986),230 +X CT N CX 1.0 2 180.0 ! JCC,7,(1986),230 (was X -CT-N -CT) +X X CA HA 1.1 2 180.0 ! bsd.on C6H6 nmodes +X X CW H4 1.1 2 180.0 ! +X X CR H5 1.1 2 180.0 ! +X X CV H4 1.1 2 180.0 ! +X X CQ H5 1.1 2 180.0 ! +X X CK H5 1.1 2 180.0 ! +X X CP H5 1.1 2 180.0 ! +X X CM H4 1.1 2 180.0 ! +X X CM HA 1.1 2 180.0 ! +X X CS H4 1.1 2 180.0 ! +X X CS HA 1.1 2 180.0 ! +X X CA H4 1.1 2 180.0 ! bsd.on C6H6 nmodes +X X CA H5 1.1 2 180.0 ! bsd.on C6H6 nmodes +CB CK NG CT 1.0 2 180.0 ! +CB CP NG CT 1.0 2 180.0 ! +C CM NG CT 1.0 2 180.0 ! dac guess, 9/94 +C CS NG CT 1.0 2 180.0 ! dac guess, 9/94 +C CS CM CT 1.1 2 180.0 ! +CT O C OH 10.5 2 180.0 ! +CT CV CC NA 1.1 2 180.0 ! +CT CW CC NB 1.1 2 180.0 ! +CT CW CC NA 1.1 2 180.0 ! +CB CT CG CW 1.1 2 180.0 ! +CA CA CA CT 1.1 2 180.0 ! +C CM CM CT 1.1 2 180.0 ! dac guess, 9/94 +C CS CS CT 1.1 2 180.0 ! dac guess, 9/94 +CM N2 CA NC 1.1 2 180.0 ! dac guess, 9/94 +CS N2 CA NC 1.1 2 180.0 ! dac guess, 9/94 +CB N2 CA NC 1.1 2 180.0 ! dac, 10/94 +N2 NA CA NC 1.1 2 180.0 ! dac, 10/94 +CA CA C OH 1.1 2 180.0 ! (not used in tyr!) +CA CA CA OH 1.1 2 180.0 ! in tyr +H5 O C OH 1.1 2 180.0 ! Junmei et al.1999 +H5 O C OS 1.1 2 180.0 ! +CM CT CM HA 1.1 2 180.0 ! Junmei et al.1999 +CS CT CS HA 1.1 2 180.0 ! Junmei et al.1999 +Br CA CA CA 1.1 2 180.0 ! Junmei et al.1999 +CM H4 C O 1.1 2 180.0 ! Junmei et al.1999 +CS H4 C O 1.1 2 180.0 ! Junmei et al.1999 +C CT N H 1.1 2 180.0 ! Junmei et al.1999 +C CX N H 1.1 2 180.0 ! Junmei et al.1999 (was C -CT-N -H ) +C CT N O 1.1 2 180.0 ! Junmei et al.1999 +X X C5 H5 1.1 2 180.0 ! +CB C5 NG CT 1.0 2 180.0 ! +X X C4 H4 1.1 2 180.0 ! +X X C4 HA 1.1 2 180.0 ! +C C4 NG CT 1.0 2 180.0 ! dac guess, 9/94 +C C4 C4 CT 1.1 2 180.0 ! dac guess, 9/94 +C4 N2 CA NC 1.1 2 180.0 ! dac guess, 9/94 +CA CA C OS 1.1 2 180.0 ! phosphotyrosine +CR CC NA P 1.1 2 180.0 ! phosphohistine +X O2 CO O2 10.5 2 180.0 ! +2C O C OH 10.5 2 180.0 ! +CA CA CA 2C 1.1 2 180.0 ! + +! +! Note: the HO and HW parameters, although zero in Cornell et al. +! should not have a 0.0 vdw radius in CHARMM to avoid difficulties +! with the 0.0/0.0 in the FAST OFF van der Waal code... +! +! NOTE: the defaults chosen here are to match AMBER. It is not +! recommended that users actually run with GROUP based truncation +! and a switch. Better would be ATOM based FSHIFT VSHIFT +NONBONDED NBXMOD 5 GROUP SWITCH CDIEL - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 0.83333333 WMIN 1.4 +! Emin Rmin/2 Emin/2 Rmin (for 1-4's) +! (kcal/mol) (A) +H 0.0 -0.015700 0.600000 0.0 -0.0078500 0.600000 ! Ferguson base pair geom. +HO 0.0 -0.000000 0.000000 0.0 -0.0000000 0.000000 ! OPLS Jorgensen, JACS,110,(1988),1657 +HS 0.0 -0.015700 0.600000 0.0 -0.0078500 0.600000 ! W. Cornell CH3SH --> CH3OH FEP +HC 0.0 -0.015700 1.487000 0.0 -0.0078500 1.487000 ! OPLS +H1 0.0 -0.015700 1.387000 0.0 -0.0078500 1.387000 ! Veenstra et al JCC,8,(1992),963 +H2 0.0 -0.015700 1.287000 0.0 -0.0078500 1.287000 ! Veenstra et al JCC,8,(1992),963 +H3 0.0 -0.015700 1.187000 0.0 -0.0078500 1.187000 ! Veenstra et al JCC,8,(1992),963 +HP 0.0 -0.015700 1.100000 0.0 -0.0078500 1.100000 ! Veenstra et al JCC,8,(1992),963 +HA 0.0 -0.015000 1.459000 0.0 -0.0075000 1.459000 ! Spellmeyer +H4 0.0 -0.015000 1.409000 0.0 -0.0075000 1.409000 ! Spellmeyer, one electrowithdr. neighbor +H5 0.0 -0.015000 1.359000 0.0 -0.0075000 1.359000 ! Spellmeyer, two electrowithdr. neighbor +HW 0.0 -0.000000 0.000000 0.0 -0.0000000 0.000000 ! TIP3P water model +HZ 0.0 -0.015000 1.459000 0.0 -0.0075000 1.459000 ! H bonded to sp C (Howard et al JCC 16) +O 0.0 -0.210000 1.661200 0.0 -0.1050000 1.661200 ! OPLS +O2 0.0 -0.210000 1.661200 0.0 -0.1050000 1.661200 ! OPLS +OW 0.0 -0.152000 1.768300 0.0 -0.0760000 1.768300 ! TIP3P water model +OH 0.0 -0.210400 1.721000 0.0 -0.1052000 1.721000 ! OPLS +OS 0.0 -0.170000 1.683700 0.0 -0.0850000 1.683700 ! OPLS ether +OP 0.0 -0.170000 1.850000 0.0 -0.0850000 1.850000 ! Steinbrecher/Latzer for 2- phosphate +CG 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CA 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CB 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CC 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CD 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CK 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CM 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CN 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CQ 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CR 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CV 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CW 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CY 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CZ 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CP 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CS 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CI 0.0 -0.109400 1.908000 0.0 -0.0547000 1.908000 ! parmbsc0 +C5 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +C4 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer +CT 0.0 -0.109400 1.908000 0.0 -0.0547000 1.908000 ! Spellmeyer +CX 0.0 -0.109400 1.908000 0.0 -0.0547000 1.908000 ! Spellmeyer (was CT) +C 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS +N 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +NA 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +N2 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +NG 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +NC 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +NB 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +NT 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +NY 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +N3 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS +S 0.0 -0.250000 2.000000 0.0 -0.1250000 2.000000 ! W. Cornell CH3SH and CH3SCH3 FEP's +SH 0.0 -0.250000 2.000000 0.0 -0.1250000 2.000000 ! W. Cornell CH3SH and CH3SCH3 FEP's +P 0.0 -0.200000 2.100000 0.0 -0.1000000 2.100000 ! JCC,7,(1986),230; +MG 0.0 -0.894700 0.792600 0.0 -0.4473500 0.792600 ! Mg2+ Aqvist JPC 1990,94,8021.(adapted) +C0 0.0 -0.459789 1.713100 0.0 -0.2298945 1.713100 ! Ca2+ Aqvist JPC 1990,94,8021.(adapted) +Zn 0.0 -0.012500 1.100000 0.0 -0.0062500 1.100000 ! Zn2+, Merz,PAK, JACS,113,8262,(1991) +F 0.0 -0.061000 1.750000 0.0 -0.0305000 1.750000 ! Gough et al. JCC 13,(1992),963. +Cl 0.0 -0.265000 1.948000 0.0 -0.1325000 1.948000 ! Fox, JPCB,102,8070,(98),flex.mdl CHCl3 +Br 0.0 -0.320000 2.220000 0.0 -0.1600000 2.220000 ! Junmei(?) +I 0.0 -0.400000 2.350000 0.0 -0.2000000 2.350000 ! JCC,7,(1986),230; +EP 0.0 -0.000000 0.000000 0.0 -0.0000000 0.000000 ! lone pair +2C 0.0 -0.109400 1.908000 0.0 -0.0547000 1.908000 ! Spellmeyer +3C 0.0 -0.109400 1.908000 0.0 -0.0547000 1.908000 ! Spellmeyer +C8 0.0 -0.109400 1.908000 0.0 -0.0547000 1.908000 ! Spellmeyer +CO 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS +SOD 0.0 -0.002770 1.8680 0.0 -0.001385 1.8680 ! Na+ Aqvist JPC 1990,94,8021. (adapted) +POT 0.0 -0.000328 2.6580 0.0 -0.000164 2.6580 ! K+ Aqvist JPC 1990,94,8021. (adapted) +CLA 0.0 -0.1 2.47 0.0 -0.05 2.47 ! Cl- Smith, JCP 1994,100:5,3757. + + +END diff --git a/charmm/toppar/non_charmm/parm14sb_all.rtf b/charmm/toppar/non_charmm/parm14sb_all.rtf new file mode 100644 index 00000000..48c59362 --- /dev/null +++ b/charmm/toppar/non_charmm/parm14sb_all.rtf @@ -0,0 +1,4269 @@ +* AMBER 2014SB force-field conversion +* See: http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00255 +* J. Chem. Theory Comput., DOI: 10.1021/acs.jctc.5b00255 +* +23 1 + +! This is a semi-automated conversion of the AMBER ff14SB force-field, done by +! Dr. Xibing He at Florida State University, in July 2015 +! Email: +! +! This conversion work is based on the previous work of: +! +! (a) Dr. Thomas E. Cheatham, III, who converted the AMBER Cornell force +! field (ff94): +! http://home.chpc.utah.edu/~cheatham/software.html +! Here is the title section of his conversion file: +! AMBER Cornell et al. (parm94) force field conversion +! See: JACS (1995) 117, 5179-5197. +! nucleic acid part converted by tec3, march 1997 +! protein part converted by tec3, february 1999 +! +! (b) Dr. Jeff Klauda, who converted the AMBER99 & AMBER99SB in october 2003: +! http://terpconnect.umd.edu/~jbklauda/research/download.html +! Dr. Klauda's conversion work was based on Dr. Cheatham's work. +! For references about AMBER99 & AMBER99SB, see: +! J Comp. Chem. (2000) 21, 1049-1074. +! Proteins, Structure, Function, and Bioinformatics. (2006) 65, 712-725. +! +! What I have done is as following: +! (1) Install AmberTools15, take files described in +! $AMBERHOME/dat/leap/cmd/leaprc.ff14SB: +! parm10.dat, frcmod.ff14SB, amino12.lib, aminoct12.lib, aminont12.lib, +! nucleic12.lib, atomic_ions.lib, and solvents.lib +! (2) Convert parameters in parm10.dat & frcmod.ff14SB to parm14sb_all.prm, +! using Dr. Klauda's parm99SB_all.prm as template. +! (3) Convert the AMBER library files to parm14sb_all.rtf, using Dr. Klauda's +! parm99sb_all.rtf as template. +! (4) Set up tri-neucleic-acid systems (RNA or DNA), such as ADE5-ADE-ADE3 +! (RNA), or DOA5-DOA-DOA3 (DNA), for ADE, THY, GUA, CYT, URA. +! load the pdb files into CHARMM and AMBER(Sander) programs, print out the +! bond-, angle-, torsion-, and electrostatic energies, and compare. +! Also, the X-,Y-,Z-forces on each atom are printed out and compared. +! The pdb files fed to CHARMM and AMBER(Sander) have different atom names +! according to their conventions, but with the same atom sequences. +! (5) Set up tri-peptides of all amino acid residues, such as ALA-ALA-ALA, +! ARG-ARG-ARG, ..., patch the N- and C-termini at the ends respectively, +! load the pdb files into CHARMM and AMBER(Sander) programs, print out the +! bond-, angle-, torsion-, and electrostatic energies, and compare. +! Also, the X-,Y-,Z-forces on each atom are printed out and compared. +! The pdb files fed to CHARMM and AMBER(Sander) have different atom names +! according to their conventions, but with the same atom sequences. +! (6) PRES DISU does not exist in Dr. Cheatham's & Dr. Klauda's files. +! it is copied from $CHARMMHOME/toppar/non_charmm/top_amber_cornell.inp +! and modified according to AMBER ff14SB (changing some atom types). +! A small system of two chains is set up, chain A: GLY-CYS-GLY, chain +! B: GLY-CYS-GLY, and S-S bond is formed by patch command. This system +! is tested using CHARMM and AMBER(Sander) respectively, and the resulted +! energies and forces are printed out and compared. +! (7) The topologies of TIP3 water, SOD (Na+), POT (K+) and CLA (Cl-), and the +! parameters are copied from Dr. Cheatham's & Dr. Klauda's files. By the way, +! the VDW parameter of Na+, K+ and Cl- cannot be found in parm10.dat or +! frcmod.ff14SB under the AMBER directory $AmberTools15/dat/leap/parm/, but +! still can be found in parm99.dat, and the parameters agree with those in +! Dr. Cheatham's & Dr. Klauda's files. +! (8) Some orders of atoms in the topology file are adjusted in order to get +! same values of energies and forces from CHARMM and AMBER(Sander). +! For example: +! It's said in Dr. Cheatham & Dr. Klauda's conversion files: +! "TRP: the impropers on "CD1 CD2 CG CB" are giving a slight +! energy and force error that I do not understand at present." +! This problem is solved by changing the atom orders in the declaration +! of improper torsion in TRP from "IMPROPER CD1 CD2 CG CB" to +! "IMPROPER CD2 CB CG CD1". +! Another example: +! In HID, HIE, & HIP, "IMPROPER ND1 CD2 CG CB" is changed to +! "IMPROPER CB CD2 CG ND1" +! (9) The BILD tables from top_all36_na.rtf are used to replace the IC tables +! in Dr. Klauda & Dr. Cheatham's conversion files for: +! ADE, URA, THY, CYT, GUA +! These tables matter if you want to generate coordinates automatically +! using CHARMM program instead of reading coordinates from files. +! The old IC tables for nucleic residues are abandoned because they bring +! a "level -1" error for a test case. Thanks to Prof. Alexander MacKerell +! (University of Maryland, Baltimore) for the test case. +! +! Note: The energies and forces agree to within ~0.0002 (mostly within ~0.0001) +! using both CHARMM and AMBER. A longrange cutoff of 80 Angstroms was used +! for both AMBER and CHARMM. +! +! Note: In order to compare energies and forces correctly, CHARMM program should +! "be compiled with the AMBER keyword added to pref.dat, to get an exact match: +! a hard-coded electrostatic constant is different for CHARMM and AMBER force +! fields" (said by Rick Venable, et al. on CHARMM Forum). +! Also see below for details about the constant. +! +! Note: Although I have done some test jobs, there is NO guarantee. Therefore, +! USE AT YOUR OWN RISK! +! +! For protein residues, changes of atom types from AMBER ff99SB to ff14SB: +! CT -> CX, for p3 aliphatic C, alpha-C in protein residues. +! CT -> C8, for sp3 aliphatic C, -CH2-, in side chain of ARG & LYS +! CT -> 2C, for sp3 aliphatic C, -CH2-, in side chain of ASN ASP CYS CYX GLH GLH +! GLN GLU ILE LEU MET SER +! CT -> 3C, for sp3 aliphatic C, -CH-, in side chain of ILE LEU THR VAL +! C -> CO, for sp2 C carboxylate group, in side chain of ASP & GLU +! SH -> S , for S in CYX +! +! As to the nucleic acids, some atom types are also changed from ff99SB to ff14SB: +! CT -> CI, for atom name C5' in ADE URA THY CYT GUA and their patches +! CM -> CS, for atom names C6 & C5 in URA (not in patches) +! CM -> C4, for atom names C6 & C5 in CYT (not in patches) +! CK -> CP, for atom name C8 in GUA (not in patches) +! +! In Dr. Cheatham & Dr. Klauda's conversion files, AMBER atom types with "*" +! in the name, N* and C*, were renamed to NS and CS, respectively. However, +! in AMBER ff14SB, atom type CS already exists. Therefore, here N* and C* +! are renamed to NG and CG, respectively. +! +! +! The following remarks are copied from Dr. Cheatham & Dr. Klauda's conversion +! files: +! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! WARNING! Please read through all the comments here in order to +! properly understand how to set up a CHARMM run with this force +! field and to properly understand the limitations and potential +! errors... +! +! NOTE: the charges here are un-scaled and represent the +! exact AMBER charges. See the comment on the electrostatics below. +! +! Standard CHARMM residue names are utilized: +! +! ADE, THY, GUA, CYT, URA. +! +! ALA, ARG, ASN, ASP, CYS, CYM, CYX, GLN, GLU, GLH, +! GLY, HID, HIE, HIP, ILE, LEU, LYS, MET, PHE, PRO, +! SER, THR, TRP, TYR, VAL, ACE, NME +! +! +! Atom type names conform to the AMBER Cornell et. al. 1995, +! parm99.dat, all_nuc94.in, and all_amino* naming conventions +! where possible. Exceptions to this rule include types with "*" +! in the name (i.e. N*, C*). CHARMM atom names are utilized +! except for sodium. +! To build the residues, the BILD arrays from the top_all22_na.inp were +! utilized (since these are actually probably more trustworthy then +! those supplied in AMBER) and modified where necessary (i.e. THY). +! They may not be reliable in all cases. BONDS were also copied from +! top_all22_na.inp and all angles and dihedrals autogenerated. +! The impropers were taken straight from the AMBER residue topology +! files (and placed in proper order). All this was done by hand editing. +! +! Results were checked by comparing energies and forces for all the +! residues defined herein. In general, in simulations performing a +! single energy and force evaluation with a cutoff large enough to +! span the entire system the energies and forces agree +! to within ~0.0005 using both CHARMM and AMBER. A longrange cutoff +! of 80 Angs. was used for both AMBER and CHARMM. The AMBER energies +! and forces were calculated using AMBER 7 sander +! (with &debugf to print out atomic forces to forcedump.dat) and CHARMM +! c31a1 (ener and coor force comp and print coor comp). Note that +! differences in the forces may be apparent if the coordinates do not +! match exactly or in cases where different constants are used between +! AMBER and CHARMM. These points require a little more elaboration. +! +! Differences in the coordinates: +! +! (*) incorrect mapping between AMBER and CHARMM coordinates +! (i.e. not 1-to-1). This is possible with hand editting of the +! AMBER names to convert to CHARMM if the correct mapping isn't +! followed. The only case that was readily apparent in this +! analysis was incorrect mapping of H2' and H2'' in the DNA +! residues of ADE, GUA and CYT. The rename command can be used +! to swap names and alleviate this problem (which is not a real +! problem except when comparing forces). +! +! (*) parm coordinate precision. If the parm coordinates were +! created from a PDB file using the link-edit-parm path, improper +! conversion from text->binary->text in edit/parm leads to +! differences in the parm coordinates from the PDB file. +! Therefore, the coordinates will be different than those +! generated by CHARMM using the same PDB coordinates. Therefore, +! prior to comparing forces, the PDB should be converted directly +! to the parm coordinates (which can be done using xleap). +! +! Differences in the electrostatic energies: +! +! (*) The conversion from charge units to kcal/mol in CHARMM is based +! on the value 332.0716 whereas AMBER uses 18.2223**2 or 332.0522173. +! The actual value is somewhat lower than both these values +! (~331.843)! To convert the charges to "CHARMM", they should be +! multiplied by 1.000058372. This was not done within this file. +! [When this is done, the charges are not rounded and therefore +! non-integral charges for the residues are apparent.] To get around +! this problem either the charges can be scaled within CHARMM (which +! will still lead to non-integral charge) or in versions of CHARMM +! beyond c25n3, and through the application of the "AMBER" keyword in +! pref.dat, the AMBER constant can be used. By default, the "fast" +! routines cannot be used with the AMBER-style impropers. In the +! later versions of CHARMM, the AMBER keyword circumvents this +! problem. +! +! BUILDING NUCLEIC ACID STRUCTURES: +! +! To build residues, use the standard naming conventions. By default +! the 5ter and 3ter patchs are applied which convert the first +! residue to a 5'-hydroxyl (no terminal phosphate) and the last +! residue to a 3'-hydroxyl. +! +! NOTE that in the case of case of ADE, GUA and CYT, by default the +! system is RIBONUCLEIC acid. To convert to deoxyribose, use the +! following patchs: +! +! patch DOA5 segid residue <-- 5'-terminal ADE +! patch DOA segid residue <-- standard ADE +! patch DOA3 segid residue <-- 3'-terminal ADE +! patch DOC5 segid residue <-- 5'-terminal CYT +! patch DOC segid residue <-- standard CYT +! patch DOC3 segid residue <-- 3'-terminal CYT +! patch DOG5 segid residue <-- 5'-terminal GUA +! patch DOG segid residue <-- standard GUA +! patch DOG3 segid residue <-- 3'-terminal GUA +! +! ...where "segid" is the current segment and "residue" is the +! residue number +! +! As an example, let's build a single stranded DNA, d[CATG]. We need +! to apply 5' and 3' terminal patches and also patches to turn the +! RNA into DNA for each residue (except THY which is DNA). +! +! read sequence card +! 4 +! CYT ADE THY GUA +! generate s1 setup +! patch doc5 s1 1 +! patch doa s1 2 +! patch dog3 s1 4 +! +! +! PROTEIN PARAMETERS: +! +! note: isolated amino acids have not been tested, only tri-peptides +! with the same amino acids in the chain, i.e. ala-ala-ala, etc. +! have been tested with charged terminii (i.e. nala-ala-cala). +! The patches to the terminii (for each residue append N for the +! N-terminal or C for the C terminal) are applied automatically +! to the first/last residues. In general the energy/force comparison +! is as good as with the nucleic acid parameters, but do note that as +! the energy increases (such as with large van der Waals overlap) the +! absolute agreement no longer is as good. This may relate to (1) +! slight coordinate differences between AMBER/CHARMM and (2) +! numerical differences due to differing operations in the +! calculation. In any event, equivalent parameters are used and +! there is an equivalent number of bonds/angles/dihedrals, etc. +! between the CHARMM PSF files and AMBER prmtop files. +! +! PROTEIN CONVERSION NOTES: +! +! (1) there are no terminal CYM (negatively charged CYS) residues +! within the Cornell et al. force field. The CYM and CYX +! residues were not tested for reliability. Use at own risk. +! (2) GLH, or neutral glutamic acid isn't available as a C- or N- +! terminal residue. This has not been tested for reliability; +! use at own risk. Note also that the IC table was not modified +! to include the extra hydrogen... +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! +! AMBER atom types and masses (from parm10.dat & frcmod.ff14SB) +! + +MASS 1 C 12.01 ! sp2 C carbonyl group +MASS 2 CA 12.01 ! sp2 C pure aromatic (benzene) +MASS 3 CB 12.01 ! sp2 aromatic C, 5&6 membered ring junction +MASS 4 CC 12.01 ! sp2 aromatic C, 5 memb. ring HIS +MASS 5 CD 12.01 ! sp2 C atom in the middle of: C=CD-CD=C +MASS 6 CI 12.01 ! parmbsc0 +MASS 7 CK 12.01 ! sp2 C 5 memb.ring in purines (dA,dG) +MASS 8 CP 12.01 ! sp2 C 5 memb.ring in purines (G) +MASS 9 CM 12.01 ! sp2 C pyrimidines in pos. 5 & 6 (dT,dC) +MASS 10 CS 12.01 ! sp2 C pyrimidines in pos. 5 & 6 (U) +MASS 11 CN 12.01 ! sp2 C aromatic 5&6 memb.ring junct.(TRP) +MASS 12 CQ 12.01 ! sp2 C in 5 mem.ring of purines between 2 N +MASS 13 CR 12.01 ! sp2 arom as CQ but in HIS +MASS 14 CT 12.01 ! sp3 aliphatic C +MASS 15 CV 12.01 ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +MASS 16 CW 12.01 ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +MASS 17 CG 12.01 ! sp2 arom. 5 memb.ring w/1 subst. (TRP) +MASS 18 CX 12.01 ! protein C-alpha (new to ff10) +MASS 19 CY 12.01 ! nitrile C (Howard et al.JCC,16,243,1995) +MASS 20 CZ 12.01 ! sp C (Howard et al.JCC,16,243,1995) +MASS 21 C5 12.01 ! sp2 C 5 memb.ring in purines (A) +MASS 22 C4 12.01 ! sp2 C pyrimidines in pos. 5 & 6 (C) +MASS 23 CO 12.01 ! sp2 C carboxylate group +MASS 24 2C 12.01 ! sp3 aliphatic C with two (duo) heavy atoms +MASS 25 3C 12.01 ! sp3 aliphatic C with three (tres) heavy atoms +MASS 26 C8 12.01 ! sp3 aliphatic C basic AA side chain +MASS 27 C0 40.08 ! calcium +MASS 28 H 1.008 ! H bonded to nitrogen atoms +MASS 29 HC 1.008 ! H aliph. bond. to C without electrwd.group +MASS 30 H1 1.008 ! H aliph. bond. to C with 1 electrwd. group +MASS 31 H2 1.008 ! H aliph. bond. to C with 2 electrwd.groups +MASS 32 H3 1.008 ! H aliph. bond. to C with 3 eletrwd.groups +MASS 33 HA 1.008 ! H arom. bond. to C without elctrwd. groups +MASS 34 H4 1.008 ! H arom. bond. to C with 1 electrwd. group +MASS 35 H5 1.008 ! H arom.at C with 2 elctrwd. gr,+HCOO group +MASS 36 HO 1.008 ! hydroxyl group +MASS 37 HS 1.008 ! hydrogen bonded to sulphur (pol?) +MASS 38 HW 1.008 ! H in TIP3P water +MASS 39 HP 1.008 ! H bonded to C next to positively charged gr +MASS 40 HZ 1.008 ! H bond sp C (Howard et al.JCC,16,243,1995) +MASS 41 F 19.00 ! fluorine (not fluoride!) +MASS 42 Cl 35.45 ! chlorine (Applequist) (not chloride!) +MASS 43 Br 79.90 ! bromine (Applequist) (not bromide!) +MASS 44 I 126.9 ! iodine (Applequist) (not iodide!) +MASS 45 MG 24.305 ! magnesium +MASS 46 N 14.01 ! sp2 nitrogen in amide groups +MASS 47 NA 14.01 ! sp2 N in 5 memb.ring w/H atom (HIS) +MASS 48 NB 14.01 ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +MASS 49 NC 14.01 ! sp2 N in 6 memb.ring w/LP (ADE,GUA) +MASS 50 N2 14.01 ! sp2 N in amino groups +MASS 51 N3 14.01 ! sp3 N for charged amino groups (Lys, etc) +MASS 52 NT 14.01 ! sp3 N for amino groups amino groups +MASS 53 NG 14.01 ! sp2 N +MASS 54 NY 14.01 ! nitrile N (Howard et al.JCC,16,243,1995) +MASS 55 O 16.00 ! carbonyl group oxygen +MASS 56 O2 16.00 ! carboxyl and phosphate group oxygen +MASS 57 OW 16.00 ! oxygen in TIP3P water +MASS 58 OH 16.00 ! oxygen in hydroxyl group +MASS 59 OS 16.00 ! ether and ester oxygen +MASS 60 OP 16.00 ! 2- phosphate oxygen +MASS 61 P 30.97 ! phosphate,pol:JACS,112,8543,90,K.J.Miller +MASS 62 S 32.06 ! S in disulfide linkage,pol:JPC,102,2399,98 +MASS 63 SH 32.06 ! S in cystine +!MASS 64 CU 63.55 ! copper +!MASS 65 FE 55.00 ! iron +MASS 66 Zn 65.4 ! Zn2+ +MASS 67 EP 0.00 ! extra point +MASS 68 SOD 22.99 ! Na+ +MASS 69 POT 39.10 ! K+ +MASS 70 CLA 35.45 ! Cl- + + +DECL -CA ! proteins +DECL -C +DECL -O +DECL +N +DECL +H +DECL +CA +DECL +P ! nucleic acids +DECL +O1P +DECL +O2P +DECL +O5' +DECL -O3' + +DEFAULT FIRST NTER LAST CTER +AUTOGENERATE ANGLES DIHEDRAL + +! +! WATER & IONS +! + +RESI TIP3 0.00 ! TIPS3P WATER MODEL + ! GENERATE USING NOANGLE NODIHEDRAL +GROUP +ATOM OH2 OW -0.834 +ATOM H1 HW 0.417 +ATOM H2 HW 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +ANGLE H1 OH2 H2 ! REQUIRED +PATCHING FIRS NONE LAST NONE + +RESI SOD 1.00 ! Na+ Aqvist JPC 1990,94,8021. (adapted) +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! K+ Aqvist JPC 1990,94,8021. (adapted) +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Cl- Smith, JCP 1994,100:5,3757. +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +! +! nucleic +! + +RESI ADE -1.0 ! note: this is RNA, resname A in ff14SB, RA in ff99SB +GROUP ! patches to make terminal or deoxyribose are required +ATOM P P 1.1662 +ATOM O1P O2 -0.7760 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7760 ! note: name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4989 +ATOM C5' CI 0.0558 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0679 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0679 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1065 +ATOM H4' H1 0.1174 +ATOM O4' OS -0.3548 +ATOM C1' CT 0.0394 +ATOM H1' H2 0.2007 +ATOM N9 NG -0.0251 ! note: type is N* in ff14SB & ff99SB +ATOM C8 C5 0.2006 +ATOM H8 H5 0.1553 +ATOM N7 NB -0.6073 +ATOM C5 CB 0.0515 +ATOM C6 CA 0.7009 +ATOM N6 N2 -0.9019 +ATOM H61 H 0.4115 +ATOM H62 H 0.4115 +ATOM N1 NC -0.7615 +ATOM C2 CQ 0.5875 +ATOM H2 H5 0.0473 +ATOM N3 NC -0.6997 +ATOM C4 CB 0.3053 +ATOM C3' CT 0.2022 +ATOM H3' H1 0.0615 +ATOM C2' CT 0.0670 +ATOM H2'' H1 0.0972 ! note: name is H2' in ff14SB, H2'1 in ff99SB +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 ! note: name is HO2' in ff14SB, HO'2 in ff99SB +ATOM O3' OS -0.5246 + +! using charmm bond lists (top_all22_na.inp) +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 +BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 + +IMPROPER C4 C8 N9 C1' +IMPROPER C6 H61 N6 H62 +IMPROPER N7 N9 C8 H8 +IMPROPER N1 N3 C2 H2 +IMPROPER C5 N6 C6 N1 + +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +! build array from charmm (top_all36_na.rtf) +IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST ADE5 LAST ADE3 + + +RESI URA -1.0 ! note: this is RNA, resname U in ff14SB, RU in ff99SB +GROUP ! patches to make terminal or deoxyribose are required +ATOM P P 1.1662 +ATOM O1P O2 -0.7760 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7760 ! note: name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4989 +ATOM C5' CI 0.0558 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0679 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0679 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1065 +ATOM H4' H1 0.1174 +ATOM O4' OS -0.3548 +ATOM C1' CT 0.0674 +ATOM H1' H2 0.1824 +ATOM N1 NG 0.0418 ! note: type is N* in ff14SB & ff99SB +ATOM C6 CS -0.1126 ! note: type changed from CM (ff99SB) to CS (ff14SB) +ATOM H6 H4 0.2188 +ATOM C5 CS -0.3635 ! note: type changed from CM (ff99SB) to CS (ff14SB) +ATOM H5 HA 0.1811 +ATOM C4 C 0.5952 +ATOM O4 O -0.5761 +ATOM N3 NA -0.3549 +ATOM H3 H 0.3154 +ATOM C2 C 0.4687 +ATOM O2 O -0.5477 +ATOM C3' CT 0.2022 +ATOM H3' H1 0.0615 +ATOM C2' CT 0.0670 +ATOM H2'' H1 0.0972 ! note: name is H2' in ff14SB, H2'1 in ff99SB +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 ! note: name is HO2' in ff14SB, HO'2 in ff99SB +ATOM O3' OS -0.5246 + +! bonds from charmm (top_all22_na.inp) +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 + +IMPROPER C2 C6 N1 C1' +IMPROPER C4 C6 C5 H5 +IMPROPER N1 N3 C2 O2 +IMPROPER C5 N3 C4 O4 +IMPROPER C2 C4 N3 H3 +IMPROPER N1 C5 C6 H6 + +DONO H3 N3 +DONO H2' O2' +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +! build array from charmm (top_all36_na.rtf) +IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 +IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 +IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 +IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 +IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 +IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 +IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 +IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST URA5 LAST URA3 + + +RESI THY -1.0 ! note: this is DNA,resname DT in ff14SB & ff99SB +GROUP ! patches to make terminal are required +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7761 ! note: name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4954 +ATOM C5' CI -0.0069 ! type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0680 +ATOM H1' H2 0.1804 +ATOM N1 NG -0.0239 ! type is N* in ff14SB & ff99SB +ATOM C6 CM -0.2209 +ATOM H6 H4 0.2607 +ATOM C5 CM 0.0025 +ATOM C7 CT -0.2269 +ATOM H71 HC 0.0770 +ATOM H72 HC 0.0770 +ATOM H73 HC 0.0770 +ATOM C4 C 0.5194 +ATOM O4 O -0.5563 +ATOM N3 NA -0.4340 +ATOM H3 H 0.3420 +ATOM C2 C 0.5677 +ATOM O2 O -0.5881 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! name is H2'2 in ff99SB +ATOM O3' OS -0.5232 + +! bonds from charmm (top_all22_na.inp) +! swapped C5M with C7 +! swapped H5? with H7? +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C7 C5 C6 C2' C3' C3' O3' O3' +P +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C6 H6 C7 H71 C7 H72 C7 H73 +BOND C2' H2' + +IMPROPER C2 C6 N1 C1' +IMPROPER C4 C6 C5 C7 +IMPROPER N1 N3 C2 O2 +IMPROPER C5 N3 C4 O4 +IMPROPER C2 C4 N3 H3 +IMPROPER N1 C5 C6 H6 + + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O3' +ACCE O4' +ACCE O5' + +! build from charmm (top_all36_na.rtf) +! name swapping as above, delete references to O2' +IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C7 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C7 H71 0.0 0.0 0.0 0.0 0.0 +IC C5 H71 *C7 H72 0.0 0.0 115.0 0.0 0.0 +IC H71 H72 *C7 H73 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 !kept from Klauda's f99sb rtf file +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 + +PATCH FIRST THY5 LAST THY3 + + +RESI CYT -1.0 ! note: this is RNA, resname C in ff14SB, RC in ff99SB +GROUP ! patches to make terminal or deoxyribose are required +ATOM P P 1.1662 +ATOM O1P O2 -0.7760 ! name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7760 ! name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4989 +ATOM C5' CI 0.0558 ! type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0679 ! name is H5'1 in ff99SB +ATOM H5'' H1 0.0679 ! name is H5'2 in ff99SB +ATOM C4' CT 0.1065 +ATOM H4' H1 0.1174 +ATOM O4' OS -0.3548 +ATOM C1' CT 0.0066 +ATOM H1' H2 0.2029 +ATOM N1 NG -0.0484 ! name is type N* in ff14SB & ff99SB +ATOM C6 C4 0.0053 ! type changed from CM (ff99SB) to C4 (ff14SB) +ATOM H6 H4 0.1958 +ATOM C5 C4 -0.5215 ! type changed from CM (ff99SB) to C4 (ff14SB) +ATOM H5 HA 0.1928 +ATOM C4 CA 0.8185 +ATOM N4 N2 -0.9530 +ATOM H41 H 0.4234 +ATOM H42 H 0.4234 +ATOM N3 NC -0.7584 +ATOM C2 C 0.7538 +ATOM O2 O -0.6252 +ATOM C3' CT 0.2022 +ATOM H3' H1 0.0615 +ATOM C2' CT 0.0670 +ATOM H2'' H1 0.0972 ! name is H2' in ff14SB, H2'1 in ff99SB +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 ! name is HO2' in ff14SB, HO'2 in ff99SB +ATOM O3' OS -0.5246 + +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 + +IMPROPER C2 C6 N1 C1' +IMPROPER N1 N3 C2 O2 +IMPROPER C4 H41 N4 H42 +IMPROPER N1 C5 C6 H6 +IMPROPER C6 C4 C5 H5 +IMPROPER C5 N4 C4 N3 + +DONO H42 N4 +DONO H2' O2' +DONO H41 N4 +ACCE O2 C2 +ACCE N3 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +! build array from charmm (top_all36_na.rtf) +IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST CYT5 LAST CYT3 + + +RESI GUA -1.0 ! note: this is RNA, resname G in ff14SB, RG in ff99SB +GROUP ! patches to make terminal or deoxyribose are required +ATOM P P 1.1662 +ATOM O1P O2 -0.7760 ! name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7760 ! name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4989 +ATOM C5' CI 0.0558 ! type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0679 ! name is H5'1 in ff99SB +ATOM H5'' H1 0.0679 ! name is H5'2 in ff99SB +ATOM C4' CT 0.1065 +ATOM H4' H1 0.1174 +ATOM O4' OS -0.3548 +ATOM C1' CT 0.0191 +ATOM H1' H2 0.2006 +ATOM N9 NG 0.0492 ! type is N* in ff14SB & ff99SB +ATOM C8 CP 0.1374 ! type changed from CK (ff99SB) to CP (ff14SB) +ATOM H8 H5 0.1640 +ATOM N7 NB -0.5709 +ATOM C5 CB 0.1744 +ATOM C6 C 0.4770 +ATOM O6 O -0.5597 +ATOM N1 NA -0.4787 +ATOM H1 H 0.3424 +ATOM C2 CA 0.7657 +ATOM N2 N2 -0.9672 +ATOM H21 H 0.4364 +ATOM H22 H 0.4364 +ATOM N3 NC -0.6323 +ATOM C4 CB 0.1222 +ATOM C3' CT 0.2022 +ATOM H3' H1 0.0615 +ATOM C2' CT 0.0670 +ATOM H2'' H1 0.0972 ! name is H2' in ff14SB, H2'1 in ff99SB +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 ! name is HO2' in ff14SB, HO'2 in ff99SB +ATOM O3' OS -0.5246 + +! bonds from charmm (top_all22_na.inp) +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 + +IMPROPER C4 C8 N9 C1' +IMPROPER C5 N1 C6 O6 +IMPROPER C6 C2 N1 H1 +IMPROPER C2 H21 N2 H22 +IMPROPER N7 N9 C8 H8 +IMPROPER N2 N1 C2 N3 + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +DONO H2' O2' +ACCE O6 C6 +ACCE N3 +ACCE N7 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +! build array from charmm (top_all36_na.rtf) +! Chi and sugar-phosphate backbone in B-DNA like conformation (top_all36_na.rtf) +IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST GUA5 LAST GUA3 + +! +! PROTEIN RESIDUES +! + +RESI ALA 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX 0.03370 ! | HB1 +ATOM HA H1 0.08230 ! | / +ATOM CB CT -0.18250 ! HA-CA--CB-HB2 ALANINE +ATOM HB1 HC 0.06030 ! | \ +ATOM HB2 HC 0.06030 ! | HB2 +ATOM HB3 HC 0.06030 ! O=C +ATOM C C 0.59730 ! | +ATOM O O -0.56790 + +BOND CB CA N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CB HB3 C O + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C + +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +PATCH FIRST NALA LAST CALA + + +RESI ARG 1.00 +GROUP +ATOM N N -0.34790 ! | HH11 +ATOM HN H 0.27470 ! HN-N | +ATOM CA CX -0.26370 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA H1 0.15600 ! | | | | | //(+) +ATOM CB C8 -0.00070 ! HA-CA--CB--CG--CD--NE--CZ +ATOM HB1 HC 0.03270 ! | | | | \ +ATOM HB2 HC 0.03270 ! | HB2 HG2 HD2 NH2-HH22 +ATOM CG C8 0.03900 ! O=C | +ATOM HG1 HC 0.02850 ! | HH21 +ATOM HG2 HC 0.02850 +ATOM CD C8 0.04860 +ATOM HD1 H1 0.06870 +ATOM HD2 H1 0.06870 +ATOM NE N2 -0.52950 +ATOM HE H 0.34560 +ATOM CZ CA 0.80760 +ATOM NH1 N2 -0.86270 +ATOM HH11 H 0.44780 +ATOM HH12 H 0.44780 +ATOM NH2 N2 -0.86270 +ATOM HH21 H 0.44780 +ATOM HH22 H 0.44780 +ATOM C C 0.73410 +ATOM O O -0.58940 + +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +BOND O C CZ NH1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER NE NH1 CZ NH2 +IMPROPER CD CZ NE HE +IMPROPER CZ HH11 NH1 HH12 +IMPROPER CZ HH21 NH2 HH22 + +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C + +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +PATCH FIRST NARG LAST CARG + + +RESI ASN 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX 0.01430 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA H1 0.10480 ! | | || / +ATOM CB 2C -0.20410 ! HA-CA--CB--CG--ND2 +ATOM HB1 HC 0.07970 ! | | \ +ATOM HB2 HC 0.07970 ! | HB2 HD22 (trans to OD1) +ATOM CG C 0.71300 ! O=C +ATOM OD1 O -0.59310 ! | +ATOM ND2 N -0.91910 +ATOM HD21 H 0.41960 +ATOM HD22 H 0.41960 +ATOM C C 0.59730 +ATOM O O -0.56790 + +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +BOND C O CG OD1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CB ND2 CG OD1 +IMPROPER CG HD21 ND2 HD22 + +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +PATCH FIRST NASN LAST CASN + + +RESI ASP -1.00 +GROUP +ATOM N N -0.51630 ! | +ATOM HN H 0.29360 ! HN-N +ATOM CA CX 0.03810 ! | HB1 OD1 +ATOM HA H1 0.08800 ! | | // +ATOM CB 2C -0.03030 ! HA-CA--CB--CG +ATOM HB1 HC -0.01220 ! | | \ +ATOM HB2 HC -0.01220 ! | HB2 OD2(-) +ATOM CG CO 0.79940 ! O=C +ATOM OD1 O2 -0.80140 ! | +ATOM OD2 O2 -0.80140 +ATOM C C 0.53660 +ATOM O O -0.58190 +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +BOND O C CG OD1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CB OD1 CG OD2 + +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C + +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +PATCH FIRST NASP LAST CASP + + +RESI CYS 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX 0.02130 ! | HB1 +ATOM HA H1 0.11240 ! | | +ATOM CB 2C -0.12310 ! HA-CA--CB--SG +ATOM HB1 H1 0.11120 ! | | \ +ATOM HB2 H1 0.11120 ! | HB2 HG1 +ATOM SG SH -0.31190 ! O=C +ATOM HG1 HS 0.19330 ! | +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C + +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +PATCH FIRST NCYS LAST CCYS + + +RESI CYM -1.00 ! NOTE: there is no terminal negative CYS +GROUP ! residues within Cornell et al.!!! +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX -0.03510 ! | HB1 +ATOM HA H1 0.05080 ! | | +ATOM CB CT -0.24130 ! HA-CA--CB--SG +ATOM HB1 H1 0.11220 ! | | (-) +ATOM HB2 H1 0.11220 ! | HB2 +ATOM SG SH -0.88440 ! O=C +ATOM C C 0.59730 ! | +ATOM O O -0.56790 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C + +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 + +PATCH FIRST NONE LAST NONE + + +RESI CYX 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX 0.04290 ! | HB1 +ATOM HA H1 0.07660 ! | | +ATOM CB 2C -0.07900 ! HA-CA--CB--SG +ATOM HB1 H1 0.09100 ! | | (-) +ATOM HB2 H1 0.09100 ! | HB2 +ATOM SG S -0.10810 ! O=C +ATOM C C 0.59730 ! | +ATOM O O -0.56790 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C + +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 + +PATCH FIRST NCYX LAST CCYX + + +RESI GLN 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX -0.00310 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA H1 0.08500 ! | | | || / +ATOM CB 2C -0.00360 ! HA-CA--CB--CG--CD--NE2 +ATOM HB1 HC 0.01710 ! | | | \ +ATOM HB2 HC 0.01710 ! | HB2 HG2 HE22 (trans to OE1) +ATOM CG 2C -0.06450 ! O=C +ATOM HG1 HC 0.03520 ! | +ATOM HG2 HC 0.03520 +ATOM CD C 0.69510 +ATOM OE1 O -0.60860 +ATOM NE2 N -0.94070 +ATOM HE21 H 0.42510 +ATOM HE22 H 0.42510 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +BOND O C CD OE1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG NE2 CD OE1 +IMPROPER CD HE21 NE2 HE22 + +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +PATCH FIRST NGLN LAST CGLN + + +RESI GLU -1.00 +ATOM N N -0.51630 ! | +ATOM HN H 0.29360 ! HN-N +ATOM CA CX 0.03970 ! | HB1 HG1 OE1 +ATOM HA H1 0.11050 ! | | | // +ATOM CB 2C 0.05600 ! HA-CA--CB--CG--CD +ATOM HB1 HC -0.01730 ! | | | \ +ATOM HB2 HC -0.01730 ! | HB2 HG2 OE2(-) +ATOM CG 2C 0.01360 ! O=C +ATOM HG1 HC -0.04250 ! | +ATOM HG2 HC -0.04250 +ATOM CD CO 0.80540 +ATOM OE1 O2 -0.81880 +ATOM OE2 O2 -0.81880 +ATOM C C 0.53660 +ATOM O O -0.58190 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 O C CD OE1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG OE1 CD OE2 + +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +PATCH FIRST NGLU LAST CGLU + + +RESI GLH 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX 0.01450 ! | HB1 HG1 OE1 +ATOM HA H1 0.07790 ! | | | // +ATOM CB 2C -0.00710 ! HA-CA--CB--CG--CD +ATOM HB1 HC 0.02560 ! | | | \ +ATOM HB2 HC 0.02560 ! | HB2 HG2 OE2(-) +ATOM CG 2C -0.01740 ! O=C +ATOM HG1 HC 0.04300 ! | +ATOM HG2 HC 0.04300 +ATOM CD C 0.68010 +ATOM OE1 O -0.58380 +ATOM OE2 OH -0.65110 +ATOM HE2 HO 0.46410 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 O C CD OE1 OE2 HE2 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG OE1 CD OE2 + +DONOR HN N +DONOR HE2 OE2 +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +PATCH FIRST NONE LAST NONE + + +RESI GLY 0.00 +GROUP ! | +ATOM N N -0.41570 ! N-H +ATOM HN H 0.27190 ! | +ATOM CA CX -0.02520 ! | +ATOM HA1 H1 0.06980 ! HA1-CA-HA2 +ATOM HA2 H1 0.06980 ! | +ATOM C C 0.59730 ! | +ATOM O O -0.56790 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 + +PATCH FIRST NGLY LAST CGLY + + +RESI HID 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N N -0.41570 ! | HD1 HE1 +ATOM HN H 0.27190 ! HN-N | / +ATOM CA CX 0.01880 ! | HB1 ND1--CE1 +ATOM HA H1 0.08810 ! | | / || +ATOM ND1 NA -0.38110 ! HA-CA--CB--CG || +ATOM HD1 H 0.36490 ! | | \\ || +ATOM CG CC -0.02660 ! | HB2 CD2--NE2 +ATOM CB CT -0.04620 ! O=C | +ATOM HB1 HC 0.04020 ! | HD2 +ATOM HB2 HC 0.04020 +ATOM NE2 NB -0.57270 +ATOM CD2 CV 0.12920 +ATOM HD2 H4 0.11470 +ATOM CE1 CR 0.20570 +ATOM HE1 H5 0.13920 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +BOND O C CG CD2 CE1 NE2 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG CE1 ND1 HD1 +IMPROPER CG NE2 CD2 HD2 +IMPROPER ND1 NE2 CE1 HE1 +IMPROPER CB CD2 CG ND1 +!!IMPROPER ND1 CD2 CG CB !! from Klauda, this order gives wrong improper energy. + +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +PATCH FIRST NHID LAST CHID + + +RESI HIE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N N -0.41570 ! | HE1 +ATOM HN H 0.27190 ! HN-N __ / +ATOM CA CX -0.05810 ! | HB1 ND1--CE1 +ATOM HA H1 0.13600 ! | | / | +ATOM NE2 NA -0.27950 ! HA-CA--CB--CG | +ATOM HE2 H 0.33390 ! | | \\ | +ATOM CD2 CW -0.22070 ! | HB2 CD2--NE2 +ATOM HD2 H4 0.18620 ! O=C | \ +ATOM ND1 NB -0.54320 ! | HD2 HE2 +ATOM CG CC 0.18680 +ATOM CE1 CR 0.16350 +ATOM HE1 H5 0.14350 +ATOM CB CT -0.00740 +ATOM HB1 HC 0.03670 +ATOM HB2 HC 0.03670 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +BOND O C CD2 CG CE1 ND1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CE1 CD2 NE2 HE2 +IMPROPER CG NE2 CD2 HD2 +IMPROPER ND1 NE2 CE1 HE1 +IMPROPER CB CD2 CG ND1 +!!IMPROPER ND1 CD2 CG CB !! from Klauda, this order gives wrong improper energy. + +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +PATCH FIRST NHIE LAST CHIE + + +RESI HIP 1.00 ! Protonated His +GROUP +ATOM N N -0.34790 ! | HD1 HE1 +ATOM HN H 0.27470 ! HN-N | / +ATOM CA CX -0.13540 ! | HB1 ND1--CE1 +ATOM HA H1 0.12120 ! | | / || +ATOM ND1 NA -0.15130 ! HA-CA--CB--CG || +ATOM HD1 H 0.38660 ! | | \\ || +ATOM NE2 NA -0.17180 ! | HB2 CD2--NE2(+) +ATOM HE2 H 0.39110 ! O=C | \ +ATOM CE1 CR -0.01700 ! | HD2 HE2 +ATOM HE1 H5 0.26810 +ATOM CD2 CW -0.11410 +ATOM HD2 H4 0.23170 +ATOM CG CC -0.00120 +ATOM CB CT -0.04140 +ATOM HB1 HC 0.08100 +ATOM HB2 HC 0.08100 +ATOM C C 0.73410 +ATOM O O -0.58940 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +BOND O C CD2 CG NE2 CE1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG CE1 ND1 HD1 +IMPROPER CE1 CD2 NE2 HE2 +IMPROPER CG NE2 CD2 HD2 +IMPROPER ND1 NE2 CE1 HE1 +IMPROPER CB CD2 CG ND1 +!!IMPROPER ND1 CD2 CG CB !! from Klauda, this order gives wrong improper energy. + +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +PATCH FIRST NHIP LAST CHIP + + +RESI ILE 0.00 +GROUP +ATOM N N -0.41570 ! | HG21 HG22 +ATOM HN H 0.27190 ! HN-N | / +ATOM CA CX -0.05970 ! | CG2--HG23 +ATOM HA H1 0.08690 ! | / +ATOM CB 3C 0.13030 ! HA-CA--CB-HB HD1 +ATOM HB HC 0.01870 ! | \ / +ATOM CG2 CT -0.32040 ! | CG1--CD--HD2 +ATOM HG21 HC 0.08820 ! O=C / \ \ +ATOM HG22 HC 0.08820 ! | HG11 HG12 HD3 +ATOM HG23 HC 0.08820 +ATOM CG1 2C -0.04300 +ATOM HG11 HC 0.02360 +ATOM HG12 HC 0.02360 +ATOM CD CT -0.06600 +ATOM HD1 HC 0.01860 +ATOM HD2 HC 0.01860 +ATOM HD3 HC 0.01860 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + +PATCH FIRST NILE LAST CILE + + +RESI LEU 0.00 +GROUP +ATOM N N -0.41570 ! | HD11 HD12 +ATOM HN H 0.27190 ! HN-N | / +ATOM CA CX -0.05180 ! | HB1 CD1--HD13 +ATOM HA H1 0.09220 ! | | / +ATOM CB 2C -0.11020 ! HA-CA--CB--CG-HG +ATOM HB1 HC 0.04570 ! | | \ +ATOM HB2 HC 0.04570 ! | HB2 CD2--HD23 +ATOM CG 3C 0.35310 ! O=C | \ +ATOM HG HC -0.03610 ! | HD21 HD22 +ATOM CD1 CT -0.41210 +ATOM HD11 HC 0.10000 +ATOM HD12 HC 0.10000 +ATOM HD13 HC 0.10000 +ATOM CD2 CT -0.41210 +ATOM HD21 HC 0.10000 +ATOM HD22 HC 0.10000 +ATOM HD23 HC 0.10000 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +PATCH FIRST NLEU LAST CLEU + + +RESI LYS 1.00 +GROUP +ATOM N N -0.34790 ! | +ATOM HN H 0.27470 ! HN-N +ATOM CA CX -0.24000 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA H1 0.14260 ! | | | | | / +ATOM CB C8 -0.00940 ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM HB1 HC 0.03620 ! | | | | | \ +ATOM HB2 HC 0.03620 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM CG C8 0.01870 ! O=C +ATOM HG1 HC 0.01030 ! | +ATOM HG2 HC 0.01030 +ATOM CD C8 -0.04790 +ATOM HD1 HC 0.06210 +ATOM HD2 HC 0.06210 +ATOM CE C8 -0.01430 +ATOM HE1 HP 0.11350 +ATOM HE2 HP 0.11350 +ATOM NZ N3 -0.38540 +ATOM HZ1 H 0.34000 +ATOM HZ2 H 0.34000 +ATOM HZ3 H 0.34000 +ATOM C C 0.73410 +ATOM O O -0.58940 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +BOND O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +PATCH FIRST NLYS LAST CLYS + + +RESI MET 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX -0.02370 ! | HB1 HG1 HE1 +ATOM HA H1 0.08800 ! | | | | +ATOM CB 2C 0.03420 ! HA-CA--CB--CG--SD--CE--HE3 +ATOM HB1 HC 0.02410 ! | | | | +ATOM HB2 HC 0.02410 ! | HB2 HG2 HE2 +ATOM CG 2C 0.00180 ! O=C +ATOM HG1 H1 0.04400 ! | +ATOM HG2 H1 0.04400 +ATOM SD S -0.27370 +ATOM CE CT -0.05360 +ATOM HE1 H1 0.06840 +ATOM HE2 H1 0.06840 +ATOM HE3 H1 0.06840 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +PATCH FIRST NMET LAST CMET + + +RESI PHE 0.00 +GROUP +ATOM N N -0.41570 ! | HD1 HE1 +ATOM HN H 0.27190 ! HN-N | | +ATOM CA CX -0.00240 ! | HB1 CD1--CE1 +ATOM HA H1 0.09780 ! | | // \\ +ATOM CB CT -0.03430 ! HA-CA--CB--CG CZ--HZ +ATOM HB1 HC 0.02950 ! | | \ __ / +ATOM HB2 HC 0.02950 ! | HB2 CD2--CE2 +ATOM CG CA 0.01180 ! O=C | | +ATOM CD1 CA -0.12560 ! | HD2 HE2 +ATOM HD1 HA 0.13300 +ATOM CE1 CA -0.17040 +ATOM HE1 HA 0.14300 +ATOM CZ CA -0.10720 +ATOM HZ HA 0.12970 +ATOM CE2 CA -0.17040 +ATOM HE2 HA 0.14300 +ATOM CD2 CA -0.12560 +ATOM HD2 HA 0.13300 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +BOND O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG CE2 CD2 HD2 +!IMPROPER CD2 CZ CE2 HE2 +IMPROPER CZ CD2 CE2 HE2 +IMPROPER CE1 CE2 CZ HZ +IMPROPER CD1 CZ CE1 HE1 +IMPROPER CG CE1 CD1 HD1 +IMPROPER CD1 CD2 CG CB + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +PATCH FIRST NPHE LAST CPHE + + +RESI PRO 0.00 +GROUP +ATOM N N -0.25480 ! HD1 HD2 +ATOM CD CT 0.01920 ! | \ / +ATOM HD1 H1 0.03910 ! N---CD HG1 +ATOM HD2 H1 0.03910 ! | \ / +ATOM CG CT 0.01890 ! | CG +ATOM HG1 HC 0.02130 ! | / \ +ATOM HG2 HC 0.02130 ! HA-CA--CB HG2 +ATOM CB CT -0.00700 ! | / \ +ATOM HB1 HC 0.02530 ! | HB1 HB2 +ATOM HB2 HC 0.02530 ! O=C +ATOM CA CX -0.02660 ! | +ATOM HA H1 0.06410 +ATOM C C 0.58960 +ATOM O O -0.57480 +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +BOND O C + +IMPROPER -C CD N CA +IMPROPER CA +N C O + +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 + +PATCH FIRST NPRO LAST CPRO + + +RESI SER 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX -0.02490 ! | HB1 +ATOM HA H1 0.08430 ! | | +ATOM CB 2C 0.21170 ! HA-CA--CB--OG +ATOM HB1 H1 0.03520 ! | | \ +ATOM HB2 H1 0.03520 ! | HB2 HG1 +ATOM OG OH -0.65460 ! O=C +ATOM HG1 HO 0.42750 ! | +ATOM C C 0.59730 +ATOM O O -0.56790 + +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +PATCH FIRST NSER LAST CSER + + +RESI THR 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CX -0.03890 ! | OG1--HG1 +ATOM HA H1 0.10070 ! | / +ATOM CB 3C 0.36540 ! HA-CA--CB-HB +ATOM HB H1 0.00430 ! | \ +ATOM CG2 CT -0.24380 ! | CG2--HG21 +ATOM HG21 HC 0.06420 ! O=C / \ +ATOM HG22 HC 0.06420 ! | HG21 HG22 +ATOM HG23 HC 0.06420 +ATOM OG1 OH -0.67610 +ATOM HG1 HO 0.41020 +ATOM C C 0.59730 +ATOM O O -0.56790 + +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +PATCH FIRST NTHR LAST CTHR + + +RESI TRP 0.00 +GROUP +ATOM N N -0.41570 ! | HE3 +ATOM HN H 0.27190 ! HN-N | +ATOM CA CX -0.02750 ! | HB1 CE3 +ATOM HA H1 0.11230 ! | | / \\ +ATOM CB CT -0.00500 ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM HB1 HC 0.03390 ! | | || || | +ATOM HB2 HC 0.03390 ! | HB2 CD1 CE2 CH2-HH2 +ATOM CG CG -0.14150 ! O=C / \ / \ // +ATOM CD1 CW -0.16380 ! | HD1 NE1 CZ2 +ATOM HD1 H4 0.20620 ! | | +ATOM NE1 NA -0.34180 ! HE1 HZ2 +ATOM HE1 H 0.34120 +ATOM CE2 CN 0.13800 +ATOM CZ2 CA -0.26010 +ATOM HZ2 HA 0.15720 +ATOM CH2 CA -0.11340 +ATOM HH2 HA 0.14170 +ATOM CZ3 CA -0.19720 +ATOM HZ3 HA 0.14470 +ATOM CE3 CA -0.23870 +ATOM HE3 HA 0.17000 +ATOM CD2 CB 0.12430 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +BOND O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CD1 CE2 NE1 HE1 +IMPROPER CE2 CH2 CZ2 HZ2 +IMPROPER CZ2 CZ3 CH2 HH2 +IMPROPER CH2 CE3 CZ3 HZ3 +IMPROPER CZ3 CD2 CE3 HE3 +IMPROPER CG NE1 CD1 HD1 +IMPROPER CD2 CB CG CD1 +!!IMPROPER CD1 CD2 CG CB !! from Klauda, this order gives wrong improper energy. + +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +PATCH FIRST NTRP LAST CTRP + + +RESI TYR 0.00 +GROUP +ATOM N N -0.41570 ! | HD1 HE1 +ATOM HN H 0.27190 ! HN-N | | +ATOM CA CX -0.00140 ! | HB1 CD1--CE1 +ATOM HA H1 0.08760 ! | | // \\ +ATOM CB CT -0.01520 ! HA-CA--CB--CG CZ--OH +ATOM HB1 HC 0.02950 ! | | \ __ / \ +ATOM HB2 HC 0.02950 ! | HB2 CD2--CE2 HH +ATOM CG CA -0.00110 ! O=C | | +ATOM CD1 CA -0.19060 ! | HD2 HE2 +ATOM HD1 HA 0.16990 +ATOM CE1 CA -0.23410 +ATOM HE1 HA 0.16560 +ATOM CZ C 0.32260 +ATOM OH OH -0.55790 +ATOM HH HO 0.39920 +ATOM CE2 CA -0.23410 +ATOM HE2 HA 0.16560 +ATOM CD2 CA -0.19060 +ATOM HD2 HA 0.16990 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +BOND O C CD1 CG CE1 CZ CE2 CD2 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG CE2 CD2 HD2 +!IMPROPER CD2 CZ CE2 HE2 +IMPROPER CZ CD2 CE2 HE2 +IMPROPER CD1 CZ CE1 HE1 +IMPROPER CG CE1 CD1 HD1 +IMPROPER CD1 CD2 CG CB +IMPROPER CE1 CE2 CZ OH + + +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +PATCH FIRST NTYR LAST CTYR + + +RESI VAL 0.00 +GROUP +ATOM N N -0.41570 ! | HG11 HG12 +ATOM HN H 0.27190 ! HN-N | / +ATOM CA CX -0.08750 ! | CG1--HG13 +ATOM HA H1 0.09690 ! | / +ATOM CB 3C 0.29850 ! HA-CA--CB-HB +ATOM HB HC -0.02970 ! | \ +ATOM CG1 CT -0.31920 ! | CG2--HG21 +ATOM HG11 HC 0.07910 ! O=C / \ +ATOM HG12 HC 0.07910 ! | HG21 HG22 +ATOM HG13 HC 0.07910 +ATOM CG2 CT -0.31920 +ATOM HG21 HC 0.07910 +ATOM HG22 HC 0.07910 +ATOM HG23 HC 0.07910 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +PATCH FIRST NVAL LAST CVAL + + +RESI ACE 0.00 ! acetylated N-terminus +GROUP ! +ATOM HY1 HC 0.11230 ! HY1 HY2 HY3 +ATOM CAY CT -0.36620 ! \ | / +ATOM HY2 HC 0.11230 ! CAY +ATOM HY3 HC 0.11230 ! | +ATOM C C 0.59720 ! C=O +ATOM O O -0.56790 ! | + +BOND C CAY C +N CAY HY1 CAY HY2 CAY HY3 +BOND O C + +IMPROPER CAY +N C O + +ACCEPTOR O C + +IC C N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC C CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY C N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O C CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O C CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC O C CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PATCH FIRST NONE LAST NONE + + +RESI NME 0.00 ! N-Methylamide C-terminus +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! N-HN +ATOM CAT CT -0.14900 ! | +ATOM HT1 H1 0.09760 ! HT1-CAT-HT3 +ATOM HT2 H1 0.09760 ! | +ATOM HT3 H1 0.09760 ! HT2 + + +BOND N HN N CAT CAT HT1 CAT HT2 CAT HT3 + +IMPROPER -C CAT N HN + +DONOR HN N +IC N CA -C -O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC -C CAT *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C N CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C N CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C N CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PATCH FIRST NONE LAST NONE + + +PRES NALA 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.14140 ! +ATOM HT1 H 0.19970 ! HT2 +ATOM HT2 H 0.19970 ! |(+) +ATOM HT3 H 0.19970 ! HT1-N-HT3 +ATOM CA CX 0.09620 ! | HB1 +ATOM HA HP 0.08890 ! | / +ATOM CB CT -0.05970 ! HA-CA--CB-HB2 ALANINE +ATOM HB1 HC 0.03000 ! | \ +ATOM HB2 HC 0.03000 ! | HB2 +ATOM HB3 HC 0.03000 ! O=C +ATOM C C 0.61630 ! | +ATOM O O -0.57220 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CALA -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 ! | +ATOM HN H 0.26810 ! HN-N +ATOM CA CX -0.17470 ! | HB1 +ATOM HA H1 0.10670 ! | / +ATOM CB CT -0.20930 ! HA-CA--CB-HB2 ALANINE +ATOM HB1 HC 0.07640 ! | \ +ATOM HB2 HC 0.07640 ! | HB2 +ATOM HB3 HC 0.07640 ! OT1=C +ATOM C C 0.77310 ! | +ATOM OT1 O2 -0.80550 ! OT2 +ATOM OT2 O2 -0.80550 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NARG 2.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.13050 +ATOM HT1 H 0.20830 +ATOM HT2 H 0.20830 ! HT2 +ATOM HT3 H 0.20830 ! |(+) HH11 +ATOM CA CX -0.02230 ! HT1-N-HT3 | +ATOM HA HP 0.12420 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM CB C8 0.01180 ! | | | | | //(+) +ATOM HB1 HC 0.02260 ! HA-CA--CB--CG--CD--NE--CZ +ATOM HB2 HC 0.02260 ! | | | | \ +ATOM CG C8 0.02360 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HG1 HC 0.03090 ! O=C | +ATOM HG2 HC 0.03090 ! | HH21 +ATOM CD C8 0.09350 +ATOM HD1 H1 0.05270 +ATOM HD2 H1 0.05270 +ATOM NE N2 -0.56500 +ATOM HE H 0.35920 +ATOM CZ CA 0.82810 +ATOM NH1 N2 -0.86930 +ATOM HH11 H 0.44940 +ATOM HH12 H 0.44940 +ATOM NH2 N2 -0.86930 +ATOM HH21 H 0.44940 +ATOM HH22 H 0.44940 +ATOM C C 0.72140 +ATOM O O -0.60130 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CARG 0.0 +GROUP +DELETE ATOM O +ATOM N N -0.34810 ! | HH11 +ATOM HN H 0.27640 ! HN-N | +ATOM CA CX -0.30680 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA H1 0.14470 ! | | | | | //(+) +ATOM CB C8 -0.03740 ! HA-CA--CB--CG--CD--NE--CZ +ATOM HB1 HC 0.03710 ! | | | | \ +ATOM HB2 HC 0.03710 ! | HB2 HG2 HD2 NH2-HH22 +ATOM CG C8 0.07440 ! OT1=C | +ATOM HG1 HC 0.01850 ! | HH21 +ATOM HG2 HC 0.01850 ! OT2 +ATOM CD C8 0.11140 +ATOM HD1 H1 0.04680 +ATOM HD2 H1 0.04680 +ATOM NE N2 -0.55640 +ATOM HE H 0.34790 +ATOM CZ CA 0.83680 +ATOM NH1 N2 -0.87370 +ATOM HH11 H 0.44930 +ATOM HH12 H 0.44930 +ATOM NH2 N2 -0.87370 +ATOM HH21 H 0.44930 +ATOM HH22 H 0.44930 +ATOM C C 0.85570 +ATOM OT1 O2 -0.82660 +ATOM OT2 O2 -0.82660 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NASN 1.0 +GROUP +DELETE ATOM HN +ATOM N N3 0.18010 +ATOM HT1 H 0.19210 +ATOM HT2 H 0.19210 +ATOM HT3 H 0.19210 +ATOM CA CX 0.03680 +ATOM HA HP 0.12310 +ATOM CB 2C -0.02830 +ATOM HB1 HC 0.05150 +ATOM HB2 HC 0.05150 +ATOM CG C 0.58330 +ATOM OD1 O -0.57440 +ATOM ND2 N -0.86340 +ATOM HD21 H 0.40970 +ATOM HD22 H 0.40970 +ATOM C C 0.61630 +ATOM O O -0.57220 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CASN -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.20800 +ATOM HA H1 0.13580 +ATOM CB 2C -0.22990 +ATOM HB1 HC 0.10230 +ATOM HB2 HC 0.10230 +ATOM CG C 0.71530 +ATOM OD1 O -0.60100 +ATOM ND2 N -0.90840 +ATOM HD21 H 0.41500 +ATOM HD22 H 0.41500 +ATOM C C 0.80500 +ATOM OT1 O2 -0.81470 +ATOM OT2 O2 -0.81470 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NASP 0.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.07820 +ATOM HT1 H 0.22000 +ATOM HT2 H 0.22000 +ATOM HT3 H 0.22000 +ATOM CA CX 0.02920 +ATOM HA HP 0.11410 +ATOM CB 2C -0.02350 +ATOM HB1 HC -0.01690 +ATOM HB2 HC -0.01690 +ATOM CG CO 0.81940 +ATOM OD1 O2 -0.80840 +ATOM OD2 O2 -0.80840 +ATOM C C 0.56210 +ATOM O O -0.58890 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CASP -2.0 +DELETE ATOM O +GROUP +ATOM N N -0.51920 +ATOM HN H 0.30550 +ATOM CA CX -0.18170 +ATOM HA H1 0.10460 +ATOM CB 2C -0.06770 +ATOM HB1 HC -0.02120 +ATOM HB2 HC -0.02120 +ATOM CG CO 0.88510 +ATOM OD1 O2 -0.81620 +ATOM OD2 O2 -0.81620 +ATOM C C 0.72560 +ATOM OT1 O2 -0.78870 +ATOM OT2 O2 -0.78870 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NCYS 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.13250 +ATOM HT1 H 0.20230 +ATOM HT2 H 0.20230 +ATOM HT3 H 0.20230 +ATOM CA CX 0.09270 +ATOM HA HP 0.14110 +ATOM CB 2C -0.11950 +ATOM HB1 H1 0.11880 +ATOM HB2 H1 0.11880 +ATOM SG SH -0.32980 +ATOM HG1 HS 0.19750 +ATOM C C 0.61230 +ATOM O O -0.57130 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CCYS -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.16350 +ATOM HA H1 0.13960 +ATOM CB 2C -0.19960 +ATOM HB1 H1 0.14370 +ATOM HB2 H1 0.14370 +ATOM SG SH -0.31020 +ATOM HG1 HS 0.20680 +ATOM C C 0.74970 +ATOM OT1 O2 -0.79810 +ATOM OT2 O2 -0.79810 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NCYX 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.20690 +ATOM HT1 H 0.18150 +ATOM HT2 H 0.18150 +ATOM HT3 H 0.18150 +ATOM CA CX 0.10550 +ATOM HA HP 0.09220 +ATOM CB 2C -0.02770 +ATOM HB1 H1 0.06800 +ATOM HB2 H1 0.06800 +ATOM SG S -0.09840 +ATOM C C 0.61230 +ATOM O O -0.57130 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CCYX -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.13180 +ATOM HA H1 0.09380 +ATOM CB 2C -0.19430 +ATOM HB1 H1 0.12280 +ATOM HB2 H1 0.12280 +ATOM SG S -0.05290 +ATOM C C 0.76180 +ATOM OT1 O2 -0.80410 +ATOM OT2 O2 -0.80410 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NGLN +1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.14930 +ATOM HT1 H 0.19960 +ATOM HT2 H 0.19960 +ATOM HT3 H 0.19960 +ATOM CA CX 0.05360 +ATOM HA HP 0.10150 +ATOM CB 2C 0.06510 +ATOM HB1 HC 0.00500 +ATOM HB2 HC 0.00500 +ATOM CG 2C -0.09030 +ATOM HG1 HC 0.03310 +ATOM HG2 HC 0.03310 +ATOM CD C 0.73540 +ATOM OE1 O -0.61330 +ATOM NE2 N -1.00310 +ATOM HE21 H 0.44290 +ATOM HE22 H 0.44290 +ATOM C C 0.61230 +ATOM O O -0.57130 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CGLN -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.22480 +ATOM HA H1 0.12320 +ATOM CB 2C -0.06640 +ATOM HB1 HC 0.04520 +ATOM HB2 HC 0.04520 +ATOM CG 2C -0.02100 +ATOM HG1 HC 0.02030 +ATOM HG2 HC 0.02030 +ATOM CD C 0.70930 +ATOM OE1 O -0.60980 +ATOM NE2 N -0.95740 +ATOM HE21 H 0.43040 +ATOM HE22 H 0.43040 +ATOM C C 0.77750 +ATOM OT1 O2 -0.80420 +ATOM OT2 O2 -0.80420 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NGLU 0.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.00170 +ATOM HT1 H 0.23910 +ATOM HT2 H 0.23910 +ATOM HT3 H 0.23910 +ATOM CA CX 0.05880 +ATOM HA HP 0.12020 +ATOM CB 2C 0.09090 +ATOM HB1 HC -0.02320 +ATOM HB2 HC -0.02320 +ATOM CG 2C -0.02360 +ATOM HG1 HC -0.03150 +ATOM HG2 HC -0.03150 +ATOM CD CO 0.80870 +ATOM OE1 O2 -0.81890 +ATOM OE2 O2 -0.81890 +ATOM C C 0.56210 +ATOM O O -0.58890 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CGLU -2.0 +DELETE ATOM O +GROUP +ATOM N N -0.51920 +ATOM HN H 0.30550 +ATOM CA CX -0.20590 +ATOM HA H1 0.13990 +ATOM CB 2C 0.00710 +ATOM HB1 HC -0.00780 +ATOM HB2 HC -0.00780 +ATOM CG 2C 0.06750 +ATOM HG1 HC -0.05480 +ATOM HG2 HC -0.05480 +ATOM CD CO 0.81830 +ATOM OE1 O2 -0.82200 +ATOM OE2 O2 -0.82200 +ATOM C C 0.74200 +ATOM OT1 O2 -0.79300 +ATOM OT2 O2 -0.79300 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NGLY 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.29430 +ATOM HT1 H 0.16420 +ATOM HT2 H 0.16420 +ATOM HT3 H 0.16420 +ATOM CA CX -0.01000 +ATOM HA1 HP 0.08950 +ATOM HA2 HP 0.08950 +ATOM C C 0.61630 +ATOM O O -0.57220 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CGLY -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.24930 +ATOM HA1 H1 0.10560 +ATOM HA2 H1 0.10560 +ATOM C C 0.72310 +ATOM OT1 O2 -0.78550 +ATOM OT2 O2 -0.78550 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NHID 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.15420 +ATOM HT1 H 0.19630 +ATOM HT2 H 0.19630 +ATOM HT3 H 0.19630 +ATOM CA CX 0.09640 +ATOM HA HP 0.09580 +ATOM ND1 NA -0.38190 +ATOM HD1 H 0.36320 +ATOM CG CC -0.03990 +ATOM CB CT 0.02590 +ATOM HB1 HC 0.02090 +ATOM HB2 HC 0.02090 +ATOM NE2 NB -0.57110 +ATOM CD2 CV 0.10460 +ATOM HD2 H4 0.12990 +ATOM CE1 CR 0.21270 +ATOM HE1 H5 0.13850 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CHID -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.17390 +ATOM HA H1 0.11000 +ATOM ND1 NA -0.38920 +ATOM HD1 H 0.37550 +ATOM CG CC 0.02930 +ATOM CB CT -0.10460 +ATOM HB1 HC 0.05650 +ATOM HB2 HC 0.05650 +ATOM NE2 NB -0.56290 +ATOM CD2 CV 0.10010 +ATOM HD2 H4 0.12410 +ATOM CE1 CR 0.19250 +ATOM HE1 H5 0.14180 +ATOM C C 0.76150 +ATOM OT1 O2 -0.80160 +ATOM OT2 O2 -0.80160 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NHIE 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.14720 +ATOM HT1 H 0.20160 +ATOM HT2 H 0.20160 +ATOM HT3 H 0.20160 +ATOM CA CX 0.02360 +ATOM HA HP 0.13800 +ATOM NE2 NA -0.27810 +ATOM HE2 H 0.33240 +ATOM CD2 CW -0.23490 +ATOM HD2 H4 0.19630 +ATOM ND1 NB -0.55790 +ATOM CG CC 0.17400 +ATOM CE1 CR 0.18040 +ATOM HE1 H5 0.13970 +ATOM CB CT 0.04890 +ATOM HB1 HC 0.02230 +ATOM HB2 HC 0.02230 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CHIE -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.26990 +ATOM HA H1 0.16500 +ATOM NE2 NA -0.26700 +ATOM HE2 H 0.33190 +ATOM CD2 CW -0.25880 +ATOM HD2 H4 0.19570 +ATOM ND1 NB -0.55170 +ATOM CG CC 0.27240 +ATOM CE1 CR 0.15580 +ATOM HE1 H5 0.14480 +ATOM CB CT -0.10680 +ATOM HB1 HC 0.06200 +ATOM HB2 HC 0.06200 +ATOM C C 0.79160 +ATOM OT1 O2 -0.80650 +ATOM OT2 O2 -0.80650 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NHIP 2.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.25600 +ATOM HT1 H 0.17040 +ATOM HT2 H 0.17040 +ATOM HT3 H 0.17040 +ATOM CA CX 0.05810 +ATOM HA HP 0.10470 +ATOM ND1 NA -0.15100 +ATOM HD1 H 0.38210 +ATOM NE2 NA -0.17390 +ATOM HE2 H 0.39210 +ATOM CE1 CR -0.00110 +ATOM HE1 H5 0.26450 +ATOM CD2 CW -0.14330 +ATOM HD2 H4 0.24950 +ATOM CG CC -0.02360 +ATOM CB CT 0.04840 +ATOM HB1 HC 0.05310 +ATOM HB2 HC 0.05310 +ATOM C C 0.72140 +ATOM O O -0.60130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CHIP 0.0 +DELETE ATOM O +GROUP +ATOM N N -0.34810 +ATOM HN H 0.27640 +ATOM CA CX -0.14450 +ATOM HA H1 0.11150 +ATOM ND1 NA -0.15010 +ATOM HD1 H 0.38830 +ATOM NE2 NA -0.16830 +ATOM HE2 H 0.39130 +ATOM CE1 CR -0.02510 +ATOM HE1 H5 0.26940 +ATOM CD2 CW -0.12560 +ATOM HD2 H4 0.23360 +ATOM CG CC 0.02980 +ATOM CB CT -0.08000 +ATOM HB1 HC 0.08680 +ATOM HB2 HC 0.08680 +ATOM C C 0.80320 +ATOM OT1 O2 -0.81770 +ATOM OT2 O2 -0.81770 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NILE 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.03110 +ATOM HT1 H 0.23290 +ATOM HT2 H 0.23290 +ATOM HT3 H 0.23290 +ATOM CA CX 0.02570 +ATOM HA HP 0.10310 +ATOM CB 3C 0.18850 +ATOM HB HC 0.02130 +ATOM CG2 CT -0.37200 +ATOM HG21 HC 0.09470 +ATOM HG22 HC 0.09470 +ATOM HG23 HC 0.09470 +ATOM CG1 2C -0.03870 +ATOM HG11 HC 0.02010 +ATOM HG12 HC 0.02010 +ATOM CD CT -0.09080 +ATOM HD1 HC 0.02260 +ATOM HD2 HC 0.02260 +ATOM HD3 HC 0.02260 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CILE -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.31000 +ATOM HA H1 0.13750 +ATOM CB 3C 0.03630 +ATOM HB HC 0.07660 +ATOM CG2 CT -0.34980 +ATOM HG21 HC 0.10210 +ATOM HG22 HC 0.10210 +ATOM HG23 HC 0.10210 +ATOM CG1 2C -0.03230 +ATOM HG11 HC 0.03210 +ATOM HG12 HC 0.03210 +ATOM CD CT -0.06990 +ATOM HD1 HC 0.01960 +ATOM HD2 HC 0.01960 +ATOM HD3 HC 0.01960 +ATOM C C 0.83430 +ATOM OT1 O2 -0.81900 +ATOM OT2 O2 -0.81900 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NLEU 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.10100 +ATOM HT1 H 0.21480 +ATOM HT2 H 0.21480 +ATOM HT3 H 0.21480 +ATOM CA CX 0.01040 +ATOM HA HP 0.10530 +ATOM CB 2C -0.02440 +ATOM HB1 HC 0.02560 +ATOM HB2 HC 0.02560 +ATOM CG 3C 0.34210 +ATOM HG HC -0.03800 +ATOM CD1 CT -0.41060 +ATOM HD11 HC 0.09800 +ATOM HD12 HC 0.09800 +ATOM HD13 HC 0.09800 +ATOM CD2 CT -0.41040 +ATOM HD21 HC 0.09800 +ATOM HD22 HC 0.09800 +ATOM HD23 HC 0.09800 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CLEU -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.28470 +ATOM HA H1 0.13460 +ATOM CB 2C -0.24690 +ATOM HB1 HC 0.09740 +ATOM HB2 HC 0.09740 +ATOM CG 3C 0.37060 +ATOM HG HC -0.03740 +ATOM CD1 CT -0.41630 +ATOM HD11 HC 0.10380 +ATOM HD12 HC 0.10380 +ATOM HD13 HC 0.10380 +ATOM CD2 CT -0.41630 +ATOM HD21 HC 0.10380 +ATOM HD22 HC 0.10380 +ATOM HD23 HC 0.10380 +ATOM C C 0.83260 +ATOM OT1 O2 -0.81990 +ATOM OT2 O2 -0.81990 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NLYS 2.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.09660 +ATOM HT1 H 0.21650 +ATOM HT2 H 0.21650 +ATOM HT3 H 0.21650 +ATOM CA CX -0.00150 +ATOM HA HP 0.11800 +ATOM CB C8 0.02120 +ATOM HB1 HC 0.02830 +ATOM HB2 HC 0.02830 +ATOM CG C8 -0.00480 +ATOM HG1 HC 0.01210 +ATOM HG2 HC 0.01210 +ATOM CD C8 -0.06080 +ATOM HD1 HC 0.06330 +ATOM HD2 HC 0.06330 +ATOM CE C8 -0.01810 +ATOM HE1 HP 0.11710 +ATOM HE2 HP 0.11710 +ATOM NZ N3 -0.37640 +ATOM HZ1 H 0.33820 +ATOM HZ2 H 0.33820 +ATOM HZ3 H 0.33820 +ATOM C C 0.72140 +ATOM O O -0.60130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CLYS 0.0 +DELETE ATOM O +GROUP +ATOM N N -0.34810 +ATOM HN H 0.27640 +ATOM CA CX -0.29030 +ATOM HA H1 0.14380 +ATOM CB C8 -0.05380 +ATOM HB1 HC 0.04820 +ATOM HB2 HC 0.04820 +ATOM CG C8 0.02270 +ATOM HG1 HC 0.01340 +ATOM HG2 HC 0.01340 +ATOM CD C8 -0.03920 +ATOM HD1 HC 0.06110 +ATOM HD2 HC 0.06110 +ATOM CE C8 -0.01760 +ATOM HE1 HP 0.11210 +ATOM HE2 HP 0.11210 +ATOM NZ N3 -0.37410 +ATOM HZ1 H 0.33740 +ATOM HZ2 H 0.33740 +ATOM HZ3 H 0.33740 +ATOM C C 0.84880 +ATOM OT1 O2 -0.82520 +ATOM OT2 O2 -0.82520 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NMET 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.15920 +ATOM HT1 H 0.19840 +ATOM HT2 H 0.19840 +ATOM HT3 H 0.19840 +ATOM CA CX 0.02210 +ATOM HA HP 0.11160 +ATOM CB 2C 0.08650 +ATOM HB1 HC 0.01250 +ATOM HB2 HC 0.01250 +ATOM CG 2C 0.03340 +ATOM HG1 H1 0.02920 +ATOM HG2 H1 0.02920 +ATOM SD S -0.27740 +ATOM CE CT -0.03410 +ATOM HE1 H1 0.05970 +ATOM HE2 H1 0.05970 +ATOM HE3 H1 0.05970 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CMET -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.25970 +ATOM HA H1 0.12770 +ATOM CB 2C -0.02360 +ATOM HB1 HC 0.04800 +ATOM HB2 HC 0.04800 +ATOM CG 2C 0.04920 +ATOM HG1 H1 0.03170 +ATOM HG2 H1 0.03170 +ATOM SD S -0.26920 +ATOM CE CT -0.03760 +ATOM HE1 H1 0.06250 +ATOM HE2 H1 0.06250 +ATOM HE3 H1 0.06250 +ATOM C C 0.80130 +ATOM OT1 O2 -0.81050 +ATOM OT2 O2 -0.81050 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NPHE 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.17370 +ATOM HT1 H 0.19210 +ATOM HT2 H 0.19210 +ATOM HT3 H 0.19210 +ATOM CA CX 0.07330 +ATOM HA HP 0.10410 +ATOM CB CT 0.03300 +ATOM HB1 HC 0.01040 +ATOM HB2 HC 0.01040 +ATOM CG CA 0.00310 +ATOM CD1 CA -0.13920 +ATOM HD1 HA 0.13740 +ATOM CE1 CA -0.16020 +ATOM HE1 HA 0.14330 +ATOM CZ CA -0.12080 +ATOM HZ HA 0.13290 +ATOM CE2 CA -0.16030 +ATOM HE2 HA 0.14330 +ATOM CD2 CA -0.13910 +ATOM HD2 HA 0.13740 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CPHE -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.18250 +ATOM HA H1 0.10980 +ATOM CB CT -0.09590 +ATOM HB1 HC 0.04430 +ATOM HB2 HC 0.04430 +ATOM CG CA 0.05520 +ATOM CD1 CA -0.13000 +ATOM HD1 HA 0.14080 +ATOM CE1 CA -0.18470 +ATOM HE1 HA 0.14610 +ATOM CZ CA -0.09440 +ATOM HZ HA 0.12800 +ATOM CE2 CA -0.18470 +ATOM HE2 HA 0.14610 +ATOM CD2 CA -0.13000 +ATOM HD2 HA 0.14080 +ATOM C C 0.76600 +ATOM OT1 O2 -0.80260 +ATOM OT2 O2 -0.80260 + +BOND C OT2 +BOND C OT1 +!IMPROPER CA OT2 C OT1 +IMPROPER CA OT1 C OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NPRO 1.0 +GROUP +ATOM N N3 -0.20200 +ATOM HN1 H 0.31200 +ATOM HN2 H 0.31200 +ATOM CD CT -0.01200 +ATOM HD1 HP 0.10000 +ATOM HD2 HP 0.10000 +ATOM CG CT -0.12100 +ATOM HG1 HC 0.10000 +ATOM HG2 HC 0.10000 +ATOM CB CT -0.11500 +ATOM HB1 HC 0.10000 +ATOM HB2 HC 0.10000 +ATOM CA CX 0.10000 +ATOM HA HP 0.10000 +ATOM C C 0.52600 +ATOM O O -0.50000 + +BOND HN1 N HN2 N ! HD1 HD2 +DONOR HN1 N +DONOR HN2 N +IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CPRO -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.28020 +ATOM CD CT 0.04340 +ATOM HD1 H1 0.03310 +ATOM HD2 H1 0.03310 +ATOM CG CT 0.04660 +ATOM HG1 HC 0.01720 +ATOM HG2 HC 0.01720 +ATOM CB CT -0.05430 +ATOM HB1 HC 0.03810 +ATOM HB2 HC 0.03810 +ATOM CA CX -0.13360 +ATOM HA H1 0.07760 +ATOM C C 0.66310 +ATOM OT1 O2 -0.76970 +ATOM OT2 O2 -0.76970 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NSER 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.18490 +ATOM HT1 H 0.18980 +ATOM HT2 H 0.18980 +ATOM HT3 H 0.18980 +ATOM CA CX 0.05670 +ATOM HA HP 0.07820 +ATOM CB 2C 0.25960 +ATOM HB1 H1 0.02730 +ATOM HB2 H1 0.02730 +ATOM OG OH -0.67140 +ATOM HG1 HO 0.42390 +ATOM C C 0.61630 +ATOM O O -0.57220 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CSER -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.27220 +ATOM HA H1 0.13040 +ATOM CB 2C 0.11230 +ATOM HB1 H1 0.08130 +ATOM HB2 H1 0.08130 +ATOM OG OH -0.65140 +ATOM HG1 HO 0.44740 +ATOM C C 0.81130 +ATOM OT1 O2 -0.81320 +ATOM OT2 O2 -0.81320 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NTHR 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.18120 +ATOM HT1 H 0.19340 +ATOM HT2 H 0.19340 +ATOM HT3 H 0.19340 +ATOM CA CX 0.00340 +ATOM HA HP 0.10870 +ATOM CB 3C 0.45140 +ATOM HB H1 -0.03230 +ATOM CG2 CT -0.25540 +ATOM HG21 HC 0.06270 +ATOM HG22 HC 0.06270 +ATOM HG23 HC 0.06270 +ATOM OG1 OH -0.67640 +ATOM HG1 HO 0.40700 +ATOM C C 0.61630 +ATOM O O -0.57220 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CTHR -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.24200 +ATOM HA H1 0.12070 +ATOM CB 3C 0.30250 +ATOM HB H1 0.00780 +ATOM CG2 CT -0.18530 +ATOM HG21 HC 0.05860 +ATOM HG22 HC 0.05860 +ATOM HG23 HC 0.05860 +ATOM OG1 OH -0.64960 +ATOM HG1 HO 0.41190 +ATOM C C 0.78100 +ATOM OT1 O2 -0.80440 +ATOM OT2 O2 -0.80440 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT1 C OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NTRP 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.19130 +ATOM HT1 H 0.18880 +ATOM HT2 H 0.18880 +ATOM HT3 H 0.18880 +ATOM CA CX 0.04210 +ATOM HA HP 0.11620 +ATOM CB CT 0.05430 +ATOM HB1 HC 0.02220 +ATOM HB2 HC 0.02220 +ATOM CG CG -0.16540 +ATOM CD1 CW -0.17880 +ATOM HD1 H4 0.21950 +ATOM NE1 NA -0.34440 +ATOM HE1 H 0.34120 +ATOM CE2 CN 0.15750 +ATOM CZ2 CA -0.27100 +ATOM HZ2 HA 0.15890 +ATOM CH2 CA -0.10800 +ATOM HH2 HA 0.14110 +ATOM CZ3 CA -0.20340 +ATOM HZ3 HA 0.14580 +ATOM CE3 CA -0.22650 +ATOM HE3 HA 0.16460 +ATOM CD2 CB 0.11320 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CTRP -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.20840 +ATOM HA H1 0.12720 +ATOM CB CT -0.07420 +ATOM HB1 HC 0.04970 +ATOM HB2 HC 0.04970 +ATOM CG CG -0.07960 +ATOM CD1 CW -0.18080 +ATOM HD1 H4 0.20430 +ATOM NE1 NA -0.33160 +ATOM HE1 H 0.34130 +ATOM CE2 CN 0.12220 +ATOM CZ2 CA -0.25940 +ATOM HZ2 HA 0.15670 +ATOM CH2 CA -0.10200 +ATOM HH2 HA 0.14010 +ATOM CZ3 CA -0.22870 +ATOM HZ3 HA 0.15070 +ATOM CE3 CA -0.18370 +ATOM HE3 HA 0.14910 +ATOM CD2 CB 0.10780 +ATOM C C 0.76580 +ATOM OT1 O2 -0.80110 +ATOM OT2 O2 -0.80110 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NTYR 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.19400 +ATOM HT1 H 0.18730 +ATOM HT2 H 0.18730 +ATOM HT3 H 0.18730 +ATOM CA CX 0.05700 +ATOM HA HP 0.09830 +ATOM CB CT 0.06590 +ATOM HB1 HC 0.01020 +ATOM HB2 HC 0.01020 +ATOM CG CA -0.02050 +ATOM CD1 CA -0.20020 +ATOM HD1 HA 0.17200 +ATOM CE1 CA -0.22390 +ATOM HE1 HA 0.16500 +ATOM CZ C 0.31390 +ATOM OH OH -0.55780 +ATOM HH HO 0.40010 +ATOM CE2 CA -0.22390 +ATOM HE2 HA 0.16500 +ATOM CD2 CA -0.20020 +ATOM HD2 HA 0.17200 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CTYR -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.20150 +ATOM HA H1 0.10920 +ATOM CB CT -0.07520 +ATOM HB1 HC 0.04900 +ATOM HB2 HC 0.04900 +ATOM CG CA 0.02430 +ATOM CD1 CA -0.19220 +ATOM HD1 HA 0.17800 +ATOM CE1 CA -0.24580 +ATOM HE1 HA 0.16730 +ATOM CZ C 0.33950 +ATOM OH OH -0.56430 +ATOM HH HO 0.40170 +ATOM CE2 CA -0.24580 +ATOM HE2 HA 0.16730 +ATOM CD2 CA -0.19220 +ATOM HD2 HA 0.17800 +ATOM C C 0.78170 +ATOM OT1 O2 -0.80700 +ATOM OT2 O2 -0.80700 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT1 C OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NVAL 1.0 +DELETE ATOM HN +GROUP +ATOM N N3 0.05770 +ATOM HT1 H 0.22720 +ATOM HT2 H 0.22720 +ATOM HT3 H 0.22720 +ATOM CA CX -0.00540 +ATOM HA HP 0.10930 +ATOM CB 3C 0.31960 +ATOM HB HC -0.02210 +ATOM CG1 CT -0.31290 +ATOM HG11 HC 0.07350 +ATOM HG12 HC 0.07350 +ATOM HG13 HC 0.07350 +ATOM CG2 CT -0.31290 +ATOM HG21 HC 0.07350 +ATOM HG22 HC 0.07350 +ATOM HG23 HC 0.07350 +ATOM C C 0.61630 +ATOM O O -0.57220 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CVAL -1.0 +DELETE ATOM O +GROUP +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CX -0.34380 +ATOM HA H1 0.14380 +ATOM CB 3C 0.19400 +ATOM HB HC 0.03080 +ATOM CG1 CT -0.30640 +ATOM HG11 HC 0.08360 +ATOM HG12 HC 0.08360 +ATOM HG13 HC 0.08360 +ATOM CG2 CT -0.30640 +ATOM HG21 HC 0.08360 +ATOM HG22 HC 0.08360 +ATOM HG23 HC 0.08360 +ATOM C C 0.83500 +ATOM OT1 O2 -0.81730 +ATOM OT2 O2 -0.81730 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES DISU 0.2288 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. +GROUP ! use in a patch statement + ! originally added by adm jr. based on CYX for top_amber_cornell.inp + ! modified by Xibing He for parm14sb_all.rtf +!1st cys +ATOM 1CA CX 0.042900 +ATOM 1HA H1 0.076600 +ATOM 1CB 2C -0.079000 +ATOM 1HB1 H1 0.091000 ! 2SG--2CB-- +ATOM 1HB2 H1 0.091000 ! / +ATOM 1SG S -0.108100 ! -1CB--1SG +!2nd cys +ATOM 2CA CX 0.042900 +ATOM 2HA H1 0.076600 +ATOM 2CB 2C -0.079000 +ATOM 2HB1 H1 0.091000 +ATOM 2HB2 H1 0.091000 +ATOM 2SG S -0.108100 +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +ANGLE 1CB 1SG 2SG 1SG 2SG 2CB +DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG +DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG +DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA +DIHE 1CB 1SG 2SG 2CB +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +! +! 5'-terminal adenine, replace phosphate by hydroxyl +! +PRES ADE5 -0.1928 +ATOM H5T HO 0.4295 ! note: name is HO5' in ff14SB, H5T in ff99SB +ATOM O5' OH -0.6223 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +! +! 5'-terminal uracil, replace phosphate by hydroxyl +! +PRES URA5 -0.1928 +ATOM H5T HO 0.4295 ! note: name is HO5' in ff14SB, H5T in ff99SB +ATOM O5' OH -0.6223 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +! +! 5'-terminal thymine, replace phosphate by hydroxyl +! +PRES THY5 -0.1896 +ATOM H5T HO 0.4422 ! note: name is HO5' in ff14SB, H5T in ff99SB +ATOM O5' OH -0.6318 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +! +! 5'-terminal cytosine, replace phosphate by hydroxyl +! +PRES CYT5 -0.1928 +ATOM H5T HO 0.4295 ! note: name is HO5' in ff14SB, H5T in ff99SB +ATOM O5' OH -0.6223 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + +! +! 5'-terminal guanine, replace phosphate by hydroxyl +! +PRES GUA5 -0.1928 +ATOM H5T HO 0.4295 ! note: name is HO5' in ff14SB, H5T in ff99SB +ATOM O5' OH -0.6223 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +! +! 3'-terminal adenine, add terminal hydrogen +! +PRES ADE3 -0.2165 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 ! note: name is HO3' in ff14SB, H3T in ff99SB + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! 3'-terminal uracil, add terminal hydrogen +! +PRES URA3 -0.2165 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 ! note: name is HO3' in ff14SB, H3T in ff99SB + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! 3'-terminal thymine, add terminal hydrogen +! +PRES THY3 -0.2153 +ATOM O3' OH -0.6549 +ATOM H3T HO 0.4396 ! note: name is HO3' in ff14SB, H3T in ff99SB + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! 3'-terminal cytosine, add terminal hydrogen +! +PRES CYT3 -0.2165 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 ! note: name is HO3' in ff14SB, H3T in ff99SB + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! 3'-terminal guanine, add terminal hydrogen +! +PRES GUA3 -0.2165 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 ! note: name is HO3' in ff14SB, H3T in ff99SB + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! DEOXYRIBOSE PATCHES, NOTE: these are made extra tricky by the fact +! that all the charges change upon conversion from RNA to DNA and +! some atom types change as well. This requires special patches for +! 5'-terminal, standard and 3'-terminal residues. +! + +! +! deoxyribose patch for adenine 5'-terminal +! +PRES DOA5 -0.3079 ! note: resname DA5 in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM H5T HO 0.4422 ! note: name is HO5' in ff14SB, H5T in ff99SB +ATOM O5' OH -0.6318 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0431 +ATOM H1' H2 0.1838 +ATOM N9 NG -0.0268 ! note: type is N* in ff14SB & ff99SB +ATOM C8 CK 0.1607 +ATOM H8 H5 0.1877 +ATOM N7 NB -0.6175 +ATOM C5 CB 0.0725 +ATOM C6 CA 0.6897 +ATOM N6 N2 -0.9123 +ATOM H61 H 0.4167 +ATOM H62 H 0.4167 +ATOM N1 NC -0.7624 +ATOM C2 CQ 0.5716 +ATOM H2 H5 0.0598 +ATOM N3 NC -0.7417 +ATOM C4 CB 0.3800 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! note: name is H2'2 in ff99SB +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for adenine +! +PRES DOA -1.0 ! note: resname DA in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7761 ! note: name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4954 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0431 +ATOM H1' H2 0.1838 +ATOM N9 NG -0.0268 ! note: type is N* in ff14SB & ff99SB +ATOM C8 CK 0.1607 +ATOM H8 H5 0.1877 +ATOM N7 NB -0.6175 +ATOM C5 CB 0.0725 +ATOM C6 CA 0.6897 +ATOM N6 N2 -0.9123 +ATOM H61 H 0.4167 +ATOM H62 H 0.4167 +ATOM N1 NC -0.7624 +ATOM C2 CQ 0.5716 +ATOM H2 H5 0.0598 +ATOM N3 NC -0.7417 +ATOM C4 CB 0.3800 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! note: name is H2'2 in ff99SB +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for 3'-terminal adenine +! +PRES DOA3 -0.6921 ! note: resname is DA3 in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7761 ! note: name is OP2 in ff14SB, O1P in ff99SB +ATOM O5' OS -0.4954 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0431 +ATOM H1' H2 0.1838 +ATOM N9 NG -0.0268 ! note: type is N* in ff14SB & ff99SB +ATOM C8 CK 0.1607 +ATOM H8 H5 0.1877 +ATOM N7 NB -0.6175 +ATOM C5 CB 0.0725 +ATOM C6 CA 0.6897 +ATOM N6 N2 -0.9123 +ATOM H61 H 0.4167 +ATOM H62 H 0.4167 +ATOM N1 NC -0.7624 +ATOM C2 CQ 0.5716 +ATOM H2 H5 0.0598 +ATOM N3 NC -0.7417 +ATOM C4 CB 0.3800 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! note: name is H2'2 in ff99SB +ATOM O3' OH -0.6549 +ATOM H3T HO 0.4396 ! name is HO3' in ff14SB, H3T in ff99SB + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + + +! +! deoxyribose patch for 5'-terminal cytosine +! +PRES DOC5 -0.3079 ! note: resname is DC5 in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM H5T HO 0.4422 ! note: name is HO5' in ff14SB, H5T in ff99SB +ATOM O5' OH -0.6318 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT -0.0116 +ATOM H1' H2 0.1963 +ATOM N1 NG -0.0339 ! note: type is N* in ff14SB & ff99SB +ATOM C6 CM -0.0183 +ATOM H6 H4 0.2293 +ATOM C5 CM -0.5222 +ATOM H5 HA 0.1863 +ATOM C4 CA 0.8439 +ATOM N4 N2 -0.9773 +ATOM H41 H 0.4314 +ATOM H42 H 0.4314 +ATOM N3 NC -0.7748 +ATOM C2 C 0.7959 +ATOM O2 O -0.6548 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! this is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! this is H2'2 in ff99SB -- ? need to check +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + + +! +! deoxyribose patch for cytosine +! +PRES DOC -1.00 ! note: resname is DC in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7761 ! note: name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4954 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT -0.0116 +ATOM H1' H2 0.1963 +ATOM N1 NG -0.0339 ! note: type is N* in ff14SB & ff99SB +ATOM C6 CM -0.0183 +ATOM H6 H4 0.2293 +ATOM C5 CM -0.5222 +ATOM H5 HA 0.1863 +ATOM C4 CA 0.8439 +ATOM N4 N2 -0.9773 +ATOM H41 H 0.4314 +ATOM H42 H 0.4314 +ATOM N3 NC -0.7748 +ATOM C2 C 0.7959 +ATOM O2 O -0.6548 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! note: name is H2'2 in ff99SB +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + + +! +! deoxyribose patch for 3'-terminal cytosine +! +PRES DOC3 -0.6921 ! note: resname is DC3 in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7761 ! note: name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4954 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT -0.0116 +ATOM H1' H2 0.1963 +ATOM N1 NG -0.0339 ! note: type is N* in ff14SB & ff99SB +ATOM C6 CM -0.0183 +ATOM H6 H4 0.2293 +ATOM C5 CM -0.5222 +ATOM H5 HA 0.1863 +ATOM C4 CA 0.8439 +ATOM N4 N2 -0.9773 +ATOM H41 H 0.4314 +ATOM H42 H 0.4314 +ATOM N3 NC -0.7748 +ATOM C2 C 0.7959 +ATOM O2 O -0.6548 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! note: name is H2'2 in ff99SB +ATOM O3' OH -0.6549 +ATOM H3T HO 0.4396 ! note: name is HO3' in ff14SB, H3T in ff99SB + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + + +! +! deoxyribose patch for 5'-terminal guanine +! +PRES DOG5 -0.3079 ! note: resname is DG5 in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM H5T HO 0.4422 ! note: name is HO5' in ff14SB, H5T in ff99SB +ATOM O5' OH -0.6318 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0358 +ATOM H1' H2 0.1746 +ATOM N9 NG 0.0577 ! note: type is N* in ff14SB & ff99SB +ATOM C8 CK 0.0736 +ATOM H8 H5 0.1997 +ATOM N7 NB -0.5725 +ATOM C5 CB 0.1991 +ATOM C6 C 0.4918 +ATOM O6 O -0.5699 +ATOM N1 NA -0.5053 +ATOM H1 H 0.3520 +ATOM C2 CA 0.7432 +ATOM N2 N2 -0.9230 +ATOM H21 H 0.4235 +ATOM H22 H 0.4235 +ATOM N3 NC -0.6636 +ATOM C4 CB 0.1814 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! note: name is H2'2 in ff99SB +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for guanine +! +PRES DOG -1.00 ! note: resname is DG in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7761 ! note: name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4954 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0358 +ATOM H1' H2 0.1746 +ATOM N9 NG 0.0577 ! note: type is N* in ff14SB & ff99SB +ATOM C8 CK 0.0736 +ATOM H8 H5 0.1997 +ATOM N7 NB -0.5725 +ATOM C5 CB 0.1991 +ATOM C6 C 0.4918 +ATOM O6 O -0.5699 +ATOM N1 NA -0.5053 +ATOM H1 H 0.3520 +ATOM C2 CA 0.7432 +ATOM N2 N2 -0.9230 +ATOM H21 H 0.4235 +ATOM H22 H 0.4235 +ATOM N3 NC -0.6636 +ATOM C4 CB 0.1814 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! note: name is H2'2 in ff99SB +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + + +! +! deoxyribose patch for 3'-terminal guanine +! +PRES DOG3 -0.6921 ! note: resname is DG3 in ff14SB & ff99SB +DELETE ATOM O2' +GROUP +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 ! note: name is OP1 in ff14SB, O1P in ff99SB +ATOM O2P O2 -0.7761 ! note: name is OP2 in ff14SB, O2P in ff99SB +ATOM O5' OS -0.4954 +ATOM C5' CI -0.0069 ! note: type changed from CT (ff99SB) to CI (ff14SB) +ATOM H5' H1 0.0754 ! note: name is H5'1 in ff99SB +ATOM H5'' H1 0.0754 ! note: name is H5'2 in ff99SB +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0358 +ATOM H1' H2 0.1746 +ATOM N9 NG 0.0577 ! note: type is N* in ff14SB & ff99SB +ATOM C8 CK 0.0736 +ATOM H8 H5 0.1997 +ATOM N7 NB -0.5725 +ATOM C5 CB 0.1991 +ATOM C6 C 0.4918 +ATOM O6 O -0.5699 +ATOM N1 NA -0.5053 +ATOM H1 H 0.3520 +ATOM C2 CA 0.7432 +ATOM N2 N2 -0.9230 +ATOM H21 H 0.4235 +ATOM H22 H 0.4235 +ATOM N3 NC -0.6636 +ATOM C4 CB 0.1814 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: name is H2'1 in ff99SB +ATOM H2'' HC 0.0718 ! note: name is H2'2 in ff99SB +ATOM O3' OH -0.6549 +ATOM H3T HO 0.4396 ! note: name is HO3' in ff14SB, H3T in ff99SB + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +END + diff --git a/charmm/toppar/non_charmm/top_amber_cornell.inp b/charmm/toppar/non_charmm/top_amber_cornell.inp new file mode 100644 index 00000000..320904e2 --- /dev/null +++ b/charmm/toppar/non_charmm/top_amber_cornell.inp @@ -0,0 +1,4050 @@ +* AMBER Cornell et al. (parm94) force field conversion +* See: JACS (1995) 117, 5179-5197. +* converted by tec3, march 1997 +* +23 1 + +!GROUP statements added around the bases in an attempt +!to avoid parallel crashes + +! NOTE: the charges here are un-scaled and represent the +! exact AMBER charges. +! +! Standard CHARMM residue names are utilized: +! +! ADE, THY, GUA, CYT, URA. +! +! Atom type names conform to the AMBER Cornell et. al. 1995, +! parm94.dat & all_nuc94.in naming conventions where possible. +! Exceptions to this rule include types with "*" in the name +! (i.e. N*->NS, C*->CS). CHARMM atom names are utilized. To build +! the residues, the BILD arrays from the top_all22_na.inp were +! utilized (since these are actually probably more trustworthy then +! those supplied in AMBER) and modified where necessary (i.e. THY). +! BONDS were also copied from top_all22_na.inp and all angles and +! dihedrals autogenerated. The impropers were taken straight from the +! all_nuc94.in. All this was done by hand editing. +! +! Results were checked by comparing energies and forces for all the +! residues defined herein. In general, in simulations performing a +! single energy and force evaluation with a cutoff large enough to +! span the entire system the energies and forces agree +! to within ~0.00005 using both CHARMM and AMBER. The AMBER energies +! and forces were calculated using AMBER 4.1/5.0_alpha sander +! (minimization or dynamics) and CHARMM c25n3 (ener). Note that +! differences in the forces may be apparent if the coordinates do not +! match exactly or in cases where different constants are used between +! AMBER and CHARMM. These points require a little more elaboration. +! +! Differences in the coordinates: +! +! (*) incorrect mapping between AMBER and CHARMM coordinates +! (i.e. not 1-to-1). This is possible with hand editting of the +! AMBER names to convert to CHARMM if the correct mapping isn't +! followed. The only case that was readily apparent in this +! analysis was incorrect mapping of H2' and H2'' in the DNA +! residues of ADE, GUA and CYT. The rename command can be used +! to swap names and alleviate this problem (which is not a real +! problem except when comparing forces). +! +! (*) parm coordinate precision. If the parm coordinates were +! created from a PDB file using the link-edit-parm path, improper +! conversion from text->binary->text in edit/parm leads to +! differences in the parm coordinates from the PDB file. +! Therefore, the coordinates will be different than those +! generated by CHARMM using the same PDB coordinates. Therefore, +! prior to comparing forces, the PDB should be converted directly +! to the parm coordinates (which can be done using carnal). +! +! Differences in the electrostatic energies: +! +! (*) The conversion from charge units to kcal/mol in CHARMM is based +! on the value 332.0716 whereas AMBER uses 18.2223**2 or 332.0522173. +! The actual value is somewhat lower than both these values +! (~331.843)! To convert the charges to "CHARMM", they should be +! multiplied by 1.000058372. This was not done within this file. +! [When this is done, the charges are not rounded and therefore +! non-integral charges for the residues are apparent.] To get around +! this problem either the charges can be scaled within CHARMM (which +! will still lead to non-integral charge) or in versions of CHARMM +! beyond c25n3, and through the application of the "AMBER" keyword in +! pref.dat, the AMBER constant can be used. By default, the "fast" +! routines cannot be used with the AMBER-style impropers. In the +! later versions of CHARMM, the AMBER keyword circumvents this +! problem. +! +! BUILDING NUCLEIC ACID STRUCTURES: +! +! To build residues, use the standard naming conventions. By default +! the 5ter and 3ter patchs are applied which convert the first +! residue to a 5'-hydroxyl (no terminal phosphate) and the last +! residue to a 3'-hydroxyl. +! +! NOTE that in the case of case of ADE, GUA and CYT, by default the +! system is RIBONUCLEIC acid. To convert to deoxyribose, use the +! following patchs: +! +! patch DOA5 segid residue <-- 5'-terminal ADE +! patch DOA segid residue <-- standard ADE +! patch DOA3 segid residue <-- 3'-terminal ADE +! patch DOC5 segid residue <-- 5'-terminal CYT +! patch DOC segid residue <-- standard CYT +! patch DOC3 segid residue <-- 3'-terminal CYT +! patch DOG5 segid residue <-- 5'-terminal GUA +! patch DOG segid residue <-- standard GUA +! patch DOG3 segid residue <-- 3'-terminal GUA +! +! ...where "segid" is the current segment and "residue" is the +! residue number +! +! As an example, let's build a single stranded DNA, d[CATG]. We need +! to apply 5' and 3' terminal patches and also patches to turn the +! RNA into DNA for each residue (except THY which is DNA). +! +! read sequence card +! 4 +! CYT ADE THY GUA +! generate s1 setup +! patch doc5 s1 1 +! patch doa s1 2 +! patch dog3 s1 4 +! +! +! Any problems? Let me know... +! cheatham@helix.nih.gov, cheatham@cgl.ucsf.edu +! +! +! +! AMBER atom types and masses (from all_nuc94.in) +! +MASS 1 BR 79.90 ! bromine +MASS 2 C 12.01 ! sp2 C carbonyl group +MASS 3 CA 12.01 ! sp2 C pure aromatic (benzene) +MASS 4 CB 12.01 ! sp2 aromatic C, 5&6 membered ring junction +MASS 5 CC 12.01 ! sp2 aromatic C, 5 memb. ring HIS +MASS 6 CK 12.01 ! sp2 C 5 memb.ring in purines +MASS 7 CM 12.01 ! sp2 C pyrimidines in pos. 5 & 6 +MASS 8 CN 12.01 ! sp2 C aromatic 5&6 memb.ring junct.(TRP) +MASS 9 CQ 12.01 ! sp2 C in 5 mem.ring of purines between 2 N +MASS 10 CR 12.01 ! sp2 arom as CQ but in HIS +MASS 11 CT 12.01 ! sp3 aliphatic C +MASS 12 CV 12.01 ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +MASS 13 CW 12.01 ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +MASS 14 CS 12.01 ! sp2 arom. 5 memb.ring w/1 subst. (TRP) +MASS 15 C0 40.08 ! calcium +MASS 16 H 1.008 ! H bonded to nitrogen atoms +MASS 17 HC 1.008 ! H aliph. bond. to C without electrwd.group +MASS 18 H1 1.008 ! H aliph. bond. to C with 1 electrwd. group +MASS 19 H2 1.008 ! H aliph. bond. to C with 2 electrwd.groups +MASS 20 H3 1.008 ! H aliph. bond. to C with 3 eletrwd.groups +MASS 21 HA 1.008 ! H arom. bond. to C without elctrwd. groups +MASS 22 H4 1.008 ! H arom. bond. to C with 1 electrwd. group +MASS 23 H5 1.008 ! H arom. bond. to C with 2 electrwd. groups +MASS 24 HO 1.008 ! hydroxyl group +MASS 25 HS 1.008 ! hydrogen bonded to sulphur +MASS 26 HW 1.008 ! H in TIP3P water +MASS 27 HP 1.008 ! H bonded to C next to positively charged gr +MASS 28 F 19.00 ! fluorine +MASS 29 I 126.9 ! iodine +MASS 30 IM 35.45 ! assumed to be Cl- +!MASS 31 IP 22.99 ! assumed to be Na+ +MASS 31 SOD 22.99 ! niu +MASS 32 IB 131.0 ! 'big ion w/ waters' for vacuum (Na+, 6H2O) +MASS 33 MG 24.305 ! magnesium +MASS 34 N 14.01 ! sp2 nitrogen in amide groups +MASS 35 NA 14.01 ! sp2 N in 5 memb.ring w/H atom (HIS) +MASS 36 NB 14.01 ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +MASS 37 NC 14.01 ! sp2 N in 6 memb.ring w/LP (ADE,GUA) +MASS 38 N2 14.01 ! sp2 N in amino groups +MASS 39 N3 14.01 ! sp3 N for charged amino groups (Lys, etc) +MASS 40 NS 14.01 ! sp2 N; note N* --> NS to avoid confusion with wildcard +MASS 41 O 16.00 ! carbonyl group oxygen +MASS 42 OW 16.00 ! oxygen in TIP3P water +MASS 43 OH 16.00 ! oxygen in hydroxyl group +MASS 44 OS 16.00 ! ether and ester oxygen +MASS 45 O2 16.00 ! carboxyl and phosphate group oxygen +MASS 46 P 30.97 ! phosphate +MASS 47 S 32.06 ! sulphur in disulfide linkage +MASS 48 SH 32.06 ! sulphur in cystine +MASS 49 CU 63.55 ! copper +MASS 50 FE 55.00 ! iron +MASS 51 Li 6.94 ! lithium +MASS 52 K 39.10 ! potassium +MASS 53 Rb 85.47 ! rubidium + +DECL -CA ! proteins +DECL -C +DECL -O +DECL +N +DECL +H +DECL +CA +DECL +P ! nucleic acids +DECL +O1P +DECL +O2P +DECL +O5' +DECL -O3' + +DEFAULT FIRST NTER LAST CTER +AUTOGENERATE ANGLES DIHEDRAL + +RESIDUE ADE -1.0 ! note: this is RNA (RA); patches to make +GROUP ! terminal or deoxyribose are required +ATOM P P 1.1662 +ATOM O1P O2 -0.7760 +ATOM O2P O2 -0.7760 +ATOM O5' OS -0.4989 +ATOM C5' CT 0.0558 +ATOM H5' H1 0.0679 ! note: type is H5'1 --> this should be checked +ATOM H5'' H1 0.0679 ! note: type is H5'2 +ATOM C4' CT 0.1065 +ATOM H4' H1 0.1174 +ATOM O4' OS -0.3548 +ATOM C1' CT 0.0394 +ATOM H1' H2 0.2007 +GROUP +ATOM N9 NS -0.0251 ! note: type is N* +ATOM C8 CK 0.2006 +ATOM H8 H5 0.1553 +ATOM N7 NB -0.6073 +ATOM C5 CB 0.0515 +ATOM C6 CA 0.7009 +ATOM N6 N2 -0.9019 +ATOM H61 H 0.4115 +ATOM H62 H 0.4115 +ATOM N1 NC -0.7615 +ATOM C2 CQ 0.5875 +ATOM H2 H5 0.0473 +ATOM N3 NC -0.6997 +ATOM C4 CB 0.3053 +GROUP +ATOM C3' CT 0.2022 +ATOM H3' H1 0.0615 +ATOM C2' CT 0.0670 +ATOM H2'' H1 0.0972 ! note: this is H2'1 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 ! note: this is HO'2 +ATOM O3' OS -0.5246 + +! using charmm bond lists (top_all22_na.inp) +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 +BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 + +IMPROPER C8 C4 N9 C1' +IMPROPER C6 H61 N6 H62 +IMPROPER N7 N9 C8 H8 +IMPROPER N1 N3 C2 H2 +IMPROPER C5 N1 C6 N6 + +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +! using charmm geometry (top_all22_na.inp) +IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST ADE5 LAST ADE3 + + +RESIDUE URA -1.0 ! note: this is RNA (RA); patches to make +GROUP ! terminal are required. +ATOM P P 1.1662 +ATOM O1P O2 -0.7760 +ATOM O2P O2 -0.7760 +ATOM O5' OS -0.4989 +ATOM C5' CT 0.0558 +ATOM H5' H1 0.0679 ! note: name is H5'1 +ATOM H5'' H1 0.0679 ! note: name is H5'2 +ATOM C4' CT 0.1065 +ATOM H4' H1 0.1174 +ATOM O4' OS -0.3548 +ATOM C1' CT 0.0674 +ATOM H1' H2 0.1824 +GROUP +ATOM N1 NS 0.0418 ! note: type is N* +ATOM C6 CM -0.1126 +ATOM H6 H4 0.2188 +ATOM C5 CM -0.3635 +ATOM H5 HA 0.1811 +ATOM C4 C 0.5952 +ATOM O4 O -0.5761 +ATOM N3 NA -0.3549 +ATOM H3 H 0.3154 +ATOM C2 C 0.4687 +ATOM O2 O -0.5477 +GROUP +ATOM C3' CT 0.2022 +ATOM H3' H1 0.0615 +ATOM C2' CT 0.0670 +ATOM H2'' H1 0.0972 ! note: name is H2'1 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 ! note: name is HO'2 +ATOM O3' OS -0.5246 + +! bonds from charmm (top_all22_na.inp) +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 + +IMPROPER C6 C2 N1 C1' +IMPROPER C4 C6 C5 H5 +IMPROPER N1 N3 C2 O2 +IMPROPER C5 N3 C4 O4 +IMPROPER C2 C4 N3 H3 +IMPROPER N1 C5 C6 H6 + +DONO H3 N3 +DONO H2' O2' +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +! build from charmm (top_all22_na.inp) +IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 +IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 +IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 +IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 +IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 +IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 +IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 +IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST URA5 LAST URA3 + + +RESIDUE THY -1.0 ! note: this is DNA (DT); patches to make +GROUP ! terminal are required +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 +ATOM O2P O2 -0.7761 +ATOM O5' OS -0.4954 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! this is H5'1 +ATOM H5'' H1 0.0754 ! this is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0680 +ATOM H1' H2 0.1804 +GROUP +ATOM N1 NS -0.0239 ! this is atom type N* +ATOM C6 CM -0.2209 +ATOM H6 H4 0.2607 +ATOM C5 CM 0.0025 +ATOM C7 CT -0.2269 +ATOM H71 HC 0.0770 +ATOM H72 HC 0.0770 +ATOM H73 HC 0.0770 +ATOM C4 C 0.5194 +ATOM O4 O -0.5563 +ATOM N3 NA -0.4340 +ATOM H3 H 0.3420 +ATOM C2 C 0.5677 +ATOM O2 O -0.5881 +GROUP +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! this is H2'1 +ATOM H2'' HC 0.0718 ! this is H2'2 +ATOM O3' OS -0.5232 + +! bonds from charmm (top_all22_na.inp) +! swapped C5M with C7 +! swapped H5? with H7? +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C7 C5 C6 C2' C3' C3' O3' O3' +P +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C6 H6 C7 H71 C7 H72 C7 H73 +BOND C2' H2' + +IMPROPER C6 C2 N1 C1' +IMPROPER C4 C6 C5 C7 +IMPROPER N1 N3 C2 O2 +IMPROPER C5 N3 C4 O4 +IMPROPER C2 C4 N3 H3 +IMPROPER N1 C5 C6 H6 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O3' +ACCE O4' +ACCE O5' + +! build from charmm (top_all22_na.inp) +! name swapping as above, delete references to O2' +IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C7 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C7 H71 0.0 0.0 0.0 0.0 0.0 +IC C5 H71 *C7 H72 0.0 0.0 115.0 0.0 0.0 +IC H71 H72 *C7 H73 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST THY5 LAST THY3 + + +RESI CYT -1.0 ! note: this is RNA (RC); patches to make +GROUP ! terminal or deoxyribose are required +ATOM P P 1.1662 +ATOM O1P O2 -0.7760 +ATOM O2P O2 -0.7760 +ATOM O5' OS -0.4989 +ATOM C5' CT 0.0558 +ATOM H5' H1 0.0679 ! this is H5'1 +ATOM H5'' H1 0.0679 ! this is H5'2 +ATOM C4' CT 0.1065 +ATOM H4' H1 0.1174 +ATOM O4' OS -0.3548 +ATOM C1' CT 0.0066 +ATOM H1' H2 0.2029 +GROUP +ATOM N1 NS -0.0484 ! this is type N* +ATOM C6 CM 0.0053 +ATOM H6 H4 0.1958 +ATOM C5 CM -0.5215 +ATOM H5 HA 0.1928 +ATOM C4 CA 0.8185 +ATOM N4 N2 -0.9530 +ATOM H41 H 0.4234 +ATOM H42 H 0.4234 +ATOM N3 NC -0.7584 +ATOM C2 C 0.7538 +ATOM O2 O -0.6252 +GROUP +ATOM C3' CT 0.2022 +ATOM H3' H1 0.0615 +ATOM C2' CT 0.0670 +ATOM H2'' H1 0.0972 ! this is H2'1 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 ! this is HO'2 +ATOM O3' OS -0.5246 + +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 + +IMPROPER C6 C2 N1 C1' +IMPROPER N1 N3 C2 O2 +IMPROPER C4 H41 N4 H42 +IMPROPER N1 C5 C6 H6 +IMPROPER C6 C4 C5 H5 +IMPROPER N3 C5 C4 N4 + +DONO H42 N4 +DONO H2' O2' +DONO H41 N4 +ACCE O2 C2 +ACCE N3 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.79 1.399 +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST CYT5 LAST CYT3 + + +RESI GUA -1.0 ! note: this is GUA (RG); patches to make +GROUP ! terminal or deoxyribose are required +ATOM P P 1.1662 +ATOM O1P O2 -0.7760 +ATOM O2P O2 -0.7760 +ATOM O5' OS -0.4989 +ATOM C5' CT 0.0558 +ATOM H5' H1 0.0679 ! this is H5'1 +ATOM H5'' H1 0.0679 ! this is H5'2 +ATOM C4' CT 0.1065 +ATOM H4' H1 0.1174 +ATOM O4' OS -0.3548 +ATOM C1' CT 0.0191 +ATOM H1' H2 0.2006 +GROUP +ATOM N9 NS 0.0492 ! this is type N* +ATOM C8 CK 0.1374 +ATOM H8 H5 0.1640 +ATOM N7 NB -0.5709 +ATOM C5 CB 0.1744 +ATOM C6 C 0.4770 +ATOM O6 O -0.5597 +ATOM N1 NA -0.4787 +ATOM H1 H 0.3424 +ATOM C2 CA 0.7657 +ATOM N2 N2 -0.9672 +ATOM H21 H 0.4364 +ATOM H22 H 0.4364 +ATOM N3 NC -0.6323 +ATOM C4 CB 0.1222 +GROUP +ATOM C3' CT 0.2022 +ATOM H3' H1 0.0615 +ATOM C2' CT 0.0670 +ATOM H2'' H1 0.0972 ! this is H2'1 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 ! this is HO'2 +ATOM O3' OS -0.5246 + +! bonds from charmm (top_all22_na.inp) +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 + +IMPROPER C8 C4 N9 C1' +IMPROPER C5 N1 C6 O6 +IMPROPER C6 C2 N1 H1 +IMPROPER C2 H21 N2 H22 +IMPROPER N7 N9 C8 H8 +IMPROPER N1 N3 C2 N2 + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +DONO H2' O2' +ACCE O6 C6 +ACCE N3 +ACCE N7 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +! build array from charmm (top_all22_na.inp) +IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 +IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 +IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -96.0 125.59 1.3783 +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +PATCH FIRST GUA5 LAST GUA3 + + +!RESI WAT 0.00 ! TIPS3P WATER MODEL + ! GENERATE USING NOANGLE NODIHEDRAL +RESI TIP3 0.00 ! niu +GROUP +ATOM OH2 OW -0.834 +ATOM H1 HW 0.417 +ATOM H2 HW 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +ANGLE H1 OH2 H2 ! REQUIRED +PATCHING FIRS NONE LAST NONE + +!RESI CIP 1.00 ! Sodium Ion +!GROUP +!ATOM NA IP 1.00 +!PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion ! niu +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +! +! Definition of patch residues +! + +! +! 5'-terminal adenine, replace phosphate by hydroxyl +! +PRES ADE5 -0.1928 +ATOM H5T HO 0.4295 +ATOM O5' OH -0.6223 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +! +! 5'-terminal uracil, replace phosphate by hydroxyl +! +PRES URA5 -0.1928 +ATOM H5T HO 0.4295 +ATOM O5' OH -0.6223 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +! +! 5'-terminal thymine, replace phosphate by hydroxyl +! +PRES THY5 -0.1896 +ATOM H5T HO 0.4422 +ATOM O5' OH -0.6318 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +! +! 5'-terminal cytosine, replace phosphate by hydroxyl +! +PRES CYT5 -0.1928 +ATOM H5T HO 0.4295 +ATOM O5' OH -0.6223 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + +! +! 5'-terminal guanine, replace phosphate by hydroxyl +! +PRES GUA5 -0.1928 +ATOM H5T HO 0.4295 +ATOM O5' OH -0.6223 + +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P + +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + + +! +! 3'-terminal adenine, add terminal hydrogen +! +PRES ADE3 -0.2165 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! 3'-terminal uracil, add terminal hydrogen +! +PRES URA3 -0.2165 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! 3'-terminal thymine, add terminal hydrogen +! +PRES THY3 -0.2153 +ATOM O3' OH -0.6549 +ATOM H3T HO 0.4396 + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! 3'-terminal cytosine, add terminal hydrogen +! +PRES CYT3 -0.2165 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + + +! +! 3'-terminal guanine, add terminal hydrogen +! +PRES GUA3 -0.2165 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 + +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + +! +! DEOXYRIBOSE PATCHES, NOTE: these are made extra tricky by the fact +! that all the charges change upon conversion from RNA to DNA and +! some atom types change as well. This requires special patches for +! 5'-terminal, standard and 3'-terminal residues. +! + +! +! deoxyribose patch for adenine 5'-terminal +! +PRES DOA5 -0.3079 +DELETE ATOM O2' +ATOM H5T HO 0.4422 +ATOM O5' OH -0.6318 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked +ATOM H5'' H1 0.0754 ! note: type is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0431 +ATOM H1' H2 0.1838 +ATOM N9 NS -0.0268 ! note: type is N* +ATOM C8 CK 0.1607 +ATOM H8 H5 0.1877 +ATOM N7 NB -0.6175 +ATOM C5 CB 0.0725 +ATOM C6 CA 0.6897 +ATOM N6 N2 -0.9123 +ATOM H61 H 0.4167 +ATOM H62 H 0.4167 +ATOM N1 NC -0.7624 +ATOM C2 CQ 0.5716 +ATOM H2 H5 0.0598 +ATOM N3 NC -0.7417 +ATOM C4 CB 0.3800 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2'' HC 0.0718 ! note: this is H2'2 +ATOM H2' HC 0.0718 ! note: this is H2'1 +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for adenine +! +PRES DOA -1.0 +DELETE ATOM O2' +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 +ATOM O2P O2 -0.7761 +ATOM O5' OS -0.4954 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked +ATOM H5'' H1 0.0754 ! note: type is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0431 +ATOM H1' H2 0.1838 +ATOM N9 NS -0.0268 ! note: type is N* +ATOM C8 CK 0.1607 +ATOM H8 H5 0.1877 +ATOM N7 NB -0.6175 +ATOM C5 CB 0.0725 +ATOM C6 CA 0.6897 +ATOM N6 N2 -0.9123 +ATOM H61 H 0.4167 +ATOM H62 H 0.4167 +ATOM N1 NC -0.7624 +ATOM C2 CQ 0.5716 +ATOM H2 H5 0.0598 +ATOM N3 NC -0.7417 +ATOM C4 CB 0.3800 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: this is H2'1 +ATOM H2'' HC 0.0718 ! note: this is H2'2 +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for 3'-terminal adenine +! +PRES DOA3 -0.6921 +DELETE ATOM O2' +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 +ATOM O2P O2 -0.7761 +ATOM O5' OS -0.4954 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked +ATOM H5'' H1 0.0754 ! note: type is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0431 +ATOM H1' H2 0.1838 +ATOM N9 NS -0.0268 ! note: type is N* +ATOM C8 CK 0.1607 +ATOM H8 H5 0.1877 +ATOM N7 NB -0.6175 +ATOM C5 CB 0.0725 +ATOM C6 CA 0.6897 +ATOM N6 N2 -0.9123 +ATOM H61 H 0.4167 +ATOM H62 H 0.4167 +ATOM N1 NC -0.7624 +ATOM C2 CQ 0.5716 +ATOM H2 H5 0.0598 +ATOM N3 NC -0.7417 +ATOM C4 CB 0.3800 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2' HC 0.0718 ! note: this is H2'1 +ATOM H2'' HC 0.0718 ! note: this is H2'2 +ATOM O3' OH -0.6549 +ATOM H3T HO 0.4396 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for 5'-terminal cytosine +! +PRES DOC5 -0.3079 +DELETE ATOM O2' + +ATOM H5T HO 0.4422 +ATOM O5' OH -0.6318 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! this is H5'1 +ATOM H5'' H1 0.0754 ! this is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT -0.0116 +ATOM H1' H2 0.1963 +ATOM N1 NS -0.0339 ! this is type N* +ATOM C6 CM -0.0183 +ATOM H6 H4 0.2293 +ATOM C5 CM -0.5222 +ATOM H5 HA 0.1863 +ATOM C4 CA 0.8439 +ATOM N4 N2 -0.9773 +ATOM H41 H 0.4314 +ATOM H42 H 0.4314 +ATOM N3 NC -0.7748 +ATOM C2 C 0.7959 +ATOM O2 O -0.6548 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2'' HC 0.0718 ! this is H2'1 +ATOM H2' HC 0.0718 ! this is HO'2 +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + + +! +! deoxyribose patch for cytosine +! +PRES DOC -1.00 +DELETE ATOM O2' +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 +ATOM O2P O2 -0.7761 +ATOM O5' OS -0.4954 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! this is H5'1 +ATOM H5'' H1 0.0754 ! this is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT -0.0116 +ATOM H1' H2 0.1963 +ATOM N1 NS -0.0339 ! this is type N* +ATOM C6 CM -0.0183 +ATOM H6 H4 0.2293 +ATOM C5 CM -0.5222 +ATOM H5 HA 0.1863 +ATOM C4 CA 0.8439 +ATOM N4 N2 -0.9773 +ATOM H41 H 0.4314 +ATOM H42 H 0.4314 +ATOM N3 NC -0.7748 +ATOM C2 C 0.7959 +ATOM O2 O -0.6548 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2'' HC 0.0718 ! this is H2'2 +ATOM H2' HC 0.0718 ! this is H2'1 +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for 3'-terminal cytosine +! +PRES DOC3 -0.6921 +DELETE ATOM O2' +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 +ATOM O2P O2 -0.7761 +ATOM O5' OS -0.4954 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! this is H5'1 +ATOM H5'' H1 0.0754 ! this is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT -0.0116 +ATOM H1' H2 0.1963 +ATOM N1 NS -0.0339 ! this is type N* +ATOM C6 CM -0.0183 +ATOM H6 H4 0.2293 +ATOM C5 CM -0.5222 +ATOM H5 HA 0.1863 +ATOM C4 CA 0.8439 +ATOM N4 N2 -0.9773 +ATOM H41 H 0.4314 +ATOM H42 H 0.4314 +ATOM N3 NC -0.7748 +ATOM C2 C 0.7959 +ATOM O2 O -0.6548 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2'' HC 0.0718 ! this is H2'2 +ATOM H2' HC 0.0718 ! this is H2'1 +ATOM O3' OH -0.6549 +ATOM H3T HO 0.4396 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for 5'-terminal guanine +! +PRES DOG5 -0.3079 +DELETE ATOM O2' +ATOM H5T HO 0.4422 +ATOM O5' OH -0.6318 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! this is H5'1 +ATOM H5'' H1 0.0754 ! this is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0358 +ATOM H1' H2 0.1746 +ATOM N9 NS 0.0577 ! this is type N* +ATOM C8 CK 0.0736 +ATOM H8 H5 0.1997 +ATOM N7 NB -0.5725 +ATOM C5 CB 0.1991 +ATOM C6 C 0.4918 +ATOM O6 O -0.5699 +ATOM N1 NA -0.5053 +ATOM H1 H 0.3520 +ATOM C2 CA 0.7432 +ATOM N2 N2 -0.9230 +ATOM H21 H 0.4235 +ATOM H22 H 0.4235 +ATOM N3 NC -0.6636 +ATOM C4 CB 0.1814 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2'' HC 0.0718 ! this is H2'2 +ATOM H2' HC 0.0718 ! this is H2'1 +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! deoxyribose patch for guanine +! +PRES DOG -1.00 +DELETE ATOM O2' +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 +ATOM O2P O2 -0.7761 +ATOM O5' OS -0.4954 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! this is H5'1 +ATOM H5'' H1 0.0754 ! this is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0358 +ATOM H1' H2 0.1746 +ATOM N9 NS 0.0577 ! this is type N* +ATOM C8 CK 0.0736 +ATOM H8 H5 0.1997 +ATOM N7 NB -0.5725 +ATOM C5 CB 0.1991 +ATOM C6 C 0.4918 +ATOM O6 O -0.5699 +ATOM N1 NA -0.5053 +ATOM H1 H 0.3520 +ATOM C2 CA 0.7432 +ATOM N2 N2 -0.9230 +ATOM H21 H 0.4235 +ATOM H22 H 0.4235 +ATOM N3 NC -0.6636 +ATOM C4 CB 0.1814 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2'' HC 0.0718 ! this is H2'2 +ATOM H2' HC 0.0718 ! this is H2'1 +ATOM O3' OS -0.5232 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + + +! +! deoxyribose patch for 3'-terminal guanine +! +PRES DOG3 -0.6921 +DELETE ATOM O2' +ATOM P P 1.1659 +ATOM O1P O2 -0.7761 +ATOM O2P O2 -0.7761 +ATOM O5' OS -0.4954 +ATOM C5' CT -0.0069 +ATOM H5' H1 0.0754 ! this is H5'1 +ATOM H5'' H1 0.0754 ! this is H5'2 +ATOM C4' CT 0.1629 +ATOM H4' H1 0.1176 +ATOM O4' OS -0.3691 +ATOM C1' CT 0.0358 +ATOM H1' H2 0.1746 +ATOM N9 NS 0.0577 ! this is type N* +ATOM C8 CK 0.0736 +ATOM H8 H5 0.1997 +ATOM N7 NB -0.5725 +ATOM C5 CB 0.1991 +ATOM C6 C 0.4918 +ATOM O6 O -0.5699 +ATOM N1 NA -0.5053 +ATOM H1 H 0.3520 +ATOM C2 CA 0.7432 +ATOM N2 N2 -0.9230 +ATOM H21 H 0.4235 +ATOM H22 H 0.4235 +ATOM N3 NC -0.6636 +ATOM C4 CB 0.1814 +ATOM C3' CT 0.0713 +ATOM H3' H1 0.0985 +ATOM C2' CT -0.0854 +ATOM H2'' HC 0.0718 ! this is H2'2 +ATOM H2' HC 0.0718 ! this is H2'1 +ATOM O3' OH -0.6549 +ATOM H3T HO 0.4396 + +BOND C2' H2' +THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' +DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' +DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' +IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +! +! PROTEIN RESIDUES +! + + +RESI ALA 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT 0.03370 ! | HB1 +ATOM HA H1 0.08230 ! | / +ATOM CB CT -0.18250 ! HA-CA--CB-HB2 ALANINE +ATOM HB1 HC 0.06030 ! | \ +ATOM HB2 HC 0.06030 ! | HB2 +ATOM HB3 HC 0.06030 ! O=C +ATOM C C 0.59730 ! | +ATOM O O -0.56790 + +BOND CB CA N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CB HB3 C O + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C + +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +PATCH FIRST NALA LAST CALA + + + +RESI ARG 1.00 +GROUP +ATOM N N -0.34790 ! | HH11 +ATOM HN H 0.27470 ! HN-N | +ATOM CA CT -0.26370 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA H1 0.15600 ! | | | | | //(+) +ATOM CB CT -0.00070 ! HA-CA--CB--CG--CD--NE--CZ +ATOM HB1 HC 0.03270 ! | | | | \ +ATOM HB2 HC 0.03270 ! | HB2 HG2 HD2 NH2-HH22 +ATOM CG CT 0.03900 ! O=C | +ATOM HG1 HC 0.02850 ! | HH21 +ATOM HG2 HC 0.02850 +ATOM CD CT 0.04860 +ATOM HD1 H1 0.06870 +ATOM HD2 H1 0.06870 +ATOM NE N2 -0.52950 +ATOM HE H 0.34560 +ATOM CZ CA 0.80760 +ATOM NH1 N2 -0.86270 +ATOM HH11 H 0.44780 +ATOM HH12 H 0.44780 +ATOM NH2 N2 -0.86270 +ATOM HH21 H 0.44780 +ATOM HH22 H 0.44780 +ATOM C C 0.73410 +ATOM O O -0.58940 + +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +BOND O C CZ NH1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER NE NH1 CZ NH2 +IMPROPER CD CZ NE HE +IMPROPER CZ HH11 NH1 HH12 +IMPROPER CZ HH21 NH2 HH22 + +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C + +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +PATCH FIRST NARG LAST CARG + + +RESI ASN 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT 0.01430 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA H1 0.10480 ! | | || / +ATOM CB CT -0.20410 ! HA-CA--CB--CG--ND2 +ATOM HB1 HC 0.07970 ! | | \ +ATOM HB2 HC 0.07970 ! | HB2 HD22 (trans to OD1) +ATOM CG C 0.71300 ! O=C +ATOM OD1 O -0.59310 ! | +ATOM ND2 N -0.91910 +ATOM HD21 H 0.41960 +ATOM HD22 H 0.41960 +ATOM C C 0.59730 +ATOM O O -0.56790 + +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +BOND C O CG OD1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CB ND2 CG OD1 +IMPROPER CG HD21 ND2 HD22 + +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +PATCH FIRST NASN LAST CASN + + +RESI ASP -1.00 +GROUP +ATOM N N -0.51630 ! | +ATOM HN H 0.29360 ! HN-N +ATOM CA CT 0.03810 ! | HB1 OD1 +ATOM HA H1 0.08800 ! | | // +ATOM CB CT -0.03030 ! HA-CA--CB--CG +ATOM HB1 HC -0.01220 ! | | \ +ATOM HB2 HC -0.01220 ! | HB2 OD2(-) +ATOM CG C 0.79940 ! O=C +ATOM OD1 O2 -0.80140 ! | +ATOM OD2 O2 -0.80140 +ATOM C C 0.53660 +ATOM O O -0.58190 +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +BOND O C CG OD1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CB OD1 CG OD2 + +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C + +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +PATCH FIRST NASP LAST CASP + +RESI CYS 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT 0.02130 ! | HB1 +ATOM HA H1 0.11240 ! | | +ATOM CB CT -0.12310 ! HA-CA--CB--SG +ATOM HB1 H1 0.11120 ! | | \ +ATOM HB2 H1 0.11120 ! | HB2 HG1 +ATOM SG SH -0.31190 ! O=C +ATOM HG1 HS 0.19330 ! | +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C + +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +PATCH FIRST NCYS LAST CCYS + + +RESI CYM -1.00 ! NOTE: there is no terminal negative CYS +GROUP ! residues within Cornell et al.!!! +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT -0.03510 ! | HB1 +ATOM HA H1 0.05080 ! | | +ATOM CB CT -0.24130 ! HA-CA--CB--SG +ATOM HB1 H1 0.11220 ! | | (-) +ATOM HB2 H1 0.11220 ! | HB2 +ATOM SG SH -0.88440 ! O=C +ATOM C C 0.59730 ! | +ATOM O O -0.56790 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C + +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 + +PATCH FIRST NONE LAST NONE + + +RESI CYX 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT 0.04290 ! | HB1 +ATOM HA H1 0.07660 ! | | +ATOM CB CT -0.07900 ! HA-CA--CB--SG +ATOM HB1 H1 0.09100 ! | | (-) +ATOM HB2 H1 0.09100 ! | HB2 +ATOM SG SH -0.10810 ! O=C +ATOM C C 0.59730 ! | +ATOM O O -0.56790 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C + +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 + +PATCH FIRST NCYX LAST CCYX + + +RESI GLN 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT -0.00310 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA H1 0.08500 ! | | | || / +ATOM CB CT -0.00360 ! HA-CA--CB--CG--CD--NE2 +ATOM HB1 HC 0.01710 ! | | | \ +ATOM HB2 HC 0.01710 ! | HB2 HG2 HE22 (trans to OE1) +ATOM CG CT -0.06450 ! O=C +ATOM HG1 HC 0.03520 ! | +ATOM HG2 HC 0.03520 +ATOM CD C 0.69510 +ATOM OE1 O -0.60860 +ATOM NE2 N -0.94070 +ATOM HE21 H 0.42510 +ATOM HE22 H 0.42510 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +BOND O C CD OE1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG NE2 CD OE1 +IMPROPER CD HE21 NE2 HE22 + +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +PATCH FIRST NGLN LAST CGLN + + +RESI GLU -1.00 +ATOM N N -0.51630 ! | +ATOM HN H 0.29360 ! HN-N +ATOM CA CT 0.03970 ! | HB1 HG1 OE1 +ATOM HA H1 0.11050 ! | | | // +ATOM CB CT 0.05600 ! HA-CA--CB--CG--CD +ATOM HB1 HC -0.01730 ! | | | \ +ATOM HB2 HC -0.01730 ! | HB2 HG2 OE2(-) +ATOM CG CT 0.01360 ! O=C +ATOM HG1 HC -0.04250 ! | +ATOM HG2 HC -0.04250 +ATOM CD C 0.80540 +ATOM OE1 O2 -0.81880 +ATOM OE2 O2 -0.81880 +ATOM C C 0.53660 +ATOM O O -0.58190 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 O C CD OE1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG OE1 CD OE2 + +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +PATCH FIRST NGLU LAST CGLU + + + +RESI GLH 0.00 +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT 0.01450 ! | HB1 HG1 OE1 +ATOM HA H1 0.07790 ! | | | // +ATOM CB CT -0.00710 ! HA-CA--CB--CG--CD +ATOM HB1 HC 0.02560 ! | | | \ +ATOM HB2 HC 0.02560 ! | HB2 HG2 OE2(-) +ATOM CG CT -0.01740 ! O=C +ATOM HG1 HC 0.04300 ! | +ATOM HG2 HC 0.04300 +ATOM CD C 0.68010 +ATOM OE1 O -0.58380 +ATOM OE2 OH -0.65110 +ATOM HE2 HO 0.46410 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 O C CD OE1 OE2 HE2 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG OE1 CD OE2 + +DONOR HN N +DONOR HE2 OE2 +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +PATCH FIRST NONE LAST NONE + + +RESI GLY 0.00 +GROUP ! | +ATOM N N -0.41570 ! N-H +ATOM HN H 0.27190 ! | +ATOM CA CT -0.02520 ! | +ATOM HA1 H1 0.06980 ! HA1-CA-HA2 +ATOM HA2 H1 0.06980 ! | +ATOM C C 0.59730 ! | +ATOM O O -0.56790 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 + +PATCH FIRST NGLY LAST CGLY + + + +RESI HID 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N N -0.41570 ! | HD1 HE1 +ATOM HN H 0.27190 ! HN-N | / +ATOM CA CT 0.01880 ! | HB1 ND1--CE1 +ATOM HA H1 0.08810 ! | | / || +ATOM ND1 NA -0.38110 ! HA-CA--CB--CG || +ATOM HD1 H 0.36490 ! | | \\ || +ATOM CG CC -0.02660 ! | HB2 CD2--NE2 +ATOM CB CT -0.04620 ! O=C | +ATOM HB1 HC 0.04020 ! | HD2 +ATOM HB2 HC 0.04020 +ATOM NE2 NB -0.57270 +ATOM CD2 CV 0.12920 +ATOM HD2 H4 0.11470 +ATOM CE1 CR 0.20570 +ATOM HE1 H5 0.13920 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +BOND O C CG CD2 CE1 NE2 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG CE1 ND1 HD1 +IMPROPER CG NE2 CD2 HD2 +IMPROPER ND1 NE2 CE1 HE1 +IMPROPER ND1 CD2 CG CB + +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +PATCH FIRST NHID LAST CHID + + +RESI HIE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N N -0.41570 ! | HE1 +ATOM HN H 0.27190 ! HN-N __ / +ATOM CA CT -0.05810 ! | HB1 ND1--CE1 +ATOM HA H1 0.13600 ! | | / | +ATOM NE2 NA -0.27950 ! HA-CA--CB--CG | +ATOM HE2 H 0.33390 ! | | \\ | +ATOM CD2 CW -0.22070 ! | HB2 CD2--NE2 +ATOM HD2 H4 0.18620 ! O=C | \ +ATOM ND1 NB -0.54320 ! | HD2 HE2 +ATOM CG CC 0.18680 +ATOM CE1 CR 0.16350 +ATOM HE1 H5 0.14350 +ATOM CB CT -0.00740 +ATOM HB1 HC 0.03670 +ATOM HB2 HC 0.03670 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +BOND O C CD2 CG CE1 ND1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CE1 CD2 NE2 HE2 +IMPROPER CG NE2 CD2 HD2 +IMPROPER ND1 NE2 CE1 HE1 +IMPROPER ND1 CD2 CG CB + +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +PATCH FIRST NHIE LAST CHIE + +RESI HIP 1.00 ! Protonated His +GROUP +ATOM N N -0.34790 ! | HD1 HE1 +ATOM HN H 0.27470 ! HN-N | / +ATOM CA CT -0.13540 ! | HB1 ND1--CE1 +ATOM HA H1 0.12120 ! | | / || +ATOM ND1 NA -0.15130 ! HA-CA--CB--CG || +ATOM HD1 H 0.38660 ! | | \\ || +ATOM NE2 NA -0.17180 ! | HB2 CD2--NE2(+) +ATOM HE2 H 0.39110 ! O=C | \ +ATOM CE1 CR -0.01700 ! | HD2 HE2 +ATOM HE1 H5 0.26810 +ATOM CD2 CW -0.11410 +ATOM HD2 H4 0.23170 +ATOM CG CC -0.00120 +ATOM CB CT -0.04140 +ATOM HB1 HC 0.08100 +ATOM HB2 HC 0.08100 +ATOM C C 0.73410 +ATOM O O -0.58940 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +BOND O C CD2 CG NE2 CE1 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG CE1 ND1 HD1 +IMPROPER CE1 CD2 NE2 HE2 +IMPROPER CG NE2 CD2 HD2 +IMPROPER ND1 NE2 CE1 HE1 +IMPROPER ND1 CD2 CG CB + +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +PATCH FIRST NHIP LAST CHIP + + +RESI ILE 0.00 +GROUP +ATOM N N -0.41570 ! | HG21 HG22 +ATOM HN H 0.27190 ! HN-N | / +ATOM CA CT -0.05970 ! | CG2--HG23 +ATOM HA H1 0.08690 ! | / +ATOM CB CT 0.13030 ! HA-CA--CB-HB HD1 +ATOM HB HC 0.01870 ! | \ / +ATOM CG2 CT -0.32040 ! | CG1--CD--HD2 +ATOM HG21 HC 0.08820 ! O=C / \ \ +ATOM HG22 HC 0.08820 ! | HG11 HG12 HD3 +ATOM HG23 HC 0.08820 +ATOM CG1 CT -0.04300 +ATOM HG11 HC 0.02360 +ATOM HG12 HC 0.02360 +ATOM CD CT -0.06600 +ATOM HD1 HC 0.01860 +ATOM HD2 HC 0.01860 +ATOM HD3 HC 0.01860 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + +PATCH FIRST NILE LAST CILE + + +RESI LEU 0.00 +GROUP +ATOM N N -0.41570 ! | HD11 HD12 +ATOM HN H 0.27190 ! HN-N | / +ATOM CA CT -0.05180 ! | HB1 CD1--HD13 +ATOM HA H1 0.09220 ! | | / +ATOM CB CT -0.11020 ! HA-CA--CB--CG-HG +ATOM HB1 HC 0.04570 ! | | \ +ATOM HB2 HC 0.04570 ! | HB2 CD2--HD23 +ATOM CG CT 0.35310 ! O=C | \ +ATOM HG HC -0.03610 ! | HD21 HD22 +ATOM CD1 CT -0.41210 +ATOM HD11 HC 0.10000 +ATOM HD12 HC 0.10000 +ATOM HD13 HC 0.10000 +ATOM CD2 CT -0.41210 +ATOM HD21 HC 0.10000 +ATOM HD22 HC 0.10000 +ATOM HD23 HC 0.10000 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +PATCH FIRST NLEU LAST CLEU + + + +RESI LYS 1.00 +GROUP +ATOM N N -0.34790 ! | +ATOM HN H 0.27470 ! HN-N +ATOM CA CT -0.24000 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA H1 0.14260 ! | | | | | / +ATOM CB CT -0.00940 ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM HB1 HC 0.03620 ! | | | | | \ +ATOM HB2 HC 0.03620 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM CG CT 0.01870 ! O=C +ATOM HG1 HC 0.01030 ! | +ATOM HG2 HC 0.01030 +ATOM CD CT -0.04790 +ATOM HD1 HC 0.06210 +ATOM HD2 HC 0.06210 +ATOM CE CT -0.01430 +ATOM HE1 HP 0.11350 +ATOM HE2 HP 0.11350 +ATOM NZ N3 -0.38540 +ATOM HZ1 H 0.34000 +ATOM HZ2 H 0.34000 +ATOM HZ3 H 0.34000 +ATOM C C 0.73410 +ATOM O O -0.58940 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +BOND O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +PATCH FIRST NLYS LAST CLYS + + +RESI MET 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT -0.02370 ! | HB1 HG1 HE1 +ATOM HA H1 0.08800 ! | | | | +ATOM CB CT 0.03420 ! HA-CA--CB--CG--SD--CE--HE3 +ATOM HB1 HC 0.02410 ! | | | | +ATOM HB2 HC 0.02410 ! | HB2 HG2 HE2 +ATOM CG CT 0.00180 ! O=C +ATOM HG1 H1 0.04400 ! | +ATOM HG2 H1 0.04400 +ATOM SD S -0.27370 +ATOM CE CT -0.05360 +ATOM HE1 H1 0.06840 +ATOM HE2 H1 0.06840 +ATOM HE3 H1 0.06840 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +PATCH FIRST NMET LAST CMET + + +RESI PHE 0.00 +GROUP +ATOM N N -0.41570 ! | HD1 HE1 +ATOM HN H 0.27190 ! HN-N | | +ATOM CA CT -0.00240 ! | HB1 CD1--CE1 +ATOM HA H1 0.09780 ! | | // \\ +ATOM CB CT -0.03430 ! HA-CA--CB--CG CZ--HZ +ATOM HB1 HC 0.02950 ! | | \ __ / +ATOM HB2 HC 0.02950 ! | HB2 CD2--CE2 +ATOM CG CA 0.01180 ! O=C | | +ATOM CD1 CA -0.12560 ! | HD2 HE2 +ATOM HD1 HA 0.13300 +ATOM CE1 CA -0.17040 +ATOM HE1 HA 0.14300 +ATOM CZ CA -0.10720 +ATOM HZ HA 0.12970 +ATOM CE2 CA -0.17040 +ATOM HE2 HA 0.14300 +ATOM CD2 CA -0.12560 +ATOM HD2 HA 0.13300 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +BOND O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG CE2 CD2 HD2 +!IMPROPER CD2 CZ CE2 HE2 +IMPROPER CZ CD2 CE2 HE2 +IMPROPER CE1 CE2 CZ HZ +IMPROPER CD1 CZ CE1 HE1 +IMPROPER CG CE1 CD1 HD1 +IMPROPER CD1 CD2 CG CB + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +PATCH FIRST NPHE LAST CPHE + +RESI PRO 0.00 +GROUP +ATOM N N -0.25480 ! HD1 HD2 +ATOM CD CT 0.01920 ! | \ / +ATOM HD1 H1 0.03910 ! N---CD HG1 +ATOM HD2 H1 0.03910 ! | \ / +ATOM CG CT 0.01890 ! | CG +ATOM HG1 HC 0.02130 ! | / \ +ATOM HG2 HC 0.02130 ! HA-CA--CB HG2 +ATOM CB CT -0.00700 ! | / \ +ATOM HB1 HC 0.02530 ! | HB1 HB2 +ATOM HB2 HC 0.02530 ! O=C +ATOM CA CT -0.02660 ! | +ATOM HA H1 0.06410 +ATOM C C 0.58960 +ATOM O O -0.57480 +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +BOND O C + +IMPROPER -C CD N CA +IMPROPER CA +N C O + +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 + +PATCH FIRST NPRO LAST CPRO + + +RESI SER 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT -0.02490 ! | HB1 +ATOM HA H1 0.08430 ! | | +ATOM CB CT 0.21170 ! HA-CA--CB--OG +ATOM HB1 H1 0.03520 ! | | \ +ATOM HB2 H1 0.03520 ! | HB2 HG1 +ATOM OG OH -0.65460 ! O=C +ATOM HG1 HO 0.42750 ! | +ATOM C C 0.59730 +ATOM O O -0.56790 + +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +PATCH FIRST NSER LAST CSER + + +RESI THR 0.00 +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! HN-N +ATOM CA CT -0.03890 ! | OG1--HG1 +ATOM HA H1 0.10070 ! | / +ATOM CB CT 0.36540 ! HA-CA--CB-HB +ATOM HB H1 0.00430 ! | \ +ATOM CG2 CT -0.24380 ! | CG2--HG21 +ATOM HG21 HC 0.06420 ! O=C / \ +ATOM HG22 HC 0.06420 ! | HG21 HG22 +ATOM HG23 HC 0.06420 +ATOM OG1 OH -0.67610 +ATOM HG1 HO 0.41020 +ATOM C C 0.59730 +ATOM O O -0.56790 + +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +PATCH FIRST NTHR LAST CTHR + + +RESI TRP 0.00 +GROUP +ATOM N N -0.41570 ! | HE3 +ATOM HN H 0.27190 ! HN-N | +ATOM CA CT -0.02750 ! | HB1 CE3 +ATOM HA H1 0.11230 ! | | / \\ +ATOM CB CT -0.00500 ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM HB1 HC 0.03390 ! | | || || | +ATOM HB2 HC 0.03390 ! | HB2 CD1 CE2 CH2-HH2 +ATOM CG CS -0.14150 ! O=C / \ / \ // +ATOM CD1 CW -0.16380 ! | HD1 NE1 CZ2 +ATOM HD1 H4 0.20620 ! | | +ATOM NE1 NA -0.34180 ! HE1 HZ2 +ATOM HE1 H 0.34120 +ATOM CE2 CN 0.13800 +ATOM CZ2 CA -0.26010 +ATOM HZ2 HA 0.15720 +ATOM CH2 CA -0.11340 +ATOM HH2 HA 0.14170 +ATOM CZ3 CA -0.19720 +ATOM HZ3 HA 0.14470 +ATOM CE3 CA -0.23870 +ATOM HE3 HA 0.17000 +ATOM CD2 CB 0.12430 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +BOND O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CD1 CE2 NE1 HE1 +IMPROPER CE2 CH2 CZ2 HZ2 +IMPROPER CZ2 CZ3 CH2 HH2 +IMPROPER CH2 CE3 CZ3 HZ3 +IMPROPER CZ3 CD2 CE3 HE3 +IMPROPER CG NE1 CD1 HD1 +IMPROPER CD1 CD2 CG CB + +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +PATCH FIRST NTRP LAST CTRP + + + +RESI TYR 0.00 +GROUP +ATOM N N -0.41570 ! | HD1 HE1 +ATOM HN H 0.27190 ! HN-N | | +ATOM CA CT -0.00140 ! | HB1 CD1--CE1 +ATOM HA H1 0.08760 ! | | // \\ +ATOM CB CT -0.01520 ! HA-CA--CB--CG CZ--OH +ATOM HB1 HC 0.02950 ! | | \ __ / \ +ATOM HB2 HC 0.02950 ! | HB2 CD2--CE2 HH +ATOM CG CA -0.00110 ! O=C | | +ATOM CD1 CA -0.19060 ! | HD2 HE2 +ATOM HD1 HA 0.16990 +ATOM CE1 CA -0.23410 +ATOM HE1 HA 0.16560 +ATOM CZ C 0.32260 +ATOM OH OH -0.55790 +ATOM HH HO 0.39920 +ATOM CE2 CA -0.23410 +ATOM HE2 HA 0.16560 +ATOM CD2 CA -0.19060 +ATOM HD2 HA 0.16990 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +BOND O C CD1 CG CE1 CZ CE2 CD2 + +IMPROPER -C CA N HN +IMPROPER CA +N C O +IMPROPER CG CE2 CD2 HD2 +!IMPROPER CD2 CZ CE2 HE2 +IMPROPER CZ CD2 CE2 HE2 +IMPROPER CD1 CZ CE1 HE1 +IMPROPER CG CE1 CD1 HD1 +IMPROPER CD1 CD2 CG CB +IMPROPER CE1 CE2 CZ OH + + +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +PATCH FIRST NTYR LAST CTYR + + +RESI VAL 0.00 +GROUP +ATOM N N -0.41570 ! | HG11 HG12 +ATOM HN H 0.27190 ! HN-N | / +ATOM CA CT -0.08750 ! | CG1--HG13 +ATOM HA H1 0.09690 ! | / +ATOM CB CT 0.29850 ! HA-CA--CB-HB +ATOM HB HC -0.02970 ! | \ +ATOM CG1 CT -0.31920 ! | CG2--HG21 +ATOM HG11 HC 0.07910 ! O=C / \ +ATOM HG12 HC 0.07910 ! | HG21 HG22 +ATOM HG13 HC 0.07910 +ATOM CG2 CT -0.31920 +ATOM HG21 HC 0.07910 +ATOM HG22 HC 0.07910 +ATOM HG23 HC 0.07910 +ATOM C C 0.59730 +ATOM O O -0.56790 +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +BOND O C + +IMPROPER -C CA N HN +IMPROPER CA +N C O + +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +PATCH FIRST NVAL LAST CVAL + + +RESI ACE 0.00 ! acetylated N-terminus +GROUP ! +ATOM HY1 HC 0.11230 ! HY1 HY2 HY3 +ATOM CAY CT -0.36620 ! \ | / +ATOM HY2 HC 0.11230 ! CAY +ATOM HY3 HC 0.11230 ! | +ATOM C C 0.59720 ! C=O +ATOM O O -0.56790 ! | + +BOND C CAY C +N CAY HY1 CAY HY2 CAY HY3 +BOND O C + +IMPROPER CAY +N C O + +ACCEPTOR O C + +IC C N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC C CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY C N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O C CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O C CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC O C CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PATCH FIRST NONE LAST NONE + + +RESI NME 0.00 ! N-Methylamide C-terminus +GROUP +ATOM N N -0.41570 ! | +ATOM HN H 0.27190 ! N-HN +ATOM CAT CT -0.14900 ! | +ATOM HT1 H1 0.09760 ! HT1-CAT-HT3 +ATOM HT2 H1 0.09760 ! | +ATOM HT3 H1 0.09760 ! HT2 + + +BOND N HN N CAT CAT HT1 CAT HT2 CAT HT3 + +IMPROPER -C CAT N HN + +DONOR HN N +IC N CA -C -O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC -C CAT *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C N CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C N CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C N CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI WAT 0.00 ! TIPS3P WATER MODEL + ! GENERATE USING NOANGLE NODIHEDRAL +GROUP +ATOM OH2 OW -0.834 +ATOM H1 HW 0.417 +ATOM H2 HW 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +ANGLE H1 OH2 H2 ! REQUIRED +PATCHING FIRS NONE LAST NONE + +!RESI CIP 1.00 ! Sodium Ion +!GROUP +!ATOM NA IP 1.00 +!PATCHING FIRST NONE LAST NONE + +!protein patches + +PRES NALA 1.0 +DELETE ATOM HN +ATOM N N3 0.14140 ! +ATOM HT1 H 0.19970 ! HT2 +ATOM HT2 H 0.19970 ! |(+) +ATOM HT3 H 0.19970 ! HT1-N-HT3 +ATOM CA CT 0.09620 ! | HB1 +ATOM HA HP 0.08890 ! | / +ATOM CB CT -0.05970 ! HA-CA--CB-HB2 ALANINE +ATOM HB1 HC 0.03000 ! | \ +ATOM HB2 HC 0.03000 ! | HB2 +ATOM HB3 HC 0.03000 ! O=C +ATOM C C 0.61630 ! | +ATOM O O -0.57220 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CALA -1.0 +DELETE ATOM O +ATOM N N -0.38210 ! | +ATOM HN H 0.26810 ! HN-N +ATOM CA CT -0.17470 ! | HB1 +ATOM HA H1 0.10670 ! | / +ATOM CB CT -0.20930 ! HA-CA--CB-HB2 ALANINE +ATOM HB1 HC 0.07640 ! | \ +ATOM HB2 HC 0.07640 ! | HB2 +ATOM HB3 HC 0.07640 ! OT1=C +ATOM C C 0.77310 ! | +ATOM OT1 O2 -0.80550 ! OT2 +ATOM OT2 O2 -0.80550 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NARG 2.0 +DELETE ATOM HN +ATOM N N3 0.13050 +ATOM HT1 H 0.20830 +ATOM HT2 H 0.20830 ! HT2 +ATOM HT3 H 0.20830 ! |(+) HH11 +ATOM CA CT -0.02230 ! HT1-N-HT3 | +ATOM HA HP 0.12420 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM CB CT 0.01180 ! | | | | | //(+) +ATOM HB1 HC 0.02260 ! HA-CA--CB--CG--CD--NE--CZ +ATOM HB2 HC 0.02260 ! | | | | \ +ATOM CG CT 0.02360 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HG1 HC 0.03090 ! O=C | +ATOM HG2 HC 0.03090 ! | HH21 +ATOM CD CT 0.09350 +ATOM HD1 H1 0.05270 +ATOM HD2 H1 0.05270 +ATOM NE N2 -0.56500 +ATOM HE H 0.35920 +ATOM CZ CA 0.82810 +ATOM NH1 N2 -0.86930 +ATOM HH11 H 0.44940 +ATOM HH12 H 0.44940 +ATOM NH2 N2 -0.86930 +ATOM HH21 H 0.44940 +ATOM HH22 H 0.44940 +ATOM C C 0.72140 +ATOM O O -0.60130 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CARG 0.0 +DELETE ATOM O +ATOM N N -0.34810 ! | HH11 +ATOM HN H 0.27640 ! HN-N | +ATOM CA CT -0.30680 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA H1 0.14470 ! | | | | | //(+) +ATOM CB CT -0.03740 ! HA-CA--CB--CG--CD--NE--CZ +ATOM HB1 HC 0.03710 ! | | | | \ +ATOM HB2 HC 0.03710 ! | HB2 HG2 HD2 NH2-HH22 +ATOM CG CT 0.07440 ! OT1=C | +ATOM HG1 HC 0.01850 ! | HH21 +ATOM HG2 HC 0.01850 ! OT2 +ATOM CD CT 0.11140 +ATOM HD1 H1 0.04680 +ATOM HD2 H1 0.04680 +ATOM NE N2 -0.55640 +ATOM HE H 0.34790 +ATOM CZ CA 0.83680 +ATOM NH1 N2 -0.87370 +ATOM HH11 H 0.44930 +ATOM HH12 H 0.44930 +ATOM NH2 N2 -0.87370 +ATOM HH21 H 0.44930 +ATOM HH22 H 0.44930 +ATOM C C 0.85570 +ATOM OT1 O2 -0.82660 +ATOM OT2 O2 -0.82660 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NASN 1.0 +DELETE ATOM HN +ATOM N N3 0.18010 +ATOM HT1 H 0.19210 +ATOM HT2 H 0.19210 +ATOM HT3 H 0.19210 +ATOM CA CT 0.03680 +ATOM HA HP 0.12310 +ATOM CB CT -0.02830 +ATOM HB1 HC 0.05150 +ATOM HB2 HC 0.05150 +ATOM CG C 0.58330 +ATOM OD1 O -0.57440 +ATOM ND2 N -0.86340 +ATOM HD21 H 0.40970 +ATOM HD22 H 0.40970 +ATOM C C 0.61630 +ATOM O O -0.57220 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CASN -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.20800 +ATOM HA H1 0.13580 +ATOM CB CT -0.22990 +ATOM HB1 HC 0.10230 +ATOM HB2 HC 0.10230 +ATOM CG C 0.71530 +ATOM OD1 O -0.60100 +ATOM ND2 N -0.90840 +ATOM HD21 H 0.41500 +ATOM HD22 H 0.41500 +ATOM C C 0.80500 +ATOM OT1 O2 -0.81470 +ATOM OT2 O2 -0.81470 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NASP 0.0 +DELETE ATOM HN +ATOM N N3 0.07820 +ATOM HT1 H 0.22000 +ATOM HT2 H 0.22000 +ATOM HT3 H 0.22000 +ATOM CA CT 0.02920 +ATOM HA HP 0.11410 +ATOM CB CT -0.02350 +ATOM HB1 HC -0.01690 +ATOM HB2 HC -0.01690 +ATOM CG C 0.81940 +ATOM OD1 O2 -0.80840 +ATOM OD2 O2 -0.80840 +ATOM C C 0.56210 +ATOM O O -0.58890 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CASP -2.0 +DELETE ATOM O +ATOM N N -0.51920 +ATOM HN H 0.30550 +ATOM CA CT -0.18170 +ATOM HA H1 0.10460 +ATOM CB CT -0.06770 +ATOM HB1 HC -0.02120 +ATOM HB2 HC -0.02120 +ATOM CG C 0.88510 +ATOM OD1 O2 -0.81620 +ATOM OD2 O2 -0.81620 +ATOM C C 0.72560 +ATOM OT1 O2 -0.78870 +ATOM OT2 O2 -0.78870 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NCYS 1.0 +DELETE ATOM HN +ATOM N N3 0.13250 +ATOM HT1 H 0.20230 +ATOM HT2 H 0.20230 +ATOM HT3 H 0.20230 +ATOM CA CT 0.09270 +ATOM HA HP 0.14110 +ATOM CB CT -0.11950 +ATOM HB1 H1 0.11880 +ATOM HB2 H1 0.11880 +ATOM SG SH -0.32980 +ATOM HG1 HS 0.19750 +ATOM C C 0.61230 +ATOM O O -0.57130 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CCYS -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.16350 +ATOM HA H1 0.13960 +ATOM CB CT -0.19960 +ATOM HB1 H1 0.14370 +ATOM HB2 H1 0.14370 +ATOM SG SH -0.31020 +ATOM HG1 HS 0.20680 +ATOM C C 0.74970 +ATOM OT1 O2 -0.79810 +ATOM OT2 O2 -0.79810 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NCYX 1.0 +DELETE ATOM HN +ATOM N N3 0.20690 +ATOM HT1 H 0.18150 +ATOM HT2 H 0.18150 +ATOM HT3 H 0.18150 +ATOM CA CT 0.10550 +ATOM HA HP 0.09220 +ATOM CB CT -0.02770 +ATOM HB1 H1 0.06800 +ATOM HB2 H1 0.06800 +ATOM SG SH -0.09840 +ATOM C C 0.61230 +ATOM O O -0.57130 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CCYX -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.13180 +ATOM HA H1 0.09380 +ATOM CB CT -0.19430 +ATOM HB1 H1 0.12280 +ATOM HB2 H1 0.12280 +ATOM SG SH -0.05290 +ATOM C C 0.76180 +ATOM OT1 O2 -0.80410 +ATOM OT2 O2 -0.80410 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + + +PRES NGLN +1.0 +DELETE ATOM HN +ATOM N N3 0.14930 +ATOM HT1 H 0.19960 +ATOM HT2 H 0.19960 +ATOM HT3 H 0.19960 +ATOM CA CT 0.05360 +ATOM HA HP 0.10150 +ATOM CB CT 0.06510 +ATOM HB1 HC 0.00500 +ATOM HB2 HC 0.00500 +ATOM CG CT -0.09030 +ATOM HG1 HC 0.03310 +ATOM HG2 HC 0.03310 +ATOM CD C 0.73540 +ATOM OE1 O -0.61330 +ATOM NE2 N -1.00310 +ATOM HE21 H 0.44290 +ATOM HE22 H 0.44290 +ATOM C C 0.61230 +ATOM O O -0.57130 +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CGLN -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.22480 +ATOM HA H1 0.12320 +ATOM CB CT -0.06640 +ATOM HB1 HC 0.04520 +ATOM HB2 HC 0.04520 +ATOM CG CT -0.02100 +ATOM HG1 HC 0.02030 +ATOM HG2 HC 0.02030 +ATOM CD C 0.70930 +ATOM OE1 O -0.60980 +ATOM NE2 N -0.95740 +ATOM HE21 H 0.43040 +ATOM HE22 H 0.43040 +ATOM C C 0.77750 +ATOM OT1 O2 -0.80420 +ATOM OT2 O2 -0.80420 +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NGLU 0.0 +DELETE ATOM HN +ATOM N N3 0.00170 +ATOM HT1 H 0.23910 +ATOM HT2 H 0.23910 +ATOM HT3 H 0.23910 +ATOM CA CT 0.05880 +ATOM HA HP 0.12020 +ATOM CB CT 0.09090 +ATOM HB1 HC -0.02320 +ATOM HB2 HC -0.02320 +ATOM CG CT -0.02360 +ATOM HG1 HC -0.03150 +ATOM HG2 HC -0.03150 +ATOM CD C 0.80870 +ATOM OE1 O2 -0.81890 +ATOM OE2 O2 -0.81890 +ATOM C C 0.56210 +ATOM O O -0.58890 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + + +PRES CGLU -2.0 +DELETE ATOM O +ATOM N N -0.51920 +ATOM HN H 0.30550 +ATOM CA CT -0.20590 +ATOM HA H1 0.13990 +ATOM CB CT 0.00710 +ATOM HB1 HC -0.00780 +ATOM HB2 HC -0.00780 +ATOM CG CT 0.06750 +ATOM HG1 HC -0.05480 +ATOM HG2 HC -0.05480 +ATOM CD C 0.81830 +ATOM OE1 O2 -0.82200 +ATOM OE2 O2 -0.82200 +ATOM C C 0.74200 +ATOM OT1 O2 -0.79300 +ATOM OT2 O2 -0.79300 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NGLY 1.0 +DELETE ATOM HN +ATOM N N3 0.29430 +ATOM HT1 H 0.16420 +ATOM HT2 H 0.16420 +ATOM HT3 H 0.16420 +ATOM CA CT -0.01000 +ATOM HA1 HP 0.08950 +ATOM HA2 HP 0.08950 +ATOM C C 0.61630 +ATOM O O -0.57220 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CGLY -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.24930 +ATOM HA1 H1 0.10560 +ATOM HA2 H1 0.10560 +ATOM C C 0.72310 +ATOM OT1 O2 -0.78550 +ATOM OT2 O2 -0.78550 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NHID 1.0 +DELETE ATOM HN +ATOM N N3 0.15420 +ATOM HT1 H 0.19630 +ATOM HT2 H 0.19630 +ATOM HT3 H 0.19630 +ATOM CA CT 0.09640 +ATOM HA HP 0.09580 +ATOM ND1 NA -0.38190 +ATOM HD1 H 0.36320 +ATOM CG CC -0.03990 +ATOM CB CT 0.02590 +ATOM HB1 HC 0.02090 +ATOM HB2 HC 0.02090 +ATOM NE2 NB -0.57110 +ATOM CD2 CV 0.10460 +ATOM HD2 H4 0.12990 +ATOM CE1 CR 0.21270 +ATOM HE1 H5 0.13850 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CHID -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.17390 +ATOM HA H1 0.11000 +ATOM ND1 NA -0.38920 +ATOM HD1 H 0.37550 +ATOM CG CC 0.02930 +ATOM CB CT -0.10460 +ATOM HB1 HC 0.05650 +ATOM HB2 HC 0.05650 +ATOM NE2 NB -0.56290 +ATOM CD2 CV 0.10010 +ATOM HD2 H4 0.12410 +ATOM CE1 CR 0.19250 +ATOM HE1 H5 0.14180 +ATOM C C 0.76150 +ATOM OT1 O2 -0.80160 +ATOM OT2 O2 -0.80160 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NHIE 1.0 +DELETE ATOM HN +ATOM N N3 0.14720 +ATOM HT1 H 0.20160 +ATOM HT2 H 0.20160 +ATOM HT3 H 0.20160 +ATOM CA CT 0.02360 +ATOM HA HP 0.13800 +ATOM NE2 NA -0.27810 +ATOM HE2 H 0.33240 +ATOM CD2 CW -0.23490 +ATOM HD2 H4 0.19630 +ATOM ND1 NB -0.55790 +ATOM CG CC 0.17400 +ATOM CE1 CR 0.18040 +ATOM HE1 H5 0.13970 +ATOM CB CT 0.04890 +ATOM HB1 HC 0.02230 +ATOM HB2 HC 0.02230 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + + +PRES CHIE -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.26990 +ATOM HA H1 0.16500 +ATOM NE2 NA -0.26700 +ATOM HE2 H 0.33190 +ATOM CD2 CW -0.25880 +ATOM HD2 H4 0.19570 +ATOM ND1 NB -0.55170 +ATOM CG CC 0.27240 +ATOM CE1 CR 0.15580 +ATOM HE1 H5 0.14480 +ATOM CB CT -0.10680 +ATOM HB1 HC 0.06200 +ATOM HB2 HC 0.06200 +ATOM C C 0.79160 +ATOM OT1 O2 -0.80650 +ATOM OT2 O2 -0.80650 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NHIP 2.0 +DELETE ATOM HN +ATOM N N3 0.25600 +ATOM HT1 H 0.17040 +ATOM HT2 H 0.17040 +ATOM HT3 H 0.17040 +ATOM CA CT 0.05810 +ATOM HA HP 0.10470 +ATOM ND1 NA -0.15100 +ATOM HD1 H 0.38210 +ATOM NE2 NA -0.17390 +ATOM HE2 H 0.39210 +ATOM CE1 CR -0.00110 +ATOM HE1 H5 0.26450 +ATOM CD2 CW -0.14330 +ATOM HD2 H4 0.24950 +ATOM CG CC -0.02360 +ATOM CB CT 0.04840 +ATOM HB1 HC 0.05310 +ATOM HB2 HC 0.05310 +ATOM C C 0.72140 +ATOM O O -0.60130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CHIP 0.0 +DELETE ATOM O +ATOM N N -0.34810 +ATOM HN H 0.27640 +ATOM CA CT -0.14450 +ATOM HA H1 0.11150 +ATOM ND1 NA -0.15010 +ATOM HD1 H 0.38830 +ATOM NE2 NA -0.16830 +ATOM HE2 H 0.39130 +ATOM CE1 CR -0.02510 +ATOM HE1 H5 0.26940 +ATOM CD2 CW -0.12560 +ATOM HD2 H4 0.23360 +ATOM CG CC 0.02980 +ATOM CB CT -0.08000 +ATOM HB1 HC 0.08680 +ATOM HB2 HC 0.08680 +ATOM C C 0.80320 +ATOM OT1 O2 -0.81770 +ATOM OT2 O2 -0.81770 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES NILE 1.0 +DELETE ATOM HN +ATOM N N3 0.03110 +ATOM HT1 H 0.23290 +ATOM HT2 H 0.23290 +ATOM HT3 H 0.23290 +ATOM CA CT 0.02570 +ATOM HA HP 0.10310 +ATOM CB CT 0.18850 +ATOM HB HC 0.02130 +ATOM CG2 CT -0.37200 +ATOM HG21 HC 0.09470 +ATOM HG22 HC 0.09470 +ATOM HG23 HC 0.09470 +ATOM CG1 CT -0.03870 +ATOM HG11 HC 0.02010 +ATOM HG12 HC 0.02010 +ATOM CD CT -0.09080 +ATOM HD1 HC 0.02260 +ATOM HD2 HC 0.02260 +ATOM HD3 HC 0.02260 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CILE -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.31000 +ATOM HA H1 0.13750 +ATOM CB CT 0.03630 +ATOM HB HC 0.07660 +ATOM CG2 CT -0.34980 +ATOM HG21 HC 0.10210 +ATOM HG22 HC 0.10210 +ATOM HG23 HC 0.10210 +ATOM CG1 CT -0.03230 +ATOM HG11 HC 0.03210 +ATOM HG12 HC 0.03210 +ATOM CD CT -0.06990 +ATOM HD1 HC 0.01960 +ATOM HD2 HC 0.01960 +ATOM HD3 HC 0.01960 +ATOM C C 0.83430 +ATOM OT1 O2 -0.81900 +ATOM OT2 O2 -0.81900 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES NLEU 1.0 +DELETE ATOM HN +ATOM N N3 0.10100 +ATOM HT1 H 0.21480 +ATOM HT2 H 0.21480 +ATOM HT3 H 0.21480 +ATOM CA CT 0.01040 +ATOM HA HP 0.10530 +ATOM CB CT -0.02440 +ATOM HB1 HC 0.02560 +ATOM HB2 HC 0.02560 +ATOM CG CT 0.34210 +ATOM HG HC -0.03800 +ATOM CD1 CT -0.41060 +ATOM HD11 HC 0.09800 +ATOM HD12 HC 0.09800 +ATOM HD13 HC 0.09800 +ATOM CD2 CT -0.41040 +ATOM HD21 HC 0.09800 +ATOM HD22 HC 0.09800 +ATOM HD23 HC 0.09800 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CLEU -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.28470 +ATOM HA H1 0.13460 +ATOM CB CT -0.24690 +ATOM HB1 HC 0.09740 +ATOM HB2 HC 0.09740 +ATOM CG CT 0.37060 +ATOM HG HC -0.03740 +ATOM CD1 CT -0.41630 +ATOM HD11 HC 0.10380 +ATOM HD12 HC 0.10380 +ATOM HD13 HC 0.10380 +ATOM CD2 CT -0.41630 +ATOM HD21 HC 0.10380 +ATOM HD22 HC 0.10380 +ATOM HD23 HC 0.10380 +ATOM C C 0.83260 +ATOM OT1 O2 -0.81990 +ATOM OT2 O2 -0.81990 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES NLYS 2.0 +DELETE ATOM HN +ATOM N N3 0.09660 +ATOM HT1 H 0.21650 +ATOM HT2 H 0.21650 +ATOM HT3 H 0.21650 +ATOM CA CT -0.00150 +ATOM HA HP 0.11800 +ATOM CB CT 0.02120 +ATOM HB1 HC 0.02830 +ATOM HB2 HC 0.02830 +ATOM CG CT -0.00480 +ATOM HG1 HC 0.01210 +ATOM HG2 HC 0.01210 +ATOM CD CT -0.06080 +ATOM HD1 HC 0.06330 +ATOM HD2 HC 0.06330 +ATOM CE CT -0.01810 +ATOM HE1 HP 0.11710 +ATOM HE2 HP 0.11710 +ATOM NZ N3 -0.37640 +ATOM HZ1 H 0.33820 +ATOM HZ2 H 0.33820 +ATOM HZ3 H 0.33820 +ATOM C C 0.72140 +ATOM O O -0.60130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CLYS 0.0 +DELETE ATOM O +ATOM N N -0.34810 +ATOM HN H 0.27640 +ATOM CA CT -0.29030 +ATOM HA H1 0.14380 +ATOM CB CT -0.05380 +ATOM HB1 HC 0.04820 +ATOM HB2 HC 0.04820 +ATOM CG CT 0.02270 +ATOM HG1 HC 0.01340 +ATOM HG2 HC 0.01340 +ATOM CD CT -0.03920 +ATOM HD1 HC 0.06110 +ATOM HD2 HC 0.06110 +ATOM CE CT -0.01760 +ATOM HE1 HP 0.11210 +ATOM HE2 HP 0.11210 +ATOM NZ N3 -0.37410 +ATOM HZ1 H 0.33740 +ATOM HZ2 H 0.33740 +ATOM HZ3 H 0.33740 +ATOM C C 0.84880 +ATOM OT1 O2 -0.82520 +ATOM OT2 O2 -0.82520 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES NMET 1.0 +DELETE ATOM HN +ATOM N N3 0.15920 +ATOM HT1 H 0.19840 +ATOM HT2 H 0.19840 +ATOM HT3 H 0.19840 +ATOM CA CT 0.02210 +ATOM HA HP 0.11160 +ATOM CB CT 0.08650 +ATOM HB1 HC 0.01250 +ATOM HB2 HC 0.01250 +ATOM CG CT 0.03340 +ATOM HG1 H1 0.02920 +ATOM HG2 H1 0.02920 +ATOM SD S -0.27740 +ATOM CE CT -0.03410 +ATOM HE1 H1 0.05970 +ATOM HE2 H1 0.05970 +ATOM HE3 H1 0.05970 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CMET -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.25970 +ATOM HA H1 0.12770 +ATOM CB CT -0.02360 +ATOM HB1 HC 0.04800 +ATOM HB2 HC 0.04800 +ATOM CG CT 0.04920 +ATOM HG1 H1 0.03170 +ATOM HG2 H1 0.03170 +ATOM SD S -0.26920 +ATOM CE CT -0.03760 +ATOM HE1 H1 0.06250 +ATOM HE2 H1 0.06250 +ATOM HE3 H1 0.06250 +ATOM C C 0.80130 +ATOM OT1 O2 -0.81050 +ATOM OT2 O2 -0.81050 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NPHE 1.0 +DELETE ATOM HN +ATOM N N3 0.17370 +ATOM HT1 H 0.19210 +ATOM HT2 H 0.19210 +ATOM HT3 H 0.19210 +ATOM CA CT 0.07330 +ATOM HA HP 0.10410 +ATOM CB CT 0.03300 +ATOM HB1 HC 0.01040 +ATOM HB2 HC 0.01040 +ATOM CG CA 0.00310 +ATOM CD1 CA -0.13920 +ATOM HD1 HA 0.13740 +ATOM CE1 CA -0.16020 +ATOM HE1 HA 0.14330 +ATOM CZ CA -0.12080 +ATOM HZ HA 0.13290 +ATOM CE2 CA -0.16030 +ATOM HE2 HA 0.14330 +ATOM CD2 CA -0.13910 +ATOM HD2 HA 0.13740 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CPHE -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.18250 +ATOM HA H1 0.10980 +ATOM CB CT -0.09590 +ATOM HB1 HC 0.04430 +ATOM HB2 HC 0.04430 +ATOM CG CA 0.05520 +ATOM CD1 CA -0.13000 +ATOM HD1 HA 0.14080 +ATOM CE1 CA -0.18470 +ATOM HE1 HA 0.14610 +ATOM CZ CA -0.09440 +ATOM HZ HA 0.12800 +ATOM CE2 CA -0.18470 +ATOM HE2 HA 0.14610 +ATOM CD2 CA -0.13000 +ATOM HD2 HA 0.14080 +ATOM C C 0.76600 +ATOM OT1 O2 -0.80260 +ATOM OT2 O2 -0.80260 + +BOND C OT2 +BOND C OT1 +!IMPROPER CA OT2 C OT1 +IMPROPER CA OT1 C OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + + +PRES NPRO 1.0 +ATOM N N3 -0.20200 +ATOM HN1 H 0.31200 +ATOM HN2 H 0.31200 +ATOM CD CT -0.01200 +ATOM HD1 HP 0.10000 +ATOM HD2 HP 0.10000 +ATOM CG CT -0.12100 +ATOM HG1 HC 0.10000 +ATOM HG2 HC 0.10000 +ATOM CB CT -0.11500 +ATOM HB1 HC 0.10000 +ATOM HB2 HC 0.10000 +ATOM CA CT 0.10000 +ATOM HA HP 0.10000 +ATOM C C 0.52600 +ATOM O O -0.50000 + +BOND HN1 N HN2 N ! HD1 HD2 +DONOR HN1 N +DONOR HN2 N +IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CPRO -1.0 +DELETE ATOM O +ATOM N N -0.28020 +ATOM CD CT 0.04340 +ATOM HD1 H1 0.03310 +ATOM HD2 H1 0.03310 +ATOM CG CT 0.04660 +ATOM HG1 HC 0.01720 +ATOM HG2 HC 0.01720 +ATOM CB CT -0.05430 +ATOM HB1 HC 0.03810 +ATOM HB2 HC 0.03810 +ATOM CA CT -0.13360 +ATOM HA H1 0.07760 +ATOM C C 0.66310 +ATOM OT1 O2 -0.76970 +ATOM OT2 O2 -0.76970 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + + +PRES NSER 1.0 +DELETE ATOM HN +ATOM N N3 0.18490 +ATOM HT1 H 0.18980 +ATOM HT2 H 0.18980 +ATOM HT3 H 0.18980 +ATOM CA CT 0.05670 +ATOM HA HP 0.07820 +ATOM CB CT 0.25960 +ATOM HB1 H1 0.02730 +ATOM HB2 H1 0.02730 +ATOM OG OH -0.67140 +ATOM HG1 HO 0.42390 +ATOM C C 0.61630 +ATOM O O -0.57220 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CSER -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.27220 +ATOM HA H1 0.13040 +ATOM CB CT 0.11230 +ATOM HB1 H1 0.08130 +ATOM HB2 H1 0.08130 +ATOM OG OH -0.65140 +ATOM HG1 HO 0.44740 +ATOM C C 0.81130 +ATOM OT1 O2 -0.81320 +ATOM OT2 O2 -0.81320 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NTHR 1.0 +DELETE ATOM HN +ATOM N N3 0.18120 +ATOM HT1 H 0.19340 +ATOM HT2 H 0.19340 +ATOM HT3 H 0.19340 +ATOM CA CT 0.00340 +ATOM HA HP 0.10870 +ATOM CB CT 0.45140 +ATOM HB H1 -0.03230 +ATOM CG2 CT -0.25540 +ATOM HG21 HC 0.06270 +ATOM HG22 HC 0.06270 +ATOM HG23 HC 0.06270 +ATOM OG1 OH -0.67640 +ATOM HG1 HO 0.40700 +ATOM C C 0.61630 +ATOM O O -0.57220 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CTHR -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.24200 +ATOM HA H1 0.12070 +ATOM CB CT 0.30250 +ATOM HB H1 0.00780 +ATOM CG2 CT -0.18530 +ATOM HG21 HC 0.05860 +ATOM HG22 HC 0.05860 +ATOM HG23 HC 0.05860 +ATOM OG1 OH -0.64960 +ATOM HG1 HO 0.41190 +ATOM C C 0.78100 +ATOM OT1 O2 -0.80440 +ATOM OT2 O2 -0.80440 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT1 C OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NTRP 1.0 +DELETE ATOM HN +ATOM N N3 0.19130 +ATOM HT1 H 0.18880 +ATOM HT2 H 0.18880 +ATOM HT3 H 0.18880 +ATOM CA CT 0.04210 +ATOM HA HP 0.11620 +ATOM CB CT 0.05430 +ATOM HB1 HC 0.02220 +ATOM HB2 HC 0.02220 +ATOM CG CS -0.16540 +ATOM CD1 CW -0.17880 +ATOM HD1 H4 0.21950 +ATOM NE1 NA -0.34440 +ATOM HE1 H 0.34120 +ATOM CE2 CN 0.15750 +ATOM CZ2 CA -0.27100 +ATOM HZ2 HA 0.15890 +ATOM CH2 CA -0.10800 +ATOM HH2 HA 0.14110 +ATOM CZ3 CA -0.20340 +ATOM HZ3 HA 0.14580 +ATOM CE3 CA -0.22650 +ATOM HE3 HA 0.16460 +ATOM CD2 CB 0.11320 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES CTRP -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.20840 +ATOM HA H1 0.12720 +ATOM CB CT -0.07420 +ATOM HB1 HC 0.04970 +ATOM HB2 HC 0.04970 +ATOM CG CS -0.07960 +ATOM CD1 CW -0.18080 +ATOM HD1 H4 0.20430 +ATOM NE1 NA -0.33160 +ATOM HE1 H 0.34130 +ATOM CE2 CN 0.12220 +ATOM CZ2 CA -0.25940 +ATOM HZ2 HA 0.15670 +ATOM CH2 CA -0.10200 +ATOM HH2 HA 0.14010 +ATOM CZ3 CA -0.22870 +ATOM HZ3 HA 0.15070 +ATOM CE3 CA -0.18370 +ATOM HE3 HA 0.14910 +ATOM CD2 CB 0.10780 +ATOM C C 0.76580 +ATOM OT1 O2 -0.80110 +ATOM OT2 O2 -0.80110 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT1 C OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NTYR 1.0 +DELETE ATOM HN +ATOM N N3 0.19400 +ATOM HT1 H 0.18730 +ATOM HT2 H 0.18730 +ATOM HT3 H 0.18730 +ATOM CA CT 0.05700 +ATOM HA HP 0.09830 +ATOM CB CT 0.06590 +ATOM HB1 HC 0.01020 +ATOM HB2 HC 0.01020 +ATOM CG CA -0.02050 +ATOM CD1 CA -0.20020 +ATOM HD1 HA 0.17200 +ATOM CE1 CA -0.22390 +ATOM HE1 HA 0.16500 +ATOM CZ C 0.31390 +ATOM OH OH -0.55780 +ATOM HH HO 0.40010 +ATOM CE2 CA -0.22390 +ATOM HE2 HA 0.16500 +ATOM CD2 CA -0.20020 +ATOM HD2 HA 0.17200 +ATOM C C 0.61230 +ATOM O O -0.57130 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + + +PRES CTYR -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.20150 +ATOM HA H1 0.10920 +ATOM CB CT -0.07520 +ATOM HB1 HC 0.04900 +ATOM HB2 HC 0.04900 +ATOM CG CA 0.02430 +ATOM CD1 CA -0.19220 +ATOM HD1 HA 0.17800 +ATOM CE1 CA -0.24580 +ATOM HE1 HA 0.16730 +ATOM CZ C 0.33950 +ATOM OH OH -0.56430 +ATOM HH HO 0.40170 +ATOM CE2 CA -0.24580 +ATOM HE2 HA 0.16730 +ATOM CD2 CA -0.19220 +ATOM HD2 HA 0.17800 +ATOM C C 0.78170 +ATOM OT1 O2 -0.80700 +ATOM OT2 O2 -0.80700 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT1 C OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES NVAL 1.0 +DELETE ATOM HN +ATOM N N3 0.05770 +ATOM HT1 H 0.22720 +ATOM HT2 H 0.22720 +ATOM HT3 H 0.22720 +ATOM CA CT -0.00540 +ATOM HA HP 0.10930 +ATOM CB CT 0.31960 +ATOM HB HC -0.02210 +ATOM CG1 CT -0.31290 +ATOM HG11 HC 0.07350 +ATOM HG12 HC 0.07350 +ATOM HG13 HC 0.07350 +ATOM CG2 CT -0.31290 +ATOM HG21 HC 0.07350 +ATOM HG22 HC 0.07350 +ATOM HG23 HC 0.07350 +ATOM C C 0.61630 +ATOM O O -0.57220 + +BOND HT1 N HT2 N HT3 N + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N + +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CVAL -1.0 +DELETE ATOM O +ATOM N N -0.38210 +ATOM HN H 0.26810 +ATOM CA CT -0.34380 +ATOM HA H1 0.14380 +ATOM CB CT 0.19400 +ATOM HB HC 0.03080 +ATOM CG1 CT -0.30640 +ATOM HG11 HC 0.08360 +ATOM HG12 HC 0.08360 +ATOM HG13 HC 0.08360 +ATOM CG2 CT -0.30640 +ATOM HG21 HC 0.08360 +ATOM HG22 HC 0.08360 +ATOM HG23 HC 0.08360 +ATOM C C 0.83500 +ATOM OT1 O2 -0.81730 +ATOM OT2 O2 -0.81730 + +BOND C OT2 +BOND C OT1 +IMPROPER CA OT2 C OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES DISU 0.2288 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. +GROUP ! use in a patch statement + ! added by adm jr. based on CYX +!1st cys +ATOM 1CA CT 0.042900 +ATOM 1HA H1 0.076600 +ATOM 1CB CT -0.079000 +ATOM 1HB1 H1 0.091000 ! 2SG--2CB-- +ATOM 1HB2 H1 0.091000 ! / +ATOM 1SG S -0.108100 ! -1CB--1SG +!2nd cys +ATOM 2CA CT 0.042900 +ATOM 2HA H1 0.076600 +ATOM 2CB CT -0.079000 +ATOM 2HB1 H1 0.091000 +ATOM 2HB2 H1 0.091000 +ATOM 2SG S -0.108100 +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +ANGLE 1CB 1SG 2SG 1SG 2SG 2CB +DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG +DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG +DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA +DIHE 1CB 1SG 2SG 2CB +!DIHE 1CB 1SG 2SG 2CB +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +END diff --git a/charmm/toppar/non_charmm/top_bms_dec03.inp b/charmm/toppar/non_charmm/top_bms_dec03.inp new file mode 100644 index 00000000..794737f2 --- /dev/null +++ b/charmm/toppar/non_charmm/top_bms_dec03.inp @@ -0,0 +1,1280 @@ +* \\\\\\\ All-Hydrogen Nucleic Acid Topology File //////// +* \\\\\\\\\\\\\\\\\\ Developmental /////////////////////// +* David R. Langley +* Version 1.00, August 1995 +* Version 1.05, June 1999 +* Version 1.10, November 2000 +* Version 1.15, April 2003 +*.................................................................. +*.................................................................. +* David R. Langley, Molecular Dynamic Simulations of Environment +* and Sequence Dependent DNA Conformations: The Development of +* the BMS Nucleic Acid Force Field and Comparison with Experimental +* Results. J. Biomol. Struct. Dyn., 1998, 16, 487-509. +*.................................................................. +*.................................................................. +* Parameters for 2'-deoxy-6-thioguanine (patch residue id: TG) were added 11-22-00. +* - +* The modeified TIPS3P WATER MODEL with 5% reduced charges (residue id: T95) +* provides stable (4M NaCl) A-DNA simulations by balancing the +* Na-H2O, Cl-H2O, DNA-Na, DNA-Cl, DNA-H2O interactions. +* + +22 1 +MASS 1 CA 12.011000 ! Nucleic acid aromatic carbon to amide +MASS 2 CB 12.011000 ! Nucleic acid purine C4 and C5 +MASS 3 CE 12.011000 ! Nucleic acid purine C8 and ADE C2 +MASS 4 CF 12.011000 ! Nucleic acid aromatic carbon +MASS 5 CK 12.011000 ! Nucleic acid carbonyl carbon +MASS 6 CT5 12.011000 ! Nucleic acid sp3 ribose ring carbon +MASS 7 CTT 12.011000 ! Nucleic acid carbon (equivalent to protein CT3) +MASS 8 CT 12.011000 ! ethanol +MASS 9 CF3 12.011000 ! trifloroethanol + +MASS 10 HA 1.008000 ! ethanol and trifloroethanol +MASS 11 HA5 1.008000 ! Nucleic acid ribose aliphatic proton +MASS 12 HAR 1.008000 ! Nucleic acid aromatic carbon proton +MASS 13 HAT 1.008000 ! Nucleic acid proton (equivalent to protein HA) +MASS 14 HB 1.008000 ! Nucleic acid ring nitrogen proton +MASS 15 HNA 1.008000 ! Nucleic acid amine proton +MASS 16 HO 1.008000 ! Nucleic acid ribose hydroxyl proton +MASS 17 HOP 1.008000 ! Nucleic acid phosphate hydroxyl proton +MASS 18 HT 1.008000 ! TIPS3P WATER HYDROGEN + +MASS 19 NAN 14.007000 ! Nucleic acid amide nitrogen +MASS 20 NAG 14.007000 ! Nucleic acid protonated ring nitrogen, gua N1 +MASS 21 NAT 14.007000 ! Nucleic acid protonated ring nitrogen, ura N3 +MASS 22 NB 14.007000 ! Nucleic acid purine ADE N7 +MASS 23 NBG 14.007000 ! Nucleic acid purine GUA N7 +MASS 24 NC 14.007000 ! Nucleic acid unprotonated ring nitrogen +MASS 25 NCA 14.007000 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 +MASS 26 NS 14.007000 ! Nucleic acid protonated ring nitrogen (N9 of ADE,GUA) +MASS 27 NSP 14.007000 ! Nucleic acid protonated ring nitrogen (N1 of THY,CYT) +MASS 28 NSR 14.007000 ! RNA Nucleic acid protonated ring nitrogen (N1 of URA,CYT or N9 of ADE, GUA) + +MASS 29 OCP 15.999400 ! Nucleic acid =O in phosphate +MASS 30 OE 15.999400 ! Nucleic acid ribose ring oxygen +MASS 31 OH 15.999400 ! Nucleic acid ribose hydroxyl oxygen +MASS 32 OHP 15.999400 ! Nucleic acid phosphate hydroxyl oxygen +MASS 33 OK 15.999400 ! Nucleic acid carbonyl oxygen +MASS 34 OKC 15.999400 ! Nucleic acid carbonyl oxygen, CYT O2 +MASS 35 OKG 15.999400 ! Nucleic acid carbonyl oxygen, GUA O6 +MASS 36 OS 15.999400 ! Nucleic acid phosphate ester oxygen +MASS 37 OT 15.999400 ! TIPS3P WATER OXYGEN + +MASS 38 S 32.06 ! Nucleic acid sulphur in 6-thioguanine + +MASS 39 P 30.974000 ! phosphorus +MASS 40 MG 24.305000 ! Magnesium Ion +MASS 41 SOD 22.989770 ! Sodium Ion +MASS 42 XCL 35.45300 ! Chlorine Ion +MASS 43 XF 18.998403 ! Fluorine, trifloroethanol +MASS 44 K 39.0983 ! potassium +MASS 45 HE 4.0026 ! Helium +MASS 46 NE 20.179 ! Neon +MASS 47 AR 39.948 ! Argon +MASS 100 DUM 0.001 ! dummy atom + +MASS 101 OW 15.999400 ! TIP3P water model, J. Chem. Phys., 79, 926, 1983. +MASS 102 HW 1.008000 ! TIP3P water model, J. Chem. Phys., 79, 926, 1983. + +DECL +P +DECL +O1P +DECL +O2P +DECL +O5' +DECL -O3' + +DEFA FIRS 5TER LAST 3TER +AUTOGENERATE ANGLES DIHEDRALS + +RESI A -1.00 +ATOM P P 1.1659 ! 1.36 +ATOM O1P OCP -0.7761 !-0.72 +ATOM O2P OCP -0.7761 !-0.72 +ATOM O5' OS -0.4954 !-0.46 +GROUP +ATOM C5' CTT -0.0069 !-0.070 +ATOM H5' HAT 0.0754 ! 0.070 +ATOM H5'' HAT 0.0754 ! 0.070 +GROUP +ATOM C4' CT5 0.1629 ! 0.065 +ATOM H4' HA5 0.1176 ! 0.035 +ATOM O4' OE -0.3691 !-0.37 +ATOM C1' CT5 0.0431 ! 0.165 +ATOM H1' HA5 0.1838 ! 0.035 +GROUP +ATOM N9 NS -0.0268 !-0.35 +ATOM C4 CB 0.3800 ! 0.55 +GROUP +ATOM N3 NCA -0.7417 !-0.73 +ATOM C2 CE 0.5716 ! 0.66 +ATOM H2 HAR 0.0598 ! 0.13 +GROUP +ATOM N1 NCA -0.7624 !-0.77 +ATOM C6 CA 0.6897 ! 0.77 +GROUP +ATOM N6 NAN -0.9123 !-0.77 +ATOM H61 HNA 0.4167 ! 0.33 trans to N1 +ATOM H62 HNA 0.4167 ! 0.33 cis to N1 (involved in BP h-bond) +GROUP +ATOM C5 CB 0.0725 !-0.10 +ATOM N7 NB -0.6175 !-0.54 +ATOM C8 CE 0.1607 ! 0.26 +ATOM H8 HAR 0.1877 ! 0.16 +GROUP +ATOM C2' CT5 -0.0854 !-0.070 +ATOM H2'' HA5 0.0718 ! 0.07 +ATOM H2' HA5 0.0718 ! 0.07 +GROUP +ATOM C3' CT5 0.0713 !-0.035 +ATOM H3' HA5 0.0985 ! 0.035 +GROUP +ATOM O3' OS -0.5232 !-0.46 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 +BOND C2' C3' C2' H2' C3' O3' O3' +P +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +IMPH H62 C6 H61 N6 N6 N1 C5 C6 H2 N1 N3 C2 +IMPH H8 N7 N9 C8 +DONO H61 N6 +DONO H62 N6 +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1P P +ACCE O2P P +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 101.45 -39.00 119.00 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.6100 119.00 -151.00 110.04 1.5400!beta +IC O5' C5' C4' C3' 1.4201 111.04 31.00 114.78 1.5284!gamma +IC C5' C4' C3' O3' 1.5400 114.78 156.00 109.42 1.421!delta +IC C4' C3' O3' +P 1.5284 109.42 159.00 119.05 1.6100!epsil +IC C3' O3' +P +O5' 1.4212 119.05 -98.00 101.45 1.610!eta +IC C5' C3' *C4' O4' 1.5400 113.37 119.62 105.78 1.4500 +IC C5' C3' *C4' H4' 1.5400 113.37 -119.62 105.78 1.0900 +IC C4' C3' C2' C1' 1.5284 102.38 -34.00 101.97 1.5251!nu2 +IC C4' O3' *C3' C2' 1.5284 109.48 -120.16 110.92 1.5412 +IC C4' O3' *C3' H3' 1.5284 109.48 120.16 110.92 1.0900 +!IC C3' C2' C1' N9 1.5284 101.97 93.39 113.71 1.4897 +IC O4' C1' N9 C4 1.4197 108.06 -95.42 125.97 1.3703!chi +IC C1' C4 *N9 C8 1.4897 125.97 -179.94 105.00 1.3768 +IC C4 N9 C8 N7 1.3703 105.00 -0.07 113.93 1.2970 +IC C8 N9 C4 C5 1.3768 105.00 0.06 106.60 1.3650 +IC N9 C5 *C4 N3 1.3703 106.60 -179.93 126.69 1.3486 +IC C5 C4 N3 C2 1.3650 126.69 -0.04 111.18 1.3130 +IC C4 N3 C2 N1 1.3486 111.18 -0.02 128.64 1.3399 +IC N3 C2 N1 C6 1.3130 128.64 0.06 118.95 1.3456 +IC C5 N1 *C6 N6 1.4034 117.43 -179.96 119.06 1.3410 +IC N1 C6 N6 H61 1.3456 119.06 179.96 120.00 1.0100 +IC H61 C6 *N6 H62 1.0100 120.00 -180.00 120.00 1.0100 +IC C1' C3' *C2' H2' 1.5251 101.97 114.67 114.31 1.0912 +IC C1' C3' *C2' H2'' 1.5251 101.97 -114.67 114.31 1.0912 +IC O4' C2' *C1' H1' 1.4197 105.77 -115.00 109.47 1.0900 +IC O4' C2' *C1' N9 0.0000 105.77 120.00 114.5 0.0000 +IC C5' C3' *C4' H4' 1.5400 114.37 -115.00 109.47 1.0900 +IC C4' O5' *C5' H5' 1.4500 111.84 115.00 109.47 1.0900 +IC C4' O5' *C5' H5'' 1.4500 111.84 -115.00 109.47 1.0900 +IC N9 N7 *C8 H8 1.3768 113.93 180.00 122.00 1.0800 +IC N1 N3 *C2 H2 1.3399 128.64 180.00 120.00 1.0800 + +RESI C -1.000 +ATOM P P 1.1659 ! 1.36 +ATOM O1P OCP -0.7761 !-0.72 +ATOM O2P OCP -0.7761 !-0.72 +ATOM O5' OS -0.4954 !-0.46 +GROUP +ATOM C5' CTT -0.0069 !-0.070 +ATOM H5' HAT 0.0754 ! 0.070 +ATOM H5'' HAT 0.0754 ! 0.070 +GROUP +ATOM C4' CT5 0.1629 ! 0.065 +ATOM H4' HA5 0.1176 ! 0.035 +ATOM O4' OE -0.3691 !-0.37 +ATOM C1' CT5 -0.0116 ! 0.165 +ATOM H1' HA5 0.1963 ! 0.035 +GROUP +ATOM N1 NSP -0.0339 !-0.21 +ATOM C6 CF -0.0183 ! 0.23 +ATOM H6 HAR 0.2293 ! 0.12 +GROUP +ATOM C2 CK 0.7959 ! 0.86 +ATOM O2 OKC -0.6548 !-0.55 +GROUP +ATOM N3 NC -0.7748 !-0.86 +ATOM C4 CA 0.8439 ! 0.94 +GROUP +ATOM N4 NAN -0.9773 !-0.83 +ATOM H41 HNA 0.4314 ! 0.33 trans to N3 +ATOM H42 HNA 0.4314 ! 0.33 cis to N3 (involved in BP h-bond) +GROUP +ATOM C5 CF -0.5222 !-0.58 +ATOM H5 HAR 0.1863 ! 0.15 +GROUP +ATOM C2' CT5 -0.0854 !-0.070 +ATOM H2'' HA5 0.0718 ! 0.07 +ATOM H2' HA5 0.0718 ! 0.07 +GROUP +ATOM C3' CT5 0.0713 !-0.035 +ATOM H3' HA5 0.0985 ! 0.035 +GROUP +ATOM O3' OS -0.5232 !-0.46 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 +IMPH O2 N1 N3 C2 N4 N3 C5 C4 +IMPH H5 C4 C6 C5 H6 C5 N1 C6 +IMPH H42 C4 H41 N4 +DONO H42 N4 +DONO H41 N4 +ACCE O2 C2 +ACCE N3 +ACCE O1P P +ACCE O2P P +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 101.45 -39.00 119.00 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.6100 119.00 -151.00 110.04 1.5400!beta +IC O5' C5' C4' C3' 1.4201 111.04 31.00 115.78 1.5284!gamma +IC C5' C4' C3' O3' 1.5400 114.78 156.0 111.92 1.4212!delta +IC C4' C3' O3' +P 1.5284 109.42 159.00 119.05 1.600!epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -98.00 101.45 1.6100!eta +IC C5' C3' *C4' O4' 1.5400 113.37 119.62 106.78 1.4560 +IC C5' C3' *C4' H4' 1.5400 113.37 -119.62 101.78 1.0900 +IC C4' O3' *C3' C2' 1.528 109.47 -120.00 110.00 1.5400 +IC C4' O3' *C3' H3' 1.528 109.47 120.00 109.47 1.0900 +IC C4' C3' C2' C1' 1.5284 102.78 -34.00 101.97 1.5251!nu2 +!IC C3' C2' C1' N1 1.5284 101.97 93.39 113.71 1.4896 +IC O4' C1' N1 C2 1.4197 108.06 -95.44 117.79 1.3923!chi +IC C1' C2 *N1 C6 1.4896 117.79 -179.99 121.13 1.3595 +IC C2 N1 C6 C5 1.3923 121.13 0.02 121.13 1.3570 +IC C6 N1 C2 N3 1.3595 121.13 0.01 118.71 1.3578 +IC N1 N3 *C2 O2 1.3923 118.71 179.98 122.46 1.2378 +IC N1 C2 N3 C4 1.3923 118.71 -0.03 120.61 1.3386 +IC C5 N3 *C4 N4 1.4331 121.58 180.00 118.32 1.3246 +IC N3 C4 N4 H41 1.3386 118.32 -180.00 117.70 1.0100 +IC H41 C4 *N4 H42 1.0100 117.70 -180.00 120.27 1.0100 +IC O4' C2' *C1' H1' 1.4197 105.77 -115.00 109.47 1.0900 +IC O4' C2' *C1' N1 1.4197 105.77 115.00 0.0000 0.0000 +IC C1' C3' *C2' H2' 1.5251 101.97 114.67 110.81 1.0912 +IC C1' C3' *C2' H2'' 1.5251 101.97 -114.67 110.81 1.0912 +IC C4' O5' *C5' H5' 1.4500 111.84 115.00 109.47 1.0900 +IC C4' O5' *C5' H5'' 1.4500 111.84 -115.00 109.47 1.0900 +IC C6 C4 *C5 H5 1.3570 116.83 180.00 120.00 1.0800 +IC N1 C5 *C6 H6 1.3595 121.13 180.00 120.00 1.0800 + +RESI G -1.00 +ATOM P P 1.1659 ! 1.36 +ATOM O1P OCP -0.7761 !-0.72 +ATOM O2P OCP -0.7761 !-0.72 +ATOM O5' OS -0.4954 !-0.46 +GROUP +ATOM C5' CTT -0.0069 !-0.070 +ATOM H5' HAT 0.0754 ! 0.070 +ATOM H5'' HAT 0.0754 ! 0.070 +GROUP +ATOM C4' CT5 0.1629 ! 0.065 +ATOM H4' HA5 0.1176 ! 0.035 +ATOM O4' OE -0.3691 !-0.37 +ATOM C1' CT5 0.0358 ! 0.165 +ATOM H1' HA5 0.1746 ! 0.035 +GROUP +ATOM N9 NS 0.0577 !-0.11 +ATOM C4 CB 0.1814 ! 0.39 +ATOM N3 NCA -0.6636 !-0.71 +ATOM C2 CA 0.7432 ! 0.87 +ATOM N2 NAN -0.9230 !-0.78 +ATOM H21 HNA 0.4235 ! 0.33 cis to N1 (involved in BP h-bond) +ATOM H22 HNA 0.4235 ! 0.33 trans to N1 +GROUP +ATOM N1 NAG -0.5053 !-0.59 +ATOM H1 HB 0.3520 ! 0.34 +GROUP +ATOM C6 CK 0.4918 ! 0.69 +ATOM O6 OKG -0.5699 !-0.55 +GROUP +ATOM C5 CB 0.1991 !-0.06 +ATOM N7 NBG -0.5725 !-0.54 +ATOM C8 CE 0.0736 ! 0.27 +ATOM H8 HAR 0.1997 ! 0.05 +GROUP +ATOM C2' CT5 -0.0854 !-0.070 +ATOM H2'' HA5 0.0718 ! 0.07 +ATOM H2' HA5 0.0718 ! 0.07 +GROUP +ATOM C3' CT5 0.0713 !-0.035 +ATOM H3' HA5 0.0985 ! 0.035 +GROUP +ATOM O3' OS -0.5232 !-0.46 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P +BOND C2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 +IMPH N2 N3 N1 C2 H1 C2 C6 N1 O6 N1 C5 C6 +IMPH H8 N7 N9 C8 H22 H21 C2 N2 +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +ACCE O6 C6 +ACCE N3 +ACCE N7 +ACCE O1P P +ACCE O2P P +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 102.60 -039.00 120.50 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 102.60 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.6100 120.50 -151.00 111.84 1.5400!beta +IC O5' C5' C4' C3' 1.4401 108.04 31.00 113.78 1.5400!gamma +IC C5' C4' C3' O3' 1.5400 113.78 156.00 109.20 1.4212!delta +IC C4' C3' O3' +P 1.5400 111.92 159.00 119.05 1.6100!epsil +IC C3' O3' +P +O5' 1.4212 119.05 -98.00 101.45 1.6100!eta +IC C5' C3' *C4' O4' 1.5400 113.37 120.00 106.48 1.4560 +IC C5' C3' *C4' H4' 1.5400 113.37 -120.00 109.47 1.090 +IC C4' C3' C2' C1' 1.5400 100.78 -34.00 101.97 1.5400!nu2 +IC C4' O3' *C3' C2' 1.5284 109.48 -115.00 110.000 1.54 +IC C4' O3' *C3' H3' 1.5284 109.48 120.00 109.47 1.0900 +IC O4' C1' N9 C4 1.4597 108.06 -095.00 125.59 1.3783!chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 105.19 1.3777 +IC C4 N9 C8 N7 1.3783 105.19 0.02 114.02 1.3107 +IC C8 N9 C4 C5 1.3777 105.19 -0.01 106.45 1.3750 +IC N9 C5 *C4 N3 1.3783 106.45 179.96 128.52 1.3591 +IC C5 C4 N3 C2 1.3750 128.52 0.04 112.23 1.3310 +IC C4 N3 C2 N1 1.3591 112.23 0.00 123.30 1.3813 +IC N1 N3 *C2 N2 1.3813 123.30 179.93 120.68 1.3349 +IC N3 C2 N2 H21 1.3310 120.68 179.25 127.00 1.0100 +IC H21 C2 *N2 H22 1.0100 127.00 -178.62 116.53 1.0100 +IC N3 C2 N1 C6 1.3310 123.30 -0.04 125.24 1.4021 +IC C6 C2 *N1 H1 1.4021 125.24 -180.00 117.40 1.0000 +IC C5 N1 *C6 O6 1.4188 111.38 179.92 119.80 1.2276 +IC C1' C3' *C2' H2' 1.5251 101.97 114.67 110.81 1.0912 +IC C1' C3' *C2' H2'' 1.5251 101.97 -114.67 110.81 1.0912 +IC O4' C2' *C1' H1' 1.4197 105.77 -115.00 109.47 1.0900 +IC O4' C2' *C1' N9 1.4197 105.77 115.00 0.00 0.000 +IC C4' O5' *C5' H5' 1.4500 111.04 115.00 109.47 1.0900 +IC C4' O5' *C5' H5'' 1.4500 111.04 -115.00 109.47 1.0900 +IC N9 N7 *C8 H8 1.3777 114.02 180.00 122.00 1.0800 + +RESI T -1.000 +ATOM P P 1.1659 ! 1.36 +ATOM O1P OCP -0.7761 !-0.72 +ATOM O2P OCP -0.7761 !-0.72 +ATOM O5' OS -0.4954 !-0.46 +GROUP +ATOM C5' CTT -0.0069 !-0.070 +ATOM H5' HAT 0.0754 ! 0.070 +ATOM H5'' HAT 0.0754 ! 0.070 +GROUP +ATOM C4' CT5 0.1629 ! 0.065 +ATOM H4' HA5 0.1176 ! 0.035 +ATOM O4' OE -0.3691 !-0.37 +ATOM C1' CT5 0.0680 ! 0.165 +ATOM H1' HA5 0.1804 ! 0.035 +GROUP +ATOM N1 NSP -0.0239 !-0.18 +ATOM C6 CF -0.2209 ! 0.03 +ATOM H6 HAR 0.2607 ! 0.13 +GROUP +ATOM C2 CK 0.5677 ! 0.80 +ATOM O2 OK -0.5881 !-0.55 +GROUP +ATOM N3 NAT -0.4340 ! 0.85 +ATOM H3 HB 0.3420 ! 0.45 +GROUP +ATOM C4 CK 0.5194 ! 0.87 +ATOM O4 OK -0.5563 !-0.55 +GROUP +ATOM C5 CF 0.0025 !-0.17 +ATOM C5A CTT -0.2269 !-0.38 +ATOM H51 HAT 0.0770 ! 0.11 +ATOM H52 HAT 0.0770 ! 0.11 +ATOM H53 HAT 0.0770 ! 0.11 +GROUP +ATOM C2' CT5 -0.0854 !-0.070 +ATOM H2'' HA5 0.0718 ! 0.07 +ATOM H2' HA5 0.0718 ! 0.07 +GROUP +ATOM C3' CT5 0.0713 !-0.035 +ATOM H3' HA5 0.0985 ! 0.035 +GROUP +ATOM O3' OS -0.5232 !-0.46 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C5A C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C6 H6 C5A H51 C5A H52 C5A H53 +IMPH O2 N1 N3 C2 H3 C2 C4 N3 +IMPH O4 N3 C5 C4 H6 N1 C5 C6 +IMPH C5A C4 C6 C5 +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 101.45 -39.00 119.00 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.00 109.80 1.4801 +IC P O5' C5' C4' 1.6100 119.00 -151.00 111.04 1.5400!beta +IC O5' C5' C4' C3' 1.4401 111.84 31.00 115.78 1.5284!gamma +IC C5' C4' C3' O3' 1.5400 114.78 156.00 111.92 1.4212!delta +IC C4' C3' O3' +P 1.5284 109.42 159.00 119.05 1.6100!epsil +IC C3' O3' +P +O5' 1.4212 119.05 -98.00 101.45 1.6100!eta +IC C5' C3' *C4' O4' 1.5400 113.37 119.62 106.48 1.4500 +IC C5' C3' *C4' H4' 1.5400 113.37 -119.62 106.48 1.0900 +IC C4' C3' C2' C1' 1.5284 102.78 -34.00 101.97 1.5251!nu2 +IC C4' O3' *C3' C2' 1.5284 109.78 -120.16 110.42 1.5412 +IC C4' O3' *C3' H3' 1.5284 109.78 120.16 110.42 1.0912 +!IC C3' C2' C1' N1 1.5284 101.97 93.39 113.71 1.4896 +IC O4' C1' N1 C2 1.4197 108.06 -95.43 117.06 1.3746!chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3431 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4440 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 -180.00 116.77 1.0900 +IC C4 C6 *C5 C5A 1.4440 120.78 -179.94 121.63 1.5000 +IC C1' C3' *C2' H2' 1.5251 101.97 114.67 114.81 1.0912 +IC C1' C3' *C2' H2'' 1.5251 101.97 -114.67 114.81 1.0912 +IC O4' C2' *C1' H1' 1.4197 106.77 -115.00 109.47 1.0900 +IC O4' C2' *C1' N1 1.4197 106.77 115.00 000.00 0.0000 +IC C4' O5' *C5' H5' 1.4500 111.84 115.00 109.47 1.0900 +IC C4' O5' *C5' H5'' 1.4500 111.84 -115.00 109.47 1.0900 +IC N1 C5 *C6 H6 1.3704 121.23 180.00 120.00 1.0800 +IC C6 C5 C5A H51 1.3431 121.63 90.00 109.47 1.0900 +IC C6 C5 C5A H52 1.3431 121.63 -30.00 109.47 1.0900 +IC C6 C5 C5A H53 1.3431 121.63 -150.00 109.47 1.0900 + +! +!RNA residues +! + +RESI RA -1.00 +ATOM P P 1.1662 +ATOM O1P OCP -0.7760 +ATOM O2P OCP -0.7760 +ATOM O5' OS -0.4989 +GROUP +ATOM C5' CTT 0.0558 +ATOM H5' HAT 0.0679 +ATOM H5'' HAT 0.0679 +GROUP +ATOM C4' CT5 0.1065 +ATOM H4' HA5 0.1174 +ATOM O4' OE -0.3548 +ATOM C1' CT5 0.0394 +ATOM H1' HA5 0.2007 +GROUP +ATOM N9 NSR -0.0251 +ATOM C4 CB 0.3053 +GROUP +ATOM N3 NCA -0.6997 +ATOM C2 CE 0.5875 +ATOM H2 HAR 0.0473 +GROUP +ATOM N1 NCA -0.7615 +ATOM C6 CA 0.7009 +GROUP +ATOM N6 NAN -0.9019 +ATOM H61 HNA 0.4115 +ATOM H62 HNA 0.4115 +GROUP +ATOM C5 CB 0.0515 +ATOM N7 NB -0.6073 +ATOM C8 CE 0.2006 +ATOM H8 HAR 0.1553 +GROUP +ATOM C2' CT5 0.0670 +ATOM H2'' HA5 0.0972 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 +GROUP +ATOM C3' CT5 0.2022 +ATOM H3' HA5 0.0615 +GROUP +ATOM O3' OS -0.5246 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 +BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +IMPH H62 C6 H61 N6 N6 N1 C5 C6 H2 N1 N3 C2 +IMPH H8 N7 N9 C8 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 101.45 -88.00 119.00 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.6100 119.00 -153.00 110.04 1.5400!beta +IC O5' C5' C4' C3' 1.4201 111.04 47.00 114.78 1.5284!gamma +IC C5' C4' C3' O3' 1.5400 114.78 83.00 109.42 1.421!delta +IC C4' C3' O3' +P 1.5284 109.42 171.00 119.05 1.6100!epsil +IC C3' O3' +P +O5' 1.4212 119.05 -44.00 101.45 1.610!eta +IC C5' C3' *C4' O4' 1.5400 113.37 119.62 105.78 1.4500 +IC C5' C3' *C4' H4' 1.5400 113.37 -119.62 105.78 1.0900 +IC C4' C3' C2' C1' 1.5284 102.38 37.00 101.97 1.5251!nu2 +IC C4' O3' *C3' C2' 1.5284 109.48 -120.16 110.92 1.5412 +IC C4' O3' *C3' H3' 1.5284 109.48 120.16 110.92 1.0900 +!IC C3' C2' C1' N9 1.5284 101.97 93.39 113.71 1.4897 +IC O4' C1' N9 C4 1.4197 108.06 -153.42 125.97 1.3703!chi +IC C1' C4 *N9 C8 1.4897 125.97 -179.94 105.00 1.3768 +IC C4 N9 C8 N7 1.3703 105.00 -0.07 113.93 1.2970 +IC C8 N9 C4 C5 1.3768 105.00 0.06 106.60 1.3650 +IC N9 C5 *C4 N3 1.3703 106.60 -179.93 126.69 1.3486 +IC C5 C4 N3 C2 1.3650 126.69 -0.04 111.18 1.3130 +IC C4 N3 C2 N1 1.3486 111.18 -0.02 128.64 1.3399 +IC N3 C2 N1 C6 1.3130 128.64 0.06 118.95 1.3456 +IC C5 N1 *C6 N6 1.4034 117.43 -179.96 119.06 1.3410 +IC N1 C6 N6 H61 1.3456 119.06 179.96 120.00 1.0100 +IC H61 C6 *N6 H62 1.0100 120.00 -180.00 120.00 1.0100 +IC C1' C3' *C2' O2' 1.5251 101.97 -114.67 114.31 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 114.31 1.5284 +IC O4' C2' *C1' H1' 1.4197 105.77 -115.00 109.47 1.0900 +IC O4' C2' *C1' N9 0.0000 105.77 120.00 114.5 0.0000 +IC C1' C3' *C2' H2'' 1.5400 101.97 115.00 109.47 1.0900 +IC C5' C3' *C4' H4' 1.5400 114.37 -115.00 109.47 1.0900 +IC C4' O5' *C5' H5' 1.4500 111.84 -115.00 109.47 1.0900 +IC C4' O5' *C5' H5'' 1.4500 111.84 115.00 109.47 1.0900 +IC N9 N7 *C8 H8 1.3768 113.93 180.00 122.00 1.0800 +IC N1 N3 *C2 H2 1.3399 128.64 180.00 120.00 1.0800 + +RESI RC -1.00 +ATOM P P 1.1662 +ATOM O1P OCP -0.7760 +ATOM O2P OCP -0.7760 +ATOM O5' OS -0.4989 +GROUP +ATOM C5' CTT 0.0558 +ATOM H5' HAT 0.0679 +ATOM H5'' HAT 0.0679 +GROUP +ATOM C4' CT5 0.1065 +ATOM H4' HA5 0.1174 +ATOM O4' OE -0.3548 +ATOM C1' CT5 0.0066 +ATOM H1' HA5 0.2029 +GROUP +ATOM N1 NSR -0.0484 +ATOM C6 CF 0.0053 +ATOM H6 HAR 0.1958 +GROUP +ATOM C2 CK 0.7538 +ATOM O2 OKC -0.6252 +GROUP +ATOM N3 NC -0.7584 +ATOM C4 CA 0.8185 +GROUP +ATOM N4 NAN -0.9530 +ATOM H41 HNA 0.4234 +ATOM H42 HNA 0.4234 +GROUP +ATOM C5 CF -0.5215 +ATOM H5 HAR 0.1928 +GROUP +ATOM C2' CT5 0.0670 +ATOM H2'' HA5 0.0972 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 +GROUP +ATOM C3' CT5 0.2022 +ATOM H3' HA5 0.0615 +GROUP +ATOM O3' OS -0.5246 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 +IMPH O2 N1 N3 C2 N4 N3 C5 C4 +IMPH H5 C4 C6 C5 H6 C5 N1 C6 +IMPH H42 C4 H41 N4 +DONO H42 N4 +DONO H2' O2' +DONO H41 N4 +ACCE O2 C2 +ACCE N3 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 101.45 -88.00 119.00 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.6100 119.00 -153.00 110.04 1.5400!beta +IC O5' C5' C4' C3' 1.4201 111.04 47.00 115.78 1.5284!gamma +IC C5' C4' C3' O3' 1.5400 114.78 83.00 111.92 1.4212!delta +IC C4' C3' O3' +P 1.5284 109.42 171.00 119.05 1.600!epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -44.00 101.45 1.6100!eta +IC C5' C3' *C4' O4' 1.5400 113.37 119.62 106.78 1.4560 +IC C5' C3' *C4' H4' 1.5400 113.37 -119.62 101.78 1.0900 +IC C4' O3' *C3' C2' 1.528 109.47 -120.00 110.00 1.5400 +IC C4' O3' *C3' H3' 1.528 109.47 120.00 109.47 1.0900 +IC C4' C3' C2' C1' 1.5284 102.78 37.00 101.97 1.5251!nu2 +!IC C3' C2' C1' N1 1.5284 101.97 93.39 113.71 1.4896 +IC O4' C1' N1 C2 1.4197 108.06 -155.44 117.79 1.3923!chi +IC C1' C2 *N1 C6 1.4896 117.79 -179.99 121.13 1.3595 +IC C2 N1 C6 C5 1.3923 121.13 0.02 121.13 1.3570 +IC C6 N1 C2 N3 1.3595 121.13 0.01 118.71 1.3578 +IC N1 N3 *C2 O2 1.3923 118.71 179.98 122.46 1.2378 +IC N1 C2 N3 C4 1.3923 118.71 -0.03 120.61 1.3386 +IC C5 N3 *C4 N4 1.4331 121.58 180.00 118.32 1.3246 +IC N3 C4 N4 H41 1.3386 118.32 -180.00 117.70 1.0100 +IC H41 C4 *N4 H42 1.0100 117.70 -180.00 120.27 1.0100 +IC C1' C3' *C2' O2' 1.5251 101.97 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC C1' C3' *C2' H2'' 1.5251 101.97 115.00 109.47 1.0900 +IC O4' C2' *C1' H1' 1.4197 105.77 -115.00 109.47 1.0900 +IC O4' C2' *C1' N1 1.4197 105.77 115.00 0.0000 0.0000 +IC C4' O5' *C5' H5' 1.4500 111.84 -115.00 109.47 1.0900 +IC C4' O5' *C5' H5'' 1.4500 111.84 115.00 109.47 1.0900 +IC C6 C4 *C5 H5 1.3570 116.83 180.00 120.00 1.0800 +IC N1 C5 *C6 H6 1.3595 121.13 180.00 120.00 1.0800 + +RESI RG -1.00 +ATOM P P 1.1662 +ATOM O1P OCP -0.7760 +ATOM O2P OCP -0.7760 +ATOM O5' OS -0.4989 +GROUP +ATOM C5' CTT 0.0558 +ATOM H5' HAT 0.0679 +ATOM H5'' HAT 0.0679 +GROUP +ATOM C4' CT5 0.1065 +ATOM H4' HA5 0.1174 +ATOM O4' OE -0.3548 +GROUP +ATOM C1' CT5 0.0191 +ATOM H1' HA5 0.2006 +GROUP +ATOM N9 NSR 0.0492 +ATOM C4 CB 0.1222 +GROUP +ATOM N3 NCA -0.6323 +ATOM C2 CA 0.7657 +GROUP +ATOM N2 NAN -0.9672 +ATOM H21 HNA 0.4364 +ATOM H22 HNA 0.4364 +GROUP +ATOM N1 NAG -0.4787 +ATOM H1 HB 0.3424 +GROUP +ATOM C6 CK 0.4770 +ATOM O6 OKG -0.5597 +GROUP +ATOM C5 CB 0.1744 +ATOM N7 NBG -0.5709 +ATOM C8 CE 0.1374 +ATOM H8 HAR 0.1640 +GROUP +ATOM C2' CT5 0.0670 +ATOM H2'' HA5 0.0972 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 +GROUP +ATOM C3' CT5 0.2022 +ATOM H3' HA5 0.0615 +GROUP +ATOM O3' OS -0.5246 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 +IMPH N2 N3 N1 C2 H1 C2 C6 N1 O6 N1 C5 C6 +IMPH H8 N7 N9 C8 H22 H21 C2 N2 +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +DONO H2' O2' +ACCE O6 C6 +ACCE N3 +ACCE N7 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 102.60 -088.00 120.50 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 102.60 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.6100 120.50 -153.00 111.84 1.5400!beta +IC O5' C5' C4' C3' 1.4401 108.04 47.00 113.78 1.5400!gamma +IC C5' C4' C3' O3' 1.5400 113.78 83.00 109.20 1.4212!delta +IC C4' C3' O3' +P 1.5400 111.92 171.00 119.05 1.6100!epsil +IC C3' O3' +P +O5' 1.4212 119.05 -44.00 101.45 1.6100!eta +IC C5' C3' *C4' O4' 1.5400 113.37 120.00 106.48 1.4560 +IC C5' C3' *C4' H4' 1.5400 113.37 -120.00 109.47 1.090 +IC C4' C3' C2' C1' 1.5400 100.78 37.00 101.97 1.5400!nu2 +IC C4' O3' *C3' C2' 1.5284 109.48 -115.00 110.000 1.54 +IC C4' O3' *C3' H3' 1.5284 109.48 120.00 109.47 1.0900 +IC O4' C1' N9 C4 1.4597 108.06 -153.00 125.59 1.3783!chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 105.19 1.3777 +IC C4 N9 C8 N7 1.3783 105.19 0.02 114.02 1.3107 +IC C8 N9 C4 C5 1.3777 105.19 -0.01 106.45 1.3750 +IC N9 C5 *C4 N3 1.3783 106.45 179.96 128.52 1.3591 +IC C5 C4 N3 C2 1.3750 128.52 0.04 112.23 1.3310 +IC C4 N3 C2 N1 1.3591 112.23 0.00 123.30 1.3813 +IC N1 N3 *C2 N2 1.3813 123.30 179.93 120.68 1.3349 +IC N3 C2 N2 H21 1.3310 120.68 179.25 127.00 1.0100 +IC H21 C2 *N2 H22 1.0100 127.00 -178.62 116.53 1.0100 +IC N3 C2 N1 C6 1.3310 123.30 -0.04 125.24 1.4021 +IC C6 C2 *N1 H1 1.4021 125.24 -180.00 117.40 1.0000 +IC C5 N1 *C6 O6 1.4188 111.38 179.92 119.80 1.2276 +IC C1' C3' *C2' O2' 1.5251 101.97 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5400 +IC O4' C2' *C1' H1' 1.4197 105.77 -115.00 109.47 1.0900 +IC O4' C2' *C1' N9 1.4197 105.77 115.00 0.00 0.0000 +IC C1' C3' *C2' H2'' 1.5251 101.97 115.00 109.47 1.0900 +IC C4' O5' *C5' H5' 1.4500 111.04 -115.00 109.47 1.0900 +IC C4' O5' *C5' H5'' 1.4500 111.04 115.00 109.47 1.0900 +IC N9 N7 *C8 H8 1.3777 114.02 180.00 122.00 1.0800 + +RESI RU -1.00 +ATOM P P 1.1662 +ATOM O1P OCP -0.7760 +ATOM O2P OCP -0.7760 +ATOM O5' OS -0.4989 +GROUP +ATOM C5' CTT 0.0558 +ATOM H5' HAT 0.0679 +ATOM H5'' HAT 0.0679 +GROUP +ATOM C4' CT5 0.1065 +ATOM H4' HA5 0.1174 +ATOM O4' OE -0.3548 +ATOM C1' CT5 0.0674 +ATOM H1' HA5 0.1824 +GROUP +ATOM N1 NSR 0.0418 +ATOM C6 CF -0.1126 +ATOM H6 HAR 0.2188 +GROUP +ATOM C2 CK 0.4687 +ATOM O2 OK -0.5477 +GROUP +ATOM N3 NAT -0.3549 +ATOM H3 HB 0.3154 +GROUP +ATOM C4 CK 0.5952 +ATOM O4 OK -0.5761 +GROUP +ATOM C5 CF -0.3635 +ATOM H5 HAR 0.1811 +GROUP +ATOM C2' CT5 0.0670 +ATOM H2'' HA5 0.0972 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 +GROUP +ATOM C3' CT5 0.2022 +ATOM H3' HA5 0.0615 +GROUP +ATOM O3' OS -0.5246 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 +IMPH O2 N1 N3 C2 H3 C2 C4 N3 H5 C4 C6 C5 +IMPH O4 N3 C5 C4 H6 N1 C5 C6 +DONO H3 N3 +DONO H2' O2' +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 101.45 -88.00 119.00 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.6100 119.00 -153.00 110.04 1.5400!beta +IC O5' C5' C4' C3' 1.4401 111.83 047.00 116.10 1.5284!gamma +IC C5' C4' C3' O3' 1.5400 115.10 83.00 115.12 1.4212!delta +IC C4' C3' O3' +P 1.5284 109.92 171.00 119.05 1.6000!epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -44.00 101.45 1.6100!eta +IC C5' C3' *C4' O4' 1.5472 113.36 119.04 106.10 1.4500 +IC C5' C3' *C4' H4' 1.5472 113.36 -119.04 109.10 1.0900 +IC C4' C3' C2' C1' 1.5400 100.00 37.00 101.97 1.5400! nu2 +IC C4' O3' *C3' C2' 1.5284 109.47 -120.00 110.00 1.5400 +IC C4' O3' *C3' H3' 1.5284 109.47 120.00 109.47 1.0900 +!IC C3' C2' C1' N1 1.5284 101.97 93.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 108.71 -153.00 117.06 1.3746 +IC C1' C2 *N1 C6 1.4896 117.06 -179.00 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 0.00 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.00 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C1' C3' *C2' O2' 1.5284 101.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 105.6 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 101.0 115.0 0.0 0.0 +IC O4' C2' *C1' N1 0.0 105.6 115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 + +RESI PSU -1.00 +ATOM P P 1.1662 +ATOM O1P OCP -0.7760 +ATOM O2P OCP -0.7760 +ATOM O5' OS -0.4989 +GROUP +ATOM C5' CTT 0.0558 +ATOM H5' HAT 0.0679 +ATOM H5'' HAT 0.0679 +GROUP +ATOM C4' CT5 0.1065 +ATOM H4' HA5 0.1174 +ATOM O4' OE -0.3548 +ATOM C1' CT5 0.0674 +ATOM H1' HA5 0.1824 +GROUP !SP/EPS rhf/6-31g* +ATOM C5 CF -0.3635 !C -0.452815 +ATOM N1 NSR -0.3082 !N -0.664803 +ATOM H1 HB 0.3811 !H 0.386406 +ATOM C6 CF 0.0374 !-0.0126 !C 0.284660 +ATOM H6 HAR 0.2188 !H 0.140854 +GROUP +ATOM C2 CK 0.5687 ! 0.4687 !C 0.941655 +ATOM O2 OK -0.6477 !-0.5477 !O -0.656752 +GROUP +ATOM N3 NAT -0.3549 !N -0.733468 +ATOM H3 HB 0.3154 !H 0.385064 +GROUP +ATOM C4 CK 0.6952 ! 0.5952 !C 0.886158 +ATOM O4 OK -0.6761 !-0.5761 !O -0.642212 +GROUP +ATOM C2' CT5 0.0670 +ATOM H2'' HA5 0.0972 +ATOM O2' OH -0.6139 +ATOM H2' HO 0.4186 +GROUP +ATOM C3' CT5 0.2022 +ATOM H3' HA5 0.0615 +GROUP +ATOM O3' OS -0.5246 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' C5 C1' C2' N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C6 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' N1 H1 C6 H6 +IMPH O2 N1 N3 C2 H3 C2 C4 N3 !H5 C4 C6 C5 +IMPH O4 N3 C5 C4 H6 N1 C5 C6 +DONO H3 N3 +DONO H2' O2' +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +IC -O3' P O5' C5' 1.6100 101.45 -88.00 119.00 1.4401!alpha +IC -O3' O5' *P O1P 1.6100 101.45 -115.82 109.74 1.4802 +IC -O3' O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 +IC P O5' C5' C4' 1.6100 119.00 -153.00 110.04 1.5400!beta +IC O5' C5' C4' C3' 1.4401 111.83 047.00 116.10 1.5284!gamma +IC C5' C4' C3' O3' 1.5400 115.10 83.00 115.12 1.4212!delta +IC C4' C3' O3' +P 1.5284 109.92 171.00 119.05 1.6000!epsilon +IC C3' O3' +P +O5' 1.4212 119.05 -44.00 101.45 1.6100!eta +IC C5' C3' *C4' O4' 1.5472 113.36 119.04 106.10 1.4500 +IC C5' C3' *C4' H4' 1.5472 113.36 -119.04 109.10 1.0900 +IC C4' C3' C2' C1' 1.5400 100.00 37.00 101.97 1.5400! nu2 +IC C4' O3' *C3' C2' 1.5284 109.47 -120.00 110.00 1.5400 +IC C4' O3' *C3' H3' 1.5284 109.47 120.00 109.47 1.0900 +!IC C3' C2' C1' N1 1.5284 101.97 93.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 108.71 -153.00 117.06 1.3746 +IC C1' C2 *N1 C6 1.4896 117.06 -179.00 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 0.00 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.00 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C1' C3' *C2' O2' 1.5284 101.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 105.6 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 101.0 115.0 0.0 0.0 +IC O4' C2' *C1' N1 0.0 105.6 115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 +!IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 + + +PATC FIRS NONE LAST NONE +RESI DIME -1.00 !dimethylphosphate +GROUP +ATOM P1 P 1.1656 +ATOM O2 OCP -0.7761 +ATOM O3 OCP -0.7761 +ATOM O4 OS -0.4954 +ATOM O5 OS -0.4954 +ATOM C6 CTT -0.0069 +ATOM C7 CTT -0.0069 +ATOM H8 HAT 0.0652 +ATOM H9 HAT 0.0652 +ATOM H10 HAT 0.0652 +ATOM H11 HAT 0.0652 +ATOM H12 HAT 0.0652 +ATOM H13 HAT 0.0652 +BOND P1 O4 +BOND P1 O5 +BOND P1 O3 +BOND P1 O2 +BOND O4 C7 +BOND O5 C6 +BOND C6 H11 +BOND C6 H12 +BOND C6 H13 +BOND C7 H8 +BOND C7 H9 +BOND C7 H10 +IC O5 P1 O4 C7 1.56 109.47 180.00 118.01 1.42 +IC O3 P1 O4 C7 1.50 113.00 53.10 118.01 1.42 +IC O2 P1 O4 + + +! +!SOLVENTS +! +PATC FIRS NONE LAST NONE +RESI ETHA 0.000 !ETHANOL +GROUP +ATOM C2 CT 0.165 +ATOM H6 HA 0.034 +ATOM H5 HA 0.034 +ATOM C3 CT -0.105 +ATOM H9 HA 0.044 +ATOM H8 HA 0.044 +ATOM H7 HA 0.044 +ATOM O1 OT -0.655 +ATOM H4 HO 0.395 +BOND C2 H6 +BOND C2 H5 +BOND C2 C3 +BOND C2 O1 +BOND C3 H9 +BOND C3 H8 +BOND C3 H7 +BOND O1 H4 +IC H6 C2 C3 H9 1.10 110.25 -60.05 110.35 1.10 +IC H5 C2 C3 H9 1.10 109.39 -178.96 110.35 1.10 +IC O1 C2 C3 H9 1.44 111.19 62.54 110.35 1.10 +IC H6 C2 C3 H8 1.10 110.25 60.00 110.29 1.10 +IC H6 C2 C3 H7 1.10 110.25 -179.99 109.92 1.10 +IC H6 C2 O1 H4 1.10 110.25 -52.31 112.52 0.95 +IC H5 C2 O1 H4 1.10 107.44 65.42 112.52 0.95 +IC C3 C2 O1 H4 1.55 111.19 -174.91 112.52 0.95 + +PATC FIRS NONE LAST NONE + +RESI TRIF 0.000 !TRIFLOROETHANOL +GROUP +ATOM C2 CT -0.083 +ATOM H6 HA 0.116 +ATOM H5 HA 0.117 +ATOM C3 CF3 1.000 +ATOM F2 XF -0.300 +ATOM F3 XF -0.300 +ATOM F1 XF -0.300 +ATOM O1 OT -0.650 +ATOM H4 HO 0.400 +BOND C2 H6 +BOND C2 H5 +BOND C2 C3 +BOND C2 O1 +BOND C3 F2 +BOND C3 F3 +BOND C3 F1 +BOND O1 H4 +IC H6 C2 C3 F2 1.09 109.24 -65.62 110.97 1.09 +IC H5 C2 C3 F2 1.09 109.49 175.95 110.97 1.09 +IC O1 C2 C3 F2 1.42 109.48 55.25 110.97 1.09 +IC H6 C2 C3 F3 1.09 109.24 54.22 110.87 1.09 +IC H6 C2 C3 F1 1.09 109.24 174.26 111.14 1.09 +IC H6 C2 O1 H4 1.09 110.29 -56.82 111.01 0.95 +IC H5 C2 O1 H4 1.09 110.03 62.58 111.01 0.95 +IC C3 C2 O1 H4 1.53 109.48 -177.04 111.01 0.95 + +! +! Water models +! +PATC FIRS NONE LAST NONE +RESI TIP3 0.000 ! TIPS3P WATER MODEL +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +ANGL H1 OH2 H2 +!ACCE OH2 + +PATC FIRS NONE LAST NONE +RESI T95 0.000 ! TIPS3P WATER MODEL with 5% reduced charge +GROUP ! This model provides stable A-DNA simulations by balancing the +ATOM OH2 OT -0.7923 ! Na-H2O, Cl-H2O, DNA-Na, DNA-Cl, DNA-H2O interactions. +ATOM H1 HT 0.39615 ! +ATOM H2 HT 0.39615 ! +BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +ANGL H1 OH2 H2 +!ACCE OH2 + +PATC FIRS NONE LAST NONE +RESI TIPS 0.000 !!TIP3P water model, J. Chem. Phys., 79, 926, 1983. +GROUP +ATOM OH2 OW -0.834 +ATOM H1 HW 0.417 +ATOM H2 HW 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +ANGL H1 OH2 H2 +!ACCE OH2 + +! +!Noble Gases +! +PATC FIRS NONE LAST NONE +RESI HE 0.00 !Helium +GROUP +ATOM HE HE 0.00 + +PATC FIRS NONE LAST NONE +RESI NE 0.00 !Neon +GROUP +ATOM NE NE 0.00 + +PATC FIRS NONE LAST NONE +RESI AR 0.00 !Argon +GROUP +ATOM AR AR 0.00 + +! +!IONS +! +PATC FIRS NONE LAST NONE +RESI NA 1.00 +GROUP +ATOM NA SOD 1.00 + +PATC FIRS NONE LAST NONE +GROUP +RESI K 1.00 +ATOM K K 1.00 + +PATC FIRS NONE LAST NONE +RESI CL -1.00 +GROUP +ATOM CL XCL -1.00 + +PATC FIRS NONE LAST NONE + + +PRES 5MU -0.1824 !Patch to make 5-methyluridine from uridine +DELETE ATOM H5 +ATOM C5 CF -0.3635 +ATOM C5A CTT -0.0499 +ATOM H51 HAT 0.0770 +ATOM H52 HAT 0.0770 +ATOM H53 HAT 0.0770 +BOND C5 C5A C5A H51 C5A H52 C5A H53 +ANGL C4 C5 C5A C6 C5 C5A C5 C5A H51 C5 C5A H52 C5 C5A H53 +ANGL H51 C5A H52 H51 C5A H53 H52 C5A H53 +DIHE N3 C4 C5 C5A O4 C4 C5 C5A N1 C6 C5 C5A H6 C6 C5 C5A +DIHE C4 C5 C5A H51 C4 C5 C5A H52 C4 C5 C5A H53 +DIHE C6 C5 C5A H51 C6 C5 C5A H52 C6 C5 C5A H53 +IMPH C5A C4 C6 C5 +IC C4 C6 *C5 C5A 1.4440 120.78 -179.94 121.63 1.5000 +IC C6 C5 C5A H51 1.3431 121.63 90.00 109.47 1.0900 +IC C6 C5 C5A H52 1.3431 121.63 -30.00 109.47 1.0900 +IC C6 C5 C5A H53 1.3431 121.63 -150.00 109.47 1.0900 + +PRES 1MG -0.1363 !Patch to make 1-methylguanine from guanine +DELETE ATOM H1 +ATOM N1 NAG -0.3635 +ATOM C1A CTT -0.0038 +ATOM H11 HAT 0.0770 +ATOM H12 HAT 0.0770 +ATOM H13 HAT 0.0770 +BOND N1 C1A C1A H11 C1A H12 C1A H13 +ANGL C2 N1 C1A C6 N1 C1A N1 C1A H11 N1 C1A H12 N1 C1A H13 +ANGL H11 C1A H12 H11 C1A H13 H12 C1A H13 +DIHE N2 C2 N1 C1A N3 C2 N1 C1A C5 C6 N1 C1A O6 C6 N1 C1A +DIHE C2 N1 C1A H11 C2 N1 C1A H12 C2 N1 C1A H13 +DIHE C6 N1 C1A H11 C6 N1 C1A H12 C6 N1 C1A H13 +IMPH C1A C2 C6 N1 + IC C6 C1A *N1 C2 1.37 118.74 -178.88 118.62 1.36 + IC C5 C6 N1 C1A 1.42 114.51 -179.37 118.74 1.44 + IC O6 C6 N1 C1A 1.24 119.19 0.52 118.74 1.44 + IC C6 N1 C1A H11 1.37 118.74 180.00 109.47 1.09 + IC C6 N1 C1A H12 1.37 118.74 60.00 109.47 1.09 + IC C6 N1 C1A H13 1.37 118.74 -59.98 109.55 1.09 + IC C2 N1 C1A H13 1.36 118.62 121.14 109.55 1.09 + +PRES TG -0.0888 ! Patch to make 2'-deoxy-6-ThioGuanine +DELETE ATOM O6 ! Charges were obtained by normalizing the +ATOM N9 NS 0.0616 ! 0.0577 ! DFT/6-31+G** charges between B-Form deoxygua, +ATOM C4 CB 0.1402 ! 0.1814 ! deoxythiogua and amber RESP charges. +ATOM N3 NCA -0.6051 !-0.6636 ! The sugar charges were retained from the RESP charges. +ATOM C2 CA 0.5343 ! 0.7432 ! (deoxythiogua/deoxygua)*RESP charges = new charges. +ATOM N2 NAN -0.8500 !-0.9230 +ATOM H21 HNA 0.4160 ! 0.4235 ! cis to N1 (involved in BP h-bond) +ATOM H22 HNA 0.4160 ! 0.4235 ! trans to N1 +GROUP +ATOM N1 NAG -0.1325 !-0.5053 +ATOM H1 HB 0.1975 ! 0.3520 +GROUP +ATOM C6 CK -0.2531 ! 0.4918 +ATOM S6 S -0.2917 !-0.5699 +GROUP +ATOM C5 CB 0.5781 ! 0.1991 +ATOM N7 NBG -0.6538 !-0.5725 +ATOM C8 CE 0.0723 ! 0.0736 +ATOM H8 HAR 0.2814 ! 0.1997 +BOND C6 S6 +ANGL C5 C6 S6 N1 C6 S6 +DIHE H1 N1 C6 S6 C2 N1 C6 S6 C4 C5 C6 S6 N7 C5 C6 S6 +IMPH S6 N1 C5 C6 +ACCE S6 C6 +IC C5 N1 *C6 S6 1.4188 111.38 179.92 119.80 1.2276 + +PRES 5PHO -0.54 ! places a phosphate at the 5' end of DNA after generation of psf +ATOM O5T OHP -0.60 +ATOM H5T HOP 0.40 +ATOM P P 0.90 +ATOM O1P OCP -0.62 +ATOM O2P OCP -0.62 +BOND H5T O5T O5T P +DONO H5T O5T +IC H5T O5T P O5' 1.0000 115.00 180.00 101.45 1.6100 +IC C5' O5' P O5T 1.4461 119.00 -39.52 101.45 1.6100 +IC O5T O5' *P O1P 1.6100 101.45 -115.82 109.74 1.4802 +IC O5T O5' *P O2P 1.6100 101.45 115.90 109.80 1.4801 + +PRES 5TER -0.0457 ! 0.070 ! Places hydroxyl at 5' end of DNA (default) +ATOM H5T HO 0.4422 ! 0.40 +ATOM O5' OH -0.6318 !-0.65 +ATOM C5' CTT -0.0069 ! 0.250 +ATOM H5' HAT 0.0754 ! 0.035 +ATOM H5'' HAT 0.0754 ! 0.035 +! +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P +DELETE ATOM O5T +! +BOND H5T O5' +!ANGL H5T O5' C5' +!DIHE H5T O5' C5' C4' H5T O5' C5' H5' H5T O5' C5' H5'' +DONO H5T O5' +IC H5T O5' C5' C4' 1.0000 110.00 180.00 110.04 1.5400 + +PRES 3TER -0.0455 ! 0.00 ! Places hydroxyl at 3' end of DNA (default) +ATOM C3' CT5 0.0713 ! 0.25 +ATOM H3' HA5 0.0985 ! 0.00 +ATOM O3' OH -0.6549 !-0.65 +ATOM H3T HO 0.4396 ! 0.40 +BOND O3' H3T +!ANGL C3' O3' H3T +!DIHE H3' C3' O3' H3T C4' C3' O3' H3T C5' C3' O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + +PRES 5RTE -0.0012 ! Places hydroxyl at 5' end of RNA after generation of psf +ATOM H5T HO 0.4295 +ATOM O5' OH -0.6223 +ATOM C5' CTT 0.0558 +ATOM H5' HAT 0.0679 +ATOM H5'' HAT 0.0679 +! +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P +DELETE ATOM O5T +! +BOND H5T O5' +DONO H5T O5' +IC H5T O5' C5' C4' 1.0000 110.00 180.00 110.04 1.5400 + +PRES 3RTE 0.0472 ! Places hydroxyl at 3' end of DNA (default) +ATOM C3' CT5 0.2022 +ATOM H3' HA5 0.0615 +ATOM O3' OH -0.6541 +ATOM H3T HO 0.4376 +BOND O3' H3T +DONO H3T O3' +IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + +PRES 2END 0.00 ! Patch to put ribose in 2*endo conformation +IC C5' C4' C3' O3' 1.5400 116.10 150.88 115.12 1.4212 +IC O4' C3' *C4' C5' 1.4572 104.06 -121.24 116.10 1.5400 +IC C2' C4' *C3' O3' 1.5284 101.91 -114.59 110.88 1.4212 +IC C4' C3' C2' C1' 1.5284 101.78 -39.92 101.97 1.5251 +IC C1' C3' *C2' O2' 1.5284 100.04 -124.67 115.81 1.4212 !INFERENCE + +END diff --git a/charmm/toppar/non_charmm/top_opls_aa.inp b/charmm/toppar/non_charmm/top_opls_aa.inp new file mode 100644 index 00000000..68b7b8bd --- /dev/null +++ b/charmm/toppar/non_charmm/top_opls_aa.inp @@ -0,0 +1,1583 @@ +*>>>>>>>>>>> OPLS All-atom Toplogy File for Proteins <<<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>>>> Nov 2000 <<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>> Generated automatically from pepz database files <<<<< +*>>>>>>>>>> script in perl, available from D. Price <<<<<<<<<< +*>>>>>>>>>>>>>>>> email: priced at scripps.edu <<<<<<<<<<<<<<< +* +27 1 + +!README for CHARMM topology/parameter files for OPLS-AA (opls.rtf, opls.prm) +!** reference for OPLS-AA for proteins: +!** Jorgensen, W.L. et al., J. Am. Chem. Soc. 118:11225-11236 (1996) +!and see additional reference below +! +!Proper usage of these files requires CHARMM software version c28b1 or greater. +!If you are presently using c28b1, please check that you have the latest release, +!as not all of the pertinant code was included in the initial release, but was +!included in a later bugfix. Compilation of CHARMM requires that the OPLS +!keyword be included in pref.dat at compile time. The relevant code has added +!the ability to combine Lennard-Jones radii with a geometric average, and use +!V2-Fourier terms for improper dihedrals. The CHARMM program compiled with the +!OPLS option in pref.dat can still use all other previously released topology and +!parameter files (CHARMM22, CHARMM19, etc.). +! +!Atom and residue names in the OPLS-AA topology file agree with that in CHARMM22. +!Consequently, any CHARMM script that reads CHARMM22 topology and parameter files +!can be converted to using OPLS-AA by adjusting the appropriate file OPEN +!statements. The atom types have the OPLS atom type embedded within them for +!easy cross-reference. For example, type H140 in opls.rtf and opls.prm is +!type 140 the OPLS-AA parameter files available from Prof. Jorgensen. +! +!The topology and parameter files here include only the protein portion of the +!OPLS-AA force field. User-defined topology and parameter files are required for +!other functionalities. +! +!While the OPLS-AA topology and parameter files are compatible with all +!functionality within CHARMM that is also compatible with CHARMM22, minimizations +!and simulations with a distance-dependent dielectric (RDIE) is not recommended +!as collapse of atoms with hydrogens on heteroatoms is possible, causing +!unreasonable structures and energies. Also, there is no current +!optimzied parameter set for the linearized form of the Generalized Born equation +!as currently implemented in CHARMM. +! +!Any questions, email priced@scripps.edu +! +!**** These files were created in the laboratory of: +!**** Prof. C.L. Brooks III +!**** Dept. of Mol. Biol. +!**** The Scripps Research Institute +! +!**** OPLS-AA is developed in the laboratory of: +!**** Prof. W.L. Jorgensen +!**** Dept. of Chemistry +!**** Yale University + +!Additional References +! +!OPLS All-Atom Model for Amines: Resolution of the Amine Hydration +!Problem. R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc., 121, +!4827-4836 (1999). +! +!Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro +!Compounds with the OPLS-AA Force Field. M. L. P. Price, D. Ostrovsky, +!and W. L. Jorgensen, J. Comput. Chem., 22, 1340-1352 (2001). +! +!Evaluation and Reparameterization of the OPLS-AA Force Field for +!Proteins via Comparison with Accurate Quantum Chemical Calculations on +!Peptides. G. Kaminski, R. A. Friesner, J. Tirado-Rives and W. L. +!Jorgensen, J. Phys. Chem. B, 105, 6474-6487 (2001). +! +!Perfluoroalkanes: Conformational Analysis and Liquid-State Properties +!from Ab Initio and Monte Carlo Calculations. E. K. Watkins and +!W. L. Jorgensen, J. Phys. Chem. A, 105, 4118-4125 (2001). +! +!Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic +!Charges.Blagovif, M. U.; Jorgensen, W. L., J. Comput. Chem. 2004, 25, +!0000-0000. Submitted. +! +!A five-site model for liquid water and the reproduction of the density +!anomaly by rigid, non-polarizable models. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 112, 8910-8922 (2000). +! +!Diffusion constant of the TIP5P model of liquid water. M. W. Mahoney +!and W. L. Jorgensen, J. Chem. Phys., 114, 363-366 (2001). +! +!Rapid Estimation of Electronic Degrees of Freedom in Monte Carlo +!Calculations for Polarizable Models of Liquid Water. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 114, 9337-9349 (2001). +! +!Quantum, intramolecular flexibility, and polarizability effects on the +!reproduction of the density anomaly of liquid water by simple +!potential functions. M. W. Mahoney and W. L. Jorgensen, +!J. Chem. Phys., 115, 10758-10768 (2001). +! + +MASS 1 C135 12.01100 C ! CH3 all-atom C: alkanes ALL-ATOM +MASS 2 C136 12.01100 C ! CH2 all-atom C: alkanes PARAMETERS +MASS 3 C137 12.01100 C ! CH all-atom C: alkanes FROM HERE ON +MASS 4 C145 12.01100 C ! Benzene C - 12 site JACS,112,4768-90 +MASS 5 C149 12.01100 C ! all-atom C: CH2, ethyl benzene +MASS 6 C157 12.01100 C ! all-atom C: CH3 & CH2, alcohols +MASS 7 C158 12.01100 C ! all-atom C: CH, alcohols +MASS 8 C166 12.01100 C ! C(OH) phenol Use with all +MASS 9 C206 12.01100 C ! all-atom C: CH2, thiols +MASS 10 C209 12.01100 C ! all-atom C: CH3, sulfides +MASS 11 C210 12.01100 C ! all-atom C: CH2, sulfides +MASS 12 C214 12.01100 C ! all-atom C: CH2, disulfides +MASS 13 C223 12.01100 C ! C in RCH2NH2 and Gly CA (See 900 for amines) +MASS 14 C224 12.01100 C ! C in R2CHNH2 and Ala CA +MASS 15 C235 12.01100 C ! C: C=O in amide. Acyl R in amides +MASS 16 C242 12.01100 C ! C on N: secondary N-Me amide +MASS 17 C245 12.01100 C ! C on N: tertiary N-CH2R amide (Pro Cdelta) +MASS 18 C246 12.01100 C ! C on N: tertiary N-CHR2 amide (Pro Calpha) +MASS 19 C267 12.01100 C ! Co in CCOOH carboxylic acid +MASS 20 C271 12.01100 C ! C in COO- carboxylate +MASS 21 C274 12.01100 C ! C: CH2, carboxylate ion +MASS 22 C283 12.01100 C ! AA C-alpha on C-terminal ALA +MASS 23 C284 12.01100 C ! AA C-alpha on C-terminal GLY +MASS 24 C285 12.01100 C ! AA C-alpha on C-terminal PRO +MASS 25 C292 12.01100 C ! C in RCH2NH3+ & CA in N-term Gly +MASS 26 C293 12.01100 C ! C in R2CHNH3+ & CA in N-term Ala, etc. +MASS 27 C295 12.01100 C ! AA:C-alpha in N-term PRO +MASS 28 C296 12.01100 C ! AA:C-delta in N-term PRO +MASS 29 C302 12.01100 C ! C: guanidinium C+ +MASS 30 C307 12.01100 C ! C: CH2(D), ARG, ethylguanidinium +MASS 31 C308 12.01100 C ! C: CH2(G), ARG +MASS 32 C500 12.01100 C ! CG in TRP +MASS 33 C501 12.01100 C ! CD C in TRP +MASS 34 C502 12.01100 C ! CE C in TRP +MASS 35 C505 12.01100 C ! CB in HIS +MASS 36 C506 12.01100 C ! CE1 in HID, HIE +MASS 37 C507 12.01100 C ! CD2 in HID, CG in HIE +MASS 38 C508 12.01100 C ! CG in HID, CD2 in HIE +MASS 39 C509 12.01100 C ! CE1 in HIP +MASS 40 C510 12.01100 C ! CG, CD2 in HIP +MASS 41 C514 12.01100 C ! CD1 in TRP +MASS 42 C748 12.01100 C ! CD of neutral ARG +MASS 43 C752 12.01100 C ! CZ " " " +MASS 44 C906 12.01100 C ! CH2(N) primary aliphatic amines, H(C) type 911 +MASS 45 H140 1.00800 H ! H all-atom H: alkanes +MASS 46 H146 1.00800 H ! Benzene H - 12 site " +MASS 47 H155 1.00800 H ! all-atom H(O): mono alcohols +MASS 48 H168 1.00800 H ! H phenol 145 & 146 +MASS 49 H204 1.00800 H ! all-atom H(S): thiols (mod 11/99) +MASS 50 H240 1.00800 H ! H on N: primary amide +MASS 51 H241 1.00800 H ! H on N: secondary amide +MASS 52 H270 1.00800 H ! H in CCOOH +MASS 53 H290 1.00800 H ! H (RNH3+) " +MASS 54 H301 1.00800 H ! H: guanidinium NH2 +MASS 55 H304 1.00800 H ! H: guanidinium NHR +MASS 56 H310 1.00800 H ! H (R2NH2+) +MASS 57 H504 1.00800 H ! H on NE in TRP +MASS 58 H513 1.00800 H ! H on N in HIP +MASS 59 H909 1.00800 H ! H(N) primary amines +MASS 60 H910 1.00800 H ! H(N) secondary amines +MASS 61 H911 1.00800 H ! H(C) for Carbons directly bonded to N in amines, diamines +MASS 62 N237 14.00700 N ! N: primary amide. alkane parameters. +MASS 63 N238 14.00700 N ! N: secondary amide 279 for formyl H. +MASS 64 N239 14.00700 N ! N: tertiary amide +MASS 65 N287 14.00700 N ! N (RNH3+) " +MASS 66 N300 14.00700 N ! N: guanidinium NH2 +MASS 67 N303 14.00700 N ! N: guanidinium NHR +MASS 68 N309 14.00700 N ! N (R2NH2+) +MASS 69 N503 14.00700 N ! NE in TRP +MASS 70 N511 14.00700 N ! NE in HID, ND in HIE +MASS 71 N512 14.00700 N ! N in HIP +MASS 72 N749 14.00700 N ! NE " +MASS 73 N750 14.00700 N ! N1 " " " (HN=CZ) +MASS 74 N751 14.00700 N ! N2 " " " (H2N-CZ) +MASS 75 N900 14.00700 N ! N primary amines +MASS 76 O154 15.99940 O ! all-atom O: mono alcohols +MASS 77 O167 15.99940 O ! O phenol atom C, H +MASS 78 O236 15.99940 O ! O: C=O in amide. is neutral - use +MASS 79 O268 15.99940 O ! Oh in CCOOH R in RCOOH is +MASS 80 O269 15.99940 O ! Oc in CCOOH neutral; use 135-140 +MASS 81 O272 15.99940 O ! O: O in COO- carboxylate +MASS 82 S200 32.06000 S ! all-atom S: thiols (mod 11/99) +MASS 83 S202 32.06000 S ! all-atom S: sulfides +MASS 84 S203 32.06000 S ! all-atom S: disulfides +MASS 85 OT 15.99940 O +MASS 86 HT 1.00800 H + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI ALA 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 +ATOM HA H140 0.060 ! | / +GROUP ! HA-CA--CB-HB2 +ATOM CB C135 -0.180 ! | \ +ATOM HB1 H140 0.060 ! | HB3 +ATOM HB2 H140 0.060 ! O=C +ATOM HB3 H140 0.060 ! | +GROUP ! +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA N HN N CA +BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +RESI ARG 1.00 +GROUP +ATOM N N238 -0.500 ! | HH11 +ATOM HN H241 0.300 ! HN-N | +ATOM CA C224 0.140 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA H140 0.060 ! | | | | | //(+) +GROUP ! HA-CA--CB--CG--CD--NE--CZ +ATOM CB C136 -0.120 ! | | | | \ +ATOM HB1 H140 0.060 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HB2 H140 0.060 ! O=C | +GROUP ! | HH21 +ATOM CG C308 -0.050 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +ATOM CD C307 0.190 ! +ATOM HD1 H140 0.060 ! +ATOM HD2 H140 0.060 ! +ATOM NE N303 -0.700 ! +ATOM HE H304 0.440 ! +ATOM CZ C302 0.640 ! +ATOM NH1 N300 -0.800 ! +ATOM HH11 H301 0.460 ! +ATOM HH12 H301 0.460 ! +ATOM NH2 N300 -0.800 ! +ATOM HH21 H301 0.460 ! +ATOM HH22 H301 0.460 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE O C CZ NH1 +IMPR HN N -C CA O C CA +N +IMPR NH2 CZ NE NH1 HE NE CD CZ +IMPR HH12 NH1 CZ HH11 HH22 NH2 CZ HH21 +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +RESI ASN 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA H140 0.060 ! | | || / +GROUP ! HA-CA--CB--CG--ND2 +ATOM CB C136 -0.120 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 HD22 (trans to OD1) +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C235 0.500 ! +ATOM OD1 O236 -0.500 ! +GROUP +ATOM ND2 N237 -0.760 ! +ATOM HD21 H240 0.380 ! +ATOM HD22 H240 0.380 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +DOUBLE C O CG OD1 +IMPR HN N -C CA O C CA +N +IMPR OD1 CG CB ND2 +IMPR HD22 ND2 CG HD21 +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +RESI ASP -1.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 OD1 +ATOM HA H140 0.060 ! | | // +GROUP ! HA-CA--CB--CG +ATOM CB C274 -0.220 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 OD2(-) +ATOM HB2 H140 0.060 ! O=C +ATOM CG C271 0.700 ! | +ATOM OD1 O272 -0.800 ! +ATOM OD2 O272 -0.800 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +DOUBLE O C CG OD1 +IMPR HN N -C CA O C CA +N +IMPR OD2 CG CB OD1 +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +RESI CYS 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 +ATOM HA H140 0.060 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB C206 0.060 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 HG1 +ATOM HB2 H140 0.060 ! O=C +ATOM SG S200 -0.335 ! | +ATOM HG1 H204 0.155 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +RESI GLN 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA H140 0.060 ! | | | || / +GROUP ! HA-CA--CB--CG--CD--NE2 +ATOM CB C136 -0.120 ! | | | \ +ATOM HB1 H140 0.060 ! | HB2 HG2 HE22 (trans to OE1) +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C136 -0.120 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +GROUP +ATOM CD C235 0.500 ! +ATOM OE1 O236 -0.500 ! +GROUP +ATOM NE2 N237 -0.760 ! +ATOM HE21 H240 0.380 ! +ATOM HE22 H240 0.380 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +DOUBLE O C CD OE1 +IMPR HN N -C CA O C CA +N +IMPR OE1 CD CG NE2 +IMPR HE22 NE2 CD HE21 +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +RESI GLU -1.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 HG1 OE1 +ATOM HA H140 0.060 ! | | | // +GROUP ! HA-CA--CB--CG--CD +ATOM CB C136 -0.120 ! | | | \ +ATOM HB1 H140 0.060 ! | HB2 HG2 OE2(-) +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C274 -0.220 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +ATOM CD C271 0.700 ! +ATOM OE1 O272 -0.800 ! +ATOM OE2 O272 -0.800 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 +DOUBLE O C CD OE1 +IMPR HN N -C CA O C CA +N +IMPR OE2 CD CG OE1 +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI GLY 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! N-H +ATOM CA C223 0.080 ! | +ATOM HA1 H140 0.060 ! | +ATOM HA2 H140 0.060 ! HA1-CA-HA2 +GROUP ! | +ATOM C C235 0.500 ! | +ATOM O O236 -0.500 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 +PATCHING FIRS GLYP LAST GLYC + +RESI HSD 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N N238 -0.500 ! | HD1 HE1 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | HB1 ND1--CE1 +ATOM HA H140 0.060 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB C505 -0.005 ! | | \\ || +ATOM HB1 H140 0.060 ! | HB2 CD2--NE2 +ATOM HB2 H140 0.060 ! O=C | +ATOM ND1 N503 -0.570 ! | HD2 +ATOM HD1 H504 0.420 ! +ATOM CG C508 0.015 ! +ATOM CE1 C506 0.295 ! +ATOM HE1 H146 0.115 ! +ATOM NE2 N511 -0.490 ! +ATOM CD2 C507 -0.015 ! +ATOM HD2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +IMPR HD1 ND1 CG CE1 HD2 CD2 NE2 CG HE1 CE1 ND1 NE2 +IMPR CB CG ND1 CD2 +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +RESI HSE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N N238 -0.500 ! | HE1 +ATOM HN H241 0.300 ! HN-N __ / +ATOM CA C224 0.140 ! | HB1 ND1--CE1 +ATOM HA H140 0.060 ! | | / | +GROUP ! HA-CA--CB--CG | +ATOM CB C505 -0.005 ! | | \\ | +ATOM HB1 H140 0.060 ! | HB2 CD2--NE2 +ATOM HB2 H140 0.060 ! O=C | \ +ATOM ND1 N511 -0.490 ! | HD2 HE2 +ATOM CG C507 -0.015 ! +ATOM CE1 C506 0.295 ! +ATOM HE1 H146 0.115 ! +ATOM NE2 N503 -0.570 ! +ATOM HE2 H504 0.420 ! +ATOM CD2 C508 0.015 ! +ATOM HD2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG CE1 ND1 +IMPR HE2 NE2 CE1 CD2 HD2 CD2 NE2 CG HE1 CE1 ND1 NE2 +IMPR CB CG ND1 CD2 +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +RESI HSP 1.00 ! Protonated His +GROUP +ATOM N N238 -0.500 ! | HD1 HE1 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | HB1 ND1--CE1 +ATOM HA H140 0.060 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB C505 -0.005 ! | | \\ || +ATOM HB1 H140 0.060 ! | HB2 CD2--NE2(+) +ATOM HB2 H140 0.060 ! O=C | \ +ATOM CD2 C510 0.215 ! | HD2 HE2 +ATOM HD2 H146 0.115 ! +ATOM CG C510 0.215 ! +ATOM NE2 N512 -0.540 ! +ATOM HE2 H513 0.460 ! +ATOM ND1 N512 -0.540 ! +ATOM HD1 H513 0.460 ! +ATOM CE1 C509 0.385 ! +ATOM HE1 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG NE2 CE1 +IMPR HD1 ND1 CG CE1 HE1 CE1 ND1 NE2 +IMPR HE2 NE2 CE1 CD2 HD2 CD2 NE2 CG +IMPR CB CG ND1 CD2 +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +RESI ILE 0.00 +GROUP +ATOM N N238 -0.500 ! | HG21 HG22 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | CG2--HG23 +ATOM HA H140 0.060 ! | / +GROUP ! HA-CA--CB-HB HD1 +ATOM CB C137 -0.060 ! | \ / +ATOM HB H140 0.060 ! | CG1--CD--HD2 +GROUP ! O=C / \ \ +ATOM CG2 C135 -0.180 ! | HG11 HG12 HD3 +ATOM HG21 H140 0.060 ! +ATOM HG22 H140 0.060 ! +ATOM HG23 H140 0.060 ! +GROUP +ATOM CG1 C136 -0.120 ! +ATOM HG11 H140 0.060 ! +ATOM HG12 H140 0.060 ! +GROUP +ATOM CD C135 -0.180 ! +ATOM HD1 H140 0.060 ! +ATOM HD2 H140 0.060 ! +ATOM HD3 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + +RESI LEU 0.00 +GROUP +ATOM N N238 -0.500 ! | HD11 HD12 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | HB1 CD1--HD13 +ATOM HA H140 0.060 ! | | / +GROUP ! HA-CA--CB--CG-HG +ATOM CB C136 -0.120 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 CD2--HD23 +ATOM HB2 H140 0.060 ! O=C | \ +GROUP ! | HD21 HD22 +ATOM CG C137 -0.060 ! +ATOM HG H140 0.060 ! +GROUP +ATOM CD1 C135 -0.180 ! +ATOM HD11 H140 0.060 ! +ATOM HD12 H140 0.060 ! +ATOM HD13 H140 0.060 ! +GROUP +ATOM CD2 C135 -0.180 ! +ATOM HD21 H140 0.060 ! +ATOM HD22 H140 0.060 ! +ATOM HD23 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +RESI LYS 1.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA H140 0.060 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM CB C136 -0.120 ! | | | | | \ +ATOM HB1 H140 0.060 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C136 -0.120 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +GROUP +ATOM CD C136 -0.120 ! +ATOM HD1 H140 0.060 ! +ATOM HD2 H140 0.060 ! +GROUP +ATOM CE C292 0.190 ! +ATOM HE1 H140 0.060 ! +ATOM HE2 H140 0.060 ! +ATOM NZ N287 -0.300 ! +ATOM HZ1 H290 0.330 ! +ATOM HZ2 H290 0.330 ! +ATOM HZ3 H290 0.330 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUBLE O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI MET 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 HG1 HE1 +ATOM HA H140 0.060 ! | | | | +GROUP ! HA-CA--CB--CG--SD--CE--HE3 +ATOM CB C136 -0.120 ! | | | | +ATOM HB1 H140 0.060 ! | HB2 HG2 HE2 +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C210 0.0975 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +ATOM SD S202 -0.435 ! +ATOM CE C209 0.0375 ! +ATOM HE1 H140 0.060 ! +ATOM HE2 H140 0.060 ! +ATOM HE3 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +RESI PHE 0.00 +GROUP +ATOM N N238 -0.500 ! | HD1 HE1 +ATOM HN H241 0.300 ! HN-N | | +ATOM CA C224 0.140 ! | HB1 CD1--CE1 +ATOM HA H140 0.060 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--HZ +ATOM CB C149 -0.005 ! | | \ __ / +ATOM HB1 H140 0.060 ! | HB2 CD2--CE2 +ATOM HB2 H140 0.060 ! O=C | | +ATOM CG C145 -0.115 ! | HD2 HE2 +GROUP +ATOM CD1 C145 -0.115 ! +ATOM HD1 H146 0.115 ! +GROUP +ATOM CE1 C145 -0.115 ! +ATOM HE1 H146 0.115 ! +GROUP +ATOM CZ C145 -0.115 ! +ATOM HZ H146 0.115 ! +GROUP +ATOM CD2 C145 -0.115 ! +ATOM HD2 H146 0.115 ! +GROUP +ATOM CE2 C145 -0.115 ! +ATOM HE2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ +IMPR HN N -C CA O C CA +N +IMPR HD1 CD1 CG CE1 HE1 CE1 CD1 CZ HZ CZ CE1 CE2 +IMPR CB CG CD1 CD2 HD2 CD2 CE2 CG HE2 CE2 CZ CD2 +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +RESI PRO 0.00 +GROUP ! HD1 HD2 +ATOM N N239 -0.140 ! | \ / +ATOM CD C245 -0.050 ! N---CD HG1 ATOM CA CP1 0.02 +ATOM HD1 H140 0.060 ! | \ / +ATOM HD2 H140 0.060 ! | CG +ATOM CA C246 0.010 ! | / \ +ATOM HA H140 0.060 ! HA-CA--CB HG2 +GROUP ! | / \ +ATOM CB C136 -0.120 ! | HB1 HB2 +ATOM HB1 H140 0.060 ! O=C +ATOM HB2 H140 0.060 ! | +GROUP +ATOM CG C136 -0.120 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +DOUBLE O C +IMPR CD N -C CA +IMPR O C CA +N +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 +PATCHING FIRS PROP LAST PROC + +RESI SER 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 +ATOM HA H140 0.060 ! | | +GROUP ! HA-CA--CB--OG +ATOM CB C157 0.145 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 HG1 +ATOM HB2 H140 0.060 ! O=C +ATOM OG O154 -0.683 ! | +ATOM HG1 H155 0.418 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +RESI THR 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | OG1--HG1 +ATOM HA H140 0.060 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB C158 0.205 ! | \ +ATOM HB H140 0.060 ! | CG2--HG21 +ATOM OG1 O154 -0.683 ! O=C / \ +ATOM HG1 H155 0.418 ! | HG21 HG22 +GROUP +ATOM CG2 C135 -0.180 ! +ATOM HG21 H140 0.060 ! +ATOM HG22 H140 0.060 ! +ATOM HG23 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +RESI TRP 0.00 +GROUP +ATOM N N238 -0.500 ! | HE3 +ATOM HN H241 0.300 ! HN-N | +ATOM CA C224 0.140 ! | HB1 CE3 +ATOM HA H140 0.060 ! | | / \\ +GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM CB C136 -0.120 ! | | || || | +ATOM HB1 H140 0.060 ! | HB2 CD1 CE2 CH2-HH2 +ATOM HB2 H140 0.060 ! O=C / \ / \ // +GROUP ! | HD1 NE1 CZ2 +ATOM CG C500 0.075 ! | | +ATOM CD1 C514 -0.115 ! HE1 HZ2 +ATOM HD1 H146 0.115 ! +ATOM NE1 N503 -0.570 ! +ATOM HE1 H504 0.420 ! +ATOM CE2 C502 0.130 ! +ATOM CD2 C501 -0.055 ! +GROUP +ATOM CE3 C145 -0.115 ! +ATOM HE3 H146 0.115 ! +GROUP +ATOM CZ3 C145 -0.115 ! +ATOM HZ3 H146 0.115 ! +GROUP +ATOM CZ2 C145 -0.115 ! +ATOM HZ2 H146 0.115 ! +GROUP +ATOM CH2 C145 -0.115 ! +ATOM HH2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 +IMPR HN N -C CA O C CA +N +IMPR CB CG CD1 CD2 HD1 CD1 CG NE1 HE1 NE1 CD1 CE2 +IMPR HZ2 CZ2 CE2 CH2 HH2 CH2 CZ2 CZ3 HZ3 CZ3 CH2 CE3 +IMPR HE3 CE3 CZ3 CD2 CE2 CD2 CE3 CG CZ2 CE2 CD2 NE1 +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI TYR 0.00 +GROUP +ATOM N N238 -0.500 ! | HD1 HE1 +ATOM HN H241 0.300 ! HN-N | | +ATOM CA C224 0.140 ! | HB1 CD1--CE1 +ATOM HA H140 0.060 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--OH +ATOM CB C149 -0.005 ! | | \ __ / \ +ATOM HB1 H140 0.060 ! | HB2 CD2--CE2 HH +ATOM HB2 H140 0.060 ! O=C | | +ATOM CG C145 -0.115 ! | HD2 HE2 +GROUP +ATOM CD1 C145 -0.115 ! +ATOM HD1 H146 0.115 ! +GROUP +ATOM CE1 C145 -0.115 ! +ATOM HE1 H146 0.115 ! +GROUP +ATOM CZ C166 0.150 ! +ATOM OH O167 -0.585 ! +ATOM HH H168 0.435 ! +GROUP +ATOM CD2 C145 -0.115 ! +ATOM HD2 H146 0.115 ! +GROUP +ATOM CE2 C145 -0.115 ! +ATOM HE2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +DOUBLE O C CD1 CG CE1 CZ CE2 CD2 +IMPR HN N -C CA O C CA +N +IMPR HD1 CD1 CG CE1 HE1 CE1 CD1 CZ OH CZ CE1 CE2 +IMPR CB CG CD1 CD2 HD2 CD2 CE2 CG HE2 CE2 CZ CD2 +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +RESI VAL 0.00 +GROUP +ATOM N N238 -0.500 ! | HG11 HG12 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | CG1--HG13 +ATOM HA H140 0.060 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB C137 -0.060 ! | \ +ATOM HB H140 0.060 ! | CG2--HG21 +GROUP ! O=C / \ +ATOM CG1 C135 -0.180 ! | HG21 HG22 +ATOM HG11 H140 0.060 ! +ATOM HG12 H140 0.060 ! +ATOM HG13 H140 0.060 ! +GROUP +ATOM CG2 C135 -0.180 ! +ATOM HG21 H140 0.060 ! +ATOM HG22 H140 0.060 ! +ATOM HG23 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +PRES NTER 1.00 ! standard N-terminus +GROUP ! use in generate statement +ATOM N N287 -0.300 ! +ATOM HT1 H290 0.330 ! HT1 +ATOM HT2 H290 0.330 ! (+)/ +ATOM HT3 H290 0.330 ! --CA--N--HT2 +ATOM CA C293 0.250 ! | \ +ATOM HA H140 0.060 ! HA HT3 +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES GLYP 1.00 ! Glycine N-terminus +GROUP ! use in generate statement +ATOM N N287 -0.300 ! +ATOM HT1 H290 0.330 ! HA1 HT1 +ATOM HT2 H290 0.330 ! | (+)/ +ATOM HT3 H290 0.330 ! --CA--N--HT2 +ATOM CA C292 0.190 ! | \ +ATOM HA1 H140 0.060 ! HA2 HT3 +ATOM HA2 H140 0.060 ! +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES PROP 1.00 ! Proline N-Terminal +GROUP ! use in generate statement +ATOM N N309 -0.200 ! HA +ATOM HN1 H310 0.310 ! | +ATOM HN2 H310 0.310 ! -CA HN1 +ATOM CD C296 0.170 ! / \ / +ATOM HD1 H140 0.060 ! N(+) +ATOM HD2 H140 0.060 ! / \ +ATOM CA C295 0.230 ! -CD HN2 +ATOM HA H140 0.060 ! | \ +BOND HN1 N HN2 N ! HD1 HD2 +DONOR HN1 N +DONOR HN2 N +IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES ACE 0.00 ! acetylated N-terminus +GROUP ! use in generate statement +ATOM CAY C135 -0.180 ! +ATOM HY1 H140 0.060 ! HY1 HY2 HY3 +ATOM HY2 H140 0.060 ! \ | / +ATOM HY3 H140 0.060 ! CAY +GROUP ! | +ATOM CY C235 0.500 ! CY=OY +ATOM OY O236 -0.500 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR OY CY CAY N +IMPR HN N CY CA +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACP 0.00 ! acetylated N-terminus for proline +GROUP ! use in generate statement +ATOM CAY C135 -0.180 ! +ATOM HY1 H140 0.060 ! HY1 HY2 HY3 +ATOM HY2 H140 0.060 ! \ | / +ATOM HY3 H140 0.060 ! CAY +GROUP ! | +ATOM CY C235 0.500 ! CY=OY +ATOM OY O236 -0.500 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR OY CY CAY N +IMPR CD N CY CA +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES CTER -0.86 ! standard C-terminus +GROUP ! use in generate statement +ATOM CA C283 0.040 ! line added in template for script pepz2rtf +ATOM C C271 0.700 ! OT2(-) +ATOM OT1 O272 -0.800 ! / +ATOM OT2 O272 -0.800 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +IMPR OT2 C CA OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT3 0.00 ! N-Methylamide C-terminus use in generate statement +GROUP ! C=O +ATOM NT N238 -0.500 ! | +ATOM HNT H241 0.300 ! NT-HNT +ATOM CAT C242 0.020 ! | +ATOM HT1 H140 0.060 ! HT1-CAT-HT3 +ATOM HT2 H140 0.060 ! | +ATOM HT3 H140 0.060 ! HT2 + ! +BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 +!DIHE CA C NT CAT +IMPR HNT NT C CAT O C CA NT +DONOR HNT NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES GLYC -0.92 ! standard C-terminus +GROUP ! use in generate statement +ATOM CA C284 -0.020 ! line added in template for script pepz2rtf +ATOM C C271 0.700 ! OT2(-) +ATOM OT1 O272 -0.800 ! / +ATOM OT2 O272 -0.800 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +IMPR OT1 C CA OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES PROC -0.99 ! standard C-terminus +GROUP ! use in generate statement +ATOM CA C285 -0.090 ! line added in template for script pepz2rtf +ATOM C C271 0.700 ! OT2(-) +ATOM OT1 O272 -0.800 ! / +ATOM OT2 O272 -0.800 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +IMPR OT1 C CA OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 +GROUP ! via acetic acid, use in a patch statement +ATOM CB C136 -0.120 ! +ATOM HB1 H140 0.060 ! HB1 OD1 +ATOM HB2 H140 0.060 ! | // +ATOM CG C267 0.520 ! -CB--CG +ATOM OD1 O269 -0.440 ! | \ +ATOM OD2 O268 -0.530 ! HB2 OD2-HD2 +ATOM HD2 H270 0.450 ! +BOND OD2 HD2 +ANGLE HD2 OD2 CG +DIHE HD2 OD2 CG OD1 HD2 OD2 CG CB +DONOR HD2 OD2 +IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 +GROUP ! via acetic acid, use in a patch statement +ATOM CG C136 -0.120 ! +ATOM HG1 H140 0.060 ! HG1 OE1 +ATOM HG2 H140 0.060 ! | // +ATOM CD C267 0.520 ! -CG--CD +ATOM OE1 O269 -0.440 ! | \ +ATOM OE2 O268 -0.530 ! HG2 OE2-HE2 +ATOM HE2 H270 0.450 ! +BOND OE2 HE2 +ANGLE HE2 OE2 CD +DIHE HE2 OE2 CD OE1 HE2 OE2 CD CG +DONOR HE2 OE2 +IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES LINK 0.00 ! linkage for IMAGES or for joining segments + ! 1 refers to previous (N terminal) + ! 2 refers to next (C terminal) + ! use in a patch statement +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +IMPR 2HN 2N 1C 2CA 1O 1C 1CA 2N +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES DISU -0.24 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. +GROUP ! use in a patch statement +ATOM 1CB C214 0.0975! +ATOM 1SG S203 -0.2175 ! 2SG--2CB-- +ATOM 2SG S203 -0.2175 ! / +ATOM 2CB C214 0.0975! -1CB--1SG +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +ANGLE 1CB 1SG 2SG 1SG 2SG 2CB +DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG +DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG +DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA +DIHE 1CB 1SG 2SG 2CB +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG1 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2HN 2N 1C 2CA 1O 1C 1CA 2N +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG2 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 +DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2HN 2N 1C 2CA 1O 1C 1CA 2N +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG3 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 +DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2HN 2N 1C 2CA 1O 1C 1CA 2N +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +END diff --git a/charmm/toppar/non_charmm/top_opls_aam.inp b/charmm/toppar/non_charmm/top_opls_aam.inp new file mode 100644 index 00000000..e66cdc97 --- /dev/null +++ b/charmm/toppar/non_charmm/top_opls_aam.inp @@ -0,0 +1,1638 @@ +*>>>>>>>>>>> OPLS-AA/M All-atom Toplogy File for Proteins <<<< +*>>>>>>>>>>>>>>>>>>>>>>>> Jun 2015 <<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>> Generated automatically from pepz database files <<<<< +*>>>>>>>>>> script in perl, available from D. Price <<<<<<<<<< +*>>>>>>>>>>> Edited by M.J. Robertson to OPLS-AA/M <<<<<<<<<<<<< +*>>>>>>>>>>>>>>>> email: michael.robertson at yale.edu <<<<<<< +* +27 1 + +!README for CHARMM topology/parameter files for OPLS-AA (opls.rtf, opls.prm) +!** reference for OPLS-AA for proteins: +!** Jorgensen, W.L. et al., J. Am. Chem. Soc. 118:11225-11236 (1996) +!** reference for OPLS-AA/M: +!** Robertson, M.J. et al., J. Chem. Theory Comput., (2015) +!and see additional reference below +! +!PLEASE ENSURE USE OF PROPER LJ COMBINING RULES AND 1-4 SCALING TO ENSURE +!PROPER IMPLEMENTATION OF THE OPLS-AA/M FORCE FIELD +! +! +!Proper usage of these files requires CHARMM software version c28b1 or greater. +!If you are presently using c28b1, please check that you have the latest release, +!as not all of the pertinant code was included in the initial release, but was +!included in a later bugfix. Compilation of CHARMM requires that the OPLS +!keyword be included in pref.dat at compile time. The relevant code has added +!the ability to combine Lennard-Jones radii with a geometric average, and use +!V2-Fourier terms for improper dihedrals. The CHARMM program compiled with the +!OPLS option in pref.dat can still use all other previously released topology and +!parameter files (CHARMM22, CHARMM19, etc.). +! +!Atom and residue names in the OPLS-AA topology file agree with that in CHARMM22. +!Consequently, any CHARMM script that reads CHARMM22 topology and parameter files +!can be converted to using OPLS-AA by adjusting the appropriate file OPEN +!statements. The atom types have the OPLS atom type embedded within them for +!easy cross-reference. For example, type H140 in opls.rtf and opls.prm is +!type 140 the OPLS-AA parameter files available from Prof. Jorgensen. +! +!The topology and parameter files here include only the protein portion of the +!OPLS-AA force field. User-defined topology and parameter files are required for +!other functionalities. +! +!While the OPLS-AA topology and parameter files are compatible with all +!functionality within CHARMM that is also compatible with CHARMM22, minimizations +!and simulations with a distance-dependent dielectric (RDIE) is not recommended +!as collapse of atoms with hydrogens on heteroatoms is possible, causing +!unreasonable structures and energies. Also, there is no current +!optimzied parameter set for the linearized form of the Generalized Born equation +!as currently implemented in CHARMM. +! +!Any questions, email priced@scripps.edu +! +!**** These files were created in the laboratory of: +!**** Prof. C.L. Brooks III +!**** Dept. of Mol. Biol. +!**** The Scripps Research Institute +! +!**** OPLS-AA is developed in the laboratory of: +!**** Prof. W.L. Jorgensen +!**** Dept. of Chemistry +!**** Yale University + +!Additional References +! +!OPLS All-Atom Model for Amines: Resolution of the Amine Hydration +!Problem. R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc., 121, +!4827-4836 (1999). +! +!Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro +!Compounds with the OPLS-AA Force Field. M. L. P. Price, D. Ostrovsky, +!and W. L. Jorgensen, J. Comput. Chem., 22, 1340-1352 (2001). +! +!Evaluation and Reparameterization of the OPLS-AA Force Field for +!Proteins via Comparison with Accurate Quantum Chemical Calculations on +!Peptides. G. Kaminski, R. A. Friesner, J. Tirado-Rives and W. L. +!Jorgensen, J. Phys. Chem. B, 105, 6474-6487 (2001). +! +!Perfluoroalkanes: Conformational Analysis and Liquid-State Properties +!from Ab Initio and Monte Carlo Calculations. E. K. Watkins and +!W. L. Jorgensen, J. Phys. Chem. A, 105, 4118-4125 (2001). +! +!Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic +!Charges.Blagovif, M. U.; Jorgensen, W. L., J. Comput. Chem. 2004, 25, +!0000-0000. Submitted. +! +!A five-site model for liquid water and the reproduction of the density +!anomaly by rigid, non-polarizable models. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 112, 8910-8922 (2000). +! +!Diffusion constant of the TIP5P model of liquid water. M. W. Mahoney +!and W. L. Jorgensen, J. Chem. Phys., 114, 363-366 (2001). +! +!Rapid Estimation of Electronic Degrees of Freedom in Monte Carlo +!Calculations for Polarizable Models of Liquid Water. M. W. Mahoney and +!W. L. Jorgensen, J. Chem. Phys., 114, 9337-9349 (2001). +! +!Quantum, intramolecular flexibility, and polarizability effects on the +!reproduction of the density anomaly of liquid water by simple +!potential functions. M. W. Mahoney and W. L. Jorgensen, +!J. Chem. Phys., 115, 10758-10768 (2001). +! +!Improved Peptide and Protein Torsional Energetics with the OPLS-AA +!Force Field M. J. Robertson, J. Tirado-Rives and W. L. Jorgensen, +!J. Chem. Theory. Comput. (2015) + +MASS 1 C135 12.01100 C ! CH3 all-atom C: alkanes ALL-ATOM +MASS 2 C136 12.01100 C ! CH2 all-atom C: alkanes PARAMETERS +MASS 3 C137 12.01100 C ! CH all-atom C: alkanes FROM HERE ON +MASS 4 C145 12.01100 C ! Benzene C - 12 site JACS,112,4768-90 +MASS 5 C149 12.01100 C ! all-atom C: CH2, ethyl benzene +MASS 6 C157 12.01100 C ! all-atom C: CH3 & CH2, alcohols +MASS 7 C158 12.01100 C ! all-atom C: CH, alcohols +MASS 8 C166 12.01100 C ! C(OH) phenol Use with all +MASS 9 C206 12.01100 C ! all-atom C: CH2, thiols +MASS 10 C209 12.01100 C ! all-atom C: CH3, sulfides +MASS 11 C210 12.01100 C ! all-atom C: CH2, sulfides +MASS 12 C214 12.01100 C ! all-atom C: CH2, disulfides +MASS 13 C223 12.01100 C ! C in RCH2NH2 and Gly CA (See 900 for amines) +MASS 14 C224 12.01100 C ! C in R2CHNH2 and Ala CA +MASS 15 C235 12.01100 C ! C: C=O in amide. Acyl R in amides +MASS 16 C242 12.01100 C ! C on N: secondary N-Me amide +MASS 17 C245 12.01100 C ! C on N: tertiary N-CH2R amide (Pro Cdelta) +MASS 18 C246 12.01100 C ! C on N: tertiary N-CHR2 amide (Pro Calpha) +MASS 19 C267 12.01100 C ! Co in CCOOH carboxylic acid +MASS 20 C271 12.01100 C ! C in COO- carboxylate +MASS 21 C274 12.01100 C ! C: CH2, carboxylate ion +MASS 22 C283 12.01100 C ! AA C-alpha on C-terminal ALA +MASS 23 C284 12.01100 C ! AA C-alpha on C-terminal GLY +MASS 24 C285 12.01100 C ! AA C-alpha on C-terminal PRO +MASS 25 C292 12.01100 C ! C in RCH2NH3+ & CA in N-term Gly +MASS 26 C293 12.01100 C ! C in R2CHNH3+ & CA in N-term Ala, etc. +MASS 27 C295 12.01100 C ! AA:C-alpha in N-term PRO +MASS 28 C296 12.01100 C ! AA:C-delta in N-term PRO +MASS 29 C302 12.01100 C ! C: guanidinium C+ +MASS 30 C307 12.01100 C ! C: CH2(D), ARG, ethylguanidinium +MASS 31 C308 12.01100 C ! C: CH2(G), ARG +MASS 32 C500 12.01100 C ! CG in TRP +MASS 33 C501 12.01100 C ! CD C in TRP +MASS 34 C502 12.01100 C ! CE C in TRP +MASS 35 C505 12.01100 C ! CB in HIS +MASS 36 C506 12.01100 C ! CE1 in HID, HIE +MASS 37 C507 12.01100 C ! CD2 in HID, CG in HIE +MASS 38 C508 12.01100 C ! CG in HID, CD2 in HIE +MASS 39 C509 12.01100 C ! CE1 in HIP +MASS 40 C510 12.01100 C ! CG, CD2 in HIP +MASS 41 C514 12.01100 C ! CD1 in TRP +!MASS 42 C748 12.01100 C ! CD of neutral ARG, adm jr. +!MASS 43 C752 12.01100 C ! CZ " " ", adm jr. +!MASS 44 C906 12.01100 C ! CH2(N) primary aliphatic amines, H(C) type 911 +MASS 45 H140 1.00800 H ! H all-atom H: alkanes +MASS 46 H146 1.00800 H ! Benzene H - 12 site " +MASS 47 H155 1.00800 H ! all-atom H(O): mono alcohols +MASS 48 H168 1.00800 H ! H phenol 145 & 146 +MASS 49 H204 1.00800 H ! all-atom H(S): thiols (mod 11/99) +MASS 50 H240 1.00800 H ! H on N: primary amide +MASS 51 H241 1.00800 H ! H on N: secondary amide +MASS 52 H270 1.00800 H ! H in CCOOH +MASS 53 H290 1.00800 H ! H (RNH3+) " +MASS 54 H301 1.00800 H ! H: guanidinium NH2 +MASS 55 H304 1.00800 H ! H: guanidinium NHR +MASS 56 H310 1.00800 H ! H (R2NH2+) +MASS 57 H504 1.00800 H ! H on NE in TRP +MASS 58 H513 1.00800 H ! H on N in HIP +!MASS 59 H909 1.00800 H ! H(N) primary amines, adm jr. +!MASS 60 H910 1.00800 H ! H(N) secondary amines, adm jr. +!MASS 61 H911 1.00800 H ! H(C) for Carbons directly bonded to N in amines, diamines, adm jr. +MASS 62 N237 14.00700 N ! N: primary amide. alkane parameters. +MASS 63 N238 14.00700 N ! N: secondary amide 279 for formyl H. +MASS 64 N239 14.00700 N ! N: tertiary amide +MASS 65 N287 14.00700 N ! N (RNH3+) " +MASS 66 N300 14.00700 N ! N: guanidinium NH2 +MASS 67 N303 14.00700 N ! N: guanidinium NHR +MASS 68 N309 14.00700 N ! N (R2NH2+) +MASS 69 N503 14.00700 N ! NE in TRP +MASS 70 N511 14.00700 N ! NE in HID, ND in HIE +MASS 71 N512 14.00700 N ! N in HIP +!MASS 72 N749 14.00700 N ! NE ", adm jr. +!MASS 73 N750 14.00700 N ! N1 " " " (HN=CZ), adm jr. +!MASS 74 N751 14.00700 N ! N2 " " " (H2N-CZ), adm jr. +!MASS 75 N900 14.00700 N ! N primary amines, adm jr. +MASS 76 O154 15.99940 O ! all-atom O: mono alcohols +MASS 77 O167 15.99940 O ! O phenol atom C, H +MASS 78 O236 15.99940 O ! O: C=O in amide. is neutral - use +MASS 79 O268 15.99940 O ! Oh in CCOOH R in RCOOH is +MASS 80 O269 15.99940 O ! Oc in CCOOH neutral; use 135-140 +MASS 81 O272 15.99940 O ! O: O in COO- carboxylate +MASS 82 S200 32.06000 S ! all-atom S: thiols (mod 11/99) +MASS 83 S202 32.06000 S ! all-atom S: sulfides +MASS 84 S203 32.06000 S ! all-atom S: disulfides +MASS 85 OT 15.99940 O +MASS 86 HT 1.00800 H +MASS 90 SOD 22.98977 NA ! Sodium Ion, adm jr. +MASS 91 CLA 35.45000 CL ! Chloride Ion, adm jr. + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI ALA 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 +ATOM HA H140 0.060 ! | / +GROUP ! HA-CA--CB-HB2 +ATOM CB C135 -0.180 ! | \ +ATOM HB1 H140 0.060 ! | HB3 +ATOM HB2 H140 0.060 ! O=C +ATOM HB3 H140 0.060 ! | +GROUP ! +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA N HN N CA +BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +RESI ARG 1.00 +GROUP +ATOM N N238 -0.500 ! | HH11 +ATOM HN H241 0.300 ! HN-N | +ATOM CA C224 0.140 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA H140 0.060 ! | | | | | //(+) +GROUP ! HA-CA--CB--CG--CD--NE--CZ +ATOM CB C136 -0.120 ! | | | | \ +ATOM HB1 H140 0.060 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HB2 H140 0.060 ! O=C | +GROUP ! | HH21 +ATOM CG C308 -0.050 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +ATOM CD C307 0.190 ! +ATOM HD1 H140 0.060 ! +ATOM HD2 H140 0.060 ! +ATOM NE N303 -0.700 ! +ATOM HE H304 0.440 ! +ATOM CZ C302 0.640 ! +ATOM NH1 N300 -0.800 ! +ATOM HH11 H301 0.460 ! +ATOM HH12 H301 0.460 ! +ATOM NH2 N300 -0.800 ! +ATOM HH21 H301 0.460 ! +ATOM HH22 H301 0.460 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE O C CZ NH1 +IMPR HN N -C CA O C CA +N +IMPR NH2 CZ NE NH1 HE NE CD CZ +IMPR HH12 NH1 CZ HH11 HH22 NH2 CZ HH21 +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +RESI ASN 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA H140 0.060 ! | | || / +GROUP ! HA-CA--CB--CG--ND2 +ATOM CB C136 -0.120 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 HD22 (trans to OD1) +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C235 0.500 ! +ATOM OD1 O236 -0.500 ! +GROUP +ATOM ND2 N237 -0.760 ! +ATOM HD21 H240 0.380 ! +ATOM HD22 H240 0.380 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +DOUBLE C O CG OD1 +IMPR HN N -C CA O C CA +N +IMPR OD1 CG CB ND2 +IMPR HD22 ND2 CG HD21 +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +RESI ASP -1.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 OD1 +ATOM HA H140 0.060 ! | | // +GROUP ! HA-CA--CB--CG +ATOM CB C274 -0.220 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 OD2(-) +ATOM HB2 H140 0.060 ! O=C +ATOM CG C271 0.700 ! | +ATOM OD1 O272 -0.800 ! +ATOM OD2 O272 -0.800 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +DOUBLE O C CG OD1 +IMPR HN N -C CA O C CA +N +IMPR OD2 CG CB OD1 +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +RESI CYS 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 +ATOM HA H140 0.060 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB C206 0.060 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 HG1 +ATOM HB2 H140 0.060 ! O=C +ATOM SG S200 -0.335 ! | +ATOM HG1 H204 0.155 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +RESI GLN 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA H140 0.060 ! | | | || / +GROUP ! HA-CA--CB--CG--CD--NE2 +ATOM CB C136 -0.120 ! | | | \ +ATOM HB1 H140 0.060 ! | HB2 HG2 HE22 (trans to OE1) +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C136 -0.120 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +GROUP +ATOM CD C235 0.500 ! +ATOM OE1 O236 -0.500 ! +GROUP +ATOM NE2 N237 -0.760 ! +ATOM HE21 H240 0.380 ! +ATOM HE22 H240 0.380 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +DOUBLE O C CD OE1 +IMPR HN N -C CA O C CA +N +IMPR OE1 CD CG NE2 +IMPR HE22 NE2 CD HE21 +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +RESI GLU -1.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 HG1 OE1 +ATOM HA H140 0.060 ! | | | // +GROUP ! HA-CA--CB--CG--CD +ATOM CB C136 -0.120 ! | | | \ +ATOM HB1 H140 0.060 ! | HB2 HG2 OE2(-) +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C274 -0.220 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +ATOM CD C271 0.700 ! +ATOM OE1 O272 -0.800 ! +ATOM OE2 O272 -0.800 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 +DOUBLE O C CD OE1 +IMPR HN N -C CA O C CA +N +IMPR OE2 CD CG OE1 +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI GLY 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! N-H +ATOM CA C223 0.080 ! | +ATOM HA1 H140 0.060 ! | +ATOM HA2 H140 0.060 ! HA1-CA-HA2 +GROUP ! | +ATOM C C235 0.500 ! | +ATOM O O236 -0.500 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 +PATCHING FIRS GLYP LAST GLYC + +RESI HSD 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N N238 -0.500 ! | HD1 HE1 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | HB1 ND1--CE1 +ATOM HA H140 0.060 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB C505 -0.005 ! | | \\ || +ATOM HB1 H140 0.060 ! | HB2 CD2--NE2 +ATOM HB2 H140 0.060 ! O=C | +ATOM ND1 N503 -0.570 ! | HD2 +ATOM HD1 H504 0.420 ! +ATOM CG C508 0.015 ! +ATOM CE1 C506 0.295 ! +ATOM HE1 H146 0.115 ! +ATOM NE2 N511 -0.490 ! +ATOM CD2 C507 -0.015 ! +ATOM HD2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +IMPR HD1 ND1 CG CE1 HD2 CD2 NE2 CG HE1 CE1 ND1 NE2 +IMPR CB CG ND1 CD2 +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +RESI HSE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N N238 -0.500 ! | HE1 +ATOM HN H241 0.300 ! HN-N __ / +ATOM CA C224 0.140 ! | HB1 ND1--CE1 +ATOM HA H140 0.060 ! | | / | +GROUP ! HA-CA--CB--CG | +ATOM CB C505 -0.005 ! | | \\ | +ATOM HB1 H140 0.060 ! | HB2 CD2--NE2 +ATOM HB2 H140 0.060 ! O=C | \ +ATOM ND1 N511 -0.490 ! | HD2 HE2 +ATOM CG C507 -0.015 ! +ATOM CE1 C506 0.295 ! +ATOM HE1 H146 0.115 ! +ATOM NE2 N503 -0.570 ! +ATOM HE2 H504 0.420 ! +ATOM CD2 C508 0.015 ! +ATOM HD2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG CE1 ND1 +IMPR HE2 NE2 CE1 CD2 HD2 CD2 NE2 CG HE1 CE1 ND1 NE2 +IMPR CB CG ND1 CD2 +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +RESI HSP 1.00 ! Protonated His +GROUP +ATOM N N238 -0.500 ! | HD1 HE1 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | HB1 ND1--CE1 +ATOM HA H140 0.060 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB C505 -0.005 ! | | \\ || +ATOM HB1 H140 0.060 ! | HB2 CD2--NE2(+) +ATOM HB2 H140 0.060 ! O=C | \ +ATOM CD2 C510 0.215 ! | HD2 HE2 +ATOM HD2 H146 0.115 ! +ATOM CG C510 0.215 ! +ATOM NE2 N512 -0.540 ! +ATOM HE2 H513 0.460 ! +ATOM ND1 N512 -0.540 ! +ATOM HD1 H513 0.460 ! +ATOM CE1 C509 0.385 ! +ATOM HE1 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG NE2 CE1 +IMPR HD1 ND1 CG CE1 HE1 CE1 ND1 NE2 +IMPR HE2 NE2 CE1 CD2 HD2 CD2 NE2 CG +IMPR CB CG ND1 CD2 +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +RESI ILE 0.00 +GROUP +ATOM N N238 -0.500 ! | HG21 HG22 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | CG2--HG23 +ATOM HA H140 0.060 ! | / +GROUP ! HA-CA--CB-HB HD1 +ATOM CB C137 -0.060 ! | \ / +ATOM HB H140 0.060 ! | CG1--CD--HD2 +GROUP ! O=C / \ \ +ATOM CG2 C135 -0.180 ! | HG11 HG12 HD3 +ATOM HG21 H140 0.060 ! +ATOM HG22 H140 0.060 ! +ATOM HG23 H140 0.060 ! +GROUP +ATOM CG1 C136 -0.120 ! +ATOM HG11 H140 0.060 ! +ATOM HG12 H140 0.060 ! +GROUP +ATOM CD C135 -0.180 ! +ATOM HD1 H140 0.060 ! +ATOM HD2 H140 0.060 ! +ATOM HD3 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + +RESI LEU 0.00 +GROUP +ATOM N N238 -0.500 ! | HD11 HD12 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | HB1 CD1--HD13 +ATOM HA H140 0.060 ! | | / +GROUP ! HA-CA--CB--CG-HG +ATOM CB C136 -0.120 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 CD2--HD23 +ATOM HB2 H140 0.060 ! O=C | \ +GROUP ! | HD21 HD22 +ATOM CG C137 -0.060 ! +ATOM HG H140 0.060 ! +GROUP +ATOM CD1 C135 -0.180 ! +ATOM HD11 H140 0.060 ! +ATOM HD12 H140 0.060 ! +ATOM HD13 H140 0.060 ! +GROUP +ATOM CD2 C135 -0.180 ! +ATOM HD21 H140 0.060 ! +ATOM HD22 H140 0.060 ! +ATOM HD23 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +RESI LYS 1.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA H140 0.060 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM CB C136 -0.120 ! | | | | | \ +ATOM HB1 H140 0.060 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C136 -0.120 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +GROUP +ATOM CD C136 -0.120 ! +ATOM HD1 H140 0.060 ! +ATOM HD2 H140 0.060 ! +GROUP +ATOM CE C292 0.190 ! +ATOM HE1 H140 0.060 ! +ATOM HE2 H140 0.060 ! +ATOM NZ N287 -0.300 ! +ATOM HZ1 H290 0.330 ! +ATOM HZ2 H290 0.330 ! +ATOM HZ3 H290 0.330 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUBLE O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI MET 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 HG1 HE1 +ATOM HA H140 0.060 ! | | | | +GROUP ! HA-CA--CB--CG--SD--CE--HE3 +ATOM CB C136 -0.120 ! | | | | +ATOM HB1 H140 0.060 ! | HB2 HG2 HE2 +ATOM HB2 H140 0.060 ! O=C +GROUP ! | +ATOM CG C210 0.0475 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +ATOM SD S202 -0.335 ! +ATOM CE C209 -0.0125 ! +ATOM HE1 H140 0.060 ! +ATOM HE2 H140 0.060 ! +ATOM HE3 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +RESI PHE 0.00 +GROUP +ATOM N N238 -0.500 ! | HD1 HE1 +ATOM HN H241 0.300 ! HN-N | | +ATOM CA C224 0.140 ! | HB1 CD1--CE1 +ATOM HA H140 0.060 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--HZ +ATOM CB C149 -0.005 ! | | \ __ / +ATOM HB1 H140 0.060 ! | HB2 CD2--CE2 +ATOM HB2 H140 0.060 ! O=C | | +ATOM CG C145 -0.115 ! | HD2 HE2 +GROUP +ATOM CD1 C145 -0.115 ! +ATOM HD1 H146 0.115 ! +GROUP +ATOM CE1 C145 -0.115 ! +ATOM HE1 H146 0.115 ! +GROUP +ATOM CZ C145 -0.115 ! +ATOM HZ H146 0.115 ! +GROUP +ATOM CD2 C145 -0.115 ! +ATOM HD2 H146 0.115 ! +GROUP +ATOM CE2 C145 -0.115 ! +ATOM HE2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ +IMPR HN N -C CA O C CA +N +IMPR HD1 CD1 CG CE1 HE1 CE1 CD1 CZ HZ CZ CE1 CE2 +IMPR CB CG CD1 CD2 HD2 CD2 CE2 CG HE2 CE2 CZ CD2 +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +RESI PRO 0.00 +GROUP ! HD1 HD2 +ATOM N N239 -0.140 ! | \ / +ATOM CD C245 -0.050 ! N---CD HG1 ATOM CA CP1 0.02 +ATOM HD1 H140 0.060 ! | \ / +ATOM HD2 H140 0.060 ! | CG +ATOM CA C246 0.010 ! | / \ +ATOM HA H140 0.060 ! HA-CA--CB HG2 +GROUP ! | / \ +ATOM CB C136 -0.120 ! | HB1 HB2 +ATOM HB1 H140 0.060 ! O=C +ATOM HB2 H140 0.060 ! | +GROUP +ATOM CG C136 -0.120 ! +ATOM HG1 H140 0.060 ! +ATOM HG2 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +DOUBLE O C +IMPR CD N -C CA +IMPR O C CA +N +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 +PATCHING FIRS PROP LAST PROC + +RESI SER 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | HB1 +ATOM HA H140 0.060 ! | | +GROUP ! HA-CA--CB--OG +ATOM CB C157 0.145 ! | | \ +ATOM HB1 H140 0.060 ! | HB2 HG1 +ATOM HB2 H140 0.060 ! O=C +ATOM OG O154 -0.683 ! | +ATOM HG1 H155 0.418 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +RESI THR 0.00 +GROUP +ATOM N N238 -0.500 ! | +ATOM HN H241 0.300 ! HN-N +ATOM CA C224 0.140 ! | OG1--HG1 +ATOM HA H140 0.060 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB C158 0.205 ! | \ +ATOM HB H140 0.060 ! | CG2--HG21 +ATOM OG1 O154 -0.683 ! O=C / \ +ATOM HG1 H155 0.418 ! | HG21 HG22 +GROUP +ATOM CG2 C135 -0.180 ! +ATOM HG21 H140 0.060 ! +ATOM HG22 H140 0.060 ! +ATOM HG23 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +RESI TRP 0.00 +GROUP +ATOM N N238 -0.500 ! | HE3 +ATOM HN H241 0.300 ! HN-N | +ATOM CA C224 0.140 ! | HB1 CE3 +ATOM HA H140 0.060 ! | | / \\ +GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM CB C136 -0.120 ! | | || || | +ATOM HB1 H140 0.060 ! | HB2 CD1 CE2 CH2-HH2 +ATOM HB2 H140 0.060 ! O=C / \ / \ // +GROUP ! | HD1 NE1 CZ2 +ATOM CG C500 0.075 ! | | +ATOM CD1 C514 -0.115 ! HE1 HZ2 +ATOM HD1 H146 0.115 ! +ATOM NE1 N503 -0.570 ! +ATOM HE1 H504 0.420 ! +ATOM CE2 C502 0.130 ! +ATOM CD2 C501 -0.055 ! +GROUP +ATOM CE3 C145 -0.115 ! +ATOM HE3 H146 0.115 ! +GROUP +ATOM CZ3 C145 -0.115 ! +ATOM HZ3 H146 0.115 ! +GROUP +ATOM CZ2 C145 -0.115 ! +ATOM HZ2 H146 0.115 ! +GROUP +ATOM CH2 C145 -0.115 ! +ATOM HH2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 +IMPR HN N -C CA O C CA +N +IMPR CB CG CD1 CD2 HD1 CD1 CG NE1 HE1 NE1 CD1 CE2 +IMPR HZ2 CZ2 CE2 CH2 HH2 CH2 CZ2 CZ3 HZ3 CZ3 CH2 CE3 +IMPR HE3 CE3 CZ3 CD2 CE2 CD2 CE3 CG CZ2 CE2 CD2 NE1 +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI TYR 0.00 +GROUP +ATOM N N238 -0.500 ! | HD1 HE1 +ATOM HN H241 0.300 ! HN-N | | +ATOM CA C224 0.140 ! | HB1 CD1--CE1 +ATOM HA H140 0.060 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--OH +ATOM CB C149 -0.005 ! | | \ __ / \ +ATOM HB1 H140 0.060 ! | HB2 CD2--CE2 HH +ATOM HB2 H140 0.060 ! O=C | | +ATOM CG C145 -0.115 ! | HD2 HE2 +GROUP +ATOM CD1 C145 -0.115 ! +ATOM HD1 H146 0.115 ! +GROUP +ATOM CE1 C145 -0.115 ! +ATOM HE1 H146 0.115 ! +GROUP +ATOM CZ C166 0.150 ! +ATOM OH O167 -0.585 ! +ATOM HH H168 0.435 ! +GROUP +ATOM CD2 C145 -0.115 ! +ATOM HD2 H146 0.115 ! +GROUP +ATOM CE2 C145 -0.115 ! +ATOM HE2 H146 0.115 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +DOUBLE O C CD1 CG CE1 CZ CE2 CD2 +IMPR HN N -C CA O C CA +N +IMPR HD1 CD1 CG CE1 HE1 CE1 CD1 CZ OH CZ CE1 CE2 +IMPR CB CG CD1 CD2 HD2 CD2 CE2 CG HE2 CE2 CZ CD2 +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +RESI VAL 0.00 +GROUP +ATOM N N238 -0.500 ! | HG11 HG12 +ATOM HN H241 0.300 ! HN-N | / +ATOM CA C224 0.140 ! | CG1--HG13 +ATOM HA H140 0.060 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB C137 -0.060 ! | \ +ATOM HB H140 0.060 ! | CG2--HG21 +GROUP ! O=C / \ +ATOM CG1 C135 -0.180 ! | HG21 HG22 +ATOM HG11 H140 0.060 ! +ATOM HG12 H140 0.060 ! +ATOM HG13 H140 0.060 ! +GROUP +ATOM CG2 C135 -0.180 ! +ATOM HG21 H140 0.060 ! +ATOM HG22 H140 0.060 ! +ATOM HG23 H140 0.060 ! +GROUP +ATOM C C235 0.500 ! +ATOM O O236 -0.500 ! +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR HN N -C CA O C CA +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +PRES NTER 1.00 ! standard N-terminus +GROUP ! use in generate statement +ATOM N N287 -0.300 ! +ATOM HT1 H290 0.330 ! HT1 +ATOM HT2 H290 0.330 ! (+)/ +ATOM HT3 H290 0.330 ! --CA--N--HT2 +ATOM CA C293 0.250 ! | \ +ATOM HA H140 0.060 ! HA HT3 +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES GLYP 1.00 ! Glycine N-terminus +GROUP ! use in generate statement +ATOM N N287 -0.300 ! +ATOM HT1 H290 0.330 ! HA1 HT1 +ATOM HT2 H290 0.330 ! | (+)/ +ATOM HT3 H290 0.330 ! --CA--N--HT2 +ATOM CA C292 0.190 ! | \ +ATOM HA1 H140 0.060 ! HA2 HT3 +ATOM HA2 H140 0.060 ! +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES PROP 1.00 ! Proline N-Terminal +GROUP ! use in generate statement +ATOM N N309 -0.200 ! HA +ATOM HN1 H310 0.310 ! | +ATOM HN2 H310 0.310 ! -CA HN1 +ATOM CD C296 0.170 ! / \ / +ATOM HD1 H140 0.060 ! N(+) +ATOM HD2 H140 0.060 ! / \ +ATOM CA C295 0.230 ! -CD HN2 +ATOM HA H140 0.060 ! | \ +BOND HN1 N HN2 N ! HD1 HD2 +DONOR HN1 N +DONOR HN2 N +IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES ACE 0.00 ! acetylated N-terminus +GROUP ! use in generate statement +ATOM CAY C135 -0.180 ! +ATOM HY1 H140 0.060 ! HY1 HY2 HY3 +ATOM HY2 H140 0.060 ! \ | / +ATOM HY3 H140 0.060 ! CAY +GROUP ! | +ATOM CY C235 0.500 ! CY=OY +ATOM OY O236 -0.500 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR OY CY CAY N +IMPR HN N CY CA +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACP 0.00 ! acetylated N-terminus for proline +GROUP ! use in generate statement +ATOM CAY C135 -0.180 ! +ATOM HY1 H140 0.060 ! HY1 HY2 HY3 +ATOM HY2 H140 0.060 ! \ | / +ATOM HY3 H140 0.060 ! CAY +GROUP ! | +ATOM CY C235 0.500 ! CY=OY +ATOM OY O236 -0.500 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR OY CY CAY N +IMPR CD N CY CA +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES CTER -0.86 ! standard C-terminus +GROUP ! use in generate statement +ATOM CA C283 0.040 ! line added in template for script pepz2rtf +ATOM C C271 0.700 ! OT2(-) +ATOM OT1 O272 -0.800 ! / +ATOM OT2 O272 -0.800 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +IMPR OT2 C CA OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CTP 0.14 ! protonated C-terminus, corrected adm jr. +GROUP ! use in generate statement +ATOM CA C224 0.14 ! line added in template for script pepz2rtf +ATOM C C267 0.52 ! OT2--HT2 +ATOM OT1 O269 -0.44 ! / +ATOM OT2 O268 -0.53 ! -C +ATOM HT2 H270 0.45 ! \\ +DELETE ATOM O ! OT1 +BOND C OT2 OT2 HT2 ! +DOUBLE C OT1 +IMPR OT2 C CA OT1 +ACCEPTOR OT1 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +! protonated C-terminal Gly, adm jr. +PRES CTPG 0.08 ! protonated C-terminal Gly +GROUP ! use in generate statement +ATOM CA C223 0.08 ! line added in template for script pepz2rtf +ATOM C C267 0.52 ! OT2--HT2 +ATOM OT1 O269 -0.44 ! / +ATOM OT2 O268 -0.53 ! -C +ATOM HT2 H270 0.45 ! \\ +DELETE ATOM O ! OT1 +BOND C OT2 OT2 HT2 ! +DOUBLE C OT1 +IMPR OT2 C CA OT1 +ACCEPTOR OT1 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT3 0.00 ! N-Methylamide C-terminus use in generate statement +GROUP ! C=O +ATOM NT N238 -0.500 ! | +ATOM HNT H241 0.300 ! NT-HNT +ATOM CAT C242 0.020 ! | +ATOM HT1 H140 0.060 ! HT1-CAT-HT3 +ATOM HT2 H140 0.060 ! | +ATOM HT3 H140 0.060 ! HT2 + ! +BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 +!DIHE CA C NT CAT +IMPR HNT NT C CAT O C CA NT +DONOR HNT NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES GLYC -0.92 ! standard C-terminus +GROUP ! use in generate statement +ATOM CA C284 -0.020 ! line added in template for script pepz2rtf +ATOM C C271 0.700 ! OT2(-) +ATOM OT1 O272 -0.800 ! / +ATOM OT2 O272 -0.800 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +IMPR OT1 C CA OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES PROC -0.99 ! standard C-terminus +GROUP ! use in generate statement +ATOM CA C285 -0.090 ! line added in template for script pepz2rtf +ATOM C C271 0.700 ! OT2(-) +ATOM OT1 O272 -0.800 ! / +ATOM OT2 O272 -0.800 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +IMPR OT1 C CA OT2 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 +GROUP ! via acetic acid, use in a patch statement +ATOM CB C136 -0.120 ! +ATOM HB1 H140 0.060 ! HB1 OD1 +ATOM HB2 H140 0.060 ! | // +ATOM CG C267 0.520 ! -CB--CG +ATOM OD1 O269 -0.440 ! | \ +ATOM OD2 O268 -0.530 ! HB2 OD2-HD2 +ATOM HD2 H270 0.450 ! +BOND OD2 HD2 +ANGLE HD2 OD2 CG +DIHE HD2 OD2 CG OD1 HD2 OD2 CG CB +DONOR HD2 OD2 +IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 +GROUP ! via acetic acid, use in a patch statement +ATOM CG C136 -0.120 ! +ATOM HG1 H140 0.060 ! HG1 OE1 +ATOM HG2 H140 0.060 ! | // +ATOM CD C267 0.520 ! -CG--CD +ATOM OE1 O269 -0.440 ! | \ +ATOM OE2 O268 -0.530 ! HG2 OE2-HE2 +ATOM HE2 H270 0.450 ! +BOND OE2 HE2 +ANGLE HE2 OE2 CD +DIHE HE2 OE2 CD OE1 HE2 OE2 CD CG +DONOR HE2 OE2 +IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES LINK 0.00 ! linkage for IMAGES or for joining segments + ! 1 refers to previous (N terminal) + ! 2 refers to next (C terminal) + ! use in a patch statement +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +IMPR 2HN 2N 1C 2CA 1O 1C 1CA 2N +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES DISU -0.24 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. +GROUP ! use in a patch statement +ATOM 1CB C214 0.0975! +ATOM 1SG S203 -0.2175 ! 2SG--2CB-- +ATOM 2SG S203 -0.2175 ! / +ATOM 2CB C214 0.0975! -1CB--1SG +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +ANGLE 1CB 1SG 2SG 1SG 2SG 2CB +DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG +DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG +DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA +DIHE 1CB 1SG 2SG 2CB +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG1 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2HN 2N 1C 2CA 1O 1C 1CA 2N +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG2 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 +DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2HN 2N 1C 2CA 1O 1C 1CA 2N +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG3 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 +DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2HN 2N 1C 2CA 1O 1C 1CA 2N +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion, adm jr. +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion, adm jr. +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END diff --git a/charmm/toppar/non_charmm/toppar_chloroform_dh.str b/charmm/toppar/non_charmm/toppar_chloroform_dh.str new file mode 100644 index 00000000..e10eb075 --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_chloroform_dh.str @@ -0,0 +1,70 @@ +* chloroform topper file in CHARMM format +* + +! Chloroform based on the original DH model from Dietz and Heinzinger (DH model) +! (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 968) +! Translated into CHARMM format for the following work +! (Yu, W., He, X., Vanommeslaeghe, K. and MacKerell, A. D., J. Comput. Chem., 2012, 33, 2451–2468) +! Tested in CHARMM and shown to be compatible with CHARMM protein and CGenFF force fields. +! Just use "stream toppar_chloroform_dh.str" in your CHARMM input file + + +read rtf card append +* chloroform +* + +MASS 480 HCM 1.0080 ! +MASS 481 CLCM 35.4500 ! +MASS 482 CCM 12.0110 ! + +RESI CCL3 0.000 +GROUP +ATOM C CCM 0.179 +ATOM CL1 CLCM -0.087 +ATOM CL2 CLCM -0.087 +ATOM CL3 CLCM -0.087 +ATOM HX HCM 0.082 +BOND C CL1 C CL2 C CL3 C HX +BOND CL1 CL2 CL1 CL3 !for shake +BOND CL1 HX CL2 HX CL3 HX ! for shake +ANGLE HX C CL1 HX C CL2 HX C CL3 +ANGLE CL1 C CL2 CL1 C CL3 CL2 C CL3 +PATCHING FIRS NONE LAST NONE + +END + +read param card flex append +* chloroform +* + +ATOMS +MASS 480 HCM 1.0080 ! +MASS 481 CLCM 35.4500 ! +MASS 482 CCM 12.0110 ! + +BONDS +CCM CLCM 500.0 1.758 +CCM HCM 500.0 1.100 +CLCM CLCM 0.0 2.9028314 +HCM CLCM 0.0 2.3383924 + +ANGLES +CLCM CCM CLCM 0.0 111.30 +HCM CCM CLCM 0.0 107.57 + + +DIHEDRALS + +IMPROPERS + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +CCM 0.0 -0.102 1.9082 ! +CLCM 0.0 -0.300 1.9306 ! +HCM 0.0 -0.020 1.2347 ! + +END + +RETURN + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_spc.str b/charmm/toppar/non_charmm/toppar_water_ions_spc.str new file mode 100644 index 00000000..ea78f839 --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_spc.str @@ -0,0 +1,300 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the SPC water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!SPC +! +!H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans, +!In Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, +!1981), p. 331! +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN, SPC +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion + +default first none last none + +RESI SPC 0.0000 ! SPC water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.8068 +ATOM H1 HT 0.4034 +ATOM H2 HT 0.4034 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +DONOR H1 OH2 +DONOR H2 OH2 +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.633 ! SPC/(E) +HT OT 450.0 1.000 ! SPC/(E) +OX HX 545.0 0.9700 ! hydroxide ion + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 109.47 ! SPC(/E) + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!SPC +HT 0.000000 -0.000001 0.0001 !SPC(/E) HYDROGEN PARAMETERS +OT 0.000000 -0.15529 1.762827 !SPC(/E) OXYGEN PARAMETERS + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_spc_e.str b/charmm/toppar/non_charmm/toppar_water_ions_spc_e.str new file mode 100644 index 00000000..23c26a31 --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_spc_e.str @@ -0,0 +1,300 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the SPC/E water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!SPC/E +! +! +!H.J.C. Berendsen, J. R. Grigera, and T. P. Straatsma. The Missing +!Term in Effective Pair Potentials. J. Phys. Chem 1987, 91, 6269-6271. +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN, SPC/E +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion + +default first none last none + +RESI SPCE 0.0000 ! SPC/E water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.8476 +ATOM H1 HT 0.4238 +ATOM H2 HT 0.4238 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +!DONOR H1 OH2 +!DONOR H2 OH2 +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.633 ! SPC/(E) +HT OT 450.0 1.000 ! SPC/(E) +OX HX 545.0 0.9700 ! hydroxide ion + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 109.47 ! SPC(/E) + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!SPC/E +HT 0.000000 -0.000001 0.0001 !SPC(/E) HYDROGEN PARAMETERS +OT 0.000000 -0.15529 1.762827 !SPC(/E) OXYGEN PARAMETERS + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str b/charmm/toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str new file mode 100644 index 00000000..746a9592 --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str @@ -0,0 +1,295 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the TIP3P-PME, model B water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!TIP3P-PME +!D.J. Price; C.L. Brooks III, J. Chem. Phys., 121:10096-10103 (2004). +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN, TIP3P-PME, model B +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion + +default first none last none + +RESI TP3B 0.000 ! tip3p-PME water model B, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.830 +ATOM H1 HT 0.415 +ATOM H2 HT 0.415 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +OX HX 545.0 0.9700 ! hydroxide ion + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!TIP3P-PME, model B +HT 0.0 -0.0 0.0 +OT 0.0 -0.102 1.7892 + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str b/charmm/toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str new file mode 100644 index 00000000..d734f783 --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str @@ -0,0 +1,297 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the TIP3P-PME, model F water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!TIP3P-PME +!D.J. Price; C.L. Brooks III, J. Chem. Phys., 121:10096-10103 (2004). +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN, TIP3P-PME, model F +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion + +default first none last none + +RESI TP3F 0.000 ! tip3p-PME water model F, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.83 +ATOM H1 HT 0.415 +ATOM H2 HT 0.415 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +DONOR H1 OH2 +DONOR H2 OH2 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +OX HX 545.0 0.9700 ! hydroxide ion + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!TIP3P-PME, model F +HT 0.0 -0.0 0.0 +OT 0.0 -0.098 1.7926 + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_tip4p.str b/charmm/toppar/non_charmm/toppar_water_ions_tip4p.str new file mode 100644 index 00000000..a43deba3 --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_tip4p.str @@ -0,0 +1,309 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the TIP4P water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!TIP4P water model +! +!W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; +!M.L. Klein; "Comparison of simple potential functions for +!simulating liquid water", J. Chem. Phys. 79 926-935 (1983). +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN, TIP4P +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion +MASS 16 LP 0.00000 H ! virtual particle for M-site/lone pairs + +default first none last none + +RESI TIP4 0.000 ! tip4p water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT 0.0 +ATOM OM LP -1.04 +ATOM H1 HT 0.52 +ATOM H2 HT 0.52 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +BOND OH2 OM +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +!DONOR H1 OH2 +!DONOR H2 OH2 +LONEPAIR bisector OM OH2 H1 H2 distance 0.15 angle 0.0 dihe 0.0 +IC H1 OM *OH2 H2 0.9572 52.26 180.00 52.26 0.9572 +IC H2 H1 OH2 OM 0.0000 0.00 0.00 52.26 0.15 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion +MASS 16 LP 0.00000 ! virtual particle for M-site/lone pairs + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +OX HX 545.0 0.9700 ! hydroxide ion +OT LP 0.0 0.15 ! from TIP4P geometry + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!TIP4P +HT 0.0 -0.0 0.0 +OT 0.0 -0.155 1.7699 +LP 0.0 -0.00 0.0 + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_tip4p_2005.str b/charmm/toppar/non_charmm/toppar_water_ions_tip4p_2005.str new file mode 100644 index 00000000..71bd5c7f --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_tip4p_2005.str @@ -0,0 +1,306 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the TIP4P-2005 water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!TIP4P-2005 +!J.L.F. Abascal; C. Vega, J. Chem. Phys., 123: 234505 (2005) +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN, TIP4P-2005 +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion +MASS 16 LP 0.00000 H ! virtual particle for M-site/lone pairs + +default first none last none + +RESI TP45 0.000 ! tip4p-2005 water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT 0.0 +ATOM OM LP -1.1128 +ATOM H1 HT 0.5564 +ATOM H2 HT 0.5564 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +BOND OH2 OM +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +!DONOR H1 OH2 +!DONOR H2 OH2 +LONEPAIR bisector OM OH2 H1 H2 distance 0.1546 angle 0.0 dihe 0.0 +IC H1 OM *OH2 H2 0.9572 52.26 180.00 52.26 0.9572 +IC H2 H1 OH2 OM 0.0000 0.00 0.00 52.26 0.15 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion +MASS 16 LP 0.00000 ! virtual particle for M-site/lone pairs + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +OX HX 545.0 0.9700 ! hydroxide ion +OT LP 0.0 0.15 ! from TIP4P geometry + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!TIP4P-2005 +HT 0.0 -0.0 0.0 +OT 0.0 -0.1852 1.7726 +LP 0.0 -0.00 0.0 + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_tip4p_ew.str b/charmm/toppar/non_charmm/toppar_water_ions_tip4p_ew.str new file mode 100644 index 00000000..364bba77 --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_tip4p_ew.str @@ -0,0 +1,307 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the TIP4P-Ewald water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!TIP4P-Ewald +!H.W. Horn; W.C Swope; J.W. Pitera; J.D. Madura; T.J. Dick; +!G.L. Hura; T. Head-Gordon, J. Chem. Phys., 120: 9665-9678 (2004) +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN, TIP4P-Ewald +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion +MASS 16 LP 0.00000 H ! virtual particle for M-site/lone pairs + +default first none last none + +RESI TP4E 0.000 ! tip4p-Ewald water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT 0.0 +ATOM OM LP -1.04844 +ATOM H1 HT 0.52422 +ATOM H2 HT 0.52422 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +BOND OH2 OM +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +!DONOR H1 OH2 +!DONOR H2 OH2 +LONEPAIR bisector OM OH2 H1 H2 distance 0.125 angle 0.0 dihe 0.0 +IC H1 OM *OH2 H2 0.9572 52.26 180.00 52.26 0.9572 +IC H2 H1 OH2 OM 0.0000 0.00 0.00 52.26 0.125 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion +MASS 16 LP 0.00000 ! virtual particle for M-site/lone pairs + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +OX HX 545.0 0.9700 ! hydroxide ion +OT LP 0.0 0.15 ! from TIP4P geometry + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!TIP4P-Ewald +HT 0.0 -0.0 0.0 +OT 0.0 -0.16275 1.7759 +LP 0.0 -0.00 0.0 + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_tip5p.str b/charmm/toppar/non_charmm/toppar_water_ions_tip5p.str new file mode 100644 index 00000000..0c46fb3f --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_tip5p.str @@ -0,0 +1,306 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the TIP5P water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!TIP5P +!M.W. Mahoney; W.L. Jorgensen, J. Chem Phys., 112: 8910-8922, (2000) +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN, TIP5P +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion +MASS 16 LP 0.00000 H ! virtual particle for M-site/lone pairs + +default first none last none + +RESI TIP5 0.000 ! tip5p water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT 0.0 +ATOM H1 HT 0.241 +ATOM H2 HT 0.241 +ATOM LP1 LP -0.241 +ATOM LP2 LP -0.241 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +BOND OH2 LP1 OH2 LP2 +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +!DONOR H1 OH2 +!DONOR H2 OH2 +LONEPAIR bisector LP1 OH2 H1 H2 distance 0.70 angle 125.265 dihedral 90.0 +LONEPAIR bisector LP2 OH2 H1 H2 distance 0.70 angle 125.265 dihedral -90.0 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion +MASS 16 LP 0.00000 ! virtual particle for M-site/lone pairs + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +OX HX 545.0 0.9700 ! hydroxide ion +OT LP 0.0 0.7 ! from TIP5P geometry + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!TIP5P +HT 0.0 -0.0 0.0 +OT 0.0 -0.16 1.7508 +LP 0.0 -0.00 0.0 + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/non_charmm/toppar_water_ions_tip5p_ew.str b/charmm/toppar/non_charmm/toppar_water_ions_tip5p_ew.str new file mode 100644 index 00000000..a6739f16 --- /dev/null +++ b/charmm/toppar/non_charmm/toppar_water_ions_tip5p_ew.str @@ -0,0 +1,306 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions_non_charmm.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +! Toppar stream file for the TIP5P-Ewald water model and ions. +! Note that the ions have not been optimized for the non-TIP3P water model. + +!references +! +!TIP5P-Ewald +!S.W. Rick, J. Chem. Phys., 120:6085-6093, (2004) +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN: TIP5P-Ewald +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion +MASS 16 LP 0.00000 H ! virtual particle for M-site/lone pairs + +default first none last none + +RESI TP5E 0.000 ! tip5p-Ewald water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT 0.0 +ATOM H1 HT 0.241 +ATOM H2 HT 0.241 +ATOM LP1 LP -0.241 +ATOM LP2 LP -0.241 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +BOND OH2 LP1 OH2 LP2 +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +DONOR H1 OH2 +DONOR H2 OH2 +LONEPAIR bisector LP1 OH2 H1 H2 distance 0.70 angle 125.265 dihedral 90.0 +LONEPAIR bisector LP2 OH2 H1 H2 distance 0.70 angle 125.265 dihedral -90.0 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion +MASS 16 LP 0.00000 ! virtual particle for M-site/lone pairs + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +OX HX 545.0 0.9700 ! hydroxide ion +OT LP 0.0 0.7 ! from TIP5P geometry + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!TIP5P-Ewald LJ parameters +HT 0.0 -0.0 0.0 +OT 0.0 -0.16275 1.7379 +LP 0.0 -0.00 0.0 + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX +SOD OC -0.075020 3.190 ! For prot carboxylate groups +SOD OCL -0.075020 3.190 ! For lipid carboxylate groups +SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups +SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + diff --git a/charmm/toppar/par_all22_prot.prm b/charmm/toppar/par_all22_prot.prm new file mode 100644 index 00000000..b4d1b9f3 --- /dev/null +++ b/charmm/toppar/par_all22_prot.prm @@ -0,0 +1,3125 @@ +*>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<< +*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< +*>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<< +* All comments to ADM jr. via the CHARMM web site: www.charmm.org +* parameter set discussion forum +* + +! references +! +!PROTEINS +! +!MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the +!treatment of backbone energetics in protein force fields: limitations +!of gas-phase quantum mechanics in reproducing protein conformational +!distributions in molecular dynamics simulations, Journal of +!Computational Chemistry, 25: 1400-1415, 2004. +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. +! +!IONS (see lipid and nucleic acid topology and parameter files for +!additional ions +! +!ZINC +! +!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) +! + +ATOMS +MASS 41 H 1.00800 ! polar H +MASS 42 HC 1.00800 ! N-ter H +MASS 43 HA 1.00800 ! nonpolar H +MASS 44 HP 1.00800 ! aromatic H +MASS 45 HB 1.00800 ! backbone H +MASS 46 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS 47 HR2 1.00800 ! (+) his HE1 +MASS 48 HR3 1.00800 ! neutral his HG, HD2 +MASS 49 HS 1.00800 ! thiol hydrogen +MASS 50 HE1 1.00800 ! for alkene; RHC=CR +MASS 51 HE2 1.00800 ! for alkene; H2C=CR +MASS 52 C 12.01100 ! carbonyl C, peptide backbone +MASS 53 CA 12.01100 ! aromatic C +MASS 54 CT1 12.01100 ! aliphatic sp3 C for CH +MASS 55 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS 56 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS 57 CPH1 12.01100 ! his CG and CD2 carbons +MASS 58 CPH2 12.01100 ! his CE1 carbon +MASS 59 CPT 12.01100 ! trp C between rings +MASS 60 CY 12.01100 ! TRP C in pyrrole ring +MASS 61 CP1 12.01100 ! tetrahedral C (proline CA) +MASS 62 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS 63 CP3 12.01100 ! tetrahedral C (proline CD) +MASS 64 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS 65 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS 66 CS 12.01100 ! thiolate carbon +MASS 67 CE1 12.01100 ! for alkene; RHC=CR +MASS 68 CE2 12.01100 ! for alkene; H2C=CR +MASS 69 C3 12.01100 ! cyclopropyl carbon +MASS 70 N 14.00700 ! proline N +MASS 71 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS 72 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS 73 NR3 14.00700 ! charged his ring nitrogen +MASS 74 NH1 14.00700 ! peptide nitrogen +MASS 75 NH2 14.00700 ! amide nitrogen +MASS 76 NH3 14.00700 ! ammonium nitrogen +MASS 77 NC2 14.00700 ! guanidinium nitroogen +MASS 78 NY 14.00700 ! TRP N in pyrrole ring +MASS 79 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS 80 O 15.99900 ! carbonyl oxygen +MASS 81 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS 82 OC 15.99900 ! carboxylate oxygen +MASS 83 OH1 15.99900 ! hydroxyl oxygen +MASS 84 OS 15.99940 ! ester oxygen +MASS 85 S 32.06000 ! sulphur +MASS 86 SM 32.06000 ! sulfur C-S-S-C type +MASS 87 SS 32.06000 ! thiolate sulfur + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +NH2 CT1 240.00 1.455 ! From LSN NH2-CT2 +CA CA 305.000 1.3750 ! ALLOW ARO + ! benzene, JES 8/25/89 +CE1 CE1 440.000 1.3400 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CE2 500.000 1.3420 ! + ! for propene, yin/adm jr., 12/95 +CE1 CT2 365.000 1.5020 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CT3 383.000 1.5040 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE2 510.000 1.3300 ! + ! for ethene, yin/adm jr., 12/95 +CP1 C 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CC 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CD 200.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 222.500 1.5270 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH1 CPH1 410.000 1.3600 ! ALLOW ARO + ! histidine, adm jr., 6/27/90 +CPT CA 305.000 1.3680 ! ALLOW ARO + ! adm jr., 12/30/91, for jwk +CPT CPT 360.000 1.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT1 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT1 222.500 1.5000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT2 CA 230.000 1.4900 ! ALLOW ALI ARO + ! phe,tyr, JES 8/25/89 +CT2 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT2 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT3 CA 230.000 1.4900 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +CT3 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT3 CS 190.000 1.5310 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CT3 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 222.500 1.5280 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT3 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CY CA 350.000 1.3650 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CY CPT 350.000 1.4400 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 230.000 1.5100 ! ALLOW ARO + !JWK Kb from alkane freq.. b0 from TRP crystal +H CD 330.000 1.1100 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CA 340.000 1.0830 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA CC 317.130 1.1000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +HA CP2 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT1 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 322.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CY 330.000 1.0800 ! ALLOW ARO + ! JWK 05/14/91 new r0 from indole +HE1 CE1 360.500 1.1000 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 365.000 1.1000 ! + ! for ethene, yin/adm jr., 12/95 +HB CP1 330.000 1.0800 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HP CA 340.000 1.0800 ! ALLOW ARO + ! phe,tyr JES 8/25/89 +HP CY 350.000 1.0800 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HR1 CPH1 375.000 1.0830 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 340.000 1.0900 ! ALLOW ARO + ! his, adm jr., 6/28/29 +HR2 CPH2 333.000 1.0700 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR3 CPH1 365.000 1.0830 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 320.000 1.4340 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 320.000 1.4550 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO + ! 403.0->463.0, 1.305->1.365 guanidinium (KK) +NC2 CT2 261.000 1.4900 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 261.000 1.4900 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NC2 HC 455.000 1.0000 ! ALLOW POL + ! 405.0->455.0 GUANIDINIUM (KK) +NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO + ! (DS) +NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +NH2 CT2 240.000 1.4550 + ! from NH2 CT3, neutral glycine, adm jr. +NH2 CT3 240.000 1.4550 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH2 H 480.000 1.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 HC 460.000 1.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT3 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 HC 403.000 1.0400 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 320.000 1.4850 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 320.000 1.5020 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP HC 460.000 1.0060 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH2 400.000 1.3600 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 H 466.000 1.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 400.000 1.3200 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 380.000 1.3700 ! ALLOW ARO + ! his, adm jr., 6/28/90 +NR3 CPH2 380.000 1.3200 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 H 453.000 1.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA 270.000 1.3700 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT 270.000 1.3750 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY H 465.000 0.9760 ! ALLOW ARO + ! indole JWK 08/28/89 +O C 620.000 1.2300 ! ALLOW PEP POL ARO + ! Peptide geometry, condensed phase (LK) +O CC 650.000 1.2300 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +OB CC 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid vibrations and geom. +OB CD 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 8/27/91, phenoxide +OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 7/23/91, acetic acid +OC CT2 450.000 1.3300 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 450.000 1.3300 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA 334.300 1.4110 ! ALLOW ARO ALC + ! MeOH, EMB 10/10/89, +OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC + ! adm jr. 5/02/91, acetic acid pure solvent +OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 H 545.000 0.9600 ! ALLOW ALC ARO + ! EMB 11/21/89 methanol vib fit +OS CD 150.000 1.3340 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +OS CT3 340.000 1.4300 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +S CT2 198.000 1.8180 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S CT3 240.000 1.8160 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S HS 275.000 1.3250 ! ALLOW SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +SM CT2 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM CT3 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM SM 173.000 2.0290 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SS CS 205.000 1.8360 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HR1 CD 330.000 1.1100 ! acetaldehyde, benzaldehyde, 3ALP +O CD 720.000 1.2050 ! acetaldehyde, benzaldehyde, 3ALP. DIFFERENT COPY OF SAME PARAMETER IN stream/toppar_all27_na_bkb_modifications.str + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +H NH2 CT1 50.000 111.00 ! From LSN HC-NH2-CT2 +NH2 CT1 CT2 67.700 110.00 ! From LSN NH2-CT2-CT2 +NH2 CT1 CT3 67.700 110.00 ! From LSN NH2-CT2-CT2 +CT1 CD OH1 55.000 110.50 ! From ASPP CT2-CD-OH1 +CT3 CT1 CD 52.000 108.00 ! Ala cter +NH2 CT1 HB 38.000 109.50 50.00 2.1400 ! From LSN NH2-CT2-HA +NH2 CT1 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C +! +CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO + ! JES 8/25/89 +CE1 CE1 CT2 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CE1 CT3 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CT2 CT3 32.00 112.20 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT2 48.00 126.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT3 47.00 125.20 ! + ! for propene, yin/adm jr., 12/95 +CP1 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 C 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 100.000 114.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 100.000 111.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPT CA CA 60.000 118.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CPT CA 60.000 122.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT NY CA 110.000 108.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 6/27/2012, for Thr with CT1 patch +CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! from CT2 CT1 C, for lactams, adm jr. +CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CY CA 45.800 129.4000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 CY CPT 45.800 124.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! 107.5->120.0 to make planar Arg (KK) +CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/09/92, for ALA cter +CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! methylguanidinium, adm jr., 3/26/92 +CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 CT1 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +CY CT2 CT3 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO + ! his, adm jr. 8/13/90 acetamide geometry and vibrations +H NH2 H 23.000 120.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NY CA 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO + ! JES 8/25/89 phenol +H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA CA CPT 41.000 122.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd + ! based on HA CT2 HA +HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT2 CE1 45.00 111.50 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 CY 33.430 109.5000 ! ALLOW ARO + ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA +HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT3 CE1 42.00 111.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HE1 CE1 CE1 52.00 119.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HE1 CE1 CE2 42.00 118.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 40.00 116.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HE1 CE1 CT3 22.00 117.00 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE1 45.00 120.50 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE2 55.50 120.50 ! + ! for ethene, yin/adm jr., 12/95 +HE2 CE2 HE2 19.00 119.00 ! + ! for propene, yin/adm jr., 12/95 +HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB CT1 CT1 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CT2 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CT3 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB CT2 HB 36.000 115.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO + ! 35.3->49.0 GUANIDINIUM (KK) +HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI + ! 107.5->120.0 to make planar Arg (KK) +HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI + ! methylguanidinium, adm jr., 3/26/92 +HC NC2 HC 25.000 120.0000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH2 CT2 50.000 111.0000 ! ALLOW POL + ! from HC NH2 CT3, neutral glycine, adm jr. +HC NH2 CT3 50.000 111.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +HC NH2 HC 39.000 106.5000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 HC 44.000 109.5000 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP HC 51.000 107.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 20.000 112.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 C 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CC 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CP2 70.000 110.8000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 CP2 70.000 110.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO + ! changed from 60.0/120.3 for guanidinium (KK) +NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/20/92, for asn,asp,gln,glu and cters +NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT1 CT2, for lactams, adm jr. +NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT3 HA, for lactams, adm jr. +NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! NMA crystal (JCS) +NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +NH2 CT2 HA 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral lysine +NH2 CT2 HB 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral glycine, adm jr. +NH2 CT2 CD 52.000 108.0000 + !from CT2 CT2 CD, neutral glycine, adm jr. +NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + !from NH3 CT2 CT2, neutral lysine +NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP + ! new aliphatics, adm jr., 2/3/92 +NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! alanine (JCS) +NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + ! alanine (JCS) +NH3 CT2 CT3 67.700 110.0000 ! ALLOW ALI POL + ! alanine (JCS) +NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP + ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) +NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 C 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +O C CP1 80.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C H 50.000 121.7000 ! ALLOW PEP POL ARO + ! acetaldehyde (JCS) +O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC HA 44.000 122.0000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO + ! adm jr. 4/10/91, acetamide update +OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA CA 40.000 120.0000 ! ALLOW POL ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CT2 CT3 65.000 122.0000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT2 HA 65.000 118.3000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 HA 65.000 118.3000 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC + ! PARALLH19 WITH [122.3] (JES) +OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 CT2 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 CT3 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 55.000 118.0000 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +O CD HR1 75.000 121.0000 ! acetaldehyde, benzaldehyde, 3ALP, retinal + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +!Neutral N terminus +NH2 CT1 C O 0.0000 1 0.00 +NH2 CT1 C NH1 0.0000 1 0.00 +H NH2 CT1 CT1 0.0000 1 0.00 +H NH2 CT1 C 0.000 1 0.00 +H NH2 CT1 HB 0.110 3 0.00 ! From LSN HC-NH2-CT2-HA +H NH2 CT1 CT2 0.110 3 0.00 ! From LSN HC-NH2-CT2-CT2 +H NH2 CT1 CT3 0.110 3 0.00 ! From LSN HC-NH2-CT2-CT2 + +C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 +CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c +CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c +CE1 CE1 CT3 HA 0.0300 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 CT3 0.5000 1 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 CT3 1.3000 3 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 HA 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT3 HA 0.0500 3 180.00 ! + ! for propene, yin/adm jr., 12/95 +CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 +CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 +CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! from CT2 CT1 NH1 C, for lactams, adm jr. +CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK +CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + !JWK +CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +CT3 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION + ! DTN 8/24/90 +CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from H NH1 CT2 CT3, for lactams, adm jr. +H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/20/89 +H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NY CA CY 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC + ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO + ! adm jr., 10/02/89 +HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO + ! ADM JR., 10/02/89 +HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! TRP (JES) +HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK +HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK +HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA NY H 1.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL + ! adm jr. 4/10/91, acetamide update +HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HE1 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +CT3 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +HE1 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 HA 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE1 CE1 CT2 CT3 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT3 HA 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE2 CE2 CE1 CT2 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NH2 CT2 CT2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral lysine +HC NH2 CT2 HA 0.1100 3 0.00 + !from X CT3 NH2 X, neutral lysine +HC NH2 CT2 HB 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CD 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA NY H 0.4000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, his +HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, YES, 0.0 +HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from NH1 C CT1 CT2, for lactams, adm jr. +NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO + ! adm jr. 3/24/92, for PRES GLYP +NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO + ! JWK +NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP + ! from O C CT1 CT2, for lactams, adm jr. +O C CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT3 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 H 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO + ! 9.0->2.25 GUANIDINIUM (KK) +X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier +X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CE1 CE1 X 0.1500 1 0.00 + ! 2-butene, adm jr., 2/00 update +X CE1 CE1 X 8.5000 2 180.00 + ! 2-butene, adm jr., 2/00 update +X CE2 CE2 X 4.9000 2 180.00 ! + ! for ethene, yin/adm jr., 12/95 +X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP + ! changed to 0.0 RLD 5/19/92 +X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI + ! rotation barrier in Ethane (SF) +X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL + ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 +X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +HE2 HE2 CE2 CE2 3.0 0 0.00 ! + ! for ethene, yin/adm jr., 12/95 +HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO + ! 5.75->40.0 GUANIDINIUM (KK) +NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +NH2 X X H 4.0000 0 0.0000 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO + !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf. +O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! adm jr., 5/13/91, formamide geometry and vibrations +O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL + ! adm jr., 10/17/90, acetic acid vibrations +OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) + +CMAP +! 2D grid correction data. The following surfaces are the correction +! to the CHARMM22 phi, psi alanine, proline and glycine dipeptide surfaces. +! Use of CMAP requires generation with the topology file containing the +! CMAP specifications along with version 31 or later of CHARMM. Note that +! use of "skip CMAP" yields the charmm22 energy surfaces. +! +! references +!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Accurate Treatment of +!Protein Backbone Conformational Energetics in Empirical Force Fields, Submitted +!for publication. + +!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Improved Treatment of the +!Protein Backbone in Empirical Force Fields, Journal of the American Chemical +!Society, In Press. + + +! alanine map +C NH1 CT1 C NH1 CT1 C NH1 24 + +!-180 +0.126790 0.768700 0.971260 1.250970 2.121010 +2.695430 2.064440 1.764790 0.755870 -0.713470 +0.976130 -2.475520 -5.455650 -5.096450 -5.305850 +-3.975630 -3.088580 -2.784200 -2.677120 -2.646060 +-2.335350 -2.010440 -1.608040 -0.482250 + +!-165 +-0.802290 1.377090 1.577020 1.872290 2.398990 +2.461630 2.333840 1.904070 1.061460 0.518400 +-0.116320 -3.575440 -5.284480 -5.160310 -4.196010 +-3.276210 -2.715340 -1.806200 -1.101780 -1.210320 +-1.008810 -0.637100 -1.603360 -1.776870 + +!-150 +-0.634810 1.156210 1.624350 2.047200 2.653910 +2.691410 2.296420 1.960450 1.324930 2.038290 +-1.151510 -3.148610 -4.058280 -4.531850 -3.796370 +-2.572090 -1.727250 -0.961410 -0.282910 -0.479120 +-1.039340 -1.618060 -1.725460 -1.376360 + +!-135 +0.214000 1.521370 1.977440 2.377950 2.929470 +2.893410 2.435810 2.162970 1.761500 1.190090 +-1.218610 -2.108900 -2.976100 -3.405340 -2.768440 +-1.836030 -0.957950 0.021790 -0.032760 -0.665880 +-1.321170 -1.212320 -0.893170 -0.897040 + +!-120 +0.873950 1.959160 2.508990 2.841100 3.698960 +3.309330 2.614300 2.481720 2.694660 1.082440 +-0.398320 -1.761800 -2.945110 -3.294690 -2.308300 +-0.855480 -0.087320 0.439040 0.691880 -0.586330 +-1.027210 -0.976640 -0.467580 0.104020 + +!-105 +1.767380 2.286650 2.818030 3.065500 3.370620 +3.397440 2.730310 2.878790 2.542010 1.545240 +-0.092150 -1.694440 -2.812310 -2.802430 -1.856360 +-0.306240 -0.122440 0.444680 0.810150 -0.058630 +-0.270290 -0.178830 0.202360 0.493810 + +!-90 +1.456010 2.743180 2.589450 3.046230 3.451510 +3.319160 3.052900 3.873720 2.420650 0.949100 +0.008370 -1.382980 -2.138930 -2.087380 -1.268300 +-0.494370 0.267580 0.908250 0.537520 0.306260 +0.069540 0.097460 0.263060 0.603220 + +!-75 +1.396790 3.349090 2.180920 2.942960 3.814070 +3.675800 3.555310 3.887290 2.101260 -0.190940 +-0.732240 -1.382040 -0.673880 -0.817390 -0.826980 +-0.111800 0.053710 0.296400 0.692240 0.428960 +-0.036100 -0.033820 -0.194300 0.400210 + +!-60 +0.246650 1.229980 1.716960 3.168570 4.208190 +4.366860 4.251080 3.348110 0.997540 -1.287540 +-1.179900 -0.684300 -0.853660 -1.158760 -0.347550 +0.114810 0.242800 0.322420 0.370140 -0.374950 +-0.676940 -1.323430 -1.366650 -0.218770 + +!-45 +-1.196730 0.078060 2.347410 4.211350 5.376000 +5.364940 4.355200 2.436510 0.408470 -0.590840 +-0.435960 -0.501210 -0.822230 -0.607210 0.057910 +0.246580 -0.070570 0.379430 0.247770 -0.571680 +-1.282910 -1.715770 -1.839820 -1.987110 + +!-30 +-1.174720 1.067030 4.180460 6.741610 6.070770 +4.781470 2.758340 1.295810 0.571150 -0.196480 +0.251860 -0.732140 1.289360 1.497590 1.890550 +2.198490 0.169290 0.534000 0.331780 -1.276320 +-2.550070 -3.312150 -3.136670 -2.642260 + +!-15 +0.293590 5.588070 3.732620 3.217620 3.272450 +2.492320 1.563700 1.356760 0.831410 0.630170 +1.591970 0.821920 0.486070 0.715760 0.996020 +1.591580 -0.367400 0.181770 -0.613920 -2.267900 +-3.516460 -3.597700 -3.043340 -1.765020 + +!0 +2.832310 0.787990 0.323280 0.479230 0.628600 +0.976330 1.238750 1.671950 1.645480 2.520340 +1.606970 0.776350 0.119780 0.070390 0.121170 +-1.569230 -1.213010 -1.846360 -2.744510 -3.792530 +-3.934880 -3.615930 -2.675750 -0.924170 + +!15 +-0.778340 -1.912680 -2.052140 -1.846280 -1.047430 +0.183400 1.682950 2.223500 1.358370 2.448660 +1.436920 0.678570 -0.237060 -0.535320 -0.790380 +-2.182580 -3.251140 -4.195110 -4.269270 -3.908210 +-3.455620 -2.773970 1.755370 0.313410 + +!30 +-2.963810 -3.483730 -3.517080 -2.724860 -1.405510 +0.336200 1.428450 1.394630 0.970370 2.462720 +1.522430 0.553620 -0.407380 -1.482950 -3.613920 +-4.159810 -4.945580 -4.784040 -3.764540 -2.959140 +-1.963850 -1.071260 -1.599580 -2.445320 + +!45 +-4.029070 -3.932660 -3.558480 -2.513980 -1.037320 +0.362000 0.814380 0.754110 0.502370 1.903420 +0.770220 -0.416420 -3.286310 -3.875270 -4.907800 +-5.704430 -5.645660 -4.396040 -2.865450 -2.368170 +-2.860490 -3.416560 -3.666490 -3.859070 + +!60 +-3.338270 -2.960220 -2.311700 -1.272890 -0.246470 +0.722610 0.668070 0.438130 2.395330 1.632470 +-2.041450 -3.218100 -3.915080 -4.852510 -5.696500 +-6.314370 -5.683690 -4.170620 -3.141000 -3.508820 +-3.756430 -3.640810 -3.640430 -3.550690 + +!75 +-2.244860 -1.632100 -1.000640 -0.170440 0.526440 +0.823710 0.517140 -0.013120 -0.370910 -1.213720 +-2.305650 -3.420580 -4.484960 -5.693140 -6.199150 +-6.253870 -5.211310 -4.174380 -3.685150 -4.151360 +-4.161970 -3.725150 -3.715310 -2.606760 + +!90 +-1.720840 -1.177830 -0.428430 0.277730 0.807900 +0.803260 0.482510 -0.336900 -0.786270 -1.774070 +-2.793220 -3.828560 -5.211800 -6.636850 -6.989940 +-6.108800 -5.452410 -3.911450 -4.321000 -4.587240 +-4.102610 -3.772820 -3.157300 -2.648390 + +!105 +-1.850640 -1.092420 -0.445020 0.128490 1.005520 +0.884820 0.485850 -0.218470 -0.857670 -1.682330 +-3.014400 -4.481110 -6.053510 -6.865400 -6.871130 +-5.728240 -3.912230 -4.802110 -5.034640 -4.715990 +-4.601080 -4.086220 -3.274630 -2.410940 + +!120 +-1.969230 -1.116650 -0.540250 -0.150330 0.763520 +1.038890 0.758480 0.313530 -0.333050 -1.872770 +-3.366270 -5.008260 -6.124810 -7.034830 -6.724320 +-3.700200 -4.510620 -5.185650 -5.361620 -4.847490 +-4.444320 -4.004260 -3.415720 -2.751230 + +!135 +-2.111250 -1.168960 -0.322790 -0.006920 0.316660 +1.086270 0.939170 0.625340 -0.166360 -1.830310 +-3.469470 -4.946030 -6.112560 -1.915580 -4.047310 +-4.996740 -4.996730 -4.842690 -4.886620 -4.300540 +-4.494620 -4.442210 -4.163570 -3.183510 + +!150 +-1.757590 -0.403620 0.023920 0.362390 0.634520 +1.264920 1.361360 0.948420 -0.073680 -1.483560 +-3.152820 1.835120 -1.762860 -5.093660 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-0.756620 -1.859410 +-2.986660 -3.675410 -5.708500 -5.536170 -4.492140 +-3.715530 -1.945510 -1.105500 -1.664160 -2.345360 +-3.228630 -3.892550 -4.485310 -4.995210 + +!90 +-3.879190 -2.939990 -2.420970 -1.794480 -1.141350 +-1.020680 -1.065550 -0.971340 -1.139090 -1.898510 +-2.864390 -4.359900 -5.446890 -4.981430 -4.181160 +-2.808170 -0.971860 -1.452040 -1.975250 -2.406460 +-3.040850 -3.611370 -3.902110 -3.713610 + +!105 +-2.793280 -2.412680 -1.959970 -1.401500 -0.950190 +-0.540540 -0.467320 -0.633810 -0.893140 -1.695490 +-2.776760 -4.255190 -4.662850 -4.448210 -3.332800 +-2.567680 -1.195390 -1.681850 -1.951490 -2.266680 +-2.626630 -3.013710 -3.178150 -3.079570 + +!120 +-2.330190 -1.914850 -1.601800 -1.068330 -0.661220 +-0.297950 -0.173830 -0.158900 -0.553910 -1.455320 +-2.394430 -3.215190 -3.975820 -3.783210 -3.014390 +-0.975570 -1.358170 -1.289220 -1.435540 -1.705860 +-1.970070 -2.364070 -2.596140 -2.593790 + +!135 +-1.796120 -1.465530 -1.267450 -0.880610 -0.288370 +-0.055650 0.100910 -0.207560 -0.758950 -1.718060 +-2.220710 -2.435890 -4.372310 0.338010 -1.062570 +-1.337360 -1.020630 -0.851590 -0.801350 -0.886880 +-1.567160 -1.803720 -2.143020 -2.117750 + +!150 +-1.263610 -0.710760 -0.794980 -0.563330 -0.339050 +-0.092820 0.033160 0.000490 -0.628990 -1.664160 +-2.225630 -2.949180 0.753400 -1.546500 -2.165440 +-1.626260 -0.887080 -0.290670 -0.054220 -1.642540 +-1.119780 -1.656770 -1.665900 -1.482430 + +!165 +-0.684660 -0.477660 -0.348750 -0.462500 -0.271890 +-0.000430 0.196710 0.180860 -0.410680 -1.810120 +-2.675640 1.822690 -1.636020 -3.153350 -2.780320 +-1.715700 -0.534910 0.258100 0.329180 -0.126160 +-0.940260 -1.319240 -0.990850 -0.896700 + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!carbons +C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO + ! NMA pure solvent, adm jr., 3/3/93 +CA 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! benzene (JES) +CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO + ! adm jr. 3/3/92, acetic acid heat of solvation +CD 0.000000 -0.070000 2.000000 ! ALLOW POL + ! adm jr. 3/19/92, acetate a.i. and dH of solvation +CE1 0.000000 -0.068000 2.090000 ! + ! for propene, yin/adm jr., 12/95 +CE2 0.000000 -0.064000 2.080000 ! + ! for ethene, yin/adm jr., 12/95 +CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO + ! benzene (JES) +CS 0.000000 -0.110000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! isobutane pure solvent properties, adm jr, 2/3/92 +CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! propane pure solvent properties, adm jr, 2/3/92 +CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +CY 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! TRP, JWK 08/29/89 +! hydrogens +H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 +HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HE1 0.000000 -0.031000 1.250000 ! + ! for propene, yin/adm jr., 12/95 +HE2 0.000000 -0.026000 1.260000 ! + ! for ethene, yin/adm jr., 12/95 +HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HC 0.000000 -0.046000 0.224500 ! ALLOW POL + ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 +HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO + ! JES 8/25/89 values from Jorgensen fit to hydration energy +HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS 0.000000 -0.100000 0.450000 ! ALLOW SUL + ! methanethiol pure solvent, adm jr., 6/22/92 +!nitrogens +N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! JG 8/27/89; note: NH1 in ARG was changed to NC2. +NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +NH2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NH3 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NP 0.000000 -0.200000 1.850000 ! ALLOW PRO + ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 +NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NY 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! trp, JWK +! oxygens +O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid carbonyl O +OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) +OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 9/17/90, avoid O* wildcard +! sulfurs +S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION + ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent +SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION + ! adm jr., 3/3/92, dimethyldisulphide pure solvent +SS 0.000000 -0.470000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +!protein model compounds (see toppar_all22_prot_model.str) +C3 0.000000 -0.020000 2.275000 ! cyclopropane, JMW and CBP 4/04 + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/par_all35_ethers.prm b/charmm/toppar/par_all35_ethers.prm new file mode 100644 index 00000000..ae860956 --- /dev/null +++ b/charmm/toppar/par_all35_ethers.prm @@ -0,0 +1,254 @@ +*>>>>>>>>>>>>>>>>> All-hydrogen parameters <<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>>>>>>>>>>> CHARMM32 ether force field <<<<<<<<<<<<<<<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>> December 2006 <<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< +*>>>>>>>>>>>> via the CHARMM forum: www.charmm.org <<<<<<<<<<<<<<< +* + +!Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., +!Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude +!Polarizable Force Fields for Linear and Cyclic Ethers," Journal of +!Chemical Theory and Computing, 3: 1120-1133, 2007 +! +! O-C-C-O torsion modified; HK Lee, RM Venable, RW Pastor August 2007 +! +!Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor +!Molecular dynamics studies of polyethylene oxide and polyethylene glycol: +!Hydrodynamic radius and shape anisotropy +!Biophysical J., 95: 1590-1599, 2008 +! +! ********* V(bond) = Kb(b - b0)**2 +ATOMS +MASS 241 HCA1A 1.00800 ! Alkane H attached to C(sp3)H (eq. HA1) +MASS 242 HCA2A 1.00800 ! Alkane H attached to C(sp3)H2 (eq. HA2) +MASS 243 HCA3A 1.00800 ! Alkane H attached to C(sp3)H3 (eq. HA3) +MASS 244 HCA25A 1.00800 ! Alkane H attached to C(sp3)H2 in 5-membered ring +MASS 245 CC30A 12.01100 ! -C(sp3) Carbon (eq. CT) +MASS 246 CC31A 12.01100 ! -C(sp3)H Carbon (eq. CT1) +MASS 247 CC32A 12.01100 ! -C(sp3)H2 Carbon (eq. CT2) +MASS 248 CC33A 12.01100 ! -C(sp3)H3 Carbon (eq. CT3) +MASS 249 CC325A 12.01100 ! -C(sp3)H2 Carbon in 5-membered ring +MASS 250 CC325B 12.01100 ! -C(sp3)H2 Carbon in THF (tetrahydrofuran) +MASS 251 CC326A 12.01100 ! -C(sp3)H2 Carbon in THP (tetrahydropyran) +MASS 252 OC30A 15.99940 ! Ether Oxygen +MASS 253 OC305A 15.99940 ! Ether Oxygen in THF + +BONDS +!! Alkane standard C27 parameeters. Not modified from original. +CC31A HCA1A 309.00 1.111 ! alkanes, 4/98 +CC32A HCA2A 309.00 1.111 ! alkanes, 4/98 +CC33A HCA3A 322.00 1.111 ! alkanes, 4/98 +CC30A CC32A 222.50 1.538 ! 10/98 +CC30A CC33A 222.50 1.538 ! 10/98 +CC31A CC31A 222.50 1.500 ! alkanes, 3/92 +CC31A CC32A 222.50 1.538 ! alkanes, 3/92 +CC31A CC33A 222.50 1.538 ! alkanes, 3/92 +CC32A CC32A 222.50 1.530 ! alkanes, 3/92 +CC32A CC33A 222.50 1.528 ! alkanes, 3/92 +CC33A CC33A 222.50 1.530 ! alkanes, 3/92 +CC325A CC325A 195.00 1.548 ! cyclopentane CPEN 10/17/05 viv +CC325A HCA25A 307.00 1.116 ! cyclopentane CPEN 10/17/05 viv +CC325B OC305A 350.00 1.425 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv +CC325B CC325B 195.00 1.518 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv +CC325B HCA25A 307.00 1.100 ! THF, THF neutron diffr., 5/30/06, viv +CC325B CC33A 222.50 1.528 ! TF2M, viv +CC32A OC30A 360.00 1.415 ! DEET, diethylether, alex +CC33A OC30A 360.00 1.415 ! DEET, diethylether, alex +CC326A HCA2A 309.00 1.111 ! THP, viv +CC326A CC326A 222.50 1.530 ! THP, viv +CC326A OC30A 360.00 1.415 ! DEET, diethylether, viv + +! ********* V(angle) = Ktheta(Theta - Theta0)**2 +ANGLES +!! Alkane standard C27 parameeters. Not modified from original. +HCA1A CC31A CC31A 34.500 110.10 22.53 2.179 ! alkane, 3/92 +HCA1A CC31A CC32A 34.500 110.10 22.53 2.179 ! alkane, 3/92 +HCA1A CC31A CC33A 34.500 110.10 22.53 2.179 ! alkane, 3/92 +HCA2A CC32A CC30A 26.500 110.10 22.53 2.179 ! alkane, 4/98 +HCA2A CC32A CC31A 26.500 110.10 22.53 2.179 ! alkane, 4/98 +HCA2A CC32A CC32A 26.500 110.10 22.53 2.179 ! alkane, 4/98 +HCA2A CC32A CC33A 34.600 110.10 22.53 2.179 ! alkane, 4/98 +HCA3A CC33A CC30A 33.430 110.10 22.53 2.179 ! alkane, 4/98 +HCA3A CC33A CC31A 33.430 110.10 22.53 2.179 ! alkane, 4/98 +HCA3A CC33A CC32A 34.600 110.10 22.53 2.179 ! alkane, 4/98 +HCA3A CC33A CC33A 37.500 110.10 22.53 2.179 ! alkane, 4/98 +HCA2A CC32A HCA2A 35.50 109.00 5.40 1.802 ! alkane, 3/92 +HCA3A CC33A HCA3A 35.50 108.40 5.40 1.802 ! alkane, 3/92 +CC30A CC32A CC32A 58.350 113.50 11.16 2.561 ! glycerol +CC30A CC32A CC33A 58.350 113.50 11.16 2.561 ! glycerol +CC31A CC31A CC31A 53.350 111.00 8.00 2.561 ! alkane, 3/92 +CC31A CC31A CC32A 58.350 113.50 11.16 2.561 ! glycerol +CC31A CC31A CC33A 53.350 108.50 8.00 2.561 ! alkane, 3/92 +CC31A CC32A CC31A 58.350 113.50 11.16 2.561 ! glycerol +CC31A CC32A CC32A 58.350 113.50 11.16 2.561 ! glycerol +CC31A CC32A CC33A 58.350 113.50 11.16 2.561 ! glycerol +CC32A CC30A CC32A 58.350 113.50 11.16 2.561 ! glycerol +CC32A CC31A CC32A 58.350 113.50 11.16 2.561 ! glycerol +CC32A CC32A CC32A 58.350 113.60 11.16 2.561 ! alkane, 3/92 +CC32A CC32A CC33A 58.000 115.00 8.00 2.561 ! alkane, 3/92 +CC33A CC30A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 +CC33A CC31A CC32A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 +CC33A CC31A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 +CC33A CC32A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 +!! 5-membered ring cyclopentane (cpen) ring parameters. viv modified Oct. 05 +CC325A CC325A CC325A 58.00 106.00 11.16 2.561 ! CPEN 10/17/05 viv +HCA25A CC325A CC325A 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +HCA25A CC325A HCA25A 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv +HCA25A CC325B CC325B 35.00 111.40 22.53 2.179 ! TF2M, viv +HCA25A CC325B HCA25A 38.50 106.80 5.40 1.802 ! THF, 10/17/05 viv +CC325B CC325B CC325B 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv +OC305A CC325B CC325B 45.00 111.10 ! THF 10/21/05, viv +CC325B OC305A CC325B 95.00 111.00 ! THF 10/21/05, viv +HCA25A CC325B OC305A 70.00 107.30 ! THF 10/21/05, viv +HCA3A CC33A CC325B 34.600 110.10 22.53 2.179 ! TF2M viv +CC325B CC325B CC33A 58.000 115.00 8.00 2.561 ! TF2M viv +HCA25A CC325B CC33A 34.600 110.10 22.53 2.179 ! TF2M viv +OC305A CC325B CC33A 45.00 111.50 ! TF2M, viv +CC32A OC30A CC32A 95.00 109.70 ! DEET, diethylether, alex +CC33A OC30A CC32A 95.00 109.70 ! DEET, diethylether, alex +CC33A OC30A CC33A 95.00 109.70 ! DEET, diethylether, alex +OC30A CC32A CC32A 45.00 111.50 ! DEET, diethylether, alex +OC30A CC32A CC33A 45.00 111.50 ! DEET, diethylether, alex +HCA3A CC33A OC30A 60.00 109.50 ! phosphate, alex +HCA2A CC32A OC30A 60.00 109.50 ! phosphate, alex +HCA2A CC326A CC326A 34.500 110.10 22.53 2.179 ! THP, sng cyclohexane 12/05 +HCA2A CC326A HCA2A 35.50 109.00 5.40 1.80200! THP, viv +CC326A CC326A CC326A 58.350 112.00 11.16 2.561 ! THP, sng cyclohexane 12/05 +OC30A CC326A CC326A 45.00 111.50 ! THP, viv +CC326A OC30A CC326A 95.00 109.70 ! THP, viv +HCA2A CC326A OC30A 45.00 109.50 ! THP, sng 02/06 + +! ******** V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +DIHEDRALS +!! Alkane standard C27 parameters. Not modified from original. +CC31A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 +CC32A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 +CC33A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 +CC31A CC30A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 +CC32A CC30A CC32A HCA3A 0.20000 3 0.00 ! alkane, 3/92 +CC33A CC30A CC32A HCA3A 0.20000 3 0.00 ! alkane, 3/92 +HCA1A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92 +CC31A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92 +CC32A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92 +CC33A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92 +HCA1A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 +HCA1A CC31A CC32A CC31A 0.20000 3 0.00 ! alkane, 3/92 +HCA1A CC31A CC32A CC32A 0.20000 3 0.00 ! alkane, 3/92 +HCA1A CC31A CC32A CC33A 0.20000 3 0.00 ! alkane, 3/92 +CC31A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 +CC32A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 +CC33A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 +HCA1A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 +CC31A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 +CC32A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 +CC33A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 +HCA2A CC32A CC32A HCA2A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell +CC30A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell +CC31A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell +CC32A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell +CC33A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell +HCA2A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell +CC30A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell +CC31A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell +CC32A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell +CC33A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell +CC33A CC32A CC32A CC33A 0.03179 6 180.0 ! alkane, c27r klauda et al 2004 +CC33A CC32A CC32A CC33A 0.03819 2 0.0 ! alkane, c27r klauda et al 2004 +CC33A CC32A CC32A CC32A 0.20391 5 0.0 ! alkane, c27r klauda et al 2004 +CC33A CC32A CC32A CC32A 0.10824 4 0.0 ! alkane, c27r klauda et al 2004 +CC33A CC32A CC32A CC32A 0.08133 3 180.0 ! alkane, c27r klauda et al 2004 +CC33A CC32A CC32A CC32A 0.15051 2 0.0 ! alkane, c27r klauda et al 2004 +CC32A CC32A CC32A CC32A 0.11251 5 0.0 ! alkane, c27r klauda et al 2004 +CC32A CC32A CC32A CC32A 0.09458 4 0.0 ! alkane, c27r klauda et al.2004 +CC32A CC32A CC32A CC32A 0.14975 3 180.0 ! alkane, c27r klauda et al 2004 +CC32A CC32A CC32A CC32A 0.06450 2 0.0 ! alkane, c27r klauda et al 2004 +CC33A CC325A CC325A CC33A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv +CC33A CC325A CC325A CC325A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv +CC33A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv +HCA25A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv +CC325A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv +CC325A CC325A CC325A CC325A 0.41000 3 180.0 ! cpen, cyclopentane, viv 10/4/05 +CC33A CC325B CC325B CC33A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv +CC33A CC325B CC325B CC325B 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv +CC33A CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv +HCA25A CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv +CC325B CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv +OC305A CC325B CC325B HCA25A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell, thf viv +HCA25A CC325B CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv +CC325B CC325B CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv +OC305A CC325B CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv +CC325B CC325B CC325B CC325B 0.41000 3 180.0 ! CPEN viv 10/4/05 +HCA25A CC325B OC305A CC325B 0.3000 3 0.0 ! THF, 05/30/06, viv +OC305A CC325B CC325B CC325B 0.0000 3 0.0 ! THF, 05/30/06, viv +CC325B CC325B OC305A CC325B 0.5000 3 0.0 ! THF, 05/30/06, viv +CC33A CC325B OC305A CC325B 0.3000 3 0.0 ! THF, 05/30/06, viv +CC33A CC326A CC326A CC33A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv +CC33A CC326A CC326A CC326A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv +CC33A CC326A CC326A HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv +HCA2A CC326A CC326A HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv +HCA2A CC326A CC326A CC326A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv +OC30A CC326A CC326A HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp viv +HCA2A CC326A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv +CC326A CC326A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv +OC30A CC326A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv +CC326A CC326A CC326A CC326A 0.49829 2 0.0 ! THP, viv +CC326A CC326A CC326A CC326A -0.59844 3 0.0 ! THP, viv +CC326A CC326A CC326A CC326A 0.41746 4 0.0 ! THP, viv +CC326A CC326A CC326A CC326A -0.24829 5 0.0 ! THP, viv +OC30A CC326A CC326A CC326A -0.19225 1 0.0 ! THP, sng 1/06 +OC30A CC326A CC326A CC326A -1.00000 2 0.0 ! THP, sng 1/06 +OC30A CC326A CC326A CC326A 0.59457 3 0.0 ! THP, sng 1/06 +OC30A CC326A CC326A CC326A -0.07862 4 0.0 ! THP, sng 1/06 +HCA3A CC33A CC33A HCA3A 0.15250 3 0.00 ! ETHA, ethane, 4/98, yin and mackerell +CC326A OC30A CC326A CC326A -0.52702 1 0.0 ! THP, sng 1/06 +CC326A OC30A CC326A CC326A 0.68297 2 0.0 ! THP, sng 1/06 +CC326A OC30A CC326A CC326A -0.20977 3 0.0 ! THP, sng 1/06 +CC326A OC30A CC326A CC326A 0.15037 4 0.0 ! THP, sng 1/06 +CC326A OC30A CC326A HCA2A 0.28400 3 0.0 ! DMET, viv +HCA2A CC32A CC32A OC30A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell +OC30A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell +HCA2A CC32A OC30A CC32A 0.28400 3 0.0 ! DEET, diethylether, alex +HCA3A CC33A OC30A CC32A 0.28400 3 0.0 ! DEET, diethylether, alex +HCA2A CC32A OC30A CC33A 0.28400 3 0.0 ! DEET, diethylether, alex +HCA3A CC33A OC30A CC33A 0.28400 3 0.0 ! DME, viv +CC33A CC32A OC30A CC32A 0.40 1 0.0 ! diethylether, 2/12/05, ATM +CC33A CC32A OC30A CC32A 0.49 3 0.0 ! diethylether +CC33A CC32A OC30A CC33A 0.40 1 0.0 ! diethylether, 2/12/05, ATM, MEE viv +CC33A CC32A OC30A CC33A 0.49 3 0.0 ! diethylether, MEE viv +CC32A CC32A OC30A CC33A 0.57 1 0.0 ! 1,2 dimethoxyethane (DME), 2/12/05, ATM +CC32A CC32A OC30A CC33A 0.29 2 0.0 ! 1,2 dimethoxyethane (DME) +CC32A CC32A OC30A CC33A 0.43 3 0.0 ! 1,2 dimethoxyethane (DME) +CC32A CC32A OC30A CC32A 0.57 1 0.0 ! 1,2 dimethoxyethane, 2/12/05, ATM +CC32A CC32A OC30A CC32A 0.29 2 0.0 ! 1,2 dimethoxyethane +CC32A CC32A OC30A CC32A 0.43 3 0.0 ! 1,2 dimethoxyethane +OC30A CC32A CC32A OC30A 0.59 1 180.0 ! 1,2 dimethoxyethane, Aug 2007, HK Lee +OC30A CC32A CC32A OC30A 1.16 2 0.0 ! 1,2 dimethoxyethane +OC30A CC32A CC32A CC33A 0.16 1 180.0 ! methylpropylether, 2/12/05, ATM +OC30A CC32A CC32A CC33A 0.39 2 0.0 ! methylpropylether +OC30A CC32A CC32A CC32A 0.16 1 180.0 ! methylpropylether, 2/12/05, ATM +OC30A CC32A CC32A CC32A 0.39 2 0.0 ! methylpropylether + + +!********* V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 + +HCA1A 0.0 -0.0450 1.3400 ! alkane,isobutane 1/5/05 viv +HCA2A 0.0 -0.0350 1.3400 ! alkane,propane 11/16/04 viv +HCA3A 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 +!HT 0.0 -0.0460 0.2245 ! TIP3P water +CC30A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! from CC31A +CC31A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC32A 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CC33A 0.0 -0.0780 2.0400 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CC326A 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! THP, tetrahyropyran, viv +HCA25A 0.0 -0.0350 1.3000 ! CPEN, cyclopentane, 8/06 viv +CC325A 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv +CC325B 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv +OC305A 0.0 -0.1000 1.6500 ! THP, tetrahydropyran sng 1/06 +OC30A 0.0 -0.1000 1.6500 ! THP, tetrahydropyran sng 1/06 + +END + + + diff --git a/charmm/toppar/par_all36_carb.prm b/charmm/toppar/par_all36_carb.prm new file mode 100644 index 00000000..1ac26cda --- /dev/null +++ b/charmm/toppar/par_all36_carb.prm @@ -0,0 +1,2628 @@ +* $Id: par_allxx_sugar.inp,v 1.132 2014/08/19 19:03:21 alex Exp $ +*>>>>>>>>>>>> All-hydrogen parameters used in the <<<<<<<<<<<<<<<< +*>>>>> development of the CHARMM carbohydrate force field<<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>>>>> June 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< +*>>>>>>>>>> via the CHARMM web site: www.charmm.org <<<<<<<<<<<<<< +*>>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<< +* + +! please reference the following: + +! pyranose monosaccharides +!Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M., +!Pastor, R.W., MacKerell, Jr., A.D. "Additive empirical force field for +!hexopyranose monosaccharides," Journal of Computational Chemistry, 29: +!2543-2564, 2008. PMID: 18470966 + +! linear sugars, sugar alcohols, and inositol +!Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. "CHARMM Additive +!All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates +!and Inositol," Journal of Chemical Theory and Computation, 5: +!1315-1327, 2009, DOI: 10.1021/ct9000608. + +! hexopyranose glycosidic linkages +!Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell, Jr., +!A. D. "Additive Empirical CHARMM Force Field for glycosyl linked +!hexopyranoses," Journal of Chemical Theory and Computation, 5, +!2353-2370, 2009, DOI: 10.1021/ct900242e + +! furanose monosaccharides +!Hatcher, E. R.; Guvench, O. and MacKerell, Jr., A.D. +!"CHARMM Additive All-Atom Force Field for Aldopentofuranose +! Carbohydrates and Fructofuranose." Journal of Physical Chemistry B. +! 113:12466-76, 2009, PMID: 19694450 + +! glycosidic linkages involving furanoses +!Raman, E. P., Guvench, O., MacKerell, Jr., A.D., "CHARMM Additive All-Atom +!Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses," +!Journal of Physical Chemistry B, 114: 12981-12994, 2010, PMID: 20845956 + +! carbohydrate derivatives and glycosidic linkages for glycoproteins +!Guvench, O.; Mallajosyula, S. S.; Raman, E. P.; Hatcher, E. R.; +!Vanommeslaeghe, K.; Foster, T. J.; Jamison, F. W. and MacKerell, Jr., A.D., +!"CHARMM additive all-atom force field for carbohydrate derivatives and its +!utility in polysaccharide and carbohydrate-protein modeling," +!Journal of Chemical Theory and Computation 2011 7 (10), 3162-3180 + +!O-glycan linkages +!Mallajosyula, S. S. and MacKerell, Jr., A.D., "Influence of Solvent and +!Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked +!Glycopeptides," +!The Journal of Physical Chemistry B 2011 115 (38), 11215-11229. + +! Phosphates and sulfates +! Mallajosyula, S. S.; Guvench, O; Hatcher E. R. and MacKerell, Jr., A.D., +! "CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates" +! Journal of Chemical Theory and Computation 2012 8 (2), 759-776. + + +! adm: Alex MacKerell +! sng: Shannon Greene +! og: Olgun Guvench +! erh: Elizabeth Hatcher +! rmv: Rick Venable +! viv: Igor Vorobyov +! pram: E.Prabhu Raman +! sai: Sairam S. Mallajosyula +! my: Mingjun Yang +! par22: par_all22_prot.inp +! par27: par_all27_lipid.prm +! par35: par_all35_ethers.prm + + +ATOMS +! tip3p water +!MASS 1 HCTIP3 1.00800 ! TIP3P water hydrogen +!MASS 2 OCTIP3 15.99940 ! TIP3P water oxygen + +! C6H12O6 pyranose monosaccharide atom types +MASS 171 CC301 12.01100 ! aliphatic C, no H's +MASS 172 CC311 12.01100 ! generic acyclic CH carbon +MASS 173 CC312 12.01100 ! CH carbon in linear polyols +MASS 174 CC3161 12.01100 ! C2, C3, C4 CH bound to OH +MASS 175 CC3162 12.01100 ! C1 (anomeric) CH bound to OH +MASS 176 CC3163 12.01100 ! C5 CH bound to exocylic CH2OH +MASS 177 CC321 12.01100 ! generic acyclic CH2 carbon (hexopyranose C6) +MASS 178 CC322 12.01100 ! CH2 carbon in linear polyols erh +MASS 179 CC3263 12.01100 ! C5 in xylose +MASS 180 CC331 12.01100 ! generic acyclic CH3 carbon (xyl C6, glcna/galna CT) +MASS 181 CC2O1 12.01100 ! sp2 carbon in amides, aldoses +MASS 182 CC2O2 12.01100 ! sp2 carbon in carboxylates +MASS 183 CC2O3 12.01100 ! sp2 carbon in acetone, ketoses +MASS 184 CC2O4 12.01100 ! c22 CD +MASS 185 HCA1 1.00800 ! aliphatic proton, CH +MASS 186 HCA2 1.00800 ! aliphatic proton, CH2 +MASS 187 HCA3 1.00800 ! aliphatic proton, CH3 +MASS 188 HCP1 1.00800 ! polar H +MASS 189 HCR1 1.00800 ! c22 HR1 +MASS 191 OC311 15.99940 ! hydroxyl oxygen +MASS 192 OC3C61 15.99940 ! ether in six membered ring +MASS 193 OC301 15.99940 ! generic linear ether +MASS 194 OC302 15.99940 ! linear ether in 1-1 glycosidic linkage +MASS 195 OC2D1 15.99940 ! sp2 oxygen in amides, aldoses +MASS 196 OC2D2 15.99940 ! sp2 oxygen in carboxylates +MASS 197 OC2D3 15.99940 ! sp2 oxygen in acetone, ketoses +MASS 198 OC2D4 15.99940 ! par22 O +MASS 200 NC2D1 14.00700 ! peptide, NMA, IPAA nitrogen (C=NHR) +! model compound atom types +MASS 201 CC321C 12.01100 ! cyclohexane, thp CH2 +MASS 202 HCA3M 1.00800 ! alcohol aliphatic proton, CH3 +MASS 203 HCP1M 1.00800 ! EGLY hydroxyl H +MASS 204 OC311M 15.99940 ! MEOH, ETOH, PRO2, EGLY hydroxyl O +MASS 205 CC321D 12.01100 ! cyclohexane, thp CH2 model for 1-1 linkage +MASS 206 CC311C 12.01100 ! patch C1 in model compound +MASS 207 CC311D 12.01100 ! patch C1 in model compound +! THF atom types +MASS 208 OC3C5M 15.99940 ! thf ring oxygen +MASS 209 CC322C 12.01100 ! cyclopentane, thf CH2 +MASS 210 HCA2C2 1.00800 ! cyclopentane, thp aliphatic proton, CH2 +MASS 211 CC312C 12.01100 ! tf2m CH1 +MASS 212 HCA1C2 1.00800 ! tf2m aliphatic proton, CH1 +! Furanose atom types; erh 10/24/07 +MASS 213 OC3C51 15.99940 ! furan ring oxygen +MASS 214 CC3152 12.01100 ! furan ring carbon +MASS 215 CC3153 12.01100 ! furan ring carbon +MASS 216 CC3251 12.01100 ! furan ring carbon; C2 deoxy +MASS 217 CC3151 12.01100 ! furan ring carbon +MASS 218 CC3051 12.01100 ! furan ring carbon; C2 fructose +! pyranose derivatives +MASS 219 CC3062 12.01100 ! C2 on NE5AC +MASS 220 CC3261 12.01100 ! C3 on NE5AC +!Added by sai for modelling phosphate +MASS 221 OC312 15.99940 ! OH in PO3H (phosphate) || OHL in top_all27_lipid.rtf +MASS 222 OC30P 15.99940 ! ester O in PO3H (phosphate) || OSL in top_all27_lipid.rtf +MASS 223 OC2DP 15.99940 ! =0 in P03H (phosphate) || O2L in top_all27_lipid.rtf +MASS 224 PC 30.97400 ! phosphorus || PL in top_all27_lipid.rtf +MASS 225 SC 32.06000 ! Sulfate sulfur +!pram, furanosyl linkages +MASS 226 CC312D 12.01100 ! from CC322C; THF anomeric carbon +MASS 227 OC303 15.99940 ! from OC301; linear ether in P1->F3 pyranose-furanose glycosidic linkage +!o-acetyl on ABEQ and ARHM, my +MASS 228 CC2O5 12.01100 ! carbonyl C on acetyl + +BONDS +!V(bond) = Kb(b - b0)**2 +!Kb: kcal/mole/A**2 +!b0: A +! +! atom types Kb b0 +! +! aldose, ketose, new!!!!! adm, 11/08 +OC2D3 CC2O3 700.00 1.215 ! ketone MP2/6-31g*, CSD geometry +CC2O3 CC331 330.00 1.500 ! ketone MP2/6-31g*, CSD geometry +CC2O3 CC312 330.00 1.500 ! ketone +CC2O3 CC322 330.00 1.500 ! ketone +OC2D4 CC2O4 700.00 1.215 ! acetaldehyde, adm +HCR1 CC2O4 330.00 1.110 ! acetaldehyde, adm +CC2O4 CC331 250.00 1.500 ! acetaldehyde, adm +CC2O4 CC312 250.00 1.500 ! acetaldehyde, adm +! monosaccharide CC +CC311 CC311 222.50 1.500 ! par22 CT1 CT1 +CC312 CC312 222.50 1.485 ! adm 11/08, glycerol +CC3161 CC3163 222.50 1.500 ! par22 CT1 CT1 +CC3161 CC3263 222.50 1.500 ! CC3161 CC3163 og xtal xylose +CC312 CC322 222.50 1.485 ! adm 11/08, glycerol +CC301 CC331 222.50 1.538 ! genff CG301 CG331 +CC311 CC321 222.50 1.538 ! par22 CT2 CT1 +CC311 CC331 222.50 1.538 ! par22 CT3 CT1 +CC331 CC3163 222.50 1.538 ! par22 CT3 CT1 og xtal alfuco +CC3161 CC3161 222.50 1.480 ! sng qm and crystal analysis +CC3261 CC3161 222.50 1.480 ! from CC3161 CC3161 +CC3161 CC3162 222.50 1.480 ! sng qm and crystal analysis +CC3261 CC3062 222.50 1.515 ! og xtal kemyac +CC321 CC3163 222.50 1.490 ! sng qm and crystal analysis +CC312 CC3163 222.50 1.490 ! from CC321 CC3163 +CC301 CC2O2 200.00 1.522 ! par22 CT1 CC +CC311 CC2O2 200.00 1.522 ! par22 CT1 CC +CC3163 CC2O2 200.00 1.480 ! og xtal +CC3062 CC2O2 200.00 1.480 ! og xtal +CC2O1 CC331 250.00 1.520 ! og ipaa and xtal acglua11 agalam10 nacman10 +! model compound CC +CC321 CC331 222.50 1.528 ! par22 CT3 CT2 +CC321 CC321 222.50 1.530 ! par22 CT2 CT2 +CC321C CC321C 222.50 1.530 ! par22 CT2 CT2 +CC321C CC321D 222.50 1.530 ! par22 CT2 CT2 +CC321C CC311C 222.50 1.538 ! par22 CT2 CT1 +CC321 CC311C 222.50 1.490 ! from CC321 CC3163 +CC321C CC311D 222.50 1.538 ! par22 CT2 CT1 +CC321D CC311C 222.50 1.538 ! par22 CT2 CT1 +CC321 CC2O2 200.00 1.522 ! par22 CT2 CC + +! CO +! hydroxyls +CC3161 OC311 410.00 1.410 ! og crystal analysis +CC3162 OC311 428.00 1.400 ! og crystal analysis +CC3062 OC311 428.00 1.400 ! from CC3162 OC311 +CC301 OC311 428.00 1.420 ! par22 OH1 CT1 +CC311 OC311 428.00 1.420 ! par22 OH1 CT1 +CC312 OC311 400.00 1.420 ! adm 11/08, glycerol +CC311 OC311M 428.00 1.420 ! par22 OH1 CT1 +CC321 OC311 428.00 1.420 ! par22 OH1 CT2 +CC321 OC311M 428.00 1.420 ! par22 OH1 CT2 +CC331 OC311M 428.00 1.420 ! par22 OH1 CT3 +CC322 OC311 400.00 1.420 ! adm 11/08, glycerol +! sp2 +CC2O1 OC2D1 620.00 1.230 ! par22 O C +CC2O2 OC2D2 525.00 1.260 ! par22 OC CC +! ethers +CC301 OC301 360.00 1.415 ! par35 CC32A OC30A +CC311 OC301 360.00 1.415 ! par35 CC32A OC30A +CC321 OC301 360.00 1.415 ! par35 CC32A OC30A +CC331 OC301 360.00 1.415 ! par35 CC33A OC30A +CC311D OC301 360.00 1.395 ! og disac model compounds 2 and 3 +CC3162 OC301 360.00 1.395 ! og disac model compounds 2 3 og/rmv crystals +CC3062 OC301 360.00 1.395 ! from CC3162 OC301 +CC311D OC302 360.00 1.415 ! og disac model compounds 4 5 6 +CC3162 OC302 360.00 1.415 ! og disac model comps 4 5 6 og/rmv crystals +CC311C OC301 360.00 1.435 ! og disac model compounds 7 8 9 and 10 +CC3161 OC301 360.00 1.415 ! og/rmv disac crystals +! pyran ring ethers +CC321D OC3C61 360.00 1.415 ! par34 CC326A OC30A +CC311D OC3C61 360.00 1.415 ! par34 CC326A OC30A +CC3162 OC3C61 360.00 1.425 ! og crystal analysis +CC3062 OC3C61 360.00 1.425 ! from CC3162 OC3C61 +CC321C OC3C61 360.00 1.415 ! par34 CC326A OC30A +CC311C OC3C61 360.00 1.415 ! par34 CC326A OC30A +CC3163 OC3C61 360.00 1.425 ! sng qm and crystal analysis +CC3263 OC3C61 360.00 1.425 ! CC3263 OC3C61 og xylose xtal ok + +! CN +NC2D1 CC311 320.00 1.430 ! par22 NH1 CT1 +NC2D1 CC3161 320.00 1.430 ! par22 NH1 CT1 +NC2D1 CC331 320.00 1.430 ! par22 NH1 CT3 +NC2D1 CC2O1 370.00 1.345 ! par22 NH1 C + +! CH +CC311 HCA1 309.00 1.111 ! par22 HA CT1 +CC312 HCA1 309.00 1.111 ! par22 HA CT1 +CC3161 HCA1 309.00 1.111 ! par22 HA CT1 +CC3162 HCA1 309.00 1.111 ! par22 HA CT1 +CC3163 HCA1 309.00 1.111 ! par22 HA CT1 +CC311C HCA1 309.00 1.111 ! par22 HA CT1 +CC311D HCA1 309.00 1.111 ! par22 HA CT1 +CC321 HCA2 309.00 1.111 ! par22 HA CT2 +CC322 HCA2 309.00 1.111 ! par22 HA CT2 +CC3263 HCA2 309.00 1.111 ! par22 HA CT2 +CC331 HCA3 322.00 1.111 ! par22 HA CT3 +CC321C HCA2 309.00 1.111 ! par22 HA CT2 +CC321D HCA2 309.00 1.111 ! par22 HA CT2 +CC3261 HCA2 309.00 1.111 ! par22 HA CT2 + +! OH +OC311 HCP1 545.00 0.960 ! par22 OH1 H +OC311M HCP1 545.00 0.960 ! par22 OH1 H +OC311M HCP1M 545.00 0.960 ! par22 OH1 H + +! NH +NC2D1 HCP1 440.00 0.997 ! par22 NH1 H + +! THF parameters for furanoses; viv, added by erh +CC322C OC3C5M 350.00 1.425 ! par34 CC325B OC305A +CC322C CC322C 195.00 1.518 ! par34 CC325B CC325B +CC322C HCA2C2 307.00 1.100 ! par34 CC325B HCA25A +! THF w/methyl for furanoses; viv, +! erh added and corrected for atom type, giving better pure solvent results 7/08 +CC312C CC331 222.50 1.528 ! par34 CC325B CC33A +CC312C OC3C5M 350.00 1.425 ! par34 CC325B OC305A +CC312C CC322C 195.00 1.518 ! par34 CC325B CC325B +CC312C HCA1C2 307.00 1.100 ! par34 CC325B HCA25A + +! OMe-THF param for omef patch +CC312C OC301 360.00 1.395 ! erh xtal analysis on disac + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! monosaccharide furanoses; erh modified 10/25/07!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! CO +OC3C51 CC3152 350.00 1.425 ! par34 CC325B OC305A +OC3C51 CC3051 350.00 1.425 ! par34 CC325B OC305A +OC3C51 CC3153 350.00 1.425 ! par34 CC325B OC305A +OC311 CC3152 428.00 1.395 ! erh crystal analysis on furanose 3/09 +OC311 CC3051 428.00 1.395 ! erh crystal analysis on furanose 3/09 +OC311 CC3151 410.00 1.395 ! erh crystal analysis on furanose 3/09 + +! CH +CC3152 HCA1 309.00 1.111 ! par22 HA CT1 +CC3251 HCA2 307.00 1.100 ! par_carb CC322C HCA2C2 +CC3151 HCA1 309.00 1.111 ! par22 HA CT1 +CC3153 HCA1 309.00 1.111 ! par22 HA CT1 + +! CC +CC3152 CC3251 195.00 1.508 ! erh crystal analysis on furanose 3/09 +CC3051 CC3251 195.00 1.508 ! erh crystal analysis on furanose 3/09 +CC3251 CC3151 195.00 1.508 ! erh crystal analysis on furanose 3/09 +CC3151 CC3153 195.00 1.508 ! erh crystal analysis on furanose 3/09 +CC3151 CC3152 195.00 1.508 ! erh crystal analysis on furanose 3/09 +CC3151 CC3051 195.00 1.508 ! erh crystal analysis on furanose 3/09 +CC3151 CC3151 195.00 1.508 ! erh crystal analysis on furanose 3/09 +CC3153 CC321 222.50 1.490 ! par_carb CC321 CC3163 (sng qm/crystal mod); erh 2/09 +CC3051 CC321 222.50 1.490 ! par_carb CC321 CC3163 (sng qm/crystal mod); erh 2/09 + +! OMe-furanose param for fomea/b patch +CC3152 OC301 360.00 1.395 ! erh xtal analysis on disac + +!*******************end of furanoses************************************ +!Added by sai for modelling phosphate + +CC321D CC311D 222.50 1.538 ! par22 CT2 CT1 +CC311D CC311D 222.50 1.538 ! par22 CT2 CT1 +CC3161 OC30P 360.00 1.425 ! +CC311D OC30P 360.00 1.425 ! +CC3162 OC30P 360.00 1.425 ! +CC321 OC30P 360.00 1.452 ! + +OC30P PC 270.0 1.675 ! +OC2DP PC 580.0 1.525 ! +OC312 PC 237.0 1.61 ! + +OC312 HCP1 545.0 0.960 ! + +SC OC2DP 540.0 1.448 ! methylsulfate +SC OC30P 250.0 1.610 ! methylsulfate + +!*******************end of phosphates*********************************** + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! pyranose/furanose-furanose linkages, pram +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +!model compounds +CC312D OC301 360.00 1.395 ! OMe-THF CC312C OC301 +CC312D OC3C5M 350.00 1.425 ! OMe-THF CC312C OC3C5M +CC312D CC322C 195.00 1.518 ! THF w/me CC312C CC322C +CC312D HCA1 307.00 1.100 ! THF w/me CC312C HCA1C2 +CC312D OC302 360.00 1.425 ! pram, modified (from OMe-THF) to match model comp 1(raman et al.) QM minima geometry and SUCROS04 crystal +CC312C HCA1 307.00 1.100 ! THF w/me CC312C HCA1C2 +CC312C CC321 222.50 1.500 ! pram, modified 12/26/2010 (from THF w/me) to match model comp 2(raman et al.) QM minima geometry +CC331 OC303 360.00 1.415 ! Ome-THF CC331 OC301 +CC312C OC303 360.00 1.425 ! pram, modified (from OMe-THF) to match model comp 3(raman et al.) QM minima geometry +CC311D OC303 360.00 1.395 ! CC311D OC301 + +!full sugars +CC3051 OC302 360.00 1.425 ! CC312D OC301 - model compound 1 (raman et. al.), crystal analysis +CC3162 OC303 360.00 1.395 ! CC311D OC303 - model compound 3 (raman et. al.) +OC303 CC3151 360.00 1.425 ! CC312C OC303 - model compound 3 (raman et. al.) +OC301 CC3051 360.00 1.395 ! CC312C OC301 - Ome-THF + +!!!!!!disialic acid!!!!!!, Mingjun +OC301 CC312 400.00 1.420 ! from CC312 OC311 +OC301 CC322 400.00 1.420 ! from CC312 OC311 +!O-acetyl on ARHM and ABEQ +CC2O5 OC301 150.00 1.3340 ! CG2O2 OG302 +CC2O5 CC331 200.00 1.5220 ! CG2O2 CG331 +CC2O5 OC2D1 750.00 1.2200 ! CG2O2 OG2D1 + +!*******************end of pyranose-fruanose**************************** + +! Original TIP3P water parameters +!HCTIP3 HCTIP3 0.00 1.5139 ! TIPS3P GEOMETRY (FOR SHAKE/W PARAM) +!OCTIP3 HCTIP3 450.00 0.9572 ! TIPS3P GEOMETRY + +!****************** ANGLES ************ +ANGLES +!V(angle) = Ktheta(Theta - Theta0)**2 +!V(Urey-Bradley) = Kub(S - S0)**2 +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +! atom types Ktheta Theta0 Kub S0 +! +! polyol, aldose, ketose, new!!!!! adm, 11/08 +CC311 CC311 CC321 53.35 111.00 8.00 2.561 ! par22 CT2 CT1 CT1 +CC322 CC312 CC322 45.00 111.00 ! adm 11/08, glycerol +CC312 CC312 CC322 45.00 111.00 ! adm 11/08, glycerol +CC312 CC2O3 OC2D3 75.00 121.50 ! ketone, par22 O CD CT2 +CC331 CC2O3 OC2D3 75.00 121.50 ! ketone, par22 aldehydes.str +CC322 CC2O3 OC2D3 75.00 121.50 ! ketone, par22 O CD CT2 +CC331 CC2O3 CC331 35.00 116.00 ! ketone, C-C-C +CC312 CC2O3 CC322 35.00 116.00 ! ketone +CC322 CC2O3 CC322 35.00 116.00 ! ketone +CC312 CC312 CC2O3 60.00 113.80 ! ketone, par22 str CT3 CT2 CD +CC2O3 CC331 HCA3 50.00 109.50 ! ketone +CC2O3 CC322 HCA2 50.00 109.50 ! ketone, par22 HB CT2 CD +HCA1 CC312 CC2O3 50.00 109.50 ! ketone, par22 HB CT1 CD +OC311 CC312 CC2O3 55.00 108.89 ! ketone, og 1/06 EtOH NIST IR fit +CC2O3 CC322 OC311 55.00 108.89 ! ketone, og 1/06 EtOH NIST IR fit + +OC2D4 CC2O4 HCR1 65.00 118.00 ! acetaldehyde, adm +HCR1 CC2O4 CC331 65.00 116.00 ! acetaldehyde, adm +HCR1 CC2O4 CC312 65.00 116.00 ! acetaldehyde, adm + +CC312 CC2O4 OC2D4 45.00 126.00 ! acetaldehyde, adm +CC331 CC2O4 OC2D4 45.00 126.00 ! acetaldehyde, adm + +CC312 CC312 CC2O4 60.00 113.80 ! aldehyde, par22 CT3 CT2 CD +OC311 CC312 CC2O4 55.00 108.89 ! aldehyde, og 1/06 EtOH NIST IR fit +CC2O4 CC312 HCA1 33.00 109.50 30.00 2.16300 ! acetaldehyde, adm +CC2O4 CC331 HCA3 33.00 109.50 30.00 2.16300 ! acetaldehyde, adm + +! monosacharide CCC +CC3161 CC3161 CC3161 53.35 111.00 8.00 2.561 ! par22 CT1 CT1 CT1 +CC3261 CC3161 CC3161 53.35 111.00 8.00 2.561 ! par22 CT2 CT1 CT1 +CC3161 CC3161 CC3163 53.35 111.00 8.00 2.561 ! par22 CT1 CT1 CT1 +CC3161 CC3161 CC3263 53.35 111.00 8.00 2.561 ! par22 CT1 CT1 CT1; erh transferred by analogy +CC312 CC312 CC312 45.00 111.00 ! adm 11/08, glycerol +CC3162 CC3161 CC3161 53.35 111.00 8.00 2.561 ! par22 CT1 CT1 CT1 +CC3163 CC312 CC312 53.35 111.00 8.00 2.561 ! par22 CT1 CT1 CT1 +CC3062 CC3261 CC3161 58.35 113.50 11.16 2.561 ! par22 CT1 CT2 CT1 +CC3161 CC3163 CC321 58.35 113.50 11.16 2.561 ! sng +CC3161 CC3163 CC312 58.35 113.50 11.16 2.561 ! from CC3161 CC3163 CC321 +CC3161 CC3163 CC331 58.35 113.50 11.16 2.561 ! CC3161 CC3163 CC321 og xylose xtal ok +CC2O2 CC311 CC331 52.00 108.00 ! par22 CT3 CT1 CC +CC2O2 CC3163 CC3161 52.00 108.00 ! par22 CT1 CT1 CC +CC2O2 CC301 CC331 52.00 112.00 ! og amol mp2/6-31g* +CC2O2 CC3062 CC3261 52.00 112.00 ! from CC2O2 CC301 CC331 for ne5ac +! other +CC321 CC321 CC321 58.35 113.60 11.16 2.561 ! par22 CT2 CT2 CT2 +CC331 CC321 CC321 58.00 115.00 8.00 2.561 ! par22 CT3 CT2 CT2 +CC331 CC311 CC331 53.35 114.00 8.00 2.561 ! par22 CT3 CT1 CT3 +CC321C CC321C CC321C 58.35 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC321C CC311C CC321C 58.35 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC321D CC321C CC311C 58.35 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC321D CC311C CC321C 58.35 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC321D CC321C CC321C 58.35 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC311D CC321C CC321C 58.35 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC311C CC321C CC321C 58.35 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC321C CC321D CC321C 58.35 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC321 CC311C CC321C 58.35 113.50 11.16 2.561 ! from CC3161 CC3163 CC321 +CC2O2 CC321 CC331 52.00 108.00 ! par22 CT2 CT2 CC + +! monosacharide CCH +CC312 CC312 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT1 +CC312 CC3163 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT1 +CC3161 CC3161 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT1 +CC3161 CC3162 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT1 +CC3261 CC3161 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +CC3162 CC3161 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT1 +CC3163 CC3161 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT1 +CC3161 CC3163 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT1 +CC3163 CC312 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT1 +CC322 CC312 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +CC321 CC3163 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +CC331 CC311 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT3 +CC331 CC3163 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT3 +CC3263 CC3161 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +CC321 CC311 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +CC312 CC322 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1 +CC3163 CC321 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1 +CC3062 CC3261 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1 +CC3161 CC3261 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1 +CC311 CC321 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1 +CC3161 CC3263 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1 +CC3163 CC331 HCA3 33.43 110.10 22.53 2.179 ! par22 HA CT3 CT1 +CC311 CC331 HCA3 33.43 110.10 22.53 2.179 ! par22 HA CT3 CT1 +CC301 CC331 HCA3 33.43 110.10 22.53 2.179 ! par22 HA CT3 CT1 +CC2O2 CC3163 HCA1 50.00 109.50 ! par 22 HB CT1 CC +CC2O2 CC311 HCA1 50.00 109.50 ! par 22 HB CT1 CC +CC2O1 CC331 HCA3 33.00 109.50 30.00 2.163 ! par22 HA CT3 C +! model compound CCH +HCA1 CC311C CC321 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +HCA1 CC311D CC321C 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +HCA1 CC311C CC321C 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +HCA1 CC311C CC321D 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 +HCA2 CC321 CC311C 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1 +HCA2 CC321 CC321 26.50 110.10 22.53 2.179 ! par22 HA CT2 CT2 +HCA2 CC321 CC331 34.60 110.10 22.53 2.179 ! par22 HA CT2 CT3 +HCA3 CC331 CC321 34.60 110.10 22.53 2.179 ! par22 HA CT3 CT2 +HCA2 CC321C CC321C 34.50 110.10 22.53 2.179 ! sng cyclohexane 12/05 +HCA2 CC321D CC321C 34.50 110.10 22.53 2.179 ! sng cyclohexane 12/05 +HCA2 CC321C CC321D 34.50 110.10 22.53 2.179 ! sng cyclohexane 12/05 +HCA2 CC321C CC311D 34.50 110.10 22.53 2.179 ! sng cyclohexane 12/05 +HCA2 CC321C CC311C 34.50 110.10 22.53 2.179 ! sng cyclohexane 12/05 +HCA2 CC321D CC311C 34.50 110.10 22.53 2.179 ! sng cyclohexane 12/05 +CC2O2 CC321 HCA2 33.00 109.50 30.00 2.163 ! par22 HA CT2 CC + +! CCN +CC3161 CC3161 NC2D1 70.00 113.50 ! par22 NH1 CT1 CT1 +CC3162 CC3161 NC2D1 70.00 113.50 ! par22 NH1 CT1 CT1 +CC3163 CC3161 NC2D1 70.00 113.50 ! par22 NH1 CT1 CT1 +CC331 CC311 NC2D1 70.00 113.50 ! par22 NH1 CT1 CT3 +NC2D1 CC2O1 CC331 80.00 116.50 ! par22 NH1 C CT3 +! CNC +CC3161 NC2D1 CC2O1 50.00 120.00 ! par22 CT1 NH1 C +CC2O1 NC2D1 CC311 50.00 120.00 ! par22 CT1 NH1 C +CC2O1 NC2D1 CC331 50.00 120.00 ! par22 CT3 NH1 C +! NCO +NC2D1 CC2O1 OC2D1 80.00 122.50 ! par22 O C NH1 +! NCH +NC2D1 CC3161 HCA1 48.00 108.00 ! par22 NH1 CT1 HB +NC2D1 CC311 HCA1 48.00 108.00 ! par22 NH1 CT1 HB +NC2D1 CC331 HCA3 51.50 109.50 ! par22 NH1 CT3 HA +! HNC +HCP1 NC2D1 CC2O1 34.00 123.00 ! par22 H NH1 C +CC3161 NC2D1 HCP1 35.00 117.00 ! par22 H NH1 CT1 +HCP1 NC2D1 CC311 35.00 117.00 ! par22 H NH1 CT1 +HCP1 NC2D1 CC331 35.00 117.00 ! par22 H NH1 CT3 +! HCH +HCA2 CC321 HCA2 35.50 109.00 5.40 1.802 ! par22 HA CT2 HA +HCA2 CC322 HCA2 35.50 109.00 5.40 1.802 ! par22 HA CT2 HA +HCA2 CC321C HCA2 35.50 109.00 5.40 1.802 ! par22 HA CT2 HA +HCA2 CC321D HCA2 35.50 109.00 5.40 1.802 ! par22 HA CT2 HA +HCA2 CC3261 HCA2 35.50 109.00 5.40 1.802 ! par22 HA CT2 HA +HCA2 CC3263 HCA2 35.50 109.00 5.40 1.802 ! par22 HA CT2 HA +HCA3 CC331 HCA3 35.50 108.40 5.40 1.802 ! par22 HA CT3 HA + +! monosaccharide CCO +CC3161 CC3163 OC3C61 45.00 110.00 ! sng mod (qm and crystal data) +CC3161 CC3263 OC3C61 45.00 110.00 ! CC3161 CC3163 OC3C61 + og xtal xylose +CC3161 CC3162 OC3C61 45.00 106.00 ! og crystal analysis +OC3C61 CC3062 CC3261 45.00 111.50 ! og xtal kemyac +CC321 CC3163 OC3C61 45.00 109.00 ! sng mod (qm and crystal data) II +CC312 CC3163 OC3C61 45.00 109.00 ! from C321 CC3163 OC3C61 +CC331 CC3163 OC3C61 45.00 111.50 ! par34 OC30A CC32A CC33A +CC2O2 CC311 OC301 45.00 103.00 ! og amop mp2/631gd +CC2O2 CC3163 OC3C61 45.00 103.00 ! og amop mp2/631gd + xtals +CC2O2 CC301 OC301 45.00 103.00 ! from CC2O2 CC311 OC301; og amol ok +CC2O2 CC3062 OC301 45.00 103.00 ! from CC2O2 CC301 OC301 +CC2O2 CC3062 OC3C61 45.00 103.00 ! from CC2O2 CC301 OC301 +CC3161 CC3162 OC311 75.70 107.00 ! sng mod (qm and crystal data) III +CC312 CC312 OC311 75.70 108.00 ! adm 11/08, glycerol +CC3161 CC3161 OC311 75.70 110.10 ! par22 OH1 CT1 CT1 +CC3261 CC3161 OC311 75.70 110.10 ! par22 OH1 CT1 CT1 +CC3162 CC3161 OC311 75.70 110.10 ! par22 OH1 CT1 CT1 +CC3163 CC3161 OC311 75.70 110.10 ! par22 OH1 CT1 CT1 +CC3163 CC312 OC311 75.70 110.10 ! par22 OH1 CT1 CT1 +CC3263 CC3161 OC311 75.70 110.10 ! par22 OH1 CT1 CT1 +CC312 CC322 OC311 50.00 106.00 ! adm 11/08, glycerol +CC3163 CC321 OC311 75.70 110.10 ! par22 OH1 CT2 CT1 +CC311 CC321 OC311 75.70 110.10 ! par22 OH1 CT2 CT1 +CC321 CC311 OC311 75.70 110.10 ! par22 OH1 CT1 CT1/CT3 +CC322 CC312 OC311 75.70 108.00 ! adm 11/08, glycerol +CC331 CC301 OC311 75.70 113.00 ! og amol mp2/631g* +CC3261 CC3062 OC311 75.70 113.00 ! from CC331 CC301 OC311 for ne5ac +CC2O2 CC301 OC311 75.70 110.10 ! par22 OH1 CT1 CT3; og amol ok +CC2O2 CC3062 OC311 75.70 110.10 ! from CC2O2 CC301 OC311 for ne5ac +CC3163 CC2O2 OC2D2 40.00 114.00 50.00 2.388 ! og amop amol and xtals +CC3062 CC2O2 OC2D2 40.00 114.00 50.00 2.388 ! og amop amol and xtals +CC311 CC2O2 OC2D2 40.00 114.00 50.00 2.388 ! og amop amol and xtals +CC301 CC2O2 OC2D2 40.00 114.00 50.00 2.388 ! og amop amol and xtals +CC321 CC2O2 OC2D2 40.00 114.00 50.00 2.388 ! og amop amol and xtals +OC2D1 CC2O1 CC331 80.00 121.00 ! par22 O C CT3 +OC301 CC311 CC331 45.00 111.50 ! par35 OC30A CC32A CC33A +OC301 CC321 CC321 45.00 111.50 ! par35 OC30A CC32A CC32A +OC301 CC301 CC331 45.00 109.00 ! og amol mp2/631g* +! model compound CCO +OC3C61 CC311C CC321 45.00 109.00 ! from CC321 CC3163 OC3C61 +OC3C61 CC311C CC321C 45.00 111.50 ! par34 OC30A CC326A CC326A +OC3C61 CC321C CC321C 45.00 111.50 ! par34 OC30A CC326A CC326A +OC3C61 CC321C CC311C 45.00 111.50 ! par34 OC30A CC326A CC326A +OC3C61 CC321D CC321C 45.00 111.50 ! par34 OC30A CC326A CC326A +OC3C61 CC321D CC311C 45.00 111.50 ! par34 OC30A CC326A CC326A +OC3C61 CC311D CC321C 45.00 111.50 ! par34 OC30A CC326A CC326A +OC301 CC311D CC321C 45.00 109.00 ! og OMeTHP qm compounds 2 and 3 +OC301 CC3162 CC3161 45.00 105.00 ! og/rmv disac crystal analysis +OC301 CC3062 CC3261 45.00 105.00 ! from OC301 CC3162 CC3161 +OC302 CC311D CC321C 45.00 109.00 ! og OMeTHP qm compounds 2 and 3 +OC302 CC3162 CC3161 45.00 105.00 ! og/rmv disac crystal analysis +OC301 CC311C CC321C 45.00 109.00 ! og OMeTHP qm compounds 2 and 3 +OC301 CC3161 CC3161 45.00 109.00 ! og OMeTHP qm compounds 2 and 3 +OC301 CC3161 CC3163 45.00 109.00 ! og OMeTHP qm compounds 2 and 3 +OC301 CC311C CC321D 45.00 109.00 ! og OMeTHP qm compounds 2 and 3 +OC301 CC3161 CC3162 45.00 109.00 ! og OMeTHP qm compounds 2 and 3 +OC301 CC321 CC311C 45.00 106.00 ! og fit compounds 11 and 12 +OC301 CC321 CC3163 45.00 106.00 ! og fit compounds 11 and 12 +CC321 CC321 OC311M 75.70 110.10 ! From CN7 CN8B ON5 +CC331 CC321 OC311M 75.70 110.10 ! par22 OH1 CT2 CT3 +CC331 CC311 OC311M 75.70 110.10 ! par22 OH1 CT2 CT3 +! COH +CC3161 OC311 HCP1 50.00 109.00 ! sng mod (qm and crystal data) II +CC321 OC311 HCP1 50.00 109.00 ! sng mod (qm and crystal data) +CC3162 OC311 HCP1 50.00 109.00 ! sng mod (qm and crystal data) II +CC3062 OC311 HCP1 50.00 109.00 ! from CC3162 OC311 HCP1 for ne5ac +HCP1 OC311 CC311 50.00 106.00 ! og 1/06 EtOH IR fit +HCP1 OC311 CC312 50.00 106.00 ! og 1/06 EtOH IR fit +HCP1 OC311 CC301 50.00 106.00 ! og 1/06 EtOH IR fit +HCP1 OC311 CC322 50.00 106.00 ! og 1/06 EtOH IR fit +HCP1 OC311M CC321 50.00 106.00 ! og 1/06 EtOH IR fit +HCP1M OC311M CC321 50.00 106.00 ! og 1/06 EtOH IR fit for egly +HCP1 OC311M CC311 50.00 106.00 ! og 1/06 EtOH IR fit +HCP1 OC311M CC331 57.50 106.00 ! par22 H OH1 CT3 +! monosaccharide OCO +OC311 CC3162 OC3C61 45.00 116.50 ! og crystal analysis +OC311 CC301 OC301 45.00 116.50 ! OC311 CC3162 OC3C61; og amol ok +OC311 CC3062 OC3C61 45.00 113.00 ! og xtal kemyac +OC2D2 CC2O2 OC2D2 100.00 132.00 70.00 2.225 ! og amop amol and xtals +! model compound OCO +OC301 CC311D OC3C61 90.00 110.00 ! og OMeTHP qm compounds 2 and 3 +OC301 CC3162 OC3C61 90.00 112.00 ! og/rmv disac crystal analysis +OC301 CC3062 OC3C61 90.00 112.00 ! from OC301 CC3162 OC3C61 +OC302 CC311D OC3C61 90.00 110.00 ! og OMeTHP qm compounds 2 and 3 +OC302 CC3162 OC3C61 90.00 112.00 ! og/rmv disac crystal analysis + +! COC +CC3163 OC3C61 CC3162 95.00 109.70 ! par35 CC326A OC30A CC326A +CC3163 OC3C61 CC3062 95.00 109.70 ! par35 CC326A OC30A CC326A +CC3263 OC3C61 CC3162 95.00 109.70 ! par35 CC326A OC30A CC326A +CC311 OC301 CC331 95.00 109.70 ! par35 CC32A OC30A CC32A +CC301 OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +CC321C OC3C61 CC321C 95.00 109.70 ! par35 CC326A OC30A CC326A +CC321D OC3C61 CC321C 95.00 109.70 ! par35 CC326A OC30A CC326A +CC321D OC3C61 CC311C 95.00 109.70 ! par35 CC326A OC30A CC326A +CC311D OC3C61 CC321C 95.00 109.70 ! par35 CC326A OC30A CC326A +CC311D OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +CC3162 OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +CC3162 OC301 CC321 95.00 109.70 ! par35 CC33A OC30A CC32A +CC321 OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +CC311D OC302 CC311D 50.00 111.50 ! og QM theta vs phi/psi comp 4 to 6 +CC3162 OC302 CC3162 50.00 111.50 ! og QM theta vs phi/psi comp 4 to 6 +CC311C OC301 CC311D 50.00 109.20 ! og QM theta vs phi/psi comp 7 to 10 +CC3161 OC301 CC3162 50.00 109.20 ! og QM theta vs phi/psi comp 7 to 10 +CC3161 OC301 CC3062 50.00 109.20 ! from CC3161 OC301 CC3162 + +! monosaccharide HCO +HCA1 CC312 OC311 55.00 108.89 ! og 1/06 EtOH NIST IR fit +HCA1 CC3161 OC311 55.00 108.89 ! og 1/06 EtOH NIST IR fit +HCA1 CC3162 OC311 55.00 108.89 ! og 1/06 EtOH NIST IR fit +HCA1 CC3163 OC311 55.00 108.89 ! og 1/06 EtOH NIST IR fit +HCA2 CC321 OC311 55.00 108.89 ! og 1/06 EtOH NIST IR fit +HCA2 CC322 OC311 55.00 108.89 ! og 1/06 EtOH NIST IR fit +HCA1 CC3162 OC3C61 45.00 109.50 ! sng from thp +HCA1 CC3163 OC3C61 45.00 109.50 ! sng from thp +HCA2 CC3263 OC3C61 45.00 109.50 ! sng from thp +HCA1 CC311 OC301 60.00 109.50 ! par34 HCA2 CC32A OC30A +OC301 CC321 HCA2 60.00 109.50 ! par34 HCA2 CC32A OC30A +OC301 CC331 HCA3 60.00 109.50 ! par34 HCA3 CC33A OC30A +! model compound HCO +HCA3 CC331 OC311M 55.00 108.89 ! og 1/06 MeOH NIST IR fit +HCA2 CC321 OC311M 55.00 108.89 ! og 1/06 EtOH NIST IR fit +HCA1 CC311 OC311M 55.00 108.89 ! og 1/06 EtOH NIST IR fit +HCA2 CC321C OC3C61 45.00 109.50 ! sng from thp +HCA2 CC321D OC3C61 45.00 109.50 ! sng from thp +HCA1 CC311C OC3C61 45.00 109.50 ! sng from thp +HCA1 CC311D OC3C61 45.00 109.50 ! sng from thp +HCA1 CC311D OC301 60.00 109.50 ! par35 HCA2 CC32A OC30A +HCA1 CC3162 OC301 60.00 109.50 ! par35 HCA2 CC32A OC30A +HCA1 CC311D OC302 60.00 109.50 ! par35 HCA2 CC32A OC30A +HCA1 CC3162 OC302 60.00 109.50 ! par35 HCA2 CC32A OC30A +HCA1 CC311C OC301 60.00 109.50 ! par35 HCA2 CC32A OC30A +HCA1 CC3161 OC301 60.00 109.50 ! par35 HCA2 CC32A OC30A + +! +! THF parameters for furanoses; viv, added by erh +CC322C CC322C CC322C 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv +HCA2C2 CC322C CC322C 35.00 111.40 22.53 2.179 ! viv cyclopentane 10/17/05 +HCA2C2 CC322C HCA2C2 38.50 106.80 5.40 1.802 ! viv cyclopentane 10/17/05 +OC3C5M CC322C CC322C 45.00 111.10 ! viv THF 10/21/05 +CC322C OC3C5M CC322C 95.00 111.00 ! viv THF 10/21/05 +HCA2C2 CC322C OC3C5M 70.00 107.30 ! viv THF 10/21/05 +! THF ww/Methylw parameter for furanoses; viv, +! erh aadded anad corrected for atom type, giving better pure solvent results 7/08 +HCA3 CC331 CC312C 33.43 110.10 22.53 2.179 ! par22 HA CT3 CT1 +CC322C CC312C CC331 53.35 114.00 8.00 2.561 ! par22 CT3 CT1 CT2 +HCA1C2 CC312C CC331 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT3 +OC3C5M CC312C CC331 45.00 111.50 ! viv TF2M (DEE) +HCA1C2 CC312C CC322C 35.00 111.40 22.53 2.179 ! viv cyclopentane 10/17/05; erh 7/08 +HCA2C2 CC322C CC312C 35.00 111.40 22.53 2.179 ! viv cyclopentane 10/17/05; erh 7/08 +CC312C CC322C CC322C 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv ; erh 7/08 +CC322C CC312C CC322C 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv ; erh 7/08 +OC3C5M CC312C CC322C 45.00 111.10 ! viv THF 10/21/05; erh 7/08 +CC312C OC3C5M CC322C 95.00 111.00 ! viv THF 10/21/05; erh 7/08 +HCA1C2 CC312C OC3C5M 70.00 107.30 ! viv THF 10/21/05; erh 7/08 + +! OMe-THF param for omef patch +HCA1C2 CC312C OC301 60.00 109.50 ! par35 HCA2 CC32A OC30A +OC301 CC312C CC322C 45.00 106.50 ! erh xtal analysis on disac +CC312C OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +OC301 CC312C OC3C5M 90.00 112.00 ! og,erh xtal analysis on disac + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! monosaccharide furanoses; erh modified 10/23/07!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +! OCC +OC3C51 CC3152 CC3251 45.00 111.10 ! THF par_carb OC3C5M CC322C CC322C +OC3C51 CC3051 CC3251 45.00 111.10 ! THF par_carb OC3C5M CC322C CC322C +OC3C51 CC3152 CC3151 45.00 111.10 ! THF par_carb OC3C5M CC322C CC322C +OC3C51 CC3051 CC3151 45.00 111.10 ! THF par_carb OC3C5M CC322C CC322C +OC3C51 CC3153 CC3151 45.00 111.10 ! THF par_carb OC3C5M CC322C CC322C +OC3C51 CC3153 CC321 45.00 108.00 ! erh crystal analysis on furanose 3/09 +OC3C51 CC3051 CC321 45.00 108.00 ! erh crystal analysis on furanose 3/09 +OC311 CC3151 CC3251 75.70 110.10 ! par22 OH1 CT1 CT1; par_Sugars, CC3263 CC3161 OC311 +OC311 CC3151 CC3153 75.70 110.10 ! par22 OH1 CT1 CT1 +OC311 CC3151 CC3152 75.70 110.10 ! par22 OH1 CT1 CT1 +OC311 CC3151 CC3051 75.70 110.10 ! par22 OH1 CT1 CT1 +OC311 CC3151 CC3151 75.70 110.10 ! par22 OH1 CT1 CT1 +OC311 CC321 CC3153 75.70 110.10 ! par22 OH1 CT2 CT1 +OC311 CC321 CC3152 75.70 110.10 ! par22 OH1 CT2 CT1; erh 3/08 +OC311 CC321 CC3051 75.70 110.10 ! par22 OH1 CT2 CT1; erh 3/08 +OC311 CC3152 CC3251 75.70 110.10 ! par22 OH1 CT1 CT1; par_carb, CC3263 CC3161 OC311 +OC311 CC3051 CC3251 75.70 110.10 ! par22 OH1 CT1 CT1; par_carb, CC3263 CC3161 OC311 +OC311 CC3152 CC321 75.70 110.10 ! par22 OH1 CT1 CT1/CT3 +OC311 CC3051 CC321 75.70 110.10 ! par22 OH1 CT1 CT1/CT3 +OC311 CC3152 CC3151 75.70 110.10 ! par22 OH1 CT1 CT1 +OC311 CC3051 CC3151 75.70 110.10 ! par22 OH1 CT1 CT1 + +! OCO +OC3C51 CC3152 OC311 45.00 116.50 ! par_carb, OC3C61 CC3162 OC311 +OC3C51 CC3051 OC311 45.00 116.50 ! par_carb, OC3C61 CC3162 OC311 + +! OCH +OC3C51 CC3152 HCA1 70.00 107.30 ! THF, par_carb, OC3C5M CC322C HCA2C2 +OC3C51 CC3153 HCA1 70.00 107.30 ! THF, par_carb, OC3C5M CC322C HCA2C2 +OC311 CC3152 HCA1 55.00 108.89 ! og 1/06 EtOH NIST IR fit; par_carb, HCA1 CC3162 OC311 +OC311 CC3151 HCA1 55.00 108.89 ! og 1/06 EtOH NIST IR fit; par_carb, HCA1 CC3161 OC311 + +! COH +CC3152 OC311 HCP1 50.00 109.00 ! par_carb CC3162 OC311 HCP1 +CC3051 OC311 HCP1 50.00 109.00 ! par_carb CC3162 OC311 HCP1 +CC3151 OC311 HCP1 50.00 109.00 ! par_carb CC3161 OC311 HCP1 + +! COC +CC3153 OC3C51 CC3152 95.00 111.00 ! THF, par_carb CC322C OC3C5M CC322C +CC3153 OC3C51 CC3051 95.00 111.00 ! THF, par_carb CC322C OC3C5M CC322C + +! CCC +CC3152 CC3251 CC3151 58.00 109.50 11.16 2.561 ! THF, par_carb CC322C CC322C CC322C +CC3051 CC3251 CC3151 58.00 109.50 11.16 2.561 ! THF, par_carb CC322C CC322C CC322C +CC3152 CC3151 CC3151 58.00 109.50 11.16 2.561 ! THF, par_carb CC322C CC322C CC322C +CC3051 CC3151 CC3151 58.00 109.50 11.16 2.561 ! THF, par_carb CC322C CC322C CC322C +CC3251 CC3151 CC3153 58.00 109.50 11.16 2.561 ! THF, par_carb CC322C CC322C CC322C +CC3151 CC3151 CC3153 58.00 109.50 11.16 2.561 ! THF, par_carb CC322C CC322C CC322C +CC3151 CC3153 CC321 58.35 113.50 11.16 2.561 ! sng, par_carb CC3161 CC3163 CC321; erh 7/08 +CC3151 CC3051 CC321 58.35 113.50 11.16 2.561 ! sng, par_carb CC3161 CC3163 CC321; erh 7/08 + +! CCH +CC3152 CC3251 HCA2 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3051 CC3251 HCA2 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3251 CC3152 HCA1 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3251 CC3151 HCA1 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3151 CC3251 HCA2 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3153 CC3151 HCA1 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3152 CC3151 HCA1 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3051 CC3151 HCA1 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3151 CC3151 HCA1 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3151 CC3152 HCA1 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3151 CC3153 HCA1 35.00 111.40 22.53 2.179 ! cyclopentane, par_carb HCA2C2 CC322C CC322C +CC3153 CC321 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1; erh 7/08 +CC3152 CC321 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1; erh 7/08 +CC3051 CC321 HCA2 33.43 110.10 22.53 2.179 ! par22 HA CT2 CT1; erh 7/08 +CC321 CC3153 HCA1 34.50 110.10 22.53 2.179 ! par22 HA CT1 CT2 + +! HCH +HCA2 CC3251 HCA2 38.50 106.80 5.40 1.802 ! cyclopentane, par_carb HCA2C2 CC322C HCA2C2 + +! OMe-furanose param for fomea/b patch +HCA1 CC3152 OC301 60.00 109.50 ! par35 HCA2 CC32A OC30A +OC301 CC3152 CC3151 45.00 105.00 ! erh xtal anal on disac/furanose 3/09 +CC3152 OC301 CC331 95.00 111.00 ! erh xtal anal on furanose 3/09 +OC301 CC3152 OC3C51 90.00 112.00 ! erh xtal anal on disac + +!***********************end of furnanose*************************************** +!Added by sai for modelling phosphate + +CC321C CC311D CC321C 58.350 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC321D CC311D CC321C 58.350 112.00 11.16 2.561 ! sng cyclohexane 12/05 +CC311D CC311D CC321C 58.350 112.00 11.16 2.561 ! sng cyclohexane 12/05 +OC3C61 CC311D CC311D 45.00 111.50 ! par34 OC30A CC326A CC326A +OC3C61 CC321D CC311D 45.00 111.50 ! par34 OC30A CC326A CC326A +HCA1 CC311D CC311D 34.500 110.10 22.53 2.179 ! par22 HA CT1 CT2 +HCA2 CC321D CC311D 34.500 110.10 22.53 2.179 ! sng cyclohexane 12/05 +HCA1 CC311D CC321D 34.500 110.10 22.53 2.179 ! par22 HA CT1 CT2 + +OC30P CC311D CC321C 45.00 107.00 ! og OMeTHP qm compounds 2 and 3 +OC30P CC311D CC311D 45.000 107.00 ! og OMeTHP qm compounds 2 and 3 +OC30P CC3161 CC3161 45.00 107.00 ! og OMeTHP qm compounds 2 and 3 +OC30P CC3161 CC3163 45.00 107.00 ! og OMeTHP qm compounds 2 and 3 +OC30P CC311D CC321D 45.00 109.00 +OC30P CC3162 CC3161 45.00 109.00 +OC30P CC3161 CC3162 45.00 109.00 +OC30P CC321 CC311C 75.700 107.50 ! +OC30P CC321 CC3163 75.700 107.50 ! +OC30P CC311D OC3C61 90.00 110.00 ! og OMeTHP qm compounds 2 and 3 +OC30P CC3162 OC3C61 90.00 110.00 +OC30P CC321 HCA2 60.0 109.5 ! +OC30P CC3162 HCA1 60.00 109.50 ! par35 HCA2 CC32A OC30A +OC30P CC3161 HCA1 60.00 109.50 ! par35 HCA2 CC32A OC30A +OC30P CC311D HCA1 60.00 109.50 ! par35 HCA2 CC32A OC30A + +OC30P PC OC2DP 98.9 111.6 ! +OC2DP PC OC2DP 120.0 120.0 ! +OC2DP PC OC312 98.9 113.23 ! ON3 P ON4 98.9 108.23 !MP_1, ADM Jr. ! +OC312 PC OC312 98.9 104.413 ! ON4 P ON4 98.9 104.0 !MP_0, ADM Jr. ! +OC30P PC OC312 48.1 108.0 ! ON2 P ON4 48.1 108.0 !MP_1, ADM Jr. ! +HCP1 OC312 PC 30.0 115.0 40.0 2.35 ! + +CC3161 OC30P PC 20.0 120.0 35.0 2.33 ! +CC311D OC30P PC 20.0 120.0 35.0 2.33 ! +CC3162 OC30P PC 20.0 120.0 35.0 2.33 ! + +CC311D OC30P SC 15.0 109.00 27.00 1.90 ! methylsulfate +CC3161 OC30P SC 15.0 109.00 27.00 1.90 ! methylsulfate +CC321 OC30P SC 15.0 110.10 27.00 1.90 ! methylsulfate + +OC2DP SC OC2DP 130.0 109.47 35.0 2.45 ! methylsulfate +OC30P SC OC2DP 85.0 98.0 ! methylsulfate + +!*******************end of phosphates*********************************** + +!O-ethyl THP +CC311D OC301 CC321 95.00 109.70 ! pram, OMeTHP CC311D OC301 CC331 +OC301 CC321 CC331 45.00 111.50 ! pram, par35 OC3C7M CC321 CC331 + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! pyranose/furanose-furanose link; pram +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +!model compounds +OC301 CC312D OC3C5M 90.00 112.00 ! OMe-THF OC301 CC312C OC3C5M +HCA1 CC312D OC301 60.00 109.50 ! OMe-THF HCA1C2 CC312C OC301 +OC301 CC312D CC322C 45.00 106.50 ! OMe-THF OC301 CC312C CC322C +CC312D OC301 CC331 95.00 109.70 ! OMe-THF CC312C OC301 CC331 +CC311D OC302 CC312D 50.00 111.50 ! THP-O-THP CC311D OC302 CC311D +CC312D OC3C5M CC322C 95.00 111.00 ! THF w/me CC312C OC3C5M CC322C +OC302 CC312D OC3C5M 90.00 112.00 ! OMe-THF OC301 CC312C OC3C5M +HCA2C2 CC322C CC312D 35.00 111.40 22.53 2.179 ! THF w/me HCA2C2 CC322C CC312C +CC312D CC322C CC322C 58.00 109.50 11.16 2.561 ! THF w/me CC312C CC322C CC322C +OC3C5M CC312D CC322C 45.00 111.10 ! THF w/me OC3C5M CC312C CC322C +OC302 CC312D CC322C 45.00 106.50 ! OMe-THF OC301 CC312C CC322C +HCA1 CC312D OC302 60.00 109.50 ! OMe-THF HCA1C2 CC312C OC301 +HCA1 CC312D OC3C5M 70.00 107.30 ! THF w/me HCA1C2 CC312C OC3C5M +HCA1 CC312D CC322C 35.00 111.40 22.53 2.179 ! THF w/me HCA1C2 CC312C CC322C +HCA1 CC312C OC3C5M 70.00 107.30 ! THF w/me HCA1C2 CC312C OC3C5M +HCA1 CC312C CC322C 35.00 111.40 22.53 2.179 ! THF w/me HCA1C2 CC312C CC322C +CC321 CC312C CC322C 58.350 113.00 11.16 2.561 ! pram, angle eq. value modified (from CC321 CC311C CC321C),QM minima, MOLVIB on model compound 2 (raman et. al) +HCA1 CC312C CC321 34.50 110.10 22.53 2.179 ! THF w/me HCA1C2 CC312C CC331 +HCA2 CC321 CC312C 33.43 110.10 22.53 2.179 ! COCA-THP2 HCA2 CC321 CC311C +OC301 CC321 CC312C 45.00 106.00 ! COCA-THP2 OC301 CC321 CC311C +OC3C5M CC312C CC321 60.00 109.00 ! pram, modified (from OC3C61 CC311C CC321),QM minima, MOLVIB on model compound 2 (raman et. al) +CC312C OC303 CC331 95.00 109.70 ! OMe-THF CC312C OC301 CC331 +OC303 CC331 HCA3 60.00 109.50 ! OMe-THF +OC303 CC311D CC321C 45.00 109.00 ! OC301 CC311D CC321C +OC303 CC311D OC3C61 90.00 110.00 ! OC301 CC311D OC3C61 +HCA1 CC311D OC303 60.00 109.50 ! HCA1 CC311D OC301 +HCA1 CC312C OC303 60.00 109.50 ! HCA1C2 CC312C OC301 +OC303 CC312C CC322C 45.00 110.50 ! pram, modified (from OC301 CC312C CC322C), model compound 3 (raman et. al) QM minima +CC311D OC303 CC312C 50.00 109.50 ! pram, modified (from CC311D OC302 CC311D), model compound 3 (raman et. al) QM minima, MOLVIB +OC3C5M CC322C CC312C 45.00 111.10 ! THF OC3C5M CC322C CC322C +CC311C OC301 CC312D 50.00 109.20 ! CC311C OC301 CC311D + +!full sugars +CC3162 OC302 CC3051 50.00 111.50 ! CC3162 OC302 CC3162 +OC302 CC3051 OC3C51 90.00 112.00 ! OC301 CC312C OC3C51 +OC302 CC3051 CC321 75.70 110.10 ! OC311 CC3051 CC321 +OC302 CC3051 CC3151 45.00 105.00 ! OC301 CC3152 CC3151 +HCA1 CC3162 OC303 60.00 109.50 ! pram, model compound 3(raman et al) HCA1 CC311D OC303 +OC303 CC3162 OC3C61 90.00 112.00 ! OC301 CC3162 OC3C61 +OC303 CC3162 CC3161 45.00 105.00 ! OC301 CC3162 CC3161 +CC3162 OC303 CC3151 50.00 109.50 ! pram, model compound 3(raman et al) CC311D OC303 CC312C +OC303 CC3151 CC3153 45.00 110.50 ! pram, model compound 3(raman et al) OC303 CC312C CC322C +OC303 CC3151 CC3151 45.00 110.50 ! pram, model compound 3(raman et al) OC303 CC312C CC322C +OC303 CC3151 HCA1 60.00 109.50 ! pram, model compound 3(raman et al) HCA1 CC312C OC303 +OC303 CC3151 CC3051 45.00 110.50 ! pram, model compound 3(raman et al) OC303 CC312C CC322C +CC3051 CC321 OC301 45.00 106.00 ! pram, model compound 2 OC301 CC321 CC312C +CC321 OC301 CC3051 95.00 112.20 ! pram, modified based on KESTOS,CELGIJ,PEKHES(2) crystal simulations (from OMe-thf CC312C OC301 CC331) 2/15/2010 +OC301 CC3051 OC3C51 90.00 112.00 ! OMe-THF OC301 CC312C OC3C5M +OC301 CC3051 CC321 75.70 110.10 ! OC311 CC3051 CC321 +OC301 CC3051 CC3151 45.00 106.50 ! OMe-thf OC301 CC312C CC322C +CC3153 CC321 OC301 45.00 106.00 ! pram, model compound 2(raman et al) OC301 CC321 CC312C +CC3152 OC301 CC321 95.00 111.00 ! CC3152 OC301 CC331 +CC3161 OC301 CC3152 50.00 109.20 ! CC311C OC301 CC311D, model compound 4 +!*******************end of pyranose/furanose**************************** + +!for xyl(1->4)xyl, transferred from hexopyranose disac, pram +OC301 CC3161 CC3263 45.00 109.00 ! from OC301 CC3161 CC3163 +CC3162 OC30P SC 15.00 109.00 27.00 1.90 ! sairam +CC321 OC301 CC3062 95.00 109.70 !from CC3162 OC301 CC321; mjyang + +!!!!!!disialic acid!!!!!!, Mingjun +OC301 CC312 CC312 45.00 106.00 ! OC301 CC321 CC3163 +OC301 CC312 CC322 45.00 106.00 ! OC301 CC321 CC3163 +CC312 OC301 CC3062 95.00 109.70 ! from CC3162 OC301 CC321 +OC301 CC312 HCA1 60.00 109.50 ! OC301 CC321 HCA2 +OC301 CC322 HCA2 60.00 109.50 ! OC301 CC321 HCA2 +OC301 CC322 CC312 45.00 106.00 ! OC301 CC321 CC3163 +CC322 OC301 CC3062 95.00 109.70 ! from CC3162 OC301 CC321 +!ABEQ +CC3162 CC3161 CC3261 53.35 111.00 8.00 2.561 ! from CC3162 CC3161 CC3161 +CC3161 CC3261 CC3161 53.35 111.00 8.00 2.561 ! from CC3161 CC3161 CC3161 +CC3261 CC3161 CC3163 53.35 111.00 8.00 2.561 ! from CC3161 CC3161 CC3163 +!O-acetyl on ARHM and ABEQ +CC3261 CC3161 OC301 75.70 110.10 ! CC3261 CC3161 OC311 +CC331 CC2O5 OC301 55.00 109.00 20.00 2.3260 ! CG331 CG2O2 OG302 +CC331 CC2O5 OC2D1 70.00 125.00 20.00 2.4420 ! CG331 CG2O2 OG2D1 +CC2O5 CC331 HCA3 33.00 109.50 30.00 2.1630 ! CG2O2 CG331 HGA3 +OC2D1 CC2O5 OC301 90.00 125.90 160.00 2.2576 ! OG2D1 CG2O2 OG302 +CC2O5 OC301 CC3161 40.00 109.60 30.00 2.2651 ! CG2O2 OG302 CG311 + +! tip3p water +!HCTIP3 OCTIP3 HCTIP3 55.00 104.52 ! TIP3P GEOMETRY + +! ******** V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +DIHEDRALS +! aldose, ketose, new!!!! adm, 11/08 + +! ketose, for D-psicose +CC312 CC312 CC312 CC2O3 0.02 1 180.0 ! erh ketone, n=6 polyol +CC312 CC312 CC312 CC2O3 0.06 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC312 CC2O3 2.47 3 0.0 ! " C2-C3-C4-C5 +CC312 CC312 CC2O3 CC322 0.02 1 180.0 ! erh ketone, n=6 polyol +CC312 CC312 CC2O3 CC322 0.06 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC2O3 CC322 2.47 3 0.0 ! " C2-C3-C4-C5 +CC2O3 CC312 CC312 OC311 2.62 1 180.0 ! erh ketone, fit psicose +CC2O3 CC312 CC312 OC311 0.28 2 180.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC2O3 CC312 CC312 OC311 2.28 3 0.0 ! " C2-C3-C4-O4 +CC312 CC312 CC2O3 OC2D3 2.06 1 0.0 ! erh ketone, fit psicose +CC312 CC312 CC2O3 OC2D3 0.13 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC2O3 OC2D3 2.87 3 0.0 ! " C4-C3-C2-O2 +CC312 CC2O3 CC322 OC311 2.94 1 0.0 ! erh ketone, fit psicose +CC312 CC2O3 CC322 OC311 1.48 2 180.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC2O3 CC322 OC311 0.50 3 180.0 ! " C3-C2-C1-O1 +CC322 CC2O3 CC322 OC311 1.03 1 0.0 ! erh ketone, fit psicose +CC322 CC2O3 CC322 OC311 2.44 2 180.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC322 CC2O3 CC322 OC311 1.24 3 180.0 ! " C1-C2-C3-O3 +CC322 CC2O3 CC312 OC311 1.03 1 0.0 ! erh ketone, fit psicose +CC322 CC2O3 CC312 OC311 2.44 2 180.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC322 CC2O3 CC312 OC311 1.24 3 180.0 ! " C1-C2-C3-O3 +OC2D3 CC2O3 CC312 OC311 2.09 1 0.0 ! erh ketone, fit psicose +OC2D3 CC2O3 CC312 OC311 0.17 2 180.0 ! " RIMP2/cc-pVTZ//MP2/631gd +OC2D3 CC2O3 CC312 OC311 2.15 3 180.0 ! " O2-C2-C3-O3 +OC2D3 CC2O3 CC322 OC311 2.80 1 0.0 ! erh ketone, fit psicose +OC2D3 CC2O3 CC322 OC311 0.75 2 180.0 ! " RIMP2/cc-pVTZ//MP2/631gd +OC2D3 CC2O3 CC322 OC311 0.32 3 180.0 ! " O2-C2-C1-O1 +CC331 CC2O3 CC331 HCA3 0.10 3 0.0 ! erh ketone RIMP2/cc-pVTZ//MP2/6-31G(d) +CC2O3 CC312 CC312 HCA1 0.10 3 0.0 ! erh ketone RIMP2/cc-pVTZ//MP2/6-31G(d) +CC322 CC2O3 CC312 HCA1 0.10 3 0.0 ! erh ketone RIMP2/cc-pVTZ//MP2/6-31G(d) +CC312 CC2O3 CC322 HCA2 0.10 3 0.0 ! erh ketone RIMP2/cc-pVTZ//MP2/6-31G(d) +CC322 CC2O3 CC322 HCA2 0.10 3 0.0 ! erh ketone RIMP2/cc-pVTZ//MP2/6-31G(d) +OC2D3 CC2O3 CC331 HCA3 0.00 3 0.0 ! erh ketone RIMP2/cc-pVTZ//MP2/6-31G(d) +OC2D3 CC2O3 CC322 HCA2 0.00 3 0.0 ! erh ketone RIMP2/cc-pVTZ//MP2/6-31G(d) +OC2D3 CC2O3 CC312 HCA1 0.00 3 0.0 ! erh ketone RIMP2/cc-pVTZ//MP2/6-31G(d) +CC2O3 CC312 OC311 HCP1 0.35 1 0.0 ! erh ketone, n=6 polyol +CC2O3 CC312 OC311 HCP1 0.37 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC2O3 CC312 OC311 HCP1 0.19 3 180.0 ! " C-C-O-H +CC2O3 CC322 OC311 HCP1 0.35 1 0.0 ! erh ketone, n=6 polyol +CC2O3 CC322 OC311 HCP1 0.37 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC2O3 CC322 OC311 HCP1 0.19 3 180.0 ! " C-C-O-H + +! aldehyde, for allose +CC312 CC312 CC312 CC2O4 0.02 1 180.0 ! erh aldehyde, n=6 polyol +CC312 CC312 CC312 CC2O4 0.06 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC312 CC2O4 2.47 3 0.0 ! " C2-C3-C4-C5 +CC312 CC312 CC2O4 OC2D4 0.17 1 180.0 ! erh aldehyde, fit allose +CC312 CC312 CC2O4 OC2D4 0.26 2 180.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC2O4 OC2D4 1.04 3 180.0 ! " C3-C2-C1-O1 +CC2O4 CC312 CC312 OC311 1.15 1 0.0 ! erh aldehyde, fit allose +CC2O4 CC312 CC312 OC311 3.00 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC2O4 CC312 CC312 OC311 2.39 3 180.0 ! " C1-C2-C3-O3 +OC2D4 CC2O4 CC312 OC311 0.56 1 180.0 ! erh aldehyde, fit allose +OC2D4 CC2O4 CC312 OC311 1.60 2 180.0 ! " RIMP2/cc-pVTZ//MP2/631gd +OC2D4 CC2O4 CC312 OC311 0.93 3 0.0 ! " O1-C1-C2-O2 +HCP1 OC311 CC312 CC2O4 0.35 1 0.0 ! erh aldehyde, n=6 polyol +HCP1 OC311 CC312 CC2O4 0.37 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +HCP1 OC311 CC312 CC2O4 0.19 3 180.0 ! " C-C-O-H +HCR1 CC2O4 CC331 HCA3 0.00 3 180.0 ! acetaldehyde, adm +OC2D4 CC2O4 CC331 HCA3 0.20 3 180.0 ! acetaldehyde, adm +CC312 CC312 CC2O4 HCR1 0.00 6 180.0 ! aldehdye par22 X CT1 CD X +CC2O4 CC312 CC312 HCA1 0.20 3 0.0 ! aldehyde par22 X CT1 CT1 X +OC2D4 CC2O4 CC312 HCA1 0.00 6 180.0 ! aldehdye par22 X CT1 CD X +OC311 CC312 CC2O4 HCR1 0.00 6 180.0 ! aldehdye par22 X CT1 CD X + +! monosaccharide CCCC +! C4-C3-C2-C1(anomeric) +CC3161 CC3161 CC3161 CC3162 0.19 3 180.0 ! og/sng cyclohexane +CC3161 CC3161 CC3261 CC3062 0.19 3 180.0 ! og/sng cyclohexane +! C2-C3-C4-C5 +CC3161 CC3161 CC3161 CC3163 0.19 3 180.0 ! og/sng cyclohexane +CC3161 CC3161 CC3161 CC3263 0.19 3 180.0 ! og/sng cyclohexane +CC3261 CC3161 CC3161 CC3163 0.19 3 180.0 ! og/sng cyclohexane +! C3-C4-C5-C6 +CC3161 CC3161 CC3163 CC321 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3161 CC3163 CC331 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3161 CC3163 CC2O2 0.20 3 0.0 ! par27 X CTL1 CTL1 X +! other +CC3161 CC3261 CC3062 CC2O2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC3163 CC312 CC312 CC322 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3161 CC3163 CC312 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3163 CC312 CC312 0.20 3 0.0 ! par27 X CTL1 CTL1 X +! polyol +CC312 CC312 CC312 CC322 0.02 1 180.0 ! erh n=6 polyol +CC312 CC312 CC312 CC322 0.06 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC312 CC322 2.47 3 0.0 ! " C2-C3-C4-C5 +CC322 CC312 CC312 CC322 0.02 1 180.0 ! erh glycerol, n=6 polyol +CC322 CC312 CC312 CC322 0.06 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC322 CC312 CC312 CC322 2.47 3 0.0 ! " C2-C3-C4-C5 +CC312 CC312 CC312 CC312 0.02 1 180.0 ! erh n=6 polyol +CC312 CC312 CC312 CC312 0.06 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC312 CC312 2.47 3 0.0 ! " C2-C3-C4-C5 +CC3161 CC3161 CC3161 CC3161 2.31 3 180.0 ! erh fit inositol RIMP2/cc-pVTZ//MP2/631gd C1-C2-C3-C4 +! model compound CCCC +CC311C CC321C CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC321C CC311C CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC321C CC321C CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC321D CC321C CC311C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC321D CC321C CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC321D CC321C CC321C CC311C 0.19 3 180.0 ! og/sng cyclohexane +CC321D CC311C CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC311D CC321C CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC3162 CC3163 CC3161 CC3161 0.19 3 180.0 ! og/sng cyclohexane +CC321 CC311C CC321C CC321C 0.20 3 0.0 ! par27 X CTL1 CTL2 X og preserve ring def energy + +! monosaccharide CCCO +! C3-C2-C1(anomeric)-O5 +CC3161 CC3161 CC3162 OC3C61 0.31 3 180.0 ! og/sng thp +CC3161 CC3261 CC3062 OC3C61 0.31 3 180.0 ! og/sng thp +! C3-C4-C5-O5 +CC3161 CC3161 CC3163 OC3C61 0.31 3 180.0 ! og/sng thp +CC3161 CC3161 CC3263 OC3C61 0.31 3 180.0 ! og/sng thp +! C-C-C-O(H) +CC3161 CC3161 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3161 CC3162 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3163 CC312 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3163 CC321 OC311 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC3161 CC3261 CC3062 OC311 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC3162 CC3161 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3062 CC3261 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC3163 CC3161 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3163 CC312 CC312 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3263 CC3161 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC321 CC3163 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC331 CC3163 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC331 CC3163 CC3161 OC301 0.20 3 0.0 ! CC331 CC3163 CC3161 OC311, pram +CC2O2 CC3163 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC2O2 CC3163 CC3161 OC301 0.20 3 0.0 ! par27 X CTL1 CTL1 X +! C-C-C-O(C) +CC321 CC3163 CC3161 OC301 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3161 CC3161 OC301 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3161 CC3162 OC301 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3161 CC3161 CC3162 OC302 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3162 CC3161 CC3161 OC301 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3163 CC3161 CC3161 OC301 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC312 CC312 CC3163 OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC321 CC321 CC321 OC301 0.19 3 0.0 ! par27 X CTL2 CTL2 X + +! polyols +CC322 CC312 CC312 OC311 0.35 1 0.0 ! erh n=6 polyol +CC322 CC312 CC312 OC311 0.69 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC322 CC312 CC312 OC311 2.79 3 180.0 ! " C1-C2-C3-O3 +CC312 CC312 CC322 OC311 0.35 1 0.0 ! erh n=6 polyol +CC312 CC312 CC322 OC311 0.69 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC322 OC311 2.79 3 180.0 ! " C3-C2-C1-O1 +CC312 CC312 CC312 OC311 0.35 1 0.0 ! erh n=6 polyol +CC312 CC312 CC312 OC311 0.69 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 CC312 OC311 2.79 3 180.0 ! " C4-C3-C2-O2 +CC322 CC312 CC322 OC311 0.35 1 0.0 ! erh glycerol, n=6 polyol +CC322 CC312 CC322 OC311 0.69 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC322 CC312 CC322 OC311 2.79 3 180.0 ! " C1-C2-C3-O3 +! C4-C5-C6-O6 in aglca, bglca, aidoa, bidoa and C3-C2-C1-O1 in ne5ac +CC3161 CC3163 CC2O2 OC2D2 0.05 6 180.00 ! par22 X CT1 CC X +OC2D2 CC2O2 CC311 CC331 0.05 6 180.00 ! par22 X CT1 CC X +OC2D2 CC2O2 CC301 CC331 0.05 6 180.00 ! par22 X CT1 CC X +OC2D2 CC2O2 CC3062 CC3261 0.05 6 180.00 ! par22 X CT1 CC X +! model compound CCCO +CC321C CC321C CC321C OC3C61 0.31 3 180.0 ! og/sng thp +CC321C CC321C CC311C OC3C61 0.31 3 180.0 ! og/sng thp +CC321C CC311C CC321C OC3C61 0.31 3 180.0 ! og/sng thp +CC321C CC321C CC321D OC3C61 0.31 3 180.0 ! og/sng thp +CC321C CC311C CC321D OC3C61 0.31 3 180.0 ! og/sng thp +CC321C CC321C CC311D OC3C61 0.31 3 180.0 ! og/sng thp +CC311C CC321C CC321C OC3C61 0.31 3 180.0 ! og/sng thp +CC311C CC321C CC321D OC3C61 0.31 3 180.0 ! og/sng thp +OC301 CC311C CC321C CC321C 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC311C CC321C CC321D 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC311D CC321C CC321C 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC302 CC311D CC321C CC321C 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC2D2 CC2O2 CC321 CC331 0.05 6 180.0 ! par22 X CT2 CC X +CC321C CC311C CC321 OC301 1.10 1 180.0 ! og compounds 11 and 12 +CC321C CC311C CC321 OC301 0.07 2 180.0 ! " MCSA fit +CC321C CC311C CC321 OC301 0.15 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +!CC3161 CC3163 CC321 OC301 1.10 1 180.0 ! og compounds 11 and 12 +!CC3161 CC3163 CC321 OC301 0.07 2 180.0 ! " MCSA fit +!CC3161 CC3163 CC321 OC301 0.15 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 CC3163 CC321 OC301 0.50 1 180.0 ! dpatel, modified +CC3161 CC3163 CC321 OC301 0.37 2 180.0 ! LS fit +CC3161 CC3163 CC321 OC301 0.15 3 0.0 ! + +! monosaccharide CCCN +NC2D1 CC3161 CC3161 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL1 X +NC2D1 CC3161 CC3161 CC3261 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC312 CC3163 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X + +! monosaccharide CCOC +! C2-C1-O5-C5 +CC3161 CC3162 OC3C61 CC3163 0.20 3 0.0 ! og/sng thp +CC3161 CC3162 OC3C61 CC3263 0.20 3 0.0 ! og/sng thp +! C4-C5-O5-C1 +CC3161 CC3163 OC3C61 CC3162 0.20 3 0.0 ! og/sng thp +CC3161 CC3163 OC3C61 CC3062 0.20 3 0.0 ! og/sng thp +CC3161 CC3263 OC3C61 CC3162 0.20 3 0.0 ! og/sng thp +! C6-C5-O5-C1(anomeric) +CC321 CC3163 OC3C61 CC3162 0.20 3 0.0 ! og/sng thp +CC312 CC3163 OC3C61 CC3062 0.20 3 0.0 ! og/sng thp +CC331 CC3163 OC3C61 CC3162 0.20 3 0.0 ! og/sng thp +CC2O2 CC3163 OC3C61 CC3162 0.20 3 0.0 ! og/sng thp +CC2O2 CC3062 OC3C61 CC3163 0.20 3 0.0 ! og/sng thp +! other +CC331 OC301 CC311 CC331 0.40 1 0.0 ! par35 +CC331 OC301 CC311 CC331 0.49 3 0.0 ! " CC33A CC32A OC30A CC33A +CC331 OC301 CC301 CC331 0.40 1 0.0 ! par35 +CC331 OC301 CC301 CC331 0.49 3 0.0 ! " CC33A CC32A OC30A CC33A +CC3162 OC301 CC321 CC321 0.40 1 0.0 ! par35 +CC3162 OC301 CC321 CC321 0.49 3 0.0 ! " CC33A CC32A OC30A CC32A +CC2O2 CC301 OC301 CC331 0.20 3 0.0 ! og/sng thp CC321C CC321C OC3C61 CC321C +CC2O2 CC311 OC301 CC331 0.20 3 0.0 ! og/sng thp CC321C CC321C OC3C61 CC321C +CC3261 CC3062 OC3C61 CC3163 0.20 3 0.0 ! og/sng thp +! model compound CCOC +CC311C CC321C OC3C61 CC321D 0.20 3 0.0 ! og/sng thp +CC321C CC321C OC3C61 CC321C 0.20 3 0.0 ! og/sng thp +CC321C CC321C OC3C61 CC321D 0.20 3 0.0 ! og/sng thp +CC321C CC321D OC3C61 CC311C 0.20 3 0.0 ! og/sng thp +CC321C CC321C OC3C61 CC311D 0.20 3 0.0 ! og/sng thp +CC321C CC321D OC3C61 CC321C 0.20 3 0.0 ! og/sng thp +CC311C CC321D OC3C61 CC321C 0.20 3 0.0 ! og/sng thp +CC321C CC311C OC3C61 CC321D 0.20 3 0.0 ! og/sng thp +CC321C CC311D OC3C61 CC321C 0.20 3 0.0 ! og/sng thp +CC321C CC311D OC301 CC331 0.22 1 0.0 ! og OMeTHP compounds 2 and 3 +CC321C CC311D OC301 CC331 0.28 2 180.0 ! " MCSA fit +CC321C CC311D OC301 CC331 0.89 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 CC3162 OC301 CC331 0.22 1 0.0 ! og OMeTHP compounds 2 and 3 +CC3161 CC3162 OC301 CC331 0.28 2 180.0 ! " MCSA fit +CC3161 CC3162 OC301 CC331 0.89 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 CC3162 OC301 CC321 0.22 1 0.0 ! og OMeTHP compounds 2 and 3 +CC3161 CC3162 OC301 CC321 0.28 2 180.0 ! " MCSA fit +CC3161 CC3162 OC301 CC321 0.89 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC321C CC311D OC302 CC311D 0.73 1 0.0 ! og THP-1-O-1-THP +CC321C CC311D OC302 CC311D 0.61 2 180.0 ! " MCSA fit +CC321C CC311D OC302 CC311D 0.00 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 CC3162 OC302 CC3162 0.73 1 0.0 ! og THP-1-O-1-THP +CC3161 CC3162 OC302 CC3162 0.61 2 180.0 ! " MCSA fit +CC3161 CC3162 OC302 CC3162 0.00 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC321C CC311D OC301 CC311C 0.41 1 180.0 ! og THP-1-O-2-CYHX +CC321C CC311D OC301 CC311C 0.66 2 180.0 ! " MCSA fit +CC321C CC311D OC301 CC311C 1.60 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 CC3162 OC301 CC3161 0.41 1 180.0 ! og THP-1-O-2-CYHX +CC3161 CC3162 OC301 CC3161 0.66 2 180.0 ! " MCSA fit +CC3161 CC3162 OC301 CC3161 1.60 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC321D CC311C OC301 CC311D 0.13 1 180.0 ! og THP-1-O-2-CYHX +CC321D CC311C OC301 CC311D 0.25 2 180.0 ! " MCSA fit +CC321D CC311C OC301 CC311D 0.06 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3162 CC3161 OC301 CC3162 0.13 1 180.0 ! og THP-1-O-2-CYHX +CC3162 CC3161 OC301 CC3162 0.25 2 180.0 ! " MCSA fit +CC3162 CC3161 OC301 CC3162 0.06 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC321C CC311C OC301 CC311D 0.13 1 180.0 ! og THP-1-O-2-CYHX +CC321C CC311C OC301 CC311D 0.25 2 180.0 ! " MCSA fit +CC321C CC311C OC301 CC311D 0.06 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 CC3161 OC301 CC3162 0.13 1 180.0 ! og THP-1-O-2-CYHX +CC3161 CC3161 OC301 CC3162 0.25 2 180.0 ! " MCSA fit +CC3161 CC3161 OC301 CC3162 0.06 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3163 CC3161 OC301 CC3162 0.13 1 180.0 ! og THP-1-O-2-CYHX +CC3163 CC3161 OC301 CC3162 0.25 2 180.0 ! " MCSA fit +CC3163 CC3161 OC301 CC3162 0.06 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC321D OC3C61 CC311C CC321 0.284 3 0.0 ! from CC321C OC3C61 CC311D HCA1 + +CC311C CC321 OC301 CC331 0.64 1 180.0 ! og compounds 11 and 12 +CC311C CC321 OC301 CC331 0.03 2 180.0 ! " MCSA fit +CC311C CC321 OC301 CC331 0.61 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3163 CC321 OC301 CC3162 0.64 1 180.0 ! og compounds 11 and 12 +CC3163 CC321 OC301 CC3162 0.03 2 180.0 ! " MCSA fit +CC3163 CC321 OC301 CC3162 0.61 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + + +! monosaccharide OCCO +! (H)O-C-C-O(H) +OC311 CC3161 CC3161 OC311 2.65 1 180.0 ! og ethylene glycol combo +OC311 CC3161 CC3161 OC311 0.00 2 0.0 ! " +OC311 CC3161 CC3161 OC311 0.13 3 180.0 ! " +! (H)O-C(anomeric)-C-O(H) +OC311 CC3162 CC3161 OC311 2.65 1 180.0 ! og ethylene glycol combo +OC311 CC3162 CC3161 OC311 0.00 2 0.0 ! " +OC311 CC3162 CC3161 OC311 0.13 3 180.0 ! " +! (C)O-C(anomeric)-C-O(H) +OC301 CC3162 CC3161 OC311 2.65 1 180.0 ! og ethylene glycol combo +OC301 CC3162 CC3161 OC311 0.00 2 0.0 ! " +OC301 CC3162 CC3161 OC311 0.13 3 180.0 ! " +OC302 CC3162 CC3161 OC311 2.65 1 180.0 ! og ethylene glycol combo +OC302 CC3162 CC3161 OC311 0.00 2 0.0 ! " +OC302 CC3162 CC3161 OC311 0.13 3 180.0 ! " +! (C)O-C-C-O(H) +OC301 CC3161 CC3161 OC311 2.65 1 180.0 ! og ethylene glycol combo +OC301 CC3161 CC3161 OC311 0.00 2 0.0 ! " +OC301 CC3161 CC3161 OC311 0.13 3 180.0 ! " +OC301 CC3161 CC3162 OC311 2.65 1 180.0 ! og ethylene glycol combo +OC301 CC3161 CC3162 OC311 0.00 2 0.0 ! " +OC301 CC3161 CC3162 OC311 0.13 3 180.0 ! " +! (C)O-C-C-O(C) +OC301 CC3161 CC3162 OC301 0.59 1 180.0 ! par35 OC30A CC32A CC32A OC30A +OC301 CC3161 CC3162 OC301 1.16 2 0.0 ! " og/rmv RESMOR and FABYOW10 +! polyol OCCO +! (H)O-C-C-O(H) +OC311 CC312 CC322 OC311 1.34 1 180.0 ! erh n=6 polyol +OC311 CC312 CC322 OC311 1.19 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +OC311 CC312 CC322 OC311 2.58 3 0.0 ! " O2-C2-C1-O1 +OC311 CC312 CC312 OC311 1.34 1 180.0 ! erh n=6 polyol +OC311 CC312 CC312 OC311 1.19 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +OC311 CC312 CC312 OC311 2.58 3 0.0 ! " O2-C2-C3-O3 +! other +OC301 CC3161 CC3162 OC3C61 2.75 1 180.0 ! from +OC301 CC3161 CC3162 OC3C61 0.26 2 180.0 ! " OC311 CC3161 CC3162 OC3C61 +OC301 CC3161 CC3162 OC3C61 0.10 3 0.0 ! " +OC301 CC3161 CC3163 OC3C61 1.36 1 180.0 ! from +OC301 CC3161 CC3163 OC3C61 0.16 2 0.0 ! " OC311 CC3161 CC3163 OC3C61 +OC301 CC3161 CC3163 OC3C61 1.01 3 0.0 ! " +OC2D2 CC2O2 CC311 OC301 0.64 2 180.0 ! og amop mp2/ccpvtz +OC301 CC301 CC2O2 OC2D2 0.64 2 180.0 ! og amop mp2/ccpvtz +OC3C61 CC3163 CC2O2 OC2D2 0.64 2 180.0 ! og amop mp2/ccpvtz +OC3C61 CC3062 CC2O2 OC2D2 0.64 2 180.0 ! from OC301 CC301 CC2O2 OC2D2 +OC311 CC301 CC2O2 OC2D2 1.11 2 180.0 ! og amol mp2/ccpvtz +OC311 CC3062 CC2O2 OC2D2 1.11 2 180.0 ! from OC311 CC301 CC2O2 OC2D2 +! model compound OCCO +OC311M CC321 CC321 OC311M 0.33 1 0.0 ! og ethylene glycol combo_star +OC311M CC321 CC321 OC311M 2.17 2 0.0 ! " *** ONLY for RESI EGLY *** +OC311M CC321 CC321 OC311M 0.45 3 0.0 ! " use "combo" for all else +OC301 CC311C CC321C OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC311C CC321D OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC321 CC311C OC3C61 1.93 1 180.0 ! og compounds 11 and 12 +OC301 CC321 CC311C OC3C61 0.43 2 0.0 ! " MCSA fit +OC301 CC321 CC311C OC3C61 0.12 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC301 CC321 CC3163 OC3C61 1.4906 1 180.00 !dpatel modified by LS fitting +OC301 CC321 CC3163 OC3C61 0.3759 2 0.00 ! " +OC301 CC321 CC3163 OC3C61 0.5916 3 0.00 ! " + + +! monosaccharide HOCH +HCP1 OC311 CC3161 HCA1 0.18 3 0.0 ! og methanol +HCP1 OC311 CC3162 HCA1 0.18 3 0.0 ! og methanol +HCP1 OC311 CC321 HCA2 0.18 3 0.0 ! og methanol +! polyols HOCH +HCP1 OC311 CC322 HCA2 0.18 3 0.0 ! og methanol +HCP1 OC311 CC312 HCA1 0.18 3 0.0 ! og methanol +! model compound HCOH +HCA3 CC331 OC311M HCP1 0.18 3 0.0 ! og methanol +HCA2 CC321 OC311M HCP1 0.18 3 0.0 ! og methanol +HCA2 CC321 OC311M HCP1M 0.18 3 0.0 ! og methanol for egly +HCA1 CC311 OC311M HCP1 0.18 3 0.0 ! og methanol + +! monosaccharide HCCO +HCA1 CC3161 CC3161 OC311 0.14 3 0.0 ! og ethanol +HCA1 CC3161 CC3162 OC311 0.14 3 0.0 ! og ethanol +HCA2 CC3261 CC3161 OC311 0.14 3 0.0 ! og ethanol +HCA2 CC3261 CC3062 OC311 0.14 3 0.0 ! og ethanol +HCA1 CC3162 CC3161 OC311 0.14 3 0.0 ! og ethanol +HCA1 CC3163 CC3161 OC311 0.14 3 0.0 ! og ethanol +HCA1 CC3163 CC321 OC311 0.14 3 0.0 ! og ethanol +HCA1 CC3163 CC312 OC311 0.14 3 0.0 ! og ethanol +HCA2 CC3263 CC3161 OC311 0.14 3 0.0 ! og ethanol +HCA3 CC331 CC301 OC311 0.14 3 0.0 ! og ethanol +HCA1 CC3161 CC3163 OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3263 OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC3161 CC3162 OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA2 CC3261 CC3062 OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC3161 CC3162 OC301 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3162 OC302 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC312 CC3163 OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA2 CC321 CC3163 OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA3 CC331 CC3163 OC3C61 0.20 3 0.0 ! par27 X CTL1 CTL3 X +HCA3 CC331 CC311 OC301 0.20 3 0.0 ! par27 X CTL1 CTL3 X +HCA3 CC331 CC301 OC301 0.20 3 0.0 ! par27 X CTL1 CTL3 X +HCA2 CC321 CC321 OC301 0.19 3 0.0 ! par27 X CTL2 CTL2 X +HCA1 CC311 CC2O2 OC2D2 0.05 6 180.0 ! par22 X CT1 CC X +HCA1 CC3163 CC2O2 OC2D2 0.05 6 180.0 ! par22 X CT1 CC X +HCA3 CC331 CC2O1 OC2D1 0.00 3 180.0 ! par22 O C CT3 HA + +! polyols +HCA2 CC322 CC312 OC311 0.14 3 0.0 ! og ethanol +HCA1 CC312 CC322 OC311 0.14 3 0.0 ! og ethanol +HCA1 CC312 CC312 OC311 0.14 3 0.0 ! og ethanol +! model compound HCCO +OC311M CC321 CC331 HCA3 0.14 3 0.0 ! og ethanol +OC311M CC311 CC331 HCA3 0.14 3 0.0 ! og ethanol +OC311M CC321 CC321 HCA2 0.14 3 0.0 ! og ethanol +OC3C61 CC321C CC321C HCA2 0.16 3 0.0 ! thp H-Cring-Cring-O +OC3C61 CC321D CC321C HCA2 0.16 3 0.0 ! thp H-Cring-Cring-O +OC3C61 CC311C CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC3C61 CC311D CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC3C61 CC311C CC321 HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC3C61 CC321C CC311C HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC3C61 CC321D CC311C HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC311D CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC302 CC311D CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC311C CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC321 CC311C HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC321 CC3163 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC3161 CC3161 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC301 CC311C CC321D HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC301 CC3161 CC3162 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC301 CC3161 CC3163 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA2 CC321 CC2O2 OC2D2 0.05 6 180.0 ! par22 X CT2 CC X + +! HCCN +HCA1 CC3161 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3162 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3163 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +NC2D1 CC311 CC331 HCA3 0.20 3 0.0 ! par27 X CTL1 CTL3 X +NC2D1 CC2O1 CC331 HCA3 0.00 3 0.0 ! par22 NH1 C CT3 HA + +! OCCN +OC301 CC3162 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC311 CC3162 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC301 CC3161 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC311 CC3161 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC3C61 CC3162 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC3C61 CC3163 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X + +! OCNC +OC2D1 CC2O1 NC2D1 CC311 2.50 2 180.0 ! par22 O C NH1 CT1 +OC2D1 CC2O1 NC2D1 CC3161 2.50 2 180.0 ! par22 O C NH1 CT1 +OC2D1 CC2O1 NC2D1 CC331 2.50 2 180.0 ! par22 O C NH1 CT3 + +! CNCC +CC311 NC2D1 CC2O1 CC331 1.60 1 0.0 ! par22 CT1 NH1 C CT3 +CC311 NC2D1 CC2O1 CC331 2.50 2 180.0 ! " +CC3161 NC2D1 CC2O1 CC331 1.60 1 0.0 ! par22 CT1 NH1 C CT3 +CC3161 NC2D1 CC2O1 CC331 2.50 2 180.0 ! " +CC331 NC2D1 CC2O1 CC331 1.60 1 0.0 ! par22 CT3 NH1 C CT3 +CC331 NC2D1 CC2O1 CC331 2.50 2 180.0 ! " +CC2O1 NC2D1 CC311 CC331 0.50 1 180.0 ! og fit to IPAA +CC2O1 NC2D1 CC3161 CC3162 0.50 1 180.0 ! og fit to IPAA +CC2O1 NC2D1 CC3161 CC3161 0.50 1 180.0 ! og fit to IPAA +CC2O1 NC2D1 CC3161 CC3163 0.50 1 180.0 ! og fit to IPAA + +! monosaccharide HCCH +HCA1 CC3161 CC3161 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3162 CC3161 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3163 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3263 HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA2 CC3261 CC3161 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC3163 CC321 HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC3163 CC312 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC311C CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC311C CC321D HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC311C CC321 HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC311D CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC311 CC331 HCA3 0.20 3 0.0 ! par27 X CTL1 CTL3 X +HCA1 CC3163 CC331 HCA3 0.20 3 0.0 ! par27 X CTL1 CTL3 X +HCA2 CC321 CC321 HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +HCA2 CC321C CC321C HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +HCA2 CC321D CC321C HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +HCA2 CC321 CC331 HCA3 0.16 3 0.0 ! par27 X CTL2 CTL3 X +! polyols HCCH +HCA1 CC312 CC322 HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC312 CC312 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC312 CC2O4 HCR1 0.00 6 180.0 ! par22 X CT3 CD X + +! pyranose HCOC +HCA1 CC3162 OC3C61 CC3163 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +HCA1 CC3162 OC3C61 CC3263 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A;erh transferred by analogy +HCA1 CC3163 OC3C61 CC3162 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +HCA1 CC3163 OC3C61 CC3062 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +HCA2 CC3263 OC3C61 CC3162 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A;erh transferred by analogy +HCA1 CC311 OC301 CC331 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC311 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CC301 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CC331 OC301 CC311D HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC331 OC301 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC321 OC301 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC321C OC3C61 CC321C HCA2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC321D OC3C61 CC321C HCA2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC311D OC3C61 CC321C HCA2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC321C OC3C61 CC321D HCA2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC311C OC3C61 CC321D HCA2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC321C OC3C61 CC311D HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC321D OC3C61 CC311C HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC311C OC301 CC311D HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC3161 OC301 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC311D OC302 CC311D HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC3162 OC302 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC311D OC301 CC311C HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC3162 OC301 CC3161 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC321 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CC311D OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CC3162 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CC3162 OC301 CC321 HCA2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC331 OC301 CC321 HCA2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC33A + +! monosaccharide HCCC +HCA1 CC3161 CC3161 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3162 CC3161 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3161 CC3163 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3161 CC3261 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3161 CC3263 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3163 CC312 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC312 CC312 CC322 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC312 CC3163 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3161 CC3162 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3163 CC3161 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3163 CC312 CC312 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA2 CC3263 CC3161 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC3161 CC3163 CC321 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3163 CC331 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3163 CC2O2 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCA1 CC3161 CC3261 CC3062 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA2 CC321 CC311C CC321C 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA2 CC321 CC3163 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA2 CC3261 CC3062 CC2O2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA2 CC3261 CC3161 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA3 CC331 CC3163 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL3 X +CC2O2 CC311 CC331 HCA3 0.20 3 0.0 ! par27 X CTL1 CTL3 X +CC2O2 CC301 CC331 HCA3 0.20 3 0.0 ! par27 X CTL1 CTL3 X +! polyols HCCC +CC312 CC312 CC312 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC3163 CC312 CC312 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC312 CC312 CC322 HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC322 CC312 CC322 HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +! model compound HCCC +CC321C CC321C CC311C HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321C CC321C CC311D HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321D CC321C CC311C HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321 CC311C CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321C CC311C CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321C CC311C CC321D HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321D CC311C CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC331 CC311 CC331 HCA3 0.20 3 0.0 ! par27 X CTL1 CTL3 X +CC311C CC321C CC321C HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC311C CC321C CC321D HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC321 CC321 CC321 HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC331 CC321 CC321 HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC321C CC321C CC321C HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC321C CC321C CC321D HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC321D CC321C CC321C HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC311D CC321C CC321C HCA2 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC321 CC321 CC331 HCA3 0.16 3 0.0 ! par27 X CTL2 CTL3 X +CC2O2 CC321 CC331 HCA3 0.16 3 0.0 ! par27 X CTL2 CTL3 X + +! HNCC +HCP1 NC2D1 CC3161 CC3161 0.00 1 0.0 ! par22 H NH1 CT1 CT1 +HCP1 NC2D1 CC3161 CC3162 0.00 1 0.0 ! par22 H NH1 CT1 CT1 +HCP1 NC2D1 CC3161 CC3163 0.00 1 0.0 ! par22 H NH1 CT1 CT1 +HCP1 NC2D1 CC311 CC331 0.00 1 0.00 ! par22 H NH1 CT1 CT3 +HCP1 NC2D1 CC2O1 CC331 2.50 2 180.0 ! par22 H NH1 C CT3 + +! HNCH +HCP1 NC2D1 CC3161 HCA1 0.00 1 0.0 ! par22 HB CT1 NH1 H +HCP1 NC2D1 CC311 HCA1 0.00 1 0.0 ! par22 HB CT1 NH1 H +HCP1 NC2D1 CC331 HCA3 0.00 3 0.0 ! par22 HA CT3 NH1 H + +! HNCO +HCP1 NC2D1 CC2O1 OC2D1 2.50 2 180.0 ! par22 O C NH1 H + +! CNCH +CC2O1 NC2D1 CC3161 HCA1 0.00 1 0.0 ! par22 HB CT1 NH1 C +CC2O1 NC2D1 CC311 HCA1 0.00 1 0.0 ! par22 HB CT1 NH1 C +CC2O1 NC2D1 CC331 HCA3 0.00 3 0.0 ! par22 HA CT3 NH1 C + +! polyols HOCC +CC312 CC322 OC311 HCP1 0.35 1 0.0 ! erh n=6 polyol +CC312 CC322 OC311 HCP1 0.37 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC322 OC311 HCP1 0.19 3 180.0 ! " C2-C1-O1-HO1 +CC322 CC312 OC311 HCP1 0.35 1 0.0 ! erh n=6 polyol +CC322 CC312 OC311 HCP1 0.37 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC322 CC312 OC311 HCP1 0.19 3 180.0 ! " C1-C2-O2-HO2 +CC312 CC312 OC311 HCP1 0.35 1 0.0 ! erh n=6 polyol +CC312 CC312 OC311 HCP1 0.37 2 0.0 ! " RIMP2/cc-pVTZ//MP2/631gd +CC312 CC312 OC311 HCP1 0.19 3 180.0 ! " C2-C3-O3-HO3 +! model compound HOCC +CC2O2 CC301 OC311 HCP1 0.82 3 180.0 ! og amol mp2/ccpvtz +CC2O2 CC3062 OC311 HCP1 0.82 3 180.0 ! from CC2O2 CC301 OC311 HCP1 +HCP1 OC311 CC301 CC331 0.24 3 0.0 ! og ethanol +HCP1 OC311 CC301 CC331 0.14 2 0.0 ! " +HCP1 OC311 CC301 CC331 1.13 1 0.0 ! " +HCP1 OC311M CC321 CC331 0.24 3 0.0 ! og ethanol +HCP1 OC311M CC321 CC331 0.14 2 0.0 ! " +HCP1 OC311M CC321 CC331 1.13 1 0.0 ! " +HCP1 OC311M CC311 CC331 0.24 3 0.0 ! og ethanol +HCP1 OC311M CC311 CC331 0.14 2 0.0 ! " +HCP1 OC311M CC311 CC331 1.13 1 0.0 ! " +HCP1M OC311M CC321 CC321 0.40 1 180.0 ! og ethylene glycol combo_star +HCP1M OC311M CC321 CC321 0.01 2 0.0 ! " *** NOT suitable for +HCP1M OC311M CC321 CC321 0.26 3 0.0 ! " *** HO-C-C-C- type alcohols + +! model compound OCOC +OC311 CC301 OC301 CC331 0.41 1 180.0 ! from +OC311 CC301 OC301 CC331 0.89 2 0.0 ! " CC3163 OC3C61 CC3162 OC311 +OC311 CC301 OC301 CC331 0.05 3 0.0 ! " +CC321C OC3C61 CC311D OC301 0.62 1 0.0 ! og OMeTHP compounds 2 and 3 +CC321C OC3C61 CC311D OC301 1.54 2 0.0 ! " MCSA fit +CC321C OC3C61 CC311D OC301 0.48 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC321C OC3C61 CC311D OC302 0.62 1 0.0 ! og OMeTHP compounds 2 and 3 +CC321C OC3C61 CC311D OC302 1.54 2 0.0 ! " MCSA fit +CC321C OC3C61 CC311D OC302 0.48 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3163 OC3C61 CC3162 OC301 0.41 1 180.0 ! og from +CC3163 OC3C61 CC3162 OC301 0.89 2 0.0 ! " CC3163 OC3C61 CC3162 OC311 +CC3163 OC3C61 CC3162 OC301 0.05 3 0.0 ! " +CC3163 OC3C61 CC3162 OC302 0.41 1 180.0 ! og from +CC3163 OC3C61 CC3162 OC302 0.89 2 0.0 ! " CC3163 OC3C61 CC3162 OC311 +CC3163 OC3C61 CC3162 OC302 0.05 3 0.0 ! " +CC331 OC301 CC311D OC3C61 0.14 1 0.0 ! og OMeTHP compounds 2 and 3 +CC331 OC301 CC311D OC3C61 0.97 2 0.0 ! " MCSA fit +CC331 OC301 CC311D OC3C61 0.11 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC331 OC301 CC3162 OC3C61 0.14 1 0.0 ! og OMeTHP compounds 2 and 3 +CC331 OC301 CC3162 OC3C61 0.97 2 0.0 ! " MCSA fit +CC331 OC301 CC3162 OC3C61 0.11 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC321 OC301 CC3162 OC3C61 0.14 1 0.0 ! og OMeTHP compounds 2 and 3 +CC321 OC301 CC3162 OC3C61 0.97 2 0.0 ! " MCSA fit +CC321 OC301 CC3162 OC3C61 0.11 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC311D OC302 CC311D OC3C61 0.53 1 0.0 ! og THP-1-O-1-THP +CC311D OC302 CC311D OC3C61 0.74 2 0.0 ! " MCSA fit +CC311D OC302 CC311D OC3C61 0.16 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3162 OC302 CC3162 OC3C61 0.53 1 0.0 ! og THP-1-O-1-THP +CC3162 OC302 CC3162 OC3C61 0.74 2 0.0 ! " MCSA fit +CC3162 OC302 CC3162 OC3C61 0.16 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC311C OC301 CC311D OC3C61 0.05 1 180.0 ! og THP-1-O-2-CYHX +CC311C OC301 CC311D OC3C61 0.91 2 0.0 ! " MCSA fit +CC311C OC301 CC311D OC3C61 1.27 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 OC301 CC3162 OC3C61 0.05 1 180.0 ! og THP-1-O-2-CYHX +CC3161 OC301 CC3162 OC3C61 0.91 2 0.0 ! " MCSA fit +CC3161 OC301 CC3162 OC3C61 1.27 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +! HOCO +HCP1 OC311 CC301 OC301 1.55 1 0.0 !from HCP1 OC311 CC3162 OC3C61 +HCP1 OC311 CC301 OC301 1.17 2 0.0 ! " +HCP1 OC311 CC301 OC301 1.07 3 0.0 ! " + + +! og and sng automated fitting of monosaccahride energies +! RMSE of 1.68 kcal/mol for 1860 hexopyranose MP2/cc-pVTZ//MP2/6-31G(d) energies +! +CC3163 CC321 OC311 HCP1 0.29 1 0.0 +CC3163 CC321 OC311 HCP1 0.62 2 0.0 +CC3163 CC321 OC311 HCP1 0.05 3 0.0 +CC3161 CC3162 OC311 HCP1 0.29 1 0.0 +CC3161 CC3162 OC311 HCP1 0.62 2 0.0 +CC3161 CC3162 OC311 HCP1 0.05 3 0.0 +HCP1 OC311 CC3162 OC3C61 1.55 1 0.0 +HCP1 OC311 CC3162 OC3C61 1.17 2 0.0 +HCP1 OC311 CC3162 OC3C61 1.07 3 0.0 +CC3162 CC3161 OC311 HCP1 0.29 1 0.0 +CC3162 CC3161 OC311 HCP1 0.62 2 0.0 +CC3162 CC3161 OC311 HCP1 0.05 3 0.0 +CC3161 CC3161 OC311 HCP1 0.29 1 0.0 +CC3161 CC3161 OC311 HCP1 0.62 2 0.0 +CC3161 CC3161 OC311 HCP1 0.05 3 0.0 +CC3163 CC3161 OC311 HCP1 0.29 1 0.0 +CC3163 CC3161 OC311 HCP1 0.62 2 0.0 +CC3163 CC3161 OC311 HCP1 0.05 3 0.0 +OC311 CC3161 CC3162 OC3C61 2.75 1 180.0 +OC311 CC3161 CC3162 OC3C61 0.26 2 180.0 +OC311 CC3161 CC3162 OC3C61 0.10 3 0.0 +CC3163 OC3C61 CC3162 OC311 0.41 1 180.0 +CC3163 OC3C61 CC3162 OC311 0.89 2 0.0 +CC3163 OC3C61 CC3162 OC311 0.05 3 0.0 +OC311 CC3161 CC3163 OC3C61 1.36 1 180.0 +OC311 CC3161 CC3163 OC3C61 0.16 2 0.0 +OC311 CC3161 CC3163 OC3C61 1.01 3 0.0 +OC311 CC321 CC3163 OC3C61 0.75 1 180.0 +OC311 CC321 CC3163 OC3C61 0.17 2 0.0 +OC311 CC321 CC3163 OC3C61 0.25 3 180.0 ! og empirical lower barrier by 1.5 kcal + +! og transferred by analogy from above for ne5ac +CC3163 OC3C61 CC3062 OC311 0.41 1 180.0 !from CC3163 OC3C61 CC3162 OC311 +CC3163 OC3C61 CC3062 OC311 0.89 2 0.0 ! " +CC3163 OC3C61 CC3062 OC311 0.05 3 0.0 ! " +HCP1 OC311 CC3062 OC3C61 1.55 1 0.0 ! from HCP1 OC311 CC3162 OC3C61 +HCP1 OC311 CC3062 OC3C61 1.17 2 0.0 ! " +HCP1 OC311 CC3062 OC3C61 1.07 3 0.0 ! " +CC3261 CC3062 OC311 HCP1 0.29 1 0.0 ! from CC3161 CC3162 OC311 HCP1 +CC3261 CC3062 OC311 HCP1 0.62 2 0.0 ! " +CC3261 CC3062 OC311 HCP1 0.05 3 0.0 ! " +CC3163 CC312 OC311 HCP1 0.29 1 0.0 ! from CC3163 CC321 OC311 HCP1 +CC3163 CC312 OC311 HCP1 0.62 2 0.0 ! " +CC3163 CC312 OC311 HCP1 0.05 3 0.0 ! +OC311 CC312 CC3163 OC3C61 0.75 1 180.0 ! from OC311 CC321 CC3163 OC3C61 +OC311 CC312 CC3163 OC3C61 0.17 2 0.0 ! " +OC311 CC312 CC3163 OC3C61 0.25 3 180.0 ! " +CC3261 CC3161 OC311 HCP1 0.29 1 0.0 ! from CC3161 CC3161 OC311 HCP1 +CC3261 CC3161 OC311 HCP1 0.62 2 0.0 ! " +CC3261 CC3161 OC311 HCP1 0.05 3 0.0 ! " + +! og transferred from above by analogy for xyl +CC3263 CC3161 OC311 HCP1 0.29 1 0.0 +CC3263 CC3161 OC311 HCP1 0.62 2 0.0 +CC3263 CC3161 OC311 HCP1 0.05 3 0.0 +CC3263 OC3C61 CC3162 OC311 0.41 1 180.0 +CC3263 OC3C61 CC3162 OC311 0.89 2 0.0 +CC3263 OC3C61 CC3162 OC311 0.05 3 0.0 +OC311 CC3161 CC3263 OC3C61 1.36 1 180.0 +OC311 CC3161 CC3263 OC3C61 0.16 2 0.0 +OC311 CC3161 CC3263 OC3C61 1.01 3 0.0 + +! og transferred from hexopyranose disac by analogy for ne5ac +CC3161 CC3161 OC301 CC3062 0.13 1 180.0 !from CC3161 CC3161 OC301 CC3162 +CC3161 CC3161 OC301 CC3062 0.25 2 180.0 ! " +CC3161 CC3161 OC301 CC3062 0.06 3 180.0 ! " + +CC3161 OC301 CC3062 OC3C61 0.05 1 180.0 !from CC3161 OC301 CC3162 OC3C61 +CC3161 OC301 CC3062 OC3C61 0.91 2 0.0 ! " +CC3161 OC301 CC3062 OC3C61 1.27 3 180.0 ! " + +CC3261 CC3062 OC301 CC3161 0.41 1 180.0 !from CC3161 CC3162 OC301 CC3161 +CC3261 CC3062 OC301 CC3161 0.66 2 180.0 ! " +CC3261 CC3062 OC301 CC3161 1.60 3 0.0 ! " + +CC3161 OC301 CC3062 CC2O2 0.284 3 0.0 !from CC3161 OC301 CC3162 HCA1 + +CC3062 OC301 CC3161 HCA1 0.284 3 0.0 !from CC3162 OC301 CC3161 HCA1 + +OC301 CC3062 CC2O2 OC2D2 0.64 2 180.0 !from OC301 CC301 CC2O2 OC2D2 + +CC3163 OC3C61 CC3062 OC301 0.41 1 180.0 !from CC3163 OC3C61 CC3162 OC301 +CC3163 OC3C61 CC3062 OC301 0.89 2 0.0 ! " +CC3163 OC3C61 CC3062 OC301 0.05 3 0.0 ! " + +HCA2 CC3261 CC3062 OC301 0.20 3 0.0 !from HCA1 CC3161 CC3162 OC301 + +CC3161 CC3261 CC3062 OC301 0.20 3 0.0 !from CC3161 CC3161 CC3162 OC301 + +OC301 CC3161 CC3161 OC301 0.59 1 180.0 !from OC301 CC3161 CC3162 OC301 +OC301 CC3161 CC3161 OC301 1.16 2 0.0 ! " + +! pram transferred from hexopyranose disac for xyl +CC3263 CC3161 OC301 CC3162 0.13 1 180.0 ! from CC3163 CC3161 OC301 CC3162 +CC3263 CC3161 OC301 CC3162 0.25 2 180.0 ! " +CC3263 CC3161 OC301 CC3162 0.06 3 180.0 ! " + +OC301 CC3161 CC3263 HCA2 0.20 3 0.0 ! from OC301 CC3161 CC3163 HCA1 + +OC301 CC3161 CC3263 OC3C61 1.36 1 180.0 ! from OC301 CC3161 CC3163 OC3C61 +OC301 CC3161 CC3263 OC3C61 0.16 2 0.0 ! " +OC301 CC3161 CC3263 OC3C61 1.01 3 0.0 ! " + +CC3263 OC3C61 CC3162 OC301 0.41 1 180.0 ! from CC3163 OC3C61 CC3162 OC301 +CC3263 OC3C61 CC3162 OC301 0.89 2 0.0 ! " +CC3263 OC3C61 CC3162 OC301 0.05 3 0.0 ! " + + +!! THF parameters for furanoses; viv, added by erh +HCA2C2 CC322C CC322C HCA2C2 0.19 3 0.0 !alkane, 4/98, yin and mackerell!from X-CCT2-CCT2-X thf, viv +CC322C CC322C CC322C HCA2C2 0.19 3 0.0 !alkane, 4/98, yin and mackerell!from X-CCT2-CCT2-X thf, viv +OC3C5M CC322C CC322C HCA2C2 0.19 3 0.0 ! alkane, 4/98, yin and mackerell!from X-CCT2-CCT2-X thf viv +CC322C CC322C CC322C CC322C 0.41 3 180.0 !cpen viv 10/4/05 !from CCP2-CCP2-CCP2-CCP2 THF, 05/30/06, viv +HCA2C2 CC322C OC3C5M CC322C 0.30 3 0.0 ! THF, 05/30/06, viv +OC3C5M CC322C CC322C CC322C 0.00 3 0.0 ! THF, 05/30/06, viv +CC322C CC322C OC3C5M CC322C 0.50 3 0.0 ! THF, 05/30/06, viv +! THF w/Methyl +! erh added and corrected for atom type, giving better pure solvent results 7/08 +CC331 CC312C CC312C CC331 0.20 3 0.0 ! par22 X CT1 CT1 X +CC331 CC312C CC322C CC322C 0.20 3 0.0 ! par22 X CT1 CT2 X +CC331 CC312C CC322C HCA2C2 0.20 3 0.0 ! par22 X CT1 CT2 X +HCA1C2 CC312C CC331 HCA3 0.20 3 0.0 ! par22 X CT1 CT3 X +CC322C CC312C CC331 HCA3 0.20 3 0.0 ! par22 X CT1 CT3 X +OC3C5M CC312C CC331 HCA3 0.20 3 0.0 ! par22 X CT1 CT3 X +HCA1C2 CC312C CC322C HCA2C2 0.20 3 0.0 ! par22 X CT1 CT2 X +CC322C CC312C CC322C HCA2C2 0.20 3 0.0 ! par22 X CT1 CT2 X +CC322C CC322C CC312C HCA1C2 0.20 3 0.0 ! par22 X CT1 CT2 X +OC3C5M CC312C CC322C HCA2C2 0.20 3 0.0 ! par22 X CT1 CT2 X +CC312C CC322C CC322C HCA2C2 0.19 3 0.0 ! alkane, 4/98, yin and mackerell!from X-CCT2-CCT2-X thf, viv +CC312C CC322C CC322C CC322C 0.41 3 180.0 ! cpen viv 10/4/05 !from CCP2-CCP2-CCP2-CCP2 THF, 05/30/06, viv; +CC322C CC312C CC322C CC322C 0.41 3 180.0 ! cpen viv 10/4/05 !from CCP2-CCP2-CCP2-CCP2 THF, 05/30/06, viv; +HCA2C2 CC322C OC3C5M CC312C 0.30 3 0.0 ! THF, 05/30/06, viv; erh 7/08 +HCA1C2 CC312C OC3C5M CC322C 0.30 3 0.0 ! THF, 05/30/06, viv; erh 7/08 +OC3C5M CC312C CC322C CC322C 0.00 3 0.0 ! THF, 05/30/06, viv; erh 7/08 +CC322C CC312C OC3C5M CC322C 0.50 3 0.0 ! THF, 05/30/06, viv; erh 7/08 +CC322C CC322C OC3C5M CC312C 0.50 3 0.0 ! THF, 05/30/06, viv; erh 7/08 +CC331 CC312C OC3C5M CC322C 0.30 3 0.0 ! THF, 05/30/06, viv ! from TF2M viv +! + +! OMe-THF param for omef patch +CC312C OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +HCA1C2 CC312C OC301 CC331 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +OC301 CC312C CC322C HCA2C2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC322C CC322C CC312C OC301 0.20 3 0.0 ! par27 X CTL2 CTL1 X +OC301 CC312C OC3C5M CC322C 0.30 3 0.0 ! THF, 05/30/06, viv + +CC322C CC312C OC301 CC331 0.21 1 180.0 ! erh OMeTHF patch for model THF +CC322C CC312C OC301 CC331 0.34 2 180.0 ! " MCSA fit +CC322C CC312C OC301 CC331 0.74 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC331 OC301 CC312C OC3C5M 0.08 1 0.0 ! erh OMeTHF patch for model THF +CC331 OC301 CC312C OC3C5M 0.76 2 0.0 ! " MCSA fit +CC331 OC301 CC312C OC3C5M 1.18 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! monosaccharide furanoses; erh modified 10/25/07!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +! OCOH +OC3C51 CC3152 OC311 HCP1 1.17 1 0.0 ! erh aldopentose monosac +OC3C51 CC3152 OC311 HCP1 0.85 2 0.0 ! " MCSA fit +OC3C51 CC3152 OC311 HCP1 0.37 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC3C51 CC3051 OC311 HCP1 0.90 1 0.0 ! erh ketopentose monosac +OC3C51 CC3051 OC311 HCP1 1.14 2 0.0 ! " MCSA fit +OC3C51 CC3051 OC311 HCP1 0.11 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +! OCCH +OC3C51 CC3152 CC3251 HCA2 0.20 3 0.0 ! par22 X CT1 CT2 X +OC3C51 CC3051 CC3251 HCA2 0.20 3 0.0 ! par22 X CT1 CT2 X +OC3C51 CC3152 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +OC3C51 CC3051 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +OC3C51 CC3153 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +OC3C51 CC3153 CC321 HCA2 0.20 3 0.0 ! par22 X CT1 CT2 X +OC3C51 CC3152 CC321 HCA2 0.20 3 0.0 ! par22 X CT1 CT2 X +OC3C51 CC3051 CC321 HCA2 0.20 3 0.0 ! par22 X CT1 CT2 X +OC311 CC3152 CC3251 HCA2 0.14 3 0.0 ! ethanol, par_carb HCA2 CC3263 CC3161 OC311 +OC311 CC3051 CC3251 HCA2 0.14 3 0.0 ! ethanol, par_carb HCA2 CC3263 CC3161 OC311 +OC311 CC3051 CC321 HCA2 0.14 3 0.0 ! ethanol, par_carb HCA2 CC3263 CC3161 OC311; erh 3/08 +OC311 CC3151 CC3251 HCA2 0.14 3 0.0 ! ethanol, par_carb HCA2 CC3263 CC3161 OC311 +OC311 CC3151 CC3153 HCA1 0.14 3 0.0 ! ethanol, par_carb HCA1 CC3163 CC3161 OC311 +OC311 CC3151 CC3152 HCA1 0.14 3 0.0 ! ethanol, par_carb HCA1 CC3162 CC3161 OC311 +OC311 CC3151 CC3151 HCA1 0.14 3 0.0 ! ethanol, par_carb HCA1 CC3161 CC3161 OC311 +OC311 CC3152 CC3151 HCA1 0.14 3 0.0 ! ethanol, par_carb HCA1 CC3161 CC3162 OC311 +OC311 CC3051 CC3151 HCA1 0.14 3 0.0 ! ethanol, par_carb HCA1 CC3161 CC3162 OC311 +OC311 CC321 CC3153 HCA1 0.14 3 0.0 ! ethanol, par_carb HCA1 CC3163 CC321 OC311 + +! OCCO +OC3C51 CC3153 CC3151 OC311 0.14 1 0.0 ! erh aldopentose monosac +OC3C51 CC3153 CC3151 OC311 0.70 2 0.0 ! " MCSA fit +OC3C51 CC3153 CC3151 OC311 0.18 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC3C51 CC3152 CC3151 OC311 1.26 1 180.0 ! erh aldopentose monosac +OC3C51 CC3152 CC3151 OC311 1.27 2 0.0 ! " MCSA fit +OC3C51 CC3152 CC3151 OC311 0.53 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC3C51 CC3051 CC3151 OC311 0.32 1 180.0 ! erh ketopentose monosac +OC3C51 CC3051 CC3151 OC311 0.65 2 180.0 ! " MCSA fit +OC3C51 CC3051 CC3151 OC311 2.62 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC3C51 CC3153 CC321 OC311 1.50 1 180.0 ! erh aldopentose monosac +OC3C51 CC3153 CC321 OC311 0.58 2 0.0 ! " MCSA fit +OC3C51 CC3153 CC321 OC311 0.54 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC3C51 CC3051 CC321 OC311 0.52 1 0.0 ! erh ketopentose monosac +OC3C51 CC3051 CC321 OC311 1.16 2 180.0 ! " MCSA fit +OC3C51 CC3051 CC321 OC311 0.33 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC311 CC3152 CC3151 OC311 2.87 1 180.0 ! erh aldopentose monosac +OC311 CC3152 CC3151 OC311 0.03 2 0.0 ! " MCSA fit +OC311 CC3152 CC3151 OC311 0.23 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC311 CC3051 CC3151 OC311 0.12 1 180.0 ! erh ketopentose monosac +OC311 CC3051 CC3151 OC311 1.87 2 180.0 ! " MCSA fit +OC311 CC3051 CC3151 OC311 1.64 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC311 CC3151 CC3151 OC311 2.87 1 180.0 ! erh aldopentose monosac +OC311 CC3151 CC3151 OC311 0.03 2 0.0 ! " MCSA fit +OC311 CC3151 CC3151 OC311 0.23 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC311 CC3051 CC321 OC311 0.07 1 0.0 ! erh ketopentose monosac +OC311 CC3051 CC321 OC311 1.99 2 180.0 ! " MCSA fit +OC311 CC3051 CC321 OC311 1.72 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +! OCOC +OC311 CC3152 OC3C51 CC3153 0.76 1 180.0 ! erh aldopentose monosac +OC311 CC3152 OC3C51 CC3153 1.25 2 0.0 ! " MCSA fit +OC311 CC3152 OC3C51 CC3153 0.48 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC311 CC3051 OC3C51 CC3153 0.19 1 180.0 ! erh ketopentose monosac +OC311 CC3051 OC3C51 CC3153 2.85 2 180.0 ! " MCSA fit +OC311 CC3051 OC3C51 CC3153 0.86 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +! CCCC +CC3152 CC3251 CC3151 CC3153 1.83 3 0.0 ! erh deoxy aldopentose MCSA fit +CC3051 CC3251 CC3151 CC3153 1.83 3 0.0 ! erh xfer from deoxyaldopentose +CC3152 CC3151 CC3151 CC3153 0.64 3 180.0 ! erh aldopentose MCSA fit +CC3051 CC3151 CC3151 CC3153 2.37 3 0.0 ! erh ketopentose MCSA fit +CC3251 CC3151 CC3153 CC321 0.20 3 0.0 ! par22 X CT1 CT1 X +CC3151 CC3151 CC3153 CC321 0.20 3 0.0 ! par22 X CT1 CT1 X +CC3151 CC3151 CC3051 CC321 0.20 3 0.0 ! par22 X CT1 CT1 X + +! CCCO +CC3152 CC3251 CC3151 OC311 0.39 1 0.0 ! erh deoxy aldopentose monosac +CC3152 CC3251 CC3151 OC311 1.20 2 0.0 ! " MCSA fit +CC3152 CC3251 CC3151 OC311 1.42 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3051 CC3251 CC3151 OC311 0.39 1 0.0 ! erh deoxy aldopentose monosac +CC3051 CC3251 CC3151 OC311 1.20 2 0.0 ! " transferred +CC3051 CC3251 CC3151 OC311 1.42 3 180.0 ! " + +CC3153 CC3151 CC3151 OC311 0.01 1 180.0 ! erh aldopentose monosac +CC3153 CC3151 CC3151 OC311 0.72 2 0.0 ! " MCSA fit +CC3153 CC3151 CC3151 OC311 0.73 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3152 CC3151 CC3151 OC311 0.81 1 180.0 ! erh aldopentose monosac +CC3152 CC3151 CC3151 OC311 1.07 2 0.0 ! " MCSA fit +CC3152 CC3151 CC3151 OC311 0.11 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3051 CC3151 CC3151 OC311 2.07 1 0.0 ! erh ketopentose monosac +CC3051 CC3151 CC3151 OC311 2.13 2 0.0 ! " MCSA fit +CC3051 CC3151 CC3151 OC311 2.71 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3251 CC3152 OC311 0.56 1 180.0 ! erh deoxy aldopentose monosac +CC3151 CC3251 CC3152 OC311 0.30 2 180.0 ! " MCSA fit +CC3151 CC3251 CC3152 OC311 0.35 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3251 CC3051 OC311 0.56 1 180.0 ! erh deoxy aldopentose monosac +CC3151 CC3251 CC3051 OC311 0.30 2 180.0 ! " transferred +CC3151 CC3251 CC3051 OC311 0.35 3 180.0 ! " + +CC3151 CC3151 CC3152 OC311 0.11 1 180.0 ! erh aldopentose monosac +CC3151 CC3151 CC3152 OC311 0.66 2 0.0 ! " MCSA fit +CC3151 CC3151 CC3152 OC311 0.02 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3151 CC3051 OC311 2.23 1 0.0 ! erh ketopentose monosac +CC3151 CC3151 CC3051 OC311 3.00 2 0.0 ! " MCSA fit +CC3151 CC3151 CC3051 OC311 0.88 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3153 CC321 OC311 0.01 1 0.0 ! erh aldopentose monosac +CC3151 CC3153 CC321 OC311 0.14 2 0.0 ! " MCSA fit +CC3151 CC3153 CC321 OC311 0.70 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3051 CC321 OC311 1.59 1 0.0 ! erh ketopentose monosac +CC3151 CC3051 CC321 OC311 0.95 2 180.0 ! " MCSA fit +CC3151 CC3051 CC321 OC311 1.95 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC321 CC3153 CC3151 OC311 0.76 1 180.0 ! erh aldopentose monosac +CC321 CC3153 CC3151 OC311 0.40 2 180.0 ! " MCSA fit +CC321 CC3153 CC3151 OC311 0.40 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC321 CC3051 CC3151 OC311 0.94 1 0.0 ! erh ketopentose monosac +CC321 CC3051 CC3151 OC311 1.59 2 180.0 ! " MCSA fit +CC321 CC3051 CC3151 OC311 0.84 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3151 CC3153 OC3C51 1.24 3 0.0 ! erh aldopentose monosac MCSA +CC3151 CC3151 CC3152 OC3C51 1.24 3 0.0 ! erh aldopentose monosac MCSA + +CC3251 CC3151 CC3153 OC3C51 0.94 3 0.0 ! erh deoxy aldopentose MCSA +CC3151 CC3251 CC3152 OC3C51 0.94 3 0.0 ! erh deoxy aldopentose MCSA +CC3151 CC3251 CC3051 OC3C51 0.94 3 0.0 ! erh deoxy aldopentose transfer +CC3151 CC3151 CC3051 OC3C51 0.62 3 0.0 ! erh ketopentose monosac MCSA + +! CCOH +CC3251 CC3152 OC311 HCP1 0.59 1 0.0 ! erh deoxy aldopentose monosac +CC3251 CC3152 OC311 HCP1 0.38 2 0.0 ! " MCSA fit +CC3251 CC3152 OC311 HCP1 0.13 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3251 CC3051 OC311 HCP1 0.59 1 0.0 ! erh deoxy aldopentose monosac +CC3251 CC3051 OC311 HCP1 0.38 2 0.0 ! " transferred +CC3251 CC3051 OC311 HCP1 0.13 3 0.0 ! " + +CC321 CC3051 OC311 HCP1 0.40 1 180.0 ! erh ketopentose monosac +CC321 CC3051 OC311 HCP1 0.48 2 0.0 ! " MCSA fit +CC321 CC3051 OC311 HCP1 0.19 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3152 OC311 HCP1 0.29 1 0.0 ! erh aldopentose monosac +CC3151 CC3152 OC311 HCP1 0.55 2 0.0 ! " MCSA fit +CC3151 CC3152 OC311 HCP1 0.08 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3051 OC311 HCP1 0.40 1 180.0 ! erh ketopentose monosac +CC3151 CC3051 OC311 HCP1 0.48 2 0.0 ! " MCSA fit +CC3151 CC3051 OC311 HCP1 0.19 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3151 OC311 HCP1 0.29 1 0.0 ! erh aldopentose monosac +CC3151 CC3151 OC311 HCP1 0.55 2 0.0 ! " MCSA fit +CC3151 CC3151 OC311 HCP1 0.08 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3152 CC3151 OC311 HCP1 0.29 1 0.0 ! erh aldopentose monosac +CC3152 CC3151 OC311 HCP1 0.55 2 0.0 ! " MCSA fit +CC3152 CC3151 OC311 HCP1 0.08 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3051 CC3151 OC311 HCP1 0.40 1 180.0 ! erh ketopentose monosac +CC3051 CC3151 OC311 HCP1 0.48 2 0.0 ! " MCSA fit +CC3051 CC3151 OC311 HCP1 0.19 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3251 CC3151 OC311 HCP1 0.59 1 0.0 ! erh deoxy aldopentose monosac +CC3251 CC3151 OC311 HCP1 0.38 2 0.0 ! " MCSA fit +CC3251 CC3151 OC311 HCP1 0.13 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3153 CC3151 OC311 HCP1 0.29 1 0.0 ! erh aldopentose monosac +CC3153 CC3151 OC311 HCP1 0.55 2 0.0 ! " MCSA fit +CC3153 CC3151 OC311 HCP1 0.08 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3153 CC321 OC311 HCP1 0.12 1 0.0 ! erh aldopentose monosac +CC3153 CC321 OC311 HCP1 0.42 2 0.0 ! " MCSA fit +CC3153 CC321 OC311 HCP1 0.29 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3051 CC321 OC311 HCP1 0.40 1 180.0 ! erh ketopentose monosac +CC3051 CC321 OC311 HCP1 0.48 2 0.0 ! " MCSA fit +CC3051 CC321 OC311 HCP1 0.19 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + + +! CCCH +CC3152 CC3251 CC3151 HCA1 0.20 3 0.0 ! par22 X CT2 CT1 X +CC3051 CC3251 CC3151 HCA1 0.20 3 0.0 ! par22 X CT2 CT1 X +CC3151 CC3251 CC3152 HCA1 0.20 3 0.0 ! par22 X CT2 CT1 X +CC3151 CC3151 CC3152 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +CC3151 CC3151 CC3153 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +CC3151 CC3153 CC321 HCA2 0.20 3 0.0 ! par22 X CT2 CT1 X +CC3151 CC3152 CC321 HCA2 0.20 3 0.0 ! par22 X CT2 CT1 X erh 3/08 +CC3151 CC3051 CC321 HCA2 0.20 3 0.0 ! par22 X CT2 CT1 X erh 3/08 +CC3153 CC3151 CC3251 HCA2 0.20 3 0.0 ! par22 X CT2 CT1 X +CC3153 CC3151 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +CC3152 CC3151 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +CC3051 CC3151 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +CC321 CC3153 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +CC321 CC3152 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X erh3/08 +CC321 CC3051 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X erh3/08 +CC3251 CC3151 CC3153 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X + +! COCC +CC3152 OC3C51 CC3153 CC3151 1.00 3 0.0 ! erh aldopentose MCSA +CC3153 OC3C51 CC3152 CC3151 1.00 3 0.0 ! erh aldopentose MCSA +CC3153 OC3C51 CC3152 CC3251 0.45 3 0.0 ! erh deoxy aldopentose MCSA +CC3153 OC3C51 CC3051 CC3151 0.61 3 0.0 ! erh ketopentose MCSA +CC3153 OC3C51 CC3051 CC3251 0.61 3 0.0 ! erh from ketopentose +CC3051 OC3C51 CC3153 CC3151 0.43 3 0.0 ! erh ketopentose MCSA +CC3152 OC3C51 CC3153 CC321 0.30 3 0.0 ! TF2M par_carb CC331C CC322C OC3C5M CC322C + +CC3051 OC3C51 CC3153 CC321 2.58 1 0.0 ! erh ketopentose monosac +CC3051 OC3C51 CC3153 CC321 0.24 2 180.0 ! " MCSA fit +CC3051 OC3C51 CC3153 CC321 0.36 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3153 OC3C51 CC3051 CC321 0.24 1 0.0 ! erh ketopentose monosac +CC3153 OC3C51 CC3051 CC321 3.00 2 180.0 ! " MCSA fit +CC3153 OC3C51 CC3051 CC321 1.38 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +! COCH +CC3152 OC3C51 CC3153 HCA1 0.30 3 0.0 ! THF par_carb HCA2C2 CC322C OC3C5M CC322C +CC3051 OC3C51 CC3153 HCA1 0.30 3 0.0 ! THF par_carb HCA2C2 CC322C OC3C5M CC322C +CC3153 OC3C51 CC3152 HCA1 0.30 3 0.0 ! THF par_carb HCA2C2 CC322C OC3C5M CC322C + +! HCCH +HCA1 CC3152 CC3251 HCA2 0.20 3 0.0 ! par22 X CT1 CT2 X +HCA2 CC3251 CC3151 HCA1 0.20 3 0.0 ! par22 X CT2 CT1 X +HCA1 CC3151 CC3153 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +HCA1 CC3151 CC3152 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +HCA1 CC3151 CC3151 HCA1 0.20 3 0.0 ! par22 X CT1 CT1 X +HCA1 CC3153 CC321 HCA2 0.20 3 0.0 ! par22 X CT1 CT2 X + +! HOCH +HCP1 OC311 CC3152 HCA1 0.18 3 0.0 ! methanol par_carb HCP1 OC311 CC3162 HCA1 +HCP1 OC311 CC3151 HCA1 0.18 3 0.0 ! methanol par_carb HCP1 OC311 CC3161 HCA1 + +! OMe-furanose param for fomea/b patch + +OC301 CC3152 CC3151 OC311 2.87 1 180.0 ! erh aldopentose monosac +OC301 CC3152 CC3151 OC311 0.03 2 0.0 ! " MCSA fit +OC301 CC3152 CC3151 OC311 0.23 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3152 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +HCA1 CC3152 OC301 CC331 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +OC301 CC3152 CC3151 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X + +CC3151 CC3151 CC3152 OC301 0.11 1 180.0 ! erh aldopentose monosac +CC3151 CC3151 CC3152 OC301 0.66 2 0.0 ! " MCSA fit +CC3151 CC3151 CC3152 OC301 0.02 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3151 CC3051 OC301 2.23 1 0.0 ! erh ketopentose monosac +CC3151 CC3151 CC3051 OC301 3.00 2 0.0 ! " MCSA fit +CC3151 CC3151 CC3051 OC301 0.88 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC301 CC3152 OC3C51 CC3153 0.76 1 180.0 ! erh aldopentose monosac +OC301 CC3152 OC3C51 CC3153 1.25 2 0.0 ! " MCSA fit +OC301 CC3152 OC3C51 CC3153 0.48 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3153 OC3C51 CC3051 OC301 0.19 1 180.0 ! erh ketopentose monosac +CC3153 OC3C51 CC3051 OC301 2.85 2 180.0 ! " MCSA fit +CC3153 OC3C51 CC3051 OC301 0.86 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3151 CC3152 OC301 CC331 0.21 1 180.0 ! erh OMeTHF patch for model THF +CC3151 CC3152 OC301 CC331 0.34 2 180.0 ! " MCSA fit +CC3151 CC3152 OC301 CC331 0.74 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC331 OC301 CC3152 OC3C51 0.08 1 0.0 ! erh OMeTHF patch for model THF +CC331 OC301 CC3152 OC3C51 0.76 2 0.0 ! " MCSA fit +CC331 OC301 CC3152 OC3C51 1.18 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +!***********************end of furanose**************************************** +!Added by sai for modelling phosphate + +CC321D CC311D OC30P PC 0.02 3 180.0 +CC3161 CC3162 OC30P PC 0.02 3 180.0 +CC3161 CC3161 OC30P PC 0.02 3 180.0 +CC321C CC311D OC30P PC 0.02 3 180.0 +CC311D CC311D OC30P PC 0.02 3 180.0 +HCA1 CC311D OC30P PC 0.284 3 0.0 ! dmp,eps, H-C3'-O3'-P || from the par_all27_na.prm +HCA1 CC3161 OC30P PC 0.284 3 0.0 ! dmp,eps, H-C3'-O3'-P || from the par_all27_na.prm +HCA1 CC3162 OC30P PC 0.284 3 0.0 ! dmp,eps, H-C3'-O3'-P || from the par_all27_na.prm + +OC3C61 CC311D OC30P PC 0.38 2 0.0 +OC3C61 CC311D OC30P PC 0.41 3 180.0 +OC3C61 CC3162 OC30P PC 0.38 2 0.0 +OC3C61 CC3162 OC30P PC 0.41 3 180.0 + +HCA1 CC311D CC311D HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA2 CC321D CC311D HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +OC3C61 CC311D CC311D HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC3C61 CC321D CC311D HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321D CC311D CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321C CC311D CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 +CC311D CC311D CC321C HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321C CC311D CC311D HCA1 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321C CC311D CC321D HCA2 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC321C CC311D CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC311D CC311D CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +CC321D CC311D CC321C CC321C 0.19 3 180.0 ! og/sng cyclohexane +OC3C61 CC311D CC311D CC321C 0.31 3 180.0 ! og/sng thp +OC3C61 CC321D CC311D CC321C 0.31 3 180.0 ! og/sng thp +CC311D CC311D OC3C61 CC321C 0.20 3 0.0 ! og/sng thp +CC311D CC321D OC3C61 CC321C 0.20 3 0.0 ! og/sng thp + +HCA1 CC3161 CC3162 OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC3162 CC3161 OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC3163 CC3161 OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC3161 CC3161 OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC311D CC311D OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA2 CC321C CC311D OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA2 CC321D CC311D OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +HCA1 CC311C CC321 OC30P 0.00 6 180.00 +HCA1 CC3163 CC321 OC30P 0.00 6 180.00 +CC321C CC311C CC321 OC30P 0.43 3 0.0 +CC3161 CC3163 CC321 OC30P 0.43 3 0.0 + +CC3161 CC3161 CC3162 OC30P 1.76 1 0.0 +CC3161 CC3161 CC3162 OC30P 2.56 2 0.0 +CC3161 CC3161 CC3162 OC30P 0.01 3 0.0 +CC321C CC321C CC311D OC30P 1.76 1 0.0 +CC321C CC321C CC311D OC30P 2.56 2 0.0 +CC321C CC321C CC311D OC30P 0.01 3 0.0 +CC3161 CC3161 CC3161 OC30P 1.76 1 0.0 +CC3161 CC3161 CC3161 OC30P 2.56 2 0.0 +CC3161 CC3161 CC3161 OC30P 0.01 3 0.0 +CC3162 CC3161 CC3161 OC30P 1.76 1 0.0 +CC3162 CC3161 CC3161 OC30P 2.56 2 0.0 +CC3162 CC3161 CC3161 OC30P 0.01 3 0.0 +CC3163 CC3161 CC3161 OC30P 1.76 1 0.0 +CC3163 CC3161 CC3161 OC30P 2.56 2 0.0 +CC3163 CC3161 CC3161 OC30P 0.01 3 0.0 +CC321C CC311D CC311D OC30P 1.76 1 0.0 +CC321C CC311D CC311D OC30P 2.56 2 0.0 +CC321C CC311D CC311D OC30P 0.01 3 0.0 +CC321C OC3C61 CC311D OC30P 2.44 3 180.0 +CC3163 OC3C61 CC3162 OC30P 2.44 3 180.0 + +OC30P CC3161 CC3161 OC311 2.50 1 180.0 +OC30P CC3161 CC3161 OC311 2.00 2 0.0 +OC30P CC3161 CC3161 OC311 2.50 3 0.0 +OC30P CC311D CC3161 OC311 2.50 1 180.0 +OC30P CC311D CC3161 OC311 2.00 2 0.0 +OC30P CC311D CC3161 OC311 2.50 3 0.0 +OC30P CC3162 CC3161 OC311 2.50 1 180.0 +OC30P CC3162 CC3161 OC311 2.00 2 0.0 +OC30P CC3162 CC3161 OC311 2.50 3 0.0 +OC30P CC3161 CC3162 OC301 2.50 1 180.0 +OC30P CC3161 CC3162 OC301 2.00 2 0.0 +OC30P CC3161 CC3162 OC301 2.50 3 0.0 +OC30P CC3161 CC3161 OC301 2.50 1 180.0 +OC30P CC3161 CC3161 OC301 2.00 2 0.0 +OC30P CC3161 CC3161 OC301 2.50 3 0.0 + +OC30P CC3161 CC3161 OC30P 1.27 3 0.0 +OC30P CC311D CC311D OC30P 1.27 3 0.0 +OC3C61 CC311D CC311D OC30P 0.61 3 0.0 +OC3C61 CC321D CC311D OC30P 0.61 3 0.0 +OC3C61 CC3162 CC3161 OC30P 0.61 3 0.0 +OC3C61 CC3163 CC3161 OC30P 0.61 3 0.0 +OC3C61 CC311C CC321 OC30P 0.06 1 0.0 +OC3C61 CC311C CC321 OC30P 0.78 2 0.0 +OC3C61 CC311C CC321 OC30P 0.74 3 180.0 +OC3C61 CC3163 CC321 OC30P 0.06 1 0.0 +OC3C61 CC3163 CC321 OC30P 0.78 2 0.0 +OC3C61 CC3163 CC321 OC30P 0.74 3 180.0 + +CC3161 OC30P PC OC2DP 0.33 3 0.0 +CC3162 OC30P PC OC2DP 0.33 3 0.0 +CC311D OC30P PC OC2DP 0.33 3 0.0 +CC311D OC30P PC OC312 1.45 2 0.0 + +OC312 PC OC312 HCP1 0.30 3 0.00 ! terminal phosphate +OC30P PC OC312 HCP1 0.30 3 0.00 ! terminal phosphate +OC2DP PC OC312 HCP1 0.30 3 0.00 ! terminal phosphate + +CC3161 OC30P PC OC312 1.45 2 0.0 !CC311D OC30P PC OC312 1.45 2 0.0 +CC3162 OC30P PC OC312 1.45 2 0.0 + +CC321C CC311D OC30P SC 0.21 3 0.0 +CC3162 CC3161 OC30P SC 0.21 3 0.0 +CC3163 CC3161 OC30P SC 0.21 3 0.0 +CC3161 CC3161 OC30P SC 0.21 3 0.0 +HCA1 CC311D OC30P SC 0.00 3 0.00 ! methylsulfate +HCA1 CC3161 OC30P SC 0.00 3 0.00 ! methylsulfate +HCA2 CC321 OC30P SC 0.284 3 0.0 ! +OC3C61 CC311D OC30P SC 0.76 1 0.0 +OC3C61 CC311D OC30P SC 0.68 2 0.0 +OC3C61 CC311D OC30P SC 0.26 3 180.0 +CC311C CC321 OC30P SC 1.41 1 180.0 +CC311C CC321 OC30P SC 0.40 2 0.0 +CC311C CC321 OC30P SC 0.21 3 180.0 +CC3163 CC321 OC30P SC 1.41 1 180.0 +CC3163 CC321 OC30P SC 0.40 2 0.0 +CC3163 CC321 OC30P SC 0.21 3 180.0 + +CC3161 OC30P SC OC2DP 0.17 3 0.0 +CC311D OC30P SC OC2DP 0.17 3 0.0 +CC321 OC30P SC OC2DP 0.17 3 0.0 + +CC321 CC3163 CC3161 OC30P 0.20 3 0.0 ! par27 X CTL1 CTL1 X + +!*******************end of phosphates*********************************** + +!O-ethyl THP, pram +CC321 OC301 CC311D HCA1 0.284 3 0.0 ! OMeTHP CC331 OC301 CC311D HCA1 +OC301 CC321 CC331 HCA3 0.20 3 0.0 ! OC301 CC321 CC3163 HCA1 +CC311D OC301 CC321 HCA2 0.284 3 0.0 ! OMeTHP CC311D OC301 CC331 HCA3 +CC321 OC301 CC311D OC3C61 0.36 1 180.0 ! pr, 1-ethoxy-THP2 QM phi-psi scan +CC321 OC301 CC311D OC3C61 0.52 2 0.0 ! " MCSA fit " +CC321 OC301 CC311D OC3C61 0.83 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC311D OC301 CC321 CC331 0.72 1 180.0 ! pr, 1-ethoxy-THP2 QM phi-psi scan +CC311D OC301 CC321 CC331 0.34 2 180.0 ! " MCSA fit " +CC311D OC301 CC321 CC331 0.12 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC321 OC301 CC311D CC321C 0.58 1 180.0 ! pr, 1-ethoxy-THP2 QM phi-psi scan +CC321 OC301 CC311D CC321C 0.69 2 180.0 ! " MCSA fit " +CC321 OC301 CC311D CC321C 1.16 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! pyranose/furanose-furanose link; pram +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +!model compounds +CC322C CC322C CC312D OC301 1.98 1 0.0 ! pram OMeTHF compound 5 (raman et al) +CC322C CC322C CC312D OC301 2.56 2 0.0 ! " MCSA fit +CC322C CC322C CC312D OC301 1.80 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC322C OC3C5M CC312D OC301 1.88 1 0.0 ! pram OMeTHF compound 5 (raman et al) +CC322C OC3C5M CC312D OC301 2.18 2 0.0 ! " MCSA fit +CC322C OC3C5M CC312D OC301 0.24 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC322C CC312D OC301 CC331 0.97 1 180.0 ! pram OMeTHF compound 5 (raman et al) +CC322C CC312D OC301 CC331 0.44 3 180.0 ! " MCSA fit +CC331 OC301 CC312D OC3C5M 0.98 2 0.0 ! pram OMeTHF compound 5 (raman et al) +CC331 OC301 CC312D OC3C5M 1.50 3 0.0 ! " MCSA fit +CC312D OC301 CC331 HCA3 0.284 3 0.0 ! OMe-THF CC312C OC301 CC331 HCA3 +HCA1 CC312D OC301 CC331 0.284 3 0.0 ! OMe-THF HCA1C2 CC312C OC301 CC331 +OC301 CC312D CC322C HCA2C2 0.20 3 0.0 ! OMe-THF OC301 CC312C CC322C HCA2C2 + +CC312D OC302 CC311D OC3C61 0.21 1 0.0 ! pram model compound 1 (raman et al) +CC312D OC302 CC311D OC3C61 0.86 2 0.0 ! " MCSA fit +CC312D OC302 CC311D OC3C61 0.35 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC311D OC302 CC312D OC3C5M 0.70 1 180.0 ! pram model compound 1 (raman et al) +CC311D OC302 CC312D OC3C5M 1.41 2 0.0 ! " MCSA fit +CC311D OC302 CC312D OC3C5M 0.75 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC311D OC302 CC312D CC322C 1.23 1 180.0 ! pram model compound 1 (raman et al) +CC311D OC302 CC312D CC322C 0.15 2 0.0 ! " MCSA fit +CC311D OC302 CC312D CC322C 0.54 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC312D OC302 CC311D CC321C 0.18 1 180.0 ! pram model compound 1 (raman et al) +CC312D OC302 CC311D CC321C 0.45 2 180.0 ! " MCSA fit +CC312D OC302 CC311D CC321C 0.75 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC312D OC302 CC311D HCA1 0.284 3 0.0 ! CC311D OC302 CC311D HCA1 + +CC322C CC322C CC312D OC302 1.98 1 0.0 ! pram model compound 5 (raman et al) +CC322C CC322C CC312D OC302 2.56 2 0.0 ! pram model compound 5 (raman et al) +CC322C CC322C CC312D OC302 1.80 3 0.0 ! pram model compound 5 (raman et al) +CC322C OC3C5M CC312D OC302 1.88 1 0.0 ! pram model compound 5 (raman et al) +CC322C OC3C5M CC312D OC302 2.18 2 0.0 ! pram model compound 5 (raman et al) +CC322C OC3C5M CC312D OC302 0.24 3 0.0 ! pram model compound 5 (raman et al) + +OC302 CC312D CC322C HCA2C2 0.20 3 0.0 ! OMe-THF OC301 CC312C CC322C HCA2C2 +OC3C5M CC312D CC322C HCA2C2 0.20 3 0.0 ! THF w/me OC3C5M CC312C CC322C HCA2C2 +OC3C5M CC312D CC322C CC322C 0.00 3 0.0 ! THF w/me OC3C5M CC312C CC322C CC322C +CC322C CC322C OC3C5M CC312D 0.50 3 0.0 ! THF w/me CC322C CC322C OC3C5M CC322C +CC312D CC322C CC322C HCA2C2 0.19 3 0.0 ! THF w/me CC312C CC322C CC322C HCA2C2 +CC312D CC322C CC322C CC322C 0.41 3 180.0 ! THF w/me CC312C CC322C CC322C CC322C + +HCA1 CC312D OC3C5M CC322C 0.30 3 0.0 ! THF w/me HCA1C2 CC312C OC3C5M CC322C +HCA1 CC312D CC322C HCA2C2 0.20 3 0.0 ! THF w/me HCA1C2 CC312C CC322C HCA2C2 +CC322C CC322C CC312D HCA1 0.20 3 0.0 ! THF w/me CC322C CC322C CC312C HCA1C2 +CC322C CC312D OC3C5M CC322C 0.50 3 0.0 ! THF w/me CC322C CC312C OC3C5M CC322C +HCA1 CC312D OC302 CC311D 0.284 3 0.0 ! OMe-THF HCA1C2 CC312C OC301 CC331 +HCA2C2 CC322C OC3C5M CC312D 0.30 3 0.0 ! THF w/me HCA2C2 CC322C OC3C5M CC312C + +OC3C5M CC312C CC321 HCA2 0.20 3 0.0 ! COCA-THP2 OC3C61 CC311C CC321 HCA2 +HCA1 CC312C OC3C5M CC322C 0.30 3 0.0 ! THF w/me HCA1C2 CC312C OC3C5M CC322C +CC322C CC322C CC312C HCA1 0.20 3 0.0 ! THF w/me CC322C CC322C CC312C HCA1C2 +CC322C CC312C CC321 HCA2 0.20 3 0.0 ! THF w/me CC322C CC312C CC331 HCA3 +HCA2C2 CC322C CC312C HCA1 0.20 3 0.0 ! THF w/me HCA1C2 CC312C CC322C HCA2C2 +HCA2C2 CC322C CC312C CC321 0.20 3 0.0 ! THF w/me CC331 CC312C CC322C HCA2C2 +HCA1 CC312C CC321 HCA2 0.20 3 0.0 ! THF w/me HCA1C2 CC312C CC331 HCA3 +HCA1 CC312C CC321 OC301 0.20 3 0.0 ! OC301 CC321 CC3163 HCA1 + +CC321 CC312C OC3C5M CC322C 1.17 3 180.0 ! pram 11/2009, model comp2 (raman et al) +CC321 CC312C CC322C CC322C 1.92 3 180.0 ! MCSA fit to (psi=-180 1-D MP2/cc-pVTZ//MP2/6-31G*) + +OC301 CC321 CC312C OC3C5M 1.93 1 180.0 ! COCA-THP2 OC301 CC321 CC311C OC3C61 +OC301 CC321 CC312C OC3C5M 0.43 2 0.0 ! " +OC301 CC321 CC312C OC3C5M 0.12 3 180.0 ! " +CC322C CC312C CC321 OC301 1.10 1 180.0 ! COCA-THP2 CC322C CC312C CC321 OC301 +CC322C CC312C CC321 OC301 0.07 2 180.0 ! " +CC322C CC312C CC321 OC301 0.15 3 0.0 ! " +CC312C CC321 OC301 CC331 0.64 1 180.0 ! COCA-THP2 CC311C CC321 OC301 CC331 +CC312C CC321 OC301 CC331 0.03 2 180.0 ! " +CC312C CC321 OC301 CC331 0.61 3 0.0 ! " + +CC322C CC312C OC303 CC331 0.41 1 180.0 ! pram model compound 6 (raman et al) +CC322C CC312C OC303 CC331 0.29 2 0.0 ! " MCSA fit +CC322C CC312C OC303 CC331 0.42 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +OC303 CC312C CC322C OC3C5M 0.73 1 0.0 ! pram model compound 6 (raman et al) +OC303 CC312C CC322C OC3C5M 2.96 2 0.0 ! " MCSA fit +OC303 CC312C CC322C OC3C5M 1.39 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC312C OC303 CC331 HCA3 0.284 3 0.0 ! CC312C OC301 CC331 HCA3 +HCA1 CC312C OC303 CC331 0.284 3 0.0 ! THF w/me HCA1C2 CC312C OC301 CC331 +CC322C CC322C CC312C OC303 0.20 3 0.0 ! CC322C CC322C CC312C OC301 + +OC3C5M CC322C CC312C HCA1 0.20 3 0.0 ! THF OC3C5M CC312C CC322C HCA2C2 +CC312C CC322C OC3C5M CC322C 0.50 3 0.0 ! THF CC322C CC322C OC3C5M CC322C +OC3C5M CC322C CC312C CC322C 0.00 3 0.0 ! THF OC3C5M CC322C CC322C CC322C +OC3C5M CC322C CC322C CC312C 0.00 3 0.0 ! THF OC3C5M CC322C CC322C CC322C +HCA1 CC312C OC303 CC311D 0.284 3 0.0 ! OMe-THF HCA1C2 CC312C OC301 CC331 +CC312C OC303 CC311D HCA1 0.284 3 0.0 ! CC311D OC302 CC311D HCA1 +OC303 CC311D CC321C CC321C 0.20 3 0.0 ! OC301 CC311D CC321C CC321C +OC303 CC311D CC321C HCA2 0.20 3 0.0 ! OC301 CC311D CC321C HCA2 +CC321C OC3C61 CC311D OC303 0.62 1 0.0 ! CC321C OC3C61 CC311D OC301 +CC321C OC3C61 CC311D OC303 1.54 2 0.0 ! " +CC321C OC3C61 CC311D OC303 0.48 3 0.0 ! " +OC303 CC312C CC322C HCA2C2 0.20 3 0.0 ! OC301 CC312C CC322C HCA2C2 +CC312C OC303 CC311D OC3C61 0.08 1 0.0 ! pram model compound 3 (raman et al) +CC312C OC303 CC311D OC3C61 0.93 2 0.0 ! " MCSA fit +CC312C OC303 CC311D OC3C61 0.05 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC312C OC303 CC311D CC321C 0.05 1 180.0 ! pram model compound 3 (raman et al) +CC312C OC303 CC311D CC321C 0.38 2 180.0 ! " MCSA fit +CC312C OC303 CC311D CC321C 0.36 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC311D OC303 CC312C CC322C 0.07 1 180.0 ! pram model compound 3 (raman et al) +CC311D OC303 CC312C CC322C 0.04 2 0.0 ! " MCSA fit +CC311D OC303 CC312C CC322C 0.14 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +HCA1 CC312D OC301 CC311C 0.284 3 0.0 ! OMe-THF HCA1C2 CC312C OC301 CC331 +CC312D OC301 CC311C HCA1 0.284 3 0.0 ! CC311D OC301 CC311C HCA1 +CC312D OC301 CC311C CC321C 0.12 1 180.0 ! pram model compound 4 (raman et al) +CC312D OC301 CC311C CC321C 0.03 2 180.0 ! " MCSA fit +CC312D OC301 CC311C CC321C 0.14 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC311C OC301 CC312D OC3C5M 0.52 1 180.0 ! pram model compound 4 (raman et al) +CC311C OC301 CC312D OC3C5M 1.50 2 0.0 ! " MCSA fit +CC311C OC301 CC312D OC3C5M 0.98 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC311C OC301 CC312D CC322C 1.19 1 180.0 ! pram model compound 4 (raman et al) +CC311C OC301 CC312D CC322C 0.16 2 180.0 ! " MCSA fit +CC311C OC301 CC312D CC322C 0.49 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + + +!full sugars +CC3051 OC302 CC3162 OC3C61 0.21 1 0.0 ! pram model compound 1 (raman et al) +CC3051 OC302 CC3162 OC3C61 0.86 2 0.0 ! " MCSA fit +CC3051 OC302 CC3162 OC3C61 0.35 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3162 OC302 CC3051 OC3C51 0.70 1 180.0 ! pram model compound 1 (raman et al) +CC3162 OC302 CC3051 OC3C51 1.41 2 0.0 ! " MCSA fit +CC3162 OC302 CC3051 OC3C51 0.75 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3162 OC302 CC3051 CC3151 1.23 1 180.0 ! pram model compound 1 (raman et al) +CC3162 OC302 CC3051 CC3151 0.15 2 0.0 ! " MCSA fit +CC3162 OC302 CC3051 CC3151 0.54 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3051 OC302 CC3162 CC3161 0.18 1 180.0 ! pram model compound 1 (raman et al) +CC3051 OC302 CC3162 CC3161 0.45 2 180.0 ! " MCSA fit +CC3051 OC302 CC3162 CC3161 0.75 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC302 CC3051 OC3C51 CC3153 0.19 1 180.0 ! OC311 CC3051 OC3C51 CC3153 BFRU +OC302 CC3051 OC3C51 CC3153 2.85 2 180.0 ! " +OC302 CC3051 OC3C51 CC3153 0.86 3 0.0 ! " +CC3151 CC3151 CC3051 OC302 2.23 1 0.0 ! CC3151 CC3151 CC3051 OC311 +CC3151 CC3151 CC3051 OC302 3.00 2 0.0 ! " +CC3151 CC3151 CC3051 OC302 0.88 3 180.0 ! " + +OC302 CC3051 CC321 HCA2 0.14 3 0.0 ! OC311 CC3051 CC321 HCA2 +OC302 CC3051 CC3151 HCA1 0.14 3 0.0 ! OC311 CC3051 CC3151 HCA1 + +OC302 CC3051 CC321 OC311 0.07 1 0.0 ! OC311 CC3051 CC321 OC311 +OC302 CC3051 CC321 OC311 1.99 2 180.0 ! " +OC302 CC3051 CC321 OC311 1.72 3 180.0 ! " + +OC302 CC3051 CC3151 OC311 0.12 1 180.0 ! OC311 CC3051 CC3151 OC311 +OC302 CC3051 CC3151 OC311 1.87 2 180.0 ! " +OC302 CC3051 CC3151 OC311 1.64 3 180.0 ! " + +CC3051 OC302 CC3162 HCA1 0.284 3 0.0 ! CC3162 OC302 CC3162 HCA1 + +CC321 CC3051 OC302 CC3162 0.40 1 180.0 ! CC321 CC3051 OC311 HCP1 Fructose +CC321 CC3051 OC302 CC3162 0.48 2 0.0 ! " +CC321 CC3051 OC302 CC3162 0.19 3 0.0 ! " + +OC3C61 CC3162 OC303 CC3151 0.08 1 0.0 ! pram model compound 3 (raman et al) +OC3C61 CC3162 OC303 CC3151 0.93 2 0.0 ! " MCSA fit +OC3C61 CC3162 OC303 CC3151 0.05 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 CC3162 OC303 CC3151 0.05 1 180.0 ! pram model compound 3 (raman et al) +CC3161 CC3162 OC303 CC3151 0.38 2 180.0 ! " MCSA fit +CC3161 CC3162 OC303 CC3151 0.36 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3162 OC303 CC3151 CC3153 0.07 1 180.0 ! pram model compound 3 (raman et al) +CC3162 OC303 CC3151 CC3153 0.04 2 0.0 ! " MCSA fit +CC3162 OC303 CC3151 CC3153 0.14 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3162 OC303 CC3151 CC3151 0.07 1 180.0 ! pram model compound 3 (raman et al) +CC3162 OC303 CC3151 CC3151 0.04 2 0.0 ! " MCSA fit +CC3162 OC303 CC3151 CC3151 0.14 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3162 OC303 CC3151 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +HCA1 CC3162 OC303 CC3151 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC3163 OC3C61 CC3162 OC303 0.41 1 180.0 ! CC3163 OC3C61 CC3162 OC301 +CC3163 OC3C61 CC3162 OC303 0.89 2 0.0 ! " +CC3163 OC3C61 CC3162 OC303 0.05 3 0.0 ! " +OC303 CC3162 CC3161 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC303 CC3162 CC3161 OC311 2.65 1 180.0 ! OC301 CC3162 CC3161 OC311 +OC303 CC3162 CC3161 OC311 0.00 2 0.0 ! " +OC303 CC3162 CC3161 OC311 0.13 3 180.0 ! " +CC3161 CC3161 CC3162 OC303 0.20 3 0.0 ! CC3161 CC3161 CC3162 OC301 + +OC3C51 CC3153 CC3151 OC303 0.14 1 0.0 ! OC3C51 CC3153 CC3151 OC311 +OC3C51 CC3153 CC3151 OC303 0.70 2 0.0 ! " +OC3C51 CC3153 CC3151 OC303 0.18 3 0.0 ! " +CC3051 CC3151 CC3151 OC303 2.07 1 0.0 ! CC3051 CC3151 CC3151 OC311 +CC3051 CC3151 CC3151 OC303 2.13 2 0.0 ! " +CC3051 CC3151 CC3151 OC303 2.71 3 180.0 ! " + +CC321 CC3153 CC3151 OC303 0.76 1 180.0 ! CC321 CC3153 CC3151 OC311 +CC321 CC3153 CC3151 OC303 0.40 2 180.0 ! " +CC321 CC3153 CC3151 OC303 0.40 3 180.0 ! " +OC303 CC3151 CC3151 OC311 2.87 1 180.0 ! OC311 CC3151 CC3151 OC311 +OC303 CC3151 CC3151 OC311 0.03 2 0.0 ! " +OC303 CC3151 CC3151 OC311 0.23 3 0.0 ! " + +OC303 CC3151 CC3151 HCA1 0.14 3 0.0 ! OC311 CC3151 CC3151 HCA1 +OC303 CC3151 CC3153 HCA1 0.14 3 0.0 ! OC311 CC3151 CC3153 HCA1 + +CC3162 OC303 CC3151 CC3051 0.07 1 180.0 ! pram model compound 3 (raman et al) +CC3162 OC303 CC3151 CC3051 0.04 2 0.0 ! " MCSA fit +CC3162 OC303 CC3151 CC3051 0.14 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +OC302 CC3051 CC3151 OC303 0.12 1 180.0 ! OC311 CC3051 CC3151 OC311 +OC302 CC3051 CC3151 OC303 1.87 2 180.0 ! " +OC302 CC3051 CC3151 OC303 1.64 3 180.0 ! " + +OC3C51 CC3051 CC3151 OC303 0.32 1 180.0 ! OC3C51 CC3051 CC3151 OC311, ketopentose monosac +OC3C51 CC3051 CC3151 OC303 0.65 2 180.0 ! " +OC3C51 CC3051 CC3151 OC303 2.62 3 0.0 ! " +CC3153 CC3151 CC3151 OC303 0.01 1 180.0 ! CC3153 CC3151 CC3151 OC311, aldopentose monosac +CC3153 CC3151 CC3151 OC303 0.72 2 0.0 ! " +CC3153 CC3151 CC3151 OC303 0.73 3 0.0 ! " +CC321 CC3051 CC3151 OC303 0.94 1 0.0 ! CC321 CC3051 CC3151 OC311, ketopentose monosac +CC321 CC3051 CC3151 OC303 1.59 2 180.0 ! " +CC321 CC3051 CC3151 OC303 0.84 3 0.0 ! " + +OC302 CC3051 CC321 OC301 0.07 1 0.0 ! OC311 CC3051 CC321 OC311, ketopentose monosac +OC302 CC3051 CC321 OC301 1.99 2 180.0 ! +OC302 CC3051 CC321 OC301 1.72 3 180.0 ! + +CC321 OC301 CC3051 OC3C51 0.98 2 0.0 ! pram model compound 5 (raman et al) +CC321 OC301 CC3051 OC3C51 1.50 3 0.0 ! " MCSA fit MP2/cc-pVTZ//MP2/6-31G* +CC321 OC301 CC3051 CC3151 0.97 1 180.0 ! pram model compound 5 (raman et al) +CC321 OC301 CC3051 CC3151 0.44 3 180.0 ! " MCSA fit MP2/cc-pVTZ//MP2/6-31G* +HCA2 CC321 OC301 CC3051 0.284 3 0.0 ! OMe-THF CC312D OC301 CC331 HCA3 + +CC321 OC301 CC3051 CC321 0.40 1 180.0 ! CC321 CC3051 OC311 HCP1, ketopentose monosac +CC321 OC301 CC3051 CC321 0.48 2 0.0 ! " +CC321 OC301 CC3051 CC321 0.19 3 0.0 ! " + +OC301 CC3051 CC321 HCA2 0.14 3 0.0 ! OC311 CC3051 CC321 HCA2 +OC301 CC3051 CC3151 HCA1 0.14 3 0.0 ! OC311 CC3051 CC3151 HCA1 + +OC301 CC3051 CC321 OC311 0.07 1 0.0 ! OC311 CC3051 CC321 OC311, ketopentose monosac +OC301 CC3051 CC321 OC311 1.99 2 180.0 ! " +OC301 CC3051 CC321 OC311 1.72 3 180.0 ! " + +OC301 CC3051 CC3151 OC311 0.12 1 180.0 ! OC311 CC3051 CC3151 OC311, ketopentose monosac +OC301 CC3051 CC3151 OC311 1.87 2 180.0 ! " +OC301 CC3051 CC3151 OC311 1.64 3 180.0 ! " + +OC3C51 CC3051 CC321 OC301 1.93 1 180.0 ! COCA-THP2 OC301 CC321 CC311C OC3C61 +OC3C51 CC3051 CC321 OC301 0.43 2 0.0 ! ", pram, validated by model compound 2 (raman et al) +OC3C51 CC3051 CC321 OC301 0.12 3 180.0 ! ", pram, MP2/cc-pVTZ//MP2/6-31G* + +OC301 CC321 CC3051 CC3151 1.10 1 180.0 ! COCA-THP2 CC322C CC312C CC321 OC301 +OC301 CC321 CC3051 CC3151 0.07 2 180.0 ! ", pram, validated by model compound 2 (raman et al) +OC301 CC321 CC3051 CC3151 0.15 3 0.0 ! ", pram, MP2/cc-pVTZ//MP2/6-31G* + +CC3051 CC321 OC301 CC3051 0.64 1 180.0 ! COCA-THP2 CC311C CC321 OC301 CC331, validated by mc2 scan +CC3051 CC321 OC301 CC3051 0.03 2 180.0 ! ", pram, validated by model compound 2 (raman et al) +CC3051 CC321 OC301 CC3051 0.61 3 0.0 ! ", pram, MP2/cc-pVTZ//MP2/6-31G* + +OC3C51 CC3153 CC321 OC301 1.93 1 180.0 ! COCA-THP2 OC301 CC321 CC311C OC3C61 +OC3C51 CC3153 CC321 OC301 0.43 2 0.0 ! ", pram, validated by model compound 2 (raman et al) +OC3C51 CC3153 CC321 OC301 0.12 3 180.0 ! ", pram, MP2/cc-pVTZ//MP2/6-31G* + +CC3153 CC321 OC301 CC3051 0.64 1 180.0 ! COCA-THP2 CC311C CC321 OC301 CC331 +CC3153 CC321 OC301 CC3051 0.03 2 180.0 ! ", pram, validated by model compound 2 (raman et al) +CC3153 CC321 OC301 CC3051 0.61 3 0.0 ! ", pram, MP2/cc-pVTZ//MP2/6-31G* + +OC301 CC321 CC3153 HCA1 0.14 3 0.0 ! OC311 CC321 CC3153 HCA1 + +OC301 CC321 CC3153 CC3151 1.10 1 180.0 ! COCA-THP2 CC322C CC312C CC321 OC301 +OC301 CC321 CC3153 CC3151 0.07 2 180.0 ! ", pram, validated by model compound 2 (raman et al) +OC301 CC321 CC3153 CC3151 0.15 3 0.0 ! ", pram, MP2/cc-pVTZ//MP2/6-31G* + +CC3153 CC321 OC301 CC3162 0.64 1 180.0 ! COCA-THP2 CC311C CC321 OC301 CC331, validated by mc2 scan +CC3153 CC321 OC301 CC3162 0.03 2 180.0 ! ", pram, validated by model compound 2 (raman et al) +CC3153 CC321 OC301 CC3162 0.61 3 0.0 ! ", pram, MP2/cc-pVTZ//MP2/6-31G* + +OC301 CC3051 CC321 OC301 0.07 1 0.0 ! OC311 CC3051 CC321 OC311, ketopentose monosac +OC301 CC3051 CC321 OC301 1.99 2 180.0 ! " +OC301 CC3051 CC321 OC301 1.72 3 180.0 ! " + +CC321 OC301 CC3152 OC3C51 0.98 2 0.0 ! pram model compound 5 (raman et al) +CC321 OC301 CC3152 OC3C51 1.50 3 0.0 ! " MCSA fit MP2/cc-pVTZ//MP2/6-31G* +CC321 OC301 CC3152 CC3151 0.97 1 180.0 ! pram model compound 5 (raman et al) +CC321 OC301 CC3152 CC3151 0.44 3 180.0 ! " MCSA fit MP2/cc-pVTZ//MP2/6-31G* +CC3153 CC321 OC301 CC3152 0.64 1 180.0 ! COCA-THP2 CC311C CC321 OC301 CC331 +CC3153 CC321 OC301 CC3152 0.03 2 180.0 ! ", pram, validated by model compound 2 (raman et al) " +CC3153 CC321 OC301 CC3152 0.61 3 0.0 ! ", pram, MP2/cc-pVTZ//MP2/6-31G* +HCA2 CC321 OC301 CC3152 0.284 3 0.0 ! OMe-THF CC312D OC301 CC331 HCA3 +HCA1 CC3152 OC301 CC321 0.284 3 0.0 ! HCA1 CC3152 OC301 CC331 + +CC3152 OC301 CC3161 CC3162 0.12 1 180.0 ! pram model compound 4 (raman et al) +CC3152 OC301 CC3161 CC3162 0.03 2 180.0 ! " MCSA fit +CC3152 OC301 CC3161 CC3162 0.14 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3152 OC301 CC3161 CC3161 0.12 1 180.0 ! pram model compound 4 (raman et al) +CC3152 OC301 CC3161 CC3161 0.03 2 180.0 ! " MCSA fit +CC3152 OC301 CC3161 CC3161 0.14 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 OC301 CC3152 OC3C51 0.52 1 180.0 ! pram model compound 4 (raman et al) +CC3161 OC301 CC3152 OC3C51 1.50 2 0.0 ! " MCSA fit +CC3161 OC301 CC3152 OC3C51 0.98 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 OC301 CC3152 CC3151 1.19 1 180.0 ! pram model compound 4 (raman et al) +CC3161 OC301 CC3152 CC3151 0.16 2 180.0 ! " MCSA fit +CC3161 OC301 CC3152 CC3151 0.49 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 OC301 CC3152 HCA1 0.284 3 0.0 ! OMe-THF HCA1C2 CC312C OC301 CC331 +HCA1 CC3161 OC301 CC3152 0.284 3 0.0 ! CC311D OC301 CC311C HCA1 +CC3263 CC3161 CC3161 OC301 0.20 3 0.0 ! CC3263 CC3161 CC3161 OC311 +!*******************end of pyranose-furanose******* +!sulphate params by sairam +CC3162 OC30P SC OC2DP 0.17 3 0.0 ! CC3161 OC30P SC OC2DP 0.17 3 0.0 +SC OC30P CC3162 OC3C61 0.76 1 0.0 ! OC3C61 CC311D OC30P SC 0.76 1 0.0 +SC OC30P CC3162 OC3C61 0.68 2 0.0 ! OC3C61 CC311D OC30P SC 0.68 2 0.0 +SC OC30P CC3162 OC3C61 0.26 3 180.0 ! OC3C61 CC311D OC30P SC 0.26 3 180.0 +SC OC30P CC3162 CC3161 0.21 3 0.0 ! CC3162 CC3161 OC30P SC 0.21 3 0.0 +SC OC30P CC3162 HCA1 0.00 3 0.0 ! HCA1 CC3161 OC30P SC 0.00 3 0.0 +OC311 CC3162 CC3161 OC30P 2.50 1 180.0 ! OC30P CC3162 CC3161 OC311 2.50 1 180.0 +OC311 CC3162 CC3161 OC30P 2.00 2 0.0 ! OC30P CC3162 CC3161 OC311 2.00 2 0.0 +OC311 CC3162 CC3161 OC30P 2.50 3 0.0 ! OC30P CC3162 CC3161 OC311 2.50 3 0.0 +!linkage btw sialic acid and other saccharide through 2 (sialic acid) - 6 +CC3062 OC301 CC321 HCA2 0.284 3 0.0 ! from CC3162 OC301 CC321 HCA2 +CC321 OC301 CC3062 OC3C61 0.14 1 0.0 ! from CC321 OC301 CC3162 OC3C61 +CC321 OC301 CC3062 OC3C61 0.97 2 0.0 ! " +CC321 OC301 CC3062 OC3C61 0.11 3 180.0 ! " +CC3163 CC321 OC301 CC3062 0.64 1 180.0 ! from CC3163 CC321 OC301 CC3162 +CC3163 CC321 OC301 CC3062 0.03 2 180.0 ! " +CC3163 CC321 OC301 CC3062 0.61 3 0.0 ! " +CC3261 CC3062 OC301 CC321 0.22 1 0.0 ! from C3161 CC3162 OC301 CC321 +CC3261 CC3062 OC301 CC321 0.28 2 180.0 ! " +CC3261 CC3062 OC301 CC321 0.89 3 0.0 ! " +CC321 OC301 CC3062 CC2O2 0.284 3 0.0 ! from CC3161 OC301 CC3062 CC2O2 +!end sialic acid para + +!!!!!!disialic acid!!!!!!, Mingjun +OC3C61 CC3062 OC301 CC312 1.3464 1 0.00 ! RMSE = 1.59697 +OC3C61 CC3062 OC301 CC312 3.0743 2 0.00 ! RMSE = 1.59697 +OC3C61 CC3062 OC301 CC312 0.8378 3 180.00 ! RMSE = 1.59697 +CC312 CC312 OC301 CC3062 3.0937 1 180.00 ! RMSE = 1.59697 +CC312 CC312 OC301 CC3062 0.7096 2 180.00 ! RMSE = 1.59697 +CC312 CC312 OC301 CC3062 0.0245 3 0.00 ! RMSE = 1.59697 +OC301 CC312 CC322 OC311 1.7749 1 180.00 ! RMSE = 1.59697 +OC301 CC312 CC322 OC311 1.5713 2 0.00 ! RMSE = 1.59697 +OC301 CC312 CC322 OC311 1.8214 3 0.00 ! RMSE = 1.59697 +CC322 CC312 OC301 CC3062 4.2905 1 180.00 ! RMSE = 1.59697 +CC322 CC312 OC301 CC3062 0.4831 2 180.00 ! RMSE = 1.59697 +CC322 CC312 OC301 CC3062 0.0488 3 180.00 ! RMSE = 1.59697 +OC301 CC312 CC312 OC311 1.7164 1 180.00 ! RMSE = 1.59697 +OC301 CC312 CC312 OC311 0.3973 2 180.00 ! RMSE = 1.59697 +OC301 CC312 CC312 OC311 1.9793 3 0.00 ! RMSE = 1.59697 +CC3163 CC312 CC312 OC301 0.2524 1 180.00 ! RMSE = 1.59697 +CC3163 CC312 CC312 OC301 0.4587 2 0.00 ! RMSE = 1.59697 +CC3163 CC312 CC312 OC301 1.1807 3 180.00 ! RMSE = 1.59697 +CC2O2 CC3062 OC301 CC312 1.1671 1 180.00 ! RMSE = 1.59697 +CC2O2 CC3062 OC301 CC312 1.5207 2 0.00 ! RMSE = 1.59697 +CC2O2 CC3062 OC301 CC312 1.0160 3 180.00 ! RMSE = 1.59697 +CC3261 CC3062 OC301 CC312 1.5334 1 180.00 ! RMSE = 1.59697 +CC3261 CC3062 OC301 CC312 1.5933 2 0.00 ! RMSE = 1.59697 +CC3261 CC3062 OC301 CC312 1.3811 3 0.00 ! RMSE = 1.59697 +OC301 CC312 CC312 HCA1 0.1400 3 0.00 ! from HCA1 CC312 CC312 OC311 +HCA1 CC312 OC301 CC3062 0.2840 3 0.00 ! from CC3162 OC301 CC321 HCA2 +OC301 CC312 CC322 HCA2 0.1400 3 0.00 ! from HCA2 CC322 CC312 OC311 +! +OC3C61 CC3062 OC301 CC322 2.1018 1 0.00 ! RMSE = 1.5934 +OC3C61 CC3062 OC301 CC322 1.4102 2 0.00 ! RMSE = 1.5934 +OC3C61 CC3062 OC301 CC322 0.4570 3 0.00 ! RMSE = 1.5934 +CC312 CC322 OC301 CC3062 2.5455 1 180.00 ! RMSE = 1.5934 +CC312 CC322 OC301 CC3062 0.7918 2 180.00 ! RMSE = 1.5934 +CC312 CC322 OC301 CC3062 0.9628 3 180.00 ! RMSE = 1.5934 +OC311 CC312 CC322 OC301 3.3150 1 180.00 ! RMSE = 1.5934 +OC311 CC312 CC322 OC301 1.6828 2 180.00 ! RMSE = 1.5934 +OC311 CC312 CC322 OC301 2.9534 3 180.00 ! RMSE = 1.5934 +CC312 CC312 CC322 OC301 0.5927 1 0.00 ! RMSE = 1.5934 +CC312 CC312 CC322 OC301 1.2961 2 180.00 ! RMSE = 1.5934 +CC312 CC312 CC322 OC301 2.1767 3 0.00 ! RMSE = 1.5934 +CC2O2 CC3062 OC301 CC322 0.4128 1 180.00 ! RMSE = 1.5934 +CC2O2 CC3062 OC301 CC322 0.2875 2 180.00 ! RMSE = 1.5934 +CC2O2 CC3062 OC301 CC322 0.0685 3 0.00 ! RMSE = 1.5934 +CC3261 CC3062 OC301 CC322 0.3336 1 180.00 ! RMSE = 1.5934 +CC3261 CC3062 OC301 CC322 0.0342 2 0.00 ! RMSE = 1.5934 +CC3261 CC3062 OC301 CC322 0.7301 3 180.00 ! RMSE = 1.5934 +OC301 CC322 CC312 HCA1 0.1400 3 0.0 ! from HCA1 CC312 CC312 OC311 +HCA2 CC322 OC301 CC3062 0.2840 3 0.0 ! from CC3162 OC301 CC321 HCA2 +! ABEQ, my +HCA1 CC3162 CC3161 CC3261 0.20 3 0.0 ! from HCA1 CC3162 CC3161 CC3161 +HCA2 CC3261 CC3161 CC3162 0.20 3 0.0 ! from HCA1 CC3161 CC3161 CC3162 +CC3161 CC3261 CC3161 CC3162 0.19 3 180.0 ! from CC3161 CC3161 CC3161 CC3162 +CC3261 CC3161 CC3163 CC331 0.20 3 0.0 ! from CC3161 CC3161 CC3163 CC331 +CC3161 CC3261 CC3161 CC3163 0.19 3 180.0 ! from CC3161 CC3161 CC3161 CC3163 +HCA2 CC3261 CC3161 CC3163 0.20 3 0.0 ! from HCA1 CC3161 CC3161 CC3163 +HCA1 CC3163 CC3161 CC3261 0.20 3 0.0 ! from HCA1 CC3163 CC3161 CC3161 +HCA1 CC3161 CC3261 CC3161 0.20 3 0.0 ! from HCA1 CC3161 CC3161 CC3161 +CC3161 CC3261 CC3161 OC311 0.20 3 0.0 ! from CC3161 CC3161 CC3161 OC311 +CC3261 CC3161 CC3163 OC3C61 0.31 3 180.0 ! from CC3161 CC3161 CC3163 OC3C61 +CC3261 CC3161 CC3162 OC3C61 0.31 3 180.0 ! from CC3161 CC3161 CC3162 OC3C61 +CC3261 CC3161 CC3162 OC311 0.20 3 0.0 ! from CC3161 CC3161 CC3162 OC311 +CC3261 CC3161 CC3162 OC301 0.20 3 0.0 ! from CC3161 CC3161 CC3162 OC301 +!O-acetyl on ARHM and ABEQ, my +CC3162 CC3161 OC301 CC2O5 0.1300 1 180.0 ! CC3162 CC3161 OC301 CC3162 +CC3162 CC3161 OC301 CC2O5 0.2500 2 180.0 ! CC3162 CC3161 OC301 CC3162 +CC3162 CC3161 OC301 CC2O5 0.0600 3 180.0 ! CC3162 CC3161 OC301 CC3162 +CC3261 CC3161 OC301 CC2O5 1.0150 1 180.0 ! RMSE = 2.28686 +CC3261 CC3161 OC301 CC2O5 0.4550 2 0.0 ! RMSE = 2.28686 +CC3261 CC3161 OC301 CC2O5 1.0330 3 180.0 ! RMSE = 2.28686 +OC2D1 CC2O5 CC331 HCA3 0.0000 6 180.0 ! OG2D1 CG2O2 CG331 HGA3 +OC301 CC2O5 CC331 HCA3 0.0000 6 180.0 ! OG302 CG2O2 CG331 HGA3 +HCA2 CC3261 CC3161 OC301 0.1400 3 0.0 ! HCA2 CC3261 CC3161 OC311 +HCA1 CC3161 OC301 CC2O5 0.0000 3 0.0 ! HGA1 CG311 OG302 CG2O2 +CC3161 OC301 CC2O5 OC2D1 0.9650 1 180.0 ! OG2D1 CG2O2 OG302 CG301 +CC3161 OC301 CC2O5 OC2D1 3.8500 2 180.0 ! OG2D1 CG2O2 OG302 CG301 +CC3161 OC301 CC2O5 CC331 2.0500 2 180.0 ! CG311 CG2O2 OG302 CG331 +CC3161 CC3261 CC3161 OC301 0.2000 3 0.0 ! from CC3161 CC3161 CC3161 OC311 +CC3161 CC3161 OC301 CC2O5 0.1300 1 180.0 ! CC3161 CC3161 OC301 CC3162 +CC3161 CC3161 OC301 CC2O5 0.2500 2 180.0 ! CC3161 CC3161 OC301 CC3162 +CC3161 CC3161 OC301 CC2O5 0.0600 3 180.0 ! CC3161 CC3161 OC301 CC3162 + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +! +!atom types Kpsi psi0 +! monosaccharides +CC2O1 CC331 NC2D1 OC2D1 120.00 0 0.00 ! par22 O X X C +NC2D1 CC2O1 CC3161 HCP1 20.00 0 0.00 ! par22 NH1 X X H +NC2D1 CC2O1 CC3062 HCP1 20.00 0 0.00 ! par22 NH1 X X H +CC2O2 CC311 OC2D2 OC2D2 96.00 0 0.00 ! par22 OC X X CC +CC2O2 CC301 OC2D2 OC2D2 96.00 0 0.00 ! par22 OC X X CC +CC2O2 CC3163 OC2D2 OC2D2 96.00 0 0.00 ! par22 OC X X CC +CC2O2 CC3062 OC2D2 OC2D2 96.00 0 0.00 ! par22 OC X X CC +CC2O2 CC321 OC2D2 OC2D2 96.00 0 0.00 ! par22 OC X X CC +NC2D1 CC2O1 CC331 HCP1 20.00 0 0.00 ! par22 NH1 X X H +NC2D1 CC2O1 CC311 HCP1 20.00 0 0.00 ! par22 NH1 X X H +! aldoses, ketoses +CC2O4 CC331 OC2D4 HCR1 50.00 0 0.00 ! acetaldehyde adm +CC2O4 CC312 OC2D4 HCR1 50.00 0 0.00 ! acetaldehyde adm +OC2D3 CC331 CC331 CC2O3 70.00 0 0.00 ! ketone, acetone +OC2D3 CC312 CC322 CC2O3 70.00 0 0.00 ! " + +!********* V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 +! monosaccharide +CC301 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! cgenff CG301 +CC3062 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! cgenff CG301 +CC311 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC3161 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC3162 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC3163 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC321 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! par22, CT2x +CC3261 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! par22, CT2x +CC3263 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! par22, CT2x +CC331 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! par22, CT3x +CC2O1 0.0 -0.1100 2.000 ! par22, C +CC2O2 0.0 -0.0700 2.000 ! par22, CC +CC2O3 0.0 -0.0900 2.000 ! adm, acetone, 11/08 +CC2O4 0.0 -0.0600 1.800 ! adm, acetaldehyde, 11/08 +CC2O5 0.0 -0.0980 1.700 ! O-acetyl carbonyl C, 04/15, methyl acetate viv 12/29/06 +OC2D1 0.0 -0.1200 1.700 0.0 -0.12 1.40 ! par22, OB +OC2D2 0.0 -0.1200 1.700 ! par22, OC +OC2D3 0.0 -0.0500 1.700 0.0 -0.12 1.40 ! adm, acetone, 11/08 +OC2D4 0.0 -0.1200 1.700 0.0 -0.12 1.40 ! adm, acetaldehyde, 11/08 +OC3C61 0.0 -0.1000 1.650 ! sng thp 1/06 +OC311 0.0 -0.1921 1.765 ! og MeOH and EtOH 1/06 +NC2D1 0.0 -0.2000 1.850 0.0 -0.20 1.55 ! par22 NH1 +HCP1 0.0 -0.0460 0.2245 ! CHARMM polar H +HCA1 0.0 -0.0450 1.340 ! alkane,isobutane 1/5/05 igor +HCA2 0.0 -0.0350 1.340 ! alkane, igor, 6/05 +HCA3 0.0 -0.0240 1.340 ! alkane, yin and mackerell, 4/98 + +! tip3p +!HCTIP3 0.0 -0.0460 0.2245 ! TIP3P water +!OCTIP3 0.0 -0.1521 1.7682 ! TIP3P water +! +! linear sugars +CC312 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC322 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! par22, CT2x +HCR1 0.0 -0.0460 0.8000 ! adm jr., 6/27/90, his (verified for acetaldehyde, 11/08) + +! model compounds +HCA3M 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 +CC321C 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CC321D 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CC311C 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC311D 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +OC301 0.0 -0.1000 1.6500 ! tetrahydropyran sng, all34_ethers_1a OC30A +OC302 0.0 -0.1000 1.6500 ! tetrahydropyran sng, all34_ethers_1a OC30A +HCP1M 0.0 -0.0460 0.2245 ! CHARMM polar H, og, 1/20/06 +OC311M 0.0 -0.1921 1.765 ! MeOH and EtOH optimized, og, 1/20/06 + +! THF parameters for furanoses; viv, added by erh +OC3C5M 0.0 -0.1000 1.6500 ! tetrahydrofuran sng 1/06 +CC322C 0.0 -0.0600 2.02 0.0 -0.01 1.9 ! CPEN, cyclopentane, MD sim. 8/06 viv !from CCP2, THF viv +HCA2C2 0.0 -0.0350 1.3000 ! alkane,propane 11/16/04 viv +! THF w/Methyl parameters for furanoses; viv, added by erh +CC312C 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +HCA1C2 0.0 -0.0450 1.340 ! alkane,isobutane 1/5/05 igor + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! monosaccharide furanoses; erh added 10/24/07!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +OC3C51 0.0 -0.1000 1.6500 ! THF, par_carb, OC3C5M +CC3152 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC3051 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! cgenff CG301 +CC3251 0.0 -0.0600 2.02 0.0 -0.01 1.9 ! cyclopentane, THF +CC3151 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv +CC3153 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv + +!*******************end of furanoses************************************ + +!New Non-bond for the phosphates || Added by sai +OC2DP 0.0 -0.12 1.70 +OC312 0.0 -0.1521 1.77 +OC30P 0.0 -0.1521 1.77 +PC 0.0 -0.585 2.15 ! ADM Jr. +SC 0.0 -0.47 2.1 ! methylsulfate +!*******************end of phosphates*********************************** + +! pyranose/furanose-furanose linkages, pram +CC312D 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! CC312C +OC303 0.0 -0.1000 1.6500 ! OC301 +!*********************************************************************** + +END + diff --git a/charmm/toppar/par_all36_cgenff.prm b/charmm/toppar/par_all36_cgenff.prm new file mode 100644 index 00000000..f2ddf687 --- /dev/null +++ b/charmm/toppar/par_all36_cgenff.prm @@ -0,0 +1,6570 @@ +* -------------------------------------------------------------------------- * +* CGenFF: Parameters for the Charmm General Force Field v. 3.1 * +* for Small Molecule Drug Design * +* -------------------------------------------------------------------------- * +* + +! -------------------------------------------------------------------------- ! +! References: - K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, ! +! J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov and ! +! A. D. Mackerell Jr., J. Comput. Chem. 2010, 31, 671-690. ! +! - W. Yu, X. He, K. Vanommeslaeghe, A. D. MacKerell Jr., ! +! J. Comput. Chem. 2012, 33, 2451-2468. ! +! -------------------------------------------------------------------------- ! +! Notes: - CGenFF is an ongoing project that is updated regularly. Please ! +! check http://mackerell.umaryland.edu/~kenno/cgenff/download.html ! +! and/or http://mackerell.umaryland.edu/ for updates! ! +! - As more functional groups will be introduced, small changes in ! +! existing parameters and/or charges may occur. ! +! - Comments in this file may be misleading. ! +! -------------------------------------------------------------------------- ! +! Contributors: abar = Arghya Barman ! +! adm = Alexander D. MacKerell Jr. ! +! alr = Ashley L. Ringer ! +! cacha = Chayan Acharya ! +! ctsai = Cheng-Chieh Tsai ! +! ed = Eva Darian ! +! ejd = Elizabeth J. Denning ! +! erh = Elizabeth R. Hatcher Frush ! +! fylin = Fang-Yu Lin ! +! isg = Ignacio Soteras Gutiérrez ! +! jal = Justin A. Lemkul ! +! jhs = JiHyun Shim ! +! kevo = Kenno VanOmmeslaeghe ! +! kundu = Sibsankar Kundu ! +! lf = Lei Fang ! +! lsk = Lakkaraju Sirish Kaushik ! +! mcs = Meagan C. Small ! +! mnoon = Muhammad Noon ! +! my = Mingjun Yang ! +! oashi = Taiji Oashi ! +! og = Olgun Guvench ! +! peml = Pedro Lopes ! +! pram = E. Prabhu Raman ! +! rima = Madhurima Jana ! +! rting = Ting Ran ! +! sc = Sherry (Hua) Chen ! +! sna = Shanthi Nagarajan ! +! sz = Shijun Zhong ! +! viv = Igor Vorobyov ! +! xhe = Xibing He ! +! xxwy = Wenbo Yu ! +! yapol = Iakov Polyak ! +! yin = Daxu Yin ! +! yxu = You Xu ! +! -------------------------------------------------------------------------- ! +! All comments to ADM jr. via the CHARMM web site: www.charmm.org ! +! parameter set discussion forum ! +! -------------------------------------------------------------------------- ! +! ORDER OF PREFERENCE FOR SORTING PARAMETERS: ! +! + C < N < O < P < S < HALOGENS (LOW TO HIGH Z) < MISC. (BY Z) < H ! +! + ATOMS TYPES WITHIN THE SAME ELEMENT ARE SORTED ALPHABETICALLY ! +! -------------------------------------------------------------------------- ! +! RULES FOR SORTING THE COLUMS ON EACH LINE: ! +! + IN BONDS, THE LOWEST PRIORITY ATOM ALWAYS COMES FIRST ! +! + FOR ANGLES, IF COLUMN 3 HAS A LOWER PRIORITY THAN COLUMN 1, ! +! COLUMNS 1 & 3 ARE SWAPPED ! +! + FOR DIHEDRALS, IF COLUMN 3 HAS LOWER PRIORITY THAN COLUMN 2, THE ! +! ORDER FOR THE ENTIRE DIHEDRAL IS REVERSED ! +! + FOR DIHEDRALS, IF COLUMNS 2 & 3 HAVE THE SAME PRIORITY, COLUMS ! +! 1 & 4 ARE CONSIDERED INSTEAD. IF 4 HAS LOWER PRIORITY THAN 1, THE ! +! ORDER FOR THE ENTIRE DIHEDRAL IS REVERSED ! +! + FOR IMPROPERS, NO SORTING IS PERFORMED *AFTER* PARAMETRIZATION, ! +! BUT THE FOLLOWING RULES APPLY *DURING* PARAMETRIZATION: ! +! - COLUMN 1 IS ALWAYS THE CENTRAL ATOM ! +! - IF 2 OF THE SUBSTITUENTS HAVE IDENTICAL TYPES, THESE SHOULD ! +! BE IN COLUMNS 2 & 3 (BUT THEY CANNOT BE MOVED AROUND ! +! WITHOUT RE-OPTIMIZING THE PARAMETER) ! +! - IF THE SUBSTITUENTS ARE ALL DIFFERENT, COLUMNS 2, 3 & 4 ! +! SHOULD BE SORTED BY INCREASING PRIORITY. COLUMNS 2 AND 3 ! +! CAN BE SWAPPED WITHOUT CHANGING THE PARAMETER BUT OTHER ! +! PERMUTATIONS MANDATE RE-OPTIMIZATION ! +! -------------------------------------------------------------------------- ! +! PRIORITY OF COLUMNS FOR THE PURPOSE OF SORTING THE LINES IN EACH SECTION: ! +! BONDS -- 1,2 ! +! ANGLES -- 2,1,3 ! +! DIHEDRALS -- 2,3,1,4 ! +! IMPROPERS -- 1,4,2,3 ! +! WHERE 1,2,3,4 INDICATE COLUMN NO, EG. DIHEDRALS ARE FIRST SORTED BY COLUMN ! +! 2, THEN (IF COLUMN 2 IS THE SAME) BY COLUMN 3, THEN BY COLUMN 1 AND THEN 4 ! +! -------------------------------------------------------------------------- ! + +ATOMS +!hydrogens +MASS 256 HGA1 1.00800 ! alphatic proton, CH +MASS 257 HGA2 1.00800 ! alphatic proton, CH2 +MASS 258 HGA3 1.00800 ! alphatic proton, CH3 +MASS 259 HGA4 1.00800 ! alkene proton; RHC= +MASS 260 HGA5 1.00800 ! alkene proton; H2C=CR +MASS 261 HGA6 1.00800 ! aliphatic H on fluorinated C, monofluoro +MASS 262 HGA7 1.00800 ! aliphatic H on fluorinated C, difluoro +MASS 263 HGAAM0 1.00800 ! aliphatic H, NEUTRAL trimethylamine (#) +MASS 264 HGAAM1 1.00800 ! aliphatic H, NEUTRAL dimethylamine (#) +MASS 265 HGAAM2 1.00800 ! aliphatic H, NEUTRAL methylamine (#) +!(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY +!on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens +MASS 266 HGP1 1.00800 ! polar H +MASS 267 HGP2 1.00800 ! polar H, +ve charge +MASS 268 HGP3 1.00800 ! polar H, thiol +MASS 269 HGP4 1.00800 ! polar H, neutral conjugated -NH2 group (NA bases) +MASS 270 HGP5 1.00800 ! polar H on quarternary ammonium salt (choline) +MASS 271 HGPAM1 1.00800 ! polar H, NEUTRAL dimethylamine (#), terminal alkyne H +MASS 272 HGPAM2 1.00800 ! polar H, NEUTRAL methylamine (#) +MASS 273 HGPAM3 1.00800 ! polar H, NEUTRAL ammonia (#) +!(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY +!on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens +MASS 274 HGR51 1.00800 ! nonpolar H, neutral 5-mem planar ring C, LJ based on benzene +MASS 275 HGR52 1.00800 ! Aldehyde H, formamide H (RCOH); nonpolar H, neutral 5-mem planar ring C adjacent to heteroatom or + charge +MASS 276 HGR53 1.00800 ! nonpolar H, +ve charge HIS he1(+1) +MASS 277 HGR61 1.00800 ! aromatic H +MASS 278 HGR62 1.00800 ! nonpolar H, neutral 6-mem planar ring C adjacent to heteroatom +MASS 279 HGR63 1.00800 ! nonpolar H, NAD+ nicotineamide all ring CH hydrogens +MASS 280 HGR71 1.00800 ! nonpolar H, neutral 7-mem arom ring, AZUL, azulene, kevo +!carbons +MASS 281 CG1T1 12.01100 ! internal alkyne R-C#C +MASS 282 CG1T2 12.01100 ! terminal alkyne H-C#C +MASS 283 CG1N1 12.01100 ! C for cyano group +MASS 284 CG2D1 12.01100 ! alkene; RHC= ; imine C +MASS 285 CG2D2 12.01100 ! alkene; H2C= +MASS 286 CG2D1O 12.01100 ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC1. +MASS 287 CG2D2O 12.01100 ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC2. +MASS 288 CG2DC1 12.01100 ! conjugated alkenes, R2C=CR2 +MASS 289 CG2DC2 12.01100 ! conjugated alkenes, R2C=CR2 +MASS 290 CG2DC3 12.01100 ! conjugated alkenes, H2C= +MASS 291 CG2N1 12.01100 ! conjugated C in guanidine/guanidinium +MASS 292 CG2N2 12.01100 ! conjugated C in amidinium cation +MASS 293 CG2O1 12.01100 ! carbonyl C: amides +MASS 294 CG2O2 12.01100 ! carbonyl C: esters, [neutral] carboxylic acids +MASS 295 CG2O3 12.01100 ! carbonyl C: [negative] carboxylates +MASS 296 CG2O4 12.01100 ! carbonyl C: aldehydes +MASS 297 CG2O5 12.01100 ! carbonyl C: ketones +MASS 298 CG2O6 12.01100 ! carbonyl C: urea, carbonate +MASS 299 CG2O7 12.01100 ! CO2 carbon +MASS 300 CG2R51 12.01100 ! 5-mem ring, his CG, CD2(0), trp +MASS 301 CG2R52 12.01100 ! 5-mem ring, double bound to N, PYRZ, pyrazole +MASS 302 CG2R53 12.01100 ! 5-mem ring, double bound to N and adjacent to another heteroatom, purine C8, his CE1 (0,+1), 2PDO, kevo +MASS 303 CG2R57 12.01100 ! 5-mem ring, bipyrroles +MASS 304 CG25C1 12.01100 ! same as CG2DC1 but in 5-membered ring with exocyclic double bond +MASS 305 CG25C2 12.01100 ! same as CG2DC2 but in 5-membered ring with exocyclic double bond +MASS 306 CG251O 12.01100 ! same as CG2D1O but in 5-membered ring with exocyclic double bond +MASS 307 CG252O 12.01100 ! same as CG2D2O but in 5-membered ring with exocyclic double bond +MASS 308 CG2R61 12.01100 ! 6-mem aromatic C +MASS 309 CG2R62 12.01100 ! 6-mem aromatic C for protonated pyridine (NIC) and rings containing carbonyls (see CG2R63) (NA) +MASS 310 CG2R63 12.01100 ! 6-mem aromatic amide carbon (NA) (and other 6-mem aromatic carbonyls?) +MASS 311 CG2R64 12.01100 ! 6-mem aromatic amidine and guanidine carbon (between 2 or 3 Ns and double-bound to one of them), NA, PYRM +MASS 312 CG2R66 12.01100 ! 6-mem aromatic carbon bound to F +MASS 313 CG2R67 12.01100 ! 6-mem aromatic carbon of biphenyl +MASS 314 CG2RC0 12.01100 ! 6/5-mem ring bridging C, guanine C4,C5, trp +MASS 315 CG2R71 12.01100 ! 7-mem ring arom C, AZUL, azulene, kevo +MASS 316 CG2RC7 12.01100 ! sp2 ring connection with single bond(!), AZUL, azulene, kevo +MASS 317 CG301 12.01100 ! aliphatic C, no hydrogens, neopentane +MASS 318 CG302 12.01100 ! aliphatic C, no hydrogens, trifluoromethyl +MASS 319 CG311 12.01100 ! aliphatic C with 1 H, CH +MASS 320 CG312 12.01100 ! aliphatic C with 1 H, difluoromethyl +MASS 321 CG314 12.01100 ! aliphatic C with 1 H, adjacent to positive N (PROT NTER) (+) +MASS 322 CG321 12.01100 ! aliphatic C for CH2 +MASS 323 CG322 12.01100 ! aliphatic C for CH2, monofluoromethyl +MASS 324 CG323 12.01100 ! aliphatic C for CH2, thiolate carbon +MASS 325 CG324 12.01100 ! aliphatic C for CH2, adjacent to positive N (piperidine) (+) +MASS 326 CG331 12.01100 ! aliphatic C for methyl group (-CH3) +MASS 327 CG334 12.01100 ! aliphatic C for methyl group (-CH3), adjacent to positive N (PROT NTER) (+) +MASS 328 CG3AM0 12.01100 ! aliphatic C for CH3, NEUTRAL trimethylamine methyl carbon (#) +MASS 329 CG3AM1 12.01100 ! aliphatic C for CH3, NEUTRAL dimethylamine methyl carbon (#) +MASS 330 CG3AM2 12.01100 ! aliphatic C for CH3, NEUTRAL methylamine methyl carbon (#) +!(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY +!on NEUTRAL METHYLAMINE groups, NOT ETHYL, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens +MASS 331 CG3C31 12.01100 ! cyclopropyl carbon +MASS 332 CG3C41 12.01100 ! cyclobutyl carbon +MASS 333 CG3C50 12.01100 ! 5-mem ring aliphatic quaternary C (cholesterol, bile acids) +MASS 334 CG3C51 12.01100 ! 5-mem ring aliphatic CH (proline CA, furanoses) +MASS 335 CG3C52 12.01100 ! 5-mem ring aliphatic CH2 (proline CB/CG/CD, THF, deoxyribose) +MASS 336 CG3C53 12.01100 ! 5-mem ring aliphatic CH adjacent to positive N (proline.H+ CA) (+) +MASS 337 CG3C54 12.01100 ! 5-mem ring aliphatic CH2 adjacent to positive N (proline.H+ CD) (+) +MASS 338 CG3RC1 12.01100 ! bridgehead in bicyclic systems containing at least one 5-membered or smaller ring +!(+) Includes protonated Shiff base (NG3D5, NG2R52 in 2HPP) but NOT amidinium (NG2R52 in IMIM), guanidinium +!nitrogens +MASS 339 NG1T1 14.00700 ! N for cyano group +!MASS 340 NG1D1 14.00700 ! terminal N in azides, lsk +MASS 341 NG2D1 14.00700 ! N for neutral imine/Schiff's base (C=N-R, acyclic amidine, gunaidine) +MASS 342 NG2S0 14.00700 ! N,N-disubstituted amide, proline N (CO=NRR') +MASS 343 NG2S1 14.00700 ! peptide nitrogen (CO=NHR) +MASS 344 NG2S2 14.00700 ! terminal amide nitrogen (CO=NH2) +MASS 345 NG2S3 14.00700 ! external amine ring nitrogen (planar/aniline), phosphoramidate +!MASS 346 NG2S4 14.00700 ! neutral hydroxamic acid +MASS 347 NG2O1 14.00700 ! NITB, nitrobenzene +MASS 348 NG2P1 14.00700 ! N for protonated imine/Schiff's base (C=N(+)H-R, acyclic amidinium, guanidinium) +MASS 349 NG2R43 14.00700 ! amide in 4-memebered ring (planar), AZDO, lsk +MASS 350 NG2R50 14.00700 ! double bound neutral 5-mem planar ring, purine N7 +MASS 351 NG2R51 14.00700 ! single bound neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused) +MASS 352 NG2R52 14.00700 ! protonated schiff base, amidinium, guanidinium in 5-membered ring, HIS, 2HPP, kevo +MASS 353 NG2R53 14.00700 ! amide in 5-memebered NON-SP2 ring (slightly pyramidized), 2PDO, kevo +MASS 354 NG2R57 14.00700 ! 5-mem ring, bipyrroles +MASS 355 NG2R60 14.00700 ! double bound neutral 6-mem planar ring, pyr1, pyzn +MASS 356 NG2R61 14.00700 ! single bound neutral 6-mem planar ring imino nitrogen; glycosyl linkage +MASS 357 NG2R62 14.00700 ! double bound 6-mem planar ring with heteroatoms in o or m, pyrd, pyrm +MASS 358 NG2R67 14.00700 ! 6-mem planar ring substituted with 6-mem planar ring (N-phenyl pyridinones etc.) +MASS 359 NG2RC0 14.00700 ! 6/5-mem ring bridging N, indolizine, INDZ, kevo +MASS 360 NG301 14.00700 ! neutral trimethylamine nitrogen +MASS 361 NG311 14.00700 ! neutral dimethylamine nitrogen +MASS 362 NG321 14.00700 ! neutral methylamine nitrogen +MASS 363 NG331 14.00700 ! neutral ammonia nitrogen +MASS 364 NG3C51 14.00700 ! secondary sp3 amine in 5-membered ring +MASS 365 NG3N1 14.00700 ! N in hydrazine, HDZN +MASS 366 NG3P0 14.00700 ! quarternary N+, choline +MASS 367 NG3P1 14.00700 ! tertiary NH+ (PIP) +MASS 368 NG3P2 14.00700 ! secondary NH2+ (proline) +MASS 369 NG3P3 14.00700 ! primary NH3+, phosphatidylethanolamine +!oxygens +MASS 370 OG2D1 15.99940 ! carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera +MASS 371 OG2D2 15.99940 ! carbonyl O: negative groups: carboxylates, carbonate +MASS 372 OG2D3 15.99940 ! carbonyl O: ketones +MASS 373 OG2D4 15.99940 ! 6-mem aromatic carbonyl oxygen (nucleic bases) +MASS 374 OG2D5 15.99940 ! CO2 oxygen +MASS 375 OG2N1 15.99940 ! NITB, nitrobenzene +MASS 376 OG2P1 15.99940 ! =O in phosphate or sulfate +MASS 377 OG2R50 15.99940 ! FURA, furan +MASS 378 OG3R60 15.99940 ! O in 6-mem cyclic enol ether (PY01, PY02) or ester +MASS 379 OG301 15.99940 ! ether -O- !SHOULD WE HAVE A SEPARATE ENOL ETHER??? IF YES, SHOULD WE MERGE IT WITH OG3R60??? +MASS 380 OG302 15.99940 ! ester -O- +MASS 381 OG303 15.99940 ! phosphate/sulfate ester oxygen +MASS 382 OG304 15.99940 ! linkage oxygen in pyrophosphate/pyrosulphate +MASS 383 OG311 15.99940 ! hydroxyl oxygen +MASS 384 OG312 15.99940 ! ionized alcohol oxygen +MASS 385 OG3C31 15.99940 ! epoxide oxygen, 1EOX, 1BOX, sc +MASS 386 OG3C51 15.99940 ! 5-mem furanose ring oxygen (ether) +MASS 387 OG3C61 15.99940 ! DIOX, dioxane, ether in 6-membered ring !SHOULD WE MERGE THIS WITH OG3R60??? +!sulphurs +MASS 388 SG2D1 32.06000 ! thiocarbonyl S +MASS 389 SG2R50 32.06000 ! THIP, thiophene +MASS 390 SG311 32.06000 ! sulphur, SH, -S- +MASS 391 SG301 32.06000 ! sulfur C-S-S-C type +MASS 392 SG302 32.06000 ! thiolate sulfur (-1) +MASS 393 SG3O1 32.06000 ! sulfate -1 sulfur +MASS 394 SG3O2 32.06000 ! neutral sulfone/sulfonamide sulfur +MASS 395 SG3O3 32.06000 ! neutral sulfoxide sulfur +!halogens +MASS 396 CLGA1 35.45300 ! CLET, DCLE, chloroethane, 1,1-dichloroethane +MASS 397 CLGA3 35.45300 ! TCLE, 1,1,1-trichloroethane +MASS 398 CLGR1 35.45300 ! CHLB, chlorobenzene +MASS 399 BRGA1 79.90400 ! BRET, bromoethane +MASS 400 BRGA2 79.90400 ! DBRE, 1,1-dibromoethane +MASS 401 BRGA3 79.90400 ! TBRE, 1,1,1-dibromoethane +MASS 402 BRGR1 79.90400 ! BROB, bromobenzene +MASS 403 IGR1 126.90447 ! IODB, iodobenzene +MASS 404 FGA1 18.99800 ! aliphatic fluorine, monofluoro +MASS 405 FGA2 18.99800 ! aliphatic fluorine, difluoro +MASS 406 FGA3 18.99800 ! aliphatic fluorine, trifluoro +MASS 407 FGP1 18.99800 ! anionic F, for ALF4 AlF4- +MASS 408 FGR1 18.99800 ! aromatic flourine +!miscellaneous +MASS 409 PG0 30.97380 ! neutral phosphate +MASS 410 PG1 30.97380 ! phosphate -1 +MASS 411 PG2 30.97380 ! phosphate -2 +MASS 412 ALG1 26.98154 ! Aluminum, for ALF4, AlF4- +!MASS 414 HGTIP3 1.00800 ! polar H, TIPS3P WATER HYDROGEN +!MASS 415 OGTIP3 15.99940 ! TIPS3P WATER OXYGEN +!MASS 416 DUM 0.00000 ! dummy atom +!MASS 417 HE 4.00260 ! helium +!MASS 418 NE 20.17970 ! neon + +BONDS +CG1N1 CG2R61 345.00 1.4350 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN) (MP2 by kevo) +CG1N1 CG331 400.00 1.4700 ! ACN, acetonitrile, kevo +CG1N1 NG1T1 1053.00 1.1800 ! ACN, acetonitrile; 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN) (MP2 by kevo) +CG1T1 CG1T1 960.00 1.2200 ! 2BTY, 2-butyne, kevo +CG1T1 CG1T2 980.00 1.2200 ! PRPY, propyne, kevo +CG1T1 CG331 410.00 1.4650 ! 2BTY, 2-butyne, kevo +CG1T2 HGPAM1 426.00 1.0700 ! PRPY, propyne, xxwy & kevo +CG251O CG25C1 440.00 1.3400 ! OIRD, oxindol-3-ylidene rhodanine; from PY02, 2h-pyran (re-optimize); kevo +CG251O CG2DC3 570.00 1.3400 ! MRDN, methylidene rhodanine, kevo & xxwy +CG251O CG2R53 255.00 1.4800 ! MRDN, methylidene rhodanine, kevo & xxwy +CG251O NG2R53 200.00 1.4100 ! MHYO, 5-methylenehydantoin, xxwy +CG251O SG311 200.00 1.7700 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O CG25C2 440.00 1.3400 ! OIRD, oxindol-3-ylidene rhodanine; from PY02, 2h-pyran (re-optimize); kevo +CG252O CG2DC3 570.00 1.3400 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O CG2R53 255.00 1.4800 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O NG2R53 200.00 1.4100 ! MHYO, 5-methylenehydantoin, xxwy +CG252O SG311 200.00 1.7700 ! MRDN, methylidene rhodanine, kevo & xxwy +CG25C1 CG2DC3 500.00 1.3420 ! MEOI, methyleneoxindole; from RETINOL 13DB, 1,3-Butadiene (re-optimize); kevo +CG25C1 CG2R53 247.00 1.4900 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C1 CG2RC0 290.00 1.4800 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2DC3 500.00 1.3420 ! MEOI, methyleneoxindole; from RETINOL 13DB, 1,3-Butadiene (re-optimize); kevo +CG25C2 CG2R53 247.00 1.4900 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2RC0 290.00 1.4800 ! MEOI, methyleneoxindole, kevo & xxwy +CG2D1 CG2D1 440.00 1.3400 ! LIPID butene, yin,adm jr., 12/95 +CG2D1 CG2D1O 440.00 1.3180 ! PY01, 4h-pyran +CG2D1 CG2D2 500.00 1.3420 ! LIPID propene, yin,adm jr., 12/95 +CG2D1 CG2D2O 440.00 1.3180 ! PY01, 4h-pyran +CG2D1 CG301 240.00 1.5020 ! CHOLEST cholesterol +CG2D1 CG321 365.00 1.5020 ! LIPID butene; from propene, yin,adm jr., 12/95 +CG2D1 CG331 383.00 1.5040 ! LIPID butene, yin,adm jr., 12/95 +CG2D1 NG2D1 500.00 1.2760 ! RETINOL SCH1, Schiff's base, deprotonated +CG2D1 NG2P1 470.00 1.2830 ! RETINOL SCH2, Schiff's base, protonated +CG2D1 HGA4 360.50 1.1000 ! LIPID propene, yin,adm jr., 12/95 +CG2D1 HGR52 360.50 1.1000 ! RETINOL SCH2, Schiff's base, protonated +CG2D1O CG2D2 600.00 1.3400 ! MOET, Methoxyethene, xxwy +CG2D1O CG2DC1 440.00 1.3400 ! PY02, 2h-pyran +CG2D1O NG301 420.00 1.3550 ! NADH, NDPH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D1O NG311 420.00 1.3550 ! NICH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D1O NG321 420.00 1.4000 ! AMET, ethenamine; mp2-geom, checked molvib; pram +CG2D1O OG301 385.00 1.3600 ! MOET, Methoxyethene, xxwy +CG2D1O OG3R60 500.00 1.3470 ! PY01, 4h-pyran +CG2D1O HGA4 360.50 1.1000 ! PY01, 4h-pyran +CG2D2 CG2D2 510.00 1.3300 ! LIPID ethene yin,adm jr., 12/95 +CG2D2 CG2D2O 600.00 1.3400 ! MOET, Methoxyethene, xxwy +CG2D2 HGA5 365.00 1.1000 ! LIPID propene; from ethene, yin,adm jr., 12/95 +CG2D2O CG2DC2 440.00 1.3400 ! PY02, 2h-pyran +CG2D2O NG301 420.00 1.3550 ! NADH, NDPH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D2O NG311 420.00 1.3550 ! NICH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D2O NG321 420.00 1.4000 ! AMET, ethenamine; mp2-geom, checked molvib; pram +CG2D2O OG301 385.00 1.3600 ! MOET, Methoxyethene, xxwy +CG2D2O OG3R60 500.00 1.3470 ! PY01, 4h-pyran +CG2D2O HGA4 360.50 1.1000 ! PY01, 4h-pyran +CG2DC1 CG2DC1 440.00 1.3400 ! RETINOL BTE2, 2-butene +CG2DC1 CG2DC2 300.00 1.4500 ! RETINOL 13DB, Butadiene @@@@@ Kenno: 1.47 --> 1.45 @@@@@ +CG2DC1 CG2DC3 500.00 1.3420 ! RETINOL 13DB, Butadiene +CG2DC1 CG2O1 440.00 1.4890 ! RETINOL CROT +CG2DC1 CG2O3 440.00 1.4890 ! RETINOL PRAC +CG2DC1 CG2O4 300.00 1.4798 ! RETINOL RTAL unmodified +CG2DC1 CG2O5 300.00 1.4800 ! BEON, butenone, kevo +CG2DC1 CG2R61 365.00 1.4500 ! compromise between HDZ1B and STYR by kevo +CG2DC1 CG301 365.00 1.5020 ! RETINOL MECH +CG2DC1 CG321 365.00 1.5020 ! RETINOL MECH +CG2DC1 CG331 383.00 1.5040 ! RETINOL 13DP, 1,3-pentadiene +CG2DC1 NG2D1 500.00 1.2760 ! RETINOL SCH1, Schiff's base, deprotonated +CG2DC1 NG2P1 470.00 1.2830 ! RETINOL SCH2, Schiff's base, protonated +CG2DC1 HGA4 360.50 1.1000 ! RETINOL BTE2, 2-butene +CG2DC1 HGR52 360.50 1.1000 ! RETINOL SCH2, Schiff's base, protonated +CG2DC2 CG2DC2 440.00 1.3400 ! RETINOL BTE2, 2-butene +CG2DC2 CG2DC3 500.00 1.3420 ! RETINOL 13DB, Butadiene +CG2DC2 CG2O1 440.00 1.4890 ! RETINOL CROT +CG2DC2 CG2O3 440.00 1.4890 ! RETINOL PRAC +CG2DC2 CG2O4 300.00 1.4798 ! RETINOL RTAL unmodified +CG2DC2 CG2O5 300.00 1.4800 ! BEON, butenone, kevo +CG2DC2 CG2R61 365.00 1.4500 ! compromise between HDZ1B and STYR by kevo +CG2DC2 CG301 365.00 1.5020 ! RETINOL MECH +CG2DC2 CG321 365.00 1.5020 ! RETINOL MECH +CG2DC2 CG331 383.00 1.5040 ! RETINOL 13DP, 1,3-pentadiene +CG2DC2 NG2D1 500.00 1.2760 ! RETINOL SCH1, Schiff's base, deprotonated +CG2DC2 NG2P1 470.00 1.2830 ! RETINOL SCH2, Schiff's base, protonated +CG2DC2 HGA4 360.50 1.1000 ! RETINOL BTE2, 2-butene +CG2DC2 HGR52 360.50 1.1000 ! RETINOL SCH2, Schiff's base, protonated +CG2DC3 HGA5 365.00 1.1000 ! RETINOL BTE2, 2-butene +CG2N1 NG2D1 500.00 1.3100 ! MGU1, methylguanidine +CG2N1 NG2P1 463.00 1.3650 ! PROT 403.0->463.0, 1.305->1.365 guanidinium (KK) +CG2N1 NG311 500.00 1.4400 ! MGU2, methylguanidine2 +CG2N1 NG321 450.00 1.4400 ! MGU1, methylguanidine +CG2N2 CG2R61 300.00 1.4400 ! BAMI, benzamidinium, mp2 geom & molvib, pram +CG2N2 CG331 280.00 1.5000 ! AMDN, amidinium, sz (verified by pram) +CG2N2 NG2D1 621.00 1.2900 ! MT2A, DH3T, fylin +CG2N2 NG2P1 475.00 1.3200 ! AMDN, amidinium; BAMI, benzamidinium; mp2 geom & molvib; pram +CG2N2 NG321 365.00 1.4200 ! MT2A, DH3T, fylin +CG2N2 SG311 187.00 1.7900 ! MT2R(+), HH3R, MT2A, DH3T, fylin +CG2O1 CG2R61 300.00 1.4750 ! 3NAP, nicotamide. kevo: 1.45 -> 1.475 +CG2O1 CG2R62 302.00 1.4800 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2O1 CG311 250.00 1.4900 ! PROT Ala Dipeptide (5/91) +CG2O1 CG314 250.00 1.4900 ! PROT Ala Dipeptide (5/91) +CG2O1 CG321 250.00 1.4900 ! PROT Ala Dipeptide (5/91) +CG2O1 CG324 250.00 1.4900 ! PROT Ala Dipeptide (5/91) +CG2O1 CG331 250.00 1.4900 ! PROT Ala Dipeptide (5/91) +CG2O1 CG3C51 250.00 1.4900 ! PROT 6-31g* AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 CG3C53 250.00 1.4900 ! PROT 6-31g* AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 NG2S0 430.00 1.3500 ! DMA, Dimethylacetamide, xxwy +CG2O1 NG2S1 370.00 1.3450 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 NG2S2 430.00 1.3600 ! PROT from NG2S2 CT3, neutral glycine, adm jr. +CG2O1 OG2D1 620.00 1.2300 ! PROT Peptide geometry, condensed phase (LK) +CG2O1 HGR52 317.13 1.1000 ! FORM, formamide reverted to value from par_all22_prot.inp and par_cgenff_1d.inp +CG2O2 CG2R61 254.00 1.4800 ! ZOIC, benzoic acid, MBOA, methylbenzoate, jal +CG2O2 CG311 200.00 1.5220 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 CG321 200.00 1.5220 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 CG331 200.00 1.5220 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 OG2D1 750.00 1.2200 ! PROT adm jr. 5/02/91, acetic acid pure solvent; LIPID methyl acetate +CG2O2 OG302 150.00 1.3340 ! LIPID methyl acetate +CG2O2 OG311 230.00 1.4000 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 HGR52 348.00 1.0960 ! FORH, formic acid, xxwy +CG2O3 CG2O5 250.00 1.5200 ! COMPDS peml unmodified +CG2O3 CG2R61 200.00 1.5000 ! 3CPY, pyridine-3-carboxylate (PYRIDINE nicotinic acid), yin +CG2O3 CG301 200.00 1.5220 ! AMOL, alpha-methoxy-lactic acid, og par22 CT1 CC +CG2O3 CG311 200.00 1.5220 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG314 200.00 1.5220 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG321 200.00 1.5220 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG324 200.00 1.5220 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG331 200.00 1.5220 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG3C51 250.00 1.4900 ! PROT 6-31g* AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C53 250.00 1.4900 ! PROT 6-31g* AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 OG2D2 525.00 1.2600 ! PROT adm jr. 7/23/91, acetic acid +CG2O3 HGR52 238.00 1.1422 ! FORA, formate, kevo +CG2O4 CG2R61 300.00 1.4798 ! ALDEHYDE benzaldehyde unmodified +CG2O4 CG321 250.00 1.5000 ! PALD, propionaldehyde from AALD adm 11/08 +CG2O4 CG331 250.00 1.5000 ! AALD, acetaldehyde adm 11/08 +CG2O4 OG2D1 700.00 1.2150 ! ALDEHYDE acetaldehyde adm 11/08 +CG2O4 HGR52 330.00 1.1100 ! ALDEHYDE acetaldehyde adm 11/08 +CG2O5 CG2R61 254.00 1.4600 ! 3ACP, 3-acetylpyridine; BF6 BF7 C36 C37; PHMK, phenyl methyl ketone, mcs +CG2O5 CG311 330.00 1.5000 ! COMPDS peml re-initialized by kevo from ACO adm 11/08 +CG2O5 CG321 330.00 1.5000 ! BTON, butanone; from ACO, acetone; yapol +CG2O5 CG331 330.00 1.5000 ! ACO, acetone adm 11/08 +CG2O5 OG2D3 700.00 1.2300 ! ACO, acetone adm 11/08 +CG2O6 NG2S1 510.00 1.3700 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo +CG2O6 NG2S2 430.00 1.3600 ! UREA, Urea. Uses a slack parameter from PROT from NG2S2 CT3, neutral glycine, adm jr. ==> re-optimize +CG2O6 OG2D1 650.00 1.2300 ! UREA, Urea. Uses a slack parameter from PROT adm jr. 4/10/91, acetamide ==> re-optimize +CG2O6 OG2D2 314.50 1.2940 ! PROTMOD carbonate +CG2O6 OG302 350.00 1.3500 ! DMCB & DECB & DMCA, dimethyl & diehtyl carbamate and dimethyl carbonate, cacha & kevo & xxwy +CG2O6 OG311 185.00 1.4800 ! CO31, bicarbonate, xxwy +CG2O6 SG2D1 300.00 1.6300 ! DMTT, dimethyl trithiocarbonate, kevo +CG2O6 SG311 190.00 1.7500 ! DMTT, dimethyl trithiocarbonate, kevo +CG2O7 NG2D1 920.00 1.1900 ! MICY, EICY: isocyanates, xxwy (QM: 1.216; Crystal survey: 1.183) +CG2O7 OG2D5 986.00 1.1700 ! PROT CO2, JES; re-optimized by kevo (1.160); compromised with isocyanate, both crystal survey and QM data, kevo & xxwy +CG2R51 CG2R51 410.00 1.3600 ! PROT histidine, adm jr., 6/27/90 +CG2R51 CG2R52 360.00 1.4000 ! PYRZ, pyrazole +CG2R51 CG2R53 264.00 1.5080 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG2R57 410.00 1.3600 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51; lf +CG2R51 CG2RC0 350.00 1.4300 ! INDO/TRP +CG2R51 CG2RC7 340.00 1.4050 ! AZUL, Azulene, kevo +CG2R51 CG321 229.63 1.5000 ! PROT his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CG2R51 CG331 229.63 1.5000 ! PROT his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CG2R51 CG3C52 350.00 1.5100 ! 2PRP, 2-pyrroline.H+; 2PRL, 2-pyrroline; 3PRL, 3-pyrroline, kevo +CG2R51 CG3C54 325.00 1.4960 ! 3PRP, 3-pyrroline.H+; 2HPP, 2H-pyrrole.H+, kevo +CG2R51 NG2R50 400.00 1.3800 ! PROT his, ADM JR., 7/20/89 +CG2R51 NG2R51 400.00 1.3800 ! PROT his, ADM JR., 7/20/89 +CG2R51 NG2R52 380.00 1.3700 ! PROT his, adm jr., 6/28/90 +CG2R51 NG2R57 400.00 1.3800 ! 13BPO, 1,3-bipyrrole; from CG2R51 NG2R51; lf +CG2R51 NG2RC0 400.00 1.3710 ! INDZ, indolizine, kevo +CG2R51 NG3C51 360.00 1.4120 ! 2PRL, 2-pyrroline, kevo +CG2R51 NG3P2 330.00 1.4800 ! 2PRP, 2-pyrroline.H+, kevo +CG2R51 OG2R50 450.00 1.3710 ! FURA, furan +CG2R51 OG3C51 360.00 1.3700 ! 2DHF, 2,3-dihydrofuran, kevo +CG2R51 SG2R50 300.00 1.7300 ! THIP, thiophene +CG2R51 HGR51 350.00 1.0800 ! INDO/TRP +CG2R51 HGR52 375.00 1.0830 ! PROT his, adm jr., 6/27/90 +CG2R52 CG2R52 400.00 1.3800 ! TRZ2, 2H-1,2,3-triazole, lf +CG2R52 CG2RC0 360.00 1.4200 ! INDA, 1H-indazole, kevo +CG2R52 CG3C52 350.00 1.5050 ! 2PRZ, 2-pyrazoline, kevo +CG2R52 NG2R50 400.00 1.3150 ! PYRZ, pyrazole; 2PRZ, 2-pyrazoline, kevo +CG2R52 NG2R52 490.00 1.3000 ! 2HPP, 2H-pyrrole.H+, kevo +CG2R52 HGR52 375.00 1.0830 ! PYRZ, pyrazole +CG2R53 CG3C41 200.00 1.5600 ! AZDO, 2-azetidinone, kevo +CG2R53 CG3C52 300.00 1.5300 !300 350 2PDO, 2-pyrrolidinone, kevo +CG2R53 NG2R43 370.00 1.3800 ! AZDO, 2-azetidinone, kevo +CG2R53 NG2R50 400.00 1.3200 ! PROT his, ADM JR., 7/20/89 +CG2R53 NG2R51 320.00 1.3740 ! NA A, adm jr. 11/97 +CG2R53 NG2R52 380.00 1.3200 ! PROT his, adm jr., 6/27/90 +CG2R53 NG2R53 460.00 1.3800 !460 370 *NEW* 2PDO, 2-pyrrolidinone, kevo +CG2R53 NG3C51 380.00 1.4000 ! 1.395 2IMI, 2-imidazoline, kevo +CG2R53 OG2D1 570.00 1.2350 !560 620 *NEW* 2PDO, 2-pyrrolidinone, kevo +CG2R53 OG2R50 450.00 1.3710 ! OXAZ, oxazole +CG2R53 OG3C51 295.50 1.3570 ! GBL, Gamma-butyrolactone, ctsai & kevo +CG2R53 SG2D1 400.00 1.6300 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 SG2R50 300.00 1.7300 ! THAZ, thiazole +CG2R53 SG311 170.00 1.7700 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 HGR52 340.00 1.0900 ! PROT his, adm jr., 6/28/29 +CG2R53 HGR53 333.00 1.0700 ! PROT his, adm jr., 6/27/90 +CG2R57 CG2R57 413.00 1.4500 ! 33BPO, 3,3-bipyrrole, lf +CG2R57 NG2R57 390.00 1.3950 ! 13BPO, 1,3-bipyrrole, lf +CG2R61 CG2R61 305.00 1.3750 ! PROT benzene, JES 8/25/89 +CG2R61 CG2R62 394.00 1.3750 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R63 265.00 1.4270 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R64 250.00 1.3550 ! 18NFD, 1,8-naphthyridine, erh +CG2R61 CG2R66 305.00 1.3700 ! NAMODEL difluorotoluene +CG2R61 CG2R67 305.00 1.3750 ! COMPDS peml +CG2R61 CG2RC0 300.00 1.3600 ! INDO/TRP +CG2R61 CG311 230.00 1.4900 ! NAMODEL difluorotoluene +CG2R61 CG312 198.00 1.4500 ! BDFP, BDFD, Difuorobenzylphosphonate +CG2R61 CG321 230.00 1.4900 ! PROT phe,tyr, JES 8/25/89 +CG2R61 CG324 230.00 1.4900 ! BPIP, N-Benzyl PIP, cacha +CG2R61 CG331 230.00 1.4900 ! PROT toluene, adm jr. 3/7/92 +CG2R61 NG2O1 230.00 1.4020 ! NITB, nitrobenzene +CG2R61 NG2R60 450.00 1.3050 ! PYR1, pyridine +CG2R61 NG2R61 380.00 1.3790 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 NG2R62 450.00 1.3050 ! PYRD, pyridazine +CG2R61 NG2RC0 370.00 1.3790 ! INDZ, indolizine, kevo +CG2R61 NG2S1 305.00 1.4140 ! RETINOL PACP +CG2R61 NG2S3 400.00 1.3900 ! PYRIDINE aminopyridine, adm jr., 7/94 +CG2R61 NG301 325.00 1.4100 ! DMAN, N,N-dimethylaniline, kevo +CG2R61 NG311 330.00 1.4000 ! FEOZ, phenoxazine; PMSM N-phenylmethanesulfonamide; xxwy +CG2R61 NG3N1 680.00 1.4100 ! PHHZ, phenylhydrazine, ed +CG2R61 OG301 230.00 1.3820 ! COMPDS peml +CG2R61 OG303 340.00 1.3800 ! PROTNA phenol phosphate, 6/94, adm jr. +CG2R61 OG311 334.30 1.4110 ! PROT MeOH, EMB 10/10/89, +CG2R61 OG312 525.00 1.2600 ! PROT adm jr. 8/27/91, phenoxide +CG2R61 OG3R60 280.00 1.3500 ! FEOZ, phenoxazine, erh based on PY02, 2h-pyran +CG2R61 SG311 280.00 1.7500 ! FETZ, phenothiazine, erh based on PY02, 2h-pyran +CG2R61 SG3O1 230.00 1.7800 ! benzene sulfonate anion, og +CG2R61 SG3O2 190.00 1.7300 ! BSAM, benzenesulfonamide and other sulfonamides, xxwy +CG2R61 CLGR1 350.00 1.7400 ! CHLB, chlorobenzene +CG2R61 BRGR1 230.00 1.9030 ! BROB, bromobenzene +CG2R61 IGR1 190.00 2.1150 ! IODB, iodobenzene +CG2R61 HGR61 340.00 1.0800 ! PROT phe,tyr JES 8/25/89 +CG2R61 HGR62 340.00 1.0800 ! NA, DFT +CG2R62 CG2R62 420.00 1.3500 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R62 CG2R63 302.00 1.4030 ! NA T, adm jr. 11/97 +CG2R62 CG2R64 320.00 1.4060 ! NA C, adm jr. 11/97 +CG2R62 CG2R67 305.00 1.3800 ! PYO2B, fylin +CG2R62 CG331 230.00 1.4780 ! NA T, adm jr. 11/97 +CG2R62 NG2R61 302.00 1.3430 ! NA C, adm jr. 11/97 +CG2R62 NG2R62 340.00 1.3650 ! TC243C, 4(3H)-quinazolinone; from CG2R61 NG2R62; isg +CG2R62 NG2R67 302.00 1.3430 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from NG2R61 CG2R61; isg +CG2R62 OG3R60 330.00 1.3700 ! RIN, coumarin, isg +CG2R62 HGR62 350.00 1.0900 ! NA C,U, JWK +CG2R62 HGR63 350.00 1.0900 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R63 CG2RC0 302.00 1.3600 ! NA G, adm jr. 11/97 +CG2R63 NG2R61 340.00 1.3830 ! NA U,T adm jr. 11/97 +CG2R63 NG2R62 350.00 1.3350 ! NA C, adm jr. 11/97 +CG2R63 NG2R67 302.00 1.3430 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from NG2R67 CG2R62, 1PH4PO; isg +CG2R63 OG2D4 660.00 1.2340 ! NA U,A,G par_a4 adm jr. 10/2/91 +CG2R63 OG3R60 235.00 1.4000 ! RIN, coumarin, isg +CG2R63 SG2D1 373.00 1.6550 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R64 CG2RC0 360.00 1.3580 ! NA A, adm jr. 11/97 +CG2R64 NG2R60 450.00 1.3050 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo +CG2R64 NG2R61 400.00 1.3920 ! NA G +CG2R64 NG2R62 400.00 1.3420 ! NA A, adm jr. 11/97 +CG2R64 NG2R67 400.00 1.3920 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from CG2R64 NG2R61, NA; isg +CG2R64 NG2S1 305.00 1.4140 ! 2AMP, 2-amino pyridine, from PACP, p-acetamide-phenol, pyridine, kevo +CG2R64 NG2S3 360.00 1.3660 ! NA C,A,G JWK, adm jr. 10/2/91 +CG2R64 NG301 390.00 1.3550 ! TMC, yxu +CG2R64 SG311 262.00 1.7410 ! 2SMPYR, 2-(methylthio)-pyrimidine; from CG2R61 SG311, 4O2SM; isg +CG2R64 HGR62 380.00 1.0900 ! NA G,A, JWK par_a7 9/30/91 +CG2R66 CG2R67 305.00 1.3800 ! PYO2F, fylin +CG2R66 FGR1 400.00 1.3580 ! NAMODEL difluorotoluene +CG2R67 CG2R67 300.00 1.4900 ! COMPDS peml +CG2R67 CG2RC0 300.00 1.4200 ! CRBZ, carbazole, erh +CG2R67 NG2R60 450.00 1.3100 ! 22BPY, 2,2'-bipyridine, kevo +CG2R67 NG2R67 403.00 1.4110 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from NG2R61 CG2R61; isg +CG2R71 CG2R71 360.00 1.3850 ! AZUL, Azulene, kevo +CG2R71 CG2RC7 400.00 1.3800 ! AZUL, Azulene, kevo +CG2R71 HGR71 355.00 1.0900 ! AZUL, Azulene, kevo +CG2RC0 CG2RC0 360.00 1.3850 ! INDO/TRP +CG2RC0 CG3C52 305.00 1.5200 ! 3HIN, 3H-indole, kevo +CG2RC0 NG2R50 310.00 1.3650 ! NA G, adm jr. 11/97 +CG2RC0 NG2R51 300.00 1.3750 ! NA A, adm jr. 11/97 +CG2RC0 NG2R62 350.00 1.3150 ! NA G, adm jr. 11/97 +CG2RC0 NG2RC0 245.00 1.4170 ! INDZ, indolizine, kevo +CG2RC0 NG3C51 330.00 1.4000 ! INDI, indoline, kevo +CG2RC0 OG2R50 450.00 1.3700 ! ZFUR, benzofuran, kevo +CG2RC0 OG3C51 330.00 1.3890 !1.388 ZDOL, 1,3-benzodioxole, kevo +CG2RC0 SG2R50 300.00 1.7600 ! ZTHP, benzothiophene, kevo +CG2RC7 CG2RC7 230.00 1.5200 ! AZUL, Azulene, kevo +CG301 CG311 222.50 1.5000 ! CA, CHOLIC ACID, cacha, 03/06 +CG301 CG321 222.50 1.5380 ! RETINOL TMCH/MECH +CG301 CG331 222.50 1.5380 ! RETINOL TMCH/MECH +CG301 OG301 360.00 1.4150 ! AMOL, alpha-methoxy-lactic acid, og all34_ethers_1a CG32A OG30A +CG301 OG302 340.00 1.4300 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide +CG301 OG311 428.00 1.4200 ! AMOL, alpha-methoxy-lactic acid, og par22 OH1 CT1 +CG301 CLGA3 190.00 1.7700 ! TCLE +CG301 BRGA3 120.00 1.9540 ! TBRE +CG302 CG321 250.00 1.5200 ! FLUROALK fluoroalkanes +CG302 CG331 250.00 1.5200 ! FLUROALK fluoroalkanes +CG302 FGA3 265.00 1.3400 ! FLUROALK fluoroalkanes +CG311 CG311 222.50 1.5000 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG314 222.50 1.5000 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG321 222.50 1.5380 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG324 222.50 1.5300 ! FLAVOP PIP1,2,3 +CG311 CG331 222.50 1.5380 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG3C51 222.50 1.5280 ! TF2M, viv +CG311 CG3RC1 222.50 1.5240 ! CARBOCY carbocyclic sugars +CG311 NG2R53 320.00 1.4300 ! drug design project, xxwy +CG311 NG2S1 320.00 1.4300 ! PROT NMA Gas & Liquid Phase IR Spectra (LK) +CG311 OG301 360.00 1.4150 ! all34_ethers_1a CG32A OG30A, gk or og +CG311 OG302 340.00 1.4300 ! LIPID phosphate +CG311 OG303 340.00 1.4300 ! LIPID phosphate +CG311 OG311 428.00 1.4200 ! PROT methanol vib fit EMB 11/21/89 +CG311 OG312 358.00 1.3130 ! COMPDS peml original OG311 CG311 428.000 1.4200 +CG311 CLGA1 190.00 1.7768 ! DCLE +CG311 BRGA2 140.00 1.9560 ! DBRE +CG311 HGA1 309.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 +CG312 CG331 198.00 1.5200 ! FLUROALK fluoroalkanes +CG312 PG1 270.00 1.8800 ! BDFP, Difuorobenzylphosphonate \ re-optimize? +CG312 PG2 270.00 1.8800 ! BDFD, Difuorobenzylphosphonate / re-optimize? +CG312 FGA2 349.00 1.3530 ! FLUROALK fluoroalkanes +CG312 HGA7 346.00 1.0828 ! FLUROALK fluoroalkanes +CG314 CG321 222.50 1.5380 ! PROT alkane update, adm jr., 3/2/92 +CG314 CG331 222.50 1.5380 ! PROT alkane update, adm jr., 3/2/92 +CG314 NG3P2 200.00 1.4900 ! 2MRB, Alpha benzyl gamma 2-methyl piperidine, cacha +CG314 NG3P3 200.00 1.4800 ! PROT new stretch and bend; methylammonium (KK 03/10/92) +CG314 HGA1 309.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG321 222.50 1.5300 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG324 222.50 1.5300 ! FLAVOP PIP1,2,3 +CG321 CG331 222.50 1.5280 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG3C31 275.00 1.5000 ! 1BOX, 1-butene oxide, sc +CG321 CG3C51 222.50 1.5280 ! TF2M, viv +CG321 CG3RC1 222.50 1.5240 ! CARBOCY carbocyclic sugars +CG321 NG2D1 293.00 1.4400 ! EEPI, fylin +CG321 NG2R51 400.00 1.4580 ! ETRZ, 1-Ethyl-1,2,3-triazole, from CG331 NG2R51, kevo +CG321 NG2S1 320.00 1.4300 ! PROT NMA Gas & Liquid Phase IR Spectra (LK) +CG321 NG2S3 322.00 1.4400 ! NESM, N-ethyl-sulfamate, my & kevo +CG321 NG311 263.00 1.4740 ! AMINE aliphatic amines +CG321 NG321 263.00 1.4740 ! AMINE aliphatic amines +CG321 OG301 360.00 1.4150 ! diethylether, alex +CG321 OG302 320.00 1.4400 ! PROTNA serine/threonine phosphate +CG321 OG303 320.00 1.4400 ! PROTNA serine/threonine phosphate +CG321 OG311 428.00 1.4200 ! PROT methanol vib fit EMB 11/21/89 +CG321 OG312 450.00 1.3300 ! PROT ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +CG321 OG3C61 360.00 1.4150 ! DIOX, dioxane +CG321 OG3R60 280.00 1.4000 ! PY02, 2h-pyran +CG321 PG1 270.00 1.8900 ! BDFP, Benzylphosphonate, Sasha \ re-optimize? +CG321 PG2 270.00 1.8900 ! BDFD, Benzylphosphonate, Sasha / re-optimize? +CG321 SG301 214.00 1.8160 ! PROT improved CSSC torsion in DMDS 5/15/92 (FL) +CG321 SG311 198.00 1.8180 ! PROT fitted to C-S s 9/26/92 (FL) +CG321 SG3O1 185.00 1.8070 ! ESNA, ethyl sulfonate, xhe +CG321 SG3O2 185.00 1.7900 ! EESM, N-ethylethanesulfonamide; MESN, methyl ethyl sulfone; xxwy & xhe +CG321 SG3O3 185.00 1.8100 ! MESO, methylethylsulfoxide, kevo +CG321 CLGA1 220.00 1.7880 ! CLET, chloroethane +CG321 BRGA1 160.00 1.9660 ! BRET +CG321 HGA2 309.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 +CG322 CG331 170.00 1.5200 ! FLUROALK fluoroalkanes +CG322 FGA1 420.00 1.3740 ! FLUROALK fluoroalkanes +CG322 HGA6 342.00 1.0828 ! FLUROALK fluoroalkanes +CG323 CG331 190.00 1.5310 ! PROT ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CG323 SG302 205.00 1.8360 ! PROT methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CG323 HGA2 300.00 1.1110 ! PROT ethylthiolate +CG323 HGA3 300.00 1.1110 ! PROT methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CG324 CG331 222.50 1.5280 ! PROT alkane update, adm jr., 3/2/92 +CG324 CG3C31 222.50 1.5280 ! AMCP, aminomethyl cyclopropane; from PROT alkane update, adm jr., 3/2/92; jhs +CG324 NG2O1 226.00 1.4900 ! NIPR, nitropropane, abar +CG324 NG2P1 300.00 1.4530 ! RETINOL SCH2, Schiff's base, protonated #eq# +CG324 NG3P0 215.00 1.5100 ! LIPID tetramethylammonium +CG324 NG3P1 200.00 1.4800 ! FLAVOP PIP1,2,3 +CG324 NG3P2 200.00 1.4900 ! PIP, piperidine +CG324 NG3P3 200.00 1.4900 ! MAMM, methylammonium 1.48 -> 1.49 based on CCSDT calc (kevo) and xtal survey (pram) +CG324 HGA2 284.50 1.1000 ! FLAVOP PIP1,2,3 +CG324 HGP5 300.00 1.0800 ! LIPID tetramethylammonium +CG331 CG331 222.50 1.5300 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG3C51 222.50 1.5280 ! TF2M, viv +CG331 CG3RC1 222.50 1.5380 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG331 NG2D1 310.00 1.4400 ! RETINOL SCH1, Schiff's base, deprotonated +CG331 NG2R51 400.00 1.4580 ! NA 9-M-G/T/U, adm jr. +CG331 NG2R61 400.00 1.4560 ! NA 9-M-A/C, adm jr. +CG331 NG2S0 315.00 1.4340 ! DMA, Dimethylacetamide, xxwy +CG331 NG2S1 320.00 1.4300 ! PROT NMA Gas & Liquid Phase IR Spectra (LK) +CG331 NG2S3 266.00 1.4600 ! NMSM, N-methyl-sulfamate; PHA, phosphoramidate; my +CG331 NG301 315.00 1.4420 ! TMC, yxu +CG331 NG311 255.00 1.4630 ! MGU2, methylguanidine2 +CG331 OG301 360.00 1.4150 ! diethylether, alex +CG331 OG302 340.00 1.4300 ! PROT adm jr., 4/05/91, for PRES CG311 from methylacetate +CG331 OG303 340.00 1.4300 ! NA DMP, ADM Jr. +CG331 OG311 428.00 1.4200 ! PROT methanol vib fit EMB 11/21/89 +CG331 OG312 450.00 1.3300 ! PROT methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +CG331 SG301 214.00 1.8160 ! PROT improved CSSC torsion in DMDS 5/15/92 (FL) +CG331 SG311 240.00 1.8160 ! PROT fitted to C-S s 9/26/92 (FL) +CG331 SG3O1 195.00 1.8370 ! MSNA, methyl sulfonate, xhe +CG331 SG3O2 210.00 1.7900 ! DMSN, dimethyl sulfone; MSAM, methanesulfonamide and other sulfonamides; compromise between crystal and mp2; xxwy & xhe +CG331 SG3O3 240.00 1.8000 ! DMSO, dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz +CG331 HGA3 322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 +CG334 NG2O1 250.00 1.4800 ! NIME, nitromethane, abar +CG334 NG2P1 300.00 1.4530 ! RETINOL SCH2, Schiff's base, protonated #eq# +CG334 NG3P0 215.00 1.5100 ! LIPID tetramethylammonium +CG334 NG3P1 200.00 1.4800 ! FLAVOP PIP1,2,3 +CG334 NG3P3 200.00 1.4800 ! PROT new stretch and bend; methylammonium (KK 03/10/92) +CG334 HGA3 322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 +CG334 HGP5 300.00 1.0800 ! LIPID tetramethylammonium +CG3AM0 NG301 235.00 1.4540 ! AMINE aliphatic amines +CG3AM0 HGAAM0 311.00 1.1110 ! AMINE aliphatic amines +CG3AM1 NG311 255.00 1.4630 ! AMINE aliphatic amines +CG3AM1 HGAAM1 313.80 1.0980 ! AMINE aliphatic amines +CG3AM2 NG321 263.00 1.4740 ! AMINE aliphatic amines +CG3AM2 HGAAM2 314.50 1.0856 ! AMINE aliphatic amines +CG3C31 CG3C31 240.00 1.5010 ! PROTMOD cyclopropane +CG3C31 CG3RC1 222.50 1.5240 ! CARBOCY carbocyclic sugars +CG3C31 OG3C31 220.00 1.4500 ! 1EOX, 1-ethylene oxide, sc & kevo +CG3C31 HGA1 340.00 1.0830 ! PROTMOD cyclopropane +CG3C31 HGA2 340.00 1.0830 ! PROTMOD cyclopropane +CG3C41 CG3C41 270.00 1.5400 ! CBU, cyclobutane, AZDO, 2-azetidinone, lsk +CG3C41 NG2R43 245.00 1.4500 ! AZDO, 2-azetidinone, kevo +CG3C41 HGA2 348.00 1.0930 ! CBU, cyclobutane, AZDO, 2-azetidinone, lsk +CG3C51 CG3C51 195.00 1.5180 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv +CG3C51 CG3C52 195.00 1.5180 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv +CG3C51 CG3C53 222.50 1.5000 ! PROT alkane update, adm jr., 3/2/92 +CG3C51 CG3RC1 222.50 1.5240 ! CARBOCY carbocyclic sugars +CG3C51 NG2R51 220.00 1.4580 ! NA G/T/U +CG3C51 NG2R61 220.00 1.4560 ! NA A/C +CG3C51 NG2S0 320.00 1.4340 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 NG2S3 360.00 1.4620 ! NABAKB phosphoramidates +CG3C51 NG301 220.00 1.4560 ! NADH, NDPH; Kenno: reverted to "A/C" from par_all27_na.prm +CG3C51 NG321 263.00 1.4740 ! AMINE aliphatic amines +CG3C51 OG301 334.30 1.4110 ! THF2, THF-2'OMe, from Nucl. Acids, ed +CG3C51 OG303 340.00 1.4300 ! LIPID phosphate +CG3C51 OG311 428.00 1.4200 ! PROT methanol vib fit EMB 11/21/89 +CG3C51 OG3C51 350.00 1.4250 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv +CG3C51 FGA1 420.00 1.3740 ! FLUROALK fluoroalkanes +CG3C51 HGA1 307.00 1.1000 ! THF, THF neutron diffr., 5/30/06, viv +CG3C51 HGA6 342.00 1.0828 ! T2FU, copied from FLUROALK fluoroalkanes by kevo +CG3C52 CG3C52 195.00 1.5300 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv; increased to 1.53 by kevo +CG3C52 CG3C53 222.50 1.5270 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C54 222.50 1.5370 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3RC1 222.50 1.5240 ! CARBOCY carbocyclic sugars +CG3C52 NG2R50 400.00 1.4700 !v 2IMI, 2-imidazoline; 2HPR, 2H-pyrrole, kevo +CG3C52 NG2R53 370.00 1.4500 ! 2PDO, 2-pyrrolidinone, kevo +CG3C52 NG2S0 320.00 1.4550 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 NG3C51 400.00 1.4780 ! PRLD, pyrrolidine; 2PRL, 2-pyrroline, kevo +CG3C52 OG3C51 350.00 1.4250 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv +CG3C52 HGA2 307.00 1.1000 ! THF, THF neutron diffr., 5/30/06, viv +CG3C53 NG2R61 220.00 1.4560 ! NA A/C +CG3C53 NG3P2 320.00 1.4850 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 OG3C51 240.00 1.4460 ! NA NA +CG3C53 HGA1 330.00 1.0800 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C54 CG3C54 210.00 1.5600 !~ 2IMP, 2-imidazoline.H+ ! RE-OPTIMIZE !!!, kevo +CG3C54 NG2R52 320.00 1.4600 ! 2IMP, 2-imidazoline.H+, kevo +CG3C54 NG3C51 235.00 1.4300 ! IMDP, imidazolidine ! partial dbl bond ==> RE-OPTIMIZE?, erh and kevo +CG3C54 NG3P2 320.00 1.5150 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 kenno: 1.502 --> 1.515 (CGenFF is not for peptides!) +CG3C54 HGA2 309.00 1.1110 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3RC1 CG3RC1 222.50 1.5230 ! CARBOCY carbocyclic sugars +CG3RC1 NG2R51 220.00 1.4580 ! CARBOCY carbocyclic sugars +CG3RC1 NG2R61 220.00 1.4560 ! CARBOCY carbocyclic sugars +CG3RC1 OG3C51 260.00 1.4200 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy +CG3RC1 HGA1 309.00 1.1110 ! CARBOCY carbocyclic sugars +NG2D1 NG2S1 550.00 1.3600 ! HDZ1, hydrazone model cmpd +NG2D1 HGP1 455.00 1.0000 ! MGU2, methylguanidine2 +NG2O1 OG2N1 580.00 1.2250 ! NITB, nitrobenzene +NG2P1 HGP2 455.00 1.0000 ! RETINOL SCH2, Schiff's base, protonated +NG2R43 HGP1 403.00 1.0150 ! AZDO, 2-azetidinone, kevo +NG2R50 NG2R50 340.00 1.2900 ! OXAD, oxadiazole123 +NG2R50 NG2R51 360.00 1.3550 ! PYRZ, pyrazole +NG2R50 NG3C51 420.00 1.4110 ! 2PRZ, 2-pyrazoline, kevo +NG2R50 OG2R50 280.00 1.3950 ! ISOX, isoxazole +NG2R50 SG2R50 270.00 1.7000 ! ISOT, isothiazole +NG2R51 HGP1 474.00 1.0100 ! NA G, adm jr. 11/97 +NG2R52 HGP2 453.00 1.0000 ! PROT his, adm jr., 6/27/90 +NG2R53 HGP1 470.00 1.0150 !470 440 *NEW* 2PDO, 2-pyrrolidinone, kevo +NG2R57 NG2R57 450.00 1.3650 ! 11BPO, 1,1-bipyrrole, lf +NG2R61 HGP1 474.00 1.0100 ! NA C,U, JWK +NG2R61 HGP2 474.00 1.0100 ! NA C,U, JWK +NG2R62 NG2R62 420.00 1.3200 ! PYRD, pyridazine +NG2S1 HGP1 440.00 0.9970 ! PROT Alanine Dipeptide ab initio calc's (LK) +NG2S2 HGP1 480.00 1.0000 ! PROT adm jr. 8/13/90 acetamide geometry and vibrations +NG2S3 PG1 180.00 1.7920 ! NABAKB phosphoramidates +NG2S3 SG3O1 224.00 1.7000 ! NMSM, N-methyl-sulfamate, my (QM: 1.74; Crystal: 1.637 1.665 1.656 1.672, aver: 1.658) +NG2S3 HGP1 432.50 1.0250 ! NABAKB phosphoramidates +NG2S3 HGP4 488.00 1.0000 ! NA A,C,G, JWK, adm jr. 7/24/91 +NG311 SG3O2 235.00 1.6500 ! MMSM, N-methylmethanesulfonamide and other sulfonamides,(org 1.6950) compromise between crystal and mp2, xxwy +NG311 HGP1 442.00 1.0210 ! MMSM, N-methylmethanesulfonamide and other sulfonamides, xxwy +NG311 HGPAM1 447.80 1.0190 ! AMINE aliphatic amines +NG321 SG3O2 240.00 1.6800 ! MSAM, methanesulfonamide; BSAM, benzenesulfonamide; (org 1.730) compromise between crystal and mp2, xxwy +NG321 HGP1 454.00 1.0200 ! MSAM, methanesulfonamide; BSAM, benzenesulfonamide; xxwy +NG321 HGPAM2 453.10 1.0140 ! AMINE aliphatic amines +NG331 HGPAM3 455.50 1.0140 ! AMINE aliphatic amines +NG3C51 NG3P2 270.00 1.4400 ! PRZP, Pyrazolidine.H+, kevo +NG3C51 HGP1 450.00 1.0180 ! PRLD, pyrrolidine; 2PRL, 2-pyrroline, kevo +NG3N1 NG3N1 355.00 1.4000 ! HDZN, hydrazine, ed +NG3N1 HGP1 437.00 1.0100 ! HDZN, hydrazine, ed +NG3P0 OG311 245.00 1.4000 ! TMAOP, Hydroxy(trimethyl)Ammonium, xxwy +NG3P0 OG312 310.00 1.4000 ! TMAO, trimethylamine N-oxide, xxwy & ejd +NG3P1 HGP2 403.00 1.0400 ! PROT new stretch and bend; methylammonium (KK 03/10/92) +NG3P2 HGP2 460.00 1.0060 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG3P3 HGP2 403.00 1.0400 ! PROT new stretch and bend; methylammonium (KK 03/10/92) +OG2P1 PG0 580.00 1.4800 ! MP_0 reorganization, kevo +OG2P1 PG1 500.00 1.5100 ! MP_1 reorganization, kevo +OG2P1 PG2 400.00 1.5200 ! MP_2 reorganization, kevo +OG2P1 SG3O1 540.00 1.4480 ! LIPID methylsulfate +OG2P1 SG3O2 630.00 1.4400 ! DMSN, dimethyl sulfone; MSAM, methanesulfonamide and other sulfonamides; compromise between crystal and mp2; xxwy & xhe +OG2P1 SG3O3 540.00 1.5300 ! DMSO, dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz +OG303 PG0 230.00 1.6100 ! MP_0 reorganization, kevo +OG303 PG1 190.00 1.6500 ! MP_1 reorganization, kevo +OG303 PG2 150.00 1.6550 ! MP_2 reorganization, kevo +OG303 SG3O1 250.00 1.5750 ! LIPID methylsulfate +OG303 SG3O2 235.00 1.6000 ! MMST, methyl methanesulfonate, (org 1.640) compromise between crystal and mp2, xxwy +OG304 PG1 330.00 1.6750 ! PPI1, PPI2, METP reorganization, kevo ! pulls against attraction +OG304 PG2 300.00 1.7150 ! PPI1, METP reorganization, kevo ! pulls against very strong attraction +OG311 PG0 237.00 1.5800 ! NA MP_1, ADM Jr. !Reorganization:MP_0 RE-OPTIMIZE! +OG311 PG1 237.00 1.6100 ! MP_1 reorganization, kevo +OG311 HGP1 545.00 0.9600 ! PROT EMB 11/21/89 methanol vib fit; og tested on MeOH EtOH,... +!OGTIP3 HGTIP3 450.00 0.9572 ! PROT FROM TIPS3P GEOM +SG301 SG301 173.00 2.0290 ! PROT improved CSSC torsion in DMDS 5/15/92 (FL) +SG311 HGP3 275.00 1.3250 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +FGP1 ALG1 205.00 1.7260 ! aluminum tetrafluoride, ALF4, w/UB +!HGTIP3 HGTIP3 0.00 1.5139 ! PROT FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) + +ANGLES +CG2R61 CG1N1 NG1T1 40.00 180.00 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN), yin +CG331 CG1N1 NG1T1 21.20 180.00 ! ACN, acetonitrile, kevo +CG1T1 CG1T1 CG331 19.00 180.00 ! 2BTY, 2-butyne, kevo +CG1T2 CG1T1 CG331 11.00 180.00 ! PRPY, propyne, kevo +CG1T1 CG1T2 HGPAM1 8.00 180.00 ! PRPY, propyne, xxwy & kevo +CG25C1 CG251O CG2R53 40.00 125.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG25C1 CG251O NG2R53 40.00 124.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +CG25C1 CG251O SG311 40.00 124.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG251O CG2R53 40.00 119.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2DC3 CG251O NG2R53 40.00 130.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2DC3 CG251O SG311 40.00 130.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 CG251O NG2R53 116.00 111.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2R53 CG251O SG311 110.00 111.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG25C2 CG252O CG2R53 40.00 125.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG25C2 CG252O NG2R53 40.00 124.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +CG25C2 CG252O SG311 40.00 124.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG252O CG2R53 40.00 119.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2DC3 CG252O NG2R53 40.00 130.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2DC3 CG252O SG311 40.00 130.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 CG252O NG2R53 116.00 111.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2R53 CG252O SG311 110.00 111.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG251O CG25C1 CG2R53 33.00 113.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG251O CG25C1 CG2RC0 33.00 131.50 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG25C1 CG2R53 33.00 115.50 ! MEOI, methyleneoxindole, kevo & xxwy +CG2DC3 CG25C1 CG2RC0 33.00 130.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R53 CG25C1 CG2RC0 45.00 114.50 ! MEOI, methyleneoxindole, kevo & xxwy +CG252O CG25C2 CG2R53 33.00 113.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG252O CG25C2 CG2RC0 33.00 131.50 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG25C2 CG2R53 33.00 115.50 ! MEOI, methyleneoxindole, kevo & xxwy +CG2DC3 CG25C2 CG2RC0 33.00 130.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R53 CG25C2 CG2RC0 45.00 114.50 ! MEOI, methyleneoxindole, kevo & xxwy +CG2D1 CG2D1 CG301 48.00 123.50 ! CHOLEST cholesterol +CG2D1 CG2D1 CG321 48.00 123.50 ! LIPID 2-butene, yin,adm jr., 12/95 +CG2D1 CG2D1 CG331 48.00 123.50 ! LIPID 2-butene, yin,adm jr., 12/95 +CG2D1 CG2D1 HGA4 52.00 119.50 ! LIPID 2-butene, yin,adm jr., 12/95 +CG2D1O CG2D1 CG321 40.00 127.50 ! PY01, 4h-pyran +CG2D1O CG2D1 HGA4 52.00 119.50 ! PY01, 4h-pyran +CG2D2 CG2D1 CG321 48.00 126.00 ! LIPID 1-butene; propene, yin,adm jr., 12/95 +CG2D2 CG2D1 CG331 47.00 125.20 ! LIPID propene, yin,adm jr., 12/95 +CG2D2 CG2D1 HGA4 42.00 118.00 ! LIPID propene, yin,adm jr., 12/95 +CG2D2O CG2D1 CG321 40.00 127.50 ! PY01, 4h-pyran +CG2D2O CG2D1 HGA4 52.00 119.50 ! PY01, 4h-pyran +CG301 CG2D1 CG321 50.00 113.00 ! CHOLEST cholesterol +CG301 CG2D1 CG331 48.00 123.50 ! RETINOL TMCH +CG321 CG2D1 CG331 48.00 123.50 ! RETINOL TMCH +CG321 CG2D1 HGA4 40.00 116.00 ! LIPID 1-butene; propene, yin,adm jr., 12/95 +CG331 CG2D1 NG2D1 80.00 123.00 ! RETINOL SCH1, Schiff's base, deprotonated, adjusted for improper, xxwy +CG331 CG2D1 NG2P1 47.00 125.60 ! RETINOL SCH2, Schiff's base, protonated, adjusted for improper, xxwy +CG331 CG2D1 HGA4 22.00 117.00 ! LIPID propene, yin,adm jr., 12/95 +CG331 CG2D1 HGR52 42.00 120.40 ! RETINOL SCH2, Schiff's base, protonated +NG2D1 CG2D1 HGA4 49.00 119.50 ! RETINOL SCH1, Schiff's base, deprotonated, adjusted for improper, xxwy +NG2P1 CG2D1 HGR52 39.00 114.00 ! RETINOL SCH2, Schiff's base, protonated, adjusted for improper, xxwy +CG2D1 CG2D1O NG301 60.00 122.00 ! NADH, NDPH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D1O NG311 60.00 122.00 ! NICH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D1O OG3R60 40.00 126.00 ! PY01, 4h-pyran, maintain 360 around apex angle +CG2D1 CG2D1O HGA4 52.00 122.00 ! PY01, 4h-pyran +CG2D2 CG2D1O NG321 80.00 128.00 ! AMET, ethenamine; mp2-geom, molvib; pram +CG2D2 CG2D1O OG301 65.00 123.50 ! MOET, Methoxyethene, xxwy +CG2D2 CG2D1O HGA4 44.00 121.00 ! MOET, Methoxyethene, xxwy +CG2DC1 CG2D1O NG301 60.00 122.00 ! NADH, NDPH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2DC1 CG2D1O NG311 60.00 122.00 ! NICH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2DC1 CG2D1O OG301 56.00 124.50 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2DC1 CG2D1O OG3R60 40.00 128.00 ! PY02, 2h-pyran +CG2DC1 CG2D1O HGA4 42.00 120.00 ! PY02, 2h-pyran +NG301 CG2D1O HGA4 42.00 119.00 ! NADH, NDPH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +NG311 CG2D1O HGA4 42.00 119.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +NG321 CG2D1O HGA4 30.00 113.00 ! AMET, ethenamine; mp2-geom, molvib; pram +OG301 CG2D1O HGA4 30.00 115.50 ! MOET, Methoxyethene, xxwy +OG3R60 CG2D1O HGA4 30.00 112.00 ! PY01, 4h-pyran +CG2D1 CG2D2 HGA5 45.00 120.50 ! LIPID propene, yin,adm jr., 12/95 +CG2D1O CG2D2 HGA5 35.00 120.50 ! MOET, Methoxyethene, xxwy +CG2D2 CG2D2 HGA5 55.50 120.50 ! LIPID ethene, yin,adm jr., 12/95 +CG2D2O CG2D2 HGA5 35.00 120.50 ! MOET, Methoxyethene, xxwy +HGA5 CG2D2 HGA5 19.00 119.00 ! LIPID propene, yin,adm jr., 12/95 +CG2D1 CG2D2O NG301 60.00 122.00 ! NADH, NDPH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D2O NG311 60.00 122.00 ! NICH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D2O OG3R60 40.00 126.00 ! PY01, 4h-pyran, maintain 360 around apex angle +CG2D1 CG2D2O HGA4 52.00 122.00 ! PY01, 4h-pyran +CG2D2 CG2D2O NG321 80.00 128.00 ! AMET, ethenamine; mp2-geom, molvib; pram +CG2D2 CG2D2O OG301 65.00 123.50 ! MOET, Methoxyethene, xxwy +CG2D2 CG2D2O HGA4 44.00 121.00 ! MOET, Methoxyethene, xxwy +CG2DC2 CG2D2O NG301 60.00 122.00 ! NADH, NDPH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2DC2 CG2D2O NG311 60.00 122.00 ! NICH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2DC2 CG2D2O OG301 56.00 124.50 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2DC2 CG2D2O OG3R60 40.00 128.00 ! PY02, 2h-pyran +CG2DC2 CG2D2O HGA4 42.00 120.00 ! PY02, 2h-pyran +NG301 CG2D2O HGA4 42.00 119.00 ! NADH, NDPH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +NG311 CG2D2O HGA4 42.00 119.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +NG321 CG2D2O HGA4 30.00 113.00 ! AMET, ethenamine; mp2-geom, molvib; pram +OG301 CG2D2O HGA4 30.00 115.50 ! MOET, Methoxyethene, xxwy +OG3R60 CG2D2O HGA4 30.00 112.00 ! PY01, 4h-pyran +CG2D1O CG2DC1 CG2DC2 48.00 120.00 ! PY02, 2h-pyran +CG2D1O CG2DC1 CG2O1 65.00 113.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 5.0 107.8 but that's too unlikely ==> re-optimize +CG2D1O CG2DC1 CG321 43.50 126.50 ! NICH; Kenno: nadh/ppi, jjp1/adm jr. 7/95 says 43.50 128.00 but that's unlikely ==> re-optimize +CG2D1O CG2DC1 HGA4 42.00 122.00 ! PY02, 2h-pyran +CG2DC1 CG2DC1 CG2DC2 48.00 123.00 ! RETINOL 13DP, Pentadiene @@@@@ Kenno: 123.5-->123.0 @@@@@ +CG2DC1 CG2DC1 CG2O1 48.00 123.50 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O3 48.00 123.50 ! RETINOL PRAC +CG2DC1 CG2DC1 CG2O4 60.00 120.00 ! RETINOL RTAL unmodified +CG2DC1 CG2DC1 CG301 48.00 123.50 ! RETINOL MECH +CG2DC1 CG2DC1 CG321 48.00 123.50 ! RETINOL MECH +CG2DC1 CG2DC1 CG331 48.00 123.50 ! RETINOL BTE2, 2-butene +CG2DC1 CG2DC1 HGA4 42.00 119.00 ! RETINOL BTE2, 2-butene +CG2DC2 CG2DC1 CG2DC3 48.00 123.50 ! RETINOL 13DB, 1,3-Butadiene +CG2DC2 CG2DC1 CG301 48.00 123.50 ! RETINOL MECH +CG2DC2 CG2DC1 CG331 48.00 113.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG2DC2 CG2DC1 NG2P1 40.00 125.60 ! RETINOL SCH3, Schiff's base, protonated +CG2DC2 CG2DC1 HGA4 42.00 118.00 ! RETINOL 13DB, 1,3-Butadiene +CG2DC2 CG2DC1 HGR52 42.00 120.40 ! RETINOL SCH3, Schiff's base, protonated +CG2DC3 CG2DC1 CG2O3 40.00 119.00 35.00 2.5267 ! RETINOL PRAC +CG2DC3 CG2DC1 CG2O4 60.00 120.00 ! RETINOL PRAL unmodified +CG2DC3 CG2DC1 CG2O5 35.00 118.60 ! BEON, butenone, kevo +CG2DC3 CG2DC1 CG2R61 29.00 122.00 ! STYR, styrene, xxwy & oashi +CG2DC3 CG2DC1 CG331 48.00 123.50 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG2DC3 CG2DC1 HGA4 42.00 118.00 ! RETINOL 13DB, 1,3-Butadiene +CG2O1 CG2DC1 CG321 65.00 123.50 ! NICH; Kenno: nadh/ppi, jjp1/adm jr. 7/95 says 125.0 124.2 but that's unlikely ==> re-optimize +CG2O1 CG2DC1 HGA4 52.00 119.50 ! RETINOL CROT +CG2O3 CG2DC1 HGA4 52.00 119.50 ! RETINOL PRAC +CG2O4 CG2DC1 HGA4 32.00 122.00 ! RETINOL RTAL unmodified +CG2O5 CG2DC1 HGA4 32.00 123.40 ! BEON, butenone, kevo +CG2R61 CG2DC1 NG2D1 56.00 117.00 ! HDZ1b, hydrazone model cmpd 1b, kevo +CG2R61 CG2DC1 HGA4 32.00 120.00 ! HDZ1b, hydrazone model cmpd 1b; STYR, styrene; kevo, xxwy, oashi +CG321 CG2DC1 CG331 48.00 123.50 ! RETINOL MECH +CG321 CG2DC1 HGA4 40.00 116.00 ! RETINOL PROL +CG331 CG2DC1 CG331 47.00 113.00 ! RETINOL DMP1, 4-methyl-1,3-pentadiene +CG331 CG2DC1 HGA4 42.00 117.50 ! RETINOL BTE2, 2-butene +NG2D1 CG2DC1 HGA4 38.00 123.00 ! HDZ1b, hydrazone model cmpd 1b, kevo +NG2P1 CG2DC1 HGR52 38.00 114.00 ! RETINOL SCH2, Schiff's base, protonated +CG2D2O CG2DC2 CG2DC1 48.00 120.00 ! PY02, 2h-pyran +CG2D2O CG2DC2 CG2O1 65.00 113.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 5.0 107.8 but that's too unlikely ==> re-optimize +CG2D2O CG2DC2 CG321 43.50 126.50 ! NICH; Kenno: nadh/ppi, jjp1/adm jr. 7/95 says 43.50 128.00 but that's unlikely ==> re-optimize +CG2D2O CG2DC2 HGA4 42.00 122.00 ! PY02, 2h-pyran +CG2DC1 CG2DC2 CG2DC2 48.00 123.00 ! RETINOL 13DP, Pentadiene @@@@@ Kenno: 123.5-->123.0 @@@@@ +CG2DC1 CG2DC2 CG2DC3 48.00 123.50 ! RETINOL 13DB, 1,3-Butadiene +CG2DC1 CG2DC2 CG301 48.00 123.50 ! RETINOL MECH +CG2DC1 CG2DC2 CG331 48.00 113.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG2DC1 CG2DC2 NG2P1 40.00 125.60 ! RETINOL SCH3, Schiff's base, protonated +CG2DC1 CG2DC2 HGA4 42.00 118.00 ! RETINOL 13DB, 1,3-Butadiene +CG2DC1 CG2DC2 HGR52 42.00 120.40 ! RETINOL SCH3, Schiff's base, protonated +CG2DC2 CG2DC2 CG2O1 48.00 123.50 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O3 48.00 123.50 ! RETINOL PRAC +CG2DC2 CG2DC2 CG2O4 60.00 120.00 ! RETINOL RTAL unmodified +CG2DC2 CG2DC2 CG301 48.00 123.50 ! RETINOL MECH +CG2DC2 CG2DC2 CG321 48.00 123.50 ! RETINOL MECH +CG2DC2 CG2DC2 CG331 48.00 123.50 ! RETINOL BTE2, 2-butene +CG2DC2 CG2DC2 HGA4 42.00 119.00 ! RETINOL BTE2, 2-butene +CG2DC3 CG2DC2 CG2O3 40.00 119.00 35.00 2.5267 ! RETINOL PRAC +CG2DC3 CG2DC2 CG2O4 60.00 120.00 ! RETINOL PRAL unmodified +CG2DC3 CG2DC2 CG2O5 35.00 118.60 ! BEON, butenone, kevo +CG2DC3 CG2DC2 CG2R61 29.00 122.00 ! STYR, styrene, xxwy & oashi +CG2DC3 CG2DC2 CG331 48.00 123.50 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG2DC3 CG2DC2 HGA4 42.00 118.00 ! RETINOL 13DB, 1,3-Butadiene +CG2O1 CG2DC2 CG321 65.00 123.50 ! NICH; Kenno: nadh/ppi, jjp1/adm jr. 7/95 says 125.0 124.2 but that's unlikely ==> re-optimize +CG2O1 CG2DC2 HGA4 52.00 119.50 ! RETINOL CROT +CG2O3 CG2DC2 HGA4 52.00 119.50 ! RETINOL PRAC +CG2O4 CG2DC2 HGA4 32.00 122.00 ! RETINOL RTAL unmodified +CG2O5 CG2DC2 HGA4 32.00 123.40 ! BEON, butenone, kevo +CG2R61 CG2DC2 NG2D1 56.00 117.00 ! HDZ1b, hydrazone model cmpd 1b, kevo +CG2R61 CG2DC2 HGA4 32.00 120.00 ! HDZ1b, hydrazone model cmpd 1b; STYR, styrene; kevo, xxwy, oashi +CG321 CG2DC2 CG331 48.00 123.50 ! RETINOL MECH +CG321 CG2DC2 HGA4 40.00 116.00 ! RETINOL PROL +CG331 CG2DC2 CG331 47.00 113.00 ! RETINOL DMP1, 4-methyl-1,3-pentadiene +CG331 CG2DC2 HGA4 42.00 117.50 ! RETINOL BTE2, 2-butene +NG2D1 CG2DC2 HGA4 38.00 123.00 ! HDZ1b, hydrazone model cmpd 1b, kevo +NG2P1 CG2DC2 HGR52 38.00 114.00 ! RETINOL SCH2, Schiff's base, protonated +CG251O CG2DC3 HGA5 35.00 120.50 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O CG2DC3 HGA5 35.00 120.50 ! MRDN, methylidene rhodanine, kevo & xxwy +CG25C1 CG2DC3 HGA5 45.00 120.50 ! MEOI, methyleneoxindole; from RETINOL 13DB, 1,3-Butadiene (re-optimize); kevo +CG25C2 CG2DC3 HGA5 45.00 120.50 ! MEOI, methyleneoxindole; from RETINOL 13DB, 1,3-Butadiene (re-optimize); kevo +CG2DC1 CG2DC3 HGA5 45.00 120.50 ! RETINOL 13DB, 1,3-Butadiene +CG2DC2 CG2DC3 HGA5 45.00 120.50 ! RETINOL 13DB, 1,3-Butadiene +HGA5 CG2DC3 HGA5 19.00 119.00 ! RETINOL 13DB, 1,3-Butadiene +NG2D1 CG2N1 NG311 50.00 125.00 ! MGU2, methylguanidine2 +NG2D1 CG2N1 NG321 100.00 125.00 ! MGU1, methylguanidine; MGU2, methylguanidine2 +NG2P1 CG2N1 NG2P1 52.00 120.00 90.00 2.36420 ! PROT changed from 60.0/120.3 for guanidinium (KK) +NG311 CG2N1 NG321 50.00 113.00 ! MGU2, methylguanidine2 kevo: sum=363 (deliberate) +NG321 CG2N1 NG321 75.00 113.00 ! MGU1, methylguanidine kevo: sum=363 (deliberate) +CG2R61 CG2N2 NG2P1 80.00 118.50 ! BAMI, benzamidinium, mp2 geom & movib, pram +CG331 CG2N2 NG2P1 52.00 118.50 ! AMDN, amidinium, mp2 geom, pram +NG2D1 CG2N2 NG321 85.00 127.00 ! MT2A, fylin +NG2D1 CG2N2 SG311 37.00 116.40 ! MT2A, fylin +NG2P1 CG2N2 NG2P1 52.00 123.00 90.00 2.36420 ! AMDN, amidinium, mp2 geom & movib, pram +NG321 CG2N2 SG311 56.00 116.60 ! MT2A, fylin +CG2DC1 CG2O1 NG2S1 80.00 116.50 ! RETINOL CROT +CG2DC1 CG2O1 NG2S2 85.00 113.00 80.0 2.46 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2DC1 CG2O1 OG2D1 80.00 122.50 ! RETINOL CROT +CG2DC2 CG2O1 NG2S1 80.00 116.50 ! RETINOL CROT +CG2DC2 CG2O1 NG2S2 85.00 113.00 80.0 2.46 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2DC2 CG2O1 OG2D1 80.00 122.50 ! RETINOL CROT +CG2R61 CG2O1 NG2S1 80.00 116.50 ! HDZ2, hydrazone model cmpd 2 +CG2R61 CG2O1 NG2S2 50.00 110.23 ! 3NAP, nicotamide (PYRIDINE pyr-CONH2), yin +CG2R61 CG2O1 OG2D1 30.00 121.00 ! reverted to 3NAP, nicotamide. Kenno: compromise with NMA and HDZ2 ==> 124.5 --> 121.00 +CG2R62 CG2O1 NG2S2 85.00 113.00 80.0 2.46 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R62 CG2O1 OG2D1 85.00 118.50 20.0 2.43 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG311 CG2O1 NG2S0 20.00 112.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG2O1 NG2S1 80.00 116.50 ! PROT NMA Vib Modes (LK) +CG311 CG2O1 NG2S2 50.00 116.50 50.00 2.45000 ! PROT adm jr. 8/13/90 geometry and vibrations +CG311 CG2O1 OG2D1 80.00 121.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG314 CG2O1 NG2S0 20.00 112.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG314 CG2O1 NG2S1 80.00 116.50 ! PROT NMA Vib Modes (LK) +CG314 CG2O1 NG2S2 50.00 116.50 50.00 2.45000 ! PROT adm jr. 8/13/90 geometry and vibrations +CG314 CG2O1 OG2D1 80.00 121.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG321 CG2O1 NG2S0 20.00 112.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG321 CG2O1 NG2S1 80.00 116.50 ! PROT NMA Vib Modes (LK) +CG321 CG2O1 NG2S2 50.00 116.50 50.00 2.45000 ! PROT adm jr. 8/13/90 geometry and vibrations +CG321 CG2O1 OG2D1 80.00 121.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG324 CG2O1 NG2S0 20.00 112.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG324 CG2O1 NG2S1 80.00 116.50 ! PROT NMA Vib Modes (LK) +CG324 CG2O1 NG2S2 50.00 116.50 50.00 2.45000 ! PROT adm jr. 8/13/90 geometry and vibrations +CG324 CG2O1 OG2D1 80.00 121.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG331 CG2O1 NG2S0 40.00 115.00 ! DMF, Dimethylformamide, xxwy +CG331 CG2O1 NG2S1 80.00 116.50 ! PROT NMA Vib Modes (LK) +CG331 CG2O1 NG2S2 50.00 116.50 50.00 2.45000 ! PROT adm jr. 8/13/90 geometry and vibrations +CG331 CG2O1 OG2D1 80.00 121.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG3C51 CG2O1 NG2S0 20.00 112.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S1 80.00 116.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S2 80.00 112.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 OG2D1 80.00 118.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S0 20.00 112.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S1 80.00 116.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S2 80.00 112.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 OG2D1 80.00 118.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 OG2D1 80.00 124.00 ! DMF, Dimethylformamide, xxwy +NG2S0 CG2O1 HGR52 43.00 115.00 ! DMF, Dimethylformamide, xxwy +NG2S1 CG2O1 OG2D1 80.00 122.50 ! PROT NMA Vib Modes (LK) +NG2S2 CG2O1 OG2D1 75.00 122.50 50.00 2.37000 ! PROT adm jr. 4/10/91, acetamide update +NG2S2 CG2O1 HGR52 44.00 111.00 50.00 1.98000 ! PROT, formamide +OG2D1 CG2O1 HGR52 44.000 122.00 ! kevo reverted to adm jr., 5/13/91, formamide geometry and vibrations +CG2R61 CG2O2 OG2D1 70.00 123.10 20.00 2.4420 ! ZOIC, benzoic acid, MBOA, methylbenzoate, jal +CG2R61 CG2O2 OG302 50.00 111.00 20.00 2.3600 ! MBOA, methylbenzoate (UB term has been adjusted), jal +CG2R61 CG2O2 OG311 40.00 113.90 30.00 2.3700 ! ZOIC, benzoic acid (UB term has been adjusted), jal +CG311 CG2O2 OG2D1 70.00 125.00 20.00 2.44200 ! PROT adm jr. 5/02/91, acetic acid pure solvent; LIPID methyl acetate +CG311 CG2O2 OG302 55.00 109.00 20.00 2.3260 ! AMGA, Alpha Methyl Glut Acid CDCA Amide +CG311 CG2O2 OG311 55.00 110.50 ! drug design project, xxwy +CG321 CG2O2 OG2D1 70.00 125.00 20.00 2.44200 ! PROT adm jr. 5/02/91, acetic acid pure solvent; LIPID methyl acetate +CG321 CG2O2 OG302 55.00 109.00 20.00 2.3260 ! LIPID methyl acetate +CG321 CG2O2 OG311 55.00 110.50 ! PROT adm jr, 10/17/90, acetic acid vibrations +CG331 CG2O2 OG2D1 70.00 125.00 20.00 2.44200 ! PROT adm jr. 5/02/91, acetic acid pure solvent; LIPID methyl acetate +CG331 CG2O2 OG302 55.00 109.00 20.00 2.3260 ! LIPID methyl acetate +CG331 CG2O2 OG311 55.00 110.50 ! PROT adm jr, 10/17/90, acetic acid vibrations +OG2D1 CG2O2 OG302 90.00 125.90 160.0 2.2576 ! LIPID acetic acid +OG2D1 CG2O2 OG311 50.00 123.00 210.00 2.26200 ! PROT adm jr, 10/17/90, acetic acid vibrations +OG2D1 CG2O2 HGR52 39.00 119.00 ! FORH, formic acid, xxwy +OG311 CG2O2 HGR52 47.00 105.00 ! FORH, formic acid, xxwy +CG2DC1 CG2O3 OG2D2 40.00 116.00 50.00 2.3530 ! RETINOL PRAC +CG2DC2 CG2O3 OG2D2 40.00 116.00 50.00 2.3530 ! RETINOL PRAC +CG2O5 CG2O3 OG2D2 95.00 116.00 ! BIPHENYL ANALOGS unmodified, peml +CG2R61 CG2O3 OG2D2 40.00 116.00 50.00 2.3530 ! 3CPY, pyridine-3-carboxylate (PYRIDINE nicotinic acid), yin +CG301 CG2O3 OG2D2 40.00 116.00 50.00 2.353 ! AMOL, alpha-methoxy-lactic acid, og +CG311 CG2O3 OG2D2 40.00 116.00 50.00 2.35300 ! PROT adm jr. 7/23/91, correction, ACETATE (KK) +CG314 CG2O3 OG2D2 40.00 116.00 50.00 2.35300 ! PROT adm jr. 7/23/91, correction, ACETATE (KK) +CG321 CG2O3 OG2D2 40.00 116.00 50.00 2.35300 ! PROT adm jr. 7/23/91, correction, ACETATE (KK) +CG324 CG2O3 OG2D2 40.00 116.00 50.00 2.35300 ! PROT adm jr. 7/23/91, correction, ACETATE (KK) +CG331 CG2O3 OG2D2 40.00 116.00 50.00 2.35300 ! PROT adm jr. 7/23/91, correction, ACETATE (KK) +CG3C51 CG2O3 OG2D2 40.00 116.00 50.00 2.35300 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O3 OG2D2 40.00 116.00 50.00 2.35300 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D2 CG2O3 OG2D2 100.00 128.00 70.00 2.25870 ! PROT adm jr. 7/23/91, correction, ACETATE (KK) +OG2D2 CG2O3 HGR52 45.00 116.00 ! FORA, formate, kevo (sum=360) +CG2DC1 CG2O4 OG2D1 75.00 126.00 ! RETINOL PRAL only angle modified +CG2DC1 CG2O4 HGR52 15.00 116.00 ! RETINOL PRAL only angle modified +CG2DC2 CG2O4 OG2D1 75.00 126.00 ! RETINOL PRAL only angle modified +CG2DC2 CG2O4 HGR52 15.00 116.00 ! RETINOL PRAL only angle modified +CG2R61 CG2O4 OG2D1 75.00 126.00 ! ALDEHYDE benzaldehyde only angle unmodified +CG2R61 CG2O4 HGR52 15.00 116.00 ! ALDEHYDE benzaldehyde only angle unmodified +CG321 CG2O4 OG2D1 45.00 126.00 ! ALDEHYDE propionaldehyde adm 11/08 +CG321 CG2O4 HGR52 65.00 116.00 ! ALDEHYDE propionaldehyde adm 11/08 +CG331 CG2O4 OG2D1 45.00 126.00 ! ALDEHYDE acetaldehyde adm 11/08 +CG331 CG2O4 HGR52 65.00 116.00 ! ALDEHYDE acetaldehyde adm 11/08 +OG2D1 CG2O4 HGR52 65.00 118.00 ! ALDEHYDE acetaldehyde adm 11/08 +CG2DC1 CG2O5 CG331 35.00 116.00 ! BEON, butenone; from PHMK, phenyl methyl ketone; kevo +CG2DC1 CG2O5 OG2D3 70.00 121.80 ! BEON, butenone; from PHMK, phenyl methyl ketone; kevo +CG2DC2 CG2O5 CG331 35.00 116.00 ! BEON, butenone; from PHMK, phenyl methyl ketone; kevo +CG2DC2 CG2O5 OG2D3 70.00 121.80 ! BEON, butenone; from PHMK, phenyl methyl ketone; kevo +CG2O3 CG2O5 CG2R61 40.00 117.20 ! BIPHENYLS BF7 C37, sum of equilibrium angles, kevo +CG2O3 CG2O5 OG2D3 95.00 121.50 ! BIPHENYLS BF7, C37 new init guess by Kenno based on ACO adm 11/08 ==> re-optimize +CG2R61 CG2O5 CG311 40.00 117.20 ! BIPHENYLS BF6 C36, sum of equilibrium angles, kevo +CG2R61 CG2O5 CG321 20.00 116.50 ! PHEK, phenyl ethyl ketone; from 3ACP, 3-acetylpyridine; mcs +CG2R61 CG2O5 CG331 60.00 116.50 ! PHMK, phenyl methyl ketone, mcs +CG2R61 CG2O5 OG2D3 70.00 121.30 ! 3ACP, 3-acetylpyridine; BF6 BF7 C36 C37; PHMK, phenyl methyl ketone; verified by mcs +CG311 CG2O5 OG2D3 95.00 121.50 ! BIPHENYLS BF6, C36 new init guess by Kenno based on ACO adm 11/08 ==> re-optimize +CG321 CG2O5 CG321 35.00 115.60 ! CHON, cyclohexanone; from ACO, acetone; yapol +CG321 CG2O5 CG331 35.00 115.60 ! BTON, butanone; from ACO, acetone; yapol +CG321 CG2O5 OG2D3 75.00 122.20 ! BTON, butanone; from ACO, acetone; yapol +CG331 CG2O5 CG331 35.00 115.60 ! ACO, acetone adm 11/08 +CG331 CG2O5 OG2D3 75.00 122.20 ! ACO, acetone adm 11/08 +NG2S1 CG2O6 OG2D1 60.00 125.70 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo +NG2S1 CG2O6 OG302 90.00 110.30 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo +NG2S2 CG2O6 NG2S2 70.00 115.00 ! UREA, Urea +NG2S2 CG2O6 OG2D1 75.00 122.50 50.00 2.37000 ! UREA, Urea. Uses a slack parameter from PROT adm jr. 4/10/91, acetamide update ==> re-optimize +OG2D1 CG2O6 OG302 70.00 123.50 ! DMCB & DECB & DMCA, dimethyl & diehtyl carbamate and dimethyl carbonate, cacha & kevo +OG2D2 CG2O6 OG2D2 40.00 120.00 99.5 2.24127 ! PROTMOD carbonate +OG2D2 CG2O6 OG311 79.00 120.00 ! CO31, bicarbonate, xxwy +OG302 CG2O6 OG302 85.00 105.00 ! DMCA, dimethyl carbonate, xxwy +SG2D1 CG2O6 SG311 70.00 124.00 ! DMTT, dimethyl trithiocarbonate, kevo +SG311 CG2O6 SG311 40.00 112.00 ! DMTT, dimethyl trithiocarbonate, kevo +NG2D1 CG2O7 OG2D5 42.00 172.00 ! MICY, EICY: isocyanates, xxwy +OG2D5 CG2O7 OG2D5 45.00 180.00 ! PROT CO2, JES; re-optimized by kevo +CG2R51 CG2R51 CG2R51 90.00 107.20 ! PYRL, pyrrole +CG2R51 CG2R51 CG2R52 90.00 106.00 ! PYRZ, pyrazole +CG2R51 CG2R51 CG2R53 100.00 116.50 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG2R51 CG2R57 90.00 107.20 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51; lf +CG2R51 CG2R51 CG2RC0 85.00 105.70 25.00 2.26100 !adm,dec06(106.4) INDO/TRP +CG2R51 CG2R51 CG2RC7 70.00 106.90 ! AZUL, Azulene, kevo +CG2R51 CG2R51 CG321 45.80 130.00 ! PROT his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CG2R51 CG2R51 CG331 45.80 130.00 ! PROT his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CG2R51 CG2R51 CG3C52 115.00 109.00 ! 2PRP, 2-pyrroline.H+; 2PRL, 2-pyrroline, kevo +CG2R51 CG2R51 CG3C54 115.00 109.00 ! 3PRP, 3-pyrroline.H+; 2HPP, 2H-pyrrole.H+, kevo +CG2R51 CG2R51 NG2R50 130.00 110.00 ! PROT his, ADM JR., 7/20/89 +CG2R51 CG2R51 NG2R51 130.00 106.00 !adm,dec06 110.6, PROT his, ADM JR., 7/20/89 +CG2R51 CG2R51 NG2R52 145.00 108.00 ! PROT his, ADM JR., 7/20/89 +CG2R51 CG2R51 NG2R57 130.00 106.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 NG2R51; lf +CG2R51 CG2R51 NG2RC0 130.00 108.20 ! INDZ, indolizine, kevo +CG2R51 CG2R51 NG3C51 105.00 111.80 ! 2PRL, 2-pyrroline, kevo +CG2R51 CG2R51 NG3P2 120.00 111.00 ! 2PRP, 2-pyrroline.H+, kevo +CG2R51 CG2R51 OG2R50 130.00 111.70 ! FURA, furan @@@@@ Kenno: 108-->112 @@@@@ +CG2R51 CG2R51 OG3C51 135.00 113.20 ! 2DHF, 2,3-dihydrofuran, kevo +CG2R51 CG2R51 SG2R50 105.00 109.00 ! THIP, thiophene +CG2R51 CG2R51 HGR51 32.00 126.40 25.00 2.17300 ! INDO/TRP +CG2R51 CG2R51 HGR52 22.00 130.00 15.00 2.21500 ! PROT adm jr., 6/27/90, his +CG2R52 CG2R51 HGR51 15.00 127.60 !x 2HPR, 2H-pyrrole; 2HPP, 2H-pyrrole.H+, kevo +CG2R53 CG2R51 HGR51 10.00 117.10 ! B2FO, 5H-furan-2-one, ctsai +CG2R57 CG2R51 NG2R51 130.00 106.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 NG2R51; lf +CG2R57 CG2R51 HGR51 32.00 126.40 25.00 2.17300 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 HGR51; lf +CG2R57 CG2R51 HGR52 22.00 130.00 15.00 2.21500 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 HGR52; lf +CG2RC0 CG2R51 CG321 30.00 126.70 ! INDO/TRP +CG2RC0 CG2R51 CG331 30.00 126.70 ! INDO/TRP +CG2RC0 CG2R51 NG2R51 100.00 107.50 ! ISOI, isoindole, kevo +CG2RC0 CG2R51 HGR51 32.00 126.40 25.00 2.25500 ! INDO/TRP +CG2RC0 CG2R51 HGR52 31.00 128.50 ! ISOI, isoindole, kevo +CG2RC7 CG2R51 HGR51 32.00 126.70 ! AZUL, Azulene, kevo +CG321 CG2R51 NG2R50 45.80 120.00 ! PROT his, ADM JR., 7/22/89, FC FROM CA CT2CT +CG321 CG2R51 NG2R51 45.80 124.00 ! PROT his, ADM JR., 7/22/89, FC FROM CA CT2CT +CG321 CG2R51 NG2R52 45.80 122.00 ! PROT his, ADM JR., 7/22/89, FC FROM CA CT2CT +CG331 CG2R51 NG2R51 45.80 124.00 ! PROT his, ADM JR., 7/22/89, FC FROM CA CT2CT +CG3C52 CG2R51 HGR51 29.00 124.60 ! 2PRP, 2-pyrroline.H+; 2PRL, 2-pyrroline, kevo +CG3C54 CG2R51 HGR51 13.00 124.60 ! 124.6 3PRP, 3-pyrroline.H+; 2HPP, 2H-pyrrole.H+, kevo +NG2R50 CG2R51 HGR52 25.00 120.00 20.00 2.14000 ! PROT adm jr., 3/24/92 +NG2R51 CG2R51 HGR52 25.00 124.00 20.00 2.14000 ! PROT adm jr., 3/24/92 +NG2R52 CG2R51 HGR52 22.00 122.00 15.00 2.18000 ! PROT his, adm jr., 6/27/90 +NG2R57 CG2R51 HGR52 25.00 124.00 20.00 2.14000 ! 13BPO, 1,3-bipyrrole; from NG2R51 CG2R51 HGR52; lf +NG2RC0 CG2R51 HGR52 31.00 121.80 ! INDZ, indolizine, kevo +NG3C51 CG2R51 HGR52 35.00 118.20 ! 2PRL, 2-pyrroline, kevo +NG3P2 CG2R51 HGR52 35.00 119.00 ! 2PRP, 2-pyrroline.H+, kevo +OG2R50 CG2R51 HGR52 50.00 118.30 ! FURA, furan @@@@@ Kenno: 122 --> 118 @@@@@ +OG3C51 CG2R51 HGR52 39.00 116.80 ! 2DHF, 2,3-dihydrofuran, kevo +SG2R50 CG2R51 HGR52 45.00 121.00 ! THIP, thiophene +CG2R51 CG2R52 NG2R50 110.00 110.50 ! PYRZ, pyrazole +CG2R51 CG2R52 NG2R52 121.00 110.00 ! 2HPP, 2H-pyrrole.H+ C4-C5-N1, kevo +CG2R51 CG2R52 HGR52 32.00 126.50 ! PYRZ, pyrazole +CG2R52 CG2R52 NG2R50 70.00 106.00 ! TRZ2, 2H-1,2,3-triazole, lf +CG2R52 CG2R52 HGR52 30.00 131.00 ! TRZ2, 2H-1,2,3-triazole, lf +CG2RC0 CG2R52 NG2R50 150.00 110.40 ! INDA, 1H-indazole, kevo +CG2RC0 CG2R52 HGR52 32.00 126.60 ! INDA, 1H-indazole, kevo +CG3C52 CG2R52 NG2R50 170.00 112.00 !x 2PRZ, 2-pyrazoline; 3HPR, 3H-pyrrole N2-C3-C4, kevo +CG3C52 CG2R52 HGR52 47.00 125.00 !x 2PRZ, 2-pyrazoline; 3HPR, 3H-pyrrole H3-C3-C4, kevo +NG2R50 CG2R52 HGR52 32.00 123.00 ! PYRZ, pyrazole +NG2R52 CG2R52 HGR52 35.00 123.50 ! 2HPP, 2H-pyrrole.H+ N1-C5-H5, kevo +CG251O CG2R53 NG2R53 55.00 108.50 ! MRDN, methylidene rhodanine, kevo & xxwy +CG251O CG2R53 OG2D1 55.00 124.50 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O CG2R53 NG2R53 55.00 108.50 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O CG2R53 OG2D1 55.00 124.50 ! MRDN, methylidene rhodanine, kevo & xxwy +CG25C1 CG2R53 NG2R51 50.00 107.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C1 CG2R53 OG2D1 55.00 125.50 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2R53 NG2R51 50.00 107.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2R53 OG2D1 55.00 125.50 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R51 CG2R53 OG2D1 60.80 127.50 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG2R53 OG3C51 65.50 105.00 ! B2FO, 5H-furan-2-one, ctsai +CG3C41 CG2R53 NG2R43 120.00 104.50 ! AZDO, 2-azetidinone, kevo +CG3C41 CG2R53 OG2D1 60.00 135.70 ! AZDO, 2-azetidinone, lsk & kevo +CG3C52 CG2R53 NG2R53 120.00 105.50 ! 2PDO, 2-pyrrolidinone N1-C2-C3 v, kevo +CG3C52 CG2R53 OG2D1 65.00 126.70 ! 2PDO, 2-pyrrolidinone, kevo +CG3C52 CG2R53 OG3C51 90.00 105.80 ! GBL, Gamma-butyrolactone, ctsai & kevo +NG2R43 CG2R53 OG2D1 60.00 134.30 ! AZDO, 2-azetidinone, lsk & kevo +NG2R50 CG2R53 NG2R50 100.00 111.00 ! TRZ4, triazole124, xxwy +NG2R50 CG2R53 NG2R51 100.00 113.00 ! NA Gua 5R) +NG2R50 CG2R53 NG3C51 160.00 117.40 ! 2IMI, 2-imidazoline N1-C2-N3 d1a,d1, kevo +NG2R50 CG2R53 OG2R50 120.00 115.70 ! OXAZ, oxazole @@@@@ Kenno: 108 --> 115.7 @@@@@ +NG2R50 CG2R53 SG2R50 110.00 117.20 ! THAZ, thiazole @@@@@ Kenno: 112 --> 117.2 @@@@@ +NG2R50 CG2R53 HGR52 39.00 124.80 ! NA Ade h8, G,A +NG2R51 CG2R53 OG2D1 70.00 127.50 ! MEOI, methyleneoxindole, kevo & xxwy +NG2R51 CG2R53 HGR52 40.00 122.20 ! NA Gua h8 (NN4 CG2R53HN3 124.8) +NG2R52 CG2R53 NG2R52 145.00 108.00 ! PROT his, ADM JR., 7/20/89 +NG2R52 CG2R53 HGR53 32.00 126.00 25.00 2.14000 ! PROT his, adm jr., 6/27/90 +NG2R53 CG2R53 NG2R53 75.00 104.40 ! MHYO, 5-methylenehydantoin, xxwy +NG2R53 CG2R53 OG2D1 65.00 127.80 ! 2PDO, 2-pyrrolidinone, kevo +NG2R53 CG2R53 SG2D1 45.00 127.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R53 CG2R53 SG311 70.00 109.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG3C51 CG2R53 HGR52 32.00 117.80 ! 2IMI, 2-imidazoline N1-C2-H2, kevo +OG2D1 CG2R53 OG3C51 64.00 127.50 ! GBL, Gamma-butyrolactone, ctsai & kevo +OG2D1 CG2R53 SG311 55.00 125.00 ! MTDO, 5-methylene-2,4-thiazolidinedione, xxwy & oashi +OG2R50 CG2R53 HGR52 25.00 119.50 20.00 2.14000 ! OXAZ, oxazole @@@@@ Kenno: 120 -->119.5 @@@@@ +SG2D1 CG2R53 SG311 45.00 124.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG2R50 CG2R53 HGR52 30.00 118.00 ! THAZ, thiazole +CG2R51 CG2R57 CG2R51 90.00 107.20 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51; lf +CG2R51 CG2R57 CG2R57 33.00 126.40 ! 33BPO, 3,3-bipyrrole, lf +CG2R51 CG2R57 NG2R57 42.50 126.40 ! 13BPO, 1,3-bipyrrole, lf +CG1N1 CG2R61 CG2R61 35.00 120.00 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN) Kenno: 119 --> 120 +CG2DC1 CG2R61 CG2R61 36.00 120.00 ! STYR, styrene & HDZ2, hydrazone model cmpd 2; xxwy & oashi; verified by kevo +CG2DC2 CG2R61 CG2R61 36.00 120.00 ! STYR, styrene & HDZ2, hydrazone model cmpd 2; xxwy & oashi; verified by kevo +CG2N2 CG2R61 CG2R61 25.00 120.00 ! BAMI, benzamidinium, mp2 molvib, pram +CG2O1 CG2R61 CG2R61 45.00 119.00 ! reverted to 3NAP, nicotinamide +CG2O1 CG2R61 CG2RC0 60.00 120.00 ! HDZ2, hydrazone model cmpd 2 +CG2O2 CG2R61 CG2R61 45.00 120.00 ! ZOIC, benzoic acid, MBOA, methylbenzoate, jal +CG2O3 CG2R61 CG2R61 45.00 119.00 ! 3CB, Benzoate. Based on a slack parameter from 3ACP, 3-acetylpyridine ==> re-optimize +CG2O4 CG2R61 CG2R61 45.00 119.80 ! ALDEHYDE benzaldehyde unmodified +CG2O5 CG2R61 CG2R61 45.00 120.00 ! PHMK, PHEK, sum of equilibrium angles, kevo +CG2R61 CG2R61 CG2R61 40.00 120.00 35.00 2.41620 ! PROT JES 8/25/89 +CG2R61 CG2R61 CG2R62 40.00 119.00 35.00 2.41620 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R61 CG2R63 40.00 120.00 35.00 2.41620 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R61 CG2R64 40.00 115.50 35.00 2.41620 ! 18NFD, 1,8-naphthyridine, erh +CG2R61 CG2R61 CG2R66 40.00 119.00 35.00 2.41620 ! NAMODEL difluorotoluene +CG2R61 CG2R61 CG2R67 40.00 120.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R61 CG2RC0 50.00 120.00 !adm,dec06 113.20 ! INDO/TRP +CG2R61 CG2R61 CG311 45.80 120.00 ! modified by kevo for improved transferability +CG2R61 CG2R61 CG312 45.80 120.00 ! BDFP, BDFD, Difuorobenzylphosphonate, modified by kevo for improved transferability +CG2R61 CG2R61 CG321 45.80 120.00 ! EBEN, ethylbenzene, modified by kevo for improved transferability +CG2R61 CG2R61 CG324 45.80 120.00 ! BPIP, N-Benzyl PIP, modified by kevo for improved transferability +CG2R61 CG2R61 CG331 45.80 120.00 ! TOLU, toluene, modified by kevo for improved transferability +CG2R61 CG2R61 NG2O1 20.00 120.00 ! NITB, nitrobenzene +CG2R61 CG2R61 NG2R60 20.00 124.00 ! PYRIDINE pyridine, yin +CG2R61 CG2R61 NG2R61 125.00 120.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R61 NG2R62 20.00 124.00 ! PYRD, pyridazine +CG2R61 CG2R61 NG2RC0 100.00 121.40 ! INDZ, indolizine, kevo +CG2R61 CG2R61 NG2S1 40.00 120.00 35.00 2.4162 ! RESI PACP, FRET AND OTHERS +CG2R61 CG2R61 NG2S3 60.00 121.00 ! PYRIDINE aminopyridine, adm jr., 7/94 +CG2R61 CG2R61 NG301 42.00 120.00 ! DMAN, N,N-dimethylaniline, kevo +CG2R61 CG2R61 NG311 40.00 120.00 ! FEOZ, phenoxazine, erh +CG2R61 CG2R61 NG3N1 48.00 122.00 ! PHHZ, phenylhydrazine, ed +CG2R61 CG2R61 OG301 110.00 120.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R61 OG303 75.00 120.00 ! PROTNA phenol phosphate, 6/94, adm jr. +CG2R61 CG2R61 OG311 45.20 120.00 ! PYRIDINE phenol, yin +CG2R61 CG2R61 OG312 40.00 120.00 ! PROT adm jr. 8/27/91, phenoxide +CG2R61 CG2R61 OG3R60 40.00 120.00 ! FEOZ, phenoxazine, erh +CG2R61 CG2R61 SG311 40.00 120.00 ! FETZ, phenothiazine, erh +CG2R61 CG2R61 SG3O1 10.0 122.3000 ! benzene sulfonic acid anion, og +CG2R61 CG2R61 SG3O2 35.00 119.00 ! BSAM, benzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +CG2R61 CG2R61 CLGR1 60.00 120.00 ! CHLB, chlorobenzene +CG2R61 CG2R61 BRGR1 45.00 120.00 ! BROB, bromobenzene +CG2R61 CG2R61 IGR1 45.00 120.00 ! IODB, iodobenzene +CG2R61 CG2R61 HGR61 30.00 120.00 22.00 2.15250 ! PROT JES 8/25/89 benzene +CG2R61 CG2R61 HGR62 30.00 120.00 22.00 2.15250 ! BROB, bromobenzene +CG2R62 CG2R61 HGR61 20.00 121.00 22.00 2.15250 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R63 CG2R61 HGR62 18.00 120.00 22.00 2.15250 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from CG2R64 CG2R61 HGR61; isg +CG2R64 CG2R61 NG2R60 20.00 123.40 ! PTID, pteridine, erh +CG2R64 CG2R61 OG311 45.20 120.00 ! 2A3HPD, from PYRIDINE phenol, cacha +CG2R64 CG2R61 HGR61 30.00 120.00 22.00 2.15250 ! 2AMP, 2-amino pyridine, from PROT benzene, kevo +CG2R66 CG2R61 CG2R66 40.00 117.00 35.00 2.41620 ! NAMODEL difluorotoluene +CG2R66 CG2R61 CG331 45.80 120.00 ! NAMODEL difluorotoluene +CG2R66 CG2R61 NG2R60 20.00 124.00 ! 3FLP, 3-fluoropyridine. Kenno: copied from pyridine while retrofitting CG2R66 ==> re-optimize +CG2R66 CG2R61 NG2S1 40.00 120.00 35.00 2.4162 ! 2FBD, 2-fluoroanilide patch. Kenno: copied from RETINOL TMCH/MECH while retrofitting CG2R66 ==> re-optimize +CG2R66 CG2R61 HGR62 30.00 121.50 22.00 2.15250 ! NAMODEL difluorotoluene +CG2R67 CG2R61 NG2R60 20.00 124.00 ! PYRIDINE pyridine, yin +CG2R67 CG2R61 HGR61 30.00 120.00 ! BIPHENYL ANALOGS, peml +CG2R67 CG2R61 HGR62 30.00 120.00 ! BIPHENYL ANALOGS, peml +CG2RC0 CG2R61 NG2R62 20.00 119.00 ! PUR9, purine(N9H); PUR7, purine(N7H), kevo +CG2RC0 CG2R61 HGR61 30.00 120.00 22.00 2.14600 ! 122 INDO/TRP +CG2RC0 CG2R61 HGR62 30.00 121.50 ! 22.00 2.16830 ! PUR7, purine(N7H); PUR9, purine(N9H), kevo +CG321 CG2R61 NG2R60 45.80 122.30 ! 2AEPD, 2-ethylamino-pyridine CDCA conjugate, cacha +CG331 CG2R61 NG2R60 45.80 122.30 ! 3A2MPD, 3-amino-2-methyl-pyridine CDCA conjugate, cacha +NG2R60 CG2R61 BRGR1 45.00 120.00 ! 3A6BPD, Gamma-3-Amino-6-bromo Pyridine GA CDCA Amide, cacha +NG2R60 CG2R61 HGR62 30.00 116.00 35.00 2.10000 ! PYR1, pyridine %%% Kenno: 112->116 +NG2R61 CG2R61 HGR62 33.00 115.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione, isg +NG2R62 CG2R61 HGR62 30.00 116.00 35.00 2.10000 ! PYRD, pyridazine %%% Kenno: 112->116 +NG2RC0 CG2R61 HGR62 30.00 118.60 ! INDZ, indolizine, kevo +CG2O1 CG2R62 CG2R62 10.00 131.80 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R61 CG2R62 CG2R62 40.00 121.00 ! RIN, coumarin, isg +CG2R61 CG2R62 CG2R63 120.00 122.30 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R62 NG2R61 23.00 116.10 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R62 NG2R62 30.00 118.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R61 CG2R62 OG3R60 40.00 119.70 ! RIN, coumarin, isg +CG2R62 CG2R62 CG2R62 40.00 118.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R62 CG2R62 CG2R63 120.00 116.70 ! NA T +CG2R62 CG2R62 CG2R64 85.00 117.80 ! NA C +CG2R62 CG2R62 CG2R67 40.00 121.00 ! pyo3b, from CG2R61 CG2R62 CG2R62, fylin +CG2R62 CG2R62 CG331 40.00 124.20 ! NA 5mc, adm jr. 9/9/93 +CG2R62 CG2R62 NG2R61 85.00 122.90 ! NA C +CG2R62 CG2R62 NG2R62 20.00 121.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R62 CG2R62 NG2R67 85.00 122.90 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R62 CG2R62 NG2R61; isg +CG2R62 CG2R62 OG3R60 10.00 119.30 ! RIN, coumarin, isg +CG2R62 CG2R62 HGR62 42.00 119.00 ! NA nadh/ppi, jjp1/adm jr. 7/95 +CG2R62 CG2R62 HGR63 80.00 120.50 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R63 CG2R62 CG2R67 120.00 122.30 ! pyo2b, from CG2R61 CG2R62 CG2R63, fylin +CG2R63 CG2R62 CG331 38.00 118.70 ! NA T, c5 methyl +CG2R63 CG2R62 HGR62 30.00 120.30 ! NA U, h5 +CG2R64 CG2R62 HGR62 38.00 120.10 ! NA C h5 +CG2R67 CG2R62 NG2R61 23.00 116.10 ! pyo3b, from CG2R61 CG2R62 NG2R61, fylin +CG2R67 CG2R62 NG2R62 30.00 118.00 ! PYRF, from CG2R61 CG2R62 NG2R62, fylin +CG2R67 CG2R62 HGR62 42.00 119.00 ! pyo3b, from CG2R62 CG2R62 HGR62, fylin +CG2R67 CG2R62 HGR63 80.00 120.50 ! PIUB, from CG2R62 CG2R62 HGR63, fylin +NG2R61 CG2R62 NG2R62 50.00 124.00 ! PYRH, from NG2R61 CG2R64 NG2R62, fylin +NG2R61 CG2R62 HGR62 44.00 115.00 ! NA C, h6 +NG2R61 CG2R62 HGR63 80.00 117.50 ! NA nad/ppi, jjp1/adm jr. 7/95 +NG2R62 CG2R62 HGR62 23.50 120.00 35.00 2.10000 ! 43HPY, 4(3H)-pyrimidinone, isg. Adjusting angle without UB (from NG2R62 CG2R61 HGR62) is problematic ==> RE-OPTIMIZE! +NG2R62 CG2R62 HGR63 50.50 118.50 ! PYRH, fylin +NG2R67 CG2R62 HGR62 44.00 118.10 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone, isg +CG2R61 CG2R63 NG2R61 59.00 111.90 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R63 NG2R67 59.00 113.40 ! 3PH24S, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione; from YTS2; isg +CG2R61 CG2R63 SG2D1 38.00 125.10 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R62 CG2R63 CG2R62 10.00 120.80 ! 4PYO, 4(1H)-pyridinone; from CG2R62 CG2R62 CG2R62; isg +CG2R62 CG2R63 NG2R61 70.00 113.50 ! NA T, adm jr. 11/97 +CG2R62 CG2R63 NG2R67 70.00 115.70 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R62 CG2R62 NG2R61; isg +CG2R62 CG2R63 OG2D4 100.00 124.60 ! NA T, o4 +CG2R62 CG2R63 OG3R60 10.00 121.50 ! RIN, coumarin, isg +CG2R62 CG2R63 SG2D1 52.00 123.50 ! YT2S, 2,4(1H,3H)-quinazolinedithione, isg +CG2RC0 CG2R63 NG2R61 70.00 107.80 ! NA Gua 6R) +CG2RC0 CG2R63 OG2D4 50.00 124.70 ! NA Gua +NG2R61 CG2R63 NG2R61 50.00 114.00 ! NA U +NG2R61 CG2R63 NG2R62 50.00 116.80 ! NA C +NG2R61 CG2R63 NG2R67 50.00 114.00 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from NG2R61 CG2R63 NG2R61, NA; isg +NG2R61 CG2R63 OG2D4 130.00 119.40 ! NA C, o2 +NG2R61 CG2R63 SG2D1 56.00 123.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +NG2R62 CG2R63 OG2D4 130.00 123.80 ! NA C +NG2R67 CG2R63 OG2D4 130.00 119.70 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from NG2R61 CG2R63 OG2D4; isg +NG2R67 CG2R63 SG2D1 56.00 123.00 ! 3PH2SR, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinone; from YTS2; isg +OG2D4 CG2R63 OG3R60 20.00 113.90 ! RIN, coumarin, isg +CG2R61 CG2R64 NG2R60 20.00 124.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo +CG2R61 CG2R64 NG2R62 20.00 128.00 ! 18NFD, 1,8-naphthyridine, erh +CG2R61 CG2R64 NG2S1 40.00 120.00 35.00 2.4162 ! 2AMP, 2-Amino pyridine, from PACP, p-acetamide-phenol, kevo +CG2R62 CG2R64 NG2R62 85.00 119.30 ! NA C +CG2R62 CG2R64 NG2S3 81.00 118.40 ! NA C +CG2R62 CG2R64 NG301 67.00 120.70 ! TMC, yxu +CG2RC0 CG2R64 NG2R62 60.00 110.70 ! NA Ade 6R) +CG2RC0 CG2R64 NG2S3 50.00 118.60 ! NA Ade +CG2RC0 CG2R64 NG301 40.00 120.00 ! M6A, yxu +NG2R60 CG2R64 NG2S1 40.00 120.00 35.00 2.4162 ! 2AMP, 2-Amino pyridine, from PACP, p-acetamide-phenol, cacha (verified by kevo) +NG2R61 CG2R64 NG2R62 70.00 122.20 ! NA Gua 6R) +NG2R61 CG2R64 NG2S3 95.00 115.40 ! NA Gua n2 +NG2R61 CG2R64 SG311 20.00 121.80 ! 4O2SM, 2-(methylthio)-4(3H)-pyrimidinone; from CG2R61 CG2R61 SG311; isg +NG2R61 CG2R64 HGR62 80.00 119.00 ! TC243C, 4(3H)-quinazolinone, isg +NG2R62 CG2R64 NG2R62 60.00 128.00 ! NA Ade 6R) %%% TEST 133.0 -> 122.2 %%% +NG2R62 CG2R64 NG2R67 70.00 125.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from NG2R61 CG2R64 NG2R62; isg +NG2R62 CG2R64 NG2S3 95.00 122.40 ! NA Gua +NG2R62 CG2R64 NG301 78.00 120.00 ! TMC, yxu +NG2R62 CG2R64 SG311 54.00 116.00 ! 2SMPYR, 2-(methylthio)-pyrimidine; from CG2R61 CG2R61 SG311; isg +NG2R62 CG2R64 HGR62 38.00 116.00 ! NA Ade h2 %%% TEST 113.5 -> 118.9 %%% +NG2R67 CG2R64 HGR62 80.00 119.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from NG2R61 CG2R64 HGR62, TC243C; isg +CG2R61 CG2R66 CG2R61 40.00 122.50 35.00 2.41620 ! NAMODEL difluorotoluene +CG2R61 CG2R66 CG2R67 40.00 122.50 35.00 2.41620 ! PYO2F, from CG2R61 CG2R66 CG2R61, fylin +CG2R61 CG2R66 FGR1 60.00 118.75 ! NAMODEL difluorotoluene +CG2R67 CG2R66 FGR1 60.00 118.75 ! PYO2F, from CG2R61 CG2R66 FGR1, fylin +CG2R61 CG2R67 CG2R61 40.00 120.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R67 CG2R66 40.00 120.00 ! PYO2F, from CG2R61 CG2R67 CG2R61, fylin +CG2R61 CG2R67 CG2R67 40.00 120.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R67 CG2RC0 50.00 120.00 ! CRBZ, carbazole, erh +CG2R61 CG2R67 NG2R60 58.00 126.80 ! 22BPY, 2,2'-bipyridine, kevo +CG2R61 CG2R67 NG2R67 50.00 120.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone, isg +CG2R62 CG2R67 CG2R62 40.00 120.00 ! pyo3b, from CG2R61 CG2R67 CG2R61, fylin +CG2R62 CG2R67 CG2R67 40.00 120.00 ! pyo3b, from CG2R61 CG2R67 CG2R67, fylin +CG2R66 CG2R67 CG2R67 40.00 120.00 ! PYO2F, from CG2R61 CG2R67 CG2R67, fylin +CG2R67 CG2R67 CG2RC0 55.00 110.00 ! CRBZ, carbazole, erh +CG2R67 CG2R67 NG2R60 44.00 113.20 ! 22BPY, 2,2'-bipyridine, kevo +CG2R71 CG2R71 CG2R71 30.00 128.60 ! AZUL, Azulene, kevo +CG2R71 CG2R71 CG2RC7 90.00 129.30 ! AZUL, Azulene, kevo +CG2R71 CG2R71 HGR71 37.00 115.70 ! AZUL, Azulene, kevo +CG2RC7 CG2R71 HGR71 32.00 115.00 ! AZUL, Azulene, kevo +CG25C1 CG2RC0 CG2R61 40.00 125.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C1 CG2RC0 CG2RC0 20.00 107.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2RC0 CG2R61 40.00 125.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2RC0 CG2RC0 20.00 107.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R51 CG2RC0 CG2R61 130.00 132.00 !adm,dec06 133.50 ! INDO/TRP +CG2R51 CG2RC0 CG2RC0 85.00 108.00 ! INDO/TRP +CG2R51 CG2RC0 NG2RC0 90.00 109.20 ! INDZ, indolizine, kevo +CG2R52 CG2RC0 CG2R61 60.00 134.10 ! INDA, 1H-indazole, kevo +CG2R52 CG2RC0 CG2RC0 90.00 105.90 ! INDA, 1H-indazole, kevo +CG2R61 CG2RC0 CG2R67 50.00 120.00 ! CRBZ, carbazole, erh +CG2R61 CG2RC0 CG2RC0 50.00 120.00 !adm,dec06 110.00 ! INDO/TRP +CG2R61 CG2RC0 CG3C52 60.00 130.00 ! 3HIN, 3H-indole, kevo +CG2R61 CG2RC0 NG2R50 130.00 130.00 ! ZIMI, benzimidazole, kevo +CG2R61 CG2RC0 NG2R51 130.00 132.60 !adm,dec06 129.50 ! INDO/TRP +CG2R61 CG2RC0 NG2RC0 80.00 118.80 ! INDZ, indolizine, kevo +CG2R61 CG2RC0 NG3C51 35.00 130.70 ! INDI, indoline, kevo +CG2R61 CG2RC0 OG2R50 100.00 129.40 ! ZFUR, benzofuran, kevo +CG2R61 CG2RC0 OG3C51 50.00 125.30 !126.60 ZDOL, 1,3-benzodioxole, kevo +CG2R61 CG2RC0 SG2R50 45.00 123.70 ! ZTHP, benzothiophene, kevo +CG2R63 CG2RC0 CG2RC0 70.00 119.60 ! NA Gua 6R) bridgeC5 +CG2R63 CG2RC0 NG2R50 125.00 129.00 ! NA Gua bridgeC5 +CG2R64 CG2RC0 CG2RC0 60.00 121.00 ! NA Ade 6R) bridgeC5 +CG2R64 CG2RC0 NG2R50 100.00 129.00 ! NA Ade bridgeC5 +CG2R67 CG2RC0 CG3C52 110.00 110.00 ! FLRN, Fluorene, erh +CG2R67 CG2RC0 NG2R51 100.00 105.70 ! CRBZ, carbazole, erh +CG2RC0 CG2RC0 CG3C52 110.00 110.00 ! 3HIN, 3H-indole, kevo +CG2RC0 CG2RC0 NG2R50 100.00 110.00 ! NA Ade 5R) bridgeC5 +CG2RC0 CG2RC0 NG2R51 100.00 105.70 ! NA Ade 5R) bridgeC4 +CG2RC0 CG2RC0 NG2R62 60.00 127.40 ! NA Ade 6R) bridgeC4 +CG2RC0 CG2RC0 NG3C51 100.00 109.30 ! INDI, indoline, kevo +CG2RC0 CG2RC0 OG2R50 110.00 110.60 ! ZFUR, benzofuran, kevo +CG2RC0 CG2RC0 OG3C51 80.00 114.70 !113.50 ZDOL, 1,3-benzodioxole, kevo +CG2RC0 CG2RC0 SG2R50 70.00 116.30 ! ZTHP, benzothiophene, kevo +NG2R50 CG2RC0 NG2R62 20.00 122.60 ! PUR7, purine(N7H), kevo +NG2R51 CG2RC0 NG2R62 100.00 126.90 ! NA Ade bridgeC4 +CG2R51 CG2RC7 CG2R71 30.00 122.70 ! AZUL, Azulene, kevo +CG2R51 CG2RC7 CG2RC7 110.00 109.50 ! AZUL, Azulene, kevo +CG2R71 CG2RC7 CG2RC7 30.00 127.80 ! AZUL, Azulene, kevo +CG2D1 CG301 CG311 32.00 112.20 ! CHOLEST cholesterol +CG2D1 CG301 CG321 32.00 112.20 ! CHOLEST cholesterol +CG2D1 CG301 CG331 32.00 112.20 ! CHOLEST cholesterol +CG2DC1 CG301 CG321 32.00 112.20 ! RETINOL MECH +CG2DC1 CG301 CG331 32.00 112.20 ! RETINOL MECH +CG2DC2 CG301 CG321 32.00 112.20 ! RETINOL MECH +CG2DC2 CG301 CG331 32.00 112.20 ! RETINOL MECH +CG2O3 CG301 CG331 52.00 108.00 ! AMOL, alpha-methoxy-lactic acid, og +CG2O3 CG301 OG301 45.00 109.00 ! AMOL, alpha-methoxy-lactic acid, og +CG2O3 CG301 OG311 75.70 110.10 ! AMOL, alpha-methoxy-lactic acid, og +CG311 CG301 CG311 58.35 113.50 11.16 2.561 ! CA, CHOLIC ACID, cacha, 03/06 +CG311 CG301 CG321 58.35 113.50 11.16 2.561 ! CA, CHOLIC ACID, cacha, 03/06 +CG311 CG301 CG331 58.35 113.50 11.16 2.561 ! CA, CHOLIC ACID, cacha, 03/06 +CG321 CG301 CG321 58.35 113.50 11.16 2.561 ! CHOLEST cholesterol +CG321 CG301 CG331 58.35 113.50 11.16 2.561 ! RETINOL TMCH/MECH +CG321 CG301 OG301 45.50 114.50 ! DMBU, dimethoxybutane, sna +CG331 CG301 CG331 58.35 113.50 11.16 2.561 ! RETINOL TMCH/MECH +CG331 CG301 OG301 45.00 111.50 ! AMOL, alpha-methoxy-lactic acid, og +CG331 CG301 OG302 75.70 110.10 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha +CG331 CG301 OG311 75.70 110.10 ! AMOL, alpha-methoxy-lactic acid, og +CG331 CG301 CLGA3 97.00 111.20 ! TCLE +CG331 CG301 BRGA3 98.00 111.20 ! TBRE +OG301 CG301 OG301 70.49 107.00 ! DMOP, dimethoxypropane, sna +OG301 CG301 OG311 45.00 116.50 ! AMOL, alpha-methoxy-lactic acid, og +CLGA3 CG301 CLGA3 95.00 109.00 ! TCLE +BRGA3 CG301 BRGA3 90.00 110.50 ! TBRE +CG321 CG302 FGA3 42.00 112.00 30.00 2.357 ! TFE, trifluoroethanol +CG331 CG302 FGA3 42.00 112.00 30.00 2.357 ! FLUROALK fluoroalkanes +FGA3 CG302 FGA3 118.00 107.00 30.00 2.155 ! FLUROALK fluoroalkanes +CG2O1 CG311 CG311 52.00 108.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 CG311 CG321 52.00 108.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 CG311 CG331 52.00 108.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 CG311 NG2S1 50.00 107.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 CG311 HGA1 50.00 109.50 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O2 CG311 CG321 52.00 108.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 CG311 NG2R53 50.00 107.00 ! drug design project, xxwy +CG2O2 CG311 NG2S1 50.00 107.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 CG311 HGA1 50.00 109.50 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O3 CG311 CG2R61 51.80 107.50 ! FBIF, Fatty acid Binding protein Inhibitor F, cacha +CG2O3 CG311 CG311 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG311 CG321 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG311 CG331 52.00 108.00 ! PROT adm jr. 4/09/92, for ALA cter +CG2O3 CG311 NG2R53 50.00 107.00 ! drug design project, xxwy +CG2O3 CG311 NG2S1 50.00 107.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG311 OG301 45.00 109.00 ! CC321 CC3163 OC3C61 optimize on PROA, gk (not affected by mistake) +CG2O3 CG311 HGA1 50.00 109.50 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O5 CG311 OG311 112.00 111.00 ! BIPHENYL ANALOGS unmodified, peml ! reset by kevo to value from CG2O5 CG311 OG312 (see discussion with Dan Arlow) ==> RE-OPTIMIZE !!! +CG2O5 CG311 OG312 130.00 111.00 ! BIPHENYL ANALOGS unmodified, peml +CG2O5 CG311 HGA1 50.00 109.50 ! BIPHENYL ANALOGS from PROT Alanine Dipeptide ab initio calc's (LK) consistent with adm 11/08 +CG2R61 CG311 CG321 51.80 107.50 ! Slack parameter from difluorotoluene picked up by FBIC ==> RE-OPTIMIZE !!! +CG2R61 CG311 CG331 51.80 107.50 ! FBIB, Fatty Binding Inhibitior B, cacha +CG2R61 CG311 HGA1 43.00 111.00 ! NAMODEL difluorotoluene +CG301 CG311 CG311 52.00 108.00 ! CA, CHOLIC ACID, cacha, 03/06 +CG301 CG311 CG321 58.35 113.50 11.16 2.561 ! CA, CHOLIC ACID, cacha, 03/06 +CG301 CG311 HGA1 34.60 110.10 22.53 2.179 ! CA, CHOLIC ACID, cacha, 03/06 +CG311 CG311 CG311 53.35 111.00 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG311 CG321 53.35 111.00 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG311 CG331 53.35 108.50 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG311 CG3RC1 53.35 103.70 8.00 2.561 ! CARBOCY carbocyclic sugars +CG311 CG311 NG2S1 70.00 113.50 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG311 CG311 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG311 CG311 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG314 CG311 CG321 53.35 111.00 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG314 CG311 CG331 53.35 108.50 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG314 CG311 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG321 58.35 113.50 11.16 2.561 ! LIPID glycerol +CG321 CG311 CG324 58.35 110.50 11.16 2.56100 ! FLAVOP PIP1,2,3 +CG321 CG311 CG331 53.35 114.00 8.00 2.561 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG3C51 53.35 111.00 8.00 2.561 ! CA, Cholic acid, cacha, 02/08 +CG321 CG311 CG3RC1 53.35 103.70 8.00 2.561 ! CARBOCY carbocyclic sugars +CG321 CG311 NG2R53 70.00 113.50 ! drug design project, xxwy +CG321 CG311 NG2S1 70.00 113.50 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG321 CG311 OG302 115.00 109.70 ! NA +CG321 CG311 OG311 75.70 110.00 ! NA +CG321 CG311 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG324 CG311 NG2S1 70.00 113.50 ! G3P(R/S), 01OH04 +CG324 CG311 OG311 75.70 112.10 ! FLAVOP PIP1,2,3 +CG324 CG311 HGA1 26.50 111.80 22.53 2.17900 ! FLAVOP PIP1,2,3 +CG331 CG311 CG331 53.35 114.00 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG3C51 53.35 108.50 8.00 2.561 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG331 CG311 NG2S1 70.00 113.50 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG331 CG311 OG301 45.00 111.50 ! all34_ethers_1a OC30A CC32A CC33A, gk or og (not affected by mistake) +CG331 CG311 OG302 75.70 110.10 ! LIPID acetic acid +CG331 CG311 OG303 115.00 109.70 ! PROTNA Ser-Phos +CG331 CG311 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG331 CG311 CLGA1 88.00 111.20 ! DCLE +CG331 CG311 BRGA2 75.00 111.00 ! DBRE +CG331 CG311 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG3C51 CG311 HGA1 34.60 110.10 22.53 2.179 ! TF2M viv +CG3RC1 CG311 OG311 75.70 110.10 ! CARBOCY ncarbocyclic sugars +CG3RC1 CG311 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +NG2R53 CG311 HGA1 48.00 108.00 ! drug design project, xxwy +NG2S1 CG311 HGA1 48.00 108.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +OG301 CG311 HGA1 60.00 109.50 ! all34_ethers_1a HCA2 CC32A OC30A, gk or og (not affected by mistake) +OG302 CG311 HGA1 60.00 109.50 ! PROTNA Ser-Phos +OG303 CG311 HGA1 60.00 109.50 ! PROTNA Ser-Phos +OG311 CG311 OG312 111.90 111.00 100.00 2.35000 ! BIPHENYL ANALOGS, peml +OG311 CG311 HGA1 45.90 108.89 ! PROT MeOH, EMB, 10/10/89 +OG312 CG311 HGA1 65.90 117.80 ! BIPHENYL ANALOGS, peml +CLGA1 CG311 CLGA1 95.00 109.00 ! DCLE +CLGA1 CG311 HGA1 44.00 108.50 ! DCLE +BRGA2 CG311 BRGA2 95.00 110.00 ! DBRE +BRGA2 CG311 HGA1 36.00 107.00 ! DBRE +CG2R61 CG312 PG1 90.00 117.00 20.0 2.30 ! BDFP, Difuorobenzylphosphonate \ re-optimize? +CG2R61 CG312 PG2 90.00 117.00 20.0 2.30 ! BDFD, Difuorobenzylphosphonate / re-optimize? +CG2R61 CG312 FGA2 50.00 115.00 30.0 2.357 ! BDFP, BDFD, Difuorobenzylphosphonate +CG331 CG312 FGA2 50.00 112.00 30.00 2.357 ! FLUROALK fluoroalkanes +CG331 CG312 HGA7 32.00 112.00 3.00 2.168 ! FLUROALK fluoroalkanes +PG1 CG312 FGA2 50.00 122.00 30.0 2.357 ! BDFP, Difuorobenzylphosphonate \ re-optimize? +PG2 CG312 FGA2 50.00 122.00 30.0 2.357 ! BDFD, Difuorobenzylphosphonate / re-optimize? +FGA2 CG312 FGA2 150.00 107.00 10.00 2.170 ! FLUROALK fluoroalkanes +FGA2 CG312 HGA7 41.90 108.89 5.00 1.980 ! FLUROALK fluoroalkanes +CG2O1 CG314 CG311 52.00 108.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 CG314 CG321 52.00 108.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 CG314 CG331 52.00 108.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 CG314 NG3P3 43.70 110.00 ! PROT new aliphatics, adm jr., 2/3/92 +CG2O1 CG314 HGA1 50.00 109.50 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O3 CG314 CG311 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG314 CG321 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG314 CG331 52.00 108.00 ! PROT adm jr. 4/09/92, for ALA cter +CG2O3 CG314 NG3P3 43.70 110.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG314 HGA1 50.00 109.50 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG311 CG314 NG3P3 67.70 110.00 ! PROT new aliphatics, adm jr., 2/3/92 +CG311 CG314 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG314 CG321 58.35 113.50 11.16 2.561 ! 2MRB, Alpha benzyl gamma 2-methyl piperidine, cacha +CG321 CG314 NG3P2 40.00 110.00 ! 2MRB, Alpha benzyl gamma 2-methyl piperidine, cacha +CG321 CG314 NG3P3 67.70 110.00 ! PROT new aliphatics, adm jr., 2/3/92 +CG321 CG314 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG314 NG3P3 67.70 110.00 ! PROT new aliphatics, adm jr., 2/3/92 +CG331 CG314 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +NG3P2 CG314 HGA1 45.00 102.30 35.00 2.10100 ! 2MRB, Alpha benzyl gamma 2-methyl piperidine, cacha +NG3P3 CG314 HGA1 51.50 107.50 ! PROT new aliphatics, adm jr., 2/3/92 +CG2D1 CG321 CG2D1 30.00 114.00 ! LIPID 1,4-dipentene, adm jr., 2/00 +CG2D1 CG321 CG2DC1 125.00 108.00 ! NICH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 ! force constant is unlikely high +CG2D1 CG321 CG2DC2 125.00 108.00 ! NICH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 ! force constant is unlikely high +CG2D1 CG321 CG311 32.00 112.20 ! CHOLEST cholesterol +CG2D1 CG321 CG321 32.00 112.20 ! LIPID 1-butene; propene, yin,adm jr., 12/95 +CG2D1 CG321 CG331 32.00 112.20 ! LIPID 1-butene; propene, yin,adm jr., 12/95 +CG2D1 CG321 OG311 75.70 110.10 ! RETINOL PROL +CG2D1 CG321 HGA2 45.00 111.50 ! LIPID 1-butene; propene, yin,adm jr., 12/95 +CG2DC1 CG321 CG321 32.00 112.20 ! RETINOL MECH +CG2DC1 CG321 OG311 75.70 110.10 ! RETINOL PROL +CG2DC1 CG321 OG3R60 20.00 99.00 ! PY02, 2h-pyran +CG2DC1 CG321 HGA2 45.00 111.50 ! RETINOL BTE2, 2-butene +CG2DC2 CG321 CG321 32.00 112.20 ! RETINOL MECH +CG2DC2 CG321 OG311 75.70 110.10 ! RETINOL PROL +CG2DC2 CG321 OG3R60 20.00 99.00 ! PY02, 2h-pyran +CG2DC2 CG321 HGA2 45.00 111.50 ! RETINOL BTE2, 2-butene +CG2O1 CG321 CG311 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O1 CG321 CG314 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O1 CG321 CG321 52.00 108.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O1 CG321 CG331 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O1 CG321 NG2S1 50.00 107.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O1 CG321 HGA2 33.00 109.50 30.00 2.16300 ! PROT alanine dipeptide, 5/09/91 +CG2O2 CG321 CG311 52.00 108.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 CG321 CG314 52.00 108.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 CG321 CG321 52.00 108.00 ! LIPID alkane +CG2O2 CG321 CG331 52.00 108.00 ! LIPID alkane +CG2O2 CG321 NG2S1 50.00 107.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 CG321 NG321 43.70 110.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O2 CG321 HGA2 33.00 109.50 30.00 2.16300 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O3 CG321 CG311 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG321 CG314 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG321 CG321 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG321 CG331 52.00 108.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG321 NG2S1 50.00 107.00 ! PROT adm jr. 5/20/92, for asn,asp,gln,glu and cters +CG2O3 CG321 HGA1 50.00 109.50 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG321 HGA2 33.00 109.50 30.00 2.16300 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O4 CG321 CG331 60.00 113.80 ! ALDEHYDE propionaldehyde unmodified +CG2O4 CG321 CLGA1 65.00 111.82 ! ALDEHYDE chloroacetaldehyde unmodified +CG2O4 CG321 HGA2 33.00 109.50 30.00 2.16300 ! PALD, propionaldehyde from PROT adm jr. 5/02/91, acetic acid pure solvent. Consistent with adm 11/08 +CG2O5 CG321 CG321 60.00 113.80 ! CHON, cyclohexanone; from PALD, propionaldehyde; yapol +CG2O5 CG321 CG331 60.00 111.50 ! PHEK, phenyl ethyl ketone; from BTON, butanone; mcs +CG2O5 CG321 HGA2 50.00 109.50 ! BTON, butanone; from ACO, acetone; yapol +CG2R51 CG321 CG311 58.35 114.00 ! INDO/TRP +CG2R51 CG321 CG314 58.35 114.00 ! PROT N-terminal AA - standard parameter collided with INDO/TRP +CG2R51 CG321 CG331 58.35 114.00 ! INDO/TRP +CG2R51 CG321 HGA2 55.00 109.50 ! INDO/TRP +CG2R61 CG321 CG2R61 51.80 107.50 ! PYRIDINE pyr_CH2C6H5, yin +CG2R61 CG321 CG311 51.80 107.50 ! PROT PARALLH19 (JES) +CG2R61 CG321 CG314 51.80 107.50 ! PROT PARALLH19 (JES) +CG2R61 CG321 CG321 51.80 107.50 ! PYRIDINE butylpyridine, yin +CG2R61 CG321 CG331 51.80 107.50 ! PROT ethylbenzene, adm jr., 3/7/92 +CG2R61 CG321 NG2S1 53.00 115.20 ! NZAD, N-benzylacetamide; from CG2O2 CG321 NG2S1; isg +CG2R61 CG321 OG302 75.70 110.10 ! ABGA, Alpha Benzyl Glu Acid CDCA Amide, corrected by kevo +CG2R61 CG321 OG311 75.70 110.10 ! toppar_all22_prot_pyridines.str has 115.1 but that appears to be a copy-paste error! - kevo +CG2R61 CG321 PG1 90.00 111.00 20.0 2.300 ! BDFP, Benzylphosphonate \ re-optimize? +CG2R61 CG321 PG2 90.00 111.00 20.0 2.300 ! BDFD, Benzylphosphonate / re-optimize? +CG2R61 CG321 HGA2 49.30 107.50 ! PYRIDINE pyridines, yin +CG301 CG321 CG321 58.35 113.50 11.16 2.561 ! RETINOL TMCH/MECH +CG301 CG321 CG331 65.35 113.50 ! DMBU, dimethoxybutane, sna +CG301 CG321 HGA2 26.50 110.10 22.53 2.179 ! RETINOL TMCH/MECH +CG302 CG321 OG311 75.70 110.10 ! TFE, triflouroethanol +CG302 CG321 HGA2 34.60 110.10 22.53 2.179 ! TFE, trifluoroethanol +CG311 CG321 CG311 58.35 113.50 11.16 2.56100 ! PROT alkanes +CG311 CG321 CG314 58.35 113.50 11.16 2.56100 ! PROT alkanes +CG311 CG321 CG321 58.35 113.50 11.16 2.56100 ! PROT alkanes +CG311 CG321 CG324 58.35 110.50 11.16 2.56100 ! FLAVOP PIP1,2,3 +CG311 CG321 CG331 58.35 113.50 11.16 2.56100 ! PROT alkanes +CG311 CG321 NG2S1 70.00 113.50 ! G3P(R/S), 01OH04, cacha from CG311 CG311 NG2S1 ==> non-ideal analogy ==> re-optimize??? +CG311 CG321 OG302 75.70 110.10 ! LIPID acetic acid +CG311 CG321 OG303 75.70 110.10 ! LIPID acetic acid +CG311 CG321 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG311 CG321 SG311 58.00 112.50 ! PROT as in expt.MeEtS & DALC crystal, 5/15/92 +CG311 CG321 HGA2 33.43 110.10 22.53 2.17900 ! PROT alkanes +CG314 CG321 CG321 58.35 113.50 11.16 2.56100 ! PROT alkanes +CG314 CG321 NG2S1 70.00 113.50 ! 2MRB, Alpha benzyl gamma 2-methyl piperidine, cacha from CG311 CG311 NG2S1 ==> non-ideal analogy ==> re-optimize??? +CG314 CG321 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG314 CG321 SG311 58.00 112.50 ! PROT as in expt.MeEtS & DALC crystal, 5/15/92 +CG314 CG321 HGA2 33.43 110.10 22.53 2.17900 ! PROT alkanes +CG321 CG321 CG321 58.35 113.60 11.16 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG321 CG324 58.35 110.50 11.16 2.56100 ! FLAVOP PIP1,2,3 +CG321 CG321 CG331 58.00 115.00 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG321 CG3RC1 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG321 CG321 NG2D1 103.00 112.00 ! EEPI, from CG321 CG321 NG2S1, fylin +CG321 CG321 NG2S1 70.00 113.50 ! slack parameter picked up by 3CPD ==> re-optimize? +CG321 CG321 NG311 43.70 110.00 ! K2Cn, cgenff_compromise, kevo +CG321 CG321 OG301 45.00 111.50 ! diethylether, alex +CG321 CG321 OG302 75.70 110.10 ! LIPID acetic acid +CG321 CG321 OG303 75.70 110.10 ! LIPID acetic acid +CG321 CG321 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG321 CG321 OG3C61 45.00 111.50 ! DIOX, dioxane +CG321 CG321 SG311 58.00 114.50 ! PROT expt. MeEtS, 3/26/92 (FL) +CG321 CG321 SG3O1 43.00 105.50 ! PSNA, propyl sulfonate, xhe +CG321 CG321 HGA2 26.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG324 CG321 CG331 58.35 110.50 11.16 2.56100 ! NIPR, nitropropane, abar +CG324 CG321 OG302 75.70 110.10 ! LIPID acetic acid +CG324 CG321 OG303 75.70 110.10 ! LIPID acetic acid +CG324 CG321 OG311 75.70 112.10 ! FLAVOP PIP1,2,3 +CG324 CG321 OG3C61 50.00 106.50 ! MORP, morpholine +CG324 CG321 SG311 70.00 110.00 ! TMOR, thiomorpholine +CG324 CG321 HGA2 26.50 110.10 22.53 2.17900 ! FLAVOP PIP1,2,3 +CG331 CG321 CG331 53.35 114.00 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG321 CG3C31 53.35 111.00 ! 1BOX, 1-butene oxide, sc +CG331 CG321 NG2D1 62.00 114.00 ! EICY, ethyl isocyanate, xxwy +CG331 CG321 NG2R51 70.00 120.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from CG331 CG321 NG2S1, kevo +CG331 CG321 NG2S1 70.00 120.00 ! DECB, diethyl carbamate, cacha & xxwy ! 120, really??? DBLCHECK WITH WENBO!!! +CG331 CG321 NG2S3 27.30 109.70 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 CG321 NG311 43.70 112.20 ! PEI polymers, kevo +CG331 CG321 OG301 45.00 111.50 ! diethylether, alex +CG331 CG321 OG302 75.70 110.10 ! LIPID acetic acid +CG331 CG321 OG303 70.00 108.40 ! PROTNA Thr-Phos +CG331 CG321 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG331 CG321 OG312 65.00 122.00 ! PROT ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +CG331 CG321 SG301 58.00 112.50 ! PROT as in expt.MeEtS & DALC crystal, 5/15/92 +CG331 CG321 SG311 58.00 114.50 ! PROT expt. MeEtS, 3/26/92 (FL) +CG331 CG321 SG3O1 50.00 105.50 ! ESNA, ethyl sulfonate, xhe +CG331 CG321 SG3O2 45.00 105.00 ! EESM, N-ethylethanesulfonamide; MESN, methyl ethyl sulfone; xxwy & xhe +CG331 CG321 SG3O3 45.00 105.00 ! MESO, methylethylsulfoxide, mnoon +CG331 CG321 CLGA1 71.00 112.20 ! CLET +CG331 CG321 BRGA1 71.00 111.00 ! BRET +CG331 CG321 HGA2 34.60 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG3C31 CG321 HGA2 42.00 109.00 ! 1BOX, 1-butene oxide, sc +CG3C51 CG321 OG301 75.70 110.10 ! 3POMP, 3-phenoxymethylpyrrolidine; standard parameter; kevo +CG3C51 CG321 OG303 75.70 110.10 ! LIPID acetic acid +CG3C51 CG321 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG3C51 CG321 SG311 58.00 112.50 ! PROT as in expt.MeEtS & DALC crystal, 5/15/92 +CG3C51 CG321 HGA2 34.60 110.10 22.53 2.179 ! TF2M viv +CG3RC1 CG321 OG303 75.70 110.10 ! CARBOCY carbocyclic sugars +CG3RC1 CG321 HGA2 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +NG2D1 CG321 HGA2 45.00 107.50 ! EEPI, from NG2D1 CG331 HGA3, fylin +NG2R51 CG321 HGA2 33.43 110.10 ! ETRZ, 1-Ethyl-1,2,3-triazole, from NG2R51 CG331 HGA3, kevo +NG2S1 CG321 HGA2 51.50 109.50 ! PROT from NG2S1 CG331 HA, for lactams, adm jr. +NG2S3 CG321 HGA2 38.30 105.20 ! NESM, N-ethyl-sulfamate, my & kevo +NG311 CG321 NG311 90.00 113.00 ! OBTZ, 1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine, xxwy +NG311 CG321 HGA2 32.40 109.50 50.00 2.1300 ! PEI polymers, kevo +NG321 CG321 HGA2 32.40 109.50 50.00 2.1400 ! AMINE aliphatic amines +OG301 CG321 HGA2 45.90 108.89 ! ETOB, Ethoxybenzene, cacha +OG302 CG321 HGA2 60.00 109.50 ! PROT adm jr. 4/05/91, methyl acetate +OG303 CG321 HGA2 60.00 109.50 ! PROTNA Thr-Phos +OG311 CG321 HGA2 45.90 108.89 ! PROT MeOH, EMB, 10/10/89 +OG312 CG321 HGA2 65.00 118.30 ! PROT ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OG3C61 CG321 OG3C61 45.00 110.50 ! DIXB, dioxane +OG3C61 CG321 HGA2 45.00 109.50 ! DIOX, dioxane +OG3R60 CG321 HGA2 55.00 111.50 ! PY02, 2h-pyran +PG1 CG321 HGA2 90.00 110.00 5.40 1.802 ! BDFP, Benzylphosphonate \ re-optimize? +PG2 CG321 HGA2 90.00 110.00 5.40 1.802 ! BDFD, Benzylphosphonate / re-optimize? +SG301 CG321 HGA2 38.00 111.00 ! PROT new S-S atom type 8/24/90 +SG311 CG321 SG311 100.00 117.00 ! THIT, trithiazine +SG311 CG321 HGA2 46.10 111.30 ! PROT vib. freq. and HF/geo. (DTN) 8/24/90 +SG3O1 CG321 HGA2 49.00 109.00 ! ESNA, ethyl sulfonate, xhe +SG3O2 CG321 HGA2 45.00 107.00 ! EESM, N-ethylethanesulfonamide; MESN, methyl ethyl sulfone; xxwy & xhe +SG3O3 CG321 HGA2 45.00 107.00 ! MESO, methylethylsulfoxide, mnoon +CLGA1 CG321 HGA2 42.00 107.00 ! CLET, chloroethane +BRGA1 CG321 HGA2 36.00 106.00 ! BRET +HGA2 CG321 HGA2 35.50 109.00 5.40 1.802 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG322 FGA1 44.00 112.00 30.00 2.369 ! FLUROALK fluoroalkanes +CG331 CG322 HGA6 31.00 112.00 3.00 2.168 ! FLUROALK fluoroalkanes +FGA1 CG322 HGA6 57.50 108.89 5.00 1.997 ! FLUROALK fluoroalkanes +HGA6 CG322 HGA6 35.50 108.40 10.40 1.746 ! FLUROALK fluoroalkanes +CG331 CG323 SG302 55.00 118.00 ! PROT ethylthiolate, adm jr., 6/1/92 +CG331 CG323 HGA2 34.60 110.10 22.53 2.17900 ! PROT ethylthiolate, adm jr., 6/1/92 +SG302 CG323 HGA2 40.00 112.30 ! PROT methylthiolate, adm jr., 6/1/92 +SG302 CG323 HGA3 40.00 112.30 ! PROT methylthiolate, adm jr., 6/1/92 +HGA2 CG323 HGA2 35.50 108.40 14.00 1.77500 ! PROT methylthiolate, adm jr., 6/1/92 +HGA3 CG323 HGA3 35.50 108.40 14.00 1.77500 ! PROT methylthiolate, adm jr., 6/1/92 +CG2O1 CG324 NG3P3 43.70 110.00 ! PROT alanine (JCS) +CG2O1 CG324 HGA2 33.00 109.50 30.00 2.16300 ! PROT alanine dipeptide, 5/09/91 +CG2O3 CG324 NG3P3 43.70 110.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O3 CG324 HGA2 33.00 109.50 30.00 2.16300 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2R61 CG324 NG3P1 45.00 102.30 35.00 2.10100 ! BPIP, N-Benzyl PIP, cacha +CG2R61 CG324 HGA2 49.30 107.50 ! BPIP, N-Benzyl PIP, cacha +CG311 CG324 NG3P1 100.00 110.00 ! FLAVOP PIP1,2,3 +CG311 CG324 NG3P2 40.00 110.00 ! G3P(R/S), 01OH04 +CG311 CG324 HGA2 26.50 111.80 22.53 2.17900 ! FLAVOP PIP1,2,3 +CG321 CG324 NG2O1 56.80 109.00 ! NIPR, nitropropane, abar +CG321 CG324 NG2P1 67.70 110.00 ! RETINOL SCK1, protonated Schiff's base #eq# +CG321 CG324 NG3P0 67.70 115.00 ! LIPID tetramethylammonium +CG321 CG324 NG3P1 100.00 110.00 ! FLAVOP PIP1,2,3 +CG321 CG324 NG3P2 40.00 110.00 ! PIP, piperidine +CG321 CG324 NG3P3 67.70 110.00 ! LIPID ethanolamine +CG321 CG324 HGA2 26.50 111.80 22.53 2.17900 ! FLAVOP PIP1,2,3 +CG321 CG324 HGP5 33.43 110.10 22.53 2.17900 ! LIPID alkane +CG331 CG324 NG3P0 67.70 115.00 ! LIPID tetramethylammonium +CG331 CG324 NG3P3 67.70 110.00 ! PROT new aliphatics, adm jr., 2/3/92 +CG331 CG324 HGA2 34.60 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG324 HGP5 33.43 110.10 22.53 2.17900 ! LIPID alkane +CG3C31 CG324 NG3P3 67.70 110.00 ! AMCP, aminomethyl cyclopropane; from PROT new aliphatics, adm jr., 2/3/92m; jhs +CG3C31 CG324 HGA2 34.60 110.10 ! AMCP, aminomethyl cyclopropane; from PROT alkane update, adm jr., 3/2/92; jhs, UB term deleted +NG2O1 CG324 HGA2 60.00 106.30 ! NIPR, nitropropane, abar +NG2P1 CG324 HGA2 42.00 110.10 ! RETINOL SCK1, deprotonated Schiff's base #eq# +NG3P0 CG324 HGP5 40.00 109.50 27.00 2.130 ! LIPID tetramethylammonium +NG3P1 CG324 HGA2 45.00 102.30 35.00 2.10100 ! FLAVOP PIP1,2,3 +NG3P2 CG324 HGA2 45.00 102.30 35.00 2.10100 ! PIP, piperidine +NG3P3 CG324 HGA2 45.00 107.50 35.00 2.101 ! NA methylammonium +HGA2 CG324 HGA2 35.50 109.00 5.40 1.80200 ! PIP1,2,3 +HGP5 CG324 HGP5 24.00 109.50 28.00 1.767 ! LIPID tetramethylammonium +CG1N1 CG331 HGA3 50.00 110.50 ! ACN, acetonitrile, kevo +CG1T1 CG331 HGA3 47.00 111.50 ! 2BTY, 2-butyne, kevo +CG2D1 CG331 HGA3 42.00 111.50 ! LIPID 2-butene, yin,adm jr., 12/95 +CG2DC1 CG331 HGA3 42.00 111.50 ! RETINOL BTE2, 2-butene +CG2DC2 CG331 HGA3 42.00 111.50 ! RETINOL BTE2, 2-butene +CG2N2 CG331 HGA3 33.00 109.50 30.00 2.13000 ! AMDN, amidinium, mp2 geom, pram +CG2O1 CG331 HGA3 33.00 109.50 30.00 2.16300 ! PROT alanine dipeptide, 5/09/91 +CG2O2 CG331 HGA3 33.00 109.50 30.00 2.16300 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O3 CG331 HGA3 33.00 109.50 30.00 2.16300 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG2O4 CG331 HGA3 33.00 109.50 30.00 2.16300 ! AALD, acetaldehyde from PROT adm jr. 5/02/91, acetic acid pure solvent consistent with adm 11/08 +CG2O5 CG331 HGA3 50.00 109.50 ! methylketones 3ACP, ACO; from PROT Alanine Dipeptide ab initio calc's (LK) consistent with adm 11/08 +CG2R51 CG331 HGA3 55.00 109.50 ! INDO/TRP +CG2R61 CG331 HGA3 49.30 107.50 ! PROT toluene, adm jr. 3/7/92 +CG2R62 CG331 HGA3 33.43 110.10 22.53 2.17900 ! NA Alkanes, sacred +CG301 CG331 HGA3 33.43 110.10 22.53 2.17900 ! RETINOL TMCH/MECH +CG302 CG331 HGA3 33.00 110.50 39.00 2.15500 ! FLUROALK fluoroalkanes +CG311 CG331 HGA3 33.43 110.10 22.53 2.17900 ! PROT alkanes +CG312 CG331 HGA3 33.00 110.50 37.00 2.16800 ! FLUROALK fluoroalkanes +CG314 CG331 HGA3 33.43 110.10 22.53 2.17900 ! PROT alkanes +CG321 CG331 HGA3 34.60 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG322 CG331 HGA3 33.00 110.50 38.00 2.18100 ! FLUROALK fluoroalkanes +CG323 CG331 HGA3 34.60 110.10 22.53 2.17900 ! PROT ethylthiolate, adm jr., 6/1/92 +CG324 CG331 HGA3 34.60 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG331 HGA3 37.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG3C51 CG331 HGA3 34.60 110.10 22.53 2.179 ! TF2M viv +CG3RC1 CG331 HGA3 33.43 110.10 22.53 2.179 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +NG2D1 CG331 HGA3 42.00 113.50 ! RETINOL SCH1, Schiff's base, deprotonated +NG2R51 CG331 HGA3 33.43 110.10 ! NA FOR 9-M-G(C), adm jr. +NG2R61 CG331 HGA3 33.43 110.10 22.53 2.179 ! 1MTH, 1-Methyl-Thymine, kevo for gsk/ibm +NG2S0 CG331 HGA3 50.00 105.00 ! DMF, Dimethylformamide, xxwy +NG2S1 CG331 HGA3 51.50 109.50 ! PROT NMA crystal (JCS) +NG2S3 CG331 HGA3 51.50 107.50 ! Was introduced for 'PROT methylguanidiniumi (MGU1, MGU2)', then (questionably) transferred to 'Phosphoramidate (PHA)'. In 2008, the atom types were split ==> RE-OPTIMIZE!!! +NG301 CG331 HGA3 30.50 109.70 50.00 2.1400 ! TMC, from NG311 CG331 HGA3, yxu +NG311 CG331 HGA3 30.50 109.70 50.00 2.1400 ! MGU2, methylguanidine2 +OG301 CG331 HGA3 45.90 108.89 ! MEOB, Methoxybenzene, cacha +OG302 CG331 HGA3 60.00 109.50 ! PROT adm jr. 4/05/91, methyl acetate +OG303 CG331 HGA3 60.00 109.50 ! NA DMP, ADM Jr. +OG311 CG331 HGA3 45.90 108.89 ! PROT MeOH, EMB, 10/10/89 +OG312 CG331 HGA3 65.00 118.30 ! PROT methoxide, adm jr., 6/1/92 +SG301 CG331 HGA3 38.00 111.00 ! PROT new S-S atom type 8/24/90 +SG311 CG331 HGA3 46.10 111.30 ! PROT vib. freq. and HF/geo. (DTN) 8/24/90 +SG3O1 CG331 HGA3 42.00 110.60 ! MSNA, methyl sulfonate, xhe +SG3O2 CG331 HGA3 45.00 108.50 ! DMSN, dimethyl sulfone; MSAM, methanesulfonamide and other sulfonamides; xxwy & xhe +SG3O3 CG331 HGA3 46.10 111.30 ! DMSO, dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz +HGA3 CG331 HGA3 35.50 108.40 5.40 1.80200 ! PROT alkane update, adm jr., 3/2/92 +NG2O1 CG334 HGA3 47.80 108.00 ! NIME, nitromethane, abar +NG2P1 CG334 HGA3 42.00 110.10 ! RETINOL SCH2, Schiff's base, protonated #eq# +NG3P0 CG334 HGP5 40.00 109.50 27.00 2.13000 ! LIPID tetramethylammonium +NG3P1 CG334 HGA3 45.00 102.30 35.00 2.10100 ! FLAVOP PIP1,2,3 +NG3P3 CG334 HGA3 45.00 107.50 35.00 2.10100 ! PROT methylammonium (KK 03/10/92) +HGA3 CG334 HGA3 35.50 108.40 5.40 1.80200 ! PROT alkane update, adm jr., 3/2/92 +HGP5 CG334 HGP5 24.00 109.50 28.00 1.76700 ! LIPID tetramethylammonium +NG301 CG3AM0 HGAAM0 35.00 109.50 50.00 2.1400 ! AMINE aliphatic amines +HGAAM0 CG3AM0 HGAAM0 35.50 108.40 5.40 1.8020 ! AMINE aliphatic amines +NG311 CG3AM1 HGAAM1 30.50 109.70 50.00 2.1400 ! AMINE aliphatic amines +HGAAM1 CG3AM1 HGAAM1 35.80 109.00 5.40 1.8020 ! AMINE aliphatic amines +NG321 CG3AM2 HGAAM2 32.40 109.50 50.00 2.1400 ! AMINE aliphatic amines +HGAAM2 CG3AM2 HGAAM2 35.00 109.47 5.40 1.8020 ! AMINE aliphatic amines +CG321 CG3C31 CG3C31 67.35 116.70 ! 1BOX, 1-butene oxide, sc +CG321 CG3C31 OG3C31 60.35 115.50 ! 1BOX, 1-butene oxide, sc +CG321 CG3C31 HGA1 30.00 115.40 ! 1BOX, 1-butene oxide, sc +CG324 CG3C31 CG3C31 58.35 120.00 ! AMCP, aminomethyl cyclopropane; from FLAVOP PIP1,2,3; jhs ! Kenno: "outside angle" of a 3-membered ring; the QM value is ~119 and the MM ~115. +CG324 CG3C31 HGA1 34.60 110.10 ! AMCP, aminomethyl cyclopropane; from PROT alkane update, adm jr., 3/2/92; jhs, UB term deleted +CG3C31 CG3C31 CG3C31 77.35 111.00 8.00 2.56100 ! PROTMOD cyclopropane +CG3C31 CG3C31 OG3C31 30.00 103.00 ! 1EOX, 1-ethylene oxide, sc +CG3C31 CG3C31 HGA1 23.00 117.10 22.53 2.17900 ! PROTMOD cyclopropane +CG3C31 CG3C31 HGA2 23.00 117.10 22.53 2.17900 ! PROTMOD cyclopropane +CG3RC1 CG3C31 CG3RC1 53.35 58.50 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C31 HGA2 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +OG3C31 CG3C31 HGA1 64.00 118.50 ! 1BOX, 1-butene oxide, sc +OG3C31 CG3C31 HGA2 68.50 115.00 ! 1EOX, 1-ethylene oxide, sc +HGA2 CG3C31 HGA2 23.00 117.00 5.40 1.80200 ! PROTMOD cyclopropane +CG2R53 CG3C41 CG3C41 90.00 106.00 ! AZDO, 2-azetidinone, lsk & kevo +CG2R53 CG3C41 HGA2 46.00 112.30 ! AZDO, 2-azetidinone, lsk & kevo +CG3C41 CG3C41 CG3C41 70.00 106.00 ! CBU, cyclobutane; QM by Nikolay Simakov; lsk +CG3C41 CG3C41 NG2R43 90.00 104.50 ! AZDO, 2-azetidinone, lsk & kevo +CG3C41 CG3C41 HGA2 46.00 110.50 ! CBU, cyclobutane; QM by Nikolay Simakov; lsk +NG2R43 CG3C41 HGA2 51.00 110.80 ! AZDO, 2-azetidinone, lsk & kevo +HGA2 CG3C41 HGA2 28.00 105.00 5.40 1.8067 ! CBU, cyclobutane; AZDO, 2-azetidinone; QM by Nikolay Simakov; lsk & kevo +CG2O1 CG3C51 CG3C52 52.00 112.30 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 CG3C51 NG2S0 50.00 108.20 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 CG3C51 HGA1 50.00 112.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C51 CG3C52 52.00 112.30 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C51 NG2S0 50.00 108.20 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C51 HGA1 50.00 112.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG3C51 CG3C52 58.00 115.00 8.00 2.561 ! TF2M viv +CG311 CG3C51 CG3RC1 52.00 108.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG311 CG3C51 HGA1 34.60 110.10 22.53 2.179 ! TF2M viv +CG321 CG3C51 CG3C51 58.00 115.00 8.00 2.561 ! TF2M viv +CG321 CG3C51 CG3C52 58.00 115.00 8.00 2.561 ! TF2M viv +CG321 CG3C51 CG3RC1 53.35 103.70 8.00 2.561 ! CARBOCY carbocyclic sugars +CG321 CG3C51 OG3C51 45.00 111.50 ! TF2M, viv +CG321 CG3C51 HGA1 34.60 110.10 22.53 2.179 ! TF2M viv +CG331 CG3C51 CG3C51 58.00 115.00 8.00 2.561 ! TF2M viv +CG331 CG3C51 CG3C52 58.00 115.00 8.00 2.561 ! TF2M viv +CG331 CG3C51 CG3RC1 53.35 108.50 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG3C51 OG3C51 45.00 111.50 ! TF2M, viv +CG331 CG3C51 HGA1 34.60 110.10 22.53 2.179 ! TF2M viv +CG3C51 CG3C51 CG3C51 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv +CG3C51 CG3C51 CG3C52 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv +CG3C51 CG3C51 CG3C53 53.35 111.00 8.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 +CG3C51 CG3C51 CG3RC1 53.35 103.70 8.00 2.561 ! CARBOCY carbocyclic sugars +CG3C51 CG3C51 NG2R51 110.00 111.00 ! NA T/U/G, Arabinose (NF) +CG3C51 CG3C51 NG2R61 110.00 111.00 ! NA C/A, RNA +CG3C51 CG3C51 NG2S3 43.70 110.00 ! NABAKB phosphoramidates +CG3C51 CG3C51 NG301 110.00 111.00 ! NADH, NDPH; Kenno: reverted to "C/A, RNA" from par_all27_na.prm +CG3C51 CG3C51 NG321 67.70 107.50 ! PROT arg, (DS) +CG3C51 CG3C51 OG303 115.00 109.70 ! PROTNA Ser-Phos +CG3C51 CG3C51 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG3C51 CG3C51 OG3C51 45.00 111.10 ! THF 10/21/05, viv +CG3C51 CG3C51 FGA1 44.00 112.00 30.00 2.369 ! FLUROALK fluoroalkanes +CG3C51 CG3C51 HGA1 35.00 111.40 22.53 2.179 ! TF2M, viv +CG3C51 CG3C51 HGA6 35.00 111.40 22.53 2.179 ! TF2M, viv +CG3C52 CG3C51 CG3C52 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv +CG3C52 CG3C51 CG3RC1 53.35 103.70 8.00 2.561 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 NG2R51 140.00 113.70 ! NA +CG3C52 CG3C51 NG2R61 110.00 113.70 ! NA C/A +CG3C52 CG3C51 NG2S0 70.00 110.80 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C51 NG2S3 43.70 110.00 ! NABAKB phosphoramidates +CG3C52 CG3C51 NG321 67.70 107.50 ! PROT arg, (DS) +CG3C52 CG3C51 OG301 58.00 106.50 8.00 2.561 ! THF2, THF-2'OMe c3'-c2'-om, from Nucl. Acids, ed +CG3C52 CG3C51 OG303 115.00 109.70 ! NA +CG3C52 CG3C51 OG311 75.70 110.00 ! NA +CG3C52 CG3C51 OG3C51 45.00 111.10 ! THF 10/21/05, viv +CG3C52 CG3C51 FGA1 44.00 112.00 30.00 2.369 ! FLUROALK fluoroalkanes +CG3C52 CG3C51 HGA1 35.00 111.40 22.53 2.179 ! TF2M, viv +CG3C52 CG3C51 HGA6 35.00 111.40 22.53 2.179 ! TF2M, viv +CG3C53 CG3C51 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89 +CG3C53 CG3C51 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG3RC1 CG3C51 NG2R51 110.00 108.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 NG2R61 110.00 108.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 OG303 75.70 110.10 ! CARBOCY ncarbocyclic sugars +CG3RC1 CG3C51 OG311 75.70 110.10 ! CARBOCY ncarbocyclic sugars +CG3RC1 CG3C51 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +NG2R51 CG3C51 OG3C51 140.00 108.00 ! NA +NG2R51 CG3C51 HGA1 43.00 111.00 ! NA From HGA1 CG3C51 NN2 +NG2R61 CG3C51 OG3C51 110.00 108.00 ! NA C/A DNA +NG2R61 CG3C51 HGA1 43.00 111.00 ! NA +NG2S0 CG3C51 HGA1 48.00 112.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S3 CG3C51 HGA1 48.00 110.00 ! NABAKB phosphoramidates +NG301 CG3C51 OG3C51 110.00 112.00 ! NADH, NDPH; Kenno: reverted to "C/A RNA" from par_all27_na.prm +NG301 CG3C51 HGA1 43.00 111.00 ! NADH, NDPH; Kenno: reverted to uncommented parameter from par_all27_na.prm +NG321 CG3C51 HGA1 32.40 109.50 50.00 2.1400 ! AMINE aliphatic amines +OG301 CG3C51 HGA1 45.90 108.50 ! THF2, THF-2'OMe h2''-c2'-om, from Nucl. Acids, ed +OG303 CG3C51 HGA1 60.00 109.50 ! PROTNA Ser-Phos +OG311 CG3C51 HGA1 45.90 108.89 ! PROT MeOH, EMB, 10/10/89 +OG3C51 CG3C51 HGA1 70.00 107.30 ! THF 10/21/05, viv +FGA1 CG3C51 HGA6 57.50 108.89 5.00 1.997 ! FLUROALK fluoroalkanes +CG2R51 CG3C52 CG2R51 76.00 107.60 ! CPDE, cyclopentadiene, kevo +CG2R51 CG3C52 CG2R52 84.00 106.00 ! 3HPR, 3H-pyrrole, kevo +CG2R51 CG3C52 CG2R53 45.00 108.00 ! A2FO, 3H-furan-2-one, ctsai +CG2R51 CG3C52 CG2RC0 40.00 107.30 ! INDE, indene, kevo +CG2R51 CG3C52 CG3C52 52.00 106.00 ! 105 2PRL, 2-pyrroline, kevo +CG2R51 CG3C52 CG3C54 52.00 103.30 ! 106 2PRL, 2-pyrroline RE-OPTIMIZE!, kevo +CG2R51 CG3C52 NG2R50 105.00 111.60 ! 115.00 111.60 2HPR, 2H-pyrrole 1, kevo +CG2R51 CG3C52 NG3C51 70.00 105.10 ! 3PRL, 3-pyrroline, kevo +CG2R51 CG3C52 OG3C51 75.00 102.40 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG3C52 HGA2 52.00 112.60 ! 2PRP, 2-pyrroline.H+; 2PRL, 2-pyrroline, kevo +CG2R52 CG3C52 CG2RC0 70.00 105.00 ! 3HIN, 3H-indole, kevo +CG2R52 CG3C52 CG3C52 80.00 99.00 !~ 99.5 99 2PRZ, 2-pyrazoline C3-C4-C5, kevo +CG2R52 CG3C52 HGA2 58.00 112.20 !x 112.2 2PRZ, 2-pyrazoline; 3HPR, 3H-pyrrole C3-C4-H4x, kevo +CG2R53 CG3C52 CG3C52 70.00 106.50 ! 2PDO, 2-pyrrolidinone C2-C3-C4, kevo +CG2R53 CG3C52 HGA2 58.00 111.00 ! 2PDO, 2-pyrrolidinone, kevo +CG2RC0 CG3C52 CG2RC0 40.00 95.00 ! FLRN, Fluorene, erh +CG2RC0 CG3C52 CG3C52 65.00 108.20 ! INDI, indoline, kevo +CG2RC0 CG3C52 HGA2 38.00 114.00 ! 3HIN, 3H-indole, kevo +CG3C51 CG3C52 CG3C51 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv +CG3C51 CG3C52 CG3C52 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv +CG3C51 CG3C52 CG3RC1 80.00 105.50 8.00 2.56100 ! CARBOCY carbocyclic sugars +CG3C51 CG3C52 NG3C51 84.00 107.60 ! 3POMP, 3-phenoxymethylpyrrolidine; from PRLD etc; kevo +CG3C51 CG3C52 OG3C51 45.00 111.10 ! THF 10/21/05, viv +CG3C51 CG3C52 HGA2 35.00 111.40 22.53 2.179 ! TF2M, viv +CG3C52 CG3C52 CG3C52 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv +CG3C52 CG3C52 CG3C53 70.00 108.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 CG3C54 70.00 108.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 CG3RC1 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 NG2R50 40.00 107.10 !~ 104.2 ! 105.80 2IMI, 2-imidazoline N3-C4-C5 d1,d1a, kevo +CG3C52 CG3C52 NG2R53 90.00 104.50 ! 2PDO, 2-pyrrolidinone C4-C5-N1, kevo +CG3C52 CG3C52 NG2S0 70.00 110.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 NG3C51 84.00 107.60 !x 107 PRLD, pyrrolidine; 103.3 2PRL, 2-pyrroline; 100.4 2IMI, 2-imidazoline; 2PRZ, 2-pyrazoline, kevo +CG3C52 CG3C52 OG3C51 45.00 111.10 ! THF 10/21/05, viv +CG3C52 CG3C52 HGA2 35.00 111.40 22.53 2.179 ! TF2M, viv +CG3C53 CG3C52 HGA2 33.43 110.10 22.53 2.17900 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C54 CG3C52 NG3C51 87.00 110.40 ! IMDP, imidazolidine, erh and kevo +CG3C54 CG3C52 HGA2 26.50 110.10 22.53 2.17900 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3RC1 CG3C52 CG3RC1 58.00 105.30 ! NORB, Norbornane, kevo +CG3RC1 CG3C52 HGA2 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +NG2R50 CG3C52 HGA2 44.00 109.80 !x 2IMI, 2-imidazoline; 2HPR, 2H-pyrrole, kevo +NG2R53 CG3C52 HGA2 59.00 111.00 ! 2PDO, 2-pyrrolidinone, kevo +NG2S0 CG3C52 HGA2 48.00 108.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG3C51 CG3C52 HGA2 54.00 109.00 !v 107.7 PRLD, pyrrolidine; 110.8 2PRL, 2-pyrroline; 110.4 3PRL, 3-pyrroline; 111.4 2IMI, 2-imidazoline; 111.7 2PRZ, 2-pyrazoline, kevo +OG3C51 CG3C52 OG3C51 85.00 108.10 ! DIOL, 1,3-Dioxolane, erh +OG3C51 CG3C52 HGA2 70.00 107.30 ! THF 10/21/05, viv +HGA2 CG3C52 HGA2 38.50 106.80 5.40 1.802 ! THF, 10/17/05 viv +CG2O1 CG3C53 CG3C52 52.00 112.30 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 CG3C53 NG3P2 50.00 106.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 CG3C53 HGA1 50.00 112.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C53 CG3C52 52.00 112.30 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C53 NG3P2 50.00 106.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C53 HGA1 50.00 112.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG3C53 NG2R61 110.00 111.00 ! NA C/A, RNA +CG3C51 CG3C53 OG3C51 120.00 106.25 ! NA +CG3C51 CG3C53 HGA1 34.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92 +CG3C52 CG3C53 NG3P2 70.00 108.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C53 HGA1 35.00 118.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2R61 CG3C53 OG3C51 110.00 108.00 ! NA C/A DNA +NG2R61 CG3C53 HGA1 43.00 111.00 ! NA +NG3P2 CG3C53 HGA1 51.50 107.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG3C51 CG3C53 HGA1 45.20 107.24 ! NA +CG2R51 CG3C54 NG2R52 138.00 103.10 ! 2HPP, 2H-pyrrole.H+ N1-C2-C3, kevo +CG2R51 CG3C54 NG3P2 62.00 103.00 ! 3PRP, 3-pyrroline.H+, kevo +CG2R51 CG3C54 HGA2 41.00 114.80 ! 109.8 3PRP, 3-pyrroline.H+; 2HPP, 2H-pyrrole.H+, kevo +CG3C52 CG3C54 NG3P2 70.00 108.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C54 HGA2 26.50 110.10 22.53 2.17900 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C54 CG3C54 NG2R52 68.00 106.00 ! 2IMP, 2-imidazoline.H+ 1a,1, kevo +CG3C54 CG3C54 HGA2 26.50 110.10 22.53 2.17900 !~ 2IMP, 2-imidazoline.H+ ! RE-OPTIMIZE !!!, kevo +NG2R52 CG3C54 HGA2 54.00 107.00 !x 2IMP, 2-imidazoline.H+; 2HPP, 2H-pyrrole.H+, kevo +NG3C51 CG3C54 NG3P2 86.00 119.00 ! IMDP, imidazolidine ! questionable - RE-OPTIMIZE?, erh and kevo +NG3C51 CG3C54 HGA2 53.00 114.60 ! IMDP, imidazolidine, erh and kevo +NG3P2 CG3C54 HGA2 51.50 109.15 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C54 HGA2 35.50 109.00 5.40 1.80200 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG3RC1 CG331 58.35 113.50 11.16 2.561 ! CA, Cholic acid, cacha, 02/08 +CG311 CG3RC1 CG3C51 58.35 113.50 11.16 2.561 ! CA, Cholic acid, cacha, 02/08 +CG311 CG3RC1 CG3C52 53.35 111.00 8.00 2.561 ! CA, Cholic acid, cacha, 02/08 +CG311 CG3RC1 CG3RC1 53.35 108.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG311 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +CG321 CG3RC1 CG331 58.35 113.50 11.16 2.561 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG321 CG3RC1 CG3C31 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG321 CG3RC1 CG3C51 53.35 111.00 8.00 2.561 ! CARBOCY carbocyclic sugars +CG321 CG3RC1 CG3C52 58.35 113.50 11.16 2.561 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG321 CG3RC1 CG3RC1 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG321 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +CG331 CG3RC1 CG3C51 58.35 113.50 11.16 2.561 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG331 CG3RC1 CG3RC1 58.35 113.50 11.16 2.561 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG3C31 CG3RC1 CG3C51 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 CG3C52 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 CG3RC1 53.35 62.50 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 NG2R51 70.00 113.70 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 NG2R61 70.00 113.70 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +CG3C51 CG3RC1 CG3C52 70.00 109.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy +CG3C51 CG3RC1 CG3RC1 53.35 108.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG3C51 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 CG3C52 56.00 109.40 ! NORB, Norbornane, kevo +CG3C52 CG3RC1 CG3RC1 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 NG2R51 70.00 113.70 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 NG2R61 70.00 113.70 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +CG3RC1 CG3RC1 NG2R51 70.00 113.70 ! CARBOCY carbocyclic sugars +CG3RC1 CG3RC1 NG2R61 70.00 113.70 ! CARBOCY carbocyclic sugars +CG3RC1 CG3RC1 OG3C51 50.00 109.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy +CG3RC1 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars +OG3C51 CG3RC1 OG3C51 70.00 105.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy +OG3C51 CG3RC1 HGA1 55.00 106.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy +CG2D1 NG2D1 CG321 74.50 111.00 ! EEPI, from CG2D1 NG2D1 CG331, fylin +CG2D1 NG2D1 CG331 67.00 111.00 ! RETINOL SCH1, Schiff's base, deprotonated +CG2D1 NG2D1 NG2S1 100.00 115.00 ! HDZ1, hydrazone model cmpd +CG2DC1 NG2D1 NG2S1 100.00 115.00 ! HDZ2, hydrazone model cmpd +CG2DC2 NG2D1 NG2S1 100.00 115.00 ! HDZ2, hydrazone model cmpd +CG2N1 NG2D1 CG331 50.00 108.00 ! MGU1, methylguanidine +CG2N1 NG2D1 HGP1 49.00 113.00 ! MGU2, methylguanidine2 +CG2N2 NG2D1 CG321 45.00 103.80 ! MT2A, fylin, re-opt +CG2O7 NG2D1 CG331 9.00 136.00 ! MICY, methyl isocyanate, xxwy +CG2R61 NG2O1 OG2N1 65.00 116.00 ! NITB, nitrobenzene +CG324 NG2O1 OG2N1 56.00 117.00 ! NIPR, nitropropane, abar +CG334 NG2O1 OG2N1 60.00 120.00 ! NIME, nitromethane, abar ! we'll tolerate the angle strain in this specific case - Kenno +OG2N1 NG2O1 OG2N1 105.00 128.00 ! NITB, nitrobenzene +CG2D1 NG2P1 CG334 67.00 123.60 ! RETINOL SCH2, Schiff's base, protonated +CG2D1 NG2P1 HGP2 38.00 118.80 ! RETINOL SCH2, Schiff's base, protonated +CG2DC1 NG2P1 CG334 67.00 123.60 ! RETINOL SCH2, Schiff's base, protonated +CG2DC1 NG2P1 HGP2 38.00 118.80 ! RETINOL SCH2, Schiff's base, protonated +CG2DC2 NG2P1 CG334 67.00 123.60 ! RETINOL SCH2, Schiff's base, protonated +CG2DC2 NG2P1 HGP2 38.00 118.80 ! RETINOL SCH2, Schiff's base, protonated +CG2N1 NG2P1 CG324 62.30 120.00 ! PROT 107.5->120.0 to make planar Arg (KK) +CG2N1 NG2P1 CG334 62.30 120.00 ! PROT methylguanidinium, adm jr., 3/26/92 +CG2N1 NG2P1 HGP2 49.00 120.00 ! PROT 35.3->49.0 GUANIDINIUM (KK) +CG2N2 NG2P1 HGP2 40.00 120.00 ! AMDN, amidinium; BAMI, benzamidinium; mp2 molvib; pram +CG324 NG2P1 HGP2 40.40 120.00 ! PROT 107.5->120.0 to make planar Arg (KK) +CG334 NG2P1 HGP2 40.40 120.00 ! PROT methylguanidinium, adm jr., 3/26/92 +HGP2 NG2P1 HGP2 25.00 120.00 ! PROT 40.0->25.0 GUANIDINIUM (KK) +CG2R53 NG2R43 CG3C41 85.00 111.50 ! AZDO, 2-azetidinone, kevo +CG2R53 NG2R43 HGP1 34.00 129.70 ! AZDO, 2-azetidinone, kevo +CG3C41 NG2R43 HGP1 34.00 125.30 ! AZDO, 2-azetidinone, kevo +CG2R51 NG2R50 CG2R52 58.00 103.00 ! 3HPR, 3H-pyrrole, kevo +CG2R51 NG2R50 CG2R53 130.00 103.50 ! PROT his, adm jr., 6/27/90 @@@@@ Kenno: 104 --> 103.5 @@@@@ +CG2R51 NG2R50 NG2R50 110.00 106.80 ! OXAD, oxadiazole123 @@@@@ Kenno: 107.1 --> 106.8 @@@@@ +CG2R52 NG2R50 CG2RC0 60.00 103.00 ! 3HIN, 3H-indole, kevo +CG2R52 NG2R50 CG3C52 115.00 102.90 ! 105.00 102.90 2HPR, 2H-pyrrole 1,1a, kevo +CG2R52 NG2R50 NG2R51 160.00 103.50 ! PYRZ, pyrazole +CG2R52 NG2R50 NG3C51 160.00 105.50 !~ 107.5 2PRZ, 2-pyrazoline N1-N2-C3, kevo +CG2R52 NG2R50 OG2R50 150.00 103.30 ! ISOX, isoxazole @@@@@ Kenno: 105.6 --> 103.3 @@@@@ +CG2R52 NG2R50 SG2R50 150.00 111.00 ! ISOT, isothiazole +CG2R53 NG2R50 CG2R53 100.00 101.00 ! TRZ4, triazole124, xxwy +CG2R53 NG2R50 CG2RC0 120.00 103.80 ! NA Gua 5R) +CG2R53 NG2R50 CG3C52 160.00 101.90 ! 101.0 ! 104.50 2IMI, 2-imidazoline C2-N3-C4 d1a, kevo +CG2R53 NG2R50 NG2R51 100.00 101.00 ! TRZ4, triazole124, xxwy +CG2R53 NG2R50 OG2R50 50.00 103.00 ! OXD4, oxadiazole124, xxwy +NG2R50 NG2R50 NG2R51 160.00 102.20 ! TRZ3, triazole123 @@@@@ Kenno: 101.9 --> 102.2 @@@@@ +NG2R50 NG2R50 OG2R50 110.00 103.00 ! OXAD, oxadiazole123 @@@@@ Kenno: 105.5 --> 103.0 @@@@@ +CG2R51 NG2R51 CG2R51 100.00 109.00 ! PYRL, pyrrole +CG2R51 NG2R51 CG2R53 130.00 107.50 ! PROT his, adm jr., 6/27/90 +CG2R51 NG2R51 CG2RC0 85.00 110.00 ! adm,dec06(112.0)INDO/TRP +CG2R51 NG2R51 CG321 70.00 127.10 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +CG2R51 NG2R51 CG3C51 130.00 126.00 ! NA +CG2R51 NG2R51 NG2R50 160.00 115.00 ! PYRZ, pyrazole +CG2R51 NG2R51 HGP1 30.00 125.50 20.00 2.15000 ! PROT his, adm jr., 6/27/90 +CG2R53 NG2R51 CG2RC0 100.00 107.20 ! NA Gua 5R) +CG2R53 NG2R51 CG331 70.00 127.80 ! NA 9-M-A, adm jr. +CG2R53 NG2R51 CG3C51 45.00 126.30 ! NA G +CG2R53 NG2R51 CG3RC1 45.00 127.60 ! CARBOCY carbocyclic sugars +CG2R53 NG2R51 NG2R50 130.00 114.00 ! TRZ4, triazole124, xxwy +CG2R53 NG2R51 HGP1 30.00 127.00 20.00 2.14000 ! PROT his, adm jr., 6/27/90 +CG2RC0 NG2R51 CG2RC0 85.00 110.00 ! CRBZ, carbazole, erh +CG2RC0 NG2R51 CG331 70.00 125.90 ! NA 9-M-G, adm jr. +CG2RC0 NG2R51 CG3C51 45.00 126.50 ! NA G +CG2RC0 NG2R51 CG3RC1 45.00 126.50 ! CARBOCY carbocyclic sugars +CG2RC0 NG2R51 NG2R50 190.00 114.50 ! INDA, 1H-indazole, kevo +CG2RC0 NG2R51 HGP1 28.00 126.00 ! INDO/TRP +CG321 NG2R51 NG2R50 70.00 117.90 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +NG2R50 NG2R51 NG2R50 90.00 121.00 ! TRZ2, 2H-1,2,3-triazole, lf +NG2R50 NG2R51 HGP1 32.00 119.50 ! PYRZ, pyrazole +CG2R51 NG2R52 CG2R53 145.00 108.00 ! PROT his, ADM JR., 7/20/89 +CG2R51 NG2R52 HGP2 25.00 124.90 15.00 2.13000 ! PROT his, adm jr., 6/27/90 +CG2R52 NG2R52 CG3C54 101.00 111.90 !x 2HPP, 2H-pyrrole.H+ C5-N1-C2, kevo +CG2R52 NG2R52 HGP2 29.00 123.20 !x 2IMP, 2-imidazoline.H+; 2HPP, 2H-pyrrole.H+, kevo +CG2R53 NG2R52 CG3C54 140.00 108.00 ! 2IMP, 2-imidazoline.H+ 1,1a, kevo +CG2R53 NG2R52 HGP2 25.00 127.10 15.00 2.09000 ! PROT his, adm jr., 6/27/90 +CG3C54 NG2R52 HGP2 29.00 124.90 !x 2IMP, 2-imidazoline.H+; 2HPP, 2H-pyrrole.H+, kevo +CG251O NG2R53 CG2R53 116.00 117.50 ! MHYO, 5-methylenehydantoin, xxwy +CG251O NG2R53 HGP1 38.00 123.00 ! MHYO, 5-methylenehydantoin, xxwy +CG252O NG2R53 CG2R53 116.00 117.50 ! MHYO, 5-methylenehydantoin, xxwy +CG252O NG2R53 HGP1 38.00 123.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2R53 NG2R53 CG2R53 55.00 120.50 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 NG2R53 CG311 50.00 120.00 ! drug design project, xxwy +CG2R53 NG2R53 CG3C52 75.00 111.00 ! 2PDO, 2-pyrrolidinone C5-N1-C2 v, kevo +CG2R53 NG2R53 HGP1 38.00 119.50 ! 2PDO, 2-pyrrolidinone (H1-N1-C2), kevo +CG3C52 NG2R53 HGP1 38.00 116.00 ! 2PDO, 2-pyrrolidinone (C5-N1-H1), kevo +CG2R51 NG2R57 CG2R51 100.00 109.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 NG2R51 CG2R51; lf +CG2R51 NG2R57 CG2R57 42.00 125.50 ! 13BPO, 1,3-bipyrrole, lf +CG2R51 NG2R57 NG2R57 54.00 125.50 ! 11BPO, 1,1-bipyrrole, lf +CG2R61 NG2R60 CG2R61 20.00 112.00 ! PYRIDINE pyridine, yin +CG2R61 NG2R60 CG2R64 20.00 112.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo +CG2R61 NG2R60 CG2R67 20.00 109.20 ! 22BPY, 2,2'-bipyridine, kevo +CG2R61 NG2R61 CG2R63 10.00 123.90 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 NG2R61 HGP1 33.00 120.70 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R62 NG2R61 CG2R62 30.00 120.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R62 NG2R61 CG2R63 70.00 122.00 ! NA U, adm jr. 11/97 +CG2R62 NG2R61 CG331 70.00 120.50 ! NA 1-M-C, adm jr. 7/24/91 +CG2R62 NG2R61 CG3C51 45.00 118.40 ! CARBOCY carbocyclic sugars +CG2R62 NG2R61 CG3C53 45.00 118.40 ! CARBOCY carbocyclic sugars +CG2R62 NG2R61 CG3RC1 45.00 115.90 ! CARBOCY carbocyclic sugars +CG2R62 NG2R61 HGP1 32.00 117.40 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R62 NG2R61 HGP2 32.00 117.40 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R63 NG2R61 CG2R63 50.00 130.20 ! NA U +CG2R63 NG2R61 CG2R64 70.00 131.10 ! NA Gua 6R)G, adm jr. 11/97 +CG2R63 NG2R61 CG331 70.00 115.40 ! NA 1-M-C, adm jr. +CG2R63 NG2R61 CG3C51 45.00 118.40 ! CARBOCY carbocyclic sugars +CG2R63 NG2R61 CG3RC1 45.00 120.00 ! CARBOCY carbocyclic sugars +CG2R63 NG2R61 HGP1 40.50 115.40 ! NA U +CG2R64 NG2R61 HGP1 45.00 115.60 ! NA Gua +CG2R61 NG2R62 CG2R64 40.00 110.50 ! PYRM, pyrimidine %%% TEST 108.0 -> 113.4 %%% +CG2R61 NG2R62 NG2R62 10.00 120.00 ! PYRD, pyridazine +CG2R62 NG2R62 CG2R62 25.00 114.10 ! PYRH , from CG2R62 NG2R62 CG2R64, fylin +CG2R62 NG2R62 CG2R64 70.00 115.50 ! TC243C, 4(3H)-quinazolinone, isg +CG2R63 NG2R62 CG2R64 85.00 119.10 ! NA C +CG2R64 NG2R62 CG2R64 90.00 117.80 ! NA Ade 6R) adm jr. 11/97 +CG2R64 NG2R62 CG2RC0 90.00 115.10 ! NA Ade 6R) %%% TEST 110.1 -> 120.9 %%% +CG2R64 NG2R62 NG2R62 65.00 121.00 ! TRIB, triazine124 +CG2R62 NG2R67 CG2R62 30.00 120.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R62 NG2R61 CG2R62; isg +CG2R62 NG2R67 CG2R63 70.00 128.70 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R61 NG2R61 CG2R63; isg +CG2R62 NG2R67 CG2R67 52.00 120.0 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone, isg +CG2R63 NG2R67 CG2R63 50.00 128.70 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from CG2R63 NG2R61 CG2R63, NA; isg +CG2R63 NG2R67 CG2R64 70.00 126.10 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from CG2R63 NG2R61 CG2R64; isg +CG2R63 NG2R67 CG2R67 33.00 111.30 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R62 NG2R61 CG2R63; isg +CG2R64 NG2R67 CG2R67 55.00 121.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from CG2R63 NG2R61 CG2R64; isg +CG2R51 NG2RC0 CG2R61 15.00 130.50 ! INDZ, indolizine, kevo +CG2R51 NG2RC0 CG2RC0 100.00 109.70 ! INDZ, indolizine, kevo +CG2R61 NG2RC0 CG2RC0 15.00 119.80 ! INDZ, indolizine, kevo +CG2O1 NG2S0 CG331 42.00 119.50 ! DMF, Dimethylformamide, xxwy +CG2O1 NG2S0 CG3C51 60.00 117.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 NG2S0 CG3C52 60.00 117.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG331 NG2S0 CG331 45.00 121.00 ! DMF, Dimethylformamide, xxwy +CG3C51 NG2S0 CG3C52 100.00 114.20 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 NG2S1 CG2R61 50.00 120.00 ! RESI PACP, FRET AND OTHERS +CG2O1 NG2S1 CG2R64 50.00 120.00 ! 2AMP, 2-amino pyridine, from PACP, p-acetamide-phenol, pyridine, kevo +CG2O1 NG2S1 CG311 50.00 120.00 ! PROT NMA Vib Modes (LK) +CG2O1 NG2S1 CG321 50.00 120.00 ! PROT NMA Vib Modes (LK) +CG2O1 NG2S1 CG331 50.00 120.00 ! PROT NMA Vib Modes (LK) +CG2O1 NG2S1 NG2D1 50.00 115.00 ! HDZ1, hydrazone model cmpd +CG2O1 NG2S1 HGP1 34.00 123.00 ! PROT NMA Vib Modes (LK) +CG2O6 NG2S1 CG321 60.00 120.00 ! DECB, diehtyl carbamate, from DMCB, cacha & kevo & xxwy +CG2O6 NG2S1 CG331 60.00 120.00 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo & xxwy +CG2O6 NG2S1 HGP1 40.00 121.50 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo & xxwy +CG2R61 NG2S1 HGP1 34.00 117.00 ! RESI PACP, FRET AND OTHERS +CG2R64 NG2S1 HGP1 34.00 117.00 ! 2AMP, 2-amino pyridine, from PACP, p-acetamide-phenol, pyridine, kevo +CG311 NG2S1 HGP1 35.00 117.00 ! PROT NMA Vibrational Modes (LK) +CG321 NG2S1 HGP1 35.00 117.00 ! PROT NMA Vibrational Modes (LK) +CG331 NG2S1 HGP1 35.00 117.00 ! PROT NMA Vibrational Modes (LK) +NG2D1 NG2S1 HGP1 34.00 122.00 ! HDZ1, hydrazone model cmpd +CG2O1 NG2S2 HGP1 50.00 120.00 ! PROT his, adm jr. 8/13/90 geometry and vibrations +CG2O6 NG2S2 HGP1 50.00 120.00 ! PROT his, adm jr. 8/13/90 geometry and vibrations NOW UREA ==> re-optimize??? +HGP1 NG2S2 HGP1 23.00 120.00 ! PROT adm jr. 8/13/90 geometry and vibrations +CG2R61 NG2S3 HGP4 60.00 111.60 ! PYRIDINE aminopyridine, adm jr., 7/94 kevo: 120 --> 111.6 +CG2R64 NG2S3 HGP4 40.00 121.50 ! NA Ade h61,h62, C,A,G +CG321 NG2S3 SG3O1 58.70 104.90 ! NESM, N-ethyl-sulfamate, my & kevo +CG321 NG2S3 HGP1 51.80 109.50 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 NG2S3 PG1 110.00 118.30 35.0 2.33 ! NABAKB phosphoramidates +CG331 NG2S3 SG3O1 39.50 103.10 ! NMSM, N-methyl-sulfamate, my +CG331 NG2S3 HGP1 35.00 109.00 ! NABAKB phosphoramidates +CG3C51 NG2S3 PG1 110.00 118.30 35.0 2.33 ! NABAKB phosphoramidates +CG3C51 NG2S3 HGP1 35.00 109.00 ! NABAKB phosphoramidates +PG1 NG2S3 HGP1 30.00 123.60 40.0 2.35 ! NABAKB phosphoramidates +SG3O1 NG2S3 HGP1 47.00 113.10 ! NMSM, N-methyl-sulfamate, my +HGP4 NG2S3 HGP4 31.00 117.00 ! NA Ade C,A,G +CG2D1O NG301 CG2D1O 20.00 114.00 ! NADH, NDPH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D1O NG301 CG3C51 70.00 121.70 ! NADH, NDPH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D2O NG301 CG2D2O 20.00 114.00 ! NADH, NDPH; Kenno: reverted to nadh/ppi, jjp1/adm jr. 7/95 +CG2D2O NG301 CG3C51 70.00 121.70 ! NADH, NDPH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2R61 NG301 CG331 48.00 113.50 ! TMC, trimethylcytosine, yxu; DMAN, N,N-dimethylaniline, kevo +CG2R64 NG301 CG331 48.00 113.50 ! TMC, trimethylcytosine, yxu +CG331 NG301 CG331 42.50 116.00 ! TMC, trimethylcytosine, yxu; DMAN, N,N-dimethylaniline, kevo +CG3AM0 NG301 CG3AM0 53.00 110.90 ! AMINE aliphatic amines +CG2D1O NG311 CG2D1O 20.00 114.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D1O NG311 HGPAM1 39.00 123.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D2O NG311 CG2D2O 20.00 114.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D2O NG311 HGPAM1 39.00 123.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2N1 NG311 CG331 43.00 106.00 ! MGU2, methylguanidine2 +CG2N1 NG311 HGPAM1 45.00 106.00 ! MGU2, methylguanidine2 Kenno: 104 -> 106 +CG2R61 NG311 CG2R61 40.00 109.00 ! FEOZ, phenoxazine, erh +CG2R61 NG311 CG321 55.00 113.00 ! OBTZ, 1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine, xxwy +CG2R61 NG311 SG3O2 35.00 115.00 ! PMSM, N-phenylmethanesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +CG2R61 NG311 HGP1 40.00 114.00 ! PMSM, N-phenylmethanesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +CG2R61 NG311 HGPAM1 45.00 115.00 ! FEOZ, phenoxazine, erh +CG321 NG311 CG321 40.50 109.60 ! 5UHG, from nmgn, cgenff_compromise, kevo +CG321 NG311 SG3O2 60.00 115.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG321 NG311 HGP1 46.00 111.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG321 NG311 HGPAM1 35.00 111.00 ! compromise between PEI0 on the one hand and OBTZ AOBT on the other hand, kevo & xxwy +CG331 NG311 SG3O2 68.00 114.00 ! MMSM, N-methylmethanesulfonamide; MBSM, N-methylbenzenesulfonamide; xxwy +CG331 NG311 HGP1 42.30 111.50 ! MMSM, N-methylmethanesulfonamide; MBSM, N-methylbenzenesulfonamide; xxwy +CG331 NG311 HGPAM1 45.00 104.00 ! MGU2, methylguanidine2 +CG3AM1 NG311 CG3AM1 40.50 112.20 5.00 2.4217 ! AMINE aliphatic amines +CG3AM1 NG311 HGPAM1 42.10 108.90 5.00 2.0292 ! AMINE aliphatic amines +SG3O2 NG311 HGP1 42.30 113.20 ! MMSM, N-methylmethanesulfonamide and other sulfonamides, xxwy +CG2D1O NG321 HGPAM2 55.00 113.00 ! AMET, ethenamine; mp2-geom, molvib; pram & kevo +CG2D2O NG321 HGPAM2 55.00 113.00 ! AMET, ethenamine; mp2-geom, molvib; pram & kevo +CG2N1 NG321 HGPAM2 55.00 108.00 ! MGU1, methylguanidine +CG2N2 NG321 HGPAM2 50.00 115.80 ! MT2A, fylin +CG321 NG321 HGPAM2 41.00 112.10 ! AMINE aliphatic amines +CG3AM2 NG321 HGPAM2 41.00 112.10 ! AMINE aliphatic amines +CG3C51 NG321 HGPAM2 41.00 112.10 ! AMINE aliphatic amines +SG3O2 NG321 HGP1 49.00 115.00 ! MSAM, methanesulfonamide; BSAM, benzenesulfonamide; xxwy +HGP1 NG321 HGP1 38.00 110.00 ! MSAM, methanesulfonamide; BSAM, benzenesulfonamide; xxwy +HGPAM2 NG321 HGPAM2 42.00 105.85 ! AMINE aliphatic amines kevo: 29.50 -> 42.00 based on MAM1 molvib & AMET scans +HGPAM3 NG331 HGPAM3 41.50 107.10 ! AMINE aliphatic amines kevo: 29.00 -> 41.50 based on MAM1 molvib & AMET scans +CG2R51 NG3C51 CG3C52 45.00 104.80 ! 2PRL, 2-pyrroline, kevo +CG2R51 NG3C51 HGP1 43.00 113.90 ! 2PRL, 2-pyrroline, kevo +CG2R53 NG3C51 CG3C52 40.00 107.00 !x 104.60 77 2IMI, 2-imidazoline C5-N1-C2 d1, kevo +CG2R53 NG3C51 HGP1 43.00 115.60 !~ 117.7 ! 112.5 ! 30 116.5 2IMI, 2-imidazoline H1-N1-C2, kevo +CG2RC0 NG3C51 CG3C52 60.00 106.90 ! INDI, indoline, kevo +CG2RC0 NG3C51 HGP1 41.00 114.50 ! INDI, indoline, kevo +CG3C52 NG3C51 CG3C52 140.00 103.70 !v 102.9 PRLD, pyrrolidine; 105.4 3PRL, 3-pyrroline, kevo +CG3C52 NG3C51 CG3C54 67.00 104.10 ! IMDP, imidazolidine, erh and kevo +CG3C52 NG3C51 NG2R50 47.00 109.00 !~ 107.5 2PRZ, 2-pyrazoline C5-N1-N2, kevo +CG3C52 NG3C51 NG3P2 47.00 103.90 ! PRZP, Pyrazolidine.H+, kevo +CG3C52 NG3C51 HGP1 43.00 112.00 !x 108 PRLD, pyrrolidine; 113 2PRL, 2-pyrroline; 106(v) 3PRL, 3-pyrroline; 117 2IMI, 2-imidazoline; 2PRZ, 2-pyrazoline, kevo +CG3C54 NG3C51 HGP1 50.00 109.25 ! IMDP, imidazolidine, erh and kevo +NG2R50 NG3C51 HGP1 50.00 103.60 !~ 104.9 2PRZ, 2-pyrazoline, kevo +NG3P2 NG3C51 HGP1 56.00 100.60 ! PRZP, Pyrazolidine.H+, kevo +CG2R61 NG3N1 NG3N1 60.00 112.00 ! PHHZ, phenylhydrazine, decrease angle to make HN become out of plane, ed +CG2R61 NG3N1 HGP1 52.00 115.00 ! PHHZ, phenylhydrazine, decrease angle to make HN become out of plane, ed +NG3N1 NG3N1 HGP1 55.00 102.00 ! HDZN, hydrazine, ed +HGP1 NG3N1 HGP1 50.00 102.00 ! HDZN, hydrazine, ed +CG324 NG3P0 CG324 60.00 109.50 26. 2.466 ! LIPID tetraethylammonium, from CG334 NG3P0 CG324 +CG324 NG3P0 CG334 60.00 109.50 26. 2.466 ! LIPID tetramethylammonium +CG334 NG3P0 CG334 60.00 109.50 26. 2.466 ! LIPID tetramethylammonium +CG334 NG3P0 OG311 69.00 100.00 ! TMAOP, Hydroxy(trimethyl)Ammonium, xxwy +CG334 NG3P0 OG312 80.00 112.00 ! TMAO, trimethylamine N-oxide, xxwy & ejd +CG324 NG3P1 CG324 45.00 115.20 ! FLAVOP PIP1,2,3 ! tweaked 115.50 --> 115.20 by kevo +CG324 NG3P1 CG334 45.00 109.50 ! FLAVOP PIP1,2,3 +CG324 NG3P1 HGP2 30.00 110.80 27.00 2.07400 ! FLAVOP PIP1,2,3 +CG334 NG3P1 HGP2 30.00 110.80 27.00 2.07400 ! FLAVOP PIP1,2,3 +CG2R51 NG3P2 CG3C54 85.00 107.00 ! 2PRP, 2-pyrroline.H+, kevo +CG2R51 NG3P2 HGP2 38.00 112.00 ! 2PRP, 2-pyrroline.H+, kevo +CG314 NG3P2 CG324 45.00 115.20 ! 2MRB, Alpha benzyl gamma 2-methyl piperidine, cacha ! tweaked 115.50 --> 115.20 by kevo +CG314 NG3P2 HGP2 30.00 110.80 27.00 2.07400 ! 2MRB, Alpha benzyl gamma 2-methyl piperidine, cacha +CG324 NG3P2 CG324 40.00 115.20 ! PIP, piperidine ! tweaked 115.50 --> 115.20 by kevo +CG324 NG3P2 HGP2 30.00 110.80 27.00 2.07400 ! PIP, piperidine +CG3C53 NG3P2 CG3C54 100.00 111.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 NG3P2 HGP2 33.00 109.50 4.00 2.05600 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C54 NG3P2 CG3C54 104.00 113.00 ! PRLP, pyrrolidine.H+, kevo +CG3C54 NG3P2 NG3C51 135.00 114.20 ! PRZP, Pyrazolidine.H+, kevo +CG3C54 NG3P2 HGP2 33.00 109.50 4.00 2.05600 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG3C51 NG3P2 HGP2 42.00 106.30 ! PRZP, Pyrazolidine.H+, kevo +HGP2 NG3P2 HGP2 51.00 107.50 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG314 NG3P3 HGP2 30.00 109.50 20.00 2.07400 ! PROT new stretch and bend; methylammonium (KK 03/10/92) +CG324 NG3P3 HGP2 30.00 109.50 20.00 2.07400 ! PROT new stretch and bend; methylammonium (KK 03/10/92) +CG334 NG3P3 HGP2 30.00 109.50 20.00 2.07400 ! PROT new stretch and bend; methylammonium (KK 03/10/92) +HGP2 NG3P3 HGP2 44.00 109.50 ! PROT new stretch and bend; methylammonium (KK 03/10/92) +CG2R51 OG2R50 CG2R51 100.00 106.00 ! FURA, furan +CG2R51 OG2R50 CG2R53 140.00 104.00 ! OXAZ, oxazole +CG2R51 OG2R50 CG2RC0 50.00 104.00 ! ZFUR, benzofuran, kevo +CG2R51 OG2R50 NG2R50 150.00 108.50 ! ISOX, isoxazole @@@@@ Kenno: 109.9 --> 108.5 @@@@@ +CG2R53 OG2R50 NG2R50 165.00 109.30 ! OXD4, oxadiazole124, xxwy +CG2D1O OG301 CG331 53.00 109.00 ! MOET, Methoxyethene, xxwy +CG2D2O OG301 CG331 53.00 109.00 ! MOET, Methoxyethene, xxwy +CG2R61 OG301 CG2R61 185.00 120.00 ! BIPHENYL ANALOGS, peml +CG2R61 OG301 CG321 65.00 108.00 ! ETOB, Ethoxybenzene, cacha +CG2R61 OG301 CG331 65.00 108.00 ! MEOB, Methoxybenzene, cacha +CG301 OG301 CG331 95.00 109.70 ! AMOL, alpha-methoxy-lactic acid, og +CG311 OG301 CG331 95.00 109.70 ! all34_ethers_1a CC33A OC30A CC32A, gk or og (not affected by mistake) +CG321 OG301 CG321 95.00 109.70 ! diethylether, alex +CG321 OG301 CG331 95.00 109.70 ! diethylether, alex +CG331 OG301 CG331 95.00 109.70 ! diethylether, alex!from CG321 OG301 CCT2, DME viv +CG331 OG301 CG3C51 65.00 107.00 ! THF2, THF-2'OMe c2'-om-cm, from Nucl. Acids, ed +CG2O2 OG302 CG301 40.00 109.60 30.00 2.2651 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha +CG2O2 OG302 CG311 40.00 109.60 30.00 2.2651 ! LIPID methyl acetate +CG2O2 OG302 CG321 40.00 109.60 30.00 2.2651 ! LIPID methyl acetate +CG2O2 OG302 CG331 40.00 109.60 30.00 2.2651 ! LIPID methyl acetate +CG2O6 OG302 CG321 40.00 111.00 ! DECB, diehtyl carbamate, from DMCB, cacha & kevo & xxwy +CG2O6 OG302 CG331 40.00 111.00 ! DMCB & DMCA, dimethyl carbamate & carbonate, cacha & kevo & xxwy +CG2R61 OG303 PG1 90.00 120.00 20.00 2.30 ! PROTNA phenol phosphate, 6/94, adm jr. +CG2R61 OG303 SG3O2 33.00 108.00 ! PMST, phenyl methanesulfonate, PSMT, phenyl sulfamate, xxwy +CG311 OG303 PG2 20.00 120.00 35.00 2.33 ! NA IP_2 +CG321 OG303 PG1 20.00 120.00 35.00 2.33 ! NA !Reorganization: PC and others +CG321 OG303 PG2 20.00 120.00 35.00 2.33 ! NA !Reorganization: TH5P and others +CG321 OG303 SG3O1 15.00 109.00 27.00 1.90 ! LIPID methylsulfate +CG331 OG303 PG0 20.00 120.00 35.0 2.33 ! LIPID phosphate !Reorganization:MP_0 +CG331 OG303 PG1 20.00 120.00 35.0 2.33 ! LIPID phosphate !Reorganization:MP_1 +CG331 OG303 PG2 20.00 120.00 35.0 2.33 ! LIPID phosphate !Reorganization:MP_2 +CG331 OG303 SG3O1 15.00 109.00 27.00 1.90 ! LIPID methylsulfate +CG331 OG303 SG3O2 48.00 113.00 ! MMST, methyl methanesulfonate, xxwy +CG3C51 OG303 PG1 20.00 120.00 35.0 2.33 ! BPNP and others +CG3C51 OG303 PG2 20.00 120.00 35.0 2.33 ! TH3P and others +PG1 OG304 PG1 45.00 143.00 40.0 3.25 ! PPI2, METP reorganization, kevo +PG1 OG304 PG2 45.00 139.50 40.0 3.05 ! PPI1, METP reorganization, kevo +CG2O2 OG311 HGP1 55.00 115.00 ! PROT adm jr. 5/02/91, acetic acid pure solvent +CG2O6 OG311 HGP1 61.00 116.00 ! CO31, bicarbonate, xxwy +CG2R61 OG311 HGP1 65.00 108.00 ! PROT JES 8/25/89 phenol +CG301 OG311 HGP1 50.00 106.00 ! AMOL, alpha-methoxy-lactic acid, og +CG311 OG311 HGP1 50.00 106.00 ! og 1/06 EtOH IR fit; was 57.5 106 +CG321 OG311 HGP1 50.00 106.00 ! sng mod (qm and crystal data); was 57.5 106 +CG331 OG311 HGP1 57.50 106.00 ! Team Sugar, HCP1M OC311M CC331M; unchanged +CG3C51 OG311 HGP1 50.00 109.00 ! par_Sugars, CC315x OC311 HCP1; was 57.5 106 +NG3P0 OG311 HGP1 60.00 101.50 ! TMAOP, Hydroxy(trimethyl)Ammonium, xxwy +PG0 OG311 HGP1 30.00 115.00 40.00 2.3500 ! NA MP_1, ADM Jr. !Reorganization:MP_0 +PG1 OG311 HGP1 30.00 115.00 40.00 2.3500 ! NA MP_1, ADM Jr. !Reorganization:MP_1 +CG3C31 OG3C31 CG3C31 50.35 97.00 ! 1EOX, 1-ethylene oxide, sc +CG2R51 OG3C51 CG2R53 85.00 104.00 ! A2FO, 3H-furan-2-one, ctsai +CG2R51 OG3C51 CG3C52 125.00 104.40 ! 2DHF, 2,3-dihydrofuran, kevo +CG2R53 OG3C51 CG3C52 90.00 107.10 ! GBL, Gamma-butyrolactone, ctsai +CG2RC0 OG3C51 CG3C52 76.00 108.05 !107.15 ZDOL, 1,3-benzodioxole, kevo +CG3C51 OG3C51 CG3C51 95.00 111.00 ! THF 10/21/05, viv +CG3C51 OG3C51 CG3C52 95.00 111.00 ! THF 10/21/05, viv +CG3C51 OG3C51 CG3C53 110.00 108.00 ! NA +CG3C52 OG3C51 CG3C52 95.00 111.00 ! THF 10/21/05, viv +CG3C52 OG3C51 CG3RC1 170.00 109.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol, xxwy +CG321 OG3C61 CG321 95.00 109.70 ! DIOX, dioxane +CG2D1O OG3R60 CG2D1O 40.00 99.00 ! PY01, 4h-pyran, maintain 720 in ring +CG2D1O OG3R60 CG321 20.00 99.00 ! PY02, 2h-pyran +CG2D2O OG3R60 CG2D2O 40.00 99.00 ! PY01, 4h-pyran, maintain 720 in ring +CG2D2O OG3R60 CG321 20.00 99.00 ! PY02, 2h-pyran +CG2R61 OG3R60 CG2R61 40.00 115.00 ! FEOZ, phenoxazine, erh +CG2R62 OG3R60 CG2R63 102.00 126.50 ! RIN, coumarin, isg +!HGTIP3 OGTIP3 HGTIP3 55.00 104.52 ! PROT TIP3P GEOMETRY, ADM JR. +OG2P1 PG0 OG303 98.90 111.60 ! LIPID phosphate !Reorganization:MP_0 RE-OPTIMIZE! +OG2P1 PG0 OG311 98.90 108.23 ! NA MP_1, ADM Jr. !Reorganization:MP_0 RE-OPTIMIZE! +OG303 PG0 OG311 48.10 108.00 ! NA MP_1, ADM Jr. !Reorganization:MP_0 RE-OPTIMIZE! +OG311 PG0 OG311 98.90 104.00 ! NA MP_0, ADM Jr. +CG312 PG1 OG2P1 98.90 94.00 ! BDFP, Difuorobenzylphosphonate \ re-optimize? +CG312 PG1 OG311 90.10 90.00 ! BDFP, BDFD, Difuorobenzylphosphonate +CG321 PG1 OG2P1 98.90 103.00 ! BDFP, Benzylphosphonate \ re-optimize? +CG321 PG1 OG311 90.10 94.00 ! BDFP, BDFD, Benzylphosphonate +NG2S3 PG1 OG2P1 140.00 110.60 ! NABAKB phosphoramidates +NG2S3 PG1 OG303 60.00 103.20 ! NABAKB phosphoramidates +OG2P1 PG1 OG2P1 104.00 120.00 ! MP_1 reorganization, kevo +OG2P1 PG1 OG303 98.90 107.50 ! MP_1 reorganization, kevo +OG2P1 PG1 OG304 88.90 111.60 ! NA nad/ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1, PPI2 +OG2P1 PG1 OG311 98.90 111.00 ! MP_1 reorganization, kevo +OG303 PG1 OG303 80.00 104.30 ! NA DMP, ADM Jr. !Reorganization: PC and others +OG303 PG1 OG304 48.10 105.00 ! PPI1, PPI2, METP reorganization, kevo +OG303 PG1 OG311 48.10 108.00 ! MP_1 reorganization, kevo +OG304 PG1 OG304 48.10 107.50 ! METP reorganization, kevo +OG304 PG1 OG311 48.10 111.00 ! PPI2 reorganization, kevo +CG312 PG2 OG2P1 98.90 94.00 ! BDFD, Difuorobenzylphosphonate / re-optimize? +CG321 PG2 OG2P1 98.90 103.00 ! BDFD, Benzylphosphonate / re-optimize? +OG2P1 PG2 OG2P1 104.00 121.00 ! MP_2 reorganization, kevo +OG2P1 PG2 OG303 88.90 111.00 ! MP_2 reorganization, kevo +OG2P1 PG2 OG304 88.90 111.60 ! NA nad/ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1, PPI2 +CG2R51 SG2R50 CG2R51 105.00 95.00 ! THIP, thiophene +CG2R51 SG2R50 CG2R53 110.00 97.00 ! THAZ, thiazole @@@@@ Kenno: 95 --> 97 @@@@@ +CG2R51 SG2R50 CG2RC0 70.00 99.50 ! ZTHP, benzothiophene, kevo +CG2R51 SG2R50 NG2R50 150.00 103.00 ! ISOT, isothiazole +CG2R53 SG2R50 CG2RC0 110.00 97.00 ! ZTHZ, benzothiazole, kevo +CG321 SG301 SG301 72.50 103.30 ! PROT expt. dimethyldisulfide, 3/26/92 (FL) +CG331 SG301 SG301 72.50 103.30 ! PROT expt. dimethyldisulfide, 3/26/92 (FL) +CG251O SG311 CG2R53 75.00 92.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O SG311 CG2R53 75.00 92.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2N2 SG311 CG321 59.00 94.70 ! DH3T, transferred from MT2A , fylin +CG2N2 SG311 CG331 59.00 94.70 ! MT2A, fylin +CG2O6 SG311 CG331 60.00 96.00 ! DMTT, dimethyl trithiocarbonate, kevo +CG2R61 SG311 CG2R61 50.00 109.00 ! FETZ, phenothiazine, erh +CG2R64 SG311 CG331 66.00 91.00 ! 2SMPYR, 2-(methylthio)-pyrimidine; from CG2O6 SG311 CG331; isg (may need to be re-evaluated because yxu got "a QM value of 100.8" for RESI 2MSA) +CG321 SG311 CG321 34.00 95.00 ! PROTNA sahc +CG321 SG311 CG331 34.00 95.00 ! PROT expt. MeEtS, 3/26/92 (FL) +CG321 SG311 HGP3 38.80 95.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG331 SG311 HGP3 43.00 95.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG2R61 SG3O1 OG2P1 85.0 98.0 ! benzene sulfonic acid anion, og +CG321 SG3O1 OG2P1 80.00 99.00 ! ESNA, ethyl sulfonate, xhe +CG331 SG3O1 OG2P1 85.00 100.00 ! MSNA, methyl sulfonate, xhe +NG2S3 SG3O1 OG2P1 33.20 94.20 ! NMSM, N-methyl-sulfamate, my +OG2P1 SG3O1 OG2P1 130.00 109.47 35.0 2.45 ! LIPID methylsulfate +OG2P1 SG3O1 OG303 85.00 98.00 ! LIPID methylsulfate +CG2R61 SG3O2 NG311 70.00 97.00 ! MBSM, N-methylbenzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +CG2R61 SG3O2 NG321 60.00 98.00 ! BSAM, benzenesulfonamide, xxwy +CG2R61 SG3O2 OG2P1 60.00 101.00 ! BSAM, benzenesulfonamide, xxwy +CG321 SG3O2 CG331 80.00 102.00 ! MESN, methyl ethyl sulfone, xhe +CG321 SG3O2 NG311 62.00 101.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG321 SG3O2 OG2P1 75.00 107.50 ! EESM, N-ethylethanesulfonamide; MESN, methyl ethyl sulfone; xxwy & xhe +CG331 SG3O2 CG331 80.00 102.00 ! DMSN, dimethyl sulfone, xhe +CG331 SG3O2 NG311 73.00 103.00 ! MMSM, N-methylmethanesulfonamide; PMSM, N-phenylmethanesulfonamide; xxwy +CG331 SG3O2 NG321 83.00 101.00 ! MSAM, methanesulfonamide, xxwy +CG331 SG3O2 OG2P1 79.00 108.50 ! DMSN, dimethyl sulfone; MSAM, methanesulfonamide and other sulfonamides; xxwy & xhe +CG331 SG3O2 OG303 93.00 96.00 ! MMST, methyl methanesulfonate, xxwy +NG311 SG3O2 NG311 83.10 102.30 ! MESI, N-methyl,N'-ethylsulfamide, rting +NG311 SG3O2 OG2P1 75.00 110.50 ! MMSM, N-methylmethanesulfonamide and other sulfonamides, xxwy +NG321 SG3O2 OG2P1 80.00 111.00 ! MSAM, methanesulfonamide; BSAM, benzenesulfonamide; xxwy +NG321 SG3O2 OG303 100.00 102.00 ! MSMT, methyl sulfamate, & PSMT, xxwy +OG2P1 SG3O2 OG2P1 85.00 121.00 ! DMSN, dimethyl sulfone; MSAM, methanesulfonamide and other sulfonamides; xxwy & xhe +OG2P1 SG3O2 OG303 90.00 109.00 ! MMST, methyl methanesulfonate, xxwy +CG321 SG3O3 CG331 85.00 95.00 ! MESO, methylethylsulfoxide, mnoon +CG321 SG3O3 OG2P1 65.00 106.50 ! MESO, methylethylsulfoxide, mnoon +CG331 SG3O3 CG331 34.00 95.00 ! DMSO, dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz +CG331 SG3O3 OG2P1 79.00 106.75 ! DMSO, dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz +FGP1 ALG1 FGP1 23.00 109.47 15.0 2.81855 ! aluminum tetrafluoride, ALF4, tetrahedral + +DIHEDRALS +!HGA3 CG1T1 CG1T1 HGA3 0.0005 3 180.00 !!Just a test! 2BTY, 2-butyne, kevo +CG2R53 CG251O CG25C1 CG2R53 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2R53 CG251O CG25C1 CG2RC0 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +NG2R53 CG251O CG25C1 CG2R53 3.4000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +NG2R53 CG251O CG25C1 CG2RC0 3.4000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +SG311 CG251O CG25C1 CG2R53 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +SG311 CG251O CG25C1 CG2RC0 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2R53 CG251O CG2DC3 HGA5 3.9000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R53 CG251O CG2DC3 HGA5 4.6000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +SG311 CG251O CG2DC3 HGA5 5.3000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG25C1 CG251O CG2R53 NG2R53 5.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG25C1 CG251O CG2R53 OG2D1 4.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG251O CG2R53 NG2R53 0.2000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2DC3 CG251O CG2R53 OG2D1 0.8000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R53 CG251O CG2R53 NG2R53 0.2000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +NG2R53 CG251O CG2R53 OG2D1 4.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +SG311 CG251O CG2R53 NG2R53 1.2000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG311 CG251O CG2R53 OG2D1 0.8000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG25C1 CG251O NG2R53 CG2R53 4.0000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +CG25C1 CG251O NG2R53 HGP1 0.4000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +CG2DC3 CG251O NG2R53 CG2R53 1.0000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2DC3 CG251O NG2R53 HGP1 0.4000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2R53 CG251O NG2R53 CG2R53 0.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2R53 CG251O NG2R53 HGP1 0.4000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +CG25C1 CG251O SG311 CG2R53 4.0000 3 0.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG251O SG311 CG2R53 0.2000 3 0.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 CG251O SG311 CG2R53 1.2000 3 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 CG252O CG25C2 CG2R53 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2R53 CG252O CG25C2 CG2RC0 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +NG2R53 CG252O CG25C2 CG2R53 3.4000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +NG2R53 CG252O CG25C2 CG2RC0 3.4000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +SG311 CG252O CG25C2 CG2R53 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +SG311 CG252O CG25C2 CG2RC0 6.4000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2R53 CG252O CG2DC3 HGA5 3.9000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R53 CG252O CG2DC3 HGA5 4.6000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +SG311 CG252O CG2DC3 HGA5 5.3000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG25C2 CG252O CG2R53 NG2R53 5.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG25C2 CG252O CG2R53 OG2D1 4.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG252O CG2R53 NG2R53 0.2000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2DC3 CG252O CG2R53 OG2D1 0.8000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R53 CG252O CG2R53 NG2R53 0.2000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +NG2R53 CG252O CG2R53 OG2D1 4.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +SG311 CG252O CG2R53 NG2R53 1.2000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG311 CG252O CG2R53 OG2D1 0.8000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG25C2 CG252O NG2R53 CG2R53 4.0000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +CG25C2 CG252O NG2R53 HGP1 0.4000 2 180.00 ! OIHY, 5-(oxindol-3-ylidene)hydantoin, complete ring system, xxwy +CG2DC3 CG252O NG2R53 CG2R53 1.0000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2DC3 CG252O NG2R53 HGP1 0.4000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2R53 CG252O NG2R53 CG2R53 0.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +CG2R53 CG252O NG2R53 HGP1 0.4000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +CG25C2 CG252O SG311 CG2R53 4.0000 3 0.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG252O SG311 CG2R53 0.2000 3 0.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 CG252O SG311 CG2R53 1.2000 3 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R53 CG25C1 CG2DC3 HGA5 4.4000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2RC0 CG25C1 CG2DC3 HGA5 4.4000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG251O CG25C1 CG2R53 NG2R51 3.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG251O CG25C1 CG2R53 OG2D1 4.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG25C1 CG2R53 NG2R51 0.1000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2DC3 CG25C1 CG2R53 OG2D1 1.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2RC0 CG25C1 CG2R53 NG2R51 1.2000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2RC0 CG25C1 CG2R53 OG2D1 1.2000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG251O CG25C1 CG2RC0 CG2R61 4.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG251O CG25C1 CG2RC0 CG2RC0 4.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG25C1 CG2RC0 CG2R61 0.1000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2DC3 CG25C1 CG2RC0 CG2RC0 0.1000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R53 CG25C1 CG2RC0 CG2R61 3.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R53 CG25C1 CG2RC0 CG2RC0 3.5000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R53 CG25C2 CG2DC3 HGA5 4.4000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2RC0 CG25C2 CG2DC3 HGA5 4.4000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG252O CG25C2 CG2R53 NG2R51 3.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG252O CG25C2 CG2R53 OG2D1 4.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG25C2 CG2R53 NG2R51 0.1000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2DC3 CG25C2 CG2R53 OG2D1 1.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2RC0 CG25C2 CG2R53 NG2R51 1.2000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2RC0 CG25C2 CG2R53 OG2D1 1.2000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG252O CG25C2 CG2RC0 CG2R61 4.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG252O CG25C2 CG2RC0 CG2RC0 4.0000 2 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy +CG2DC3 CG25C2 CG2RC0 CG2R61 0.1000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2DC3 CG25C2 CG2RC0 CG2RC0 0.1000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R53 CG25C2 CG2RC0 CG2R61 3.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R53 CG25C2 CG2RC0 CG2RC0 3.5000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG301 CG2D1 CG2D1 CG321 0.4500 1 180.00 ! CHL1, cholesterol +CG301 CG2D1 CG2D1 CG321 8.5000 2 180.00 ! CHL1, cholesterol +CG301 CG2D1 CG2D1 CG331 10.0000 2 180.00 ! RETINOL TMCH +CG301 CG2D1 CG2D1 HGA4 1.0000 2 180.00 ! LIPID 2-butene, adm jr., 8/98 update +CG321 CG2D1 CG2D1 CG321 0.4500 1 180.00 ! LIPID 2-butene, adm jr., 4/04 +CG321 CG2D1 CG2D1 CG321 8.5000 2 180.00 ! LIPID +CG321 CG2D1 CG2D1 CG331 0.4500 1 180.00 ! LIPID 2-butene, adm jr., 4/04 +CG321 CG2D1 CG2D1 CG331 8.5000 2 180.00 ! LIPID +CG321 CG2D1 CG2D1 HGA4 1.0000 2 180.00 ! LIPID 2-butene, adm jr., 8/98 update +CG331 CG2D1 CG2D1 CG331 0.4500 1 180.00 ! LIPID 2-butene, adm jr., 4/04 +CG331 CG2D1 CG2D1 CG331 8.5000 2 180.00 ! LIPID +CG331 CG2D1 CG2D1 HGA4 1.0000 2 180.00 ! LIPID 2-butene, adm jr., 8/98 update +HGA4 CG2D1 CG2D1 HGA4 1.0000 2 180.00 ! LIPID 2-butene, adm jr., 8/98 update +CG321 CG2D1 CG2D1O NG301 3.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +CG321 CG2D1 CG2D1O NG311 3.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +CG321 CG2D1 CG2D1O OG3R60 3.0000 2 180.00 ! PY01, 4h-pyran +CG321 CG2D1 CG2D1O HGA4 6.0000 2 180.00 ! PY01, 4h-pyran +HGA4 CG2D1 CG2D1O NG301 1.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +HGA4 CG2D1 CG2D1O NG311 1.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +HGA4 CG2D1 CG2D1O OG3R60 8.0000 2 180.00 ! PY01, 4h-pyran +HGA4 CG2D1 CG2D1O HGA4 1.0000 2 180.00 ! PY01, 4h-pyran +CG321 CG2D1 CG2D2 HGA5 5.2000 2 180.00 ! LIPID propene, yin,adm jr., 12/95 +CG331 CG2D1 CG2D2 HGA5 5.2000 2 180.00 ! LIPID propene, yin,adm jr., 12/95 +HGA4 CG2D1 CG2D2 HGA5 5.2000 2 180.00 ! LIPID propene, yin,adm jr., 12/95 +CG321 CG2D1 CG2D2O NG301 3.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +CG321 CG2D1 CG2D2O NG311 3.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +CG321 CG2D1 CG2D2O OG3R60 3.0000 2 180.00 ! PY01, 4h-pyran +CG321 CG2D1 CG2D2O HGA4 6.0000 2 180.00 ! PY01, 4h-pyran +HGA4 CG2D1 CG2D2O NG301 1.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +HGA4 CG2D1 CG2D2O NG311 1.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +HGA4 CG2D1 CG2D2O OG3R60 8.0000 2 180.00 ! PY01, 4h-pyran +HGA4 CG2D1 CG2D2O HGA4 1.0000 2 180.00 ! PY01, 4h-pyran +CG2D1 CG2D1 CG301 CG311 0.5000 1 180.00 ! CHOLEST cholesterol +CG2D1 CG2D1 CG301 CG311 1.3000 3 180.00 ! CHOLEST cholesterol +CG2D1 CG2D1 CG301 CG321 0.5000 1 180.00 ! CHOLEST cholesterol +CG2D1 CG2D1 CG301 CG321 1.3000 3 180.00 ! CHOLEST cholesterol +CG2D1 CG2D1 CG301 CG331 0.5000 1 180.00 ! CHOLEST cholesterol +CG2D1 CG2D1 CG301 CG331 1.3000 3 180.00 ! CHOLEST cholesterol +CG321 CG2D1 CG301 CG311 0.0000 3 180.00 ! CHOLEST cholesterol +CG321 CG2D1 CG301 CG321 0.3000 3 180.00 ! CHOLEST cholesterol +CG321 CG2D1 CG301 CG331 0.0000 3 180.00 ! CHOLEST cholesterol +CG331 CG2D1 CG301 CG321 0.4000 3 0.00 ! RETINOL TMCH +CG331 CG2D1 CG301 CG331 0.4000 3 0.00 ! RETINOL TMCH +CG2D1 CG2D1 CG321 CG2D1 1.0000 1 180.00 ! LIPID 2,5-diheptane +CG2D1 CG2D1 CG321 CG2D1 0.1000 2 0.00 ! LIPID 2,5-diheptane +CG2D1 CG2D1 CG321 CG2D1 0.3000 3 180.00 ! LIPID 2,5-diheptane +CG2D1 CG2D1 CG321 CG2D1 0.2000 4 0.00 ! LIPID 2,5-diheptane +CG2D1 CG2D1 CG321 CG311 0.5000 1 180.00 ! CHOLEST cholesterol +CG2D1 CG2D1 CG321 CG311 1.3000 3 180.00 ! CHOLEST cholesterol +CG2D1 CG2D1 CG321 CG321 0.6000 1 180.00 ! LIPID alkenes +CG2D1 CG2D1 CG321 CG331 0.9000 1 180.00 ! LIPID alkenes +CG2D1 CG2D1 CG321 CG331 0.2000 2 180.00 ! LIPID alkenes +CG2D1 CG2D1 CG321 HGA2 0.3000 3 180.00 ! LIPID alkenes +CG2D1O CG2D1 CG321 CG2D1 0.5000 2 0.00 ! PY01, 4h-pyran +CG2D1O CG2D1 CG321 CG2D1 0.4500 4 0.00 ! PY01, 4h-pyran +CG2D1O CG2D1 CG321 CG2DC1 0.0000 3 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG2D1O CG2D1 CG321 HGA2 0.1000 3 0.00 ! PY01, 4h-pyran +CG2D2 CG2D1 CG321 CG2D1 1.2000 1 180.00 ! LIPID 1,4-dipentene +CG2D2 CG2D1 CG321 CG2D1 0.4000 2 180.00 ! LIPID 1,4-dipentene +CG2D2 CG2D1 CG321 CG2D1 1.3000 3 180.00 ! LIPID 1,4-dipentene +CG2D2 CG2D1 CG321 CG331 0.5000 1 180.00 ! LIPID 1-butene, adm jr., 2/00 update +CG2D2 CG2D1 CG321 CG331 1.3000 3 180.00 ! LIPID 1-butene, adm jr., 2/00 update +CG2D2 CG2D1 CG321 OG311 1.9000 1 180.00 ! RETINOL PROL +CG2D2 CG2D1 CG321 OG311 0.4000 2 180.00 ! RETINOL PROL +CG2D2 CG2D1 CG321 OG311 0.6000 3 180.00 ! RETINOL PROL +CG2D2 CG2D1 CG321 HGA2 0.1200 3 0.00 ! LIPID 1-butene, yin,adm jr., 12/95 +CG2D2O CG2D1 CG321 CG2D1 0.5000 2 0.00 ! PY01, 4h-pyran +CG2D2O CG2D1 CG321 CG2D1 0.4500 4 0.00 ! PY01, 4h-pyran +CG2D2O CG2D1 CG321 CG2DC2 0.0000 3 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG2D2O CG2D1 CG321 HGA2 0.1000 3 0.00 ! PY01, 4h-pyran +CG301 CG2D1 CG321 CG311 0.3000 3 180.00 ! CHOLEST cholesterol +CG301 CG2D1 CG321 HGA2 0.0300 3 0.00 ! CHOLEST cholesterol +CG331 CG2D1 CG321 CG321 0.1900 3 0.00 ! RETINOL TMCH +CG331 CG2D1 CG321 HGA2 0.1900 3 0.00 ! RETINOL TMCH +HGA4 CG2D1 CG321 CG2D1 0.0000 3 0.00 ! LIPID 1,4-dipentene +HGA4 CG2D1 CG321 CG2DC1 0.0000 3 0.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +HGA4 CG2D1 CG321 CG2DC2 0.0000 3 0.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +HGA4 CG2D1 CG321 CG311 0.0000 3 0.00 ! CHOLEST cholesterol +HGA4 CG2D1 CG321 CG321 0.1200 3 0.00 ! LIPID butene, yin,adm jr., 12/95 +HGA4 CG2D1 CG321 CG331 0.1200 3 0.00 ! LIPID butene, yin,adm jr., 12/95 +HGA4 CG2D1 CG321 OG311 0.2000 3 0.00 ! RETINOL PROL +HGA4 CG2D1 CG321 HGA2 0.0000 3 0.00 ! LIPID butene, adm jr., 2/00 update +CG2D1 CG2D1 CG331 HGA3 0.3000 3 180.00 ! LIPID alkenes +CG2D2 CG2D1 CG331 HGA3 0.0500 3 180.00 ! LIPID propene, yin,adm jr., 12/95 +CG301 CG2D1 CG331 HGA3 0.1600 3 0.00 ! RETINOL TMCH +CG321 CG2D1 CG331 HGA3 0.1600 3 0.00 ! RETINOL TMCH +NG2D1 CG2D1 CG331 HGA3 0.1000 3 180.00 ! RETINOL SCH1, Schiff's base, deprotonated +NG2P1 CG2D1 CG331 HGA3 0.1500 3 180.00 ! RETINOL SCH2, Schiff's base, protonated +HGA4 CG2D1 CG331 HGA3 0.0000 3 0.00 ! LIPID butene, adm jr., 2/00 update +HGR52 CG2D1 CG331 HGA3 0.1500 3 0.00 ! RETINOL SCH2, Schiff's base, protonated +CG331 CG2D1 NG2D1 CG321 12.0000 2 180.00 ! EEPI, from CG331 CG2D1 NG2D1 CG331, fylin +CG331 CG2D1 NG2D1 CG331 12.0000 2 180.00 ! RETINOL SCH1, Schiff's base, deprotonated +CG331 CG2D1 NG2D1 NG2S1 12.0000 2 180.00 ! HDZ1, hydrazone model cmpd +HGA4 CG2D1 NG2D1 CG321 8.5000 2 180.00 ! EEPI, from HGA4 CG2D1 NG2D1 CG331, fylin +HGA4 CG2D1 NG2D1 CG331 8.5000 2 180.00 ! RETINOL SCH1, Schiff's base, deprotonated +HGA4 CG2D1 NG2D1 NG2S1 4.0000 2 180.00 ! HDZ1, hydrazone model cmpd +CG331 CG2D1 NG2P1 CG334 7.0000 2 180.00 ! RETINOL SCH2, Schiff's base, protonated +CG331 CG2D1 NG2P1 HGP2 5.0000 2 180.00 ! RETINOL SCH2, Schiff's base, protonated +HGR52 CG2D1 NG2P1 CG334 8.5000 2 180.00 ! RETINOL SCH2, Schiff's base, protonated +HGR52 CG2D1 NG2P1 HGP2 5.0000 2 180.00 ! RETINOL SCH2, Schiff's base, protonated +NG321 CG2D1O CG2D2 HGA5 2.0000 2 180.00 ! AMET, ethenamine, 1.0->2.0 to improve molvib; pram +OG301 CG2D1O CG2D2 HGA5 9.0000 2 180.00 ! MOET, Methoxyethene, xxwy +HGA4 CG2D1O CG2D2 HGA5 2.0000 2 180.00 ! MOET, Methoxyethene, xxwy +NG301 CG2D1O CG2DC1 CG2O1 2.5000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +NG301 CG2D1O CG2DC1 CG321 2.5000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +NG311 CG2D1O CG2DC1 CG2O1 2.5000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +NG311 CG2D1O CG2DC1 CG321 2.5000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +OG301 CG2D1O CG2DC1 CG2DC2 1.5000 1 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +OG301 CG2D1O CG2DC1 CG2DC2 15.0000 2 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +OG301 CG2D1O CG2DC1 HGA4 3.0000 2 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +OG3R60 CG2D1O CG2DC1 CG2DC2 2.0000 2 180.00 ! PY02, 2h-pyran +OG3R60 CG2D1O CG2DC1 HGA4 7.0000 2 180.00 ! PY02, 2h-pyran +HGA4 CG2D1O CG2DC1 CG2DC2 6.0000 2 180.00 ! PY02, 2h-pyran +HGA4 CG2D1O CG2DC1 CG2O1 1.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +HGA4 CG2D1O CG2DC1 CG321 1.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +HGA4 CG2D1O CG2DC1 HGA4 2.5000 2 180.00 ! PY02, 2h-pyran +CG2D1 CG2D1O NG301 CG2D1O 0.1000 2 180.00 ! NADH, NDPH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D1O NG301 CG3C51 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2DC1 CG2D1O NG301 CG2D1O 0.5000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +CG2DC1 CG2D1O NG301 CG3C51 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +HGA4 CG2D1O NG301 CG2D1O 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +HGA4 CG2D1O NG301 CG3C51 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D1O NG311 CG2D1O 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D1O NG311 HGPAM1 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2DC1 CG2D1O NG311 CG2D1O 0.5000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +CG2DC1 CG2D1O NG311 HGPAM1 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +HGA4 CG2D1O NG311 CG2D1O 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +HGA4 CG2D1O NG311 HGPAM1 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D2 CG2D1O NG321 HGPAM2 1.7000 1 0.00 ! 1.66 w/o 4-fold; AMET, ethenamine, lsfitdih run 9 w 113, kevo +CG2D2 CG2D1O NG321 HGPAM2 3.0600 2 180.00 ! 3.02 w/o 4-fold; AMET, ethenamine, lsfitdih run 9 w 113, kevo +CG2D2 CG2D1O NG321 HGPAM2 0.2300 3 180.00 ! 0.24 w/o 4-fold; AMET, ethenamine, lsfitdih run 9 w 113, kevo +CG2D2 CG2D1O NG321 HGPAM2 0.1200 4 0.00 ! needed for OOP but poorly transferable; AMET, ethenamine, lsfitdih run 9 w 113, kevo +HGA4 CG2D1O NG321 HGPAM2 0.1600 3 0.00 ! AMET, ethenamine; from MAM1, methylamine; kevo +CG2D2 CG2D1O OG301 CG331 0.9000 1 180.00 ! MOET, Methoxyethene, xxwy +CG2D2 CG2D1O OG301 CG331 3.1000 2 180.00 ! MOET, Methoxyethene, xxwy +CG2D2 CG2D1O OG301 CG331 1.2000 3 180.00 ! MOET, Methoxyethene, xxwy +CG2DC1 CG2D1O OG301 CG331 0.8000 1 180.00 ! MOET, Methoxyethene, xxwy +CG2DC1 CG2D1O OG301 CG331 3.0000 2 180.00 ! MOET, Methoxyethene, xxwy +CG2DC1 CG2D1O OG301 CG331 1.1000 3 180.00 ! MOET, Methoxyethene, xxwy +HGA4 CG2D1O OG301 CG331 0.0000 2 180.00 ! MOET, Methoxyethene, xxwy +CG2D1 CG2D1O OG3R60 CG2D1O 3.0000 2 180.00 ! PY01, 4h-pyran seems reasonable - kevo +CG2D1 CG2D1O OG3R60 CG2D2O 3.0000 2 180.00 ! PY01, 4h-pyran seems reasonable - kevo +CG2DC1 CG2D1O OG3R60 CG321 2.0000 2 0.00 ! PY02, 2h-pyran seems reasonable - kevo +HGA4 CG2D1O OG3R60 CG2D1O 0.0000 2 180.00 ! PY01, 4h-pyran; re-initialized from MOET, Methoxyethene; kevo +HGA4 CG2D1O OG3R60 CG2D2O 0.0000 2 180.00 ! PY01, 4h-pyran; re-initialized from MOET, Methoxyethene; kevo +HGA4 CG2D1O OG3R60 CG321 0.0000 2 180.00 ! PY02, 2h-pyran; re-initialized from MOET, Methoxyethene; kevo +HGA5 CG2D2 CG2D2 HGA5 4.9000 2 180.00 ! LIPID ethene, yin,adm jr., 12/95 +HGA5 CG2D2 CG2D2O NG321 2.0000 2 180.00 ! AMET, ethenamine, 1.0->2.0 to improve molvib; pram +HGA5 CG2D2 CG2D2O OG301 9.0000 2 180.00 ! MOET, Methoxyethene, xxwy +HGA5 CG2D2 CG2D2O HGA4 2.0000 2 180.00 ! MOET, Methoxyethene, xxwy +NG301 CG2D2O CG2DC2 CG2O1 2.5000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +NG301 CG2D2O CG2DC2 CG321 2.5000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +NG311 CG2D2O CG2DC2 CG2O1 2.5000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +NG311 CG2D2O CG2DC2 CG321 2.5000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +OG301 CG2D2O CG2DC2 CG2DC1 1.5000 1 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +OG301 CG2D2O CG2DC2 CG2DC1 15.0000 2 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +OG301 CG2D2O CG2DC2 HGA4 3.0000 2 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +OG3R60 CG2D2O CG2DC2 CG2DC1 2.0000 2 180.00 ! PY02, 2h-pyran +OG3R60 CG2D2O CG2DC2 HGA4 7.0000 2 180.00 ! PY02, 2h-pyran +HGA4 CG2D2O CG2DC2 CG2DC1 6.0000 2 180.00 ! PY02, 2h-pyran +HGA4 CG2D2O CG2DC2 CG2O1 1.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +HGA4 CG2D2O CG2DC2 CG321 1.0000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +HGA4 CG2D2O CG2DC2 HGA4 2.5000 2 180.00 ! PY02, 2h-pyran +CG2D1 CG2D2O NG301 CG2D2O 0.1000 2 180.00 ! NADH, NDPH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D2O NG301 CG3C51 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2DC2 CG2D2O NG301 CG2D2O 0.5000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +CG2DC2 CG2D2O NG301 CG3C51 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +HGA4 CG2D2O NG301 CG2D2O 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +HGA4 CG2D2O NG301 CG3C51 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D2O NG311 CG2D2O 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D1 CG2D2O NG311 HGPAM1 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2DC2 CG2D2O NG311 CG2D2O 0.5000 2 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 0.1 but that's unlikely ==> re-optimize +CG2DC2 CG2D2O NG311 HGPAM1 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +HGA4 CG2D2O NG311 CG2D2O 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +HGA4 CG2D2O NG311 HGPAM1 0.1000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2D2 CG2D2O NG321 HGPAM2 1.7000 1 0.00 ! 1.66 w/o 4-fold; AMET, ethenamine, lsfitdih run 9 w 113, kevo +CG2D2 CG2D2O NG321 HGPAM2 3.0600 2 180.00 ! 3.02 w/o 4-fold; AMET, ethenamine, lsfitdih run 9 w 113, kevo +CG2D2 CG2D2O NG321 HGPAM2 0.2300 3 180.00 ! 0.24 w/o 4-fold; AMET, ethenamine, lsfitdih run 9 w 113, kevo +CG2D2 CG2D2O NG321 HGPAM2 0.1200 4 0.00 ! needed for OOP but poorly transferable; AMET, ethenamine, lsfitdih run 9 w 113, kevo +HGA4 CG2D2O NG321 HGPAM2 0.1600 3 0.00 ! AMET, ethenamine; from MAM1, methylamine; kevo +CG2D2 CG2D2O OG301 CG331 0.9000 1 180.00 ! MOET, Methoxyethene, xxwy +CG2D2 CG2D2O OG301 CG331 3.1000 2 180.00 ! MOET, Methoxyethene, xxwy +CG2D2 CG2D2O OG301 CG331 1.2000 3 180.00 ! MOET, Methoxyethene, xxwy +CG2DC2 CG2D2O OG301 CG331 0.8000 1 180.00 ! MOET, Methoxyethene, xxwy +CG2DC2 CG2D2O OG301 CG331 3.0000 2 180.00 ! MOET, Methoxyethene, xxwy +CG2DC2 CG2D2O OG301 CG331 1.1000 3 180.00 ! MOET, Methoxyethene, xxwy +HGA4 CG2D2O OG301 CG331 0.0000 2 180.00 ! MOET, Methoxyethene, xxwy +CG2D1 CG2D2O OG3R60 CG2D1O 3.0000 2 180.00 ! PY01, 4h-pyran seems reasonable - kevo +CG2D1 CG2D2O OG3R60 CG2D2O 3.0000 2 180.00 ! PY01, 4h-pyran seems reasonable - kevo +CG2DC2 CG2D2O OG3R60 CG321 2.0000 2 0.00 ! PY02, 2h-pyran seems reasonable - kevo +HGA4 CG2D2O OG3R60 CG2D1O 0.0000 2 180.00 ! PY01, 4h-pyran; re-initialized from MOET, Methoxyethene; kevo +HGA4 CG2D2O OG3R60 CG2D2O 0.0000 2 180.00 ! PY01, 4h-pyran; re-initialized from MOET, Methoxyethene; kevo +HGA4 CG2D2O OG3R60 CG321 0.0000 2 180.00 ! PY02, 2h-pyran; re-initialized from MOET, Methoxyethene; kevo +CG2DC2 CG2DC1 CG2DC1 CG2DC2 0.5600 1 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC2 CG2DC1 CG2DC1 CG2DC2 7.0000 2 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC2 CG2DC1 CG2DC1 CG2O1 0.5600 1 180.00 ! RETINOL FRET +CG2DC2 CG2DC1 CG2DC1 CG2O1 7.0000 2 180.00 ! RETINOL FRET +CG2DC2 CG2DC1 CG2DC1 CG2O3 0.5600 1 180.00 ! RETINOL PRAC +CG2DC2 CG2DC1 CG2DC1 CG2O3 7.0000 2 180.00 ! RETINOL PRAC +CG2DC2 CG2DC1 CG2DC1 CG2O4 0.5600 1 180.00 ! RETINOL RTAL unmodified +CG2DC2 CG2DC1 CG2DC1 CG2O4 7.0000 2 180.00 ! RETINOL RTAL unmodified +CG2DC2 CG2DC1 CG2DC1 CG321 0.5600 1 180.00 ! RETINOL MECH +CG2DC2 CG2DC1 CG2DC1 CG321 7.0000 2 180.00 ! RETINOL MECH +CG2DC2 CG2DC1 CG2DC1 CG331 0.5600 1 180.00 ! RETINOL 13DP, 1,3-Pentadiene +CG2DC2 CG2DC1 CG2DC1 CG331 7.0000 2 180.00 ! RETINOL 13DP, 1,3-Pentadiene +CG2DC2 CG2DC1 CG2DC1 HGA4 5.2000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +CG2O1 CG2DC1 CG2DC1 CG331 0.5600 1 180.00 ! RETINOL CROT +CG2O1 CG2DC1 CG2DC1 CG331 7.0000 2 180.00 ! RETINOL CROT +CG2O3 CG2DC1 CG2DC1 CG331 0.5600 1 180.00 ! RETINOL PRAC +CG2O3 CG2DC1 CG2DC1 CG331 7.0000 2 180.00 ! RETINOL PRAC +CG2O4 CG2DC1 CG2DC1 CG331 0.5600 1 180.00 ! RETINOL RTAL +CG2O4 CG2DC1 CG2DC1 CG331 7.0000 2 180.00 ! RETINOL RTAL Kenno: 0.5 -> 7.0 for the sake of transferability +CG301 CG2DC1 CG2DC1 CG321 10.0000 2 180.00 ! RETINOL TMCH +CG301 CG2DC1 CG2DC1 CG331 10.0000 2 180.00 ! RETINOL MECH +CG321 CG2DC1 CG2DC1 CG331 10.0000 2 180.00 ! RETINOL BTE2, 2-butene +CG321 CG2DC1 CG2DC1 HGA4 5.2000 2 180.00 ! PY02, 2h-pyran; re-initialized from BTE2, 2-butene; kevo +CG331 CG2DC1 CG2DC1 HGA4 5.2000 2 180.00 ! RETINOL BTE2, 2-butene +HGA4 CG2DC1 CG2DC1 HGA4 5.2000 2 180.00 ! RETINOL BTE2, 2-butene +CG2D1O CG2DC1 CG2DC2 CG2DC2 1.5000 1 180.00 ! PY02, 2h-pyran; re-initialized from MOBU, 1-Methoxy-1,3-butadiene; xxwy +CG2D1O CG2DC1 CG2DC2 CG2DC2 1.0000 2 180.00 ! PY02, 2h-pyran; re-initialized from MOBU, 1-Methoxy-1,3-butadiene; xxwy +CG2D1O CG2DC1 CG2DC2 CG2DC2 1.5000 3 0.00 ! PY02, 2h-pyran; re-initialized from MOBU, 1-Methoxy-1,3-butadiene; xxwy +CG2D1O CG2DC1 CG2DC2 CG2DC3 1.5000 1 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2D1O CG2DC1 CG2DC2 CG2DC3 1.0000 2 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2D1O CG2DC1 CG2DC2 CG2DC3 1.5000 3 0.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2D1O CG2DC1 CG2DC2 HGA4 1.0000 2 180.00 ! PY02, 2h-pyran; re-initialized from MOBU, 1-Methoxy-1,3-butadiene; xxwy +CG2DC1 CG2DC1 CG2DC2 CG2D2O 1.5000 1 180.00 ! PY02, 2h-pyran; re-initialized from MOBU, 1-Methoxy-1,3-butadiene; xxwy +CG2DC1 CG2DC1 CG2DC2 CG2D2O 1.0000 2 180.00 ! PY02, 2h-pyran; re-initialized from MOBU, 1-Methoxy-1,3-butadiene; xxwy +CG2DC1 CG2DC1 CG2DC2 CG2D2O 1.5000 3 0.00 ! PY02, 2h-pyran; re-initialized from MOBU, 1-Methoxy-1,3-butadiene; xxwy +CG2DC1 CG2DC1 CG2DC2 CG2DC2 0.5000 1 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC1 CG2DC1 CG2DC2 CG2DC2 2.0000 2 0.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC1 CG2DC1 CG2DC2 CG2DC2 1.0000 3 0.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC1 CG2DC1 CG2DC2 CG2DC3 0.5000 1 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC1 CG2DC1 CG2DC2 CG2DC3 2.0000 2 0.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC1 CG2DC1 CG2DC2 CG2DC3 1.0000 3 0.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC1 CG2DC1 CG2DC2 CG301 0.9000 1 0.00 ! RETINOL MECH +CG2DC1 CG2DC1 CG2DC2 CG301 2.1000 2 180.00 ! RETINOL MECH +CG2DC1 CG2DC1 CG2DC2 CG301 0.2200 3 0.00 ! RETINOL MECH +CG2DC1 CG2DC1 CG2DC2 CG301 0.2500 5 180.00 ! RETINOL MECH +CG2DC1 CG2DC1 CG2DC2 CG301 0.1000 6 0.00 ! RETINOL MECH +CG2DC1 CG2DC1 CG2DC2 CG331 1.1000 1 180.00 ! RETINOL DMP2, 2-methyl-1,3-pentadiene +CG2DC1 CG2DC1 CG2DC2 CG331 0.7000 2 180.00 ! RETINOL DMP2, 2-methyl-1,3-pentadiene +CG2DC1 CG2DC1 CG2DC2 HGA4 1.0000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +CG2DC3 CG2DC1 CG2DC2 CG2D2O 1.5000 1 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2DC3 CG2DC1 CG2DC2 CG2D2O 1.0000 2 180.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2DC3 CG2DC1 CG2DC2 CG2D2O 1.5000 3 0.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2DC3 CG2DC1 CG2DC2 CG2DC2 0.5000 1 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC3 CG2DC1 CG2DC2 CG2DC2 2.0000 2 0.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC3 CG2DC1 CG2DC2 CG2DC2 1.0000 3 0.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC3 CG2DC1 CG2DC2 CG2DC3 0.4000 1 180.00 ! RETINOL 13DB, 1,3-Butadiene +CG2DC3 CG2DC1 CG2DC2 CG2DC3 0.4000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +CG2DC3 CG2DC1 CG2DC2 CG2DC3 1.3000 3 0.00 ! RETINOL 13DB, 1,3-Butadiene +CG2DC3 CG2DC1 CG2DC2 CG301 0.9000 1 0.00 ! RETINOL MECH +CG2DC3 CG2DC1 CG2DC2 CG301 2.1000 2 180.00 ! RETINOL MECH +CG2DC3 CG2DC1 CG2DC2 CG301 0.2200 3 0.00 ! RETINOL MECH +CG2DC3 CG2DC1 CG2DC2 CG301 0.2500 5 180.00 ! RETINOL MECH +CG2DC3 CG2DC1 CG2DC2 CG301 0.1000 6 0.00 ! RETINOL MECH +CG2DC3 CG2DC1 CG2DC2 CG331 1.1000 1 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG2DC3 CG2DC1 CG2DC2 CG331 0.7000 2 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG2DC3 CG2DC1 CG2DC2 NG2P1 0.5000 1 0.00 ! RETINOL SCH3, Schiff's base, protonated +CG2DC3 CG2DC1 CG2DC2 NG2P1 2.2000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +CG2DC3 CG2DC1 CG2DC2 NG2P1 1.1000 3 0.00 ! RETINOL SCH3, Schiff's base, protonated +CG2DC3 CG2DC1 CG2DC2 NG2P1 0.6000 4 0.00 ! RETINOL SCH3, Schiff's base, protonated +CG2DC3 CG2DC1 CG2DC2 HGA4 1.0000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +CG2DC3 CG2DC1 CG2DC2 HGR52 1.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +CG301 CG2DC1 CG2DC2 CG2DC2 0.9000 1 0.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC2 2.1000 2 180.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC2 0.2200 3 0.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC2 0.2500 5 180.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC2 0.1000 6 0.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC3 0.9000 1 0.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC3 2.1000 2 180.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC3 0.2200 3 0.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC3 0.2500 5 180.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 CG2DC3 0.1000 6 0.00 ! RETINOL MECH +CG301 CG2DC1 CG2DC2 HGA4 1.0000 2 180.00 ! RETINOL MECH +CG331 CG2DC1 CG2DC2 CG2DC2 1.1000 1 180.00 ! RETINOL DMP2, 2-methyl-1,3-pentadiene +CG331 CG2DC1 CG2DC2 CG2DC2 0.7000 2 180.00 ! RETINOL DMP2, 2-methyl-1,3-pentadiene +CG331 CG2DC1 CG2DC2 CG2DC3 1.1000 1 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG331 CG2DC1 CG2DC2 CG2DC3 0.7000 2 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG331 CG2DC1 CG2DC2 HGA4 1.0000 2 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +NG2P1 CG2DC1 CG2DC2 CG2DC3 0.5000 1 0.00 ! RETINOL SCH3, Schiff's base, protonated +NG2P1 CG2DC1 CG2DC2 CG2DC3 2.2000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +NG2P1 CG2DC1 CG2DC2 CG2DC3 1.1000 3 0.00 ! RETINOL SCH3, Schiff's base, protonated +NG2P1 CG2DC1 CG2DC2 CG2DC3 0.6000 4 0.00 ! RETINOL SCH3, Schiff's base, protonated +NG2P1 CG2DC1 CG2DC2 HGA4 1.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +HGA4 CG2DC1 CG2DC2 CG2D2O 1.0000 2 180.00 ! PY02, 2h-pyran; re-initialized from MOBU, 1-Methoxy-1,3-butadiene; xxwy +HGA4 CG2DC1 CG2DC2 CG2DC2 1.0000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +HGA4 CG2DC1 CG2DC2 CG2DC3 1.0000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +HGA4 CG2DC1 CG2DC2 CG301 1.0000 2 180.00 ! RETINOL MECH +HGA4 CG2DC1 CG2DC2 CG331 1.0000 2 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +HGA4 CG2DC1 CG2DC2 NG2P1 1.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +HGA4 CG2DC1 CG2DC2 HGA4 0.0000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +HGA4 CG2DC1 CG2DC2 HGR52 0.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +HGR52 CG2DC1 CG2DC2 CG2DC3 1.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +HGR52 CG2DC1 CG2DC2 HGA4 0.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +CG2DC2 CG2DC1 CG2DC3 HGA5 5.0000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +CG2O3 CG2DC1 CG2DC3 HGA5 4.2000 2 180.00 ! RETINOL PRAC +CG2O4 CG2DC1 CG2DC3 HGA5 3.2000 2 180.00 ! RETINOL PRAL unmodified +CG2O5 CG2DC1 CG2DC3 HGA5 3.2000 2 180.00 ! BEON, butenone; from PRAL, acrolein; mcs +CG2R61 CG2DC1 CG2DC3 HGA5 3.5000 2 180.00 ! STYR, styrene, xxwy & oashi +CG331 CG2DC1 CG2DC3 HGA5 5.2000 2 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +HGA4 CG2DC1 CG2DC3 HGA5 5.2000 2 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2D1O CG2DC1 CG2O1 NG2S2 1.1000 1 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG2D1O CG2DC1 CG2O1 NG2S2 1.9500 2 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG2D1O CG2DC1 CG2O1 OG2D1 0.3000 1 0.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG2D1O CG2DC1 CG2O1 OG2D1 1.9500 2 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG2DC1 CG2DC1 CG2O1 NG2S1 0.7000 1 0.00 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O1 NG2S1 1.2000 2 180.00 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O1 NG2S1 0.1000 3 0.00 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O1 NG2S1 0.1500 4 0.00 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O1 OG2D1 0.7000 1 180.00 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O1 OG2D1 1.2000 2 180.00 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O1 OG2D1 0.1000 3 180.00 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O1 OG2D1 0.2000 4 0.00 ! RETINOL CROT +CG321 CG2DC1 CG2O1 NG2S2 0.5000 2 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC1 CG2O1 NG2S2 0.3500 3 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC1 CG2O1 NG2S2 0.4000 6 0.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC1 CG2O1 OG2D1 1.0000 2 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC1 CG2O1 OG2D1 1.0000 3 0.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC1 CG2O1 OG2D1 0.4000 6 0.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +HGA4 CG2DC1 CG2O1 NG2S1 0.3000 3 180.00 ! RETINOL CROT +HGA4 CG2DC1 CG2O1 OG2D1 0.3000 3 180.00 ! RETINOL CROT +CG2DC1 CG2DC1 CG2O3 OG2D2 1.3000 2 180.00 ! RETINOL PRAC +CG2DC3 CG2DC1 CG2O3 OG2D2 1.3000 2 180.00 ! RETINOL PRAC +HGA4 CG2DC1 CG2O3 OG2D2 0.0000 2 180.00 ! RETINOL PRAC +CG2DC1 CG2DC1 CG2O4 OG2D1 1.0000 2 180.00 ! RETINOL PRAL unmodified +CG2DC1 CG2DC1 CG2O4 HGR52 3.2000 2 180.00 ! RETINOL PRAL unmodified +CG2DC3 CG2DC1 CG2O4 OG2D1 1.0000 2 180.00 ! RETINOL PRAL unmodified +CG2DC3 CG2DC1 CG2O4 HGR52 3.2000 2 180.00 ! RETINOL PRAL unmodified +HGA4 CG2DC1 CG2O4 OG2D1 0.0000 2 180.00 ! RETINOL PRAL unmodified +HGA4 CG2DC1 CG2O4 HGR52 0.0000 2 180.00 ! RETINOL PRAL unmodified +CG2DC3 CG2DC1 CG2O5 CG331 1.4000 2 180.00 ! BEON, butenone, kevo +CG2DC3 CG2DC1 CG2O5 OG2D3 1.4000 2 180.00 ! BEON, butenone, kevo +HGA4 CG2DC1 CG2O5 CG331 0.0000 2 180.00 ! BEON, butenone, from PRAL, acrolein; mcs +HGA4 CG2DC1 CG2O5 OG2D3 0.0000 2 180.00 ! BEON, butenone, from PRAL, acrolein; mcs +CG2DC3 CG2DC1 CG2R61 CG2R61 0.7500 2 180.00 ! STYR, styrene, xxwy & oashi +CG2DC3 CG2DC1 CG2R61 CG2R61 0.1900 4 0.00 ! STYR, styrene, xxwy & oashi +NG2D1 CG2DC1 CG2R61 CG2R61 1.6000 2 180.00 ! HDZ1b, hydrazone model cmpd 1b, kevo +HGA4 CG2DC1 CG2R61 CG2R61 0.6000 2 180.00 ! HDZ1b, hydrazone model cmpd 1b, kevo +CG2DC1 CG2DC1 CG301 CG321 0.5000 2 0.00 ! RETINOL TMCH +CG2DC1 CG2DC1 CG301 CG321 0.3000 3 0.00 ! RETINOL TMCH +CG2DC1 CG2DC1 CG301 CG331 0.5000 2 0.00 ! RETINOL TMCH +CG2DC1 CG2DC1 CG301 CG331 0.4000 3 0.00 ! RETINOL TMCH +CG2DC2 CG2DC1 CG301 CG321 0.3000 3 0.00 ! RETINOL MECH +CG2DC2 CG2DC1 CG301 CG331 0.3000 3 0.00 ! RETINOL MECH +CG2D1O CG2DC1 CG321 CG2D1 0.0000 3 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG2D1O CG2DC1 CG321 HGA2 0.0000 3 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG2DC1 CG2DC1 CG321 CG321 0.5000 2 0.00 ! RETINOL TMCH +CG2DC1 CG2DC1 CG321 CG321 0.3000 3 0.00 ! RETINOL TMCH +CG2DC1 CG2DC1 CG321 OG311 1.9000 1 180.00 ! RETINOL PROL +CG2DC1 CG2DC1 CG321 OG311 0.4000 2 180.00 ! RETINOL PROL +CG2DC1 CG2DC1 CG321 OG311 0.6000 3 180.00 ! RETINOL PROL +CG2DC1 CG2DC1 CG321 OG3R60 0.7000 3 0.00 ! PY02, 2h-pyran +CG2DC1 CG2DC1 CG321 HGA2 0.0300 3 0.00 ! RETINOL PROL +CG2O1 CG2DC1 CG321 CG2D1 0.0000 3 0.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG2O1 CG2DC1 CG321 HGA2 0.0000 3 0.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG331 CG2DC1 CG321 CG321 0.1900 3 0.00 ! RETINOL TMCH +CG331 CG2DC1 CG321 HGA2 0.1900 3 0.00 ! RETINOL TMCH +HGA4 CG2DC1 CG321 OG311 0.2000 3 0.00 ! RETINOL PROL +HGA4 CG2DC1 CG321 OG3R60 0.2000 3 0.00 ! PY02, 2h-pyran; re-initialized from PROL, 3-propenol; kevo +HGA4 CG2DC1 CG321 HGA2 0.2000 3 0.00 ! RETINOL PROL +CG2DC1 CG2DC1 CG331 HGA3 0.3000 3 180.00 ! RETINOL BTE2, 2-butene @@@@@ Kenno: 0 --> 180 to fix minimum @@@@@ +CG2DC2 CG2DC1 CG331 HGA3 0.3000 3 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG2DC3 CG2DC1 CG331 HGA3 0.3000 3 0.00 ! RETINOL DMP2, 2-methyl-1,3-pentadiene +CG321 CG2DC1 CG331 HGA3 0.1600 3 0.00 ! RETINOL MECH +CG331 CG2DC1 CG331 HGA3 0.3000 3 0.00 ! RETINOL DMP1, 4-methyl-1,3-pentadiene +HGA4 CG2DC1 CG331 HGA3 0.0000 3 0.00 ! RETINOL BTE2, 2-butene @@@@@ Kenno: 0.3 --> 0.0 to fix planarity around CG2DCx @@@@@ +CG2R61 CG2DC1 NG2D1 NG2S1 12.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +HGA4 CG2DC1 NG2D1 NG2S1 4.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC2 CG2DC1 NG2P1 CG334 7.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +CG2DC2 CG2DC1 NG2P1 HGP2 5.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +HGR52 CG2DC1 NG2P1 CG334 8.5000 2 180.00 ! RETINOL SCH2, Schiff's base, protonated +HGR52 CG2DC1 NG2P1 HGP2 5.0000 2 180.00 ! RETINOL SCH2, Schiff's base, protonated +CG2DC1 CG2DC2 CG2DC2 CG2DC1 0.5600 1 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC1 CG2DC2 CG2DC2 CG2DC1 7.0000 2 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2DC1 CG2DC2 CG2DC2 CG2O1 0.5600 1 180.00 ! RETINOL FRET +CG2DC1 CG2DC2 CG2DC2 CG2O1 7.0000 2 180.00 ! RETINOL FRET +CG2DC1 CG2DC2 CG2DC2 CG2O3 0.5600 1 180.00 ! RETINOL PRAC +CG2DC1 CG2DC2 CG2DC2 CG2O3 7.0000 2 180.00 ! RETINOL PRAC +CG2DC1 CG2DC2 CG2DC2 CG2O4 0.5600 1 180.00 ! RETINOL RTAL unmodified +CG2DC1 CG2DC2 CG2DC2 CG2O4 7.0000 2 180.00 ! RETINOL RTAL unmodified +CG2DC1 CG2DC2 CG2DC2 CG321 0.5600 1 180.00 ! RETINOL MECH +CG2DC1 CG2DC2 CG2DC2 CG321 7.0000 2 180.00 ! RETINOL MECH +CG2DC1 CG2DC2 CG2DC2 CG331 0.5600 1 180.00 ! RETINOL 13DP, 1,3-Pentadiene +CG2DC1 CG2DC2 CG2DC2 CG331 7.0000 2 180.00 ! RETINOL 13DP, 1,3-Pentadiene +CG2DC1 CG2DC2 CG2DC2 HGA4 5.2000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +CG2O1 CG2DC2 CG2DC2 CG331 0.5600 1 180.00 ! RETINOL CROT +CG2O1 CG2DC2 CG2DC2 CG331 7.0000 2 180.00 ! RETINOL CROT +CG2O3 CG2DC2 CG2DC2 CG331 0.5600 1 180.00 ! RETINOL PRAC +CG2O3 CG2DC2 CG2DC2 CG331 7.0000 2 180.00 ! RETINOL PRAC +CG2O4 CG2DC2 CG2DC2 CG331 0.5600 1 180.00 ! RETINOL RTAL +CG2O4 CG2DC2 CG2DC2 CG331 7.0000 2 180.00 ! RETINOL RTAL Kenno: 0.5 -> 7.0 for the sake of transferability +CG301 CG2DC2 CG2DC2 CG321 10.0000 2 180.00 ! RETINOL TMCH +CG301 CG2DC2 CG2DC2 CG331 10.0000 2 180.00 ! RETINOL MECH +CG321 CG2DC2 CG2DC2 CG331 10.0000 2 180.00 ! RETINOL BTE2, 2-butene +CG321 CG2DC2 CG2DC2 HGA4 5.2000 2 180.00 ! PY02, 2h-pyran; re-initialized from BTE2, 2-butene; kevo +CG331 CG2DC2 CG2DC2 HGA4 5.2000 2 180.00 ! RETINOL BTE2, 2-butene +HGA4 CG2DC2 CG2DC2 HGA4 5.2000 2 180.00 ! RETINOL BTE2, 2-butene +CG2DC1 CG2DC2 CG2DC3 HGA5 5.0000 2 180.00 ! RETINOL 13DB, 1,3-Butadiene +CG2O3 CG2DC2 CG2DC3 HGA5 4.2000 2 180.00 ! RETINOL PRAC +CG2O4 CG2DC2 CG2DC3 HGA5 3.2000 2 180.00 ! RETINOL PRAL unmodified +CG2O5 CG2DC2 CG2DC3 HGA5 3.2000 2 180.00 ! BEON, butenone; from PRAL, acrolein; mcs +CG2R61 CG2DC2 CG2DC3 HGA5 3.5000 2 180.00 ! STYR, styrene, xxwy & oashi +CG331 CG2DC2 CG2DC3 HGA5 5.2000 2 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +HGA4 CG2DC2 CG2DC3 HGA5 5.2000 2 180.00 ! RETINOL HEP3, 1,3,5-heptatriene +CG2D2O CG2DC2 CG2O1 NG2S2 1.1000 1 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG2D2O CG2DC2 CG2O1 NG2S2 1.9500 2 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG2D2O CG2DC2 CG2O1 OG2D1 0.3000 1 0.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG2D2O CG2DC2 CG2O1 OG2D1 1.9500 2 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG2DC2 CG2DC2 CG2O1 NG2S1 0.7000 1 0.00 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O1 NG2S1 1.2000 2 180.00 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O1 NG2S1 0.1000 3 0.00 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O1 NG2S1 0.1500 4 0.00 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O1 OG2D1 0.7000 1 180.00 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O1 OG2D1 1.2000 2 180.00 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O1 OG2D1 0.1000 3 180.00 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O1 OG2D1 0.2000 4 0.00 ! RETINOL CROT +CG321 CG2DC2 CG2O1 NG2S2 0.5000 2 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC2 CG2O1 NG2S2 0.3500 3 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC2 CG2O1 NG2S2 0.4000 6 0.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC2 CG2O1 OG2D1 1.0000 2 180.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC2 CG2O1 OG2D1 1.0000 3 0.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +CG321 CG2DC2 CG2O1 OG2D1 0.4000 6 0.00 ! NICH; Kenno: reverted to nadh, jjp1,adm jr. 4/95 +HGA4 CG2DC2 CG2O1 NG2S1 0.3000 3 180.00 ! RETINOL CROT +HGA4 CG2DC2 CG2O1 OG2D1 0.3000 3 180.00 ! RETINOL CROT +CG2DC2 CG2DC2 CG2O3 OG2D2 1.3000 2 180.00 ! RETINOL PRAC +CG2DC3 CG2DC2 CG2O3 OG2D2 1.3000 2 180.00 ! RETINOL PRAC +HGA4 CG2DC2 CG2O3 OG2D2 0.0000 2 180.00 ! RETINOL PRAC +CG2DC2 CG2DC2 CG2O4 OG2D1 1.0000 2 180.00 ! RETINOL PRAL unmodified +CG2DC2 CG2DC2 CG2O4 HGR52 3.2000 2 180.00 ! RETINOL PRAL unmodified +CG2DC3 CG2DC2 CG2O4 OG2D1 1.0000 2 180.00 ! RETINOL PRAL unmodified +CG2DC3 CG2DC2 CG2O4 HGR52 3.2000 2 180.00 ! RETINOL PRAL unmodified +HGA4 CG2DC2 CG2O4 OG2D1 0.0000 2 180.00 ! RETINOL PRAL unmodified +HGA4 CG2DC2 CG2O4 HGR52 0.0000 2 180.00 ! RETINOL PRAL unmodified +CG2DC3 CG2DC2 CG2O5 CG331 1.4000 2 180.00 ! BEON, butenone, kevo +CG2DC3 CG2DC2 CG2O5 OG2D3 1.4000 2 180.00 ! BEON, butenone, kevo +HGA4 CG2DC2 CG2O5 CG331 0.0000 2 180.00 ! BEON, butenone, from PRAL, acrolein; mcs +HGA4 CG2DC2 CG2O5 OG2D3 0.0000 2 180.00 ! BEON, butenone, from PRAL, acrolein; mcs +CG2DC3 CG2DC2 CG2R61 CG2R61 0.7500 2 180.00 ! STYR, styrene, xxwy & oashi +CG2DC3 CG2DC2 CG2R61 CG2R61 0.1900 4 0.00 ! STYR, styrene, xxwy & oashi +NG2D1 CG2DC2 CG2R61 CG2R61 1.6000 2 180.00 ! HDZ1b, hydrazone model cmpd 1b, kevo +HGA4 CG2DC2 CG2R61 CG2R61 0.6000 2 180.00 ! HDZ1b, hydrazone model cmpd 1b, kevo +CG2DC1 CG2DC2 CG301 CG321 0.3000 3 0.00 ! RETINOL MECH +CG2DC1 CG2DC2 CG301 CG331 0.3000 3 0.00 ! RETINOL MECH +CG2DC2 CG2DC2 CG301 CG321 0.5000 2 0.00 ! RETINOL TMCH +CG2DC2 CG2DC2 CG301 CG321 0.3000 3 0.00 ! RETINOL TMCH +CG2DC2 CG2DC2 CG301 CG331 0.5000 2 0.00 ! RETINOL TMCH +CG2DC2 CG2DC2 CG301 CG331 0.4000 3 0.00 ! RETINOL TMCH +CG2D2O CG2DC2 CG321 CG2D1 0.0000 3 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG2D2O CG2DC2 CG321 HGA2 0.0000 3 180.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG2DC2 CG2DC2 CG321 CG321 0.5000 2 0.00 ! RETINOL TMCH +CG2DC2 CG2DC2 CG321 CG321 0.3000 3 0.00 ! RETINOL TMCH +CG2DC2 CG2DC2 CG321 OG311 1.9000 1 180.00 ! RETINOL PROL +CG2DC2 CG2DC2 CG321 OG311 0.4000 2 180.00 ! RETINOL PROL +CG2DC2 CG2DC2 CG321 OG311 0.6000 3 180.00 ! RETINOL PROL +CG2DC2 CG2DC2 CG321 OG3R60 0.7000 3 0.00 ! PY02, 2h-pyran +CG2DC2 CG2DC2 CG321 HGA2 0.0300 3 0.00 ! RETINOL PROL +CG2O1 CG2DC2 CG321 CG2D1 0.0000 3 0.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG2O1 CG2DC2 CG321 HGA2 0.0000 3 0.00 ! NICH; Kenno: nad/ppi, jjp1/adm jr. 7/95 says 1.0 3 180 but that's unlikely ==> re-optimize +CG331 CG2DC2 CG321 CG321 0.1900 3 0.00 ! RETINOL TMCH +CG331 CG2DC2 CG321 HGA2 0.1900 3 0.00 ! RETINOL TMCH +HGA4 CG2DC2 CG321 OG311 0.2000 3 0.00 ! RETINOL PROL +HGA4 CG2DC2 CG321 OG3R60 0.2000 3 0.00 ! PY02, 2h-pyran; re-initialized from PROL, 3-propenol; kevo +HGA4 CG2DC2 CG321 HGA2 0.2000 3 0.00 ! RETINOL PROL +CG2DC1 CG2DC2 CG331 HGA3 0.3000 3 180.00 ! RETINOL DMB1, 2-methyl-1,3-butadiene +CG2DC2 CG2DC2 CG331 HGA3 0.3000 3 180.00 ! RETINOL BTE2, 2-butene @@@@@ Kenno: 0 --> 180 to fix minimum @@@@@ +CG2DC3 CG2DC2 CG331 HGA3 0.3000 3 0.00 ! RETINOL DMP2, 2-methyl-1,3-pentadiene +CG321 CG2DC2 CG331 HGA3 0.1600 3 0.00 ! RETINOL MECH +CG331 CG2DC2 CG331 HGA3 0.3000 3 0.00 ! RETINOL DMP1, 4-methyl-1,3-pentadiene +HGA4 CG2DC2 CG331 HGA3 0.0000 3 0.00 ! RETINOL BTE2, 2-butene @@@@@ Kenno: 0.3 --> 0.0 to fix planarity around CG2DCx @@@@@ +CG2R61 CG2DC2 NG2D1 NG2S1 12.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +HGA4 CG2DC2 NG2D1 NG2S1 4.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC1 CG2DC2 NG2P1 CG334 7.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +CG2DC1 CG2DC2 NG2P1 HGP2 5.0000 2 180.00 ! RETINOL SCH3, Schiff's base, protonated +HGR52 CG2DC2 NG2P1 CG334 8.5000 2 180.00 ! RETINOL SCH2, Schiff's base, protonated +HGR52 CG2DC2 NG2P1 HGP2 5.0000 2 180.00 ! RETINOL SCH2, Schiff's base, protonated +NG311 CG2N1 NG2D1 HGP1 5.2000 2 180.00 ! MGU2, methylguanidine2 +NG321 CG2N1 NG2D1 CG331 6.5000 2 180.00 ! MGU1, methylguanidine +NG321 CG2N1 NG2D1 HGP1 5.2000 2 180.00 ! MGU2, methylguanidine2 +NG2P1 CG2N1 NG2P1 CG324 2.2500 2 180.00 ! PROT 9.0->2.25 GUANIDINIUM (KK) +NG2P1 CG2N1 NG2P1 CG334 2.2500 2 180.00 ! PROT 9.0->2.25 GUANIDINIUM (KK) +NG2P1 CG2N1 NG2P1 HGP2 2.2500 2 180.00 ! PROT 9.0->2.25 GUANIDINIUM (KK) +NG2D1 CG2N1 NG311 CG331 0.5000 2 180.00 ! MGU2, methylguanidine2 +NG2D1 CG2N1 NG311 HGPAM1 2.8000 2 180.00 ! MGU2, methylguanidine2 kevo: 3 --> 2 (counteracting forces). May benefit optimization. +NG321 CG2N1 NG311 CG331 0.5000 2 180.00 ! MGU2, methylguanidine2 +NG321 CG2N1 NG311 HGPAM1 2.8000 2 180.00 ! MGU2, methylguanidine2 kevo: 3 --> 2 (counteracting forces). May benefit optimization. +NG2D1 CG2N1 NG321 HGPAM2 0.2000 2 180.00 ! MGU1, methylguanidine; MGU2, methylguanidine2 kevo: new. Needs to be further optimized. +NG2D1 CG2N1 NG321 HGPAM2 0.1500 6 0.00 ! MGU1, methylguanidine; MGU2, methylguanidine2 kevo: new. Needs to be further optimized. +NG311 CG2N1 NG321 HGPAM2 0.2000 2 180.00 ! MGU2, methylguanidine2 kevo: new. Needs to be further optimized. +NG311 CG2N1 NG321 HGPAM2 0.1500 6 0.00 ! MGU2, methylguanidine2 kevo: new. Needs to be further optimized. +NG321 CG2N1 NG321 HGPAM2 0.2000 2 180.00 ! MGU1, methylguanidine kevo: new. Needs to be further optimized. +NG321 CG2N1 NG321 HGPAM2 0.1500 6 0.00 ! MGU1, methylguanidine kevo: new. Needs to be further optimized. +NG2P1 CG2N2 CG2R61 CG2R61 0.8200 2 180.00 ! BAMI, benzamidinium, sz (verified by pram) +NG2P1 CG2N2 CG2R61 CG2R61 0.2900 4 0.00 ! BAMI, benzamidinium, sz (verified by pram) +NG2P1 CG2N2 CG2R61 CG2R61 0.0900 6 0.00 ! BAMI, benzamidinium, sz (verified by pram) +NG2P1 CG2N2 CG331 HGA3 0.2500 3 0.00 ! AMDN, amidinium amidinium, mp2 scan, pram +NG321 CG2N2 NG2D1 CG321 6.5000 2 180.00 ! MT2A , from NG321 CG2N1 NG2D1 CG331, fylin +SG311 CG2N2 NG2D1 CG321 2.3600 1 180.00 ! MT2A, fylin +SG311 CG2N2 NG2D1 CG321 2.0800 2 180.00 ! MT2A, fylin +SG311 CG2N2 NG2D1 CG321 0.0600 3 0.00 ! MT2A, fylin +SG311 CG2N2 NG2D1 CG321 1.0700 4 180.00 ! MT2A, fylin +SG311 CG2N2 NG2D1 CG321 0.2800 6 0.00 ! MT2A, fylin +CG2R61 CG2N2 NG2P1 HGP2 2.0000 2 180.00 ! BAMI, benzamidinium, mp2 scan, pram +CG331 CG2N2 NG2P1 HGP2 3.5000 2 180.00 ! AMDN, amidinium, mp2 scan, pram +NG2P1 CG2N2 NG2P1 HGP2 3.5000 2 180.00 ! AMDN, amidinium, mp2 scan, pram +NG2D1 CG2N2 NG321 HGPAM2 0.2000 2 180.00 ! MT2A , from NG2D1 CG2N1 NG321 HGPAM2, fylin +NG2D1 CG2N2 NG321 HGPAM2 0.1500 6 0.00 ! MT2A , from NG2D1 CG2N1 NG321 HGPAM2, fylin +SG311 CG2N2 NG321 HGPAM2 0.0200 1 180.00 ! MT2A, fylin +SG311 CG2N2 NG321 HGPAM2 2.8700 2 180.00 ! MT2A, fylin +SG311 CG2N2 NG321 HGPAM2 0.1200 3 0.00 ! MT2A, fylin +SG311 CG2N2 NG321 HGPAM2 0.2000 4 180.00 ! MT2A, fylin +SG311 CG2N2 NG321 HGPAM2 0.2000 6 180.00 ! MT2A, fylin +NG2D1 CG2N2 SG311 CG321 1.1200 2 180.00 ! DH3T, fylin +NG2D1 CG2N2 SG311 CG331 1.1200 2 180.00 ! MT2A, fylin +NG321 CG2N2 SG311 CG321 0.6400 1 180.00 ! DH3T, fylin +NG321 CG2N2 SG311 CG321 1.1200 2 180.00 ! DH3T, fylin +NG321 CG2N2 SG311 CG321 0.3300 4 0.00 ! DH3T, fylin +NG321 CG2N2 SG311 CG331 0.6400 1 180.00 ! MT2A, fylin +NG321 CG2N2 SG311 CG331 1.1200 2 180.00 ! MT2A, fylin +NG321 CG2N2 SG311 CG331 0.3300 4 0.00 ! MT2A, fylin +NG2S1 CG2O1 CG2R61 CG2R61 1.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +NG2S1 CG2O1 CG2R61 CG2RC0 1.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +NG2S2 CG2O1 CG2R61 CG2R61 1.0000 2 180.00 ! 3NAP, nicotinamide (PYRIDINE pyr-CONH2), yin +OG2D1 CG2O1 CG2R61 CG2R61 1.0000 2 180.00 ! 3NAP, nicotinamide (PYRIDINE pyr-CONH2), yin +OG2D1 CG2O1 CG2R61 CG2RC0 1.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +NG2S2 CG2O1 CG2R62 CG2R62 0.3500 1 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +NG2S2 CG2O1 CG2R62 CG2R62 0.6200 2 0.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +OG2D1 CG2O1 CG2R62 CG2R62 2.3800 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +NG2S0 CG2O1 CG311 CG311 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG311 CG321 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG311 CG323 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG311 CG331 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG311 NG2S1 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG311 HGA1 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG311 CG311 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S1 CG2O1 CG311 CG321 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S1 CG2O1 CG311 CG323 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S1 CG2O1 CG311 CG331 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S1 CG2O1 CG311 NG2S1 0.6000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93 +NG2S1 CG2O1 CG311 HGA1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +NG2S2 CG2O1 CG311 CG311 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S2 CG2O1 CG311 CG321 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S2 CG2O1 CG311 CG323 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S2 CG2O1 CG311 CG331 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S2 CG2O1 CG311 NG2S1 0.6000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93 +NG2S2 CG2O1 CG311 HGA1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +OG2D1 CG2O1 CG311 CG311 1.4000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +OG2D1 CG2O1 CG311 CG321 1.4000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +OG2D1 CG2O1 CG311 CG323 1.4000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +OG2D1 CG2O1 CG311 CG331 1.4000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +OG2D1 CG2O1 CG311 NG2S1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +OG2D1 CG2O1 CG311 HGA1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +NG2S0 CG2O1 CG314 CG311 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG314 CG321 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG314 CG323 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG314 CG331 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG314 NG3P3 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG314 HGA1 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG314 CG311 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S1 CG2O1 CG314 CG321 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S1 CG2O1 CG314 CG323 0.0000 1 0.00 ! NOT OPTIMIZED! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S1 CG2O1 CG314 CG331 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S1 CG2O1 CG314 NG3P3 0.6000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93 +NG2S1 CG2O1 CG314 HGA1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +NG2S2 CG2O1 CG314 CG311 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S2 CG2O1 CG314 CG321 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S2 CG2O1 CG314 CG323 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S2 CG2O1 CG314 CG331 0.0000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, 4/10/93 (LK) +NG2S2 CG2O1 CG314 NG3P3 0.6000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93 +NG2S2 CG2O1 CG314 HGA1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +OG2D1 CG2O1 CG314 CG311 1.4000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +OG2D1 CG2O1 CG314 CG321 1.4000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +OG2D1 CG2O1 CG314 CG323 1.4000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +OG2D1 CG2O1 CG314 CG331 1.4000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +OG2D1 CG2O1 CG314 NG3P3 0.0000 1 0.00 ! PROT Backbone parameter set made complete RLD 8/8/90 +OG2D1 CG2O1 CG314 HGA1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +NG2S0 CG2O1 CG321 CG331 1.5000 1 0.00 ! DMPR, dimethylpropanamide, mnoon +NG2S0 CG2O1 CG321 NG2S1 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG321 HGA2 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG321 CG321 0.0000 1 0.00 ! PROT from NG2S1 CG2O1 CG311 CT2, for lactams, adm jr. +NG2S1 CG2O1 CG321 NG2S1 0.6000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93 +NG2S1 CG2O1 CG321 HGA1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +NG2S1 CG2O1 CG321 HGA2 0.0000 3 0.00 ! PROT, sp2-methyl, no torsion potential +NG2S2 CG2O1 CG321 CG311 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +NG2S2 CG2O1 CG321 CG314 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +NG2S2 CG2O1 CG321 CG321 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +NG2S2 CG2O1 CG321 CG331 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +NG2S2 CG2O1 CG321 NG2S1 0.6000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93 +NG2S2 CG2O1 CG321 HGA2 0.0000 3 180.00 ! PROT adm jr., 8/13/90 geometry and vibrations +OG2D1 CG2O1 CG321 CG311 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D1 CG2O1 CG321 CG314 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D1 CG2O1 CG321 CG321 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D1 CG2O1 CG321 CG331 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D1 CG2O1 CG321 NG2S1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +OG2D1 CG2O1 CG321 HGA2 0.0000 3 180.00 ! PROT adm jr., 8/13/90 geometry and vibrations +NG2S0 CG2O1 CG324 NG3P3 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG324 HGA2 0.0000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG324 NG3P3 0.4000 1 0.00 ! PROT adm jr. 3/24/92, for PRES GLYP +NG2S1 CG2O1 CG324 HGA2 0.0000 3 0.00 ! PROT, sp2-methyl, no torsion potential +NG2S2 CG2O1 CG324 NG3P3 0.4000 1 0.00 ! PROT adm jr. 3/24/92, for PRES GLYP +NG2S2 CG2O1 CG324 HGA2 0.0000 3 180.00 ! PROT adm jr., 8/13/90 geometry and vibrations +OG2D1 CG2O1 CG324 NG3P3 0.0000 1 0.00 ! PROT Backbone parameter set made complete RLD 8/8/90 +OG2D1 CG2O1 CG324 HGA2 0.0000 3 180.00 ! PROT adm jr., 8/13/90 geometry and vibrations +NG2S0 CG2O1 CG331 HGA3 0.0000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG331 HGA3 0.0000 3 0.00 ! PROT, sp2-methyl, no torsion potential +NG2S2 CG2O1 CG331 HGA3 0.0000 3 0.00 ! PROT, sp2-methyl, no torsion potential +OG2D1 CG2O1 CG331 HGA3 0.0000 3 180.00 ! PROT adm jr., 8/13/90 geometry and vibrations +NG2S0 CG2O1 CG3C51 CG3C52 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C51 CG3C52 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C51 NG2S0 0.3000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C51 NG2S0 -0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C51 HGA1 0.4000 1 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C51 HGA1 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C51 CG3C52 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C51 CG3C52 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C51 NG2S0 0.3000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C51 NG2S0 -0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C51 HGA1 0.4000 1 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C51 HGA1 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C51 CG3C52 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C51 CG3C52 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C51 NG2S0 0.3000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C51 NG2S0 -0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C51 HGA1 0.4000 1 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C51 HGA1 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C51 CG3C52 0.4000 1 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C51 CG3C52 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C51 NG2S0 -0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C51 HGA1 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C51 HGA1 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C53 CG3C52 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C53 CG3C52 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C53 NG3P2 0.3000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C53 HGA1 0.4000 1 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG2O1 CG3C53 HGA1 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C53 CG3C52 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C53 CG3C52 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C53 NG3P2 0.3000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C53 HGA1 0.4000 1 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S1 CG2O1 CG3C53 HGA1 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C53 CG3C52 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C53 CG3C52 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C53 NG3P2 0.3000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C53 HGA1 0.4000 1 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S2 CG2O1 CG3C53 HGA1 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C53 CG3C52 0.4000 1 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C53 CG3C52 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C53 NG3P2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C53 HGA1 0.4000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 CG3C53 HGA1 0.6000 2 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG2O1 NG2S0 CG3C51 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG2O1 NG2S0 CG3C51 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG2O1 NG2S0 CG3C52 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG2O1 NG2S0 CG3C52 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG314 CG2O1 NG2S0 CG3C51 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG314 CG2O1 NG2S0 CG3C51 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG314 CG2O1 NG2S0 CG3C52 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG314 CG2O1 NG2S0 CG3C52 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG321 CG2O1 NG2S0 CG331 2.6000 2 180.00 ! DMPR, dimethylpropanamide; from DMF, Dimethylformamide; kevo +CG321 CG2O1 NG2S0 CG3C51 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG321 CG2O1 NG2S0 CG3C51 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG321 CG2O1 NG2S0 CG3C52 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG321 CG2O1 NG2S0 CG3C52 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG324 CG2O1 NG2S0 CG3C51 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG324 CG2O1 NG2S0 CG3C51 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG324 CG2O1 NG2S0 CG3C52 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG324 CG2O1 NG2S0 CG3C52 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG331 CG2O1 NG2S0 CG331 2.6000 2 180.00 ! DMF, Dimethylformamide, xxwy +CG331 CG2O1 NG2S0 CG3C51 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG331 CG2O1 NG2S0 CG3C51 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG331 CG2O1 NG2S0 CG3C52 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG331 CG2O1 NG2S0 CG3C52 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S0 CG3C51 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S0 CG3C51 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S0 CG3C52 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S0 CG3C52 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S0 CG3C51 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S0 CG3C51 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S0 CG3C52 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S0 CG3C52 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 NG2S0 CG331 2.6000 2 180.00 ! DMF, Dimethylformamide, xxwy +OG2D1 CG2O1 NG2S0 CG3C51 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 NG2S0 CG3C51 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 NG2S0 CG3C52 2.7500 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 NG2S0 CG3C52 0.3000 4 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGR52 CG2O1 NG2S0 CG331 2.6000 2 180.00 ! DMF, Dimethylformamide, xxwy +CG2DC1 CG2O1 NG2S1 CG2R61 1.6000 1 0.00 ! RETINOL FRET +CG2DC1 CG2O1 NG2S1 CG2R61 2.5000 2 180.00 ! RETINOL FRET +CG2DC1 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! RETINOL CROT +CG2DC1 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! RETINOL CROT +CG2DC1 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! RETINOL CROT +CG2DC2 CG2O1 NG2S1 CG2R61 1.6000 1 0.00 ! RETINOL FRET +CG2DC2 CG2O1 NG2S1 CG2R61 2.5000 2 180.00 ! RETINOL FRET +CG2DC2 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! RETINOL CROT +CG2DC2 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! RETINOL CROT +CG2DC2 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! RETINOL CROT +CG2R61 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! 3CPD, Gamma-3-Amide Pyridine Lysine CDCA Amide; from HDZ2, hydrazone model cmpd 2; cacha +CG2R61 CG2O1 NG2S1 CG321 4.0000 2 180.00 ! 3CPD, Gamma-3-Amide Pyridine Lysine CDCA Amide; from HDZ2, hydrazone model cmpd 2; cacha +CG2R61 CG2O1 NG2S1 NG2D1 1.6000 1 0.00 ! HDZ2, hydrazone model cmpd 2 +CG2R61 CG2O1 NG2S1 NG2D1 4.0000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2R61 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG311 CG2O1 NG2S1 CG311 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG311 CG2O1 NG2S1 CG311 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG311 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG311 CG2O1 NG2S1 CG321 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG311 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG311 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG311 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG314 CG2O1 NG2S1 CG311 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG314 CG2O1 NG2S1 CG311 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG314 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG314 CG2O1 NG2S1 CG321 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG314 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG314 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG314 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG321 CG2O1 NG2S1 CG2R61 1.6000 1 0.00 ! 3APP, Alpha-Benzyl Gamma-3-Amino Pyridine GA CDCA Amide, cacha +CG321 CG2O1 NG2S1 CG2R61 2.5000 2 180.00 ! 3APP, Alpha-Benzyl Gamma-3-Amino Pyridine GA CDCA Amide, cacha +CG321 CG2O1 NG2S1 CG2R64 1.6000 1 0.00 ! 2APP, Alpha-Benzyl Gamma-2-Amino Pyridine GA CDCA Amide, cacha +CG321 CG2O1 NG2S1 CG2R64 2.5000 2 180.00 ! 2APP, Alpha-Benzyl Gamma-2-Amino Pyridine GA CDCA Amide, cacha +CG321 CG2O1 NG2S1 CG311 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG321 CG2O1 NG2S1 CG311 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG321 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG321 CG2O1 NG2S1 CG321 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG321 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! PROT from CG321 CG2O1 NG2S1 CT2, adm jr. 10/21/96 +CG321 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! PROT from CG321 CG2O1 NG2S1 CT2, adm jr. 10/21/96 +CG321 CG2O1 NG2S1 NG2D1 0.9000 1 0.00 ! PMHA, hydrazone-containing model compound:, sz +CG321 CG2O1 NG2S1 NG2D1 3.5000 2 180.00 ! PMHA, hydrazone-containing model compound: HDZ1, hydrazone model cmpd, sz +CG321 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG324 CG2O1 NG2S1 CG311 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG324 CG2O1 NG2S1 CG311 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG324 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG324 CG2O1 NG2S1 CG321 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG324 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! PROT from CG321 CG2O1 NG2S1 CT2, adm jr. 10/21/96 +CG324 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! PROT from CG321 CG2O1 NG2S1 CT2, adm jr. 10/21/96 +CG324 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG331 CG2O1 NG2S1 CG2R61 1.6000 1 0.00 ! RETINOL PACP 1-fold added by kevo +CG331 CG2O1 NG2S1 CG2R61 2.5000 2 180.00 ! RETINOL PACP +CG331 CG2O1 NG2S1 CG2R64 1.6000 1 0.00 ! 2AMP, 2-amino pyridine, from PACP, p-acetamide-phenol, pyridine, kevo +CG331 CG2O1 NG2S1 CG2R64 2.5000 2 180.00 ! 2AMP, 2-amino pyridine, from PACP, p-acetamide-phenol, pyridine, kevo +CG331 CG2O1 NG2S1 CG311 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG331 CG2O1 NG2S1 CG311 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG331 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! PROT for acetylated GLY N-terminus, adm jr. +CG331 CG2O1 NG2S1 CG321 2.5000 2 180.00 ! PROT for acetylated GLY N-terminus, adm jr. +CG331 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! PROT NMA cis/trans energy difference. (LK) +CG331 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG331 CG2O1 NG2S1 NG2D1 0.9000 1 0.00 ! HDZ1, hydrazone model cmpd +CG331 CG2O1 NG2S1 NG2D1 3.5000 2 180.00 ! HDZ1, hydrazone model cmpd +CG331 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG3C51 CG2O1 NG2S1 CG311 1.6000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S1 CG311 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S1 CG321 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S1 CG311 1.6000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S1 CG311 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S1 CG321 1.6000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S1 CG321 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S1 CG331 1.6000 1 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 NG2S1 CG2R61 2.5000 2 180.00 ! RETINOL PACP +OG2D1 CG2O1 NG2S1 CG2R64 2.5000 2 180.00 ! 2AMP, 2-amino pyridine, from PACP, p-acetamide-phenol, pyridine, kevo +OG2D1 CG2O1 NG2S1 CG311 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +OG2D1 CG2O1 NG2S1 CG321 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +OG2D1 CG2O1 NG2S1 CG331 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +OG2D1 CG2O1 NG2S1 NG2D1 2.5000 2 180.00 ! HDZ1, hydrazone model cmpd +OG2D1 CG2O1 NG2S1 HGP1 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG2DC1 CG2O1 NG2S2 HGP1 2.5000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2DC2 CG2O1 NG2S2 HGP1 2.5000 2 180.00 ! NICH; Kenno: reverted to nad/ppi, jjp1/adm jr. 7/95 +CG2R61 CG2O1 NG2S2 HGP1 1.0000 2 180.00 ! 3NAP, nicotamide (PYRIDINE pyr-CONH2), yin +CG2R62 CG2O1 NG2S2 HGP1 2.5000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG311 CG2O1 NG2S2 HGP1 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG314 CG2O1 NG2S2 HGP1 2.5000 2 180.00 ! PROT Gives appropriate NMA cis/trans barrier. (LK) +CG321 CG2O1 NG2S2 HGP1 1.4000 2 180.00 ! PROT adm jr. 4/10/91, acetamide update +CG324 CG2O1 NG2S2 HGP1 1.4000 2 180.00 ! PROT adm jr. 4/10/91, acetamide update +CG331 CG2O1 NG2S2 HGP1 1.4000 2 180.00 ! PROT adm jr. 4/10/91, acetamide update +CG3C51 CG2O1 NG2S2 HGP1 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG2O1 NG2S2 HGP1 2.5000 2 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O1 NG2S2 HGP1 1.4000 2 180.00 ! PROT adm jr. 4/10/91, acetamide update +HGR52 CG2O1 NG2S2 HGP1 1.4000 2 180.00 ! PROT, formamide +OG2D1 CG2O2 CG2R61 CG2R61 1.0250 2 180.00 ! ZOIC, benzoic acid, MBOA, methylbenzoate, jal +OG302 CG2O2 CG2R61 CG2R61 0.8500 2 180.00 ! MBOA, methylbenzoate, jal +OG311 CG2O2 CG2R61 CG2R61 1.0250 2 180.00 ! ZOIC, benzoic acid, jal +OG2D1 CG2O2 CG311 CG321 0.0500 6 180.00 ! AMGA, Alpha Methyl Tert Butyl Glu Acid, cacha, 05/06 ! corrected kevo, 01/08 +OG2D1 CG2O2 CG311 NG2R53 0.0000 1 0.00 ! drug design project, xxwy +OG2D1 CG2O2 CG311 NG2S1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +OG2D1 CG2O2 CG311 HGA1 0.0000 3 0.00 ! AMGA, Alpha Methyl Glu Acid CDCA Amide, cacha, 03/06 +OG302 CG2O2 CG311 CG321 0.0500 6 180.00 ! AMGA, Alpha Methyl Glu Acid CDCA Amide, cacha +OG302 CG2O2 CG311 NG2R53 0.0000 1 0.00 ! B5HE, B5H6 ethyl ester, xxwy +OG302 CG2O2 CG311 NG2S1 0.0000 1 0.00 ! AMGA, Alpha Methyl Glut Acid CDCA Amide, cacha, 05/06 +OG302 CG2O2 CG311 HGA1 0.0000 1 0.00 ! AMGA, Alpha Methyl Glut Acid CDCA Amide, cacha, 05/06 +OG311 CG2O2 CG311 CG321 0.0500 6 180.00 ! drug design project, xxwy +OG311 CG2O2 CG311 NG2R53 0.0000 1 0.00 ! drug design project, xxwy +OG311 CG2O2 CG311 HGA1 0.0500 6 180.00 ! drug design project, xxwy +OG2D1 CG2O2 CG321 CG311 0.0000 6 180.00 ! 576P, standard param [0.05 also acceptable] +OG2D1 CG2O2 CG321 CG321 0.0500 6 180.00 ! LIPID methyl acetate +OG2D1 CG2O2 CG321 CG331 0.0500 6 180.00 ! LIPID methyl acetate +OG2D1 CG2O2 CG321 NG321 0.0000 6 180.00 ! PROT adm jr. 3/19/92, from lipid methyl acetate +OG2D1 CG2O2 CG321 HGA2 0.0000 6 180.00 ! PROT adm jr. 3/19/92, from lipid methyl acetate; LIPID acetic Acid +OG302 CG2O2 CG321 CG321 0.5300 2 180.00 ! LIPID methyl propionate, 12/92 +OG302 CG2O2 CG321 CG331 -0.1500 1 180.00 ! LIPID methyl propionate, 12/92 +OG302 CG2O2 CG321 HGA2 0.0000 3 0.00 ! LIPID acetic Acid +OG311 CG2O2 CG321 CG311 0.0000 6 180.00 ! 576P, standard param [0.05 also acceptable] +OG311 CG2O2 CG321 NG321 0.0000 6 180.00 ! PROT adm jr. 3/19/92, from lipid methyl acetate +OG311 CG2O2 CG321 HGA2 0.0000 6 180.00 ! PROT adm jr. 3/19/92, from lipid methyl acetate +OG2D1 CG2O2 CG331 HGA3 0.0000 6 180.00 ! PROT adm jr. 3/19/92, from lipid methyl acetate; LIPID acetic Acid +OG302 CG2O2 CG331 HGA3 0.0000 3 0.00 ! LIPID acetic Acid +OG311 CG2O2 CG331 HGA3 0.0000 6 180.00 ! PROT adm jr. 3/19/92, from lipid methyl acetate +CG2R61 CG2O2 OG302 CG331 1.2500 1 180.00 ! MBOA, methylbenzoate, jal +CG2R61 CG2O2 OG302 CG331 1.5000 2 180.00 ! MBOA, methylbenzoate, jal +CG2R61 CG2O2 OG302 CG331 0.0500 6 180.00 ! MBOA, methylbenzoate, jal +CG311 CG2O2 OG302 CG301 2.0500 2 180.00 ! ATGM, GAMMA METHYL ALPHA TERT BUTYL GLU ACID CDCA AMIDE, cacha +CG311 CG2O2 OG302 CG321 2.0500 2 180.00 ! ABGA, ALPHA BENZYL GLU ACID CDCA AMIDE, cacha +CG311 CG2O2 OG302 CG331 2.0500 2 180.00 ! AMGA, Alpha Methyl Glu Acid CDCA Amide, cacha +CG321 CG2O2 OG302 CG301 2.0500 2 180.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha +CG321 CG2O2 OG302 CG311 2.0500 2 180.00 ! LIPID methyl acetate +CG321 CG2O2 OG302 CG321 2.0500 2 180.00 ! LIPID methyl acetate ! corrected kevo, 01/08 +CG321 CG2O2 OG302 CG331 2.0500 2 180.00 ! LIPID methyl acetate ! corrected kevo, 01/08 +CG331 CG2O2 OG302 CG311 2.0500 2 180.00 ! LIPID methyl acetate +CG331 CG2O2 OG302 CG321 2.0500 2 180.00 ! LIPID methyl acetate +CG331 CG2O2 OG302 CG331 2.0500 2 180.00 ! LIPID methyl acetate ! corrected kevo, 01/08 +OG2D1 CG2O2 OG302 CG301 0.9650 1 180.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide !cacha,corrected kevo, 01/08 +OG2D1 CG2O2 OG302 CG301 3.8500 2 180.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide !cacha,corrected kevo, 01/08 +OG2D1 CG2O2 OG302 CG311 0.9650 1 180.00 ! LIPID methyl acetate +OG2D1 CG2O2 OG302 CG311 3.8500 2 180.00 ! LIPID methyl acetate +OG2D1 CG2O2 OG302 CG321 0.9650 1 180.00 ! LIPID methyl acetate +OG2D1 CG2O2 OG302 CG321 3.8500 2 180.00 ! LIPID methyl acetate +OG2D1 CG2O2 OG302 CG331 0.9650 1 180.00 ! LIPID methyl acetate +OG2D1 CG2O2 OG302 CG331 3.8500 2 180.00 ! LIPID methyl acetate ! corrected kevo, 01/08 +CG2R61 CG2O2 OG311 HGP1 0.9750 1 180.00 ! ZOIC, benzoic acid, jal +CG2R61 CG2O2 OG311 HGP1 2.7000 2 180.00 ! ZOIC, benzoic acid, jal +CG2R61 CG2O2 OG311 HGP1 0.0500 3 180.00 ! ZOIC, benzoic acid, jal +CG2R61 CG2O2 OG311 HGP1 0.2500 6 180.00 ! ZOIC, benzoic acid, jal +CG311 CG2O2 OG311 HGP1 2.0500 2 180.00 ! drug design project, xxwy +CG321 CG2O2 OG311 HGP1 2.0500 2 180.00 ! PROT adm jr, 10/17/90, acetic Acid C-Oh rotation barrier +CG331 CG2O2 OG311 HGP1 2.0500 2 180.00 ! PROT adm jr, 10/17/90, acetic Acid C-Oh rotation barrier +OG2D1 CG2O2 OG311 HGP1 2.0500 2 180.00 ! PROT adm jr, 10/17/90, acetic Acid C-Oh rotation barrier +HGR52 CG2O2 OG311 HGP1 3.4500 2 180.00 ! FORH, formic acid, xxwy +OG2D2 CG2O3 CG2O5 CG2R61 0.3000 2 180.00 ! BIPHENYL ANALOGS unmodified, peml +OG2D2 CG2O3 CG2O5 OG2D3 0.3000 2 180.00 ! BIPHENYL ANALOGS unmodified, peml +OG2D2 CG2O3 CG2R61 CG2R61 3.1000 2 180.00 ! BIPHENYL ANALOGS, peml +OG2D2 CG2O3 CG301 CG331 0.0500 6 180.00 ! AMOL, alpha-methoxy-lactic acid, og +OG2D2 CG2O3 CG301 OG301 0.5500 2 180.00 ! AMOL, alpha-methoxy-lactic acid, og +OG2D2 CG2O3 CG301 OG311 1.1100 2 180.00 ! AMOL, alpha-methoxy-lactic acid, og +OG2D2 CG2O3 CG311 CG2R61 0.0000 1 0.00 ! FBIF, Fatty acid Binding protein Inhibitor F, cacha. Was 3.1 2 180 ==> reset by kevo. re-optimize!!! +OG2D2 CG2O3 CG311 CG311 0.0500 6 180.00 ! PROT C-terminal AA - standard parameter +OG2D2 CG2O3 CG311 CG321 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG311 CG331 0.0500 6 180.00 ! deleteme DELETEME (we want to use wildcarting) +OG2D2 CG2O3 CG311 NG2R53 0.0000 1 0.00 ! drug design project, xxwy +OG2D2 CG2O3 CG311 NG2S1 0.0000 6 180.00 ! GA, Glut Acid CDCA Amide, cacha +OG2D2 CG2O3 CG311 OG301 0.5500 2 180.00 ! og amop mp2/ccpvtz +OG2D2 CG2O3 CG311 HGA1 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG314 CG311 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG314 CG321 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG314 CG331 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG314 NG3P3 3.2000 2 180.00 ! PROT adm jr. 4/17/94, zwitterionic glycine +OG2D2 CG2O3 CG314 HGA1 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG321 CG311 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG321 CG314 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG321 CG321 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG321 CG331 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG321 NG2S1 0.0500 6 180.00 ! GCA, Glycocholic Acid, cacha, 03/06 +OG2D2 CG2O3 CG321 HGA2 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG324 NG3P3 3.2000 2 180.00 ! PROT adm jr. 4/17/94, zwitterionic glycine +OG2D2 CG2O3 CG324 HGA2 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG331 HGA3 0.0500 6 180.00 ! PROT For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +OG2D2 CG2O3 CG3C51 CG3C52 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D2 CG2O3 CG3C51 NG2S0 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D2 CG2O3 CG3C51 HGA1 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D2 CG2O3 CG3C53 CG3C52 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D2 CG2O3 CG3C53 NG3P2 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D2 CG2O3 CG3C53 HGA1 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +OG2D1 CG2O4 CG2R61 CG2R61 1.0800 2 180.00 ! ALDEHYDE benzaldehyde unmodified +HGR52 CG2O4 CG2R61 CG2R61 1.0800 2 180.00 ! ALDEHYDE benzaldehyde unmodified +OG2D1 CG2O4 CG321 CG331 1.0500 1 180.00 ! ALDEHYDE propionaldehyde unmodified +OG2D1 CG2O4 CG321 CG331 0.4000 2 180.00 ! ALDEHYDE propionaldehyde unmodified +OG2D1 CG2O4 CG321 CG331 0.6000 3 180.00 ! ALDEHYDE propionaldehyde unmodified +OG2D1 CG2O4 CG321 CG331 0.1000 4 180.00 ! ALDEHYDE propionaldehyde unmodified +OG2D1 CG2O4 CG321 CLGA1 0.1000 1 0.00 ! ALDEHYDE chloracetaldehyde unmodified +OG2D1 CG2O4 CG321 CLGA1 1.0000 2 180.00 ! ALDEHYDE chloracetaldehyde unmodified +OG2D1 CG2O4 CG321 CLGA1 0.5500 3 180.00 ! ALDEHYDE chloracetaldehyde unmodified +OG2D1 CG2O4 CG321 HGA2 0.0000 3 180.00 ! PALD, Propionaldehyde, PROT adm jr. 3/19/92, from lipid methyl acetate (unmodified because this may not be analogous to AALD) +HGR52 CG2O4 CG321 CG331 0.0000 3 180.00 ! PALD, Propionaldehyde, PROT adm jr. 3/19/92, from lipid methyl acetate unmodified +HGR52 CG2O4 CG321 CLGA1 0.0000 3 180.00 ! CALD, Chloroacetaldehyde, PROT adm jr. 3/19/92, from lipid methyl acetate unmodified +HGR52 CG2O4 CG321 HGA2 0.0000 3 180.00 ! acetaldehyde, adm 11/08 +OG2D1 CG2O4 CG331 HGA3 0.2000 3 180.00 ! AALD, acetaldehyde, adm 11/08 +HGR52 CG2O4 CG331 HGA3 0.0000 3 180.00 ! acetaldehyde, adm 11/08 +CG2O3 CG2O5 CG2R61 CG2R61 1.5850 2 180.00 ! BIPHENYL ANALOGS unmodified, peml; verified by mcs +CG311 CG2O5 CG2R61 CG2R61 1.5850 2 180.00 ! BIPHENYL ANALOGS unmodified, peml +CG321 CG2O5 CG2R61 CG2R61 0.2700 2 180.00 ! PHEK, phenyl ethyl ketone, mcs +CG331 CG2O5 CG2R61 CG2R61 0.2500 2 180.00 ! PHMK, phenyl methyl ketone, mcs +OG2D3 CG2O5 CG2R61 CG2R61 1.5850 2 180.00 ! BIPHENYL ANALOGS unmodified, peml; verified by mcs +CG2R61 CG2O5 CG311 OG311 0.0000 2 180.00 ! BIPHENYL ANALOGS unmodified, peml +CG2R61 CG2O5 CG311 OG312 0.0000 2 0.00 ! BIPHENYL ANALOGS unmodified, peml +CG2R61 CG2O5 CG311 HGA1 0.0000 1 180.00 ! BIPHENYL ANALOGS unmodified, peml +OG2D3 CG2O5 CG311 OG311 0.0000 2 0.00 ! reverted to BIPHENYL ANALOGS unmodified, peml +OG2D3 CG2O5 CG311 OG312 0.0000 2 180.00 ! reverted to BIPHENYL ANALOGS unmodified, peml +OG2D3 CG2O5 CG311 HGA1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) unmodified +CG2R61 CG2O5 CG321 CG331 0.4000 1 0.00 ! PHEK, phenyl ethyl ketone, mcs +CG2R61 CG2O5 CG321 CG331 0.1700 2 180.00 ! PHEK, phenyl ethyl ketone, mcs +CG2R61 CG2O5 CG321 CG331 0.1300 3 180.00 ! PHEK, phenyl ethyl ketone, mcs +CG2R61 CG2O5 CG321 CG331 0.1000 6 180.00 ! PHEK, phenyl ethyl ketone, mcs +CG2R61 CG2O5 CG321 HGA2 0.1000 3 0.00 ! PHEK, phenyl ethyl ketone; from 3ACP, 3-acetylpyridine; mcs +CG321 CG2O5 CG321 CG321 0.7500 1 0.00 ! CHON, cyclohexanone; from BTON, butanone; yapol +CG321 CG2O5 CG321 CG321 0.1800 2 180.00 ! CHON, cyclohexanone; from BTON, butanone; yapol +CG321 CG2O5 CG321 CG321 0.0650 3 0.00 ! CHON, cyclohexanone; from BTON, butanone; yapol +CG321 CG2O5 CG321 CG321 0.0300 6 0.00 ! CHON, cyclohexanone; from BTON, butanone; yapol +CG321 CG2O5 CG321 HGA2 0.1000 3 0.00 ! CHON, cyclohexanone; from ACO, acetone; yapol +CG331 CG2O5 CG321 CG331 0.7500 1 0.00 ! BTON, butanone, yapol +CG331 CG2O5 CG321 CG331 0.1800 2 180.00 ! BTON, butanone, yapol +CG331 CG2O5 CG321 CG331 0.0650 3 0.00 ! BTON, butanone, yapol +CG331 CG2O5 CG321 CG331 0.0300 6 0.00 ! BTON, butanone, yapol +CG331 CG2O5 CG321 HGA2 0.1000 3 0.00 ! BTON, butanone; from ACO, acetone; yapol +OG2D3 CG2O5 CG321 CG321 0.7500 1 180.00 ! CHON, cyclohexanone; from BTON, butanone; yapol +OG2D3 CG2O5 CG321 CG321 0.1800 2 180.00 ! CHON, cyclohexanone; from BTON, butanone; yapol +OG2D3 CG2O5 CG321 CG321 0.0650 3 180.00 ! CHON, cyclohexanone; from BTON, butanone; yapol +OG2D3 CG2O5 CG321 CG321 0.0300 6 0.00 ! CHON, cyclohexanone; from BTON, butanone; yapol +OG2D3 CG2O5 CG321 CG331 0.7500 1 180.00 ! BTON, butanone, yapol +OG2D3 CG2O5 CG321 CG331 0.1800 2 180.00 ! BTON, butanone, yapol +OG2D3 CG2O5 CG321 CG331 0.0650 3 180.00 ! BTON, butanone, yapol +OG2D3 CG2O5 CG321 CG331 0.0300 6 0.00 ! BTON, butanone, yapol +OG2D3 CG2O5 CG321 HGA2 0.0000 3 0.00 ! BTON, butanone; from ACO, acetone; yapol +CG2DC1 CG2O5 CG331 HGA3 0.1000 3 0.00 ! BEON, butenone; from ACO, acetone; mcs +CG2DC2 CG2O5 CG331 HGA3 0.1000 3 0.00 ! BEON, butenone; from ACO, acetone; mcs +CG2R61 CG2O5 CG331 HGA3 0.1000 3 0.00 ! 3ACP, 3-acetylpyridine; reset by kevo to ketone, RIMP2/cc-pVTZ//MP2/6-31G(d), adm 11/08 +CG321 CG2O5 CG331 HGA3 0.1000 3 0.00 ! BTON, butanone; from ACO, acetone; yapol +CG331 CG2O5 CG331 HGA3 0.1000 3 0.00 ! ketone, RIMP2/cc-pVTZ//MP2/6-31G(d), adm 11/08 +OG2D3 CG2O5 CG331 HGA3 0.0000 3 0.00 ! 3ACP, ACO; ketone, RIMP2/cc-pVTZ//MP2/6-31G(d), adm 11/08 +NG2S1 CG2O6 NG2S1 CG331 1.6000 1 0.00 ! S132R, from NMTU, pram +NG2S1 CG2O6 NG2S1 CG331 2.5000 2 180.00 ! S132R, from NMTU, pram +OG2D1 CG2O6 NG2S1 CG321 4.0000 2 180.00 ! DECB, diethyl carbamate, from DMCB, cacha & xxwy +OG2D1 CG2O6 NG2S1 CG321 0.9500 4 0.00 ! DECB, diethyl carbamate, from DMCB, cacha & xxwy +OG2D1 CG2O6 NG2S1 CG331 4.0000 2 180.00 ! DMCB, dimethyl carbamate, cacha & xxwy +OG2D1 CG2O6 NG2S1 CG331 0.9500 4 0.00 ! DMCB, dimethyl carbamate, cacha & xxwy +OG2D1 CG2O6 NG2S1 HGP1 0.0000 2 180.00 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo +OG302 CG2O6 NG2S1 CG321 4.0000 2 180.00 ! DECB, diethyl carbamate, from DMCB, cacha & xxwy +OG302 CG2O6 NG2S1 CG321 0.9500 4 0.00 ! DECB, diethyl carbamate, from DMCB, cacha & xxwy +OG302 CG2O6 NG2S1 CG331 4.0000 2 180.00 ! DMCB, dimethyl carbamate, cacha & xxwy +OG302 CG2O6 NG2S1 CG331 0.9500 4 0.00 ! DMCB, dimethyl carbamate, cacha & xxwy +OG302 CG2O6 NG2S1 HGP1 0.0000 2 180.00 ! DMCB & DECB, dimethyl & diehtyl carbamate, cacha & kevo +NG2S2 CG2O6 NG2S2 HGP1 1.5000 2 180.00 ! UREA, Urea +OG2D1 CG2O6 NG2S2 HGP1 1.4000 2 180.00 ! PROT adm jr. 4/10/91, acetamide update NOW UREA ==> re-optimize??? +NG2S1 CG2O6 OG302 CG321 0.1500 1 180.00 ! DECB, diethyl carbamate, cacha & xxwy +NG2S1 CG2O6 OG302 CG321 2.2000 2 180.00 ! DECB, diethyl carbamate, cacha & xxwy +NG2S1 CG2O6 OG302 CG321 0.1000 3 180.00 ! DECB, diethyl carbamate, cacha & xxwy +NG2S1 CG2O6 OG302 CG331 0.2500 1 0.00 ! DMCB, dimethyl carbamate, cacha & xxwy +NG2S1 CG2O6 OG302 CG331 1.8500 2 180.00 ! DMCB, dimethyl carbamate, cacha & xxwy +NG2S1 CG2O6 OG302 CG331 0.1200 3 180.00 ! DMCB, dimethyl carbamate, cacha & xxwy +OG2D1 CG2O6 OG302 CG321 0.1500 1 0.00 ! DECB, diethyl carbamate, cacha & xxwy +OG2D1 CG2O6 OG302 CG321 2.2000 2 180.00 ! DECB, diethyl carbamate, cacha & xxwy +OG2D1 CG2O6 OG302 CG321 0.1000 3 0.00 ! DECB, diethyl carbamate, cacha & xxwy +OG2D1 CG2O6 OG302 CG331 0.2500 1 180.00 ! DMCB, dimethyl carbamate, cacha & xxwy +OG2D1 CG2O6 OG302 CG331 1.8500 2 180.00 ! DMCB, dimethyl carbamate, cacha & xxwy +OG2D1 CG2O6 OG302 CG331 0.1200 3 0.00 ! DMCB, dimethyl carbamate, cacha & xxwy +OG302 CG2O6 OG302 CG321 0.1000 1 180.00 ! DECA, diethyl carbonate, xxwy +OG302 CG2O6 OG302 CG321 3.1000 2 180.00 ! DECA, diethyl carbonate, xxwy +OG302 CG2O6 OG302 CG331 0.5500 1 180.00 ! DMCA, dimethyl carbonate, xxwy +OG302 CG2O6 OG302 CG331 2.9500 2 180.00 ! DMCA, dimethyl carbonate, xxwy +OG2D2 CG2O6 OG311 HGP1 2.0000 2 180.00 ! CO31, bicarbonate, MP2/6-31G* dihedral scan, xxwy +SG2D1 CG2O6 SG311 CG331 0.1000 1 180.00 ! DMTT, dimethyl trithiocarbonate, kevo +SG2D1 CG2O6 SG311 CG331 2.1300 2 180.00 ! DMTT, dimethyl trithiocarbonate, kevo +SG311 CG2O6 SG311 CG331 0.1000 1 0.00 ! DMTT, dimethyl trithiocarbonate, kevo +SG311 CG2O6 SG311 CG331 2.1300 2 180.00 ! DMTT, dimethyl trithiocarbonate, kevo +OG2D5 CG2O7 NG2D1 CG331 0.4000 2 180.00 ! MICY, methyl isocyanate, xxwy +CG2R51 CG2R51 CG2R51 CG2R51 15.0000 2 180.00 ! PYRL, pyrrole +CG2R51 CG2R51 CG2R51 CG2RC0 2.0000 2 180.00 ! INDZ, indolizine, kevo +CG2R51 CG2R51 CG2R51 CG2RC7 9.0000 2 180.00 ! AZUL, Azulene, kevo +CG2R51 CG2R51 CG2R51 CG3C52 4.0000 2 180.00 ! CPDE, cyclopentadiene, kevo +CG2R51 CG2R51 CG2R51 NG2R51 4.0000 2 180.00 ! PYRL, pyrrole +CG2R51 CG2R51 CG2R51 NG2R57 4.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 NG2R51; lf +CG2R51 CG2R51 CG2R51 NG2RC0 16.0000 2 180.00 ! INDZ, indolizine, kevo +CG2R51 CG2R51 CG2R51 OG2R50 8.5000 2 180.00 ! FURA, furan +CG2R51 CG2R51 CG2R51 SG2R50 8.5000 2 180.00 ! THIP, thiophene +CG2R51 CG2R51 CG2R51 HGR51 1.0000 2 180.00 ! PYRL, pyrrole +CG2R51 CG2R51 CG2R51 HGR52 1.5000 2 180.00 ! PYRL, pyrrole +CG2R52 CG2R51 CG2R51 CG3C52 6.6000 2 180.00 ! 2HPR, 2H-pyrrole !1,(1a), kevo +CG2R52 CG2R51 CG2R51 CG3C54 7.5000 2 180.00 ! 2HPP, 2H-pyrrole.H+ 1a, kevo +CG2R52 CG2R51 CG2R51 NG2R51 12.0000 2 180.00 ! PYRZ, pyrazole +CG2R52 CG2R51 CG2R51 OG2R50 9.5000 2 180.00 ! ISOX, isoxazole +CG2R52 CG2R51 CG2R51 SG2R50 8.5000 2 180.00 ! ISOT, isothiazole +CG2R52 CG2R51 CG2R51 HGR51 2.6000 2 180.00 ! 2HPR, 2H-pyrrole; 2HPP, 2H-pyrrole.H+, kevo +CG2R52 CG2R51 CG2R51 HGR52 1.5000 2 180.00 ! PYRZ, pyrazole +CG2R53 CG2R51 CG2R51 CG3C52 6.6000 2 180.00 ! B2FO, from CG2R52 CG2R51 CG2R51 CG3C52, ctsai +CG2R53 CG2R51 CG2R51 HGR51 2.6000 2 180.00 ! B2FO, from CG2R52 CG2R51 CG2R51 HGR51, ctsai +CG2R57 CG2R51 CG2R51 NG2R51 4.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 NG2R51; lf +CG2R57 CG2R51 CG2R51 HGR52 1.5000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 HGR52; lf +CG2RC0 CG2R51 CG2R51 CG3C52 6.9000 2 180.00 ! INDE, indene, kevo +CG2RC0 CG2R51 CG2R51 NG2R51 4.0000 2 180.00 ! PROT JWK 05/14/91 fit to indole +CG2RC0 CG2R51 CG2R51 OG2R50 8.5000 2 180.00 ! ZFUR, benzofuran, kevo +CG2RC0 CG2R51 CG2R51 SG2R50 8.5000 2 180.00 ! ZTHP, benzothiophene, kevo +CG2RC0 CG2R51 CG2R51 HGR51 2.8000 2 180.00 ! INDO/TRP +CG2RC0 CG2R51 CG2R51 HGR52 2.8000 2 180.00 ! INDO/TRP +CG2RC7 CG2R51 CG2R51 HGR51 2.7000 2 180.00 ! AZUL, Azulene, kevo +CG321 CG2R51 CG2R51 NG2R50 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89 +CG321 CG2R51 CG2R51 NG2R51 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89 +CG321 CG2R51 CG2R51 NG2R52 2.5000 2 180.00 ! PROT his, adm jr., 6/27/90 +CG321 CG2R51 CG2R51 HGR52 1.0000 2 180.00 ! PROT his, adm jr., 6/27/90 +CG331 CG2R51 CG2R51 NG2R50 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89 +CG331 CG2R51 CG2R51 NG2R51 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89 +CG331 CG2R51 CG2R51 HGR52 1.0000 2 180.00 ! PROT his, adm jr., 6/27/90 +CG3C52 CG2R51 CG2R51 CG3C52 12.0000 2 180.00 ! 3PRL, 3-pyrroline, kevo +CG3C52 CG2R51 CG2R51 NG2R50 7.5000 2 180.00 ! 3HPR, 3H-pyrrole, kevo +CG3C52 CG2R51 CG2R51 NG3C51 11.0000 2 180.00 ! 2PRL, 2-pyrroline, kevo +CG3C52 CG2R51 CG2R51 NG3P2 10.5000 2 180.00 ! 2PRP, 2-pyrroline.H+, kevo +CG3C52 CG2R51 CG2R51 OG3C51 8.8900 2 180.00 ! 2DHF, 2,3-dihydrofuran, kevo +CG3C52 CG2R51 CG2R51 HGR51 2.9000 2 180.00 ! 2HPR, 2H-pyrrole, kevo +CG3C52 CG2R51 CG2R51 HGR52 5.8000 2 180.00 ! 2PRP, 2-pyrroline.H+; 2PRL, 2-pyrroline, kevo +CG3C54 CG2R51 CG2R51 CG3C54 11.5000 2 180.00 ! 3PRP, 3-pyrroline.H+, kevo +CG3C54 CG2R51 CG2R51 HGR51 4.2500 2 180.00 ! 3PRP, 3-pyrroline.H+; 2HPP, 2H-pyrrole.H+, kevo +NG2R50 CG2R51 CG2R51 NG2R51 14.0000 2 180.00 ! PROT his, ADM JR., 7/20/89 +NG2R50 CG2R51 CG2R51 OG2R50 14.0000 2 180.00 ! OXAZ, oxazole +NG2R50 CG2R51 CG2R51 SG2R50 7.0000 2 180.00 ! THAZ, thiazole +NG2R50 CG2R51 CG2R51 HGR51 2.7000 2 180.00 ! 3HPR, 3H-pyrrole, kevo +NG2R50 CG2R51 CG2R51 HGR52 3.0000 2 180.00 ! PROT adm jr., 3/24/92 +NG2R51 CG2R51 CG2R51 HGR51 3.5000 2 180.00 ! INDO/TRP +NG2R51 CG2R51 CG2R51 HGR52 3.0000 2 180.00 ! PROT adm jr., 3/24/92 +NG2R52 CG2R51 CG2R51 NG2R52 12.0000 2 180.00 ! PROT his, adm jr., 6/27/90 +NG2R52 CG2R51 CG2R51 HGR52 2.5000 2 180.00 ! PROT his, adm jr., 6/27/90 +NG2R57 CG2R51 CG2R51 HGR51 3.5000 2 180.00 ! 13BPO, 1,3-bipyrrole; from NG2R51 CG2R51 CG2R51 HGR51; lf +NG2RC0 CG2R51 CG2R51 HGR51 3.7000 2 180.00 ! INDZ, indolizine, kevo +NG3C51 CG2R51 CG2R51 HGR51 3.5000 2 180.00 ! 2PRL, 2-pyrroline, kevo +NG3P2 CG2R51 CG2R51 HGR51 7.0000 2 180.00 ! 7.0 2PRP, 2-pyrroline.H+, kevo +OG2R50 CG2R51 CG2R51 HGR51 4.5000 2 180.00 ! FURA, furan +OG2R50 CG2R51 CG2R51 HGR52 3.0000 2 180.00 ! OXAZ, oxazole +OG3C51 CG2R51 CG2R51 HGR51 3.7000 2 180.00 ! 2DHF, 2,3-dihydrofuran, kevo +SG2R50 CG2R51 CG2R51 HGR51 4.0000 2 180.00 ! THIP, thiophene +SG2R50 CG2R51 CG2R51 HGR52 5.5000 2 180.00 ! THAZ, thiazole +HGR51 CG2R51 CG2R51 HGR51 1.0000 2 180.00 ! INDO/TRP +HGR51 CG2R51 CG2R51 HGR52 1.0000 2 180.00 ! PYRL, pyrrole +HGR52 CG2R51 CG2R51 HGR52 1.0000 2 180.00 ! PROT his, adm jr., 6/27/90, his +CG2R51 CG2R51 CG2R52 NG2R50 8.5000 2 180.00 ! PYRZ, pyrazole +CG2R51 CG2R51 CG2R52 NG2R52 4.1500 2 180.00 ! 4.1 2HPP, 2H-pyrrole.H+ 1, kevo +CG2R51 CG2R51 CG2R52 HGR52 3.8000 2 180.00 ! PYRZ, pyrazole +HGR51 CG2R51 CG2R52 NG2R50 4.5000 2 180.00 !v 4.25 2HPR, 2H-pyrrole !wC4H !coupled with pyrz, pyrazole, kevo +HGR51 CG2R51 CG2R52 NG2R52 4.5000 2 180.00 ! 2HPP, 2H-pyrrole.H+, kevo +HGR51 CG2R51 CG2R52 HGR52 0.1000 2 180.00 ! 2HPR, 2H-pyrrole; 2HPP, 2H-pyrrole.H+, kevo +CG2R51 CG2R51 CG2R53 OG2D1 1.2000 2 180.00 ! B2FO, from CG2RC0 CG25C1 CG2R53 OG2D1, ctsai +CG2R51 CG2R51 CG2R53 OG3C51 0.4100 1 180.00 ! B2FO, 5H-furan-2-one, ctsai +HGR51 CG2R51 CG2R53 OG2D1 4.5000 2 180.00 ! B2FO, from OG2R50 CG2R51 CG2R51 HGR51, ctsai +HGR51 CG2R51 CG2R53 OG3C51 3.7000 2 180.00 ! B2FO, from OG3C51 CG2R51 CG2R51 HGR51, ctsai +CG2R51 CG2R51 CG2R57 CG2R51 15.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 CG2R51; lf +CG2R51 CG2R51 CG2R57 CG2R57 2.1000 2 180.00 ! 33BPO, 3,3-bipyrrole, lf +CG2R51 CG2R51 CG2R57 NG2R57 1.9000 2 180.00 ! 13BPO, 1,3-bipyrrole, lf +CG2R51 CG2R51 CG2R57 HGR52 1.5000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 HGR52; lf +NG2R51 CG2R51 CG2R57 CG2R51 4.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 NG2R51; lf +NG2R51 CG2R51 CG2R57 CG2R57 2.1000 2 180.00 ! 33BPO, 3,3-bipyrrole, lf +NG2R51 CG2R51 CG2R57 NG2R57 1.9000 2 180.00 ! 13BPO, 1,3-bipyrrole, lf +HGR51 CG2R51 CG2R57 CG2R51 1.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 HGR51; lf +HGR51 CG2R51 CG2R57 CG2R57 3.5000 2 180.00 ! 33BPO, 3,3-bipyrrole; from NG2R51 CG2R51 CG2R51 HGR51; lf +HGR51 CG2R51 CG2R57 NG2R57 3.5000 2 180.00 ! 13BPO, 1,3-bipyrrole; from NG2R51 CG2R51 CG2R51 HGR51; lf +HGR52 CG2R51 CG2R57 CG2R51 1.5000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 CG2R51 HGR52; lf +HGR52 CG2R51 CG2R57 CG2R57 3.0000 2 180.00 ! 33BPO, 3,3-bipyrrole, lf +HGR52 CG2R51 CG2R57 NG2R57 3.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from NG2R51 CG2R51 CG2R51 HGR52; lf +CG2R51 CG2R51 CG2RC0 CG2R61 3.0000 2 180.00 ! PROT JWK 09/05/89 +CG2R51 CG2R51 CG2RC0 CG2RC0 4.0000 2 180.00 ! PROT JWK 05/14/91 fit to indole +CG2R51 CG2R51 CG2RC0 NG2RC0 12.0000 2 180.00 ! INDZ, indolizine, kevo +CG321 CG2R51 CG2RC0 CG2R61 2.5000 2 180.00 ! INDO/TRP +CG321 CG2R51 CG2RC0 CG2RC0 3.0000 2 180.00 ! INDO/TRP +CG331 CG2R51 CG2RC0 CG2R61 2.5000 2 180.00 ! INDO/TRP +CG331 CG2R51 CG2RC0 CG2RC0 2.5000 2 180.00 ! INDO/TRP +NG2R51 CG2R51 CG2RC0 CG2R61 1.5000 2 180.00 ! ISOI, isoindole, kevo +NG2R51 CG2R51 CG2RC0 CG2RC0 9.0000 2 180.00 ! ISOI, isoindole, kevo +HGR51 CG2R51 CG2RC0 CG2R61 2.8000 2 180.00 ! INDO/TRP +HGR51 CG2R51 CG2RC0 CG2RC0 2.6000 2 180.00 ! INDO/TRP +HGR51 CG2R51 CG2RC0 NG2RC0 0.8000 2 180.00 ! INDZ, indolizine, kevo +HGR52 CG2R51 CG2RC0 CG2R61 0.2500 2 180.00 ! ISOI, isoindole, kevo +HGR52 CG2R51 CG2RC0 CG2RC0 0.2500 2 180.00 ! ISOI, isoindole, kevo +CG2R51 CG2R51 CG2RC7 CG2R71 2.0000 2 180.00 ! AZUL, Azulene, kevo +CG2R51 CG2R51 CG2RC7 CG2RC7 4.0000 2 180.00 ! AZUL, Azulene, kevo +HGR51 CG2R51 CG2RC7 CG2R71 2.2000 2 180.00 ! AZUL, Azulene, kevo +HGR51 CG2R51 CG2RC7 CG2RC7 2.2000 2 180.00 ! AZUL, Azulene, kevo +CG2R51 CG2R51 CG321 CG311 0.2000 1 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 CG311 0.2700 2 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 CG311 0.0000 3 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 CG314 0.2000 1 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 CG314 0.2700 2 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 CG314 0.0000 3 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 CG331 0.2000 1 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 CG331 0.2700 2 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 CG331 0.0000 3 0.00 ! PROT 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CG2R51 CG2R51 CG321 HGA2 0.0000 3 0.00 ! PROT 4-methylimidazole 4-21G//rot bar. adm jr., 9/4/89 +CG2RC0 CG2R51 CG321 CG311 0.0900 2 180.00 ! INDO/TRP +CG2RC0 CG2R51 CG321 CG311 0.5700 3 0.00 ! INDO/TRP +CG2RC0 CG2R51 CG321 CG314 0.0900 2 180.00 ! INDO/TRP +CG2RC0 CG2R51 CG321 CG314 0.5700 3 0.00 ! INDO/TRP +CG2RC0 CG2R51 CG321 CG331 0.2500 2 180.00 ! INDO/TRP +CG2RC0 CG2R51 CG321 HGA2 0.2000 3 0.00 ! INDO/TRP +NG2R50 CG2R51 CG321 CG311 0.1900 3 0.00 ! PROT HIS CB-CG TORSION, +NG2R50 CG2R51 CG321 CG314 0.1900 3 0.00 ! PROT HIS CB-CG TORSION, +NG2R50 CG2R51 CG321 HGA2 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +NG2R51 CG2R51 CG321 CG311 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +NG2R51 CG2R51 CG321 CG314 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +NG2R51 CG2R51 CG321 CG331 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +NG2R51 CG2R51 CG321 HGA2 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +NG2R52 CG2R51 CG321 CG311 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +NG2R52 CG2R51 CG321 CG314 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +NG2R52 CG2R51 CG321 CG331 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +NG2R52 CG2R51 CG321 HGA2 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +CG2R51 CG2R51 CG331 HGA3 0.0000 3 0.00 ! PROT 4-methylimidazole 4-21G//rot bar. adm jr., 9/4/89 +CG2RC0 CG2R51 CG331 HGA3 0.2000 3 0.00 ! INDO/TRP +NG2R51 CG2R51 CG331 HGA3 0.1900 3 0.00 ! PROT 4-METHYLIMIDAZOLE 4-21G//ROT BAR. ADM JR., 9/4/89 +CG2R51 CG2R51 CG3C52 CG2R51 2.0500 3 180.00 ! CPDE, cyclopentadiene, kevo +CG2R51 CG2R51 CG3C52 CG2R52 3.5000 3 180.00 ! 3HPR, 3H-pyrrole, kevo +CG2R51 CG2R51 CG3C52 CG2R53 3.5000 3 180.00 ! A2FO, from CG2R51 CG2R51 CG3C52 CG2R52, ctsai +CG2R51 CG2R51 CG3C52 CG2RC0 1.5000 3 180.00 ! INDE, indene, kevo +CG2R51 CG2R51 CG3C52 CG3C52 0.0500 3 180.00 ! 2PRL, 2-pyrroline, kevo +CG2R51 CG2R51 CG3C52 CG3C54 0.5000 3 180.00 ! 0.05 2PRL, 2-pyrroline, kevo +CG2R51 CG2R51 CG3C52 NG2R50 3.6000 2 180.00 ! 2HPR, 2H-pyrrole !1a, kevo +CG2R51 CG2R51 CG3C52 NG3C51 0.7000 3 180.00 ! 0.70 0.50 3PRL, 3-pyrroline, kevo +CG2R51 CG2R51 CG3C52 OG3C51 0.2800 1 180.00 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG2R51 CG3C52 OG3C51 0.9800 2 180.00 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG2R51 CG3C52 OG3C51 1.7500 3 180.00 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG2R51 CG3C52 HGA2 0.0000 3 0.00 ! 2PRP, 2-pyrroline.H+; 2PRL, 2-pyrroline, kevo +HGR51 CG2R51 CG3C52 CG2R51 2.0500 3 0.00 ! CPDE, cyclopentadiene, kevo +HGR51 CG2R51 CG3C52 CG2R52 1.5000 3 0.00 ! 3HPR, 3H-pyrrole, kevo +HGR51 CG2R51 CG3C52 CG2R53 1.5000 3 0.00 ! A2FO, from HGR51 CG2R51 CG3C52 CG2R52, ctsai +HGR51 CG2R51 CG3C52 CG2RC0 1.9000 3 0.00 ! INDE, indene, kevo +HGR51 CG2R51 CG3C52 CG3C52 2.0000 2 180.00 ! 2PRL, 2-pyrroline, kevo +HGR51 CG2R51 CG3C52 CG3C54 1.5000 2 180.00 ! 2.00 2PRL, 2-pyrroline, kevo +HGR51 CG2R51 CG3C52 NG2R50 4.3000 2 180.00 !v 2.6 2HPR, 2H-pyrrole !wC3H, kevo +HGR51 CG2R51 CG3C52 NG3C51 3.1000 2 180.00 ! 3PRL, 3-pyrroline, kevo +HGR51 CG2R51 CG3C52 OG3C51 3.1000 2 180.00 ! B2FO, from HGR51 CG2R51 CG3C52 NG3C51, ctsai +HGR51 CG2R51 CG3C52 HGA2 0.0000 3 0.00 ! 2PRP, 2-pyrroline.H+; 2PRL, 2-pyrroline, kevo +CG2R51 CG2R51 CG3C54 NG2R52 2.8000 2 180.00 ! 2.7 2.4 2HPP, 2H-pyrrole.H+ 1a, kevo +CG2R51 CG2R51 CG3C54 NG3P2 0.9000 3 180.00 ! 0.9 3PRP, 3-pyrroline.H+, kevo +CG2R51 CG2R51 CG3C54 HGA2 0.0000 3 0.00 ! 3PRP, 3-pyrroline.H+; 2HPP, 2H-pyrrole.H+, kevo +HGR51 CG2R51 CG3C54 NG2R52 5.0000 2 180.00 ! 2HPP, 2H-pyrrole.H+, kevo +HGR51 CG2R51 CG3C54 NG3P2 1.7000 2 180.00 ! 3PRP, 3-pyrroline.H+, kevo +HGR51 CG2R51 CG3C54 HGA2 0.0000 3 0.00 ! 3PRP, 3-pyrroline.H+; 2HPP, 2H-pyrrole.H+, kevo +CG2R51 CG2R51 NG2R50 CG2R52 5.4000 2 180.00 ! 3HPR, 3H-pyrrole, kevo +CG2R51 CG2R51 NG2R50 CG2R53 14.0000 2 180.00 ! PROT his, ADM JR., 7/20/89 +CG2R51 CG2R51 NG2R50 NG2R50 8.5000 2 180.00 ! OXAD, oxadiazole123 +CG321 CG2R51 NG2R50 CG2R53 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89, FROM HGR52 CG2R51 NG2R50CPH2 +HGR52 CG2R51 NG2R50 CG2R52 2.0000 2 180.00 ! 3HPR, 3H-pyrrole, kevo +HGR52 CG2R51 NG2R50 CG2R53 3.0000 2 180.00 ! PROT adm jr., 3/24/92 +HGR52 CG2R51 NG2R50 NG2R50 5.5000 2 180.00 ! OXAD, oxadiazole123 +CG2R51 CG2R51 NG2R51 CG2R51 10.0000 2 180.00 ! PYRL, pyrrole +CG2R51 CG2R51 NG2R51 CG2R53 14.0000 2 180.00 ! PROT his, ADM JR., 7/20/89 +CG2R51 CG2R51 NG2R51 CG2RC0 5.0000 2 180.00 ! PROT JWK 05/14/91 fit to indole +CG2R51 CG2R51 NG2R51 CG321 0.0000 1 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from CG2R51 CG2R51 NG2R51 CG3C51, kevo +CG2R51 CG2R51 NG2R51 CG3C51 0.0000 1 0.00 ! NA, glycosyl linkage +CG2R51 CG2R51 NG2R51 NG2R50 10.0000 2 180.00 ! PYRZ, pyrazole +CG2R51 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! PROT his, adm jr., 7/20/89 +CG2R57 CG2R51 NG2R51 CG2R51 10.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 NG2R51 CG2R51; lf +CG2R57 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 NG2R51 HGP1; lf +CG2RC0 CG2R51 NG2R51 CG2R51 6.0000 2 180.00 ! ISOI, isoindole, kevo +CG2RC0 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! ISOI, isoindole, kevo +CG321 CG2R51 NG2R51 CG2R53 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89, FROM HGR52 CG2R51 NG2R51CPH2 +CG321 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! PROT his, adm jr., 7/22/89, FROM HGR52 CG2R51 NG2R51H +CG331 CG2R51 NG2R51 CG2R53 3.0000 2 180.00 ! PROT his, ADM JR., 7/22/89, FROM HGR52 CG2R51 NG2R51CPH2 +CG331 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! PROT his, adm jr., 7/22/89, FROM HGR52 CG2R51 NG2R51H +HGR52 CG2R51 NG2R51 CG2R51 2.6000 2 180.00 ! PYRL, pyrrole +HGR52 CG2R51 NG2R51 CG2R53 3.0000 2 180.00 ! PROT adm jr., 3/24/92 +HGR52 CG2R51 NG2R51 CG2RC0 2.6000 2 180.00 ! INDO/TRP +HGR52 CG2R51 NG2R51 CG321 0.0000 2 180.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from HGR52 CG2R53 NG2R51 CG331, kevo +HGR52 CG2R51 NG2R51 CG3C51 0.0000 2 180.00 ! NA, glycosyl linkage +HGR52 CG2R51 NG2R51 NG2R50 3.0000 2 180.00 ! PYRZ, pyrazole +HGR52 CG2R51 NG2R51 HGP1 1.0000 2 180.00 ! PROT adm jr., 3/24/92 +CG2R51 CG2R51 NG2R52 CG2R53 12.0000 2 180.00 ! PROT his, ADM JR., 7/20/89 +CG2R51 CG2R51 NG2R52 HGP2 1.4000 2 180.00 ! PROT his, adm jr., 6/27/90 +CG321 CG2R51 NG2R52 CG2R53 2.5000 2 180.00 ! PROT his, adm jr., 6/27/90 +CG321 CG2R51 NG2R52 HGP2 3.0000 2 180.00 ! PROT his, adm jr., 7/22/89, FROM HC NG2R52CPH1 HA +HGR52 CG2R51 NG2R52 CG2R53 2.5000 2 180.00 ! PROT his, adm jr., 6/27/90 +HGR52 CG2R51 NG2R52 HGP2 3.0000 2 180.00 ! PROT his, adm jr., 6/27/90 +CG2R51 CG2R51 NG2R57 CG2R51 10.0000 2 180.00 ! 13BPO, 1,3-bipyrrole; from CG2R51 CG2R51 NG2R51 CG2R51; lf +CG2R51 CG2R51 NG2R57 CG2R57 0.2000 2 180.00 ! 13BPO, 1,3-bipyrrole, lf +CG2R51 CG2R51 NG2R57 NG2R57 0.2000 2 180.00 ! 11BPO, 1,1-bipyrrole, lf +HGR52 CG2R51 NG2R57 CG2R51 2.6000 2 180.00 ! 13BPO, 1,3-bipyrrole; from HGR52 CG2R51 NG2R51 CG2R51; lf +HGR52 CG2R51 NG2R57 CG2R57 1.5000 2 180.00 ! 13BPO, 1,3-bipyrrole, lf +HGR52 CG2R51 NG2R57 NG2R57 1.1000 2 180.00 ! 11BPO, 1,1-bipyrrole, lf +CG2R51 CG2R51 NG2RC0 CG2R61 3.0000 2 180.00 ! INDZ, indolizine, kevo +CG2R51 CG2R51 NG2RC0 CG2RC0 9.0000 2 180.00 ! INDZ, indolizine, kevo +HGR52 CG2R51 NG2RC0 CG2R61 1.4000 2 180.00 ! INDZ, indolizine, kevo +HGR52 CG2R51 NG2RC0 CG2RC0 1.4000 2 180.00 ! INDZ, indolizine, kevo +CG2R51 CG2R51 NG3C51 CG3C52 8.0000 2 180.00 ! 2PRL, 2-pyrroline, kevo +CG2R51 CG2R51 NG3C51 HGP1 0.0000 3 0.00 ! 2PRL, 2-pyrroline, kevo +HGR52 CG2R51 NG3C51 CG3C52 3.0000 2 180.00 ! 2PRL, 2-pyrroline, kevo +HGR52 CG2R51 NG3C51 HGP1 0.0000 3 0.00 ! 2PRL, 2-pyrroline, kevo +CG2R51 CG2R51 NG3P2 CG3C54 0.3000 3 0.00 ! 2PRP, 2-pyrroline.H+, kevo +CG2R51 CG2R51 NG3P2 HGP2 0.3000 3 180.00 ! 2PRP, 2-pyrroline.H+, kevo +HGR52 CG2R51 NG3P2 CG3C54 0.0000 3 180.00 ! 2PRP, 2-pyrroline.H+, kevo +HGR52 CG2R51 NG3P2 HGP2 0.0000 3 180.00 ! 2PRP, 2-pyrroline.H+, kevo +CG2R51 CG2R51 OG2R50 CG2R51 7.5000 2 180.00 ! FURA, furan @@@@@ Kenno: 8.5 --> 7.5 @@@@@ +CG2R51 CG2R51 OG2R50 CG2R53 8.5000 2 180.00 ! OXAZ, oxazole +CG2R51 CG2R51 OG2R50 CG2RC0 8.5000 2 180.00 ! ZFUR, benzofuran, kevo +CG2R51 CG2R51 OG2R50 NG2R50 8.5000 2 180.00 ! ISOX, isoxazole +HGR52 CG2R51 OG2R50 CG2R51 3.8000 2 180.00 ! FURA, furan +HGR52 CG2R51 OG2R50 CG2R53 3.8000 2 180.00 ! OXAZ, oxazole +HGR52 CG2R51 OG2R50 CG2RC0 3.0000 2 180.00 ! ZFUR, benzofuran, kevo +HGR52 CG2R51 OG2R50 NG2R50 5.5000 2 180.00 ! ISOX, isoxazole +CG2R51 CG2R51 OG3C51 CG2R53 1.2310 2 180.00 ! A2FO, 3H-furan-2-one, ctsai +CG2R51 CG2R51 OG3C51 CG2R53 2.2940 3 180.00 ! A2FO, 3H-furan-2-one, ctsai +CG2R51 CG2R51 OG3C51 CG3C52 4.3400 2 180.00 ! 2DHF, 2,3-dihydrofuran, kevo +HGR52 CG2R51 OG3C51 CG2R53 2.1000 2 180.00 ! A2FO, from HGR52 CG2R51 OG3C51 CG3C52, ctsai +HGR52 CG2R51 OG3C51 CG3C52 2.1000 2 180.00 ! 2DHF, 2,3-dihydrofuran, kevo +CG2R51 CG2R51 SG2R50 CG2R51 8.5000 2 180.00 ! THIP, thiophene +CG2R51 CG2R51 SG2R50 CG2R53 8.5000 2 180.00 ! THAZ, thiazole @@@@@ Kenno: 8.0 --> 8.5 @@@@@ +CG2R51 CG2R51 SG2R50 CG2RC0 8.5000 2 180.00 ! ZTHP, benzothiophene, kevo +CG2R51 CG2R51 SG2R50 NG2R50 9.0000 2 180.00 ! ISOT, isothiazole +HGR52 CG2R51 SG2R50 CG2R51 4.0000 2 180.00 ! THIP, thiophene +HGR52 CG2R51 SG2R50 CG2R53 5.5000 2 180.00 ! THAZ, thiazole +HGR52 CG2R51 SG2R50 CG2RC0 3.9000 2 180.00 ! ZTHP, benzothiophene, kevo +HGR52 CG2R51 SG2R50 NG2R50 4.5000 2 180.00 ! ISOT, isothiazole +NG2R50 CG2R52 CG2R52 NG2R50 9.5000 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf +NG2R50 CG2R52 CG2R52 HGR52 3.9000 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf +HGR52 CG2R52 CG2R52 HGR52 0.1700 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf +NG2R50 CG2R52 CG2RC0 CG2R61 2.0000 2 180.00 ! INDA, 1H-indazole, kevo +NG2R50 CG2R52 CG2RC0 CG2RC0 8.0000 2 180.00 ! INDA, 1H-indazole, kevo +HGR52 CG2R52 CG2RC0 CG2R61 2.4000 2 180.00 ! INDA, 1H-indazole, kevo +HGR52 CG2R52 CG2RC0 CG2RC0 2.4000 2 180.00 ! INDA, 1H-indazole, kevo +NG2R50 CG2R52 CG3C52 CG2R51 3.5000 3 180.00 ! 3HPR, 3H-pyrrole, kevo +NG2R50 CG2R52 CG3C52 CG2RC0 3.5000 3 180.00 ! 3HIN, 3H-indole, kevo +NG2R50 CG2R52 CG3C52 CG3C52 2.8000 3 180.00 ! 2.85 2PRZ, 2-pyrazoline, kevo +NG2R50 CG2R52 CG3C52 HGA2 1.4000 3 0.00 ! 2PRZ, 2-pyrazoline, kevo +HGR52 CG2R52 CG3C52 CG2R51 1.3000 3 0.00 ! 3HPR, 3H-pyrrole, kevo +HGR52 CG2R52 CG3C52 CG2RC0 2.0000 3 0.00 ! 3HIN, 3H-indole, kevo +HGR52 CG2R52 CG3C52 CG3C52 4.0000 2 180.00 ! 2PRZ, 2-pyrazoline, kevo +HGR52 CG2R52 CG3C52 HGA2 0.0000 3 0.00 ! 2PRZ, 2-pyrazoline, kevo +CG2R51 CG2R52 NG2R50 CG3C52 5.5000 2 180.00 ! 2HPR, 2H-pyrrole !1,1a, kevo +CG2R51 CG2R52 NG2R50 NG2R51 12.0000 2 180.00 ! PYRZ, pyrazole +CG2R51 CG2R52 NG2R50 OG2R50 12.0000 2 180.00 ! ISOX, isoxazole +CG2R51 CG2R52 NG2R50 SG2R50 8.5000 2 180.00 ! ISOT, isothiazole +CG2R52 CG2R52 NG2R50 NG2R51 12.0000 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf +CG2RC0 CG2R52 NG2R50 NG2R51 13.5000 2 180.00 ! INDA, 1H-indazole, kevo +CG3C52 CG2R52 NG2R50 CG2R51 6.5000 2 180.00 ! 3HPR, 3H-pyrrole, kevo +CG3C52 CG2R52 NG2R50 CG2RC0 13.0000 2 180.00 ! 3HIN, 3H-indole, kevo +CG3C52 CG2R52 NG2R50 NG3C51 17.0000 2 180.00 ! 2PRZ, 2-pyrazoline, kevo +HGR52 CG2R52 NG2R50 CG2R51 5.0000 2 180.00 ! 3HPR, 3H-pyrrole, kevo +HGR52 CG2R52 NG2R50 CG2RC0 4.0000 2 180.00 ! 3HIN, 3H-indole, kevo +HGR52 CG2R52 NG2R50 CG3C52 7.6000 2 180.00 !v 7.1 2HPR, 2H-pyrrole !wC5H, kevo +HGR52 CG2R52 NG2R50 NG2R51 3.8000 2 180.00 ! PYRZ, pyrazole +HGR52 CG2R52 NG2R50 NG3C51 5.0000 2 180.00 ! 2PRZ, 2-pyrazoline, kevo +HGR52 CG2R52 NG2R50 OG2R50 5.5000 2 180.00 ! ISOX, isoxazole +HGR52 CG2R52 NG2R50 SG2R50 4.5000 2 180.00 ! ISOT, isothiazole +CG2R51 CG2R52 NG2R52 CG3C54 6.0000 2 180.00 ! 2HPP, 2H-pyrrole.H+ 1a, kevo +CG2R51 CG2R52 NG2R52 HGP2 2.7000 2 180.00 ! 2.5 2HPP, 2H-pyrrole.H+, kevo +HGR52 CG2R52 NG2R52 CG3C54 9.0000 2 180.00 ! 2HPP, 2H-pyrrole.H+, kevo +HGR52 CG2R52 NG2R52 HGP2 0.0000 2 180.00 ! 2HPP, 2H-pyrrole.H+, kevo +NG2R43 CG2R53 CG3C41 CG3C41 3.0000 3 0.00 ! AZDO, 2-azetidinone, kevo +NG2R43 CG2R53 CG3C41 HGA2 0.5700 3 0.00 ! AZDO, 2-azetidinone; lsk & kevo +OG2D1 CG2R53 CG3C41 CG3C41 0.5700 3 0.00 ! AZDO, 2-azetidinone, kevo +OG2D1 CG2R53 CG3C41 HGA2 0.5700 3 0.00 ! AZDO, 2-azetidinone, kevo +NG2R53 CG2R53 CG3C52 CG3C52 1.0500 3 180.00 ! 2PDO, 2-pyrrolidinone, kevo +NG2R53 CG2R53 CG3C52 HGA2 0.0000 3 180.00 ! 2PDO, 2-pyrrolidinone, kevo +OG2D1 CG2R53 CG3C52 CG2R51 0.0800 3 0.00 ! A2FO, from OG2D1 CG2R53 CG3C52 CG3C52, ctsai +OG2D1 CG2R53 CG3C52 CG3C52 0.0800 3 0.00 ! 2PDO, 2-pyrrolidinone, kevo +OG2D1 CG2R53 CG3C52 HGA2 0.0000 3 0.00 != 2PDO, 2-pyrrolidinone, kevo +OG3C51 CG2R53 CG3C52 CG2R51 0.2190 3 0.00 ! A2FO, 3H-furan-2-one, ctsai +OG3C51 CG2R53 CG3C52 CG2R51 0.2890 4 0.00 ! A2FO, 3H-furan-2-one, ctsai +OG3C51 CG2R53 CG3C52 CG3C52 2.3700 2 0.00 ! GBL, Gamma-batyrolactone, ctsai +OG3C51 CG2R53 CG3C52 HGA2 0.0000 3 180.00 ! GBL, from NG2R53 CG2R53 CG3C52 HGA2, ctsai +CG3C41 CG2R53 NG2R43 CG3C41 1.5000 2 180.00 ! AZDO, 2-azetidinone, kevo +CG3C41 CG2R53 NG2R43 HGP1 0.0000 1 0.00 ! AZDO, 2-azetidinone, kevo +OG2D1 CG2R53 NG2R43 CG3C41 2.5000 2 180.00 ! AZDO, 2-azetidinone, kevo +OG2D1 CG2R53 NG2R43 HGP1 2.5000 2 180.00 ! AZDO, 2-azetidinone, kevo +NG2R50 CG2R53 NG2R50 CG2R53 10.0000 2 180.00 ! TRZ4, triazole124, xxwy +NG2R50 CG2R53 NG2R50 NG2R51 12.0000 2 180.00 ! TRZ4, triazole124, xxwy +NG2R50 CG2R53 NG2R50 OG2R50 12.0000 2 180.00 ! OXD4, oxadiazole124, xxwy +NG2R51 CG2R53 NG2R50 CG2R51 14.0000 2 180.00 ! PROT his, ADM JR., 7/20/89 +NG2R51 CG2R53 NG2R50 CG2R53 12.0000 2 180.00 ! TRZ4, triazole124, xxwy +NG2R51 CG2R53 NG2R50 CG2RC0 14.0000 2 180.00 ! NA A +NG3C51 CG2R53 NG2R50 CG3C52 18.0000 2 180.00 ! 14 ! 13 2IMI, 2-imidazoline 1, kevo +OG2R50 CG2R53 NG2R50 CG2R51 14.0000 2 180.00 ! OXAZ, oxazole +OG2R50 CG2R53 NG2R50 CG2R53 12.0000 2 180.00 ! OXD4, oxadiazole124, xxwy +SG2R50 CG2R53 NG2R50 CG2R51 6.0000 2 180.00 ! THAZ, thiazole @@@@@ Kenno: 7.0 --> 6.0 @@@@@ +SG2R50 CG2R53 NG2R50 CG2RC0 12.5000 2 180.00 ! ZTHZ, benzothiazole, kevo +HGR52 CG2R53 NG2R50 CG2R51 2.0000 2 180.00 ! NA bases +HGR52 CG2R53 NG2R50 CG2R53 5.5000 2 180.00 ! TRZ4, triazole124, xxwy +HGR52 CG2R53 NG2R50 CG2RC0 5.2000 2 180.00 ! NA A +HGR52 CG2R53 NG2R50 CG3C52 11.4000 2 180.00 ! 2IMI, 2-imidazoline, kevo +HGR52 CG2R53 NG2R50 NG2R51 3.3000 2 180.00 ! TRZ4, triazole124, xxwy +HGR52 CG2R53 NG2R50 OG2R50 3.8000 2 180.00 ! OXD4, oxadiazole124, xxwy +CG25C1 CG2R53 NG2R51 CG2RC0 2.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C1 CG2R53 NG2R51 HGP1 0.3000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2R53 NG2R51 CG2RC0 2.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2R53 NG2R51 HGP1 0.3000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +NG2R50 CG2R53 NG2R51 CG2R51 14.0000 2 180.00 ! PROT his, ADM JR., 7/20/89 +NG2R50 CG2R53 NG2R51 CG2RC0 6.0000 2 180.00 ! NA A +NG2R50 CG2R53 NG2R51 CG331 11.0000 2 180.00 ! 9MAD, 9-Methyl-Adenine, kevo for gsk/ibm +NG2R50 CG2R53 NG2R51 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage +NG2R50 CG2R53 NG2R51 CG3RC1 1.5000 2 180.00 ! NA bases +NG2R50 CG2R53 NG2R51 NG2R50 10.0000 2 180.00 ! TRZ4, triazole124, xxwy +NG2R50 CG2R53 NG2R51 HGP1 1.0000 2 180.00 ! PROT his, ADM JR., 7/20/89 +OG2D1 CG2R53 NG2R51 CG2RC0 2.5000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +OG2D1 CG2R53 NG2R51 HGP1 0.8600 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +HGR52 CG2R53 NG2R51 CG2R51 3.0000 2 180.00 ! PROT his, adm jr., 6/27/90 +HGR52 CG2R53 NG2R51 CG2RC0 5.6000 2 180.00 ! NA G +HGR52 CG2R53 NG2R51 CG331 0.0000 2 180.00 ! 9MAD, 9-Methyl-Adenine, kevo for gsk/ibm +HGR52 CG2R53 NG2R51 CG3C51 0.0000 2 180.00 ! NA, glycosyl linkage +HGR52 CG2R53 NG2R51 CG3RC1 1.5000 2 180.00 ! NA bases +HGR52 CG2R53 NG2R51 NG2R50 1.7000 2 180.00 ! TRZ4, triazole124, xxwy +HGR52 CG2R53 NG2R51 HGP1 1.0000 2 180.00 ! PROT his, adm jr., 6/27/90 +NG2R52 CG2R53 NG2R52 CG2R51 12.0000 2 180.00 ! PROT his, ADM JR., 7/20/89 +NG2R52 CG2R53 NG2R52 CG3C54 7.7000 2 180.00 ! 7.7 2IMP, 2-imidazoline.H+, kevo +NG2R52 CG2R53 NG2R52 HGP2 1.4000 2 180.00 ! PROT his, adm jr., 6/27/90 +HGR53 CG2R53 NG2R52 CG2R51 3.0000 2 180.00 ! PROT his, adm jr., 6/27/90 +HGR53 CG2R53 NG2R52 CG3C54 6.3000 2 180.00 ! 2IMP, 2-imidazoline.H+, kevo +HGR53 CG2R53 NG2R52 HGP2 0.0000 2 180.00 ! PROT his, adm jr., 6/27/90, YES, 0.0 +CG251O CG2R53 NG2R53 CG2R53 1.5000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG251O CG2R53 NG2R53 CG311 1.6000 1 0.00 ! drug design project, xxwy +CG251O CG2R53 NG2R53 CG311 2.5000 2 180.00 ! drug design project, xxwy +CG251O CG2R53 NG2R53 HGP1 1.7000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O CG2R53 NG2R53 CG2R53 1.5000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG252O CG2R53 NG2R53 CG311 1.6000 1 0.00 ! drug design project, xxwy +CG252O CG2R53 NG2R53 CG311 2.5000 2 180.00 ! drug design project, xxwy +CG252O CG2R53 NG2R53 HGP1 1.7000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG3C52 CG2R53 NG2R53 CG3C52 0.4000 2 180.00 ! 2PDO, 2-pyrrolidinone, kevo +CG3C52 CG2R53 NG2R53 HGP1 1.2700 2 180.00 ! 2PDO, 2-pyrrolidinone, kevo +NG2R53 CG2R53 NG2R53 CG251O 0.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +NG2R53 CG2R53 NG2R53 CG252O 0.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +NG2R53 CG2R53 NG2R53 CG2R53 0.5000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +NG2R53 CG2R53 NG2R53 CG311 0.5000 2 180.00 ! drug design project, xxwy +NG2R53 CG2R53 NG2R53 HGP1 0.8000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +OG2D1 CG2R53 NG2R53 CG251O 6.0000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +OG2D1 CG2R53 NG2R53 CG252O 6.0000 2 180.00 ! MHYO, 5-methylenehydantoin, xxwy +OG2D1 CG2R53 NG2R53 CG2R53 1.1000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +OG2D1 CG2R53 NG2R53 CG311 2.5000 2 180.00 ! drug design project, xxwy +OG2D1 CG2R53 NG2R53 CG3C52 2.5900 2 180.00 ! 2PDO, 2-pyrrolidinone, kevo +OG2D1 CG2R53 NG2R53 HGP1 0.8600 2 180.00 ! 2PDO, 2-pyrrolidinone, kevo +SG2D1 CG2R53 NG2R53 CG2R53 1.5000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG2D1 CG2R53 NG2R53 CG311 1.5000 2 180.00 ! drug design project, xxwy +SG2D1 CG2R53 NG2R53 HGP1 1.0000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG311 CG2R53 NG2R53 CG2R53 1.5000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG311 CG2R53 NG2R53 CG311 1.5000 2 180.00 ! drug design project, xxwy +SG311 CG2R53 NG2R53 HGP1 1.7000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R50 CG2R53 NG3C51 CG3C52 4.0000 2 180.00 ! 4 2IMI, 2-imidazoline x, kevo +NG2R50 CG2R53 NG3C51 HGP1 1.2000 3 0.00 ! .85 ! 0 ! 0.6 3 0 2IMI, 2-imidazoline -wN1H, kevo +HGR52 CG2R53 NG3C51 CG3C52 0.0000 2 180.00 ! 4.6 2IMI, 2-imidazoline, kevo +HGR52 CG2R53 NG3C51 HGP1 0.0000 3 0.00 ! 2IMI, 2-imidazoline, kevo +NG2R50 CG2R53 OG2R50 CG2R51 8.5000 2 180.00 ! OXAZ, oxazole +NG2R50 CG2R53 OG2R50 NG2R50 9.0000 2 180.00 ! OXD4, oxadiazole124, xxwy +HGR52 CG2R53 OG2R50 CG2R51 3.8000 2 180.00 ! OXAZ, oxazole +HGR52 CG2R53 OG2R50 NG2R50 4.0000 2 180.00 ! OXD4, oxadiazole124, xxwy +CG2R51 CG2R53 OG3C51 CG3C52 1.2400 2 180.00 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG2R53 OG3C51 CG3C52 2.2700 3 180.00 ! B2FO, 5H-furan-2-one, ctsai +CG3C52 CG2R53 OG3C51 CG2R51 0.2960 2 180.00 ! A2FO, 3H-furan-2-one, ctsai +CG3C52 CG2R53 OG3C51 CG2R51 0.5120 3 180.00 ! A2FO, 3H-furan-2-one, ctsai +CG3C52 CG2R53 OG3C51 CG3C52 3.8000 2 180.00 ! GBL, Gamma-butyrolactone, ctsai +OG2D1 CG2R53 OG3C51 CG2R51 4.3400 2 180.00 ! A2FO, from CG2R51 CG2R51 OG3C51 CG3C52, ctsai +OG2D1 CG2R53 OG3C51 CG3C52 4.3400 2 180.00 ! GBL, from CG2R51 CG2R51 OG3C51 CG3C52, ctsai +NG2R50 CG2R53 SG2R50 CG2R51 8.5000 2 180.00 ! THAZ, thiazole @@@@@ Kenno: 8.0 --> 8.5 @@@@@ +NG2R50 CG2R53 SG2R50 CG2RC0 3.0000 2 180.00 ! ZTHZ, benzothiazole, kevo +HGR52 CG2R53 SG2R50 CG2R51 5.5000 2 180.00 ! THAZ, thiazole +HGR52 CG2R53 SG2R50 CG2RC0 3.0000 2 180.00 ! ZTHZ, benzothiazole, kevo +NG2R53 CG2R53 SG311 CG251O 0.2500 1 0.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R53 CG2R53 SG311 CG251O 1.3000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R53 CG2R53 SG311 CG252O 0.2500 1 0.00 ! MRDN, methylidene rhodanine, kevo & xxwy +NG2R53 CG2R53 SG311 CG252O 1.3000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +OG2D1 CG2R53 SG311 CG251O 0.2500 1 0.00 ! MTDO, 5-methylene-2,4-thiazolidinedione, xxwy & oashi +OG2D1 CG2R53 SG311 CG251O 1.3000 2 180.00 ! MTDO, 5-methylene-2,4-thiazolidinedione, xxwy & oashi +OG2D1 CG2R53 SG311 CG252O 0.2500 1 0.00 ! MTDO, 5-methylene-2,4-thiazolidinedione, xxwy & oashi +OG2D1 CG2R53 SG311 CG252O 1.3000 2 180.00 ! MTDO, 5-methylene-2,4-thiazolidinedione, xxwy & oashi +SG2D1 CG2R53 SG311 CG251O 0.2500 1 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG2D1 CG2R53 SG311 CG251O 0.6000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG2D1 CG2R53 SG311 CG252O 0.2500 1 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +SG2D1 CG2R53 SG311 CG252O 0.6000 2 180.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R51 CG2R57 CG2R57 CG2R51 0.4500 2 180.00 ! 33BPO, 3,3-bipyrrole, lf +CG2R51 CG2R57 CG2R57 CG2R51 0.0800 4 0.00 ! 33BPO, 3,3-bipyrrole, lf +CG2R51 CG2R57 NG2R57 CG2R51 0.3200 2 180.00 ! 13BPO, 1,3-bipyrrole, lf +CG2R51 CG2R57 NG2R57 CG2R51 0.1200 4 0.00 ! 13BPO, 1,3-bipyrrole, lf +CG2R51 CG2R57 NG2R57 CG2R51 0.0150 6 0.00 ! 13BPO, 1,3-bipyrrole, lf +CG1N1 CG2R61 CG2R61 CG2R61 2.0000 2 180.00 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN), yin +CG1N1 CG2R61 CG2R61 CG2RC0 1.3000 2 180.00 ! CYIN, 5-cyanoindole; from 3CYP, 3-Cyanopyridine; alr +CG1N1 CG2R61 CG2R61 NG2R60 1.0000 2 180.00 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN), yin +CG1N1 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN) Kenno: was 5.0 1 0.0 (sic!) ==> reset to default. +CG1N1 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN) Kenno: was 5.0 1 0.0 (sic!) ==> reset to default. +CG2DC1 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC1 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! HDZ2, hydrazone model cmpd 2 Kenno: 4.2 -> 2.4 +CG2DC2 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC2 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! HDZ2, hydrazone model cmpd 2 Kenno: 4.2 -> 2.4 +CG2N2 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! BAMI, benzamidinium; default parameter; sz +CG2N2 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! BAMI, benzamidinium; default parameter; sz +CG2O1 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! 3NAP, nicotinamide Kenno: 1.0 -> 3.1 +CG2O1 CG2R61 CG2R61 NG2R60 5.0000 2 180.00 ! 3NAP, nicotinamide +CG2O1 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! 3NAP, nicotinamide Kenno: 4.2 -> 2.4 +CG2O1 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! 3NAP, nicotinamide Kenno: 4.2 -> 2.4 +CG2O2 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! ZOIC, benzoic acid, MBOA, methylbenzoate; default parameter; kevo & jal +CG2O2 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! ZOIC, benzoic acid, MBOA, methylbenzoate; default parameter; kevo & jal +CG2O3 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! BIPHENYL ANALOGS, peml +CG2O3 CG2R61 CG2R61 NG2R60 1.0000 2 180.00 ! PYRIDINE pyridine, yin +CG2O3 CG2R61 CG2R61 NG2S1 2.4000 2 180.00 ! 2XBD, Gamma 2-carboxy phenyl GA CDCA amide, corrected by kevo +CG2O3 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PYRIDINE aminopyridine Kenno: 4.2 -> 2.4 +CG2O3 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! PYRIDINE aminopyridine Kenno: 4.2 -> 2.4 +CG2O4 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! 3ALP, nicotinaldehyde (PYRIDINE pyr-aldehyde) unmodified, yin +CG2O4 CG2R61 CG2R61 NG2R60 1.0000 2 180.00 ! 3ALP, nicotinaldehyde (PYRIDINE pyr-aldehyde) unmodified, yin +CG2O4 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! 3ALP, nicotinaldehyde (PYRIDINE pyr-aldehyde) Kenno: 4.2 -> 2.4 unmodified +CG2O4 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! 3ALP, nicotinaldehyde (PYRIDINE pyr-aldehyde) Kenno: 4.2 -> 2.4 unmodified +CG2O5 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! BIPHENYL ANALOGS unmodified, peml +CG2O5 CG2R61 CG2R61 NG2R60 5.0000 2 180.00 ! 3ACP, 3-acetylpyridine unmodified +CG2O5 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! 3ACP, 3-acetylpyridine reset to default by kevo; verified by mcs +CG2O5 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! 3ACP, 3-acetylpyridine reset to default by kevo; verified by mcs +CG2R61 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! PROT JES 8/25/89 +CG2R61 CG2R61 CG2R61 CG2R62 0.5000 2 180.00 ! RIN, coumarin, isg +CG2R61 CG2R61 CG2R61 CG2R63 3.2000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R61 CG2R61 CG2R64 3.1000 2 180.00 ! 18NFD, 1,8-naphthyridine, erh +CG2R61 CG2R61 CG2R61 CG2R66 3.1000 2 180.00 ! NAMODEL difluorotoluene +CG2R61 CG2R61 CG2R61 CG2R67 3.1000 2 180.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R61 CG2R61 CG2RC0 3.0000 2 180.00 ! INDO/TRP +CG2R61 CG2R61 CG2R61 CG311 3.1000 2 180.00 ! NAMODEL difluorotoluene +CG2R61 CG2R61 CG2R61 CG312 3.1000 2 180.00 ! BDFP, BDFD, Difuorobenzylphosphonate +CG2R61 CG2R61 CG2R61 CG321 3.1000 2 180.00 ! PROT JES 8/25/89 toluene and ethylbenzene +CG2R61 CG2R61 CG2R61 CG324 3.1000 2 180.00 ! BPIP, N-Benzyl PIP, cacha +CG2R61 CG2R61 CG2R61 CG331 3.1000 2 180.00 ! PROT toluene, adm jr., 3/7/92 +CG2R61 CG2R61 CG2R61 NG2O1 2.0000 2 180.00 ! NITB, nitrobenzene +CG2R61 CG2R61 CG2R61 NG2R60 1.2000 2 180.00 ! PYR1, pyridine, yin +CG2R61 CG2R61 CG2R61 NG2R61 3.7000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R61 CG2R61 NG2R62 1.2000 2 180.00 ! PYRD, pyridazine (also applies to PYRM, pyrimidine); from PYR1, pyridine, yin; adm +CG2R61 CG2R61 CG2R61 NG2RC0 1.5000 2 180.00 ! INDZ, indolizine, kevo +CG2R61 CG2R61 CG2R61 NG2S1 3.1000 2 180.00 ! RETINOL PACP +CG2R61 CG2R61 CG2R61 NG2S3 5.0000 2 180.00 ! PYRIDINE aminopyridine, yin +CG2R61 CG2R61 CG2R61 NG301 1.4000 2 180.00 ! DMAN, N,N-dimethylaniline, kevo +CG2R61 CG2R61 CG2R61 NG311 3.1000 2 180.00 ! FEOZ, phenoxazine, erh based on PROT toluene, adm jr., 3/7/92 +CG2R61 CG2R61 CG2R61 NG3N1 3.1000 2 180.00 ! PHHZ, phenylhydrazine, ed; reset to default param by kevo +CG2R61 CG2R61 CG2R61 OG301 3.1000 2 180.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R61 CG2R61 OG303 3.1000 2 180.00 ! PROTNA phenol phosphate, 6/94, adm jr. +CG2R61 CG2R61 CG2R61 OG311 3.1000 2 180.00 ! PYRIDINE phenol, yin +CG2R61 CG2R61 CG2R61 OG312 3.1000 2 180.00 ! PROT adm jr. 8/27/91, phenoxide +CG2R61 CG2R61 CG2R61 OG3R60 3.1000 2 180.00 ! FEOZ, phenoxazine, erh based on PROT toluene, adm jr., 3/7/92 +CG2R61 CG2R61 CG2R61 SG311 4.5000 2 180.00 ! FETZ, phenothiazine, erh based on toluene, adm jr., 3/7/92 +CG2R61 CG2R61 CG2R61 SG3O1 3.1000 2 180.00 ! based on toluene, adm jr., 3/7/92 +CG2R61 CG2R61 CG2R61 SG3O2 3.0000 2 180.00 ! BSAM, benzenesulfonamide and other sulfonamides, xxwy +CG2R61 CG2R61 CG2R61 CLGR1 3.0000 2 180.00 ! CHLB, chlorobenzene +CG2R61 CG2R61 CG2R61 BRGR1 3.0000 2 180.00 ! BROB, bromobenzene +CG2R61 CG2R61 CG2R61 IGR1 2.1000 2 180.00 ! IODB, iodobenzene +CG2R61 CG2R61 CG2R61 HGR61 4.2000 2 180.00 ! PROT JES 8/25/89 benzene +CG2R61 CG2R61 CG2R61 HGR62 4.2000 2 180.00 ! BROB, bromobenzene +CG2R62 CG2R61 CG2R61 HGR61 4.2000 2 180.00 ! RIN, coumarin, isg +CG2R63 CG2R61 CG2R61 NG2R61 0.5000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R63 CG2R61 CG2R61 NG2R62 1.2000 2 180.00 ! 43HSPY, 4(3H)-pyrimidinethione; from CG2R64 CG2R61 CG2R61 NG2R62; isg +CG2R63 CG2R61 CG2R61 HGR61 1.0000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R63 CG2R61 CG2R61 HGR62 0.5000 2 180.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from CG2R64 CG2R61 CG2R61 HGR62; isg +CG2R64 CG2R61 CG2R61 CG331 3.1000 2 180.00 ! 2A46PD, 2-Amino-4,6-dimethyl-pyridine CDCA conjugate, cacha +CG2R64 CG2R61 CG2R61 NG2R62 1.2000 2 180.00 ! PTID, pteridine, erh +CG2R64 CG2R61 CG2R61 HGR61 1.0000 2 180.00 ! 18NFD, 1,8-naphthyridine, erh +CG2R64 CG2R61 CG2R61 HGR62 0.5000 2 180.00 ! PTID, pteridine, erh +CG2R66 CG2R61 CG2R61 NG2S1 3.1000 2 180.00 ! 3FBD, 3-fluoroanilide patch. Kenno: copied from RETINOL PACP while retrofitting CG2R66 ==> re-optimize +CG2R66 CG2R61 CG2R61 HGR61 4.2000 2 180.00 ! NAMODEL difluorotoluene +CG2R67 CG2R61 CG2R61 HGR61 4.2000 2 180.00 ! BIPHENYL ANALOGS, peml +CG2RC0 CG2R61 CG2R61 BRGR1 3.1000 2 180.00 ! drug design project, xxwy +CG2RC0 CG2R61 CG2R61 HGR61 3.0000 2 180.00 ! INDO/TRP +CG2RC0 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! drug design project, xxwy +CG311 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! FBIB, Fatty Binding Inhibitior B, cacha Kenno: 4.2 -> 2.4 +CG311 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! NAMODEL difluorotoluene Kenno: 4.2 -> 2.4 +CG312 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! BDFP, BDFD, Difuorobenzylphosphonate Kenno: 4.2 -> 2.4 +CG321 CG2R61 CG2R61 NG2R60 1.0000 2 180.00 ! PYRIDINE 3-ethylpyridine, yin +CG321 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PROT JES 8/25/89 toluene and ethylbenzene Kenno: 4.2 -> 2.4 +CG321 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! PROT JES 8/25/89 toluene and ethylbenzene Kenno: 4.2 -> 2.4 +CG324 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! BPIP, N-Benzyl PIP, cacha Kenno: 4.2 -> 2.4 +CG331 CG2R61 CG2R61 CG331 2.4000 2 180.00 ! OXYL, o-xylene, kevo for gsk/ibm +CG331 CG2R61 CG2R61 NG2R60 1.0000 2 180.00 ! PYRIDINE 3-methylpyridine, yin +CG331 CG2R61 CG2R61 NG2S1 2.4000 2 180.00 ! 3A2MPD, 3-amino-2-methyl-pyridine CDCA conjugate, corrected by kevo +CG331 CG2R61 CG2R61 OG301 2.4000 2 180.00 ! FBID, Fatty acid Binding protein Inhibitor D, cacha Kenno: 4.2 -> 2.4 +CG331 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! FBIA, Fatty Binding Inhibitior B, cacha Kenno: 4.2 -> 2.4 +CG331 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PROT toluene, adm jr., 3/7/92 Kenno: 4.2 -> 2.4 +CG331 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! PROT toluene, adm jr., 3/7/92 Kenno: 4.2 -> 2.4 +NG2O1 CG2R61 CG2R61 HGR61 1.0000 2 180.00 ! NITB, nitrobenzene +NG2R60 CG2R61 CG2R61 NG2R60 0.9000 2 180.00 ! PYZN, pyrazine +NG2R60 CG2R61 CG2R61 NG2R62 3.0000 2 180.00 ! PTID, pteridine, erh +NG2R60 CG2R61 CG2R61 NG2S1 5.0000 2 180.00 ! 3AMP, 3-Amino pyridine, cacha +NG2R60 CG2R61 CG2R61 NG2S3 5.0000 2 180.00 ! PYRIDINE aminopyridine, yin +NG2R60 CG2R61 CG2R61 OG311 1.0000 2 180.00 ! PYRIDINE 3-hydroxypyridine Kenno: 0.0 (unlikely) -> 1.0 from 3-methylpyridine, yin +NG2R60 CG2R61 CG2R61 BRGR1 3.0000 2 180.00 ! 3A5BPD, Gamma-3-Amino-5-bromo Pyridine GA CDCA Amide, cacha +NG2R60 CG2R61 CG2R61 HGR61 2.8000 2 180.00 ! PYRIDINE pyridine, yin +NG2R60 CG2R61 CG2R61 HGR62 6.0000 2 180.00 ! PYZN, pyrazine +NG2R61 CG2R61 CG2R61 HGR61 0.8000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg (may need to be re-evaluated; ideally re-check INDZ with molvib_energy script and also look at URA2S molvib) +NG2R61 CG2R61 CG2R61 HGR62 0.8000 2 180.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from NG2RC0 CG2R61 CG2R61 HGR61; isg (may need to be re-evaluated; ideally re-check INDZ with molvib_energy script and also look at URA2S molvib) +NG2R62 CG2R61 CG2R61 NG2R62 0.5000 2 180.00 ! TRIB, triazine124 +NG2R62 CG2R61 CG2R61 HGR61 2.8000 2 180.00 ! PYRD, pyridazine +NG2R62 CG2R61 CG2R61 HGR62 6.0000 2 180.00 ! TRIB, triazine124 +NG2RC0 CG2R61 CG2R61 HGR61 0.8000 2 180.00 ! INDZ, indolizine, kevo +NG2S1 CG2R61 CG2R61 OG301 2.4000 2 180.00 ! 2AMFD, Gamma 2-amino phenyl methyl ether, corrected by kevo +NG2S1 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! 2AMF, 2-acetamide phenol, cacha Kenno: 4.2 -> 2.4 +NG2S1 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! RETINOL PACP Kenno: 4.2 -> 2.4 +NG2S1 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! 3AMP, 3-Amino pyridine, cacha Kenno: 4.2 -> 2.4 +NG2S3 CG2R61 CG2R61 NG2S3 3.1000 2 180.00 ! PYRIDINE diaminopyridine. Kenno: Change to 2.4 ??? +NG2S3 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PYRIDINE aminopyridine Kenno: 4.2 -> 2.4 +NG2S3 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! PYRIDINE aminopyridine Kenno: 4.2 -> 2.4 +NG301 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! DMAN, N,N-dimethylaniline; from NG311 CG2R61 CG2R61 HGR61; sc +NG311 CG2R61 CG2R61 OG3R60 2.5800 2 180.00 ! FEOZ, phenoxazine fit_dihedral, erh +NG311 CG2R61 CG2R61 SG311 3.5700 2 180.00 ! FETZ, phenothiazine fit_dihedral, erh +NG311 CG2R61 CG2R61 SG3O2 2.4000 2 180.00 ! OBTZ, sulfonamide heterocycle in drug HCTZ, xxwy +NG311 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! FEOZ, phenoxazine, erh +NG3N1 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PHHZ, phenylhydrazine, ed; reset to default param by kevo +OG301 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! BIPHENYL ANALOGS, peml. Kenno: 4.2 -> 2.4 +OG303 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PROTNA phenol phosphate, 6/94, adm jr. Kenno: 4.2 -> 2.4 +OG311 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PROT JES 8/25/89 phenol Kenno: 4.2 -> 2.4 +OG311 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! PROT JES 8/25/89 phenol Kenno: 4.2 -> 2.4 +OG312 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PROT adm jr. 8/27/91, phenoxide Kenno: 4.2 -> 2.4 +OG3R60 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! FEOZ, phenoxazine, erh +SG311 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! FETZ, phenothiazine, erh based on toluene, adm jr., 3/7/92 Kenno: 4.2 -> 2.4 +SG3O1 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! based on toluene, adm jr., 3/7/92 Kenno: 4.2 -> 2.4 +SG3O2 CG2R61 CG2R61 HGR61 2.1000 2 180.00 ! BSAM, benzenesulfonamide and other sulfonamides, xxwy +CLGR1 CG2R61 CG2R61 HGR62 3.0000 2 180.00 ! CHLB, chlorobenzene +BRGR1 CG2R61 CG2R61 HGR62 3.0000 2 180.00 ! BROB, bromobenzene +IGR1 CG2R61 CG2R61 HGR62 3.0000 2 180.00 ! IODB, iodobenzene +HGR61 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! PROT JES 8/25/89 benzene +HGR61 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! BROB, bromobenzene +HGR62 CG2R61 CG2R61 HGR62 2.4000 2 180.00 ! TRIB, triazine124 +CG2R61 CG2R61 CG2R62 CG2R62 0.5000 2 180.00 ! RIN, coumarin, isg +CG2R61 CG2R61 CG2R62 CG2R63 3.1000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R61 CG2R62 NG2R61 7.0000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R61 CG2R62 NG2R62 1.2000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R61 CG2R61 CG2R62 OG3R60 3.1000 2 180.00 ! RIN, coumarin, isg +HGR61 CG2R61 CG2R62 CG2R62 3.1000 2 180.00 ! RIN, coumarin, isg +HGR61 CG2R61 CG2R62 CG2R63 1.0000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +HGR61 CG2R61 CG2R62 NG2R61 0.4000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +HGR61 CG2R61 CG2R62 NG2R62 2.8000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +HGR61 CG2R61 CG2R62 OG3R60 2.4000 2 180.00 ! RIN, coumarin, isg +CG2R61 CG2R61 CG2R63 NG2R61 0.5000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R61 CG2R63 NG2R67 0.5000 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from CG2R61 CG2R61 CG2R63 NG2R61, YTS2; isg +CG2R61 CG2R61 CG2R63 SG2D1 4.5000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +HGR62 CG2R61 CG2R63 NG2R61 1.0000 2 180.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from HGR62 CG2R62 CG2R63 NG2R61; isg +HGR62 CG2R61 CG2R63 NG2R67 1.0000 2 180.00 ! 3PH24S, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione; from HGR62 CG2R62 CG2R63 NG2R61, NA; isg +HGR62 CG2R61 CG2R63 SG2D1 2.4000 2 180.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from SG311 CG2R61 CG2R61 HGR61; isg +CG2R61 CG2R61 CG2R64 NG2R60 1.2000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo +CG2R61 CG2R61 CG2R64 NG2R62 1.2000 2 180.00 ! 18NFD, 1,8-naphthyridine, from PYR1, pyridine, erh +CG2R61 CG2R61 CG2R64 NG2S1 3.1000 2 180.00 ! 2AMP, 2-amino pyridine, from PACP, p-acetamide-phenol, pyridine, kevo +NG2R60 CG2R61 CG2R64 NG2R62 1.5000 2 0.00 ! PTID, pteridine, erh +OG311 CG2R61 CG2R64 NG2R60 3.1000 2 180.00 ! 2A3HPD, cacha +OG311 CG2R61 CG2R64 NG2S1 2.4000 2 180.00 ! 2A3HPD, cacha +HGR61 CG2R61 CG2R64 NG2R60 2.8000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo +HGR61 CG2R61 CG2R64 NG2S1 2.4000 2 180.00 ! 2AMP, 2-amino pyridine, default parameter by analogy to PACP, kevo +CG2R61 CG2R61 CG2R66 CG2R61 3.1000 2 180.00 ! NAMODEL difluorotoluene +CG2R61 CG2R61 CG2R66 CG2R67 3.10 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R66 CG2R61, penalty= 0.5 +CG2R61 CG2R61 CG2R66 FGR1 4.5000 2 180.00 ! NAMODEL difluorotoluene +CG2R66 CG2R61 CG2R66 CG2R61 3.1000 2 180.00 ! NAMODEL difluorotoluene +CG2R66 CG2R61 CG2R66 FGR1 4.5000 2 180.00 ! NAMODEL difluorotoluene +CG331 CG2R61 CG2R66 CG2R61 3.1000 2 180.00 ! NAMODEL difluorotoluene +CG331 CG2R61 CG2R66 FGR1 4.5000 2 180.00 ! NAMODEL difluorotoluene +NG2R60 CG2R61 CG2R66 CG2R61 1.2000 2 180.00 ! 3FLP, 3-fluoropyridine. Kenno: copied from pyridine while retrofitting CG2R66 ==> re-optimize +NG2R60 CG2R61 CG2R66 FGR1 3.1000 2 180.00 ! PYRIDINE fluoropyridine, yin +NG2S1 CG2R61 CG2R66 CG2R61 3.1000 2 180.00 ! 2FBD, 2-fluoroanilide patch. Kenno: copied from RETINOL PACP while retrofitting CG2R66 ==> re-optimize +NG2S1 CG2R61 CG2R66 FGR1 2.4000 2 180.00 ! 2FBD, Gamma 2-Fluoro amino benzene glutamic acid CDCA amide, cacha Kenno: 3.1 -> 2.4 +HGR62 CG2R61 CG2R66 CG2R61 4.2000 2 180.00 ! NAMODEL difluorotoluene +HGR62 CG2R61 CG2R66 CG2R67 4.20 2 180.00 ! PYO2F , from HGR62 CG2R61 CG2R66 CG2R61, penalty= 0.5 +HGR62 CG2R61 CG2R66 FGR1 2.4000 2 180.00 ! NAMODEL difluorotoluene +CG2R61 CG2R61 CG2R67 CG2R61 3.1000 2 180.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R61 CG2R67 CG2R66 3.10 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 1.5 +CG2R61 CG2R61 CG2R67 CG2R67 3.1000 2 180.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R61 CG2R67 CG2RC0 0.2500 2 180.00 ! CRBZ, carbazole, erh +CG2R61 CG2R61 CG2R67 NG2R60 1.2000 2 180.00 ! 22BPY, 2,2'-bipyridine, from CG2R61 CG2R61 CG2R61 NG2R60, kevo +CG2R61 CG2R61 CG2R67 NG2R67 3.1000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R61 CG2R61 CG2R61 CG2R61; isg +NG2R60 CG2R61 CG2R67 CG2R61 1.2000 2 180.00 ! 3PHP, 3-phenyl-pyridine; Kenno: 3.1 -> 1.2 from PYRIDINE pyridine, yin +NG2R60 CG2R61 CG2R67 CG2R67 1.0000 2 180.00 ! 3PHP, 3-phenyl-pyridine, Kenno: 3.1 -> 1.0 from 3-methylpyridine, yin +HGR61 CG2R61 CG2R67 CG2R61 4.2000 2 180.00 ! BIPHENYL ANALOGS, peml +HGR61 CG2R61 CG2R67 CG2R66 4.20 2 180.00 ! PYO2F , from HGR61 CG2R61 CG2R67 CG2R61, penalty= 1.5 +HGR61 CG2R61 CG2R67 CG2R67 4.2000 2 180.00 ! BIPHENYL ANALOGS, peml +HGR61 CG2R61 CG2R67 CG2RC0 3.0000 2 180.00 ! CRBZ, carbazole, erh +HGR61 CG2R61 CG2R67 NG2R60 2.8000 2 180.00 ! 22BPY, 2,2'-bipyridine, from NG2R60 CG2R61 CG2R61 HGR61, kevo +HGR61 CG2R61 CG2R67 NG2R67 2.8000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from NG2R60 CG2R61 CG2R61 HGR61; isg +HGR62 CG2R61 CG2R67 CG2R61 4.2000 2 180.00 ! BIPHENYL ANALOGS, peml +HGR62 CG2R61 CG2R67 CG2R67 4.2000 2 180.00 ! BIPHENYL ANALOGS, peml +CG2O1 CG2R61 CG2RC0 CG2RC0 3.1000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2O1 CG2R61 CG2RC0 NG2R51 2.8000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2R61 CG2R61 CG2RC0 CG25C1 3.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R61 CG2R61 CG2RC0 CG25C2 3.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R61 CG2R61 CG2RC0 CG2R51 4.0000 2 180.00 ! INDO/TRP +CG2R61 CG2R61 CG2RC0 CG2R52 1.5000 2 180.00 ! INDA, 1H-indazole, kevo +CG2R61 CG2R61 CG2RC0 CG2R67 0.2500 2 180.00 ! CRBZ, carbazole, erh +CG2R61 CG2R61 CG2RC0 CG2RC0 3.0000 2 180.00 ! INDO/TRP +CG2R61 CG2R61 CG2RC0 CG3C52 0.0000 2 180.00 ! 3HIN, 3H-indole, kevo +CG2R61 CG2R61 CG2RC0 NG2R50 1.5000 2 180.00 ! ZIMI, benzimidazole, kevo +CG2R61 CG2R61 CG2RC0 NG2R51 3.0000 2 180.00 ! INDO/TRP +CG2R61 CG2R61 CG2RC0 NG2RC0 3.5000 2 180.00 ! INDZ, indolizine, kevo +CG2R61 CG2R61 CG2RC0 NG3C51 6.0000 2 180.00 ! INDI, indoline, kevo +CG2R61 CG2R61 CG2RC0 OG2R50 0.0000 2 180.00 ! ZFUR, benzofuran, kevo +CG2R61 CG2R61 CG2RC0 OG3C51 2.0000 2 180.00 ! ZDOL, 1,3-benzodioxole, pram & oashi +CG2R61 CG2R61 CG2RC0 SG2R50 0.0000 2 180.00 ! ZTHP, benzothiophene, kevo +NG2R62 CG2R61 CG2RC0 CG2RC0 2.2000 2 180.00 ! PUR9, purine(N9H), kevo +NG2R62 CG2R61 CG2RC0 NG2R50 0.0000 2 180.00 ! PUR9, purine(N9H), kevo +NG2R62 CG2R61 CG2RC0 NG2R51 0.0000 2 180.00 ! PUR7, purine(N7H), kevo +HGR61 CG2R61 CG2RC0 CG25C1 3.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +HGR61 CG2R61 CG2RC0 CG25C2 3.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +HGR61 CG2R61 CG2RC0 CG2R51 4.0000 2 180.00 ! INDO/TRP +HGR61 CG2R61 CG2RC0 CG2R52 0.0000 2 180.00 ! INDA, 1H-indazole, kevo +HGR61 CG2R61 CG2RC0 CG2R67 3.0000 2 180.00 ! CRBZ, carbazole, erh +HGR61 CG2R61 CG2RC0 CG2RC0 3.0000 2 180.00 ! INDO/TRP +HGR61 CG2R61 CG2RC0 CG3C52 0.0000 2 180.00 ! 3HIN, 3H-indole, kevo +HGR61 CG2R61 CG2RC0 NG2R50 0.8000 2 180.00 ! ZIMI, benzimidazole, kevo +HGR61 CG2R61 CG2RC0 NG2R51 3.0000 2 180.00 ! INDO/TRP +HGR61 CG2R61 CG2RC0 NG2RC0 0.0000 2 180.00 ! INDZ, indolizine, kevo +HGR61 CG2R61 CG2RC0 NG3C51 0.0000 2 180.00 ! INDI, indoline, kevo +HGR61 CG2R61 CG2RC0 OG2R50 0.0000 2 180.00 ! ZFUR, benzofuran, kevo +HGR61 CG2R61 CG2RC0 OG3C51 2.4000 2 180.00 ! ZDOL, 1,3-benzodioxole, pram & oashi +HGR61 CG2R61 CG2RC0 SG2R50 0.0000 2 180.00 ! ZTHP, benzothiophene, kevo +HGR62 CG2R61 CG2RC0 CG25C1 2.4000 2 180.00 ! drug design project, xxwy +HGR62 CG2R61 CG2RC0 CG25C2 2.4000 2 180.00 ! drug design project, xxwy +HGR62 CG2R61 CG2RC0 CG2RC0 4.2000 2 180.00 ! PUR7, purine(N7H); PUR9, purine(N9H), kevo +HGR62 CG2R61 CG2RC0 NG2R50 1.0000 2 180.00 ! PUR9, purine(N9H), kevo +HGR62 CG2R61 CG2RC0 NG2R51 0.0000 2 180.00 ! PUR7, purine(N7H), kevo +CG2R61 CG2R61 CG311 CG2O3 0.2300 2 180.00 ! FBIF, Fatty acid Binding protein Inhibitor F, cacha +CG2R61 CG2R61 CG311 CG321 0.2300 2 180.00 ! Slack parameter from difluorotoluene picked up by FBIC ==> RE-OPTIMIZE !!! +CG2R61 CG2R61 CG311 CG331 0.2300 2 180.00 ! FBIB, Fatty Binding Inhibitior B, cacha +CG2R61 CG2R61 CG311 HGA1 0.1000 6 180.00 ! NAMODEL difluorotoluene +CG2R61 CG2R61 CG312 PG1 0.1500 2 180.00 ! BDFP, Difuorobenzylphosphonate \ re-optimize? +CG2R61 CG2R61 CG312 PG2 0.1500 2 180.00 ! BDFD, Difuorobenzylphosphonate / re-optimize? +CG2R61 CG2R61 CG312 FGA2 0.3000 2 0.00 ! BDFP, BDFD, Difuorobenzylphosphonate +CG2R61 CG2R61 CG321 CG2R61 0.2300 2 180.00 ! PYRIDINE pyr-CH2C6H5, yin +CG2R61 CG2R61 CG321 CG311 0.2300 2 180.00 ! PROT ethylbenzene ethyl rotation, adm jr. 3/7/92 +CG2R61 CG2R61 CG321 CG314 0.2300 2 180.00 ! PROT ethylbenzene ethyl rotation, adm jr. 3/7/92 +CG2R61 CG2R61 CG321 CG321 0.2300 2 180.00 ! PROT ethylbenzene ethyl rotation, adm jr. 3/7/92 +CG2R61 CG2R61 CG321 CG331 0.2300 2 180.00 ! PROT ethylbenzene ethyl rotation, adm jr. 3/7/92 +CG2R61 CG2R61 CG321 NG2S1 0.1190 2 0.00 ! NZAD, N-benzylacetamide, isg +CG2R61 CG2R61 CG321 NG2S1 0.1320 4 180.00 ! NZAD, N-benzylacetamide, isg +CG2R61 CG2R61 CG321 NG2S1 0.0130 6 180.00 ! NZAD, N-benzylacetamide, isg +CG2R61 CG2R61 CG321 OG302 0.0000 2 0.00 ! ABGA, ALPHA BENZYL GLU ACID CDCA AMIDE, cacha +CG2R61 CG2R61 CG321 OG311 0.0000 2 0.00 ! 3CAP, carbinol-pyridine (PYRIDINE pyr-CH2OH), yin +CG2R61 CG2R61 CG321 PG1 0.2000 2 180.00 ! BDFP, Benzylphosphonate \ re-optimize? +CG2R61 CG2R61 CG321 PG2 0.2000 2 180.00 ! BDFD, Benzylphosphonate / re-optimize? +CG2R61 CG2R61 CG321 HGA2 0.0020 6 0.00 ! PROT toluene, adm jr., 3/7/92 +NG2R60 CG2R61 CG321 CG321 0.2300 2 180.00 ! 2AEPD, 2-ethylamino-pyridine CDCA conjugate, corrected by kevo +NG2R60 CG2R61 CG321 HGA2 0.0020 6 0.00 ! 2AEPD, 2-ethylamino-pyridine CDCA conjugate, corrected by kevo +CG2R61 CG2R61 CG324 NG3P1 0.1500 2 180.00 ! BPIP, N-Benzyl PIP, cacha +CG2R61 CG2R61 CG324 NG3P3 0.3300 2 0.00 ! 4FBA, optimized using CCCN mp2 scan, pram +CG2R61 CG2R61 CG324 HGA2 0.0000 2 0.00 ! BPIP, N-Benzyl PIP, cacha +CG2R61 CG2R61 CG331 HGA3 0.0020 6 0.00 ! PYRIDINE toluene Kenno: 180 -> 0 +CG2R66 CG2R61 CG331 HGA3 0.0020 6 0.00 ! PYRIDINE toluene Kenno: 180 -> 0 +NG2R60 CG2R61 CG331 HGA3 0.0030 6 180.00 ! 3A2MPD, 3-amino-2-methyl-pyridine CDCA conjugate, cacha +CG2R61 CG2R61 NG2O1 OG2N1 0.9000 2 180.00 ! NITB, nitrobenzene +CG2R61 CG2R61 NG2R60 CG2R61 1.2000 2 180.00 ! PYRIDINE pyridine, yin +CG2R61 CG2R61 NG2R60 CG2R64 1.2000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo +CG2R61 CG2R61 NG2R60 CG2R67 1.2000 2 180.00 ! 22BPY, 2,2'-bipyridine, from CG2R61 CG2R61 NG2R60 CG2R61, kevo +CG2R64 CG2R61 NG2R60 CG2R61 2.2000 2 180.00 ! PTID, pteridine, erh +CG2R66 CG2R61 NG2R60 CG2R61 1.2000 2 180.00 ! 3FLP, 3-fluoropyridine. Kenno: copied from pyridine while retrofitting CG2R66 ==> re-optimize +CG2R67 CG2R61 NG2R60 CG2R61 1.2000 2 180.00 ! 3PHP, 3-phenyl-pyridine, yin +CG321 CG2R61 NG2R60 CG2R61 3.1000 2 180.00 ! 2AEPD, 2-ethylamino-pyridine CDCA conjugate, cacha +CG331 CG2R61 NG2R60 CG2R61 3.1000 2 180.00 ! 3A2MPD, 3-amino-2-methyl-pyridine CDCA conjugate, cacha +CG331 CG2R61 NG2R60 CG2R64 3.1000 2 180.00 ! 2A46PD, 2-Amino-4,6-dimethyl-pyridine CDCA conjugate, cacha +BRGR1 CG2R61 NG2R60 CG2R61 3.0000 2 180.00 ! 3A6BPD, Gamma-3-Amino-6-bromo Pyridine GA CDCA Amide, cacha +HGR62 CG2R61 NG2R60 CG2R61 5.8000 2 180.00 ! PYR1 pyridine, yin ! got overwritten with "slack parameter" during big renaming operation (par_cgenff_1e_unsorted). Restored to original from toppar_all22_prot_pyridines. +HGR62 CG2R61 NG2R60 CG2R64 5.8000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo +HGR62 CG2R61 NG2R60 CG2R67 5.2500 2 180.00 ! 22BPY, 2,2'-bipyridine, kevo +CG2R61 CG2R61 NG2R61 CG2R63 0.5000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R61 NG2R61 HGP1 1.0000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +HGR62 CG2R61 NG2R61 CG2R63 4.6000 2 180.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from HGR62 CG2R62 NG2R61 CG2R63; isg +HGR62 CG2R61 NG2R61 HGP1 1.2000 2 180.00 ! URA24S, 2,4(1H,3H)-pyrimidinedithione; from HGR62 CG2R62 NG2R61 HGP1; isg +CG2R61 CG2R61 NG2R62 CG2R64 2.0000 2 180.00 ! PYRM, pyrimidine +CG2R61 CG2R61 NG2R62 NG2R62 0.8000 2 180.00 ! PYRD, pyridazine +CG2RC0 CG2R61 NG2R62 CG2R64 2.2000 2 180.00 ! PUR9, purine(N9H), kevo +HGR62 CG2R61 NG2R62 CG2R64 7.3000 2 180.00 ! PYRM, pyrimidine +HGR62 CG2R61 NG2R62 NG2R62 2.8000 2 180.00 ! PYRD, pyridazine +CG2R61 CG2R61 NG2RC0 CG2R51 0.0000 2 180.00 ! INDZ, indolizine, kevo +CG2R61 CG2R61 NG2RC0 CG2RC0 0.5000 2 180.00 ! INDZ, indolizine, kevo +HGR62 CG2R61 NG2RC0 CG2R51 0.0000 2 180.00 ! INDZ, indolizine, kevo +HGR62 CG2R61 NG2RC0 CG2RC0 1.9000 2 180.00 ! INDZ, indolizine, kevo +CG2R61 CG2R61 NG2S1 CG2O1 1.2000 2 180.00 ! RETINOL PACP +CG2R61 CG2R61 NG2S1 HGP1 0.5000 2 180.00 ! RETINOL PACP +CG2R66 CG2R61 NG2S1 CG2O1 1.2000 2 180.00 ! 2FBD, 2-fluoroanilide patch. Kenno: copied from RETINOL PACP while retrofitting CG2R66 ==> re-optimize +CG2R66 CG2R61 NG2S1 CG2O1 1.0000 3 180.00 ! 2FBD, 2-fluoroanilide patch. Kenno: copied from RETINOL PACP while retrofitting CG2R66 ==> re-optimize +CG2R66 CG2R61 NG2S1 HGP1 0.5000 2 180.00 ! 2FBD, 2-fluoroanilide patch. Kenno: copied from RETINOL PACP while retrofitting CG2R66 ==> re-optimize +CG2R61 CG2R61 NG2S3 HGP4 1.3500 2 180.00 ! PYRIDINE aminopyridine. kevo: 1.80 --> 1.35 +CG2R61 CG2R61 NG301 CG331 0.9600 2 180.00 ! DMAN, N,N-dimethylaniline, kevo +CG2R61 CG2R61 NG301 CG331 0.1050 4 0.00 ! DMAN, N,N-dimethylaniline, kevo +CG2R61 CG2R61 NG301 CG331 0.0350 6 180.00 ! DMAN, N,N-dimethylaniline, kevo +CG2R61 CG2R61 NG311 CG2R61 0.4400 2 0.00 ! FEOZ, phenoxazine fit_dihedral, erh +CG2R61 CG2R61 NG311 CG321 1.2000 2 180.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +CG2R61 CG2R61 NG311 CG321 0.3000 4 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +CG2R61 CG2R61 NG311 SG3O2 0.2000 2 180.00 ! PMSM, N-phenylmethanesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +CG2R61 CG2R61 NG311 HGP1 0.5000 2 180.00 ! PMSM, N-phenylmethanesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +CG2R61 CG2R61 NG311 HGPAM1 0.3200 2 180.00 ! FEOZ, phenoxazine fit_dihedral, erh +CG2R61 CG2R61 NG3N1 NG3N1 2.3700 2 180.00 ! PHHZ, phenylhydrazine, ed +CG2R61 CG2R61 NG3N1 HGP1 0.0000 2 0.00 ! PHHZ, phenylhydrazine, ed +CG2R61 CG2R61 OG301 CG2R61 1.2000 2 180.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R61 OG301 CG321 1.6200 2 180.00 ! ETOB, Ethoxybenzene, cacha +CG2R61 CG2R61 OG301 CG321 0.1900 4 180.00 ! ETOB, Ethoxybenzene, cacha +CG2R61 CG2R61 OG301 CG331 1.5800 2 180.00 ! MEOB, Methoxybenzene update, yxu +CG2R61 CG2R61 OG301 CG331 0.2000 4 180.00 ! MEOB, Methoxybenzene update, yxu +CG2R61 CG2R61 OG303 PG1 1.4000 2 180.00 ! PROTNA phenol phosphate, 6/94, adm jr. +CG2R61 CG2R61 OG303 SG3O2 0.5100 2 180.00 ! PMST, phenyl methanesulfonate, PSMT, phenyl sulfamate, xxwy +CG2R61 CG2R61 OG303 SG3O2 0.1500 4 0.00 ! PMST, phenyl methanesulfonate, PSMT, phenyl sulfamate, xxwy +CG2R61 CG2R61 OG311 HGP1 0.9900 2 180.00 ! PROT phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +CG2R64 CG2R61 OG311 HGP1 0.9900 2 180.00 ! 2A3HPD, from PROT phenol, cacha +CG2R61 CG2R61 OG3R60 CG2R61 0.7600 2 0.00 ! FEOZ, phenoxazine fit_dihedral, erh +CG2R61 CG2R61 SG311 CG2R61 1.7500 2 0.00 ! FETZ, phenothiazine fit_dihedral, erh +CG2R61 CG2R61 SG3O1 OG2P1 0.0040 6 0.00 ! benzene sulfonic acid anion, og +CG2R61 CG2R61 SG3O2 NG311 0.2200 2 0.00 ! MBSM, N-methylbenzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +CG2R61 CG2R61 SG3O2 NG321 0.3500 2 0.00 ! BSAM, benzenesulfonamide, xxwy +CG2R61 CG2R61 SG3O2 OG2P1 0.0000 6 0.00 ! BSAM, benzenesulfonamide and other sulfonamides, xxwy +CG2O1 CG2R62 CG2R62 CG2R62 3.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2O1 CG2R62 CG2R62 NG2R61 2.5000 2 180.00 ! NA ppi, jjp1/adm jr. 7/95 +CG2O1 CG2R62 CG2R62 HGR63 1.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R61 CG2R62 CG2R62 CG2R61 2.5000 2 180.00 ! RIN, coumarin, isg +CG2R61 CG2R62 CG2R62 CG2R62 2.0000 2 180.00 ! RIN, coumarin, isg +CG2R61 CG2R62 CG2R62 CG2R63 3.7000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R62 CG2R62 NG2R61 3.5000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R62 CG2R62 NG2R62 3.1000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R61 CG2R62 CG2R62 OG3R60 3.9000 2 180.00 ! RIN, coumarin, isg +CG2R61 CG2R62 CG2R62 HGR62 1.0000 2 180.00 ! RIN, coumarin, isg +CG2R62 CG2R62 CG2R62 CG2R62 6.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R62 CG2R62 CG2R62 CG2R63 3.0000 2 180.00 ! 2PYO, 2-Pyridone, xxwy +CG2R62 CG2R62 CG2R62 NG2R61 7.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R62 CG2R62 CG2R62 NG2R62 1.2000 2 180.00 ! 5FOP, PYRH; from CG2R61 CG2R61 CG2R61 NG2R62, PYRD, PYRM and CG2R61 CG2R61 CG2R61 NG2R60, PYR1; yxu +CG2R62 CG2R62 CG2R62 NG2R67 3.5000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R61 CG2R62 CG2R62 NG2R61, YTHY; isg +CG2R62 CG2R62 CG2R62 OG3R60 0.4000 2 180.00 ! RIN, coumarin, isg +CG2R62 CG2R62 CG2R62 HGR62 1.0000 2 180.00 ! 2PYO, 2-Pyridone, xxwy +CG2R62 CG2R62 CG2R62 HGR63 1.0000 2 180.00 ! NA bases +CG2R63 CG2R62 CG2R62 CG2R67 3.70 2 180.00 ! pyo3b , from CG2R61 CG2R62 CG2R62 CG2R63, penalty= 0.5 +CG2R63 CG2R62 CG2R62 NG2R61 3.0000 2 180.00 ! NA T +CG2R63 CG2R62 CG2R62 NG2R62 0.5000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R63 CG2R62 CG2R62 NG2R67 3.0000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R63 CG2R62 CG2R62 NG2R61; isg +CG2R63 CG2R62 CG2R62 HGR62 1.0000 2 180.00 ! NA bases +CG2R64 CG2R62 CG2R62 NG2R61 6.0000 2 180.00 ! NA C +CG2R64 CG2R62 CG2R62 HGR62 4.0000 2 180.00 ! NA 5mc, adm jr. 9/9/93 +CG2R67 CG2R62 CG2R62 NG2R61 3.50 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R62 NG2R61, penalty= 0.5 +CG2R67 CG2R62 CG2R62 HGR62 1.00 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R62 HGR62, penalty= 0.5 +CG2R67 CG2R62 CG2R62 HGR63 1.00 2 180.00 ! PIUB , from CG2R61 CG2R62 CG2R62 HGR62, penalty= 1.5 +CG331 CG2R62 CG2R62 NG2R61 4.0000 2 180.00 ! NA 5mc, adm jr. 9/9/93 +CG331 CG2R62 CG2R62 HGR62 4.0000 2 180.00 ! NA 5mc, adm jr. 9/9/93 +NG2R61 CG2R62 CG2R62 HGR62 3.4000 2 180.00 ! NA C +NG2R61 CG2R62 CG2R62 HGR63 7.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +NG2R62 CG2R62 CG2R62 HGR62 6.0000 2 180.00 ! 43HPY, 4(3H)-pyrimidinone; from NG2R62 CG2R61 CG2R61 HGR62; isg +NG2R62 CG2R62 CG2R62 HGR63 1.10 2 180.00 ! PYRH ,6.0000 2 180.00 ! from NG2R62 CG2R62 CG2R62 HGR62, penalty= 1 +NG2R67 CG2R62 CG2R62 HGR62 3.4000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from NG2R61 CG2R62 CG2R62 HGR62; isg +HGR62 CG2R62 CG2R62 HGR62 3.0000 2 180.00 ! NA U +HGR63 CG2R62 CG2R62 HGR63 2.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R61 CG2R62 CG2R63 NG2R61 1.8000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R62 CG2R63 OG2D4 1.0000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R62 CG2R63 SG2D1 4.5000 2 180.00 ! YT2S, 3,4-dihydro-4-thioxo-2(1H)-quinazolinone; from CG2R61 CG2R61 CG2R61 SG311, FETZ; isg +CG2R62 CG2R62 CG2R63 CG2R62 1.6000 2 180.00 ! 4PYO, 4(1H)-pyridinone, isg +CG2R62 CG2R62 CG2R63 NG2R61 1.8000 2 180.00 ! NA T +CG2R62 CG2R62 CG2R63 NG2R67 1.8000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R61 CG2R62 CG2R63 NG2R61, YTHY; isg +CG2R62 CG2R62 CG2R63 OG2D4 1.0000 2 180.00 ! NA bases +CG2R62 CG2R62 CG2R63 OG3R60 0.4000 2 180.00 ! RIN, coumarin, isg +CG2R62 CG2R62 CG2R63 SG2D1 4.5000 2 180.00 ! YT2S, 3,4-dihydro-4-thioxo-2(1H)-quinazolinone; from CG2R61 CG2R61 CG2R61 SG311, FETZ; isg +CG2R67 CG2R62 CG2R63 NG2R61 1.80 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R63 NG2R61, penalty= 0.5 +CG2R67 CG2R62 CG2R63 OG2D4 1.00 2 180.00 ! pyo2b , from CG2R61 CG2R62 CG2R63 OG2D4, penalty= 0.5 +CG331 CG2R62 CG2R63 NG2R61 5.6000 2 180.00 ! NA T +CG331 CG2R62 CG2R63 OG2D4 1.0000 2 180.00 ! NA bases +HGR62 CG2R62 CG2R63 CG2R62 0.5000 2 180.00 ! 4PYO, 4(1H)-pyridinone, isg +HGR62 CG2R62 CG2R63 NG2R61 1.0000 2 180.00 ! NA bases +HGR62 CG2R62 CG2R63 NG2R67 0.8000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from NG2R61 CG2R61 CG2R61 HGR61 , YTS2; isg +HGR62 CG2R62 CG2R63 OG2D4 6.0000 2 180.00 ! NA U +HGR62 CG2R62 CG2R63 OG3R60 2.4000 2 180.00 ! RIN, coumarin, isg +HGR62 CG2R62 CG2R63 SG2D1 2.4000 2 180.00 ! URA4S, 3,4-dihydro-4-thioxo-2(1H)-pyrimidinone; from SG311 CG2R61 CG2R61 HGR61; isg +CG2R62 CG2R62 CG2R64 NG2R62 0.6000 2 180.00 ! NA C +CG2R62 CG2R62 CG2R64 NG2S3 2.0000 2 180.00 ! NA C +CG2R62 CG2R62 CG2R64 NG301 3.1000 2 180.00 ! TMC, from 4MC, yxu +HGR62 CG2R62 CG2R64 NG2R62 3.4000 2 180.00 ! NA C +HGR62 CG2R62 CG2R64 NG2S3 2.0000 2 180.00 ! NA C +HGR62 CG2R62 CG2R64 NG301 0.0000 2 180.00 ! TMC, from 4MC, yxu +CG2R62 CG2R62 CG2R67 CG2R62 3.10 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 6 +CG2R62 CG2R62 CG2R67 CG2R67 3.10 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 5.5 +CG2R63 CG2R62 CG2R67 CG2R62 3.10 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 8.5 +CG2R63 CG2R62 CG2R67 CG2R67 3.10 2 180.00 ! pyo2b , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 8 +NG2R61 CG2R62 CG2R67 CG2R62 1.20 2 180.00 ! pyo3b , from NG2R60 CG2R61 CG2R67 CG2R61, penalty= 27.5 +NG2R61 CG2R62 CG2R67 CG2R67 1.00 2 180.00 ! pyo3b , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 27 +NG2R62 CG2R62 CG2R67 CG2R62 1.20 2 180.00 ! PYRF , from NG2R60 CG2R61 CG2R67 CG2R61, penalty= 6.5 +NG2R62 CG2R62 CG2R67 CG2R67 1.00 2 180.00 ! PYRF , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 6 +HGR62 CG2R62 CG2R67 CG2R62 4.20 2 180.00 ! pyo2b , from HGR62 CG2R61 CG2R67 CG2R61, penalty= 5.5 +HGR62 CG2R62 CG2R67 CG2R67 4.20 2 180.00 ! pyo2b , from HGR62 CG2R61 CG2R67 CG2R67, penalty= 5 +HGR63 CG2R62 CG2R67 CG2R62 4.20 2 180.00 ! PIUB , from HGR62 CG2R61 CG2R67 CG2R61, penalty= 6.5 +HGR63 CG2R62 CG2R67 CG2R67 4.20 2 180.00 ! PIUB , from HGR62 CG2R61 CG2R67 CG2R67, penalty= 6 +CG2R62 CG2R62 CG331 HGA3 0.4600 3 0.00 ! NA T +CG2R63 CG2R62 CG331 HGA3 0.4600 3 0.00 ! NA T +CG2R61 CG2R62 NG2R61 CG2R63 0.6000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R61 CG2R62 NG2R61 HGP1 1.0000 2 180.00 ! YTHY, 2,4(1H,3H)-quinazolinedione, isg +CG2R62 CG2R62 NG2R61 CG2R62 4.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R62 CG2R62 NG2R61 CG2R63 0.6000 2 180.00 ! NA C +CG2R62 CG2R62 NG2R61 CG331 11.0000 2 180.00 ! 1MTH, 1-Methyl-Thymine, kevo for gsk/ibm +CG2R62 CG2R62 NG2R61 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage +CG2R62 CG2R62 NG2R61 CG3C53 11.0000 2 180.00 ! NA, glycosyl linkage +CG2R62 CG2R62 NG2R61 CG3RC1 1.0000 2 180.00 ! NA bases +CG2R62 CG2R62 NG2R61 HGP1 1.0000 2 180.00 ! NA base +CG2R62 CG2R62 NG2R61 HGP2 1.0000 2 180.00 ! NA base +CG2R67 CG2R62 NG2R61 CG2R62 4.00 2 180.00 ! PYRF , from CG2R62 CG2R62 NG2R61 CG2R62, penalty= 1.5 +CG2R67 CG2R62 NG2R61 CG2R63 0.60 2 180.00 ! pyo3b , from CG2R61 CG2R62 NG2R61 CG2R63, penalty= 0.5 +CG2R67 CG2R62 NG2R61 HGP1 1.00 2 180.00 ! pyo3b , from CG2R61 CG2R62 NG2R61 HGP1, penalty= 0.5 +CG2R67 CG2R62 NG2R61 HGP2 1.00 2 180.00 ! PYRF , from CG2R62 CG2R62 NG2R61 HGP2, penalty= 1.5 +NG2R62 CG2R62 NG2R61 CG2R62 0.15 2 180.00 ! PYRH ,0.2000 2 180.00 ! from NG2R62 CG2R64 NG2R61 CG2R63, penalty= 17 +NG2R62 CG2R62 NG2R61 HGP2 3.20 2 180.00 ! PYRH ,3.6000 2 180.00 ! from NG2R62 CG2R64 NG2R61 HGP1, penalty= 18 +HGR62 CG2R62 NG2R61 CG2R62 5.6000 2 180.00 ! 4PYO, 4(1H)-pyridinone, isg +HGR62 CG2R62 NG2R61 CG2R63 4.6000 2 180.00 ! NA C +HGR62 CG2R62 NG2R61 CG331 0.3000 2 180.00 ! 1MTH, 1-Methyl-Thymine, kevo for gsk/ibm +HGR62 CG2R62 NG2R61 CG3C51 0.3000 2 180.00 ! NA, glycosyl linkage +HGR62 CG2R62 NG2R61 CG3RC1 1.0000 2 180.00 ! NA bases +HGR62 CG2R62 NG2R61 HGP1 1.2000 2 180.00 ! adjusted for 2PYO,URAC,4PYO, kevo,isg,xxwy 8/13 +HGR63 CG2R62 NG2R61 CG2R62 7.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +HGR63 CG2R62 NG2R61 CG3C53 1.0000 2 180.00 ! NA base +HGR63 CG2R62 NG2R61 HGP2 3.0000 2 180.00 ! NA nad/ppi, jjp1/adm jr. 7/95 +CG2R61 CG2R62 NG2R62 CG2R64 2.0000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R62 CG2R62 NG2R62 CG2R62 2.70 2 180.00 ! PYRH ,0.5000 2 180.00 ! from CG2R62 CG2R62 NG2R62 CG2R64, penalty= 2.5 +CG2R62 CG2R62 NG2R62 CG2R64 0.5000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R67 CG2R62 NG2R62 CG2R62 2.00 2 180.00 ! PYRF , from CG2R61 CG2R62 NG2R62 CG2R64, penalty= 3 +NG2R61 CG2R62 NG2R62 CG2R62 3.00 2 180.00 ! PYRH ,4.0000 2 180.00 ! from NG2R61 CG2R64 NG2R62 CG2R62, penalty= 15 +HGR62 CG2R62 NG2R62 CG2R64 7.3000 2 180.00 ! 43HPY, 4(3H)-pyrimidinone; from HGR62 CG2R61 NG2R62 CG2R64; isg +HGR63 CG2R62 NG2R62 CG2R62 7.40 2 180.00 ! PYRH ,7.3000 2 180.00 ! from HGR62 CG2R62 NG2R62 CG2R64, penalty= 3.5 +CG2R62 CG2R62 NG2R67 CG2R62 4.0000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R62 CG2R62 NG2R61 CG2R62; isg +CG2R62 CG2R62 NG2R67 CG2R63 0.6000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R62 CG2R62 NG2R61 CG2R63, NA; isg +CG2R62 CG2R62 NG2R67 CG2R67 4.0000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R62 CG2R62 NG2R61 CG2R62; isg +HGR62 CG2R62 NG2R67 CG2R62 2.8000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from NG2R60 CG2R61 CG2R61 HGR61; isg +HGR62 CG2R62 NG2R67 CG2R63 4.6000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from HGR62 CG2R62 NG2R61 CG2R63, NA; isg +HGR62 CG2R62 NG2R67 CG2R67 1.0000 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone; from CG2R62 CG2R62 CG2R62 HGR62; isg +CG2R61 CG2R62 OG3R60 CG2R63 0.7600 2 0.00 ! RIN, coumarin, isg +CG2R62 CG2R62 OG3R60 CG2R63 0.9400 2 0.00 ! RIN, coumarin, isg +NG2R61 CG2R63 CG2RC0 CG2RC0 0.2000 2 180.00 ! NA G +NG2R61 CG2R63 CG2RC0 NG2R50 2.0000 2 180.00 ! NA G +OG2D4 CG2R63 CG2RC0 CG2RC0 14.0000 2 180.00 ! NA G +OG2D4 CG2R63 CG2RC0 NG2R50 0.0000 2 180.00 ! NA G +CG2R61 CG2R63 NG2R61 CG2R63 0.5000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R61 CG2R63 NG2R61 CG2R64 1.5000 2 180.00 ! 43HSPY, 4(3H)-pyrimidinethione; from CG2R62 CG2R63 NG2R61 CG2R63; isg +CG2R61 CG2R63 NG2R61 HGP1 4.8000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R62 CG2R63 NG2R61 CG2R62 1.5000 2 180.00 ! 2PYO, 2-Pyridone, xxwy +CG2R62 CG2R63 NG2R61 CG2R63 1.5000 2 180.00 ! NA U +CG2R62 CG2R63 NG2R61 CG2R64 0.5000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R62 CG2R63 NG2R61 HGP1 4.8000 2 180.00 ! NA T +CG2RC0 CG2R63 NG2R61 CG2R64 0.2000 2 180.00 ! NA G +CG2RC0 CG2R63 NG2R61 HGP1 3.6000 2 180.00 ! NA G +NG2R61 CG2R63 NG2R61 CG2R61 0.5000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +NG2R61 CG2R63 NG2R61 CG2R62 1.5000 2 180.00 ! NA U +NG2R61 CG2R63 NG2R61 CG2R63 3.0000 2 180.00 ! NA T +NG2R61 CG2R63 NG2R61 CG331 11.0000 2 180.00 ! 1MTH, 1-Methyl-Thymine, kevo for gsk/ibm +NG2R61 CG2R63 NG2R61 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage +NG2R61 CG2R63 NG2R61 CG3RC1 1.0000 2 180.00 ! NA base +NG2R61 CG2R63 NG2R61 HGP1 3.3000 2 180.00 ! NAMODEL cytosine tautomer +NG2R62 CG2R63 NG2R61 CG2R62 0.6000 2 180.00 ! NA C +NG2R62 CG2R63 NG2R61 CG331 11.0000 2 180.00 ! CYT, BTMC,...; not optimized; yxu +NG2R62 CG2R63 NG2R61 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage +NG2R62 CG2R63 NG2R61 CG3RC1 0.9000 2 180.00 ! NA bases +NG2R67 CG2R63 NG2R61 CG2R61 1.5000 2 180.00 ! 3PH24S, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione; from NG2R61 CG2R63 NG2R61 CG2R62, NA; isg +NG2R67 CG2R63 NG2R61 CG2R62 1.5000 2 180.00 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from NG2R61 CG2R63 NG2R61 CG2R62, NA; isg +NG2R67 CG2R63 NG2R61 HGP1 3.3000 2 180.00 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from NG2R61 CG2R63 NG2R61 HGP1, NA; isg +OG2D4 CG2R63 NG2R61 CG2R62 1.6000 2 180.00 ! NA C +OG2D4 CG2R63 NG2R61 CG2R63 0.9000 2 180.00 ! NA bases +OG2D4 CG2R63 NG2R61 CG2R64 14.0000 2 180.00 ! NA G +OG2D4 CG2R63 NG2R61 CG331 11.0000 2 180.00 ! 1MTH, 1-Methyl-Thymine, kevo for gsk/ibm +OG2D4 CG2R63 NG2R61 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage +OG2D4 CG2R63 NG2R61 CG3RC1 1.0000 2 180.00 ! NA base +OG2D4 CG2R63 NG2R61 HGP1 0.0000 2 180.00 ! NA G +SG2D1 CG2R63 NG2R61 CG2R61 1.6000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +SG2D1 CG2R63 NG2R61 CG2R62 1.6000 2 180.00 ! YT4S, 2,3-dihydro-2-thioxo-4(1H)-quinazolinone; from OG2D4 CG2R63 NG2R61 CG2R62, NA; isg +SG2D1 CG2R63 NG2R61 CG2R63 0.9000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +SG2D1 CG2R63 NG2R61 CG2R64 14.0000 2 180.00 ! 43HSPY, 4(3H)-pyrimidinethione; from OG2D4 CG2R63 NG2R61 CG2R64; isg +SG2D1 CG2R63 NG2R61 HGP1 0.5000 2 180.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +NG2R61 CG2R63 NG2R62 CG2R64 0.6000 2 180.00 ! NA C +OG2D4 CG2R63 NG2R62 CG2R64 1.6000 2 180.00 ! NA C +CG2R61 CG2R63 NG2R67 CG2R63 1.5000 2 180.00 ! 3PH24S, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione; from CG2R62 CG2R63 NG2R61 CG2R63, NA; isg +CG2R61 CG2R63 NG2R67 CG2R64 1.5000 2 180.00 ! 43HSPP, 3-phenyl-4(3H)-pyrimidinethione; from 43HSPY; isg +CG2R61 CG2R63 NG2R67 CG2R67 1.5000 2 180.00 ! 3PH24S, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione; from CG2R62 CG2R63 NG2R67 CG2R67; isg +CG2R62 CG2R63 NG2R67 CG2R62 1.5000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R62 CG2R63 NG2R61 CG2R62, 2PYO; isg +CG2R62 CG2R63 NG2R67 CG2R63 1.5000 2 180.00 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from CG2R62 CG2R63 NG2R61 CG2R63, NA; isg +CG2R62 CG2R63 NG2R67 CG2R64 0.5000 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from CG2R62 CG2R63 NG2R61 CG2R64, TC243C; isg +CG2R62 CG2R63 NG2R67 CG2R67 1.5000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R62 CG2R63 NG2R61 CG2R62, 2PYO; isg +NG2R61 CG2R63 NG2R67 CG2R63 3.0000 2 180.00 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from NG2R61 CG2R63 NG2R61 CG2R63, NA; isg +NG2R61 CG2R63 NG2R67 CG2R67 11.0000 2 180.00 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from NG2R61 CG2R63 NG2R61 CG3C51, NA; isg +OG2D4 CG2R63 NG2R67 CG2R62 1.6000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from OG2D4 CG2R63 NG2R61 CG2R62, NA; isg +OG2D4 CG2R63 NG2R67 CG2R63 0.9000 2 180.00 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from OG2D4 CG2R63 NG2R61 CG2R63, NA; isg +OG2D4 CG2R63 NG2R67 CG2R64 14.0000 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from OG2D4 CG2R63 NG2R61 CG2R64, TC243C; isg +OG2D4 CG2R63 NG2R67 CG2R67 1.6000 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from OG2D4 CG2R63 NG2R61 CG2R62, NA; isg +SG2D1 CG2R63 NG2R67 CG2R63 0.9000 2 180.00 ! 3PH2SR, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinone; from CG2R63 NG2R61 CG2R63 SG2D1, YTS2; isg +SG2D1 CG2R63 NG2R67 CG2R64 0.9000 2 180.00 ! 43HSPP, 3-phenyl-4(3H)-pyrimidinethione; from SG2D1 CG2R63 NG2R61 CG2R63, YTS2; isg +SG2D1 CG2R63 NG2R67 CG2R67 1.6000 2 180.00 ! 3PH2SR, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinone; from OG2D4 CG2R63 NG2R61 CG2R62, NA; isg +CG2R62 CG2R63 OG3R60 CG2R62 0.6000 2 0.00 ! RIN, coumarin, isg +OG2D4 CG2R63 OG3R60 CG2R62 0.7600 2 0.00 ! RIN, coumarin, isg +NG2R62 CG2R64 CG2RC0 CG2RC0 1.8000 2 180.00 ! NA A +NG2R62 CG2R64 CG2RC0 NG2R50 2.0000 2 180.00 ! NA A +NG2S3 CG2R64 CG2RC0 CG2RC0 4.0000 2 180.00 ! NA A +NG2S3 CG2R64 CG2RC0 NG2R50 0.0000 2 180.00 ! NA A +NG301 CG2R64 CG2RC0 CG2RC0 4.0000 2 180.00 ! M6A, yxu +NG301 CG2R64 CG2RC0 NG2R50 4.7000 2 180.00 ! M6A, yxu +CG2R61 CG2R64 NG2R60 CG2R61 1.2000 2 180.00 ! 2AMP, 2-amino pyridine, from PYR1, pyridine, kevo +NG2S1 CG2R64 NG2R60 CG2R61 3.1000 2 180.00 ! 2AMP, 2-Amino pyridine, cacha (verified by kevo) +NG2R62 CG2R64 NG2R61 CG2R63 0.2000 2 180.00 ! NA G +NG2R62 CG2R64 NG2R61 HGP1 3.6000 2 180.00 ! NA G +NG2S3 CG2R64 NG2R61 CG2R63 4.0000 2 180.00 ! NA G +NG2S3 CG2R64 NG2R61 HGP1 0.0000 2 180.00 ! NA G +SG311 CG2R64 NG2R61 CG2R63 4.0000 2 180.00 ! 4O2SM, 2-(methylthio)-4(3H)-pyrimidinone; from NG2S3 CG2R64 NG2R61 CG2R63; isg +SG311 CG2R64 NG2R61 HGP1 0.0000 2 180.00 ! 4O2SM, 2-(methylthio)-4(3H)-pyrimidinone; from NG2S3 CG2R64 NG2R61 HGP1; isg +HGR62 CG2R64 NG2R61 CG2R63 5.5000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +HGR62 CG2R64 NG2R61 HGP1 0.5000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +CG2R61 CG2R64 NG2R62 CG2R61 2.0000 2 180.00 ! 18NFD, 1,8-naphthyridine, erh +CG2R61 CG2R64 NG2R62 CG2R64 2.0000 2 0.00 ! PTID, pteridine, erh +CG2R62 CG2R64 NG2R62 CG2R63 6.0000 2 180.00 ! NA C +CG2RC0 CG2R64 NG2R62 CG2R64 1.8000 2 180.00 ! NA A +NG2R61 CG2R64 NG2R62 CG2R61 2.0000 2 180.00 ! 43HSPY, 4(3H)-pyrimidinethione; from NG2R61 CG2R64 NG2R62 CG2RC0; isg +NG2R61 CG2R64 NG2R62 CG2R62 4.0000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +NG2R61 CG2R64 NG2R62 CG2RC0 2.0000 2 180.00 ! NA G +NG2R62 CG2R64 NG2R62 CG2R61 2.0000 2 180.00 ! PYRM, pyrimidine +NG2R62 CG2R64 NG2R62 CG2R64 1.8000 2 180.00 ! NA A +NG2R62 CG2R64 NG2R62 CG2RC0 2.0000 2 180.00 ! NAMODEL guanine tautomer +NG2R62 CG2R64 NG2R62 NG2R62 0.5000 2 180.00 ! TRIB, triazine124 +NG2R67 CG2R64 NG2R62 CG2R61 2.0000 2 180.00 ! 43HSPP, 3-phenyl-4(3H)-pyrimidinethione; from NG2R62 CG2R64 NG2R62 CG2R61, PYRM; isg +NG2R67 CG2R64 NG2R62 CG2R62 4.0000 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from NG2R61 CG2R64 NG2R62 CG2R62, TC243C; isg +NG2S3 CG2R64 NG2R62 CG2R63 2.0000 2 180.00 ! NA C +NG2S3 CG2R64 NG2R62 CG2R64 1.8000 2 180.00 ! NA A +NG2S3 CG2R64 NG2R62 CG2RC0 4.0000 2 180.00 ! NA G +NG301 CG2R64 NG2R62 CG2R63 3.1000 2 180.00 ! TMC, from 4MC, yxu +NG301 CG2R64 NG2R62 CG2R64 3.8000 2 180.00 ! M6A, yxu +SG311 CG2R64 NG2R62 CG2R61 10.2000 2 180.00 ! 2SMPYR, 2-(methylthio)-pyrimidine; from NG2S1 CG2R64 NG2R60 CG2R61; isg +SG311 CG2R64 NG2R62 CG2R62 2.0000 2 180.00 ! 4O2SM, 2-(methylthio)-4(3H)-pyrimidinone; from NG2S3 CG2R64 NG2R62 CG2R63; isg +HGR62 CG2R64 NG2R62 CG2R61 7.3000 2 180.00 ! PYRM, pyrimidine +HGR62 CG2R64 NG2R62 CG2R62 7.3000 2 180.00 ! TC243C, 4(3H)-quinazolinone, isg +HGR62 CG2R64 NG2R62 CG2R64 8.5000 2 180.00 ! NA A +HGR62 CG2R64 NG2R62 CG2RC0 8.5000 2 180.00 ! NA A +HGR62 CG2R64 NG2R62 NG2R62 6.0000 2 180.00 ! TRIB, triazine124 +NG2R62 CG2R64 NG2R67 CG2R63 0.2000 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from NG2R62 CG2R64 NG2R61 CG2R63, TC243C; isg +NG2R62 CG2R64 NG2R67 CG2R67 0.2000 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from NG2R62 CG2R64 NG2R61 CG2R63, TC243C; isg +HGR62 CG2R64 NG2R67 CG2R63 5.5000 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from HGR62 CG2R64 NG2R61 CG2R63, TC243C; isg +HGR62 CG2R64 NG2R67 CG2R67 1.0000 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone; from HGR62 CG2R62 NG2R67 CG2R67, TC243C; isg +CG2R61 CG2R64 NG2S1 CG2O1 1.2000 2 180.00 ! 2AMP, 2-amino pyridine, from PACP, cacha ! not fitted because cacha's original atom typing didn't allow it ==> re-optimize +CG2R61 CG2R64 NG2S1 HGP1 0.5000 2 180.00 ! 2AMP, 2-amino pyridine, from PACP, cacha ! this one does not require re-optimization +NG2R60 CG2R64 NG2S1 CG2O1 1.5000 1 180.00 ! 2AMP, 2-Amino pyridine, dihedral fit by cacha +NG2R60 CG2R64 NG2S1 CG2O1 2.6000 2 180.00 ! 2AMP, 2-Amino pyridine, dihedral fit by cacha +NG2R60 CG2R64 NG2S1 CG2O1 0.1800 3 180.00 ! 2AMP, 2-Amino pyridine, dihedral fit by cacha +NG2R60 CG2R64 NG2S1 HGP1 0.5000 2 180.00 ! 2AMP, 2-Amino pyridine, dihedral fit by cacha +CG2R62 CG2R64 NG2S3 HGP4 2.0000 2 180.00 ! NA 5mc, adm jr. 9/9/93 +CG2RC0 CG2R64 NG2S3 HGP4 0.5000 2 180.00 ! NA A +NG2R61 CG2R64 NG2S3 HGP4 1.2000 2 180.00 ! NA G +NG2R62 CG2R64 NG2S3 HGP4 1.0000 2 180.00 ! NA C +CG2R62 CG2R64 NG301 CG331 1.9800 2 180.00 ! TMC, yxu, pyramid can be increased by adding term of 4-fold & 0.0-phase +CG2RC0 CG2R64 NG301 CG331 2.8500 2 180.00 ! M6A, yxu +CG2RC0 CG2R64 NG301 CG331 0.9000 4 0.00 ! M6A, yxu, pyramid can be increased by increasing this term +NG2R62 CG2R64 NG301 CG331 1.9800 2 180.00 ! TMC, yxu +NG2R61 CG2R64 SG311 CG331 1.4500 1 0.00 ! 4O2SM, 2-(methylthio)-4(3H)-pyrimidinone, isg +NG2R62 CG2R64 SG311 CG331 2.1200 2 180.00 ! 2SMPYR, 2-(methylthio)-pyrimidine, isg +NG2R62 CG2R64 SG311 CG331 0.1900 4 180.00 ! 2SMPYR, 2-(methylthio)-pyrimidine, isg +CG2R61 CG2R66 CG2R67 CG2R61 3.10 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R61, penalty= 5 +CG2R61 CG2R66 CG2R67 CG2R67 3.10 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R67 CG2R67, penalty= 5 +FGR1 CG2R66 CG2R67 CG2R61 4.50 2 180.00 ! PYO2F , from CG2R61 CG2R61 CG2R66 FGR1, penalty= 30 +FGR1 CG2R66 CG2R67 CG2R67 1.00 2 180.00 ! PYO2F , from NG2R60 CG2R61 CG2R67 CG2R67, penalty= 89 +CG2R61 CG2R67 CG2R67 CG2R61 0.8900 2 180.00 ! BIPHENYL ANALOGS, peml +CG2R61 CG2R67 CG2R67 CG2R62 0.46 2 180.00 ! pyo2b ,tune the middle 180 from CG2R61 CG2R67 CG2R67 CG2R61, penalty= 0.5 +CG2R61 CG2R67 CG2R67 CG2R62 0.23 4 0.00 ! low will down the two peaks;phs 4, 0 pyo2b , from CG2R61 CG2R67 CG2R67 CG2R61, penalty= 0.5 +CG2R61 CG2R67 CG2R67 CG2RC0 2.0000 2 180.00 ! CRBZ, carbazole, erh +CG2R61 CG2R67 CG2R67 NG2R60 0.3750 1 0.00 ! 22BPY, 2,2'-bipyridine, kevo +CG2R61 CG2R67 CG2R67 NG2R60 0.9400 2 180.00 ! 22BPY, 2,2'-bipyridine, kevo +CG2R61 CG2R67 CG2R67 NG2R60 0.1900 3 180.00 ! 22BPY, 2,2'-bipyridine, kevo +CG2R61 CG2R67 CG2R67 NG2R60 0.1600 4 0.00 ! 22BPY, 2,2'-bipyridine, kevo +CG2R62 CG2R67 CG2R67 CG2R66 0.43 2 180.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin +CG2R62 CG2R67 CG2R67 CG2R66 0.12 4 0.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin +CG2R62 CG2R67 CG2R67 CG2R66 0.02 6 180.00 ! compromise between pyo2f, pyo3f, piuf using weight on maxmin +CG2RC0 CG2R67 CG2R67 CG2RC0 1.5000 2 180.00 ! CRBZ, carbazole, erh +NG2R60 CG2R67 CG2R67 NG2R60 0.3750 1 180.00 ! 22BPY, 2,2'-bipyridine, kevo +NG2R60 CG2R67 CG2R67 NG2R60 0.9400 2 180.00 ! 22BPY, 2,2'-bipyridine, kevo +NG2R60 CG2R67 CG2R67 NG2R60 0.1900 3 0.00 ! 22BPY, 2,2'-bipyridine, kevo +NG2R60 CG2R67 CG2R67 NG2R60 0.1600 4 0.00 ! 22BPY, 2,2'-bipyridine, kevo +CG2R61 CG2R67 CG2RC0 CG2R61 0.0500 2 180.00 ! CRBZ, carbazole, erh +CG2R61 CG2R67 CG2RC0 CG3C52 6.7500 2 180.00 ! FLRN, Fluorene, erh +CG2R61 CG2R67 CG2RC0 NG2R51 3.0000 2 180.00 ! CRBZ, carbazole, erh +CG2R67 CG2R67 CG2RC0 CG2R61 3.5000 2 180.00 ! CRBZ, carbazole, erh +CG2R67 CG2R67 CG2RC0 CG3C52 5.0000 3 180.00 ! FLRN, Fluorene, erh +CG2R67 CG2R67 CG2RC0 NG2R51 0.2500 2 180.00 ! CRBZ, carbazole, erh +CG2R61 CG2R67 NG2R60 CG2R61 1.2000 2 180.00 ! 22BPY, 2,2'-bipyridine, from CG2R61 CG2R61 NG2R60 CG2R61, kevo +CG2R67 CG2R67 NG2R60 CG2R61 3.1000 2 180.00 ! 22BPY, 2,2'-bipyridine, kevo +CG2R61 CG2R67 NG2R67 CG2R62 0.3700 2 180.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone, isg +CG2R61 CG2R67 NG2R67 CG2R62 0.2700 4 0.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone, isg +CG2R61 CG2R67 NG2R67 CG2R62 0.0200 6 0.00 ! 1PH4PO, 1-phenyl-4(1H)-pyridinone, isg +CG2R61 CG2R67 NG2R67 CG2R63 1.4500 2 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from 1PH4PO; isg +CG2R61 CG2R67 NG2R67 CG2R63 0.1400 4 180.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from 1PH4PO; isg +CG2R61 CG2R67 NG2R67 CG2R64 0.3700 2 180.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone, isg +CG2R61 CG2R67 NG2R67 CG2R64 0.2600 4 0.00 ! 43PPY, 3-phenyl-4(3H)-pyrimidinone, isg +CG2R71 CG2R71 CG2R71 CG2R71 1.6000 2 180.00 ! AZUL, Azulene, kevo +CG2R71 CG2R71 CG2R71 CG2RC7 1.6000 2 180.00 ! AZUL, Azulene, kevo +CG2R71 CG2R71 CG2R71 HGR71 3.2000 2 180.00 ! AZUL, Azulene, kevo +CG2RC7 CG2R71 CG2R71 HGR71 4.2000 2 180.00 ! AZUL, Azulene, kevo +HGR71 CG2R71 CG2R71 HGR71 2.4000 2 180.00 ! AZUL, Azulene, kevo +CG2R71 CG2R71 CG2RC7 CG2R51 3.0000 2 180.00 ! AZUL, Azulene, kevo +CG2R71 CG2R71 CG2RC7 CG2RC7 3.0000 2 180.00 ! AZUL, Azulene, kevo +HGR71 CG2R71 CG2RC7 CG2R51 3.1000 2 180.00 ! AZUL, Azulene, kevo +HGR71 CG2R71 CG2RC7 CG2RC7 3.1000 2 180.00 ! AZUL, Azulene, kevo +CG25C1 CG2RC0 CG2RC0 CG2R61 1.5000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C1 CG2RC0 CG2RC0 NG2R51 1.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2RC0 CG2RC0 CG2R61 1.5000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG25C2 CG2RC0 CG2RC0 NG2R51 1.0000 2 180.00 ! MEOI, methyleneoxindole, kevo & xxwy +CG2R51 CG2RC0 CG2RC0 CG2R51 0.0000 2 180.00 ! ISOI, isoindole, kevo +CG2R51 CG2RC0 CG2RC0 CG2R61 1.5000 2 180.00 ! INDO/TRP (Kenno: 4.0 --> 1.5) +CG2R51 CG2RC0 CG2RC0 CG3C52 5.0000 2 180.00 ! INDE, indene, kevo +CG2R51 CG2RC0 CG2RC0 NG2R51 6.5000 2 180.00 ! INDO/TRP +CG2R51 CG2RC0 CG2RC0 OG2R50 8.5000 2 180.00 ! ZFUR, benzofuran, kevo +CG2R51 CG2RC0 CG2RC0 SG2R50 8.5000 2 180.00 ! ZTHP, benzothiophene, kevo +CG2R52 CG2RC0 CG2RC0 CG2R61 1.5000 2 180.00 ! INDA, 1H-indazole, kevo +CG2R52 CG2RC0 CG2RC0 NG2R51 12.0000 2 180.00 ! INDA, 1H-indazole, kevo +CG2R61 CG2RC0 CG2RC0 CG2R61 3.0000 2 180.00 ! INDO/TRP +CG2R61 CG2RC0 CG2RC0 CG3C52 6.5000 2 180.00 ! 3HIN, 3H-indole, kevo +CG2R61 CG2RC0 CG2RC0 NG2R50 1.5000 2 180.00 ! ZIMI, benzimidazole, kevo +CG2R61 CG2RC0 CG2RC0 NG2R51 1.5000 2 180.00 ! INDO/TRP (Kenno: 4.0 --> 1.5) +CG2R61 CG2RC0 CG2RC0 NG2R62 0.0000 2 180.00 ! PUR9, purine(N9H), kevo +CG2R61 CG2RC0 CG2RC0 NG3C51 6.0000 2 180.00 ! INDI, indoline, kevo +CG2R61 CG2RC0 CG2RC0 OG2R50 0.0000 2 180.00 ! ZFUR, benzofuran, kevo +CG2R61 CG2RC0 CG2RC0 OG3C51 4.0000 2 180.00 ! ZDOL, 1,3-benzodioxole, pram & oashi +CG2R61 CG2RC0 CG2RC0 SG2R50 0.0000 2 180.00 ! ZTHP, benzothiophene, kevo +CG2R63 CG2RC0 CG2RC0 NG2R51 10.0000 2 180.00 ! NA G +CG2R63 CG2RC0 CG2RC0 NG2R62 2.0000 2 180.00 ! NA G +CG2R64 CG2RC0 CG2RC0 NG2R51 7.0000 2 180.00 ! NA A +CG2R64 CG2RC0 CG2RC0 NG2R62 2.0000 2 180.00 ! NA A +CG3C52 CG2RC0 CG2RC0 NG2R50 6.5000 2 180.00 ! 3HIN, 3H-indole, kevo +CG3C52 CG2RC0 CG2RC0 NG3C51 6.0000 2 180.00 ! INDI, indoline, kevo +NG2R50 CG2RC0 CG2RC0 NG2R51 10.0000 2 180.00 ! NA G +NG2R50 CG2RC0 CG2RC0 NG2R62 7.0000 2 180.00 ! NA A +NG2R50 CG2RC0 CG2RC0 SG2R50 4.0000 2 180.00 ! ZTHZ, benzothiazole, kevo +NG2R51 CG2RC0 CG2RC0 NG2R62 8.5000 2 180.00 ! PUR7, purine(N7H), kevo +OG3C51 CG2RC0 CG2RC0 OG3C51 7.7000 2 180.00 ! ZDOL, 1,3-benzodioxole, pram & oashi +CG2R61 CG2RC0 CG3C52 CG2R51 0.9000 3 0.00 ! INDE, indene, kevo +CG2R61 CG2RC0 CG3C52 CG2R52 3.5000 3 0.00 ! 3HIN, 3H-indole, kevo +CG2R61 CG2RC0 CG3C52 CG2RC0 0.9000 3 0.00 ! FLRN, Fluorene, erh +CG2R61 CG2RC0 CG3C52 CG3C52 3.0000 2 180.00 ! INDI, indoline, kevo +CG2R61 CG2RC0 CG3C52 HGA2 0.5000 3 180.00 ! 3HIN, 3H-indole, kevo +CG2R67 CG2RC0 CG3C52 CG2RC0 0.7500 3 180.00 ! FLRN, Fluorene, erh +CG2R67 CG2RC0 CG3C52 HGA2 0.5000 3 0.00 ! FLRN, Fluorene, erh +CG2RC0 CG2RC0 CG3C52 CG2R51 1.0000 3 180.00 ! INDE, indene, kevo +CG2RC0 CG2RC0 CG3C52 CG2R52 2.0000 3 180.00 ! 3HIN, 3H-indole, kevo +CG2RC0 CG2RC0 CG3C52 CG3C52 1.0300 3 180.00 ! INDI, indoline, kevo +CG2RC0 CG2RC0 CG3C52 HGA2 0.5000 3 0.00 ! 3HIN, 3H-indole, kevo +CG2R61 CG2RC0 NG2R50 CG2R52 4.0000 2 180.00 ! 3HIN, 3H-indole, kevo +CG2R61 CG2RC0 NG2R50 CG2R53 15.0000 2 180.00 ! ZIMI, benzimidazole, kevo +CG2R63 CG2RC0 NG2R50 CG2R53 2.0000 2 180.00 ! NA G +CG2R64 CG2RC0 NG2R50 CG2R53 2.0000 2 180.00 ! NA A +CG2RC0 CG2RC0 NG2R50 CG2R52 4.0000 2 180.00 ! 3HIN, 3H-indole, kevo +CG2RC0 CG2RC0 NG2R50 CG2R53 6.0000 2 180.00 ! NA G +NG2R62 CG2RC0 NG2R50 CG2R53 2.0000 2 180.00 ! PUR7, purine(N7H), kevo +CG2R61 CG2RC0 NG2R51 CG2R51 1.5000 2 180.00 ! NA bases +CG2R61 CG2RC0 NG2R51 CG2R53 19.0000 2 180.00 ! ZIMI, benzimidazole, kevo +CG2R61 CG2RC0 NG2R51 CG2RC0 0.5000 2 180.00 ! CRBZ, carbazole, erh +CG2R61 CG2RC0 NG2R51 NG2R50 3.0000 2 180.00 ! INDA, 1H-indazole, kevo +CG2R61 CG2RC0 NG2R51 HGP1 0.2000 2 180.00 ! INDO/TRP +CG2R67 CG2RC0 NG2R51 CG2RC0 0.5000 2 180.00 ! CRBZ, carbazole, erh +CG2R67 CG2RC0 NG2R51 HGP1 0.2500 2 180.00 ! CRBZ, carbazole, erh +CG2RC0 CG2RC0 NG2R51 CG2R51 1.5000 2 180.00 ! NA bases +CG2RC0 CG2RC0 NG2R51 CG2R53 6.0000 2 180.00 ! NA G +CG2RC0 CG2RC0 NG2R51 CG331 11.0000 2 180.00 ! 9MAD, 9-Methyl-Adenine, kevo for gsk/ibm +CG2RC0 CG2RC0 NG2R51 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage +CG2RC0 CG2RC0 NG2R51 CG3RC1 1.2000 2 180.00 ! PYRIDINE pyridine, yin +CG2RC0 CG2RC0 NG2R51 NG2R50 6.5000 2 180.00 ! INDA, 1H-indazole, kevo +CG2RC0 CG2RC0 NG2R51 HGP1 0.8500 2 180.00 ! INDO/TRP +NG2R62 CG2RC0 NG2R51 CG2R53 2.0000 2 180.00 ! NA G +NG2R62 CG2RC0 NG2R51 CG331 11.0000 2 180.00 ! 9MAD, 9-Methyl-Adenine, kevo for gsk/ibm +NG2R62 CG2RC0 NG2R51 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage +NG2R62 CG2RC0 NG2R51 CG3RC1 1.2000 2 180.00 ! PYRIDINE pyridine, yin +NG2R62 CG2RC0 NG2R51 HGP1 1.2000 2 180.00 ! NA G +CG2RC0 CG2RC0 NG2R62 CG2R64 0.2000 2 180.00 ! NA G +NG2R50 CG2RC0 NG2R62 CG2R64 2.0000 2 180.00 ! PUR7, purine(N7H), kevo +NG2R51 CG2RC0 NG2R62 CG2R64 2.0000 2 180.00 ! NA G +CG2R51 CG2RC0 NG2RC0 CG2R51 8.0000 2 180.00 ! INDZ, indolizine, kevo +CG2R51 CG2RC0 NG2RC0 CG2R61 1.0000 2 180.00 ! INDZ, indolizine, kevo +CG2R61 CG2RC0 NG2RC0 CG2R51 1.0000 2 180.00 ! INDZ, indolizine, kevo +CG2R61 CG2RC0 NG2RC0 CG2R61 0.8000 2 180.00 ! INDZ, indolizine, kevo +CG2R61 CG2RC0 NG3C51 CG3C52 4.0000 2 180.00 ! INDI, indoline, kevo +CG2R61 CG2RC0 NG3C51 HGP1 0.0000 3 0.00 ! INDI, indoline, kevo +CG2RC0 CG2RC0 NG3C51 CG3C52 1.9600 3 0.00 ! INDI, indoline, kevo +CG2RC0 CG2RC0 NG3C51 HGP1 0.0000 3 0.00 ! INDI, indoline, kevo +CG2R61 CG2RC0 OG2R50 CG2R51 8.5000 2 180.00 ! ZFUR, benzofuran, kevo +CG2RC0 CG2RC0 OG2R50 CG2R51 8.5000 2 180.00 ! ZFUR, benzofuran, kevo +CG2R61 CG2RC0 OG3C51 CG3C52 0.3000 2 180.00 ! ZDOL, 1,3-benzodioxole, pram & oashi +CG2RC0 CG2RC0 OG3C51 CG3C52 0.3000 2 180.00 ! ZDOL, 1,3-benzodioxole, pram & oashi & kevo +CG2R61 CG2RC0 SG2R50 CG2R51 8.5000 2 180.00 ! ZTHP, benzothiophene, kevo +CG2R61 CG2RC0 SG2R50 CG2R53 3.0000 2 180.00 ! ZTHZ, benzothiazole, kevo +CG2RC0 CG2RC0 SG2R50 CG2R51 8.5000 2 180.00 ! ZTHP, benzothiophene, kevo +CG2RC0 CG2RC0 SG2R50 CG2R53 3.0000 2 180.00 ! ZTHZ, benzothiazole, kevo +CG2R51 CG2RC7 CG2RC7 CG2R51 3.0000 2 180.00 ! AZUL, Azulene, kevo +CG2R51 CG2RC7 CG2RC7 CG2R71 0.0000 2 180.00 ! AZUL, Azulene, kevo +CG2R71 CG2RC7 CG2RC7 CG2R71 0.0000 2 180.00 ! AZUL, Azulene, kevo +CG2D1 CG301 CG311 CG311 0.2000 3 0.00 ! CHL1, Cholesterol from X CTL1 CTL1 X; also consistent with RETINOL TMCH +CG2D1 CG301 CG311 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2D1 CG301 CG311 HGA1 0.1950 3 0.00 ! NA, sugar +CG311 CG301 CG311 CG311 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG311 CG301 CG311 CG321 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG311 CG301 CG311 HGA1 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG321 CG301 CG311 CG311 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG321 CG301 CG311 CG321 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG321 CG301 CG311 HGA1 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG331 CG301 CG311 CG311 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG331 CG301 CG311 CG321 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG331 CG301 CG311 HGA1 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG2D1 CG301 CG321 CG321 0.2000 3 0.00 ! CHL1, Cholesterol from X CTL1 CTL2 X; also consistent with RETINOL TMCH +CG2D1 CG301 CG321 HGA2 0.1950 3 0.00 ! NA, sugar +CG2DC1 CG301 CG321 CG321 0.2000 3 0.00 ! RETINOL TMCH +CG2DC1 CG301 CG321 HGA2 0.1900 3 0.00 ! RETINOL TMCH +CG2DC2 CG301 CG321 CG321 0.2000 3 0.00 ! RETINOL TMCH +CG2DC2 CG301 CG321 HGA2 0.1900 3 0.00 ! RETINOL TMCH +CG311 CG301 CG321 CG321 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 +CG311 CG301 CG321 HGA2 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG321 CG301 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG301 CG321 HGA2 0.1950 3 0.00 ! CHOLEST cholesterol reset to default by kevo +CG331 CG301 CG321 CG321 0.2000 3 0.00 ! RETINOL TMCH +CG331 CG301 CG321 CG331 0.4400 1 0.00 ! DMBU, dimethoxybutane, sna +CG331 CG301 CG321 CG331 0.0200 2 180.00 ! DMBU, dimethoxybutane, sna +CG331 CG301 CG321 CG331 0.7300 3 180.00 ! DMBU, dimethoxybutane, sna +CG331 CG301 CG321 HGA2 0.1950 3 0.00 ! RETINOL TMCH kevo: reset to default +OG301 CG301 CG321 CG331 0.8000 3 0.00 ! DMBU, dimethoxybutane, sna +OG301 CG301 CG321 HGA2 0.1600 3 0.00 ! DMBU, dimethoxybutane, sna +CG2D1 CG301 CG331 HGA3 0.1600 3 0.00 ! CHL1, Cholesterol from RETINOL TMCH (X CTL1 CTL3 X seems woefully inaccurate) +CG2DC1 CG301 CG331 HGA3 0.1600 3 0.00 ! RETINOL TMCH +CG2DC2 CG301 CG331 HGA3 0.1600 3 0.00 ! RETINOL TMCH +CG2O3 CG301 CG331 HGA3 0.2000 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +CG311 CG301 CG331 HGA3 0.1600 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG321 CG301 CG331 HGA3 0.1600 3 0.00 ! RETINOL TMCH +CG331 CG301 CG331 HGA3 0.1600 3 0.00 ! RETINOL TMCH +OG301 CG301 CG331 HGA3 0.1600 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +OG302 CG301 CG331 HGA3 0.1600 3 0.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha reset to default by kevo +OG311 CG301 CG331 HGA3 0.1400 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +CLGA3 CG301 CG331 HGA3 0.2700 3 0.00 ! TCLE +BRGA3 CG301 CG331 HGA3 0.2600 3 0.00 ! TBRE +CG2O3 CG301 OG301 CG331 0.2000 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +CG321 CG301 OG301 CG331 1.1500 1 0.00 ! DMBU, dimethoxybutane, sna +CG321 CG301 OG301 CG331 0.2300 2 180.00 ! DMBU, dimethoxybutane, sna +CG321 CG301 OG301 CG331 0.4900 3 0.00 ! DMBU, dimethoxybutane, sna +CG331 CG301 OG301 CG331 0.4000 1 0.00 ! AMOL, alpha-methoxy-lactic acid, og +CG331 CG301 OG301 CG331 0.4900 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +OG301 CG301 OG301 CG331 0.5100 1 0.00 ! DMOP, dimethoxypropane, sna +OG301 CG301 OG301 CG331 0.6700 2 0.00 ! DMOP, dimethoxypropane, sna +OG301 CG301 OG301 CG331 0.2600 3 0.00 ! DMOP, dimethoxypropane, sna +OG311 CG301 OG301 CG331 0.4100 1 180.00 ! AMOL, alpha-methoxy-lactic acid, og +OG311 CG301 OG301 CG331 0.8900 2 0.00 ! AMOL, alpha-methoxy-lactic acid, og +OG311 CG301 OG301 CG331 0.0500 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +CG331 CG301 OG302 CG2O2 0.0000 3 0.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha +CG2O3 CG301 OG311 HGP1 0.8200 3 180.00 ! AMOL, alpha-methoxy-lactic acid, og +CG331 CG301 OG311 HGP1 1.1300 1 0.00 ! AMOL, alpha-methoxy-lactic acid, og +CG331 CG301 OG311 HGP1 0.1400 2 0.00 ! AMOL, alpha-methoxy-lactic acid, og +CG331 CG301 OG311 HGP1 0.2400 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +OG301 CG301 OG311 HGP1 1.5500 1 0.00 ! AMOL, alpha-methoxy-lactic acid, og +OG301 CG301 OG311 HGP1 1.1700 2 0.00 ! AMOL, alpha-methoxy-lactic acid, og +OG301 CG301 OG311 HGP1 1.0700 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +FGA3 CG302 CG321 OG311 0.2500 3 0.00 ! TFE, Trifluoroethanol +FGA3 CG302 CG321 HGA2 0.1580 3 0.00 ! TFE, Trifluoroethanol +FGA3 CG302 CG331 HGA3 0.1580 3 0.00 ! FLUROALK fluoro_alkanes +CG2O1 CG311 CG311 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG311 CG331 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG311 OG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG311 HGA1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG311 CG311 CG321 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG311 CG331 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG311 OG311 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG311 HGA1 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG301 CG311 CG311 CG311 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 +CG301 CG311 CG311 CG321 0.2000 3 0.00 ! DCA, Deoxycholic Acid, cacha, 03/06 +CG301 CG311 CG311 CG3RC1 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG301 CG311 CG311 HGA1 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG311 CG311 CG311 CG321 0.5000 4 180.00 ! NA bkb +CG311 CG311 CG311 OG311 0.1400 3 0.00 ! PROT, hydroxyl wild card +CG311 CG311 CG311 HGA1 0.1950 3 0.00 ! NA, sugar +CG321 CG311 CG311 CG321 0.5000 4 180.00 ! NA, sugar +CG321 CG311 CG311 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG311 CG311 NG2S1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG311 HGA1 0.1950 3 0.00 ! NA, sugar +CG331 CG311 CG311 NG2S1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG311 HGA1 0.1950 3 0.00 ! NA, sugar +CG3RC1 CG311 CG311 OG311 0.6000 1 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG311 CG311 OG311 0.7000 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG311 CG311 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugar +NG2S1 CG311 CG311 OG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG311 HGA1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG311 CG311 CG311 HGA1 0.1950 3 0.00 ! NA, sugar +HGA1 CG311 CG311 HGA1 0.1950 3 0.00 ! NA, sugar +CG321 CG311 CG314 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG314 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG314 NG3P3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG314 HGA1 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter collided with NA, sugar +CG331 CG311 CG314 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG314 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG314 NG3P3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG314 HGA1 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter collided with NA, sugar +HGA1 CG311 CG314 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG311 CG314 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG311 CG314 NG3P3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG311 CG314 HGA1 0.1950 3 0.00 ! NPROT N-terminal AA - standard parameter collided with A, sugar +CG2O1 CG311 CG321 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG321 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG321 CG2R51 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG321 CG2R61 0.0400 3 0.00 ! PROT 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CG2O1 CG311 CG321 CG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG321 OG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG321 SG301 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG321 SG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG311 CG321 HGA2 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O2 CG311 CG321 CG2O2 0.2000 3 0.00 ! 576P, standard param +CG2O2 CG311 CG321 CG321 0.2000 3 0.00 ! AMGA, Alpha Methyl Glu Acid CDCA Amide, cacha +CG2O2 CG311 CG321 HGA2 0.2000 3 0.00 ! AMGA, Alpha Methyl Glu Acid CDCA Amide, cacha +CG2O3 CG311 CG321 CG2O1 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG321 CG2O3 0.2000 3 0.00 ! drug design project, xxwy +CG2O3 CG311 CG321 CG2R51 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG321 CG2R61 0.0400 3 0.00 ! PROT 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CG2O3 CG311 CG321 CG311 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG311 CG321 OG311 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG321 SG301 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG321 SG311 0.2000 3 0.00 ! PROT C-terminal AA - standard parameter +CG2O3 CG311 CG321 HGA2 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2R61 CG311 CG321 CG2O3 0.0400 3 0.00 ! FBIC(R/S), Fatty Binding Inhibitior C, cacha +CG2R61 CG311 CG321 HGA2 0.0000 3 0.00 ! Slack parameter from difluorotoluene picked up by FBIC ==> RE-OPTIMIZE !!! +CG301 CG311 CG321 CG311 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 +CG301 CG311 CG321 CG321 0.2000 3 0.00 ! DCA, Deoxycholic Acid, cacha, 03/06 +CG301 CG311 CG321 HGA2 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 03/06 reset to default by kevo +CG311 CG311 CG321 CG2D1 0.2000 3 0.00 ! CHL1, Cholesterol +CG311 CG311 CG321 CG311 0.2000 3 0.00 ! CA, Cholic Acid, reset to default by kevo +CG311 CG311 CG321 CG321 0.2000 3 0.00 ! CHL1, Cholesterol reset to default by kevo +CG311 CG311 CG321 CG331 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG311 CG321 HGA2 0.1950 3 0.00 ! NA, sugar +CG314 CG311 CG321 CG331 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG314 CG311 CG321 HGA2 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter collided with NA, sugar +CG321 CG311 CG321 CG2D1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG321 CG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG321 CG324 0.2000 3 0.00 ! G4MP, Gamma-4-Methyl piperidine Glu Acid CDCA Amide, cacha reset to default by kevo +CG321 CG311 CG321 NG2S1 0.2000 3 0.00 ! G4MP, Gamma-4-Methyl piperidine Glu Acid CDCA Amide, cacha +CG321 CG311 CG321 OG302 0.2000 3 180.00 ! NA, sugar +CG321 CG311 CG321 OG303 0.2000 3 180.00 ! NA, sugar +CG321 CG311 CG321 OG311 0.2000 3 180.00 ! CARBOCY carbocyclic sugars +CG321 CG311 CG321 HGA2 0.1950 1 0.00 ! NA, sugar +CG324 CG311 CG321 CG321 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG324 CG311 CG321 NG2S1 0.2000 3 0.00 ! 3MSB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +CG324 CG311 CG321 HGA2 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG331 CG311 CG321 CG2O3 0.2000 3 0.00 ! FBIC(R/S), Fatty Binding Inhibitior C +CG331 CG311 CG321 CG2R61 0.0400 3 0.00 ! FBIF, Fatty acid Binding protein Inhibitor F, cacha +CG331 CG311 CG321 CG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG321 CG314 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG321 CG331 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG321 OG302 0.2000 3 0.00 ! LIPID methyl acetate +CG331 CG311 CG321 HGA2 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG3C51 CG311 CG321 CG321 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 02/08 reset to default by kevo +CG3C51 CG311 CG321 HGA2 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG3RC1 CG311 CG321 CG2D1 0.2000 3 0.00 ! CHL1, Cholesterol +CG3RC1 CG311 CG321 CG311 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG311 CG321 CG321 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG311 CG321 HGA2 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R53 CG311 CG321 CG2O2 0.2000 3 0.00 ! drug design project, xxwy +NG2R53 CG311 CG321 CG2O3 0.2000 3 0.00 ! drug design project, xxwy +NG2R53 CG311 CG321 HGA2 0.2000 3 0.00 ! drug design project, xxwy +NG2S1 CG311 CG321 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG321 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG321 CG2R51 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG321 CG2R61 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG321 CG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG321 CG324 0.2000 3 0.00 ! G4P, 01OH02 +NG2S1 CG311 CG321 OG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG321 SG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG2S1 CG311 CG321 HGA2 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG302 CG311 CG321 OG302 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG302 CG311 CG321 OG303 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG302 CG311 CG321 HGA2 0.1950 3 0.00 ! NA, sugar +OG311 CG311 CG321 CG2D1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG311 CG311 CG321 CG311 2.0000 3 180.00 ! NA, sugar +OG311 CG311 CG321 CG311 0.4000 5 0.00 ! NA, sugar +OG311 CG311 CG321 CG311 0.8000 6 0.00 ! NA, sugar +OG311 CG311 CG321 CG321 0.5000 1 180.00 ! NA elevates energy at 0 (c3'endo), adm +OG311 CG311 CG321 CG321 0.7000 2 0.00 ! NA elevates energy at 0 (c3'endo), adm +OG311 CG311 CG321 CG321 0.4000 3 0.00 ! NA abasic nucleoside +OG311 CG311 CG321 CG321 0.4000 5 0.00 ! NA abasic nucleoside +OG311 CG311 CG321 CG331 0.1400 3 0.00 ! 2BOH, 2-butanol, kevo for gsk/ibm +OG311 CG311 CG321 OG303 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG311 CG311 CG321 OG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG311 CG311 CG321 HGA2 0.1950 3 180.00 ! NA, sugar +HGA1 CG311 CG321 CG2D1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG311 CG321 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG311 CG321 CG2O2 0.2000 3 0.00 ! 576P, standard param +HGA1 CG311 CG321 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG311 CG321 CG2R51 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG311 CG321 CG2R61 0.0400 3 0.00 ! PROT 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HGA1 CG311 CG321 CG311 0.1950 3 0.00 ! NA, sugar +HGA1 CG311 CG321 CG314 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter collided with NA, sugar +HGA1 CG311 CG321 CG321 0.1950 3 0.00 ! NA abasic nucleoside +HGA1 CG311 CG321 CG324 0.1950 3 0.00 ! G4MP, 01OH03, cacha +HGA1 CG311 CG321 CG331 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG311 CG321 NG2S1 0.2000 3 0.00 ! G4MP, 01OH03, cacha +HGA1 CG311 CG321 OG302 0.1950 3 0.00 ! NA, sugar +HGA1 CG311 CG321 OG303 0.1950 3 0.00 ! NA, sugar +HGA1 CG311 CG321 OG311 0.1950 3 0.00 ! NA, sugar +HGA1 CG311 CG321 SG311 0.1950 3 0.00 ! PROTNA sahc +HGA1 CG311 CG321 HGA2 0.1950 3 0.00 ! NA, sugar +CG321 CG311 CG324 NG3P1 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG321 CG311 CG324 NG3P2 0.1950 3 0.00 ! G3P(R/S), Gamma-3-piperidine Glu Acid CDCA Amide, cacha +CG321 CG311 CG324 HGA2 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +NG2S1 CG311 CG324 NG3P2 0.1950 3 0.00 ! G3P(R/S), Gamma-3-piperidine Glu Acid CDCA Amide, cacha +NG2S1 CG311 CG324 HGA2 0.2000 3 0.00 ! G3P(R/S), Gamma-3-piperidine Glu Acid CDCA Amide, cacha +OG311 CG311 CG324 NG3P1 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +OG311 CG311 CG324 HGA2 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +HGA1 CG311 CG324 NG3P1 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +HGA1 CG311 CG324 NG3P2 0.1950 3 0.00 ! G3P(R/S), Gamma-3-piperidine Glu Acid CDCA Amide, cacha +HGA1 CG311 CG324 HGA2 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG2O1 CG311 CG331 HGA3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG311 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG2R61 CG311 CG331 HGA3 0.0400 3 0.00 ! FBIB, Fatty Binding Inhibitior B, cacha +CG311 CG311 CG331 HGA3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG314 CG311 CG331 HGA3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG311 CG331 HGA3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG311 CG331 HGA3 0.1950 3 0.00 ! PROTNA alkanes phospho-ser/thr +CG3C51 CG311 CG331 HGA3 0.2000 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +NG2S1 CG311 CG331 HGA3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG301 CG311 CG331 HGA3 0.1600 3 0.00 ! all34_ethers_1a +OG302 CG311 CG331 HGA3 0.2000 3 0.00 ! LIPID methyl acetate +OG303 CG311 CG331 HGA3 0.1950 3 0.00 ! PROTNA phospho-ser/thr phospho-ser/thr +OG311 CG311 CG331 HGA3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CLGA1 CG311 CG331 HGA3 0.2500 3 0.00 ! DCLE +BRGA2 CG311 CG331 HGA3 0.2600 3 0.00 ! DBRE +HGA1 CG311 CG331 HGA3 0.1950 3 0.00 ! NA, sugar +CG321 CG311 CG3C51 CG3C52 0.5000 4 180.00 ! CA, Cholic Acid, cacha, 02/08 +CG321 CG311 CG3C51 CG3RC1 0.1500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG321 CG311 CG3C51 HGA1 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG331 CG311 CG3C51 CG3C52 0.2500 1 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG331 CG311 CG3C51 CG3C52 0.2500 2 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG331 CG311 CG3C51 CG3C52 0.4500 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG331 CG311 CG3C51 CG3RC1 0.2000 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG331 CG311 CG3C51 HGA1 0.1950 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA1 CG311 CG3C51 CG3C52 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA1 CG311 CG3C51 CG3RC1 0.2000 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA1 CG311 CG3C51 HGA1 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +CG311 CG311 CG3RC1 CG3C52 0.1500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG311 CG311 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG311 CG311 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG311 CG3RC1 CG331 0.0500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG321 CG311 CG3RC1 CG3C51 0.0500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG321 CG311 CG3RC1 CG3C52 0.5000 4 180.00 ! DCA, Deoxycholic Acid, cacha, 02/08 +CG321 CG311 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG311 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +OG311 CG311 CG3RC1 CG331 0.1580 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +OG311 CG311 CG3RC1 CG3C51 0.1580 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +OG311 CG311 CG3RC1 CG3RC1 0.4500 2 0.00 ! CARBOCY carbocyclic sugars +HGA1 CG311 CG3RC1 CG331 0.0500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +HGA1 CG311 CG3RC1 CG3C51 0.0500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +HGA1 CG311 CG3RC1 CG3C52 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +HGA1 CG311 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA1 CG311 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG2O2 CG311 NG2R53 CG2R53 0.0000 1 180.00 ! drug design project, xxwy +CG2O3 CG311 NG2R53 CG2R53 0.0000 1 180.00 ! drug design project, xxwy +CG321 CG311 NG2R53 CG2R53 0.0000 1 0.00 ! drug design project, xxwy +HGA1 CG311 NG2R53 CG2R53 0.0000 1 0.00 ! drug design project, xxwy +CG2O1 CG311 NG2S1 CG2O1 0.2000 1 180.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +CG2O1 CG311 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O2 CG311 NG2S1 CG2O1 0.2000 1 180.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +CG2O2 CG311 NG2S1 HGP1 0.0000 1 0.00 ! PROT adm jr. 5/02/91, acetic Acid pure solvent +CG2O3 CG311 NG2S1 CG2O1 0.2000 1 180.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +CG2O3 CG311 NG2S1 HGP1 0.0000 1 0.00 ! PROT adm jr. 4/05/91, for asn,asp,gln,glu and cters +CG311 CG311 NG2S1 CG2O1 1.8000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +CG311 CG311 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG321 CG311 NG2S1 CG2O1 1.8000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +CG321 CG311 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG324 CG311 NG2S1 CG2O1 1.8000 1 0.00 ! G3P(R/S), Gamma-3-piperidine Glu Acid CDCA Amide, cacha +CG324 CG311 NG2S1 HGP1 0.0000 1 0.00 ! G3P(R/S), Gamma-3-piperidine Glu Acid CDCA Amide, cacha +CG331 CG311 NG2S1 CG2O1 1.8000 1 0.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +CG331 CG311 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +HGA1 CG311 NG2S1 CG2O1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +HGA1 CG311 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O3 CG311 OG301 CG331 0.2000 3 0.00 ! og/sng thp CG321C CG321C OG3C6M CG321C +CG331 CG311 OG301 CG331 0.4000 1 0.00 ! all34_ethers_1a og/gk (not affected by mistake) +CG331 CG311 OG301 CG331 0.4900 3 0.00 ! " CC33A CC32A OC30A CC33A og/gk (not affected by mistake) +HGA1 CG311 OG301 CG331 0.2840 3 0.00 ! all34_ethers_1a og/gk (not affected by mistake) +CG321 CG311 OG302 CG2O2 0.7000 1 180.00 ! LIPID ethyl acetate, 12/92 +CG331 CG311 OG302 CG2O2 0.0000 3 0.00 ! LIPID methyl acetate +HGA1 CG311 OG302 CG2O2 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +CG331 CG311 OG303 PG2 0.4000 1 180.00 ! IP_2 phospho-ser/thr +CG331 CG311 OG303 PG2 0.3000 2 0.00 ! IP_2 phospho-ser/thr +CG331 CG311 OG303 PG2 0.1000 3 0.00 ! IP_2 phospho-ser/thr +HGA1 CG311 OG303 PG2 0.0000 3 0.00 ! IP_2 phospho-ser/thr +CG2O5 CG311 OG311 HGP1 0.3500 1 0.00 ! BIPHENYL re-initialized from CC2O3 CC312 OC311 HCP1 ! erh ketone, n=6 polyol +CG2O5 CG311 OG311 HGP1 0.3700 2 0.00 ! BIPHENYL re-initialized from CC2O3 CC312 OC311 HCP1 ! erh ketone, n=6 polyol +CG2O5 CG311 OG311 HGP1 0.0100 3 180.00 ! BIPHENYL re-initialized from CC2O3 CC312 OC311 HCP1 ! erh ketone, n=6 polyol with compensation for HCA1 CC311 OC311M HCP1 0.18 --> HGA1 CG311 OG311 HGP1 0.00 kevo ==> re-evaluate? +CG311 CG311 OG311 HGP1 1.3300 1 0.00 ! PROT PRO2, 2-propanol OH hf/torsional surface, adm jr., 3/2/93 +CG311 CG311 OG311 HGP1 0.1800 2 0.00 ! PROT PRO2, 2-propanol OH hf/torsional surface, adm jr., 3/2/93 +CG311 CG311 OG311 HGP1 0.4600 3 0.00 ! PROT PRO2, 2-propanol OH hf/torsional surface, adm jr., 3/2/93 ! compensated for X CG311 OG311 X 0.14 --> HGA1 CG311 OG311 HGP1 0.00 kevo ==> re-optimize? +CG321 CG311 OG311 HGP1 0.3000 1 0.00 ! CARBOCY carbocyclic sugars +CG321 CG311 OG311 HGP1 0.3000 3 0.00 ! CHOLEST cholesterol +CG324 CG311 OG311 HGP1 0.5000 1 0.00 ! FLAVOP PIP3 +CG324 CG311 OG311 HGP1 0.7000 2 0.00 ! FLAVOP PIP3 +CG331 CG311 OG311 HGP1 1.3300 1 0.00 ! PROT PRO2, 2-propanol OH hf/torsional surface, adm jr., 3/2/93 +CG331 CG311 OG311 HGP1 0.1800 2 0.00 ! PROT PRO2, 2-propanol OH hf/torsional surface, adm jr., 3/2/93 +CG331 CG311 OG311 HGP1 0.4600 3 0.00 ! PROT PRO2, 2-propanol OH hf/torsional surface, adm jr., 3/2/93 ! compensated for X CG311 OG311 X 0.14 --> HGA1 CG311 OG311 HGP1 0.00 kevo ==> re-optimize? +CG3RC1 CG311 OG311 HGP1 1.5000 1 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG311 OG311 HGP1 0.3000 2 180.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG311 OG311 HGP1 0.5000 3 0.00 ! CARBOCY carbocyclic sugars +OG312 CG311 OG311 HGP1 0.2800 3 0.00 ! PROT EMB 11/21/89 methanol vib fit ! compensated for X CG311 OG311 X 0.14 --> HGA1 CG311 OG311 HGP1 0.00 kevo ==> re-optimize? +HGA1 CG311 OG311 HGP1 0.0000 3 0.00 ! NA backbone. PRO2 not properly optimized in new carbohydrate FF ==> unmodified. +FGA2 CG312 CG331 HGA3 0.1780 3 0.00 ! FLUROALK fluoro_alkanes +HGA7 CG312 CG331 HGA3 0.1780 3 0.00 ! FLUROALK fluoro_alkanes +CG2R61 CG312 PG1 OG2P1 0.0000 3 0.00 ! BDFP, Difuorobenzylphosphonate \ re-optimize? +CG2R61 CG312 PG1 OG311 0.1000 2 0.00 ! BDFP, BDFD, Difuorobenzylphosphonate +CG2R61 CG312 PG1 OG311 0.4000 3 0.00 ! BDFP, BDFD, Difuorobenzylphosphonate +FGA2 CG312 PG1 OG2P1 0.0000 3 0.00 ! BDFP, Difuorobenzylphosphonate \ re-optimize? +FGA2 CG312 PG1 OG311 0.1000 3 0.00 ! BDFP, BDFD, Difuorobenzylphosphonate +CG2R61 CG312 PG2 OG2P1 0.0000 3 0.00 ! BDFD, Difuorobenzylphosphonate / re-optimize? +FGA2 CG312 PG2 OG2P1 0.0000 3 0.00 ! BDFD, Difuorobenzylphosphonate / re-optimize? +CG2O1 CG314 CG321 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG314 CG321 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG314 CG321 CG2R51 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG314 CG321 CG2R61 0.0400 3 0.00 ! PROT 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CG2O1 CG314 CG321 CG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG314 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG314 CG321 OG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG314 CG321 SG301 0.2000 3 0.00 ! deleteme DELETEME (we want to use wildcarting) +CG2O1 CG314 CG321 SG311 0.2000 3 0.00 ! PROT N-terminal AA - standard parameter +CG2O1 CG314 CG321 HGA2 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG321 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG321 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG321 CG2R51 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG321 CG2R61 0.0400 3 0.00 ! PROT 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CG2O3 CG314 CG321 CG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG321 OG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG321 SG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG321 HGA2 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG314 CG321 CG321 0.2000 3 0.00 ! 3MRB,Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +CG321 CG314 CG321 NG2S1 0.2000 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +CG321 CG314 CG321 HGA2 0.1950 3 0.00 ! 3MRB,Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha reset to default by kevo +NG3P2 CG314 CG321 CG321 0.1950 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +NG3P2 CG314 CG321 NG2S1 0.1950 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +NG3P2 CG314 CG321 HGA2 0.1950 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +NG3P3 CG314 CG321 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG3P3 CG314 CG321 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG3P3 CG314 CG321 CG2R51 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG3P3 CG314 CG321 CG2R61 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG3P3 CG314 CG321 CG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG3P3 CG314 CG321 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG3P3 CG314 CG321 OG311 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +NG3P3 CG314 CG321 SG311 0.2000 3 0.00 ! PROT N-terminal AA - standard parameter +NG3P3 CG314 CG321 HGA2 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG314 CG321 CG2O1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG314 CG321 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG314 CG321 CG2R51 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA1 CG314 CG321 CG2R61 0.0400 3 0.00 ! PROT 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HGA1 CG314 CG321 CG311 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter collided with NA, sugar +HGA1 CG314 CG321 CG321 0.1950 3 0.00 ! NA abasic nucleoside +HGA1 CG314 CG321 NG2S1 0.2000 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +HGA1 CG314 CG321 OG311 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter collided with NA, sugar +HGA1 CG314 CG321 SG311 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter collided with PROTNA sahc +HGA1 CG314 CG321 HGA2 0.1950 3 0.00 ! NA, sugar +CG2O1 CG314 CG331 HGA3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG314 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +NG3P3 CG314 CG331 HGA3 0.2000 3 0.00 ! PROT N-terminal AA - standard parameter +HGA1 CG314 CG331 HGA3 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter +CG321 CG314 NG3P2 CG324 0.1000 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +CG321 CG314 NG3P2 HGP2 0.1000 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +HGA1 CG314 NG3P2 CG324 0.1000 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +HGA1 CG314 NG3P2 HGP2 0.1000 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +CG2O1 CG314 NG3P3 HGP2 0.1000 3 0.00 ! PROT N-terminal AA - standard parameter +CG2O3 CG314 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +CG311 CG314 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +CG321 CG314 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +CG331 CG314 NG3P3 HGP2 0.1000 3 0.00 ! PROT N-terminal AA - standard parameter +HGA1 CG314 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +CG2D1 CG321 CG321 CG2O3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2D1 CG321 CG321 CG321 0.1400 1 180.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG321 0.1700 2 0.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG321 0.0500 3 180.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG331 0.1400 1 180.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG331 0.1700 2 0.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG331 0.0500 3 180.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2DC1 CG321 CG321 CG321 0.1900 3 0.00 ! RETINOL TMCH +CG2DC1 CG321 CG321 HGA2 0.1900 3 0.00 ! RETINOL TMCH +CG2DC2 CG321 CG321 CG321 0.1900 3 0.00 ! RETINOL TMCH +CG2DC2 CG321 CG321 HGA2 0.1900 3 0.00 ! RETINOL TMCH +CG2O1 CG321 CG321 CG2O1 0.2000 3 0.00 ! PMHA, hydrazone-containing model compound: PROT alkane update, adm jr., 3/2/92, sz +CG2O1 CG321 CG321 CG311 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O1 CG321 CG321 CG314 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter +CG2O1 CG321 CG321 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O2 CG321 CG321 CG311 0.1950 3 0.00 ! GMGA, cacha +CG2O2 CG321 CG321 CG321 0.2100 1 180.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG321 0.3900 2 0.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG321 0.3500 3 180.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG321 0.1100 4 0.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG321 0.0900 6 180.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG331 0.2100 1 180.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG331 0.3900 2 0.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG331 0.3500 3 180.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG331 0.1100 4 0.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 CG331 0.0900 6 180.00 ! LIPID methylbutyrate +CG2O2 CG321 CG321 HGA2 0.1950 3 0.00 ! deleteme DELETEME (we want to use wildcarting) +CG2O3 CG321 CG321 CG2R61 0.0400 3 0.00 ! FBIB, Fatty Binding Inhibitior B, cacha +CG2O3 CG321 CG321 CG311 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O3 CG321 CG321 CG314 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter +CG2O3 CG321 CG321 CG321 0.06450 2 0.00 ! LIPID alkane, 4/04, jbk +CG2O3 CG321 CG321 CG321 0.14975 3 180.00 ! LIPID alkane, 4/04, jbk +CG2O3 CG321 CG321 CG321 0.09458 4 0.00 ! LIPID alkane, 4/04, jbk +CG2O3 CG321 CG321 CG321 0.11251 5 0.00 ! LIPID alkane, 4/04, jbk +CG2O3 CG321 CG321 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2O5 CG321 CG321 CG321 0.2100 1 180.00 ! CHON, cyclohexanone; from LIPID methylbutyrate; yapol +CG2O5 CG321 CG321 CG321 0.3900 2 0.00 ! CHON, cyclohexanone; from LIPID methylbutyrate; yapol +CG2O5 CG321 CG321 CG321 0.3500 3 180.00 ! CHON, cyclohexanone; from LIPID methylbutyrate; yapol +CG2O5 CG321 CG321 CG321 0.1100 4 0.00 ! CHON, cyclohexanone; from LIPID methylbutyrate; yapol +CG2O5 CG321 CG321 CG321 0.0900 6 180.00 ! CHON, cyclohexanone; from LIPID methylbutyrate; yapol +CG2O5 CG321 CG321 HGA2 0.1950 3 0.00 ! CHON, cyclohexanone; from CG2O2 CG321 CG321 HGA2; yapol +CG2R61 CG321 CG321 CG321 0.0400 3 0.00 ! PROT ethylbenzene +CG2R61 CG321 CG321 NG2S1 0.1900 3 0.00 ! 2AEPD, 2-ethylamino-pyridine CDCA conjugate, corrected by kevo +CG2R61 CG321 CG321 HGA2 0.0400 3 0.00 ! PROT ethylbenzene +CG301 CG321 CG321 CG311 0.2000 3 0.00 ! CA, Cholic Acid, cacha, 03/06 +CG301 CG321 CG321 CG321 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG301 CG321 CG321 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG321 CG321 CG311 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG321 CG321 CG321 0.5000 3 0.00 ! CARBOCY carbocyclic sugars +CG311 CG321 CG321 CG321 0.5000 6 180.00 ! CARBOCY carbocyclic sugars +CG311 CG321 CG321 CG324 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG311 CG321 CG321 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG311 CG321 CG321 SG311 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG311 CG321 CG321 HGA2 0.1950 3 0.00 ! NA abasic nucleoside +CG314 CG321 CG321 CG321 0.5000 3 0.00 ! CARBOCY carbocyclic sugars +CG314 CG321 CG321 CG321 0.5000 6 180.00 ! CARBOCY carbocyclic sugars +CG314 CG321 CG321 CG324 0.1950 3 0.00 ! PROT N-terminal AA - standard parameter collided with FLAVOP PIP1,2,3 +CG314 CG321 CG321 SG311 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG314 CG321 CG321 HGA2 0.1950 3 0.00 ! NA abasic nucleoside +CG321 CG321 CG321 CG321 0.06450 2 0.00 ! LIPID alkane, 4/04, jbk (Jeff Klauda) +CG321 CG321 CG321 CG321 0.14975 3 180.00 ! LIPID alkane, 4/04, jbk +CG321 CG321 CG321 CG321 0.09458 4 0.00 ! LIPID alkane, 4/04, jbk +CG321 CG321 CG321 CG321 0.11251 5 0.00 ! LIPID alkane, 4/04, jbk +CG321 CG321 CG321 CG324 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG321 CG321 CG321 CG331 0.15051 2 0.00 ! LIPID alkane, 4/04, jbk (Jeff Klauda) +CG321 CG321 CG321 CG331 0.08133 3 180.00 ! LIPID alkane, 4/04, jbk +CG321 CG321 CG321 CG331 0.10824 4 0.00 ! LIPID alkane, 4/04, jbk +CG321 CG321 CG321 CG331 0.20391 5 0.00 ! LIPID alkane, 4/04, jbk +CG321 CG321 CG321 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG321 CG321 NG2D1 0.7900 1 180.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin +CG321 CG321 CG321 NG2D1 0.2000 2 0.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin +CG321 CG321 CG321 NG2D1 0.1200 3 0.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin +CG321 CG321 CG321 NG2D1 0.1500 4 0.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin +CG321 CG321 CG321 NG2D1 0.0500 6 180.00 ! from EEPI's CG331 CG321 CG321 NG2D1, fylin +CG321 CG321 CG321 NG2S1 0.2000 3 0.00 ! ALBE, Alpha Lysine Benzyl Ester CDCA Amide, cacha +CG321 CG321 CG321 OG301 0.1600 1 180.00 ! methylpropylether, 2/12/05, ATM +CG321 CG321 CG321 OG301 0.3900 2 0.00 ! methylpropylether +CG321 CG321 CG321 OG302 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG321 CG321 OG303 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG321 CG321 OG311 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG321 CG321 OG3C61 0.1900 1 180.00 ! THP, tetrahydropyran +CG321 CG321 CG321 OG3C61 1.0000 2 180.00 ! THP, tetrahydropyran +CG321 CG321 CG321 OG3C61 0.6000 3 0.00 ! THP, tetrahydropyran +CG321 CG321 CG321 OG3C61 0.0800 4 180.00 ! THP, tetrahydropyran +CG321 CG321 CG321 SG311 0.1950 3 0.00 ! THPS, thiopyran +CG321 CG321 CG321 HGA2 0.1950 3 0.00 ! LIPID alkanes +CG324 CG321 CG321 HGA2 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG331 CG321 CG321 CG331 0.03819 2 0.00 ! LIPID alkane, 4/04, jbk +CG331 CG321 CG321 CG331 0.03178 6 180.00 ! LIPID alkane, 4/04, jbk +CG331 CG321 CG321 NG2D1 0.7900 1 180.00 ! EEPI, fylin +CG331 CG321 CG321 NG2D1 0.2000 2 0.00 ! EEPI, fylin +CG331 CG321 CG321 NG2D1 0.1200 3 0.00 ! EEPI, fylin +CG331 CG321 CG321 NG2D1 0.1500 4 0.00 ! EEPI, fylin +CG331 CG321 CG321 NG2D1 0.0500 6 180.00 ! EEPI, fylin +CG331 CG321 CG321 OG301 0.1600 1 180.00 ! methylpropylether, 2/12/05, ATM +CG331 CG321 CG321 OG301 0.3900 2 0.00 ! methylpropylether +CG331 CG321 CG321 OG311 0.1950 3 0.00 ! PROH, n-propanol, kevo for gsk/ibm +CG331 CG321 CG321 SG311 0.1950 3 0.00 ! PRSH, n-thiopropanol, kevo for gsk/ibm +CG331 CG321 CG321 SG3O1 0.9400 1 180.00 ! PSNA, propyl sulfonate, xhe +CG331 CG321 CG321 SG3O1 0.3800 2 0.00 ! PSNA, propyl sulfonate, xhe +CG331 CG321 CG321 SG3O1 0.1100 3 0.00 ! PSNA, propyl sulfonate, xhe +CG331 CG321 CG321 HGA2 0.1800 3 0.00 ! LIPID alkane +CG3RC1 CG321 CG321 HGA2 0.1950 3 0.00 ! LIPID alkanes +NG2D1 CG321 CG321 HGA2 0.2000 3 0.00 ! EEPI, from NG2S1 CG321 CG321 HGA2, fylin +NG2S1 CG321 CG321 SG3O1 0.9500 1 180.00 ! NACT, N-acetyltaurine, compromise between 6-31G* and 6-31+G*, xxwy & kevo +NG2S1 CG321 CG321 SG3O1 1.3300 2 0.00 ! NACT, N-acetyltaurine, compromise between 6-31G* and 6-31+G*, xxwy & kevo +NG2S1 CG321 CG321 SG3O1 0.0800 3 180.00 ! NACT, N-acetyltaurine, compromise between 6-31G* and 6-31+G*, xxwy & kevo +NG2S1 CG321 CG321 HGA2 0.1950 3 0.00 ! TCA, Taurocholic Acid, cacha, 03/06 OK +NG311 CG321 CG321 HGA2 0.1950 3 0.00 ! K2Cn, cgenff_compromise, kevo +OG301 CG321 CG321 OG301 0.2500 1 180.00 ! 1,2 dimethoxyethane, 2/12/05, ATM +OG301 CG321 CG321 OG301 1.2400 2 0.00 ! 1,2 dimethoxyethane +OG301 CG321 CG321 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell +OG302 CG321 CG321 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG303 CG321 CG321 OG303 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG303 CG321 CG321 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG311 CG321 CG321 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG3C61 CG321 CG321 OG3C61 0.1950 3 0.00 ! DIOX, dioxane +OG3C61 CG321 CG321 HGA2 0.1950 3 0.00 ! DIOX, dioxane +SG311 CG321 CG321 SG311 0.1000 3 0.00 ! DITH, dithiane +SG311 CG321 CG321 HGA2 0.0100 3 0.00 ! PROT DTN 8/24/90 +SG3O1 CG321 CG321 HGA2 0.0100 1 0.00 ! PSNA, propyl sulfonate, xhe +HGA2 CG321 CG321 HGA2 0.2200 3 0.00 ! LIPID alkanes +CG311 CG321 CG324 NG3P1 1.0000 3 0.00 ! BPAB, Gamma N-benzyl piperidine alpha benzyl CDCA amide, cacha ! @@@ Kenno: 0.1950 -> 1.0000 +CG311 CG321 CG324 NG3P2 1.0000 3 0.00 ! G4MP, Gamma-4-Methyl Piperidine Glu Acid CDCA Amide, cacha ! @@@ Kenno: 0.1950 -> 1.0000 +CG311 CG321 CG324 HGA2 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG321 CG321 CG324 NG2P1 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG321 CG324 NG3P1 1.0000 3 0.00 ! FLAVOP PIP1,2,3 ! @@@ Kenno: 0.1950 -> 1.0000 +CG321 CG321 CG324 NG3P2 1.0000 3 0.00 ! PIP, piperidine ! @@@ Kenno: 0.1950 -> 1.0000 +CG321 CG321 CG324 NG3P3 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG321 CG321 CG324 HGA2 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +CG331 CG321 CG324 NG2O1 0.8773 1 180.00 ! NIPR, nitropropane, abar +CG331 CG321 CG324 NG2O1 0.2382 2 0.00 ! NIPR, nitropropane, abar +CG331 CG321 CG324 NG2O1 0.1465 3 180.00 ! NIPR, nitropropane, abar +CG331 CG321 CG324 HGA2 0.1950 3 0.00 ! NIPR, nitropropane; from CG321 CG321 CG324 HGA2; abar +OG302 CG321 CG324 NG3P0 3.3000 1 180.00 ! LIPID choline, 12/92 +OG302 CG321 CG324 NG3P0 -0.4000 3 180.00 ! LIPID choline, 12/92 +OG302 CG321 CG324 HGP5 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG303 CG321 CG324 NG3P0 3.3000 1 180.00 ! LIPID choline, 12/92 +OG303 CG321 CG324 NG3P0 -0.4000 3 180.00 ! LIPID choline, 12/92 +OG303 CG321 CG324 NG3P3 0.7000 1 180.00 ! LIPID ethanolamine +OG303 CG321 CG324 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG303 CG321 CG324 HGP5 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG311 CG321 CG324 NG3P0 4.3000 1 180.00 ! LIPID choline, 12/92 +OG311 CG321 CG324 NG3P0 -0.4000 3 180.00 ! LIPID choline, 12/92 +OG311 CG321 CG324 NG3P3 0.7000 1 180.00 ! LIPID ethanolamine +OG311 CG321 CG324 HGA2 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG311 CG321 CG324 HGP5 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG3C61 CG321 CG324 NG3P2 0.8000 3 0.00 ! MORP, morpholine +OG3C61 CG321 CG324 HGA2 0.1950 3 0.00 ! MORP, morpholine +SG311 CG321 CG324 NG3P2 0.8000 3 0.00 ! TMOR, thiomorpholine +SG311 CG321 CG324 HGA2 0.1950 3 0.00 ! TMOR, thiomorpholine +HGA2 CG321 CG324 NG2O1 0.1950 3 0.00 ! NIPR, nitropropane; from NG2S1 CG321 CG321 HGA2; abar +HGA2 CG321 CG324 NG2P1 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA2 CG321 CG324 NG3P0 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA2 CG321 CG324 NG3P1 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +HGA2 CG321 CG324 NG3P2 0.1950 3 0.00 ! PIP, piperidine +HGA2 CG321 CG324 NG3P3 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA2 CG321 CG324 HGA2 0.1950 3 0.00 ! FLAVOP PIP1,2,3 +HGA2 CG321 CG324 HGP5 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2D1 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG2O1 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG2O2 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG2O3 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG2O4 CG321 CG331 HGA3 0.1600 3 0.00 ! PALD, propionaldehyde from PROT rotation barrier in Ethane (SF) unmodified +CG2O5 CG321 CG331 HGA3 0.1600 3 0.00 ! Methyl group torsion, kevo +CG2R51 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG2R61 CG321 CG331 HGA3 0.0400 3 0.00 ! PROT 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CG301 CG321 CG331 HGA3 0.1600 3 0.00 ! DMBU, dimethoxybutane, sna +CG311 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG321 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG324 CG321 CG331 HGA3 0.2000 3 0.00 ! NIPR, nitropropane; from CG314 CG311 CG331 HGA3; abar +CG331 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG3C31 CG321 CG331 HGA3 0.1600 3 0.00 ! 1BOX, 1-butene oxide; default from CG321 CG321 CG331 HGA3; sc +NG2D1 CG321 CG331 HGA3 0.1500 3 0.00 ! EICY, ethyl isocyanate, xxwy +NG2R51 CG321 CG331 HGA3 0.1950 3 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from NG2S1 CG321 CG331 HGA3, kevo +NG2S1 CG321 CG331 HGA3 0.1950 3 0.00 ! DECB, diethyl carbamate, cacha +NG2S3 CG321 CG331 HGA3 0.1950 3 0.00 ! NESM, N-ethyl-sulfamate; from NG2S1 CG321 CG331 HGA3; my +NG311 CG321 CG331 HGA3 0.1600 3 0.00 ! PEI polymers, default parameter, kevo +OG301 CG321 CG331 HGA3 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell +OG302 CG321 CG331 HGA3 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG303 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +OG311 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +OG312 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +SG301 CG321 CG331 HGA3 0.0100 3 0.00 ! PROT DTN 8/24/90 +SG311 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +SG3O1 CG321 CG331 HGA3 0.1100 3 0.00 ! ESNA, ethyl sulfonate, xhe +SG3O2 CG321 CG331 HGA3 0.0770 3 0.00 ! EESM, N-ethylethanesulfonamide; MESN, methyl ethyl sulfone; xxwy & xhe +SG3O3 CG321 CG331 HGA3 0.1600 3 0.00 ! MESO, methylethylsulfoxide; default parameter; kevo +CLGA1 CG321 CG331 HGA3 0.3000 3 0.00 ! CLET +BRGA1 CG321 CG331 HGA3 0.3000 3 0.00 ! BRET +HGA2 CG321 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +CG331 CG321 CG3C31 CG3C31 0.0000 3 0.00 ! 1BOX, 1-butene oxide, kevo +CG331 CG321 CG3C31 OG3C31 0.4700 1 180.00 ! 1BOX, 1-butene oxide, kevo +CG331 CG321 CG3C31 OG3C31 0.1300 3 0.00 ! 1BOX, 1-butene oxide, kevo +CG331 CG321 CG3C31 HGA1 0.1800 1 0.00 ! 1BOX, 1-butene oxide, kevo +CG331 CG321 CG3C31 HGA1 1.0700 3 0.00 ! 1BOX, 1-butene oxide, kevo +HGA2 CG321 CG3C31 CG3C31 0.0100 1 0.00 ! 1BOX, 1-butene oxide, kevo +HGA2 CG321 CG3C31 CG3C31 0.0200 3 0.00 ! 1BOX, 1-butene oxide, kevo +HGA2 CG321 CG3C31 OG3C31 0.5000 1 0.00 ! 1BOX, 1-butene oxide, kevo +HGA2 CG321 CG3C31 OG3C31 0.2700 3 0.00 ! 1BOX, 1-butene oxide, kevo +HGA2 CG321 CG3C31 HGA1 0.0000 3 0.00 ! 1BOX, 1-butene oxide; kept at 0; sc +OG301 CG321 CG3C51 CG3C52 0.2000 3 180.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from NA, sugar; kevo +OG301 CG321 CG3C51 HGA1 0.1950 3 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from NA, sugar; kevo +OG303 CG321 CG3C51 CG3C51 2.5000 1 180.00 ! NA, sugar +OG303 CG321 CG3C51 CG3C51 0.4000 2 0.00 ! NA, sugar +OG303 CG321 CG3C51 CG3C51 0.8000 3 180.00 ! NA, sugar +OG303 CG321 CG3C51 CG3C51 0.2000 4 180.00 ! NA, sugar +OG303 CG321 CG3C51 CG3C52 0.2000 3 180.00 ! NA, sugar +OG303 CG321 CG3C51 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +OG303 CG321 CG3C51 OG3C51 3.4000 1 180.00 ! NA, sugar +OG303 CG321 CG3C51 HGA1 0.1950 3 0.00 ! NA, sugar +OG311 CG321 CG3C51 CG3C51 2.5000 1 180.00 ! NA, sugar +OG311 CG321 CG3C51 CG3C51 0.4000 2 0.00 ! NA, sugar +OG311 CG321 CG3C51 CG3C51 0.8000 3 180.00 ! NA, sugar +OG311 CG321 CG3C51 CG3C51 0.2000 4 180.00 ! NA, sugar +OG311 CG321 CG3C51 CG3C52 0.2000 3 180.00 ! CARBOCY carbocyclic sugars +OG311 CG321 CG3C51 OG3C51 3.4000 1 180.00 ! NA, sugar +OG311 CG321 CG3C51 HGA1 0.1950 3 0.00 ! NA, sugar +SG311 CG321 CG3C51 CG3C51 2.5000 1 180.00 ! PROTNA sahc +SG311 CG321 CG3C51 CG3C51 0.4000 2 0.00 ! PROTNA sahc +SG311 CG321 CG3C51 CG3C51 0.8000 3 180.00 ! PROTNA sahc +SG311 CG321 CG3C51 CG3C51 0.2000 4 180.00 ! PROTNA sahc +SG311 CG321 CG3C51 OG3C51 3.4000 1 180.00 ! PROTNA sahc +SG311 CG321 CG3C51 HGA1 0.1950 3 0.00 ! PROTNA sahc +HGA2 CG321 CG3C51 CG3C51 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA2 CG321 CG3C51 CG3C52 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA2 CG321 CG3C51 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG321 CG3C51 OG3C51 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA2 CG321 CG3C51 HGA1 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +CG321 CG321 CG3RC1 CG331 0.2000 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG321 CG321 CG3RC1 CG3C51 0.1580 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG321 CG321 CG3RC1 CG3C52 0.2000 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG321 CG321 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG321 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +OG303 CG321 CG3RC1 CG3C31 0.1500 1 180.00 ! CARBOCY carbocyclic sugars +OG303 CG321 CG3RC1 CG3C51 0.5000 2 0.00 ! CARBOCY carbocyclic sugars +OG303 CG321 CG3RC1 CG3RC1 0.6000 1 0.00 ! CARBOCY carbocyclic sugars +OG303 CG321 CG3RC1 CG3RC1 0.4500 2 0.00 ! CARBOCY carbocyclic sugars +OG303 CG321 CG3RC1 CG3RC1 0.7000 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG321 CG3RC1 CG331 0.1900 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA2 CG321 CG3RC1 CG3C31 0.1950 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG321 CG3RC1 CG3C51 0.1950 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG321 CG3RC1 CG3C52 0.1950 1 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA2 CG321 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG321 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG321 NG2D1 CG2D1 0.6100 1 0.00 ! EEPI, fylin +CG321 CG321 NG2D1 CG2D1 0.6200 2 180.00 ! EEPI, fylin +CG321 CG321 NG2D1 CG2D1 0.2500 3 0.00 ! EEPI, fylin +CG321 CG321 NG2D1 CG2D1 0.6000 4 0.00 ! EEPI, fylin +CG321 CG321 NG2D1 CG2D1 0.2500 6 0.00 ! EEPI, fylin +CG321 CG321 NG2D1 CG2N2 0.1900 1 180.00 ! DH3T, fylin +CG321 CG321 NG2D1 CG2N2 0.3400 2 180.00 ! DH3T, fylin +CG321 CG321 NG2D1 CG2N2 0.5600 3 180.00 ! DH3T, fylin +CG321 CG321 NG2D1 CG2N2 0.1200 4 0.00 ! DH3T, fylin +CG321 CG321 NG2D1 CG2N2 0.1200 6 180.00 ! DH3T, fylin +CG331 CG321 NG2D1 CG2N2 0.1900 1 0.00 ! MT2A, fylin +CG331 CG321 NG2D1 CG2N2 0.3400 2 180.00 ! MT2A, fylin +CG331 CG321 NG2D1 CG2N2 0.5600 3 180.00 ! MT2A, fylin +CG331 CG321 NG2D1 CG2N2 0.1200 4 0.00 ! MT2A, fylin +CG331 CG321 NG2D1 CG2N2 0.1200 6 180.00 ! MT2A, fylin +HGA2 CG321 NG2D1 CG2D1 0.1000 3 0.00 ! EEPI, from HGA3 CG331 NG2D1 CG2D1, fylin +HGA2 CG321 NG2D1 CG2N2 0.1100 3 180.00 ! MT2A, from HGA3 CG331 NG2D1 CG2N1, fylin +CG331 CG321 NG2R51 CG2R51 0.3850 1 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +CG331 CG321 NG2R51 CG2R51 0.4200 2 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +CG331 CG321 NG2R51 CG2R51 0.0800 3 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +CG331 CG321 NG2R51 CG2R51 0.0550 4 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +CG331 CG321 NG2R51 NG2R50 0.3850 1 180.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +CG331 CG321 NG2R51 NG2R50 0.4200 2 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +CG331 CG321 NG2R51 NG2R50 0.0800 3 180.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +CG331 CG321 NG2R51 NG2R50 0.0550 4 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, kevo +HGA2 CG321 NG2R51 CG2R51 0.0000 3 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from HGA3 CG331 NG2R51 CG2R53, kevo +HGA2 CG321 NG2R51 NG2R50 0.0000 3 0.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from HGA3 CG331 NG2R51 CG2R53, kevo +CG2O1 CG321 NG2S1 CG2O1 0.2000 1 180.00 ! PROT ala dipeptide, new C VDW Rmin, adm jr., 3/3/93c +CG2O1 CG321 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +CG2O2 CG321 NG2S1 CG2O1 0.2000 1 180.00 ! PROT Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c +CG2O2 CG321 NG2S1 HGP1 0.0000 1 0.00 ! PROT adm jr. 5/02/91, acetic Acid pure solvent +CG2O3 CG321 NG2S1 CG2O1 0.2000 1 180.00 ! PROT Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c +CG2O3 CG321 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +CG2R61 CG321 NG2S1 CG2O1 0.0150 1 0.00 ! NZAD, N-benzylacetamide, isg +CG2R61 CG321 NG2S1 CG2O1 0.2980 2 0.00 ! NZAD, N-benzylacetamide, isg +CG2R61 CG321 NG2S1 CG2O1 0.0760 3 180.00 ! NZAD, N-benzylacetamide, isg +CG2R61 CG321 NG2S1 CG2O1 0.6190 4 0.00 ! NZAD, N-benzylacetamide, isg +CG2R61 CG321 NG2S1 CG2O1 0.1480 6 0.00 ! NZAD, N-benzylacetamide, isg +CG2R61 CG321 NG2S1 HGP1 0.0000 1 0.00 ! NZAD, N-benzylacetamide; from CG2O2 CG321 NG2S1 HGP1; isg +CG311 CG321 NG2S1 CG2O1 1.8000 1 0.00 ! G4MP, Gamma-4-Methyl Piperidine Glu Acid CDCA Amide, cacha +CG311 CG321 NG2S1 HGP1 0.0000 1 0.00 ! G4MP, Gamma-4-Methyl Piperidine Glu Acid CDCA Amide, cacha +CG314 CG321 NG2S1 CG2O1 1.8000 1 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +CG314 CG321 NG2S1 HGP1 0.0000 1 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha +CG321 CG321 NG2S1 CG2O1 1.8000 1 0.00 ! slack parameter picked up by 3CPD ==> re-optimize? +CG321 CG321 NG2S1 HGP1 0.0000 1 0.00 ! PROT from HGP1 NG2S1 CG321 CT3, for lactams, adm jr. +CG331 CG321 NG2S1 CG2O6 0.3500 1 180.00 ! DECB, diethyl carbamate, cacha & xxwy +CG331 CG321 NG2S1 CG2O6 0.7500 2 0.00 ! DECB, diethyl carbamate, cacha & xxwy +CG331 CG321 NG2S1 CG2O6 0.1500 4 0.00 ! DECB, diethyl carbamate, cacha & xxwy +CG331 CG321 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +HGA1 CG321 NG2S1 CG2O1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +HGA1 CG321 NG2S1 HGP1 0.0000 1 0.00 ! PROT Alanine Dipeptide ab initio calc's (LK) +HGA2 CG321 NG2S1 CG2O1 0.0000 3 0.00 ! PROT, sp2-methyl, no torsion potential +HGA2 CG321 NG2S1 CG2O6 0.0000 3 0.00 ! DECB, diethyl carbamate, from DMCB, kevo +HGA2 CG321 NG2S1 HGP1 0.0000 3 0.00 ! PROT, sp2-methyl, no torsion potential +CG331 CG321 NG2S3 SG3O1 0.7550 1 180.00 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 CG321 NG2S3 SG3O1 0.8660 2 0.00 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 CG321 NG2S3 SG3O1 0.6280 3 0.00 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 CG321 NG2S3 SG3O1 0.1510 4 180.00 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 CG321 NG2S3 SG3O1 0.1130 6 0.00 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 CG321 NG2S3 HGP1 0.7410 1 0.00 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 CG321 NG2S3 HGP1 0.3210 2 0.00 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 CG321 NG2S3 HGP1 0.2350 3 180.00 ! NESM, N-ethyl-sulfamate, my & kevo +HGA2 CG321 NG2S3 SG3O1 0.1500 3 0.00 ! NESM, N-ethyl-sulfamate; from HGA3 CG331 NG2S3 PG1; my +HGA2 CG321 NG2S3 HGP1 0.0100 3 0.00 ! NESM, N-ethyl-sulfamate; from HGA3 CG331 NG2S3 HGP1; my +CG321 CG321 NG311 HGPAM1 0.3000 3 0.00 ! K2Cn, cgenff_compromise, kevo +CG331 CG321 NG311 SG3O2 0.1000 1 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG331 CG321 NG311 SG3O2 0.7000 2 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG331 CG321 NG311 SG3O2 0.1000 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG331 CG321 NG311 HGP1 0.1000 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +NG311 CG321 NG311 CG2R61 2.5000 1 180.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +NG311 CG321 NG311 CG2R61 1.5000 2 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +NG311 CG321 NG311 CG2R61 0.5000 3 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +NG311 CG321 NG311 SG3O2 1.4000 1 180.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +NG311 CG321 NG311 SG3O2 0.5000 2 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +NG311 CG321 NG311 SG3O2 0.1000 3 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +NG311 CG321 NG311 HGP1 0.1000 3 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +NG311 CG321 NG311 HGPAM1 1.7000 2 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +NG311 CG321 NG311 HGPAM1 0.3000 3 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +HGA2 CG321 NG311 CG2R61 0.0000 3 180.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +HGA2 CG321 NG311 CG321 0.0000 3 0.00 ! 5UHG, cgenff_compromise, kevo +HGA2 CG321 NG311 SG3O2 0.1000 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +HGA2 CG321 NG311 HGP1 0.0500 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +HGA2 CG321 NG311 HGPAM1 0.0500 3 0.00 ! PEI0, OBTZ, AOBT, kevo & xxwy +CG2O2 CG321 NG321 HGPAM2 0.1600 3 0.00 ! GLYN, Glycine neutral from AMINE aliphatic amines +HGA2 CG321 NG321 HGPAM2 0.0100 3 0.00 ! amines +CG321 CG321 OG301 CG2R61 0.2400 1 0.00 ! PNTM, pentamidine; from ETOB, Ethoxybenzene; kevo +CG321 CG321 OG301 CG2R61 0.2900 2 0.00 ! PNTM, pentamidine; from ETOB, Ethoxybenzene; kevo +CG321 CG321 OG301 CG2R61 0.0200 3 0.00 ! PNTM, pentamidine; from ETOB, Ethoxybenzene; kevo +CG321 CG321 OG301 CG321 0.5700 1 0.00 ! 1,2 dimethoxyethane, 2/12/05, ATM +CG321 CG321 OG301 CG321 0.2900 2 0.00 ! 1,2 dimethoxyethane +CG321 CG321 OG301 CG321 0.4300 3 0.00 ! 1,2 dimethoxyethane +CG321 CG321 OG301 CG331 0.5700 1 0.00 ! 1,2 dimethoxyethane (DME), 2/12/05, ATM +CG321 CG321 OG301 CG331 0.2900 2 0.00 ! 1,2 dimethoxyethane (DME) +CG321 CG321 OG301 CG331 0.4300 3 0.00 ! 1,2 dimethoxyethane (DME) +CG331 CG321 OG301 CG2R61 0.2400 1 0.00 ! ETOB, Ethoxybenzene, cacha +CG331 CG321 OG301 CG2R61 0.2900 2 0.00 ! ETOB, Ethoxybenzene, cacha +CG331 CG321 OG301 CG2R61 0.0200 3 0.00 ! ETOB, Ethoxybenzene, cacha +CG331 CG321 OG301 CG321 0.4000 1 0.00 ! diethylether, 2/12/05, ATM +CG331 CG321 OG301 CG321 0.4900 3 0.00 ! diethylether +CG331 CG321 OG301 CG331 0.4000 1 0.00 ! diethylether, 2/12/05, ATM!from CCT3-CCT2-OCE-CG321 MEE viv +CG331 CG321 OG301 CG331 0.4900 3 0.00 ! diethylether !from CCT3-CCT2-OCE-CG321 MEE viv +CG3C51 CG321 OG301 CG2R61 0.2000 1 180.00 ! 3POMP, 3-phenoxymethylpyrrolidine, kevo +CG3C51 CG321 OG301 CG2R61 0.1000 2 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine, kevo +CG3C51 CG321 OG301 CG2R61 0.1000 3 180.00 ! 3POMP, 3-phenoxymethylpyrrolidine, kevo +HGA2 CG321 OG301 CG2R61 0.0950 3 0.00 ! ETOB, Ethoxybenzene, cacha +HGA2 CG321 OG301 CG321 0.2840 3 0.00 ! diethylether, alex +HGA2 CG321 OG301 CG331 0.2840 3 0.00 ! diethylether, alex +CG2R61 CG321 OG302 CG2O2 0.0000 3 0.00 ! ABGA, ALPHA BENZYL GLU ACID CDCA AMIDE +CG311 CG321 OG302 CG2O2 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +CG321 CG321 OG302 CG2O2 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +CG324 CG321 OG302 CG2O2 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +CG331 CG321 OG302 CG2O2 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +CG331 CG321 OG302 CG2O6 0.1000 1 180.00 ! DECB & DECA, diethyl carbamate & carbonate, cacha & xxwy +CG331 CG321 OG302 CG2O6 0.6000 2 0.00 ! DECB, diethyl carbamate, cacha & xxwy +CG331 CG321 OG302 CG2O6 0.1000 3 180.00 ! DECB, diethyl carbamate, cacha & xxwy +HGA2 CG321 OG302 CG2O2 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +HGA2 CG321 OG302 CG2O6 0.0000 3 0.00 ! DECB, diethyl carbamate, from DMCB, kevo +CG311 CG321 OG303 PG1 0.6000 1 180.00 ! EP_2 phospho-ser/thr !Reorganization: GPC and others +CG311 CG321 OG303 PG1 0.6500 2 0.00 ! EP_2 phospho-ser/thr !Reorganization: GPC and others +CG311 CG321 OG303 PG1 0.0500 3 0.00 ! EP_2 phospho-ser/thr !Reorganization: GPC and others +CG321 CG321 OG303 PG1 0.6000 1 180.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others +CG321 CG321 OG303 PG1 0.6500 2 0.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others +CG321 CG321 OG303 PG1 0.0500 3 0.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others +CG321 CG321 OG303 SG3O1 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +CG324 CG321 OG303 PG1 0.6000 1 180.00 ! EP_2 phospho-ser/thr !Reorganization: PC and others +CG324 CG321 OG303 PG1 0.6500 2 0.00 ! EP_2 phospho-ser/thr !Reorganization: PC and others +CG324 CG321 OG303 PG1 0.0500 3 0.00 ! EP_2 phospho-ser/thr !Reorganization: PC and others +CG331 CG321 OG303 PG2 0.6000 1 180.00 ! EP_2 phospho-ser/thr +CG331 CG321 OG303 PG2 0.6500 2 0.00 ! EP_2 phospho-ser/thr +CG331 CG321 OG303 PG2 0.0500 3 0.00 ! EP_2 phospho-ser/thr +CG3C51 CG321 OG303 PG1 0.6000 1 180.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr +CG3C51 CG321 OG303 PG1 0.6500 2 0.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr +CG3C51 CG321 OG303 PG1 0.0500 3 0.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr +CG3C51 CG321 OG303 PG2 0.6000 1 180.00 ! TH5P carbocyclic sugars reset to EP_2 phospho-ser/thr +CG3C51 CG321 OG303 PG2 0.6500 2 0.00 ! TH5P carbocyclic sugars reset to EP_2 phospho-ser/thr +CG3C51 CG321 OG303 PG2 0.0500 3 0.00 ! TH5P carbocyclic sugars reset to EP_2 phospho-ser/thr +CG3RC1 CG321 OG303 PG1 0.6000 1 180.00 ! B5NP carbocyclic sugars reset to EP_2 phospho-ser/thr +CG3RC1 CG321 OG303 PG1 0.6500 2 0.00 ! B5NP carbocyclic sugars reset to EP_2 phospho-ser/thr +CG3RC1 CG321 OG303 PG1 0.0500 3 0.00 ! B5NP carbocyclic sugars reset to EP_2 phospho-ser/thr +HGA2 CG321 OG303 PG1 0.0000 3 0.00 ! NA dmp !Reorganization: PC and others +HGA2 CG321 OG303 PG2 0.0000 3 0.00 ! NA dmp !Reorganization: TH5P and others +HGA2 CG321 OG303 SG3O1 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +CG2D1 CG321 OG311 HGP1 1.3000 1 0.00 ! RETINOL PROL +CG2D1 CG321 OG311 HGP1 0.7000 2 0.00 ! RETINOL PROL +CG2D1 CG321 OG311 HGP1 0.1400 3 0.00 ! RETINOL PROL; Kenno: empirically corrected for HGA2 CG321 OG311 HGP1 from Team sugar ==> re-evaluate. +CG2DC1 CG321 OG311 HGP1 1.3000 1 0.00 ! RETINOL PROL +CG2DC1 CG321 OG311 HGP1 0.7000 2 0.00 ! RETINOL PROL +CG2DC1 CG321 OG311 HGP1 0.1400 3 0.00 ! RETINOL PROL; Kenno: empirically corrected for HGA2 CG321 OG311 HGP1 from Team sugar ==> re-evaluate. +CG2DC2 CG321 OG311 HGP1 1.3000 1 0.00 ! RETINOL PROL +CG2DC2 CG321 OG311 HGP1 0.7000 2 0.00 ! RETINOL PROL +CG2DC2 CG321 OG311 HGP1 0.1400 3 0.00 ! RETINOL PROL; Kenno: empirically corrected for HGA2 CG321 OG311 HGP1 from Team sugar ==> re-evaluate. +CG2R61 CG321 OG311 HGP1 2.1000 1 0.00 ! 3ALP, nicotinaldehyde (PYRIDINE pyr-CH2OH), yin +CG2R61 CG321 OG311 HGP1 1.4000 2 0.00 ! 3ALP, nicotinaldehyde (PYRIDINE pyr-CH2OH), yin +CG2R61 CG321 OG311 HGP1 0.7400 3 0.00 ! 3ALP, nicotinaldehyde (PYRIDINE pyr-CH2OH), yin; Kenno: empirically corrected for HGA2 CG321 OG311 HGP1 from Team sugar ==> re-evaluate. +CG302 CG321 OG311 HGP1 0.4000 1 0.00 ! TFE, Trifluoroethanol +CG302 CG321 OG311 HGP1 0.9000 2 0.00 ! TFE, Trifluoroethanol +CG302 CG321 OG311 HGP1 0.3400 3 0.00 ! TFE, Trifluoroethanol; Kenno: empirically corrected for HGA2 CG321 OG311 HGP1 from Team sugar ==> re-evaluate. +CG302 CG321 OG311 HGP1 0.1200 4 0.00 ! TFE, Trifluoroethanol +CG311 CG321 OG311 HGP1 1.1300 1 0.00 ! og ethanol +CG311 CG321 OG311 HGP1 0.1400 2 0.00 ! og ethanol +CG311 CG321 OG311 HGP1 0.2400 3 0.00 ! og ethanol +CG314 CG321 OG311 HGP1 1.1300 1 0.00 ! og ethanol +CG314 CG321 OG311 HGP1 0.1400 2 0.00 ! og ethanol +CG314 CG321 OG311 HGP1 0.2400 3 0.00 ! og ethanol +CG321 CG321 OG311 HGP1 1.1300 1 0.00 ! og ethanol +CG321 CG321 OG311 HGP1 0.1400 2 0.00 ! og ethanol +CG321 CG321 OG311 HGP1 0.2400 3 0.00 ! og ethanol +CG324 CG321 OG311 HGP1 1.1300 1 0.00 ! ETAM, ethanolamine (transferred from og ethanol) +CG324 CG321 OG311 HGP1 0.1400 2 0.00 ! ETAM, ethanolamine (transferred from og ethanol) +CG324 CG321 OG311 HGP1 0.2400 3 0.00 ! ETAM, ethanolamine (transferred from og ethanol) +CG331 CG321 OG311 HGP1 1.1300 1 0.00 ! og ethanol +CG331 CG321 OG311 HGP1 0.1400 2 0.00 ! og ethanol +CG331 CG321 OG311 HGP1 0.2400 3 0.00 ! og ethanol +CG3C51 CG321 OG311 HGP1 1.1300 1 0.00 ! og ethanol +CG3C51 CG321 OG311 HGP1 0.1400 2 0.00 ! og ethanol +CG3C51 CG321 OG311 HGP1 0.2400 3 0.00 ! og ethanol +HGA2 CG321 OG311 HGP1 0.1800 3 0.00 ! og methanol +CG321 CG321 OG3C61 CG321 0.5300 1 180.00 ! DIOX, dioxane +CG321 CG321 OG3C61 CG321 0.6800 2 0.00 ! DIOX, dioxane +CG321 CG321 OG3C61 CG321 0.2100 3 180.00 ! DIOX, dioxane +CG321 CG321 OG3C61 CG321 0.1500 4 0.00 ! DIOX, dioxane +CG324 CG321 OG3C61 CG321 0.5000 3 0.00 ! MORP, morpholine +OG3C61 CG321 OG3C61 CG321 1.0000 3 0.00 ! DIXB, 13dioxane +HGA2 CG321 OG3C61 CG321 0.1950 3 0.00 ! DIOX, dioxane +CG2DC1 CG321 OG3R60 CG2D2O 0.7000 3 0.00 ! PY02, 2h-pyran +CG2DC2 CG321 OG3R60 CG2D1O 0.7000 3 0.00 ! PY02, 2h-pyran +HGA2 CG321 OG3R60 CG2D1O 0.9000 3 0.00 ! PY02, 2h-pyran +HGA2 CG321 OG3R60 CG2D2O 0.9000 3 0.00 ! PY02, 2h-pyran +CG2R61 CG321 PG1 OG2P1 0.0500 3 0.00 ! BDFP, Benzylphosphonate \ re-optimize? +CG2R61 CG321 PG1 OG311 1.6500 1 180.00 ! BDFP, BDFD, Benzylphosphonate +CG2R61 CG321 PG1 OG311 0.5000 2 0.00 ! BDFP, BDFD, Benzylphosphonate +HGA2 CG321 PG1 OG2P1 0.1000 3 0.00 ! BDFP, Benzylphosphonate \ re-optimize? +HGA2 CG321 PG1 OG311 0.1000 3 0.00 ! BDFP, BDFD, Benzylphosphonate +CG2R61 CG321 PG2 OG2P1 0.0500 3 0.00 ! BDFD, Benzylphosphonate / re-optimize? +HGA2 CG321 PG2 OG2P1 0.1000 3 0.00 ! BDFD, Benzylphosphonate / re-optimize? +CG331 CG321 SG301 SG301 0.3100 3 0.00 ! PROT S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +HGA2 CG321 SG301 SG301 0.1580 3 0.00 ! PROT expt. dimethyldisulfide, 3/26/92 (FL) +CG311 CG321 SG311 HGP3 0.2400 1 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG311 CG321 SG311 HGP3 0.1500 2 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG311 CG321 SG311 HGP3 0.2700 3 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG314 CG321 SG311 HGP3 0.2400 1 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG314 CG321 SG311 HGP3 0.1500 2 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG314 CG321 SG311 HGP3 0.2700 3 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG321 CG321 SG311 CG2N2 0.24 1 180.00 ! DH3T , from CG321 CG321 SG311 CG321, penalty= 69 no opt. +CG321 CG321 SG311 CG2N2 0.37 3 0.00 ! DH3T , from CG321 CG321 SG311 CG321, penalty= 69 no opt. +CG321 CG321 SG311 CG321 0.2400 1 180.00 ! PROT expt. MeEtS, 3/26/92 (FL) +CG321 CG321 SG311 CG321 0.3700 3 0.00 ! PROT expt. MeEtS, 3/26/92 (FL) +CG321 CG321 SG311 CG331 0.2400 1 180.00 ! PROT expt. MeEtS, 3/26/92 (FL) +CG321 CG321 SG311 CG331 0.3700 3 0.00 ! PROT expt. MeEtS, 3/26/92 (FL) +CG321 CG321 SG311 HGP3 0.2400 1 0.00 ! PRSH, n-thiopropanol, kevo for gsk/ibm +CG321 CG321 SG311 HGP3 0.1500 2 0.00 ! PRSH, n-thiopropanol, kevo for gsk/ibm +CG321 CG321 SG311 HGP3 0.2700 3 0.00 ! PRSH, n-thiopropanol, kevo for gsk/ibm +CG324 CG321 SG311 CG321 0.1950 3 0.00 ! TMOR, thiomorpholine +CG331 CG321 SG311 CG331 0.2400 1 180.00 ! PROT expt. MeEtS, 3/26/92 (FL) +CG331 CG321 SG311 CG331 0.3700 3 0.00 ! PROT DTN 8/24/90 +CG331 CG321 SG311 HGP3 0.2400 1 0.00 ! PROT ethanethiol C-C-S-H surface, adm jr., 4/18/93 +CG331 CG321 SG311 HGP3 0.1500 2 0.00 ! PROT ethanethiol C-C-S-H surface, adm jr., 4/18/93 +CG331 CG321 SG311 HGP3 0.2700 3 0.00 ! PROT ethanethiol C-C-S-H surface, adm jr., 4/18/93 +CG3C51 CG321 SG311 CG321 0.2400 1 180.00 ! PROT MeEtS reset by kevo +CG3C51 CG321 SG311 CG321 0.3700 3 0.00 ! PROT MeEtS reset by kevo +SG311 CG321 SG311 CG321 1.3000 3 0.00 ! TRIT, trithiane +HGA2 CG321 SG311 CG2N2 0.36 3 0.00 ! DH3T , from HGA3 CG331 SG311 CG2O6, penalty= 19.5 no opt. +HGA2 CG321 SG311 CG321 0.2800 3 0.00 ! PROT DTN 8/24/90 +HGA2 CG321 SG311 CG331 0.2800 3 0.00 ! PROT DTN 8/24/90 +HGA2 CG321 SG311 HGP3 0.2000 3 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +CG321 CG321 SG3O1 OG2P1 0.2300 3 0.00 ! PSNA, propyl sulfonate, xhe +CG331 CG321 SG3O1 OG2P1 0.2600 3 0.00 ! ESNA, ethyl sulfonate, xhe +HGA2 CG321 SG3O1 OG2P1 0.1900 3 0.00 ! ESNA, ethyl sulfonate, xhe +CG331 CG321 SG3O2 CG331 0.9000 1 0.00 ! MESN, methyl ethyl sulfone, xhe & kevo +CG331 CG321 SG3O2 CG331 0.3500 2 0.00 ! MESN, methyl ethyl sulfone, xhe & kevo +CG331 CG321 SG3O2 CG331 0.1250 3 0.00 ! MESN, methyl ethyl sulfone, xhe & kevo +CG331 CG321 SG3O2 NG311 0.1000 1 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG331 CG321 SG3O2 NG311 0.4000 2 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG331 CG321 SG3O2 NG311 0.3600 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG331 CG321 SG3O2 OG2P1 0.1800 3 0.00 ! EESM, N-ethylethanesulfonamide; MESN, methyl ethyl sulfone; xxwy & xhe +HGA2 CG321 SG3O2 CG331 0.1250 3 0.00 ! MESN, methyl ethyl sulfone, xhe +HGA2 CG321 SG3O2 NG311 0.1600 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +HGA2 CG321 SG3O2 OG2P1 0.1600 3 0.00 ! EESM, N-ethylethanesulfonamide; MESN, methyl ethyl sulfone; xxwy & xhe +CG331 CG321 SG3O3 CG331 0.1800 1 180.0 ! MESO, methylethylsulfoxide, kevo +CG331 CG321 SG3O3 CG331 0.5700 3 0.0 ! MESO, methylethylsulfoxide, kevo +CG331 CG321 SG3O3 OG2P1 1.6000 1 180.0 ! MESO, methylethylsulfoxide, kevo +CG331 CG321 SG3O3 OG2P1 0.2400 2 180.0 ! MESO, methylethylsulfoxide, kevo +CG331 CG321 SG3O3 OG2P1 0.0300 3 180.0 ! MESO, methylethylsulfoxide, kevo +HGA2 CG321 SG3O3 CG331 0.2000 3 0.00 ! MESO, methylethylsulfoxide; from DMSO, dimethylsulfoxide; mnoon +HGA2 CG321 SG3O3 OG2P1 0.2000 3 0.00 ! MESO, methylethylsulfoxide; from DMSO, dimethylsulfoxide; mnoon +FGA1 CG322 CG331 HGA3 0.1850 3 0.00 ! FLUROALK fluoro_alkanes +HGA6 CG322 CG331 HGA3 0.1850 3 0.00 ! FLUROALK fluoro_alkanes +SG302 CG323 CG331 HGA3 0.1500 3 0.00 ! PROT ethylthiolate, adm jr., 6/1/92 +HGA2 CG323 CG331 HGA3 0.1600 3 0.00 ! PROT ethylthiolate, adm jr., 6/1/92 +NG3P0 CG324 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +NG3P3 CG324 CG331 HGA3 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA2 CG324 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +HGP5 CG324 CG331 HGA3 0.1600 3 0.00 ! PROT rotation barrier in Ethane (SF) +NG3P3 CG324 CG3C31 CG3C31 0.1950 3 0.00 ! AMCP, aminomethyl cyclopropane; from PROT alkane update, adm jr., 3/2/92; jhs +NG3P3 CG324 CG3C31 HGA1 0.2000 3 0.00 ! AMCP, aminomethyl cyclopropane; from PROT alkane update, adm jr., 3/2/92; jhs +HGA2 CG324 CG3C31 CG3C31 0.1950 3 0.00 ! AMCP, aminomethyl cyclopropane; from FLAVOP PIP1,2,3; jhs +HGA2 CG324 CG3C31 HGA1 0.1950 3 0.00 ! AMCP, aminomethyl cyclopropane; from FLAVOP PIP1,2,3; jhs +CG321 CG324 NG2O1 OG2N1 0.0840 2 180.00 ! NIPR, nitropropane, kevo & abar +CG321 CG324 NG2O1 OG2N1 0.0330 4 0.00 ! NIPR, nitropropane, kevo & abar +CG321 CG324 NG2O1 OG2N1 0.0242 6 0.00 ! NIPR, nitropropane, kevo & abar ! we'll tolerate the slight dihedral strain for the sake of transferability - Kenno +HGA2 CG324 NG2O1 OG2N1 0.0150 6 180.00 ! NIPR, nitropropane, abar +CG321 CG324 NG2P1 CG2N1 0.0000 6 180.00 ! PROT methylguanidinium, adm jr., 3/26/92 +CG321 CG324 NG2P1 HGP2 0.0000 6 180.00 ! PROT methylguanidinium, adm jr., 3/26/92 +HGA2 CG324 NG2P1 CG2N1 0.0000 6 180.00 ! PROT methylguanidinium, adm jr., 3/26/92 +HGA2 CG324 NG2P1 HGP2 0.0000 6 180.00 ! PROT methylguanidinium, adm jr., 3/26/92 +CG321 CG324 NG3P0 CG334 0.2600 3 0.00 ! LIPID tetramethylammonium +CG331 CG324 NG3P0 CG324 0.2600 3 0.00 ! LIPID tetramethylammonium +CG331 CG324 NG3P0 CG334 0.2600 3 0.00 ! LIPID tetramethylammonium +HGP5 CG324 NG3P0 CG324 0.2600 3 0.00 ! LIPID tetramethylammonium +HGP5 CG324 NG3P0 CG334 0.2600 3 0.00 ! LIPID tetramethylammonium +CG2R61 CG324 NG3P1 CG324 1.7000 1 180.00 ! BPIP, N-Benzyl PIP, cacha +CG2R61 CG324 NG3P1 CG324 0.8000 2 180.00 ! BPIP, N-Benzyl PIP, cacha +CG2R61 CG324 NG3P1 CG324 0.5800 3 0.00 ! BPIP, N-Benzyl PIP, cacha +CG2R61 CG324 NG3P1 HGP2 0.0400 3 0.00 ! BPIP, N-Benzyl PIP, cacha +CG311 CG324 NG3P1 CG324 0.1000 3 0.00 ! FLAVOP PIP1,2,3; PEI polymers, kevo +CG311 CG324 NG3P1 CG334 0.1000 3 0.00 ! FLAVOP PIP1,2,3; PEI polymers, kevo +CG311 CG324 NG3P1 HGP2 0.1000 3 0.00 ! FLAVOP PIP1,2,3 +CG321 CG324 NG3P1 CG324 0.1000 3 0.00 ! FLAVOP PIP1,2,3; PEI polymers, kevo +CG321 CG324 NG3P1 CG334 0.1000 3 0.00 ! FLAVOP PIP1,2,3; PEI polymers, kevo +CG321 CG324 NG3P1 HGP2 0.1000 3 0.00 ! FLAVOP PIP1,2,3 +HGA2 CG324 NG3P1 CG324 0.1000 3 0.00 ! FLAVOP PIP1,2,3; PEI polymers, kevo +HGA2 CG324 NG3P1 CG334 0.1000 3 0.00 ! FLAVOP PIP1,2,3; PEI polymers, kevo +HGA2 CG324 NG3P1 HGP2 0.1000 3 0.00 ! FLAVOP PIP1,2,3 +CG311 CG324 NG3P2 CG324 0.4000 1 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG311 CG324 NG3P2 CG324 0.2500 2 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG311 CG324 NG3P2 CG324 0.6000 3 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG311 CG324 NG3P2 HGP2 0.1000 3 0.00 ! G3P(R/S), Gamma-3-Piperidine Glu Acid CDCA Amide, cacha +CG321 CG324 NG3P2 CG314 0.4000 1 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG321 CG324 NG3P2 CG314 0.2500 2 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG321 CG324 NG3P2 CG314 0.6000 3 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG321 CG324 NG3P2 CG324 0.4000 1 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG321 CG324 NG3P2 CG324 0.2500 2 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG321 CG324 NG3P2 CG324 0.6000 3 0.00 ! *** Developmental params for PEI polymers and PIP. Will be tweaked, then applied to existing PIP derivatives *** kevo +CG321 CG324 NG3P2 HGP2 0.1000 3 0.00 ! PIP, piperidine +HGA2 CG324 NG3P2 CG314 0.1000 3 0.00 ! 3MRB, Gamma-3 methyl piperidine, alpha-benzyl GA CDCA amide, cacha; PEI polymers, kevo +HGA2 CG324 NG3P2 CG324 0.1000 3 0.00 ! PIP, piperidine; PEI polymers, kevo +HGA2 CG324 NG3P2 HGP2 0.1000 3 0.00 ! PIP, piperidine +CG2O1 CG324 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +CG2O3 CG324 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +CG321 CG324 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +CG331 CG324 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +CG3C31 CG324 NG3P3 HGP2 0.1000 3 0.00 ! AMCP, aminomethyl cyclopropane; from PROT 0.715->0.10 METHYLAMMONIUM (KK); jhs +HGA2 CG324 NG3P3 HGP2 0.1000 3 0.00 ! PROT 0.715->0.10 METHYLAMMONIUM (KK) +HGA3 CG331 CG331 HGA3 0.1550 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +HGA3 CG331 CG3C51 CG3C51 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA3 CG331 CG3C51 CG3C52 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA3 CG331 CG3C51 CG3RC1 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA3 CG331 CG3C51 OG3C51 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA3 CG331 CG3C51 HGA1 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv +HGA3 CG331 CG3RC1 CG311 0.1500 3 180.00 ! CA, Cholic Acid, cacha, 02/08 +HGA3 CG331 CG3RC1 CG321 0.1600 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA3 CG331 CG3RC1 CG3C51 0.1500 3 180.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA3 CG331 CG3RC1 CG3RC1 0.1500 3 180.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA3 CG331 NG2D1 CG2D1 0.1000 3 0.00 ! RETINOL SCH1, Schiff's base, deprotonated +HGA3 CG331 NG2D1 CG2N1 0.1100 3 180.00 ! MGU1, methylguanidine +HGA3 CG331 NG2D1 CG2O7 0.0300 3 0.00 ! MICY, methyl isocyanate, xxwy +HGA3 CG331 NG2R51 CG2R53 0.0000 3 0.00 ! NA 9-M-A +HGA3 CG331 NG2R51 CG2RC0 0.1900 3 0.00 ! NA 9-M-G +HGA3 CG331 NG2R61 CG2R62 0.0000 3 0.00 ! NA 1-M-C +HGA3 CG331 NG2R61 CG2R63 0.1900 3 0.00 ! NA 1-M-C +HGA3 CG331 NG2S0 CG2O1 0.0000 3 0.00 ! DMA, dimethylacetamide; from PROT, sp2-methyl, no torsion potential; xxwy & jhs +HGA3 CG331 NG2S0 CG331 0.4200 3 0.00 ! DMF, Dimethylformamide, xxwy +HGA3 CG331 NG2S1 CG2O1 0.0000 3 0.00 ! PROT, sp2-methyl, no torsion potential +HGA3 CG331 NG2S1 CG2O6 0.0000 3 0.00 ! DMCB, diethyl carbamate, kevo +HGA3 CG331 NG2S1 HGP1 0.0000 3 0.00 ! PROT, sp2-methyl, no torsion potential +HGA3 CG331 NG2S3 PG1 0.1500 3 0.00 ! NABAKB phosphoramidates +HGA3 CG331 NG2S3 SG3O1 0.1500 3 0.00 ! NMSM, N-methyl-sulfamate; from HGA3 CG331 NG2S3 PG1; my +HGA3 CG331 NG2S3 HGP1 0.0100 3 0.00 ! NABAKB phosphoramidates +HGA3 CG331 NG301 CG2R61 0.4300 3 0.00 ! DMAN, N,N-dimethylaniline, kevo +HGA3 CG331 NG301 CG2R64 0.0000 3 180.00 ! TMC, from HGA3 CG331 NG311 CG2N1, yxu +HGA3 CG331 NG301 CG331 0.0000 3 180.00 ! TMC, from HGA3 CG331 NG311 CG2N1, yxu +HGA3 CG331 NG311 CG2N1 0.0000 3 180.00 ! MGU2, methylguanidine2 \ Taken together, these two params don't make much sense +HGA3 CG331 NG311 SG3O2 0.1000 3 0.00 ! MMSM, N-methylmethanesulfonamide; MBSM, N-methylbenzenesulfonamide; xxwy +HGA3 CG331 NG311 HGP1 0.0500 3 0.00 ! MMSM, N-methylmethanesulfonamide; MBSM, N-methylbenzenesulfonamide; xxwy +HGA3 CG331 NG311 HGPAM1 0.4200 3 0.00 ! MGU2, methylguanidine2 / Taken together, these two params don't make much sense +HGA3 CG331 OG301 CG2D1O 0.0650 3 0.00 ! MOET, Methoxyethene, xxwy +HGA3 CG331 OG301 CG2D2O 0.0650 3 0.00 ! MOET, Methoxyethene, xxwy +HGA3 CG331 OG301 CG2R61 0.0850 3 0.00 ! MEOB, Methoxybenzene, cacha +HGA3 CG331 OG301 CG301 0.2840 3 0.00 ! AMOL, alpha-methoxy-lactic acid, og +HGA3 CG331 OG301 CG311 0.2840 3 0.00 ! all34_ethers_1a og/gk (not affected by mistake) +HGA3 CG331 OG301 CG321 0.2840 3 0.00 ! diethylether, alex +HGA3 CG331 OG301 CG331 0.2840 3 0.00 ! diethylether, alex !from HCT2-CCT2-OCE-CG321 DME, viv +HGA3 CG331 OG301 CG3C51 0.2000 1 180.00 ! THF2, THF-2'OMe C2'-OM-CM-H, from Nucl. Acids, ed +HGA3 CG331 OG301 CG3C51 1.2000 2 180.00 ! THF2, THF-2'OMe C2'-OM-CM-H, from Nucl. Acids, ed +HGA3 CG331 OG302 CG2O2 0.0000 3 0.00 ! LIPID phosphate, new NA, 4/98, adm jr. +HGA3 CG331 OG302 CG2O6 0.0000 3 0.00 ! DMCB & DMCA, dimethyl carbamate & carbonate, kevo +HGA3 CG331 OG303 PG0 0.0000 3 0.00 ! NA dmp !Reorganization:MP_0 RE-OPTIMIZE! +HGA3 CG331 OG303 PG1 0.0000 3 0.00 ! NA dmp !Reorganization:MP_1 +HGA3 CG331 OG303 PG2 0.0000 3 0.00 ! NA dmp !Reorganization:MP_2 +HGA3 CG331 OG303 SG3O1 0.0000 3 0.00 ! LIPID methylsulfate +HGA3 CG331 OG303 SG3O2 0.0000 3 0.00 ! MMST, methyl methanesulfonate, xxwy +HGA3 CG331 OG311 HGP1 0.1800 3 0.00 ! og methanol +HGA3 CG331 SG301 SG301 0.1580 3 0.00 ! PROT expt. dimethyldisulfide, 3/26/92 (FL) +HGA3 CG331 SG311 CG2N2 0.36 3 0.00 ! MT2A , from HGA3 CG331 SG311 CG2O6 +HGA3 CG331 SG311 CG2O6 0.3600 3 0.00 ! DMTT, dimethyl trithiocarbonate, kevo +HGA3 CG331 SG311 CG2R64 0.1500 3 180.00 ! 2SMPYR, 2-(methylthio)-pyrimidine; from HGA3 CG331 SG311 CG2O6; isg +HGA3 CG331 SG311 CG321 0.2800 3 0.00 ! PROT DTN 8/24/90 +HGA3 CG331 SG311 HGP3 0.2000 3 0.00 ! PROT methanethiol pure solvent, adm jr., 6/22/92 +HGA3 CG331 SG3O1 OG2P1 0.2300 3 0.00 ! MSNA, methyl sulfonate, xhe +HGA3 CG331 SG3O2 CG321 0.0850 3 0.00 ! MESN, methyl ethyl sulfone, xhe +HGA3 CG331 SG3O2 CG331 0.1150 3 0.00 ! DMSN, dimethyl sulfone, xhe +HGA3 CG331 SG3O2 NG311 0.1000 3 0.00 ! MMSM, N-methylmethanesulfonamide; PMSM, N-phenylmethanesulfonamide; xxwy +HGA3 CG331 SG3O2 NG321 0.1900 3 0.00 ! MSAM, methanesulfonamide, xxwy +HGA3 CG331 SG3O2 OG2P1 0.1800 3 0.00 ! DMSN, dimethyl sulfone; MSAM, methanesulfonamide and other sulfonamides; xxwy & xhe +HGA3 CG331 SG3O2 OG303 0.0000 3 0.00 ! MMST, methyl methanesulfonate, xxwy +HGA3 CG331 SG3O3 CG321 0.2000 3 0.00 ! MESO, methylethylsulfoxide; from DMSO, dimethylsulfoxide; mnoon +HGA3 CG331 SG3O3 CG331 0.2000 3 0.00 ! DMSO, dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz +HGA3 CG331 SG3O3 OG2P1 0.2000 3 0.00 ! DMSO, dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz +HGA3 CG334 NG2O1 OG2N1 0.0010 6 0.00 ! NIME, nitromethane, abar +HGA3 CG334 NG2P1 CG2D1 0.1500 3 180.00 ! RETINOL SCH2, Schiff's base, protonated +HGA3 CG334 NG2P1 CG2DC1 0.1500 3 180.00 ! RETINOL SCH2, Schiff's base, protonated +HGA3 CG334 NG2P1 CG2DC2 0.1500 3 180.00 ! RETINOL SCH2, Schiff's base, protonated +HGA3 CG334 NG2P1 CG2N1 0.0000 6 180.00 ! PROT methylguanidinium, adm jr., 3/26/92 +HGA3 CG334 NG2P1 HGP2 0.0000 6 180.00 ! PROT methylguanidinium, adm jr., 3/26/92 +HGP5 CG334 NG3P0 CG324 0.2600 3 0.00 ! LIPID tetramethylammonium +HGP5 CG334 NG3P0 CG334 0.2600 3 0.00 ! LIPID tetramethylammonium +HGP5 CG334 NG3P0 OG311 0.1000 3 0.00 ! TMAOP, Hydroxy(trimethyl)Ammonium, xxwy +HGP5 CG334 NG3P0 OG312 0.3500 3 0.00 ! TMAO, xxwy & ejd +HGA3 CG334 NG3P1 CG324 0.1000 3 0.00 ! FLAVOP PIP1,2,3 +HGA3 CG334 NG3P1 HGP2 0.9000 3 0.00 ! FLAVOP PIP1,2,3 +HGA3 CG334 NG3P3 HGP2 0.0900 3 0.00 ! PROT fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 +HGAAM0 CG3AM0 NG301 CG3AM0 0.3150 3 0.00 ! AMINE aliphatic amines +HGAAM1 CG3AM1 NG311 CG3AM1 0.0800 3 0.00 ! AMINE aliphatic amines +HGAAM1 CG3AM1 NG311 HGPAM1 0.4200 3 0.00 ! AMINE aliphatic amines +HGAAM2 CG3AM2 NG321 HGPAM2 0.1600 3 0.00 ! AMINE aliphatic amines +CG321 CG3C31 CG3C31 OG3C31 0.1100 6 180.00 ! 1BOX, 1-butene oxide; from OG3C31 CG3C31 CG3C31 HGA2 from 1EOX, 1-ethylene oxide; kevo +CG321 CG3C31 CG3C31 HGA2 0.2000 5 180.00 ! 1BOX, 1-butene oxide; from CG324 CG3C31 CG3C31 HGA2 from PROTMOD hf/cyclopropane; sc +CG324 CG3C31 CG3C31 CG3C31 0.1000 6 0.00 ! AMCP, aminomethyl cyclopropane; from PROTMOD hf/cyclopropane; jhs +CG324 CG3C31 CG3C31 HGA2 0.2000 5 180.00 ! AMCP, aminomethyl cyclopropane; from PROTMOD hf/cyclopropane; jhs +CG3C31 CG3C31 CG3C31 HGA1 0.1000 6 0.00 ! AMCP, aminomethyl cyclopropane; from PROTMOD hf/cyclopropane; jhs +CG3C31 CG3C31 CG3C31 HGA2 0.1000 6 0.00 ! PROTMOD hf/cyclopropane +OG3C31 CG3C31 CG3C31 HGA1 0.1100 6 180.00 ! 1BOX, 1-butene oxide; from OG3C31 CG3C31 CG3C31 HGA2 from 1EOX, 1-ethylene oxide; kevo +OG3C31 CG3C31 CG3C31 HGA2 0.1100 6 180.00 ! 1EOX, 1-ethylene oxide, kevo +HGA1 CG3C31 CG3C31 HGA2 0.2000 5 180.00 ! AMCP, aminomethyl cyclopropane; from PROTMOD hf/cyclopropane; jhs +HGA2 CG3C31 CG3C31 HGA2 0.2000 5 180.00 ! PROTMOD hf/cyclopropane +CG3RC1 CG3C31 CG3RC1 CG321 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C31 CG3RC1 CG3C51 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C31 CG3RC1 CG3C52 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C31 CG3RC1 NG2R51 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C31 CG3RC1 NG2R61 0.7000 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C31 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C31 CG3RC1 CG321 0.1950 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C31 CG3RC1 CG3C51 0.1950 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C31 CG3RC1 CG3C52 0.1950 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C31 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C31 CG3RC1 NG2R51 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C31 CG3RC1 NG2R61 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C31 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG3C31 OG3C31 CG3C31 0.6400 5 0.00 ! 1BOX, 1-butene oxide; from HGA2 CG3C31 OG3C31 CG3C31 from 1EOX, 1-ethylene oxide; kevo +CG321 CG3C31 OG3C31 CG3C31 0.8100 6 180.00 ! 1BOX, 1-butene oxide; from HGA2 CG3C31 OG3C31 CG3C31 from 1EOX, 1-ethylene oxide; kevo +HGA1 CG3C31 OG3C31 CG3C31 0.6400 5 0.00 ! 1BOX, 1-butene oxide; from HGA2 CG3C31 OG3C31 CG3C31 from 1EOX, 1-ethylene oxide; kevo +HGA1 CG3C31 OG3C31 CG3C31 0.8100 6 180.00 ! 1BOX, 1-butene oxide; from HGA2 CG3C31 OG3C31 CG3C31 from 1EOX, 1-ethylene oxide; kevo +HGA2 CG3C31 OG3C31 CG3C31 0.6400 5 0.00 ! 1EOX, 1-ethylene oxide, kevo +HGA2 CG3C31 OG3C31 CG3C31 0.8100 6 180.00 ! 1EOX, 1-ethylene oxide, kevo +CG2R53 CG3C41 CG3C41 NG2R43 3.0000 3 0.00 ! AZDO, 2-azetidinone, kevo +CG2R53 CG3C41 CG3C41 HGA2 0.5700 3 0.00 ! AZDO, 2-azetidinone; lsk & kevo +CG3C41 CG3C41 CG3C41 CG3C41 1.4300 3 0.00 ! CBU, cyclobutane; QM by Nikolay Simakov; lsk +CG3C41 CG3C41 CG3C41 HGA2 0.5700 3 0.00 ! CBU, cyclobutane; QM by Nikolay Simakov; lsk +NG2R43 CG3C41 CG3C41 HGA2 0.5700 3 0.00 ! AZDO, 2-azetidinone; lsk & kevo +HGA2 CG3C41 CG3C41 HGA2 0.0000 3 0.00 ! CBU, cyclobutane, kevo +CG3C41 CG3C41 NG2R43 CG2R53 3.0000 3 0.00 ! AZDO, 2-azetidinone, kevo +CG3C41 CG3C41 NG2R43 HGP1 0.2000 3 180.00 ! AZDO, 2-azetidinone, kevo +HGA2 CG3C41 NG2R43 CG2R53 0.5700 3 0.00 ! AZDO, 2-azetidinone; lsk & kevo +HGA2 CG3C41 NG2R43 HGP1 0.0000 3 0.00 ! AZDO, 2-azetidinone, lsk & kevo +CG321 CG3C51 CG3C51 CG3C51 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG321 CG3C51 CG3C51 CG3C52 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG321 CG3C51 CG3C51 NG2S3 0.5000 2 180.00 ! NABAKB phosphoramidates +CG321 CG3C51 CG3C51 NG321 0.3000 3 180.00 ! amines +CG321 CG3C51 CG3C51 OG303 0.8000 3 180.00 ! NA, sugar +CG321 CG3C51 CG3C51 OG303 0.2000 4 0.00 ! NA, sugar +CG321 CG3C51 CG3C51 OG311 0.1400 3 0.00 ! PROT, hydroxyl wild card +CG321 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG331 CG3C51 CG3C51 CG3C51 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG331 CG3C51 CG3C51 CG3C52 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG331 CG3C51 CG3C51 OG303 0.8000 3 180.00 ! NA, sugar +CG331 CG3C51 CG3C51 OG311 0.1400 3 0.00 ! PROT, hydroxyl wild card +CG331 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C51 CG3C51 CG3C51 CG3C51 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C51 CG3C51 CG3C51 CG3C52 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C51 CG3C51 CG3C51 CG3C53 0.4000 6 0.00 ! NA bkb +CG3C51 CG3C51 CG3C51 NG2R51 0.0000 3 0.00 ! NA, glycosyl linkage +CG3C51 CG3C51 CG3C51 NG2R61 0.0000 3 0.00 ! NA, glycosyl linkage +CG3C51 CG3C51 CG3C51 NG301 0.0000 3 0.00 ! NADH, NDPH; Kenno: reverted to uncommented parameter from par_all27_na.prm +CG3C51 CG3C51 CG3C51 OG303 2.0000 3 180.00 ! NA, sugar +CG3C51 CG3C51 CG3C51 OG303 0.4000 5 0.00 ! NA, sugar +CG3C51 CG3C51 CG3C51 OG303 0.8000 6 0.00 ! NA, sugar +CG3C51 CG3C51 CG3C51 OG311 0.2000 3 0.00 ! par22, X CT1 CT2 X; erh 3/08 +CG3C51 CG3C51 CG3C51 OG3C51 0.0000 3 0.00 ! THF, 05/30/06, viv +CG3C51 CG3C51 CG3C51 FGA1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG3C51 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C51 CG3C51 CG3C51 HGA6 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C52 CG3C51 CG3C51 CG3C52 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C52 CG3C51 CG3C51 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3C51 NG2R51 0.0000 3 0.00 ! NA, glycosyl linkage +CG3C52 CG3C51 CG3C51 OG303 0.8000 3 180.00 ! NA, sugar +CG3C52 CG3C51 CG3C51 OG303 0.2000 4 0.00 ! NA, sugar +CG3C52 CG3C51 CG3C51 OG311 0.2000 3 0.00 ! par22, X CT1 CT2 X; erh 3/08 +CG3C52 CG3C51 CG3C51 OG3C51 0.0000 3 0.00 ! THF, 05/30/06, viv +CG3C52 CG3C51 CG3C51 FGA1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG3C52 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C52 CG3C51 CG3C51 HGA6 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C53 CG3C51 CG3C51 OG311 0.1400 3 0.00 ! PROT, hydroxyl wild card +CG3C53 CG3C51 CG3C51 HGA1 0.1950 3 0.00 ! NA, sugar +CG3RC1 CG3C51 CG3C51 OG311 0.6000 1 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 CG3C51 OG311 0.7000 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 CG3C51 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugar +NG2R51 CG3C51 CG3C51 OG303 0.0000 3 0.00 ! NA nadp/nadph +NG2R51 CG3C51 CG3C51 OG311 0.0000 3 0.00 ! NA Guanine and uracil +NG2R51 CG3C51 CG3C51 HGA1 0.0000 3 0.00 ! NA, glycosyl linkage +NG2R61 CG3C51 CG3C51 OG311 0.0000 3 0.00 ! NA Adenine and cytosine +NG2R61 CG3C51 CG3C51 HGA1 0.1950 3 0.00 ! NA nadp/nadph +NG2S3 CG3C51 CG3C51 OG3C51 0.2000 3 0.00 ! NABAKB tphc phosphoramidates +NG2S3 CG3C51 CG3C51 HGA1 0.1950 3 0.00 ! NABAKB tphc phosphoramidates +NG301 CG3C51 CG3C51 OG311 0.0000 3 0.00 ! NADH, NDPH; Kenno: reverted to "Adenine and cytosine" from par_all27_na.prm +NG301 CG3C51 CG3C51 HGA1 0.1950 3 0.00 ! NADH, NDPH; Kenno: reverted to uncommented parameter from par_all27_na.prm +NG321 CG3C51 CG3C51 OG3C51 0.2000 3 0.00 ! NABAKB tphc phosphoramidates +NG321 CG3C51 CG3C51 HGA1 0.1950 3 0.00 ! NABAKB tphc phosphoramidates +OG303 CG3C51 CG3C51 OG311 0.0000 3 0.00 ! NA bkb +OG303 CG3C51 CG3C51 OG3C51 0.2000 3 0.00 ! NA bkb +OG303 CG3C51 CG3C51 OG3C51 0.6000 4 180.00 ! NA bkb +OG303 CG3C51 CG3C51 OG3C51 0.3000 5 0.00 ! NA bkb +OG303 CG3C51 CG3C51 OG3C51 0.5000 6 0.00 ! NA bkb +OG303 CG3C51 CG3C51 FGA1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +OG303 CG3C51 CG3C51 HGA1 0.1950 3 0.00 ! NA, sugar +OG303 CG3C51 CG3C51 HGA6 0.1950 3 0.00 ! NA, sugar +OG311 CG3C51 CG3C51 OG311 0.0000 3 0.00 ! NA bkb +OG311 CG3C51 CG3C51 OG3C51 0.2000 3 0.00 ! NA, sugar +OG311 CG3C51 CG3C51 OG3C51 0.6000 4 180.00 ! NA, sugar +OG311 CG3C51 CG3C51 OG3C51 0.3000 5 0.00 ! NA, sugar +OG311 CG3C51 CG3C51 OG3C51 0.5000 6 0.00 ! NA, sugar +OG311 CG3C51 CG3C51 HGA1 0.1950 3 0.00 ! NA, sugar +OG3C51 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf viv +FGA1 CG3C51 CG3C51 HGA1 0.1850 3 0.00 ! FLUROALK fluoro_alkanes +HGA1 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +HGA1 CG3C51 CG3C51 HGA6 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG2O1 CG3C51 CG3C52 CG3C52 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 CG3C51 CG3C52 HGA2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C51 CG3C52 CG3C52 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C51 CG3C52 HGA2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG3C51 CG3C52 CG3C52 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG311 CG3C51 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG321 CG3C51 CG3C52 CG3C52 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG321 CG3C51 CG3C52 NG3C51 0.0000 3 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from PRLD etc; kevo +CG321 CG3C51 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG331 CG3C51 CG3C52 CG3C52 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG331 CG3C51 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C51 CG3C51 CG3C52 CG3C51 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C51 CG3C51 CG3C52 CG3C52 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C51 CG3C51 CG3C52 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3C51 CG3C52 OG3C51 0.0000 3 0.00 ! THF, 05/30/06, viv +CG3C51 CG3C51 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C52 CG3C51 CG3C52 CG3C52 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C52 CG3C51 CG3C52 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3C52 NG3C51 0.6900 3 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from PRLD etc; kevo +CG3C52 CG3C51 CG3C52 OG3C51 0.0000 3 0.00 ! THF, 05/30/06, viv +CG3C52 CG3C51 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3RC1 CG3C51 CG3C52 CG3C52 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 CG3C52 OG3C51 0.0000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from THF; xxwy +CG3RC1 CG3C51 CG3C52 HGA2 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R51 CG3C51 CG3C52 CG3C51 0.0000 3 0.00 ! NA, glycosyl linkage +NG2R51 CG3C51 CG3C52 CG3C52 0.0000 3 0.00 ! NA, glycosyl linkage +NG2R51 CG3C51 CG3C52 HGA2 0.0000 3 0.00 ! NA, glycosyl linkage +NG2R61 CG3C51 CG3C52 CG3C51 0.0000 3 0.00 ! NA, glycosyl linkage +NG2R61 CG3C51 CG3C52 CG3C52 0.0000 3 0.00 ! NA, glycosyl linkage +NG2R61 CG3C51 CG3C52 HGA2 0.0000 3 0.00 ! NA, glycosyl linkage +NG2S0 CG3C51 CG3C52 CG3C52 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S0 CG3C51 CG3C52 HGA2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG2S3 CG3C51 CG3C52 CG3C51 1.3500 1 180.00 ! NABAKB phosphoramidates +NG2S3 CG3C51 CG3C52 CG3C51 1.0000 2 0.00 ! NABAKB phosphoramidates +NG2S3 CG3C51 CG3C52 CG3C51 0.2000 3 180.00 ! NABAKB phosphoramidates +NG2S3 CG3C51 CG3C52 CG3C52 1.3500 1 180.00 ! NABAKB phosphoramidates +NG2S3 CG3C51 CG3C52 CG3C52 1.0000 2 0.00 ! NABAKB phosphoramidates +NG2S3 CG3C51 CG3C52 CG3C52 0.2000 3 180.00 ! NABAKB phosphoramidates +NG2S3 CG3C51 CG3C52 OG3C51 0.2000 3 0.00 ! NABAKB tphc phosphoramidates +NG2S3 CG3C51 CG3C52 HGA2 0.1950 3 0.00 ! NABAKB tphc phosphoramidates +NG321 CG3C51 CG3C52 CG3C51 0.3000 3 180.00 ! amines +NG321 CG3C51 CG3C52 HGA2 0.1500 3 180.00 ! amines +OG301 CG3C51 CG3C52 CG3C52 2.0000 3 180.00 ! THF2, THF-2'OMe from NA, sugar, ed Kenno: was 1.0 - reset to 2.0 +OG301 CG3C51 CG3C52 CG3C52 0.4000 5 0.00 ! THF2, THF-2'OMe from NA, sugar, ed +OG301 CG3C51 CG3C52 CG3C52 0.8000 6 0.00 ! THF2, THF-2'OMe from NA, sugar, ed +OG301 CG3C51 CG3C52 OG3C51 0.2000 3 0.00 ! THF2, THF-2'OMe, standard parameter, ed +OG301 CG3C51 CG3C52 HGA2 0.1950 3 180.00 ! THF2, THF-2'OMe from NA, sugar, ed. Kenno: was 1.395 - problematic when substituting away hydrogens. +OG303 CG3C51 CG3C52 CG3C51 2.0000 3 180.00 ! NA, sugar +OG303 CG3C51 CG3C52 CG3C51 0.4000 5 0.00 ! NA, sugar +OG303 CG3C51 CG3C52 CG3C51 0.8000 6 0.00 ! NA, sugar +OG303 CG3C51 CG3C52 CG3C52 0.5000 1 180.00 ! NA +OG303 CG3C51 CG3C52 CG3C52 0.7000 2 0.00 ! NA +OG303 CG3C51 CG3C52 CG3C52 0.4000 3 0.00 ! NA +OG303 CG3C51 CG3C52 CG3C52 0.4000 5 0.00 ! NA +OG303 CG3C51 CG3C52 CG3RC1 1.9000 2 0.00 ! CARBOCY carbocyclic sugars +OG303 CG3C51 CG3C52 OG3C51 0.2000 3 0.00 ! NA, sugar +OG303 CG3C51 CG3C52 OG3C51 0.6000 4 180.00 ! NA, sugar +OG303 CG3C51 CG3C52 OG3C51 0.3000 5 0.00 ! NA, sugar +OG303 CG3C51 CG3C52 OG3C51 0.5000 6 0.00 ! NA, sugar +OG303 CG3C51 CG3C52 HGA2 0.1950 3 0.00 ! NA, sugar +OG311 CG3C51 CG3C52 CG3C51 2.0000 3 180.00 ! NA, sugar +OG311 CG3C51 CG3C52 CG3C51 0.4000 5 0.00 ! NA, sugar +OG311 CG3C51 CG3C52 CG3C51 0.8000 6 0.00 ! NA, sugar +OG311 CG3C51 CG3C52 CG3C52 0.5000 1 180.00 ! NA elevates energy at 0 (c3'endo), adm +OG311 CG3C51 CG3C52 CG3C52 0.7000 2 0.00 ! NA elevates energy at 0 (c3'endo), adm +OG311 CG3C51 CG3C52 CG3C52 0.4000 3 0.00 ! NA abasic nucleoside +OG311 CG3C51 CG3C52 CG3C52 0.4000 5 0.00 ! NA abasic nucleoside +OG311 CG3C51 CG3C52 CG3RC1 1.9000 2 0.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3C52 OG3C51 0.2000 3 0.00 ! NA, sugar +OG311 CG3C51 CG3C52 OG3C51 0.6000 4 180.00 ! NA, sugar +OG311 CG3C51 CG3C52 OG3C51 0.3000 5 0.00 ! NA, sugar +OG311 CG3C51 CG3C52 OG3C51 0.5000 6 0.00 ! NA, sugar +OG311 CG3C51 CG3C52 HGA2 0.1950 3 180.00 ! NA, sugar +OG3C51 CG3C51 CG3C52 CG3C51 0.0000 3 0.00 ! THF, 05/30/06, viv +OG3C51 CG3C51 CG3C52 CG3C52 0.0000 3 0.00 ! THF, 05/30/06, viv +OG3C51 CG3C51 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf viv +FGA1 CG3C51 CG3C52 OG3C51 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +FGA1 CG3C51 CG3C52 HGA2 0.1850 3 0.00 ! FLUROALK fluoro_alkanes +HGA1 CG3C51 CG3C52 CG3C51 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +HGA1 CG3C51 CG3C52 CG3C52 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +HGA1 CG3C51 CG3C52 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA1 CG3C51 CG3C52 NG3C51 0.0000 3 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from PRLD etc; kevo +HGA1 CG3C51 CG3C52 OG3C51 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf viv +HGA1 CG3C51 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +HGA6 CG3C51 CG3C52 OG3C51 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf viv +HGA6 CG3C51 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C51 CG3C51 CG3C53 NG2R61 0.0000 3 0.00 ! NA, glycosyl linkage +CG3C51 CG3C51 CG3C53 OG3C51 0.6000 6 0.00 ! NA, sugar +CG3C51 CG3C51 CG3C53 HGA1 0.1950 3 0.00 ! NA, sugar +OG311 CG3C51 CG3C53 NG2R61 0.0000 3 0.00 ! NA Adenine and cytosine +OG311 CG3C51 CG3C53 OG3C51 0.2000 3 0.00 ! NA, sugar +OG311 CG3C51 CG3C53 OG3C51 0.6000 4 180.00 ! NA, sugar +OG311 CG3C51 CG3C53 OG3C51 0.3000 5 0.00 ! NA, sugar +OG311 CG3C51 CG3C53 OG3C51 0.5000 6 0.00 ! NA, sugar +OG311 CG3C51 CG3C53 HGA1 0.1950 3 0.00 ! NA, sugar +HGA1 CG3C51 CG3C53 NG2R61 0.1950 3 0.00 ! NA nadp/nadph +HGA1 CG3C51 CG3C53 OG3C51 0.1950 3 0.00 ! NA, sugar +HGA1 CG3C51 CG3C53 HGA1 0.1950 3 0.00 ! NA, sugar +CG311 CG3C51 CG3RC1 CG311 0.1580 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG311 CG3C51 CG3RC1 CG321 0.0500 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG311 CG3C51 CG3RC1 CG331 0.1580 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG311 CG3C51 CG3RC1 CG3RC1 0.1580 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG321 CG3C51 CG3RC1 CG3C31 2.2000 2 180.00 ! CARBOCY carbocyclic sugars +CG321 CG3C51 CG3RC1 CG3C31 4.0000 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG3C51 CG3RC1 CG3C31 0.5500 6 180.00 ! CARBOCY carbocyclic sugars +CG321 CG3C51 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG3C51 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG331 CG3C51 CG3RC1 CG321 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG3C51 CG3RC1 CG331 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG331 CG3C51 CG3RC1 CG3RC1 0.2000 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG3C51 CG3C51 CG3RC1 CG3C31 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3C51 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3C51 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3RC1 CG311 0.0500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG3C52 CG3C51 CG3RC1 CG321 2.2000 2 180.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3RC1 CG321 4.0000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3RC1 CG321 0.5500 6 180.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3RC1 CG331 0.0500 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG3C52 CG3C51 CG3RC1 CG3C31 2.2000 2 180.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3RC1 CG3C31 4.0000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3RC1 CG3C31 0.5500 6 180.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3RC1 CG3C52 0.0000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; xxwy +CG3C52 CG3C51 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C51 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R51 CG3C51 CG3RC1 CG3C31 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R51 CG3C51 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R51 CG3C51 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R61 CG3C51 CG3RC1 CG3C31 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R61 CG3C51 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R61 CG3C51 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +OG303 CG3C51 CG3RC1 CG3C31 0.4500 2 0.00 ! CARBOCY carbocyclic sugars +OG303 CG3C51 CG3RC1 CG3C31 0.8000 3 180.00 ! CARBOCY carbocyclic sugars +OG303 CG3C51 CG3RC1 CG3C31 0.2000 4 0.00 ! CARBOCY carbocyclic sugars +OG303 CG3C51 CG3RC1 CG3RC1 0.4500 2 0.00 ! CARBOCY carbocyclic sugars +OG303 CG3C51 CG3RC1 CG3RC1 0.9000 6 0.00 ! CARBOCY carbocyclic sugars +OG303 CG3C51 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3RC1 CG321 0.4500 2 0.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3RC1 CG321 0.8000 3 180.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3RC1 CG321 0.2000 4 0.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3RC1 CG3C31 0.4500 2 0.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3RC1 CG3C31 0.8000 3 180.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3RC1 CG3C31 0.2000 4 0.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3RC1 CG3C52 0.4500 2 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from CARBOCY; xxwy +OG311 CG3C51 CG3RC1 CG3RC1 0.4500 2 0.00 ! CARBOCY carbocyclic sugars +OG311 CG3C51 CG3RC1 HGA1 0.1500 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from CARBOCY; xxwy +HGA1 CG3C51 CG3RC1 CG311 0.0500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +HGA1 CG3C51 CG3RC1 CG321 0.1950 3 0.00 ! CARBOCY carbocyclic sugars +HGA1 CG3C51 CG3RC1 CG331 0.0500 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA1 CG3C51 CG3RC1 CG3C31 0.1950 3 0.00 ! CARBOCY carbocyclic sugars +HGA1 CG3C51 CG3RC1 CG3C52 0.1500 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from CARBOCY; xxwy +HGA1 CG3C51 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA1 CG3C51 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3C51 NG2R51 CG2R51 0.2000 4 0.00 ! NA, glycosyl linkage +CG3C51 CG3C51 NG2R51 CG2R53 0.0000 3 180.00 ! NA, glycosyl linkage +CG3C51 CG3C51 NG2R51 CG2RC0 0.0000 3 0.00 ! NA, glycosyl linkage +CG3C52 CG3C51 NG2R51 CG2R51 0.2000 4 0.00 ! NA, glycosyl linkage +CG3C52 CG3C51 NG2R51 CG2R53 0.0000 3 180.00 ! NA, glycosyl linkage +CG3C52 CG3C51 NG2R51 CG2RC0 0.0000 3 0.00 ! NA, glycosyl linkage +CG3RC1 CG3C51 NG2R51 CG2R53 0.5000 1 180.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 NG2R51 CG2RC0 1.1000 1 180.00 ! CARBOCY carbocyclic sugars +OG3C51 CG3C51 NG2R51 CG2R51 0.6000 1 180.00 ! NA, glycosyl linkage 0.5 2 -70 removed by kevo +OG3C51 CG3C51 NG2R51 CG2R51 0.2000 3 0.00 ! NA, glycosyl linkage 0.5 2 -70 removed by kevo +OG3C51 CG3C51 NG2R51 CG2R53 1.1000 1 0.00 ! NA, glycosyl linkage +OG3C51 CG3C51 NG2R51 CG2RC0 1.1000 1 180.00 ! NA, glycosyl linkage +OG3C51 CG3C51 NG2R51 CG2RC0 0.2000 3 0.00 ! NA, glycosyl linkage +HGA1 CG3C51 NG2R51 CG2R51 0.2500 2 180.00 ! NA, glycosyl linkage 0.25 2 180 to compensate for removal of OG3C51 CG3C51 NG2R51 CG2R51 0.5 2 -70 +HGA1 CG3C51 NG2R51 CG2R53 0.2500 2 180.00 ! NA, glycosyl linkage 0.25 2 180 to compensate for removal of OG3C51 CG3C51 NG2R51 CG2R51 0.5 2 -70 +HGA1 CG3C51 NG2R51 CG2R53 0.1950 3 0.00 ! NA, glycosyl linkage +HGA1 CG3C51 NG2R51 CG2RC0 0.2500 2 180.00 ! NA, glycosyl linkage 0.25 2 180 to compensate for removal of OG3C51 CG3C51 NG2R51 CG2R51 0.5 2 -70 +CG3C51 CG3C51 NG2R61 CG2R62 0.0000 3 180.00 ! NA, glycosyl linkage +CG3C51 CG3C51 NG2R61 CG2R63 1.0000 3 0.00 ! NA, glycosyl linkage +CG3C52 CG3C51 NG2R61 CG2R62 0.0000 3 180.00 ! NA, glycosyl linkage +CG3C52 CG3C51 NG2R61 CG2R63 1.0000 3 0.00 ! NA, glycosyl linkage +CG3RC1 CG3C51 NG2R61 CG2R62 0.4000 4 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 NG2R61 CG2R63 1.0000 3 0.00 ! CARBOCY carbocyclic sugars +OG3C51 CG3C51 NG2R61 CG2R62 1.0000 1 0.00 ! NA, glycosyl linkage +OG3C51 CG3C51 NG2R61 CG2R63 0.0000 3 0.00 ! NA, glycosyl linkage +HGA1 CG3C51 NG2R61 CG2R62 0.1950 3 0.00 ! NA, glycosyl linkage +HGA1 CG3C51 NG2R61 CG2R63 0.1950 3 0.00 ! NA, glycosyl linkage +CG2O1 CG3C51 NG2S0 CG2O1 0.8000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 CG3C51 NG2S0 CG3C52 0.1000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C51 NG2S0 CG2O1 0.8000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C51 NG2S0 CG3C52 0.1000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C51 NG2S0 CG2O1 0.8000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C51 NG2S0 CG3C52 0.1000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA1 CG3C51 NG2S0 CG2O1 0.8000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA1 CG3C51 NG2S0 CG3C52 0.1000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG3C51 NG2S3 PG1 1.5000 1 180.00 ! Questionable THNP parameters ignored +CG3C51 CG3C51 NG2S3 PG1 0.6500 2 180.00 ! Questionable THNP parameters ignored +CG3C51 CG3C51 NG2S3 PG1 1.0000 3 0.00 ! Questionable THNP parameters ignored +CG3C51 CG3C51 NG2S3 HGP1 0.3000 1 0.00 ! NABAKB TPHC phosphoramidates +CG3C52 CG3C51 NG2S3 PG1 1.5000 1 180.00 ! Questionable TPHC parameters ignored +CG3C52 CG3C51 NG2S3 PG1 0.6500 2 180.00 ! Questionable TPHC parameters ignored +CG3C52 CG3C51 NG2S3 PG1 1.0000 3 0.00 ! Questionable TPHC parameters ignored +CG3C52 CG3C51 NG2S3 HGP1 0.3000 1 0.00 ! NABAKB TPHC phosphoramidates +HGA1 CG3C51 NG2S3 PG1 0.1500 3 0.00 ! NABAKB TPHC phosphoramidates +HGA1 CG3C51 NG2S3 HGP1 0.0100 3 0.00 ! NABAKB TPHC phosphoramidates +CG3C51 CG3C51 NG301 CG2D1O 0.0000 3 0.00 ! NADH, NDPH; Kenno: reverted to uncommented parameter from par_all27_na.prm +CG3C51 CG3C51 NG301 CG2D2O 0.0000 3 0.00 ! NADH, NDPH; Kenno: reverted to uncommented parameter from par_all27_na.prm +OG3C51 CG3C51 NG301 CG2D1O 0.0000 3 0.00 ! NADH, NDPH; Kenno: reverted to "for NADPH" from par_all27_na.prm +OG3C51 CG3C51 NG301 CG2D2O 0.0000 3 0.00 ! NADH, NDPH; Kenno: reverted to "for NADPH" from par_all27_na.prm +HGA1 CG3C51 NG301 CG2D1O 0.1950 3 0.00 ! NADH, NDPH; Kenno: reverted to uncommented parameter from par_all27_na.prm +HGA1 CG3C51 NG301 CG2D2O 0.1950 3 0.00 ! NADH, NDPH; Kenno: reverted to uncommented parameter from par_all27_na.prm +CG3C51 CG3C51 NG321 HGPAM2 0.3000 3 180.00 ! amines +CG3C52 CG3C51 NG321 HGPAM2 0.3000 3 180.00 ! amines +HGA1 CG3C51 NG321 HGPAM2 0.0100 3 0.00 ! amines +CG3C52 CG3C51 OG301 CG331 0.1000 1 180.00 ! THF2, THF-2'OMe c-C2'-OM-cm, from Nucl. Acids, ed +CG3C52 CG3C51 OG301 CG331 1.6500 2 180.00 ! THF2, THF-2'OMe c-C2'-OM-cm, from Nucl. Acids, ed +CG3C52 CG3C51 OG301 CG331 0.4500 3 0.00 ! THF2, THF-2'OMe c-C2'-OM-cm, from Nucl. Acids, ed +HGA1 CG3C51 OG301 CG331 0.6000 1 0.00 ! THF2, THF-2'OMe h-C2'-OM-cm, from Nucl. Acids, ed +HGA1 CG3C51 OG301 CG331 1.8000 2 180.00 ! THF2, THF-2'OMe h-C2'-OM-cm, from Nucl. Acids, ed +HGA1 CG3C51 OG301 CG331 0.4800 3 0.00 ! THF2, THF-2'OMe h-C2'-OM-cm, from Nucl. Acids, ed +CG3C51 CG3C51 OG303 PG1 2.5000 1 180.00 ! reverted to NA, sugar by kevo +CG3C51 CG3C51 OG303 PG2 2.5000 1 180.00 ! reverted to NA, sugar by kevo +CG3C52 CG3C51 OG303 PG1 2.5000 1 180.00 ! NA, sugar ! verified by kevo +CG3C52 CG3C51 OG303 PG2 2.5000 1 180.00 ! NA, sugar ! verified by kevo +CG3RC1 CG3C51 OG303 PG1 2.4000 1 180.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 OG303 PG1 0.4000 2 180.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 OG303 PG1 1.5000 3 180.00 ! CARBOCY carbocyclic sugars ! phase adjusted for CGenFF by kevo +HGA1 CG3C51 OG303 PG1 0.0000 3 0.00 ! NA, sugar ! verified by kevo +HGA1 CG3C51 OG303 PG2 0.0000 3 0.00 ! NA, sugar ! verified by kevo +CG3C51 CG3C51 OG311 HGP1 0.2900 1 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1 +CG3C51 CG3C51 OG311 HGP1 0.6200 2 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1 +CG3C51 CG3C51 OG311 HGP1 0.0500 3 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1 +CG3C52 CG3C51 OG311 HGP1 0.2900 1 0.00 ! Team sugar, CC3251 CC3152 OC311 HCP1 +CG3C52 CG3C51 OG311 HGP1 0.6200 2 0.00 ! Team sugar, CC3251 CC3152 OC311 HCP1 +CG3C52 CG3C51 OG311 HGP1 0.0500 3 0.00 ! Team sugar, CC3251 CC3152 OC311 HCP1 +CG3C53 CG3C51 OG311 HGP1 0.2900 1 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1 +CG3C53 CG3C51 OG311 HGP1 0.6200 2 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1 +CG3C53 CG3C51 OG311 HGP1 0.0500 3 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1 +CG3RC1 CG3C51 OG311 HGP1 1.5000 1 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 OG311 HGP1 0.3000 2 180.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C51 OG311 HGP1 0.3200 3 0.00 ! CARBOCY carbocyclic sugars; Kenno: empirically corrected for HGA1 CG3C51 OG311 HGP1 from Team sugar ==> re-evaluate. +HGA1 CG3C51 OG311 HGP1 0.1800 3 0.00 ! Team sugar, HCP1 OC311 CC3151 HCA1 +CG321 CG3C51 OG3C51 CG3C51 0.3000 3 0.00 ! THF, 05/30/06, viv +CG321 CG3C51 OG3C51 CG3C52 0.3000 3 0.00 ! THF, 05/30/06, viv +CG321 CG3C51 OG3C51 CG3C53 0.8000 3 0.00 ! NA, sugar +CG331 CG3C51 OG3C51 CG3C51 0.3000 3 0.00 ! THF, 05/30/06, viv +CG331 CG3C51 OG3C51 CG3C52 0.3000 3 0.00 ! THF, 05/30/06, viv +CG3C51 CG3C51 OG3C51 CG3C51 0.5000 3 0.00 ! THF, 05/30/06, viv +CG3C51 CG3C51 OG3C51 CG3C52 0.5000 3 0.00 ! THF, 05/30/06, viv +CG3C51 CG3C51 OG3C51 CG3C53 0.0000 6 0.00 ! NA, sugar +CG3C52 CG3C51 OG3C51 CG3C51 0.5000 3 0.00 ! THF, 05/30/06, viv +CG3C52 CG3C51 OG3C51 CG3C52 0.5000 3 0.00 ! THF, 05/30/06, viv +NG2R51 CG3C51 OG3C51 CG3C51 0.0000 3 0.00 ! NA, sugar +NG2R51 CG3C51 OG3C51 CG3C52 0.0000 3 0.00 ! NA, glycosyl linkage +NG2R61 CG3C51 OG3C51 CG3C51 0.0000 3 0.00 ! NA, glycosyl linkage +NG2R61 CG3C51 OG3C51 CG3C52 0.0000 3 0.00 ! NA, glycosyl linkage +NG301 CG3C51 OG3C51 CG3C51 0.0000 3 0.00 ! NADH, NDPH; Kenno: reverted to uncommented parameter from par_all27_na.prm +HGA1 CG3C51 OG3C51 CG3C51 0.3000 3 0.00 ! THF, 05/30/06, viv +HGA1 CG3C51 OG3C51 CG3C52 0.3000 3 0.00 ! THF, 05/30/06, viv +HGA1 CG3C51 OG3C51 CG3C53 0.1950 3 0.00 ! NA, sugar +CG2R51 CG3C52 CG3C52 CG3C52 3.7000 3 180.00 ! CYPE, cyclopentene, abar & rima +CG2R51 CG3C52 CG3C52 CG3C52 2.2500 4 0.00 ! CYPE, cyclopentene, abar & rima +CG2R51 CG3C52 CG3C52 CG3C52 0.2300 6 180.00 ! CYPE, cyclopentene, abar & rima +CG2R51 CG3C52 CG3C52 NG3C51 1.7000 3 0.00 ! 2PRL, 2-pyrroline, kevo +CG2R51 CG3C52 CG3C52 OG3C51 0.2500 3 180.00 ! 2DHF, 2,3-dihydrofuran, kevo +CG2R51 CG3C52 CG3C52 HGA2 0.1400 3 0.00 ! 2PRL, 2-pyrroline, kevo +CG2R52 CG3C52 CG3C52 NG3C51 0.0000 3 0.00 ! 0 2PRZ, 2-pyrazoline, kevo +CG2R52 CG3C52 CG3C52 HGA2 1.0000 3 0.00 ! 2PRZ, 2-pyrazoline, kevo +CG2R53 CG3C52 CG3C52 CG3C52 0.3400 3 180.00 ! 2PDO, 2-pyrrolidinone, kevo +CG2R53 CG3C52 CG3C52 HGA2 0.0000 3 0.00 ! 2PDO, 2-pyrrolidinone, kevo +CG2RC0 CG3C52 CG3C52 NG3C51 2.4800 3 0.00 ! INDI, indoline, kevo +CG2RC0 CG3C52 CG3C52 HGA2 0.0000 3 0.00 ! INDI, indoline, kevo +CG3C51 CG3C52 CG3C52 CG3C51 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C51 CG3C52 CG3C52 CG3C52 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C51 CG3C52 CG3C52 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3C52 CG3C52 NG3C51 0.6900 3 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from PRLD etc; kevo +CG3C51 CG3C52 CG3C52 OG3C51 0.0000 3 0.00 ! THF, 05/30/06, viv +CG3C51 CG3C52 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C52 CG3C52 CG3C52 CG3C52 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05 +CG3C52 CG3C52 CG3C52 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 CG3C52 NG2R53 2.1300 3 0.00 ! 2PDO, 2-pyrrolidinone, kevo +CG3C52 CG3C52 CG3C52 NG2S0 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 CG3C52 NG3C51 0.6900 3 0.00 ! PRLD, pyrrolidine fit_dihedral run 31, kevo +CG3C52 CG3C52 CG3C52 OG3C51 0.0000 3 0.00 ! THF, 05/30/06, viv +CG3C52 CG3C52 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C53 CG3C52 CG3C52 CG3C54 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C53 CG3C52 CG3C52 HGA2 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C54 CG3C52 CG3C52 CG3C54 0.3700 3 180.00 ! 0.8 3 180 ! 0.15 3 0 PRLP, pyrrolidine.H+, kevo +CG3C54 CG3C52 CG3C52 CG3C54 0.0300 6 180.00 ! 0.31 6 0 ! 0.10 6 0 PRLP, pyrrolidine.H+, kevo +CG3C54 CG3C52 CG3C52 NG3C51 0.0400 3 0.00 ! PRZP, Pyrazolidine.H+, fit_dihedral run 14, kevo +CG3C54 CG3C52 CG3C52 HGA2 0.1600 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3RC1 CG3C52 CG3C52 CG3RC1 0.2100 3 180.00 ! NORB, Norbornane, kevo +CG3RC1 CG3C52 CG3C52 OG3C51 0.0000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from THF; xxwy +CG3RC1 CG3C52 CG3C52 HGA2 0.1950 3 0.00 ! LIPID alkanes +NG2R50 CG3C52 CG3C52 NG3C51 1.0000 3 0.00 ! 0 2IMI, 2-imidazoline ! 1a,1,NCCN+, kevo +NG2R50 CG3C52 CG3C52 HGA2 0.3000 3 0.00 ! 2IMI, 2-imidazoline, kevo +NG2R53 CG3C52 CG3C52 HGA2 0.0000 3 180.00 ! 2PDO, 2-pyrrolidinone, kevo +NG2S0 CG3C52 CG3C52 HGA2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG3C51 CG3C52 CG3C52 HGA2 0.0000 3 0.00 ! 2PRL, 2-pyrroline; 2IMI, 2-imidazoline, kevo +OG3C51 CG3C52 CG3C52 OG3C51 0.2600 3 0.0 ! DIOL, 1,3-Dioxolane fit_dihedral, erh +OG3C51 CG3C52 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf viv +HGA2 CG3C52 CG3C52 HGA2 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv +CG3C52 CG3C52 CG3C53 CG2O1 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 CG3C53 CG2O3 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 CG3C53 NG3P2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 CG3C53 HGA1 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C52 CG3C53 CG2O1 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C52 CG3C53 CG2O3 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C52 CG3C53 NG3P2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C52 CG3C53 HGA1 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2R51 CG3C52 CG3C54 NG3P2 0.6000 3 180.00 ! 0.5 0.4 2PRP, 2-pyrroline.H+, kevo +CG2R51 CG3C52 CG3C54 HGA2 0.1400 3 0.00 ! 2PRL, 2-pyrroline, kevo +CG3C52 CG3C52 CG3C54 NG3P2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 CG3C54 HGA2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG3C51 CG3C52 CG3C54 NG3P2 0.4900 3 0.00 ! IMDP, imidazolidine fit_dihedral, erh +NG3C51 CG3C52 CG3C54 HGA2 0.3700 3 180.00 ! IMDP, imidazolidine fit_dihedral, erh +HGA2 CG3C52 CG3C54 NG3P2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C52 CG3C54 HGA2 0.1400 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG3C52 CG3RC1 CG3C31 4.0000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3C52 CG3RC1 CG3RC1 1.7500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3C52 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 CG3RC1 CG311 0.1000 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG3C52 CG3C52 CG3RC1 CG311 0.5000 4 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG3C52 CG3C52 CG3RC1 CG321 0.2000 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG3C52 CG3C52 CG3RC1 CG3C31 2.2000 2 180.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 CG3RC1 CG3C31 4.0000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 CG3RC1 CG3C31 0.5500 6 180.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 CG3RC1 CG3C51 0.0000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from NORB; xxwy +CG3C52 CG3C52 CG3RC1 CG3C52 0.0000 3 0.00 ! NORB, Norbornane, kevo +CG3C52 CG3C52 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 CG3RC1 NG2R51 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 CG3RC1 NG2R61 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3C52 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3C52 CG3RC1 CG3C52 0.0000 3 0.00 ! NORB, Norbornane, kevo +CG3RC1 CG3C52 CG3RC1 HGA1 0.0000 3 0.00 ! NORB, Norbornane, kevo +HGA2 CG3C52 CG3RC1 CG311 0.1950 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +HGA2 CG3C52 CG3RC1 CG321 0.1950 1 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HGA2 CG3C52 CG3RC1 CG3C31 0.1950 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C52 CG3RC1 CG3C51 0.0000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from NORB; xxwy +HGA2 CG3C52 CG3RC1 CG3C52 0.0000 3 0.00 ! NORB, Norbornane, kevo +HGA2 CG3C52 CG3RC1 CG3RC1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C52 CG3RC1 NG2R51 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C52 CG3RC1 NG2R61 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +HGA2 CG3C52 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG2R51 CG3C52 NG2R50 CG2R52 2.0000 2 180.00 ! 2HPR, 2H-pyrrole !???, kevo +CG3C52 CG3C52 NG2R50 CG2R53 1.9000 3 180.00 ! 2.0 2IMI, 2-imidazoline -1a, kevo +HGA2 CG3C52 NG2R50 CG2R52 0.0000 3 0.00 !x 2HPR, 2H-pyrrole !x, kevo +HGA2 CG3C52 NG2R50 CG2R53 0.6000 3 0.00 ! 2IMI, 2-imidazoline, kevo +CG3C52 CG3C52 NG2R53 CG2R53 2.3100 3 180.00 ! 2PDO, 2-pyrrolidinone, kevo +CG3C52 CG3C52 NG2R53 HGP1 0.7600 3 0.00 ! 2PDO, 2-pyrrolidinone, kevo +HGA2 CG3C52 NG2R53 CG2R53 0.0000 3 0.00 ! 2PDO, 2-pyrrolidinone, kevo +HGA2 CG3C52 NG2R53 HGP1 0.0000 3 180.00 != 2PDO, 2-pyrrolidinone, kevo +CG3C52 CG3C52 NG2S0 CG2O1 0.0000 3 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C52 NG2S0 CG3C51 0.1000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C52 NG2S0 CG2O1 0.0000 3 180.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C52 NG2S0 CG3C51 0.1000 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2R51 CG3C52 NG3C51 CG3C52 2.0500 3 180.00 ! 2.05 2.02 2.05 1.4 1.38 3PRL, 3-pyrroline, kevo +CG2R51 CG3C52 NG3C51 HGP1 1.7700 1 180.00 ! 1.77 1.60 1.0 *new* 3PRL, 3-pyrroline, kevo +CG2R51 CG3C52 NG3C51 HGP1 0.7000 3 0.00 ! 0.70 0.75 0.5 1.10 3PRL, 3-pyrroline, kevo +CG3C51 CG3C52 NG3C51 CG3C52 0.1800 3 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from PRLD etc; kevo +CG3C51 CG3C52 NG3C51 HGP1 0.5500 1 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from PRLD etc; kevo +CG3C51 CG3C52 NG3C51 HGP1 0.8500 3 0.00 ! 3POMP, 3-phenoxymethylpyrrolidine; from PRLD etc; kevo +CG3C52 CG3C52 NG3C51 CG2R51 0.0500 3 180.00 ! 2PRL, 2-pyrroline, kevo +CG3C52 CG3C52 NG3C51 CG2R53 1.9000 3 180.00 ! 1.6 ! 2.5 1.5 2IMI, 2-imidazoline -1a, kevo +CG3C52 CG3C52 NG3C51 CG2RC0 1.4500 3 180.00 ! INDI, indoline, kevo +CG3C52 CG3C52 NG3C51 CG3C52 0.1800 3 0.00 ! PRLD, pyrrolidine fit_dihedral run 31, kevo +CG3C52 CG3C52 NG3C51 NG2R50 2.8000 3 180.00 ! 2.9 2PRZ, 2-pyrazoline, kevo +CG3C52 CG3C52 NG3C51 NG3P2 0.9000 3 0.00 ! PRZP, Pyrazolidine.H+, fit_dihedral run 14, kevo +CG3C52 CG3C52 NG3C51 HGP1 0.5500 1 0.00 ! PRLD, pyrrolidine fit_dihedral run 31, kevo +CG3C52 CG3C52 NG3C51 HGP1 0.8500 3 0.00 ! PRLD, pyrrolidine fit_dihedral run 31, kevo +CG3C54 CG3C52 NG3C51 CG3C54 1.5800 3 180.00 ! IMDP, imidazolidine fit_dihedral, erh +CG3C54 CG3C52 NG3C51 HGP1 1.6500 1 0.00 ! IMDP, imidazolidine fit_dihedral, erh +CG3C54 CG3C52 NG3C51 HGP1 0.7400 3 0.00 ! IMDP, imidazolidine fit_dihedral, erh +HGA2 CG3C52 NG3C51 CG2R51 0.0000 3 0.00 ! 2PRL, 2-pyrroline, kevo +HGA2 CG3C52 NG3C51 CG2R53 0.1000 3 0.00 ! 2IMI, 2-imidazoline, kevo +HGA2 CG3C52 NG3C51 CG2RC0 0.0000 3 0.00 ! INDI, indoline, kevo +HGA2 CG3C52 NG3C51 CG3C52 0.0000 3 0.00 ! 3PRL, 3-pyrroline, kevo +HGA2 CG3C52 NG3C51 CG3C54 0.4800 3 0.00 ! IMDP, imidazolidine fit_dihedral, erh +HGA2 CG3C52 NG3C51 NG2R50 0.3000 3 0.00 ! 2PRZ, 2-pyrazoline, kevo +HGA2 CG3C52 NG3C51 NG3P2 0.0000 3 0.00 ! PRZP, Pyrazolidine.H+, kevo +HGA2 CG3C52 NG3C51 HGP1 0.0000 3 0.00 ! 2PRL, 2-pyrroline, kevo +CG2R51 CG3C52 OG3C51 CG2R53 0.3100 1 180.00 ! B2FO, 5H-furan-2-one, ctsai +CG2R51 CG3C52 OG3C51 CG2R53 0.2800 6 0.00 ! B2FO, 5H-furan-2-one, ctsai +CG3C51 CG3C52 OG3C51 CG3C51 0.5000 3 0.00 ! THF, 05/30/06, viv +CG3C51 CG3C52 OG3C51 CG3C52 0.5000 3 0.00 ! THF, 05/30/06, viv +CG3C51 CG3C52 OG3C51 CG3RC1 0.5000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from THF; xxwy +CG3C52 CG3C52 OG3C51 CG2R51 0.7300 3 0.00 ! 2DHF, 2,3-dihydrofuran, kevo +CG3C52 CG3C52 OG3C51 CG2R53 2.2200 2 0.00 ! GBL, Gamma-butyrolactone, ctsai +CG3C52 CG3C52 OG3C51 CG3C51 0.5000 3 0.00 ! THF, 05/30/06, viv +CG3C52 CG3C52 OG3C51 CG3C52 0.5000 3 0.00 ! THF, 05/30/06, viv +CG3C52 CG3C52 OG3C51 CG3RC1 0.5000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from THF; xxwy +OG3C51 CG3C52 OG3C51 CG2RC0 0.5000 3 0.00 !0.3 ZDOL, 1,3-benzodioxole; from THF, tetrahydofuran; kevo +OG3C51 CG3C52 OG3C51 CG3C52 1.6500 3 180.00 ! DIOL, 1,3-Dioxolane fit_dihedral, erh +HGA2 CG3C52 OG3C51 CG2R51 0.0000 3 0.00 ! 2DHF, 2,3-dihydrofuran, kevo +HGA2 CG3C52 OG3C51 CG2R53 0.0000 3 0.00 ! GBL, from HGA2 CG3C52 OG3C51 CG2R51, ctsai +HGA2 CG3C52 OG3C51 CG2RC0 0.3000 3 0.00 ! ZDOL, 1,3-benzodioxole; from THF, tetrahydofuran; kevo +HGA2 CG3C52 OG3C51 CG3C51 0.3000 3 0.00 ! THF, 05/30/06, viv +HGA2 CG3C52 OG3C51 CG3C52 0.3000 3 0.00 ! THF, 05/30/06, viv +HGA2 CG3C52 OG3C51 CG3RC1 0.3000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from THF; xxwy +CG3C51 CG3C53 NG2R61 CG2R62 0.0000 3 180.00 ! NA, glycosyl linkage +OG3C51 CG3C53 NG2R61 CG2R62 1.0000 1 0.00 ! NA, glycosyl linkage +HGA1 CG3C53 NG2R61 CG2R62 0.1950 3 0.00 ! NA, glycosyl linkage +CG2O1 CG3C53 NG3P2 CG3C54 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O1 CG3C53 NG3P2 HGP2 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C53 NG3P2 CG3C54 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG2O3 CG3C53 NG3P2 HGP2 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C53 NG3P2 CG3C54 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C53 NG3P2 HGP2 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA1 CG3C53 NG3P2 CG3C54 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA1 CG3C53 NG3P2 HGP2 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C51 CG3C53 OG3C51 CG3C51 0.0000 6 0.00 ! NA, sugar +NG2R61 CG3C53 OG3C51 CG3C51 0.0000 3 0.00 ! NA, glycosyl linkage +HGA1 CG3C53 OG3C51 CG3C51 0.1950 3 0.00 ! NA, sugar +NG2R52 CG3C54 CG3C54 NG2R52 0.0700 3 0.00 ! 0 2IMP, 2-imidazoline.H+, kevo +NG2R52 CG3C54 CG3C54 HGA2 0.3000 3 0.00 ! 2IMP, 2-imidazoline.H+, kevo +HGA2 CG3C54 CG3C54 HGA2 0.1400 3 0.00 ! 2IMP, 2-imidazoline.H+ ! RE-OPTIMIZE !!!, kevo +CG2R51 CG3C54 NG2R52 CG2R52 2.8000 2 180.00 ! 2.7 2.3 2HPP, 2H-pyrrole.H+ 1a, kevo +CG2R51 CG3C54 NG2R52 HGP2 2.7000 2 180.00 ! 2HPP, 2H-pyrrole.H+, kevo +CG3C54 CG3C54 NG2R52 CG2R53 0.2500 3 180.00 ! 0.21 2IMP, 2-imidazoline.H+, kevo +CG3C54 CG3C54 NG2R52 HGP2 0.6000 3 0.00 ! 2IMP, 2-imidazoline.H+, kevo +HGA2 CG3C54 NG2R52 CG2R52 0.0000 3 180.00 ! 2HPP, 2H-pyrrole.H+, kevo +HGA2 CG3C54 NG2R52 CG2R53 0.0000 3 180.00 ! 2IMP, 2-imidazoline.H+, kevo +HGA2 CG3C54 NG2R52 HGP2 0.0000 3 0.00 ! 2IMP, 2-imidazoline.H+; 2HPP, 2H-pyrrole.H+, kevo +NG3P2 CG3C54 NG3C51 CG3C52 1.7700 3 0.00 ! IMDP, imidazolidine fit_dihedral, erh +NG3P2 CG3C54 NG3C51 HGP1 1.8400 1 180.00 ! IMDP, imidazolidine fit_dihedral, erh +NG3P2 CG3C54 NG3C51 HGP1 0.9600 3 180.00 ! IMDP, imidazolidine fit_dihedral, erh +HGA2 CG3C54 NG3C51 CG3C52 0.4800 3 0.00 ! IMDP, imidazolidine fit_dihedral, erh +HGA2 CG3C54 NG3C51 HGP1 0.0000 3 0.00 ! IMDP, imidazolidine, erh and kevo +CG2R51 CG3C54 NG3P2 CG3C54 1.8800 3 180.00 ! 1.9 1.5 3PRP, 3-pyrroline.H+, kevo +CG2R51 CG3C54 NG3P2 HGP2 0.3000 3 0.00 ! 3PRP, 3-pyrroline.H+, kevo +CG3C52 CG3C54 NG3P2 CG2R51 0.7000 3 180.00 ! 0.7 2PRP, 2-pyrroline.H+, kevo +CG3C52 CG3C54 NG3P2 CG3C53 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG3C52 CG3C54 NG3P2 CG3C54 0.1000 3 0.00 ! PRLP, pyrrolidine.H+, kevo +CG3C52 CG3C54 NG3P2 NG3C51 0.0400 3 0.00 ! PRZP, Pyrazolidine.H+, fit_dihedral run 14, kevo +CG3C52 CG3C54 NG3P2 HGP2 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +NG3C51 CG3C54 NG3P2 CG3C54 2.7400 3 180.00 ! IMDP, imidazolidine fit_dihedral, erh +NG3C51 CG3C54 NG3P2 HGP2 0.1600 3 180.00 ! IMDP, imidazolidine fit_dihedral, erh +HGA2 CG3C54 NG3P2 CG2R51 0.2000 3 0.00 ! 2PRP, 2-pyrroline.H+, kevo +HGA2 CG3C54 NG3P2 CG3C53 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +HGA2 CG3C54 NG3P2 CG3C54 0.1000 3 0.00 ! PRLP, pyrrolidine.H+, kevo +HGA2 CG3C54 NG3P2 NG3C51 0.1000 3 0.00 ! PRZP, Pyrazolidine.H+, kevo +HGA2 CG3C54 NG3P2 HGP2 0.0800 3 0.00 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD 4/23/93 +CG311 CG3RC1 CG3RC1 CG311 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG311 CG3RC1 CG3RC1 CG321 4.0000 3 0.00 ! CARBOCY carbocyclic sugars +CG311 CG3RC1 CG3RC1 CG331 0.1580 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG311 CG3RC1 CG3RC1 CG3C51 0.1500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 +CG311 CG3RC1 CG3RC1 CG3C52 0.1500 3 0.00 ! CA, Cholic Acid, cacha, 02/08 corrected by kevo +CG311 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG3RC1 CG3RC1 CG321 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG3RC1 CG3RC1 CG331 0.0500 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG321 CG3RC1 CG3RC1 CG3C31 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG3RC1 CG3RC1 CG3C51 0.0500 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG321 CG3RC1 CG3RC1 CG3C52 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG321 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG331 CG3RC1 CG3RC1 CG3C52 0.0500 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG331 CG3RC1 CG3RC1 HGA1 0.0500 3 0.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +CG3C31 CG3RC1 CG3RC1 CG3C51 4.0000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 CG3RC1 CG3C52 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 CG3RC1 NG2R51 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 CG3RC1 NG2R61 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3RC1 CG3RC1 CG3C52 4.0000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C51 CG3RC1 CG3RC1 OG3C51 1.2000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; xxwy +CG3C51 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 CG3RC1 CG3C52 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 CG3RC1 NG2R51 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 CG3RC1 NG2R61 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 CG3RC1 OG3C51 1.2000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; xxwy +CG3C52 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R51 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +NG2R61 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +OG3C51 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from CARBOCY; xxwy +HGA1 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 NG2R51 CG2R53 1.1000 1 180.00 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 NG2R51 CG2RC0 0.3000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 NG2R51 CG2R53 0.1000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 NG2R51 CG2RC0 0.3000 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3RC1 NG2R51 CG2R53 1.1000 1 180.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3RC1 NG2R51 CG2RC0 1.1000 1 180.00 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 NG2R61 CG2R62 0.0000 3 180.00 ! CARBOCY carbocyclic sugars +CG3C31 CG3RC1 NG2R61 CG2R63 0.3000 3 0.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 NG2R61 CG2R62 0.0000 3 180.00 ! CARBOCY carbocyclic sugars +CG3C52 CG3RC1 NG2R61 CG2R63 0.3000 3 0.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3RC1 NG2R61 CG2R62 0.0000 3 180.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3RC1 NG2R61 CG2R63 0.2000 3 180.00 ! CARBOCY carbocyclic sugars +CG3RC1 CG3RC1 OG3C51 CG3C52 0.0000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; xxwy +OG3C51 CG3RC1 OG3C51 CG3C52 0.0000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; xxwy +HGA1 CG3RC1 OG3C51 CG3C52 0.3000 3 0.00 ! RSRF, 4,6-dioxabicyclo[3.3.0]octan-8-ol; from THF; xxwy +CG2D1 NG2D1 NG2S1 CG2O1 3.4000 1 180.00 ! HDZ1, hydrazone model cmpd +CG2D1 NG2D1 NG2S1 CG2O1 1.3000 2 180.00 ! HDZ1, hydrazone model cmpd +CG2D1 NG2D1 NG2S1 HGP1 2.5000 2 180.00 ! HDZ1, hydrazone model cmpd +CG2DC1 NG2D1 NG2S1 CG2O1 3.4000 1 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC1 NG2D1 NG2S1 CG2O1 1.3000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC1 NG2D1 NG2S1 HGP1 2.5000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC2 NG2D1 NG2S1 CG2O1 3.4000 1 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC2 NG2D1 NG2S1 CG2O1 1.3000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2DC2 NG2D1 NG2S1 HGP1 2.5000 2 180.00 ! HDZ2, hydrazone model cmpd 2 +CG2R51 NG2R50 NG2R50 NG2R51 14.0000 2 180.00 ! TRZ3, triazole123 +CG2R51 NG2R50 NG2R50 OG2R50 14.0000 2 180.00 ! OXAD, oxadiazole123 +CG2R52 NG2R50 NG2R51 CG2R51 12.0000 2 180.00 ! PYRZ, pyrazole +CG2R52 NG2R50 NG2R51 CG2RC0 8.5000 2 180.00 ! INDA, 1H-indazole, kevo +CG2R52 NG2R50 NG2R51 NG2R50 9.5000 2 180.00 ! TRZ2, 2H-1,2,3-triazole, lf +CG2R52 NG2R50 NG2R51 HGP1 1.4000 2 180.00 ! PYRZ, pyrazole +CG2R53 NG2R50 NG2R51 CG2R53 10.0000 2 180.00 ! TRZ4, triazole124, xxwy +CG2R53 NG2R50 NG2R51 HGP1 2.3000 2 180.00 ! TRZ4, triazole124, xxwy +NG2R50 NG2R50 NG2R51 CG2R51 8.5000 2 180.00 ! TRZ3, triazole123 +NG2R50 NG2R50 NG2R51 CG321 2.5000 2 180.00 ! ETRZ, 1-Ethyl-1,2,3-triazole, from NG2R50 NG2R50 NG2R51 HGP1, kevo +NG2R50 NG2R50 NG2R51 HGP1 2.5000 2 180.00 ! TRZ3, triazole123 +CG2R52 NG2R50 NG3C51 CG3C52 0.5000 2 180.00 ! 9 2PRZ, 2-pyrazoline, kevo +CG2R52 NG2R50 NG3C51 HGP1 0.2500 3 0.00 ! 0.7 1.3 2PRZ, 2-pyrazoline, kevo +CG2R52 NG2R50 OG2R50 CG2R51 12.0000 2 180.00 ! ISOX, isoxazole +CG2R53 NG2R50 OG2R50 CG2R53 9.0000 2 180.00 ! OXD4, oxadiazole124, xxwy +NG2R50 NG2R50 OG2R50 CG2R51 8.5000 2 180.00 ! OXAD, oxadiazole123 +CG2R52 NG2R50 SG2R50 CG2R51 9.0000 2 180.00 ! ISOT, isothiazole +CG2R51 NG2R57 NG2R57 CG2R51 0.3000 2 000.00 ! 11BPO, 1,1-bipyrrole, lf +CG2R61 NG2R62 NG2R62 CG2R61 1.2000 2 180.00 ! PYRD, pyridazine +CG2R61 NG2R62 NG2R62 CG2R64 0.5000 2 180.00 ! TRIB, triazine124 +CG331 NG2S3 PG1 OG2P1 0.4000 3 0.00 ! NABAKB phosphoramidates +CG331 NG2S3 PG1 OG2P1 0.5000 4 0.00 ! NABAKB phosphoramidates +CG331 NG2S3 PG1 OG303 1.9000 2 0.00 ! NABAKB phosphoramidates ! eliminated 0.8 2 120 for OG2P1 and compensated 1.5 -> 1.9 here +CG3C51 NG2S3 PG1 OG2P1 0.4000 3 0.00 ! NABAKB phosphoramidates +CG3C51 NG2S3 PG1 OG2P1 0.5000 4 0.00 ! NABAKB phosphoramidates +CG3C51 NG2S3 PG1 OG303 1.9000 2 0.00 ! NABAKB phosphoramidates ! eliminated 0.8 2 120 for OG2P1 and compensated 1.5 -> 1.9 here +HGP1 NG2S3 PG1 OG2P1 0.0500 3 0.00 ! NABAKB phosphoramidates +HGP1 NG2S3 PG1 OG303 0.0500 3 0.00 ! NABAKB phosphoramidates +CG321 NG2S3 SG3O1 OG2P1 0.5520 3 0.00 ! NESM, N-ethyl-sulfamate, my & kevo +CG331 NG2S3 SG3O1 OG2P1 0.5370 3 0.00 ! NMSM, N-methyl-sulfamate, my +HGP1 NG2S3 SG3O1 OG2P1 0.0500 3 0.00 ! NMSM, N-methyl-sulfamate; from HGP1 NG2S3 PG1 OG2P1; my +CG2R61 NG311 SG3O2 CG2R61 1.2000 1 180.00 ! PBSM, N-phenylbenzenesulfonamide, xxwy +CG2R61 NG311 SG3O2 CG2R61 1.4000 2 0.00 ! PBSM, N-phenylbenzenesulfonamide, xxwy +CG2R61 NG311 SG3O2 CG331 2.2000 2 0.00 ! PMSM, N-phenylmethanesulfonamide, xxwy +CG2R61 NG311 SG3O2 CG331 0.2000 3 0.00 ! PMSM, N-phenylmethanesulfonamide, xxwy +CG2R61 NG311 SG3O2 OG2P1 0.2000 3 0.00 ! PMSM, N-phenylmethanesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +CG321 NG311 SG3O2 CG2R61 1.5000 2 0.00 ! OBTZ, sulfonamide heterocycle in drug HCTZ, xxwy +CG321 NG311 SG3O2 CG2R61 0.5000 3 0.00 ! OBTZ, sulfonamide heterocycle in drug HCTZ, xxwy +CG321 NG311 SG3O2 CG321 2.0000 2 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG321 NG311 SG3O2 CG321 0.3000 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG321 NG311 SG3O2 CG331 2.0000 2 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +CG321 NG311 SG3O2 CG331 0.3000 3 0.00 ! AOBT, acyclic model introduced for OBTZ to optimize related dihedrals, xxwy +CG321 NG311 SG3O2 NG311 0.9020 1 180.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG321 NG311 SG3O2 NG311 0.6350 2 0.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG321 NG311 SG3O2 NG311 1.4440 3 0.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG321 NG311 SG3O2 NG311 0.3320 4 180.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG321 NG311 SG3O2 OG2P1 0.2000 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +CG331 NG311 SG3O2 CG2R61 1.5000 2 0.00 ! MBSM, N-methylbenzenesulfonamide, xxwy +CG331 NG311 SG3O2 CG2R61 0.5000 3 0.00 ! MBSM, N-methylbenzenesulfonamide, xxwy +CG331 NG311 SG3O2 CG331 2.0000 2 0.00 ! MMSM, N-methylmethanesulfonamide, xxwy +CG331 NG311 SG3O2 CG331 0.2000 3 0.00 ! MMSM, N-methylmethanesulfonamide, xxwy +CG331 NG311 SG3O2 NG311 1.2560 1 180.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG331 NG311 SG3O2 NG311 0.6240 2 0.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG331 NG311 SG3O2 NG311 1.8260 3 0.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG331 NG311 SG3O2 NG311 0.2140 4 180.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG331 NG311 SG3O2 NG311 0.2630 6 180.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +CG331 NG311 SG3O2 OG2P1 0.2000 3 0.00 ! MMSM, N-methylmethanesulfonamide; MBSM, N-methylbenzenesulfonamide; xxwy +HGP1 NG311 SG3O2 CG2R61 1.2000 1 180.00 ! MBSM, N-methylbenzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +HGP1 NG311 SG3O2 CG2R61 1.1000 2 0.00 ! MBSM, N-methylbenzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +HGP1 NG311 SG3O2 CG2R61 0.5000 3 0.00 ! MBSM, N-methylbenzenesulfonamide; PBSM, N-phenylbenzenesulfonamide; xxwy +HGP1 NG311 SG3O2 CG321 1.3000 1 180.00 ! EESM, N-ethylethanesulfonamide, xxwy +HGP1 NG311 SG3O2 CG321 1.2000 2 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +HGP1 NG311 SG3O2 CG321 0.2000 3 0.00 ! EESM, N-ethylethanesulfonamide, xxwy +HGP1 NG311 SG3O2 CG331 1.0000 1 180.00 ! MMSM, N-methylmethanesulfonamide; PMSM, N-phenylmethanesulfonamide; xxwy +HGP1 NG311 SG3O2 CG331 1.1000 2 0.00 ! MMSM, N-methylmethanesulfonamide; PMSM, N-phenylmethanesulfonamide; xxwy +HGP1 NG311 SG3O2 CG331 0.2000 3 0.00 ! MMSM, N-methylmethanesulfonamide; PMSM, N-phenylmethanesulfonamide; xxwy +HGP1 NG311 SG3O2 NG311 0.5750 1 180.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +HGP1 NG311 SG3O2 NG311 1.0830 2 0.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +HGP1 NG311 SG3O2 NG311 0.9590 3 180.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +HGP1 NG311 SG3O2 NG311 0.1990 4 180.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +HGP1 NG311 SG3O2 NG311 0.2380 6 0.00 ! MESI, N-methyl,N'-ethylsulfamide, rting +HGP1 NG311 SG3O2 OG2P1 0.2000 3 0.00 ! MMSM, N-methylmethanesulfonamide and other sulfonamides, xxwy +HGP1 NG321 SG3O2 CG2R61 1.5000 1 180.00 ! BSAM, benzenesulfonamide, xxwy +HGP1 NG321 SG3O2 CG2R61 1.2000 2 0.00 ! BSAM, benzenesulfonamide, xxwy +HGP1 NG321 SG3O2 CG2R61 0.1000 3 0.00 ! BSAM, benzenesulfonamide, xxwy +HGP1 NG321 SG3O2 CG331 0.9000 1 180.00 ! MSAM, methanesulfonamide, xxwy +HGP1 NG321 SG3O2 CG331 1.6000 2 0.00 ! MSAM, methanesulfonamide, xxwy +HGP1 NG321 SG3O2 CG331 0.1000 3 0.00 ! MSAM, methanesulfonamide, xxwy +HGP1 NG321 SG3O2 OG2P1 0.2000 3 0.00 ! MSAM, methanesulfonamide; BSAM, benzenesulfonamide; xxwy +HGP1 NG321 SG3O2 OG303 0.4000 3 0.00 ! MSMT, methyl sulfamate, PSMT, phenyl sulfamate, xxwy +CG3C52 NG3C51 NG3P2 CG3C54 1.0200 3 0.00 ! PRZP, Pyrazolidine.H+, fit_dihedral run 14, kevo +CG3C52 NG3C51 NG3P2 HGP2 0.0800 3 0.00 ! PRZP, Pyrazolidine.H+, kevo +HGP1 NG3C51 NG3P2 CG3C54 2.4500 1 0.00 ! PRZP, Pyrazolidine.H+, fit_dihedral run 14, kevo +HGP1 NG3C51 NG3P2 CG3C54 0.0200 3 0.00 ! PRZP, Pyrazolidine.H+, fit_dihedral run 14, kevo +HGP1 NG3C51 NG3P2 HGP2 0.0000 3 0.00 ! PRZP, Pyrazolidine.H+, kevo +CG2R61 NG3N1 NG3N1 HGP1 1.6000 2 180.00 ! PHHZ, phenylhydrazine, ed +HGP1 NG3N1 NG3N1 HGP1 1.1000 1 180.00 ! HDZN, hydrazine, ed +HGP1 NG3N1 NG3N1 HGP1 4.5000 2 0.00 ! HDZN, hydrazine, ed +HGP1 NG3N1 NG3N1 HGP1 0.0500 3 0.00 ! HDZN, hydrazine, ed +CG334 NG3P0 OG311 HGP1 0.2770 3 0.00 ! TMAOP, Hydroxy(trimethyl)Ammonium, xxwy +CG331 OG303 PG0 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization:MP_0 RE-OPTIMIZE! +CG331 OG303 PG0 OG311 0.9500 2 0.00 ! NA MP_1, adm jr. !Reorganization:MP_0 RE-OPTIMIZE! +CG331 OG303 PG0 OG311 0.5000 3 0.00 ! NA MP_1, adm jr. !Reorganization:MP_0 RE-OPTIMIZE! +CG2R61 OG303 PG1 OG2P1 0.1000 3 0.00 ! PROTNA phenol phosphate, 6/94, adm jr. +CG2R61 OG303 PG1 OG311 0.9500 2 0.00 ! PROTNA phenol phosphate, 6/94, adm jr. +CG2R61 OG303 PG1 OG311 0.5000 3 0.00 ! PROTNA phenol phosphate, 6/94, adm jr. +CG321 OG303 PG1 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization: PC and others +CG321 OG303 PG1 OG303 1.2000 1 180.00 ! NA 10/97, DMP, adm jr. !Reorganization: PC and others +CG321 OG303 PG1 OG303 0.1000 2 180.00 ! NA 10/97, DMP, adm jr. !Reorganization: PC and others +CG321 OG303 PG1 OG303 0.1000 3 180.00 ! NA 10/97, DMP, adm jr. !Reorganization: PC and others +CG321 OG303 PG1 OG304 1.2000 1 180.00 ! NA dmp !Reorganization:ADP +CG321 OG303 PG1 OG304 0.1000 2 180.00 ! NA dmp !Reorganization:ADP +CG321 OG303 PG1 OG304 0.1000 3 180.00 ! NA dmp !Reorganization:ADP +CG321 OG303 PG1 OG311 0.9500 2 0.00 ! NA MP_1, adm jr. +CG321 OG303 PG1 OG311 0.5000 3 0.00 ! NA MP_1, adm jr. +CG331 OG303 PG1 NG2S3 0.4000 1 0.00 ! NABAKB phosphoramidates +CG331 OG303 PG1 NG2S3 0.2600 2 0.00 ! NABAKB phosphoramidates ! changed 0.4 2 50 into 0.4cos(50)=0.26 2 0 +CG331 OG303 PG1 NG2S3 0.3500 3 0.00 ! NABAKB phosphoramidates +CG331 OG303 PG1 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization:MP_1 +CG331 OG303 PG1 OG303 1.2000 1 180.00 ! NA dmp !Reorganization: PC and others +CG331 OG303 PG1 OG303 0.1000 2 180.00 ! NA dmp !Reorganization: PC and others +CG331 OG303 PG1 OG303 0.1000 3 180.00 ! NA dmp !Reorganization: PC and others +CG331 OG303 PG1 OG304 1.2000 1 180.00 ! NA dmp !Reorganization:PPI1 +CG331 OG303 PG1 OG304 0.1000 2 180.00 ! NA dmp !Reorganization:PPI1 +CG331 OG303 PG1 OG304 0.1000 3 180.00 ! NA dmp !Reorganization:PPI1 +CG331 OG303 PG1 OG311 0.9500 2 0.00 ! NA MP_1, adm jr. !Reorganization:MP_1 +CG331 OG303 PG1 OG311 0.5000 3 0.00 ! NA MP_1, adm jr. !Reorganization:MP_1 +CG3C51 OG303 PG1 OG2P1 0.1000 3 0.00 ! BPNP and others dmp,eps, O1P-P-O3'-C3' +CG3C51 OG303 PG1 OG303 1.2000 1 180.00 ! BPNP and others 10/97, DMP, adm jr. +CG3C51 OG303 PG1 OG303 0.1000 2 180.00 ! BPNP and others 10/97, DMP, adm jr. +CG3C51 OG303 PG1 OG303 0.1000 3 180.00 ! BPNP and others 10/97, DMP, adm jr. +CG3C51 OG303 PG1 OG311 0.9500 2 0.00 ! NA T3PH, adm jr. +CG3C51 OG303 PG1 OG311 0.5000 3 0.00 ! NA T3PH, adm jr. +CG311 OG303 PG2 OG2P1 0.1000 3 0.00 ! IP_2 NA dmp,eps, O1P-P-O3'-C3' +CG321 OG303 PG2 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization: TH5P and others +CG331 OG303 PG2 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization:MP_2 +CG3C51 OG303 PG2 OG2P1 0.1000 3 0.00 ! TH3P and others dmp,eps, O1P-P-O3'-C3' +CG321 OG303 SG3O1 OG2P1 0.0000 3 0.00 ! LIPID methylsulfate +CG331 OG303 SG3O1 OG2P1 0.0000 3 0.00 ! LIPID methylsulfate +CG2R61 OG303 SG3O2 CG331 1.6000 1 180.00 ! PMST, phenyl methanesulfonate, xxwy +CG2R61 OG303 SG3O2 CG331 0.8000 2 0.00 ! PMST, phenyl methanesulfonate, xxwy +CG2R61 OG303 SG3O2 CG331 0.1000 3 0.00 ! PMST, phenyl methanesulfonate, xxwy +CG2R61 OG303 SG3O2 NG321 3.2000 1 180.00 ! PSMT, phenyl sulfamate, xxwy +CG2R61 OG303 SG3O2 NG321 0.2000 2 0.00 ! PSMT, phenyl sulfamate, xxwy +CG2R61 OG303 SG3O2 NG321 0.2000 3 0.00 ! PSMT, phenyl sulfamate, xxwy +CG2R61 OG303 SG3O2 OG2P1 0.3000 3 0.00 ! PMST, phenyl methanesulfonate, PSMT, phenyl sulfamate, xxwy +CG331 OG303 SG3O2 CG331 1.1000 1 180.00 ! MMST, methyl methanesulfonate, xxwy +CG331 OG303 SG3O2 CG331 0.7000 2 0.00 ! MMST, methyl methanesulfonate, xxwy +CG331 OG303 SG3O2 CG331 0.3000 3 0.00 ! MMST, methyl methanesulfonate, xxwy +CG331 OG303 SG3O2 NG321 1.8000 1 180.00 ! MSMT, methyl sulfamate, xxwy +CG331 OG303 SG3O2 NG321 0.5000 2 0.00 ! MSMT, methyl sulfamate, xxwy +CG331 OG303 SG3O2 NG321 0.4000 3 0.00 ! MSMT, methyl sulfamate, xxwy +CG331 OG303 SG3O2 OG2P1 0.3000 3 0.00 ! MMST, methyl methanesulfonate, xxwy +PG1 OG304 PG1 OG2P1 0.1000 2 0.00 ! NA ppi2 !Reorganization:PPI2 +PG1 OG304 PG1 OG2P1 0.0300 3 0.00 ! NA ppi2 !Reorganization:PPI2 +PG1 OG304 PG1 OG303 0.0300 2 0.00 ! NA ppi2 !Reorganization:PPI2 +PG1 OG304 PG1 OG303 0.0300 3 0.00 ! NA ppi2 !Reorganization:PPI2 +PG1 OG304 PG1 OG304 0.0300 2 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize? +PG1 OG304 PG1 OG304 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize? +PG1 OG304 PG1 OG311 0.1000 2 0.00 ! NA ppi2 !Reorganization:PPI2 +PG1 OG304 PG1 OG311 0.0300 3 0.00 ! NA ppi2 !Reorganization:PPI2 +PG2 OG304 PG1 OG2P1 0.1000 2 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1 +PG2 OG304 PG1 OG2P1 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1 +PG2 OG304 PG1 OG303 0.0300 2 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1 +PG2 OG304 PG1 OG303 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1 +PG2 OG304 PG1 OG304 0.0300 2 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize? +PG2 OG304 PG1 OG304 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize? +PG1 OG304 PG2 OG2P1 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1 +HGP1 OG311 PG0 OG2P1 0.3000 3 0.00 ! NA MP_1, adm jr. !Reorganization:MP_0 RE-OPTIMIZE! +HGP1 OG311 PG0 OG303 1.6000 1 180.00 ! PROTNA phenol phosphate !Reorganization:MP_0 RE-OPTIMIZE! +HGP1 OG311 PG0 OG303 0.9000 2 0.00 ! PROTNA phenol phosphate !Reorganization:MP_0 RE-OPTIMIZE! +HGP1 OG311 PG0 OG311 0.3000 3 0.00 ! NA MP_0, adm jr. +HGP1 OG311 PG1 CG312 0.2000 1 180.00 ! BDFP, BDFD, Difuorobenzylphosphonate +HGP1 OG311 PG1 CG312 1.6000 2 0.00 ! BDFP, BDFD, Difuorobenzylphosphonate +HGP1 OG311 PG1 CG321 0.6000 1 180.00 ! BDFP, BDFD, Benzylphosphonate +HGP1 OG311 PG1 CG321 1.1000 2 0.00 ! BDFP, BDFD, Benzylphosphonate +HGP1 OG311 PG1 OG2P1 0.3000 3 0.00 ! NA MP_1, adm jr. !Reorganization:MP_1 +HGP1 OG311 PG1 OG303 1.6000 1 180.00 ! PROTNA phenol phosphate !Reorganization:MP_1 +HGP1 OG311 PG1 OG303 0.9000 2 0.00 ! PROTNA phenol phosphate !Reorganization:MP_1 +HGP1 OG311 PG1 OG304 1.6000 1 180.00 ! PROTNA phenol phosphate !Reorganization:PPI2 +HGP1 OG311 PG1 OG304 0.9000 2 0.00 ! PROTNA phenol phosphate !Reorganization:PPI2 +CG321 SG301 SG301 CG321 1.0000 1 0.00 ! PROT DMDS 5/15/92 (FL) +CG321 SG301 SG301 CG321 4.1000 2 0.00 ! PROT mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CG321 SG301 SG301 CG321 0.9000 3 0.00 ! PROT DMDS 5/15/92 (FL) +CG321 SG301 SG301 CG331 1.0000 1 0.00 ! PROT DMDS 5/15/92 (FL) +CG321 SG301 SG301 CG331 4.1000 2 0.00 ! PROT mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CG321 SG301 SG301 CG331 0.9000 3 0.00 ! PROT DMDS 5/15/92 (FL) +CG331 SG301 SG301 CG331 1.0000 1 0.00 ! PROT DMDS 5/15/92 (FL) +CG331 SG301 SG301 CG331 4.1000 2 0.00 ! PROT mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CG331 SG301 SG301 CG331 0.9000 3 0.00 ! PROT DMDS 5/15/92 (FL) + +IMPROPERS +!! -------------------------------------------------------------------------- ! +!! Rules: - The multiplicity of impropers should always be 0 so that a harmonic ! +!! potential is used rather than a cosine function. ! +!! - The phase of impropers should always be 0. Due to an algorithmic ! +!! quirk, Discontinuities will occur if CHARMM is given a harmonic potential ! +!! with a phase other than 0. ! +!! - The first atom in the definition should always be the central atom ! +!! to which the three other atoms are connected. Otherwise, the planar ! +!! structure will be a maximum in the potential instead of a minimum. ! +!! -------------------------------------------------------------------------- ! +CG2D1 CG331 NG2D1 HGA4 25.0000 0 0.00 ! SCH1, xxwy +CG2D1 CG331 NG2P1 HGR52 18.0000 0 0.00 ! SCH2, xxwy +CG2D1O CG2D1 NG301 HGA4 53.0000 0 0.00 ! NA NICH, adm jr. WILDCARD +CG2D1O CG2D1 NG311 HGA4 53.0000 0 0.00 ! NA NICH, adm jr. WILDCARD +CG2D1O CG2D2 NG321 HGA4 53.0000 0 0.00 ! AMET, ethenamine, from NA NICH WILDCARD; pram +CG2D1O CG2D2 OG301 HGA4 23.0000 0 0.00 ! MOET, Methoxyethene, xxwy +CG2D1O CG2DC1 NG301 HGA4 53.0000 0 0.00 ! NA NICH, adm jr. WILDCARD +CG2D1O CG2DC1 NG311 HGA4 53.0000 0 0.00 ! NA NICH, adm jr. WILDCARD +CG2D1O CG2DC1 OG301 HGA4 10.0000 0 0.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2D2O CG2D1 NG301 HGA4 53.0000 0 0.00 ! NA NICH, adm jr. WILDCARD +CG2D2O CG2D1 NG311 HGA4 53.0000 0 0.00 ! NA NICH, adm jr. WILDCARD +CG2D2O CG2D2 NG321 HGA4 53.0000 0 0.00 ! AMET, ethenamine, from NA NICH WILDCARD; pram +CG2D2O CG2D2 OG301 HGA4 23.0000 0 0.00 ! MOET, Methoxyethene, xxwy +CG2D2O CG2DC2 NG301 HGA4 53.0000 0 0.00 ! NA NICH, adm jr. WILDCARD +CG2D2O CG2DC2 NG311 HGA4 53.0000 0 0.00 ! NA NICH, adm jr. WILDCARD +CG2D2O CG2DC2 OG301 HGA4 10.0000 0 0.00 ! MOBU, 1-Methoxy-1,3-butadiene, xxwy +CG2DC1 CG2R61 NG2D1 HGA4 30.0000 0 0.00 ! HDZ1B, xxwy +CG2DC1 CG2DC2 NG2P1 HGR52 13.0000 0 0.00 ! SCH3, xxwy +CG2DC2 CG2R61 NG2D1 HGA4 30.0000 0 0.00 ! HDZ1B, xxwy +CG2DC2 CG2DC1 NG2P1 HGR52 13.0000 0 0.00 ! SCH3, xxwy +CG2N1 NG321 NG321 NG2D1 85.0000 0 0.00 ! MGU1, methylguanidine +CG2N1 NG2P1 NG2P1 NG2P1 40.0000 0 0.00 ! PROT 5.75->40.0 GUANIDINIUM (KK) +CG2N1 NG2D1 NG311 NG321 85.0000 0 0.00 ! MGU2, methylguanidine2 +CG2N2 NG2P1 NG2P1 CG2R61 30.0000 0 0.00 ! BAMI, benzamidinium; from AMDN, amidinium; pram +CG2N2 NG2P1 NG2P1 CG331 30.0000 0 0.00 ! AMDN, amidinium, sz (verified by pram) +CG2N2 NG2D1 NG321 SG311 32.0000 0 0.00 ! MT2A, fylin +CG2O1 CG2DC1 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG2DC1 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG2DC2 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG2DC2 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG2R61 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG2R61 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG2R62 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG311 NG2S0 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG311 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG311 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG311 NG311 OG2D1 120.0000 0 0.00 ! AMS1, xxwy, from PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG321 NG2S0 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG321 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG321 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG331 NG2S0 OG2D1 71.0000 0 0.00 ! DMA, Dimethylacetamide, xxwy +CG2O1 CG331 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG331 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG3C51 NG2S0 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG3C51 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG3C51 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG3C53 NG2S0 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG3C53 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 CG3C53 NG2S2 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK) WILDCARD +CG2O1 NG2S0 OG2D1 HGR52 50.0000 0 0.00 ! DMF, Dimethylformamide, xxwy +CG2O1 NG2S2 OG2D1 HGR52 66.0000 0 0.00 ! FORM, formamide, xxwy +CG2O2 CG2R61 OG2D1 OG302 72.0000 0 0.00 ! MBOA, methyl benzoate; MOLVIB looks good; jal +CG2O2 CG311 OG2D1 OG302 62.0000 0 0.00 ! PROT & LIPID WILDCARD; from MAS, methyl acetate; xxwy +CG2O2 CG321 OG2D1 OG302 62.0000 0 0.00 ! PROT & LIPID WILDCARD; from MAS, methyl acetate; xxwy +CG2O2 CG331 OG2D1 OG302 62.0000 0 0.00 ! MAS, methyl acetate, xxwy +CG2O2 CG2R61 OG2D1 OG311 53.0000 0 0.00 ! ZOIC, benzoic acid; MOLVIB 1% low (55 would be spot on); jal +CG2O2 CG311 OG2D1 OG311 65.0000 0 0.00 ! PROT & LIPID WILDCARD; ACEH, acetic acid; xxwy +CG2O2 CG321 OG2D1 OG311 65.0000 0 0.00 ! PROT & LIPID WILDCARD; ACEH, acetic acid; xxwy +CG2O2 CG331 OG2D1 OG311 65.0000 0 0.00 ! ACEH, acetic acid, xxwy +CG2O2 OG2D1 OG311 HGR52 75.0000 0 0.00 ! FORH, formic acid, xxwy +CG2O3 OG2D2 OG2D2 CG2DC1 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) WILDCARD +CG2O3 OG2D2 OG2D2 CG2DC2 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) WILDCARD +CG2O3 OG2D2 OG2D2 CG2O5 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) WILDCARD +CG2O3 OG2D2 OG2D2 CG2R61 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) WILDCARD +CG2O3 OG2D2 OG2D2 CG301 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) WILDCARD +CG2O3 OG2D2 OG2D2 CG311 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) correct conversion from wildcard CC X X CT1 which itself may or may not be correct +CG2O3 OG2D2 OG2D2 CG314 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) WILDCARD +CG2O3 OG2D2 OG2D2 CG321 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) correct conversion from wildcard CC X X CT2 which itself may or may not be correct +CG2O3 OG2D2 OG2D2 CG331 96.0000 0 0.00 ! PROT 90.0->96.0 acetate, single impr (KK) correct conversion from wildcard CC X X CT3 which itself may or may not be correct +CG2O3 OG2D2 OG2D2 HGR52 67.0000 0 0.00 ! FORA, formate, sz +CG2O4 CG2DC1 OG2D1 HGR52 14.0000 0 0.00 ! RETINOL RTAL unmodified +CG2O4 CG2DC2 OG2D1 HGR52 14.0000 0 0.00 ! RETINOL RTAL unmodified +CG2O4 CG2R61 OG2D1 HGR52 53.0000 0 0.00 ! ALDEHYDE benzaldehyde unmodified +CG2O4 CG321 OG2D1 HGR52 50.0000 0 0.00 ! PALD from acetaldehyde adm 11/08 +CG2O4 CG331 OG2D1 HGR52 50.0000 0 0.00 ! AALD acetaldehyde adm 11/08 +CG2O5 CG2DC1 CG331 OG2D3 88.0000 0 0.00 ! BEON, butenone, kevo +CG2O5 CG2DC2 CG331 OG2D3 88.0000 0 0.00 ! BEON, butenone, kevo +CG2O5 CG2O3 CG2R61 OG2D3 72.0000 0 0.00 ! BIPHENYL re-initialized by kevo from PHEK, phenyl ethyl ketone, mcs +CG2O5 CG2R61 CG311 OG2D3 72.0000 0 0.00 ! BIPHENYL re-initialized by kevo from PHEK, phenyl ethyl ketone; mcs +CG2O5 CG2R61 CG321 OG2D3 72.0000 0 0.00 ! PHEK, phenyl ethyl ketone; mcs +CG2O5 CG2R61 CG331 OG2D3 60.0000 0 0.00 ! 3ACP, 3-acetylpyridine; PHMK, phenyl methyl ketone; mcs +CG2O5 CG321 CG321 OG2D3 70.0000 0 0.00 ! CHON, cyclohexanone; from ACO, acetone; yapol +CG2O5 CG321 CG331 OG2D3 70.0000 0 0.00 ! BTON, butanone; from ACO, acetone; yapol +CG2O5 CG331 CG331 OG2D3 70.0000 0 0.00 ! ketone, acetone adm 11/08 +CG2O6 NG2S2 NG2S2 OG2D1 80.0000 0 0.00 ! UREA, Urea +CG2O6 OG302 OG302 OG2D1 145.0000 0 0.00 ! DMCA, dimethyl carbonate, xxwy +CG2O6 OG2D2 OG2D2 OG2D2 107.0000 0 0.00 ! PROTMOD carbonate +CG2O6 NG2S1 OG2D1 OG302 62.0000 0 0.00 ! DMCB, dimehtyl carbamate, xxwy +CG2O6 OG2D2 OG2D2 OG311 85.0000 0 0.00 ! CO31, bicarbonate, xxwy +CG2O6 SG311 SG311 SG2D1 80.0000 0 0.00 ! DMTT, dimethyl trithiocarbonate, kevo +CG2R53 CG251O NG2R53 OG2D1 90.0000 0 0.00 ! MRDN, methylidene rhodanine, kevo & xxwy from 2PDO WILDCARD +CG2R53 CG252O NG2R53 OG2D1 90.0000 0 0.00 ! MRDN, methylidene rhodanine, kevo & xxwy from 2PDO WILDCARD +CG2R53 CG25C1 NG2R51 OG2D1 90.0000 0 0.00 ! MEOI, methyleneoxindole, kevo & xxwy from 2PDO WILDCARD +CG2R53 CG25C2 NG2R51 OG2D1 90.0000 0 0.00 ! MEOI, methyleneoxindole, kevo & xxwy from 2PDO WILDCARD +CG2R53 CG3C41 NG2R43 OG2D1 120.0000 0 0.00 ! AZDO, 2-azetidinone, kevo +CG2R53 CG3C52 NG2R53 OG2D1 90.0000 0 0.00 !90 120 2PDO, 2-pyrrolidinone, kevo +CG2R53 NG2R53 NG2R53 OG2D1 90.0000 0 0.00 ! MHYO, 5-methylenehydantoin, xxwy from 2PDO WILDCARD +CG2R53 CG2R51 OG2D1 OG3C51 28.6000 0 0.00 ! B2FO, 5H-furan-2-one, ctsai +CG2R53 CG3C52 OG2D1 OG3C51 45.0000 0 0.00 ! GBL, Gamma-butyrolactone, ctsai +CG2R53 NG2R53 OG2D1 SG311 43.0000 0 0.00 ! MTDO, 5-methylene-2,4-thiazolidinedione, xxwy +CG2R53 NG2R53 SG2D1 SG311 43.0000 0 0.00 ! MRDN, methylidene rhodanine, kevo & xxwy +CG2R63 CG2R62 CG2R62 OG2D4 15.0000 0 0.00 ! 4PYO, 4(1H)-pyridinone, isg +CG2R63 CG2R62 NG2R61 OG2D4 90.0000 0 0.00 ! NA T/O4, adm jr. 11/97 correct conversion +CG2R63 CG2R62 NG2R67 OG2D4 90.0000 0 0.00 ! 1PH2PO, 1-phenyl-2(1H)-pyridinone; from CG2R63 CG2R62 NG2R61 OG2D4, NA; isg +CG2R63 CG2RC0 NG2R61 OG2D4 90.0000 0 0.00 ! NA G correct conversion +CG2R63 NG2R61 NG2R61 OG2D4 90.0000 0 0.00 ! RESI URAC, uracil, xxwy, from NA U WILDCARD +CG2R63 NG2R61 NG2R62 OG2D4 90.0000 0 0.00 ! RESI CYT, cytosine, NA U WILDCARD +CG2R63 NG2R61 NG2R67 OG2D4 90.0000 0 0.00 ! 3PHURA, 3-phenyl-2,4(1H,3H)-pyrimidinedione; from CG2R63 NG2R61 NG2R61 OG2D4, URAC from NA; isg +CG2R63 CG2R62 OG2D4 OG3R60 51.0000 0 0.00 ! RIN, coumarin, isg +CG2R63 CG2R61 NG2R61 SG2D1 31.0000 0 0.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R63 CG2R61 NG2R67 SG2D1 39.0000 0 0.00 ! 3PH24S, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione; from CG2R63 CG2R62 NG2R61 SG2D1, YTS2; isg +CG2R63 CG2R62 NG2R61 SG2D1 39.0000 0 0.00 ! YT2S, 3,4-dihydro-4-thioxo-2(1H)-quinazolinone, isg +CG2R63 CG2R62 NG2R67 SG2D1 39.0000 0 0.00 ! 3PH4SR, 2,3-dihydro-3-phenyl-2-oxo-4(1H)pyrimidinethione; from CG2R63 CG2R62 NG2R61 SG2D1, YTS2; isg +CG2R63 NG2R61 NG2R61 SG2D1 84.0000 0 0.00 ! YTS2, 2,4(1H,3H)-quinazolinedithione, isg +CG2R63 NG2R61 NG2R67 SG2D1 84.0000 0 0.00 ! 3PH2SR, 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinone; from CG2R63 NG2R61 NG2R61 SG2D1, YTS2; isg +CG2R64 CG2R61 NG2R60 NG2S1 19.0000 0 0.00 ! 2AMP, 2-acetamide pyridine,xxwy +CG2R64 CG2R62 NG2R62 NG2S3 60.0000 0 0.00 ! NA C +CG2R64 CG2RC0 NG2R62 NG2S3 40.0000 0 0.00 ! NA A +CG2R64 NG2R61 NG2R62 NG2S3 40.0000 0 0.00 ! NA G +CG2R64 CG2R62 NG2R62 NG301 40.0000 0 0.00 ! TMC, yxu +CG2R64 CG2RC0 NG2R62 NG301 40.0000 0 0.00 ! M6A, yxu +NG2O1 OG2N1 OG2N1 CG324 53.6000 0 0.00 ! NIPR, nitropropane, abar +NG2O1 OG2N1 OG2N1 CG334 50.8000 0 0.00 ! NIME, nitromethane, abar +NG2S3 HGP4 HGP4 CG2R61 -2.5000 0 0.00 ! -2.0 PYRIDINE aminopyridine 11/10 kevo: sic! Compensates for in-plane force from CG2R61 CG2R61 NG2S3 HGP4 +NG2S3 HGP4 HGP4 CG2R64 9.0000 0 0.00 ! NA GUA ADE CYT; from artificially planar 2APY, 2-aminopyridine parameter set (12/2010); xxwy & kevo + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!see mass list above for better description of atom types +!hydrogens +HGA1 0.0 -0.0450 1.3400 ! alkane, igor, 6/05 +HGA2 0.0 -0.0350 1.3400 ! alkane, igor, 6/05 +HGA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 +HGA4 0.0 -0.0310 1.2500 ! alkene, yin,adm jr., 12/95 +HGA5 0.0 -0.0260 1.2600 ! alkene, yin,adm jr., 12/95 +HGA6 0.0 -0.0280 1.3200 ! fluoro_alkanes +HGA7 0.0 -0.0300 1.3000 ! fluoro_alkanes +HGAAM0 0.0 -0.0280 1.2800 ! aliphatic amines +HGAAM1 0.0 -0.0280 1.2800 ! aliphatic amines +HGAAM2 0.0 -0.0400 1.2600 ! aliphatic amines +HGP1 0.0 -0.0460 0.2245 ! polar H +HGP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged systems +HGP3 0.0 -0.1000 0.4500 ! methanethiol pure solvent, adm jr., 6/22/92 +HGP4 0.0 -0.0460 0.2245 ! polar H, conjugated amines (NA bases) +HGP5 0.0 -0.0460 0.7000 ! polar H on quarternary amine (choline) +HGPAM1 0.0 -0.0090 0.8750 ! aliphatic amines +HGPAM2 0.0 -0.0100 0.8750 ! aliphatic amines +HGPAM3 0.0 -0.0120 0.8700 ! aliphatic amines +HGR51 0.0 -0.0300 1.3582 ! benzene +HGR52 0.0 -0.0460 0.9000 ! adm jr., 6/27/90, his +HGR53 0.0 -0.0460 0.7000 ! adm jr., 6/27/90, his +HGR61 0.0 -0.0300 1.3582 ! benzene +HGR62 0.0 -0.0460 1.1000 ! intermediate aromatic Hvdw +HGR63 0.0 -0.0460 0.9000 ! nad/ppi, jjp1/adm jr. +HGR71 0.0 -0.0300 1.3582 ! benzene +!HGTIP3 0.0 -0.0460 0.2245 ! PROT TIP3P HYDROGEN PARAMETERS +!carbons +CG1T1 0.0 -0.1670 1.8400 ! 2BTY, 2-butyne, kevo & rima +CG1T2 0.0 -0.1032 1.9925 ! PRPY, propyne, rima & kevo +CG1N1 0.0 -0.1800 1.8700 ! ACN, acetonitrile; 3CYP, 3-cyanopyridine, kevo +CG2D1 0.0 -0.0680 2.0900 ! alkene, yin,adm jr., 12/95 +CG2D2 0.0 -0.0640 2.0800 ! alkene, yin,adm jr., 12/95 +CG2D1O 0.0 -0.0680 2.0900 ! double bond carbon adjacent to O (pyran) +CG2D2O 0.0 -0.0680 2.0900 ! double bond carbon adjacent to O (pyran) +CG2DC1 0.0 -0.0680 2.0900 ! Butadiene +CG2DC2 0.0 -0.0680 2.0900 ! Butadiene +CG2DC3 0.0 -0.0640 2.0800 ! Butadiene +CG2N1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93 +CG2N2 0.0 -0.1100 2.0000 ! same as CG2N1 of NMA pure solvent, adm jr., 3/3/93 +CG2O1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93 +CG2O2 0.0 -0.0980 1.7000 ! methyl acetate update viv 12/29/06 +CG2O3 0.0 -0.0700 2.0000 ! acetate heat of solvation +CG2O4 0.0 -0.0600 1.8000 ! adm, acetaldehyde, 11/08 +CG2O5 0.0 -0.0900 2.0000 ! adm, acetone, 11/08 +CG2O6 0.0 -0.0700 2.0000 ! UREA, CO3 (carbonate) from acetate heat of solvation +CG2O7 0.0 -0.0580 1.5630 ! carbon dioxide, JES +CG2R51 0.0 -0.0500 2.1000 ! INDO/TRP; bulk solvent of 10 maybridge cmpds (kevo) +CG2R52 0.0 -0.0200 2.2000 ! PYRZ, pyrazole; bulk solvent of 3 maybridge cmpds (kevo); consistent with CG2R64 +CG2R53 0.0 -0.0200 2.2000 ! IMIA, imidazole; bulk solvent of 5 maybridge cmpds (kevo); consistent with CG2R64 +CG2R57 0.0 -0.0500 2.1000 ! bipyrroles; from CG2R51; lf +CG25C1 0.0 -0.0680 2.0900 ! same as CG2DC1 but in 5-membered ring with exocyclic double bond +CG25C2 0.0 -0.0680 2.0900 ! same as CG2DC2 but in 5-membered ring with exocyclic double bond +CG251O 0.0 -0.0680 2.0900 ! same as CG2D1O but in 5-membered ring with exocyclic double bond +CG252O 0.0 -0.0680 2.0900 ! same as CG2D2O but in 5-membered ring with exocyclic double bond +CG2R61 0.0 -0.0700 1.9924 ! INDO/TRP +CG2R62 0.0 -0.0900 1.9000 ! NA +CG2R63 0.0 -0.1000 1.9000 ! NA +CG2R64 0.0 -0.0400 2.1000 ! PYRM, pyrimidine +CG2R66 0.0 -0.0700 1.9000 ! NA dft +CG2R67 0.0 -0.0700 1.9924 ! biphenyl +CG2RC0 0.0 -0.0990 1.8600 ! INDO/TRP +CG2R71 0.0 -0.0670 1.9948 ! Questionable extrapolation. TO BE REFINED! +CG2RC7 0.0 -0.0990 1.8600 ! copied from INDO/TRP, ignoring single bond character ==> TO BE REFINED! +! THESE ARE IGOR'S ALKANE AND THF PARAMS +CG301 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! alkane (CT0), neopentane, from CT1, viv +CG302 0.0 -0.0200 2.3000 ! fluoro_alkanes +CG311 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! alkane (CT1), isobutane, 6/05 viv +CG312 0.0 -0.0420 2.0500 ! fluoro_alkanes +CG314 0.0 -0.0310 2.1650 0.0 -0.01 1.9 ! extrapolation based on CG311, CG321 and CG324, kevo +CG321 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! alkane (CT2), 4/98, yin, adm jr, also used by viv +CG322 0.0 -0.0600 1.9000 ! fluoro_alkanes +CG323 0.0 -0.1100 2.2000 ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +CG324 0.0 -0.0550 2.1750 0.0 -0.01 1.9 ! PIP1,2,3 +CG331 0.0 -0.0780 2.0500 0.0 -0.01 1.9 ! alkane (CT3), 4/98, yin, adm jr; Rmin/2 modified from 2.04 to 2.05 +CG334 0.0 -0.0770 2.2150 0.0 -0.01 1.9 ! extrapolation based on CG331, CG321 and CG324, kevo +CG3C50 0.0 -0.0360 2.0100 0.0 -0.01 1.9 ! extrapolation based on CG301, CG321 and CG3C52, kevo +CG3C51 0.0 -0.0360 2.0100 0.0 -0.01 1.9 ! extrapolation based on CG311, CG321 and CG3C52, kevo +CG3C52 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv +CG3C53 0.0 -0.0350 2.1750 0.0 -0.01 1.9 ! extrapolation based on (CG324, CG321 and CG3C51(ex)) or (CG311, CG321 and CG3C54(ex)), kevo +CG3C54 0.0 -0.0590 2.1850 0.0 -0.01 1.9 ! extrapolation based on CG324, CG321 and CG3C52, kevo +CG3C31 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! cyclopropane JMW (CT2), viv +CG3C41 0.0 -0.0650 2.0200 0.0 -0.01 1.9 ! CBU, cyclobutane, lsk +CG3RC1 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! alkane (CT1), viv +! "highly specialized amine parameters" +CG3AM0 0.0 -0.0700 1.9700 ! aliphatic amines +CG3AM1 0.0 -0.0780 1.9800 ! aliphatic amines +CG3AM2 0.0 -0.0800 1.9900 ! aliphatic amines +!nitrogens +NG1T1 0.0 -0.1800 1.7900 ! ACN, acetonitrile; 3CYP, 3-cyanopyridine, kevo +!NG1D1 0.0 -0.0350 2.0300 ! terminal N in azides, lsk +NG2D1 0.0 -0.2000 1.8500 ! deprotonated Schiff's base +NG2S0 0.0 -0.2000 1.8500 0.0 -0.0001 1.85 ! PROT AcProNH2, ProNH2, AcProNHCH3 RLD +NG2S1 0.0 -0.2000 1.8500 0.0 -0.20 1.55 ! 1,4 vdW allows the C5 dipeptide minimum to exist +NG2S2 0.0 -0.2000 1.8500 ! PROT +NG2S3 0.0 -0.2000 1.8500 ! PROT +NG2O1 0.0 -0.2000 1.8500 ! NITR, nitrobenzene +NG2P1 0.0 -0.2000 1.8500 ! protonated Schiff's base +NG2R43 0.0 -0.2000 1.8500 ! AZDO, 2-azetidinone; from 2PDO; lsk +NG2R50 0.0 -0.2000 1.8500 ! IMIA, Imidazole from IMIA/HS[DE]; originally from prot backbone - probably not ideal +NG2R51 0.0 -0.2000 1.8500 ! PYRL, Pyrrole; IMIA, Imidazole from IMIA/HS[DE] and INDO/TRP; originally from prot backbone - probably not ideal +NG2R52 0.0 -0.2000 1.8500 ! IMIM, imidazolium from IMIM/HSP; originally from prot backbone - probably not ideal +NG2R53 0.0 -0.2000 1.8500 ! amide in 5-memebered ring (slightly pyramidized), 2PDO, kevo +NG2R57 0.0 -0.2000 1.8500 ! bipyrroles; from NG2R51; lf +NG2R60 0.0 -0.0600 1.8900 ! PYR1, pyridine +NG2R61 0.0 -0.2000 1.8500 ! NA +NG2R62 0.0 -0.0500 2.0600 ! PYRM, pyrimidine +NG2R67 0.0 -0.2000 1.8500 ! N-phenyl pyridinones etc.; from NG2R61; isg +NG2RC0 0.0 -0.2000 1.8500 ! 6/5-mem ring bridging N, indolizine, INDZ, kevo +NG301 0.0 -0.0350 2.0000 ! aliphatic amines +NG311 0.0 -0.0450 2.0000 ! aliphatic amines +NG321 0.0 -0.0600 1.9900 ! aliphatic amines +NG331 0.0 -0.0700 1.9800 ! aliphatic amines +NG3C51 0.0 -0.2000 1.8500 ! 2PRL, 2-pyrroline, kevo +NG3N1 0.0 -0.0600 2.0500 ! HDZN, hydrazine, ed +NG3P0 0.0 -0.2000 1.8500 ! LIPID, quarternary amine +NG3P1 0.0 -0.2000 1.8500 ! PIP, tertiary amine +NG3P2 0.0 -0.2000 1.8500 ! N-terminal proline; from +ProNH2 RLD 9/28/90 +NG3P3 0.0 -0.2000 1.8500 ! NA +OG2D1 0.0 -0.1200 1.7000 0.0 -0.12 1.40 ! carbonyl. Also consistent with adm, acetaldehyde, 11/08 +OG2D2 0.0 -0.1200 1.7000 ! PROT +OG2D3 0.0 -0.0500 1.7000 0.0 -0.12 1.40 ! adm, acetone, 11/08 +OG2D4 0.0 -0.1200 1.7000 ! NA +OG2D5 0.0 -0.1650 1.6920 ! carbon dioxide, JES +OG2N1 0.0 -0.1200 1.7000 ! NITR, nitrobenzene +OG2P1 0.0 -0.1200 1.7000 ! NA +OG2R50 0.0 -0.1200 1.7000 ! FURA, furan +OG3R60 0.0 -0.1000 1.6500 ! PY01, PY02, pyran; LJ from THP, sng 1/06 +OG301 0.0 -0.1000 1.6500 ! ether; LJ from THP, sng 1/06 !SHOULD WE HAVE A SEPARATE ENOL ETHER??? IF YES, SHOULD WE MERGE IT WITH OG3R60??? +OG302 0.0 -0.1000 1.6500 ! ester; LJ from THP, sng 1/06 +OG303 0.0 -0.1000 1.6500 ! phosphate/sulfate ester; LJ from THP, sng 1/06 +OG304 0.0 -0.1000 1.6500 ! linkage oxygen in pyrophosphate/pyrosulphate +OG311 0.0 -0.1921 1.7650 ! og MeOH and EtOH 1/06 (was -0.1521 1.7682) +OG312 0.0 -0.1200 1.7500 ! PROT, anionic alcohol oxygen +OG3C31 0.0 -0.1000 1.6500 ! epoxide; from ethers; sc +OG3C51 0.0 -0.1000 1.6500 ! THF; LJ from THP, tetrahydropyran sng 1/06 +OG3C61 0.0 -0.1000 1.6500 ! DIOX, dioxane; THP, tetrahydropyran sng 1/06 !SHOULD WE MERGE THIS WITH OG3R60??? +!OGTIP3 0.0 -0.1521 1.7682 ! TIP3P OXYGEN PARAMETERS +!sulphurs +SG2D1 0.0 -0.5650 2.0500 ! DMTT, dimethyl trithiocarbonate, kevo +SG2R50 0.0 -0.4500 2.0000 ! THIP, thiophene +SG311 0.0 -0.4500 2.0000 ! methanethiol/ethylmethylsulfide pure solvent +SG301 0.0 -0.3800 1.9750 ! dimethyldisulphide pure solvent +SG302 0.0 -0.4700 2.2000 ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +SG3O1 0.0 -0.4700 2.1000 ! methylsulfate +SG3O2 0.0 -0.3500 2.0000 ! from SG3O3 (ML Strader, SE Feller, JPC-A106(6),1074(2002)), xxwy +SG3O3 0.0 -0.3500 2.0000 ! ML Strader, SE Feller, JPC-A106(6),1074(2002), sz +!halogens +FGA1 0.0 -0.1350 1.6300 ! fluoro_alkanes +FGA2 0.0 -0.1050 1.6300 ! fluoro_alkanes +FGA3 0.0 -0.0970 1.6000 ! fluoro_alkanes +FGP1 0.0 -0.0970 1.6000 ! Aluminum tetraflouride, ALF4 +FGR1 0.0 -0.1200 1.7000 ! aromatic F, 1,3-difluorobenzene pure solvent +CLGA1 0.0 -0.3430 1.9100 ! CLET, DCLE, chloroethane, 1,1-dichloroethane +CLGA3 0.0 -0.3100 1.9100 ! TCLE +CLGR1 0.0 -0.3200 1.9300 ! CHLB, chlorobenzene +BRGA1 0.0 -0.4800 1.9700 ! BRET +BRGA2 0.0 -0.5300 2.0500 ! DBRE +BRGA3 0.0 -0.5400 2.0000 ! TBRE +BRGR1 0.0 -0.4200 2.0700 ! BROM, bromobenzene +IGR1 0.0 -0.5500 2.1900 ! IODB, iodobenzene +!miscellaneous +!DUM 0.0 -0.0000 0.0000 ! dummy atom +!HE 0.0 -0.02127 1.4800 ! helium +!NE 0.0 -0.08545 1.5300 ! neon +PG0 0.0 -0.5850 2.1500 ! neutral phosphate +PG1 0.0 -0.5850 2.1500 ! phosphate -1 +PG2 0.0 -0.5850 2.1500 ! phosphate -2 +ALG1 0.0 -0.6500 2.0000 ! Aluminum tetraflouride, ALF4 + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/par_all36_lipid.prm b/charmm/toppar/par_all36_lipid.prm new file mode 100644 index 00000000..12dcf43a --- /dev/null +++ b/charmm/toppar/par_all36_lipid.prm @@ -0,0 +1,532 @@ +* \\\\\\\ CHARMM36 All-Hydrogen Lipid Parameter File /////// +* All comments and questions should be submitted to the +* parameter forum at the CHARMM website: www.charmm.org +* + +!references +! +!Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph +!W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor +!Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of +!the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six +!Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843 +! +! PUFA Modifications +!Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving +!the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B. +!2012 ASAP http://dx.doi.org/10.1021/jp304056p + +ATOMS +MASS 136 HL 1.008000 ! polar H (equivalent to protein H) +MASS 137 HCL 1.008000 ! charged H for PE (equivalent to protein HC) +MASS 138 HOL 1.008000 ! Nucleic acid phosphate hydroxyl proton +MASS 139 HAL1 1.008000 ! alphatic proton +MASS 140 HAL2 1.008000 ! alphatic proton +MASS 141 HAL3 1.008000 ! alphatic proton +MASS 142 HEL1 1.008000 ! for alkene; RHC=CR +MASS 143 HEL2 1.008000 ! for alkene; H2C=CR +MASS 144 HBL 1.008000 ! POPS SER backbone H +MASS 145 CL 12.011000 ! carbonyl C (acetic acid/methyl acetate) +MASS 146 CTL1 12.011000 ! sp3 carbon with 1 H (-CH1-) +MASS 147 CTL2 12.011000 ! carbon of methylene group (-CH2-) +MASS 148 CTL3 12.011000 ! carbon of methyl group (-CH3) +MASS 149 CTL5 12.011000 ! carbon of methyl group (-CH3) for tetramethylammonium +MASS 150 CEL1 12.011000 ! for alkene; RHC=CR +MASS 151 CEL2 12.011000 ! for alkene; H2C=CR +MASS 152 CCL 12.011000 ! for POPS +MASS 153 NTL 14.007000 ! ammonium nitrogen +MASS 154 NH3L 14.007000 ! nitrogen phosphatidylethanolamine +MASS 155 OBL 15.999400 ! acetic acid carboxyl oxygen (e. to protein OB) +MASS 156 OCL 15.999400 ! acetate oxygen +MASS 157 OSL 15.999400 ! ester oxygen +MASS 158 O2L 15.999400 ! Nucleic acid =O in phosphate or sulfate +MASS 159 OHL 15.999400 ! Nucleic acid phosphate hydroxyl oxygen +MASS 160 OSLP 15.999400 ! Phosphate oxygen, to avoid conflict with methylacetate type O +MASS 161 PL 30.974000 ! phosphorus +MASS 162 SL 32.060000 ! Sulfate sulfur +MASS 163 CRL1 12.011000 ! sp3 carbon with 1 H on a ring (-CH1-) for sterols +MASS 164 CRL2 12.011000 ! carbon of methylene group on a ring (-CH2-) for sterols + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +CTL3 CL 200.0 1.522 ! methyl acetate +CTL2 CL 200.0 1.522 ! methyl acetate +CTL1 CL 200.0 1.522 ! methyl acetate +CTL1 CCL 200.0 1.522 ! for POPS +OBL CL 750.0 1.220 ! methyl acetate +OCL CL 525.0 1.260 ! acetate, protein +OCL CCL 525.0 1.260 ! for POPS +OSL CL 150.0 1.334 ! methyl acetate +OSLP CL 150.0 1.334 ! methyl acetate +OHL CL 230.0 1.40 ! methyl acetate +HOL OHL 545.0 0.960 ! acetic acid +CTL1 HAL1 309.00 1.111 ! alkanes, 3/92 +CTL1 HBL 330.00 1.080 ! for POPS +CTL2 HAL2 309.00 1.111 ! alkanes, 4/98 +CTL3 HAL3 322.00 1.111 ! alkanes, 4/98 +CTL3 OSL 340.0 1.43 ! phosphate +CTL2 OSL 340.0 1.43 ! phosphate +CTL1 OSL 340.0 1.43 ! phosphate +CTL3 OSLP 340.0 1.43 ! +CTL2 OSLP 340.0 1.43 ! +CTL1 OSLP 340.0 1.43 ! +OSL PL 270.0 1.60 ! phosphate +OSLP PL 270.0 1.60 ! +O2L PL 580.0 1.48 ! phosphate +OHL PL 237.0 1.59 ! phosphate +NH3L HCL 410.0 1.04 ! ethanolamine +NH3L CTL1 200.0 1.48 ! for POPS +NH3L CTL2 261.0 1.51 ! ethanolamine +NTL CTL2 215.00 1.51 ! tetramethylammonium +NTL CTL5 215.00 1.51 ! tetramethylammonium +CTL5 HL 300.00 1.08 ! tetramethylammonium +CTL2 HL 300.00 1.08 ! tetramethylammonium +CTL1 CTL1 222.500 1.500 ! alkanes, 3/92 +CTL1 CTL2 222.500 1.538 ! alkanes, 3/92 +CTL1 CTL3 222.500 1.538 ! alkanes, 3/92 +CTL2 CTL2 222.500 1.530 ! alkanes, 3/92 +CTL2 CTL3 222.500 1.528 ! alkanes, 3/92 +CTL3 CTL3 222.500 1.530 ! alkanes, 3/92 +OHL CTL1 428.0 1.420 ! glycerol +OHL CTL2 428.0 1.420 ! glycerol +OHL CTL3 428.0 1.420 ! glycerol +SL O2L 540.0 1.448 ! methylsulfate +SL OSL 250.0 1.575 ! methylsulfate +CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95 +HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95 +CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95 +CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95 +HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95 +CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95 +CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95 + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +! +OBL CL CTL3 70.0 125.0 20.0 2.442 ! methyl acetate +OBL CL CTL2 70.0 125.0 20.0 2.442 ! methyl acetate +OBL CL CTL1 70.0 125.0 20.0 2.442 ! methyl acetate +OSL CL OBL 90.0 125.9 160.0 2.2576 ! acetic acid +CL OSL CTL1 40.0 109.6 30.0 2.2651 ! methyl acetate +CL OSL CTL2 40.0 109.6 30.0 2.2651 ! methyl acetate +CL OSL CTL3 40.0 109.6 30.0 2.2651 ! methyl acetate +HAL2 CTL2 CL 33.00 109.50 30.00 2.163 ! methyl acetate +HAL3 CTL3 CL 33.00 109.50 30.00 2.163 ! methyl acetate +CTL2 CTL2 CL 52.0 108.00 ! alkane +CTL2 CTL1 CCL 52.0 108.00 ! for POPS +CTL3 CTL2 CL 52.0 108.00 ! alkane +OSL CL CTL3 55.0 109.0 20.00 2.3260 ! methyl acetate +OSL CL CTL2 55.0 109.0 20.00 2.3260 ! methyl acetate +OSL CL CTL1 55.0 109.0 20.00 2.3260 ! methyl acetate +OHL CL OBL 50.0 123.0 210.0 2.2620 ! acetic acid +OCL CL CTL2 40.0 118.0 50.0 2.3880 ! acetate +OCL CL CTL3 40.0 118.0 50.0 2.3880 ! acetate +OCL CL OCL 100.0 124.0 70.0 2.2250 ! acetate +OCL CCL OCL 100.0 124.0 70.0 2.2250 ! for POPS +OCL CCL CTL1 40.0 118.0 50.0 2.3880 ! for POPS +OHL CL CTL3 55.0 110.50 ! acetic acid +OHL CL CTL2 55.0 110.50 ! acetic acid +HOL OHL CL 55.0 115.0 ! acetic acid +OSL CTL1 CTL1 75.700 110.10 ! acetic acid, PIP +OSL CTL1 CTL2 75.700 110.10 ! acetic acid +OSL CTL1 CTL3 75.700 110.10 ! acetic acid +OSL CTL2 CTL1 75.700 110.10 ! acetic acid +OSL CTL2 CTL2 75.700 110.10 ! acetic acid +OSL CTL2 CTL3 75.700 110.10 ! acetic acid +OSLP CTL1 CTL1 75.700 110.10 ! acetic acid, PIP +OSLP CTL1 CTL2 75.700 110.10 ! acetic acid +OSLP CTL1 CTL3 75.700 110.10 ! acetic acid +OSLP CTL2 CTL1 75.700 110.10 ! acetic acid +OSLP CTL2 CTL2 75.700 110.10 ! acetic acid +OSLP CTL2 CTL3 75.700 110.10 ! acetic acid +HAL2 CTL2 HAL2 35.500 109.00 5.40 1.80200 ! alkane, 3/92 +HAL3 CTL3 HAL3 35.500 108.40 5.40 1.80200 ! alkane, 3/92 +HAL1 CTL1 OSL 60.0 109.5 ! phosphate +HAL2 CTL2 OSL 60.0 109.5 ! phosphate +HAL3 CTL3 OSL 60.0 109.5 ! phosphate +HAL1 CTL1 OSLP 60.0 109.5 ! phosphate +HAL2 CTL2 OSLP 60.0 109.5 ! phosphate +HAL3 CTL3 OSLP 60.0 109.5 ! phosphate +CTL1 OSL PL 20.0 120.0 35.0 2.33 ! phosphate, PIP +CTL2 OSL PL 20.0 120.0 35.0 2.33 ! phosphate +CTL3 OSL PL 20.0 120.0 35.0 2.33 ! phosphate +CTL1 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate, PIP +CTL2 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate +CTL3 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate +HOL OHL PL 30.0 115.0 40.0 2.30 ! phosphate +OSL PL OSL 80.0 104.3 ! phosphate +OSL PL O2L 98.9 111.6 ! phosphate +OSL PL OHL 48.1 108.0 ! phosphate +OSLP PL OSLP 80.0 104.3 ! phosphate +OSLP PL O2L 98.9 111.6 ! phosphate +OSLP PL OHL 48.1 108.0 ! phosphate +O2L PL O2L 120.0 120.0 ! phosphate +O2L PL OHL 98.9 108.23 ! phosphate +NTL CTL2 HL 40.0 109.5 27. 2.13 ! tetramethylammonium +NTL CTL5 HL 40.0 109.5 27. 2.13 ! tetramethylammonium +HL CTL2 HL 24.0 109.50 28. 1.767 ! tetramethylammonium +HL CTL5 HL 24.0 109.50 28. 1.767 ! tetramethylammonium +CTL2 NTL CTL2 60.0 109.5 26. 2.466 ! tetraethylammonium, from CTL5 NTL CTL2 +CTL5 NTL CTL2 60.0 109.5 26. 2.466 ! tetramethylammonium +CTL5 NTL CTL5 60.0 109.5 26. 2.466 ! tetramethylammonium +HL CTL2 CTL2 33.430 110.10 22.53 2.179 ! alkane +HL CTL2 CTL3 33.430 110.10 22.53 2.179 ! alkane +HAL1 CTL1 CTL1 34.500 110.10 22.53 2.179 ! alkane, 3/92 +HAL1 CTL1 CTL2 34.500 110.10 22.53 2.179 ! alkane, 3/92 +HAL1 CTL1 CTL3 34.500 110.10 22.53 2.179 ! alkane, 3/92 +HAL2 CTL2 CTL1 26.500 110.10 22.53 2.179 ! alkane, 4/98 +HAL2 CTL2 CTL2 26.500 110.10 22.53 2.179 ! alkane, 4/98 +HAL2 CTL2 CTL3 34.600 110.10 22.53 2.179 ! alkane, 4/98 +HAL3 CTL3 CTL1 33.430 110.10 22.53 2.179 ! alkane, 4/98 +HAL3 CTL3 CTL2 34.600 110.10 22.53 2.179 ! alkane, 4/98 +HAL3 CTL3 CTL3 37.500 110.10 22.53 2.179 ! alkane, 4/98 +HBL CTL1 CCL 50.000 109.50 ! for POPS +HBL CTL1 CTL2 35.000 111.00 ! for POPS +NTL CTL2 CTL2 67.7 115.00 ! tetramethylammonium +NTL CTL2 CTL3 67.7 115.00 ! tetramethylammonium +HCL NH3L CTL2 33.0 109.50 4.00 2.056 ! ethanolamine +HCL NH3L CTL1 30.0 109.50 20.00 2.074 ! for POPS +HCL NH3L HCL 41.0 109.50 ! ethanolamine +NH3L CTL2 CTL2 67.7 110.00 ! ethanolamine +NH3L CTL2 HAL2 45.0 107.50 35.00 2.0836 ! ethanolamine +CTL1 CTL1 CTL1 53.350 111.00 8.00 2.561 ! alkane, 3/92 +NH3L CTL1 CCL 43.7 110.00 ! for POPS +NH3L CTL1 CTL2 67.7 110.00 ! for POPS +NH3L CTL1 HBL 51.5 107.50 ! for POPS +CTL1 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol +CTL1 CTL1 CTL3 53.350 108.50 8.00 2.561 ! alkane, 3/92 +CTL1 CTL2 CTL1 58.350 113.50 11.16 2.561 ! glycerol +CTL1 CTL2 CTL2 58.350 113.50 11.16 2.561 ! glycerol +CTL1 CTL2 CTL3 58.350 113.50 11.16 2.561 ! glycerol +CTL2 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol +CTL2 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol +CTL2 CTL2 CTL2 58.350 113.60 11.16 2.561 ! alkane, 3/92 +CTL2 CTL2 CTL3 58.000 115.00 8.00 2.561 ! alkane, 3/92 +CTL3 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol +HOL OHL CTL1 57.500 106.00 ! glycerol +HOL OHL CTL2 57.500 106.00 ! glycerol +HOL OHL CTL3 57.500 106.00 ! glycerol +OHL CTL1 CTL1 75.700 110.10 ! glycerol, PIP +OHL CTL1 CTL2 75.700 110.10 ! glycerol +OHL CTL2 CTL1 75.700 110.10 ! glycerol +OHL CTL2 CTL2 75.700 110.10 ! glycerol +OHL CTL2 CTL3 75.700 110.10 ! glycerol +OHL CTL1 HAL1 45.900 108.89 ! glycerol +OHL CTL2 HAL2 45.900 108.89 ! glycerol +OHL CTL3 HAL3 45.900 108.89 ! glycerol +O2L SL O2L 130.0 109.47 35.0 2.45 ! methylsulfate +O2L SL OSL 85.0 98.0 ! methylsulfate +CTL2 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate +CTL3 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate +CEL1 CEL1 CTL2 48.00 123.50 ! from 2-butene, yin,adm jr., 12/95 +CEL1 CEL1 CTL3 48.00 123.50 ! 2-butene, yin,adm jr., 12/95 +CEL2 CEL1 CTL2 48.00 126.00 ! 1-butene; from propene, yin,adm jr., 12/95 +CEL2 CEL1 CTL3 47.00 125.20 ! propene, yin,adm jr., 12/95 +HEL1 CEL1 CEL1 52.00 119.50 ! 2-butene, yin,adm jr., 12/95 +HEL1 CEL1 CEL2 42.00 118.00 ! propene, yin,adm jr., 12/95 +HEL1 CEL1 CTL2 40.00 116.00 ! 1-butene; from propene, yin,adm jr., 12/95 +HEL1 CEL1 CTL3 22.00 117.00 ! propene, yin,adm jr., 12/95 +HEL2 CEL2 CEL1 45.00 120.50 ! propene, yin,adm jr., 12/95 +HEL2 CEL2 CEL2 55.50 120.50 ! ethene, yin,adm jr., 12/95 +HEL2 CEL2 HEL2 19.00 119.00 ! propene, yin,adm jr., 12/95 +CEL1 CTL2 CTL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 +CEL1 CTL2 CTL3 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 +HAL2 CTL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95 +HAL3 CTL3 CEL1 42.00 111.50 ! 2-butene, yin,adm jr., 12/95 +CEL1 CTL2 CEL1 30.0 114.0 ! 1,4-dipentene, adm jr., 2/00 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +X CTL1 OHL X 0.14 3 0.00 ! glycerol +X CTL2 OHL X 0.14 3 0.00 ! glycerol +X CTL3 OHL X 0.14 3 0.00 ! glycerol +OCL CCL CTL1 NH3L 3.20 2 180.00 ! for POPS +OBL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid +OBL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid +OSL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid +OSL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid +OSLP CL CTL2 HAL2 0.00 6 180.00 ! acetic acid +OSLP CL CTL3 HAL3 0.00 6 180.00 ! acetic acid +OBL CL OSL CTL1 0.965 1 180.00 ! methyl acetate +OBL CL OSL CTL1 3.85 2 180.00 ! methyl acetate +OBL CL OSL CTL2 0.965 1 180.00 ! methyl acetate +OBL CL OSL CTL2 3.85 2 180.00 ! methyl acetate +OBL CL OSL CTL3 0.965 1 180.00 ! methyl acetate +OBL CL OSL CTL3 3.85 2 180.00 ! methyl acetate +X CL OSL X 2.05 2 180.00 ! methyl acetate +X CTL2 CL X 0.05 6 180.00 ! methyl acetate +X CTL3 CL X 0.05 6 180.00 ! methyl acetate +X CL OHL X 2.05 2 180.00 ! acetic acid +X CTL1 CCL X 0.05 6 180.00 ! for POPS +HAL2 CTL2 CL OHL 0.00 6 180.00 +HAL3 CTL3 CL OHL 0.00 6 180.00 +PL OSLP CTL2 CTL1 0.407 2 0.00 ! Phos-gly, 8/05 +PL OSLP CTL2 CTL1 0.241 1 180.00 ! Phos-gly, 8/05 +PL OSLP CTL2 CTL2 0.407 2 0.00 ! Phos-gly, 8/05 +PL OSLP CTL2 CTL2 0.241 1 180.00 ! Phos-gly, 8/05 +OSL PL OSL CTL1 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr., PIP +OSL PL OSL CTL1 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr., PIP +OSL PL OSL CTL1 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr., PIP +OSLP PL OSLP CTL1 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr., PIP +OSLP PL OSLP CTL1 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr., PIP +OSLP PL OSLP CTL1 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr., PIP +OSLP PL OSLP CTL2 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr. +OSLP PL OSLP CTL2 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr. +OSLP PL OSLP CTL2 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr. +O2L PL OSLP CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. +O2L PL OSL CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. +OSLP PL OSLP CTL3 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr. +OSLP PL OSLP CTL3 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr. +OSLP PL OSLP CTL3 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr. +O2L PL OSLP CTL1 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr., PIP +O2L PL OSL CTL1 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr., PIP +O2L PL OSLP CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. +O2L PL OSL CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. +OHL PL OSL CTL1 0.95 2 0.00 ! terminal phosphate, PIP +OHL PL OSL CTL1 0.50 3 0.00 ! terminal phosphate, PIP +OHL PL OSL CTL2 0.95 2 0.00 ! terminal phosphate +OHL PL OSL CTL2 0.50 3 0.00 ! terminal phosphate +OHL PL OSL CTL3 0.95 2 0.00 ! terminal phosphate +OHL PL OSL CTL3 0.50 3 0.00 ! terminal phosphate +OHL PL OSLP CTL2 0.95 2 0.00 ! terminal phosphate +OHL PL OSLP CTL2 0.50 3 0.00 ! terminal phosphate +OHL PL OSLP CTL3 0.95 2 0.00 ! terminal phosphate +OHL PL OSLP CTL3 0.50 3 0.00 ! terminal phosphate +X OHL PL X 0.30 3 0.00 ! terminal phosphate +X CTL1 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. +X CTL2 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. +X CTL3 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. +X CTL1 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. +X CTL2 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. +X CTL3 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. +CTL1 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92 +CTL1 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92 +CTL2 CTL2 CL OSL 0.000 6 0.00 ! glycerol & propl ester, 6/07 +CTL2 CTL2 CL OSL 0.030 3 180.00 ! glycerol & propl ester, 6/07 +CTL2 CTL2 CL OSL 0.432 2 180.00 ! glycerol & propl ester, 6/07 +CTL2 CTL2 CL OSL 0.332 1 0.00 ! glycerol & propl ester, 6/07 +CTL3 CTL2 CL OSL 0.000 6 0.00 ! glycerol & propl ester, 6/07 +CTL3 CTL2 CL OSL 0.030 3 180.00 ! glycerol & propl ester, 6/07 +CTL3 CTL2 CL OSL 0.432 2 180.00 ! glycerol & propl ester, 6/07 +CTL3 CTL2 CL OSL 0.332 1 0.00 ! glycerol & propl ester, 6/07 +CTL3 CTL2 CTL2 CL 0.000 5 180.00 ! propyl ester, 6/07 +CTL3 CTL2 CTL2 CL 0.317 3 180.00 ! propyl ester, 6/07 +CTL3 CTL2 CTL2 CL 0.557 2 0.00 ! propyl ester, 6/07 +CTL3 CTL2 CTL2 CL 0.753 1 0.00 ! propyl ester, 6/07 +CTL2 CTL2 CTL2 CL 0.000 5 180.00 ! propyl ester, 6/07 +CTL2 CTL2 CTL2 CL 0.317 3 180.00 ! propyl ester, 6/07 +CTL2 CTL2 CTL2 CL 0.557 2 0.00 ! propyl ester, 6/07 +CTL2 CTL2 CTL2 CL 0.753 1 0.00 ! propyl ester, 6/07 +OSL CTL2 CTL1 OSL -0.429 4 60.00 ! glycerol, 8/08 +OSL CTL2 CTL1 OSL 0.614 3 0.00 ! glycerol, 8/08 +OSL CTL2 CTL1 OSL -0.115 2 60.00 ! glycerol, 8/08 +OSL CTL2 CTL1 OSL 0.703 1 180.00 ! glycerol, 8/08 +OSLP CTL2 CTL1 OSL 0.000 4 0.00 ! Fit to QM, theta2, 07/08 jbk +OSLP CTL2 CTL1 OSL 0.607 3 180.00 ! Fit to QM, theta2, 07/08 jbk +OSLP CTL2 CTL1 OSL 0.254 2 60.00 ! Fit to QM, theta2, 07/08 jbk +OSLP CTL2 CTL1 OSL 2.016 1 180.00 ! Fit to QM, theta2, 07/08 jbk +OSLP CTL2 CTL2 OSL 0.000 4 0.00 ! Fit to QM, theta2, 07/08 jbk +OSLP CTL2 CTL2 OSL 0.607 3 180.00 ! Fit to QM, theta2, 07/08 jbk +OSLP CTL2 CTL2 OSL 0.254 2 60.00 ! Fit to QM, theta2, 07/08 jbk +OSLP CTL2 CTL2 OSL 2.016 1 180.00 ! Fit to QM, theta2, 07/08 jbk +CTL3 CTL1 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3 +CTL2 CTL1 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3 +CTL3 CTL2 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3 +CTL2 CTL2 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3 +CL OSL CTL1 CTL2 0.000 4 0.00 ! glycerol, beta1 6/07 +CL OSL CTL1 CTL2 0.150 3 180.00 ! glycerol, beta1 6/07 +CL OSL CTL1 CTL2 1.453 2 180.00 ! glycerol, beta1 6/07 +CL OSL CTL1 CTL2 0.837 1 180.00 ! glycerol, beta1 6/07 +CL OSL CTL1 CTL3 0.000 4 0.00 ! glycerol, beta1 6/07 +CL OSL CTL1 CTL3 0.150 3 180.00 ! glycerol, beta1 6/07 +CL OSL CTL1 CTL3 1.453 2 180.00 ! glycerol, beta1 6/07 +CL OSL CTL1 CTL3 0.837 1 180.00 ! glycerol, beta1 6/07 +CL OSL CTL2 CTL1 0.267 3 180.00 ! glycerol, gamma1 6/07 +CL OSL CTL2 CTL1 0.173 2 0.00 ! glycerol, gamma1 6/07 +CL OSL CTL2 CTL1 0.781 1 180.00 ! glycerol, gamma1 6/07 +X CTL2 NTL X 0.26 3 0.00 ! tetramethylammonium +X CTL5 NTL X 0.23 3 0.00 ! tetramethylammonium +X CTL1 NH3L X 0.10 3 0.00 ! for POPS +X CTL2 NH3L X 0.10 3 0.00 ! ethanolamine +NH3L CTL2 CTL2 OHL 0.7 1 180.00 ! ethanolamine +NH3L CTL2 CTL2 OSLP 0.7 1 180.00 ! ethanolamine +NTL CTL2 CTL2 OHL 4.3 1 180.00 ! choline, 12/92 +NTL CTL2 CTL2 OHL -0.4 3 180.00 ! choline, 12/92 +NTL CTL2 CTL2 OSLP 3.3 1 180.00 ! choline, 12/92 +NTL CTL2 CTL2 OSLP -0.4 3 180.00 ! choline, 12/92 +X CTL1 CTL1 X 0.200 3 0.00 ! alkane, 3/92 +X CTL1 CTL2 X 0.200 3 0.00 ! alkane, 3/92 +X CTL1 CTL3 X 0.200 3 0.00 ! alkane, 3/92 +X CTL2 CTL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell +X CTL2 CTL3 X 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell +X CTL3 CTL3 X 0.1525 3 0.00 ! alkane, 4/98, yin and mackerell +!alkane CCCC dihedrals based on pentane, heptane and hexane vdz/vqz/ccsd(t) QM data +CTL3 CTL2 CTL2 CTL3 0.060 2 0.00 ! alkane, 7/08, jbk +CTL3 CTL2 CTL2 CTL3 0.035 5 0.00 ! alkane, 7/08, jbk +CTL2 CTL2 CTL2 CTL3 0.162 2 0.00 ! alkane, 7/08, jbk +CTL2 CTL2 CTL2 CTL3 0.047 3 180.00 ! alkane, 7/08, jbk +CTL2 CTL2 CTL2 CTL3 0.105 4 0.00 ! alkane, 7/08, jbk +CTL2 CTL2 CTL2 CTL3 0.177 5 0.00 ! alkane, 7/08, jbk +CTL2 CTL2 CTL2 CTL2 0.101 2 0.00 ! alkane, 7/08, jbk +CTL2 CTL2 CTL2 CTL2 0.142 3 180.00 ! alkane, 7/08, jbk +CTL2 CTL2 CTL2 CTL2 0.074 4 0.00 ! alkane, 7/08, jbk +CTL2 CTL2 CTL2 CTL2 0.097 5 0.00 ! alkane, 7/08, jbk +HAL3 CTL3 OSL SL 0.00 3 0.00 ! methylsulfate +CTL2 OSL SL O2L 0.00 3 0.00 ! methylsulfate +CTL3 OSL SL O2L 0.00 3 0.00 ! methylsulfate +HEL1 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update +CTL3 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update +X CEL1 CEL1 X 0.4500 1 180.00 ! 2-butene, adm jr., 4/04 +X CEL1 CEL1 X 8.5000 2 180.00 ! +X CEL2 CEL2 X 4.9000 2 180.00 ! ethene, yin,adm jr., 12/95 +CTL2 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 +CTL3 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 +HEL1 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 +!alkene update, 2004,2009 +CEL1 CEL1 CTL2 HAL2 0.3000 3 180.00 !2-butene, adm jr., 4/04 +CEL1 CEL1 CTL3 HAL3 0.3000 3 180.00 !2-butene, adm jr., 4/04 +!CEL1 CEL1 CTL2 CTL3 0.9000 1 180.00 !2-pentene and 3-heptene +!CEL1 CEL1 CTL2 CTL3 0.2000 2 180.00 !2-pentene and 3-heptene +CEL1 CEL1 CTL2 CTL3 0.9100 1 180.0 !2-hexene, adm jr., 11/09, end fix jbk +CEL1 CEL1 CTL2 CTL3 0.1800 2 180.0 !2-hexene, adm jr., 11/09 +CEL1 CEL1 CTL2 CTL3 0.1700 3 180.0 !2-hexene, adm jr., 11/09 +CEL1 CEL1 CTL2 CTL2 0.9100 1 180.0 !2-hexene, adm jr., 11/09 +CEL1 CEL1 CTL2 CTL2 0.1800 2 180.0 !2-hexene, adm jr., 11/09 +CEL1 CEL1 CTL2 CTL2 0.1700 3 180.0 !2-hexene, adm jr., 11/09 +CEL1 CTL2 CTL2 CL 0.1400 1 180.0 !2-hexene, adm jr., 11/09, add jbk for DHA +CEL1 CTL2 CTL2 CL 0.1700 2 0.0 !2-hexene, adm jr., 11/09, add jbk for DHA +CEL1 CTL2 CTL2 CL 0.0500 3 180.0 !2-hexene, adm jr., 11/09, add jbk for DHA +CEL1 CTL2 CTL2 CTL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 +CEL1 CTL2 CTL2 CTL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 +CEL1 CTL2 CTL2 CTL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 +CEL1 CTL2 CTL2 CTL3 0.1400 1 180.0 !2-hexene, adm jr., 11/09 +CEL1 CTL2 CTL2 CTL3 0.1700 2 0.0 !2-hexene, adm jr., 11/09 +CEL1 CTL2 CTL2 CTL3 0.0500 3 180.0 !2-hexene, adm jr., 11/09 +CEL2 CEL1 CTL2 CTL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CTL2 CTL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CTL2 CTL3 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CTL2 CTL3 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CTL2 HAL2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95 +CEL2 CEL1 CTL3 HAL3 0.0500 3 180.00 ! propene, yin,adm jr., 12/95 +HEL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 +HEL1 CEL1 CTL2 CTL3 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 +HEL1 CEL1 CTL2 HAL2 0.0000 3 0.00 ! butene, adm jr., 2/00 update +HEL1 CEL1 CTL3 HAL3 0.0000 3 0.00 ! butene, adm jr., 2/00 update +! 1,4-dipentene, adm jr., 2/00 +CEL2 CEL1 CTL2 CEL1 1.200 1 180.00 !1,4-dipentene +CEL2 CEL1 CTL2 CEL1 0.400 2 180.00 !1,4-dipentene +CEL2 CEL1 CTL2 CEL1 1.300 3 180.00 !1,4-dipentene +CEL1 CTL2 CEL1 HEL1 0.000 2 0.00 !1,4-dipentene +CEL1 CTL2 CEL1 HEL1 0.000 3 0.00 !1,4-dipentene +! 2,5-diheptene, jbk., 9/2010 +! for CIS double bonds in polyunsaturated lipids (default) +CEL1 CEL1 CTL2 CEL1 0.850 1 180.00 !2,5-diheptane +CEL1 CEL1 CTL2 CEL1 0.300 2 180.00 !2,5-diheptane +CEL1 CEL1 CTL2 CEL1 0.260 3 0.00 !2,5-diheptane +CEL1 CEL1 CTL2 CEL1 0.096 4 0.00 !2,5-diheptane +! for TRANS double bonds in polyunsaturated lipids +! uncomment following 4 lines and comment previous 4 lines to use +!CEL1 CEL1 CTL2 CEL1 1.200 1 180.00 !2,5-diheptane +!CEL1 CEL1 CTL2 CEL1 0.200 2 180.00 !2,5-diheptane +!CEL1 CEL1 CTL2 CEL1 1.200 3 180.00 !2,5-diheptane +!CEL1 CEL1 CTL2 CEL1 0.100 4 180.00 !2,5-diheptane + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +OBL X X CL 100.00 0 0.00 ! acetic acid +HEL2 HEL2 CEL2 CEL2 3.00 0 0.00 ! ethene, yin,adm jr., 12/95 +OCL X X CL 96.00 0 0.00 ! acetate +OCL X X CCL 96.00 0 0.00 ! for POPS + + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +HOL 0.0 -0.046 0.2245 +HAL1 0.0 -0.022 1.3200 ! alkane, 3/92 +HAL2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98 +HAL3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98 +HBL 0.0 -0.022 1.3200 ! for POPS +HCL 0.0 -0.046 0.2245 ! ethanolamine +HL 0.0 -0.046 0.7 ! polar H on NC4+ +HEL1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95 +HEL2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95 +! +CL 0.0 -0.0700 2.00 ! methyl acetate update +CCL 0.0 -0.0700 2.00 ! for POPS +CTL1 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92 +CTL2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CTL3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CTL5 0.0 -0.0800 2.06 0.0 -0.01 1.9 ! old CTL3 + ! maintained for tetramethylammonium +CEL1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95 +CEL2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95 +CRL1 0.0 -0.0360 2.010 0.0 -0.01 1.9 ! CGAFF, jbk add for cholesterol +CRL2 0.0 -0.0600 2.020 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv (jbk add) + +! +OBL 0.0 -0.12 1.70 0.0 -0.12 1.4 +OCL 0.0 -0.12 1.70 +O2L 0.0 -0.12 1.70 +OHL 0.0 -0.1521 1.77 +OSL 0.0 -0.1000 1.6500 !viv dec06 ether parameter +OSLP 0.0 -0.1000 1.6500 !viv dec06 ether parameter +! +NH3L 0.0 -0.20 1.85 ! ethanolamine +NTL 0.0 -0.20 1.85 ! as all other nitogens +! +SL 0.0 -0.47 2.1 ! methylsulfate +PL 0.0 -0.585 2.15 ! ADM Jr. + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +! + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/par_all36_na.prm b/charmm/toppar/par_all36_na.prm new file mode 100644 index 00000000..47876b41 --- /dev/null +++ b/charmm/toppar/par_all36_na.prm @@ -0,0 +1,1253 @@ +* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Parameter File //// +* Alexander D. MacKerell Jr. and coworkers +* April 2011 +* All comments to the CHARMM web site: www.charmm.org parameter +* set discussion forum +* + +!2010/2011 additions +! ejd, 2010 RNA update +! adm, 2011 DNA update +! For DNA update, new atom type required for P of DNA. This required +! replication of a number of parameters and the creation of new +! patches, DEOX and DEO5, to convert RNA to DNA, such that previous +! CHARMM scripts to generate DNA will no longer work. Note that the +! atom type change to P3 ONLY applies to the phosphodester linkage in +! DNA and NOT to terminal phosphates, DMP etc. +! +! +!references +! +!NUCLEIC ACIDS +! +!Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and +!MacKerell Jr., A.D. “Optimization of the CHARMM additive force field +!for DNA: Improved treatment of the BI/BII conformational +!equilibrium,” Journal of Chemical Theory and Computation, 8:348–362, +!2012, http://dx.doi.org/10.1021/ct200723y +! +!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D., +!“Impact of 2’-hydroxyl sampling on the conformational properties of +!RNA: Update of the CHARMM all-atom additive force field for RNA,” +!JCC, In Press, 2011, NIHMSID #272247 + +!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for +!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and +!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104. +! +!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for +!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA +!and RNA in Solution. JCC, 2000, 21: 105-120. +! + +ATOMS +MASS 91 HN1 1.008000 ! Nucleic acid amine proton +MASS 92 HN2 1.008000 ! Nucleic acid ring nitrogen proton +MASS 93 HN3 1.008000 ! Nucleic acid aromatic carbon proton +MASS 94 HN4 1.008000 ! Nucleic acid phosphate hydroxyl proton +MASS 95 HN5 1.008000 ! Nucleic acid ribose hydroxyl proton +MASS 96 HN6 1.008000 ! Nucleic acid ribose aliphatic proton +MASS 97 HN7 1.008000 ! Nucleic acid proton (equivalent to protein HA) +MASS 98 HN8 1.008000 ! Bound to CN8 in nucleic acids/model compounds +MASS 99 HN9 1.008000 ! Bound to CN9 in nucleic acids/model compounds +MASS 100 CN1 12.011000 ! Nucleic acid carbonyl carbon +MASS 101 CN1T 12.011000 ! Nucleic acid carbonyl carbon (T/U C2) +MASS 102 CN2 12.011000 ! Nucleic acid aromatic carbon to amide +MASS 103 CN3 12.011000 ! Nucleic acid aromatic carbon +MASS 104 CN3T 12.011000 ! Nucleic acid aromatic carbon, Thy C5 +MASS 105 CN4 12.011000 ! Nucleic acid purine C8 and ADE C2 +MASS 106 CN5 12.011000 ! Nucleic acid purine C4 and C5 +MASS 107 CN5G 12.011000 ! Nucleic acid guanine C5 +MASS 108 CN7 12.011000 ! Nucleic acid carbon (equivalent to protein CT1) +MASS 109 CN7B 12.011000 ! Nucleic acid aliphatic carbon for C1' +MASS 110 CN8 12.011000 ! Nucleic acid carbon (equivalent to protein CT2) +MASS 111 CN8B 12.011000 ! Nucleic acid carbon (equivalent to protein CT2) +MASS 112 CN9 12.011000 ! Nucleic acid carbon (equivalent to protein CT3) +MASS 113 NN1 14.007000 ! Nucleic acid amide nitrogen +MASS 114 NN2 14.007000 ! Nucleic acid protonated ring nitrogen +MASS 115 NN2B 14.007000 ! From NN2, for N9 in GUA different from ADE +MASS 116 NN2U 14.007000 ! Nucleic acid protonated ring nitrogen, ura N3 +MASS 117 NN2G 14.007000 ! Nucleic acid protonated ring nitrogen, gua N1 +MASS 118 NN3 14.007000 ! Nucleic acid unprotonated ring nitrogen +MASS 119 NN3A 14.007000 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 +MASS 120 NN3G 14.007000 ! Nucleic acid unprotonated ring nitrogen, gua N3 +MASS 121 NN4 14.007000 ! Nucleic acid purine N7 +MASS 122 NN6 14.007000 ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3) +MASS 123 ON1 15.999400 ! Nucleic acid carbonyl oxygen +MASS 124 ON1C 15.999400 ! Nucleic acid carbonyl oxygen, cyt O2 +MASS 125 ON2 15.999400 ! Nucleic acid phosphate ester oxygen +MASS 126 ON3 15.999400 ! Nucleic acid =O in phosphate +MASS 127 ON4 15.999400 ! Nucleic acid phosphate hydroxyl oxygen +MASS 128 ON5 15.999400 ! Nucleic acid ribose hydroxyl oxygen +MASS 129 ON6 15.999400 ! Nucleic acid deoxyribose ring oxygen +MASS 130 ON6B 15.999400 ! Nucleic acid ribose ring oxygen +MASS 131 P 30.974000 ! phosphorus +MASS 132 P2 30.974000 ! phosphorus, adm, 2011 DNA update + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +!2-(aminobutyl)-1,3-propandiol terms +CN8 NN6 200.000 1.480 ! methylammonium +NN6 HN1 403.000 1.040 ! methylammonium +!abasic deoxynucleoside +ON6 CN8B 260.0 1.420 ! susil +CN8 CN8B 222.50 1.528 ! Alkanes, sacred +! +CN1 CN3 302.0 1.409 !U, adm jr. 11/97 +CN1 CN3T 302.0 1.403 !T, adm jr. 11/97 +CN1 CN5G 302.0 1.360 !G, adm jr. 11/97 +CN1 NN2 380.0 1.367 !C, adm jr. 11/97 +CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97 +CN1 NN2G 340.0 1.396 !G, adm jr. 11/97 +CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97 +CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97 +CN1 NN3 350.0 1.335 !C, adm jr. 11/97 +CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95 +CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91 +CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91 +CN2 CN3 320.0 1.406 !C, adm jr. 11/97 +CN2 CN5 360.0 1.358 !A, adm jr. 11/97 +CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91 +CN2 NN2G 400.0 1.392 !G +CN2 NN3 450.0 1.343 !C +CN2 NN3A 400.0 1.342 !A, adm jr. 11/97 +CN2 NN3G 320.0 1.326 !G, adm jr. 11/97 +CN3 CN3 500.0 1.326 !C,U adm jr. 11/97 +CN3 CN3T 560.0 1.320 !T, adm jr. 11/97 +CN3T CN9 230.0 1.478 !T, adm jr. 11/97 +CN3 HN3 350.0 1.09 !C,U, JWK +CN3T HN3 350.0 1.09 !T, JWK +CN3 NN2 302.0 1.343 !C, adm jr. 11/97 +CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97 +CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91 +CN4 NN2 320.0 1.374 !A, adm jr. 11/97 +CN4 NN2B 300.0 1.378 !G, adm jr. 11/97 +CN4 NN3A 420.0 1.322 !A, adm jr. 11/97 +CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97 +CN5 CN5 310.0 1.361 !A, adm jr. 11/97 +CN5 CN5G 320.0 1.350 !G, adm jr. 11/97 +CN5 NN2 300.0 1.375 !A, adm jr. 11/97 +CN5 NN2B 302.0 1.375 !G, adm jr. 11/97 +CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91 +CN5 NN3G 350.0 1.315 !G, adm jr. 11/97 +CN5 NN4 310.0 1.355 !A, adm jr. 11/97 +CN5G NN4 310.0 1.365 !G, adm jr. 11/97 +CN8 CN8 222.50 1.528 !Alkanes, sacred +CN8 CN9 222.50 1.528 !Alkanes, sacred +CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR. +CN8 ON5 428.0 1.42 !RIBOSE, MeOH +CN9 HN9 322.0 1.111 !alkanes +CN9 ON2 340.0 1.43 !DMP, ADM Jr. +HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91 +HN2 NN2 474.0 1.01 !C,U, JWK +HN2 NN2B 474.0 1.01 !G, adm jr. 11/97 +HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91 +HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91 +HN4 ON4 545.0 0.960 !MP_1, ADM Jr. +ON2 P 270.0 1.60 !DMP, ADM Jr. +ON2 P2 270.0 1.60 !DMP, ADM Jr., adm, 2011 DNA update +ON3 P 580.0 1.48 !DMP, ADM Jr. +ON3 P2 580.0 1.48 !DMP, ADM Jr., adm, 2011 DNA update +ON4 P 237.0 1.58 !MP_1, ADM Jr. +ON4 P2 237.0 1.58 !MP_1, ADM Jr., adm, 2011 DNA update +!NN5 HN1 460.0 1.01 !sugar model, adm jr. +!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@ +CN7B ON6 260.0 1.420 ! From exp +CN7B CN8 200.0 1.518 ! From exp +CN7 ON6 240.0 1.446 ! Fom exp. +CN7 CN7 222.5 1.529 ! From exp +CN7 CN8 222.5 1.516 ! From exp. +CN7 CN9 222.5 1.516 ! for 5MET, From alkanes +CN7 HN7 309.0 1.111 !Alkanes, sacred +CN8 HN8 309.0 1.111 !Alkanes, sacred +CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF) +!@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@ +!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@ +CN7B ON6B 260.0 1.420 ! From CN7B ON6 +CN7 ON6B 240.0 1.480 ! From CN7 ON6 +CN7B CN7B 200.0 1.450 ! +CN7 CN7B 222.5 1.460 ! Specific to RNA +!@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@ + +!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@ +CN7 CN8B 222.5 1.512 ! From exp. +CN8B ON2 320.0 1.44 ! From exp +!CN8B ON5 250.0 1.44 ! From CN8B ON2 +CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98 +CN7 ON2 310.0 1.433 ! From exp +CN7B ON2 310.0 1.433 ! From exp, for NADPH and bkbmod +!CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO +CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98 +! C1'-N9 (purines)/C1'-N1 (pyrimidines) +CN9 NN2 400.0 1.456 !9-M-A/C, adm jr. +CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr. +CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr. +CN7B NN2 220.0 1.456 !A/C +CN7B NN2B 220.0 1.458 !G/T/U +! C5'-H in model compounds and DNA +CN8B HN8 309.0 1.111 !Alkanes, sacred +ON5 HN5 545.0 0.960 !RIBOSE, MeOH +!@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@ + +!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@ +!CN7B ON5 250.0 1.400 ! From CN7 ON5 +CN7B ON5 428.0 1.400 ! check adm jr., +!FC should be 428.000 based on Meoh +!@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@ + +!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@ +CN8 ON2 340.0 1.44 ! +!@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@ + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +! angle parameters have been rearranged based on model +! compounds and functional groups. Additional angle +! parameters follow sorted based on the central atom +! +!2-(aminobutyl)-1,3-propandiol terms +CN7 CN8 CN8 58.35 113.60 11.16 2.561 !alkane +CN8 CN7 CN8 58.35 113.60 11.16 2.561 !alkane +CN8 CN8 CN8 58.35 113.60 11.16 2.561 !alkane +HN1 NN6 CN8 30.00 109.50 20.00 2.074 !methylammonium +NN6 CN8 HN8 45.00 107.50 35.00 2.101 !methylammonium +CN7 CN8 ON2 115.00 109.70 !DNA exocyclic angles +NN6 CN8 CN8 67.70 110.00 !methylammonium +HN1 NN6 HN1 44.00 109.50 !methylammonium +!abasic propyl linkage +ON2 CN8 CN8 115.0 109.7 !DNA exocyclic angles +!abasic deoxynucleoside +CN7 ON6 CN8B 110.0 109.0 +ON6 CN8B CN8 90.0 106.0 +CN8B CN8 CN7 80.0 106.0 +ON6 CN8B HN8 45.2 107.24 ! +HN8 CN8B CN8 34.53 110.10 22.53 2.179 ! alkane +HN8 CN8 CN8B 34.53 110.10 22.53 2.179 ! alkane + +! pyrmidines +!@@@@@@@@ Adenine +! ade 6-mem ring +CN2 NN3A CN4 90.0 117.8 !6R) adm jr. 11/97 +NN3A CN4 NN3A 60.0 133.0 !6R) +CN4 NN3A CN5 90.0 110.1 !6R) +CN5 CN5 NN3A 60.0 127.4 !6R) bridgeC4 +CN2 CN5 CN5 60.0 121.0 !6R) bridgeC5 +CN5 CN2 NN3A 60.0 110.7 !6R) +CN5 CN5 NN2 100.0 105.7 !5R) bridgeC4 +CN5 CN5 NN4 100.0 110.0 !5R) bridgeC5 +CN4 NN4 CN5 120.0 104.6 !5R) +NN2 CN4 NN4 100.0 113.4 !5R) +CN4 NN2 CN5 100.0 106.3 !5R) +NN2 CN5 NN3A 100.0 126.9 !bridgeC4 +CN2 CN5 NN4 100.0 129.0 !bridgeC5 +HN3 CN4 NN3A 38.0 113.5 !h2 +NN3A CN2 NN1 50.0 130.7 !n6 +CN5 CN2 NN1 50.0 118.6 ! +CN2 NN1 HN1 40.0 121.5 !h61,h62, C,A,G +HN1 NN1 HN1 31.0 117.0 !C,A,G +NN4 CN4 HN3 39.0 124.8 !h8, G,A +NN2 CN4 HN3 39.0 121.8 ! +CN5 NN2 HN2 30.0 129.4 !h9 +CN4 NN2 HN2 30.0 125.0 ! +!@@@@@@@@ Guanine +! gua 6-mem ring +CN1 NN2G CN2 70.0 131.1 !6R)G, adm jr. 11/97 +NN2G CN2 NN3G 70.0 122.2 !6R) +CN2 NN3G CN5 90.0 109.4 !6R) +CN5G CN5 NN3G 70.0 129.9 !6R) bridgeC4 +CN1 CN5G CN5 70.0 119.6 !6R) bridgeC5 +CN5G CN1 NN2G 70.0 107.8 !6R) +CN5G CN5 NN2B 100.0 104.6 !5R) bridgeC4 +CN5 CN5G NN4 100.0 111.4 !5R) bridgeC5 +CN4 NN4 CN5G 120.0 103.8 !5R) +NN2B CN4 NN4 100.0 113.0 !5R) +CN4 NN2B CN5 100.0 107.2 !5R) +NN2B CN5 NN3G 140.0 125.5 ! bridgeC4 +CN1 CN5G NN4 125.0 129.0 ! bridgeC5 +CN1 NN2G HN2 45.0 113.3 ! h1 +CN2 NN2G HN2 45.0 115.6 ! +NN1 CN2 NN2G 95.0 115.4 ! n2 +NN1 CN2 NN3G 95.0 122.4 ! +NN2G CN1 ON1 50.0 127.5 ! o6 +CN5G CN1 ON1 50.0 124.7 ! +HN3 CN4 NN2B 40.0 122.2 ! h8 (NN4 CN4 HN3 124.8) +CN4 NN2B HN2 30.0 124.6 ! h9 +CN5 NN2B HN2 30.0 129.3 ! +!@@@@@@@@ Cytosine +! cyt 6-mem ring +CN1 NN2 CN3 50.0 124.1 !C, adm jr. 11/97 +NN2 CN1 NN3 50.0 116.8 !C +CN1 NN3 CN2 85.0 119.1 !C +CN3 CN2 NN3 85.0 119.3 !C +CN2 CN3 CN3 85.0 117.8 !C +CN3 CN3 NN2 85.0 122.9 !C +CN1 NN2 HN2 37.0 121.2 !C, h1 +CN3 NN2 HN2 37.0 114.7 !C +NN2 CN1 ON1C 130.0 119.4 !C, o2 +NN3 CN1 ON1C 130.0 123.8 !C +NN3 CN2 NN1 81.0 122.3 !C, n4 +CN3 CN2 NN1 81.0 118.4 !C +CN2 CN3 HN3 38.0 120.1 !C h5 +CN3 CN3 HN3 38.0 122.1 !C,U +HN3 CN3 NN2 44.0 115.0 !C, h6 +!@@@@@@@@ Uracil +! ura 6-mem ring +CN1T NN2B CN3 70.0 122.0 !U, adm jr. 11/97 +NN2B CN1T NN2U 50.0 114.0 !U +CN1T NN2U CN1 50.0 130.2 !U +NN2U CN1 CN3 70.0 112.6 !U +CN1 CN3 CN3 100.0 117.6 !U +CN3 CN3 NN2B 100.0 123.6 !U +CN1T NN2B HN2 40.5 122.0 !U, h1 +CN3 NN2B HN2 32.0 116.0 !U +NN2B CN1T ON1 100.0 121.6 !U, o2 +NN2U CN1T ON1 100.0 124.4 !U +CN1T NN2U HN2 40.5 114.4 !U, h3 +CN1 NN2U HN2 40.5 115.4 !U +NN2U CN1 ON1 100.0 121.9 !U, o4 +CN3 CN1 ON1 100.0 125.5 !U, +CN1 CN3 HN3 30.0 120.3 !U, h5 +HN3 CN3 NN2B 30.0 114.3 !U, h6 +! thymine 6-mem ring (unique from ura) +CN3T CN1 NN2U 70.0 113.5 !T, adm jr. 11/97 +CN1 CN3T CN3 120.0 116.7 !T +CN3T CN3 NN2B 120.0 123.6 !125.3 !T +CN3T CN1 ON1 100.0 124.6 !T, o4 +CN1 CN3T CN9 38.0 118.7 !T, c5 methyl +CN3 CN3T CN9 38.0 124.6 !T +CN3T CN3 HN3 30.0 122.1 !T, h6 +! base to methyl connection +CN1T NN2B CN9 70.0 116.0 !1-M-T/U, adm jr. +CN3 NN2B CN9 70.0 122.0 !1-M-T/U, adm jr. 7/24/91 +CN1 NN2 CN9 70.0 115.4 !1-M-C, adm jr. +CN3 NN2 CN9 70.0 120.5 !1-M-C, adm jr. 7/24/91 +CN5 NN2 CN9 70.0 125.9 !9-M-A, adm jr. +CN4 NN2 CN9 70.0 127.8 !9-M-A, adm jr. +CN5 NN2B CN9 70.0 125.9 !9-M-G, adm jr. +CN4 NN2B CN9 70.0 126.9 !9-M-G, adm jr. +CN5 NN2B CN8 70.0 125.9 !9-E-G, adm jr. +CN4 NN2B CN8 70.0 126.9 !9-E-G, adm jr. +NN2B CN8 CN9 70.0 113.7 !9-E-G, adm jr. +!===== For glycosydic linkage, base to c1' +CN1T NN2B CN7B 45.0 118.4 !U/T, FC from A +CN3 NN2B CN7B 45.0 119.6 !U/T +CN1 NN2 CN7B 45.0 120.0 !C, FC from A +CN3 NN2 CN7B 45.0 115.9 !C +CN5 NN2 CN7B 45.0 126.1 !A +CN4 NN2 CN7B 45.0 127.6 !A +CN5 NN2B CN7B 45.0 126.5 !G +CN4 NN2B CN7B 45.0 126.3 !G +ON6 CN7B NN2 110.0 108.0 !C/A DNA +ON6B CN7B NN2 110.0 112.0 !C/A RNA +CN8 CN7B NN2 110.0 113.7 !C/A +CN7B CN7B NN2 110.0 111.0 !C/A, RNA +ON6 CN7B NN2B 110.0 108.0 !T/U/G (DNA) FC from A +ON6B CN7B NN2B 110.0 112.0 !T/U/G (RNA) FC from A +CN8 CN7B NN2B 110.0 113.7 !T/U/G +CN7B CN7B NN2B 110.0 111.0 !T/U/G, RNA +HN7 CN7B NN2 43.0 111.0 ! +HN7 CN7B NN2B 43.0 111.0 !From HN7 CN7B NN2 +!===== End of glycosydic linkage +! remaining terms ordered based on central atom +CN9 CN8 HN8 34.6 110.10 22.53 2.179 ! Alkanes, sacred +CN9 CN7 HN7 34.6 110.10 22.53 2.179 ! Alkanes, sacred +HN8 CN8 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM +HN8 CN8 ON5 45.9 108.89 !RIBOSE, Adm Jr. MeOH +CN3 CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred +CN3T CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred +CN8 CN9 HN9 34.60 110.10 22.53 2.179 ! Alkanes, sacred +HN9 CN9 CN7 33.43 110.1 22.53 2.179 ! Alkanes, sacred +HN9 CN9 NN2 33.43 110.1 !FOR 9-M-A(T), adm jr. +HN9 CN9 NN2B 33.43 110.1 !FOR 9-M-G(C), adm jr. +HN8 CN8 NN2B 33.43 110.1 !FOR 9-E-G, adm jr. +HN9 CN9 ON2 60.0 109.5 !DMP, ADM Jr. +!HN1 NN5 HN1 39.0 106.0 ! sugar model, adm jr. +CN9 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr. +HN4 ON4 P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. +HN4 ON4 P2 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. , adm, 2011 DNA update +HN5 ON5 CN8 57.5 106.0 !RIBOSE, Adm Jr. MeOH +HN5 ON5 CN9 57.5 106.0 !RIBOSE, Adm Jr. MeOH +ON2 P ON2 80.0 104.3 !DMP, ADM Jr. +ON2 P2 ON2 80.0 104.3 !DMP, ADM Jr., adm, 2011 DNA update +ON2 P ON4 48.1 108.0 !MP_1, ADM Jr. +ON2 P2 ON4 48.1 108.0 !MP_1, ADM Jr., adm, 2011 DNA update +ON3 P ON4 98.9 108.23 !MP_1, ADM Jr. +ON3 P2 ON4 98.9 108.23 !MP_1, ADM Jr., adm, 2011 DNA update +ON4 P ON4 98.9 104.0 !MP_0, ADM Jr. +ON4 P2 ON4 98.9 104.0 !MP_0, ADM Jr., adm, 2011 DNA update +CN7 CN8 ON5 75.7 110.10 !RIBOSE, adm jr. MeOH +HN9 CN9 HN9 35.500 108.40 5.40 1.802 !alkane update, adm jr. 3/2/92 +!@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@ +CN7 ON6 CN7B 110.0 108.0 ! NF, 11/97, C4'O4'C1' +ON6 CN7B CN8 90.0 102.0 ! NF, 11/97, C4'O4'C1' +CN7B CN8 CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3' +CN8 CN7 CN7 60.00 102.0 8.0 2.561 !NF, 11/97, C2'C3'C4' +CN9 CN7 CN7 60.00 102.0 8.0 2.561 !for 5MET, adm jr. +CN7 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4' +HN7 CN7 ON6 45.2 107.24 ! +HN7 CN7B ON6 45.2 107.24 ! +HN7 CN7 CN7 40.0 108.00 ! +CN7B CN8 HN8 33.4 110.10 22.53 2.179 ! following terms directly +CN8 CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes +HN7 CN7 CN8 34.5 110.1 22.53 2.179 ! +HN8 CN8 CN7 34.53 110.10 22.53 2.179 ! +HN8 CN8 CN8 34.53 110.10 22.53 2.179 ! +HN8 CN8 HN8 35.5 109.00 5.40 1.802 ! +HN7 CN7 HN7 35.5 109.00 5.40 1.802 ! +!@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@ + +!@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@ +CN7 ON6B CN7B 110.0 115.0 ! From CN7 ON6 CN7B +CN7 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6 +ON6B CN7B CN7B 90.0 106.0 ! 030998 +CN7B CN7B CN7 110.0 96.0 ! +CN7B CN7 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4' +HN7 CN7 ON6B 45.2 107.24 ! +HN7 CN7B ON6B 45.2 107.24 ! +CN7B CN7B HN7 33.4 110.10 22.53 2.179 ! following terms directly +HN7 CN7B HN7 35.5 109.00 5.40 1.802 ! +!@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@ + +!@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@ +ON6 CN7 CN8B 90.0 108.2 !NF, 11/97, O4'C4'C5' +ON6 CN7 CN9 90.0 108.2 !for 5MET, adm jr. +CN7 CN7 CN8B 45.0 110.0 !NF, 11/97, C3'C4'C5' +CN8 CN7 CN8B 58.35 113.60 11.16 2.561 ! from alkane, 25P1 +CN7 CN8B ON2 70.0 108.4 !NF, 11/97, C4'C5'O5' +CN7 CN7 ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' +CN7B CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH and bkbmod +CN8 CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3' +CN8B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P +CN8B ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P, adm, 2011 DNA update +CN7 ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P +CN7 ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, adm, 2011 DNA update +CN7B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod +CN7B ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod, adm, 2011 DNA update +! sugar +HN7 CN7 CN8B 34.5 110.1 22.53 2.179 ! From HN7 CN7 CN8 +HN8 CN8B ON2 60.0 109.5 ! From HN7 CN8 ON2 +HN5 ON5 CN8B 57.5 106.0 ! From HN5 ON5 CN8 +HN8 CN8B HN8 35.5 109.0 5.40 1.802 ! Alkanes, sacred +HN8 CN8B CN7 34.53 110.1 22.53 2.179 ! Alkanes, sacred +HN7 CN7 ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2 +HN7 CN7B ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2, for NADPH and bkbmod +!===== For 5ter patch: +CN7 CN8B ON5 75.7 110.10 ! From CN7 CN8B ON5 +CN8B CN7 ON5 90.0 108.2 ! phosphoramidate, carbocyclic +HN8 CN8B ON5 45.9 108.89 ! From HN7 CN8 ON5 +!===== For 3ter patch: +ON5 CN7 CN8 75.7 110.0 ! from CHARMM22 +ON5 CN7 CN7 75.7 110.1 ! +HN7 CN7 ON5 60.0 109.5 ! +HN5 ON5 CN7 57.5 109.0 ! +!@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@ + +!@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@ +!O4'-C4'-C5' +ON6B CN7 CN8B 90.0 108.2 ! +ON6B CN7 CN9 90.0 108.2 ! for 5MET patch, adm jr. +!O3'-C3'-C2' +ON2 CN7 CN7B 90.0 110.0 ! +ON5 CN7 CN7B 90.0 110.0 ! From ON5 CN7 CN8 +!O2'-C2'-C1' +ON5 CN7B CN7B 80.0 108.4 ! +!O2'-C2'-C3' +ON5 CN7B CN7 90.0 108.0 ! +HN7 CN7B ON5 60.0 109.5 ! +HN5 ON5 CN7B 57.5 109.0 ! +HN7 CN7B CN7 34.53 110.10 22.53 2.179 +HN7 CN7 CN7B 34.53 110.10 22.53 2.179 + +!@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@ + +!@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@ +CN8 ON2 P 20.0 120.0 35. 2.33 !DMP, adm jr. +CN8 ON2 P2 20.0 120.0 35. 2.33 !DMP, adm jr., adm 2011 DNA update +!@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@ +ON2 P ON3 98.9 111.6 !DMP, adm jr. +ON2 P2 ON3 98.9 111.6 !DMP, adm jr., adm, 2011 DNA update +ON3 P ON3 120.0 120.0 !DMP, adm jr. +ON3 P2 ON3 120.0 120.0 !DMP, adm jr., adm, 2011 DNA update +HN8 CN8 ON2 60.0 109.5 !DMP, adm jr. +ON5 P ON3 98.9 111.6 ! From ON2 P ON3 +!------------------------ added for araim ---------------------- +ON6 CN7B CN7 120.0 106.25 ! +CN7B CN7 CN8 58.35 113.6 11.16 2.561 ! + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +!2-(aminobutyl)-1,3-propandiol terms +X CN8 ON2 X -0.10 3 0.0 ! phosphate ester +X CN7 CN8 X 0.20 3 0.0 ! alkane +X CN8 NN6 X 0.10 3 0.0 ! methylammonium +!abasic nucleoside terms - susil +CN7 ON6 CN8B HN8 0.195 1 0.0 +ON6 CN8B CN8 HN8 0.195 1 0.0 +HN7 CN7 ON6 CN8B 0.195 3 0.0 +CN8B CN8 CN7 HN7 0.195 3 0.0 +HN8 CN8B CN8 HN8 0.195 3 0.0 +HN8 CN8B CN8 CN7 0.195 3 0.0 +! c5'-c4'-o4'-c1', exo +CN8B CN7 ON6 CN8B 0.5 5 0.0 ! min at 150 310 max at 25 200 +CN8B CN7 ON6 CN8B 0.1 3 180.0 +CN8B CN7 ON6 CN8B 0.5 1 0.0 +! c1'-c2'-c3'-o3', exo +CN8B CN8 CN7 ON5 0.4 5 0.0 +CN8B CN8 CN7 ON5 0.4 3 0.0 +CN8B CN8 CN7 ON5 0.7 2 0.0 !elevates energy at 0 (c3'endo), adm +CN8B CN8 CN7 ON5 0.5 1 180.0 !elevates energy at 0 (c3'endo), adm +CN8B CN8 CN7 ON2 0.4 5 0.0 !terms for oligonuclotide +CN8B CN8 CN7 ON2 0.4 3 0.0 +CN8B CN8 CN7 ON2 0.7 2 0.0 +CN8B CN8 CN7 ON2 0.5 1 180.0 +! c4'-o4'-c1'-c2', tau0 +CN7 ON6 CN8B CN8 0.6 6 180.0 +CN7 ON6 CN8B CN8 0.6 3 0.0 +! o4'-c1'-c2'-c3', tau1 +ON6 CN8B CN8 CN7 0.7 5 180.0 !lowers 90, shifts c2endo minimum towards 200 +ON6 CN8B CN8 CN7 0.4 4 0.0 !lowers 90, shifts c2endo minimum towards 200 +ON6 CN8B CN8 CN7 0.4 3 180.0 !lowers 90, shifts c2endo minimum towards 200 +! c4'-c3'-c2'-c1', tau2 +CN7 CN7 CN8 CN8B 0.5 4 0.0 +CN7 CN7 CN8 CN8B 0.1 3 0.0 !lowers energy in 150 to 250 range +! c1'-o4'-c4'-c3', tau4 +CN8B ON6 CN7 CN7 0.5 3 0.0 !effects surface in 200-360 region + +! PHOSPHATE +ON2 P2 ON2 CN7 0.90 1 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set +ON2 P2 ON2 CN7 0.40 2 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set +ON2 P2 ON2 CN7 0.20 3 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set +ON2 P ON2 CN7 1.20 1 180.0 !10/97, DMP, adm jr., RNA +ON2 P ON2 CN7 0.10 2 180.0 !10/97, DMP, adm jr., RNA +ON2 P ON2 CN7 0.10 3 180.0 !10/97, DMP, adm jr., RNA +ON2 P ON2 CN7 0.00 6 0.0 !10/97, DMP, adm jr., RNA +ON2 P ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr. +ON2 P ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr. +ON2 P ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr. +ON2 P ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr. +ON2 P2 ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr., adm 2011 DNA update +ON2 P2 ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr., adm 2011 DNA update +ON2 P2 ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr., adm 2011 DNA update +ON2 P2 ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr., adm 2011 DNA update +! Added when C5' defined as CN8B (NF 041497): +ON2 P2 ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update +ON2 P2 ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update +ON2 P2 ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update +ON2 P2 ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr., adm, 2011 DNA update +ON2 P ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr., RNA +ON2 P ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr., RNA +ON2 P ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr., RNA +ON2 P ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr., RNA +ON2 P ON2 CN9 1.20 1 180.0 !dmp +ON2 P ON2 CN9 0.10 2 180.0 !dmp +ON2 P ON2 CN9 0.10 3 180.0 !dmp +ON2 P ON2 CN9 0.00 6 0.0 !dmp +ON2 P2 ON2 CN9 1.20 1 180.0 !dmp, adm, 2011 DNA update +ON2 P2 ON2 CN9 0.10 2 180.0 !dmp, adm, 2011 DNA update +ON2 P2 ON2 CN9 0.10 3 180.0 !dmp, adm, 2011 DNA update +ON2 P2 ON2 CN9 0.00 6 0.0 !dmp, adm, 2011 DNA update +! +ON3 P ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3' +ON3 P2 ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3', adm, 2011 DNA update +ON3 P ON2 CN7B 0.10 3 0.0 !for NADPH and bkbmod +ON3 P ON2 CN8 0.10 3 0.0 !dmp +ON3 P2 ON2 CN8 0.10 3 0.0 !dmp, adm 2011 DNA update +ON3 P ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5' +ON3 P2 ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5', adm, 2011 DNA update +ON3 P ON2 CN9 0.10 3 0.0 !dmp +ON3 P2 ON2 CN9 0.10 3 0.0 !dmp, adm, 2011 DNA update +! terminal phosphate terms, adm jr. +ON4 P ON2 CN7 0.95 2 0.0 !MP_1, adm jr. +ON4 P ON2 CN7 0.50 3 0.0 !MP_1, adm jr. +ON4 P2 ON2 CN7 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update +ON4 P2 ON2 CN7 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update +ON4 P ON2 CN8 0.95 2 0.0 !MP_1, adm jr. +ON4 P ON2 CN8 0.50 3 0.0 !MP_1, adm jr. +ON4 P ON2 CN8B 0.95 2 0.0 !MP_1, adm jr. +ON4 P ON2 CN8B 0.50 3 0.0 !MP_1, adm jr. +ON4 P2 ON2 CN8B 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update +ON4 P2 ON2 CN8B 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update +ON4 P ON2 CN9 0.95 2 0.0 !MP_1, adm jr. +ON4 P ON2 CN9 0.50 3 0.0 !MP_1, adm jr. +ON4 P2 ON2 CN9 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update +ON4 P2 ON2 CN9 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update +X ON4 P X 0.30 3 0.0 !MP_1, adm jr. +X ON4 P2 X 0.30 3 0.0 !MP_1, adm jr., adm, 2011 DNA update +! When O5' is ON2 (phosphodiester linkage): +P ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P +P2 ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P, adm, 2011 DNA update +P ON2 CN7B HN7 0.000 3 0.0 !for NADPH and bkbmod +P ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P +P2 ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P, adm, 2011 DNA update +P ON2 CN8 HN8 0.000 3 0.0 !dmp +P ON2 CN9 HN9 0.000 3 0.0 !dmp +P2 ON2 CN9 HN9 0.000 3 0.0 !dmp, adm, 2011 DNA update +! butane gauche terms +cn9 cn8 cn8 cn9 0.15 1 0.0 +cn9 cn8 cn8 cn8 0.15 1 0.0 +! BASES +! Uracil +NN2B CN1T NN2U CN1 1.5 2 180.0 ! adm jr. 11/97 +CN1T NN2U CN1 CN3 1.5 2 180.0 ! adm jr. 11/97 +NN2U CN1 CN3 CN3 1.5 2 180.0 ! adm jr. 11/97 +CN1 CN3 CN3 NN2B 6.0 2 180.0 ! adm jr. 11/97 +CN3 CN3 NN2B CN1T 1.5 2 180.0 ! adm jr. 11/97 +CN3 NN2B CN1T NN2U 1.5 2 180.0 ! adm jr. 11/97 +HN3 CN3 CN3 HN3 3.0 2 180.0 ! adm jr. 11/97 +HN3 CN3 CN1 ON1 6.0 2 180.0 ! adm jr. 11/97 +ON1 CN1T NN2B HN2 0.0 2 180.0 ! adm jr. 11/97 +ON1 CN1 NN2U HN2 0.0 2 180.0 ! adm jr. 11/97 +ON1 CN1T NN2U HN2 0.0 2 180.0 ! adm jr. 11/97 +HN2 NN2B CN3 HN3 1.5 2 180.0 ! adm jr. 11/97 +NN2B CN1T NN2U HN2 3.8 2 180.0 ! adm jr. 11/97 +CN3 CN1 NN2U HN2 3.8 2 180.0 ! adm jr. 11/97 +CN3 CN3 NN2B HN2 1.6 2 180.0 ! adm jr. 11/97 +NN2U CN1T NN2B HN2 1.6 2 180.0 ! adm jr. 11/97 +!Thymine +CN1T NN2B CN3 CN3T 1.8 2 180.0 ! adm jr. 11/97 +NN2U CN1 CN3T CN3 1.8 2 180.0 ! adm jr. 11/97 +CN1 CN3T CN3 NN2B 3.0 2 180.0 ! adm jr. 11/97 +NN2B CN1 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97 +NN2B CN3 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97 +CN1 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97 +CN3 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97 +CN3T CN1 NN2U HN2 4.8 2 180.0 ! adm jr. 11/97 +! Cytosine +CN3 NN2 CN1 NN3 0.6 2 180.0 ! adm jr. 11/97 +NN2 CN1 NN3 CN2 0.6 2 180.0 ! adm jr. 11/97 +CN1 NN3 CN2 CN3 6.0 2 180.0 ! adm jr. 11/97 +NN3 CN2 CN3 CN3 0.6 2 180.0 ! adm jr. 11/97 +CN2 CN3 CN3 NN2 6.0 2 180.0 ! adm jr. 11/97 +CN3 CN3 NN2 CN1 0.6 2 180.0 ! adm jr. 11/97 +NN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97 +CN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97 +NN1 CN2 NN3 CN1 2.0 2 180.0 ! adm jr. 11/97 +NN1 CN2 CN3 CN3 2.0 2 180.0 ! adm jr. 11/97 +NN1 CN2 CN3 HN3 2.0 2 180.0 ! adm jr. 11/97 +ON1C CN1 NN2 HN2 3.0 2 180.0 ! adm jr. 11/97 +ON1C CN1 NN3 CN2 1.6 2 180.0 ! adm jr. 11/97 +ON1C CN1 NN2 CN3 1.6 2 180.0 ! adm jr. 11/97 +NN3 CN2 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97 +NN2 CN3 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97 +CN2 CN3 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97 +CN1 NN2 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97 +X CN2 NN3 X 2.0 2 180.0 ! adm jr. 11/97 +! Adenine +CN2 NN3A CN4 NN3A 1.8 2 180.0 ! adm jr. 11/97, 6-mem +NN3A CN4 NN3A CN5 2.0 2 180.0 ! +CN4 NN3A CN5 CN5 1.8 2 180.0 ! +NN3A CN5 CN5 CN2 2.0 2 180.0 ! treated 2x +CN5 CN5 CN2 NN3A 1.8 2 180.0 ! +CN5 CN2 NN3A CN4 10.0 2 180.0 ! +CN5 CN5 NN4 CN4 6.0 2 180.0 ! 5-mem +CN5 NN4 CN4 NN2 14.0 2 180.0 ! +NN4 CN4 NN2 CN5 6.0 2 180.0 ! +CN4 NN2 CN5 CN5 6.0 2 180.0 ! +NN2 CN5 CN5 NN4 14.0 2 180.0 ! treated 2x +CN2 NN3A CN4 HN3 8.5 2 180.0 ! H2 +CN5 NN3A CN4 HN3 8.5 2 180.0 ! H2 +CN5 NN4 CN4 HN3 5.2 2 180.0 ! H8 +CN5 NN2 CN4 HN3 5.2 2 180.0 ! H8 +CN5 CN5 NN2 HN2 1.2 2 180.0 ! H9 +NN4 CN4 NN2 HN2 1.2 2 180.0 ! H9 +HN2 NN2 CN4 HN3 0.0 2 180.0 ! H8-C-N-H9 +CN4 NN3A CN2 NN1 4.0 2 180.0 ! N6 +CN5 CN5 CN2 NN1 4.0 2 180.0 ! N6 +NN4 CN5 CN2 NN1 0.0 2 180.0 ! N6 +CN5 CN2 NN1 HN1 0.5 2 180.0 ! 6-NH2 +NN3A CN2 NN1 HN1 0.5 2 180.0 ! +! Butterfly motion +NN3A CN5 CN5 NN4 7.0 2 180.0 !A, adm jr. 11/97 +CN2 CN5 CN5 NN2 7.0 2 180.0 !A +NN3A CN2 CN5 NN4 2.0 2 180.0 !A +CN2 CN5 NN4 CN4 2.0 2 180.0 !A +CN4 NN3A CN5 NN2 2.0 2 180.0 !A +NN3A CN5 NN2 CN4 2.0 2 180.0 !A +! Guanine +CN1 NN2G CN2 NN3G 0.2 2 180.0 !adm jr. 11/97, 6-mem +NN2G CN2 NN3G CN5 2.0 2 180.0 ! +CN2 NN3G CN5 CN5G 0.2 2 180.0 ! +NN3G CN5 CN5G CN1 2.0 2 180.0 ! +CN5 CN5G CN1 NN2G 0.2 2 180.0 ! +CN5G CN1 NN2G CN2 0.2 2 180.0 ! +CN5 CN5G NN4 CN4 6.0 2 180.0 !5-mem +CN5G NN4 CN4 NN2B 16.0 2 180.0 ! +NN4 CN4 NN2B CN5 6.0 2 180.0 ! +CN4 NN2B CN5 CN5G 6.0 2 180.0 ! +NN2B CN5 CN5G NN4 10.0 2 180.0 ! +! substitutents +ON1 CN1 CN5G CN5 14.0 2 180.0 !G, O6 +ON1 CN1 CN5G NN4 0.0 2 180.0 ! +ON1 CN1 NN2G CN2 14.0 2 180.0 ! +ON1 CN1 NN2G HN2 0.0 2 180.0 ! +NN1 CN2 NN2G CN1 4.0 2 180.0 !G, N2 +NN1 CN2 NN3G CN5 4.0 2 180.0 ! +NN1 CN2 NN2G HN2 0.0 2 180.0 ! +NN2G CN2 NN1 HN1 1.2 2 180.0 ! +NN3G CN2 NN1 HN1 1.2 2 180.0 ! +HN2 NN2G CN1 CN5G 3.6 2 180.0 !G, H1 +HN2 NN2G CN2 NN3G 3.6 2 180.0 ! +HN3 CN4 NN4 CN5G 5.6 2 180.0 !G, H8 +HN3 CN4 NN2B CN5 5.6 2 180.0 ! +HN3 CN4 NN2B HN2 0.0 2 180.0 ! +HN2 NN2B CN5 CN5G 1.2 2 180.0 !G, H9 +HN2 NN2B CN5 NN3G 1.2 2 180.0 ! +HN2 NN2B CN4 NN4 1.2 2 180.0 ! +! Butterfly motion +NN3G CN5 CN5G NN4 10.0 2 180.0 !adm jr. 11/97 +CN1 CN5G CN5 NN2 10.0 2 180.0 ! +NN2G CN1 CN5G NN4 2.0 2 180.0 ! +CN1 CN5G NN4 CN4 2.0 2 180.0 ! +CN2 NN3G CN5 NN2B 2.0 2 180.0 ! +NN3G CN5 NN2B CN4 2.0 2 180.0 ! +! Wild cards for uracil, thymine and cytosine +X CN1 NN3 X 1.0 2 180.0 ! c22 +X CN1 NN2 X 0.9 2 180.0 ! c22 +X CN1T NN2B X 0.9 2 180.0 ! From X CN1 NN2 X, for thymines +X CN1 NN2G X 0.9 2 180.0 ! c22 +X CN1 NN2U X 0.9 2 180.0 ! c22 +X CN1T NN2U X 0.9 2 180.0 ! c22 +X CN3 NN2 X 1.0 2 180.0 ! c22 +X CN3 NN2B X 1.0 2 180.0 ! From X CN3 NN2 X, for thymines +X CN3 CN3 X 1.0 2 180.0 ! c22 +X CN3 CN3T X 1.0 2 180.0 !T, adm jr. 11/97 +X CN1 CN3 X 1.0 2 180.0 ! c22 +X CN1 CN3T X 1.0 2 180.0 !T, adm jr. 11/97 +X CN2 CN3 X 0.8 2 180.0 ! c22 +! Wild cards for adenine and guanine +X CN1 CN5G X 1.0 2 180.0 ! adm jr. 11/97 +X CN2 NN2G X 1.0 2 180.0 ! +X CN2 CN5 X 1.0 2 180.0 ! +X CN4 NN2 X 1.5 2 180.0 ! +X CN4 NN2B X 1.5 2 180.0 ! From X CN4 NN2 X +X CN4 NN3A X 3.5 2 180.0 ! +X CN4 NN4 X 2.0 2 180.0 ! A,G +X CN5 CN5 X 0.0 2 180.0 ! +X CN5G CN5 X 0.0 2 180.0 ! adm jr. 11/97 +X CN5 NN2 X 1.5 2 180.0 ! +X CN5 NN2B X 1.5 2 180.0 ! From X CN5 NN2 X +X CN5 NN3A X 1.0 2 180.0 ! +X CN5 NN3G X 1.0 2 180.0 ! adm jr. 11/97 +X CN5 NN4 X 1.0 2 180.0 ! +X CN5G NN4 X 1.0 2 180.0 ! adm jr. 11/97 +X CN2 NN3A X 1.0 2 180.0 ! +X CN2 NN3G X 1.0 2 180.0 ! adm jr. 11/97 +! MISC. +CN1 NN2 CN9 HN9 0.19 3 0.0 ! 1-M-C +CN3 NN2 CN9 HN9 0.00 3 0.0 ! 1-M-C +CN4 NN2 CN9 HN9 0.00 3 0.0 ! 9-M-A +CN5 NN2 CN9 HN9 0.19 3 0.0 ! 9-M-A +CN1 NN2B CN9 HN9 0.19 3 0.0 ! 1-M-U +CN1T NN2B CN9 HN9 0.19 3 0.0 ! 1-M-T +CN3 NN2B CN9 HN9 0.00 3 0.0 ! 1-M-T/U +CN4 NN2B CN9 HN9 0.00 3 0.0 ! 9-M-G +CN5 NN2B CN9 HN9 0.19 3 0.0 ! 9-M-G +CN4 NN2B CN8 HN8 0.00 3 0.0 ! 9-E-G +CN5 NN2B CN8 HN8 0.19 3 0.0 ! 9-E-G +CN4 NN2B CN8 CN9 0.00 3 0.0 ! 9-E-G +CN5 NN2B CN8 CN9 0.19 3 0.0 ! 9-E-G +X CN8 CN8 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) +X CN8 CN9 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) +!for nadp/nadph, adm jr. +HN7 CN7B CN7B ON2 0.195 3 0.0 !for NADPH and bkbmod +ON2 CN7B CN7B NN2 0.0 3 0.0 !for NADPH and bkbmod + +! sugar, replace with ribose terms 021998 +CN7 CN7B ON6 CN7 0.6 6 180.0 +CN7B CN7 CN7 CN7 0.4 6 0.0 ! good for amplitudes +CN7B CN7 CN7 CN9 0.4 6 0.0 ! good for amplitudes, 5MET +CN7 CN7 CN7 ON6 0.6 6 0.0 +CN7 CN7 CN7B ON6 0.6 6 0.0 +ON2 CN7 CN7 CN7 0.8 6 0.0 ! +ON2 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right +ON2 CN7 CN7 CN7 2.0 3 180.0 ! +! for ndph +ON2 CN7B CN7 CN7 0.8 6 0.0 ! +ON2 CN7B CN7 CN7 0.4 5 0.0 ! Moves the barrier right +ON2 CN7B CN7 CN7 2.0 3 180.0 ! +! +ON5 CN7 CN7 CN7 0.8 6 0.0 ! +ON5 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right +ON5 CN7 CN7 CN7 2.0 3 180.0 ! +ON5 CN7 CN7 ON5 0.0 3 0.0 ! +ON5 CN7 CN7 ON2 0.0 3 0.0 ! +ON2 CN7 CN7B ON6 0.5 6 0.0 !good for amplitudes +ON2 CN7 CN7B ON6 0.3 5 0.0 !impact on amplitudes +ON2 CN7 CN7B ON6 0.6 4 180.0 !increases c2'endo +ON2 CN7 CN7B ON6 0.2 3 0.0 ! +CN7 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg. + +!%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%% +! The following is for: THF3P (model for espilon), THFM3P (model for puckering), +! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue +!@@@@@@ Begining of chi +!============= added for torsion about chi in adenine ============ +!For link from sugar to base: +CN7B NN2 CN4 HN3 0.3 2 180.0 ! NF +CN7B NN2 CN5 CN5 11.0 2 180.0 ! adm jr. +CN7B NN2 CN4 NN4 11.0 2 180.0 ! adm jr. +CN7B NN2 CN4 NN3A 11.0 2 180.0 ! adm jr. +!For chi itself: + !DNA: +ON6 CN7B NN2 CN5 1.1 1 180.0 ! +ON6 CN7B NN2 CN4 1.1 1 0.0 ! NF + !RNA: +ON6B CN7B NN2 CN5 1.1 1 180.0 ! +ON6B CN7B NN2 CN4 1.1 1 0.0 ! + !DNA: +CN8 CN7B NN2 CN5 0.3 3 0.0 ! NF +CN8 CN7B NN2 CN4 0.0 3 180.0 ! NF + !RNA: +CN7B CN7B NN2 CN5 0.3 3 0.0 ! NF +CN7B CN7B NN2 CN4 0.0 3 180.0 ! NF + +HN7 CN7B NN2 CN5 0.0 3 0.0 ! NF +HN7 CN7B NN2 CN4 0.195 3 0.0 ! NF +!@@@@@@ End of chi in adenines + +!============== terms for torsion about chi in cytosines =========== +CN7B NN2 CN3 HN3 0.3 2 180.0 ! NF +CN7B NN2 CN1 ON1C 11.0 2 180.0 ! adm jr. from A +CN7B NN2 CN1 NN3 11.0 2 180.0 ! adm jr. +CN7B NN2 CN3 CN3 11.0 2 180.0 ! adm jr. + !DNA: +ON6 CN7B NN2 CN1 0.0 3 0.0 ! +ON6 CN7B NN2 CN3 1.0 1 0.0 ! NF + !RNA: +ON6B CN7B NN2 CN1 0.0 3 0.0 ! +ON6B CN7B NN2 CN3 1.0 1 0.0 ! + !DNA: +CN8 CN7B NN2 CN1 1.0 3 0.0 ! +CN8 CN7B NN2 CN3 0.0 3 180.0 ! NF 030697 + !RNA: +CN7B CN7B NN2 CN1 1.0 3 0.0 ! +CN7B CN7B NN2 CN3 0.0 3 180.0 ! + +HN7 CN7B NN2 CN1 0.0 3 0.0 ! NF +HN7 CN7B NN2 CN3 0.195 3 0.0 ! NF +!@@@@@@ End of chi in cytosines + +!=========== terms for torsion about chi in uracils/thymines =========== +CN7B NN2B CN3 HN3 0.3 2 180.0 ! NF +CN7B NN2B CN1T ON1 11.0 2 180.0 ! adm jr. from A +CN7B NN2B CN1T NN2U 11.0 2 180.0 ! adm jr. +CN7B NN2B CN3 CN3T 11.0 2 180.0 ! adm jr. + !DNA: +ON6 CN7B NN2B CN1 0.0 3 0.0 ! +ON6 CN7B NN2B CN1T 0.7 3 0.0 ! +ON6 CN7B NN2B CN1T 0.8 1 180.0 ! +ON6 CN7B NN2B CN3 0.9 1 0.0 ! NF + !RNA: +ON6B CN7B NN2B CN1 0.0 3 0.0 ! +ON6B CN7B NN2B CN1T 0.7 3 0.0 ! +ON6B CN7B NN2B CN1T 0.8 1 180.0 ! +ON6B CN7B NN2B CN3 0.9 1 0.0 ! + !DNA: +CN8 CN7B NN2B CN1T 0.2 3 180.0 ! +CN8 CN7B NN2B CN3 0.0 3 180.0 ! NF + !RNA: +CN7B CN7B NN2B CN1T 0.2 3 180.0 ! +CN7B CN7B NN2B CN3 0.0 3 180.0 ! + +HN7 CN7B NN2B CN1T 0.0 3 0.0 ! NF +HN7 CN7B NN2B CN3 0.195 3 0.0 ! NF +!@@@@@@ End of chi in thymines + +!============= added for torsion about chi in guanine ============ +CN7B NN2B CN4 HN3 0.3 2 180.0 ! NF +CN7B NN2B CN4 NN4 11.0 2 180.0 ! adm jr. +CN7B NN2B CN5 CN5G 11.0 2 180.0 ! adm jr. from U +CN7B NN2B CN5 NN3G 11.0 2 180.0 ! adm jr. + !DNA: +ON6 CN7B NN2B CN5 0.2 3 0.0 ! +ON6 CN7B NN2B CN5 1.1 1 180.0 ! +ON6 CN7B NN2B CN4 1.4 1 0.0 ! NF + !RNA: +ON6B CN7B NN2B CN5 0.2 3 0.0 ! +ON6B CN7B NN2B CN5 1.1 1 180.0 ! +ON6B CN7B NN2B CN4 1.4 1 0.0 ! + !DNA: +CN8 CN7B NN2B CN5 0.0 3 0.0 ! NF +CN8 CN7B NN2B CN4 0.0 3 180.0 ! NF 030697 + !RNA: +CN7B CN7B NN2B CN5 0.0 3 0.0 ! NF +CN7B CN7B NN2B CN4 0.0 3 180.0 ! + +HN7 CN7B NN2B CN5 0.0 3 0.0 ! NF +HN7 CN7B NN2B CN4 0.195 3 0.0 ! NF +!@@@@@@ End of chi in guanines +!@@@@@@ link (not chi) between base and sugar for both purines and pyrimidines: + !DNA: +CN7 ON6 CN7B NN2 0.0 3 0.0 +CN7 ON6 CN7B NN2B 0.0 3 0.0 + !RNA: +CN7 ON6B CN7B NN2 0.0 3 0.0 +CN7 ON6B CN7B NN2B 0.0 3 0.0 + !DNA: +CN7 CN8 CN7B NN2 0.0 3 0.0 +CN7 CN8 CN7B NN2B 0.0 3 0.0 +HN8 CN8 CN7B NN2 0.0 3 0.0 +HN8 CN8 CN7B NN2B 0.0 3 0.0 + !RNA: +CN7 CN7B CN7B NN2 0.0 3 0.0 +CN7 CN7B CN7B NN2B 0.0 3 0.0 + !RNA +HN7 CN7B CN7B NN2 0.0 3 0.0 +HN7 CN7B CN7B NN2B 0.0 3 0.0 + +!@@@@@@ Begining of torsions involving exocyclic sugar atoms: +!======= CN7 CN8B ON2 P = C4'-C5'-O5'-P +CN7 CN8B ON2 P 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr. +CN7 CN8B ON2 P2 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr., adm, 2011 DNA update +! the following differ significantly from the alcohols +! in the protein (based on ethanol), they also differ from other +! NA C-C-OH-H parameters (see below) +! The two following terms have been replaced by their ethanol +! counterpart (NF, 083098) +CN7 CN8B ON5 HN5 1.3300 1 0.00 +CN7 CN8B ON5 HN5 0.1800 2 0.00 +CN7 CN8B ON5 HN5 0.3200 3 0.00 +!======= HN8 CN8B ON2 P = H-C5'-O5'-P )beta +HN8 CN8B ON5 HN5 0.0 3 0.0 !bet +!======== CN7 CN7 CN8B ON2 = C3'-C4'-C5'-O5' +! When O5' is ON2 (phosphodiester linkage): +CN7 CN7 CN8B ON2 0.20 4 180.0 !gam adm jr. +CN7 CN7 CN8B ON2 0.80 3 180.0 !gam C3'-C4'-C5'-O5' +CN7 CN7 CN8B ON2 0.40 2 0.0 !gam +CN7 CN7 CN8B ON2 2.50 1 180.0 !gam +! +CN8 CN7 CN8B ON2 0.2 3 180.0 ! from gam, carbocyclic and 25P1 +! When O5' is ON5 (5TER patch): +CN7 CN7 CN8B ON5 0.20 4 180.0 !gam adm jr. +CN7 CN7 CN8B ON5 0.80 3 180.0 !gam C3'-C4'-C5'-O5' +CN7 CN7 CN8B ON5 0.40 2 0.0 !gam +CN7 CN7 CN8B ON5 2.50 1 180.0 !gam +!======== ON6 CN7 CN8B ON2 = O4'-C4'-C5'-O5' +! When O5' is ON2 (3'-5' phosphodiester linkage) +ON6 CN7 CN8B ON2 3.4 1 180.0 !gam O4'-C4'-C5'-O5',influences +60 +ON6B CN7 CN8B ON2 3.4 1 180.0 !gam, RNA +! When O5' is ON5 (5TER patch): +ON6 CN7 CN8B ON5 3.4 1 180.0 !gam +ON6B CN7 CN8B ON5 3.4 1 180.0 !gam, RNA +!======== HN8 CN8B CN7 CN7 = H-C5'-C4'-H +HN8 CN8B CN7 CN7 0.195 3 0.0 !gam,H-C5'-C4'-H +HN8 CN8B CN7 CN8 0.195 1 0.0 !gam, carbocylic, 25P1 +!======== HN7 CN8B CN7 ON6 = H-C5'-C4'-O4' +HN8 CN8B CN7 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4' +HN8 CN8B CN7 ON6B 0.195 1 0.0 !gam, RNA +!======== HN7 CN7 CN8B ON2 = H-C4'-C5'-O5' +! When O5' is ON2 (phosphodiester linkage): +HN7 CN7 CN8B ON2 0.195 3 0.0 !gam H-C4'-C5'-O5' +! When O5' is ON5 (5TER patch): +HN7 CN7 CN8B ON5 0.195 3 0.0 !gam +HN8 CN8 CN8 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4' +! terms for 5MET patch +CN9 CN7 CN7 CN8B 0.5 4 180.0 !cn8 -> cn9 +HN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9 +CN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9 +ON6 CN7 CN9 HN9 0.195 3 0.0 !cn7 -> cn9 +HN7 CN7 CN7 CN9 0.195 3 0.0 !cn8 -> cn9 +ON2 CN7 CN7 CN9 0.2 4 0.0 !cn8b -> cn9 +ON2 CN7 CN7 CN9 0.8 3 180.0 !cn8b -> cn9 +CN8 CN7 CN7 CN9 0.5 4 180.0 !cn8b -> cn9 + +!======== CN8 CN7 CN7 CN8B = C2'-C3'-C4'-C5' +! This term is well suited to modify the puckering surfaces, in +! particular because it is present in THF5P +CN8 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg. +CN7B CN7 CN7 CN8B 0.2 4 180.0 !del, RNA +!======== CN8B CN7 CN7 ON2 = C5'-C4'-C3'-O3' +! These terms affect the c2endo/c3endo energy difference +! When O3' is ON2 (3'-5' phosphodiester linkage) +ON2 CN7 CN7 CN8B 0.2 4 0.0 !del +! the following term controls the location of the barrier at ~75 deg. +ON2 CN7 CN7 CN8B 0.8 3 180.0 !del,decreases P [100,250] +! When O3' is ON5 (patch 3TER) +ON5 CN7 CN7 CN8B 0.2 4 0.0 ! +ON5 CN7 CN7 CN8B 0.8 3 180.0 ! +!======== ON6 CN7 CN7 ON2 = O4'-C4'-C3'-O3' +! These terms contribute to delta +! These terms are present in THF3P and THFM3P but not in THF5P +! When O3' is ON2 (3'-5' phosphodiester linkage) +ON2 CN7 CN7 ON6 0.5 6 0.0 !del, good for amplitudes +ON2 CN7 CN7 ON6 0.3 5 0.0 !del, impact on amplitudes +ON2 CN7 CN7 ON6 0.6 4 180.0 !del, increases c2'endo +ON2 CN7 CN7 ON6 0.2 3 0.0 ! +ON2 CN7 CN7 ON6B 0.4 6 0.0 !del, RNA, good for amplitudes +ON2 CN7 CN7 ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes +ON2 CN7 CN7 ON6B 0.0 4 180.0 !del, RNA, increases c2'endo +ON2 CN7 CN7 ON6B 1.6 3 0.0 !del, RNA, increases C2'endo +! for ndph: make identical to ON2 CN7 CN7 ON6B +ON2 CN7B CN7B ON6B 0.4 6 0.0 !del, RNA, good for amplitudes +ON2 CN7B CN7B ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes +ON2 CN7B CN7B ON6B 0.0 4 180.0 !del, RNA, increases c2'endo +ON2 CN7B CN7B ON6B 1.6 3 0.0 !del, RNA, increases C2'endo +! When O3' is ON5 (patch 3TER) +ON5 CN7 CN7 ON6 0.5 6 0.0 ! +ON5 CN7 CN7 ON6 0.3 5 0.0 ! +ON5 CN7 CN7 ON6 0.6 4 180.0 ! +ON5 CN7 CN7 ON6 0.2 3 0.0 ! +ON5 CN7 CN7 ON6B 0.4 6 0.0 !RNA +ON5 CN7 CN7 ON6B 0.0 5 0.0 !RNA +ON5 CN7 CN7 ON6B 0.0 4 180.0 !RNA +ON5 CN7 CN7 ON6B 1.6 3 0.0 !RNA. increases c2'endo + +!======== CN8B CN7 ON6 CN7B = C5'-C4'-O4'-C1' +! This term can be used to adjust the c2'endo/c3'endo +! energy difference in THF5P +CN7B ON6 CN7 CN8B 0.8 3 0.0 ! P [30,80] +CN7B ON6B CN7 CN8B 2.0 3 0.0 ! To lower barrier in RNA +CN7B ON6B CN7 CN9 2.0 3 0.0 ! To lower barrier in RNA, 5MET +!======== ON2 CN7 CN8 CN7B = O3'-C3'-C2'-C1' +! This term can be used to adjust the c2'endo/c3'endo +! When O3' is ON2 +ON2 CN7 CN8 CN7B 0.8 6 0.0 ! +ON2 CN7 CN8 CN7B 0.4 5 0.0 ! Moves the barrier right +ON2 CN7 CN8 CN7B 2.0 3 180.0 ! +ON2 CN7 CN7B CN7B 0.6 6 0.0 ! RNA +ON2 CN7 CN7B CN7B 0.0 5 0.0 ! RNA c2/c3 endo in RNA +ON2 CN7 CN7B CN7B 1.6 3 180.0 ! +!When O3' is ON5 (patch 3TER) +ON5 CN7 CN8 CN7B 0.8 6 0.0 ! +ON5 CN7 CN8 CN7B 0.4 5 0.0 ! +ON5 CN7 CN8 CN7B 2.0 3 180.0 ! +ON5 CN7 CN7B CN7B 0.6 6 0.0 ! RNA, c2/c3 endo +ON5 CN7 CN7B CN7B 0.0 5 0.0 ! RNA +ON5 CN7 CN7B CN7B 1.6 3 180.0 ! RNA +!======== ON2 CN7 CN8 HN8 = O3'-C3'-C2'-H +ON2 CN7 CN8 HN8 0.195 3 0.0 ! +ON5 CN7 CN8 HN8 0.195 3 180.0 ! +ON2 CN7 CN7B HN7 0.195 3 0.0 ! RNA +ON5 CN7 CN7B HN7 0.195 3 180.0 ! RNA +!======== HN7 CN7 CN7 ON2 = H-C4'-C3'-O3' +HN7 CN7 CN7 ON2 0.195 3 0.0 +HN7 CN7 CN7 ON5 0.195 3 0.0 +!======== CN7 CN7 ON2 P = C4'-C3'-O3'-P +CN7 CN7 ON2 P2 0.6 5 0.0 !eps, adm, 2011 DNA update +CN7 CN7 ON2 P2 0.2 4 0.0 !eps, locat of 200 mimima, adm, 2011 DNA update +CN7 CN7 ON2 P2 0.0 3 180.0 !eps, barE beteen minima, adm, 2011 DNA update +CN7 CN7 ON2 P2 0.4 2 0.0 !eps, relE of 200 vs 275 min, adm, 2011 DNA update +CN7 CN7 ON2 P2 1.9 1 180.0 !eps, adm, 2011 DNA update +CN7 CN7 ON2 P 0.6 5 0.0 !eps, RNA +CN7 CN7 ON2 P 0.2 4 0.0 !eps, locat of 200 mimima, RNA +CN7 CN7 ON2 P 0.0 3 180.0 !eps, barE beteen minima, RNA +CN7 CN7 ON2 P 0.4 2 0.0 !eps, relE of 200 vs 275 min, RNA +CN7 CN7 ON2 P 1.9 1 180.0 !eps, RNA +!======== CN8 CN7 ON2 P = C2'-C3'-O3'-P +! This term is involved in epsilon +CN8 CN7 ON2 P 2.5 1 180.0 ! 3-terminal phosphate +CN8 CN7 ON2 P2 1.9 1 180.0 ! adm, 2011 DNA update new param, eps +CN7B CN7 ON2 P 2.5 1 180.0 !eps, RNA +CN7B CN7B ON2 P 2.5 1 180.0 !eps, NADPH and bkbmod +CN7 CN7B ON2 P 2.5 1 180.0 !eps, NADPH and bkbmod +! base on thfalloh +! the following differ significantly from the protein based +! alcohol parameters (based on ethanol, see above) +CN7 CN7 ON5 HN5 0.5 3 0.0 +CN7 CN7 ON5 HN5 0.3 2 180.0 +CN7 CN7 ON5 HN5 1.5 1 0.0 +CN8 CN7 ON5 HN5 0.5 3 0.0 +CN8 CN7 ON5 HN5 1.0 2 180.0 +CN8 CN7 ON5 HN5 0.3 1 0.0 +CN7B CN7 ON5 HN5 0.8 3 0.0 ! RNA +CN7B CN7 ON5 HN5 0.5 1 0.0 ! RNA +! Was simply transfered from HN7 CN7 ON2 P +! adm jr. should convert to alcohol term (see ribose etc) +HN7 CN7 ON5 HN5 0.0 3 0.0 +HN7 CN7 CN8B HN8 0.195 3 0.0 !gam H-C4'-C5'-H +HN7 CN7 CN7 CN8B 0.195 3 0.0 !gam H-C3'-C4'-C5' +!@@@@@@ End of torsions involving exocyclic atoms: +!@@@@@@ Begining of torsions for endocyclic atoms only: +CN8 CN7B ON6 CN7 0.6 6 180.0 !C2'-C1'-O4'-C4' +CN8 CN7 CN7 ON6 1.0 4 0.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; lowers c3'endo +CN8 CN7 CN7 ON6 0.3 5 180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima +CN8 CN7 CN7 ON6 0.3 6 180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima +CN7B CN7B ON6B CN7 0.0 6 0.0 ! RNA, Lowers barrier +CN7B CN7 CN7 ON6B 0.0 3 0.0 ! RNA +!======== CN7 CN8 CN7B ON6 for nucleosides, transfered from ========= +!======== CN7 CN8 CN8 ON6 from thfoh ============================== +CN7 CN8 CN7B ON6 0.6 6 0.0 ! C3'-C2'-C1'-O4', adjust barrier +CN7 CN7B CN7B ON6B 0.4 6 0.0 ! RNA +!======== C1'-C2'-C3'-C4' ======== +CN7B CN8 CN7 CN7 0.4 6 0.0 ! good for amplitudes +CN7B CN7B CN7 CN7 0.0 6 0.0 ! RNA +!======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ======== +!======== CN7 CN7 ON6 CN8 from thfohch3 ============================ +CN7 CN7 ON6 CN7B 0.6 6 180.0 ! C3'-C4'-O4'-C1' +CN7 CN7 ON6B CN7B 0.0 6 180.0 ! RNA +!======== Directly adjusted with TM3P +HN7 CN7 CN7 CN8 0.0 3 0.0 !puc,H-C3'-C4'-C5' +!======== HN7 CN7 CN7 ON6 = H-C2'-C3'-O4' +HN7 CN7 CN8 CN7B 0.195 3 0.0 !H-C3'-C2'-C1' +HN7 CN7B CN8 CN7 0.195 3 0.0 !H-C1'-C2'-C3' +HN7 CN7 CN7 ON6 0.195 3 180.0 ! useful +HN8 CN8 CN7B ON6 0.195 3 0.0 !H-C2'-C1'-O4' +HN7 CN7 CN7 HN7 0.195 3 0.0 !H-C4'-C3'-H +HN7 CN7B CN8 HN8 0.195 3 0.0 !H-C1'-C2'-H +HN7 CN7 CN8 HN8 0.195 3 0.0 !H-C3'-C2'-H +HN8 CN8 CN7 CN7 0.195 3 0.0 ! useful *cccc* +HN7 CN7 ON6 CN7B 0.195 3 0.0 !H-C3'-C2'-C1' +HN7 CN7B ON6 CN7 0.000 3 0.0 !H-C1'-O4'-C4' +HN7 CN7 CN7 ON6B 0.195 3 180.0 ! RNA +HN9 CN9 CN7 ON6B 0.195 3 180.0 ! RNA, 5MET +HN8 CN8 CN7B ON6B 0.195 3 0.0 ! RNA +HN7 CN7B ON6B CN7 0.000 3 0.0 ! RNA +HN7 CN7 ON6B CN7B 0.195 3 0.0 ! RNA +HN7 CN7 CN7B CN7B 0.195 3 0.0 ! RNA, H-C3'-C2'-C1' +HN7 CN7B CN7B CN7 0.195 3 0.0 ! RNA, H-C1'-C2'-C3' +HN7 CN7B CN7B ON6B 0.195 3 0.0 ! RNA, H-C2'-C1'-O4' +!@@@@@@ End of torsions for endocyclic atoms only + +!@@@@@@ Begining of torsions specifically defined for RNA @@@@@@ +! N9-C1'-C2'-O2': +NN2 CN7B CN7B ON5 0.000 3 0.0 ! Adenine and cytosine +NN2B CN7B CN7B ON5 0.000 3 0.0 ! Guanine and uracil +ON5 CN7B CN7B HN7 0.000 3 0.0 ! +HN7 CN7B CN7B HN7 0.000 3 0.0 ! +CN7 CN7 CN7B ON5 0.000 3 0.0 +ON6B CN7B CN7B ON5 0.000 3 0.0 +ON5 CN7B CN7 ON2 0.000 3 0.0 +! for ndph +ON5 CN7 CN7B ON2 0.000 3 0.0 +ON5 CN7B CN7 ON5 0.000 3 0.0 +HN7 CN7B ON5 HN5 0.000 3 0.0 +!ejd, 2010 RNA update +HN5 ON5 CN7B CN7B 0.000 6 180.0 ! ejd, 2010 RNA update +HN5 ON5 CN7B CN7B 0.400 3 0.0 ! shifts min, ejd, 2010 RNA update +HN5 ON5 CN7B CN7B 0.400 2 0.0 ! ejd, 2010 RNA update +HN5 ON5 CN7B CN7B 0.800 1 0.0 ! height of right barrier and can shift min, ejd, 2010 RNA update +!to C3' +HN5 ON5 CN7B CN7 0.200 3 0.0 ! ejd, 2010 RNA update +HN5 ON5 CN7B CN7 0.000 2 180.0 ! ejd, 2010 RNA update +HN5 ON5 CN7B CN7 2.000 1 0.0 ! height of left side barrier, ejd, 2010 RNA update +!@@@@@@ End of torsions specifically defined for RNA @@@@@@ + +!Collection of parameters that were previously incorrectly categorized or labeled +CN7B ON6 CN7 CN9 0.0 3 0.0 ! added for sugar model compounds +HN7 CN7 CN7B ON5 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr. +HN7 CN7B CN7 CN7 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr. +HN7 CN7 CN7 CN7B 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr. +HN7 CN7 CN7B HN7 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr. + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +! +HN2 X X NN2 1.0 0 0.0 !C, adm jr. 11/97 +NN2B CN4 CN5 HN2 7.0 0 0.0 !G, adm jr. 11/97 +HN1 X X NN1 4.0 0 0.0 !G, adm jr. 11/97 +NN1 CN2 HN1 HN1 6.0 0 0.0 !A,C adm jr. 11/97 +CN1 X X ON1 90.0 0 0.0 !U +CN1T X X ON1 90.0 0 0.0 !U +CN1 NN2G CN5G ON1 90.0 0 0.0 !G +CN1T NN2B NN2U ON1 110.0 0 0.0 !T/O2, adm jr. 11/97 +CN1 NN2U CN3T ON1 90.0 0 0.0 !T/O4, adm jr. 11/97 +CN1 X X ON1C 80.0 0 0.0 !C, par_32, adm jr. 10/2/91 +CN2 X X NN1 90.0 0 0.0 !C, +CN2 NN3G NN2G NN1 40.0 0 0.0 !G +CN2 NN3A CN5 NN1 40.0 0 0.0 !A +CN2 NN3 CN3 NN1 60.0 0 0.0 !C, +CN9 X X CN3T 14.0 0 0.0 !T, adm jr. 11/97 + +! Wildcards used to minimize memory requirements +NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +HN1 0.0 -0.0460 0.2245 +HN2 0.0 -0.0460 0.2245 +HN3 0.0 -0.046 1.1000 !adm jr. aromatic Hvdw +HN4 0.0 -0.0460 0.2245 +HN5 0.0 -0.0460 0.2245 +HN6 0.0 -0.0220 1.3200 +HN7 0.0 -0.0220 1.3200 +HN8 0.0 -0.0280 1.3400 ! Hydrogen bound to CN8 +HN9 0.0 -0.0240 1.3400 ! Hydrogen bound to CN9 +! +NN1 0.0 -0.20 1.85 +NN2 0.0 -0.20 1.85 +NN2B 0.0 -0.20 1.85 ! From NN2, for N9 in guanines +NN2G 0.0 -0.20 1.85 +NN2U 0.0 -0.20 1.85 +NN3 0.0 -0.20 1.85 +NN3A 0.0 -0.20 1.85 +NN3G 0.0 -0.20 1.85 +NN4 0.0 -0.20 1.85 +NN6 0.0 -0.20 1.85 +! +ON1 0.0 -0.1200 1.70 +ON1C 0.0 -0.1200 1.70 +ON2 0.0 -0.1521 1.77 +ON3 0.0 -0.1200 1.70 +ON4 0.0 -0.1521 1.77 +ON5 0.0 -0.1521 1.77 +ON6 0.0 -0.1521 1.77 +ON6B 0.0 -0.1521 1.77 +! +! base ring C vdw param, 11/14/97, adm jr +CN1 0.0 -0.10 1.9000 +CN1T 0.0 -0.10 1.9000 +CN2 0.0 -0.10 1.9000 +CN3 0.0 -0.09 1.9000 +CN3T 0.0 -0.09 1.9000 ! T, adm jr. +CN4 0.0 -0.075 1.9000 +CN5 0.0 -0.075 1.9000 +CN5G 0.0 -0.075 1.9000 +CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 +CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 +! alkane optimized terms below, Yin and MacKerell, 1998, JCC, In press +CN8 0.0 -0.0560 2.010 0.0 -0.01 1.90 ! +CN8B 0.0 -0.0560 2.010 0.0 -0.01 1.90 ! +CN9 0.0 -0.0780 2.040 0.0 -0.01 1.90 ! +! +P 0.0 -0.585 2.15 +P2 0.0 -0.585 2.15 + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +! + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/par_all36_prot.prm b/charmm/toppar/par_all36_prot.prm new file mode 100644 index 00000000..38fb06dc --- /dev/null +++ b/charmm/toppar/par_all36_prot.prm @@ -0,0 +1,3399 @@ +*>>>> CHARMM36 All-Hydrogen Parameter File for Proteins <<<<<<<<<< +*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>>>>>> Feb. 2012 <<<<<<<<<<<<<<<<<<<<<<<<<<<< +* All comments to the CHARMM web site: www.charmm.org +* parameter set discussion forum +* + +!references +! +!Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P. +!Mittal, J., Feig, M. and MacKerell, A.D., Jr. Optimization of the +!additive CHARMM all-atom protein force field targeting improved +!sampling of the backbone phi, psi and sidechain chi1 and chi2 +!dihedral angles. In preparation +! +!MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved +!treatment of the protein backbone in empirical force fields," Journal +!of the American Chemical Society, 126: 698-699, 2004 +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. + +ATOMS +MASS 31 H 1.00800 ! polar H +MASS 32 HC 1.00800 ! N-ter H +MASS 33 HA 1.00800 ! nonpolar H +MASS 34 HP 1.00800 ! aromatic H +MASS 35 HB1 1.00800 ! backbone H +MASS 36 HB2 1.00800 ! aliphatic backbone H, to CT2 +MASS 37 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS 38 HR2 1.00800 ! (+) his HE1 +MASS 39 HR3 1.00800 ! neutral his HG, HD2 +MASS 40 HS 1.00800 ! thiol hydrogen +MASS 41 HE1 1.00800 ! for alkene; RHC=CR +MASS 42 HE2 1.00800 ! for alkene; H2C=CR +MASS 43 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS 44 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS 45 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS 46 C 12.01100 ! carbonyl C, peptide backbone +MASS 47 CA 12.01100 ! aromatic C +MASS 48 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters +MASS 49 CT1 12.01100 ! aliphatic sp3 C for CH +MASS 50 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS 51 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu +MASS 52 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS 53 CPH1 12.01100 ! his CG and CD2 carbons +MASS 54 CPH2 12.01100 ! his CE1 carbon +MASS 55 CPT 12.01100 ! trp C between rings +MASS 56 CY 12.01100 ! TRP C in pyrrole ring +MASS 57 CP1 12.01100 ! tetrahedral C (proline CA) +MASS 58 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS 59 CP3 12.01100 ! tetrahedral C (proline CD) +MASS 60 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS 61 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS 62 CS 12.01100 ! thiolate carbon +MASS 63 CE1 12.01100 ! for alkene; RHC=CR +MASS 64 CE2 12.01100 ! for alkene; H2C=CR +MASS 65 CAI 12.01100 ! aromatic C next to CPT in trp +MASS 66 N 14.00700 ! proline N +MASS 67 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS 68 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS 69 NR3 14.00700 ! charged his ring nitrogen +MASS 70 NH1 14.00700 ! peptide nitrogen +MASS 71 NH2 14.00700 ! amide nitrogen +MASS 72 NH3 14.00700 ! ammonium nitrogen +MASS 73 NC2 14.00700 ! guanidinium nitrogen +MASS 74 NY 14.00700 ! TRP N in pyrrole ring +MASS 75 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS 76 O 15.99900 ! carbonyl oxygen +MASS 77 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS 78 OC 15.99900 ! carboxylate oxygen +MASS 79 OH1 15.99900 ! hydroxyl oxygen +MASS 80 OS 15.99940 ! ester oxygen +MASS 81 S 32.06000 ! sulphur +MASS 82 SM 32.06000 ! sulfur C-S-S-C type +MASS 83 SS 32.06000 ! thiolate sulfur + + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +NH2 CT1 240.000 1.4550 ! From LSN NH2-CT2 +! +!Indole/Tryptophan +CA CAI 305.000 1.3750 ! from CA CA +CAI CAI 305.000 1.3750 ! atm, methylindole, fit CCDSS +CPT CA 300.000 1.3600 ! atm, methylindole, fit CCDSS +CPT CAI 300.000 1.3600 ! atm, methylindole, fit CCDSS +CPT CPT 360.000 1.3850 ! atm, methylindole, fit CCDSS +CY CA 350.000 1.3650 ! trj, adm jr., 5/08/91, indole CCDB structure search +CY CAI 350.000 1.3650 ! from CY CA +CY CPT 350.000 1.4300 ! atm, methylindole, fit CDS data +CY CT3 375.000 1.4920 ! atm, methylindole, fit CDS data +CY CT2 375.000 1.4920 ! atm, methylindole, fit CDS data +HP CAI 340.000 1.0800 ! from HP CA +HP CY 350.000 1.0800 ! trp, adm jr., 12/30/91 +NY CA 270.000 1.3700 ! trp, adm jr., 12/30/91 +NY CPT 270.000 1.3700 ! atm, methylindole, from CCDS 1/17/04 +NY H 537.500 0.9760 ! atm, methylindole, 1/17/04 +CA CA 305.000 1.3750 ! ALLOW ARO + ! benzene, JES 8/25/89 +CE1 CE1 440.000 1.3400 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CE2 500.000 1.3420 ! + ! for propene, yin/adm jr., 12/95 +CE1 CT2 365.000 1.5020 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CT3 383.000 1.5040 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE2 510.000 1.3300 ! + ! for ethene, yin/adm jr., 12/95 +CP1 C 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CC 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CD 200.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 222.500 1.5270 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH1 CPH1 410.000 1.3600 ! ALLOW ARO + ! histidine, adm jr., 6/27/90 +CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT1 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT1 222.500 1.5000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT2 CA 230.000 1.4900 ! ALLOW ALI ARO + ! phe,tyr, JES 8/25/89 +CT2 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT2 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT3 CA 230.000 1.4900 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +CT3 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT3 CS 190.000 1.5310 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CT3 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 222.500 1.5280 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT3 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +H CD 330.000 1.1100 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA1 CC 317.130 1.1000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +HA2 CP2 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA1 CT1 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 322.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +!HA CY 330.000 1.0800 ! ALLOW ARO + ! JWK 05/14/91 new r0 from indole +HE1 CE1 360.500 1.1000 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 365.000 1.1000 ! + ! for ethene, yin/adm jr., 12/95 +HB1 CP1 330.000 1.0800 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +!HB3 CT3 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HP CA 340.000 1.0800 ! ALLOW ARO + ! phe,tyr JES 8/25/89 +HR1 CPH1 375.000 1.0830 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 340.000 1.0900 ! ALLOW ARO + ! his, adm jr., 6/28/29 +HR2 CPH2 333.000 1.0700 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR3 CPH1 365.000 1.0830 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 320.000 1.4340 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 320.000 1.4550 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C 450.000 1.3650 ! ALLOW PEP POL ARO + ! mp2/6-311g** mgua vib. data, adm jr., 1/04 +NC2 CT2 390.000 1.4900 ! ALLOW ALI POL + ! mp2/6-311g** mgua vib. data, adm jr., 1/04 +NC2 CT3 390.000 1.4900 ! ALLOW ALI POL + ! mp2/6-311g** mgua vib. data, adm jr., 1/04 +NC2 HC 455.000 1.0000 ! ALLOW POL + ! 405.0->455.0 GUANIDINIUM (KK) +NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO + ! (DS) +NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +NH2 CT2 240.000 1.4550 + ! from NH2 CT3, neutral glycine, adm jr. +NH2 CT3 240.000 1.4550 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH2 H 480.000 1.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 HC 460.000 1.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT3 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 HC 403.000 1.0400 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 320.000 1.4850 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 320.000 1.5020 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP HC 460.000 1.0060 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH2 400.000 1.3600 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 H 466.000 1.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 400.000 1.3200 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 380.000 1.3700 ! ALLOW ARO + ! his, adm jr., 6/28/90 +NR3 CPH2 380.000 1.3200 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 H 453.000 1.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +O C 620.000 1.2300 ! ALLOW PEP POL ARO + ! Peptide geometry, condensed phase (LK) +O CC 650.000 1.2300 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +OB CC 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid vibrations and geom. +OB CD 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 8/27/91, phenoxide +OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 7/23/91, acetic acid +OC CT2 450.000 1.3300 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 450.000 1.3300 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA 334.300 1.4110 ! ALLOW ARO ALC + ! MeOH, EMB 10/10/89, +OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC + ! adm jr. 5/02/91, acetic acid pure solvent +OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 H 545.000 0.9600 ! ALLOW ALC ARO + ! EMB 11/21/89 methanol vib fit +OS CD 150.000 1.3340 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +OS CT3 340.000 1.4300 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +S CT2 198.000 1.8180 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S CT3 240.000 1.8160 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S HS 275.000 1.3250 ! ALLOW SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +SM CT2 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC surface in DMDS 5/15/92 (FL) +SM CT3 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC surface in DMDS 5/15/92 (FL) +SM SM 173.000 2.0290 ! ALLOW SUL ION + ! improved CSSC surface in DMDS 5/15/92 (FL) +SS CS 205.000 1.8360 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HR1 CD 330.000 1.1100 ! acetaldehyde, benzaldehyde, 3ALP +O CD 720.000 1.2050 ! acetaldehyde, benzaldehyde, 3ALP. from stream/toppar_all27_na_bkb_modifications.str +CT2A CT1 222.500 1.5380 ! from CT2 CT1, Zhu +CT2 CT2A 222.500 1.5300 ! from CT2 CT2, Zhu +CT2A HA2 309.000 1.1110 ! from HA2 CT2, Zhu +CT2A CPH1 229.630 1.5000 ! from CT2 CPH1, Zhu +!ASP, CT2->CT2A +CT2A CC 200.000 1.5220 ! from CT2 CC, jshim +! RESI CYSM and PRES CYSD +CT1 CS 190.000 1.5380 ! from CT3 CS but lengthened; compare CT3 CT2 with CT2 CT1; kevo + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +H NH2 CT1 50.000 111.00 ! From LSN HC-NH2-CT2 +H NH2 CT2 50.000 111.00 ! From LSN HC-NH2-CT2, Neutral Gly Nterminus +NH2 CT1 CT1 67.700 110.00 ! From LSN NH2-CT2-CT2 +NH2 CT1 CT2 67.700 110.00 ! From LSN NH2-CT2-CT2 +NH2 CT1 CT3 67.700 110.00 ! From LSN NH2-CT2-CT2 +CT1 CD OH1 55.000 110.50 ! From ASPP CT2-CD-OH1 +CT3 CT1 CD 52.000 108.00 ! Ala cter +NH2 CT1 HB1 38.000 109.50 50.00 2.1400 ! From LSN NH2-CT2-HA +NH2 CT1 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C +NH2 CT2 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C, Neutral Gly Nterminus + +! +!Indole/Tryptophan +CAI CAI CA 40.000 120.00 35.00 2.41620 ! from CA CA CA +CAI CA CA 40.000 120.00 35.00 2.41620 ! from CA CA CA +CPT CA CA 50.000 113.20 ! atm, methylindole, 1/17/04 +CPT CPT CA 50.000 110.00 ! atm, methylindole, 1/17/04 +CPT CAI CA 50.000 113.20 ! atm, methylindole, 1/17/04 +CPT CPT CAI 50.000 110.00 ! atm, methylindole, 1/17/04 +CPT CY CA 85.000 106.40 25.00 2.26100 ! atm, methylindole, 1/17/04 +CPT NY CA 85.000 112.00 ! atm, methylindole, 1/17/04 +CT2 CY CA 30.000 127.00 ! atm, methylindole, CT3 CY CA +CT2 CY CPT 30.000 126.70 ! atm, methylindole, 1/17/04 +CT3 CY CA 30.000 127.00 ! atm, methylindole, CT3 CY CA +CT3 CY CPT 30.000 126.70 ! atm, methylindole, 1/17/04 +CY CPT CA 130.000 133.50 ! atm, methylindole, 1/17/04 +CY CPT CAI 130.000 133.50 ! atm, methylindole, 1/17/04 +CY CPT CPT 85.000 108.00 ! atm, methylindole, 1/17/04 +CY CT2 CT1 58.350 114.00 ! from TRP crystal, JWK +CY CT2 CT3 58.350 114.00 ! from TRP crystal, JWK +H NY CA 28.000 126.00 ! trp, adm jr., 12/30/91 +H NY CAI 28.000 126.00 ! trp, adm jr., 12/30/91 +H NY CPT 28.000 126.00 ! trp, adm jr., 12/30/91 +HA2 CT2 CY 55.000 109.50 ! atm, methylindole, 1/17/04 +HA3 CT3 CY 55.000 109.50 ! atm, methylindole, 1/17/04 +HP CA CAI 30.000 120.00 22.00 2.15250 ! from HP CA CA +HP CAI CA 30.000 120.00 22.00 2.15250 ! from HP CA CA +HP CA CPT 30.000 122.00 22.00 2.14600 ! trp, adm jr., 12/30/91 +HP CAI CPT 30.000 122.00 22.00 2.14600 ! from HP CA CPT +HP CA CY 32.000 125.00 25.00 2.17300 ! JWK 05/14/91 new theta0 and r0UB from indole +HP CY CA 32.000 126.40 25.00 2.18600 ! trp, adm jr., 12/30/91 +HP CY CPT 32.000 126.40 25.00 2.25500 ! JWK 05/14/91 new theta0 and r0UB from indole +NY CA CY 85.000 110.50 25.00 2.24000 ! trp, adm jr., 12/30/91 +NY CA HP 32.000 125.00 25.00 2.17700 ! JWK 05/14/91 new theta0 and r0UB from indole +NY CPT CA 130.000 129.50 ! atm, methylindole, 1/17/04 +NY CPT CAI 130.000 129.50 ! atm, methylindole, 1/17/04 +NY CPT CPT 95.000 107.40 ! atm, methylindole, 1/17/04 +CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO + ! JES 8/25/89 +CE1 CE1 CT2 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CE1 CT3 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CT2 CT3 32.00 112.20 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT2 48.00 126.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT3 47.00 125.20 ! + ! for propene, yin/adm jr., 12/95 +CP1 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 C 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 100.000 114.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 100.000 111.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 6/27/2012, for Thr with CT1 patch +CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2A CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! from CT2 CT1 C, for lactams, adm jr. +CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2A CT2 CD 52.000 108.0000 ! for GLUP, ZHU +CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! 107.5->120.0 to make planar Arg (KK) +CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/09/92, for ALA cter +CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! methylguanidinium, adm jr., 3/26/92 +CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO + ! his, adm jr. 8/13/90 acetamide geometry and vibrations +H NH2 H 23.000 120.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO + ! JES 8/25/89 phenol +H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +HA2 CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA2 CS HA2 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CS HA3 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA1 CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA1 CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA1 CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 HA1 35.500 109.00 5.40 1.80200 ! TEST for test cpd + ! based on HA CT2 HA +HA2 CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA2 CT2 CA 49.300 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +HA2 CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA2 CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA2 CT2 CE1 45.00 111.50 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HA2 CT2 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA2 CT2 CT1 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA2 CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA3 CT3 CA 49.300 107.5000 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +HA3 CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA3 CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA3 CT3 CE1 42.00 111.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HA3 CT3 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA3 CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA3 CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 HA3 35.500 108.40 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HE1 CE1 CE1 52.00 119.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HE1 CE1 CE2 42.00 118.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 40.00 116.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HE1 CE1 CT3 22.00 117.00 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE1 45.00 120.50 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE2 55.50 120.50 ! + ! for ethene, yin/adm jr., 12/95 +HE2 CE2 HE2 19.00 119.00 ! + ! for propene, yin/adm jr., 12/95 +HB1 CP1 C 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CC 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB1 CT1 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB1 CT1 CT1 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CT2 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CT3 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB2 CT2 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB2 CT2 HB2 36.000 115.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO + ! 35.3->49.0 GUANIDINIUM (KK) +HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI + ! 107.5->120.0 to make planar Arg (KK) +HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI + ! methylguanidinium, adm jr., 3/26/92 +HC NC2 HC 25.000 120.0000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH2 CT2 50.000 111.0000 ! ALLOW POL + ! from HC NH2 CT3, neutral glycine, adm jr. +HC NH2 CT3 50.000 111.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +HC NH2 HC 39.000 106.5000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 HC 44.000 109.5000 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP HC 51.000 107.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO + ! JES 8/25/89 benzene +HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 20.000 112.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 C 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CC 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CP2 70.000 110.8000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 HB1 48.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 CP2 70.000 110.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 HA2 48.000 108.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C NC2 40.000 120.00 70.00 2.31 + ! mp2/6-311g** mgua vib data, adm jr., 1/04 + ! N-N distances: 2.29001, 2.31146, 2.33240 +NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT2 HA2 56.500 107.5000 ! ALLOW ALI POL + ! mp2/6-311g** mgua vib data, adm jr., 1/04 +NC2 CT3 HA3 56.5000 107.5000 ! ALLOW ALI POL + ! mp2/6-311g** mgua vib data, adm jr., 1/04 +NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 HB1 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/20/92, for asn,asp,gln,glu and cters +NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT1 CT2, for lactams, adm jr. +NH1 CT2 HA2 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT3 HA, for lactams, adm jr. +NH1 CT2 HB2 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT3 HA3 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! NMA crystal (JCS) +NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC HA1 44.000 111.00 50.00 1.98000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +NH2 CT2 HB2 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral glycine, adm jr. +NH2 CT2 CD 52.000 108.0000 + !from CT2 CT2 CD, neutral glycine, adm jr. +NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + !from NH3 CT2 CT2, neutral lysine +NH2 CT2 HA2 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral lysine +NH2 CT3 HA3 38.000 109.50 50.00 2.14000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP + ! new aliphatics, adm jr., 2/3/92 +NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! alanine (JCS) +NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + ! methylammonium +NH3 CT2 CT3 67.700 110.0000 ! ALLOW ALI POL + ! ethylammonium +NH3 CT2 HA2 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 HB2 51.500 107.5000 ! ALLOW ALI POL PEP + ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) +NH3 CT3 HA3 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 C 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 HA2 51.500 109.1500 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +O C CP1 80.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C H 50.000 121.7000 ! ALLOW PEP POL ARO + ! acetaldehyde (JCS) +O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC HA1 44.000 122.0000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO + ! adm jr. 4/10/91, acetamide update +OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA CA 40.000 120.0000 ! ALLOW POL ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CT2 CT3 65.000 122.0000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT2 HA2 65.000 118.3000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 HA3 65.000 118.3000 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC + ! PARALLH19 WITH [122.3] (JES) +OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 HA1 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 HA2 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT3 HA3 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OS CT2 HA2 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +OS CT3 HA3 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 HA2 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +S CT3 HA3 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 CT3 58.000 112.5000 ! ALLOW ALI SUL ION + ! diethyldisulfide, as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 HA2 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM CT3 HA3 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 55.000 118.0000 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA2 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA3 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +O CD HR1 75.000 121.0000 ! acetaldehyde, benzaldehyde, 3ALP, retinal +!For GLU/HSP, Zhu +NH1 CT1 CT2A 70.000 113.5000 ! from NH1 CT1 CT2 +HB1 CT1 CT2A 35.000 111.0000 ! from HB1 CT1 CT2 +CT2A CT1 C 52.000 108.0000 ! from CT2 CT1 C +CT1 CT2A HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT1 +CT1 CT2A CT2 58.350 113.5000 11.16 2.56100 ! from CT2 CT2 CT1 +HA2 CT2A HA2 35.500 109.0000 5.40 1.80200 ! from HA2 CT2 HA2 +HA2 CT2A CT2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT2 +CT2A CT2 HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT2 +CT2A CT2 CC 52.000 108.0000 ! from CT2 CT2 CC +CT1 CT2A CPH1 58.350 113.0000 ! from CT1 CT2 CPH1 +HA2 CT2A CPH1 33.430 109.5000 ! from HA2 CT2 CPH1 +CT2A CPH1 CPH1 45.800 130.0000 ! from CT2 CPH1 CPH1 +CT2A CPH1 NR3 45.800 122.0000 ! from NR3 CPH1 CT2 +!ASP, CT2->CT2A, jshim +CT1 CT2A CC 52.000 108.0000 ! from CT1 CT2 CC +HA2 CT2A CC 33.000 109.5000 30.00 2.16300 ! from HA2 CT2 CC +OC CC CT2A 40.000 118.0000 50.00 2.38800 ! from OC CC CT2 +NH3 CT1 CT2A 67.700 110.0000 ! from NH3 CT1 CT2 +CT2A CT1 CD 52.000 108.0000 ! from CT2 CT1 CD +! RESI CYSM and PRES CYSD +NH2 CT1 CS 67.700 110.0000 ! from NH2 CT1 CT2 , kevo +CS CT1 C 52.000 108.0000 ! from CT2 CT1 C , kevo +CS CT1 CC 52.000 108.0000 ! from CT2 CT1 CC , kevo +CS CT1 CD 52.000 108.0000 ! from CT2 CT1 CD , kevo +HB1 CT1 CS 35.000 111.0000 ! from HB1 CT1 CT2 , kevo +NH1 CT1 CS 70.000 113.5000 ! from NH1 CT1 CT2 , kevo +NH3 CT1 CS 67.700 110.0000 ! from NH3 CT1 CT2 , kevo +SS CS CT1 55.000 118.0000 ! from SS CS CT3 , kevo +HA2 CS CT1 34.600 110.10 22.53 2.17900 ! from HA2 CS CT3 to be consistent with SS CS CT1, kevo +! PRES SERD +OC CT2 CT1 65.000 122.0000 ! from OC CT2 CT3 , kevo + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +!Neutral N terminus +NH2 CT1 C O 0.0000 1 0.00 +NH2 CT2 C O 0.0000 1 0.00 ! Neutral Gly Nterminus +NH2 CT1 C NH1 0.0000 1 0.00 +NH2 CT2 C NH1 0.0000 1 0.00 ! Neutral Gly Nterminus +H NH2 CT1 CT1 0.0000 1 0.00 +H NH2 CT1 C 0.0000 1 0.00 +H NH2 CT2 C 0.0000 1 0.00 ! Neutral Gly Nterminus +H NH2 CT1 HB1 0.1100 3 0.00 ! From LSN HC-NH2-CT2-HA +H NH2 CT2 HB2 0.1100 3 0.00 ! From LSN HC-NH2-CT2-HA, Neutral Gly Nterminus +H NH2 CT1 CT2 0.1100 3 0.00 ! From LSN HC-NH2-CT2-CT2 +H NH2 CT1 CT3 0.1100 3 0.00 ! From LSN HC-NH2-CT2-CT2 +!Indole/Tryptophan +CAI CA CA CAI 3.1000 2 180.00 ! from CA CA CA CA +CA CPT CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CAI CPT CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CA CY CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CA CY CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CA NY CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CPT CA CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +CPT CPT CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +CA NY CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CPT CAI CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +CPT CPT CAI CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +CPT CPT CY CA 5.0000 2 180.00 ! atm, methylindole, 1/17/04 +CPT CPT NY CA 6.5000 2 180.00 ! atm, methylindole, 1/17/04 +CT3 CY CPT CA 2.5000 2 180.00 ! atm, methylindole, r6r5 +CT3 CY CPT CAI 2.5000 2 180.00 ! atm, methylindole, r6r5 +CT3 CY CPT CPT 3.0000 2 180.00 ! atm, methylindole, meth +CT2 CY CPT CA 2.5000 2 180.00 ! atm, methylindole, r6r5 +CT2 CY CPT CAI 2.5000 2 180.00 ! atm, methylindole, r6r5 +CT2 CY CPT CPT 3.0000 2 180.00 ! atm, methylindole, meth +CY CA NY CPT 6.0000 2 180.00 ! atm, methylindole, 1/17/04 +CY CPT CA CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +CY CPT CPT CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +CY CPT CAI CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +CY CPT CPT CAI 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +H NY CA CY 0.0500 2 180.00 ! atm, methylindole, 1/17/04 +H NY CPT CA 0.2000 2 180.00 ! atm, methylindole, 1/17/04 +H NY CPT CAI 0.2000 2 180.00 ! atm, methylindole, 1/17/04 +H NY CPT CPT 0.8500 2 180.00 ! atm, methylindole, 1/17/04 +HP CAI CA CA 4.2000 2 180.00 ! from HP CA CA CA +HP CA CA CPT 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +HP CA CPT CPT 3.0000 2 180.00 ! JWK indole 05/14/91 +HP CA CPT CY 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +HP CA CA CAI 4.2000 2 180.00 ! from HP CA CA CA +HP CA CAI CPT 3.0000 2 180.00 ! from HP CA CA CPT +HP CAI CA HP 2.4000 2 180.00 ! from HP CA CA HP +HP CAI CPT CPT 3.0000 2 180.00 ! from HP CA CPT CPT +HP CAI CPT CY 4.0000 2 180.00 ! from HP CA CPT CY, r6r5 +HP CA CY CPT 2.8000 2 180.00 ! adm jr., 12/30/91, for jwk +HP CA CY CT3 1.2000 2 180.00 ! atm, methylindole +HP CA CY CT2 1.2000 2 180.00 ! atm, methylindole +HP CA NY CPT 2.6000 2 180.00 ! adm jr., 12/30/91, for jwk +HP CA NY H 0.4000 2 180.00 ! JWK 05/14/91 fit to indole +HP CY CA HP 1.0000 2 180.00 ! JWK 05/14/91 fit to indole +HP CY CPT CA 2.8000 2 180.00 ! JWK 05/14/91 fit to indole +HP CY CPT CAI 2.8000 2 180.00 ! JWK 05/14/91 fit to indole +HP CY CPT CPT 2.6000 2 180.00 ! JWK 05/14/91 fit to indole +NY CA CY CPT 5.0000 2 180.00 ! atm, methylindole, 1/17/04 +NY CA CY CT3 2.5000 2 180.00 ! atm, methylindole, from NY CA CY CT3 +NY CA CY CT2 2.5000 2 180.00 ! atm, methylindole, from NY CA CY CT3 +NY CA CY HP 3.5000 2 180.00 ! JWK indole 05/14/91 +NY CPT CA CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04, r6r5 +NY CPT CA HP 3.0000 2 180.00 ! JWK 05/14/91 fit to indole, r6r5 +NY CPT CPT CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04, bfly +NY CPT CAI CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +NY CPT CAI HP 3.0000 2 180.00 ! JWK 05/14/91 fit to indole, r6r5 +NY CPT CPT CAI 4.0000 2 180.00 ! atm, methylindole, 1/17/04, bfly +NY CPT CPT CY 6.5000 2 180.00 ! JWK 05/14/91 fit to indole, r5 t1 +CT3 CT2 CY CA 0.3800 2 0.00 ! trp, from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CY CPT 0.2500 2 180.00 ! atm 1/14/04 3-ethylindole +CT3 CT2 CY CPT 0.3000 3 0.00 ! atm 1/14/04 3-ethylindole +HA3 CT3 CY CA 0.0100 3 0.00 ! atm, methylindole, 1/17/04 +HA3 CT3 CY CPT 0.2000 3 0.00 ! atm, methylindole, 1/17/04 +HA2 CT2 CY CA 0.0100 3 0.00 ! atm, methylindole, 1/17/04 +HA2 CT2 CY CPT 0.2000 3 0.00 ! atm, methylindole, 1/17/04 +X CS SS X 0.0000 3 0.20 ! guess + !from methanethiol, HS S CT3 HA + !adm jr., 7/01 +C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 +!CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +!CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL +! ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c +CC CT2 NH1 C 2.0000 1 180.00 ! ALLOW PEP POL + ! Based on Gly3 data from graf et al, RB 7/1/11 +CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +!CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL +! ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c +CD CT2 NH1 C 2.0000 1 180.00 ! ALLOW PEP POL + ! Based on Gly3 data from graf et al, RB 7/1/11 +CE1 CE1 CT3 HA3 0.0300 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 CT3 0.5000 1 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 CT3 1.3000 3 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 HA2 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT3 HA3 0.0500 3 180.00 ! + ! for propene, yin/adm jr., 12/95 +CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 +CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 +!aliphatic chain parameters compatible with the revised side-chain parameters, from all22_carb>>all27_lip>>all31 + ! lower butane gauche conformer +CT2 CT2 CT2 CT2 0.10 2 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT2 0.15 4 0.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT2 0.10 6 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.10 2 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.15 4 0.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.10 6 180.00 ! alkane, 4/98, adm jr. +! +CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! from CT2 CT1 NH1 C, for lactams, adm jr. +CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +CT3 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION + ! DTN 8/24/90 +CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from H NH1 CT2 CT3, for lactams, adm jr. +H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/20/89 +H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC + ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HA1 CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL + ! adm jr. 4/10/91, acetamide update +HA2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA1 CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA2 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA2 CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA2 CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA2 CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA3 CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA3 CT3 CS HA2 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CS HA3 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA3 CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA3 CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA3 CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HE1 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +CT3 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +HE1 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 HA2 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE1 CE1 CT2 CT3 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT3 HA3 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE2 CE2 CE1 CT2 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +HB1 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NH2 CT2 HB2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CD 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CT2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral lysine +HC NH2 CT2 HA2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral lysine +HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 HB1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 HA2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, his +HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, YES, 0.0 +HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 HA2 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 HA3 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 HA3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from NH1 C CT1 CT2, for lactams, adm jr. +NH1 C CT2 HA2 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT3 HA3 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +!!!NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO +!!! ! adm jr. 3/24/92, for PRES GLYP +NH3 CT2 C NH1 1.0000 1 0.00 ! ALLOW PEP PRO + ! RB 1/07/11, based on graf et al Gly 3 N-ter J-couplings for PRES GLYP +NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +!NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB1 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP + ! from O C CT1 CT2, for lactams, adm jr. +O C CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT3 HA3 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 H 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB1 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 HB1 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +S CT2 CT2 HA2 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM CT2 CT2 HA2 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT3 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 HA2 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 HA3 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 HA3 0.1500 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO + ! 9.0->2.25 GUANIDINIUM (KK) +X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier +X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CE1 CE1 X 0.1500 1 0.00 + ! 2-butene, adm jr., 2/00 update +X CE1 CE1 X 8.5000 2 180.00 + ! 2-butene, adm jr., 2/00 update +X CE2 CE2 X 4.9000 2 180.00 ! + ! for ethene, yin/adm jr., 12/95 +X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP + ! changed to 0.0 RLD 5/19/92 +X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CT2 X 0.1900 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CT3 X 0.1525 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL + ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 +X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate + +!chi1/chi2 fitting, Zhu, 2011 +!directly transferred parameters +NH1 CT1 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT1 X +HB1 CT1 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT1 X +HB1 CT1 CT1 CT3 0.2000 3 0.00 ! From X CT1 CT1 X +HA1 CT1 CT1 C 0.2000 3 0.00 ! From X CT1 CT1 X +! +NH1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2 OH1 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2 CT2 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2 CT1 C 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2 OH1 H 0.1400 3 0.00 ! From X CT2 OH1 X +! +CT1 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2 CT2 CC 0.1900 3 0.00 ! From X CT2 CT2 X +! +HB1 CT1 CT2 S 0.2000 3 0.00 ! From X CT1 CT2 X +!Arg +CT2 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +CT2 CT2 CT2 NC2 0.1900 3 0.00 ! From X CT2 CT2 X +CT2 CT2 NC2 HC 0.0000 6 180.00 ! From X CT2 NC2 X +CT2 CT2 NC2 C 0.0000 6 180.00 ! From X CT2 NC2 X +HA2 CT2 CT2 NC2 0.1900 3 0.00 ! From X CT2 CT2 X +CT2 NC2 C NC2 2.2500 2 180.00 ! From X C NC2 X +HA2 CT2 NC2 HC 0.0000 6 180.00 ! From X CT2 NC2 X +HA2 CT2 NC2 C 0.0000 6 180.00 ! From X CT2 NC2 X +NC2 C NC2 HC 2.2500 2 180.00 ! From X C NC2 X +!Asn +HB1 CT1 CT2 CC 0.2000 3 0.00 ! From X CT1 CT2 X +!Trp +HB1 CT1 CT2 CY 0.2000 3 0.00 ! From X CT1 CT2 X +!Asp +HA2 CT2 CC OC 0.0500 6 180.00 ! From X CT2 CC X +!Hsd/Hse +HB1 CT1 CT2 CPH1 0.2000 3 0.00 ! From X CT1 CT2 X +!Ile,Leu,Val +CT1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X +CT1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT1 CT2 0.2000 3 0.00 ! From X CT1 CT1 X +CT1 CT2 CT3 HA3 0.1600 3 0.00 ! From X CT2 CT3 X +HA1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X +HA1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HA1 CT1 CT2 CT3 0.2000 3 0.00 ! From X CT1 CT2 X +CT3 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +CT3 CT1 CT2 CT3 0.2000 3 0.00 ! From X CT1 CT2 X +HA3 CT3 CT1 CT2 0.2000 3 0.00 ! From X CT1 CT3 X +HA2 CT2 CT3 HA3 0.1600 3 0.00 ! From X CT2 CT3 X +CT1 CT2 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2 CT1 0.2000 3 0.00 ! From X CT1 CT2 X +CT3 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X +!Lys +CT2 CT2 CT2 NH3 0.1900 3 0.00 ! From X CT2 CT2 X +CT2 CT2 NH3 HC 0.1000 3 0.00 ! From X CT2 NH3 X +HA2 CT2 CT2 NH3 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2 NH3 HC 0.1000 3 0.00 ! From X CT2 NH3 X +!Tyr/Phe +HB1 CT1 CT2 CA 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2 CA CA 0.0000 6 0.00 ! From X CT2 CA X +!Thr +HB1 CT1 CT1 OH1 0.2000 3 0.00 ! From X CT1 CT1 X +HA1 CT1 OH1 H 0.1400 3 0.00 ! From X CT1 OH1 X +OH1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X +!Gln +CT2 CT2 CC O 0.0500 6 180.00 ! From X CT2 CC X +CT2 CT2 CC NH2 0.0500 6 180.00 ! From X CT2 CC X +!Glu +CT2 CT2 CC OC 0.0500 6 180.00 ! From X CT2 CC X +!Glu/Hsp +NH1 CT1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X +NH3 CT1 CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X !N terminus +CT1 CT2A CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HB1 CT1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2A CT1 C 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2A CT1 CC 0.2000 3 0.00 ! RB: added for C-ter Glu +HA2 CT2A CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2A CT2 CC 0.1900 3 0.00 ! From X CT2 CT2 X +HB1 CT1 CT2A CPH1 0.2000 3 0.00 ! From X CT1 CT2 X +C NH1 CT1 CT2A 1.8000 1 0.00 ! from CT2 CT1 NH1 C +H NH1 CT1 CT2A 0.0000 1 0.00 ! from H NH1 CT1 CT2 +CT2A CT1 C O 1.4000 1 0.00 ! from O C CT1 CT2 +CT2A CT1 C NH1 0.0000 1 0.00 ! NH1 C CT1 CT2 +CT2A CT1 C N 0.0000 1 0.00 ! RB: added for GLU-PRO in UBQ +! Glup +CT1 CT2A CT2 CD 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2A CT2 CD 0.1900 3 0.00 ! From X CT2 CT2 X +CT2A CPH1 CPH1 HR1 1.0000 2 180.00 ! from HR1 CPH1 CPH1 CT2 +CT2A CPH1 CPH1 NR3 2.5000 2 180.00 ! from NR3 CPH1 CPH1 CT2 +CT2A CPH1 NR3 H 3.0000 2 180.00 ! from H NR3 CPH1 CT2 +CT2A CPH1 NR3 CPH2 2.5000 2 180.00 ! from CT2 CPH1 NR3 CPH2 +HA2 CT2A CPH1 CPH1 0.0000 3 0.00 ! from HA2 CT2 CPH1 CPH1 +HA2 CT2A CPH1 NR3 0.1900 3 0.00 ! from NR3 CPH1 CT2 HA2 + +! Fit dihedrals +! Variable cutoff based on QM and weighted in favor of alphaR and EXT (5:5:1) +! Shared dihedrals were fitted simultaneously + +! Group-fitted for Lys/Arg/Gln/Met +C CT1 CT2 CT2 0.3500 1 180.00 +C CT1 CT2 CT2 0.4200 2 180.00 +C CT1 CT2 CT2 1.9100 3 180.00 +CT2 CT2 CT1 NH1 0.8800 1 180.00 +CT2 CT2 CT1 NH1 0.0000 2 180.00 +CT2 CT2 CT1 NH1 1.9000 3 0.00 +CC CT2 CT2 CT1 1.8400 1 180.00 +CC CT2 CT2 CT1 0.8400 2 180.00 +CC CT2 CT2 CT1 0.3900 3 180.00 +CT1 CT2 CT2 CT2 0.6300 1 180.00 +CT1 CT2 CT2 CT2 0.0100 2 0.00 +CT1 CT2 CT2 CT2 0.1500 3 0.00 +CT1 CT2 CT2 S 0.1400 1 180.00 +CT1 CT2 CT2 S 0.5400 2 0.00 +CT1 CT2 CT2 S 0.6900 3 0.00 +! Fitted Asn +C CT1 CT2 CC 1.4100 1 180.00 +C CT1 CT2 CC 1.2900 2 180.00 +C CT1 CT2 CC 0.5900 3 180.00 +CC CT2 CT1 NH1 0.2800 1 180.00 +CC CT2 CT1 NH1 0.5000 2 180.00 +CC CT2 CT1 NH1 0.3800 3 0.00 +CT1 CT2 CC NH2 0.6200 1 180.00 +CT1 CT2 CC NH2 0.6600 2 180.00 +CT1 CT2 CC NH2 0.7200 3 180.00 +CT1 CT2 CC O 0.4200 1 180.00 +CT1 CT2 CC O 0.1500 2 180.00 +CT1 CT2 CC O 0.9500 3 180.00 +! Fitted Asp +C CT1 CT2A CC 1.6100 1 180.00 +C CT1 CT2A CC 1.2900 2 180.00 +C CT1 CT2A CC 0.5900 3 180.00 +CC CT2A CT1 NH1 0.6800 1 180.00 +CC CT2A CT1 NH1 0.1000 2 180.00 +CC CT2A CT1 NH1 0.3800 3 0.00 +CT1 CT2A CC OC 0.8400 1 0.00 +CT1 CT2A CC OC 0.9800 2 180.00 +CT1 CT2A CC OC 1.4600 3 0.00 +! Fitted Cys +CT1 CT2 S HS 0.2000 1 0.00 +CT1 CT2 S HS 0.6500 2 0.00 +CT1 CT2 S HS 0.2200 3 0.00 +C CT1 CT2 S 0.2400 1 180.00 +C CT1 CT2 S 0.7500 2 180.00 +C CT1 CT2 S 1.3500 3 180.00 +NH1 CT1 CT2 S 0.3400 1 0.00 +NH1 CT1 CT2 S 0.5000 2 180.00 +NH1 CT1 CT2 S 1.4300 3 0.00 +! Fitted Glu +CC CT2 CT2A CT1 0.0000 1 180.00 +CC CT2 CT2A CT1 0.3800 2 180.00 +CC CT2 CT2A CT1 0.5900 3 180.00 +C CT1 CT2A CT2 0.1100 1 0.00 +C CT1 CT2A CT2 0.9800 2 180.00 +C CT1 CT2A CT2 1.6000 3 180.00 +CC CT1 CT2A CT2 1.6000 3 180.00 +CT2 CT2A CT1 NH1 0.3000 1 0.00 +CT2 CT2A CT1 NH1 0.3500 2 0.00 +CT2 CT2A CT1 NH1 1.7600 3 0.00 +! Group-fitted for Hsd/Hse +CPH1 CPH1 CT2 CT1 1.7400 1 0.00 +CPH1 CPH1 CT2 CT1 0.1500 2 0.00 +CPH1 CPH1 CT2 CT1 0.7700 3 180.00 +CT1 CT2 CPH1 NR1 1.4900 1 0.00 +CT1 CT2 CPH1 NR1 0.0900 2 180.00 +CT1 CT2 CPH1 NR1 0.7900 3 180.00 +CT1 CT2 CPH1 NR2 1.0900 1 0.00 +CT1 CT2 CPH1 NR2 0.0900 2 0.00 +CT1 CT2 CPH1 NR2 0.6700 3 180.00 +C CT1 CT2 CPH1 0.1800 1 180.00 +C CT1 CT2 CPH1 0.6400 2 180.00 +C CT1 CT2 CPH1 0.8700 3 180.00 +CPH1 CT2 CT1 NH1 0.0000 1 0.00 +CPH1 CT2 CT1 NH1 0.0000 2 180.00 +CPH1 CT2 CT1 NH1 0.9000 3 0.00 +! Fitted Hsp +CPH1 CPH1 CT2A CT1 2.0400 1 0.00 +CPH1 CPH1 CT2A CT1 0.4400 2 0.00 +CPH1 CPH1 CT2A CT1 0.1300 3 180.00 +CT1 CT2A CPH1 NR3 0.5300 1 180.00 +CT1 CT2A CPH1 NR3 0.4200 2 180.00 +CT1 CT2A CPH1 NR3 0.3000 3 180.00 +C CT1 CT2A CPH1 1.7500 1 180.00 +C CT1 CT2A CPH1 0.1300 2 0.00 +C CT1 CT2A CPH1 1.8600 3 180.00 +CPH1 CT2A CT1 NH1 1.0900 1 180.00 +CPH1 CT2A CT1 NH1 0.2200 2 180.00 +CPH1 CT2A CT1 NH1 2.3200 3 0.00 +! Group-fitted for Ile/Thr +CT1 CT1 CT2 CT3 0.3800 1 180.00 +CT1 CT1 CT2 CT3 0.1300 2 180.00 +CT1 CT1 CT2 CT3 0.2900 3 180.00 +C CT1 CT1 CT2 0.1000 1 180.00 +C CT1 CT1 CT2 0.5200 2 180.00 +C CT1 CT1 CT2 0.2900 3 180.00 +CT2 CT1 CT1 NH1 0.1200 1 180.00 +CT2 CT1 CT1 NH1 0.3600 2 180.00 +CT2 CT1 CT1 NH1 0.4100 3 0.00 +! Fitted Leu +CT1 CT2 CT1 CT3 0.0500 1 0.00 +CT1 CT2 CT1 CT3 0.1000 2 180.00 +CT1 CT2 CT1 CT3 0.0100 3 180.00 +C CT1 CT2 CT1 0.3200 1 180.00 +C CT1 CT2 CT1 0.6100 2 180.00 +C CT1 CT2 CT1 0.7200 3 180.00 +CT1 CT2 CT1 NH1 0.4800 1 180.00 +CT1 CT2 CT1 NH1 0.4200 2 180.00 +CT1 CT2 CT1 NH1 0.6500 3 0.00 +! Group-fitted for Phe/Tyr +CA CA CT2 CT1 1.0700 1 0.00 +CA CA CT2 CT1 0.2400 2 180.00 +CA CA CT2 CT1 0.1700 3 180.00 +C CT1 CT2 CA 1.2800 1 180.00 +C CT1 CT2 CA 0.9400 2 180.00 +C CT1 CT2 CA 1.5700 3 180.00 +CA CT2 CT1 NH1 0.5200 1 180.00 +CA CT2 CT1 NH1 0.6200 2 180.00 +CA CT2 CT1 NH1 1.5800 3 0.00 +! Fitted Ser +CT1 CT2 OH1 H 0.0200 1 0.00 +CT1 CT2 OH1 H 0.5600 2 0.00 +CT1 CT2 OH1 H 0.4900 3 0.00 +C CT1 CT2 OH1 0.6500 1 180.00 +C CT1 CT2 OH1 0.2500 2 180.00 +C CT1 CT2 OH1 1.1700 3 180.00 +NH1 CT1 CT2 OH1 0.1800 1 180.00 +NH1 CT1 CT2 OH1 0.1900 2 180.00 +NH1 CT1 CT2 OH1 1.4600 3 0.00 +! Group-fitted for Ile/Thr +CT1 CT1 OH1 H 0.1800 1 0.00 +CT1 CT1 OH1 H 0.0600 2 0.00 +CT1 CT1 OH1 H 0.2500 3 0.00 +C CT1 CT1 OH1 0.7900 1 180.00 +C CT1 CT1 OH1 0.3900 2 180.00 +C CT1 CT1 OH1 0.9900 3 180.00 +NH1 CT1 CT1 OH1 0.0900 1 0.00 +NH1 CT1 CT1 OH1 0.1900 2 180.00 +NH1 CT1 CT1 OH1 0.1700 3 0.00 +! Fitted Trp +CA CY CT2 CT1 0.0300 1 0.00 +CA CY CT2 CT1 0.5500 2 0.00 +CA CY CT2 CT1 0.3900 3 180.00 +CPT CY CT2 CT1 0.3600 1 180.00 +CPT CY CT2 CT1 0.0500 2 0.00 +CPT CY CT2 CT1 0.1900 3 180.00 +C CT1 CT2 CY 1.0900 1 180.00 +C CT1 CT2 CY 0.5000 2 180.00 +C CT1 CT2 CY 1.1700 3 180.00 +CY CT2 CT1 NH1 0.2900 1 180.00 +CY CT2 CT1 NH1 0.6600 2 180.00 +CY CT2 CT1 NH1 1.1700 3 0.00 +! Fitted Val +C CT1 CT1 CT3 0.1400 1 180.00 +C CT1 CT1 CT3 0.2600 2 180.00 +C CT1 CT1 CT3 0.3300 3 180.00 +CT3 CT1 CT1 NH1 0.1800 1 0.00 +CT3 CT1 CT1 NH1 0.0600 2 0.00 +CT3 CT1 CT1 NH1 0.5900 3 0.00 +!ASP, CT2->CT2A, jshim +H NH1 CT2A CC 0.0000 1 0.00 +X CT2A CC X 0.0500 6 180.00 +HB1 CT1 CT2A CC 0.2000 3 0.00 +HA2 CT2A CC OC 0.0500 6 180.00 +NH3 CT1 CT2A HA2 0.2000 3 0.00 +NH3 CT1 CT2A CC 0.2000 3 0.00 +CC CT2A CT1 CC 0.2000 3 0.00 +!termini specific terms +CPH1 CT2A CT1 CC 0.2000 3 0.00 +CPH1 CT2A CT1 NH3 0.2000 3 0.00 +CPH1 CT2A CT1 CD 0.2000 3 0.00 +HA2 CT2A CT1 CD 0.2000 3 0.00 +CT2 CT2A CT1 CD 0.2000 3 0.00 +! RESI CYSM and PRES CYSD +H NH2 CT1 CS 0.1100 3 0.00 ! from H NH2 CT1 CT2 or H NH2 CT1 CT2 , kevo +CS CT1 NH1 C 1.8000 1 0.00 ! from CT2 CT1 NH1 C or CT2A CT1 NH1 C , kevo +H NH1 CT1 CS 0.0000 1 0.00 ! from H NH1 CT1 CT2 or H NH1 CT1 CT2 , kevo +N C CT1 CS 0.0000 1 0.00 ! from N C CT1 CT2 or N C CT1 CT2 , kevo +NH1 C CT1 CS 0.0000 1 0.00 ! from NH1 C CT1 CT2 or NH1 C CT1 CT2 , kevo +O C CT1 CS 1.4000 1 0.00 ! from O C CT1 CT2 or O C CT1 CT2 , kevo +HA2 CS CT1 C 0.2000 3 0.00 ! from HA2 CT2 CT1 C or HA2 CT2A CT1 C , kevo +NH1 CT1 CS HA2 0.2000 3 0.00 ! from NH1 CT1 CT2 HA2 or NH1 CT1 CT2A HA2 , kevo +HB1 CT1 CS HA2 0.2000 3 0.00 ! from HB1 CT1 CT2 HA2 or HB1 CT1 CT2A HA2 , kevo +HB1 CT1 CS SS 0.2000 3 0.00 ! from HB1 CT1 CT2 S or HB1 CT1 CT2A S , kevo +C CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH1 CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +! Termini +NH3 CT1 CS HA2 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH3 CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH2 CT1 CS HA2 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH2 CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CC CT1 CS HA2 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CC CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CD CT1 CS HA2 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CD CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +! PRES SERD +NH1 CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH2 CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH3 CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +C CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CC CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CD CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +HB1 CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +HE2 HE2 CE2 CE2 3.0 0 0.00 ! + ! for ethene, yin/adm jr., 12/95 +HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +NC2 X X C 45.0000 0 0.0000 ! ALLOW PEP POL ARO + ! mp2/6-311g** guan vibrational data, adm jr., 1/04 +C HC HC NC2 0.0 0 0.0 + ! mp2/6-311g** guan vibrational data, adm jr., 1/04 +NC2 X X HC -2.0 0 0.0 + ! mp2/6-311g** guan vibrational data, adm jr., 1/04 +NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +NH2 X X H 4.0000 0 0.0000 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O HA1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! adm jr., 5/13/91, formamide geometry and vibrations +O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 HA1 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL + ! adm jr., 10/17/90, acetic acid vibrations +OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) + +CMAP +! 2D grid correction data. +! Finalfix3, Feig/Best/MacKerell 2010 + +! alanine map +C NH1 CT1 C NH1 CT1 C NH1 24 + +! phi = -180.0 + 0.126790 0.768700 0.971260 1.250970 2.121010 + 2.720430 2.089440 1.789790 0.780870 -0.688474 + 1.001130 -2.200520 -4.827670 -4.821447 -4.913223 + -3.591106 -2.766446 -2.784200 -2.454589 -2.346991 + -2.335350 -1.522656 -0.951542 -0.036650 + +! phi = -165.0 + -0.127133 1.377090 1.577020 1.872290 2.398990 + 2.486630 2.436754 1.929070 1.086456 0.643400 + 0.258676 -2.800440 -4.009477 -4.135306 -3.420090 + -2.602140 -2.299128 -1.501241 -1.101780 -0.861434 + -0.640168 -0.207701 -1.076344 -1.122030 + +! phi = -150.0 + 0.084069 1.420317 1.624350 2.047200 2.653910 + 2.716410 2.321416 1.985454 1.557466 2.463293 + -0.225720 -1.815886 -2.583256 -3.006154 -2.551995 + -1.890683 -1.354215 -0.727243 0.068512 -0.225016 + -0.765479 -1.283444 -1.293226 -0.816303 + +! phi = -135.0 + 0.927992 1.521370 2.242218 2.546305 3.111384 + 2.918410 2.460813 2.187970 2.058314 1.852278 + 0.115935 -1.183897 -1.995479 -2.278329 -1.959136 + -1.340467 -0.932949 0.021790 0.313725 -0.517358 + -1.152891 -0.983285 -0.566518 -0.442565 + +! phi = -120.0 + 1.357468 1.959160 2.698894 3.037857 3.698960 + 3.558453 2.639296 2.773853 2.719664 1.627997 + 0.705667 -0.785637 -2.118268 -2.628489 -1.803113 + -0.425969 -0.062320 0.439040 0.910952 -0.546994 + -0.968118 -0.856791 -0.250116 0.449309 + +! phi = -105.0 + 2.045006 2.544424 2.818030 3.088582 3.370620 + 3.551568 3.073520 2.903794 2.956634 2.124759 + 0.906487 -0.823628 -2.090819 -2.241579 -1.456524 + 0.206160 0.082195 0.771710 1.040241 -0.124647 + -0.316550 -0.164333 0.314474 0.733747 + +! phi = -90.0 + 1.451735 2.748481 2.738185 3.156796 3.450028 + 3.344157 3.180200 3.898724 3.335030 2.440579 + 0.912671 -0.606502 -1.511772 -1.620864 -0.962798 + -0.020653 0.415153 0.908250 0.459433 0.145910 + -0.071054 0.017622 0.280839 0.748823 + +! phi = -75.0 + 1.378160 3.345958 2.352424 3.063543 3.814070 + 3.700796 3.580310 4.212293 3.536425 1.693809 + 0.095172 -0.682452 -0.123614 -0.427765 -0.598368 + 0.226352 0.423308 0.301999 0.551890 0.191719 + -0.253585 -0.190548 -0.253412 0.468922 + +! phi = -60.0 + 0.237754 1.229980 1.716960 3.168570 4.208190 + 4.391860 4.276080 3.673107 2.272295 -0.482789 + -0.406695 -0.038919 -0.357600 -0.823341 -0.173146 + 0.139806 0.267796 0.322420 0.309664 -0.666399 + -0.948631 -1.534365 -1.479968 -0.204264 + +! phi = -45.0 + -1.184837 0.078060 2.347410 4.211350 5.376000 + 5.389940 4.380200 2.461506 1.123713 0.107016 + 0.007574 -0.149443 -0.797230 -0.582210 0.082910 + 0.271580 -0.045570 0.379430 0.247770 -0.890956 + -1.582430 -1.954532 -1.980965 -2.000433 + +! phi = -30.0 + -1.174720 1.067030 4.180460 6.741610 6.070770 + 4.806470 2.783340 1.320806 0.765978 -0.008448 + 0.276860 -0.707140 1.314360 1.522590 1.915550 + 2.223490 0.194290 0.534000 0.331780 -1.595147 + -2.849141 -3.550465 -3.277369 -2.655135 + +! phi = -15.0 + 0.293590 5.588070 3.732620 3.217620 3.272450 + 2.517320 1.588700 1.381760 0.856410 0.655170 + 1.616970 0.846920 0.511070 0.740760 1.021020 + 1.616580 -0.342400 0.181770 -0.613920 -2.558037 + -3.786839 -3.807325 -3.155346 -1.749204 + +! phi = 0.0 + 2.832310 0.787990 0.323280 0.479230 0.628600 + 0.976330 1.238750 1.671950 1.645480 2.520340 + 1.606970 0.776350 0.119780 0.070390 0.121170 + -1.569230 -1.213010 -1.846360 -2.744510 -3.792530 + -3.934880 -3.615930 -2.675750 -0.924170 + +! phi = 15.0 + -0.778340 -1.912680 -2.052140 -1.846280 -1.047430 + 0.183400 1.682950 2.223500 1.358370 2.448660 + 1.436920 0.678570 -0.237060 -0.535320 -0.790380 + -2.182580 -3.251140 -4.195110 -4.269270 -3.908210 + -3.455620 -2.773970 1.755370 0.313410 + +! phi = 30.0 + -2.963810 -3.483730 -3.441809 -2.400349 -1.125083 + 0.336200 1.428450 1.394630 0.970370 2.462720 + 1.522430 0.553620 -0.407380 -1.482950 -3.613920 + -4.159810 -4.709721 -4.496271 -3.764540 -2.959140 + -1.963850 -1.071260 -1.599580 -2.445320 + +! phi = 45.0 + -4.021496 -3.836549 -3.365327 -2.334377 -0.984725 + 0.362000 0.814380 0.754110 0.502370 1.903420 + 0.770220 -0.416420 -3.286310 -3.875270 -4.611550 + -5.287977 -5.146239 -4.038627 -2.865450 -2.368170 + -2.860490 -3.416560 -3.666490 -3.595217 + +! phi = 60.0 + -3.353683 -2.984416 -2.317412 -1.240143 -0.257890 + 0.722610 0.668070 0.438130 2.395330 1.632470 + -2.041450 -3.218100 -3.915080 -4.568574 -5.096776 + -5.526955 -5.005312 -3.777879 -2.840678 -3.508820 + -3.756430 -3.640810 -3.451845 -3.342810 + +! phi = 75.0 + -2.248733 -1.641080 -1.010583 0.039656 0.636063 + 0.823710 0.517140 -0.013120 -0.370910 -1.192809 + -2.305650 -3.420580 -4.484960 -5.597237 -5.601264 + -5.727739 -4.740525 -3.819378 -3.685150 -4.151360 + -4.170739 -3.725589 -3.736732 -2.620673 + +! phi = 90.0 + -1.720840 -1.177830 -0.428430 0.277730 0.807900 + 0.803260 0.482510 -0.336900 -0.786270 -1.774070 + -2.793220 -3.828560 -5.211800 -6.294328 -6.617221 + -5.763953 -5.072995 -3.911450 -4.158306 -4.473413 + -4.099325 -3.769822 -3.157300 -2.651694 + +! phi = 105.0 + -1.850640 -1.092420 -0.445020 0.128490 1.005520 + 0.884820 0.485850 -0.218470 -0.857670 -1.682330 + -3.014400 -4.481110 -6.053510 -6.865400 -6.871130 + -5.728240 -3.912230 -4.802110 -5.034640 -4.715990 + -4.600554 -4.086721 -3.274630 -2.410940 + +! phi = 120.0 + -1.969230 -1.116650 -0.540250 -0.150330 0.763520 + 1.038890 0.758480 0.313530 -0.333050 -1.872770 + -3.366270 -5.008260 -6.124810 -7.034830 -6.724320 + -3.700200 -4.510620 -5.185650 -5.361620 -4.847490 + -4.444320 -4.004260 -3.415720 -2.751230 + +! phi = 135.0 + -2.111250 -1.168960 -0.322790 -0.006920 0.316660 + 1.086270 0.939170 0.625340 -0.166360 -1.830310 + -3.469470 -4.946030 -6.112560 -1.915580 -4.047310 + -4.996740 -4.996730 -4.842690 -4.886620 -4.300540 + -4.494620 -4.442210 -4.163570 -3.183510 + +! phi = 150.0 + -1.757590 -0.403620 0.023920 0.362390 0.634520 + 1.264920 1.361360 0.948420 -0.073680 -1.483560 + -3.152820 1.835120 -1.762860 -5.093660 -5.744830 + -5.390070 -4.783930 -4.190630 -4.115420 -4.042280 + -4.125570 -4.028550 -4.026100 -2.937910 + +! phi = 165.0 + -0.810590 -0.071500 0.378890 0.543310 1.277880 + 1.641310 1.698840 1.519950 0.631950 -1.088670 + -2.736530 -0.735240 -4.563830 -6.408350 -5.889450 + -5.141750 -4.194970 -3.666490 -3.843450 -3.555000 + -3.548722 -3.246995 -2.751289 -1.814368 + + +! alanine before proline map + +C NH1 CT1 C NH1 CT1 C N 24 + +! phi = -180.0 + 0.126790 0.768700 0.971260 1.250970 2.121010 + 2.720430 2.089440 1.789790 0.780870 -0.688474 + 1.001130 -2.200520 -4.827670 -4.821447 -4.913223 + -3.591106 -2.766446 -2.784200 -2.454589 -2.346991 + -2.335350 -1.522656 -0.951542 -0.036650 + +! phi = -165.0 + -0.127133 1.377090 1.577020 1.872290 2.398990 + 2.486630 2.436754 1.929070 1.086456 0.643400 + 0.258676 -2.800440 -4.009477 -4.135306 -3.420090 + -2.602140 -2.299128 -1.501241 -1.101780 -0.861434 + -0.640168 -0.207701 -1.076344 -1.122030 + +! phi = -150.0 + 0.084069 1.420317 1.624350 2.047200 2.653910 + 2.716410 2.321416 1.985454 1.557466 2.463293 + -0.225720 -1.815886 -2.583256 -3.006154 -2.551995 + -1.890683 -1.354215 -0.727243 0.068512 -0.225016 + -0.765479 -1.283444 -1.293226 -0.816303 + +! phi = -135.0 + 0.927992 1.521370 2.242218 2.546305 3.111384 + 2.918410 2.460813 2.187970 2.058314 1.852278 + 0.115935 -1.183897 -1.995479 -2.278329 -1.959136 + -1.340467 -0.932949 0.021790 0.313725 -0.517358 + -1.152891 -0.983285 -0.566518 -0.442565 + +! phi = -120.0 + 1.357468 1.959160 2.698894 3.037857 3.698960 + 3.558453 2.639296 2.773853 2.719664 1.627997 + 0.705667 -0.785637 -2.118268 -2.628489 -1.803113 + -0.425969 -0.062320 0.439040 0.910952 -0.546994 + -0.968118 -0.856791 -0.250116 0.449309 + +! phi = -105.0 + 2.045006 2.544424 2.818030 3.088582 3.370620 + 3.551568 3.073520 2.903794 2.956634 2.124759 + 0.906487 -0.823628 -2.090819 -2.241579 -1.456524 + 0.206160 0.082195 0.771710 1.040241 -0.124647 + -0.316550 -0.164333 0.314474 0.733747 + +! phi = -90.0 + 1.451735 2.748481 2.738185 3.156796 3.450028 + 3.344157 3.180200 3.898724 3.335030 2.440579 + 0.912671 -0.606502 -1.511772 -1.620864 -0.962798 + -0.020653 0.415153 0.908250 0.459433 0.145910 + -0.071054 0.017622 0.280839 0.748823 + +! phi = -75.0 + 1.378160 3.345958 2.352424 3.063543 3.814070 + 3.700796 3.580310 4.212293 3.536425 1.693809 + 0.095172 -0.682452 -0.123614 -0.427765 -0.598368 + 0.226352 0.423308 0.301999 0.551890 0.191719 + -0.253585 -0.190548 -0.253412 0.468922 + +! phi = -60.0 + 0.237754 1.229980 1.716960 3.168570 4.208190 + 4.391860 4.276080 3.673107 2.272295 -0.482789 + -0.406695 -0.038919 -0.357600 -0.823341 -0.173146 + 0.139806 0.267796 0.322420 0.309664 -0.666399 + -0.948631 -1.534365 -1.479968 -0.204264 + +! phi = -45.0 + -1.184837 0.078060 2.347410 4.211350 5.376000 + 5.389940 4.380200 2.461506 1.123713 0.107016 + 0.007574 -0.149443 -0.797230 -0.582210 0.082910 + 0.271580 -0.045570 0.379430 0.247770 -0.890956 + -1.582430 -1.954532 -1.980965 -2.000433 + +! phi = -30.0 + -1.174720 1.067030 4.180460 6.741610 6.070770 + 4.806470 2.783340 1.320806 0.765978 -0.008448 + 0.276860 -0.707140 1.314360 1.522590 1.915550 + 2.223490 0.194290 0.534000 0.331780 -1.595147 + -2.849141 -3.550465 -3.277369 -2.655135 + +! phi = -15.0 + 0.293590 5.588070 3.732620 3.217620 3.272450 + 2.517320 1.588700 1.381760 0.856410 0.655170 + 1.616970 0.846920 0.511070 0.740760 1.021020 + 1.616580 -0.342400 0.181770 -0.613920 -2.558037 + -3.786839 -3.807325 -3.155346 -1.749204 + +! phi = 0.0 + 2.832310 0.787990 0.323280 0.479230 0.628600 + 0.976330 1.238750 1.671950 1.645480 2.520340 + 1.606970 0.776350 0.119780 0.070390 0.121170 + -1.569230 -1.213010 -1.846360 -2.744510 -3.792530 + -3.934880 -3.615930 -2.675750 -0.924170 + +! phi = 15.0 + -0.778340 -1.912680 -2.052140 -1.846280 -1.047430 + 0.183400 1.682950 2.223500 1.358370 2.448660 + 1.436920 0.678570 -0.237060 -0.535320 -0.790380 + -2.182580 -3.251140 -4.195110 -4.269270 -3.908210 + -3.455620 -2.773970 1.755370 0.313410 + +! phi = 30.0 + -2.963810 -3.483730 -3.441809 -2.400349 -1.125083 + 0.336200 1.428450 1.394630 0.970370 2.462720 + 1.522430 0.553620 -0.407380 -1.482950 -3.613920 + -4.159810 -4.709721 -4.496271 -3.764540 -2.959140 + -1.963850 -1.071260 -1.599580 -2.445320 + +! phi = 45.0 + -4.021496 -3.836549 -3.365327 -2.334377 -0.984725 + 0.362000 0.814380 0.754110 0.502370 1.903420 + 0.770220 -0.416420 -3.286310 -3.875270 -4.611550 + -5.287977 -5.146239 -4.038627 -2.865450 -2.368170 + -2.860490 -3.416560 -3.666490 -3.595217 + +! phi = 60.0 + -3.353683 -2.984416 -2.317412 -1.240143 -0.257890 + 0.722610 0.668070 0.438130 2.395330 1.632470 + -2.041450 -3.218100 -3.915080 -4.568574 -5.096776 + -5.526955 -5.005312 -3.777879 -2.840678 -3.508820 + -3.756430 -3.640810 -3.451845 -3.342810 + +! phi = 75.0 + -2.248733 -1.641080 -1.010583 0.039656 0.636063 + 0.823710 0.517140 -0.013120 -0.370910 -1.192809 + -2.305650 -3.420580 -4.484960 -5.597237 -5.601264 + -5.727739 -4.740525 -3.819378 -3.685150 -4.151360 + -4.170739 -3.725589 -3.736732 -2.620673 + +! phi = 90.0 + -1.720840 -1.177830 -0.428430 0.277730 0.807900 + 0.803260 0.482510 -0.336900 -0.786270 -1.774070 + -2.793220 -3.828560 -5.211800 -6.294328 -6.617221 + -5.763953 -5.072995 -3.911450 -4.158306 -4.473413 + -4.099325 -3.769822 -3.157300 -2.651694 + +! phi = 105.0 + -1.850640 -1.092420 -0.445020 0.128490 1.005520 + 0.884820 0.485850 -0.218470 -0.857670 -1.682330 + -3.014400 -4.481110 -6.053510 -6.865400 -6.871130 + -5.728240 -3.912230 -4.802110 -5.034640 -4.715990 + -4.600554 -4.086721 -3.274630 -2.410940 + +! phi = 120.0 + -1.969230 -1.116650 -0.540250 -0.150330 0.763520 + 1.038890 0.758480 0.313530 -0.333050 -1.872770 + -3.366270 -5.008260 -6.124810 -7.034830 -6.724320 + -3.700200 -4.510620 -5.185650 -5.361620 -4.847490 + -4.444320 -4.004260 -3.415720 -2.751230 + +! phi = 135.0 + -2.111250 -1.168960 -0.322790 -0.006920 0.316660 + 1.086270 0.939170 0.625340 -0.166360 -1.830310 + -3.469470 -4.946030 -6.112560 -1.915580 -4.047310 + -4.996740 -4.996730 -4.842690 -4.886620 -4.300540 + -4.494620 -4.442210 -4.163570 -3.183510 + +! phi = 150.0 + -1.757590 -0.403620 0.023920 0.362390 0.634520 + 1.264920 1.361360 0.948420 -0.073680 -1.483560 + -3.152820 1.835120 -1.762860 -5.093660 -5.744830 + -5.390070 -4.783930 -4.190630 -4.115420 -4.042280 + -4.125570 -4.028550 -4.026100 -2.937910 + +! phi = 165.0 + -0.810590 -0.071500 0.378890 0.543310 1.277880 + 1.641310 1.698840 1.519950 0.631950 -1.088670 + -2.736530 -0.735240 -4.563830 -6.408350 -5.889450 + -5.141750 -4.194970 -3.666490 -3.843450 -3.555000 + -3.548722 -3.246995 -2.751289 -1.814368 + + +! proline +! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map +C N CP1 C N CP1 C NH1 24 + +! phi = -180 + 2.973500 3.348200 3.062900 2.113400 1.040500 + 0.770600 0.785200 0.263300 -0.479000 -0.583000 + -0.463800 -0.292600 0.000000 0.259100 0.177100 + -0.151200 -0.173500 0.211700 0.348900 -0.135600 + -0.950000 -1.256600 -0.292800 1.560000 + +! phi = -165 + 5.674100 6.011400 5.562700 4.467300 3.390800 + 3.008800 2.848600 2.311200 1.661400 1.468400 + 1.142700 1.437400 2.113200 2.799500 2.989100 + 2.869000 3.016100 3.328500 3.232900 2.547600 + 1.647200 1.422700 2.517100 4.339800 + +! phi = -150 + 6.752800 6.973200 6.444300 5.389800 4.438600 + 4.046000 3.832800 3.442400 3.303500 3.010000 + 2.838100 3.162200 3.778300 4.362800 4.603600 + 4.546200 4.702100 4.837200 4.549500 3.849600 + 3.099200 3.031800 4.060200 5.624800 + +! phi = -135 + 7.627800 8.153400 7.342500 5.893500 4.799200 + 4.433400 4.551500 4.442800 2.222200 0.776300 + 0.790000 2.152300 3.932900 5.274900 5.830800 + 5.988600 5.588500 5.211000 4.918000 4.292100 + 3.495500 3.449800 4.617700 6.311700 + +! phi = -120 + 8.115600 8.477200 7.754300 6.585000 5.537900 + 4.964300 4.929000 4.421200 2.336100 1.257800 + 1.769300 3.359900 5.018000 6.055500 6.217600 + 5.726100 5.512200 5.820200 5.716700 4.872300 + 4.066800 4.094600 5.284900 6.931500 + +! phi = -105 + 9.249700 9.483000 8.668500 7.525300 7.003200 + 6.834600 6.822100 5.287600 3.320600 2.640300 + 3.464800 5.100300 6.537600 6.885600 5.842000 + 5.248700 5.540200 6.652400 7.196700 6.625400 + 5.710100 5.581700 6.651500 8.192800 + +! phi = -90 + 9.335600 9.208000 8.564600 8.010200 7.885100 + 8.212200 8.737100 8.429100 7.306500 6.474200 + 6.651300 7.484700 8.195300 8.295000 7.407200 + 6.529900 6.242000 6.227500 6.347300 6.449700 + 6.404700 6.579300 7.391700 8.570700 + +! phi = -75 + 10.955200 11.455400 11.173300 10.428700 10.062400 + 10.044500 9.279600 6.965100 5.361500 5.102700 + 6.267600 7.871600 8.009800 7.104500 6.616400 + 6.733700 7.504000 8.664700 9.282800 8.795900 + 7.872500 7.612400 8.498100 9.894000 + +! phi = -60 + 8.422900 8.529200 8.608500 9.306400 10.239400 + 11.025900 11.510800 9.283500 7.566000 6.624600 + 7.038700 8.222400 8.786400 8.512000 8.103500 + 7.988200 8.192900 8.291000 8.055600 7.436800 + 6.651800 6.317000 6.802500 7.746300 + +! phi = -45 + 6.913200 7.937400 8.610800 9.316600 9.388500 + 9.408400 8.828800 7.297900 5.456400 4.742700 + 5.793100 7.118800 7.565400 7.598500 7.438700 + 7.512500 7.878100 8.082200 7.642700 6.320500 + 4.680400 3.830500 4.215800 5.435200 + +! phi = -30 + 5.466700 7.116000 8.908800 8.347200 7.413500 + 7.047000 6.031600 4.193100 2.674800 3.023700 + 4.485300 5.451700 6.214900 6.422600 6.229300 + 6.191100 6.488900 6.646400 5.833400 3.751300 + 1.719800 1.064900 1.955800 3.860800 + +! phi = -15 + 3.061500 5.603800 12.179500 6.295200 5.323400 + 4.826500 3.705600 2.461500 2.291600 3.145900 + 3.562100 4.443600 5.337500 5.728800 5.694800 + 5.641600 5.943300 6.169000 4.759500 2.569400 + 1.357100 1.669800 3.212300 5.031900 + +! phi = 0 + 8.085900 8.051100 5.023600 3.450800 2.836100 + 2.192500 1.566200 1.456300 2.039300 1.945200 + 2.188400 2.921300 3.467500 3.543500 3.374500 + 3.472300 4.069900 3.615600 2.082200 0.958600 + 0.792600 1.494200 2.794900 4.853100 + +! phi = 15 + 6.639500 5.177400 3.252300 1.952700 1.078400 + 0.888300 1.505400 2.442300 2.178600 1.578600 + 1.777400 2.395400 2.820200 2.795200 2.662400 + 2.917100 2.562100 1.557900 1.322300 1.631400 + 2.051200 2.555600 3.039100 4.915000 + +! phi = 30 + 7.548800 5.095500 2.747000 0.955200 0.444500 + 1.318700 2.733300 3.223200 2.565500 2.150900 + 2.394400 2.939300 3.266000 3.210000 3.113400 + 2.491300 0.978300 0.815300 1.522700 2.055600 + 2.199900 2.327600 3.474200 7.977800 + +! phi = 45 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 60 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 75 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 90 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 105 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 120 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 135 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 150 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 165 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +!2 adjacent prolines +! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map +C N CP1 C N CP1 C N 24 + +! phi = -180 + 2.973500 3.348200 3.062900 2.113400 1.040500 + 0.770600 0.785200 0.263300 -0.479000 -0.583000 + -0.463800 -0.292600 0.000000 0.259100 0.177100 + -0.151200 -0.173500 0.211700 0.348900 -0.135600 + -0.950000 -1.256600 -0.292800 1.560000 + +! phi = -165 + 5.674100 6.011400 5.562700 4.467300 3.390800 + 3.008800 2.848600 2.311200 1.661400 1.468400 + 1.142700 1.437400 2.113200 2.799500 2.989100 + 2.869000 3.016100 3.328500 3.232900 2.547600 + 1.647200 1.422700 2.517100 4.339800 + +! phi = -150 + 6.752800 6.973200 6.444300 5.389800 4.438600 + 4.046000 3.832800 3.442400 3.303500 3.010000 + 2.838100 3.162200 3.778300 4.362800 4.603600 + 4.546200 4.702100 4.837200 4.549500 3.849600 + 3.099200 3.031800 4.060200 5.624800 + +! phi = -135 + 7.627800 8.153400 7.342500 5.893500 4.799200 + 4.433400 4.551500 4.442800 2.222200 0.776300 + 0.790000 2.152300 3.932900 5.274900 5.830800 + 5.988600 5.588500 5.211000 4.918000 4.292100 + 3.495500 3.449800 4.617700 6.311700 + +! phi = -120 + 8.115600 8.477200 7.754300 6.585000 5.537900 + 4.964300 4.929000 4.421200 2.336100 1.257800 + 1.769300 3.359900 5.018000 6.055500 6.217600 + 5.726100 5.512200 5.820200 5.716700 4.872300 + 4.066800 4.094600 5.284900 6.931500 + +! phi = -105 + 9.249700 9.483000 8.668500 7.525300 7.003200 + 6.834600 6.822100 5.287600 3.320600 2.640300 + 3.464800 5.100300 6.537600 6.885600 5.842000 + 5.248700 5.540200 6.652400 7.196700 6.625400 + 5.710100 5.581700 6.651500 8.192800 + +! phi = -90 + 9.335600 9.208000 8.564600 8.010200 7.885100 + 8.212200 8.737100 8.429100 7.306500 6.474200 + 6.651300 7.484700 8.195300 8.295000 7.407200 + 6.529900 6.242000 6.227500 6.347300 6.449700 + 6.404700 6.579300 7.391700 8.570700 + +! phi = -75 + 10.955200 11.455400 11.173300 10.428700 10.062400 + 10.044500 9.279600 6.965100 5.361500 5.102700 + 6.267600 7.871600 8.009800 7.104500 6.616400 + 6.733700 7.504000 8.664700 9.282800 8.795900 + 7.872500 7.612400 8.498100 9.894000 + +! phi = -60 + 8.422900 8.529200 8.608500 9.306400 10.239400 + 11.025900 11.510800 9.283500 7.566000 6.624600 + 7.038700 8.222400 8.786400 8.512000 8.103500 + 7.988200 8.192900 8.291000 8.055600 7.436800 + 6.651800 6.317000 6.802500 7.746300 + +! phi = -45 + 6.913200 7.937400 8.610800 9.316600 9.388500 + 9.408400 8.828800 7.297900 5.456400 4.742700 + 5.793100 7.118800 7.565400 7.598500 7.438700 + 7.512500 7.878100 8.082200 7.642700 6.320500 + 4.680400 3.830500 4.215800 5.435200 + +! phi = -30 + 5.466700 7.116000 8.908800 8.347200 7.413500 + 7.047000 6.031600 4.193100 2.674800 3.023700 + 4.485300 5.451700 6.214900 6.422600 6.229300 + 6.191100 6.488900 6.646400 5.833400 3.751300 + 1.719800 1.064900 1.955800 3.860800 + +! phi = -15 + 3.061500 5.603800 12.179500 6.295200 5.323400 + 4.826500 3.705600 2.461500 2.291600 3.145900 + 3.562100 4.443600 5.337500 5.728800 5.694800 + 5.641600 5.943300 6.169000 4.759500 2.569400 + 1.357100 1.669800 3.212300 5.031900 + +! phi = 0 + 8.085900 8.051100 5.023600 3.450800 2.836100 + 2.192500 1.566200 1.456300 2.039300 1.945200 + 2.188400 2.921300 3.467500 3.543500 3.374500 + 3.472300 4.069900 3.615600 2.082200 0.958600 + 0.792600 1.494200 2.794900 4.853100 + +! phi = 15 + 6.639500 5.177400 3.252300 1.952700 1.078400 + 0.888300 1.505400 2.442300 2.178600 1.578600 + 1.777400 2.395400 2.820200 2.795200 2.662400 + 2.917100 2.562100 1.557900 1.322300 1.631400 + 2.051200 2.555600 3.039100 4.915000 + +! phi = 30 + 7.548800 5.095500 2.747000 0.955200 0.444500 + 1.318700 2.733300 3.223200 2.565500 2.150900 + 2.394400 2.939300 3.266000 3.210000 3.113400 + 2.491300 0.978300 0.815300 1.522700 2.055600 + 2.199900 2.327600 3.474200 7.977800 + +! phi = 45 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 60 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 75 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 90 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 105 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 120 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 135 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 150 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! phi = 165 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +! glycine map +! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map +C NH1 CT2 C NH1 CT2 C NH1 24 + +! phi = -180 + 0.235350 0.182300 0.177200 0.396800 0.859400 + 1.489700 2.092500 2.297700 1.808600 0.696200 + -0.563300 -1.432700 -1.015100 1.426300 -0.564300 + 0.696200 1.808200 2.301700 2.092600 1.489100 + 0.859500 0.396900 0.176900 0.182400 + +! phi = -165 + 0.020100 -0.203800 -0.269700 0.014200 0.620800 + 1.392400 2.046200 2.188200 1.683900 0.688500 + -0.373700 -0.703500 0.837800 3.704000 -0.730100 + 0.594100 1.713100 2.205800 2.026400 1.529800 + 1.027400 0.623800 0.348400 0.182800 + +! phi = -150 + -0.533600 -0.807400 -0.804600 -0.379800 0.365300 + 1.168000 1.641000 1.618100 1.302200 0.615100 + 0.065700 0.738500 2.959500 -2.036600 -0.934600 + 0.407900 1.517000 1.984800 1.833100 1.435200 + 0.995600 0.562200 0.150600 -0.209000 + +! phi = -135 + -1.208500 -1.429400 -1.319200 -0.817500 -0.112400 + 0.454400 0.737600 0.879300 0.850100 0.670300 + 0.943500 -2.651200 -2.829400 -2.199100 -1.065700 + 0.279600 1.322000 1.668300 1.521300 1.193900 + 0.765300 0.246000 -0.315500 -0.823200 + +! phi = -120 + -1.789100 -1.965500 -1.860700 -1.447900 -0.896500 + -0.401000 -0.015100 0.321300 0.634600 0.976300 + -1.977500 -2.883200 -2.848500 -2.137900 -0.960300 + 0.308700 1.098100 1.245300 1.133600 0.881800 + 0.448200 -0.153900 -0.823700 -1.404300 + +! phi = -105 + -2.246700 -2.487000 -2.473700 -2.135600 -1.577700 + -0.980600 -0.429100 0.144700 0.734000 -0.918300 + -2.299200 -2.882200 -2.668600 -1.847100 -0.719800 + 0.107000 0.496000 0.553500 0.584300 0.494000 + 0.098300 -0.529800 -1.237900 -1.840100 + +! phi = -90 + -2.851100 -3.181100 -3.199500 -2.785300 -2.054300 + -1.242900 -0.476500 0.288100 -0.045300 -1.470600 + -2.558800 -2.869400 -2.450300 -1.582200 -0.930800 + -0.426400 -0.022700 0.000000 -0.097400 -0.136100 + -0.439600 -1.038600 -1.741000 -2.373200 + +! phi = -75 + -3.961800 -4.268200 -4.109000 -3.364700 -2.252200 + -1.140400 -0.209800 0.487300 -0.746200 -2.127700 + -2.932100 -2.898500 -2.247900 -1.730400 -1.177200 + -0.448200 0.034900 -0.073300 -0.531600 -0.933300 + -1.360700 -2.009200 -2.745700 -3.424900 + +! phi = -60 + -5.408000 -5.355100 -4.640100 -3.283200 -1.710200 + -0.423800 0.354400 -0.103700 -1.577700 -2.828300 + -3.151200 -2.649200 -2.183000 -1.761200 -0.981700 + -0.174700 0.262600 0.039200 -0.663000 -1.530700 + -2.478200 -3.465600 -4.334200 -5.011200 + +! phi = -45 + -6.093200 -5.298400 -3.816620 -1.922530 -0.196160 + 0.768200 0.568500 -0.831300 -2.343900 -3.037100 + -2.663700 -2.191100 -2.022900 -1.438500 -0.649000 + 0.077000 0.441500 0.257500 -0.491100 -1.820600 + -3.473100 -4.895200 -5.790700 -6.205900 + +! phi = -30 + -5.258225 -3.675795 -1.631110 0.430085 1.496470 + 0.318200 -0.555100 -1.695500 -2.434200 -2.192600 + -1.691300 -1.890000 -1.708500 -1.206300 -0.567400 + 0.054300 0.497200 0.599600 -0.171000 -2.137600 + -4.237000 -5.584100 -6.135100 -6.067000 + +! phi = -15 + -3.161820 -0.902080 1.432450 -1.452885 -1.560780 + -1.665600 -1.783100 -1.755100 -1.329300 -0.731100 + -1.317000 -1.662800 -1.601200 -1.294900 -0.817300 + -0.197100 0.549500 0.850400 -0.689700 -2.819900 + -4.393000 -5.111500 -5.205690 -4.654785 + +! phi = 0 + 0.034035 -2.349860 -3.412065 -3.620070 -3.450950 + -2.875650 -1.787800 -0.541250 0.410450 -0.372500 + -1.126850 -1.498450 -1.608700 -1.498450 -1.126850 + -0.372500 0.410450 -0.541250 -1.787800 -2.875650 + -3.450950 -3.620070 -3.412065 -2.349860 + +! phi = 15 + -3.162345 -4.654785 -5.205690 -5.111500 -4.393000 + -2.819900 -0.689700 0.850400 0.549500 -0.197100 + -0.817300 -1.294900 -1.601200 -1.662800 -1.317000 + -0.731100 -1.329300 -1.755100 -1.783100 -1.665600 + -1.560780 -1.452885 1.432450 -0.902080 + +! phi = 30 + -5.258220 -6.067000 -6.135100 -5.584100 -4.237000 + -2.137600 -0.171000 0.599600 0.497200 0.054300 + -0.567400 -1.206300 -1.708500 -1.890000 -1.691300 + -2.192600 -2.434200 -1.695500 -0.555100 0.318200 + 1.496470 0.430085 -1.631110 -3.675795 + +! phi = 45 + -6.093300 -6.205900 -5.790700 -4.895200 -3.473100 + -1.820600 -0.491100 0.257500 0.441500 0.077000 + -0.649000 -1.438500 -2.022900 -2.191100 -2.663700 + -3.037100 -2.343900 -0.831300 0.568500 0.768200 + -0.196160 -1.922530 -3.816620 -5.298400 + +! phi = 60 + -5.407500 -5.011200 -4.334200 -3.465600 -2.478200 + -1.530700 -0.663000 0.039200 0.262600 -0.174700 + -0.981700 -1.761200 -2.183000 -2.649200 -3.151200 + -2.828300 -1.577700 -0.103700 0.354400 -0.423800 + -1.710200 -3.283200 -4.640100 -5.355100 + +! phi = 75 + -3.961900 -3.424900 -2.745700 -2.009200 -1.360700 + -0.933300 -0.531600 -0.073300 0.034900 -0.448200 + -1.177200 -1.730400 -2.247900 -2.898500 -2.932100 + -2.127700 -0.746200 0.487300 -0.209800 -1.140400 + -2.252200 -3.364700 -4.109000 -4.268200 + +! phi = 90 + -2.854500 -2.373200 -1.741000 -1.038600 -0.439600 + -0.136100 -0.097400 0.000000 -0.022700 -0.426400 + -0.930800 -1.582200 -2.450300 -2.869400 -2.558800 + -1.470600 -0.045300 0.288100 -0.476500 -1.242900 + -2.054300 -2.785300 -3.199500 -3.181100 + +! phi = 105 + -2.246400 -1.840100 -1.237900 -0.529800 0.098300 + 0.494000 0.584300 0.553500 0.496000 0.107000 + -0.719800 -1.847100 -2.668600 -2.882200 -2.299200 + -0.918300 0.734000 0.144700 -0.429100 -0.980600 + -1.577700 -2.135600 -2.473700 -2.487000 + +! phi = 120 + -1.788800 -1.404300 -0.823700 -0.153900 0.448200 + 0.881800 1.133600 1.245300 1.098100 0.308700 + -0.960300 -2.137900 -2.848500 -2.883200 -1.977500 + 0.976300 0.634600 0.321300 -0.015100 -0.401000 + -0.896500 -1.447900 -1.860700 -1.965500 + +! phi = 135 + -1.208900 -0.823200 -0.315500 0.246000 0.765300 + 1.193900 1.521300 1.668300 1.322000 0.279600 + -1.065700 -2.199100 -2.829400 -2.651200 0.943500 + 0.670300 0.850100 0.879300 0.737600 0.454400 + -0.112400 -0.817500 -1.319200 -1.429400 + +! phi = 150 + -0.533400 -0.209000 0.150600 0.562200 0.995600 + 1.435200 1.833100 1.984800 1.517000 0.407900 + -0.934600 -2.036600 2.959500 0.738500 0.065700 + 0.615100 1.302200 1.618100 1.641000 1.168000 + 0.365300 -0.379800 -0.804600 -0.807400 + +! phi = 165 + 0.019900 0.182800 0.348400 0.623800 1.027400 + 1.529800 2.026400 2.205800 1.713100 0.594100 + -0.730100 3.704000 0.837800 -0.703500 -0.373700 + 0.688500 1.683900 2.188200 2.046200 1.392400 + 0.620800 0.014200 -0.269700 -0.203800 + +! glycine before proline map: use glycine map +! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map +C NH1 CT2 C NH1 CT2 C N 24 + +! phi = -180 + 0.235350 0.182300 0.177200 0.396800 0.859400 + 1.489700 2.092500 2.297700 1.808600 0.696200 + -0.563300 -1.432700 -1.015100 1.426300 -0.564300 + 0.696200 1.808200 2.301700 2.092600 1.489100 + 0.859500 0.396900 0.176900 0.182400 + +! phi = -165 + 0.020100 -0.203800 -0.269700 0.014200 0.620800 + 1.392400 2.046200 2.188200 1.683900 0.688500 + -0.373700 -0.703500 0.837800 3.704000 -0.730100 + 0.594100 1.713100 2.205800 2.026400 1.529800 + 1.027400 0.623800 0.348400 0.182800 + +! phi = -150 + -0.533600 -0.807400 -0.804600 -0.379800 0.365300 + 1.168000 1.641000 1.618100 1.302200 0.615100 + 0.065700 0.738500 2.959500 -2.036600 -0.934600 + 0.407900 1.517000 1.984800 1.833100 1.435200 + 0.995600 0.562200 0.150600 -0.209000 + +! phi = -135 + -1.208500 -1.429400 -1.319200 -0.817500 -0.112400 + 0.454400 0.737600 0.879300 0.850100 0.670300 + 0.943500 -2.651200 -2.829400 -2.199100 -1.065700 + 0.279600 1.322000 1.668300 1.521300 1.193900 + 0.765300 0.246000 -0.315500 -0.823200 + +! phi = -120 + -1.789100 -1.965500 -1.860700 -1.447900 -0.896500 + -0.401000 -0.015100 0.321300 0.634600 0.976300 + -1.977500 -2.883200 -2.848500 -2.137900 -0.960300 + 0.308700 1.098100 1.245300 1.133600 0.881800 + 0.448200 -0.153900 -0.823700 -1.404300 + +! phi = -105 + -2.246700 -2.487000 -2.473700 -2.135600 -1.577700 + -0.980600 -0.429100 0.144700 0.734000 -0.918300 + -2.299200 -2.882200 -2.668600 -1.847100 -0.719800 + 0.107000 0.496000 0.553500 0.584300 0.494000 + 0.098300 -0.529800 -1.237900 -1.840100 + +! phi = -90 + -2.851100 -3.181100 -3.199500 -2.785300 -2.054300 + -1.242900 -0.476500 0.288100 -0.045300 -1.470600 + -2.558800 -2.869400 -2.450300 -1.582200 -0.930800 + -0.426400 -0.022700 0.000000 -0.097400 -0.136100 + -0.439600 -1.038600 -1.741000 -2.373200 + +! phi = -75 + -3.961800 -4.268200 -4.109000 -3.364700 -2.252200 + -1.140400 -0.209800 0.487300 -0.746200 -2.127700 + -2.932100 -2.898500 -2.247900 -1.730400 -1.177200 + -0.448200 0.034900 -0.073300 -0.531600 -0.933300 + -1.360700 -2.009200 -2.745700 -3.424900 + +! phi = -60 + -5.408000 -5.355100 -4.640100 -3.283200 -1.710200 + -0.423800 0.354400 -0.103700 -1.577700 -2.828300 + -3.151200 -2.649200 -2.183000 -1.761200 -0.981700 + -0.174700 0.262600 0.039200 -0.663000 -1.530700 + -2.478200 -3.465600 -4.334200 -5.011200 + +! phi = -45 + -6.093200 -5.298400 -3.816620 -1.922530 -0.196160 + 0.768200 0.568500 -0.831300 -2.343900 -3.037100 + -2.663700 -2.191100 -2.022900 -1.438500 -0.649000 + 0.077000 0.441500 0.257500 -0.491100 -1.820600 + -3.473100 -4.895200 -5.790700 -6.205900 + +! phi = -30 + -5.258225 -3.675795 -1.631110 0.430085 1.496470 + 0.318200 -0.555100 -1.695500 -2.434200 -2.192600 + -1.691300 -1.890000 -1.708500 -1.206300 -0.567400 + 0.054300 0.497200 0.599600 -0.171000 -2.137600 + -4.237000 -5.584100 -6.135100 -6.067000 + +! phi = -15 + -3.161820 -0.902080 1.432450 -1.452885 -1.560780 + -1.665600 -1.783100 -1.755100 -1.329300 -0.731100 + -1.317000 -1.662800 -1.601200 -1.294900 -0.817300 + -0.197100 0.549500 0.850400 -0.689700 -2.819900 + -4.393000 -5.111500 -5.205690 -4.654785 + +! phi = 0 + 0.034035 -2.349860 -3.412065 -3.620070 -3.450950 + -2.875650 -1.787800 -0.541250 0.410450 -0.372500 + -1.126850 -1.498450 -1.608700 -1.498450 -1.126850 + -0.372500 0.410450 -0.541250 -1.787800 -2.875650 + -3.450950 -3.620070 -3.412065 -2.349860 + +! phi = 15 + -3.162345 -4.654785 -5.205690 -5.111500 -4.393000 + -2.819900 -0.689700 0.850400 0.549500 -0.197100 + -0.817300 -1.294900 -1.601200 -1.662800 -1.317000 + -0.731100 -1.329300 -1.755100 -1.783100 -1.665600 + -1.560780 -1.452885 1.432450 -0.902080 + +! phi = 30 + -5.258220 -6.067000 -6.135100 -5.584100 -4.237000 + -2.137600 -0.171000 0.599600 0.497200 0.054300 + -0.567400 -1.206300 -1.708500 -1.890000 -1.691300 + -2.192600 -2.434200 -1.695500 -0.555100 0.318200 + 1.496470 0.430085 -1.631110 -3.675795 + +! phi = 45 + -6.093300 -6.205900 -5.790700 -4.895200 -3.473100 + -1.820600 -0.491100 0.257500 0.441500 0.077000 + -0.649000 -1.438500 -2.022900 -2.191100 -2.663700 + -3.037100 -2.343900 -0.831300 0.568500 0.768200 + -0.196160 -1.922530 -3.816620 -5.298400 + +! phi = 60 + -5.407500 -5.011200 -4.334200 -3.465600 -2.478200 + -1.530700 -0.663000 0.039200 0.262600 -0.174700 + -0.981700 -1.761200 -2.183000 -2.649200 -3.151200 + -2.828300 -1.577700 -0.103700 0.354400 -0.423800 + -1.710200 -3.283200 -4.640100 -5.355100 + +! phi = 75 + -3.961900 -3.424900 -2.745700 -2.009200 -1.360700 + -0.933300 -0.531600 -0.073300 0.034900 -0.448200 + -1.177200 -1.730400 -2.247900 -2.898500 -2.932100 + -2.127700 -0.746200 0.487300 -0.209800 -1.140400 + -2.252200 -3.364700 -4.109000 -4.268200 + +! phi = 90 + -2.854500 -2.373200 -1.741000 -1.038600 -0.439600 + -0.136100 -0.097400 0.000000 -0.022700 -0.426400 + -0.930800 -1.582200 -2.450300 -2.869400 -2.558800 + -1.470600 -0.045300 0.288100 -0.476500 -1.242900 + -2.054300 -2.785300 -3.199500 -3.181100 + +! phi = 105 + -2.246400 -1.840100 -1.237900 -0.529800 0.098300 + 0.494000 0.584300 0.553500 0.496000 0.107000 + -0.719800 -1.847100 -2.668600 -2.882200 -2.299200 + -0.918300 0.734000 0.144700 -0.429100 -0.980600 + -1.577700 -2.135600 -2.473700 -2.487000 + +! phi = 120 + -1.788800 -1.404300 -0.823700 -0.153900 0.448200 + 0.881800 1.133600 1.245300 1.098100 0.308700 + -0.960300 -2.137900 -2.848500 -2.883200 -1.977500 + 0.976300 0.634600 0.321300 -0.015100 -0.401000 + -0.896500 -1.447900 -1.860700 -1.965500 + +! phi = 135 + -1.208900 -0.823200 -0.315500 0.246000 0.765300 + 1.193900 1.521300 1.668300 1.322000 0.279600 + -1.065700 -2.199100 -2.829400 -2.651200 0.943500 + 0.670300 0.850100 0.879300 0.737600 0.454400 + -0.112400 -0.817500 -1.319200 -1.429400 + +! phi = 150 + -0.533400 -0.209000 0.150600 0.562200 0.995600 + 1.435200 1.833100 1.984800 1.517000 0.407900 + -0.934600 -2.036600 2.959500 0.738500 0.065700 + 0.615100 1.302200 1.618100 1.641000 1.168000 + 0.365300 -0.379800 -0.804600 -0.807400 + +! phi = 165 + 0.019900 0.182800 0.348400 0.623800 1.027400 + 1.529800 2.026400 2.205800 1.713100 0.594100 + -0.730100 3.704000 0.837800 -0.703500 -0.373700 + 0.688500 1.683900 2.188200 2.046200 1.392400 + 0.620800 0.014200 -0.269700 -0.203800 + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 2013 correction +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!carbons +C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO + ! NMA pure solvent, adm jr., 3/3/93 +CA 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! benzene (JES) +CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO + ! adm jr. 3/3/92, acetic acid heat of solvation +CD 0.000000 -0.070000 2.000000 ! ALLOW POL + ! adm jr. 3/19/92, acetate a.i. and dH of solvation +CE1 0.000000 -0.068000 2.090000 ! + ! for propene, yin/adm jr., 12/95 +CE2 0.000000 -0.064000 2.080000 ! + ! for ethene, yin/adm jr., 12/95 +CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CS 0.000000 -0.110000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +CPT 0.000000 -0.099000 1.860000 ! atm, indole vaporization 5/05 +CY 0.000000 -0.073000 1.990000 ! atm, indole vaporization 5/05 +CAI 0.000000 -0.073000 1.990000 ! atm, indole vaporization 5/05 + ! TRP, JWK 08/29/89 +!new alkanes atoms types for conversion to new LJ parameters for c27 +CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! +CT1 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane, 4/07, viv and adm jr. +CT2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CT2A 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! from CT2 (GLU, HSP), 05282010, zhu +CT3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +! hydrogens +H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 +HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HB1 0.000000 -0.022000 1.320000 ! + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HB2 0.000000 -0.028000 1.340000 ! + ! Yin and MacKerell, adm jr., 5/30/02 +HE1 0.000000 -0.031000 1.250000 ! + ! for propene, yin/adm jr., 12/95 +HE2 0.000000 -0.026000 1.260000 ! + ! for ethene, yin/adm jr., 12/95 +!HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HC 0.000000 -0.046000 0.224500 ! ALLOW POL + ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 +HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO + ! JES 8/25/89 values from Jorgensen fit to hydration energy +HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS 0.000000 -0.100000 0.450000 ! ALLOW SUL + ! methanethiol pure solvent, adm jr., 6/22/92 +!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str) +HA1 0.0 -0.045 1.3400 ! alkane, viv and adm jr., 4/07 +HA2 0.0 -0.034 1.3400 ! alkane, viv and adm jr., 4/07 +HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98 +!nitrogens +N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! JG 8/27/89; note: NH1 in ARG was changed to NC2. +NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +NH2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NH3 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NP 0.000000 -0.200000 1.850000 ! ALLOW PRO + ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 +NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NY 0.000000 -0.200000 1.850000 ! atm, indole vaporization 5/05 +! oxygens +O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid carbonyl O +OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) +OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 9/17/90, avoid O* wildcard +! sulfurs +S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION + ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent +SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION + ! adm jr., 3/3/92, dimethyldisulphide pure solvent +SS 0.000000 -0.470000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 + + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/par_hbond.inp b/charmm/toppar/par_hbond.inp new file mode 100644 index 00000000..627715da --- /dev/null +++ b/charmm/toppar/par_hbond.inp @@ -0,0 +1,88 @@ +* This parameter append file is for Hydrogen bond analysis ONLY. +* Use the command: READ PARAM APPEND CARD ... +* It WILL change your energy function (not for the better) +* by adding an HBOND energy term. Use at your own risk. +* NOTE: The charmm potential energy function is designed NOT +* to include an explicit hydrogen bond term. Therefore, use +* of the following hydrogen bond parameters will lead to incorrect +* results. +* + +HBOND AEXP 4 REXP 6 HAEX 2 AAEX 2 NOACCEPTORS HBNOEXCLUSIONS ALL - +CUTHB 6.0 CTOFHB 5.0 CTONHB 4.0 CUTHA 100.0 CTOFHA 90.0 CTONHA 90.0 +N N -5.000 3.0000 +N N% -5.000 3.0000 +N N%% -5.000 3.0000 +N N%%% -5.000 3.0000 +N% N -5.000 3.0000 +N% N% -5.000 3.0000 +N% N%% -5.000 3.0000 +N% N%%% -5.000 3.0000 +N%% N -5.000 3.0000 +N%% N% -5.000 3.0000 +N%% N%% -5.000 3.0000 +N%% N%%% -5.000 3.0000 +N%%% N -5.000 3.0000 +N%%% N% -5.000 3.0000 +N%%% N%% -5.000 3.0000 +N%%% N%%% -5.000 3.0000 +N O -4.900 2.9000 +N O% -4.900 2.9000 +N O%% -4.900 2.9000 +N O%%% -4.900 2.9000 +N% O -4.900 2.9000 +N% O% -4.900 2.9000 +N% O%% -4.900 2.9000 +N% O%%% -4.900 2.9000 +N%% O -4.900 2.9000 +N%% O% -4.900 2.9000 +N%% O%% -4.900 2.9000 +N%% O%%% -4.900 2.9000 +N%%% O -4.900 2.9000 +N%%% O% -4.900 2.9000 +N%%% O%% -4.900 2.9000 +N%%% O%%% -4.900 2.9000 +O N -4.850 2.8500 +O N% -4.850 2.8500 +O N%% -4.850 2.8500 +O N%%% -4.850 2.8500 +O% N -4.850 2.8500 +O% N% -4.850 2.8500 +O% N%% -4.850 2.8500 +O% N%%% -4.850 2.8500 +O%% N -4.850 2.8500 +O%% N% -4.850 2.8500 +O%% N%% -4.850 2.8500 +O%% N%%% -4.850 2.8500 +O%%% N -4.850 2.8500 +O%%% N% -4.850 2.8500 +O%%% N%% -4.850 2.8500 +O%%% N%%% -4.850 2.8500 +O O -4.750 2.7500 +O O% -4.750 2.7500 +O O%% -4.750 2.7500 +O O%%% -4.750 2.7500 +O% O -4.750 2.7500 +O% O% -4.750 2.7500 +O% O%% -4.750 2.7500 +O% O%%% -4.750 2.7500 +O%% O -4.750 2.7500 +O%% O% -4.750 2.7500 +O%% O%% -4.750 2.7500 +O%% O%%% -4.750 2.7500 +O%%% O -4.750 2.7500 +O%%% O% -4.750 2.7500 +O%%% O%% -4.750 2.7500 +O%%% O%%% -4.750 2.7500 +S N -3.500 3.0000 +S N% -3.500 3.0000 +S N%% -3.500 3.0000 +S N%%% -3.500 3.0000 +S O -3.500 2.9000 +S O% -3.500 2.9000 +S O%% -3.500 2.9000 +S O%%% -3.500 2.9000 + +END + + diff --git a/charmm/toppar/param19.inp b/charmm/toppar/param19.inp new file mode 100644 index 00000000..4de66f63 --- /dev/null +++ b/charmm/toppar/param19.inp @@ -0,0 +1,438 @@ +* - parameter file PARAM19 - +* PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) +* TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) +* JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 +* + +!* - PEPTIDE GEOMETRY TO GIVE RAMACHANDRAN ET AL BBA 359:298 (1974) +!* - PEPTIDE TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) +!* - NONBONDED TERMS JORGENSEN JACS 103:3976 W/ RC1-4 = 1.80 EC1-4 = 0.1 +!* The default h-bond exponents are now 6-repul 4-attr +!* ++++++++ ATOMTYPE OS (IN METHYL ESTER) ADDED FOR CHARMM COURSE /LN ++++ +!* SOLVENT PARAMETERS: SUPPORTING ST2 AND MODIFIED TIP3P MODEL +!* Switched from Slater-Kirkwood to simple mixing rules - AB +!* Hbond parameters based on comparisons of dimer results with +!* ab initio calculations. - WER 12/19/84 +!* Grouping of atom types for VDW parameters - BRB 1/3/85 +!* + +!references +!Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D. +!Thesis, Department of Chemistry, Harvard University, Cambridge, MA, +!USA, 1985 +! +!and +! +!Neria, E., Fischer, S., and Karplus, M. Simulation of Activation Free +!Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105: +!1902-21. + +BOND +C C 450.0 1.38! FROM B. R. GELIN THESIS AMIDE AND DIPEPTIDES +C CH1E 405.0 1.52! EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT +C CH2E 405.0 1.52! ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED +C CH3E 405.0 1.52 +C CR1E 450.0 1.38 +C CT 405.0 1.53 +C N 471.0 1.33 +C NC2 400.0 1.33! BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE +C NH1 471.0 1.33 +C NH2 471.0 1.33 +C NP 471.0 1.33 +C NR 471.0 1.33 +C O 580.0 1.23 +C OC 580.0 1.23! FORCE DECREASE AND LENGTH INCREASE FROM C O +C OH1 450.0 1.38! FROM PARMFIX9 (NO VALUE IN GELIN THESIS) +C OS 292.0 1.43! FROM DEP NORMAL MODE FIT +CH1E CH1E 225.0 1.53 +CH1E CH2E 225.0 1.52 +CH1E CH3E 225.0 1.52 +CH1E N 422.0 1.45 +CH1E NH1 422.0 1.45 +CH1E NH2 422.0 1.45 +CH1E NH3 422.0 1.45 +CH1E OH1 400.0 1.42! FROM PARMFIX9 (NO VALUE IN GELIN THESIS) +CH2E CH2E 225.0 1.52 +CH2E CH3E 225.0 1.54 +CH2E CR1E 250.0 1.45! FROM WARSHEL AND KARPLUS 1972 JACS 96:5612 +CH2E N 422.0 1.45 +CH2E NH1 422.0 1.45 +CH2E NH2 422.0 1.45 +CH2E NH3 422.0 1.45 +CH2E OH1 400.0 1.42 +CH2E S 450.0 1.81! FROM PARMFIX9 +CH2E SH1E 450.0 1.81 +CH3E NH1 422.0 1.49 +CH3E NR 422.0 1.49 ! FOR NETROPSIN +CH3E S 450.0 1.77! FROM PARMFIX9 +CH3E OS 292.0 1.38! FROM DEP NORMAL MODE FIT +CM OM 1115.0 1.128! FROM CAUGHEY ET AL(1978),CARBON MONOXIDE +CR1E CR1E 450.0 1.38 +CR1E NH1 450.0 1.305 +CR1E NR 450.0 1.305 +CT CT 200.0 1.53 +CT N 422.0 1.45 +CT NC2 422.0 1.45 +CT NH1 422.0 1.45 +CT NH2 422.0 1.45 +CT NH3 422.0 1.45 +CT OH1 400.0 1.42 +CT S 450.0 1.81 +FE CM 258.0 1.79! FROM KROEKER ET AL(JCP:72:4846) +FE NP 500.0 2.09 +FE NR 65.0 1.98! FROM NAGAI ET AL(1980) +FE OM 250.0 1.8! JUST A GUESS. +H NH1 405.0 0.98! GELIN AND IR STRETCH 3200 CM 1 +H NH2 405.0 0.98 +H OH1 450.0 0.96! FROM IR STRETCH 3400 CM 1 +H OH2 450.0 1.00 ! from ST2 geometry +LP OH2 450.0 0.80 ! ditto +H H 0.0 1.6329931 ! from ST2 geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HA C 350.0 1.08 +HA CT 300.0 1.08 +HC NC2 405.0 1.00 +HC NH1 405.0 0.98 +HC NH3 405.0 1.04 +OC S 400.0 1.43 +OM OM 600.0 1.23! STRETCHING CONSTANT JUST A GUESS. +S S 500.0 2.02 +THETAS +C C C 70.0 106.5! FROM B. R. GELIN THESIS WITH HARMONIC +C C CH2E 65.0 126.5! PART OF F TERMS INCORPORATED. ATOMS +C C CH3E 65.0 126.5! WITH EXTENDED H COMPENSATED FOR LACK +C C CR1E 70.0 122.5! OF H ANGLES. +C C CT 70.0 126.5 +C C HA 40.0 120.0! AMIDE PARAMETERS FIT BY LEAST SQUARES +C C NH1 65.0 109.0! TO N-METHYL ACETAMIDE VIBRATIONS. +C C NP 65.0 112.5! MINIMIZATION OF N-METHYL ACETAMIDE. +C C NR 65.0 112.5 +C C OH1 65.0 119.0 +C C O 65.0 119.0 ! FOR NETROPSIN +CH1E C N 20.0 117.5 +CH1E C NH1 20.0 117.5 +CH1E C O 85.0 121.5 +CH1E C OC 85.0 117.5 +CH1E C OH1 85.0 120.0 +CH2E C CR1E 70.0 121.5 +CH2E C N 20.0 117.5 +CH2E C NH1 20.0 117.5 +CH2E C NH2 20.0 117.5 +CH2E C NC2 20.0 117.5 ! FOR NETROPSIN +CH2E C NR 60.0 116.0 +CH2E C O 85.0 121.6 +CH2E C OC 85.0 118.5 +CH2E C OH1 85.0 120.0 +CH3E C N 20.0 117.5 +CH3E C NH1 20.0 117.5 +CH3E C O 85.0 121.5 +CR1E C CR1E 65.0 120.5 +CR1E C NH1 65.0 110.5! USED ONLY IN HIS, NOT IT TRP +CR1E C NP 65.0 122.5 +CR1E C NR 65.0 122.5 +CR1E C OH1 65.0 119.0 +CT C N 20.0 117.5 +CT C NH1 20.0 117.5 +CT C NH2 20.0 117.5 +CT C O 85.0 121.5 +CT C OC 85.0 118.5 +CT C OH1 85.0 120.0 +HA C NH1 40.0 120.0 +HA C NH2 40.0 120.0 +HA C NR 40.0 120.0 +HA C O 85.0 121.5 +N C O 85.0 121.0 +NC2 C NC2 70.0 120.0 +NC2 C NH1 70.0 120.0 +NH1 C NR 70.0 120.0 +NH1 C O 65.0 121.0 +NH2 C O 65.0 121.0 +O C OH1 85.0 120.0 +OC C OC 85.0 122.5 +OS C CH1E 70.0 125.3! FROM PARDNA10 +OS C CH2E 70.0 125.3! - " - +OS C O 70.0 120.0! - " - +C CH1E CH1E 70.0 110.0 +C CH1E CH2E 70.0 109.5 +C CH1E CH3E 70.0 106.5 +C CH1E N 45.0 111.6 +C CH1E NH1 45.0 111.6 +C CH1E NH2 45.0 111.6 +C CH1E NH3 45.0 111.6 +CH1E CH1E CH2E 45.0 112.5 +CH1E CH1E CH3E 45.0 111.0 +CH1E CH1E NH1 50.0 110.0 +CH1E CH1E NH2 50.0 109.5 +CH1E CH1E NH3 50.0 107.5 +CH1E CH1E OH1 50.0 104.5 +CH2E CH1E CH3E 50.0 111.5 +CH2E CH1E N 65.0 104.0 +CH2E CH1E NH1 65.0 110.0 +CH2E CH1E NH2 65.0 110.0 +CH2E CH1E NH3 65.0 110.0 +CH3E CH1E CH3E 50.0 111.0 +CH3E CH1E NH1 65.0 108.5 +CH3E CH1E NH2 65.0 109.5 +CH3E CH1E NH3 65.0 109.5 +CH3E CH1E OH1 60.0 110.5 +C CH2E CH1E 70.0 112.5 +C CH2E CH2E 70.0 113.0 +C CH2E NH1 70.0 111.6 +C CH2E NH2 70.0 111.6 +C CH2E NH3 70.0 111.6 +CH1E CH2E CH1E 45.0 117.0 +CH1E CH2E CH2E 45.0 112.5 +CH1E CH2E CH3E 45.0 113.0 +CH1E CH2E OH1 45.0 111.0 +CH3E CH2E OH1 45.0 111.0 +CH1E CH2E S 50.0 112.5 +CH1E CH2E SH1E 50.0 112.5 +CH2E CH2E CH2E 45.0 110.0 +CH2E CH2E CH3E 45.0 111.0 +CH2E CH2E N 65.0 105.0 +CH2E CH2E NH1 65.0 111.0 +CH2E CH2E NH2 65.0 109.5 +CH2E CH2E NH3 65.0 110.5 +CH2E CH2E S 50.0 112.5 +C CR1E C 90.0 126.5 +C CR1E CH2E 90.0 122.0 +C CR1E CR1E 90.0 119.0 +C CR1E NH1 90.0 109.5 +C CR1E NR 90.0 106.5 +CR1E CR1E CR1E 90.0 120.5 +NH1 CR1E NH1 70.0 109.0 +NH1 CR1E NR 70.0 109.0 +C CT CT 70.0 109.5 +C CT HA 70.0 109.5 +C CT N 70.0 111.6 +C CT NH1 70.0 111.6 +C CT NH2 70.0 111.6 +C CT NH3 70.0 111.6 +CT CT CT 45.0 111.00 +CT CT HA 40.0 109.50 +CT CT N 65.0 105.00 +CT CT NC2 65.0 110.00 +CT CT NH1 65.0 110.00 +CT CT NH2 65.0 110.00 +CT CT NH3 65.0 110.00 +CT CT OH1 50.0 109.50 +CT CT S 50.0 112.50 +HA CT HA 40.0 109.5 +HA CT N 50.0 109.5 +HA CT NC2 50.0 109.5 +HA CT NH1 50.0 109.5 +HA CT NH3 50.0 109.5 +HA CT OH1 50.0 109.5 +HA CT S 40.0 109.5 +FE CM OM 5.0 90.0! FROM KROEKER ET AL(1980) +C N CH1E 80.0 120.0 +C N CH2E 80.0 120.0 +C N CT 80.0 120.0 +CH1E N CH2E 60.0 110.0 +CH1E N CH3E 60.0 110.0 +CH2E N CH3E 60.0 109.5 +CT N CT 60.0 110.0 +C NC2 CT 80.0 120.0 +C NC2 HC 35.0 120.0 +CT NC2 HC 35.0 120.0 +HC NC2 HC 40.0 120.0 +C NH1 C 60.0 102.5 ! UNUSED (AND PROBABLY WRONG) +C NH1 CH1E 77.5 120.0 +C NH1 CH2E 77.5 120.0 +C NH1 CH3E 77.5 120.0 +C NH1 CR1E 60.0 108.0 +C NH1 CT 80.0 120.0 +C NH1 H 30.0 120.0 +CH1E NH1 CH3E 60.0 120.0 +CH1E NH1 H 35.0 120.0 +CH2E NH1 CH3E 60.0 120.0 +CH2E NH1 H 35.0 120.0 +CH3E NH1 H 35.0 120.0 +CR1E NH1 CR1E 65.0 110.0 +CR1E NH1 H 35.0 120.0 +CT NH1 H 35.0 120.0 +C NH2 H 30.0 120.0 +CH1E NH2 CH2E 60.0 120.0 +CH1E NH2 H 35.0 120.0 +CH2E NH2 H 35.0 120.0 +CT NH2 H 35.0 120.0 +H NH2 H 40.0 125.0 +C NP C 70.0 102.5 +C NP FE 50.0 128.0! FORCE CONSTANT FROM PARMFIX9 +C NR C 70.0 102.5 +C NR CR1E 70.0 109.5 +CH3E NR CR1E 70.0 109.5 ! FOR NETROPSIN +CH3E NR C 70.0 109.5 ! FOR NETROPSIN +CR1E NR CR1E 65.0 110.0 +CR1E NR FE 30.0 124.8! FORCE CONSTANT FROM PARMFIX9 +CH1E NH3 HC 35.0 109.5 +CH1E NH3 CH2E 35.0 109.5 +CH2E NH3 HC 35.0 109.5 +CT NH3 HC 35.0 109.5 +HC NH3 HC 40.0 109.5 +C OH1 H 50.0 109.5 +CH1E OH1 H 35.0 109.5 +CH2E OH1 H 35.0 109.5 +CT OH1 H 35.0 109.5 +H OH2 H 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S +H OH2 LP 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S +LP OH2 LP 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S +FE OM OM 0.0 180.0! DUMMY PARAMETER FOR PATCH AND ANALYSIS. +C OS CH3E 46.5 120.5! FROM PARDNA10 +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY +CH2E S CH3E 50.0 99.5! FROM PARMFIX9, CHECK WITH IR +CH2E S S 50.0 104.2 +CT S CT 50.0 99.5! FORCE CONSTANTS FROM PARMFIX9 +CT S S 50.0 104.2 +OC S OC 85.0 109.5! FORCE CONSTANT JST A GUESS. +NP FE CM 5.0 90.0 +NP FE NP 50.0 90.0 +NP FE NR 5.0 115.0 +NP FE OM 5.0 90.0! JUST A GUESS FROM EXISTING FE CM DATA +!NR FE CM 5.0 180.0 +!NR FE OM 5.0 180.0! JUST A GUESS FROM EXISTING FE CM DATA +PHI +CH1E C N CH1E 10.0 2 180.0! PRO ISOM. BARRIER 20 KCAL/MOL. +CH2E C N CH1E 10.0 2 180.0 +CR1E C C CR1E 5.0 2 180.0! => TRP OOP. VIB 170CM 1 +CR1E C C C 2.5 2 180.0! SEE BEHLEN ET AL JCP 75:5685 81 +CR1E C C NH1 2.5 2 180.0 +X C CH1E X 0.0 3 0.0! FROM GELIN THESIS AMIDES +X C CH2E X 0.0 3 0.0! USING A SINGLE +X C CR1E X 10.0 2 180.0! DIHEDRAL PER BOND RATHER +X C CT X 0.0 3 0.0! THAN MULTIPLE TORSIONS. +X C N X 8.2 2 180.0! ALKANE TORSION REDUCED TO +X C NC2 X 8.2 2 180.0! 1.6 FROM 1.8 TO COINCIDE WITH +X C NH1 X 8.2 2 180.0! THE EXPERIMENTAL BARRIER. +X C NH2 X 8.2 2 180.0 +X C OH1 X 1.8 2 180.0 +X C OS X 1.8 2 180.0 ! INFERRED FROM C-OH1 +X CH1E CH1E X 1.6 3 0.0 +X CH1E CH2E X 1.6 3 0.0 +X CH1E N X 0.3 3 0.0! FROM HAGLER ET AL TABULATION OF +X CH1E NH1 X 0.3 3 0.0! EXP. DATA AND 6 31G CALC. +X CH1E NH2 X 1.8 3 0.0! PROTONATED SECONDARY AMINE +X CH1E NH3 X 0.6 3 0.0! 1/PROTON SO 3 FOR THE BOND +X CH1E OH1 X 0.5 3 0.0! CHANGED TO ROUGHLY MEOH +X CH2E CH2E X 1.6 3 0.0 +X CH2E N X 0.3 3 0.0! SEE CH1E COMMENTS +X CH2E NH1 X 0.3 3 0.0 +X CH2E NH2 X 0.6 3 0.0 +X CH2E NH3 X 0.6 3 0.0 +X CH2E OH1 X 0.5 3 0.0 +X CH2E S X 1.2 2 0.0 +X CT CT X 1.6 3 0.0 +X CT N X 0.3 3 0.0! SEE CH1E COMMENTS +X CT NC2 X 0.3 3 0.0 +X CT NH1 X 0.3 3 0.0 +X CT NH2 X 0.6 3 0.0 +X CT NH3 X 0.6 3 0.0 +X CT OH1 X 0.5 3 0.0 +X CT S X 1.2 2 0.0 +X FE NR X 0.05 4 0.0 +X FE CM X 0.05 4 0.0 +X FE OM X 0.00 4 0.0 +X S S X 4.0 2 0.0! FROM EXP. NMR BARRIER +IMPHI +C C CR1E CH2E 90.0 0 0.0! GIVE 220 CM 1 METHYL OOP FOR TOLUENE. +C CR1E C CH2E 90.0 0 0.0! USED HERE FOR TRP CG OUT OF PLANE +C CR1E CR1E CH2E 90.0 0 0.0! PHE, AND TYR CG OOP +C CR1E NH1 CH2E 90.0 0 0.0! HIS CG RING OOP +C NH1 CR1E CH2E 90.0 0 0.0! +C CR1E CR1E OH1 150.0 0 0.0! GIVE 249 CM 1 PHENOL OH OOP. +C H H NH2 45.0 0 0.0! PRIMARY AMIDES (ASN AND GLN) OOP +C OC OC CH1E 100.0 0 0.0! CARBOXYL OUT OF PLANE. +C OC OC CH2E 100.0 0 0.0! +C X X C 25.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS +C X X CH2E 90.0 0 0.0! FROM TOLUENE METHYL OOP. 217 CM 1 +C X X CH3E 90.0 0 0.0 +C X X CR1E 25.0 0 0.0 +C X X H 75.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS +C X X HA 75.0 0 0.0! +C X X NH1 100.0 0 0.0! AMIDES FIT TO N METHYL ACETAMIDE. +C X X O 100.0 0 0.0 +C X X OC 100.0 0 0.0 +C X X OH1 150.0 0 0.0! USED FOR TYR HYDROXYL OOP +CH1E X X CH1E 55.0 0 35.26439! CALCULATED TO BE THE SAME AS THE 3 +CH1E X X CH2E 55.0 0 35.26439! H CH1E X ANGLES WITH K=40 +CH1E X X CH3E 55.0 0 35.26439 +CR1E X X CR1E 25.0 0 0.0! EXTENDED ATOM VERSION OF BENZENE +CR1E X X NH1 25.0 0 0.0! SAME AS ABOVE FOR LACK OF VALUES +FE X X NP 20.0 0 0.0! FROM PARMFIX9 +H X X O 45.0 0 0.0 +N CH1E CH2E C 45.0 0 0.0! PROLINE NITROGENS +N X X CH2E 45.0 0 0.0 +N X X CT 45.0 0 0.0 +NC2 X X CT 45.0 0 0.0 +NC2 X X HC 45.0 0 0.0 +NH1 X X CH1E 45.0 0 0.0 +NH1 X X CH2E 45.0 0 0.0 +NH1 X X CH3E 45.0 0 0.0 +NH1 X X CT 45.0 0 0.0 +NH1 X X H 45.0 0 0.0! AMIDES PROTON OOP +NH1 X X NH1 25.0 0 0.0! +NH1 X X NR 25.0 0 0.0 +NH2 X X H 45.0 0 0.0 +NR X X C 25.0 0 0.0 +NR X X CR1E 25.0 0 0.0 +NR X X CT 25.0 0 0.0 +NR X X CH3E 25.0 0 0.0 ! FOR NETROPSIN +! +NONBONDED NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSHIFT - + CUTNB 8.0 CTOFNB 7.5 CTONNB 6.5 EPS 1.0 E14FAC 0.4 WMIN 1.5 +! +! Emin Rmin +! (kcal/mol) (A) +H 0.0440 -0.0498 0.8000 +HC 0.0440 -0.0498 0.6000 ! charged group. Reduced vdw radius +HA 0.1000 -0.0450 1.4680 +HT 0.0440 -0.0498 0.8000 !TIP3P water hydrogen, see NBFIX below +! +C 1.65 -0.1200 2.100 1.65 -0.1 1.9 ! carbonyl carbon +CH1E 1.35 -0.0486 2.365 1.35 -0.1 1.9 ! \ +CH2E 1.77 -0.1142 2.235 1.77 -0.1 1.9 ! extended carbons +CH3E 2.17 -0.1811 2.165 1.77 -0.1 1.9 ! / +CR1E 1.35 -0.1200 2.100 1.35 -0.1 1.9 ! ring carbons +C% 1.65 -0.0262 2.490 1.65 -0.1 1.9 ! includes CT and CM +! +N* 1.1000 -0.2384 1.6000 ! includes N,NC2,NH1,NH2,NH3,NP,and NR +! +O* 0.8400 -0.1591 1.6000 ! includes O, OH1, OM, and OS +OC 2.1400 -0.6469 1.6000 +OT 0.8400 -0.1591 1.6000 !TIP3P water oxygen, see NBFIX below +OH2 0.0000 -0.0758 1.7398 !ST2 water oxygen +! +LP 0.0000 -0.04598 0.2245 !ST2 lone pair +FE 0.0100 0.000 0.6500 +S* 0.3400 -0.0430 1.890 ! includes S and SH1E +! +!CM 0.000000 -0.0262 2.150 ! CO 3-point model. +!OM 0.000000 -0.1591 1.750 ! CO 3-point model. + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +! +! We're gonna NBFIX the TIP3P water-water interactions +! here to make them more like Jorgensen's. The vdW parameters +! specified above will be in effect, therefore, for ONLY +! protein (read, protein OR nucleic acid)-water interactions. +! OT-OT is exactly Jorgensen's; HT interactions are added +! here. +! +OT OT -0.152073 3.5365 ! TIPS3P VDW INTERACTION +HT HT -0.04598 0.4490 +HT OT -0.08363 1.9927 +! +! All protein-protein NBFIXes removed + +! +HBOND AEXP 4 REXP 6 HAEX 0 AAEX 0 NOACCEPTORS HBNOEXCLUSIONS ALL - + CUTHB 0.5 CTOFHB 5.0 CTONHB 4.0 CUTHA 90.0 CTOFHA 90.0 CTONHA 90.0 +! +N*+* N% -0.0 3.0 ! dummy parameters +N*+* O* -0.00 2.9 ! +OH* N% -0.00 2.85 +OH* O* -0.00 2.75 +END diff --git a/charmm/toppar/rush/par_rush_058.inp b/charmm/toppar/rush/par_rush_058.inp new file mode 100755 index 00000000..4a286041 --- /dev/null +++ b/charmm/toppar/rush/par_rush_058.inp @@ -0,0 +1,2219 @@ +* RUSH all-hydrogen parameter file for proteins, based largely on +* the: +* CHARMM22 All-Hydrogen Parameter File for Proteins +* due to MacKerell et al. +* + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +C C 600.000 1.3350 ! ALLOW ARO HEM + ! Heme vinyl substituent (KK, from propene (JCS)) +CA CA 305.000 1.3750 ! ALLOW ARO + ! benzene, JES 8/25/89 +CE1 CE1 440.000 1.3400 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CE2 500.000 1.3420 ! + ! for propene, yin/adm jr., 12/95 +CE1 CT2 365.000 1.5020 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CT3 383.000 1.5040 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE2 510.000 1.3300 ! + ! for ethene, yin/adm jr., 12/95 +CP1 C 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CC 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CD 200.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 222.500 1.5270 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPB C 450.000 1.3800 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPA 299.800 1.4432 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB CPB 340.700 1.3464 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH1 CPH1 410.000 1.3600 ! ALLOW ARO + ! histidine, adm jr., 6/27/90 +CPM CPA 360.000 1.3716 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT CA 305.000 1.3680 ! ALLOW ARO + ! adm jr., 12/30/91, for jwk +CPT CPT 360.000 1.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT1 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT1 222.500 1.5000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT2 CA 230.000 1.4900 ! ALLOW ALI ARO + ! phe,tyr, JES 8/25/89 +CT2 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT2 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT3 CA 230.000 1.4900 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +CT3 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT3 CS 190.000 1.5310 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CT3 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 222.500 1.5280 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT3 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CY CA 350.000 1.3650 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CY CPT 350.000 1.4400 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 230.000 1.5100 ! ALLOW ARO + !JWK Kb from alkane freq.. b0 from TRP crystal +FE CM 258.000 1.9000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +FE CPM 0.000 3.3814 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +H CD 330.000 1.1100 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA C 330.000 1.1000 ! ALLOW ARO HEM + ! Heme vinyl substituent (KK, from propene (JCS)) +HA CA 340.000 1.0830 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA CC 317.130 1.1000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +HA CP2 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CPM 367.600 1.0900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT1 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 322.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CY 330.000 1.0800 ! ALLOW ARO + ! JWK 05/14/91 new r0 from indole +HE1 CE1 360.500 1.1000 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 365.000 1.1000 ! + ! for ethene, yin/adm jr., 12/95 +HB CP1 330.000 1.0800 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HP CA 340.000 1.0800 ! ALLOW ARO + ! phe,tyr JES 8/25/89 +HP CY 350.000 1.0800 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HR1 CPH1 375.000 1.0830 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 340.000 1.0900 ! ALLOW ARO + ! his, adm jr., 6/28/29 +HR2 CPH2 333.000 1.0700 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR3 CPH1 365.000 1.0830 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HT HT 0.000 1.5139 ! ALLOW WAT + ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) +N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 320.000 1.4340 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 320.000 1.4550 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO + ! 403.0->463.0, 1.305->1.365 guanidinium (KK) +NC2 CT2 261.000 1.4900 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 261.000 1.4900 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NC2 HC 455.000 1.0000 ! ALLOW POL + ! 405.0->455.0 GUANIDINIUM (KK) +NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO + ! (DS) +NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +NH2 CT2 240.000 1.4550 + ! from NH2 CT3, neutral glycine, adm jr. +NH2 CT3 240.000 1.4550 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH2 H 480.000 1.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 HC 460.000 1.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT3 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 HC 403.000 1.0400 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 320.000 1.4850 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 320.000 1.5020 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP HC 460.000 1.0060 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NPH CPA 377.200 1.3757 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE 270.200 1.9580 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH2 400.000 1.3600 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 H 466.000 1.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 400.000 1.3200 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 FE 65.000 2.2000 ! ALLOW HEM + ! Heme (6-liganded): His ligand (KK 05/13/91) +NR2 HM 466.000 1.2500 ! ALLOW ARO + ! og copied from his, ADM JR., 7/20/89 +NR3 CPH1 380.000 1.3700 ! ALLOW ARO + ! his, adm jr., 6/28/90 +NR3 CPH2 380.000 1.3200 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 H 453.000 1.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA 270.000 1.3700 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT 270.000 1.3750 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY H 465.000 0.9760 ! ALLOW ARO + ! indole JWK 08/28/89 +O C 620.000 1.2300 ! ALLOW PEP POL ARO + ! Peptide geometry, condensed phase (LK) +O CC 650.000 1.2300 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +OB CC 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid vibrations and geom. +OB CD 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 8/27/91, phenoxide +OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 7/23/91, acetic acid +OC CT2 450.000 1.3300 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 450.000 1.3300 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA 334.300 1.4110 ! ALLOW ARO ALC + ! MeOH, EMB 10/10/89, +OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC + ! adm jr. 5/02/91, acetic acid pure solvent +OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 H 545.000 0.9600 ! ALLOW ALC ARO + ! EMB 11/21/89 methanol vib fit +OH1 HM 545.000 1.2500 ! ALLOW ALC ARO + ! og copied from OH1 H methanol vib fit +OM CM 1115.000 1.1280 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +OM FE 250.000 1.8000 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OM OM 600.000 1.2300 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OS CD 150.000 1.3340 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +OS CT3 340.000 1.4300 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OT HT 450.000 0.9572 ! ALLOW WAT + ! FROM TIPS3P GEOM +OT HM 545.000 1.2500 ! ALLOW ALC ARO + ! og copied from OH1 H methanol vib fit +S CT2 198.000 1.8180 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S CT3 240.000 1.8160 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S HS 275.000 1.3250 ! ALLOW SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +SM CT2 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM CT3 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM SM 173.000 2.0290 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SS CS 205.000 1.8360 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO + ! JES 8/25/89 +CE1 CE1 CT3 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CT2 CT3 32.00 112.20 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT2 48.00 126.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT3 47.00 125.20 ! + ! for propene, yin/adm jr., 12/95 +CP1 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 C 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 100.000 114.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 100.000 111.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPA CPB C 70.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPA CPM CPA 94.200 125.1200 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPA NPH CPA 139.300 103.9000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB C C 70.000 121.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB C 70.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB CPA 30.800 106.5100 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR2 HM 130.000 52.0000 ! ALLOW ARO + ! og copied from: his, adm jr., 6/27/90 +CPH1 NR2 HM 130.000 52.0000 ! ALLOW ARO + ! og copied from: his, adm jr., 6/27/90 +CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPM CPA CPB 61.600 124.0700 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT CA CA 60.000 118.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CPT CA 60.000 122.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT NY CA 110.000 108.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! from CT2 CT1 C, for lactams, adm jr. +CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CY CA 45.800 129.4000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 CY CPT 45.800 124.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! 107.5->120.0 to make planar Arg (KK) +CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/09/92, for ALA cter +CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! methylguanidinium, adm jr., 3/26/92 +CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 CT1 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +CY CT2 CT3 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +FE NPH CPA 96.150 128.0500 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO + ! his, adm jr. 8/13/90 acetamide geometry and vibrations +H NH2 H 23.000 120.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NY CA 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO + ! JES 8/25/89 phenol +HM OH1 CA 65.000 55.0000 ! ALLOW ALC ARO + ! og copied from: JES 8/25/89 phenol +HM OH1 H 65.000 53.0000 ! ALLOW ALC ARO + ! og copied from: JES 8/25/89 phenol +H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +HM OH1 CT2 57.500 53.0000 ! ALLOW ALC ARO ALI + ! og methanol vib fit EMB 11/21/89 +HM OH1 CT1 57.500 53.0000 ! ALLOW ALC ARO ALI + ! og methanol vib fit EMB 11/21/89 +H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +HA C C 50.000 120.5000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK from propene (JCS)) +HA C CPB 50.000 120.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK from propene (JCS)) +HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA CA CPT 41.000 122.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CPM CPA 12.700 117.4400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CPM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd + ! based on HA CT2 HA +HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT2 CE1 45.00 111.50 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HA CT2 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 CY 33.430 109.5000 ! ALLOW ARO + ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA +HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT3 CE1 42.00 111.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HA CT3 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HE1 CE1 CE1 52.00 119.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HE1 CE1 CE2 42.00 118.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 40.00 116.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HE1 CE1 CT3 22.00 117.00 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE1 45.00 120.50 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE2 55.50 120.50 ! + ! for ethene, yin/adm jr., 12/95 +HE2 CE2 HE2 19.00 119.00 ! + ! for propene, yin/adm jr., 12/95 +HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB CT1 CT1 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CT2 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CT3 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB CT2 HB 36.000 115.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO + ! 35.3->49.0 GUANIDINIUM (KK) +HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI + ! 107.5->120.0 to make planar Arg (KK) +HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI + ! methylguanidinium, adm jr., 3/26/92 +HC NC2 HC 25.000 120.0000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH2 CT2 50.000 111.0000 ! ALLOW POL + ! from HC NH2 CT3, neutral glycine, adm jr. +HC NH2 CT3 50.000 111.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +HC NH2 HC 39.000 106.5000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 HC 44.000 109.5000 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP HC 51.000 107.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HT OT HT 55.000 104.5200 ! ALLOW WAT + ! TIP3P GEOMETRY, ADM JR. +HT OT HM 27.500 52.2600 ! ALLOW WAT + ! og copied from: TIP3P GEOMETRY, ADM JR. +N C CP1 20.000 112.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 C 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CC 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CP2 70.000 110.8000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 CP2 70.000 110.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO + ! changed from 60.0/120.3 for guanidinium (KK) +NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/20/92, for asn,asp,gln,glu and cters +NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT1 CT2, for lactams, adm jr. +NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT3 HA, for lactams, adm jr. +NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! NMA crystal (JCS) +NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +NH2 CT2 HB 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral glycine, adm jr. +NH2 CT2 CD 52.000 108.0000 + !from CT2 CT2 CD, neutral glycine, adm jr. +NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP + ! new aliphatics, adm jr., 2/3/92 +NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! alanine (JCS) +NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + ! alanine (JCS) +NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP + ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) +NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 C 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NPH CPA CPB 122.000 111.5400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM 88.000 124.3900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE CM 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NPH FE CPM 0.000 45.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +NPH FE NPH 14.390 90.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 FE CM 50.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR2 FE NPH 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +O C CP1 80.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C H 50.000 121.7000 ! ALLOW PEP POL ARO + ! acetaldehyde (JCS) +O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC HA 44.000 122.0000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO + ! adm jr. 4/10/91, acetamide update +OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA CA 40.000 120.0000 ! ALLOW POL ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CT2 CT3 65.000 122.0000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT2 HA 65.000 118.3000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 HA 65.000 118.3000 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC + ! PARALLH19 WITH [122.3] (JES) +OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OM CM FE 35.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM FE NPH 5.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM OM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 55.000 118.0000 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 +CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c +CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c +CE1 CE1 CT3 HA 0.0300 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 CT3 0.5000 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 HA 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT3 HA 0.0500 3 180.00 ! + ! for propene, yin/adm jr., 12/95 +CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 +CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 +CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! from CT2 CT1 NH1 C, for lactams, adm jr. +CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK +CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + !JWK +CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +CT3 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION + ! DTN 8/24/90 +CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from H NH1 CT2 CT3, for lactams, adm jr. +H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/20/89 +HM NR2 CPH2 NR1 0.0010 2 0.00 ! ALLOW ARO + ! og copied from: his, adm jr., 7/20/89 +HM NR2 CPH1 CPH1 0.0010 2 0.00 ! ALLOW ARO + ! og copied from: his, adm jr., 7/20/89 +HM NR2 CPH1 HR3 0.0010 2 180.00 ! ALLOW ARO + ! og copied from: his, adm jr., 7/20/89 +HM NR2 CPH1 CT2 0.0010 2 180.00 ! ALLOW ARO + ! og copied from: his, adm jr., 7/20/89 +HM NR2 CPH2 HR1 0.0010 2 180.00 ! ALLOW ARO + ! og copied from: his, adm jr., 7/20/89 +H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NY CA CY 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC + ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +HM OH1 CA CA 0.0000 2 180.00 ! ALLOW ARO ALC + ! og copied from: phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT1 CT1 0.0000 1 0.00 ! ALLOW ALC + ! og copied from: 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT1 CT1 0.0000 2 0.00 ! ALLOW ALC + ! og copied from: 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT1 CT1 0.0000 3 0.00 ! ALLOW ALC + ! og copied from: 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT1 CT3 0.0000 1 0.00 ! ALLOW ALC + ! og copied from: 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT1 CT3 0.0000 2 0.00 ! ALLOW ALC + ! og copied from: 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT1 CT3 0.0000 3 0.00 ! ALLOW ALC + ! og copied from: 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT2 CT1 0.0000 1 0.00 ! ALLOW ALC + ! og copied from: ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT2 CT1 0.0000 2 0.00 ! ALLOW ALC + ! og copied from: ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HM OH1 CT2 CT1 0.0000 3 0.00 ! ALLOW ALC + ! og copied from: ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO + ! adm jr., 10/02/89 +HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO + ! ADM JR., 10/02/89 +HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! TRP (JES) +HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK +HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK +HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA NY H 1.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL + ! adm jr. 4/10/91, acetamide update +HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HE1 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 HA 0.8700 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT2 CT3 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT3 HA 0.3400 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE2 CE2 CE1 CT2 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NH2 CT2 HB 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CD 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA NY H 0.4000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, his +HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, YES, 0.0 +HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from NH1 C CT1 CT2, for lactams, adm jr. +NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO + ! adm jr. 3/24/92, for PRES GLYP +NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO + ! JWK +NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP + ! from O C CT1 CT2, for lactams, adm jr. +O C CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT3 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 H 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +X C C X 4.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO + ! 9.0->2.25 GUANIDINIUM (KK) +X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier +X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CE1 CE1 X 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +X CE2 CE2 X 4.9000 2 180.00 ! + ! for ethene, yin/adm jr., 12/95 +X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP + ! changed to 0.0 RLD 5/19/92 +X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB C X 3.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI + ! rotation barrier in Ethane (SF) +X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL + ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 +X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X FE CM X 0.0500 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X FE NPH X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +X FE OM X 0.0000 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB X X C 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK, from propene (JCS)) +HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO + ! Heme (6-liganded): substituents (KK 05/13/91) +HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK, from propene (JCS)) +HE2 HE2 CE2 CE2 3.0 0 0.00 ! + ! for ethene, yin/adm jr., 12/95 +HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO + ! 5.75->40.0 GUANIDINIUM (KK) +NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +NH2 X X H 4.0000 0 0.0000 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO + !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf. +O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! adm jr., 5/13/91, formamide geometry and vibrations +O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL + ! adm jr., 10/17/90, acetic acid vibrations +OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) + +NONBONDED cutnb 6.0 ctofnb 5.0 ctonnb 4.9 wmin 0.75 + !og RUSH-appropriate cutoff scheme + !og accomodates CT1 : CT1 repulsion, rmin = 4.55 + +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO + ! NMA pure solvent, adm jr., 3/3/93 +CA 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! benzene (JES) +CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO + ! adm jr. 3/3/92, acetic acid heat of solvation +CD 0.000000 -0.070000 2.000000 ! ALLOW POL + ! adm jr. 3/19/92, acetate a.i. and dH of solvation +CE1 0.000000 -0.068000 2.090000 ! + ! for propene, yin/adm jr., 12/95 +CE2 0.000000 -0.064000 2.080000 ! + ! for ethene, yin/adm jr., 12/95 +CM 0.000000 -0.110000 2.100000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand carbon (KK 05/13/91) +CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO + ! benzene (JES) +CS 0.000000 -0.110000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! isobutane pure solvent properties, adm jr, 2/3/92 +CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! propane pure solvent properties, adm jr, 2/3/92 +CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +CY 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! TRP, JWK 08/29/89 +! carbon wildcards, following atom order is essential for accurate results +!C* 0.000000 -0.070000 2.000000 +!CP% 0.000000 -0.090000 1.800000 +!C%1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 +!C%2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 +!C%3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 +!CPH+ 0.000000 -0.050000 1.800000 +!C 0.000000 -0.110000 2.000000 +!CA 0.000000 -0.070000 1.992400 +!CE1 0.000000 -0.068000 2.090000 +!CE2 0.000000 -0.064000 2.080000 +!CM 0.000000 -0.110000 2.100000 +!CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI +!CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 +!CS 0.000000 -0.110000 2.200000 +!CY 0.000000 -0.070000 1.992400 + +H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 +HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HE1 0.000000 -0.031000 1.250000 ! + ! for propene, yin/adm jr., 12/95 +HE2 0.000000 -0.026000 1.260000 ! + ! for ethene, yin/adm jr., 12/95 +HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HC 0.000000 -0.046000 0.224500 ! ALLOW POL + ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 +HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO + ! JES 8/25/89 values from Jorgensen fit to hydration energy +HM 0.000000 0.000000 0.000000 ! og +HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS 0.000000 -0.100000 0.450000 ! ALLOW SUL + ! methanethiol pure solvent, adm jr., 6/22/92 +HT 0.000000 -0.046000 0.224500 ! ALLOW WAT + !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete +! hydrogen wildcards +!H* 0.000000 -0.046000 0.224500 +!HA 0.000000 -0.022000 1.320000 +!HE1 0.000000 -0.031000 1.250000 +!HE2 0.000000 -0.026000 1.260000 +!HB 0.000000 -0.022000 1.320000 +!HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 +!HR1 0.000000 -0.046000 0.900000 +!HR2 0.000000 -0.046000 0.700000 +!HR3 0.000000 -0.007800 1.468000 +!HS 0.000000 -0.100000 0.450000 +! +N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! JG 8/27/89; note: NH1 in ARG was changed to NC2. +NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +NH2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NH3 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NP 0.000000 -0.200000 1.850000 ! ALLOW PRO + ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 +NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NY 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! trp, JWK +! nitrogen wildcards +!N* 0.000000 -0.200000 1.850000 +!N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 +!NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 +! +O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid carbonyl O +OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) +OM 0.000000 -0.120000 1.700000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91) +OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 9/17/90, avoid O* wildcard +OT 0.000000 -0.152100 1.768200 ! ALLOW WAT + !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete +! oxygen wildcards +!O* 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 +!OC 0.000000 -0.120000 1.700000 +!OH1 0.000000 -0.152100 1.770000 +!OM 0.000000 -0.120000 1.700000 +!OS 0.000000 -0.152100 1.770000 +!OT 0.000000 -0.152100 1.768200 + +CAL 0.000000 -0.120000 1.710000 ! ALLOW ION + !Calcium (BP) +FE 0.010000 0.000000 0.650000 ! ALLOW HEM + ! Heme (6-liganded): Iron atom (KK 05/13/91) +S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION + ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent +SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION + ! adm jr., 3/3/92, dimethyldisulphide pure solvent +SS 0.000000 -0.470000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +ZN 0.000000 -0.250000 1.090000 ! ALLOW ION + ! RHS March 18, 1990 +DUM 0.000000 -0.000000 0.000000 ! + ! dummy atom +HE 0.000000 -0.021270 1.4800 ! + ! helium, experimental pot. energy surface, adm jr., 12/95 +NE 0.000000 -0.086000 1.5300 + ! neon, semiempirical pot. energy surface, adm jr., 12/95 + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/rush/par_rush_058_a.cmap b/charmm/toppar/rush/par_rush_058_a.cmap new file mode 100755 index 00000000..6f8162a3 --- /dev/null +++ b/charmm/toppar/rush/par_rush_058_a.cmap @@ -0,0 +1,925 @@ +CMAP ! Parameterized to Richardson's PDB phi/psi frequency data. + ! The data is taken from .kin files at: + ! http://kinemage.biochem.duke.edu/validation/model.html#rama + ! and the accompanying publication is: + ! Lovell et al. Proteins: Structure, Function, and Genetics. + ! 50:437-450 (2003). + ! For our parameterization: + ! a) All data regardless of B factor are used except cis proline + ! residue data which are _not_ used. Expect energy errors if your + ! system contains cis proline. + ! b) No distinction is made between pre-PRO residues and non-pre-PRO + ! residues. + ! + ! Olgun Guvench 1/9/05 + +! non-GLY non-PRO residues; based on alanine dipeptide +! based on corrections to adiabatic surface; +0.00 kcal/mol to alpha +! /cb/morisot2/guvench/devel/058/parameterization/ +! cmap/a/ala2/adiabatic_cmap/cmap + +C CT1 NH1 C NH1 C CT1 NH1 24 + + 4.71223 5.80272 6.14468 6.20720 6.11110 !-180 + 6.09600 6.06400 5.90570 4.87552 4.68820 + 2.86660 0.33360 0.00000 0.00000 1.00750 + 2.23350 2.90510 3.29278 3.79498 3.92012 + 4.89248 5.03222 4.41478 3.84450 + + 4.33615 5.42613 6.95132 7.51450 7.49070 !-165 + 6.80212 7.15880 6.27402 6.53120 5.55680 + 3.51380 1.37440 0.32682 1.27722 2.44432 + 3.34072 3.20594 3.09648 3.21548 3.49063 + 3.84704 3.66787 3.51457 3.50142 + + 4.59734 5.69017 6.86419 8.07298 8.18280 !-150 + 7.12029 7.01752 6.10424 5.72384 5.63568 + 2.38491 1.17549 0.87143 1.26747 2.42838 + 2.77711 2.56755 2.54270 2.69150 3.27580 + 3.60339 3.64417 3.59015 3.91239 + + 5.17971 6.47890 7.49091 7.98142 7.20194 !-135 + 7.58212 6.83006 5.74015 5.28158 3.99983 + 2.41317 1.36658 1.24942 1.69174 2.04328 + 2.22125 2.13371 2.01836 3.14859 3.14040 + 3.00402 3.14358 3.47688 4.01024 + + 5.63649 6.38843 6.88363 7.49701 7.23029 !-120 + 7.49479 6.39772 5.90145 4.88288 3.85821 + 2.56282 1.54414 1.33410 1.19133 1.31974 + 2.32558 3.20227 3.14374 3.19400 2.98531 + 2.76283 3.11259 3.86397 4.58254 + + 5.85752 6.75626 7.68926 8.03742 7.77069 !-105 + 7.31371 6.71321 5.99909 5.06023 3.84875 + 2.78159 1.95510 1.13551 0.98555 2.00039 + 3.18584 3.72230 3.72530 3.20612 2.82846 + 2.90561 3.49606 4.33593 5.03073 + + 5.55963 6.34192 8.23258 7.70092 7.68322 ! -90 + 7.22556 8.08080 5.92046 4.85237 3.59587 + 3.10683 2.40767 1.55588 1.53220 2.42967 + 2.37570 2.03194 1.93717 2.21020 2.34068 + 2.63110 3.59879 4.68433 5.16508 + + 5.21884 6.06543 7.39200 7.21370 7.25310 ! -75 + 7.38560 7.52380 6.17549 4.23622 2.21850 + 1.90400 1.44107 1.06052 1.49324 1.66141 + 1.04073 0.62714 2.04683 1.71744 2.40270 + 2.95288 3.45924 4.01681 4.42856 + + 5.28181 5.46240 4.73370 4.51420 4.55408 ! -60 + 5.24580 5.75678 5.25869 2.99426 0.58263 + 0.22688 -0.30336 -0.20063 -0.40361 0.00000 + -0.17662 1.93820 2.97588 2.58471 3.19766 + 2.38680 2.15459 2.79141 3.64129 + + 3.15500 1.77960 0.97480 1.26920 2.58320 ! -45 + 3.99890 4.93230 4.19986 1.88879 0.23464 + -0.49865 -0.58474 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 1.54908 2.36359 + 1.23626 1.20232 2.17157 3.88858 + + 0.00000 0.00000 0.00000 0.00000 0.77008 ! -30 + 2.26390 2.72158 2.11929 1.29794 0.47091 + -0.17662 -0.58558 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 1.48408 + 1.26901 3.07150 2.61648 1.60990 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! -15 + 1.47830 2.10590 1.84058 1.10140 -0.17662 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.12378 + 0.52440 0.04498 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.49070 ! 0 + 0.93370 0.62658 0.02320 -0.17662 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.17300 1.13950 ! 15 + 1.57390 1.26390 -0.17662 -0.17662 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 -0.17662 0.00000 0.00000 + + 0.00000 0.77720 2.07620 2.68760 2.76210 ! 30 + 2.22898 1.39920 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + -0.82481 -1.40349 -0.58558 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 1.71900 2.68280 2.41689 1.72103 2.16021 ! 45 + 2.76509 2.70610 0.85440 0.97240 0.00000 + 0.00000 0.00000 0.00000 -0.17662 -2.32280 + -2.78970 -1.88138 -0.52884 0.60922 0.04992 + 0.00000 0.00000 0.00000 0.29140 + + 2.65079 3.51296 3.48861 3.34508 2.96935 ! 60 + 2.95489 3.27170 1.13882 1.53369 -0.58558 + -0.82481 -0.82481 -1.53515 -2.42743 -2.52917 + -2.17922 -1.16155 0.00908 1.31788 0.17146 + 0.98510 1.44950 2.42210 3.33230 + + 3.42341 4.73650 4.60208 4.67170 4.40750 ! 75 + 3.98870 3.31080 3.47040 0.72323 -1.53938 + 0.22142 -0.70798 -1.51711 -1.85569 -1.45717 + -0.01176 0.25276 0.42649 1.16628 1.14212 + 1.87932 2.48142 2.59656 3.27199 + + 3.74240 3.81600 3.64398 3.71860 3.49450 ! 90 + 3.19130 2.80490 2.27930 1.75760 1.50510 + 1.22550 0.27602 -0.30141 -0.51951 0.24300 + 0.20040 0.02368 0.15778 0.64260 0.89548 + 1.68768 2.56758 3.13258 3.66290 + + 2.68560 2.69960 2.68760 2.61790 2.45640 ! 105 + 2.24350 2.03170 1.80750 1.43230 0.70340 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.52380 + 1.13560 1.64210 2.05980 2.31070 + + 1.50840 1.37790 1.23070 1.11010 0.93930 ! 120 + 0.93710 1.38980 1.55670 1.29330 0.69850 + 0.00000 -0.17662 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.71250 1.29880 1.67000 1.83640 + + 1.71870 1.48000 1.44400 1.50940 1.54720 ! 135 + 1.60420 1.65200 1.69730 1.50740 0.45362 + 0.18830 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.28770 + 1.05420 1.64180 1.97600 1.98940 + + 2.82330 2.60090 2.56140 2.65090 2.71650 ! 150 + 2.77750 2.88840 2.96640 2.77730 2.19960 + 0.76898 0.00000 0.00000 0.00000 0.00000 + 0.00000 -0.17662 0.00000 0.52070 1.34130 + 1.86798 2.36288 2.82720 2.90930 + + 4.39620 4.06518 4.21550 4.23380 4.26240 ! 165 + 4.30040 4.37760 4.40480 4.10340 3.27580 + 1.58028 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.99050 1.50760 2.20570 2.91080 + 3.48810 3.98220 4.22248 4.37448 + + +! pre-PRO non-GLY non-PRO residues; based on alanine dipeptide +! based on corrections to adiabatic surface; +0.00 kcal/mol to alpha +! /cb/morisot2/guvench/devel/058/parameterization/ +! cmap/a/ala2/adiabatic_cmap/cmap + +C CT1 NH1 C N C CT1 NH1 24 + + 4.71223 5.80272 6.14468 6.20720 6.11110 !-180 + 6.09600 6.06400 5.90570 4.87552 4.68820 + 2.86660 0.33360 0.00000 0.00000 1.00750 + 2.23350 2.90510 3.29278 3.79498 3.92012 + 4.89248 5.03222 4.41478 3.84450 + + 4.33615 5.42613 6.95132 7.51450 7.49070 !-165 + 6.80212 7.15880 6.27402 6.53120 5.55680 + 3.51380 1.37440 0.32682 1.27722 2.44432 + 3.34072 3.20594 3.09648 3.21548 3.49063 + 3.84704 3.66787 3.51457 3.50142 + + 4.59734 5.69017 6.86419 8.07298 8.18280 !-150 + 7.12029 7.01752 6.10424 5.72384 5.63568 + 2.38491 1.17549 0.87143 1.26747 2.42838 + 2.77711 2.56755 2.54270 2.69150 3.27580 + 3.60339 3.64417 3.59015 3.91239 + + 5.17971 6.47890 7.49091 7.98142 7.20194 !-135 + 7.58212 6.83006 5.74015 5.28158 3.99983 + 2.41317 1.36658 1.24942 1.69174 2.04328 + 2.22125 2.13371 2.01836 3.14859 3.14040 + 3.00402 3.14358 3.47688 4.01024 + + 5.63649 6.38843 6.88363 7.49701 7.23029 !-120 + 7.49479 6.39772 5.90145 4.88288 3.85821 + 2.56282 1.54414 1.33410 1.19133 1.31974 + 2.32558 3.20227 3.14374 3.19400 2.98531 + 2.76283 3.11259 3.86397 4.58254 + + 5.85752 6.75626 7.68926 8.03742 7.77069 !-105 + 7.31371 6.71321 5.99909 5.06023 3.84875 + 2.78159 1.95510 1.13551 0.98555 2.00039 + 3.18584 3.72230 3.72530 3.20612 2.82846 + 2.90561 3.49606 4.33593 5.03073 + + 5.55963 6.34192 8.23258 7.70092 7.68322 ! -90 + 7.22556 8.08080 5.92046 4.85237 3.59587 + 3.10683 2.40767 1.55588 1.53220 2.42967 + 2.37570 2.03194 1.93717 2.21020 2.34068 + 2.63110 3.59879 4.68433 5.16508 + + 5.21884 6.06543 7.39200 7.21370 7.25310 ! -75 + 7.38560 7.52380 6.17549 4.23622 2.21850 + 1.90400 1.44107 1.06052 1.49324 1.66141 + 1.04073 0.62714 2.04683 1.71744 2.40270 + 2.95288 3.45924 4.01681 4.42856 + + 5.28181 5.46240 4.73370 4.51420 4.55408 ! -60 + 5.24580 5.75678 5.25869 2.99426 0.58263 + 0.22688 -0.30336 -0.20063 -0.40361 0.00000 + -0.17662 1.93820 2.97588 2.58471 3.19766 + 2.38680 2.15459 2.79141 3.64129 + + 3.15500 1.77960 0.97480 1.26920 2.58320 ! -45 + 3.99890 4.93230 4.19986 1.88879 0.23464 + -0.49865 -0.58474 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 1.54908 2.36359 + 1.23626 1.20232 2.17157 3.88858 + + 0.00000 0.00000 0.00000 0.00000 0.77008 ! -30 + 2.26390 2.72158 2.11929 1.29794 0.47091 + -0.17662 -0.58558 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 1.48408 + 1.26901 3.07150 2.61648 1.60990 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! -15 + 1.47830 2.10590 1.84058 1.10140 -0.17662 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.12378 + 0.52440 0.04498 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.49070 ! 0 + 0.93370 0.62658 0.02320 -0.17662 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.17300 1.13950 ! 15 + 1.57390 1.26390 -0.17662 -0.17662 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 -0.17662 0.00000 0.00000 + + 0.00000 0.77720 2.07620 2.68760 2.76210 ! 30 + 2.22898 1.39920 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + -0.82481 -1.40349 -0.58558 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 1.71900 2.68280 2.41689 1.72103 2.16021 ! 45 + 2.76509 2.70610 0.85440 0.97240 0.00000 + 0.00000 0.00000 0.00000 -0.17662 -2.32280 + -2.78970 -1.88138 -0.52884 0.60922 0.04992 + 0.00000 0.00000 0.00000 0.29140 + + 2.65079 3.51296 3.48861 3.34508 2.96935 ! 60 + 2.95489 3.27170 1.13882 1.53369 -0.58558 + -0.82481 -0.82481 -1.53515 -2.42743 -2.52917 + -2.17922 -1.16155 0.00908 1.31788 0.17146 + 0.98510 1.44950 2.42210 3.33230 + + 3.42341 4.73650 4.60208 4.67170 4.40750 ! 75 + 3.98870 3.31080 3.47040 0.72323 -1.53938 + 0.22142 -0.70798 -1.51711 -1.85569 -1.45717 + -0.01176 0.25276 0.42649 1.16628 1.14212 + 1.87932 2.48142 2.59656 3.27199 + + 3.74240 3.81600 3.64398 3.71860 3.49450 ! 90 + 3.19130 2.80490 2.27930 1.75760 1.50510 + 1.22550 0.27602 -0.30141 -0.51951 0.24300 + 0.20040 0.02368 0.15778 0.64260 0.89548 + 1.68768 2.56758 3.13258 3.66290 + + 2.68560 2.69960 2.68760 2.61790 2.45640 ! 105 + 2.24350 2.03170 1.80750 1.43230 0.70340 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.52380 + 1.13560 1.64210 2.05980 2.31070 + + 1.50840 1.37790 1.23070 1.11010 0.93930 ! 120 + 0.93710 1.38980 1.55670 1.29330 0.69850 + 0.00000 -0.17662 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.71250 1.29880 1.67000 1.83640 + + 1.71870 1.48000 1.44400 1.50940 1.54720 ! 135 + 1.60420 1.65200 1.69730 1.50740 0.45362 + 0.18830 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.28770 + 1.05420 1.64180 1.97600 1.98940 + + 2.82330 2.60090 2.56140 2.65090 2.71650 ! 150 + 2.77750 2.88840 2.96640 2.77730 2.19960 + 0.76898 0.00000 0.00000 0.00000 0.00000 + 0.00000 -0.17662 0.00000 0.52070 1.34130 + 1.86798 2.36288 2.82720 2.90930 + + 4.39620 4.06518 4.21550 4.23380 4.26240 ! 165 + 4.30040 4.37760 4.40480 4.10340 3.27580 + 1.58028 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.99050 1.50760 2.20570 2.91080 + 3.48810 3.98220 4.22248 4.37448 + + +! 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135 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 150 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 165 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + +! pre-PRO PRO residues; based on proline dipeptide +! based on corrections to 298 K PMF +! /cb/morisot2/guvench/devel/051/parameterization/ +! cmap/0.00/pro2/alpha_c31a1_cmap/cmap + +C CP1 N C N C CP1 N 24 + + 0.00000 0.00000 0.00000 0.00000 0.00000 !-180 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 !-165 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 !-150 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 !-135 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.40896 0.00000 0.00000 0.00000 !-120 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.64818 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 1.61592 2.70513 0.94957 0.00000 0.00000 !-105 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.40896 -0.02285 0.56316 1.00195 -0.15451 + -0.69512 0.00000 0.81791 0.64818 0.00000 + 0.00000 -1.27381 0.00029 0.91238 + + 2.14691 1.66561 0.43151 0.00000 -1.92199 ! -90 + 0.00000 0.00000 0.00000 0.00000 0.81791 + 0.55878 0.35617 0.66094 1.28184 -0.05757 + -0.62563 -1.92200 -1.43058 -0.45590 -0.43181 + -0.45590 -0.10911 0.35217 1.18556 + + 1.79850 2.13895 2.28401 -1.92199 -1.92199 ! -75 + -1.92199 0.00000 0.64818 -0.77390 -0.66633 + -0.83481 -0.34895 0.45688 1.05490 2.63489 + -1.60892 -2.40045 -1.81442 -0.61480 -0.58532 + -0.50379 -0.40464 0.00020 0.84098 + + 1.94230 3.04722 0.64818 0.00000 0.00000 ! -60 + 0.00000 -1.92199 -1.27381 -2.02956 -3.36420 + -2.71146 -1.49351 -0.09584 0.02255 -1.51303 + -1.92199 -1.92199 0.00000 1.22687 -0.24179 + -1.20432 -1.53333 -0.84297 0.52000 + + 2.00671 0.64818 0.00000 0.00000 0.00000 ! -45 + 0.00000 0.00000 -1.92199 -3.43531 -4.84176 + -3.78043 -1.92200 0.40896 0.00000 0.00000 + 0.00000 0.00000 0.00000 -1.92199 -1.92199 + -2.46261 -2.38967 -1.26406 0.80674 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! -30 + -1.92199 0.00000 0.00000 -3.07008 -2.33095 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 -2.33095 + -2.33095 0.00000 -1.92199 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! -15 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 -1.92199 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 0 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 15 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 30 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 45 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 60 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 75 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 90 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 105 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 120 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 135 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 150 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 + + 0.00000 0.00000 0.00000 0.00000 0.00000 ! 165 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 diff --git a/charmm/toppar/rush/top_rush_058.inp b/charmm/toppar/rush/top_rush_058.inp new file mode 100755 index 00000000..c9dd1149 --- /dev/null +++ b/charmm/toppar/rush/top_rush_058.inp @@ -0,0 +1,1810 @@ +* RUSH all-hydrogen topology file for proteins, based largely on +* the: +* CHARMM22 All-Hydrogen topology File for Proteins +* due to MacKerell et al. +* +27 1 + +MASS 1 H 12.01100 H ! polar H +MASS 2 HC 12.01100 H ! N-ter H +MASS 3 HA 12.01100 H ! nonpolar H +MASS 4 HT 12.01100 H ! TIPS3P WATER HYDROGEN +MASS 5 HP 12.01100 H ! aromatic H +MASS 6 HB 12.01100 H ! backbone H +MASS 7 HR1 12.01100 H ! his he1, (+) his HG,HD2 +MASS 8 HR2 12.01100 H ! (+) his HE1 +MASS 9 HR3 12.01100 H ! neutral his HG, HD2 +MASS 10 HS 12.01100 H ! thiol hydrogen +MASS 11 HE1 12.01100 H ! for alkene; RHC=CR +MASS 12 HE2 12.01100 H ! for alkene; H2C=CR +MASS 15 HM 12.01100 H ! og acceptor antecedent +MASS 20 C 12.01100 C ! carbonyl C, peptide backbone +MASS 21 CA 12.01100 C ! aromatic C +MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH +MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 +MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 +MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons +MASS 26 CPH2 12.01100 C ! his CE1 carbon +MASS 27 CPT 12.01100 C ! trp C between rings +MASS 28 CY 12.01100 C ! TRP C in pyrrole ring +MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) +MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) +MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) +MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 +MASS 34 CPA 12.01100 C ! heme alpha-C +MASS 35 CPB 12.01100 C ! heme beta-C +MASS 36 CPM 12.01100 C ! heme meso-C +MASS 37 CM 12.01100 C ! heme CO carbon +MASS 38 CS 12.01100 C ! thiolate carbon +MASS 39 CE1 12.01100 C ! for alkene; RHC=CR +MASS 40 CE2 12.01100 C ! for alkene; H2C=CR +MASS 50 N 14.00700 N ! proline N +MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen +MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen +MASS 53 NR3 14.00700 N ! charged his ring nitrogen +MASS 54 NH1 14.00700 N ! peptide nitrogen +MASS 55 NH2 14.00700 N ! amide nitrogen +MASS 56 NH3 14.00700 N ! ammonium nitrogen +MASS 57 NC2 14.00700 N ! guanidinium nitroogen +MASS 58 NY 14.00700 N ! TRP N in pyrrole ring +MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) +MASS 60 NPH 14.00700 N ! heme pyrrole N +MASS 70 O 15.99900 O ! carbonyl oxygen +MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid +MASS 72 OC 15.99900 O ! carboxylate oxygen +MASS 73 OH1 15.99900 O ! hydroxyl oxygen +MASS 74 OS 15.99940 O ! ester oxygen +MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN +MASS 76 OM 15.99900 O ! heme CO/O2 oxygen +MASS 81 S 32.06000 S ! sulphur +MASS 82 SM 32.06000 S ! sulfur C-S-S-C type +MASS 83 SS 32.06000 S ! thiolate sulfur +MASS 85 HE 4.00260 HE ! helium +MASS 86 NE 20.17970 NE ! neon +MASS 90 CAL 40.08000 CA ! calcium 2+ +MASS 91 ZN 65.37000 ZN ! zinc (II) cation +MASS 92 FE 55.84700 Fe ! heme iron 56 +MASS 99 DUM 0.00000 H ! dummy atom + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI ALA 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 +ATOM HA HB 0.00 ! | / +GROUP ! HA-CA--CB-HB2 +ATOM CB CT3 0.00 ! | \ +ATOM HB1 HA 0.00 ! | HB3 +ATOM HB2 HA 0.00 ! O=C +ATOM HB3 HA 0.00 ! | +GROUP ! +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA N HN N CA +BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +ACCEPTOR O C +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +RESI ARG 0.00 +GROUP +ATOM N NH1 0.00 ! | HH11 +ATOM HN H 0.00 ! HN-N | +ATOM CA CT1 0.00 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA HB 0.00 ! | | | | | //(+) +GROUP ! HA-CA--CB--CG--CD--NE--CZ +ATOM CB CT2 0.00 ! | | | | \ +ATOM HB1 HA 0.00 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HB2 HA 0.00 ! O=C | +GROUP ! | HH21 +ATOM CG CT2 0.00 +ATOM HG1 HA 0.00 +ATOM HG2 HA 0.00 +GROUP +ATOM CD CT2 0.00 +ATOM HD1 HA 0.00 +ATOM HD2 HA 0.00 +ATOM NE NC2 0.00 +ATOM HE HC 0.00 +ATOM CZ C 0.00 +ATOM NH1 NC2 0.00 +ATOM HH11 HC 0.00 +ATOM HH12 HC 0.00 +ATOM NH2 NC2 0.00 +ATOM HH21 HC 0.00 +ATOM HH22 HC 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE O C CZ NH1 +IMPR N -C CA HN C CA +N O +IMPR CZ NH1 NH2 NE +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +RESI ASN 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA HB 0.00 ! | | || / +GROUP ! HA-CA--CB--CG--ND2 +ATOM CB CT2 0.00 ! | | \ +ATOM HB1 HA 0.00 ! | HB2 HD22 (trans to OD1) +ATOM HB2 HA 0.00 ! O=C +GROUP ! | +ATOM CG CC 0.00 +ATOM OD1 O 0.00 +GROUP +ATOM ND2 NH2 0.00 +ATOM HD21 H 0.00 +ATOM HD22 H 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +DOUBLE C O CG OD1 +IMPR N -C CA HN C CA +N O +IMPR CG ND2 CB OD1 CG CB ND2 OD1 +IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +RESI ASP 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 OD1 +ATOM HA HB 0.00 ! | | // +GROUP ! HA-CA--CB--CG +ATOM CB CT2 0.00 ! | | \ +ATOM HB1 HA 0.00 ! | HB2 OD2(-) +ATOM HB2 HA 0.00 ! O=C +ATOM CG CC 0.00 ! | +ATOM OD1 OC 0.00 +ATOM OD2 OC 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +DOUBLE O C CG OD1 +IMPR N -C CA HN C CA +N O +!IMPR OD1 CB OD2 CG +IMPR CG CB OD2 OD1 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +RESI CYS 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 +ATOM HA HB 0.00 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB CT2 0.00 ! | | \ +ATOM HB1 HA 0.00 ! | HB2 HG1 +ATOM HB2 HA 0.00 ! O=C +ATOM SG S 0.00 ! | +ATOM HG1 HS 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +RESI GLN 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA HB 0.00 ! | | | || / +GROUP ! HA-CA--CB--CG--CD--NE2 +ATOM CB CT2 0.00 ! | | | \ +ATOM HB1 HA 0.00 ! | HB2 HG2 HE22 (trans to OE1) +ATOM HB2 HA 0.00 ! O=C +GROUP ! | +ATOM CG CT2 0.00 +ATOM HG1 HA 0.00 +ATOM HG2 HA 0.00 +GROUP +ATOM CD CC 0.00 +ATOM OE1 O 0.00 +GROUP +ATOM NE2 NH2 0.00 +ATOM HE21 H 0.00 +ATOM HE22 H 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD NE2 CG OE1 CD CG NE2 OE1 +IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +RESI GLU 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 HG1 OE1 +ATOM HA HB 0.00 ! | | | // +GROUP ! HA-CA--CB--CG--CD +ATOM CB CT2 0.00 ! | | | \ +ATOM HB1 HA 0.00 ! | HB2 HG2 OE2(-) +ATOM HB2 HA 0.00 ! O=C +GROUP ! | +ATOM CG CT2 0.00 +ATOM HG1 HA 0.00 +ATOM HG2 HA 0.00 +ATOM CD CC 0.00 +ATOM OE1 OC 0.00 +ATOM OE2 OC 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +!IMPR OE1 CG OE2 CD +IMPR CD CG OE2 OE1 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI GLY 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! N-H +ATOM CA CT2 0.00 ! | +ATOM HA1 HB 0.00 ! | +ATOM HA2 HB 0.00 ! HA1-CA-HA2 +GROUP ! | +ATOM C C 0.00 ! | +ATOM O O 0.00 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA1 CA +DONOR HA2 CA +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 +PATCHING FIRS GLYP + +RESI HSD 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N NH1 0.00 ! | HD1 HE1 +ATOM HN H 0.00 ! HN-N | / +ATOM CA CT1 0.00 ! | HB1 ND1--CE1 +ATOM HA HB 0.00 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 0.00 ! | | \\ || +ATOM HB1 HA 0.00 ! | HB2 CD2--NE2 +ATOM HB2 HA 0.00 ! O=C | +ATOM ND1 NR1 0.00 ! | HD2 +ATOM HD1 H 0.00 +ATOM CG CPH1 0.00 +GROUP +ATOM CE1 CPH2 0.00 +ATOM HE1 HR1 0.00 +ATOM NE2 NR2 0.00 +ATOM CD2 CPH1 0.00 +ATOM HD2 HR3 0.00 +ATOM HE2 HM 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +BOND NE2 HE2 +IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HD1 ND1 +ACCEPTOR NE2 HE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 +IC CG CD2 NE2 HE2 1.3597 110.0300 0.0000 60.0000 1.2500 + +RESI HSE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N NH1 0.00 ! | HE1 +ATOM HN H 0.00 ! HN-N __ / +ATOM CA CT1 0.00 ! | HB1 ND1--CE1 +ATOM HA HB 0.00 ! | | / | +GROUP ! HA-CA--CB--CG | +ATOM CB CT2 0.00 ! | | \\ | +ATOM HB1 HA 0.00 ! | HB2 CD2--NE2 +ATOM HB2 HA 0.00 ! O=C | \ +ATOM ND1 NR2 0.00 ! | HD2 HE2 +ATOM CG CPH1 0.00 +ATOM CE1 CPH2 0.00 +ATOM HE1 HR1 0.00 +ATOM HD1 HM 0.00 +GROUP +ATOM NE2 NR1 0.00 +ATOM HE2 H 0.00 +ATOM CD2 CPH1 0.00 +ATOM HD2 HR3 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +BOND ND1 HD1 +DOUBLE O C CD2 CG CE1 ND1 +IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HE2 NE2 +ACCEPTOR ND1 HD1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 +IC CB CG ND1 HD1 1.5109 120.1700 180.0000 60.0000 1.2500 + +RESI HSP 0.00 ! Protonated His +GROUP +ATOM N NH1 0.00 ! | HD1 HE1 +ATOM HN H 0.00 ! HN-N | / +ATOM CA CT1 0.00 ! | HB1 ND1--CE1 +ATOM HA HB 0.00 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 0.00 ! | | \\ || +ATOM HB1 HA 0.00 ! | HB2 CD2--NE2(+) +ATOM HB2 HA 0.00 ! O=C | \ +ATOM CD2 CPH1 0.00 ! | HD2 HE2 +ATOM HD2 HR1 0.00 +ATOM CG CPH1 0.00 +GROUP +ATOM NE2 NR3 0.00 +ATOM HE2 H 0.00 +ATOM ND1 NR3 0.00 +ATOM HD1 H 0.00 +ATOM CE1 CPH2 0.00 +ATOM HE1 HR2 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG NE2 CE1 +IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +RESI ILE 0.00 +GROUP +ATOM N NH1 0.00 ! | HG21 HG22 +ATOM HN H 0.00 ! HN-N | / +ATOM CA CT1 0.00 ! | CG2--HG23 +ATOM HA HB 0.00 ! | / +GROUP ! HA-CA--CB-HB HD1 +ATOM CB CT1 0.00 ! | \ / +ATOM HB HA 0.00 ! | CG1--CD--HD2 +GROUP ! O=C / \ \ +ATOM CG2 CT3 0.00 ! | HG11 HG12 HD3 +ATOM HG21 HA 0.00 +ATOM HG22 HA 0.00 +ATOM HG23 HA 0.00 +GROUP +ATOM CG1 CT2 0.00 +ATOM HG11 HA 0.00 +ATOM HG12 HA 0.00 +GROUP +ATOM CD CT3 0.00 +ATOM HD1 HA 0.00 +ATOM HD2 HA 0.00 +ATOM HD3 HA 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + +RESI LEU 0.00 +GROUP +ATOM N NH1 0.00 ! | HD11 HD12 +ATOM HN H 0.00 ! HN-N | / +ATOM CA CT1 0.00 ! | HB1 CD1--HD13 +ATOM HA HB 0.00 ! | | / +GROUP ! HA-CA--CB--CG-HG +ATOM CB CT2 0.00 ! | | \ +ATOM HB1 HA 0.00 ! | HB2 CD2--HD23 +ATOM HB2 HA 0.00 ! O=C | \ +GROUP ! | HD21 HD22 +ATOM CG CT1 0.00 +ATOM HG HA 0.00 +GROUP +ATOM CD1 CT3 0.00 +ATOM HD11 HA 0.00 +ATOM HD12 HA 0.00 +ATOM HD13 HA 0.00 +GROUP +ATOM CD2 CT3 0.00 +ATOM HD21 HA 0.00 +ATOM HD22 HA 0.00 +ATOM HD23 HA 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 +!IC CD1 CB *CG HG 1.5361 110.4800 116.6300 108.6800 1.1168 old +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +RESI LYS 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA HB 0.00 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM CB CT2 0.00 ! | | | | | \ +ATOM HB1 HA 0.00 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM HB2 HA 0.00 ! O=C +GROUP ! | +ATOM CG CT2 0.00 +ATOM HG1 HA 0.00 +ATOM HG2 HA 0.00 +GROUP +ATOM CD CT2 0.00 +ATOM HD1 HA 0.00 +ATOM HD2 HA 0.00 +GROUP +ATOM CE CT2 0.00 +ATOM HE1 HA 0.00 +ATOM HE2 HA 0.00 +ATOM NZ NH3 0.00 +ATOM HZ1 HC 0.00 +ATOM HZ2 HC 0.00 +ATOM HZ3 HC 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUBLE O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI MET 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 HG1 HE1 +ATOM HA HB 0.00 ! | | | | +GROUP ! HA-CA--CB--CG--SD--CE--HE3 +ATOM CB CT2 0.00 ! | | | | +ATOM HB1 HA 0.00 ! | HB2 HG2 HE2 +ATOM HB2 HA 0.00 ! O=C +GROUP ! | +ATOM CG CT2 0.00 +ATOM HG1 HA 0.00 +ATOM HG2 HA 0.00 +ATOM SD S 0.00 +ATOM CE CT3 0.00 +ATOM HE1 HA 0.00 +ATOM HE2 HA 0.00 +ATOM HE3 HA 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +RESI PHE 0.00 +GROUP +ATOM N NH1 0.00 ! | HD1 HE1 +ATOM HN H 0.00 ! HN-N | | +ATOM CA CT1 0.00 ! | HB1 CD1--CE1 +ATOM HA HB 0.00 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--HZ +ATOM CB CT2 0.00 ! | | \ __ / +ATOM HB1 HA 0.00 ! | HB2 CD2--CE2 +ATOM HB2 HA 0.00 ! O=C | | +ATOM CG CA 0.00 ! | HD2 HE2 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA -0.115 +ATOM HZ HP 0.115 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +RESI PRO 0.00 +GROUP ! HD1 HD2 +ATOM N N 0.00 ! | \ / +ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02 +ATOM HD1 HA 0.00 ! | \ / +ATOM HD2 HA 0.00 ! | CG +ATOM CA CP1 0.00 ! | / \ +ATOM HA HB 0.00 ! HA-CA--CB HG2 +GROUP ! | / \ +ATOM CB CP2 0.00 ! | HB1 HB2 +ATOM HB1 HA 0.00 ! O=C +ATOM HB2 HA 0.00 ! | +GROUP +ATOM CG CP2 0.00 +ATOM HG1 HA 0.00 +ATOM HG2 HA 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +DOUBLE O C +IMPR N -C CA CD +IMPR C CA +N O +CMAP -C N CA C N CA C +N +DONOR HA CA +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 +PATCHING FIRS PROP + +RESI SER 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | HB1 +ATOM HA HB 0.00 ! | | +GROUP ! HA-CA--CB--OG +ATOM CB CT2 0.00 ! | | \ +ATOM HB1 HA 0.00 ! | HB2 HG1 +ATOM HB2 HA 0.00 ! O=C +ATOM OG OH1 0.00 ! | +ATOM HG1 H 0.00 +ATOM HG2 HM 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +BOND OG HG2 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HG1 OG +ACCEPTOR OG HG2 +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 180.0000 107.0800 0.9655 +IC CA CB OG HG2 1.5585 112.4500 180.0000 53.5400 1.2500 + +RESI THR 0.00 +GROUP +ATOM N NH1 0.00 ! | +ATOM HN H 0.00 ! HN-N +ATOM CA CT1 0.00 ! | OG1--HG1 +ATOM HA HB 0.00 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 0.00 ! | \ +ATOM HB HA 0.00 ! | CG2--HG21 +ATOM OG1 OH1 0.00 ! O=C / \ +ATOM HG11 H 0.00 ! | HG21 HG22 +ATOM HG12 HM 0.00 +GROUP +ATOM CG2 CT3 0.00 +ATOM HG21 HA 0.00 +ATOM HG22 HA 0.00 +ATOM HG23 HA 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG11 CG2 HG21 CG2 HG22 CG2 HG23 +BOND OG1 HG12 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HG11 OG1 +ACCEPTOR OG1 HG12 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG11 1.5693 112.1600 180.0000 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 +IC CA CB OG1 HG12 1.5693 112.1600 180.0000 52.7500 1.2500 + +RESI TRP 0.00 +GROUP +ATOM N NH1 0.00 ! | HE3 +ATOM HN H 0.00 ! HN-N | +ATOM CA CT1 0.00 ! | HB1 CE3 +ATOM HA HB 0.00 ! | | / \\ +GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM CB CT2 0.00 ! | | || || | +ATOM HB1 HA 0.00 ! | HB2 CD1 CE2 CH2-HH2 +ATOM HB2 HA 0.00 ! O=C / \ / \ // +ATOM CG CY 0.00 ! | HD1 NE1 CZ2 +ATOM CD1 CA -0.115 ! | | +ATOM HD1 HP 0.115 ! HE1 HZ2 +ATOM NE1 NY -0.115 +ATOM HE1 H 0.115 +ATOM CE2 CPT 0.00 +ATOM CD2 CPT 0.00 +GROUP +ATOM CE3 CA -0.115 +ATOM HE3 HP 0.115 +GROUP +ATOM CZ3 CA -0.115 +ATOM HZ3 HP 0.115 +GROUP +ATOM CZ2 CA -0.115 +ATOM HZ2 HP 0.115 +GROUP +ATOM CH2 CA -0.115 +ATOM HH2 HP 0.115 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI TYR 0.00 +GROUP +ATOM N NH1 0.00 ! | HD1 HE1 +ATOM HN H 0.00 ! HN-N | | +ATOM CA CT1 0.00 ! | HB1 CD1--CE1 +ATOM HA HB 0.00 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--OH +ATOM CB CT2 0.00 ! | | \ __ / \ +ATOM HB1 HA 0.00 ! | HB2 CD2--CE2 HH +ATOM HB2 HA 0.00 ! O=C | | +ATOM CG CA 0.00 ! | HD2 HE2 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA 0.11 +ATOM OH OH1 -0.11 +ATOM HH1 H 0.00 +ATOM HH2 HM 0.00 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH1 +BOND OH HH2 +DOUBLE O C CD1 CG CE1 CZ CE2 CD2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +DONOR HH1 OH +ACCEPTOR OH HH2 +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH1 1.3978 119.6800 180.0000 107.4700 0.9594 +IC CE1 CZ OH HH2 1.3978 119.6800 180.0000 53.7400 1.2500 + +RESI VAL 0.00 +GROUP +ATOM N NH1 0.00 ! | HG11 HG12 +ATOM HN H 0.00 ! HN-N | / +ATOM CA CT1 0.00 ! | CG1--HG13 +ATOM HA HB 0.00 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 0.00 ! | \ +ATOM HB HA 0.00 ! | CG2--HG21 +GROUP ! O=C / \ +ATOM CG1 CT3 0.00 ! | HG21 HG22 +ATOM HG11 HA 0.00 +ATOM HG12 HA 0.00 +ATOM HG13 HA 0.00 +GROUP +ATOM CG2 CT3 0.00 +ATOM HG21 HA 0.00 +ATOM HG22 HA 0.00 +ATOM HG23 HA 0.00 +GROUP +ATOM C C 0.00 +ATOM O O 0.00 +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HA CA +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +ATOM H3 HM 0.000 +BOND OH2 H1 OH2 H2 OH2 H3 +ANGLE H1 OH2 H2 ! required +ANGLE H1 OH2 H3 ! +ANGLE H2 OH2 H3 ! +DONOR H1 OH2 +DONOR H2 OH2 +ACCEPTOR OH2 H3 +PATCHING FIRS NONE LAST NONE + +RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p +GROUP +ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup +ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup +ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup +BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI CAL 2.00 ! Calcium ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc ion +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI HEME -2.00 ! 6-liganded planar heme +GROUP +ATOM FE FE 0.24 ! O2A O1A O2D O1D +ATOM NA NPH -0.18 ! \\ // \\ // +ATOM NB NPH -0.18 ! CGA CGD +ATOM NC NPH -0.18 ! | | +ATOM ND NPH -0.18 ! HBA1--CBA--HBA2 HA HBD1--CBD--HBD2 +ATOM C1A CPA 0.12 ! | | | +ATOM C2A CPB -0.06 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2 +ATOM C3A CPB -0.06 ! | / \ | +ATOM C4A CPA 0.12 ! C2A---C1A C4D---C3D +ATOM C1B CPA 0.12 ! | | | | +ATOM C2B CPB -0.06 !HMA1\ | | | | /HMD1 +ATOM C3B CPB -0.06 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2 +ATOM C4B CPA 0.12 !HMA3/ \ / \ / \ / \HMD3 +ATOM C1C CPA 0.12 ! C4A \ / C1D +ATOM C2C CPB -0.06 ! / \ / \ +ATOM C3C CPB -0.06 ! HB--CHB FE CHD--HD +ATOM C4C CPA 0.12 ! \ / \ / +ATOM C1D CPA 0.12 ! C1B / \ C4C HAC +ATOM C2D CPB -0.06 !HMB1\ / \ / \ / \ / +ATOM C3D CPB -0.06 !HMB2-CMB--C2B NB NC C3C--CAC +ATOM C4D CPA 0.12 !HMB3/ | | | | \\ /HBC1 +GROUP ! | | | | CBC +ATOM CHA CPM -0.10 ! C3B---C4B C1C---C2C \HBC2 +ATOM HA HA 0.10 ! | \_CHC_/ | +GROUP ! CAB | CMC--HMC3 +ATOM CHB CPM -0.10 ! // \ HC / | +ATOM HB HA 0.10 ! CBB HAB HMC1 HMC2 +GROUP ! / \ +ATOM CHC CPM -0.10 ! HBB1 HBB2 +ATOM HC HA 0.10 ! +GROUP +ATOM CHD CPM -0.10 +ATOM HD HA 0.10 +GROUP +ATOM CMA CT3 -0.27 +ATOM HMA1 HA 0.09 +ATOM HMA2 HA 0.09 +ATOM HMA3 HA 0.09 +GROUP +ATOM CAA CT2 -0.18 +ATOM HAA1 HA 0.09 +ATOM HAA2 HA 0.09 +GROUP +ATOM CBA CT2 -0.28 +ATOM HBA1 HA 0.09 +ATOM HBA2 HA 0.09 +ATOM CGA CC 0.62 +ATOM O1A OC -0.76 +ATOM O2A OC -0.76 +GROUP +ATOM CMB CT3 -0.27 +ATOM HMB1 HA 0.09 +ATOM HMB2 HA 0.09 +ATOM HMB3 HA 0.09 +GROUP +ATOM CAB C -0.20 +ATOM HAB HA 0.20 +GROUP +ATOM CBB C -0.20 +ATOM HBB1 HA 0.10 +ATOM HBB2 HA 0.10 +GROUP +ATOM CMC CT3 -0.27 +ATOM HMC1 HA 0.09 +ATOM HMC2 HA 0.09 +ATOM HMC3 HA 0.09 +GROUP +ATOM CAC C -0.20 +ATOM HAC HA 0.20 +GROUP +ATOM CBC C -0.20 +ATOM HBC1 HA 0.10 +ATOM HBC2 HA 0.10 +GROUP +ATOM CMD CT3 -0.27 +ATOM HMD1 HA 0.09 +ATOM HMD2 HA 0.09 +ATOM HMD3 HA 0.09 +GROUP +ATOM CAD CT2 -0.18 +ATOM HAD1 HA 0.09 +ATOM HAD2 HA 0.09 +GROUP +ATOM CBD CT2 -0.28 +ATOM HBD1 HA 0.09 +ATOM HBD2 HA 0.09 +ATOM CGD CC 0.62 +ATOM O1D OC -0.76 +ATOM O2D OC -0.76 +BOND FE NA FE NB FE NC FE ND NA C1A +BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA +BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA +BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B +BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB +BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C +BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC +BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D +BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD +BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A +BOND CHA HA CHB HB CHC HC CHD HD +BOND CAA HAA1 CAA HAA2 CBA HBA1 CBA HBA2 +BOND CMA HMA1 CMA HMA2 CMA HMA3 +BOND CMB HMB1 CMB HMB2 CMB HMB3 +BOND CAB HAB CBB HBB1 CBB HBB2 +BOND CMC HMC1 CMC HMC2 CMC HMC3 +BOND CAC HAC CBC HBC1 CBC HBC2 +BOND CMD HMD1 CMD HMD2 CMD HMD3 +BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2 +IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB +IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC +IMPR C2D C1D C3D CMD C3D C2D C4D CAD +IMPR CGA CBA O2A O1A CGD CBD O2D O1D +IMPR C4A NA C1A C2A C1A NA C4A C3A +IMPR C4B NB C1B C2B C1B NB C4B C3B +IMPR C4C NC C1C C2C C1C NC C4C C3C +IMPR C4D ND C1D C2D C1D ND C4D C3D +IMPR NA C1A C2A C3A NA C4A C3A C2A +IMPR NB C1B C2B C3B NB C4B C3B C2B +IMPR NC C1C C2C C3C NC C4C C3C C2C +IMPR ND C1D C2D C3D ND C4D C3D C2D +IMPR NA C1A CHA C4D NA C4A CHB C1B +IMPR NB C1B CHB C4A NB C4B CHC C1C +IMPR NC C1C CHC C4B NC C4C CHD C1D +IMPR ND C1D CHD C4C ND C4D CHA C1A +IMPR CHA C1A C4D HA +IMPR CHB C1B C4A HB +IMPR CHC C1C C4B HC +IMPR CHD C1D C4C HD +IMPR C1A C2A CHA NA C4A C3A CHB NA +IMPR C1B C2B CHB NB C4B C3B CHC NB +IMPR C1C C2C CHC NC C4C C3C CHD NC +IMPR C1D C2D CHD ND C4D C3D CHA ND +IMPR NA C1A C4A FE +IMPR NB C1B C4B FE +IMPR NC C1C C4C FE +IMPR ND C1D C4D FE +IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1 +IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1 +ACCEPTOR NA +ACCEPTOR O1A ! CGA +ACCEPTOR O2A ! CGA +ACCEPTOR NB +ACCEPTOR NC +ACCEPTOR ND +ACCEPTOR O1D ! CGD +ACCEPTOR O2D ! CGD +IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NA FE CHB HB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NB FE CHC HC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NC FE CHD HD 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC ND FE CHA HA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION +IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION +IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 +PATCHING FIRS NONE LAST NONE + +PRES NTER 0.00 ! standard N-terminus +GROUP ! use in generate statement +ATOM N NH3 0.00 ! +ATOM HT1 HC 0.00 ! HT1 +ATOM HT2 HC 0.00 ! (+)/ +ATOM HT3 HC 0.00 ! --CA--N--HT2 +ATOM CA CT1 0.00 ! | \ +ATOM HA HB 0.00 ! HA HT3 +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT1 HT2 *N CA 0.0000 109.0000 120.0000 0.0000 0.0000 +IC HT2 HT3 *N CA 0.0000 109.0000 120.0000 0.0000 0.0000 +IC HT3 HT1 *N CA 0.0000 109.0000 120.0000 0.0000 0.0000 + + +PRES GLYP 0.00 ! Glycine N-terminus +GROUP ! use in generate statement +ATOM N NH3 0.00 ! +ATOM HT1 HC 0.00 ! HA1 HT1 +ATOM HT2 HC 0.00 ! | (+)/ +ATOM HT3 HC 0.00 ! --CA--N--HT2 +ATOM CA CT2 0.00 ! | \ +ATOM HA1 HB 0.00 ! HA2 HT3 +ATOM HA2 HB 0.00 ! +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES PROP 0.00 ! Proline N-Terminal +GROUP ! use in generate statement +ATOM N NP 0.00 ! HA +ATOM HN1 HC 0.00 ! | +ATOM HN2 HC 0.00 ! -CA HN1 +ATOM CD CP3 0.00 ! / \ / +ATOM HD1 HA 0.00 ! N(+) +ATOM HD2 HA 0.00 ! / \ +ATOM CA CP1 0.00 ! -CD HN2 +ATOM HA HB 0.00 ! | \ +BOND HN1 N HN2 N ! HD1 HD2 +DONOR HN1 N +DONOR HN2 N +IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES ACE 0.00 ! acetylated N-terminus +GROUP ! use in generate statement +ATOM CAY CT3 0.00 ! +ATOM HY1 HA 0.00 ! HY1 HY2 HY3 +ATOM HY2 HA 0.00 ! \ | / +ATOM HY3 HA 0.00 ! CAY +GROUP ! | +ATOM CY C 0.00 ! CY=OY +ATOM OY O 0.00 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA HN +CMAP CY N CA C N CA C +N +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACP 0.00 ! acetylated N-terminus for proline +GROUP ! use in generate statement +ATOM CAY CT3 0.00 ! +ATOM HY1 HA 0.00 ! HY1 HY2 HY3 +ATOM HY2 HA 0.00 ! \ | / +ATOM HY3 HA 0.00 ! CAY +GROUP ! | +ATOM CY C 0.00 ! CY=OY +ATOM OY O 0.00 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA CD +CMAP CY N CA C N CA C +N +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES CTER 0.00 ! standard C-terminus +GROUP ! use in generate statement +ATOM C CC 0.00 ! OT2(-) +ATOM OT1 OC 0.00 ! / +ATOM OT2 OC 0.00 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +!IMPR OT1 CA OT2 C +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT1 0.00 ! methylated C-terminus from methyl acetate +GROUP ! use in generate statement +ATOM N NH1 0.00 ! +ATOM HN H 0.00 ! OT1 +ATOM CA CT1 0.00 ! | // +ATOM HA HB 0.00 ! -N--CA--C HT1 +ATOM C CD 0.00 ! | | \ / +ATOM OT1 OB 0.00 ! HN HA OT2--CT--HT2 +ATOM OT2 OS 0.00 ! \ +ATOM CT CT3 0.00 ! HT3 +ATOM HT1 HA 0.00 ! +ATOM HT2 HA 0.00 ! +ATOM HT3 HA 0.00 ! +DELETE ATOM O +BOND C OT2 OT2 CT +BOND CT HT1 CT HT2 CT HT3 +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 + +PRES CT2 0.00 ! amidated C-terminus +GROUP ! use in generate statement +ATOM C CC 0.00 ! +ATOM O O 0.00 ! | +GROUP ! O=C +ATOM NT NH2 0.00 ! | +ATOM HT1 H 0.00 ! NT +ATOM HT2 H 0.00 ! / \ +BOND C NT ! HT1 HT2 (HT1 is cis to O) +BOND NT HT1 NT HT2 ! +IMPR C NT CA O C CA NT O +IMPR NT C HT1 HT2 NT C HT2 HT1 +DONOR HT1 NT +DONOR HT2 NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT3 0.00 ! N-Methylamide C-terminus +GROUP ! use in generate statement +ATOM C C 0.00 ! +ATOM O O 0.00 ! | +GROUP ! C=O +ATOM NT NH1 0.00 ! | +ATOM HNT H 0.00 ! NT-HNT +ATOM CAT CT3 0.00 ! | +ATOM HT1 HA 0.00 ! HT1-CAT-HT3 +ATOM HT2 HA 0.00 ! | +ATOM HT3 HA 0.00 ! HT2 + ! +BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 +IMPR NT C CAT HNT C CA NT O +CMAP -C N CA C N CA C NT +DONOR HNT NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES DIP 0.00 ! N-Methylamide C-terminus +GROUP ! use in generate statement for creating dipeptides +ATOM C C 0.00 ! +ATOM O O 0.00 ! | +GROUP ! C=O +ATOM NT NH1 0.00 ! | +ATOM HNT H 0.00 ! NT-HNT +ATOM CAT CT3 0.00 ! | +ATOM HT1 HA 0.00 ! HT1-CAT-HT3 +ATOM HT2 HA 0.00 ! | +ATOM HT3 HA 0.00 ! HT2 + ! +BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 +IMPR NT C CAT HNT C CA NT O +CMAP CY N CA C N CA C NT +DONOR HNT NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 + ! via acetic acid, use in a patch statement and + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM CB CT2 0.00 ! +ATOM HB1 HA 0.00 ! HB1 OD1 +ATOM HB2 HA 0.00 ! | // +ATOM CG CD 0.00 ! -CB--CG +ATOM OD1 OB 0.00 ! | \ +ATOM OD2 OH1 0.00 ! HB2 OD2-HD2 +ATOM HD2 H 0.00 ! +BOND OD2 HD2 +DONOR HD2 OD2 +IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 + ! via acetic acid, use in a patch statement and + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM CG CT2 0.00 ! +ATOM HG1 HA 0.00 ! HG1 OE1 +ATOM HG2 HA 0.00 ! | // +ATOM CD CD 0.00 ! -CG--CD +ATOM OE1 OB 0.00 ! | \ +ATOM OE2 OH1 0.00 ! HG2 OE2-HE2 +ATOM HE2 H 0.00 ! +BOND OE2 HE2 +DONOR HE2 OE2 +IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES LINK 0.00 ! linkage for IMAGES or for joining segments + ! 1 refers to previous (N terminal) + ! 2 refers to next (C terminal) + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +!the need for the explicit specification of angles and dihedrals in +!patches linking images has not been tested +!ANGLE 1C 2N 2CA 1CA 1C 2N +!ANGLE 1O 1C 2N 1C 2N 2HN +!DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +!DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +!DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +!DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES DISU 0.00 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. + ! use in a patch statement and + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM 1CB CT2 0.00 ! +ATOM 1SG SM 0.00 ! 2SG--2CB-- +GROUP ! / +ATOM 2SG SM 0.00 ! -1CB--1SG +ATOM 2CB CT2 0.00 ! +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 + ! use in a patch statement and + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM CE1 CPH2 0.00 ! HE1 +ATOM HE1 HR1 0.00 ! / +ATOM ND1 NR2 0.00 ! HB1 ND1--CE1 +ATOM CG CPH1 0.00 ! | / | +ATOM CB CT2 0.00 ! -CB--CG | +ATOM HB1 HA 0.00 ! | \ | +ATOM HB2 HA 0.00 ! HB2 CD2--NE2 +GROUP ! | \ +ATOM NE2 NR1 0.00 ! HD2 HE2 +ATOM HE2 H 0.00 +ATOM CD2 CPH1 0.00 +ATOM HD2 HR3 0.00 +DELETE ATOM HD1 +DELETE ACCE NE2 +BOND NE2 HE2 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +DONOR HE2 NE2 +ACCEPTOR ND1 +IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 + +! patches for cyclic peptides +PRES LIG1 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus + ! use in a patch statement, perform initial + ! generation using first NONE last NONE and + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG2 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE and + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG3 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE and + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +END + + + diff --git a/charmm/toppar/silicates/00README b/charmm/toppar/silicates/00README new file mode 100644 index 00000000..4f45d6b3 --- /dev/null +++ b/charmm/toppar/silicates/00README @@ -0,0 +1,78 @@ + +CHARMM force field parameters have been recently developed for +silicates and aluminumsilicates. This document shows how to set up +input files for a slab of (011) quartz surface, taking advantage of +the ability of CHARMM to perform MD simulations of peridic systems. + +Pedro Lopes and Alexander D. MacKerell, Jr. + +An auxiliary program, patchfind, has been developed to help in the +definition of the patches between atoms in the primitive cell and +neighbouring cells. Lists of bonds, angles and dihedrals, with the +assignment of atoms along particular directions, are produced. You +can find patchfind.x in ./code directory. + +The topology and parameter file is in the ./toppar subdirectory + +Steps for successful use of silicates and aluminumsilicates parameters +in modeling surfaces: + +1) Primitive unit cell of the surface in XYZ format (input.xyz): the +surface has to be oriented along the X-Y plane. X is made to +correspond to the crystalline a-vector and Y to the crystalline +b-vector. c is orthogonal to a and b. + +2) crystal.dat file: contains the a, b, c, alpha, beta and gamma +crystal parameters: + +7.3000 +4.9100 +44.5000 +90.0 +90.0 +109.6517 + +3) run the program patchfind.x: if no mistakes were made it produces a +list of bonds, angles and torsions that can be used to define the +patches between the primitive and neigbouring cells. Common mistakes +are made in the definition of the crystal parameters. The space is +divided according to the following drawing. The priminitve cell is +always 1. Replica along the a-vector is refered as XX or 2 and replica +along the b-vector is refered as YY or 3. XY or 4 is the cell +resulting from a+b. + +To run patchfind.x ./code/patchfind.x > patches.dat + +----------------------- +| | | +| 3 | 4 | +| YY | XY | +| | | +----------------------- +| | | +| 1 | 2 | +|Primitive | XX | +| | | +----------------------- + +Example output is: + +Torsions along XX and YY + 17 1 9 25 3 1 1 2 + 18 22 30 27 2 1 1 3 + +In this case both torsions span tree cells: primitive, XX and YY. + +With this information the creation of the topology file is +straightforward. + +4) Create topology file: an example for quartz (011), +is available in ./toppar/top_silicates.inp + +5) A CHARMM input file, test.inp, is included. It reads the primitive +cell, replicates 8x5 times the primitive cell to create the unit cell, +then generates the images and patches the images. Required files are +top_silicates.inp, par_silicates.inp, params.str, crystal.img and +image_patch.str. + + diff --git a/charmm/toppar/silicates/code/cell.f b/charmm/toppar/silicates/code/cell.f new file mode 100644 index 00000000..160f8d23 --- /dev/null +++ b/charmm/toppar/silicates/code/cell.f @@ -0,0 +1,40 @@ + subroutine cell(alen,blen,clen,alpha,beta,gamma) + implicit none +c + double precision alpha,beta,gamma + double precision alen,blen,clen + integer iout +c +c initialize periodic lengths and angles +c + iout = 6 + + alen = 0.0d0 + blen = 0.0d0 + clen = 0.0d0 + alpha = 0.0d0 + beta = 0.0d0 + gamma = 0.0d0 + + open (11,file='crystal.dat',status='old') + read(11,*) alen,blen,clen,alpha,beta,gamma + close (11) +c +c checck unspecified periodic lengths and angles +c + if (alen .eq. 0.0d0) write(iout,'(/,a)') 'a lenght not set' + if (blen .eq. 0.0d0) write(iout,'(/,a)') 'b lenght not set' + if (clen .eq. 0.0d0) write(iout,'(/,a)') 'c lenght not set' + if (alpha .eq. 0.0d0) write(iout,'(/,a)') 'alpha not set' + if (beta .eq. 0.0d0) write(iout,'(/,a)') 'beta not set' + if (gamma .eq. 0.0d0) write(iout,'(/,a)') 'gamma not set' +c +c stop if lengths or angles are nought +c + if (alen.eq.0.0d0 .or. blen.eq.0.0d0 + & .or. clen.eq.90.0d0) stop + if (alpha.eq.0.0d0 .or. beta.eq.0.0d0 + & .or. gamma.eq.90.0d0) stop + + return + end diff --git a/charmm/toppar/silicates/code/compile.txt b/charmm/toppar/silicates/code/compile.txt new file mode 100644 index 00000000..a65ccb64 --- /dev/null +++ b/charmm/toppar/silicates/code/compile.txt @@ -0,0 +1,3 @@ + +g77 -o patchfind.x patchfind.f crystal.f cell.f + diff --git a/charmm/toppar/silicates/code/crystal.dat b/charmm/toppar/silicates/code/crystal.dat new file mode 100644 index 00000000..0d121dab --- /dev/null +++ b/charmm/toppar/silicates/code/crystal.dat @@ -0,0 +1,7 @@ +7.3000 +4.9100 +44.5000 +90.0 +90.0 +109.6517 + diff --git a/charmm/toppar/silicates/code/crystal.f b/charmm/toppar/silicates/code/crystal.f new file mode 100644 index 00000000..b8631858 --- /dev/null +++ b/charmm/toppar/silicates/code/crystal.f @@ -0,0 +1,133 @@ +c +c +c "crystal" is a utility program which converts between +c fractional and Cartesian coordinates, and can generate +c full unit cells from asymmetric units +c +c + subroutine crystal(n,name,valence,x,y,z) + implicit none + + integer mxatm + parameter (mxatm=1000) + integer n + integer iout + integer valence(mxatm) + double precision radian + parameter (radian=57.295780d0) + double precision alpha,beta,gamma + double precision adim,bdim,cdim + double precision aleng(3),bleng(3),cleng(3) + double precision x(mxatm),y(mxatm),z(mxatm) + logical orthogonal,triclinic + character*4 name(mxatm) +c + call cell(adim,bdim,cdim,alpha,beta,gamma) +c +c + iout = 6 + + orthogonal = .false. + triclinic = .false. + + if (alpha.eq. 90.0d0 .and. beta .eq. 90.0d0 + $ .and. gamma.eq.90.0d0) then + orthogonal = .true. + else + triclinic = .true. + end if +c +c determina as coordenadas de cada crystal system +c + if (orthogonal) then + aleng(1) = adim + aleng(2) = 0.0d0 + aleng(3) = 0.0d0 + bleng(1) = 0.0d0 + bleng(2) = bdim + bleng(3) = 0.0d0 + cleng(1) = 0.0d0 + cleng(2) = 0.0d0 + cleng(3) = cdim + else if (triclinic) then + aleng(1) = adim*sin(alpha/radian) + aleng(2) = adim*cos(alpha/radian) + aleng(3) = 0.0d0 + bleng(1) = bdim*cos(gamma/radian) + bleng(2) = bdim*sin(gamma/radian) + bleng(3) = 0.0d0 + cleng(1) = 0.0d0 + cleng(2) = 0.0d0 + cleng(3) = cdim + end if +c +c print out the initial cell dimensions to be used +c + write (iout,10) adim,bdim,cdim,alpha,beta,gamma + 10 format (/,'Unit Cell Dimensions :' + $ /,' a =',f10.4, + $ /,' b =',f10.4, + $ /,' c =',f10.4, + $ /,' alpha =',f10.4, + $ /,' beta =',f10.4, + $ /,' gamma =',f10.4) +c +c replicate the unit cell to make a block of unit cells +c + call replicate + $ (n,name,valence,x,y,z,aleng,bleng,cleng) +c +c + return + end +c + subroutine replicate + $ (n,name,valence,x,y,z,aleng,bleng,cleng) + implicit none + + integer mxatm + parameter (mxatm=1000) + integer i,n,nunit !nunit number of atoms in unit cell PEML + integer valence(mxatm) + character*4 name(mxatm) + double precision aleng(3),bleng(3),cleng(3) + double precision x(mxatm),y(mxatm),z(mxatm) +c +c translate along XX +c + nunit = n + do i = 1, nunit + n = n + 1 + x(n) = x(i) + aleng(1) + y(n) = y(i) + aleng(2) + z(n) = z(i) + aleng(3) + + name(n) = name(i) + valence(n) = valence(i) + + end do +c +c translate along YY +c + do i = 1, nunit + n = n + 1 + x(n) = x(i) + bleng(1) + y(n) = y(i) + bleng(2) + z(n) = z(i) + bleng(3) + name(n) = name(i) + valence(n) = valence(i) + end do +c +c translate along XY +c + do i = 1, nunit + n = n + 1 + x(n) = x(i) + aleng(1) + bleng(1) + y(n) = y(i) + aleng(2) + bleng(2) + z(n) = z(i) + aleng(3) + bleng(3) + name(n) = name(i) + valence(n) = valence(i) + end do + + return + end diff --git a/charmm/toppar/silicates/code/input.xyz b/charmm/toppar/silicates/code/input.xyz new file mode 100644 index 00000000..a8e4ff3c --- /dev/null +++ b/charmm/toppar/silicates/code/input.xyz @@ -0,0 +1,42 @@ +40 + + Si 4.118 4.481 -12.830 + Si 0.121 3.053 -9.489 + Si 3.423 1.626 -6.147 + Si 6.726 0.198 -2.806 + O 3.980 2.880 -12.662 + O -0.018 1.453 -9.320 + O 3.285 0.025 -5.979 + O 4.936 3.222 -2.638 + O 5.654 4.910 -12.703 + O 1.656 3.483 -9.362 + O 4.959 2.055 -6.020 + O 0.961 0.628 -2.679 + O -0.396 3.385 -10.982 + O 2.906 1.958 -7.641 + O 6.209 0.530 -4.300 + O 2.211 -0.897 -0.959 + O 4.828 0.576 -11.756 + O -0.821 3.772 -8.414 + O 2.481 2.345 -5.073 + O 5.784 0.917 -1.732 + Si 3.707 1.727 -11.588 + Si 5.358 4.923 -8.246 + Si 1.360 3.496 -4.905 + Si 4.663 2.068 -1.564 + Si -0.198 4.393 -12.209 + Si 3.105 2.966 -8.867 + Si 6.407 1.538 -5.526 + Si 2.410 0.110 -2.185 + O 3.896 2.311 -10.094 + O 5.547 5.508 -6.753 + O 1.550 4.080 -3.411 + O 4.852 2.653 -0.070 + O 2.246 1.087 -11.715 + O 3.898 4.283 -8.373 + O -0.100 2.856 -5.032 + O 3.203 1.428 -1.691 + H 3.601 4.813 -14.324 + H 2.728 -1.229 0.535 + H 0.594 3.739 -13.435 + H 4.061 3.307 1.156 diff --git a/charmm/toppar/silicates/code/patches.dat b/charmm/toppar/silicates/code/patches.dat new file mode 100644 index 00000000..73880f15 --- /dev/null +++ b/charmm/toppar/silicates/code/patches.dat @@ -0,0 +1,219 @@ + +Unit Cell Dimensions : + a = 7.3000 + b = 4.9100 + c = 44.5000 + alpha = 90.0000 + beta = 90.0000 + gamma = 109.6517 + + + +Bonds inside unit cell + 1 5 1 1 + 1 9 1 1 + 1 37 1 1 + 2 6 1 1 + 2 10 1 1 + 2 13 1 1 + 2 18 1 1 + 3 7 1 1 + 3 11 1 1 + 3 14 1 1 + 3 19 1 1 + 4 15 1 1 + 4 20 1 1 + 5 21 1 1 + 8 24 1 1 + 10 26 1 1 + 11 27 1 1 + 12 28 1 1 + 13 25 1 1 + 14 26 1 1 + 15 27 1 1 + 16 28 1 1 + 17 21 1 1 + 19 23 1 1 + 20 24 1 1 + 21 29 1 1 + 21 33 1 1 + 22 30 1 1 + 22 34 1 1 + 23 31 1 1 + 23 35 1 1 + 24 32 1 1 + 24 36 1 1 + 25 39 1 1 + 26 29 1 1 + 28 36 1 1 + + +Bonds along XX + 4 12 1 2 + 9 25 1 2 + 22 18 1 2 + 27 35 1 2 + +Bonds along YY + 1 17 1 3 + 8 4 1 3 + 23 7 1 3 + 25 33 1 3 + 30 27 1 3 + 31 28 1 3 + +Bonds along XY + 22 6 1 4 + + +Angles along XX + 1 9 25 1 1 2 + 12 4 15 2 1 1 + 12 4 20 2 1 1 + 4 12 28 1 2 2 + 9 25 13 1 2 2 + 9 25 39 1 2 2 + 11 27 35 1 1 2 + 15 27 35 1 1 2 + 18 22 30 2 1 1 + 18 22 34 2 1 1 + 22 18 2 1 2 2 + 27 35 23 1 2 2 + +Angles along YY + 17 1 5 3 1 1 + 17 1 9 3 1 1 + 17 1 37 3 1 1 + 1 17 21 1 3 3 + 4 8 24 3 1 1 + 8 4 15 1 3 3 + 8 4 20 1 3 3 + 13 25 33 1 1 3 + 19 23 7 1 1 3 + 22 30 27 1 1 3 + 23 31 28 1 1 3 + 7 23 31 3 1 1 + 7 23 35 3 1 1 + 23 7 3 1 3 3 + 33 25 39 3 1 1 + 25 33 21 1 3 3 + 30 27 11 1 3 3 + 30 27 15 1 3 3 + 31 28 12 1 3 3 + 31 28 16 1 3 3 + 31 28 36 1 3 3 + +Angles along XY + 6 22 30 4 1 1 + 6 22 34 4 1 1 + 22 6 2 1 4 4 + +Angles along XX and YY + +Angles along XX and XY + 9 25 33 1 2 4 + 6 22 18 4 1 2 + +Angles along YY and XY + 8 4 12 1 3 4 + 30 27 35 1 3 4 + +All angles are accounted for + + +Torsions along XX + 25 9 1 5 2 1 1 1 + 1 9 25 13 1 1 2 2 + 1 9 25 39 1 1 2 2 + 37 1 9 25 1 1 1 2 + 3 11 27 35 1 1 1 2 + 4 15 27 35 1 1 1 2 + 12 4 15 27 2 1 1 1 + 28 12 4 15 2 2 1 1 + 12 4 20 24 2 1 1 1 + 28 12 4 20 2 2 1 1 + 4 12 28 16 1 2 2 2 + 4 12 28 36 1 2 2 2 + 9 25 13 2 1 2 2 2 + 11 27 35 23 1 1 2 2 + 15 27 35 23 1 1 2 2 + 2 18 22 30 2 2 1 1 + 18 22 34 26 2 1 1 1 + 2 18 22 34 2 2 1 1 + 22 18 2 6 1 2 2 2 + 22 18 2 10 1 2 2 2 + 22 18 2 13 1 2 2 2 + 27 35 23 19 1 2 2 2 + 27 35 23 31 1 2 2 2 + +Torsions along YY + 17 1 5 21 3 1 1 1 + 21 17 1 5 3 3 1 1 + 21 17 1 9 3 3 1 1 + 21 17 1 37 3 3 1 1 + 1 17 21 5 1 3 3 3 + 1 17 21 29 1 3 3 3 + 1 17 21 33 1 3 3 3 + 2 13 25 33 1 1 1 3 + 3 19 23 7 1 1 1 3 + 4 8 24 20 3 1 1 1 + 4 8 24 32 3 1 1 1 + 4 8 24 36 3 1 1 1 + 15 4 8 24 3 3 1 1 + 20 4 8 24 3 3 1 1 + 8 4 15 27 1 3 3 3 + 8 4 20 24 1 3 3 3 + 13 25 33 21 1 1 3 3 + 19 23 31 28 1 1 1 3 + 19 23 7 3 1 1 3 3 + 22 30 27 11 1 1 3 3 + 22 30 27 15 1 1 3 3 + 34 22 30 27 1 1 1 3 + 23 31 28 12 1 1 3 3 + 23 31 28 16 1 1 3 3 + 23 31 28 36 1 1 3 3 + 35 23 31 28 1 1 1 3 + 7 23 31 28 3 1 1 3 + 3 7 23 31 3 3 1 1 + 3 7 23 35 3 3 1 1 + 23 7 3 11 1 3 3 3 + 23 7 3 14 1 3 3 3 + 23 7 3 19 1 3 3 3 + 21 33 25 39 3 3 1 1 + 25 33 21 5 1 3 3 3 + 25 33 21 17 1 3 3 3 + 25 33 21 29 1 3 3 3 + 30 27 11 3 1 3 3 3 + 30 27 15 4 1 3 3 3 + 31 28 36 24 1 3 3 3 + +Torsions along XY + 2 6 22 30 4 4 1 1 + 6 22 34 26 4 1 1 1 + 2 6 22 34 4 4 1 1 + 22 6 2 10 1 4 4 4 + 22 6 2 13 1 4 4 4 + 22 6 2 18 1 4 4 4 + +Torsions along XX and YY + 17 1 9 25 3 1 1 2 + 18 22 30 27 2 1 1 3 + +Torsions along XX and XY + 1 9 25 33 1 1 2 4 + 9 25 33 21 1 2 4 4 + 6 22 18 2 4 1 2 2 + 2 6 22 18 4 4 1 2 + 27 35 23 7 1 2 2 4 + +Torsions along YY and XY + 12 4 8 24 4 3 1 1 + 8 4 12 28 1 3 4 4 + 22 30 27 35 1 1 3 4 + 6 22 30 27 4 1 1 3 + 30 27 35 23 1 3 4 4 + +Torsions along XX and XY and XY + + +All torsions are accounted for diff --git a/charmm/toppar/silicates/code/patchfind.f b/charmm/toppar/silicates/code/patchfind.f new file mode 100644 index 00000000..6238a15f --- /dev/null +++ b/charmm/toppar/silicates/code/patchfind.f @@ -0,0 +1,668 @@ +C ****************************************************************************** +C DISCLAIMER +C Everything that is free comes with NO warranty!!! +C Pedro E M Lopes +C ****************************************************************************** + program patchfind + implicit none + + integer mxatm + parameter (mxatm=1000) + integer mxcon + parameter (mxcon=8) + integer i,j,k,l + integer n,nunit + integer ia,ib,ic,id + integer ncryst + integer valence(mxatm) + integer ncon(mxatm),nval(mxatm) + integer icon(mxatm,mxcon),cel(mxatm,mxcon) + integer nbnd,nang,ntor + integer ibond(2000,2),bcel(2000,2) + integer iangl(2000,3),acel(2000,3) + integer itor(2000,4),tcel(2000,4) + integer indcel,jtrans + integer indx + integer celind(2000,8) + integer nprim,nxx,nxy,nyy,nxxyy,nxxxy,nyyxy,nxxyyxy + double precision radii(mxatm) + double precision dist, rcut + double precision x(mxatm),y(mxatm),z(mxatm) + character*4 name(mxatm) + logical primitive,similar + logical xx,yy,xy + logical skip,skip1,skip2,skip3,skip4 +c +c read the unit cell coordinates +c + open(3,file='input.xyz',status='old') + + read(3,*) n + do i = 1, n + read(3,*) name(i),x(i),y(i),z(i) + end do +c +c create a supercell by replicating the unit cell along X, Y and XY PEML +c + nunit = n ! NUNIT is the number of atoms in the unit cell PEML + + call crystal(n,name,valence,x,y,z) ! CRYSTAL replicates the unit cell along X, Y and XY PEML + + ncryst = n + + n = nunit + +c do i = 1, ncryst +c write(6,*) name(i),x(i),y(i),z(i) +c end do + +c +c determine valences of atoms +c + do i = 1, n + if ((name(i)(1:1) .eq. 'S') .or. (name(i)(1:1) .eq. 's')) + $ valence(i) = 4 + if ((name(i)(1:1) .eq. 'O') .or. (name(i)(1:1) .eq. 'o')) + $ valence(i) = 2 + if ((name(i)(1:1) .eq. 'H') .or. (name(i)(1:1) .eq. 'h')) + $ valence(i) = 1 + end do +c + do i = 1, ncryst + if ((name(i)(1:1) .eq. 'S') .or. (name(i)(1:1) .eq. 's')) + $ radii(i) = 1.09d0 + if ((name(i)(1:1) .eq. 'O') .or. (name(i)(1:1) .eq. 'o')) + $ radii(i) = 0.66d0 + if ((name(i)(1:1) .eq. 'H') .or. (name(i)(1:1) .eq. 'h')) + $ radii(i) = 0.30d0 + end do +c +c + do i = 1, mxatm + ncon(i) = 0 + nval(i) = 0 + do j = 1, mxcon + icon(i,j) = 0 + end do + end do +c + primitive = .false. + similar = .false. + do i = 1, n-1 + do j = i+1, n + rcut = 1.35d0*(radii(i)+radii(j)) + dist =sqrt((x(i)-x(j))**2 + (y(i)-y(j))**2 + (z(i)-z(j))**2) + if (dist .le. rcut) then + ncon(i) = ncon(i) + 1 + nval(i) = nval(i) + 1 + ncon(j) = ncon(j) + 1 + nval(j) = nval(j) + 1 + icon(i,ncon(i)) = j + cel(i,ncon(i)) = 1 + icon(j,ncon(j)) = i + cel(j,ncon(j)) = 1 + end if + end do + end do +c + do i = 1, n + do j = n+1, ncryst + rcut = 1.35d0*(radii(i)+radii(j)) + dist =sqrt((x(i)-x(j))**2 + + $ (y(i)-y(j))**2 + (z(i)-z(j))**2) + if (dist .le. rcut) then + indcel = int(j/n) + 1 + jtrans = j - (indcel-1)*n + ncon(i) = ncon(i) + 1 + nval(i) = nval(i) + 1 +c ncon(jtrans) = ncon(jtrans) + 1 +c nval(jtrans) = nval(jtrans) + 1 + icon(i,ncon(i)) = jtrans + cel(i,ncon(i)) = indcel +c icon(jtrans,ncon(jtrans)) = i +c cel(jtrans,ncon(jtrans)) = 1 + end if + end do + end do +c + do i = 1, 2000 + ibond(i,1) = 0 + ibond(i,2) = 0 + iangl(i,1) = 0 + iangl(i,2) = 0 + iangl(i,3) = 0 + itor(i,1) = 0 + itor(i,2) = 0 + itor(i,3) = 0 + itor(i,4) = 0 + end do +c + nbnd = 0 + do i = 1, n + ia = i + if (ncon(ia) .gt. 0) then + do j = 1, ncon(ia) + ib = icon(ia,j) + nbnd = nbnd + 1 + ibond(nbnd,1) = ia + ibond(nbnd,2) = ib + bcel(nbnd,1) = 1 + bcel(nbnd,2) = cel(ia,j) + + if (nbnd .ge. 2) then + skip = .false. + skip1 = .false. + skip2 = .false. + do k = 1, nbnd-1 + if ((ibond(k,1) .eq. ibond(nbnd,2)) .and. + $ (bcel(k,1) .eq. bcel(nbnd,2))) skip1 = .true. + if ((ibond(k,2) .eq. ibond(nbnd,1)) .and. + $ (bcel(k,2) .eq. bcel(nbnd,1))) skip2 = .true. + if (skip1 .and. skip2) skip = .true. + if (skip) then + nbnd = nbnd - 1 + skip = .false. + skip1 = .false. + skip2 = .false. + goto 550 + end if + end do + skip = .false. + skip1 = .false. + skip2 = .false. + do k = 1, nbnd-1 + if ((ibond(k,1) .eq. ibond(nbnd,1)) .and. + $ (bcel(k,1) .eq. bcel(nbnd,1))) skip1 = .true. + if ((ibond(k,2) .eq. ibond(nbnd,2)) .and. + $ (bcel(k,2) .eq. bcel(nbnd,2))) skip2 = .true. + if (skip1 .and. skip2) skip = .true. + if (skip) then + nbnd = nbnd - 1 + skip = .false. + skip1 = .false. + skip2 = .false. + goto 550 + end if + end do + 550 continue + end if + end do + end if + end do +c + nang = 0 + do i = 1, nbnd + ia = ibond(i,1) + ib = ibond(i,2) + if (ncon(ib) .gt. 0) then + do j = 1, ncon(ib) + ic = icon(ib,j) + if (ic .ne. ia) then + nang = nang + 1 + iangl(nang,1) = ia + iangl(nang,2) = ib + iangl(nang,3) = ic + acel(nang,1) = bcel(i,1) + acel(nang,2) = bcel(i,2) + acel(nang,3) = bcel(i,2) + cel(ib,j) - 1 + end if + end do + end if +c + if (ncon(ia) .gt. 0) then + do j = 1, ncon(ia) + ic = icon(ia,j) + if (ic .ne. ib) then + nang = nang + 1 + iangl(nang,1) = ic + iangl(nang,2) = ia + iangl(nang,3) = ib + acel(nang,1) = bcel(i,1) + cel(ia,j) - 1 + acel(nang,2) = bcel(i,1) + acel(nang,3) = bcel(i,2) + end if + end do + end if + end do +c + do i = 1, nang-1 + do k = i+1, nang + skip = .false. + skip1 = .false. + skip2 = .false. + skip3 = .false. + if ((iangl(i,1) .eq. iangl(k,1)) .and. + $ (acel(i,1) .eq. acel(k,1))) skip1 = .true. + if ((iangl(i,2) .eq. iangl(k,2)) .and. + $ (acel(i,2) .eq. acel(k,2))) skip2 = .true. + if ((iangl(i,3) .eq. iangl(k,3)) .and. + $ (acel(i,3) .eq. acel(k,3))) skip3 = .true. + if (skip1 .and. skip2 .and. skip3) skip = .true. + if (skip) then + do l = k, nang-1 + iangl(l,1) = iangl(l+1,1) + acel(l,1) = acel(l+1,1) + iangl(l,2) = iangl(l+1,2) + acel(l,2) = acel(l+1,2) + iangl(l,3) = iangl(l+1,3) + acel(l,3) = acel(l+1,3) + end do + nang = nang - 1 + end if + end do + end do + do i = 1, nang-1 + do k = i+1, nang + skip = .false. + skip1 = .false. + skip2 = .false. + skip3 = .false. + if ((iangl(i,1) .eq. iangl(k,3)) .and. + $ (acel(i,1) .eq. acel(k,3))) skip1 = .true. + if ((iangl(i,2) .eq. iangl(k,2)) .and. + $ (acel(i,2) .eq. acel(k,2))) skip2 = .true. + if ((iangl(i,3) .eq. iangl(k,1)) .and. + $ (acel(i,3) .eq. acel(k,1))) skip3 = .true. + if (skip1 .and. skip2 .and. skip3) skip = .true. + if (skip) then + do l = k, nang-1 + iangl(l,1) = iangl(l+1,1) + acel(l,1) = acel(l+1,1) + iangl(l,2) = iangl(l+1,2) + acel(l,2) = acel(l+1,2) + iangl(l,3) = iangl(l+1,3) + acel(l,3) = acel(l+1,3) + end do + nang = nang - 1 + end if + end do + end do +c + ntor = 0 + do i = 1, nang + ia = iangl(i,1) + ib = iangl(i,2) + ic = iangl(i,3) + if (ncon(ic) .gt. 0) then + do j = 1, ncon(ic) + id = icon(ic,j) + if (id .ne. ib) then + ntor = ntor + 1 + itor(ntor,1) = ia + itor(ntor,2) = ib + itor(ntor,3) = ic + itor(ntor,4) = id + tcel(ntor,1) = acel(i,1) + tcel(ntor,2) = acel(i,2) + tcel(ntor,3) = acel(i,3) + tcel(ntor,4) = acel(i,3) + cel(ic,j) - 1 + end if + end do + end if +c + if (ncon(ia) .gt. 0) then + do j = 1, ncon(ia) + id = icon(ia,j) + if (id .ne. ib) then + ntor = ntor + 1 + itor(ntor,1) = id + itor(ntor,2) = ia + itor(ntor,3) = ib + itor(ntor,4) = ic + tcel(ntor,1) = acel(i,1) + cel(ia,j) - 1 + tcel(ntor,2) = acel(i,1) + tcel(ntor,3) = acel(i,2) + tcel(ntor,4) = acel(i,3) + end if + end do + end if + end do +c + do i = 1, ntor-1 + do k = i+1, ntor + skip = .false. + skip1 = .false. + skip2 = .false. + skip3 = .false. + skip4 = .false. + if ((itor(i,1) .eq. itor(k,1)) .and. + $ (tcel(i,1) .eq. tcel(k,1))) skip1 = .true. + if ((itor(i,2) .eq. itor(k,2)) .and. + $ (tcel(i,2) .eq. tcel(k,2))) skip2 = .true. + if ((itor(i,3) .eq. itor(k,3)) .and. + $ (tcel(i,3) .eq. tcel(k,3))) skip3 = .true. + if ((itor(i,4) .eq. itor(k,4)) .and. + $ (tcel(i,4) .eq. tcel(k,4))) skip4 = .true. + if (skip1 .and. skip2 .and. skip3 .and. skip4) skip = .true. + if (skip) then + do l = k, ntor-1 + itor(l,1) = itor(l+1,1) + tcel(l,1) = tcel(l+1,1) + itor(l,2) = itor(l+1,2) + tcel(l,2) = tcel(l+1,2) + itor(l,3) = itor(l+1,3) + tcel(l,3) = tcel(l+1,3) + itor(l,4) = itor(l+1,4) + tcel(l,4) = tcel(l+1,4) + end do + ntor = ntor - 1 + end if + end do + end do + do i = 1, ntor-1 + do k = i+1, ntor + skip = .false. + skip1 = .false. + skip2 = .false. + skip3 = .false. + skip4 = .false. + if ((itor(i,1) .eq. itor(k,4)) .and. + $ (tcel(i,1) .eq. tcel(k,4))) skip1 = .true. + if ((itor(i,2) .eq. itor(k,3)) .and. + $ (tcel(i,2) .eq. tcel(k,3))) skip2 = .true. + if ((itor(i,3) .eq. itor(k,2)) .and. + $ (tcel(i,3) .eq. tcel(k,2))) skip3 = .true. + if ((itor(i,4) .eq. itor(k,1)) .and. + $ (tcel(i,4) .eq. tcel(k,1))) skip4 = .true. + if (skip1 .and. skip2 .and. skip3 .and. skip4) skip = .true. + if (skip) then + do l = k, ntor-1 + itor(l,1) = itor(l+1,1) + tcel(l,1) = tcel(l+1,1) + itor(l,2) = itor(l+1,2) + tcel(l,2) = tcel(l+1,2) + itor(l,3) = itor(l+1,3) + tcel(l,3) = tcel(l+1,3) + itor(l,4) = itor(l+1,4) + tcel(l,4) = tcel(l+1,4) + end do + ntor = ntor - 1 + end if + end do + end do + +c +c PRINT SECTION +c +c +c print bonds +c + + write(6,'(///,a)')'Bonds inside unit cell' + do i = 1,nbnd + if (bcel(i,2) .eq. 1) then + write(6,200) ibond(i,1),ibond(i,2),bcel(i,1),bcel(i,2) + end if + end do + + write(6,'(//,a)')'Bonds along XX' + do i = 1,nbnd + if (bcel(i,2) .eq. 2) then + write(6,200)ibond(i,1),ibond(i,2),bcel(i,1),bcel(i,2) + end if + end do + write(6,'(/,a)')'Bonds along YY' + do i = 1,nbnd + if (bcel(i,2) .eq. 3) then + write(6,200)ibond(i,1),ibond(i,2),bcel(i,1),bcel(i,2) + end if + end do + write(6,'(/,a)')'Bonds along XY' + do i = 1,nbnd + if (bcel(i,2) .eq. 4) then + write(6,200)ibond(i,1),ibond(i,2),bcel(i,1),bcel(i,2) + end if + end do + 200 format (2i5,4x,2i3) + +c write(6,*)'Nang=',nang + + do i = 1, 2000 + celind(i,1) = 0 + celind(i,2) = 0 + celind(i,3) = 0 + celind(i,4) = 0 + celind(i,5) = 0 + celind(i,6) = 0 + celind(i,7) = 0 + celind(i,8) = 0 + end do + + nprim = 0 + nxx = 0 + nxy = 0 + nyy = 0 + nxxyy = 0 + nxxxy = 0 + nyyxy = 0 + do i = 1, nang + xx = .false. + xy = .false. + yy = .false. + do j = 1, 3 + if (acel(i,j) .eq. 2) xx = .true. + if (acel(i,j) .eq. 3) yy = .true. + if (acel(i,j) .eq. 4) xy = .true. + end do + + if (.not. xx .and. .not. yy .and. .not. xy) then + nprim = nprim + 1 + celind(nprim,1) = i + end if + + if (xx .and. .not. yy .and. .not. xy) then + nxx = nxx + 1 + celind(nxx,2) = i + end if + + if (yy .and. .not. xx .and. .not. xy) then + nyy = nyy + 1 + celind(nyy,3) = i + end if +c + if (xy .and. .not. xx .and. .not. yy) then + nxy = nxy + 1 + celind(nxy,4) = i + end if +c + if (xx .and. yy .and. .not. xy) then + nxxyy = nxxyy + 1 + celind(nxxyy,5) = i + end if +c + if (xx .and. .not. yy .and. xy) then + nxxxy = nxxxy + 1 + celind(nxxxy,6) = i + end if +c + if (.not. xx .and. yy .and. xy) then + nyyxy = nyyxy + 1 + celind(nyyxy,7) = i + end if + end do +c +c print angles +c + +c write(6,'(///,a)')'Angles inside unit cell' +c do i = 1, nprim +c indx = celind(i,1) +c write(6,201)(iangl(indx,k),k=1,3),(acel(indx,k),k=1,3) +c end do + + write(6,'(//,a)')'Angles along XX' + do i = 1, nxx + indx = celind(i,2) + write(6,201)(iangl(indx,k),k=1,3),(acel(indx,k),k=1,3) + end do + write(6,'(/,a)')'Angles along YY' + do i = 1, nyy + indx = celind(i,3) + write(6,201)(iangl(indx,k),k=1,3),(acel(indx,k),k=1,3) + end do + write(6,'(/,a)')'Angles along XY' + do i = 1, nxy + indx = celind(i,4) + write(6,201)(iangl(indx,k),k=1,3),(acel(indx,k),k=1,3) + end do + write(6,'(/,a)')'Angles along XX and YY' + do i = 1, nxxyy + indx = celind(i,5) + write(6,201)(iangl(indx,k),k=1,3),(acel(indx,k),k=1,3) + end do + write(6,'(/,a)')'Angles along XX and XY' + do i = 1, nxxxy + indx = celind(i,6) + write(6,201)(iangl(indx,k),k=1,3),(acel(indx,k),k=1,3) + end do + write(6,'(/,a)')'Angles along YY and XY' + do i = 1, nyyxy + indx = celind(i,7) + write(6,201)(iangl(indx,k),k=1,3),(acel(indx,k),k=1,3) + end do + + 201 format (3i5,4x,3i3) + + nang = nang - (nprim+nxx+nyy+nxy+nxxyy+nxxxy+nyyxy) + + if (nang .eq. 0) then + write(6,'(/,a)') 'All angles are accounted for' + else + write(6,202)'Angles missing: ',nang + write(6,'(/,a)')'You have to change the code, print all angles' + write(6,'(a)')'and see which ones are missing' + end if + 202 format (/,a16,i6) + +c write(6,*)'ntor=',ntor + + do i = 1, 2000 + celind(i,1) = 0 + celind(i,2) = 0 + celind(i,3) = 0 + celind(i,4) = 0 + celind(i,5) = 0 + celind(i,6) = 0 + celind(i,7) = 0 + celind(i,8) = 0 + end do + + nprim = 0 + nxx = 0 + nxy = 0 + nyy = 0 + nxxyy = 0 + nxxxy = 0 + nyyxy = 0 + nxxyyxy = 0 + do i = 1, ntor + xx = .false. + yy = .false. + xy = .false. + do j = 1, 4 + if (tcel(i,j) .eq. 2) xx = .true. + if (tcel(i,j) .eq. 3) yy = .true. + if (tcel(i,j) .eq. 4) xy = .true. + end do +c + if (.not. xx .and. .not. yy .and. .not. xy) then + nprim = nprim + 1 + celind(nprim,1) = i + end if +c + if (xx .and. .not. yy .and. .not. xy) then + nxx = nxx + 1 + celind(nxx,2) = i + end if + + if (yy .and. .not. xx .and. .not. xy) then + nyy = nyy + 1 + celind(nyy,3) = i + end if +c + if (xy .and. .not. xx .and. .not. yy) then + nxy = nxy + 1 + celind(nxy,4) = i + end if +c + if (xx .and. yy .and. .not. xy) then + nxxyy = nxxyy + 1 + celind(nxxyy,5) = i + end if +c + if (xx .and. .not. yy .and. xy) then + nxxxy = nxxxy + 1 + celind(nxxxy,6) = i + end if +c + if (.not. xx .and. yy .and. xy) then + nyyxy = nyyxy + 1 + celind(nyyxy,7) = i + end if +c + if (xx .and. yy .and. xy) then + nxxyyxy = nxxyyxy + 1 + celind(nxxyyxy,8) = i + end if + end do + +c +c print torsions +c + +c write(6,'(///,a)')'Torsions inside unit cell' +c do i = 1, nprim +c indx = celind(i,1) +c write(6,203)(itor(indx,k),k=1,4),(tcel(indx,k),k=1,4) +c end do + + write(6,'(//,a)')'Torsions along XX' + do i = 1, nxx + indx = celind(i,2) + write(6,203)(itor(indx,k),k=1,4),(tcel(indx,k),k=1,4) + end do + write(6,'(/,a)')'Torsions along YY' + do i = 1, nyy + indx = celind(i,3) + write(6,203)(itor(indx,k),k=1,4),(tcel(indx,k),k=1,4) + end do + write(6,'(/,a)')'Torsions along XY' + do i = 1, nxy + indx = celind(i,4) + write(6,203)(itor(indx,k),k=1,4),(tcel(indx,k),k=1,4) + end do + write(6,'(/,a)')'Torsions along XX and YY' + do i = 1, nxxyy + indx = celind(i,5) + write(6,203)(itor(indx,k),k=1,4),(tcel(indx,k),k=1,4) + end do + write(6,'(/,a)')'Torsions along XX and XY' + do i = 1, nxxxy + indx = celind(i,6) + write(6,203)(itor(indx,k),k=1,4),(tcel(indx,k),k=1,4) + end do + write(6,'(/,a)')'Torsions along YY and XY' + do i = 1, nyyxy + indx = celind(i,7) + write(6,203)(itor(indx,k),k=1,4),(tcel(indx,k),k=1,4) + end do + write(6,'(/,a)')'Torsions along XX and XY and XY' + do i = 1, nxxyyxy + indx = celind(i,8) + write(6,203)(itor(indx,k),k=1,4),(tcel(indx,k),k=1,4) + end do + + 203 format (4i5,4x,4i3) + + ntor = ntor - (nprim+nxx+nyy+nxy+nxxyy+nxxxy+nyyxy+nxxyyxy) + + if (ntor .eq. 0) then + write(6,'(//,a)') 'All torsions are accounted for' + else + write(6,204)'Torsions missing: ',ntor + write(6,'(/,a)')'You have to change the code, print all angles' + write(6,'(a)')'and see which ones are missing' + end if + 204 format (//,a18,i6) + + end diff --git a/charmm/toppar/silicates/code/patchfind.x b/charmm/toppar/silicates/code/patchfind.x new file mode 100755 index 0000000000000000000000000000000000000000..d3d36ff1aca92819631d1f94ec727b26664bb03c GIT binary patch literal 113019 zcmeFa3w%`7wLg9)nZN*v6EqQ29;2cXMNAYc5vY+cfMPTc!b6Q3AvlR4iOC!uErHk} zHK)h1>8)#J43NMydQe}QC z;MT=SE?)awiqbXCA?js*0?>B+8JC*m;?)kA7x`ixyj-Zn^{~^$%LAB~m3K{L`Tf^a zF1)(3yh>d*zOH)wwK5N+1#dHMFUFIshjo#!%W!4m^58lb7u(NvuukTW$Hjj);2MdG z{sxG297xYBW5jB7M5H?BdrhT*yt*Oj>V zFGJpxG~6j${!7L+Ry--nHMoy4pR>%n{YDuk>rNMCM14%fH3IMty%HV_<%|Qoz|3Ed z`(zt@7vS3f|Jlqx2>iPNKMa_9+YGo8@R!Z}j{vU#e4_~maeox>r$}f0f57!5VCso* zBd%uv>n2=@`-^~+P5hy_?*UA^CH`hy2LUIV`NMJV0&LaS0Qdyp@4>K$|98O2k2+mB zcqZHgcm!bD5aH#3#{quLgueuMGT_T`XZ}mLTBjwsHV8ObX#>0|H_7BLS*bw!ZNRtM zzY+O&1FkXa&qRJDV0Hr1n~eJkz<1)A@VmGk1^f)|l;><*YnLRsXg5P)F|&cc!3LAh zCxM@C(til~&j7v#9fkBx;(8JAUvMY<1LW_q<-Y;=AmCeYXa0ZU-Uavt6Tc4k6M+8> 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Q(M-1)*N+1 Q(M-1)*N+2 ..... QM*N +! ---------------------------------------- +! . . . . . +! . . . . . +! . . . . . +! ----------------------------------------- +! QN+1 QN+2 +! ----------------------------------------- +! Q1 Q2 Q3 Q4 Q5 .... QN +! ----------------------------------------- +! +! +! Based on the PBC for the surface one has to set the values of U (a-vector), +! V (b-vector) and Z (c-vector). The angle between U and V is theta. + +!PBC 7.3000 4.9100 109.6517 (P1) + +set U = 7.3000 +set V = 4.9100 +set Z = 50.000 + +set theta = 109.6517 + +set radian = 57.29577951308232088 +calc theta = @theta - 90.0 +calc theta = @theta/@radian + + +!unit cell translation parameters +set u1 @U +set u2 0.0 +set u3 0.0 + +calc v1 @V*sin(@theta) +calc v1 = -1*@v1 +calc v2 @V*cos(@theta) +set v3 0.0 + +set w1 0.0 +set w2 0.0 +set w3 @Z + +!Define translational vectors for images + +calc bigu1 = @n * @u1 +calc bigu2 = @n * @u2 +calc bigu3 = @n * @u3 + +calc bigv1 = @m * @v1 +calc bigv2 = @m * @v2 +calc bigv3 = @m * @v3 + +calc bigw1 = @k * @w1 +calc bigw2 = @k * @w2 +calc bigw3 = @k * @w3 + + diff --git a/charmm/toppar/silicates/patches.dat b/charmm/toppar/silicates/patches.dat new file mode 100644 index 00000000..db27c651 --- /dev/null +++ b/charmm/toppar/silicates/patches.dat @@ -0,0 +1,256 @@ + +Unit Cell Dimensions : + a = 7.3000 + b = 4.9100 + c = 44.5000 + alpha = 90.0000 + beta = 90.0000 + gamma = 109.6517 + + + +Bonds inside unit cell + 1 5 1 1 + 1 9 1 1 + 1 37 1 1 + 2 6 1 1 + 2 10 1 1 + 2 13 1 1 + 2 18 1 1 + 3 7 1 1 + 3 11 1 1 + 3 14 1 1 + 3 19 1 1 + 4 15 1 1 + 4 20 1 1 + 5 1 1 1 + 5 21 1 1 + 6 2 1 1 + 7 3 1 1 + 8 24 1 1 + 9 1 1 1 + 10 2 1 1 + 10 26 1 1 + 11 3 1 1 + 11 27 1 1 + 12 28 1 1 + 13 2 1 1 + 13 25 1 1 + 14 3 1 1 + 14 26 1 1 + 15 4 1 1 + 15 27 1 1 + 16 28 1 1 + 17 21 1 1 + 18 2 1 1 + 19 3 1 1 + 19 23 1 1 + 20 4 1 1 + 20 24 1 1 + 21 5 1 1 + 21 17 1 1 + 21 29 1 1 + 21 33 1 1 + 22 30 1 1 + 22 34 1 1 + 23 19 1 1 + 23 31 1 1 + 23 35 1 1 + 24 8 1 1 + 24 20 1 1 + 24 32 1 1 + 24 36 1 1 + 25 13 1 1 + 25 39 1 1 + 26 10 1 1 + 26 14 1 1 + 26 29 1 1 + 26 34 1 1 + 27 11 1 1 + 27 15 1 1 + 28 12 1 1 + 28 16 1 1 + 28 36 1 1 + 29 21 1 1 + 29 26 1 1 + 30 22 1 1 + 31 23 1 1 + 32 24 1 1 + 33 21 1 1 + 34 22 1 1 + 34 26 1 1 + 35 23 1 1 + 36 24 1 1 + 36 28 1 1 + 37 1 1 1 + 39 25 1 1 + + +Bonds along XX + 4 12 1 2 + 9 25 1 2 + 22 18 1 2 + 27 35 1 2 + +Bonds along YY + 1 17 1 3 + 8 4 1 3 + 23 7 1 3 + 25 33 1 3 + 30 27 1 3 + 31 28 1 3 + +Bonds along XY + 22 6 1 4 + + +Angles along XX + 1 9 25 1 1 2 + 4 12 28 1 2 2 + 9 25 13 1 2 2 + 9 25 39 1 2 2 + 11 27 35 1 1 2 + 15 4 12 1 1 2 + 15 27 35 1 1 2 + 20 4 12 1 1 2 + 22 18 2 1 2 2 + 27 35 23 1 2 2 + 30 22 18 1 1 2 + 34 22 18 1 1 2 + +Angles along YY + 1 17 21 1 3 3 + 5 1 17 1 1 3 + 8 4 15 1 3 3 + 8 4 20 1 3 3 + 9 1 17 1 1 3 + 13 25 33 1 1 3 + 19 23 7 1 1 3 + 22 30 27 1 1 3 + 23 31 28 1 1 3 + 23 7 3 1 3 3 + 24 8 4 1 1 3 + 25 33 21 1 3 3 + 30 27 11 1 3 3 + 30 27 15 1 3 3 + 31 23 7 1 1 3 + 31 28 12 1 3 3 + 31 28 16 1 3 3 + 31 28 36 1 3 3 + 35 23 7 1 1 3 + 37 1 17 1 1 3 + 39 25 33 1 1 3 + +Angles along XY + 22 6 2 1 4 4 + 30 22 6 1 1 4 + 34 22 6 1 1 4 + +Angles along XX and YY + +Angles along XX and XY + 9 25 33 1 2 4 + +Angles along YY and XY + 8 4 12 1 3 4 + 30 27 35 1 3 4 + +All angles are accounted for + + +Torsions along XX + 1 9 25 13 1 1 2 2 + 1 9 25 39 1 1 2 2 + 5 1 9 25 1 1 1 2 + 37 1 9 25 1 1 1 2 + 3 11 27 35 1 1 1 2 + 4 15 27 35 1 1 1 2 + 12 4 15 27 2 1 1 1 + 12 4 20 24 2 1 1 1 + 4 12 28 16 1 2 2 2 + 4 12 28 36 1 2 2 2 + 15 4 12 28 1 1 2 2 + 20 4 12 28 1 1 2 2 + 9 25 13 2 1 2 2 2 + 11 27 35 23 1 1 2 2 + 15 27 35 23 1 1 2 2 + 18 22 34 26 2 1 1 1 + 22 18 2 6 1 2 2 2 + 22 18 2 10 1 2 2 2 + 22 18 2 13 1 2 2 2 + 30 22 18 2 1 1 2 2 + 34 22 18 2 1 1 2 2 + 27 35 23 19 1 2 2 2 + 27 35 23 31 1 2 2 2 + +Torsions along YY + 17 1 5 21 3 1 1 1 + 1 17 21 5 1 3 3 3 + 1 17 21 29 1 3 3 3 + 1 17 21 33 1 3 3 3 + 5 1 17 21 1 1 3 3 + 9 1 17 21 1 1 3 3 + 37 1 17 21 1 1 3 3 + 2 13 25 33 1 1 1 3 + 3 19 23 7 1 1 1 3 + 4 8 24 20 3 1 1 1 + 4 8 24 32 3 1 1 1 + 4 8 24 36 3 1 1 1 + 8 4 15 27 1 3 3 3 + 24 8 4 15 1 1 3 3 + 8 4 20 24 1 3 3 3 + 24 8 4 20 1 1 3 3 + 13 25 33 21 1 1 3 3 + 19 23 31 28 1 1 1 3 + 19 23 7 3 1 1 3 3 + 22 30 27 11 1 1 3 3 + 22 30 27 15 1 1 3 3 + 34 22 30 27 1 1 1 3 + 23 31 28 12 1 1 3 3 + 23 31 28 16 1 1 3 3 + 23 31 28 36 1 1 3 3 + 23 7 3 11 1 3 3 3 + 23 7 3 14 1 3 3 3 + 23 7 3 19 1 3 3 3 + 25 33 21 5 1 3 3 3 + 25 33 21 17 1 3 3 3 + 25 33 21 29 1 3 3 3 + 30 27 11 3 1 3 3 3 + 30 27 15 4 1 3 3 3 + 28 31 23 35 3 1 1 1 + 31 23 7 3 1 1 3 3 + 28 31 23 7 3 1 1 3 + 31 28 36 24 1 3 3 3 + 35 23 7 3 1 1 3 3 + 39 25 33 21 1 1 3 3 + +Torsions along XY + 6 22 34 26 4 1 1 1 + 22 6 2 10 1 4 4 4 + 22 6 2 13 1 4 4 4 + 22 6 2 18 1 4 4 4 + 30 22 6 2 1 1 4 4 + 34 22 6 2 1 1 4 4 + +Torsions along XX and YY + 17 1 9 25 3 1 1 2 + 18 22 30 27 2 1 1 3 + +Torsions along XX and XY + 1 9 25 33 1 1 2 4 + 9 25 33 21 1 2 4 4 + 6 22 18 2 4 1 2 2 + 18 22 6 2 2 1 4 4 + 27 35 23 7 1 2 2 4 + +Torsions along YY and XY + 8 4 12 28 1 3 4 4 + 24 8 4 12 1 1 3 4 + 22 30 27 35 1 1 3 4 + 6 22 30 27 4 1 1 3 + 30 27 35 23 1 3 4 4 + +Torsions along XX and XY and XY + + +All torsions are accounted for diff --git a/charmm/toppar/silicates/quartz_init.pdb b/charmm/toppar/silicates/quartz_init.pdb new file mode 100644 index 00000000..2e911247 --- /dev/null +++ b/charmm/toppar/silicates/quartz_init.pdb @@ -0,0 +1,85 @@ +REMARK 4 quar COMPLIES WITH FORMAT V. 2.0 +HETATM 1 SI1 Q011 1 4.118 4.481 -12.830 1.00 0.00 SI3- +HETATM 2 SI2 Q011 1 0.121 3.053 -9.489 1.00 0.00 SI +HETATM 3 SI3 Q011 1 3.423 1.626 -6.147 1.00 0.00 SI +HETATM 4 SI4 Q011 1 6.726 0.198 -2.806 1.00 0.00 SI2- +HETATM 5 O5 Q011 1 3.980 2.880 -12.662 1.00 0.00 O +HETATM 6 O6 Q011 1 -0.018 1.453 -9.320 1.00 0.00 O1- +HETATM 7 O7 Q011 1 3.285 0.025 -5.979 1.00 0.00 O1- +HETATM 8 O8 Q011 1 4.936 3.222 -2.638 1.00 0.00 O1- +HETATM 9 O9 Q011 1 5.654 4.910 -12.703 1.00 0.00 O2- +HETATM 10 O10 Q011 1 1.656 3.483 -9.362 1.00 0.00 O +HETATM 11 O11 Q011 1 4.959 2.055 -6.020 1.00 0.00 O +HETATM 12 O12 Q011 1 0.961 0.628 -2.679 1.00 0.00 O1- +HETATM 13 O13 Q011 1 -0.396 3.385 -10.982 1.00 0.00 O +HETATM 14 O14 Q011 1 2.906 1.958 -7.641 1.00 0.00 O +HETATM 15 O15 Q011 1 6.209 0.530 -4.300 1.00 0.00 O +HETATM 16 O16 Q011 1 2.211 -0.897 -0.959 1.00 0.00 O2- +HETATM 17 O17 Q011 1 4.828 0.576 -11.756 1.00 0.00 O1- +HETATM 18 O18 Q011 1 -0.821 3.772 -8.414 1.00 0.00 O1- +HETATM 19 O19 Q011 1 2.481 2.345 -5.073 1.00 0.00 O +HETATM 20 O20 Q011 1 5.784 0.917 -1.732 1.00 0.00 O +HETATM 21 SI21 Q011 1 3.707 1.727 -11.588 1.00 0.00 SI +HETATM 22 SI22 Q011 1 5.358 4.923 -8.246 1.00 0.00 SI4- +HETATM 23 SI23 Q011 1 1.360 3.496 -4.905 1.00 0.00 SI1- +HETATM 24 SI24 Q011 1 4.663 2.068 -1.564 1.00 0.00 SI +HETATM 25 SI25 Q011 1 -0.198 4.393 -12.209 1.00 0.00 SI3- +HETATM 26 SI26 Q011 1 3.105 2.966 -8.867 1.00 0.00 SI +HETATM 27 SI27 Q011 1 6.407 1.538 -5.526 1.00 0.00 SI2- +HETATM 28 SI28 Q011 1 2.410 0.110 -2.185 1.00 0.00 SI2- +HETATM 29 O29 Q011 1 3.896 2.311 -10.094 1.00 0.00 O +HETATM 30 O30 Q011 1 5.547 5.508 -6.753 1.00 0.00 O2- +HETATM 31 O31 Q011 1 1.550 4.080 -3.411 1.00 0.00 O1- +HETATM 32 O32 Q011 1 4.852 2.653 -0.070 1.00 0.00 O1- +HETATM 33 O33 Q011 1 2.246 1.087 -11.715 1.00 0.00 O1- +HETATM 34 O34 Q011 1 3.898 4.283 -8.373 1.00 0.00 O1- +HETATM 35 O35 Q011 1 -0.100 2.856 -5.032 1.00 0.00 O1- +HETATM 36 O36 Q011 1 3.203 1.428 -1.691 1.00 0.00 O +HETATM 37 H37 Q011 1 3.601 4.813 -14.324 1.00 0.00 X +HETATM 38 H38 Q011 1 2.728 -1.229 0.535 1.00 0.00 X +HETATM 39 H39 Q011 1 0.594 3.739 -13.435 1.00 0.00 X +HETATM 40 H40 Q011 1 4.061 3.307 1.156 1.00 0.00 X +TER 41 Q011 1 +CONECT 1 5 37 +CONECT 2 6 10 13 18 +CONECT 3 7 11 14 19 +CONECT 4 15 20 +CONECT 5 1 21 +CONECT 6 2 +CONECT 7 3 +CONECT 8 24 +CONECT 10 2 26 +CONECT 11 3 27 +CONECT 12 28 +CONECT 13 2 25 +CONECT 14 3 26 +CONECT 15 4 27 +CONECT 16 38 +CONECT 17 21 +CONECT 18 2 +CONECT 19 3 23 +CONECT 20 4 24 +CONECT 21 5 17 29 33 +CONECT 23 19 31 35 +CONECT 24 8 20 32 36 +CONECT 25 13 39 +CONECT 26 10 14 29 34 +CONECT 27 11 15 +CONECT 28 12 36 +CONECT 29 21 26 +CONECT 31 23 +CONECT 32 24 40 +CONECT 33 21 +CONECT 34 26 +CONECT 35 23 +CONECT 36 24 28 +CONECT 37 1 +CONECT 38 16 +CONECT 39 25 +CONECT 40 32 +END + + + + + diff --git a/charmm/toppar/silicates/supp_mat_oct05.tar b/charmm/toppar/silicates/supp_mat_oct05.tar new file mode 100644 index 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zZQN<$#WXYQPJ|CklLy}E_4%*Bkq-He6^N#xq`7DI44~{9tN(GaRV5x)7hnbA;B^>olGueoVAjuIXvGqKis?7%mIQk?h~wpU=z}d|002$Kc-n&{@E)9l@sqJH^?nkH2;Aj{g0I zKfQ&`(yO<)!|qz1zOle*0objB{kwj0l4%G2{F%}YQ?CcAp5MU6LN>qvaH|UWthO0;GMs@XuAXdEoIn8@=#BCahAQN%hQrS(-EedBh!VqSN;mrPer0u) z{oi=HQIStZzm9P7V=#8{Xu}52>V>@Y>GxiZ#AAdq-GMul;7S^e7(*O&4f zAmsrw+$ozf9-IPWPP8cWsnvU={qu=7XFQ4PYt4DSgwaCsJvKEjtGK+Tr00gYY{%v! zp>8|txoIx1Iqms2?6zeK50K-Q&GMcbX7`n!f#VTzh_dL8hS_cBJvYp5ecob&YxT0j ze5b>sFqGZh;1{{Rz;hK2fw=pi>efPZrOXZIfV%Ygnr!cTN!>i$M4Bz$Af50+R$L2}}~0Brr)}lE5T^Ndl7uCJ9Uum?SVsV3NQjfk^_B1SSbg u5||_~Nnnz|B!Ni+lLRISOcIzRFiBvNz$Af50+R$L2}}~0B=E * GENERATION OF CRYSTAL SLAB FOLLOWED BY MINIMIZATION + RDTITL> * THE SURFACE IS GENERATED BY CREATING THE APPROPRIATE + RDTITL> * IMAGES OF THE CENTRAL UNITCELL USING THE IMAGE + RDTITL> * FACILITY OF CHARMM + RDTITL> + + CHARMM> + + CHARMM> stream params.str + VOPEN> Attempting to open::params.str:: + OPNLGU> Unit 99 opened for READONLY access to params.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * PARAMETERS FOR SIMULATION OF ON CRYSTAL SURFACES + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> ! Generation of n cells along U and m cells along V + CHARMM> ! Used to specify the surface size from the primitive cell + CHARMM> ! k is the number of replicas along Z + CHARMM> + + CHARMM> set n 5 + Parameter: N <- "5" + + CHARMM> set m 8 + Parameter: M <- "8" + + CHARMM> set k 1 + Parameter: K <- "1" + + CHARMM> + + CHARMM> calc nm = @n * @m * @k + Parameter: N -> "5" + Parameter: M -> "8" + Parameter: K -> "1" +Evaluating: 5*8*1 + Parameter: NM <- "40" + + CHARMM> + + CHARMM> ! + CHARMM> ! U |__2| V + CHARMM> !|__1|__2| 1-->2 |__1| 1-->2 + CHARMM> ! + CHARMM> ! + CHARMM> ! Q(M-1)*N+1 Q(M-1)*N+2 ..... QM*N + CHARMM> ! ---------------------------------------- + CHARMM> ! . . . . . + CHARMM> ! . . . . . + CHARMM> ! . . . . . + CHARMM> ! ----------------------------------------- + CHARMM> ! QN+1 QN+2 + CHARMM> ! ----------------------------------------- + CHARMM> ! Q1 Q2 Q3 Q4 Q5 .... QN + CHARMM> ! ----------------------------------------- + CHARMM> ! + CHARMM> ! + CHARMM> ! Based on the PBC for the surface one has to set the values of U (a-vector), + CHARMM> ! V (b-vector) and Z (c-vector). The angle between U and V is theta. + CHARMM> + + CHARMM> !PBC 7.3000 4.9100 109.6517 (P1) + CHARMM> + + CHARMM> set U = 7.3000 + Parameter: U <- "7.3000" + + CHARMM> set V = 4.9100 + Parameter: V <- "4.9100" + + CHARMM> set Z = 50.000 + Parameter: Z <- "50.000" + + CHARMM> + + CHARMM> set theta = 109.6517 + Parameter: THETA <- "109.6517" + + CHARMM> + + CHARMM> set radian = 57.29577951308232088 + Parameter: RADIAN <- "57.29577951308232088" + + CHARMM> calc theta = @theta - 90.0 + Parameter: THETA -> "109.6517" +Evaluating: 109.6517-90.0 + Parameter: THETA <- "19.6517" + + CHARMM> calc theta = @theta/@radian + Parameter: THETA -> "19.6517" + Parameter: RADIAN -> "57.29577951308232088" +Evaluating: 19.6517/57.29577951308232088 + Parameter: THETA <- "0.342987" + + CHARMM> + + CHARMM> + + CHARMM> !unit cell translation parameters + CHARMM> set u1 @U + Parameter: U -> "7.3000" + Parameter: U1 <- "7.3000" + + CHARMM> set u2 0.0 + Parameter: U2 <- "0.0" + + CHARMM> set u3 0.0 + Parameter: U3 <- "0.0" + + CHARMM> + + CHARMM> calc v1 @V*sin(@theta) + Parameter: V -> "4.9100" + Parameter: THETA -> "0.342987" +Evaluating: 4.9100*SIN(0.342987) + Parameter: V1 <- "1.65124" + + CHARMM> calc v1 = -1*@v1 + Parameter: V1 -> "1.65124" +Evaluating: -1*1.65124 + Parameter: V1 <- "-1.65124" + + CHARMM> calc v2 @V*cos(@theta) + Parameter: V -> "4.9100" + Parameter: THETA -> "0.342987" +Evaluating: 4.9100*COS(0.342987) + Parameter: V2 <- "4.62401" + + CHARMM> set v3 0.0 + Parameter: V3 <- "0.0" + + CHARMM> + + CHARMM> set w1 0.0 + Parameter: W1 <- "0.0" + + CHARMM> set w2 0.0 + Parameter: W2 <- "0.0" + + CHARMM> set w3 @Z + Parameter: Z -> "50.000" + Parameter: W3 <- "50.000" + + CHARMM> + + CHARMM> !Define translational vectors for images + CHARMM> + + CHARMM> calc bigu1 = @n * @u1 + Parameter: N -> "5" + Parameter: U1 -> "7.3000" +Evaluating: 5*7.3000 + Parameter: BIGU1 <- "36.5" + + CHARMM> calc bigu2 = @n * @u2 + Parameter: N -> "5" + Parameter: U2 -> "0.0" +Evaluating: 5*0.0 + Parameter: BIGU2 <- "0" + + CHARMM> calc bigu3 = @n * @u3 + Parameter: N -> "5" + Parameter: U3 -> "0.0" +Evaluating: 5*0.0 + Parameter: BIGU3 <- "0" + + CHARMM> + + CHARMM> calc bigv1 = @m * @v1 + Parameter: M -> "8" + Parameter: V1 -> "-1.65124" +Evaluating: 8*-1.65124 + Parameter: BIGV1 <- "-13.2099" + + CHARMM> calc bigv2 = @m * @v2 + Parameter: M -> "8" + Parameter: V2 -> "4.62401" +Evaluating: 8*4.62401 + Parameter: BIGV2 <- "36.9921" + + CHARMM> calc bigv3 = @m * @v3 + Parameter: M -> "8" + Parameter: V3 -> "0.0" +Evaluating: 8*0.0 + Parameter: BIGV3 <- "0" + + CHARMM> + + CHARMM> calc bigw1 = @k * @w1 + Parameter: K -> "1" + Parameter: W1 -> "0.0" +Evaluating: 1*0.0 + Parameter: BIGW1 <- "0" + + CHARMM> calc bigw2 = @k * @w2 + Parameter: K -> "1" + Parameter: W2 -> "0.0" +Evaluating: 1*0.0 + Parameter: BIGW2 <- "0" + + CHARMM> calc bigw3 = @k * @w3 + Parameter: K -> "1" + Parameter: W3 -> "50.000" +Evaluating: 1*50.000 + Parameter: BIGW3 <- "50" + + CHARMM> + + CHARMM> + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> + + CHARMM> bomlev -2 + + CHARMM> + + CHARMM> ! 3: cutim + CHARMM> ! 4: cutnb + CHARMM> ! 5: ctonnb + CHARMM> ! 6: ctofnb + CHARMM> set 3 14.0 ! cutim + Parameter: 3 <- "14.0" + + CHARMM> set 4 14.0 ! cutnb + Parameter: 4 <- "14.0" + + CHARMM> set 5 10.0 ! ctonnb + Parameter: 5 <- "10.0" + + CHARMM> set 6 12.0 ! ctofnb + Parameter: 6 <- "12.0" + + CHARMM> + + CHARMM> + + CHARMM> ! Read in the topology file + CHARMM> open unit 20 read card name ./toppar/top_quartz_011.inp + VOPEN> Attempting to open::./toppar/top_quartz_011.inp:: + OPNLGU> Unit 20 opened for READONLY access to ./toppar/top_quartz_011.inp + + CHARMM> read rtf card unit 20 + MAINIO> Residue topology file being read from unit 20. + TITLE> * <<<<<>>>>> + TITLE> * ALEXANDER D. MACKERELL JR. AND MOUHSINE TAZI + TITLE> * NOVEMBER 2001 + TITLE> *ALL COMMENTS TO ADM JR. EMAIL: ALEX::OUTERBANKS.UMARYLAND.EDU + TITLE> * TELEPHONE: 410-706-7442 + TITLE> * + + CHARMM> close unit 20 + VCLOSE: Closing unit 20 with status "KEEP" + + CHARMM> + + CHARMM> ! Read in the parameter file + CHARMM> open unit 20 read card name ./toppar/par_silicates.inp + VOPEN> Attempting to open::./toppar/par_silicates.inp:: + OPNLGU> Unit 20 opened for READONLY access to ./toppar/par_silicates.inp + + CHARMM> read para card unit 20 + + PARAMETER FILE BEING READ FROM UNIT 20 + TITLE> * <<<<<>>>>> + TITLE> * ALEXANDER D. MACKERELL JR. AND MOUHSINE TAZI + TITLE> * NOVEMBER 2001 + TITLE> *ALL COMMENTS TO ADM JR. EMAIL: ALEX::OUTERBANKS.UMARYLAND.EDU + TITLE> * TELEPHONE: 410-706-7442 + TITLE> * + PARRDR> WARNING: ATOMS IN HBOND S N% 0.00000 3.00000 DONT EXIST + PARRDR> WARNING: ATOMS IN HBOND S O* 0.00000 2.90000 DONT EXIST + PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. + + CHARMM> close unit 20 + VCLOSE: Closing unit 20 with status "KEEP" + + CHARMM> + + CHARMM> ! Read in PSF and CRD file + CHARMM> open read form unit 30 name geom_ini.psf + VOPEN> Attempting to open::geom_ini.psf:: + OPNLGU> Unit 30 opened for READONLY access to geom_ini.psf + + CHARMM> read psf card unit 30 + MAINIO> Protein structure file being read from unit 30. + TITLE> * PSF + TITLE> * DATE: 7/13/ 5 13:50: 3 CREATED BY USER: mbdtslo + TITLE> * + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1926 Number of angles = 3555 + Number of dihedrals = 4908 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> open unit 30 read form name geom_ini.crd + OPNLGU> Unit already open. The old file will be closed first. + VCLOSE: Closing unit 30 with status "KEEP" + VOPEN> Attempting to open::geom_ini.crd:: + OPNLGU> Unit 30 opened for READONLY access to geom_ini.crd + + CHARMM> read coor cards unit 30 + SPATIAL COORDINATES BEING READ FROM UNIT 30 + TITLE> * COORDINATES + TITLE> * DATE: 7/13/ 5 13:50: 3 CREATED BY USER: MBDTSLO + TITLE> * + + CHARMM> close unit 30 + VCLOSE: Closing unit 30 with status "KEEP" + + CHARMM> + + CHARMM> ! Create images now + CHARMM> open unit 8 read card name crystal.img + VOPEN> Attempting to open::crystal.img:: + OPNLGU> Unit 8 opened for READONLY access to crystal.img + + CHARMM> read imag print init unit 8 + TITLE> * IMAGE GENERATION + TITLE> * + + READING IMAGE FILE FROM UNIT 8 + + + IMREAD> scale 1 1 1 + + IMREAD> + + IMREAD> IMAGE qi1 + + IMREAD> TRANslate @bigu1 @bigu2 @bigu3 + Parameter: BIGU1 -> "36.5" + Parameter: BIGU2 -> "0" + Parameter: BIGU3 -> "0" + TRANSLATION VECTOR 36.500000 0.000000 0.000000 + + IMREAD> + + IMREAD> IMAGE qi2 + + TRANSFORMATION 1 NAME: QI1 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 36.500000 0.000000 0.000000 + + IMREAD> DEFIne INVErse qi1 + + IMREAD> + + IMREAD> IMAGE qi3 + + TRANSFORMATION 2 NAME: QI2 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -36.500000 0.000000 0.000000 + + IMREAD> TRANslate @bigv1 @bigv2 @bigv3 + Parameter: BIGV1 -> "-13.2099" + Parameter: BIGV2 -> "36.9921" + Parameter: BIGV3 -> "0" + TRANSLATION VECTOR -13.209900 36.992100 0.000000 + + IMREAD> + + IMREAD> IMAGE qi4 + + TRANSFORMATION 3 NAME: QI3 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -13.209900 36.992100 0.000000 + + IMREAD> DEFIne INVErse qi3 + + IMREAD> + + IMREAD> IMAGE qi5 + + TRANSFORMATION 4 NAME: QI4 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 13.209900-36.992100 0.000000 + + IMREAD> DEFIne qi1 qi3 + + IMREAD> + + IMREAD> IMAGE qi6 + + TRANSFORMATION 5 NAME: QI5 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 23.290100 36.992100 0.000000 + + IMREAD> DEFIne INVErse qi5 + + IMREAD> + + IMREAD> IMAGE qi7 + + TRANSFORMATION 6 NAME: QI6 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -23.290100-36.992100 0.000000 + + IMREAD> DEFIne qi1 qi4 + + IMREAD> + + IMREAD> IMAGE qi8 + + TRANSFORMATION 7 NAME: QI7 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 49.709900-36.992100 0.000000 + + IMREAD> DEFIne INVErse qi7 + + IMREAD> + + IMREAD> IMAGE qi9 + + TRANSFORMATION 8 NAME: QI8 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -49.709900 36.992100 0.000000 + + IMREAD> TRANslate @bigw1 @bigw2 @bigw3 + Parameter: BIGW1 -> "0" + Parameter: BIGW2 -> "0" + Parameter: BIGW3 -> "50" + TRANSLATION VECTOR 0.000000 0.000000 50.000000 + + IMREAD> + + IMREAD> IMAGE qi10 + + TRANSFORMATION 9 NAME: QI9 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 0.000000 0.000000 50.000000 + + IMREAD> DEFIne INVErse qi9 + + IMREAD> + + IMREAD> IMAGE qi11 + + TRANSFORMATION 10 NAME: QI10 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 0.000000 0.000000-50.000000 + + IMREAD> DEFIne qi1 qi9 + + IMREAD> + + IMREAD> IMAGE qi12 + + TRANSFORMATION 11 NAME: QI11 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 36.500000 0.000000 50.000000 + + IMREAD> DEFIne INVErse qi11 + + IMREAD> + + IMREAD> IMAGE qi13 + + TRANSFORMATION 12 NAME: QI12 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -36.500000 0.000000-50.000000 + + IMREAD> DEFIne qi2 qi9 + + IMREAD> + + IMREAD> IMAGE qi14 + + TRANSFORMATION 13 NAME: QI13 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -36.500000 0.000000 50.000000 + + IMREAD> DEFIne INVErse qi13 + + IMREAD> + + IMREAD> IMAGE qi15 + + TRANSFORMATION 14 NAME: QI14 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 36.500000 0.000000-50.000000 + + IMREAD> DEFIne qi3 qi9 + + IMREAD> + + IMREAD> IMAGE qi16 + + TRANSFORMATION 15 NAME: QI15 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -13.209900 36.992100 50.000000 + + IMREAD> DEFIne INVErse qi15 + + IMREAD> + + IMREAD> IMAGE qi17 + + TRANSFORMATION 16 NAME: QI16 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 13.209900-36.992100-50.000000 + + IMREAD> DEFIne qi4 qi9 + + IMREAD> + + IMREAD> IMAGE qi18 + + TRANSFORMATION 17 NAME: QI17 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 13.209900-36.992100 50.000000 + + IMREAD> DEFIne INVErse qi17 + + IMREAD> + + IMREAD> IMAGE qi19 + + TRANSFORMATION 18 NAME: QI18 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -13.209900 36.992100-50.000000 + + IMREAD> DEFIne qi5 qi9 + + IMREAD> + + IMREAD> IMAGE qi20 + + TRANSFORMATION 19 NAME: QI19 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 23.290100 36.992100 50.000000 + + IMREAD> DEFIne INVErse qi19 + + IMREAD> + + IMREAD> IMAGE qi21 + + TRANSFORMATION 20 NAME: QI20 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -23.290100-36.992100-50.000000 + + IMREAD> DEFIne qi8 qi9 + + IMREAD> + + IMREAD> IMAGE qi22 + + TRANSFORMATION 21 NAME: QI21 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -49.709900 36.992100 50.000000 + + IMREAD> DEFIne INVErse qi21 + + IMREAD> + + IMREAD> IMAGE qi23 + + TRANSFORMATION 22 NAME: QI22 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 49.709900-36.992100-50.000000 + + IMREAD> DEFIne qi6 qi9 + + IMREAD> + + IMREAD> IMAGE qi24 + + TRANSFORMATION 23 NAME: QI23 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -23.290100-36.992100 50.000000 + + IMREAD> DEFIne INVErse qi23 + + IMREAD> + + IMREAD> IMAGE qi25 + + TRANSFORMATION 24 NAME: QI24 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 23.290100 36.992100-50.000000 + + IMREAD> DEFIne qi7 qi9 + + IMREAD> + + IMREAD> IMAGE qi26 + + TRANSFORMATION 25 NAME: QI25 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 49.709900-36.992100 50.000000 + + IMREAD> DEFIne INVErse qi25 + + IMREAD> + + IMREAD> end + + 26 TRANSFORMATIONS HAVE BEEN READ + + THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET + + CHARMM> close unit 8 + VCLOSE: Closing unit 8 with status "KEEP" + + CHARMM> + + CHARMM> ! Manipulation of images + CHARMM> update inbf 0 ihbf 0 imgfrq 100 cutim @3 + Parameter: 3 -> "14.0" + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 920 23 23 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 440 11 11 0.00 + 7 QI7 has 240 6 6 0.00 + 9 QI9 has 0 0 0 35.07 + 11 QI11 has 0 0 0 35.07 + 13 QI13 has 0 0 0 35.07 + 15 QI15 has 0 0 0 35.07 + 17 QI17 has 0 0 0 35.07 + 19 QI19 has 0 0 0 35.07 + 21 QI21 has 0 0 0 35.10 + 23 QI23 has 0 0 0 35.07 + 25 QI25 has 0 0 0 35.10 + Total of 4000 atoms and 100 groups and 100 residues were included + + + CHARMM> stream image_patch.str + VOPEN> Attempting to open::image_patch.str:: + OPNLGU> Unit 99 opened for READONLY access to image_patch.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> + RDTITL> No title read. + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> update inbf 0 ihbf 0 imgfrq 011 cutim @3 + Parameter: 3 -> "14.0" + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 920 23 23 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 440 11 11 0.00 + 7 QI7 has 240 6 6 0.00 + 9 QI9 has 0 0 0 35.07 + 11 QI11 has 0 0 0 35.07 + 13 QI13 has 0 0 0 35.07 + 15 QI15 has 0 0 0 35.07 + 17 QI17 has 0 0 0 35.07 + 19 QI19 has 0 0 0 35.07 + 21 QI21 has 0 0 0 35.10 + 23 QI23 has 0 0 0 35.07 + 25 QI25 has 0 0 0 35.10 + Total of 4000 atoms and 100 groups and 100 residues were included + + + CHARMM> + + CHARMM> ! Now apply patches around the perimeter + CHARMM> ! + CHARMM> + + CHARMM> !In x direction + CHARMM> ! + CHARMM> ! py | iy + CHARMM> ! prim px | ix image + CHARMM> ! + CHARMM> + + CHARMM> set counn 1 + Parameter: COUNN <- "1" + + CHARMM> label loop2 + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "1" + Parameter: N -> "5" +Evaluating: 1*5 + Parameter: PX <- "5" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "5" + Parameter: N -> "5" +Evaluating: 5-5+1 + Parameter: IX <- "1" + + CHARMM> calc py = @px + @n + Parameter: PX -> "5" + Parameter: N -> "5" +Evaluating: 5+5 + Parameter: PY <- "10" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "10" + Parameter: N -> "5" +Evaluating: 10-5+1 + Parameter: IY <- "6" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "5" + Parameter: IX -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 4 12 23 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "5" + Parameter: IY -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 5 19 29 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "10" + Parameter: IY -> "6" + Parameter: PX -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 5 19 29 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "10" + Parameter: PX -> "5" + Parameter: IX -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 5 19 31 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "5" + Parameter: IX -> "1" + Parameter: IY -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 5 21 36 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "5" + Parameter: PY -> "10" + Parameter: IY -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 5 21 41 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "1" +Evaluating: 1+1 + Parameter: COUNN <- "2" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "2" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "2" + Parameter: N -> "5" +Evaluating: 2*5 + Parameter: PX <- "10" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "10" + Parameter: N -> "5" +Evaluating: 10-5+1 + Parameter: IX <- "6" + + CHARMM> calc py = @px + @n + Parameter: PX -> "10" + Parameter: N -> "5" +Evaluating: 10+5 + Parameter: PY <- "15" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "15" + Parameter: N -> "5" +Evaluating: 15-5+1 + Parameter: IY <- "11" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "10" + Parameter: IX -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 9 33 64 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "10" + Parameter: IY -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 10 40 70 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "15" + Parameter: IY -> "11" + Parameter: PX -> "10" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 10 40 70 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "15" + Parameter: PX -> "10" + Parameter: IX -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 10 40 72 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "10" + Parameter: IX -> "6" + Parameter: IY -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 10 42 77 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "10" + Parameter: PY -> "15" + Parameter: IY -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 10 42 82 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "2" +Evaluating: 2+1 + Parameter: COUNN <- "3" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "3" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "3" + Parameter: N -> "5" +Evaluating: 3*5 + Parameter: PX <- "15" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "15" + Parameter: N -> "5" +Evaluating: 15-5+1 + Parameter: IX <- "11" + + CHARMM> calc py = @px + @n + Parameter: PX -> "15" + Parameter: N -> "5" +Evaluating: 15+5 + Parameter: PY <- "20" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "20" + Parameter: N -> "5" +Evaluating: 20-5+1 + Parameter: IY <- "16" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "15" + Parameter: IX -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 14 54 105 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "15" + Parameter: IY -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 15 61 111 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "20" + Parameter: IY -> "16" + Parameter: PX -> "15" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 15 61 111 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "20" + Parameter: PX -> "15" + Parameter: IX -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 15 61 113 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "15" + Parameter: IX -> "11" + Parameter: IY -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 15 63 118 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "15" + Parameter: PY -> "20" + Parameter: IY -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 15 63 123 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "3" +Evaluating: 3+1 + Parameter: COUNN <- "4" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "4" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "4" + Parameter: N -> "5" +Evaluating: 4*5 + Parameter: PX <- "20" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "20" + Parameter: N -> "5" +Evaluating: 20-5+1 + Parameter: IX <- "16" + + CHARMM> calc py = @px + @n + Parameter: PX -> "20" + Parameter: N -> "5" +Evaluating: 20+5 + Parameter: PY <- "25" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "25" + Parameter: N -> "5" +Evaluating: 25-5+1 + Parameter: IY <- "21" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "20" + Parameter: IX -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 19 75 146 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "20" + Parameter: IY -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 20 82 152 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "25" + Parameter: IY -> "21" + Parameter: PX -> "20" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 20 82 152 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "25" + Parameter: PX -> "20" + Parameter: IX -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 20 82 154 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "20" + Parameter: IX -> "16" + Parameter: IY -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 20 84 159 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "20" + Parameter: PY -> "25" + Parameter: IY -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 20 84 164 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "4" +Evaluating: 4+1 + Parameter: COUNN <- "5" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "5" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "5" + Parameter: N -> "5" +Evaluating: 5*5 + Parameter: PX <- "25" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "25" + Parameter: N -> "5" +Evaluating: 25-5+1 + Parameter: IX <- "21" + + CHARMM> calc py = @px + @n + Parameter: PX -> "25" + Parameter: N -> "5" +Evaluating: 25+5 + Parameter: PY <- "30" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "30" + Parameter: N -> "5" +Evaluating: 30-5+1 + Parameter: IY <- "26" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "25" + Parameter: IX -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 24 96 187 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "25" + Parameter: IY -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 25 103 193 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "30" + Parameter: IY -> "26" + Parameter: PX -> "25" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 25 103 193 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "30" + Parameter: PX -> "25" + Parameter: IX -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 25 103 195 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "25" + Parameter: IX -> "21" + Parameter: IY -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 25 105 200 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "25" + Parameter: PY -> "30" + Parameter: IY -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 25 105 205 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "5" +Evaluating: 5+1 + Parameter: COUNN <- "6" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "6" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "6" + Parameter: N -> "5" +Evaluating: 6*5 + Parameter: PX <- "30" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "30" + Parameter: N -> "5" +Evaluating: 30-5+1 + Parameter: IX <- "26" + + CHARMM> calc py = @px + @n + Parameter: PX -> "30" + Parameter: N -> "5" +Evaluating: 30+5 + Parameter: PY <- "35" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "35" + Parameter: N -> "5" +Evaluating: 35-5+1 + Parameter: IY <- "31" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "30" + Parameter: IX -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 29 117 228 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "30" + Parameter: IY -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 30 124 234 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "35" + Parameter: IY -> "31" + Parameter: PX -> "30" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 30 124 234 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "35" + Parameter: PX -> "30" + Parameter: IX -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 30 124 236 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "30" + Parameter: IX -> "26" + Parameter: IY -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 30 126 241 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "30" + Parameter: PY -> "35" + Parameter: IY -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 30 126 246 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "6" +Evaluating: 6+1 + Parameter: COUNN <- "7" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "7" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "7" + Parameter: N -> "5" +Evaluating: 7*5 + Parameter: PX <- "35" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "35" + Parameter: N -> "5" +Evaluating: 35-5+1 + Parameter: IX <- "31" + + CHARMM> calc py = @px + @n + Parameter: PX -> "35" + Parameter: N -> "5" +Evaluating: 35+5 + Parameter: PY <- "40" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "40" + Parameter: N -> "5" +Evaluating: 40-5+1 + Parameter: IY <- "36" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "35" + Parameter: IX -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 34 138 269 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "35" + Parameter: IY -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 35 145 275 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "40" + Parameter: IY -> "36" + Parameter: PX -> "35" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 35 145 275 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "40" + Parameter: PX -> "35" + Parameter: IX -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 35 145 277 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "35" + Parameter: IX -> "31" + Parameter: IY -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 35 147 282 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "35" + Parameter: PY -> "40" + Parameter: IY -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 35 147 287 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "7" +Evaluating: 7+1 + Parameter: COUNN <- "8" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "8" and "8". + IF test evaluated as false. Skipping command + + CHARMM> ! corner cells will be treated later + CHARMM> + + CHARMM> ! In y direction + CHARMM> ! + CHARMM> ! image + CHARMM> ! iy ix + CHARMM> ! --------------- + CHARMM> ! py px + CHARMM> ! prim + CHARMM> + + CHARMM> set counm 1 + Parameter: COUNM <- "1" + + CHARMM> label loop3 + + CHARMM> calc py = (@m - 1) * @n + @counm + Parameter: M -> "8" + Parameter: N -> "5" + Parameter: COUNM -> "1" +Evaluating: (8-1)*5+1 + Parameter: PY <- "36" + + CHARMM> calc iy = @counm + Parameter: COUNM -> "1" +Evaluating: 1 + Parameter: IY <- "1" + + CHARMM> calc px = @py + 1 + Parameter: PY -> "36" +Evaluating: 36+1 + Parameter: PX <- "37" + + CHARMM> calc ix = @iy + 1 + Parameter: IY -> "1" +Evaluating: 1+1 + Parameter: IX <- "2" + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "36" + Parameter: IY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 41 168 326 0 0 + + CHARMM> impa 011C prim q@py 1 qi3 q@ix 1 setup warn + Parameter: PY -> "36" + Parameter: IX -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 42 175 332 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn + Parameter: PY -> "36" + Parameter: IX -> "2" + Parameter: IY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 42 175 332 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn + Parameter: IY -> "1" + Parameter: PY -> "36" + Parameter: PX -> "37" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 42 175 334 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn + Parameter: PY -> "36" + Parameter: PX -> "37" + Parameter: IX -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 42 177 339 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn + Parameter: PY -> "36" + Parameter: IY -> "1" + Parameter: IX -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 42 177 344 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counm = @counm +1 + Parameter: COUNM -> "1" +Evaluating: 1+1 + Parameter: COUNM <- "2" + + CHARMM> if counm lt @n goto loop3 + Parameter: N -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> calc py = (@m - 1) * @n + @counm + Parameter: M -> "8" + Parameter: N -> "5" + Parameter: COUNM -> "2" +Evaluating: (8-1)*5+2 + Parameter: PY <- "37" + + CHARMM> calc iy = @counm + Parameter: COUNM -> "2" +Evaluating: 2 + Parameter: IY <- "2" + + CHARMM> calc px = @py + 1 + Parameter: PY -> "37" +Evaluating: 37+1 + Parameter: PX <- "38" + + CHARMM> calc ix = @iy + 1 + Parameter: IY -> "2" +Evaluating: 2+1 + Parameter: IX <- "3" + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "37" + Parameter: IY -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 48 198 383 0 0 + + CHARMM> impa 011C prim q@py 1 qi3 q@ix 1 setup warn + Parameter: PY -> "37" + Parameter: IX -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 49 205 389 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn + Parameter: PY -> "37" + Parameter: IX -> "3" + Parameter: IY -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 49 205 389 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn + Parameter: IY -> "2" + Parameter: PY -> "37" + Parameter: PX -> "38" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 49 205 391 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn + Parameter: PY -> "37" + Parameter: PX -> "38" + Parameter: IX -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 49 207 396 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn + Parameter: PY -> "37" + Parameter: IY -> "2" + Parameter: IX -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 49 207 401 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counm = @counm +1 + Parameter: COUNM -> "2" +Evaluating: 2+1 + Parameter: COUNM <- "3" + + CHARMM> if counm lt @n goto loop3 + Parameter: N -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> calc py = (@m - 1) * @n + @counm + Parameter: M -> "8" + Parameter: N -> "5" + Parameter: COUNM -> "3" +Evaluating: (8-1)*5+3 + Parameter: PY <- "38" + + CHARMM> calc iy = @counm + Parameter: COUNM -> "3" +Evaluating: 3 + Parameter: IY <- "3" + + CHARMM> calc px = @py + 1 + Parameter: PY -> "38" +Evaluating: 38+1 + Parameter: PX <- "39" + + CHARMM> calc ix = @iy + 1 + Parameter: IY -> "3" +Evaluating: 3+1 + Parameter: IX <- "4" + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "38" + Parameter: IY -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 55 228 440 0 0 + + CHARMM> impa 011C prim q@py 1 qi3 q@ix 1 setup warn + Parameter: PY -> "38" + Parameter: IX -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 56 235 446 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn + Parameter: PY -> "38" + Parameter: IX -> "4" + Parameter: IY -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 56 235 446 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn + Parameter: IY -> "3" + Parameter: PY -> "38" + Parameter: PX -> "39" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 56 235 448 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn + Parameter: PY -> "38" + Parameter: PX -> "39" + Parameter: IX -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 56 237 453 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn + Parameter: PY -> "38" + Parameter: IY -> "3" + Parameter: IX -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 56 237 458 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counm = @counm +1 + Parameter: COUNM -> "3" +Evaluating: 3+1 + Parameter: COUNM <- "4" + + CHARMM> if counm lt @n goto loop3 + Parameter: N -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> calc py = (@m - 1) * @n + @counm + Parameter: M -> "8" + Parameter: N -> "5" + Parameter: COUNM -> "4" +Evaluating: (8-1)*5+4 + Parameter: PY <- "39" + + CHARMM> calc iy = @counm + Parameter: COUNM -> "4" +Evaluating: 4 + Parameter: IY <- "4" + + CHARMM> calc px = @py + 1 + Parameter: PY -> "39" +Evaluating: 39+1 + Parameter: PX <- "40" + + CHARMM> calc ix = @iy + 1 + Parameter: IY -> "4" +Evaluating: 4+1 + Parameter: IX <- "5" + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "39" + Parameter: IY -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 62 258 497 0 0 + + CHARMM> impa 011C prim q@py 1 qi3 q@ix 1 setup warn + Parameter: PY -> "39" + Parameter: IX -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 63 265 503 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn + Parameter: PY -> "39" + Parameter: IX -> "5" + Parameter: IY -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 63 265 503 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn + Parameter: IY -> "4" + Parameter: PY -> "39" + Parameter: PX -> "40" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 63 265 505 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn + Parameter: PY -> "39" + Parameter: PX -> "40" + Parameter: IX -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 63 267 510 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn + Parameter: PY -> "39" + Parameter: IY -> "4" + Parameter: IX -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 63 267 515 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counm = @counm +1 + Parameter: COUNM -> "4" +Evaluating: 4+1 + Parameter: COUNM <- "5" + + CHARMM> if counm lt @n goto loop3 + Parameter: N -> "5" + Comparing "5" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> ! Now corner cells + CHARMM> calc py = (@m - 1) * @n + 1 + Parameter: M -> "8" + Parameter: N -> "5" +Evaluating: (8-1)*5+1 + Parameter: PY <- "36" + + CHARMM> calc iy = 1 +Evaluating: 1 + Parameter: IY <- "1" + + CHARMM> calc ix = @n + Parameter: N -> "5" +Evaluating: 5 + Parameter: IX <- "5" + + CHARMM> + + CHARMM> calc py = @m*@n + Parameter: M -> "8" + Parameter: N -> "5" +Evaluating: 8*5 + Parameter: PY <- "40" + + CHARMM> calc ix = (@m - 1) * @n + 1 + Parameter: M -> "8" + Parameter: N -> "5" +Evaluating: (8-1)*5+1 + Parameter: IX <- "36" + + CHARMM> calc iy = @n + Parameter: N -> "5" +Evaluating: 5 + Parameter: IY <- "5" + + CHARMM> set ixy 1 + Parameter: IXY <- "1" + + CHARMM> impa 011A prim q@py 1 qi1 q@ix 1 setup warn + Parameter: PY -> "40" + Parameter: IX -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 67 279 538 0 0 + + CHARMM> + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "40" + Parameter: IY -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 73 300 577 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@py 1 qi5 q@ixy 1 setup warn + Parameter: PY -> "40" + Parameter: IXY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 74 307 583 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi5 q@ixy 1 qi3 q@iy 1 setup warn + Parameter: PY -> "40" + Parameter: IXY -> "1" + Parameter: IY -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 74 307 583 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 qi1 q@ix 1 setup warn + Parameter: IY -> "5" + Parameter: PY -> "40" + Parameter: IX -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 74 307 585 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 qi1 q@ix 1 qi5 q@ixy 1 setup warn + Parameter: PY -> "40" + Parameter: IX -> "36" + Parameter: IXY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 74 309 590 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi5 q@ixy 1 setup warn + Parameter: PY -> "40" + Parameter: IY -> "5" + Parameter: IXY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2400 74 309 595 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> ! Below info for testing only + CHARMM> ! PRINT IMAG PSF + CHARMM> + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> + + CHARMM> !PRINT PSF + CHARMM> !PRINT IMAG PSF + CHARMM> + + CHARMM> update inbfrq -1 imgfrq -1 ihbfrq 0 - + CHARMM> nbonds atom fshift cdie vdw vshift - + CHARMM> cutnb @4 ctofnb @6 ctonnb @5 wmin 1.5 eps 1.0 + Parameter: 4 -> "14.0" + Parameter: 6 -> "12.0" + Parameter: 5 -> "10.0" + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 920 23 23 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 440 11 11 0.00 + 7 QI7 has 240 6 6 0.00 + 9 QI9 has 0 0 0 35.07 + 11 QI11 has 0 0 0 35.07 + 13 QI13 has 0 0 0 35.07 + 15 QI15 has 0 0 0 35.07 + 17 QI17 has 0 0 0 35.07 + 19 QI19 has 0 0 0 35.07 + 21 QI21 has 0 0 0 35.10 + 23 QI23 has 0 0 0 35.07 + 25 QI25 has 0 0 0 35.10 + Total of 4000 atoms and 100 groups and 100 residues were included + + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec FSHIft VATOm VSHIft + BYGRoup NOEXtnd NOEWald + CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 5481 exclusions and 4908 interactions(1-4) + found 123 group exclusions. + with mode 5 found 348 exclusions and 576 interactions(1-4) + found 36 image group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 459762 ATOM PAIRS AND 0 GROUP PAIRS + NBONDA>> Maximum group spatial extent (12A) exceeded. + Size is 14.93 Angstroms and starts with atom: 161 + Please check group boundary definitions. + + General atom nonbond list generation found: + 329036 ATOM PAIRS WERE FOUND FOR ATOM LIST + 523 GROUP PAIRS REQUIRED ATOM SEARCHES + + SPACE FOR 497818 ATOM PAIRS AND 0 GROUP PAIRS + + Image nonbond list generation found: + 135266 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 ATOM PAIRS WERE FOUND FOR ATOM SELF LIST + 437 GROUP PAIRS REQUIRED ATOM SEARCHES + + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + NBONDS + + CHARMM> + + CHARMM> mini sd nsteps 500 nprint 50 + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 920 23 23 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 440 11 11 0.00 + 7 QI7 has 240 6 6 0.00 + 9 QI9 has 0 0 0 35.07 + 11 QI11 has 0 0 0 35.07 + 13 QI13 has 0 0 0 35.07 + 15 QI15 has 0 0 0 35.07 + 17 QI17 has 0 0 0 35.07 + 19 QI19 has 0 0 0 35.07 + 21 QI21 has 0 0 0 35.10 + 23 QI23 has 0 0 0 35.07 + 25 QI25 has 0 0 0 35.10 + Total of 4000 atoms and 100 groups and 100 residues were included + + with mode 5 found 348 exclusions and 576 interactions(1-4) + found 36 image group exclusions. + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec FSHIft VATOm VSHIft + BYGRoup NOEXtnd NOEWald + CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 329036 atom pairs and 10389 atom exclusions. + There are 0 group pairs and 123 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 459762 ATOM PAIRS AND 0 GROUP PAIRS + NBONDA>> Maximum group spatial extent (12A) exceeded. + Size is 14.93 Angstroms and starts with atom: 161 + Please check group boundary definitions. + + General atom nonbond list generation found: + 329036 ATOM PAIRS WERE FOUND FOR ATOM LIST + 523 GROUP PAIRS REQUIRED ATOM SEARCHES + + SPACE FOR 497818 ATOM PAIRS AND 0 GROUP PAIRS + + Image nonbond list generation found: + 135266 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 ATOM PAIRS WERE FOUND FOR ATOM SELF LIST + 437 GROUP PAIRS REQUIRED ATOM SEARCHES + + + + STEEPD> An energy minimization has been requested. + + NSTEP = 500 NPRINT = 50 + STEP = 0.0200000 TOLFUN = 0.0000000 + TOLGRD = 0.0000000 TOLSTP = 0.0000000 + +MINI MIN: Cycle ENERgy Delta-E GRMS Step-size +MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +MINI EXTERN: VDWaals ELEC HBONds ASP USER +MINI IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec + ---------- --------- --------- --------- --------- --------- +MINI> 0 -50514.41281 0.00000 18.13075 0.02000 +MINI INTERN> 4438.95176 6722.92844 0.00000 974.08237 0.00000 +MINI EXTERN> -5486.56921 -50578.13673 0.00000 0.00000 0.00000 +MINI IMAGES> -915.38266 -5670.28678 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 50 -52195.81342 1681.40061 0.81707 0.00087 +MINI INTERN> 1814.02780 6909.08002 0.00000 943.02603 0.00000 +MINI EXTERN> -5318.98045 -49997.88139 0.00000 0.00000 0.00000 +MINI IMAGES> -883.39359 -5661.69184 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 100 -52272.47798 76.66456 0.49071 0.00052 +MINI INTERN> 1759.33153 6850.89147 0.00000 912.71176 0.00000 +MINI EXTERN> -5316.40360 -49936.86637 0.00000 0.00000 0.00000 +MINI IMAGES> -879.68309 -5662.45969 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 150 -52306.38863 33.91064 0.97493 0.00074 +MINI INTERN> 1742.06033 6823.86060 0.00000 900.07465 0.00000 +MINI EXTERN> -5318.37063 -49913.80158 0.00000 0.00000 0.00000 +MINI IMAGES> -878.30040 -5661.91160 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 200 -52323.30793 16.91930 0.58339 0.00044 +MINI INTERN> 1737.10869 6812.01701 0.00000 896.70442 0.00000 +MINI EXTERN> -5319.62144 -49908.81412 0.00000 0.00000 0.00000 +MINI IMAGES> -877.69214 -5663.01037 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 250 -52332.29950 8.99158 0.17452 0.00027 +MINI INTERN> 1734.17169 6807.58529 0.00000 896.09804 0.00000 +MINI EXTERN> -5320.21660 -49908.22190 0.00000 0.00000 0.00000 +MINI IMAGES> -877.33178 -5664.38423 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 300 -52337.54187 5.24237 0.50977 0.00038 +MINI INTERN> 1733.17908 6805.63544 0.00000 896.49883 0.00000 +MINI EXTERN> -5320.61211 -49909.14653 0.00000 0.00000 0.00000 +MINI IMAGES> -877.15593 -5665.94064 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 350 -52341.39249 3.85062 0.30129 0.00023 +MINI INTERN> 1732.96067 6804.56330 0.00000 897.37540 0.00000 +MINI EXTERN> -5320.90107 -49910.57995 0.00000 0.00000 0.00000 +MINI IMAGES> -877.10741 -5667.70343 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 400 -52344.07058 2.67809 0.09965 0.00014 +MINI INTERN> 1732.16325 6804.12020 0.00000 898.19351 0.00000 +MINI EXTERN> -5321.12900 -49911.42801 0.00000 0.00000 0.00000 +MINI IMAGES> -877.09566 -5668.89487 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 450 -52346.03713 1.96654 0.25319 0.00020 +MINI INTERN> 1731.58023 6803.90716 0.00000 899.06892 0.00000 +MINI EXTERN> -5321.33044 -49912.17600 0.00000 0.00000 0.00000 +MINI IMAGES> -877.12223 -5669.96476 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 500 -52347.61211 1.57498 0.07820 0.00012 +MINI INTERN> 1731.16935 6803.83827 0.00000 899.96567 0.00000 +MINI EXTERN> -5321.48410 -49912.90249 0.00000 0.00000 0.00000 +MINI IMAGES> -877.17253 -5671.02628 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. + +STPD MIN: Cycle ENERgy Delta-E GRMS Step-size +STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +STPD EXTERN: VDWaals ELEC HBONds ASP USER +STPD IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec + ---------- --------- --------- --------- --------- --------- +STPD> 500 -52347.61211 1.57498 0.07820 0.00014 +STPD INTERN> 1731.16935 6803.83827 0.00000 899.96567 0.00000 +STPD EXTERN> -5321.48410 -49912.90249 0.00000 0.00000 0.00000 +STPD IMAGES> -877.17253 -5671.02628 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> energy + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 920 23 23 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 440 11 11 0.00 + 7 QI7 has 280 7 7 0.00 + 9 QI9 has 0 0 0 35.12 + 11 QI11 has 0 0 0 35.21 + 13 QI13 has 0 0 0 35.12 + 15 QI15 has 0 0 0 35.13 + 17 QI17 has 0 0 0 35.17 + 19 QI19 has 0 0 0 35.31 + 21 QI21 has 0 0 0 35.15 + 23 QI23 has 0 0 0 35.17 + 25 QI25 has 0 0 0 35.24 + Total of 4040 atoms and 101 groups and 101 residues were included + + with mode 5 found 348 exclusions and 576 interactions(1-4) + found 36 image group exclusions. + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec FSHIft VATOm VSHIft + BYGRoup NOEXtnd NOEWald + CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 329036 atom pairs and 10389 atom exclusions. + There are 0 group pairs and 123 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 459762 ATOM PAIRS AND 0 GROUP PAIRS + NBONDA>> Maximum group spatial extent (12A) exceeded. + Size is 14.84 Angstroms and starts with atom: 161 + Please check group boundary definitions. + + General atom nonbond list generation found: + 329161 ATOM PAIRS WERE FOUND FOR ATOM LIST + 538 GROUP PAIRS REQUIRED ATOM SEARCHES + + SPACE FOR 497818 ATOM PAIRS AND 0 GROUP PAIRS + + Image nonbond list generation found: + 136223 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 ATOM PAIRS WERE FOUND FOR ATOM SELF LIST + 464 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER +ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec + ---------- --------- --------- --------- --------- --------- +ENER> 0 -52347.61211 1.57498 0.07820 +ENER INTERN> 1731.16935 6803.83827 0.00000 899.96567 0.00000 +ENER EXTERN> -5321.48410 -49912.90249 0.00000 0.00000 0.00000 +ENER IMAGES> -877.17253 -5671.02628 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> open write card unit 20 name test_opt.pdb + VOPEN> Attempting to open::test_opt.pdb:: + OPNLGU> Unit 20 opened for WRITE access to test_opt.pdb + + CHARMM> write coor pdb unit 20 + RDTITL> * COORDINATES + RDTITL> * + + CHARMM> close unit 20 + VCLOSE: Closing unit 20 with status "KEEP" + + CHARMM> + + CHARMM> open write form unit 20 name test_opt.crd + VOPEN> Attempting to open::test_opt.crd:: + OPNLGU> Unit 20 opened for WRITE access to test_opt.crd + + CHARMM> write coor cards unit 20 + RDTITL> * COORDINATES + RDTITL> * + VCLOSE: Closing unit 20 with status "KEEP" + + CHARMM> close unit 20 + CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. + + CHARMM> + + CHARMM> open unit 20 write form name test_opt.psf + VOPEN> Attempting to open::test_opt.psf:: + OPNLGU> Unit 20 opened for WRITE access to test_opt.psf + + CHARMM> write psf cards unit 20 + RDTITL> * PSFFILE + RDTITL> * + + CHARMM> close unit 20 + VCLOSE: Closing unit 20 with status "KEEP" + + CHARMM> + + CHARMM> stop +$$$$$$ New timer profile $$$$$ + Nonbond force 16.89984 Other: 0.00000 + Bond energy 0.10693 Other: 0.00000 + Angle energy 0.62793 Other: 0.00000 + Dihedral energy 0.63496 Other: 0.00000 + Restraints energy 0.00131 Other: 0.00000 + INTRNL energy 1.42178 Other: 0.05064 + Energy time 18.41402 Other: 0.09240 + Total time 19.62556 Other: 1.21154 + + NORMAL TERMINATION BY NORMAL STOP + MAXIMUM STACK SPACE USED IS 242614 + STACK CURRENTLY IN USE IS 0 + NO WARNINGS WERE ISSUED + HEAP PRINTOUT- HEAP SIZE 2048000 + SPACE CURRENTLY IN USE IS 0 + MAXIMUM SPACE USED IS 1519420 + FREE LIST + PRINHP> ADDRESS: 1 LENGTH: 2048000 NEXT: 0 + + $$$$$ JOB ACCOUNTING INFORMATION $$$$$ + ELAPSED TIME: 19.63 SECONDS + CPU TIME: 16.68 SECONDS diff --git a/charmm/toppar/silicates/test.out b/charmm/toppar/silicates/test.out new file mode 100644 index 00000000..8c36882a --- /dev/null +++ b/charmm/toppar/silicates/test.out @@ -0,0 +1,13316 @@ +1 + Chemistry at HARvard Macromolecular Mechanics + (CHARMM) - Developmental Version 32a1 August 15, 2004 + Copyright(c) 1984-2001 President and Fellows of Harvard College + All Rights Reserved + Current operating system: Linux-2.4.9-e.38smp(i686)@psc-raid1 + Created on 7/14/ 5 at 16:12:16 by user: alex + + Maximum number of ATOMS: 25140, and RESidues: 14000 + Current HEAP size: 2048000, and STACK size: 500000 + + RDTITL> * GENERATION OF CRYSTAL SLAB FOLLOWED BY MINIMIZATION + RDTITL> * PEDRO LOPES, JUL 2005 + RDTITL> * + + CHARMM> + + CHARMM> ! The surface is generated by creating the appropriate + CHARMM> ! images of the central unitcell using the IMAGE + CHARMM> ! facility of charmm. The user starts from a pdb file + CHARMM> ! of the primitive cell, with the surface on the XY + CHARMM> ! plane. This script assumes this file is file.pdb. + CHARMM> ! From the primitive cell a surface is created by + CHARMM> ! replicating it 8x5 times. The crystal parameters and + CHARMM> ! number of replicas are defined in params.dat + CHARMM> ! Other files needed to run this script are: + CHARMM> ! crystal.img and image_patch.str + CHARMM> + + CHARMM> + + CHARMM> bomlev -2 + + CHARMM> + + CHARMM> ! read the topology and parameter file + CHARMM> + + CHARMM> open read formatted unit 12 name toppar/top_silicates.inp + VOPEN> Attempting to open::toppar/top_silicates.inp:: + OPNLGU> Unit 12 opened for READONLY access to toppar/top_silicates.inp + + CHARMM> read rtf card unit 12 + MAINIO> Residue topology file being read from unit 12. + TITLE> * <<<<<>>>>> + TITLE> * ALEXANDER D. MACKERELL JR., PEDRO LOPES AND MOUHSINE TAZI + TITLE> * JULY 2005 + TITLE> *ALL COMMENTS TO ADM JR. CHARMM FORUM: WWW.CHARMM.ORG + TITLE> * + + CHARMM> close unit 12 + VCLOSE: Closing unit 12 with status "KEEP" + + CHARMM> open read formatted unit 12 name toppar/par_silicates.inp + VOPEN> Attempting to open::toppar/par_silicates.inp:: + OPNLGU> Unit 12 opened for READONLY access to toppar/par_silicates.inp + + CHARMM> read para card unit 12 + + PARAMETER FILE BEING READ FROM UNIT 12 + TITLE> * <<<<<>>>>> + TITLE> * ALEXANDER D. MACKERELL JR., PEDRO LOPES AND MOUHSINE TAZI + TITLE> * JULY 2005 + TITLE> *ALL COMMENTS TO ADM JR. CHARMM FORUM: WWW.CHARMM.ORG + TITLE> * + PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. + + CHARMM> close unit 12 + VCLOSE: Closing unit 12 with status "KEEP" + + CHARMM> + + CHARMM> ! Generate "unit cell" psf and coordinates + CHARMM> + + CHARMM> ! Generate the molecule, corresponing to the "unit cell" + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate q1 noangle nodihedral first none last none setup warn + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 1 has been generated. Its identifier is Q1. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 40 Number of groups = 1 + Number of bonds = 39 Number of angles = 0 + Number of dihedrals = 0 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> open unit 30 read form name quartz_init.pdb + VOPEN> Attempting to open::quartz_init.pdb:: + OPNLGU> Unit 30 opened for READONLY access to quartz_init.pdb + + CHARMM> read coor pdb unit 30 + SPATIAL COORDINATES BEING READ FROM UNIT 30 + TITLE> 4 QUAR COMPLIES WITH FORMAT V. 2.0 + TITLE> * + + CHARMM> close unit 30 + VCLOSE: Closing unit 30 with status "KEEP" + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 1 Number of residues = 1 + Number of atoms = 40 Number of groups = 1 + Number of bonds = 39 Number of angles = 56 + Number of dihedrals = 56 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> !PRINT COOR + CHARMM> !PRINT PSF + CHARMM> + + CHARMM> !====================================================== + CHARMM> ! Set up periodic images + CHARMM> !====================================================== + CHARMM> + + CHARMM> stream params.str + VOPEN> Attempting to open::params.str:: + OPNLGU> Unit 99 opened for READONLY access to params.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> * PARAMETERS FOR SIMULATION OF ON CRYSTAL SURFACES + RDTITL> * + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> ! Generation of n cells along U and m cells along V + CHARMM> ! Used to specify the surface size from the primitive cell + CHARMM> ! k is the number of replicas along Z + CHARMM> + + CHARMM> set n 5 + Parameter: N <- "5" + + CHARMM> set m 8 + Parameter: M <- "8" + + CHARMM> set k 1 + Parameter: K <- "1" + + CHARMM> + + CHARMM> calc nm = @n * @m * @k + Parameter: N -> "5" + Parameter: M -> "8" + Parameter: K -> "1" +Evaluating: 5*8*1 + Parameter: NM <- "40" + + CHARMM> + + CHARMM> ! + CHARMM> ! U |__2| V + CHARMM> !|__1|__2| 1-->2 |__1| 1-->2 + CHARMM> ! + CHARMM> ! + CHARMM> ! Q(M-1)*N+1 Q(M-1)*N+2 ..... QM*N + CHARMM> ! ---------------------------------------- + CHARMM> ! . . . . . + CHARMM> ! . . . . . + CHARMM> ! . . . . . + CHARMM> ! ----------------------------------------- + CHARMM> ! QN+1 QN+2 + CHARMM> ! ----------------------------------------- + CHARMM> ! Q1 Q2 Q3 Q4 Q5 .... QN + CHARMM> ! ----------------------------------------- + CHARMM> ! + CHARMM> ! + CHARMM> ! Based on the PBC for the surface one has to set the values of U (a-vector), + CHARMM> ! V (b-vector) and Z (c-vector). The angle between U and V is theta. + CHARMM> + + CHARMM> !PBC 7.3000 4.9100 109.6517 (P1) + CHARMM> + + CHARMM> set U = 7.3000 + Parameter: U <- "7.3000" + + CHARMM> set V = 4.9100 + Parameter: V <- "4.9100" + + CHARMM> set Z = 50.000 + Parameter: Z <- "50.000" + + CHARMM> + + CHARMM> set theta = 109.6517 + Parameter: THETA <- "109.6517" + + CHARMM> + + CHARMM> set radian = 57.29577951308232088 + Parameter: RADIAN <- "57.29577951308232088" + + CHARMM> calc theta = @theta - 90.0 + Parameter: THETA -> "109.6517" +Evaluating: 109.6517-90.0 + Parameter: THETA <- "19.6517" + + CHARMM> calc theta = @theta/@radian + Parameter: THETA -> "19.6517" + Parameter: RADIAN -> "57.29577951308232088" +Evaluating: 19.6517/57.29577951308232088 + Parameter: THETA <- "0.342987" + + CHARMM> + + CHARMM> + + CHARMM> !unit cell translation parameters + CHARMM> set u1 @U + Parameter: U -> "7.3000" + Parameter: U1 <- "7.3000" + + CHARMM> set u2 0.0 + Parameter: U2 <- "0.0" + + CHARMM> set u3 0.0 + Parameter: U3 <- "0.0" + + CHARMM> + + CHARMM> calc v1 @V*sin(@theta) + Parameter: V -> "4.9100" + Parameter: THETA -> "0.342987" +Evaluating: 4.9100*SIN(0.342987) + Parameter: V1 <- "1.65124" + + CHARMM> calc v1 = -1*@v1 + Parameter: V1 -> "1.65124" +Evaluating: -1*1.65124 + Parameter: V1 <- "-1.65124" + + CHARMM> calc v2 @V*cos(@theta) + Parameter: V -> "4.9100" + Parameter: THETA -> "0.342987" +Evaluating: 4.9100*COS(0.342987) + Parameter: V2 <- "4.62401" + + CHARMM> set v3 0.0 + Parameter: V3 <- "0.0" + + CHARMM> + + CHARMM> set w1 0.0 + Parameter: W1 <- "0.0" + + CHARMM> set w2 0.0 + Parameter: W2 <- "0.0" + + CHARMM> set w3 @Z + Parameter: Z -> "50.000" + Parameter: W3 <- "50.000" + + CHARMM> + + CHARMM> !Define translational vectors for images + CHARMM> + + CHARMM> calc bigu1 = @n * @u1 + Parameter: N -> "5" + Parameter: U1 -> "7.3000" +Evaluating: 5*7.3000 + Parameter: BIGU1 <- "36.5" + + CHARMM> calc bigu2 = @n * @u2 + Parameter: N -> "5" + Parameter: U2 -> "0.0" +Evaluating: 5*0.0 + Parameter: BIGU2 <- "0" + + CHARMM> calc bigu3 = @n * @u3 + Parameter: N -> "5" + Parameter: U3 -> "0.0" +Evaluating: 5*0.0 + Parameter: BIGU3 <- "0" + + CHARMM> + + CHARMM> calc bigv1 = @m * @v1 + Parameter: M -> "8" + Parameter: V1 -> "-1.65124" +Evaluating: 8*-1.65124 + Parameter: BIGV1 <- "-13.2099" + + CHARMM> calc bigv2 = @m * @v2 + Parameter: M -> "8" + Parameter: V2 -> "4.62401" +Evaluating: 8*4.62401 + Parameter: BIGV2 <- "36.9921" + + CHARMM> calc bigv3 = @m * @v3 + Parameter: M -> "8" + Parameter: V3 -> "0.0" +Evaluating: 8*0.0 + Parameter: BIGV3 <- "0" + + CHARMM> + + CHARMM> calc bigw1 = @k * @w1 + Parameter: K -> "1" + Parameter: W1 -> "0.0" +Evaluating: 1*0.0 + Parameter: BIGW1 <- "0" + + CHARMM> calc bigw2 = @k * @w2 + Parameter: K -> "1" + Parameter: W2 -> "0.0" +Evaluating: 1*0.0 + Parameter: BIGW2 <- "0" + + CHARMM> calc bigw3 = @k * @w3 + Parameter: K -> "1" + Parameter: W3 -> "50.000" +Evaluating: 1*50.000 + Parameter: BIGW3 <- "50" + + CHARMM> + + CHARMM> + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> + + CHARMM> !initialise number of replicas along U and V + CHARMM> set maxU @n + Parameter: N -> "5" + Parameter: MAXU <- "5" + + CHARMM> set maxV @m + Parameter: M -> "8" + Parameter: MAXV <- "8" + + CHARMM> + + CHARMM> !initialise unitcell counters and total cell count + CHARMM> set countU 2 + Parameter: COUNTU <- "2" + + CHARMM> set countV 1 + Parameter: COUNTV <- "1" + + CHARMM> set count 1 + Parameter: COUNT <- "1" + + CHARMM> + + CHARMM> !start loops + CHARMM> + + CHARMM> label loopV + + CHARMM> + + CHARMM> label loopU + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "2" +Evaluating: 2-1.0 + Parameter: VECTU <- "1" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "1" +Evaluating: 1-1.0 + Parameter: VECTV <- "0" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "1" +Evaluating: 1+1 + Parameter: COUNT <- "2" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "2" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 2 has been generated. Its identifier is Q2. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 80 Number of groups = 2 + Number of bonds = 78 Number of angles = 56 + Number of dihedrals = 56 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "2" + SELRPN> 40 atoms have been selected out of 80 + SELRPN> 40 atoms have been selected out of 80 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "2" + SELRPN> 40 atoms have been selected out of 80 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "2" + SELRPN> 40 atoms have been selected out of 80 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "2" + SELRPN> 40 atoms have been selected out of 80 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "2" + SELRPN> 40 atoms have been selected out of 80 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "2" + SELRPN> 40 atoms have been selected out of 80 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "2" + SELRPN> 40 atoms have been selected out of 80 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 2 Number of residues = 2 + Number of atoms = 80 Number of groups = 2 + Number of bonds = 78 Number of angles = 112 + Number of dihedrals = 112 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "2" +Evaluating: 2+1 + Parameter: COUNTU <- "3" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "3" +Evaluating: 3-1.0 + Parameter: VECTU <- "2" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "1" +Evaluating: 1-1.0 + Parameter: VECTV <- "0" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "2" +Evaluating: 2+1 + Parameter: COUNT <- "3" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "3" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 3 has been generated. Its identifier is Q3. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 3 Number of residues = 3 + Number of atoms = 120 Number of groups = 3 + Number of bonds = 117 Number of angles = 112 + Number of dihedrals = 112 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "3" + SELRPN> 40 atoms have been selected out of 120 + SELRPN> 40 atoms have been selected out of 120 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "3" + SELRPN> 40 atoms have been selected out of 120 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "3" + SELRPN> 40 atoms have been selected out of 120 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "3" + SELRPN> 40 atoms have been selected out of 120 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "3" + SELRPN> 40 atoms have been selected out of 120 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "3" + SELRPN> 40 atoms have been selected out of 120 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "3" + SELRPN> 40 atoms have been selected out of 120 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 3 Number of residues = 3 + Number of atoms = 120 Number of groups = 3 + Number of bonds = 117 Number of angles = 168 + Number of dihedrals = 168 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "3" +Evaluating: 3+1 + Parameter: COUNTU <- "4" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "4" +Evaluating: 4-1.0 + Parameter: VECTU <- "3" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "1" +Evaluating: 1-1.0 + Parameter: VECTV <- "0" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "3" +Evaluating: 3+1 + Parameter: COUNT <- "4" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "4" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 4 has been generated. Its identifier is Q4. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 4 Number of residues = 4 + Number of atoms = 160 Number of groups = 4 + Number of bonds = 156 Number of angles = 168 + Number of dihedrals = 168 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "4" + SELRPN> 40 atoms have been selected out of 160 + SELRPN> 40 atoms have been selected out of 160 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "4" + SELRPN> 40 atoms have been selected out of 160 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "4" + SELRPN> 40 atoms have been selected out of 160 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "4" + SELRPN> 40 atoms have been selected out of 160 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "4" + SELRPN> 40 atoms have been selected out of 160 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "4" + SELRPN> 40 atoms have been selected out of 160 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "4" + SELRPN> 40 atoms have been selected out of 160 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 4 Number of residues = 4 + Number of atoms = 160 Number of groups = 4 + Number of bonds = 156 Number of angles = 224 + Number of dihedrals = 224 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "4" +Evaluating: 4+1 + Parameter: COUNTU <- "5" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "5" +Evaluating: 5-1.0 + Parameter: VECTU <- "4" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "1" +Evaluating: 1-1.0 + Parameter: VECTV <- "0" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "4" +Evaluating: 4+1 + Parameter: COUNT <- "5" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "5" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 5 has been generated. Its identifier is Q5. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 5 Number of residues = 5 + Number of atoms = 200 Number of groups = 5 + Number of bonds = 195 Number of angles = 224 + Number of dihedrals = 224 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "5" + SELRPN> 40 atoms have been selected out of 200 + SELRPN> 40 atoms have been selected out of 200 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "5" + SELRPN> 40 atoms have been selected out of 200 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "5" + SELRPN> 40 atoms have been selected out of 200 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "5" + SELRPN> 40 atoms have been selected out of 200 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "5" + SELRPN> 40 atoms have been selected out of 200 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "5" + SELRPN> 40 atoms have been selected out of 200 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "0" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "5" + SELRPN> 40 atoms have been selected out of 200 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 5 Number of residues = 5 + Number of atoms = 200 Number of groups = 5 + Number of bonds = 195 Number of angles = 280 + Number of dihedrals = 280 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "5" +Evaluating: 5+1 + Parameter: COUNTU <- "6" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set countU 1 + Parameter: COUNTU <- "1" + + CHARMM> + + CHARMM> calc countV = @countV + 1 + Parameter: COUNTV -> "1" +Evaluating: 1+1 + Parameter: COUNTV <- "2" + + CHARMM> + + CHARMM> if countV le @maxV goto loopV + Parameter: MAXV -> "8" + Comparing "2" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> label loopU + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "1" +Evaluating: 1-1.0 + Parameter: VECTU <- "0" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "2" +Evaluating: 2-1.0 + Parameter: VECTV <- "1" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "5" +Evaluating: 5+1 + Parameter: COUNT <- "6" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "6" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 6 has been generated. Its identifier is Q6. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 6 Number of residues = 6 + Number of atoms = 240 Number of groups = 6 + Number of bonds = 234 Number of angles = 280 + Number of dihedrals = 280 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "6" + SELRPN> 40 atoms have been selected out of 240 + SELRPN> 40 atoms have been selected out of 240 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "6" + SELRPN> 40 atoms have been selected out of 240 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "6" + SELRPN> 40 atoms have been selected out of 240 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "6" + SELRPN> 40 atoms have been selected out of 240 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "6" + SELRPN> 40 atoms have been selected out of 240 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "6" + SELRPN> 40 atoms have been selected out of 240 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "6" + SELRPN> 40 atoms have been selected out of 240 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 6 Number of residues = 6 + Number of atoms = 240 Number of groups = 6 + Number of bonds = 234 Number of angles = 336 + Number of dihedrals = 336 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "1" +Evaluating: 1+1 + Parameter: COUNTU <- "2" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "2" +Evaluating: 2-1.0 + Parameter: VECTU <- "1" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "2" +Evaluating: 2-1.0 + Parameter: VECTV <- "1" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "6" +Evaluating: 6+1 + Parameter: COUNT <- "7" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "7" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 7 has been generated. Its identifier is Q7. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 7 Number of residues = 7 + Number of atoms = 280 Number of groups = 7 + Number of bonds = 273 Number of angles = 336 + Number of dihedrals = 336 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "7" + SELRPN> 40 atoms have been selected out of 280 + SELRPN> 40 atoms have been selected out of 280 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "7" + SELRPN> 40 atoms have been selected out of 280 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "7" + SELRPN> 40 atoms have been selected out of 280 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "7" + SELRPN> 40 atoms have been selected out of 280 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "7" + SELRPN> 40 atoms have been selected out of 280 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "7" + SELRPN> 40 atoms have been selected out of 280 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "7" + SELRPN> 40 atoms have been selected out of 280 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 7 Number of residues = 7 + Number of atoms = 280 Number of groups = 7 + Number of bonds = 273 Number of angles = 392 + Number of dihedrals = 392 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "2" +Evaluating: 2+1 + Parameter: COUNTU <- "3" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "3" +Evaluating: 3-1.0 + Parameter: VECTU <- "2" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "2" +Evaluating: 2-1.0 + Parameter: VECTV <- "1" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "7" +Evaluating: 7+1 + Parameter: COUNT <- "8" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "8" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 8 has been generated. Its identifier is Q8. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 8 Number of residues = 8 + Number of atoms = 320 Number of groups = 8 + Number of bonds = 312 Number of angles = 392 + Number of dihedrals = 392 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "8" + SELRPN> 40 atoms have been selected out of 320 + SELRPN> 40 atoms have been selected out of 320 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "8" + SELRPN> 40 atoms have been selected out of 320 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "8" + SELRPN> 40 atoms have been selected out of 320 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "8" + SELRPN> 40 atoms have been selected out of 320 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "8" + SELRPN> 40 atoms have been selected out of 320 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "8" + SELRPN> 40 atoms have been selected out of 320 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "8" + SELRPN> 40 atoms have been selected out of 320 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 8 Number of residues = 8 + Number of atoms = 320 Number of groups = 8 + Number of bonds = 312 Number of angles = 448 + Number of dihedrals = 448 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "3" +Evaluating: 3+1 + Parameter: COUNTU <- "4" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "4" +Evaluating: 4-1.0 + Parameter: VECTU <- "3" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "2" +Evaluating: 2-1.0 + Parameter: VECTV <- "1" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "8" +Evaluating: 8+1 + Parameter: COUNT <- "9" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "9" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 9 has been generated. Its identifier is Q9. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 9 Number of residues = 9 + Number of atoms = 360 Number of groups = 9 + Number of bonds = 351 Number of angles = 448 + Number of dihedrals = 448 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "9" + SELRPN> 40 atoms have been selected out of 360 + SELRPN> 40 atoms have been selected out of 360 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "9" + SELRPN> 40 atoms have been selected out of 360 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "9" + SELRPN> 40 atoms have been selected out of 360 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "9" + SELRPN> 40 atoms have been selected out of 360 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "9" + SELRPN> 40 atoms have been selected out of 360 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "9" + SELRPN> 40 atoms have been selected out of 360 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "9" + SELRPN> 40 atoms have been selected out of 360 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 9 Number of residues = 9 + Number of atoms = 360 Number of groups = 9 + Number of bonds = 351 Number of angles = 504 + Number of dihedrals = 504 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "4" +Evaluating: 4+1 + Parameter: COUNTU <- "5" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "5" +Evaluating: 5-1.0 + Parameter: VECTU <- "4" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "2" +Evaluating: 2-1.0 + Parameter: VECTV <- "1" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "9" +Evaluating: 9+1 + Parameter: COUNT <- "10" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "10" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 10 has been generated. Its identifier is Q10. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 10 Number of residues = 10 + Number of atoms = 400 Number of groups = 10 + Number of bonds = 390 Number of angles = 504 + Number of dihedrals = 504 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "10" + SELRPN> 40 atoms have been selected out of 400 + SELRPN> 40 atoms have been selected out of 400 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "10" + SELRPN> 40 atoms have been selected out of 400 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "10" + SELRPN> 40 atoms have been selected out of 400 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "10" + SELRPN> 40 atoms have been selected out of 400 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "10" + SELRPN> 40 atoms have been selected out of 400 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "10" + SELRPN> 40 atoms have been selected out of 400 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "1" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "10" + SELRPN> 40 atoms have been selected out of 400 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 10 Number of residues = 10 + Number of atoms = 400 Number of groups = 10 + Number of bonds = 390 Number of angles = 560 + Number of dihedrals = 560 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "5" +Evaluating: 5+1 + Parameter: COUNTU <- "6" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set countU 1 + Parameter: COUNTU <- "1" + + CHARMM> + + CHARMM> calc countV = @countV + 1 + Parameter: COUNTV -> "2" +Evaluating: 2+1 + Parameter: COUNTV <- "3" + + CHARMM> + + CHARMM> if countV le @maxV goto loopV + Parameter: MAXV -> "8" + Comparing "3" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> label loopU + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "1" +Evaluating: 1-1.0 + Parameter: VECTU <- "0" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "3" +Evaluating: 3-1.0 + Parameter: VECTV <- "2" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "10" +Evaluating: 10+1 + Parameter: COUNT <- "11" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "11" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 11 has been generated. Its identifier is Q11. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 11 Number of residues = 11 + Number of atoms = 440 Number of groups = 11 + Number of bonds = 429 Number of angles = 560 + Number of dihedrals = 560 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "11" + SELRPN> 40 atoms have been selected out of 440 + SELRPN> 40 atoms have been selected out of 440 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "11" + SELRPN> 40 atoms have been selected out of 440 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "11" + SELRPN> 40 atoms have been selected out of 440 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "11" + SELRPN> 40 atoms have been selected out of 440 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "11" + SELRPN> 40 atoms have been selected out of 440 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "11" + SELRPN> 40 atoms have been selected out of 440 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "11" + SELRPN> 40 atoms have been selected out of 440 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 11 Number of residues = 11 + Number of atoms = 440 Number of groups = 11 + Number of bonds = 429 Number of angles = 616 + Number of dihedrals = 616 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "1" +Evaluating: 1+1 + Parameter: COUNTU <- "2" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "2" +Evaluating: 2-1.0 + Parameter: VECTU <- "1" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "3" +Evaluating: 3-1.0 + Parameter: VECTV <- "2" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "11" +Evaluating: 11+1 + Parameter: COUNT <- "12" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "12" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 12 has been generated. Its identifier is Q12. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 12 Number of residues = 12 + Number of atoms = 480 Number of groups = 12 + Number of bonds = 468 Number of angles = 616 + Number of dihedrals = 616 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "12" + SELRPN> 40 atoms have been selected out of 480 + SELRPN> 40 atoms have been selected out of 480 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "12" + SELRPN> 40 atoms have been selected out of 480 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "12" + SELRPN> 40 atoms have been selected out of 480 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "12" + SELRPN> 40 atoms have been selected out of 480 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "12" + SELRPN> 40 atoms have been selected out of 480 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "12" + SELRPN> 40 atoms have been selected out of 480 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "12" + SELRPN> 40 atoms have been selected out of 480 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 12 Number of residues = 12 + Number of atoms = 480 Number of groups = 12 + Number of bonds = 468 Number of angles = 672 + Number of dihedrals = 672 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "2" +Evaluating: 2+1 + Parameter: COUNTU <- "3" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "3" +Evaluating: 3-1.0 + Parameter: VECTU <- "2" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "3" +Evaluating: 3-1.0 + Parameter: VECTV <- "2" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "12" +Evaluating: 12+1 + Parameter: COUNT <- "13" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "13" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 13 has been generated. Its identifier is Q13. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 13 Number of residues = 13 + Number of atoms = 520 Number of groups = 13 + Number of bonds = 507 Number of angles = 672 + Number of dihedrals = 672 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "13" + SELRPN> 40 atoms have been selected out of 520 + SELRPN> 40 atoms have been selected out of 520 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "13" + SELRPN> 40 atoms have been selected out of 520 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "13" + SELRPN> 40 atoms have been selected out of 520 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "13" + SELRPN> 40 atoms have been selected out of 520 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "13" + SELRPN> 40 atoms have been selected out of 520 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "13" + SELRPN> 40 atoms have been selected out of 520 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "13" + SELRPN> 40 atoms have been selected out of 520 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 13 Number of residues = 13 + Number of atoms = 520 Number of groups = 13 + Number of bonds = 507 Number of angles = 728 + Number of dihedrals = 728 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "3" +Evaluating: 3+1 + Parameter: COUNTU <- "4" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "4" +Evaluating: 4-1.0 + Parameter: VECTU <- "3" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "3" +Evaluating: 3-1.0 + Parameter: VECTV <- "2" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "13" +Evaluating: 13+1 + Parameter: COUNT <- "14" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "14" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 14 has been generated. Its identifier is Q14. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 14 Number of residues = 14 + Number of atoms = 560 Number of groups = 14 + Number of bonds = 546 Number of angles = 728 + Number of dihedrals = 728 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "14" + SELRPN> 40 atoms have been selected out of 560 + SELRPN> 40 atoms have been selected out of 560 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "14" + SELRPN> 40 atoms have been selected out of 560 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "14" + SELRPN> 40 atoms have been selected out of 560 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "14" + SELRPN> 40 atoms have been selected out of 560 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "14" + SELRPN> 40 atoms have been selected out of 560 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "14" + SELRPN> 40 atoms have been selected out of 560 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "14" + SELRPN> 40 atoms have been selected out of 560 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 14 Number of residues = 14 + Number of atoms = 560 Number of groups = 14 + Number of bonds = 546 Number of angles = 784 + Number of dihedrals = 784 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "4" +Evaluating: 4+1 + Parameter: COUNTU <- "5" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "5" +Evaluating: 5-1.0 + Parameter: VECTU <- "4" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "3" +Evaluating: 3-1.0 + Parameter: VECTV <- "2" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "14" +Evaluating: 14+1 + Parameter: COUNT <- "15" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "15" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 15 has been generated. Its identifier is Q15. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 15 Number of residues = 15 + Number of atoms = 600 Number of groups = 15 + Number of bonds = 585 Number of angles = 784 + Number of dihedrals = 784 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "15" + SELRPN> 40 atoms have been selected out of 600 + SELRPN> 40 atoms have been selected out of 600 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "15" + SELRPN> 40 atoms have been selected out of 600 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "15" + SELRPN> 40 atoms have been selected out of 600 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "15" + SELRPN> 40 atoms have been selected out of 600 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "15" + SELRPN> 40 atoms have been selected out of 600 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "15" + SELRPN> 40 atoms have been selected out of 600 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "2" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "15" + SELRPN> 40 atoms have been selected out of 600 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 15 Number of residues = 15 + Number of atoms = 600 Number of groups = 15 + Number of bonds = 585 Number of angles = 840 + Number of dihedrals = 840 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "5" +Evaluating: 5+1 + Parameter: COUNTU <- "6" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set countU 1 + Parameter: COUNTU <- "1" + + CHARMM> + + CHARMM> calc countV = @countV + 1 + Parameter: COUNTV -> "3" +Evaluating: 3+1 + Parameter: COUNTV <- "4" + + CHARMM> + + CHARMM> if countV le @maxV goto loopV + Parameter: MAXV -> "8" + Comparing "4" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> label loopU + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "1" +Evaluating: 1-1.0 + Parameter: VECTU <- "0" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "4" +Evaluating: 4-1.0 + Parameter: VECTV <- "3" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "15" +Evaluating: 15+1 + Parameter: COUNT <- "16" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "16" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 16 has been generated. Its identifier is Q16. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 16 Number of residues = 16 + Number of atoms = 640 Number of groups = 16 + Number of bonds = 624 Number of angles = 840 + Number of dihedrals = 840 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "16" + SELRPN> 40 atoms have been selected out of 640 + SELRPN> 40 atoms have been selected out of 640 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "16" + SELRPN> 40 atoms have been selected out of 640 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "16" + SELRPN> 40 atoms have been selected out of 640 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "16" + SELRPN> 40 atoms have been selected out of 640 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "16" + SELRPN> 40 atoms have been selected out of 640 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "16" + SELRPN> 40 atoms have been selected out of 640 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "16" + SELRPN> 40 atoms have been selected out of 640 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 16 Number of residues = 16 + Number of atoms = 640 Number of groups = 16 + Number of bonds = 624 Number of angles = 896 + Number of dihedrals = 896 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "1" +Evaluating: 1+1 + Parameter: COUNTU <- "2" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "2" +Evaluating: 2-1.0 + Parameter: VECTU <- "1" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "4" +Evaluating: 4-1.0 + Parameter: VECTV <- "3" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "16" +Evaluating: 16+1 + Parameter: COUNT <- "17" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "17" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 17 has been generated. Its identifier is Q17. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 17 Number of residues = 17 + Number of atoms = 680 Number of groups = 17 + Number of bonds = 663 Number of angles = 896 + Number of dihedrals = 896 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "17" + SELRPN> 40 atoms have been selected out of 680 + SELRPN> 40 atoms have been selected out of 680 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "17" + SELRPN> 40 atoms have been selected out of 680 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "17" + SELRPN> 40 atoms have been selected out of 680 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "17" + SELRPN> 40 atoms have been selected out of 680 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "17" + SELRPN> 40 atoms have been selected out of 680 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "17" + SELRPN> 40 atoms have been selected out of 680 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "17" + SELRPN> 40 atoms have been selected out of 680 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 17 Number of residues = 17 + Number of atoms = 680 Number of groups = 17 + Number of bonds = 663 Number of angles = 952 + Number of dihedrals = 952 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "2" +Evaluating: 2+1 + Parameter: COUNTU <- "3" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "3" +Evaluating: 3-1.0 + Parameter: VECTU <- "2" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "4" +Evaluating: 4-1.0 + Parameter: VECTV <- "3" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "17" +Evaluating: 17+1 + Parameter: COUNT <- "18" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "18" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 18 has been generated. Its identifier is Q18. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 18 Number of residues = 18 + Number of atoms = 720 Number of groups = 18 + Number of bonds = 702 Number of angles = 952 + Number of dihedrals = 952 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "18" + SELRPN> 40 atoms have been selected out of 720 + SELRPN> 40 atoms have been selected out of 720 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "18" + SELRPN> 40 atoms have been selected out of 720 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "18" + SELRPN> 40 atoms have been selected out of 720 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "18" + SELRPN> 40 atoms have been selected out of 720 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "18" + SELRPN> 40 atoms have been selected out of 720 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "18" + SELRPN> 40 atoms have been selected out of 720 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "18" + SELRPN> 40 atoms have been selected out of 720 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 18 Number of residues = 18 + Number of atoms = 720 Number of groups = 18 + Number of bonds = 702 Number of angles = 1008 + Number of dihedrals = 1008 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "3" +Evaluating: 3+1 + Parameter: COUNTU <- "4" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "4" +Evaluating: 4-1.0 + Parameter: VECTU <- "3" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "4" +Evaluating: 4-1.0 + Parameter: VECTV <- "3" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "18" +Evaluating: 18+1 + Parameter: COUNT <- "19" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "19" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 19 has been generated. Its identifier is Q19. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 19 Number of residues = 19 + Number of atoms = 760 Number of groups = 19 + Number of bonds = 741 Number of angles = 1008 + Number of dihedrals = 1008 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "19" + SELRPN> 40 atoms have been selected out of 760 + SELRPN> 40 atoms have been selected out of 760 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "19" + SELRPN> 40 atoms have been selected out of 760 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "19" + SELRPN> 40 atoms have been selected out of 760 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "19" + SELRPN> 40 atoms have been selected out of 760 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "19" + SELRPN> 40 atoms have been selected out of 760 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "19" + SELRPN> 40 atoms have been selected out of 760 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "19" + SELRPN> 40 atoms have been selected out of 760 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 19 Number of residues = 19 + Number of atoms = 760 Number of groups = 19 + Number of bonds = 741 Number of angles = 1064 + Number of dihedrals = 1064 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "4" +Evaluating: 4+1 + Parameter: COUNTU <- "5" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "5" +Evaluating: 5-1.0 + Parameter: VECTU <- "4" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "4" +Evaluating: 4-1.0 + Parameter: VECTV <- "3" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "19" +Evaluating: 19+1 + Parameter: COUNT <- "20" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "20" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 20 has been generated. Its identifier is Q20. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 20 Number of residues = 20 + Number of atoms = 800 Number of groups = 20 + Number of bonds = 780 Number of angles = 1064 + Number of dihedrals = 1064 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "20" + SELRPN> 40 atoms have been selected out of 800 + SELRPN> 40 atoms have been selected out of 800 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "20" + SELRPN> 40 atoms have been selected out of 800 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "20" + SELRPN> 40 atoms have been selected out of 800 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "20" + SELRPN> 40 atoms have been selected out of 800 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "20" + SELRPN> 40 atoms have been selected out of 800 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "20" + SELRPN> 40 atoms have been selected out of 800 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "3" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "20" + SELRPN> 40 atoms have been selected out of 800 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 20 Number of residues = 20 + Number of atoms = 800 Number of groups = 20 + Number of bonds = 780 Number of angles = 1120 + Number of dihedrals = 1120 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "5" +Evaluating: 5+1 + Parameter: COUNTU <- "6" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set countU 1 + Parameter: COUNTU <- "1" + + CHARMM> + + CHARMM> calc countV = @countV + 1 + Parameter: COUNTV -> "4" +Evaluating: 4+1 + Parameter: COUNTV <- "5" + + CHARMM> + + CHARMM> if countV le @maxV goto loopV + Parameter: MAXV -> "8" + Comparing "5" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> label loopU + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "1" +Evaluating: 1-1.0 + Parameter: VECTU <- "0" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "5" +Evaluating: 5-1.0 + Parameter: VECTV <- "4" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "20" +Evaluating: 20+1 + Parameter: COUNT <- "21" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "21" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 21 has been generated. Its identifier is Q21. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 21 Number of residues = 21 + Number of atoms = 840 Number of groups = 21 + Number of bonds = 819 Number of angles = 1120 + Number of dihedrals = 1120 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "21" + SELRPN> 40 atoms have been selected out of 840 + SELRPN> 40 atoms have been selected out of 840 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "21" + SELRPN> 40 atoms have been selected out of 840 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "21" + SELRPN> 40 atoms have been selected out of 840 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "21" + SELRPN> 40 atoms have been selected out of 840 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "21" + SELRPN> 40 atoms have been selected out of 840 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "21" + SELRPN> 40 atoms have been selected out of 840 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "21" + SELRPN> 40 atoms have been selected out of 840 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 21 Number of residues = 21 + Number of atoms = 840 Number of groups = 21 + Number of bonds = 819 Number of angles = 1176 + Number of dihedrals = 1176 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "1" +Evaluating: 1+1 + Parameter: COUNTU <- "2" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "2" +Evaluating: 2-1.0 + Parameter: VECTU <- "1" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "5" +Evaluating: 5-1.0 + Parameter: VECTV <- "4" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "21" +Evaluating: 21+1 + Parameter: COUNT <- "22" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "22" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 22 has been generated. Its identifier is Q22. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 22 Number of residues = 22 + Number of atoms = 880 Number of groups = 22 + Number of bonds = 858 Number of angles = 1176 + Number of dihedrals = 1176 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "22" + SELRPN> 40 atoms have been selected out of 880 + SELRPN> 40 atoms have been selected out of 880 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "22" + SELRPN> 40 atoms have been selected out of 880 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "22" + SELRPN> 40 atoms have been selected out of 880 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "22" + SELRPN> 40 atoms have been selected out of 880 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "22" + SELRPN> 40 atoms have been selected out of 880 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "22" + SELRPN> 40 atoms have been selected out of 880 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "22" + SELRPN> 40 atoms have been selected out of 880 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 22 Number of residues = 22 + Number of atoms = 880 Number of groups = 22 + Number of bonds = 858 Number of angles = 1232 + Number of dihedrals = 1232 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "2" +Evaluating: 2+1 + Parameter: COUNTU <- "3" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "3" +Evaluating: 3-1.0 + Parameter: VECTU <- "2" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "5" +Evaluating: 5-1.0 + Parameter: VECTV <- "4" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "22" +Evaluating: 22+1 + Parameter: COUNT <- "23" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "23" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 23 has been generated. Its identifier is Q23. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 23 Number of residues = 23 + Number of atoms = 920 Number of groups = 23 + Number of bonds = 897 Number of angles = 1232 + Number of dihedrals = 1232 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "23" + SELRPN> 40 atoms have been selected out of 920 + SELRPN> 40 atoms have been selected out of 920 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "23" + SELRPN> 40 atoms have been selected out of 920 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "23" + SELRPN> 40 atoms have been selected out of 920 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "23" + SELRPN> 40 atoms have been selected out of 920 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "23" + SELRPN> 40 atoms have been selected out of 920 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "23" + SELRPN> 40 atoms have been selected out of 920 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "23" + SELRPN> 40 atoms have been selected out of 920 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 23 Number of residues = 23 + Number of atoms = 920 Number of groups = 23 + Number of bonds = 897 Number of angles = 1288 + Number of dihedrals = 1288 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "3" +Evaluating: 3+1 + Parameter: COUNTU <- "4" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "4" +Evaluating: 4-1.0 + Parameter: VECTU <- "3" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "5" +Evaluating: 5-1.0 + Parameter: VECTV <- "4" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "23" +Evaluating: 23+1 + Parameter: COUNT <- "24" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "24" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 24 has been generated. Its identifier is Q24. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 24 Number of residues = 24 + Number of atoms = 960 Number of groups = 24 + Number of bonds = 936 Number of angles = 1288 + Number of dihedrals = 1288 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "24" + SELRPN> 40 atoms have been selected out of 960 + SELRPN> 40 atoms have been selected out of 960 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "24" + SELRPN> 40 atoms have been selected out of 960 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "24" + SELRPN> 40 atoms have been selected out of 960 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "24" + SELRPN> 40 atoms have been selected out of 960 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "24" + SELRPN> 40 atoms have been selected out of 960 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "24" + SELRPN> 40 atoms have been selected out of 960 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "24" + SELRPN> 40 atoms have been selected out of 960 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 24 Number of residues = 24 + Number of atoms = 960 Number of groups = 24 + Number of bonds = 936 Number of angles = 1344 + Number of dihedrals = 1344 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "4" +Evaluating: 4+1 + Parameter: COUNTU <- "5" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "5" +Evaluating: 5-1.0 + Parameter: VECTU <- "4" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "5" +Evaluating: 5-1.0 + Parameter: VECTV <- "4" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "24" +Evaluating: 24+1 + Parameter: COUNT <- "25" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "25" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 25 has been generated. Its identifier is Q25. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 25 Number of residues = 25 + Number of atoms = 1000 Number of groups = 25 + Number of bonds = 975 Number of angles = 1344 + Number of dihedrals = 1344 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "25" + SELRPN> 40 atoms have been selected out of 1000 + SELRPN> 40 atoms have been selected out of 1000 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "25" + SELRPN> 40 atoms have been selected out of 1000 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "25" + SELRPN> 40 atoms have been selected out of 1000 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "25" + SELRPN> 40 atoms have been selected out of 1000 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "25" + SELRPN> 40 atoms have been selected out of 1000 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "25" + SELRPN> 40 atoms have been selected out of 1000 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "4" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "25" + SELRPN> 40 atoms have been selected out of 1000 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 25 Number of residues = 25 + Number of atoms = 1000 Number of groups = 25 + Number of bonds = 975 Number of angles = 1400 + Number of dihedrals = 1400 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "5" +Evaluating: 5+1 + Parameter: COUNTU <- "6" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set countU 1 + Parameter: COUNTU <- "1" + + CHARMM> + + CHARMM> calc countV = @countV + 1 + Parameter: COUNTV -> "5" +Evaluating: 5+1 + Parameter: COUNTV <- "6" + + CHARMM> + + CHARMM> if countV le @maxV goto loopV + Parameter: MAXV -> "8" + Comparing "6" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> label loopU + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "1" +Evaluating: 1-1.0 + Parameter: VECTU <- "0" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "6" +Evaluating: 6-1.0 + Parameter: VECTV <- "5" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "25" +Evaluating: 25+1 + Parameter: COUNT <- "26" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "26" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 26 has been generated. Its identifier is Q26. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 26 Number of residues = 26 + Number of atoms = 1040 Number of groups = 26 + Number of bonds = 1014 Number of angles = 1400 + Number of dihedrals = 1400 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "26" + SELRPN> 40 atoms have been selected out of 1040 + SELRPN> 40 atoms have been selected out of 1040 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "26" + SELRPN> 40 atoms have been selected out of 1040 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "26" + SELRPN> 40 atoms have been selected out of 1040 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "26" + SELRPN> 40 atoms have been selected out of 1040 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "26" + SELRPN> 40 atoms have been selected out of 1040 + TRANSLATION VECTOR 5.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "26" + SELRPN> 40 atoms have been selected out of 1040 + TRANSLATION VECTOR 0.000000 5.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "26" + SELRPN> 40 atoms have been selected out of 1040 + TRANSLATION VECTOR 0.000000 0.000000 5.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 26 Number of residues = 26 + Number of atoms = 1040 Number of groups = 26 + Number of bonds = 1014 Number of angles = 1456 + Number of dihedrals = 1456 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "1" +Evaluating: 1+1 + Parameter: COUNTU <- "2" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "2" +Evaluating: 2-1.0 + Parameter: VECTU <- "1" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "6" +Evaluating: 6-1.0 + Parameter: VECTV <- "5" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "26" +Evaluating: 26+1 + Parameter: COUNT <- "27" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "27" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 27 has been generated. Its identifier is Q27. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 27 Number of residues = 27 + Number of atoms = 1080 Number of groups = 27 + Number of bonds = 1053 Number of angles = 1456 + Number of dihedrals = 1456 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "27" + SELRPN> 40 atoms have been selected out of 1080 + SELRPN> 40 atoms have been selected out of 1080 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "27" + SELRPN> 40 atoms have been selected out of 1080 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "27" + SELRPN> 40 atoms have been selected out of 1080 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "27" + SELRPN> 40 atoms have been selected out of 1080 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "27" + SELRPN> 40 atoms have been selected out of 1080 + TRANSLATION VECTOR 5.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "27" + SELRPN> 40 atoms have been selected out of 1080 + TRANSLATION VECTOR 0.000000 5.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "27" + SELRPN> 40 atoms have been selected out of 1080 + TRANSLATION VECTOR 0.000000 0.000000 5.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 27 Number of residues = 27 + Number of atoms = 1080 Number of groups = 27 + Number of bonds = 1053 Number of angles = 1512 + Number of dihedrals = 1512 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "2" +Evaluating: 2+1 + Parameter: COUNTU <- "3" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "3" +Evaluating: 3-1.0 + Parameter: VECTU <- "2" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "6" +Evaluating: 6-1.0 + Parameter: VECTV <- "5" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "27" +Evaluating: 27+1 + Parameter: COUNT <- "28" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "28" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 28 has been generated. Its identifier is Q28. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 28 Number of residues = 28 + Number of atoms = 1120 Number of groups = 28 + Number of bonds = 1092 Number of angles = 1512 + Number of dihedrals = 1512 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "28" + SELRPN> 40 atoms have been selected out of 1120 + SELRPN> 40 atoms have been selected out of 1120 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "28" + SELRPN> 40 atoms have been selected out of 1120 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "28" + SELRPN> 40 atoms have been selected out of 1120 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "28" + SELRPN> 40 atoms have been selected out of 1120 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "28" + SELRPN> 40 atoms have been selected out of 1120 + TRANSLATION VECTOR 5.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "28" + SELRPN> 40 atoms have been selected out of 1120 + TRANSLATION VECTOR 0.000000 5.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "28" + SELRPN> 40 atoms have been selected out of 1120 + TRANSLATION VECTOR 0.000000 0.000000 5.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 28 Number of residues = 28 + Number of atoms = 1120 Number of groups = 28 + Number of bonds = 1092 Number of angles = 1568 + Number of dihedrals = 1568 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "3" +Evaluating: 3+1 + Parameter: COUNTU <- "4" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "4" +Evaluating: 4-1.0 + Parameter: VECTU <- "3" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "6" +Evaluating: 6-1.0 + Parameter: VECTV <- "5" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "28" +Evaluating: 28+1 + Parameter: COUNT <- "29" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "29" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 29 has been generated. Its identifier is Q29. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 29 Number of residues = 29 + Number of atoms = 1160 Number of groups = 29 + Number of bonds = 1131 Number of angles = 1568 + Number of dihedrals = 1568 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "29" + SELRPN> 40 atoms have been selected out of 1160 + SELRPN> 40 atoms have been selected out of 1160 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "29" + SELRPN> 40 atoms have been selected out of 1160 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "29" + SELRPN> 40 atoms have been selected out of 1160 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "29" + SELRPN> 40 atoms have been selected out of 1160 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "29" + SELRPN> 40 atoms have been selected out of 1160 + TRANSLATION VECTOR 5.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "29" + SELRPN> 40 atoms have been selected out of 1160 + TRANSLATION VECTOR 0.000000 5.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "29" + SELRPN> 40 atoms have been selected out of 1160 + TRANSLATION VECTOR 0.000000 0.000000 5.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 29 Number of residues = 29 + Number of atoms = 1160 Number of groups = 29 + Number of bonds = 1131 Number of angles = 1624 + Number of dihedrals = 1624 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "4" +Evaluating: 4+1 + Parameter: COUNTU <- "5" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "5" +Evaluating: 5-1.0 + Parameter: VECTU <- "4" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "6" +Evaluating: 6-1.0 + Parameter: VECTV <- "5" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "29" +Evaluating: 29+1 + Parameter: COUNT <- "30" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "30" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 30 has been generated. Its identifier is Q30. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 30 Number of residues = 30 + Number of atoms = 1200 Number of groups = 30 + Number of bonds = 1170 Number of angles = 1624 + Number of dihedrals = 1624 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "30" + SELRPN> 40 atoms have been selected out of 1200 + SELRPN> 40 atoms have been selected out of 1200 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "30" + SELRPN> 40 atoms have been selected out of 1200 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "30" + SELRPN> 40 atoms have been selected out of 1200 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "30" + SELRPN> 40 atoms have been selected out of 1200 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "30" + SELRPN> 40 atoms have been selected out of 1200 + TRANSLATION VECTOR 5.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "30" + SELRPN> 40 atoms have been selected out of 1200 + TRANSLATION VECTOR 0.000000 5.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "5" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "30" + SELRPN> 40 atoms have been selected out of 1200 + TRANSLATION VECTOR 0.000000 0.000000 5.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 30 Number of residues = 30 + Number of atoms = 1200 Number of groups = 30 + Number of bonds = 1170 Number of angles = 1680 + Number of dihedrals = 1680 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "5" +Evaluating: 5+1 + Parameter: COUNTU <- "6" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set countU 1 + Parameter: COUNTU <- "1" + + CHARMM> + + CHARMM> calc countV = @countV + 1 + Parameter: COUNTV -> "6" +Evaluating: 6+1 + Parameter: COUNTV <- "7" + + CHARMM> + + CHARMM> if countV le @maxV goto loopV + Parameter: MAXV -> "8" + Comparing "7" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> label loopU + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "1" +Evaluating: 1-1.0 + Parameter: VECTU <- "0" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "7" +Evaluating: 7-1.0 + Parameter: VECTV <- "6" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "30" +Evaluating: 30+1 + Parameter: COUNT <- "31" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "31" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 31 has been generated. Its identifier is Q31. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 31 Number of residues = 31 + Number of atoms = 1240 Number of groups = 31 + Number of bonds = 1209 Number of angles = 1680 + Number of dihedrals = 1680 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "31" + SELRPN> 40 atoms have been selected out of 1240 + SELRPN> 40 atoms have been selected out of 1240 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "31" + SELRPN> 40 atoms have been selected out of 1240 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "31" + SELRPN> 40 atoms have been selected out of 1240 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "31" + SELRPN> 40 atoms have been selected out of 1240 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "31" + SELRPN> 40 atoms have been selected out of 1240 + TRANSLATION VECTOR 6.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "31" + SELRPN> 40 atoms have been selected out of 1240 + TRANSLATION VECTOR 0.000000 6.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "31" + SELRPN> 40 atoms have been selected out of 1240 + TRANSLATION VECTOR 0.000000 0.000000 6.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 31 Number of residues = 31 + Number of atoms = 1240 Number of groups = 31 + Number of bonds = 1209 Number of angles = 1736 + Number of dihedrals = 1736 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "1" +Evaluating: 1+1 + Parameter: COUNTU <- "2" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "2" +Evaluating: 2-1.0 + Parameter: VECTU <- "1" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "7" +Evaluating: 7-1.0 + Parameter: VECTV <- "6" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "31" +Evaluating: 31+1 + Parameter: COUNT <- "32" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "32" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 32 has been generated. Its identifier is Q32. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 32 Number of residues = 32 + Number of atoms = 1280 Number of groups = 32 + Number of bonds = 1248 Number of angles = 1736 + Number of dihedrals = 1736 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "32" + SELRPN> 40 atoms have been selected out of 1280 + SELRPN> 40 atoms have been selected out of 1280 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "32" + SELRPN> 40 atoms have been selected out of 1280 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "32" + SELRPN> 40 atoms have been selected out of 1280 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "32" + SELRPN> 40 atoms have been selected out of 1280 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "32" + SELRPN> 40 atoms have been selected out of 1280 + TRANSLATION VECTOR 6.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "32" + SELRPN> 40 atoms have been selected out of 1280 + TRANSLATION VECTOR 0.000000 6.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "32" + SELRPN> 40 atoms have been selected out of 1280 + TRANSLATION VECTOR 0.000000 0.000000 6.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 32 Number of residues = 32 + Number of atoms = 1280 Number of groups = 32 + Number of bonds = 1248 Number of angles = 1792 + Number of dihedrals = 1792 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "2" +Evaluating: 2+1 + Parameter: COUNTU <- "3" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "3" +Evaluating: 3-1.0 + Parameter: VECTU <- "2" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "7" +Evaluating: 7-1.0 + Parameter: VECTV <- "6" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "32" +Evaluating: 32+1 + Parameter: COUNT <- "33" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "33" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 33 has been generated. Its identifier is Q33. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 33 Number of residues = 33 + Number of atoms = 1320 Number of groups = 33 + Number of bonds = 1287 Number of angles = 1792 + Number of dihedrals = 1792 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "33" + SELRPN> 40 atoms have been selected out of 1320 + SELRPN> 40 atoms have been selected out of 1320 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "33" + SELRPN> 40 atoms have been selected out of 1320 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "33" + SELRPN> 40 atoms have been selected out of 1320 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "33" + SELRPN> 40 atoms have been selected out of 1320 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "33" + SELRPN> 40 atoms have been selected out of 1320 + TRANSLATION VECTOR 6.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "33" + SELRPN> 40 atoms have been selected out of 1320 + TRANSLATION VECTOR 0.000000 6.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "33" + SELRPN> 40 atoms have been selected out of 1320 + TRANSLATION VECTOR 0.000000 0.000000 6.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 33 Number of residues = 33 + Number of atoms = 1320 Number of groups = 33 + Number of bonds = 1287 Number of angles = 1848 + Number of dihedrals = 1848 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "3" +Evaluating: 3+1 + Parameter: COUNTU <- "4" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "4" +Evaluating: 4-1.0 + Parameter: VECTU <- "3" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "7" +Evaluating: 7-1.0 + Parameter: VECTV <- "6" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "33" +Evaluating: 33+1 + Parameter: COUNT <- "34" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "34" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 34 has been generated. Its identifier is Q34. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 34 Number of residues = 34 + Number of atoms = 1360 Number of groups = 34 + Number of bonds = 1326 Number of angles = 1848 + Number of dihedrals = 1848 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "34" + SELRPN> 40 atoms have been selected out of 1360 + SELRPN> 40 atoms have been selected out of 1360 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "34" + SELRPN> 40 atoms have been selected out of 1360 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "34" + SELRPN> 40 atoms have been selected out of 1360 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "34" + SELRPN> 40 atoms have been selected out of 1360 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "34" + SELRPN> 40 atoms have been selected out of 1360 + TRANSLATION VECTOR 6.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "34" + SELRPN> 40 atoms have been selected out of 1360 + TRANSLATION VECTOR 0.000000 6.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "34" + SELRPN> 40 atoms have been selected out of 1360 + TRANSLATION VECTOR 0.000000 0.000000 6.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 34 Number of residues = 34 + Number of atoms = 1360 Number of groups = 34 + Number of bonds = 1326 Number of angles = 1904 + Number of dihedrals = 1904 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "4" +Evaluating: 4+1 + Parameter: COUNTU <- "5" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "5" +Evaluating: 5-1.0 + Parameter: VECTU <- "4" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "7" +Evaluating: 7-1.0 + Parameter: VECTV <- "6" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "34" +Evaluating: 34+1 + Parameter: COUNT <- "35" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "35" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 35 has been generated. Its identifier is Q35. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 35 Number of residues = 35 + Number of atoms = 1400 Number of groups = 35 + Number of bonds = 1365 Number of angles = 1904 + Number of dihedrals = 1904 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "35" + SELRPN> 40 atoms have been selected out of 1400 + SELRPN> 40 atoms have been selected out of 1400 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "35" + SELRPN> 40 atoms have been selected out of 1400 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "35" + SELRPN> 40 atoms have been selected out of 1400 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "35" + SELRPN> 40 atoms have been selected out of 1400 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "35" + SELRPN> 40 atoms have been selected out of 1400 + TRANSLATION VECTOR 6.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "35" + SELRPN> 40 atoms have been selected out of 1400 + TRANSLATION VECTOR 0.000000 6.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "6" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "35" + SELRPN> 40 atoms have been selected out of 1400 + TRANSLATION VECTOR 0.000000 0.000000 6.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 35 Number of residues = 35 + Number of atoms = 1400 Number of groups = 35 + Number of bonds = 1365 Number of angles = 1960 + Number of dihedrals = 1960 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "5" +Evaluating: 5+1 + Parameter: COUNTU <- "6" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set countU 1 + Parameter: COUNTU <- "1" + + CHARMM> + + CHARMM> calc countV = @countV + 1 + Parameter: COUNTV -> "7" +Evaluating: 7+1 + Parameter: COUNTV <- "8" + + CHARMM> + + CHARMM> if countV le @maxV goto loopV + Parameter: MAXV -> "8" + Comparing "8" and "8". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> label loopU + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "1" +Evaluating: 1-1.0 + Parameter: VECTU <- "0" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "8" +Evaluating: 8-1.0 + Parameter: VECTV <- "7" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "35" +Evaluating: 35+1 + Parameter: COUNT <- "36" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "36" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 36 has been generated. Its identifier is Q36. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 36 Number of residues = 36 + Number of atoms = 1440 Number of groups = 36 + Number of bonds = 1404 Number of angles = 1960 + Number of dihedrals = 1960 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "36" + SELRPN> 40 atoms have been selected out of 1440 + SELRPN> 40 atoms have been selected out of 1440 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "36" + SELRPN> 40 atoms have been selected out of 1440 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "36" + SELRPN> 40 atoms have been selected out of 1440 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "0" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "36" + SELRPN> 40 atoms have been selected out of 1440 + TRANSLATION VECTOR 0.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "36" + SELRPN> 40 atoms have been selected out of 1440 + TRANSLATION VECTOR 7.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "36" + SELRPN> 40 atoms have been selected out of 1440 + TRANSLATION VECTOR 0.000000 7.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "36" + SELRPN> 40 atoms have been selected out of 1440 + TRANSLATION VECTOR 0.000000 0.000000 7.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 36 Number of residues = 36 + Number of atoms = 1440 Number of groups = 36 + Number of bonds = 1404 Number of angles = 2016 + Number of dihedrals = 2016 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "1" +Evaluating: 1+1 + Parameter: COUNTU <- "2" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "2" +Evaluating: 2-1.0 + Parameter: VECTU <- "1" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "8" +Evaluating: 8-1.0 + Parameter: VECTV <- "7" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "36" +Evaluating: 36+1 + Parameter: COUNT <- "37" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "37" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 37 has been generated. Its identifier is Q37. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 37 Number of residues = 37 + Number of atoms = 1480 Number of groups = 37 + Number of bonds = 1443 Number of angles = 2016 + Number of dihedrals = 2016 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "37" + SELRPN> 40 atoms have been selected out of 1480 + SELRPN> 40 atoms have been selected out of 1480 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "37" + SELRPN> 40 atoms have been selected out of 1480 + TRANSLATION VECTOR 1.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "37" + SELRPN> 40 atoms have been selected out of 1480 + TRANSLATION VECTOR 0.000000 1.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "1" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "37" + SELRPN> 40 atoms have been selected out of 1480 + TRANSLATION VECTOR 0.000000 0.000000 1.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "37" + SELRPN> 40 atoms have been selected out of 1480 + TRANSLATION VECTOR 7.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "37" + SELRPN> 40 atoms have been selected out of 1480 + TRANSLATION VECTOR 0.000000 7.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "37" + SELRPN> 40 atoms have been selected out of 1480 + TRANSLATION VECTOR 0.000000 0.000000 7.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 37 Number of residues = 37 + Number of atoms = 1480 Number of groups = 37 + Number of bonds = 1443 Number of angles = 2072 + Number of dihedrals = 2072 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "2" +Evaluating: 2+1 + Parameter: COUNTU <- "3" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "3" +Evaluating: 3-1.0 + Parameter: VECTU <- "2" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "8" +Evaluating: 8-1.0 + Parameter: VECTV <- "7" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "37" +Evaluating: 37+1 + Parameter: COUNT <- "38" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "38" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 38 has been generated. Its identifier is Q38. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 38 Number of residues = 38 + Number of atoms = 1520 Number of groups = 38 + Number of bonds = 1482 Number of angles = 2072 + Number of dihedrals = 2072 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "38" + SELRPN> 40 atoms have been selected out of 1520 + SELRPN> 40 atoms have been selected out of 1520 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "38" + SELRPN> 40 atoms have been selected out of 1520 + TRANSLATION VECTOR 2.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "38" + SELRPN> 40 atoms have been selected out of 1520 + TRANSLATION VECTOR 0.000000 2.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "2" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "38" + SELRPN> 40 atoms have been selected out of 1520 + TRANSLATION VECTOR 0.000000 0.000000 2.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "38" + SELRPN> 40 atoms have been selected out of 1520 + TRANSLATION VECTOR 7.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "38" + SELRPN> 40 atoms have been selected out of 1520 + TRANSLATION VECTOR 0.000000 7.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "38" + SELRPN> 40 atoms have been selected out of 1520 + TRANSLATION VECTOR 0.000000 0.000000 7.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 38 Number of residues = 38 + Number of atoms = 1520 Number of groups = 38 + Number of bonds = 1482 Number of angles = 2128 + Number of dihedrals = 2128 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "3" +Evaluating: 3+1 + Parameter: COUNTU <- "4" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "4" +Evaluating: 4-1.0 + Parameter: VECTU <- "3" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "8" +Evaluating: 8-1.0 + Parameter: VECTV <- "7" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "38" +Evaluating: 38+1 + Parameter: COUNT <- "39" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "39" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 39 has been generated. Its identifier is Q39. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 39 Number of residues = 39 + Number of atoms = 1560 Number of groups = 39 + Number of bonds = 1521 Number of angles = 2128 + Number of dihedrals = 2128 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "39" + SELRPN> 40 atoms have been selected out of 1560 + SELRPN> 40 atoms have been selected out of 1560 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "39" + SELRPN> 40 atoms have been selected out of 1560 + TRANSLATION VECTOR 3.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "39" + SELRPN> 40 atoms have been selected out of 1560 + TRANSLATION VECTOR 0.000000 3.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "3" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "39" + SELRPN> 40 atoms have been selected out of 1560 + TRANSLATION VECTOR 0.000000 0.000000 3.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "39" + SELRPN> 40 atoms have been selected out of 1560 + TRANSLATION VECTOR 7.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "39" + SELRPN> 40 atoms have been selected out of 1560 + TRANSLATION VECTOR 0.000000 7.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "39" + SELRPN> 40 atoms have been selected out of 1560 + TRANSLATION VECTOR 0.000000 0.000000 7.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 39 Number of residues = 39 + Number of atoms = 1560 Number of groups = 39 + Number of bonds = 1521 Number of angles = 2184 + Number of dihedrals = 2184 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "4" +Evaluating: 4+1 + Parameter: COUNTU <- "5" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "5" and "5". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> ! generate copy of unit cell. name it Q@COUNT + CHARMM> + + CHARMM> calc vectU = @countU - 1.0 + Parameter: COUNTU -> "5" +Evaluating: 5-1.0 + Parameter: VECTU <- "4" + + CHARMM> calc vectV = @countV - 1.0 + Parameter: COUNTV -> "8" +Evaluating: 8-1.0 + Parameter: VECTV <- "7" + + CHARMM> + + CHARMM> calc count = @count + 1 + Parameter: COUNT -> "39" +Evaluating: 39+1 + Parameter: COUNT <- "40" + + CHARMM> + + CHARMM> read sequ card + MAINIO> Sequence information being read from unit 5. + RDTITL> * QUARTZ + RDTITL> * + + SEQRDR> 1 + + SEQRDR> Q011 + + RESIDUE SEQUENCE -- 1 RESIDUES + Q011 + + CHARMM> + + CHARMM> generate Q@count noangle nodihedral first none last none setup warn + Parameter: COUNT -> "40" + NO PATCHING WILL BE DONE ON THE FIRST RESIDUE + NO PATCHING WILL BE DONE ON THE LAST RESIDUE + GENPSF> Segment 40 has been generated. Its identifier is Q40. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1560 Number of angles = 2184 + Number of dihedrals = 2184 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> coor dupl sele segi q1 end sele segi q@count end + Parameter: COUNT -> "40" + SELRPN> 40 atoms have been selected out of 1600 + SELRPN> 40 atoms have been selected out of 1600 + + CHARMM> + + CHARMM> coor trans XDir @vectU YDIR 0.0 ZDIR 0.0 FACT @u1 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U1 -> "7.3000" + Parameter: COUNT -> "40" + SELRPN> 40 atoms have been selected out of 1600 + TRANSLATION VECTOR 4.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectU ZDIR 0.0 FACT @u2 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U2 -> "0.0" + Parameter: COUNT -> "40" + SELRPN> 40 atoms have been selected out of 1600 + TRANSLATION VECTOR 0.000000 4.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectU FACT @u3 SELE SEGI q@count END + Parameter: VECTU -> "4" + Parameter: U3 -> "0.0" + Parameter: COUNT -> "40" + SELRPN> 40 atoms have been selected out of 1600 + TRANSLATION VECTOR 0.000000 0.000000 4.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> coor trans XDir @vectV YDIR 0.0 ZDIR 0.0 FACT @v1 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V1 -> "-1.65124" + Parameter: COUNT -> "40" + SELRPN> 40 atoms have been selected out of 1600 + TRANSLATION VECTOR 7.000000 0.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR @vectV ZDIR 0.0 FACT @v2 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V2 -> "4.62401" + Parameter: COUNT -> "40" + SELRPN> 40 atoms have been selected out of 1600 + TRANSLATION VECTOR 0.000000 7.000000 0.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> coor trans XDir 0.0 YDIR 0.0 ZDIR @vectV FACT @v3 SELE SEGI q@count END + Parameter: VECTV -> "7" + Parameter: V3 -> "0.0" + Parameter: COUNT -> "40" + SELRPN> 40 atoms have been selected out of 1600 + TRANSLATION VECTOR 0.000000 0.000000 7.000000 + SELECTED COORDINATES TRANSLATED IN THE MAIN SET. + + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1560 Number of angles = 2240 + Number of dihedrals = 2240 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc countU = @countU + 1 + Parameter: COUNTU -> "5" +Evaluating: 5+1 + Parameter: COUNTU <- "6" + + CHARMM> + + CHARMM> ! PRINT COOR + CHARMM> ! PRINT PSF + CHARMM> + + CHARMM> if countU le @maxU goto loopU + Parameter: MAXU -> "5" + Comparing "6" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set countU 1 + Parameter: COUNTU <- "1" + + CHARMM> + + CHARMM> calc countV = @countV + 1 + Parameter: COUNTV -> "8" +Evaluating: 8+1 + Parameter: COUNTV <- "9" + + CHARMM> + + CHARMM> if countV le @maxV goto loopV + Parameter: MAXV -> "8" + Comparing "9" and "8". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !PRINT COOR + CHARMM> !PRINT PSF + CHARMM> + + CHARMM> ! apply patches + CHARMM> + + CHARMM> set count 0 + Parameter: COUNT <- "0" + + CHARMM> + + CHARMM> calc endXloop = @maxU - 1.0 + Parameter: MAXU -> "5" +Evaluating: 5-1.0 + Parameter: ENDXLOOP <- "4" + + CHARMM> calc endYloop = @maxV - 1.0 + Parameter: MAXV -> "8" +Evaluating: 8-1.0 + Parameter: ENDYLOOP <- "7" + + CHARMM> + + CHARMM> set incX 1 + Parameter: INCX <- "1" + + CHARMM> set incY 1 + Parameter: INCY <- "1" + + CHARMM> + + CHARMM> label loopY + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "0" +Evaluating: 0+1.0 + Parameter: COUNT <- "1" + + CHARMM> + + CHARMM> label loopX + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "1" +Evaluating: 1+1.0 + Parameter: X <- "2" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "1" + Parameter: X -> "2" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1564 Number of angles = 2252 + Number of dihedrals = 2263 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1564 Number of angles = 2252 + Number of dihedrals = 2263 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "1" + Parameter: MAXU -> "5" +Evaluating: 1+5 + Parameter: Y <- "6" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "1" + Parameter: Y -> "6" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1570 Number of angles = 2273 + Number of dihedrals = 2302 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1570 Number of angles = 2273 + Number of dihedrals = 2305 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "2" + Parameter: MAXU -> "5" +Evaluating: 2+5 + Parameter: XY <- "7" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "1" + Parameter: XY -> "7" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1571 Number of angles = 2280 + Number of dihedrals = 2311 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1571 Number of angles = 2277 + Number of dihedrals = 2314 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "1" +Evaluating: 1+1.0 + Parameter: COUNT <- "2" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "1" +Evaluating: 1+1.0 + Parameter: INCX <- "2" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "2" +Evaluating: 2+1.0 + Parameter: X <- "3" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "2" + Parameter: X -> "3" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1575 Number of angles = 2289 + Number of dihedrals = 2337 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1575 Number of angles = 2289 + Number of dihedrals = 2337 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "2" + Parameter: MAXU -> "5" +Evaluating: 2+5 + Parameter: Y <- "7" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "2" + Parameter: Y -> "7" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1581 Number of angles = 2310 + Number of dihedrals = 2376 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1581 Number of angles = 2311 + Number of dihedrals = 2382 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "3" + Parameter: MAXU -> "5" +Evaluating: 3+5 + Parameter: XY <- "8" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "2" + Parameter: XY -> "8" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1582 Number of angles = 2318 + Number of dihedrals = 2388 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1582 Number of angles = 2315 + Number of dihedrals = 2391 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "2" +Evaluating: 2+1.0 + Parameter: COUNT <- "3" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "2" +Evaluating: 2+1.0 + Parameter: INCX <- "3" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "3" +Evaluating: 3+1.0 + Parameter: X <- "4" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "3" + Parameter: X -> "4" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1586 Number of angles = 2327 + Number of dihedrals = 2414 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1586 Number of angles = 2327 + Number of dihedrals = 2414 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "3" + Parameter: MAXU -> "5" +Evaluating: 3+5 + Parameter: Y <- "8" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "3" + Parameter: Y -> "8" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1592 Number of angles = 2348 + Number of dihedrals = 2453 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1592 Number of angles = 2349 + Number of dihedrals = 2459 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "4" + Parameter: MAXU -> "5" +Evaluating: 4+5 + Parameter: XY <- "9" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "3" + Parameter: XY -> "9" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1593 Number of angles = 2356 + Number of dihedrals = 2465 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1593 Number of angles = 2353 + Number of dihedrals = 2468 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "3" +Evaluating: 3+1.0 + Parameter: COUNT <- "4" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "3" +Evaluating: 3+1.0 + Parameter: INCX <- "4" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "4" +Evaluating: 4+1.0 + Parameter: X <- "5" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "4" + Parameter: X -> "5" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1597 Number of angles = 2365 + Number of dihedrals = 2491 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1597 Number of angles = 2365 + Number of dihedrals = 2491 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "4" + Parameter: MAXU -> "5" +Evaluating: 4+5 + Parameter: Y <- "9" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "4" + Parameter: Y -> "9" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1603 Number of angles = 2386 + Number of dihedrals = 2530 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1603 Number of angles = 2387 + Number of dihedrals = 2536 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "5" + Parameter: MAXU -> "5" +Evaluating: 5+5 + Parameter: XY <- "10" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "4" + Parameter: XY -> "10" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1604 Number of angles = 2394 + Number of dihedrals = 2542 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1604 Number of angles = 2391 + Number of dihedrals = 2545 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "4" +Evaluating: 4+1.0 + Parameter: COUNT <- "5" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "4" +Evaluating: 4+1.0 + Parameter: INCX <- "5" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set incX 1 + Parameter: INCX <- "1" + + CHARMM> + + CHARMM> calc incY = @incY + 1.0 + Parameter: INCY -> "1" +Evaluating: 1+1.0 + Parameter: INCY <- "2" + + CHARMM> + + CHARMM> calc lastX = @X + @maxU + Parameter: X -> "5" + Parameter: MAXU -> "5" +Evaluating: 5+5 + Parameter: LASTX <- "10" + + CHARMM> + + CHARMM> patch 011B q@X 1 q@lastX 1 setup warn ! patch last column along V + Parameter: X -> "5" + Parameter: LASTX -> "10" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1610 Number of angles = 2412 + Number of dihedrals = 2584 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1610 Number of angles = 2413 + Number of dihedrals = 2588 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> if incY le @endYloop goto loopY + Parameter: ENDYLOOP -> "7" + Comparing "2" and "7". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "5" +Evaluating: 5+1.0 + Parameter: COUNT <- "6" + + CHARMM> + + CHARMM> label loopX + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "6" +Evaluating: 6+1.0 + Parameter: X <- "7" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "6" + Parameter: X -> "7" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1614 Number of angles = 2425 + Number of dihedrals = 2611 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1614 Number of angles = 2427 + Number of dihedrals = 2616 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "6" + Parameter: MAXU -> "5" +Evaluating: 6+5 + Parameter: Y <- "11" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "6" + Parameter: Y -> "11" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1620 Number of angles = 2448 + Number of dihedrals = 2655 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1620 Number of angles = 2448 + Number of dihedrals = 2658 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "7" + Parameter: MAXU -> "5" +Evaluating: 7+5 + Parameter: XY <- "12" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "6" + Parameter: XY -> "12" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1621 Number of angles = 2455 + Number of dihedrals = 2664 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1621 Number of angles = 2452 + Number of dihedrals = 2667 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "6" +Evaluating: 6+1.0 + Parameter: COUNT <- "7" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "1" +Evaluating: 1+1.0 + Parameter: INCX <- "2" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "7" +Evaluating: 7+1.0 + Parameter: X <- "8" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "7" + Parameter: X -> "8" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1625 Number of angles = 2464 + Number of dihedrals = 2690 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1625 Number of angles = 2466 + Number of dihedrals = 2695 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "7" + Parameter: MAXU -> "5" +Evaluating: 7+5 + Parameter: Y <- "12" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "7" + Parameter: Y -> "12" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1631 Number of angles = 2487 + Number of dihedrals = 2734 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1631 Number of angles = 2488 + Number of dihedrals = 2740 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "8" + Parameter: MAXU -> "5" +Evaluating: 8+5 + Parameter: XY <- "13" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "7" + Parameter: XY -> "13" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1632 Number of angles = 2495 + Number of dihedrals = 2746 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1632 Number of angles = 2492 + Number of dihedrals = 2749 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "7" +Evaluating: 7+1.0 + Parameter: COUNT <- "8" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "2" +Evaluating: 2+1.0 + Parameter: INCX <- "3" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "8" +Evaluating: 8+1.0 + Parameter: X <- "9" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "8" + Parameter: X -> "9" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1636 Number of angles = 2504 + Number of dihedrals = 2772 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1636 Number of angles = 2506 + Number of dihedrals = 2777 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "8" + Parameter: MAXU -> "5" +Evaluating: 8+5 + Parameter: Y <- "13" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "8" + Parameter: Y -> "13" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1642 Number of angles = 2527 + Number of dihedrals = 2816 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1642 Number of angles = 2528 + Number of dihedrals = 2822 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "9" + Parameter: MAXU -> "5" +Evaluating: 9+5 + Parameter: XY <- "14" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "8" + Parameter: XY -> "14" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1643 Number of angles = 2535 + Number of dihedrals = 2828 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1643 Number of angles = 2532 + Number of dihedrals = 2831 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "8" +Evaluating: 8+1.0 + Parameter: COUNT <- "9" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "3" +Evaluating: 3+1.0 + Parameter: INCX <- "4" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "9" +Evaluating: 9+1.0 + Parameter: X <- "10" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "9" + Parameter: X -> "10" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1647 Number of angles = 2544 + Number of dihedrals = 2854 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1647 Number of angles = 2546 + Number of dihedrals = 2859 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "9" + Parameter: MAXU -> "5" +Evaluating: 9+5 + Parameter: Y <- "14" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "9" + Parameter: Y -> "14" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1653 Number of angles = 2567 + Number of dihedrals = 2898 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1653 Number of angles = 2568 + Number of dihedrals = 2904 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "10" + Parameter: MAXU -> "5" +Evaluating: 10+5 + Parameter: XY <- "15" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "9" + Parameter: XY -> "15" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1654 Number of angles = 2575 + Number of dihedrals = 2910 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1654 Number of angles = 2572 + Number of dihedrals = 2913 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "9" +Evaluating: 9+1.0 + Parameter: COUNT <- "10" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "4" +Evaluating: 4+1.0 + Parameter: INCX <- "5" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set incX 1 + Parameter: INCX <- "1" + + CHARMM> + + CHARMM> calc incY = @incY + 1.0 + Parameter: INCY -> "2" +Evaluating: 2+1.0 + Parameter: INCY <- "3" + + CHARMM> + + CHARMM> calc lastX = @X + @maxU + Parameter: X -> "10" + Parameter: MAXU -> "5" +Evaluating: 10+5 + Parameter: LASTX <- "15" + + CHARMM> + + CHARMM> patch 011B q@X 1 q@lastX 1 setup warn ! patch last column along V + Parameter: X -> "10" + Parameter: LASTX -> "15" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1660 Number of angles = 2593 + Number of dihedrals = 2952 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1660 Number of angles = 2594 + Number of dihedrals = 2956 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> if incY le @endYloop goto loopY + Parameter: ENDYLOOP -> "7" + Comparing "3" and "7". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "10" +Evaluating: 10+1.0 + Parameter: COUNT <- "11" + + CHARMM> + + CHARMM> label loopX + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "11" +Evaluating: 11+1.0 + Parameter: X <- "12" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "11" + Parameter: X -> "12" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1664 Number of angles = 2606 + Number of dihedrals = 2979 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1664 Number of angles = 2608 + Number of dihedrals = 2984 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "11" + Parameter: MAXU -> "5" +Evaluating: 11+5 + Parameter: Y <- "16" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "11" + Parameter: Y -> "16" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1670 Number of angles = 2629 + Number of dihedrals = 3023 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1670 Number of angles = 2629 + Number of dihedrals = 3026 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "12" + Parameter: MAXU -> "5" +Evaluating: 12+5 + Parameter: XY <- "17" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "11" + Parameter: XY -> "17" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1671 Number of angles = 2636 + Number of dihedrals = 3032 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1671 Number of angles = 2633 + Number of dihedrals = 3035 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "11" +Evaluating: 11+1.0 + Parameter: COUNT <- "12" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "1" +Evaluating: 1+1.0 + Parameter: INCX <- "2" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "12" +Evaluating: 12+1.0 + Parameter: X <- "13" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "12" + Parameter: X -> "13" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1675 Number of angles = 2645 + Number of dihedrals = 3058 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1675 Number of angles = 2647 + Number of dihedrals = 3063 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "12" + Parameter: MAXU -> "5" +Evaluating: 12+5 + Parameter: Y <- "17" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "12" + Parameter: Y -> "17" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1681 Number of angles = 2668 + Number of dihedrals = 3102 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1681 Number of angles = 2669 + Number of dihedrals = 3108 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "13" + Parameter: MAXU -> "5" +Evaluating: 13+5 + Parameter: XY <- "18" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "12" + Parameter: XY -> "18" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1682 Number of angles = 2676 + Number of dihedrals = 3114 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1682 Number of angles = 2673 + Number of dihedrals = 3117 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "12" +Evaluating: 12+1.0 + Parameter: COUNT <- "13" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "2" +Evaluating: 2+1.0 + Parameter: INCX <- "3" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "13" +Evaluating: 13+1.0 + Parameter: X <- "14" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "13" + Parameter: X -> "14" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1686 Number of angles = 2685 + Number of dihedrals = 3140 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1686 Number of angles = 2687 + Number of dihedrals = 3145 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "13" + Parameter: MAXU -> "5" +Evaluating: 13+5 + Parameter: Y <- "18" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "13" + Parameter: Y -> "18" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1692 Number of angles = 2708 + Number of dihedrals = 3184 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1692 Number of angles = 2709 + Number of dihedrals = 3190 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "14" + Parameter: MAXU -> "5" +Evaluating: 14+5 + Parameter: XY <- "19" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "13" + Parameter: XY -> "19" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1693 Number of angles = 2716 + Number of dihedrals = 3196 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1693 Number of angles = 2713 + Number of dihedrals = 3199 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "13" +Evaluating: 13+1.0 + Parameter: COUNT <- "14" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "3" +Evaluating: 3+1.0 + Parameter: INCX <- "4" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "14" +Evaluating: 14+1.0 + Parameter: X <- "15" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "14" + Parameter: X -> "15" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1697 Number of angles = 2725 + Number of dihedrals = 3222 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1697 Number of angles = 2727 + Number of dihedrals = 3227 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "14" + Parameter: MAXU -> "5" +Evaluating: 14+5 + Parameter: Y <- "19" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "14" + Parameter: Y -> "19" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1703 Number of angles = 2748 + Number of dihedrals = 3266 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1703 Number of angles = 2749 + Number of dihedrals = 3272 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "15" + Parameter: MAXU -> "5" +Evaluating: 15+5 + Parameter: XY <- "20" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "14" + Parameter: XY -> "20" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1704 Number of angles = 2756 + Number of dihedrals = 3278 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1704 Number of angles = 2753 + Number of dihedrals = 3281 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "14" +Evaluating: 14+1.0 + Parameter: COUNT <- "15" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "4" +Evaluating: 4+1.0 + Parameter: INCX <- "5" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set incX 1 + Parameter: INCX <- "1" + + CHARMM> + + CHARMM> calc incY = @incY + 1.0 + Parameter: INCY -> "3" +Evaluating: 3+1.0 + Parameter: INCY <- "4" + + CHARMM> + + CHARMM> calc lastX = @X + @maxU + Parameter: X -> "15" + Parameter: MAXU -> "5" +Evaluating: 15+5 + Parameter: LASTX <- "20" + + CHARMM> + + CHARMM> patch 011B q@X 1 q@lastX 1 setup warn ! patch last column along V + Parameter: X -> "15" + Parameter: LASTX -> "20" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1710 Number of angles = 2774 + Number of dihedrals = 3320 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1710 Number of angles = 2775 + Number of dihedrals = 3324 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> if incY le @endYloop goto loopY + Parameter: ENDYLOOP -> "7" + Comparing "4" and "7". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "15" +Evaluating: 15+1.0 + Parameter: COUNT <- "16" + + CHARMM> + + CHARMM> label loopX + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "16" +Evaluating: 16+1.0 + Parameter: X <- "17" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "16" + Parameter: X -> "17" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1714 Number of angles = 2787 + Number of dihedrals = 3347 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1714 Number of angles = 2789 + Number of dihedrals = 3352 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "16" + Parameter: MAXU -> "5" +Evaluating: 16+5 + Parameter: Y <- "21" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "16" + Parameter: Y -> "21" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1720 Number of angles = 2810 + Number of dihedrals = 3391 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1720 Number of angles = 2810 + Number of dihedrals = 3394 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "17" + Parameter: MAXU -> "5" +Evaluating: 17+5 + Parameter: XY <- "22" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "16" + Parameter: XY -> "22" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1721 Number of angles = 2817 + Number of dihedrals = 3400 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1721 Number of angles = 2814 + Number of dihedrals = 3403 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "16" +Evaluating: 16+1.0 + Parameter: COUNT <- "17" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "1" +Evaluating: 1+1.0 + Parameter: INCX <- "2" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "17" +Evaluating: 17+1.0 + Parameter: X <- "18" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "17" + Parameter: X -> "18" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1725 Number of angles = 2826 + Number of dihedrals = 3426 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1725 Number of angles = 2828 + Number of dihedrals = 3431 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "17" + Parameter: MAXU -> "5" +Evaluating: 17+5 + Parameter: Y <- "22" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "17" + Parameter: Y -> "22" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1731 Number of angles = 2849 + Number of dihedrals = 3470 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1731 Number of angles = 2850 + Number of dihedrals = 3476 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "18" + Parameter: MAXU -> "5" +Evaluating: 18+5 + Parameter: XY <- "23" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "17" + Parameter: XY -> "23" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1732 Number of angles = 2857 + Number of dihedrals = 3482 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1732 Number of angles = 2854 + Number of dihedrals = 3485 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "17" +Evaluating: 17+1.0 + Parameter: COUNT <- "18" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "2" +Evaluating: 2+1.0 + Parameter: INCX <- "3" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "18" +Evaluating: 18+1.0 + Parameter: X <- "19" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "18" + Parameter: X -> "19" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1736 Number of angles = 2866 + Number of dihedrals = 3508 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1736 Number of angles = 2868 + Number of dihedrals = 3513 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "18" + Parameter: MAXU -> "5" +Evaluating: 18+5 + Parameter: Y <- "23" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "18" + Parameter: Y -> "23" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1742 Number of angles = 2889 + Number of dihedrals = 3552 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1742 Number of angles = 2890 + Number of dihedrals = 3558 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "19" + Parameter: MAXU -> "5" +Evaluating: 19+5 + Parameter: XY <- "24" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "18" + Parameter: XY -> "24" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1743 Number of angles = 2897 + Number of dihedrals = 3564 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1743 Number of angles = 2894 + Number of dihedrals = 3567 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "18" +Evaluating: 18+1.0 + Parameter: COUNT <- "19" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "3" +Evaluating: 3+1.0 + Parameter: INCX <- "4" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "19" +Evaluating: 19+1.0 + Parameter: X <- "20" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "19" + Parameter: X -> "20" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1747 Number of angles = 2906 + Number of dihedrals = 3590 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1747 Number of angles = 2908 + Number of dihedrals = 3595 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "19" + Parameter: MAXU -> "5" +Evaluating: 19+5 + Parameter: Y <- "24" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "19" + Parameter: Y -> "24" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1753 Number of angles = 2929 + Number of dihedrals = 3634 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1753 Number of angles = 2930 + Number of dihedrals = 3640 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "20" + Parameter: MAXU -> "5" +Evaluating: 20+5 + Parameter: XY <- "25" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "19" + Parameter: XY -> "25" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1754 Number of angles = 2937 + Number of dihedrals = 3646 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1754 Number of angles = 2934 + Number of dihedrals = 3649 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "19" +Evaluating: 19+1.0 + Parameter: COUNT <- "20" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "4" +Evaluating: 4+1.0 + Parameter: INCX <- "5" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set incX 1 + Parameter: INCX <- "1" + + CHARMM> + + CHARMM> calc incY = @incY + 1.0 + Parameter: INCY -> "4" +Evaluating: 4+1.0 + Parameter: INCY <- "5" + + CHARMM> + + CHARMM> calc lastX = @X + @maxU + Parameter: X -> "20" + Parameter: MAXU -> "5" +Evaluating: 20+5 + Parameter: LASTX <- "25" + + CHARMM> + + CHARMM> patch 011B q@X 1 q@lastX 1 setup warn ! patch last column along V + Parameter: X -> "20" + Parameter: LASTX -> "25" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1760 Number of angles = 2955 + Number of dihedrals = 3688 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1760 Number of angles = 2956 + Number of dihedrals = 3692 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> if incY le @endYloop goto loopY + Parameter: ENDYLOOP -> "7" + Comparing "5" and "7". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "20" +Evaluating: 20+1.0 + Parameter: COUNT <- "21" + + CHARMM> + + CHARMM> label loopX + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "21" +Evaluating: 21+1.0 + Parameter: X <- "22" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "21" + Parameter: X -> "22" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1764 Number of angles = 2968 + Number of dihedrals = 3715 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1764 Number of angles = 2970 + Number of dihedrals = 3720 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "21" + Parameter: MAXU -> "5" +Evaluating: 21+5 + Parameter: Y <- "26" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "21" + Parameter: Y -> "26" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1770 Number of angles = 2991 + Number of dihedrals = 3759 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1770 Number of angles = 2991 + Number of dihedrals = 3762 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "22" + Parameter: MAXU -> "5" +Evaluating: 22+5 + Parameter: XY <- "27" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "21" + Parameter: XY -> "27" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1771 Number of angles = 2998 + Number of dihedrals = 3768 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1771 Number of angles = 2995 + Number of dihedrals = 3771 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "21" +Evaluating: 21+1.0 + Parameter: COUNT <- "22" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "1" +Evaluating: 1+1.0 + Parameter: INCX <- "2" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "22" +Evaluating: 22+1.0 + Parameter: X <- "23" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "22" + Parameter: X -> "23" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1775 Number of angles = 3007 + Number of dihedrals = 3794 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1775 Number of angles = 3009 + Number of dihedrals = 3799 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "22" + Parameter: MAXU -> "5" +Evaluating: 22+5 + Parameter: Y <- "27" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "22" + Parameter: Y -> "27" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1781 Number of angles = 3030 + Number of dihedrals = 3838 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1781 Number of angles = 3031 + Number of dihedrals = 3844 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "23" + Parameter: MAXU -> "5" +Evaluating: 23+5 + Parameter: XY <- "28" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "22" + Parameter: XY -> "28" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1782 Number of angles = 3038 + Number of dihedrals = 3850 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1782 Number of angles = 3035 + Number of dihedrals = 3853 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "22" +Evaluating: 22+1.0 + Parameter: COUNT <- "23" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "2" +Evaluating: 2+1.0 + Parameter: INCX <- "3" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "23" +Evaluating: 23+1.0 + Parameter: X <- "24" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "23" + Parameter: X -> "24" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1786 Number of angles = 3047 + Number of dihedrals = 3876 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1786 Number of angles = 3049 + Number of dihedrals = 3881 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "23" + Parameter: MAXU -> "5" +Evaluating: 23+5 + Parameter: Y <- "28" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "23" + Parameter: Y -> "28" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1792 Number of angles = 3070 + Number of dihedrals = 3920 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1792 Number of angles = 3071 + Number of dihedrals = 3926 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "24" + Parameter: MAXU -> "5" +Evaluating: 24+5 + Parameter: XY <- "29" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "23" + Parameter: XY -> "29" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1793 Number of angles = 3078 + Number of dihedrals = 3932 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1793 Number of angles = 3075 + Number of dihedrals = 3935 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "23" +Evaluating: 23+1.0 + Parameter: COUNT <- "24" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "3" +Evaluating: 3+1.0 + Parameter: INCX <- "4" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "24" +Evaluating: 24+1.0 + Parameter: X <- "25" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "24" + Parameter: X -> "25" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1797 Number of angles = 3087 + Number of dihedrals = 3958 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1797 Number of angles = 3089 + Number of dihedrals = 3963 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "24" + Parameter: MAXU -> "5" +Evaluating: 24+5 + Parameter: Y <- "29" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "24" + Parameter: Y -> "29" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1803 Number of angles = 3110 + Number of dihedrals = 4002 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1803 Number of angles = 3111 + Number of dihedrals = 4008 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "25" + Parameter: MAXU -> "5" +Evaluating: 25+5 + Parameter: XY <- "30" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "24" + Parameter: XY -> "30" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1804 Number of angles = 3118 + Number of dihedrals = 4014 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1804 Number of angles = 3115 + Number of dihedrals = 4017 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "24" +Evaluating: 24+1.0 + Parameter: COUNT <- "25" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "4" +Evaluating: 4+1.0 + Parameter: INCX <- "5" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set incX 1 + Parameter: INCX <- "1" + + CHARMM> + + CHARMM> calc incY = @incY + 1.0 + Parameter: INCY -> "5" +Evaluating: 5+1.0 + Parameter: INCY <- "6" + + CHARMM> + + CHARMM> calc lastX = @X + @maxU + Parameter: X -> "25" + Parameter: MAXU -> "5" +Evaluating: 25+5 + Parameter: LASTX <- "30" + + CHARMM> + + CHARMM> patch 011B q@X 1 q@lastX 1 setup warn ! patch last column along V + Parameter: X -> "25" + Parameter: LASTX -> "30" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1810 Number of angles = 3136 + Number of dihedrals = 4056 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1810 Number of angles = 3137 + Number of dihedrals = 4060 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> if incY le @endYloop goto loopY + Parameter: ENDYLOOP -> "7" + Comparing "6" and "7". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "25" +Evaluating: 25+1.0 + Parameter: COUNT <- "26" + + CHARMM> + + CHARMM> label loopX + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "26" +Evaluating: 26+1.0 + Parameter: X <- "27" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "26" + Parameter: X -> "27" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1814 Number of angles = 3149 + Number of dihedrals = 4083 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1814 Number of angles = 3151 + Number of dihedrals = 4088 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "26" + Parameter: MAXU -> "5" +Evaluating: 26+5 + Parameter: Y <- "31" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "26" + Parameter: Y -> "31" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1820 Number of angles = 3172 + Number of dihedrals = 4127 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1820 Number of angles = 3172 + Number of dihedrals = 4130 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "27" + Parameter: MAXU -> "5" +Evaluating: 27+5 + Parameter: XY <- "32" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "26" + Parameter: XY -> "32" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1821 Number of angles = 3179 + Number of dihedrals = 4136 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1821 Number of angles = 3176 + Number of dihedrals = 4139 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "26" +Evaluating: 26+1.0 + Parameter: COUNT <- "27" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "1" +Evaluating: 1+1.0 + Parameter: INCX <- "2" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "27" +Evaluating: 27+1.0 + Parameter: X <- "28" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "27" + Parameter: X -> "28" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1825 Number of angles = 3188 + Number of dihedrals = 4162 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1825 Number of angles = 3190 + Number of dihedrals = 4167 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "27" + Parameter: MAXU -> "5" +Evaluating: 27+5 + Parameter: Y <- "32" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "27" + Parameter: Y -> "32" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1831 Number of angles = 3211 + Number of dihedrals = 4206 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1831 Number of angles = 3212 + Number of dihedrals = 4212 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "28" + Parameter: MAXU -> "5" +Evaluating: 28+5 + Parameter: XY <- "33" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "27" + Parameter: XY -> "33" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1832 Number of angles = 3219 + Number of dihedrals = 4218 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1832 Number of angles = 3216 + Number of dihedrals = 4221 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "27" +Evaluating: 27+1.0 + Parameter: COUNT <- "28" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "2" +Evaluating: 2+1.0 + Parameter: INCX <- "3" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "28" +Evaluating: 28+1.0 + Parameter: X <- "29" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "28" + Parameter: X -> "29" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1836 Number of angles = 3228 + Number of dihedrals = 4244 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1836 Number of angles = 3230 + Number of dihedrals = 4249 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "28" + Parameter: MAXU -> "5" +Evaluating: 28+5 + Parameter: Y <- "33" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "28" + Parameter: Y -> "33" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1842 Number of angles = 3251 + Number of dihedrals = 4288 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1842 Number of angles = 3252 + Number of dihedrals = 4294 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "29" + Parameter: MAXU -> "5" +Evaluating: 29+5 + Parameter: XY <- "34" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "28" + Parameter: XY -> "34" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1843 Number of angles = 3259 + Number of dihedrals = 4300 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1843 Number of angles = 3256 + Number of dihedrals = 4303 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "28" +Evaluating: 28+1.0 + Parameter: COUNT <- "29" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "3" +Evaluating: 3+1.0 + Parameter: INCX <- "4" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "29" +Evaluating: 29+1.0 + Parameter: X <- "30" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "29" + Parameter: X -> "30" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1847 Number of angles = 3268 + Number of dihedrals = 4326 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1847 Number of angles = 3270 + Number of dihedrals = 4331 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "29" + Parameter: MAXU -> "5" +Evaluating: 29+5 + Parameter: Y <- "34" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "29" + Parameter: Y -> "34" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1853 Number of angles = 3291 + Number of dihedrals = 4370 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1853 Number of angles = 3292 + Number of dihedrals = 4376 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "30" + Parameter: MAXU -> "5" +Evaluating: 30+5 + Parameter: XY <- "35" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "29" + Parameter: XY -> "35" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1854 Number of angles = 3299 + Number of dihedrals = 4382 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1854 Number of angles = 3296 + Number of dihedrals = 4385 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "29" +Evaluating: 29+1.0 + Parameter: COUNT <- "30" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "4" +Evaluating: 4+1.0 + Parameter: INCX <- "5" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set incX 1 + Parameter: INCX <- "1" + + CHARMM> + + CHARMM> calc incY = @incY + 1.0 + Parameter: INCY -> "6" +Evaluating: 6+1.0 + Parameter: INCY <- "7" + + CHARMM> + + CHARMM> calc lastX = @X + @maxU + Parameter: X -> "30" + Parameter: MAXU -> "5" +Evaluating: 30+5 + Parameter: LASTX <- "35" + + CHARMM> + + CHARMM> patch 011B q@X 1 q@lastX 1 setup warn ! patch last column along V + Parameter: X -> "30" + Parameter: LASTX -> "35" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1860 Number of angles = 3317 + Number of dihedrals = 4424 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1860 Number of angles = 3318 + Number of dihedrals = 4428 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> if incY le @endYloop goto loopY + Parameter: ENDYLOOP -> "7" + Comparing "7" and "7". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "30" +Evaluating: 30+1.0 + Parameter: COUNT <- "31" + + CHARMM> + + CHARMM> label loopX + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "31" +Evaluating: 31+1.0 + Parameter: X <- "32" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "31" + Parameter: X -> "32" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1864 Number of angles = 3330 + Number of dihedrals = 4451 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1864 Number of angles = 3332 + Number of dihedrals = 4456 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "31" + Parameter: MAXU -> "5" +Evaluating: 31+5 + Parameter: Y <- "36" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "31" + Parameter: Y -> "36" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1870 Number of angles = 3353 + Number of dihedrals = 4495 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1870 Number of angles = 3353 + Number of dihedrals = 4498 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "32" + Parameter: MAXU -> "5" +Evaluating: 32+5 + Parameter: XY <- "37" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "31" + Parameter: XY -> "37" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1871 Number of angles = 3360 + Number of dihedrals = 4504 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1871 Number of angles = 3357 + Number of dihedrals = 4507 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "31" +Evaluating: 31+1.0 + Parameter: COUNT <- "32" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "1" +Evaluating: 1+1.0 + Parameter: INCX <- "2" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "32" +Evaluating: 32+1.0 + Parameter: X <- "33" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "32" + Parameter: X -> "33" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1875 Number of angles = 3369 + Number of dihedrals = 4530 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1875 Number of angles = 3371 + Number of dihedrals = 4535 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "32" + Parameter: MAXU -> "5" +Evaluating: 32+5 + Parameter: Y <- "37" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "32" + Parameter: Y -> "37" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1881 Number of angles = 3392 + Number of dihedrals = 4574 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1881 Number of angles = 3393 + Number of dihedrals = 4580 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "33" + Parameter: MAXU -> "5" +Evaluating: 33+5 + Parameter: XY <- "38" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "32" + Parameter: XY -> "38" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1882 Number of angles = 3400 + Number of dihedrals = 4586 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1882 Number of angles = 3397 + Number of dihedrals = 4589 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "32" +Evaluating: 32+1.0 + Parameter: COUNT <- "33" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "2" +Evaluating: 2+1.0 + Parameter: INCX <- "3" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "33" +Evaluating: 33+1.0 + Parameter: X <- "34" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "33" + Parameter: X -> "34" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1886 Number of angles = 3409 + Number of dihedrals = 4612 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1886 Number of angles = 3411 + Number of dihedrals = 4617 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "33" + Parameter: MAXU -> "5" +Evaluating: 33+5 + Parameter: Y <- "38" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "33" + Parameter: Y -> "38" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1892 Number of angles = 3432 + Number of dihedrals = 4656 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1892 Number of angles = 3433 + Number of dihedrals = 4662 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "34" + Parameter: MAXU -> "5" +Evaluating: 34+5 + Parameter: XY <- "39" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "33" + Parameter: XY -> "39" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1893 Number of angles = 3440 + Number of dihedrals = 4668 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1893 Number of angles = 3437 + Number of dihedrals = 4671 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "33" +Evaluating: 33+1.0 + Parameter: COUNT <- "34" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "3" +Evaluating: 3+1.0 + Parameter: INCX <- "4" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc X = @count + 1.0 + Parameter: COUNT -> "34" +Evaluating: 34+1.0 + Parameter: X <- "35" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@x 1 setup warn ! patch along U + Parameter: COUNT -> "34" + Parameter: X -> "35" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1897 Number of angles = 3449 + Number of dihedrals = 4694 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1897 Number of angles = 3451 + Number of dihedrals = 4699 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc Y = @count + @maxU + Parameter: COUNT -> "34" + Parameter: MAXU -> "5" +Evaluating: 34+5 + Parameter: Y <- "39" + + CHARMM> + + CHARMM> patch 011B q@count 1 q@y 1 setup warn ! patch along V + Parameter: COUNT -> "34" + Parameter: Y -> "39" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1903 Number of angles = 3472 + Number of dihedrals = 4738 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1903 Number of angles = 3473 + Number of dihedrals = 4744 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc XY = @X + @maxU + Parameter: X -> "35" + Parameter: MAXU -> "5" +Evaluating: 35+5 + Parameter: XY <- "40" + + CHARMM> + + CHARMM> patch 011C q@count 1 q@xy 1 setup warn ! patch along UV + Parameter: COUNT -> "34" + Parameter: XY -> "40" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1904 Number of angles = 3480 + Number of dihedrals = 4750 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1904 Number of angles = 3477 + Number of dihedrals = 4753 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> ! patch + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "34" +Evaluating: 34+1.0 + Parameter: COUNT <- "35" + + CHARMM> + + CHARMM> calc incX = @incX + 1.0 + Parameter: INCX -> "4" +Evaluating: 4+1.0 + Parameter: INCX <- "5" + + CHARMM> + + CHARMM> if incX le @endXloop goto loopX + Parameter: ENDXLOOP -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set incX 1 + Parameter: INCX <- "1" + + CHARMM> + + CHARMM> calc incY = @incY + 1.0 + Parameter: INCY -> "7" +Evaluating: 7+1.0 + Parameter: INCY <- "8" + + CHARMM> + + CHARMM> calc lastX = @X + @maxU + Parameter: X -> "35" + Parameter: MAXU -> "5" +Evaluating: 35+5 + Parameter: LASTX <- "40" + + CHARMM> + + CHARMM> patch 011B q@X 1 q@lastX 1 setup warn ! patch last column along V + Parameter: X -> "35" + Parameter: LASTX -> "40" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1910 Number of angles = 3498 + Number of dihedrals = 4792 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1910 Number of angles = 3499 + Number of dihedrals = 4796 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> if incY le @endYloop goto loopY + Parameter: ENDYLOOP -> "7" + Comparing "8" and "7". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> set incXend 1 + Parameter: INCXEND <- "1" + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "35" +Evaluating: 35+1.0 + Parameter: COUNT <- "36" + + CHARMM> + + CHARMM> label loopXend + + CHARMM> + + CHARMM> calc Xend = @count + 1.0 + Parameter: COUNT -> "36" +Evaluating: 36+1.0 + Parameter: XEND <- "37" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@Xend 1 setup warn ! patch along U + Parameter: COUNT -> "36" + Parameter: XEND -> "37" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1914 Number of angles = 3511 + Number of dihedrals = 4819 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1914 Number of angles = 3513 + Number of dihedrals = 4824 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc incXend = @incXend + 1.0 + Parameter: INCXEND -> "1" +Evaluating: 1+1.0 + Parameter: INCXEND <- "2" + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "36" +Evaluating: 36+1.0 + Parameter: COUNT <- "37" + + CHARMM> + + CHARMM> if incXend le @endXloop goto loopXend + Parameter: ENDXLOOP -> "4" + Comparing "2" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc Xend = @count + 1.0 + Parameter: COUNT -> "37" +Evaluating: 37+1.0 + Parameter: XEND <- "38" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@Xend 1 setup warn ! patch along U + Parameter: COUNT -> "37" + Parameter: XEND -> "38" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1918 Number of angles = 3525 + Number of dihedrals = 4847 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1918 Number of angles = 3527 + Number of dihedrals = 4852 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc incXend = @incXend + 1.0 + Parameter: INCXEND -> "2" +Evaluating: 2+1.0 + Parameter: INCXEND <- "3" + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "37" +Evaluating: 37+1.0 + Parameter: COUNT <- "38" + + CHARMM> + + CHARMM> if incXend le @endXloop goto loopXend + Parameter: ENDXLOOP -> "4" + Comparing "3" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc Xend = @count + 1.0 + Parameter: COUNT -> "38" +Evaluating: 38+1.0 + Parameter: XEND <- "39" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@Xend 1 setup warn ! patch along U + Parameter: COUNT -> "38" + Parameter: XEND -> "39" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1922 Number of angles = 3539 + Number of dihedrals = 4875 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1922 Number of angles = 3541 + Number of dihedrals = 4880 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc incXend = @incXend + 1.0 + Parameter: INCXEND -> "3" +Evaluating: 3+1.0 + Parameter: INCXEND <- "4" + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "38" +Evaluating: 38+1.0 + Parameter: COUNT <- "39" + + CHARMM> + + CHARMM> if incXend le @endXloop goto loopXend + Parameter: ENDXLOOP -> "4" + Comparing "4" and "4". + IF test evaluated as true. Performing command + + CHARMM> + + CHARMM> calc Xend = @count + 1.0 + Parameter: COUNT -> "39" +Evaluating: 39+1.0 + Parameter: XEND <- "40" + + CHARMM> + + CHARMM> patch 011A q@count 1 q@Xend 1 setup warn ! patch along U + Parameter: COUNT -> "39" + Parameter: XEND -> "40" + PATCH: Check angles and dihedrals autogenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1926 Number of angles = 3553 + Number of dihedrals = 4903 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> AUTOgenerate ANGLES DIHEdrals + AUTOGEN: All angles are removed and regenerated. + AUTOGEN: All dihedrals are removed and regenerated. + PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. + PSFSUM> Summary of the structure file counters : + Number of segments = 40 Number of residues = 40 + Number of atoms = 1600 Number of groups = 40 + Number of bonds = 1926 Number of angles = 3555 + Number of dihedrals = 4908 Number of impropers = 0 + Number of cross-terms = 0 + Number of HB acceptors = 0 Number of HB donors = 0 + Number of NB exclusions = 0 Total charge = 0.00000 + + CHARMM> + + CHARMM> calc incXend = @incXend + 1.0 + Parameter: INCXEND -> "4" +Evaluating: 4+1.0 + Parameter: INCXEND <- "5" + + CHARMM> + + CHARMM> calc count = @count + 1.0 + Parameter: COUNT -> "39" +Evaluating: 39+1.0 + Parameter: COUNT <- "40" + + CHARMM> + + CHARMM> if incXend le @endXloop goto loopXend + Parameter: ENDXLOOP -> "4" + Comparing "5" and "4". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> !PRINT COOR + CHARMM> !PRINT PSF + CHARMM> + + CHARMM> ! Minimize initial structure. + CHARMM> ! Only hydrogens are allowed to move. + CHARMM> cons harm force 10000.0 mass select .not. type H* end + SELRPN> 1440 atoms have been selected out of 1600 + CSTRAN: Harmonic Restraints + ABSOlute type as set number 1. Number of selected atoms: 1440 + Reference coordinates set to main coordinates. + Mass weighting will be used for new restraints. + The force constant of 10000.00000 will be used. + An exponent of 2 will be used. + The XYZ scale factors are: 1.00000 1.00000 1.00000 + A total of 1440 atoms are restrained. + + CHARMM> mini sd nsteps 500 nprint 50 + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec FSWItch VATOm VFSWIt + BYGRoup NOEXtnd NOEWald + CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 5481 exclusions and 4908 interactions(1-4) + found 123 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 459762 ATOM PAIRS AND 0 GROUP PAIRS + NBONDA>> Maximum group spatial extent (12A) exceeded. + Size is 15.48 Angstroms and starts with atom: 1 + Please check group boundary definitions. + + General atom nonbond list generation found: + 327059 ATOM PAIRS WERE FOUND FOR ATOM LIST + 538 GROUP PAIRS REQUIRED ATOM SEARCHES + + + + STEEPD> An energy minimization has been requested. + + NSTEP = 500 NPRINT = 50 + STEP = 0.0200000 TOLFUN = 0.0000000 + TOLGRD = 0.0000000 TOLSTP = 0.0000000 + +MINI MIN: Cycle ENERgy Delta-E GRMS Step-size +MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +MINI EXTERN: VDWaals ELEC HBONds ASP USER + ---------- --------- --------- --------- --------- --------- +MINI> 0 -46195.24541 0.00000 134.64992 0.02000 +MINI INTERN> 22498.93956 3124.52289 0.00000 876.59902 0.00000 +MINI EXTERN> -5496.48615 -67198.82074 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 50 -55568.15140 9372.90599 263.07717 0.00087 +MINI INTERN> 12917.98679 3114.13400 0.00000 876.78912 0.00000 +MINI EXTERN> -5497.74334 -67317.30211 0.00000 0.00000 0.00000 +MINI CONSTR> 337.98414 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 100 -59397.50928 3829.35788 172.43999 0.00052 +MINI INTERN> 9371.26401 3112.43770 0.00000 875.99642 0.00000 +MINI EXTERN> -5498.03232 -67380.44402 0.00000 0.00000 0.00000 +MINI CONSTR> 121.26892 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 150 -61646.16005 2248.65077 54.59150 0.00031 +MINI INTERN> 7280.45792 3101.84003 0.00000 876.12341 0.00000 +MINI EXTERN> -5498.69449 -67429.66521 0.00000 0.00000 0.00000 +MINI CONSTR> 23.77828 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 200 -62965.02361 1318.86356 42.07711 0.00019 +MINI INTERN> 6022.96304 3094.07754 0.00000 875.83443 0.00000 +MINI EXTERN> -5499.08283 -67468.83639 0.00000 0.00000 0.00000 +MINI CONSTR> 10.02060 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 250 -63736.22552 771.20191 79.84704 0.00027 +MINI INTERN> 5277.71205 3085.53756 0.00000 875.56606 0.00000 +MINI EXTERN> -5499.41901 -67499.73408 0.00000 0.00000 0.00000 +MINI CONSTR> 24.11189 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 300 -64233.84493 497.61940 49.24221 0.00016 +MINI INTERN> 4823.20642 3074.41192 0.00000 875.53538 0.00000 +MINI EXTERN> -5499.82669 -67524.50754 0.00000 0.00000 0.00000 +MINI CONSTR> 17.33558 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 350 -64533.39325 299.54832 15.19451 0.00010 +MINI INTERN> 4566.53764 3065.46807 0.00000 875.25123 0.00000 +MINI EXTERN> -5500.05242 -67543.68378 0.00000 0.00000 0.00000 +MINI CONSTR> 3.08600 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 400 -64721.23083 187.83758 12.30136 0.00006 +MINI INTERN> 4405.27272 3055.31082 0.00000 875.04048 0.00000 +MINI EXTERN> -5500.29105 -67559.70403 0.00000 0.00000 0.00000 +MINI CONSTR> 3.14024 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 450 -64837.27014 116.03931 24.87330 0.00008 +MINI INTERN> 4309.47502 3045.06099 0.00000 874.84199 0.00000 +MINI EXTERN> -5500.50234 -67572.57449 0.00000 0.00000 0.00000 +MINI CONSTR> 6.42869 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 500 -64915.33800 78.06786 7.92194 0.00005 +MINI INTERN> 4256.05558 3035.63432 0.00000 874.58347 0.00000 +MINI EXTERN> -5500.65031 -67582.81561 0.00000 0.00000 0.00000 +MINI CONSTR> 1.85455 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. + +STPD MIN: Cycle ENERgy Delta-E GRMS Step-size +STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +STPD EXTERN: VDWaals ELEC HBONds ASP USER +STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE + ---------- --------- --------- --------- --------- --------- +STPD> 500 -64915.33800 78.06786 7.92194 0.00006 +STPD INTERN> 4256.05558 3035.63432 0.00000 874.58347 0.00000 +STPD EXTERN> -5500.65031 -67582.81561 0.00000 0.00000 0.00000 +STPD CONSTR> 1.85455 0.00000 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> cons harm force 0.0 mass select all end + SELRPN> 1600 atoms have been selected out of 1600 + CSTRAN: Harmonic Restraints + ABSOlute type as set number 1. Number of selected atoms: 1600 + Reference coordinates set to main coordinates. + Mass weighting will be used for new restraints. + The force constant of 0.00000 will be used. + An exponent of 2 will be used. + The XYZ scale factors are: 1.00000 1.00000 1.00000 + A total of 0 atoms are restrained. + + CHARMM> + + CHARMM> + + CHARMM> !======================================================== + CHARMM> ! Generation of crystal slab followed by minimization + CHARMM> ! The surface is generated by creating the appropriate + CHARMM> ! images of the central unitcell using the IMAGE + CHARMM> ! facility of charmm + CHARMM> !======================================================== + CHARMM> + + CHARMM> + + CHARMM> ! 3: cutim + CHARMM> ! 4: cutnb + CHARMM> ! 5: ctonnb + CHARMM> ! 6: ctofnb + CHARMM> set 3 16.0 ! cutim + Parameter: 3 <- "16.0" + + CHARMM> set 4 16.0 ! cutnb + Parameter: 4 <- "16.0" + + CHARMM> set 5 10.0 ! ctonnb + Parameter: 5 <- "10.0" + + CHARMM> set 6 12.0 ! ctofnb + Parameter: 6 <- "12.0" + + CHARMM> + + CHARMM> ! Create images now + CHARMM> open unit 8 read card name crystal.img + VOPEN> Attempting to open::crystal.img:: + OPNLGU> Unit 8 opened for READONLY access to crystal.img + + CHARMM> read imag print init unit 8 + TITLE> * IMAGE GENERATION + TITLE> * + + READING IMAGE FILE FROM UNIT 8 + + + IMREAD> scale 1 1 1 + + IMREAD> + + IMREAD> IMAGE qi1 + + IMREAD> TRANslate @bigu1 @bigu2 @bigu3 + Parameter: BIGU1 -> "36.5" + Parameter: BIGU2 -> "0" + Parameter: BIGU3 -> "0" + TRANSLATION VECTOR 36.500000 0.000000 0.000000 + + IMREAD> + + IMREAD> IMAGE qi2 + + TRANSFORMATION 1 NAME: QI1 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 36.500000 0.000000 0.000000 + + IMREAD> DEFIne INVErse qi1 + + IMREAD> + + IMREAD> IMAGE qi3 + + TRANSFORMATION 2 NAME: QI2 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -36.500000 0.000000 0.000000 + + IMREAD> TRANslate @bigv1 @bigv2 @bigv3 + Parameter: BIGV1 -> "-13.2099" + Parameter: BIGV2 -> "36.9921" + Parameter: BIGV3 -> "0" + TRANSLATION VECTOR -13.209900 36.992100 0.000000 + + IMREAD> + + IMREAD> IMAGE qi4 + + TRANSFORMATION 3 NAME: QI3 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -13.209900 36.992100 0.000000 + + IMREAD> DEFIne INVErse qi3 + + IMREAD> + + IMREAD> IMAGE qi5 + + TRANSFORMATION 4 NAME: QI4 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 13.209900-36.992100 0.000000 + + IMREAD> DEFIne qi1 qi3 + + IMREAD> + + IMREAD> IMAGE qi6 + + TRANSFORMATION 5 NAME: QI5 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 23.290100 36.992100 0.000000 + + IMREAD> DEFIne INVErse qi5 + + IMREAD> + + IMREAD> IMAGE qi7 + + TRANSFORMATION 6 NAME: QI6 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -23.290100-36.992100 0.000000 + + IMREAD> DEFIne qi1 qi4 + + IMREAD> + + IMREAD> IMAGE qi8 + + TRANSFORMATION 7 NAME: QI7 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 49.709900-36.992100 0.000000 + + IMREAD> DEFIne INVErse qi7 + + IMREAD> + + IMREAD> IMAGE qi9 + + TRANSFORMATION 8 NAME: QI8 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -49.709900 36.992100 0.000000 + + IMREAD> TRANslate @bigw1 @bigw2 @bigw3 + Parameter: BIGW1 -> "0" + Parameter: BIGW2 -> "0" + Parameter: BIGW3 -> "50" + TRANSLATION VECTOR 0.000000 0.000000 50.000000 + + IMREAD> + + IMREAD> IMAGE qi10 + + TRANSFORMATION 9 NAME: QI9 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 0.000000 0.000000 50.000000 + + IMREAD> DEFIne INVErse qi9 + + IMREAD> + + IMREAD> IMAGE qi11 + + TRANSFORMATION 10 NAME: QI10 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 0.000000 0.000000-50.000000 + + IMREAD> DEFIne qi1 qi9 + + IMREAD> + + IMREAD> IMAGE qi12 + + TRANSFORMATION 11 NAME: QI11 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 36.500000 0.000000 50.000000 + + IMREAD> DEFIne INVErse qi11 + + IMREAD> + + IMREAD> IMAGE qi13 + + TRANSFORMATION 12 NAME: QI12 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -36.500000 0.000000-50.000000 + + IMREAD> DEFIne qi2 qi9 + + IMREAD> + + IMREAD> IMAGE qi14 + + TRANSFORMATION 13 NAME: QI13 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -36.500000 0.000000 50.000000 + + IMREAD> DEFIne INVErse qi13 + + IMREAD> + + IMREAD> IMAGE qi15 + + TRANSFORMATION 14 NAME: QI14 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 36.500000 0.000000-50.000000 + + IMREAD> DEFIne qi3 qi9 + + IMREAD> + + IMREAD> IMAGE qi16 + + TRANSFORMATION 15 NAME: QI15 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -13.209900 36.992100 50.000000 + + IMREAD> DEFIne INVErse qi15 + + IMREAD> + + IMREAD> IMAGE qi17 + + TRANSFORMATION 16 NAME: QI16 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 13.209900-36.992100-50.000000 + + IMREAD> DEFIne qi4 qi9 + + IMREAD> + + IMREAD> IMAGE qi18 + + TRANSFORMATION 17 NAME: QI17 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 13.209900-36.992100 50.000000 + + IMREAD> DEFIne INVErse qi17 + + IMREAD> + + IMREAD> IMAGE qi19 + + TRANSFORMATION 18 NAME: QI18 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -13.209900 36.992100-50.000000 + + IMREAD> DEFIne qi5 qi9 + + IMREAD> + + IMREAD> IMAGE qi20 + + TRANSFORMATION 19 NAME: QI19 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 23.290100 36.992100 50.000000 + + IMREAD> DEFIne INVErse qi19 + + IMREAD> + + IMREAD> IMAGE qi21 + + TRANSFORMATION 20 NAME: QI20 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -23.290100-36.992100-50.000000 + + IMREAD> DEFIne qi8 qi9 + + IMREAD> + + IMREAD> IMAGE qi22 + + TRANSFORMATION 21 NAME: QI21 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -49.709900 36.992100 50.000000 + + IMREAD> DEFIne INVErse qi21 + + IMREAD> + + IMREAD> IMAGE qi23 + + TRANSFORMATION 22 NAME: QI22 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 49.709900-36.992100-50.000000 + + IMREAD> DEFIne qi6 qi9 + + IMREAD> + + IMREAD> IMAGE qi24 + + TRANSFORMATION 23 NAME: QI23 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + -23.290100-36.992100 50.000000 + + IMREAD> DEFIne INVErse qi23 + + IMREAD> + + IMREAD> IMAGE qi25 + + TRANSFORMATION 24 NAME: QI24 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 23.290100 36.992100-50.000000 + + IMREAD> DEFIne qi7 qi9 + + IMREAD> + + IMREAD> IMAGE qi26 + + TRANSFORMATION 25 NAME: QI25 + 1.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 + 49.709900-36.992100 50.000000 + + IMREAD> DEFIne INVErse qi25 + + IMREAD> + + IMREAD> end + + 26 TRANSFORMATIONS HAVE BEEN READ + + THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET + + CHARMM> close unit 8 + VCLOSE: Closing unit 8 with status "KEEP" + + CHARMM> + + CHARMM> ! Manipulation of images + CHARMM> update inbf 0 ihbf 0 imgfrq 100 cutim @3 + Parameter: 3 -> "16.0" + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 960 24 24 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 480 12 12 0.00 + 7 QI7 has 280 7 7 0.00 + 9 QI9 has 0 0 0 35.07 + 11 QI11 has 0 0 0 35.07 + 13 QI13 has 0 0 0 35.07 + 15 QI15 has 0 0 0 35.07 + 17 QI17 has 0 0 0 35.08 + 19 QI19 has 0 0 0 35.07 + 21 QI21 has 0 0 0 35.10 + 23 QI23 has 0 0 0 35.08 + 25 QI25 has 0 0 0 35.10 + Total of 4120 atoms and 103 groups and 103 residues were included + + found 0 image group exclusions. + + CHARMM> stream image_patch.str + VOPEN> Attempting to open::image_patch.str:: + OPNLGU> Unit 99 opened for READONLY access to image_patch.str + + INPUT STREAM SWITCHING TO UNIT 99 + RDTITL> + RDTITL> No title read. + Parameter: IN1 <- "" + + CHARMM> + + CHARMM> update inbf 0 ihbf 0 imgfrq 011 cutim @3 + Parameter: 3 -> "16.0" + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 960 24 24 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 480 12 12 0.00 + 7 QI7 has 280 7 7 0.00 + 9 QI9 has 0 0 0 35.07 + 11 QI11 has 0 0 0 35.07 + 13 QI13 has 0 0 0 35.07 + 15 QI15 has 0 0 0 35.07 + 17 QI17 has 0 0 0 35.08 + 19 QI19 has 0 0 0 35.07 + 21 QI21 has 0 0 0 35.10 + 23 QI23 has 0 0 0 35.08 + 25 QI25 has 0 0 0 35.10 + Total of 4120 atoms and 103 groups and 103 residues were included + + found 0 image group exclusions. + + CHARMM> + + CHARMM> ! Now apply patches around the perimeter + CHARMM> ! + CHARMM> + + CHARMM> !In x direction + CHARMM> ! + CHARMM> ! py | iy + CHARMM> ! prim px | ix image + CHARMM> ! + CHARMM> + + CHARMM> set counn 1 + Parameter: COUNN <- "1" + + CHARMM> label loop2 + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "1" + Parameter: N -> "5" +Evaluating: 1*5 + Parameter: PX <- "5" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "5" + Parameter: N -> "5" +Evaluating: 5-5+1 + Parameter: IX <- "1" + + CHARMM> calc py = @px + @n + Parameter: PX -> "5" + Parameter: N -> "5" +Evaluating: 5+5 + Parameter: PY <- "10" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "10" + Parameter: N -> "5" +Evaluating: 10-5+1 + Parameter: IY <- "6" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "5" + Parameter: IX -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 4 12 23 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "5" + Parameter: IY -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 5 19 29 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "10" + Parameter: IY -> "6" + Parameter: PX -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 5 19 29 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "10" + Parameter: PX -> "5" + Parameter: IX -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 5 19 31 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "5" + Parameter: IX -> "1" + Parameter: IY -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 5 21 36 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "5" + Parameter: PY -> "10" + Parameter: IY -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 5 21 41 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "1" +Evaluating: 1+1 + Parameter: COUNN <- "2" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "2" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "2" + Parameter: N -> "5" +Evaluating: 2*5 + Parameter: PX <- "10" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "10" + Parameter: N -> "5" +Evaluating: 10-5+1 + Parameter: IX <- "6" + + CHARMM> calc py = @px + @n + Parameter: PX -> "10" + Parameter: N -> "5" +Evaluating: 10+5 + Parameter: PY <- "15" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "15" + Parameter: N -> "5" +Evaluating: 15-5+1 + Parameter: IY <- "11" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "10" + Parameter: IX -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 9 33 64 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "10" + Parameter: IY -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 10 40 70 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "15" + Parameter: IY -> "11" + Parameter: PX -> "10" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 10 40 70 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "15" + Parameter: PX -> "10" + Parameter: IX -> "6" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 10 40 72 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "10" + Parameter: IX -> "6" + Parameter: IY -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 10 42 77 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "10" + Parameter: PY -> "15" + Parameter: IY -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 10 42 82 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "2" +Evaluating: 2+1 + Parameter: COUNN <- "3" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "3" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "3" + Parameter: N -> "5" +Evaluating: 3*5 + Parameter: PX <- "15" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "15" + Parameter: N -> "5" +Evaluating: 15-5+1 + Parameter: IX <- "11" + + CHARMM> calc py = @px + @n + Parameter: PX -> "15" + Parameter: N -> "5" +Evaluating: 15+5 + Parameter: PY <- "20" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "20" + Parameter: N -> "5" +Evaluating: 20-5+1 + Parameter: IY <- "16" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "15" + Parameter: IX -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 14 54 105 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "15" + Parameter: IY -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 15 61 111 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "20" + Parameter: IY -> "16" + Parameter: PX -> "15" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 15 61 111 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "20" + Parameter: PX -> "15" + Parameter: IX -> "11" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 15 61 113 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "15" + Parameter: IX -> "11" + Parameter: IY -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 15 63 118 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "15" + Parameter: PY -> "20" + Parameter: IY -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 15 63 123 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "3" +Evaluating: 3+1 + Parameter: COUNN <- "4" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "4" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "4" + Parameter: N -> "5" +Evaluating: 4*5 + Parameter: PX <- "20" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "20" + Parameter: N -> "5" +Evaluating: 20-5+1 + Parameter: IX <- "16" + + CHARMM> calc py = @px + @n + Parameter: PX -> "20" + Parameter: N -> "5" +Evaluating: 20+5 + Parameter: PY <- "25" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "25" + Parameter: N -> "5" +Evaluating: 25-5+1 + Parameter: IY <- "21" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "20" + Parameter: IX -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 19 75 146 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "20" + Parameter: IY -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 20 82 152 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "25" + Parameter: IY -> "21" + Parameter: PX -> "20" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 20 82 152 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "25" + Parameter: PX -> "20" + Parameter: IX -> "16" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 20 82 154 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "20" + Parameter: IX -> "16" + Parameter: IY -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 20 84 159 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "20" + Parameter: PY -> "25" + Parameter: IY -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 20 84 164 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "4" +Evaluating: 4+1 + Parameter: COUNN <- "5" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "5" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "5" + Parameter: N -> "5" +Evaluating: 5*5 + Parameter: PX <- "25" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "25" + Parameter: N -> "5" +Evaluating: 25-5+1 + Parameter: IX <- "21" + + CHARMM> calc py = @px + @n + Parameter: PX -> "25" + Parameter: N -> "5" +Evaluating: 25+5 + Parameter: PY <- "30" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "30" + Parameter: N -> "5" +Evaluating: 30-5+1 + Parameter: IY <- "26" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "25" + Parameter: IX -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 24 96 187 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "25" + Parameter: IY -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 25 103 193 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "30" + Parameter: IY -> "26" + Parameter: PX -> "25" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 25 103 193 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "30" + Parameter: PX -> "25" + Parameter: IX -> "21" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 25 103 195 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "25" + Parameter: IX -> "21" + Parameter: IY -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 25 105 200 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "25" + Parameter: PY -> "30" + Parameter: IY -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 25 105 205 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "5" +Evaluating: 5+1 + Parameter: COUNN <- "6" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "6" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "6" + Parameter: N -> "5" +Evaluating: 6*5 + Parameter: PX <- "30" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "30" + Parameter: N -> "5" +Evaluating: 30-5+1 + Parameter: IX <- "26" + + CHARMM> calc py = @px + @n + Parameter: PX -> "30" + Parameter: N -> "5" +Evaluating: 30+5 + Parameter: PY <- "35" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "35" + Parameter: N -> "5" +Evaluating: 35-5+1 + Parameter: IY <- "31" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "30" + Parameter: IX -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 29 117 228 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "30" + Parameter: IY -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 30 124 234 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "35" + Parameter: IY -> "31" + Parameter: PX -> "30" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 30 124 234 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "35" + Parameter: PX -> "30" + Parameter: IX -> "26" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 30 124 236 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "30" + Parameter: IX -> "26" + Parameter: IY -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 30 126 241 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "30" + Parameter: PY -> "35" + Parameter: IY -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 30 126 246 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "6" +Evaluating: 6+1 + Parameter: COUNN <- "7" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "7" and "8". + IF test evaluated as true. Performing command + + CHARMM> calc px = @counn * @n + Parameter: COUNN -> "7" + Parameter: N -> "5" +Evaluating: 7*5 + Parameter: PX <- "35" + + CHARMM> calc ix = @px - @n + 1 + Parameter: PX -> "35" + Parameter: N -> "5" +Evaluating: 35-5+1 + Parameter: IX <- "31" + + CHARMM> calc py = @px + @n + Parameter: PX -> "35" + Parameter: N -> "5" +Evaluating: 35+5 + Parameter: PY <- "40" + + CHARMM> calc iy = @py - @n + 1 + Parameter: PY -> "40" + Parameter: N -> "5" +Evaluating: 40-5+1 + Parameter: IY <- "36" + + CHARMM> impa 011A prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PX -> "35" + Parameter: IX -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 34 138 269 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@px 1 qi1 q@iy 1 setup warn + Parameter: PX -> "35" + Parameter: IY -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 35 145 275 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi1 q@iy 1 prim q@px 1 setup warn + Parameter: PY -> "40" + Parameter: IY -> "36" + Parameter: PX -> "35" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 35 145 275 0 0 + + CHARMM> + + CHARMM> impa 011E prim q@py 1 prim q@px 1 qi1 q@ix 1 setup warn + Parameter: PY -> "40" + Parameter: PX -> "35" + Parameter: IX -> "31" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 35 145 277 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@px 1 qi1 q@ix 1 qi1 q@iy 1 setup warn + Parameter: PX -> "35" + Parameter: IX -> "31" + Parameter: IY -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 35 147 282 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@px 1 prim q@py 1 qi1 q@iy 1 setup warn + Parameter: PX -> "35" + Parameter: PY -> "40" + Parameter: IY -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 35 147 287 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counn = @counn + 1 + Parameter: COUNN -> "7" +Evaluating: 7+1 + Parameter: COUNN <- "8" + + CHARMM> if counn lt @m goto loop2 + Parameter: M -> "8" + Comparing "8" and "8". + IF test evaluated as false. Skipping command + + CHARMM> ! corner cells will be treated later + CHARMM> + + CHARMM> ! In y direction + CHARMM> ! + CHARMM> ! image + CHARMM> ! iy ix + CHARMM> ! --------------- + CHARMM> ! py px + CHARMM> ! prim + CHARMM> + + CHARMM> set counm 1 + Parameter: COUNM <- "1" + + CHARMM> label loop3 + + CHARMM> calc py = (@m - 1) * @n + @counm + Parameter: M -> "8" + Parameter: N -> "5" + Parameter: COUNM -> "1" +Evaluating: (8-1)*5+1 + Parameter: PY <- "36" + + CHARMM> calc iy = @counm + Parameter: COUNM -> "1" +Evaluating: 1 + Parameter: IY <- "1" + + CHARMM> calc px = @py + 1 + Parameter: PY -> "36" +Evaluating: 36+1 + Parameter: PX <- "37" + + CHARMM> calc ix = @iy + 1 + Parameter: IY -> "1" +Evaluating: 1+1 + Parameter: IX <- "2" + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "36" + Parameter: IY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 41 168 326 0 0 + + CHARMM> impa 011C prim q@py 1 qi3 q@ix 1 setup warn + Parameter: PY -> "36" + Parameter: IX -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 42 175 332 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn + Parameter: PY -> "36" + Parameter: IX -> "2" + Parameter: IY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 42 175 332 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn + Parameter: IY -> "1" + Parameter: PY -> "36" + Parameter: PX -> "37" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 42 175 334 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn + Parameter: PY -> "36" + Parameter: PX -> "37" + Parameter: IX -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 42 177 339 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn + Parameter: PY -> "36" + Parameter: IY -> "1" + Parameter: IX -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 42 177 344 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counm = @counm +1 + Parameter: COUNM -> "1" +Evaluating: 1+1 + Parameter: COUNM <- "2" + + CHARMM> if counm lt @n goto loop3 + Parameter: N -> "5" + Comparing "2" and "5". + IF test evaluated as true. Performing command + + CHARMM> calc py = (@m - 1) * @n + @counm + Parameter: M -> "8" + Parameter: N -> "5" + Parameter: COUNM -> "2" +Evaluating: (8-1)*5+2 + Parameter: PY <- "37" + + CHARMM> calc iy = @counm + Parameter: COUNM -> "2" +Evaluating: 2 + Parameter: IY <- "2" + + CHARMM> calc px = @py + 1 + Parameter: PY -> "37" +Evaluating: 37+1 + Parameter: PX <- "38" + + CHARMM> calc ix = @iy + 1 + Parameter: IY -> "2" +Evaluating: 2+1 + Parameter: IX <- "3" + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "37" + Parameter: IY -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 48 198 383 0 0 + + CHARMM> impa 011C prim q@py 1 qi3 q@ix 1 setup warn + Parameter: PY -> "37" + Parameter: IX -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 49 205 389 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn + Parameter: PY -> "37" + Parameter: IX -> "3" + Parameter: IY -> "2" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 49 205 389 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn + Parameter: IY -> "2" + Parameter: PY -> "37" + Parameter: PX -> "38" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 49 205 391 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn + Parameter: PY -> "37" + Parameter: PX -> "38" + Parameter: IX -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 49 207 396 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn + Parameter: PY -> "37" + Parameter: IY -> "2" + Parameter: IX -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 49 207 401 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counm = @counm +1 + Parameter: COUNM -> "2" +Evaluating: 2+1 + Parameter: COUNM <- "3" + + CHARMM> if counm lt @n goto loop3 + Parameter: N -> "5" + Comparing "3" and "5". + IF test evaluated as true. Performing command + + CHARMM> calc py = (@m - 1) * @n + @counm + Parameter: M -> "8" + Parameter: N -> "5" + Parameter: COUNM -> "3" +Evaluating: (8-1)*5+3 + Parameter: PY <- "38" + + CHARMM> calc iy = @counm + Parameter: COUNM -> "3" +Evaluating: 3 + Parameter: IY <- "3" + + CHARMM> calc px = @py + 1 + Parameter: PY -> "38" +Evaluating: 38+1 + Parameter: PX <- "39" + + CHARMM> calc ix = @iy + 1 + Parameter: IY -> "3" +Evaluating: 3+1 + Parameter: IX <- "4" + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "38" + Parameter: IY -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 55 228 440 0 0 + + CHARMM> impa 011C prim q@py 1 qi3 q@ix 1 setup warn + Parameter: PY -> "38" + Parameter: IX -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 56 235 446 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn + Parameter: PY -> "38" + Parameter: IX -> "4" + Parameter: IY -> "3" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 56 235 446 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn + Parameter: IY -> "3" + Parameter: PY -> "38" + Parameter: PX -> "39" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 56 235 448 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn + Parameter: PY -> "38" + Parameter: PX -> "39" + Parameter: IX -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 56 237 453 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn + Parameter: PY -> "38" + Parameter: IY -> "3" + Parameter: IX -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 56 237 458 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counm = @counm +1 + Parameter: COUNM -> "3" +Evaluating: 3+1 + Parameter: COUNM <- "4" + + CHARMM> if counm lt @n goto loop3 + Parameter: N -> "5" + Comparing "4" and "5". + IF test evaluated as true. Performing command + + CHARMM> calc py = (@m - 1) * @n + @counm + Parameter: M -> "8" + Parameter: N -> "5" + Parameter: COUNM -> "4" +Evaluating: (8-1)*5+4 + Parameter: PY <- "39" + + CHARMM> calc iy = @counm + Parameter: COUNM -> "4" +Evaluating: 4 + Parameter: IY <- "4" + + CHARMM> calc px = @py + 1 + Parameter: PY -> "39" +Evaluating: 39+1 + Parameter: PX <- "40" + + CHARMM> calc ix = @iy + 1 + Parameter: IY -> "4" +Evaluating: 4+1 + Parameter: IX <- "5" + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "39" + Parameter: IY -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 62 258 497 0 0 + + CHARMM> impa 011C prim q@py 1 qi3 q@ix 1 setup warn + Parameter: PY -> "39" + Parameter: IX -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 63 265 503 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi3 q@ix 1 qi3 q@iy 1 setup warn + Parameter: PY -> "39" + Parameter: IX -> "5" + Parameter: IY -> "4" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 63 265 503 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 prim q@px 1 setup warn + Parameter: IY -> "4" + Parameter: PY -> "39" + Parameter: PX -> "40" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 63 265 505 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 prim q@px 1 qi3 q@ix 1 setup warn + Parameter: PY -> "39" + Parameter: PX -> "40" + Parameter: IX -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 63 267 510 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi3 q@ix 1 setup warn + Parameter: PY -> "39" + Parameter: IY -> "4" + Parameter: IX -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 63 267 515 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> calc counm = @counm +1 + Parameter: COUNM -> "4" +Evaluating: 4+1 + Parameter: COUNM <- "5" + + CHARMM> if counm lt @n goto loop3 + Parameter: N -> "5" + Comparing "5" and "5". + IF test evaluated as false. Skipping command + + CHARMM> + + CHARMM> ! Now corner cells + CHARMM> calc py = (@m - 1) * @n + 1 + Parameter: M -> "8" + Parameter: N -> "5" +Evaluating: (8-1)*5+1 + Parameter: PY <- "36" + + CHARMM> calc iy = 1 +Evaluating: 1 + Parameter: IY <- "1" + + CHARMM> calc ix = @n + Parameter: N -> "5" +Evaluating: 5 + Parameter: IX <- "5" + + CHARMM> + + CHARMM> calc py = @m*@n + Parameter: M -> "8" + Parameter: N -> "5" +Evaluating: 8*5 + Parameter: PY <- "40" + + CHARMM> calc ix = (@m - 1) * @n + 1 + Parameter: M -> "8" + Parameter: N -> "5" +Evaluating: (8-1)*5+1 + Parameter: IX <- "36" + + CHARMM> calc iy = @n + Parameter: N -> "5" +Evaluating: 5 + Parameter: IY <- "5" + + CHARMM> set ixy 1 + Parameter: IXY <- "1" + + CHARMM> impa 011A prim q@py 1 qi1 q@ix 1 setup warn + Parameter: PY -> "40" + Parameter: IX -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 67 279 538 0 0 + + CHARMM> + + CHARMM> impa 011B prim q@py 1 qi3 q@iy 1 setup warn + Parameter: PY -> "40" + Parameter: IY -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 73 300 577 0 0 + + CHARMM> + + CHARMM> impa 011C prim q@py 1 qi5 q@ixy 1 setup warn + Parameter: PY -> "40" + Parameter: IXY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 74 307 583 0 0 + + CHARMM> + + CHARMM> impa 011D prim q@py 1 qi5 q@ixy 1 qi3 q@iy 1 setup warn + Parameter: PY -> "40" + Parameter: IXY -> "1" + Parameter: IY -> "5" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 74 307 583 0 0 + + CHARMM> + + CHARMM> impa 011E qi3 q@iy 1 prim q@py 1 qi1 q@ix 1 setup warn + Parameter: IY -> "5" + Parameter: PY -> "40" + Parameter: IX -> "36" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 74 307 585 0 0 + + CHARMM> + + CHARMM> impa 011F prim q@py 1 qi1 q@ix 1 qi5 q@ixy 1 setup warn + Parameter: PY -> "40" + Parameter: IX -> "36" + Parameter: IXY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 74 309 590 0 0 + + CHARMM> + + CHARMM> impa 011G prim q@py 1 qi3 q@iy 1 qi5 q@ixy 1 setup warn + Parameter: PY -> "40" + Parameter: IY -> "5" + Parameter: IXY -> "1" + CURRENT IMAGE INTERNAL COORDINATE COUNTS: + NATOM NBOND NTHETA NPHI NIMPHI NCRT + 2520 74 309 595 0 0 + + CHARMM> + + CHARMM> + + CHARMM> + + CHARMM> ! Below info for testing only + CHARMM> ! PRINT IMAG PSF + CHARMM> + + VCLOSE: Closing unit 99 with status "KEEP" + + RETURNING TO INPUT STREAM 5 + + CHARMM> + + CHARMM> !PRINT PSF + CHARMM> !PRINT IMAG PSF + CHARMM> + + CHARMM> update inbfrq -1 imgfrq -1 ihbfrq 0 - + CHARMM> nbonds atom fshift cdie vdw vshift - + CHARMM> cutnb @4 ctofnb @6 ctonnb @5 wmin 1.5 eps 1.0 + Parameter: 4 -> "16.0" + Parameter: 6 -> "12.0" + Parameter: 5 -> "10.0" + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 960 24 24 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 480 12 12 0.00 + 7 QI7 has 280 7 7 0.00 + 9 QI9 has 0 0 0 35.07 + 11 QI11 has 0 0 0 35.07 + 13 QI13 has 0 0 0 35.07 + 15 QI15 has 0 0 0 35.07 + 17 QI17 has 0 0 0 35.08 + 19 QI19 has 0 0 0 35.07 + 21 QI21 has 0 0 0 35.10 + 23 QI23 has 0 0 0 35.08 + 25 QI25 has 0 0 0 35.10 + Total of 4120 atoms and 103 groups and 103 residues were included + + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec FSHIft VATOm VSHIft + BYGRoup NOEXtnd NOEWald + CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 0 atom pairs and 0 atom exclusions. + There are 0 group pairs and 0 group exclusions. + with mode 5 found 5481 exclusions and 4908 interactions(1-4) + found 123 group exclusions. + with mode 5 found 348 exclusions and 576 interactions(1-4) + found 36 image group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 686292 ATOM PAIRS AND 0 GROUP PAIRS + NBONDA>> Maximum group spatial extent (12A) exceeded. + Size is 14.93 Angstroms and starts with atom: 161 + Please check group boundary definitions. + + General atom nonbond list generation found: + 432259 ATOM PAIRS WERE FOUND FOR ATOM LIST + 562 GROUP PAIRS REQUIRED ATOM SEARCHES + + VEHEAP> Expanding heap size by 950272 words. + SPACE FOR 686368 ATOM PAIRS AND 0 GROUP PAIRS + + Image nonbond list generation found: + 214609 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 ATOM PAIRS WERE FOUND FOR ATOM SELF LIST + 518 GROUP PAIRS REQUIRED ATOM SEARCHES + + **** Warning **** The following extraneous characters + were found while command processing in CHARMM + NBONDS + + CHARMM> + + CHARMM> mini sd nsteps 500 nprint 50 + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 960 24 24 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 480 12 12 0.00 + 7 QI7 has 280 7 7 0.00 + 9 QI9 has 0 0 0 35.07 + 11 QI11 has 0 0 0 35.07 + 13 QI13 has 0 0 0 35.07 + 15 QI15 has 0 0 0 35.07 + 17 QI17 has 0 0 0 35.08 + 19 QI19 has 0 0 0 35.07 + 21 QI21 has 0 0 0 35.10 + 23 QI23 has 0 0 0 35.08 + 25 QI25 has 0 0 0 35.10 + Total of 4120 atoms and 103 groups and 103 residues were included + + with mode 5 found 348 exclusions and 576 interactions(1-4) + found 36 image group exclusions. + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec FSHIft VATOm VSHIft + BYGRoup NOEXtnd NOEWald + CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 432259 atom pairs and 10389 atom exclusions. + There are 0 group pairs and 123 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 686292 ATOM PAIRS AND 0 GROUP PAIRS + NBONDA>> Maximum group spatial extent (12A) exceeded. + Size is 14.93 Angstroms and starts with atom: 161 + Please check group boundary definitions. + + General atom nonbond list generation found: + 432259 ATOM PAIRS WERE FOUND FOR ATOM LIST + 562 GROUP PAIRS REQUIRED ATOM SEARCHES + + VEHEAP> Expanding heap size by 950272 words. + SPACE FOR 686368 ATOM PAIRS AND 0 GROUP PAIRS + + Image nonbond list generation found: + 214609 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 ATOM PAIRS WERE FOUND FOR ATOM SELF LIST + 518 GROUP PAIRS REQUIRED ATOM SEARCHES + + + + STEEPD> An energy minimization has been requested. + + NSTEP = 500 NPRINT = 50 + STEP = 0.0200000 TOLFUN = 0.0000000 + TOLGRD = 0.0000000 TOLSTP = 0.0000000 + +MINI MIN: Cycle ENERgy Delta-E GRMS Step-size +MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +MINI EXTERN: VDWaals ELEC HBONds ASP USER +MINI IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec + ---------- --------- --------- --------- --------- --------- +MINI> 0 -50525.41123 -14389.92677 17.87600 0.02000 +MINI INTERN> 4430.59567 6721.43029 0.00000 974.05019 0.00000 +MINI EXTERN> -5486.58944 -50579.40355 0.00000 0.00000 0.00000 +MINI IMAGES> -915.37881 -5670.11558 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 50 -52195.87549 1670.46426 0.81713 0.00087 +MINI INTERN> 1814.22802 6909.22686 0.00000 943.01888 0.00000 +MINI EXTERN> -5318.90488 -49998.42246 0.00000 0.00000 0.00000 +MINI IMAGES> -883.41706 -5661.60485 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 100 -52272.51477 76.63927 0.49075 0.00052 +MINI INTERN> 1759.44919 6850.96834 0.00000 912.70140 0.00000 +MINI EXTERN> -5316.36680 -49937.15423 0.00000 0.00000 0.00000 +MINI IMAGES> -879.68967 -5662.42300 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 150 -52306.40676 33.89199 0.97512 0.00074 +MINI INTERN> 1742.12722 6823.91011 0.00000 900.06821 0.00000 +MINI EXTERN> -5318.34901 -49913.96582 0.00000 0.00000 0.00000 +MINI IMAGES> -878.30173 -5661.89574 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 200 -52323.31715 16.91040 0.58335 0.00044 +MINI INTERN> 1737.15764 6812.04694 0.00000 896.70532 0.00000 +MINI EXTERN> -5319.60938 -49908.92130 0.00000 0.00000 0.00000 +MINI IMAGES> -877.69474 -5663.00164 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 250 -52332.30414 8.98699 0.17450 0.00027 +MINI INTERN> 1734.19934 6807.60591 0.00000 896.09834 0.00000 +MINI EXTERN> -5320.20849 -49908.28671 0.00000 0.00000 0.00000 +MINI IMAGES> -877.33304 -5664.37948 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 300 -52337.54421 5.24007 0.50976 0.00038 +MINI INTERN> 1733.19273 6805.65025 0.00000 896.49811 0.00000 +MINI EXTERN> -5320.60616 -49909.18565 0.00000 0.00000 0.00000 +MINI IMAGES> -877.15684 -5665.93665 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 350 -52341.39375 3.84953 0.30132 0.00023 +MINI INTERN> 1732.97330 6804.57029 0.00000 897.37733 0.00000 +MINI EXTERN> -5320.89759 -49910.60673 0.00000 0.00000 0.00000 +MINI IMAGES> -877.10837 -5667.70199 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 400 -52344.07121 2.67746 0.09964 0.00014 +MINI INTERN> 1732.16950 6804.12536 0.00000 898.19432 0.00000 +MINI EXTERN> -5321.12613 -49911.44483 0.00000 0.00000 0.00000 +MINI IMAGES> -877.09656 -5668.89286 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 450 -52346.03741 1.96621 0.25321 0.00020 +MINI INTERN> 1731.58226 6803.91114 0.00000 899.06890 0.00000 +MINI EXTERN> -5321.32801 -49912.18624 0.00000 0.00000 0.00000 +MINI IMAGES> -877.12311 -5669.96235 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- +MINI> 500 -52347.61223 1.57481 0.07820 0.00012 +MINI INTERN> 1731.17196 6803.84001 0.00000 899.96647 0.00000 +MINI EXTERN> -5321.48236 -49912.91031 0.00000 0.00000 0.00000 +MINI IMAGES> -877.17330 -5671.02470 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. + +STPD MIN: Cycle ENERgy Delta-E GRMS Step-size +STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +STPD EXTERN: VDWaals ELEC HBONds ASP USER +STPD IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec + ---------- --------- --------- --------- --------- --------- +STPD> 500 -52347.61223 1.57481 0.07820 0.00014 +STPD INTERN> 1731.17196 6803.84001 0.00000 899.96647 0.00000 +STPD EXTERN> -5321.48236 -49912.91031 0.00000 0.00000 0.00000 +STPD IMAGES> -877.17330 -5671.02470 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> energy + + : updating the image atom lists and remapping + Transformation Atoms Groups Residues Upper-Bound + 1 QI1 has 960 24 24 0.00 + 3 QI3 has 800 20 20 0.00 + 5 QI5 has 480 12 12 0.00 + 7 QI7 has 320 8 8 0.00 + 9 QI9 has 0 0 0 35.12 + 11 QI11 has 0 0 0 35.21 + 13 QI13 has 0 0 0 35.12 + 15 QI15 has 0 0 0 35.13 + 17 QI17 has 0 0 0 35.17 + 19 QI19 has 0 0 0 35.31 + 21 QI21 has 0 0 0 35.15 + 23 QI23 has 0 0 0 35.17 + 25 QI25 has 0 0 0 35.24 + Total of 4160 atoms and 104 groups and 104 residues were included + + with mode 5 found 348 exclusions and 576 interactions(1-4) + found 36 image group exclusions. + + NONBOND OPTION FLAGS: + ELEC VDW ATOMs CDIElec FSHIft VATOm VSHIft + BYGRoup NOEXtnd NOEWald + CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 + WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 + NBXMOD = 5 + There are 432259 atom pairs and 10389 atom exclusions. + There are 0 group pairs and 123 group exclusions. + Generating nonbond list with Exclusion mode = 5 + == PRIMARY == SPACE FOR 686292 ATOM PAIRS AND 0 GROUP PAIRS + NBONDA>> Maximum group spatial extent (12A) exceeded. + Size is 14.84 Angstroms and starts with atom: 161 + Please check group boundary definitions. + + General atom nonbond list generation found: + 432087 ATOM PAIRS WERE FOUND FOR ATOM LIST + 562 GROUP PAIRS REQUIRED ATOM SEARCHES + + SPACE FOR 686368 ATOM PAIRS AND 0 GROUP PAIRS + + Image nonbond list generation found: + 215605 ATOM PAIRS WERE FOUND FOR ATOM LIST + 0 ATOM PAIRS WERE FOUND FOR ATOM SELF LIST + 540 GROUP PAIRS REQUIRED ATOM SEARCHES + +ENER ENR: Eval# ENERgy Delta-E GRMS +ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers +ENER EXTERN: VDWaals ELEC HBONds ASP USER +ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec + ---------- --------- --------- --------- --------- --------- +ENER> 0 -52347.61223 1.57481 0.07820 +ENER INTERN> 1731.17196 6803.84001 0.00000 899.96647 0.00000 +ENER EXTERN> -5321.48236 -49912.91031 0.00000 0.00000 0.00000 +ENER IMAGES> -877.17330 -5671.02470 0.00000 0.00000 0.00000 + ---------- --------- --------- --------- --------- --------- + + CHARMM> + + CHARMM> open write card unit 20 name test_opt.pdb + VOPEN> Attempting to open::test_opt.pdb:: + OPNLGU> Unit 20 opened for WRITE access to test_opt.pdb + + CHARMM> write coor pdb unit 20 + RDTITL> * COORDINATES + RDTITL> * + + CHARMM> close unit 20 + VCLOSE: Closing unit 20 with status "KEEP" + + CHARMM> + + CHARMM> open write form unit 20 name test_opt.crd + VOPEN> Attempting to open::test_opt.crd:: + OPNLGU> Unit 20 opened for WRITE access to test_opt.crd + + CHARMM> write coor cards unit 20 + RDTITL> * COORDINATES + RDTITL> * + VCLOSE: Closing unit 20 with status "KEEP" + + CHARMM> close unit 20 + CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. + + CHARMM> + + CHARMM> open unit 20 write form name test_opt.psf + VOPEN> Attempting to open::test_opt.psf:: + OPNLGU> Unit 20 opened for WRITE access to test_opt.psf + + CHARMM> write psf cards unit 20 + RDTITL> * PSFFILE + RDTITL> * + + CHARMM> close unit 20 + VCLOSE: Closing unit 20 with status "KEEP" + + CHARMM> + + CHARMM> stop +$$$$$$ New timer profile $$$$$ + Nonbond force 35.72844 Other: 0.00000 + Bond energy 0.14775 Other: 0.00000 + Angle energy 1.48916 Other: 0.00000 + Dihedral energy 1.82762 Other: 0.00000 + Restraints energy 0.00245 Other: 0.00000 + INTRNL energy 3.58538 Other: 0.11841 + Energy time 39.46469 Other: 0.15087 + Total time 43.88100 Other: 4.41631 + + NORMAL TERMINATION BY NORMAL STOP + MAXIMUM STACK SPACE USED IS 242652 + STACK CURRENTLY IN USE IS 0 + NO WARNINGS WERE ISSUED + HEAP PRINTOUT- HEAP SIZE 2048000 + SPACE CURRENTLY IN USE IS 0 + MAXIMUM SPACE USED IS 1935148 + FREE LIST + PRINHP> ADDRESS: 1 LENGTH: 2048000 NEXT: 229011097 + PRINHP> ADDRESS: 229011097 LENGTH: 950272 NEXT: 229962393 + PRINHP> ADDRESS: 229962393 LENGTH: 950272 NEXT: 0 + + $$$$$ JOB ACCOUNTING INFORMATION $$$$$ + ELAPSED TIME: 43.88 SECONDS + CPU TIME: 43.68 SECONDS diff --git a/charmm/toppar/silicates/test_opt.crd b/charmm/toppar/silicates/test_opt.crd new file mode 100644 index 00000000..d2c6c9de --- /dev/null +++ b/charmm/toppar/silicates/test_opt.crd @@ -0,0 +1,1604 @@ +* COORDINATES +* DATE: 7/14/ 5 16:13: 0 CREATED BY USER: alex +* + 1600 + 1 1 Q011 SI1 3.95209 4.58869 -12.92325 Q1 1 0.00000 + 2 1 Q011 SI2 0.08583 3.06171 -9.50702 Q1 1 0.00000 + 3 1 Q011 SI3 3.33729 1.69673 -6.11317 Q1 1 0.00000 + 4 1 Q011 SI4 6.63254 0.11246 -2.78686 Q1 1 0.00000 + 5 1 Q011 O5 3.72324 2.97986 -12.70992 Q1 1 0.00000 + 6 1 Q011 O6 0.01876 1.44432 -9.37400 Q1 1 0.00000 + 7 1 Q011 O7 3.13706 0.07943 -5.96637 Q1 1 0.00000 + 8 1 Q011 O8 5.00737 3.09472 -2.57977 Q1 1 0.00000 + 9 1 Q011 O9 5.54167 4.88903 -12.64165 Q1 1 0.00000 + 10 1 Q011 O10 1.61202 3.62675 -9.34382 Q1 1 0.00000 + 11 1 Q011 O11 4.90987 2.13473 -6.00454 Q1 1 0.00000 + 12 1 Q011 O12 0.80195 0.91449 -2.54462 Q1 1 0.00000 + 13 1 Q011 O13 -0.52277 3.43809 -10.98792 Q1 1 0.00000 + 14 1 Q011 O14 2.76895 2.02541 -7.60845 Q1 1 0.00000 + 15 1 Q011 O15 6.10128 0.42514 -4.30414 Q1 1 0.00000 + 16 1 Q011 O16 2.18101 -0.77311 -0.83002 Q1 1 0.00000 + 17 1 Q011 O17 4.98443 0.74286 -11.86844 Q1 1 0.00000 + 18 1 Q011 O18 -0.82943 3.62251 -8.27623 Q1 1 0.00000 + 19 1 Q011 O19 2.47526 2.44155 -4.93111 Q1 1 0.00000 + 20 1 Q011 O20 5.56014 0.67690 -1.67403 Q1 1 0.00000 + 21 1 Q011 SI21 3.73282 1.79430 -11.55899 Q1 1 0.00000 + 22 1 Q011 SI22 5.37180 4.92249 -8.18324 Q1 1 0.00000 + 23 1 Q011 SI23 1.31150 3.58687 -4.78740 Q1 1 0.00000 + 24 1 Q011 SI24 4.68598 2.03888 -1.37006 Q1 1 0.00000 + 25 1 Q011 SI25 -0.21020 4.31961 -12.33025 Q1 1 0.00000 + 26 1 Q011 SI26 3.05956 3.05877 -8.84699 Q1 1 0.00000 + 27 1 Q011 SI27 6.34253 1.54455 -5.48039 Q1 1 0.00000 + 28 1 Q011 SI28 2.25893 0.31961 -2.06339 Q1 1 0.00000 + 29 1 Q011 O29 3.94407 2.35198 -10.02796 Q1 1 0.00000 + 30 1 Q011 O30 5.58172 5.51868 -6.67129 Q1 1 0.00000 + 31 1 Q011 O31 1.50695 4.29387 -3.31620 Q1 1 0.00000 + 32 1 Q011 O32 4.93542 2.63725 0.14661 Q1 1 0.00000 + 33 1 Q011 O33 2.21220 1.13633 -11.57639 Q1 1 0.00000 + 34 1 Q011 O34 3.83513 4.37443 -8.26732 Q1 1 0.00000 + 35 1 Q011 O35 -0.16673 2.89415 -4.80547 Q1 1 0.00000 + 36 1 Q011 O36 3.11505 1.66367 -1.66682 Q1 1 0.00000 + 37 1 Q011 H37 3.54471 5.02327 -14.28066 Q1 1 0.00000 + 38 1 Q011 H38 3.00010 -1.24260 -0.60513 Q1 1 0.00000 + 39 1 Q011 H39 0.86119 3.69883 -13.14229 Q1 1 0.00000 + 40 1 Q011 H40 4.51571 3.48074 0.37926 Q1 1 0.00000 + 41 2 Q011 SI1 11.31306 4.50797 -12.97765 Q2 1 0.00000 + 42 2 Q011 SI2 7.41600 3.07610 -9.46821 Q2 1 0.00000 + 43 2 Q011 SI3 10.66075 1.64082 -6.13694 Q2 1 0.00000 + 44 2 Q011 SI4 13.93424 0.09184 -2.79920 Q2 1 0.00000 + 45 2 Q011 O5 11.03886 2.90835 -12.75678 Q2 1 0.00000 + 46 2 Q011 O6 7.38533 1.45188 -9.29955 Q2 1 0.00000 + 47 2 Q011 O7 10.48229 0.02163 -5.98173 Q2 1 0.00000 + 48 2 Q011 O8 12.35667 3.11868 -2.58495 Q2 1 0.00000 + 49 2 Q011 O9 12.92090 4.78520 -12.78455 Q2 1 0.00000 + 50 2 Q011 O10 8.94804 3.62620 -9.31633 Q2 1 0.00000 + 51 2 Q011 O11 12.22156 2.11276 -6.00252 Q2 1 0.00000 + 52 2 Q011 O12 8.09653 0.85414 -2.53571 Q2 1 0.00000 + 53 2 Q011 O13 6.85278 3.39428 -10.97571 Q2 1 0.00000 + 54 2 Q011 O14 10.12337 1.96511 -7.64379 Q2 1 0.00000 + 55 2 Q011 O15 13.40703 0.40805 -4.31587 Q2 1 0.00000 + 56 2 Q011 O16 9.54071 -0.76120 -0.80628 Q2 1 0.00000 + 57 2 Q011 O17 12.26298 0.68563 -11.87517 Q2 1 0.00000 + 58 2 Q011 O18 6.47054 3.71549 -8.29016 Q2 1 0.00000 + 59 2 Q011 O19 9.76193 2.35871 -4.96943 Q2 1 0.00000 + 60 2 Q011 O20 12.86652 0.67367 -1.69053 Q2 1 0.00000 + 61 2 Q011 SI21 11.00870 1.74169 -11.58731 Q2 1 0.00000 + 62 2 Q011 SI22 12.70090 4.90637 -8.19527 Q2 1 0.00000 + 63 2 Q011 SI23 8.61900 3.52191 -4.84221 Q2 1 0.00000 + 64 2 Q011 SI24 11.98837 2.03965 -1.40781 Q2 1 0.00000 + 65 2 Q011 SI25 7.05941 4.40982 -12.23889 Q2 1 0.00000 + 66 2 Q011 SI26 10.39618 3.02589 -8.86276 Q2 1 0.00000 + 67 2 Q011 SI27 13.65926 1.52973 -5.48712 Q2 1 0.00000 + 68 2 Q011 SI28 9.57706 0.28717 -2.08039 Q2 1 0.00000 + 69 2 Q011 O29 11.25164 2.32922 -10.07091 Q2 1 0.00000 + 70 2 Q011 O30 12.92130 5.51722 -6.69148 Q2 1 0.00000 + 71 2 Q011 O31 8.82638 4.18328 -3.35521 Q2 1 0.00000 + 72 2 Q011 O32 12.18826 2.62799 0.12017 Q2 1 0.00000 + 73 2 Q011 O33 9.47927 1.09501 -11.61106 Q2 1 0.00000 + 74 2 Q011 O34 11.17249 4.33670 -8.27070 Q2 1 0.00000 + 75 2 Q011 O35 7.11822 2.87406 -4.86422 Q2 1 0.00000 + 76 2 Q011 O36 10.42949 1.65211 -1.74940 Q2 1 0.00000 + 77 2 Q011 H37 10.84195 4.96187 -14.30781 Q2 1 0.00000 + 78 2 Q011 H38 10.37362 -1.19817 -0.56933 Q2 1 0.00000 + 79 2 Q011 H39 7.78342 3.77737 -13.36659 Q2 1 0.00000 + 80 2 Q011 H40 11.77473 3.47830 0.33877 Q2 1 0.00000 + 81 3 Q011 SI1 18.63865 4.50547 -12.97560 Q3 1 0.00000 + 82 3 Q011 SI2 14.72825 3.04941 -9.47117 Q3 1 0.00000 + 83 3 Q011 SI3 17.97612 1.63339 -6.13415 Q3 1 0.00000 + 84 3 Q011 SI4 21.24893 0.08201 -2.79793 Q3 1 0.00000 + 85 3 Q011 O5 18.36622 2.90596 -12.74973 Q3 1 0.00000 + 86 3 Q011 O6 14.68994 1.42436 -9.30627 Q3 1 0.00000 + 87 3 Q011 O7 17.80645 0.01343 -5.98034 Q3 1 0.00000 + 88 3 Q011 O8 19.66535 3.10570 -2.58522 Q3 1 0.00000 + 89 3 Q011 O9 20.24598 4.78714 -12.78366 Q3 1 0.00000 + 90 3 Q011 O10 16.26052 3.60271 -9.32874 Q3 1 0.00000 + 91 3 Q011 O11 19.53594 2.10840 -5.99722 Q3 1 0.00000 + 92 3 Q011 O12 15.39840 0.83345 -2.54730 Q3 1 0.00000 + 93 3 Q011 O13 14.14435 3.39372 -10.96478 Q3 1 0.00000 + 94 3 Q011 O14 17.43497 1.95695 -7.63982 Q3 1 0.00000 + 95 3 Q011 O15 20.72438 0.39667 -4.31630 Q3 1 0.00000 + 96 3 Q011 O16 16.82071 -0.78592 -0.81139 Q3 1 0.00000 + 97 3 Q011 O17 19.58834 0.68149 -11.86976 Q3 1 0.00000 + 98 3 Q011 O18 13.80189 3.70138 -8.28711 Q3 1 0.00000 + 99 3 Q011 O19 17.07456 2.34580 -4.96582 Q3 1 0.00000 + 100 3 Q011 O20 20.17454 0.66138 -1.69367 Q3 1 0.00000 + 101 3 Q011 SI21 18.33612 1.73880 -11.58047 Q3 1 0.00000 + 102 3 Q011 SI22 20.00973 4.90339 -8.19794 Q3 1 0.00000 + 103 3 Q011 SI23 15.93435 3.51128 -4.83758 Q3 1 0.00000 + 104 3 Q011 SI24 19.29040 2.02391 -1.41200 Q3 1 0.00000 + 105 3 Q011 SI25 14.41559 4.35200 -12.26028 Q3 1 0.00000 + 106 3 Q011 SI26 17.70924 3.01616 -8.85986 Q3 1 0.00000 + 107 3 Q011 SI27 20.97365 1.52103 -5.48598 Q3 1 0.00000 + 108 3 Q011 SI28 16.87526 0.26518 -2.08272 Q3 1 0.00000 + 109 3 Q011 O29 18.57454 2.32302 -10.06265 Q3 1 0.00000 + 110 3 Q011 O30 20.23561 5.51048 -6.69326 Q3 1 0.00000 + 111 3 Q011 O31 16.15278 4.17135 -3.35057 Q3 1 0.00000 + 112 3 Q011 O32 19.48881 2.61338 0.11581 Q3 1 0.00000 + 113 3 Q011 O33 16.80703 1.09272 -11.59945 Q3 1 0.00000 + 114 3 Q011 O34 18.48147 4.33099 -8.27002 Q3 1 0.00000 + 115 3 Q011 O35 14.43408 2.86072 -4.86870 Q3 1 0.00000 + 116 3 Q011 O36 17.73123 1.62914 -1.74975 Q3 1 0.00000 + 117 3 Q011 H37 18.16683 4.95484 -14.30710 Q3 1 0.00000 + 118 3 Q011 H38 17.64902 -1.22778 -0.56732 Q3 1 0.00000 + 119 3 Q011 H39 15.21907 3.68006 -13.30826 Q3 1 0.00000 + 120 3 Q011 H40 19.07828 3.46573 0.33224 Q3 1 0.00000 + 121 4 Q011 SI1 26.01691 4.52053 -12.94120 Q4 1 0.00000 + 122 4 Q011 SI2 22.04127 3.04797 -9.47118 Q4 1 0.00000 + 123 4 Q011 SI3 25.29524 1.61208 -6.13238 Q4 1 0.00000 + 124 4 Q011 SI4 28.57817 0.07779 -2.78753 Q4 1 0.00000 + 125 4 Q011 O5 25.71673 2.92159 -12.73861 Q4 1 0.00000 + 126 4 Q011 O6 21.99393 1.42226 -9.31087 Q4 1 0.00000 + 127 4 Q011 O7 25.11991 -0.00626 -5.97850 Q4 1 0.00000 + 128 4 Q011 O8 26.99336 3.09999 -2.57954 Q4 1 0.00000 + 129 4 Q011 O9 27.62127 4.78774 -12.69555 Q4 1 0.00000 + 130 4 Q011 O10 23.57513 3.59376 -9.32233 Q4 1 0.00000 + 131 4 Q011 O11 26.85982 2.07364 -5.99873 Q4 1 0.00000 + 132 4 Q011 O12 22.71433 0.82225 -2.54376 Q4 1 0.00000 + 133 4 Q011 O13 21.46628 3.40093 -10.96630 Q4 1 0.00000 + 134 4 Q011 O14 24.74579 1.93734 -7.63505 Q4 1 0.00000 + 135 4 Q011 O15 28.03983 0.38521 -4.30094 Q4 1 0.00000 + 136 4 Q011 O16 24.14015 -0.78866 -0.80511 Q4 1 0.00000 + 137 4 Q011 O17 26.88936 0.66657 -11.87245 Q4 1 0.00000 + 138 4 Q011 O18 21.11206 3.69960 -8.28913 Q4 1 0.00000 + 139 4 Q011 O19 24.39733 2.32871 -4.96307 Q4 1 0.00000 + 140 4 Q011 O20 27.50199 0.65694 -1.68422 Q4 1 0.00000 + 141 4 Q011 SI21 25.65165 1.74044 -11.58335 Q4 1 0.00000 + 142 4 Q011 SI22 27.33509 4.84621 -8.16585 Q4 1 0.00000 + 143 4 Q011 SI23 23.25518 3.49252 -4.83133 Q4 1 0.00000 + 144 4 Q011 SI24 26.61214 2.01736 -1.40916 Q4 1 0.00000 + 145 4 Q011 SI25 21.74285 4.35617 -12.26328 Q4 1 0.00000 + 146 4 Q011 SI26 25.01993 2.99742 -8.85410 Q4 1 0.00000 + 147 4 Q011 SI27 28.29964 1.49366 -5.48164 Q4 1 0.00000 + 148 4 Q011 SI28 24.19399 0.25792 -2.08008 Q4 1 0.00000 + 149 4 Q011 O29 25.88491 2.30454 -10.05729 Q4 1 0.00000 + 150 4 Q011 O30 27.56072 5.46574 -6.66677 Q4 1 0.00000 + 151 4 Q011 O31 23.47435 4.15293 -3.34421 Q4 1 0.00000 + 152 4 Q011 O32 26.80247 2.61028 0.11839 Q4 1 0.00000 + 153 4 Q011 O33 24.11809 1.10435 -11.61460 Q4 1 0.00000 + 154 4 Q011 O34 25.79731 4.30480 -8.25597 Q4 1 0.00000 + 155 4 Q011 O35 21.75317 2.84623 -4.86180 Q4 1 0.00000 + 156 4 Q011 O36 25.05384 1.62123 -1.75234 Q4 1 0.00000 + 157 4 Q011 H37 25.59106 4.98718 -14.28231 Q4 1 0.00000 + 158 4 Q011 H38 24.96879 -1.22856 -0.55887 Q4 1 0.00000 + 159 4 Q011 H39 22.54191 3.67869 -13.31106 Q4 1 0.00000 + 160 4 Q011 H40 26.39253 3.46414 0.33001 Q4 1 0.00000 + 161 5 Q011 SI1 33.22574 4.37958 -13.18237 Q5 1 0.00000 + 162 5 Q011 SI2 29.35025 2.98508 -9.43443 Q5 1 0.00000 + 163 5 Q011 SI3 32.64255 1.60938 -6.13783 Q5 1 0.00000 + 164 5 Q011 SI4 35.91177 0.01774 -2.82188 Q5 1 0.00000 + 165 5 Q011 O5 32.78837 2.84979 -12.79487 Q5 1 0.00000 + 166 5 Q011 O6 29.35349 1.36202 -9.27421 Q5 1 0.00000 + 167 5 Q011 O7 32.46350 -0.01033 -5.98517 Q5 1 0.00000 + 168 5 Q011 O8 34.46809 3.05850 -2.53535 Q5 1 0.00000 + 169 5 Q011 O9 34.87691 4.33609 -13.20294 Q5 1 0.00000 + 170 5 Q011 O10 30.86335 3.57585 -9.27502 Q5 1 0.00000 + 171 5 Q011 O11 34.20577 2.07974 -6.00982 Q5 1 0.00000 + 172 5 Q011 O12 30.04234 0.82720 -2.55058 Q5 1 0.00000 + 173 5 Q011 O13 28.80661 3.31074 -10.94371 Q5 1 0.00000 + 174 5 Q011 O14 32.09765 1.92623 -7.64409 Q5 1 0.00000 + 175 5 Q011 O15 35.40474 0.40093 -4.33665 Q5 1 0.00000 + 176 5 Q011 O16 31.48277 -0.76846 -0.81319 Q5 1 0.00000 + 177 5 Q011 O17 34.16751 0.67283 -11.92096 Q5 1 0.00000 + 178 5 Q011 O18 28.40646 3.61563 -8.25372 Q5 1 0.00000 + 179 5 Q011 O19 31.73125 2.32833 -4.97868 Q5 1 0.00000 + 180 5 Q011 O20 34.82347 0.57982 -1.72453 Q5 1 0.00000 + 181 5 Q011 SI21 32.90093 1.70845 -11.60528 Q5 1 0.00000 + 182 5 Q011 SI22 34.61481 4.89270 -8.25689 Q5 1 0.00000 + 183 5 Q011 SI23 30.57776 3.48299 -4.85095 Q5 1 0.00000 + 184 5 Q011 SI24 33.97907 1.95947 -1.42051 Q5 1 0.00000 + 185 5 Q011 SI25 29.11231 4.30027 -12.20448 Q5 1 0.00000 + 186 5 Q011 SI26 32.32665 2.99408 -8.86639 Q5 1 0.00000 + 187 5 Q011 SI27 35.66435 1.52709 -5.51055 Q5 1 0.00000 + 188 5 Q011 SI28 31.52672 0.26614 -2.09838 Q5 1 0.00000 + 189 5 Q011 O29 33.15965 2.32850 -10.10582 Q5 1 0.00000 + 190 5 Q011 O30 34.86964 5.44544 -6.73579 Q5 1 0.00000 + 191 5 Q011 O31 30.78591 4.14086 -3.36213 Q5 1 0.00000 + 192 5 Q011 O32 34.12477 2.50532 0.12926 Q5 1 0.00000 + 193 5 Q011 O33 31.39452 1.02166 -11.57475 Q5 1 0.00000 + 194 5 Q011 O34 33.08362 4.33454 -8.31963 Q5 1 0.00000 + 195 5 Q011 O35 29.07649 2.83186 -4.87995 Q5 1 0.00000 + 196 5 Q011 O36 32.41922 1.62000 -1.81748 Q5 1 0.00000 + 197 5 Q011 H37 32.67773 4.79890 -14.49431 Q5 1 0.00000 + 198 5 Q011 H38 32.30109 -1.24841 -0.60951 Q5 1 0.00000 + 199 5 Q011 H39 29.87836 3.63313 -13.28238 Q5 1 0.00000 + 200 5 Q011 H40 33.73935 3.37018 0.34170 Q5 1 0.00000 + 201 6 Q011 SI1 2.28343 9.21132 -12.94684 Q6 1 0.00000 + 202 6 Q011 SI2 -1.58554 7.70392 -9.49811 Q6 1 0.00000 + 203 6 Q011 SI3 1.69203 6.31140 -6.13042 Q6 1 0.00000 + 204 6 Q011 SI4 4.97460 4.71971 -2.79141 Q6 1 0.00000 + 205 6 Q011 O5 2.02748 7.60269 -12.75449 Q6 1 0.00000 + 206 6 Q011 O6 -1.59813 6.08458 -9.36525 Q6 1 0.00000 + 207 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0.00000 + 1510 38 Q011 O30 8.64443 37.81887 -6.69923 Q38 1 0.00000 + 1511 38 Q011 O31 4.49321 36.57463 -3.33120 Q38 1 0.00000 + 1512 38 Q011 O32 7.85269 34.95745 0.11930 Q38 1 0.00000 + 1513 38 Q011 O33 5.22411 33.44258 -11.67611 Q38 1 0.00000 + 1514 38 Q011 O34 6.84650 36.73965 -8.31451 Q38 1 0.00000 + 1515 38 Q011 O35 2.84474 35.23074 -4.90582 Q38 1 0.00000 + 1516 38 Q011 O36 6.25387 33.89242 -1.81881 Q38 1 0.00000 + 1517 38 Q011 H37 6.58897 37.28605 -14.40674 Q38 1 0.00000 + 1518 38 Q011 H38 6.18562 31.02897 -0.55825 Q38 1 0.00000 + 1519 38 Q011 H39 3.90129 36.07788 -13.13634 Q38 1 0.00000 + 1520 38 Q011 H40 7.40421 35.79846 0.30168 Q38 1 0.00000 + 1521 39 Q011 SI1 14.41813 36.83528 -13.09832 Q39 1 0.00000 + 1522 39 Q011 SI2 10.39700 35.39461 -9.49417 Q39 1 0.00000 + 1523 39 Q011 SI3 13.71857 33.99999 -6.12097 Q39 1 0.00000 + 1524 39 Q011 SI4 17.04687 32.42909 -2.82457 Q39 1 0.00000 + 1525 39 Q011 O5 14.06549 35.26648 -12.78794 Q39 1 0.00000 + 1526 39 Q011 O6 10.34263 33.76824 -9.35316 Q39 1 0.00000 + 1527 39 Q011 O7 13.57261 32.37368 -5.99371 Q39 1 0.00000 + 1528 39 Q011 O8 15.55870 35.43665 -2.55245 Q39 1 0.00000 + 1529 39 Q011 O9 16.07499 36.87724 -13.10587 Q39 1 0.00000 + 1530 39 Q011 O10 11.92277 35.95673 -9.30284 Q39 1 0.00000 + 1531 39 Q011 O11 15.28508 34.46005 -5.99872 Q39 1 0.00000 + 1532 39 Q011 O12 11.27488 33.03571 -2.61825 Q39 1 0.00000 + 1533 39 Q011 O13 9.84046 35.81604 -10.97904 Q39 1 0.00000 + 1534 39 Q011 O14 13.15469 34.33187 -7.62035 Q39 1 0.00000 + 1535 39 Q011 O15 16.49489 32.76592 -4.32671 Q39 1 0.00000 + 1536 39 Q011 O16 12.67064 31.45111 -0.82343 Q39 1 0.00000 + 1537 39 Q011 O17 15.23517 33.02529 -11.76724 Q39 1 0.00000 + 1538 39 Q011 O18 9.45336 36.02851 -8.31410 Q39 1 0.00000 + 1539 39 Q011 O19 12.82002 34.71490 -4.94283 Q39 1 0.00000 + 1540 39 Q011 O20 16.06656 33.04667 -1.65596 Q39 1 0.00000 + 1541 39 Q011 SI21 14.02471 34.12986 -11.58967 Q39 1 0.00000 + 1542 39 Q011 SI22 15.73863 37.20569 -8.19506 Q39 1 0.00000 + 1543 39 Q011 SI23 11.66099 35.87026 -4.81236 Q39 1 0.00000 + 1544 39 Q011 SI24 15.09600 34.35083 -1.41512 Q39 1 0.00000 + 1545 39 Q011 SI25 10.21968 36.74355 -12.27018 Q39 1 0.00000 + 1546 39 Q011 SI26 13.38544 35.39092 -8.85157 Q39 1 0.00000 + 1547 39 Q011 SI27 16.73492 33.87982 -5.50474 Q39 1 0.00000 + 1548 39 Q011 SI28 12.73649 32.49555 -2.09907 Q39 1 0.00000 + 1549 39 Q011 O29 14.23426 34.72084 -10.07335 Q39 1 0.00000 + 1550 39 Q011 O30 15.97718 37.76083 -6.67348 Q39 1 0.00000 + 1551 39 Q011 O31 11.81251 36.56291 -3.32610 Q39 1 0.00000 + 1552 39 Q011 O32 15.16436 34.94739 0.12139 Q39 1 0.00000 + 1553 39 Q011 O33 12.54154 33.42199 -11.67016 Q39 1 0.00000 + 1554 39 Q011 O34 14.18400 36.70987 -8.30458 Q39 1 0.00000 + 1555 39 Q011 O35 10.16421 35.21920 -4.89894 Q39 1 0.00000 + 1556 39 Q011 O36 13.57165 33.88752 -1.82397 Q39 1 0.00000 + 1557 39 Q011 H37 13.87903 37.26657 -14.41038 Q39 1 0.00000 + 1558 39 Q011 H38 13.49986 31.02790 -0.55069 Q39 1 0.00000 + 1559 39 Q011 H39 11.22071 36.07806 -13.13470 Q39 1 0.00000 + 1560 39 Q011 H40 14.72056 35.79112 0.30290 Q39 1 0.00000 + 1561 40 Q011 SI1 21.67740 36.80605 -13.13405 Q40 1 0.00000 + 1562 40 Q011 SI2 17.71606 35.32064 -9.51511 Q40 1 0.00000 + 1563 40 Q011 SI3 21.05922 33.99764 -6.12420 Q40 1 0.00000 + 1564 40 Q011 SI4 24.40358 32.43581 -2.80384 Q40 1 0.00000 + 1565 40 Q011 O5 21.33907 35.24252 -12.78367 Q40 1 0.00000 + 1566 40 Q011 O6 17.66909 33.69709 -9.35887 Q40 1 0.00000 + 1567 40 Q011 O7 20.91496 32.37102 -6.00364 Q40 1 0.00000 + 1568 40 Q011 O8 22.68891 35.33895 -2.65050 Q40 1 0.00000 + 1569 40 Q011 O9 23.33519 36.85182 -13.14827 Q40 1 0.00000 + 1570 40 Q011 O10 19.25225 35.86698 -9.37681 Q40 1 0.00000 + 1571 40 Q011 O11 22.62958 34.44535 -5.98644 Q40 1 0.00000 + 1572 40 Q011 O12 18.57270 32.99723 -2.62934 Q40 1 0.00000 + 1573 40 Q011 O13 17.13349 35.73533 -10.99232 Q40 1 0.00000 + 1574 40 Q011 O14 20.49177 34.30630 -7.62919 Q40 1 0.00000 + 1575 40 Q011 O15 23.88718 32.73317 -4.33264 Q40 1 0.00000 + 1576 40 Q011 O16 19.92601 31.35248 -0.85566 Q40 1 0.00000 + 1577 40 Q011 O17 22.72594 33.04852 -11.95547 Q40 1 0.00000 + 1578 40 Q011 O18 16.79506 35.96243 -8.31822 Q40 1 0.00000 + 1579 40 Q011 O19 20.14443 34.70036 -4.95056 Q40 1 0.00000 + 1580 40 Q011 O20 23.30241 32.96852 -1.70502 Q40 1 0.00000 + 1581 40 Q011 SI21 21.47088 34.07998 -11.61717 Q40 1 0.00000 + 1582 40 Q011 SI22 22.97778 37.23227 -8.28965 Q40 1 0.00000 + 1583 40 Q011 SI23 18.98776 35.85923 -4.82726 Q40 1 0.00000 + 1584 40 Q011 SI24 22.35940 34.28831 -1.43604 Q40 1 0.00000 + 1585 40 Q011 SI25 17.50304 36.68204 -12.27222 Q40 1 0.00000 + 1586 40 Q011 SI26 20.71393 35.32706 -8.89537 Q40 1 0.00000 + 1587 40 Q011 SI27 24.08767 33.87022 -5.50314 Q40 1 0.00000 + 1588 40 Q011 SI28 20.01811 32.43102 -2.10075 Q40 1 0.00000 + 1589 40 Q011 O29 21.61980 34.64705 -10.08075 Q40 1 0.00000 + 1590 40 Q011 O30 23.22932 37.70817 -6.74806 Q40 1 0.00000 + 1591 40 Q011 O31 19.13134 36.54597 -3.33876 Q40 1 0.00000 + 1592 40 Q011 O32 22.57330 34.91707 0.07420 Q40 1 0.00000 + 1593 40 Q011 O33 19.99590 33.35738 -11.63628 Q40 1 0.00000 + 1594 40 Q011 O34 21.43972 36.69737 -8.37975 Q40 1 0.00000 + 1595 40 Q011 O35 17.48873 35.20970 -4.91297 Q40 1 0.00000 + 1596 40 Q011 O36 20.81122 33.81859 -1.71703 Q40 1 0.00000 + 1597 40 Q011 H37 21.12752 37.20309 -14.45229 Q40 1 0.00000 + 1598 40 Q011 H38 20.75882 30.96882 -0.53923 Q40 1 0.00000 + 1599 40 Q011 H39 18.50692 36.03623 -13.14812 Q40 1 0.00000 + 1600 40 Q011 H40 22.11143 35.74186 0.29370 Q40 1 0.00000 diff --git a/charmm/toppar/silicates/test_opt.pdb b/charmm/toppar/silicates/test_opt.pdb new file mode 100644 index 00000000..25208b31 --- /dev/null +++ b/charmm/toppar/silicates/test_opt.pdb @@ -0,0 +1,1604 @@ +REMARK COORDINATES +REMARK DATE: 7/14/ 5 16:13: 0 CREATED BY USER: alex +ATOM 1 SI1 Q011 1 3.952 4.589 -12.923 1.00 0.00 Q1 +ATOM 2 SI2 Q011 1 0.086 3.062 -9.507 1.00 0.00 Q1 +ATOM 3 SI3 Q011 1 3.337 1.697 -6.113 1.00 0.00 Q1 +ATOM 4 SI4 Q011 1 6.633 0.112 -2.787 1.00 0.00 Q1 +ATOM 5 O5 Q011 1 3.723 2.980 -12.710 1.00 0.00 Q1 +ATOM 6 O6 Q011 1 0.019 1.444 -9.374 1.00 0.00 Q1 +ATOM 7 O7 Q011 1 3.137 0.079 -5.966 1.00 0.00 Q1 +ATOM 8 O8 Q011 1 5.007 3.095 -2.580 1.00 0.00 Q1 +ATOM 9 O9 Q011 1 5.542 4.889 -12.642 1.00 0.00 Q1 +ATOM 10 O10 Q011 1 1.612 3.627 -9.344 1.00 0.00 Q1 +ATOM 11 O11 Q011 1 4.910 2.135 -6.005 1.00 0.00 Q1 +ATOM 12 O12 Q011 1 0.802 0.914 -2.545 1.00 0.00 Q1 +ATOM 13 O13 Q011 1 -0.523 3.438 -10.988 1.00 0.00 Q1 +ATOM 14 O14 Q011 1 2.769 2.025 -7.608 1.00 0.00 Q1 +ATOM 15 O15 Q011 1 6.101 0.425 -4.304 1.00 0.00 Q1 +ATOM 16 O16 Q011 1 2.181 -0.773 -0.830 1.00 0.00 Q1 +ATOM 17 O17 Q011 1 4.984 0.743 -11.868 1.00 0.00 Q1 +ATOM 18 O18 Q011 1 -0.829 3.623 -8.276 1.00 0.00 Q1 +ATOM 19 O19 Q011 1 2.475 2.442 -4.931 1.00 0.00 Q1 +ATOM 20 O20 Q011 1 5.560 0.677 -1.674 1.00 0.00 Q1 +ATOM 21 SI21 Q011 1 3.733 1.794 -11.559 1.00 0.00 Q1 +ATOM 22 SI22 Q011 1 5.372 4.922 -8.183 1.00 0.00 Q1 +ATOM 23 SI23 Q011 1 1.311 3.587 -4.787 1.00 0.00 Q1 +ATOM 24 SI24 Q011 1 4.686 2.039 -1.370 1.00 0.00 Q1 +ATOM 25 SI25 Q011 1 -0.210 4.320 -12.330 1.00 0.00 Q1 +ATOM 26 SI26 Q011 1 3.060 3.059 -8.847 1.00 0.00 Q1 +ATOM 27 SI27 Q011 1 6.343 1.545 -5.480 1.00 0.00 Q1 +ATOM 28 SI28 Q011 1 2.259 0.320 -2.063 1.00 0.00 Q1 +ATOM 29 O29 Q011 1 3.944 2.352 -10.028 1.00 0.00 Q1 +ATOM 30 O30 Q011 1 5.582 5.519 -6.671 1.00 0.00 Q1 +ATOM 31 O31 Q011 1 1.507 4.294 -3.316 1.00 0.00 Q1 +ATOM 32 O32 Q011 1 4.935 2.637 0.147 1.00 0.00 Q1 +ATOM 33 O33 Q011 1 2.212 1.136 -11.576 1.00 0.00 Q1 +ATOM 34 O34 Q011 1 3.835 4.374 -8.267 1.00 0.00 Q1 +ATOM 35 O35 Q011 1 -0.167 2.894 -4.805 1.00 0.00 Q1 +ATOM 36 O36 Q011 1 3.115 1.664 -1.667 1.00 0.00 Q1 +ATOM 37 H37 Q011 1 3.545 5.023 -14.281 1.00 0.00 Q1 +ATOM 38 H38 Q011 1 3.000 -1.243 -0.605 1.00 0.00 Q1 +ATOM 39 H39 Q011 1 0.861 3.699 -13.142 1.00 0.00 Q1 +ATOM 40 H40 Q011 1 4.516 3.481 0.379 1.00 0.00 Q1 +ATOM 41 SI1 Q011 1 11.313 4.508 -12.978 1.00 0.00 Q2 +ATOM 42 SI2 Q011 1 7.416 3.076 -9.468 1.00 0.00 Q2 +ATOM 43 SI3 Q011 1 10.661 1.641 -6.137 1.00 0.00 Q2 +ATOM 44 SI4 Q011 1 13.934 0.092 -2.799 1.00 0.00 Q2 +ATOM 45 O5 Q011 1 11.039 2.908 -12.757 1.00 0.00 Q2 +ATOM 46 O6 Q011 1 7.385 1.452 -9.300 1.00 0.00 Q2 +ATOM 47 O7 Q011 1 10.482 0.022 -5.982 1.00 0.00 Q2 +ATOM 48 O8 Q011 1 12.357 3.119 -2.585 1.00 0.00 Q2 +ATOM 49 O9 Q011 1 12.921 4.785 -12.785 1.00 0.00 Q2 +ATOM 50 O10 Q011 1 8.948 3.626 -9.316 1.00 0.00 Q2 +ATOM 51 O11 Q011 1 12.222 2.113 -6.003 1.00 0.00 Q2 +ATOM 52 O12 Q011 1 8.097 0.854 -2.536 1.00 0.00 Q2 +ATOM 53 O13 Q011 1 6.853 3.394 -10.976 1.00 0.00 Q2 +ATOM 54 O14 Q011 1 10.123 1.965 -7.644 1.00 0.00 Q2 +ATOM 55 O15 Q011 1 13.407 0.408 -4.316 1.00 0.00 Q2 +ATOM 56 O16 Q011 1 9.541 -0.761 -0.806 1.00 0.00 Q2 +ATOM 57 O17 Q011 1 12.263 0.686 -11.875 1.00 0.00 Q2 +ATOM 58 O18 Q011 1 6.471 3.715 -8.290 1.00 0.00 Q2 +ATOM 59 O19 Q011 1 9.762 2.359 -4.969 1.00 0.00 Q2 +ATOM 60 O20 Q011 1 12.867 0.674 -1.691 1.00 0.00 Q2 +ATOM 61 SI21 Q011 1 11.009 1.742 -11.587 1.00 0.00 Q2 +ATOM 62 SI22 Q011 1 12.701 4.906 -8.195 1.00 0.00 Q2 +ATOM 63 SI23 Q011 1 8.619 3.522 -4.842 1.00 0.00 Q2 +ATOM 64 SI24 Q011 1 11.988 2.040 -1.408 1.00 0.00 Q2 +ATOM 65 SI25 Q011 1 7.059 4.410 -12.239 1.00 0.00 Q2 +ATOM 66 SI26 Q011 1 10.396 3.026 -8.863 1.00 0.00 Q2 +ATOM 67 SI27 Q011 1 13.659 1.530 -5.487 1.00 0.00 Q2 +ATOM 68 SI28 Q011 1 9.577 0.287 -2.080 1.00 0.00 Q2 +ATOM 69 O29 Q011 1 11.252 2.329 -10.071 1.00 0.00 Q2 +ATOM 70 O30 Q011 1 12.921 5.517 -6.691 1.00 0.00 Q2 +ATOM 71 O31 Q011 1 8.826 4.183 -3.355 1.00 0.00 Q2 +ATOM 72 O32 Q011 1 12.188 2.628 0.120 1.00 0.00 Q2 +ATOM 73 O33 Q011 1 9.479 1.095 -11.611 1.00 0.00 Q2 +ATOM 74 O34 Q011 1 11.172 4.337 -8.271 1.00 0.00 Q2 +ATOM 75 O35 Q011 1 7.118 2.874 -4.864 1.00 0.00 Q2 +ATOM 76 O36 Q011 1 10.429 1.652 -1.749 1.00 0.00 Q2 +ATOM 77 H37 Q011 1 10.842 4.962 -14.308 1.00 0.00 Q2 +ATOM 78 H38 Q011 1 10.374 -1.198 -0.569 1.00 0.00 Q2 +ATOM 79 H39 Q011 1 7.783 3.777 -13.367 1.00 0.00 Q2 +ATOM 80 H40 Q011 1 11.775 3.478 0.339 1.00 0.00 Q2 +ATOM 81 SI1 Q011 1 18.639 4.505 -12.976 1.00 0.00 Q3 +ATOM 82 SI2 Q011 1 14.728 3.049 -9.471 1.00 0.00 Q3 +ATOM 83 SI3 Q011 1 17.976 1.633 -6.134 1.00 0.00 Q3 +ATOM 84 SI4 Q011 1 21.249 0.082 -2.798 1.00 0.00 Q3 +ATOM 85 O5 Q011 1 18.366 2.906 -12.750 1.00 0.00 Q3 +ATOM 86 O6 Q011 1 14.690 1.424 -9.306 1.00 0.00 Q3 +ATOM 87 O7 Q011 1 17.806 0.013 -5.980 1.00 0.00 Q3 +ATOM 88 O8 Q011 1 19.665 3.106 -2.585 1.00 0.00 Q3 +ATOM 89 O9 Q011 1 20.246 4.787 -12.784 1.00 0.00 Q3 +ATOM 90 O10 Q011 1 16.261 3.603 -9.329 1.00 0.00 Q3 +ATOM 91 O11 Q011 1 19.536 2.108 -5.997 1.00 0.00 Q3 +ATOM 92 O12 Q011 1 15.398 0.833 -2.547 1.00 0.00 Q3 +ATOM 93 O13 Q011 1 14.144 3.394 -10.965 1.00 0.00 Q3 +ATOM 94 O14 Q011 1 17.435 1.957 -7.640 1.00 0.00 Q3 +ATOM 95 O15 Q011 1 20.724 0.397 -4.316 1.00 0.00 Q3 +ATOM 96 O16 Q011 1 16.821 -0.786 -0.811 1.00 0.00 Q3 +ATOM 97 O17 Q011 1 19.588 0.681 -11.870 1.00 0.00 Q3 +ATOM 98 O18 Q011 1 13.802 3.701 -8.287 1.00 0.00 Q3 +ATOM 99 O19 Q011 1 17.075 2.346 -4.966 1.00 0.00 Q3 +ATOM 100 O20 Q011 1 20.175 0.661 -1.694 1.00 0.00 Q3 +ATOM 101 SI21 Q011 1 18.336 1.739 -11.580 1.00 0.00 Q3 +ATOM 102 SI22 Q011 1 20.010 4.903 -8.198 1.00 0.00 Q3 +ATOM 103 SI23 Q011 1 15.934 3.511 -4.838 1.00 0.00 Q3 +ATOM 104 SI24 Q011 1 19.290 2.024 -1.412 1.00 0.00 Q3 +ATOM 105 SI25 Q011 1 14.416 4.352 -12.260 1.00 0.00 Q3 +ATOM 106 SI26 Q011 1 17.709 3.016 -8.860 1.00 0.00 Q3 +ATOM 107 SI27 Q011 1 20.974 1.521 -5.486 1.00 0.00 Q3 +ATOM 108 SI28 Q011 1 16.875 0.265 -2.083 1.00 0.00 Q3 +ATOM 109 O29 Q011 1 18.575 2.323 -10.063 1.00 0.00 Q3 +ATOM 110 O30 Q011 1 20.236 5.510 -6.693 1.00 0.00 Q3 +ATOM 111 O31 Q011 1 16.153 4.171 -3.351 1.00 0.00 Q3 +ATOM 112 O32 Q011 1 19.489 2.613 0.116 1.00 0.00 Q3 +ATOM 113 O33 Q011 1 16.807 1.093 -11.599 1.00 0.00 Q3 +ATOM 114 O34 Q011 1 18.481 4.331 -8.270 1.00 0.00 Q3 +ATOM 115 O35 Q011 1 14.434 2.861 -4.869 1.00 0.00 Q3 +ATOM 116 O36 Q011 1 17.731 1.629 -1.750 1.00 0.00 Q3 +ATOM 117 H37 Q011 1 18.167 4.955 -14.307 1.00 0.00 Q3 +ATOM 118 H38 Q011 1 17.649 -1.228 -0.567 1.00 0.00 Q3 +ATOM 119 H39 Q011 1 15.219 3.680 -13.308 1.00 0.00 Q3 +ATOM 120 H40 Q011 1 19.078 3.466 0.332 1.00 0.00 Q3 +ATOM 121 SI1 Q011 1 26.017 4.521 -12.941 1.00 0.00 Q4 +ATOM 122 SI2 Q011 1 22.041 3.048 -9.471 1.00 0.00 Q4 +ATOM 123 SI3 Q011 1 25.295 1.612 -6.132 1.00 0.00 Q4 +ATOM 124 SI4 Q011 1 28.578 0.078 -2.788 1.00 0.00 Q4 +ATOM 125 O5 Q011 1 25.717 2.922 -12.739 1.00 0.00 Q4 +ATOM 126 O6 Q011 1 21.994 1.422 -9.311 1.00 0.00 Q4 +ATOM 127 O7 Q011 1 25.120 -0.006 -5.978 1.00 0.00 Q4 +ATOM 128 O8 Q011 1 26.993 3.100 -2.580 1.00 0.00 Q4 +ATOM 129 O9 Q011 1 27.621 4.788 -12.696 1.00 0.00 Q4 +ATOM 130 O10 Q011 1 23.575 3.594 -9.322 1.00 0.00 Q4 +ATOM 131 O11 Q011 1 26.860 2.074 -5.999 1.00 0.00 Q4 +ATOM 132 O12 Q011 1 22.714 0.822 -2.544 1.00 0.00 Q4 +ATOM 133 O13 Q011 1 21.466 3.401 -10.966 1.00 0.00 Q4 +ATOM 134 O14 Q011 1 24.746 1.937 -7.635 1.00 0.00 Q4 +ATOM 135 O15 Q011 1 28.040 0.385 -4.301 1.00 0.00 Q4 +ATOM 136 O16 Q011 1 24.140 -0.789 -0.805 1.00 0.00 Q4 +ATOM 137 O17 Q011 1 26.889 0.667 -11.872 1.00 0.00 Q4 +ATOM 138 O18 Q011 1 21.112 3.700 -8.289 1.00 0.00 Q4 +ATOM 139 O19 Q011 1 24.397 2.329 -4.963 1.00 0.00 Q4 +ATOM 140 O20 Q011 1 27.502 0.657 -1.684 1.00 0.00 Q4 +ATOM 141 SI21 Q011 1 25.652 1.740 -11.583 1.00 0.00 Q4 +ATOM 142 SI22 Q011 1 27.335 4.846 -8.166 1.00 0.00 Q4 +ATOM 143 SI23 Q011 1 23.255 3.493 -4.831 1.00 0.00 Q4 +ATOM 144 SI24 Q011 1 26.612 2.017 -1.409 1.00 0.00 Q4 +ATOM 145 SI25 Q011 1 21.743 4.356 -12.263 1.00 0.00 Q4 +ATOM 146 SI26 Q011 1 25.020 2.997 -8.854 1.00 0.00 Q4 +ATOM 147 SI27 Q011 1 28.300 1.494 -5.482 1.00 0.00 Q4 +ATOM 148 SI28 Q011 1 24.194 0.258 -2.080 1.00 0.00 Q4 +ATOM 149 O29 Q011 1 25.885 2.305 -10.057 1.00 0.00 Q4 +ATOM 150 O30 Q011 1 27.561 5.466 -6.667 1.00 0.00 Q4 +ATOM 151 O31 Q011 1 23.474 4.153 -3.344 1.00 0.00 Q4 +ATOM 152 O32 Q011 1 26.802 2.610 0.118 1.00 0.00 Q4 +ATOM 153 O33 Q011 1 24.118 1.104 -11.615 1.00 0.00 Q4 +ATOM 154 O34 Q011 1 25.797 4.305 -8.256 1.00 0.00 Q4 +ATOM 155 O35 Q011 1 21.753 2.846 -4.862 1.00 0.00 Q4 +ATOM 156 O36 Q011 1 25.054 1.621 -1.752 1.00 0.00 Q4 +ATOM 157 H37 Q011 1 25.591 4.987 -14.282 1.00 0.00 Q4 +ATOM 158 H38 Q011 1 24.969 -1.229 -0.559 1.00 0.00 Q4 +ATOM 159 H39 Q011 1 22.542 3.679 -13.311 1.00 0.00 Q4 +ATOM 160 H40 Q011 1 26.393 3.464 0.330 1.00 0.00 Q4 +ATOM 161 SI1 Q011 1 33.226 4.380 -13.182 1.00 0.00 Q5 +ATOM 162 SI2 Q011 1 29.350 2.985 -9.434 1.00 0.00 Q5 +ATOM 163 SI3 Q011 1 32.643 1.609 -6.138 1.00 0.00 Q5 +ATOM 164 SI4 Q011 1 35.912 0.018 -2.822 1.00 0.00 Q5 +ATOM 165 O5 Q011 1 32.788 2.850 -12.795 1.00 0.00 Q5 +ATOM 166 O6 Q011 1 29.353 1.362 -9.274 1.00 0.00 Q5 +ATOM 167 O7 Q011 1 32.464 -0.010 -5.985 1.00 0.00 Q5 +ATOM 168 O8 Q011 1 34.468 3.059 -2.535 1.00 0.00 Q5 +ATOM 169 O9 Q011 1 34.877 4.336 -13.203 1.00 0.00 Q5 +ATOM 170 O10 Q011 1 30.863 3.576 -9.275 1.00 0.00 Q5 +ATOM 171 O11 Q011 1 34.206 2.080 -6.010 1.00 0.00 Q5 +ATOM 172 O12 Q011 1 30.042 0.827 -2.551 1.00 0.00 Q5 +ATOM 173 O13 Q011 1 28.807 3.311 -10.944 1.00 0.00 Q5 +ATOM 174 O14 Q011 1 32.098 1.926 -7.644 1.00 0.00 Q5 +ATOM 175 O15 Q011 1 35.405 0.401 -4.337 1.00 0.00 Q5 +ATOM 176 O16 Q011 1 31.483 -0.768 -0.813 1.00 0.00 Q5 +ATOM 177 O17 Q011 1 34.168 0.673 -11.921 1.00 0.00 Q5 +ATOM 178 O18 Q011 1 28.406 3.616 -8.254 1.00 0.00 Q5 +ATOM 179 O19 Q011 1 31.731 2.328 -4.979 1.00 0.00 Q5 +ATOM 180 O20 Q011 1 34.823 0.580 -1.725 1.00 0.00 Q5 +ATOM 181 SI21 Q011 1 32.901 1.708 -11.605 1.00 0.00 Q5 +ATOM 182 SI22 Q011 1 34.615 4.893 -8.257 1.00 0.00 Q5 +ATOM 183 SI23 Q011 1 30.578 3.483 -4.851 1.00 0.00 Q5 +ATOM 184 SI24 Q011 1 33.979 1.959 -1.421 1.00 0.00 Q5 +ATOM 185 SI25 Q011 1 29.112 4.300 -12.204 1.00 0.00 Q5 +ATOM 186 SI26 Q011 1 32.327 2.994 -8.866 1.00 0.00 Q5 +ATOM 187 SI27 Q011 1 35.664 1.527 -5.511 1.00 0.00 Q5 +ATOM 188 SI28 Q011 1 31.527 0.266 -2.098 1.00 0.00 Q5 +ATOM 189 O29 Q011 1 33.160 2.328 -10.106 1.00 0.00 Q5 +ATOM 190 O30 Q011 1 34.870 5.445 -6.736 1.00 0.00 Q5 +ATOM 191 O31 Q011 1 30.786 4.141 -3.362 1.00 0.00 Q5 +ATOM 192 O32 Q011 1 34.125 2.505 0.129 1.00 0.00 Q5 +ATOM 193 O33 Q011 1 31.395 1.022 -11.575 1.00 0.00 Q5 +ATOM 194 O34 Q011 1 33.084 4.335 -8.320 1.00 0.00 Q5 +ATOM 195 O35 Q011 1 29.076 2.832 -4.880 1.00 0.00 Q5 +ATOM 196 O36 Q011 1 32.419 1.620 -1.817 1.00 0.00 Q5 +ATOM 197 H37 Q011 1 32.678 4.799 -14.494 1.00 0.00 Q5 +ATOM 198 H38 Q011 1 32.301 -1.248 -0.610 1.00 0.00 Q5 +ATOM 199 H39 Q011 1 29.878 3.633 -13.282 1.00 0.00 Q5 +ATOM 200 H40 Q011 1 33.739 3.370 0.342 1.00 0.00 Q5 +ATOM 201 SI1 Q011 1 2.283 9.211 -12.947 1.00 0.00 Q6 +ATOM 202 SI2 Q011 1 -1.586 7.704 -9.498 1.00 0.00 Q6 +ATOM 203 SI3 Q011 1 1.692 6.311 -6.130 1.00 0.00 Q6 +ATOM 204 SI4 Q011 1 4.975 4.720 -2.791 1.00 0.00 Q6 +ATOM 205 O5 Q011 1 2.027 7.603 -12.754 1.00 0.00 Q6 +ATOM 206 O6 Q011 1 -1.598 6.085 -9.365 1.00 0.00 Q6 +ATOM 207 O7 Q011 1 1.498 4.694 -5.973 1.00 0.00 Q6 +ATOM 208 O8 Q011 1 3.371 7.728 -2.577 1.00 0.00 Q6 +ATOM 209 O9 Q011 1 3.890 9.484 -12.734 1.00 0.00 Q6 +ATOM 210 O10 Q011 1 -0.083 8.303 -9.286 1.00 0.00 Q6 +ATOM 211 O11 Q011 1 3.254 6.766 -6.024 1.00 0.00 Q6 +ATOM 212 O12 Q011 1 -0.770 5.494 -2.492 1.00 0.00 Q6 +ATOM 213 O13 Q011 1 -2.167 8.087 -10.989 1.00 0.00 Q6 +ATOM 214 O14 Q011 1 1.122 6.649 -7.623 1.00 0.00 Q6 +ATOM 215 O15 Q011 1 4.429 5.060 -4.297 1.00 0.00 Q6 +ATOM 216 O16 Q011 1 0.648 3.807 -0.800 1.00 0.00 Q6 +ATOM 217 O17 Q011 1 3.049 5.310 -11.765 1.00 0.00 Q6 +ATOM 218 O18 Q011 1 -2.521 8.242 -8.275 1.00 0.00 Q6 +ATOM 219 O19 Q011 1 0.854 7.059 -4.937 1.00 0.00 Q6 +ATOM 220 O20 Q011 1 3.991 5.347 -1.631 1.00 0.00 Q6 +ATOM 221 SI21 Q011 1 1.857 6.438 -11.594 1.00 0.00 Q6 +ATOM 222 SI22 Q011 1 3.706 9.552 -8.192 1.00 0.00 Q6 +ATOM 223 SI23 Q011 1 -0.317 8.194 -4.802 1.00 0.00 Q6 +ATOM 224 SI24 Q011 1 3.076 6.686 -1.351 1.00 0.00 Q6 +ATOM 225 SI25 Q011 1 -1.846 8.968 -12.329 1.00 0.00 Q6 +ATOM 226 SI26 Q011 1 1.370 7.711 -8.845 1.00 0.00 Q6 +ATOM 227 SI27 Q011 1 4.671 6.170 -5.480 1.00 0.00 Q6 +ATOM 228 SI28 Q011 1 0.694 4.909 -2.028 1.00 0.00 Q6 +ATOM 229 O29 Q011 1 2.159 7.002 -10.082 1.00 0.00 Q6 +ATOM 230 O30 Q011 1 3.925 10.147 -6.681 1.00 0.00 Q6 +ATOM 231 O31 Q011 1 -0.139 8.896 -3.326 1.00 0.00 Q6 +ATOM 232 O32 Q011 1 3.303 7.313 0.158 1.00 0.00 Q6 +ATOM 233 O33 Q011 1 0.349 5.750 -11.701 1.00 0.00 Q6 +ATOM 234 O34 Q011 1 2.167 9.017 -8.276 1.00 0.00 Q6 +ATOM 235 O35 Q011 1 -1.776 7.469 -4.842 1.00 0.00 Q6 +ATOM 236 O36 Q011 1 1.516 6.273 -1.634 1.00 0.00 Q6 +ATOM 237 H37 Q011 1 1.844 9.666 -14.287 1.00 0.00 Q6 +ATOM 238 H38 Q011 1 1.477 3.349 -0.589 1.00 0.00 Q6 +ATOM 239 H39 Q011 1 -0.775 8.344 -13.138 1.00 0.00 Q6 +ATOM 240 H40 Q011 1 2.848 8.141 0.380 1.00 0.00 Q6 +ATOM 241 SI1 Q011 1 9.675 9.155 -12.984 1.00 0.00 Q7 +ATOM 242 SI2 Q011 1 5.711 7.680 -9.482 1.00 0.00 Q7 +ATOM 243 SI3 Q011 1 9.014 6.265 -6.143 1.00 0.00 Q7 +ATOM 244 SI4 Q011 1 12.329 4.747 -2.794 1.00 0.00 Q7 +ATOM 245 O5 Q011 1 9.444 7.549 -12.770 1.00 0.00 Q7 +ATOM 246 O6 Q011 1 5.663 6.056 -9.316 1.00 0.00 Q7 +ATOM 247 O7 Q011 1 8.852 4.643 -6.006 1.00 0.00 Q7 +ATOM 248 O8 Q011 1 10.665 7.736 -2.603 1.00 0.00 Q7 +ATOM 249 O9 Q011 1 11.284 9.438 -12.811 1.00 0.00 Q7 +ATOM 250 O10 Q011 1 7.245 8.231 -9.328 1.00 0.00 Q7 +ATOM 251 O11 Q011 1 10.575 6.738 -6.003 1.00 0.00 Q7 +ATOM 252 O12 Q011 1 6.500 5.305 -2.599 1.00 0.00 Q7 +ATOM 253 O13 Q011 1 5.129 8.032 -10.975 1.00 0.00 Q7 +ATOM 254 O14 Q011 1 8.458 6.591 -7.644 1.00 0.00 Q7 +ATOM 255 O15 Q011 1 11.790 5.053 -4.307 1.00 0.00 Q7 +ATOM 256 O16 Q011 1 7.925 3.711 -0.832 1.00 0.00 Q7 +ATOM 257 O17 Q011 1 10.506 5.263 -11.774 1.00 0.00 Q7 +ATOM 258 O18 Q011 1 4.787 8.331 -8.296 1.00 0.00 Q7 +ATOM 259 O19 Q011 1 8.101 6.965 -4.974 1.00 0.00 Q7 +ATOM 260 O20 Q011 1 11.303 5.363 -1.661 1.00 0.00 Q7 +ATOM 261 SI21 Q011 1 9.336 6.404 -11.584 1.00 0.00 Q7 +ATOM 262 SI22 Q011 1 11.020 9.531 -8.206 1.00 0.00 Q7 +ATOM 263 SI23 Q011 1 6.953 8.126 -4.849 1.00 0.00 Q7 +ATOM 264 SI24 Q011 1 10.314 6.657 -1.420 1.00 0.00 Q7 +ATOM 265 SI25 Q011 1 5.390 9.011 -12.257 1.00 0.00 Q7 +ATOM 266 SI26 Q011 1 8.702 7.662 -8.860 1.00 0.00 Q7 +ATOM 267 SI27 Q011 1 12.019 6.161 -5.492 1.00 0.00 Q7 +ATOM 268 SI28 Q011 1 7.973 4.779 -2.088 1.00 0.00 Q7 +ATOM 269 O29 Q011 1 9.567 6.987 -10.068 1.00 0.00 Q7 +ATOM 270 O30 Q011 1 11.256 10.137 -6.703 1.00 0.00 Q7 +ATOM 271 O31 Q011 1 7.168 8.781 -3.360 1.00 0.00 Q7 +ATOM 272 O32 Q011 1 10.468 7.281 0.100 1.00 0.00 Q7 +ATOM 273 O33 Q011 1 7.834 5.738 -11.678 1.00 0.00 Q7 +ATOM 274 O34 Q011 1 9.485 8.974 -8.276 1.00 0.00 Q7 +ATOM 275 O35 Q011 1 5.447 7.487 -4.891 1.00 0.00 Q7 +ATOM 276 O36 Q011 1 8.775 6.174 -1.743 1.00 0.00 Q7 +ATOM 277 H37 Q011 1 9.191 9.601 -14.313 1.00 0.00 Q7 +ATOM 278 H38 Q011 1 8.764 3.297 -0.574 1.00 0.00 Q7 +ATOM 279 H39 Q011 1 6.156 8.347 -13.338 1.00 0.00 Q7 +ATOM 280 H40 Q011 1 10.016 8.116 0.299 1.00 0.00 Q7 +ATOM 281 SI1 Q011 1 17.003 9.147 -12.985 1.00 0.00 Q8 +ATOM 282 SI2 Q011 1 13.041 7.667 -9.488 1.00 0.00 Q8 +ATOM 283 SI3 Q011 1 16.338 6.255 -6.140 1.00 0.00 Q8 +ATOM 284 SI4 Q011 1 19.651 4.735 -2.792 1.00 0.00 Q8 +ATOM 285 O5 Q011 1 16.758 7.542 -12.769 1.00 0.00 Q8 +ATOM 286 O6 Q011 1 12.985 6.042 -9.331 1.00 0.00 Q8 +ATOM 287 O7 Q011 1 16.174 4.633 -6.000 1.00 0.00 Q8 +ATOM 288 O8 Q011 1 17.994 7.731 -2.598 1.00 0.00 Q8 +ATOM 289 O9 Q011 1 18.614 9.425 -12.823 1.00 0.00 Q8 +ATOM 290 O10 Q011 1 14.571 8.221 -9.323 1.00 0.00 Q8 +ATOM 291 O11 Q011 1 17.897 6.731 -6.001 1.00 0.00 Q8 +ATOM 292 O12 Q011 1 13.851 5.330 -2.586 1.00 0.00 Q8 +ATOM 293 O13 Q011 1 12.482 8.030 -10.987 1.00 0.00 Q8 +ATOM 294 O14 Q011 1 15.783 6.579 -7.641 1.00 0.00 Q8 +ATOM 295 O15 Q011 1 19.107 5.044 -4.304 1.00 0.00 Q8 +ATOM 296 O16 Q011 1 15.246 3.704 -0.826 1.00 0.00 Q8 +ATOM 297 O17 Q011 1 17.830 5.263 -11.775 1.00 0.00 Q8 +ATOM 298 O18 Q011 1 12.112 8.319 -8.306 1.00 0.00 Q8 +ATOM 299 O19 Q011 1 15.428 6.957 -4.969 1.00 0.00 Q8 +ATOM 300 O20 Q011 1 18.638 5.358 -1.653 1.00 0.00 Q8 +ATOM 301 SI21 Q011 1 16.646 6.391 -11.589 1.00 0.00 Q8 +ATOM 302 SI22 Q011 1 18.338 9.529 -8.210 1.00 0.00 Q8 +ATOM 303 SI23 Q011 1 14.287 8.123 -4.845 1.00 0.00 Q8 +ATOM 304 SI24 Q011 1 17.652 6.655 -1.411 1.00 0.00 Q8 +ATOM 305 SI25 Q011 1 12.771 8.991 -12.276 1.00 0.00 Q8 +ATOM 306 SI26 Q011 1 16.027 7.649 -8.858 1.00 0.00 Q8 +ATOM 307 SI27 Q011 1 19.339 6.152 -5.489 1.00 0.00 Q8 +ATOM 308 SI28 Q011 1 15.312 4.775 -2.079 1.00 0.00 Q8 +ATOM 309 O29 Q011 1 16.881 6.971 -10.071 1.00 0.00 Q8 +ATOM 310 O30 Q011 1 18.576 10.134 -6.706 1.00 0.00 Q8 +ATOM 311 O31 Q011 1 14.499 8.768 -3.351 1.00 0.00 Q8 +ATOM 312 O32 Q011 1 17.808 7.282 0.107 1.00 0.00 Q8 +ATOM 313 O33 Q011 1 15.153 5.702 -11.694 1.00 0.00 Q8 +ATOM 314 O34 Q011 1 16.806 8.965 -8.278 1.00 0.00 Q8 +ATOM 315 O35 Q011 1 12.780 7.488 -4.906 1.00 0.00 Q8 +ATOM 316 O36 Q011 1 16.115 6.167 -1.726 1.00 0.00 Q8 +ATOM 317 H37 Q011 1 16.513 9.595 -14.310 1.00 0.00 Q8 +ATOM 318 H38 Q011 1 16.077 3.277 -0.566 1.00 0.00 Q8 +ATOM 319 H39 Q011 1 13.583 8.323 -13.321 1.00 0.00 Q8 +ATOM 320 H40 Q011 1 17.349 8.114 0.306 1.00 0.00 Q8 +ATOM 321 SI1 Q011 1 24.382 9.158 -12.949 1.00 0.00 Q9 +ATOM 322 SI2 Q011 1 20.361 7.665 -9.489 1.00 0.00 Q9 +ATOM 323 SI3 Q011 1 23.653 6.234 -6.135 1.00 0.00 Q9 +ATOM 324 SI4 Q011 1 26.970 4.729 -2.785 1.00 0.00 Q9 +ATOM 325 O5 Q011 1 24.122 7.552 -12.755 1.00 0.00 Q9 +ATOM 326 O6 Q011 1 20.293 6.039 -9.334 1.00 0.00 Q9 +ATOM 327 O7 Q011 1 23.488 4.613 -5.995 1.00 0.00 Q9 +ATOM 328 O8 Q011 1 25.323 7.727 -2.589 1.00 0.00 Q9 +ATOM 329 O9 Q011 1 25.991 9.426 -12.742 1.00 0.00 Q9 +ATOM 330 O10 Q011 1 21.894 8.210 -9.321 1.00 0.00 Q9 +ATOM 331 O11 Q011 1 25.214 6.704 -5.999 1.00 0.00 Q9 +ATOM 332 O12 Q011 1 21.174 5.315 -2.589 1.00 0.00 Q9 +ATOM 333 O13 Q011 1 19.803 8.037 -10.986 1.00 0.00 Q9 +ATOM 334 O14 Q011 1 23.094 6.560 -7.635 1.00 0.00 Q9 +ATOM 335 O15 Q011 1 26.413 5.035 -4.290 1.00 0.00 Q9 +ATOM 336 O16 Q011 1 22.560 3.698 -0.818 1.00 0.00 Q9 +ATOM 337 O17 Q011 1 25.163 5.258 -11.759 1.00 0.00 Q9 +ATOM 338 O18 Q011 1 19.434 8.320 -8.307 1.00 0.00 Q9 +ATOM 339 O19 Q011 1 22.748 6.940 -4.964 1.00 0.00 Q9 +ATOM 340 O20 Q011 1 25.962 5.353 -1.642 1.00 0.00 Q9 +ATOM 341 SI21 Q011 1 23.980 6.390 -11.588 1.00 0.00 Q9 +ATOM 342 SI22 Q011 1 25.680 9.467 -8.181 1.00 0.00 Q9 +ATOM 343 SI23 Q011 1 21.608 8.107 -4.837 1.00 0.00 Q9 +ATOM 344 SI24 Q011 1 24.973 6.649 -1.405 1.00 0.00 Q9 +ATOM 345 SI25 Q011 1 20.102 8.988 -12.281 1.00 0.00 Q9 +ATOM 346 SI26 Q011 1 23.345 7.629 -8.851 1.00 0.00 Q9 +ATOM 347 SI27 Q011 1 26.657 6.132 -5.481 1.00 0.00 Q9 +ATOM 348 SI28 Q011 1 22.634 4.763 -2.075 1.00 0.00 Q9 +ATOM 349 O29 Q011 1 24.202 6.952 -10.063 1.00 0.00 Q9 +ATOM 350 O30 Q011 1 25.908 10.085 -6.680 1.00 0.00 Q9 +ATOM 351 O31 Q011 1 21.822 8.756 -3.345 1.00 0.00 Q9 +ATOM 352 O32 Q011 1 25.118 7.277 0.113 1.00 0.00 Q9 +ATOM 353 O33 Q011 1 22.483 5.709 -11.708 1.00 0.00 Q9 +ATOM 354 O34 Q011 1 24.138 8.931 -8.260 1.00 0.00 Q9 +ATOM 355 O35 Q011 1 20.100 7.476 -4.898 1.00 0.00 Q9 +ATOM 356 O36 Q011 1 23.438 6.156 -1.729 1.00 0.00 Q9 +ATOM 357 H37 Q011 1 23.932 9.620 -14.284 1.00 0.00 Q9 +ATOM 358 H38 Q011 1 23.390 3.275 -0.548 1.00 0.00 Q9 +ATOM 359 H39 Q011 1 20.916 8.310 -13.317 1.00 0.00 Q9 +ATOM 360 H40 Q011 1 24.661 8.111 0.307 1.00 0.00 Q9 +ATOM 361 SI1 Q011 1 31.595 9.015 -13.189 1.00 0.00 Q10 +ATOM 362 SI2 Q011 1 27.689 7.592 -9.465 1.00 0.00 Q10 +ATOM 363 SI3 Q011 1 30.998 6.234 -6.141 1.00 0.00 Q10 +ATOM 364 SI4 Q011 1 34.308 4.696 -2.780 1.00 0.00 Q10 +ATOM 365 O5 Q011 1 31.195 7.477 -12.794 1.00 0.00 Q10 +ATOM 366 O6 Q011 1 27.643 5.969 -9.305 1.00 0.00 Q10 +ATOM 367 O7 Q011 1 30.820 4.613 -6.004 1.00 0.00 Q10 +ATOM 368 O8 Q011 1 32.804 7.672 -2.549 1.00 0.00 Q10 +ATOM 369 O9 Q011 1 33.247 9.000 -13.210 1.00 0.00 Q10 +ATOM 370 O10 Q011 1 29.217 8.154 -9.328 1.00 0.00 Q10 +ATOM 371 O11 Q011 1 32.563 6.692 -5.987 1.00 0.00 Q10 +ATOM 372 O12 Q011 1 28.490 5.322 -2.604 1.00 0.00 Q10 +ATOM 373 O13 Q011 1 27.147 7.947 -10.968 1.00 0.00 Q10 +ATOM 374 O14 Q011 1 30.455 6.546 -7.650 1.00 0.00 Q10 +ATOM 375 O15 Q011 1 33.790 4.997 -4.308 1.00 0.00 Q10 +ATOM 376 O16 Q011 1 29.894 3.736 -0.822 1.00 0.00 Q10 +ATOM 377 O17 Q011 1 32.628 5.306 -11.960 1.00 0.00 Q10 +ATOM 378 O18 Q011 1 26.762 8.244 -8.280 1.00 0.00 Q10 +ATOM 379 O19 Q011 1 30.078 6.941 -4.981 1.00 0.00 Q10 +ATOM 380 O20 Q011 1 33.234 5.245 -1.665 1.00 0.00 Q10 +ATOM 381 SI21 Q011 1 31.371 6.333 -11.615 1.00 0.00 Q10 +ATOM 382 SI22 Q011 1 32.938 9.521 -8.262 1.00 0.00 Q10 +ATOM 383 SI23 Q011 1 28.928 8.101 -4.859 1.00 0.00 Q10 +ATOM 384 SI24 Q011 1 32.326 6.591 -1.409 1.00 0.00 Q10 +ATOM 385 SI25 Q011 1 27.473 8.932 -12.227 1.00 0.00 Q10 +ATOM 386 SI26 Q011 1 30.682 7.598 -8.886 1.00 0.00 Q10 +ATOM 387 SI27 Q011 1 34.015 6.117 -5.490 1.00 0.00 Q10 +ATOM 388 SI28 Q011 1 29.955 4.778 -2.100 1.00 0.00 Q10 +ATOM 389 O29 Q011 1 31.562 6.935 -10.098 1.00 0.00 Q10 +ATOM 390 O30 Q011 1 33.207 10.074 -6.745 1.00 0.00 Q10 +ATOM 391 O31 Q011 1 29.133 8.745 -3.364 1.00 0.00 Q10 +ATOM 392 O32 Q011 1 32.434 7.182 0.127 1.00 0.00 Q10 +ATOM 393 O33 Q011 1 29.907 5.588 -11.599 1.00 0.00 Q10 +ATOM 394 O34 Q011 1 31.410 8.956 -8.338 1.00 0.00 Q10 +ATOM 395 O35 Q011 1 27.420 7.467 -4.913 1.00 0.00 Q10 +ATOM 396 O36 Q011 1 30.788 6.167 -1.806 1.00 0.00 Q10 +ATOM 397 H37 Q011 1 31.036 9.419 -14.500 1.00 0.00 Q10 +ATOM 398 H38 Q011 1 30.730 3.325 -0.551 1.00 0.00 Q10 +ATOM 399 H39 Q011 1 28.255 8.264 -13.293 1.00 0.00 Q10 +ATOM 400 H40 Q011 1 32.021 8.041 0.312 1.00 0.00 Q10 +ATOM 401 SI1 Q011 1 0.635 13.847 -12.948 1.00 0.00 Q11 +ATOM 402 SI2 Q011 1 -3.237 12.331 -9.502 1.00 0.00 Q11 +ATOM 403 SI3 Q011 1 0.037 10.932 -6.131 1.00 0.00 Q11 +ATOM 404 SI4 Q011 1 3.327 9.351 -2.796 1.00 0.00 Q11 +ATOM 405 O5 Q011 1 0.383 12.239 -12.753 1.00 0.00 Q11 +ATOM 406 O6 Q011 1 -3.262 10.711 -9.370 1.00 0.00 Q11 +ATOM 407 O7 Q011 1 -0.145 9.313 -5.978 1.00 0.00 Q11 +ATOM 408 O8 Q011 1 1.713 12.351 -2.583 1.00 0.00 Q11 +ATOM 409 O9 Q011 1 2.242 14.120 -12.734 1.00 0.00 Q11 +ATOM 410 O10 Q011 1 -1.733 12.928 -9.291 1.00 0.00 Q11 +ATOM 411 O11 Q011 1 1.598 11.393 -6.023 1.00 0.00 Q11 +ATOM 412 O12 Q011 1 -2.418 10.100 -2.510 1.00 0.00 Q11 +ATOM 413 O13 Q011 1 -3.818 12.715 -10.992 1.00 0.00 Q11 +ATOM 414 O14 Q011 1 -0.535 11.275 -7.621 1.00 0.00 Q11 +ATOM 415 O15 Q011 1 2.780 9.687 -4.302 1.00 0.00 Q11 +ATOM 416 O16 Q011 1 -1.007 8.409 -0.817 1.00 0.00 Q11 +ATOM 417 O17 Q011 1 1.418 9.950 -11.769 1.00 0.00 Q11 +ATOM 418 O18 Q011 1 -4.171 12.870 -8.278 1.00 0.00 Q11 +ATOM 419 O19 Q011 1 -0.803 11.676 -4.936 1.00 0.00 Q11 +ATOM 420 O20 Q011 1 2.341 9.975 -1.636 1.00 0.00 Q11 +ATOM 421 SI21 Q011 1 0.225 11.076 -11.590 1.00 0.00 Q11 +ATOM 422 SI22 Q011 1 2.053 14.179 -8.193 1.00 0.00 Q11 +ATOM 423 SI23 Q011 1 -1.969 12.815 -4.802 1.00 0.00 Q11 +ATOM 424 SI24 Q011 1 1.415 11.307 -1.359 1.00 0.00 Q11 +ATOM 425 SI25 Q011 1 -3.497 13.597 -12.332 1.00 0.00 Q11 +ATOM 426 SI26 Q011 1 -0.283 12.336 -8.842 1.00 0.00 Q11 +ATOM 427 SI27 Q011 1 3.018 10.796 -5.486 1.00 0.00 Q11 +ATOM 428 SI28 Q011 1 -0.957 9.513 -2.041 1.00 0.00 Q11 +ATOM 429 O29 Q011 1 0.519 11.635 -10.076 1.00 0.00 Q11 +ATOM 430 O30 Q011 1 2.272 14.773 -6.682 1.00 0.00 Q11 +ATOM 431 O31 Q011 1 -1.791 13.516 -3.325 1.00 0.00 Q11 +ATOM 432 O32 Q011 1 1.633 11.935 0.151 1.00 0.00 Q11 +ATOM 433 O33 Q011 1 -1.284 10.392 -11.692 1.00 0.00 Q11 +ATOM 434 O34 Q011 1 0.513 13.643 -8.272 1.00 0.00 Q11 +ATOM 435 O35 Q011 1 -3.430 12.093 -4.843 1.00 0.00 Q11 +ATOM 436 O36 Q011 1 -0.141 10.880 -1.647 1.00 0.00 Q11 +ATOM 437 H37 Q011 1 0.194 14.301 -14.289 1.00 0.00 Q11 +ATOM 438 H38 Q011 1 -0.180 7.945 -0.608 1.00 0.00 Q11 +ATOM 439 H39 Q011 1 -2.425 12.973 -13.141 1.00 0.00 Q11 +ATOM 440 H40 Q011 1 1.176 12.762 0.370 1.00 0.00 Q11 +ATOM 441 SI1 Q011 1 8.015 13.772 -12.985 1.00 0.00 Q12 +ATOM 442 SI2 Q011 1 4.058 12.308 -9.487 1.00 0.00 Q12 +ATOM 443 SI3 Q011 1 7.355 10.880 -6.142 1.00 0.00 Q12 +ATOM 444 SI4 Q011 1 10.667 9.365 -2.804 1.00 0.00 Q12 +ATOM 445 O5 Q011 1 7.774 12.167 -12.771 1.00 0.00 Q12 +ATOM 446 O6 Q011 1 4.006 10.684 -9.325 1.00 0.00 Q12 +ATOM 447 O7 Q011 1 7.197 9.257 -6.003 1.00 0.00 Q12 +ATOM 448 O8 Q011 1 9.014 12.359 -2.608 1.00 0.00 Q12 +ATOM 449 O9 Q011 1 9.625 14.054 -12.818 1.00 0.00 Q12 +ATOM 450 O10 Q011 1 5.592 12.854 -9.328 1.00 0.00 Q12 +ATOM 451 O11 Q011 1 8.914 11.359 -6.005 1.00 0.00 Q12 +ATOM 452 O12 Q011 1 4.854 9.930 -2.603 1.00 0.00 Q12 +ATOM 453 O13 Q011 1 3.480 12.661 -10.981 1.00 0.00 Q12 +ATOM 454 O14 Q011 1 6.799 11.208 -7.644 1.00 0.00 Q12 +ATOM 455 O15 Q011 1 10.127 9.676 -4.316 1.00 0.00 Q12 +ATOM 456 O16 Q011 1 6.281 8.323 -0.841 1.00 0.00 Q12 +ATOM 457 O17 Q011 1 8.848 9.891 -11.781 1.00 0.00 Q12 +ATOM 458 O18 Q011 1 3.134 12.958 -8.300 1.00 0.00 Q12 +ATOM 459 O19 Q011 1 6.442 11.581 -4.974 1.00 0.00 Q12 +ATOM 460 O20 Q011 1 9.652 9.987 -1.666 1.00 0.00 Q12 +ATOM 461 SI21 Q011 1 7.663 11.017 -11.590 1.00 0.00 Q12 +ATOM 462 SI22 Q011 1 9.364 14.152 -8.210 1.00 0.00 Q12 +ATOM 463 SI23 Q011 1 5.300 12.748 -4.851 1.00 0.00 Q12 +ATOM 464 SI24 Q011 1 8.660 11.280 -1.427 1.00 0.00 Q12 +ATOM 465 SI25 Q011 1 3.741 13.643 -12.261 1.00 0.00 Q12 +ATOM 466 SI26 Q011 1 7.047 12.277 -8.861 1.00 0.00 Q12 +ATOM 467 SI27 Q011 1 10.360 10.784 -5.500 1.00 0.00 Q12 +ATOM 468 SI28 Q011 1 6.324 9.393 -2.095 1.00 0.00 Q12 +ATOM 469 O29 Q011 1 7.901 11.597 -10.074 1.00 0.00 Q12 +ATOM 470 O30 Q011 1 9.601 14.759 -6.707 1.00 0.00 Q12 +ATOM 471 O31 Q011 1 5.515 13.401 -3.361 1.00 0.00 Q12 +ATOM 472 O32 Q011 1 8.805 11.902 0.094 1.00 0.00 Q12 +ATOM 473 O33 Q011 1 6.164 10.340 -11.689 1.00 0.00 Q12 +ATOM 474 O34 Q011 1 7.831 13.590 -8.279 1.00 0.00 Q12 +ATOM 475 O35 Q011 1 3.792 12.114 -4.898 1.00 0.00 Q12 +ATOM 476 O36 Q011 1 7.126 10.790 -1.757 1.00 0.00 Q12 +ATOM 477 H37 Q011 1 7.528 14.220 -14.312 1.00 0.00 Q12 +ATOM 478 H38 Q011 1 7.120 7.914 -0.577 1.00 0.00 Q12 +ATOM 479 H39 Q011 1 4.505 12.982 -13.344 1.00 0.00 Q12 +ATOM 480 H40 Q011 1 8.354 12.738 0.291 1.00 0.00 Q12 +ATOM 481 SI1 Q011 1 15.350 13.774 -12.984 1.00 0.00 Q13 +ATOM 482 SI2 Q011 1 11.385 12.290 -9.493 1.00 0.00 Q13 +ATOM 483 SI3 Q011 1 14.682 10.874 -6.140 1.00 0.00 Q13 +ATOM 484 SI4 Q011 1 17.994 9.360 -2.801 1.00 0.00 Q13 +ATOM 485 O5 Q011 1 15.110 12.169 -12.766 1.00 0.00 Q13 +ATOM 486 O6 Q011 1 11.317 10.665 -9.340 1.00 0.00 Q13 +ATOM 487 O7 Q011 1 14.536 9.251 -5.999 1.00 0.00 Q13 +ATOM 488 O8 Q011 1 16.330 12.350 -2.607 1.00 0.00 Q13 +ATOM 489 O9 Q011 1 16.961 14.056 -12.823 1.00 0.00 Q13 +ATOM 490 O10 Q011 1 12.918 12.839 -9.330 1.00 0.00 Q13 +ATOM 491 O11 Q011 1 16.240 11.358 -6.001 1.00 0.00 Q13 +ATOM 492 O12 Q011 1 12.196 9.932 -2.600 1.00 0.00 Q13 +ATOM 493 O13 Q011 1 10.821 12.656 -10.989 1.00 0.00 Q13 +ATOM 494 O14 Q011 1 14.124 11.199 -7.640 1.00 0.00 Q13 +ATOM 495 O15 Q011 1 17.452 9.669 -4.313 1.00 0.00 Q13 +ATOM 496 O16 Q011 1 13.577 8.299 -0.837 1.00 0.00 Q13 +ATOM 497 O17 Q011 1 16.193 9.894 -11.778 1.00 0.00 Q13 +ATOM 498 O18 Q011 1 10.460 12.944 -8.309 1.00 0.00 Q13 +ATOM 499 O19 Q011 1 13.769 11.571 -4.970 1.00 0.00 Q13 +ATOM 500 O20 Q011 1 16.982 9.983 -1.661 1.00 0.00 Q13 +ATOM 501 SI21 Q011 1 15.005 11.017 -11.587 1.00 0.00 Q13 +ATOM 502 SI22 Q011 1 16.683 14.152 -8.213 1.00 0.00 Q13 +ATOM 503 SI23 Q011 1 12.631 12.741 -4.847 1.00 0.00 Q13 +ATOM 504 SI24 Q011 1 15.987 11.272 -1.421 1.00 0.00 Q13 +ATOM 505 SI25 Q011 1 11.114 13.613 -12.280 1.00 0.00 Q13 +ATOM 506 SI26 Q011 1 14.372 12.268 -8.857 1.00 0.00 Q13 +ATOM 507 SI27 Q011 1 17.684 10.777 -5.498 1.00 0.00 Q13 +ATOM 508 SI28 Q011 1 13.653 9.375 -2.085 1.00 0.00 Q13 +ATOM 509 O29 Q011 1 15.233 11.593 -10.068 1.00 0.00 Q13 +ATOM 510 O30 Q011 1 16.921 14.756 -6.709 1.00 0.00 Q13 +ATOM 511 O31 Q011 1 12.844 13.383 -3.352 1.00 0.00 Q13 +ATOM 512 O32 Q011 1 16.139 11.900 0.098 1.00 0.00 Q13 +ATOM 513 O33 Q011 1 13.511 10.330 -11.692 1.00 0.00 Q13 +ATOM 514 O34 Q011 1 15.151 13.584 -8.277 1.00 0.00 Q13 +ATOM 515 O35 Q011 1 11.123 12.110 -4.913 1.00 0.00 Q13 +ATOM 516 O36 Q011 1 14.453 10.769 -1.732 1.00 0.00 Q13 +ATOM 517 H37 Q011 1 14.859 14.220 -14.310 1.00 0.00 Q13 +ATOM 518 H38 Q011 1 14.407 7.879 -0.561 1.00 0.00 Q13 +ATOM 519 H39 Q011 1 11.928 12.942 -13.321 1.00 0.00 Q13 +ATOM 520 H40 Q011 1 15.681 12.733 0.295 1.00 0.00 Q13 +ATOM 521 SI1 Q011 1 22.731 13.785 -12.950 1.00 0.00 Q14 +ATOM 522 SI2 Q011 1 18.709 12.291 -9.494 1.00 0.00 Q14 +ATOM 523 SI3 Q011 1 22.002 10.853 -6.138 1.00 0.00 Q14 +ATOM 524 SI4 Q011 1 25.314 9.356 -2.792 1.00 0.00 Q14 +ATOM 525 O5 Q011 1 22.474 12.178 -12.753 1.00 0.00 Q14 +ATOM 526 O6 Q011 1 18.630 10.666 -9.344 1.00 0.00 Q14 +ATOM 527 O7 Q011 1 21.852 9.232 -5.995 1.00 0.00 Q14 +ATOM 528 O8 Q011 1 23.663 12.349 -2.597 1.00 0.00 Q14 +ATOM 529 O9 Q011 1 24.340 14.054 -12.745 1.00 0.00 Q14 +ATOM 530 O10 Q011 1 20.244 12.831 -9.326 1.00 0.00 Q14 +ATOM 531 O11 Q011 1 23.562 11.328 -6.004 1.00 0.00 Q14 +ATOM 532 O12 Q011 1 19.522 9.928 -2.599 1.00 0.00 Q14 +ATOM 533 O13 Q011 1 18.152 12.665 -10.990 1.00 0.00 Q14 +ATOM 534 O14 Q011 1 21.439 11.179 -7.637 1.00 0.00 Q14 +ATOM 535 O15 Q011 1 24.760 9.661 -4.299 1.00 0.00 Q14 +ATOM 536 O16 Q011 1 20.901 8.301 -0.828 1.00 0.00 Q14 +ATOM 537 O17 Q011 1 23.527 9.887 -11.762 1.00 0.00 Q14 +ATOM 538 O18 Q011 1 17.783 12.947 -8.311 1.00 0.00 Q14 +ATOM 539 O19 Q011 1 21.094 11.556 -4.966 1.00 0.00 Q14 +ATOM 540 O20 Q011 1 24.308 9.981 -1.648 1.00 0.00 Q14 +ATOM 541 SI21 Q011 1 22.338 11.013 -11.588 1.00 0.00 Q14 +ATOM 542 SI22 Q011 1 24.027 14.089 -8.184 1.00 0.00 Q14 +ATOM 543 SI23 Q011 1 19.956 12.726 -4.841 1.00 0.00 Q14 +ATOM 544 SI24 Q011 1 23.311 11.271 -1.414 1.00 0.00 Q14 +ATOM 545 SI25 Q011 1 18.450 13.617 -12.285 1.00 0.00 Q14 +ATOM 546 SI26 Q011 1 21.693 12.248 -8.852 1.00 0.00 Q14 +ATOM 547 SI27 Q011 1 25.007 10.754 -5.493 1.00 0.00 Q14 +ATOM 548 SI28 Q011 1 20.978 9.372 -2.081 1.00 0.00 Q14 +ATOM 549 O29 Q011 1 22.555 11.573 -10.061 1.00 0.00 Q14 +ATOM 550 O30 Q011 1 24.256 14.708 -6.684 1.00 0.00 Q14 +ATOM 551 O31 Q011 1 20.169 13.371 -3.347 1.00 0.00 Q14 +ATOM 552 O32 Q011 1 23.453 11.899 0.105 1.00 0.00 Q14 +ATOM 553 O33 Q011 1 20.841 10.333 -11.709 1.00 0.00 Q14 +ATOM 554 O34 Q011 1 22.486 13.550 -8.261 1.00 0.00 Q14 +ATOM 555 O35 Q011 1 18.447 12.100 -4.906 1.00 0.00 Q14 +ATOM 556 O36 Q011 1 21.780 10.767 -1.736 1.00 0.00 Q14 +ATOM 557 H37 Q011 1 22.278 14.244 -14.285 1.00 0.00 Q14 +ATOM 558 H38 Q011 1 21.731 7.884 -0.548 1.00 0.00 Q14 +ATOM 559 H39 Q011 1 19.262 12.940 -13.322 1.00 0.00 Q14 +ATOM 560 H40 Q011 1 22.996 12.734 0.298 1.00 0.00 Q14 +ATOM 561 SI1 Q011 1 29.946 13.642 -13.190 1.00 0.00 Q15 +ATOM 562 SI2 Q011 1 26.038 12.216 -9.470 1.00 0.00 Q15 +ATOM 563 SI3 Q011 1 29.346 10.855 -6.145 1.00 0.00 Q15 +ATOM 564 SI4 Q011 1 32.657 9.309 -2.798 1.00 0.00 Q15 +ATOM 565 O5 Q011 1 29.550 12.103 -12.796 1.00 0.00 Q15 +ATOM 566 O6 Q011 1 25.983 10.593 -9.318 1.00 0.00 Q15 +ATOM 567 O7 Q011 1 29.186 9.233 -6.007 1.00 0.00 Q15 +ATOM 568 O8 Q011 1 31.150 12.291 -2.557 1.00 0.00 Q15 +ATOM 569 O9 Q011 1 31.597 13.630 -13.213 1.00 0.00 Q15 +ATOM 570 O10 Q011 1 27.567 12.775 -9.335 1.00 0.00 Q15 +ATOM 571 O11 Q011 1 30.907 11.322 -5.986 1.00 0.00 Q15 +ATOM 572 O12 Q011 1 26.839 9.937 -2.614 1.00 0.00 Q15 +ATOM 573 O13 Q011 1 25.495 12.575 -10.972 1.00 0.00 Q15 +ATOM 574 O14 Q011 1 28.803 11.165 -7.655 1.00 0.00 Q15 +ATOM 575 O15 Q011 1 32.139 9.614 -4.323 1.00 0.00 Q15 +ATOM 576 O16 Q011 1 28.236 8.342 -0.832 1.00 0.00 Q15 +ATOM 577 O17 Q011 1 30.987 9.933 -11.966 1.00 0.00 Q15 +ATOM 578 O18 Q011 1 25.113 12.870 -8.284 1.00 0.00 Q15 +ATOM 579 O19 Q011 1 28.420 11.556 -4.986 1.00 0.00 Q15 +ATOM 580 O20 Q011 1 31.583 9.862 -1.683 1.00 0.00 Q15 +ATOM 581 SI21 Q011 1 29.727 10.957 -11.620 1.00 0.00 Q15 +ATOM 582 SI22 Q011 1 31.285 14.147 -8.266 1.00 0.00 Q15 +ATOM 583 SI23 Q011 1 27.275 12.720 -4.864 1.00 0.00 Q15 +ATOM 584 SI24 Q011 1 30.674 11.206 -1.421 1.00 0.00 Q15 +ATOM 585 SI25 Q011 1 25.822 13.561 -12.231 1.00 0.00 Q15 +ATOM 586 SI26 Q011 1 29.031 12.218 -8.890 1.00 0.00 Q15 +ATOM 587 SI27 Q011 1 32.360 10.745 -5.496 1.00 0.00 Q15 +ATOM 588 SI28 Q011 1 28.301 9.389 -2.107 1.00 0.00 Q15 +ATOM 589 O29 Q011 1 29.914 11.557 -10.100 1.00 0.00 Q15 +ATOM 590 O30 Q011 1 31.554 14.698 -6.748 1.00 0.00 Q15 +ATOM 591 O31 Q011 1 27.479 13.361 -3.367 1.00 0.00 Q15 +ATOM 592 O32 Q011 1 30.784 11.791 0.118 1.00 0.00 Q15 +ATOM 593 O33 Q011 1 28.264 10.214 -11.605 1.00 0.00 Q15 +ATOM 594 O34 Q011 1 29.757 13.576 -8.340 1.00 0.00 Q15 +ATOM 595 O35 Q011 1 25.767 12.089 -4.924 1.00 0.00 Q15 +ATOM 596 O36 Q011 1 29.136 10.777 -1.815 1.00 0.00 Q15 +ATOM 597 H37 Q011 1 29.384 14.047 -14.501 1.00 0.00 Q15 +ATOM 598 H38 Q011 1 29.070 7.935 -0.551 1.00 0.00 Q15 +ATOM 599 H39 Q011 1 26.605 12.893 -13.297 1.00 0.00 Q15 +ATOM 600 H40 Q011 1 30.371 12.649 0.307 1.00 0.00 Q15 +ATOM 601 SI1 Q011 1 -1.016 18.475 -12.950 1.00 0.00 Q16 +ATOM 602 SI2 Q011 1 -4.890 16.957 -9.502 1.00 0.00 Q16 +ATOM 603 SI3 Q011 1 -1.616 15.555 -6.130 1.00 0.00 Q16 +ATOM 604 SI4 Q011 1 1.673 13.974 -2.798 1.00 0.00 Q16 +ATOM 605 O5 Q011 1 -1.270 16.868 -12.754 1.00 0.00 Q16 +ATOM 606 O6 Q011 1 -4.917 15.337 -9.373 1.00 0.00 Q16 +ATOM 607 O7 Q011 1 -1.796 13.936 -5.977 1.00 0.00 Q16 +ATOM 608 O8 Q011 1 0.059 16.974 -2.583 1.00 0.00 Q16 +ATOM 609 O9 Q011 1 0.590 18.747 -12.736 1.00 0.00 Q16 +ATOM 610 O10 Q011 1 -3.385 17.553 -9.290 1.00 0.00 Q16 +ATOM 611 O11 Q011 1 -0.056 16.018 -6.023 1.00 0.00 Q16 +ATOM 612 O12 Q011 1 -4.071 14.721 -2.512 1.00 0.00 Q16 +ATOM 613 O13 Q011 1 -5.470 17.342 -10.992 1.00 0.00 Q16 +ATOM 614 O14 Q011 1 -2.188 15.897 -7.621 1.00 0.00 Q16 +ATOM 615 O15 Q011 1 1.126 14.312 -4.304 1.00 0.00 Q16 +ATOM 616 O16 Q011 1 -2.663 13.029 -0.818 1.00 0.00 Q16 +ATOM 617 O17 Q011 1 -0.232 14.582 -11.770 1.00 0.00 Q16 +ATOM 618 O18 Q011 1 -5.823 17.495 -8.278 1.00 0.00 Q16 +ATOM 619 O19 Q011 1 -2.456 16.298 -4.935 1.00 0.00 Q16 +ATOM 620 O20 Q011 1 0.688 14.598 -1.637 1.00 0.00 Q16 +ATOM 621 SI21 Q011 1 -1.427 15.705 -11.591 1.00 0.00 Q16 +ATOM 622 SI22 Q011 1 0.400 18.803 -8.193 1.00 0.00 Q16 +ATOM 623 SI23 Q011 1 -3.622 17.438 -4.801 1.00 0.00 Q16 +ATOM 624 SI24 Q011 1 -0.238 15.929 -1.360 1.00 0.00 Q16 +ATOM 625 SI25 Q011 1 -5.148 18.222 -12.333 1.00 0.00 Q16 +ATOM 626 SI26 Q011 1 -1.936 16.960 -8.841 1.00 0.00 Q16 +ATOM 627 SI27 Q011 1 1.365 15.421 -5.487 1.00 0.00 Q16 +ATOM 628 SI28 Q011 1 -2.610 14.133 -2.042 1.00 0.00 Q16 +ATOM 629 O29 Q011 1 -1.134 16.262 -10.076 1.00 0.00 Q16 +ATOM 630 O30 Q011 1 0.620 19.398 -6.682 1.00 0.00 Q16 +ATOM 631 O31 Q011 1 -3.444 18.138 -3.325 1.00 0.00 Q16 +ATOM 632 O32 Q011 1 -0.021 16.557 0.150 1.00 0.00 Q16 +ATOM 633 O33 Q011 1 -2.935 15.020 -11.693 1.00 0.00 Q16 +ATOM 634 O34 Q011 1 -1.140 18.266 -8.271 1.00 0.00 Q16 +ATOM 635 O35 Q011 1 -5.082 16.716 -4.843 1.00 0.00 Q16 +ATOM 636 O36 Q011 1 -1.794 15.501 -1.647 1.00 0.00 Q16 +ATOM 637 H37 Q011 1 -1.457 18.929 -14.290 1.00 0.00 Q16 +ATOM 638 H38 Q011 1 -1.836 12.566 -0.606 1.00 0.00 Q16 +ATOM 639 H39 Q011 1 -4.076 17.599 -13.141 1.00 0.00 Q16 +ATOM 640 H40 Q011 1 -0.478 17.385 0.369 1.00 0.00 Q16 +ATOM 641 SI1 Q011 1 6.365 18.398 -12.986 1.00 0.00 Q17 +ATOM 642 SI2 Q011 1 2.405 16.934 -9.488 1.00 0.00 Q17 +ATOM 643 SI3 Q011 1 5.702 15.502 -6.144 1.00 0.00 Q17 +ATOM 644 SI4 Q011 1 9.015 13.988 -2.807 1.00 0.00 Q17 +ATOM 645 O5 Q011 1 6.126 16.792 -12.771 1.00 0.00 Q17 +ATOM 646 O6 Q011 1 2.350 15.310 -9.326 1.00 0.00 Q17 +ATOM 647 O7 Q011 1 5.548 13.879 -6.004 1.00 0.00 Q17 +ATOM 648 O8 Q011 1 7.361 16.980 -2.610 1.00 0.00 Q17 +ATOM 649 O9 Q011 1 7.975 18.679 -12.819 1.00 0.00 Q17 +ATOM 650 O10 Q011 1 3.940 17.478 -9.330 1.00 0.00 Q17 +ATOM 651 O11 Q011 1 7.261 15.983 -6.007 1.00 0.00 Q17 +ATOM 652 O12 Q011 1 3.201 14.550 -2.606 1.00 0.00 Q17 +ATOM 653 O13 Q011 1 1.828 17.287 -10.982 1.00 0.00 Q17 +ATOM 654 O14 Q011 1 5.147 15.831 -7.645 1.00 0.00 Q17 +ATOM 655 O15 Q011 1 8.474 14.300 -4.318 1.00 0.00 Q17 +ATOM 656 O16 Q011 1 4.623 12.944 -0.842 1.00 0.00 Q17 +ATOM 657 O17 Q011 1 7.197 14.513 -11.780 1.00 0.00 Q17 +ATOM 658 O18 Q011 1 1.483 17.584 -8.300 1.00 0.00 Q17 +ATOM 659 O19 Q011 1 4.789 16.202 -4.975 1.00 0.00 Q17 +ATOM 660 O20 Q011 1 8.000 14.609 -1.669 1.00 0.00 Q17 +ATOM 661 SI21 Q011 1 6.015 15.643 -11.590 1.00 0.00 Q17 +ATOM 662 SI22 Q011 1 7.711 18.776 -8.211 1.00 0.00 Q17 +ATOM 663 SI23 Q011 1 3.649 17.371 -4.851 1.00 0.00 Q17 +ATOM 664 SI24 Q011 1 7.007 15.901 -1.429 1.00 0.00 Q17 +ATOM 665 SI25 Q011 1 2.089 18.268 -12.262 1.00 0.00 Q17 +ATOM 666 SI26 Q011 1 5.394 16.901 -8.861 1.00 0.00 Q17 +ATOM 667 SI27 Q011 1 8.707 15.407 -5.503 1.00 0.00 Q17 +ATOM 668 SI28 Q011 1 4.670 14.013 -2.097 1.00 0.00 Q17 +ATOM 669 O29 Q011 1 6.251 16.223 -10.073 1.00 0.00 Q17 +ATOM 670 O30 Q011 1 7.949 19.382 -6.708 1.00 0.00 Q17 +ATOM 671 O31 Q011 1 3.863 18.022 -3.361 1.00 0.00 Q17 +ATOM 672 O32 Q011 1 7.152 16.523 0.092 1.00 0.00 Q17 +ATOM 673 O33 Q011 1 4.514 14.969 -11.688 1.00 0.00 Q17 +ATOM 674 O34 Q011 1 6.178 18.213 -8.278 1.00 0.00 Q17 +ATOM 675 O35 Q011 1 2.140 16.739 -4.898 1.00 0.00 Q17 +ATOM 676 O36 Q011 1 5.473 15.409 -1.758 1.00 0.00 Q17 +ATOM 677 H37 Q011 1 5.878 18.844 -14.313 1.00 0.00 Q17 +ATOM 678 H38 Q011 1 5.462 12.536 -0.573 1.00 0.00 Q17 +ATOM 679 H39 Q011 1 2.854 17.606 -13.345 1.00 0.00 Q17 +ATOM 680 H40 Q011 1 6.701 17.359 0.288 1.00 0.00 Q17 +ATOM 681 SI1 Q011 1 13.698 18.398 -12.985 1.00 0.00 Q18 +ATOM 682 SI2 Q011 1 9.731 16.913 -9.494 1.00 0.00 Q18 +ATOM 683 SI3 Q011 1 13.029 15.494 -6.141 1.00 0.00 Q18 +ATOM 684 SI4 Q011 1 16.339 13.980 -2.806 1.00 0.00 Q18 +ATOM 685 O5 Q011 1 13.456 16.793 -12.768 1.00 0.00 Q18 +ATOM 686 O6 Q011 1 9.660 15.288 -9.342 1.00 0.00 Q18 +ATOM 687 O7 Q011 1 12.885 13.871 -5.999 1.00 0.00 Q18 +ATOM 688 O8 Q011 1 14.679 16.972 -2.609 1.00 0.00 Q18 +ATOM 689 O9 Q011 1 15.309 18.679 -12.825 1.00 0.00 Q18 +ATOM 690 O10 Q011 1 11.264 17.461 -9.330 1.00 0.00 Q18 +ATOM 691 O11 Q011 1 14.586 15.980 -6.003 1.00 0.00 Q18 +ATOM 692 O12 Q011 1 10.544 14.554 -2.604 1.00 0.00 Q18 +ATOM 693 O13 Q011 1 9.170 17.280 -10.990 1.00 0.00 Q18 +ATOM 694 O14 Q011 1 12.470 15.819 -7.641 1.00 0.00 Q18 +ATOM 695 O15 Q011 1 15.797 14.292 -4.317 1.00 0.00 Q18 +ATOM 696 O16 Q011 1 11.921 12.921 -0.838 1.00 0.00 Q18 +ATOM 697 O17 Q011 1 14.537 14.519 -11.778 1.00 0.00 Q18 +ATOM 698 O18 Q011 1 8.807 17.568 -8.310 1.00 0.00 Q18 +ATOM 699 O19 Q011 1 12.115 16.191 -4.971 1.00 0.00 Q18 +ATOM 700 O20 Q011 1 15.330 14.604 -1.663 1.00 0.00 Q18 +ATOM 701 SI21 Q011 1 13.347 15.641 -11.589 1.00 0.00 Q18 +ATOM 702 SI22 Q011 1 15.030 18.774 -8.215 1.00 0.00 Q18 +ATOM 703 SI23 Q011 1 10.979 17.363 -4.849 1.00 0.00 Q18 +ATOM 704 SI24 Q011 1 14.334 15.893 -1.424 1.00 0.00 Q18 +ATOM 705 SI25 Q011 1 9.463 18.238 -12.281 1.00 0.00 Q18 +ATOM 706 SI26 Q011 1 12.718 16.889 -8.858 1.00 0.00 Q18 +ATOM 707 SI27 Q011 1 16.031 15.400 -5.501 1.00 0.00 Q18 +ATOM 708 SI28 Q011 1 12.000 13.995 -2.088 1.00 0.00 Q18 +ATOM 709 O29 Q011 1 13.577 16.215 -10.070 1.00 0.00 Q18 +ATOM 710 O30 Q011 1 15.269 19.379 -6.711 1.00 0.00 Q18 +ATOM 711 O31 Q011 1 11.193 18.004 -3.354 1.00 0.00 Q18 +ATOM 712 O32 Q011 1 14.484 16.521 0.095 1.00 0.00 Q18 +ATOM 713 O33 Q011 1 11.853 14.954 -11.697 1.00 0.00 Q18 +ATOM 714 O34 Q011 1 13.498 18.205 -8.278 1.00 0.00 Q18 +ATOM 715 O35 Q011 1 9.470 16.733 -4.917 1.00 0.00 Q18 +ATOM 716 O36 Q011 1 12.801 15.389 -1.737 1.00 0.00 Q18 +ATOM 717 H37 Q011 1 13.207 18.844 -14.311 1.00 0.00 Q18 +ATOM 718 H38 Q011 1 12.750 12.502 -0.558 1.00 0.00 Q18 +ATOM 719 H39 Q011 1 10.277 17.567 -13.322 1.00 0.00 Q18 +ATOM 720 H40 Q011 1 14.027 17.354 0.291 1.00 0.00 Q18 +ATOM 721 SI1 Q011 1 21.080 18.410 -12.951 1.00 0.00 Q19 +ATOM 722 SI2 Q011 1 17.055 16.914 -9.495 1.00 0.00 Q19 +ATOM 723 SI3 Q011 1 20.349 15.475 -6.139 1.00 0.00 Q19 +ATOM 724 SI4 Q011 1 23.660 13.978 -2.797 1.00 0.00 Q19 +ATOM 725 O5 Q011 1 20.825 16.803 -12.754 1.00 0.00 Q19 +ATOM 726 O6 Q011 1 16.973 15.289 -9.346 1.00 0.00 Q19 +ATOM 727 O7 Q011 1 20.203 13.852 -5.997 1.00 0.00 Q19 +ATOM 728 O8 Q011 1 22.009 16.970 -2.600 1.00 0.00 Q19 +ATOM 729 O9 Q011 1 22.689 18.680 -12.745 1.00 0.00 Q19 +ATOM 730 O10 Q011 1 18.591 17.453 -9.327 1.00 0.00 Q19 +ATOM 731 O11 Q011 1 21.909 15.951 -6.007 1.00 0.00 Q19 +ATOM 732 O12 Q011 1 17.868 14.544 -2.605 1.00 0.00 Q19 +ATOM 733 O13 Q011 1 16.499 17.289 -10.991 1.00 0.00 Q19 +ATOM 734 O14 Q011 1 19.786 15.801 -7.638 1.00 0.00 Q19 +ATOM 735 O15 Q011 1 23.106 14.285 -4.303 1.00 0.00 Q19 +ATOM 736 O16 Q011 1 19.243 12.920 -0.830 1.00 0.00 Q19 +ATOM 737 O17 Q011 1 21.876 14.513 -11.761 1.00 0.00 Q19 +ATOM 738 O18 Q011 1 16.130 17.570 -8.312 1.00 0.00 Q19 +ATOM 739 O19 Q011 1 19.440 16.176 -4.968 1.00 0.00 Q19 +ATOM 740 O20 Q011 1 22.655 14.603 -1.652 1.00 0.00 Q19 +ATOM 741 SI21 Q011 1 20.687 15.639 -11.589 1.00 0.00 Q19 +ATOM 742 SI22 Q011 1 22.374 18.712 -8.185 1.00 0.00 Q19 +ATOM 743 SI23 Q011 1 18.304 17.348 -4.843 1.00 0.00 Q19 +ATOM 744 SI24 Q011 1 21.656 15.891 -1.418 1.00 0.00 Q19 +ATOM 745 SI25 Q011 1 16.798 18.241 -12.286 1.00 0.00 Q19 +ATOM 746 SI26 Q011 1 20.040 16.871 -8.852 1.00 0.00 Q19 +ATOM 747 SI27 Q011 1 23.354 15.378 -5.497 1.00 0.00 Q19 +ATOM 748 SI28 Q011 1 19.324 13.989 -2.085 1.00 0.00 Q19 +ATOM 749 O29 Q011 1 20.903 16.197 -10.061 1.00 0.00 Q19 +ATOM 750 O30 Q011 1 22.603 19.331 -6.685 1.00 0.00 Q19 +ATOM 751 O31 Q011 1 18.517 17.992 -3.348 1.00 0.00 Q19 +ATOM 752 O32 Q011 1 21.796 16.520 0.101 1.00 0.00 Q19 +ATOM 753 O33 Q011 1 19.190 14.962 -11.711 1.00 0.00 Q19 +ATOM 754 O34 Q011 1 20.833 18.173 -8.261 1.00 0.00 Q19 +ATOM 755 O35 Q011 1 16.794 16.722 -4.908 1.00 0.00 Q19 +ATOM 756 O36 Q011 1 20.126 15.384 -1.740 1.00 0.00 Q19 +ATOM 757 H37 Q011 1 20.627 18.869 -14.286 1.00 0.00 Q19 +ATOM 758 H38 Q011 1 20.072 12.505 -0.545 1.00 0.00 Q19 +ATOM 759 H39 Q011 1 17.610 17.563 -13.323 1.00 0.00 Q19 +ATOM 760 H40 Q011 1 21.340 17.354 0.293 1.00 0.00 Q19 +ATOM 761 SI1 Q011 1 28.295 18.268 -13.191 1.00 0.00 Q20 +ATOM 762 SI2 Q011 1 24.385 16.840 -9.471 1.00 0.00 Q20 +ATOM 763 SI3 Q011 1 27.694 15.477 -6.146 1.00 0.00 Q20 +ATOM 764 SI4 Q011 1 31.004 13.930 -2.801 1.00 0.00 Q20 +ATOM 765 O5 Q011 1 27.900 16.729 -12.797 1.00 0.00 Q20 +ATOM 766 O6 Q011 1 24.328 15.217 -9.320 1.00 0.00 Q20 +ATOM 767 O7 Q011 1 27.538 13.854 -6.009 1.00 0.00 Q20 +ATOM 768 O8 Q011 1 29.497 16.913 -2.558 1.00 0.00 Q20 +ATOM 769 O9 Q011 1 29.946 18.256 -13.214 1.00 0.00 Q20 +ATOM 770 O10 Q011 1 25.915 17.398 -9.335 1.00 0.00 Q20 +ATOM 771 O11 Q011 1 29.254 15.946 -5.987 1.00 0.00 Q20 +ATOM 772 O12 Q011 1 25.186 14.556 -2.619 1.00 0.00 Q20 +ATOM 773 O13 Q011 1 23.843 17.200 -10.973 1.00 0.00 Q20 +ATOM 774 O14 Q011 1 27.152 15.786 -7.657 1.00 0.00 Q20 +ATOM 775 O15 Q011 1 30.486 14.238 -4.326 1.00 0.00 Q20 +ATOM 776 O16 Q011 1 26.579 12.962 -0.835 1.00 0.00 Q20 +ATOM 777 O17 Q011 1 29.336 14.559 -11.966 1.00 0.00 Q20 +ATOM 778 O18 Q011 1 23.460 17.494 -8.285 1.00 0.00 Q20 +ATOM 779 O19 Q011 1 26.767 16.176 -4.987 1.00 0.00 Q20 +ATOM 780 O20 Q011 1 29.929 14.481 -1.686 1.00 0.00 Q20 +ATOM 781 SI21 Q011 1 28.077 15.583 -11.620 1.00 0.00 Q20 +ATOM 782 SI22 Q011 1 29.631 18.771 -8.266 1.00 0.00 Q20 +ATOM 783 SI23 Q011 1 25.624 17.342 -4.865 1.00 0.00 Q20 +ATOM 784 SI24 Q011 1 29.020 15.825 -1.424 1.00 0.00 Q20 +ATOM 785 SI25 Q011 1 24.171 18.186 -12.232 1.00 0.00 Q20 +ATOM 786 SI26 Q011 1 27.378 16.842 -8.890 1.00 0.00 Q20 +ATOM 787 SI27 Q011 1 30.707 15.369 -5.498 1.00 0.00 Q20 +ATOM 788 SI28 Q011 1 26.647 14.007 -2.110 1.00 0.00 Q20 +ATOM 789 O29 Q011 1 28.263 16.183 -10.101 1.00 0.00 Q20 +ATOM 790 O30 Q011 1 29.901 19.322 -6.748 1.00 0.00 Q20 +ATOM 791 O31 Q011 1 25.828 17.982 -3.368 1.00 0.00 Q20 +ATOM 792 O32 Q011 1 29.129 16.410 0.115 1.00 0.00 Q20 +ATOM 793 O33 Q011 1 26.613 14.842 -11.607 1.00 0.00 Q20 +ATOM 794 O34 Q011 1 28.105 18.199 -8.339 1.00 0.00 Q20 +ATOM 795 O35 Q011 1 24.115 16.713 -4.927 1.00 0.00 Q20 +ATOM 796 O36 Q011 1 27.483 15.395 -1.819 1.00 0.00 Q20 +ATOM 797 H37 Q011 1 27.733 18.672 -14.501 1.00 0.00 Q20 +ATOM 798 H38 Q011 1 27.413 12.559 -0.548 1.00 0.00 Q20 +ATOM 799 H39 Q011 1 24.953 17.518 -13.298 1.00 0.00 Q20 +ATOM 800 H40 Q011 1 28.717 17.268 0.304 1.00 0.00 Q20 +ATOM 801 SI1 Q011 1 -2.669 23.101 -12.950 1.00 0.00 Q21 +ATOM 802 SI2 Q011 1 -6.542 21.581 -9.502 1.00 0.00 Q21 +ATOM 803 SI3 Q011 1 -3.268 20.178 -6.130 1.00 0.00 Q21 +ATOM 804 SI4 Q011 1 0.021 18.596 -2.799 1.00 0.00 Q21 +ATOM 805 O5 Q011 1 -2.923 21.493 -12.755 1.00 0.00 Q21 +ATOM 806 O6 Q011 1 -6.570 19.962 -9.373 1.00 0.00 Q21 +ATOM 807 O7 Q011 1 -3.448 18.559 -5.976 1.00 0.00 Q21 +ATOM 808 O8 Q011 1 -1.591 21.595 -2.584 1.00 0.00 Q21 +ATOM 809 O9 Q011 1 -1.062 23.371 -12.737 1.00 0.00 Q21 +ATOM 810 O10 Q011 1 -5.037 22.177 -9.290 1.00 0.00 Q21 +ATOM 811 O11 Q011 1 -1.708 20.641 -6.022 1.00 0.00 Q21 +ATOM 812 O12 Q011 1 -5.723 19.343 -2.512 1.00 0.00 Q21 +ATOM 813 O13 Q011 1 -7.122 21.966 -10.992 1.00 0.00 Q21 +ATOM 814 O14 Q011 1 -3.840 20.520 -7.621 1.00 0.00 Q21 +ATOM 815 O15 Q011 1 -0.526 18.935 -4.304 1.00 0.00 Q21 +ATOM 816 O16 Q011 1 -4.315 17.651 -0.817 1.00 0.00 Q21 +ATOM 817 O17 Q011 1 -1.883 19.209 -11.771 1.00 0.00 Q21 +ATOM 818 O18 Q011 1 -7.475 22.119 -8.277 1.00 0.00 Q21 +ATOM 819 O19 Q011 1 -4.108 20.921 -4.935 1.00 0.00 Q21 +ATOM 820 O20 Q011 1 -0.963 19.220 -1.637 1.00 0.00 Q21 +ATOM 821 SI21 Q011 1 -3.079 20.331 -11.591 1.00 0.00 Q21 +ATOM 822 SI22 Q011 1 -1.252 23.426 -8.193 1.00 0.00 Q21 +ATOM 823 SI23 Q011 1 -5.274 22.061 -4.801 1.00 0.00 Q21 +ATOM 824 SI24 Q011 1 -1.890 20.551 -1.360 1.00 0.00 Q21 +ATOM 825 SI25 Q011 1 -6.800 22.847 -12.333 1.00 0.00 Q21 +ATOM 826 SI26 Q011 1 -3.588 21.584 -8.841 1.00 0.00 Q21 +ATOM 827 SI27 Q011 1 -0.288 20.045 -5.487 1.00 0.00 Q21 +ATOM 828 SI28 Q011 1 -4.262 18.756 -2.042 1.00 0.00 Q21 +ATOM 829 O29 Q011 1 -2.786 20.887 -10.076 1.00 0.00 Q21 +ATOM 830 O30 Q011 1 -1.032 24.021 -6.683 1.00 0.00 Q21 +ATOM 831 O31 Q011 1 -5.095 22.762 -3.325 1.00 0.00 Q21 +ATOM 832 O32 Q011 1 -1.673 21.179 0.150 1.00 0.00 Q21 +ATOM 833 O33 Q011 1 -4.587 19.646 -11.693 1.00 0.00 Q21 +ATOM 834 O34 Q011 1 -2.792 22.889 -8.270 1.00 0.00 Q21 +ATOM 835 O35 Q011 1 -6.734 21.340 -4.843 1.00 0.00 Q21 +ATOM 836 O36 Q011 1 -3.446 20.123 -1.647 1.00 0.00 Q21 +ATOM 837 H37 Q011 1 -3.110 23.555 -14.291 1.00 0.00 Q21 +ATOM 838 H38 Q011 1 -3.489 17.190 -0.604 1.00 0.00 Q21 +ATOM 839 H39 Q011 1 -5.728 22.223 -13.141 1.00 0.00 Q21 +ATOM 840 H40 Q011 1 -2.128 22.008 0.368 1.00 0.00 Q21 +ATOM 841 SI1 Q011 1 4.712 23.023 -12.987 1.00 0.00 Q22 +ATOM 842 SI2 Q011 1 0.753 21.557 -9.489 1.00 0.00 Q22 +ATOM 843 SI3 Q011 1 4.050 20.125 -6.144 1.00 0.00 Q22 +ATOM 844 SI4 Q011 1 7.363 18.609 -2.808 1.00 0.00 Q22 +ATOM 845 O5 Q011 1 4.474 21.418 -12.772 1.00 0.00 Q22 +ATOM 846 O6 Q011 1 0.696 19.934 -9.327 1.00 0.00 Q22 +ATOM 847 O7 Q011 1 3.897 18.502 -6.004 1.00 0.00 Q22 +ATOM 848 O8 Q011 1 5.709 21.599 -2.612 1.00 0.00 Q22 +ATOM 849 O9 Q011 1 6.322 23.304 -12.820 1.00 0.00 Q22 +ATOM 850 O10 Q011 1 2.288 22.101 -9.330 1.00 0.00 Q22 +ATOM 851 O11 Q011 1 5.609 20.605 -6.007 1.00 0.00 Q22 +ATOM 852 O12 Q011 1 1.549 19.172 -2.606 1.00 0.00 Q22 +ATOM 853 O13 Q011 1 0.175 21.911 -10.983 1.00 0.00 Q22 +ATOM 854 O14 Q011 1 3.495 20.453 -7.645 1.00 0.00 Q22 +ATOM 855 O15 Q011 1 6.822 18.921 -4.319 1.00 0.00 Q22 +ATOM 856 O16 Q011 1 2.970 17.565 -0.842 1.00 0.00 Q22 +ATOM 857 O17 Q011 1 5.546 19.138 -11.781 1.00 0.00 Q22 +ATOM 858 O18 Q011 1 -0.169 22.207 -8.300 1.00 0.00 Q22 +ATOM 859 O19 Q011 1 3.137 20.825 -4.976 1.00 0.00 Q22 +ATOM 860 O20 Q011 1 6.348 19.229 -1.669 1.00 0.00 Q22 +ATOM 861 SI21 Q011 1 4.363 20.268 -11.591 1.00 0.00 Q22 +ATOM 862 SI22 Q011 1 6.059 23.398 -8.211 1.00 0.00 Q22 +ATOM 863 SI23 Q011 1 1.997 21.994 -4.852 1.00 0.00 Q22 +ATOM 864 SI24 Q011 1 5.355 20.521 -1.429 1.00 0.00 Q22 +ATOM 865 SI25 Q011 1 0.436 22.892 -12.263 1.00 0.00 Q22 +ATOM 866 SI26 Q011 1 3.742 21.523 -8.862 1.00 0.00 Q22 +ATOM 867 SI27 Q011 1 7.056 20.029 -5.504 1.00 0.00 Q22 +ATOM 868 SI28 Q011 1 3.018 18.635 -2.097 1.00 0.00 Q22 +ATOM 869 O29 Q011 1 4.600 20.847 -10.074 1.00 0.00 Q22 +ATOM 870 O30 Q011 1 6.298 24.004 -6.708 1.00 0.00 Q22 +ATOM 871 O31 Q011 1 2.212 22.645 -3.362 1.00 0.00 Q22 +ATOM 872 O32 Q011 1 5.502 21.144 0.091 1.00 0.00 Q22 +ATOM 873 O33 Q011 1 2.863 19.594 -11.689 1.00 0.00 Q22 +ATOM 874 O34 Q011 1 4.526 22.835 -8.278 1.00 0.00 Q22 +ATOM 875 O35 Q011 1 0.488 21.362 -4.898 1.00 0.00 Q22 +ATOM 876 O36 Q011 1 3.821 20.030 -1.757 1.00 0.00 Q22 +ATOM 877 H37 Q011 1 4.226 23.469 -14.315 1.00 0.00 Q22 +ATOM 878 H38 Q011 1 3.809 17.158 -0.572 1.00 0.00 Q22 +ATOM 879 H39 Q011 1 1.201 22.231 -13.346 1.00 0.00 Q22 +ATOM 880 H40 Q011 1 5.052 21.981 0.287 1.00 0.00 Q22 +ATOM 881 SI1 Q011 1 12.046 23.023 -12.987 1.00 0.00 Q23 +ATOM 882 SI2 Q011 1 8.080 21.536 -9.496 1.00 0.00 Q23 +ATOM 883 SI3 Q011 1 11.377 20.116 -6.142 1.00 0.00 Q23 +ATOM 884 SI4 Q011 1 14.688 18.601 -2.807 1.00 0.00 Q23 +ATOM 885 O5 Q011 1 11.804 21.418 -12.768 1.00 0.00 Q23 +ATOM 886 O6 Q011 1 8.007 19.911 -9.344 1.00 0.00 Q23 +ATOM 887 O7 Q011 1 11.235 18.493 -6.000 1.00 0.00 Q23 +ATOM 888 O8 Q011 1 13.030 21.592 -2.610 1.00 0.00 Q23 +ATOM 889 O9 Q011 1 13.657 23.303 -12.826 1.00 0.00 Q23 +ATOM 890 O10 Q011 1 9.612 22.084 -9.331 1.00 0.00 Q23 +ATOM 891 O11 Q011 1 12.934 20.603 -6.004 1.00 0.00 Q23 +ATOM 892 O12 Q011 1 8.892 19.175 -2.605 1.00 0.00 Q23 +ATOM 893 O13 Q011 1 7.518 21.904 -10.992 1.00 0.00 Q23 +ATOM 894 O14 Q011 1 10.818 20.441 -7.643 1.00 0.00 Q23 +ATOM 895 O15 Q011 1 14.145 18.915 -4.318 1.00 0.00 Q23 +ATOM 896 O16 Q011 1 10.269 17.542 -0.839 1.00 0.00 Q23 +ATOM 897 O17 Q011 1 12.886 19.143 -11.779 1.00 0.00 Q23 +ATOM 898 O18 Q011 1 7.155 22.190 -8.311 1.00 0.00 Q23 +ATOM 899 O19 Q011 1 10.463 20.812 -4.972 1.00 0.00 Q23 +ATOM 900 O20 Q011 1 13.679 19.224 -1.665 1.00 0.00 Q23 +ATOM 901 SI21 Q011 1 11.696 20.265 -11.590 1.00 0.00 Q23 +ATOM 902 SI22 Q011 1 13.378 23.396 -8.217 1.00 0.00 Q23 +ATOM 903 SI23 Q011 1 9.327 21.984 -4.850 1.00 0.00 Q23 +ATOM 904 SI24 Q011 1 12.683 20.513 -1.425 1.00 0.00 Q23 +ATOM 905 SI25 Q011 1 7.810 22.862 -12.282 1.00 0.00 Q23 +ATOM 906 SI26 Q011 1 11.066 21.511 -8.859 1.00 0.00 Q23 +ATOM 907 SI27 Q011 1 14.379 20.023 -5.502 1.00 0.00 Q23 +ATOM 908 SI28 Q011 1 10.348 18.616 -2.089 1.00 0.00 Q23 +ATOM 909 O29 Q011 1 11.926 20.838 -10.070 1.00 0.00 Q23 +ATOM 910 O30 Q011 1 13.618 23.999 -6.713 1.00 0.00 Q23 +ATOM 911 O31 Q011 1 9.541 22.625 -3.354 1.00 0.00 Q23 +ATOM 912 O32 Q011 1 12.833 21.141 0.094 1.00 0.00 Q23 +ATOM 913 O33 Q011 1 10.202 19.578 -11.697 1.00 0.00 Q23 +ATOM 914 O34 Q011 1 11.846 22.827 -8.280 1.00 0.00 Q23 +ATOM 915 O35 Q011 1 7.819 21.355 -4.917 1.00 0.00 Q23 +ATOM 916 O36 Q011 1 11.150 20.010 -1.739 1.00 0.00 Q23 +ATOM 917 H37 Q011 1 11.555 23.469 -14.312 1.00 0.00 Q23 +ATOM 918 H38 Q011 1 11.098 17.125 -0.557 1.00 0.00 Q23 +ATOM 919 H39 Q011 1 8.624 22.192 -13.323 1.00 0.00 Q23 +ATOM 920 H40 Q011 1 12.377 21.975 0.290 1.00 0.00 Q23 +ATOM 921 SI1 Q011 1 19.428 23.035 -12.952 1.00 0.00 Q24 +ATOM 922 SI2 Q011 1 15.404 21.537 -9.497 1.00 0.00 Q24 +ATOM 923 SI3 Q011 1 18.698 20.097 -6.141 1.00 0.00 Q24 +ATOM 924 SI4 Q011 1 22.008 18.599 -2.799 1.00 0.00 Q24 +ATOM 925 O5 Q011 1 19.172 21.428 -12.755 1.00 0.00 Q24 +ATOM 926 O6 Q011 1 15.321 19.911 -9.348 1.00 0.00 Q24 +ATOM 927 O7 Q011 1 18.552 18.475 -5.997 1.00 0.00 Q24 +ATOM 928 O8 Q011 1 20.359 21.591 -2.602 1.00 0.00 Q24 +ATOM 929 O9 Q011 1 21.037 23.304 -12.746 1.00 0.00 Q24 +ATOM 930 O10 Q011 1 16.939 22.076 -9.328 1.00 0.00 Q24 +ATOM 931 O11 Q011 1 20.257 20.574 -6.008 1.00 0.00 Q24 +ATOM 932 O12 Q011 1 16.217 19.166 -2.607 1.00 0.00 Q24 +ATOM 933 O13 Q011 1 14.848 21.912 -10.994 1.00 0.00 Q24 +ATOM 934 O14 Q011 1 18.134 20.423 -7.639 1.00 0.00 Q24 +ATOM 935 O15 Q011 1 21.454 18.907 -4.305 1.00 0.00 Q24 +ATOM 936 O16 Q011 1 17.591 17.542 -0.831 1.00 0.00 Q24 +ATOM 937 O17 Q011 1 20.224 19.137 -11.763 1.00 0.00 Q24 +ATOM 938 O18 Q011 1 14.478 22.192 -8.314 1.00 0.00 Q24 +ATOM 939 O19 Q011 1 17.789 20.798 -4.969 1.00 0.00 Q24 +ATOM 940 O20 Q011 1 21.004 19.225 -1.653 1.00 0.00 Q24 +ATOM 941 SI21 Q011 1 19.035 20.263 -11.590 1.00 0.00 Q24 +ATOM 942 SI22 Q011 1 20.722 23.336 -8.186 1.00 0.00 Q24 +ATOM 943 SI23 Q011 1 16.653 21.971 -4.845 1.00 0.00 Q24 +ATOM 944 SI24 Q011 1 20.005 20.513 -1.420 1.00 0.00 Q24 +ATOM 945 SI25 Q011 1 15.146 22.865 -12.287 1.00 0.00 Q24 +ATOM 946 SI26 Q011 1 18.388 21.494 -8.853 1.00 0.00 Q24 +ATOM 947 SI27 Q011 1 21.703 20.001 -5.498 1.00 0.00 Q24 +ATOM 948 SI28 Q011 1 17.673 18.610 -2.086 1.00 0.00 Q24 +ATOM 949 O29 Q011 1 19.251 20.821 -10.063 1.00 0.00 Q24 +ATOM 950 O30 Q011 1 20.953 23.957 -6.687 1.00 0.00 Q24 +ATOM 951 O31 Q011 1 16.866 22.615 -3.350 1.00 0.00 Q24 +ATOM 952 O32 Q011 1 20.145 21.142 0.099 1.00 0.00 Q24 +ATOM 953 O33 Q011 1 17.538 19.585 -11.712 1.00 0.00 Q24 +ATOM 954 O34 Q011 1 19.181 22.796 -8.261 1.00 0.00 Q24 +ATOM 955 O35 Q011 1 15.143 21.345 -4.911 1.00 0.00 Q24 +ATOM 956 O36 Q011 1 18.475 20.006 -1.742 1.00 0.00 Q24 +ATOM 957 H37 Q011 1 18.976 23.493 -14.287 1.00 0.00 Q24 +ATOM 958 H38 Q011 1 18.419 17.128 -0.544 1.00 0.00 Q24 +ATOM 959 H39 Q011 1 15.958 22.188 -13.326 1.00 0.00 Q24 +ATOM 960 H40 Q011 1 19.690 21.977 0.291 1.00 0.00 Q24 +ATOM 961 SI1 Q011 1 26.643 22.892 -13.191 1.00 0.00 Q25 +ATOM 962 SI2 Q011 1 22.733 21.464 -9.472 1.00 0.00 Q25 +ATOM 963 SI3 Q011 1 26.042 20.099 -6.147 1.00 0.00 Q25 +ATOM 964 SI4 Q011 1 29.352 18.552 -2.801 1.00 0.00 Q25 +ATOM 965 O5 Q011 1 26.248 21.353 -12.797 1.00 0.00 Q25 +ATOM 966 O6 Q011 1 22.674 19.840 -9.321 1.00 0.00 Q25 +ATOM 967 O7 Q011 1 25.888 18.476 -6.010 1.00 0.00 Q25 +ATOM 968 O8 Q011 1 27.845 21.536 -2.558 1.00 0.00 Q25 +ATOM 969 O9 Q011 1 28.294 22.880 -13.214 1.00 0.00 Q25 +ATOM 970 O10 Q011 1 24.263 22.021 -9.336 1.00 0.00 Q25 +ATOM 971 O11 Q011 1 27.602 20.570 -5.986 1.00 0.00 Q25 +ATOM 972 O12 Q011 1 23.534 19.177 -2.621 1.00 0.00 Q25 +ATOM 973 O13 Q011 1 22.191 21.824 -10.974 1.00 0.00 Q25 +ATOM 974 O14 Q011 1 25.500 20.409 -7.657 1.00 0.00 Q25 +ATOM 975 O15 Q011 1 28.834 18.860 -4.326 1.00 0.00 Q25 +ATOM 976 O16 Q011 1 24.926 17.584 -0.835 1.00 0.00 Q25 +ATOM 977 O17 Q011 1 27.685 19.184 -11.966 1.00 0.00 Q25 +ATOM 978 O18 Q011 1 21.809 22.118 -8.285 1.00 0.00 Q25 +ATOM 979 O19 Q011 1 25.115 20.799 -4.988 1.00 0.00 Q25 +ATOM 980 O20 Q011 1 28.277 19.103 -1.686 1.00 0.00 Q25 +ATOM 981 SI21 Q011 1 26.426 20.208 -11.620 1.00 0.00 Q25 +ATOM 982 SI22 Q011 1 27.979 23.394 -8.265 1.00 0.00 Q25 +ATOM 983 SI23 Q011 1 23.972 21.966 -4.865 1.00 0.00 Q25 +ATOM 984 SI24 Q011 1 27.368 20.448 -1.425 1.00 0.00 Q25 +ATOM 985 SI25 Q011 1 22.519 22.810 -12.232 1.00 0.00 Q25 +ATOM 986 SI26 Q011 1 25.726 21.465 -8.890 1.00 0.00 Q25 +ATOM 987 SI27 Q011 1 29.055 19.992 -5.497 1.00 0.00 Q25 +ATOM 988 SI28 Q011 1 24.995 18.628 -2.111 1.00 0.00 Q25 +ATOM 989 O29 Q011 1 26.611 20.806 -10.101 1.00 0.00 Q25 +ATOM 990 O30 Q011 1 28.249 23.946 -6.747 1.00 0.00 Q25 +ATOM 991 O31 Q011 1 24.177 22.605 -3.368 1.00 0.00 Q25 +ATOM 992 O32 Q011 1 27.476 21.032 0.114 1.00 0.00 Q25 +ATOM 993 O33 Q011 1 24.961 19.466 -11.606 1.00 0.00 Q25 +ATOM 994 O34 Q011 1 26.452 22.822 -8.339 1.00 0.00 Q25 +ATOM 995 O35 Q011 1 22.463 21.336 -4.928 1.00 0.00 Q25 +ATOM 996 O36 Q011 1 25.831 20.017 -1.821 1.00 0.00 Q25 +ATOM 997 H37 Q011 1 26.081 23.297 -14.502 1.00 0.00 Q25 +ATOM 998 H38 Q011 1 25.760 17.182 -0.547 1.00 0.00 Q25 +ATOM 999 H39 Q011 1 23.301 22.142 -13.298 1.00 0.00 Q25 +ATOM 1000 H40 Q011 1 27.065 21.890 0.304 1.00 0.00 Q25 +ATOM 1001 SI1 Q011 1 -4.323 27.727 -12.950 1.00 0.00 Q26 +ATOM 1002 SI2 Q011 1 -8.195 26.204 -9.502 1.00 0.00 Q26 +ATOM 1003 SI3 Q011 1 -4.920 24.802 -6.130 1.00 0.00 Q26 +ATOM 1004 SI4 Q011 1 -1.630 23.218 -2.800 1.00 0.00 Q26 +ATOM 1005 O5 Q011 1 -4.577 26.120 -12.755 1.00 0.00 Q26 +ATOM 1006 O6 Q011 1 -8.223 24.585 -9.373 1.00 0.00 Q26 +ATOM 1007 O7 Q011 1 -5.100 23.183 -5.976 1.00 0.00 Q26 +ATOM 1008 O8 Q011 1 -3.236 26.217 -2.583 1.00 0.00 Q26 +ATOM 1009 O9 Q011 1 -2.716 27.997 -12.736 1.00 0.00 Q26 +ATOM 1010 O10 Q011 1 -6.691 26.800 -9.290 1.00 0.00 Q26 +ATOM 1011 O11 Q011 1 -3.359 25.264 -6.022 1.00 0.00 Q26 +ATOM 1012 O12 Q011 1 -7.374 23.967 -2.512 1.00 0.00 Q26 +ATOM 1013 O13 Q011 1 -8.775 26.590 -10.992 1.00 0.00 Q26 +ATOM 1014 O14 Q011 1 -5.492 25.144 -7.621 1.00 0.00 Q26 +ATOM 1015 O15 Q011 1 -2.177 23.557 -4.305 1.00 0.00 Q26 +ATOM 1016 O16 Q011 1 -5.966 22.276 -0.817 1.00 0.00 Q26 +ATOM 1017 O17 Q011 1 -3.535 23.835 -11.772 1.00 0.00 Q26 +ATOM 1018 O18 Q011 1 -9.128 26.740 -8.276 1.00 0.00 Q26 +ATOM 1019 O19 Q011 1 -5.759 25.546 -4.935 1.00 0.00 Q26 +ATOM 1020 O20 Q011 1 -2.614 23.841 -1.638 1.00 0.00 Q26 +ATOM 1021 SI21 Q011 1 -4.732 24.956 -11.592 1.00 0.00 Q26 +ATOM 1022 SI22 Q011 1 -2.905 28.048 -8.194 1.00 0.00 Q26 +ATOM 1023 SI23 Q011 1 -6.925 26.686 -4.801 1.00 0.00 Q26 +ATOM 1024 SI24 Q011 1 -3.539 25.173 -1.360 1.00 0.00 Q26 +ATOM 1025 SI25 Q011 1 -8.454 27.471 -12.332 1.00 0.00 Q26 +ATOM 1026 SI26 Q011 1 -5.241 26.207 -8.841 1.00 0.00 Q26 +ATOM 1027 SI27 Q011 1 -1.939 24.668 -5.487 1.00 0.00 Q26 +ATOM 1028 SI28 Q011 1 -5.913 23.380 -2.042 1.00 0.00 Q26 +ATOM 1029 O29 Q011 1 -4.439 25.511 -10.076 1.00 0.00 Q26 +ATOM 1030 O30 Q011 1 -2.683 28.642 -6.683 1.00 0.00 Q26 +ATOM 1031 O31 Q011 1 -6.745 27.388 -3.325 1.00 0.00 Q26 +ATOM 1032 O32 Q011 1 -3.321 25.800 0.150 1.00 0.00 Q26 +ATOM 1033 O33 Q011 1 -6.239 24.270 -11.694 1.00 0.00 Q26 +ATOM 1034 O34 Q011 1 -4.445 27.513 -8.270 1.00 0.00 Q26 +ATOM 1035 O35 Q011 1 -8.385 25.963 -4.841 1.00 0.00 Q26 +ATOM 1036 O36 Q011 1 -5.095 24.747 -1.650 1.00 0.00 Q26 +ATOM 1037 H37 Q011 1 -4.763 28.181 -14.290 1.00 0.00 Q26 +ATOM 1038 H38 Q011 1 -5.139 21.814 -0.604 1.00 0.00 Q26 +ATOM 1039 H39 Q011 1 -7.382 26.849 -13.140 1.00 0.00 Q26 +ATOM 1040 H40 Q011 1 -3.776 26.629 0.368 1.00 0.00 Q26 +ATOM 1041 SI1 Q011 1 3.055 27.650 -12.987 1.00 0.00 Q27 +ATOM 1042 SI2 Q011 1 -0.900 26.180 -9.491 1.00 0.00 Q27 +ATOM 1043 SI3 Q011 1 2.399 24.748 -6.146 1.00 0.00 Q27 +ATOM 1044 SI4 Q011 1 5.712 23.228 -2.810 1.00 0.00 Q27 +ATOM 1045 O5 Q011 1 2.816 26.044 -12.772 1.00 0.00 Q27 +ATOM 1046 O6 Q011 1 -0.956 24.557 -9.328 1.00 0.00 Q27 +ATOM 1047 O7 Q011 1 2.245 23.125 -6.005 1.00 0.00 Q27 +ATOM 1048 O8 Q011 1 4.066 26.218 -2.612 1.00 0.00 Q27 +ATOM 1049 O9 Q011 1 4.666 27.927 -12.821 1.00 0.00 Q27 +ATOM 1050 O10 Q011 1 0.635 26.725 -9.331 1.00 0.00 Q27 +ATOM 1051 O11 Q011 1 3.958 25.227 -6.008 1.00 0.00 Q27 +ATOM 1052 O12 Q011 1 -0.102 23.795 -2.606 1.00 0.00 Q27 +ATOM 1053 O13 Q011 1 -1.477 26.532 -10.985 1.00 0.00 Q27 +ATOM 1054 O14 Q011 1 1.843 25.076 -7.647 1.00 0.00 Q27 +ATOM 1055 O15 Q011 1 5.170 23.542 -4.321 1.00 0.00 Q27 +ATOM 1056 O16 Q011 1 1.320 22.189 -0.842 1.00 0.00 Q27 +ATOM 1057 O17 Q011 1 3.893 23.764 -11.783 1.00 0.00 Q27 +ATOM 1058 O18 Q011 1 -1.823 26.828 -8.302 1.00 0.00 Q27 +ATOM 1059 O19 Q011 1 1.486 25.449 -4.977 1.00 0.00 Q27 +ATOM 1060 O20 Q011 1 4.697 23.847 -1.670 1.00 0.00 Q27 +ATOM 1061 SI21 Q011 1 2.710 24.893 -11.593 1.00 0.00 Q27 +ATOM 1062 SI22 Q011 1 4.406 28.019 -8.212 1.00 0.00 Q27 +ATOM 1063 SI23 Q011 1 0.346 26.618 -4.854 1.00 0.00 Q27 +ATOM 1064 SI24 Q011 1 3.708 25.141 -1.430 1.00 0.00 Q27 +ATOM 1065 SI25 Q011 1 -1.218 27.517 -12.263 1.00 0.00 Q27 +ATOM 1066 SI26 Q011 1 2.088 26.147 -8.863 1.00 0.00 Q27 +ATOM 1067 SI27 Q011 1 5.404 24.651 -5.504 1.00 0.00 Q27 +ATOM 1068 SI28 Q011 1 1.368 23.258 -2.098 1.00 0.00 Q27 +ATOM 1069 O29 Q011 1 2.946 25.472 -10.075 1.00 0.00 Q27 +ATOM 1070 O30 Q011 1 4.646 28.624 -6.709 1.00 0.00 Q27 +ATOM 1071 O31 Q011 1 0.563 27.270 -3.364 1.00 0.00 Q27 +ATOM 1072 O32 Q011 1 3.853 25.763 0.091 1.00 0.00 Q27 +ATOM 1073 O33 Q011 1 1.210 24.218 -11.690 1.00 0.00 Q27 +ATOM 1074 O34 Q011 1 2.872 27.458 -8.279 1.00 0.00 Q27 +ATOM 1075 O35 Q011 1 -1.163 25.984 -4.898 1.00 0.00 Q27 +ATOM 1076 O36 Q011 1 2.173 24.653 -1.760 1.00 0.00 Q27 +ATOM 1077 H37 Q011 1 2.570 28.096 -14.315 1.00 0.00 Q27 +ATOM 1078 H38 Q011 1 2.158 21.782 -0.573 1.00 0.00 Q27 +ATOM 1079 H39 Q011 1 -0.452 26.859 -13.348 1.00 0.00 Q27 +ATOM 1080 H40 Q011 1 3.406 26.601 0.286 1.00 0.00 Q27 +ATOM 1081 SI1 Q011 1 10.388 27.651 -12.986 1.00 0.00 Q28 +ATOM 1082 SI2 Q011 1 6.426 26.157 -9.497 1.00 0.00 Q28 +ATOM 1083 SI3 Q011 1 9.725 24.738 -6.143 1.00 0.00 Q28 +ATOM 1084 SI4 Q011 1 13.037 23.221 -2.809 1.00 0.00 Q28 +ATOM 1085 O5 Q011 1 10.149 26.046 -12.769 1.00 0.00 Q28 +ATOM 1086 O6 Q011 1 6.354 24.532 -9.344 1.00 0.00 Q28 +ATOM 1087 O7 Q011 1 9.582 23.114 -6.001 1.00 0.00 Q28 +ATOM 1088 O8 Q011 1 11.374 26.205 -2.614 1.00 0.00 Q28 +ATOM 1089 O9 Q011 1 11.999 27.931 -12.823 1.00 0.00 Q28 +ATOM 1090 O10 Q011 1 7.958 26.705 -9.331 1.00 0.00 Q28 +ATOM 1091 O11 Q011 1 11.282 25.222 -6.005 1.00 0.00 Q28 +ATOM 1092 O12 Q011 1 7.240 23.795 -2.607 1.00 0.00 Q28 +ATOM 1093 O13 Q011 1 5.863 26.521 -10.994 1.00 0.00 Q28 +ATOM 1094 O14 Q011 1 9.166 25.062 -7.644 1.00 0.00 Q28 +ATOM 1095 O15 Q011 1 12.495 23.534 -4.320 1.00 0.00 Q28 +ATOM 1096 O16 Q011 1 8.616 22.160 -0.840 1.00 0.00 Q28 +ATOM 1097 O17 Q011 1 11.233 23.769 -11.781 1.00 0.00 Q28 +ATOM 1098 O18 Q011 1 5.501 26.810 -8.313 1.00 0.00 Q28 +ATOM 1099 O19 Q011 1 8.811 25.436 -4.974 1.00 0.00 Q28 +ATOM 1100 O20 Q011 1 12.026 23.841 -1.666 1.00 0.00 Q28 +ATOM 1101 SI21 Q011 1 10.043 24.891 -11.592 1.00 0.00 Q28 +ATOM 1102 SI22 Q011 1 11.724 28.012 -8.211 1.00 0.00 Q28 +ATOM 1103 SI23 Q011 1 7.675 26.607 -4.852 1.00 0.00 Q28 +ATOM 1104 SI24 Q011 1 11.031 25.130 -1.425 1.00 0.00 Q28 +ATOM 1105 SI25 Q011 1 6.153 27.484 -12.282 1.00 0.00 Q28 +ATOM 1106 SI26 Q011 1 9.411 26.133 -8.859 1.00 0.00 Q28 +ATOM 1107 SI27 Q011 1 12.728 24.642 -5.504 1.00 0.00 Q28 +ATOM 1108 SI28 Q011 1 8.696 23.235 -2.089 1.00 0.00 Q28 +ATOM 1109 O29 Q011 1 10.273 25.462 -10.072 1.00 0.00 Q28 +ATOM 1110 O30 Q011 1 11.966 28.616 -6.708 1.00 0.00 Q28 +ATOM 1111 O31 Q011 1 7.891 27.250 -3.358 1.00 0.00 Q28 +ATOM 1112 O32 Q011 1 11.183 25.759 0.092 1.00 0.00 Q28 +ATOM 1113 O33 Q011 1 8.550 24.202 -11.698 1.00 0.00 Q28 +ATOM 1114 O34 Q011 1 10.192 27.446 -8.276 1.00 0.00 Q28 +ATOM 1115 O35 Q011 1 6.167 25.976 -4.917 1.00 0.00 Q28 +ATOM 1116 O36 Q011 1 9.497 24.628 -1.737 1.00 0.00 Q28 +ATOM 1117 H37 Q011 1 9.900 28.096 -14.312 1.00 0.00 Q28 +ATOM 1118 H38 Q011 1 9.445 21.745 -0.556 1.00 0.00 Q28 +ATOM 1119 H39 Q011 1 6.970 26.818 -13.325 1.00 0.00 Q28 +ATOM 1120 H40 Q011 1 10.729 26.594 0.287 1.00 0.00 Q28 +ATOM 1121 SI1 Q011 1 17.771 27.663 -12.950 1.00 0.00 Q29 +ATOM 1122 SI2 Q011 1 13.751 26.158 -9.499 1.00 0.00 Q29 +ATOM 1123 SI3 Q011 1 17.047 24.720 -6.143 1.00 0.00 Q29 +ATOM 1124 SI4 Q011 1 20.358 23.220 -2.802 1.00 0.00 Q29 +ATOM 1125 O5 Q011 1 17.516 26.056 -12.755 1.00 0.00 Q29 +ATOM 1126 O6 Q011 1 13.669 24.533 -9.350 1.00 0.00 Q29 +ATOM 1127 O7 Q011 1 16.902 23.098 -5.999 1.00 0.00 Q29 +ATOM 1128 O8 Q011 1 18.716 26.210 -2.604 1.00 0.00 Q29 +ATOM 1129 O9 Q011 1 19.380 27.931 -12.743 1.00 0.00 Q29 +ATOM 1130 O10 Q011 1 15.285 26.700 -9.330 1.00 0.00 Q29 +ATOM 1131 O11 Q011 1 18.607 25.199 -6.010 1.00 0.00 Q29 +ATOM 1132 O12 Q011 1 14.566 23.788 -2.608 1.00 0.00 Q29 +ATOM 1133 O13 Q011 1 13.193 26.535 -10.995 1.00 0.00 Q29 +ATOM 1134 O14 Q011 1 16.483 25.047 -7.641 1.00 0.00 Q29 +ATOM 1135 O15 Q011 1 19.804 23.530 -4.308 1.00 0.00 Q29 +ATOM 1136 O16 Q011 1 15.942 22.167 -0.832 1.00 0.00 Q29 +ATOM 1137 O17 Q011 1 18.571 23.763 -11.765 1.00 0.00 Q29 +ATOM 1138 O18 Q011 1 12.825 26.808 -8.314 1.00 0.00 Q29 +ATOM 1139 O19 Q011 1 16.138 25.422 -4.972 1.00 0.00 Q29 +ATOM 1140 O20 Q011 1 19.354 23.844 -1.656 1.00 0.00 Q29 +ATOM 1141 SI21 Q011 1 17.382 24.889 -11.592 1.00 0.00 Q29 +ATOM 1142 SI22 Q011 1 19.068 27.964 -8.196 1.00 0.00 Q29 +ATOM 1143 SI23 Q011 1 15.001 26.593 -4.848 1.00 0.00 Q29 +ATOM 1144 SI24 Q011 1 18.358 25.133 -1.422 1.00 0.00 Q29 +ATOM 1145 SI25 Q011 1 13.489 27.491 -12.287 1.00 0.00 Q29 +ATOM 1146 SI26 Q011 1 16.734 26.118 -8.855 1.00 0.00 Q29 +ATOM 1147 SI27 Q011 1 20.052 24.626 -5.499 1.00 0.00 Q29 +ATOM 1148 SI28 Q011 1 16.023 23.234 -2.088 1.00 0.00 Q29 +ATOM 1149 O29 Q011 1 17.597 25.445 -10.065 1.00 0.00 Q29 +ATOM 1150 O30 Q011 1 19.301 28.581 -6.696 1.00 0.00 Q29 +ATOM 1151 O31 Q011 1 15.214 27.234 -3.353 1.00 0.00 Q29 +ATOM 1152 O32 Q011 1 18.497 25.761 0.097 1.00 0.00 Q29 +ATOM 1153 O33 Q011 1 15.885 24.209 -11.714 1.00 0.00 Q29 +ATOM 1154 O34 Q011 1 17.527 27.422 -8.266 1.00 0.00 Q29 +ATOM 1155 O35 Q011 1 13.492 25.965 -4.913 1.00 0.00 Q29 +ATOM 1156 O36 Q011 1 16.826 24.629 -1.747 1.00 0.00 Q29 +ATOM 1157 H37 Q011 1 17.322 28.122 -14.287 1.00 0.00 Q29 +ATOM 1158 H38 Q011 1 16.771 21.753 -0.545 1.00 0.00 Q29 +ATOM 1159 H39 Q011 1 14.301 26.817 -13.327 1.00 0.00 Q29 +ATOM 1160 H40 Q011 1 18.043 26.598 0.287 1.00 0.00 Q29 +ATOM 1161 SI1 Q011 1 24.989 27.517 -13.190 1.00 0.00 Q30 +ATOM 1162 SI2 Q011 1 21.080 26.087 -9.475 1.00 0.00 Q30 +ATOM 1163 SI3 Q011 1 24.391 24.723 -6.147 1.00 0.00 Q30 +ATOM 1164 SI4 Q011 1 27.701 23.176 -2.800 1.00 0.00 Q30 +ATOM 1165 O5 Q011 1 24.595 25.977 -12.797 1.00 0.00 Q30 +ATOM 1166 O6 Q011 1 21.021 24.464 -9.323 1.00 0.00 Q30 +ATOM 1167 O7 Q011 1 24.236 23.100 -6.010 1.00 0.00 Q30 +ATOM 1168 O8 Q011 1 26.196 26.164 -2.557 1.00 0.00 Q30 +ATOM 1169 O9 Q011 1 26.640 27.505 -13.213 1.00 0.00 Q30 +ATOM 1170 O10 Q011 1 22.610 26.644 -9.337 1.00 0.00 Q30 +ATOM 1171 O11 Q011 1 25.951 25.194 -5.986 1.00 0.00 Q30 +ATOM 1172 O12 Q011 1 21.884 23.800 -2.623 1.00 0.00 Q30 +ATOM 1173 O13 Q011 1 20.540 26.444 -10.979 1.00 0.00 Q30 +ATOM 1174 O14 Q011 1 23.848 25.033 -7.657 1.00 0.00 Q30 +ATOM 1175 O15 Q011 1 27.183 23.484 -4.326 1.00 0.00 Q30 +ATOM 1176 O16 Q011 1 23.276 22.210 -0.836 1.00 0.00 Q30 +ATOM 1177 O17 Q011 1 26.033 23.808 -11.967 1.00 0.00 Q30 +ATOM 1178 O18 Q011 1 20.154 26.744 -8.292 1.00 0.00 Q30 +ATOM 1179 O19 Q011 1 23.464 25.424 -4.989 1.00 0.00 Q30 +ATOM 1180 O20 Q011 1 26.626 23.729 -1.686 1.00 0.00 Q30 +ATOM 1181 SI21 Q011 1 24.773 24.832 -11.621 1.00 0.00 Q30 +ATOM 1182 SI22 Q011 1 26.327 28.016 -8.263 1.00 0.00 Q30 +ATOM 1183 SI23 Q011 1 22.321 26.591 -4.867 1.00 0.00 Q30 +ATOM 1184 SI24 Q011 1 25.717 25.074 -1.426 1.00 0.00 Q30 +ATOM 1185 SI25 Q011 1 20.863 27.434 -12.235 1.00 0.00 Q30 +ATOM 1186 SI26 Q011 1 24.073 26.089 -8.891 1.00 0.00 Q30 +ATOM 1187 SI27 Q011 1 27.404 24.616 -5.497 1.00 0.00 Q30 +ATOM 1188 SI28 Q011 1 23.345 23.253 -2.113 1.00 0.00 Q30 +ATOM 1189 O29 Q011 1 24.959 25.430 -10.101 1.00 0.00 Q30 +ATOM 1190 O30 Q011 1 26.597 28.567 -6.745 1.00 0.00 Q30 +ATOM 1191 O31 Q011 1 22.528 27.234 -3.372 1.00 0.00 Q30 +ATOM 1192 O32 Q011 1 25.824 25.657 0.113 1.00 0.00 Q30 +ATOM 1193 O33 Q011 1 23.309 24.090 -11.607 1.00 0.00 Q30 +ATOM 1194 O34 Q011 1 24.800 27.446 -8.339 1.00 0.00 Q30 +ATOM 1195 O35 Q011 1 20.813 25.960 -4.929 1.00 0.00 Q30 +ATOM 1196 O36 Q011 1 24.181 24.642 -1.824 1.00 0.00 Q30 +ATOM 1197 H37 Q011 1 24.427 27.922 -14.500 1.00 0.00 Q30 +ATOM 1198 H38 Q011 1 24.110 21.808 -0.547 1.00 0.00 Q30 +ATOM 1199 H39 Q011 1 21.644 26.772 -13.305 1.00 0.00 Q30 +ATOM 1200 H40 Q011 1 25.414 26.516 0.302 1.00 0.00 Q30 +ATOM 1201 SI1 Q011 1 -5.981 32.355 -12.950 1.00 0.00 Q31 +ATOM 1202 SI2 Q011 1 -9.849 30.826 -9.497 1.00 0.00 Q31 +ATOM 1203 SI3 Q011 1 -6.572 29.426 -6.131 1.00 0.00 Q31 +ATOM 1204 SI4 Q011 1 -3.275 27.839 -2.801 1.00 0.00 Q31 +ATOM 1205 O5 Q011 1 -6.235 30.747 -12.754 1.00 0.00 Q31 +ATOM 1206 O6 Q011 1 -9.873 29.207 -9.368 1.00 0.00 Q31 +ATOM 1207 O7 Q011 1 -6.754 27.807 -5.976 1.00 0.00 Q31 +ATOM 1208 O8 Q011 1 -4.868 30.835 -2.584 1.00 0.00 Q31 +ATOM 1209 O9 Q011 1 -4.375 32.623 -12.732 1.00 0.00 Q31 +ATOM 1210 O10 Q011 1 -8.346 31.426 -9.285 1.00 0.00 Q31 +ATOM 1211 O11 Q011 1 -5.011 29.886 -6.022 1.00 0.00 Q31 +ATOM 1212 O12 Q011 1 -9.022 28.597 -2.514 1.00 0.00 Q31 +ATOM 1213 O13 Q011 1 -10.429 31.205 -10.989 1.00 0.00 Q31 +ATOM 1214 O14 Q011 1 -7.143 29.766 -7.623 1.00 0.00 Q31 +ATOM 1215 O15 Q011 1 -3.825 28.178 -4.305 1.00 0.00 Q31 +ATOM 1216 O16 Q011 1 -7.615 26.907 -0.817 1.00 0.00 Q31 +ATOM 1217 O17 Q011 1 -5.190 28.462 -11.771 1.00 0.00 Q31 +ATOM 1218 O18 Q011 1 -10.785 31.363 -8.274 1.00 0.00 Q31 +ATOM 1219 O19 Q011 1 -7.414 30.176 -4.942 1.00 0.00 Q31 +ATOM 1220 O20 Q011 1 -4.260 28.459 -1.639 1.00 0.00 Q31 +ATOM 1221 SI21 Q011 1 -6.387 29.583 -11.591 1.00 0.00 Q31 +ATOM 1222 SI22 Q011 1 -4.559 32.669 -8.188 1.00 0.00 Q31 +ATOM 1223 SI23 Q011 1 -8.581 31.316 -4.810 1.00 0.00 Q31 +ATOM 1224 SI24 Q011 1 -5.179 29.794 -1.361 1.00 0.00 Q31 +ATOM 1225 SI25 Q011 1 -10.109 32.086 -12.329 1.00 0.00 Q31 +ATOM 1226 SI26 Q011 1 -6.896 30.833 -8.839 1.00 0.00 Q31 +ATOM 1227 SI27 Q011 1 -3.590 29.290 -5.488 1.00 0.00 Q31 +ATOM 1228 SI28 Q011 1 -7.561 28.011 -2.043 1.00 0.00 Q31 +ATOM 1229 O29 Q011 1 -6.093 30.140 -10.077 1.00 0.00 Q31 +ATOM 1230 O30 Q011 1 -4.335 33.279 -6.682 1.00 0.00 Q31 +ATOM 1231 O31 Q011 1 -8.399 32.013 -3.334 1.00 0.00 Q31 +ATOM 1232 O32 Q011 1 -4.958 30.421 0.149 1.00 0.00 Q31 +ATOM 1233 O33 Q011 1 -7.894 28.895 -11.692 1.00 0.00 Q31 +ATOM 1234 O34 Q011 1 -6.100 32.136 -8.261 1.00 0.00 Q31 +ATOM 1235 O35 Q011 1 -10.041 30.592 -4.849 1.00 0.00 Q31 +ATOM 1236 O36 Q011 1 -6.737 29.375 -1.654 1.00 0.00 Q31 +ATOM 1237 H37 Q011 1 -6.419 32.806 -14.292 1.00 0.00 Q31 +ATOM 1238 H38 Q011 1 -6.789 26.445 -0.605 1.00 0.00 Q31 +ATOM 1239 H39 Q011 1 -9.035 31.466 -13.137 1.00 0.00 Q31 +ATOM 1240 H40 Q011 1 -5.408 31.253 0.366 1.00 0.00 Q31 +ATOM 1241 SI1 Q011 1 1.391 32.283 -12.984 1.00 0.00 Q32 +ATOM 1242 SI2 Q011 1 -2.557 30.802 -9.489 1.00 0.00 Q32 +ATOM 1243 SI3 Q011 1 0.747 29.371 -6.150 1.00 0.00 Q32 +ATOM 1244 SI4 Q011 1 4.067 27.847 -2.813 1.00 0.00 Q32 +ATOM 1245 O5 Q011 1 1.153 30.676 -12.770 1.00 0.00 Q32 +ATOM 1246 O6 Q011 1 -2.608 29.179 -9.327 1.00 0.00 Q32 +ATOM 1247 O7 Q011 1 0.590 27.749 -6.007 1.00 0.00 Q32 +ATOM 1248 O8 Q011 1 2.439 30.832 -2.610 1.00 0.00 Q32 +ATOM 1249 O9 Q011 1 3.002 32.557 -12.814 1.00 0.00 Q32 +ATOM 1250 O10 Q011 1 -1.025 31.353 -9.326 1.00 0.00 Q32 +ATOM 1251 O11 Q011 1 2.307 29.848 -6.011 1.00 0.00 Q32 +ATOM 1252 O12 Q011 1 -1.749 28.421 -2.608 1.00 0.00 Q32 +ATOM 1253 O13 Q011 1 -3.134 31.152 -10.984 1.00 0.00 Q32 +ATOM 1254 O14 Q011 1 0.189 29.699 -7.650 1.00 0.00 Q32 +ATOM 1255 O15 Q011 1 3.522 28.162 -4.322 1.00 0.00 Q32 +ATOM 1256 O16 Q011 1 -0.327 26.816 -0.844 1.00 0.00 Q32 +ATOM 1257 O17 Q011 1 2.237 28.394 -11.784 1.00 0.00 Q32 +ATOM 1258 O18 Q011 1 -3.479 31.448 -8.298 1.00 0.00 Q32 +ATOM 1259 O19 Q011 1 -0.165 30.080 -4.986 1.00 0.00 Q32 +ATOM 1260 O20 Q011 1 3.053 28.461 -1.671 1.00 0.00 Q32 +ATOM 1261 SI21 Q011 1 1.052 29.522 -11.593 1.00 0.00 Q32 +ATOM 1262 SI22 Q011 1 2.746 32.643 -8.208 1.00 0.00 Q32 +ATOM 1263 SI23 Q011 1 -1.308 31.247 -4.862 1.00 0.00 Q32 +ATOM 1264 SI24 Q011 1 2.069 29.758 -1.430 1.00 0.00 Q32 +ATOM 1265 SI25 Q011 1 -2.877 32.142 -12.259 1.00 0.00 Q32 +ATOM 1266 SI26 Q011 1 0.429 30.775 -8.862 1.00 0.00 Q32 +ATOM 1267 SI27 Q011 1 3.752 29.271 -5.506 1.00 0.00 Q32 +ATOM 1268 SI28 Q011 1 -0.279 27.885 -2.100 1.00 0.00 Q32 +ATOM 1269 O29 Q011 1 1.287 30.104 -10.076 1.00 0.00 Q32 +ATOM 1270 O30 Q011 1 2.988 33.262 -6.709 1.00 0.00 Q32 +ATOM 1271 O31 Q011 1 -1.083 31.882 -3.367 1.00 0.00 Q32 +ATOM 1272 O32 Q011 1 2.217 30.379 0.091 1.00 0.00 Q32 +ATOM 1273 O33 Q011 1 -0.446 28.842 -11.687 1.00 0.00 Q32 +ATOM 1274 O34 Q011 1 1.211 32.083 -8.269 1.00 0.00 Q32 +ATOM 1275 O35 Q011 1 -2.815 30.609 -4.903 1.00 0.00 Q32 +ATOM 1276 O36 Q011 1 0.532 29.278 -1.765 1.00 0.00 Q32 +ATOM 1277 H37 Q011 1 0.910 32.728 -14.314 1.00 0.00 Q32 +ATOM 1278 H38 Q011 1 0.512 26.409 -0.575 1.00 0.00 Q32 +ATOM 1279 H39 Q011 1 -2.109 31.490 -13.346 1.00 0.00 Q32 +ATOM 1280 H40 Q011 1 1.775 31.221 0.285 1.00 0.00 Q32 +ATOM 1281 SI1 Q011 1 8.715 32.278 -12.985 1.00 0.00 Q33 +ATOM 1282 SI2 Q011 1 4.765 30.781 -9.495 1.00 0.00 Q33 +ATOM 1283 SI3 Q011 1 8.071 29.362 -6.148 1.00 0.00 Q33 +ATOM 1284 SI4 Q011 1 11.384 27.834 -2.813 1.00 0.00 Q33 +ATOM 1285 O5 Q011 1 8.468 30.674 -12.767 1.00 0.00 Q33 +ATOM 1286 O6 Q011 1 4.700 29.156 -9.343 1.00 0.00 Q33 +ATOM 1287 O7 Q011 1 7.925 27.738 -6.004 1.00 0.00 Q33 +ATOM 1288 O8 Q011 1 9.754 30.822 -2.610 1.00 0.00 Q33 +ATOM 1289 O9 Q011 1 10.329 32.541 -12.823 1.00 0.00 Q33 +ATOM 1290 O10 Q011 1 6.294 31.335 -9.325 1.00 0.00 Q33 +ATOM 1291 O11 Q011 1 9.630 29.843 -6.010 1.00 0.00 Q33 +ATOM 1292 O12 Q011 1 5.593 28.420 -2.609 1.00 0.00 Q33 +ATOM 1293 O13 Q011 1 4.204 31.141 -10.993 1.00 0.00 Q33 +ATOM 1294 O14 Q011 1 7.509 29.686 -7.647 1.00 0.00 Q33 +ATOM 1295 O15 Q011 1 10.839 28.154 -4.321 1.00 0.00 Q33 +ATOM 1296 O16 Q011 1 6.972 26.791 -0.842 1.00 0.00 Q33 +ATOM 1297 O17 Q011 1 9.573 28.398 -11.782 1.00 0.00 Q33 +ATOM 1298 O18 Q011 1 3.838 31.431 -8.310 1.00 0.00 Q33 +ATOM 1299 O19 Q011 1 7.160 30.068 -4.984 1.00 0.00 Q33 +ATOM 1300 O20 Q011 1 10.380 28.454 -1.666 1.00 0.00 Q33 +ATOM 1301 SI21 Q011 1 8.379 29.517 -11.591 1.00 0.00 Q33 +ATOM 1302 SI22 Q011 1 10.062 32.639 -8.210 1.00 0.00 Q33 +ATOM 1303 SI23 Q011 1 6.020 31.237 -4.861 1.00 0.00 Q33 +ATOM 1304 SI24 Q011 1 9.393 29.748 -1.425 1.00 0.00 Q33 +ATOM 1305 SI25 Q011 1 4.489 32.109 -12.278 1.00 0.00 Q33 +ATOM 1306 SI26 Q011 1 7.749 30.763 -8.858 1.00 0.00 Q33 +ATOM 1307 SI27 Q011 1 11.073 29.263 -5.504 1.00 0.00 Q33 +ATOM 1308 SI28 Q011 1 7.050 27.864 -2.092 1.00 0.00 Q33 +ATOM 1309 O29 Q011 1 8.609 30.094 -10.073 1.00 0.00 Q33 +ATOM 1310 O30 Q011 1 10.304 33.257 -6.711 1.00 0.00 Q33 +ATOM 1311 O31 Q011 1 6.245 31.863 -3.362 1.00 0.00 Q33 +ATOM 1312 O32 Q011 1 9.545 30.375 0.094 1.00 0.00 Q33 +ATOM 1313 O33 Q011 1 6.889 28.822 -11.691 1.00 0.00 Q33 +ATOM 1314 O34 Q011 1 8.529 32.075 -8.269 1.00 0.00 Q33 +ATOM 1315 O35 Q011 1 4.515 30.599 -4.922 1.00 0.00 Q33 +ATOM 1316 O36 Q011 1 7.858 29.256 -1.747 1.00 0.00 Q33 +ATOM 1317 H37 Q011 1 8.230 32.725 -14.312 1.00 0.00 Q33 +ATOM 1318 H38 Q011 1 7.801 26.374 -0.560 1.00 0.00 Q33 +ATOM 1319 H39 Q011 1 5.306 31.450 -13.324 1.00 0.00 Q33 +ATOM 1320 H40 Q011 1 9.099 31.215 0.287 1.00 0.00 Q33 +ATOM 1321 SI1 Q011 1 16.102 32.298 -12.949 1.00 0.00 Q34 +ATOM 1322 SI2 Q011 1 12.085 30.774 -9.491 1.00 0.00 Q34 +ATOM 1323 SI3 Q011 1 15.393 29.344 -6.145 1.00 0.00 Q34 +ATOM 1324 SI4 Q011 1 18.710 27.839 -2.808 1.00 0.00 Q34 +ATOM 1325 O5 Q011 1 15.854 30.689 -12.754 1.00 0.00 Q34 +ATOM 1326 O6 Q011 1 12.014 29.149 -9.342 1.00 0.00 Q34 +ATOM 1327 O7 Q011 1 15.247 27.722 -6.001 1.00 0.00 Q34 +ATOM 1328 O8 Q011 1 17.030 30.801 -2.626 1.00 0.00 Q34 +ATOM 1329 O9 Q011 1 17.711 32.568 -12.734 1.00 0.00 Q34 +ATOM 1330 O10 Q011 1 13.619 31.320 -9.323 1.00 0.00 Q34 +ATOM 1331 O11 Q011 1 16.954 29.819 -6.013 1.00 0.00 Q34 +ATOM 1332 O12 Q011 1 12.913 28.400 -2.613 1.00 0.00 Q34 +ATOM 1333 O13 Q011 1 11.524 31.128 -10.991 1.00 0.00 Q34 +ATOM 1334 O14 Q011 1 14.827 29.665 -7.643 1.00 0.00 Q34 +ATOM 1335 O15 Q011 1 18.158 28.147 -4.314 1.00 0.00 Q34 +ATOM 1336 O16 Q011 1 14.279 26.766 -0.839 1.00 0.00 Q34 +ATOM 1337 O17 Q011 1 16.914 28.394 -11.765 1.00 0.00 Q34 +ATOM 1338 O18 Q011 1 11.158 31.430 -8.310 1.00 0.00 Q34 +ATOM 1339 O19 Q011 1 14.482 30.054 -4.981 1.00 0.00 Q34 +ATOM 1340 O20 Q011 1 17.697 28.451 -1.663 1.00 0.00 Q34 +ATOM 1341 SI21 Q011 1 15.723 29.519 -11.593 1.00 0.00 Q34 +ATOM 1342 SI22 Q011 1 17.399 32.587 -8.197 1.00 0.00 Q34 +ATOM 1343 SI23 Q011 1 13.342 31.222 -4.857 1.00 0.00 Q34 +ATOM 1344 SI24 Q011 1 16.697 29.736 -1.426 1.00 0.00 Q34 +ATOM 1345 SI25 Q011 1 11.812 32.090 -12.279 1.00 0.00 Q34 +ATOM 1346 SI26 Q011 1 15.070 30.741 -8.854 1.00 0.00 Q34 +ATOM 1347 SI27 Q011 1 18.400 29.245 -5.506 1.00 0.00 Q34 +ATOM 1348 SI28 Q011 1 14.365 27.840 -2.089 1.00 0.00 Q34 +ATOM 1349 O29 Q011 1 15.937 30.078 -10.066 1.00 0.00 Q34 +ATOM 1350 O30 Q011 1 17.633 33.228 -6.706 1.00 0.00 Q34 +ATOM 1351 O31 Q011 1 13.562 31.850 -3.358 1.00 0.00 Q34 +ATOM 1352 O32 Q011 1 16.853 30.375 0.087 1.00 0.00 Q34 +ATOM 1353 O33 Q011 1 14.228 28.835 -11.712 1.00 0.00 Q34 +ATOM 1354 O34 Q011 1 15.859 32.041 -8.253 1.00 0.00 Q34 +ATOM 1355 O35 Q011 1 11.836 30.588 -4.917 1.00 0.00 Q34 +ATOM 1356 O36 Q011 1 15.162 29.233 -1.729 1.00 0.00 Q34 +ATOM 1357 H37 Q011 1 15.659 32.753 -14.288 1.00 0.00 Q34 +ATOM 1358 H38 Q011 1 15.109 26.359 -0.544 1.00 0.00 Q34 +ATOM 1359 H39 Q011 1 12.635 31.432 -13.320 1.00 0.00 Q34 +ATOM 1360 H40 Q011 1 16.401 31.213 0.276 1.00 0.00 Q34 +ATOM 1361 SI1 Q011 1 23.335 32.138 -13.185 1.00 0.00 Q35 +ATOM 1362 SI2 Q011 1 19.421 30.720 -9.479 1.00 0.00 Q35 +ATOM 1363 SI3 Q011 1 22.737 29.348 -6.153 1.00 0.00 Q35 +ATOM 1364 SI4 Q011 1 26.054 27.804 -2.800 1.00 0.00 Q35 +ATOM 1365 O5 Q011 1 22.937 30.599 -12.796 1.00 0.00 Q35 +ATOM 1366 O6 Q011 1 19.363 29.095 -9.330 1.00 0.00 Q35 +ATOM 1367 O7 Q011 1 22.582 27.725 -6.013 1.00 0.00 Q35 +ATOM 1368 O8 Q011 1 24.560 30.798 -2.553 1.00 0.00 Q35 +ATOM 1369 O9 Q011 1 24.985 32.119 -13.210 1.00 0.00 Q35 +ATOM 1370 O10 Q011 1 20.951 31.276 -9.339 1.00 0.00 Q35 +ATOM 1371 O11 Q011 1 24.297 29.817 -5.990 1.00 0.00 Q35 +ATOM 1372 O12 Q011 1 20.234 28.425 -2.625 1.00 0.00 Q35 +ATOM 1373 O13 Q011 1 18.884 31.081 -10.983 1.00 0.00 Q35 +ATOM 1374 O14 Q011 1 22.190 29.659 -7.661 1.00 0.00 Q35 +ATOM 1375 O15 Q011 1 25.530 28.112 -4.324 1.00 0.00 Q35 +ATOM 1376 O16 Q011 1 21.631 26.843 -0.837 1.00 0.00 Q35 +ATOM 1377 O17 Q011 1 24.378 28.431 -11.965 1.00 0.00 Q35 +ATOM 1378 O18 Q011 1 18.492 31.374 -8.295 1.00 0.00 Q35 +ATOM 1379 O19 Q011 1 21.812 30.053 -4.996 1.00 0.00 Q35 +ATOM 1380 O20 Q011 1 24.982 28.358 -1.685 1.00 0.00 Q35 +ATOM 1381 SI21 Q011 1 23.117 29.454 -11.619 1.00 0.00 Q35 +ATOM 1382 SI22 Q011 1 24.671 32.640 -8.265 1.00 0.00 Q35 +ATOM 1383 SI23 Q011 1 20.668 31.218 -4.874 1.00 0.00 Q35 +ATOM 1384 SI24 Q011 1 24.073 29.704 -1.428 1.00 0.00 Q35 +ATOM 1385 SI25 Q011 1 19.200 32.071 -12.243 1.00 0.00 Q35 +ATOM 1386 SI26 Q011 1 22.414 30.718 -8.892 1.00 0.00 Q35 +ATOM 1387 SI27 Q011 1 25.750 29.241 -5.497 1.00 0.00 Q35 +ATOM 1388 SI28 Q011 1 21.698 27.883 -2.116 1.00 0.00 Q35 +ATOM 1389 O29 Q011 1 23.301 30.057 -10.101 1.00 0.00 Q35 +ATOM 1390 O30 Q011 1 24.941 33.205 -6.752 1.00 0.00 Q35 +ATOM 1391 O31 Q011 1 20.872 31.839 -3.369 1.00 0.00 Q35 +ATOM 1392 O32 Q011 1 24.172 30.287 0.112 1.00 0.00 Q35 +ATOM 1393 O33 Q011 1 21.654 28.712 -11.605 1.00 0.00 Q35 +ATOM 1394 O34 Q011 1 23.142 32.072 -8.335 1.00 0.00 Q35 +ATOM 1395 O35 Q011 1 19.162 30.580 -4.937 1.00 0.00 Q35 +ATOM 1396 O36 Q011 1 22.537 29.272 -1.831 1.00 0.00 Q35 +ATOM 1397 H37 Q011 1 22.772 32.548 -14.494 1.00 0.00 Q35 +ATOM 1398 H38 Q011 1 22.466 26.441 -0.549 1.00 0.00 Q35 +ATOM 1399 H39 Q011 1 19.967 31.403 -13.320 1.00 0.00 Q35 +ATOM 1400 H40 Q011 1 23.759 31.144 0.299 1.00 0.00 Q35 +ATOM 1401 SI1 Q011 1 -7.514 36.896 -13.099 1.00 0.00 Q36 +ATOM 1402 SI2 Q011 1 -11.517 35.441 -9.505 1.00 0.00 Q36 +ATOM 1403 SI3 Q011 1 -8.228 34.067 -6.126 1.00 0.00 Q36 +ATOM 1404 SI4 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1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + + 0 0 !NUMLP NUMLPH + + 0 !NCRTERM: cross-terms + diff --git a/charmm/toppar/silicates/toppar/par_silicates.inp b/charmm/toppar/silicates/toppar/par_silicates.inp new file mode 100644 index 00000000..b5f2355e --- /dev/null +++ b/charmm/toppar/silicates/toppar/par_silicates.inp @@ -0,0 +1,153 @@ +* <<<<<>>>>> +* Alexander D. MacKerell Jr., Pedro Lopes and Mouhsine Tazi +* July 2005 +*All comments to adm jr. charmm forum: www.charmm.org +* + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +! atom type Kb b0 +! +Si OSiE 302.000 1.698 +AL OSIE 302.000 1.698 +Si OSiA 302.000 1.698 +Si OSiH 325.000 1.68 +Al OAl 302.000 2.00 +Sih3 OSiE 304.000 1.682 +HSiO OSiH 566.000 0.975 +HAl OAl 566.000 0.9600 +Al HAl 450.000 0.9572 +SI HSIA 204.0 1.489 +HSiA Sih3 204.0 1.489 +Si OAl 304.000 1.682 +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +OSiE Si OSiE 30.000 117.00 !quartz, from sim1 +OSiE Sih3 OSiE 30.000 121.50 !quartz, from sim1 +Si OSiE Sih3 34.000 150.50 !quartz, from sim1 +Si OSiE Si 34.000 150.00 !quartz, from sim1 +Si OSiA Si 34.000 150.00 !quartz, from sim1 +OSIA SI OSIH 32.000 126.00 !quartz, from sim1 +OSIA SI OSIA 30.000 121.50 !quartz, from sim1 +OSIA SI OSIE 30.000 121.50 !quartz, from sim1 +Sih3 OSiE Sih3 34.000 159.00 !quartz, from sim1 +HSiA Sih3 HSiA 30.00 119.00 !quartz, from sim1 +HSiA Sih3 OSiE 44.000 118.00 !quartz, from sim1 +Si OSiH HSiO 34.00 122.50 !122 quartz, from sim2 +OSiE Si OSiH 32.000 126.00 !quartz, from sim2 +OSiH Si OSiH 30.000 117.00 !quartz, from sim2 +Al OAl Al 30.000 98.00 +Al OAl Si 30.000 117.00 +OAl Si OSiE 30.000 117.00 +HAl OAl Al 35.000 93.40 +OAl Al HAl 35.000 93.40 +OAl Al OAl 30.000 90.00 +OSIE AL OSIE 30.000 117.00 +OSIE AL OAL 30.000 117.00 +OSIE AL HAL 30.00 119.00 +AL OSIE SI 30.000 117.00 +AL OSIE AL 30.000 117.00 +OSIE SI HSIA 44.000 118.00 +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +OSiE Si OSIE Sih3 0.18000 5 0.00 ! quartz, from sim1 +OSIE SI OSIE SI 0.18000 5 0.00 ! quartz, from sim1 +OSIA SI OSIA SI 0.18000 5 0.00 ! quartz, from sim1 +OSIE SI OSIA SI 0.18000 5 0.00 ! quartz, from sim1 +OSIE SIH3 OSIE SI 0.18000 5 0.00 ! quartz, from sim1 +OSiH Si OSIE Sih3 0.12000 5 0.00 ! quartz, from sim1 +SI OSIE SI OSIA 0.12000 5 0.00 ! quartz, from sim1 +HSiA Sih3 OSiE Si 0.20000 3 0.00 ! quartz, from sim1 +HSiA Sih3 OSiE Sih3 0.20000 3 0.00 ! quartz, from sim1 +OSiE Si OSiH HSiO 0.30000 3 0.00 ! quartz, from sim2 +OSiH Si OSiH HSiO 0.35000 3 0.00 ! quartz, from sim2 +SI OSIA SI OSIH 0.12000 5 0.00 ! quartz, from sim1 +SIH3 OSIE SIH3 OSIE 0.18000 5 0.00 ! quartz, from sim1 +SI OSIE SI HSIA 0.20000 3 0.00 +SI OSIE SI OSIH 0.18000 5 0.00 +SIH3 OSIE SI OSIA 0.18000 5 0.00 +OSIA SI OSIH HSIO 0.35000 3 0.00 ! quartz, from sim2 +OAl Al OAl HAl 0.10000 3 0.00 +Al OAl Si OSIE 0.10000 3 0.00 +Al OAl Al OAl 0.10000 3 0.00 +AL OAL AL HAL 0.30000 3 0.00 +SI OAL AL OAL 0.10000 3 0.00 +SI OSIE SI OAL 0.10000 3 0.00 +SI OAL AL HAL 0.30000 3 0.00 +HAL OAL AL HAL 0.30000 3 0.00 +AL OSIE SI OSIE 0.10000 3 0.00 +AL OSIE AL OSIE 0.10000 3 0.00 +AL OSIE AL OAL 0.10000 3 0.00 +AL OAL AL OSIE 0.10000 3 0.00 +AL OSIE AL HAL 0.30000 3 0.00 +SI OSIE AL OSIE 0.30000 3 0.00 +SI OSIE AL OAL 0.30000 3 0.00 +SI OSIE AL HAL 0.10000 3 0.00 +OSIE AL OAL HAL 0.10000 3 0.00 +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel fswitch vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +HSiO 0.000000 -0.0460 0.2245 ! from proteins +HSiA 0.000000 -0.022 1.3200 ! from alkane +HAl 0.000000 -0.022 1.3200 ! from alkane +AL 0.000000 -0.650 2.2000 ! relative to Phos +Si 0.000000 -0.600 2.2000 ! relative to Phos +Sih3 0.000000 -0.600 2.2000 ! relative to Phos +OSiH 0.000000 -0.1521 1.7700 ! from proteins +OSiE 0.000000 -0.1521 1.7700 ! from nucleic acids +OSiA 0.000000 -0.1521 1.7700 ! from nucleic acids +OAl 0.000000 -0.1521 1.7700 ! from proteins +! +HT 0.0 -0.046 0.2245 ! TIP3P water +OT 0.0 -0.1521 1.7682 ! TIP3P water +DUM 0.0 -0.0000 0.0000 ! dummy atom + + +END diff --git a/charmm/toppar/silicates/toppar/top_silicates.inp b/charmm/toppar/silicates/toppar/top_silicates.inp new file mode 100644 index 00000000..b7381847 --- /dev/null +++ b/charmm/toppar/silicates/toppar/top_silicates.inp @@ -0,0 +1,371 @@ +* <<<<<>>>>> +* Alexander D. MacKerell Jr., Pedro Lopes and Mouhsine Tazi +* July 2005 +*All comments to adm jr. charmm forum: www.charmm.org +* +27 1 + +! +!topology for development of quartz and kaolinite parameters +! +MASS 1 HT 1.008000 H ! TIPS3P WATER HYDROGEN +MASS 2 OT 15.99940 O ! TIPS3P WATER OXYGEN +MASS 3 DUM 1.008000 H ! dummy atom +MASS 100 HSiO 1.008000 H ! Si hydroxyl hydrogen; +MASS 101 HSiA 1.008000 H ! Si aliphatic hydrogen; +MASS 102 HAl 1.008000 H ! Si aliphatic hydrogen; +MASS 103 OSiH 15.999000 O ! Si Hydroxyl Oxygen; +MASS 104 OSiE 15.999000 O ! Si Ester Oxygen; +MASS 105 OSiA 15.999000 O ! Si Ester Oxygen; +MASS 106 OAl 15.999000 O ! Si Hydroxyl Oxygen; +MASS 107 Si 28.085500 Si ! Si Atom; +MASS 108 Sih3 28.085500 Si ! Si Atom; +MASS 110 Al 26.981540 AL ! Aluminum Atom; + +AUTO ANGLES DIHE + +RESI SiO4 0.00 +GROUP +ATOM Si2 Si 0.76 ! OH +ATOM O1 OSiH -0.51 ! | +ATOM O3 OSiH -0.51 ! | +ATOM O4 OSiH -0.51 ! Si +ATOM O5 OSiH -0.51 ! /|\ +ATOM H6 HSiO 0.32 ! / | \ +ATOM H7 HSiO 0.32 ! OH OH OH +ATOM H8 HSiO 0.32 ! +ATOM H9 HSiO 0.32 ! +BOND Si2 O1 Si2 O3 Si2 O5 Si2 O4 +BOND O1 H6 O3 H9 O5 H8 O4 H7 + +RESI SiM1 0.00 +GROUP +ATOM Si2 Si 1.00 ! +ATOM Si6 Si 0.80 ! +ATOM Si7 Si 0.80 ! H1 H3 +ATOM O5 OSiE -0.70 ! \ / +ATOM O4 OSiE -0.70 ! H3Si7 Si2 Si6H3:8,9,10 +ATOM H1 HSiA -0.15 ! \ / \ / +ATOM H3 HSiA -0.15 ! O5 O4 +ATOM H8 HSiA -0.15 ! +ATOM H9 HSiA -0.15 !H:11,12,13 +ATOM H10 HSiA -0.15 ! +ATOM H11 HSiA -0.15 ! +ATOM H12 HSiA -0.15 ! +ATOM H13 HSiA -0.15 ! +BOND Si2 H1 Si2 H3 Si2 O4 Si2 O5 +BOND Si6 O4 Si6 H8 Si6 H9 Si6 H10 +BOND Si7 O5 Si7 H11 Si7 H12 Si7 H13 + +RESI SiM2 0.00 +GROUP +ATOM Si2 Si 1.08 ! +ATOM O1 OSiE -0.70 ! +ATOM O3 OSiE -0.70 ! +ATOM O4 OSiH -0.51 ! H14 H15 +ATOM H14 HSiO 0.32 ! | | +ATOM O5 OSiH -0.51 ! O4 O5 +ATOM H15 HSiO 0.32 ! \ / +ATOM Si6 Sih3 0.80 ! H3-Si10 Si2 Si6-H7,8,9 +ATOM H7 HSiA -0.15 ! \ / \ / +ATOM H8 HSiA -0.15 ! O1 O3 +ATOM H9 HSiA -0.15 ! +ATOM Si10 Sih3 0.80 ! H3:11,12,13 +ATOM H11 HSiA -0.15 ! +ATOM H12 HSiA -0.15 ! +ATOM H13 HSiA -0.15 ! +BOND Si2 O1 Si2 O3 Si2 O4 Si2 O5 +BOND O3 Si6 Si6 H7 Si6 H8 Si6 H9 +BOND O1 Si10 Si10 H11 Si10 H12 Si10 H13 +BOND O4 H14 O5 H15 + +RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI DUM 0.00 ! DUMMY ATOM +GROUP +ATOM DUM DUM 0.00 +PATCHING FIRST NONE LAST NONE + +RESI Q011 0.0 + +ATOM SI1 Sih3 0.80 +ATOM SI2 Si 1.08 +ATOM SI3 Si 1.08 +ATOM SI4 Si 1.08 +ATOM O5 OSiE -0.53 +ATOM O6 OSiE -0.53 +ATOM O7 OSiE -0.53 +ATOM O8 OSiE -0.53 +ATOM O9 OSiE -0.53 +ATOM O10 OSiE -0.53 +ATOM O11 OSiE -0.53 +ATOM O12 OSiE -0.53 +ATOM O13 OSiE -0.53 +ATOM O14 OSiE -0.53 +ATOM O15 OSiE -0.53 +ATOM O16 OSiH -0.54 +ATOM O17 OSiE -0.53 +ATOM O18 OSiE -0.53 +ATOM O19 OSiE -0.53 +ATOM O20 OSiE -0.53 +ATOM SI21 Si 1.08 +ATOM SI22 Si 1.08 +ATOM SI23 Si 1.08 +ATOM SI24 Si 1.08 +ATOM SI25 Sih3 0.80 +ATOM SI26 Si 1.08 +ATOM SI27 Si 1.08 +ATOM SI28 Si 1.08 +ATOM O29 OSiE -0.53 +ATOM O30 OSiE -0.53 +ATOM O31 OSiE -0.53 +ATOM O32 OSiH -0.54 +ATOM O33 OSiE -0.53 +ATOM O34 OSiE -0.53 +ATOM O35 OSiE -0.53 +ATOM O36 OSiE -0.53 +ATOM H37 HSiA -0.15 +ATOM H38 HSiO 0.32 +ATOM H39 HSiA -0.15 +ATOM H40 HSiO 0.32 + +BOND O5 SI1 +BOND O9 SI1 +BOND H37 SI1 +BOND O6 SI2 +BOND O10 SI2 +BOND O13 SI2 +BOND O18 SI2 +BOND O7 SI3 +BOND O11 SI3 +BOND O14 SI3 +BOND O19 SI3 +BOND O15 SI4 +BOND O20 SI4 +BOND SI21 O5 +BOND SI24 O8 +BOND SI26 O10 +BOND SI27 O11 +BOND SI28 O12 +BOND SI25 O13 +BOND SI26 O14 +BOND SI27 O15 +BOND SI28 O16 +BOND SI21 O17 +BOND SI23 O19 +BOND SI24 O20 +BOND O29 SI21 +BOND O33 SI21 +BOND O30 SI22 +BOND O34 SI22 +BOND O31 SI23 +BOND O35 SI23 +BOND O32 SI24 +BOND O36 SI24 +BOND H39 SI25 +BOND O29 SI26 +BOND O34 SI26 +BOND O36 SI28 +BOND H40 O32 +BOND O16 H38 + +! Patches to finish Quartz surface + +! Patch 011A between |_1||_2| along U + +PRES 011A 0.00 +BOND 1SI4 2O12 +BOND 1SI27 2O35 +BOND 1SI22 2O18 +BOND 1O9 2SI25 + +! Angles along XX +ANGLE 1O15 1SI4 2O12 +ANGLE 1O20 1SI4 2O12 +ANGLE 1SI1 1O9 2SI25 +ANGLE 2SI28 2O12 1SI4 +ANGLE 2SI2 2O18 1SI22 +ANGLE 1O30 1SI22 2O18 +ANGLE 1O34 1SI22 2O18 +ANGLE 2O13 2SI25 1O9 +ANGLE 2H39 2SI25 1O9 +ANGLE 1O11 1SI27 2O35 +ANGLE 1O15 1SI27 2O35 +ANGLE 2SI23 2O35 1SI27 + +! Dihedrals along XX +DIHEDRAL 1O5 1SI1 1O9 2SI25 +DIHEDRAL 1H37 1SI1 1O9 2SI25 +DIHEDRAL 2O6 2SI2 2O18 1SI22 +DIHEDRAL 2O10 2SI2 2O18 1SI22 +DIHEDRAL 2O13 2SI2 2O18 1SI22 +DIHEDRAL 2O12 1SI4 1O15 1SI27 +DIHEDRAL 2O12 1SI4 1O20 1SI24 +DIHEDRAL 1SI3 1O11 1SI27 2O35 +DIHEDRAL 1SI4 2O12 2SI28 2O16 +DIHEDRAL 1SI4 2O12 2SI28 2O36 +DIHEDRAL 2SI2 2O13 2SI25 1O9 +DIHEDRAL 1SI4 1O15 1SI27 2O35 +DIHEDRAL 2O18 1SI22 1O34 1SI26 +DIHEDRAL 2O19 2SI23 2O35 1SI27 +DIHEDRAL 2O31 2SI23 2O35 1SI27 +DIHEDRAL 1O15 1SI4 2O12 2SI28 +DIHEDRAL 1O20 1SI4 2O12 2SI28 +DIHEDRAL 1SI1 1O9 2SI25 2O13 +DIHEDRAL 1SI1 1O9 2SI25 2H39 +DIHEDRAL 1O30 1SI22 2O18 2SI2 +DIHEDRAL 1O34 1SI22 2O18 2SI2 +DIHEDRAL 1O11 1SI27 2O35 2SI23 +DIHEDRAL 1O15 1SI27 2O35 2SI23 + + +! Patch 011B between |_2| along V +! |_1| + +PRES 011B 0.00 +BOND 1SI1 2O17 +BOND 1SI25 2O33 +BOND 1O30 2SI27 +BOND 1O8 2SI4 +BOND 1SI23 2O7 +BOND 1O31 2SI28 + +! Angles along YY +ANGLE 1O5 1SI1 2O17 +ANGLE 1O9 1SI1 2O17 +ANGLE 1H37 1SI1 2O17 +ANGLE 2O15 2SI4 1O8 +ANGLE 2O20 2SI4 1O8 +ANGLE 2SI3 2O7 1SI23 +ANGLE 1SI24 1O8 2SI4 +ANGLE 2SI21 2O17 1SI1 +ANGLE 1O19 1SI23 2O7 +ANGLE 1O31 1SI23 2O7 +ANGLE 1O35 1SI23 2O7 +ANGLE 1O13 1SI25 2O33 +ANGLE 1H39 1SI25 2O33 +ANGLE 2O11 2SI27 1O30 +ANGLE 2O15 2SI27 1O30 +ANGLE 2O12 2SI28 1O31 +ANGLE 2O16 2SI28 1O31 +ANGLE 2O36 2SI28 1O31 +ANGLE 1SI22 1O30 2SI27 +ANGLE 1SI23 1O31 2SI28 +ANGLE 2SI21 2O33 1SI25 + +! Dihedrals along YY +DIHEDRAL 2O17 1SI1 1O5 1SI21 +DIHEDRAL 2O11 2SI3 2O7 1SI23 +DIHEDRAL 2O14 2SI3 2O7 1SI23 +DIHEDRAL 2O19 2SI3 2O7 1SI23 +DIHEDRAL 1O8 2SI4 2O15 2SI27 +DIHEDRAL 1O8 2SI4 2O20 2SI24 +DIHEDRAL 2SI4 1O8 1SI24 1O20 +DIHEDRAL 2SI4 1O8 1SI24 1O32 +DIHEDRAL 2SI4 1O8 1SI24 1O36 +DIHEDRAL 2SI3 2O11 2SI27 1O30 +DIHEDRAL 1SI2 1O13 1SI25 2O33 +DIHEDRAL 2SI4 2O15 2SI27 1O30 +DIHEDRAL 1SI1 2O17 2SI21 2O5 +DIHEDRAL 1SI1 2O17 2SI21 2O29 +DIHEDRAL 1SI1 2O17 2SI21 2O33 +DIHEDRAL 1SI3 1O19 1SI23 2O7 +DIHEDRAL 2O5 2SI21 2O33 1SI25 +DIHEDRAL 2O17 2SI21 2O33 1SI25 +DIHEDRAL 2O29 2SI21 2O33 1SI25 +DIHEDRAL 1O34 1SI22 1O30 2SI27 +DIHEDRAL 1O19 1SI23 1O31 2SI28 +DIHEDRAL 1O35 1SI23 1O31 2SI28 +DIHEDRAL 2O7 1SI23 1O31 2SI28 +DIHEDRAL 1O31 2SI28 2O36 2SI24 +DIHEDRAL 1O5 1SI1 2O17 2SI21 +DIHEDRAL 1O9 1SI1 2O17 2SI21 +DIHEDRAL 1H37 1SI1 2O17 2SI21 +DIHEDRAL 1SI24 1O8 2SI4 2O15 +DIHEDRAL 1SI24 1O8 2SI4 2O20 +DIHEDRAL 1O19 1SI23 2O7 2SI3 +DIHEDRAL 1O31 1SI23 2O7 2SI3 +DIHEDRAL 1O35 1SI23 2O7 2SI3 +DIHEDRAL 1O13 1SI25 2O33 2SI21 +DIHEDRAL 1H39 1SI25 2O33 2SI21 +DIHEDRAL 1SI22 1O30 2SI27 2O11 +DIHEDRAL 1SI22 1O30 2SI27 2O15 +DIHEDRAL 1SI23 1O31 2SI28 2O12 +DIHEDRAL 1SI23 1O31 2SI28 2O16 +DIHEDRAL 1SI23 1O31 2SI28 2O36 + +! Patch 011C between |_2| along UV +! |_1| + +PRES 011C 0.00 +BOND 1SI22 2O6 + +! Angles along XY +ANGLE 2O12 2SI4 1O8 +ANGLE 2SI2 2O6 1SI22 +ANGLE 1O30 1SI22 2O6 +ANGLE 1O34 1SI22 2O6 +ANGLE 1O18 1SI22 2O6 +ANGLE 1O9 1SI25 2O33 +ANGLE 2O35 2SI27 1O30 + +! Dihedrals along XY +DIHEDRAL 2O10 2SI2 2O6 1SI22 +DIHEDRAL 2O13 2SI2 2O6 1SI22 +DIHEDRAL 2O18 2SI2 2O6 1SI22 +DIHEDRAL 2O6 1SI22 1O34 1SI26 +DIHEDRAL 1O30 1SI22 2O6 2SI2 +DIHEDRAL 1O34 1SI22 2O6 2SI2 + +!*************************************************** + +! Patch 011D between |_3||_2| +! |_1| + +PRES 011D 0.00 + + + +! Patch 011E between |_3| +! |_1||_2| + +PRES 011E 0.00 + +DIHEDRAL 3O17 1SI1 1O9 2SI25 +DIHEDRAL 2O18 1SI22 1O30 3SI27 + + +! Patch 011F between |_3| +! |_1||_2| + +PRES 011F 0.00 + +ANGLE 2O18 1SI22 3O6 +ANGLE 1O9 2SI25 3O33 + +DIHEDRAL 3O7 2SI23 2O35 1SI27 +DIHEDRAL 1SI1 1O9 2SI25 3O33 +DIHEDRAL 3O6 1SI22 2O18 2SI2 +DIHEDRAL 1O9 2SI25 3O33 3SI21 +DIHEDRAL 2O18 1SI22 3O6 3SI2 + +! Patch 011G between |_2||_3| +! |_1| + +PRES 011G 0.00 + +DIHEDRAL 3O6 1SI22 1O30 2SI27 +DIHEDRAL 1O8 2SI4 3O12 3SI28 +DIHEDRAL 1O30 2SI27 3O35 3SI23 +DIHEDRAL 1SI24 1O8 2SI4 3O12 +DIHEDRAL 1SI22 1O30 2SI27 3O35 + +END diff --git a/charmm/toppar/stream/carb/.toppar_all36_carb_model.str.swp b/charmm/toppar/stream/carb/.toppar_all36_carb_model.str.swp new file mode 100644 index 0000000000000000000000000000000000000000..d56f0f50c3556140879e55de4ddf144cd4072775 GIT binary patch literal 16384 zcmeHOYm6jS6)r#!aTgR&(L}i;D7))+P2GBSFD7nJ@67b1d0S0yS5s1Zp}BMEB!L5u-6q6iAeO9lPTxwraJ)3ZAS zC1|R$Usp|?Tj!p8?s-=C&RUmE>=A+K7&zW!7`LB$%Vlr>@x4awO2cTiqh@VR66Lr@ zwRNx}-CS_oK_GryGaPO;=Y|W5;Yzr-P3Pv)lH(s38yjxd8;!6z+-f(YaA|lhY|iRi z2f}IWd*K7l2ktd|+;^GS*Gzw~jLzCW9wzohAl`u=wl^cOXK zO5YcHf_R>PYWk$6Hxl%JX!<3Zes_ZY_r&vO=>^67U(oa&`uY6{`tzC|cSK)K(4W)v zSpH`d^k+4Fr{+I)in@sBe@4^yY5GkG`rkDD3Qhk*g8sCoe^Ap$Uf0k6sRaFV3Hp+I}-FKG(Fbesi*Zn|G1{lYyOuf=zrGqX-)q@g8rDM zmo)wC*Z1@Plcry;>0yHYM@^6Qe^-M3sHWq!7awPzuFmoP>FqEMXnHL{*SFJCs)1Ak zsRmLFq#8&ykZK^+K&pXM1E~gHvlwy}u57-WD2A)R`d^d0u_!{te zU>|S}@C)?UHv;3pDZo8wAg=`i-~!-byg#6K3?Bi`2i^s|6L69@&x_3g1j_>|ZOy-9z zdN^t?u2iF1Bo?YGbM@+0QD4B^LlXtT9C^l~1oNV_@igYd(K*X(;)Wi;3?P^2Bq@nlg#oVRSbb~J+e}O2qq7$2nj~w+cTEejN-51O$qYGMdmxY1`p`TC z@c=I=1Jlnc9+oW!$wAx1M?wzhBWK!pR$8{{(kRGbE1fFe!0fz1MW=TyS<9z+c`X^~ z=O8@s$adC}%PBdCCGCmk(Yuyj9zyt71Kfc2$)iz_!_#X?@aSDjACHV1=)L8=CLXl; z#t@raWlqd4SE^+rUnq>i){Gsc$r76zu189fJ2)7yXVS{qJJki570|JyiA60*cBw8LPnYM?ToKIvkihUwzUHD!&5Da#RhUh-)O zhEI+-xp-c1qFdmp2eP6IQ+l9lV<2`llVO1{vfv<+J6cMXx>Rta+#@oU>3f>(mBf$^ zT;GsLVk|Jvr{sF^SV^Jz$OigPg5o3y)U}0w(&3YrOQKksXOX8}g zd9kQPhefF<=J1ogg{XxLBIK~`4qHAl38I~fa%``hQ#daWPcnJWrFcTV=uu4Y9Fxpd zT8MXuSrjvU$!&8%9Hf?gQhaY@uy^x-?;&h0Safp#%sRIQBVucasqKyxA zu_}&WN?weLK%^FccZhCd!(*>VICOlQ*!TE(e4CzKb(>e&8%K1Jqau|K2w>RtyPoZ# zQmHEr*ENNF-(Wl!`;r!emyqyK8}(Iz5IZJB6$2fU9X@tS8Wq=X@F;d)Rxkx}=u0m} z)oU~GsrbEslLnK| z3pY#E668Upr94&2Y@qFWT-!AyDUEBp9)Ui<35zO@Kq9T64v|-kRb%zq21t9orYPbR zMUVFr@Haab1nseWnl3pG0}`f2+A1bYO|qF$g|B4cEgfWPip(3;bq`Aie%WhUdq!8A z))G2__1KohwlyU9_t;{tzSO8M*UBwp$LLsIj7?1M6_cgOQL#I}cZRQwp=Q*I+M*oI zhs)KrXoT&##i)gL%NEkuBJi)iuuaSqr;taYa!Z7wQJHHmHzQEm^>Te1&gE#K8BuDP z7xTC%*Ox#NvylkfqP-YZnj$)cYN;~YtSm2ytHbJY)Y{C?3;cw4ac-CX=N-wgBrwkwmEVe zM5!+_nXJi^WP5~0d5993edZNO~CKaP6Hl8Z~p*rCvZD(6>t&oTlDic1D6120zXCHem~Fz z=71Ss5^#X?fEUrrKMYWBe+0MWaQw}Ec~v=3hg1|7`^-cSQ&baDqisiG2g(a8%N zsc?%;b+s%}9Ht7z@o_&D{HB7^MWBio*YZ^Hf@x_o z62HrbCULERW`z`35c)nBce*TTfP)ndHCmNe6iOid%$SeesVAv^LjRc4t0P4bAJ0K2 z(pZf7&_a5&5-XM#4T91Fw1U2mCZsx5D;5G9+@DO45_ZxDa;*@%=|hO=O%uB|<2-}& zPP!0NMH)G?Y3Hup^!M~8oK?;ueW+x_n(14Xit@a9$S1T09LU?~Ff@sjz?J_FMS|cl ziB^NuLCF$n+cF(LCb2;cX2=^u3~jQ!crNv33I8XDf-vGS7>pR*KOx|VF@-`#OpQ4s zTs+Xj^f=6DNHm(^(#46$C!E`1YZm=x%f3XDxK@^Y0Jatc@Bz;^RhQ$${fL`Iv_G*AI6+pw zQ*tRNcuEA#mnR}w*X09j^GXYN@xr|bEs6MQfnN_?Y7vy`q z;P`G3uG0;a`H<%g%mu#3Eh8d!7UmFs0Ssa!w- zJg)m`$9*?8;{F)k@dKKK9#OMO58g;p;ct2=Ni3wT+TmpQ?(qY93zYL_oWVOdY?2efEBr@9{~7J-JB$b3P7i zB;|S3LkNz#I3s82XUB8dtP=Ff_-29MsMEW0>b)spkuW4Jc|pu*t&#}q#(1p=X`^}P z^uUan5oCTf+~B{N4*t`Q(31|<>j>e?a|9cW0af)JKDmCRy}&mnRDPhMVF$owaSVe) zxY`6QCl13ZlE($TT_8^(yTAyX)gySBh_Zw$8kb9IHXJ`@QG^s^d+05=o`(0a6t>5Y zNE0@Q$cbv4O$K!qe2Q4O>YEr`Cs^>;2ego07F-;8WWET-R4ict-Y9F2?rK0uLB7C~ zsD;3j@md@n;Bi7E-NaI4vywePCs^uh63m#7>Xc#~()VnfEtxM5z-rhh*C^{_)iCe4 fu!rW>DrqpD3;W(WoL_tLHdA5GD@+vjgBboBP$o6( literal 0 HcmV?d00001 diff --git a/charmm/toppar/stream/carb/toppar_all36_carb_glycolipid.str b/charmm/toppar/stream/carb/toppar_all36_carb_glycolipid.str new file mode 100644 index 00000000..f230dee8 --- /dev/null +++ b/charmm/toppar/stream/carb/toppar_all36_carb_glycolipid.str @@ -0,0 +1,3692 @@ +read rtf card append +* Topology for inositol-based lipids +* +32 1 + +!*** Changes Made to this file by sairam *** +! Critical changes made to SAPI and DMPI +! +!1) OSLP has been changed to OC30P only at pos O12. +!3) Checked the charges on the phosphates. They are all consistent with the lipid FF. + +!************ +! Stream file to the following lipids. Additional residues and patches +! to extend the glycan or modify the sugar moieties (ie. PIPs etc.) are +! in the parent sugar topology file. +! RESI SAPI ! Phosphatidylinositol +! RESI DMPI ! Di-myristol-inositol +!********************************* + +!LLO (DOL/UND added July 2014) +!Nathan R. Kern, Hui Sun Lee, Emilia L. Wu, Kenno Vanommeslaeghe, Alexander D. MacKerell, Jr., Jeffery B. Klauda, Sunhwan Jo, and Wonpil Im +!Lipid-Linked Oligosaccharides in Membranes Sample Conformations that Facilitate Binding to Oligosaccharyltransferase. +!Submitted + + +RESI SAPI -1.00 ! Phosphatidylinositol +! +! Stearoyl - CH2 Uses RESI INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH RESI SAPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | +ATOM C12 CC3161 0.14 ! | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5-HO5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 !5 / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 !10 | H2--C12----------C13--O3-HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 !15 | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 !20 \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 !25 P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 !30 | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5530 107.31 -59.93 109.11 1.5612 +IC C12 C13 C14 C15 1.4341 109.11 59.27 114.44 1.4654 +IC C13 C12 C11 O12 1.4341 107.31 -175.79 117.69 1.4086 +IC C13 C14 C15 C16 1.5612 114.44 -55.48 109.80 1.5350 +IC C14 C15 C16 C11 1.4654 109.80 55.05 107.18 1.5598 +IC C12 C13 C14 O4 1.4341 109.11 -177.27 106.06 1.4595 +IC C13 C14 C15 O5 1.5612 114.44 171.27 114.28 1.4386 +IC C12 C13 C14 H4 1.4341 109.11 -64.25 106.39 1.1684 +IC O12 C12 *C11 H1 1.4086 117.69 -121.05 110.98 1.1834 +IC O12 C11 C12 O2 1.4086 117.69 51.01 111.79 1.4490 +IC O12 C11 C12 H2 1.4086 117.69 -61.28 98.22 1.1105 +IC C13 C14 C15 H5 1.5612 114.44 52.34 110.34 1.0922 +IC O2 C11 *C12 C13 1.4490 111.79 133.20 107.31 1.4341 +IC O3 C14 *C13 H3 1.4537 110.99 114.31 113.73 1.1394 +IC O3 C12 *C13 C14 1.4537 105.59 119.36 109.11 1.5612 +IC O4 C13 *C14 C15 1.4595 106.06 -123.46 114.44 1.4654 +IC C16 C14 *C15 O5 1.5350 109.80 -133.25 114.28 1.4386 +IC C14 C15 O5 HO5 1.4654 114.28 -73.20 108.55 0.9726 +IC C14 C15 C16 O6 1.4654 109.80 -179.24 110.87 1.4043 +IC C16 C11 O12 P 1.5530 117.69 300.00 114.27 0.9451 ! gauche +IC C11 C12 O2 HO2 1.5530 111.79 -31.80 115.65 0.9404 +IC C12 C13 O3 HO3 1.4341 105.59 37.19 107.10 0.9920 +IC C13 C14 O4 HO4 1.5612 106.06 35.00 105.15 0.9686 +IC C15 C16 O6 HO6 1.5350 110.87 51.35 112.65 0.9879 +IC C14 C15 C16 H6 1.4654 109.80 -58.40 111.34 1.0796 +! Phosphate Linker +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 ! trans +IC P O11 C1 C2 1.5867 122.31 180.00 111.45 1.5517 ! trans +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +! Backbone +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +! Acyl Chain 1 +IC C21 C22 C23 C24 1.5329 113.78 180.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 !cis db +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 120.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 120.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 !cis db +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 120.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 120.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 !cis db +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 120.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 120.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 !cis db +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI DMPI -1.00 ! Di-myristol-inositol +! +! myristol - CH2 Uses RESI INI1 - cyclic myi-inositol, +! | +! myristoyl - CH RESI DMPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | +ATOM C12 CC3161 0.14 ! | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5-HO5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 !5 / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 !10 | H2--C12----------C13--O3-HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 !15 | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 !20 | +GROUP ! / +ATOM C11 CC3161 0.01 ! | +ATOM H1 HCA1 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL3 -0.27 ! | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5530 107.31 -59.93 109.11 1.5612 +IC C12 C13 C14 C15 1.4341 109.11 59.27 114.44 1.4654 +IC C13 C12 C11 O12 1.4341 107.31 -175.79 117.69 1.4086 +IC C13 C14 C15 C16 1.5612 114.44 -55.48 109.80 1.5350 +IC C14 C15 C16 C11 1.4654 109.80 55.05 107.18 1.5598 +IC C12 C13 C14 O4 1.4341 109.11 -177.27 106.06 1.4595 +IC C13 C14 C15 O5 1.5612 114.44 171.27 114.28 1.4386 +IC C12 C13 C14 H4 1.4341 109.11 -64.25 106.39 1.1684 +IC O12 C12 *C11 H1 1.4086 117.69 -121.05 110.98 1.1834 +IC O12 C11 C12 O2 1.4086 117.69 51.01 111.79 1.4490 +IC O12 C11 C12 H2 1.4086 117.69 -61.28 98.22 1.1105 +IC C13 C14 C15 H5 1.5612 114.44 52.34 110.34 1.0922 +IC O2 C11 *C12 C13 1.4490 111.79 133.20 107.31 1.4341 +IC O3 C14 *C13 H3 1.4537 110.99 114.31 113.73 1.1394 +IC O3 C12 *C13 C14 1.4537 105.59 119.36 109.11 1.5612 +IC O4 C13 *C14 C15 1.4595 106.06 -123.46 114.44 1.4654 +IC C16 C14 *C15 O5 1.5350 109.80 -133.25 114.28 1.4386 +IC C14 C15 O5 HO5 1.4654 114.28 -73.20 108.55 0.9726 +IC C14 C15 C16 O6 1.4654 109.80 -179.24 110.87 1.4043 +IC C16 C11 O12 P 1.5530 117.69 300.00 114.27 0.9451 ! gauche +IC C11 C12 O2 HO2 1.5530 111.79 -31.80 115.65 0.9404 +IC C12 C13 O3 HO3 1.4341 105.59 37.19 107.10 0.9920 +IC C13 C14 O4 HO4 1.5612 106.06 35.00 105.15 0.9686 +IC C15 C16 O6 HO6 1.5350 110.87 51.35 112.65 0.9879 +IC C14 C15 C16 H6 1.4654 109.80 -58.40 111.34 1.0796 +! Phosphate Linker +IC C11 O12 P O11 1.4234 118.40 -166.94 104.13 1.5782 +IC O11 O12 *P O13 1.5782 104.13 117.91 108.15 1.4793 +IC O11 O12 *P O14 1.5782 104.13 -117.27 106.75 1.4823 +IC O12 P O11 C1 1.5875 104.13 177.32 118.17 1.4318 +IC P O11 C1 C2 1.5782 118.17 167.65 110.87 1.5511 +IC C2 O11 *C1 HA 1.5511 110.87 -119.11 111.42 1.1172 +IC HA O11 *C1 HB 1.1172 111.42 -120.82 110.01 1.1145 +IC O11 C1 C2 C3 1.4318 110.87 177.69 110.63 1.5578 +IC C3 C1 *C2 O21 1.5578 110.63 120.78 108.07 1.4415 !defines S chirality +IC C3 C1 *C2 HS 1.5578 110.63 -118.30 106.69 1.1168 !defines S chirality +IC C1 C2 O21 C21 1.5511 108.07 147.89 115.06 1.3179 +IC C2 O21 C21 C22 1.4415 115.06 179.61 108.77 1.5289 +IC C22 O21 *C21 O22 1.5289 108.77 -179.08 126.52 1.2183 +IC O21 C21 C22 C23 1.3179 108.77 -173.00 112.01 1.5450 +IC C23 C21 *C22 H2R 1.5450 112.01 -121.50 107.73 1.1091 +IC H2R C21 *C22 H2S 1.1091 107.73 -117.24 107.85 1.1091 +IC C1 C2 C3 O31 1.5511 110.63 175.48 112.70 1.4436 +IC O31 C2 *C3 HX 1.4436 112.70 -118.48 106.61 1.1129 +IC HX C2 *C3 HY 1.1129 106.61 -115.12 109.44 1.1145 +IC C2 C3 O31 C31 1.5578 112.70 87.10 115.14 1.3313 +IC C3 O31 C31 C32 1.4436 115.14 -172.45 108.40 1.5287 +IC C32 O31 *C31 O32 1.5287 108.40 -178.98 125.63 1.2169 +IC O31 C31 C32 C33 1.3313 108.40 -169.89 113.40 1.5448 +IC C33 C31 *C32 H2X 1.5448 113.40 -121.09 107.19 1.1104 +IC H2X C31 *C32 H2Y 1.1104 107.19 -116.85 108.01 1.1089 +IC C21 C22 C23 C24 1.5289 112.01 177.45 112.54 1.5336 +IC C24 C22 *C23 H3R 1.5336 112.54 -120.79 109.48 1.1146 +IC H3R C22 *C23 H3S 1.1146 109.48 -117.62 109.70 1.1144 +IC C22 C23 C24 C25 1.5450 112.54 -177.78 112.24 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.24 -121.51 109.37 1.1130 +IC H4R C23 *C24 H4S 1.1130 109.37 -117.64 109.09 1.1133 +IC C23 C24 C25 C26 1.5336 112.24 178.33 112.83 1.5342 +IC C26 C24 *C25 H5R 1.5342 112.83 -121.07 108.90 1.1136 +IC H5R C24 *C25 H5S 1.1136 108.90 -117.22 109.21 1.1132 +IC C24 C25 C26 C27 1.5346 112.83 -177.92 112.39 1.5344 +IC C27 C25 *C26 H6R 1.5344 112.39 -121.57 109.28 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.28 -117.51 109.01 1.1133 +IC C25 C26 C27 C28 1.5342 112.39 178.43 112.74 1.5342 +IC C28 C26 *C27 H7R 1.5342 112.74 -121.06 108.92 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.92 -117.29 109.22 1.1131 +IC C26 C27 C28 C29 1.5344 112.74 -178.17 112.46 1.5345 +IC C29 C27 *C28 H8R 1.5345 112.46 -121.56 109.25 1.1130 +IC H8R C27 *C28 H8S 1.1130 109.25 -117.46 109.01 1.1133 +IC C27 C28 C29 C210 1.5342 112.46 178.92 112.68 1.5343 +IC C210 C28 *C29 H9R 1.5343 112.68 -121.11 108.98 1.1135 +IC H9R C28 *C29 H9S 1.1135 108.98 -117.36 109.19 1.1131 +IC C28 C29 C210 C211 1.5345 112.68 -178.62 112.55 1.5345 +IC C211 C29 *C210 H10R 1.5345 112.55 -121.48 109.19 1.1130 +IC H10R C29 *C210 H10S 1.1130 109.19 -117.42 109.05 1.1132 +IC C29 C210 C211 C212 1.5343 112.55 179.33 112.62 1.5345 +IC C212 C210 *C211 H11R 1.5345 112.62 -121.19 109.03 1.1133 +IC H11R C210 *C211 H11S 1.1133 109.03 -117.37 109.14 1.1131 +IC C210 C211 C212 C213 1.5345 112.62 -179.30 112.67 1.5338 +IC C213 C211 *C212 H12R 1.5338 112.67 -121.40 109.15 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.15 -117.41 109.09 1.1133 +IC C211 C212 C213 C214 1.5345 112.67 179.80 113.26 1.5308 +IC C214 C212 *C213 H13R 1.5308 113.26 -121.66 108.77 1.1142 +IC H13R C212 *C213 H13S 1.1142 108.77 -116.66 108.78 1.1140 +IC C212 C213 C214 H14R 1.5338 113.26 -59.87 110.43 1.1113 +IC H14R C213 *C214 H14S 1.1113 110.43 119.85 110.46 1.1113 +IC H14R C213 *C214 H14T 1.1113 110.43 -120.04 110.62 1.1112 +IC C31 C32 C33 C34 1.5287 113.40 179.64 111.32 1.5341 +IC C34 C32 *C33 H3X 1.5341 111.32 -120.86 109.71 1.1137 +IC H3X C32 *C33 H3Y 1.1137 109.71 -118.09 109.81 1.1143 +IC C32 C33 C34 C35 1.5448 111.32 -176.82 113.37 1.5345 +IC C35 C33 *C34 H4X 1.5345 113.37 -121.80 109.05 1.1135 +IC H4X C33 *C34 H4Y 1.1135 109.05 -117.12 108.83 1.1136 +IC C33 C34 C35 C36 1.5341 113.37 178.26 111.94 1.5348 +IC C36 C34 *C35 H5X 1.5348 111.94 -120.83 109.02 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.02 -117.61 109.44 1.1129 +IC C34 C35 C36 C37 1.5345 111.94 -176.79 113.19 1.5342 +IC C37 C35 *C36 H6X 1.5342 113.19 -121.90 109.15 1.1132 +IC H6X C35 *C36 H6Y 1.1132 109.15 -117.14 108.76 1.1136 +IC C35 C36 C37 C38 1.5348 113.19 177.72 112.13 1.5346 +IC C38 C36 *C37 H7X 1.5346 112.13 -120.80 109.00 1.1133 +IC H7X C36 *C37 H7Y 1.1133 109.00 -117.59 109.40 1.1128 +IC C36 C37 C38 C39 1.5342 112.13 -177.62 112.99 1.5342 +IC C39 C37 *C38 H8X 1.5342 112.99 -121.75 109.20 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.20 -117.24 108.86 1.1136 +IC C37 C38 C39 C310 1.5346 112.99 178.21 112.22 1.5344 +IC C310 C38 *C39 H9X 1.5344 112.22 -120.97 109.07 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.07 -117.54 109.30 1.1130 +IC C38 C39 C310 C311 1.5342 112.22 -178.81 112.83 1.5339 +IC C311 C39 *C310 H10X 1.5339 112.83 -121.55 109.12 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.12 -117.29 108.97 1.1134 +IC C39 C310 C311 C312 1.5344 112.83 179.12 112.41 1.5346 +IC C312 C310 *C311 H11X 1.5346 112.41 -121.13 109.11 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.11 -117.49 109.19 1.1130 +IC C310 C311 C312 C313 1.5339 112.41 -179.72 112.68 1.5336 +IC C313 C311 *C312 H12X 1.5336 112.68 -121.39 109.14 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.14 -117.34 109.09 1.1133 +IC C311 C312 C313 C314 1.5346 112.68 179.81 113.29 1.5308 +IC C314 C312 *C313 H13X 1.5308 113.29 -121.66 108.73 1.1141 +IC H13X C312 *C313 H13Y 1.1141 108.73 -116.66 108.73 1.1141 +IC C312 C313 C314 H14X 1.5336 113.29 -59.97 110.46 1.1113 +IC H14X C313 *C314 H14Y 1.1113 110.46 119.87 110.46 1.1113 +IC H14X C313 *C314 H14Z 1.1113 110.46 -120.06 110.59 1.1112 + +PRES OCTA 0.11 ! og axial octyl patch to C1 +dele atom HO1 +GROUP +ATOM C1 CC3162 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM C1P CTL2 0.00 ! +ATOM H1P1 HAL2 0.09 ! +ATOM H1P2 HAL2 0.09 ! +GROUP +ATOM C2P CTL2 -0.18 ! +ATOM H2P1 HAL2 0.09 ! +ATOM H2P2 HAL2 0.09 ! +GROUP +ATOM C3P CTL2 -0.18 ! +ATOM H3P1 HAL2 0.09 ! +ATOM H3P2 HAL2 0.09 ! +GROUP +ATOM C4P CTL2 -0.18 ! +ATOM H4P1 HAL2 0.09 ! +ATOM H4P2 HAL2 0.09 ! +GROUP +ATOM C5P CTL2 -0.18 ! +ATOM H5P1 HAL2 0.09 ! +ATOM H5P2 HAL2 0.09 ! +GROUP +ATOM C6P CTL2 -0.18 ! +ATOM H6P1 HAL2 0.09 ! +ATOM H6P2 HAL2 0.09 ! +GROUP +ATOM C7P CTL2 -0.18 ! +ATOM H7P1 HAL2 0.09 ! +ATOM H7P2 HAL2 0.09 ! +GROUP +ATOM C8P CTL3 -0.27 ! +ATOM H8P1 HAL3 0.09 ! +ATOM H8P2 HAL3 0.09 ! +ATOM H8P3 HAL3 0.09 ! +BOND O1 C1P C1P C2P +BOND C2P C3P C3P C4P +BOND C4P C5P C5P C6P +BOND C6P C7P C7P C8P +BOND C1P H1P1 C1P H1P2 +BOND C2P H2P1 C2P H2P2 +BOND C3P H3P1 C3P H3P2 +BOND C4P H4P1 C4P H4P2 +BOND C5P H5P1 C5P H5P2 +BOND C6P H6P1 C6P H6P2 +BOND C7P H7P1 C7P H7P2 +BOND C8P H8P1 C8P H8P2 C8P H8P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C1 O1 C1P 1.4326 113.39 76.24 112.41 1.4390 +IC C1 O1 C1P C2P 1.3743 112.41 -174.48 113.71 1.5661 +IC O1 C1P C2P C3P 1.4390 113.71 171.35 116.60 1.5435 +IC C1P C2P C3P C4P 1.5661 116.60 167.78 109.45 1.5162 +IC C2P C3P C4P C5P 1.5435 109.45 176.22 113.48 1.5169 +IC C3P C4P C5P C6P 1.5162 113.48 -170.18 109.85 1.5192 +IC C4P C5P C6P C7P 1.5169 109.85 -178.66 113.31 1.5327 +IC C5P C6P C7P C8P 1.5192 113.31 168.96 112.74 1.5011 +IC C2P O1 *C1P H1P1 1.5661 113.71 -128.80 113.66 1.0672 +IC C2P O1 *C1P H1P2 1.5661 113.71 111.70 104.83 1.1576 +IC C3P C1P *C2P H2P1 1.5435 116.60 -122.44 111.35 1.1341 +IC C3P C1P *C2P H2P2 1.5435 116.60 120.83 104.33 1.0593 +IC C4P C2P *C3P H3P1 1.5162 109.45 -122.81 111.56 1.0873 +IC C4P C2P *C3P H3P2 1.5162 109.45 119.63 108.38 1.1453 +IC C5P C3P *C4P H4P1 1.5169 113.48 -113.66 106.44 1.1732 +IC C5P C3P *C4P H4P2 1.5169 113.48 127.08 117.15 1.0636 +IC C6P C4P *C5P H5P1 1.5192 109.85 -123.11 112.49 1.0773 +IC C6P C4P *C5P H5P2 1.5192 109.85 118.20 103.00 1.1136 +IC C7P C5P *C6P H6P1 1.5327 113.31 -120.77 104.09 1.1135 +IC C7P C5P *C6P H6P2 1.5327 113.31 121.24 102.96 1.1126 +IC C8P C6P *C7P H7P1 1.5011 112.74 -120.21 106.53 1.0732 +IC C8P C6P *C7P H7P2 1.5011 112.74 122.52 101.92 1.1138 +IC C6P C7P C8P H8P1 1.5327 112.74 68.12 110.42 1.0685 +IC H8P1 C7P *C8P H8P2 1.0685 110.42 -123.66 113.02 1.1341 +IC H8P1 C7P *C8P H8P3 1.0685 110.42 117.47 111.97 1.1299 + +PRES OCTB 0.11 ! og equatorial octyl patch to C1 +dele atom HO1 +GROUP +ATOM C1 CC3162 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM C1P CTL2 0.00 ! +ATOM H1P1 HAL2 0.09 ! +ATOM H1P2 HAL2 0.09 ! +GROUP +ATOM C2P CTL2 -0.18 ! +ATOM H2P1 HAL2 0.09 ! +ATOM H2P2 HAL2 0.09 ! +GROUP +ATOM C3P CTL2 -0.18 ! +ATOM H3P1 HAL2 0.09 ! +ATOM H3P2 HAL2 0.09 ! +GROUP +ATOM C4P CTL2 -0.18 ! +ATOM H4P1 HAL2 0.09 ! +ATOM H4P2 HAL2 0.09 ! +GROUP +ATOM C5P CTL2 -0.18 ! +ATOM H5P1 HAL2 0.09 ! +ATOM H5P2 HAL2 0.09 ! +GROUP +ATOM C6P CTL2 -0.18 ! +ATOM H6P1 HAL2 0.09 ! +ATOM H6P2 HAL2 0.09 ! +GROUP +ATOM C7P CTL2 -0.18 ! +ATOM H7P1 HAL2 0.09 ! +ATOM H7P2 HAL2 0.09 ! +GROUP +ATOM C8P CTL3 -0.27 ! +ATOM H8P1 HAL3 0.09 ! +ATOM H8P2 HAL3 0.09 ! +ATOM H8P3 HAL3 0.09 ! +BOND O1 C1P C1P C2P +BOND C2P C3P C3P C4P +BOND C4P C5P C5P C6P +BOND C6P C7P C7P C8P +BOND C1P H1P1 C1P H1P2 +BOND C2P H2P1 C2P H2P2 +BOND C3P H3P1 C3P H3P2 +BOND C4P H4P1 C4P H4P2 +BOND C5P H5P1 C5P H5P2 +BOND C6P H6P1 C6P H6P2 +BOND C7P H7P1 C7P H7P2 +BOND C8P H8P1 C8P H8P2 C8P H8P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C1 O1 C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC C1 O1 C1P C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC O1 C1P C2P C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC C1P C2P C3P C4P 1.5408 111.72 174.29 118.38 1.4860 +IC C2P C3P C4P C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC C3P C4P C5P C6P 1.4860 117.15 176.92 116.91 1.5223 +IC C4P C5P C6P C7P 1.5882 116.91 166.99 109.72 1.5200 +IC C5P C6P C7P C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC C2P O1 *C1P H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC C2P O1 *C1P H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC C3P C1P *C2P H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC C3P C1P *C2P H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC C4P C2P *C3P H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC C4P C2P *C3P H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC C5P C3P *C4P H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC C5P C3P *C4P H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC C6P C4P *C5P H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC C6P C4P *C5P H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC C7P C5P *C6P H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC C7P C5P *C6P H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC C8P C6P *C7P H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C8P C6P *C7P H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC C6P C7P C8P H8P1 1.5200 108.36 67.85 108.61 1.0625 +IC H8P1 C7P *C8P H8P2 1.0625 108.61 -118.96 114.90 1.1259 +IC H8P1 C7P *C8P H8P3 1.0625 108.61 126.50 111.01 1.1613 + +PRES DDMB 0.11 ! og equatorial dodecyl patch to C1 +dele atom HO1 +GROUP +ATOM C1 CC3162 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM C1P CTL2 0.00 ! +ATOM H1P1 HAL2 0.09 ! +ATOM H1P2 HAL2 0.09 ! +GROUP +ATOM C2P CTL2 -0.18 ! +ATOM H2P1 HAL2 0.09 ! +ATOM H2P2 HAL2 0.09 ! +GROUP +ATOM C3P CTL2 -0.18 ! +ATOM H3P1 HAL2 0.09 ! +ATOM H3P2 HAL2 0.09 ! +GROUP +ATOM C4P CTL2 -0.18 ! +ATOM H4P1 HAL2 0.09 ! +ATOM H4P2 HAL2 0.09 ! +GROUP +ATOM C5P CTL2 -0.18 ! +ATOM H5P1 HAL2 0.09 ! +ATOM H5P2 HAL2 0.09 ! +GROUP +ATOM C6P CTL2 -0.18 ! +ATOM H6P1 HAL2 0.09 ! +ATOM H6P2 HAL2 0.09 ! +GROUP +ATOM C7P CTL2 -0.18 ! +ATOM H7P1 HAL2 0.09 ! +ATOM H7P2 HAL2 0.09 ! +GROUP +ATOM C8P CTL2 -0.18 ! +ATOM H8P1 HAL2 0.09 ! +ATOM H8P2 HAL2 0.09 ! +GROUP +ATOM C9P CTL2 -0.18 ! +ATOM H9P1 HAL2 0.09 ! +ATOM H9P2 HAL2 0.09 ! +GROUP +ATOM C10P CTL2 -0.18 ! +ATOM H10P1 HAL2 0.09 ! +ATOM H10P2 HAL2 0.09 ! +GROUP +ATOM C11P CTL2 -0.18 ! +ATOM H11P1 HAL2 0.09 ! +ATOM H11P2 HAL2 0.09 ! +GROUP +ATOM C12P CTL3 -0.27 ! +ATOM H12P1 HAL3 0.09 ! +ATOM H12P2 HAL3 0.09 ! +ATOM H12P3 HAL3 0.09 ! +BOND O1 C1P C1P C2P +BOND C2P C3P C3P C4P +BOND C4P C5P C5P C6P +BOND C6P C7P C7P C8P +BOND C8P C9P C9P C10P +BOND C10P C11P C11P C12P +BOND C1P H1P1 C1P H1P2 +BOND C2P H2P1 C2P H2P2 +BOND C3P H3P1 C3P H3P2 +BOND C4P H4P1 C4P H4P2 +BOND C5P H5P1 C5P H5P2 +BOND C6P H6P1 C6P H6P2 +BOND C7P H7P1 C7P H7P2 +BOND C8P H8P1 C8P H8P2 +BOND C9P H9P1 C9P H9P2 +BOND C10P H10P1 C10P H10P2 +BOND C11P H11P1 C11P H11P2 +BOND C12P H12P1 C12P H12P2 C12P H12P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C1 O1 C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC C1 O1 C1P C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC O1 C1P C2P C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC C1P C2P C3P C4P 1.5408 111.72 174.29 118.38 1.4860 +IC C2P C3P C4P C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC C3P C4P C5P C6P 1.4860 117.15 176.92 116.91 1.5223 +IC C4P C5P C6P C7P 1.5882 116.91 166.99 109.72 1.5200 +IC C5P C6P C7P C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC C6P C7P C8P C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC C7P C8P C9P C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC C8P C9P C10P C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC C9P C10P C11P C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC C2P O1 *C1P H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC C2P O1 *C1P H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC C3P C1P *C2P H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC C3P C1P *C2P H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC C4P C2P *C3P H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC C4P C2P *C3P H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC C5P C3P *C4P H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC C5P C3P *C4P H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC C6P C4P *C5P H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC C6P C4P *C5P H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC C7P C5P *C6P H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC C7P C5P *C6P H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC C8P C6P *C7P H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C8P C6P *C7P H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC C9P C7P *C8P H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C9P C7P *C8P H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC C10P C8P *C9P H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C10P C8P *C9P H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC C11P C9P *C10P H10P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C11P C9P *C10P H10P2 1.5091 108.36 126.14 108.14 1.1445 +IC C12P C10P *C11P H11P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C12P C10P *C11P H11P2 1.5091 108.36 126.14 108.14 1.1445 +IC C10P C11P C12P H12P1 1.5200 108.36 67.85 108.61 1.0625 +IC H12P1 C11P *C12P H12P2 1.0625 108.61 -118.96 114.90 1.1259 +IC H12P1 C11P *C12P H12P3 1.0625 108.61 126.50 111.01 1.1613 + + +RESI BDDM 0.000 ! added by pram +! ! Beta, do-decyl maltoside residue +GROU ! +ATOM 1C1 CC3162 0.290 ! +ATOM 1H1 HCA1 0.090 ! +ATOM 1C5 CC3163 0.110 ! +ATOM 1H5 HCA1 0.090 ! +ATOM 1O5 OC3C61 -0.400 ! +GROU ! +ATOM 1C2 CC3161 0.140 ! +ATOM 1H2 HCA1 0.090 ! +ATOM 1O2 OC311 -0.650 ! +ATOM 1HO2 HCP1 0.420 ! +GROU ! +ATOM 1C3 CC3161 0.140 ! +ATOM 1H3 HCA1 0.090 ! +ATOM 1O3 OC311 -0.650 ! +ATOM 1HO3 HCP1 0.420 ! +GROU +ATOM 1C4 CC3161 0.140 +ATOM 1H4 HCA1 0.090 +ATOM 1O4 OC311 -0.650 +ATOM 1HO4 HCP1 0.420 +GROU +ATOM 1C6 CC321 0.050 +ATOM 1H61 HCA2 0.090 +ATOM 1H62 HCA2 0.090 +ATOM 1O6 OC311 -0.650 +ATOM 1HO6 HCP1 0.420 +! ! BGLC +GROU ! +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.090 ! +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC301 -0.360 ! +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +! +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL2 -0.18 ! +ATOM 3H10P1 HAL2 0.09 ! +ATOM 3H10P2 HAL2 0.09 ! +GROUP +ATOM 3C11P CTL2 -0.18 ! +ATOM 3H11P1 HAL2 0.09 ! +ATOM 3H11P2 HAL2 0.09 ! +GROUP +ATOM 3C12P CTL3 -0.27 ! +ATOM 3H12P1 HAL3 0.09 ! +ATOM 3H12P2 HAL3 0.09 ! +ATOM 3H12P3 HAL3 0.09 ! +! +BOND 1C1 1H1 1C1 1O5 1C1 1C2 +BOND 1C2 1H2 1C2 1O2 1O2 1HO2 1C2 1C3 1C3 1H3 +BOND 1C3 1O3 1O3 1HO3 1C3 1C4 1C4 1H4 1C4 1O4 +BOND 1O4 1HO4 1C4 1C5 1C5 1H5 1C5 1C6 1C6 1H61 +BOND 1C6 1H62 1C6 1O6 1O6 1HO6 1C5 1O5 +BOND 2O4 1C1 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 2C3 2H3 +BOND 2C3 2O3 2O3 2HO3 2C3 2C4 2C4 2H4 2C4 2O4 +BOND 2C4 2C5 2C5 2H5 2C5 2C6 2C6 2H61 +BOND 2C6 2H62 2C6 2O6 2O6 2HO6 2C5 2O5 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C10P 3C11P 3C11P 3C12P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 +BOND 3C11P 3H11P1 3C11P 3H11P2 +BOND 3C12P 3H12P1 3C12P 3H12P2 3C12P 3H12P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O2 1C3 *1C2 1H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 1O2 1C1 *1C2 1C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 1O3 1C4 *1C3 1H3 1.4122 110.86 120.36 107.49 1.1219 +IC 1O3 1C2 *1C3 1C4 1.4122 109.00 121.20 109.13 1.5315 +IC 1O4 1C5 *1C4 1H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 1O4 1C3 *1C4 1C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 1C6 1O5 *1C5 1H5 1.4718 112.19 113.05 108.36 1.1212 +IC 1C6 1C4 *1C5 1O5 1.4718 112.04 128.71 113.93 1.4175 +IC 1O6 1H62 *1C6 1H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 1O6 1C5 *1C6 1H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 1O5 1C1 1C2 1C3 1.4351 112.62 51.83 113.63 1.4880 +IC 1C1 1C2 1C3 1C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 1C2 1C3 1C4 1C5 1.4880 109.13 47.85 114.40 1.5087 +IC 1C3 1C4 1C5 1O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 1C4 1C5 1O5 1C1 1.5087 113.93 51.43 114.13 1.4351 +IC 1C5 1O5 1C1 1C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 1C4 1C5 1C6 1O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 1C1 1C2 1O2 1HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 1C2 1C3 1O3 1HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC 1C3 1C4 1O4 1HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 1C5 1C6 1O6 1HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2C3 2C4 2O4 1C1 1.5010 117.73 72.71 118.66 1.4036 ! psi +IC 2C4 2O4 1C1 1O5 1.4919 118.66 48.64 109.48 1.4570 ! phi +IC 1O5 2O4 *1C1 1C2 1.4570 109.48 124.57 110.72 1.5065 +IC 1O5 2O4 *1C1 1H1 1.4570 109.48 -116.61 107.55 1.1057 +IC 2O1 2C2 *2C1 2H1 1.3899 110.90 120.10 104.58 1.0836 +IC 2O1 2O5 *2C1 2C2 1.3899 108.62 122.10 110.88 1.5316 +IC 2O2 2C3 *2C2 2H2 1.4594 108.12 -118.78 111.06 1.1375 +IC 2O2 2C1 *2C2 2C3 1.4594 115.65 -125.60 113.28 1.4983 +IC 2O3 2C4 *2C3 2H3 1.4071 113.48 122.06 103.39 1.0895 +IC 2O3 2C2 *2C3 2C4 1.4071 108.48 124.18 109.26 1.5497 +IC 2O4 2C5 *2C4 2H4 1.3940 111.12 -110.35 108.66 1.0857 +IC 2O4 2C3 *2C4 2C5 1.3940 112.77 -129.39 115.62 1.5530 +IC 2C6 2O5 *2C5 2H5 1.5597 111.17 120.85 110.98 1.1092 +IC 2C6 2C4 *2C5 2O5 1.5597 109.90 122.92 110.30 1.4512 +IC 2O6 2H62 *2C6 2H61 1.4589 116.11 -112.93 103.57 1.1467 +IC 2O6 2C5 *2C6 2H62 1.4589 109.41 -135.95 118.22 1.0853 +IC 2O5 2C1 2C2 2C3 1.4620 110.88 57.82 113.28 1.4983 +IC 2C1 2C2 2C3 2C4 1.5316 113.28 -48.40 109.26 1.5497 +IC 2C2 2C3 2C4 2C5 1.4983 109.26 45.07 115.62 1.5530 +IC 2C3 2C4 2C5 2O5 1.5497 115.62 -49.19 110.30 1.4512 +IC 2C4 2C5 2O5 2C1 1.5530 110.30 56.36 112.12 1.4620 +IC 2C5 2O5 2C1 2C2 1.4512 112.12 -61.39 110.88 1.5316 +IC 2C4 2C5 2C6 2O6 1.5530 109.90 -177.46 109.41 1.4589 +IC 2O5 2C1 2O1 2HO1 1.4620 108.62 72.25 106.48 0.9328 +IC 2C1 2C2 2O2 2HO2 1.5316 115.65 135.41 116.81 0.9527 +IC 2C2 2C3 2O3 2HO3 1.4983 108.48 -71.46 120.86 0.9441 +!IC 2C3 2C4 2O4 2HO4 1.5497 112.77 47.45 109.31 0.9911 +IC 2C5 2C6 2O6 2HO6 1.5597 109.41 -54.60 118.82 0.95210 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C11P 3C9P *3C10P 3H10P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C11P 3C9P *3C10P 3H10P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C12P 3C10P *3C11P 3H11P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C12P 3C10P *3C11P 3H11P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C11P 3C12P 3H12P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H12P1 3C11P *3C12P 3H12P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H12P1 3C11P *3C12P 3H12P3 1.0625 108.61 126.50 111.01 1.1613 + + +RESI ADDM 0.000 ! added by pram +GROU ! alpha, do-decyl maltoside residue +ATOM 1C1 CC3162 0.290 ! +ATOM 1H1 HCA1 0.090 ! +ATOM 1C5 CC3163 0.110 ! +ATOM 1H5 HCA1 0.090 ! +ATOM 1O5 OC3C61 -0.400 ! +GROU ! +ATOM 1C2 CC3161 0.140 ! +ATOM 1H2 HCA1 0.090 ! +ATOM 1O2 OC311 -0.650 ! +ATOM 1HO2 HCP1 0.420 ! +GROU ! +ATOM 1C3 CC3161 0.140 ! +ATOM 1H3 HCA1 0.090 ! +ATOM 1O3 OC311 -0.650 ! +ATOM 1HO3 HCP1 0.420 ! +GROU +ATOM 1C4 CC3161 0.140 +ATOM 1H4 HCA1 0.090 +ATOM 1O4 OC311 -0.650 +ATOM 1HO4 HCP1 0.420 +GROU +ATOM 1C6 CC321 0.050 +ATOM 1H61 HCA2 0.090 +ATOM 1H62 HCA2 0.090 +ATOM 1O6 OC311 -0.650 +ATOM 1HO6 HCP1 0.420 +GROU ! +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.090 ! +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC301 -0.360 ! +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL2 -0.18 ! +ATOM 3H10P1 HAL2 0.09 ! +ATOM 3H10P2 HAL2 0.09 ! +GROUP +ATOM 3C11P CTL2 -0.18 ! +ATOM 3H11P1 HAL2 0.09 ! +ATOM 3H11P2 HAL2 0.09 ! +GROUP +ATOM 3C12P CTL3 -0.27 ! +ATOM 3H12P1 HAL3 0.09 ! +ATOM 3H12P2 HAL3 0.09 ! +ATOM 3H12P3 HAL3 0.09 ! +BOND 1C1 1H1 1C1 1O5 1C1 1C2 +BOND 1C2 1H2 1C2 1O2 1O2 1HO2 1C2 1C3 1C3 1H3 +BOND 1C3 1O3 1O3 1HO3 1C3 1C4 1C4 1H4 1C4 1O4 +BOND 1O4 1HO4 1C4 1C5 1C5 1H5 1C5 1C6 1C6 1H61 +BOND 1C6 1H62 1C6 1O6 1O6 1HO6 1C5 1O5 +BOND 2O4 1C1 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 2C3 2H3 +BOND 2C3 2O3 2O3 2HO3 2C3 2C4 2C4 2H4 2C4 2O4 +BOND 2C4 2C5 2C5 2H5 2C5 2C6 2C6 2H61 +BOND 2C6 2H62 2C6 2O6 2O6 2HO6 2C5 2O5 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C10P 3C11P 3C11P 3C12P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 +BOND 3C11P 3H11P1 3C11P 3H11P2 +BOND 3C12P 3H12P1 3C12P 3H12P2 3C12P 3H12P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O2 1C3 *1C2 1H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 1O2 1C1 *1C2 1C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 1O3 1C4 *1C3 1H3 1.4122 110.86 120.36 107.49 1.1219 +IC 1O3 1C2 *1C3 1C4 1.4122 109.00 121.20 109.13 1.5315 +IC 1O4 1C5 *1C4 1H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 1O4 1C3 *1C4 1C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 1C6 1O5 *1C5 1H5 1.4718 112.19 113.05 108.36 1.1212 +IC 1C6 1C4 *1C5 1O5 1.4718 112.04 128.71 113.93 1.4175 +IC 1O6 1H62 *1C6 1H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 1O6 1C5 *1C6 1H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 1O5 1C1 1C2 1C3 1.4351 112.62 51.83 113.63 1.4880 +IC 1C1 1C2 1C3 1C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 1C2 1C3 1C4 1C5 1.4880 109.13 47.85 114.40 1.5087 +IC 1C3 1C4 1C5 1O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 1C4 1C5 1O5 1C1 1.5087 113.93 51.43 114.13 1.4351 +IC 1C5 1O5 1C1 1C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 1C4 1C5 1C6 1O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 1C1 1C2 1O2 1HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 1C2 1C3 1O3 1HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC 1C3 1C4 1O4 1HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 1C5 1C6 1O6 1HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2C3 2C4 2O4 1C1 1.5010 117.73 72.71 118.66 1.4036 ! psi +IC 2C4 2O4 1C1 1O5 1.4919 118.66 48.64 109.48 1.4570 ! phi +IC 1O5 2O4 *1C1 1C2 1.4570 109.48 124.57 110.72 1.5065 +IC 1O5 2O4 *1C1 1H1 1.4570 109.48 -116.61 107.55 1.1057 +IC 2O1 2C2 *2C1 2H1 1.4077 108.33 -123.34 103.67 1.1200 +IC 2O1 2O5 *2C1 2C2 1.4077 108.39 -119.83 112.62 1.5516 +IC 2O2 2C3 *2C2 2H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 2O2 2C1 *2C2 2C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 2O3 2C4 *2C3 2H3 1.4122 110.86 120.36 107.49 1.1219 +IC 2O3 2C2 *2C3 2C4 1.4122 109.00 121.20 109.13 1.5315 +IC 2O4 2C5 *2C4 2H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 2O4 2C3 *2C4 2C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 2C6 2O5 *2C5 2H5 1.4718 112.19 113.05 108.36 1.1212 +IC 2C6 2C4 *2C5 2O5 1.4718 112.04 128.71 113.93 1.4175 +IC 2O6 2H62 *2C6 2H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 2O6 2C5 *2C6 2H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 2O5 2C1 2C2 2C3 1.4351 112.62 51.83 113.63 1.4880 +IC 2C1 2C2 2C3 2C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 2C2 2C3 2C4 2C5 1.4880 109.13 47.85 114.40 1.5087 +IC 2C3 2C4 2C5 2O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 2C4 2C5 2O5 2C1 1.5087 113.93 51.43 114.13 1.4351 +IC 2C5 2O5 2C1 2C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 2C4 2C5 2C6 2O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 2O5 2C1 2O1 2HO1 1.4351 108.39 47.62 101.41 0.9789 +IC 2C1 2C2 2O2 2HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 2C2 2C3 2O3 2HO3 1.4880 109.00 -28.48 103.99 0.9971 +!IC 2C3 2C4 2O4 2HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 2C5 2C6 2O6 2HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C11P 3C9P *3C10P 3H10P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C11P 3C9P *3C10P 3H10P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C12P 3C10P *3C11P 3H11P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C12P 3C10P *3C11P 3H11P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C11P 3C12P 3H12P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H12P1 3C11P *3C12P 3H12P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H12P1 3C11P *3C12P 3H12P3 1.0625 108.61 126.50 111.01 1.1613 + +!LLO section + +RESI ABAC 0.000 ! 2,4-diacetamido-2,4,6-trideoxyglucose + ! (beta bacillosamine or Bac) +GROU ! +ATOM C1 CC3162 0.340 ! H63 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! HT41 ON4 C4 | C1 +ATOM C2 CC3161 0.070 ! | || / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HT41-CT4--CN4--N4 \| | / O1-HO1 +ATOM N NC2D1 -0.470 ! | | C3---C2 +ATOM HN HCP1 0.310 ! HT43 HN4 | | +GROU ! H3 N-HN +ATOM C CC2O1 0.510 ! / +ATOM O OC2D1 -0.510 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.070 ! +ATOM H4 HCA1 0.090 ! +ATOM N4 NC2D1 -0.470 ! +ATOM HN4 HCP1 0.310 ! +GROU ! +ATOM CN4 CC2O1 0.510 ! +ATOM ON4 OC2D1 -0.510 ! +GROU ! +ATOM CT4 CC331 -0.270 ! +ATOM HT41 HCA3 0.090 ! +ATOM HT42 HCA3 0.090 ! +ATOM HT43 HCA3 0.090 ! +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 N4 N4 HN4 C4 C5 +BOND C5 H5 C5 C6 C5 O5 +BOND C6 H61 C6 H62 C6 H63 +BOND N C C O C CT +BOND CT HT1 CT HT2 CT HT3 +BOND N4 CN4 CN4 ON4 CN4 CT4 +BOND CT4 HT41 CT4 HT42 CT4 HT43 +IMPR C CT N O +IMPR N C C2 HN +IMPR CN4 CT4 N4 ON4 +IMPR N4 CN4 C4 HN4 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.0000 120.00 -120.00 120.00 1.0000 +IC O1 O5 *C1 C2 1.3949 110.13 120.34 109.32 1.5156 +IC N C3 *C2 H2 1.4607 113.70 -119.19 107.08 1.1227 +IC N C1 *C2 C3 1.4607 112.62 -127.32 109.20 1.5149 +IC O3 C4 *C3 H3 1.4246 110.45 117.60 108.58 1.1171 +IC O3 C2 *C3 C4 1.4246 111.13 123.24 110.86 1.5168 +IC N4 C5 *C4 H4 1.4204 110.47 -117.94 108.07 1.1172 +IC N4 C3 *C4 C5 1.4204 110.88 -123.03 110.79 1.5206 +IC C6 O5 *C5 H5 1.5134 108.06 117.57 109.86 1.1171 +IC C6 C4 *C5 O5 1.5134 113.35 119.99 108.45 1.4386 +IC H63 H62 *C6 H61 1.4280 109.26 -117.58 107.87 1.1141 +IC H63 C5 *C6 H62 1.4280 111.18 -121.26 110.14 1.1132 +IC O5 C1 C2 C3 1.4220 109.32 58.90 109.20 1.5149 +IC C1 C2 C3 C4 1.5156 109.20 -52.68 110.86 1.5168 +IC C2 C3 C4 C5 1.5149 110.86 52.13 110.79 1.5206 +IC C3 C4 C5 O5 1.5168 110.79 -56.10 108.45 1.4386 +IC C4 C5 O5 C1 1.5206 108.45 64.09 111.47 1.4220 +IC C5 O5 C1 C2 1.4386 111.47 -66.18 109.32 1.5156 +IC C4 C5 C6 H63 1.5206 113.35 -179.21 111.18 1.4280 +IC O5 C1 O1 HO1 1.4220 110.13 53.79 107.03 0.9601 +IC C1 C2 N HN 1.5156 112.62 -21.73 117.18 0.9940 +IC C2 C3 O3 HO3 1.5149 111.13 0.20 109.43 0.9762 +IC C3 C4 N4 HN4 1.5156 112.62 -21.73 117.18 0.9940 +IC C N C2 C3 1.3365 123.04 -84.98 113.70 1.5149 +IC C C2 *N HN 1.3365 123.04 -171.85 117.18 0.9940 +IC CT C N C2 1.4798 117.02 -173.18 123.04 1.4607 +IC N CT *C O 1.3365 117.02 178.97 121.63 1.2235 +IC O C CT HT1 1.2235 121.63 116.39 110.28 1.1105 +IC O C CT HT2 1.2235 121.63 -3.06 109.29 1.1121 +IC O C CT HT3 1.2235 121.63 -122.59 110.33 1.1105 +IC CN4 N4 C4 C5 1.3365 123.04 -84.98 113.70 1.5149 +IC CN4 C2 *N4 HN4 1.3365 123.04 -171.85 117.18 0.9940 +IC CT4 CN4 N4 C4 1.4798 117.02 -173.18 123.04 1.4607 +IC N4 CT4 *CN4 ON4 1.3365 117.02 178.97 121.63 1.2235 +IC ON4 CN4 CT4 HT41 1.2235 121.63 116.39 110.28 1.1105 +IC ON4 CN4 CT4 HT42 1.2235 121.63 -3.06 109.29 1.1121 +IC ON4 CN4 CT4 HT43 1.2235 121.63 -122.59 110.33 1.1105 +PATC FIRS NONE LAST NONE + +RESI BBAC 0.000 ! 2,4-diacetamido-2,4,6-trideoxyglucose + ! (beta bacillosamine or Bac) +GROU ! +ATOM C1 CC3162 0.340 ! H63 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! HT41 ON4 C4 | C1 +ATOM C2 CC3161 0.070 ! | || / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HT41-CT4--CN4--N4 \| | / H1 +ATOM N NC2D1 -0.470 ! | | C3---C2 +ATOM HN HCP1 0.310 ! HT43 HN4 | | +GROU ! H3 N-HN +ATOM C CC2O1 0.510 ! / +ATOM O OC2D1 -0.510 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.070 ! +ATOM H4 HCA1 0.090 ! +ATOM N4 NC2D1 -0.470 ! +ATOM HN4 HCP1 0.310 ! +GROU ! +ATOM CN4 CC2O1 0.510 ! +ATOM ON4 OC2D1 -0.510 ! +GROU ! +ATOM CT4 CC331 -0.270 ! +ATOM HT41 HCA3 0.090 ! +ATOM HT42 HCA3 0.090 ! +ATOM HT43 HCA3 0.090 ! +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 N4 N4 HN4 C4 C5 +BOND C5 H5 C5 C6 C5 O5 +BOND C6 H61 C6 H62 C6 H63 +BOND N C C O C CT +BOND CT HT1 CT HT2 CT HT3 +BOND N4 CN4 CN4 ON4 CN4 CT4 +BOND CT4 HT41 CT4 HT42 CT4 HT43 +IMPR C CT N O +IMPR N C C2 HN +IMPR CN4 CT4 N4 ON4 +IMPR N4 CN4 C4 HN4 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 -120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 -118.92 111.32 1.5218 +IC N C3 *C2 H2 1.4607 113.70 -119.19 107.08 1.1227 +IC N C1 *C2 C3 1.4607 112.62 -127.32 109.20 1.5149 +IC O3 C4 *C3 H3 1.4246 110.45 117.60 108.58 1.1171 +IC O3 C2 *C3 C4 1.4246 111.13 123.24 110.86 1.5168 +IC N4 C5 *C4 H4 1.4204 110.47 -117.94 108.07 1.1172 +IC N4 C3 *C4 C5 1.4204 110.88 -123.03 110.79 1.5206 +IC C6 O5 *C5 H5 1.5134 108.06 117.57 109.86 1.1171 +IC C6 C4 *C5 O5 1.5134 113.35 119.99 108.45 1.4386 +IC H63 H62 *C6 H61 1.4280 109.26 -117.58 107.87 1.1141 +IC H63 C5 *C6 H62 1.4280 111.18 -121.26 110.14 1.1132 +IC O5 C1 C2 C3 1.4220 109.32 58.90 109.20 1.5149 +IC C1 C2 C3 C4 1.5156 109.20 -52.68 110.86 1.5168 +IC C2 C3 C4 C5 1.5149 110.86 52.13 110.79 1.5206 +IC C3 C4 C5 O5 1.5168 110.79 -56.10 108.45 1.4386 +IC C4 C5 O5 C1 1.5206 108.45 64.09 111.47 1.4220 +IC C5 O5 C1 C2 1.4386 111.47 -66.18 109.32 1.5156 +IC C4 C5 C6 H63 1.5206 113.35 -179.21 111.18 1.4280 +IC O5 C1 O1 HO1 1.4220 110.13 53.79 107.03 0.9601 +IC C1 C2 N HN 1.5156 112.62 -21.73 117.18 0.9940 +IC C2 C3 O3 HO3 1.5149 111.13 0.20 109.43 0.9762 +IC C3 C4 N4 HN4 1.5156 112.62 -21.73 117.18 0.9940 +IC C N C2 C3 1.3365 123.04 -84.98 113.70 1.5149 +IC C C2 *N HN 1.3365 123.04 -171.85 117.18 0.9940 +IC CT C N C2 1.4798 117.02 -173.18 123.04 1.4607 +IC N CT *C O 1.3365 117.02 178.97 121.63 1.2235 +IC O C CT HT1 1.2235 121.63 116.39 110.28 1.1105 +IC O C CT HT2 1.2235 121.63 -3.06 109.29 1.1121 +IC O C CT HT3 1.2235 121.63 -122.59 110.33 1.1105 +IC CN4 N4 C4 C5 1.3365 123.04 -84.98 113.70 1.5149 +IC CN4 C2 *N4 HN4 1.3365 123.04 -171.85 117.18 0.9940 +IC CT4 CN4 N4 C4 1.4798 117.02 -173.18 123.04 1.4607 +IC N4 CT4 *CN4 ON4 1.3365 117.02 178.97 121.63 1.2235 +IC ON4 CN4 CT4 HT41 1.2235 121.63 116.39 110.28 1.1105 +IC ON4 CN4 CT4 HT42 1.2235 121.63 -3.06 109.29 1.1121 +IC ON4 CN4 CT4 HT43 1.2235 121.63 -122.59 110.33 1.1105 +PATC FIRS NONE LAST NONE + +RESI DL16PP -2.00 ! [name] +GROUP +ATOM P2 PG1 1.34 ! HO22 +ATOM O22 OG311 -0.71 ! | +ATOM HO22 HGP1 0.44 ! O22 !! based on RESI PPI2 +ATOM O23 OG2P1 -0.86 ! | +ATOM O24 OG2P1 -0.86 ! O23==P2==O24 (-) + ! | +ATOM P1 PG1 1.46 ! O12 +ATOM O12 OG304 -0.63 ! | +ATOM O13 OG2P1 -0.83 ! O13==P1==O14 (-) +ATOM O14 OG2P1 -0.83 ! | +ATOM O11 OG303 -0.62 ! O11 + ! | +ATOM C1 CG321 -0.08 ! H11--C1--H12 +ATOM H11 HGA2 0.09 ! | +ATOM H12 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C2 CG321 -0.18 ! H21--C2--H12 +ATOM H21 HGA2 0.09 ! ! +ATOM H22 HGA2 0.09 ! | H41 +GROUP 0.00 ! ! | +ATOM C3 CG311 -0.09 ! H3--C3---C4--H42 +ATOM H3 HGA1 0.09 ! | | +GROUP 0.00 ! | H43 +ATOM C4 CG331 -0.27 ! | +ATOM H41 HGA3 0.09 ! | +ATOM H42 HGA3 0.09 ! | +ATOM H43 HGA3 0.09 ! | +GROUP 0.00 ! | +ATOM C5 CG321 -0.18 ! H51--C5--H52 +ATOM H51 HGA2 0.09 ! | +ATOM H52 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C1A CG321 -0.18 ! H1A1--C1A--H1A2 +ATOM H1A1 HGA2 0.09 ! | +ATOM H1A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C1B CG2D1 -0.15 ! C1B--H1B (cis) +ATOM H1B HGA4 0.15 ! || +GROUP 0.00 ! || H1D1 +ATOM C1C CG2D1 0.00 ! || | +GROUP 0.00 ! C1C--C1D--H1D2 +ATOM C1D CG331 -0.27 ! | | +ATOM H1D1 HGA3 0.09 ! | H1D3 +ATOM H1D2 HGA3 0.09 ! ! +ATOM H1D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C1E CG321 -0.18 ! H1E1--C1E--H1E2 +ATOM H1E1 HGA2 0.09 ! ! +ATOM H1E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C2A CG321 -0.18 ! H2A1--C2A--H2A2 +ATOM H2A1 HGA2 0.09 ! | +ATOM H2A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C2B CG2D1 -0.15 ! C2B--H2B (cis) +ATOM H2B HGA4 0.15 ! || +GROUP 0.00 ! || H2D1 +ATOM C2C CG2D1 0.00 ! || | +GROUP 0.00 ! C2C--C2D--H2D2 +ATOM C2D CG331 -0.27 ! | | +ATOM H2D1 HGA3 0.09 ! | H2D3 +ATOM H2D2 HGA3 0.09 ! ! +ATOM H2D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C2E CG321 -0.18 ! H2E1--C2E--H2E2 +ATOM H2E1 HGA2 0.09 ! ! +ATOM H2E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C3A CG321 -0.18 ! H3A1--C3A--H3A2 +ATOM H3A1 HGA2 0.09 ! | +ATOM H3A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C3B CG2D1 -0.15 ! C3B--H3B (cis) +ATOM H3B HGA4 0.15 ! || +GROUP 0.00 ! || H3D1 +ATOM C3C CG2D1 0.00 ! || | +GROUP 0.00 ! C3C--C3D--H3D2 +ATOM C3D CG331 -0.27 ! | | +ATOM H3D1 HGA3 0.09 ! | H3D3 +ATOM H3D2 HGA3 0.09 ! ! +ATOM H3D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C3E CG321 -0.18 ! H3E1--C3E--H3E2 +ATOM H3E1 HGA2 0.09 ! ! +ATOM H3E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C4A CG321 -0.18 ! H4A1--C4A--H4A2 +ATOM H4A1 HGA2 0.09 ! | +ATOM H4A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C4B CG2D1 -0.15 ! C4B--H4B (cis) +ATOM H4B HGA4 0.15 ! || +GROUP 0.00 ! || H4D1 +ATOM C4C CG2D1 0.00 ! || | +GROUP 0.00 ! C4C--C4D--H4D2 +ATOM C4D CG331 -0.27 ! | | +ATOM H4D1 HGA3 0.09 ! | H4D3 +ATOM H4D2 HGA3 0.09 ! ! +ATOM H4D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C4E CG321 -0.18 ! H4E1--C4E--H4E2 +ATOM H4E1 HGA2 0.09 ! ! +ATOM H4E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C5A CG321 -0.18 ! H5A1--C5A--H5A2 +ATOM H5A1 HGA2 0.09 ! | +ATOM H5A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C5B CG2D1 -0.15 ! C5B--H5B (cis) +ATOM H5B HGA4 0.15 ! || +GROUP 0.00 ! || H5D1 +ATOM C5C CG2D1 0.00 ! || | +GROUP 0.00 ! C5C--C5D--H5D2 +ATOM C5D CG331 -0.27 ! | | +ATOM H5D1 HGA3 0.09 ! | H5D3 +ATOM H5D2 HGA3 0.09 ! ! +ATOM H5D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C5E CG321 -0.18 ! H5E1--C5E--H5E2 +ATOM H5E1 HGA2 0.09 ! ! +ATOM H5E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C6A CG321 -0.18 ! H6A1--C6A--H6A2 +ATOM H6A1 HGA2 0.09 ! | +ATOM H6A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C6B CG2D1 -0.15 ! C6B--H6B (cis) +ATOM H6B HGA4 0.15 ! || +GROUP 0.00 ! || H6D1 +ATOM C6C CG2D1 0.00 ! || | +GROUP 0.00 ! C6C--C6D--H6D2 +ATOM C6D CG331 -0.27 ! | | +ATOM H6D1 HGA3 0.09 ! | H6D3 +ATOM H6D2 HGA3 0.09 ! ! +ATOM H6D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C6E CG321 -0.18 ! H6E1-C6E--H6E2 +ATOM H6E1 HGA2 0.09 ! ! +ATOM H6E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C7A CG321 -0.18 ! H7A1--C7A--H7A2 +ATOM H7A1 HGA2 0.09 ! | +ATOM H7A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C7B CG2D1 -0.15 ! C7B--H7B (cis) +ATOM H7B HGA4 0.15 ! || +GROUP 0.00 ! || H7D1 +ATOM C7C CG2D1 0.00 ! || | +GROUP 0.00 ! C7C--C7D--H7D2 +ATOM C7D CG331 -0.27 ! | | +ATOM H7D1 HGA3 0.09 ! | H7D3 +ATOM H7D2 HGA3 0.09 ! ! +ATOM H7D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C7E CG321 -0.18 ! H7E1-C7E--H7E2 +ATOM H7E1 HGA2 0.09 ! ! +ATOM H7E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C8A CG321 -0.18 ! H8A1--C8A--H8A2 +ATOM H8A1 HGA2 0.09 ! | +ATOM H8A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C8B CG2D1 -0.15 ! C8B--H8B (cis) +ATOM H8B HGA4 0.15 ! || +GROUP 0.00 ! || H8D1 +ATOM C8C CG2D1 0.00 ! || | +GROUP 0.00 ! C8C--C8D--H8D2 +ATOM C8D CG331 -0.27 ! | | +ATOM H8D1 HGA3 0.09 ! | H8D3 +ATOM H8D2 HGA3 0.09 ! ! +ATOM H8D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C8E CG321 -0.18 ! H8E1-C8E--H8E2 +ATOM H8E1 HGA2 0.09 ! ! +ATOM H8E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C9A CG321 -0.18 ! H9A1--C9A--H9A2 +ATOM H9A1 HGA2 0.09 ! | +ATOM H9A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C9B CG2D1 -0.15 ! C9B--H9B (cis) +ATOM H9B HGA4 0.15 ! || +GROUP 0.00 ! || H9D1 +ATOM C9C CG2D1 0.00 ! || | +GROUP 0.00 ! C9C--C9D--H9D2 +ATOM C9D CG331 -0.27 ! | | +ATOM H9D1 HGA3 0.09 ! | H9D3 +ATOM H9D2 HGA3 0.09 ! ! +ATOM H9D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C9E CG321 -0.18 ! H9E1-C9E--H9E2 +ATOM H9E1 HGA2 0.09 ! ! +ATOM H9E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C10A CG321 -0.18 ! H10A1--C10A--H10A2 +ATOM H10A1 HGA2 0.09 ! | +ATOM H10A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C10B CG2D1 -0.15 ! C10B--H110B (cis) +ATOM H10B HGA4 0.15 ! || +GROUP 0.00 ! || H10D1 +ATOM C10C CG2D1 0.00 ! || | +GROUP 0.00 ! C10C-C10D--H10D2 +ATOM C10D CG331 -0.27 ! | | +ATOM H10D1 HGA3 0.09 ! | H10D3 +ATOM H10D2 HGA3 0.09 ! ! +ATOM H10D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C10E CG321 -0.18 ! H10E1-C10E--H10E2 +ATOM H10E1 HGA2 0.09 ! ! +ATOM H10E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C11A CG321 -0.18 ! H11A1--C11A--H11A2 +ATOM H11A1 HGA2 0.09 ! | +ATOM H11A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C11B CG2D1 -0.15 ! C11B--H11B (cis) +ATOM H11B HGA4 0.15 ! || +GROUP 0.00 ! || H11D1 +ATOM C11C CG2D1 0.00 ! || | +GROUP 0.00 ! C11C-C11D--H11D2 +ATOM C11D CG331 -0.27 ! | | +ATOM H11D1 HGA3 0.09 ! | H11D3 +ATOM H11D2 HGA3 0.09 ! ! +ATOM H11D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C11E CG321 -0.18 ! H11E1-C11E--H11E2 +ATOM H11E1 HGA2 0.09 ! ! +ATOM H11E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C12A CG321 -0.18 ! H12A1--C12A--H12A2 +ATOM H12A1 HGA2 0.09 ! | +ATOM H12A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C12B CG2D1 -0.15 ! C12B--H12B (cis) +ATOM H12B HGA4 0.15 ! || +GROUP 0.00 ! || H12D1 +ATOM C12C CG2D1 0.00 ! || | +GROUP 0.00 ! C12C-C12D--H12D2 +ATOM C12D CG331 -0.27 ! | | +ATOM H12D1 HGA3 0.09 ! | H12D3 +ATOM H12D2 HGA3 0.09 ! ! +ATOM H12D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C12E CG321 -0.18 ! H1E12-C12E--H12E2 +ATOM H12E1 HGA2 0.09 ! ! +ATOM H12E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C13A CG321 -0.18 ! H13A1--C13A--H13A2 +ATOM H13A1 HGA2 0.09 ! | +ATOM H13A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C13B CG2D1 -0.15 ! C13B--H13B (trans) +ATOM H13B HGA4 0.15 ! || +GROUP 0.00 ! || H13D1 +ATOM C13C CG2D1 0.00 ! || | +GROUP 0.00 ! C13C-C13D--H13D2 +ATOM C13D CG331 -0.27 ! | | +ATOM H13D1 HGA3 0.09 ! | H13D3 +ATOM H13D2 HGA3 0.09 ! ! +ATOM H13D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C13E CG321 -0.18 ! H13E1-C13E--H13E2 +ATOM H13E1 HGA2 0.09 ! ! +ATOM H13E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C14A CG321 -0.18 ! H14A1--C14A--H14A2 +ATOM H14A1 HGA2 0.09 ! | +ATOM H14A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C14B CG2D1 -0.15 ! C14B--H14B (trans) +ATOM H14B HGA4 0.15 ! || +GROUP 0.00 ! || H14D1 +ATOM C14C CG2D1 0.00 ! || | +GROUP 0.00 ! C14C-C14D--H14D2 +ATOM C14D CG331 -0.27 ! | | +ATOM H14D1 HGA3 0.09 ! | H14D3 +ATOM H14D2 HGA3 0.09 ! ! +ATOM H14D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C14E CG321 -0.18 ! H14E1-C14E--H14E2 +ATOM H14E1 HGA2 0.09 ! ! +ATOM H14E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C15A CG321 -0.18 ! H15A1--C15A--H15A2 +ATOM H15A1 HGA2 0.09 ! | +ATOM H15A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C15B CG2D1 -0.15 ! C15B--H15B +ATOM H15B HGA4 0.15 ! || +GROUP 0.00 ! || H15D1 +ATOM C15C CG2D1 0.00 ! || | +GROUP 0.00 ! C15C-C15D--H15D2 +ATOM C15D CG331 -0.27 ! | | +ATOM H15D1 HGA3 0.09 ! | H15D3 +ATOM H15D2 HGA3 0.09 ! ! +ATOM H15D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C15E CG331 -0.27 ! H15E1-C15E--H15E2 +ATOM H15E1 HGA3 0.09 ! ! +ATOM H15E2 HGA3 0.09 ! H15E3 +ATOM H15E3 HGA3 0.09 ! + +BOND O22 HO22 P2 O22 P2 O23 P2 O24 P2 O12 ! Phosphate group 2 +BOND P1 O12 P1 O13 P1 O14 P1 O11 O11 C1 ! Phosphate group 1 +BOND C1 C2 C2 C3 C3 C4 C3 C5 ! Alpha isoprene backbone carbons +BOND C1 H11 C1 H12 ! C1 hydrogens +BOND C2 H21 C2 H22 ! C2 hydrogens +BOND C3 H3 ! C3 hydrogen +BOND C4 H41 C4 H42 C4 H43 ! C4 hydrogens +BOND C5 H51 C5 H52 ! C5 hydrogens +BOND C5 C1A ! isoprene linking bond +BOND C1A C1B C1C C1D C1C C1E ! cis isoprene backbone carbons +DOUBLE C1B C1C ! cis double bond +BOND C1A H1A1 C1A H1A2 ! C1A hydrogens +BOND C1B H1B ! C1B hydrogen +BOND C1D H1D1 C1D H1D2 C1D H1D3 ! C1D hydrogens +BOND C1E H1E1 C1E H1E2 ! C1E hydrogens +BOND C1E C2A ! isoprene linking bond +BOND C2A C2B C2C C2D C2C C2E ! cis isoprene backbone carbons +DOUBLE C2B C2C ! cis double bond +BOND C2A H2A1 C2A H2A2 ! C2A hydrogens +BOND C2B H2B ! C2B hydrogen +BOND C2D H2D1 C2D H2D2 C2D H2D3 ! C2D hydrogens +BOND C2E H2E1 C2E H2E2 ! C2E hydrogens +BOND C2E C3A ! isoprene linking bond +BOND C3A C3B C3C C3D C3C C3E ! cis isoprene backbone carbons +DOUBLE C3B C3C ! cis double bond +BOND C3A H3A1 C3A H3A2 ! C3A hydrogens +BOND C3B H3B ! C3B hydrogen +BOND C3D H3D1 C3D H3D2 C3D H3D3 ! C3D hydrogens +BOND C3E H3E1 C3E H3E2 ! C3E hydrogens +BOND C3E C4A ! isoprene linking bond +BOND C4A C4B C4C C4D C4C C4E ! cis isoprene backbone carbons +DOUBLE C4B C4C ! cis double bond +BOND C4A H4A1 C4A H4A2 ! C4A hydrogens +BOND C4B H4B ! C4B hydrogen +BOND C4D H4D1 C4D H4D2 C4D H4D3 ! C4D hydrogens +BOND C4E H4E1 C4E H4E2 ! C4E hydrogens +BOND C4E C5A ! isoprene linking bond +BOND C5A C5B C5C C5D C5C C5E ! cis isoprene backbone carbons +DOUBLE C5B C5C ! cis double bond +BOND C5A H5A1 C5A H5A2 ! C5A hydrogens +BOND C5B H5B ! C5B hydrogen +BOND C5D H5D1 C5D H5D2 C5D H5D3 ! C5D hydrogens +BOND C5E H5E1 C5E H5E2 ! C5E hydrogens +BOND C5E C6A ! isoprene linking bond +BOND C6A C6B C6C C6D C6C C6E ! cis isoprene backbone carbons +DOUBLE C6B C6C ! cis double bond +BOND C6A H6A1 C6A H6A2 ! C6A hydrogens +BOND C6B H6B ! C6B hydrogen +BOND C6D H6D1 C6D H6D2 C6D H6D3 ! C6D hydrogens +BOND C6E H6E1 C6E H6E2 ! C6E hydrogens +BOND C6E C7A ! isoprene linking bond +BOND C7A C7B C7C C7D C7C C7E ! cis isoprene backbone carbons +DOUBLE C7B C7C ! cis double bond +BOND C7A H7A1 C7A H7A2 ! C7A hydrogens +BOND C7B H7B ! C7B hydrogen +BOND C7D H7D1 C7D H7D2 C7D H7D3 ! C7D hydrogens +BOND C7E H7E1 C7E H7E2 ! C7E hydrogens +BOND C7E C8A ! isoprene linking bond +BOND C8A C8B C8C C8D C8C C8E ! cis isoprene backbone carbons +DOUBLE C8B C8C ! cis double bond +BOND C8A H8A1 C8A H8A2 ! C8A hydrogens +BOND C8B H8B ! C8B hydrogen +BOND C8D H8D1 C8D H8D2 C8D H8D3 ! C8D hydrogens +BOND C8E H8E1 C8E H8E2 ! C8E hydrogens +BOND C8E C9A ! isoprene linking bond +BOND C9A C9B C9C C9D C9C C9E ! cis isoprene backbone carbons +DOUBLE C9B C9C ! cis double bond +BOND C9A H9A1 C9A H9A2 ! C9A hydrogens +BOND C9B H9B ! C9B hydrogen +BOND C9D H9D1 C9D H9D2 C9D H9D3 ! C9D hydrogens +BOND C9E H9E1 C9E H9E2 ! C9E hydrogens +BOND C9E C10A ! isoprene linking bond +BOND C10A C10B C10C C10D C10C C10E ! cis isoprene backbone carbons +DOUBLE C10B C10C ! cis double bond +BOND C10A H10A1 C10A H10A2 ! C10A hydrogens +BOND C10B H10B ! C10B hydrogen +BOND C10D H10D1 C10D H10D2 C10D H10D3 ! C10D hydrogens +BOND C10E H10E1 C10E H10E2 ! C10E hydrogens +BOND C10E C11A ! isoprene linking bond +BOND C11A C11B C11C C11D C11C C11E ! cis isoprene backbone carbons +DOUBLE C11B C11C ! cis double bond +BOND C11A H11A1 C11A H11A2 ! C11A hydrogens +BOND C11B H11B ! C11B hydrogen +BOND C11D H11D1 C11D H11D2 C11D H11D3 ! C11D hydrogens +BOND C11E H11E1 C11E H11E2 ! C11E hydrogens +BOND C11E C12A ! isoprene linking bond +BOND C12A C12B C12C C12D C12C C12E ! cis isoprene backbone carbons +DOUBLE C12B C12C ! cis double bond +BOND C12A H12A1 C12A H12A2 ! C12A hydrogens +BOND C12B H12B ! C12B hydrogen +BOND C12D H12D1 C12D H12D2 C12D H12D3 ! C12D hydrogens +BOND C12E H12E1 C12E H12E2 ! C12E hydrogens +BOND C12E C13A ! isoprene linking bond +BOND C13A C13B C13C C13D C13C C13E ! cis isoprene backbone carbons +DOUBLE C13B C13C ! cis double bond +BOND C13A H13A1 C13A H13A2 ! C13A hydrogens +BOND C13B H13B ! C13B hydrogen +BOND C13D H13D1 C13D H13D2 C13D H13D3 ! C13D hydrogens +BOND C13E H13E1 C13E H13E2 ! C13E hydrogens +BOND C13E C14A ! isoprene linking bond +BOND C14A C14B C14C C14D C14C C14E ! cis isoprene backbone carbons +DOUBLE C14B C14C ! cis double bond +BOND C14A H14A1 C14A H14A2 ! C14A hydrogens +BOND C14B H14B ! C14B hydrogen +BOND C14D H14D1 C14D H14D2 C14D H14D3 ! C14D hydrogens +BOND C14E H14E1 C14E H14E2 ! C14E hydrogens +BOND C14E C15A ! isoprene linking bond +BOND C15A C15B C15C C15D C15C C15E ! cis isoprene backbone carbons +DOUBLE C15B C15C ! cis double bond +BOND C15A H15A1 C15A H15A2 ! C15A hydrogens +BOND C15B H15B ! C15B hydrogen +BOND C15D H15D1 C15D H15D2 C15D H15D3 ! C15D hydrogens +BOND C15E H15E1 C15E H15E2 C15E H15E3 ! C15E hydrogens +IC O22 O12 *P2 O23 1.6100 111.00 120.00 111.60 1.5100 +IC O22 O12 *P2 O24 1.6100 111.00 -120.00 111.60 1.5100 +IC O12 P2 O22 HO22 1.6750 111.00 180.00 115.00 0.9600 +IC O22 P2 O12 P1 1.6100 111.00 180.00 143.00 1.6750 +IC P2 O12 P1 O11 1.6750 143.00 180.00 105.00 1.6500 +IC O11 O12 *P1 O13 1.6500 105.00 120.00 111.60 1.5100 +IC O11 O12 *P1 O14 1.5100 111.60 -120.00 111.60 1.5100 +IC O12 P1 O11 C1 1.6750 105.00 180.00 120.00 1.4400 +IC P1 O11 C1 C2 1.6500 120.00 180.00 110.10 1.5300 +IC C2 O11 *C1 H11 1.5300 110.10 120.00 109.50 1.1110 +IC C2 O11 *C1 H12 1.5300 110.10 -120.00 109.50 1.1110 +IC O11 C1 C2 C3 1.4400 110.10 180.00 113.50 1.5380 +IC C3 C1 *C2 H21 1.5380 113.50 120.00 110.10 1.1110 +IC C3 C1 *C2 H22 1.5380 113.50 -120.00 110.10 1.1110 +IC C1 C2 C3 C5 1.5280 113.50 180.00 113.50 1.5380 +IC C5 C2 *C3 C4 1.5380 113.50 120.00 114.00 1.5380 +IC C5 C2 *C3 H3 1.5380 114.00 -120.00 110.10 1.1110 +IC C2 C3 C4 H41 1.5380 114.00 180.00 110.10 1.1110 +IC H41 C3 *C4 H42 1.1110 110.10 120.00 110.10 1.1110 +IC H41 C3 *C4 H43 1.1110 110.10 -120.00 110.10 1.1110 +IC C2 C3 C5 C1A 1.5380 113.50 180.00 113.50 1.5300 +IC C1A C3 *C5 H51 1.5300 113.50 120.00 110.10 1.1110 +IC C1A C3 *C5 H52 1.1110 110.10 -120.00 110.10 1.1110 +IC C3 C5 C1A C1B 1.5380 113.50 180.00 112.20 1.5020 +IC C1B C5 *C1A H1A1 1.5020 112.20 120.00 110.10 1.1110 +IC C1B C5 *C1A H1A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C5 C1A C1B C1C 1.5300 112.20 180.00 123.50 1.3400 +IC C1C C1A *C1B H1B 1.3400 123.50 180.00 116.00 1.1000 +IC C1A C1B C1C C1D 1.5020 123.50 180.00 123.50 1.5020 +IC C1E C1B *C1C C1D 1.5020 123.50 180.00 123.50 1.5040 +IC C1B C1C C1D H1D1 1.3400 123.50 180.00 111.50 1.1110 +IC H1D1 C1C *C1D H1D2 1.1110 111.50 120.00 111.50 1.1110 +IC H1D1 C1C *C1D H1D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C1B C1C C1E C2A 1.3400 123.50 180.00 112.20 1.5300 +IC C2A C1C *C1E H1E1 1.5300 112.20 120.00 111.50 1.1110 +IC C2A C1C *C1E H1E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C1C C1E C2A C2B 1.5020 112.20 180.00 112.20 1.5020 +IC C2B C1E *C2A H2A1 1.5020 112.20 120.00 110.10 1.1110 +IC C2B C1E *C2A H2A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C1E C2A C2B C2C 1.5300 112.20 180.00 123.50 1.3400 +IC C2C C2A *C2B H2B 1.3400 123.50 180.00 116.00 1.1000 +IC C2A C2B C2C C2D 1.5020 123.50 180.00 123.50 1.5020 +IC C2E C2B *C2C C2D 1.5020 123.50 180.00 123.50 1.5040 +IC C2B C2C C2D H2D1 1.3400 123.50 180.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D2 1.1110 111.50 120.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C2B C2C C2E C3A 1.3400 123.50 180.00 112.20 1.5300 +IC C3A C2C *C2E H2E1 1.5300 112.20 120.00 111.50 1.1110 +IC C3A C2C *C2E H2E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C2C C2E C3A C3B 1.5020 112.20 180.00 112.20 1.5020 +IC C3B C2E *C3A H3A1 1.5020 112.20 120.00 110.10 1.1110 +IC C3B C2E *C3A H3A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C2E C3A C3B C3C 1.5300 112.20 180.00 123.50 1.3400 +IC C3C C3A *C3B H3B 1.3400 123.50 180.00 116.00 1.1000 +IC C3A C3B C3C C3D 1.5020 123.50 180.00 123.50 1.5020 +IC C3E C3B *C3C C3D 1.5020 123.50 180.00 123.50 1.5040 +IC C3B C3C C3D H3D1 1.3400 123.50 180.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D2 1.1110 111.50 120.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C3B C3C C3E C4A 1.3400 123.50 180.00 112.20 1.5300 +IC C4A C3C *C3E H3E1 1.5300 112.20 120.00 111.50 1.1110 +IC C4A C3C *C3E H3E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C3C C3E C4A C4B 1.5020 112.20 180.00 112.20 1.5020 +IC C4B C3E *C4A H4A1 1.5020 112.20 120.00 110.10 1.1110 +IC C4B C3E *C4A H4A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C3E C4A C4B C4C 1.5300 112.20 180.00 123.50 1.3400 +IC C4C C4A *C4B H4B 1.3400 123.50 180.00 116.00 1.1000 +IC C4A C4B C4C C4D 1.5020 123.50 180.00 123.50 1.5020 +IC C4E C4B *C4C C4D 1.5020 123.50 180.00 123.50 1.5040 +IC C4B C4C C4D H4D1 1.3400 123.50 180.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D2 1.1110 111.50 120.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C4B C4C C4E C5A 1.3400 123.50 180.00 112.20 1.5300 +IC C5A C4C *C4E H4E1 1.5300 112.20 120.00 111.50 1.1110 +IC C5A C4C *C4E H4E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C4C C4E C5A C5B 1.5020 112.20 180.00 112.20 1.5020 +IC C5B C4E *C5A H5A1 1.5020 112.20 120.00 110.10 1.1110 +IC C5B C4E *C5A H5A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C4E C5A C5B C5C 1.5300 112.20 180.00 123.50 1.3400 +IC C5C C5A *C5B H5B 1.3400 123.50 180.00 116.00 1.1000 +IC C5A C5B C5C C5D 1.5020 123.50 180.00 123.50 1.5020 +IC C5E C5B *C5C C5D 1.5020 123.50 180.00 123.50 1.5040 +IC C5B C5C C5D H5D1 1.3400 123.50 180.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D2 1.1110 111.50 120.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C5B C5C C5E C6A 1.3400 123.50 180.00 112.20 1.5300 +IC C6A C5C *C5E H5E1 1.5300 112.20 120.00 111.50 1.1110 +IC C6A C5C *C5E H5E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C5C C5E C6A C6B 1.5020 112.20 180.00 112.20 1.5020 +IC C6B C5E *C6A H6A1 1.5020 112.20 120.00 110.10 1.1110 +IC C6B C5E *C6A H6A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C5E C6A C6B C6C 1.5300 112.20 180.00 123.50 1.3400 +IC C6C C6A *C6B H6B 1.3400 123.50 180.00 116.00 1.1000 +IC C6A C6B C6C C6D 1.5020 123.50 180.00 123.50 1.5020 +IC C6E C6B *C6C C6D 1.5020 123.50 180.00 123.50 1.5040 +IC C6B C6C C6D H6D1 1.3400 123.50 180.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D2 1.1110 111.50 120.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C6B C6C C6E C7A 1.3400 123.50 180.00 112.20 1.5300 +IC C7A C6C *C6E H6E1 1.5300 112.20 120.00 111.50 1.1110 +IC C7A C6C *C6E H6E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C6C C6E C7A C7B 1.5020 112.20 180.00 112.20 1.5020 +IC C7B C6E *C7A H7A1 1.5020 112.20 120.00 110.10 1.1110 +IC C7B C6E *C7A H7A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C6E C7A C7B C7C 1.5300 112.20 180.00 123.50 1.3400 +IC C7C C7A *C7B H7B 1.3400 123.50 180.00 116.00 1.1000 +IC C7A C7B C7C C7D 1.5020 123.50 180.00 123.50 1.5020 +IC C7E C7B *C7C C7D 1.5020 123.50 180.00 123.50 1.5040 +IC C7B C7C C7D H7D1 1.3400 123.50 180.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D2 1.1110 111.50 120.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C7B C7C C7E C8A 1.3400 123.50 180.00 112.20 1.5300 +IC C8A C7C *C7E H7E1 1.5300 112.20 120.00 111.50 1.1110 +IC C8A C7C *C7E H7E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C7C C7E C8A C8B 1.5020 112.20 180.00 112.20 1.5020 +IC C8B C7E *C8A H8A1 1.5020 112.20 120.00 110.10 1.1110 +IC C8B C7E *C8A H8A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C7E C8A C8B C8C 1.5300 112.20 180.00 123.50 1.3400 +IC C8C C8A *C8B H8B 1.3400 123.50 180.00 116.00 1.1000 +IC C8A C8B C8C C8D 1.5020 123.50 180.00 123.50 1.5020 +IC C8E C8B *C8C C8D 1.5020 123.50 180.00 123.50 1.5040 +IC C8B C8C C8D H8D1 1.3400 123.50 180.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D2 1.1110 111.50 120.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C8B C8C C8E C9A 1.3400 123.50 180.00 112.20 1.5300 +IC C9A C8C *C8E H8E1 1.5300 112.20 120.00 111.50 1.1110 +IC C9A C8C *C8E H8E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C8C C8E C9A C9B 1.5020 112.20 180.00 112.20 1.5020 +IC C9B C8E *C9A H9A1 1.5020 112.20 120.00 110.10 1.1110 +IC C9B C8E *C9A H9A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C8E C9A C9B C9C 1.5300 112.20 180.00 123.50 1.3400 +IC C9C C9A *C9B H9B 1.3400 123.50 180.00 116.00 1.1000 +IC C9A C9B C9C C9D 1.5020 123.50 180.00 123.50 1.5020 +IC C9E C9B *C9C C9D 1.5020 123.50 180.00 123.50 1.5040 +IC C9B C9C C9D H9D1 1.3400 123.50 180.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D2 1.1110 111.50 120.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C9B C9C C9E C10A 1.3400 123.50 180.00 112.20 1.5300 +IC C10A C9C *C9E H9E1 1.5300 112.20 120.00 111.50 1.1110 +IC C10A C9C *C9E H9E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C9C C9E C10A C10B 1.5020 112.20 180.00 112.20 1.5020 +IC C10B C9E *C10A H10A1 1.5020 112.20 120.00 110.10 1.1110 +IC C10B C9E *C10A H10A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C9E C10A C10B C10C 1.5300 112.20 180.00 123.50 1.3400 +IC C10C C10A *C10B H10B 1.3400 123.50 180.00 116.00 1.1000 +IC C10A C10B C10C C10D 1.5020 123.50 180.00 123.50 1.5020 +IC C10E C10B *C10C C10D 1.5020 123.50 180.00 123.50 1.5040 +IC C10B C10C C10D H10D1 1.3400 123.50 180.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D2 1.1110 111.50 120.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C10B C10C C10E C11A 1.3400 123.50 180.00 112.20 1.5300 +IC C11A C10C *C10E H10E1 1.5300 112.20 120.00 111.50 1.1110 +IC C11A C10C *C10E H10E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C10C C10E C11A C11B 1.5020 112.20 180.00 112.20 1.5020 +IC C11B C10E *C11A H11A1 1.5020 112.20 120.00 110.10 1.1110 +IC C11B C10E *C11A H11A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C10E C11A C11B C11C 1.5300 112.20 180.00 123.50 1.3400 +IC C11C C11A *C11B H11B 1.3400 123.50 180.00 116.00 1.1000 +IC C11A C11B C11C C11D 1.5020 123.50 180.00 123.50 1.5020 +IC C11E C11B *C11C C11D 1.5020 123.50 180.00 123.50 1.5040 +IC C11B C11C C11D H11D1 1.3400 123.50 180.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D2 1.1110 111.50 120.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C11B C11C C11E C12A 1.3400 123.50 180.00 112.20 1.5300 +IC C12A C11C *C11E H11E1 1.5300 112.20 120.00 111.50 1.1110 +IC C12A C11C *C11E H11E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C11C C11E C12A C12B 1.5020 112.20 180.00 112.20 1.5020 +IC C12B C11E *C12A H12A1 1.5020 112.20 120.00 110.10 1.1110 +IC C12B C11E *C12A H12A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C11E C12A C12B C12C 1.5300 112.20 180.00 123.50 1.3400 +IC C12C C12A *C12B H12B 1.3400 123.50 180.00 116.00 1.1000 +IC C12A C12B C12C C12D 1.5020 123.50 180.00 123.50 1.5020 +IC C12E C12B *C12C C12D 1.5020 123.50 180.00 123.50 1.5040 +IC C12B C12C C12D H12D1 1.3400 123.50 180.00 111.50 1.1110 +IC H12D1 C12C *C12D H12D2 1.1110 111.50 120.00 111.50 1.1110 +IC H12D1 C12C *C12D H12D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C12B C12C C12E C13A 1.3400 123.50 180.00 112.20 1.5300 +IC C13A C12C *C12E H12E1 1.5300 112.20 120.00 111.50 1.1110 +IC C13A C12C *C12E H12E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C12C C12E C13A C13B 1.5020 112.20 180.00 112.20 1.5020 +IC C13B C12E *C13A H13A1 1.5020 112.20 120.00 110.10 1.1110 +IC C13B C12E *C13A H13A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C12E C13A C13B C13C 1.5300 112.20 180.00 123.50 1.3400 +IC C13C C13A *C13B H13B 1.3400 123.50 180.00 116.00 1.1000 +IC C13A C13B C13C C13E 1.5020 123.50 180.00 123.50 1.5040 +IC C13D C13B *C13C C13E 1.5040 123.50 180.00 123.50 1.5020 +IC C13B C13C C13D H13D1 1.3400 123.50 180.00 111.50 1.1110 +IC H13D1 C13C *C13D H13D2 1.1110 111.50 120.00 111.50 1.1110 +IC H13D1 C13C *C13D H13D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C13C C14A *C13E H13E1 1.3400 123.50 120.00 111.50 1.1110 +IC C13C C14A *C13E H13E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C13B C13C C13E C14A 1.3400 123.50 180.00 112.20 1.5300 +IC C13C C13E C14A C14B 1.5020 112.20 180.00 112.20 1.5020 +IC C14B C13E *C14A H14A1 1.5020 112.20 120.00 110.10 1.1110 +IC C14B C13E *C14A H14A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C13E C14A C14B C14C 1.5300 112.20 180.00 123.50 1.3400 +IC C14C C14A *C14B H14B 1.3400 123.50 180.00 116.00 1.1000 +IC C14A C14B C14C C14E 1.5020 123.50 180.00 123.50 1.5020 +IC C14E C14B *C14C C14D 1.5020 123.50 180.00 123.50 1.5040 +IC C14B C14C C14D H14D1 1.3400 123.50 180.00 111.50 1.1110 +IC H14D1 C14C *C14D H14D2 1.1110 111.50 120.00 111.50 1.1110 +IC H14D1 C14C *C14D H14D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C14B C14C C14E C15A 1.3400 123.50 180.00 112.20 1.5300 +IC C15A C14C *C14E H14E1 1.5300 112.20 120.00 111.50 1.1110 +IC C15A C14C *C14E H14E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C14C C14E C15A C15B 1.5020 112.20 180.00 112.20 1.5020 +IC C15B C14E *C15A H15A1 1.5020 112.20 120.00 110.10 1.1110 +IC C15B C14E *C15A H15A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C14E C15A C15B C15C 1.5300 112.20 180.00 123.50 1.3400 +IC C15C C15A *C15B H15B 1.3400 123.50 180.00 116.00 1.1000 +IC C15A C15B C15C C15E 1.5020 123.50 180.00 123.50 1.5040 +IC C15D C15B *C15C C15E 1.5040 123.50 180.00 123.50 1.5040 +IC C15B C15C C15D H15D1 1.3400 123.50 180.00 111.50 1.1110 +IC H15D1 C15C *C15D H15D2 1.1110 111.50 120.00 111.50 1.1110 +IC H15D1 C15C *C15D H15D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C15B C15C C15E H15E1 1.3400 123.50 180.00 111.50 1.1110 +IC H15E1 C15C *C15E H15E2 1.1110 111.50 120.00 111.50 1.1110 +IC H15E1 C15C *C15E H15E3 1.1110 111.50 -120.00 111.50 1.1110 + +RESI DL19PP -2.00 ! [name] +GROUP +ATOM P2 PG1 1.34 ! HO22 +ATOM O22 OG311 -0.71 ! | +ATOM HO22 HGP1 0.44 ! O22 !! based on RESI PPI2 +ATOM O23 OG2P1 -0.86 ! | +ATOM O24 OG2P1 -0.86 ! O23==P2==O24 (-) + ! | +ATOM P1 PG1 1.46 ! O12 +ATOM O12 OG304 -0.63 ! | +ATOM O13 OG2P1 -0.83 ! O13==P1==O14 (-) +ATOM O14 OG2P1 -0.83 ! | +ATOM O11 OG303 -0.62 ! O11 + ! | +ATOM C1A CG321 -0.08 ! H1A1--C1A--H1A2 +ATOM H1A1 HGA2 0.09 ! | +ATOM H1A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C1B CG321 -0.18 ! H1B1--C1B--H1B2 +ATOM H1B1 HGA2 0.09 ! | +ATOM H1B2 HGA2 0.09 ! | H1D1 +GROUP 0.00 ! | | +ATOM C1C CG311 -0.09 ! H1C--C1C--C1D--H1D2 +ATOM H1C HGA1 0.09 ! | | +GROUP 0.00 ! | H1D3 +ATOM C1D CG331 -0.27 ! | +ATOM H1D1 HGA3 0.09 ! | +ATOM H1D2 HGA3 0.09 ! | +ATOM H1D3 HGA3 0.09 ! H1E1--C1E--H1E2 +GROUP 0.00 ! | +ATOM C1E CG321 -0.18 ! | +ATOM H1E1 HGA2 0.09 ! | +ATOM H1E2 HGA2 0.09 ! H2A1--C2A--H2A2 +GROUP 0.00 ! | +ATOM C2A CG321 -0.18 ! | +ATOM H2A1 HGA2 0.09 ! | +ATOM H2A2 HGA2 0.09 ! C2B--H2B (cis) +GROUP 0.00 ! || +ATOM C2B CG2D1 -0.15 ! || H2D1 +ATOM H2B HGA4 0.15 ! || | +GROUP 0.00 ! C2C--C2D--H2D2 +ATOM C2C CG2D1 0.00 ! | | +GROUP 0.00 ! | H2D3 +ATOM C2D CG331 -0.27 ! ! +ATOM H2D1 HGA3 0.09 ! ! +ATOM H2D2 HGA3 0.09 ! ! +ATOM H2D3 HGA3 0.09 ! H2E1--C2E--H2E2 +GROUP 0.00 ! ! +ATOM C2E CG321 -0.18 ! ! +ATOM H2E1 HGA2 0.09 ! | +ATOM H2E2 HGA2 0.09 ! H3A1--C3A--H3A2 +GROUP 0.00 ! | +ATOM C3A CG321 -0.18 ! | +ATOM H3A1 HGA2 0.09 ! | +ATOM H3A2 HGA2 0.09 ! C3B--H3B (cis) +GROUP 0.00 ! || +ATOM C3B CG2D1 -0.15 ! || H3D1 +ATOM H3B HGA4 0.15 ! || | +GROUP 0.00 ! C3C--C3D--H3D2 +ATOM C3C CG2D1 0.00 ! | | +GROUP 0.00 ! | H3D3 +ATOM C3D CG331 -0.27 ! ! +ATOM H3D1 HGA3 0.09 ! ! +ATOM H3D2 HGA3 0.09 ! ! +ATOM H3D3 HGA3 0.09 ! H3E1--C3E--H3E2 +GROUP 0.00 ! ! +ATOM C3E CG321 -0.18 ! ! +ATOM H3E1 HGA2 0.09 ! | +ATOM H3E2 HGA2 0.09 ! H4A1--C4A--H4A2 +GROUP 0.00 ! | +ATOM C4A CG321 -0.18 ! | +ATOM H4A1 HGA2 0.09 ! | +ATOM H4A2 HGA2 0.09 ! C4B--H4B (cis) +GROUP 0.00 ! || +ATOM C4B CG2D1 -0.15 ! || H4D1 +ATOM H4B HGA4 0.15 ! || | +GROUP 0.00 ! C4C--C4D--H4D2 +ATOM C4C CG2D1 0.00 ! | | +GROUP 0.00 ! | H4D3 +ATOM C4D CG331 -0.27 ! ! +ATOM H4D1 HGA3 0.09 ! ! +ATOM H4D2 HGA3 0.09 ! ! +ATOM H4D3 HGA3 0.09 ! H4E1--C4E--H4E2 +GROUP 0.00 ! ! +ATOM C4E CG321 -0.18 ! ! +ATOM H4E1 HGA2 0.09 ! | +ATOM H4E2 HGA2 0.09 ! H5A1--C5A--H5A2 +GROUP 0.00 ! | +ATOM C5A CG321 -0.18 ! | +ATOM H5A1 HGA2 0.09 ! | +ATOM H5A2 HGA2 0.09 ! C5B--H5B (cis) +GROUP 0.00 ! || +ATOM C5B CG2D1 -0.15 ! || H5D1 +ATOM H5B HGA4 0.15 ! || | +GROUP 0.00 ! C5C--C5D--H5D2 +ATOM C5C CG2D1 0.00 ! | | +GROUP 0.00 ! | H5D3 +ATOM C5D CG331 -0.27 ! ! +ATOM H5D1 HGA3 0.09 ! ! +ATOM H5D2 HGA3 0.09 ! ! +ATOM H5D3 HGA3 0.09 ! H5E1--C5E--H5E2 +GROUP 0.00 ! ! +ATOM C5E CG321 -0.18 ! ! +ATOM H5E1 HGA2 0.09 ! | +ATOM H5E2 HGA2 0.09 ! H6A1--C6A--H6A2 +GROUP 0.00 ! | +ATOM C6A CG321 -0.18 ! | +ATOM H6A1 HGA2 0.09 ! | +ATOM H6A2 HGA2 0.09 ! C6B--H6B (cis) +GROUP 0.00 ! || +ATOM C6B CG2D1 -0.15 ! || H6D1 +ATOM H6B HGA4 0.15 ! || | +GROUP 0.00 ! C6C--C6D--H6D2 +ATOM C6C CG2D1 0.00 ! | | +GROUP 0.00 ! | H6D3 +ATOM C6D CG331 -0.27 ! ! +ATOM H6D1 HGA3 0.09 ! ! +ATOM H6D2 HGA3 0.09 ! ! +ATOM H6D3 HGA3 0.09 ! H6E1-C6E--H6E2 +GROUP 0.00 ! ! +ATOM C6E CG321 -0.18 ! ! +ATOM H6E1 HGA2 0.09 ! | +ATOM H6E2 HGA2 0.09 ! H7A1--C7A--H7A2 +GROUP 0.00 ! | +ATOM C7A CG321 -0.18 ! | +ATOM H7A1 HGA2 0.09 ! | +ATOM H7A2 HGA2 0.09 ! C7B--H7B (cis) +GROUP 0.00 ! || +ATOM C7B CG2D1 -0.15 ! || H7D1 +ATOM H7B HGA4 0.15 ! || | +GROUP 0.00 ! C7C--C7D--H7D2 +ATOM C7C CG2D1 0.00 ! | | +GROUP 0.00 ! | H7D3 +ATOM C7D CG331 -0.27 ! ! +ATOM H7D1 HGA3 0.09 ! ! +ATOM H7D2 HGA3 0.09 ! ! +ATOM H7D3 HGA3 0.09 ! H7E1-C7E--H7E2 +GROUP 0.00 ! ! +ATOM C7E CG321 -0.18 ! ! +ATOM H7E1 HGA2 0.09 ! | +ATOM H7E2 HGA2 0.09 ! H8A1--C8A--H8A2 +GROUP 0.00 ! | +ATOM C8A CG321 -0.18 ! | +ATOM H8A1 HGA2 0.09 ! | +ATOM H8A2 HGA2 0.09 ! C8B--H8B (cis) +GROUP 0.00 ! || +ATOM C8B CG2D1 -0.15 ! || H8D1 +ATOM H8B HGA4 0.15 ! || | +GROUP 0.00 ! C8C--C8D--H8D2 +ATOM C8C CG2D1 0.00 ! | | +GROUP 0.00 ! | H8D3 +ATOM C8D CG331 -0.27 ! ! +ATOM H8D1 HGA3 0.09 ! ! +ATOM H8D2 HGA3 0.09 ! ! +ATOM H8D3 HGA3 0.09 ! H8E1-C8E--H8E2 +GROUP 0.00 ! ! +ATOM C8E CG321 -0.18 ! ! +ATOM H8E1 HGA2 0.09 ! | +ATOM H8E2 HGA2 0.09 ! H9A1--C9A--H9A2 +GROUP 0.00 ! | +ATOM C9A CG321 -0.18 ! | +ATOM H9A1 HGA2 0.09 ! | +ATOM H9A2 HGA2 0.09 ! C9B--H9B (cis) +GROUP 0.00 ! || +ATOM C9B CG2D1 -0.15 ! || H9D1 +ATOM H9B HGA4 0.15 ! || | +GROUP 0.00 ! C9C--C9D--H9D2 +ATOM C9C CG2D1 0.00 ! | | +GROUP 0.00 ! | H9D3 +ATOM C9D CG331 -0.27 ! ! +ATOM H9D1 HGA3 0.09 ! ! +ATOM H9D2 HGA3 0.09 ! ! +ATOM H9D3 HGA3 0.09 ! H9E1-C9E--H9E2 +GROUP 0.00 ! ! +ATOM C9E CG321 -0.18 ! ! +ATOM H9E1 HGA2 0.09 ! | +ATOM H9E2 HGA2 0.09 ! H10A1--C10A--H10A2 +GROUP 0.00 ! | +ATOM C10A CG321 -0.18 ! | +ATOM H10A1 HGA2 0.09 ! | +ATOM H10A2 HGA2 0.09 ! C10B--H110B (cis) +GROUP 0.00 ! || +ATOM C10B CG2D1 -0.15 ! || H10D1 +ATOM H10B HGA4 0.15 ! || | +GROUP 0.00 ! C10C-C10D--H10D2 +ATOM C10C CG2D1 0.00 ! | | +GROUP 0.00 ! | H10D3 +ATOM C10D CG331 -0.27 ! ! +ATOM H10D1 HGA3 0.09 ! ! +ATOM H10D2 HGA3 0.09 ! ! +ATOM H10D3 HGA3 0.09 ! H10E1-C10E--H10E2 +GROUP 0.00 ! ! +ATOM C10E CG321 -0.18 ! ! +ATOM H10E1 HGA2 0.09 ! | +ATOM H10E2 HGA2 0.09 ! H11A1--C11A--H11A2 +GROUP 0.00 ! | +ATOM C11A CG321 -0.18 ! | +ATOM H11A1 HGA2 0.09 ! | +ATOM H11A2 HGA2 0.09 ! C11B--H11B (cis) +GROUP 0.00 ! || +ATOM C11B CG2D1 -0.15 ! || H11D1 +ATOM H11B HGA4 0.15 ! || | +GROUP 0.00 ! C11C-C11D--H11D2 +ATOM C11C CG2D1 0.00 ! | | +GROUP 0.00 ! | H11D3 +ATOM C11D CG331 -0.27 ! ! +ATOM H11D1 HGA3 0.09 ! ! +ATOM H11D2 HGA3 0.09 ! ! +ATOM H11D3 HGA3 0.09 ! H11E1-C11E--H11E2 +GROUP 0.00 ! ! +ATOM C11E CG321 -0.18 ! ! +ATOM H11E1 HGA2 0.09 ! | +ATOM H11E2 HGA2 0.09 ! H12A1--C12A--H12A2 +GROUP 0.00 ! | +ATOM C12A CG321 -0.18 ! | +ATOM H12A1 HGA2 0.09 ! | +ATOM H12A2 HGA2 0.09 ! C12B--H12B (cis) +GROUP 0.00 ! || +ATOM C12B CG2D1 -0.15 ! || H12D1 +ATOM H12B HGA4 0.15 ! || | +GROUP 0.00 ! C12C-C12D--H12D2 +ATOM C12C CG2D1 0.00 ! | | +GROUP 0.00 ! | H12D3 +ATOM C12D CG331 -0.27 ! ! +ATOM H12D1 HGA3 0.09 ! ! +ATOM H12D2 HGA3 0.09 ! ! +ATOM H12D3 HGA3 0.09 ! H1E12-C12E--H12E2 +GROUP 0.00 ! ! +ATOM C12E CG321 -0.18 ! ! +ATOM H12E1 HGA2 0.09 ! | +ATOM H12E2 HGA2 0.09 ! H13A1--C13A--H13A2 +GROUP 0.00 ! | +ATOM C13A CG321 -0.18 ! | +ATOM H13A1 HGA2 0.09 ! | +ATOM H13A2 HGA2 0.09 ! C13B--H13B (cis) +GROUP 0.00 ! || +ATOM C13B CG2D1 -0.15 ! || H13D1 +ATOM H13B HGA4 0.15 ! || | +GROUP 0.00 ! C13C-C13D--H13D2 +ATOM C13C CG2D1 0.00 ! | | +GROUP 0.00 ! | H13D3 +ATOM C13D CG331 -0.27 ! ! +ATOM H13D1 HGA3 0.09 ! ! +ATOM H13D2 HGA3 0.09 ! ! +ATOM H13D3 HGA3 0.09 ! H13E1-C13E--H13E2 +GROUP 0.00 ! ! +ATOM C13E CG321 -0.18 ! ! +ATOM H13E1 HGA2 0.09 ! | +ATOM H13E2 HGA2 0.09 ! H14A1--C14A--H14A2 +GROUP 0.00 ! | +ATOM C14A CG321 -0.18 ! | +ATOM H14A1 HGA2 0.09 ! | +ATOM H14A2 HGA2 0.09 ! C14B--H14B (cis) +GROUP 0.00 ! || +ATOM C14B CG2D1 -0.15 ! || H14D1 +ATOM H14B HGA4 0.15 ! || | +GROUP 0.00 ! C14C-C14D--H14D2 +ATOM C14C CG2D1 0.00 ! | | +GROUP 0.00 ! | H14D3 +ATOM C14D CG331 -0.27 ! ! +ATOM H14D1 HGA3 0.09 ! ! +ATOM H14D2 HGA3 0.09 ! ! +ATOM H14D3 HGA3 0.09 ! H14E1-C14E--H14E2 +GROUP 0.00 ! | +ATOM C14E CG321 -0.18 ! | +ATOM H14E1 HGA2 0.09 ! | +ATOM H14E2 HGA2 0.09 ! H15A1--C15A--H15A2 +GROUP 0.00 ! | +ATOM C15A CG321 -0.18 ! | +ATOM H15A1 HGA2 0.09 ! | +ATOM H15A2 HGA2 0.09 ! C15B--H15B (cis) +GROUP 0.00 ! || +ATOM C15B CG2D1 -0.15 ! || H15D1 +ATOM H15B HGA4 0.15 ! || | +GROUP 0.00 ! C15C-C15D--H15D2 +ATOM C15C CG2D1 0.00 ! | | +GROUP 0.00 ! | H15D3 +ATOM C15D CG331 -0.27 ! | +ATOM H15D1 HGA3 0.09 ! | +ATOM H15D2 HGA3 0.09 ! | +ATOM H15D3 HGA3 0.09 ! H15E1-C15E--H15E2 +GROUP 0.00 ! | +ATOM C15E CG321 -0.18 ! | +ATOM H15E1 HGA2 0.09 ! | +ATOM H15E2 HGA2 0.09 ! H16A1--C16A--H16A2 +GROUP 0.00 ! | +ATOM C16A CG321 -0.18 ! | +ATOM H16A1 HGA2 0.09 ! | +ATOM H16A2 HGA2 0.09 ! C16B--H16B (cis) +GROUP 0.00 ! || +ATOM C16B CG2D1 -0.15 ! || H16D1 +ATOM H16B HGA4 0.15 ! || | +GROUP 0.00 ! C16C-C16D--H16D2 +ATOM C16C CG2D1 0.00 ! | | +GROUP 0.00 ! | H16D3 +ATOM C16D CG331 -0.27 ! | +ATOM H16D1 HGA3 0.09 ! | +ATOM H16D2 HGA3 0.09 ! | +ATOM H16D3 HGA3 0.09 ! H16E1-C16E--H16E2 +GROUP 0.00 ! | +ATOM C16E CG321 -0.18 ! | +ATOM H16E1 HGA2 0.09 ! | +ATOM H16E2 HGA2 0.09 ! H17A1--C17A--H17A2 +GROUP 0.00 ! | +ATOM C17A CG321 -0.18 ! | +ATOM H17A1 HGA2 0.09 ! | +ATOM H17A2 HGA2 0.09 ! C17B--H17B (trans) +GROUP 0.00 ! || +ATOM C17B CG2D1 -0.15 ! || H17D1 +ATOM H17B HGA4 0.15 ! || | +GROUP 0.00 ! C17C-C17D--H17D2 +ATOM C17C CG2D1 0.00 ! | | +GROUP 0.00 ! | H17D3 +ATOM C17D CG331 -0.27 ! | +ATOM H17D1 HGA3 0.09 ! | +ATOM H17D2 HGA3 0.09 ! | +ATOM H17D3 HGA3 0.09 ! H17E1-C17E--H17E2 +GROUP 0.00 ! | +ATOM C17E CG321 -0.18 ! | +ATOM H17E1 HGA2 0.09 ! | +ATOM H17E2 HGA2 0.09 ! H18A1--C18A--H18A2 +GROUP 0.00 ! | +ATOM C18A CG321 -0.18 ! | +ATOM H18A1 HGA2 0.09 ! | +ATOM H18A2 HGA2 0.09 ! C18B--H18B (trans) +GROUP 0.00 ! || +ATOM C18B CG2D1 -0.15 ! || H18D1 +ATOM H18B HGA4 0.15 ! || | +GROUP 0.00 ! C18C-C18D--H18D2 +ATOM C18C CG2D1 0.00 ! | | +GROUP 0.00 ! | H18D3 +ATOM C18D CG331 -0.27 ! | +ATOM H18D1 HGA3 0.09 ! | +ATOM H18D2 HGA3 0.09 ! | +ATOM H18D3 HGA3 0.09 ! H18E1-C18E--H18E2 +GROUP 0.00 ! | +ATOM C18E CG321 -0.18 ! | +ATOM H18E1 HGA2 0.09 ! | +ATOM H18E2 HGA2 0.09 ! H19A1--C19A--H19A2 +GROUP 0.00 ! | +ATOM C19A CG321 -0.18 ! | +ATOM H19A1 HGA2 0.09 ! | +ATOM H19A2 HGA2 0.09 ! C19B--H19B +GROUP 0.00 ! || +ATOM C19B CG2D1 -0.15 ! || H19D1 +ATOM H19B HGA4 0.15 ! || | +GROUP 0.00 ! C19C-C19D--H19D2 +ATOM C19C CG2D1 0.00 ! | | +GROUP 0.00 ! | H19D3 +ATOM C19D CG331 -0.27 ! | +ATOM H19D1 HGA3 0.09 ! | +ATOM H19D2 HGA3 0.09 ! | +ATOM H19D3 HGA3 0.09 ! H19E1-C19E--H19E2 +GROUP 0.00 ! +ATOM C19E CG331 -0.27 ! +ATOM H19E1 HGA3 0.09 ! +ATOM H19E2 HGA3 0.09 ! +ATOM H19E3 HGA3 0.09 ! + +BOND O22 HO22 P2 O22 P2 O23 P2 O24 P2 O12 ! Phosphate group 2 +BOND P1 O12 P1 O13 P1 O14 P1 O11 O11 C1A ! Phosphate group 1 +BOND C1A C1B C1B C1C C1C C1D C1C C1E ! alpha isoprene backbone carbons +BOND C1A H1A1 C1A H1A2 ! C1A hydrogens +BOND C1B H1B1 C1B H1B2 ! C1B hydrogens +BOND C1C H1C ! C1C hydrogen +BOND C1D H1D1 C1D H1D2 C1D H1D3 ! C1D hydrogens +BOND C1E H1E1 C1E H1E2 ! C1E hydrogens +BOND C1E C2A ! isoprene linking bond +BOND C2A C2B C2C C2D C2C C2E ! cis isoprene backbone carbons +DOUBLE C2B C2C ! cis double bond +BOND C2A H2A1 C2A H2A2 ! C2A hydrogens +BOND C2B H2B ! C2B hydrogen +BOND C2D H2D1 C2D H2D2 C2D H2D3 ! C2D hydrogens +BOND C2E H2E1 C2E H2E2 ! C2E hydrogens +BOND C2E C3A ! isoprene linking bond +BOND C3A C3B C3C C3D C3C C3E ! cis isoprene backbone carbons +DOUBLE C3B C3C ! cis double bond +BOND C3A H3A1 C3A H3A2 ! C3A hydrogens +BOND C3B H3B ! C3B hydrogen +BOND C3D H3D1 C3D H3D2 C3D H3D3 ! C3D hydrogens +BOND C3E H3E1 C3E H3E2 ! C3E hydrogens +BOND C3E C4A ! isoprene linking bond +BOND C4A C4B C4C C4D C4C C4E ! cis isoprene backbone carbons +DOUBLE C4B C4C ! cis double bond +BOND C4A H4A1 C4A H4A2 ! C4A hydrogens +BOND C4B H4B ! C4B hydrogen +BOND C4D H4D1 C4D H4D2 C4D H4D3 ! C4D hydrogens +BOND C4E H4E1 C4E H4E2 ! C4E hydrogens +BOND C4E C5A ! isoprene linking bond +BOND C5A C5B C5C C5D C5C C5E ! cis isoprene backbone carbons +DOUBLE C5B C5C ! cis double bond +BOND C5A H5A1 C5A H5A2 ! C5A hydrogens +BOND C5B H5B ! C5B hydrogen +BOND C5D H5D1 C5D H5D2 C5D H5D3 ! C5D hydrogens +BOND C5E H5E1 C5E H5E2 ! C5E hydrogens +BOND C5E C6A ! isoprene linking bond +BOND C6A C6B C6C C6D C6C C6E ! cis isoprene backbone carbons +DOUBLE C6B C6C ! cis double bond +BOND C6A H6A1 C6A H6A2 ! C6A hydrogens +BOND C6B H6B ! C6B hydrogen +BOND C6D H6D1 C6D H6D2 C6D H6D3 ! C6D hydrogens +BOND C6E H6E1 C6E H6E2 ! C6E hydrogens +BOND C6E C7A ! isoprene linking bond +BOND C7A C7B C7C C7D C7C C7E ! cis isoprene backbone carbons +DOUBLE C7B C7C ! cis double bond +BOND C7A H7A1 C7A H7A2 ! C7A hydrogens +BOND C7B H7B ! C7B hydrogen +BOND C7D H7D1 C7D H7D2 C7D H7D3 ! C7D hydrogens +BOND C7E H7E1 C7E H7E2 ! C7E hydrogens +BOND C7E C8A ! isoprene linking bond +BOND C8A C8B C8C C8D C8C C8E ! cis isoprene backbone carbons +DOUBLE C8B C8C ! cis double bond +BOND C8A H8A1 C8A H8A2 ! C8A hydrogens +BOND C8B H8B ! C8B hydrogen +BOND C8D H8D1 C8D H8D2 C8D H8D3 ! C8D hydrogens +BOND C8E H8E1 C8E H8E2 ! C8E hydrogens +BOND C8E C9A ! isoprene linking bond +BOND C9A C9B C9C C9D C9C C9E ! cis isoprene backbone carbons +DOUBLE C9B C9C ! cis double bond +BOND C9A H9A1 C9A H9A2 ! C9A hydrogens +BOND C9B H9B ! C9B hydrogen +BOND C9D H9D1 C9D H9D2 C9D H9D3 ! C9D hydrogens +BOND C9E H9E1 C9E H9E2 ! C9E hydrogens +BOND C9E C10A ! isoprene linking bond +BOND C10A C10B C10C C10D C10C C10E ! cis isoprene backbone carbons +DOUBLE C10B C10C ! cis double bond +BOND C10A H10A1 C10A H10A2 ! C10A hydrogens +BOND C10B H10B ! C10B hydrogen +BOND C10D H10D1 C10D H10D2 C10D H10D3 ! C10D hydrogens +BOND C10E H10E1 C10E H10E2 ! C10E hydrogens +BOND C10E C11A ! isoprene linking bond +BOND C11A C11B C11C C11D C11C C11E ! cis isoprene backbone carbons +DOUBLE C11B C11C ! cis double bond +BOND C11A H11A1 C11A H11A2 ! C11A hydrogens +BOND C11B H11B ! C11B hydrogen +BOND C11D H11D1 C11D H11D2 C11D H11D3 ! C11D hydrogens +BOND C11E H11E1 C11E H11E2 ! C11E hydrogens +BOND C11E C12A ! isoprene linking bond +BOND C12A C12B C12C C12D C12C C12E ! cis isoprene backbone carbons +DOUBLE C12B C12C ! cis double bond +BOND C12A H12A1 C12A H12A2 ! C12A hydrogens +BOND C12B H12B ! C12B hydrogen +BOND C12D H12D1 C12D H12D2 C12D H12D3 ! C12D hydrogens +BOND C12E H12E1 C12E H12E2 ! C12E hydrogens +BOND C12E C13A ! isoprene linking bond +BOND C13A C13B C13C C13D C13C C13E ! cis isoprene backbone carbons +DOUBLE C13B C13C ! cis double bond +BOND C13A H13A1 C13A H13A2 ! C13A hydrogens +BOND C13B H13B ! C13B hydrogen +BOND C13D H13D1 C13D H13D2 C13D H13D3 ! C13D hydrogens +BOND C13E H13E1 C13E H13E2 ! C13E hydrogens +BOND C13E C14A ! isoprene linking bond +BOND C14A C14B C14C C14D C14C C14E ! cis isoprene backbone carbons +DOUBLE C14B C14C ! cis double bond +BOND C14A H14A1 C14A H14A2 ! C14A hydrogens +BOND C14B H14B ! C14B hydrogen +BOND C14D H14D1 C14D H14D2 C14D H14D3 ! C14D hydrogens +BOND C14E H14E1 C14E H14E2 ! C14E hydrogens +BOND C14E C15A ! isoprene linking bond +BOND C15A C15B C15C C15D C15C C15E ! cis isoprene backbone carbons +DOUBLE C15B C15C ! cis double bond +BOND C15A H15A1 C15A H15A2 ! C15A hydrogens +BOND C15B H15B ! C15B hydrogen +BOND C15D H15D1 C15D H15D2 C15D H15D3 ! C15D hydrogens +BOND C15E H15E1 C15E H15E2 ! C15E hydrogens +BOND C15E C16A ! isoprene linking bond +BOND C16A C16B C16C C16D C16C C16E ! cis isoprene backbone carbons +DOUBLE C16B C16C ! cis double bond +BOND C16A H16A1 C16A H16A2 ! C16A hydrogens +BOND C16B H16B ! C16B hydrogen +BOND C16D H16D1 C16D H16D2 C16D H16D3 ! C16D hydrogens +BOND C16E H16E1 C16E H16E2 ! C16E hydrogens +BOND C16E C17A ! isoprene linking bond +BOND C17A C17B C17C C17D C17C C17E ! trans isoprene backbone carbons +DOUBLE C17B C17C ! trans double bond +BOND C17A H17A1 C17A H17A2 ! C17A hydrogens +BOND C17B H17B ! C17B hydrogen +BOND C17D H17D1 C17D H17D2 C17D H17D3 ! C17D hydrogens +BOND C17E H17E1 C17E H17E2 ! C17E hydrogens +BOND C17E C18A ! isoprene linking bond +BOND C18A C18B C18C C18D C18C C18E ! trans isoprene backbone carbons +DOUBLE C18B C18C ! trans double bond +BOND C18A H18A1 C18A H18A2 ! C18A hydrogens +BOND C18B H18B ! C18B hydrogen +BOND C18D H18D1 C18D H18D2 C18D H18D3 ! C18D hydrogens +BOND C18E H18E1 C18E H18E2 ! C18E hydrogens +BOND C18E C19A ! isoprene linking bond +BOND C19A C19B C19C C19D C19C C19E ! omega isoprene backbone carbons +DOUBLE C19B C19C ! omega double bond +BOND C19A H19A1 C19A H19A2 ! C19A hydrogens +BOND C19B H19B ! C19B hydrogen +BOND C19D H19D1 C19D H19D2 C19D H19D3 ! C19D hydrogens +BOND C19E H19E1 C19E H19E2 C19E H19E3 ! C19E hydrogens +IC O22 O12 *P2 O23 1.6100 111.00 120.00 111.60 1.5100 +IC O22 O12 *P2 O24 1.6100 111.00 -120.00 111.60 1.5100 +IC O12 P2 O22 HO22 1.6750 111.00 180.00 115.00 0.9600 +IC O22 P2 O12 P1 1.6100 111.00 180.00 143.00 1.6750 +IC P2 O12 P1 O11 1.6750 143.00 180.00 105.00 1.6500 +IC O11 O12 *P1 O13 1.6500 105.00 120.00 111.60 1.5100 +IC O11 O12 *P1 O14 1.5100 111.60 -120.00 111.60 1.5100 +IC O12 P1 O11 C1A 1.6750 105.00 180.00 120.00 1.4400 +IC P1 O11 C1A C1B 1.6500 120.00 180.00 110.10 1.5300 +IC C1B O11 *C1A H1A1 1.5300 110.10 120.00 109.50 1.1110 +IC C1B O11 *C1A H1A2 1.5300 110.10 -120.00 109.50 1.1110 +IC O11 C1A C1B C1C 1.4400 110.10 180.00 113.50 1.5380 +IC C1C C1A *C1B H1B1 1.5380 113.50 120.00 110.10 1.1110 +IC C1C C1A *C1B H1B2 1.5380 113.50 -120.00 110.10 1.1110 +IC C1A C1B C1C C1E 1.5300 113.50 180.00 113.50 1.5380 +IC C1E C1B *C1C C1D 1.5380 113.50 -120.00 114.00 1.5380 +IC C1E C1B *C1C H1C 1.5380 114.00 120.00 110.10 1.1110 +IC C1B C1C C1D H1D1 1.5380 114.00 180.00 110.10 1.1110 +IC H1D1 C1C *C1D H1D2 1.1110 110.10 120.00 110.10 1.1110 +IC H1D1 C1C *C1D H1D3 1.1110 110.10 -120.00 110.10 1.1110 +IC C1B C1C C1E C2A 1.5380 113.50 180.00 113.50 1.5300 +IC C2A C1C *C1E H1E1 1.5300 113.50 120.00 110.10 1.1110 +IC C2A C1C *C1E H1E2 1.1110 110.10 -120.00 110.10 1.1110 +IC C1C C1E C2A C2B 1.5380 113.50 180.00 112.20 1.5020 +IC C2B C1E *C2A H2A1 1.5020 112.20 120.00 110.10 1.1110 +IC C2B C1E *C2A H2A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C1E C2A C2B C2C 1.5300 112.20 180.00 123.50 1.3400 +IC C2C C2A *C2B H2B 1.3400 123.50 180.00 116.00 1.1000 +IC C2A C2B C2C C2D 1.5020 123.50 180.00 123.50 1.5020 +IC C2E C2B *C2C C2D 1.5020 123.50 180.00 123.50 1.5040 +IC C2B C2C C2D H2D1 1.3400 123.50 180.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D2 1.1110 111.50 120.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C2B C2C C2E C3A 1.3400 123.50 180.00 112.20 1.5300 +IC C3A C2C *C2E H2E1 1.5300 112.20 120.00 111.50 1.1110 +IC C3A C2C *C2E H2E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C2C C2E C3A C3B 1.5020 112.20 180.00 112.20 1.5020 +IC C3B C2E *C3A H3A1 1.5020 112.20 120.00 110.10 1.1110 +IC C3B C2E *C3A H3A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C2E C3A C3B C3C 1.5300 112.20 180.00 123.50 1.3400 +IC C3C C3A *C3B H3B 1.3400 123.50 180.00 116.00 1.1000 +IC C3A C3B C3C C3D 1.5020 123.50 180.00 123.50 1.5020 +IC C3E C3B *C3C C3D 1.5020 123.50 180.00 123.50 1.5040 +IC C3B C3C C3D H3D1 1.3400 123.50 180.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D2 1.1110 111.50 120.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C3B C3C C3E C4A 1.3400 123.50 180.00 112.20 1.5300 +IC C4A C3C *C3E H3E1 1.5300 112.20 120.00 111.50 1.1110 +IC C4A C3C *C3E H3E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C3C C3E C4A C4B 1.5020 112.20 180.00 112.20 1.5020 +IC C4B C3E *C4A H4A1 1.5020 112.20 120.00 110.10 1.1110 +IC C4B C3E *C4A H4A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C3E C4A C4B C4C 1.5300 112.20 180.00 123.50 1.3400 +IC C4C C4A *C4B H4B 1.3400 123.50 180.00 116.00 1.1000 +IC C4A C4B C4C C4D 1.5020 123.50 180.00 123.50 1.5020 +IC C4E C4B *C4C C4D 1.5020 123.50 180.00 123.50 1.5040 +IC C4B C4C C4D H4D1 1.3400 123.50 180.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D2 1.1110 111.50 120.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C4B C4C C4E C5A 1.3400 123.50 180.00 112.20 1.5300 +IC C5A C4C *C4E H4E1 1.5300 112.20 120.00 111.50 1.1110 +IC C5A C4C *C4E H4E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C4C C4E C5A C5B 1.5020 112.20 180.00 112.20 1.5020 +IC C5B C4E *C5A H5A1 1.5020 112.20 120.00 110.10 1.1110 +IC C5B C4E *C5A H5A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C4E C5A C5B C5C 1.5300 112.20 180.00 123.50 1.3400 +IC C5C C5A *C5B H5B 1.3400 123.50 180.00 116.00 1.1000 +IC C5A C5B C5C C5D 1.5020 123.50 180.00 123.50 1.5020 +IC C5E C5B *C5C C5D 1.5020 123.50 180.00 123.50 1.5040 +IC C5B C5C C5D H5D1 1.3400 123.50 180.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D2 1.1110 111.50 120.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C5B C5C C5E C6A 1.3400 123.50 180.00 112.20 1.5300 +IC C6A C5C *C5E H5E1 1.5300 112.20 120.00 111.50 1.1110 +IC C6A C5C *C5E H5E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C5C C5E C6A C6B 1.5020 112.20 180.00 112.20 1.5020 +IC C6B C5E *C6A H6A1 1.5020 112.20 120.00 110.10 1.1110 +IC C6B C5E *C6A H6A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C5E C6A C6B C6C 1.5300 112.20 180.00 123.50 1.3400 +IC C6C C6A *C6B H6B 1.3400 123.50 180.00 116.00 1.1000 +IC C6A C6B C6C C6D 1.5020 123.50 180.00 123.50 1.5020 +IC C6E C6B *C6C C6D 1.5020 123.50 180.00 123.50 1.5040 +IC C6B C6C C6D H6D1 1.3400 123.50 180.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D2 1.1110 111.50 120.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C6B C6C C6E C7A 1.3400 123.50 180.00 112.20 1.5300 +IC C7A C6C *C6E H6E1 1.5300 112.20 120.00 111.50 1.1110 +IC C7A C6C *C6E H6E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C6C C6E C7A C7B 1.5020 112.20 180.00 112.20 1.5020 +IC C7B C6E *C7A H7A1 1.5020 112.20 120.00 110.10 1.1110 +IC C7B C6E *C7A H7A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C6E C7A C7B C7C 1.5300 112.20 180.00 123.50 1.3400 +IC C7C C7A *C7B H7B 1.3400 123.50 180.00 116.00 1.1000 +IC C7A C7B C7C C7D 1.5020 123.50 180.00 123.50 1.5020 +IC C7E C7B *C7C C7D 1.5020 123.50 180.00 123.50 1.5040 +IC C7B C7C C7D H7D1 1.3400 123.50 180.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D2 1.1110 111.50 120.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C7B C7C C7E C8A 1.3400 123.50 180.00 112.20 1.5300 +IC C8A C7C *C7E H7E1 1.5300 112.20 120.00 111.50 1.1110 +IC C8A C7C *C7E H7E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C7C C7E C8A C8B 1.5020 112.20 180.00 112.20 1.5020 +IC C8B C7E *C8A H8A1 1.5020 112.20 120.00 110.10 1.1110 +IC C8B C7E *C8A H8A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C7E C8A C8B C8C 1.5300 112.20 180.00 123.50 1.3400 +IC C8C C8A *C8B H8B 1.3400 123.50 180.00 116.00 1.1000 +IC C8A C8B C8C C8D 1.5020 123.50 180.00 123.50 1.5020 +IC C8E C8B *C8C C8D 1.5020 123.50 180.00 123.50 1.5040 +IC C8B C8C C8D H8D1 1.3400 123.50 180.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D2 1.1110 111.50 120.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C8B C8C C8E C9A 1.3400 123.50 180.00 112.20 1.5300 +IC C9A C8C *C8E H8E1 1.5300 112.20 120.00 111.50 1.1110 +IC C9A C8C *C8E H8E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C8C C8E C9A C9B 1.5020 112.20 180.00 112.20 1.5020 +IC C9B C8E *C9A H9A1 1.5020 112.20 120.00 110.10 1.1110 +IC C9B C8E *C9A H9A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C8E C9A C9B C9C 1.5300 112.20 180.00 123.50 1.3400 +IC C9C C9A *C9B H9B 1.3400 123.50 180.00 116.00 1.1000 +IC C9A C9B C9C C9D 1.5020 123.50 180.00 123.50 1.5020 +IC C9E C9B *C9C C9D 1.5020 123.50 180.00 123.50 1.5040 +IC C9B C9C C9D H9D1 1.3400 123.50 180.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D2 1.1110 111.50 120.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C9B C9C C9E C10A 1.3400 123.50 180.00 112.20 1.5300 +IC C10A C9C *C9E H9E1 1.5300 112.20 120.00 111.50 1.1110 +IC C10A C9C *C9E H9E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C9C C9E C10A C10B 1.5020 112.20 180.00 112.20 1.5020 +IC C10B C9E *C10A H10A1 1.5020 112.20 120.00 110.10 1.1110 +IC C10B C9E *C10A H10A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C9E C10A C10B C10C 1.5300 112.20 180.00 123.50 1.3400 +IC C10C C10A *C10B H10B 1.3400 123.50 180.00 116.00 1.1000 +IC C10A C10B C10C C10D 1.5020 123.50 180.00 123.50 1.5020 +IC C10E C10B *C10C C10D 1.5020 123.50 180.00 123.50 1.5040 +IC C10B C10C C10D H10D1 1.3400 123.50 180.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D2 1.1110 111.50 120.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C10B C10C C10E C11A 1.3400 123.50 180.00 112.20 1.5300 +IC C11A C10C *C10E H10E1 1.5300 112.20 120.00 111.50 1.1110 +IC C11A C10C *C10E H10E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C10C C10E C11A C11B 1.5020 112.20 180.00 112.20 1.5020 +IC C11B C10E *C11A H11A1 1.5020 112.20 120.00 110.10 1.1110 +IC C11B C10E *C11A H11A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C10E C11A C11B C11C 1.5300 112.20 180.00 123.50 1.3400 +IC C11C C11A *C11B H11B 1.3400 123.50 180.00 116.00 1.1000 +IC C11A C11B C11C C11D 1.5020 123.50 180.00 123.50 1.5020 +IC C11E C11B *C11C C11D 1.5020 123.50 180.00 123.50 1.5040 +IC C11B C11C C11D H11D1 1.3400 123.50 180.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D2 1.1110 111.50 120.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C11B C11C C11E C12A 1.3400 123.50 180.00 112.20 1.5300 +IC C12A C11C *C11E H11E1 1.5300 112.20 120.00 111.50 1.1110 +IC C12A C11C *C11E H11E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C11C C11E C12A C12B 1.5020 112.20 180.00 112.20 1.5020 +IC C12B C11E *C12A H12A1 1.5020 112.20 120.00 110.10 1.1110 +IC C12B C11E *C12A H12A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C11E C12A C12B C12C 1.5300 112.20 180.00 123.50 1.3400 +IC C12C C12A *C12B H12B 1.3400 123.50 180.00 116.00 1.1000 +IC C12A C12B C12C C12D 1.5020 123.50 180.00 123.50 1.5020 +IC C12E C12B *C12C C12D 1.5020 123.50 180.00 123.50 1.5040 +IC C12B C12C C12D H12D1 1.3400 123.50 180.00 111.50 1.1110 +IC H12D1 C12C *C12D H12D2 1.1110 111.50 120.00 111.50 1.1110 +IC H12D1 C12C *C12D H12D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C12B C12C C12E C13A 1.3400 123.50 180.00 112.20 1.5300 +IC C13A C12C *C12E H12E1 1.5300 112.20 120.00 111.50 1.1110 +IC C13A C12C *C12E H12E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C12C C12E C13A C13B 1.5020 112.20 180.00 112.20 1.5020 +IC C13B C12E *C13A H13A1 1.5020 112.20 120.00 110.10 1.1110 +IC C13B C12E *C13A H13A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C12E C13A C13B C13C 1.5300 112.20 180.00 123.50 1.3400 +IC C13C C13A *C13B H13B 1.3400 123.50 180.00 116.00 1.1000 +IC C13A C13B C13C C13D 1.5020 123.50 180.00 123.50 1.5020 +IC C13E C13B *C13C C13D 1.5020 123.50 180.00 123.50 1.5040 +IC C13B C13C C13D H13D1 1.3400 123.50 180.00 111.50 1.1110 +IC H13D1 C13C *C13D H13D2 1.1110 111.50 120.00 111.50 1.1110 +IC H13D1 C13C *C13D H13D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C13B C13C C13E C14A 1.3400 123.50 180.00 112.20 1.5300 +IC C14A C13C *C13E H13E1 1.5300 112.20 120.00 111.50 1.1110 +IC C14A C13C *C13E H13E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C13C C13E C14A C14B 1.5020 112.20 180.00 112.20 1.5020 +IC C14B C13E *C14A H14A1 1.5020 112.20 120.00 110.10 1.1110 +IC C14B C13E *C14A H14A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C13E C14A C14B C14C 1.5300 112.20 180.00 123.50 1.3400 +IC C14C C14A *C14B H14B 1.3400 123.50 180.00 116.00 1.1000 +IC C14A C14B C14C C14D 1.5020 123.50 180.00 123.50 1.5020 +IC C14E C14B *C14C C14D 1.5020 123.50 180.00 123.50 1.5040 +IC C14B C14C C14D H14D1 1.3400 123.50 180.00 111.50 1.1110 +IC H14D1 C14C *C14D H14D2 1.1110 111.50 120.00 111.50 1.1110 +IC H14D1 C14C *C14D H14D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C14B C14C C14E C15A 1.3400 123.50 180.00 112.20 1.5300 +IC C15A C14C *C14E H14E1 1.5300 112.20 120.00 111.50 1.1110 +IC C15A C14C *C14E H14E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C14C C14E C15A C15B 1.5020 112.20 180.00 112.20 1.5020 +IC C15B C14E *C15A H15A1 1.5020 112.20 120.00 110.10 1.1110 +IC C15B C14E *C15A H15A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C14E C15A C15B C15C 1.5300 112.20 180.00 123.50 1.3400 +IC C15C C15A *C15B H15B 1.3400 123.50 180.00 116.00 1.1000 +IC C15A C15B C15C C15D 1.5020 123.50 180.00 123.50 1.5020 +IC C15E C15B *C15C C15D 1.5020 123.50 180.00 123.50 1.5040 +IC C15B C15C C15D H15D1 1.3400 123.50 180.00 111.50 1.1110 +IC H15D1 C15C *C15D H15D2 1.1110 111.50 120.00 111.50 1.1110 +IC H15D1 C15C *C15D H15D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C15B C15C C15E C16A 1.3400 123.50 180.00 112.20 1.5300 +IC C16A C15C *C15E H15E1 1.5300 112.20 120.00 111.50 1.1110 +IC C16A C15C *C15E H15E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C15C C15E C16A C16B 1.5020 112.20 180.00 112.20 1.5020 +IC C16B C15E *C16A H16A1 1.5020 112.20 120.00 110.10 1.1110 +IC C16B C15E *C16A H16A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C15E C16A C16B C16C 1.5300 112.20 180.00 123.50 1.3400 +IC C16C C16A *C16B H16B 1.3400 123.50 180.00 116.00 1.1000 +IC C16A C16B C16C C16D 1.5020 123.50 180.00 123.50 1.5020 +IC C16E C16B *C16C C16D 1.5020 123.50 180.00 123.50 1.5040 +IC C16B C16C C16D H16D1 1.3400 123.50 180.00 111.50 1.1110 +IC H16D1 C16C *C16D H16D2 1.1110 111.50 120.00 111.50 1.1110 +IC H16D1 C16C *C16D H16D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C16B C16C C16E C17A 1.3400 123.50 180.00 112.20 1.5300 +IC C17A C16C *C16E H16E1 1.5300 112.20 120.00 111.50 1.1110 +IC C17A C16C *C16E H16E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C16C C16E C17A C17B 1.5020 112.20 180.00 112.20 1.5020 +IC C17B C16E *C17A H17A1 1.5020 112.20 120.00 110.10 1.1110 +IC C17B C16E *C17A H17A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C16E C17A C17B C17C 1.5300 112.20 180.00 123.50 1.3400 +IC C17C C17A *C17B H17B 1.3400 123.50 180.00 116.00 1.1000 +IC C17A C17B C17C C17E 1.5020 123.50 180.00 123.50 1.5020 +IC C17E C17B *C17C C17D 1.5020 123.50 180.00 123.50 1.5040 +IC C17B C17C C17D H17D1 1.3400 123.50 180.00 111.50 1.1110 +IC H17D1 C17C *C17D H17D2 1.1110 111.50 120.00 111.50 1.1110 +IC H17D1 C17C *C17D H17D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C17B C17C C17E C18A 1.3400 123.50 180.00 112.20 1.5300 +IC C18A C17C *C17E H17E1 1.5300 112.20 120.00 111.50 1.1110 +IC C18A C17C *C17E H17E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C17C C17E C18A C18B 1.5020 112.20 180.00 112.20 1.5020 +IC C18B C17E *C18A H18A1 1.5020 112.20 120.00 110.10 1.1110 +IC C18B C17E *C18A H18A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C17E C18A C18B C18C 1.5300 112.20 180.00 123.50 1.3400 +IC C18C C18A *C18B H18B 1.3400 123.50 180.00 116.00 1.1000 +IC C18A C18B C18C C18E 1.5020 123.50 180.00 123.50 1.5020 +IC C18E C18B *C18C C18D 1.5020 123.50 180.00 123.50 1.5040 +IC C18B C18C C18D H18D1 1.3400 123.50 180.00 111.50 1.1110 +IC H18D1 C18C *C18D H18D2 1.1110 111.50 120.00 111.50 1.1110 +IC H18D1 C18C *C18D H18D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C18B C18C C18E C19A 1.3400 123.50 180.00 112.20 1.5300 +IC C19A C18C *C18E H18E1 1.5300 112.20 120.00 111.50 1.1110 +IC C19A C18C *C18E H18E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C18C C18E C19A C19B 1.5020 112.20 180.00 112.20 1.5020 +IC C19B C18E *C19A H19A1 1.5020 112.20 120.00 110.10 1.1110 +IC C19B C18E *C19A H19A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C18E C19A C19B C19C 1.5300 112.20 180.00 123.50 1.3400 +IC C19C C19A *C19B H19B 1.3400 123.50 180.00 116.00 1.1000 +IC C19A C19B C19C C19D 1.5020 123.50 180.00 123.50 1.5040 +IC C19D C19B *C19C C19E 1.5040 123.50 180.00 123.50 1.5040 +IC C19B C19C C19D H19D1 1.3400 123.50 180.00 111.50 1.1110 +IC H19D1 C19C *C19D H19D2 1.1110 111.50 120.00 111.50 1.1110 +IC H19D1 C19C *C19D H19D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C19B C19C C19E H19E1 1.3400 123.50 180.00 111.50 1.1110 +IC H19E1 C19C *C19E H19E2 1.1110 111.50 120.00 111.50 1.1110 +IC H19E1 C19C *C19E H19E3 1.1110 111.50 -120.00 111.50 1.1110 + +RESI UNDPP -2.00 ! [name] +GROUP +ATOM P2 PG1 1.34 ! HO22 +ATOM O22 OG311 -0.71 ! | +ATOM HO22 HGP1 0.44 ! O22 !! based on RESI PPI2 +ATOM O23 OG2P1 -0.86 ! | +ATOM O24 OG2P1 -0.86 ! O23==P2==O24 (-) + ! | +ATOM P1 PG1 1.46 ! O12 +ATOM O12 OG304 -0.63 ! | +ATOM O13 OG2P1 -0.83 ! O13==P1==O14 (-) +ATOM O14 OG2P1 -0.83 ! | +ATOM O11 OG303 -0.62 ! O11 + ! | +ATOM C1A CG321 -0.08 ! H1A1--C1A--H1A2 +ATOM H1A1 HGA2 0.09 ! | +ATOM H1A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C1B CG2D1 -0.15 ! C1B--H1B (cis) +ATOM H1B HGA4 0.15 ! || +GROUP 0.00 ! || H1D1 +ATOM C1C CG2D1 0.00 ! || | +GROUP 0.00 ! C1C--C1D--H1D2 +ATOM C1D CG331 -0.27 ! | | +ATOM H1D1 HGA3 0.09 ! | H1D3 +ATOM H1D2 HGA3 0.09 ! ! +ATOM H1D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C1E CG321 -0.18 ! H1E1--C1E--H1E2 +ATOM H1E1 HGA2 0.09 ! ! +ATOM H1E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C2A CG321 -0.18 ! H2A1--C2A--H2A2 +ATOM H2A1 HGA2 0.09 ! | +ATOM H2A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C2B CG2D1 -0.15 ! C2B--H2B (cis) +ATOM H2B HGA4 0.15 ! || +GROUP 0.00 ! || H2D1 +ATOM C2C CG2D1 0.00 ! || | +GROUP 0.00 ! C2C--C2D--H2D2 +ATOM C2D CG331 -0.27 ! | | +ATOM H2D1 HGA3 0.09 ! | H2D3 +ATOM H2D2 HGA3 0.09 ! ! +ATOM H2D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C2E CG321 -0.18 ! H2E1--C2E--H2E2 +ATOM H2E1 HGA2 0.09 ! ! +ATOM H2E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C3A CG321 -0.18 ! H3A1--C3A--H3A2 +ATOM H3A1 HGA2 0.09 ! | +ATOM H3A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C3B CG2D1 -0.15 ! C3B--H3B (cis) +ATOM H3B HGA4 0.15 ! || +GROUP 0.00 ! || H3D1 +ATOM C3C CG2D1 0.00 ! || | +GROUP 0.00 ! C3C--C3D--H3D2 +ATOM C3D CG331 -0.27 ! | | +ATOM H3D1 HGA3 0.09 ! | H3D3 +ATOM H3D2 HGA3 0.09 ! ! +ATOM H3D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C3E CG321 -0.18 ! H3E1--C3E--H3E2 +ATOM H3E1 HGA2 0.09 ! ! +ATOM H3E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C4A CG321 -0.18 ! H4A1--C4A--H4A2 +ATOM H4A1 HGA2 0.09 ! | +ATOM H4A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C4B CG2D1 -0.15 ! C4B--H4B (cis) +ATOM H4B HGA4 0.15 ! || +GROUP 0.00 ! || H4D1 +ATOM C4C CG2D1 0.00 ! || | +GROUP 0.00 ! C4C--C4D--H4D2 +ATOM C4D CG331 -0.27 ! | | +ATOM H4D1 HGA3 0.09 ! | H4D3 +ATOM H4D2 HGA3 0.09 ! ! +ATOM H4D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C4E CG321 -0.18 ! H4E1--C4E--H4E2 +ATOM H4E1 HGA2 0.09 ! ! +ATOM H4E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C5A CG321 -0.18 ! H5A1--C5A--H5A2 +ATOM H5A1 HGA2 0.09 ! | +ATOM H5A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C5B CG2D1 -0.15 ! C5B--H5B (cis) +ATOM H5B HGA4 0.15 ! || +GROUP 0.00 ! || H5D1 +ATOM C5C CG2D1 0.00 ! || | +GROUP 0.00 ! C5C--C5D--H5D2 +ATOM C5D CG331 -0.27 ! | | +ATOM H5D1 HGA3 0.09 ! | H5D3 +ATOM H5D2 HGA3 0.09 ! ! +ATOM H5D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C5E CG321 -0.18 ! H5E1--C5E--H5E2 +ATOM H5E1 HGA2 0.09 ! ! +ATOM H5E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C6A CG321 -0.18 ! H6A1--C6A--H6A2 +ATOM H6A1 HGA2 0.09 ! | +ATOM H6A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C6B CG2D1 -0.15 ! C6B--H6B (cis) +ATOM H6B HGA4 0.15 ! || +GROUP 0.00 ! || H6D1 +ATOM C6C CG2D1 0.00 ! || | +GROUP 0.00 ! C6C--C6D--H6D2 +ATOM C6D CG331 -0.27 ! | | +ATOM H6D1 HGA3 0.09 ! | H6D3 +ATOM H6D2 HGA3 0.09 ! ! +ATOM H6D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C6E CG321 -0.18 ! H6E1-C6E--H6E2 +ATOM H6E1 HGA2 0.09 ! ! +ATOM H6E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C7A CG321 -0.18 ! H7A1--C7A--H7A2 +ATOM H7A1 HGA2 0.09 ! | +ATOM H7A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C7B CG2D1 -0.15 ! C7B--H7B (cis) +ATOM H7B HGA4 0.15 ! || +GROUP 0.00 ! || H7D1 +ATOM C7C CG2D1 0.00 ! || | +GROUP 0.00 ! C7C--C7D--H7D2 +ATOM C7D CG331 -0.27 ! | | +ATOM H7D1 HGA3 0.09 ! | H7D3 +ATOM H7D2 HGA3 0.09 ! ! +ATOM H7D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C7E CG321 -0.18 ! H7E1-C7E--H7E2 +ATOM H7E1 HGA2 0.09 ! ! +ATOM H7E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C8A CG321 -0.18 ! H8A1--C8A--H8A2 +ATOM H8A1 HGA2 0.09 ! | +ATOM H8A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C8B CG2D1 -0.15 ! C8B--H8B (trans) +ATOM H8B HGA4 0.15 ! || +GROUP 0.00 ! || H8D1 +ATOM C8C CG2D1 0.00 ! || | +GROUP 0.00 ! C8C--C8D--H8D2 +ATOM C8D CG331 -0.27 ! | | +ATOM H8D1 HGA3 0.09 ! | H8D3 +ATOM H8D2 HGA3 0.09 ! ! +ATOM H8D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C8E CG321 -0.18 ! H8E1-C8E--H8E2 +ATOM H8E1 HGA2 0.09 ! ! +ATOM H8E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C9A CG321 -0.18 ! H9A1--C9A--H9A2 +ATOM H9A1 HGA2 0.09 ! | +ATOM H9A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C9B CG2D1 -0.15 ! C9B--H9B (trans) +ATOM H9B HGA4 0.15 ! || +GROUP 0.00 ! || H9D1 +ATOM C9C CG2D1 0.00 ! || | +GROUP 0.00 ! C9C--C9D--H9D2 +ATOM C9D CG331 -0.27 ! | | +ATOM H9D1 HGA3 0.09 ! | H9D3 +ATOM H9D2 HGA3 0.09 ! ! +ATOM H9D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C9E CG321 -0.18 ! H9E1-C9E--H9E2 +ATOM H9E1 HGA2 0.09 ! ! +ATOM H9E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C10A CG321 -0.18 ! H10A1--C10A--H10A2 +ATOM H10A1 HGA2 0.09 ! | +ATOM H10A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C10B CG2D1 -0.15 ! C10B--H110B (trans) +ATOM H10B HGA4 0.15 ! || +GROUP 0.00 ! || H10D1 +ATOM C10C CG2D1 0.00 ! || | +GROUP 0.00 ! C10C-C10D--H10D2 +ATOM C10D CG331 -0.27 ! | | +ATOM H10D1 HGA3 0.09 ! | H10D3 +ATOM H10D2 HGA3 0.09 ! ! +ATOM H10D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C10E CG321 -0.18 ! H10E1-C10E--H10E2 +ATOM H10E1 HGA2 0.09 ! ! +ATOM H10E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C11A CG321 -0.18 ! H11A1--C11A--H11A2 +ATOM H11A1 HGA2 0.09 ! | +ATOM H11A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C11B CG2D1 -0.15 ! C11B--H11B +ATOM H11B HGA4 0.15 ! || +GROUP 0.00 ! || H11D1 +ATOM C11C CG2D1 0.00 ! || | +GROUP 0.00 ! C11C-C11D--H11D2 +ATOM C11D CG331 -0.27 ! | | +ATOM H11D1 HGA3 0.09 ! | H11D3 +ATOM H11D2 HGA3 0.09 ! ! +ATOM H11D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C11E CG331 -0.27 ! H11E1-C11E--H11E2 +ATOM H11E1 HGA3 0.09 ! ! +ATOM H11E2 HGA3 0.09 ! ! +ATOM H11E3 HGA3 0.09 ! H11E3 + +BOND O22 HO22 P2 O22 P2 O23 P2 O24 P2 O12 ! Phosphate group 2 +BOND P1 O12 P1 O13 P1 O14 P1 O11 O11 C1A ! Phosphate group 1 +BOND C1A C1B C1C C1D C1C C1E ! cis isoprene backbone carbons +DOUBLE C1B C1C ! cis double bond +BOND C1A H1A1 C1A H1A2 ! C1A hydrogens +BOND C1B H1B ! C1B hydrogen +BOND C1D H1D1 C1D H1D2 C1D H1D3 ! C1D hydrogens +BOND C1E H1E1 C1E H1E2 ! C1E hydrogens +BOND C1E C2A ! isoprene linking bond +BOND C2A C2B C2C C2D C2C C2E ! cis isoprene backbone carbons +DOUBLE C2B C2C ! cis double bond +BOND C2A H2A1 C2A H2A2 ! C2A hydrogens +BOND C2B H2B ! C2B hydrogen +BOND C2D H2D1 C2D H2D2 C2D H2D3 ! C2D hydrogens +BOND C2E H2E1 C2E H2E2 ! C2E hydrogens +BOND C2E C3A ! isoprene linking bond +BOND C3A C3B C3C C3D C3C C3E ! cis isoprene backbone carbons +DOUBLE C3B C3C ! cis double bond +BOND C3A H3A1 C3A H3A2 ! C3A hydrogens +BOND C3B H3B ! C3B hydrogen +BOND C3D H3D1 C3D H3D2 C3D H3D3 ! C3D hydrogens +BOND C3E H3E1 C3E H3E2 ! C3E hydrogens +BOND C3E C4A ! isoprene linking bond +BOND C4A C4B C4C C4D C4C C4E ! cis isoprene backbone carbons +DOUBLE C4B C4C ! cis double bond +BOND C4A H4A1 C4A H4A2 ! C4A hydrogens +BOND C4B H4B ! C4B hydrogen +BOND C4D H4D1 C4D H4D2 C4D H4D3 ! C4D hydrogens +BOND C4E H4E1 C4E H4E2 ! C4E hydrogens +BOND C4E C5A ! isoprene linking bond +BOND C5A C5B C5C C5D C5C C5E ! cis isoprene backbone carbons +DOUBLE C5B C5C ! cis double bond +BOND C5A H5A1 C5A H5A2 ! C5A hydrogens +BOND C5B H5B ! C5B hydrogen +BOND C5D H5D1 C5D H5D2 C5D H5D3 ! C5D hydrogens +BOND C5E H5E1 C5E H5E2 ! C5E hydrogens +BOND C5E C6A ! isoprene linking bond +BOND C6A C6B C6C C6D C6C C6E ! cis isoprene backbone carbons +DOUBLE C6B C6C ! cis double bond +BOND C6A H6A1 C6A H6A2 ! C6A hydrogens +BOND C6B H6B ! C6B hydrogen +BOND C6D H6D1 C6D H6D2 C6D H6D3 ! C6D hydrogens +BOND C6E H6E1 C6E H6E2 ! C6E hydrogens +BOND C6E C7A ! isoprene linking bond +BOND C7A C7B C7C C7D C7C C7E ! cis isoprene backbone carbons +DOUBLE C7B C7C ! cis double bond +BOND C7A H7A1 C7A H7A2 ! C7A hydrogens +BOND C7B H7B ! C7B hydrogen +BOND C7D H7D1 C7D H7D2 C7D H7D3 ! C7D hydrogens +BOND C7E H7E1 C7E H7E2 ! C7E hydrogens +BOND C7E C8A ! isoprene linking bond +BOND C8A C8B C8C C8D C8C C8E ! trans isoprene backbone carbons +DOUBLE C8B C8C ! trans double bond +BOND C8A H8A1 C8A H8A2 ! C8A hydrogens +BOND C8B H8B ! C8B hydrogen +BOND C8D H8D1 C8D H8D2 C8D H8D3 ! C8D hydrogens +BOND C8E H8E1 C8E H8E2 ! C8E hydrogens +BOND C8E C9A ! isoprene linking bond +BOND C9A C9B C9C C9D C9C C9E ! trans isoprene backbone carbons +DOUBLE C9B C9C ! trans double bond +BOND C9A H9A1 C9A H9A2 ! C9A hydrogens +BOND C9B H9B ! C9B hydrogen +BOND C9D H9D1 C9D H9D2 C9D H9D3 ! C9D hydrogens +BOND C9E H9E1 C9E H9E2 ! C9E hydrogens +BOND C9E C10A ! isoprene linking bond +BOND C10A C10B C10C C10D C10C C10E ! trans isoprene backbone carbons +DOUBLE C10B C10C ! trans double bond +BOND C10A H10A1 C10A H10A2 ! C10A hydrogens +BOND C10B H10B ! C10B hydrogen +BOND C10D H10D1 C10D H10D2 C10D H10D3 ! C10D hydrogens +BOND C10E H10E1 C10E H10E2 ! C10E hydrogens +BOND C10E C11A ! isoprene linking bond +BOND C11A C11B C11C C11D C11C C11E ! isoprene backbone carbons +DOUBLE C11B C11C ! double bond +BOND C11A H11A1 C11A H11A2 ! C11A hydrogens +BOND C11B H11B ! C11B hydrogen +BOND C11D H11D1 C11D H11D2 C11D H11D3 ! C11D hydrogens +BOND C11E H11E1 C11E H11E2 C11E H11E3 ! C11E hydrogens +IC O22 O12 *P2 O23 1.6100 111.00 120.00 111.60 1.5100 +IC O22 O12 *P2 O24 1.6100 111.00 -120.00 111.60 1.5100 +IC O12 P2 O22 HO22 1.6750 111.00 180.00 115.00 0.9600 +IC O22 P2 O12 P1 1.6100 111.00 180.00 143.00 1.6750 +IC P2 O12 P1 O11 1.6750 143.00 180.00 105.00 1.6500 +IC O11 O12 *P1 O13 1.6500 105.00 120.00 111.60 1.5100 +IC O11 O12 *P1 O14 1.5100 111.60 -120.00 111.60 1.5100 +IC O12 P1 O11 C1A 1.6750 105.00 180.00 120.00 1.4400 +IC P1 O11 C1A C1B 1.6500 120.00 180.00 110.10 1.5300 +IC C1B O11 *C1A H1A1 1.5300 110.10 120.00 109.50 1.1110 +IC C1B O11 *C1A H1A2 1.5300 110.10 -120.00 109.50 1.1110 +IC O11 C1A C1B C1C 1.4400 110.10 180.00 113.50 1.5380 +IC C1C C1A *C1B H1B 1.3400 123.50 180.00 116.00 1.1000 +IC C1A C1B C1C C1D 1.5020 123.50 180.00 123.50 1.5020 +IC C1E C1B *C1C C1D 1.5020 123.50 180.00 123.50 1.5040 +IC C1B C1C C1D H1D1 1.3400 123.50 180.00 111.50 1.1110 +IC H1D1 C1C *C1D H1D2 1.1110 111.50 120.00 111.50 1.1110 +IC H1D1 C1C *C1D H1D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C1B C1C C1E C2A 1.3400 123.50 180.00 112.20 1.5300 +IC C2A C1C *C1E H1E1 1.5300 112.20 120.00 111.50 1.1110 +IC C2A C1C *C1E H1E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C1C C1E C2A C2B 1.5020 112.20 180.00 112.20 1.5020 +IC C2B C1E *C2A H2A1 1.5020 112.20 120.00 110.10 1.1110 +IC C2B C1E *C2A H2A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C1E C2A C2B C2C 1.5300 112.20 180.00 123.50 1.3400 +IC C2C C2A *C2B H2B 1.3400 123.50 180.00 116.00 1.1000 +IC C2A C2B C2C C2D 1.5020 123.50 180.00 123.50 1.5020 +IC C2E C2B *C2C C2D 1.5020 123.50 180.00 123.50 1.5040 +IC C2B C2C C2D H2D1 1.3400 123.50 180.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D2 1.1110 111.50 120.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C2B C2C C2E C3A 1.3400 123.50 180.00 112.20 1.5300 +IC C3A C2C *C2E H2E1 1.5300 112.20 120.00 111.50 1.1110 +IC C3A C2C *C2E H2E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C2C C2E C3A C3B 1.5020 112.20 180.00 112.20 1.5020 +IC C3B C2E *C3A H3A1 1.5020 112.20 120.00 110.10 1.1110 +IC C3B C2E *C3A H3A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C2E C3A C3B C3C 1.5300 112.20 180.00 123.50 1.3400 +IC C3C C3A *C3B H3B 1.3400 123.50 180.00 116.00 1.1000 +IC C3A C3B C3C C3D 1.5020 123.50 180.00 123.50 1.5020 +IC C3E C3B *C3C C3D 1.5020 123.50 180.00 123.50 1.5040 +IC C3B C3C C3D H3D1 1.3400 123.50 180.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D2 1.1110 111.50 120.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C3B C3C C3E C4A 1.3400 123.50 180.00 112.20 1.5300 +IC C4A C3C *C3E H3E1 1.5300 112.20 120.00 111.50 1.1110 +IC C4A C3C *C3E H3E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C3C C3E C4A C4B 1.5020 112.20 180.00 112.20 1.5020 +IC C4B C3E *C4A H4A1 1.5020 112.20 120.00 110.10 1.1110 +IC C4B C3E *C4A H4A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C3E C4A C4B C4C 1.5300 112.20 180.00 123.50 1.3400 +IC C4C C4A *C4B H4B 1.3400 123.50 180.00 116.00 1.1000 +IC C4A C4B C4C C4D 1.5020 123.50 180.00 123.50 1.5020 +IC C4E C4B *C4C C4D 1.5020 123.50 180.00 123.50 1.5040 +IC C4B C4C C4D H4D1 1.3400 123.50 180.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D2 1.1110 111.50 120.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C4B C4C C4E C5A 1.3400 123.50 180.00 112.20 1.5300 +IC C5A C4C *C4E H4E1 1.5300 112.20 120.00 111.50 1.1110 +IC C5A C4C *C4E H4E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C4C C4E C5A C5B 1.5020 112.20 180.00 112.20 1.5020 +IC C5B C4E *C5A H5A1 1.5020 112.20 120.00 110.10 1.1110 +IC C5B C4E *C5A H5A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C4E C5A C5B C5C 1.5300 112.20 180.00 123.50 1.3400 +IC C5C C5A *C5B H5B 1.3400 123.50 180.00 116.00 1.1000 +IC C5A C5B C5C C5D 1.5020 123.50 180.00 123.50 1.5020 +IC C5E C5B *C5C C5D 1.5020 123.50 180.00 123.50 1.5040 +IC C5B C5C C5D H5D1 1.3400 123.50 180.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D2 1.1110 111.50 120.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C5B C5C C5E C6A 1.3400 123.50 180.00 112.20 1.5300 +IC C6A C5C *C5E H5E1 1.5300 112.20 120.00 111.50 1.1110 +IC C6A C5C *C5E H5E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C5C C5E C6A C6B 1.5020 112.20 180.00 112.20 1.5020 +IC C6B C5E *C6A H6A1 1.5020 112.20 120.00 110.10 1.1110 +IC C6B C5E *C6A H6A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C5E C6A C6B C6C 1.5300 112.20 180.00 123.50 1.3400 +IC C6C C6A *C6B H6B 1.3400 123.50 180.00 116.00 1.1000 +IC C6A C6B C6C C6D 1.5020 123.50 180.00 123.50 1.5020 +IC C6E C6B *C6C C6D 1.5020 123.50 180.00 123.50 1.5040 +IC C6B C6C C6D H6D1 1.3400 123.50 180.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D2 1.1110 111.50 120.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C6B C6C C6E C7A 1.3400 123.50 180.00 112.20 1.5300 +IC C7A C6C *C6E H6E1 1.5300 112.20 120.00 111.50 1.1110 +IC C7A C6C *C6E H6E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C6C C6E C7A C7B 1.5020 112.20 180.00 112.20 1.5020 +IC C7B C6E *C7A H7A1 1.5020 112.20 120.00 110.10 1.1110 +IC C7B C6E *C7A H7A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C6E C7A C7B C7C 1.5300 112.20 180.00 123.50 1.3400 +IC C7C C7A *C7B H7B 1.3400 123.50 180.00 116.00 1.1000 +IC C7A C7B C7C C7D 1.5020 123.50 180.00 123.50 1.5020 +IC C7E C7B *C7C C7D 1.5020 123.50 180.00 123.50 1.5040 +IC C7B C7C C7D H7D1 1.3400 123.50 180.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D2 1.1110 111.50 120.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C7B C7C C7E C8A 1.3400 123.50 180.00 112.20 1.5300 +IC C8A C7C *C7E H7E1 1.5300 112.20 120.00 111.50 1.1110 +IC C8A C7C *C7E H7E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C7C C7E C8A C8B 1.5020 112.20 180.00 112.20 1.5020 +IC C8B C7E *C8A H8A1 1.5020 112.20 120.00 110.10 1.1110 +IC C8B C7E *C8A H8A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C7E C8A C8B C8C 1.5300 112.20 180.00 123.50 1.3400 +IC C8C C8A *C8B H8B 1.3400 123.50 180.00 116.00 1.1000 +IC C8A C8B C8C C8D 1.5020 123.50 0.00 123.50 1.5020 +IC C8E C8B *C8C C8D 1.5020 123.50 180.00 123.50 1.5040 +IC C8B C8C C8D H8D1 1.3400 123.50 180.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D2 1.1110 111.50 120.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C8B C8C C8E C9A 1.3400 123.50 180.00 112.20 1.5300 +IC C9A C8C *C8E H8E1 1.5300 112.20 120.00 111.50 1.1110 +IC C9A C8C *C8E H8E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C8C C8E C9A C9B 1.5020 112.20 180.00 112.20 1.5020 +IC C9B C8E *C9A H9A1 1.5020 112.20 120.00 110.10 1.1110 +IC C9B C8E *C9A H9A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C8E C9A C9B C9C 1.5300 112.20 180.00 123.50 1.3400 +IC C9C C9A *C9B H9B 1.3400 123.50 180.00 116.00 1.1000 +IC C9A C9B C9C C9D 1.5020 123.50 0.00 123.50 1.5020 +IC C9E C9B *C9C C9D 1.5020 123.50 180.00 123.50 1.5040 +IC C9B C9C C9D H9D1 1.3400 123.50 180.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D2 1.1110 111.50 120.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C9B C9C C9E C10A 1.3400 123.50 180.00 112.20 1.5300 +IC C10A C9C *C9E H9E1 1.5300 112.20 120.00 111.50 1.1110 +IC C10A C9C *C9E H9E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C9C C9E C10A C10B 1.5020 112.20 180.00 112.20 1.5020 +IC C10B C9E *C10A H10A1 1.5020 112.20 120.00 110.10 1.1110 +IC C10B C9E *C10A H10A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C9E C10A C10B C10C 1.5300 112.20 180.00 123.50 1.3400 +IC C10C C10A *C10B H10B 1.3400 123.50 180.00 116.00 1.1000 +IC C10A C10B C10C C10D 1.5020 123.50 0.00 123.50 1.5020 +IC C10E C10B *C10C C10D 1.5020 123.50 180.00 123.50 1.5040 +IC C10B C10C C10D H10D1 1.3400 123.50 180.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D2 1.1110 111.50 120.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C10B C10C C10E C11A 1.3400 123.50 180.00 112.20 1.5300 +IC C11A C10C *C10E H10E1 1.5300 112.20 120.00 111.50 1.1110 +IC C11A C10C *C10E H10E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C10C C10E C11A C11B 1.5020 112.20 180.00 112.20 1.5020 +IC C11B C10E *C11A H11A1 1.5020 112.20 120.00 110.10 1.1110 +IC C11B C10E *C11A H11A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C10E C11A C11B C11C 1.5300 112.20 180.00 123.50 1.3400 +IC C11C C11A *C11B H11B 1.3400 123.50 180.00 116.00 1.1000 +IC C11A C11B C11C C11D 1.5020 123.50 180.00 123.50 1.5020 +IC C11E C11B *C11C C11D 1.5020 123.50 180.00 123.50 1.5040 +IC C11B C11C C11D H11D1 1.3400 123.50 180.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D2 1.1110 111.50 120.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C11B C11C C11E H11E1 1.5300 112.20 180.00 111.50 1.1110 +IC C11B C11C *C11E H11E2 1.1110 111.50 120.00 111.50 1.1110 +IC C11B C11C *C11E H11E3 1.1110 111.50 -120.00 111.50 1.1110 + +PRES LLLO -2.00 ! linkage for dol-P-P and sugar +dele atom 1HO1 ! +dele atom 1O1 ! +dele atom 2HO22 ! +GROUP ! +ATOM 1C1 CC3162 0.30 ! adjust to make this section charge 0.1 (same as the dol part) +ATOM 1H1 HCA1 0.09 ! +ATOM 1C5 CC3163 0.02 ! H5 +ATOM 1H5 HCA1 0.09 ! \ +ATOM 1O5 OC3C61 -0.40 ! C5-------O5 + ! / \ H1 + ! / \ / + ! C4 C1 + ! \ / \ + ! \ / \ + ! C3------C2 \ + ! \ + ! \ + ! \ +ATOM 2P2 PG1 1.50 ! \ +ATOM 2O22 OG303 -0.62 ! O22 +ATOM 2O23 OG2P1 -0.82 ! | +ATOM 2O24 OG2P1 -0.82 ! O23==P2==O24 (-) + ! | +ATOM 2O12 OG304 -0.68 ! O12 +ATOM 2P1 PG1 1.50 ! | +ATOM 2O13 OG2P1 -0.82 ! O13==P1==O14 (-) +ATOM 2O14 OG2P1 -0.82 ! | +ATOM 2O11 OG303 -0.62 ! O11 + ! | +!ATOM 2C1 CG321 -0.08! H11--C1--H12 +!ATOM 2H11 HGA2 0.09! | +!ATOM 2H12 HGA2 0.09! | + +BOND 1C1 2O22 + +!Thermalized IC +!IC 1C3 1C2 1C1 2O22 1.5364 112.47 -174.92 109.44 1.4102 +!IC 1C2 2O22 *1C1 1H1 1.5323 109.44 -120.96 109.46 1.1223 +IC 1C3 1C2 1C1 1H1 1.5364 112.47 180.00 109.44 1.4102 +IC 1C2 1H1 *1C1 2O22 1.5323 109.44 -120.00 109.46 1.1223 +IC 1C2 1C1 2O22 2P2 1.5323 109.44 -84.54 127.66 1.5968 +IC 1C1 2O22 2P2 2O12 1.4102 127.66 -174.21 102.94 1.5071 +IC 2O22 2O12 *2P2 2O23 1.5968 102.94 113.03 118.81 1.5471 +IC 2O22 2O12 *2P2 2O24 1.5968 102.94 -113.60 109.37 1.4811 + +END + +read param card flex append +* PIP related parameters +* +! Parameters have been transferred from two FF +! sugar FF and lipid FF +! +! Important atom def: +! Sugar FF phosphate : PC +! Lipid FF phosphate : PL +! NA FF phosphate : P +! +! phosphate =O , sug (OC2DP), lipid (O2L), NA (ON3) +! phosphate -O , sug (OC30P), lipid (OSLP), NA (ON2) +! phosphate -OH , sug (OC312), lipid (OHL), NA (ON4) +! + +BONDS +!** sugar FF *** +OC30P PL 270.0 1.675 ! +OC2DP PL 580.0 1.525 ! +OC312 PL 237.0 1.61 ! +CTL2 OC301 360.00 1.415 ! par35 CC32A OC30A +!LLO +CC3162 OG303 360.00 1.425 !! from CC3162 OC30P 360.00 1.425 ! + +ANGLES +!** sugar FF *** +OC30P PL OC2DP 98.9 111.6 +OC2DP PL OC2DP 120.0 120.0 +OC30P PL OC30P 80.0 104.3 ! ON2 P ON2 !DMP, ADM Jr. +CC3161 OC30P PL 20.0 120.0 35.0 2.33 !CTL2 OSLP PL ! phosphate, PIP +OC301 CTL2 CTL2 45.00 111.50 ! par35 OC30A CC32A CC32A +CC3162 OC301 CTL2 95.00 109.70 ! par35 CC33A OC30A CC32A +CC311D OC301 CTL2 95.00 109.70 ! pram, OMeTHP CC311D OC301 CC331 +OC301 CTL2 HAL2 60.00 109.50 ! par34 HCA2 CC32A OC30A +!*** lipid FF *** +OC30P PL O2L 98.9 111.6 ! OSLP PL O2L ! phosphate +OC30P PL OSLP 80.0 104.3 ! OSLP PL OSLP ! phosphate +!LLO +!DOL-PP +CG331 CG2D1 CG331 48.00 123.50 !! from CG321 CG2D1 CG331 48.00 123.50 ! RETINOL TMCH +!LLLO +OG303 CC3162 HCA1 60.00 109.50 !! from OC30P CC3162 HCA1 60.00 109.50 ! par35 HCA2 CC32A OC30A +OG303 CC3162 OC3C61 90.00 110.00 !! from OC30P CC3162 OC3C61 90.00 110.00 +OG303 CC3162 CC3161 45.00 109.00 !! from OC30P CC3162 CC3161 45.00 109.00 +CC3162 OG303 PG1 20.0 120.0 35.0 2.33 !! from CC3162 OC30P PC 20.0 120.0 35.0 2.33 ! same in CGenFF (CG311 OG303 PG1 from CG321 OG303 PG1) +!UND-PP +CG2D1 CG321 OG303 75.70 110.10 !! from CG2D1 CG321 OG311 75.70 110.10 ! RETINOL PROL + + +DIHEDRALS +!** sugar FF *** +CC3161 CC3161 OC30P PL 0.02 3 180.0 +CC3161 OC30P PL OC2DP 0.33 3 0.0 +HCA1 CC3161 OC30P PL 0.284 3 0.0 ! dmp,eps, H-C3'-O3'-P || from the par_all27_na.prm +CC3161 OC30P PL OSLP 1.45 2 0.0 !CC311D OC30P PC OC312 +CC3161 OC30P PL O2L 0.33 3 0.0 !CC311D OC30P PC OC2DP +CTL2 CTL2 CTL2 OC301 0.19 3 0.0 ! par27 X CTL2 CTL2 X + +CC3162 OC301 CTL2 CTL2 0.72 1 180.0 ! pram, 1-ethoxy-THP2 QM phi-psi scan, updated param +CC3162 OC301 CTL2 CTL2 0.34 2 180.0 ! " MCSA fit " +CC3162 OC301 CTL2 CTL2 0.12 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CC3161 CC3162 OC301 CTL2 0.58 1 180.0 ! pram, 1-ethoxy-THP2 QM phi-psi scan, updated param +CC3161 CC3162 OC301 CTL2 0.69 2 180.0 ! " MCSA fit " +CC3161 CC3162 OC301 CTL2 1.16 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +HAL2 CTL2 CTL2 OC301 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC3162 OC301 CTL2 HAL2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A + +OC3C61 CC3162 OC301 CTL2 0.36 1 180.0 ! pram, 1-ethoxy-THP2 QM phi-psi scan, updated param +OC3C61 CC3162 OC301 CTL2 0.52 2 0.0 ! " MCSA fit " +OC3C61 CC3162 OC301 CTL2 0.83 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* + +CTL2 OC301 CTL1 HAL1 0.284 3 0.0 ! OMeTHP CC331 OC301 CC311D HCA1 +OC301 CTL2 CTL3 HAL3 0.20 3 0.0 ! OC301 CTL2 CC3163 HCA1 +CTL2 OC301 CC311D OC3C61 0.36 1 180.0 ! pr, 1-ethoxy-THP2 QM phi-psi scan +CTL2 OC301 CC311D OC3C61 0.52 2 0.0 ! " MCSA fit " +CTL2 OC301 CC311D OC3C61 0.83 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CTL2 OC301 CC311D CC321C 0.58 1 180.0 ! pr, 1-ethoxy-THP2 QM phi-psi scan +CTL2 OC301 CC311D CC321C 0.69 2 180.0 ! " MCSA fit " +CTL2 OC301 CC311D CC321C 1.16 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +HAL2 CTL2 OC301 CC3051 0.284 3 0.0 ! OMe-THF CC312D OC301 CC331 HCA3 +HAL2 CTL2 OC301 CC3152 0.284 3 0.0 ! OMe-THF CC312D OC301 CC331 HCA3 +HAL1 CC3152 OC301 CTL2 0.284 3 0.0 ! HCA1 CC3152 OC301 CC331 +CTL2 OC301 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +!*** lipid FF *** +OC30P PL OSLP CTL2 1.20 1 180.00 !OSLP PL OSLP CTL2 ! phosphate, new NA, 4/98, adm jr. +OC30P PL OSLP CTL2 0.10 2 180.00 ! +OC30P PL OSLP CTL2 0.10 3 180.00 ! +!LLO +DIHEDRALS +!DOL-PP +CG311 CG321 CG321 OG303 0.1950 3 0.00 !! from CG321 CG321 CG321 OG303 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2D1 CG321 CG321 CG311 0.1400 1 180.0 !! from CG2D1 CG321 CG321 CG321 0.1400 1 180.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG311 0.1700 2 0.0 !! from CG2D1 CG321 CG321 CG321 0.1700 2 0.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG311 0.0500 3 180.0 !! from CG2D1 CG321 CG321 CG321 0.0500 3 180.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG2D1 0.1400 1 180.0 !! from CG2D1 CG321 CG321 CG321 0.1400 1 180.0 ! 2-hexene, adm jr., 11/09 ; potential candidate for optimization -- kevo +CG2D1 CG321 CG321 CG2D1 0.1700 2 0.0 !! from CG2D1 CG321 CG321 CG321 0.1700 2 0.0 ! 2-hexene, adm jr., 11/09 ; potential candidate for optimization -- kevo +CG2D1 CG321 CG321 CG2D1 0.0500 3 180.0 !! from CG2D1 CG321 CG321 CG321 0.0500 3 180.0 ! 2-hexene, adm jr., 11/09 ; potential candidate for optimization -- kevo +CG331 CG2D1 CG331 HGA3 0.3000 3 0.00 !! from CG331 CG2DC1 CG331 HGA3 0.3000 3 0.00 ! RETINOL DMP1, 4-methyl-1,3-pentadiene ; alternative CG321 CG2D1 CG331 HGA3, RETINOL TMCH is cyclic so probably worse -- kevo +!LLLO +CC3162 OG303 PG1 OG2P1 0.33 3 0.0 !! from CC3162 OC30P PC OC2DP 0.33 3 0.0 ! probably better with the old phosphate charges in the topology (and the L-J haven't changed) -- kevo +CC3162 OG303 PG1 OG304 1.45 2 0.0 !! from CC3162 OC30P PC OC312 1.45 2 0.0 ! probably better with the old phosphate charges in the topology (and the L-J haven't changed) -- kevo +HCA1 CC3162 OG303 PG1 0.284 3 0.0 !! from HCA1 CC3162 OC30P PC 0.284 3 0.0 ! dmp,eps, H-C3'-O3'-P || from the par_all27_na.prm +OC3C61 CC3162 OG303 PG1 0.38 2 0.0 !! from OC3C61 CC3162 OC30P PC 0.38 2 0.0 +OC3C61 CC3162 OG303 PG1 0.41 3 180.0 !! from OC3C61 CC3162 OC30P PC 0.41 3 180.0 +CC3161 CC3162 OG303 PG1 0.02 3 180.0 !! from CC3161 CC3162 OC30P PC 0.02 3 180.0 +CC3163 OC3C61 CC3162 OG303 2.44 3 180.0 !! from CC3163 OC3C61 CC3162 OC30P 2.44 3 180.0 +HCA1 CC3161 CC3162 OG303 0.20 3 0.0 !! from HCA1 CC3161 CC3162 OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC3161 CC3161 CC3162 OG303 1.76 1 0.0 !! from CC3161 CC3161 CC3162 OC30P 1.76 1 0.0 +CC3161 CC3161 CC3162 OG303 2.56 2 0.0 !! from CC3161 CC3161 CC3162 OC30P 2.56 2 0.0 +CC3161 CC3161 CC3162 OG303 0.01 3 0.0 !! from CC3161 CC3161 CC3162 OC30P 0.01 3 0.0 +OG303 CC3162 CC3161 NC2D1 0.20 3 0.0 !! from OC301 CC3162 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +!BBAC +CC331 CC3163 CC3161 NC2D1 0.20 3 0.0 !! from CC312 CC3163 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +!UND-PP +CG2D1 CG2D1 CG321 OG303 1.9000 1 180.00 !! from CG2D2 CG2D1 CG321 OG311 and CG2DC1 CG2DC1 CG321 OG311 , RETINOL PROL +CG2D1 CG2D1 CG321 OG303 0.4000 2 180.00 !! from CG2D2 CG2D1 CG321 OG311 and CG2DC1 CG2DC1 CG321 OG311 , RETINOL PROL +CG2D1 CG2D1 CG321 OG303 0.6000 3 180.00 !! from CG2D2 CG2D1 CG321 OG311 and CG2DC1 CG2DC1 CG321 OG311 , RETINOL PROL +HGA4 CG2D1 CG321 OG303 0.2000 3 0.00 !! from HGA4 CG2D1 CG321 OG311 and HGA4 CG2DC1 CG321 OG311 , RETINOL PROL +CG2D1 CG321 OG303 PG1 0.6000 1 180.00 !! from CG321 CG321 OG303 PG1 0.6000 1 180.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others ; potential candidate for optimization -- kevo +CG2D1 CG321 OG303 PG1 0.6500 2 0.00 !! from CG321 CG321 OG303 PG1 0.6500 2 0.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others ; potential candidate for optimization -- kevo +CG2D1 CG321 OG303 PG1 0.0500 3 0.00 !! from CG321 CG321 OG303 PG1 0.0500 3 0.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others ; potential candidate for optimization -- kevo + +END + +RETURN + diff --git a/charmm/toppar/stream/carb/toppar_all36_carb_glycopeptide.str b/charmm/toppar/stream/carb/toppar_all36_carb_glycopeptide.str new file mode 100644 index 00000000..454765a2 --- /dev/null +++ b/charmm/toppar/stream/carb/toppar_all36_carb_glycopeptide.str @@ -0,0 +1,485 @@ +read rtf card append +* Topology for glycopeptide linkages +* +32 1 + +! | | * change charges +! HN-N HN-N +! | HB1 | HB1 +! | | | | * * +! HA-CA--CB--OG ==> HA-CA--CB--OG +! | | \ | | \ * +! | HB2 HG1 | HB2 C1(sugar) +! O=C O=C +! | | + +PRES SGPA -0.07 ! for connecting SER at the alpha position +dele atom 1HG1 +dele atom 2O1 +dele atom 2HO1 + +GROUP + +ATOM 1CB CT2 0.00 !Charge assigned by adding +ATOM 1OG OC301 -0.36 ! Charge from OMEA + +GROUP + +ATOM 2C1 CC3162 0.29 ! Charge from OMEA + +BOND 1OG 2C1 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) + +!IC 1CA 1CB 1OG 2C1 0.0000 0.0000 167.06 0.0000 0.0000 +!IC 1CB 1OG 2C1 2O5 0.0000 0.0000 71.26 0.0000 0.0000 +!IC 1CB 1OG 2C1 2H1 0.0000 0.0000 -50.07 0.0000 0.0000 +!IC 1OG 2C1 2O5 2C5 0.0000 0.0000 70.42 0.0000 0.0000 + +!Thermalized IC +IC 1CA 1CB 1OG 2C1 1.5246 112.48 -174.87 115.72 1.4191 +IC 1CB 1OG 2C1 2O5 1.4218 115.72 45.37 110.03 1.4241 +IC 1CB 1OG 2C1 2H1 1.4218 115.72 -71.61 112.01 1.1125 +IC 1OG 2C1 2O5 2C5 1.4191 110.03 63.29 109.91 1.4591 + +! | | +! HN-N HN-N +! | OG1--HG1 | OG1--C1(sugar) +! | / | / +! HA-CA--CB-HB ==> HA-CA--CB-HB +! | \ | \ +! | CG2--HG21 | CG2--HG21 +! O=C / \ O=C / \ +! | HG21 HG22 | HG21 HG22 + +PRES TGPA 0.02 ! for connecting THR at the alpha position +dele atom 1HG1 +dele atom 2O1 +dele atom 2HO1 + +GROUP + +ATOM 1CB CT1 0.09 !Charge assigned by adding +ATOM 1OG1 OC301 -0.36 ! Charge from OMEA + +GROUP + +ATOM 2C1 CC3162 0.29 ! Charge from OMEA + +BOND 1OG1 2C1 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) + +!IC 1CA 1CB 1OG1 2C1 0.0000 0.0000 167.06 0.0000 0.0000 +!IC 1CB 1OG1 2C1 2O5 0.0000 0.0000 71.26 0.0000 0.0000 +!IC 1CB 1OG1 2C1 2H1 0.0000 0.0000 -50.07 0.0000 0.0000 +!IC 1OG1 2C1 2O5 2C5 0.0000 0.0000 70.42 0.0000 0.0000 + +!Thermalized IC +IC 1CA 1CB 1OG1 2C1 1.5900 102.09 161.11 116.78 1.4047 +IC 1CB 1OG1 2C1 2O5 1.5040 116.78 69.90 114.66 1.4346 +IC 1CB 1OG1 2C1 2H1 1.5040 116.78 -51.01 110.33 1.1436 +IC 1OG1 2C1 2O5 2C5 1.4047 114.66 71.63 114.71 1.4751 + +! | | * change charges +! HN-N HN-N +! | HB1 | HB1 +! | | | | * * +! HA-CA--CB--OG ==> HA-CA--CB--OG +! | | \ | | \ * +! | HB2 HG1 | HB2 C1(sugar) +! O=C O=C +! | | + +PRES SGPB -0.07 ! for connecting SER at the beta position +dele atom 1HG1 +dele atom 2O1 +dele atom 2HO1 + +GROUP + +ATOM 1CB CT2 0.00 !Charge assigned by adding +ATOM 1OG OC301 -0.36 ! Charge from OMEA + +GROUP + +ATOM 2C1 CC3162 0.29 ! Charge from OMEA + +BOND 1OG 2C1 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) + +!IC 1CA 1CB 1OG 2C1 0.0000 0.0000 167.06 0.0000 0.0000 +!IC 1CB 1OG 2C1 2O5 0.0000 0.0000 41.65 0.0000 0.0000 +!IC 1CB 1OG 2C1 2H1 0.0000 0.0000 164.59 0.0000 0.0000 +!IC 1OG 2C1 2O5 2C5 0.0000 0.0000 177.84 0.0000 0.0000 + +!Thermalized IC +IC 1CA 1CB 1OG 2C1 1.5288 114.42 160.15 116.19 1.4222 +IC 1CB 1OG 2C1 2O5 1.5026 116.19 19.87 107.74 1.4694 +IC 1CB 1OG 2C1 2H1 1.5026 116.19 149.79 108.46 1.1232 +IC 1OG 2C1 2O5 2C5 1.4222 107.74 173.59 112.12 1.4637 + +! | | +! HN-N HN-N +! | OG1--HG1 | OG1--C1(sugar) +! | / | / +! HA-CA--CB-HB ==> HA-CA--CB-HB +! | \ | \ +! | CG2--HG21 | CG2--HG21 +! O=C / \ O=C / \ +! | HG21 HG22 | HG21 HG22 + +PRES TGPB 0.02 ! for connecting THR at the beta position +dele atom 1HG1 +dele atom 2O1 +dele atom 2HO1 + +GROUP + +ATOM 1CB CT1 0.09 !Charge assigned by adding +ATOM 1OG1 OC301 -0.36 ! Charge from OMEA + +GROUP + +ATOM 2C1 CC3162 0.29 ! Charge from OMEA + +BOND 1OG1 2C1 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) + +!IC 1CA 1CB 1OG1 2C1 0.0000 0.0000 167.06 0.0000 0.0000 +!IC 1CB 1OG1 2C1 2O5 0.0000 0.0000 41.65 0.0000 0.0000 +!IC 1CB 1OG1 2C1 2H1 0.0000 0.0000 164.59 0.0000 0.0000 +!IC 1OG1 2C1 2O5 2C5 0.0000 0.0000 177.84 0.0000 0.0000 + +!Thermalized IC +IC 1CA 1CB 1OG1 2C1 1.5466 109.42 84.79 119.34 1.4626 +IC 1CB 1OG1 2C1 2O5 1.4452 119.34 33.16 108.68 1.4170 +IC 1CB 1OG1 2C1 2H1 1.4452 119.34 142.21 103.58 1.0859 +IC 1OG1 2C1 2O5 2C5 1.4626 108.68 167.53 109.99 1.4643 + +PRES NGLB 0.00 ! og make model compound 3 by adding equat +dele atom 1HD21 ! +dele atom 2O1 ! O-methyl to C1; apply to THP2 +dele atom 2HO1 ! O-methyl to C1; apply to THP2 + +GROUP +ATOM 2C1 CC3162 0.27 ! | +ATOM 2H1 HCA1 0.09 ! HN-N +ATOM 1ND2 NC2D1 -0.47 ! | HB1 OD1 HD21 (cis to OD1) +ATOM 1HD22 HCP1 0.31 ! | | || / +ATOM 2C5 CC3163 0.11 ! HA-CA--CB--CG--ND2 +ATOM 2H5 HCA1 0.09 ! | | \ +ATOM 2O5 OC3C61 -0.40 ! | HB2 HD22 (trans to OD1) +GROUP ! O=C +ATOM 1CG CC2O1 0.510 ! | +ATOM 1OD1 OC2D1 -0.510 ! +GROUP ! | Sugar +ATOM 1CB CC321 -0.180 ! HN-N | +ATOM 1HB1 HCA2 0.090 ! | HB1 OD1 C1 (cis to OD1) +ATOM 1HB2 HCA2 0.090 ! | | || / + ! HA-CA--CB--CG--ND2 + ! | | \ + ! | HB2 HD22 (trans to OD1) + ! O=C + ! | +BOND 2C1 1ND2 ! +IMPR 1ND2 1CG 2C1 1HD22 ! + + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +!IC 1CB 1CG 1ND2 2C1 1.4000 120.00 180.00 120.00 1.4000 +!IC 1CG 1ND2 2C1 2O5 1.4000 120.00 -120.00 120.00 1.4000 +!IC 1HD22 1ND2 2C1 2O5 1.4000 120.00 0.00 120.00 1.4000 +!IC 2C5 2O5 2C1 2H1 1.4773 111.49 60.14 108.74 1.0555 +!IC 1ND2 2C1 2O5 2C5 1.4000 120.00 180.00 120.00 1.4000 + +!Thermalized +IC 1CB 1CG 1ND2 2C1 1.5479 118.86 -175.68 128.70 1.3783 +IC 1CG 1ND2 2C1 2O5 1.3126 128.70 -70.91 104.39 1.4413 +IC 1HD22 1ND2 2C1 2O5 1.0117 111.10 108.04 104.39 1.4413 +IC 2C5 2O5 2C1 2H1 1.4242 116.13 41.53 110.40 1.1136 +IC 1ND2 2C1 2O5 2C5 1.3783 104.39 165.66 116.13 1.4242 + +PRES NGLA 0.00 ! og make model compound 3 by adding equat +dele atom 1HD21 ! +dele atom 2O1 ! O-methyl to C1; apply to THP2 +dele atom 2HO1 ! O-methyl to C1; apply to THP2 + +GROUP +ATOM 2C1 CC3162 0.27 ! | +ATOM 2H1 HCA1 0.09 ! HN-N +ATOM 1ND2 NC2D1 -0.47 ! | HB1 OD1 HD21 (cis to OD1) +ATOM 1HD22 HCP1 0.31 ! | | || / +ATOM 2C5 CC3163 0.11 ! HA-CA--CB--CG--ND2 +ATOM 2H5 HCA1 0.09 ! | | \ +ATOM 2O5 OC3C61 -0.40 ! | HB2 HD22 (trans to OD1) +GROUP ! O=C +ATOM 1CG CC2O1 0.510 ! | +ATOM 1OD1 OC2D1 -0.510 ! +GROUP ! | Sugar +ATOM 1CB CC321 -0.180 ! HN-N | +ATOM 1HB1 HCA2 0.090 ! | HB1 OD1 C1 (cis to OD1) +ATOM 1HB2 HCA2 0.090 ! | | || / + ! HA-CA--CB--CG--ND2 + ! | | \ + ! | HB2 HD22 (trans to OD1) + ! O=C + ! | +BOND 2C1 1ND2 ! +IMPR 1ND2 1CG 2C1 1HD22 ! + + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +!IC 1CB 1CG 1ND2 2C1 1.4000 120.00 180.00 120.00 1.4000 +!IC 1CG 1ND2 2C1 2O5 1.4000 120.00 -180.00 120.00 1.4000 +!IC 1HD22 1ND2 2C1 2O5 1.4000 120.00 0.00 120.00 1.4000 +!IC 2C5 2O5 2C1 2H1 1.4773 111.49 -180.14 108.74 1.0555 +!IC 1ND2 2C1 2O5 2C5 1.4000 120.00 60.00 120.00 1.4000 + +!Thermalized +IC 1CB 1CG 1ND2 2C1 1.5278 116.61 179.92 128.01 1.4551 +IC 1CG 1ND2 2C1 2O5 1.3341 128.01 168.99 103.48 1.4210 +IC 1HD22 1ND2 2C1 2O5 0.9855 112.93 -12.55 103.48 1.4210 +IC 2C5 2O5 2C1 2H1 1.4292 117.47 -174.95 108.88 1.0797 +IC 1ND2 2C1 2O5 2C5 1.4551 103.48 75.29 117.47 1.4292 + +END + +read param card flex append +* new parametes +* +BONDS + +!Nglycan +CC311D NC2D1 320.00 1.430 ! 320.00 1.430 ! par22 NH1 CT1 +CC3162 NC2D1 320.00 1.430 ! 320.00 1.430 ! par22 NH1 CT1 + +CC321 CT1 222.500 1.5380 ! CT2 CT1 222.500 1.5380 ! ALLOW ALI +CC2O1 CC321 200.000 1.5220 ! CT2 CC 200.000 1.5220 ! ALLOW POL + +!Oglycan +OC301 CT2 360.00 1.425 ! CC311 OC301 360.00 1.415 ! par35 CC32A OC30A +OC301 CT1 360.00 1.425 ! CC311 OC301 360.00 1.415 ! par35 CC32A OC30A + +ANGLES + +!Nglycan +NC2D1 CC311D OC3C61 90.00 110.00 ! 90.00 110.00 ! OC301 CC311D OC3C61 90.00 110.00 +HCA1 CC311D NC2D1 48.00 108.00 ! par22 NH1 CT1 HB +NC2D1 CC311D CC321C 70.00 113.50 ! par22 NH1 CT1 CT1 +NC2D1 CC311D CC311D 70.00 113.50 ! par22 NH1 CT1 CT1 +CC311D NC2D1 HCP1 35.00 117.00 ! par22 H NH1 CT1 +CC311D NC2D1 CC2O1 50.00 120.00 ! par22 CT1 NH1 C +NC2D1 CC3162 OC3C61 90.00 110.00 ! 90.00 110.00 ! OC301 CC311D OC3C61 90.00 110.00 +HCA1 CC3162 NC2D1 48.00 108.00 ! par22 NH1 CT1 HB +NC2D1 CC3162 CC3161 70.00 113.50 ! par22 NH1 CT1 CT1 +CC3162 NC2D1 HCP1 35.00 117.00 ! par22 H NH1 CT1 +CC3162 NC2D1 CC2O1 50.00 120.00 ! par22 CT1 NH1 C + +NH3 CT1 CC321 67.700 110.0000 ! NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL +CC321 CT1 CC 52.000 108.0000 ! CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +NH1 CT1 CC321 70.000 113.5000 ! NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO +HB1 CT1 CC321 35.000 111.0000 ! HB CT1 CT2 35.000 111.0000 ! ALLOW PEP +CC321 CT1 C 52.000 108.0000 ! CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT1 CC321 CC2O1 52.000 108.0000 ! CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT1 CC321 HCA2 33.430 110.10 22.53 2.17900 ! HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI +HCA2 CC321 CC2O1 33.000 109.50 30.00 2.16300 ! HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO +CC321 CC2O1 OC2D1 15.000 121.00 50.00 2.44000 ! O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO +CC321 CC2O1 NC2D1 50.000 116.50 50.00 2.45000 ! NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + +!Oglycan +CT1 CT2 OC301 45.000 107.00 ! OC301 CC311 CC331 45.00 111.50 ! par35 OC30A CC32A CC33A +CT1 CT1 OC301 45.000 107.00 ! OC301 CC311 CC331 45.00 111.50 ! par35 OC30A CC32A CC33A +CT2 OC301 CC311D 95.00 110.70 ! CC311D OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +CT1 OC301 CC311D 95.00 110.70 ! CC311D OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +CT2 OC301 CC3162 95.00 110.70 ! CC3162 OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +CT1 OC301 CC3162 95.00 110.70 ! CC3162 OC301 CC331 95.00 109.70 ! par35 CC33A OC30A CC32A +CT3 CT1 OC301 45.000 110.00 ! OC301 CC311 CC331 45.00 111.50 ! par35 OC30A CC32A CC33A +HA CT2 OC301 60.00 109.50 ! HCA1 CC311 OC301 60.00 109.50 ! par34 HCA2 CC32A OC30A +HA2 CT2 OC301 60.00 109.50 ! HCA1 CC311 OC301 60.00 109.50 ! par34 HCA2 CC32A OC30A +HA CT1 OC301 60.00 109.50 ! HCA1 CC311 OC301 60.00 109.50 ! par34 HCA2 CC32A OC30A +HA1 CT1 OC301 60.00 109.50 ! HCA1 CC311 OC301 60.00 109.50 ! par34 HCA2 CC32A OC30A + +DIHEDRALS + +!Nglycan +CC321C OC3C61 CC311D NC2D1 0.62 1 0.0 ! og OMeTHP compounds 2 and 3 +CC321C OC3C61 CC311D NC2D1 1.54 2 0.0 ! OC301 CC311D OC3C61 CC321C +CC321C OC3C61 CC311D NC2D1 0.48 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +HCP1 NC2D1 CC311D OC3C61 0.00 1 0.0 ! par22 H NH1 CT1 CT1 +NC2D1 CC311D CC311D NC2D1 0.59 1 180.0 ! OC301 CC3161 CC3162 OC301 ! par35 OC30A CC32A CC32A OC30A +NC2D1 CC311D CC311D NC2D1 1.16 2 0.0 ! OC301 CC3161 CC3162 OC301 ! " og/rmv RESMOR and FABYOW10 +CC311D NC2D1 CC2O1 OC2D1 2.50 2 180.0 ! par22 O C NH1 CT1 +CC311D NC2D1 CC2O1 CC331 1.60 1 0.0 ! par22 CT1 NH1 C CT3 +CC311D NC2D1 CC2O1 CC331 2.50 2 180.0 ! " +HCP1 NC2D1 CC311D HCA1 0.00 1 0.0 ! par22 HB CT1 NH1 H +CC2O1 NC2D1 CC311D HCA1 0.00 1 0.0 ! par22 HB CT1 NH1 C +HCP1 NC2D1 CC311D CC321C 0.00 1 0.0 ! par22 H NH1 CT1 CT1 +HCA2 CC321C CC311D NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC321C CC321C CC311D NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC311D CC311D NC2D1 HCP1 0.00 1 0.0 ! par22 H NH1 CT1 CT1 +HCA1 CC311D CC311D NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +NC2D1 CC311D CC311D CC321C 0.20 3 0.0 ! par27 X CTL1 CTL1 X +OC3C61 CC311D CC311D NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +NC2D1 CC3162 OC3C61 CC3163 0.62 1 0.0 ! og OMeTHP compounds 2 and 3 +NC2D1 CC3162 OC3C61 CC3163 1.54 2 0.0 ! OC301 CC311D OC3C61 CC321C +NC2D1 CC3162 OC3C61 CC3163 0.48 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +NC2D1 CC3162 OC3C61 CC3263 0.62 1 0.0 ! og OMeTHP compounds 2 and 3 +NC2D1 CC3162 OC3C61 CC3263 1.54 2 0.0 ! OC301 CC311D OC3C61 CC321C +NC2D1 CC3162 OC3C61 CC3263 0.48 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +HCP1 NC2D1 CC3162 OC3C61 0.00 1 0.0 ! par22 H NH1 CT1 CT1 +NC2D1 CC3162 CC3161 NC2D1 0.59 1 180.0 ! OC301 CC3161 CC3162 OC301 ! par35 OC30A CC32A CC32A OC30A +NC2D1 CC3162 CC3161 NC2D1 1.16 2 0.0 ! OC301 CC3161 CC3162 OC301 ! " og/rmv RESMOR and FABYOW10 +CC3162 NC2D1 CC2O1 OC2D1 2.50 2 180.0 ! par22 O C NH1 CT1 +CC3162 NC2D1 CC2O1 CC331 1.60 1 0.0 ! par22 CT1 NH1 C CT3 +CC3162 NC2D1 CC2O1 CC331 2.50 2 180.0 ! " +HCA1 CC3162 NC2D1 HCP1 0.00 1 0.0 ! par22 HB CT1 NH1 H +HCA1 CC3162 NC2D1 CC2O1 0.00 1 0.0 ! par22 HB CT1 NH1 C +NC2D1 CC3162 CC3161 HCA1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +NC2D1 CC3162 CC3161 CC3161 0.20 3 0.0 ! par27 X CTL1 CTL1 X +HCP1 NC2D1 CC3162 CC3161 0.00 1 0.0 ! par22 H NH1 CT1 CT1 +NC2D1 CC3162 CC3161 OC311 0.20 3 0.0 ! par27 X CTL1 CTL1 X +CC311D CC311D NC2D1 CC2O1 0.50 1 180.0 ! og fit to IPAA +CC2O1 NC2D1 CC311D CC321C 0.50 1 180.0 ! og fit to IPAA +CC2O1 NC2D1 CC311D OC3C61 2.70 1 180.0 +CC2O1 NC2D1 CC311D OC3C61 1.28 2 0.0 +CC2O1 NC2D1 CC3162 CC3161 0.50 1 180.0 ! og fit to IPAA +CC2O1 NC2D1 CC3162 OC3C61 2.70 1 180.0 +CC2O1 NC2D1 CC3162 OC3C61 1.28 2 0.0 + +NH3 CT1 CC321 HCA2 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +NH1 CT1 CC321 HCA2 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW AL +NH3 CT1 CC321 CC2O1 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +NH1 CT1 CC321 CC2O1 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +CT1 CC321 CC2O1 OC2D1 0.0500 6 180.0 ! X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP +CT1 CC321 CC2O1 NC2D1 0.0500 6 180.0 ! X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP +HB1 CT1 CC321 HCA2 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +HB1 CT1 CC321 CC2O1 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +CC321 CC2O1 NC2D1 HCP1 2.50 2 180.0 ! HCP1 NC2D1 CC2O1 CC331 2.50 2 180.0 ! par22 H NH1 C CT3 +CC321 CC2O1 NC2D1 CC3162 1.60 1 0.0 ! CC3161 NC2D1 CC2O1 CC331 1.60 1 0.0 ! par22 CT1 NH1 C CT3 +CC321 CC2O1 NC2D1 CC3162 2.50 2 180.0 ! CC3161 NC2D1 CC2O1 CC331 2.50 2 180.0 ! " +HCA2 CC321 CT1 CC 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +HCA2 CC321 CT1 C 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +HCA2 CC321 CC2O1 OC2D1 0.00 3 180.0 ! HCA3 CC331 CC2O1 OC2D1 0.00 3 180.0 ! par22 O C CT3 HA +HCA2 CC321 CC2O1 NC2D1 0.00 3 0.0 ! NC2D1 CC2O1 CC331 HCA3 0.00 3 0.0 ! par22 NH1 C CT3 HA +CC2O1 CC321 CT1 CC 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +CC2O1 CC321 CT1 C 0.2000 3 0.0 ! X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +CC321 CT1 C O 1.4000 1 0.0 ! O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP +H NH1 CT1 CC321 0.0000 1 0.0 ! H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP +C NH1 CT1 CC321 1.8000 1 0.0 ! CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP +CC321 CT1 C NH1 0.0000 1 0.0 ! NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + +!Oglycan Transferred +CC311D OC301 CT2 HA 0.284 3 0.0 !CC311D OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CC311D OC301 CT2 HA2 0.284 3 0.0 !CC311D OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +HA CT2 OC301 CC3162 0.284 3 0.0 !CC3162 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +HA2 CT2 OC301 CC3162 0.284 3 0.0 !CC3162 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CC311D OC301 CT1 HA 0.284 3 0.0 !CC311D OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CC311D OC301 CT1 HA1 0.284 3 0.0 !CC311D OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +HA CT1 OC301 CC3162 0.284 3 0.0 !CC3162 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +HA1 CT1 OC301 CC3162 0.284 3 0.0 !CC3162 OC301 CC331 HCA3 0.284 3 0.0 ! par35 HCA3 CC33A OC30A CC32A +CT2 OC301 CC311D HCA1 0.284 3 0.0 !CC331 OC301 CC311D HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CT2 OC301 CC3162 HCA1 0.284 3 0.0 !CC331 OC301 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CT1 OC301 CC311D HCA1 0.284 3 0.0 !CC331 OC301 CC311D HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CT1 OC301 CC3162 HCA1 0.284 3 0.0 !CC331 OC301 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A + + +!Oglycan Optimized + +!!!C2 C1 OG CB +CC321C CC311D OC301 CT2 1.38 1 180.0 +CC321C CC311D OC301 CT2 1.23 2 180.0 +CC321C CC311D OC301 CT2 0.25 3 0.0 +CC321C CC311D OC301 CT1 1.15 1 180.0 +CC321C CC311D OC301 CT1 1.54 2 180.0 +CC321C CC311D OC301 CT1 0.39 3 0.0 + +!!O5 C1 OG CB +CT2 OC301 CC311D OC3C61 0.27 1 0.0 +CT2 OC301 CC311D OC3C61 0.22 2 0.0 +CT2 OC301 CC311D OC3C61 0.07 3 0.0 +CT1 OC301 CC311D OC3C61 0.43 1 180.0 +CT1 OC301 CC311D OC3C61 0.05 2 0.0 +CT1 OC301 CC311D OC3C61 0.56 3 180.0 + +!!C1 OG CB CG +CC311D OC301 CT1 CT3 1.52 1 180.0 +CC311D OC301 CT1 CT3 0.04 2 180.0 +CC311D OC301 CT1 CT3 0.45 3 180.0 + +!!C1 OG CB CA +CC311D OC301 CT2 CT1 2.02 1 180.0 +CC311D OC301 CT2 CT1 0.04 2 0.0 +CC311D OC301 CT2 CT1 0.97 3 180.0 +CC311D OC301 CT1 CT1 2.21 1 180.0 +CC311D OC301 CT1 CT1 0.01 2 180.0 +CC311D OC301 CT1 CT1 0.03 3 0.0 + +!!N CA CB OG +NH1 CT1 CT2 OC301 0.42 1 180.0 +NH1 CT1 CT2 OC301 0.68 2 180.0 +NH1 CT1 CT2 OC301 1.06 3 0.0 +NH1 CT1 CT1 OC301 0.47 1 0.0 +NH1 CT1 CT1 OC301 1.60 2 0.0 +NH1 CT1 CT1 OC301 0.39 3 180.0 + +NH3 CT1 CT2 OC301 0.42 1 180.0 +NH3 CT1 CT2 OC301 0.68 2 180.0 +NH3 CT1 CT2 OC301 1.06 3 0.0 +NH3 CT1 CT1 OC301 0.47 1 0.0 +NH3 CT1 CT1 OC301 1.60 2 0.0 +NH3 CT1 CT1 OC301 0.39 3 180.0 + +!!C CA CB OG +C CT1 CT2 OC301 0.41 1 180.0 +C CT1 CT2 OC301 0.32 2 180.0 +C CT1 CT2 OC301 1.19 3 180.0 +C CT1 CT1 OC301 1.03 1 0.0 +C CT1 CT1 OC301 1.41 2 0.0 +C CT1 CT1 OC301 0.66 3 0.0 + +!GALNAc +!!!C2 C1 OG CB +CC3161 CC3162 OC301 CT2 1.38 1 180.0 +CC3161 CC3162 OC301 CT2 1.23 2 180.0 +CC3161 CC3162 OC301 CT2 0.25 3 0.0 +CC3161 CC3162 OC301 CT1 1.15 1 180.0 +CC3161 CC3162 OC301 CT1 1.54 2 180.0 +CC3161 CC3162 OC301 CT1 0.39 3 0.0 + +!!O5 C1 OG CB +CT2 OC301 CC3162 OC3C61 0.27 1 0.0 +CT2 OC301 CC3162 OC3C61 0.22 2 0.0 +CT2 OC301 CC3162 OC3C61 0.07 3 0.0 +CT1 OC301 CC3162 OC3C61 0.43 1 180.0 +CT1 OC301 CC3162 OC3C61 0.05 2 0.0 +CT1 OC301 CC3162 OC3C61 0.56 3 180.0 + +!!C1 OG CB CG +CC3162 OC301 CT1 CT3 1.52 1 180.0 +CC3162 OC301 CT1 CT3 0.04 2 180.0 +CC3162 OC301 CT1 CT3 0.45 3 180.0 + +!!C1 OG CB CA +CC3162 OC301 CT2 CT1 2.02 1 180.0 +CC3162 OC301 CT2 CT1 0.04 2 0.0 +CC3162 OC301 CT2 CT1 0.97 3 180.0 +CC3162 OC301 CT1 CT1 2.21 1 180.0 +CC3162 OC301 CT1 CT1 0.01 2 180.0 +CC3162 OC301 CT1 CT1 0.03 3 0.0 + +IMPROPER + +NC2D1 CC2O1 CC311D HCP1 20.00 0 0.00 ! par22 NH1 X X H +NC2D1 CC2O1 CC3162 HCP1 20.00 0 0.00 ! par22 NH1 X X H + +CC2O1 NC2D1 CC321 OC2D1 45.0000 0 0.0000 ! O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL +CC2O1 CC321 NC2D1 OC2D1 45.0000 0 0.0000 ! O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + +END + + +RETURN + diff --git a/charmm/toppar/stream/carb/toppar_all36_carb_model.str b/charmm/toppar/stream/carb/toppar_all36_carb_model.str new file mode 100644 index 00000000..0c40bda8 --- /dev/null +++ b/charmm/toppar/stream/carb/toppar_all36_carb_model.str @@ -0,0 +1,2252 @@ +* $Id: toppar_allxx_sugar_model.str,v 1.45 2010-06-21 23:31:00 oguvench Exp $ +read rtf card append +* Topology for sugar related model compounds +* Geometry for all compounds is after dyna leap nstep 1000 ihtfrq 10 +* to allow for testing of all energetic terms (i.e. we dont want any +* degrees of freedom to be at their equilibrium values) +* todo: +* og: THP needs a picture +* +32 1 + +!reset default patches +DEFA FIRS NONE LAST NONE +! model compounds + +RESI MEOH 0.00 ! methanol, adm jr.; new OH charges og 1/20/06 +GROUP +ATOM CB CC331 -0.04 ! H11 +ATOM OG OC311M -0.65 ! \ +ATOM HG1 HCP1 0.42 ! H12--C1--O1 +ATOM HB1 HCA3 0.09 ! / \ +ATOM HB2 HCA3 0.09 ! H13 HO1 +ATOM HB3 HCA3 0.09 ! +BOND CB OG OG HG1 +BOND CB HB1 CB HB2 CB HB3 +DONO HG1 OG +ACCE OG +IC HG1 OG CB HB1 0.9545 108.11 48.03 106.95 1.1187 +IC HG1 OG CB HB2 0.9545 108.11 168.15 114.07 1.1104 +IC HG1 OG CB HB3 0.9545 108.11 -71.70 115.01 1.1744 +IC OG CB HB3 BLNK 1.3957 115.01 0.00 0.00 0.0000 + + +RESI ETOH 0.00 ! Ethanol, adm jr.; new OH charges og 1/23/06 +GROUP +ATOM C1 CC321 0.05 ! H21 H11 H12 +ATOM O1 OC311M -0.65 ! \ \ / +ATOM HO1 HCP1 0.42 ! H22--C2--C1 +ATOM H11 HCA2 0.09 ! / \ +ATOM H12 HCA2 0.09 ! H23 O1--HO1 +GROUP +ATOM C2 CC331 -0.27 +ATOM H21 HCA3 0.09 +ATOM H22 HCA3 0.09 +ATOM H23 HCA3 0.09 +BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 H21 C2 H22 C2 H23 +DONO HO1 O1 +ACCE O1 +IC O1 C1 C2 H21 1.4449 108.58 -167.34 108.13 1.1172 +IC O1 C1 C2 H22 1.4449 108.58 71.26 112.88 1.0611 +IC O1 C1 C2 H23 1.4449 108.58 -53.49 123.68 1.1048 +IC H21 C2 C1 H11 1.1172 108.13 66.57 107.85 1.0962 +IC H21 C2 C1 H12 1.1172 108.13 -57.24 108.08 1.1278 +IC C2 C1 O1 HO1 1.5482 108.58 53.32 103.07 0.9621 + + +RESI PRO2 0.00 ! 2-propanol, adm jr.; new OH charges og 1/24/06 +GROUP +ATOM C2 CC311 0.14 ! H12 H13 H33 H32 +ATOM O2 OC311M -0.65 ! \ / \ / +ATOM HO2 HCP1 0.42 ! H11--C1 C3--H31 +ATOM H21 HCA1 0.09 ! \ / +GROUP ! C2 +ATOM C1 CC331 -0.27 ! / \ +ATOM H11 HCA3 0.09 ! O2 H21 +ATOM H12 HCA3 0.09 ! | +ATOM H13 HCA3 0.09 ! HO2 +GROUP ! +ATOM C3 CC331 -0.27 ! +ATOM H31 HCA3 0.09 +ATOM H32 HCA3 0.09 +ATOM H33 HCA3 0.09 +BOND C1 C2 C2 C3 C2 O2 C2 H21 O2 HO2 +BOND C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 C3 H33 +DONO HO2 O2 +ACCE O2 +! for ic build +IC C1 C2 C3 H31 1.5806 114.31 -47.47 110.03 1.0829 +IC C1 C2 C3 H32 1.5806 114.31 67.60 110.52 1.1521 +IC C1 C2 C3 H33 1.5806 114.31 -169.14 108.82 1.1991 +IC C3 C2 C1 H11 1.5327 114.31 -179.28 102.41 1.1274 +IC C3 C2 C1 H12 1.5327 114.31 64.01 117.68 1.1021 +IC C3 C2 C1 H13 1.5327 114.31 -64.02 111.82 1.1420 +IC H31 C3 C2 O2 1.0829 110.03 73.17 100.87 1.4030 +IC H31 C3 C2 H21 1.0829 110.03 -171.47 113.09 1.1612 +IC C3 C2 O2 HO2 1.5327 100.87 178.34 106.99 0.9874 +! only for analysis +!IC HO1 O1 C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC HO1 O1 C1 H12 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC HO1 O1 C1 H13 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC O1 C1 H11 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + + +RESI EGLY 0.00 ! ethylene glycol, og +GROUP +ATOM C1 CC321 0.05 ! HO1--O1 O2--HO2 +ATOM H11 HCA2 0.09 ! \ / +ATOM H12 HCA2 0.09 ! C1-------C2 +ATOM O1 OC311M -0.65 ! / \ / \ +ATOM HO1 HCP1M 0.42 ! H11 H12 H21 H22 +GROUP +ATOM C2 CC321 0.05 ! +ATOM H21 HCA2 0.09 ! +ATOM H22 HCA2 0.09 ! +ATOM O2 OC311M -0.65 ! +ATOM HO2 HCP1M 0.42 ! +BOND C1 O1 C1 H11 C1 H12 +BOND O1 HO1 C1 C2 +BOND C2 O2 C2 H21 C2 H22 +BOND O2 HO2 +IC O1 C1 C2 O2 1.4049 111.18 75.89 106.30 1.4246 +IC O1 C2 *C1 H11 1.4049 111.18 128.43 116.00 1.0458 +IC O1 C2 *C1 H12 1.4049 111.18 -111.56 109.09 1.0837 +IC C2 C1 O1 HO1 1.5188 111.18 148.98 103.82 0.9491 +IC O2 C1 *C2 H21 1.4246 106.30 111.73 108.49 1.1258 +IC O2 C1 *C2 H22 1.4246 106.30 -125.60 108.10 1.1425 +IC C1 C2 O2 HO2 1.5188 106.30 -54.72 106.27 0.9709 + + +RESI CYHX 0.00 ! cyclohexane viv; og optimized dihedrals +GROUP +ATOM C1 CC321C -0.18 ! H1A H1B H2A H2B +ATOM H1A HCA2 0.09 ! \ / \ / +ATOM H1B HCA2 0.09 ! C1------C2 +GROUP ! H6A / \ H3A +ATOM C2 CC321C -0.18 ! \ / \ / +ATOM H2A HCA2 0.09 ! C6 C3 +ATOM H2B HCA2 0.09 ! / \ / \ +GROUP ! H6B \ / H3B +ATOM C3 CC321C -0.18 ! C5------C4 +ATOM H3A HCA2 0.09 ! / \ / \ +ATOM H3B HCA2 0.09 ! H5A H5B H4A H4B +GROUP +ATOM C4 CC321C -0.18 +ATOM H4A HCA2 0.09 +ATOM H4B HCA2 0.09 +GROUP +ATOM C5 CC321C -0.18 +ATOM H5A HCA2 0.09 +ATOM H5B HCA2 0.09 +GROUP +ATOM C6 CC321C -0.18 +ATOM H6A HCA2 0.09 +ATOM H6B HCA2 0.09 +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C6 +BOND C6 H6A C6 H6B C6 C1 +! og ic table +IC C2 C6 *C1 H1A 1.5577 109.50 116.67 118.32 1.1443 +IC H1A C6 *C1 H1B 1.1443 118.32 124.65 107.86 1.1345 +IC C6 C1 C2 C3 1.5158 109.50 -59.08 110.22 1.5977 +IC C3 C1 *C2 H2A 1.5977 110.22 124.22 105.15 1.1217 +IC H2A C1 *C2 H2B 1.1217 105.15 111.74 108.71 1.1035 +IC C1 C2 C3 C4 1.5577 110.22 47.64 115.10 1.5469 +IC C4 C2 *C3 H3A 1.5469 115.10 129.92 106.77 1.1292 +IC H3A C2 *C3 H3B 1.1292 106.77 111.27 106.42 1.1158 +IC C2 C3 C4 C5 1.5977 115.10 -43.10 111.15 1.5735 +IC C5 C3 *C4 H4A 1.5735 111.15 121.37 109.21 1.1871 +IC H4A C3 *C4 H4B 1.1871 109.21 115.43 112.13 1.0395 +IC C6 C4 *C5 H5A 1.5631 112.23 135.64 115.89 1.1188 +IC H5A C4 *C5 H5B 1.1188 115.89 107.70 107.68 1.1603 +IC C5 C1 *C6 H6A 1.5631 107.66 -115.78 108.70 1.1108 +IC C5 C1 *C6 H6B 1.5631 107.66 124.95 110.76 1.1187 +patc firs none last none + + +RESI ACO 0.0 ! Acetone, adm, Oct 08 +GROUP +ATOM O1 OC2D3 -0.48 ! H22 O1 H32 +ATOM C1 CC2O3 0.40 ! | || | +ATOM C2 CC331 -0.23 ! H21-C2--C1--C3-H31 +ATOM C3 CC331 -0.23 ! | | +ATOM H21 HCA3 0.09 ! H23 H33 +ATOM H22 HCA3 0.09 ! +ATOM H23 HCA3 0.09 ! +ATOM H31 HCA3 0.09 ! +ATOM H32 HCA3 0.09 ! +ATOM H33 HCA3 0.09 ! +BOND C1 C2 C1 C3 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +DOUBLE O1 C1 +IMPR C1 C2 C3 O1 +ACCE O1 +IC C2 C1 C3 H31 1.5366 110.58 135.22 109.51 1.1328 +IC O1 C1 C3 H31 1.2237 122.95 -42.47 109.51 1.1328 +IC O1 C1 C3 H32 1.2237 122.95 77.28 104.63 1.1325 +IC O1 C1 C3 H33 1.2237 122.95 -161.85 105.76 1.0732 +IC C3 C1 C2 H21 1.5233 110.58 -153.74 111.52 1.1204 +IC O1 C1 C2 H21 1.2237 126.42 23.85 111.52 1.1204 +IC O1 C1 C2 H22 1.2237 126.42 148.26 114.11 1.1296 +IC O1 C1 C2 H23 1.2237 126.42 -90.21 101.67 1.1375 + +!og DHA is not fit for use +!og PATCH FIRST NONE LAST NONE +!og RESI DHA 0.0 ! DiHydroxyAcetone +!og GROUP +!og ATOM O1 OC2D3 -0.28 ! +!og ATOM C1 CC2O3 0.28 ! +!og ATOM C2 CC325 0.05 ! +!og ATOM C3 CC325 0.05 ! H22 O1 H32 +!og ATOM H23 HCA2 0.09 ! | || | +!og ATOM H22 HCA2 0.09 ! HO2-O2-C2--C1--C3-O3-HO3 +!og ATOM O2 OC311 -0.65 ! | | +!og ATOM HO2 HCP1 0.42 ! H23 H33 +!og ATOM H33 HCA2 0.09 ! +!og ATOM H32 HCA2 0.09 ! +!og ATOM O3 OC311 -0.65 ! +!og ATOM HO3 HCP1 0.42 ! +!og BOND C1 C2 C1 C3 +!og BOND C2 H23 C2 H22 C2 O2 +!og BOND O2 HO2 +!og BOND C3 H33 C3 H32 C3 O3 +!og BOND O3 HO3 +!og DOUBLE O1 C1 +!og IMPR C2 C1 O1 C3 +!og ACCE O1 +!og ACCE O2 +!og ACCE O3 +!og IC C2 C1 C3 O3 1.5753 104.65 -142.60 114.18 1.3826 +!og IC O1 C1 C3 O3 1.2044 129.46 35.16 114.18 1.3826 +!og IC O1 C1 C3 H32 1.2044 129.46 156.19 109.33 1.1226 +!og IC O1 C1 C3 H33 1.2044 129.46 -87.35 100.41 1.0682 +!og IC C3 C1 C2 O2 1.5724 104.65 -148.30 119.57 1.4192 +!og IC O1 C1 C2 O2 1.2044 125.86 33.83 119.57 1.4192 +!og IC O1 C1 C2 H22 1.2044 125.86 158.40 107.83 1.1409 +!og IC O1 C1 C2 H23 1.2044 125.86 -92.15 104.50 1.0275 +!og IC C1 C2 O2 HO2 1.5753 119.57 -147.48 106.96 0.9437 +!og IC C1 C3 O3 HO3 1.5724 114.18 164.66 116.28 0.9640 +!og PATCH FIRST NONE LAST NONE + + +RESI AALD 0.00 ! Acetaldehyde, adm, Oct 2008 +GROUP ! +ATOM HA HCR1 0.09 ! HB3 +ATOM C CC2O4 0.20 ! | +ATOM O OC2D4 -0.40 !HB1-CB-HB2 +ATOM CB CC331 -0.16 ! | +ATOM HB1 HCA3 0.09 ! O=C +ATOM HB2 HCA3 0.09 ! | +ATOM HB3 HCA3 0.09 ! HA + +BOND HA C C CB CB HB1 CB HB2 CB HB3 +DOUB C O +IMPH C CB O HA +ACCE O + +IC O C CB HB1 1.2074 123.73 -0.46 108.58 1.1053 +IC HB2 CB C O 1.0625 110.65 118.23 123.73 1.2074 +IC HB3 CB C O 1.0898 105.98 -126.83 123.73 1.2074 +IC HA O *C CB 1.1347 126.86 -176.51 123.73 1.5462 +PATCHING FIRST NONE LAST NONE + + +RESI THP 0.00 ! cyclic ether, tetrahydropyran sng; og dihedrals +GROUP +ATOM O1 OC3C61 -0.40 +ATOM C1 CC321C 0.02 +ATOM H1A HCA2 0.09 +ATOM H1B HCA2 0.09 +ATOM C5 CC321C 0.02 +ATOM H5A HCA2 0.09 +ATOM H5B HCA2 0.09 +GROUP +ATOM C2 CC321C -0.18 +ATOM H2A HCA2 0.09 +ATOM H2B HCA2 0.09 +GROUP +ATOM C3 CC321C -0.18 +ATOM H3A HCA2 0.09 +ATOM H3B HCA2 0.09 +GROUP +ATOM C4 CC321C -0.18 +ATOM H4A HCA2 0.09 +ATOM H4B HCA2 0.09 +BOND O1 C1 C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 O1 +ACCE O1 +! og ic table +IC C5 O1 C1 C2 1.4904 108.31 72.27 107.28 1.5434 +IC C2 O1 *C1 H1A 1.5434 107.28 107.92 103.81 1.1412 +IC H1A O1 *C1 H1B 1.1412 103.81 120.92 119.22 1.0624 +IC C1 O1 C5 C4 1.4311 108.31 -67.46 109.85 1.5276 +IC C4 O1 *C5 H5A 1.5276 109.85 -120.99 108.92 1.1306 +IC C4 O1 *C5 H5B 1.5276 109.85 122.89 111.76 1.1083 +IC O1 C1 C2 C3 1.4311 107.28 -65.14 109.39 1.5277 +IC C3 C1 *C2 H2A 1.5277 109.39 117.82 109.98 1.1491 +IC H2A C1 *C2 H2B 1.1491 109.98 124.17 105.47 1.0938 +IC C4 C2 *C3 H3A 1.6111 110.58 117.60 108.00 1.0977 +IC H3A C2 *C3 H3B 1.0977 108.00 113.88 116.20 1.0489 +IC C3 C5 *C4 H4A 1.6111 110.34 -125.17 106.02 1.1192 +IC C3 C5 *C4 H4B 1.6111 110.34 124.54 119.02 1.0688 + + +RESI NMA 0.00 ! og NOT FOR USE from par22 for parameter transfer only +GROUP +ATOM CL CC331 -0.27 ! CT3 +ATOM HL1 HCA3 0.09 ! HA +ATOM HL2 HCA3 0.09 ! HA +ATOM HL3 HCA3 0.09 ! HA +ATOM C CC2O1 0.51 ! C +ATOM O OC2D1 -0.51 ! O +ATOM N NC2D1 -0.47 ! NH1 +ATOM H HCP1 0.31 ! H +ATOM CR CC331 -0.11 ! CT3 +ATOM HR1 HCA3 0.09 ! HA +ATOM HR2 HCA3 0.09 ! HA +ATOM HR3 HCA3 0.09 ! HA +BOND HL1 CL HL2 CL HL3 CL ! N-Methylacetamide: +BOND CL C C N N CR ! HL1\ O /HR1 +BOND N H ! HL2-- CL -- C -- N -- CR --HR2 +BOND HR1 CR HR2 CR HR3 CR ! HL3/ H \HR3 +DOUBLE C O +IMPR N C CR H +IMPR C CL N O +IC O C N H 1.2170 122.19 -172.63 117.71 1.0174 +IC H N C CL 1.0174 117.71 10.44 116.80 1.4705 +IC O C N CR 1.2170 122.19 -1.67 127.03 1.4271 +IC N C CL HL1 1.3649 116.80 145.76 103.37 1.1542 +IC N C CL HL2 1.3649 116.80 23.93 112.45 1.1269 +IC N C CL HL3 1.3649 116.80 -97.81 110.31 1.0862 +IC C N CR HR1 1.3649 127.03 -173.51 106.23 1.0877 +IC C N CR HR2 1.3649 127.03 63.92 119.80 1.1663 +IC C N CR HR3 1.3649 127.03 -68.31 110.26 1.0837 + + +RESI IPAA 0.00 ! og isopropyl acetamide +GROUP ! +ATOM CL CC331 -0.27 ! +ATOM HL1 HCA3 0.09 ! +ATOM HL2 HCA3 0.09 ! H211 H212 H213 +ATOM HL3 HCA3 0.09 ! \ | / +GROUP ! C21 +ATOM C CC2O1 0.51 ! C HL1\ O / +ATOM O OC2D1 -0.51 ! O HL2-- CL -- C -- N -- CR --HR +ATOM N NC2D1 -0.47 ! NH1 HL3/ H \ +ATOM H HCP1 0.31 ! H C22 +ATOM CR CC311 0.07 ! CT1 / | \ +ATOM HR HCA1 0.09 ! H221 H222 H223 +GROUP ! +ATOM C21 CC331 -0.27 ! +ATOM H211 HCA3 0.09 ! +ATOM H212 HCA3 0.09 ! +ATOM H213 HCA3 0.09 ! +GROUP +ATOM C22 CC331 -0.27 ! +ATOM H221 HCA3 0.09 ! +ATOM H222 HCA3 0.09 ! +ATOM H223 HCA3 0.09 ! +BOND HL1 CL HL2 CL HL3 CL ! +BOND CL C C N N CR ! +BOND N H ! +BOND HR CR C21 CR C22 CR ! +BOND C21 H211 C21 H212 C21 H213 +BOND C22 H221 C22 H222 C22 H223 +DOUBLE C O +IMPR N C CR H +IMPR C CL N O +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O C N H 1.2155 122.35 -164.87 110.88 1.0016 +IC H N C CL 1.0016 110.88 17.10 117.67 1.3978 +IC O C N CR 1.2155 122.35 -4.65 130.13 1.4829 +IC N C CL HL1 1.2940 117.67 -165.10 107.63 1.0780 +IC N C CL HL2 1.2940 117.67 75.06 110.90 1.1098 +IC N C CL HL3 1.2940 117.67 -47.51 110.65 1.1556 +IC C N CR HR 1.2940 130.13 171.27 103.75 1.1568 +IC C N CR C21 1.2940 130.13 48.14 115.66 1.5028 +IC C N CR C22 1.2940 130.13 -78.47 108.40 1.5882 +IC N CR C21 H211 1.4829 115.66 62.05 107.27 1.1345 +IC N CR C21 H212 1.4829 115.66 -59.32 109.83 1.1523 +IC N CR C21 H213 1.4829 115.66 -175.32 115.02 1.0858 +IC N CR C22 H221 1.4829 108.40 61.94 112.51 1.1415 +IC N CR C22 H222 1.4829 108.40 -59.32 113.98 1.0642 +IC N CR C22 H223 1.4829 108.40 -175.46 104.61 1.0857 + + +RESI PROA -1.00 ! og NOT FOR USE from par22 for parameter transfer only +GROUP +ATOM C1 CC321 -0.28 ! CT2 +ATOM C2 CC2O2 0.62 ! CC H1 O1 (-) +ATOM H1 HCA2 0.09 ! HA | / +ATOM H2 HCA2 0.09 ! HA H2--C1--C2 + ! | \\ +ATOM O1 OC2D2 -0.76 ! OC | O2 +ATOM O2 OC2D2 -0.76 ! OC H01--C0 +GROUP ! | \ +ATOM C0 CC331 -0.27 ! CT3 H02 H03 +ATOM H01 HCA3 0.09 ! HA +ATOM H02 HCA3 0.09 ! HA +ATOM H03 HCA3 0.09 ! HA +Bond c1 h1 c1 h2 c1 c0 +Bond c1 c2 c2 o1 +Bond c0 h01 c0 h02 c0 h03 +Double c2 o2 +impr c2 c1 o2 o1 +IC H1 C1 C2 O1 1.1253 109.12 -137.07 128.49 1.2966 +IC H2 C1 C2 O1 1.1036 108.72 108.43 128.49 1.2966 +IC H1 C1 C2 O2 1.1253 109.12 44.26 110.77 1.2526 +IC H2 C1 C2 O2 1.1036 108.72 -70.24 110.77 1.2526 +IC O1 O2 *C2 C1 1.2966 120.73 178.79 110.77 1.4700 +IC O2 C2 C1 C0 1.2526 110.77 163.40 111.67 1.5339 +IC C2 C1 C0 H01 1.4700 111.67 66.43 112.03 1.1071 +IC C2 C1 C0 H02 1.4700 111.67 -45.94 110.20 1.1306 +IC C2 C1 C0 H03 1.4700 111.67 -176.01 119.82 1.1022 +patc firs none last none + + +RESI AMOP -1.00 ! alpha-methoxy-propionic acid, og +GROUP +ATOM C1 CC311 -0.02 ! CT1 HM1 HM2 HM3 +ATOM C2 CC2O2 0.62 ! CC \ | / +ATOM H1 HCA1 0.09 ! HA CM +ATOM OM OC301 -0.34 ! ethers | +ATOM CM CC331 -0.10 ! CT3 OM O1 (-) +ATOM HM1 HCA3 0.09 ! HA | / +ATOM HM2 HCA3 0.09 ! HA H1--C1--C2 +ATOM HM3 HCA3 0.09 ! HA | \\ +ATOM O1 OC2D2 -0.76 ! OC | O2 +ATOM O2 OC2D2 -0.76 ! OC H01--C0 +GROUP ! | \ +ATOM C0 CC331 -0.27 ! CT3 H02 H03 +ATOM H01 HCA3 0.09 ! HA +ATOM H02 HCA3 0.09 ! HA +ATOM H03 HCA3 0.09 ! HA +BOND C1 H1 C1 OM C1 C0 +BOND C1 C2 C2 O1 +BOND C0 H01 C0 H02 C0 H03 +BOND OM CM +BOND CM HM1 CM HM2 CM HM3 +DOUBLE C2 O2 +IMPR C2 C1 O2 O1 +IC C2 C1 OM CM 1.5252 115.91 -163.98 110.47 1.4137 +IC OM C2 *C1 C0 1.4518 115.91 127.11 106.96 1.5476 +IC OM C2 *C1 H1 1.4518 115.91 -115.97 105.08 1.0909 +IC C1 OM CM HM1 1.4518 110.47 45.69 109.01 1.0989 +IC HM1 OM *CM HM2 1.0989 109.01 -131.94 114.65 1.0712 +IC HM1 OM *CM HM3 1.0989 109.01 114.35 108.56 1.1268 +IC H1 C1 C2 O1 1.0909 105.08 177.07 118.55 1.2873 +IC O1 C1 *C2 O2 1.2873 118.55 -179.93 117.50 1.2467 +IC H1 C1 C0 H01 1.0909 110.01 -49.49 109.27 1.0665 +IC H01 C1 *C0 H02 1.0665 109.27 -122.70 108.49 1.0942 +IC H01 C1 *C0 H03 1.0665 109.27 120.34 108.58 1.0708 +patc firs none last none + + +RESI AMOL -1.00 ! alpha-methoxy-lactic acid, og +GROUP +ATOM C1 CC301 0.30 ! CT1 HM1 HM2 HM3 +ATOM C2 CC2O2 0.30 ! CC \ | / +ATOM OH OC311 -0.65 ! OH1 CM +ATOM HO HCP1 0.42 ! H | +ATOM OM OC301 -0.34 ! ethers OM O1 (-) +ATOM CM CC331 -0.10 ! CT3 | / +ATOM HM1 HCA3 0.09 ! HA OH--C1--C2 +ATOM HM2 HCA3 0.09 ! HA / | \\ +ATOM HM3 HCA3 0.09 ! HA HO | O2 +ATOM O1 OC2D2 -0.60 ! OC H01--C0 +ATOM O2 OC2D2 -0.60 ! OC | \ +GROUP ! H02 H03 +ATOM C0 CC331 -0.27 ! CT3 +ATOM H01 HCA3 0.09 ! HA +ATOM H02 HCA3 0.09 ! HA +ATOM H03 HCA3 0.09 ! HA +BOND C1 OH OH HO C1 OM C1 C0 +BOND C1 C2 C2 O1 +BOND C0 H01 C0 H02 C0 H03 +BOND OM CM +BOND CM HM1 CM HM2 CM HM3 +DOUBLE C2 O2 +IMPR C2 C1 O2 O1 +IC C2 C1 OM CM 1.6681 105.74 -166.75 112.34 1.4412 +IC OM C2 *C1 C0 1.3543 105.74 122.28 111.78 1.5273 +IC OM C2 *C1 OH 1.3543 105.74 -119.79 108.83 1.4185 +IC C2 C1 OH HO 1.6681 108.83 1.59 91.98 0.9590 +IC C1 OM CM HM1 1.3543 112.34 64.47 115.10 1.1624 +IC HM1 OM *CM HM2 1.1624 115.10 -125.06 110.12 1.1195 +IC HM1 OM *CM HM3 1.1624 115.10 121.32 109.80 1.1277 +IC OH C1 C2 O1 1.4185 108.83 155.75 117.95 1.2344 +IC O1 C1 *C2 O2 1.2344 117.95 -172.28 112.81 1.2801 +IC OH C1 C0 H01 1.4185 106.97 -71.89 103.07 1.1263 +IC H01 C1 *C0 H02 1.1263 103.07 -114.48 109.08 1.0786 +IC H01 C1 *C0 H03 1.1263 103.07 118.43 113.39 1.1086 +patc firs none last none + + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!! Cyclic ethers from top_all27_carb_jul2o.inp!!!!!!!!!!!!!!! +!! - written by viv; added erh !!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +RESI THF 0.00 ! cyclic ether, Tetra-Hydro-Furan +GROUP +ATOM O1 OC3C5M -0.40 ! +ATOM C1 CC322C 0.02 ! +ATOM H1A HCA2C2 0.09 ! O1 +ATOM H1B HCA2C2 0.09 ! H4A / \ H1A +ATOM C2 CC322C -0.18 ! \ / \ / +ATOM H2A HCA2C2 0.09 ! C4 C1 +ATOM H2B HCA2C2 0.09 ! / \ / \ +ATOM C3 CC322C -0.18 ! H4B \ / H1B +ATOM H3A HCA2C2 0.09 ! C3----C2 +ATOM H3B HCA2C2 0.09 ! / \ / \ +ATOM C4 CC322C 0.02 ! H3A H3B H2A H2B +ATOM H4A HCA2C2 0.09 ! +ATOM H4B HCA2C2 0.09 ! +BOND O1 C1 C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 O1 +!! +IC O1 C1 C2 C3 1.4360 101.32 37.98 103.21 1.5433 +IC C1 C2 C3 C4 1.5237 103.21 -41.00 99.36 1.5882 +IC C2 C3 C4 O1 1.5433 99.36 28.95 103.42 1.4134 +IC C3 C4 O1 C1 1.5882 103.42 -6.17 114.90 1.4360 +IC C4 O1 C1 C2 1.4134 114.90 -19.85 101.32 1.5237 +IC O1 C2 *C1 H1A 1.4360 101.32 112.58 114.19 1.1457 +IC O1 C2 *C1 H1B 1.4360 101.32 -113.28 118.93 1.0941 +IC C1 C3 *C2 H2A 1.5237 103.21 118.50 110.42 1.0754 +IC C1 C3 *C2 H2B 1.5237 103.21 -124.27 110.08 1.1915 +IC C2 C4 *C3 H3A 1.5433 99.36 124.21 112.48 1.1275 +IC C2 C4 *C3 H3B 1.5433 99.36 -113.45 108.07 1.1155 +IC C3 O1 *C4 H4A 1.5882 103.42 115.42 113.34 1.1051 +IC C3 O1 *C4 H4B 1.5882 103.42 -119.16 106.17 1.0807 +patc firs none last none + + +RESI TF2M 0.00 ! cyclic ether, 2-Methyl-Tetra-Hydro-Furan +GROUP +ATOM O1 OC3C5M -0.40 ! +ATOM C1 CC312C 0.11 ! H5A +ATOM H1 HCA1C2 0.09 ! O1 | +ATOM C2 CC322C -0.18 ! H4A / \ C5-H5B +ATOM H2A HCA2C2 0.09 ! \ / \ / \ +ATOM H2B HCA2C2 0.09 ! C4 C1 H5C +ATOM C3 CC322C -0.18 ! / \ / \ +ATOM H3A HCA2C2 0.09 ! H4B \ / H1 +ATOM H3B HCA2C2 0.09 ! C3----C2 +ATOM C4 CC322C 0.02 ! / \ / \ +ATOM H4A HCA2C2 0.09 ! H3A H3B H2A H2B +ATOM H4B HCA2C2 0.09 ! +ATOM C5 CC331 -0.27 ! +ATOM H5A HCA3 0.09 ! +ATOM H5B HCA3 0.09 ! +ATOM H5C HCA3 0.09 ! +BOND O1 C1 C1 H1 C1 C2 C1 C5 +BOND C5 H5A C5 H5B C5 H5C +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 O1 +IC O1 C1 C2 C3 1.4040 99.92 -23.40 101.04 1.5499 +IC C4 O1 C1 C2 1.4038 110.12 47.12 99.92 1.6003 +IC O1 C1 C5 H5A 1.4040 115.16 72.23 115.84 1.1039 +IC C2 O1 *C1 C5 1.6003 99.92 127.51 115.16 1.4891 +IC C2 O1 *C1 H1 1.6003 99.92 -111.47 106.70 1.1317 +IC C3 C1 *C2 H2A 1.5499 101.04 120.73 112.60 1.1356 +IC H2A C1 *C2 H2B 1.1356 112.60 123.04 114.57 1.0401 +IC C4 C2 *C3 H3A 1.5176 106.88 125.54 106.84 1.0941 +IC H3A C2 *C3 H3B 1.0941 106.84 122.26 113.57 1.0368 +IC C3 O1 *C4 H4A 1.5176 98.99 -115.57 106.84 1.1102 +IC C3 O1 *C4 H4B 1.5176 98.99 119.80 114.56 1.1058 +IC H5A C1 *C5 H5B 1.1039 115.84 125.85 119.74 1.1039 +IC H5A C1 *C5 H5C 1.1039 115.84 -119.92 109.77 1.1311 +patc firs none last none + +!!model compounds and patches for disaccharide analogs !!!!!!!! +!!! These compounds were used for determing the dihedral parameters for the +!!! glycosidic linkage, partial charge and LJ on the glycosidic oxygen and +!!! the bonded terms. +!!! Reference: +!!! pending +!!! + +RESI CYHX2 0.0 ! og CYHX with different atom names for use in +GROUP ! disaccharide model compounds; +ATOM C1 CC321C -0.18 ! C5O corresponds to the position of hexopyranose O5; +ATOM H1A HCA2 0.09 ! compatible with PRES A1A2M etc; +ATOM H1B HCA2 0.09 ! H?A are axial, H?B are equatorial +GROUP ! +ATOM C2 CC321C -0.18 ! +ATOM H2A HCA2 0.09 ! H5A H5B H5OA H5OB +ATOM H2B HCA2 0.09 ! \ / \/ +GROUP ! C5-------C5O +ATOM C3 CC321C -0.18 ! H4A / \ H1B +ATOM H3A HCA2 0.09 ! \/ \ / +ATOM H3B HCA2 0.09 ! C4 C1 +GROUP ! / \ / \ +ATOM C4 CC321C -0.18 ! H4B \ / H1A +ATOM H4A HCA2 0.09 ! C3------C2 +ATOM H4B HCA2 0.09 ! /\ /\ +GROUP ! H3A H3B H2A H2B +ATOM C5 CC321C -0.18 ! +ATOM H5A HCA2 0.09 ! +ATOM H5B HCA2 0.09 ! +GROUP +ATOM C5O CC321C -0.18 ! +ATOM H5OA HCA2 0.09 ! +ATOM H5OB HCA2 0.09 ! +BOND C1 H1B C1 H1A C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C5O +BOND C5O H5OA C5O H5OB C5O C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC H1A C2 *C1 H1B 1.0819 113.09 -112.79 110.23 1.1580 +IC H1A C5O *C1 C2 1.0819 113.40 -128.57 110.98 1.4734 +IC H2B C3 *C2 H2A 1.1122 119.93 -113.35 114.30 1.0471 +IC H2B C1 *C2 C3 1.1122 109.47 -133.64 109.85 1.5102 +IC H3B C4 *C3 H3A 1.0583 107.43 113.71 111.34 1.0962 +IC H3B C2 *C3 C4 1.0583 113.73 118.21 106.61 1.5310 +IC H4B C5 *C4 H4A 1.1481 103.95 -122.84 108.77 1.1271 +IC H4B C3 *C4 C5 1.1481 109.54 -115.03 112.42 1.5413 +IC H5A C5O *C5 H5B 1.0812 108.12 -122.12 108.01 1.1656 +IC H5A C4 *C5 C5O 1.0812 106.22 -116.61 109.67 1.3746 +IC H5OA C1 *C5O H5OB 1.0812 108.12 122.12 108.01 1.1656 +IC H5OA C5 *C5O C1 1.0812 106.22 116.61 109.67 1.3746 +IC C5O C1 C2 C3 1.4247 110.98 63.25 109.85 1.5102 +IC C1 C2 C3 C4 1.4734 109.85 -53.97 106.61 1.5310 +IC C2 C3 C4 C5 1.5102 106.61 50.83 112.42 1.5413 +IC C3 C4 C5 C5O 1.5310 112.42 -55.85 109.67 1.3746 +IC C4 C5 C5O C1 1.5413 109.67 61.26 109.77 1.4247 +IC C5 C5O C1 C2 1.3746 109.77 -67.11 110.98 1.4734 + +RESI THP2 0.00 ! og THP with different atom names for use in +GROUP ! disaccharide model compounds ; +ATOM C1 CC321D 0.02 ! O5 corresponds to the position of hexopyranose O5 ; +ATOM H1A HCA2 0.09 ! compatible with PRES 11ABM etc; +ATOM H1B HCA2 0.09 ! H?A are axial and H?B are equatorial +ATOM O5 OC3C61 -0.40 ! +ATOM C5 CC321C 0.02 ! +ATOM H5A HCA2 0.09 ! H5A H5B +ATOM H5B HCA2 0.09 ! \/ +GROUP ! C5-------O5 +ATOM C2 CC321C -0.18 ! H4A / \ H1B +ATOM H2A HCA2 0.09 ! \/ \ / +ATOM H2B HCA2 0.09 ! C4 C1 +GROUP ! / \ / \ +ATOM C3 CC321C -0.18 ! H4B \ / H1A +ATOM H3A HCA2 0.09 ! C3------C2 +ATOM H3B HCA2 0.09 ! /\ /\ +GROUP ! H3A H3B H2A H2B +ATOM C4 CC321C -0.18 ! +ATOM H4A HCA2 0.09 ! +ATOM H4B HCA2 0.09 ! +BOND C1 H1B C1 H1A C1 C2 O5 C5 +BOND C2 H2A C2 H2B C2 C3 C3 H3A +BOND C3 H3B C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5A C5 H5B C1 O5 +ACCE O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC H1A C2 *C1 H1B 1.0819 113.09 -112.79 110.23 1.1580 +IC H1A O5 *C1 C2 1.0819 113.40 -128.57 110.98 1.4734 +IC H2B C3 *C2 H2A 1.1122 119.93 -113.35 114.30 1.0471 +IC H2B C1 *C2 C3 1.1122 109.47 -133.64 109.85 1.5102 +IC H3B C4 *C3 H3A 1.0583 107.43 113.71 111.34 1.0962 +IC H3B C2 *C3 C4 1.0583 113.73 118.21 106.61 1.5310 +IC H4B C5 *C4 H4A 1.1481 103.95 -122.84 108.77 1.1271 +IC H4B C3 *C4 C5 1.1481 109.54 -115.03 112.42 1.5413 +IC H5A O5 *C5 H5B 1.0812 108.12 -122.12 108.01 1.1656 +IC H5A C4 *C5 O5 1.0812 106.22 -116.61 109.67 1.3746 +IC O5 C1 C2 C3 1.4247 110.98 63.25 109.85 1.5102 +IC C1 C2 C3 C4 1.4734 109.85 -53.97 106.61 1.5310 +IC C2 C3 C4 C5 1.5102 106.61 50.83 112.42 1.5413 +IC C3 C4 C5 O5 1.5310 112.42 -55.85 109.67 1.3746 +IC C4 C5 O5 C1 1.5413 109.67 61.26 109.77 1.4247 +IC C5 O5 C1 C2 1.3746 109.77 -67.11 110.98 1.4734 + +RESI THF2 0.00 ! pram; copied from THF with Fructose IUPAC naming +GROUP +ATOM O5 OC3C5M -0.40 ! +ATOM C2 CC322C 0.02 ! +ATOM H2A HCA2C2 0.09 ! O5 +ATOM H2B HCA2C2 0.09 ! H5B / \ H2B +ATOM C3 CC322C -0.18 ! \ / \ / +ATOM H3A HCA2C2 0.09 ! C5 C2 +ATOM H3B HCA2C2 0.09 ! / \ / \ +ATOM C4 CC322C -0.18 ! H5A \ / H2A +ATOM H4A HCA2C2 0.09 ! C4----C3 +ATOM H4B HCA2C2 0.09 ! / \ / \ +ATOM C5 CC322C 0.02 ! H4B H4A H3B H3A +ATOM H5A HCA2C2 0.09 ! +ATOM H5B HCA2C2 0.09 ! +BOND O5 C2 C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C2 C3 C4 1.4360 101.32 37.98 103.21 1.5433 +IC C2 C3 C4 C5 1.5237 103.21 -41.00 99.36 1.5882 +IC C3 C4 C5 O5 1.5433 99.36 28.95 103.42 1.4134 +IC C4 C5 O5 C2 1.5882 103.42 -6.17 114.90 1.4360 +IC C5 O5 C2 C3 1.4134 114.90 -19.85 101.32 1.5237 +IC O5 C3 *C2 H2B 1.4360 101.32 112.58 114.19 1.1457 +IC O5 C3 *C2 H2A 1.4360 101.32 -113.28 118.93 1.0941 +IC C2 C4 *C3 H3B 1.5237 103.21 118.50 110.42 1.0754 +IC C2 C4 *C3 H3A 1.5237 103.21 -124.27 110.08 1.1915 +IC C3 C5 *C4 H4B 1.5433 99.36 124.21 112.48 1.1275 +IC C3 C5 *C4 H4A 1.5433 99.36 -113.45 108.07 1.1155 +IC C4 O5 *C5 H5B 1.5882 103.42 115.42 113.34 1.1051 +IC C4 O5 *C5 H5A 1.5882 103.42 -119.16 106.17 1.0807 +patc firs none last none + + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! disaccharide model compound patches ! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +PRES OMEAM 0.00 ! og make model compound 2 by adding axial +dele atom H1A ! O-methyl to C1; apply to THP2 +GROUP +ATOM C1 CC311D 0.29 ! +ATOM H1B HCA1 0.09 ! +ATOM OM OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +ATOM C5 CC321C 0.02 ! +ATOM H5A HCA2 0.09 ! +ATOM H5B HCA2 0.09 ! +ATOM O5 OC3C61 -0.40 ! +BOND OM C1 OM CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC OM C1 O5 C5 1.4552 103.73 70.41 111.65 1.4477 +IC O5 C1 OM CM 1.4735 103.73 71.27 114.58 1.4525 +IC C1 OM CM HM1 1.4552 114.58 47.22 110.08 1.1158 +IC C5 O5 C1 H1B 1.4477 111.65 -168.02 112.12 1.1401 +IC HM1 OM *CM HM2 1.1158 110.08 119.89 110.78 1.1344 +IC HM3 OM *CM HM2 1.1501 109.28 -117.02 110.78 1.1344 + +PRES OMEBM 0.00 ! og make model compound 3 by adding equat +dele atom H1B ! O-methyl to C1; apply to THP2 +GROUP +ATOM C1 CC311D 0.29 ! +ATOM H1A HCA1 0.09 ! +ATOM OM OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +ATOM C5 CC321C 0.02 ! +ATOM H5A HCA2 0.09 ! +ATOM H5B HCA2 0.09 ! +ATOM O5 OC3C61 -0.40 ! +BOND OM C1 OM CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC OM C1 O5 C5 1.4076 115.06 177.85 112.70 1.4132 +IC O5 C1 OM CM 1.3742 115.06 41.63 111.09 1.4240 +IC C1 OM CM HM1 1.4076 111.09 46.35 109.37 1.1094 +IC O5 OM *C1 H1A 1.3742 115.06 118.51 107.07 1.1324 +IC HM1 OM *CM HM2 1.1094 109.37 124.73 105.27 1.1288 +IC HM3 OM *CM HM2 1.0920 106.02 -112.54 105.27 1.1288 + +! patches for disaccharide model compounds 5 through 10: +! first 4 letters indicate type of linkage as in the main topology file +! letter 5 "m" indicates that this is a model compound patch +! for all patches, first residue must be THP2 +! for 11??mo patches only: +! letter 6 "o" indicates that residue 2 must be THP2 +! i.e. 11aamo is a C1_axial - C1_axial linkage for res1=THP2 and res2=THP2 +! for 12??m patches: +! lack of letter 6 "o" indicates that residue 2 must be CYHX2 +! +PRES 11aamo 0.40 ! og disac model compound 5 C1_axial -> C1_axial +dele atom 1H1A +dele atom 2H1A +GROUP +ATOM 1H1B HCA1 0.09 ! atom type change +ATOM 1C1 CC311D 0.29 ! atom type and charge change +ATOM 1O11 OC302 -0.36 ! new atom +ATOM 2C1 CC311D 0.29 ! atom type and charge change +ATOM 2H1B HCA1 0.09 ! atom type change +BOND 1O11 1C1 1O11 2C1 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C5 1O5 1C1 1O11 1.4381 110.11 64.51 109.50 1.3767 +IC 1O5 1C1 1O11 2C1 1.4355 109.50 63.09 119.52 1.3634 ! PHI +IC 1C1 1O11 2C1 2O5 1.3767 119.52 70.86 111.74 1.4224 ! PSI +IC 1O11 2C1 2O5 2C5 1.3634 111.74 57.99 110.76 1.4474 +IC 1H1B 1O5 *1C1 1C2 1.1061 111.88 120.00 112.57 1.5609 +IC 2H1B 2O5 *2C1 1O11 1.1122 119.93 -120.35 114.30 1.0471 + +PRES 11abmo 0.40 ! og disac model compound 4 C1_axial -> C1_equat +dele atom 1H1A +dele atom 2H1B +ATOM 1H1B HCA1 0.09 ! atom type change +ATOM 1C1 CC311D 0.29 ! atom type and charge change +ATOM 1O11 OC302 -0.36 ! new atom +ATOM 2C1 CC311D 0.29 ! atom type and charge change +ATOM 2H1A HCA1 0.09 ! atom type change +BOND 1O11 1C1 1O11 2C1 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C5 1O5 1C1 1O11 1.4457 108.86 55.88 110.23 1.3751 +IC 1O5 1C1 1O11 2C1 1.4581 110.23 75.76 123.58 1.3651 ! PHI +IC 1C1 1O11 2C1 2O5 1.3751 123.58 124.09 106.90 1.4243 ! PSI +IC 1O11 2C1 2O5 2C5 1.3651 106.90 174.55 113.60 1.4121 +IC 1H1B 1O5 *1C1 1C2 1.1061 111.88 120.00 112.57 1.5609 +IC 2H1A 2O5 *2C1 1O11 1.1122 119.93 120.35 114.30 1.0471 + +PRES 11bamo 0.40 ! og disac model compound 4 C1_equat -> C1_axial +dele atom 1H1B +dele atom 2H1A +ATOM 1H1A HCA1 0.09 ! atom type change +ATOM 1C1 CC311D 0.29 ! atom type and charge change +ATOM 1O11 OC302 -0.36 ! new atom +ATOM 2C1 CC311D 0.29 ! atom type and charge change +ATOM 2H1B HCA1 0.09 ! atom type change +BOND 1O11 1C1 1O11 2C1 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C5 1O5 1C1 1O11 1.4457 108.86 -180.00 110.23 1.3751 +IC 1O5 1C1 1O11 2C1 1.4581 110.23 75.76 123.58 1.3651 ! PHI +IC 1C1 1O11 2C1 2O5 1.3751 123.58 124.09 106.90 1.4243 ! PSI +IC 1O11 2C1 2O5 2C5 1.3651 106.90 60.55 113.60 1.4121 +IC 1H1A 1O5 *1C1 1C2 1.1061 111.88 -120.00 112.57 1.5609 +IC 2H1B 2O5 *2C1 1O11 1.1122 119.93 -120.35 114.30 1.0471 + +PRES 11bbmo 0.40 ! og disac model compound 6 C1_equat -> C1_equat +dele atom 1H1B +dele atom 2H1B +GROUP +ATOM 1H1A HCA1 0.09 ! atom type change +ATOM 1C1 CC311D 0.29 ! atom type and charge change +ATOM 1O11 OC302 -0.36 ! new atom +ATOM 2C1 CC311D 0.29 ! atom type and charge change +ATOM 2H1A HCA1 0.09 ! atom type change +BOND 1O11 1C1 1O11 2C1 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C5 1O5 1C1 1O11 1.4890 115.18 -167.87 105.32 1.3850 +IC 1O5 1C1 1O11 2C1 1.4085 105.32 -52.34 114.84 1.3651 ! PHI +IC 1C1 1O11 2C1 2O5 1.3850 114.84 -60.01 112.27 1.4608 ! PSI +IC 1O11 2C1 2O5 2C5 1.3651 112.27 172.44 109.51 1.4158 +IC 1H1A 1O5 *1C1 1C2 1.1061 111.88 -120.00 112.57 1.5609 +IC 2H1A 2O5 *2C1 1O11 1.1122 119.93 120.35 114.30 1.0471 + +PRES 12aam 0.20 ! og disac model compound 7 C1_axial -> C2_axial +dele atom 1H1A +dele atom 2H2A +ATOM 1C1 CC311D 0.29 ! atom type and charge change +ATOM 1H1B HCA1 0.09 ! atom type change +ATOM 1O12 OC301 -0.36 ! new atom +ATOM 2C2 CC311C 0.09 ! atom type and charge change +ATOM 2H2B HCA1 0.09 ! atom type change +BOND 1C1 1O12 1O12 2C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O12 1C1 1O5 1C5 1.3623 108.15 64.23 113.01 1.4139 +IC 1O5 1C1 1O12 2C2 1.4386 108.15 60.13 116.04 1.4913 ! PHI +IC 1C1 1O12 2C2 2C1 1.3623 116.04 -150.33 114.55 1.5295 ! PSI +IC 1H1B 1O5 *1C1 1C2 1.1061 111.88 120.00 112.57 1.5609 +IC 2H2B 2C1 *2C2 1O12 1.1122 119.93 120.35 114.30 1.0471 + +PRES 12abm 0.20 ! og disac model compound 8 C1_axial -> C2_equat +dele atom 1H1A +dele atom 2H2B +ATOM 1C1 CC311D 0.29 ! atom type and charge change +ATOM 1H1B HCA1 0.09 ! atom type change +ATOM 1O12 OC301 -0.36 ! new atom +ATOM 2C2 CC311C 0.09 ! atom type and charge change +ATOM 2H2A HCA1 0.09 ! atom type change +BOND 1C1 1O12 1O12 2C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O12 1C1 1O5 1C5 1.3623 108.15 64.23 113.01 1.4139 +IC 1O5 1C1 1O12 2C2 1.4386 108.15 90.13 116.04 1.4913 ! PHI +IC 1C1 1O12 2C2 2C1 1.3623 116.04 90.33 114.55 1.5295 ! PSI +IC 1H1B 1O5 *1C1 1C2 1.1061 111.88 120.00 112.57 1.5609 +IC 2H2A 2C1 *2C2 1O12 1.1122 119.93 -120.35 114.30 1.0471 +IC 2H2A 2C1 *2C2 2C3 1.1122 109.47 120.64 109.85 1.5102 + +PRES 12bam 0.20 ! og disac model compound 9 C1_equat -> C2_axial +dele atom 1H1B +dele atom 2H2A +ATOM 1C1 CC311D 0.29 ! atom type and charge change +ATOM 1H1A HCA1 0.09 ! atom type change +ATOM 1O12 OC301 -0.36 ! new atom +ATOM 2C2 CC311C 0.09 ! atom type and charge change +ATOM 2H2B HCA1 0.09 ! atom type change +BOND 1C1 1O12 1O12 2C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O12 1C1 1O5 1C5 1.3623 108.15 180.23 113.01 1.4139 +IC 1O5 1C1 1O12 2C2 1.4386 108.15 -60.00 116.04 1.4913 ! PHI +IC 1C1 1O12 2C2 2C1 1.3623 116.04 -60.00 114.55 1.5295 ! PSI +IC 1H1A 1O5 *1C1 1C2 1.1061 111.88 -120.00 112.57 1.5609 +IC 2H2B 2C1 *2C2 1O12 1.1122 119.93 120.35 114.30 1.0471 + +PRES 12bbm 0.20 ! og disac model compound 10 C1_equat -> C2_equat +dele atom 1H1B +dele atom 2H2B +ATOM 1C1 CC311D 0.29 ! atom type and charge change +ATOM 1H1A HCA1 0.09 ! atom type change +ATOM 1O12 OC301 -0.36 ! new atom +ATOM 2C2 CC311C 0.09 ! atom type and charge change +ATOM 2H2A HCA1 0.09 ! atom type change +BOND 1C1 1O12 1O12 2C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O12 1C1 1O5 1C5 1.3623 108.15 180.23 113.01 1.4139 +IC 1O5 1C1 1O12 2C2 1.4386 108.15 -60.00 116.04 1.4913 ! PHI +IC 1C1 1O12 2C2 2C1 1.3623 116.04 150.00 114.55 1.5295 ! PSI +IC 1H1A 1O5 *1C1 1C2 1.1061 111.88 -120.00 112.57 1.5609 +IC 2H2A 2C1 *2C2 1O12 1.1122 119.93 -120.35 114.30 1.0471 +IC 2H2A 2C1 *2C2 2C3 1.1122 109.47 120.64 109.85 1.5102 + +PRES COCA 0.20 ! og make disaccharide model compound 11 by adding +dele atom H5A ! axial -CH2-O-CH3 to C5; apply to THP2 +ATOM C5 CC311C 0.11 ! +ATOM H5B HCA1 0.09 ! +ATOM C6 CC321 0.00 ! +ATOM H61 HCA2 0.09 ! +ATOM H62 HCA2 0.09 ! +ATOM O1P OC301 -0.36 ! +ATOM C1P CC331 -0.09 ! +ATOM H11P HCA3 0.09 ! +ATOM H12P HCA3 0.09 ! +ATOM H13P HCA3 0.09 ! +BOND C5 C6 +BOND C6 H61 C6 H62 C6 O1P +BOND O1P C1P +BOND C1P H11P C1P H12P C1P H13P +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1P O1P C6 C5 1.4194 111.22 179.14 111.34 1.5489 +IC O1P C6 C5 O5 1.4232 111.34 -169.45 110.62 1.4282 +IC C6 C4 *C5 O5 1.5489 113.77 -126.20 111.80 1.4282 +IC C6 O5 *C5 H5B 1.5489 110.62 -115.09 106.68 1.1152 +IC O1P C5 *C6 H61 1.4232 111.34 120.30 108.27 1.1119 +IC H61 C5 *C6 H62 1.1119 108.27 118.30 110.00 1.1087 +IC C6 O1P C1P H11P 1.4232 111.22 60.60 110.47 1.1115 +IC H11P O1P *C1P H12P 1.1115 110.47 119.52 109.62 1.1114 +IC H13P O1P *C1P H12P 1.1116 110.46 -119.50 109.62 1.1114 + +PRES COCB 0.20 ! og make disaccharide model compound 12 by adding +dele atom H5B ! equatorial -CH2-O-CH3 to C5; apply to THP2 +ATOM C5 CC311C 0.11 ! +ATOM H5A HCA1 0.09 ! +ATOM C6 CC321 0.00 ! +ATOM H61 HCA2 0.09 ! +ATOM H62 HCA2 0.09 ! +ATOM O1P OC301 -0.36 ! +ATOM C1P CC331 -0.09 ! +ATOM H11P HCA3 0.09 ! +ATOM H12P HCA3 0.09 ! +ATOM H13P HCA3 0.09 ! +BOND C5 C6 +BOND C6 H61 C6 H62 C6 O1P +BOND O1P C1P +BOND C1P H11P C1P H12P C1P H13P +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1P O1P C6 C5 1.4194 111.22 179.14 111.34 1.5489 +IC O1P C6 C5 O5 1.4232 111.34 -169.45 110.62 1.4282 +IC C6 C4 *C5 O5 1.5489 113.77 126.20 111.80 1.4282 +IC C6 O5 *C5 H5A 1.5489 110.62 -115.09 106.68 1.1152 +IC O1P C5 *C6 H61 1.4232 111.34 120.30 108.27 1.1119 +IC H61 C5 *C6 H62 1.1119 108.27 118.30 110.00 1.1087 +IC C6 O1P C1P H11P 1.4232 111.22 60.60 110.47 1.1115 +IC H11P O1P *C1P H12P 1.1115 110.47 119.52 109.62 1.1114 +IC H13P O1P *C1P H12P 1.1116 110.46 -119.50 109.62 1.1114 + +!RESI DUM 0.0 +!GROUP +!ATOM DUM DUM 0.0 + +!RESI MP_1 -1.00 ! Methylphosphate, anionic +!GROUP ! +! atom order for molvib +!ATOM C1 CTL3 -0.17 ! +!ATOM O1 OSL -0.62 ! H11 +!ATOM P1 PL 1.50 ! | +!ATOM O2 OHL -0.68 ! H13--C1--H12 +!ATOM O3 O2L -0.82 ! | +!ATOM O4 O2L -0.82 ! O1 +!ATOM H11 HAL3 0.09 ! | +!ATOM H12 HAL3 0.09 ! O4==P1==O3 (-) +!ATOM H13 HAL3 0.09 ! | +!ATOM H2 HOL 0.34 ! O2 + ! \ + ! H2 + +!BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +!BOND C1 H11 C1 H12 C1 H13 O2 H2 + +!IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +!IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +!IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +!IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +!IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +!IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +!IC H2 O2 P1 O1 0.0000 000.00 000.0 000.00 0.0000 + +!********************* +!Added by sai for modelling phosphate +!Patch Residue for attaching phosphate +!In this patch we are adding the phosphate at the axial position of C1 +!********************* + +PRES PH_A -1.00 ! The phsophate is added to the axial group +dele atom H1A ! O-PO3H is added to C1; apply to THP2 +GROUP +ATOM C1 CC311D 0.21 ! +ATOM H1B HCA1 0.09 ! Equitorial Hydrogen +ATOM O1 OC30P -0.62 ! All the phosphate atom types have been borrowed from the +ATOM P1 PC 1.50 ! top_all27_lipid.rtf topology file +ATOM O2 OC312 -0.68 ! +ATOM O3 OC2DP -0.82 ! H5A H5B +ATOM O4 OC2DP -0.82 ! \/ +ATOM H2 HCP1 0.34 ! C5-------O5 +ATOM C5 CC321C 0.02 ! H4A / \ H1B +ATOM H5A HCA2 0.09 ! \/ \ / +ATOM H5B HCA2 0.09 ! C4 C1 +ATOM O5 OC3C61 -0.40 ! / \ / \ + ! H4B \ / O1 + ! C3------C2 | + ! /\ /\ O4==P1==O3 (-) + ! H3A H3B H2A H2B | + ! O2 + ! \ + ! H2 +BOND C1 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +!Thermalized IC +IC C5 O5 C1 O1 1.4251 113.39 64.42 111.42 1.4611 +IC O5 O1 *C1 H1B 1.4053 111.42 -123.36 114.66 1.1221 +IC O5 C1 O1 P1 1.4053 111.42 66.60 112.24 1.6183 +IC C1 O1 P1 O2 1.4611 112.24 163.11 83.39 1.5985 +IC O1 O2 *P1 O3 1.6183 83.39 106.51 113.61 1.5067 +IC O1 O2 *P1 O4 1.6183 83.39 -110.58 108.15 1.5473 +IC O1 P1 O2 H2 1.6183 83.39 29.06 99.90 0.9669 + +!********************* +!Patch Residue for attaching phosphate +!In this patch we are adding the phosphate at the equitorial position of C1 +!********************* + +PRES PH_B -1.00 ! The phsophate is added to the equitorial group +dele atom H1B ! O-PO3H is added to C1; apply to THP2 +GROUP +ATOM C1 CC311D 0.21 ! +ATOM H1A HCA1 0.09 ! Axial Hydrogen +ATOM O1 OC30P -0.62 ! All the phosphate atom types have been borrowed from the +ATOM P1 PC 1.50 ! top_all27_lipid.rtf topology file +ATOM O2 OC312 -0.68 ! +ATOM O3 OC2DP -0.82 ! H2 +ATOM O4 OC2DP -0.82 ! / +ATOM H2 HCP1 0.34 ! O2 +ATOM C5 CC321C 0.02 ! H5A H5B | +ATOM H5A HCA2 0.09 ! \/ O3=P1=O4(-) +ATOM H5B HCA2 0.09 ! C5-------O5 | +ATOM O5 OC3C61 -0.40 ! H4A / \ O1 + ! \/ \ / + ! C4 C1 + ! / \ / \ + ! H4B \ / H1A + ! C3------C2 + ! /\ /\ + ! H3A H3B H2A H2B +BOND C1 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +!Thermalized IC +IC C5 O5 C1 O1 1.4283 117.17 172.83 114.29 1.4190 +IC O5 O1 *C1 H1A 1.3757 114.29 111.68 100.52 1.1176 +IC O5 C1 O1 P1 1.3757 114.29 83.65 117.50 1.6236 +IC C1 O1 P1 O2 1.4190 117.50 -157.34 82.18 1.5598 +IC O1 O2 *P1 O3 1.6236 82.18 102.65 111.48 1.5066 +IC O1 O2 *P1 O4 1.6236 82.18 -112.23 110.54 1.5464 +IC O1 P1 O2 H2 1.6236 82.18 7.21 102.26 0.9628 + +!************************ +!dianionic methylphosphate +!************************ +!RESI MP_2 -2.00 ! Methylphosphate, dianionic +!GROUP ! +!ATOM P1 PL 1.10 ! +!ATOM O1 OSL -0.40 ! H11 +!ATOM O2 O2L -0.90 ! | +!ATOM O3 O2L -0.90 ! H13--C1--H12 +!ATOM O4 O2L -0.90 ! | +!GROUP ! O1 +!ATOM C1 CTL3 -0.27 ! | +!ATOM H11 HAL3 0.09 ! (-) O4--P1(+)--O3 (-) +!ATOM H12 HAL3 0.09 ! | +!ATOM H13 HAL3 0.09 ! O2 (-) +! ! +!BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +!BOND C1 H11 C1 H12 C1 H13 +! +!IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +!IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +!IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +!IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +!IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +!IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +! dummy to analyze cetain angles +!IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 + +!********************* +!Patch Residue for attaching dianionic phosphate +!In this patch we are adding the phosphate at the axial position of C1 +!********************* + +PRES DPH_A -2.00 ! The phsophate is added to the axial group +dele atom H1A ! O-PO3 is added to C1; apply to THP2 +GROUP +ATOM C1 CC311D 0.11 ! +ATOM H1B HCA1 0.09 ! Equitorial Hydrogen +ATOM O1 OC30P -0.40 ! All the phosphate atom types have been borrowed from the +ATOM P1 PC 1.10 ! top_all27_lipid.rtf topology file +ATOM O2 OC2DP -0.90 ! +ATOM O3 OC2DP -0.90 ! H5A H5B +ATOM O4 OC2DP -0.90 ! \/ +ATOM C5 CC321C 0.02 ! C5-------O5 +ATOM H5A HCA2 0.09 ! H4A / \ H1B +ATOM H5B HCA2 0.09 ! \/ \ / +ATOM O5 OC3C61 -0.40 ! C4 C1 + ! / \ / \ + ! H4B \ / O1 + ! C3------C2 (-) | + ! /\ /\ O4--P1--O3 (-) + ! H3A H3B H2A H2B | + ! O2 (-) +! ! +BOND C1 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 + +!Thermalized IC +IC C5 O5 C1 O1 1.4560 110.91 68.94 115.15 1.3655 +IC O5 O1 *C1 H1B 1.4599 115.15 -120.56 109.91 1.1324 +IC O5 C1 O1 P1 1.4599 115.15 97.33 121.23 1.6405 +IC C1 O1 P1 O2 1.3655 121.23 153.36 102.74 1.5058 +IC O1 O2 *P1 O3 1.6405 102.74 111.69 114.50 1.5585 +IC O1 O2 *P1 O4 1.6405 102.74 -111.64 112.24 1.5030 + +!********************* +!Patch Residue for attaching dianionic phosphate +!In this patch we are adding the phosphate at the equitorial position of C1 +!********************* + +PRES DPH_B -2.00 ! The phsophate is added to the equitorial group +dele atom H1B ! O-PO3 is added to C1; apply to THP2 +GROUP +ATOM C1 CC311D 0.11 ! +ATOM H1A HCA1 0.09 ! axial Hydrogen +ATOM O1 OC30P -0.40 ! All the phosphate atom types have been borrowed from the +ATOM P1 PC 1.10 ! top_all27_lipid.rtf topology file +ATOM O2 OC2DP -0.90 ! +ATOM O3 OC2DP -0.90 ! O2(-) +ATOM O4 OC2DP -0.90 ! H5A H5B (-) | +ATOM C5 CC321C 0.02 ! \/ O3-P1-O4(-) +ATOM H5A HCA2 0.09 ! C5-------O5 | +ATOM H5B HCA2 0.09 ! H4A / \ O1 +ATOM O5 OC3C61 -0.40 ! \/ \ / + ! C4 C1 + ! / \ / \ + ! H4B \ / H1A + ! C3------C2 + ! /\ /\ + ! H3A H3B H2A H2B + ! +BOND C1 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 + +!Thermalized IC +IC C5 O5 C1 O1 1.4281 112.18 172.29 110.68 1.4066 +IC O5 O1 *C1 H1A 1.4357 110.68 109.11 99.38 1.1519 +IC O5 C1 O1 P1 1.4357 110.68 108.53 128.86 1.6405 +IC C1 O1 P1 O2 1.4066 128.86 -173.99 99.00 1.5251 +IC O1 O2 *P1 O3 1.6405 99.00 110.81 112.21 1.5323 +IC O1 O2 *P1 O4 1.6405 99.00 -112.66 112.82 1.5482 + +!********************* +! Adding the phosphates to cyclohexane, the phosphates are added +! to the C2 carbon and not to the C1 carbon as in the case of THP. +! In this patch phosphate is added to the axial position. +!********************* + +PRES CHPHA -1.00 ! The phsophate is added to the axial group +dele atom H2A ! O-PO3H is added to C2; apply to CYHX2 +GROUP +ATOM C2 CC311D 0.01 ! +ATOM H2B HCA1 0.09 ! Equitorial Hydrogen +ATOM O1 OC30P -0.62 ! All the phosphate atom types have been borrowed from the +ATOM P1 PC 1.50 ! top_all27_lipid.rtf topology file +ATOM O2 OC312 -0.68 ! +ATOM O3 OC2DP -0.82 ! H5A H5B H5OA H5OB | H5A H5B +ATOM O4 OC2DP -0.82 ! \ / \/ | \/ +ATOM H2 HCP1 0.34 ! C5-------C5O | C5-------O5 + ! H4A / \ H1B | H4A / \ H1B + ! \/ \ / | \/ \ / + ! C4 C1 | C4 C1 + ! / \ / \ | / \ / \ + ! H4B \ / H1A | H4B \ / O1 + ! C3------C2 | C3------C2 | + ! /\ /\ | /\ /\ O4==P1==O3 (-) + ! H3A H3B O1 H2B | H3A H3B H2A H2B | + ! | | O2 + ! O4==P1==O3(-) | \ + ! | | H2 + ! O2 + ! \ + ! H2 +BOND C2 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +!Thermalized IC +IC C5O C1 C2 O1 1.5416 112.35 -78.20 109.11 1.3987 +IC C1 O1 *C2 H2B 1.5568 109.11 120.34 110.30 1.1057 +IC C1 C2 O1 P1 1.5568 109.11 -87.89 118.45 1.6239 +IC C2 O1 P1 O2 1.3987 118.45 -176.89 90.38 1.5567 +IC O1 O2 *P1 O3 1.6239 90.38 114.28 105.52 1.5304 +IC O1 O2 *P1 O4 1.6239 90.38 -111.43 110.08 1.5252 +IC O1 P1 O2 H2 1.6239 90.38 27.23 100.22 0.9790 + +!********************* +! Adding the phosphates to cyclohexane, the phosphates are added +! to the C2 carbon and not to the C1 carbon as in the case of THP. +! In this patch phosphate is added to the equitorial position. +!********************* + +PRES CHPHB -1.00 ! The phsophate is added to the equitorial group +dele atom H2B ! O-PO3H is added to C2; apply to CYHX2 +GROUP +ATOM C2 CC311D 0.01 ! +ATOM H2A HCA1 0.09 ! axial Hydrogen +ATOM O1 OC30P -0.62 ! All the phosphate atom types have been borrowed from the +ATOM P1 PC 1.50 ! top_all27_lipid.rtf topology file +ATOM O2 OC312 -0.68 ! +ATOM O3 OC2DP -0.82 ! H5A H5B H5OA H5OB +ATOM O4 OC2DP -0.82 ! \ / \/ +ATOM H2 HCP1 0.34 ! C5-------C5O + ! H4A / \ H1B + ! \/ \ / + ! C4 C1 + ! / \ / \ + ! H4B \ / H1A + ! C3------C2 + ! /\ /\ + ! H3A H3B H1A O1 + ! | + ! O4==P1==O3(-) + ! | + ! O2 + ! \ + ! H2 +BOND C2 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +!Thermalized IC +IC C5O C1 C2 O1 1.5681 108.70 -177.62 105.41 1.4032 +IC C1 O1 *C2 H2A 1.5490 105.41 -116.28 107.56 1.1543 +IC C1 C2 O1 P1 1.5490 105.41 -70.04 127.83 1.6634 +IC C2 O1 P1 O2 1.4032 127.83 175.35 92.04 1.5992 +IC O1 O2 *P1 O3 1.6634 92.04 108.70 112.55 1.5284 +IC O1 O2 *P1 O4 1.6634 92.04 -108.48 113.68 1.5672 +IC O1 P1 O2 H2 1.6634 92.04 17.38 110.00 0.9486 + +!********************* +! dianionic phosphate patch to cyclohexane, the phosphates are added +! to the C2 carbon and not to the C1 carbon as in the case of THP. +! In this patch the phosphate group is added to the axial position. +!********************* + +PRES CHDPA -2.00 ! The phsophate is added to the axial group +dele atom H2A ! O-PO3 is added to C2; apply to CYHX2 +GROUP +ATOM C2 CC311D -0.09 ! +ATOM H2B HCA1 0.09 ! Equitorial Hydrogen +ATOM O1 OC30P -0.40 ! All the phosphate atom types have been borrowed from the +ATOM P1 PC 1.10 ! top_all27_lipid.rtf topology file +ATOM O2 OC2DP -0.90 ! +ATOM O3 OC2DP -0.90 ! H5A H5B H5OA H5OB | H5A H5B +ATOM O4 OC2DP -0.90 ! \ / \/ | \/ + ! C5-------C5O | C5-------O5 + ! H4A / \ H1B | H4A / \ H1B + ! \/ \ / | \/ \ / + ! C4 C1 | C4 C1 + ! / \ / \ | / \ / \ + ! H4B \ / H1A | H4B \ / O1 + ! C3------C2 | C3------C2 (-) | + ! /\ /\ | /\ /\ O4--P1--O3 (-) + ! H3A H3B O1 H2B | H3A H3B H2A H2B | + ! | | O2(-) + ! (-)O4--P1--O3(-) | + ! | | + ! O2(-) + ! +BOND C2 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 + +!Thermalized IC +IC C5O C1 C2 O1 1.5498 116.69 -69.52 108.10 1.3887 +IC C1 O1 *C2 H2B 1.5506 108.10 116.34 109.76 1.0909 +IC C1 C2 O1 P1 1.5506 108.10 -111.50 122.41 1.6642 +IC C2 O1 P1 O2 1.3887 122.41 -172.81 106.99 1.5327 +IC O1 O2 *P1 O3 1.6642 106.99 114.35 116.44 1.5605 +IC O1 O2 *P1 O4 1.6642 106.99 -115.54 112.29 1.5247 + +!********************* +! dianionic phosphate patch to cyclohexane, the phosphates are added +! to the C2 carbon and not to the C1 carbon as in the case of THP. +! In this patch the phosphate group is added to the equitorial position. +!********************* + +PRES CHDPB -2.00 ! The phsophate is added to the equitorial group +dele atom H2B ! O-PO3 is added to C2; apply to CYHX2 +GROUP +ATOM C2 CC311D -0.09 ! +ATOM H2A HCA1 0.09 ! axial Hydrogen +ATOM O1 OC30P -0.40 ! All the phosphate atom types have been borrowed from the +ATOM P1 PC 1.10 ! top_all27_lipid.rtf topology file +ATOM O2 OC2DP -0.90 ! +ATOM O3 OC2DP -0.90 ! H5A H5B H5OA H5OB +ATOM O4 OC2DP -0.90 ! \ / \/ + ! C5-------C5O + ! H4A / \ H1B + ! \/ \ / + ! C4 C1 + ! / \ / \ + ! H4B \ / H1A + ! C3------C2 + ! /\ /\ + ! H3A H3B H1A O1 + ! | + ! (-)O4--P1--O3(-) + ! | + ! O2(-) + ! + ! +BOND C2 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 + +!Thermalized IC +IC C5O C1 C2 O1 1.5364 112.47 -174.92 109.44 1.4102 +IC C1 O1 *C2 H2A 1.5323 109.44 -120.96 109.46 1.1223 +IC C1 C2 O1 P1 1.5323 109.44 -84.54 127.66 1.5968 +IC C2 O1 P1 O2 1.4102 127.66 -174.21 102.94 1.5071 +IC O1 O2 *P1 O3 1.5968 102.94 113.03 118.81 1.5471 +IC O1 O2 *P1 O4 1.5968 102.94 -113.60 109.37 1.4811 + +!****************** +! Di phosphates +!****************** + +PRES P2HAA -2.00 ! +dele atom H1A +dele atom H2A +GROUP +ATOM C1 CC311D 0.21 ! +ATOM H1B HCA1 0.09 ! +ATOM O1 OC30P -0.62 ! +ATOM P1 PC 1.50 ! +ATOM O2 OC312 -0.68 ! +ATOM O3 OC2DP -0.82 ! H5A H5B +ATOM O4 OC2DP -0.82 ! \/ +ATOM H2 HCP1 0.34 ! C5-------O5 +ATOM C5 CC321C 0.02 ! H4A / \ H1B +ATOM H5A HCA2 0.09 ! \/ \ / +ATOM H5B HCA2 0.09 ! C4 C1 +ATOM O5 OC3C61 -0.40 ! / \ / \ + ! H4B \ / O1 + ! C3------C2 | +GROUP ! /\ /\ O4==P1==O3(-) +ATOM C2 CC311D 0.01 ! H3A H3B O1A H2B | +ATOM H2B HCA1 0.09 ! | O2 +ATOM O1A OC30P -0.62 ! O4A==P2==O3A(-) \ +ATOM P2 PC 1.50 ! | H2 +ATOM O2A OC312 -0.68 ! O2A +ATOM O3A OC2DP -0.82 ! \ +ATOM O4A OC2DP -0.82 ! H3 +ATOM H3 HCP1 0.34 ! + +BOND C1 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +BOND C2 O1A +BOND O1A P2 O2A P2 O3A P2 O4A P2 +BOND O2A H3 + +!Thermalized IC +IC C5 O5 C1 O1 1.4282 115.23 62.90 110.07 1.4195 +IC O5 O1 *C1 H1B 1.4271 110.07 -115.42 105.97 1.1319 +IC O5 C1 O1 P1 1.4271 110.07 57.27 117.04 1.6373 +IC C1 O1 P1 O2 1.4195 117.04 -178.66 78.79 1.5370 +IC O1 O2 *P1 O3 1.6373 78.79 107.09 112.80 1.5582 +IC O1 O2 *P1 O4 1.6373 78.79 -112.88 107.93 1.5166 +IC O1 P1 O2 H2 1.6373 78.79 -0.06 97.73 0.9887 +IC O1 C1 C2 O1A 1.4195 101.59 172.29 107.09 1.4581 +IC C1 O1A *C2 H2B 1.5620 107.09 124.33 116.74 1.1261 +IC C1 C2 O1A P2 1.5620 107.09 -114.48 111.86 1.6490 +IC C2 O1A P2 O2A 1.4581 111.86 -142.10 76.47 1.6332 +IC O1A O2A *P2 O3A 1.6490 76.47 110.49 112.74 1.5305 +IC O1A O2A *P2 O4A 1.6490 76.47 -113.06 108.88 1.4937 +IC O1A P2 O2A H3 1.6490 76.47 17.07 99.28 0.9665 + +!********************* + +PRES P2HAB -2.00 ! +dele atom H1A +dele atom H2B +GROUP +ATOM C1 CC311D 0.21 ! +ATOM H1B HCA1 0.09 ! +ATOM O1 OC30P -0.62 ! +ATOM P1 PC 1.50 ! +ATOM O2 OC312 -0.68 ! +ATOM O3 OC2DP -0.82 ! H5A H5B +ATOM O4 OC2DP -0.82 ! \/ +ATOM H2 HCP1 0.34 ! C5-------O5 +ATOM C5 CC321C 0.02 ! H4A / \ H1B +ATOM H5A HCA2 0.09 ! \/ \ / +ATOM H5B HCA2 0.09 ! C4 C1 +ATOM O5 OC3C61 -0.40 ! / \ / \ + ! H4B \ / O1 + ! C3------C2 | +GROUP ! /\ /\ O4==P1==O3(-) +ATOM C2 CC311D 0.01 ! H3A H3B O1A H2A | +ATOM H2A HCA1 0.09 ! | O2 +ATOM O1A OC30P -0.62 ! O4A==P1==O3A(-) \ +ATOM P2 PC 1.50 ! | H2 +ATOM O2A OC312 -0.68 ! O2A +ATOM O3A OC2DP -0.82 ! \ +ATOM O4A OC2DP -0.82 ! H3 +ATOM H3 HCP1 0.34 ! + +BOND C1 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +BOND C2 O1A +BOND O1A P2 O2A P2 O3A P2 O4A P2 +BOND O2A H3 + +!Thermalized IC +IC C5 O5 C1 O1 1.4123 111.30 56.44 112.83 1.3833 +IC O5 O1 *C1 H1B 1.4305 112.83 -116.12 106.77 1.1639 +IC O5 C1 O1 P1 1.4305 112.83 61.75 112.64 1.6157 +IC C1 O1 P1 O2 1.3833 112.64 162.73 78.67 1.6270 +IC O1 O2 *P1 O3 1.6157 78.67 110.11 111.56 1.5434 +IC O1 O2 *P1 O4 1.6157 78.67 -108.49 113.38 1.5158 +IC O1 P1 O2 H2 1.6157 78.67 -4.63 95.96 0.9275 +IC O1 C1 C2 O1A 1.3833 113.03 49.13 119.38 1.4302 +IC C1 O1A *C2 H2A 1.6104 119.38 -127.92 116.43 1.1748 +IC C1 C2 O1A P2 1.6104 119.38 109.82 118.84 1.6437 +IC C2 O1A P2 O2A 1.4302 118.84 151.65 79.32 1.6151 +IC O1A O2A *P2 O3A 1.6437 79.32 111.04 111.60 1.5482 +IC O1A O2A *P2 O4A 1.6437 79.32 -110.83 111.70 1.5064 +IC O1A P2 O2A H3 1.6437 79.32 0.86 99.84 0.9402 + +!********************* + +PRES P2HBB -2.00 ! +dele atom H1B +dele atom H2B +GROUP +ATOM C1 CC311D 0.21 ! +ATOM H1A HCA1 0.09 ! +ATOM O1 OC30P -0.62 ! +ATOM P1 PC 1.50 ! +ATOM O2 OC312 -0.68 ! +ATOM O3 OC2DP -0.82 ! H5A H5B +ATOM O4 OC2DP -0.82 ! \/ +ATOM H2 HCP1 0.34 ! C5-------O5 +ATOM C5 CC321C 0.02 ! H4A / \ H1A +ATOM H5A HCA2 0.09 ! \/ \ / +ATOM H5B HCA2 0.09 ! C4 C1 +ATOM O5 OC3C61 -0.40 ! / \ / \ + ! H4B \ / O1 + ! C3------C2 | +GROUP ! /\ /\ O4==P1==O3(-) +ATOM C2 CC311D 0.01 ! H3A H3B O1A H2A | +ATOM H2A HCA1 0.09 ! | O2 +ATOM O1A OC30P -0.62 ! O4A==P1==O3A(-) \ +ATOM P2 PC 1.50 ! | H2 +ATOM O2A OC312 -0.68 ! O2A +ATOM O3A OC2DP -0.82 ! \ +ATOM O4A OC2DP -0.82 ! H3 +ATOM H3 HCP1 0.34 ! + +BOND C1 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +BOND C2 O1A +BOND O1A P2 O2A P2 O3A P2 O4A P2 +BOND O2A H3 + +!Thermalized IC +IC C5 O5 C1 O1 1.4437 115.80 167.55 107.74 1.4184 +IC O5 O1 *C1 H1A 1.4723 107.74 112.27 106.11 1.1493 +IC O5 C1 O1 P1 1.4723 107.74 84.92 113.86 1.6128 +IC C1 O1 P1 O2 1.4184 113.86 90.78 91.30 1.6764 +IC O1 O2 *P1 O3 1.6128 91.30 119.13 112.41 1.5141 +IC O1 O2 *P1 O4 1.6128 91.30 -113.34 110.46 1.5144 +IC O1 P1 O2 H2 1.6128 91.30 -35.67 106.61 0.9464 +IC O1 C1 C2 O1A 1.4184 120.73 -57.27 109.92 1.3939 +IC C1 O1A *C2 H2A 1.5553 109.92 -113.45 111.07 1.1407 +IC C1 C2 O1A P2 1.5553 109.92 174.68 128.19 1.6454 +IC C2 O1A P2 O2A 1.3939 128.19 110.92 88.39 1.6055 +IC O1A O2A *P2 O3A 1.6454 88.39 110.02 113.52 1.5245 +IC O1A O2A *P2 O4A 1.6454 88.39 -113.23 111.25 1.5397 +IC O1A P2 O2A H3 1.6454 88.39 7.99 106.81 0.9527 + +!********************* + +PRES P2HBA -2.00 ! +dele atom H1B +dele atom H2A +GROUP +ATOM C1 CC311D 0.21 ! +ATOM H1A HCA1 0.09 ! +ATOM O1 OC30P -0.62 ! +ATOM P1 PC 1.50 ! +ATOM O2 OC312 -0.68 ! +ATOM O3 OC2DP -0.82 ! H5A H5B +ATOM O4 OC2DP -0.82 ! \/ +ATOM H2 HCP1 0.34 ! C5-------O5 +ATOM C5 CC321C 0.02 ! H4A / \ H1A +ATOM H5A HCA2 0.09 ! \/ \ / +ATOM H5B HCA2 0.09 ! C4 C1 +ATOM O5 OC3C61 -0.40 ! / \ / \ + ! H4B \ / O1 + ! C3------C2 | +GROUP ! /\ /\ O4==P1==O3(-) +ATOM C2 CC311D 0.01 ! H3A H3B O1A H2B | +ATOM H2B HCA1 0.09 ! | O2 +ATOM O1A OC30P -0.62 ! O4A==P1==O3A(-) \ +ATOM P2 PC 1.50 ! | H2 +ATOM O2A OC312 -0.68 ! O2A +ATOM O3A OC2DP -0.82 ! \ +ATOM O4A OC2DP -0.82 ! H3 +ATOM H3 HCP1 0.34 ! + +BOND C1 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +BOND C2 O1A +BOND O1A P2 O2A P2 O3A P2 O4A P2 +BOND O2A H3 + +!Thermalized IC +IC C5 O5 C1 O1 1.4168 109.99 160.88 110.83 1.4214 +IC O5 O1 *C1 H1A 1.4275 110.83 120.32 109.13 1.1208 +IC O5 C1 O1 P1 1.4275 110.83 -69.97 115.66 1.6410 +IC C1 O1 P1 O2 1.4214 115.66 80.54 91.08 1.5848 +IC O1 O2 *P1 O3 1.6410 91.08 112.26 110.34 1.5219 +IC O1 O2 *P1 O4 1.6410 91.08 -113.80 111.08 1.5199 +IC O1 P1 O2 H2 1.6410 91.08 -28.53 102.00 0.9730 +IC O1 C1 C2 O1A 1.4214 115.12 64.86 115.16 1.4317 +IC C1 O1A *C2 H2B 1.5832 115.16 119.48 109.95 1.1155 +IC C1 C2 O1A P2 1.5832 115.16 -168.70 120.38 1.6420 +IC C2 O1A P2 O2A 1.4317 120.38 -108.17 82.18 1.5834 +IC O1A O2A *P2 O3A 1.6420 82.18 111.54 110.62 1.5188 +IC O1A O2A *P2 O4A 1.6420 82.18 -111.53 111.20 1.5212 +IC O1A P2 O2A H3 1.6420 82.18 -3.46 99.00 0.9711 + +!********************* + +PRES PH2A -1.00 ! +dele atom H2A ! H5A H5B +GROUP ! \/ +ATOM C2 CC311D 0.01 ! C5-------O5 +ATOM H2B HCA1 0.09 ! H4A / \ H1B +ATOM O1 OC30P -0.62 ! \/ \ / +ATOM P1 PC 1.50 ! C4 C1 +ATOM O2 OC312 -0.68 ! / \ / \ +ATOM O3 OC2DP -0.82 ! H4B \ / H1A +ATOM O4 OC2DP -0.82 ! C3------C2 +ATOM H2 HCP1 0.34 ! /\ /\ + ! H3A H3B O1 H2B + ! | + ! O4==P1==O3(-) + ! | + ! O2 + ! \ + ! H2 + ! + +BOND C2 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +!Thermalized IC +IC O5 C1 C2 O1 1.4466 115.81 -68.25 112.45 1.4565 +IC C1 O1 *C2 H2B 1.5413 112.45 122.90 110.29 1.0934 +IC C1 C2 O1 P1 1.5413 112.45 -88.90 115.31 1.6176 +IC C2 O1 P1 O2 1.4565 115.31 140.43 87.18 1.6056 +IC O1 O2 *P1 O3 1.6176 87.18 111.89 108.49 1.5075 +IC O1 O2 *P1 O4 1.6176 87.18 -110.46 116.26 1.5340 +IC O1 P1 O2 H2 1.6176 87.18 -27.94 107.23 0.9329 + +!********************* + +PRES PH2B -1.00 ! +dele atom H2B ! H5A H5B +GROUP ! \/ +ATOM C2 CC311D 0.01 ! C5-------O5 +ATOM H2A HCA1 0.09 ! H4A / \ H1B +ATOM O1 OC30P -0.62 ! \/ \ / +ATOM P1 PC 1.50 ! C4 C1 +ATOM O2 OC312 -0.68 ! / \ / \ +ATOM O3 OC2DP -0.82 ! H4B \ / H1A +ATOM O4 OC2DP -0.82 ! C3------C2 +ATOM H2 HCP1 0.34 ! /\ /\ + ! H3A H3B O1 H2B + ! | + ! O4==P1==O3(-) + ! | + ! O2 + ! \ + ! H2 + ! + +BOND C2 O1 +BOND O1 P1 O2 P1 O3 P1 O4 P1 +BOND O2 H2 + +!Thermalized IC +IC O5 C1 C2 O1 1.4069 113.21 -179.48 115.05 1.4246 +IC C1 O1 *C2 H2A 1.5523 115.05 -112.84 107.69 1.1244 +IC C1 C2 O1 P1 1.5523 115.05 -60.42 126.59 1.5831 +IC C2 O1 P1 O2 1.4246 126.59 178.54 87.53 1.5648 +IC O1 O2 *P1 O3 1.5831 87.53 109.66 112.66 1.5278 +IC O1 O2 *P1 O4 1.5831 87.53 -111.18 109.18 1.5039 +IC O1 P1 O2 H2 1.5831 87.53 2.03 102.84 0.9870 + +!********************* +!Added by sai for modelling sulfate +!Patch Residue for attaching sulfate +!In this patch we are adding the sulfate at the axial position of C1 +!********************* + +PRES SH_A -1.00 ! +dele atom H1A ! +GROUP +ATOM C1 CC311D 0.01 ! +ATOM H1B HCA1 0.09 ! +ATOM O1 OC30P -0.28 ! +ATOM S1 SC 1.33 ! +ATOM O2 OC2DP -0.65 ! +ATOM O3 OC2DP -0.65 ! H5A H5B +ATOM O4 OC2DP -0.65 ! \/ + ! C5-------O5 +ATOM C5 CC321C 0.02 ! H4A / \ H1B +ATOM H5A HCA2 0.09 ! \/ \ / +ATOM H5B HCA2 0.09 ! C4 C1 +ATOM O5 OC3C61 -0.40 ! / \ / \ + ! H4B \ / O1 + ! C3------C2 (-) |(+2) + ! /\ /\ O4--S1--O3 (-) + ! H3A H3B H2A H2B | + ! O2 (-) +! ! +BOND C1 O1 +BOND O1 S1 O2 S1 O3 S1 O4 S1 + +!Thermalized IC +IC C5 O5 C1 O1 1.4310 116.99 78.97 115.55 1.3813 +IC O5 O1 *C1 H1B 1.4311 115.55 -119.64 114.20 1.1304 +IC O5 C1 O1 S1 1.4311 115.55 79.86 115.54 1.5969 +IC C1 O1 S1 O2 1.3813 115.54 168.67 102.54 1.4562 +IC O1 O2 *S1 O3 1.5969 102.54 118.16 113.46 1.5020 +IC O1 O2 *S1 O4 1.5969 102.54 -110.63 108.22 1.4480 + +!********************* +!Patch Residue for attaching sulfate +!In this patch we are adding the sulfate at the axial position of C1 +!********************* + +PRES SH_B -1.00 ! +dele atom H1B ! +GROUP +ATOM C1 CC311D 0.01 ! +ATOM H1A HCA1 0.09 ! +ATOM O1 OC30P -0.28 ! +ATOM S1 SC 1.33 ! +ATOM O2 OC2DP -0.65 ! +ATOM O3 OC2DP -0.65 ! O2(-) +ATOM O4 OC2DP -0.65 ! | + ! H5A H5B (-) |(+2) +ATOM C5 CC321C 0.02 ! \/ O3-S1-O4(-) +ATOM H5A HCA2 0.09 ! C5-------O5 | +ATOM H5B HCA2 0.09 ! H4A / \ O1 +ATOM O5 OC3C61 -0.40 ! \/ \ / + ! C4 C1 + ! / \ / \ + ! H4B \ / H1A + ! C3------C2 + ! /\ /\ +! ! H3A H3B H2A H2B +BOND C1 O1 +BOND O1 S1 O2 S1 O3 S1 O4 S1 + +!Thermalized IC +IC C5 O5 C1 O1 1.4406 109.78 152.17 115.69 1.4053 +IC O5 O1 *C1 H1A 1.4332 115.69 102.69 93.50 1.1611 +IC O5 C1 O1 S1 1.4332 115.69 88.20 109.04 1.6159 +IC C1 O1 S1 O2 1.4053 109.04 -158.88 104.33 1.4389 +IC O1 O2 *S1 O3 1.6159 104.33 108.64 112.19 1.4409 +IC O1 O2 *S1 O4 1.6159 104.33 -120.67 114.72 1.4475 + +!********************* +! Sulfate patch to cyclohexane, the sulfate is added to the +! C2 carbon and not to the C1 carbon as in the case of THP2. +!********************* + +PRES CHSHA -1.00 ! +dele atom H2A ! +GROUP +ATOM C2 CC311D -0.19 ! +ATOM H2B HCA1 0.09 ! Equitorial Hydrogen +ATOM O1 OC30P -0.28 ! +ATOM S1 SC 1.33 ! +ATOM O2 OC2DP -0.65 ! +ATOM O3 OC2DP -0.65 ! H5A H5B H5OA H5OB | H5A H5B +ATOM O4 OC2DP -0.65 ! \ / \/ | \/ + ! C5-------C5O | C5-------O5 + ! H4A / \ H1B | H4A / \ H1B + ! \/ \ / | \/ \ / + ! C4 C1 | C4 C1 + ! / \ / \ | / \ / \ + ! H4B \ / H1A | H4B \ / O1 + ! C3------C2 | C3------C2 (-) |(+2) + ! /\ /\ | /\ /\ O4--S1--O3 (-) + ! H3A H3B O1 H2B | H3A H3B H2A H2B | + ! |(+2) | O2(-) + ! (-)O4--S1--O3(-) | + ! | | + ! O2(-) + ! +BOND C2 O1 +BOND O1 S1 O2 S1 O3 S1 O4 S1 + +!Thermalized IC +IC C5O C1 C2 O1 1.5440 109.55 -61.18 109.61 1.3756 +IC C1 O1 *C2 H2B 1.5823 109.61 119.48 110.25 1.0740 +IC C1 C2 O1 S1 1.5823 109.61 -108.10 124.06 1.5412 +IC C2 O1 S1 O2 1.3756 124.06 -170.79 110.18 1.4689 +IC O1 O2 *S1 O3 1.5412 110.18 115.90 110.99 1.4191 +IC O1 O2 *S1 O4 1.5412 110.18 -113.88 109.72 1.4534 + + +!********************* +! sulfate group is added to the equitorial position. +!********************* + +PRES CHSHB -1.00 ! +dele atom H2B ! +GROUP +ATOM C2 CC311D -0.19 ! +ATOM H2A HCA1 0.09 ! +ATOM O1 OC30P -0.28 ! +ATOM S1 SC 1.33 ! +ATOM O2 OC2DP -0.65 ! +ATOM O3 OC2DP -0.65 ! H5A H5B H5OA H5OB +ATOM O4 OC2DP -0.65 ! \ / \/ + ! C5-------C5O + ! H4A / \ H1B + ! \/ \ / + ! C4 C1 + ! / \ / \ + ! H4B \ / H1A + ! C3------C2 + ! /\ /\ + ! H3A H3B H1A O1 + ! |(+2) + ! (-)O4--S1--O3(-) + ! | + ! O2(-) + ! + ! +BOND C2 O1 +BOND O1 S1 O2 S1 O3 S1 O4 S1 + +!Thermalized IC +IC C5O C1 C2 O1 1.5681 109.22 -168.30 110.37 1.4193 +IC C1 O1 *C2 H2A 1.5679 110.37 -118.19 108.04 1.1500 +IC C1 C2 O1 S1 1.5679 110.37 -79.13 125.57 1.5912 +IC C2 O1 S1 O2 1.4193 125.57 -173.80 98.45 1.4760 +IC O1 O2 *S1 O3 1.5912 98.45 104.93 115.42 1.4071 +IC O1 O2 *S1 O4 1.5912 98.45 -109.45 116.89 1.4224 + +!********************* + +PRES SHOM -0.80 ! The sulfate is added to C6 +dele atom H5B ! OS2 + ! | +GROUP ! OS3-S1-OS4 +ATOM C5 CC311C 0.110 ! | +ATOM H5A HCA1 0.09 ! OS1 +ATOM C6 CC321 -0.28 ! | +ATOM H61 HCA2 0.090 ! H61-C6-H62 +ATOM H62 HCA2 0.090 ! | +ATOM OS1 OC30P -0.28 ! H5A-C5------O5 +ATOM S1 SC 1.33 ! H4A / \ H1B +ATOM OS2 OC2DP -0.65 ! \ / \ / +ATOM OS3 OC2DP -0.65 ! C4 C1 +ATOM OS4 OC2DP -0.65 ! / \ / \ + ! H4B \ / H1A + ! C3------C2 + ! /\ /\ + ! H3A H3B H2A H2B + ! + ! +BOND C5 C6 +BOND C6 H61 C6 H62 +BOND C6 OS1 +BOND OS1 S1 OS2 S1 OS3 S1 OS4 S1 + +!Thermalized IC +IC C2 C3 C4 C5 1.4900 110.86 51.81 111.20 1.5199 +IC C6 O5 *C5 H5A 1.5514 109.15 114.44 106.87 1.0951 +IC C6 C4 *C5 O5 1.5514 112.49 124.74 113.74 1.4277 +IC OS1 H62 *C6 H61 1.4265 113.86 112.96 109.28 1.1586 +IC OS1 C5 *C6 H62 1.4265 112.10 127.71 109.94 1.0972 +IC C4 C5 C6 OS1 1.5199 112.49 52.86 112.10 1.4265 +IC C5 OS1 *C6 H61 1.5514 112.10 116.99 101.72 1.1586 +IC C5 OS1 *C6 H62 1.5514 112.10 -125.59 113.86 1.0972 +IC C5 C6 OS1 S1 1.5514 112.10 -179.74 111.93 1.6431 +IC C6 OS1 S1 OS2 1.4265 111.93 172.41 104.68 1.4202 +IC OS1 OS2 *S1 OS3 1.6431 104.68 116.86 113.70 1.4534 +IC OS1 OS2 *S1 OS4 1.6431 104.68 -110.72 111.01 1.4884 + + +PRES POEA 0.20 ! pram, make model compound 1-ethoxy-THP by adding axial +dele atom H1A ! O-ethyl to C1; apply to THP2 +GROUP +ATOM C1 CC311D 0.29 ! +ATOM H1B HCA1 0.09 ! +ATOM OE OC301 -0.36 ! +ATOM C6 CC321 0.00 ! +ATOM H61 HCA2 0.09 ! +ATOM H62 HCA2 0.09 ! +ATOM C7 CC331 -0.27 ! +ATOM H71 HCA3 0.09 ! +ATOM H72 HCA3 0.09 ! +ATOM H73 HCA3 0.09 ! +BOND OE C1 OE C6 C6 C7 +BOND C6 H61 C6 H62 +BOND C7 H71 C7 H72 C7 H73 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) (Thermalized IC) +IC OE C1 O5 C5 1.3697 108.86 68.68 116.37 1.4397 +IC O5 C1 OE C6 1.4279 108.86 60.91 116.74 1.4512 +IC C1 OE C6 H61 1.3697 116.74 53.97 105.24 1.1186 +IC C5 O5 C1 H1B 1.4397 116.37 -171.79 105.66 1.0872 +IC H61 OE *C6 H62 1.1186 105.24 -115.79 110.34 1.1048 +IC C1 OE C6 C7 1.3697 116.74 175.08 112.08 1.4895 +IC OE C6 C7 H71 1.4512 112.08 81.73 106.78 1.1072 +IC H71 C6 *C7 H72 1.1072 106.78 116.68 109.17 1.1407 +IC H73 C6 *C7 H72 1.1791 110.11 -123.76 109.17 1.1407 + + +PRES POEB 0.20 ! pram, make model compound 1-ethoxy-THP by adding equatorial +dele atom H1B ! O-ethyl to C1; apply to THP2 +GROUP +ATOM C1 CC311D 0.29 ! +ATOM H1A HCA1 0.09 ! +ATOM OE OC301 -0.36 ! +ATOM C6 CC321 0.00 ! +ATOM H61 HCA2 0.09 ! +ATOM H62 HCA2 0.09 ! +ATOM C7 CC331 -0.27 ! +ATOM H71 HCA3 0.09 ! +ATOM H72 HCA3 0.09 ! +ATOM H73 HCA3 0.09 ! + +BOND OE C1 OE C6 C6 C7 +BOND C6 H61 C6 H62 +BOND C7 H71 C7 H72 C7 H73 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) (Thermalized IC) +IC OE C1 O5 C5 1.3877 109.94 179.05 111.49 1.4773 +IC O5 C1 OE C6 1.4000 109.94 50.09 114.51 1.4195 +IC C1 OE C6 H61 1.3877 114.51 64.37 109.77 1.1110 +IC C5 O5 C1 H1A 1.4773 111.49 60.14 108.74 1.0555 +IC H61 OE *C6 H62 1.1110 109.77 -116.22 114.54 1.1610 +IC C1 OE C6 C7 1.3877 114.51 -171.94 105.76 1.5887 +IC OE C6 C7 H71 1.4195 105.76 47.18 107.35 1.0932 +IC H71 C6 *C7 H72 1.0932 107.35 122.35 108.56 1.0788 +IC H73 C6 *C7 H72 1.0693 106.58 -115.60 108.56 1.0788 + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! pyranose-furanose disaccharide model compound patches ! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +PRES OMEFB 0.00 ! pram; model compound 5b (raman et al.), OMe-THF add beta-O-methyl to C2; apply to THF2 +dele atom H2B ! +GROUP +ATOM C2 CC312D 0.29 ! +ATOM H2A HCA1 0.09 ! +ATOM OM OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +ATOM C5 CC322C 0.02 ! +ATOM H5A HCA2C2 0.09 ! +ATOM H5B HCA2C2 0.09 ! +ATOM O5 OC3C5M -0.40 ! +BOND OM C2 OM CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC OM C2 O5 C5 1.4262 110.39 -132.64 111.11 1.4440 +IC O5 C2 OM CM 1.4608 110.39 37.67 111.87 1.4590 +IC O5 C3 *C2 OM 1.4608 104.27 118.06 109.37 1.4262 +IC C2 OM CM HM1 1.4262 111.87 75.44 111.66 1.1146 +IC O5 OM *C2 H2A 1.4608 110.39 120.87 110.17 1.0756 +IC HM1 OM *CM HM2 1.1146 111.66 116.60 112.36 1.1028 +IC HM3 OM *CM HM2 1.1382 106.78 -113.45 112.36 1.1028 + +PRES OMEFA 0.00 ! pram; model compound 5a (raman et al.) OMe-THF add alpha-O-methyl to C2; apply to THF2 +dele atom H2A ! +GROUP +ATOM C2 CC312D 0.29 ! +ATOM H2B HCA1 0.09 ! +ATOM OM OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +ATOM C5 CC322C 0.02 ! +ATOM H5A HCA2C2 0.09 ! +ATOM H5B HCA2C2 0.09 ! +ATOM O5 OC3C5M -0.40 ! +BOND OM C2 OM CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC OM C2 O5 C5 1.3890 117.62 96.68 108.36 1.4125 +IC O5 C2 OM CM 1.4182 117.62 72.05 117.33 1.4176 !phi +IC O5 C3 *C2 OM 1.4182 104.62 -126.40 108.61 1.3890 +IC C2 OM CM HM1 1.3890 117.33 74.42 112.96 1.1873 +IC C5 O5 C2 H2B 1.4125 108.36 -146.31 102.20 1.1158 +IC HM1 OM *CM HM2 1.1873 112.96 123.66 111.70 1.0904 +IC HM3 OM *CM HM2 1.0743 116.43 -115.60 111.70 1.0904 + +PRES OM3FA 0.00 ! pram; make model compound 6 (raman et al.) (3-OMe-THF) by adding O-methyl to C3; apply to THF2 +dele atom H3A ! +GROUP +ATOM C3 CC312C 0.09 ! +ATOM H3B HCA1 0.09 ! +ATOM OM OC303 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +BOND OM C3 OM CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC OM C3 C2 O5 1.4423 111.50 145.16 110.09 1.3943 +IC C2 C3 OM CM 1.4615 111.50 67.07 111.78 1.4313 +IC C2 C4 *C3 OM 1.4615 101.47 -120.02 114.08 1.4423 +IC C3 OM CM HM1 1.4423 111.78 80.41 110.06 1.0756 +IC O5 C2 C3 H3B 1.3943 110.09 -89.94 112.82 1.0824 +IC HM1 OM *CM HM2 1.0756 110.06 123.52 113.51 1.1208 +IC HM3 OM *CM HM2 1.2034 115.51 -118.76 113.51 1.1208 + +PRES PFAA 0.40 ! pram; model compound 1aa (raman et al.) THP2-O-THF2 apply to THP2,THF2 +dele atom 1H1A +dele atom 2H2A +GROUP +ATOM 2C2 CC312D 0.29 ! +ATOM 1O11 OC302 -0.36 ! +ATOM 1C1 CC311D 0.29 ! +ATOM 1H1B HCA1 0.09 ! +ATOM 2H2B HCA1 0.09 ! +BOND 1O11 1C1 1O11 2C2 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) THERMALIZED +IC 1C2 1O5 *1C1 1O11 1.5510 112.63 119.66 106.38 1.3630 +IC 1O5 1C1 1O11 2C2 1.4439 106.38 71.59 113.52 1.4364 !phi +IC 1C1 1O11 2C2 2O5 1.3630 113.52 61.37 107.48 1.4378 !psi +IC 1O11 2C2 2O5 2C5 1.4364 107.48 89.10 111.56 1.5134 +IC 1H1B 1O5 *1C1 1C2 1.0878 105.31 123.05 112.63 1.5510 +IC 2H2B 2O5 *2C2 1O11 1.0740 112.55 -116.05 107.48 1.4364 + +PRES PFBA 0.40 ! pram; model compound 1ba (raman et al.) THP2-O-THF2 apply to THP2,THF2 +dele atom 1H1B +dele atom 2H2A +GROUP +ATOM 2C2 CC312D 0.29 ! +ATOM 1O11 OC302 -0.36 ! +ATOM 1C1 CC311D 0.29 ! +ATOM 1H1A HCA1 0.09 ! +ATOM 2H2B HCA1 0.09 ! +BOND 1O11 1C1 1O11 2C2 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1O5 *1C1 1O11 1.5360 111.33 -122.30 108.74 1.4121 +IC 1O5 1C1 1O11 2C2 1.4501 108.74 56.96 113.69 1.4241 !phi +IC 1C1 1O11 2C2 2O5 1.4121 113.69 108.56 109.48 1.4474 !psi +IC 1O11 2C2 2O5 2C5 1.4241 109.48 81.20 113.97 1.4756 +IC 1H1A 1O5 *1C1 1C2 1.1622 100.94 -121.84 111.33 1.5360 +IC 2H2B 2O5 *2C2 1O11 1.1203 106.41 -120.94 109.48 1.4241 + +PRES PFAB 0.40 ! pram; model compound 1ab (raman et al.) THP2-O-THF2 apply to THP2,THF2 +dele atom 1H1A +dele atom 2H2B +GROUP +ATOM 2C2 CC312D 0.29 ! +ATOM 1O11 OC302 -0.36 ! +ATOM 1C1 CC311D 0.29 ! +ATOM 1H1B HCA1 0.09 ! +ATOM 2H2A HCA1 0.09 ! +BOND 1O11 1C1 1O11 2C2 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1O5 *1C1 1O11 1.5500 104.88 112.39 119.22 1.4034 +IC 1O5 1C1 1O11 2C2 1.4723 119.22 86.14 119.83 1.4283 !phi +IC 1C1 1O11 2C2 2O5 1.4034 119.83 66.28 114.05 1.4624 !psi +IC 1O11 2C2 2O5 2C5 1.4283 114.05 -143.91 110.27 1.4121 +IC 1H1B 1O5 *1C1 1C2 1.0673 113.85 121.01 104.88 1.5500 +IC 2H2A 2O5 *2C2 1O11 1.0471 111.86 125.94 114.05 1.4283 + +PRES PFBB 0.40 ! pram; model compound 1bb (raman et al.) THP2-O-THF2 apply to THP2,THF2 +dele atom 1H1B +dele atom 2H2B +GROUP +ATOM 2C2 CC312D 0.29 ! +ATOM 1O11 OC302 -0.36 ! +ATOM 1C1 CC311D 0.29 ! +ATOM 1H1A HCA1 0.09 ! +ATOM 2H2A HCA1 0.09 ! +BOND 1O11 1C1 1O11 2C2 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1O5 *1C1 1O11 1.5446 113.68 -132.00 111.60 1.4189 +IC 1O5 1C1 1O11 2C2 1.4232 111.60 89.26 123.35 1.4838 !phi +IC 1C1 1O11 2C2 2O5 1.4189 123.35 72.10 115.09 1.4352 !psi +IC 1O11 2C2 2O5 2C5 1.4838 115.09 -139.72 112.23 1.4335 +IC 1H1A 1O5 *1C1 1C2 1.1282 107.59 -117.94 113.31 1.5517 +IC 2H2A 2O5 *2C2 1O11 1.1012 105.03 114.76 117.59 1.4175 + + +PRES COCFA 0.20 ! pram; model compound 2b (raman et al.), add -CH2-O-CH3 to C5; apply to THF2 +dele atom H5A ! +ATOM C5 CC312C 0.11 ! +ATOM H5B HCA1 0.09 ! +ATOM C6 CC321 0.00 ! +ATOM H61 HCA2 0.09 ! +ATOM H62 HCA2 0.09 ! +ATOM O1P OC301 -0.36 ! +ATOM C1P CC331 -0.09 ! +ATOM H11P HCA3 0.09 ! +ATOM H12P HCA3 0.09 ! +ATOM H13P HCA3 0.09 ! +BOND C5 C6 +BOND C6 H61 C6 H62 C6 O1P +BOND O1P C1P +BOND C1P H11P C1P H12P C1P H13P +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1P O1P C6 C5 1.3888 112.13 -175.22 105.16 1.4586 +IC O1P C6 C5 O5 1.4148 105.16 -163.59 108.02 1.4619 +IC C6 C4 *C5 O5 1.4586 115.45 -119.50 105.95 1.4619 +IC C6 O5 *C5 H5B 1.4586 108.02 -119.47 105.97 1.1555 +IC O1P C5 *C6 H61 1.4148 105.16 113.31 111.22 1.1326 +IC H61 C5 *C6 H62 1.1326 111.22 123.63 106.71 1.1801 +IC C6 O1P C1P H11P 1.4148 112.13 65.17 110.74 1.1107 +IC H11P O1P *C1P H12P 1.1107 110.74 113.46 105.59 1.1220 +IC H13P O1P *C1P H12P 1.0950 113.13 -117.42 105.59 1.1220 + +PRES COCFB 0.20 ! pram; model compound 2a (raman et al.), add -CH2-O-CH3 to C5; apply to THF2 +dele atom H5B ! +ATOM C5 CC312C 0.11 ! +ATOM H5A HCA1 0.09 ! +ATOM C6 CC321 0.00 ! +ATOM H61 HCA2 0.09 ! +ATOM H62 HCA2 0.09 ! +ATOM O1P OC301 -0.36 ! +ATOM C1P CC331 -0.09 ! +ATOM H11P HCA3 0.09 ! +ATOM H12P HCA3 0.09 ! +ATOM H13P HCA3 0.09 ! +BOND C5 C6 +BOND C6 H61 C6 H62 C6 O1P +BOND O1P C1P +BOND C1P H11P C1P H12P C1P H13P +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1P O1P C6 C5 1.4328 110.66 175.35 106.09 1.5903 +IC O1P C6 C5 O5 1.3578 106.09 157.99 110.58 1.4483 +IC C6 C4 *C5 O5 1.5903 108.99 119.30 106.48 1.4483 +IC C6 H5A *C5 O5 1.5903 109.40 -121.74 110.13 1.4483 +IC O1P C5 *C6 H61 1.3578 106.09 118.03 119.23 1.117 +IC H61 C5 *C6 H62 1.1170 119.23 124.31 105.47 1.1501 +IC C6 O1P C1P H11P 1.3578 110.66 41.15 103.52 1.1297 +IC H11P O1P *C1P H12P 1.1297 103.52 123.44 113.67 1.0505 +IC H13P O1P *C1P H12P 1.1142 109.41 -117.61 113.67 1.0505 + +PRES CHFAA 0.20 ! pram; model compound 4aa (raman et. al.), CYHX2-O-THF2, apply to CYHX2,THF2 +dele atom 1H2A +dele atom 2H2A +GROUP +ATOM 2C2 CC312D 0.29 ! +ATOM 2H2B HCA1 0.09 ! +ATOM 1O11 OC301 -0.36 ! +ATOM 1C2 CC311C 0.09 ! +ATOM 1H2B HCA1 0.09 ! +BOND 1O11 1C2 1O11 2C2 +ACCE 1O11 +IC 2O5 2C2 1O11 1C2 1.4540 110.47 56.72 116.77 1.4445 !psi +IC 2C2 1O11 1C2 1C1 1.4270 116.77 -128.42 109.24 1.5358 !phi +IC 1H2B 1C1 *1C2 1O11 1.1348 112.89 127.18 109.24 1.4445 +IC 1O11 2C2 2O5 2C5 1.4270 110.47 78.09 107.07 1.4761 +IC 2H2B 2O5 *2C2 1O11 1.1337 103.17 -116.99 110.47 1.4270 + + +PRES CHFBA 0.20 ! pram; model compound 4ba (raman et. al.), CYHX2-O-THF2, apply to CYHX2,THF2 +dele atom 1H2B +dele atom 2H2A +GROUP +ATOM 2C2 CC312D 0.29 ! +ATOM 2H2B HCA1 0.09 ! +ATOM 1O11 OC301 -0.36 ! +ATOM 1C2 CC311C 0.09 ! +ATOM 1H2A HCA1 0.09 ! +BOND 1O11 1C2 1O11 2C2 +ACCE 1O11 +IC 2O5 2C2 1O11 1C2 1.4602 117.40 75.76 116.64 1.4020 !psi +IC 2C2 1O11 1C2 1C1 1.4042 116.64 166.98 106.23 1.5646 !phi +IC 1H2A 1C1 *1C2 1C3 1.1396 105.05 114.39 113.20 1.5443 +IC 1H2A 1C1 *1C2 1O11 1.1396 105.05 -119.63 106.23 1.4020 +IC 1O11 2C2 2O5 2C5 1.4042 117.40 81.81 108.37 1.3613 +IC 2H2B 2O5 *2C2 1O11 1.1290 103.96 -118.53 117.40 1.4042 + +PRES CHFAB 0.20 ! pram; model compound 4ab (raman et. al.), CYHX2-O-THF2, apply to CYHX2,THF2 +dele atom 1H2A +dele atom 2H2B +GROUP +ATOM 2C2 CC312D 0.29 ! +ATOM 2H2A HCA1 0.09 ! +ATOM 1O11 OC301 -0.36 ! +ATOM 1C2 CC311C 0.09 ! +ATOM 1H2B HCA1 0.09 ! +BOND 1O11 1C2 1O11 2C2 +ACCE 1O11 +IC 2O5 2C2 1O11 1C2 1.3721 117.42 54.65 116.24 1.4701 !psi +IC 2C2 1O11 1C2 1C1 1.3640 116.24 -112.21 114.93 1.5708 !phi +IC 1H2B 1C1 *1C2 1O11 1.1056 108.77 124.20 114.93 1.4701 +IC 1O11 2C2 2O5 2C5 1.3640 117.42 -145.86 111.37 1.4398 +IC 2H2A 2O5 *2C2 1O11 1.1253 105.07 111.93 117.42 1.3640 + + +PRES CHFBB 0.20 ! pram; model compound 4bb (raman et. al.), CYHX2-O-THF2, apply to CYHX2,THF2 +dele atom 1H2B +dele atom 2H2B +GROUP +ATOM 2C2 CC312D 0.29 ! +ATOM 2H2A HCA1 0.09 ! +ATOM 1O11 OC301 -0.36 ! +ATOM 1C2 CC311C 0.09 ! +ATOM 1H2A HCA1 0.09 ! +BOND 1O11 1C2 1O11 2C2 +ACCE 1O11 +IC 2O5 2C2 1O11 1C2 1.4211 121.43 73.18 118.14 1.4491 !psi +IC 2C2 1O11 1C2 1C1 1.4038 118.14 -175.58 103.30 1.4881 !phi +IC 1H2A 1C1 *1C2 1C3 1.1251 111.63 120.53 108.83 1.5483 +IC 1H2A 1C1 *1C2 1O11 1.1251 111.63 -119.95 103.30 1.4491 +IC 1O11 2C2 2O5 2C5 1.4038 121.43 -160.71 114.91 1.4268 +IC 2H2A 2O5 *2C2 1O11 1.1021 103.74 124.46 121.43 1.4038 + +PRES PF3AA 0.20 ! pram; model compound 3aa (raman et. al.), apply to THP2,THF2 +dele atom 1H1A +dele atom 2H3A +GROUP +ATOM 2C3 CC312C 0.09 ! +ATOM 2H3B HCA1 0.09 ! +ATOM 1O11 OC303 -0.36 ! +ATOM 1C1 CC311D 0.29 ! +ATOM 1H1B HCA1 0.09 ! +BOND 1O11 1C1 1O11 2C3 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1O5 *1C1 1O11 1.5189 107.98 124.05 106.47 1.4144 +IC 1O5 1C1 1O11 2C3 1.4263 106.47 -179.33 114.87 1.4273 !phi +IC 1C1 1O11 2C3 2C2 1.4144 114.87 -172.32 111.75 1.5129 !psi +IC 1O11 2C3 2C2 2O5 1.4273 111.75 158.04 100.93 1.4547 +IC 1H1B 1O5 *1C1 1C2 1.0524 107.99 118.20 107.98 1.5189 +IC 2H3B 2C2 *2C3 1O11 1.0863 110.11 -121.74 111.75 1.4273 + +PRES PF3BA 0.20 ! pram; model compound 3ba (raman et. al.), apply to THP2,THF2 +dele atom 1H1B +dele atom 2H3A +GROUP +ATOM 2C3 CC312C 0.09 ! +ATOM 2H3B HCA1 0.09 ! +ATOM 1O11 OC303 -0.36 ! +ATOM 1C1 CC311D 0.29 ! +ATOM 1H1A HCA1 0.09 ! +BOND 1O11 1C1 1O11 2C3 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1O5 *1C1 1O11 1.4646 108.11 -116.50 106.68 1.4000 +IC 1O5 1C1 1O11 2C3 1.3967 106.68 -142.16 115.25 1.3990 !phi +IC 1C1 1O11 2C3 2C2 1.4000 115.25 162.99 107.58 1.4712 !psi +IC 1O11 2C3 2C2 2O5 1.3990 107.58 155.06 107.17 1.4128 +IC 1H1A 1O5 *1C1 1C2 1.1088 113.75 -125.78 108.11 1.4646 +IC 2H3B 2C2 *2C3 1O11 1.0656 111.58 -118.99 107.58 1.3990 + + +PRES PF3AB 0.20 ! pram; model compound 3ab (raman et. al.), apply to THP2,THF2 +dele atom 1H1A +dele atom 2H3B +GROUP +ATOM 2C3 CC312C 0.09 ! +ATOM 2H3A HCA1 0.09 ! +ATOM 1O11 OC303 -0.36 ! +ATOM 1C1 CC311D 0.29 ! +ATOM 1H1B HCA1 0.09 ! +BOND 1O11 1C1 1O11 2C3 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1O5 *1C1 1O11 1.5725 109.62 127.88 110.48 1.4083 +IC 1O5 1C1 1O11 2C3 1.3789 110.48 150.28 120.77 1.4287 !phi +IC 1C1 1O11 2C3 2C2 1.4083 120.77 -156.72 103.85 1.4845 !psi +IC 1O11 2C3 2C2 2O5 1.4287 103.85 -75.61 110.28 1.3796 +IC 1H1B 1O5 *1C1 1C2 1.1026 103.31 116.57 109.62 1.5725 +IC 2H3A 2C2 *2C3 1O11 1.0941 116.55 125.04 103.85 1.4287 + +PRES PF3BB 0.20 ! pram; model compound 3bb (raman et. al.), apply to THP2,THF2 +dele atom 1H1B +dele atom 2H3B +GROUP +ATOM 2C3 CC312C 0.09 ! +ATOM 2H3A HCA1 0.09 ! +ATOM 1O11 OC303 -0.36 ! +ATOM 1C1 CC311D 0.29 ! +ATOM 1H1A HCA1 0.09 ! +BOND 1O11 1C1 1O11 2C3 +ACCE 1O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1O5 *1C1 1O11 1.5729 105.20 -120.55 103.06 1.4073 +IC 1O5 1C1 1O11 2C3 1.4232 103.06 179.91 116.61 1.4537 !phi +IC 1C1 1O11 2C3 2C2 1.4073 116.61 -174.40 107.06 1.4398 !psi +IC 1O11 2C3 2C2 2O5 1.4537 107.06 -82.05 108.78 1.4051 +IC 1H1A 1O5 *1C1 1C2 1.1211 116.09 -125.13 105.20 1.5729 +IC 2H3A 2C2 *2C3 1O11 1.0361 111.98 125.34 107.06 1.4537 + + +END + + +return diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_bacterial.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_bacterial.str new file mode 100644 index 00000000..5634b70d --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_bacterial.str @@ -0,0 +1,5474 @@ +* Toppar stream file for Branched and Cyclic Chained lipids. Following reading of +* top_all36_lipid.rtf +* and +* par_all36_lipid.rtf +* + +! REFERENCES +! +! Branched Lipids +! +! Lim, J.B. & Klauda, J.B. Branching at the Iso- and Anteiso- Positions in Complex Chlamydia +! Membranes: A Molecular Dynamics Study. Biochimica et Biophysica Acta (BBA) - Biomembranes +! 1808:323-331 (2011). +! +! Cyclic-replacement of double bond +! +! Pandit, K.R. & Klauda, J.B. Membrane models of E. coli containing cyclic moieties in +! the aliphatic lipid chain. Biochimica et Biophysica Acta (BBA) - Biomembranes +! 1818:1205-1210 (2012). +! + +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have proirity, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* cholesterol residues +* +36 1 + +RESI PVPG -1.00 ! 16:0 (palmitoyl) - 18:1 cis-11 (vaccenyl) Phosphatidylglycerol +! +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H111 HEL1 0.15 ! H111---C211 | +GROUP ! || (CIS) | +ATOM C212 CEL1 -0.15 ! || | +ATOM H121 HEL1 0.15 ! H121---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H111 +DOUBLE C211 C212 +BOND C212 H121 C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 C12 C11 O12 1.5527 112.85 -172.43 115.75 1.4326 +IC OC3 C13 C12 C11 1.4270 111.28 66.71 112.85 1.5633 +IC C11 C13 *C12 OC2 1.5633 112.85 -123.90 110.15 1.4283 +IC OC3 C12 *C13 H13A 1.4270 111.28 119.84 108.43 1.1124 +IC OC3 C12 *C13 H13B 1.4270 111.28 -121.62 109.64 1.1108 +IC C12 C13 OC3 HO3 1.5527 111.28 31.95 102.00 0.9699 +IC OC2 C13 *C12 H12A 1.4283 110.15 -117.28 107.28 1.1148 +IC C13 C12 OC2 HO2 1.5527 110.15 -171.78 103.00 0.9822 +IC O12 C12 *C11 H11A 1.4326 115.75 -123.85 108.44 1.1130 +IC H11A C12 *C11 H11B 1.1130 108.44 -115.56 107.30 1.1122 +IC C12 C11 O12 P 1.5633 115.75 -47.69 121.24 1.5793 +IC C11 O12 P O11 1.4326 121.24 -163.05 101.81 1.5842 +IC O11 O12 *P O13 1.5842 101.81 115.87 108.46 1.4772 +IC O11 O12 *P O14 1.5842 101.81 -115.89 106.55 1.4794 +IC O12 P O11 C1 1.5793 101.81 52.06 120.97 1.4307 +IC P O11 C1 C2 1.5842 120.97 -123.35 111.16 1.5486 +IC C2 O11 *C1 HA 1.5486 111.16 -119.56 109.11 1.1121 +IC HA O11 *C1 HB 1.1121 109.11 -119.08 113.21 1.1182 +IC O11 C1 C2 O21 1.4307 111.16 174.21 106.66 1.4420 +IC O21 C1 *C2 C3 1.4420 106.66 -120.98 111.16 1.5605 !defines S chirality +IC C3 C1 *C2 HS 1.5605 111.16 -118.20 107.43 1.1163 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.66 151.72 115.89 1.3162 +IC C2 O21 C21 C22 1.4420 115.89 174.64 108.39 1.5300 +IC C22 O21 *C21 O22 1.5300 108.39 179.62 126.87 1.2174 +IC O21 C21 C22 C23 1.3162 108.39 -178.91 112.40 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.40 -121.55 107.75 1.1090 +IC H2R C21 *C22 H2S 1.1090 107.75 -117.07 107.65 1.1094 +IC C1 C2 C3 O31 1.5486 111.16 173.26 113.08 1.4465 +IC O31 C2 *C3 HX 1.4465 113.08 126.36 109.19 1.1155 +IC HX C2 *C3 HY 1.1155 109.19 114.42 106.70 1.1130 +IC C2 C3 O31 C31 1.5605 113.08 85.33 114.98 1.3287 +IC C3 O31 C31 C32 1.4465 114.98 -175.76 108.36 1.5299 +IC C32 O31 *C31 O32 1.5299 108.36 -179.46 126.35 1.2156 +IC O31 C31 C32 C33 1.3287 108.36 179.34 112.58 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.58 -120.90 107.34 1.1099 +IC H2X C31 *C32 H2Y 1.1099 107.34 -117.24 107.84 1.1085 +IC C21 C22 C23 C24 1.5300 112.40 179.84 112.28 1.5340 +IC C24 C22 *C23 H3R 1.5340 112.28 -121.15 109.56 1.1144 +IC H3R C22 *C23 H3S 1.1144 109.56 -117.66 109.59 1.1144 +IC C22 C23 C24 C25 1.5451 112.28 -179.93 112.52 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.52 -121.28 109.14 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.14 -117.44 109.11 1.1133 +IC C23 C24 C25 C26 1.5340 112.52 179.89 112.69 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.69 -121.36 109.01 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.01 -117.25 109.07 1.1133 +IC C24 C25 C26 C27 1.5348 112.69 -179.62 112.61 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.61 -121.31 109.08 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.08 -117.38 109.05 1.1131 +IC C25 C26 C27 C28 1.5347 112.61 179.89 112.39 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.39 -121.64 108.41 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.41 -116.93 108.78 1.1140 +IC C26 C27 C28 C29 1.5356 112.39 -177.47 111.53 1.5098 +IC C29 C27 *C28 H8R 1.5098 111.53 -123.70 107.68 1.1128 +IC H8R C27 *C28 H8S 1.1128 107.68 -115.21 108.48 1.1128 +IC C27 C28 C29 C210 1.5356 112.39 -177.47 111.53 1.5098 +IC C210 C28 *C29 H9R 1.5098 111.53 -123.70 107.68 1.1128 +IC H9R C28 *C29 H9S 1.1128 107.68 -115.21 108.48 1.1128 +IC C28 C29 C210 C211 1.5356 112.39 -177.47 111.53 1.5098 +IC C211 C29 *C210 H10R 1.5098 111.53 -123.70 107.68 1.1128 +IC H10R C29 *C210 H10S 1.1128 107.68 -115.21 108.48 1.1128 +IC C29 C210 C211 C212 1.5398 111.53 -118.23 126.87 1.3467 +IC C212 C210 *C211 H111 1.3467 126.87 178.64 114.46 1.1012 +IC C210 C211 C212 C213 1.5098 126.87 -1.03 126.59 1.5093 +IC C213 C211 *C212 H121 1.5093 126.59 179.83 118.67 1.1011 +IC C211 C212 C213 C214 1.3467 126.59 93.85 111.91 1.5393 +IC C214 C212 *C213 H13R 1.5393 111.91 -121.29 111.52 1.1130 +IC H13R C212 *C213 H13S 1.1130 111.52 -117.67 110.00 1.1125 +IC C212 C213 C214 C215 1.5355 112.61 179.58 112.66 1.5348 +IC C215 C213 *C214 H14R 1.5348 112.66 -121.34 109.11 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.11 -117.35 109.06 1.1134 +IC C213 C214 C215 C216 1.5347 112.66 -179.86 112.61 1.5349 +IC C216 C214 *C215 H15R 1.5349 112.61 -121.26 109.07 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.07 -117.41 109.12 1.1130 +IC C214 C215 C216 C217 1.5348 112.61 179.90 112.71 1.5340 +IC C217 C215 *C216 H16R 1.5340 112.71 -121.38 109.14 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.33 109.09 1.1134 +IC C215 C216 C217 C218 1.5349 112.71 180.00 113.31 1.5310 +IC C218 C216 *C217 H17R 1.5310 113.31 -121.61 108.71 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.71 -116.68 108.78 1.1140 +IC C216 C217 C218 H18R 1.5340 113.31 -59.87 110.43 1.1115 +IC H18R C217 *C218 H18S 1.1115 110.43 119.84 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1115 110.43 -120.02 110.62 1.1112 +IC C31 C32 C33 C34 1.5299 112.58 -179.46 112.10 1.5339 +IC C34 C32 *C33 H3X 1.5339 112.10 -121.48 109.72 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.72 -117.58 109.31 1.1149 +IC C32 C33 C34 C35 1.5448 112.10 179.21 112.66 1.5346 +IC C35 C33 *C34 H4X 1.5346 112.66 -121.16 108.94 1.1134 +IC H4X C33 *C34 H4Y 1.1134 108.94 -117.41 109.10 1.1130 +IC C33 C34 C35 C36 1.5339 112.66 -179.91 112.56 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.56 -121.46 109.07 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.07 -117.21 108.96 1.1134 +IC C34 C35 C36 C37 1.5346 112.56 179.56 112.70 1.5346 +IC C37 C35 *C36 H6X 1.5346 112.70 -121.29 108.98 1.1132 +IC H6X C35 *C36 H6Y 1.1132 108.98 -117.32 109.02 1.1131 +IC C35 C36 C37 C38 1.5346 112.70 179.89 112.56 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.56 -121.38 109.07 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.07 -117.30 109.01 1.1133 +IC C36 C37 C38 C39 1.5346 112.56 179.63 112.69 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.69 -121.30 109.02 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.02 -117.33 109.03 1.1132 +IC C37 C38 C39 C310 1.5347 112.69 179.94 112.58 1.5346 +IC C310 C38 *C39 H9X 1.5346 112.58 -121.36 109.09 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.09 -117.34 109.04 1.1132 +IC C38 C39 C310 C311 1.5346 112.58 179.62 112.67 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.67 -121.29 109.04 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.04 -117.34 109.06 1.1132 +IC C39 C310 C311 C312 1.5346 112.67 -179.93 112.59 1.5346 +IC C312 C310 *C311 H11X 1.5346 112.59 -121.36 109.10 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.10 -117.36 109.05 1.1132 +IC C310 C311 C312 C313 1.5346 112.59 179.64 112.65 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.65 -121.28 109.06 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.06 -117.36 109.08 1.1132 +IC C311 C312 C313 C314 1.5346 112.65 -179.95 112.60 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.60 -121.34 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.37 109.06 1.1132 +IC C312 C313 C314 C315 1.5346 112.60 179.75 112.70 1.5339 +IC C315 C313 *C314 H14X 1.5339 112.70 -121.31 109.09 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.09 -117.35 109.10 1.1132 +IC C313 C314 C315 C316 1.5348 112.70 179.98 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.75 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.75 -116.64 108.73 1.1141 +IC C314 C315 C316 H16X 1.5339 113.30 -59.99 110.44 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.44 119.85 110.44 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.44 -120.07 110.60 1.1112 + +RESI PVPE 0.00 ! 16:0 (palmitoyl) - 18:1 cis-11 (vaccenyl) Phosphatidylethanolamine +! +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H111 HEL1 0.15 ! H111---C211 | +GROUP ! || (CIS) | +ATOM C212 CEL1 -0.15 ! || | +ATOM H121 HEL1 0.15 ! H121---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H111 +DOUBLE C211 C212 +BOND C212 H121 C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.5078 111.09 68.79 110.33 1.4254 +IC C11 N *C12 H12A 1.5400 111.09 -122.33 108.17 1.1079 +IC H12A N *C12 H12B 1.1079 108.17 -118.40 107.74 1.1112 +IC C11 C12 N HN1 1.5400 111.09 -35.27 106.06 1.0664 +IC HN1 C12 *N HN2 1.0664 106.06 114.05 112.10 1.0358 +IC HN1 C12 *N HN3 1.0664 106.06 -118.21 113.62 1.0353 +IC O12 C12 *C11 H11A 1.4254 110.33 -126.01 111.43 1.1173 +IC H11A C12 *C11 H11B 1.1173 111.43 -116.40 108.25 1.1146 +IC C12 C11 O12 P 1.5400 110.33 -98.67 122.01 1.5838 +IC C11 O12 P O11 1.4254 122.01 175.28 101.96 1.5733 +IC O11 O12 *P O13 1.5733 101.96 118.35 108.16 1.4702 +IC O11 O12 *P O14 1.5733 101.96 -114.83 104.73 1.4823 +IC O12 P O11 C1 1.5838 101.96 61.31 122.26 1.4287 +IC P O11 C1 C2 1.5733 122.26 -120.45 111.00 1.5491 +IC C2 O11 *C1 HA 1.5491 111.00 -118.16 108.31 1.1134 +IC HA O11 *C1 HB 1.1134 108.31 -118.72 113.73 1.1170 +IC O11 C1 C2 O21 1.4287 111.00 -170.08 107.01 1.4406 +IC O21 C1 *C2 C3 1.4406 107.01 -121.48 111.36 1.5593 !defines S chirality +IC C3 C1 *C2 HS 1.5593 111.36 -118.41 106.90 1.1168 !defines S chirality +IC C1 C2 O21 C21 1.5491 107.01 151.66 115.21 1.3219 +IC C2 O21 C21 C22 1.4406 115.21 176.14 108.47 1.5289 +IC C22 O21 *C21 O22 1.5289 108.47 179.75 126.36 1.2176 +IC O21 C21 C22 C23 1.3219 108.47 -177.19 112.65 1.5452 +IC C23 C21 *C22 H2R 1.5452 112.65 -121.46 107.75 1.1093 +IC H2R C21 *C22 H2S 1.1093 107.75 -117.05 107.80 1.1094 +IC C1 C2 C3 O31 1.5491 111.36 174.62 112.78 1.4451 +IC O31 C2 *C3 HX 1.4451 112.78 126.20 108.61 1.1134 +IC HX C2 *C3 HY 1.1134 108.61 114.63 106.76 1.1126 +IC C2 C3 O31 C31 1.5593 112.78 94.47 115.64 1.3298 +IC C3 O31 C31 C32 1.4451 115.64 -170.85 108.57 1.5287 +IC C32 O31 *C31 O32 1.5287 108.57 -178.35 125.82 1.2178 +IC O31 C31 C32 C33 1.3298 108.57 176.09 113.01 1.5453 +IC C33 C31 *C32 H2X 1.5453 113.01 -120.86 107.43 1.1106 +IC H2X C31 *C32 H2Y 1.1106 107.43 -117.02 107.94 1.1084 +IC C21 C22 C23 C24 1.5289 112.65 179.22 112.12 1.5344 +IC C24 C22 *C23 H3R 1.5344 112.12 -120.98 109.71 1.1144 +IC H3R C22 *C23 H3S 1.1144 109.71 -117.88 109.69 1.1144 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5359 112.47 -179.09 111.48 1.5100 +IC C210 C28 *C29 H9R 1.5100 111.48 -123.55 107.71 1.1131 +IC H9R C28 *C29 H9S 1.1131 107.71 -115.31 108.52 1.1127 +IC C28 C29 C210 C211 1.5359 112.47 -179.09 111.48 1.5100 +IC C211 C29 *C210 H10R 1.5100 111.48 -123.55 107.71 1.1131 +IC H10R C29 *C210 H10S 1.1131 107.71 -115.31 108.52 1.1127 +IC C29 C210 C211 C212 1.5399 111.48 -120.51 126.65 1.3465 +IC C212 C210 *C211 H111 1.3465 126.65 178.55 114.65 1.1012 +IC C210 C211 C212 C213 1.5100 126.65 -1.33 126.32 1.5088 +IC C213 C211 *C212 H121 1.5088 126.32 -179.89 118.81 1.1013 +IC C211 C212 C213 C214 1.3465 126.32 90.84 112.10 1.5393 +IC C214 C212 *C213 H13R 1.5393 112.10 -121.27 111.29 1.1133 +IC H13R C212 *C213 H13S 1.1133 111.29 -117.47 110.08 1.1126 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5344 112.29 -121.35 109.32 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.32 -117.49 109.04 1.1133 +IC C213 C214 C215 C216 1.5344 112.29 178.10 112.83 1.5343 +IC C216 C214 *C215 H15R 1.5343 112.83 -121.22 109.06 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.06 -117.27 109.05 1.1132 +IC C214 C215 C216 C217 1.5344 112.83 179.20 112.48 1.5338 +IC C217 C215 *C216 H16R 1.5338 112.48 -121.30 109.23 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.23 -117.48 109.17 1.1133 +IC C215 C216 C217 C218 1.5343 112.48 179.30 113.32 1.5307 +IC C218 C216 *C217 H17R 1.5307 113.32 -121.67 108.76 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.76 -116.60 108.71 1.1141 +IC C216 C217 C218 H18R 1.5338 113.32 -60.32 110.45 1.1114 +IC H18R C217 *C218 H18S 1.1114 110.45 119.86 110.49 1.1113 +IC H18R C217 *C218 H18T 1.1114 110.45 -120.04 110.58 1.1112 +IC C31 C32 C33 C34 1.5287 113.01 -179.36 111.84 1.5345 +IC C34 C32 *C33 H3X 1.5345 111.84 -121.48 110.04 1.1135 +IC H3X C32 *C33 H3Y 1.1135 110.04 -117.95 109.39 1.1149 +IC C32 C33 C34 C35 1.5453 111.84 178.35 112.93 1.5350 +IC C35 C33 *C34 H4X 1.5350 112.93 -121.06 108.92 1.1138 +IC H4X C33 *C34 H4Y 1.1138 108.92 -117.32 109.20 1.1130 +IC C33 C34 C35 C36 1.5345 112.93 -179.86 112.46 1.5352 +IC C36 C34 *C35 H5X 1.5352 112.46 -121.45 109.25 1.1129 +IC H5X C34 *C35 H5Y 1.1129 109.25 -117.43 109.01 1.1134 +IC C34 C35 C36 C37 1.5350 112.46 179.21 112.88 1.5352 +IC C37 C35 *C36 H6X 1.5352 112.88 -121.25 109.00 1.1134 +IC H6X C35 *C36 H6Y 1.1134 109.00 -117.27 109.08 1.1131 +IC C35 C36 C37 C38 1.5352 112.88 179.79 112.50 1.5352 +IC C38 C36 *C37 H7X 1.5352 112.50 -121.35 109.17 1.1130 +IC H7X C36 *C37 H7Y 1.1130 109.17 -117.42 109.08 1.1132 +IC C36 C37 C38 C39 1.5352 112.50 179.41 112.91 1.5352 +IC C39 C37 *C38 H8X 1.5352 112.91 -121.30 109.04 1.1133 +IC H8X C37 *C38 H8Y 1.1133 109.04 -117.27 109.05 1.1132 +IC C37 C38 C39 C310 1.5352 112.91 179.74 112.46 1.5353 +IC C310 C38 *C39 H9X 1.5353 112.46 -121.33 109.17 1.1131 +IC H9X C38 *C39 H9Y 1.1131 109.17 -117.42 109.10 1.1132 +IC C38 C39 C310 C311 1.5352 112.46 179.50 112.91 1.5350 +IC C311 C39 *C310 H10X 1.5350 112.91 -121.32 109.05 1.1133 +IC H10X C39 *C310 H10Y 1.1133 109.05 -117.29 109.05 1.1132 +IC C39 C310 C311 C312 1.5353 112.91 179.80 112.52 1.5354 +IC C312 C310 *C311 H11X 1.5354 112.52 -121.32 109.16 1.1131 +IC H11X C310 *C311 H11Y 1.1131 109.16 -117.41 109.11 1.1132 +IC C310 C311 C312 C313 1.5350 112.52 179.66 112.78 1.5349 +IC C313 C311 *C312 H12X 1.5349 112.78 -121.30 109.08 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.08 -117.35 109.09 1.1132 +IC C311 C312 C313 C314 1.5354 112.78 179.95 112.66 1.5353 +IC C314 C312 *C313 H13X 1.5353 112.66 -121.33 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.38 109.07 1.1132 +IC C312 C313 C314 C315 1.5349 112.66 179.95 112.69 1.5341 +IC C315 C313 *C314 H14X 1.5341 112.69 -121.30 109.17 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.17 -117.38 109.15 1.1132 +IC C313 C314 C315 C316 1.5353 112.69 179.98 113.37 1.5312 +IC C316 C314 *C315 H15X 1.5312 113.37 -121.71 108.74 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.74 -116.61 108.74 1.1141 +IC C314 C315 C316 H16X 1.5341 113.37 -59.94 110.51 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.51 119.91 110.52 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.51 -120.06 110.58 1.1112 + +RESI PPPE 0.00 ! 16:0 (palmitoyl) - 16:1 cis-9 (palmitoleoyl) Phosphatidylethanolamine +! +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.5078 111.09 68.79 110.33 1.4254 +IC C11 N *C12 H12A 1.5400 111.09 -122.33 108.17 1.1079 +IC H12A N *C12 H12B 1.1079 108.17 -118.40 107.74 1.1112 +IC C11 C12 N HN1 1.5400 111.09 -35.27 106.06 1.0664 +IC HN1 C12 *N HN2 1.0664 106.06 114.05 112.10 1.0358 +IC HN1 C12 *N HN3 1.0664 106.06 -118.21 113.62 1.0353 +IC O12 C12 *C11 H11A 1.4254 110.33 -126.01 111.43 1.1173 +IC H11A C12 *C11 H11B 1.1173 111.43 -116.40 108.25 1.1146 +IC C12 C11 O12 P 1.5400 110.33 -98.67 122.01 1.5838 +IC C11 O12 P O11 1.4254 122.01 175.28 101.96 1.5733 +IC O11 O12 *P O13 1.5733 101.96 118.35 108.16 1.4702 +IC O11 O12 *P O14 1.5733 101.96 -114.83 104.73 1.4823 +IC O12 P O11 C1 1.5838 101.96 61.31 122.26 1.4287 +IC P O11 C1 C2 1.5733 122.26 -120.45 111.00 1.5491 +IC C2 O11 *C1 HA 1.5491 111.00 -118.16 108.31 1.1134 +IC HA O11 *C1 HB 1.1134 108.31 -118.72 113.73 1.1170 +IC O11 C1 C2 O21 1.4287 111.00 -170.08 107.01 1.4406 +IC O21 C1 *C2 C3 1.4406 107.01 -121.48 111.36 1.5593 !defines S chirality +IC C3 C1 *C2 HS 1.5593 111.36 -118.41 106.90 1.1168 !defines S chirality +IC C1 C2 O21 C21 1.5491 107.01 151.66 115.21 1.3219 +IC C2 O21 C21 C22 1.4406 115.21 176.14 108.47 1.5289 +IC C22 O21 *C21 O22 1.5289 108.47 179.75 126.36 1.2176 +IC O21 C21 C22 C23 1.3219 108.47 -177.19 112.65 1.5452 +IC C23 C21 *C22 H2R 1.5452 112.65 -121.46 107.75 1.1093 +IC H2R C21 *C22 H2S 1.1093 107.75 -117.05 107.80 1.1094 +IC C1 C2 C3 O31 1.5491 111.36 174.62 112.78 1.4451 +IC O31 C2 *C3 HX 1.4451 112.78 126.20 108.61 1.1134 +IC HX C2 *C3 HY 1.1134 108.61 114.63 106.76 1.1126 +IC C2 C3 O31 C31 1.5593 112.78 94.47 115.64 1.3298 +IC C3 O31 C31 C32 1.4451 115.64 -170.85 108.57 1.5287 +IC C32 O31 *C31 O32 1.5287 108.57 -178.35 125.82 1.2178 +IC O31 C31 C32 C33 1.3298 108.57 176.09 113.01 1.5453 +IC C33 C31 *C32 H2X 1.5453 113.01 -120.86 107.43 1.1106 +IC H2X C31 *C32 H2Y 1.1106 107.43 -117.02 107.94 1.1084 +IC C21 C22 C23 C24 1.5289 112.65 179.22 112.12 1.5344 +IC C24 C22 *C23 H3R 1.5344 112.12 -120.98 109.71 1.1144 +IC H3R C22 *C23 H3S 1.1144 109.71 -117.88 109.69 1.1144 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5348 112.82 179.61 112.29 1.5344 +IC C213 C211 *C212 H13R 1.5344 112.29 -121.35 109.32 1.1131 +IC H12R C211 *C212 H13S 1.1131 109.32 -117.49 109.04 1.1133 +IC C211 C212 C213 C214 1.5344 112.29 178.10 112.83 1.5343 +IC C214 C212 *C213 H13R 1.5343 112.83 -121.22 109.06 1.1133 +IC H13R C212 *C213 H13S 1.1133 109.06 -117.27 109.05 1.1132 +IC C212 C213 C214 C215 1.5344 112.83 179.20 112.48 1.5338 +IC C215 C213 *C214 H14R 1.5338 112.48 -121.30 109.23 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.23 -117.48 109.17 1.1133 +IC C213 C214 C215 C216 1.5343 112.48 179.30 113.32 1.5307 +IC C216 C214 *C215 H15R 1.5307 113.32 -121.67 108.76 1.1142 +IC H15R C214 *C215 H15S 1.1142 108.76 -116.60 108.71 1.1141 +IC C214 C215 C216 H16R 1.5338 113.32 -60.32 110.45 1.1114 +IC H16R C215 *C216 H16S 1.1114 110.45 119.86 110.49 1.1113 +IC H16R C215 *C216 H16T 1.1114 110.45 -120.04 110.58 1.1112 +IC C31 C32 C33 C34 1.5287 113.01 -179.36 111.84 1.5345 +IC C34 C32 *C33 H3X 1.5345 111.84 -121.48 110.04 1.1135 +IC H3X C32 *C33 H3Y 1.1135 110.04 -117.95 109.39 1.1149 +IC C32 C33 C34 C35 1.5453 111.84 178.35 112.93 1.5350 +IC C35 C33 *C34 H4X 1.5350 112.93 -121.06 108.92 1.1138 +IC H4X C33 *C34 H4Y 1.1138 108.92 -117.32 109.20 1.1130 +IC C33 C34 C35 C36 1.5345 112.93 -179.86 112.46 1.5352 +IC C36 C34 *C35 H5X 1.5352 112.46 -121.45 109.25 1.1129 +IC H5X C34 *C35 H5Y 1.1129 109.25 -117.43 109.01 1.1134 +IC C34 C35 C36 C37 1.5350 112.46 179.21 112.88 1.5352 +IC C37 C35 *C36 H6X 1.5352 112.88 -121.25 109.00 1.1134 +IC H6X C35 *C36 H6Y 1.1134 109.00 -117.27 109.08 1.1131 +IC C35 C36 C37 C38 1.5352 112.88 179.79 112.50 1.5352 +IC C38 C36 *C37 H7X 1.5352 112.50 -121.35 109.17 1.1130 +IC H7X C36 *C37 H7Y 1.1130 109.17 -117.42 109.08 1.1132 +IC C36 C37 C38 C39 1.5352 112.50 179.41 112.91 1.5352 +IC C39 C37 *C38 H8X 1.5352 112.91 -121.30 109.04 1.1133 +IC H8X C37 *C38 H8Y 1.1133 109.04 -117.27 109.05 1.1132 +IC C37 C38 C39 C310 1.5352 112.91 179.74 112.46 1.5353 +IC C310 C38 *C39 H9X 1.5353 112.46 -121.33 109.17 1.1131 +IC H9X C38 *C39 H9Y 1.1131 109.17 -117.42 109.10 1.1132 +IC C38 C39 C310 C311 1.5352 112.46 179.50 112.91 1.5350 +IC C311 C39 *C310 H10X 1.5350 112.91 -121.32 109.05 1.1133 +IC H10X C39 *C310 H10Y 1.1133 109.05 -117.29 109.05 1.1132 +IC C39 C310 C311 C312 1.5353 112.91 179.80 112.52 1.5354 +IC C312 C310 *C311 H11X 1.5354 112.52 -121.32 109.16 1.1131 +IC H11X C310 *C311 H11Y 1.1131 109.16 -117.41 109.11 1.1132 +IC C310 C311 C312 C313 1.5350 112.52 179.66 112.78 1.5349 +IC C313 C311 *C312 H12X 1.5349 112.78 -121.30 109.08 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.08 -117.35 109.09 1.1132 +IC C311 C312 C313 C314 1.5354 112.78 179.95 112.66 1.5353 +IC C314 C312 *C313 H13X 1.5353 112.66 -121.33 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.38 109.07 1.1132 +IC C312 C313 C314 C315 1.5349 112.66 179.95 112.69 1.5341 +IC C315 C313 *C314 H14X 1.5341 112.69 -121.30 109.17 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.17 -117.38 109.15 1.1132 +IC C313 C314 C315 C316 1.5353 112.69 179.98 113.37 1.5312 +IC C316 C314 *C315 H15X 1.5312 113.37 -121.71 108.74 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.74 -116.61 108.74 1.1141 +IC C314 C315 C316 H16X 1.5341 113.37 -59.94 110.51 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.51 119.91 110.52 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.51 -120.06 110.58 1.1112 + +RESI PMPE 0.00 ! 1-palmytoil-2-CIS-9,10-METHYLENEHEXADECANOYL- +! Phosphatidylethanolamine +! +! (April 7, 2010 Kunal Pandit) +! +! Palmytoil - CH2 +! | +! Oleyl - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CG3RC1 -0.09 ! | | +ATOM H9R HGA1 0.09 ! H9R ---C29 H17R | +GROUP ! |\ / | +ATOM C217 CG3C31 -0.18 ! | \ / | +ATOM H17R HGA2 0.09 ! | C217 | +ATOM H17S HGA2 0.09 ! | / \ | +GROUP ! |/ \ | +ATOM C210 CG3RC1 -0.09 ! H10R ---C210 H17S | +ATOM H10R HGA1 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H121 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 C210 C29 C217 +BOND C210 H10R C210 C211 C210 C217 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +BOND C217 H17R C217 H17S +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from minimize coord +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5740 108.03 62.34 109.55 1.4587 +IC O12 C12 *C11 H11A 1.4587 109.55 -133.45 104.51 1.1111 +IC H11A C12 *C11 H11B 1.1111 104.51 -102.24 107.44 1.1106 +IC C12 C11 O12 P 1.6269 109.55 -163.53 109.35 1.5489 +IC C11 O12 P O11 1.4587 109.35 45.61 102.47 1.5319 +IC O11 O12 *P O13 1.5319 102.47 -122.17 109.86 1.4873 +IC O11 O12 *P O14 1.5319 102.47 113.34 104.82 1.5089 +IC O12 P O11 C1 1.5489 102.47 -127.21 119.35 1.4081 +IC P O11 C1 C2 1.5319 119.35 168.57 109.93 1.5357 +IC C2 O11 *C1 HA 1.5357 109.93 -115.95 114.29 1.1113 +IC HA O11 *C1 HB 1.1113 114.29 -119.43 108.09 1.1105 +IC O11 C1 C2 O21 1.4081 109.93 48.51 107.78 1.3985 +IC O21 C1 *C2 C3 1.3985 107.78 -124.83 112.50 1.5189 +IC C3 C1 *C2 HS 1.5189 112.50 -116.89 107.38 1.1110 +IC C1 C2 O21 C21 1.5357 107.78 69.98 118.97 1.3059 +IC C2 O21 C21 C22 1.3985 118.97 166.82 107.13 1.5380 +IC C22 O21 *C21 O22 1.5380 107.13 -170.88 125.96 1.1735 +IC O21 C21 C22 C23 1.3059 107.13 -129.04 116.72 1.5340 +IC C23 C21 *C22 H2R 1.5340 116.72 -121.20 110.01 1.1106 +IC H2R C21 *C22 H2S 1.1106 110.01 -115.57 107.31 1.1116 +IC C1 C2 C3 O31 1.5357 112.50 -174.65 112.28 1.4522 +IC O31 C2 *C3 HX 1.4522 112.28 -114.36 112.03 1.1112 +IC HX C2 *C3 HY 1.1112 112.03 -119.01 106.04 1.1105 +IC C2 C3 O31 C31 1.5189 112.28 103.03 115.31 1.4071 +IC C3 O31 C31 C32 1.4522 115.31 179.90 110.84 1.5158 +IC C32 O31 *C31 O32 1.5158 110.84 172.37 122.14 1.2201 +IC O31 C31 C32 C33 1.4071 110.84 -166.46 116.58 1.5719 +IC C33 C31 *C32 H2X 1.5719 116.58 -117.94 109.57 1.1109 +IC H2X C31 *C32 H2Y 1.1109 109.57 -123.57 102.64 1.1107 +IC C21 C22 C23 C24 1.5380 116.72 -80.26 109.08 1.5218 +IC C24 C22 *C23 H3R 1.5218 109.08 -124.90 105.17 1.1108 +IC H3R C22 *C23 H3S 1.1108 105.17 -108.19 105.63 1.1108 +IC C22 C23 C24 C25 1.5340 109.08 -159.22 112.40 1.5136 +IC C23 C24 C25 C26 1.5218 112.40 -43.61 120.64 1.5087 +IC C24 C25 C26 C27 1.5136 120.64 178.93 113.39 1.5700 +IC C25 C26 C27 C28 1.5087 113.39 72.57 109.72 1.5767 +IC C26 C27 C28 C29 1.5700 109.72 -173.11 106.46 1.5083 +IC C27 C28 C29 C210 1.5767 106.46 -147.88 120.94 1.4723 +IC C28 C29 C210 C211 1.5083 120.94 -1.64 121.09 1.5792 +IC C29 C210 C211 C212 1.4723 121.09 164.86 109.30 1.5195 +IC C210 C211 C212 C213 1.5792 109.30 174.67 109.83 1.5417 +IC C211 C212 C213 C214 1.5195 109.83 152.45 110.39 1.5837 +IC C212 C213 C214 C215 1.5417 110.39 -161.02 117.34 1.5467 +IC C213 C214 C215 C216 1.5837 117.34 136.15 109.27 1.5335 +IC C27 C28 C29 C217 1.5767 106.46 -77.30 114.54 1.5040 +IC C28 C29 C217 C210 1.5083 114.54 -113.36 58.10 1.5281 +IC C29 C217 C210 C211 1.5040 58.10 112.25 116.55 1.5792 +IC C217 C210 C211 C212 1.5281 116.55 95.28 109.30 1.5195 +IC C31 C32 C33 C34 1.5158 116.58 -156.33 110.79 1.5385 +IC C34 C32 *C33 H3X 1.5385 110.79 -119.46 105.53 1.1099 +IC H3X C32 *C33 H3Y 1.1099 105.53 -124.63 112.06 1.1108 +IC C32 C33 C34 C35 1.5719 110.79 -164.94 113.24 1.5570 +IC C35 C33 *C34 H4X 1.5570 113.24 -115.88 103.84 1.1106 +IC H4X C33 *C34 H4Y 1.1106 103.84 -117.83 112.15 1.1111 +IC C33 C34 C35 C36 1.5385 113.24 -175.74 108.09 1.4998 +IC C36 C34 *C35 H5X 1.4998 108.09 -124.22 112.64 1.1110 +IC H5X C34 *C35 H5Y 1.1110 112.64 -112.55 111.15 1.1109 +IC C34 C35 C36 C37 1.5570 108.09 -170.32 111.91 1.6017 +IC C37 C35 *C36 H6X 1.6017 111.91 -113.57 111.94 1.1104 +IC H6X C35 *C36 H6Y 1.1104 111.94 -125.88 112.72 1.1112 +IC C35 C36 C37 C38 1.4998 111.91 -166.01 112.78 1.5291 +IC C38 C36 *C37 H7X 1.5291 112.78 -123.46 107.25 1.1111 +IC H7X C36 *C37 H7Y 1.1111 107.25 -118.21 107.27 1.1106 +IC C36 C37 C38 C39 1.6017 112.78 -59.37 115.90 1.4988 +IC C39 C37 *C38 H8X 1.4988 115.90 -121.29 104.94 1.1119 +IC H8X C37 *C38 H8Y 1.1119 104.94 -122.24 111.41 1.1102 +IC C37 C38 C39 C310 1.5291 115.90 173.72 114.97 1.5808 +IC C310 C38 *C39 H9X 1.5808 114.97 -120.44 103.80 1.1109 +IC H9X C38 *C39 H9Y 1.1109 103.80 -119.52 109.32 1.1115 +IC C38 C39 C310 C311 1.4988 114.97 165.18 107.22 1.5315 +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5740 108.03 62.34 109.55 1.4587 +IC O12 C12 *C11 H11A 1.4587 109.55 -133.45 104.51 1.1111 +IC H11A C12 *C11 H11B 1.1111 104.51 -102.24 107.44 1.1106 +IC C12 C11 O12 P 1.6269 109.55 -163.53 109.35 1.5489 +IC C11 O12 P O11 1.4587 109.35 45.61 102.47 1.5319 +IC O11 O12 *P O13 1.5319 102.47 -122.17 109.86 1.4873 +IC O11 O12 *P O14 1.5319 102.47 113.34 104.82 1.5089 +IC O12 P O11 C1 1.5489 102.47 -127.21 119.35 1.4081 +IC P O11 C1 C2 1.5319 119.35 168.57 109.93 1.5357 +IC C2 O11 *C1 HA 1.5357 109.93 -115.95 114.29 1.1113 +IC HA O11 *C1 HB 1.1113 114.29 -119.43 108.09 1.1105 +IC O11 C1 C2 C3 1.4081 109.93 -76.32 112.50 1.5189 +IC C3 C1 *C2 O21 1.5189 112.50 124.83 107.78 1.3985 +IC C3 C1 *C2 HS 1.5189 112.50 -116.89 107.38 1.1110 +IC C1 C2 O21 C21 1.5357 107.78 69.98 118.97 1.3059 +IC C2 O21 C21 C22 1.3985 118.97 166.82 107.13 1.5380 +IC C22 O21 *C21 O22 1.5380 107.13 -170.88 125.96 1.1735 +IC O21 C21 C22 C23 1.3059 107.13 -129.04 116.72 1.5340 +IC C23 C21 *C22 H2R 1.5340 116.72 -121.20 110.01 1.1106 +IC H2R C21 *C22 H2S 1.1106 110.01 -115.57 107.31 1.1116 +IC C1 C2 C3 O31 1.5357 112.50 -174.65 112.28 1.4522 +IC O31 C2 *C3 HX 1.4522 112.28 -114.36 112.03 1.1112 +IC HX C2 *C3 HY 1.1112 112.03 -119.01 106.04 1.1105 +IC C2 C3 O31 C31 1.5189 112.28 103.03 115.31 1.4071 +IC C3 O31 C31 C32 1.4522 115.31 179.90 110.84 1.5158 +IC C32 O31 *C31 O32 1.5158 110.84 172.37 122.14 1.2201 +IC O31 C31 C32 C33 1.4071 110.84 -166.46 116.58 1.5719 +IC C33 C31 *C32 H2X 1.5719 116.58 -117.94 109.57 1.1109 +IC H2X C31 *C32 H2Y 1.1109 109.57 -123.57 102.64 1.1107 +IC C21 C22 C23 C24 1.5380 116.72 -80.26 109.08 1.5218 +IC C24 C22 *C23 H3R 1.5218 109.08 -124.90 105.17 1.1108 +IC H3R C22 *C23 H3S 1.1108 105.17 -108.19 105.63 1.1108 +IC C22 C23 C24 C25 1.5340 109.08 -159.22 112.40 1.5136 +IC C25 C23 *C24 H4R 1.5136 112.40 -135.93 110.03 1.1105 +IC H4R C23 *C24 H4S 1.1105 110.03 -107.07 104.29 1.1111 +IC C23 C24 C25 C26 1.5218 112.40 -43.61 120.64 1.5087 +IC C26 C24 *C25 H5R 1.5087 120.64 -131.32 113.13 1.1109 +IC H5R C24 *C25 H5S 1.1109 113.13 -114.79 101.24 1.1106 +IC C24 C25 C26 C27 1.5136 120.64 178.93 113.39 1.5700 +IC C27 C25 *C26 H6R 1.5700 113.39 -116.18 110.80 1.1108 +IC H6R C25 *C26 H6S 1.1108 110.80 -118.75 104.13 1.1118 +IC C25 C26 C27 C28 1.5087 113.39 72.57 109.72 1.5767 +IC C28 C26 *C27 H7R 1.5767 109.72 -120.46 112.93 1.1112 +IC H7R C26 *C27 H7S 1.1112 112.93 -119.62 110.82 1.1117 +IC C26 C27 C28 C29 1.5700 109.72 -173.11 106.46 1.5083 +IC C29 C27 *C28 H8R 1.5083 106.46 -122.48 110.55 1.1113 +IC H8R C27 *C28 H8S 1.1113 110.55 -116.67 104.62 1.1100 +IC C27 C28 C29 C210 1.5767 106.46 -147.88 120.94 1.4723 +IC C210 C28 *C29 C217 1.4723 120.94 70.58 114.54 1.5040 +IC C210 C28 *C29 H9R 1.4723 120.94 -159.53 113.14 1.1112 +IC C210 C29 *C217 H17R 1.5281 58.10 -112.42 111.09 1.0831 +IC C210 C29 *C217 H17S 1.5281 58.10 108.07 115.73 1.0825 +IC C217 C29 *C210 C211 1.5281 60.13 -104.81 121.09 1.5792 +IC C211 C29 *C210 H10R 1.5792 121.09 -151.97 117.51 1.1105 +IC C29 C210 C211 C212 1.4723 121.09 164.86 109.30 1.5195 +IC C212 C210 *C211 H11R 1.5195 109.30 -117.57 109.62 1.1114 +IC H11R C210 *C211 H11S 1.1114 109.62 -121.30 102.02 1.1114 +IC C210 C211 C212 C213 1.5792 109.30 174.67 109.83 1.5417 +IC C213 C211 *C212 H12R 1.5417 109.83 -120.12 111.78 1.1111 +IC H12R C211 *C212 H12S 1.1111 111.78 -117.04 109.60 1.1108 +IC C211 C212 C213 C214 1.5195 109.83 152.45 110.39 1.5837 +IC C214 C212 *C213 H13R 1.5837 110.39 -109.14 112.03 1.1114 +IC H13R C212 *C213 H13S 1.1114 112.03 -121.91 105.98 1.1107 +IC C212 C213 C214 C215 1.5417 110.39 -161.02 117.34 1.5467 +IC C215 C213 *C214 H14R 1.5467 117.34 -128.35 108.55 1.1111 +IC H14R C213 *C214 H14S 1.1111 108.55 -120.77 103.11 1.1107 +IC C213 C214 C215 C216 1.5837 117.34 136.15 109.27 1.5335 +IC C216 C214 *C215 H15R 1.5335 109.27 -117.30 111.58 1.1111 +IC H15R C214 *C215 H15S 1.1111 111.58 -116.62 107.49 1.1099 +IC C214 C215 C216 H16R 1.5467 109.27 77.67 107.75 1.1107 +IC H16R C215 *C216 H16S 1.1107 107.75 127.18 111.70 1.1109 +IC H16R C215 *C216 H16T 1.1107 107.75 -106.85 112.98 1.1113 +IC C31 C32 C33 C34 1.5158 116.58 -156.33 110.79 1.5385 +IC C34 C32 *C33 H3X 1.5385 110.79 -119.46 105.53 1.1099 +IC H3X C32 *C33 H3Y 1.1099 105.53 -124.63 112.06 1.1108 +IC C32 C33 C34 C35 1.5719 110.79 -164.94 113.24 1.5570 +IC C35 C33 *C34 H4X 1.5570 113.24 -115.88 103.84 1.1106 +IC H4X C33 *C34 H4Y 1.1106 103.84 -117.83 112.15 1.1111 +IC C33 C34 C35 C36 1.5385 113.24 -175.74 108.09 1.4998 +IC C36 C34 *C35 H5X 1.4998 108.09 -124.22 112.64 1.1110 +IC H5X C34 *C35 H5Y 1.1110 112.64 -112.55 111.15 1.1109 +IC C34 C35 C36 C37 1.5570 108.09 -170.32 111.91 1.6017 +IC C37 C35 *C36 H6X 1.6017 111.91 -113.57 111.94 1.1104 +IC H6X C35 *C36 H6Y 1.1104 111.94 -125.88 112.72 1.1112 +IC C35 C36 C37 C38 1.4998 111.91 -166.01 112.78 1.5291 +IC C38 C36 *C37 H7X 1.5291 112.78 -123.46 107.25 1.1111 +IC H7X C36 *C37 H7Y 1.1111 107.25 -118.21 107.27 1.1106 +IC C36 C37 C38 C39 1.6017 112.78 -59.37 115.90 1.4988 +IC C39 C37 *C38 H8X 1.4988 115.90 -121.29 104.94 1.1119 +IC H8X C37 *C38 H8Y 1.1119 104.94 -122.24 111.41 1.1102 +IC C37 C38 C39 C310 1.5291 115.90 173.72 114.97 1.5808 +IC C310 C38 *C39 H9X 1.5808 114.97 -120.44 103.80 1.1109 +IC H9X C38 *C39 H9Y 1.1109 103.80 -119.52 109.32 1.1115 +IC C38 C39 C310 C311 1.4988 114.97 165.18 107.22 1.5315 +IC C311 C39 *C310 H10X 1.5315 107.22 -112.11 98.67 1.1109 +IC H10X C39 *C310 H10Y 1.1109 98.67 -115.14 117.96 1.1111 +IC C39 C310 C311 C312 1.5808 107.22 -175.37 118.03 1.5172 +IC C312 C310 *C311 H11X 1.5172 118.03 -113.87 110.17 1.1112 +IC H11X C310 *C311 H11Y 1.1112 110.17 -114.37 110.15 1.1116 +IC C310 C311 C312 C313 1.5315 118.03 -173.25 108.85 1.5385 +IC C313 C311 *C312 H12X 1.5385 108.85 -124.55 114.43 1.1104 +IC H12X C311 *C312 H12Y 1.1104 114.43 -112.22 110.77 1.1108 +IC C311 C312 C313 C314 1.5172 108.85 -166.98 112.56 1.5808 +IC C314 C312 *C313 H13X 1.5808 112.56 -123.12 106.98 1.1111 +IC H13X C312 *C313 H13Y 1.1111 106.98 -119.68 107.09 1.1107 +IC C312 C313 C314 C315 1.5385 112.56 167.58 110.45 1.5917 +IC C315 C313 *C314 H14X 1.5917 110.45 -128.77 103.10 1.1105 +IC H14X C313 *C314 H14Y 1.1105 103.10 -111.23 111.53 1.1114 +IC C313 C314 C315 C316 1.5808 110.45 -172.95 109.13 1.6003 +IC C316 C314 *C315 H15X 1.6003 109.13 -127.12 115.64 1.1105 +IC H15X C314 *C315 H15Y 1.1105 115.64 -113.13 111.62 1.1114 +IC C314 C315 C316 H16X 1.5917 109.13 -79.50 115.10 1.1121 +IC H16X C315 *C316 H16Y 1.1121 115.10 -111.72 108.87 1.1109 +IC H16X C315 *C316 H16Z 1.1121 115.10 128.91 106.88 1.1103 + +RESI QMPE 0.00 ! PE-15:0/cy17:0 +! +! (June, 2010 Kunal Pandit) +! +! C15:0 - CH2 +! | +! cyC17:0 - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CG3RC1 -0.09 ! | | +ATOM H9R HGA1 0.09 ! H9R ---C29 H17R | +GROUP ! |\ / | +ATOM C217 CG3C31 -0.18 ! | \ / | +ATOM H17R HGA2 0.09 ! | C217 | +ATOM H17S HGA2 0.09 ! | / \ | +GROUP ! |/ \ | +ATOM C210 CG3RC1 -0.09 ! H10R ---C210 H17S | +ATOM H10R HGA1 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H121 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL3 -0.27 ! | +ATOM H15X HAL3 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL3 0.09 ! | +ATOM H15Z HAL3 0.09 ! H15Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 C210 C29 C217 +BOND C210 H10R C210 C211 C210 C217 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +BOND C217 H17R C217 H17S +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 H15Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, geometry from after equilib +IC HN1 C12 *N HN2 1.0398 108.49 120.70 111.21 1.0403 +IC HN1 C12 *N HN3 1.0398 108.49 -114.45 119.45 1.0398 +IC HN1 N C12 C11 1.0398 108.49 68.06 106.74 1.5427 +IC C11 N *C12 H12A 1.5427 106.74 -122.52 112.85 1.1111 +IC H12A N *C12 H12B 1.1111 112.85 -122.65 108.20 1.1115 +IC N C12 C11 O12 1.5033 106.74 64.41 108.34 1.4799 +IC O12 C12 *C11 H11A 1.4799 108.34 -130.75 109.17 1.1114 +IC H11A C12 *C11 H11B 1.1114 109.17 -107.67 107.31 1.1105 +IC C12 C11 O12 P 1.5427 108.34 -176.97 113.52 1.5614 +IC C11 O12 P O11 1.4799 113.52 73.49 102.39 1.5972 +IC O11 O12 *P O13 1.5972 102.39 -114.83 112.06 1.5001 +IC O11 O12 *P O14 1.5972 102.39 113.28 112.25 1.4988 +IC O12 P O11 C1 1.5614 102.39 42.14 117.80 1.4263 +IC P O11 C1 C2 1.5972 117.80 134.14 113.11 1.5665 +IC C2 O11 *C1 HA 1.5665 113.11 -121.46 108.89 1.1118 +IC HA O11 *C1 HB 1.1118 108.89 -119.56 112.88 1.1103 +IC O11 C1 C2 O21 1.4263 113.11 35.92 109.15 1.4167 +IC O21 C1 *C2 C3 1.4167 109.15 -118.43 114.81 1.5651 +IC C3 C1 *C2 HS 1.5651 114.81 -121.92 105.60 1.1115 +IC C1 C2 O21 C21 1.5665 109.15 69.86 114.03 1.3052 +IC C2 O21 C21 C22 1.4167 114.03 -178.62 109.36 1.4816 +IC C22 O21 *C21 O22 1.4816 109.36 -177.70 124.43 1.2156 +IC O21 C21 C22 C23 1.3052 109.36 -116.49 110.93 1.5398 +IC C23 C21 *C22 H2R 1.5398 110.93 -124.04 107.56 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.56 -117.99 109.45 1.1107 +IC C1 C2 C3 O31 1.5665 114.81 -175.15 110.73 1.3859 +IC O31 C2 *C3 HX 1.3859 110.73 -136.04 115.98 1.1110 +IC HX C2 *C3 HY 1.1110 115.98 -108.95 103.79 1.1115 +IC C2 C3 O31 C31 1.5651 110.73 -123.66 120.14 1.2986 +IC C3 O31 C31 C32 1.3859 120.14 -152.92 109.96 1.5052 +IC C32 O31 *C31 O32 1.5052 109.96 175.08 126.64 1.2334 +IC O31 C31 C32 C33 1.2986 109.96 -166.68 117.67 1.5245 +IC C33 C31 *C32 H2X 1.5245 117.67 124.10 109.07 1.1116 +IC H2X C31 *C32 H2Y 1.1116 109.07 117.19 104.21 1.1103 +IC C21 C22 C23 C24 1.4816 110.93 56.07 120.07 1.5366 +IC C24 C22 *C23 H3R 1.5366 120.07 -121.56 109.69 1.1109 +IC H3R C22 *C23 H3S 1.1109 109.69 -117.64 105.26 1.1101 +IC C22 C23 C24 C25 1.5398 120.07 63.29 114.83 1.4944 +IC C25 C23 *C24 H4R 1.4944 114.83 -120.76 105.54 1.1110 +IC H4R C23 *C24 H4S 1.1110 105.54 -120.05 113.18 1.1108 +IC C23 C24 C25 C26 1.5366 114.83 65.38 114.43 1.5286 +IC C24 C25 C26 C27 1.4944 114.43 72.51 109.88 1.4637 +IC C25 C26 C27 C28 1.5286 109.88 162.96 107.19 1.5822 +IC C26 C27 C28 C29 1.4637 107.19 -172.56 108.02 1.5492 +IC C27 C28 C29 C210 1.5822 108.02 -146.15 123.80 1.5401 +IC C28 C29 C210 C211 1.5492 123.80 -5.82 126.41 1.5802 +IC C29 C210 C211 C212 1.5401 126.41 -79.49 101.59 1.5101 +IC C210 C211 C212 C213 1.5802 101.59 -74.31 115.26 1.5320 +IC C211 C212 C213 C214 1.5101 115.26 -169.28 108.36 1.5416 +IC C212 C213 C214 C215 1.5320 108.36 -179.78 112.10 1.5699 +IC C213 C214 C215 C216 1.5416 112.10 -155.14 113.39 1.5161 +IC C27 C28 C29 C217 1.5822 108.02 -80.69 112.07 1.5545 +IC C28 C29 C217 C210 1.5492 112.07 -117.05 60.48 1.5021 +IC C29 C217 C210 C211 1.5545 60.48 119.15 115.86 1.5802 +IC C217 C210 C211 C212 1.5021 115.86 -151.88 101.59 1.5101 +IC C31 C32 C33 C34 1.5052 117.67 84.12 107.31 1.5220 +IC C34 C32 *C33 H3X 1.5220 107.31 -124.27 113.40 1.1113 +IC H3X C32 *C33 H3Y 1.1113 113.40 -112.17 114.59 1.1114 +IC C32 C33 C34 C35 1.5245 107.31 171.93 111.53 1.5255 +IC C35 C33 *C34 H4X 1.5255 111.53 -115.65 107.80 1.1109 +IC H4X C33 *C34 H4Y 1.1109 107.80 -119.94 104.52 1.1108 +IC C33 C34 C35 C36 1.5220 111.53 170.20 117.99 1.5486 +IC C36 C34 *C35 H5X 1.5486 117.99 -117.18 111.93 1.1112 +IC H5X C34 *C35 H5Y 1.1112 111.93 -117.44 113.54 1.1111 +IC C34 C35 C36 C37 1.5255 117.99 -164.96 120.25 1.5368 +IC C37 C35 *C36 H6X 1.5368 120.25 -122.07 109.99 1.1109 +IC H6X C35 *C36 H6Y 1.1109 109.99 -116.37 104.19 1.1112 +IC C35 C36 C37 C38 1.5486 120.25 -49.68 114.29 1.5306 +IC C38 C36 *C37 H7X 1.5306 114.29 120.09 110.67 1.1110 +IC H7X C36 *C37 H7Y 1.1110 110.67 118.73 103.85 1.1110 +IC C36 C37 C38 C39 1.5368 114.29 -175.31 112.39 1.6625 +IC C39 C37 *C38 H8X 1.6625 112.39 125.03 111.00 1.1110 +IC H8X C37 *C38 H8Y 1.1110 111.00 119.11 110.20 1.1104 +IC C37 C38 C39 C310 1.5306 112.39 -70.93 114.13 1.5153 +IC C310 C38 *C39 H9X 1.5153 114.13 -121.79 105.54 1.1110 +IC H9X C38 *C39 H9Y 1.1110 105.54 -112.48 106.93 1.1109 +IC C38 C39 C310 C311 1.6625 114.13 -159.26 114.48 1.5717 +IC HN1 C12 *N HN2 1.0398 108.49 120.70 111.21 1.0403 +IC HN1 C12 *N HN3 1.0398 108.49 -114.45 119.45 1.0398 +IC HN1 N C12 C11 1.0398 108.49 68.06 106.74 1.5427 +IC C11 N *C12 H12A 1.5427 106.74 -122.52 112.85 1.1111 +IC H12A N *C12 H12B 1.1111 112.85 -122.65 108.20 1.1115 +IC N C12 C11 O12 1.5033 106.74 64.41 108.34 1.4799 +IC O12 C12 *C11 H11A 1.4799 108.34 -130.75 109.17 1.1114 +IC H11A C12 *C11 H11B 1.1114 109.17 -107.67 107.31 1.1105 +IC C12 C11 O12 P 1.5427 108.34 -176.97 113.52 1.5614 +IC C11 O12 P O11 1.4799 113.52 73.49 102.39 1.5972 +IC O11 O12 *P O13 1.5972 102.39 -114.83 112.06 1.5001 +IC O11 O12 *P O14 1.5972 102.39 113.28 112.25 1.4988 +IC O12 P O11 C1 1.5614 102.39 42.14 117.80 1.4263 +IC P O11 C1 C2 1.5972 117.80 134.14 113.11 1.5665 +IC C2 O11 *C1 HA 1.5665 113.11 -121.46 108.89 1.1118 +IC HA O11 *C1 HB 1.1118 108.89 -119.56 112.88 1.1103 +IC O11 C1 C2 O21 1.4263 113.11 35.92 109.15 1.4167 +IC O21 C1 *C2 C3 1.4167 109.15 -118.43 114.81 1.5651 +IC C3 C1 *C2 HS 1.5651 114.81 -121.92 105.60 1.1115 +IC C1 C2 O21 C21 1.5665 109.15 69.86 114.03 1.3052 +IC C2 O21 C21 C22 1.4167 114.03 -178.62 109.36 1.4816 +IC C22 O21 *C21 O22 1.4816 109.36 -177.70 124.43 1.2156 +IC O21 C21 C22 C23 1.3052 109.36 -116.49 110.93 1.5398 +IC C23 C21 *C22 H2R 1.5398 110.93 -124.04 107.56 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.56 -117.99 109.45 1.1107 +IC C1 C2 C3 O31 1.5665 114.81 -175.15 110.73 1.3859 +IC O31 C2 *C3 HX 1.3859 110.73 -136.04 115.98 1.1110 +IC HX C2 *C3 HY 1.1110 115.98 -108.95 103.79 1.1115 +IC C2 C3 O31 C31 1.5651 110.73 -123.66 120.14 1.2986 +IC C3 O31 C31 C32 1.3859 120.14 -152.92 109.96 1.5052 +IC C32 O31 *C31 O32 1.5052 109.96 175.08 126.64 1.2334 +IC O31 C31 C32 C33 1.2986 109.96 -166.68 117.67 1.5245 +IC C33 C31 *C32 H2X 1.5245 117.67 124.10 109.07 1.1116 +IC H2X C31 *C32 H2Y 1.1116 109.07 117.19 104.21 1.1103 +IC C21 C22 C23 C24 1.4816 110.93 56.07 120.07 1.5366 +IC C24 C22 *C23 H3R 1.5366 120.07 -121.56 109.69 1.1109 +IC H3R C22 *C23 H3S 1.1109 109.69 -117.64 105.26 1.1101 +IC C22 C23 C24 C25 1.5398 120.07 63.29 114.83 1.4944 +IC C25 C23 *C24 H4R 1.4944 114.83 -120.76 105.54 1.1110 +IC H4R C23 *C24 H4S 1.1110 105.54 -120.05 113.18 1.1108 +IC C23 C24 C25 C26 1.5366 114.83 65.38 114.43 1.5286 +IC C26 C24 *C25 H5R 1.5286 114.43 -126.04 115.81 1.1112 +IC H5R C24 *C25 H5S 1.1112 115.81 -120.48 106.68 1.1105 +IC C24 C25 C26 C27 1.4944 114.43 72.51 109.88 1.4637 +IC C27 C25 *C26 H6R 1.4637 109.88 -134.30 119.35 1.1112 +IC H6R C25 *C26 H6S 1.1112 119.35 -117.00 103.34 1.1115 +IC C25 C26 C27 C28 1.5286 109.88 162.96 107.19 1.5822 +IC C28 C26 *C27 H7R 1.5822 107.19 -114.78 105.46 1.1114 +IC H7R C26 *C27 H7S 1.1114 105.46 -116.74 115.88 1.1110 +IC C26 C27 C28 C29 1.4637 107.19 -172.56 108.02 1.5492 +IC C29 C27 *C28 H8R 1.5492 108.02 -120.93 113.31 1.1108 +IC H8R C27 *C28 H8S 1.1108 113.31 -123.30 109.35 1.1106 +IC C27 C28 C29 C210 1.5822 108.02 -146.15 123.80 1.5401 +IC C210 C28 *C29 C217 1.5401 123.80 65.46 112.07 1.5545 +IC C210 C28 *C29 H9R 1.5401 123.80 -159.53 116.49 1.1108 +IC C210 C29 *C217 H17R 1.5021 60.48 102.40 112.44 1.0822 +IC C210 C29 *C217 H17S 1.5021 60.48 -101.70 111.32 1.0830 +IC C217 C29 *C210 C211 1.5021 61.44 -102.46 126.41 1.5802 +IC C211 C29 *C210 H10R 1.5802 126.41 -166.30 115.43 1.1107 +IC C29 C210 C211 C212 1.5401 126.41 -79.49 101.59 1.5101 +IC C212 C210 *C211 H11R 1.5101 101.59 117.92 106.95 1.1111 +IC H11R C210 *C211 H11S 1.1111 106.95 116.16 109.60 1.1106 +IC C210 C211 C212 C213 1.5802 101.59 -74.31 115.26 1.5320 +IC C213 C211 *C212 H12R 1.5320 115.26 -118.75 104.97 1.1118 +IC H12R C211 *C212 H12S 1.1118 104.97 -113.03 112.81 1.1108 +IC C211 C212 C213 C214 1.5101 115.26 -169.28 108.36 1.5416 +IC C214 C212 *C213 H13R 1.5416 108.36 -125.71 116.43 1.1103 +IC H13R C212 *C213 H13S 1.1103 116.43 -120.83 111.50 1.1106 +IC C212 C213 C214 C215 1.5320 108.36 -179.78 112.10 1.5699 +IC C215 C213 *C214 H14R 1.5699 112.10 -119.81 100.36 1.1104 +IC H14R C213 *C214 H14S 1.1104 100.36 -116.36 112.10 1.1112 +IC C213 C214 C215 C216 1.5416 112.10 -155.14 113.39 1.5161 +IC C216 C214 *C215 H15R 1.5161 113.39 -123.06 111.63 1.1110 +IC H15R C214 *C215 H15S 1.1110 111.63 -120.45 108.54 1.1114 +IC C214 C215 C216 H16R 1.5699 113.39 -178.84 109.17 1.1118 +IC H16R C215 *C216 H16S 1.1118 109.17 -111.81 105.59 1.1104 +IC H16R C215 *C216 H16T 1.1118 109.17 128.03 107.11 1.1106 +IC C31 C32 C33 C34 1.5052 117.67 84.12 107.31 1.5220 +IC C34 C32 *C33 H3X 1.5220 107.31 -124.27 113.40 1.1113 +IC H3X C32 *C33 H3Y 1.1113 113.40 -112.17 114.59 1.1114 +IC C32 C33 C34 C35 1.5245 107.31 171.93 111.53 1.5255 +IC C35 C33 *C34 H4X 1.5255 111.53 -115.65 107.80 1.1109 +IC H4X C33 *C34 H4Y 1.1109 107.80 -119.94 104.52 1.1108 +IC C33 C34 C35 C36 1.5220 111.53 170.20 117.99 1.5486 +IC C36 C34 *C35 H5X 1.5486 117.99 -117.18 111.93 1.1112 +IC H5X C34 *C35 H5Y 1.1112 111.93 -117.44 113.54 1.1111 +IC C34 C35 C36 C37 1.5255 117.99 -164.96 120.25 1.5368 +IC C37 C35 *C36 H6X 1.5368 120.25 -122.07 109.99 1.1109 +IC H6X C35 *C36 H6Y 1.1109 109.99 -116.37 104.19 1.1112 +IC C35 C36 C37 C38 1.5486 120.25 -49.68 114.29 1.5306 +IC C38 C36 *C37 H7X 1.5306 114.29 120.09 110.67 1.1110 +IC H7X C36 *C37 H7Y 1.1110 110.67 118.73 103.85 1.1110 +IC C36 C37 C38 C39 1.5368 114.29 -175.31 112.39 1.6625 +IC C39 C37 *C38 H8X 1.6625 112.39 125.03 111.00 1.1110 +IC H8X C37 *C38 H8Y 1.1110 111.00 119.11 110.20 1.1104 +IC C37 C38 C39 C310 1.5306 112.39 -70.93 114.13 1.5153 +IC C310 C38 *C39 H9X 1.5153 114.13 -121.79 105.54 1.1110 +IC H9X C38 *C39 H9Y 1.1110 105.54 -112.48 106.93 1.1109 +IC C38 C39 C310 C311 1.6625 114.13 -159.26 114.48 1.5717 +IC C311 C39 *C310 H10X 1.5717 114.48 -123.50 105.06 1.1117 +IC H10X C39 *C310 H10Y 1.1117 105.06 -106.86 112.47 1.1116 +IC C39 C310 C311 C312 1.5153 114.48 -71.88 118.27 1.5909 +IC C312 C310 *C311 H11X 1.5909 118.27 -130.45 105.63 1.1107 +IC H11X C310 *C311 H11Y 1.1107 105.63 -112.51 105.79 1.1113 +IC C310 C311 C312 C313 1.5717 118.27 168.05 115.70 1.5434 +IC C313 C311 *C312 H12X 1.5434 115.70 -124.69 106.80 1.1109 +IC H12X C311 *C312 H12Y 1.1109 106.80 -115.23 106.21 1.1114 +IC C311 C312 C313 C314 1.5909 115.70 -179.90 106.30 1.5984 +IC C314 C312 *C313 H13X 1.5984 106.30 125.90 113.51 1.1113 +IC H13X C312 *C313 H13Y 1.1113 113.51 113.08 105.32 1.1113 +IC C312 C313 C314 C315 1.5434 106.30 -173.09 113.30 1.5317 +IC C315 C313 *C314 H14X 1.5317 113.30 -118.71 112.10 1.1114 +IC H14X C313 *C314 H14Y 1.1114 112.10 -117.61 110.72 1.1104 +IC C313 C314 C315 H15X 1.5984 113.30 38.53 114.00 1.1117 +IC H15X C314 *C315 H15Y 1.1117 114.00 122.60 103.30 1.1109 +IC H15X C314 *C315 H15Z 1.1117 114.00 -119.17 112.56 1.1108 + +RESI OSPE 0.00 ! 1-palmytoil-2-oleoyl-sn-glycero-3-Phosphatidylethanolamine (jun07_1d_0.09 ester charges) +! +! (June, 2010 Kunal Pandit) +! +! Oleyl - CH2 +! | +! Sapienyl- CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || (CIS) +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, geometry is optimized +IC HN1 C12 *N HN2 1.0404 106.34 113.99 106.80 1.0405 +IC HN1 C12 *N HN3 1.0404 106.34 -126.93 118.51 1.0401 +IC HN1 N C12 C11 1.0404 106.34 65.98 109.57 1.5189 +IC C11 N *C12 H12A 1.5189 109.57 -124.87 113.96 1.1106 +IC H12A N *C12 H12B 1.1106 113.96 -116.01 108.13 1.1113 +IC N C12 C11 O12 1.4532 109.57 -91.00 111.09 1.4004 +IC O12 C12 *C11 H11A 1.4004 111.09 -120.66 102.68 1.1106 +IC H11A C12 *C11 H11B 1.1106 102.68 -118.87 114.36 1.1110 +IC C12 C11 O12 P 1.5189 111.09 -94.89 122.55 1.5678 +IC C11 O12 P O11 1.4004 122.55 -97.36 102.05 1.5777 +IC O11 O12 *P O13 1.5777 102.05 -118.18 105.42 1.4559 +IC O11 O12 *P O14 1.5777 102.05 115.61 112.94 1.5066 +IC O12 P O11 C1 1.5678 102.05 -32.17 120.35 1.4391 +IC P O11 C1 C2 1.5777 120.35 133.40 113.82 1.5437 +IC C2 O11 *C1 HA 1.5437 113.82 -116.79 109.98 1.1104 +IC HA O11 *C1 HB 1.1104 109.98 -116.24 109.93 1.1109 +IC O11 C1 C2 O21 1.4391 113.82 59.55 105.26 1.4954 +IC O21 C1 *C2 C3 1.4954 105.26 -118.34 113.34 1.5094 +IC C3 C1 *C2 HS 1.5094 113.34 -123.85 103.48 1.1108 +IC C1 C2 O21 C21 1.5437 105.26 79.30 114.36 1.2853 +IC C2 O21 C21 C22 1.4954 114.36 175.69 103.31 1.5206 +IC C22 O21 *C21 O22 1.5206 103.31 176.88 126.70 1.1735 +IC O21 C21 C22 C23 1.2853 103.31 -139.28 107.70 1.5451 +IC C23 C21 *C22 H2R 1.5451 107.70 -123.93 108.08 1.1109 +IC H2R C21 *C22 H2S 1.1109 108.08 -118.18 111.84 1.1106 +IC C1 C2 C3 O31 1.5437 113.34 -171.03 110.16 1.4822 +IC O31 C2 *C3 HX 1.4822 110.16 -133.56 114.42 1.1115 +IC HX C2 *C3 HY 1.1115 114.42 -115.92 105.00 1.1101 +IC C2 C3 O31 C31 1.5094 110.16 -127.22 112.79 1.3758 +IC C3 O31 C31 C32 1.4822 112.79 171.14 112.83 1.5026 +IC C32 O31 *C31 O32 1.5026 112.83 179.53 119.25 1.2029 +IC O31 C31 C32 C33 1.3758 112.83 -179.03 110.92 1.5498 +IC C33 C31 *C32 H2X 1.5498 110.92 114.27 108.67 1.1109 +IC H2X C31 *C32 H2Y 1.1109 108.67 120.62 109.24 1.1107 +IC C21 C22 C23 C24 1.5206 107.70 66.12 113.81 1.5683 +IC C24 C22 *C23 H3R 1.5683 113.81 -118.21 112.06 1.1116 +IC H3R C22 *C23 H3S 1.1116 112.06 -120.09 108.20 1.1106 +IC C22 C23 C24 C25 1.5451 113.81 61.56 110.87 1.5851 +IC C25 C23 *C24 H4R 1.5851 110.87 -124.43 111.86 1.1106 +IC H4R C23 *C24 H4S 1.1106 111.86 -114.23 112.18 1.1111 +IC C23 C24 C25 C26 1.5683 110.87 158.22 112.90 1.5880 +IC C26 C24 *C25 H5R 1.5880 112.90 -119.61 110.88 1.1110 +IC H5R C24 *C25 H5S 1.1110 110.88 -128.44 110.21 1.1106 +IC C24 C25 C26 C27 1.5851 112.90 44.43 116.71 1.5441 +IC C27 C25 *C26 H6R 1.5441 116.71 -127.96 111.27 1.1109 +IC H6R C25 *C26 H6S 1.1109 111.27 -113.35 108.47 1.1107 +IC C25 C26 C27 C28 1.5880 116.71 169.49 114.17 1.5757 +IC C28 C26 *C27 H7R 1.5757 114.17 -121.65 108.14 1.1111 +IC H7R C26 *C27 H7S 1.1111 108.14 -116.38 112.13 1.1110 +IC C26 C27 C28 C29 1.5441 114.17 -68.77 111.18 1.5005 +IC C29 C27 *C28 H8R 1.5005 111.18 -114.50 105.38 1.1106 +IC H8R C27 *C28 H8S 1.1106 105.38 -114.72 104.33 1.1114 +IC C27 C28 C29 C210 1.5757 111.18 -98.02 127.21 1.3150 +IC C28 C29 C210 C211 1.5005 127.21 8.98 131.89 1.4783 +IC C29 C210 C211 C212 1.3150 131.89 -93.02 109.57 1.5301 +IC C31 C32 C33 C34 1.5026 110.92 -171.55 105.74 1.4894 +IC C34 C32 *C33 H3X 1.4894 105.74 -122.53 113.04 1.1114 +IC H3X C32 *C33 H3Y 1.1114 113.04 -127.30 111.94 1.1116 +IC C32 C33 C34 C35 1.5498 105.74 158.44 113.31 1.5775 +IC C35 C33 *C34 H4X 1.5775 113.31 129.09 117.98 1.1116 +IC H4X C33 *C34 H4Y 1.1116 117.98 114.50 105.12 1.1110 +IC C33 C34 C35 C36 1.4894 113.31 -178.41 117.04 1.5784 +IC C36 C34 *C35 H5X 1.5784 117.04 -116.07 109.82 1.1105 +IC H5X C34 *C35 H5Y 1.1105 109.82 -118.00 104.69 1.1105 +IC C34 C35 C36 C37 1.5775 117.04 -75.56 108.42 1.5409 +IC C37 C35 *C36 H6X 1.5409 108.42 124.40 109.51 1.1100 +IC H6X C35 *C36 H6Y 1.1100 109.51 119.06 102.21 1.1112 +IC C35 C36 C37 C38 1.5784 108.42 171.66 109.49 1.5256 +IC C38 C36 *C37 H7X 1.5256 109.49 119.29 108.23 1.1107 +IC H7X C36 *C37 H7Y 1.1107 108.23 129.15 104.13 1.1104 +IC C36 C37 C38 C39 1.5409 109.49 172.55 110.52 1.5303 +IC C39 C37 *C38 H8X 1.5303 110.52 121.46 114.78 1.1108 +IC H8X C37 *C38 H8Y 1.1108 114.78 117.08 105.83 1.1113 +IC C37 C38 C39 C310 1.5256 110.52 -156.58 120.38 1.3404 +IC C39 C310 C311 C312 1.3404 128.10 153.38 113.65 1.5340 +IC C314 C315 C316 C317 1.5703 113.05 176.49 113.95 1.5795 +IC C315 C316 C317 C318 1.5309 113.95 175.69 114.09 1.5595 +IC HN1 C12 *N HN2 1.0404 106.34 113.99 106.80 1.0405 +IC HN1 C12 *N HN3 1.0404 106.34 -126.93 118.51 1.0401 +IC HN1 N C12 C11 1.0404 106.34 65.98 109.57 1.5189 +IC C11 N *C12 H12A 1.5189 109.57 -124.87 113.96 1.1106 +IC H12A N *C12 H12B 1.1106 113.96 -116.01 108.13 1.1113 +IC N C12 C11 O12 1.4532 109.57 -91.00 111.09 1.4004 +IC O12 C12 *C11 H11A 1.4004 111.09 -120.66 102.68 1.1106 +IC H11A C12 *C11 H11B 1.1106 102.68 -118.87 114.36 1.1110 +IC C12 C11 O12 P 1.5189 111.09 -94.89 122.55 1.5678 +IC C11 O12 P O11 1.4004 122.55 -97.36 102.05 1.5777 +IC O11 O12 *P O13 1.5777 102.05 -118.18 105.42 1.4559 +IC O11 O12 *P O14 1.5777 102.05 115.61 112.94 1.5066 +IC O12 P O11 C1 1.5678 102.05 -32.17 120.35 1.4391 +IC P O11 C1 C2 1.5777 120.35 133.40 113.82 1.5437 +IC C2 O11 *C1 HA 1.5437 113.82 -116.79 109.98 1.1104 +IC HA O11 *C1 HB 1.1104 109.98 -116.24 109.93 1.1109 +IC O11 C1 C2 C3 1.4391 113.82 -58.79 113.34 1.5094 +IC C3 C1 *C2 O21 1.5094 113.34 118.34 105.26 1.4954 +IC C3 C1 *C2 HS 1.5094 113.34 -123.85 103.48 1.1108 +IC C1 C2 O21 C21 1.5437 105.26 79.30 114.36 1.2853 +IC C2 O21 C21 C22 1.4954 114.36 175.69 103.31 1.5206 +IC C22 O21 *C21 O22 1.5206 103.31 176.88 126.70 1.1735 +IC O21 C21 C22 C23 1.2853 103.31 -139.28 107.70 1.5451 +IC C23 C21 *C22 H2R 1.5451 107.70 -123.93 108.08 1.1109 +IC H2R C21 *C22 H2S 1.1109 108.08 -118.18 111.84 1.1106 +IC C1 C2 C3 O31 1.5437 113.34 -171.03 110.16 1.4822 +IC O31 C2 *C3 HX 1.4822 110.16 -133.56 114.42 1.1115 +IC HX C2 *C3 HY 1.1115 114.42 -115.92 105.00 1.1101 +IC C2 C3 O31 C31 1.5094 110.16 -127.22 112.79 1.3758 +IC C3 O31 C31 C32 1.4822 112.79 171.14 112.83 1.5026 +IC C32 O31 *C31 O32 1.5026 112.83 179.53 119.25 1.2029 +IC O31 C31 C32 C33 1.3758 112.83 -179.03 110.92 1.5498 +IC C33 C31 *C32 H2X 1.5498 110.92 114.27 108.67 1.1109 +IC H2X C31 *C32 H2Y 1.1109 108.67 120.62 109.24 1.1107 +IC C21 C22 C23 C24 1.5206 107.70 66.12 113.81 1.5683 +IC C24 C22 *C23 H3R 1.5683 113.81 -118.21 112.06 1.1116 +IC H3R C22 *C23 H3S 1.1116 112.06 -120.09 108.20 1.1106 +IC C22 C23 C24 C25 1.5451 113.81 61.56 110.87 1.5851 +IC C25 C23 *C24 H4R 1.5851 110.87 -124.43 111.86 1.1106 +IC H4R C23 *C24 H4S 1.1106 111.86 -114.23 112.18 1.1111 +IC C23 C24 C25 C26 1.5683 110.87 158.22 112.90 1.5880 +IC C26 C24 *C25 H5R 1.5880 112.90 -119.61 110.88 1.1110 +IC H5R C24 *C25 H5S 1.1110 110.88 -128.44 110.21 1.1106 +IC C24 C25 C26 C27 1.5851 112.90 44.43 116.71 1.5441 +IC C27 C25 *C26 H6R 1.5441 116.71 -127.96 111.27 1.1109 +IC H6R C25 *C26 H6S 1.1109 111.27 -113.35 108.47 1.1107 +IC C25 C26 C27 C28 1.5880 116.71 169.49 114.17 1.5757 +IC C28 C26 *C27 H7R 1.5757 114.17 -121.65 108.14 1.1111 +IC H7R C26 *C27 H7S 1.1111 108.14 -116.38 112.13 1.1110 +IC C26 C27 C28 C29 1.5441 114.17 -68.77 111.18 1.5005 +IC C29 C27 *C28 H8R 1.5005 111.18 -114.50 105.38 1.1106 +IC H8R C27 *C28 H8S 1.1106 105.38 -114.72 104.33 1.1114 +IC C27 C28 C29 C210 1.5757 111.18 -98.02 127.21 1.3150 +IC C210 C28 *C29 H9R 1.3150 127.21 -176.13 118.43 1.0995 +IC C28 C29 C210 C211 1.5005 127.21 8.98 131.89 1.4783 +IC C211 C29 *C210 H10R 1.4783 131.89 166.68 111.76 1.0998 +IC C29 C210 C211 C212 1.3150 131.89 -93.02 109.57 1.5301 +IC C212 C210 *C211 H11R 1.5301 109.57 -113.33 112.63 1.1108 +IC H11R C210 *C211 H11S 1.1108 112.63 -120.21 113.73 1.1113 +IC C210 C211 C212 C213 1.4783 109.57 -70.77 112.58 1.5470 +IC C213 C211 *C212 H12R 1.5470 112.58 -121.08 109.36 1.1107 +IC H12R C211 *C212 H12S 1.1107 109.36 -113.48 107.05 1.1114 +IC C211 C212 C213 C214 1.5301 112.58 176.12 112.10 1.4804 +IC C214 C212 *C213 H13R 1.4804 112.10 -114.96 106.41 1.1111 +IC H13R C212 *C213 H13S 1.1111 106.41 -122.58 110.52 1.1105 +IC C212 C213 C214 C215 1.5470 112.10 176.80 113.58 1.5562 +IC C215 C213 *C214 H14R 1.5562 113.58 -124.82 110.07 1.1117 +IC H14R C213 *C214 H14S 1.1117 110.07 -110.18 110.21 1.1107 +IC C213 C214 C215 C216 1.4804 113.58 174.37 112.69 1.4794 +IC C216 C214 *C215 H15R 1.4794 112.69 -120.63 100.31 1.1108 +IC H15R C214 *C215 H15S 1.1108 100.31 -119.13 108.76 1.1113 +IC C214 C215 C216 H16R 1.5562 112.69 -70.47 109.45 1.1118 +IC H16R C215 *C216 H16S 1.1118 109.45 -119.27 117.08 1.1114 +IC H16R C215 *C216 H16T 1.1118 109.45 111.51 112.83 1.1111 +IC C31 C32 C33 C34 1.5026 110.92 -171.55 105.74 1.4894 +IC C34 C32 *C33 H3X 1.4894 105.74 -122.53 113.04 1.1114 +IC H3X C32 *C33 H3Y 1.1114 113.04 -127.30 111.94 1.1116 +IC C32 C33 C34 C35 1.5498 105.74 158.44 113.31 1.5775 +IC C35 C33 *C34 H4X 1.5775 113.31 129.09 117.98 1.1116 +IC H4X C33 *C34 H4Y 1.1116 117.98 114.50 105.12 1.1110 +IC C33 C34 C35 C36 1.4894 113.31 -178.41 117.04 1.5784 +IC C36 C34 *C35 H5X 1.5784 117.04 -116.07 109.82 1.1105 +IC H5X C34 *C35 H5Y 1.1105 109.82 -118.00 104.69 1.1105 +IC C34 C35 C36 C37 1.5775 117.04 -75.56 108.42 1.5409 +IC C37 C35 *C36 H6X 1.5409 108.42 124.40 109.51 1.1100 +IC H6X C35 *C36 H6Y 1.1100 109.51 119.06 102.21 1.1112 +IC C35 C36 C37 C38 1.5784 108.42 171.66 109.49 1.5256 +IC C38 C36 *C37 H7X 1.5256 109.49 119.29 108.23 1.1107 +IC H7X C36 *C37 H7Y 1.1107 108.23 129.15 104.13 1.1104 +IC C36 C37 C38 C39 1.5409 109.49 172.55 110.52 1.5303 +IC C39 C37 *C38 H8X 1.5303 110.52 121.46 114.78 1.1108 +IC H8X C37 *C38 H8Y 1.1108 114.78 117.08 105.83 1.1113 +IC C37 C38 C39 C310 1.5256 110.52 -156.58 120.38 1.3404 +IC C310 C38 *C39 H9X 1.3404 120.38 -170.76 120.04 1.0998 +IC C38 C39 C310 C311 1.5303 120.38 6.62 128.10 1.4972 +IC C311 C39 *C310 H10X 1.4972 128.10 179.88 115.30 1.0995 +IC C39 C310 C311 C312 1.3404 128.10 153.38 113.65 1.5340 +IC C312 C310 *C311 H11X 1.5340 113.65 120.38 109.64 1.1104 +IC H11X C310 *C311 H11Y 1.1104 109.64 125.44 113.60 1.1114 +IC C310 C311 C312 C313 1.4972 113.65 -171.92 110.74 1.5242 +IC C313 C311 *C312 H12X 1.5242 110.74 -115.22 107.62 1.1108 +IC H12X C311 *C312 H12Y 1.1108 107.62 -125.34 111.30 1.1113 +IC C311 C312 C313 C314 1.5340 110.74 -168.86 112.68 1.5508 +IC C314 C312 *C313 H13X 1.5508 112.68 123.52 109.69 1.1106 +IC H13X C312 *C313 H13Y 1.1106 109.69 112.67 112.39 1.1110 +IC C312 C313 C314 C315 1.5242 112.68 176.45 110.39 1.5703 +IC C315 C313 *C314 H14X 1.5703 110.39 -127.56 109.72 1.1105 +IC H14X C313 *C314 H14Y 1.1105 109.72 -118.49 110.40 1.1107 +IC C313 C314 C315 C316 1.5508 110.39 56.35 113.05 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.05 -121.73 109.73 1.1114 +IC H15X C314 *C315 H15Y 1.1114 109.73 -118.09 109.07 1.1114 +IC C314 C315 C316 C317 1.5703 113.05 176.49 113.95 1.5795 +IC C317 C315 *C316 H16X 1.5795 113.95 -128.63 111.32 1.1111 +IC H16X C315 *C316 H16Y 1.1111 111.32 -126.51 101.03 1.1111 +IC C315 C316 C317 C318 1.5309 113.95 175.69 114.09 1.5595 +IC C318 C316 *C317 H17X 1.5595 114.09 -127.09 112.35 1.1107 +IC H17X C316 *C317 H17Y 1.1107 112.35 -118.73 101.41 1.1111 +IC C316 C317 C318 H18X 1.5795 114.09 55.80 106.86 1.1112 +IC H18X C317 *C318 H18Y 1.1112 106.86 123.78 110.51 1.1113 +IC H18X C317 *C318 H18Z 1.1112 106.86 -116.14 106.87 1.1105 + +RESI PSPG -1.00 ! PG-16:0/16:1 +! (June, 2010 Kunal Pandit) +! +! Palmytoil - CH2 +! | +! Sapienyl- CH +! | +! CH2 - PO4 - CH2 - CH(OH) - CH2OH +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.66 ! | +ATOM HO3 HOL 0.43 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.66 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.43 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! ||(cis) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, geometry is guessed +IC O12 C11 C12 C13 1.4509 114.21 165.56 117.48 1.5704 +IC O12 C11 C12 OC2 1.4509 114.21 -73.69 110.87 1.4782 +IC C11 C12 C13 OC3 1.5204 117.48 -61.28 112.21 1.4532 +IC OC2 C12 C13 OC3 1.4782 105.03 174.98 112.21 1.4532 +IC C12 C11 O12 P 1.5204 114.21 -92.56 121.65 1.6004 +IC C11 O12 P O11 1.4509 121.65 -47.76 105.22 1.6251 +IC O11 O12 *P O13 1.6251 105.22 -115.08 110.24 1.4953 +IC O11 O12 *P O14 1.6251 105.22 115.98 108.20 1.4712 +IC O12 P O11 C1 1.6004 105.22 98.75 114.06 1.4856 +IC P O11 C1 C2 1.6251 114.06 -166.06 109.38 1.4913 +IC C2 O11 *C1 HA 1.4913 109.38 -108.65 107.97 1.1116 +IC HA O11 *C1 HB 1.1116 107.97 -129.35 122.45 1.1106 +IC O11 C1 C2 O21 1.4856 109.38 -78.70 111.99 1.4830 +IC O21 C1 *C2 C3 1.4830 111.99 -126.22 112.96 1.5836 +IC C3 C1 *C2 HS 1.5836 112.96 -114.71 112.27 1.1110 +IC C1 C2 O21 C21 1.4913 111.99 156.97 118.33 1.2837 +IC C2 O21 C21 C22 1.4830 118.33 -175.15 106.26 1.5296 +IC C22 O21 *C21 O22 1.5296 106.26 177.78 128.83 1.2139 +IC O21 C21 C22 C23 1.2837 106.26 -65.42 111.80 1.5340 +IC C23 C21 *C22 H2R 1.5340 111.80 -123.52 110.15 1.1118 +IC H2R C21 *C22 H2S 1.1118 110.15 -114.43 113.12 1.1108 +IC C1 C2 C3 O31 1.4913 112.96 67.86 110.41 1.4280 +IC O31 C2 *C3 HX 1.4280 110.41 -117.67 110.41 1.1106 +IC HX C2 *C3 HY 1.1106 110.41 -116.34 104.49 1.1106 +IC C2 C3 O31 C31 1.5836 110.41 158.38 111.76 1.3559 +IC C3 O31 C31 C32 1.4280 111.76 173.15 111.04 1.5651 +IC C32 O31 *C31 O32 1.5651 111.04 -178.50 125.22 1.2028 +IC O31 C31 C32 C33 1.3559 111.04 136.55 111.38 1.5412 +IC C33 C31 *C32 H2X 1.5412 111.38 115.03 113.20 1.1108 +IC H2X C31 *C32 H2Y 1.1108 113.20 123.96 111.62 1.1110 +IC C21 C22 C23 C24 1.5296 111.80 -74.89 116.02 1.5995 +IC C24 C22 *C23 H3R 1.5995 116.02 -116.95 110.31 1.1115 +IC H3R C22 *C23 H3S 1.1115 110.31 -117.60 113.33 1.1109 +IC C22 C23 C24 C25 1.5340 116.02 -58.62 114.95 1.5046 +IC C25 C23 *C24 H4R 1.5046 114.95 -126.86 112.82 1.1113 +IC H4R C23 *C24 H4S 1.1113 112.82 -107.67 103.55 1.1100 +IC C23 C24 C25 C26 1.5995 114.95 -167.81 111.59 1.5208 +IC C26 C24 *C25 H5R 1.5208 111.59 -121.19 103.95 1.1114 +IC H5R C24 *C25 H5S 1.1114 103.95 -106.49 111.36 1.1104 +IC C24 C25 C26 C27 1.5046 111.59 92.34 113.87 1.6002 +IC C27 C25 *C26 H6R 1.6002 113.87 -124.06 120.25 1.1102 +IC H6R C25 *C26 H6S 1.1102 120.25 -120.61 109.89 1.1105 +IC C25 C26 C27 C28 1.5208 113.87 91.52 112.36 1.5242 +IC C28 C26 *C27 H7R 1.5242 112.36 -129.80 108.86 1.1107 +IC H7R C26 *C27 H7S 1.1107 108.86 -110.77 103.17 1.1108 +IC C26 C27 C28 C29 1.6002 112.36 172.49 113.33 1.4719 +IC C29 C27 *C28 H8R 1.4719 113.33 -131.49 112.98 1.1109 +IC H8R C27 *C28 H8S 1.1109 112.98 -112.64 102.49 1.1107 +IC C27 C28 C29 C210 1.5242 113.33 -160.05 124.09 1.3612 +IC C28 C29 C210 C211 1.4719 124.09 -10.52 119.71 1.5230 +IC C29 C210 C211 C212 1.3612 119.71 -129.35 115.15 1.5486 +IC C31 C32 C33 C34 1.5651 111.38 -63.42 115.22 1.5491 +IC C34 C32 *C33 H3X 1.5491 115.22 -125.27 107.87 1.1109 +IC H3X C32 *C33 H3Y 1.1109 107.87 -105.68 108.54 1.1108 +IC C32 C33 C34 C35 1.5412 115.22 -155.96 112.59 1.4766 +IC C35 C33 *C34 H4X 1.4766 112.59 -134.43 113.31 1.1104 +IC H4X C33 *C34 H4Y 1.1104 113.31 -114.78 108.67 1.1104 +IC C33 C34 C35 C36 1.5491 112.59 -70.29 110.90 1.5777 +IC C36 C34 *C35 H5X 1.5777 110.90 -112.47 110.51 1.1104 +IC H5X C34 *C35 H5Y 1.1104 110.51 -125.12 122.47 1.1114 +IC C34 C35 C36 C37 1.4766 110.90 -174.16 116.43 1.4425 +IC C37 C35 *C36 H6X 1.4425 116.43 -133.72 116.59 1.1108 +IC H6X C35 *C36 H6Y 1.1108 116.59 -112.44 101.91 1.1110 +IC C35 C36 C37 C38 1.5777 116.43 67.71 115.60 1.5665 +IC C38 C36 *C37 H7X 1.5665 115.60 117.40 108.66 1.1104 +IC H7X C36 *C37 H7Y 1.1104 108.66 119.92 108.24 1.1115 +IC C36 C37 C38 C39 1.4425 115.60 174.91 112.85 1.5424 +IC C39 C37 *C38 H8X 1.5424 112.85 -112.21 104.00 1.1108 +IC H8X C37 *C38 H8Y 1.1108 104.00 -115.84 111.16 1.1104 +IC C37 C38 C39 C310 1.5665 112.85 179.65 109.95 1.5726 +IC C38 C39 C310 C311 1.5424 109.95 174.69 114.71 1.5266 +IC C39 C310 C311 C312 1.5726 114.71 -179.58 111.40 1.5149 +IC OC3 C12 *C13 H13A 1.4532 112.21 129.28 111.82 1.1101 +IC OC3 C12 *C13 H13B 1.4532 112.21 -118.99 108.98 1.1107 +IC C12 C13 OC3 HO3 1.5704 112.21 141.02 102.28 0.9599 +IC OC3 C13 C12 C11 1.4532 112.21 -61.28 117.48 1.5204 +IC C11 C13 *C12 OC2 1.5204 117.48 -123.75 105.03 1.4782 +IC OC2 C13 *C12 H12A 1.4782 105.03 -113.86 103.70 1.1104 +IC C13 C12 OC2 HO2 1.5704 105.03 -132.36 107.09 0.9594 +IC C13 C12 C11 O12 1.5704 117.48 165.56 114.21 1.4509 +IC O12 C12 *C11 H11A 1.4509 114.21 -120.96 108.64 1.1109 +IC H11A C12 *C11 H11B 1.1109 108.64 -105.17 114.83 1.1114 +IC C12 C11 O12 P 1.5204 114.21 -92.56 121.65 1.6004 +IC C11 O12 P O11 1.4509 121.65 -47.76 105.22 1.6251 +IC O11 O12 *P O13 1.6251 105.22 -115.08 110.24 1.4953 +IC O11 O12 *P O14 1.6251 105.22 115.98 108.20 1.4712 +IC O12 P O11 C1 1.6004 105.22 98.75 114.06 1.4856 +IC P O11 C1 C2 1.6251 114.06 -166.06 109.38 1.4913 +IC C2 O11 *C1 HA 1.4913 109.38 -108.65 107.97 1.1116 +IC HA O11 *C1 HB 1.1116 107.97 -129.35 122.45 1.1106 +IC O11 C1 C2 C3 1.4856 109.38 155.08 112.96 1.5836 +IC C3 C1 *C2 O21 1.5836 112.96 126.22 111.99 1.4830 +IC C3 C1 *C2 HS 1.5836 112.96 -114.71 112.27 1.1110 +IC C1 C2 O21 C21 1.4913 111.99 156.97 118.33 1.2837 +IC C2 O21 C21 C22 1.4830 118.33 -175.15 106.26 1.5296 +IC C22 O21 *C21 O22 1.5296 106.26 177.78 128.83 1.2139 +IC O21 C21 C22 C23 1.2837 106.26 -65.42 111.80 1.5340 +IC C23 C21 *C22 H2R 1.5340 111.80 -123.52 110.15 1.1118 +IC H2R C21 *C22 H2S 1.1118 110.15 -114.43 113.12 1.1108 +IC C1 C2 C3 O31 1.4913 112.96 67.86 110.41 1.4280 +IC O31 C2 *C3 HX 1.4280 110.41 -117.67 110.41 1.1106 +IC HX C2 *C3 HY 1.1106 110.41 -116.34 104.49 1.1106 +IC C2 C3 O31 C31 1.5836 110.41 158.38 111.76 1.3559 +IC C3 O31 C31 C32 1.4280 111.76 173.15 111.04 1.5651 +IC C32 O31 *C31 O32 1.5651 111.04 -178.50 125.22 1.2028 +IC O31 C31 C32 C33 1.3559 111.04 136.55 111.38 1.5412 +IC C33 C31 *C32 H2X 1.5412 111.38 115.03 113.20 1.1108 +IC H2X C31 *C32 H2Y 1.1108 113.20 123.96 111.62 1.1110 +IC C21 C22 C23 C24 1.5296 111.80 -74.89 116.02 1.5995 +IC C24 C22 *C23 H3R 1.5995 116.02 -116.95 110.31 1.1115 +IC H3R C22 *C23 H3S 1.1115 110.31 -117.60 113.33 1.1109 +IC C22 C23 C24 C25 1.5340 116.02 -58.62 114.95 1.5046 +IC C25 C23 *C24 H4R 1.5046 114.95 -126.86 112.82 1.1113 +IC H4R C23 *C24 H4S 1.1113 112.82 -107.67 103.55 1.1100 +IC C23 C24 C25 C26 1.5995 114.95 -167.81 111.59 1.5208 +IC C26 C24 *C25 H5R 1.5208 111.59 -121.19 103.95 1.1114 +IC H5R C24 *C25 H5S 1.1114 103.95 -106.49 111.36 1.1104 +IC C24 C25 C26 C27 1.5046 111.59 92.34 113.87 1.6002 +IC C27 C25 *C26 H6R 1.6002 113.87 -124.06 120.25 1.1102 +IC H6R C25 *C26 H6S 1.1102 120.25 -120.61 109.89 1.1105 +IC C25 C26 C27 C28 1.5208 113.87 91.52 112.36 1.5242 +IC C28 C26 *C27 H7R 1.5242 112.36 -129.80 108.86 1.1107 +IC H7R C26 *C27 H7S 1.1107 108.86 -110.77 103.17 1.1108 +IC C26 C27 C28 C29 1.6002 112.36 172.49 113.33 1.4719 +IC C29 C27 *C28 H8R 1.4719 113.33 -131.49 112.98 1.1109 +IC H8R C27 *C28 H8S 1.1109 112.98 -112.64 102.49 1.1107 +IC C27 C28 C29 C210 1.5242 113.33 -160.05 124.09 1.3612 +IC C210 C28 *C29 H9R 1.3612 124.09 173.62 116.31 1.0997 +IC C28 C29 C210 C211 1.4719 124.09 -10.52 119.71 1.5230 +IC C211 C29 *C210 H10R 1.5230 119.71 -169.05 121.07 1.1002 +IC C29 C210 C211 C212 1.3612 119.71 -129.35 115.15 1.5486 +IC C212 C210 *C211 H11R 1.5486 115.15 -124.35 112.65 1.1114 +IC H11R C210 *C211 H11S 1.1114 112.65 -119.37 120.31 1.1110 +IC C210 C211 C212 C213 1.5230 115.15 150.63 113.58 1.5610 +IC C213 C211 *C212 H12R 1.5610 113.58 -114.24 101.75 1.1110 +IC H12R C211 *C212 H12S 1.1110 101.75 -112.62 114.50 1.1109 +IC C211 C212 C213 C214 1.5486 113.58 -177.85 108.65 1.5785 +IC C214 C212 *C213 H13R 1.5785 108.65 -115.14 109.89 1.1112 +IC H13R C212 *C213 H13S 1.1112 109.89 -119.96 126.15 1.1107 +IC C212 C213 C214 C215 1.5610 108.65 -68.84 114.63 1.5299 +IC C215 C213 *C214 H14R 1.5299 114.63 125.97 117.34 1.1106 +IC H14R C213 *C214 H14S 1.1106 117.34 115.82 107.25 1.1106 +IC C213 C214 C215 C216 1.5785 114.63 -42.96 118.96 1.5637 +IC C216 C214 *C215 H15R 1.5637 118.96 -124.91 108.26 1.1110 +IC H15R C214 *C215 H15S 1.1110 108.26 -118.61 110.50 1.1110 +IC C214 C215 C216 H16R 1.5299 118.96 173.57 108.10 1.1109 +IC H16R C215 *C216 H16S 1.1109 108.10 -118.04 116.31 1.1111 +IC H16R C215 *C216 H16T 1.1109 108.10 115.60 116.71 1.1117 +IC C31 C32 C33 C34 1.5651 111.38 -63.42 115.22 1.5491 +IC C34 C32 *C33 H3X 1.5491 115.22 -125.27 107.87 1.1109 +IC H3X C32 *C33 H3Y 1.1109 107.87 -105.68 108.54 1.1108 +IC C32 C33 C34 C35 1.5412 115.22 -155.96 112.59 1.4766 +IC C35 C33 *C34 H4X 1.4766 112.59 -134.43 113.31 1.1104 +IC H4X C33 *C34 H4Y 1.1104 113.31 -114.78 108.67 1.1104 +IC C33 C34 C35 C36 1.5491 112.59 -70.29 110.90 1.5777 +IC C36 C34 *C35 H5X 1.5777 110.90 -112.47 110.51 1.1104 +IC H5X C34 *C35 H5Y 1.1104 110.51 -125.12 122.47 1.1114 +IC C34 C35 C36 C37 1.4766 110.90 -174.16 116.43 1.4425 +IC C37 C35 *C36 H6X 1.4425 116.43 -133.72 116.59 1.1108 +IC H6X C35 *C36 H6Y 1.1108 116.59 -112.44 101.91 1.1110 +IC C35 C36 C37 C38 1.5777 116.43 67.71 115.60 1.5665 +IC C38 C36 *C37 H7X 1.5665 115.60 117.40 108.66 1.1104 +IC H7X C36 *C37 H7Y 1.1104 108.66 119.92 108.24 1.1115 +IC C36 C37 C38 C39 1.4425 115.60 174.91 112.85 1.5424 +IC C39 C37 *C38 H8X 1.5424 112.85 -112.21 104.00 1.1108 +IC H8X C37 *C38 H8Y 1.1108 104.00 -115.84 111.16 1.1104 +IC C37 C38 C39 C310 1.5665 112.85 179.65 109.95 1.5726 +IC C310 C38 *C39 H9X 1.5726 109.95 -111.46 106.98 1.1111 +IC H9X C38 *C39 H9Y 1.1111 106.98 -126.65 118.05 1.1107 +IC C38 C39 C310 C311 1.5424 109.95 174.69 114.71 1.5266 +IC C311 C39 *C310 H10X 1.5266 114.71 -123.56 108.17 1.1108 +IC H10X C39 *C310 H10Y 1.1108 108.17 -117.87 107.18 1.1116 +IC C39 C310 C311 C312 1.5726 114.71 -179.58 111.40 1.5149 +IC C312 C310 *C311 H11X 1.5149 111.40 -119.72 105.00 1.1114 +IC H11X C310 *C311 H11Y 1.1114 105.00 -117.51 115.97 1.1105 +IC C310 C311 C312 C313 1.5266 111.40 70.34 113.13 1.5947 +IC C313 C311 *C312 H12X 1.5947 113.13 131.55 112.69 1.1108 +IC H12X C311 *C312 H12Y 1.1108 112.69 116.69 109.34 1.1111 +IC C311 C312 C313 C314 1.5149 113.13 178.91 112.17 1.5328 +IC C314 C312 *C313 H13X 1.5328 112.17 133.76 111.53 1.1106 +IC H13X C312 *C313 H13Y 1.1106 111.53 103.52 101.22 1.1114 +IC C312 C313 C314 C315 1.5947 112.17 -166.34 107.41 1.5628 +IC C315 C313 *C314 H14X 1.5628 107.41 124.18 110.43 1.1107 +IC H14X C313 *C314 H14Y 1.1107 110.43 119.98 113.93 1.1110 +IC C313 C314 C315 C316 1.5328 107.41 -171.11 113.26 1.5900 +IC C316 C314 *C315 H15X 1.5900 113.26 111.62 106.71 1.1112 +IC H15X C314 *C315 H15Y 1.1112 106.71 119.51 111.74 1.1110 +IC C314 C315 C316 H16X 1.5628 113.26 -73.48 109.62 1.1109 +IC H16X C315 *C316 H16Y 1.1109 109.62 -123.41 115.43 1.1108 +IC H16X C315 *C316 H16Z 1.1109 109.62 119.08 108.61 1.1113 + + +RESI IPPC 0.00 ! 14-methyl pentadecanoic acid and palmitic acid with PC headgroup +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - N(CH3)3 +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL1 -0.09 ! | | +ATOM H14R HAL1 0.09 ! H14R---C214-- H16R +ATOM C216 CTL3 -0.27 ! | | / +ATOM H16R HAL3 0.09 ! | C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! | | | +GROUP ! | H16T +ATOM C215 CTL3 -0.27 ! | | +ATOM H15R HAL3 0.09 ! H15R---C215--H15S +ATOM H15S HAL3 0.09 ! | | +ATOM H15T HAL3 0.09 ! H15T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 C216 C214 C215 +BOND C215 H15R C215 H15S C215 H15T +BOND C216 H16R C216 H16S C216 H16T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! Polar head (angle names from Sundaralingam) +IC C2 C1 O11 P 1.5440 110.61 177.94 117.00 1.5815 +IC C1 O11 P O12 1.4329 117.00 -65.03 103.02 1.5888 +IC O11 O12 *P O13 1.5815 103.02 -117.16 107.52 1.4800 +IC O11 O12 *P O14 1.5815 103.02 117.64 106.67 1.4804 +IC O11 P O12 C11 1.5815 103.02 165.83 118.57 1.4229 +IC O12 C12 *C11 H11A 1.4229 108.54 -118.43 109.15 1.1128 +IC O12 C12 *C11 H11B 1.4229 108.54 123.01 113.14 1.1135 +IC P O12 C11 C12 1.5888 118.57 65.71 108.54 1.5421 +IC N C11 *C12 H12A 1.5218 116.67 119.58 104.69 1.0973 +IC N C11 *C12 H12B 1.5218 116.67 -127.82 108.90 1.0788 +IC O12 C11 C12 N 1.4229 108.54 -128.09 116.67 1.5218 +IC C11 C12 N C13 1.5421 116.67 178.75 109.65 1.4975 +IC C12 C13 *N C14 1.5218 109.65 117.57 107.83 1.5030 +IC C12 C13 *N C15 1.5218 109.65 -122.44 111.03 1.4955 +IC O11 C1 C2 C3 1.4329 110.61 56.66 111.41 1.5598 +IC C1 C2 C3 O31 1.5440 111.41 66.59 110.61 1.4439 +IC C1 C3 *C2 O21 1.5440 111.41 -119.92 112.55 1.4386 +IC O11 C2 *C1 HA 1.4329 110.61 121.99 107.69 1.1162 +IC O11 C2 *C1 HB 1.4329 110.61 -121.13 107.38 1.1172 +IC O21 C1 *C2 HS 1.4386 106.80 118.56 107.31 1.1155 +IC O31 C2 *C3 HX 1.4439 110.61 -121.09 106.51 1.1169 +IC O31 C2 *C3 HY 1.4439 110.61 122.29 109.97 1.1114 +IC C1 C2 O21 C21 1.5440 106.80 172.86 116.04 1.3143 +IC C2 O21 C21 C22 1.4386 116.04 170.45 108.50 1.5279 +IC O21 C21 C22 C23 1.3143 108.50 -73.81 111.99 1.5471 +IC C22 O21 *C21 O22 1.5279 108.50 179.35 126.50 1.2177 +IC C21 C22 C23 C24 1.5279 111.99 165.39 113.18 1.5372 +IC C22 C23 C24 C25 1.5471 113.18 56.95 113.80 1.5365 +IC C23 C24 C25 C26 1.5372 113.80 170.70 113.64 1.5385 +IC C24 C25 C26 C27 1.5365 113.64 60.20 114.05 1.5367 +IC C25 C26 C27 C28 1.5385 114.05 176.20 112.34 1.5355 +IC C26 C27 C28 C29 1.5367 112.34 176.30 113.02 1.5353 +IC C27 C28 C29 C210 1.5355 113.02 -179.85 112.36 1.5352 +IC C28 C29 C210 C211 1.5353 112.36 177.09 112.99 1.5359 +IC C29 C210 C211 C212 1.5352 112.99 179.47 112.29 1.5355 +IC C210 C211 C212 C213 1.5359 112.29 169.44 115.50 1.5422 +IC C211 C212 C213 C214 1.5355 115.50 67.02 115.75 1.5456 +IC C212 C213 C214 C215 1.5422 115.75 -90.47 112.50 1.5385 +IC C212 C213 C214 C216 1.5422 115.75 146.98 110.57 1.5388 +IC C2 C3 O31 C31 1.5598 110.61 -167.95 113.85 1.3247 +IC C3 O31 C31 C32 1.4439 113.85 178.20 109.08 1.5271 +IC O31 C31 C32 C33 1.3247 109.08 88.08 111.58 1.5458 +IC C32 O31 *C31 O32 1.5271 109.08 179.11 125.88 1.2171 +IC C31 C32 C33 C34 1.5271 111.58 -176.50 113.53 1.5370 +IC C32 C33 C34 C35 1.5458 113.53 65.92 113.17 1.5369 +IC C33 C34 C35 C36 1.5370 113.17 173.97 114.01 1.5376 +IC C34 C35 C36 C37 1.5369 114.01 -66.39 113.55 1.5357 +IC C35 C36 C37 C38 1.5376 113.55 -168.87 112.65 1.5348 +IC C36 C37 C38 C39 1.5357 112.65 177.26 112.52 1.5346 +IC C37 C38 C39 C310 1.5348 112.52 -173.25 112.63 1.5345 +IC C38 C39 C310 C311 1.5346 112.63 177.34 112.59 1.5345 +IC C39 C310 C311 C312 1.5345 112.59 -174.13 112.60 1.5350 +IC C310 C311 C312 C313 1.5345 112.60 178.42 112.48 1.5357 +IC C311 C312 C313 C314 1.5350 112.48 179.67 113.88 1.5378 +IC C312 C313 C314 C315 1.5357 113.88 65.20 113.76 1.5355 +IC C313 C314 C315 C316 1.5378 113.76 175.05 113.27 1.5312 +IC C13 C12 *N C14 1.4975 109.65 -117.35 108.18 1.5030 +IC C13 C12 *N C15 1.4975 109.65 122.73 110.54 1.4955 +IC C12 N C13 H13A 1.5218 109.65 -58.54 109.61 1.0881 +IC H13A N *C13 H13B 1.0881 109.61 -118.65 110.91 1.0819 +IC H13A N *C13 H13C 1.0881 109.61 119.68 111.54 1.0810 +IC C12 N C14 H14A 1.5218 108.18 -177.50 113.84 1.0741 +IC H14A N *C14 H14B 1.0741 113.84 -123.78 110.45 1.0927 +IC H14A N *C14 H14C 1.0741 113.84 123.84 111.11 1.0953 +IC C12 N C15 H15A 1.5218 110.54 58.36 109.41 1.0867 +IC H15A N *C15 H15B 1.0867 109.41 -118.96 111.25 1.0814 +IC H15A N *C15 H15C 1.0867 109.41 119.11 111.16 1.0813 +IC C13 N C12 C11 1.4975 109.65 178.75 116.67 1.5421 +IC C11 N *C12 H12A 1.5421 116.67 -117.66 108.24 1.0973 +IC H12A N *C12 H12B 1.0973 108.24 -116.00 111.90 1.0788 +IC N C12 C11 O12 1.5218 116.67 -128.09 108.54 1.4229 +IC O12 C12 *C11 H11A 1.4229 108.54 -118.43 109.15 1.1128 +IC H11A C12 *C11 H11B 1.1128 109.15 -118.56 113.14 1.1135 +IC C12 C11 O12 P 1.5421 108.54 65.71 118.57 1.5888 +IC C11 O12 P O11 1.4229 118.57 165.83 103.02 1.5815 +IC O11 O12 *P O13 1.5815 103.02 -117.16 107.52 1.4800 +IC O11 O12 *P O14 1.5815 103.02 117.64 106.67 1.4804 +IC O12 P O11 C1 1.5888 103.02 -65.03 117.00 1.4329 +IC P O11 C1 C2 1.5815 117.00 177.94 110.61 1.5440 +IC C2 O11 *C1 HA 1.5440 110.61 -119.76 111.44 1.1162 +IC HA O11 *C1 HB 1.1162 111.44 -121.21 110.89 1.1172 +IC O11 C1 C2 C3 1.4329 110.61 56.66 111.41 1.5598 +IC C3 C1 *C2 O21 1.5598 111.41 123.27 106.80 1.4386 +IC C3 C1 *C2 HS 1.5598 111.41 -118.17 107.31 1.1155 +IC C1 C2 O21 C21 1.5440 106.80 172.86 116.04 1.3143 +IC C2 O21 C21 C22 1.4386 116.04 170.45 108.50 1.5279 +IC C22 O21 *C21 O22 1.5279 108.50 179.35 126.50 1.2177 +IC O21 C21 C22 C23 1.3143 108.50 -73.81 111.99 1.5471 +IC C23 C21 *C22 H2R 1.5471 111.99 -122.07 107.94 1.1081 +IC H2R C21 *C22 H2S 1.1081 107.94 -117.27 107.60 1.1098 +IC C1 C2 C3 O31 1.5440 111.41 66.59 110.61 1.4439 +IC O31 C2 *C3 HX 1.4439 110.61 -121.09 106.51 1.1169 +IC HX C2 *C3 HY 1.1169 106.51 -116.62 109.97 1.1114 +IC C2 C3 O31 C31 1.5598 110.61 -167.95 113.85 1.3247 +IC C3 O31 C31 C32 1.4439 113.85 178.20 109.08 1.5271 +IC C32 O31 *C31 O32 1.5271 109.08 179.11 125.88 1.2171 +IC O31 C31 C32 C33 1.3247 109.08 88.08 111.58 1.5458 +IC C33 C31 *C32 H2X 1.5458 111.58 -122.03 107.83 1.1090 +IC H2X C31 *C32 H2Y 1.1090 107.83 -117.05 107.60 1.1089 +IC C21 C22 C23 C24 1.5279 111.99 165.39 113.18 1.5372 +IC C24 C22 *C23 H3R 1.5372 113.18 -120.00 109.61 1.1164 +IC H3R C22 *C23 H3S 1.1164 109.61 -117.59 109.40 1.1133 +IC C22 C23 C24 C25 1.5471 113.18 56.95 113.80 1.5365 +IC C25 C23 *C24 H4R 1.5365 113.80 -121.86 108.70 1.1130 +IC H4R C23 *C24 H4S 1.1130 108.70 -116.69 108.53 1.1137 +IC C23 C24 C25 C26 1.5372 113.80 170.70 113.64 1.5385 +IC C26 C24 *C25 H5R 1.5385 113.64 -120.74 108.61 1.1138 +IC H5R C24 *C25 H5S 1.1138 108.61 -117.23 109.42 1.1127 +IC C24 C25 C26 C27 1.5365 113.64 60.20 114.05 1.5367 +IC C27 C25 *C26 H6R 1.5367 114.05 -121.86 108.99 1.1134 +IC H6R C25 *C26 H6S 1.1134 108.99 -116.89 108.53 1.1138 +IC C25 C26 C27 C28 1.5385 114.05 176.20 112.34 1.5355 +IC C28 C26 *C27 H7R 1.5355 112.34 -121.36 109.33 1.1129 +IC H7R C26 *C27 H7S 1.1129 109.33 -117.84 109.43 1.1127 +IC C26 C27 C28 C29 1.5367 112.34 176.30 113.02 1.5353 +IC C29 C27 *C28 H8R 1.5353 113.02 -121.00 108.91 1.1133 +IC H8R C27 *C28 H8S 1.1133 108.91 -117.21 109.13 1.1128 +IC C27 C28 C29 C210 1.5355 113.02 -179.85 112.36 1.5352 +IC C210 C28 *C29 H9R 1.5352 112.36 -121.50 109.37 1.1129 +IC H9R C28 *C29 H9S 1.1129 109.37 -117.52 108.96 1.1133 +IC C28 C29 C210 C211 1.5353 112.36 177.09 112.99 1.5359 +IC C29 C210 C211 C212 1.5352 112.99 179.47 112.29 1.5355 +IC C210 C211 C212 C213 1.5359 112.29 169.44 115.50 1.5422 +IC C211 C212 C213 C214 1.5355 115.50 67.02 115.75 1.5456 +IC C212 C213 C214 C216 1.5422 115.75 146.98 110.57 1.5388 +IC C213 C214 C216 H16R 1.5456 110.57 -58.72 110.52 1.1106 +IC C213 C214 C215 H15R 1.5456 112.50 59.19 111.39 1.1078 +IC C31 C32 C33 C34 1.5271 111.58 -176.50 113.53 1.5370 +IC C34 C32 *C33 H3X 1.5370 113.53 -121.24 109.04 1.1148 +IC H3X C32 *C33 H3Y 1.1148 109.04 -117.55 109.70 1.1145 +IC C32 C33 C34 C35 1.5458 113.53 65.92 113.17 1.5369 +IC C35 C33 *C34 H4X 1.5369 113.17 -122.53 109.63 1.1124 +IC H4X C33 *C34 H4Y 1.1124 109.63 -116.83 107.85 1.1132 +IC C33 C34 C35 C36 1.5370 113.17 173.97 114.01 1.5376 +IC C36 C34 *C35 H5X 1.5376 114.01 -121.80 109.03 1.1135 +IC H5X C34 *C35 H5Y 1.1135 109.03 -117.06 109.02 1.1131 +IC C34 C35 C36 C37 1.5369 114.01 -66.39 113.55 1.5357 +IC C37 C35 *C36 H6X 1.5357 113.55 -119.96 107.94 1.1144 +IC H6X C35 *C36 H6Y 1.1144 107.94 -116.96 109.76 1.1123 +IC C35 C36 C37 C38 1.5376 113.55 -168.87 112.65 1.5348 +IC C38 C36 *C37 H7X 1.5348 112.65 -122.05 109.82 1.1121 +IC H7X C36 *C37 H7Y 1.1121 109.82 -117.60 108.70 1.1137 +IC C36 C37 C38 C39 1.5357 112.65 177.26 112.52 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.52 -120.49 108.62 1.1137 +IC H8X C37 *C38 H8Y 1.1137 108.62 -117.43 109.59 1.1126 +IC C37 C38 C39 C310 1.5348 112.52 -173.25 112.63 1.5345 +IC C310 C38 *C39 H9X 1.5345 112.63 -122.20 109.44 1.1127 +IC H9X C38 *C39 H9Y 1.1127 109.44 -117.35 108.75 1.1138 +IC C38 C39 C310 C311 1.5346 112.63 177.34 112.59 1.5345 +IC C39 C310 C311 C312 1.5345 112.59 -174.13 112.60 1.5350 +IC C310 C311 C312 C313 1.5345 112.60 178.42 112.48 1.5357 +IC C311 C312 C313 C314 1.5350 112.48 179.67 113.88 1.5378 +IC C312 C313 C314 C315 1.5357 113.88 65.20 113.76 1.5355 +IC C313 C314 C315 C316 1.5378 113.76 175.05 113.27 1.5312 +IC C314 C315 C316 H16X 1.5355 113.27 -60.18 110.47 1.1113 +IC C13 C12 *N C14 1.4975 109.65 -117.35 108.18 1.5030 +IC C13 C12 *N C15 1.4975 109.65 122.73 110.54 1.4955 +IC C12 N C13 H13A 1.5218 109.65 -58.54 109.61 1.0881 +IC H13A N *C13 H13B 1.0881 109.61 -118.65 110.91 1.0819 +IC H13A N *C13 H13C 1.0881 109.61 119.68 111.54 1.0810 +IC C12 N C14 H14A 1.5218 108.18 -177.50 113.84 1.0741 +IC H14A N *C14 H14B 1.0741 113.84 -123.78 110.45 1.0927 +IC H14A N *C14 H14C 1.0741 113.84 123.84 111.11 1.0953 +IC C12 N C15 H15A 1.5218 110.54 58.36 109.41 1.0867 +IC H15A N *C15 H15B 1.0867 109.41 -118.96 111.25 1.0814 +IC H15A N *C15 H15C 1.0867 109.41 119.11 111.16 1.0813 +IC C13 N C12 C11 1.4975 109.65 178.75 116.67 1.5421 +IC C11 N *C12 H12A 1.5421 116.67 -117.66 108.24 1.0973 +IC H12A N *C12 H12B 1.0973 108.24 -116.00 111.90 1.0788 +IC N C12 C11 O12 1.5218 116.67 -128.09 108.54 1.4229 +IC O12 C12 *C11 H11A 1.4229 108.54 -118.43 109.15 1.1128 +IC H11A C12 *C11 H11B 1.1128 109.15 -118.56 113.14 1.1135 +IC C12 C11 O12 P 1.5421 108.54 65.71 118.57 1.5888 +IC C11 O12 P O11 1.4229 118.57 165.83 103.02 1.5815 +IC O11 O12 *P O13 1.5815 103.02 -117.16 107.52 1.4800 +IC O11 O12 *P O14 1.5815 103.02 117.64 106.67 1.4804 +IC O12 P O11 C1 1.5888 103.02 -65.03 117.00 1.4329 +IC P O11 C1 C2 1.5815 117.00 177.94 110.61 1.5440 +IC C2 O11 *C1 HA 1.5440 110.61 -119.76 111.44 1.1162 +IC HA O11 *C1 HB 1.1162 111.44 -121.21 110.89 1.1172 +IC O11 C1 C2 C3 1.4329 110.61 56.66 111.41 1.5598 +IC C3 C1 *C2 O21 1.5598 111.41 123.27 106.80 1.4386 +IC C3 C1 *C2 HS 1.5598 111.41 -118.17 107.31 1.1155 +IC C1 C2 O21 C21 1.5440 106.80 172.86 116.04 1.3143 +IC C2 O21 C21 C22 1.4386 116.04 170.45 108.50 1.5279 +IC C22 O21 *C21 O22 1.5279 108.50 179.35 126.50 1.2177 +IC O21 C21 C22 C23 1.3143 108.50 -73.81 111.99 1.5471 +IC C23 C21 *C22 H2R 1.5471 111.99 -122.07 107.94 1.1081 +IC H2R C21 *C22 H2S 1.1081 107.94 -117.27 107.60 1.1098 +IC C1 C2 C3 O31 1.5440 111.41 66.59 110.61 1.4439 +IC O31 C2 *C3 HX 1.4439 110.61 -121.09 106.51 1.1169 +IC HX C2 *C3 HY 1.1169 106.51 -116.62 109.97 1.1114 +IC C2 C3 O31 C31 1.5598 110.61 -167.95 113.85 1.3247 +IC C3 O31 C31 C32 1.4439 113.85 178.20 109.08 1.5271 +IC C32 O31 *C31 O32 1.5271 109.08 179.11 125.88 1.2171 +IC O31 C31 C32 C33 1.3247 109.08 88.08 111.58 1.5458 +IC C33 C31 *C32 H2X 1.5458 111.58 -122.03 107.83 1.1090 +IC H2X C31 *C32 H2Y 1.1090 107.83 -117.05 107.60 1.1089 +IC C21 C22 C23 C24 1.5279 111.99 165.39 113.18 1.5372 +IC C24 C22 *C23 H3R 1.5372 113.18 -120.00 109.61 1.1164 +IC H3R C22 *C23 H3S 1.1164 109.61 -117.59 109.40 1.1133 +IC C22 C23 C24 C25 1.5471 113.18 56.95 113.80 1.5365 +IC C25 C23 *C24 H4R 1.5365 113.80 -121.86 108.70 1.1130 +IC H4R C23 *C24 H4S 1.1130 108.70 -116.69 108.53 1.1137 +IC C23 C24 C25 C26 1.5372 113.80 170.70 113.64 1.5385 +IC C26 C24 *C25 H5R 1.5385 113.64 -120.74 108.61 1.1138 +IC H5R C24 *C25 H5S 1.1138 108.61 -117.23 109.42 1.1127 +IC C24 C25 C26 C27 1.5365 113.64 60.20 114.05 1.5367 +IC C27 C25 *C26 H6R 1.5367 114.05 -121.86 108.99 1.1134 +IC H6R C25 *C26 H6S 1.1134 108.99 -116.89 108.53 1.1138 +IC C25 C26 C27 C28 1.5385 114.05 176.20 112.34 1.5355 +IC C28 C26 *C27 H7R 1.5355 112.34 -121.36 109.33 1.1129 +IC H7R C26 *C27 H7S 1.1129 109.33 -117.84 109.43 1.1127 +IC C26 C27 C28 C29 1.5367 112.34 176.30 113.02 1.5353 +IC C29 C27 *C28 H8R 1.5353 113.02 -121.00 108.91 1.1133 +IC H8R C27 *C28 H8S 1.1133 108.91 -117.21 109.13 1.1128 +IC C27 C28 C29 C210 1.5355 113.02 -179.85 112.36 1.5352 +IC C210 C28 *C29 H9R 1.5352 112.36 -121.50 109.37 1.1129 +IC H9R C28 *C29 H9S 1.1129 109.37 -117.52 108.96 1.1133 +IC C28 C29 C210 C211 1.5353 112.36 177.09 112.99 1.5359 +IC C211 C29 *C210 H10R 1.5359 112.99 -121.11 108.95 1.1135 +IC H10R C29 *C210 H10S 1.1135 108.95 -117.30 109.08 1.1132 +IC C29 C210 C211 C212 1.5352 112.99 179.47 112.29 1.5355 +IC C212 C210 *C211 H11R 1.5355 112.29 -121.39 108.78 1.1121 +IC H11R C210 *C211 H11S 1.1121 108.78 -117.61 108.96 1.1131 +IC C210 C211 C212 C213 1.5359 112.29 169.44 115.50 1.5422 +IC C213 C211 *C212 H12R 1.5422 115.50 -120.25 107.83 1.1147 +IC H12R C211 *C212 H12S 1.1147 107.83 -116.21 109.15 1.1126 +IC C211 C212 C213 C214 1.5355 115.50 67.02 115.75 1.5456 +IC C214 C212 *C213 H13R 1.5456 115.75 119.39 106.55 1.1147 +IC H13R C212 *C213 H13S 1.1147 106.55 115.84 110.25 1.1106 +IC C212 C213 C214 C216 1.5422 115.75 146.98 110.57 1.5388 +IC C216 C213 *C214 C215 1.5388 110.57 122.56 112.50 1.5385 +IC C216 C213 *C214 H14R 1.5388 110.57 -117.50 107.90 1.1158 +IC C213 C214 C216 H16R 1.5456 110.57 -58.72 110.52 1.1106 +IC H16R C214 *C216 H16S 1.1106 110.52 120.08 110.21 1.1106 +IC H16R C214 *C216 H16T 1.1106 110.52 -120.02 110.36 1.1106 +IC C213 C214 C215 H15R 1.5456 112.50 59.19 111.39 1.1078 +IC H15R C214 *C215 H15S 1.1078 111.39 -120.26 110.08 1.1106 +IC H15R C214 *C215 H15T 1.1078 111.39 120.24 110.19 1.1106 +IC C31 C32 C33 C34 1.5271 111.58 -176.50 113.53 1.5370 +IC C34 C32 *C33 H3X 1.5370 113.53 -121.24 109.04 1.1148 +IC H3X C32 *C33 H3Y 1.1148 109.04 -117.55 109.70 1.1145 +IC C32 C33 C34 C35 1.5458 113.53 65.92 113.17 1.5369 +IC C35 C33 *C34 H4X 1.5369 113.17 -122.53 109.63 1.1124 +IC H4X C33 *C34 H4Y 1.1124 109.63 -116.83 107.85 1.1132 +IC C33 C34 C35 C36 1.5370 113.17 173.97 114.01 1.5376 +IC C36 C34 *C35 H5X 1.5376 114.01 -121.80 109.03 1.1135 +IC H5X C34 *C35 H5Y 1.1135 109.03 -117.06 109.02 1.1131 +IC C34 C35 C36 C37 1.5369 114.01 -66.39 113.55 1.5357 +IC C37 C35 *C36 H6X 1.5357 113.55 -119.96 107.94 1.1144 +IC H6X C35 *C36 H6Y 1.1144 107.94 -116.96 109.76 1.1123 +IC C35 C36 C37 C38 1.5376 113.55 -168.87 112.65 1.5348 +IC C38 C36 *C37 H7X 1.5348 112.65 -122.05 109.82 1.1121 +IC H7X C36 *C37 H7Y 1.1121 109.82 -117.60 108.70 1.1137 +IC C36 C37 C38 C39 1.5357 112.65 177.26 112.52 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.52 -120.49 108.62 1.1137 +IC H8X C37 *C38 H8Y 1.1137 108.62 -117.43 109.59 1.1126 +IC C37 C38 C39 C310 1.5348 112.52 -173.25 112.63 1.5345 +IC C310 C38 *C39 H9X 1.5345 112.63 -122.20 109.44 1.1127 +IC H9X C38 *C39 H9Y 1.1127 109.44 -117.35 108.75 1.1138 +IC C38 C39 C310 C311 1.5346 112.63 177.34 112.59 1.5345 +IC C311 C39 *C310 H10X 1.5345 112.59 -120.58 108.66 1.1137 +IC H10X C39 *C310 H10Y 1.1137 108.66 -117.39 109.55 1.1127 +IC C39 C310 C311 C312 1.5345 112.59 -174.13 112.60 1.5350 +IC C312 C310 *C311 H11X 1.5350 112.60 -122.03 109.34 1.1127 +IC H11X C310 *C311 H11Y 1.1127 109.34 -117.39 108.86 1.1136 +IC C310 C311 C312 C313 1.5345 112.60 178.42 112.48 1.5357 +IC C313 C311 *C312 H12X 1.5357 112.48 -121.21 108.42 1.1126 +IC H12X C311 *C312 H12Y 1.1126 108.42 -117.23 109.32 1.1128 +IC C311 C312 C313 C314 1.5350 112.48 179.67 113.88 1.5378 +IC C314 C312 *C313 H13X 1.5378 113.88 -121.12 108.42 1.1138 +IC H13X C312 *C313 H13Y 1.1138 108.42 -116.84 109.16 1.1130 +IC C312 C313 C314 C315 1.5357 113.88 65.20 113.76 1.5355 +IC C315 C313 *C314 H14X 1.5355 113.76 -122.46 109.35 1.1127 +IC H14X C313 *C314 H14Y 1.1127 109.35 -116.97 108.43 1.1140 +IC C313 C314 C315 C316 1.5378 113.76 175.05 113.27 1.5312 +IC C316 C314 *C315 H15X 1.5312 113.27 -121.48 108.68 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.68 -116.94 109.24 1.1133 +IC C314 C315 C316 H16X 1.5355 113.27 -60.18 110.47 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.47 -120.01 110.57 1.1112 +IC H16X C315 *C316 H16Z 1.1113 110.47 119.95 110.47 1.1112 +PATCHING FIRST NONE LAST NONE + +RESI APPC 0.00 ! 13-methyl pentadecanoic acid and palmitic acid with PC headgroup +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - N(CH3)3 +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL1 -0.09 ! | H16R | +ATOM H13R HAL1 0.09 ! H13R---C213-- / +ATOM C216 CTL3 -0.27 ! | | / +ATOM H16R HAL3 0.09 ! | C216-H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! | | | +GROUP ! | H16T +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | +GROUP ! +ATOM C215 CTL3 -0.27 ! | | +ATOM H15R HAL3 0.09 ! H15R---C215--H15S +ATOM H15S HAL3 0.09 ! | | +ATOM H15T HAL3 0.09 ! H15T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 C214 C213 C216 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 H15T +BOND C216 H16R C216 H16S C216 H16T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! Polar head (angle names from Sundaralingam) +IC C2 C1 O11 P 1.5510 111.51 131.98 121.74 1.5784 +IC C1 O11 P O12 1.4308 121.74 -107.38 104.29 1.5894 +IC O11 O12 *P O13 1.5784 104.29 -118.38 107.71 1.4804 +IC O11 O12 *P O14 1.5784 104.29 117.25 106.45 1.4817 +IC O11 P O12 C11 1.5784 104.29 166.63 118.15 1.4249 +IC O12 C12 *C11 H11A 1.4249 108.84 -118.47 109.01 1.1128 +IC O12 C12 *C11 H11B 1.4249 108.84 123.14 113.02 1.1135 +IC P O12 C11 C12 1.5894 118.15 65.93 108.84 1.5438 +IC N C11 *C12 H12A 1.5234 116.91 119.55 104.56 1.0972 +IC N C11 *C12 H12B 1.5234 116.91 -127.85 108.82 1.0787 +IC O12 C11 C12 N 1.4249 108.84 -127.58 116.91 1.5234 +IC C11 C12 N C13 1.5438 116.91 179.44 109.76 1.4977 +IC C12 C13 *N C14 1.5234 109.76 117.57 107.80 1.5027 +IC C12 C13 *N C15 1.5234 109.76 -122.63 110.99 1.4953 +IC O11 C1 C2 C3 1.4308 111.51 175.42 110.00 1.5574 +IC C1 C2 C3 O31 1.5510 110.00 164.12 112.50 1.4443 +IC C1 C3 *C2 O21 1.5510 110.00 -119.83 110.61 1.4410 +IC O11 C2 *C1 HA 1.4308 111.51 124.39 106.68 1.1176 +IC O11 C2 *C1 HB 1.4308 111.51 -119.84 108.60 1.1122 +IC O21 C1 *C2 HS 1.4410 108.48 121.27 106.73 1.1166 +IC O31 C2 *C3 HX 1.4443 112.50 -120.23 107.27 1.1140 +IC O31 C2 *C3 HY 1.4443 112.50 123.54 107.12 1.1157 +IC C1 C2 O21 C21 1.5510 108.48 145.04 114.43 1.3209 +IC C2 O21 C21 C22 1.4410 114.43 179.80 109.39 1.5280 +IC O21 C21 C22 C23 1.3209 109.39 -67.84 112.26 1.5462 +IC C22 O21 *C21 O22 1.5280 109.39 179.74 126.64 1.2169 +IC C21 C22 C23 C24 1.5280 112.26 -178.01 113.07 1.5375 +IC C22 C23 C24 C25 1.5462 113.07 72.04 114.47 1.5401 +IC C23 C24 C25 C26 1.5375 114.47 72.07 114.75 1.5399 +IC C24 C25 C26 C27 1.5401 114.75 69.41 113.42 1.5375 +IC C25 C26 C27 C28 1.5399 113.42 175.01 112.75 1.5366 +IC C26 C27 C28 C29 1.5375 112.75 -170.66 113.89 1.5396 +IC C27 C28 C29 C210 1.5366 113.89 -94.88 115.55 1.5409 +IC C28 C29 C210 C211 1.5396 115.55 71.26 115.51 1.5429 +IC C29 C210 C211 C212 1.5409 115.51 -113.00 113.55 1.5944 +IC C210 C211 C212 C213 1.5429 113.55 124.84 129.45 1.6033 +IC C211 C212 C213 C214 1.5944 129.45 134.05 112.60 1.5516 +IC C212 C213 C214 C215 1.6033 112.60 -70.19 115.90 1.5355 +IC C211 C212 C213 C216 1.5944 129.45 -104.04 112.35 1.5453 +IC C2 C3 O31 C31 1.5574 112.50 171.18 113.30 1.3281 +IC C3 O31 C31 C32 1.4443 113.30 172.65 109.66 1.5265 +IC O31 C31 C32 C33 1.3281 109.66 118.29 112.92 1.5439 +IC C32 O31 *C31 O32 1.5265 109.66 -176.72 125.32 1.2176 +IC C31 C32 C33 C34 1.5265 112.92 174.13 112.74 1.5375 +IC C32 C33 C34 C35 1.5439 112.74 54.96 113.41 1.5363 +IC C33 C34 C35 C36 1.5375 113.41 164.07 112.78 1.5344 +IC C34 C35 C36 C37 1.5363 112.78 -178.38 112.60 1.5352 +IC C35 C36 C37 C38 1.5344 112.60 155.96 112.41 1.5346 +IC C36 C37 C38 C39 1.5352 112.41 -175.46 113.04 1.5394 +IC C37 C38 C39 C310 1.5346 113.04 155.31 113.10 1.5857 +IC C38 C39 C310 C311 1.5394 113.10 115.61 128.44 1.6440 +IC C39 C310 C311 C312 1.5857 128.44 100.24 125.90 1.5875 +IC C310 C311 C312 C313 1.6440 125.90 105.39 114.86 1.5415 +IC C311 C312 C313 C314 1.5875 114.86 174.34 112.59 1.5359 +IC C312 C313 C314 C315 1.5415 112.59 168.88 113.53 1.5375 +IC C313 C314 C315 C316 1.5359 113.53 59.07 114.65 1.5320 +IC C13 C12 *N C14 1.4977 109.76 -117.35 108.14 1.5027 +IC C13 C12 *N C15 1.4977 109.76 122.83 110.65 1.4953 +IC C12 N C13 H13A 1.5234 109.76 -58.20 109.63 1.0879 +IC H13A N *C13 H13B 1.0879 109.63 -118.63 110.88 1.0821 +IC H13A N *C13 H13C 1.0879 109.63 119.78 111.58 1.0810 +IC C12 N C14 H14A 1.5234 108.14 -178.85 113.94 1.0739 +IC H14A N *C14 H14B 1.0739 113.94 -123.80 110.35 1.0933 +IC H14A N *C14 H14C 1.0739 113.94 123.94 111.04 1.0955 +IC C12 N C15 H15A 1.5234 110.65 58.28 109.35 1.0868 +IC H15A N *C15 H15B 1.0868 109.35 -119.04 111.31 1.0812 +IC H15A N *C15 H15C 1.0868 109.35 119.05 111.13 1.0813 +IC C13 N C12 C11 1.4977 109.76 179.44 116.91 1.5438 +IC C11 N *C12 H12A 1.5438 116.91 -117.61 108.17 1.0972 +IC H12A N *C12 H12B 1.0972 108.17 -116.02 111.83 1.0787 +IC N C12 C11 O12 1.5234 116.91 -127.58 108.84 1.4249 +IC O12 C12 *C11 H11A 1.4249 108.84 -118.47 109.01 1.1128 +IC H11A C12 *C11 H11B 1.1128 109.01 -118.39 113.02 1.1135 +IC C12 C11 O12 P 1.5438 108.84 65.93 118.15 1.5894 +IC C11 O12 P O11 1.4249 118.15 166.63 104.29 1.5784 +IC O11 O12 *P O13 1.5784 104.29 -118.38 107.71 1.4804 +IC O11 O12 *P O14 1.5784 104.29 117.25 106.45 1.4817 +IC O12 P O11 C1 1.5894 104.29 -107.38 121.74 1.4308 +IC P O11 C1 C2 1.5784 121.74 131.98 111.51 1.5510 +IC C2 O11 *C1 HA 1.5510 111.51 -120.49 113.46 1.1176 +IC HA O11 *C1 HB 1.1176 113.46 -119.77 108.77 1.1122 +IC O11 C1 C2 C3 1.4308 111.51 175.42 110.00 1.5574 +IC C3 C1 *C2 O21 1.5574 110.00 121.11 108.48 1.4410 +IC C3 C1 *C2 HS 1.5574 110.00 -117.62 106.73 1.1166 +IC C1 C2 O21 C21 1.5510 108.48 145.04 114.43 1.3209 +IC C2 O21 C21 C22 1.4410 114.43 179.80 109.39 1.5280 +IC C22 O21 *C21 O22 1.5280 109.39 179.74 126.64 1.2169 +IC O21 C21 C22 C23 1.3209 109.39 -67.84 112.26 1.5462 +IC C23 C21 *C22 H2R 1.5462 112.26 -121.28 106.69 1.1085 +IC H2R C21 *C22 H2S 1.1085 106.69 -116.77 107.90 1.1093 +IC C1 C2 C3 O31 1.5510 110.00 164.12 112.50 1.4443 +IC O31 C2 *C3 HX 1.4443 112.50 -120.23 107.27 1.1140 +IC HX C2 *C3 HY 1.1140 107.27 -116.23 107.12 1.1157 +IC C2 C3 O31 C31 1.5574 112.50 171.18 113.30 1.3281 +IC C3 O31 C31 C32 1.4443 113.30 172.65 109.66 1.5265 +IC C32 O31 *C31 O32 1.5265 109.66 -176.72 125.32 1.2176 +IC O31 C31 C32 C33 1.3281 109.66 118.29 112.92 1.5439 +IC C33 C31 *C32 H2X 1.5439 112.92 -122.74 108.69 1.1092 +IC H2X C31 *C32 H2Y 1.1092 108.69 -117.30 106.71 1.1101 +IC C21 C22 C23 C24 1.5280 112.26 -178.01 113.07 1.5375 +IC C24 C22 *C23 H3R 1.5375 113.07 -120.13 108.37 1.1155 +IC H3R C22 *C23 H3S 1.1155 108.37 -117.16 109.92 1.1121 +IC C22 C23 C24 C25 1.5462 113.07 72.04 114.47 1.5401 +IC C25 C23 *C24 H4R 1.5401 114.47 -121.44 107.98 1.1136 +IC H4R C23 *C24 H4S 1.1136 107.98 -116.06 109.08 1.1119 +IC C23 C24 C25 C26 1.5375 114.47 72.07 114.75 1.5399 +IC C26 C24 *C25 H5R 1.5399 114.75 -122.59 109.09 1.1122 +IC H5R C24 *C25 H5S 1.1122 109.09 -116.42 108.63 1.1138 +IC C24 C25 C26 C27 1.5401 114.75 69.41 113.42 1.5375 +IC C27 C25 *C26 H6R 1.5375 113.42 -123.61 110.17 1.1112 +IC H6R C25 *C26 H6S 1.1112 110.17 -116.81 108.04 1.1144 +IC C25 C26 C27 C28 1.5399 113.42 175.01 112.75 1.5366 +IC C28 C26 *C27 H7R 1.5366 112.75 -120.37 108.41 1.1131 +IC H7R C26 *C27 H7S 1.1131 108.41 -117.31 109.76 1.1100 +IC C26 C27 C28 C29 1.5375 112.75 -170.66 113.89 1.5396 +IC C29 C27 *C28 H8R 1.5396 113.89 -124.54 110.37 1.1112 +IC H8R C27 *C28 H8S 1.1112 110.37 -116.46 107.16 1.1152 +IC C27 C28 C29 C210 1.5366 113.89 -94.88 115.55 1.5409 +IC C210 C28 *C29 H9R 1.5409 115.55 -118.30 107.09 1.1161 +IC H9R C28 *C29 H9S 1.1161 107.09 -116.01 110.08 1.1114 +IC C28 C29 C210 C211 1.5396 115.55 71.26 115.51 1.5429 +IC C29 C210 C211 C212 1.5409 115.51 -113.00 113.55 1.5944 +IC C210 C211 C212 C213 1.5429 113.55 124.84 129.45 1.6033 +IC C211 C212 C213 C214 1.5944 129.45 134.05 112.60 1.5516 +IC C212 C213 C216 H16R 1.6033 112.35 -177.11 110.41 1.1106 +IC C212 C213 C214 C215 1.6033 112.60 -70.19 115.90 1.5355 +IC C213 C214 C215 H15R 1.5516 115.90 -54.93 110.48 1.1107 +IC C31 C32 C33 C34 1.5265 112.92 174.13 112.74 1.5375 +IC C34 C32 *C33 H3X 1.5375 112.74 121.12 109.25 1.1147 +IC H3X C32 *C33 H3Y 1.1147 109.25 117.83 109.77 1.1147 +IC C32 C33 C34 C35 1.5439 112.74 54.96 113.41 1.5363 +IC C35 C33 *C34 H4X 1.5363 113.41 -121.93 109.71 1.1131 +IC H4X C33 *C34 H4Y 1.1131 109.71 -117.16 108.14 1.1144 +IC C33 C34 C35 C36 1.5375 113.41 164.07 112.78 1.5344 +IC C36 C34 *C35 H5X 1.5344 112.78 -119.88 108.50 1.1143 +IC H5X C34 *C35 H5Y 1.1143 108.50 -117.54 110.02 1.1123 +IC C34 C35 C36 C37 1.5363 112.78 -178.38 112.60 1.5352 +IC C37 C35 *C36 H6X 1.5352 112.60 -122.96 110.39 1.1117 +IC H6X C35 *C36 H6Y 1.1117 110.39 -117.16 107.71 1.1142 +IC C35 C36 C37 C38 1.5344 112.60 155.96 112.41 1.5346 +IC C38 C36 *C37 H7X 1.5346 112.41 -119.11 108.31 1.1145 +IC H7X C36 *C37 H7Y 1.1145 108.31 -117.37 109.92 1.1116 +IC C36 C37 C38 C39 1.5352 112.41 -175.46 113.04 1.5394 +IC C39 C37 *C38 H8X 1.5394 113.04 -123.81 110.27 1.1121 +IC H8X C37 *C38 H8Y 1.1121 110.27 -117.16 107.60 1.1155 +IC C37 C38 C39 C310 1.5346 113.04 155.31 113.10 1.5857 +IC C310 C38 *C39 H9X 1.5857 113.10 -118.74 106.59 1.1160 +IC H9X C38 *C39 H9Y 1.1160 106.59 -116.27 110.13 1.1104 +IC C38 C39 C310 C311 1.5394 113.10 115.61 128.44 1.6440 +IC C39 C310 C311 C312 1.5857 128.44 100.24 125.90 1.5875 +IC C310 C311 C312 C313 1.6440 125.90 105.39 114.86 1.5415 +IC C311 C312 C313 C314 1.5875 114.86 174.34 112.59 1.5359 +IC C312 C313 C314 C315 1.5415 112.59 168.88 113.53 1.5375 +IC C313 C314 C315 C316 1.5359 113.53 59.07 114.65 1.5320 +IC C314 C315 C316 H16X 1.5375 114.65 -62.80 110.72 1.1112 +IC C13 C12 *N C14 1.4977 109.76 -117.35 108.14 1.5027 +IC C13 C12 *N C15 1.4977 109.76 122.83 110.65 1.4953 +IC C12 N C13 H13A 1.5234 109.76 -58.20 109.63 1.0879 +IC H13A N *C13 H13B 1.0879 109.63 -118.63 110.88 1.0821 +IC H13A N *C13 H13C 1.0879 109.63 119.78 111.58 1.0810 +IC C12 N C14 H14A 1.5234 108.14 -178.85 113.94 1.0739 +IC H14A N *C14 H14B 1.0739 113.94 -123.80 110.35 1.0933 +IC H14A N *C14 H14C 1.0739 113.94 123.94 111.04 1.0955 +IC C12 N C15 H15A 1.5234 110.65 58.28 109.35 1.0868 +IC H15A N *C15 H15B 1.0868 109.35 -119.04 111.31 1.0812 +IC H15A N *C15 H15C 1.0868 109.35 119.05 111.13 1.0813 +IC C13 N C12 C11 1.4977 109.76 179.44 116.91 1.5438 +IC C11 N *C12 H12A 1.5438 116.91 -117.61 108.17 1.0972 +IC H12A N *C12 H12B 1.0972 108.17 -116.02 111.83 1.0787 +IC N C12 C11 O12 1.5234 116.91 -127.58 108.84 1.4249 +IC O12 C12 *C11 H11A 1.4249 108.84 -118.47 109.01 1.1128 +IC H11A C12 *C11 H11B 1.1128 109.01 -118.39 113.02 1.1135 +IC C12 C11 O12 P 1.5438 108.84 65.93 118.15 1.5894 +IC C11 O12 P O11 1.4249 118.15 166.63 104.29 1.5784 +IC O11 O12 *P O13 1.5784 104.29 -118.38 107.71 1.4804 +IC O11 O12 *P O14 1.5784 104.29 117.25 106.45 1.4817 +IC O12 P O11 C1 1.5894 104.29 -107.38 121.74 1.4308 +IC P O11 C1 C2 1.5784 121.74 131.98 111.51 1.5510 +IC C2 O11 *C1 HA 1.5510 111.51 -120.49 113.46 1.1176 +IC HA O11 *C1 HB 1.1176 113.46 -119.77 108.77 1.1122 +IC O11 C1 C2 C3 1.4308 111.51 175.42 110.00 1.5574 +IC C3 C1 *C2 O21 1.5574 110.00 121.11 108.48 1.4410 +IC C3 C1 *C2 HS 1.5574 110.00 -117.62 106.73 1.1166 +IC C1 C2 O21 C21 1.5510 108.48 145.04 114.43 1.3209 +IC C2 O21 C21 C22 1.4410 114.43 179.80 109.39 1.5280 +IC C22 O21 *C21 O22 1.5280 109.39 179.74 126.64 1.2169 +IC O21 C21 C22 C23 1.3209 109.39 -67.84 112.26 1.5462 +IC C23 C21 *C22 H2R 1.5462 112.26 -121.28 106.69 1.1085 +IC H2R C21 *C22 H2S 1.1085 106.69 -116.77 107.90 1.1093 +IC C1 C2 C3 O31 1.5510 110.00 164.12 112.50 1.4443 +IC O31 C2 *C3 HX 1.4443 112.50 -120.23 107.27 1.1140 +IC HX C2 *C3 HY 1.1140 107.27 -116.23 107.12 1.1157 +IC C2 C3 O31 C31 1.5574 112.50 171.18 113.30 1.3281 +IC C3 O31 C31 C32 1.4443 113.30 172.65 109.66 1.5265 +IC C32 O31 *C31 O32 1.5265 109.66 -176.72 125.32 1.2176 +IC O31 C31 C32 C33 1.3281 109.66 118.29 112.92 1.5439 +IC C33 C31 *C32 H2X 1.5439 112.92 -122.74 108.69 1.1092 +IC H2X C31 *C32 H2Y 1.1092 108.69 -117.30 106.71 1.1101 +IC C21 C22 C23 C24 1.5280 112.26 -178.01 113.07 1.5375 +IC C24 C22 *C23 H3R 1.5375 113.07 -120.13 108.37 1.1155 +IC H3R C22 *C23 H3S 1.1155 108.37 -117.16 109.92 1.1121 +IC C22 C23 C24 C25 1.5462 113.07 72.04 114.47 1.5401 +IC C25 C23 *C24 H4R 1.5401 114.47 -121.44 107.98 1.1136 +IC H4R C23 *C24 H4S 1.1136 107.98 -116.06 109.08 1.1119 +IC C23 C24 C25 C26 1.5375 114.47 72.07 114.75 1.5399 +IC C26 C24 *C25 H5R 1.5399 114.75 -122.59 109.09 1.1122 +IC H5R C24 *C25 H5S 1.1122 109.09 -116.42 108.63 1.1138 +IC C24 C25 C26 C27 1.5401 114.75 69.41 113.42 1.5375 +IC C27 C25 *C26 H6R 1.5375 113.42 -123.61 110.17 1.1112 +IC H6R C25 *C26 H6S 1.1112 110.17 -116.81 108.04 1.1144 +IC C25 C26 C27 C28 1.5399 113.42 175.01 112.75 1.5366 +IC C28 C26 *C27 H7R 1.5366 112.75 -120.37 108.41 1.1131 +IC H7R C26 *C27 H7S 1.1131 108.41 -117.31 109.76 1.1100 +IC C26 C27 C28 C29 1.5375 112.75 -170.66 113.89 1.5396 +IC C29 C27 *C28 H8R 1.5396 113.89 -124.54 110.37 1.1112 +IC H8R C27 *C28 H8S 1.1112 110.37 -116.46 107.16 1.1152 +IC C27 C28 C29 C210 1.5366 113.89 -94.88 115.55 1.5409 +IC C210 C28 *C29 H9R 1.5409 115.55 -118.30 107.09 1.1161 +IC H9R C28 *C29 H9S 1.1161 107.09 -116.01 110.08 1.1114 +IC C28 C29 C210 C211 1.5396 115.55 71.26 115.51 1.5429 +IC C211 C29 *C210 H10R 1.5429 115.51 -124.74 109.78 1.1124 +IC H10R C29 *C210 H10S 1.1124 109.78 -115.43 107.14 1.1152 +IC C29 C210 C211 C212 1.5409 115.51 -113.00 113.55 1.5944 +IC C212 C210 *C211 H11R 1.5944 113.55 124.78 110.23 1.1102 +IC H11R C210 *C211 H11S 1.1102 110.23 115.57 106.28 1.1164 +IC C210 C211 C212 C213 1.5429 113.55 124.84 129.45 1.6033 +IC C213 C211 *C212 H12R 1.6033 129.45 71.12 80.77 1.1280 +IC H12R C211 *C212 H12S 1.1280 80.77 -141.35 78.76 1.1274 +IC C211 C212 C213 C214 1.5944 129.45 134.05 112.60 1.5516 +IC C214 C212 *C213 C216 1.5516 112.60 121.91 112.35 1.5453 +IC C214 C212 *C213 H13R 1.5516 112.60 -119.57 108.53 1.1145 +IC C212 C213 C216 H16R 1.6033 112.35 -177.11 110.41 1.1106 +IC H16R C213 *C216 H16S 1.1106 110.41 119.94 109.73 1.1102 +IC H16R C213 *C216 H16T 1.1106 110.41 -119.78 111.42 1.1093 +IC C212 C213 C214 C215 1.6033 112.60 -70.19 115.90 1.5355 +IC C215 C213 *C214 H14R 1.5355 115.90 -120.66 107.62 1.1147 +IC H14R C213 *C214 H14S 1.1147 107.62 -115.55 108.33 1.1128 +IC C213 C214 C215 H15R 1.5516 115.90 -54.93 110.48 1.1107 +IC H15R C214 *C215 H15S 1.1107 110.48 -119.77 110.23 1.1115 +IC H15R C214 *C215 H15T 1.1107 110.48 120.66 110.97 1.1105 +IC C31 C32 C33 C34 1.5265 112.92 174.13 112.74 1.5375 +IC C34 C32 *C33 H3X 1.5375 112.74 121.12 109.25 1.1147 +IC H3X C32 *C33 H3Y 1.1147 109.25 117.83 109.77 1.1147 +IC C32 C33 C34 C35 1.5439 112.74 54.96 113.41 1.5363 +IC C35 C33 *C34 H4X 1.5363 113.41 -121.93 109.71 1.1131 +IC H4X C33 *C34 H4Y 1.1131 109.71 -117.16 108.14 1.1144 +IC C33 C34 C35 C36 1.5375 113.41 164.07 112.78 1.5344 +IC C36 C34 *C35 H5X 1.5344 112.78 -119.88 108.50 1.1143 +IC H5X C34 *C35 H5Y 1.1143 108.50 -117.54 110.02 1.1123 +IC C34 C35 C36 C37 1.5363 112.78 -178.38 112.60 1.5352 +IC C37 C35 *C36 H6X 1.5352 112.60 -122.96 110.39 1.1117 +IC H6X C35 *C36 H6Y 1.1117 110.39 -117.16 107.71 1.1142 +IC C35 C36 C37 C38 1.5344 112.60 155.96 112.41 1.5346 +IC C38 C36 *C37 H7X 1.5346 112.41 -119.11 108.31 1.1145 +IC H7X C36 *C37 H7Y 1.1145 108.31 -117.37 109.92 1.1116 +IC C36 C37 C38 C39 1.5352 112.41 -175.46 113.04 1.5394 +IC C39 C37 *C38 H8X 1.5394 113.04 -123.81 110.27 1.1121 +IC H8X C37 *C38 H8Y 1.1121 110.27 -117.16 107.60 1.1155 +IC C37 C38 C39 C310 1.5346 113.04 155.31 113.10 1.5857 +IC C310 C38 *C39 H9X 1.5857 113.10 -118.74 106.59 1.1160 +IC H9X C38 *C39 H9Y 1.1160 106.59 -116.27 110.13 1.1104 +IC C38 C39 C310 C311 1.5394 113.10 115.61 128.44 1.6440 +IC C311 C39 *C310 H10X 1.6440 128.44 -64.26 80.14 1.1359 +IC H10X C39 *C310 H10Y 1.1359 80.14 144.67 83.79 1.1359 +IC C39 C310 C311 C312 1.5857 128.44 100.24 125.90 1.5875 +IC C312 C310 *C311 H11X 1.5875 125.90 67.21 75.11 1.1333 +IC H11X C310 *C311 H11Y 1.1333 75.11 -147.67 86.45 1.1361 +IC C310 C311 C312 C313 1.6440 125.90 105.39 114.86 1.5415 +IC C313 C311 *C312 H12X 1.5415 114.86 -123.19 109.95 1.1116 +IC H12X C311 *C312 H12Y 1.1116 109.95 -117.26 108.16 1.1146 +IC C311 C312 C313 C314 1.5875 114.86 174.34 112.59 1.5359 +IC C314 C312 *C313 H13X 1.5359 112.59 120.46 109.45 1.1137 +IC H13X C312 *C313 H13Y 1.1137 109.45 117.68 109.07 1.1125 +IC C312 C313 C314 C315 1.5415 112.59 168.88 113.53 1.5375 +IC C315 C313 *C314 H14X 1.5375 113.53 122.36 109.06 1.1127 +IC H14X C313 *C314 H14Y 1.1127 109.06 117.00 108.67 1.1138 +IC C313 C314 C315 C316 1.5359 113.53 59.07 114.65 1.5320 +IC C316 C314 *C315 H15X 1.5320 114.65 -121.81 108.43 1.1144 +IC H15X C314 *C315 H15Y 1.1144 108.43 -116.12 108.44 1.1143 +IC C314 C315 C316 H16X 1.5375 114.65 -62.80 110.72 1.1112 +IC H16X C315 *C316 H16Y 1.1112 110.72 -119.94 110.43 1.1115 +IC H16X C315 *C316 H16Z 1.1112 110.72 120.13 110.53 1.1108 +PATCHING FIRST NONE LAST NONE + +RESI PhPC 0.00 ! 1,2 diphytanoyl-SN-glycero-3-Phosphorylcholine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - N(CH3)3 +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL1 -0.09 ! | | +ATOM H3R HAL1 0.09 ! H3R ---C23--C217-H17R | +ATOM C217 CTL3 -0.27 ! | | \ | +ATOM H17R HAL3 0.09 ! | | H17S | +ATOM H17S HAL3 0.09 ! | H17T | +ATOM H17T HAL3 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL1 -0.09 ! | | +ATOM H7R HAL1 0.09 ! H7R ---C27--C218-H18R | +ATOM C218 CTL3 -0.27 ! | | \ | +ATOM H18R HAL3 0.09 ! | | H18S | +ATOM H18S HAL3 0.09 ! | H18T | +ATOM H18T HAL3 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL1 -0.09 ! | | +ATOM H11R HAL1 0.09 ! H11R---C211-C219-H19R | +ATOM C219 CTL3 -0.27 ! | | \ | +ATOM H19R HAL3 0.09 ! | | H19S | +ATOM H19S HAL3 0.09 ! | H19T | +ATOM H19T HAL3 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL1 -0.09 ! | | +ATOM H15R HAL1 0.09 ! H15R---C215-C220-H20R | +ATOM C220 CTL3 -0.27 ! | | \ | +ATOM H20R HAL3 0.09 ! | | H20S | +ATOM H20S HAL3 0.09 ! | H20T | +ATOM H20T HAL3 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL1 -0.09 ! | +ATOM H3X HAL1 0.09 ! H3X ---C33--C317--H17X +ATOM C317 CTL3 -0.27 ! | | \ +ATOM H17X HAL3 0.09 ! | | \ +ATOM H17Y HAL3 0.09 ! | | H17Y +ATOM H17Z HAL3 0.09 ! | H17Z +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL1 -0.09 ! | +ATOM H7X HAL1 0.09 ! H7X ---C37--C318--H18X +ATOM C318 CTL3 -0.27 ! | | \ +ATOM H18X HAL3 0.09 ! | | \ +ATOM H18Y HAL3 0.09 ! | | H18Y +ATOM H18Z HAL3 0.09 ! | H18Z +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL1 -0.09 ! | +ATOM H11X HAL1 0.09 ! H11X---C311-C319--H19X +ATOM C319 CTL3 -0.27 ! | | \ +ATOM H19X HAL3 0.09 ! | | \ +ATOM H19Y HAL3 0.09 ! | | H19Y +ATOM H19Z HAL3 0.09 ! | H19Z +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL1 -0.09 ! | +ATOM H15X HAL1 0.09 ! H15X---C315-C320--H20X +ATOM C320 CTL3 -0.27 ! | | \ +ATOM H20X HAL3 0.09 ! | | \ +ATOM H20Y HAL3 0.09 ! | | H20Y +ATOM H20Z HAL3 0.09 ! | H20Z +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 C217 C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 C218 C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 C219 C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 C220 C215 C216 +BOND C216 H16R C216 H16S C216 H16T +BOND C217 H17R C217 H17S C217 H17T +BOND C218 H18R C218 H18S C218 H18T +BOND C219 H19R C219 H19S C219 H19T +BOND C220 H20R C220 H20S C220 H20T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 C317 C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 C318 C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 C319 C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 C320 C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z +BOND C317 H17X C317 H17Y C317 H17Z +BOND C318 H18X C318 H18Y C318 H18Z +BOND C319 H19X C319 H19Y C319 H19Z +BOND C320 H20X C320 H20Y C320 H20Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! Polar head (angle names from Sundaralingam) +IC C2 C1 O11 P 1.5491 111.37 -173.91 118.16 1.5904 +IC C1 O11 P O12 1.4304 118.16 -113.39 100.60 1.5872 +IC O11 O12 *P O13 1.5904 100.60 -113.84 106.86 1.4799 +IC O11 O12 *P O14 1.5904 100.60 116.28 109.07 1.4728 +IC O11 P O12 C11 1.5904 100.60 50.71 118.11 1.4136 +IC O12 C12 *C11 H11A 1.4136 102.76 -118.22 112.41 1.1137 +IC O12 C12 *C11 H11B 1.4136 102.76 119.32 110.63 1.1171 +IC P O12 C11 C12 1.5872 118.11 164.00 102.76 1.5198 +IC N C11 *C12 H12A 1.5162 116.25 124.05 105.45 1.0866 +IC N C11 *C12 H12B 1.5162 116.25 -124.58 105.76 1.0856 +IC O12 C11 C12 N 1.4136 102.76 179.33 116.25 1.5162 +IC C11 C12 N C13 1.5198 116.25 -60.68 109.10 1.5002 +IC C12 C13 *N C14 1.5162 109.10 120.45 109.94 1.4983 +IC C12 C13 *N C15 1.5162 109.10 -119.21 109.14 1.5010 +IC O11 C1 C2 C3 1.4304 111.37 170.15 109.23 1.5574 +IC C1 C2 C3 O31 1.5491 109.23 -179.19 113.15 1.4399 +IC C1 C3 *C2 O21 1.5491 109.23 -119.93 110.27 1.4452 +IC O11 C2 *C1 HA 1.4304 111.37 122.42 108.48 1.1135 +IC O11 C2 *C1 HB 1.4304 111.37 -120.75 107.20 1.1172 +IC O21 C1 *C2 HS 1.4452 109.14 121.79 106.46 1.1174 +IC O31 C2 *C3 HX 1.4399 113.15 -119.05 106.76 1.1127 +IC O31 C2 *C3 HY 1.4399 113.15 125.71 109.47 1.1145 +IC C1 C2 O21 C21 1.5491 109.14 150.68 114.41 1.3285 +IC C2 O21 C21 C22 1.4452 114.41 176.87 109.25 1.5285 +IC O21 C21 C22 C23 1.3285 109.25 -111.60 112.63 1.5527 +IC C22 O21 *C21 O22 1.5285 109.25 179.37 126.18 1.2162 +IC C21 C22 C23 C24 1.5285 112.63 -67.95 114.00 1.5450 +IC C22 C23 C24 C25 1.5527 114.00 -64.25 114.28 1.5363 +IC C23 C24 C25 C26 1.5450 114.28 -174.25 112.52 1.5387 +IC C24 C25 C26 C27 1.5363 112.52 168.22 113.60 1.5464 +IC C25 C26 C27 C28 1.5387 113.60 160.56 112.30 1.5456 +IC C26 C27 C28 C29 1.5464 112.30 -75.09 112.89 1.5372 +IC C27 C28 C29 C210 1.5456 112.89 179.30 113.66 1.5383 +IC C28 C29 C210 C211 1.5372 113.66 -172.26 112.87 1.5465 +IC C29 C210 C211 C212 1.5383 112.87 172.46 113.09 1.5448 +IC C210 C211 C212 C213 1.5465 113.09 -60.75 114.64 1.5370 +IC C211 C212 C213 C214 1.5448 114.64 -162.28 111.85 1.5374 +IC C212 C213 C214 C215 1.5370 111.85 -173.72 115.06 1.5438 +IC C213 C214 C215 C216 1.5374 115.06 -54.53 112.62 1.5376 +IC C21 C22 C23 C217 1.5285 112.63 57.75 111.36 1.5389 +IC C25 C26 C27 C218 1.5387 113.60 -75.44 110.81 1.5396 +IC C29 C210 C211 C219 1.5383 112.87 -63.21 111.91 1.5404 +IC C213 C214 C215 C220 1.5374 115.06 -177.66 110.12 1.5377 +IC C2 C3 O31 C31 1.5574 113.15 80.22 114.41 1.3349 +IC C3 O31 C31 C32 1.4399 114.41 -176.59 108.40 1.5182 +IC O31 C31 C32 C33 1.3349 108.40 -75.68 109.71 1.5454 +IC C32 O31 *C31 O32 1.5182 108.40 -178.01 125.70 1.2157 +IC C31 C32 C33 C34 1.5182 109.71 159.75 112.55 1.5415 +IC C32 C33 C34 C35 1.5454 112.55 -63.23 112.93 1.5379 +IC C33 C34 C35 C36 1.5415 112.93 -150.58 112.65 1.5362 +IC C34 C35 C36 C37 1.5379 112.65 176.72 113.84 1.5439 +IC C35 C36 C37 C38 1.5362 113.84 72.60 112.19 1.5458 +IC C36 C37 C38 C39 1.5439 112.19 -166.57 113.01 1.5371 +IC C37 C38 C39 C310 1.5458 113.01 172.46 113.51 1.5388 +IC C38 C39 C310 C311 1.5371 113.51 -179.74 112.96 1.5472 +IC C39 C310 C311 C312 1.5388 112.96 -167.32 113.47 1.5463 +IC C310 C311 C312 C313 1.5472 113.47 58.94 114.52 1.5362 +IC C311 C312 C313 C314 1.5463 114.52 166.86 112.83 1.5380 +IC C312 C313 C314 C315 1.5362 112.83 175.69 113.23 1.5430 +IC C313 C314 C315 C316 1.5380 113.23 160.57 111.18 1.5373 +IC C31 C32 C33 C317 1.5182 109.71 -75.36 110.58 1.5378 +IC C35 C36 C37 C318 1.5362 113.84 -162.39 110.06 1.5399 +IC C39 C310 C311 C319 1.5388 112.96 68.75 111.24 1.5407 +IC C313 C314 C315 C320 1.5380 113.23 -76.09 111.76 1.5380 +IC C13 C12 *N C14 1.5002 109.10 -120.54 109.79 1.4983 +IC C13 C12 *N C15 1.5002 109.10 119.20 109.17 1.5010 +IC C12 N C13 H13A 1.5162 109.10 -59.54 110.98 1.0839 +IC H13A N *C13 H13B 1.0839 110.98 -121.90 111.84 1.0802 +IC H13A N *C13 H13C 1.0839 110.98 117.68 109.78 1.0875 +IC C12 N C14 H14A 1.5162 109.79 58.97 110.86 1.0845 +IC H14A N *C14 H14B 1.0845 110.86 -119.40 110.72 1.0849 +IC H14A N *C14 H14C 1.0845 110.86 120.42 111.18 1.0823 +IC C12 N C15 H15A 1.5162 109.17 58.01 111.00 1.0846 +IC H15A N *C15 H15B 1.0846 111.00 -117.39 109.91 1.0875 +IC H15A N *C15 H15C 1.0846 111.00 122.00 111.98 1.0800 +IC C13 N C12 C11 1.5002 109.10 -60.68 116.25 1.5198 +IC C11 N *C12 H12A 1.5198 116.25 -120.88 111.48 1.0866 +IC H12A N *C12 H12B 1.0866 111.48 -117.64 111.70 1.0856 +IC N C12 C11 O12 1.5162 116.25 179.33 102.76 1.4136 +IC O12 C12 *C11 H11A 1.4136 102.76 -118.22 112.41 1.1137 +IC H11A C12 *C11 H11B 1.1137 112.41 -122.45 110.63 1.1171 +IC C12 C11 O12 P 1.5198 102.76 164.00 118.11 1.5872 +IC C11 O12 P O11 1.4136 118.11 50.71 100.60 1.5904 +IC O11 O12 *P O13 1.5904 100.60 -113.84 106.86 1.4799 +IC O11 O12 *P O14 1.5904 100.60 116.28 109.07 1.4728 +IC O12 P O11 C1 1.5872 100.60 -113.39 118.16 1.4304 +IC P O11 C1 C2 1.5904 118.16 -173.91 111.37 1.5491 +IC C2 O11 *C1 HA 1.5491 111.37 -120.97 110.98 1.1135 +IC HA O11 *C1 HB 1.1135 110.98 -120.12 110.31 1.1172 +IC O11 C1 C2 C3 1.4304 111.37 170.15 109.23 1.5574 +IC C3 C1 *C2 O21 1.5574 109.23 120.62 109.14 1.4452 +IC C3 C1 *C2 HS 1.5574 109.23 -117.59 106.46 1.1174 +IC C1 C2 O21 C21 1.5491 109.14 150.68 114.41 1.3285 +IC C2 O21 C21 C22 1.4452 114.41 176.87 109.25 1.5285 +IC C22 O21 *C21 O22 1.5285 109.25 179.37 126.18 1.2162 +IC O21 C21 C22 C23 1.3285 109.25 -111.60 112.63 1.5527 +IC C23 C21 *C22 H2R 1.5527 112.63 -121.74 107.41 1.1074 +IC H2R C21 *C22 H2S 1.1074 107.41 -116.96 108.74 1.1080 +IC C1 C2 C3 O31 1.5491 109.23 -179.19 113.15 1.4399 +IC O31 C2 *C3 HX 1.4399 113.15 -119.05 106.76 1.1127 +IC HX C2 *C3 HY 1.1127 106.76 -115.24 109.47 1.1145 +IC C2 C3 O31 C31 1.5574 113.15 80.22 114.41 1.3349 +IC C3 O31 C31 C32 1.4399 114.41 -176.59 108.40 1.5182 +IC C32 O31 *C31 O32 1.5182 108.40 -178.01 125.70 1.2157 +IC O31 C31 C32 C33 1.3349 108.40 -75.68 109.71 1.5454 +IC C33 C31 *C32 H2X 1.5454 109.71 -121.47 108.57 1.1076 +IC H2X C31 *C32 H2Y 1.1076 108.57 -117.26 107.31 1.1076 +IC C21 C22 C23 C24 1.5285 112.63 -67.95 114.00 1.5450 +IC C24 C22 *C23 C217 1.5450 114.00 125.71 111.36 1.5389 +IC C217 C22 *C23 H3R 1.5389 111.36 116.87 107.04 1.1178 +IC C22 C23 C217 H17R 1.5527 111.36 -67.24 110.75 1.1112 +IC C22 C23 C24 C25 1.5527 114.00 -64.25 114.28 1.5363 +IC C25 C23 *C24 H4R 1.5363 114.28 -119.34 107.37 1.1125 +IC H4R C23 *C24 H4S 1.1125 107.37 -116.53 110.36 1.1105 +IC C23 C24 C25 C26 1.5450 114.28 -174.25 112.52 1.5387 +IC C26 C24 *C25 H5R 1.5387 112.52 -120.60 109.83 1.1130 +IC H5R C24 *C25 H5S 1.1130 109.83 -117.76 108.40 1.1109 +IC C24 C25 C26 C27 1.5363 112.52 168.22 113.60 1.5464 +IC C27 C25 *C26 H6R 1.5464 113.60 -121.40 109.83 1.1119 +IC H6R C25 *C26 H6S 1.1119 109.83 -116.45 107.75 1.1116 +IC C25 C26 C27 C28 1.5387 113.60 160.56 112.30 1.5456 +IC C28 C26 *C27 C218 1.5456 112.30 124.00 110.81 1.5396 +IC C218 C26 *C27 H7R 1.5396 110.81 118.13 108.02 1.1159 +IC C26 C27 C28 C29 1.5464 112.30 -75.09 112.89 1.5372 +IC C29 C27 *C28 H8R 1.5372 112.89 -119.68 108.66 1.1131 +IC H8R C27 *C28 H8S 1.1131 108.66 -117.27 109.20 1.1112 +IC C27 C28 C29 C210 1.5456 112.89 179.30 113.66 1.5383 +IC C210 C28 *C29 H9R 1.5383 113.66 -121.19 109.51 1.1120 +IC H9R C28 *C29 H9S 1.1120 109.51 -116.95 108.20 1.1126 +IC C28 C29 C210 C211 1.5372 113.66 -172.26 112.87 1.5465 +IC C29 C210 C211 C212 1.5383 112.87 172.46 113.09 1.5448 +IC C210 C211 C212 C213 1.5465 113.09 -60.75 114.64 1.5370 +IC C211 C212 C213 C214 1.5448 114.64 -162.28 111.85 1.5374 +IC C212 C213 C214 C215 1.5370 111.85 -173.72 115.06 1.5438 +IC C213 C214 C215 C220 1.5374 115.06 -177.66 110.12 1.5377 +IC C214 C215 C216 H16R 1.5438 112.62 -56.60 110.30 1.1104 +IC C31 C32 C33 C34 1.5182 109.71 159.75 112.55 1.5415 +IC C34 C32 *C33 C317 1.5415 112.55 124.89 110.58 1.5378 +IC C317 C32 *C33 H3X 1.5378 110.58 118.15 108.74 1.1188 +IC C32 C33 C317 H17X 1.5454 110.58 179.81 110.56 1.1102 +IC C32 C33 C34 C35 1.5454 112.55 -63.23 112.93 1.5379 +IC C35 C33 *C34 H4X 1.5379 112.93 -119.35 107.22 1.1137 +IC H4X C33 *C34 H4Y 1.1137 107.22 -116.92 110.30 1.1110 +IC C33 C34 C35 C36 1.5415 112.93 -150.58 112.65 1.5362 +IC C36 C34 *C35 H5X 1.5362 112.65 -123.48 109.14 1.1113 +IC H5X C34 *C35 H5Y 1.1113 109.14 -116.94 108.81 1.1142 +IC C34 C35 C36 C37 1.5379 112.65 176.72 113.84 1.5439 +IC C37 C35 *C36 H6X 1.5439 113.84 -119.26 107.42 1.1144 +IC H6X C35 *C36 H6Y 1.1144 107.42 -117.09 110.33 1.1107 +IC C35 C36 C37 C38 1.5362 113.84 72.60 112.19 1.5458 +IC C38 C36 *C37 C318 1.5458 112.19 125.01 110.06 1.5399 +IC C318 C36 *C37 H7X 1.5399 110.06 116.88 107.24 1.1163 +IC C36 C37 C318 H18X 1.5439 110.06 58.61 110.20 1.1107 +IC C36 C37 C38 C39 1.5439 112.19 -166.57 113.01 1.5371 +IC C39 C37 *C38 H8X 1.5371 113.01 -122.96 109.28 1.1113 +IC H8X C37 *C38 H8Y 1.1113 109.28 -116.96 108.98 1.1103 +IC C37 C38 C39 C310 1.5458 113.01 172.46 113.51 1.5388 +IC C310 C38 *C39 H9X 1.5388 113.51 -121.66 107.92 1.1115 +IC H9X C38 *C39 H9Y 1.1115 107.92 -117.07 109.46 1.1125 +IC C38 C39 C310 C311 1.5371 113.51 -179.74 112.96 1.5472 +IC C39 C310 C311 C312 1.5388 112.96 -167.32 113.47 1.5463 +IC C310 C311 C319 H19X 1.5472 111.24 -59.97 111.11 1.1088 +IC C310 C311 C312 C313 1.5472 113.47 58.94 114.52 1.5362 +IC C311 C312 C313 C314 1.5463 114.52 166.86 112.83 1.5380 +IC C312 C313 C314 C315 1.5362 112.83 175.69 113.23 1.5430 +IC C313 C314 C315 C320 1.5380 113.23 -76.09 111.76 1.5380 +IC C314 C315 C320 H20X 1.5430 111.76 -70.16 110.13 1.1108 +IC C314 C315 C316 H16X 1.5430 111.18 -179.80 110.31 1.1107 +IC C13 C12 *N C14 1.5002 109.10 -120.54 109.79 1.4983 +IC C13 C12 *N C15 1.5002 109.10 119.20 109.17 1.5010 +IC C12 N C13 H13A 1.5162 109.10 -59.54 110.98 1.0839 +IC H13A N *C13 H13B 1.0839 110.98 -121.90 111.84 1.0802 +IC H13A N *C13 H13C 1.0839 110.98 117.68 109.78 1.0875 +IC C12 N C14 H14A 1.5162 109.79 58.97 110.86 1.0845 +IC H14A N *C14 H14B 1.0845 110.86 -119.40 110.72 1.0849 +IC H14A N *C14 H14C 1.0845 110.86 120.42 111.18 1.0823 +IC C12 N C15 H15A 1.5162 109.17 58.01 111.00 1.0846 +IC H15A N *C15 H15B 1.0846 111.00 -117.39 109.91 1.0875 +IC H15A N *C15 H15C 1.0846 111.00 122.00 111.98 1.0800 +IC C13 N C12 C11 1.5002 109.10 -60.68 116.25 1.5198 +IC C11 N *C12 H12A 1.5198 116.25 -120.88 111.48 1.0866 +IC H12A N *C12 H12B 1.0866 111.48 -117.64 111.70 1.0856 +IC N C12 C11 O12 1.5162 116.25 179.33 102.76 1.4136 +IC O12 C12 *C11 H11A 1.4136 102.76 -118.22 112.41 1.1137 +IC H11A C12 *C11 H11B 1.1137 112.41 -122.45 110.63 1.1171 +IC C12 C11 O12 P 1.5198 102.76 164.00 118.11 1.5872 +IC C11 O12 P O11 1.4136 118.11 50.71 100.60 1.5904 +IC O11 O12 *P O13 1.5904 100.60 -113.84 106.86 1.4799 +IC O11 O12 *P O14 1.5904 100.60 116.28 109.07 1.4728 +IC O12 P O11 C1 1.5872 100.60 -113.39 118.16 1.4304 +IC P O11 C1 C2 1.5904 118.16 -173.91 111.37 1.5491 +IC C2 O11 *C1 HA 1.5491 111.37 -120.97 110.98 1.1135 +IC HA O11 *C1 HB 1.1135 110.98 -120.12 110.31 1.1172 +IC O11 C1 C2 C3 1.4304 111.37 170.15 109.23 1.5574 +IC C3 C1 *C2 O21 1.5574 109.23 120.62 109.14 1.4452 +IC C3 C1 *C2 HS 1.5574 109.23 -117.59 106.46 1.1174 +IC C1 C2 O21 C21 1.5491 109.14 150.68 114.41 1.3285 +IC C2 O21 C21 C22 1.4452 114.41 176.87 109.25 1.5285 +IC C22 O21 *C21 O22 1.5285 109.25 179.37 126.18 1.2162 +IC O21 C21 C22 C23 1.3285 109.25 -111.60 112.63 1.5527 +IC C23 C21 *C22 H2R 1.5527 112.63 -121.74 107.41 1.1074 +IC H2R C21 *C22 H2S 1.1074 107.41 -116.96 108.74 1.1080 +IC C1 C2 C3 O31 1.5491 109.23 -179.19 113.15 1.4399 +IC O31 C2 *C3 HX 1.4399 113.15 -119.05 106.76 1.1127 +IC HX C2 *C3 HY 1.1127 106.76 -115.24 109.47 1.1145 +IC C2 C3 O31 C31 1.5574 113.15 80.22 114.41 1.3349 +IC C3 O31 C31 C32 1.4399 114.41 -176.59 108.40 1.5182 +IC C32 O31 *C31 O32 1.5182 108.40 -178.01 125.70 1.2157 +IC O31 C31 C32 C33 1.3349 108.40 -75.68 109.71 1.5454 +IC C33 C31 *C32 H2X 1.5454 109.71 -121.47 108.57 1.1076 +IC H2X C31 *C32 H2Y 1.1076 108.57 -117.26 107.31 1.1076 +IC C21 C22 C23 C24 1.5285 112.63 -67.95 114.00 1.5450 +IC C24 C22 *C23 C217 1.5450 114.00 125.71 111.36 1.5389 +IC C217 C22 *C23 H3R 1.5389 111.36 116.87 107.04 1.1178 +IC C22 C23 C217 H17R 1.5527 111.36 -67.24 110.75 1.1112 +IC H17R C23 *C217 H17S 1.1112 110.75 -119.27 110.24 1.1110 +IC H17R C23 *C217 H17T 1.1112 110.75 120.46 110.74 1.1098 +IC C22 C23 C24 C25 1.5527 114.00 -64.25 114.28 1.5363 +IC C25 C23 *C24 H4R 1.5363 114.28 -119.34 107.37 1.1125 +IC H4R C23 *C24 H4S 1.1125 107.37 -116.53 110.36 1.1105 +IC C23 C24 C25 C26 1.5450 114.28 -174.25 112.52 1.5387 +IC C26 C24 *C25 H5R 1.5387 112.52 -120.60 109.83 1.1130 +IC H5R C24 *C25 H5S 1.1130 109.83 -117.76 108.40 1.1109 +IC C24 C25 C26 C27 1.5363 112.52 168.22 113.60 1.5464 +IC C27 C25 *C26 H6R 1.5464 113.60 -121.40 109.83 1.1119 +IC H6R C25 *C26 H6S 1.1119 109.83 -116.45 107.75 1.1116 +IC C25 C26 C27 C28 1.5387 113.60 160.56 112.30 1.5456 +IC C28 C26 *C27 C218 1.5456 112.30 124.00 110.81 1.5396 +IC C218 C26 *C27 H7R 1.5396 110.81 118.13 108.02 1.1159 +IC C26 C27 C218 H18R 1.5464 110.81 -60.09 110.29 1.1107 +IC H18R C27 *C218 H18S 1.1107 110.29 -120.03 110.54 1.1100 +IC H18R C27 *C218 H18T 1.1107 110.29 120.01 110.67 1.1092 +IC C26 C27 C28 C29 1.5464 112.30 -75.09 112.89 1.5372 +IC C29 C27 *C28 H8R 1.5372 112.89 -119.68 108.66 1.1131 +IC H8R C27 *C28 H8S 1.1131 108.66 -117.27 109.20 1.1112 +IC C27 C28 C29 C210 1.5456 112.89 179.30 113.66 1.5383 +IC C210 C28 *C29 H9R 1.5383 113.66 -121.19 109.51 1.1120 +IC H9R C28 *C29 H9S 1.1120 109.51 -116.95 108.20 1.1126 +IC C28 C29 C210 C211 1.5372 113.66 -172.26 112.87 1.5465 +IC C211 C29 *C210 H10R 1.5465 112.87 -122.46 109.95 1.1111 +IC H10R C29 *C210 H10S 1.1111 109.95 -117.30 107.81 1.1120 +IC C29 C210 C211 C212 1.5383 112.87 172.46 113.09 1.5448 +IC C212 C210 *C211 C219 1.5448 113.09 124.32 111.91 1.5404 +IC C219 C210 *C211 H11R 1.5404 111.91 117.85 107.24 1.1168 +IC C210 C211 C219 H19R 1.5465 111.91 179.48 110.18 1.1106 +IC H19R C211 *C219 H19S 1.1106 110.18 -119.57 111.09 1.1092 +IC H19R C211 *C219 H19T 1.1106 110.18 119.78 110.29 1.1102 +IC C210 C211 C212 C213 1.5465 113.09 -60.75 114.64 1.5370 +IC C213 C211 *C212 H12R 1.5370 114.64 -119.75 107.17 1.1142 +IC H12R C211 *C212 H12S 1.1142 107.17 -116.41 109.65 1.1112 +IC C211 C212 C213 C214 1.5448 114.64 -162.28 111.85 1.5374 +IC C214 C212 *C213 H13R 1.5374 111.85 -121.89 109.61 1.1120 +IC H13R C212 *C213 H13S 1.1120 109.61 -117.75 108.52 1.1130 +IC C212 C213 C214 C215 1.5370 111.85 -173.72 115.06 1.5438 +IC C215 C213 *C214 H14R 1.5438 115.06 -121.85 108.56 1.1129 +IC H14R C213 *C214 H14S 1.1129 108.56 -116.70 108.75 1.1130 +IC C213 C214 C215 C220 1.5374 115.06 -177.66 110.12 1.5377 +IC C220 C214 *C215 C216 1.5377 110.12 123.13 112.62 1.5376 +IC C220 C214 *C215 H15R 1.5377 110.12 -117.80 107.84 1.1164 +IC C214 C215 C220 H20R 1.5438 110.12 -176.18 110.52 1.1102 +IC H20R C215 *C220 H20S 1.1102 110.52 -119.77 110.07 1.1111 +IC H20R C215 *C220 H20T 1.1102 110.52 120.39 110.56 1.1103 +IC C214 C215 C216 H16R 1.5438 112.62 -56.60 110.30 1.1104 +IC H16R C215 *C216 H16S 1.1104 110.30 -119.87 110.26 1.1105 +IC H16R C215 *C216 H16T 1.1104 110.30 120.39 110.82 1.1099 +IC C31 C32 C33 C34 1.5182 109.71 159.75 112.55 1.5415 +IC C34 C32 *C33 C317 1.5415 112.55 124.89 110.58 1.5378 +IC C317 C32 *C33 H3X 1.5378 110.58 118.15 108.74 1.1188 +IC C32 C33 C317 H17X 1.5454 110.58 179.81 110.56 1.1102 +IC H17X C33 *C317 H17Y 1.1102 110.56 -120.19 110.88 1.1112 +IC H17X C33 *C317 H17Z 1.1102 110.56 119.98 110.27 1.1110 +IC C32 C33 C34 C35 1.5454 112.55 -63.23 112.93 1.5379 +IC C35 C33 *C34 H4X 1.5379 112.93 -119.35 107.22 1.1137 +IC H4X C33 *C34 H4Y 1.1137 107.22 -116.92 110.30 1.1110 +IC C33 C34 C35 C36 1.5415 112.93 -150.58 112.65 1.5362 +IC C36 C34 *C35 H5X 1.5362 112.65 -123.48 109.14 1.1113 +IC H5X C34 *C35 H5Y 1.1113 109.14 -116.94 108.81 1.1142 +IC C34 C35 C36 C37 1.5379 112.65 176.72 113.84 1.5439 +IC C37 C35 *C36 H6X 1.5439 113.84 -119.26 107.42 1.1144 +IC H6X C35 *C36 H6Y 1.1144 107.42 -117.09 110.33 1.1107 +IC C35 C36 C37 C38 1.5362 113.84 72.60 112.19 1.5458 +IC C38 C36 *C37 C318 1.5458 112.19 125.01 110.06 1.5399 +IC C318 C36 *C37 H7X 1.5399 110.06 116.88 107.24 1.1163 +IC C36 C37 C318 H18X 1.5439 110.06 58.61 110.20 1.1107 +IC H18X C37 *C318 H18Y 1.1107 110.20 -119.68 110.20 1.1104 +IC H18X C37 *C318 H18Z 1.1107 110.20 119.82 111.09 1.1091 +IC C36 C37 C38 C39 1.5439 112.19 -166.57 113.01 1.5371 +IC C39 C37 *C38 H8X 1.5371 113.01 -122.96 109.28 1.1113 +IC H8X C37 *C38 H8Y 1.1113 109.28 -116.96 108.98 1.1103 +IC C37 C38 C39 C310 1.5458 113.01 172.46 113.51 1.5388 +IC C310 C38 *C39 H9X 1.5388 113.51 -121.66 107.92 1.1115 +IC H9X C38 *C39 H9Y 1.1115 107.92 -117.07 109.46 1.1125 +IC C38 C39 C310 C311 1.5371 113.51 -179.74 112.96 1.5472 +IC C311 C39 *C310 H10X 1.5472 112.96 -121.19 107.40 1.1111 +IC H10X C39 *C310 H10Y 1.1111 107.40 -116.88 109.92 1.1115 +IC C39 C310 C311 C312 1.5388 112.96 -167.32 113.47 1.5463 +IC C312 C310 *C311 C319 1.5463 113.47 -123.93 111.24 1.5407 +IC C319 C310 *C311 H11X 1.5407 111.24 -118.12 107.33 1.1162 +IC C310 C311 C319 H19X 1.5472 111.24 -59.97 111.11 1.1088 +IC H19X C311 *C319 H19Y 1.1088 111.11 -119.99 110.29 1.1102 +IC H19X C311 *C319 H19Z 1.1088 111.11 120.25 109.98 1.1108 +IC C310 C311 C312 C313 1.5472 113.47 58.94 114.52 1.5362 +IC C313 C311 *C312 H12X 1.5362 114.52 -123.20 109.44 1.1104 +IC H12X C311 *C312 H12Y 1.1104 109.44 -116.43 107.60 1.1135 +IC C311 C312 C313 C314 1.5463 114.52 166.86 112.83 1.5380 +IC C314 C312 *C313 H13X 1.5380 112.83 121.91 108.99 1.1111 +IC H13X C312 *C313 H13Y 1.1111 108.99 117.42 109.13 1.1134 +IC C312 C313 C314 C315 1.5362 112.83 175.69 113.23 1.5430 +IC C315 C313 *C314 H14X 1.5430 113.23 -122.27 110.11 1.1116 +IC H14X C313 *C314 H14Y 1.1116 110.11 -117.34 108.02 1.1132 +IC C313 C314 C315 C320 1.5380 113.23 -76.09 111.76 1.5380 +IC C320 C314 *C315 C316 1.5380 111.76 -123.35 111.18 1.5373 +IC C320 C314 *C315 H15X 1.5380 111.76 118.82 107.54 1.1166 +IC C314 C315 C320 H20X 1.5430 111.76 -70.16 110.13 1.1108 +IC H20X C315 *C320 H20Y 1.1108 110.13 -119.63 110.29 1.1104 +IC H20X C315 *C320 H20Z 1.1108 110.13 120.11 111.16 1.1091 +IC C314 C315 C316 H16X 1.5430 111.18 -179.80 110.31 1.1107 +IC H16X C315 *C316 H16Y 1.1107 110.31 -119.89 110.32 1.1105 +IC H16X C315 *C316 H16Z 1.1107 110.31 119.99 110.50 1.1104 +PATCHING FIRS NONE LAST NONE + +RESI PMPG -1.00! +! +! +! (Wonpil Im, modified based on POPG) +! (Kunal Pandit, modified again back to POPG) +! (Kunal Pandit, modified again to 4_733) +! +! C16:0 - CH2 +! | +! cyC17:0 - CH +! | +! CH2 - PO4 - CH2 - CH(OH) - CH2OH +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.66 ! | +ATOM HO3 HOL 0.43 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.66 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.43 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CG3RC1 -0.09 ! | | +ATOM H9R HGA1 0.09 ! H9R ---C29 H17R | +GROUP ! |\ / | +ATOM C217 CG3C31 -0.18 ! | \ / | +ATOM H17R HGA2 0.09 ! | C217 | +ATOM H17S HGA2 0.09 ! | / \ | +GROUP ! |/ \ | +ATOM C210 CG3RC1 -0.09 ! H10R ---C210 H17S | +ATOM H10R HGA1 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H121 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 C210 C29 C217 +BOND C210 H10R C210 C211 C210 C217 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +BOND C217 H17R C217 H17S +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, geometry minimize +IC O12 C11 C12 C13 1.4341 110.34 68.36 111.75 1.5474 +IC O12 C11 C12 OC2 1.4341 110.34 -169.48 109.34 1.4251 +IC C11 C12 C13 OC3 1.5475 111.75 -52.46 110.85 1.4270 +IC OC2 C12 C13 OC3 1.4251 110.11 -174.18 110.85 1.4270 +IC C12 C11 O12 P 1.5475 110.34 102.36 119.61 1.5931 +IC C11 O12 P O11 1.4341 119.61 -141.96 101.59 1.5838 +IC O11 O12 *P O13 1.5838 101.59 -115.76 109.03 1.4768 +IC O11 O12 *P O14 1.5838 101.59 114.36 108.79 1.4780 +IC O12 P O11 C1 1.5931 101.59 61.22 120.90 1.4293 +IC P O11 C1 C2 1.5838 120.90 90.47 112.12 1.5534 +IC C2 O11 *C1 HA 1.5534 112.12 -124.08 112.81 1.1125 +IC HA O11 *C1 HB 1.1125 112.81 -117.85 107.89 1.1127 +IC O11 C1 C2 O21 1.4293 112.12 165.36 108.44 1.4443 +IC O21 C1 *C2 C3 1.4443 108.44 -120.44 110.97 1.5541 +IC C3 C1 *C2 HS 1.5541 110.97 -116.97 108.83 1.1173 +IC C1 C2 O21 C21 1.5534 108.44 76.97 113.40 1.3245 +IC C2 O21 C21 C22 1.4443 113.40 -163.80 111.46 1.5374 +IC C22 O21 *C21 O22 1.5374 111.46 177.99 125.98 1.2162 +IC O21 C21 C22 C23 1.3245 111.46 -0.07 116.63 1.5492 +IC C23 C21 *C22 H2R 1.5492 116.63 -124.89 107.74 1.1073 +IC H2R C21 *C22 H2S 1.1073 107.74 -114.83 105.01 1.1116 +IC C1 C2 C3 O31 1.5534 110.97 -175.43 111.44 1.4475 +IC O31 C2 *C3 HX 1.4475 111.44 -122.10 108.21 1.1130 +IC HX C2 *C3 HY 1.1130 108.21 -116.48 106.55 1.1173 +IC C2 C3 O31 C31 1.5541 111.44 167.39 112.82 1.3263 +IC C3 O31 C31 C32 1.4475 112.82 -178.62 109.86 1.5284 +IC C32 O31 *C31 O32 1.5284 109.86 -177.17 125.75 1.2185 +IC O31 C31 C32 C33 1.3263 109.86 141.72 111.59 1.5474 +IC C33 C31 *C32 H2X 1.5474 111.59 -122.41 109.36 1.1083 +IC H2X C31 *C32 H2Y 1.1083 109.36 -117.27 106.19 1.1085 +IC C21 C22 C23 C24 1.5374 116.63 -83.54 112.96 1.5356 +IC C24 C22 *C23 H3R 1.5356 112.96 -118.51 107.87 1.1148 +IC H3R C22 *C23 H3S 1.1148 107.87 -116.64 110.55 1.1118 +IC C22 C23 C24 C25 1.5492 112.96 -174.20 113.28 1.5394 +IC C25 C23 *C24 H4R 1.5394 113.28 -123.19 109.36 1.1121 +IC H4R C23 *C24 H4S 1.1121 109.36 -116.67 108.42 1.1137 +IC C23 C24 C25 C26 1.5356 113.28 -65.77 114.60 1.5384 +IC C24 C25 C26 C27 1.5394 114.60 -66.19 113.33 1.5348 +IC C25 C26 C27 C28 1.5384 113.33 179.14 112.83 1.5365 +IC C26 C27 C28 C29 1.5348 112.83 173.76 110.31 1.5268 +IC C27 C28 C29 C210 1.5365 110.31 -77.38 118.89 1.5088 +IC C28 C29 C210 C211 1.5268 118.89 -8.11 121.57 1.5303 +IC C29 C210 C211 C212 1.5088 121.57 -156.81 109.50 1.5373 +IC C210 C211 C212 C213 1.5303 109.50 170.79 114.90 1.5375 +IC C211 C212 C213 C214 1.5373 114.90 -62.35 113.49 1.5376 +IC C212 C213 C214 C215 1.5375 113.49 -166.75 113.77 1.5368 +IC C213 C214 C215 C216 1.5376 113.77 73.09 114.06 1.5331 +IC C27 C28 C29 C217 1.5365 110.31 -147.53 118.13 1.5229 +IC C28 C29 C217 C210 1.5268 118.13 109.15 59.22 1.5310 +IC C29 C217 C210 C211 1.5229 59.22 -114.45 112.74 1.5303 +IC C217 C210 C211 C212 1.5310 112.74 -88.92 109.50 1.5373 +IC C31 C32 C33 C34 1.5284 111.59 167.80 113.94 1.5388 +IC C34 C32 *C33 H3X 1.5388 113.94 -121.81 109.88 1.1145 +IC H3X C32 *C33 H3Y 1.1145 109.88 -116.46 108.93 1.1143 +IC C32 C33 C34 C35 1.5474 113.94 -60.84 115.08 1.5405 +IC C35 C33 *C34 H4X 1.5405 115.08 -120.85 107.86 1.1144 +IC H4X C33 *C34 H4Y 1.1144 107.86 -116.44 108.97 1.1129 +IC C33 C34 C35 C36 1.5388 115.08 -51.92 113.77 1.5360 +IC C36 C34 *C35 H5X 1.5360 113.77 -121.36 108.56 1.1132 +IC H5X C34 *C35 H5Y 1.1132 108.56 -116.72 109.40 1.1122 +IC C34 C35 C36 C37 1.5405 113.77 -175.56 113.09 1.5343 +IC C37 C35 *C36 H6X 1.5343 113.09 -120.55 109.13 1.1139 +IC H6X C35 *C36 H6Y 1.1139 109.13 -117.44 109.41 1.1126 +IC C35 C36 C37 C38 1.5360 113.09 -173.55 111.94 1.5343 +IC C38 C36 *C37 H7X 1.5343 111.94 -121.99 109.56 1.1121 +IC H7X C36 *C37 H7Y 1.1121 109.56 -117.71 108.86 1.1135 +IC C36 C37 C38 C39 1.5343 111.94 177.58 112.98 1.5339 +IC C39 C37 *C38 H8X 1.5339 112.98 -120.59 108.43 1.1143 +IC H8X C37 *C38 H8Y 1.1143 108.43 -117.05 109.60 1.1126 +IC C37 C38 C39 C310 1.5343 112.98 -172.72 112.13 1.5349 +IC C310 C38 *C39 H9X 1.5349 112.13 -122.49 109.38 1.1119 +IC C38 C39 C310 C311 1.5339 112.13 169.28 114.08 1.5375 +IC OC3 C12 *C13 H13A 1.4270 110.85 119.79 108.69 1.1123 +IC OC3 C12 *C13 H13B 1.4270 110.85 -121.57 109.60 1.1113 +IC C12 C13 OC3 HO3 1.5474 110.85 23.87 103.97 0.9818 +IC OC3 C13 C12 C11 1.4270 110.85 -52.46 111.75 1.5475 +IC C11 C13 *C12 OC2 1.5475 111.75 -121.72 110.11 1.4251 +IC OC2 C13 *C12 H12A 1.4251 110.11 -118.95 108.53 1.1159 +IC C13 C12 OC2 HO2 1.5474 110.11 -172.38 104.03 0.9621 +IC C13 C12 C11 O12 1.5474 111.75 68.36 110.34 1.4341 +IC O12 C12 *C11 H11A 1.4341 110.34 -119.17 108.14 1.1130 +IC H11A C12 *C11 H11B 1.1130 108.14 -115.77 109.66 1.1170 +IC C12 C11 O12 P 1.5475 110.34 102.36 119.61 1.5931 +IC C11 O12 P O11 1.4341 119.61 -141.96 101.59 1.5838 +IC O11 O12 *P O13 1.5838 101.59 -115.76 109.03 1.4768 +IC O11 O12 *P O14 1.5838 101.59 114.36 108.79 1.4780 +IC O12 P O11 C1 1.5931 101.59 61.22 120.90 1.4293 +IC P O11 C1 C2 1.5838 120.90 90.47 112.12 1.5534 +IC C2 O11 *C1 HA 1.5534 112.12 -124.08 112.81 1.1125 +IC HA O11 *C1 HB 1.1125 112.81 -117.85 107.89 1.1127 +IC O11 C1 C2 C3 1.4293 112.12 44.92 110.97 1.5541 +IC C3 C1 *C2 O21 1.5541 110.97 120.44 108.44 1.4443 +IC C3 C1 *C2 HS 1.5541 110.97 -116.97 108.83 1.1173 +IC C1 C2 O21 C21 1.5534 108.44 76.97 113.40 1.3245 +IC C2 O21 C21 C22 1.4443 113.40 -163.80 111.46 1.5374 +IC C22 O21 *C21 O22 1.5374 111.46 177.99 125.98 1.2162 +IC O21 C21 C22 C23 1.3245 111.46 -0.07 116.63 1.5492 +IC C23 C21 *C22 H2R 1.5492 116.63 -124.89 107.74 1.1073 +IC H2R C21 *C22 H2S 1.1073 107.74 -114.83 105.01 1.1116 +IC C1 C2 C3 O31 1.5534 110.97 -175.43 111.44 1.4475 +IC O31 C2 *C3 HX 1.4475 111.44 -122.10 108.21 1.1130 +IC HX C2 *C3 HY 1.1130 108.21 -116.48 106.55 1.1173 +IC C2 C3 O31 C31 1.5541 111.44 167.39 112.82 1.3263 +IC C3 O31 C31 C32 1.4475 112.82 -178.62 109.86 1.5284 +IC C32 O31 *C31 O32 1.5284 109.86 -177.17 125.75 1.2185 +IC O31 C31 C32 C33 1.3263 109.86 141.72 111.59 1.5474 +IC C33 C31 *C32 H2X 1.5474 111.59 -122.41 109.36 1.1083 +IC H2X C31 *C32 H2Y 1.1083 109.36 -117.27 106.19 1.1085 +IC C21 C22 C23 C24 1.5374 116.63 -83.54 112.96 1.5356 +IC C24 C22 *C23 H3R 1.5356 112.96 -118.51 107.87 1.1148 +IC H3R C22 *C23 H3S 1.1148 107.87 -116.64 110.55 1.1118 +IC C22 C23 C24 C25 1.5492 112.96 -174.20 113.28 1.5394 +IC C25 C23 *C24 H4R 1.5394 113.28 -123.19 109.36 1.1121 +IC H4R C23 *C24 H4S 1.1121 109.36 -116.67 108.42 1.1137 +IC C23 C24 C25 C26 1.5356 113.28 -65.77 114.60 1.5384 +IC C26 C24 *C25 H5R 1.5384 114.60 -121.62 108.86 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.86 -116.75 108.38 1.1133 +IC C24 C25 C26 C27 1.5394 114.60 -66.19 113.33 1.5348 +IC C27 C25 *C26 H6R 1.5348 113.33 -120.40 108.65 1.1135 +IC H6R C25 *C26 H6S 1.1135 108.65 -117.12 109.85 1.1117 +IC C25 C26 C27 C28 1.5384 113.33 179.14 112.83 1.5365 +IC C28 C26 *C27 H7R 1.5365 112.83 -120.50 109.77 1.1136 +IC H7R C26 *C27 H7S 1.1136 109.77 -117.45 108.82 1.1115 +IC C26 C27 C28 C29 1.5348 112.83 173.76 110.31 1.5268 +IC C29 C27 *C28 H8R 1.5268 110.31 -122.73 109.79 1.1089 +IC H8R C27 *C28 H8S 1.1089 109.79 -117.24 109.17 1.1131 +IC C27 C28 C29 C210 1.5365 110.31 -77.38 118.89 1.5088 +IC C210 C28 *C29 C217 1.5088 118.89 -70.15 118.13 1.5229 +IC C210 C28 *C29 H9R 1.5088 118.89 145.80 117.46 1.1021 +IC C210 C29 *C217 H17R 1.5310 59.22 104.65 112.88 1.0808 +IC C210 C29 *C217 H17S 1.5310 59.22 -105.41 113.26 1.0793 +IC C217 C29 *C210 C211 1.5310 60.12 99.80 121.57 1.5303 +IC C211 C29 *C210 H10R 1.5303 121.57 155.57 115.53 1.1018 +IC C29 C210 C211 C212 1.5088 121.57 -156.81 109.50 1.5373 +IC C212 C210 *C211 H11R 1.5373 109.50 120.40 110.38 1.1086 +IC H11R C210 *C211 H11S 1.1086 110.38 119.13 110.06 1.1112 +IC C210 C211 C212 C213 1.5303 109.50 170.79 114.90 1.5375 +IC C213 C211 *C212 H12R 1.5375 114.90 -121.31 108.57 1.1141 +IC H12R C211 *C212 H12S 1.1141 108.57 -116.52 108.24 1.1128 +IC C211 C212 C213 C214 1.5373 114.90 -62.35 113.49 1.5376 +IC C214 C212 *C213 H13R 1.5376 113.49 -120.54 107.52 1.1130 +IC H13R C212 *C213 H13S 1.1130 107.52 -116.74 109.77 1.1121 +IC C212 C213 C214 C215 1.5375 113.49 -166.75 113.77 1.5368 +IC C215 C213 *C214 H14R 1.5368 113.77 -121.30 108.51 1.1132 +IC H14R C213 *C214 H14S 1.1132 108.51 -116.98 109.36 1.1130 +IC C213 C214 C215 C216 1.5376 113.77 73.09 114.06 1.5331 +IC C216 C214 *C215 H15R 1.5331 114.06 -123.14 108.99 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.99 -116.31 108.09 1.1149 +IC C214 C215 C216 H16R 1.5368 114.06 57.76 110.27 1.1114 +IC H16R C215 *C216 H16S 1.1114 110.27 -119.91 110.95 1.1102 +IC H16R C215 *C216 H16T 1.1114 110.27 119.85 110.62 1.1109 +IC C31 C32 C33 C34 1.5284 111.59 167.80 113.94 1.5388 +IC C34 C32 *C33 H3X 1.5388 113.94 -121.81 109.88 1.1145 +IC H3X C32 *C33 H3Y 1.1145 109.88 -116.46 108.93 1.1143 +IC C32 C33 C34 C35 1.5474 113.94 -60.84 115.08 1.5405 +IC C35 C33 *C34 H4X 1.5405 115.08 -120.85 107.86 1.1144 +IC H4X C33 *C34 H4Y 1.1144 107.86 -116.44 108.97 1.1129 +IC C33 C34 C35 C36 1.5388 115.08 -51.92 113.77 1.5360 +IC C36 C34 *C35 H5X 1.5360 113.77 -121.36 108.56 1.1132 +IC H5X C34 *C35 H5Y 1.1132 108.56 -116.72 109.40 1.1122 +IC C34 C35 C36 C37 1.5405 113.77 -175.56 113.09 1.5343 +IC C37 C35 *C36 H6X 1.5343 113.09 -120.55 109.13 1.1139 +IC H6X C35 *C36 H6Y 1.1139 109.13 -117.44 109.41 1.1126 +IC C35 C36 C37 C38 1.5360 113.09 -173.55 111.94 1.5343 +IC C38 C36 *C37 H7X 1.5343 111.94 -121.99 109.56 1.1121 +IC H7X C36 *C37 H7Y 1.1121 109.56 -117.71 108.86 1.1135 +IC C36 C37 C38 C39 1.5343 111.94 177.58 112.98 1.5339 +IC C39 C37 *C38 H8X 1.5339 112.98 -120.59 108.43 1.1143 +IC H8X C37 *C38 H8Y 1.1143 108.43 -117.05 109.60 1.1126 +IC C37 C38 C39 C310 1.5343 112.98 -172.72 112.13 1.5349 +IC C310 C38 *C39 H9X 1.5349 112.13 -122.49 109.38 1.1119 +IC H9X C38 *C39 H9Y 1.1119 109.38 -117.25 108.74 1.1113 +IC C38 C39 C310 C311 1.5339 112.13 169.28 114.08 1.5375 +IC C311 C39 *C310 H10X 1.5375 114.08 -120.50 108.50 1.1146 +IC H10X C39 *C310 H10Y 1.1146 108.50 -116.73 108.99 1.1127 +IC C39 C310 C311 C312 1.5349 114.08 58.76 113.80 1.5363 +IC C312 C310 *C311 H11X 1.5363 113.80 -121.99 109.25 1.1134 +IC H11X C310 *C311 H11Y 1.1134 109.25 -116.46 107.76 1.1126 +IC C310 C311 C312 C313 1.5375 113.80 172.81 113.45 1.5378 +IC C313 C311 *C312 H12X 1.5378 113.45 -122.01 109.39 1.1128 +IC H12X C311 *C312 H12Y 1.1128 109.39 -117.20 108.58 1.1136 +IC C311 C312 C313 C314 1.5363 113.45 -71.31 113.37 1.5364 +IC C314 C312 *C313 H13X 1.5364 113.37 -120.09 108.39 1.1139 +IC H13X C312 *C313 H13Y 1.1139 108.39 -117.14 109.45 1.1125 +IC C312 C313 C314 C315 1.5378 113.37 -175.57 112.81 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.81 -121.47 109.72 1.1122 +IC H14X C313 *C314 H14Y 1.1122 109.72 -117.50 108.87 1.1133 +IC C313 C314 C315 C316 1.5364 112.81 178.54 113.21 1.5310 +IC C316 C314 *C315 H15X 1.5310 113.21 -121.56 108.76 1.1139 +IC H15X C314 *C315 H15Y 1.1139 108.76 -116.74 108.73 1.1140 +IC C314 C315 C316 H16X 1.5340 113.21 59.81 110.45 1.1115 +IC H16X C315 *C316 H16Y 1.1115 110.45 -119.79 110.40 1.1115 +IC H16X C315 *C316 H16Z 1.1115 110.45 120.13 110.61 1.1111 + +RESI PVCL2 -2.00 ! (PVPG + PVPG) Cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 2 C16:0 + 2 C18:1 cis-11 +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 -0.08 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9--H9E H9A--CA9--H9B H9X--CD9--H9Y H9R--CC9--H9S +ATOM H13K HAL2 0.09 ! | | | | +ATOM O13 OSL -0.49 ! H10D--CB10--H10E H10A--CA10--H10B H10X--CD10--H10Y H10R--CC10--H10S +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11 H11X--CD11--H11Y H11R--CC11 +ATOM CB2 CTL2 -0.22 ! | || | || +ATOM H2D HAL2 0.09 ! H12D--CB12--H12E H12A--CA12 H12X--CD12--H12Y H12R--CC12 +ATOM H2E HAL2 0.09 ! | | | | +GROUP ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +ATOM C32 CTL1 0.17 ! | | | | +ATOM H32J HAL1 0.09 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM H2R HAL2 0.09 ! | | | | +ATOM H2S HAL2 0.09 ! H16F H17A--CA17--H17B H16Z H17R--CC17--H17S +GROUP ! | | +ATOM C33 CTL2 0.08 ! H18A--CA18--H18B H18R--CC18--H18S +ATOM H33J HAL2 0.09 ! | | +ATOM H33K HAL2 0.09 ! H18C H18T +ATOM O33 OSL -0.49 ! +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CTL2 -0.18 ! +ATOM H9A HAL2 0.09 ! +ATOM H9B HAL2 0.09 ! +GROUP ! +ATOM CA10 CTL2 -0.18 ! +ATOM H10A HAL2 0.09 ! +ATOM H10B HAL2 0.09 ! +GROUP ! +ATOM CA11 CEL1 -0.15 ! +ATOM H11A HEL1 0.15 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CTL2 -0.18 ! +ATOM H9D HAL2 0.09 ! +ATOM H9E HAL2 0.09 ! +GROUP ! +ATOM CB10 CTL2 -0.18 ! +ATOM H10D HAL2 0.09 ! +ATOM H10E HAL2 0.09 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL3 -0.27 ! +ATOM H16D HAL3 0.09 ! +ATOM H16E HAL3 0.09 ! +ATOM H16F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CTL2 -0.18 ! +ATOM H9R HAL2 0.09 ! +ATOM H9S HAL2 0.09 ! +GROUP ! +ATOM CC10 CTL2 -0.18 ! +ATOM H10R HAL2 0.09 ! +ATOM H10S HAL2 0.09 ! +GROUP ! +ATOM CC11 CEL1 -0.15 ! +ATOM H11R HEL1 0.15 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CTL2 -0.18 ! +ATOM H9X HAL2 0.09 ! +ATOM H9Y HAL2 0.09 ! +GROUP ! +ATOM CD10 CTL2 -0.18 ! +ATOM H10X HAL2 0.09 ! +ATOM H10Y HAL2 0.09 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 H9B CA9 CA10 +BOND CA10 H10A CA10 H10B CA10 CA11 +BOND CA11 H11A +DOUBLE CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 H9E CB9 CB10 +BOND CB10 H10D CB10 H10E CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 H16F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 H9S CC9 CC10 +BOND CC10 H10R CC10 H10S CC10 CC11 +BOND CC11 H11R +DOUBLE CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 H9Y CD9 CD10 +BOND CD10 H10X CD10 H10Y CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 H16Z +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4404 111.77 121.98 107.43 1.1157 +IC HG31 C2 *C3 HG32 1.1157 107.43 116.50 107.43 1.1155 +IC C2 C3 OP31 P3 1.5543 111.77 178.39 118.46 1.5903 +IC C3 OP31 P3 OP32 1.4404 118.46 53.85 101.93 1.5888 +IC OP32 OP31 *P3 OP33 1.5888 101.93 -114.83 110.16 1.4776 +IC OP32 OP31 *P3 OP34 1.5888 101.93 114.40 109.34 1.4797 +IC OP31 P3 OP32 C31 1.5903 101.93 85.61 119.24 1.4309 +IC P3 OP32 C31 C32 1.5888 119.24 -163.67 110.36 1.5555 +IC C32 OP32 *C31 H31J 1.5555 110.36 123.24 112.29 1.1149 +IC H31J OP32 *C31 H31K 1.1149 112.29 118.62 108.89 1.1140 +IC HG31 C3 C2 C1 1.1157 107.43 -65.18 112.25 1.5593 +IC C1 C3 *C2 OG12 1.5593 112.25 -122.22 106.09 1.4219 +IC C1 C3 *C2 HG22 1.5593 112.25 120.27 108.54 1.1138 +IC C3 C2 OG12 HO12 1.5543 106.09 -39.60 99.04 0.9676 +IC C3 C2 C1 OP11 1.5543 112.25 164.26 114.43 1.4378 +IC OP11 C2 *C1 HG11 1.4378 114.43 -124.62 107.10 1.1145 +IC HG11 C2 *C1 HG12 1.1145 107.10 -114.05 107.69 1.1117 +IC C2 C1 OP11 P1 1.5593 114.43 -90.31 122.18 1.5885 +IC C1 OP11 P1 OP12 1.4378 122.18 -40.47 102.50 1.5910 +IC OP12 OP11 *P1 OP13 1.5910 102.50 114.98 110.09 1.4771 +IC OP12 OP11 *P1 OP14 1.5910 102.50 -115.36 109.21 1.4819 +IC OP11 P1 OP12 C11 1.5885 102.50 -95.61 123.00 1.4265 +IC P1 OP12 C11 C12 1.5910 123.00 81.19 112.88 1.5535 +IC C12 OP12 *C11 H11J 1.5535 112.88 -123.80 111.65 1.1148 +IC H11J OP12 *C11 H11K 1.1148 111.65 -117.35 107.38 1.1110 +IC OP12 C11 C12 C13 1.4265 112.88 162.75 111.01 1.5548 +IC C13 C11 *C12 O12 1.5548 111.01 119.22 107.45 1.4324 +IC O12 C11 *C12 H12J 1.4324 107.45 121.50 107.21 1.1164 +IC C11 C12 O12 CA1 1.5535 107.45 143.54 116.43 1.3133 +IC C12 O12 CA1 CA2 1.4324 116.43 -172.80 108.02 1.5341 +IC CA2 O12 *CA1 OA1 1.5341 108.02 -175.93 126.26 1.2216 +IC O12 CA1 CA2 CA3 1.3133 108.02 -148.36 113.31 1.5470 +IC CA3 CA1 *CA2 H2A 1.5470 113.31 -123.41 107.26 1.1100 +IC H2A CA1 *CA2 H2B 1.1100 107.26 -115.53 107.24 1.1101 +IC C11 C12 C13 O13 1.5535 111.01 -179.49 112.23 1.4463 +IC O13 C12 *C13 H13J 1.4463 112.23 -118.71 106.42 1.1130 +IC H13J C12 *C13 H13K 1.1130 106.42 -115.08 109.24 1.1142 +IC C12 C13 O13 CB1 1.5548 112.23 87.75 114.75 1.3288 +IC C13 O13 CB1 CB2 1.4463 114.75 -168.75 109.29 1.5293 +IC CB2 O13 *CB1 OB1 1.5293 109.29 -177.26 125.60 1.2177 +IC O13 CB1 CB2 CB3 1.3288 109.29 -159.26 112.09 1.5474 +IC CB3 CB1 *CB2 H2D 1.5474 112.09 -120.96 107.12 1.1105 +IC H2D CB1 *CB2 H2E 1.1105 107.12 -116.84 107.85 1.1075 +IC OP32 C31 C32 C33 1.4309 110.36 -44.28 110.18 1.5546 +IC C33 C31 *C32 O32 1.5546 110.18 120.84 111.14 1.4409 +IC O32 C31 *C32 H32J 1.4409 111.14 121.75 108.07 1.1150 +IC C31 C32 O32 CC1 1.5555 111.14 69.92 113.95 1.3234 +IC C32 O32 CC1 CC2 1.4409 113.95 -163.73 108.67 1.5294 +IC CC2 O32 *CC1 OC1 1.5294 108.67 -178.62 125.27 1.2211 +IC O32 CC1 CC2 CC3 1.3234 108.67 169.29 114.76 1.5515 +IC CC3 CC1 *CC2 H2R 1.5515 114.76 -118.81 105.73 1.1128 +IC H2R CC1 *CC2 H2S 1.1128 105.73 -115.50 109.04 1.1050 +IC C31 C32 C33 O33 1.5555 110.18 -170.30 112.58 1.4492 +IC O33 C32 *C33 H33J 1.4492 112.58 125.96 108.97 1.1147 +IC H33J C32 *C33 H33K 1.1147 108.97 114.33 106.50 1.1147 +IC C32 C33 O33 CD1 1.5546 112.58 86.37 115.24 1.3207 +IC C33 O33 CD1 CD2 1.4492 115.24 -175.48 109.59 1.5292 +IC CD2 O33 *CD1 OD1 1.5292 109.59 178.66 126.37 1.2168 +IC O33 CD1 CD2 CD3 1.3207 109.59 -112.69 113.08 1.5459 +IC CD3 CD1 *CD2 H2X 1.5459 113.08 -119.64 106.06 1.1102 +IC H2X CD1 *CD2 H2Y 1.1102 106.06 -116.76 109.15 1.1084 +IC CA1 CA2 CA3 CA4 1.5341 113.31 -90.85 112.33 1.5335 +IC CA4 CA2 *CA3 H3A 1.5335 112.33 -119.04 108.72 1.1138 +IC H3A CA2 *CA3 H3B 1.1138 108.72 -117.35 110.01 1.1120 +IC CA2 CA3 CA4 CA5 1.5470 112.33 171.12 113.32 1.5388 +IC CA5 CA3 *CA4 H4A 1.5388 113.32 -123.59 109.50 1.1129 +IC H4A CA3 *CA4 H4B 1.1129 109.50 -115.18 108.13 1.1141 +IC CA3 CA4 CA5 CA6 1.5335 113.32 -70.58 114.83 1.5415 +IC CA6 CA4 *CA5 H5A 1.5415 114.83 -120.76 107.77 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 107.77 -116.12 108.97 1.1121 +IC CA4 CA5 CA6 CA7 1.5388 114.83 -54.59 113.60 1.5367 +IC CA7 CA5 *CA6 H6A 1.5367 113.60 -121.30 108.70 1.1128 +IC H6A CA5 *CA6 H6B 1.1128 108.70 -117.34 109.35 1.1124 +IC CA5 CA6 CA7 CA8 1.5415 113.60 -175.73 113.55 1.5363 +IC CA8 CA6 *CA7 H7A 1.5363 113.55 -119.83 108.95 1.1157 +IC H7A CA6 *CA7 H7B 1.1157 108.95 -117.14 109.37 1.1099 +IC CA6 CA7 CA8 CA9 1.5367 113.55 -169.18 110.39 1.5298 +IC CA9 CA7 *CA8 H8A 1.5298 110.39 -123.41 109.97 1.1091 +IC H8A CA7 *CA8 H8B 1.1091 109.97 -117.61 108.74 1.1130 +IC CA7 CA8 CA9 CA10 1.5367 113.55 -169.18 110.39 1.5298 +IC CA10 CA8 *CA9 H9A 1.5298 110.39 -123.41 109.97 1.1091 +IC H9A CA8 *CA9 H9B 1.1091 109.97 -117.61 108.74 1.1130 +IC CA8 CA9 CA10 CA11 1.5367 113.55 -169.18 110.39 1.5298 +IC CA11 CA9 *CA10 H10A 1.5298 110.39 -123.41 109.97 1.1091 +IC H10A CA9 *CA10 H10B 1.1091 109.97 -117.61 108.74 1.1130 +IC CA9 CA10 CA11 CA12 1.5398 111.53 -118.23 126.87 1.3467 +IC CA12 CA10 *CA11 H11A 1.3467 126.87 178.64 114.46 1.1012 +IC CA10 CA11 CA12 CA13 1.5098 126.87 -1.03 126.59 1.5093 +IC CA13 CA11 *CA12 H12A 1.5093 126.59 179.83 118.67 1.1011 +IC CA11 CA12 CA13 CA14 1.3467 126.59 93.85 111.91 1.5393 +IC CA14 CA12 *CA13 H13A 1.5359 113.93 -121.52 108.07 1.1129 +IC H13A CA12 *CA13 H13B 1.1129 108.07 -116.19 109.02 1.1129 +IC CA12 CA13 CA14 CA15 1.5369 113.93 -179.46 113.24 1.5368 +IC CA15 CA13 *CA14 H14A 1.5368 113.24 -120.32 108.71 1.1128 +IC H14A CA13 *CA14 H14B 1.1128 108.71 -117.34 109.56 1.1122 +IC CA13 CA14 CA15 CA16 1.5359 113.24 69.05 114.41 1.5315 +IC CA16 CA14 *CA15 H15A 1.5315 114.41 -122.58 108.59 1.1140 +IC H15A CA14 *CA15 H15B 1.1140 108.59 -115.96 108.27 1.1135 +IC CA14 CA15 CA16 CA17 1.5359 113.24 69.05 114.41 1.5315 +IC CA17 CA15 *CA16 H16A 1.5315 114.41 -122.58 108.59 1.1140 +IC H16A CA15 *CA16 H16B 1.1140 108.59 -115.96 108.27 1.1135 +IC CA15 CA16 CA17 CA18 1.5359 113.24 69.05 114.41 1.5315 +IC CA18 CA16 *CA17 H17A 1.5315 114.41 -122.58 108.59 1.1140 +IC H17A CA16 *CA17 H17B 1.1140 108.59 -115.96 108.27 1.1135 +IC CA16 CA17 CA18 H18A 1.5368 114.41 57.17 110.45 1.1111 +IC H18A CA17 *CA18 H18B 1.1111 110.45 -120.11 110.71 1.1109 +IC H18A CA17 *CA18 H18C 1.1111 110.45 120.04 110.50 1.1111 +IC CB1 CB2 CB3 CB4 1.5293 112.09 -179.75 113.77 1.5373 +IC CB4 CB2 *CB3 H3D 1.5373 113.77 -122.31 109.50 1.1133 +IC H3D CB2 *CB3 H3E 1.1133 109.50 -116.80 108.92 1.1158 +IC CB2 CB3 CB4 CB5 1.5474 113.77 -56.57 115.13 1.5384 +IC CB5 CB3 *CB4 H4D 1.5384 115.13 -121.97 108.32 1.1129 +IC H4D CB3 *CB4 H4E 1.1129 108.32 -116.05 108.73 1.1123 +IC CB3 CB4 CB5 CB6 1.5373 115.13 -55.77 113.84 1.5359 +IC CB6 CB4 *CB5 H5D 1.5359 113.84 -121.23 108.23 1.1135 +IC H5D CB4 *CB5 H5E 1.1135 108.23 -116.40 109.46 1.1127 +IC CB4 CB5 CB6 CB7 1.5384 113.84 -173.32 112.53 1.5350 +IC CB7 CB5 *CB6 H6D 1.5350 112.53 -120.96 109.26 1.1129 +IC H6D CB5 *CB6 H6E 1.1129 109.26 -117.48 109.43 1.1126 +IC CB5 CB6 CB7 CB8 1.5359 112.53 -175.82 112.56 1.5344 +IC CB8 CB6 *CB7 H7D 1.5344 112.56 -121.89 109.52 1.1131 +IC H7D CB6 *CB7 H7E 1.1131 109.52 -117.47 108.68 1.1137 +IC CB6 CB7 CB8 CB9 1.5350 112.56 176.00 112.56 1.5350 +IC CB9 CB7 *CB8 H8D 1.5350 112.56 -120.58 108.62 1.1138 +IC H8D CB7 *CB8 H8E 1.1138 108.62 -117.40 109.53 1.1128 +IC CB7 CB8 CB9 CB10 1.5344 112.56 -174.31 112.58 1.5360 +IC CB10 CB8 *CB9 H9D 1.5360 112.58 -122.42 109.13 1.1122 +IC H9D CB8 *CB9 H9E 1.1122 109.13 -117.22 108.67 1.1137 +IC CB8 CB9 CB10 CB11 1.5350 112.58 171.88 113.64 1.5381 +IC CB11 CB9 *CB10 H10D 1.5381 113.64 -120.00 108.14 1.1144 +IC H10D CB9 *CB10 H10E 1.1144 108.14 -116.92 109.62 1.1123 +IC CB9 CB10 CB11 CB12 1.5360 113.64 68.36 113.72 1.5363 +IC CB12 CB10 *CB11 H11D 1.5363 113.72 -122.24 109.08 1.1129 +IC H11D CB10 *CB11 H11E 1.1129 109.08 -116.74 108.26 1.1132 +IC CB10 CB11 CB12 CB13 1.5381 113.72 -176.80 113.72 1.5378 +IC CB13 CB11 *CB12 H12D 1.5378 113.72 -121.91 109.01 1.1125 +IC H12D CB11 *CB12 H12E 1.1125 109.01 -117.24 109.07 1.1131 +IC CB11 CB12 CB13 CB14 1.5363 113.72 -65.09 113.76 1.5357 +IC CB14 CB12 *CB13 H13D 1.5357 113.76 -120.67 108.42 1.1141 +IC H13D CB12 *CB13 H13E 1.1141 108.42 -116.91 109.24 1.1129 +IC CB12 CB13 CB14 CB15 1.5378 113.76 -175.73 112.55 1.5341 +IC CB15 CB13 *CB14 H14D 1.5341 112.55 -121.18 109.65 1.1125 +IC H14D CB13 *CB14 H14E 1.1125 109.65 -117.71 109.07 1.1133 +IC CB13 CB14 CB15 CB16 1.5357 112.55 179.96 113.22 1.5308 +IC CB16 CB14 *CB15 H15D 1.5308 113.22 -121.67 108.80 1.1142 +IC H15D CB14 *CB15 H15E 1.1142 108.80 -116.68 108.75 1.1142 +IC CB14 CB15 CB16 H16D 1.5341 113.22 59.92 110.47 1.1114 +IC H16D CB15 *CB16 H16E 1.1114 110.47 -119.86 110.47 1.1114 +IC H16D CB15 *CB16 H16F 1.1114 110.47 120.07 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5294 114.76 93.79 114.39 1.5374 +IC CC4 CC2 *CC3 H3R 1.5374 114.39 -126.95 111.10 1.1116 +IC H3R CC2 *CC3 H3S 1.1116 111.10 -115.09 106.18 1.1184 +IC CC2 CC3 CC4 CC5 1.5515 114.39 -72.23 114.19 1.5358 +IC CC5 CC3 *CC4 H4R 1.5358 114.19 -121.05 108.41 1.1133 +IC H4R CC3 *CC4 H4S 1.1133 108.41 -116.30 107.75 1.1098 +IC CC3 CC4 CC5 CC6 1.5374 114.19 -179.76 114.16 1.5387 +IC CC6 CC4 *CC5 H5R 1.5387 114.16 -121.52 108.86 1.1110 +IC H5R CC4 *CC5 H5S 1.1110 108.86 -115.95 108.61 1.1135 +IC CC4 CC5 CC6 CC7 1.5358 114.16 -59.65 113.12 1.5354 +IC CC7 CC5 *CC6 H6R 1.5354 113.12 -120.53 108.09 1.1136 +IC H6R CC5 *CC6 H6S 1.1136 108.09 -117.17 109.48 1.1121 +IC CC5 CC6 CC7 CC8 1.5387 113.12 -170.18 113.61 1.5340 +IC CC8 CC6 *CC7 H7R 1.5340 113.61 -121.71 109.29 1.1106 +IC H7R CC6 *CC7 H7S 1.1106 109.29 -117.04 108.75 1.1122 +IC CC6 CC7 CC8 CC9 1.5354 113.61 -179.71 111.74 1.5360 +IC CC9 CC7 *CC8 H8R 1.5360 111.74 -121.24 108.81 1.1116 +IC H8R CC7 *CC8 H8S 1.1116 108.81 -117.52 109.28 1.1125 +IC CC7 CC8 CC9 CC10 1.5340 111.74 179.06 113.91 1.5382 +IC CC10 CC8 *CC9 H9R 1.5382 113.91 -120.63 108.05 1.1143 +IC H9R CC8 *CC9 H9S 1.1143 108.05 -116.01 109.22 1.1120 +IC CC8 CC9 CC10 CC11 1.5360 113.91 65.10 115.15 1.5400 +IC CC11 CC9 *CC10 H10R 1.5400 115.15 -122.07 108.46 1.1136 +IC H10R CC9 *CC10 H10S 1.1136 108.46 -116.44 108.60 1.1138 +IC CC9 CC10 CC11 CC12 1.5398 111.53 -118.23 126.87 1.3467 +IC CC12 CC10 *CC11 H11R 1.3467 126.87 178.64 114.46 1.1012 +IC CC10 CC11 CC12 CC13 1.5098 126.87 -1.03 126.59 1.5093 +IC CC13 CC11 *CC12 H12R 1.5093 126.59 179.83 118.67 1.1011 +IC CC11 CC12 CC13 CC14 1.3467 126.59 93.85 111.91 1.5393 +IC CC14 CC12 *CC13 H13R 1.5356 113.78 -120.56 108.36 1.1141 +IC H13R CC12 *CC13 H13S 1.1141 108.36 -116.88 109.43 1.1125 +IC CC12 CC13 CC14 CC15 1.5382 113.78 -176.10 112.53 1.5342 +IC CC15 CC13 *CC14 H14R 1.5342 112.53 -121.11 109.65 1.1124 +IC H14R CC13 *CC14 H14S 1.1124 109.65 -117.73 109.12 1.1131 +IC CC13 CC14 CC15 CC16 1.5356 112.53 -179.76 113.22 1.5308 +IC CC16 CC14 *CC15 H15R 1.5308 113.22 -121.71 108.83 1.1141 +IC H15R CC14 *CC15 H15S 1.1141 108.83 -116.67 108.72 1.1143 +IC CC14 CC15 CC16 CC17 1.5356 112.53 -179.76 113.22 1.5308 +IC CC17 CC15 *CC16 H16R 1.5308 113.22 -121.71 108.83 1.1141 +IC H16R CC15 *CC16 H16S 1.1141 108.83 -116.67 108.72 1.1143 +IC CC15 CC16 CC17 CC18 1.5356 112.53 -179.76 113.22 1.5308 +IC CC18 CC16 *CC17 H17R 1.5308 113.22 -121.71 108.83 1.1141 +IC H17R CC16 *CC17 H17S 1.1141 108.83 -116.67 108.72 1.1143 +IC CC16 CC17 CC18 H18R 1.5342 113.22 59.93 110.47 1.1114 +IC H18R CC17 *CC18 H18S 1.1114 110.47 -119.87 110.51 1.1113 +IC H18R CC17 *CC18 H18T 1.1114 110.47 120.04 110.64 1.1113 +IC CD1 CD2 CD3 CD4 1.5292 113.08 -164.96 112.68 1.5376 +IC CD4 CD2 *CD3 H3X 1.5376 112.68 -122.71 109.48 1.1130 +IC H3X CD2 *CD3 H3Y 1.1130 109.48 -117.50 109.46 1.1158 +IC CD2 CD3 CD4 CD5 1.5459 112.68 -56.05 114.87 1.5384 +IC CD5 CD3 *CD4 H4X 1.5384 114.87 -122.39 108.88 1.1135 +IC H4X CD3 *CD4 H4Y 1.1135 108.88 -116.47 108.31 1.1144 +IC CD3 CD4 CD5 CD6 1.5376 114.87 -62.08 113.82 1.5352 +IC CD6 CD4 *CD5 H5X 1.5352 113.82 -120.45 108.15 1.1142 +IC H5X CD4 *CD5 H5Y 1.1142 108.15 -116.65 110.02 1.1126 +IC CD4 CD5 CD6 CD7 1.5384 113.82 -173.93 112.13 1.5346 +IC CD7 CD5 *CD6 H6X 1.5346 112.13 -121.46 109.73 1.1130 +IC H6X CD5 *CD6 H6Y 1.1130 109.73 -117.82 108.98 1.1132 +IC CD5 CD6 CD7 CD8 1.5352 112.13 176.71 112.86 1.5339 +IC CD8 CD6 *CD7 H7X 1.5339 112.86 -120.99 108.98 1.1134 +IC H7X CD6 *CD7 H7Y 1.1134 108.98 -117.24 109.24 1.1129 +IC CD6 CD7 CD8 CD9 1.5346 112.86 -179.51 112.25 1.5346 +IC CD9 CD7 *CD8 H8X 1.5346 112.25 -121.44 109.34 1.1134 +IC H8X CD7 *CD8 H8Y 1.1134 109.34 -117.57 109.03 1.1134 +IC CD7 CD8 CD9 CD10 1.5339 112.25 176.04 112.66 1.5351 +IC CD10 CD8 *CD9 H9X 1.5351 112.66 -121.53 108.95 1.1125 +IC H9X CD8 *CD9 H9Y 1.1125 108.95 -117.19 108.86 1.1136 +IC CD8 CD9 CD10 CD11 1.5346 112.66 172.88 113.48 1.5371 +IC CD11 CD9 *CD10 H10X 1.5371 113.48 -120.25 108.40 1.1141 +IC H10X CD9 *CD10 H10Y 1.1141 108.40 -116.97 109.60 1.1125 +IC CD9 CD10 CD11 CD12 1.5351 113.48 67.69 114.12 1.5358 +IC CD12 CD10 *CD11 H11X 1.5358 114.12 -121.84 108.97 1.1121 +IC H11X CD10 *CD11 H11Y 1.1121 108.97 -116.62 108.19 1.1132 +IC CD10 CD11 CD12 CD13 1.5371 114.12 -176.72 113.29 1.5381 +IC CD13 CD11 *CD12 H12X 1.5381 113.29 -122.08 109.14 1.1128 +IC H12X CD11 *CD12 H12Y 1.1128 109.14 -117.38 109.15 1.1128 +IC CD11 CD12 CD13 CD14 1.5358 113.29 -62.39 113.71 1.5354 +IC CD14 CD12 *CD13 H13X 1.5354 113.71 -120.88 108.48 1.1139 +IC H13X CD12 *CD13 H13Y 1.1139 108.48 -117.04 109.24 1.1131 +IC CD12 CD13 CD14 CD15 1.5381 113.71 -174.33 112.64 1.5333 +IC CD15 CD13 *CD14 H14X 1.5333 112.64 -121.18 109.76 1.1129 +IC H14X CD13 *CD14 H14Y 1.1129 109.76 -117.80 109.00 1.1133 +IC CD13 CD14 CD15 CD16 1.5354 112.64 178.46 112.96 1.5300 +IC CD16 CD14 *CD15 H15X 1.5300 112.96 -121.49 108.86 1.1141 +IC H15X CD14 *CD15 H15Y 1.1141 108.86 -116.85 108.85 1.1141 +IC CD14 CD15 CD16 H16X 1.5333 112.96 60.23 110.39 1.1115 +IC H16X CD15 *CD16 H16Y 1.1115 110.39 -119.86 110.53 1.1112 +IC H16X CD15 *CD16 H16Z 1.1115 110.39 120.03 110.61 1.1112 + +end + +read para card flex @app +* new parameters +* + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! Cyclopropane Moeity Addition +CTL2 CG3RC1 222.500 1.530 ! alkanes, 3/92 +CTL3 CG3RC1 222.50 1.5380 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08, from genFF +CTL3 CG3C31 240.00 1.5010 ! PROTMOD cyclopropane, taken from CG321 CG3C31, genFF +CTL2 CG3C31 240.00 1.5010 ! PROTMOD cyclopropane, from genFF +! + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! For Propane Ring +CTL2 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! propane ring, MacKerell +CTL2 CTL2 CG3RC1 53.35 111.00 8.0 2.561 ! propane ring, MacKerell +HAL2 CTL2 CG3RC1 34.50 110.10 22.53 2.179 ! propane ring, MacKerell +CTL2 CG3RC1 CG3C31 53.35 111.00 8.0 2.561 ! propane ring, MacKerell +CTL2 CG3RC1 CG3RC1 53.35 111.00 8.0 2.561 ! propane ring, MacKerell +! For Dihedral Mapping with Propane Ring +CG3RC1 CTL3 HAL3 33.43 110.10 22.53 2.179 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08, from GenFF +CTL3 CG3RC1 CG3RC1 58.35 113.50 11.16 2.561 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08, from GenFF +CTL3 CG3RC1 HGA1 34.50 110.10 22.53 2.179 ! CARBOCY carbocyclic sugars, taken from CG321-CG3RC1-HGA1, from GenFF +CTL3 CG3RC1 CG3C31 53.35 111.00 8.0 2.561 ! CARBOCY carbocyclic sugars, taken from CG321-CG3RC1-HGA1, from GenFF +CG3C31 CTL2 HAL2 26.50 110.10 22.53 2.17900 ! PROT alkane update, adm jr., 3/2/92, from genFF +CTL1 CTL2 CL 52.0 108.00 ! best guess made by jbl for PhPC + + +! +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! Taken from C36 GenFF for Propane Ring in Lipid +CTL2 CTL2 CG3RC1 HGA1 0.1500 3 0.00 ! propane ring, MacKerell +CTL2 CTL2 CG3RC1 CG3C31 0.0000 2 180.00 ! propane ring, MacKerell +HGA2 CG3C31 CG3RC1 CTL2 0.1950 3 0.00 ! propane ring, MacKerell +CG3RC1 CG3C31 CG3RC1 CTL2 0.1500 3 0.00 ! propane ring, MacKerell +CTL2 CG3RC1 CG3RC1 CG3C31 0.1500 3 0.00 ! propane ring, MacKerell +CTL2 CG3RC1 CG3RC1 HGA1 0.1500 3 0.00 ! propane ring, MacKerell +CTL2 CG3RC1 CG3RC1 CTL2 0.1500 3 0.00 ! propane ring, MacKerell +HAL2 CTL2 CG3RC1 CG3C31 0.1950 3 0.00 ! propane ring, MacKerell +HAL2 CTL2 CG3RC1 CG3RC1 0.1500 3 0.00 ! propane ring, MacKerell +HAL2 CTL2 CG3RC1 HGA1 0.1500 3 0.00 ! propane ring, MacKerell +! Take from C36 Gen FF for Ring on small molecule studies +CG3RC1 CG3C31 CG3RC1 CTL3 0.1500 3 0.00 ! CARBOCY carbocyclic sugars, taken from CG3RC1 CG3C31 CG3RC1 CG321, genFF +HGA2 CG3C31 CG3RC1 CTL3 0.1950 3 0.00 ! CARBOCY carbocyclic sugars, taken from HGA2 CG3C31 CG3RC1 CG321, genFF +HAL3 CTL3 CG3RC1 CG3RC1 0.1500 3 180.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08 +HAL3 CTL3 CG3RC1 HGA1 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv, taken from HGA3 CG331 CG3C51 HGA1, genFF +HAL3 CTL3 CG3RC1 CG3C31 0.1500 3 180.00 ! BAM1, bile acid steroidal C-D ring, cacha, 02/08, taken from HGA3 CG331 CG3RC1 CG3C51, genFF +! For Propane Ring added by K.R.P. 07/10 +X CG3RC1 CG3RC1 X 0.4500 1 180.00 ! 2-butene, adm jr., 4/04 from C36 GenFF +X CG3RC1 CG3RC1 X 8.5000 2 180.00 !from C36 GenFF +CG3RC1 CG3RC1 CTL2 CTL2 1.71 1 159.6 !ring, KRP +CG3RC1 CG3RC1 CTL2 CTL2 0.37 2 165.1 !ring, KRP +CG3RC1 CG3RC1 CTL2 CTL2 0.58 3 47.6 !ring, KRP +CG3RC1 CTL2 CTL2 CTL2 0.16 1 180.0 ! ring, KRP +CG3RC1 CTL2 CTL2 CTL2 0.01 2 180.0 ! ring, KRP +CG3RC1 CTL2 CTL2 CTL2 0.17 3 180.0 ! ring, KRP + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!Cylcopropane moeity addition + + +end + +return + + diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_cardiolipin.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_cardiolipin.str new file mode 100644 index 00000000..ef40cd95 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_cardiolipin.str @@ -0,0 +1,14152 @@ +read rtf card append flex + +!* cardiolipin molecule assembly kit; append this file to the all36_lipid set +!* begun may 2010 rick venable, nih/nhlbi Lab of computational biology +!* venabler at nhlbi*nih*gov +!* + +RESI TOCL1 -1.00 ! Tetraoleoyl Cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 4 oleoly chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12--H12E H12A--CA12--H12B H12X--CD12--H12Y H12R--CC12--H12S +ATOM H2E HAL2 0.09 ! | | | | +GROUP ! | | | | +ATOM C32 CTL1 0.17 ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM CC2 CTL2 -0.22 ! | | | | +ATOM H2R HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18F H18C H18Z H18T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z +! +!IC TABLE +! +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +IC OP31 C2 *C3 HG31 1.4478 115.81 120.77 107.21 1.1103 +IC HG31 C2 *C3 HG32 1.1103 107.21 113.79 109.44 1.1116 +IC C2 C3 OP31 P3 1.5391 115.81 179.54 116.48 1.6311 +IC C3 OP31 P3 OP32 1.4478 116.48 -24.68 104.81 1.5590 +IC OP32 OP31 *P3 OP33 1.5590 104.81 -115.81 107.08 1.5202 +IC OP32 OP31 *P3 OP34 1.5590 104.81 119.46 112.11 1.4755 +IC OP31 P3 OP32 C31 1.6311 104.81 118.48 124.90 1.4204 +IC P3 OP32 C31 C32 1.5590 124.90 -177.96 114.46 1.5293 +IC C32 OP32 *C31 H31J 1.5293 114.46 121.21 110.94 1.1113 +IC H31J OP32 *C31 H31K 1.1113 110.94 118.18 111.26 1.1114 +IC HG31 C3 C2 C1 1.1103 107.21 59.15 111.81 1.5775 +IC C1 C3 *C2 OG12 1.5775 111.81 -123.03 104.24 1.4529 +IC C1 C3 *C2 HG22 1.5775 111.81 120.08 109.60 1.1109 +IC C3 C2 OG12 HO12 1.5391 104.24 -67.25 112.57 0.9601 +IC C3 C2 C1 OP11 1.5391 111.81 56.67 113.71 1.4252 +IC OP11 C2 *C1 HG11 1.4252 113.71 -129.69 102.65 1.1114 +IC HG11 C2 *C1 HG12 1.1114 102.65 -108.19 113.55 1.1117 +IC C2 C1 OP11 P1 1.5775 113.71 -137.16 115.79 1.5694 +IC C1 OP11 P1 OP12 1.4252 115.79 -38.56 101.17 1.5512 +IC OP12 OP11 *P1 OP13 1.5512 101.17 120.92 110.23 1.6318 +IC OP12 OP11 *P1 OP14 1.5512 101.17 -119.69 108.21 1.4683 +IC OP11 P1 OP13 HP13 1.5694 110.23 80.36 103.88 0.9590 +IC OP11 P1 OP12 C11 1.5694 101.17 -165.75 116.90 1.4487 +IC P1 OP12 C11 C12 1.5512 116.90 -70.20 120.82 1.5785 +IC C12 OP12 *C11 H11J 1.5785 120.82 -121.59 102.98 1.1110 +IC H11J OP12 *C11 H11K 1.1110 102.98 -117.94 115.12 1.1109 +IC OP12 C11 C12 C13 1.4487 120.82 -158.44 110.14 1.4806 +IC C13 C11 *C12 O12 1.4806 110.14 123.75 104.19 1.4203 +IC O12 C11 *C12 H12J 1.4203 104.19 117.29 108.71 1.1108 +IC C11 C12 O12 CA1 1.5785 104.19 152.63 121.75 1.3357 +IC C12 O12 CA1 CA2 1.4203 121.75 -172.10 105.98 1.5689 +IC CA2 O12 *CA1 OA1 1.5689 105.98 172.32 128.82 1.2022 +IC O12 CA1 CA2 CA3 1.3357 105.98 -133.79 106.00 1.5485 +IC CA3 CA1 *CA2 H2A 1.5485 106.00 -117.84 100.88 1.1105 +IC H2A CA1 *CA2 H2B 1.1105 100.88 -120.79 109.17 1.1118 +IC C11 C12 C13 O13 1.5785 110.14 52.09 108.48 1.4206 +IC O13 C12 *C13 H13J 1.4206 108.48 -117.15 111.73 1.1103 +IC H13J C12 *C13 H13K 1.1103 111.73 -117.14 109.17 1.1115 +IC C12 C13 O13 CB1 1.4806 108.48 100.89 115.21 1.3485 +IC C13 O13 CB1 CB2 1.4206 115.21 -166.50 102.03 1.4979 +IC CB2 O13 *CB1 OB1 1.4979 102.03 172.46 124.90 1.2074 +IC O13 CB1 CB2 CB3 1.3485 102.03 145.94 108.15 1.5439 +IC CB3 CB1 *CB2 H2D 1.5439 108.15 -115.82 109.51 1.1113 +IC H2D CB1 *CB2 H2E 1.1113 109.51 -110.90 114.30 1.1103 +IC OP32 C31 C32 C33 1.4204 114.46 -60.29 108.40 1.5604 +IC C33 C31 *C32 O32 1.5604 108.40 121.34 111.13 1.4494 +IC O32 C31 *C32 H32J 1.4494 111.13 122.24 106.35 1.1110 +IC C31 C32 O32 CC1 1.5293 111.13 68.14 114.89 1.3105 +IC C32 O32 CC1 CC2 1.4494 114.89 176.15 108.12 1.4876 +IC CC2 O32 *CC1 OC1 1.4876 108.12 -170.27 125.63 1.2266 +IC O32 CC1 CC2 CC3 1.3105 108.12 -76.46 108.70 1.5560 +IC CC3 CC1 *CC2 H2R 1.5560 108.70 -122.84 112.77 1.1107 +IC H2R CC1 *CC2 H2S 1.1107 112.77 -123.28 108.97 1.1110 +IC C31 C32 C33 O33 1.5293 108.40 176.96 112.72 1.4640 +IC O33 C32 *C33 H33J 1.4640 112.72 117.22 113.13 1.1108 +IC H33J C32 *C33 H33K 1.1108 113.13 115.83 106.47 1.1118 +IC C32 C33 O33 CD1 1.5604 112.72 -151.26 113.15 1.3113 +IC C33 O33 CD1 CD2 1.4640 113.15 173.25 112.34 1.5319 +IC CD2 O33 *CD1 OD1 1.5319 112.34 -178.05 122.67 1.2242 +IC O33 CD1 CD2 CD3 1.3113 112.34 -38.42 110.46 1.5461 +IC CD3 CD1 *CD2 H2X 1.5461 110.46 -112.49 109.00 1.1104 +IC H2X CD1 *CD2 H2Y 1.1104 109.00 -130.20 111.55 1.1111 +IC CA1 CA2 CA3 CA4 1.5689 106.00 70.58 115.07 1.5306 +IC CA4 CA2 *CA3 H3A 1.5306 115.07 -129.18 107.90 1.1109 +IC H3A CA2 *CA3 H3B 1.1109 107.90 -105.89 101.69 1.1112 +IC CA2 CA3 CA4 CA5 1.5485 115.07 158.69 108.32 1.5834 +IC CA5 CA3 *CA4 H4A 1.5834 108.32 -118.75 108.71 1.1108 +IC H4A CA3 *CA4 H4B 1.1108 108.71 -117.19 107.01 1.1110 +IC CA3 CA4 CA5 CA6 1.5306 108.32 -174.04 108.06 1.5368 +IC CA6 CA4 *CA5 H5A 1.5368 108.06 -118.82 105.90 1.1109 +IC H5A CA4 *CA5 H5B 1.1109 105.90 -121.68 106.09 1.1119 +IC CA4 CA5 CA6 CA7 1.5834 108.06 178.17 110.77 1.5223 +IC CA7 CA5 *CA6 H6A 1.5223 110.77 -132.06 116.95 1.1113 +IC H6A CA5 *CA6 H6B 1.1113 116.95 -112.47 107.63 1.1111 +IC CA5 CA6 CA7 CA8 1.5368 110.77 59.27 117.63 1.4882 +IC CA8 CA6 *CA7 H7A 1.4882 117.63 -118.56 104.37 1.1116 +IC H7A CA6 *CA7 H7B 1.1116 104.37 -114.08 107.73 1.1109 +IC CA6 CA7 CA8 CA9 1.5223 117.63 67.91 107.29 1.5222 +IC CA9 CA7 *CA8 H8A 1.5222 107.29 -124.85 113.63 1.1112 +IC H8A CA7 *CA8 H8B 1.1112 113.63 -117.04 109.09 1.1113 +IC CA7 CA8 CA9 CA10 1.4882 107.29 119.10 123.38 1.3319 +IC CA10 CA8 *CA9 H9A 1.3319 123.38 -177.89 117.11 1.0999 +IC CA8 CA9 CA10 CA11 1.5222 123.38 7.54 131.28 1.5065 +IC CA11 CA9 *CA10 H10A 1.5065 131.28 178.90 115.15 1.0997 +IC CA9 CA10 CA11 CA12 1.3319 131.28 -97.49 113.43 1.5850 +IC CA12 CA10 *CA11 H11A 1.5850 113.43 -130.41 112.16 1.1112 +IC H11A CA10 *CA11 H11B 1.1112 112.16 -109.74 101.87 1.1115 +IC CA10 CA11 CA12 CA13 1.5065 113.43 -173.72 107.65 1.4866 +IC CA13 CA11 *CA12 H12A 1.4866 107.65 -113.01 107.64 1.1113 +IC H12A CA11 *CA12 H12B 1.1113 107.64 -111.93 109.75 1.1111 +IC CA11 CA12 CA13 CA14 1.5850 107.65 -179.34 115.75 1.5000 +IC CA14 CA12 *CA13 H13A 1.5000 115.75 -115.95 103.71 1.1118 +IC H13A CA12 *CA13 H13B 1.1118 103.71 -111.93 109.06 1.1112 +IC CA12 CA13 CA14 CA15 1.4866 115.75 -54.04 114.55 1.5487 +IC CA15 CA13 *CA14 H14A 1.5487 114.55 -122.19 111.44 1.1108 +IC H14A CA13 *CA14 H14B 1.1108 111.44 -116.88 102.67 1.1109 +IC CA13 CA14 CA15 CA16 1.5000 114.55 -74.45 115.60 1.5143 +IC CA16 CA14 *CA15 H15A 1.5143 115.60 -119.98 104.04 1.1105 +IC H15A CA14 *CA15 H15B 1.1105 104.04 -110.62 108.03 1.1111 +IC CA14 CA15 CA16 CA17 1.5487 115.60 -160.42 111.25 1.6032 +IC CA17 CA15 *CA16 H16A 1.6032 111.25 -125.34 109.28 1.1106 +IC H16A CA15 *CA16 H16B 1.1106 109.28 -118.70 112.68 1.1108 +IC CA15 CA16 CA17 CA18 1.5143 111.25 -79.24 109.31 1.5207 +IC CA18 CA16 *CA17 H17A 1.5207 109.31 -117.60 110.70 1.1118 +IC H17A CA16 *CA17 H17B 1.1118 110.70 -114.15 102.66 1.1109 +IC CA16 CA17 CA18 H18A 1.6032 109.31 69.09 108.47 1.1114 +IC H18A CA17 *CA18 H18B 1.1114 108.47 -133.81 115.46 1.1115 +IC H18A CA17 *CA18 H18C 1.1114 108.47 106.76 112.60 1.1111 +IC CB1 CB2 CB3 CB4 1.4979 108.15 168.84 113.97 1.5414 +IC CB4 CB2 *CB3 H3D 1.5414 113.97 -116.57 109.36 1.1106 +IC H3D CB2 *CB3 H3E 1.1106 109.36 -121.06 112.37 1.1109 +IC CB2 CB3 CB4 CB5 1.5439 113.97 -58.59 116.14 1.5170 +IC CB5 CB3 *CB4 H4D 1.5170 116.14 -125.09 117.26 1.1105 +IC H4D CB3 *CB4 H4E 1.1105 117.26 -121.61 108.92 1.1112 +IC CB3 CB4 CB5 CB6 1.5414 116.14 -78.78 114.35 1.6375 +IC CB6 CB4 *CB5 H5D 1.6375 114.35 -119.75 109.83 1.1112 +IC H5D CB4 *CB5 H5E 1.1112 109.83 -120.87 106.11 1.1121 +IC CB4 CB5 CB6 CB7 1.5170 114.35 -70.16 112.68 1.5227 +IC CB7 CB5 *CB6 H6D 1.5227 112.68 -116.61 103.22 1.1114 +IC H6D CB5 *CB6 H6E 1.1114 103.22 -112.98 111.60 1.1115 +IC CB5 CB6 CB7 CB8 1.6375 112.68 -161.94 110.39 1.5832 +IC CB8 CB6 *CB7 H7D 1.5832 110.39 -124.11 108.30 1.1108 +IC H7D CB6 *CB7 H7E 1.1108 108.30 -115.23 115.05 1.1106 +IC CB6 CB7 CB8 CB9 1.5227 110.39 -90.27 109.83 1.5037 +IC CB9 CB7 *CB8 H8D 1.5037 109.83 -117.18 103.04 1.1116 +IC H8D CB7 *CB8 H8E 1.1116 103.04 -115.48 109.94 1.1108 +IC CB7 CB8 CB9 CB10 1.5832 109.83 -147.27 128.01 1.3511 +IC CB10 CB8 *CB9 H9D 1.3511 128.01 179.43 117.16 1.1000 +IC CB8 CB9 CB10 CB11 1.5037 128.01 -2.70 125.31 1.4853 +IC CB11 CB9 *CB10 H10D 1.4853 125.31 -164.56 115.65 1.1003 +IC CB9 CB10 CB11 CB12 1.3511 125.31 -105.03 114.69 1.5411 +IC CB12 CB10 *CB11 H11D 1.5411 114.69 -123.57 118.03 1.1101 +IC H11D CB10 *CB11 H11E 1.1101 118.03 -117.71 111.56 1.1111 +IC CB10 CB11 CB12 CB13 1.4853 114.69 66.66 113.32 1.5589 +IC CB13 CB11 *CB12 H12D 1.5589 113.32 -114.28 112.33 1.1108 +IC H12D CB11 *CB12 H12E 1.1108 112.33 -130.02 107.65 1.1105 +IC CB11 CB12 CB13 CB14 1.5411 113.32 172.82 117.09 1.5221 +IC CB14 CB12 *CB13 H13D 1.5221 117.09 -121.37 115.12 1.1107 +IC H13D CB12 *CB13 H13E 1.1107 115.12 -120.42 104.48 1.1105 +IC CB12 CB13 CB14 CB15 1.5589 117.09 -56.19 116.78 1.5397 +IC CB15 CB13 *CB14 H14D 1.5397 116.78 -118.05 107.59 1.1115 +IC H14D CB13 *CB14 H14E 1.1115 107.59 -119.10 106.18 1.1112 +IC CB13 CB14 CB15 CB16 1.5221 116.78 -61.27 110.45 1.5107 +IC CB16 CB14 *CB15 H15D 1.5107 110.45 -121.68 109.04 1.1098 +IC H15D CB14 *CB15 H15E 1.1098 109.04 -118.57 112.04 1.1110 +IC CB14 CB15 CB16 CB17 1.5397 110.45 -177.69 115.35 1.5345 +IC CB17 CB15 *CB16 H16D 1.5345 115.35 -127.17 106.89 1.1111 +IC H16D CB15 *CB16 H16E 1.1111 106.89 -114.84 99.50 1.1107 +IC CB15 CB16 CB17 CB18 1.5107 115.35 -175.38 114.56 1.5592 +IC CB18 CB16 *CB17 H17D 1.5592 114.56 -121.20 113.97 1.1109 +IC H17D CB16 *CB17 H17E 1.1109 113.97 -121.51 102.37 1.1113 +IC CB16 CB17 CB18 H18D 1.5345 114.56 110.74 111.55 1.1108 +IC H18D CB17 *CB18 H18E 1.1108 111.55 -123.62 104.19 1.1101 +IC H18D CB17 *CB18 H18F 1.1108 111.55 121.03 109.64 1.1105 +IC CC1 CC2 CC3 CC4 1.4876 108.70 166.49 115.31 1.5516 +IC CC4 CC2 *CC3 H3R 1.5516 115.31 -122.81 110.40 1.1117 +IC H3R CC2 *CC3 H3S 1.1117 110.40 -108.90 112.78 1.1110 +IC CC2 CC3 CC4 CC5 1.5560 115.31 -58.76 114.09 1.5204 +IC CC5 CC3 *CC4 H4R 1.5204 114.09 -125.99 113.90 1.1108 +IC H4R CC3 *CC4 H4S 1.1108 113.90 -118.25 104.34 1.1112 +IC CC3 CC4 CC5 CC6 1.5516 114.09 -159.82 106.26 1.5455 +IC CC6 CC4 *CC5 H5R 1.5455 106.26 -120.26 113.02 1.1112 +IC H5R CC4 *CC5 H5S 1.1112 113.02 -116.51 107.52 1.1101 +IC CC4 CC5 CC6 CC7 1.5204 106.26 -162.84 115.72 1.5093 +IC CC7 CC5 *CC6 H6R 1.5093 115.72 -125.35 109.33 1.1120 +IC H6R CC5 *CC6 H6S 1.1120 109.33 -115.83 104.84 1.1114 +IC CC5 CC6 CC7 CC8 1.5455 115.72 169.85 115.65 1.5438 +IC CC8 CC6 *CC7 H7R 1.5438 115.65 -119.94 105.61 1.1114 +IC H7R CC6 *CC7 H7S 1.1114 105.61 -109.43 118.03 1.1113 +IC CC6 CC7 CC8 CC9 1.5093 115.65 68.29 114.74 1.4947 +IC CC9 CC7 *CC8 H8R 1.4947 114.74 -125.62 104.10 1.1108 +IC H8R CC7 *CC8 H8S 1.1108 104.10 -104.85 109.88 1.1111 +IC CC7 CC8 CC9 CC10 1.5438 114.74 -94.94 122.44 1.3611 +IC CC10 CC8 *CC9 H9R 1.3611 122.44 178.47 118.28 1.0993 +IC CC8 CC9 CC10 CC11 1.4947 122.44 1.31 128.99 1.5289 +IC CC11 CC9 *CC10 H10R 1.5289 128.99 -171.44 117.81 1.0999 +IC CC9 CC10 CC11 CC12 1.3611 128.99 -117.48 117.23 1.5675 +IC CC12 CC10 *CC11 H11R 1.5675 117.23 133.47 119.59 1.1108 +IC H11R CC10 *CC11 H11S 1.1108 119.59 114.38 108.18 1.1111 +IC CC10 CC11 CC12 CC13 1.5289 117.23 -49.76 118.58 1.4935 +IC CC13 CC11 *CC12 H12R 1.4935 118.58 -124.61 111.80 1.1107 +IC H12R CC11 *CC12 H12S 1.1107 111.80 -118.72 105.83 1.1104 +IC CC11 CC12 CC13 CC14 1.5675 118.58 98.30 113.13 1.5099 +IC CC14 CC12 *CC13 H13R 1.5099 113.13 -122.89 107.50 1.1109 +IC H13R CC12 *CC13 H13S 1.1109 107.50 -117.77 111.05 1.1106 +IC CC12 CC13 CC14 CC15 1.4935 113.13 80.43 108.22 1.4802 +IC CC15 CC13 *CC14 H14R 1.4802 108.22 -129.23 111.33 1.1104 +IC H14R CC13 *CC14 H14S 1.1104 111.33 -110.13 98.50 1.1110 +IC CC13 CC14 CC15 CC16 1.5099 108.22 -167.84 114.83 1.5382 +IC CC16 CC14 *CC15 H15R 1.5382 114.83 120.52 111.86 1.1102 +IC H15R CC14 *CC15 H15S 1.1102 111.86 115.94 109.88 1.1112 +IC CC14 CC15 CC16 CC17 1.4802 114.83 170.93 115.39 1.4625 +IC CC17 CC15 *CC16 H16R 1.4625 115.39 132.70 112.02 1.1123 +IC H16R CC15 *CC16 H16S 1.1123 112.02 108.77 98.04 1.1103 +IC CC15 CC16 CC17 CC18 1.5382 115.39 71.39 116.83 1.4835 +IC CC18 CC16 *CC17 H17R 1.4835 116.83 -127.49 108.68 1.1102 +IC H17R CC16 *CC17 H17S 1.1102 108.68 -116.81 103.93 1.1106 +IC CC16 CC17 CC18 H18R 1.4625 116.83 66.76 99.69 1.1108 +IC H18R CC17 *CC18 H18S 1.1108 99.69 -115.88 114.54 1.1107 +IC H18R CC17 *CC18 H18T 1.1108 99.69 118.86 113.91 1.1111 +IC CD1 CD2 CD3 CD4 1.5319 110.46 175.03 113.67 1.6015 +IC CD4 CD2 *CD3 H3X 1.6015 113.67 -120.00 106.80 1.1112 +IC H3X CD2 *CD3 H3Y 1.1112 106.80 -113.48 108.54 1.1113 +IC CD2 CD3 CD4 CD5 1.5461 113.67 -169.91 108.66 1.5690 +IC CD5 CD3 *CD4 H4X 1.5690 108.66 -119.27 105.80 1.1112 +IC H4X CD3 *CD4 H4Y 1.1112 105.80 -120.84 111.26 1.1108 +IC CD3 CD4 CD5 CD6 1.6015 108.66 -178.21 116.73 1.5287 +IC CD6 CD4 *CD5 H5X 1.5287 116.73 -125.69 112.08 1.1102 +IC H5X CD4 *CD5 H5Y 1.1102 112.08 -118.33 106.27 1.1116 +IC CD4 CD5 CD6 CD7 1.5690 116.73 68.59 112.56 1.6088 +IC CD7 CD5 *CD6 H6X 1.6088 112.56 -130.94 112.73 1.1110 +IC H6X CD5 *CD6 H6Y 1.1110 112.73 -116.11 107.23 1.1114 +IC CD5 CD6 CD7 CD8 1.5287 112.56 -176.20 110.80 1.4652 +IC CD8 CD6 *CD7 H7X 1.4652 110.80 -124.79 106.04 1.1106 +IC H7X CD6 *CD7 H7Y 1.1106 106.04 -116.11 113.65 1.1105 +IC CD6 CD7 CD8 CD9 1.6088 110.80 -176.35 117.02 1.4890 +IC CD9 CD7 *CD8 H8X 1.4890 117.02 -130.96 111.56 1.1107 +IC H8X CD7 *CD8 H8Y 1.1107 111.56 -116.19 101.92 1.1105 +IC CD7 CD8 CD9 CD10 1.4652 117.02 -110.91 134.02 1.3183 +IC CD10 CD8 *CD9 H9X 1.3183 134.02 168.17 109.97 1.0999 +IC CD8 CD9 CD10 CD11 1.4890 134.02 -8.00 119.30 1.5217 +IC CD11 CD9 *CD10 H10X 1.5217 119.30 -161.66 119.21 1.1001 +IC CD9 CD10 CD11 CD12 1.3183 119.30 -115.70 121.90 1.5128 +IC CD12 CD10 *CD11 H11X 1.5128 121.90 -115.24 110.72 1.1108 +IC H11X CD10 *CD11 H11Y 1.1108 110.72 -117.48 110.55 1.1107 +IC CD10 CD11 CD12 CD13 1.5217 121.90 176.42 109.32 1.5755 +IC CD13 CD11 *CD12 H12X 1.5755 109.32 -127.73 103.95 1.1110 +IC H12X CD11 *CD12 H12Y 1.1110 103.95 -110.68 112.20 1.1102 +IC CD11 CD12 CD13 CD14 1.5128 109.32 166.83 111.46 1.5220 +IC CD14 CD12 *CD13 H13X 1.5220 111.46 -121.14 113.18 1.1109 +IC H13X CD12 *CD13 H13Y 1.1109 113.18 -118.01 110.96 1.1106 +IC CD12 CD13 CD14 CD15 1.5755 111.46 -61.93 118.37 1.4969 +IC CD15 CD13 *CD14 H14X 1.4969 118.37 -125.51 112.03 1.1107 +IC H14X CD13 *CD14 H14Y 1.1107 112.03 -118.45 109.75 1.1119 +IC CD13 CD14 CD15 CD16 1.5220 118.37 -169.88 114.61 1.5503 +IC CD16 CD14 *CD15 H15X 1.5503 114.61 -118.47 112.81 1.1115 +IC H15X CD14 *CD15 H15Y 1.1115 112.81 -123.12 104.45 1.1109 +IC CD14 CD15 CD16 CD17 1.4969 114.61 72.09 117.29 1.5486 +IC CD17 CD15 *CD16 H16X 1.5486 117.29 -122.17 103.46 1.1109 +IC H16X CD15 *CD16 H16Y 1.1109 103.46 -121.10 108.97 1.1104 +IC CD15 CD16 CD17 CD18 1.5503 117.29 -160.70 111.27 1.4722 +IC CD18 CD16 *CD17 H17X 1.4722 111.27 -119.79 103.29 1.1104 +IC H17X CD16 *CD17 H17Y 1.1104 103.29 -113.39 109.70 1.1108 +IC CD16 CD17 CD18 H18X 1.5486 111.27 67.81 112.96 1.1114 +IC H18X CD17 *CD18 H18Y 1.1114 112.96 -115.92 114.72 1.1111 +IC H18X CD17 *CD18 H18Z 1.1114 112.96 122.62 110.38 1.1112 + +RESI TOCL2 -2.00 ! Tetraoleoyl Cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 4 oleoly chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12--H12E H12A--CA12--H12B H12X--CD12--H12Y H12R--CC12--H12S +GROUP ! | | | | +ATOM C32 CTL1 0.17 ! | | | | +ATOM H32J HAL1 0.09 ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM H2R HAL2 0.09 ! | | | | +ATOM H2S HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +GROUP ! | | | | +ATOM C33 CTL2 0.08 ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM H33J HAL2 0.09 ! | | | | +ATOM H33K HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM O33 OSL -0.49 ! | | | | +ATOM CD1 CL 0.90 ! H18F H18C H18Z H18T +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 !! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z +! +! IC TABLE +! +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +IC OP31 C2 *C3 HG31 1.4633 109.99 126.99 106.69 1.1112 +IC HG31 C2 *C3 HG32 1.1112 106.69 120.70 112.94 1.1110 +IC C2 C3 OP31 P3 1.5211 109.99 154.06 117.47 1.5924 +IC C3 OP31 P3 OP32 1.4633 117.47 66.74 101.68 1.6525 +IC OP32 OP31 *P3 OP33 1.6525 101.68 -113.70 109.39 1.4926 +IC OP32 OP31 *P3 OP34 1.6525 101.68 112.29 106.74 1.4836 +IC OP31 P3 OP32 C31 1.5924 101.68 55.76 110.28 1.4698 +IC P3 OP32 C31 C32 1.6525 110.28 -172.41 110.74 1.5958 +IC C32 OP32 *C31 H31J 1.5958 110.74 116.75 110.82 1.1115 +IC H31J OP32 *C31 H31K 1.1115 110.82 111.29 110.26 1.1103 +IC HG31 C3 C2 C1 1.1112 106.69 -61.74 114.49 1.5241 +IC C1 C3 *C2 OG12 1.5241 114.49 -122.33 108.64 1.4665 +IC C1 C3 *C2 HG22 1.5241 114.49 124.23 104.11 1.1108 +IC C3 C2 OG12 HO12 1.5211 108.64 -38.03 96.97 0.9599 +IC C3 C2 C1 OP11 1.5211 114.49 175.92 108.99 1.3945 +IC OP11 C2 *C1 HG11 1.3945 108.99 -131.04 104.78 1.1106 +IC HG11 C2 *C1 HG12 1.1106 104.78 -113.14 109.09 1.1119 +IC C2 C1 OP11 P1 1.5241 108.99 -84.99 120.20 1.5652 +IC C1 OP11 P1 OP12 1.3945 120.20 -27.24 102.68 1.5816 +IC OP12 OP11 *P1 OP13 1.5816 102.68 118.64 109.06 1.4705 +IC OP12 OP11 *P1 OP14 1.5816 102.68 -114.38 108.43 1.4438 +IC OP11 P1 OP12 C11 1.5652 102.68 -105.08 129.51 1.3844 +IC P1 OP12 C11 C12 1.5816 129.51 79.30 113.33 1.5572 +IC C12 OP12 *C11 H11J 1.5572 113.33 -123.60 109.70 1.1106 +IC H11J OP12 *C11 H11K 1.1106 109.70 -125.75 111.37 1.1111 +IC OP12 C11 C12 C13 1.3844 113.33 172.10 111.92 1.5430 +IC C13 C11 *C12 O12 1.5430 111.92 120.38 106.67 1.4690 +IC O12 C11 *C12 H12J 1.4690 106.67 123.36 105.85 1.1110 +IC C11 C12 O12 CA1 1.5572 106.67 139.57 111.75 1.3546 +IC C12 O12 CA1 CA2 1.4690 111.75 -177.04 105.16 1.4819 +IC CA2 O12 *CA1 OA1 1.4819 105.16 175.26 126.65 1.2359 +IC O12 CA1 CA2 CA3 1.3546 105.16 -166.84 109.95 1.5144 +IC CA3 CA1 *CA2 H2A 1.5144 109.95 -122.50 115.81 1.1105 +IC H2A CA1 *CA2 H2B 1.1105 115.81 -121.44 107.35 1.1109 +IC C11 C12 C13 O13 1.5572 111.92 -172.11 107.78 1.5003 +IC O13 C12 *C13 H13J 1.5003 107.78 -115.91 112.20 1.1109 +IC H13J C12 *C13 H13K 1.1109 112.20 -121.54 112.00 1.1122 +IC C12 C13 O13 CB1 1.5430 107.78 77.67 115.10 1.2970 +IC C13 O13 CB1 CB2 1.5003 115.10 -179.81 109.11 1.4434 +IC CB2 O13 *CB1 OB1 1.4434 109.11 -173.82 130.35 1.2113 +IC O13 CB1 CB2 CB3 1.2970 109.11 173.87 116.83 1.5195 +IC CB3 CB1 *CB2 H2D 1.5195 116.83 -121.03 109.80 1.1112 +IC H2D CB1 *CB2 H2E 1.1112 109.80 -114.30 107.94 1.1107 +IC OP32 C31 C32 C33 1.4698 110.74 -72.15 111.19 1.5682 +IC C33 C31 *C32 O32 1.5682 111.19 124.56 112.11 1.3898 +IC O32 C31 *C32 H32J 1.3898 112.11 122.90 114.56 1.1112 +IC C31 C32 O32 CC1 1.5958 112.11 62.25 119.56 1.3075 +IC C32 O32 CC1 CC2 1.3898 119.56 -174.92 104.05 1.4829 +IC CC2 O32 *CC1 OC1 1.4829 104.05 -166.47 126.62 1.2264 +IC O32 CC1 CC2 CC3 1.3075 104.05 170.64 115.59 1.5435 +IC CC3 CC1 *CC2 H2R 1.5435 115.59 -124.86 107.06 1.1110 +IC H2R CC1 *CC2 H2S 1.1110 107.06 -105.63 111.30 1.1109 +IC C31 C32 C33 O33 1.5958 111.19 -173.79 110.26 1.4370 +IC O33 C32 *C33 H33J 1.4370 110.26 118.41 109.85 1.1107 +IC H33J C32 *C33 H33K 1.1107 109.85 116.35 110.86 1.1105 +IC C32 C33 O33 CD1 1.5682 110.26 -82.05 116.23 1.3711 +IC C33 O33 CD1 CD2 1.4370 116.23 156.92 111.58 1.5654 +IC CD2 O33 *CD1 OD1 1.5654 111.58 -176.12 124.80 1.1850 +IC O33 CD1 CD2 CD3 1.3711 111.58 79.99 113.19 1.5154 +IC CD3 CD1 *CD2 H2X 1.5154 113.19 -122.11 106.99 1.1106 +IC H2X CD1 *CD2 H2Y 1.1106 106.99 -114.65 110.19 1.1109 +IC CA1 CA2 CA3 CA4 1.4819 109.95 160.84 117.75 1.5645 +IC CA4 CA2 *CA3 H3A 1.5645 117.75 -127.81 109.37 1.1111 +IC H3A CA2 *CA3 H3B 1.1111 109.37 -117.63 101.55 1.1105 +IC CA2 CA3 CA4 CA5 1.5144 117.75 157.03 111.41 1.5424 +IC CA5 CA3 *CA4 H4A 1.5424 111.41 -119.03 108.09 1.1114 +IC H4A CA3 *CA4 H4B 1.1114 108.09 -126.38 120.58 1.1101 +IC CA3 CA4 CA5 CA6 1.5645 111.41 74.25 110.88 1.5499 +IC CA6 CA4 *CA5 H5A 1.5499 110.88 -125.89 112.16 1.1114 +IC H5A CA4 *CA5 H5B 1.1114 112.16 -116.89 114.30 1.1106 +IC CA4 CA5 CA6 CA7 1.5424 110.88 177.26 112.07 1.5702 +IC CA7 CA5 *CA6 H6A 1.5702 112.07 -121.41 112.61 1.1107 +IC H6A CA5 *CA6 H6B 1.1107 112.61 -124.17 99.78 1.1108 +IC CA5 CA6 CA7 CA8 1.5499 112.07 74.00 120.92 1.5501 +IC CA8 CA6 *CA7 H7A 1.5501 120.92 -128.07 104.29 1.1105 +IC H7A CA6 *CA7 H7B 1.1105 104.29 -118.23 103.40 1.1112 +IC CA6 CA7 CA8 CA9 1.5702 120.92 170.69 112.79 1.5329 +IC CA9 CA7 *CA8 H8A 1.5329 112.79 -117.60 114.99 1.1111 +IC H8A CA7 *CA8 H8B 1.1111 114.99 -115.64 104.49 1.1114 +IC CA7 CA8 CA9 CA10 1.5501 112.79 82.54 132.44 1.3410 +IC CA10 CA8 *CA9 H9A 1.3410 132.44 -165.92 110.30 1.0996 +IC CA8 CA9 CA10 CA11 1.5329 132.44 11.31 129.79 1.4668 +IC CA11 CA9 *CA10 H10A 1.4668 129.79 173.10 113.82 1.1006 +IC CA9 CA10 CA11 CA12 1.3410 129.79 -125.54 110.53 1.5132 +IC CA12 CA10 *CA11 H11A 1.5132 110.53 -124.22 111.84 1.1109 +IC H11A CA10 *CA11 H11B 1.1109 111.84 -116.05 116.75 1.1107 +IC CA10 CA11 CA12 CA13 1.4668 110.53 161.55 113.19 1.4862 +IC CA13 CA11 *CA12 H12A 1.4862 113.19 -115.99 104.44 1.1104 +IC H12A CA11 *CA12 H12B 1.1104 104.44 -109.05 111.86 1.1114 +IC CA11 CA12 CA13 CA14 1.5132 113.19 66.72 118.43 1.5736 +IC CA14 CA12 *CA13 H13A 1.5736 118.43 -112.65 104.63 1.1114 +IC H13A CA12 *CA13 H13B 1.1114 104.63 -117.70 113.84 1.1109 +IC CA12 CA13 CA14 CA15 1.4862 118.43 62.79 110.33 1.5584 +IC CA15 CA13 *CA14 H14A 1.5584 110.33 -118.07 107.82 1.1108 +IC H14A CA13 *CA14 H14B 1.1108 107.82 -113.03 108.64 1.1112 +IC CA13 CA14 CA15 CA16 1.5736 110.33 -175.93 102.80 1.5814 +IC CA16 CA14 *CA15 H15A 1.5814 102.80 -121.30 114.89 1.1112 +IC H15A CA14 *CA15 H15B 1.1112 114.89 -125.40 120.38 1.1112 +IC CA14 CA15 CA16 CA17 1.5584 102.80 -177.33 108.65 1.4920 +IC CA17 CA15 *CA16 H16A 1.4920 108.65 -121.79 105.96 1.1117 +IC H16A CA15 *CA16 H16B 1.1117 105.96 -110.08 103.15 1.1108 +IC CA15 CA16 CA17 CA18 1.5814 108.65 -168.13 114.64 1.5103 +IC CA18 CA16 *CA17 H17A 1.5103 114.64 -123.69 105.58 1.1117 +IC H17A CA16 *CA17 H17B 1.1117 105.58 -117.14 106.96 1.1108 +IC CA16 CA17 CA18 H18A 1.4920 114.64 -97.38 116.78 1.1116 +IC H18A CA17 *CA18 H18B 1.1116 116.78 -112.38 110.91 1.1109 +IC H18A CA17 *CA18 H18C 1.1116 116.78 124.13 107.97 1.1105 +IC CB1 CB2 CB3 CB4 1.4434 116.83 -155.75 114.25 1.5868 +IC CB4 CB2 *CB3 H3D 1.5868 114.25 -122.78 114.66 1.1117 +IC H3D CB2 *CB3 H3E 1.1117 114.66 -129.44 120.87 1.1109 +IC CB2 CB3 CB4 CB5 1.5195 114.25 -52.65 114.56 1.5137 +IC CB5 CB3 *CB4 H4D 1.5137 114.56 -115.68 101.27 1.1103 +IC H4D CB3 *CB4 H4E 1.1103 101.27 -119.02 105.41 1.1106 +IC CB3 CB4 CB5 CB6 1.5868 114.56 -179.99 120.50 1.5634 +IC CB6 CB4 *CB5 H5D 1.5634 120.50 -122.72 117.24 1.1113 +IC H5D CB4 *CB5 H5E 1.1113 117.24 -123.34 103.45 1.1107 +IC CB4 CB5 CB6 CB7 1.5137 120.50 39.76 116.61 1.5133 +IC CB7 CB5 *CB6 H6D 1.5133 116.61 -120.56 106.07 1.1110 +IC H6D CB5 *CB6 H6E 1.1110 106.07 -117.54 106.11 1.1114 +IC CB5 CB6 CB7 CB8 1.5634 116.61 176.57 110.49 1.5173 +IC CB8 CB6 *CB7 H7D 1.5173 110.49 -120.73 106.74 1.1106 +IC H7D CB6 *CB7 H7E 1.1106 106.74 -117.79 112.10 1.1106 +IC CB6 CB7 CB8 CB9 1.5133 110.49 -82.21 120.66 1.5172 +IC CB9 CB7 *CB8 H8D 1.5172 120.66 -115.86 108.05 1.1105 +IC H8D CB7 *CB8 H8E 1.1105 108.05 -111.89 111.52 1.1117 +IC CB7 CB8 CB9 CB10 1.5173 120.66 -107.87 126.23 1.3089 +IC CB10 CB8 *CB9 H9D 1.3089 126.23 177.32 108.46 1.0998 +IC CB8 CB9 CB10 CB11 1.5172 126.23 -9.03 129.20 1.5488 +IC CB11 CB9 *CB10 H10D 1.5488 129.20 -177.87 114.84 1.1001 +IC CB9 CB10 CB11 CB12 1.3089 129.20 89.60 118.95 1.5198 +IC CB12 CB10 *CB11 H11D 1.5198 118.95 -127.92 113.12 1.1108 +IC H11D CB10 *CB11 H11E 1.1108 113.12 -116.33 107.89 1.1110 +IC CB10 CB11 CB12 CB13 1.5488 118.95 47.44 108.85 1.4805 +IC CB13 CB11 *CB12 H12D 1.4805 108.85 -124.66 111.86 1.1106 +IC H12D CB11 *CB12 H12E 1.1106 111.86 -115.71 106.95 1.1117 +IC CB11 CB12 CB13 CB14 1.5198 108.85 158.33 114.90 1.5460 +IC CB14 CB12 *CB13 H13D 1.5460 114.90 -122.78 110.67 1.1114 +IC H13D CB12 *CB13 H13E 1.1114 110.67 -118.72 111.28 1.1107 +IC CB12 CB13 CB14 CB15 1.4805 114.90 68.37 114.96 1.5755 +IC CB15 CB13 *CB14 H14D 1.5755 114.96 -127.83 107.96 1.1104 +IC H14D CB13 *CB14 H14E 1.1104 107.96 -116.62 108.21 1.1111 +IC CB13 CB14 CB15 CB16 1.5460 114.96 166.45 117.74 1.5429 +IC CB16 CB14 *CB15 H15D 1.5429 117.74 -122.27 110.71 1.1109 +IC H15D CB14 *CB15 H15E 1.1109 110.71 -117.71 99.91 1.1101 +IC CB14 CB15 CB16 CB17 1.5755 117.74 174.50 116.45 1.5273 +IC CB17 CB15 *CB16 H16D 1.5273 116.45 -126.26 106.79 1.1119 +IC H16D CB15 *CB16 H16E 1.1119 106.79 -120.93 108.80 1.1106 +IC CB15 CB16 CB17 CB18 1.5429 116.45 176.52 110.28 1.5697 +IC CB18 CB16 *CB17 H17D 1.5697 110.28 -130.06 105.87 1.1105 +IC H17D CB16 *CB17 H17E 1.1105 105.87 -115.72 106.22 1.1106 +IC CB16 CB17 CB18 H18D 1.5273 110.28 -159.07 103.32 1.1112 +IC H18D CB17 *CB18 H18E 1.1112 103.32 -120.33 105.93 1.1103 +IC H18D CB17 *CB18 H18F 1.1112 103.32 118.79 110.62 1.1116 +IC CC1 CC2 CC3 CC4 1.4829 115.59 49.93 117.90 1.5366 +IC CC4 CC2 *CC3 H3R 1.5366 117.90 -115.05 111.28 1.1107 +IC H3R CC2 *CC3 H3S 1.1107 111.28 -122.62 109.57 1.1107 +IC CC2 CC3 CC4 CC5 1.5435 117.90 41.42 122.16 1.4856 +IC CC5 CC3 *CC4 H4R 1.4856 122.16 -129.12 107.74 1.1116 +IC H4R CC3 *CC4 H4S 1.1116 107.74 -110.63 106.93 1.1114 +IC CC3 CC4 CC5 CC6 1.5366 122.16 79.03 118.09 1.5779 +IC CC6 CC4 *CC5 H5R 1.5779 118.09 -121.27 111.33 1.1111 +IC H5R CC4 *CC5 H5S 1.1111 111.33 -121.85 103.83 1.1116 +IC CC4 CC5 CC6 CC7 1.4856 118.09 -175.62 114.14 1.5193 +IC CC7 CC5 *CC6 H6R 1.5193 114.14 -112.92 99.65 1.1104 +IC H6R CC5 *CC6 H6S 1.1104 99.65 -115.34 114.89 1.1110 +IC CC5 CC6 CC7 CC8 1.5779 114.14 86.04 111.08 1.5443 +IC CC8 CC6 *CC7 H7R 1.5443 111.08 -126.84 118.56 1.1115 +IC H7R CC6 *CC7 H7S 1.1115 118.56 -116.67 107.70 1.1111 +IC CC6 CC7 CC8 CC9 1.5193 111.08 -167.74 113.25 1.5955 +IC CC9 CC7 *CC8 H8R 1.5955 113.25 -126.88 111.16 1.1113 +IC H8R CC7 *CC8 H8S 1.1113 111.16 -113.40 107.96 1.1105 +IC CC7 CC8 CC9 CC10 1.5443 113.25 -109.87 126.39 1.3527 +IC CC10 CC8 *CC9 H9R 1.3527 126.39 -170.92 110.56 1.0998 +IC CC8 CC9 CC10 CC11 1.5955 126.39 15.86 128.70 1.4629 +IC CC11 CC9 *CC10 H10R 1.4629 128.70 175.07 123.34 1.1002 +IC CC9 CC10 CC11 CC12 1.3527 128.70 101.47 118.70 1.5861 +IC CC12 CC10 *CC11 H11R 1.5861 118.70 -125.10 109.20 1.1112 +IC H11R CC10 *CC11 H11S 1.1112 109.20 -110.25 111.88 1.1101 +IC CC10 CC11 CC12 CC13 1.4629 118.70 67.74 108.82 1.5353 +IC CC13 CC11 *CC12 H12R 1.5353 108.82 -126.41 105.67 1.1103 +IC H12R CC11 *CC12 H12S 1.1103 105.67 -116.13 112.54 1.1110 +IC CC11 CC12 CC13 CC14 1.5861 108.82 -177.19 124.76 1.5291 +IC CC14 CC12 *CC13 H13R 1.5291 124.76 -126.31 102.56 1.1109 +IC H13R CC12 *CC13 H13S 1.1109 102.56 -101.72 109.52 1.1110 +IC CC12 CC13 CC14 CC15 1.5353 124.76 -147.35 108.06 1.5835 +IC CC15 CC13 *CC14 H14R 1.5835 108.06 -127.34 119.98 1.1117 +IC H14R CC13 *CC14 H14S 1.1117 119.98 -118.05 109.10 1.1109 +IC CC13 CC14 CC15 CC16 1.5291 108.06 78.94 118.04 1.5648 +IC CC16 CC14 *CC15 H15R 1.5648 118.04 -130.95 115.54 1.1114 +IC H15R CC14 *CC15 H15S 1.1114 115.54 -107.98 103.32 1.1109 +IC CC14 CC15 CC16 CC17 1.5835 118.04 170.34 112.62 1.5605 +IC CC17 CC15 *CC16 H16R 1.5605 112.62 116.67 109.09 1.1110 +IC H16R CC15 *CC16 H16S 1.1110 109.09 118.07 101.73 1.1110 +IC CC15 CC16 CC17 CC18 1.5648 112.62 -160.59 113.48 1.5455 +IC CC18 CC16 *CC17 H17R 1.5455 113.48 -119.35 112.75 1.1111 +IC H17R CC16 *CC17 H17S 1.1111 112.75 -118.74 109.01 1.1114 +IC CC16 CC17 CC18 H18R 1.5605 113.48 -167.53 105.19 1.1114 +IC H18R CC17 *CC18 H18S 1.1114 105.19 123.30 114.77 1.1107 +IC H18R CC17 *CC18 H18T 1.1114 105.19 -120.49 105.29 1.1117 +IC CD1 CD2 CD3 CD4 1.5654 113.19 -162.40 114.80 1.5512 +IC CD4 CD2 *CD3 H3X 1.5512 114.80 -117.81 118.26 1.1102 +IC H3X CD2 *CD3 H3Y 1.1102 118.26 -125.60 110.95 1.1112 +IC CD2 CD3 CD4 CD5 1.5154 114.80 63.81 109.67 1.6095 +IC CD5 CD3 *CD4 H4X 1.6095 109.67 -112.22 109.63 1.1107 +IC H4X CD3 *CD4 H4Y 1.1107 109.63 -120.86 110.95 1.1109 +IC CD3 CD4 CD5 CD6 1.5512 109.67 -171.66 110.10 1.5117 +IC CD6 CD4 *CD5 H5X 1.5117 110.10 -113.98 105.23 1.1108 +IC H5X CD4 *CD5 H5Y 1.1108 105.23 -128.80 116.89 1.1106 +IC CD4 CD5 CD6 CD7 1.6095 110.10 170.09 111.04 1.5055 +IC CD7 CD5 *CD6 H6X 1.5055 111.04 -114.76 105.35 1.1116 +IC H6X CD5 *CD6 H6Y 1.1116 105.35 -122.63 110.38 1.1108 +IC CD5 CD6 CD7 CD8 1.5117 111.04 -172.02 115.71 1.5289 +IC CD8 CD6 *CD7 H7X 1.5289 115.71 -123.94 114.68 1.1110 +IC H7X CD6 *CD7 H7Y 1.1110 114.68 -126.78 107.85 1.1109 +IC CD6 CD7 CD8 CD9 1.5055 115.71 -61.83 117.36 1.5186 +IC CD9 CD7 *CD8 H8X 1.5186 117.36 -129.63 101.79 1.1109 +IC H8X CD7 *CD8 H8Y 1.1109 101.79 -111.91 105.86 1.1107 +IC CD7 CD8 CD9 CD10 1.5289 117.36 179.97 120.32 1.3356 +IC CD10 CD8 *CD9 H9X 1.3356 120.32 -177.34 116.78 1.1009 +IC CD8 CD9 CD10 CD11 1.5186 120.32 -9.60 131.58 1.4710 +IC CD11 CD9 *CD10 H10X 1.4710 131.58 -172.61 113.16 1.1005 +IC CD9 CD10 CD11 CD12 1.3356 131.58 -124.79 115.05 1.5361 +IC CD12 CD10 *CD11 H11X 1.5361 115.05 -128.95 111.59 1.1111 +IC H11X CD10 *CD11 H11Y 1.1111 111.59 -111.21 111.18 1.1111 +IC CD10 CD11 CD12 CD13 1.4710 115.05 -77.11 105.04 1.4788 +IC CD13 CD11 *CD12 H12X 1.4788 105.04 -112.96 106.48 1.1110 +IC H12X CD11 *CD12 H12Y 1.1110 106.48 -120.99 113.58 1.1114 +IC CD11 CD12 CD13 CD14 1.5361 105.04 168.60 110.84 1.5429 +IC CD14 CD12 *CD13 H13X 1.5429 110.84 -122.83 114.36 1.1104 +IC H13X CD12 *CD13 H13Y 1.1104 114.36 -113.84 114.06 1.1110 +IC CD12 CD13 CD14 CD15 1.4788 110.84 -80.22 114.95 1.5099 +IC CD15 CD13 *CD14 H14X 1.5099 114.95 -125.08 104.06 1.1112 +IC H14X CD13 *CD14 H14Y 1.1112 104.06 -114.53 108.61 1.1117 +IC CD13 CD14 CD15 CD16 1.5429 114.95 173.02 110.69 1.5313 +IC CD16 CD14 *CD15 H15X 1.5313 110.69 -123.13 108.31 1.1109 +IC H15X CD14 *CD15 H15Y 1.1109 108.31 -110.71 116.76 1.1116 +IC CD14 CD15 CD16 CD17 1.5099 110.69 -176.63 112.38 1.5367 +IC CD17 CD15 *CD16 H16X 1.5367 112.38 -134.03 107.87 1.1113 +IC H16X CD15 *CD16 H16Y 1.1113 107.87 -110.75 102.38 1.1114 +IC CD15 CD16 CD17 CD18 1.5313 112.38 -173.09 106.45 1.5289 +IC CD18 CD16 *CD17 H17X 1.5289 106.45 -115.92 116.45 1.1117 +IC H17X CD16 *CD17 H17Y 1.1117 116.45 -114.48 108.29 1.1110 +IC CD16 CD17 CD18 H18X 1.5367 106.45 178.60 109.03 1.1112 +IC H18X CD17 *CD18 H18Y 1.1112 109.03 -120.60 108.05 1.1107 +IC H18X CD17 *CD18 H18Z 1.1112 109.03 119.06 114.08 1.1116 + +RESI TMCL1 -1.00 ! Tetramyristoyl Cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 4 myristoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9--H9E H9A--CA9--H9B H9X--CD9--H9Y H9R--CC9--H9S +ATOM H13J HAL2 0.09 ! | | | | +ATOM H13K HAL2 0.09 ! | | | | +ATOM O13 OSL -0.49 ! H10D--CB10--H10E H10A--CA10--H10B H10X--CD10--H10Y H10R--CC10--H10S +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12--H12E H12A--CA12--H12B H12X--CD12--H12Y H12R--CC12--H12S +ATOM H2E HAL2 0.09 ! | | | | +GROUP ! | | | | +ATOM C32 CTL1 0.17 ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H14F H14C H14Z H14T +ATOM CC2 CTL2 -0.22 ! +ATOM H2R HAL2 0.09 ! +ATOM H2S HAL2 0.09 ! +GROUP ! +ATOM C33 CTL2 0.08 ! +ATOM H33J HAL2 0.09 ! +ATOM H33K HAL2 0.09 ! +ATOM O33 OSL -0.49 ! +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CTL2 -0.18 ! +ATOM H9A HAL2 0.09 ! +ATOM H9B HAL2 0.09 ! +GROUP ! +ATOM CA10 CTL2 -0.18 ! +ATOM H10A HAL2 0.09 ! +ATOM H10B HAL2 0.09 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL3 -0.27 ! +ATOM H14A HAL3 0.09 ! +ATOM H14B HAL3 0.09 ! +ATOM H14C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CTL2 -0.18 ! +ATOM H9D HAL2 0.09 ! +ATOM H9E HAL2 0.09 ! +GROUP ! +ATOM CB10 CTL2 -0.18 ! +ATOM H10D HAL2 0.09 ! +ATOM H10E HAL2 0.09 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL3 -0.27 ! +ATOM H14D HAL3 0.09 ! +ATOM H14E HAL3 0.09 ! +ATOM H14F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CTL2 -0.18 ! +ATOM H9R HAL2 0.09 ! +ATOM H9S HAL2 0.09 ! +GROUP ! +ATOM CC10 CTL2 -0.18 ! +ATOM H10R HAL2 0.09 ! +ATOM H10S HAL2 0.09 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL3 -0.27 ! +ATOM H14R HAL3 0.09 ! +ATOM H14S HAL3 0.09 ! +ATOM H14T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CTL2 -0.18 ! +ATOM H9X HAL2 0.09 ! +ATOM H9Y HAL2 0.09 ! +GROUP ! +ATOM CD10 CTL2 -0.18 ! +ATOM H10X HAL2 0.09 ! +ATOM H10Y HAL2 0.09 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL3 -0.27 ! +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 H9B CA9 CA10 +BOND CA10 H10A CA10 H10B CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 H14C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 H9E CB9 CB10 +BOND CB10 H10D CB10 H10E CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 H14F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 H9S CC9 CC10 +BOND CC10 H10R CC10 H10S CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 H14T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 H9Y CD9 CD10 +BOND CD10 H10X CD10 H10Y CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 H14Z +! +! IC TABLE +! +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +IC OP31 C2 *C3 HG31 1.4050 106.59 123.15 108.63 1.1110 +IC HG31 C2 *C3 HG32 1.1110 108.63 110.55 105.02 1.1106 +IC C2 C3 OP31 P3 1.5276 106.59 150.07 122.97 1.5260 +IC C3 OP31 P3 OP32 1.4050 122.97 48.38 103.83 1.5120 +IC OP32 OP31 *P3 OP33 1.5120 103.83 -117.10 102.39 1.4430 +IC OP32 OP31 *P3 OP34 1.5120 103.83 117.56 104.31 1.4492 +IC OP31 P3 OP32 C31 1.5260 103.83 114.60 123.88 1.4412 +IC P3 OP32 C31 C32 1.5120 123.88 -70.62 112.68 1.5463 +IC C32 OP32 *C31 H31J 1.5463 112.68 133.05 108.81 1.1113 +IC H31J OP32 *C31 H31K 1.1113 108.81 108.32 102.51 1.1109 +IC HG31 C3 C2 C1 1.1110 108.63 65.18 110.69 1.5914 +IC C1 C3 *C2 OG12 1.5914 110.69 -127.85 110.69 1.4497 +IC C1 C3 *C2 HG22 1.5914 110.69 116.32 109.28 1.1109 +IC C3 C2 OG12 HO12 1.5276 110.69 20.43 105.65 0.9602 +IC C3 C2 C1 OP11 1.5276 110.69 -177.31 118.52 1.4009 +IC OP11 C2 *C1 HG11 1.4009 118.52 -115.89 100.08 1.1109 +IC HG11 C2 *C1 HG12 1.1109 100.08 -107.32 109.71 1.1109 +IC C2 C1 OP11 P1 1.5914 118.52 -42.01 125.79 1.5517 +IC C1 OP11 P1 OP12 1.4009 125.79 -23.10 113.44 1.4932 +IC OP12 OP11 *P1 OP13 1.4932 113.44 109.11 100.93 1.5223 +IC OP12 OP11 *P1 OP14 1.4932 113.44 -136.64 112.10 1.4774 +IC OP11 P1 OP13 HP13 1.5517 100.93 -32.51 100.15 0.9598 +IC OP11 P1 OP12 C11 1.5517 113.44 -71.46 119.19 1.4281 +IC P1 OP12 C11 C12 1.4932 119.19 -174.01 114.14 1.5600 +IC C12 OP12 *C11 H11J 1.5600 114.14 -120.45 115.71 1.1106 +IC H11J OP12 *C11 H11K 1.1106 115.71 -114.22 111.43 1.1116 +IC OP12 C11 C12 C13 1.4281 114.14 -44.52 111.60 1.5856 +IC C13 C11 *C12 O12 1.5856 111.60 120.95 112.40 1.4437 +IC O12 C11 *C12 H12J 1.4437 112.40 120.80 109.72 1.1111 +IC C11 C12 O12 CA1 1.5600 112.40 76.37 118.91 1.3382 +IC C12 O12 CA1 CA2 1.4437 118.91 -170.10 106.88 1.5044 +IC CA2 O12 *CA1 OA1 1.5044 106.88 170.93 125.37 1.2190 +IC O12 CA1 CA2 CA3 1.3382 106.88 -64.01 111.06 1.5054 +IC CA3 CA1 *CA2 H2A 1.5054 111.06 -122.28 106.22 1.1109 +IC H2A CA1 *CA2 H2B 1.1109 106.22 -115.95 107.88 1.1107 +IC C11 C12 C13 O13 1.5600 111.60 -168.55 103.46 1.4220 +IC O13 C12 *C13 H13J 1.4220 103.46 -122.75 106.37 1.1110 +IC H13J C12 *C13 H13K 1.1110 106.37 -120.14 107.90 1.1108 +IC C12 C13 O13 CB1 1.5856 103.46 -147.61 113.98 1.2904 +IC C13 O13 CB1 CB2 1.4220 113.98 -172.19 109.26 1.5109 +IC CB2 O13 *CB1 OB1 1.5109 109.26 175.74 132.39 1.2034 +IC O13 CB1 CB2 CB3 1.2904 109.26 -177.33 108.28 1.5902 +IC CB3 CB1 *CB2 H2D 1.5902 108.28 -126.53 103.94 1.1113 +IC H2D CB1 *CB2 H2E 1.1113 103.94 -108.22 114.02 1.1107 +IC OP32 C31 C32 C33 1.4412 112.68 -161.31 112.42 1.5470 +IC C33 C31 *C32 O32 1.5470 112.42 119.64 107.70 1.4164 +IC O32 C31 *C32 H32J 1.4164 107.70 117.79 103.91 1.1102 +IC C31 C32 O32 CC1 1.5463 107.70 150.86 113.51 1.3489 +IC C32 O32 CC1 CC2 1.4164 113.51 171.81 109.01 1.5112 +IC CC2 O32 *CC1 OC1 1.5112 109.01 -171.00 129.68 1.2250 +IC O32 CC1 CC2 CC3 1.3489 109.01 -53.78 119.27 1.5736 +IC CC3 CC1 *CC2 H2R 1.5736 119.27 -128.35 114.39 1.1108 +IC H2R CC1 *CC2 H2S 1.1108 114.39 -114.40 111.03 1.1112 +IC C31 C32 C33 O33 1.5463 112.42 168.14 118.35 1.4413 +IC O33 C32 *C33 H33J 1.4413 118.35 129.89 106.14 1.1114 +IC H33J C32 *C33 H33K 1.1114 106.14 111.36 95.75 1.1106 +IC C32 C33 O33 CD1 1.5470 118.35 84.29 117.79 1.3116 +IC C33 O33 CD1 CD2 1.4413 117.79 177.74 108.82 1.5668 +IC CD2 O33 *CD1 OD1 1.5668 108.82 -170.98 126.29 1.2372 +IC O33 CD1 CD2 CD3 1.3116 108.82 166.31 115.76 1.5388 +IC CD3 CD1 *CD2 H2X 1.5388 115.76 -130.95 106.40 1.1110 +IC H2X CD1 *CD2 H2Y 1.1110 106.40 -111.15 109.27 1.1118 +IC CA1 CA2 CA3 CA4 1.5044 111.06 -172.27 111.95 1.5762 +IC CA4 CA2 *CA3 H3A 1.5762 111.95 -119.12 106.42 1.1118 +IC H3A CA2 *CA3 H3B 1.1118 106.42 -117.36 112.06 1.1104 +IC CA2 CA3 CA4 CA5 1.5054 111.95 162.14 109.11 1.5194 +IC CA5 CA3 *CA4 H4A 1.5194 109.11 -122.88 100.98 1.1109 +IC H4A CA3 *CA4 H4B 1.1109 100.98 -104.55 118.21 1.1106 +IC CA3 CA4 CA5 CA6 1.5762 109.11 179.46 116.32 1.5160 +IC CA6 CA4 *CA5 H5A 1.5160 116.32 -130.90 119.18 1.1102 +IC H5A CA4 *CA5 H5B 1.1102 119.18 -111.91 102.81 1.1109 +IC CA4 CA5 CA6 CA7 1.5194 116.32 173.16 108.62 1.5591 +IC CA7 CA5 *CA6 H6A 1.5591 108.62 -116.45 106.70 1.1101 +IC H6A CA5 *CA6 H6B 1.1101 106.70 -121.57 110.88 1.1109 +IC CA5 CA6 CA7 CA8 1.5160 108.62 161.59 121.05 1.5360 +IC CA8 CA6 *CA7 H7A 1.5360 121.05 -118.76 105.58 1.1107 +IC H7A CA6 *CA7 H7B 1.1107 105.58 -112.97 111.34 1.1119 +IC CA6 CA7 CA8 CA9 1.5591 121.05 92.68 112.73 1.5325 +IC CA9 CA7 *CA8 H8A 1.5325 112.73 -126.40 106.72 1.1116 +IC H8A CA7 *CA8 H8B 1.1116 106.72 -113.41 103.36 1.1107 +IC CA7 CA8 CA9 CA10 1.5360 112.73 -173.09 107.97 1.5898 +IC CA10 CA8 *CA9 H9A 1.5898 107.97 -133.03 119.80 1.1112 +IC H9A CA8 *CA9 H9B 1.1112 119.80 -111.51 99.61 1.1114 +IC CA8 CA9 CA10 CA11 1.5325 107.97 -67.89 114.22 1.5589 +IC CA11 CA9 *CA10 H10A 1.5589 114.22 -119.09 107.30 1.1107 +IC H10A CA9 *CA10 H10B 1.1107 107.30 -112.42 107.57 1.1103 +IC CA9 CA10 CA11 CA12 1.5898 114.22 -160.31 103.05 1.5729 +IC CA12 CA10 *CA11 H11A 1.5729 103.05 -118.36 104.24 1.1115 +IC H11A CA10 *CA11 H11B 1.1115 104.24 -115.25 108.98 1.1113 +IC CA10 CA11 CA12 CA13 1.5589 103.05 -170.27 114.35 1.5884 +IC CA13 CA11 *CA12 H12A 1.5884 114.35 -120.66 108.63 1.1105 +IC H12A CA11 *CA12 H12B 1.1105 108.63 -117.12 113.06 1.1107 +IC CA11 CA12 CA13 CA14 1.5729 114.35 166.69 118.61 1.5182 +IC CA14 CA12 *CA13 H13A 1.5182 118.61 -115.87 103.12 1.1111 +IC H13A CA12 *CA13 H13B 1.1111 103.12 -118.00 100.92 1.1110 +IC CA12 CA13 CA14 H14A 1.5884 118.61 148.03 112.69 1.1104 +IC H14A CA13 *CA14 H14B 1.1104 112.69 -122.08 105.10 1.1104 +IC H14A CA13 *CA14 H14C 1.1104 112.69 123.62 104.29 1.1105 +IC CB1 CB2 CB3 CB4 1.5109 108.28 81.08 109.86 1.5577 +IC CB4 CB2 *CB3 H3D 1.5577 109.86 -127.89 123.15 1.1106 +IC H3D CB2 *CB3 H3E 1.1106 123.15 -116.59 102.58 1.1117 +IC CB2 CB3 CB4 CB5 1.5902 109.86 177.90 113.44 1.4761 +IC CB5 CB3 *CB4 H4D 1.4761 113.44 -124.87 115.51 1.1111 +IC H4D CB3 *CB4 H4E 1.1111 115.51 -116.67 108.51 1.1118 +IC CB3 CB4 CB5 CB6 1.5577 113.44 -100.36 111.37 1.5155 +IC CB6 CB4 *CB5 H5D 1.5155 111.37 -114.84 111.97 1.1105 +IC H5D CB4 *CB5 H5E 1.1105 111.97 -127.96 116.57 1.1114 +IC CB4 CB5 CB6 CB7 1.4761 111.37 174.16 108.77 1.5362 +IC CB7 CB5 *CB6 H6D 1.5362 108.77 -117.02 117.49 1.1103 +IC H6D CB5 *CB6 H6E 1.1103 117.49 -132.94 112.76 1.1118 +IC CB5 CB6 CB7 CB8 1.5155 108.77 146.40 115.49 1.5845 +IC CB8 CB6 *CB7 H7D 1.5845 115.49 -116.88 108.45 1.1120 +IC H7D CB6 *CB7 H7E 1.1120 108.45 -111.34 112.25 1.1112 +IC CB6 CB7 CB8 CB9 1.5362 115.49 -72.08 117.65 1.5557 +IC CB9 CB7 *CB8 H8D 1.5557 117.65 -113.04 108.13 1.1109 +IC H8D CB7 *CB8 H8E 1.1109 108.13 -118.68 110.23 1.1118 +IC CB7 CB8 CB9 CB10 1.5845 117.65 -156.81 104.24 1.5265 +IC CB10 CB8 *CB9 H9D 1.5265 104.24 -122.89 113.93 1.1108 +IC H9D CB8 *CB9 H9E 1.1108 113.93 -127.80 108.66 1.1113 +IC CB8 CB9 CB10 CB11 1.5557 104.24 -86.15 111.07 1.5370 +IC CB11 CB9 *CB10 H10D 1.5370 111.07 -119.92 110.97 1.1106 +IC H10D CB9 *CB10 H10E 1.1106 110.97 -121.26 111.59 1.1112 +IC CB9 CB10 CB11 CB12 1.5265 111.07 -173.33 116.48 1.5027 +IC CB12 CB10 *CB11 H11D 1.5027 116.48 -131.71 106.69 1.1111 +IC H11D CB10 *CB11 H11E 1.1111 106.69 -113.55 112.18 1.1108 +IC CB10 CB11 CB12 CB13 1.5370 116.48 -36.71 111.63 1.5305 +IC CB13 CB11 *CB12 H12D 1.5305 111.63 -126.37 109.33 1.1112 +IC H12D CB11 *CB12 H12E 1.1112 109.33 -109.21 113.42 1.1103 +IC CB11 CB12 CB13 CB14 1.5027 111.63 -179.35 109.24 1.5190 +IC CB14 CB12 *CB13 H13D 1.5190 109.24 -121.77 105.36 1.1111 +IC H13D CB12 *CB13 H13E 1.1111 105.36 -118.30 111.80 1.1108 +IC CB12 CB13 CB14 H14D 1.5305 109.24 91.17 115.81 1.1112 +IC H14D CB13 *CB14 H14E 1.1112 115.81 -129.13 112.15 1.1108 +IC H14D CB13 *CB14 H14F 1.1112 115.81 111.54 104.35 1.1107 +IC CC1 CC2 CC3 CC4 1.5112 119.27 -84.82 111.07 1.5486 +IC CC4 CC2 *CC3 H3R 1.5486 111.07 -128.79 105.38 1.1109 +IC H3R CC2 *CC3 H3S 1.1109 105.38 -116.05 114.39 1.1116 +IC CC2 CC3 CC4 CC5 1.5736 111.07 -158.86 113.50 1.5532 +IC CC5 CC3 *CC4 H4R 1.5532 113.50 119.25 109.95 1.1104 +IC H4R CC3 *CC4 H4S 1.1104 109.95 116.52 106.49 1.1114 +IC CC3 CC4 CC5 CC6 1.5486 113.50 175.31 108.39 1.5673 +IC CC6 CC4 *CC5 H5R 1.5673 108.39 -121.95 112.05 1.1112 +IC H5R CC4 *CC5 H5S 1.1112 112.05 -125.98 108.85 1.1111 +IC CC4 CC5 CC6 CC7 1.5532 108.39 58.87 112.46 1.5361 +IC CC7 CC5 *CC6 H6R 1.5361 112.46 -127.53 116.00 1.1111 +IC H6R CC5 *CC6 H6S 1.1111 116.00 -116.02 103.83 1.1105 +IC CC5 CC6 CC7 CC8 1.5673 112.46 157.87 116.86 1.4675 +IC CC8 CC6 *CC7 H7R 1.4675 116.86 -118.69 110.59 1.1110 +IC H7R CC6 *CC7 H7S 1.1110 110.59 -113.76 106.32 1.1115 +IC CC6 CC7 CC8 CC9 1.5361 116.86 77.53 114.85 1.6005 +IC CC9 CC7 *CC8 H8R 1.6005 114.85 -113.75 107.33 1.1106 +IC H8R CC7 *CC8 H8S 1.1106 107.33 -127.57 118.62 1.1109 +IC CC7 CC8 CC9 CC10 1.4675 114.85 -174.60 112.33 1.4927 +IC CC10 CC8 *CC9 H9R 1.4927 112.33 -126.47 100.16 1.1110 +IC H9R CC8 *CC9 H9S 1.1110 100.16 -100.96 119.10 1.1106 +IC CC8 CC9 CC10 CC11 1.6005 112.33 67.84 110.69 1.5216 +IC CC11 CC9 *CC10 H10R 1.5216 110.69 -128.17 115.38 1.1104 +IC H10R CC9 *CC10 H10S 1.1104 115.38 -110.12 110.97 1.1103 +IC CC9 CC10 CC11 CC12 1.4927 110.69 172.42 119.51 1.5448 +IC CC12 CC10 *CC11 H11R 1.5448 119.51 -130.45 109.51 1.1109 +IC H11R CC10 *CC11 H11S 1.1109 109.51 -112.41 104.58 1.1110 +IC CC10 CC11 CC12 CC13 1.5216 119.51 175.01 110.61 1.5672 +IC CC13 CC11 *CC12 H12R 1.5672 110.61 -122.43 105.82 1.1108 +IC H12R CC11 *CC12 H12S 1.1108 105.82 -113.63 99.43 1.1116 +IC CC11 CC12 CC13 CC14 1.5448 110.61 150.51 115.86 1.5313 +IC CC14 CC12 *CC13 H13R 1.5313 115.86 -121.46 111.52 1.1113 +IC H13R CC12 *CC13 H13S 1.1113 111.52 -115.56 105.11 1.1111 +IC CC12 CC13 CC14 H14R 1.5672 115.86 -36.59 112.22 1.1116 +IC H14R CC13 *CC14 H14S 1.1116 112.22 -122.53 109.83 1.1109 +IC H14R CC13 *CC14 H14T 1.1116 112.22 116.08 103.16 1.1117 +IC CD1 CD2 CD3 CD4 1.5668 115.76 163.93 105.41 1.5236 +IC CD4 CD2 *CD3 H3X 1.5236 105.41 -129.15 113.03 1.1119 +IC H3X CD2 *CD3 H3Y 1.1119 113.03 -114.25 105.13 1.1112 +IC CD2 CD3 CD4 CD5 1.5388 105.41 168.47 108.44 1.5329 +IC CD5 CD3 *CD4 H4X 1.5329 108.44 -109.46 117.96 1.1108 +IC H4X CD3 *CD4 H4Y 1.1108 117.96 -130.57 108.16 1.1114 +IC CD3 CD4 CD5 CD6 1.5236 108.44 -178.40 112.75 1.5659 +IC CD6 CD4 *CD5 H5X 1.5659 112.75 -122.58 110.57 1.1106 +IC H5X CD4 *CD5 H5Y 1.1106 110.57 -130.67 109.90 1.1111 +IC CD4 CD5 CD6 CD7 1.5329 112.75 -177.36 117.41 1.5472 +IC CD7 CD5 *CD6 H6X 1.5472 117.41 -123.99 110.82 1.1111 +IC H6X CD5 *CD6 H6Y 1.1111 110.82 -122.26 107.55 1.1111 +IC CD5 CD6 CD7 CD8 1.5659 117.41 -165.15 117.72 1.5893 +IC CD8 CD6 *CD7 H7X 1.5893 117.72 -123.61 106.43 1.1106 +IC H7X CD6 *CD7 H7Y 1.1106 106.43 -116.65 103.21 1.1118 +IC CD6 CD7 CD8 CD9 1.5472 117.72 178.42 118.20 1.5022 +IC CD9 CD7 *CD8 H8X 1.5022 118.20 -126.93 106.15 1.1108 +IC H8X CD7 *CD8 H8Y 1.1108 106.15 -111.83 99.99 1.1104 +IC CD7 CD8 CD9 CD10 1.5893 118.20 -164.18 109.69 1.5450 +IC CD10 CD8 *CD9 H9X 1.5450 109.69 -114.64 108.89 1.1107 +IC H9X CD8 *CD9 H9Y 1.1107 108.89 -122.84 111.25 1.1105 +IC CD8 CD9 CD10 CD11 1.5022 109.69 -167.74 114.00 1.5498 +IC CD11 CD9 *CD10 H10X 1.5498 114.00 -115.78 109.31 1.1109 +IC H10X CD9 *CD10 H10Y 1.1109 109.31 -126.90 108.29 1.1108 +IC CD9 CD10 CD11 CD12 1.5450 114.00 151.20 114.13 1.5788 +IC CD12 CD10 *CD11 H11X 1.5788 114.13 -121.41 105.65 1.1113 +IC H11X CD10 *CD11 H11Y 1.1113 105.65 -117.14 111.34 1.1114 +IC CD10 CD11 CD12 CD13 1.5498 114.13 -89.48 107.29 1.5452 +IC CD13 CD11 *CD12 H12X 1.5452 107.29 -118.25 108.80 1.1106 +IC H12X CD11 *CD12 H12Y 1.1106 108.80 -115.90 107.78 1.1110 +IC CD11 CD12 CD13 CD14 1.5788 107.29 -173.08 114.52 1.5673 +IC CD14 CD12 *CD13 H13X 1.5673 114.52 -123.36 112.22 1.1108 +IC H13X CD12 *CD13 H13Y 1.1108 112.22 -118.84 107.84 1.1110 +IC CD12 CD13 CD14 H14X 1.5452 114.52 150.10 116.26 1.1110 +IC H14X CD13 *CD14 H14Y 1.1110 116.26 -124.21 105.24 1.1111 +IC H14X CD13 *CD14 H14Z 1.1110 116.26 127.23 112.28 1.1115 + +RESI TMCL2 -2.00 ! Tetramyristoyl Cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 4 myristoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9--H9E H9A--CA9--H9B H9X--CD9--H9Y H9R--CC9-H9S +ATOM H13K HAL2 0.09 ! | | | | +ATOM O13 OSL -0.49 ! | | | | +ATOM CB1 CL 0.90 ! H10D--CB10--H10E H10A--CA10--H10B H10X--CD10--H10Y H10R--CC10--H10S +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12--H12E H12A--CA12--H12B H12X--CD12--H12Y H12R--CC12--H12S +GROUP ! | | | | +ATOM C32 CTL1 0.17 ! | | | | +ATOM H32J HAL1 0.09 ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H14F H14C H14Z H14T +ATOM H2R HAL2 0.09 ! +ATOM H2S HAL2 0.09 ! +GROUP ! +ATOM C33 CTL2 0.08 ! +ATOM H33J HAL2 0.09 ! +ATOM H33K HAL2 0.09 ! +ATOM O33 OSL -0.49 ! +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CTL2 -0.18 ! +ATOM H9A HAL2 0.09 ! +ATOM H9B HAL2 0.09 ! +GROUP ! +ATOM CA10 CTL2 -0.18 ! +ATOM H10A HAL2 0.09! +ATOM H10B HAL2 0.09 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL3 -0.27 ! +ATOM H14A HAL3 0.09 ! +ATOM H14B HAL3 0.09 ! +ATOM H14C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CTL2 -0.18 ! +ATOM H9D HAL2 0.09 ! +ATOM H9E HAL2 0.09 ! +GROUP ! +ATOM CB10 CTL2 -0.18 ! +ATOM H10D HAL2 0.09 ! +ATOM H10E HAL2 0.09 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL3 -0.27 ! +ATOM H14D HAL3 0.09 ! +ATOM H14E HAL3 0.09 ! +ATOM H14F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CTL2 -0.18 ! +ATOM H9R HAL2 0.09 ! +ATOM H9S HAL2 0.09 ! +GROUP ! +ATOM CC10 CTL2 -0.18 ! +ATOM H10R HAL2 0.09 ! +ATOM H10S HAL2 0.09 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL3 -0.27 ! +ATOM H14R HAL3 0.09 ! +ATOM H14S HAL3 0.09 ! +ATOM H14T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CTL2 -0.18 ! +ATOM H9X HAL2 0.09 ! +ATOM H9Y HAL2 0.09 ! +GROUP ! +ATOM CD10 CTL2 -0.18 ! +ATOM H10X HAL2 0.09 ! +ATOM H10Y HAL2 0.09 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL3 -0.27 ! +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 H9B CA9 CA10 +BOND CA10 H10A CA10 H10B CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 H14C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 H9E CB9 CB10 +BOND CB10 H10D CB10 H10E CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 H14F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 H9S CC9 CC10 +BOND CC10 H10R CC10 H10S CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 H14T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 H9Y CD9 CD10 +BOND CD10 H10X CD10 H10Y CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 H14Z +! +! IC TABLE +! +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +IC OP31 C2 *C3 HG31 1.4123 114.11 131.84 108.14 1.1103 +IC HG31 C2 *C3 HG32 1.1103 108.14 115.64 109.73 1.1111 +IC C2 C3 OP31 P3 1.5538 114.11 78.24 123.69 1.5653 +IC C3 OP31 P3 OP32 1.4123 123.69 48.30 104.93 1.5616 +IC OP32 OP31 *P3 OP33 1.5616 104.93 -120.49 111.69 1.4907 +IC OP32 OP31 *P3 OP34 1.5616 104.93 113.19 98.21 1.4413 +IC OP31 P3 OP32 C31 1.5653 104.93 -155.09 118.42 1.4883 +IC P3 OP32 C31 C32 1.5616 118.42 145.48 113.54 1.5598 +IC C32 OP32 *C31 H31J 1.5598 113.54 117.40 107.36 1.1113 +IC H31J OP32 *C31 H31K 1.1113 107.36 111.44 115.77 1.1099 +IC HG31 C3 C2 C1 1.1103 108.14 -54.64 113.40 1.5823 +IC C1 C3 *C2 OG12 1.5823 113.40 -122.75 105.61 1.4076 +IC C1 C3 *C2 HG22 1.5823 113.40 120.16 101.82 1.1105 +IC C3 C2 OG12 HO12 1.5538 105.61 -58.96 102.08 0.9596 +IC C3 C2 C1 OP11 1.5538 113.40 51.17 113.07 1.4776 +IC OP11 C2 *C1 HG11 1.4776 113.07 -119.07 110.82 1.1108 +IC HG11 C2 *C1 HG12 1.1108 110.82 -113.40 110.20 1.1105 +IC C2 C1 OP11 P1 1.5823 113.07 146.91 118.09 1.5112 +IC C1 OP11 P1 OP12 1.4776 118.09 161.02 106.11 1.5707 +IC OP12 OP11 *P1 OP13 1.5707 106.11 120.54 110.55 1.4806 +IC OP12 OP11 *P1 OP14 1.5707 106.11 -117.61 110.74 1.4659 +IC OP11 P1 OP12 C11 1.5112 106.11 -53.10 115.48 1.4801 +IC P1 OP12 C11 C12 1.5707 115.48 136.21 111.90 1.5371 +IC C12 OP12 *C11 H11J 1.5371 111.90 -115.68 114.32 1.1105 +IC H11J OP12 *C11 H11K 1.1105 114.32 -118.73 106.02 1.1104 +IC OP12 C11 C12 C13 1.4801 111.90 -53.69 112.78 1.5450 +IC C13 C11 *C12 O12 1.5450 112.78 116.76 109.20 1.4352 +IC O12 C11 *C12 H12J 1.4352 109.20 121.04 113.41 1.1109 +IC C11 C12 O12 CA1 1.5371 109.20 145.12 122.23 1.3261 +IC C12 O12 CA1 CA2 1.4352 122.23 177.65 115.77 1.4715 +IC CA2 O12 *CA1 OA1 1.4715 115.77 -175.29 125.06 1.2159 +IC O12 CA1 CA2 CA3 1.3261 115.77 -108.99 110.99 1.5476 +IC CA3 CA1 *CA2 H2A 1.5476 110.99 -131.14 108.98 1.1115 +IC H2A CA1 *CA2 H2B 1.1115 108.98 -106.72 103.88 1.1102 +IC C11 C12 C13 O13 1.5371 112.78 170.60 115.76 1.4335 +IC O13 C12 *C13 H13J 1.4335 115.76 -126.88 109.64 1.1113 +IC H13J C12 *C13 H13K 1.1113 109.64 -106.43 106.48 1.1107 +IC C12 C13 O13 CB1 1.5450 115.76 85.85 121.32 1.3241 +IC C13 O13 CB1 CB2 1.4335 121.32 153.55 113.54 1.5621 +IC CB2 O13 *CB1 OB1 1.5621 113.54 -170.07 125.27 1.2188 +IC O13 CB1 CB2 CB3 1.3241 113.54 61.58 108.34 1.5843 +IC CB3 CB1 *CB2 H2D 1.5843 108.34 -122.68 106.79 1.1120 +IC H2D CB1 *CB2 H2E 1.1120 106.79 -120.86 94.29 1.1110 +IC OP32 C31 C32 C33 1.4883 113.54 -27.39 105.62 1.5931 +IC C33 C31 *C32 O32 1.5931 105.62 121.20 116.58 1.4539 +IC O32 C31 *C32 H32J 1.4539 116.58 131.67 110.14 1.1112 +IC C31 C32 O32 CC1 1.5598 116.58 80.56 112.20 1.2833 +IC C32 O32 CC1 CC2 1.4539 112.20 -178.92 107.85 1.5237 +IC CC2 O32 *CC1 OC1 1.5237 107.85 -177.98 127.26 1.2253 +IC O32 CC1 CC2 CC3 1.2833 107.85 -160.76 111.13 1.5467 +IC CC3 CC1 *CC2 H2R 1.5467 111.13 -117.06 100.52 1.1114 +IC H2R CC1 *CC2 H2S 1.1114 100.52 -114.48 110.77 1.1107 +IC C31 C32 C33 O33 1.5598 105.62 175.04 108.57 1.4963 +IC O33 C32 *C33 H33J 1.4963 108.57 123.32 110.69 1.1110 +IC H33J C32 *C33 H33K 1.1110 110.69 122.72 103.67 1.1113 +IC C32 C33 O33 CD1 1.5931 108.57 86.02 114.21 1.3123 +IC C33 O33 CD1 CD2 1.4963 114.21 179.35 111.83 1.5364 +IC CD2 O33 *CD1 OD1 1.5364 111.83 171.47 123.49 1.2177 +IC O33 CD1 CD2 CD3 1.3123 111.83 74.27 111.90 1.6081 +IC CD3 CD1 *CD2 H2X 1.6081 111.90 -125.71 104.19 1.1111 +IC H2X CD1 *CD2 H2Y 1.1111 104.19 -114.85 107.54 1.1103 +IC CA1 CA2 CA3 CA4 1.4715 110.99 -99.56 111.63 1.5613 +IC CA4 CA2 *CA3 H3A 1.5613 111.63 -120.89 114.81 1.1111 +IC H3A CA2 *CA3 H3B 1.1111 114.81 -122.44 112.12 1.1118 +IC CA2 CA3 CA4 CA5 1.5476 111.63 -164.46 118.20 1.5177 +IC CA5 CA3 *CA4 H4A 1.5177 118.20 -129.80 107.75 1.1115 +IC H4A CA3 *CA4 H4B 1.1115 107.75 -112.77 109.37 1.1110 +IC CA3 CA4 CA5 CA6 1.5613 118.20 -165.05 110.21 1.4960 +IC CA6 CA4 *CA5 H5A 1.4960 110.21 -119.21 110.30 1.1105 +IC H5A CA4 *CA5 H5B 1.1105 110.30 -120.60 113.94 1.1105 +IC CA4 CA5 CA6 CA7 1.5177 110.21 -162.85 112.03 1.5101 +IC CA7 CA5 *CA6 H6A 1.5101 112.03 -122.46 111.99 1.1107 +IC H6A CA5 *CA6 H6B 1.1107 111.99 -125.70 104.97 1.1117 +IC CA5 CA6 CA7 CA8 1.4960 112.03 -175.49 116.42 1.5114 +IC CA8 CA6 *CA7 H7A 1.5114 116.42 -121.55 106.98 1.1103 +IC H7A CA6 *CA7 H7B 1.1103 106.98 -122.20 105.89 1.1110 +IC CA6 CA7 CA8 CA9 1.5101 116.42 170.45 119.52 1.5556 +IC CA9 CA7 *CA8 H8A 1.5556 119.52 -124.58 108.53 1.1104 +IC H8A CA7 *CA8 H8B 1.1104 108.53 -106.84 106.46 1.1114 +IC CA7 CA8 CA9 CA10 1.5114 119.52 178.06 106.74 1.5816 +IC CA10 CA8 *CA9 H9A 1.5816 106.74 -122.44 108.78 1.1112 +IC H9A CA8 *CA9 H9B 1.1112 108.78 -121.68 111.63 1.1108 +IC CA8 CA9 CA10 CA11 1.5556 106.74 172.43 115.38 1.5312 +IC CA11 CA9 *CA10 H10A 1.5312 115.38 -125.34 115.83 1.1107 +IC H10A CA9 *CA10 H10B 1.1107 115.83 -110.84 93.66 1.1108 +IC CA9 CA10 CA11 CA12 1.5816 115.38 134.56 122.59 1.5541 +IC CA12 CA10 *CA11 H11A 1.5541 122.59 -114.06 104.68 1.1107 +IC H11A CA10 *CA11 H11B 1.1107 104.68 -118.16 106.19 1.1110 +IC CA10 CA11 CA12 CA13 1.5312 122.59 167.13 113.35 1.5666 +IC CA13 CA11 *CA12 H12A 1.5666 113.35 -122.36 108.22 1.1117 +IC H12A CA11 *CA12 H12B 1.1117 108.22 -112.28 114.20 1.1105 +IC CA11 CA12 CA13 CA14 1.5541 113.35 170.17 110.71 1.5053 +IC CA14 CA12 *CA13 H13A 1.5053 110.71 -113.56 104.89 1.1111 +IC H13A CA12 *CA13 H13B 1.1111 104.89 -126.54 111.17 1.1105 +IC CA12 CA13 CA14 H14A 1.5666 110.71 -49.73 116.43 1.1109 +IC H14A CA13 *CA14 H14B 1.1109 116.43 -119.24 111.92 1.1107 +IC H14A CA13 *CA14 H14C 1.1109 116.43 118.51 106.19 1.1109 +IC CB1 CB2 CB3 CB4 1.5621 108.34 -172.32 111.36 1.5605 +IC CB4 CB2 *CB3 H3D 1.5605 111.36 -116.74 108.43 1.1107 +IC H3D CB2 *CB3 H3E 1.1107 108.43 -114.82 122.03 1.1108 +IC CB2 CB3 CB4 CB5 1.5843 111.36 -161.34 112.89 1.5565 +IC CB5 CB3 *CB4 H4D 1.5565 112.89 -123.47 112.97 1.1114 +IC H4D CB3 *CB4 H4E 1.1114 112.97 -122.07 107.10 1.1106 +IC CB3 CB4 CB5 CB6 1.5605 112.89 169.94 110.19 1.5761 +IC CB6 CB4 *CB5 H5D 1.5761 110.19 -115.78 106.78 1.1107 +IC H5D CB4 *CB5 H5E 1.1107 106.78 -115.02 107.79 1.1104 +IC CB4 CB5 CB6 CB7 1.5565 110.19 170.22 115.75 1.5972 +IC CB7 CB5 *CB6 H6D 1.5972 115.75 -126.64 116.58 1.1111 +IC H6D CB5 *CB6 H6E 1.1111 116.58 -113.21 100.46 1.1111 +IC CB5 CB6 CB7 CB8 1.5761 115.75 154.34 112.13 1.5372 +IC CB8 CB6 *CB7 H7D 1.5372 112.13 -118.87 109.96 1.1114 +IC H7D CB6 *CB7 H7E 1.1114 109.96 -120.67 109.16 1.1111 +IC CB6 CB7 CB8 CB9 1.5972 112.13 -174.51 119.07 1.5320 +IC CB9 CB7 *CB8 H8D 1.5320 119.07 -128.68 112.83 1.1110 +IC H8D CB7 *CB8 H8E 1.1110 112.83 -111.51 96.63 1.1113 +IC CB7 CB8 CB9 CB10 1.5372 119.07 -164.45 113.21 1.5560 +IC CB10 CB8 *CB9 H9D 1.5560 113.21 -131.64 118.55 1.1110 +IC H9D CB8 *CB9 H9E 1.1110 118.55 -113.98 106.59 1.1113 +IC CB8 CB9 CB10 CB11 1.5320 113.21 -177.52 113.58 1.5741 +IC CB11 CB9 *CB10 H10D 1.5741 113.58 -124.27 109.24 1.1110 +IC H10D CB9 *CB10 H10E 1.1110 109.24 -123.30 111.99 1.1114 +IC CB9 CB10 CB11 CB12 1.5560 113.58 -75.52 112.60 1.4985 +IC CB12 CB10 *CB11 H11D 1.4985 112.60 -123.86 113.84 1.1105 +IC H11D CB10 *CB11 H11E 1.1105 113.84 -127.22 110.15 1.1113 +IC CB10 CB11 CB12 CB13 1.5741 112.60 -167.95 115.99 1.5564 +IC CB13 CB11 *CB12 H12D 1.5564 115.99 -113.80 102.16 1.1105 +IC H12D CB11 *CB12 H12E 1.1105 102.16 -113.97 112.17 1.1105 +IC CB11 CB12 CB13 CB14 1.4985 115.99 -161.74 111.86 1.4887 +IC CB14 CB12 *CB13 H13D 1.4887 111.86 -133.81 112.75 1.1114 +IC H13D CB12 *CB13 H13E 1.1114 112.75 -114.35 108.49 1.1110 +IC CB12 CB13 CB14 H14D 1.5564 111.86 145.57 116.60 1.1114 +IC H14D CB13 *CB14 H14E 1.1114 116.60 -128.22 114.97 1.1109 +IC H14D CB13 *CB14 H14F 1.1114 116.60 118.21 104.54 1.1106 +IC CC1 CC2 CC3 CC4 1.5237 111.13 -171.03 111.92 1.5265 +IC CC4 CC2 *CC3 H3R 1.5265 111.92 -116.51 107.19 1.1119 +IC H3R CC2 *CC3 H3S 1.1119 107.19 -121.78 110.51 1.1118 +IC CC2 CC3 CC4 CC5 1.5467 111.92 -169.41 111.35 1.5565 +IC CC5 CC3 *CC4 H4R 1.5565 111.35 -125.66 110.37 1.1111 +IC H4R CC3 *CC4 H4S 1.1111 110.37 -115.71 111.29 1.1112 +IC CC3 CC4 CC5 CC6 1.5265 111.35 169.94 115.34 1.4319 +IC CC6 CC4 *CC5 H5R 1.4319 115.34 -116.32 102.94 1.1111 +IC H5R CC4 *CC5 H5S 1.1111 102.94 -123.23 101.79 1.1114 +IC CC4 CC5 CC6 CC7 1.5565 115.34 75.88 113.89 1.5676 +IC CC7 CC5 *CC6 H6R 1.5676 113.89 -123.49 107.84 1.1109 +IC H6R CC5 *CC6 H6S 1.1109 107.84 -119.64 113.33 1.1110 +IC CC5 CC6 CC7 CC8 1.4319 113.89 -172.19 115.47 1.5138 +IC CC8 CC6 *CC7 H7R 1.5138 115.47 -112.82 108.85 1.1109 +IC H7R CC6 *CC7 H7S 1.1109 108.85 -118.30 110.86 1.1107 +IC CC6 CC7 CC8 CC9 1.5676 115.47 76.63 114.20 1.5551 +IC CC9 CC7 *CC8 H8R 1.5551 114.20 -122.83 112.42 1.1105 +IC H8R CC7 *CC8 H8S 1.1105 112.42 -109.89 108.80 1.1115 +IC CC7 CC8 CC9 CC10 1.5138 114.20 168.52 113.41 1.5495 +IC CC10 CC8 *CC9 H9R 1.5495 113.41 -120.00 103.82 1.1112 +IC H9R CC8 *CC9 H9S 1.1112 103.82 -114.65 112.47 1.1113 +IC CC8 CC9 CC10 CC11 1.5551 113.41 53.18 113.24 1.5294 +IC CC11 CC9 *CC10 H10R 1.5294 113.24 -120.20 109.36 1.1114 +IC H10R CC9 *CC10 H10S 1.1114 109.36 -119.23 103.43 1.1106 +IC CC9 CC10 CC11 CC12 1.5495 113.24 162.91 112.34 1.5239 +IC CC12 CC10 *CC11 H11R 1.5239 112.34 -122.79 117.98 1.1116 +IC H11R CC10 *CC11 H11S 1.1116 117.98 -117.81 105.44 1.1113 +IC CC10 CC11 CC12 CC13 1.5294 112.34 -163.12 111.66 1.5573 +IC CC13 CC11 *CC12 H12R 1.5573 111.66 -123.84 113.86 1.1112 +IC H12R CC11 *CC12 H12S 1.1112 113.86 -117.78 106.11 1.1104 +IC CC11 CC12 CC13 CC14 1.5239 111.66 168.54 114.62 1.5290 +IC CC14 CC12 *CC13 H13R 1.5290 114.62 -118.14 108.05 1.1110 +IC H13R CC12 *CC13 H13S 1.1110 108.05 -119.00 110.61 1.1104 +IC CC12 CC13 CC14 H14R 1.5573 114.62 67.10 103.74 1.1106 +IC H14R CC13 *CC14 H14S 1.1106 103.74 -123.52 110.77 1.1109 +IC H14R CC13 *CC14 H14T 1.1106 103.74 117.05 114.20 1.1112 +IC CD1 CD2 CD3 CD4 1.5364 111.90 -63.17 115.51 1.5018 +IC CD4 CD2 *CD3 H3X 1.5018 115.51 -125.99 109.85 1.1115 +IC H3X CD2 *CD3 H3Y 1.1115 109.85 -110.04 111.66 1.1108 +IC CD2 CD3 CD4 CD5 1.6081 115.51 -173.64 113.56 1.5400 +IC CD5 CD3 *CD4 H4X 1.5400 113.56 -121.35 106.16 1.1109 +IC H4X CD3 *CD4 H4Y 1.1109 106.16 -107.67 114.08 1.1115 +IC CD3 CD4 CD5 CD6 1.5018 113.56 71.26 114.10 1.5395 +IC CD6 CD4 *CD5 H5X 1.5395 114.10 -118.11 108.32 1.1113 +IC H5X CD4 *CD5 H5Y 1.1113 108.32 -121.07 103.86 1.1107 +IC CD4 CD5 CD6 CD7 1.5400 114.10 179.27 116.81 1.5485 +IC CD7 CD5 *CD6 H6X 1.5485 116.81 -120.39 111.83 1.1114 +IC H6X CD5 *CD6 H6Y 1.1114 111.83 -114.44 112.31 1.1113 +IC CD5 CD6 CD7 CD8 1.5395 116.81 -172.44 110.34 1.5139 +IC CD8 CD6 *CD7 H7X 1.5139 110.34 -123.11 109.13 1.1115 +IC H7X CD6 *CD7 H7Y 1.1115 109.13 -117.23 114.42 1.1104 +IC CD6 CD7 CD8 CD9 1.5485 110.34 -177.63 116.71 1.5986 +IC CD9 CD7 *CD8 H8X 1.5986 116.71 -122.96 114.88 1.1116 +IC H8X CD7 *CD8 H8Y 1.1116 114.88 -120.47 104.07 1.1115 +IC CD7 CD8 CD9 CD10 1.5139 116.71 -175.88 116.87 1.5306 +IC CD10 CD8 *CD9 H9X 1.5306 116.87 -120.26 101.93 1.1106 +IC H9X CD8 *CD9 H9Y 1.1106 101.93 -118.48 109.71 1.1113 +IC CD8 CD9 CD10 CD11 1.5986 116.87 179.59 117.00 1.5477 +IC CD11 CD9 *CD10 H10X 1.5477 117.00 -121.39 116.38 1.1108 +IC H10X CD9 *CD10 H10Y 1.1108 116.38 -116.93 112.75 1.1110 +IC CD9 CD10 CD11 CD12 1.5306 117.00 58.29 115.55 1.5919 +IC CD12 CD10 *CD11 H11X 1.5919 115.55 -123.93 111.02 1.1115 +IC H11X CD10 *CD11 H11Y 1.1115 111.02 -125.71 106.67 1.1106 +IC CD10 CD11 CD12 CD13 1.5477 115.55 171.82 112.65 1.5096 +IC CD13 CD11 *CD12 H12X 1.5096 112.65 -108.78 101.68 1.1113 +IC H12X CD11 *CD12 H12Y 1.1113 101.68 -123.05 109.66 1.1111 +IC CD11 CD12 CD13 CD14 1.5919 112.65 179.19 114.79 1.5673 +IC CD14 CD12 *CD13 H13X 1.5673 114.79 -126.45 112.62 1.1114 +IC H13X CD12 *CD13 H13Y 1.1114 112.62 -117.03 109.25 1.1109 +IC CD12 CD13 CD14 H14X 1.5096 114.79 54.70 110.96 1.1109 +IC H14X CD13 *CD14 H14Y 1.1109 110.96 -118.96 105.91 1.1108 +IC H14X CD13 *CD14 H14Z 1.1109 110.96 120.33 110.31 1.1115 + +RESI TLCL1 -1.00 ! Tetralinoleoyl Cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 4 linoleoly chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +ATOM H2E HAL2 0.09 ! || || || || +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM CC2 CTL2 -0.22 ! | | | | +ATOM H2R HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18F H18C H18Z H18T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4272 111.57 124.87 107.78 1.1169 +IC HG31 C2 *C3 HG32 1.1169 107.78 115.89 109.04 1.1124 +IC C2 C3 OP31 P3 1.5483 111.57 118.08 122.98 1.5819 +IC C3 OP31 P3 OP32 1.4272 122.98 37.85 102.14 1.5830 +IC OP32 OP31 *P3 OP33 1.5830 102.14 -113.92 107.98 1.4793 +IC OP32 OP31 *P3 OP34 1.5830 102.14 115.66 109.62 1.4740 +IC OP31 P3 OP32 C31 1.5819 102.14 69.85 119.33 1.4301 +IC P3 OP32 C31 C32 1.5830 119.33 176.40 110.18 1.5529 +IC C32 OP32 *C31 H31J 1.5529 110.18 120.82 110.67 1.1139 +IC H31J OP32 *C31 H31K 1.1139 110.67 119.45 110.95 1.1159 +IC HG31 C3 C2 C1 1.1169 107.78 60.13 113.14 1.5594 +IC C1 C3 *C2 OG12 1.5594 113.14 -122.65 107.36 1.4314 +IC C1 C3 *C2 HG22 1.5594 113.14 119.50 108.81 1.1137 +IC C3 C2 OG12 HO12 1.5483 107.36 -59.74 104.73 0.9611 +IC C3 C2 C1 OP11 1.5483 113.14 102.14 111.29 1.4365 +IC OP11 C2 *C1 HG11 1.4365 111.29 -124.72 105.61 1.1191 +IC HG11 C2 *C1 HG12 1.1191 105.61 -115.38 108.40 1.1138 +IC C2 C1 OP11 P1 1.5594 111.29 -157.61 115.85 1.5685 +IC C1 OP11 P1 OP12 1.4365 115.85 -14.21 104.93 1.5653 +IC OP12 OP11 *P1 OP13 1.5653 104.93 115.00 111.23 1.5595 +IC OP12 OP11 *P1 OP14 1.5653 104.93 -120.71 114.44 1.4714 +IC OP11 P1 OP13 HP13 1.5685 111.23 -49.71 108.79 0.9805 +IC OP11 P1 OP12 C11 1.5685 104.93 168.45 117.56 1.4279 +IC P1 OP12 C11 C12 1.5653 117.56 -104.42 112.05 1.5631 +IC C12 OP12 *C11 H11J 1.5631 112.05 -116.94 106.96 1.1115 +IC H11J OP12 *C11 H11K 1.1115 106.96 -117.70 114.83 1.1174 +IC OP12 C11 C12 C13 1.4279 112.05 -169.61 110.60 1.5613 +IC C13 C11 *C12 O12 1.5613 110.60 124.16 109.17 1.4428 +IC O12 C11 *C12 H12J 1.4428 109.17 118.13 106.49 1.1175 +IC C11 C12 O12 CA1 1.5631 109.17 161.88 113.49 1.3343 +IC C12 O12 CA1 CA2 1.4428 113.49 -169.35 108.84 1.5280 +IC CA2 O12 *CA1 OA1 1.5280 108.84 179.80 125.17 1.2183 +IC O12 CA1 CA2 CA3 1.3343 108.84 -146.40 113.25 1.5456 +IC CA3 CA1 *CA2 H2A 1.5456 113.25 -119.97 106.28 1.1109 +IC H2A CA1 *CA2 H2B 1.1109 106.28 -116.75 108.94 1.1073 +IC C11 C12 C13 O13 1.5631 110.60 48.04 111.75 1.4444 +IC O13 C12 *C13 H13J 1.4444 111.75 -117.92 106.48 1.1131 +IC H13J C12 *C13 H13K 1.1131 106.48 -115.07 111.40 1.1131 +IC C12 C13 O13 CB1 1.5613 111.75 88.82 115.87 1.3297 +IC C13 O13 CB1 CB2 1.4444 115.87 -174.80 108.56 1.5287 +IC CB2 O13 *CB1 OB1 1.5287 108.56 -178.49 126.34 1.2145 +IC O13 CB1 CB2 CB3 1.3297 108.56 152.47 112.16 1.5454 +IC CB3 CB1 *CB2 H2D 1.5454 112.16 -121.52 108.74 1.1089 +IC H2D CB1 *CB2 H2E 1.1089 108.74 -117.40 106.94 1.1083 +IC OP32 C31 C32 C33 1.4301 110.18 -69.33 110.65 1.5522 +IC C33 C31 *C32 O32 1.5522 110.65 120.01 111.21 1.4395 +IC O32 C31 *C32 H32J 1.4395 111.21 122.30 108.97 1.1146 +IC C31 C32 O32 CC1 1.5529 111.21 69.31 115.35 1.3120 +IC C32 O32 CC1 CC2 1.4395 115.35 -171.71 108.60 1.5297 +IC CC2 O32 *CC1 OC1 1.5297 108.60 -178.02 126.78 1.2186 +IC O32 CC1 CC2 CC3 1.3120 108.60 -59.72 112.33 1.5489 +IC CC3 CC1 *CC2 H2R 1.5489 112.33 -122.26 107.83 1.1075 +IC H2R CC1 *CC2 H2S 1.1075 107.83 -116.44 106.39 1.1097 +IC C31 C32 C33 O33 1.5529 110.65 179.11 109.99 1.4464 +IC O33 C32 *C33 H33J 1.4464 109.99 121.93 109.29 1.1119 +IC H33J C32 *C33 H33K 1.1119 109.29 116.57 106.09 1.1186 +IC C32 C33 O33 CD1 1.5522 109.99 -159.03 114.19 1.3237 +IC C33 O33 CD1 CD2 1.4464 114.19 164.21 109.32 1.5286 +IC CD2 O33 *CD1 OD1 1.5286 109.32 -178.45 126.02 1.2156 +IC O33 CD1 CD2 CD3 1.3237 109.32 -46.26 112.24 1.5470 +IC CD3 CD1 *CD2 H2X 1.5470 112.24 -120.21 106.48 1.1100 +IC H2X CD1 *CD2 H2Y 1.1100 106.48 -117.13 108.41 1.1069 +IC CA1 CA2 CA3 CA4 1.5280 113.25 70.18 112.81 1.5346 +IC CA4 CA2 *CA3 H3A 1.5346 112.81 -123.14 110.14 1.1142 +IC H3A CA2 *CA3 H3B 1.1142 110.14 -116.66 107.70 1.1125 +IC CA2 CA3 CA4 CA5 1.5456 112.81 172.40 112.79 1.5353 +IC CA5 CA3 *CA4 H4A 1.5353 112.79 -122.05 109.90 1.1116 +IC H4A CA3 *CA4 H4B 1.1116 109.90 -117.14 108.37 1.1150 +IC CA3 CA4 CA5 CA6 1.5346 112.79 167.30 112.42 1.5358 +IC CA6 CA4 *CA5 H5A 1.5358 112.42 -120.63 108.10 1.1132 +IC H5A CA4 *CA5 H5B 1.1132 108.10 -117.30 109.47 1.1120 +IC CA4 CA5 CA6 CA7 1.5353 112.42 177.91 114.45 1.5409 +IC CA7 CA5 *CA6 H6A 1.5409 114.45 -121.60 108.84 1.1121 +IC H6A CA5 *CA6 H6B 1.1121 108.84 -116.16 108.48 1.1134 +IC CA5 CA6 CA7 CA8 1.5358 114.45 53.66 115.58 1.5440 +IC CA8 CA6 *CA7 H7A 1.5440 115.58 -121.63 108.47 1.1138 +IC H7A CA6 *CA7 H7B 1.1138 108.47 -116.24 108.32 1.1141 +IC CA6 CA7 CA8 CA9 1.5409 115.58 55.01 112.73 1.5097 +IC CA9 CA7 *CA8 H8A 1.5097 112.73 -121.48 108.57 1.1114 +IC H8A CA7 *CA8 H8B 1.1114 108.57 -114.55 107.55 1.1126 +IC CA7 CA8 CA9 CA10 1.5440 112.73 109.39 127.97 1.3474 +IC CA10 CA8 *CA9 H9A 1.3474 127.97 -179.15 113.83 1.1025 +IC CA8 CA9 CA10 CA11 1.5097 127.97 0.64 127.89 1.5108 +IC CA11 CA9 *CA10 H10A 1.5108 127.89 179.31 117.75 1.1014 +IC CA9 CA10 CA11 CA12 1.3474 127.89 -112.95 111.22 1.5114 +IC CA12 CA10 *CA11 H11A 1.5114 111.22 -120.46 108.90 1.1119 +IC H11A CA10 *CA11 H11B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA10 CA11 CA12 CA13 1.5108 111.22 134.57 126.37 1.3465 +IC CA13 CA11 *CA12 H12A 1.3465 126.37 -177.01 115.27 1.1018 +IC CA11 CA12 CA13 CA14 1.5114 126.37 3.15 126.32 1.5077 +IC CA14 CA12 *CA13 H13A 1.5077 126.32 178.37 118.79 1.1003 +IC CA12 CA13 CA14 CA15 1.3465 126.32 -92.58 113.47 1.5417 +IC CA15 CA13 *CA14 H14A 1.5417 113.47 -122.01 110.01 1.1123 +IC H14A CA13 *CA14 H14B 1.1123 110.01 -116.77 110.38 1.1120 +IC CA13 CA14 CA15 CA16 1.5077 113.47 -63.55 113.58 1.5369 +IC CA16 CA14 *CA15 H15A 1.5369 113.58 -120.33 108.08 1.1132 +IC H15A CA14 *CA15 H15B 1.1132 108.08 -116.59 109.36 1.1132 +IC CA14 CA15 CA16 CA17 1.5417 113.58 -171.21 113.87 1.5374 +IC CA17 CA15 *CA16 H16A 1.5374 113.87 -121.70 108.87 1.1122 +IC H16A CA15 *CA16 H16B 1.1122 108.87 -117.00 108.72 1.1132 +IC CA15 CA16 CA17 CA18 1.5369 113.87 -61.57 114.41 1.5314 +IC CA18 CA16 *CA17 H17A 1.5314 114.41 -121.26 108.12 1.1148 +IC H17A CA16 *CA17 H17B 1.1148 108.12 -116.30 108.76 1.1136 +IC CA16 CA17 CA18 H18A 1.5374 114.41 63.53 110.93 1.1107 +IC H18A CA17 *CA18 H18B 1.1107 110.93 -119.76 110.34 1.1109 +IC H18A CA17 *CA18 H18C 1.1107 110.93 120.37 110.77 1.1100 +IC CB1 CB2 CB3 CB4 1.5287 112.16 178.44 113.36 1.5384 +IC CB4 CB2 *CB3 H3D 1.5384 113.36 -122.28 109.76 1.1140 +IC H3D CB2 *CB3 H3E 1.1140 109.76 -116.69 109.13 1.1151 +IC CB2 CB3 CB4 CB5 1.5454 113.36 -60.74 115.02 1.5414 +IC CB5 CB3 *CB4 H4D 1.5414 115.02 -121.57 108.33 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 108.33 -116.10 108.96 1.1133 +IC CB3 CB4 CB5 CB6 1.5384 115.02 -51.86 114.89 1.5394 +IC CB6 CB4 *CB5 H5D 1.5394 114.89 -121.74 108.45 1.1137 +IC H5D CB4 *CB5 H5E 1.1137 108.45 -116.35 108.99 1.1129 +IC CB4 CB5 CB6 CB7 1.5414 114.89 -57.34 113.83 1.5380 +IC CB7 CB5 *CB6 H6D 1.5380 113.83 -121.31 108.98 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.98 -116.37 108.87 1.1123 +IC CB5 CB6 CB7 CB8 1.5394 113.83 179.71 113.63 1.5423 +IC CB8 CB6 *CB7 H7D 1.5423 113.63 -122.27 109.89 1.1123 +IC H7D CB6 *CB7 H7E 1.1123 109.89 -116.77 108.48 1.1132 +IC CB6 CB7 CB8 CB9 1.5380 113.63 -63.29 112.23 1.5093 +IC CB9 CB7 *CB8 H8D 1.5093 112.23 -120.64 107.87 1.1133 +IC H8D CB7 *CB8 H8E 1.1133 107.87 -115.67 108.05 1.1129 +IC CB7 CB8 CB9 CB10 1.5423 112.23 148.17 126.47 1.3460 +IC CB10 CB8 *CB9 H9D 1.3460 126.47 -177.74 114.82 1.1018 +IC CB8 CB9 CB10 CB11 1.5093 126.47 2.77 126.58 1.5092 +IC CB11 CB9 *CB10 H10D 1.5092 126.58 177.26 118.57 1.1029 +IC CB9 CB10 CB11 CB12 1.3460 126.58 -116.82 111.69 1.5096 +IC CB12 CB10 *CB11 H11D 1.5096 111.69 -123.10 108.54 1.1115 +IC H11D CB10 *CB11 H11E 1.1115 108.54 -114.79 111.63 1.1116 +IC CB10 CB11 CB12 CB13 1.5092 111.69 -110.56 126.32 1.3473 +IC CB13 CB11 *CB12 H12D 1.3473 126.32 -178.41 114.77 1.1018 +IC CB11 CB12 CB13 CB14 1.5096 126.32 2.04 125.85 1.5088 +IC CB14 CB12 *CB13 H13D 1.5088 125.85 179.17 118.99 1.1012 +IC CB12 CB13 CB14 CB15 1.3473 125.85 -89.20 112.98 1.5413 +IC CB15 CB13 *CB14 H14D 1.5413 112.98 -121.97 110.15 1.1124 +IC H14D CB13 *CB14 H14E 1.1124 110.15 -116.85 110.43 1.1140 +IC CB13 CB14 CB15 CB16 1.5088 112.98 -66.02 113.67 1.5362 +IC CB16 CB14 *CB15 H15D 1.5362 113.67 -120.47 108.54 1.1134 +IC H15D CB14 *CB15 H15E 1.1134 108.54 -116.71 109.67 1.1135 +IC CB14 CB15 CB16 CB17 1.5413 113.67 -176.61 112.48 1.5339 +IC CB17 CB15 *CB16 H16D 1.5339 112.48 -121.15 109.47 1.1130 +IC H16D CB15 *CB16 H16E 1.1130 109.47 -117.68 109.15 1.1130 +IC CB15 CB16 CB17 CB18 1.5362 112.48 -179.94 113.24 1.5308 +IC CB18 CB16 *CB17 H17D 1.5308 113.24 -121.73 108.82 1.1141 +IC H17D CB16 *CB17 H17E 1.1141 108.82 -116.64 108.69 1.1143 +IC CB16 CB17 CB18 H18D 1.5339 113.24 59.88 110.45 1.1114 +IC H18D CB17 *CB18 H18E 1.1114 110.45 -119.87 110.50 1.1113 +IC H18D CB17 *CB18 H18F 1.1114 110.45 120.03 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5297 112.33 172.47 113.86 1.5361 +IC CC4 CC2 *CC3 H3R 1.5361 113.86 -119.64 108.94 1.1154 +IC H3R CC2 *CC3 H3S 1.1154 108.94 -117.39 109.77 1.1130 +IC CC2 CC3 CC4 CC5 1.5489 113.86 -56.98 112.74 1.5347 +IC CC5 CC3 *CC4 H4R 1.5347 112.74 -119.98 107.98 1.1143 +IC H4R CC3 *CC4 H4S 1.1143 107.98 -117.33 110.39 1.1120 +IC CC3 CC4 CC5 CC6 1.5361 112.74 -154.31 113.28 1.5321 +IC CC6 CC4 *CC5 H5R 1.5321 113.28 -123.53 109.65 1.1125 +IC H5R CC4 *CC5 H5S 1.1125 109.65 -117.22 108.68 1.1132 +IC CC4 CC5 CC6 CC7 1.5347 113.28 -174.72 112.18 1.5360 +IC CC7 CC5 *CC6 H6R 1.5360 112.18 -120.78 108.11 1.1141 +IC H6R CC5 *CC6 H6S 1.1141 108.11 -117.38 110.00 1.1122 +IC CC5 CC6 CC7 CC8 1.5321 112.18 -168.49 113.32 1.5408 +IC CC8 CC6 *CC7 H7R 1.5408 113.32 -121.00 108.07 1.1137 +IC H7R CC6 *CC7 H7S 1.1137 108.07 -116.02 109.54 1.1140 +IC CC6 CC7 CC8 CC9 1.5360 113.32 72.57 111.65 1.5102 +IC CC9 CC7 *CC8 H8R 1.5102 111.65 -124.76 108.23 1.1117 +IC H8R CC7 *CC8 H8S 1.1117 108.23 -115.30 107.95 1.1119 +IC CC7 CC8 CC9 CC10 1.5408 111.65 -134.06 127.67 1.3478 +IC CC10 CC8 *CC9 H9R 1.3478 127.67 179.52 113.97 1.1023 +IC CC8 CC9 CC10 CC11 1.5102 127.67 -0.03 127.34 1.5115 +IC CC11 CC9 *CC10 H10R 1.5115 127.34 179.73 118.07 1.1026 +IC CC9 CC10 CC11 CC12 1.3478 127.34 129.05 112.32 1.5099 +IC CC12 CC10 *CC11 H11R 1.5099 112.32 -123.72 111.60 1.1114 +IC H11R CC10 *CC11 H11S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC10 CC11 CC12 CC13 1.5115 112.32 -84.97 126.59 1.3471 +IC CC13 CC11 *CC12 H12R 1.3471 126.59 -179.05 114.79 1.1010 +IC CC11 CC12 CC13 CC14 1.5099 126.59 1.41 126.41 1.5090 +IC CC14 CC12 *CC13 H13R 1.5090 126.41 178.45 118.70 1.0998 +IC CC12 CC13 CC14 CC15 1.3471 126.41 -125.27 113.39 1.5418 +IC CC15 CC13 *CC14 H14R 1.5418 113.39 -121.44 109.86 1.1131 +IC H14R CC13 *CC14 H14S 1.1131 109.86 -117.22 111.11 1.1131 +IC CC13 CC14 CC15 CC16 1.5090 113.39 -68.63 113.68 1.5381 +IC CC16 CC14 *CC15 H15R 1.5381 113.68 123.30 109.83 1.1129 +IC H15R CC14 *CC15 H15S 1.1129 109.83 116.45 107.53 1.1136 +IC CC14 CC15 CC16 CC17 1.5418 113.68 179.76 113.73 1.5374 +IC CC17 CC15 *CC16 H16R 1.5374 113.73 121.83 108.95 1.1128 +IC H16R CC15 *CC16 H16S 1.1128 108.95 117.24 109.15 1.1127 +IC CC15 CC16 CC17 CC18 1.5381 113.73 63.65 114.54 1.5322 +IC CC18 CC16 *CC17 H17R 1.5322 114.54 -122.47 108.69 1.1141 +IC H17R CC16 *CC17 H17S 1.1141 108.69 -116.13 108.22 1.1148 +IC CC16 CC17 CC18 H18R 1.5374 114.54 56.61 110.47 1.1112 +IC H18R CC17 *CC18 H18S 1.1112 110.47 -120.21 110.86 1.1107 +IC H18R CC17 *CC18 H18T 1.1112 110.47 119.94 110.49 1.1113 +IC CD1 CD2 CD3 CD4 1.5286 112.24 -168.50 113.06 1.5318 +IC CD4 CD2 *CD3 H3X 1.5318 113.06 -122.94 109.98 1.1137 +IC H3X CD2 *CD3 H3Y 1.1137 109.98 -117.36 109.14 1.1136 +IC CD2 CD3 CD4 CD5 1.5470 113.06 175.61 111.87 1.5362 +IC CD5 CD3 *CD4 H4X 1.5362 111.87 -120.66 108.60 1.1128 +IC H4X CD3 *CD4 H4Y 1.1128 108.60 -117.59 109.56 1.1124 +IC CD3 CD4 CD5 CD6 1.5318 111.87 177.84 113.59 1.5356 +IC CD6 CD4 *CD5 H5X 1.5356 113.59 -121.15 108.45 1.1137 +IC H5X CD4 *CD5 H5Y 1.1137 108.45 -116.84 109.16 1.1138 +IC CD4 CD5 CD6 CD7 1.5362 113.59 67.64 113.35 1.5355 +IC CD7 CD5 *CD6 H6X 1.5355 113.35 -122.12 109.12 1.1128 +IC H6X CD5 *CD6 H6Y 1.1128 109.12 -117.25 108.81 1.1134 +IC CD5 CD6 CD7 CD8 1.5356 113.35 -178.50 112.28 1.5389 +IC CD8 CD6 *CD7 H7X 1.5389 112.28 -122.16 108.88 1.1140 +IC H7X CD6 *CD7 H7Y 1.1140 108.88 -116.95 109.16 1.1134 +IC CD6 CD7 CD8 CD9 1.5355 112.28 179.01 111.42 1.5083 +IC CD9 CD7 *CD8 H8X 1.5083 111.42 -122.39 108.26 1.1135 +IC H8X CD7 *CD8 H8Y 1.1135 108.26 -115.32 109.05 1.1118 +IC CD7 CD8 CD9 CD10 1.5389 111.42 -84.39 125.66 1.3464 +IC CD10 CD8 *CD9 H9X 1.3464 125.66 178.86 115.42 1.1011 +IC CD8 CD9 CD10 CD11 1.5083 125.66 0.74 126.41 1.5100 +IC CD11 CD9 *CD10 H10X 1.5100 126.41 178.33 118.71 1.1020 +IC CD9 CD10 CD11 CD12 1.3464 126.41 -119.11 111.66 1.5104 +IC CD12 CD10 *CD11 H11X 1.5104 111.66 -123.67 108.55 1.1120 +IC H11X CD10 *CD11 H11Y 1.1120 108.55 -114.62 111.55 1.1120 +IC CD10 CD11 CD12 CD13 1.5100 111.66 -113.81 126.72 1.3477 +IC CD13 CD11 *CD12 H12X 1.3477 126.72 -178.56 114.59 1.1018 +IC CD11 CD12 CD13 CD14 1.5104 126.72 1.66 126.19 1.5088 +IC CD14 CD12 *CD13 H13X 1.5088 126.19 179.37 118.90 1.1014 +IC CD12 CD13 CD14 CD15 1.3477 126.19 -100.76 112.41 1.5405 +IC CD15 CD13 *CD14 H14X 1.5405 112.41 -121.85 109.83 1.1118 +IC H14X CD13 *CD14 H14Y 1.1118 109.83 -117.23 111.23 1.1116 +IC CD13 CD14 CD15 CD16 1.5088 112.41 170.52 113.29 1.5388 +IC CD16 CD14 *CD15 H15X 1.5388 113.29 -119.71 109.05 1.1153 +IC H15X CD14 *CD15 H15Y 1.1153 109.05 -117.72 109.78 1.1127 +IC CD14 CD15 CD16 CD17 1.5405 113.29 62.69 114.08 1.5347 +IC CD17 CD15 *CD16 H16X 1.5347 114.08 -121.99 108.89 1.1132 +IC H16X CD15 *CD16 H16Y 1.1132 108.89 -116.64 108.76 1.1136 +IC CD15 CD16 CD17 CD18 1.5388 114.08 179.88 112.98 1.5311 +IC CD18 CD16 *CD17 H17X 1.5311 112.98 -121.76 108.79 1.1137 +IC H17X CD16 *CD17 H17Y 1.1137 108.79 -117.11 109.38 1.1133 +IC CD16 CD17 CD18 H18X 1.5347 112.98 60.79 110.28 1.1118 +IC H18X CD17 *CD18 H18Y 1.1118 110.28 -119.90 110.57 1.1110 +IC H18X CD17 *CD18 H18Z 1.1118 110.28 119.81 110.63 1.1110 + +RESI TLCL2 -2.00 ! Tetralinoleoyl Cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 4 linoleoly chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! || || || || +ATOM H32J HAL1 0.09 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM H2R HAL2 0.09 ! | | | | +ATOM H2S HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +GROUP ! | | | | +ATOM C33 CTL2 0.08 ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM H33J HAL2 0.09 ! | | | | +ATOM H33K HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM O33 OSL -0.49 ! | | | | +ATOM CD1 CL 0.90 ! H18F H18C H18Z H18T +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 !! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +! IC TABLE +! +IC OP31 C2 *C3 HG31 1.4399 111.73 121.27 107.98 1.1140 +IC HG31 C2 *C3 HG32 1.1140 107.98 116.42 107.18 1.1169 +IC C2 C3 OP31 P3 1.5535 111.73 -167.54 118.79 1.5904 +IC C3 OP31 P3 OP32 1.4399 118.79 79.71 101.55 1.5890 +IC OP32 OP31 *P3 OP33 1.5890 101.55 -115.28 110.31 1.4782 +IC OP32 OP31 *P3 OP34 1.5890 101.55 113.65 109.35 1.4797 +IC OP31 P3 OP32 C31 1.5904 101.55 67.83 117.77 1.4329 +IC P3 OP32 C31 C32 1.5890 117.77 -170.90 110.66 1.5522 +IC C32 OP32 *C31 H31J 1.5522 110.66 121.35 111.65 1.1158 +IC H31J OP32 *C31 H31K 1.1158 111.65 119.36 109.77 1.1144 +IC HG31 C3 C2 C1 1.1140 107.98 -59.84 112.53 1.5592 +IC C1 C3 *C2 OG12 1.5592 112.53 -122.28 106.17 1.4219 +IC C1 C3 *C2 HG22 1.5592 112.53 120.07 108.81 1.1138 +IC C3 C2 OG12 HO12 1.5535 106.17 -43.83 99.95 0.9654 +IC C3 C2 C1 OP11 1.5535 112.53 172.59 114.00 1.4374 +IC OP11 C2 *C1 HG11 1.4374 114.00 -124.71 107.54 1.1153 +IC HG11 C2 *C1 HG12 1.1153 107.54 -114.53 107.04 1.1121 +IC C2 C1 OP11 P1 1.5592 114.00 -97.83 122.51 1.5864 +IC C1 OP11 P1 OP12 1.4374 122.51 -52.87 102.45 1.5913 +IC OP12 OP11 *P1 OP13 1.5913 102.45 114.70 110.17 1.4774 +IC OP12 OP11 *P1 OP14 1.5913 102.45 -115.08 109.36 1.4815 +IC OP11 P1 OP12 C11 1.5864 102.45 -92.52 122.70 1.4285 +IC P1 OP12 C11 C12 1.5913 122.70 85.68 111.92 1.5508 +IC C12 OP12 *C11 H11J 1.5508 111.92 -123.87 112.24 1.1149 +IC H11J OP12 *C11 H11K 1.1149 112.24 -117.66 107.38 1.1110 +IC OP12 C11 C12 C13 1.4285 111.92 161.41 112.21 1.5554 +IC C13 C11 *C12 O12 1.5554 112.21 119.92 107.58 1.4348 +IC O12 C11 *C12 H12J 1.4348 107.58 121.23 105.93 1.1177 +IC C11 C12 O12 CA1 1.5508 107.58 139.57 115.43 1.3169 +IC C12 O12 CA1 CA2 1.4348 115.43 -169.02 109.20 1.5307 +IC CA2 O12 *CA1 OA1 1.5307 109.20 -177.29 125.89 1.2210 +IC O12 CA1 CA2 CA3 1.3169 109.20 -125.27 111.98 1.5453 +IC CA3 CA1 *CA2 H2A 1.5453 111.98 -121.72 106.70 1.1104 +IC H2A CA1 *CA2 H2B 1.1104 106.70 -115.79 108.58 1.1093 +IC C11 C12 C13 O13 1.5508 112.21 -165.73 111.20 1.4484 +IC O13 C12 *C13 H13J 1.4484 111.20 -119.38 107.07 1.1127 +IC H13J C12 *C13 H13K 1.1127 107.07 -115.20 109.28 1.1141 +IC C12 C13 O13 CB1 1.5554 111.20 86.74 113.94 1.3304 +IC C13 O13 CB1 CB2 1.4484 113.94 -157.19 109.85 1.5285 +IC CB2 O13 *CB1 OB1 1.5285 109.85 179.45 125.30 1.2183 +IC O13 CB1 CB2 CB3 1.3304 109.85 170.02 112.02 1.5483 +IC CB3 CB1 *CB2 H2D 1.5483 112.02 -119.03 106.46 1.1119 +IC H2D CB1 *CB2 H2E 1.1119 106.46 -117.11 109.11 1.1053 +IC OP32 C31 C32 C33 1.4329 110.66 -55.34 111.30 1.5520 +IC C33 C31 *C32 O32 1.5520 111.30 121.41 110.58 1.4400 +IC O32 C31 *C32 H32J 1.4400 110.58 121.80 108.53 1.1157 +IC C31 C32 O32 CC1 1.5522 110.58 76.00 113.72 1.3241 +IC C32 O32 CC1 CC2 1.4400 113.72 -175.40 107.92 1.5290 +IC CC2 O32 *CC1 OC1 1.5290 107.92 -174.97 125.21 1.2214 +IC O32 CC1 CC2 CC3 1.3241 107.92 -171.64 114.45 1.5483 +IC CC3 CC1 *CC2 H2R 1.5483 114.45 -120.08 106.50 1.1125 +IC H2R CC1 *CC2 H2S 1.1125 106.50 -115.84 108.14 1.1062 +IC C31 C32 C33 O33 1.5522 111.30 178.27 110.32 1.4463 +IC O33 C32 *C33 H33J 1.4463 110.32 122.56 108.16 1.1137 +IC H33J C32 *C33 H33K 1.1137 108.16 116.60 107.22 1.1149 +IC C32 C33 O33 CD1 1.5520 110.32 176.92 114.52 1.3194 +IC C33 O33 CD1 CD2 1.4463 114.52 169.48 108.39 1.5307 +IC CD2 O33 *CD1 OD1 1.5307 108.39 179.86 126.25 1.2174 +IC O33 CD1 CD2 CD3 1.3194 108.39 166.29 113.39 1.5479 +IC CD3 CD1 *CD2 H2X 1.5479 113.39 -122.94 107.91 1.1081 +IC H2X CD1 *CD2 H2Y 1.1081 107.91 -116.24 106.59 1.1103 +IC CA1 CA2 CA3 CA4 1.5307 111.98 174.09 112.77 1.5340 +IC CA4 CA2 *CA3 H3A 1.5340 112.77 -121.48 109.27 1.1128 +IC H3A CA2 *CA3 H3B 1.1128 109.27 -117.62 108.80 1.1132 +IC CA2 CA3 CA4 CA5 1.5453 112.77 176.67 112.97 1.5369 +IC CA5 CA3 *CA4 H4A 1.5369 112.97 -120.43 108.08 1.1146 +IC H4A CA3 *CA4 H4B 1.1146 108.08 -116.67 109.58 1.1123 +IC CA3 CA4 CA5 CA6 1.5340 112.97 69.98 113.98 1.5366 +IC CA6 CA4 *CA5 H5A 1.5366 113.98 -122.10 108.41 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 108.41 -116.88 108.64 1.1132 +IC CA4 CA5 CA6 CA7 1.5369 113.98 177.62 113.05 1.5384 +IC CA7 CA5 *CA6 H6A 1.5384 113.05 -120.54 108.00 1.1138 +IC H6A CA5 *CA6 H6B 1.1138 108.00 -117.16 109.92 1.1119 +IC CA5 CA6 CA7 CA8 1.5366 113.05 72.32 113.20 1.5409 +IC CA8 CA6 *CA7 H7A 1.5409 113.20 -122.31 108.58 1.1140 +IC H7A CA6 *CA7 H7B 1.1140 108.58 -116.70 108.43 1.1139 +IC CA6 CA7 CA8 CA9 1.5384 113.20 -177.88 111.67 1.5104 +IC CA9 CA7 *CA8 H8A 1.5104 111.67 -121.51 108.57 1.1127 +IC H8A CA7 *CA8 H8B 1.1127 108.57 -114.68 108.68 1.1109 +IC CA7 CA8 CA9 CA10 1.5409 111.67 106.92 126.93 1.3485 +IC CA10 CA8 *CA9 H9A 1.3485 126.93 179.93 114.52 1.1012 +IC CA8 CA9 CA10 CA11 1.5104 126.93 -0.98 126.94 1.5114 +IC CA11 CA9 *CA10 H10A 1.5114 126.94 -179.25 118.31 1.1017 +IC CA9 CA10 CA11 CA12 1.3485 126.94 -125.33 111.90 1.5094 +IC CA12 CA10 *CA11 H11A 1.5094 111.90 -120.91 109.22 1.1122 +IC H11A CA10 *CA11 H11B 1.1122 109.22 -115.26 111.36 1.1089 +IC CA10 CA11 CA12 CA13 1.5114 111.90 103.75 127.05 1.3481 +IC CA13 CA11 *CA12 H12A 1.3481 127.05 178.55 114.54 1.1015 +IC CA11 CA12 CA13 CA14 1.5094 127.05 -1.51 127.29 1.5104 +IC CA14 CA12 *CA13 H13A 1.5104 127.29 -178.83 118.45 1.1012 +IC CA12 CA13 CA14 CA15 1.3481 127.29 123.19 111.92 1.5400 +IC CA15 CA13 *CA14 H14A 1.5400 111.92 -122.30 112.60 1.1129 +IC H14A CA13 *CA14 H14B 1.1129 112.60 -117.91 109.33 1.1129 +IC CA13 CA14 CA15 CA16 1.5104 111.92 172.46 112.42 1.5358 +IC CA16 CA14 *CA15 H15A 1.5358 112.42 -120.26 109.74 1.1138 +IC H15A CA14 *CA15 H15B 1.1138 109.74 -118.26 109.67 1.1136 +IC CA14 CA15 CA16 CA17 1.5400 112.42 -176.77 112.71 1.5339 +IC CA17 CA15 *CA16 H16A 1.5339 112.71 -121.51 109.43 1.1130 +IC H16A CA15 *CA16 H16B 1.1130 109.43 -117.43 109.11 1.1131 +IC CA15 CA16 CA17 CA18 1.5358 112.71 177.47 113.22 1.5311 +IC CA18 CA16 *CA17 H17A 1.5311 113.22 -121.64 108.92 1.1137 +IC H17A CA16 *CA17 H17B 1.1137 108.92 -116.79 108.72 1.1143 +IC CA16 CA17 CA18 H18A 1.5339 113.22 -60.64 110.64 1.1108 +IC H18A CA17 *CA18 H18B 1.1108 110.64 -120.38 110.71 1.1111 +IC H18A CA17 *CA18 H18C 1.1108 110.64 119.78 110.63 1.1119 +IC CB1 CB2 CB3 CB4 1.5285 112.02 -156.49 113.16 1.5352 +IC CB4 CB2 *CB3 H3D 1.5352 113.16 -125.26 110.81 1.1108 +IC H3D CB2 *CB3 H3E 1.1108 110.81 -117.62 108.58 1.1185 +IC CB2 CB3 CB4 CB5 1.5483 113.16 -72.87 114.64 1.5362 +IC CB5 CB3 *CB4 H4D 1.5362 114.64 -121.50 107.87 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 107.87 -115.68 108.33 1.1133 +IC CB3 CB4 CB5 CB6 1.5352 114.64 173.14 113.35 1.5409 +IC CB6 CB4 *CB5 H5D 1.5409 113.35 -120.91 109.12 1.1130 +IC H5D CB4 *CB5 H5E 1.1130 109.12 -117.35 108.69 1.1125 +IC CB4 CB5 CB6 CB7 1.5362 113.35 52.82 114.03 1.5378 +IC CB7 CB5 *CB6 H6D 1.5378 114.03 -120.64 108.65 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.65 -116.83 109.17 1.1121 +IC CB5 CB6 CB7 CB8 1.5409 114.03 179.98 112.81 1.5400 +IC CB8 CB6 *CB7 H7D 1.5400 112.81 -122.98 109.09 1.1121 +IC H7D CB6 *CB7 H7E 1.1121 109.09 -117.53 108.71 1.1155 +IC CB6 CB7 CB8 CB9 1.5378 112.81 177.49 110.85 1.5102 +IC CB9 CB7 *CB8 H8D 1.5102 110.85 -122.35 107.23 1.1140 +IC H8D CB7 *CB8 H8E 1.1140 107.23 -115.61 109.26 1.1115 +IC CB7 CB8 CB9 CB10 1.5400 110.85 -111.54 126.68 1.3485 +IC CB10 CB8 *CB9 H9D 1.3485 126.68 176.66 114.61 1.1007 +IC CB8 CB9 CB10 CB11 1.5102 126.68 -2.77 127.04 1.5103 +IC CB11 CB9 *CB10 H10D 1.5103 127.04 -178.65 118.60 1.1012 +IC CB9 CB10 CB11 CB12 1.3485 127.04 96.60 112.31 1.5135 +IC CB12 CB10 *CB11 H11D 1.5135 112.31 -125.47 110.37 1.1105 +IC H11D CB10 *CB11 H11E 1.1105 110.37 -114.37 108.83 1.1122 +IC CB10 CB11 CB12 CB13 1.5103 112.31 -123.24 127.49 1.3487 +IC CB13 CB11 *CB12 H12D 1.3487 127.49 -179.18 114.92 1.1025 +IC CB11 CB12 CB13 CB14 1.5135 127.49 0.10 127.26 1.5079 +IC CB14 CB12 *CB13 H13D 1.5079 127.26 -179.25 118.69 1.1053 +IC CB12 CB13 CB14 CB15 1.3487 127.26 123.97 111.98 1.5384 +IC CB15 CB13 *CB14 H14D 1.5384 111.98 -120.79 111.90 1.1093 +IC H14D CB13 *CB14 H14E 1.1093 111.90 -118.90 109.68 1.1138 +IC CB13 CB14 CB15 CB16 1.5079 111.98 -173.48 111.85 1.5348 +IC CB16 CB14 *CB15 H15D 1.5348 111.85 -121.68 109.78 1.1147 +IC H15D CB14 *CB15 H15E 1.1147 109.78 -117.79 109.28 1.1119 +IC CB14 CB15 CB16 CB17 1.5384 111.85 179.99 113.35 1.5313 +IC CB17 CB15 *CB16 H16D 1.5313 113.35 -121.42 108.85 1.1101 +IC H16D CB15 *CB16 H16E 1.1101 108.85 -117.19 108.74 1.1110 +IC CB15 CB16 CB17 CB18 1.5348 113.35 -178.76 113.12 1.5314 +IC CB18 CB16 *CB17 H17D 1.5314 113.12 -121.82 108.25 1.1149 +IC H17D CB16 *CB17 H17E 1.1149 108.25 -115.96 109.19 1.1126 +IC CB16 CB17 CB18 H18D 1.5313 113.12 -178.27 110.36 1.1112 +IC H18D CB17 *CB18 H18E 1.1112 110.36 -120.53 110.61 1.1103 +IC H18D CB17 *CB18 H18F 1.1112 110.36 119.56 110.21 1.1112 +IC CC1 CC2 CC3 CC4 1.5290 114.45 61.17 115.54 1.5407 +IC CC4 CC2 *CC3 H3R 1.5407 115.54 -123.39 108.81 1.1159 +IC H3R CC2 *CC3 H3S 1.1159 108.81 -115.09 107.30 1.1128 +IC CC2 CC3 CC4 CC5 1.5483 115.54 48.75 115.70 1.5381 +IC CC5 CC3 *CC4 H4R 1.5381 115.70 -121.95 108.35 1.1141 +IC H4R CC3 *CC4 H4S 1.1141 108.35 -115.67 107.88 1.1118 +IC CC3 CC4 CC5 CC6 1.5407 115.70 59.37 113.26 1.5339 +IC CC6 CC4 *CC5 H5R 1.5339 113.26 -122.42 108.68 1.1122 +IC H5R CC4 *CC5 H5S 1.1122 108.68 -116.61 108.64 1.1128 +IC CC4 CC5 CC6 CC7 1.5381 113.26 175.46 114.41 1.5382 +IC CC7 CC5 *CC6 H6R 1.5382 114.41 -121.44 108.39 1.1118 +IC H6R CC5 *CC6 H6S 1.1118 108.39 -116.44 108.77 1.1127 +IC CC5 CC6 CC7 CC8 1.5339 114.41 50.21 113.91 1.5402 +IC CC8 CC6 *CC7 H7R 1.5402 113.91 -122.10 108.87 1.1136 +IC H7R CC6 *CC7 H7S 1.1136 108.87 -116.44 107.40 1.1147 +IC CC6 CC7 CC8 CC9 1.5382 113.91 171.45 111.26 1.5090 +IC CC9 CC7 *CC8 H8R 1.5090 111.26 -123.76 107.81 1.1114 +IC H8R CC7 *CC8 H8S 1.1114 107.81 -115.28 108.84 1.1122 +IC CC7 CC8 CC9 CC10 1.5402 111.26 -128.36 127.23 1.3472 +IC CC10 CC8 *CC9 H9R 1.3472 127.23 178.70 114.30 1.1010 +IC CC8 CC9 CC10 CC11 1.5090 127.23 -1.15 127.54 1.5084 +IC CC11 CC9 *CC10 H10R 1.5084 127.54 -179.59 118.30 1.1015 +IC CC9 CC10 CC11 CC12 1.3472 127.54 121.83 111.08 1.5090 +IC CC12 CC10 *CC11 H11R 1.5090 111.08 -121.38 111.45 1.1092 +IC H11R CC10 *CC11 H11S 1.1092 111.45 -115.12 108.94 1.1091 +IC CC10 CC11 CC12 CC13 1.5084 111.08 114.57 127.61 1.3469 +IC CC13 CC11 *CC12 H12R 1.3469 127.61 179.18 114.07 1.1019 +IC CC11 CC12 CC13 CC14 1.5090 127.61 -1.12 127.24 1.5089 +IC CC14 CC12 *CC13 H13R 1.5089 127.24 -179.24 118.36 1.1008 +IC CC12 CC13 CC14 CC15 1.3469 127.24 -127.92 112.49 1.5415 +IC CC15 CC13 *CC14 H14R 1.5415 112.49 -120.38 109.34 1.1135 +IC H14R CC13 *CC14 H14S 1.1135 109.34 -118.08 112.29 1.1108 +IC CC13 CC14 CC15 CC16 1.5089 112.49 64.28 113.82 1.5372 +IC CC16 CC14 *CC15 H15R 1.5372 113.82 -123.02 109.95 1.1128 +IC H15R CC14 *CC15 H15S 1.1128 109.95 -116.79 108.08 1.1141 +IC CC14 CC15 CC16 CC17 1.5415 113.82 175.12 112.35 1.5342 +IC CC17 CC15 *CC16 H16R 1.5342 112.35 121.44 109.60 1.1127 +IC H16R CC15 *CC16 H16S 1.1127 109.60 117.48 109.22 1.1130 +IC CC15 CC16 CC17 CC18 1.5372 112.35 177.84 113.41 1.5303 +IC CC18 CC16 *CC17 H17R 1.5303 113.41 -121.68 108.79 1.1140 +IC H17R CC16 *CC17 H17S 1.1140 108.79 -116.65 108.60 1.1141 +IC CC16 CC17 CC18 H18R 1.5342 113.41 177.41 110.78 1.1108 +IC H18R CC17 *CC18 H18S 1.1108 110.78 120.14 110.47 1.1110 +IC H18R CC17 *CC18 H18T 1.1108 110.78 -120.28 110.55 1.1114 +IC CD1 CD2 CD3 CD4 1.5307 113.39 169.15 112.93 1.5372 +IC CD4 CD2 *CD3 H3X 1.5372 112.93 -120.02 109.25 1.1156 +IC H3X CD2 *CD3 H3Y 1.1156 109.25 -117.49 109.59 1.1130 +IC CD2 CD3 CD4 CD5 1.5479 112.93 59.54 113.85 1.5360 +IC CD5 CD3 *CD4 H4X 1.5360 113.85 -121.33 108.32 1.1134 +IC H4X CD3 *CD4 H4Y 1.1134 108.32 -116.71 109.15 1.1132 +IC CD3 CD4 CD5 CD6 1.5372 113.85 -177.43 112.79 1.5357 +IC CD6 CD4 *CD5 H5X 1.5357 112.79 -122.43 109.70 1.1122 +IC H5X CD4 *CD5 H5Y 1.1122 109.70 -117.86 109.15 1.1139 +IC CD4 CD5 CD6 CD7 1.5360 112.79 173.65 112.21 1.5365 +IC CD7 CD5 *CD6 H6X 1.5365 112.21 -119.39 108.19 1.1136 +IC H6X CD5 *CD6 H6Y 1.1136 108.19 -117.35 110.05 1.1111 +IC CD5 CD6 CD7 CD8 1.5357 112.21 -164.07 113.53 1.5412 +IC CD8 CD6 *CD7 H7X 1.5412 113.53 -125.12 110.25 1.1118 +IC H7X CD6 *CD7 H7Y 1.1118 110.25 -116.30 107.52 1.1152 +IC CD6 CD7 CD8 CD9 1.5365 113.53 -72.33 113.26 1.5081 +IC CD9 CD7 *CD8 H8X 1.5081 113.26 -123.64 107.20 1.1122 +IC H8X CD7 *CD8 H8Y 1.1122 107.20 -114.54 108.43 1.1124 +IC CD7 CD8 CD9 CD10 1.5412 113.26 -141.33 126.38 1.3479 +IC CD10 CD8 *CD9 H9X 1.3479 126.38 -179.10 114.78 1.1010 +IC CD8 CD9 CD10 CD11 1.5081 126.38 0.12 126.84 1.5114 +IC CD11 CD9 *CD10 H10X 1.5114 126.84 -179.87 118.43 1.1016 +IC CD9 CD10 CD11 CD12 1.3479 126.84 -106.33 111.23 1.5105 +IC CD12 CD10 *CD11 H11X 1.5105 111.23 -120.37 109.03 1.1122 +IC H11X CD10 *CD11 H11Y 1.1122 109.03 -114.91 111.58 1.1099 +IC CD10 CD11 CD12 CD13 1.5114 111.23 109.38 127.41 1.3486 +IC CD13 CD11 *CD12 H12X 1.3486 127.41 179.19 114.40 1.1015 +IC CD11 CD12 CD13 CD14 1.5105 127.41 -1.41 127.65 1.5109 +IC CD14 CD12 *CD13 H13X 1.5109 127.65 -178.15 118.24 1.1012 +IC CD12 CD13 CD14 CD15 1.3486 127.65 -115.93 111.19 1.5399 +IC CD15 CD13 *CD14 H14X 1.5399 111.19 -120.10 109.72 1.1126 +IC H14X CD13 *CD14 H14Y 1.1126 109.72 -118.73 112.54 1.1122 +IC CD13 CD14 CD15 CD16 1.5109 111.19 -174.42 112.98 1.5354 +IC CD16 CD14 *CD15 H15X 1.5354 112.98 -121.07 109.22 1.1143 +IC H15X CD14 *CD15 H15Y 1.1143 109.22 -117.98 109.91 1.1138 +IC CD14 CD15 CD16 CD17 1.5399 112.98 179.46 112.15 1.5344 +IC CD17 CD15 *CD16 H16X 1.5344 112.15 -121.15 109.44 1.1128 +IC H16X CD15 *CD16 H16Y 1.1128 109.44 -117.66 109.26 1.1126 +IC CD15 CD16 CD17 CD18 1.5354 112.15 179.70 113.67 1.5310 +IC CD18 CD16 *CD17 H17X 1.5310 113.67 -121.71 108.44 1.1139 +IC H17X CD16 *CD17 H17Y 1.1139 108.44 -116.35 108.83 1.1138 +IC CD16 CD17 CD18 H18X 1.5344 113.67 -178.87 110.70 1.1108 +IC H18X CD17 *CD18 H18Y 1.1108 110.70 -120.14 110.59 1.1104 +IC H18X CD17 *CD18 H18Z 1.1108 110.70 119.96 110.62 1.1117 + +RESI PMCL1 -1.00 ! (PMPG + DPPG) Cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 3 C16:0 + 1 C17:cyc +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9--H9E H9A--CA9 H17A H9X--CD9--H9Y H9R--CC9--H9S +ATOM H13J HAL2 0.09 ! | |\ / | | +ATOM H13K HAL2 0.09 ! | | \ / | | +ATOM O13 OSL -0.49 ! | | CA17 | | +ATOM CB1 CL 0.90 ! | | / \ | | +ATOM OB1 OBL -0.63 ! | |/ \ | | +ATOM CB2 CTL2 -0.22 ! H10D--CB10--H10E H10A--CA10 H17B H10X--CD10--H10Y H10R--CC10--H10S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +GROUP ! | | | | +ATOM C32 CTL1 0.17 ! H12D--CB12--H12E H12A--CA12--H12B H12X--CD12--H12Y H12R--CC12--H12S +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC2 CTL2 -0.22 ! | | | | +ATOM H2R HAL2 0.09 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H16F H16C H16Z H16T +ATOM H33K HAL2 0.09 ! +ATOM O33 OSL -0.49 ! +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CG3RC1 -0.09 ! +ATOM H9A HGA1 0.09 ! +GROUP ! +ATOM CA17 CG3C31 -0.18 ! +ATOM H17A HGA2 0.09 ! +ATOM H17B HGA2 0.09 ! +GROUP ! +ATOM CA10 CG3RC1 -0.09 ! +ATOM H10A HGA1 0.09 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL3 -0.27 ! +ATOM H16A HAL3 0.09 ! +ATOM H16B HAL3 0.09 ! +ATOM H16C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CTL2 -0.18 ! +ATOM H9D HAL2 0.09 ! +ATOM H9E HAL2 0.09 ! +GROUP ! +ATOM CB10 CTL2 -0.18 ! +ATOM H10D HAL2 0.09 ! +ATOM H10E HAL2 0.09 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL3 -0.27 ! +ATOM H16D HAL3 0.09 ! +ATOM H16E HAL3 0.09 ! +ATOM H16F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CTL2 -0.18 ! +ATOM H9R HAL2 0.09 ! +ATOM H9S HAL2 0.09 ! +GROUP ! +ATOM CC10 CTL2 -0.18 ! +ATOM H10R HAL2 0.09 ! +ATOM H10S HAL2 0.09 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL3 -0.27 ! +ATOM H16R HAL3 0.09 ! +ATOM H16S HAL3 0.09 ! +ATOM H16T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CTL2 -0.18 ! +ATOM H9X HAL2 0.09 ! +ATOM H9Y HAL2 0.09 ! +GROUP ! +ATOM CD10 CTL2 -0.18 ! +ATOM H10X HAL2 0.09 ! +ATOM H10Y HAL2 0.09 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 CA9 CA17 +BOND CA17 H17A CA17 H17B +BOND CA10 CA17 CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 H16C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 H9E CB9 CB10 +BOND CB10 H10D CB10 H10E CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 H16F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 H9S CC9 CC10 +BOND CC10 H10R CC10 H10S CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 H16T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 H9Y CD9 CD10 +BOND CD10 H10X CD10 H10Y CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 H16Z +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4314 112.03 -126.36 110.28 1.1143 +IC HG31 C2 *C3 HG32 1.1143 110.28 -116.00 107.83 1.1134 +IC C2 C3 OP31 P3 1.5518 112.03 -85.16 123.42 1.5781 +IC C3 OP31 P3 OP32 1.4314 123.42 95.16 99.81 1.5949 +IC OP32 OP31 *P3 OP33 1.5949 99.81 114.97 109.58 1.4776 +IC OP32 OP31 *P3 OP34 1.5949 99.81 -113.53 108.98 1.4763 +IC OP31 P3 OP32 C31 1.5781 99.81 111.50 119.16 1.4360 +IC P3 OP32 C31 C32 1.5949 119.16 79.93 112.86 1.5601 +IC C32 OP32 *C31 H31J 1.5601 112.86 -123.37 111.88 1.1159 +IC H31J OP32 *C31 H31K 1.1159 111.88 -117.01 109.05 1.1115 +IC HG31 C3 C2 C1 1.1143 110.28 -38.98 114.38 1.5595 +IC C1 C3 *C2 OG12 1.5595 114.38 123.12 110.08 1.4305 +IC C1 C3 *C2 HG22 1.5595 114.38 -120.07 106.39 1.1139 +IC C3 C2 OG12 HO12 1.5518 110.08 179.61 104.21 0.9626 +IC C3 C2 C1 OP11 1.5518 114.38 -166.76 110.50 1.4418 +IC OP11 C2 *C1 HG11 1.4418 110.50 -118.63 107.02 1.1137 +IC HG11 C2 *C1 HG12 1.1137 107.02 -113.23 110.64 1.1147 +IC C2 C1 OP11 P1 1.5595 110.50 100.97 114.56 1.5701 +IC C1 OP11 P1 OP12 1.4418 114.56 -170.63 108.21 1.5719 +IC OP12 OP11 *P1 OP13 1.5719 108.21 114.04 109.87 1.5524 +IC OP12 OP11 *P1 OP14 1.5719 108.21 -124.34 113.31 1.4680 +IC OP11 P1 OP13 HP13 1.5701 109.87 78.38 110.14 0.9769 +IC OP11 P1 OP12 C11 1.5701 108.21 -174.49 113.53 1.4402 +IC P1 OP12 C11 C12 1.5719 113.53 95.22 112.08 1.5659 +IC C12 OP12 *C11 H11J 1.5659 112.08 -123.36 114.85 1.1216 +IC H11J OP12 *C11 H11K 1.1216 114.85 -116.29 108.17 1.1100 +IC OP12 C11 C12 C13 1.4402 112.08 -171.97 112.34 1.5598 +IC C13 C11 *C12 O12 1.5598 112.34 -129.73 113.48 1.4454 +IC O12 C11 *C12 H12J 1.4454 113.48 -116.13 105.54 1.1149 +IC C11 C12 O12 CA1 1.5659 113.48 64.62 118.08 1.3164 +IC C12 O12 CA1 CA2 1.4454 118.08 -179.87 109.04 1.5299 +IC CA2 O12 *CA1 OA1 1.5299 109.04 179.54 126.48 1.2178 +IC O12 CA1 CA2 CA3 1.3164 109.04 -99.68 112.46 1.5472 +IC CA3 CA1 *CA2 H2A 1.5472 112.46 -121.59 107.58 1.1084 +IC H2A CA1 *CA2 H2B 1.1084 107.58 -116.95 108.20 1.1100 +IC C11 C12 C13 O13 1.5659 112.34 171.00 110.17 1.4442 +IC O13 C12 *C13 H13J 1.4442 110.17 -120.21 106.23 1.1183 +IC H13J C12 *C13 H13K 1.1183 106.23 -116.84 110.76 1.1114 +IC C12 C13 O13 CB1 1.5598 110.17 -166.81 113.49 1.3279 +IC C13 O13 CB1 CB2 1.4442 113.49 179.07 108.91 1.5266 +IC CB2 O13 *CB1 OB1 1.5266 108.91 179.26 125.43 1.2164 +IC O13 CB1 CB2 CB3 1.3279 108.91 -168.63 112.85 1.5470 +IC CB3 CB1 *CB2 H2D 1.5470 112.85 -120.96 107.08 1.1078 +IC H2D CB1 *CB2 H2E 1.1078 107.08 -116.60 108.17 1.1083 +IC OP32 C31 C32 C33 1.4360 112.86 172.67 112.47 1.5581 +IC C33 C31 *C32 O32 1.5581 112.47 -128.34 112.49 1.4366 +IC O32 C31 *C32 H32J 1.4366 112.49 -116.07 105.95 1.1161 +IC C31 C32 O32 CC1 1.5601 112.49 63.95 119.66 1.3116 +IC C32 O32 CC1 CC2 1.4366 119.66 174.29 107.09 1.5336 +IC CC2 O32 *CC1 OC1 1.5336 107.09 -173.56 127.47 1.2207 +IC O32 CC1 CC2 CC3 1.3116 107.09 -164.46 113.36 1.5473 +IC CC3 CC1 *CC2 H2R 1.5473 113.36 -122.26 107.51 1.1095 +IC H2R CC1 *CC2 H2S 1.1095 107.51 -116.12 106.49 1.1079 +IC C31 C32 C33 O33 1.5601 112.47 172.98 110.61 1.4451 +IC O33 C32 *C33 H33J 1.4451 110.61 -120.02 107.20 1.1140 +IC H33J C32 *C33 H33K 1.1140 107.20 -116.59 109.03 1.1135 +IC C32 C33 O33 CD1 1.5581 110.61 171.79 114.01 1.3219 +IC C33 O33 CD1 CD2 1.4451 114.01 -179.82 108.63 1.5286 +IC CD2 O33 *CD1 OD1 1.5286 108.63 -179.11 125.87 1.2176 +IC O33 CD1 CD2 CD3 1.3219 108.63 -179.87 112.70 1.5466 +IC CD3 CD1 *CD2 H2X 1.5466 112.70 -121.86 107.89 1.1090 +IC H2X CD1 *CD2 H2Y 1.1090 107.89 -116.69 106.84 1.1089 +IC CA1 CA2 CA3 CA4 1.5299 112.46 -72.65 112.78 1.5357 +IC CA4 CA2 *CA3 H3A 1.5357 112.78 -119.28 108.34 1.1147 +IC H3A CA2 *CA3 H3B 1.1147 108.34 -117.06 110.05 1.1129 +IC CA2 CA3 CA4 CA5 1.5472 112.78 -174.17 113.65 1.5387 +IC CA5 CA3 *CA4 H4A 1.5387 113.65 -123.06 109.83 1.1127 +IC H4A CA3 *CA4 H4B 1.1127 109.83 -116.54 108.51 1.1143 +IC CA3 CA4 CA5 CA6 1.5357 113.65 -63.24 114.94 1.5387 +IC CA6 CA4 *CA5 H5A 1.5387 114.94 -121.33 108.45 1.1141 +IC H5A CA4 *CA5 H5B 1.1141 108.45 -116.48 108.66 1.1133 +IC CA4 CA5 CA6 CA7 1.5387 114.94 -61.54 113.57 1.5357 +IC CA7 CA5 *CA6 H6A 1.5357 113.57 -120.25 108.19 1.1142 +IC H6A CA5 *CA6 H6B 1.1142 108.19 -116.88 109.94 1.1118 +IC CA5 CA6 CA7 CA8 1.5387 113.57 -173.80 112.49 1.5368 +IC CA8 CA6 *CA7 H7A 1.5368 112.49 -121.21 109.61 1.1131 +IC H7A CA6 *CA7 H7B 1.1131 109.61 -117.26 108.90 1.1119 +IC CA6 CA7 CA8 CA9 1.5357 112.49 -179.80 111.15 1.5288 +IC CA9 CA7 *CA8 H8A 1.5288 111.15 -122.72 109.39 1.1101 +IC H8A CA7 *CA8 H8B 1.1101 109.39 -116.56 109.32 1.1116 +IC CA7 CA8 CA9 CA10 1.5368 111.15 -77.30 119.88 1.5097 +IC CA10 CA8 *CA9 CA17 1.5097 119.88 -69.78 116.66 1.5237 +IC CA10 CA8 *CA9 H9A 1.5097 119.88 146.11 117.84 1.1032 +IC CA10 CA9 *CA17 H17A 1.5298 59.26 104.14 113.33 1.0805 +IC CA10 CA9 *CA17 H17B 1.5298 59.26 -104.27 113.81 1.0797 +IC CA17 CA9 *CA10 CA11 1.5298 60.17 102.17 120.90 1.5286 +IC CA11 CA9 *CA10 H10A 1.5286 120.90 152.97 115.36 1.1029 +IC CA9 CA10 CA11 CA12 1.5097 120.90 -156.87 110.35 1.5381 +IC CA12 CA10 *CA11 H11A 1.5381 110.35 121.29 111.11 1.1086 +IC H11A CA10 *CA11 H11B 1.1086 111.11 119.10 109.17 1.1124 +IC CA10 CA11 CA12 CA13 1.5286 110.35 -174.73 113.78 1.5383 +IC CA13 CA11 *CA12 H12A 1.5383 113.78 -122.46 109.26 1.1127 +IC H12A CA11 *CA12 H12B 1.1127 109.26 -116.89 108.39 1.1140 +IC CA11 CA12 CA13 CA14 1.5381 113.78 -65.46 113.72 1.5374 +IC CA14 CA12 *CA13 H13A 1.5374 113.72 -121.14 108.03 1.1130 +IC H13A CA12 *CA13 H13B 1.1130 108.03 -116.69 109.13 1.1128 +IC CA12 CA13 CA14 CA15 1.5383 113.72 -179.99 113.77 1.5378 +IC CA15 CA13 *CA14 H14A 1.5378 113.77 -120.74 109.02 1.1129 +IC H14A CA13 *CA14 H14B 1.1129 109.02 -117.21 109.04 1.1129 +IC CA13 CA14 CA15 CA16 1.5374 113.77 64.12 114.57 1.5322 +IC CA16 CA14 *CA15 H15A 1.5322 114.57 -122.53 108.68 1.1140 +IC H15A CA14 *CA15 H15B 1.1140 108.68 -116.08 108.17 1.1148 +IC CA14 CA15 CA16 H16A 1.5378 114.57 56.51 110.44 1.1112 +IC H16A CA15 *CA16 H16B 1.1112 110.44 -120.19 110.86 1.1106 +IC H16A CA15 *CA16 H16C 1.1112 110.44 119.94 110.49 1.1113 +IC CB1 CB2 CB3 CB4 1.5266 112.85 -169.96 113.08 1.5376 +IC CB4 CB2 *CB3 H3D 1.5376 113.08 -122.66 109.52 1.1132 +IC H3D CB2 *CB3 H3E 1.1132 109.52 -117.10 109.67 1.1154 +IC CB2 CB3 CB4 CB5 1.5470 113.08 -55.83 114.87 1.5385 +IC CB5 CB3 *CB4 H4D 1.5385 114.87 -122.02 108.60 1.1138 +IC H4D CB3 *CB4 H4E 1.1138 108.60 -116.38 108.50 1.1144 +IC CB3 CB4 CB5 CB6 1.5376 114.87 -58.80 113.88 1.5356 +IC CB6 CB4 *CB5 H5D 1.5356 113.88 -120.94 108.45 1.1140 +IC H5D CB4 *CB5 H5E 1.1140 108.45 -116.62 109.60 1.1125 +IC CB4 CB5 CB6 CB7 1.5385 113.88 -177.61 112.33 1.5346 +IC CB7 CB5 *CB6 H6D 1.5346 112.33 -120.85 109.57 1.1122 +IC H6D CB5 *CB6 H6E 1.1122 109.57 -117.67 109.29 1.1129 +IC CB5 CB6 CB7 CB8 1.5356 112.33 -178.04 112.63 1.5340 +IC CB8 CB6 *CB7 H7D 1.5340 112.63 -121.54 109.17 1.1131 +IC H7D CB6 *CB7 H7E 1.1131 109.17 -117.45 109.06 1.1136 +IC CB6 CB7 CB8 CB9 1.5346 112.63 -179.44 112.56 1.5345 +IC CB9 CB7 *CB8 H8D 1.5345 112.56 -120.92 109.03 1.1131 +IC H8D CB7 *CB8 H8E 1.1131 109.03 -117.57 109.27 1.1131 +IC CB7 CB8 CB9 CB10 1.5340 112.56 -179.60 112.44 1.5356 +IC CB10 CB8 *CB9 H9D 1.5356 112.44 -121.78 108.82 1.1122 +IC H9D CB8 *CB9 H9E 1.1122 108.82 -117.28 108.99 1.1134 +IC CB8 CB9 CB10 CB11 1.5345 112.44 175.48 113.77 1.5381 +IC CB11 CB9 *CB10 H10D 1.5381 113.77 -120.54 108.30 1.1144 +IC H10D CB9 *CB10 H10E 1.1144 108.30 -116.89 109.38 1.1126 +IC CB9 CB10 CB11 CB12 1.5356 113.77 65.91 113.71 1.5369 +IC CB12 CB10 *CB11 H11D 1.5369 113.71 -122.23 109.11 1.1130 +IC H11D CB10 *CB11 H11E 1.1130 109.11 -116.62 108.06 1.1131 +IC CB10 CB11 CB12 CB13 1.5381 113.71 -179.53 113.68 1.5381 +IC CB13 CB11 *CB12 H12D 1.5381 113.68 -122.23 109.24 1.1129 +IC H12D CB11 *CB12 H12E 1.1129 109.24 -117.27 108.98 1.1131 +IC CB11 CB12 CB13 CB14 1.5369 113.68 -65.91 113.81 1.5357 +IC CB14 CB12 *CB13 H13D 1.5357 113.81 -120.61 108.41 1.1141 +IC H13D CB12 *CB13 H13E 1.1141 108.41 -116.89 109.26 1.1129 +IC CB12 CB13 CB14 CB15 1.5381 113.81 -175.66 112.54 1.5341 +IC CB15 CB13 *CB14 H14D 1.5341 112.54 -121.18 109.69 1.1124 +IC H14D CB13 *CB14 H14E 1.1124 109.69 -117.74 109.08 1.1133 +IC CB13 CB14 CB15 CB16 1.5357 112.54 179.98 113.21 1.5308 +IC CB16 CB14 *CB15 H15D 1.5308 113.21 -121.66 108.80 1.1142 +IC H15D CB14 *CB15 H15E 1.1142 108.80 -116.68 108.77 1.1142 +IC CB14 CB15 CB16 H16D 1.5341 113.21 60.10 110.47 1.1113 +IC H16D CB15 *CB16 H16E 1.1113 110.47 -119.86 110.47 1.1114 +IC H16D CB15 *CB16 H16F 1.1113 110.47 120.07 110.63 1.1112 +IC CC1 CC2 CC3 CC4 1.5336 113.36 159.10 113.65 1.5383 +IC CC4 CC2 *CC3 H3R 1.5383 113.65 -122.34 110.45 1.1133 +IC H3R CC2 *CC3 H3S 1.1133 110.45 -116.61 107.75 1.1124 +IC CC2 CC3 CC4 CC5 1.5473 113.65 -64.03 115.09 1.5403 +IC CC5 CC3 *CC4 H4R 1.5403 115.09 -120.94 108.04 1.1118 +IC H4R CC3 *CC4 H4S 1.1118 108.04 -116.36 108.75 1.1134 +IC CC3 CC4 CC5 CC6 1.5383 115.09 -53.34 114.08 1.5361 +IC CC6 CC4 *CC5 H5R 1.5361 114.08 -121.25 108.56 1.1127 +IC H5R CC4 *CC5 H5S 1.1127 108.56 -116.59 109.46 1.1125 +IC CC4 CC5 CC6 CC7 1.5403 114.08 -175.83 112.45 1.5343 +IC CC7 CC5 *CC6 H6R 1.5343 112.45 -120.54 109.39 1.1136 +IC H6R CC5 *CC6 H6S 1.1136 109.39 -117.65 109.41 1.1127 +IC CC5 CC6 CC7 CC8 1.5361 112.45 -177.91 112.51 1.5342 +IC CC8 CC6 *CC7 H7R 1.5342 112.51 -121.64 109.24 1.1129 +IC H7R CC6 *CC7 H7S 1.1129 109.24 -117.44 108.87 1.1136 +IC CC6 CC7 CC8 CC9 1.5343 112.51 179.29 112.46 1.5346 +IC CC9 CC7 *CC8 H8R 1.5346 112.46 -121.23 109.01 1.1138 +IC H8R CC7 *CC8 H8S 1.1138 109.01 -117.26 109.20 1.1133 +IC CC7 CC8 CC9 CC10 1.5342 112.46 -179.50 112.54 1.5356 +IC CC10 CC8 *CC9 H9R 1.5356 112.54 -121.79 108.89 1.1123 +IC H9R CC8 *CC9 H9S 1.1123 108.89 -117.12 108.81 1.1130 +IC CC8 CC9 CC10 CC11 1.5346 112.54 172.76 113.77 1.5381 +IC CC11 CC9 *CC10 H10R 1.5381 113.77 -120.56 108.36 1.1141 +IC H10R CC9 *CC10 H10S 1.1141 108.36 -116.76 109.34 1.1128 +IC CC9 CC10 CC11 CC12 1.5356 113.77 65.44 113.74 1.5368 +IC CC12 CC10 *CC11 H11R 1.5368 113.74 -122.13 109.19 1.1127 +IC H11R CC10 *CC11 H11S 1.1127 109.19 -116.69 108.08 1.1131 +IC CC10 CC11 CC12 CC13 1.5381 113.74 -178.80 113.65 1.5382 +IC CC13 CC11 *CC12 H12R 1.5382 113.65 -122.23 109.18 1.1129 +IC H12R CC11 *CC12 H12S 1.1129 109.18 -117.22 108.97 1.1130 +IC CC11 CC12 CC13 CC14 1.5368 113.65 -65.20 113.84 1.5357 +IC CC14 CC12 *CC13 H13R 1.5357 113.84 -120.68 108.43 1.1141 +IC H13R CC12 *CC13 H13S 1.1141 108.43 -116.91 109.25 1.1129 +IC CC12 CC13 CC14 CC15 1.5382 113.84 -175.70 112.52 1.5341 +IC CC15 CC13 *CC14 H14R 1.5341 112.52 -121.15 109.71 1.1124 +IC H14R CC13 *CC14 H14S 1.1124 109.71 -117.76 109.11 1.1133 +IC CC13 CC14 CC15 CC16 1.5357 112.52 -179.95 113.21 1.5308 +IC CC16 CC14 *CC15 H15R 1.5308 113.21 -121.66 108.79 1.1142 +IC H15R CC14 *CC15 H15S 1.1142 108.79 -116.68 108.78 1.1142 +IC CC14 CC15 CC16 H16R 1.5341 113.21 60.13 110.48 1.1114 +IC H16R CC15 *CC16 H16S 1.1114 110.48 -119.86 110.46 1.1114 +IC H16R CC15 *CC16 H16T 1.1114 110.48 120.07 110.63 1.1113 +IC CD1 CD2 CD3 CD4 1.5286 112.70 177.22 113.29 1.5381 +IC CD4 CD2 *CD3 H3X 1.5381 113.29 -122.22 109.75 1.1136 +IC H3X CD2 *CD3 H3Y 1.1136 109.75 -116.74 109.02 1.1148 +IC CD2 CD3 CD4 CD5 1.5466 113.29 -59.96 115.09 1.5393 +IC CD5 CD3 *CD4 H4X 1.5393 115.09 -121.71 108.40 1.1140 +IC H4X CD3 *CD4 H4Y 1.1140 108.40 -116.40 108.62 1.1132 +IC CD3 CD4 CD5 CD6 1.5381 115.09 -56.77 113.80 1.5358 +IC CD6 CD4 *CD5 H5X 1.5358 113.80 -120.99 108.41 1.1139 +IC H5X CD4 *CD5 H5Y 1.1139 108.41 -116.66 109.61 1.1125 +IC CD4 CD5 CD6 CD7 1.5393 113.80 -176.21 112.66 1.5348 +IC CD7 CD5 *CD6 H6X 1.5348 112.66 -120.85 109.46 1.1132 +IC H6X CD5 *CD6 H6Y 1.1132 109.46 -117.69 109.17 1.1131 +IC CD5 CD6 CD7 CD8 1.5358 112.66 -178.83 112.38 1.5345 +IC CD8 CD6 *CD7 H7X 1.5345 112.38 -121.48 109.30 1.1130 +IC H7X CD6 *CD7 H7Y 1.1130 109.30 -117.53 109.03 1.1135 +IC CD6 CD7 CD8 CD9 1.5348 112.38 179.35 112.73 1.5349 +IC CD9 CD7 *CD8 H8X 1.5349 112.73 -121.20 108.96 1.1136 +IC H8X CD7 *CD8 H8Y 1.1136 108.96 -117.31 109.19 1.1132 +IC CD7 CD8 CD9 CD10 1.5345 112.73 -178.92 112.37 1.5357 +IC CD10 CD8 *CD9 H9X 1.5357 112.37 -121.80 108.89 1.1123 +IC H9X CD8 *CD9 H9Y 1.1123 108.89 -117.31 108.99 1.1134 +IC CD8 CD9 CD10 CD11 1.5349 112.37 175.10 113.87 1.5381 +IC CD11 CD9 *CD10 H10X 1.5381 113.87 -120.54 108.27 1.1143 +IC H10X CD9 *CD10 H10Y 1.1143 108.27 -116.88 109.38 1.1128 +IC CD9 CD10 CD11 CD12 1.5357 113.87 66.07 113.71 1.5369 +IC CD12 CD10 *CD11 H11X 1.5369 113.71 -122.30 109.21 1.1128 +IC H11X CD10 *CD11 H11Y 1.1128 109.21 -116.69 108.02 1.1131 +IC CD10 CD11 CD12 CD13 1.5381 113.71 179.76 113.69 1.5383 +IC CD13 CD11 *CD12 H12X 1.5383 113.69 -122.18 109.23 1.1129 +IC H12X CD11 *CD12 H12Y 1.1129 109.23 -117.24 108.92 1.1130 +IC CD11 CD12 CD13 CD14 1.5369 113.69 -66.02 113.82 1.5359 +IC CD14 CD12 *CD13 H13X 1.5359 113.82 -120.59 108.40 1.1141 +IC H13X CD12 *CD13 H13Y 1.1141 108.40 -116.90 109.26 1.1128 +IC CD12 CD13 CD14 CD15 1.5383 113.82 -175.64 112.56 1.5342 +IC CD15 CD13 *CD14 H14X 1.5342 112.56 -121.17 109.69 1.1124 +IC H14X CD13 *CD14 H14Y 1.1124 109.69 -117.73 109.08 1.1133 +IC CD13 CD14 CD15 CD16 1.5359 112.56 179.98 113.21 1.5309 +IC CD16 CD14 *CD15 H15X 1.5309 113.21 -121.67 108.80 1.1141 +IC H15X CD14 *CD15 H15Y 1.1141 108.80 -116.68 108.75 1.1142 +IC CD14 CD15 CD16 H16X 1.5342 113.21 60.00 110.47 1.1114 +IC H16X CD15 *CD16 H16Y 1.1114 110.47 -119.85 110.47 1.1114 +IC H16X CD15 *CD16 H16Z 1.1114 110.47 120.07 110.64 1.1112 + +RESI PMCL2 -2.00 ! (PMPG + DPPG) Cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 3 C16:0 + 1 C17:CYC +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 -0.08 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM H13J HAL2 0.09 ! | | | | +ATOM H13K HAL2 0.09 ! H9D--CB9--H9E H9A--CA9 H17A H9X--CD9--H9Y H9R--CC9--H9S +ATOM O13 OSL -0.49 ! | |\ / | | +ATOM CB1 CL 0.90 ! | | \ / | | +ATOM OB1 OBL -0.63 ! | | CA17 | | +ATOM CB2 CTL2 -0.22 ! | | / \ | | +ATOM H2D HAL2 0.09 ! | |/ \ | | +ATOM H2E HAL2 0.09 ! H10D--CB10--H10E H10A--CA10 H17B H10X--CD10--H10Y H10R--CC10--H10S +GROUP ! | | | | +ATOM C32 CTL1 0.17 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H12D--CB12--H12E H12A--CA12--H12B H12X--CD12--H12Y H12R--CC12--H12S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +ATOM CC2 CTL2 -0.22 ! | | | | +ATOM H2R HAL2 0.09 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H16F H16C H16Z H16T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CG3RC1 -0.09 ! +ATOM H9A HGA1 0.09 ! +GROUP ! +ATOM CA17 CG3C31 -0.18 ! +ATOM H17A HGA2 0.09 ! +ATOM H17B HGA2 0.09 ! +GROUP ! +ATOM CA10 CG3RC1 -0.09 ! +ATOM H10A HGA1 0.09 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL3 -0.27 ! +ATOM H16A HAL3 0.09 ! +ATOM H16B HAL3 0.09 ! +ATOM H16C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CTL2 -0.18 ! +ATOM H9D HAL2 0.09 ! +ATOM H9E HAL2 0.09 ! +GROUP ! +ATOM CB10 CTL2 -0.18 ! +ATOM H10D HAL2 0.09 ! +ATOM H10E HAL2 0.09 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL3 -0.27 ! +ATOM H16D HAL3 0.09 ! +ATOM H16E HAL3 0.09 ! +ATOM H16F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CTL2 -0.18 ! +ATOM H9R HAL2 0.09 ! +ATOM H9S HAL2 0.09 ! +GROUP ! +ATOM CC10 CTL2 -0.18 ! +ATOM H10R HAL2 0.09 ! +ATOM H10S HAL2 0.09 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL3 -0.27 ! +ATOM H16R HAL3 0.09 ! +ATOM H16S HAL3 0.09 ! +ATOM H16T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CTL2 -0.18 ! +ATOM H9X HAL2 0.09 ! +ATOM H9Y HAL2 0.09 ! +GROUP ! +ATOM CD10 CTL2 -0.18 ! +ATOM H10X HAL2 0.09 ! +ATOM H10Y HAL2 0.09 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 CA9 CA17 +BOND CA17 H17A CA17 H17B CA17 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 H16C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 H9E CB9 CB10 +BOND CB10 H10D CB10 H10E CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 H16F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 H9S CC9 CC10 +BOND CC10 H10R CC10 H10S CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 H16T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 H9Y CD9 CD10 +BOND CD10 H10X CD10 H10Y CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 H16Z +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4404 111.77 121.98 107.43 1.1157 +IC HG31 C2 *C3 HG32 1.1157 107.43 116.50 107.43 1.1155 +IC C2 C3 OP31 P3 1.5543 111.77 178.39 118.46 1.5903 +IC C3 OP31 P3 OP32 1.4404 118.46 53.85 101.93 1.5888 +IC OP32 OP31 *P3 OP33 1.5888 101.93 -114.83 110.16 1.4776 +IC OP32 OP31 *P3 OP34 1.5888 101.93 114.40 109.34 1.4797 +IC OP31 P3 OP32 C31 1.5903 101.93 85.61 119.24 1.4309 +IC P3 OP32 C31 C32 1.5888 119.24 -163.67 110.36 1.5555 +IC C32 OP32 *C31 H31J 1.5555 110.36 123.24 112.29 1.1149 +IC H31J OP32 *C31 H31K 1.1149 112.29 118.62 108.89 1.1140 +IC HG31 C3 C2 C1 1.1157 107.43 -65.18 112.25 1.5593 +IC C1 C3 *C2 OG12 1.5593 112.25 -122.22 106.09 1.4219 +IC C1 C3 *C2 HG22 1.5593 112.25 120.27 108.54 1.1138 +IC C3 C2 OG12 HO12 1.5543 106.09 -39.60 99.04 0.9676 +IC C3 C2 C1 OP11 1.5543 112.25 164.26 114.43 1.4378 +IC OP11 C2 *C1 HG11 1.4378 114.43 -124.62 107.10 1.1145 +IC HG11 C2 *C1 HG12 1.1145 107.10 -114.05 107.69 1.1117 +IC C2 C1 OP11 P1 1.5593 114.43 -90.31 122.18 1.5885 +IC C1 OP11 P1 OP12 1.4378 122.18 -40.47 102.50 1.5910 +IC OP12 OP11 *P1 OP13 1.5910 102.50 114.98 110.09 1.4771 +IC OP12 OP11 *P1 OP14 1.5910 102.50 -115.36 109.21 1.4819 +IC OP11 P1 OP12 C11 1.5885 102.50 -95.61 123.00 1.4265 +IC P1 OP12 C11 C12 1.5910 123.00 81.19 112.88 1.5535 +IC C12 OP12 *C11 H11J 1.5535 112.88 -123.80 111.65 1.1148 +IC H11J OP12 *C11 H11K 1.1148 111.65 -117.35 107.38 1.1110 +IC OP12 C11 C12 C13 1.4265 112.88 162.75 111.01 1.5548 +IC C13 C11 *C12 O12 1.5548 111.01 119.22 107.45 1.4324 +IC O12 C11 *C12 H12J 1.4324 107.45 121.50 107.21 1.1164 +IC C11 C12 O12 CA1 1.5535 107.45 143.54 116.43 1.3133 +IC C12 O12 CA1 CA2 1.4324 116.43 -172.80 108.02 1.5341 +IC CA2 O12 *CA1 OA1 1.5341 108.02 -175.93 126.26 1.2216 +IC O12 CA1 CA2 CA3 1.3133 108.02 -148.36 113.31 1.5470 +IC CA3 CA1 *CA2 H2A 1.5470 113.31 -123.41 107.26 1.1100 +IC H2A CA1 *CA2 H2B 1.1100 107.26 -115.53 107.24 1.1101 +IC C11 C12 C13 O13 1.5535 111.01 -179.49 112.23 1.4463 +IC O13 C12 *C13 H13J 1.4463 112.23 -118.71 106.42 1.1130 +IC H13J C12 *C13 H13K 1.1130 106.42 -115.08 109.24 1.1142 +IC C12 C13 O13 CB1 1.5548 112.23 87.75 114.75 1.3288 +IC C13 O13 CB1 CB2 1.4463 114.75 -168.75 109.29 1.5293 +IC CB2 O13 *CB1 OB1 1.5293 109.29 -177.26 125.60 1.2177 +IC O13 CB1 CB2 CB3 1.3288 109.29 -159.26 112.09 1.5474 +IC CB3 CB1 *CB2 H2D 1.5474 112.09 -120.96 107.12 1.1105 +IC H2D CB1 *CB2 H2E 1.1105 107.12 -116.84 107.85 1.1075 +IC OP32 C31 C32 C33 1.4309 110.36 -44.28 110.18 1.5546 +IC C33 C31 *C32 O32 1.5546 110.18 120.84 111.14 1.4409 +IC O32 C31 *C32 H32J 1.4409 111.14 121.75 108.07 1.1150 +IC C31 C32 O32 CC1 1.5555 111.14 69.92 113.95 1.3234 +IC C32 O32 CC1 CC2 1.4409 113.95 -163.73 108.67 1.5294 +IC CC2 O32 *CC1 OC1 1.5294 108.67 -178.62 125.27 1.2211 +IC O32 CC1 CC2 CC3 1.3234 108.67 169.29 114.76 1.5515 +IC CC3 CC1 *CC2 H2R 1.5515 114.76 -118.81 105.73 1.1128 +IC H2R CC1 *CC2 H2S 1.1128 105.73 -115.50 109.04 1.1050 +IC C31 C32 C33 O33 1.5555 110.18 -170.30 112.58 1.4492 +IC O33 C32 *C33 H33J 1.4492 112.58 125.96 108.97 1.1147 +IC H33J C32 *C33 H33K 1.1147 108.97 114.33 106.50 1.1147 +IC C32 C33 O33 CD1 1.5546 112.58 86.37 115.24 1.3207 +IC C33 O33 CD1 CD2 1.4492 115.24 -175.48 109.59 1.5292 +IC CD2 O33 *CD1 OD1 1.5292 109.59 178.66 126.37 1.2168 +IC O33 CD1 CD2 CD3 1.3207 109.59 -112.69 113.08 1.5459 +IC CD3 CD1 *CD2 H2X 1.5459 113.08 -119.64 106.06 1.1102 +IC H2X CD1 *CD2 H2Y 1.1102 106.06 -116.76 109.15 1.1084 +IC CA1 CA2 CA3 CA4 1.5341 113.31 -90.85 112.33 1.5335 +IC CA4 CA2 *CA3 H3A 1.5335 112.33 -119.04 108.72 1.1138 +IC H3A CA2 *CA3 H3B 1.1138 108.72 -117.35 110.01 1.1120 +IC CA2 CA3 CA4 CA5 1.5470 112.33 171.12 113.32 1.5388 +IC CA5 CA3 *CA4 H4A 1.5388 113.32 -123.59 109.50 1.1129 +IC H4A CA3 *CA4 H4B 1.1129 109.50 -115.18 108.13 1.1141 +IC CA3 CA4 CA5 CA6 1.5335 113.32 -70.58 114.83 1.5415 +IC CA6 CA4 *CA5 H5A 1.5415 114.83 -120.76 107.77 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 107.77 -116.12 108.97 1.1121 +IC CA4 CA5 CA6 CA7 1.5388 114.83 -54.59 113.60 1.5367 +IC CA7 CA5 *CA6 H6A 1.5367 113.60 -121.30 108.70 1.1128 +IC H6A CA5 *CA6 H6B 1.1128 108.70 -117.34 109.35 1.1124 +IC CA5 CA6 CA7 CA8 1.5415 113.60 -175.73 113.55 1.5363 +IC CA8 CA6 *CA7 H7A 1.5363 113.55 -119.83 108.95 1.1157 +IC H7A CA6 *CA7 H7B 1.1157 108.95 -117.14 109.37 1.1099 +IC CA6 CA7 CA8 CA9 1.5367 113.55 -169.18 110.39 1.5298 +IC CA9 CA7 *CA8 H8A 1.5298 110.39 -123.41 109.97 1.1091 +IC H8A CA7 *CA8 H8B 1.1091 109.97 -117.61 108.74 1.1130 +IC CA7 CA8 CA9 CA10 1.5363 110.39 -75.06 119.81 1.5091 +IC CA10 CA8 *CA9 CA17 1.5091 119.81 -70.11 117.53 1.5234 +IC CA10 CA8 *CA9 H9A 1.5091 119.81 144.51 117.37 1.1050 +IC CA10 CA9 *CA17 H17A 1.5290 59.26 103.84 113.36 1.0808 +IC CA10 CA9 *CA17 H17B 1.5290 59.26 -104.32 113.75 1.0793 +IC CA17 CA9 *CA10 CA11 1.5290 60.19 102.01 120.98 1.5275 +IC CA11 CA9 *CA10 H10A 1.5275 120.98 152.12 114.86 1.1044 +IC CA9 CA10 CA11 CA12 1.5091 120.98 -158.05 110.02 1.5368 +IC CA12 CA10 *CA11 H11A 1.5368 110.02 122.06 111.31 1.1084 +IC H11A CA10 *CA11 H11B 1.1084 111.31 119.12 108.66 1.1115 +IC CA10 CA11 CA12 CA13 1.5275 110.02 -173.90 114.47 1.5369 +IC CA13 CA11 *CA12 H12A 1.5369 114.47 -122.88 109.11 1.1118 +IC H12A CA11 *CA12 H12B 1.1118 109.11 -117.07 107.71 1.1153 +IC CA11 CA12 CA13 CA14 1.5368 114.47 -64.73 113.93 1.5359 +IC CA14 CA12 *CA13 H13A 1.5359 113.93 -121.52 108.07 1.1129 +IC H13A CA12 *CA13 H13B 1.1129 108.07 -116.19 109.02 1.1129 +IC CA12 CA13 CA14 CA15 1.5369 113.93 -179.46 113.24 1.5368 +IC CA15 CA13 *CA14 H14A 1.5368 113.24 -120.32 108.71 1.1128 +IC H14A CA13 *CA14 H14B 1.1128 108.71 -117.34 109.56 1.1122 +IC CA13 CA14 CA15 CA16 1.5359 113.24 69.05 114.41 1.5315 +IC CA16 CA14 *CA15 H15A 1.5315 114.41 -122.58 108.59 1.1140 +IC H15A CA14 *CA15 H15B 1.1140 108.59 -115.96 108.27 1.1135 +IC CA14 CA15 CA16 H16A 1.5368 114.41 57.17 110.45 1.1111 +IC H16A CA15 *CA16 H16B 1.1111 110.45 -120.11 110.71 1.1109 +IC H16A CA15 *CA16 H16C 1.1111 110.45 120.04 110.50 1.1111 +IC CB1 CB2 CB3 CB4 1.5293 112.09 -179.75 113.77 1.5373 +IC CB4 CB2 *CB3 H3D 1.5373 113.77 -122.31 109.50 1.1133 +IC H3D CB2 *CB3 H3E 1.1133 109.50 -116.80 108.92 1.1158 +IC CB2 CB3 CB4 CB5 1.5474 113.77 -56.57 115.13 1.5384 +IC CB5 CB3 *CB4 H4D 1.5384 115.13 -121.97 108.32 1.1129 +IC H4D CB3 *CB4 H4E 1.1129 108.32 -116.05 108.73 1.1123 +IC CB3 CB4 CB5 CB6 1.5373 115.13 -55.77 113.84 1.5359 +IC CB6 CB4 *CB5 H5D 1.5359 113.84 -121.23 108.23 1.1135 +IC H5D CB4 *CB5 H5E 1.1135 108.23 -116.40 109.46 1.1127 +IC CB4 CB5 CB6 CB7 1.5384 113.84 -173.32 112.53 1.5350 +IC CB7 CB5 *CB6 H6D 1.5350 112.53 -120.96 109.26 1.1129 +IC H6D CB5 *CB6 H6E 1.1129 109.26 -117.48 109.43 1.1126 +IC CB5 CB6 CB7 CB8 1.5359 112.53 -175.82 112.56 1.5344 +IC CB8 CB6 *CB7 H7D 1.5344 112.56 -121.89 109.52 1.1131 +IC H7D CB6 *CB7 H7E 1.1131 109.52 -117.47 108.68 1.1137 +IC CB6 CB7 CB8 CB9 1.5350 112.56 176.00 112.56 1.5350 +IC CB9 CB7 *CB8 H8D 1.5350 112.56 -120.58 108.62 1.1138 +IC H8D CB7 *CB8 H8E 1.1138 108.62 -117.40 109.53 1.1128 +IC CB7 CB8 CB9 CB10 1.5344 112.56 -174.31 112.58 1.5360 +IC CB10 CB8 *CB9 H9D 1.5360 112.58 -122.42 109.13 1.1122 +IC H9D CB8 *CB9 H9E 1.1122 109.13 -117.22 108.67 1.1137 +IC CB8 CB9 CB10 CB11 1.5350 112.58 171.88 113.64 1.5381 +IC CB11 CB9 *CB10 H10D 1.5381 113.64 -120.00 108.14 1.1144 +IC H10D CB9 *CB10 H10E 1.1144 108.14 -116.92 109.62 1.1123 +IC CB9 CB10 CB11 CB12 1.5360 113.64 68.36 113.72 1.5363 +IC CB12 CB10 *CB11 H11D 1.5363 113.72 -122.24 109.08 1.1129 +IC H11D CB10 *CB11 H11E 1.1129 109.08 -116.74 108.26 1.1132 +IC CB10 CB11 CB12 CB13 1.5381 113.72 -176.80 113.72 1.5378 +IC CB13 CB11 *CB12 H12D 1.5378 113.72 -121.91 109.01 1.1125 +IC H12D CB11 *CB12 H12E 1.1125 109.01 -117.24 109.07 1.1131 +IC CB11 CB12 CB13 CB14 1.5363 113.72 -65.09 113.76 1.5357 +IC CB14 CB12 *CB13 H13D 1.5357 113.76 -120.67 108.42 1.1141 +IC H13D CB12 *CB13 H13E 1.1141 108.42 -116.91 109.24 1.1129 +IC CB12 CB13 CB14 CB15 1.5378 113.76 -175.73 112.55 1.5341 +IC CB15 CB13 *CB14 H14D 1.5341 112.55 -121.18 109.65 1.1125 +IC H14D CB13 *CB14 H14E 1.1125 109.65 -117.71 109.07 1.1133 +IC CB13 CB14 CB15 CB16 1.5357 112.55 179.96 113.22 1.5308 +IC CB16 CB14 *CB15 H15D 1.5308 113.22 -121.67 108.80 1.1142 +IC H15D CB14 *CB15 H15E 1.1142 108.80 -116.68 108.75 1.1142 +IC CB14 CB15 CB16 H16D 1.5341 113.22 59.92 110.47 1.1114 +IC H16D CB15 *CB16 H16E 1.1114 110.47 -119.86 110.47 1.1114 +IC H16D CB15 *CB16 H16F 1.1114 110.47 120.07 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5294 114.76 93.79 114.39 1.5374 +IC CC4 CC2 *CC3 H3R 1.5374 114.39 -126.95 111.10 1.1116 +IC H3R CC2 *CC3 H3S 1.1116 111.10 -115.09 106.18 1.1184 +IC CC2 CC3 CC4 CC5 1.5515 114.39 -72.23 114.19 1.5358 +IC CC5 CC3 *CC4 H4R 1.5358 114.19 -121.05 108.41 1.1133 +IC H4R CC3 *CC4 H4S 1.1133 108.41 -116.30 107.75 1.1098 +IC CC3 CC4 CC5 CC6 1.5374 114.19 -179.76 114.16 1.5387 +IC CC6 CC4 *CC5 H5R 1.5387 114.16 -121.52 108.86 1.1110 +IC H5R CC4 *CC5 H5S 1.1110 108.86 -115.95 108.61 1.1135 +IC CC4 CC5 CC6 CC7 1.5358 114.16 -59.65 113.12 1.5354 +IC CC7 CC5 *CC6 H6R 1.5354 113.12 -120.53 108.09 1.1136 +IC H6R CC5 *CC6 H6S 1.1136 108.09 -117.17 109.48 1.1121 +IC CC5 CC6 CC7 CC8 1.5387 113.12 -170.18 113.61 1.5340 +IC CC8 CC6 *CC7 H7R 1.5340 113.61 -121.71 109.29 1.1106 +IC H7R CC6 *CC7 H7S 1.1106 109.29 -117.04 108.75 1.1122 +IC CC6 CC7 CC8 CC9 1.5354 113.61 -179.71 111.74 1.5360 +IC CC9 CC7 *CC8 H8R 1.5360 111.74 -121.24 108.81 1.1116 +IC H8R CC7 *CC8 H8S 1.1116 108.81 -117.52 109.28 1.1125 +IC CC7 CC8 CC9 CC10 1.5340 111.74 179.06 113.91 1.5382 +IC CC10 CC8 *CC9 H9R 1.5382 113.91 -120.63 108.05 1.1143 +IC H9R CC8 *CC9 H9S 1.1143 108.05 -116.01 109.22 1.1120 +IC CC8 CC9 CC10 CC11 1.5360 113.91 65.10 115.15 1.5400 +IC CC11 CC9 *CC10 H10R 1.5400 115.15 -122.07 108.46 1.1136 +IC H10R CC9 *CC10 H10S 1.1136 108.46 -116.44 108.60 1.1138 +IC CC9 CC10 CC11 CC12 1.5382 115.15 62.67 113.67 1.5374 +IC CC12 CC10 *CC11 H11R 1.5374 113.67 -122.71 109.79 1.1118 +IC H11R CC10 *CC11 H11S 1.1118 109.79 -116.50 107.76 1.1130 +IC CC10 CC11 CC12 CC13 1.5400 113.67 176.65 113.83 1.5382 +IC CC13 CC11 *CC12 H12R 1.5382 113.83 -122.31 109.33 1.1126 +IC H12R CC11 *CC12 H12S 1.1126 109.33 -117.12 108.68 1.1131 +IC CC11 CC12 CC13 CC14 1.5374 113.83 -68.12 113.78 1.5356 +IC CC14 CC12 *CC13 H13R 1.5356 113.78 -120.56 108.36 1.1141 +IC H13R CC12 *CC13 H13S 1.1141 108.36 -116.88 109.43 1.1125 +IC CC12 CC13 CC14 CC15 1.5382 113.78 -176.10 112.53 1.5342 +IC CC15 CC13 *CC14 H14R 1.5342 112.53 -121.11 109.65 1.1124 +IC H14R CC13 *CC14 H14S 1.1124 109.65 -117.73 109.12 1.1131 +IC CC13 CC14 CC15 CC16 1.5356 112.53 -179.76 113.22 1.5308 +IC CC16 CC14 *CC15 H15R 1.5308 113.22 -121.71 108.83 1.1141 +IC H15R CC14 *CC15 H15S 1.1141 108.83 -116.67 108.72 1.1143 +IC CC14 CC15 CC16 H16R 1.5342 113.22 59.93 110.47 1.1114 +IC H16R CC15 *CC16 H16S 1.1114 110.47 -119.87 110.51 1.1113 +IC H16R CC15 *CC16 H16T 1.1114 110.47 120.04 110.64 1.1113 +IC CD1 CD2 CD3 CD4 1.5292 113.08 -164.96 112.68 1.5376 +IC CD4 CD2 *CD3 H3X 1.5376 112.68 -122.71 109.48 1.1130 +IC H3X CD2 *CD3 H3Y 1.1130 109.48 -117.50 109.46 1.1158 +IC CD2 CD3 CD4 CD5 1.5459 112.68 -56.05 114.87 1.5384 +IC CD5 CD3 *CD4 H4X 1.5384 114.87 -122.39 108.88 1.1135 +IC H4X CD3 *CD4 H4Y 1.1135 108.88 -116.47 108.31 1.1144 +IC CD3 CD4 CD5 CD6 1.5376 114.87 -62.08 113.82 1.5352 +IC CD6 CD4 *CD5 H5X 1.5352 113.82 -120.45 108.15 1.1142 +IC H5X CD4 *CD5 H5Y 1.1142 108.15 -116.65 110.02 1.1126 +IC CD4 CD5 CD6 CD7 1.5384 113.82 -173.93 112.13 1.5346 +IC CD7 CD5 *CD6 H6X 1.5346 112.13 -121.46 109.73 1.1130 +IC H6X CD5 *CD6 H6Y 1.1130 109.73 -117.82 108.98 1.1132 +IC CD5 CD6 CD7 CD8 1.5352 112.13 176.71 112.86 1.5339 +IC CD8 CD6 *CD7 H7X 1.5339 112.86 -120.99 108.98 1.1134 +IC H7X CD6 *CD7 H7Y 1.1134 108.98 -117.24 109.24 1.1129 +IC CD6 CD7 CD8 CD9 1.5346 112.86 -179.51 112.25 1.5346 +IC CD9 CD7 *CD8 H8X 1.5346 112.25 -121.44 109.34 1.1134 +IC H8X CD7 *CD8 H8Y 1.1134 109.34 -117.57 109.03 1.1134 +IC CD7 CD8 CD9 CD10 1.5339 112.25 176.04 112.66 1.5351 +IC CD10 CD8 *CD9 H9X 1.5351 112.66 -121.53 108.95 1.1125 +IC H9X CD8 *CD9 H9Y 1.1125 108.95 -117.19 108.86 1.1136 +IC CD8 CD9 CD10 CD11 1.5346 112.66 172.88 113.48 1.5371 +IC CD11 CD9 *CD10 H10X 1.5371 113.48 -120.25 108.40 1.1141 +IC H10X CD9 *CD10 H10Y 1.1141 108.40 -116.97 109.60 1.1125 +IC CD9 CD10 CD11 CD12 1.5351 113.48 67.69 114.12 1.5358 +IC CD12 CD10 *CD11 H11X 1.5358 114.12 -121.84 108.97 1.1121 +IC H11X CD10 *CD11 H11Y 1.1121 108.97 -116.62 108.19 1.1132 +IC CD10 CD11 CD12 CD13 1.5371 114.12 -176.72 113.29 1.5381 +IC CD13 CD11 *CD12 H12X 1.5381 113.29 -122.08 109.14 1.1128 +IC H12X CD11 *CD12 H12Y 1.1128 109.14 -117.38 109.15 1.1128 +IC CD11 CD12 CD13 CD14 1.5358 113.29 -62.39 113.71 1.5354 +IC CD14 CD12 *CD13 H13X 1.5354 113.71 -120.88 108.48 1.1139 +IC H13X CD12 *CD13 H13Y 1.1139 108.48 -117.04 109.24 1.1131 +IC CD12 CD13 CD14 CD15 1.5381 113.71 -174.33 112.64 1.5333 +IC CD15 CD13 *CD14 H14X 1.5333 112.64 -121.18 109.76 1.1129 +IC H14X CD13 *CD14 H14Y 1.1129 109.76 -117.80 109.00 1.1133 +IC CD13 CD14 CD15 CD16 1.5354 112.64 178.46 112.96 1.5300 +IC CD16 CD14 *CD15 H15X 1.5300 112.96 -121.49 108.86 1.1141 +IC H15X CD14 *CD15 H15Y 1.1141 108.86 -116.85 108.85 1.1141 +IC CD14 CD15 CD16 H16X 1.5333 112.96 60.23 110.39 1.1115 +IC H16X CD15 *CD16 H16Y 1.1115 110.39 -119.86 110.53 1.1112 +IC H16X CD15 *CD16 H16Z 1.1115 110.39 120.03 110.61 1.1112 + +RESI TXCL1 -1.00 ! Tetra-hexadecenoyl Cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 4 C16:1 +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM O13 OSL -0.49 ! | | | | +ATOM CB1 CL 0.90 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H12D--CB12--H12E H12A--CA12--H12B H12X--CD12--H12Y H12R--CC12--H12S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +GROUP ! | | | | +ATOM C32 CTL1 0.17 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM CC2 CTL2 -0.22 ! | | | | +ATOM H2R HAL2 0.09 ! H16F H16C H16Z H16T +ATOM H2S HAL2 0.09 ! +GROUP ! +ATOM C33 CTL2 0.08 ! +ATOM H33J HAL2 0.09 ! +ATOM H33K HAL2 0.09 ! +ATOM O33 OSL -0.49 ! +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL3 -0.27 ! +ATOM H16A HAL3 0.09 ! +ATOM H16B HAL3 0.09 ! +ATOM H16C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL3 -0.27 ! +ATOM H16D HAL3 0.09 ! +ATOM H16E HAL3 0.09 ! +ATOM H16F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL3 -0.27 ! +ATOM H16R HAL3 0.09 ! +ATOM H16S HAL3 0.09 ! +ATOM H16T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 H16C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 H16F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 H16T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 H16Z +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4478 115.81 120.77 107.21 1.1103 +IC HG31 C2 *C3 HG32 1.1103 107.21 113.79 109.44 1.1116 +IC C2 C3 OP31 P3 1.5391 115.81 179.54 116.48 1.6311 +IC C3 OP31 P3 OP32 1.4478 116.48 -24.68 104.81 1.5590 +IC OP32 OP31 *P3 OP33 1.5590 104.81 -115.81 107.08 1.5202 +IC OP32 OP31 *P3 OP34 1.5590 104.81 119.46 112.11 1.4755 +IC OP31 P3 OP32 C31 1.6311 104.81 118.48 124.90 1.4204 +IC P3 OP32 C31 C32 1.5590 124.90 -177.96 114.46 1.5293 +IC C32 OP32 *C31 H31J 1.5293 114.46 121.21 110.94 1.1113 +IC H31J OP32 *C31 H31K 1.1113 110.94 118.18 111.26 1.1114 +IC HG31 C3 C2 C1 1.1103 107.21 59.15 111.81 1.5775 +IC C1 C3 *C2 OG12 1.5775 111.81 -123.03 104.24 1.4529 +IC C1 C3 *C2 HG22 1.5775 111.81 120.08 109.60 1.1109 +IC C3 C2 OG12 HO12 1.5391 104.24 -67.25 112.57 0.9601 +IC C3 C2 C1 OP11 1.5391 111.81 56.67 113.71 1.4252 +IC OP11 C2 *C1 HG11 1.4252 113.71 -129.69 102.65 1.1114 +IC HG11 C2 *C1 HG12 1.1114 102.65 -108.19 113.55 1.1117 +IC C2 C1 OP11 P1 1.5775 113.71 -137.16 115.79 1.5694 +IC C1 OP11 P1 OP12 1.4252 115.79 -38.56 101.17 1.5512 +IC OP12 OP11 *P1 OP13 1.5512 101.17 120.92 110.23 1.6318 +IC OP12 OP11 *P1 OP14 1.5512 101.17 -119.69 108.21 1.4683 +IC OP11 P1 OP13 HP13 1.5694 110.23 80.36 103.88 0.9590 +IC OP11 P1 OP12 C11 1.5694 101.17 -165.75 116.90 1.4487 +IC P1 OP12 C11 C12 1.5512 116.90 -70.20 120.82 1.5785 +IC C12 OP12 *C11 H11J 1.5785 120.82 -121.59 102.98 1.1110 +IC H11J OP12 *C11 H11K 1.1110 102.98 -117.94 115.12 1.1109 +IC OP12 C11 C12 C13 1.4487 120.82 -158.44 110.14 1.4806 +IC C13 C11 *C12 O12 1.4806 110.14 123.75 104.19 1.4203 +IC O12 C11 *C12 H12J 1.4203 104.19 117.29 108.71 1.1108 +IC C11 C12 O12 CA1 1.5785 104.19 152.63 121.75 1.3357 +IC C12 O12 CA1 CA2 1.4203 121.75 -172.10 105.98 1.5689 +IC CA2 O12 *CA1 OA1 1.5689 105.98 172.32 128.82 1.2022 +IC O12 CA1 CA2 CA3 1.3357 105.98 -133.79 106.00 1.5485 +IC CA3 CA1 *CA2 H2A 1.5485 106.00 -117.84 100.88 1.1105 +IC H2A CA1 *CA2 H2B 1.1105 100.88 -120.79 109.17 1.1118 +IC C11 C12 C13 O13 1.5785 110.14 52.09 108.48 1.4206 +IC O13 C12 *C13 H13J 1.4206 108.48 -117.15 111.73 1.1103 +IC H13J C12 *C13 H13K 1.1103 111.73 -117.14 109.17 1.1115 +IC C12 C13 O13 CB1 1.4806 108.48 100.89 115.21 1.3485 +IC C13 O13 CB1 CB2 1.4206 115.21 -166.50 102.03 1.4979 +IC CB2 O13 *CB1 OB1 1.4979 102.03 172.46 124.90 1.2074 +IC O13 CB1 CB2 CB3 1.3485 102.03 145.94 108.15 1.5439 +IC CB3 CB1 *CB2 H2D 1.5439 108.15 -115.82 109.51 1.1113 +IC H2D CB1 *CB2 H2E 1.1113 109.51 -110.90 114.30 1.1103 +IC OP32 C31 C32 C33 1.4204 114.46 -60.29 108.40 1.5604 +IC C33 C31 *C32 O32 1.5604 108.40 121.34 111.13 1.4494 +IC O32 C31 *C32 H32J 1.4494 111.13 122.24 106.35 1.1110 +IC C31 C32 O32 CC1 1.5293 111.13 68.14 114.89 1.3105 +IC C32 O32 CC1 CC2 1.4494 114.89 176.15 108.12 1.4876 +IC CC2 O32 *CC1 OC1 1.4876 108.12 -170.27 125.63 1.2266 +IC O32 CC1 CC2 CC3 1.3105 108.12 -76.46 108.70 1.5560 +IC CC3 CC1 *CC2 H2R 1.5560 108.70 -122.84 112.77 1.1107 +IC H2R CC1 *CC2 H2S 1.1107 112.77 -123.28 108.97 1.1110 +IC C31 C32 C33 O33 1.5293 108.40 176.96 112.72 1.4640 +IC O33 C32 *C33 H33J 1.4640 112.72 117.22 113.13 1.1108 +IC H33J C32 *C33 H33K 1.1108 113.13 115.83 106.47 1.1118 +IC C32 C33 O33 CD1 1.5604 112.72 -151.26 113.15 1.3113 +IC C33 O33 CD1 CD2 1.4640 113.15 173.25 112.34 1.5319 +IC CD2 O33 *CD1 OD1 1.5319 112.34 -178.05 122.67 1.2242 +IC O33 CD1 CD2 CD3 1.3113 112.34 -38.42 110.46 1.5461 +IC CD3 CD1 *CD2 H2X 1.5461 110.46 -112.49 109.00 1.1104 +IC H2X CD1 *CD2 H2Y 1.1104 109.00 -130.20 111.55 1.1111 +IC CA1 CA2 CA3 CA4 1.5689 106.00 70.58 115.07 1.5306 +IC CA4 CA2 *CA3 H3A 1.5306 115.07 -129.18 107.90 1.1109 +IC H3A CA2 *CA3 H3B 1.1109 107.90 -105.89 101.69 1.1112 +IC CA2 CA3 CA4 CA5 1.5485 115.07 158.69 108.32 1.5834 +IC CA5 CA3 *CA4 H4A 1.5834 108.32 -118.75 108.71 1.1108 +IC H4A CA3 *CA4 H4B 1.1108 108.71 -117.19 107.01 1.1110 +IC CA3 CA4 CA5 CA6 1.5306 108.32 -174.04 108.06 1.5368 +IC CA6 CA4 *CA5 H5A 1.5368 108.06 -118.82 105.90 1.1109 +IC H5A CA4 *CA5 H5B 1.1109 105.90 -121.68 106.09 1.1119 +IC CA4 CA5 CA6 CA7 1.5834 108.06 178.17 110.77 1.5223 +IC CA7 CA5 *CA6 H6A 1.5223 110.77 -132.06 116.95 1.1113 +IC H6A CA5 *CA6 H6B 1.1113 116.95 -112.47 107.63 1.1111 +IC CA5 CA6 CA7 CA8 1.5368 110.77 59.27 117.63 1.4882 +IC CA8 CA6 *CA7 H7A 1.4882 117.63 -118.56 104.37 1.1116 +IC H7A CA6 *CA7 H7B 1.1116 104.37 -114.08 107.73 1.1109 +IC CA6 CA7 CA8 CA9 1.5223 117.63 67.91 107.29 1.5222 +IC CA9 CA7 *CA8 H8A 1.5222 107.29 -124.85 113.63 1.1112 +IC H8A CA7 *CA8 H8B 1.1112 113.63 -117.04 109.09 1.1113 +IC CA7 CA8 CA9 CA10 1.4882 107.29 119.10 123.38 1.3319 +IC CA10 CA8 *CA9 H9A 1.3319 123.38 -177.89 117.11 1.0999 +IC CA8 CA9 CA10 CA11 1.5222 123.38 7.54 131.28 1.5065 +IC CA11 CA9 *CA10 H10A 1.5065 131.28 178.90 115.15 1.0997 +IC CA9 CA10 CA11 CA12 1.3319 131.28 -97.49 113.43 1.5850 +IC CA12 CA10 *CA11 H11A 1.5850 113.43 -130.41 112.16 1.1112 +IC H11A CA10 *CA11 H11B 1.1112 112.16 -109.74 101.87 1.1115 +IC CA10 CA11 CA12 CA13 1.5065 113.43 -173.72 107.65 1.4866 +IC CA13 CA11 *CA12 H12A 1.4866 107.65 -113.01 107.64 1.1113 +IC H12A CA11 *CA12 H12B 1.1113 107.64 -111.93 109.75 1.1111 +IC CA11 CA12 CA13 CA14 1.5850 107.65 -179.34 115.75 1.5000 +IC CA14 CA12 *CA13 H13A 1.5000 115.75 -115.95 103.71 1.1118 +IC H13A CA12 *CA13 H13B 1.1118 103.71 -111.93 109.06 1.1112 +IC CA12 CA13 CA14 CA15 1.4866 115.75 -54.04 114.55 1.5487 +IC CA15 CA13 *CA14 H14A 1.5487 114.55 -122.19 111.44 1.1108 +IC H14A CA13 *CA14 H14B 1.1108 111.44 -116.88 102.67 1.1109 +IC CA13 CA14 CA15 CA16 1.5000 114.55 -74.45 115.60 1.5143 +IC CA16 CA14 *CA15 H15A 1.5143 115.60 -119.98 104.04 1.1105 +IC H15A CA14 *CA15 H15B 1.1105 104.04 -110.62 108.03 1.1111 +IC CA14 CA15 CA16 H16A 1.6032 109.31 69.09 108.47 1.1114 +IC H16A CA15 *CA16 H16B 1.1114 108.47 -133.81 115.46 1.1115 +IC H16A CA15 *CA16 H16C 1.1114 108.47 106.76 112.60 1.1111 +IC CB1 CB2 CB3 CB4 1.4979 108.15 168.84 113.97 1.5414 +IC CB4 CB2 *CB3 H3D 1.5414 113.97 -116.57 109.36 1.1106 +IC H3D CB2 *CB3 H3E 1.1106 109.36 -121.06 112.37 1.1109 +IC CB2 CB3 CB4 CB5 1.5439 113.97 -58.59 116.14 1.5170 +IC CB5 CB3 *CB4 H4D 1.5170 116.14 -125.09 117.26 1.1105 +IC H4D CB3 *CB4 H4E 1.1105 117.26 -121.61 108.92 1.1112 +IC CB3 CB4 CB5 CB6 1.5414 116.14 -78.78 114.35 1.6375 +IC CB6 CB4 *CB5 H5D 1.6375 114.35 -119.75 109.83 1.1112 +IC H5D CB4 *CB5 H5E 1.1112 109.83 -120.87 106.11 1.1121 +IC CB4 CB5 CB6 CB7 1.5170 114.35 -70.16 112.68 1.5227 +IC CB7 CB5 *CB6 H6D 1.5227 112.68 -116.61 103.22 1.1114 +IC H6D CB5 *CB6 H6E 1.1114 103.22 -112.98 111.60 1.1115 +IC CB5 CB6 CB7 CB8 1.6375 112.68 -161.94 110.39 1.5832 +IC CB8 CB6 *CB7 H7D 1.5832 110.39 -124.11 108.30 1.1108 +IC H7D CB6 *CB7 H7E 1.1108 108.30 -115.23 115.05 1.1106 +IC CB6 CB7 CB8 CB9 1.5227 110.39 -90.27 109.83 1.5037 +IC CB9 CB7 *CB8 H8D 1.5037 109.83 -117.18 103.04 1.1116 +IC H8D CB7 *CB8 H8E 1.1116 103.04 -115.48 109.94 1.1108 +IC CB7 CB8 CB9 CB10 1.5832 109.83 -147.27 128.01 1.3511 +IC CB10 CB8 *CB9 H9D 1.3511 128.01 179.43 117.16 1.1000 +IC CB8 CB9 CB10 CB11 1.5037 128.01 -2.70 125.31 1.4853 +IC CB11 CB9 *CB10 H10D 1.4853 125.31 -164.56 115.65 1.1003 +IC CB9 CB10 CB11 CB12 1.3511 125.31 -105.03 114.69 1.5411 +IC CB12 CB10 *CB11 H11D 1.5411 114.69 -123.57 118.03 1.1101 +IC H11D CB10 *CB11 H11E 1.1101 118.03 -117.71 111.56 1.1111 +IC CB10 CB11 CB12 CB13 1.4853 114.69 66.66 113.32 1.5589 +IC CB13 CB11 *CB12 H12D 1.5589 113.32 -114.28 112.33 1.1108 +IC H12D CB11 *CB12 H12E 1.1108 112.33 -130.02 107.65 1.1105 +IC CB11 CB12 CB13 CB14 1.5411 113.32 172.82 117.09 1.5221 +IC CB14 CB12 *CB13 H13D 1.5221 117.09 -121.37 115.12 1.1107 +IC H13D CB12 *CB13 H13E 1.1107 115.12 -120.42 104.48 1.1105 +IC CB12 CB13 CB14 CB15 1.5589 117.09 -56.19 116.78 1.5397 +IC CB15 CB13 *CB14 H14D 1.5397 116.78 -118.05 107.59 1.1115 +IC H14D CB13 *CB14 H14E 1.1115 107.59 -119.10 106.18 1.1112 +IC CB13 CB14 CB15 CB16 1.5221 116.78 -61.27 110.45 1.5107 +IC CB16 CB14 *CB15 H15D 1.5107 110.45 -121.68 109.04 1.1098 +IC H15D CB14 *CB15 H15E 1.1098 109.04 -118.57 112.04 1.1110 +IC CB14 CB15 CB16 H16D 1.5345 114.56 110.74 111.55 1.1108 +IC H16D CB15 *CB16 H16E 1.1108 111.55 -123.62 104.19 1.1101 +IC H16D CB15 *CB16 H16F 1.1108 111.55 121.03 109.64 1.1105 +IC CC1 CC2 CC3 CC4 1.4876 108.70 166.49 115.31 1.5516 +IC CC4 CC2 *CC3 H3R 1.5516 115.31 -122.81 110.40 1.1117 +IC H3R CC2 *CC3 H3S 1.1117 110.40 -108.90 112.78 1.1110 +IC CC2 CC3 CC4 CC5 1.5560 115.31 -58.76 114.09 1.5204 +IC CC5 CC3 *CC4 H4R 1.5204 114.09 -125.99 113.90 1.1108 +IC H4R CC3 *CC4 H4S 1.1108 113.90 -118.25 104.34 1.1112 +IC CC3 CC4 CC5 CC6 1.5516 114.09 -159.82 106.26 1.5455 +IC CC6 CC4 *CC5 H5R 1.5455 106.26 -120.26 113.02 1.1112 +IC H5R CC4 *CC5 H5S 1.1112 113.02 -116.51 107.52 1.1101 +IC CC4 CC5 CC6 CC7 1.5204 106.26 -162.84 115.72 1.5093 +IC CC7 CC5 *CC6 H6R 1.5093 115.72 -125.35 109.33 1.1120 +IC H6R CC5 *CC6 H6S 1.1120 109.33 -115.83 104.84 1.1114 +IC CC5 CC6 CC7 CC8 1.5455 115.72 169.85 115.65 1.5438 +IC CC8 CC6 *CC7 H7R 1.5438 115.65 -119.94 105.61 1.1114 +IC H7R CC6 *CC7 H7S 1.1114 105.61 -109.43 118.03 1.1113 +IC CC6 CC7 CC8 CC9 1.5093 115.65 68.29 114.74 1.4947 +IC CC9 CC7 *CC8 H8R 1.4947 114.74 -125.62 104.10 1.1108 +IC H8R CC7 *CC8 H8S 1.1108 104.10 -104.85 109.88 1.1111 +IC CC7 CC8 CC9 CC10 1.5438 114.74 -94.94 122.44 1.3611 +IC CC10 CC8 *CC9 H9R 1.3611 122.44 178.47 118.28 1.0993 +IC CC8 CC9 CC10 CC11 1.4947 122.44 1.31 128.99 1.5289 +IC CC11 CC9 *CC10 H10R 1.5289 128.99 -171.44 117.81 1.0999 +IC CC9 CC10 CC11 CC12 1.3611 128.99 -117.48 117.23 1.5675 +IC CC12 CC10 *CC11 H11R 1.5675 117.23 133.47 119.59 1.1108 +IC H11R CC10 *CC11 H11S 1.1108 119.59 114.38 108.18 1.1111 +IC CC10 CC11 CC12 CC13 1.5289 117.23 -49.76 118.58 1.4935 +IC CC13 CC11 *CC12 H12R 1.4935 118.58 -124.61 111.80 1.1107 +IC H12R CC11 *CC12 H12S 1.1107 111.80 -118.72 105.83 1.1104 +IC CC11 CC12 CC13 CC14 1.5675 118.58 98.30 113.13 1.5099 +IC CC14 CC12 *CC13 H13R 1.5099 113.13 -122.89 107.50 1.1109 +IC H13R CC12 *CC13 H13S 1.1109 107.50 -117.77 111.05 1.1106 +IC CC12 CC13 CC14 CC15 1.4935 113.13 80.43 108.22 1.4802 +IC CC15 CC13 *CC14 H14R 1.4802 108.22 -129.23 111.33 1.1104 +IC H14R CC13 *CC14 H14S 1.1104 111.33 -110.13 98.50 1.1110 +IC CC13 CC14 CC15 CC16 1.5099 108.22 -167.84 114.83 1.5382 +IC CC16 CC14 *CC15 H15R 1.5382 114.83 120.52 111.86 1.1102 +IC H15R CC14 *CC15 H15S 1.1102 111.86 115.94 109.88 1.1112 +IC CC14 CC15 CC16 H16R 1.4625 116.83 66.76 99.69 1.1108 +IC H16R CC15 *CC16 H16S 1.1108 99.69 -115.88 114.54 1.1107 +IC H16R CC15 *CC16 H16T 1.1108 99.69 118.86 113.91 1.1111 +IC CD1 CD2 CD3 CD4 1.5319 110.46 175.03 113.67 1.6015 +IC CD4 CD2 *CD3 H3X 1.6015 113.67 -120.00 106.80 1.1112 +IC H3X CD2 *CD3 H3Y 1.1112 106.80 -113.48 108.54 1.1113 +IC CD2 CD3 CD4 CD5 1.5461 113.67 -169.91 108.66 1.5690 +IC CD5 CD3 *CD4 H4X 1.5690 108.66 -119.27 105.80 1.1112 +IC H4X CD3 *CD4 H4Y 1.1112 105.80 -120.84 111.26 1.1108 +IC CD3 CD4 CD5 CD6 1.6015 108.66 -178.21 116.73 1.5287 +IC CD6 CD4 *CD5 H5X 1.5287 116.73 -125.69 112.08 1.1102 +IC H5X CD4 *CD5 H5Y 1.1102 112.08 -118.33 106.27 1.1116 +IC CD4 CD5 CD6 CD7 1.5690 116.73 68.59 112.56 1.6088 +IC CD7 CD5 *CD6 H6X 1.6088 112.56 -130.94 112.73 1.1110 +IC H6X CD5 *CD6 H6Y 1.1110 112.73 -116.11 107.23 1.1114 +IC CD5 CD6 CD7 CD8 1.5287 112.56 -176.20 110.80 1.4652 +IC CD8 CD6 *CD7 H7X 1.4652 110.80 -124.79 106.04 1.1106 +IC H7X CD6 *CD7 H7Y 1.1106 106.04 -116.11 113.65 1.1105 +IC CD6 CD7 CD8 CD9 1.6088 110.80 -176.35 117.02 1.4890 +IC CD9 CD7 *CD8 H8X 1.4890 117.02 -130.96 111.56 1.1107 +IC H8X CD7 *CD8 H8Y 1.1107 111.56 -116.19 101.92 1.1105 +IC CD7 CD8 CD9 CD10 1.4652 117.02 -110.91 134.02 1.3183 +IC CD10 CD8 *CD9 H9X 1.3183 134.02 168.17 109.97 1.0999 +IC CD8 CD9 CD10 CD11 1.4890 134.02 -8.00 119.30 1.5217 +IC CD11 CD9 *CD10 H10X 1.5217 119.30 -161.66 119.21 1.1001 +IC CD9 CD10 CD11 CD12 1.3183 119.30 -115.70 121.90 1.5128 +IC CD12 CD10 *CD11 H11X 1.5128 121.90 -115.24 110.72 1.1108 +IC H11X CD10 *CD11 H11Y 1.1108 110.72 -117.48 110.55 1.1107 +IC CD10 CD11 CD12 CD13 1.5217 121.90 176.42 109.32 1.5755 +IC CD13 CD11 *CD12 H12X 1.5755 109.32 -127.73 103.95 1.1110 +IC H12X CD11 *CD12 H12Y 1.1110 103.95 -110.68 112.20 1.1102 +IC CD11 CD12 CD13 CD14 1.5128 109.32 166.83 111.46 1.5220 +IC CD14 CD12 *CD13 H13X 1.5220 111.46 -121.14 113.18 1.1109 +IC H13X CD12 *CD13 H13Y 1.1109 113.18 -118.01 110.96 1.1106 +IC CD12 CD13 CD14 CD15 1.5755 111.46 -61.93 118.37 1.4969 +IC CD15 CD13 *CD14 H14X 1.4969 118.37 -125.51 112.03 1.1107 +IC H14X CD13 *CD14 H14Y 1.1107 112.03 -118.45 109.75 1.1119 +IC CD13 CD14 CD15 CD16 1.5220 118.37 -169.88 114.61 1.5503 +IC CD16 CD14 *CD15 H15X 1.5503 114.61 -118.47 112.81 1.1115 +IC H15X CD14 *CD15 H15Y 1.1115 112.81 -123.12 104.45 1.1109 +IC CD14 CD15 CD16 H16X 1.5367 106.45 178.60 109.03 1.1112 +IC H16X CD15 *CD16 H16Y 1.1112 109.03 -120.60 108.05 1.1107 +IC H16X CD15 *CD16 H16Z 1.1112 109.03 119.06 114.08 1.1116 + +RESI TXCL2 -2.00 ! Tetra-hexadecenoyl Cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 4 C16:1 +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 -0.08 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM H13J HAL2 0.09 ! | | | | +ATOM H13K HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10Y H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12--H12E H12A--CA12--H12B H12X--CD12--H12Y H12R--CC12--H12S +GROUP ! | | | | +ATOM C32 CTL1 0.17 ! H13D--CB13--H13E H13A--CA13--H13B H13X--CD13--H13Y H13R--CC13--H13S +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM CC2 CTL2 -0.22 ! | | | | +ATOM H2R HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H16F H16C H16Z H16T +ATOM C33 CTL2 0.08 ! +ATOM H33J HAL2 0.09 ! +ATOM H33K HAL2 0.09 ! +ATOM O33 OSL -0.49 ! +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL3 -0.27 ! +ATOM H16A HAL3 0.09 ! +ATOM H16B HAL3 0.09 ! +ATOM H16C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CB13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL3 -0.27 ! +ATOM H16D HAL3 0.09 ! +ATOM H16E HAL3 0.09 ! +ATOM H16F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL3 -0.27 ! +ATOM H16R HAL3 0.09 ! +ATOM H16S HAL3 0.09 ! +ATOM H16T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 H16C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 H12E CB12 CB13 +BOND CB13 H13D CB13 H13E CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 H16F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 H16T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 H12Y CD12 CD13 +BOND CD13 H13X CD13 H13Y CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 H16Z +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4633 109.99 126.99 106.69 1.1112 +IC HG31 C2 *C3 HG32 1.1112 106.69 120.70 112.94 1.1110 +IC C2 C3 OP31 P3 1.5211 109.99 154.06 117.47 1.5924 +IC C3 OP31 P3 OP32 1.4633 117.47 66.74 101.68 1.6525 +IC OP32 OP31 *P3 OP33 1.6525 101.68 -113.70 109.39 1.4926 +IC OP32 OP31 *P3 OP34 1.6525 101.68 112.29 106.74 1.4836 +IC OP31 P3 OP32 C31 1.5924 101.68 55.76 110.28 1.4698 +IC P3 OP32 C31 C32 1.6525 110.28 -172.41 110.74 1.5958 +IC C32 OP32 *C31 H31J 1.5958 110.74 116.75 110.82 1.1115 +IC H31J OP32 *C31 H31K 1.1115 110.82 111.29 110.26 1.1103 +IC HG31 C3 C2 C1 1.1112 106.69 -61.74 114.49 1.5241 +IC C1 C3 *C2 OG12 1.5241 114.49 -122.33 108.64 1.4665 +IC C1 C3 *C2 HG22 1.5241 114.49 124.23 104.11 1.1108 +IC C3 C2 OG12 HO12 1.5211 108.64 -38.03 96.97 0.9599 +IC C3 C2 C1 OP11 1.5211 114.49 175.92 108.99 1.3945 +IC OP11 C2 *C1 HG11 1.3945 108.99 -131.04 104.78 1.1106 +IC HG11 C2 *C1 HG12 1.1106 104.78 -113.14 109.09 1.1119 +IC C2 C1 OP11 P1 1.5241 108.99 -84.99 120.20 1.5652 +IC C1 OP11 P1 OP12 1.3945 120.20 -27.24 102.68 1.5816 +IC OP12 OP11 *P1 OP13 1.5816 102.68 118.64 109.06 1.4705 +IC OP12 OP11 *P1 OP14 1.5816 102.68 -114.38 108.43 1.4438 +IC OP11 P1 OP12 C11 1.5652 102.68 -105.08 129.51 1.3844 +IC P1 OP12 C11 C12 1.5816 129.51 79.30 113.33 1.5572 +IC C12 OP12 *C11 H11J 1.5572 113.33 -123.60 109.70 1.1106 +IC H11J OP12 *C11 H11K 1.1106 109.70 -125.75 111.37 1.1111 +IC OP12 C11 C12 C13 1.3844 113.33 172.10 111.92 1.5430 +IC C13 C11 *C12 O12 1.5430 111.92 120.38 106.67 1.4690 +IC O12 C11 *C12 H12J 1.4690 106.67 123.36 105.85 1.1110 +IC C11 C12 O12 CA1 1.5572 106.67 139.57 111.75 1.3546 +IC C12 O12 CA1 CA2 1.4690 111.75 -177.04 105.16 1.4819 +IC CA2 O12 *CA1 OA1 1.4819 105.16 175.26 126.65 1.2359 +IC O12 CA1 CA2 CA3 1.3546 105.16 -166.84 109.95 1.5144 +IC CA3 CA1 *CA2 H2A 1.5144 109.95 -122.50 115.81 1.1105 +IC H2A CA1 *CA2 H2B 1.1105 115.81 -121.44 107.35 1.1109 +IC C11 C12 C13 O13 1.5572 111.92 -172.11 107.78 1.5003 +IC O13 C12 *C13 H13J 1.5003 107.78 -115.91 112.20 1.1109 +IC H13J C12 *C13 H13K 1.1109 112.20 -121.54 112.00 1.1122 +IC C12 C13 O13 CB1 1.5430 107.78 77.67 115.10 1.2970 +IC C13 O13 CB1 CB2 1.5003 115.10 -179.81 109.11 1.4434 +IC CB2 O13 *CB1 OB1 1.4434 109.11 -173.82 130.35 1.2113 +IC O13 CB1 CB2 CB3 1.2970 109.11 173.87 116.83 1.5195 +IC CB3 CB1 *CB2 H2D 1.5195 116.83 -121.03 109.80 1.1112 +IC H2D CB1 *CB2 H2E 1.1112 109.80 -114.30 107.94 1.1107 +IC OP32 C31 C32 C33 1.4698 110.74 -72.15 111.19 1.5682 +IC C33 C31 *C32 O32 1.5682 111.19 124.56 112.11 1.3898 +IC O32 C31 *C32 H32J 1.3898 112.11 122.90 114.56 1.1112 +IC C31 C32 O32 CC1 1.5958 112.11 62.25 119.56 1.3075 +IC C32 O32 CC1 CC2 1.3898 119.56 -174.92 104.05 1.4829 +IC CC2 O32 *CC1 OC1 1.4829 104.05 -166.47 126.62 1.2264 +IC O32 CC1 CC2 CC3 1.3075 104.05 170.64 115.59 1.5435 +IC CC3 CC1 *CC2 H2R 1.5435 115.59 -124.86 107.06 1.1110 +IC H2R CC1 *CC2 H2S 1.1110 107.06 -105.63 111.30 1.1109 +IC C31 C32 C33 O33 1.5958 111.19 -173.79 110.26 1.4370 +IC O33 C32 *C33 H33J 1.4370 110.26 118.41 109.85 1.1107 +IC H33J C32 *C33 H33K 1.1107 109.85 116.35 110.86 1.1105 +IC C32 C33 O33 CD1 1.5682 110.26 -82.05 116.23 1.3711 +IC C33 O33 CD1 CD2 1.4370 116.23 156.92 111.58 1.5654 +IC CD2 O33 *CD1 OD1 1.5654 111.58 -176.12 124.80 1.1850 +IC O33 CD1 CD2 CD3 1.3711 111.58 79.99 113.19 1.5154 +IC CD3 CD1 *CD2 H2X 1.5154 113.19 -122.11 106.99 1.1106 +IC H2X CD1 *CD2 H2Y 1.1106 106.99 -114.65 110.19 1.1109 +IC CA1 CA2 CA3 CA4 1.4819 109.95 160.84 117.75 1.5645 +IC CA4 CA2 *CA3 H3A 1.5645 117.75 -127.81 109.37 1.1111 +IC H3A CA2 *CA3 H3B 1.1111 109.37 -117.63 101.55 1.1105 +IC CA2 CA3 CA4 CA5 1.5144 117.75 157.03 111.41 1.5424 +IC CA5 CA3 *CA4 H4A 1.5424 111.41 -119.03 108.09 1.1114 +IC H4A CA3 *CA4 H4B 1.1114 108.09 -126.38 120.58 1.1101 +IC CA3 CA4 CA5 CA6 1.5645 111.41 74.25 110.88 1.5499 +IC CA6 CA4 *CA5 H5A 1.5499 110.88 -125.89 112.16 1.1114 +IC H5A CA4 *CA5 H5B 1.1114 112.16 -116.89 114.30 1.1106 +IC CA4 CA5 CA6 CA7 1.5424 110.88 177.26 112.07 1.5702 +IC CA7 CA5 *CA6 H6A 1.5702 112.07 -121.41 112.61 1.1107 +IC H6A CA5 *CA6 H6B 1.1107 112.61 -124.17 99.78 1.1108 +IC CA5 CA6 CA7 CA8 1.5499 112.07 74.00 120.92 1.5501 +IC CA8 CA6 *CA7 H7A 1.5501 120.92 -128.07 104.29 1.1105 +IC H7A CA6 *CA7 H7B 1.1105 104.29 -118.23 103.40 1.1112 +IC CA6 CA7 CA8 CA9 1.5702 120.92 170.69 112.79 1.5329 +IC CA9 CA7 *CA8 H8A 1.5329 112.79 -117.60 114.99 1.1111 +IC H8A CA7 *CA8 H8B 1.1111 114.99 -115.64 104.49 1.1114 +IC CA7 CA8 CA9 CA10 1.5501 112.79 82.54 132.44 1.3410 +IC CA10 CA8 *CA9 H9A 1.3410 132.44 -165.92 110.30 1.0996 +IC CA8 CA9 CA10 CA11 1.5329 132.44 11.31 129.79 1.4668 +IC CA11 CA9 *CA10 H10A 1.4668 129.79 173.10 113.82 1.1006 +IC CA9 CA10 CA11 CA12 1.3410 129.79 -125.54 110.53 1.5132 +IC CA12 CA10 *CA11 H11A 1.5132 110.53 -124.22 111.84 1.1109 +IC H11A CA10 *CA11 H11B 1.1109 111.84 -116.05 116.75 1.1107 +IC CA10 CA11 CA12 CA13 1.4668 110.53 161.55 113.19 1.4862 +IC CA13 CA11 *CA12 H12A 1.4862 113.19 -115.99 104.44 1.1104 +IC H12A CA11 *CA12 H12B 1.1104 104.44 -109.05 111.86 1.1114 +IC CA11 CA12 CA13 CA14 1.5132 113.19 66.72 118.43 1.5736 +IC CA14 CA12 *CA13 H13A 1.5736 118.43 -112.65 104.63 1.1114 +IC H13A CA12 *CA13 H13B 1.1114 104.63 -117.70 113.84 1.1109 +IC CA12 CA13 CA14 CA15 1.4862 118.43 62.79 110.33 1.5584 +IC CA15 CA13 *CA14 H14A 1.5584 110.33 -118.07 107.82 1.1108 +IC H14A CA13 *CA14 H14B 1.1108 107.82 -113.03 108.64 1.1112 +IC CA13 CA14 CA15 CA16 1.5736 110.33 -175.93 102.80 1.5814 +IC CA16 CA14 *CA15 H15A 1.5814 102.80 -121.30 114.89 1.1112 +IC H15A CA14 *CA15 H15B 1.1112 114.89 -125.40 120.38 1.1112 +IC CA14 CA15 CA16 H16A 1.4920 114.64 -97.38 116.78 1.1116 +IC H16A CA15 *CA16 H16B 1.1116 116.78 -112.38 110.91 1.1109 +IC H16A CA15 *CA16 H16C 1.1116 116.78 124.13 107.97 1.1105 +IC CB1 CB2 CB3 CB4 1.4434 116.83 -155.75 114.25 1.5868 +IC CB4 CB2 *CB3 H3D 1.5868 114.25 -122.78 114.66 1.1117 +IC H3D CB2 *CB3 H3E 1.1117 114.66 -129.44 120.87 1.1109 +IC CB2 CB3 CB4 CB5 1.5195 114.25 -52.65 114.56 1.5137 +IC CB5 CB3 *CB4 H4D 1.5137 114.56 -115.68 101.27 1.1103 +IC H4D CB3 *CB4 H4E 1.1103 101.27 -119.02 105.41 1.1106 +IC CB3 CB4 CB5 CB6 1.5868 114.56 -179.99 120.50 1.5634 +IC CB6 CB4 *CB5 H5D 1.5634 120.50 -122.72 117.24 1.1113 +IC H5D CB4 *CB5 H5E 1.1113 117.24 -123.34 103.45 1.1107 +IC CB4 CB5 CB6 CB7 1.5137 120.50 39.76 116.61 1.5133 +IC CB7 CB5 *CB6 H6D 1.5133 116.61 -120.56 106.07 1.1110 +IC H6D CB5 *CB6 H6E 1.1110 106.07 -117.54 106.11 1.1114 +IC CB5 CB6 CB7 CB8 1.5634 116.61 176.57 110.49 1.5173 +IC CB8 CB6 *CB7 H7D 1.5173 110.49 -120.73 106.74 1.1106 +IC H7D CB6 *CB7 H7E 1.1106 106.74 -117.79 112.10 1.1106 +IC CB6 CB7 CB8 CB9 1.5133 110.49 -82.21 120.66 1.5172 +IC CB9 CB7 *CB8 H8D 1.5172 120.66 -115.86 108.05 1.1105 +IC H8D CB7 *CB8 H8E 1.1105 108.05 -111.89 111.52 1.1117 +IC CB7 CB8 CB9 CB10 1.5173 120.66 -107.87 126.23 1.3089 +IC CB10 CB8 *CB9 H9D 1.3089 126.23 177.32 108.46 1.0998 +IC CB8 CB9 CB10 CB11 1.5172 126.23 -9.03 129.20 1.5488 +IC CB11 CB9 *CB10 H10D 1.5488 129.20 -177.87 114.84 1.1001 +IC CB9 CB10 CB11 CB12 1.3089 129.20 89.60 118.95 1.5198 +IC CB12 CB10 *CB11 H11D 1.5198 118.95 -127.92 113.12 1.1108 +IC H11D CB10 *CB11 H11E 1.1108 113.12 -116.33 107.89 1.1110 +IC CB10 CB11 CB12 CB13 1.5488 118.95 47.44 108.85 1.4805 +IC CB13 CB11 *CB12 H12D 1.4805 108.85 -124.66 111.86 1.1106 +IC H12D CB11 *CB12 H12E 1.1106 111.86 -115.71 106.95 1.1117 +IC CB11 CB12 CB13 CB14 1.5198 108.85 158.33 114.90 1.5460 +IC CB14 CB12 *CB13 H13D 1.5460 114.90 -122.78 110.67 1.1114 +IC H13D CB12 *CB13 H13E 1.1114 110.67 -118.72 111.28 1.1107 +IC CB12 CB13 CB14 CB15 1.4805 114.90 68.37 114.96 1.5755 +IC CB15 CB13 *CB14 H14D 1.5755 114.96 -127.83 107.96 1.1104 +IC H14D CB13 *CB14 H14E 1.1104 107.96 -116.62 108.21 1.1111 +IC CB13 CB14 CB15 CB16 1.5460 114.96 166.45 117.74 1.5429 +IC CB16 CB14 *CB15 H15D 1.5429 117.74 -122.27 110.71 1.1109 +IC H15D CB14 *CB15 H15E 1.1109 110.71 -117.71 99.91 1.1101 +IC CB14 CB15 CB16 H16D 1.5273 110.28 -159.07 103.32 1.1112 +IC H16D CB15 *CB16 H16E 1.1112 103.32 -120.33 105.93 1.1103 +IC H16D CB15 *CB16 H16F 1.1112 103.32 118.79 110.62 1.1116 +IC CC1 CC2 CC3 CC4 1.4829 115.59 49.93 117.90 1.5366 +IC CC4 CC2 *CC3 H3R 1.5366 117.90 -115.05 111.28 1.1107 +IC H3R CC2 *CC3 H3S 1.1107 111.28 -122.62 109.57 1.1107 +IC CC2 CC3 CC4 CC5 1.5435 117.90 41.42 122.16 1.4856 +IC CC5 CC3 *CC4 H4R 1.4856 122.16 -129.12 107.74 1.1116 +IC H4R CC3 *CC4 H4S 1.1116 107.74 -110.63 106.93 1.1114 +IC CC3 CC4 CC5 CC6 1.5366 122.16 79.03 118.09 1.5779 +IC CC6 CC4 *CC5 H5R 1.5779 118.09 -121.27 111.33 1.1111 +IC H5R CC4 *CC5 H5S 1.1111 111.33 -121.85 103.83 1.1116 +IC CC4 CC5 CC6 CC7 1.4856 118.09 -175.62 114.14 1.5193 +IC CC7 CC5 *CC6 H6R 1.5193 114.14 -112.92 99.65 1.1104 +IC H6R CC5 *CC6 H6S 1.1104 99.65 -115.34 114.89 1.1110 +IC CC5 CC6 CC7 CC8 1.5779 114.14 86.04 111.08 1.5443 +IC CC8 CC6 *CC7 H7R 1.5443 111.08 -126.84 118.56 1.1115 +IC H7R CC6 *CC7 H7S 1.1115 118.56 -116.67 107.70 1.1111 +IC CC6 CC7 CC8 CC9 1.5193 111.08 -167.74 113.25 1.5955 +IC CC9 CC7 *CC8 H8R 1.5955 113.25 -126.88 111.16 1.1113 +IC H8R CC7 *CC8 H8S 1.1113 111.16 -113.40 107.96 1.1105 +IC CC7 CC8 CC9 CC10 1.5443 113.25 -109.87 126.39 1.3527 +IC CC10 CC8 *CC9 H9R 1.3527 126.39 -170.92 110.56 1.0998 +IC CC8 CC9 CC10 CC11 1.5955 126.39 15.86 128.70 1.4629 +IC CC11 CC9 *CC10 H10R 1.4629 128.70 175.07 123.34 1.1002 +IC CC9 CC10 CC11 CC12 1.3527 128.70 101.47 118.70 1.5861 +IC CC12 CC10 *CC11 H11R 1.5861 118.70 -125.10 109.20 1.1112 +IC H11R CC10 *CC11 H11S 1.1112 109.20 -110.25 111.88 1.1101 +IC CC10 CC11 CC12 CC13 1.4629 118.70 67.74 108.82 1.5353 +IC CC13 CC11 *CC12 H12R 1.5353 108.82 -126.41 105.67 1.1103 +IC H12R CC11 *CC12 H12S 1.1103 105.67 -116.13 112.54 1.1110 +IC CC11 CC12 CC13 CC14 1.5861 108.82 -177.19 124.76 1.5291 +IC CC14 CC12 *CC13 H13R 1.5291 124.76 -126.31 102.56 1.1109 +IC H13R CC12 *CC13 H13S 1.1109 102.56 -101.72 109.52 1.1110 +IC CC12 CC13 CC14 CC15 1.5353 124.76 -147.35 108.06 1.5835 +IC CC15 CC13 *CC14 H14R 1.5835 108.06 -127.34 119.98 1.1117 +IC H14R CC13 *CC14 H14S 1.1117 119.98 -118.05 109.10 1.1109 +IC CC13 CC14 CC15 CC16 1.5291 108.06 78.94 118.04 1.5648 +IC CC16 CC14 *CC15 H15R 1.5648 118.04 -130.95 115.54 1.1114 +IC H15R CC14 *CC15 H15S 1.1114 115.54 -107.98 103.32 1.1109 +IC CC14 CC15 CC16 H16R 1.5605 113.48 -167.53 105.19 1.1114 +IC H16R CC15 *CC16 H16S 1.1114 105.19 123.30 114.77 1.1107 +IC H16R CC15 *CC16 H16T 1.1114 105.19 -120.49 105.29 1.1117 +IC CD1 CD2 CD3 CD4 1.5654 113.19 -162.40 114.80 1.5512 +IC CD4 CD2 *CD3 H3X 1.5512 114.80 -117.81 118.26 1.1102 +IC H3X CD2 *CD3 H3Y 1.1102 118.26 -125.60 110.95 1.1112 +IC CD2 CD3 CD4 CD5 1.5154 114.80 63.81 109.67 1.6095 +IC CD5 CD3 *CD4 H4X 1.6095 109.67 -112.22 109.63 1.1107 +IC H4X CD3 *CD4 H4Y 1.1107 109.63 -120.86 110.95 1.1109 +IC CD3 CD4 CD5 CD6 1.5512 109.67 -171.66 110.10 1.5117 +IC CD6 CD4 *CD5 H5X 1.5117 110.10 -113.98 105.23 1.1108 +IC H5X CD4 *CD5 H5Y 1.1108 105.23 -128.80 116.89 1.1106 +IC CD4 CD5 CD6 CD7 1.6095 110.10 170.09 111.04 1.5055 +IC CD7 CD5 *CD6 H6X 1.5055 111.04 -114.76 105.35 1.1116 +IC H6X CD5 *CD6 H6Y 1.1116 105.35 -122.63 110.38 1.1108 +IC CD5 CD6 CD7 CD8 1.5117 111.04 -172.02 115.71 1.5289 +IC CD8 CD6 *CD7 H7X 1.5289 115.71 -123.94 114.68 1.1110 +IC H7X CD6 *CD7 H7Y 1.1110 114.68 -126.78 107.85 1.1109 +IC CD6 CD7 CD8 CD9 1.5055 115.71 -61.83 117.36 1.5186 +IC CD9 CD7 *CD8 H8X 1.5186 117.36 -129.63 101.79 1.1109 +IC H8X CD7 *CD8 H8Y 1.1109 101.79 -111.91 105.86 1.1107 +IC CD7 CD8 CD9 CD10 1.5289 117.36 179.97 120.32 1.3356 +IC CD10 CD8 *CD9 H9X 1.3356 120.32 -177.34 116.78 1.1009 +IC CD8 CD9 CD10 CD11 1.5186 120.32 -9.60 131.58 1.4710 +IC CD11 CD9 *CD10 H10X 1.4710 131.58 -172.61 113.16 1.1005 +IC CD9 CD10 CD11 CD12 1.3356 131.58 -124.79 115.05 1.5361 +IC CD12 CD10 *CD11 H11X 1.5361 115.05 -128.95 111.59 1.1111 +IC H11X CD10 *CD11 H11Y 1.1111 111.59 -111.21 111.18 1.1111 +IC CD10 CD11 CD12 CD13 1.4710 115.05 -77.11 105.04 1.4788 +IC CD13 CD11 *CD12 H12X 1.4788 105.04 -112.96 106.48 1.1110 +IC H12X CD11 *CD12 H12Y 1.1110 106.48 -120.99 113.58 1.1114 +IC CD11 CD12 CD13 CD14 1.5361 105.04 168.60 110.84 1.5429 +IC CD14 CD12 *CD13 H13X 1.5429 110.84 -122.83 114.36 1.1104 +IC H13X CD12 *CD13 H13Y 1.1104 114.36 -113.84 114.06 1.1110 +IC CD12 CD13 CD14 CD15 1.4788 110.84 -80.22 114.95 1.5099 +IC CD15 CD13 *CD14 H14X 1.5099 114.95 -125.08 104.06 1.1112 +IC H14X CD13 *CD14 H14Y 1.1112 104.06 -114.53 108.61 1.1117 +IC CD13 CD14 CD15 CD16 1.5429 114.95 173.02 110.69 1.5313 +IC CD16 CD14 *CD15 H15X 1.5313 110.69 -123.13 108.31 1.1109 +IC H15X CD14 *CD15 H15Y 1.1109 108.31 -110.71 116.76 1.1116 +IC CD14 CD15 CD16 H16X 1.5367 106.45 178.60 109.03 1.1112 +IC H16X CD15 *CD16 H16Y 1.1112 109.03 -120.60 108.05 1.1107 +IC H16X CD15 *CD16 H16Z 1.1112 109.03 119.06 114.08 1.1116 + +RESI LOACL1 -1.00 ! 3 Linoleic acid + 1 oleic acid cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 3 linoleoly + 1 oleoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12 H12A--CA12--H12B H12X--CD12 H12R--CC12 +ATOM H2E HAL2 0.09 ! || | || || +GROUP ! || | || || +ATOM C32 CTL1 0.17 ! H13D--CB13 H13A--CA13--H13B H13X--CD13 H13R--CC13 +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM CC2 CTL2 -0.22 ! | | | | +ATOM H2R HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18F H18C H18Z H18T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4272 111.57 124.87 107.78 1.1169 +IC HG31 C2 *C3 HG32 1.1169 107.78 115.89 109.04 1.1124 +IC C2 C3 OP31 P3 1.5483 111.57 118.08 122.98 1.5819 +IC C3 OP31 P3 OP32 1.4272 122.98 37.85 102.14 1.5830 +IC OP32 OP31 *P3 OP33 1.5830 102.14 -113.92 107.98 1.4793 +IC OP32 OP31 *P3 OP34 1.5830 102.14 115.66 109.62 1.4740 +IC OP31 P3 OP32 C31 1.5819 102.14 69.85 119.33 1.4301 +IC P3 OP32 C31 C32 1.5830 119.33 176.40 110.18 1.5529 +IC C32 OP32 *C31 H31J 1.5529 110.18 120.82 110.67 1.1139 +IC H31J OP32 *C31 H31K 1.1139 110.67 119.45 110.95 1.1159 +IC HG31 C3 C2 C1 1.1169 107.78 60.13 113.14 1.5594 +IC C1 C3 *C2 OG12 1.5594 113.14 -122.65 107.36 1.4314 +IC C1 C3 *C2 HG22 1.5594 113.14 119.50 108.81 1.1137 +IC C3 C2 OG12 HO12 1.5483 107.36 -59.74 104.73 0.9611 +IC C3 C2 C1 OP11 1.5483 113.14 102.14 111.29 1.4365 +IC OP11 C2 *C1 HG11 1.4365 111.29 -124.72 105.61 1.1191 +IC HG11 C2 *C1 HG12 1.1191 105.61 -115.38 108.40 1.1138 +IC C2 C1 OP11 P1 1.5594 111.29 -157.61 115.85 1.5685 +IC C1 OP11 P1 OP12 1.4365 115.85 -14.21 104.93 1.5653 +IC OP12 OP11 *P1 OP13 1.5653 104.93 115.00 111.23 1.5595 +IC OP12 OP11 *P1 OP14 1.5653 104.93 -120.71 114.44 1.4714 +IC OP11 P1 OP13 HP13 1.5685 111.23 -49.71 108.79 0.9805 +IC OP11 P1 OP12 C11 1.5685 104.93 168.45 117.56 1.4279 +IC P1 OP12 C11 C12 1.5653 117.56 -104.42 112.05 1.5631 +IC C12 OP12 *C11 H11J 1.5631 112.05 -116.94 106.96 1.1115 +IC H11J OP12 *C11 H11K 1.1115 106.96 -117.70 114.83 1.1174 +IC OP12 C11 C12 C13 1.4279 112.05 -169.61 110.60 1.5613 +IC C13 C11 *C12 O12 1.5613 110.60 124.16 109.17 1.4428 +IC O12 C11 *C12 H12J 1.4428 109.17 118.13 106.49 1.1175 +IC C11 C12 O12 CA1 1.5631 109.17 161.88 113.49 1.3343 +IC C12 O12 CA1 CA2 1.4428 113.49 -169.35 108.84 1.5280 +IC CA2 O12 *CA1 OA1 1.5280 108.84 179.80 125.17 1.2183 +IC O12 CA1 CA2 CA3 1.3343 108.84 -146.40 113.25 1.5456 +IC CA3 CA1 *CA2 H2A 1.5456 113.25 -119.97 106.28 1.1109 +IC H2A CA1 *CA2 H2B 1.1109 106.28 -116.75 108.94 1.1073 +IC C11 C12 C13 O13 1.5631 110.60 48.04 111.75 1.4444 +IC O13 C12 *C13 H13J 1.4444 111.75 -117.92 106.48 1.1131 +IC H13J C12 *C13 H13K 1.1131 106.48 -115.07 111.40 1.1131 +IC C12 C13 O13 CB1 1.5613 111.75 88.82 115.87 1.3297 +IC C13 O13 CB1 CB2 1.4444 115.87 -174.80 108.56 1.5287 +IC CB2 O13 *CB1 OB1 1.5287 108.56 -178.49 126.34 1.2145 +IC O13 CB1 CB2 CB3 1.3297 108.56 152.47 112.16 1.5454 +IC CB3 CB1 *CB2 H2D 1.5454 112.16 -121.52 108.74 1.1089 +IC H2D CB1 *CB2 H2E 1.1089 108.74 -117.40 106.94 1.1083 +IC OP32 C31 C32 C33 1.4301 110.18 -69.33 110.65 1.5522 +IC C33 C31 *C32 O32 1.5522 110.65 120.01 111.21 1.4395 +IC O32 C31 *C32 H32J 1.4395 111.21 122.30 108.97 1.1146 +IC C31 C32 O32 CC1 1.5529 111.21 69.31 115.35 1.3120 +IC C32 O32 CC1 CC2 1.4395 115.35 -171.71 108.60 1.5297 +IC CC2 O32 *CC1 OC1 1.5297 108.60 -178.02 126.78 1.2186 +IC O32 CC1 CC2 CC3 1.3120 108.60 -59.72 112.33 1.5489 +IC CC3 CC1 *CC2 H2R 1.5489 112.33 -122.26 107.83 1.1075 +IC H2R CC1 *CC2 H2S 1.1075 107.83 -116.44 106.39 1.1097 +IC C31 C32 C33 O33 1.5529 110.65 179.11 109.99 1.4464 +IC O33 C32 *C33 H33J 1.4464 109.99 121.93 109.29 1.1119 +IC H33J C32 *C33 H33K 1.1119 109.29 116.57 106.09 1.1186 +IC C32 C33 O33 CD1 1.5522 109.99 -159.03 114.19 1.3237 +IC C33 O33 CD1 CD2 1.4464 114.19 164.21 109.32 1.5286 +IC CD2 O33 *CD1 OD1 1.5286 109.32 -178.45 126.02 1.2156 +IC O33 CD1 CD2 CD3 1.3237 109.32 -46.26 112.24 1.5470 +IC CD3 CD1 *CD2 H2X 1.5470 112.24 -120.21 106.48 1.1100 +IC H2X CD1 *CD2 H2Y 1.1100 106.48 -117.13 108.41 1.1069 +IC CA1 CA2 CA3 CA4 1.5280 113.25 70.18 112.81 1.5346 +IC CA4 CA2 *CA3 H3A 1.5346 112.81 -123.14 110.14 1.1142 +IC H3A CA2 *CA3 H3B 1.1142 110.14 -116.66 107.70 1.1125 +IC CA2 CA3 CA4 CA5 1.5456 112.81 172.40 112.79 1.5353 +IC CA5 CA3 *CA4 H4A 1.5353 112.79 -122.05 109.90 1.1116 +IC H4A CA3 *CA4 H4B 1.1116 109.90 -117.14 108.37 1.1150 +IC CA3 CA4 CA5 CA6 1.5346 112.79 167.30 112.42 1.5358 +IC CA6 CA4 *CA5 H5A 1.5358 112.42 -120.63 108.10 1.1132 +IC H5A CA4 *CA5 H5B 1.1132 108.10 -117.30 109.47 1.1120 +IC CA4 CA5 CA6 CA7 1.5353 112.42 177.91 114.45 1.5409 +IC CA7 CA5 *CA6 H6A 1.5409 114.45 -121.60 108.84 1.1121 +IC H6A CA5 *CA6 H6B 1.1121 108.84 -116.16 108.48 1.1134 +IC CA5 CA6 CA7 CA8 1.5358 114.45 53.66 115.58 1.5440 +IC CA8 CA6 *CA7 H7A 1.5440 115.58 -121.63 108.47 1.1138 +IC H7A CA6 *CA7 H7B 1.1138 108.47 -116.24 108.32 1.1141 +IC CA6 CA7 CA8 CA9 1.5409 115.58 55.01 112.73 1.5097 +IC CA9 CA7 *CA8 H8A 1.5097 112.73 -121.48 108.57 1.1114 +IC H8A CA7 *CA8 H8B 1.1114 108.57 -114.55 107.55 1.1126 +IC CA7 CA8 CA9 CA10 1.5440 112.73 109.39 127.97 1.3474 +IC CA10 CA8 *CA9 H9A 1.3474 127.97 -179.15 113.83 1.1025 +IC CA8 CA9 CA10 CA11 1.5097 127.97 0.64 127.89 1.5108 +IC CA11 CA9 *CA10 H10A 1.5108 127.89 179.31 117.75 1.1014 +IC CA9 CA10 CA11 CA12 1.3474 127.89 -112.95 111.22 1.5114 +IC CA12 CA10 *CA11 H11A 1.5114 111.22 -120.46 108.90 1.1119 +IC H11A CA10 *CA11 H11B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA10 CA11 CA12 CA13 1.5108 111.22 134.57 126.37 1.3465 +IC CA13 CA11 *CA12 H12A 1.3465 126.37 -177.01 115.27 1.1018 +IC H12A CA11 *CA12 H12B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA11 CA12 CA13 CA14 1.5114 126.37 3.15 126.32 1.5077 +IC CA14 CA12 *CA13 H13A 1.5077 126.32 178.37 118.79 1.1003 +IC H13A CA12 *CA13 H13B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA12 CA13 CA14 CA15 1.3465 126.32 -92.58 113.47 1.5417 +IC CA15 CA13 *CA14 H14A 1.5417 113.47 -122.01 110.01 1.1123 +IC H14A CA13 *CA14 H14B 1.1123 110.01 -116.77 110.38 1.1120 +IC CA13 CA14 CA15 CA16 1.5077 113.47 -63.55 113.58 1.5369 +IC CA16 CA14 *CA15 H15A 1.5369 113.58 -120.33 108.08 1.1132 +IC H15A CA14 *CA15 H15B 1.1132 108.08 -116.59 109.36 1.1132 +IC CA14 CA15 CA16 CA17 1.5417 113.58 -171.21 113.87 1.5374 +IC CA17 CA15 *CA16 H16A 1.5374 113.87 -121.70 108.87 1.1122 +IC H16A CA15 *CA16 H16B 1.1122 108.87 -117.00 108.72 1.1132 +IC CA15 CA16 CA17 CA18 1.5369 113.87 -61.57 114.41 1.5314 +IC CA18 CA16 *CA17 H17A 1.5314 114.41 -121.26 108.12 1.1148 +IC H17A CA16 *CA17 H17B 1.1148 108.12 -116.30 108.76 1.1136 +IC CA16 CA17 CA18 H18A 1.5374 114.41 63.53 110.93 1.1107 +IC H18A CA17 *CA18 H18B 1.1107 110.93 -119.76 110.34 1.1109 +IC H18A CA17 *CA18 H18C 1.1107 110.93 120.37 110.77 1.1100 +IC CB1 CB2 CB3 CB4 1.5287 112.16 178.44 113.36 1.5384 +IC CB4 CB2 *CB3 H3D 1.5384 113.36 -122.28 109.76 1.1140 +IC H3D CB2 *CB3 H3E 1.1140 109.76 -116.69 109.13 1.1151 +IC CB2 CB3 CB4 CB5 1.5454 113.36 -60.74 115.02 1.5414 +IC CB5 CB3 *CB4 H4D 1.5414 115.02 -121.57 108.33 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 108.33 -116.10 108.96 1.1133 +IC CB3 CB4 CB5 CB6 1.5384 115.02 -51.86 114.89 1.5394 +IC CB6 CB4 *CB5 H5D 1.5394 114.89 -121.74 108.45 1.1137 +IC H5D CB4 *CB5 H5E 1.1137 108.45 -116.35 108.99 1.1129 +IC CB4 CB5 CB6 CB7 1.5414 114.89 -57.34 113.83 1.5380 +IC CB7 CB5 *CB6 H6D 1.5380 113.83 -121.31 108.98 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.98 -116.37 108.87 1.1123 +IC CB5 CB6 CB7 CB8 1.5394 113.83 179.71 113.63 1.5423 +IC CB8 CB6 *CB7 H7D 1.5423 113.63 -122.27 109.89 1.1123 +IC H7D CB6 *CB7 H7E 1.1123 109.89 -116.77 108.48 1.1132 +IC CB6 CB7 CB8 CB9 1.5380 113.63 -63.29 112.23 1.5093 +IC CB9 CB7 *CB8 H8D 1.5093 112.23 -120.64 107.87 1.1133 +IC H8D CB7 *CB8 H8E 1.1133 107.87 -115.67 108.05 1.1129 +IC CB7 CB8 CB9 CB10 1.5423 112.23 148.17 126.47 1.3460 +IC CB10 CB8 *CB9 H9D 1.3460 126.47 -177.74 114.82 1.1018 +IC CB8 CB9 CB10 CB11 1.5093 126.47 2.77 126.58 1.5092 +IC CB11 CB9 *CB10 H10D 1.5092 126.58 177.26 118.57 1.1029 +IC CB9 CB10 CB11 CB12 1.3460 126.58 -116.82 111.69 1.5096 +IC CB12 CB10 *CB11 H11D 1.5096 111.69 -123.10 108.54 1.1115 +IC H11D CB10 *CB11 H11E 1.1115 108.54 -114.79 111.63 1.1116 +IC CB10 CB11 CB12 CB13 1.5092 111.69 -110.56 126.32 1.3473 +IC CB13 CB11 *CB12 H12D 1.3473 126.32 -178.41 114.77 1.1018 +IC CB11 CB12 CB13 CB14 1.5096 126.32 2.04 125.85 1.5088 +IC CB14 CB12 *CB13 H13D 1.5088 125.85 179.17 118.99 1.1012 +IC CB12 CB13 CB14 CB15 1.3473 125.85 -89.20 112.98 1.5413 +IC CB15 CB13 *CB14 H14D 1.5413 112.98 -121.97 110.15 1.1124 +IC H14D CB13 *CB14 H14E 1.1124 110.15 -116.85 110.43 1.1140 +IC CB13 CB14 CB15 CB16 1.5088 112.98 -66.02 113.67 1.5362 +IC CB16 CB14 *CB15 H15D 1.5362 113.67 -120.47 108.54 1.1134 +IC H15D CB14 *CB15 H15E 1.1134 108.54 -116.71 109.67 1.1135 +IC CB14 CB15 CB16 CB17 1.5413 113.67 -176.61 112.48 1.5339 +IC CB17 CB15 *CB16 H16D 1.5339 112.48 -121.15 109.47 1.1130 +IC H16D CB15 *CB16 H16E 1.1130 109.47 -117.68 109.15 1.1130 +IC CB15 CB16 CB17 CB18 1.5362 112.48 -179.94 113.24 1.5308 +IC CB18 CB16 *CB17 H17D 1.5308 113.24 -121.73 108.82 1.1141 +IC H17D CB16 *CB17 H17E 1.1141 108.82 -116.64 108.69 1.1143 +IC CB16 CB17 CB18 H18D 1.5339 113.24 59.88 110.45 1.1114 +IC H18D CB17 *CB18 H18E 1.1114 110.45 -119.87 110.50 1.1113 +IC H18D CB17 *CB18 H18F 1.1114 110.45 120.03 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5297 112.33 172.47 113.86 1.5361 +IC CC4 CC2 *CC3 H3R 1.5361 113.86 -119.64 108.94 1.1154 +IC H3R CC2 *CC3 H3S 1.1154 108.94 -117.39 109.77 1.1130 +IC CC2 CC3 CC4 CC5 1.5489 113.86 -56.98 112.74 1.5347 +IC CC5 CC3 *CC4 H4R 1.5347 112.74 -119.98 107.98 1.1143 +IC H4R CC3 *CC4 H4S 1.1143 107.98 -117.33 110.39 1.1120 +IC CC3 CC4 CC5 CC6 1.5361 112.74 -154.31 113.28 1.5321 +IC CC6 CC4 *CC5 H5R 1.5321 113.28 -123.53 109.65 1.1125 +IC H5R CC4 *CC5 H5S 1.1125 109.65 -117.22 108.68 1.1132 +IC CC4 CC5 CC6 CC7 1.5347 113.28 -174.72 112.18 1.5360 +IC CC7 CC5 *CC6 H6R 1.5360 112.18 -120.78 108.11 1.1141 +IC H6R CC5 *CC6 H6S 1.1141 108.11 -117.38 110.00 1.1122 +IC CC5 CC6 CC7 CC8 1.5321 112.18 -168.49 113.32 1.5408 +IC CC8 CC6 *CC7 H7R 1.5408 113.32 -121.00 108.07 1.1137 +IC H7R CC6 *CC7 H7S 1.1137 108.07 -116.02 109.54 1.1140 +IC CC6 CC7 CC8 CC9 1.5360 113.32 72.57 111.65 1.5102 +IC CC9 CC7 *CC8 H8R 1.5102 111.65 -124.76 108.23 1.1117 +IC H8R CC7 *CC8 H8S 1.1117 108.23 -115.30 107.95 1.1119 +IC CC7 CC8 CC9 CC10 1.5408 111.65 -134.06 127.67 1.3478 +IC CC10 CC8 *CC9 H9R 1.3478 127.67 179.52 113.97 1.1023 +IC CC8 CC9 CC10 CC11 1.5102 127.67 -0.03 127.34 1.5115 +IC CC11 CC9 *CC10 H10R 1.5115 127.34 179.73 118.07 1.1026 +IC CC9 CC10 CC11 CC12 1.3478 127.34 129.05 112.32 1.5099 +IC CC12 CC10 *CC11 H11R 1.5099 112.32 -123.72 111.60 1.1114 +IC H11R CC10 *CC11 H11S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC10 CC11 CC12 CC13 1.5115 112.32 -84.97 126.59 1.3471 +IC CC13 CC11 *CC12 H12R 1.3471 126.59 -179.05 114.79 1.1010 +IC CC11 CC12 CC13 CC14 1.5099 126.59 1.41 126.41 1.5090 +IC CC14 CC12 *CC13 H13R 1.5090 126.41 178.45 118.70 1.0998 +IC CC12 CC13 CC14 CC15 1.3471 126.41 -125.27 113.39 1.5418 +IC CC15 CC13 *CC14 H14R 1.5418 113.39 -121.44 109.86 1.1131 +IC H14R CC13 *CC14 H14S 1.1131 109.86 -117.22 111.11 1.1131 +IC CC13 CC14 CC15 CC16 1.5090 113.39 -68.63 113.68 1.5381 +IC CC16 CC14 *CC15 H15R 1.5381 113.68 123.30 109.83 1.1129 +IC H15R CC14 *CC15 H15S 1.1129 109.83 116.45 107.53 1.1136 +IC CC14 CC15 CC16 CC17 1.5418 113.68 179.76 113.73 1.5374 +IC CC17 CC15 *CC16 H16R 1.5374 113.73 121.83 108.95 1.1128 +IC H16R CC15 *CC16 H16S 1.1128 108.95 117.24 109.15 1.1127 +IC CC15 CC16 CC17 CC18 1.5381 113.73 63.65 114.54 1.5322 +IC CC18 CC16 *CC17 H17R 1.5322 114.54 -122.47 108.69 1.1141 +IC H17R CC16 *CC17 H17S 1.1141 108.69 -116.13 108.22 1.1148 +IC CC16 CC17 CC18 H18R 1.5374 114.54 56.61 110.47 1.1112 +IC H18R CC17 *CC18 H18S 1.1112 110.47 -120.21 110.86 1.1107 +IC H18R CC17 *CC18 H18T 1.1112 110.47 119.94 110.49 1.1113 +IC CD1 CD2 CD3 CD4 1.5286 112.24 -168.50 113.06 1.5318 +IC CD4 CD2 *CD3 H3X 1.5318 113.06 -122.94 109.98 1.1137 +IC H3X CD2 *CD3 H3Y 1.1137 109.98 -117.36 109.14 1.1136 +IC CD2 CD3 CD4 CD5 1.5470 113.06 175.61 111.87 1.5362 +IC CD5 CD3 *CD4 H4X 1.5362 111.87 -120.66 108.60 1.1128 +IC H4X CD3 *CD4 H4Y 1.1128 108.60 -117.59 109.56 1.1124 +IC CD3 CD4 CD5 CD6 1.5318 111.87 177.84 113.59 1.5356 +IC CD6 CD4 *CD5 H5X 1.5356 113.59 -121.15 108.45 1.1137 +IC H5X CD4 *CD5 H5Y 1.1137 108.45 -116.84 109.16 1.1138 +IC CD4 CD5 CD6 CD7 1.5362 113.59 67.64 113.35 1.5355 +IC CD7 CD5 *CD6 H6X 1.5355 113.35 -122.12 109.12 1.1128 +IC H6X CD5 *CD6 H6Y 1.1128 109.12 -117.25 108.81 1.1134 +IC CD5 CD6 CD7 CD8 1.5356 113.35 -178.50 112.28 1.5389 +IC CD8 CD6 *CD7 H7X 1.5389 112.28 -122.16 108.88 1.1140 +IC H7X CD6 *CD7 H7Y 1.1140 108.88 -116.95 109.16 1.1134 +IC CD6 CD7 CD8 CD9 1.5355 112.28 179.01 111.42 1.5083 +IC CD9 CD7 *CD8 H8X 1.5083 111.42 -122.39 108.26 1.1135 +IC H8X CD7 *CD8 H8Y 1.1135 108.26 -115.32 109.05 1.1118 +IC CD7 CD8 CD9 CD10 1.5389 111.42 -84.39 125.66 1.3464 +IC CD10 CD8 *CD9 H9X 1.3464 125.66 178.86 115.42 1.1011 +IC CD8 CD9 CD10 CD11 1.5083 125.66 0.74 126.41 1.5100 +IC CD11 CD9 *CD10 H10X 1.5100 126.41 178.33 118.71 1.1020 +IC CD9 CD10 CD11 CD12 1.3464 126.41 -119.11 111.66 1.5104 +IC CD12 CD10 *CD11 H11X 1.5104 111.66 -123.67 108.55 1.1120 +IC H11X CD10 *CD11 H11Y 1.1120 108.55 -114.62 111.55 1.1120 +IC CD10 CD11 CD12 CD13 1.5100 111.66 -113.81 126.72 1.3477 +IC CD13 CD11 *CD12 H12X 1.3477 126.72 -178.56 114.59 1.1018 +IC CD11 CD12 CD13 CD14 1.5104 126.72 1.66 126.19 1.5088 +IC CD14 CD12 *CD13 H13X 1.5088 126.19 179.37 118.90 1.1014 +IC CD12 CD13 CD14 CD15 1.3477 126.19 -100.76 112.41 1.5405 +IC CD15 CD13 *CD14 H14X 1.5405 112.41 -121.85 109.83 1.1118 +IC H14X CD13 *CD14 H14Y 1.1118 109.83 -117.23 111.23 1.1116 +IC CD13 CD14 CD15 CD16 1.5088 112.41 170.52 113.29 1.5388 +IC CD16 CD14 *CD15 H15X 1.5388 113.29 -119.71 109.05 1.1153 +IC H15X CD14 *CD15 H15Y 1.1153 109.05 -117.72 109.78 1.1127 +IC CD14 CD15 CD16 CD17 1.5405 113.29 62.69 114.08 1.5347 +IC CD17 CD15 *CD16 H16X 1.5347 114.08 -121.99 108.89 1.1132 +IC H16X CD15 *CD16 H16Y 1.1132 108.89 -116.64 108.76 1.1136 +IC CD15 CD16 CD17 CD18 1.5388 114.08 179.88 112.98 1.5311 +IC CD18 CD16 *CD17 H17X 1.5311 112.98 -121.76 108.79 1.1137 +IC H17X CD16 *CD17 H17Y 1.1137 108.79 -117.11 109.38 1.1133 +IC CD16 CD17 CD18 H18X 1.5347 112.98 60.79 110.28 1.1118 +IC H18X CD17 *CD18 H18Y 1.1118 110.28 -119.90 110.57 1.1110 +IC H18X CD17 *CD18 H18Z 1.1118 110.28 119.81 110.63 1.1110 + +RESI LOACL2 -2.00 ! 3 linoleoic acid + 1 oleic acid chain, Cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 3 linoleoly chains + 1 oleoyl chain (chain A, sn-2) +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12 H12A--CA12--H12B H12X--CD12 H12R--CC12 +GROUP ! || | || || +ATOM C32 CTL1 0.17 ! || | || || +ATOM H32J HAL1 0.09 ! H13D--CB13 H13A--CA13--H13B H13X--CD13 H13R--CC13 +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM H2R HAL2 0.09 ! | | | | +ATOM H2S HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +GROUP ! | | | | +ATOM C33 CTL2 0.08 ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM H33J HAL2 0.09 ! | | | | +ATOM H33K HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM O33 OSL -0.49 ! | | | | +ATOM CD1 CL 0.90 ! H18F H18C H18Z H18T +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CTL2 -0.18 ! +ATOM H12A HAL2 0.09 ! +ATOM H12B HAL2 0.09 ! +GROUP ! +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 !! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 H12B CA12 CA13 +BOND CA13 H13A CA13 H13B CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +! IC TABLE +! +! +! IC TABLE +! +IC OP31 C2 *C3 HG31 1.4399 111.73 121.27 107.98 1.1140 +IC HG31 C2 *C3 HG32 1.1140 107.98 116.42 107.18 1.1169 +IC C2 C3 OP31 P3 1.5535 111.73 -167.54 118.79 1.5904 +IC C3 OP31 P3 OP32 1.4399 118.79 79.71 101.55 1.5890 +IC OP32 OP31 *P3 OP33 1.5890 101.55 -115.28 110.31 1.4782 +IC OP32 OP31 *P3 OP34 1.5890 101.55 113.65 109.35 1.4797 +IC OP31 P3 OP32 C31 1.5904 101.55 67.83 117.77 1.4329 +IC P3 OP32 C31 C32 1.5890 117.77 -170.90 110.66 1.5522 +IC C32 OP32 *C31 H31J 1.5522 110.66 121.35 111.65 1.1158 +IC H31J OP32 *C31 H31K 1.1158 111.65 119.36 109.77 1.1144 +IC HG31 C3 C2 C1 1.1140 107.98 -59.84 112.53 1.5592 +IC C1 C3 *C2 OG12 1.5592 112.53 -122.28 106.17 1.4219 +IC C1 C3 *C2 HG22 1.5592 112.53 120.07 108.81 1.1138 +IC C3 C2 OG12 HO12 1.5535 106.17 -43.83 99.95 0.9654 +IC C3 C2 C1 OP11 1.5535 112.53 172.59 114.00 1.4374 +IC OP11 C2 *C1 HG11 1.4374 114.00 -124.71 107.54 1.1153 +IC HG11 C2 *C1 HG12 1.1153 107.54 -114.53 107.04 1.1121 +IC C2 C1 OP11 P1 1.5592 114.00 -97.83 122.51 1.5864 +IC C1 OP11 P1 OP12 1.4374 122.51 -52.87 102.45 1.5913 +IC OP12 OP11 *P1 OP13 1.5913 102.45 114.70 110.17 1.4774 +IC OP12 OP11 *P1 OP14 1.5913 102.45 -115.08 109.36 1.4815 +IC OP11 P1 OP12 C11 1.5864 102.45 -92.52 122.70 1.4285 +IC P1 OP12 C11 C12 1.5913 122.70 85.68 111.92 1.5508 +IC C12 OP12 *C11 H11J 1.5508 111.92 -123.87 112.24 1.1149 +IC H11J OP12 *C11 H11K 1.1149 112.24 -117.66 107.38 1.1110 +IC OP12 C11 C12 C13 1.4285 111.92 161.41 112.21 1.5554 +IC C13 C11 *C12 O12 1.5554 112.21 119.92 107.58 1.4348 +IC O12 C11 *C12 H12J 1.4348 107.58 121.23 105.93 1.1177 +IC C11 C12 O12 CA1 1.5508 107.58 139.57 115.43 1.3169 +IC C12 O12 CA1 CA2 1.4348 115.43 -169.02 109.20 1.5307 +IC CA2 O12 *CA1 OA1 1.5307 109.20 -177.29 125.89 1.2210 +IC O12 CA1 CA2 CA3 1.3169 109.20 -125.27 111.98 1.5453 +IC CA3 CA1 *CA2 H2A 1.5453 111.98 -121.72 106.70 1.1104 +IC H2A CA1 *CA2 H2B 1.1104 106.70 -115.79 108.58 1.1093 +IC C11 C12 C13 O13 1.5508 112.21 -165.73 111.20 1.4484 +IC O13 C12 *C13 H13J 1.4484 111.20 -119.38 107.07 1.1127 +IC H13J C12 *C13 H13K 1.1127 107.07 -115.20 109.28 1.1141 +IC C12 C13 O13 CB1 1.5554 111.20 86.74 113.94 1.3304 +IC C13 O13 CB1 CB2 1.4484 113.94 -157.19 109.85 1.5285 +IC CB2 O13 *CB1 OB1 1.5285 109.85 179.45 125.30 1.2183 +IC O13 CB1 CB2 CB3 1.3304 109.85 170.02 112.02 1.5483 +IC CB3 CB1 *CB2 H2D 1.5483 112.02 -119.03 106.46 1.1119 +IC H2D CB1 *CB2 H2E 1.1119 106.46 -117.11 109.11 1.1053 +IC OP32 C31 C32 C33 1.4329 110.66 -55.34 111.30 1.5520 +IC C33 C31 *C32 O32 1.5520 111.30 121.41 110.58 1.4400 +IC O32 C31 *C32 H32J 1.4400 110.58 121.80 108.53 1.1157 +IC C31 C32 O32 CC1 1.5522 110.58 76.00 113.72 1.3241 +IC C32 O32 CC1 CC2 1.4400 113.72 -175.40 107.92 1.5290 +IC CC2 O32 *CC1 OC1 1.5290 107.92 -174.97 125.21 1.2214 +IC O32 CC1 CC2 CC3 1.3241 107.92 -171.64 114.45 1.5483 +IC CC3 CC1 *CC2 H2R 1.5483 114.45 -120.08 106.50 1.1125 +IC H2R CC1 *CC2 H2S 1.1125 106.50 -115.84 108.14 1.1062 +IC C31 C32 C33 O33 1.5522 111.30 178.27 110.32 1.4463 +IC O33 C32 *C33 H33J 1.4463 110.32 122.56 108.16 1.1137 +IC H33J C32 *C33 H33K 1.1137 108.16 116.60 107.22 1.1149 +IC C32 C33 O33 CD1 1.5520 110.32 176.92 114.52 1.3194 +IC C33 O33 CD1 CD2 1.4463 114.52 169.48 108.39 1.5307 +IC CD2 O33 *CD1 OD1 1.5307 108.39 179.86 126.25 1.2174 +IC O33 CD1 CD2 CD3 1.3194 108.39 166.29 113.39 1.5479 +IC CD3 CD1 *CD2 H2X 1.5479 113.39 -122.94 107.91 1.1081 +IC H2X CD1 *CD2 H2Y 1.1081 107.91 -116.24 106.59 1.1103 +IC CA1 CA2 CA3 CA4 1.5307 111.98 174.09 112.77 1.5340 +IC CA4 CA2 *CA3 H3A 1.5340 112.77 -121.48 109.27 1.1128 +IC H3A CA2 *CA3 H3B 1.1128 109.27 -117.62 108.80 1.1132 +IC CA2 CA3 CA4 CA5 1.5453 112.77 176.67 112.97 1.5369 +IC CA5 CA3 *CA4 H4A 1.5369 112.97 -120.43 108.08 1.1146 +IC H4A CA3 *CA4 H4B 1.1146 108.08 -116.67 109.58 1.1123 +IC CA3 CA4 CA5 CA6 1.5340 112.97 69.98 113.98 1.5366 +IC CA6 CA4 *CA5 H5A 1.5366 113.98 -122.10 108.41 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 108.41 -116.88 108.64 1.1132 +IC CA4 CA5 CA6 CA7 1.5369 113.98 177.62 113.05 1.5384 +IC CA7 CA5 *CA6 H6A 1.5384 113.05 -120.54 108.00 1.1138 +IC H6A CA5 *CA6 H6B 1.1138 108.00 -117.16 109.92 1.1119 +IC CA5 CA6 CA7 CA8 1.5366 113.05 72.32 113.20 1.5409 +IC CA8 CA6 *CA7 H7A 1.5409 113.20 -122.31 108.58 1.1140 +IC H7A CA6 *CA7 H7B 1.1140 108.58 -116.70 108.43 1.1139 +IC CA6 CA7 CA8 CA9 1.5384 113.20 -177.88 111.67 1.5104 +IC CA9 CA7 *CA8 H8A 1.5104 111.67 -121.51 108.57 1.1127 +IC H8A CA7 *CA8 H8B 1.1127 108.57 -114.68 108.68 1.1109 +IC CA7 CA8 CA9 CA10 1.5409 111.67 106.92 126.93 1.3485 +IC CA10 CA8 *CA9 H9A 1.3485 126.93 179.93 114.52 1.1012 +IC CA8 CA9 CA10 CA11 1.5104 126.93 -0.98 126.94 1.5114 +IC CA11 CA9 *CA10 H10A 1.5114 126.94 -179.25 118.31 1.1017 +IC CA9 CA10 CA11 CA12 1.3485 126.94 -125.33 111.90 1.5094 +IC CA12 CA10 *CA11 H11A 1.5094 111.90 -120.91 109.22 1.1122 +IC H11A CA10 *CA11 H11B 1.1122 109.22 -115.26 111.36 1.1089 +IC CA10 CA11 CA12 CA13 1.5114 111.90 103.75 127.05 1.3481 +IC CA13 CA11 *CA12 H12A 1.3481 127.05 -178.55 114.54 1.1015 +IC CA13 CA11 *CA12 H12B 1.3481 127.05 -178.55 114.54 1.1015 +IC CA11 CA12 CA13 CA14 1.5094 127.05 -1.51 127.29 1.5104 +IC CA14 CA12 *CA13 H13A 1.5104 127.29 -178.83 118.45 1.1012 +IC CA14 CA12 *CA13 H13B 1.5104 127.29 -178.83 118.45 1.1012 +IC CA12 CA13 CA14 CA15 1.3481 127.29 123.19 111.92 1.5400 +IC CA15 CA13 *CA14 H14A 1.5400 111.92 -122.30 112.60 1.1129 +IC H14A CA13 *CA14 H14B 1.1129 112.60 -117.91 109.33 1.1129 +IC CA13 CA14 CA15 CA16 1.5104 111.92 172.46 112.42 1.5358 +IC CA16 CA14 *CA15 H15A 1.5358 112.42 -120.26 109.74 1.1138 +IC H15A CA14 *CA15 H15B 1.1138 109.74 -118.26 109.67 1.1136 +IC CA14 CA15 CA16 CA17 1.5400 112.42 -176.77 112.71 1.5339 +IC CA17 CA15 *CA16 H16A 1.5339 112.71 -121.51 109.43 1.1130 +IC H16A CA15 *CA16 H16B 1.1130 109.43 -117.43 109.11 1.1131 +IC CA15 CA16 CA17 CA18 1.5358 112.71 177.47 113.22 1.5311 +IC CA18 CA16 *CA17 H17A 1.5311 113.22 -121.64 108.92 1.1137 +IC H17A CA16 *CA17 H17B 1.1137 108.92 -116.79 108.72 1.1143 +IC CA16 CA17 CA18 H18A 1.5339 113.22 -60.64 110.64 1.1108 +IC H18A CA17 *CA18 H18B 1.1108 110.64 -120.38 110.71 1.1111 +IC H18A CA17 *CA18 H18C 1.1108 110.64 119.78 110.63 1.1119 +IC CB1 CB2 CB3 CB4 1.5285 112.02 -156.49 113.16 1.5352 +IC CB4 CB2 *CB3 H3D 1.5352 113.16 -125.26 110.81 1.1108 +IC H3D CB2 *CB3 H3E 1.1108 110.81 -117.62 108.58 1.1185 +IC CB2 CB3 CB4 CB5 1.5483 113.16 -72.87 114.64 1.5362 +IC CB5 CB3 *CB4 H4D 1.5362 114.64 -121.50 107.87 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 107.87 -115.68 108.33 1.1133 +IC CB3 CB4 CB5 CB6 1.5352 114.64 173.14 113.35 1.5409 +IC CB6 CB4 *CB5 H5D 1.5409 113.35 -120.91 109.12 1.1130 +IC H5D CB4 *CB5 H5E 1.1130 109.12 -117.35 108.69 1.1125 +IC CB4 CB5 CB6 CB7 1.5362 113.35 52.82 114.03 1.5378 +IC CB7 CB5 *CB6 H6D 1.5378 114.03 -120.64 108.65 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.65 -116.83 109.17 1.1121 +IC CB5 CB6 CB7 CB8 1.5409 114.03 179.98 112.81 1.5400 +IC CB8 CB6 *CB7 H7D 1.5400 112.81 -122.98 109.09 1.1121 +IC H7D CB6 *CB7 H7E 1.1121 109.09 -117.53 108.71 1.1155 +IC CB6 CB7 CB8 CB9 1.5378 112.81 177.49 110.85 1.5102 +IC CB9 CB7 *CB8 H8D 1.5102 110.85 -122.35 107.23 1.1140 +IC H8D CB7 *CB8 H8E 1.1140 107.23 -115.61 109.26 1.1115 +IC CB7 CB8 CB9 CB10 1.5400 110.85 -111.54 126.68 1.3485 +IC CB10 CB8 *CB9 H9D 1.3485 126.68 176.66 114.61 1.1007 +IC CB8 CB9 CB10 CB11 1.5102 126.68 -2.77 127.04 1.5103 +IC CB11 CB9 *CB10 H10D 1.5103 127.04 -178.65 118.60 1.1012 +IC CB9 CB10 CB11 CB12 1.3485 127.04 96.60 112.31 1.5135 +IC CB12 CB10 *CB11 H11D 1.5135 112.31 -125.47 110.37 1.1105 +IC H11D CB10 *CB11 H11E 1.1105 110.37 -114.37 108.83 1.1122 +IC CB10 CB11 CB12 CB13 1.5103 112.31 -123.24 127.49 1.3487 +IC CB13 CB11 *CB12 H12D 1.3487 127.49 -179.18 114.92 1.1025 +IC CB11 CB12 CB13 CB14 1.5135 127.49 0.10 127.26 1.5079 +IC CB14 CB12 *CB13 H13D 1.5079 127.26 -179.25 118.69 1.1053 +IC CB12 CB13 CB14 CB15 1.3487 127.26 123.97 111.98 1.5384 +IC CB15 CB13 *CB14 H14D 1.5384 111.98 -120.79 111.90 1.1093 +IC H14D CB13 *CB14 H14E 1.1093 111.90 -118.90 109.68 1.1138 +IC CB13 CB14 CB15 CB16 1.5079 111.98 -173.48 111.85 1.5348 +IC CB16 CB14 *CB15 H15D 1.5348 111.85 -121.68 109.78 1.1147 +IC H15D CB14 *CB15 H15E 1.1147 109.78 -117.79 109.28 1.1119 +IC CB14 CB15 CB16 CB17 1.5384 111.85 179.99 113.35 1.5313 +IC CB17 CB15 *CB16 H16D 1.5313 113.35 -121.42 108.85 1.1101 +IC H16D CB15 *CB16 H16E 1.1101 108.85 -117.19 108.74 1.1110 +IC CB15 CB16 CB17 CB18 1.5348 113.35 -178.76 113.12 1.5314 +IC CB18 CB16 *CB17 H17D 1.5314 113.12 -121.82 108.25 1.1149 +IC H17D CB16 *CB17 H17E 1.1149 108.25 -115.96 109.19 1.1126 +IC CB16 CB17 CB18 H18D 1.5313 113.12 -178.27 110.36 1.1112 +IC H18D CB17 *CB18 H18E 1.1112 110.36 -120.53 110.61 1.1103 +IC H18D CB17 *CB18 H18F 1.1112 110.36 119.56 110.21 1.1112 +IC CC1 CC2 CC3 CC4 1.5290 114.45 61.17 115.54 1.5407 +IC CC4 CC2 *CC3 H3R 1.5407 115.54 -123.39 108.81 1.1159 +IC H3R CC2 *CC3 H3S 1.1159 108.81 -115.09 107.30 1.1128 +IC CC2 CC3 CC4 CC5 1.5483 115.54 48.75 115.70 1.5381 +IC CC5 CC3 *CC4 H4R 1.5381 115.70 -121.95 108.35 1.1141 +IC H4R CC3 *CC4 H4S 1.1141 108.35 -115.67 107.88 1.1118 +IC CC3 CC4 CC5 CC6 1.5407 115.70 59.37 113.26 1.5339 +IC CC6 CC4 *CC5 H5R 1.5339 113.26 -122.42 108.68 1.1122 +IC H5R CC4 *CC5 H5S 1.1122 108.68 -116.61 108.64 1.1128 +IC CC4 CC5 CC6 CC7 1.5381 113.26 175.46 114.41 1.5382 +IC CC7 CC5 *CC6 H6R 1.5382 114.41 -121.44 108.39 1.1118 +IC H6R CC5 *CC6 H6S 1.1118 108.39 -116.44 108.77 1.1127 +IC CC5 CC6 CC7 CC8 1.5339 114.41 50.21 113.91 1.5402 +IC CC8 CC6 *CC7 H7R 1.5402 113.91 -122.10 108.87 1.1136 +IC H7R CC6 *CC7 H7S 1.1136 108.87 -116.44 107.40 1.1147 +IC CC6 CC7 CC8 CC9 1.5382 113.91 171.45 111.26 1.5090 +IC CC9 CC7 *CC8 H8R 1.5090 111.26 -123.76 107.81 1.1114 +IC H8R CC7 *CC8 H8S 1.1114 107.81 -115.28 108.84 1.1122 +IC CC7 CC8 CC9 CC10 1.5402 111.26 -128.36 127.23 1.3472 +IC CC10 CC8 *CC9 H9R 1.3472 127.23 178.70 114.30 1.1010 +IC CC8 CC9 CC10 CC11 1.5090 127.23 -1.15 127.54 1.5084 +IC CC11 CC9 *CC10 H10R 1.5084 127.54 -179.59 118.30 1.1015 +IC CC9 CC10 CC11 CC12 1.3472 127.54 121.83 111.08 1.5090 +IC CC12 CC10 *CC11 H11R 1.5090 111.08 -121.38 111.45 1.1092 +IC H11R CC10 *CC11 H11S 1.1092 111.45 -115.12 108.94 1.1091 +IC CC10 CC11 CC12 CC13 1.5084 111.08 114.57 127.61 1.3469 +IC CC13 CC11 *CC12 H12R 1.3469 127.61 179.18 114.07 1.1019 +IC CC11 CC12 CC13 CC14 1.5090 127.61 -1.12 127.24 1.5089 +IC CC14 CC12 *CC13 H13R 1.5089 127.24 -179.24 118.36 1.1008 +IC CC12 CC13 CC14 CC15 1.3469 127.24 -127.92 112.49 1.5415 +IC CC15 CC13 *CC14 H14R 1.5415 112.49 -120.38 109.34 1.1135 +IC H14R CC13 *CC14 H14S 1.1135 109.34 -118.08 112.29 1.1108 +IC CC13 CC14 CC15 CC16 1.5089 112.49 64.28 113.82 1.5372 +IC CC16 CC14 *CC15 H15R 1.5372 113.82 -123.02 109.95 1.1128 +IC H15R CC14 *CC15 H15S 1.1128 109.95 -116.79 108.08 1.1141 +IC CC14 CC15 CC16 CC17 1.5415 113.82 175.12 112.35 1.5342 +IC CC17 CC15 *CC16 H16R 1.5342 112.35 121.44 109.60 1.1127 +IC H16R CC15 *CC16 H16S 1.1127 109.60 117.48 109.22 1.1130 +IC CC15 CC16 CC17 CC18 1.5372 112.35 177.84 113.41 1.5303 +IC CC18 CC16 *CC17 H17R 1.5303 113.41 -121.68 108.79 1.1140 +IC H17R CC16 *CC17 H17S 1.1140 108.79 -116.65 108.60 1.1141 +IC CC16 CC17 CC18 H18R 1.5342 113.41 177.41 110.78 1.1108 +IC H18R CC17 *CC18 H18S 1.1108 110.78 120.14 110.47 1.1110 +IC H18R CC17 *CC18 H18T 1.1108 110.78 -120.28 110.55 1.1114 +IC CD1 CD2 CD3 CD4 1.5307 113.39 169.15 112.93 1.5372 +IC CD4 CD2 *CD3 H3X 1.5372 112.93 -120.02 109.25 1.1156 +IC H3X CD2 *CD3 H3Y 1.1156 109.25 -117.49 109.59 1.1130 +IC CD2 CD3 CD4 CD5 1.5479 112.93 59.54 113.85 1.5360 +IC CD5 CD3 *CD4 H4X 1.5360 113.85 -121.33 108.32 1.1134 +IC H4X CD3 *CD4 H4Y 1.1134 108.32 -116.71 109.15 1.1132 +IC CD3 CD4 CD5 CD6 1.5372 113.85 -177.43 112.79 1.5357 +IC CD6 CD4 *CD5 H5X 1.5357 112.79 -122.43 109.70 1.1122 +IC H5X CD4 *CD5 H5Y 1.1122 109.70 -117.86 109.15 1.1139 +IC CD4 CD5 CD6 CD7 1.5360 112.79 173.65 112.21 1.5365 +IC CD7 CD5 *CD6 H6X 1.5365 112.21 -119.39 108.19 1.1136 +IC H6X CD5 *CD6 H6Y 1.1136 108.19 -117.35 110.05 1.1111 +IC CD5 CD6 CD7 CD8 1.5357 112.21 -164.07 113.53 1.5412 +IC CD8 CD6 *CD7 H7X 1.5412 113.53 -125.12 110.25 1.1118 +IC H7X CD6 *CD7 H7Y 1.1118 110.25 -116.30 107.52 1.1152 +IC CD6 CD7 CD8 CD9 1.5365 113.53 -72.33 113.26 1.5081 +IC CD9 CD7 *CD8 H8X 1.5081 113.26 -123.64 107.20 1.1122 +IC H8X CD7 *CD8 H8Y 1.1122 107.20 -114.54 108.43 1.1124 +IC CD7 CD8 CD9 CD10 1.5412 113.26 -141.33 126.38 1.3479 +IC CD10 CD8 *CD9 H9X 1.3479 126.38 -179.10 114.78 1.1010 +IC CD8 CD9 CD10 CD11 1.5081 126.38 0.12 126.84 1.5114 +IC CD11 CD9 *CD10 H10X 1.5114 126.84 -179.87 118.43 1.1016 +IC CD9 CD10 CD11 CD12 1.3479 126.84 -106.33 111.23 1.5105 +IC CD12 CD10 *CD11 H11X 1.5105 111.23 -120.37 109.03 1.1122 +IC H11X CD10 *CD11 H11Y 1.1122 109.03 -114.91 111.58 1.1099 +IC CD10 CD11 CD12 CD13 1.5114 111.23 109.38 127.41 1.3486 +IC CD13 CD11 *CD12 H12X 1.3486 127.41 179.19 114.40 1.1015 +IC CD11 CD12 CD13 CD14 1.5105 127.41 -1.41 127.65 1.5109 +IC CD14 CD12 *CD13 H13X 1.5109 127.65 -178.15 118.24 1.1012 +IC CD12 CD13 CD14 CD15 1.3486 127.65 -115.93 111.19 1.5399 +IC CD15 CD13 *CD14 H14X 1.5399 111.19 -120.10 109.72 1.1126 +IC H14X CD13 *CD14 H14Y 1.1126 109.72 -118.73 112.54 1.1122 +IC CD13 CD14 CD15 CD16 1.5109 111.19 -174.42 112.98 1.5354 +IC CD16 CD14 *CD15 H15X 1.5354 112.98 -121.07 109.22 1.1143 +IC H15X CD14 *CD15 H15Y 1.1143 109.22 -117.98 109.91 1.1138 +IC CD14 CD15 CD16 CD17 1.5399 112.98 179.46 112.15 1.5344 +IC CD17 CD15 *CD16 H16X 1.5344 112.15 -121.15 109.44 1.1128 +IC H16X CD15 *CD16 H16Y 1.1128 109.44 -117.66 109.26 1.1126 +IC CD15 CD16 CD17 CD18 1.5354 112.15 179.70 113.67 1.5310 +IC CD18 CD16 *CD17 H17X 1.5310 113.67 -121.71 108.44 1.1139 +IC H17X CD16 *CD17 H17Y 1.1139 108.44 -116.35 108.83 1.1138 +IC CD16 CD17 CD18 H18X 1.5344 113.67 -178.87 110.70 1.1108 +IC H18X CD17 *CD18 H18Y 1.1108 110.70 -120.14 110.59 1.1104 +IC H18X CD17 *CD18 H18Z 1.1108 110.70 119.96 110.62 1.1117 + +RESI LOCCL1 -1.00 ! 3 Linoleic acid + 1 oleic acid Cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 3 linoleoyl + 1 oleoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12--H12S +ATOM H2E HAL2 0.09 ! || || || | +GROUP ! || || || | +ATOM C32 CTL1 0.17 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13--H13S +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM CC2 CTL2 -0.22 ! | | | | +ATOM H2R HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18F H18C H18Z H18T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4272 111.57 124.87 107.78 1.1169 +IC HG31 C2 *C3 HG32 1.1169 107.78 115.89 109.04 1.1124 +IC C2 C3 OP31 P3 1.5483 111.57 118.08 122.98 1.5819 +IC C3 OP31 P3 OP32 1.4272 122.98 37.85 102.14 1.5830 +IC OP32 OP31 *P3 OP33 1.5830 102.14 -113.92 107.98 1.4793 +IC OP32 OP31 *P3 OP34 1.5830 102.14 115.66 109.62 1.4740 +IC OP31 P3 OP32 C31 1.5819 102.14 69.85 119.33 1.4301 +IC P3 OP32 C31 C32 1.5830 119.33 176.40 110.18 1.5529 +IC C32 OP32 *C31 H31J 1.5529 110.18 120.82 110.67 1.1139 +IC H31J OP32 *C31 H31K 1.1139 110.67 119.45 110.95 1.1159 +IC HG31 C3 C2 C1 1.1169 107.78 60.13 113.14 1.5594 +IC C1 C3 *C2 OG12 1.5594 113.14 -122.65 107.36 1.4314 +IC C1 C3 *C2 HG22 1.5594 113.14 119.50 108.81 1.1137 +IC C3 C2 OG12 HO12 1.5483 107.36 -59.74 104.73 0.9611 +IC C3 C2 C1 OP11 1.5483 113.14 102.14 111.29 1.4365 +IC OP11 C2 *C1 HG11 1.4365 111.29 -124.72 105.61 1.1191 +IC HG11 C2 *C1 HG12 1.1191 105.61 -115.38 108.40 1.1138 +IC C2 C1 OP11 P1 1.5594 111.29 -157.61 115.85 1.5685 +IC C1 OP11 P1 OP12 1.4365 115.85 -14.21 104.93 1.5653 +IC OP12 OP11 *P1 OP13 1.5653 104.93 115.00 111.23 1.5595 +IC OP12 OP11 *P1 OP14 1.5653 104.93 -120.71 114.44 1.4714 +IC OP11 P1 OP13 HP13 1.5685 111.23 -49.71 108.79 0.9805 +IC OP11 P1 OP12 C11 1.5685 104.93 168.45 117.56 1.4279 +IC P1 OP12 C11 C12 1.5653 117.56 -104.42 112.05 1.5631 +IC C12 OP12 *C11 H11J 1.5631 112.05 -116.94 106.96 1.1115 +IC H11J OP12 *C11 H11K 1.1115 106.96 -117.70 114.83 1.1174 +IC OP12 C11 C12 C13 1.4279 112.05 -169.61 110.60 1.5613 +IC C13 C11 *C12 O12 1.5613 110.60 124.16 109.17 1.4428 +IC O12 C11 *C12 H12J 1.4428 109.17 118.13 106.49 1.1175 +IC C11 C12 O12 CA1 1.5631 109.17 161.88 113.49 1.3343 +IC C12 O12 CA1 CA2 1.4428 113.49 -169.35 108.84 1.5280 +IC CA2 O12 *CA1 OA1 1.5280 108.84 179.80 125.17 1.2183 +IC O12 CA1 CA2 CA3 1.3343 108.84 -146.40 113.25 1.5456 +IC CA3 CA1 *CA2 H2A 1.5456 113.25 -119.97 106.28 1.1109 +IC H2A CA1 *CA2 H2B 1.1109 106.28 -116.75 108.94 1.1073 +IC C11 C12 C13 O13 1.5631 110.60 48.04 111.75 1.4444 +IC O13 C12 *C13 H13J 1.4444 111.75 -117.92 106.48 1.1131 +IC H13J C12 *C13 H13K 1.1131 106.48 -115.07 111.40 1.1131 +IC C12 C13 O13 CB1 1.5613 111.75 88.82 115.87 1.3297 +IC C13 O13 CB1 CB2 1.4444 115.87 -174.80 108.56 1.5287 +IC CB2 O13 *CB1 OB1 1.5287 108.56 -178.49 126.34 1.2145 +IC O13 CB1 CB2 CB3 1.3297 108.56 152.47 112.16 1.5454 +IC CB3 CB1 *CB2 H2D 1.5454 112.16 -121.52 108.74 1.1089 +IC H2D CB1 *CB2 H2E 1.1089 108.74 -117.40 106.94 1.1083 +IC OP32 C31 C32 C33 1.4301 110.18 -69.33 110.65 1.5522 +IC C33 C31 *C32 O32 1.5522 110.65 120.01 111.21 1.4395 +IC O32 C31 *C32 H32J 1.4395 111.21 122.30 108.97 1.1146 +IC C31 C32 O32 CC1 1.5529 111.21 69.31 115.35 1.3120 +IC C32 O32 CC1 CC2 1.4395 115.35 -171.71 108.60 1.5297 +IC CC2 O32 *CC1 OC1 1.5297 108.60 -178.02 126.78 1.2186 +IC O32 CC1 CC2 CC3 1.3120 108.60 -59.72 112.33 1.5489 +IC CC3 CC1 *CC2 H2R 1.5489 112.33 -122.26 107.83 1.1075 +IC H2R CC1 *CC2 H2S 1.1075 107.83 -116.44 106.39 1.1097 +IC C31 C32 C33 O33 1.5529 110.65 179.11 109.99 1.4464 +IC O33 C32 *C33 H33J 1.4464 109.99 121.93 109.29 1.1119 +IC H33J C32 *C33 H33K 1.1119 109.29 116.57 106.09 1.1186 +IC C32 C33 O33 CD1 1.5522 109.99 -159.03 114.19 1.3237 +IC C33 O33 CD1 CD2 1.4464 114.19 164.21 109.32 1.5286 +IC CD2 O33 *CD1 OD1 1.5286 109.32 -178.45 126.02 1.2156 +IC O33 CD1 CD2 CD3 1.3237 109.32 -46.26 112.24 1.5470 +IC CD3 CD1 *CD2 H2X 1.5470 112.24 -120.21 106.48 1.1100 +IC H2X CD1 *CD2 H2Y 1.1100 106.48 -117.13 108.41 1.1069 +IC CA1 CA2 CA3 CA4 1.5280 113.25 70.18 112.81 1.5346 +IC CA4 CA2 *CA3 H3A 1.5346 112.81 -123.14 110.14 1.1142 +IC H3A CA2 *CA3 H3B 1.1142 110.14 -116.66 107.70 1.1125 +IC CA2 CA3 CA4 CA5 1.5456 112.81 172.40 112.79 1.5353 +IC CA5 CA3 *CA4 H4A 1.5353 112.79 -122.05 109.90 1.1116 +IC H4A CA3 *CA4 H4B 1.1116 109.90 -117.14 108.37 1.1150 +IC CA3 CA4 CA5 CA6 1.5346 112.79 167.30 112.42 1.5358 +IC CA6 CA4 *CA5 H5A 1.5358 112.42 -120.63 108.10 1.1132 +IC H5A CA4 *CA5 H5B 1.1132 108.10 -117.30 109.47 1.1120 +IC CA4 CA5 CA6 CA7 1.5353 112.42 177.91 114.45 1.5409 +IC CA7 CA5 *CA6 H6A 1.5409 114.45 -121.60 108.84 1.1121 +IC H6A CA5 *CA6 H6B 1.1121 108.84 -116.16 108.48 1.1134 +IC CA5 CA6 CA7 CA8 1.5358 114.45 53.66 115.58 1.5440 +IC CA8 CA6 *CA7 H7A 1.5440 115.58 -121.63 108.47 1.1138 +IC H7A CA6 *CA7 H7B 1.1138 108.47 -116.24 108.32 1.1141 +IC CA6 CA7 CA8 CA9 1.5409 115.58 55.01 112.73 1.5097 +IC CA9 CA7 *CA8 H8A 1.5097 112.73 -121.48 108.57 1.1114 +IC H8A CA7 *CA8 H8B 1.1114 108.57 -114.55 107.55 1.1126 +IC CA7 CA8 CA9 CA10 1.5440 112.73 109.39 127.97 1.3474 +IC CA10 CA8 *CA9 H9A 1.3474 127.97 -179.15 113.83 1.1025 +IC CA8 CA9 CA10 CA11 1.5097 127.97 0.64 127.89 1.5108 +IC CA11 CA9 *CA10 H10A 1.5108 127.89 179.31 117.75 1.1014 +IC CA9 CA10 CA11 CA12 1.3474 127.89 -112.95 111.22 1.5114 +IC CA12 CA10 *CA11 H11A 1.5114 111.22 -120.46 108.90 1.1119 +IC H11A CA10 *CA11 H11B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA10 CA11 CA12 CA13 1.5108 111.22 134.57 126.37 1.3465 +IC CA13 CA11 *CA12 H12A 1.3465 126.37 -177.01 115.27 1.1018 +IC CA11 CA12 CA13 CA14 1.5114 126.37 3.15 126.32 1.5077 +IC CA14 CA12 *CA13 H13A 1.5077 126.32 178.37 118.79 1.1003 +IC CA12 CA13 CA14 CA15 1.3465 126.32 -92.58 113.47 1.5417 +IC CA15 CA13 *CA14 H14A 1.5417 113.47 -122.01 110.01 1.1123 +IC H14A CA13 *CA14 H14B 1.1123 110.01 -116.77 110.38 1.1120 +IC CA13 CA14 CA15 CA16 1.5077 113.47 -63.55 113.58 1.5369 +IC CA16 CA14 *CA15 H15A 1.5369 113.58 -120.33 108.08 1.1132 +IC H15A CA14 *CA15 H15B 1.1132 108.08 -116.59 109.36 1.1132 +IC CA14 CA15 CA16 CA17 1.5417 113.58 -171.21 113.87 1.5374 +IC CA17 CA15 *CA16 H16A 1.5374 113.87 -121.70 108.87 1.1122 +IC H16A CA15 *CA16 H16B 1.1122 108.87 -117.00 108.72 1.1132 +IC CA15 CA16 CA17 CA18 1.5369 113.87 -61.57 114.41 1.5314 +IC CA18 CA16 *CA17 H17A 1.5314 114.41 -121.26 108.12 1.1148 +IC H17A CA16 *CA17 H17B 1.1148 108.12 -116.30 108.76 1.1136 +IC CA16 CA17 CA18 H18A 1.5374 114.41 63.53 110.93 1.1107 +IC H18A CA17 *CA18 H18B 1.1107 110.93 -119.76 110.34 1.1109 +IC H18A CA17 *CA18 H18C 1.1107 110.93 120.37 110.77 1.1100 +IC CB1 CB2 CB3 CB4 1.5287 112.16 178.44 113.36 1.5384 +IC CB4 CB2 *CB3 H3D 1.5384 113.36 -122.28 109.76 1.1140 +IC H3D CB2 *CB3 H3E 1.1140 109.76 -116.69 109.13 1.1151 +IC CB2 CB3 CB4 CB5 1.5454 113.36 -60.74 115.02 1.5414 +IC CB5 CB3 *CB4 H4D 1.5414 115.02 -121.57 108.33 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 108.33 -116.10 108.96 1.1133 +IC CB3 CB4 CB5 CB6 1.5384 115.02 -51.86 114.89 1.5394 +IC CB6 CB4 *CB5 H5D 1.5394 114.89 -121.74 108.45 1.1137 +IC H5D CB4 *CB5 H5E 1.1137 108.45 -116.35 108.99 1.1129 +IC CB4 CB5 CB6 CB7 1.5414 114.89 -57.34 113.83 1.5380 +IC CB7 CB5 *CB6 H6D 1.5380 113.83 -121.31 108.98 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.98 -116.37 108.87 1.1123 +IC CB5 CB6 CB7 CB8 1.5394 113.83 179.71 113.63 1.5423 +IC CB8 CB6 *CB7 H7D 1.5423 113.63 -122.27 109.89 1.1123 +IC H7D CB6 *CB7 H7E 1.1123 109.89 -116.77 108.48 1.1132 +IC CB6 CB7 CB8 CB9 1.5380 113.63 -63.29 112.23 1.5093 +IC CB9 CB7 *CB8 H8D 1.5093 112.23 -120.64 107.87 1.1133 +IC H8D CB7 *CB8 H8E 1.1133 107.87 -115.67 108.05 1.1129 +IC CB7 CB8 CB9 CB10 1.5423 112.23 148.17 126.47 1.3460 +IC CB10 CB8 *CB9 H9D 1.3460 126.47 -177.74 114.82 1.1018 +IC CB8 CB9 CB10 CB11 1.5093 126.47 2.77 126.58 1.5092 +IC CB11 CB9 *CB10 H10D 1.5092 126.58 177.26 118.57 1.1029 +IC CB9 CB10 CB11 CB12 1.3460 126.58 -116.82 111.69 1.5096 +IC CB12 CB10 *CB11 H11D 1.5096 111.69 -123.10 108.54 1.1115 +IC H11D CB10 *CB11 H11E 1.1115 108.54 -114.79 111.63 1.1116 +IC CB10 CB11 CB12 CB13 1.5092 111.69 -110.56 126.32 1.3473 +IC CB13 CB11 *CB12 H12D 1.3473 126.32 -178.41 114.77 1.1018 +IC CB11 CB12 CB13 CB14 1.5096 126.32 2.04 125.85 1.5088 +IC CB14 CB12 *CB13 H13D 1.5088 125.85 179.17 118.99 1.1012 +IC CB12 CB13 CB14 CB15 1.3473 125.85 -89.20 112.98 1.5413 +IC CB15 CB13 *CB14 H14D 1.5413 112.98 -121.97 110.15 1.1124 +IC H14D CB13 *CB14 H14E 1.1124 110.15 -116.85 110.43 1.1140 +IC CB13 CB14 CB15 CB16 1.5088 112.98 -66.02 113.67 1.5362 +IC CB16 CB14 *CB15 H15D 1.5362 113.67 -120.47 108.54 1.1134 +IC H15D CB14 *CB15 H15E 1.1134 108.54 -116.71 109.67 1.1135 +IC CB14 CB15 CB16 CB17 1.5413 113.67 -176.61 112.48 1.5339 +IC CB17 CB15 *CB16 H16D 1.5339 112.48 -121.15 109.47 1.1130 +IC H16D CB15 *CB16 H16E 1.1130 109.47 -117.68 109.15 1.1130 +IC CB15 CB16 CB17 CB18 1.5362 112.48 -179.94 113.24 1.5308 +IC CB18 CB16 *CB17 H17D 1.5308 113.24 -121.73 108.82 1.1141 +IC H17D CB16 *CB17 H17E 1.1141 108.82 -116.64 108.69 1.1143 +IC CB16 CB17 CB18 H18D 1.5339 113.24 59.88 110.45 1.1114 +IC H18D CB17 *CB18 H18E 1.1114 110.45 -119.87 110.50 1.1113 +IC H18D CB17 *CB18 H18F 1.1114 110.45 120.03 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5297 112.33 172.47 113.86 1.5361 +IC CC4 CC2 *CC3 H3R 1.5361 113.86 -119.64 108.94 1.1154 +IC H3R CC2 *CC3 H3S 1.1154 108.94 -117.39 109.77 1.1130 +IC CC2 CC3 CC4 CC5 1.5489 113.86 -56.98 112.74 1.5347 +IC CC5 CC3 *CC4 H4R 1.5347 112.74 -119.98 107.98 1.1143 +IC H4R CC3 *CC4 H4S 1.1143 107.98 -117.33 110.39 1.1120 +IC CC3 CC4 CC5 CC6 1.5361 112.74 -154.31 113.28 1.5321 +IC CC6 CC4 *CC5 H5R 1.5321 113.28 -123.53 109.65 1.1125 +IC H5R CC4 *CC5 H5S 1.1125 109.65 -117.22 108.68 1.1132 +IC CC4 CC5 CC6 CC7 1.5347 113.28 -174.72 112.18 1.5360 +IC CC7 CC5 *CC6 H6R 1.5360 112.18 -120.78 108.11 1.1141 +IC H6R CC5 *CC6 H6S 1.1141 108.11 -117.38 110.00 1.1122 +IC CC5 CC6 CC7 CC8 1.5321 112.18 -168.49 113.32 1.5408 +IC CC8 CC6 *CC7 H7R 1.5408 113.32 -121.00 108.07 1.1137 +IC H7R CC6 *CC7 H7S 1.1137 108.07 -116.02 109.54 1.1140 +IC CC6 CC7 CC8 CC9 1.5360 113.32 72.57 111.65 1.5102 +IC CC9 CC7 *CC8 H8R 1.5102 111.65 -124.76 108.23 1.1117 +IC H8R CC7 *CC8 H8S 1.1117 108.23 -115.30 107.95 1.1119 +IC CC7 CC8 CC9 CC10 1.5408 111.65 -134.06 127.67 1.3478 +IC CC10 CC8 *CC9 H9R 1.3478 127.67 179.52 113.97 1.1023 +IC CC8 CC9 CC10 CC11 1.5102 127.67 -0.03 127.34 1.5115 +IC CC11 CC9 *CC10 H10R 1.5115 127.34 179.73 118.07 1.1026 +IC CC9 CC10 CC11 CC12 1.3478 127.34 129.05 112.32 1.5099 +IC CC12 CC10 *CC11 H11R 1.5099 112.32 -123.72 111.60 1.1114 +IC H11R CC10 *CC11 H11S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC10 CC11 CC12 CC13 1.5115 112.32 -84.97 126.59 1.3471 +IC CC13 CC11 *CC12 H12R 1.3471 126.59 -179.05 114.79 1.1010 +IC H12R CC11 *CC12 H12S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC11 CC12 CC13 CC14 1.5099 126.59 1.41 126.41 1.5090 +IC CC14 CC12 *CC13 H13R 1.5090 126.41 178.45 118.70 1.0998 +IC H13R CC12 *CC13 H13S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC12 CC13 CC14 CC15 1.3471 126.41 -125.27 113.39 1.5418 +IC CC15 CC13 *CC14 H14R 1.5418 113.39 -121.44 109.86 1.1131 +IC H14R CC13 *CC14 H14S 1.1131 109.86 -117.22 111.11 1.1131 +IC CC13 CC14 CC15 CC16 1.5090 113.39 -68.63 113.68 1.5381 +IC CC16 CC14 *CC15 H15R 1.5381 113.68 123.30 109.83 1.1129 +IC H15R CC14 *CC15 H15S 1.1129 109.83 116.45 107.53 1.1136 +IC CC14 CC15 CC16 CC17 1.5418 113.68 179.76 113.73 1.5374 +IC CC17 CC15 *CC16 H16R 1.5374 113.73 121.83 108.95 1.1128 +IC H16R CC15 *CC16 H16S 1.1128 108.95 117.24 109.15 1.1127 +IC CC15 CC16 CC17 CC18 1.5381 113.73 63.65 114.54 1.5322 +IC CC18 CC16 *CC17 H17R 1.5322 114.54 -122.47 108.69 1.1141 +IC H17R CC16 *CC17 H17S 1.1141 108.69 -116.13 108.22 1.1148 +IC CC16 CC17 CC18 H18R 1.5374 114.54 56.61 110.47 1.1112 +IC H18R CC17 *CC18 H18S 1.1112 110.47 -120.21 110.86 1.1107 +IC H18R CC17 *CC18 H18T 1.1112 110.47 119.94 110.49 1.1113 +IC CD1 CD2 CD3 CD4 1.5286 112.24 -168.50 113.06 1.5318 +IC CD4 CD2 *CD3 H3X 1.5318 113.06 -122.94 109.98 1.1137 +IC H3X CD2 *CD3 H3Y 1.1137 109.98 -117.36 109.14 1.1136 +IC CD2 CD3 CD4 CD5 1.5470 113.06 175.61 111.87 1.5362 +IC CD5 CD3 *CD4 H4X 1.5362 111.87 -120.66 108.60 1.1128 +IC H4X CD3 *CD4 H4Y 1.1128 108.60 -117.59 109.56 1.1124 +IC CD3 CD4 CD5 CD6 1.5318 111.87 177.84 113.59 1.5356 +IC CD6 CD4 *CD5 H5X 1.5356 113.59 -121.15 108.45 1.1137 +IC H5X CD4 *CD5 H5Y 1.1137 108.45 -116.84 109.16 1.1138 +IC CD4 CD5 CD6 CD7 1.5362 113.59 67.64 113.35 1.5355 +IC CD7 CD5 *CD6 H6X 1.5355 113.35 -122.12 109.12 1.1128 +IC H6X CD5 *CD6 H6Y 1.1128 109.12 -117.25 108.81 1.1134 +IC CD5 CD6 CD7 CD8 1.5356 113.35 -178.50 112.28 1.5389 +IC CD8 CD6 *CD7 H7X 1.5389 112.28 -122.16 108.88 1.1140 +IC H7X CD6 *CD7 H7Y 1.1140 108.88 -116.95 109.16 1.1134 +IC CD6 CD7 CD8 CD9 1.5355 112.28 179.01 111.42 1.5083 +IC CD9 CD7 *CD8 H8X 1.5083 111.42 -122.39 108.26 1.1135 +IC H8X CD7 *CD8 H8Y 1.1135 108.26 -115.32 109.05 1.1118 +IC CD7 CD8 CD9 CD10 1.5389 111.42 -84.39 125.66 1.3464 +IC CD10 CD8 *CD9 H9X 1.3464 125.66 178.86 115.42 1.1011 +IC CD8 CD9 CD10 CD11 1.5083 125.66 0.74 126.41 1.5100 +IC CD11 CD9 *CD10 H10X 1.5100 126.41 178.33 118.71 1.1020 +IC CD9 CD10 CD11 CD12 1.3464 126.41 -119.11 111.66 1.5104 +IC CD12 CD10 *CD11 H11X 1.5104 111.66 -123.67 108.55 1.1120 +IC H11X CD10 *CD11 H11Y 1.1120 108.55 -114.62 111.55 1.1120 +IC CD10 CD11 CD12 CD13 1.5100 111.66 -113.81 126.72 1.3477 +IC CD13 CD11 *CD12 H12X 1.3477 126.72 -178.56 114.59 1.1018 +IC CD11 CD12 CD13 CD14 1.5104 126.72 1.66 126.19 1.5088 +IC CD14 CD12 *CD13 H13X 1.5088 126.19 179.37 118.90 1.1014 +IC CD12 CD13 CD14 CD15 1.3477 126.19 -100.76 112.41 1.5405 +IC CD15 CD13 *CD14 H14X 1.5405 112.41 -121.85 109.83 1.1118 +IC H14X CD13 *CD14 H14Y 1.1118 109.83 -117.23 111.23 1.1116 +IC CD13 CD14 CD15 CD16 1.5088 112.41 170.52 113.29 1.5388 +IC CD16 CD14 *CD15 H15X 1.5388 113.29 -119.71 109.05 1.1153 +IC H15X CD14 *CD15 H15Y 1.1153 109.05 -117.72 109.78 1.1127 +IC CD14 CD15 CD16 CD17 1.5405 113.29 62.69 114.08 1.5347 +IC CD17 CD15 *CD16 H16X 1.5347 114.08 -121.99 108.89 1.1132 +IC H16X CD15 *CD16 H16Y 1.1132 108.89 -116.64 108.76 1.1136 +IC CD15 CD16 CD17 CD18 1.5388 114.08 179.88 112.98 1.5311 +IC CD18 CD16 *CD17 H17X 1.5311 112.98 -121.76 108.79 1.1137 +IC H17X CD16 *CD17 H17Y 1.1137 108.79 -117.11 109.38 1.1133 +IC CD16 CD17 CD18 H18X 1.5347 112.98 60.79 110.28 1.1118 +IC H18X CD17 *CD18 H18Y 1.1118 110.28 -119.90 110.57 1.1110 +IC H18X CD17 *CD18 H18Z 1.1118 110.28 119.81 110.63 1.1110 + +RESI LOCCL2 -2.00 ! 3 lineoleic acid + 1 oleic acid chain cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 3 lineoleoyl chain + 1 oleoyl chain +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12--H12S +GROUP ! || || || | +ATOM C32 CTL1 0.17 ! || || || | +ATOM H32J HAL1 0.09 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13--H13S +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM H2R HAL2 0.09 ! | | | | +ATOM H2S HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +GROUP ! | | | | +ATOM C33 CTL2 0.08 ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM H33J HAL2 0.09 ! | | | | +ATOM H33K HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM O33 OSL -0.49 ! | | | | +ATOM CD1 CL 0.90 ! H18F H18C H18Z H18T +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CTL2 -0.18 ! +ATOM H12R HAL2 0.09 ! +ATOM H12S HAL2 0.09 ! +GROUP ! +ATOM CC13 CTL2 -0.18 ! +ATOM H13R HAL2 0.09 ! +ATOM H13S HAL2 0.09 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 !! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 H12S CC12 CC13 +BOND CC13 H13R CC13 H13S CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +! IC TABLE +! +IC OP31 C2 *C3 HG31 1.4399 111.73 121.27 107.98 1.1140 +IC HG31 C2 *C3 HG32 1.1140 107.98 116.42 107.18 1.1169 +IC C2 C3 OP31 P3 1.5535 111.73 -167.54 118.79 1.5904 +IC C3 OP31 P3 OP32 1.4399 118.79 79.71 101.55 1.5890 +IC OP32 OP31 *P3 OP33 1.5890 101.55 -115.28 110.31 1.4782 +IC OP32 OP31 *P3 OP34 1.5890 101.55 113.65 109.35 1.4797 +IC OP31 P3 OP32 C31 1.5904 101.55 67.83 117.77 1.4329 +IC P3 OP32 C31 C32 1.5890 117.77 -170.90 110.66 1.5522 +IC C32 OP32 *C31 H31J 1.5522 110.66 121.35 111.65 1.1158 +IC H31J OP32 *C31 H31K 1.1158 111.65 119.36 109.77 1.1144 +IC HG31 C3 C2 C1 1.1140 107.98 -59.84 112.53 1.5592 +IC C1 C3 *C2 OG12 1.5592 112.53 -122.28 106.17 1.4219 +IC C1 C3 *C2 HG22 1.5592 112.53 120.07 108.81 1.1138 +IC C3 C2 OG12 HO12 1.5535 106.17 -43.83 99.95 0.9654 +IC C3 C2 C1 OP11 1.5535 112.53 172.59 114.00 1.4374 +IC OP11 C2 *C1 HG11 1.4374 114.00 -124.71 107.54 1.1153 +IC HG11 C2 *C1 HG12 1.1153 107.54 -114.53 107.04 1.1121 +IC C2 C1 OP11 P1 1.5592 114.00 -97.83 122.51 1.5864 +IC C1 OP11 P1 OP12 1.4374 122.51 -52.87 102.45 1.5913 +IC OP12 OP11 *P1 OP13 1.5913 102.45 114.70 110.17 1.4774 +IC OP12 OP11 *P1 OP14 1.5913 102.45 -115.08 109.36 1.4815 +IC OP11 P1 OP12 C11 1.5864 102.45 -92.52 122.70 1.4285 +IC P1 OP12 C11 C12 1.5913 122.70 85.68 111.92 1.5508 +IC C12 OP12 *C11 H11J 1.5508 111.92 -123.87 112.24 1.1149 +IC H11J OP12 *C11 H11K 1.1149 112.24 -117.66 107.38 1.1110 +IC OP12 C11 C12 C13 1.4285 111.92 161.41 112.21 1.5554 +IC C13 C11 *C12 O12 1.5554 112.21 119.92 107.58 1.4348 +IC O12 C11 *C12 H12J 1.4348 107.58 121.23 105.93 1.1177 +IC C11 C12 O12 CA1 1.5508 107.58 139.57 115.43 1.3169 +IC C12 O12 CA1 CA2 1.4348 115.43 -169.02 109.20 1.5307 +IC CA2 O12 *CA1 OA1 1.5307 109.20 -177.29 125.89 1.2210 +IC O12 CA1 CA2 CA3 1.3169 109.20 -125.27 111.98 1.5453 +IC CA3 CA1 *CA2 H2A 1.5453 111.98 -121.72 106.70 1.1104 +IC H2A CA1 *CA2 H2B 1.1104 106.70 -115.79 108.58 1.1093 +IC C11 C12 C13 O13 1.5508 112.21 -165.73 111.20 1.4484 +IC O13 C12 *C13 H13J 1.4484 111.20 -119.38 107.07 1.1127 +IC H13J C12 *C13 H13K 1.1127 107.07 -115.20 109.28 1.1141 +IC C12 C13 O13 CB1 1.5554 111.20 86.74 113.94 1.3304 +IC C13 O13 CB1 CB2 1.4484 113.94 -157.19 109.85 1.5285 +IC CB2 O13 *CB1 OB1 1.5285 109.85 179.45 125.30 1.2183 +IC O13 CB1 CB2 CB3 1.3304 109.85 170.02 112.02 1.5483 +IC CB3 CB1 *CB2 H2D 1.5483 112.02 -119.03 106.46 1.1119 +IC H2D CB1 *CB2 H2E 1.1119 106.46 -117.11 109.11 1.1053 +IC OP32 C31 C32 C33 1.4329 110.66 -55.34 111.30 1.5520 +IC C33 C31 *C32 O32 1.5520 111.30 121.41 110.58 1.4400 +IC O32 C31 *C32 H32J 1.4400 110.58 121.80 108.53 1.1157 +IC C31 C32 O32 CC1 1.5522 110.58 76.00 113.72 1.3241 +IC C32 O32 CC1 CC2 1.4400 113.72 -175.40 107.92 1.5290 +IC CC2 O32 *CC1 OC1 1.5290 107.92 -174.97 125.21 1.2214 +IC O32 CC1 CC2 CC3 1.3241 107.92 -171.64 114.45 1.5483 +IC CC3 CC1 *CC2 H2R 1.5483 114.45 -120.08 106.50 1.1125 +IC H2R CC1 *CC2 H2S 1.1125 106.50 -115.84 108.14 1.1062 +IC C31 C32 C33 O33 1.5522 111.30 178.27 110.32 1.4463 +IC O33 C32 *C33 H33J 1.4463 110.32 122.56 108.16 1.1137 +IC H33J C32 *C33 H33K 1.1137 108.16 116.60 107.22 1.1149 +IC C32 C33 O33 CD1 1.5520 110.32 176.92 114.52 1.3194 +IC C33 O33 CD1 CD2 1.4463 114.52 169.48 108.39 1.5307 +IC CD2 O33 *CD1 OD1 1.5307 108.39 179.86 126.25 1.2174 +IC O33 CD1 CD2 CD3 1.3194 108.39 166.29 113.39 1.5479 +IC CD3 CD1 *CD2 H2X 1.5479 113.39 -122.94 107.91 1.1081 +IC H2X CD1 *CD2 H2Y 1.1081 107.91 -116.24 106.59 1.1103 +IC CA1 CA2 CA3 CA4 1.5307 111.98 174.09 112.77 1.5340 +IC CA4 CA2 *CA3 H3A 1.5340 112.77 -121.48 109.27 1.1128 +IC H3A CA2 *CA3 H3B 1.1128 109.27 -117.62 108.80 1.1132 +IC CA2 CA3 CA4 CA5 1.5453 112.77 176.67 112.97 1.5369 +IC CA5 CA3 *CA4 H4A 1.5369 112.97 -120.43 108.08 1.1146 +IC H4A CA3 *CA4 H4B 1.1146 108.08 -116.67 109.58 1.1123 +IC CA3 CA4 CA5 CA6 1.5340 112.97 69.98 113.98 1.5366 +IC CA6 CA4 *CA5 H5A 1.5366 113.98 -122.10 108.41 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 108.41 -116.88 108.64 1.1132 +IC CA4 CA5 CA6 CA7 1.5369 113.98 177.62 113.05 1.5384 +IC CA7 CA5 *CA6 H6A 1.5384 113.05 -120.54 108.00 1.1138 +IC H6A CA5 *CA6 H6B 1.1138 108.00 -117.16 109.92 1.1119 +IC CA5 CA6 CA7 CA8 1.5366 113.05 72.32 113.20 1.5409 +IC CA8 CA6 *CA7 H7A 1.5409 113.20 -122.31 108.58 1.1140 +IC H7A CA6 *CA7 H7B 1.1140 108.58 -116.70 108.43 1.1139 +IC CA6 CA7 CA8 CA9 1.5384 113.20 -177.88 111.67 1.5104 +IC CA9 CA7 *CA8 H8A 1.5104 111.67 -121.51 108.57 1.1127 +IC H8A CA7 *CA8 H8B 1.1127 108.57 -114.68 108.68 1.1109 +IC CA7 CA8 CA9 CA10 1.5409 111.67 106.92 126.93 1.3485 +IC CA10 CA8 *CA9 H9A 1.3485 126.93 179.93 114.52 1.1012 +IC CA8 CA9 CA10 CA11 1.5104 126.93 -0.98 126.94 1.5114 +IC CA11 CA9 *CA10 H10A 1.5114 126.94 -179.25 118.31 1.1017 +IC CA9 CA10 CA11 CA12 1.3485 126.94 -125.33 111.90 1.5094 +IC CA12 CA10 *CA11 H11A 1.5094 111.90 -120.91 109.22 1.1122 +IC H11A CA10 *CA11 H11B 1.1122 109.22 -115.26 111.36 1.1089 +IC CA10 CA11 CA12 CA13 1.5114 111.90 103.75 127.05 1.3481 +IC CA13 CA11 *CA12 H12A 1.3481 127.05 178.55 114.54 1.1015 +IC CA11 CA12 CA13 CA14 1.5094 127.05 -1.51 127.29 1.5104 +IC CA14 CA12 *CA13 H13A 1.5104 127.29 -178.83 118.45 1.1012 +IC CA12 CA13 CA14 CA15 1.3481 127.29 123.19 111.92 1.5400 +IC CA15 CA13 *CA14 H14A 1.5400 111.92 -122.30 112.60 1.1129 +IC H14A CA13 *CA14 H14B 1.1129 112.60 -117.91 109.33 1.1129 +IC CA13 CA14 CA15 CA16 1.5104 111.92 172.46 112.42 1.5358 +IC CA16 CA14 *CA15 H15A 1.5358 112.42 -120.26 109.74 1.1138 +IC H15A CA14 *CA15 H15B 1.1138 109.74 -118.26 109.67 1.1136 +IC CA14 CA15 CA16 CA17 1.5400 112.42 -176.77 112.71 1.5339 +IC CA17 CA15 *CA16 H16A 1.5339 112.71 -121.51 109.43 1.1130 +IC H16A CA15 *CA16 H16B 1.1130 109.43 -117.43 109.11 1.1131 +IC CA15 CA16 CA17 CA18 1.5358 112.71 177.47 113.22 1.5311 +IC CA18 CA16 *CA17 H17A 1.5311 113.22 -121.64 108.92 1.1137 +IC H17A CA16 *CA17 H17B 1.1137 108.92 -116.79 108.72 1.1143 +IC CA16 CA17 CA18 H18A 1.5339 113.22 -60.64 110.64 1.1108 +IC H18A CA17 *CA18 H18B 1.1108 110.64 -120.38 110.71 1.1111 +IC H18A CA17 *CA18 H18C 1.1108 110.64 119.78 110.63 1.1119 +IC CB1 CB2 CB3 CB4 1.5285 112.02 -156.49 113.16 1.5352 +IC CB4 CB2 *CB3 H3D 1.5352 113.16 -125.26 110.81 1.1108 +IC H3D CB2 *CB3 H3E 1.1108 110.81 -117.62 108.58 1.1185 +IC CB2 CB3 CB4 CB5 1.5483 113.16 -72.87 114.64 1.5362 +IC CB5 CB3 *CB4 H4D 1.5362 114.64 -121.50 107.87 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 107.87 -115.68 108.33 1.1133 +IC CB3 CB4 CB5 CB6 1.5352 114.64 173.14 113.35 1.5409 +IC CB6 CB4 *CB5 H5D 1.5409 113.35 -120.91 109.12 1.1130 +IC H5D CB4 *CB5 H5E 1.1130 109.12 -117.35 108.69 1.1125 +IC CB4 CB5 CB6 CB7 1.5362 113.35 52.82 114.03 1.5378 +IC CB7 CB5 *CB6 H6D 1.5378 114.03 -120.64 108.65 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.65 -116.83 109.17 1.1121 +IC CB5 CB6 CB7 CB8 1.5409 114.03 179.98 112.81 1.5400 +IC CB8 CB6 *CB7 H7D 1.5400 112.81 -122.98 109.09 1.1121 +IC H7D CB6 *CB7 H7E 1.1121 109.09 -117.53 108.71 1.1155 +IC CB6 CB7 CB8 CB9 1.5378 112.81 177.49 110.85 1.5102 +IC CB9 CB7 *CB8 H8D 1.5102 110.85 -122.35 107.23 1.1140 +IC H8D CB7 *CB8 H8E 1.1140 107.23 -115.61 109.26 1.1115 +IC CB7 CB8 CB9 CB10 1.5400 110.85 -111.54 126.68 1.3485 +IC CB10 CB8 *CB9 H9D 1.3485 126.68 176.66 114.61 1.1007 +IC CB8 CB9 CB10 CB11 1.5102 126.68 -2.77 127.04 1.5103 +IC CB11 CB9 *CB10 H10D 1.5103 127.04 -178.65 118.60 1.1012 +IC CB9 CB10 CB11 CB12 1.3485 127.04 96.60 112.31 1.5135 +IC CB12 CB10 *CB11 H11D 1.5135 112.31 -125.47 110.37 1.1105 +IC H11D CB10 *CB11 H11E 1.1105 110.37 -114.37 108.83 1.1122 +IC CB10 CB11 CB12 CB13 1.5103 112.31 -123.24 127.49 1.3487 +IC CB13 CB11 *CB12 H12D 1.3487 127.49 -179.18 114.92 1.1025 +IC CB11 CB12 CB13 CB14 1.5135 127.49 0.10 127.26 1.5079 +IC CB14 CB12 *CB13 H13D 1.5079 127.26 -179.25 118.69 1.1053 +IC CB12 CB13 CB14 CB15 1.3487 127.26 123.97 111.98 1.5384 +IC CB15 CB13 *CB14 H14D 1.5384 111.98 -120.79 111.90 1.1093 +IC H14D CB13 *CB14 H14E 1.1093 111.90 -118.90 109.68 1.1138 +IC CB13 CB14 CB15 CB16 1.5079 111.98 -173.48 111.85 1.5348 +IC CB16 CB14 *CB15 H15D 1.5348 111.85 -121.68 109.78 1.1147 +IC H15D CB14 *CB15 H15E 1.1147 109.78 -117.79 109.28 1.1119 +IC CB14 CB15 CB16 CB17 1.5384 111.85 179.99 113.35 1.5313 +IC CB17 CB15 *CB16 H16D 1.5313 113.35 -121.42 108.85 1.1101 +IC H16D CB15 *CB16 H16E 1.1101 108.85 -117.19 108.74 1.1110 +IC CB15 CB16 CB17 CB18 1.5348 113.35 -178.76 113.12 1.5314 +IC CB18 CB16 *CB17 H17D 1.5314 113.12 -121.82 108.25 1.1149 +IC H17D CB16 *CB17 H17E 1.1149 108.25 -115.96 109.19 1.1126 +IC CB16 CB17 CB18 H18D 1.5313 113.12 -178.27 110.36 1.1112 +IC H18D CB17 *CB18 H18E 1.1112 110.36 -120.53 110.61 1.1103 +IC H18D CB17 *CB18 H18F 1.1112 110.36 119.56 110.21 1.1112 +IC CC1 CC2 CC3 CC4 1.5290 114.45 61.17 115.54 1.5407 +IC CC4 CC2 *CC3 H3R 1.5407 115.54 -123.39 108.81 1.1159 +IC H3R CC2 *CC3 H3S 1.1159 108.81 -115.09 107.30 1.1128 +IC CC2 CC3 CC4 CC5 1.5483 115.54 48.75 115.70 1.5381 +IC CC5 CC3 *CC4 H4R 1.5381 115.70 -121.95 108.35 1.1141 +IC H4R CC3 *CC4 H4S 1.1141 108.35 -115.67 107.88 1.1118 +IC CC3 CC4 CC5 CC6 1.5407 115.70 59.37 113.26 1.5339 +IC CC6 CC4 *CC5 H5R 1.5339 113.26 -122.42 108.68 1.1122 +IC H5R CC4 *CC5 H5S 1.1122 108.68 -116.61 108.64 1.1128 +IC CC4 CC5 CC6 CC7 1.5381 113.26 175.46 114.41 1.5382 +IC CC7 CC5 *CC6 H6R 1.5382 114.41 -121.44 108.39 1.1118 +IC H6R CC5 *CC6 H6S 1.1118 108.39 -116.44 108.77 1.1127 +IC CC5 CC6 CC7 CC8 1.5339 114.41 50.21 113.91 1.5402 +IC CC8 CC6 *CC7 H7R 1.5402 113.91 -122.10 108.87 1.1136 +IC H7R CC6 *CC7 H7S 1.1136 108.87 -116.44 107.40 1.1147 +IC CC6 CC7 CC8 CC9 1.5382 113.91 171.45 111.26 1.5090 +IC CC9 CC7 *CC8 H8R 1.5090 111.26 -123.76 107.81 1.1114 +IC H8R CC7 *CC8 H8S 1.1114 107.81 -115.28 108.84 1.1122 +IC CC7 CC8 CC9 CC10 1.5402 111.26 -128.36 127.23 1.3472 +IC CC10 CC8 *CC9 H9R 1.3472 127.23 178.70 114.30 1.1010 +IC CC8 CC9 CC10 CC11 1.5090 127.23 -1.15 127.54 1.5084 +IC CC11 CC9 *CC10 H10R 1.5084 127.54 -179.59 118.30 1.1015 +IC CC9 CC10 CC11 CC12 1.3472 127.54 121.83 111.08 1.5090 +IC CC12 CC10 *CC11 H11R 1.5090 111.08 -121.38 111.45 1.1092 +IC H11R CC10 *CC11 H11S 1.1092 111.45 -115.12 108.94 1.1091 +IC CC10 CC11 CC12 CC13 1.5084 111.08 114.57 127.61 1.3469 +IC CC13 CC11 *CC12 H12R 1.3469 127.61 179.18 114.07 1.1019 +IC CC13 CC11 *CC12 H12S 1.3469 127.61 179.18 114.07 1.1019 +IC CC11 CC12 CC13 CC14 1.5090 127.61 -1.12 127.24 1.5089 +IC CC14 CC12 *CC13 H13R 1.5089 127.24 -179.24 118.36 1.1008 +IC CC14 CC12 *CC13 H13S 1.5089 127.24 -179.24 118.36 1.1008 +IC CC12 CC13 CC14 CC15 1.3469 127.24 -127.92 112.49 1.5415 +IC CC15 CC13 *CC14 H14R 1.5415 112.49 -120.38 109.34 1.1135 +IC H14R CC13 *CC14 H14S 1.1135 109.34 -118.08 112.29 1.1108 +IC CC13 CC14 CC15 CC16 1.5089 112.49 64.28 113.82 1.5372 +IC CC16 CC14 *CC15 H15R 1.5372 113.82 -123.02 109.95 1.1128 +IC H15R CC14 *CC15 H15S 1.1128 109.95 -116.79 108.08 1.1141 +IC CC14 CC15 CC16 CC17 1.5415 113.82 175.12 112.35 1.5342 +IC CC17 CC15 *CC16 H16R 1.5342 112.35 121.44 109.60 1.1127 +IC H16R CC15 *CC16 H16S 1.1127 109.60 117.48 109.22 1.1130 +IC CC15 CC16 CC17 CC18 1.5372 112.35 177.84 113.41 1.5303 +IC CC18 CC16 *CC17 H17R 1.5303 113.41 -121.68 108.79 1.1140 +IC H17R CC16 *CC17 H17S 1.1140 108.79 -116.65 108.60 1.1141 +IC CC16 CC17 CC18 H18R 1.5342 113.41 177.41 110.78 1.1108 +IC H18R CC17 *CC18 H18S 1.1108 110.78 120.14 110.47 1.1110 +IC H18R CC17 *CC18 H18T 1.1108 110.78 -120.28 110.55 1.1114 +IC CD1 CD2 CD3 CD4 1.5307 113.39 169.15 112.93 1.5372 +IC CD4 CD2 *CD3 H3X 1.5372 112.93 -120.02 109.25 1.1156 +IC H3X CD2 *CD3 H3Y 1.1156 109.25 -117.49 109.59 1.1130 +IC CD2 CD3 CD4 CD5 1.5479 112.93 59.54 113.85 1.5360 +IC CD5 CD3 *CD4 H4X 1.5360 113.85 -121.33 108.32 1.1134 +IC H4X CD3 *CD4 H4Y 1.1134 108.32 -116.71 109.15 1.1132 +IC CD3 CD4 CD5 CD6 1.5372 113.85 -177.43 112.79 1.5357 +IC CD6 CD4 *CD5 H5X 1.5357 112.79 -122.43 109.70 1.1122 +IC H5X CD4 *CD5 H5Y 1.1122 109.70 -117.86 109.15 1.1139 +IC CD4 CD5 CD6 CD7 1.5360 112.79 173.65 112.21 1.5365 +IC CD7 CD5 *CD6 H6X 1.5365 112.21 -119.39 108.19 1.1136 +IC H6X CD5 *CD6 H6Y 1.1136 108.19 -117.35 110.05 1.1111 +IC CD5 CD6 CD7 CD8 1.5357 112.21 -164.07 113.53 1.5412 +IC CD8 CD6 *CD7 H7X 1.5412 113.53 -125.12 110.25 1.1118 +IC H7X CD6 *CD7 H7Y 1.1118 110.25 -116.30 107.52 1.1152 +IC CD6 CD7 CD8 CD9 1.5365 113.53 -72.33 113.26 1.5081 +IC CD9 CD7 *CD8 H8X 1.5081 113.26 -123.64 107.20 1.1122 +IC H8X CD7 *CD8 H8Y 1.1122 107.20 -114.54 108.43 1.1124 +IC CD7 CD8 CD9 CD10 1.5412 113.26 -141.33 126.38 1.3479 +IC CD10 CD8 *CD9 H9X 1.3479 126.38 -179.10 114.78 1.1010 +IC CD8 CD9 CD10 CD11 1.5081 126.38 0.12 126.84 1.5114 +IC CD11 CD9 *CD10 H10X 1.5114 126.84 -179.87 118.43 1.1016 +IC CD9 CD10 CD11 CD12 1.3479 126.84 -106.33 111.23 1.5105 +IC CD12 CD10 *CD11 H11X 1.5105 111.23 -120.37 109.03 1.1122 +IC H11X CD10 *CD11 H11Y 1.1122 109.03 -114.91 111.58 1.1099 +IC CD10 CD11 CD12 CD13 1.5114 111.23 109.38 127.41 1.3486 +IC CD13 CD11 *CD12 H12X 1.3486 127.41 179.19 114.40 1.1015 +IC CD11 CD12 CD13 CD14 1.5105 127.41 -1.41 127.65 1.5109 +IC CD14 CD12 *CD13 H13X 1.5109 127.65 -178.15 118.24 1.1012 +IC CD12 CD13 CD14 CD15 1.3486 127.65 -115.93 111.19 1.5399 +IC CD15 CD13 *CD14 H14X 1.5399 111.19 -120.10 109.72 1.1126 +IC H14X CD13 *CD14 H14Y 1.1126 109.72 -118.73 112.54 1.1122 +IC CD13 CD14 CD15 CD16 1.5109 111.19 -174.42 112.98 1.5354 +IC CD16 CD14 *CD15 H15X 1.5354 112.98 -121.07 109.22 1.1143 +IC H15X CD14 *CD15 H15Y 1.1143 109.22 -117.98 109.91 1.1138 +IC CD14 CD15 CD16 CD17 1.5399 112.98 179.46 112.15 1.5344 +IC CD17 CD15 *CD16 H16X 1.5344 112.15 -121.15 109.44 1.1128 +IC H16X CD15 *CD16 H16Y 1.1128 109.44 -117.66 109.26 1.1126 +IC CD15 CD16 CD17 CD18 1.5354 112.15 179.70 113.67 1.5310 +IC CD18 CD16 *CD17 H17X 1.5310 113.67 -121.71 108.44 1.1139 +IC H17X CD16 *CD17 H17Y 1.1139 108.44 -116.35 108.83 1.1138 +IC CD16 CD17 CD18 H18X 1.5344 113.67 -178.87 110.70 1.1108 +IC H18X CD17 *CD18 H18Y 1.1108 110.70 -120.14 110.59 1.1104 +IC H18X CD17 *CD18 H18Z 1.1108 110.70 119.96 110.62 1.1117 + +RESI LNACL1 -1.00 ! 3 linoleic acid + 1 linolenic acid cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 3 linoleoyl + 1 linolenoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +ATOM H2E HAL2 0.09 ! || || || || +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15--H15E H15A--CA15 H15X--CD15--H15Y H15R--CC15--H15S +ATOM CC2 CTL2 -0.22 ! | || | | +ATOM H2R HAL2 0.09 ! H16D--CB16--H16E H16A--CA16 H16X--CD16--H16Y H16R--CC16--H16S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18F H18C H18Z H18T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CEL1 -0.15 ! +ATOM H15A HEL1 0.15 ! +GROUP ! +ATOM CA16 CEL1 -0.15 ! +ATOM H16A HEL1 0.15 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 CA16 +BOND CA16 H16A CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4272 111.57 124.87 107.78 1.1169 +IC HG31 C2 *C3 HG32 1.1169 107.78 115.89 109.04 1.1124 +IC C2 C3 OP31 P3 1.5483 111.57 118.08 122.98 1.5819 +IC C3 OP31 P3 OP32 1.4272 122.98 37.85 102.14 1.5830 +IC OP32 OP31 *P3 OP33 1.5830 102.14 -113.92 107.98 1.4793 +IC OP32 OP31 *P3 OP34 1.5830 102.14 115.66 109.62 1.4740 +IC OP31 P3 OP32 C31 1.5819 102.14 69.85 119.33 1.4301 +IC P3 OP32 C31 C32 1.5830 119.33 176.40 110.18 1.5529 +IC C32 OP32 *C31 H31J 1.5529 110.18 120.82 110.67 1.1139 +IC H31J OP32 *C31 H31K 1.1139 110.67 119.45 110.95 1.1159 +IC HG31 C3 C2 C1 1.1169 107.78 60.13 113.14 1.5594 +IC C1 C3 *C2 OG12 1.5594 113.14 -122.65 107.36 1.4314 +IC C1 C3 *C2 HG22 1.5594 113.14 119.50 108.81 1.1137 +IC C3 C2 OG12 HO12 1.5483 107.36 -59.74 104.73 0.9611 +IC C3 C2 C1 OP11 1.5483 113.14 102.14 111.29 1.4365 +IC OP11 C2 *C1 HG11 1.4365 111.29 -124.72 105.61 1.1191 +IC HG11 C2 *C1 HG12 1.1191 105.61 -115.38 108.40 1.1138 +IC C2 C1 OP11 P1 1.5594 111.29 -157.61 115.85 1.5685 +IC C1 OP11 P1 OP12 1.4365 115.85 -14.21 104.93 1.5653 +IC OP12 OP11 *P1 OP13 1.5653 104.93 115.00 111.23 1.5595 +IC OP12 OP11 *P1 OP14 1.5653 104.93 -120.71 114.44 1.4714 +IC OP11 P1 OP13 HP13 1.5685 111.23 -49.71 108.79 0.9805 +IC OP11 P1 OP12 C11 1.5685 104.93 168.45 117.56 1.4279 +IC P1 OP12 C11 C12 1.5653 117.56 -104.42 112.05 1.5631 +IC C12 OP12 *C11 H11J 1.5631 112.05 -116.94 106.96 1.1115 +IC H11J OP12 *C11 H11K 1.1115 106.96 -117.70 114.83 1.1174 +IC OP12 C11 C12 C13 1.4279 112.05 -169.61 110.60 1.5613 +IC C13 C11 *C12 O12 1.5613 110.60 124.16 109.17 1.4428 +IC O12 C11 *C12 H12J 1.4428 109.17 118.13 106.49 1.1175 +IC C11 C12 O12 CA1 1.5631 109.17 161.88 113.49 1.3343 +IC C12 O12 CA1 CA2 1.4428 113.49 -169.35 108.84 1.5280 +IC CA2 O12 *CA1 OA1 1.5280 108.84 179.80 125.17 1.2183 +IC O12 CA1 CA2 CA3 1.3343 108.84 -146.40 113.25 1.5456 +IC CA3 CA1 *CA2 H2A 1.5456 113.25 -119.97 106.28 1.1109 +IC H2A CA1 *CA2 H2B 1.1109 106.28 -116.75 108.94 1.1073 +IC C11 C12 C13 O13 1.5631 110.60 48.04 111.75 1.4444 +IC O13 C12 *C13 H13J 1.4444 111.75 -117.92 106.48 1.1131 +IC H13J C12 *C13 H13K 1.1131 106.48 -115.07 111.40 1.1131 +IC C12 C13 O13 CB1 1.5613 111.75 88.82 115.87 1.3297 +IC C13 O13 CB1 CB2 1.4444 115.87 -174.80 108.56 1.5287 +IC CB2 O13 *CB1 OB1 1.5287 108.56 -178.49 126.34 1.2145 +IC O13 CB1 CB2 CB3 1.3297 108.56 152.47 112.16 1.5454 +IC CB3 CB1 *CB2 H2D 1.5454 112.16 -121.52 108.74 1.1089 +IC H2D CB1 *CB2 H2E 1.1089 108.74 -117.40 106.94 1.1083 +IC OP32 C31 C32 C33 1.4301 110.18 -69.33 110.65 1.5522 +IC C33 C31 *C32 O32 1.5522 110.65 120.01 111.21 1.4395 +IC O32 C31 *C32 H32J 1.4395 111.21 122.30 108.97 1.1146 +IC C31 C32 O32 CC1 1.5529 111.21 69.31 115.35 1.3120 +IC C32 O32 CC1 CC2 1.4395 115.35 -171.71 108.60 1.5297 +IC CC2 O32 *CC1 OC1 1.5297 108.60 -178.02 126.78 1.2186 +IC O32 CC1 CC2 CC3 1.3120 108.60 -59.72 112.33 1.5489 +IC CC3 CC1 *CC2 H2R 1.5489 112.33 -122.26 107.83 1.1075 +IC H2R CC1 *CC2 H2S 1.1075 107.83 -116.44 106.39 1.1097 +IC C31 C32 C33 O33 1.5529 110.65 179.11 109.99 1.4464 +IC O33 C32 *C33 H33J 1.4464 109.99 121.93 109.29 1.1119 +IC H33J C32 *C33 H33K 1.1119 109.29 116.57 106.09 1.1186 +IC C32 C33 O33 CD1 1.5522 109.99 -159.03 114.19 1.3237 +IC C33 O33 CD1 CD2 1.4464 114.19 164.21 109.32 1.5286 +IC CD2 O33 *CD1 OD1 1.5286 109.32 -178.45 126.02 1.2156 +IC O33 CD1 CD2 CD3 1.3237 109.32 -46.26 112.24 1.5470 +IC CD3 CD1 *CD2 H2X 1.5470 112.24 -120.21 106.48 1.1100 +IC H2X CD1 *CD2 H2Y 1.1100 106.48 -117.13 108.41 1.1069 +IC CA1 CA2 CA3 CA4 1.5280 113.25 70.18 112.81 1.5346 +IC CA4 CA2 *CA3 H3A 1.5346 112.81 -123.14 110.14 1.1142 +IC H3A CA2 *CA3 H3B 1.1142 110.14 -116.66 107.70 1.1125 +IC CA2 CA3 CA4 CA5 1.5456 112.81 172.40 112.79 1.5353 +IC CA5 CA3 *CA4 H4A 1.5353 112.79 -122.05 109.90 1.1116 +IC H4A CA3 *CA4 H4B 1.1116 109.90 -117.14 108.37 1.1150 +IC CA3 CA4 CA5 CA6 1.5346 112.79 167.30 112.42 1.5358 +IC CA6 CA4 *CA5 H5A 1.5358 112.42 -120.63 108.10 1.1132 +IC H5A CA4 *CA5 H5B 1.1132 108.10 -117.30 109.47 1.1120 +IC CA4 CA5 CA6 CA7 1.5353 112.42 177.91 114.45 1.5409 +IC CA7 CA5 *CA6 H6A 1.5409 114.45 -121.60 108.84 1.1121 +IC H6A CA5 *CA6 H6B 1.1121 108.84 -116.16 108.48 1.1134 +IC CA5 CA6 CA7 CA8 1.5358 114.45 53.66 115.58 1.5440 +IC CA8 CA6 *CA7 H7A 1.5440 115.58 -121.63 108.47 1.1138 +IC H7A CA6 *CA7 H7B 1.1138 108.47 -116.24 108.32 1.1141 +IC CA6 CA7 CA8 CA9 1.5409 115.58 55.01 112.73 1.5097 +IC CA9 CA7 *CA8 H8A 1.5097 112.73 -121.48 108.57 1.1114 +IC H8A CA7 *CA8 H8B 1.1114 108.57 -114.55 107.55 1.1126 +IC CA7 CA8 CA9 CA10 1.5440 112.73 109.39 127.97 1.3474 +IC CA10 CA8 *CA9 H9A 1.3474 127.97 -179.15 113.83 1.1025 +IC CA8 CA9 CA10 CA11 1.5097 127.97 0.64 127.89 1.5108 +IC CA11 CA9 *CA10 H10A 1.5108 127.89 179.31 117.75 1.1014 +IC CA9 CA10 CA11 CA12 1.3474 127.89 -112.95 111.22 1.5114 +IC CA12 CA10 *CA11 H11A 1.5114 111.22 -120.46 108.90 1.1119 +IC H11A CA10 *CA11 H11B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA10 CA11 CA12 CA13 1.5108 111.22 134.57 126.37 1.3465 +IC CA13 CA11 *CA12 H12A 1.3465 126.37 -177.01 115.27 1.1018 +IC CA11 CA12 CA13 CA14 1.5114 126.37 3.15 126.32 1.5077 +IC CA14 CA12 *CA13 H13A 1.5077 126.32 178.37 118.79 1.1003 +IC CA12 CA13 CA14 CA15 1.3465 126.32 -92.58 113.47 1.5417 +IC CA15 CA13 *CA14 H14A 1.5417 113.47 -122.01 110.01 1.1123 +IC H14A CA13 *CA14 H14B 1.1123 110.01 -116.77 110.38 1.1120 +IC CA13 CA14 CA15 CA16 1.5077 113.47 -63.55 113.58 1.5369 +IC CA16 CA14 *CA15 H15A 1.5369 113.58 -120.33 108.08 1.1132 +IC CA14 CA15 CA16 CA17 1.5417 113.58 -171.21 113.87 1.5374 +IC CA17 CA15 *CA16 H16A 1.5374 113.87 -121.70 108.87 1.1122 +IC CA15 CA16 CA17 CA18 1.5369 113.87 -61.57 114.41 1.5314 +IC CA18 CA16 *CA17 H17A 1.5314 114.41 -121.26 108.12 1.1148 +IC H17A CA16 *CA17 H17B 1.1148 108.12 -116.30 108.76 1.1136 +IC CA16 CA17 CA18 H18A 1.5374 114.41 63.53 110.93 1.1107 +IC H18A CA17 *CA18 H18B 1.1107 110.93 -119.76 110.34 1.1109 +IC H18A CA17 *CA18 H18C 1.1107 110.93 120.37 110.77 1.1100 +IC CB1 CB2 CB3 CB4 1.5287 112.16 178.44 113.36 1.5384 +IC CB4 CB2 *CB3 H3D 1.5384 113.36 -122.28 109.76 1.1140 +IC H3D CB2 *CB3 H3E 1.1140 109.76 -116.69 109.13 1.1151 +IC CB2 CB3 CB4 CB5 1.5454 113.36 -60.74 115.02 1.5414 +IC CB5 CB3 *CB4 H4D 1.5414 115.02 -121.57 108.33 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 108.33 -116.10 108.96 1.1133 +IC CB3 CB4 CB5 CB6 1.5384 115.02 -51.86 114.89 1.5394 +IC CB6 CB4 *CB5 H5D 1.5394 114.89 -121.74 108.45 1.1137 +IC H5D CB4 *CB5 H5E 1.1137 108.45 -116.35 108.99 1.1129 +IC CB4 CB5 CB6 CB7 1.5414 114.89 -57.34 113.83 1.5380 +IC CB7 CB5 *CB6 H6D 1.5380 113.83 -121.31 108.98 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.98 -116.37 108.87 1.1123 +IC CB5 CB6 CB7 CB8 1.5394 113.83 179.71 113.63 1.5423 +IC CB8 CB6 *CB7 H7D 1.5423 113.63 -122.27 109.89 1.1123 +IC H7D CB6 *CB7 H7E 1.1123 109.89 -116.77 108.48 1.1132 +IC CB6 CB7 CB8 CB9 1.5380 113.63 -63.29 112.23 1.5093 +IC CB9 CB7 *CB8 H8D 1.5093 112.23 -120.64 107.87 1.1133 +IC H8D CB7 *CB8 H8E 1.1133 107.87 -115.67 108.05 1.1129 +IC CB7 CB8 CB9 CB10 1.5423 112.23 148.17 126.47 1.3460 +IC CB10 CB8 *CB9 H9D 1.3460 126.47 -177.74 114.82 1.1018 +IC CB8 CB9 CB10 CB11 1.5093 126.47 2.77 126.58 1.5092 +IC CB11 CB9 *CB10 H10D 1.5092 126.58 177.26 118.57 1.1029 +IC CB9 CB10 CB11 CB12 1.3460 126.58 -116.82 111.69 1.5096 +IC CB12 CB10 *CB11 H11D 1.5096 111.69 -123.10 108.54 1.1115 +IC H11D CB10 *CB11 H11E 1.1115 108.54 -114.79 111.63 1.1116 +IC CB10 CB11 CB12 CB13 1.5092 111.69 -110.56 126.32 1.3473 +IC CB13 CB11 *CB12 H12D 1.3473 126.32 -178.41 114.77 1.1018 +IC CB11 CB12 CB13 CB14 1.5096 126.32 2.04 125.85 1.5088 +IC CB14 CB12 *CB13 H13D 1.5088 125.85 179.17 118.99 1.1012 +IC CB12 CB13 CB14 CB15 1.3473 125.85 -89.20 112.98 1.5413 +IC CB15 CB13 *CB14 H14D 1.5413 112.98 -121.97 110.15 1.1124 +IC H14D CB13 *CB14 H14E 1.1124 110.15 -116.85 110.43 1.1140 +IC CB13 CB14 CB15 CB16 1.5088 112.98 -66.02 113.67 1.5362 +IC CB16 CB14 *CB15 H15D 1.5362 113.67 -120.47 108.54 1.1134 +IC H15D CB14 *CB15 H15E 1.1134 108.54 -116.71 109.67 1.1135 +IC CB14 CB15 CB16 CB17 1.5413 113.67 -176.61 112.48 1.5339 +IC CB17 CB15 *CB16 H16D 1.5339 112.48 -121.15 109.47 1.1130 +IC H16D CB15 *CB16 H16E 1.1130 109.47 -117.68 109.15 1.1130 +IC CB15 CB16 CB17 CB18 1.5362 112.48 -179.94 113.24 1.5308 +IC CB18 CB16 *CB17 H17D 1.5308 113.24 -121.73 108.82 1.1141 +IC H17D CB16 *CB17 H17E 1.1141 108.82 -116.64 108.69 1.1143 +IC CB16 CB17 CB18 H18D 1.5339 113.24 59.88 110.45 1.1114 +IC H18D CB17 *CB18 H18E 1.1114 110.45 -119.87 110.50 1.1113 +IC H18D CB17 *CB18 H18F 1.1114 110.45 120.03 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5297 112.33 172.47 113.86 1.5361 +IC CC4 CC2 *CC3 H3R 1.5361 113.86 -119.64 108.94 1.1154 +IC H3R CC2 *CC3 H3S 1.1154 108.94 -117.39 109.77 1.1130 +IC CC2 CC3 CC4 CC5 1.5489 113.86 -56.98 112.74 1.5347 +IC CC5 CC3 *CC4 H4R 1.5347 112.74 -119.98 107.98 1.1143 +IC H4R CC3 *CC4 H4S 1.1143 107.98 -117.33 110.39 1.1120 +IC CC3 CC4 CC5 CC6 1.5361 112.74 -154.31 113.28 1.5321 +IC CC6 CC4 *CC5 H5R 1.5321 113.28 -123.53 109.65 1.1125 +IC H5R CC4 *CC5 H5S 1.1125 109.65 -117.22 108.68 1.1132 +IC CC4 CC5 CC6 CC7 1.5347 113.28 -174.72 112.18 1.5360 +IC CC7 CC5 *CC6 H6R 1.5360 112.18 -120.78 108.11 1.1141 +IC H6R CC5 *CC6 H6S 1.1141 108.11 -117.38 110.00 1.1122 +IC CC5 CC6 CC7 CC8 1.5321 112.18 -168.49 113.32 1.5408 +IC CC8 CC6 *CC7 H7R 1.5408 113.32 -121.00 108.07 1.1137 +IC H7R CC6 *CC7 H7S 1.1137 108.07 -116.02 109.54 1.1140 +IC CC6 CC7 CC8 CC9 1.5360 113.32 72.57 111.65 1.5102 +IC CC9 CC7 *CC8 H8R 1.5102 111.65 -124.76 108.23 1.1117 +IC H8R CC7 *CC8 H8S 1.1117 108.23 -115.30 107.95 1.1119 +IC CC7 CC8 CC9 CC10 1.5408 111.65 -134.06 127.67 1.3478 +IC CC10 CC8 *CC9 H9R 1.3478 127.67 179.52 113.97 1.1023 +IC CC8 CC9 CC10 CC11 1.5102 127.67 -0.03 127.34 1.5115 +IC CC11 CC9 *CC10 H10R 1.5115 127.34 179.73 118.07 1.1026 +IC CC9 CC10 CC11 CC12 1.3478 127.34 129.05 112.32 1.5099 +IC CC12 CC10 *CC11 H11R 1.5099 112.32 -123.72 111.60 1.1114 +IC H11R CC10 *CC11 H11S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC10 CC11 CC12 CC13 1.5115 112.32 -84.97 126.59 1.3471 +IC CC13 CC11 *CC12 H12R 1.3471 126.59 -179.05 114.79 1.1010 +IC CC11 CC12 CC13 CC14 1.5099 126.59 1.41 126.41 1.5090 +IC CC14 CC12 *CC13 H13R 1.5090 126.41 178.45 118.70 1.0998 +IC CC12 CC13 CC14 CC15 1.3471 126.41 -125.27 113.39 1.5418 +IC CC15 CC13 *CC14 H14R 1.5418 113.39 -121.44 109.86 1.1131 +IC H14R CC13 *CC14 H14S 1.1131 109.86 -117.22 111.11 1.1131 +IC CC13 CC14 CC15 CC16 1.5090 113.39 -68.63 113.68 1.5381 +IC CC16 CC14 *CC15 H15R 1.5381 113.68 123.30 109.83 1.1129 +IC H15R CC14 *CC15 H15S 1.1129 109.83 116.45 107.53 1.1136 +IC CC14 CC15 CC16 CC17 1.5418 113.68 179.76 113.73 1.5374 +IC CC17 CC15 *CC16 H16R 1.5374 113.73 121.83 108.95 1.1128 +IC H16R CC15 *CC16 H16S 1.1128 108.95 117.24 109.15 1.1127 +IC CC15 CC16 CC17 CC18 1.5381 113.73 63.65 114.54 1.5322 +IC CC18 CC16 *CC17 H17R 1.5322 114.54 -122.47 108.69 1.1141 +IC H17R CC16 *CC17 H17S 1.1141 108.69 -116.13 108.22 1.1148 +IC CC16 CC17 CC18 H18R 1.5374 114.54 56.61 110.47 1.1112 +IC H18R CC17 *CC18 H18S 1.1112 110.47 -120.21 110.86 1.1107 +IC H18R CC17 *CC18 H18T 1.1112 110.47 119.94 110.49 1.1113 +IC CD1 CD2 CD3 CD4 1.5286 112.24 -168.50 113.06 1.5318 +IC CD4 CD2 *CD3 H3X 1.5318 113.06 -122.94 109.98 1.1137 +IC H3X CD2 *CD3 H3Y 1.1137 109.98 -117.36 109.14 1.1136 +IC CD2 CD3 CD4 CD5 1.5470 113.06 175.61 111.87 1.5362 +IC CD5 CD3 *CD4 H4X 1.5362 111.87 -120.66 108.60 1.1128 +IC H4X CD3 *CD4 H4Y 1.1128 108.60 -117.59 109.56 1.1124 +IC CD3 CD4 CD5 CD6 1.5318 111.87 177.84 113.59 1.5356 +IC CD6 CD4 *CD5 H5X 1.5356 113.59 -121.15 108.45 1.1137 +IC H5X CD4 *CD5 H5Y 1.1137 108.45 -116.84 109.16 1.1138 +IC CD4 CD5 CD6 CD7 1.5362 113.59 67.64 113.35 1.5355 +IC CD7 CD5 *CD6 H6X 1.5355 113.35 -122.12 109.12 1.1128 +IC H6X CD5 *CD6 H6Y 1.1128 109.12 -117.25 108.81 1.1134 +IC CD5 CD6 CD7 CD8 1.5356 113.35 -178.50 112.28 1.5389 +IC CD8 CD6 *CD7 H7X 1.5389 112.28 -122.16 108.88 1.1140 +IC H7X CD6 *CD7 H7Y 1.1140 108.88 -116.95 109.16 1.1134 +IC CD6 CD7 CD8 CD9 1.5355 112.28 179.01 111.42 1.5083 +IC CD9 CD7 *CD8 H8X 1.5083 111.42 -122.39 108.26 1.1135 +IC H8X CD7 *CD8 H8Y 1.1135 108.26 -115.32 109.05 1.1118 +IC CD7 CD8 CD9 CD10 1.5389 111.42 -84.39 125.66 1.3464 +IC CD10 CD8 *CD9 H9X 1.3464 125.66 178.86 115.42 1.1011 +IC CD8 CD9 CD10 CD11 1.5083 125.66 0.74 126.41 1.5100 +IC CD11 CD9 *CD10 H10X 1.5100 126.41 178.33 118.71 1.1020 +IC CD9 CD10 CD11 CD12 1.3464 126.41 -119.11 111.66 1.5104 +IC CD12 CD10 *CD11 H11X 1.5104 111.66 -123.67 108.55 1.1120 +IC H11X CD10 *CD11 H11Y 1.1120 108.55 -114.62 111.55 1.1120 +IC CD10 CD11 CD12 CD13 1.5100 111.66 -113.81 126.72 1.3477 +IC CD13 CD11 *CD12 H12X 1.3477 126.72 -178.56 114.59 1.1018 +IC CD11 CD12 CD13 CD14 1.5104 126.72 1.66 126.19 1.5088 +IC CD14 CD12 *CD13 H13X 1.5088 126.19 179.37 118.90 1.1014 +IC CD12 CD13 CD14 CD15 1.3477 126.19 -100.76 112.41 1.5405 +IC CD15 CD13 *CD14 H14X 1.5405 112.41 -121.85 109.83 1.1118 +IC H14X CD13 *CD14 H14Y 1.1118 109.83 -117.23 111.23 1.1116 +IC CD13 CD14 CD15 CD16 1.5088 112.41 170.52 113.29 1.5388 +IC CD16 CD14 *CD15 H15X 1.5388 113.29 -119.71 109.05 1.1153 +IC H15X CD14 *CD15 H15Y 1.1153 109.05 -117.72 109.78 1.1127 +IC CD14 CD15 CD16 CD17 1.5405 113.29 62.69 114.08 1.5347 +IC CD17 CD15 *CD16 H16X 1.5347 114.08 -121.99 108.89 1.1132 +IC H16X CD15 *CD16 H16Y 1.1132 108.89 -116.64 108.76 1.1136 +IC CD15 CD16 CD17 CD18 1.5388 114.08 179.88 112.98 1.5311 +IC CD18 CD16 *CD17 H17X 1.5311 112.98 -121.76 108.79 1.1137 +IC H17X CD16 *CD17 H17Y 1.1137 108.79 -117.11 109.38 1.1133 +IC CD16 CD17 CD18 H18X 1.5347 112.98 60.79 110.28 1.1118 +IC H18X CD17 *CD18 H18Y 1.1118 110.28 -119.90 110.57 1.1110 +IC H18X CD17 *CD18 H18Z 1.1118 110.28 119.81 110.63 1.1110 + +RESI LNACL2 -2.00 ! 3 linoleic acid + 1 linolenic acid cardiolipin + ! Cardiolipin headgroup + 3 linoleoyl chains + 1 linolenoyl chain +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! || || || || +ATOM H32J HAL1 0.09 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H15D--CB15--H15E H15A--CA15 H15X--CD15--H15Y H15R--CC15--H15S +ATOM H2R HAL2 0.09 ! | || | | +ATOM H2S HAL2 0.09 ! | || | | +GROUP ! H16D--CB16--H16E H16A--CA16 H16X--CD16--H16Y H16R--CC16--H16S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM CD1 CL 0.90 ! | | | | +ATOM OD1 OBL -0.63 ! H18F H18C H18Z H18T +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CEL1 -0.15 ! +ATOM H15A HEL1 0.15 ! +GROUP ! +ATOM CA16 CEL1 -0.15 ! +ATOM H16A HEL1 0.15 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 !! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 CA16 +BOND CA16 H16A CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +! IC TABLE +! +IC OP31 C2 *C3 HG31 1.4399 111.73 121.27 107.98 1.1140 +IC HG31 C2 *C3 HG32 1.1140 107.98 116.42 107.18 1.1169 +IC C2 C3 OP31 P3 1.5535 111.73 -167.54 118.79 1.5904 +IC C3 OP31 P3 OP32 1.4399 118.79 79.71 101.55 1.5890 +IC OP32 OP31 *P3 OP33 1.5890 101.55 -115.28 110.31 1.4782 +IC OP32 OP31 *P3 OP34 1.5890 101.55 113.65 109.35 1.4797 +IC OP31 P3 OP32 C31 1.5904 101.55 67.83 117.77 1.4329 +IC P3 OP32 C31 C32 1.5890 117.77 -170.90 110.66 1.5522 +IC C32 OP32 *C31 H31J 1.5522 110.66 121.35 111.65 1.1158 +IC H31J OP32 *C31 H31K 1.1158 111.65 119.36 109.77 1.1144 +IC HG31 C3 C2 C1 1.1140 107.98 -59.84 112.53 1.5592 +IC C1 C3 *C2 OG12 1.5592 112.53 -122.28 106.17 1.4219 +IC C1 C3 *C2 HG22 1.5592 112.53 120.07 108.81 1.1138 +IC C3 C2 OG12 HO12 1.5535 106.17 -43.83 99.95 0.9654 +IC C3 C2 C1 OP11 1.5535 112.53 172.59 114.00 1.4374 +IC OP11 C2 *C1 HG11 1.4374 114.00 -124.71 107.54 1.1153 +IC HG11 C2 *C1 HG12 1.1153 107.54 -114.53 107.04 1.1121 +IC C2 C1 OP11 P1 1.5592 114.00 -97.83 122.51 1.5864 +IC C1 OP11 P1 OP12 1.4374 122.51 -52.87 102.45 1.5913 +IC OP12 OP11 *P1 OP13 1.5913 102.45 114.70 110.17 1.4774 +IC OP12 OP11 *P1 OP14 1.5913 102.45 -115.08 109.36 1.4815 +IC OP11 P1 OP12 C11 1.5864 102.45 -92.52 122.70 1.4285 +IC P1 OP12 C11 C12 1.5913 122.70 85.68 111.92 1.5508 +IC C12 OP12 *C11 H11J 1.5508 111.92 -123.87 112.24 1.1149 +IC H11J OP12 *C11 H11K 1.1149 112.24 -117.66 107.38 1.1110 +IC OP12 C11 C12 C13 1.4285 111.92 161.41 112.21 1.5554 +IC C13 C11 *C12 O12 1.5554 112.21 119.92 107.58 1.4348 +IC O12 C11 *C12 H12J 1.4348 107.58 121.23 105.93 1.1177 +IC C11 C12 O12 CA1 1.5508 107.58 139.57 115.43 1.3169 +IC C12 O12 CA1 CA2 1.4348 115.43 -169.02 109.20 1.5307 +IC CA2 O12 *CA1 OA1 1.5307 109.20 -177.29 125.89 1.2210 +IC O12 CA1 CA2 CA3 1.3169 109.20 -125.27 111.98 1.5453 +IC CA3 CA1 *CA2 H2A 1.5453 111.98 -121.72 106.70 1.1104 +IC H2A CA1 *CA2 H2B 1.1104 106.70 -115.79 108.58 1.1093 +IC C11 C12 C13 O13 1.5508 112.21 -165.73 111.20 1.4484 +IC O13 C12 *C13 H13J 1.4484 111.20 -119.38 107.07 1.1127 +IC H13J C12 *C13 H13K 1.1127 107.07 -115.20 109.28 1.1141 +IC C12 C13 O13 CB1 1.5554 111.20 86.74 113.94 1.3304 +IC C13 O13 CB1 CB2 1.4484 113.94 -157.19 109.85 1.5285 +IC CB2 O13 *CB1 OB1 1.5285 109.85 179.45 125.30 1.2183 +IC O13 CB1 CB2 CB3 1.3304 109.85 170.02 112.02 1.5483 +IC CB3 CB1 *CB2 H2D 1.5483 112.02 -119.03 106.46 1.1119 +IC H2D CB1 *CB2 H2E 1.1119 106.46 -117.11 109.11 1.1053 +IC OP32 C31 C32 C33 1.4329 110.66 -55.34 111.30 1.5520 +IC C33 C31 *C32 O32 1.5520 111.30 121.41 110.58 1.4400 +IC O32 C31 *C32 H32J 1.4400 110.58 121.80 108.53 1.1157 +IC C31 C32 O32 CC1 1.5522 110.58 76.00 113.72 1.3241 +IC C32 O32 CC1 CC2 1.4400 113.72 -175.40 107.92 1.5290 +IC CC2 O32 *CC1 OC1 1.5290 107.92 -174.97 125.21 1.2214 +IC O32 CC1 CC2 CC3 1.3241 107.92 -171.64 114.45 1.5483 +IC CC3 CC1 *CC2 H2R 1.5483 114.45 -120.08 106.50 1.1125 +IC H2R CC1 *CC2 H2S 1.1125 106.50 -115.84 108.14 1.1062 +IC C31 C32 C33 O33 1.5522 111.30 178.27 110.32 1.4463 +IC O33 C32 *C33 H33J 1.4463 110.32 122.56 108.16 1.1137 +IC H33J C32 *C33 H33K 1.1137 108.16 116.60 107.22 1.1149 +IC C32 C33 O33 CD1 1.5520 110.32 176.92 114.52 1.3194 +IC C33 O33 CD1 CD2 1.4463 114.52 169.48 108.39 1.5307 +IC CD2 O33 *CD1 OD1 1.5307 108.39 179.86 126.25 1.2174 +IC O33 CD1 CD2 CD3 1.3194 108.39 166.29 113.39 1.5479 +IC CD3 CD1 *CD2 H2X 1.5479 113.39 -122.94 107.91 1.1081 +IC H2X CD1 *CD2 H2Y 1.1081 107.91 -116.24 106.59 1.1103 +IC CA1 CA2 CA3 CA4 1.5307 111.98 174.09 112.77 1.5340 +IC CA4 CA2 *CA3 H3A 1.5340 112.77 -121.48 109.27 1.1128 +IC H3A CA2 *CA3 H3B 1.1128 109.27 -117.62 108.80 1.1132 +IC CA2 CA3 CA4 CA5 1.5453 112.77 176.67 112.97 1.5369 +IC CA5 CA3 *CA4 H4A 1.5369 112.97 -120.43 108.08 1.1146 +IC H4A CA3 *CA4 H4B 1.1146 108.08 -116.67 109.58 1.1123 +IC CA3 CA4 CA5 CA6 1.5340 112.97 69.98 113.98 1.5366 +IC CA6 CA4 *CA5 H5A 1.5366 113.98 -122.10 108.41 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 108.41 -116.88 108.64 1.1132 +IC CA4 CA5 CA6 CA7 1.5369 113.98 177.62 113.05 1.5384 +IC CA7 CA5 *CA6 H6A 1.5384 113.05 -120.54 108.00 1.1138 +IC H6A CA5 *CA6 H6B 1.1138 108.00 -117.16 109.92 1.1119 +IC CA5 CA6 CA7 CA8 1.5366 113.05 72.32 113.20 1.5409 +IC CA8 CA6 *CA7 H7A 1.5409 113.20 -122.31 108.58 1.1140 +IC H7A CA6 *CA7 H7B 1.1140 108.58 -116.70 108.43 1.1139 +IC CA6 CA7 CA8 CA9 1.5384 113.20 -177.88 111.67 1.5104 +IC CA9 CA7 *CA8 H8A 1.5104 111.67 -121.51 108.57 1.1127 +IC H8A CA7 *CA8 H8B 1.1127 108.57 -114.68 108.68 1.1109 +IC CA7 CA8 CA9 CA10 1.5409 111.67 106.92 126.93 1.3485 +IC CA10 CA8 *CA9 H9A 1.3485 126.93 179.93 114.52 1.1012 +IC CA8 CA9 CA10 CA11 1.5104 126.93 -0.98 126.94 1.5114 +IC CA11 CA9 *CA10 H10A 1.5114 126.94 -179.25 118.31 1.1017 +IC CA9 CA10 CA11 CA12 1.3485 126.94 -125.33 111.90 1.5094 +IC CA12 CA10 *CA11 H11A 1.5094 111.90 -120.91 109.22 1.1122 +IC H11A CA10 *CA11 H11B 1.1122 109.22 -115.26 111.36 1.1089 +IC CA10 CA11 CA12 CA13 1.5114 111.90 103.75 127.05 1.3481 +IC CA13 CA11 *CA12 H12A 1.3481 127.05 178.55 114.54 1.1015 +IC CA11 CA12 CA13 CA14 1.5094 127.05 -1.51 127.29 1.5104 +IC CA14 CA12 *CA13 H13A 1.5104 127.29 -178.83 118.45 1.1012 +IC CA12 CA13 CA14 CA15 1.3481 127.29 123.19 111.92 1.5400 +IC CA15 CA13 *CA14 H14A 1.5400 111.92 -122.30 112.60 1.1129 +IC H14A CA13 *CA14 H14B 1.1129 112.60 -117.91 109.33 1.1129 +IC CA13 CA14 CA15 CA16 1.5104 111.92 172.46 112.42 1.5358 +IC CA16 CA14 *CA15 H15A 1.5358 112.42 -120.26 109.74 1.1138 +IC CA14 CA15 CA16 CA17 1.5400 112.42 -176.77 112.71 1.5339 +IC CA17 CA15 *CA16 H16A 1.5339 112.71 -121.51 109.43 1.1130 +IC CA15 CA16 CA17 CA18 1.5358 112.71 177.47 113.22 1.5311 +IC CA18 CA16 *CA17 H17A 1.5311 113.22 -121.64 108.92 1.1137 +IC H17A CA16 *CA17 H17B 1.1137 108.92 -116.79 108.72 1.1143 +IC CA16 CA17 CA18 H18A 1.5339 113.22 -60.64 110.64 1.1108 +IC H18A CA17 *CA18 H18B 1.1108 110.64 -120.38 110.71 1.1111 +IC H18A CA17 *CA18 H18C 1.1108 110.64 119.78 110.63 1.1119 +IC CB1 CB2 CB3 CB4 1.5285 112.02 -156.49 113.16 1.5352 +IC CB4 CB2 *CB3 H3D 1.5352 113.16 -125.26 110.81 1.1108 +IC H3D CB2 *CB3 H3E 1.1108 110.81 -117.62 108.58 1.1185 +IC CB2 CB3 CB4 CB5 1.5483 113.16 -72.87 114.64 1.5362 +IC CB5 CB3 *CB4 H4D 1.5362 114.64 -121.50 107.87 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 107.87 -115.68 108.33 1.1133 +IC CB3 CB4 CB5 CB6 1.5352 114.64 173.14 113.35 1.5409 +IC CB6 CB4 *CB5 H5D 1.5409 113.35 -120.91 109.12 1.1130 +IC H5D CB4 *CB5 H5E 1.1130 109.12 -117.35 108.69 1.1125 +IC CB4 CB5 CB6 CB7 1.5362 113.35 52.82 114.03 1.5378 +IC CB7 CB5 *CB6 H6D 1.5378 114.03 -120.64 108.65 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.65 -116.83 109.17 1.1121 +IC CB5 CB6 CB7 CB8 1.5409 114.03 179.98 112.81 1.5400 +IC CB8 CB6 *CB7 H7D 1.5400 112.81 -122.98 109.09 1.1121 +IC H7D CB6 *CB7 H7E 1.1121 109.09 -117.53 108.71 1.1155 +IC CB6 CB7 CB8 CB9 1.5378 112.81 177.49 110.85 1.5102 +IC CB9 CB7 *CB8 H8D 1.5102 110.85 -122.35 107.23 1.1140 +IC H8D CB7 *CB8 H8E 1.1140 107.23 -115.61 109.26 1.1115 +IC CB7 CB8 CB9 CB10 1.5400 110.85 -111.54 126.68 1.3485 +IC CB10 CB8 *CB9 H9D 1.3485 126.68 176.66 114.61 1.1007 +IC CB8 CB9 CB10 CB11 1.5102 126.68 -2.77 127.04 1.5103 +IC CB11 CB9 *CB10 H10D 1.5103 127.04 -178.65 118.60 1.1012 +IC CB9 CB10 CB11 CB12 1.3485 127.04 96.60 112.31 1.5135 +IC CB12 CB10 *CB11 H11D 1.5135 112.31 -125.47 110.37 1.1105 +IC H11D CB10 *CB11 H11E 1.1105 110.37 -114.37 108.83 1.1122 +IC CB10 CB11 CB12 CB13 1.5103 112.31 -123.24 127.49 1.3487 +IC CB13 CB11 *CB12 H12D 1.3487 127.49 -179.18 114.92 1.1025 +IC CB11 CB12 CB13 CB14 1.5135 127.49 0.10 127.26 1.5079 +IC CB14 CB12 *CB13 H13D 1.5079 127.26 -179.25 118.69 1.1053 +IC CB12 CB13 CB14 CB15 1.3487 127.26 123.97 111.98 1.5384 +IC CB15 CB13 *CB14 H14D 1.5384 111.98 -120.79 111.90 1.1093 +IC H14D CB13 *CB14 H14E 1.1093 111.90 -118.90 109.68 1.1138 +IC CB13 CB14 CB15 CB16 1.5079 111.98 -173.48 111.85 1.5348 +IC CB16 CB14 *CB15 H15D 1.5348 111.85 -121.68 109.78 1.1147 +IC H15D CB14 *CB15 H15E 1.1147 109.78 -117.79 109.28 1.1119 +IC CB14 CB15 CB16 CB17 1.5384 111.85 179.99 113.35 1.5313 +IC CB17 CB15 *CB16 H16D 1.5313 113.35 -121.42 108.85 1.1101 +IC H16D CB15 *CB16 H16E 1.1101 108.85 -117.19 108.74 1.1110 +IC CB15 CB16 CB17 CB18 1.5348 113.35 -178.76 113.12 1.5314 +IC CB18 CB16 *CB17 H17D 1.5314 113.12 -121.82 108.25 1.1149 +IC H17D CB16 *CB17 H17E 1.1149 108.25 -115.96 109.19 1.1126 +IC CB16 CB17 CB18 H18D 1.5313 113.12 -178.27 110.36 1.1112 +IC H18D CB17 *CB18 H18E 1.1112 110.36 -120.53 110.61 1.1103 +IC H18D CB17 *CB18 H18F 1.1112 110.36 119.56 110.21 1.1112 +IC CC1 CC2 CC3 CC4 1.5290 114.45 61.17 115.54 1.5407 +IC CC4 CC2 *CC3 H3R 1.5407 115.54 -123.39 108.81 1.1159 +IC H3R CC2 *CC3 H3S 1.1159 108.81 -115.09 107.30 1.1128 +IC CC2 CC3 CC4 CC5 1.5483 115.54 48.75 115.70 1.5381 +IC CC5 CC3 *CC4 H4R 1.5381 115.70 -121.95 108.35 1.1141 +IC H4R CC3 *CC4 H4S 1.1141 108.35 -115.67 107.88 1.1118 +IC CC3 CC4 CC5 CC6 1.5407 115.70 59.37 113.26 1.5339 +IC CC6 CC4 *CC5 H5R 1.5339 113.26 -122.42 108.68 1.1122 +IC H5R CC4 *CC5 H5S 1.1122 108.68 -116.61 108.64 1.1128 +IC CC4 CC5 CC6 CC7 1.5381 113.26 175.46 114.41 1.5382 +IC CC7 CC5 *CC6 H6R 1.5382 114.41 -121.44 108.39 1.1118 +IC H6R CC5 *CC6 H6S 1.1118 108.39 -116.44 108.77 1.1127 +IC CC5 CC6 CC7 CC8 1.5339 114.41 50.21 113.91 1.5402 +IC CC8 CC6 *CC7 H7R 1.5402 113.91 -122.10 108.87 1.1136 +IC H7R CC6 *CC7 H7S 1.1136 108.87 -116.44 107.40 1.1147 +IC CC6 CC7 CC8 CC9 1.5382 113.91 171.45 111.26 1.5090 +IC CC9 CC7 *CC8 H8R 1.5090 111.26 -123.76 107.81 1.1114 +IC H8R CC7 *CC8 H8S 1.1114 107.81 -115.28 108.84 1.1122 +IC CC7 CC8 CC9 CC10 1.5402 111.26 -128.36 127.23 1.3472 +IC CC10 CC8 *CC9 H9R 1.3472 127.23 178.70 114.30 1.1010 +IC CC8 CC9 CC10 CC11 1.5090 127.23 -1.15 127.54 1.5084 +IC CC11 CC9 *CC10 H10R 1.5084 127.54 -179.59 118.30 1.1015 +IC CC9 CC10 CC11 CC12 1.3472 127.54 121.83 111.08 1.5090 +IC CC12 CC10 *CC11 H11R 1.5090 111.08 -121.38 111.45 1.1092 +IC H11R CC10 *CC11 H11S 1.1092 111.45 -115.12 108.94 1.1091 +IC CC10 CC11 CC12 CC13 1.5084 111.08 114.57 127.61 1.3469 +IC CC13 CC11 *CC12 H12R 1.3469 127.61 179.18 114.07 1.1019 +IC CC11 CC12 CC13 CC14 1.5090 127.61 -1.12 127.24 1.5089 +IC CC14 CC12 *CC13 H13R 1.5089 127.24 -179.24 118.36 1.1008 +IC CC12 CC13 CC14 CC15 1.3469 127.24 -127.92 112.49 1.5415 +IC CC15 CC13 *CC14 H14R 1.5415 112.49 -120.38 109.34 1.1135 +IC H14R CC13 *CC14 H14S 1.1135 109.34 -118.08 112.29 1.1108 +IC CC13 CC14 CC15 CC16 1.5089 112.49 64.28 113.82 1.5372 +IC CC16 CC14 *CC15 H15R 1.5372 113.82 -123.02 109.95 1.1128 +IC H15R CC14 *CC15 H15S 1.1128 109.95 -116.79 108.08 1.1141 +IC CC14 CC15 CC16 CC17 1.5415 113.82 175.12 112.35 1.5342 +IC CC17 CC15 *CC16 H16R 1.5342 112.35 121.44 109.60 1.1127 +IC H16R CC15 *CC16 H16S 1.1127 109.60 117.48 109.22 1.1130 +IC CC15 CC16 CC17 CC18 1.5372 112.35 177.84 113.41 1.5303 +IC CC18 CC16 *CC17 H17R 1.5303 113.41 -121.68 108.79 1.1140 +IC H17R CC16 *CC17 H17S 1.1140 108.79 -116.65 108.60 1.1141 +IC CC16 CC17 CC18 H18R 1.5342 113.41 177.41 110.78 1.1108 +IC H18R CC17 *CC18 H18S 1.1108 110.78 120.14 110.47 1.1110 +IC H18R CC17 *CC18 H18T 1.1108 110.78 -120.28 110.55 1.1114 +IC CD1 CD2 CD3 CD4 1.5307 113.39 169.15 112.93 1.5372 +IC CD4 CD2 *CD3 H3X 1.5372 112.93 -120.02 109.25 1.1156 +IC H3X CD2 *CD3 H3Y 1.1156 109.25 -117.49 109.59 1.1130 +IC CD2 CD3 CD4 CD5 1.5479 112.93 59.54 113.85 1.5360 +IC CD5 CD3 *CD4 H4X 1.5360 113.85 -121.33 108.32 1.1134 +IC H4X CD3 *CD4 H4Y 1.1134 108.32 -116.71 109.15 1.1132 +IC CD3 CD4 CD5 CD6 1.5372 113.85 -177.43 112.79 1.5357 +IC CD6 CD4 *CD5 H5X 1.5357 112.79 -122.43 109.70 1.1122 +IC H5X CD4 *CD5 H5Y 1.1122 109.70 -117.86 109.15 1.1139 +IC CD4 CD5 CD6 CD7 1.5360 112.79 173.65 112.21 1.5365 +IC CD7 CD5 *CD6 H6X 1.5365 112.21 -119.39 108.19 1.1136 +IC H6X CD5 *CD6 H6Y 1.1136 108.19 -117.35 110.05 1.1111 +IC CD5 CD6 CD7 CD8 1.5357 112.21 -164.07 113.53 1.5412 +IC CD8 CD6 *CD7 H7X 1.5412 113.53 -125.12 110.25 1.1118 +IC H7X CD6 *CD7 H7Y 1.1118 110.25 -116.30 107.52 1.1152 +IC CD6 CD7 CD8 CD9 1.5365 113.53 -72.33 113.26 1.5081 +IC CD9 CD7 *CD8 H8X 1.5081 113.26 -123.64 107.20 1.1122 +IC H8X CD7 *CD8 H8Y 1.1122 107.20 -114.54 108.43 1.1124 +IC CD7 CD8 CD9 CD10 1.5412 113.26 -141.33 126.38 1.3479 +IC CD10 CD8 *CD9 H9X 1.3479 126.38 -179.10 114.78 1.1010 +IC CD8 CD9 CD10 CD11 1.5081 126.38 0.12 126.84 1.5114 +IC CD11 CD9 *CD10 H10X 1.5114 126.84 -179.87 118.43 1.1016 +IC CD9 CD10 CD11 CD12 1.3479 126.84 -106.33 111.23 1.5105 +IC CD12 CD10 *CD11 H11X 1.5105 111.23 -120.37 109.03 1.1122 +IC H11X CD10 *CD11 H11Y 1.1122 109.03 -114.91 111.58 1.1099 +IC CD10 CD11 CD12 CD13 1.5114 111.23 109.38 127.41 1.3486 +IC CD13 CD11 *CD12 H12X 1.3486 127.41 179.19 114.40 1.1015 +IC CD11 CD12 CD13 CD14 1.5105 127.41 -1.41 127.65 1.5109 +IC CD14 CD12 *CD13 H13X 1.5109 127.65 -178.15 118.24 1.1012 +IC CD12 CD13 CD14 CD15 1.3486 127.65 -115.93 111.19 1.5399 +IC CD15 CD13 *CD14 H14X 1.5399 111.19 -120.10 109.72 1.1126 +IC H14X CD13 *CD14 H14Y 1.1126 109.72 -118.73 112.54 1.1122 +IC CD13 CD14 CD15 CD16 1.5109 111.19 -174.42 112.98 1.5354 +IC CD16 CD14 *CD15 H15X 1.5354 112.98 -121.07 109.22 1.1143 +IC H15X CD14 *CD15 H15Y 1.1143 109.22 -117.98 109.91 1.1138 +IC CD14 CD15 CD16 CD17 1.5399 112.98 179.46 112.15 1.5344 +IC CD17 CD15 *CD16 H16X 1.5344 112.15 -121.15 109.44 1.1128 +IC H16X CD15 *CD16 H16Y 1.1128 109.44 -117.66 109.26 1.1126 +IC CD15 CD16 CD17 CD18 1.5354 112.15 179.70 113.67 1.5310 +IC CD18 CD16 *CD17 H17X 1.5310 113.67 -121.71 108.44 1.1139 +IC H17X CD16 *CD17 H17Y 1.1139 108.44 -116.35 108.83 1.1138 +IC CD16 CD17 CD18 H18X 1.5344 113.67 -178.87 110.70 1.1108 +IC H18X CD17 *CD18 H18Y 1.1108 110.70 -120.14 110.59 1.1104 +IC H18X CD17 *CD18 H18Z 1.1108 110.70 119.96 110.62 1.1117 + +RESI LNBCL1 -1.00 ! 3 Linoleic acid + 1 linolenic acid cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 3 linoleoly + 1 linolenoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +ATOM H2E HAL2 0.09 ! || || || || +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15 H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM CC2 CTL2 -0.22 ! || | | | +ATOM H2R HAL2 0.09 ! H16D--CB16 H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18F H18C H18Z H18T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CEL1 -0.15 ! +ATOM H15D HEL1 0.15 ! +GROUP ! +ATOM CB16 CEL1 -0.15 ! +ATOM H16D HEL1 0.15 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 CB16 +BOND CB16 H16D CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4272 111.57 124.87 107.78 1.1169 +IC HG31 C2 *C3 HG32 1.1169 107.78 115.89 109.04 1.1124 +IC C2 C3 OP31 P3 1.5483 111.57 118.08 122.98 1.5819 +IC C3 OP31 P3 OP32 1.4272 122.98 37.85 102.14 1.5830 +IC OP32 OP31 *P3 OP33 1.5830 102.14 -113.92 107.98 1.4793 +IC OP32 OP31 *P3 OP34 1.5830 102.14 115.66 109.62 1.4740 +IC OP31 P3 OP32 C31 1.5819 102.14 69.85 119.33 1.4301 +IC P3 OP32 C31 C32 1.5830 119.33 176.40 110.18 1.5529 +IC C32 OP32 *C31 H31J 1.5529 110.18 120.82 110.67 1.1139 +IC H31J OP32 *C31 H31K 1.1139 110.67 119.45 110.95 1.1159 +IC HG31 C3 C2 C1 1.1169 107.78 60.13 113.14 1.5594 +IC C1 C3 *C2 OG12 1.5594 113.14 -122.65 107.36 1.4314 +IC C1 C3 *C2 HG22 1.5594 113.14 119.50 108.81 1.1137 +IC C3 C2 OG12 HO12 1.5483 107.36 -59.74 104.73 0.9611 +IC C3 C2 C1 OP11 1.5483 113.14 102.14 111.29 1.4365 +IC OP11 C2 *C1 HG11 1.4365 111.29 -124.72 105.61 1.1191 +IC HG11 C2 *C1 HG12 1.1191 105.61 -115.38 108.40 1.1138 +IC C2 C1 OP11 P1 1.5594 111.29 -157.61 115.85 1.5685 +IC C1 OP11 P1 OP12 1.4365 115.85 -14.21 104.93 1.5653 +IC OP12 OP11 *P1 OP13 1.5653 104.93 115.00 111.23 1.5595 +IC OP12 OP11 *P1 OP14 1.5653 104.93 -120.71 114.44 1.4714 +IC OP11 P1 OP13 HP13 1.5685 111.23 -49.71 108.79 0.9805 +IC OP11 P1 OP12 C11 1.5685 104.93 168.45 117.56 1.4279 +IC P1 OP12 C11 C12 1.5653 117.56 -104.42 112.05 1.5631 +IC C12 OP12 *C11 H11J 1.5631 112.05 -116.94 106.96 1.1115 +IC H11J OP12 *C11 H11K 1.1115 106.96 -117.70 114.83 1.1174 +IC OP12 C11 C12 C13 1.4279 112.05 -169.61 110.60 1.5613 +IC C13 C11 *C12 O12 1.5613 110.60 124.16 109.17 1.4428 +IC O12 C11 *C12 H12J 1.4428 109.17 118.13 106.49 1.1175 +IC C11 C12 O12 CA1 1.5631 109.17 161.88 113.49 1.3343 +IC C12 O12 CA1 CA2 1.4428 113.49 -169.35 108.84 1.5280 +IC CA2 O12 *CA1 OA1 1.5280 108.84 179.80 125.17 1.2183 +IC O12 CA1 CA2 CA3 1.3343 108.84 -146.40 113.25 1.5456 +IC CA3 CA1 *CA2 H2A 1.5456 113.25 -119.97 106.28 1.1109 +IC H2A CA1 *CA2 H2B 1.1109 106.28 -116.75 108.94 1.1073 +IC C11 C12 C13 O13 1.5631 110.60 48.04 111.75 1.4444 +IC O13 C12 *C13 H13J 1.4444 111.75 -117.92 106.48 1.1131 +IC H13J C12 *C13 H13K 1.1131 106.48 -115.07 111.40 1.1131 +IC C12 C13 O13 CB1 1.5613 111.75 88.82 115.87 1.3297 +IC C13 O13 CB1 CB2 1.4444 115.87 -174.80 108.56 1.5287 +IC CB2 O13 *CB1 OB1 1.5287 108.56 -178.49 126.34 1.2145 +IC O13 CB1 CB2 CB3 1.3297 108.56 152.47 112.16 1.5454 +IC CB3 CB1 *CB2 H2D 1.5454 112.16 -121.52 108.74 1.1089 +IC H2D CB1 *CB2 H2E 1.1089 108.74 -117.40 106.94 1.1083 +IC OP32 C31 C32 C33 1.4301 110.18 -69.33 110.65 1.5522 +IC C33 C31 *C32 O32 1.5522 110.65 120.01 111.21 1.4395 +IC O32 C31 *C32 H32J 1.4395 111.21 122.30 108.97 1.1146 +IC C31 C32 O32 CC1 1.5529 111.21 69.31 115.35 1.3120 +IC C32 O32 CC1 CC2 1.4395 115.35 -171.71 108.60 1.5297 +IC CC2 O32 *CC1 OC1 1.5297 108.60 -178.02 126.78 1.2186 +IC O32 CC1 CC2 CC3 1.3120 108.60 -59.72 112.33 1.5489 +IC CC3 CC1 *CC2 H2R 1.5489 112.33 -122.26 107.83 1.1075 +IC H2R CC1 *CC2 H2S 1.1075 107.83 -116.44 106.39 1.1097 +IC C31 C32 C33 O33 1.5529 110.65 179.11 109.99 1.4464 +IC O33 C32 *C33 H33J 1.4464 109.99 121.93 109.29 1.1119 +IC H33J C32 *C33 H33K 1.1119 109.29 116.57 106.09 1.1186 +IC C32 C33 O33 CD1 1.5522 109.99 -159.03 114.19 1.3237 +IC C33 O33 CD1 CD2 1.4464 114.19 164.21 109.32 1.5286 +IC CD2 O33 *CD1 OD1 1.5286 109.32 -178.45 126.02 1.2156 +IC O33 CD1 CD2 CD3 1.3237 109.32 -46.26 112.24 1.5470 +IC CD3 CD1 *CD2 H2X 1.5470 112.24 -120.21 106.48 1.1100 +IC H2X CD1 *CD2 H2Y 1.1100 106.48 -117.13 108.41 1.1069 +IC CA1 CA2 CA3 CA4 1.5280 113.25 70.18 112.81 1.5346 +IC CA4 CA2 *CA3 H3A 1.5346 112.81 -123.14 110.14 1.1142 +IC H3A CA2 *CA3 H3B 1.1142 110.14 -116.66 107.70 1.1125 +IC CA2 CA3 CA4 CA5 1.5456 112.81 172.40 112.79 1.5353 +IC CA5 CA3 *CA4 H4A 1.5353 112.79 -122.05 109.90 1.1116 +IC H4A CA3 *CA4 H4B 1.1116 109.90 -117.14 108.37 1.1150 +IC CA3 CA4 CA5 CA6 1.5346 112.79 167.30 112.42 1.5358 +IC CA6 CA4 *CA5 H5A 1.5358 112.42 -120.63 108.10 1.1132 +IC H5A CA4 *CA5 H5B 1.1132 108.10 -117.30 109.47 1.1120 +IC CA4 CA5 CA6 CA7 1.5353 112.42 177.91 114.45 1.5409 +IC CA7 CA5 *CA6 H6A 1.5409 114.45 -121.60 108.84 1.1121 +IC H6A CA5 *CA6 H6B 1.1121 108.84 -116.16 108.48 1.1134 +IC CA5 CA6 CA7 CA8 1.5358 114.45 53.66 115.58 1.5440 +IC CA8 CA6 *CA7 H7A 1.5440 115.58 -121.63 108.47 1.1138 +IC H7A CA6 *CA7 H7B 1.1138 108.47 -116.24 108.32 1.1141 +IC CA6 CA7 CA8 CA9 1.5409 115.58 55.01 112.73 1.5097 +IC CA9 CA7 *CA8 H8A 1.5097 112.73 -121.48 108.57 1.1114 +IC H8A CA7 *CA8 H8B 1.1114 108.57 -114.55 107.55 1.1126 +IC CA7 CA8 CA9 CA10 1.5440 112.73 109.39 127.97 1.3474 +IC CA10 CA8 *CA9 H9A 1.3474 127.97 -179.15 113.83 1.1025 +IC CA8 CA9 CA10 CA11 1.5097 127.97 0.64 127.89 1.5108 +IC CA11 CA9 *CA10 H10A 1.5108 127.89 179.31 117.75 1.1014 +IC CA9 CA10 CA11 CA12 1.3474 127.89 -112.95 111.22 1.5114 +IC CA12 CA10 *CA11 H11A 1.5114 111.22 -120.46 108.90 1.1119 +IC H11A CA10 *CA11 H11B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA10 CA11 CA12 CA13 1.5108 111.22 134.57 126.37 1.3465 +IC CA13 CA11 *CA12 H12A 1.3465 126.37 -177.01 115.27 1.1018 +IC CA11 CA12 CA13 CA14 1.5114 126.37 3.15 126.32 1.5077 +IC CA14 CA12 *CA13 H13A 1.5077 126.32 178.37 118.79 1.1003 +IC CA12 CA13 CA14 CA15 1.3465 126.32 -92.58 113.47 1.5417 +IC CA15 CA13 *CA14 H14A 1.5417 113.47 -122.01 110.01 1.1123 +IC H14A CA13 *CA14 H14B 1.1123 110.01 -116.77 110.38 1.1120 +IC CA13 CA14 CA15 CA16 1.5077 113.47 -63.55 113.58 1.5369 +IC CA16 CA14 *CA15 H15A 1.5369 113.58 -120.33 108.08 1.1132 +IC H15A CA14 *CA15 H15B 1.1132 108.08 -116.59 109.36 1.1132 +IC CA14 CA15 CA16 CA17 1.5417 113.58 -171.21 113.87 1.5374 +IC CA17 CA15 *CA16 H16A 1.5374 113.87 -121.70 108.87 1.1122 +IC H16A CA15 *CA16 H16B 1.1122 108.87 -117.00 108.72 1.1132 +IC CA15 CA16 CA17 CA18 1.5369 113.87 -61.57 114.41 1.5314 +IC CA18 CA16 *CA17 H17A 1.5314 114.41 -121.26 108.12 1.1148 +IC H17A CA16 *CA17 H17B 1.1148 108.12 -116.30 108.76 1.1136 +IC CA16 CA17 CA18 H18A 1.5374 114.41 63.53 110.93 1.1107 +IC H18A CA17 *CA18 H18B 1.1107 110.93 -119.76 110.34 1.1109 +IC H18A CA17 *CA18 H18C 1.1107 110.93 120.37 110.77 1.1100 +IC CB1 CB2 CB3 CB4 1.5287 112.16 178.44 113.36 1.5384 +IC CB4 CB2 *CB3 H3D 1.5384 113.36 -122.28 109.76 1.1140 +IC H3D CB2 *CB3 H3E 1.1140 109.76 -116.69 109.13 1.1151 +IC CB2 CB3 CB4 CB5 1.5454 113.36 -60.74 115.02 1.5414 +IC CB5 CB3 *CB4 H4D 1.5414 115.02 -121.57 108.33 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 108.33 -116.10 108.96 1.1133 +IC CB3 CB4 CB5 CB6 1.5384 115.02 -51.86 114.89 1.5394 +IC CB6 CB4 *CB5 H5D 1.5394 114.89 -121.74 108.45 1.1137 +IC H5D CB4 *CB5 H5E 1.1137 108.45 -116.35 108.99 1.1129 +IC CB4 CB5 CB6 CB7 1.5414 114.89 -57.34 113.83 1.5380 +IC CB7 CB5 *CB6 H6D 1.5380 113.83 -121.31 108.98 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.98 -116.37 108.87 1.1123 +IC CB5 CB6 CB7 CB8 1.5394 113.83 179.71 113.63 1.5423 +IC CB8 CB6 *CB7 H7D 1.5423 113.63 -122.27 109.89 1.1123 +IC H7D CB6 *CB7 H7E 1.1123 109.89 -116.77 108.48 1.1132 +IC CB6 CB7 CB8 CB9 1.5380 113.63 -63.29 112.23 1.5093 +IC CB9 CB7 *CB8 H8D 1.5093 112.23 -120.64 107.87 1.1133 +IC H8D CB7 *CB8 H8E 1.1133 107.87 -115.67 108.05 1.1129 +IC CB7 CB8 CB9 CB10 1.5423 112.23 148.17 126.47 1.3460 +IC CB10 CB8 *CB9 H9D 1.3460 126.47 -177.74 114.82 1.1018 +IC CB8 CB9 CB10 CB11 1.5093 126.47 2.77 126.58 1.5092 +IC CB11 CB9 *CB10 H10D 1.5092 126.58 177.26 118.57 1.1029 +IC CB9 CB10 CB11 CB12 1.3460 126.58 -116.82 111.69 1.5096 +IC CB12 CB10 *CB11 H11D 1.5096 111.69 -123.10 108.54 1.1115 +IC H11D CB10 *CB11 H11E 1.1115 108.54 -114.79 111.63 1.1116 +IC CB10 CB11 CB12 CB13 1.5092 111.69 -110.56 126.32 1.3473 +IC CB13 CB11 *CB12 H12D 1.3473 126.32 -178.41 114.77 1.1018 +IC CB11 CB12 CB13 CB14 1.5096 126.32 2.04 125.85 1.5088 +IC CB14 CB12 *CB13 H13D 1.5088 125.85 179.17 118.99 1.1012 +IC CB12 CB13 CB14 CB15 1.3473 125.85 -89.20 112.98 1.5413 +IC CB15 CB13 *CB14 H14D 1.5413 112.98 -121.97 110.15 1.1124 +IC H14D CB13 *CB14 H14E 1.1124 110.15 -116.85 110.43 1.1140 +IC CB13 CB14 CB15 CB16 1.5088 112.98 -66.02 113.67 1.5362 +IC CB16 CB14 *CB15 H15D 1.5362 113.67 -120.47 108.54 1.1134 +IC CB14 CB15 CB16 CB17 1.5413 113.67 -176.61 112.48 1.5339 +IC CB17 CB15 *CB16 H16D 1.5339 112.48 -121.15 109.47 1.1130 +IC CB15 CB16 CB17 CB18 1.5362 112.48 -179.94 113.24 1.5308 +IC CB18 CB16 *CB17 H17D 1.5308 113.24 -121.73 108.82 1.1141 +IC H17D CB16 *CB17 H17E 1.1141 108.82 -116.64 108.69 1.1143 +IC CB16 CB17 CB18 H18D 1.5339 113.24 59.88 110.45 1.1114 +IC H18D CB17 *CB18 H18E 1.1114 110.45 -119.87 110.50 1.1113 +IC H18D CB17 *CB18 H18F 1.1114 110.45 120.03 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5297 112.33 172.47 113.86 1.5361 +IC CC4 CC2 *CC3 H3R 1.5361 113.86 -119.64 108.94 1.1154 +IC H3R CC2 *CC3 H3S 1.1154 108.94 -117.39 109.77 1.1130 +IC CC2 CC3 CC4 CC5 1.5489 113.86 -56.98 112.74 1.5347 +IC CC5 CC3 *CC4 H4R 1.5347 112.74 -119.98 107.98 1.1143 +IC H4R CC3 *CC4 H4S 1.1143 107.98 -117.33 110.39 1.1120 +IC CC3 CC4 CC5 CC6 1.5361 112.74 -154.31 113.28 1.5321 +IC CC6 CC4 *CC5 H5R 1.5321 113.28 -123.53 109.65 1.1125 +IC H5R CC4 *CC5 H5S 1.1125 109.65 -117.22 108.68 1.1132 +IC CC4 CC5 CC6 CC7 1.5347 113.28 -174.72 112.18 1.5360 +IC CC7 CC5 *CC6 H6R 1.5360 112.18 -120.78 108.11 1.1141 +IC H6R CC5 *CC6 H6S 1.1141 108.11 -117.38 110.00 1.1122 +IC CC5 CC6 CC7 CC8 1.5321 112.18 -168.49 113.32 1.5408 +IC CC8 CC6 *CC7 H7R 1.5408 113.32 -121.00 108.07 1.1137 +IC H7R CC6 *CC7 H7S 1.1137 108.07 -116.02 109.54 1.1140 +IC CC6 CC7 CC8 CC9 1.5360 113.32 72.57 111.65 1.5102 +IC CC9 CC7 *CC8 H8R 1.5102 111.65 -124.76 108.23 1.1117 +IC H8R CC7 *CC8 H8S 1.1117 108.23 -115.30 107.95 1.1119 +IC CC7 CC8 CC9 CC10 1.5408 111.65 -134.06 127.67 1.3478 +IC CC10 CC8 *CC9 H9R 1.3478 127.67 179.52 113.97 1.1023 +IC CC8 CC9 CC10 CC11 1.5102 127.67 -0.03 127.34 1.5115 +IC CC11 CC9 *CC10 H10R 1.5115 127.34 179.73 118.07 1.1026 +IC CC9 CC10 CC11 CC12 1.3478 127.34 129.05 112.32 1.5099 +IC CC12 CC10 *CC11 H11R 1.5099 112.32 -123.72 111.60 1.1114 +IC H11R CC10 *CC11 H11S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC10 CC11 CC12 CC13 1.5115 112.32 -84.97 126.59 1.3471 +IC CC13 CC11 *CC12 H12R 1.3471 126.59 -179.05 114.79 1.1010 +IC CC11 CC12 CC13 CC14 1.5099 126.59 1.41 126.41 1.5090 +IC CC14 CC12 *CC13 H13R 1.5090 126.41 178.45 118.70 1.0998 +IC CC12 CC13 CC14 CC15 1.3471 126.41 -125.27 113.39 1.5418 +IC CC15 CC13 *CC14 H14R 1.5418 113.39 -121.44 109.86 1.1131 +IC H14R CC13 *CC14 H14S 1.1131 109.86 -117.22 111.11 1.1131 +IC CC13 CC14 CC15 CC16 1.5090 113.39 -68.63 113.68 1.5381 +IC CC16 CC14 *CC15 H15R 1.5381 113.68 123.30 109.83 1.1129 +IC H15R CC14 *CC15 H15S 1.1129 109.83 116.45 107.53 1.1136 +IC CC14 CC15 CC16 CC17 1.5418 113.68 179.76 113.73 1.5374 +IC CC17 CC15 *CC16 H16R 1.5374 113.73 121.83 108.95 1.1128 +IC H16R CC15 *CC16 H16S 1.1128 108.95 117.24 109.15 1.1127 +IC CC15 CC16 CC17 CC18 1.5381 113.73 63.65 114.54 1.5322 +IC CC18 CC16 *CC17 H17R 1.5322 114.54 -122.47 108.69 1.1141 +IC H17R CC16 *CC17 H17S 1.1141 108.69 -116.13 108.22 1.1148 +IC CC16 CC17 CC18 H18R 1.5374 114.54 56.61 110.47 1.1112 +IC H18R CC17 *CC18 H18S 1.1112 110.47 -120.21 110.86 1.1107 +IC H18R CC17 *CC18 H18T 1.1112 110.47 119.94 110.49 1.1113 +IC CD1 CD2 CD3 CD4 1.5286 112.24 -168.50 113.06 1.5318 +IC CD4 CD2 *CD3 H3X 1.5318 113.06 -122.94 109.98 1.1137 +IC H3X CD2 *CD3 H3Y 1.1137 109.98 -117.36 109.14 1.1136 +IC CD2 CD3 CD4 CD5 1.5470 113.06 175.61 111.87 1.5362 +IC CD5 CD3 *CD4 H4X 1.5362 111.87 -120.66 108.60 1.1128 +IC H4X CD3 *CD4 H4Y 1.1128 108.60 -117.59 109.56 1.1124 +IC CD3 CD4 CD5 CD6 1.5318 111.87 177.84 113.59 1.5356 +IC CD6 CD4 *CD5 H5X 1.5356 113.59 -121.15 108.45 1.1137 +IC H5X CD4 *CD5 H5Y 1.1137 108.45 -116.84 109.16 1.1138 +IC CD4 CD5 CD6 CD7 1.5362 113.59 67.64 113.35 1.5355 +IC CD7 CD5 *CD6 H6X 1.5355 113.35 -122.12 109.12 1.1128 +IC H6X CD5 *CD6 H6Y 1.1128 109.12 -117.25 108.81 1.1134 +IC CD5 CD6 CD7 CD8 1.5356 113.35 -178.50 112.28 1.5389 +IC CD8 CD6 *CD7 H7X 1.5389 112.28 -122.16 108.88 1.1140 +IC H7X CD6 *CD7 H7Y 1.1140 108.88 -116.95 109.16 1.1134 +IC CD6 CD7 CD8 CD9 1.5355 112.28 179.01 111.42 1.5083 +IC CD9 CD7 *CD8 H8X 1.5083 111.42 -122.39 108.26 1.1135 +IC H8X CD7 *CD8 H8Y 1.1135 108.26 -115.32 109.05 1.1118 +IC CD7 CD8 CD9 CD10 1.5389 111.42 -84.39 125.66 1.3464 +IC CD10 CD8 *CD9 H9X 1.3464 125.66 178.86 115.42 1.1011 +IC CD8 CD9 CD10 CD11 1.5083 125.66 0.74 126.41 1.5100 +IC CD11 CD9 *CD10 H10X 1.5100 126.41 178.33 118.71 1.1020 +IC CD9 CD10 CD11 CD12 1.3464 126.41 -119.11 111.66 1.5104 +IC CD12 CD10 *CD11 H11X 1.5104 111.66 -123.67 108.55 1.1120 +IC H11X CD10 *CD11 H11Y 1.1120 108.55 -114.62 111.55 1.1120 +IC CD10 CD11 CD12 CD13 1.5100 111.66 -113.81 126.72 1.3477 +IC CD13 CD11 *CD12 H12X 1.3477 126.72 -178.56 114.59 1.1018 +IC CD11 CD12 CD13 CD14 1.5104 126.72 1.66 126.19 1.5088 +IC CD14 CD12 *CD13 H13X 1.5088 126.19 179.37 118.90 1.1014 +IC CD12 CD13 CD14 CD15 1.3477 126.19 -100.76 112.41 1.5405 +IC CD15 CD13 *CD14 H14X 1.5405 112.41 -121.85 109.83 1.1118 +IC H14X CD13 *CD14 H14Y 1.1118 109.83 -117.23 111.23 1.1116 +IC CD13 CD14 CD15 CD16 1.5088 112.41 170.52 113.29 1.5388 +IC CD16 CD14 *CD15 H15X 1.5388 113.29 -119.71 109.05 1.1153 +IC H15X CD14 *CD15 H15Y 1.1153 109.05 -117.72 109.78 1.1127 +IC CD14 CD15 CD16 CD17 1.5405 113.29 62.69 114.08 1.5347 +IC CD17 CD15 *CD16 H16X 1.5347 114.08 -121.99 108.89 1.1132 +IC H16X CD15 *CD16 H16Y 1.1132 108.89 -116.64 108.76 1.1136 +IC CD15 CD16 CD17 CD18 1.5388 114.08 179.88 112.98 1.5311 +IC CD18 CD16 *CD17 H17X 1.5311 112.98 -121.76 108.79 1.1137 +IC H17X CD16 *CD17 H17Y 1.1137 108.79 -117.11 109.38 1.1133 +IC CD16 CD17 CD18 H18X 1.5347 112.98 60.79 110.28 1.1118 +IC H18X CD17 *CD18 H18Y 1.1118 110.28 -119.90 110.57 1.1110 +IC H18X CD17 *CD18 H18Z 1.1118 110.28 119.81 110.63 1.1110 + +RESI LNBCL2 -2.00 ! 3 linoleic acid + 1 linolenic acid chains Cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 3 linoleoyl + 1 linolenoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! || || || || +ATOM H32J HAL1 0.09 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H15D--CB15 H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM H2R HAL2 0.09 ! || | | | +ATOM H2S HAL2 0.09 ! || | | | +GROUP ! H16D--CB16 H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM CD1 CL 0.90 ! | | | | +ATOM OD1 OBL -0.63 ! H18F H18C H18Z H18T +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CEL1 -0.15 ! +ATOM H15D HEL1 0.15 ! +GROUP ! +ATOM CB16 CEL1 -0.15 ! +ATOM H16D HEL1 0.15 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 !! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 CB16 +BOND CB16 H16D CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +! IC TABLE +! +IC OP31 C2 *C3 HG31 1.4399 111.73 121.27 107.98 1.1140 +IC HG31 C2 *C3 HG32 1.1140 107.98 116.42 107.18 1.1169 +IC C2 C3 OP31 P3 1.5535 111.73 -167.54 118.79 1.5904 +IC C3 OP31 P3 OP32 1.4399 118.79 79.71 101.55 1.5890 +IC OP32 OP31 *P3 OP33 1.5890 101.55 -115.28 110.31 1.4782 +IC OP32 OP31 *P3 OP34 1.5890 101.55 113.65 109.35 1.4797 +IC OP31 P3 OP32 C31 1.5904 101.55 67.83 117.77 1.4329 +IC P3 OP32 C31 C32 1.5890 117.77 -170.90 110.66 1.5522 +IC C32 OP32 *C31 H31J 1.5522 110.66 121.35 111.65 1.1158 +IC H31J OP32 *C31 H31K 1.1158 111.65 119.36 109.77 1.1144 +IC HG31 C3 C2 C1 1.1140 107.98 -59.84 112.53 1.5592 +IC C1 C3 *C2 OG12 1.5592 112.53 -122.28 106.17 1.4219 +IC C1 C3 *C2 HG22 1.5592 112.53 120.07 108.81 1.1138 +IC C3 C2 OG12 HO12 1.5535 106.17 -43.83 99.95 0.9654 +IC C3 C2 C1 OP11 1.5535 112.53 172.59 114.00 1.4374 +IC OP11 C2 *C1 HG11 1.4374 114.00 -124.71 107.54 1.1153 +IC HG11 C2 *C1 HG12 1.1153 107.54 -114.53 107.04 1.1121 +IC C2 C1 OP11 P1 1.5592 114.00 -97.83 122.51 1.5864 +IC C1 OP11 P1 OP12 1.4374 122.51 -52.87 102.45 1.5913 +IC OP12 OP11 *P1 OP13 1.5913 102.45 114.70 110.17 1.4774 +IC OP12 OP11 *P1 OP14 1.5913 102.45 -115.08 109.36 1.4815 +IC OP11 P1 OP12 C11 1.5864 102.45 -92.52 122.70 1.4285 +IC P1 OP12 C11 C12 1.5913 122.70 85.68 111.92 1.5508 +IC C12 OP12 *C11 H11J 1.5508 111.92 -123.87 112.24 1.1149 +IC H11J OP12 *C11 H11K 1.1149 112.24 -117.66 107.38 1.1110 +IC OP12 C11 C12 C13 1.4285 111.92 161.41 112.21 1.5554 +IC C13 C11 *C12 O12 1.5554 112.21 119.92 107.58 1.4348 +IC O12 C11 *C12 H12J 1.4348 107.58 121.23 105.93 1.1177 +IC C11 C12 O12 CA1 1.5508 107.58 139.57 115.43 1.3169 +IC C12 O12 CA1 CA2 1.4348 115.43 -169.02 109.20 1.5307 +IC CA2 O12 *CA1 OA1 1.5307 109.20 -177.29 125.89 1.2210 +IC O12 CA1 CA2 CA3 1.3169 109.20 -125.27 111.98 1.5453 +IC CA3 CA1 *CA2 H2A 1.5453 111.98 -121.72 106.70 1.1104 +IC H2A CA1 *CA2 H2B 1.1104 106.70 -115.79 108.58 1.1093 +IC C11 C12 C13 O13 1.5508 112.21 -165.73 111.20 1.4484 +IC O13 C12 *C13 H13J 1.4484 111.20 -119.38 107.07 1.1127 +IC H13J C12 *C13 H13K 1.1127 107.07 -115.20 109.28 1.1141 +IC C12 C13 O13 CB1 1.5554 111.20 86.74 113.94 1.3304 +IC C13 O13 CB1 CB2 1.4484 113.94 -157.19 109.85 1.5285 +IC CB2 O13 *CB1 OB1 1.5285 109.85 179.45 125.30 1.2183 +IC O13 CB1 CB2 CB3 1.3304 109.85 170.02 112.02 1.5483 +IC CB3 CB1 *CB2 H2D 1.5483 112.02 -119.03 106.46 1.1119 +IC H2D CB1 *CB2 H2E 1.1119 106.46 -117.11 109.11 1.1053 +IC OP32 C31 C32 C33 1.4329 110.66 -55.34 111.30 1.5520 +IC C33 C31 *C32 O32 1.5520 111.30 121.41 110.58 1.4400 +IC O32 C31 *C32 H32J 1.4400 110.58 121.80 108.53 1.1157 +IC C31 C32 O32 CC1 1.5522 110.58 76.00 113.72 1.3241 +IC C32 O32 CC1 CC2 1.4400 113.72 -175.40 107.92 1.5290 +IC CC2 O32 *CC1 OC1 1.5290 107.92 -174.97 125.21 1.2214 +IC O32 CC1 CC2 CC3 1.3241 107.92 -171.64 114.45 1.5483 +IC CC3 CC1 *CC2 H2R 1.5483 114.45 -120.08 106.50 1.1125 +IC H2R CC1 *CC2 H2S 1.1125 106.50 -115.84 108.14 1.1062 +IC C31 C32 C33 O33 1.5522 111.30 178.27 110.32 1.4463 +IC O33 C32 *C33 H33J 1.4463 110.32 122.56 108.16 1.1137 +IC H33J C32 *C33 H33K 1.1137 108.16 116.60 107.22 1.1149 +IC C32 C33 O33 CD1 1.5520 110.32 176.92 114.52 1.3194 +IC C33 O33 CD1 CD2 1.4463 114.52 169.48 108.39 1.5307 +IC CD2 O33 *CD1 OD1 1.5307 108.39 179.86 126.25 1.2174 +IC O33 CD1 CD2 CD3 1.3194 108.39 166.29 113.39 1.5479 +IC CD3 CD1 *CD2 H2X 1.5479 113.39 -122.94 107.91 1.1081 +IC H2X CD1 *CD2 H2Y 1.1081 107.91 -116.24 106.59 1.1103 +IC CA1 CA2 CA3 CA4 1.5307 111.98 174.09 112.77 1.5340 +IC CA4 CA2 *CA3 H3A 1.5340 112.77 -121.48 109.27 1.1128 +IC H3A CA2 *CA3 H3B 1.1128 109.27 -117.62 108.80 1.1132 +IC CA2 CA3 CA4 CA5 1.5453 112.77 176.67 112.97 1.5369 +IC CA5 CA3 *CA4 H4A 1.5369 112.97 -120.43 108.08 1.1146 +IC H4A CA3 *CA4 H4B 1.1146 108.08 -116.67 109.58 1.1123 +IC CA3 CA4 CA5 CA6 1.5340 112.97 69.98 113.98 1.5366 +IC CA6 CA4 *CA5 H5A 1.5366 113.98 -122.10 108.41 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 108.41 -116.88 108.64 1.1132 +IC CA4 CA5 CA6 CA7 1.5369 113.98 177.62 113.05 1.5384 +IC CA7 CA5 *CA6 H6A 1.5384 113.05 -120.54 108.00 1.1138 +IC H6A CA5 *CA6 H6B 1.1138 108.00 -117.16 109.92 1.1119 +IC CA5 CA6 CA7 CA8 1.5366 113.05 72.32 113.20 1.5409 +IC CA8 CA6 *CA7 H7A 1.5409 113.20 -122.31 108.58 1.1140 +IC H7A CA6 *CA7 H7B 1.1140 108.58 -116.70 108.43 1.1139 +IC CA6 CA7 CA8 CA9 1.5384 113.20 -177.88 111.67 1.5104 +IC CA9 CA7 *CA8 H8A 1.5104 111.67 -121.51 108.57 1.1127 +IC H8A CA7 *CA8 H8B 1.1127 108.57 -114.68 108.68 1.1109 +IC CA7 CA8 CA9 CA10 1.5409 111.67 106.92 126.93 1.3485 +IC CA10 CA8 *CA9 H9A 1.3485 126.93 179.93 114.52 1.1012 +IC CA8 CA9 CA10 CA11 1.5104 126.93 -0.98 126.94 1.5114 +IC CA11 CA9 *CA10 H10A 1.5114 126.94 -179.25 118.31 1.1017 +IC CA9 CA10 CA11 CA12 1.3485 126.94 -125.33 111.90 1.5094 +IC CA12 CA10 *CA11 H11A 1.5094 111.90 -120.91 109.22 1.1122 +IC H11A CA10 *CA11 H11B 1.1122 109.22 -115.26 111.36 1.1089 +IC CA10 CA11 CA12 CA13 1.5114 111.90 103.75 127.05 1.3481 +IC CA13 CA11 *CA12 H12A 1.3481 127.05 178.55 114.54 1.1015 +IC CA11 CA12 CA13 CA14 1.5094 127.05 -1.51 127.29 1.5104 +IC CA14 CA12 *CA13 H13A 1.5104 127.29 -178.83 118.45 1.1012 +IC CA12 CA13 CA14 CA15 1.3481 127.29 123.19 111.92 1.5400 +IC CA15 CA13 *CA14 H14A 1.5400 111.92 -122.30 112.60 1.1129 +IC H14A CA13 *CA14 H14B 1.1129 112.60 -117.91 109.33 1.1129 +IC CA13 CA14 CA15 CA16 1.5104 111.92 172.46 112.42 1.5358 +IC CA16 CA14 *CA15 H15A 1.5358 112.42 -120.26 109.74 1.1138 +IC H15A CA14 *CA15 H15B 1.1138 109.74 -118.26 109.67 1.1136 +IC CA14 CA15 CA16 CA17 1.5400 112.42 -176.77 112.71 1.5339 +IC CA17 CA15 *CA16 H16A 1.5339 112.71 -121.51 109.43 1.1130 +IC H16A CA15 *CA16 H16B 1.1130 109.43 -117.43 109.11 1.1131 +IC CA15 CA16 CA17 CA18 1.5358 112.71 177.47 113.22 1.5311 +IC CA18 CA16 *CA17 H17A 1.5311 113.22 -121.64 108.92 1.1137 +IC H17A CA16 *CA17 H17B 1.1137 108.92 -116.79 108.72 1.1143 +IC CA16 CA17 CA18 H18A 1.5339 113.22 -60.64 110.64 1.1108 +IC H18A CA17 *CA18 H18B 1.1108 110.64 -120.38 110.71 1.1111 +IC H18A CA17 *CA18 H18C 1.1108 110.64 119.78 110.63 1.1119 +IC CB1 CB2 CB3 CB4 1.5285 112.02 -156.49 113.16 1.5352 +IC CB4 CB2 *CB3 H3D 1.5352 113.16 -125.26 110.81 1.1108 +IC H3D CB2 *CB3 H3E 1.1108 110.81 -117.62 108.58 1.1185 +IC CB2 CB3 CB4 CB5 1.5483 113.16 -72.87 114.64 1.5362 +IC CB5 CB3 *CB4 H4D 1.5362 114.64 -121.50 107.87 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 107.87 -115.68 108.33 1.1133 +IC CB3 CB4 CB5 CB6 1.5352 114.64 173.14 113.35 1.5409 +IC CB6 CB4 *CB5 H5D 1.5409 113.35 -120.91 109.12 1.1130 +IC H5D CB4 *CB5 H5E 1.1130 109.12 -117.35 108.69 1.1125 +IC CB4 CB5 CB6 CB7 1.5362 113.35 52.82 114.03 1.5378 +IC CB7 CB5 *CB6 H6D 1.5378 114.03 -120.64 108.65 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.65 -116.83 109.17 1.1121 +IC CB5 CB6 CB7 CB8 1.5409 114.03 179.98 112.81 1.5400 +IC CB8 CB6 *CB7 H7D 1.5400 112.81 -122.98 109.09 1.1121 +IC H7D CB6 *CB7 H7E 1.1121 109.09 -117.53 108.71 1.1155 +IC CB6 CB7 CB8 CB9 1.5378 112.81 177.49 110.85 1.5102 +IC CB9 CB7 *CB8 H8D 1.5102 110.85 -122.35 107.23 1.1140 +IC H8D CB7 *CB8 H8E 1.1140 107.23 -115.61 109.26 1.1115 +IC CB7 CB8 CB9 CB10 1.5400 110.85 -111.54 126.68 1.3485 +IC CB10 CB8 *CB9 H9D 1.3485 126.68 176.66 114.61 1.1007 +IC CB8 CB9 CB10 CB11 1.5102 126.68 -2.77 127.04 1.5103 +IC CB11 CB9 *CB10 H10D 1.5103 127.04 -178.65 118.60 1.1012 +IC CB9 CB10 CB11 CB12 1.3485 127.04 96.60 112.31 1.5135 +IC CB12 CB10 *CB11 H11D 1.5135 112.31 -125.47 110.37 1.1105 +IC H11D CB10 *CB11 H11E 1.1105 110.37 -114.37 108.83 1.1122 +IC CB10 CB11 CB12 CB13 1.5103 112.31 -123.24 127.49 1.3487 +IC CB13 CB11 *CB12 H12D 1.3487 127.49 -179.18 114.92 1.1025 +IC CB11 CB12 CB13 CB14 1.5135 127.49 0.10 127.26 1.5079 +IC CB14 CB12 *CB13 H13D 1.5079 127.26 -179.25 118.69 1.1053 +IC CB12 CB13 CB14 CB15 1.3487 127.26 123.97 111.98 1.5384 +IC CB15 CB13 *CB14 H14D 1.5384 111.98 -120.79 111.90 1.1093 +IC H14D CB13 *CB14 H14E 1.1093 111.90 -118.90 109.68 1.1138 +IC CB13 CB14 CB15 CB16 1.5079 111.98 -173.48 111.85 1.5348 +IC CB16 CB14 *CB15 H15D 1.5348 111.85 -121.68 109.78 1.1147 +IC CB14 CB15 CB16 CB17 1.5384 111.85 179.99 113.35 1.5313 +IC CB17 CB15 *CB16 H16D 1.5313 113.35 -121.42 108.85 1.1101 +IC CB15 CB16 CB17 CB18 1.5348 113.35 -178.76 113.12 1.5314 +IC CB18 CB16 *CB17 H17D 1.5314 113.12 -121.82 108.25 1.1149 +IC H17D CB16 *CB17 H17E 1.1149 108.25 -115.96 109.19 1.1126 +IC CB16 CB17 CB18 H18D 1.5313 113.12 -178.27 110.36 1.1112 +IC H18D CB17 *CB18 H18E 1.1112 110.36 -120.53 110.61 1.1103 +IC H18D CB17 *CB18 H18F 1.1112 110.36 119.56 110.21 1.1112 +IC CC1 CC2 CC3 CC4 1.5290 114.45 61.17 115.54 1.5407 +IC CC4 CC2 *CC3 H3R 1.5407 115.54 -123.39 108.81 1.1159 +IC H3R CC2 *CC3 H3S 1.1159 108.81 -115.09 107.30 1.1128 +IC CC2 CC3 CC4 CC5 1.5483 115.54 48.75 115.70 1.5381 +IC CC5 CC3 *CC4 H4R 1.5381 115.70 -121.95 108.35 1.1141 +IC H4R CC3 *CC4 H4S 1.1141 108.35 -115.67 107.88 1.1118 +IC CC3 CC4 CC5 CC6 1.5407 115.70 59.37 113.26 1.5339 +IC CC6 CC4 *CC5 H5R 1.5339 113.26 -122.42 108.68 1.1122 +IC H5R CC4 *CC5 H5S 1.1122 108.68 -116.61 108.64 1.1128 +IC CC4 CC5 CC6 CC7 1.5381 113.26 175.46 114.41 1.5382 +IC CC7 CC5 *CC6 H6R 1.5382 114.41 -121.44 108.39 1.1118 +IC H6R CC5 *CC6 H6S 1.1118 108.39 -116.44 108.77 1.1127 +IC CC5 CC6 CC7 CC8 1.5339 114.41 50.21 113.91 1.5402 +IC CC8 CC6 *CC7 H7R 1.5402 113.91 -122.10 108.87 1.1136 +IC H7R CC6 *CC7 H7S 1.1136 108.87 -116.44 107.40 1.1147 +IC CC6 CC7 CC8 CC9 1.5382 113.91 171.45 111.26 1.5090 +IC CC9 CC7 *CC8 H8R 1.5090 111.26 -123.76 107.81 1.1114 +IC H8R CC7 *CC8 H8S 1.1114 107.81 -115.28 108.84 1.1122 +IC CC7 CC8 CC9 CC10 1.5402 111.26 -128.36 127.23 1.3472 +IC CC10 CC8 *CC9 H9R 1.3472 127.23 178.70 114.30 1.1010 +IC CC8 CC9 CC10 CC11 1.5090 127.23 -1.15 127.54 1.5084 +IC CC11 CC9 *CC10 H10R 1.5084 127.54 -179.59 118.30 1.1015 +IC CC9 CC10 CC11 CC12 1.3472 127.54 121.83 111.08 1.5090 +IC CC12 CC10 *CC11 H11R 1.5090 111.08 -121.38 111.45 1.1092 +IC H11R CC10 *CC11 H11S 1.1092 111.45 -115.12 108.94 1.1091 +IC CC10 CC11 CC12 CC13 1.5084 111.08 114.57 127.61 1.3469 +IC CC13 CC11 *CC12 H12R 1.3469 127.61 179.18 114.07 1.1019 +IC CC11 CC12 CC13 CC14 1.5090 127.61 -1.12 127.24 1.5089 +IC CC14 CC12 *CC13 H13R 1.5089 127.24 -179.24 118.36 1.1008 +IC CC12 CC13 CC14 CC15 1.3469 127.24 -127.92 112.49 1.5415 +IC CC15 CC13 *CC14 H14R 1.5415 112.49 -120.38 109.34 1.1135 +IC H14R CC13 *CC14 H14S 1.1135 109.34 -118.08 112.29 1.1108 +IC CC13 CC14 CC15 CC16 1.5089 112.49 64.28 113.82 1.5372 +IC CC16 CC14 *CC15 H15R 1.5372 113.82 -123.02 109.95 1.1128 +IC H15R CC14 *CC15 H15S 1.1128 109.95 -116.79 108.08 1.1141 +IC CC14 CC15 CC16 CC17 1.5415 113.82 175.12 112.35 1.5342 +IC CC17 CC15 *CC16 H16R 1.5342 112.35 121.44 109.60 1.1127 +IC H16R CC15 *CC16 H16S 1.1127 109.60 117.48 109.22 1.1130 +IC CC15 CC16 CC17 CC18 1.5372 112.35 177.84 113.41 1.5303 +IC CC18 CC16 *CC17 H17R 1.5303 113.41 -121.68 108.79 1.1140 +IC H17R CC16 *CC17 H17S 1.1140 108.79 -116.65 108.60 1.1141 +IC CC16 CC17 CC18 H18R 1.5342 113.41 177.41 110.78 1.1108 +IC H18R CC17 *CC18 H18S 1.1108 110.78 120.14 110.47 1.1110 +IC H18R CC17 *CC18 H18T 1.1108 110.78 -120.28 110.55 1.1114 +IC CD1 CD2 CD3 CD4 1.5307 113.39 169.15 112.93 1.5372 +IC CD4 CD2 *CD3 H3X 1.5372 112.93 -120.02 109.25 1.1156 +IC H3X CD2 *CD3 H3Y 1.1156 109.25 -117.49 109.59 1.1130 +IC CD2 CD3 CD4 CD5 1.5479 112.93 59.54 113.85 1.5360 +IC CD5 CD3 *CD4 H4X 1.5360 113.85 -121.33 108.32 1.1134 +IC H4X CD3 *CD4 H4Y 1.1134 108.32 -116.71 109.15 1.1132 +IC CD3 CD4 CD5 CD6 1.5372 113.85 -177.43 112.79 1.5357 +IC CD6 CD4 *CD5 H5X 1.5357 112.79 -122.43 109.70 1.1122 +IC H5X CD4 *CD5 H5Y 1.1122 109.70 -117.86 109.15 1.1139 +IC CD4 CD5 CD6 CD7 1.5360 112.79 173.65 112.21 1.5365 +IC CD7 CD5 *CD6 H6X 1.5365 112.21 -119.39 108.19 1.1136 +IC H6X CD5 *CD6 H6Y 1.1136 108.19 -117.35 110.05 1.1111 +IC CD5 CD6 CD7 CD8 1.5357 112.21 -164.07 113.53 1.5412 +IC CD8 CD6 *CD7 H7X 1.5412 113.53 -125.12 110.25 1.1118 +IC H7X CD6 *CD7 H7Y 1.1118 110.25 -116.30 107.52 1.1152 +IC CD6 CD7 CD8 CD9 1.5365 113.53 -72.33 113.26 1.5081 +IC CD9 CD7 *CD8 H8X 1.5081 113.26 -123.64 107.20 1.1122 +IC H8X CD7 *CD8 H8Y 1.1122 107.20 -114.54 108.43 1.1124 +IC CD7 CD8 CD9 CD10 1.5412 113.26 -141.33 126.38 1.3479 +IC CD10 CD8 *CD9 H9X 1.3479 126.38 -179.10 114.78 1.1010 +IC CD8 CD9 CD10 CD11 1.5081 126.38 0.12 126.84 1.5114 +IC CD11 CD9 *CD10 H10X 1.5114 126.84 -179.87 118.43 1.1016 +IC CD9 CD10 CD11 CD12 1.3479 126.84 -106.33 111.23 1.5105 +IC CD12 CD10 *CD11 H11X 1.5105 111.23 -120.37 109.03 1.1122 +IC H11X CD10 *CD11 H11Y 1.1122 109.03 -114.91 111.58 1.1099 +IC CD10 CD11 CD12 CD13 1.5114 111.23 109.38 127.41 1.3486 +IC CD13 CD11 *CD12 H12X 1.3486 127.41 179.19 114.40 1.1015 +IC CD11 CD12 CD13 CD14 1.5105 127.41 -1.41 127.65 1.5109 +IC CD14 CD12 *CD13 H13X 1.5109 127.65 -178.15 118.24 1.1012 +IC CD12 CD13 CD14 CD15 1.3486 127.65 -115.93 111.19 1.5399 +IC CD15 CD13 *CD14 H14X 1.5399 111.19 -120.10 109.72 1.1126 +IC H14X CD13 *CD14 H14Y 1.1126 109.72 -118.73 112.54 1.1122 +IC CD13 CD14 CD15 CD16 1.5109 111.19 -174.42 112.98 1.5354 +IC CD16 CD14 *CD15 H15X 1.5354 112.98 -121.07 109.22 1.1143 +IC H15X CD14 *CD15 H15Y 1.1143 109.22 -117.98 109.91 1.1138 +IC CD14 CD15 CD16 CD17 1.5399 112.98 179.46 112.15 1.5344 +IC CD17 CD15 *CD16 H16X 1.5344 112.15 -121.15 109.44 1.1128 +IC H16X CD15 *CD16 H16Y 1.1128 109.44 -117.66 109.26 1.1126 +IC CD15 CD16 CD17 CD18 1.5354 112.15 179.70 113.67 1.5310 +IC CD18 CD16 *CD17 H17X 1.5310 113.67 -121.71 108.44 1.1139 +IC H17X CD16 *CD17 H17Y 1.1139 108.44 -116.35 108.83 1.1138 +IC CD16 CD17 CD18 H18X 1.5344 113.67 -178.87 110.70 1.1108 +IC H18X CD17 *CD18 H18Y 1.1108 110.70 -120.14 110.59 1.1104 +IC H18X CD17 *CD18 H18Z 1.1108 110.70 119.96 110.62 1.1117 + +RESI LNCCL1 -1.00 ! 3 Linoleic acid + 1 linolenic acid cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 3 linoleoyl + 1 linolenoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +ATOM H2E HAL2 0.09 ! || || || || +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15 +ATOM CC2 CTL2 -0.22 ! | | | || +ATOM H2R HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16 +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18F H18C H18Z H18T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CEL1 -0.15 ! +ATOM H15R HEL1 0.15 ! +GROUP ! +ATOM CC16 CEL1 -0.15 ! +ATOM H16R HEL1 0.15 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 CC16 +BOND CC16 H16R CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4272 111.57 124.87 107.78 1.1169 +IC HG31 C2 *C3 HG32 1.1169 107.78 115.89 109.04 1.1124 +IC C2 C3 OP31 P3 1.5483 111.57 118.08 122.98 1.5819 +IC C3 OP31 P3 OP32 1.4272 122.98 37.85 102.14 1.5830 +IC OP32 OP31 *P3 OP33 1.5830 102.14 -113.92 107.98 1.4793 +IC OP32 OP31 *P3 OP34 1.5830 102.14 115.66 109.62 1.4740 +IC OP31 P3 OP32 C31 1.5819 102.14 69.85 119.33 1.4301 +IC P3 OP32 C31 C32 1.5830 119.33 176.40 110.18 1.5529 +IC C32 OP32 *C31 H31J 1.5529 110.18 120.82 110.67 1.1139 +IC H31J OP32 *C31 H31K 1.1139 110.67 119.45 110.95 1.1159 +IC HG31 C3 C2 C1 1.1169 107.78 60.13 113.14 1.5594 +IC C1 C3 *C2 OG12 1.5594 113.14 -122.65 107.36 1.4314 +IC C1 C3 *C2 HG22 1.5594 113.14 119.50 108.81 1.1137 +IC C3 C2 OG12 HO12 1.5483 107.36 -59.74 104.73 0.9611 +IC C3 C2 C1 OP11 1.5483 113.14 102.14 111.29 1.4365 +IC OP11 C2 *C1 HG11 1.4365 111.29 -124.72 105.61 1.1191 +IC HG11 C2 *C1 HG12 1.1191 105.61 -115.38 108.40 1.1138 +IC C2 C1 OP11 P1 1.5594 111.29 -157.61 115.85 1.5685 +IC C1 OP11 P1 OP12 1.4365 115.85 -14.21 104.93 1.5653 +IC OP12 OP11 *P1 OP13 1.5653 104.93 115.00 111.23 1.5595 +IC OP12 OP11 *P1 OP14 1.5653 104.93 -120.71 114.44 1.4714 +IC OP11 P1 OP13 HP13 1.5685 111.23 -49.71 108.79 0.9805 +IC OP11 P1 OP12 C11 1.5685 104.93 168.45 117.56 1.4279 +IC P1 OP12 C11 C12 1.5653 117.56 -104.42 112.05 1.5631 +IC C12 OP12 *C11 H11J 1.5631 112.05 -116.94 106.96 1.1115 +IC H11J OP12 *C11 H11K 1.1115 106.96 -117.70 114.83 1.1174 +IC OP12 C11 C12 C13 1.4279 112.05 -169.61 110.60 1.5613 +IC C13 C11 *C12 O12 1.5613 110.60 124.16 109.17 1.4428 +IC O12 C11 *C12 H12J 1.4428 109.17 118.13 106.49 1.1175 +IC C11 C12 O12 CA1 1.5631 109.17 161.88 113.49 1.3343 +IC C12 O12 CA1 CA2 1.4428 113.49 -169.35 108.84 1.5280 +IC CA2 O12 *CA1 OA1 1.5280 108.84 179.80 125.17 1.2183 +IC O12 CA1 CA2 CA3 1.3343 108.84 -146.40 113.25 1.5456 +IC CA3 CA1 *CA2 H2A 1.5456 113.25 -119.97 106.28 1.1109 +IC H2A CA1 *CA2 H2B 1.1109 106.28 -116.75 108.94 1.1073 +IC C11 C12 C13 O13 1.5631 110.60 48.04 111.75 1.4444 +IC O13 C12 *C13 H13J 1.4444 111.75 -117.92 106.48 1.1131 +IC H13J C12 *C13 H13K 1.1131 106.48 -115.07 111.40 1.1131 +IC C12 C13 O13 CB1 1.5613 111.75 88.82 115.87 1.3297 +IC C13 O13 CB1 CB2 1.4444 115.87 -174.80 108.56 1.5287 +IC CB2 O13 *CB1 OB1 1.5287 108.56 -178.49 126.34 1.2145 +IC O13 CB1 CB2 CB3 1.3297 108.56 152.47 112.16 1.5454 +IC CB3 CB1 *CB2 H2D 1.5454 112.16 -121.52 108.74 1.1089 +IC H2D CB1 *CB2 H2E 1.1089 108.74 -117.40 106.94 1.1083 +IC OP32 C31 C32 C33 1.4301 110.18 -69.33 110.65 1.5522 +IC C33 C31 *C32 O32 1.5522 110.65 120.01 111.21 1.4395 +IC O32 C31 *C32 H32J 1.4395 111.21 122.30 108.97 1.1146 +IC C31 C32 O32 CC1 1.5529 111.21 69.31 115.35 1.3120 +IC C32 O32 CC1 CC2 1.4395 115.35 -171.71 108.60 1.5297 +IC CC2 O32 *CC1 OC1 1.5297 108.60 -178.02 126.78 1.2186 +IC O32 CC1 CC2 CC3 1.3120 108.60 -59.72 112.33 1.5489 +IC CC3 CC1 *CC2 H2R 1.5489 112.33 -122.26 107.83 1.1075 +IC H2R CC1 *CC2 H2S 1.1075 107.83 -116.44 106.39 1.1097 +IC C31 C32 C33 O33 1.5529 110.65 179.11 109.99 1.4464 +IC O33 C32 *C33 H33J 1.4464 109.99 121.93 109.29 1.1119 +IC H33J C32 *C33 H33K 1.1119 109.29 116.57 106.09 1.1186 +IC C32 C33 O33 CD1 1.5522 109.99 -159.03 114.19 1.3237 +IC C33 O33 CD1 CD2 1.4464 114.19 164.21 109.32 1.5286 +IC CD2 O33 *CD1 OD1 1.5286 109.32 -178.45 126.02 1.2156 +IC O33 CD1 CD2 CD3 1.3237 109.32 -46.26 112.24 1.5470 +IC CD3 CD1 *CD2 H2X 1.5470 112.24 -120.21 106.48 1.1100 +IC H2X CD1 *CD2 H2Y 1.1100 106.48 -117.13 108.41 1.1069 +IC CA1 CA2 CA3 CA4 1.5280 113.25 70.18 112.81 1.5346 +IC CA4 CA2 *CA3 H3A 1.5346 112.81 -123.14 110.14 1.1142 +IC H3A CA2 *CA3 H3B 1.1142 110.14 -116.66 107.70 1.1125 +IC CA2 CA3 CA4 CA5 1.5456 112.81 172.40 112.79 1.5353 +IC CA5 CA3 *CA4 H4A 1.5353 112.79 -122.05 109.90 1.1116 +IC H4A CA3 *CA4 H4B 1.1116 109.90 -117.14 108.37 1.1150 +IC CA3 CA4 CA5 CA6 1.5346 112.79 167.30 112.42 1.5358 +IC CA6 CA4 *CA5 H5A 1.5358 112.42 -120.63 108.10 1.1132 +IC H5A CA4 *CA5 H5B 1.1132 108.10 -117.30 109.47 1.1120 +IC CA4 CA5 CA6 CA7 1.5353 112.42 177.91 114.45 1.5409 +IC CA7 CA5 *CA6 H6A 1.5409 114.45 -121.60 108.84 1.1121 +IC H6A CA5 *CA6 H6B 1.1121 108.84 -116.16 108.48 1.1134 +IC CA5 CA6 CA7 CA8 1.5358 114.45 53.66 115.58 1.5440 +IC CA8 CA6 *CA7 H7A 1.5440 115.58 -121.63 108.47 1.1138 +IC H7A CA6 *CA7 H7B 1.1138 108.47 -116.24 108.32 1.1141 +IC CA6 CA7 CA8 CA9 1.5409 115.58 55.01 112.73 1.5097 +IC CA9 CA7 *CA8 H8A 1.5097 112.73 -121.48 108.57 1.1114 +IC H8A CA7 *CA8 H8B 1.1114 108.57 -114.55 107.55 1.1126 +IC CA7 CA8 CA9 CA10 1.5440 112.73 109.39 127.97 1.3474 +IC CA10 CA8 *CA9 H9A 1.3474 127.97 -179.15 113.83 1.1025 +IC CA8 CA9 CA10 CA11 1.5097 127.97 0.64 127.89 1.5108 +IC CA11 CA9 *CA10 H10A 1.5108 127.89 179.31 117.75 1.1014 +IC CA9 CA10 CA11 CA12 1.3474 127.89 -112.95 111.22 1.5114 +IC CA12 CA10 *CA11 H11A 1.5114 111.22 -120.46 108.90 1.1119 +IC H11A CA10 *CA11 H11B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA10 CA11 CA12 CA13 1.5108 111.22 134.57 126.37 1.3465 +IC CA13 CA11 *CA12 H12A 1.3465 126.37 -177.01 115.27 1.1018 +IC CA11 CA12 CA13 CA14 1.5114 126.37 3.15 126.32 1.5077 +IC CA14 CA12 *CA13 H13A 1.5077 126.32 178.37 118.79 1.1003 +IC CA12 CA13 CA14 CA15 1.3465 126.32 -92.58 113.47 1.5417 +IC CA15 CA13 *CA14 H14A 1.5417 113.47 -122.01 110.01 1.1123 +IC H14A CA13 *CA14 H14B 1.1123 110.01 -116.77 110.38 1.1120 +IC CA13 CA14 CA15 CA16 1.5077 113.47 -63.55 113.58 1.5369 +IC CA16 CA14 *CA15 H15A 1.5369 113.58 -120.33 108.08 1.1132 +IC H15A CA14 *CA15 H15B 1.1132 108.08 -116.59 109.36 1.1132 +IC CA14 CA15 CA16 CA17 1.5417 113.58 -171.21 113.87 1.5374 +IC CA17 CA15 *CA16 H16A 1.5374 113.87 -121.70 108.87 1.1122 +IC H16A CA15 *CA16 H16B 1.1122 108.87 -117.00 108.72 1.1132 +IC CA15 CA16 CA17 CA18 1.5369 113.87 -61.57 114.41 1.5314 +IC CA18 CA16 *CA17 H17A 1.5314 114.41 -121.26 108.12 1.1148 +IC H17A CA16 *CA17 H17B 1.1148 108.12 -116.30 108.76 1.1136 +IC CA16 CA17 CA18 H18A 1.5374 114.41 63.53 110.93 1.1107 +IC H18A CA17 *CA18 H18B 1.1107 110.93 -119.76 110.34 1.1109 +IC H18A CA17 *CA18 H18C 1.1107 110.93 120.37 110.77 1.1100 +IC CB1 CB2 CB3 CB4 1.5287 112.16 178.44 113.36 1.5384 +IC CB4 CB2 *CB3 H3D 1.5384 113.36 -122.28 109.76 1.1140 +IC H3D CB2 *CB3 H3E 1.1140 109.76 -116.69 109.13 1.1151 +IC CB2 CB3 CB4 CB5 1.5454 113.36 -60.74 115.02 1.5414 +IC CB5 CB3 *CB4 H4D 1.5414 115.02 -121.57 108.33 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 108.33 -116.10 108.96 1.1133 +IC CB3 CB4 CB5 CB6 1.5384 115.02 -51.86 114.89 1.5394 +IC CB6 CB4 *CB5 H5D 1.5394 114.89 -121.74 108.45 1.1137 +IC H5D CB4 *CB5 H5E 1.1137 108.45 -116.35 108.99 1.1129 +IC CB4 CB5 CB6 CB7 1.5414 114.89 -57.34 113.83 1.5380 +IC CB7 CB5 *CB6 H6D 1.5380 113.83 -121.31 108.98 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.98 -116.37 108.87 1.1123 +IC CB5 CB6 CB7 CB8 1.5394 113.83 179.71 113.63 1.5423 +IC CB8 CB6 *CB7 H7D 1.5423 113.63 -122.27 109.89 1.1123 +IC H7D CB6 *CB7 H7E 1.1123 109.89 -116.77 108.48 1.1132 +IC CB6 CB7 CB8 CB9 1.5380 113.63 -63.29 112.23 1.5093 +IC CB9 CB7 *CB8 H8D 1.5093 112.23 -120.64 107.87 1.1133 +IC H8D CB7 *CB8 H8E 1.1133 107.87 -115.67 108.05 1.1129 +IC CB7 CB8 CB9 CB10 1.5423 112.23 148.17 126.47 1.3460 +IC CB10 CB8 *CB9 H9D 1.3460 126.47 -177.74 114.82 1.1018 +IC CB8 CB9 CB10 CB11 1.5093 126.47 2.77 126.58 1.5092 +IC CB11 CB9 *CB10 H10D 1.5092 126.58 177.26 118.57 1.1029 +IC CB9 CB10 CB11 CB12 1.3460 126.58 -116.82 111.69 1.5096 +IC CB12 CB10 *CB11 H11D 1.5096 111.69 -123.10 108.54 1.1115 +IC H11D CB10 *CB11 H11E 1.1115 108.54 -114.79 111.63 1.1116 +IC CB10 CB11 CB12 CB13 1.5092 111.69 -110.56 126.32 1.3473 +IC CB13 CB11 *CB12 H12D 1.3473 126.32 -178.41 114.77 1.1018 +IC CB11 CB12 CB13 CB14 1.5096 126.32 2.04 125.85 1.5088 +IC CB14 CB12 *CB13 H13D 1.5088 125.85 179.17 118.99 1.1012 +IC CB12 CB13 CB14 CB15 1.3473 125.85 -89.20 112.98 1.5413 +IC CB15 CB13 *CB14 H14D 1.5413 112.98 -121.97 110.15 1.1124 +IC H14D CB13 *CB14 H14E 1.1124 110.15 -116.85 110.43 1.1140 +IC CB13 CB14 CB15 CB16 1.5088 112.98 -66.02 113.67 1.5362 +IC CB16 CB14 *CB15 H15D 1.5362 113.67 -120.47 108.54 1.1134 +IC H15D CB14 *CB15 H15E 1.1134 108.54 -116.71 109.67 1.1135 +IC CB14 CB15 CB16 CB17 1.5413 113.67 -176.61 112.48 1.5339 +IC CB17 CB15 *CB16 H16D 1.5339 112.48 -121.15 109.47 1.1130 +IC H16D CB15 *CB16 H16E 1.1130 109.47 -117.68 109.15 1.1130 +IC CB15 CB16 CB17 CB18 1.5362 112.48 -179.94 113.24 1.5308 +IC CB18 CB16 *CB17 H17D 1.5308 113.24 -121.73 108.82 1.1141 +IC H17D CB16 *CB17 H17E 1.1141 108.82 -116.64 108.69 1.1143 +IC CB16 CB17 CB18 H18D 1.5339 113.24 59.88 110.45 1.1114 +IC H18D CB17 *CB18 H18E 1.1114 110.45 -119.87 110.50 1.1113 +IC H18D CB17 *CB18 H18F 1.1114 110.45 120.03 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5297 112.33 172.47 113.86 1.5361 +IC CC4 CC2 *CC3 H3R 1.5361 113.86 -119.64 108.94 1.1154 +IC H3R CC2 *CC3 H3S 1.1154 108.94 -117.39 109.77 1.1130 +IC CC2 CC3 CC4 CC5 1.5489 113.86 -56.98 112.74 1.5347 +IC CC5 CC3 *CC4 H4R 1.5347 112.74 -119.98 107.98 1.1143 +IC H4R CC3 *CC4 H4S 1.1143 107.98 -117.33 110.39 1.1120 +IC CC3 CC4 CC5 CC6 1.5361 112.74 -154.31 113.28 1.5321 +IC CC6 CC4 *CC5 H5R 1.5321 113.28 -123.53 109.65 1.1125 +IC H5R CC4 *CC5 H5S 1.1125 109.65 -117.22 108.68 1.1132 +IC CC4 CC5 CC6 CC7 1.5347 113.28 -174.72 112.18 1.5360 +IC CC7 CC5 *CC6 H6R 1.5360 112.18 -120.78 108.11 1.1141 +IC H6R CC5 *CC6 H6S 1.1141 108.11 -117.38 110.00 1.1122 +IC CC5 CC6 CC7 CC8 1.5321 112.18 -168.49 113.32 1.5408 +IC CC8 CC6 *CC7 H7R 1.5408 113.32 -121.00 108.07 1.1137 +IC H7R CC6 *CC7 H7S 1.1137 108.07 -116.02 109.54 1.1140 +IC CC6 CC7 CC8 CC9 1.5360 113.32 72.57 111.65 1.5102 +IC CC9 CC7 *CC8 H8R 1.5102 111.65 -124.76 108.23 1.1117 +IC H8R CC7 *CC8 H8S 1.1117 108.23 -115.30 107.95 1.1119 +IC CC7 CC8 CC9 CC10 1.5408 111.65 -134.06 127.67 1.3478 +IC CC10 CC8 *CC9 H9R 1.3478 127.67 179.52 113.97 1.1023 +IC CC8 CC9 CC10 CC11 1.5102 127.67 -0.03 127.34 1.5115 +IC CC11 CC9 *CC10 H10R 1.5115 127.34 179.73 118.07 1.1026 +IC CC9 CC10 CC11 CC12 1.3478 127.34 129.05 112.32 1.5099 +IC CC12 CC10 *CC11 H11R 1.5099 112.32 -123.72 111.60 1.1114 +IC H11R CC10 *CC11 H11S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC10 CC11 CC12 CC13 1.5115 112.32 -84.97 126.59 1.3471 +IC CC13 CC11 *CC12 H12R 1.3471 126.59 -179.05 114.79 1.1010 +IC CC11 CC12 CC13 CC14 1.5099 126.59 1.41 126.41 1.5090 +IC CC14 CC12 *CC13 H13R 1.5090 126.41 178.45 118.70 1.0998 +IC CC12 CC13 CC14 CC15 1.3471 126.41 -125.27 113.39 1.5418 +IC CC15 CC13 *CC14 H14R 1.5418 113.39 -121.44 109.86 1.1131 +IC H14R CC13 *CC14 H14S 1.1131 109.86 -117.22 111.11 1.1131 +IC CC13 CC14 CC15 CC16 1.5090 113.39 -68.63 113.68 1.5381 +IC CC16 CC14 *CC15 H15R 1.5381 113.68 123.30 109.83 1.1129 +IC CC14 CC15 CC16 CC17 1.5418 113.68 179.76 113.73 1.5374 +IC CC17 CC15 *CC16 H16R 1.5374 113.73 121.83 108.95 1.1128 +IC CC15 CC16 CC17 CC18 1.5381 113.73 63.65 114.54 1.5322 +IC CC18 CC16 *CC17 H17R 1.5322 114.54 -122.47 108.69 1.1141 +IC H17R CC16 *CC17 H17S 1.1141 108.69 -116.13 108.22 1.1148 +IC CC16 CC17 CC18 H18R 1.5374 114.54 56.61 110.47 1.1112 +IC H18R CC17 *CC18 H18S 1.1112 110.47 -120.21 110.86 1.1107 +IC H18R CC17 *CC18 H18T 1.1112 110.47 119.94 110.49 1.1113 +IC CD1 CD2 CD3 CD4 1.5286 112.24 -168.50 113.06 1.5318 +IC CD4 CD2 *CD3 H3X 1.5318 113.06 -122.94 109.98 1.1137 +IC H3X CD2 *CD3 H3Y 1.1137 109.98 -117.36 109.14 1.1136 +IC CD2 CD3 CD4 CD5 1.5470 113.06 175.61 111.87 1.5362 +IC CD5 CD3 *CD4 H4X 1.5362 111.87 -120.66 108.60 1.1128 +IC H4X CD3 *CD4 H4Y 1.1128 108.60 -117.59 109.56 1.1124 +IC CD3 CD4 CD5 CD6 1.5318 111.87 177.84 113.59 1.5356 +IC CD6 CD4 *CD5 H5X 1.5356 113.59 -121.15 108.45 1.1137 +IC H5X CD4 *CD5 H5Y 1.1137 108.45 -116.84 109.16 1.1138 +IC CD4 CD5 CD6 CD7 1.5362 113.59 67.64 113.35 1.5355 +IC CD7 CD5 *CD6 H6X 1.5355 113.35 -122.12 109.12 1.1128 +IC H6X CD5 *CD6 H6Y 1.1128 109.12 -117.25 108.81 1.1134 +IC CD5 CD6 CD7 CD8 1.5356 113.35 -178.50 112.28 1.5389 +IC CD8 CD6 *CD7 H7X 1.5389 112.28 -122.16 108.88 1.1140 +IC H7X CD6 *CD7 H7Y 1.1140 108.88 -116.95 109.16 1.1134 +IC CD6 CD7 CD8 CD9 1.5355 112.28 179.01 111.42 1.5083 +IC CD9 CD7 *CD8 H8X 1.5083 111.42 -122.39 108.26 1.1135 +IC H8X CD7 *CD8 H8Y 1.1135 108.26 -115.32 109.05 1.1118 +IC CD7 CD8 CD9 CD10 1.5389 111.42 -84.39 125.66 1.3464 +IC CD10 CD8 *CD9 H9X 1.3464 125.66 178.86 115.42 1.1011 +IC CD8 CD9 CD10 CD11 1.5083 125.66 0.74 126.41 1.5100 +IC CD11 CD9 *CD10 H10X 1.5100 126.41 178.33 118.71 1.1020 +IC CD9 CD10 CD11 CD12 1.3464 126.41 -119.11 111.66 1.5104 +IC CD12 CD10 *CD11 H11X 1.5104 111.66 -123.67 108.55 1.1120 +IC H11X CD10 *CD11 H11Y 1.1120 108.55 -114.62 111.55 1.1120 +IC CD10 CD11 CD12 CD13 1.5100 111.66 -113.81 126.72 1.3477 +IC CD13 CD11 *CD12 H12X 1.3477 126.72 -178.56 114.59 1.1018 +IC CD11 CD12 CD13 CD14 1.5104 126.72 1.66 126.19 1.5088 +IC CD14 CD12 *CD13 H13X 1.5088 126.19 179.37 118.90 1.1014 +IC CD12 CD13 CD14 CD15 1.3477 126.19 -100.76 112.41 1.5405 +IC CD15 CD13 *CD14 H14X 1.5405 112.41 -121.85 109.83 1.1118 +IC H14X CD13 *CD14 H14Y 1.1118 109.83 -117.23 111.23 1.1116 +IC CD13 CD14 CD15 CD16 1.5088 112.41 170.52 113.29 1.5388 +IC CD16 CD14 *CD15 H15X 1.5388 113.29 -119.71 109.05 1.1153 +IC H15X CD14 *CD15 H15Y 1.1153 109.05 -117.72 109.78 1.1127 +IC CD14 CD15 CD16 CD17 1.5405 113.29 62.69 114.08 1.5347 +IC CD17 CD15 *CD16 H16X 1.5347 114.08 -121.99 108.89 1.1132 +IC H16X CD15 *CD16 H16Y 1.1132 108.89 -116.64 108.76 1.1136 +IC CD15 CD16 CD17 CD18 1.5388 114.08 179.88 112.98 1.5311 +IC CD18 CD16 *CD17 H17X 1.5311 112.98 -121.76 108.79 1.1137 +IC H17X CD16 *CD17 H17Y 1.1137 108.79 -117.11 109.38 1.1133 +IC CD16 CD17 CD18 H18X 1.5347 112.98 60.79 110.28 1.1118 +IC H18X CD17 *CD18 H18Y 1.1118 110.28 -119.90 110.57 1.1110 +IC H18X CD17 *CD18 H18Z 1.1118 110.28 119.81 110.63 1.1110 + +RESI LNCCL2 -2.00 ! 3 linoleic acid + 1 linolenic acid cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 3 linoleoly chains + 1 linolenoyl chain +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! || || || || +ATOM H32J HAL1 0.09 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15 +ATOM H2R HAL2 0.09 ! | | | || +ATOM H2S HAL2 0.09 ! | | | || +GROUP ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16 +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM CD1 CL 0.90 ! | | | | +ATOM OD1 OBL -0.63 ! H18F H18C H18Z H18T +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CEL1 -0.15 ! +ATOM H15R HEL1 0.15 ! +GROUP ! +ATOM CC16 CEL1 -0.15 ! +ATOM H16R HEL1 0.15 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL2 -0.18 ! +ATOM H16X HAL2 0.09 ! +ATOM H16Y HAL2 0.09 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 !! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 CC16 +BOND CC16 H16R CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 H15Y CD15 CD16 +BOND CD16 H16X CD16 H16Y CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +! IC TABLE +! +IC OP31 C2 *C3 HG31 1.4399 111.73 121.27 107.98 1.1140 +IC HG31 C2 *C3 HG32 1.1140 107.98 116.42 107.18 1.1169 +IC C2 C3 OP31 P3 1.5535 111.73 -167.54 118.79 1.5904 +IC C3 OP31 P3 OP32 1.4399 118.79 79.71 101.55 1.5890 +IC OP32 OP31 *P3 OP33 1.5890 101.55 -115.28 110.31 1.4782 +IC OP32 OP31 *P3 OP34 1.5890 101.55 113.65 109.35 1.4797 +IC OP31 P3 OP32 C31 1.5904 101.55 67.83 117.77 1.4329 +IC P3 OP32 C31 C32 1.5890 117.77 -170.90 110.66 1.5522 +IC C32 OP32 *C31 H31J 1.5522 110.66 121.35 111.65 1.1158 +IC H31J OP32 *C31 H31K 1.1158 111.65 119.36 109.77 1.1144 +IC HG31 C3 C2 C1 1.1140 107.98 -59.84 112.53 1.5592 +IC C1 C3 *C2 OG12 1.5592 112.53 -122.28 106.17 1.4219 +IC C1 C3 *C2 HG22 1.5592 112.53 120.07 108.81 1.1138 +IC C3 C2 OG12 HO12 1.5535 106.17 -43.83 99.95 0.9654 +IC C3 C2 C1 OP11 1.5535 112.53 172.59 114.00 1.4374 +IC OP11 C2 *C1 HG11 1.4374 114.00 -124.71 107.54 1.1153 +IC HG11 C2 *C1 HG12 1.1153 107.54 -114.53 107.04 1.1121 +IC C2 C1 OP11 P1 1.5592 114.00 -97.83 122.51 1.5864 +IC C1 OP11 P1 OP12 1.4374 122.51 -52.87 102.45 1.5913 +IC OP12 OP11 *P1 OP13 1.5913 102.45 114.70 110.17 1.4774 +IC OP12 OP11 *P1 OP14 1.5913 102.45 -115.08 109.36 1.4815 +IC OP11 P1 OP12 C11 1.5864 102.45 -92.52 122.70 1.4285 +IC P1 OP12 C11 C12 1.5913 122.70 85.68 111.92 1.5508 +IC C12 OP12 *C11 H11J 1.5508 111.92 -123.87 112.24 1.1149 +IC H11J OP12 *C11 H11K 1.1149 112.24 -117.66 107.38 1.1110 +IC OP12 C11 C12 C13 1.4285 111.92 161.41 112.21 1.5554 +IC C13 C11 *C12 O12 1.5554 112.21 119.92 107.58 1.4348 +IC O12 C11 *C12 H12J 1.4348 107.58 121.23 105.93 1.1177 +IC C11 C12 O12 CA1 1.5508 107.58 139.57 115.43 1.3169 +IC C12 O12 CA1 CA2 1.4348 115.43 -169.02 109.20 1.5307 +IC CA2 O12 *CA1 OA1 1.5307 109.20 -177.29 125.89 1.2210 +IC O12 CA1 CA2 CA3 1.3169 109.20 -125.27 111.98 1.5453 +IC CA3 CA1 *CA2 H2A 1.5453 111.98 -121.72 106.70 1.1104 +IC H2A CA1 *CA2 H2B 1.1104 106.70 -115.79 108.58 1.1093 +IC C11 C12 C13 O13 1.5508 112.21 -165.73 111.20 1.4484 +IC O13 C12 *C13 H13J 1.4484 111.20 -119.38 107.07 1.1127 +IC H13J C12 *C13 H13K 1.1127 107.07 -115.20 109.28 1.1141 +IC C12 C13 O13 CB1 1.5554 111.20 86.74 113.94 1.3304 +IC C13 O13 CB1 CB2 1.4484 113.94 -157.19 109.85 1.5285 +IC CB2 O13 *CB1 OB1 1.5285 109.85 179.45 125.30 1.2183 +IC O13 CB1 CB2 CB3 1.3304 109.85 170.02 112.02 1.5483 +IC CB3 CB1 *CB2 H2D 1.5483 112.02 -119.03 106.46 1.1119 +IC H2D CB1 *CB2 H2E 1.1119 106.46 -117.11 109.11 1.1053 +IC OP32 C31 C32 C33 1.4329 110.66 -55.34 111.30 1.5520 +IC C33 C31 *C32 O32 1.5520 111.30 121.41 110.58 1.4400 +IC O32 C31 *C32 H32J 1.4400 110.58 121.80 108.53 1.1157 +IC C31 C32 O32 CC1 1.5522 110.58 76.00 113.72 1.3241 +IC C32 O32 CC1 CC2 1.4400 113.72 -175.40 107.92 1.5290 +IC CC2 O32 *CC1 OC1 1.5290 107.92 -174.97 125.21 1.2214 +IC O32 CC1 CC2 CC3 1.3241 107.92 -171.64 114.45 1.5483 +IC CC3 CC1 *CC2 H2R 1.5483 114.45 -120.08 106.50 1.1125 +IC H2R CC1 *CC2 H2S 1.1125 106.50 -115.84 108.14 1.1062 +IC C31 C32 C33 O33 1.5522 111.30 178.27 110.32 1.4463 +IC O33 C32 *C33 H33J 1.4463 110.32 122.56 108.16 1.1137 +IC H33J C32 *C33 H33K 1.1137 108.16 116.60 107.22 1.1149 +IC C32 C33 O33 CD1 1.5520 110.32 176.92 114.52 1.3194 +IC C33 O33 CD1 CD2 1.4463 114.52 169.48 108.39 1.5307 +IC CD2 O33 *CD1 OD1 1.5307 108.39 179.86 126.25 1.2174 +IC O33 CD1 CD2 CD3 1.3194 108.39 166.29 113.39 1.5479 +IC CD3 CD1 *CD2 H2X 1.5479 113.39 -122.94 107.91 1.1081 +IC H2X CD1 *CD2 H2Y 1.1081 107.91 -116.24 106.59 1.1103 +IC CA1 CA2 CA3 CA4 1.5307 111.98 174.09 112.77 1.5340 +IC CA4 CA2 *CA3 H3A 1.5340 112.77 -121.48 109.27 1.1128 +IC H3A CA2 *CA3 H3B 1.1128 109.27 -117.62 108.80 1.1132 +IC CA2 CA3 CA4 CA5 1.5453 112.77 176.67 112.97 1.5369 +IC CA5 CA3 *CA4 H4A 1.5369 112.97 -120.43 108.08 1.1146 +IC H4A CA3 *CA4 H4B 1.1146 108.08 -116.67 109.58 1.1123 +IC CA3 CA4 CA5 CA6 1.5340 112.97 69.98 113.98 1.5366 +IC CA6 CA4 *CA5 H5A 1.5366 113.98 -122.10 108.41 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 108.41 -116.88 108.64 1.1132 +IC CA4 CA5 CA6 CA7 1.5369 113.98 177.62 113.05 1.5384 +IC CA7 CA5 *CA6 H6A 1.5384 113.05 -120.54 108.00 1.1138 +IC H6A CA5 *CA6 H6B 1.1138 108.00 -117.16 109.92 1.1119 +IC CA5 CA6 CA7 CA8 1.5366 113.05 72.32 113.20 1.5409 +IC CA8 CA6 *CA7 H7A 1.5409 113.20 -122.31 108.58 1.1140 +IC H7A CA6 *CA7 H7B 1.1140 108.58 -116.70 108.43 1.1139 +IC CA6 CA7 CA8 CA9 1.5384 113.20 -177.88 111.67 1.5104 +IC CA9 CA7 *CA8 H8A 1.5104 111.67 -121.51 108.57 1.1127 +IC H8A CA7 *CA8 H8B 1.1127 108.57 -114.68 108.68 1.1109 +IC CA7 CA8 CA9 CA10 1.5409 111.67 106.92 126.93 1.3485 +IC CA10 CA8 *CA9 H9A 1.3485 126.93 179.93 114.52 1.1012 +IC CA8 CA9 CA10 CA11 1.5104 126.93 -0.98 126.94 1.5114 +IC CA11 CA9 *CA10 H10A 1.5114 126.94 -179.25 118.31 1.1017 +IC CA9 CA10 CA11 CA12 1.3485 126.94 -125.33 111.90 1.5094 +IC CA12 CA10 *CA11 H11A 1.5094 111.90 -120.91 109.22 1.1122 +IC H11A CA10 *CA11 H11B 1.1122 109.22 -115.26 111.36 1.1089 +IC CA10 CA11 CA12 CA13 1.5114 111.90 103.75 127.05 1.3481 +IC CA13 CA11 *CA12 H12A 1.3481 127.05 178.55 114.54 1.1015 +IC CA11 CA12 CA13 CA14 1.5094 127.05 -1.51 127.29 1.5104 +IC CA14 CA12 *CA13 H13A 1.5104 127.29 -178.83 118.45 1.1012 +IC CA12 CA13 CA14 CA15 1.3481 127.29 123.19 111.92 1.5400 +IC CA15 CA13 *CA14 H14A 1.5400 111.92 -122.30 112.60 1.1129 +IC H14A CA13 *CA14 H14B 1.1129 112.60 -117.91 109.33 1.1129 +IC CA13 CA14 CA15 CA16 1.5104 111.92 172.46 112.42 1.5358 +IC CA16 CA14 *CA15 H15A 1.5358 112.42 -120.26 109.74 1.1138 +IC H15A CA14 *CA15 H15B 1.1138 109.74 -118.26 109.67 1.1136 +IC CA14 CA15 CA16 CA17 1.5400 112.42 -176.77 112.71 1.5339 +IC CA17 CA15 *CA16 H16A 1.5339 112.71 -121.51 109.43 1.1130 +IC H16A CA15 *CA16 H16B 1.1130 109.43 -117.43 109.11 1.1131 +IC CA15 CA16 CA17 CA18 1.5358 112.71 177.47 113.22 1.5311 +IC CA18 CA16 *CA17 H17A 1.5311 113.22 -121.64 108.92 1.1137 +IC H17A CA16 *CA17 H17B 1.1137 108.92 -116.79 108.72 1.1143 +IC CA16 CA17 CA18 H18A 1.5339 113.22 -60.64 110.64 1.1108 +IC H18A CA17 *CA18 H18B 1.1108 110.64 -120.38 110.71 1.1111 +IC H18A CA17 *CA18 H18C 1.1108 110.64 119.78 110.63 1.1119 +IC CB1 CB2 CB3 CB4 1.5285 112.02 -156.49 113.16 1.5352 +IC CB4 CB2 *CB3 H3D 1.5352 113.16 -125.26 110.81 1.1108 +IC H3D CB2 *CB3 H3E 1.1108 110.81 -117.62 108.58 1.1185 +IC CB2 CB3 CB4 CB5 1.5483 113.16 -72.87 114.64 1.5362 +IC CB5 CB3 *CB4 H4D 1.5362 114.64 -121.50 107.87 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 107.87 -115.68 108.33 1.1133 +IC CB3 CB4 CB5 CB6 1.5352 114.64 173.14 113.35 1.5409 +IC CB6 CB4 *CB5 H5D 1.5409 113.35 -120.91 109.12 1.1130 +IC H5D CB4 *CB5 H5E 1.1130 109.12 -117.35 108.69 1.1125 +IC CB4 CB5 CB6 CB7 1.5362 113.35 52.82 114.03 1.5378 +IC CB7 CB5 *CB6 H6D 1.5378 114.03 -120.64 108.65 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.65 -116.83 109.17 1.1121 +IC CB5 CB6 CB7 CB8 1.5409 114.03 179.98 112.81 1.5400 +IC CB8 CB6 *CB7 H7D 1.5400 112.81 -122.98 109.09 1.1121 +IC H7D CB6 *CB7 H7E 1.1121 109.09 -117.53 108.71 1.1155 +IC CB6 CB7 CB8 CB9 1.5378 112.81 177.49 110.85 1.5102 +IC CB9 CB7 *CB8 H8D 1.5102 110.85 -122.35 107.23 1.1140 +IC H8D CB7 *CB8 H8E 1.1140 107.23 -115.61 109.26 1.1115 +IC CB7 CB8 CB9 CB10 1.5400 110.85 -111.54 126.68 1.3485 +IC CB10 CB8 *CB9 H9D 1.3485 126.68 176.66 114.61 1.1007 +IC CB8 CB9 CB10 CB11 1.5102 126.68 -2.77 127.04 1.5103 +IC CB11 CB9 *CB10 H10D 1.5103 127.04 -178.65 118.60 1.1012 +IC CB9 CB10 CB11 CB12 1.3485 127.04 96.60 112.31 1.5135 +IC CB12 CB10 *CB11 H11D 1.5135 112.31 -125.47 110.37 1.1105 +IC H11D CB10 *CB11 H11E 1.1105 110.37 -114.37 108.83 1.1122 +IC CB10 CB11 CB12 CB13 1.5103 112.31 -123.24 127.49 1.3487 +IC CB13 CB11 *CB12 H12D 1.3487 127.49 -179.18 114.92 1.1025 +IC CB11 CB12 CB13 CB14 1.5135 127.49 0.10 127.26 1.5079 +IC CB14 CB12 *CB13 H13D 1.5079 127.26 -179.25 118.69 1.1053 +IC CB12 CB13 CB14 CB15 1.3487 127.26 123.97 111.98 1.5384 +IC CB15 CB13 *CB14 H14D 1.5384 111.98 -120.79 111.90 1.1093 +IC H14D CB13 *CB14 H14E 1.1093 111.90 -118.90 109.68 1.1138 +IC CB13 CB14 CB15 CB16 1.5079 111.98 -173.48 111.85 1.5348 +IC CB16 CB14 *CB15 H15D 1.5348 111.85 -121.68 109.78 1.1147 +IC H15D CB14 *CB15 H15E 1.1147 109.78 -117.79 109.28 1.1119 +IC CB14 CB15 CB16 CB17 1.5384 111.85 179.99 113.35 1.5313 +IC CB17 CB15 *CB16 H16D 1.5313 113.35 -121.42 108.85 1.1101 +IC H16D CB15 *CB16 H16E 1.1101 108.85 -117.19 108.74 1.1110 +IC CB15 CB16 CB17 CB18 1.5348 113.35 -178.76 113.12 1.5314 +IC CB18 CB16 *CB17 H17D 1.5314 113.12 -121.82 108.25 1.1149 +IC H17D CB16 *CB17 H17E 1.1149 108.25 -115.96 109.19 1.1126 +IC CB16 CB17 CB18 H18D 1.5313 113.12 -178.27 110.36 1.1112 +IC H18D CB17 *CB18 H18E 1.1112 110.36 -120.53 110.61 1.1103 +IC H18D CB17 *CB18 H18F 1.1112 110.36 119.56 110.21 1.1112 +IC CC1 CC2 CC3 CC4 1.5290 114.45 61.17 115.54 1.5407 +IC CC4 CC2 *CC3 H3R 1.5407 115.54 -123.39 108.81 1.1159 +IC H3R CC2 *CC3 H3S 1.1159 108.81 -115.09 107.30 1.1128 +IC CC2 CC3 CC4 CC5 1.5483 115.54 48.75 115.70 1.5381 +IC CC5 CC3 *CC4 H4R 1.5381 115.70 -121.95 108.35 1.1141 +IC H4R CC3 *CC4 H4S 1.1141 108.35 -115.67 107.88 1.1118 +IC CC3 CC4 CC5 CC6 1.5407 115.70 59.37 113.26 1.5339 +IC CC6 CC4 *CC5 H5R 1.5339 113.26 -122.42 108.68 1.1122 +IC H5R CC4 *CC5 H5S 1.1122 108.68 -116.61 108.64 1.1128 +IC CC4 CC5 CC6 CC7 1.5381 113.26 175.46 114.41 1.5382 +IC CC7 CC5 *CC6 H6R 1.5382 114.41 -121.44 108.39 1.1118 +IC H6R CC5 *CC6 H6S 1.1118 108.39 -116.44 108.77 1.1127 +IC CC5 CC6 CC7 CC8 1.5339 114.41 50.21 113.91 1.5402 +IC CC8 CC6 *CC7 H7R 1.5402 113.91 -122.10 108.87 1.1136 +IC H7R CC6 *CC7 H7S 1.1136 108.87 -116.44 107.40 1.1147 +IC CC6 CC7 CC8 CC9 1.5382 113.91 171.45 111.26 1.5090 +IC CC9 CC7 *CC8 H8R 1.5090 111.26 -123.76 107.81 1.1114 +IC H8R CC7 *CC8 H8S 1.1114 107.81 -115.28 108.84 1.1122 +IC CC7 CC8 CC9 CC10 1.5402 111.26 -128.36 127.23 1.3472 +IC CC10 CC8 *CC9 H9R 1.3472 127.23 178.70 114.30 1.1010 +IC CC8 CC9 CC10 CC11 1.5090 127.23 -1.15 127.54 1.5084 +IC CC11 CC9 *CC10 H10R 1.5084 127.54 -179.59 118.30 1.1015 +IC CC9 CC10 CC11 CC12 1.3472 127.54 121.83 111.08 1.5090 +IC CC12 CC10 *CC11 H11R 1.5090 111.08 -121.38 111.45 1.1092 +IC H11R CC10 *CC11 H11S 1.1092 111.45 -115.12 108.94 1.1091 +IC CC10 CC11 CC12 CC13 1.5084 111.08 114.57 127.61 1.3469 +IC CC13 CC11 *CC12 H12R 1.3469 127.61 179.18 114.07 1.1019 +IC CC11 CC12 CC13 CC14 1.5090 127.61 -1.12 127.24 1.5089 +IC CC14 CC12 *CC13 H13R 1.5089 127.24 -179.24 118.36 1.1008 +IC CC12 CC13 CC14 CC15 1.3469 127.24 -127.92 112.49 1.5415 +IC CC15 CC13 *CC14 H14R 1.5415 112.49 -120.38 109.34 1.1135 +IC H14R CC13 *CC14 H14S 1.1135 109.34 -118.08 112.29 1.1108 +IC CC13 CC14 CC15 CC16 1.5089 112.49 64.28 113.82 1.5372 +IC CC16 CC14 *CC15 H15R 1.5372 113.82 -123.02 109.95 1.1128 +IC CC14 CC15 CC16 CC17 1.5415 113.82 175.12 112.35 1.5342 +IC CC17 CC15 *CC16 H16R 1.5342 112.35 121.44 109.60 1.1127 +IC CC15 CC16 CC17 CC18 1.5372 112.35 177.84 113.41 1.5303 +IC CC18 CC16 *CC17 H17R 1.5303 113.41 -121.68 108.79 1.1140 +IC H17R CC16 *CC17 H17S 1.1140 108.79 -116.65 108.60 1.1141 +IC CC16 CC17 CC18 H18R 1.5342 113.41 177.41 110.78 1.1108 +IC H18R CC17 *CC18 H18S 1.1108 110.78 120.14 110.47 1.1110 +IC H18R CC17 *CC18 H18T 1.1108 110.78 -120.28 110.55 1.1114 +IC CD1 CD2 CD3 CD4 1.5307 113.39 169.15 112.93 1.5372 +IC CD4 CD2 *CD3 H3X 1.5372 112.93 -120.02 109.25 1.1156 +IC H3X CD2 *CD3 H3Y 1.1156 109.25 -117.49 109.59 1.1130 +IC CD2 CD3 CD4 CD5 1.5479 112.93 59.54 113.85 1.5360 +IC CD5 CD3 *CD4 H4X 1.5360 113.85 -121.33 108.32 1.1134 +IC H4X CD3 *CD4 H4Y 1.1134 108.32 -116.71 109.15 1.1132 +IC CD3 CD4 CD5 CD6 1.5372 113.85 -177.43 112.79 1.5357 +IC CD6 CD4 *CD5 H5X 1.5357 112.79 -122.43 109.70 1.1122 +IC H5X CD4 *CD5 H5Y 1.1122 109.70 -117.86 109.15 1.1139 +IC CD4 CD5 CD6 CD7 1.5360 112.79 173.65 112.21 1.5365 +IC CD7 CD5 *CD6 H6X 1.5365 112.21 -119.39 108.19 1.1136 +IC H6X CD5 *CD6 H6Y 1.1136 108.19 -117.35 110.05 1.1111 +IC CD5 CD6 CD7 CD8 1.5357 112.21 -164.07 113.53 1.5412 +IC CD8 CD6 *CD7 H7X 1.5412 113.53 -125.12 110.25 1.1118 +IC H7X CD6 *CD7 H7Y 1.1118 110.25 -116.30 107.52 1.1152 +IC CD6 CD7 CD8 CD9 1.5365 113.53 -72.33 113.26 1.5081 +IC CD9 CD7 *CD8 H8X 1.5081 113.26 -123.64 107.20 1.1122 +IC H8X CD7 *CD8 H8Y 1.1122 107.20 -114.54 108.43 1.1124 +IC CD7 CD8 CD9 CD10 1.5412 113.26 -141.33 126.38 1.3479 +IC CD10 CD8 *CD9 H9X 1.3479 126.38 -179.10 114.78 1.1010 +IC CD8 CD9 CD10 CD11 1.5081 126.38 0.12 126.84 1.5114 +IC CD11 CD9 *CD10 H10X 1.5114 126.84 -179.87 118.43 1.1016 +IC CD9 CD10 CD11 CD12 1.3479 126.84 -106.33 111.23 1.5105 +IC CD12 CD10 *CD11 H11X 1.5105 111.23 -120.37 109.03 1.1122 +IC H11X CD10 *CD11 H11Y 1.1122 109.03 -114.91 111.58 1.1099 +IC CD10 CD11 CD12 CD13 1.5114 111.23 109.38 127.41 1.3486 +IC CD13 CD11 *CD12 H12X 1.3486 127.41 179.19 114.40 1.1015 +IC CD11 CD12 CD13 CD14 1.5105 127.41 -1.41 127.65 1.5109 +IC CD14 CD12 *CD13 H13X 1.5109 127.65 -178.15 118.24 1.1012 +IC CD12 CD13 CD14 CD15 1.3486 127.65 -115.93 111.19 1.5399 +IC CD15 CD13 *CD14 H14X 1.5399 111.19 -120.10 109.72 1.1126 +IC H14X CD13 *CD14 H14Y 1.1126 109.72 -118.73 112.54 1.1122 +IC CD13 CD14 CD15 CD16 1.5109 111.19 -174.42 112.98 1.5354 +IC CD16 CD14 *CD15 H15X 1.5354 112.98 -121.07 109.22 1.1143 +IC H15X CD14 *CD15 H15Y 1.1143 109.22 -117.98 109.91 1.1138 +IC CD14 CD15 CD16 CD17 1.5399 112.98 179.46 112.15 1.5344 +IC CD17 CD15 *CD16 H16X 1.5344 112.15 -121.15 109.44 1.1128 +IC H16X CD15 *CD16 H16Y 1.1128 109.44 -117.66 109.26 1.1126 +IC CD15 CD16 CD17 CD18 1.5354 112.15 179.70 113.67 1.5310 +IC CD18 CD16 *CD17 H17X 1.5310 113.67 -121.71 108.44 1.1139 +IC H17X CD16 *CD17 H17Y 1.1139 108.44 -116.35 108.83 1.1138 +IC CD16 CD17 CD18 H18X 1.5344 113.67 -178.87 110.70 1.1108 +IC H18X CD17 *CD18 H18Y 1.1108 110.70 -120.14 110.59 1.1104 +IC H18X CD17 *CD18 H18Z 1.1108 110.70 119.96 110.62 1.1117 + +RESI LNDCL1 -1.00 ! 3 Linoleic acid + 1 linolenic acid cardiolipin with head group charge = -1 + ! Cardiolipin headgroup + 3 linoleoyl + 1 linolenoyl chains +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! HP13--OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 0.17 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 OHL -0.62 ! | | | | +ATOM HP13 HOL 0.34 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP14 O2L -0.78 ! | | | | +ATOM OP11 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM OP12 OSLP -0.57 ! | | | | +ATOM C11 CTL2 0.17 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11J HAL2 0.09 ! | | | | +ATOM H11K HAL2 0.09 ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +GROUP ! | | | | +ATOM C12 CTL1 0.17 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM H12J HAL1 0.09 ! | | | | +ATOM O12 OSL -0.49 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM CA1 CL 0.90 ! | | | | +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2A HAL2 0.09 ! | | | | +ATOM H2B HAL2 0.09 ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +GROUP ! | | | | +ATOM C13 CTL2 0.08 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13J HAL2 0.09 ! || || || || +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM CB1 CL 0.90 ! | | | | +ATOM OB1 OBL -0.63 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM CB2 CTL2 -0.22 ! | | | | +ATOM H2D HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +ATOM H2E HAL2 0.09 ! || || || || +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM H32J HAL1 0.09 ! | | | | +ATOM O32 OSL -0.49 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM CC1 CL 0.90 ! | | | | +ATOM OC1 OBL -0.63 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15 H15R--CC15--H15S +ATOM CC2 CTL2 -0.22 ! | | || | +ATOM H2R HAL2 0.09 ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16 H16R--CC16--H16S +ATOM H2S HAL2 0.09 ! | | | | +GROUP ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18F H18C H18Z H18T +ATOM CD1 CL 0.90 ! +ATOM OD1 OBL -0.63 ! +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CEL1 -0.15 ! +ATOM H15X HEL1 0.15 ! +GROUP ! +ATOM CD16 CEL1 -0.15 ! +ATOM H16X HEL1 0.15 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND OP13 HP13 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 CD16 +BOND CD16 H16X CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +!IC TABLE +! +IC OP31 C2 *C3 HG31 1.4272 111.57 124.87 107.78 1.1169 +IC HG31 C2 *C3 HG32 1.1169 107.78 115.89 109.04 1.1124 +IC C2 C3 OP31 P3 1.5483 111.57 118.08 122.98 1.5819 +IC C3 OP31 P3 OP32 1.4272 122.98 37.85 102.14 1.5830 +IC OP32 OP31 *P3 OP33 1.5830 102.14 -113.92 107.98 1.4793 +IC OP32 OP31 *P3 OP34 1.5830 102.14 115.66 109.62 1.4740 +IC OP31 P3 OP32 C31 1.5819 102.14 69.85 119.33 1.4301 +IC P3 OP32 C31 C32 1.5830 119.33 176.40 110.18 1.5529 +IC C32 OP32 *C31 H31J 1.5529 110.18 120.82 110.67 1.1139 +IC H31J OP32 *C31 H31K 1.1139 110.67 119.45 110.95 1.1159 +IC HG31 C3 C2 C1 1.1169 107.78 60.13 113.14 1.5594 +IC C1 C3 *C2 OG12 1.5594 113.14 -122.65 107.36 1.4314 +IC C1 C3 *C2 HG22 1.5594 113.14 119.50 108.81 1.1137 +IC C3 C2 OG12 HO12 1.5483 107.36 -59.74 104.73 0.9611 +IC C3 C2 C1 OP11 1.5483 113.14 102.14 111.29 1.4365 +IC OP11 C2 *C1 HG11 1.4365 111.29 -124.72 105.61 1.1191 +IC HG11 C2 *C1 HG12 1.1191 105.61 -115.38 108.40 1.1138 +IC C2 C1 OP11 P1 1.5594 111.29 -157.61 115.85 1.5685 +IC C1 OP11 P1 OP12 1.4365 115.85 -14.21 104.93 1.5653 +IC OP12 OP11 *P1 OP13 1.5653 104.93 115.00 111.23 1.5595 +IC OP12 OP11 *P1 OP14 1.5653 104.93 -120.71 114.44 1.4714 +IC OP11 P1 OP13 HP13 1.5685 111.23 -49.71 108.79 0.9805 +IC OP11 P1 OP12 C11 1.5685 104.93 168.45 117.56 1.4279 +IC P1 OP12 C11 C12 1.5653 117.56 -104.42 112.05 1.5631 +IC C12 OP12 *C11 H11J 1.5631 112.05 -116.94 106.96 1.1115 +IC H11J OP12 *C11 H11K 1.1115 106.96 -117.70 114.83 1.1174 +IC OP12 C11 C12 C13 1.4279 112.05 -169.61 110.60 1.5613 +IC C13 C11 *C12 O12 1.5613 110.60 124.16 109.17 1.4428 +IC O12 C11 *C12 H12J 1.4428 109.17 118.13 106.49 1.1175 +IC C11 C12 O12 CA1 1.5631 109.17 161.88 113.49 1.3343 +IC C12 O12 CA1 CA2 1.4428 113.49 -169.35 108.84 1.5280 +IC CA2 O12 *CA1 OA1 1.5280 108.84 179.80 125.17 1.2183 +IC O12 CA1 CA2 CA3 1.3343 108.84 -146.40 113.25 1.5456 +IC CA3 CA1 *CA2 H2A 1.5456 113.25 -119.97 106.28 1.1109 +IC H2A CA1 *CA2 H2B 1.1109 106.28 -116.75 108.94 1.1073 +IC C11 C12 C13 O13 1.5631 110.60 48.04 111.75 1.4444 +IC O13 C12 *C13 H13J 1.4444 111.75 -117.92 106.48 1.1131 +IC H13J C12 *C13 H13K 1.1131 106.48 -115.07 111.40 1.1131 +IC C12 C13 O13 CB1 1.5613 111.75 88.82 115.87 1.3297 +IC C13 O13 CB1 CB2 1.4444 115.87 -174.80 108.56 1.5287 +IC CB2 O13 *CB1 OB1 1.5287 108.56 -178.49 126.34 1.2145 +IC O13 CB1 CB2 CB3 1.3297 108.56 152.47 112.16 1.5454 +IC CB3 CB1 *CB2 H2D 1.5454 112.16 -121.52 108.74 1.1089 +IC H2D CB1 *CB2 H2E 1.1089 108.74 -117.40 106.94 1.1083 +IC OP32 C31 C32 C33 1.4301 110.18 -69.33 110.65 1.5522 +IC C33 C31 *C32 O32 1.5522 110.65 120.01 111.21 1.4395 +IC O32 C31 *C32 H32J 1.4395 111.21 122.30 108.97 1.1146 +IC C31 C32 O32 CC1 1.5529 111.21 69.31 115.35 1.3120 +IC C32 O32 CC1 CC2 1.4395 115.35 -171.71 108.60 1.5297 +IC CC2 O32 *CC1 OC1 1.5297 108.60 -178.02 126.78 1.2186 +IC O32 CC1 CC2 CC3 1.3120 108.60 -59.72 112.33 1.5489 +IC CC3 CC1 *CC2 H2R 1.5489 112.33 -122.26 107.83 1.1075 +IC H2R CC1 *CC2 H2S 1.1075 107.83 -116.44 106.39 1.1097 +IC C31 C32 C33 O33 1.5529 110.65 179.11 109.99 1.4464 +IC O33 C32 *C33 H33J 1.4464 109.99 121.93 109.29 1.1119 +IC H33J C32 *C33 H33K 1.1119 109.29 116.57 106.09 1.1186 +IC C32 C33 O33 CD1 1.5522 109.99 -159.03 114.19 1.3237 +IC C33 O33 CD1 CD2 1.4464 114.19 164.21 109.32 1.5286 +IC CD2 O33 *CD1 OD1 1.5286 109.32 -178.45 126.02 1.2156 +IC O33 CD1 CD2 CD3 1.3237 109.32 -46.26 112.24 1.5470 +IC CD3 CD1 *CD2 H2X 1.5470 112.24 -120.21 106.48 1.1100 +IC H2X CD1 *CD2 H2Y 1.1100 106.48 -117.13 108.41 1.1069 +IC CA1 CA2 CA3 CA4 1.5280 113.25 70.18 112.81 1.5346 +IC CA4 CA2 *CA3 H3A 1.5346 112.81 -123.14 110.14 1.1142 +IC H3A CA2 *CA3 H3B 1.1142 110.14 -116.66 107.70 1.1125 +IC CA2 CA3 CA4 CA5 1.5456 112.81 172.40 112.79 1.5353 +IC CA5 CA3 *CA4 H4A 1.5353 112.79 -122.05 109.90 1.1116 +IC H4A CA3 *CA4 H4B 1.1116 109.90 -117.14 108.37 1.1150 +IC CA3 CA4 CA5 CA6 1.5346 112.79 167.30 112.42 1.5358 +IC CA6 CA4 *CA5 H5A 1.5358 112.42 -120.63 108.10 1.1132 +IC H5A CA4 *CA5 H5B 1.1132 108.10 -117.30 109.47 1.1120 +IC CA4 CA5 CA6 CA7 1.5353 112.42 177.91 114.45 1.5409 +IC CA7 CA5 *CA6 H6A 1.5409 114.45 -121.60 108.84 1.1121 +IC H6A CA5 *CA6 H6B 1.1121 108.84 -116.16 108.48 1.1134 +IC CA5 CA6 CA7 CA8 1.5358 114.45 53.66 115.58 1.5440 +IC CA8 CA6 *CA7 H7A 1.5440 115.58 -121.63 108.47 1.1138 +IC H7A CA6 *CA7 H7B 1.1138 108.47 -116.24 108.32 1.1141 +IC CA6 CA7 CA8 CA9 1.5409 115.58 55.01 112.73 1.5097 +IC CA9 CA7 *CA8 H8A 1.5097 112.73 -121.48 108.57 1.1114 +IC H8A CA7 *CA8 H8B 1.1114 108.57 -114.55 107.55 1.1126 +IC CA7 CA8 CA9 CA10 1.5440 112.73 109.39 127.97 1.3474 +IC CA10 CA8 *CA9 H9A 1.3474 127.97 -179.15 113.83 1.1025 +IC CA8 CA9 CA10 CA11 1.5097 127.97 0.64 127.89 1.5108 +IC CA11 CA9 *CA10 H10A 1.5108 127.89 179.31 117.75 1.1014 +IC CA9 CA10 CA11 CA12 1.3474 127.89 -112.95 111.22 1.5114 +IC CA12 CA10 *CA11 H11A 1.5114 111.22 -120.46 108.90 1.1119 +IC H11A CA10 *CA11 H11B 1.1119 108.90 -115.57 110.84 1.1112 +IC CA10 CA11 CA12 CA13 1.5108 111.22 134.57 126.37 1.3465 +IC CA13 CA11 *CA12 H12A 1.3465 126.37 -177.01 115.27 1.1018 +IC CA11 CA12 CA13 CA14 1.5114 126.37 3.15 126.32 1.5077 +IC CA14 CA12 *CA13 H13A 1.5077 126.32 178.37 118.79 1.1003 +IC CA12 CA13 CA14 CA15 1.3465 126.32 -92.58 113.47 1.5417 +IC CA15 CA13 *CA14 H14A 1.5417 113.47 -122.01 110.01 1.1123 +IC H14A CA13 *CA14 H14B 1.1123 110.01 -116.77 110.38 1.1120 +IC CA13 CA14 CA15 CA16 1.5077 113.47 -63.55 113.58 1.5369 +IC CA16 CA14 *CA15 H15A 1.5369 113.58 -120.33 108.08 1.1132 +IC H15A CA14 *CA15 H15B 1.1132 108.08 -116.59 109.36 1.1132 +IC CA14 CA15 CA16 CA17 1.5417 113.58 -171.21 113.87 1.5374 +IC CA17 CA15 *CA16 H16A 1.5374 113.87 -121.70 108.87 1.1122 +IC H16A CA15 *CA16 H16B 1.1122 108.87 -117.00 108.72 1.1132 +IC CA15 CA16 CA17 CA18 1.5369 113.87 -61.57 114.41 1.5314 +IC CA18 CA16 *CA17 H17A 1.5314 114.41 -121.26 108.12 1.1148 +IC H17A CA16 *CA17 H17B 1.1148 108.12 -116.30 108.76 1.1136 +IC CA16 CA17 CA18 H18A 1.5374 114.41 63.53 110.93 1.1107 +IC H18A CA17 *CA18 H18B 1.1107 110.93 -119.76 110.34 1.1109 +IC H18A CA17 *CA18 H18C 1.1107 110.93 120.37 110.77 1.1100 +IC CB1 CB2 CB3 CB4 1.5287 112.16 178.44 113.36 1.5384 +IC CB4 CB2 *CB3 H3D 1.5384 113.36 -122.28 109.76 1.1140 +IC H3D CB2 *CB3 H3E 1.1140 109.76 -116.69 109.13 1.1151 +IC CB2 CB3 CB4 CB5 1.5454 113.36 -60.74 115.02 1.5414 +IC CB5 CB3 *CB4 H4D 1.5414 115.02 -121.57 108.33 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 108.33 -116.10 108.96 1.1133 +IC CB3 CB4 CB5 CB6 1.5384 115.02 -51.86 114.89 1.5394 +IC CB6 CB4 *CB5 H5D 1.5394 114.89 -121.74 108.45 1.1137 +IC H5D CB4 *CB5 H5E 1.1137 108.45 -116.35 108.99 1.1129 +IC CB4 CB5 CB6 CB7 1.5414 114.89 -57.34 113.83 1.5380 +IC CB7 CB5 *CB6 H6D 1.5380 113.83 -121.31 108.98 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.98 -116.37 108.87 1.1123 +IC CB5 CB6 CB7 CB8 1.5394 113.83 179.71 113.63 1.5423 +IC CB8 CB6 *CB7 H7D 1.5423 113.63 -122.27 109.89 1.1123 +IC H7D CB6 *CB7 H7E 1.1123 109.89 -116.77 108.48 1.1132 +IC CB6 CB7 CB8 CB9 1.5380 113.63 -63.29 112.23 1.5093 +IC CB9 CB7 *CB8 H8D 1.5093 112.23 -120.64 107.87 1.1133 +IC H8D CB7 *CB8 H8E 1.1133 107.87 -115.67 108.05 1.1129 +IC CB7 CB8 CB9 CB10 1.5423 112.23 148.17 126.47 1.3460 +IC CB10 CB8 *CB9 H9D 1.3460 126.47 -177.74 114.82 1.1018 +IC CB8 CB9 CB10 CB11 1.5093 126.47 2.77 126.58 1.5092 +IC CB11 CB9 *CB10 H10D 1.5092 126.58 177.26 118.57 1.1029 +IC CB9 CB10 CB11 CB12 1.3460 126.58 -116.82 111.69 1.5096 +IC CB12 CB10 *CB11 H11D 1.5096 111.69 -123.10 108.54 1.1115 +IC H11D CB10 *CB11 H11E 1.1115 108.54 -114.79 111.63 1.1116 +IC CB10 CB11 CB12 CB13 1.5092 111.69 -110.56 126.32 1.3473 +IC CB13 CB11 *CB12 H12D 1.3473 126.32 -178.41 114.77 1.1018 +IC CB11 CB12 CB13 CB14 1.5096 126.32 2.04 125.85 1.5088 +IC CB14 CB12 *CB13 H13D 1.5088 125.85 179.17 118.99 1.1012 +IC CB12 CB13 CB14 CB15 1.3473 125.85 -89.20 112.98 1.5413 +IC CB15 CB13 *CB14 H14D 1.5413 112.98 -121.97 110.15 1.1124 +IC H14D CB13 *CB14 H14E 1.1124 110.15 -116.85 110.43 1.1140 +IC CB13 CB14 CB15 CB16 1.5088 112.98 -66.02 113.67 1.5362 +IC CB16 CB14 *CB15 H15D 1.5362 113.67 -120.47 108.54 1.1134 +IC H15D CB14 *CB15 H15E 1.1134 108.54 -116.71 109.67 1.1135 +IC CB14 CB15 CB16 CB17 1.5413 113.67 -176.61 112.48 1.5339 +IC CB17 CB15 *CB16 H16D 1.5339 112.48 -121.15 109.47 1.1130 +IC H16D CB15 *CB16 H16E 1.1130 109.47 -117.68 109.15 1.1130 +IC CB15 CB16 CB17 CB18 1.5362 112.48 -179.94 113.24 1.5308 +IC CB18 CB16 *CB17 H17D 1.5308 113.24 -121.73 108.82 1.1141 +IC H17D CB16 *CB17 H17E 1.1141 108.82 -116.64 108.69 1.1143 +IC CB16 CB17 CB18 H18D 1.5339 113.24 59.88 110.45 1.1114 +IC H18D CB17 *CB18 H18E 1.1114 110.45 -119.87 110.50 1.1113 +IC H18D CB17 *CB18 H18F 1.1114 110.45 120.03 110.63 1.1113 +IC CC1 CC2 CC3 CC4 1.5297 112.33 172.47 113.86 1.5361 +IC CC4 CC2 *CC3 H3R 1.5361 113.86 -119.64 108.94 1.1154 +IC H3R CC2 *CC3 H3S 1.1154 108.94 -117.39 109.77 1.1130 +IC CC2 CC3 CC4 CC5 1.5489 113.86 -56.98 112.74 1.5347 +IC CC5 CC3 *CC4 H4R 1.5347 112.74 -119.98 107.98 1.1143 +IC H4R CC3 *CC4 H4S 1.1143 107.98 -117.33 110.39 1.1120 +IC CC3 CC4 CC5 CC6 1.5361 112.74 -154.31 113.28 1.5321 +IC CC6 CC4 *CC5 H5R 1.5321 113.28 -123.53 109.65 1.1125 +IC H5R CC4 *CC5 H5S 1.1125 109.65 -117.22 108.68 1.1132 +IC CC4 CC5 CC6 CC7 1.5347 113.28 -174.72 112.18 1.5360 +IC CC7 CC5 *CC6 H6R 1.5360 112.18 -120.78 108.11 1.1141 +IC H6R CC5 *CC6 H6S 1.1141 108.11 -117.38 110.00 1.1122 +IC CC5 CC6 CC7 CC8 1.5321 112.18 -168.49 113.32 1.5408 +IC CC8 CC6 *CC7 H7R 1.5408 113.32 -121.00 108.07 1.1137 +IC H7R CC6 *CC7 H7S 1.1137 108.07 -116.02 109.54 1.1140 +IC CC6 CC7 CC8 CC9 1.5360 113.32 72.57 111.65 1.5102 +IC CC9 CC7 *CC8 H8R 1.5102 111.65 -124.76 108.23 1.1117 +IC H8R CC7 *CC8 H8S 1.1117 108.23 -115.30 107.95 1.1119 +IC CC7 CC8 CC9 CC10 1.5408 111.65 -134.06 127.67 1.3478 +IC CC10 CC8 *CC9 H9R 1.3478 127.67 179.52 113.97 1.1023 +IC CC8 CC9 CC10 CC11 1.5102 127.67 -0.03 127.34 1.5115 +IC CC11 CC9 *CC10 H10R 1.5115 127.34 179.73 118.07 1.1026 +IC CC9 CC10 CC11 CC12 1.3478 127.34 129.05 112.32 1.5099 +IC CC12 CC10 *CC11 H11R 1.5099 112.32 -123.72 111.60 1.1114 +IC H11R CC10 *CC11 H11S 1.1114 111.60 -115.47 108.90 1.1121 +IC CC10 CC11 CC12 CC13 1.5115 112.32 -84.97 126.59 1.3471 +IC CC13 CC11 *CC12 H12R 1.3471 126.59 -179.05 114.79 1.1010 +IC CC11 CC12 CC13 CC14 1.5099 126.59 1.41 126.41 1.5090 +IC CC14 CC12 *CC13 H13R 1.5090 126.41 178.45 118.70 1.0998 +IC CC12 CC13 CC14 CC15 1.3471 126.41 -125.27 113.39 1.5418 +IC CC15 CC13 *CC14 H14R 1.5418 113.39 -121.44 109.86 1.1131 +IC H14R CC13 *CC14 H14S 1.1131 109.86 -117.22 111.11 1.1131 +IC CC13 CC14 CC15 CC16 1.5090 113.39 -68.63 113.68 1.5381 +IC CC16 CC14 *CC15 H15R 1.5381 113.68 123.30 109.83 1.1129 +IC H15R CC14 *CC15 H15S 1.1129 109.83 116.45 107.53 1.1136 +IC CC14 CC15 CC16 CC17 1.5418 113.68 179.76 113.73 1.5374 +IC CC17 CC15 *CC16 H16R 1.5374 113.73 121.83 108.95 1.1128 +IC H16R CC15 *CC16 H16S 1.1128 108.95 117.24 109.15 1.1127 +IC CC15 CC16 CC17 CC18 1.5381 113.73 63.65 114.54 1.5322 +IC CC18 CC16 *CC17 H17R 1.5322 114.54 -122.47 108.69 1.1141 +IC H17R CC16 *CC17 H17S 1.1141 108.69 -116.13 108.22 1.1148 +IC CC16 CC17 CC18 H18R 1.5374 114.54 56.61 110.47 1.1112 +IC H18R CC17 *CC18 H18S 1.1112 110.47 -120.21 110.86 1.1107 +IC H18R CC17 *CC18 H18T 1.1112 110.47 119.94 110.49 1.1113 +IC CD1 CD2 CD3 CD4 1.5286 112.24 -168.50 113.06 1.5318 +IC CD4 CD2 *CD3 H3X 1.5318 113.06 -122.94 109.98 1.1137 +IC H3X CD2 *CD3 H3Y 1.1137 109.98 -117.36 109.14 1.1136 +IC CD2 CD3 CD4 CD5 1.5470 113.06 175.61 111.87 1.5362 +IC CD5 CD3 *CD4 H4X 1.5362 111.87 -120.66 108.60 1.1128 +IC H4X CD3 *CD4 H4Y 1.1128 108.60 -117.59 109.56 1.1124 +IC CD3 CD4 CD5 CD6 1.5318 111.87 177.84 113.59 1.5356 +IC CD6 CD4 *CD5 H5X 1.5356 113.59 -121.15 108.45 1.1137 +IC H5X CD4 *CD5 H5Y 1.1137 108.45 -116.84 109.16 1.1138 +IC CD4 CD5 CD6 CD7 1.5362 113.59 67.64 113.35 1.5355 +IC CD7 CD5 *CD6 H6X 1.5355 113.35 -122.12 109.12 1.1128 +IC H6X CD5 *CD6 H6Y 1.1128 109.12 -117.25 108.81 1.1134 +IC CD5 CD6 CD7 CD8 1.5356 113.35 -178.50 112.28 1.5389 +IC CD8 CD6 *CD7 H7X 1.5389 112.28 -122.16 108.88 1.1140 +IC H7X CD6 *CD7 H7Y 1.1140 108.88 -116.95 109.16 1.1134 +IC CD6 CD7 CD8 CD9 1.5355 112.28 179.01 111.42 1.5083 +IC CD9 CD7 *CD8 H8X 1.5083 111.42 -122.39 108.26 1.1135 +IC H8X CD7 *CD8 H8Y 1.1135 108.26 -115.32 109.05 1.1118 +IC CD7 CD8 CD9 CD10 1.5389 111.42 -84.39 125.66 1.3464 +IC CD10 CD8 *CD9 H9X 1.3464 125.66 178.86 115.42 1.1011 +IC CD8 CD9 CD10 CD11 1.5083 125.66 0.74 126.41 1.5100 +IC CD11 CD9 *CD10 H10X 1.5100 126.41 178.33 118.71 1.1020 +IC CD9 CD10 CD11 CD12 1.3464 126.41 -119.11 111.66 1.5104 +IC CD12 CD10 *CD11 H11X 1.5104 111.66 -123.67 108.55 1.1120 +IC H11X CD10 *CD11 H11Y 1.1120 108.55 -114.62 111.55 1.1120 +IC CD10 CD11 CD12 CD13 1.5100 111.66 -113.81 126.72 1.3477 +IC CD13 CD11 *CD12 H12X 1.3477 126.72 -178.56 114.59 1.1018 +IC CD11 CD12 CD13 CD14 1.5104 126.72 1.66 126.19 1.5088 +IC CD14 CD12 *CD13 H13X 1.5088 126.19 179.37 118.90 1.1014 +IC CD12 CD13 CD14 CD15 1.3477 126.19 -100.76 112.41 1.5405 +IC CD15 CD13 *CD14 H14X 1.5405 112.41 -121.85 109.83 1.1118 +IC H14X CD13 *CD14 H14Y 1.1118 109.83 -117.23 111.23 1.1116 +IC CD13 CD14 CD15 CD16 1.5088 112.41 170.52 113.29 1.5388 +IC CD16 CD14 *CD15 H15X 1.5388 113.29 -119.71 109.05 1.1153 +IC CD14 CD15 CD16 CD17 1.5405 113.29 62.69 114.08 1.5347 +IC CD17 CD15 *CD16 H16X 1.5347 114.08 -121.99 108.89 1.1132 +IC CD15 CD16 CD17 CD18 1.5388 114.08 179.88 112.98 1.5311 +IC CD18 CD16 *CD17 H17X 1.5311 112.98 -121.76 108.79 1.1137 +IC H17X CD16 *CD17 H17Y 1.1137 108.79 -117.11 109.38 1.1133 +IC CD16 CD17 CD18 H18X 1.5347 112.98 60.79 110.28 1.1118 +IC H18X CD17 *CD18 H18Y 1.1118 110.28 -119.90 110.57 1.1110 +IC H18X CD17 *CD18 H18Z 1.1118 110.28 119.81 110.63 1.1110 + +RESI LNDCL2 -2.00 ! 3 linoleic acid + 1 linolenic acid cardiolipin with head group charge = -2 + ! Cardiolipin headgroup + 3 linoleoly chains + 1 linolenoyl chain +GROUP ! +ATOM C3 CTL2 -0.08 ! HG11 OG12--HO12 HG31 +ATOM HG31 HAL2 0.09 ! \ | / +ATOM HG32 HAL2 0.09 ! C1----------------C2--------------------C3 +ATOM P3 PL 1.50 ! / \ | / \ +ATOM OP33 O2L -0.78 ! / HG12 HG22 HG32 \ +ATOM OP34 O2L -0.78 ! OP11 OP31 +ATOM OP31 OSLP -0.57 ! | | +ATOM OP32 OSLP -0.57 ! OP13(-)--P1(+)--OP14(-) OP33(-)--P3(+)--OP34(-) +ATOM C31 CTL2 -0.08 ! | | +ATOM H31J HAL2 0.09 ! OP12 OP32 +ATOM H31K HAL2 0.09 ! | | +GROUP ! H11J--C11--H11K H31J--C31--H31K +ATOM C2 CTL1 0.14 ! | | +ATOM HG22 HAL1 0.09 ! | | +ATOM OG12 OHL -0.65 ! H12J--C12--------O12-------- H32J--C32--------O32------- +ATOM HO12 HOL 0.42 ! | | | | +GROUP ! | | | | +ATOM C1 CTL2 -0.08 ! H13J--C13--H13K | H33J--C33--H33K | +ATOM HG11 HAL2 0.09 ! | | | | +ATOM HG12 HAL2 0.09 ! | | | | +ATOM P1 PL 1.50 ! O13 | O33 | +ATOM OP13 O2L -0.78 ! | | | | +ATOM OP14 O2L -0.78 ! CB1=OB1 CA1=OA1 CD1=OD1 CC1=OC1 +ATOM OP11 OSLP -0.57 ! | | | | +ATOM OP12 OSLP -0.57 ! H2D--CB2--H2E H2A--CA2--H2B H2X--CD2--H2Y H2R--CC2--H2S +ATOM C11 CTL2 -0.08 ! | | | | +ATOM H11J HAL2 0.09 ! H3D--CB3--H3E H3A--CA3--H3B H3X--CD3--H3Y H3R--CC3--H3S +ATOM H11K HAL2 0.09 ! | | | | +GROUP ! H4D--CB4--H4E H4A--CA4--H4B H4X--CD4--H4Y H4R--CC4--H4S +ATOM C12 CTL1 0.17 ! | | | | +ATOM H12J HAL1 0.09 ! H5D--CB5--H5E H5A--CA5--H5B H5X--CD5--H5Y H5R--CC5--H5S +ATOM O12 OSL -0.49 ! | | | | +ATOM CA1 CL 0.90 ! H6D--CB6--H6E H6A--CA6--H6B H6X--CD6--H6Y H6R--CC6--H6S +ATOM OA1 OBL -0.63 ! | | | | +ATOM CA2 CTL2 -0.22 ! | | | | +ATOM H2A HAL2 0.09 ! H7D--CB7--H7E H7A--CA7--H7B H7X--CD7--H7Y H7R--CC7--H7S +ATOM H2B HAL2 0.09 ! | | | | +GROUP ! H8D--CB8--H8E H8A--CA8--H8B H8X--CD8--H8Y H8R--CC8--H8S +ATOM C13 CTL2 0.08 ! | | | | +ATOM H13J HAL2 0.09 ! H9D--CB9 H9A--CA9 H9X--CD9 H9R--CC9 +ATOM H13K HAL2 0.09 ! || || || || +ATOM O13 OSL -0.49 ! || || || || +ATOM CB1 CL 0.90 ! H10D--CB10 H10A--CA10 H10X--CD10 H10R--CC10 +ATOM OB1 OBL -0.63 ! | | | | +ATOM CB2 CTL2 -0.22 ! H11D--CB11--H11E H11A--CA11--H11B H11X--CD11--H11Y H11R--CC11--H11S +ATOM H2D HAL2 0.09 ! | | | | +ATOM H2E HAL2 0.09 ! H12D--CB12 H12A--CA12 H12X--CD12 H12R--CC12 +GROUP ! || || || || +ATOM C32 CTL1 0.17 ! || || || || +ATOM H32J HAL1 0.09 ! H13D--CB13 H13A--CA13 H13X--CD13 H13R--CC13 +ATOM O32 OSL -0.49 ! | | | | +ATOM CC1 CL 0.90 ! H14D--CB14--H14E H14A--CA14--H14B H14X--CD14--H14Y H14R--CC14--H14S +ATOM OC1 OBL -0.63 ! | | | | +ATOM CC2 CTL2 -0.22 ! H15D--CB15--H15E H15A--CA15--H15B H15X--CD15--H15Y H15R--CC15--H15S +ATOM H2R HAL2 0.09 ! | | || | +ATOM H2S HAL2 0.09 ! | | || | +GROUP ! H16D--CB16--H16E H16A--CA16--H16B H16X--CD16--H16Y H16R--CC16--H16S +ATOM C33 CTL2 0.08 ! | | | | +ATOM H33J HAL2 0.09 ! H17D--CB17--H17E H17A--CA17--H17B H17X--CD17--H17Y H17R--CC17--H17S +ATOM H33K HAL2 0.09 ! | | | | +ATOM O33 OSL -0.49 ! H18D--CB18--H18E H18A--CA18--H18B H18X--CD18--H18Y H18R--CC18--H18S +ATOM CD1 CL 0.90 ! | | | | +ATOM OD1 OBL -0.63 ! H18F H18C H18Z H18T +ATOM CD2 CTL2 -0.22 ! +ATOM H2X HAL2 0.09 ! +ATOM H2Y HAL2 0.09 ! +GROUP ! +ATOM CA3 CTL2 -0.18 ! +ATOM H3A HAL2 0.09 ! +ATOM H3B HAL2 0.09 ! +GROUP ! +ATOM CA4 CTL2 -0.18 ! +ATOM H4A HAL2 0.09 ! +ATOM H4B HAL2 0.09 ! +GROUP ! +ATOM CA5 CTL2 -0.18 ! +ATOM H5A HAL2 0.09 ! +ATOM H5B HAL2 0.09 ! +GROUP ! +ATOM CA6 CTL2 -0.18 ! +ATOM H6A HAL2 0.09 ! +ATOM H6B HAL2 0.09 ! +GROUP ! +ATOM CA7 CTL2 -0.18 ! +ATOM H7A HAL2 0.09 ! +ATOM H7B HAL2 0.09 ! +GROUP ! +ATOM CA8 CTL2 -0.18 ! +ATOM H8A HAL2 0.09 ! +ATOM H8B HAL2 0.09 ! +GROUP ! +ATOM CA9 CEL1 -0.15 ! +ATOM H9A HEL1 0.15 ! +GROUP ! +ATOM CA10 CEL1 -0.15 ! +ATOM H10A HEL1 0.15 ! +GROUP ! +ATOM CA11 CTL2 -0.18 ! +ATOM H11A HAL2 0.09 ! +ATOM H11B HAL2 0.09 ! +GROUP ! +ATOM CA12 CEL1 -0.15 ! +ATOM H12A HEL1 0.15 ! +GROUP ! +ATOM CA13 CEL1 -0.15 ! +ATOM H13A HEL1 0.15 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL2 -0.18 ! +ATOM H16A HAL2 0.09 ! +ATOM H16B HAL2 0.09 ! +GROUP ! +ATOM CA17 CTL2 -0.18 ! +ATOM H17A HAL2 0.09 ! +ATOM H17B HAL2 0.09 ! +GROUP ! +ATOM CA18 CTL3 -0.27 ! +ATOM H18A HAL3 0.09 ! +ATOM H18B HAL3 0.09 ! +ATOM H18C HAL3 0.09 ! +GROUP ! +ATOM CB3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CB4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CB5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CB6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CB7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CB8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CB9 CEL1 -0.15 ! +ATOM H9D HEL1 0.15 ! +GROUP ! +ATOM CB10 CEL1 -0.15 ! +ATOM H10D HEL1 0.15 ! +GROUP ! +ATOM CB11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CB12 CEL1 -0.15 ! +ATOM H12D HEL1 0.15 ! +GROUP ! +ATOM CB13 CEL1 -0.15 ! +ATOM H13D HEL1 0.15 ! +GROUP ! +ATOM CB14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CB15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CB16 CTL2 -0.18 ! +ATOM H16D HAL2 0.09 ! +ATOM H16E HAL2 0.09 ! +GROUP ! +ATOM CB17 CTL2 -0.18 ! +ATOM H17D HAL2 0.09 ! +ATOM H17E HAL2 0.09 ! +GROUP ! +ATOM CB18 CTL3 -0.27 ! +ATOM H18D HAL3 0.09 ! +ATOM H18E HAL3 0.09 ! +ATOM H18F HAL3 0.09 ! +GROUP ! +ATOM CC3 CTL2 -0.18 ! +ATOM H3R HAL2 0.09 ! +ATOM H3S HAL2 0.09 ! +GROUP ! +ATOM CC4 CTL2 -0.18 ! +ATOM H4R HAL2 0.09 ! +ATOM H4S HAL2 0.09 ! +GROUP ! +ATOM CC5 CTL2 -0.18 ! +ATOM H5R HAL2 0.09 ! +ATOM H5S HAL2 0.09 ! +GROUP ! +ATOM CC6 CTL2 -0.18 ! +ATOM H6R HAL2 0.09 ! +ATOM H6S HAL2 0.09 ! +GROUP ! +ATOM CC7 CTL2 -0.18 ! +ATOM H7R HAL2 0.09 ! +ATOM H7S HAL2 0.09 ! +GROUP ! +ATOM CC8 CTL2 -0.18 ! +ATOM H8R HAL2 0.09 ! +ATOM H8S HAL2 0.09 ! +GROUP ! +ATOM CC9 CEL1 -0.15 ! +ATOM H9R HEL1 0.15 ! +GROUP ! +ATOM CC10 CEL1 -0.15 ! +ATOM H10R HEL1 0.15 ! +GROUP ! +ATOM CC11 CTL2 -0.18 ! +ATOM H11R HAL2 0.09 ! +ATOM H11S HAL2 0.09 ! +GROUP ! +ATOM CC12 CEL1 -0.15 ! +ATOM H12R HEL1 0.15 ! +GROUP ! +ATOM CC13 CEL1 -0.15 ! +ATOM H13R HEL1 0.15 ! +GROUP ! +ATOM CC14 CTL2 -0.18 ! +ATOM H14R HAL2 0.09 ! +ATOM H14S HAL2 0.09 ! +GROUP ! +ATOM CC15 CTL2 -0.18 ! +ATOM H15R HAL2 0.09 ! +ATOM H15S HAL2 0.09 ! +GROUP ! +ATOM CC16 CTL2 -0.18 ! +ATOM H16R HAL2 0.09 ! +ATOM H16S HAL2 0.09 ! +GROUP ! +ATOM CC17 CTL2 -0.18 ! +ATOM H17R HAL2 0.09 ! +ATOM H17S HAL2 0.09 ! +GROUP ! +ATOM CC18 CTL3 -0.27 ! +ATOM H18R HAL3 0.09 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CD9 CEL1 -0.15 ! +ATOM H9X HEL1 0.15 ! +GROUP ! +ATOM CD10 CEL1 -0.15 ! +ATOM H10X HEL1 0.15 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CD12 CEL1 -0.15 ! +ATOM H12X HEL1 0.15 ! +GROUP ! +ATOM CD13 CEL1 -0.15 ! +ATOM H13X HEL1 0.15 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CD15 CEL1 -0.15 ! +ATOM H15X HEL1 0.15 ! +GROUP ! +ATOM CD16 CEL1 -0.15 ! +ATOM H16X HEL1 0.15 ! +GROUP ! +ATOM CD17 CTL2 -0.18 ! +ATOM H17X HAL2 0.09 ! +ATOM H17Y HAL2 0.09 ! +GROUP ! +ATOM CD18 CTL3 -0.27 ! +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 !! + +! Glycerol head +BOND C1 C2 C1 HG11 C1 HG12 +BOND C2 OG12 C2 HG22 OG12 HO12 C2 C3 +BOND C3 HG31 C3 HG32 +! Phosphates +BOND C1 OP11 C3 OP31 +BOND P1 OP11 P1 OP12 P1 OP13 P1 OP14 +BOND P3 OP31 P3 OP32 P3 OP33 P3 OP34 +! Glycerol Backbones +BOND OP12 C11 C11 H11J C11 H11K +BOND C11 C12 +BOND C12 H12J C12 O12 +BOND C12 C13 +BOND C13 H13J C13 H13K C13 O13 +BOND OP32 C31 C31 H31J C31 H31K +BOND C31 C32 +BOND C32 H32J C32 O32 +BOND C32 C33 +BOND C33 H33J C33 H33K C33 O33 +! Acyl chain 1 +BOND O12 CA1 O13 CB1 O32 CC1 O33 CD1 +BOND CA1 OA1 CA1 CA2 +BOND CA2 H2A CA2 H2B CA2 CA3 +BOND CA3 H3A CA3 H3B CA3 CA4 +BOND CA4 H4A CA4 H4B CA4 CA5 +BOND CA5 H5A CA5 H5B CA5 CA6 +BOND CA6 H6A CA6 H6B CA6 CA7 +BOND CA7 H7A CA7 H7B CA7 CA8 +BOND CA8 H8A CA8 H8B CA8 CA9 +BOND CA9 H9A CA9 CA10 +BOND CA10 H10A CA10 CA11 +BOND CA11 H11A CA11 H11B CA11 CA12 +BOND CA12 H12A CA12 CA13 +BOND CA13 H13A CA13 CA14 +BOND CA14 H14A CA14 H14B CA14 CA15 +BOND CA15 H15A CA15 H15B CA15 CA16 +BOND CA16 H16A CA16 H16B CA16 CA17 +BOND CA17 H17A CA17 H17B CA17 CA18 +BOND CA18 H18A CA18 H18B CA18 H18C +! Acyl chain 2 +BOND CB1 OB1 CB1 CB2 +BOND CB2 H2D CB2 H2E CB2 CB3 +BOND CB3 H3D CB3 H3E CB3 CB4 +BOND CB4 H4D CB4 H4E CB4 CB5 +BOND CB5 H5D CB5 H5E CB5 CB6 +BOND CB6 H6D CB6 H6E CB6 CB7 +BOND CB7 H7D CB7 H7E CB7 CB8 +BOND CB8 H8D CB8 H8E CB8 CB9 +BOND CB9 H9D CB9 CB10 +BOND CB10 H10D CB10 CB11 +BOND CB11 H11D CB11 H11E CB11 CB12 +BOND CB12 H12D CB12 CB13 +BOND CB13 H13D CB13 CB14 +BOND CB14 H14D CB14 H14E CB14 CB15 +BOND CB15 H15D CB15 H15E CB15 CB16 +BOND CB16 H16D CB16 H16E CB16 CB17 +BOND CB17 H17D CB17 H17E CB17 CB18 +BOND CB18 H18D CB18 H18E CB18 H18F +! Acyl chain 3 +BOND CC1 OC1 CC1 CC2 +BOND CC2 H2R CC2 H2S CC2 CC3 +BOND CC3 H3R CC3 H3S CC3 CC4 +BOND CC4 H4R CC4 H4S CC4 CC5 +BOND CC5 H5R CC5 H5S CC5 CC6 +BOND CC6 H6R CC6 H6S CC6 CC7 +BOND CC7 H7R CC7 H7S CC7 CC8 +BOND CC8 H8R CC8 H8S CC8 CC9 +BOND CC9 H9R CC9 CC10 +BOND CC10 H10R CC10 CC11 +BOND CC11 H11R CC11 H11S CC11 CC12 +BOND CC12 H12R CC12 CC13 +BOND CC13 H13R CC13 CC14 +BOND CC14 H14R CC14 H14S CC14 CC15 +BOND CC15 H15R CC15 H15S CC15 CC16 +BOND CC16 H16R CC16 H16S CC16 CC17 +BOND CC17 H17R CC17 H17S CC17 CC18 +BOND CC18 H18R CC18 H18S CC18 H18T +! Acyl chain 4 +BOND CD1 OD1 CD1 CD2 +BOND CD2 H2X CD2 H2Y CD2 CD3 +BOND CD3 H3X CD3 H3Y CD3 CD4 +BOND CD4 H4X CD4 H4Y CD4 CD5 +BOND CD5 H5X CD5 H5Y CD5 CD6 +BOND CD6 H6X CD6 H6Y CD6 CD7 +BOND CD7 H7X CD7 H7Y CD7 CD8 +BOND CD8 H8X CD8 H8Y CD8 CD9 +BOND CD9 H9X CD9 CD10 +BOND CD10 H10X CD10 CD11 +BOND CD11 H11X CD11 H11Y CD11 CD12 +BOND CD12 H12X CD12 CD13 +BOND CD13 H13X CD13 CD14 +BOND CD14 H14X CD14 H14Y CD14 CD15 +BOND CD15 H15X CD15 CD16 +BOND CD16 H16X CD16 CD17 +BOND CD17 H17X CD17 H17Y CD17 CD18 +BOND CD18 H18X CD18 H18Y CD18 H18Z + +IMPR CB1 O13 CB2 OB1 +IMPR CA1 O12 CA2 OA1 +IMPR CD1 O33 CD2 OD1 +IMPR CC1 O32 CC2 OC1 + +! +! IC TABLE +! +IC OP31 C2 *C3 HG31 1.4399 111.73 121.27 107.98 1.1140 +IC HG31 C2 *C3 HG32 1.1140 107.98 116.42 107.18 1.1169 +IC C2 C3 OP31 P3 1.5535 111.73 -167.54 118.79 1.5904 +IC C3 OP31 P3 OP32 1.4399 118.79 79.71 101.55 1.5890 +IC OP32 OP31 *P3 OP33 1.5890 101.55 -115.28 110.31 1.4782 +IC OP32 OP31 *P3 OP34 1.5890 101.55 113.65 109.35 1.4797 +IC OP31 P3 OP32 C31 1.5904 101.55 67.83 117.77 1.4329 +IC P3 OP32 C31 C32 1.5890 117.77 -170.90 110.66 1.5522 +IC C32 OP32 *C31 H31J 1.5522 110.66 121.35 111.65 1.1158 +IC H31J OP32 *C31 H31K 1.1158 111.65 119.36 109.77 1.1144 +IC HG31 C3 C2 C1 1.1140 107.98 -59.84 112.53 1.5592 +IC C1 C3 *C2 OG12 1.5592 112.53 -122.28 106.17 1.4219 +IC C1 C3 *C2 HG22 1.5592 112.53 120.07 108.81 1.1138 +IC C3 C2 OG12 HO12 1.5535 106.17 -43.83 99.95 0.9654 +IC C3 C2 C1 OP11 1.5535 112.53 172.59 114.00 1.4374 +IC OP11 C2 *C1 HG11 1.4374 114.00 -124.71 107.54 1.1153 +IC HG11 C2 *C1 HG12 1.1153 107.54 -114.53 107.04 1.1121 +IC C2 C1 OP11 P1 1.5592 114.00 -97.83 122.51 1.5864 +IC C1 OP11 P1 OP12 1.4374 122.51 -52.87 102.45 1.5913 +IC OP12 OP11 *P1 OP13 1.5913 102.45 114.70 110.17 1.4774 +IC OP12 OP11 *P1 OP14 1.5913 102.45 -115.08 109.36 1.4815 +IC OP11 P1 OP12 C11 1.5864 102.45 -92.52 122.70 1.4285 +IC P1 OP12 C11 C12 1.5913 122.70 85.68 111.92 1.5508 +IC C12 OP12 *C11 H11J 1.5508 111.92 -123.87 112.24 1.1149 +IC H11J OP12 *C11 H11K 1.1149 112.24 -117.66 107.38 1.1110 +IC OP12 C11 C12 C13 1.4285 111.92 161.41 112.21 1.5554 +IC C13 C11 *C12 O12 1.5554 112.21 119.92 107.58 1.4348 +IC O12 C11 *C12 H12J 1.4348 107.58 121.23 105.93 1.1177 +IC C11 C12 O12 CA1 1.5508 107.58 139.57 115.43 1.3169 +IC C12 O12 CA1 CA2 1.4348 115.43 -169.02 109.20 1.5307 +IC CA2 O12 *CA1 OA1 1.5307 109.20 -177.29 125.89 1.2210 +IC O12 CA1 CA2 CA3 1.3169 109.20 -125.27 111.98 1.5453 +IC CA3 CA1 *CA2 H2A 1.5453 111.98 -121.72 106.70 1.1104 +IC H2A CA1 *CA2 H2B 1.1104 106.70 -115.79 108.58 1.1093 +IC C11 C12 C13 O13 1.5508 112.21 -165.73 111.20 1.4484 +IC O13 C12 *C13 H13J 1.4484 111.20 -119.38 107.07 1.1127 +IC H13J C12 *C13 H13K 1.1127 107.07 -115.20 109.28 1.1141 +IC C12 C13 O13 CB1 1.5554 111.20 86.74 113.94 1.3304 +IC C13 O13 CB1 CB2 1.4484 113.94 -157.19 109.85 1.5285 +IC CB2 O13 *CB1 OB1 1.5285 109.85 179.45 125.30 1.2183 +IC O13 CB1 CB2 CB3 1.3304 109.85 170.02 112.02 1.5483 +IC CB3 CB1 *CB2 H2D 1.5483 112.02 -119.03 106.46 1.1119 +IC H2D CB1 *CB2 H2E 1.1119 106.46 -117.11 109.11 1.1053 +IC OP32 C31 C32 C33 1.4329 110.66 -55.34 111.30 1.5520 +IC C33 C31 *C32 O32 1.5520 111.30 121.41 110.58 1.4400 +IC O32 C31 *C32 H32J 1.4400 110.58 121.80 108.53 1.1157 +IC C31 C32 O32 CC1 1.5522 110.58 76.00 113.72 1.3241 +IC C32 O32 CC1 CC2 1.4400 113.72 -175.40 107.92 1.5290 +IC CC2 O32 *CC1 OC1 1.5290 107.92 -174.97 125.21 1.2214 +IC O32 CC1 CC2 CC3 1.3241 107.92 -171.64 114.45 1.5483 +IC CC3 CC1 *CC2 H2R 1.5483 114.45 -120.08 106.50 1.1125 +IC H2R CC1 *CC2 H2S 1.1125 106.50 -115.84 108.14 1.1062 +IC C31 C32 C33 O33 1.5522 111.30 178.27 110.32 1.4463 +IC O33 C32 *C33 H33J 1.4463 110.32 122.56 108.16 1.1137 +IC H33J C32 *C33 H33K 1.1137 108.16 116.60 107.22 1.1149 +IC C32 C33 O33 CD1 1.5520 110.32 176.92 114.52 1.3194 +IC C33 O33 CD1 CD2 1.4463 114.52 169.48 108.39 1.5307 +IC CD2 O33 *CD1 OD1 1.5307 108.39 179.86 126.25 1.2174 +IC O33 CD1 CD2 CD3 1.3194 108.39 166.29 113.39 1.5479 +IC CD3 CD1 *CD2 H2X 1.5479 113.39 -122.94 107.91 1.1081 +IC H2X CD1 *CD2 H2Y 1.1081 107.91 -116.24 106.59 1.1103 +IC CA1 CA2 CA3 CA4 1.5307 111.98 174.09 112.77 1.5340 +IC CA4 CA2 *CA3 H3A 1.5340 112.77 -121.48 109.27 1.1128 +IC H3A CA2 *CA3 H3B 1.1128 109.27 -117.62 108.80 1.1132 +IC CA2 CA3 CA4 CA5 1.5453 112.77 176.67 112.97 1.5369 +IC CA5 CA3 *CA4 H4A 1.5369 112.97 -120.43 108.08 1.1146 +IC H4A CA3 *CA4 H4B 1.1146 108.08 -116.67 109.58 1.1123 +IC CA3 CA4 CA5 CA6 1.5340 112.97 69.98 113.98 1.5366 +IC CA6 CA4 *CA5 H5A 1.5366 113.98 -122.10 108.41 1.1112 +IC H5A CA4 *CA5 H5B 1.1112 108.41 -116.88 108.64 1.1132 +IC CA4 CA5 CA6 CA7 1.5369 113.98 177.62 113.05 1.5384 +IC CA7 CA5 *CA6 H6A 1.5384 113.05 -120.54 108.00 1.1138 +IC H6A CA5 *CA6 H6B 1.1138 108.00 -117.16 109.92 1.1119 +IC CA5 CA6 CA7 CA8 1.5366 113.05 72.32 113.20 1.5409 +IC CA8 CA6 *CA7 H7A 1.5409 113.20 -122.31 108.58 1.1140 +IC H7A CA6 *CA7 H7B 1.1140 108.58 -116.70 108.43 1.1139 +IC CA6 CA7 CA8 CA9 1.5384 113.20 -177.88 111.67 1.5104 +IC CA9 CA7 *CA8 H8A 1.5104 111.67 -121.51 108.57 1.1127 +IC H8A CA7 *CA8 H8B 1.1127 108.57 -114.68 108.68 1.1109 +IC CA7 CA8 CA9 CA10 1.5409 111.67 106.92 126.93 1.3485 +IC CA10 CA8 *CA9 H9A 1.3485 126.93 179.93 114.52 1.1012 +IC CA8 CA9 CA10 CA11 1.5104 126.93 -0.98 126.94 1.5114 +IC CA11 CA9 *CA10 H10A 1.5114 126.94 -179.25 118.31 1.1017 +IC CA9 CA10 CA11 CA12 1.3485 126.94 -125.33 111.90 1.5094 +IC CA12 CA10 *CA11 H11A 1.5094 111.90 -120.91 109.22 1.1122 +IC H11A CA10 *CA11 H11B 1.1122 109.22 -115.26 111.36 1.1089 +IC CA10 CA11 CA12 CA13 1.5114 111.90 103.75 127.05 1.3481 +IC CA13 CA11 *CA12 H12A 1.3481 127.05 178.55 114.54 1.1015 +IC CA11 CA12 CA13 CA14 1.5094 127.05 -1.51 127.29 1.5104 +IC CA14 CA12 *CA13 H13A 1.5104 127.29 -178.83 118.45 1.1012 +IC CA12 CA13 CA14 CA15 1.3481 127.29 123.19 111.92 1.5400 +IC CA15 CA13 *CA14 H14A 1.5400 111.92 -122.30 112.60 1.1129 +IC H14A CA13 *CA14 H14B 1.1129 112.60 -117.91 109.33 1.1129 +IC CA13 CA14 CA15 CA16 1.5104 111.92 172.46 112.42 1.5358 +IC CA16 CA14 *CA15 H15A 1.5358 112.42 -120.26 109.74 1.1138 +IC H15A CA14 *CA15 H15B 1.1138 109.74 -118.26 109.67 1.1136 +IC CA14 CA15 CA16 CA17 1.5400 112.42 -176.77 112.71 1.5339 +IC CA17 CA15 *CA16 H16A 1.5339 112.71 -121.51 109.43 1.1130 +IC H16A CA15 *CA16 H16B 1.1130 109.43 -117.43 109.11 1.1131 +IC CA15 CA16 CA17 CA18 1.5358 112.71 177.47 113.22 1.5311 +IC CA18 CA16 *CA17 H17A 1.5311 113.22 -121.64 108.92 1.1137 +IC H17A CA16 *CA17 H17B 1.1137 108.92 -116.79 108.72 1.1143 +IC CA16 CA17 CA18 H18A 1.5339 113.22 -60.64 110.64 1.1108 +IC H18A CA17 *CA18 H18B 1.1108 110.64 -120.38 110.71 1.1111 +IC H18A CA17 *CA18 H18C 1.1108 110.64 119.78 110.63 1.1119 +IC CB1 CB2 CB3 CB4 1.5285 112.02 -156.49 113.16 1.5352 +IC CB4 CB2 *CB3 H3D 1.5352 113.16 -125.26 110.81 1.1108 +IC H3D CB2 *CB3 H3E 1.1108 110.81 -117.62 108.58 1.1185 +IC CB2 CB3 CB4 CB5 1.5483 113.16 -72.87 114.64 1.5362 +IC CB5 CB3 *CB4 H4D 1.5362 114.64 -121.50 107.87 1.1137 +IC H4D CB3 *CB4 H4E 1.1137 107.87 -115.68 108.33 1.1133 +IC CB3 CB4 CB5 CB6 1.5352 114.64 173.14 113.35 1.5409 +IC CB6 CB4 *CB5 H5D 1.5409 113.35 -120.91 109.12 1.1130 +IC H5D CB4 *CB5 H5E 1.1130 109.12 -117.35 108.69 1.1125 +IC CB4 CB5 CB6 CB7 1.5362 113.35 52.82 114.03 1.5378 +IC CB7 CB5 *CB6 H6D 1.5378 114.03 -120.64 108.65 1.1134 +IC H6D CB5 *CB6 H6E 1.1134 108.65 -116.83 109.17 1.1121 +IC CB5 CB6 CB7 CB8 1.5409 114.03 179.98 112.81 1.5400 +IC CB8 CB6 *CB7 H7D 1.5400 112.81 -122.98 109.09 1.1121 +IC H7D CB6 *CB7 H7E 1.1121 109.09 -117.53 108.71 1.1155 +IC CB6 CB7 CB8 CB9 1.5378 112.81 177.49 110.85 1.5102 +IC CB9 CB7 *CB8 H8D 1.5102 110.85 -122.35 107.23 1.1140 +IC H8D CB7 *CB8 H8E 1.1140 107.23 -115.61 109.26 1.1115 +IC CB7 CB8 CB9 CB10 1.5400 110.85 -111.54 126.68 1.3485 +IC CB10 CB8 *CB9 H9D 1.3485 126.68 176.66 114.61 1.1007 +IC CB8 CB9 CB10 CB11 1.5102 126.68 -2.77 127.04 1.5103 +IC CB11 CB9 *CB10 H10D 1.5103 127.04 -178.65 118.60 1.1012 +IC CB9 CB10 CB11 CB12 1.3485 127.04 96.60 112.31 1.5135 +IC CB12 CB10 *CB11 H11D 1.5135 112.31 -125.47 110.37 1.1105 +IC H11D CB10 *CB11 H11E 1.1105 110.37 -114.37 108.83 1.1122 +IC CB10 CB11 CB12 CB13 1.5103 112.31 -123.24 127.49 1.3487 +IC CB13 CB11 *CB12 H12D 1.3487 127.49 -179.18 114.92 1.1025 +IC CB11 CB12 CB13 CB14 1.5135 127.49 0.10 127.26 1.5079 +IC CB14 CB12 *CB13 H13D 1.5079 127.26 -179.25 118.69 1.1053 +IC CB12 CB13 CB14 CB15 1.3487 127.26 123.97 111.98 1.5384 +IC CB15 CB13 *CB14 H14D 1.5384 111.98 -120.79 111.90 1.1093 +IC H14D CB13 *CB14 H14E 1.1093 111.90 -118.90 109.68 1.1138 +IC CB13 CB14 CB15 CB16 1.5079 111.98 -173.48 111.85 1.5348 +IC CB16 CB14 *CB15 H15D 1.5348 111.85 -121.68 109.78 1.1147 +IC H15D CB14 *CB15 H15E 1.1147 109.78 -117.79 109.28 1.1119 +IC CB14 CB15 CB16 CB17 1.5384 111.85 179.99 113.35 1.5313 +IC CB17 CB15 *CB16 H16D 1.5313 113.35 -121.42 108.85 1.1101 +IC H16D CB15 *CB16 H16E 1.1101 108.85 -117.19 108.74 1.1110 +IC CB15 CB16 CB17 CB18 1.5348 113.35 -178.76 113.12 1.5314 +IC CB18 CB16 *CB17 H17D 1.5314 113.12 -121.82 108.25 1.1149 +IC H17D CB16 *CB17 H17E 1.1149 108.25 -115.96 109.19 1.1126 +IC CB16 CB17 CB18 H18D 1.5313 113.12 -178.27 110.36 1.1112 +IC H18D CB17 *CB18 H18E 1.1112 110.36 -120.53 110.61 1.1103 +IC H18D CB17 *CB18 H18F 1.1112 110.36 119.56 110.21 1.1112 +IC CC1 CC2 CC3 CC4 1.5290 114.45 61.17 115.54 1.5407 +IC CC4 CC2 *CC3 H3R 1.5407 115.54 -123.39 108.81 1.1159 +IC H3R CC2 *CC3 H3S 1.1159 108.81 -115.09 107.30 1.1128 +IC CC2 CC3 CC4 CC5 1.5483 115.54 48.75 115.70 1.5381 +IC CC5 CC3 *CC4 H4R 1.5381 115.70 -121.95 108.35 1.1141 +IC H4R CC3 *CC4 H4S 1.1141 108.35 -115.67 107.88 1.1118 +IC CC3 CC4 CC5 CC6 1.5407 115.70 59.37 113.26 1.5339 +IC CC6 CC4 *CC5 H5R 1.5339 113.26 -122.42 108.68 1.1122 +IC H5R CC4 *CC5 H5S 1.1122 108.68 -116.61 108.64 1.1128 +IC CC4 CC5 CC6 CC7 1.5381 113.26 175.46 114.41 1.5382 +IC CC7 CC5 *CC6 H6R 1.5382 114.41 -121.44 108.39 1.1118 +IC H6R CC5 *CC6 H6S 1.1118 108.39 -116.44 108.77 1.1127 +IC CC5 CC6 CC7 CC8 1.5339 114.41 50.21 113.91 1.5402 +IC CC8 CC6 *CC7 H7R 1.5402 113.91 -122.10 108.87 1.1136 +IC H7R CC6 *CC7 H7S 1.1136 108.87 -116.44 107.40 1.1147 +IC CC6 CC7 CC8 CC9 1.5382 113.91 171.45 111.26 1.5090 +IC CC9 CC7 *CC8 H8R 1.5090 111.26 -123.76 107.81 1.1114 +IC H8R CC7 *CC8 H8S 1.1114 107.81 -115.28 108.84 1.1122 +IC CC7 CC8 CC9 CC10 1.5402 111.26 -128.36 127.23 1.3472 +IC CC10 CC8 *CC9 H9R 1.3472 127.23 178.70 114.30 1.1010 +IC CC8 CC9 CC10 CC11 1.5090 127.23 -1.15 127.54 1.5084 +IC CC11 CC9 *CC10 H10R 1.5084 127.54 -179.59 118.30 1.1015 +IC CC9 CC10 CC11 CC12 1.3472 127.54 121.83 111.08 1.5090 +IC CC12 CC10 *CC11 H11R 1.5090 111.08 -121.38 111.45 1.1092 +IC H11R CC10 *CC11 H11S 1.1092 111.45 -115.12 108.94 1.1091 +IC CC10 CC11 CC12 CC13 1.5084 111.08 114.57 127.61 1.3469 +IC CC13 CC11 *CC12 H12R 1.3469 127.61 179.18 114.07 1.1019 +IC CC11 CC12 CC13 CC14 1.5090 127.61 -1.12 127.24 1.5089 +IC CC14 CC12 *CC13 H13R 1.5089 127.24 -179.24 118.36 1.1008 +IC CC12 CC13 CC14 CC15 1.3469 127.24 -127.92 112.49 1.5415 +IC CC15 CC13 *CC14 H14R 1.5415 112.49 -120.38 109.34 1.1135 +IC H14R CC13 *CC14 H14S 1.1135 109.34 -118.08 112.29 1.1108 +IC CC13 CC14 CC15 CC16 1.5089 112.49 64.28 113.82 1.5372 +IC CC16 CC14 *CC15 H15R 1.5372 113.82 -123.02 109.95 1.1128 +IC H15R CC14 *CC15 H15S 1.1128 109.95 -116.79 108.08 1.1141 +IC CC14 CC15 CC16 CC17 1.5415 113.82 175.12 112.35 1.5342 +IC CC17 CC15 *CC16 H16R 1.5342 112.35 121.44 109.60 1.1127 +IC H16R CC15 *CC16 H16S 1.1127 109.60 117.48 109.22 1.1130 +IC CC15 CC16 CC17 CC18 1.5372 112.35 177.84 113.41 1.5303 +IC CC18 CC16 *CC17 H17R 1.5303 113.41 -121.68 108.79 1.1140 +IC H17R CC16 *CC17 H17S 1.1140 108.79 -116.65 108.60 1.1141 +IC CC16 CC17 CC18 H18R 1.5342 113.41 177.41 110.78 1.1108 +IC H18R CC17 *CC18 H18S 1.1108 110.78 120.14 110.47 1.1110 +IC H18R CC17 *CC18 H18T 1.1108 110.78 -120.28 110.55 1.1114 +IC CD1 CD2 CD3 CD4 1.5307 113.39 169.15 112.93 1.5372 +IC CD4 CD2 *CD3 H3X 1.5372 112.93 -120.02 109.25 1.1156 +IC H3X CD2 *CD3 H3Y 1.1156 109.25 -117.49 109.59 1.1130 +IC CD2 CD3 CD4 CD5 1.5479 112.93 59.54 113.85 1.5360 +IC CD5 CD3 *CD4 H4X 1.5360 113.85 -121.33 108.32 1.1134 +IC H4X CD3 *CD4 H4Y 1.1134 108.32 -116.71 109.15 1.1132 +IC CD3 CD4 CD5 CD6 1.5372 113.85 -177.43 112.79 1.5357 +IC CD6 CD4 *CD5 H5X 1.5357 112.79 -122.43 109.70 1.1122 +IC H5X CD4 *CD5 H5Y 1.1122 109.70 -117.86 109.15 1.1139 +IC CD4 CD5 CD6 CD7 1.5360 112.79 173.65 112.21 1.5365 +IC CD7 CD5 *CD6 H6X 1.5365 112.21 -119.39 108.19 1.1136 +IC H6X CD5 *CD6 H6Y 1.1136 108.19 -117.35 110.05 1.1111 +IC CD5 CD6 CD7 CD8 1.5357 112.21 -164.07 113.53 1.5412 +IC CD8 CD6 *CD7 H7X 1.5412 113.53 -125.12 110.25 1.1118 +IC H7X CD6 *CD7 H7Y 1.1118 110.25 -116.30 107.52 1.1152 +IC CD6 CD7 CD8 CD9 1.5365 113.53 -72.33 113.26 1.5081 +IC CD9 CD7 *CD8 H8X 1.5081 113.26 -123.64 107.20 1.1122 +IC H8X CD7 *CD8 H8Y 1.1122 107.20 -114.54 108.43 1.1124 +IC CD7 CD8 CD9 CD10 1.5412 113.26 -141.33 126.38 1.3479 +IC CD10 CD8 *CD9 H9X 1.3479 126.38 -179.10 114.78 1.1010 +IC CD8 CD9 CD10 CD11 1.5081 126.38 0.12 126.84 1.5114 +IC CD11 CD9 *CD10 H10X 1.5114 126.84 -179.87 118.43 1.1016 +IC CD9 CD10 CD11 CD12 1.3479 126.84 -106.33 111.23 1.5105 +IC CD12 CD10 *CD11 H11X 1.5105 111.23 -120.37 109.03 1.1122 +IC H11X CD10 *CD11 H11Y 1.1122 109.03 -114.91 111.58 1.1099 +IC CD10 CD11 CD12 CD13 1.5114 111.23 109.38 127.41 1.3486 +IC CD13 CD11 *CD12 H12X 1.3486 127.41 179.19 114.40 1.1015 +IC CD11 CD12 CD13 CD14 1.5105 127.41 -1.41 127.65 1.5109 +IC CD14 CD12 *CD13 H13X 1.5109 127.65 -178.15 118.24 1.1012 +IC CD12 CD13 CD14 CD15 1.3486 127.65 -115.93 111.19 1.5399 +IC CD15 CD13 *CD14 H14X 1.5399 111.19 -120.10 109.72 1.1126 +IC H14X CD13 *CD14 H14Y 1.1126 109.72 -118.73 112.54 1.1122 +IC CD13 CD14 CD15 CD16 1.5109 111.19 -174.42 112.98 1.5354 +IC CD16 CD14 *CD15 H15X 1.5354 112.98 -121.07 109.22 1.1143 +IC CD14 CD15 CD16 CD17 1.5399 112.98 179.46 112.15 1.5344 +IC CD17 CD15 *CD16 H16X 1.5344 112.15 -121.15 109.44 1.1128 +IC CD15 CD16 CD17 CD18 1.5354 112.15 179.70 113.67 1.5310 +IC CD18 CD16 *CD17 H17X 1.5310 113.67 -121.71 108.44 1.1139 +IC H17X CD16 *CD17 H17Y 1.1139 108.44 -116.35 108.83 1.1138 +IC CD16 CD17 CD18 H18X 1.5344 113.67 -178.87 110.70 1.1108 +IC H18X CD17 *CD18 H18Y 1.1108 110.70 -120.14 110.59 1.1104 +IC H18X CD17 *CD18 H18Z 1.1108 110.70 119.96 110.62 1.1117 + +END + +return diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_cholesterol.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_cholesterol.str new file mode 100644 index 00000000..33122c63 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_cholesterol.str @@ -0,0 +1,1584 @@ +* Toppar stream file for cholesterol. Stream following reading of +* top_all36_lipid.rtf +* par_all36_lipid.rtf +* top_all36_cgenff.rtf +* and par_all36_cgenff.prm +* + +!topology and parameters are included for two cholesterol models. the +!model may be selected by setting variable chol_model to 1 or 2, as +!specified below +! + +set chol_model 1 !2 for original Suits et al. model + +! +!1) Revised model of Lim et al. This contains a number of NBFIXes that +!makes it unsuitable for ANTON (set chol_model 1) +! +!2) Original model of Suits et al., which is used on ANTON as well as +!being suitable for other systems (set chol_model 2 (or anything but 1....)) +! +!references +! +!Lim, J.B., Rogaski, B. and Klauda, J.B.. "Update of the Cholesterol Force Field +!Parameters in CHARMM" 116: 203-210 (2012). +! +!Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. "Molecular Level +!Organization of Saturated and Polyunsaturated Fatty Acids in a +!Phosphatidylcholine Bilayer Containing Cholesterol" Biochemistry, +!43(49):15318-28, 2004 +! + +!test "append" +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +if chol_model eq 1 then + +! reference +! Lim, J.B., Rogaski, B. and Klauda, J.B.. "Update of the Cholesterol Force Field +! Parameters in CHARMM" 116: 203-210 (2012). +! + +read rtf card @app +* Topology for cholesterol +* +31 1 + +RESI CHL1 0.00 !cholesterol v. 2(name to avoid conflict with choline) +! by Joseph Lim, based on DEC2 +! atoms names correspond to the correct cholesterol nomenclature +GROUP +ATOM C3 CRL1 0.14 +ATOM O3 OHL -0.66 +ATOM H3' HOL 0.43 +ATOM H3 HGA1 0.09 +GROUP +ATOM C4 CRL2 -0.18 +ATOM H4A HGA2 0.09 +ATOM H4B HGA2 0.09 +GROUP +ATOM C5 CEL1 0.00 +ATOM C6 CEL1 -0.15 +ATOM H6 HEL1 0.15 +GROUP +ATOM C7 CRL2 -0.18 +ATOM H7A HGA2 0.09 +ATOM H7B HGA2 0.09 +GROUP +ATOM C8 CRL1 -0.09 +ATOM H8 HGA1 0.09 +GROUP +ATOM C14 CRL1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CRL2 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CRL2 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CRL1 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CRL1 0.00 +GROUP +ATOM C18 CTL3 -0.27 !methyl at c13 +ATOM H18A HAL3 0.09 +ATOM H18B HAL3 0.09 +ATOM H18C HAL3 0.09 +GROUP +ATOM C12 CRL2 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CRL2 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CRL1 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CRL1 0.00 +GROUP +ATOM C19 CTL3 -0.27 !methyl at c10 +ATOM H19A HAL3 0.09 +ATOM H19B HAL3 0.09 +ATOM H19C HAL3 0.09 +GROUP +ATOM C1 CRL2 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CRL2 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CTL1 -0.09 +ATOM H20 HAL1 0.09 +GROUP +ATOM C21 CTL3 -0.27 +ATOM H21A HAL3 0.09 +ATOM H21B HAL3 0.09 +ATOM H21C HAL3 0.09 +GROUP +ATOM C22 CTL2 -0.18 +ATOM H22A HAL2 0.09 +ATOM H22B HAL2 0.09 +GROUP +ATOM C23 CTL2 -0.18 +ATOM H23A HAL2 0.09 +ATOM H23B HAL2 0.09 +GROUP +ATOM C24 CTL2 -0.18 !beyond this nomenclature may not be correct +ATOM H24A HAL2 0.09 +ATOM H24B HAL2 0.09 +GROUP +ATOM C25 CTL1 -0.09 !c25 +ATOM H25 HAL1 0.09 +GROUP +ATOM C26 CTL3 -0.27 !terminal methyl, c26 +ATOM H26A HAL3 0.09 +ATOM H26B HAL3 0.09 +ATOM H26C HAL3 0.09 +GROUP +ATOM C27 CTL3 -0.27 !terminal methyl, c27 +ATOM H27A HAL3 0.09 +ATOM H27B HAL3 0.09 +ATOM H27C HAL3 0.09 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C2 C2 H2A C2 H2B +BOND C2 C1 C1 H1A C1 H1B +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 +BOND C5 C10 +BOND C10 C1 +BOND C10 C19 C19 H19A C19 H19B C19 H19C +DOUBLE C5 C6 +BOND C6 H6 +BOND C6 C7 C7 H7A C7 H7B +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C13 C18 C18 H18A C18 H18B C18 H18C +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 +BOND C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 C24 C24 H24A C24 H24B +BOND C24 C25 C25 H25 +BOND C25 C26 C26 H26A C26 H26B C26 H26C +BOND C25 C27 C27 H27A C27 H27B C27 H27C +!ICs based on CHARMM optimized structure +IC C1 C2 C3 C4 1.5383 110.44 55.92 110.66 1.5367 +IC C4 C2 *C3 O3 1.5367 110.66 120.28 109.14 1.4158 +IC O3 C2 *C3 H3 1.4158 109.14 118.92 109.40 1.1155 +IC C2 C3 O3 H3' 1.5311 109.14 -58.51 105.39 0.9593 +IC C2 C3 C4 C5 1.5311 110.66 -55.96 111.70 1.5156 +IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 +IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 +IC C3 C4 C5 C10 1.5367 111.70 54.04 115.09 1.5304 +IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 +IC C4 C5 C6 C7 1.5156 121.28 -178.39 123.88 1.5018 +IC C7 C5 *C6 H6 1.5018 123.88 177.19 119.54 1.1001 +IC C5 C6 C7 C8 1.3432 123.88 14.50 112.36 1.5506 +IC C8 C6 *C7 H7A 1.5506 112.36 122.18 110.84 1.1114 +IC H7A C6 *C7 H7B 1.1114 110.84 118.17 109.17 1.1124 +IC C6 C7 C8 C14 1.5018 112.36 -165.89 110.02 1.5202 +IC C14 C7 *C8 C9 1.5202 110.02 121.07 110.84 1.5327 +IC C9 C7 *C8 H8 1.5327 110.84 119.34 108.18 1.1123 +IC C7 C8 C14 C13 1.5506 110.02 179.73 115.21 1.5247 +IC C13 C8 *C14 C15 1.5247 115.21 126.69 117.86 1.5382 +IC C13 C8 *C14 H14 1.5247 115.21 -116.05 105.83 1.1205 +IC C8 C14 C15 C16 1.5202 117.86 -163.10 103.40 1.5360 +IC C16 C14 *C15 H15A 1.5360 103.40 117.45 109.62 1.1113 +IC H15A C14 *C15 H15B 1.1113 109.62 121.32 111.94 1.1082 +IC C14 C15 C16 C17 1.5382 103.40 7.85 106.79 1.5620 +IC C17 C15 *C16 H16A 1.5620 106.79 118.96 109.25 1.1107 +IC H16A C15 *C16 H16B 1.1107 109.25 120.76 111.65 1.1090 +IC C13 C16 *C17 C20 1.5401 104.94 132.02 112.36 1.5633 +IC C13 C16 *C17 H17 1.5401 104.94 -111.76 106.42 1.1153 +IC C17 C14 *C13 C12 1.5401 100.27 122.68 106.98 1.5408 +IC C12 C14 *C13 C18 1.5408 106.98 122.91 110.83 1.5518 +IC C14 C13 C18 H18A 1.5247 110.83 60.33 111.48 1.1077 +IC H18A C13 *C18 H18B 1.1077 111.48 119.80 110.01 1.1086 +IC H18A C13 *C18 H18C 1.1077 111.48 -121.00 111.71 1.1067 +IC C14 C13 C12 C11 1.5247 106.98 56.78 111.10 1.5422 +IC C11 C13 *C12 H12A 1.5422 111.10 121.37 111.21 1.1067 +IC H12A C13 *C12 H12B 1.1067 111.21 118.82 108.68 1.1119 +IC C9 C12 *C11 H11A 1.5593 113.54 121.67 107.06 1.1093 +IC H11A C12 *C11 H11B 1.1093 107.06 115.98 108.75 1.1100 +IC C10 C8 *C9 H9 1.5531 112.73 -114.54 104.68 1.1185 +IC C9 C5 *C10 C19 1.5531 111.91 -120.04 108.03 1.5524 +IC C19 C5 *C10 C1 1.5524 108.03 -119.87 109.26 1.5579 +IC C5 C10 C19 H19A 1.5304 108.03 -172.88 110.67 1.1082 +IC H19A C10 *C19 H19B 1.1082 110.67 118.48 111.77 1.1080 +IC H19A C10 *C19 H19C 1.1082 110.67 -120.66 110.97 1.1095 +IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 +IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 +IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 +IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 +IC C16 C17 C20 C22 1.5620 112.36 55.21 110.55 1.5476 +IC C22 C17 *C20 C21 1.5476 110.55 125.88 113.32 1.5349 +IC C21 C17 *C20 H20 1.5349 113.32 118.87 107.27 1.1157 +IC C17 C20 C21 H21A 1.5633 113.32 64.90 110.93 1.1077 +IC H21A C20 *C21 H21B 1.1077 110.93 -121.00 110.41 1.1104 +IC H21A C20 *C21 H21C 1.1077 110.93 118.40 111.29 1.1085 +IC C17 C20 C22 C23 1.5633 110.55 -174.59 115.12 1.5394 +IC C23 C20 *C22 H22A 1.5394 115.12 120.23 109.35 1.1116 +IC H22A C20 *C22 H22B 1.1116 109.35 117.13 108.75 1.1121 +IC C20 C22 C23 C24 1.5476 115.12 172.50 112.25 1.5377 +IC C24 C22 *C23 H23A 1.5377 112.25 121.13 109.69 1.1108 +IC H23A C22 *C23 H23B 1.1108 109.69 118.14 108.99 1.1129 +IC C22 C23 C24 C25 1.5394 112.25 -176.23 114.06 1.5418 +IC C25 C23 *C24 H24A 1.5418 114.06 120.56 108.44 1.1132 +IC H24A C23 *C24 H24B 1.1132 108.44 117.11 109.39 1.1121 +IC C23 C24 C25 C26 1.5377 114.06 174.26 111.24 1.5378 +IC C26 C24 *C25 C27 1.5378 111.24 119.63 112.86 1.5381 +IC C26 C24 *C25 H25 1.5378 111.24 -119.50 108.47 1.1151 +IC C24 C25 C26 H26A 1.5418 111.24 -178.53 110.52 1.1105 +IC H26A C25 *C26 H26B 1.1105 110.52 120.00 110.36 1.1105 +IC H26A C25 *C26 H26C 1.1105 110.52 -120.09 110.33 1.1106 +IC C24 C25 C27 H27A 1.5418 112.86 -178.28 110.40 1.1105 +IC H27A C25 *C27 H27B 1.1105 110.40 119.95 110.31 1.1105 +IC H27A C25 *C27 H27C 1.1105 110.40 -119.82 110.77 1.1097 + +RESI CHNS 0.00 !cholesterol with sidechain beyond c18(c20) omitted +! atoms names after the comments correspond to the +! correct cholesterol nomenclature +GROUP +ATOM C1 CRL1 0.14 !C3 +ATOM O1 OHL -0.66 +ATOM HO1 HOL 0.43 +ATOM H1 HGA1 0.09 + +ATOM C2 CRL2 -0.18 !c4 +ATOM H2 HGA2 0.09 +ATOM H2' HGA2 0.09 + +ATOM C3 CEL1 0.00 !c5 +ATOM C4 CEL1 -0.15 !c6 +ATOM H4 HEL1 0.15 + +ATOM C5 CRL2 -0.18 !c7 +ATOM H5 HGA2 0.09 +ATOM H5' HGA2 0.09 + +ATOM C6 CRL1 -0.09 !c8 +ATOM H6 HGA1 0.09 + +ATOM C7 CRL1 -0.09 !c14 +ATOM H7 HGA1 0.09 + +ATOM C8 CRL2 -0.18 !c15 +ATOM H8 HGA2 0.09 +ATOM H8' HGA2 0.09 + +ATOM C9 CRL2 -0.18 !c16 +ATOM H9 HGA2 0.09 +ATOM H9' HGA2 0.09 + +ATOM C10 CRL1 -0.09 !c17 +ATOM H10 HGA1 0.09 +GROUP +ATOM C11 CRL1 0.00 ! c14 + +ATOM Cc11 CTL3 -0.27 !c18, methyl at c13 +ATOM H111 HAL3 0.09 +ATOM H112 HAL3 0.09 +ATOM H113 HAL3 0.09 + +ATOM C12 CRL2 -0.18 !c12 +ATOM H12 HGA2 0.09 +ATOM H12' HGA2 0.09 + +ATOM C13 CRL2 -0.18 !c11 +ATOM H13 HGA2 0.09 +ATOM H13' HGA2 0.09 + +ATOM C14 CRL1 -0.09 !c9 +ATOM H14 HGA1 0.09 + +ATOM C15 CRL1 0.00 !c10 + +ATOM CC15 CTL3 -0.27 !c19, methyl at c10 +ATOM H151 HAL3 0.09 +ATOM H152 HAL3 0.09 +ATOM H153 HAL3 0.09 + +ATOM C16 CRL2 -0.18 !c1 +ATOM H16 HGA2 0.09 +ATOM H16' HGA2 0.09 + +ATOM C17 CRL2 -0.18 !c2 +ATOM H17 HGA2 0.09 +ATOM H17' HGA2 0.09 + +ATOM C18 CTL3 -0.27 !c20 +ATOM H181 HAL3 0.09 +ATOM H182 HAL3 0.09 +ATOM H183 HAL3 0.09 + +BOND C1 O1 C1 H1 C1 C2 +BOND O1 HO1 +BOND C2 C3 C2 H2 C2 H2' +DOUBLE C3 C4 +BOND C4 C5 C4 H4 +BOND C5 C6 C5 H5 C5 H5' +BOND C6 C7 C6 H6 +BOND C7 C8 C7 H7 +BOND C8 C9 C8 H8 C8 H8' +BOND C9 C10 C9 H9 C9 H9' +BOND C10 C18 C10 C11 C10 H10 +BOND C11 CC11 C11 C7 C11 C12 +BOND CC11 H111 CC11 H112 CC11 H113 +BOND C12 C13 C12 H12 C12 H12' +BOND C13 C14 C13 H13 C13 H13' +BOND C14 C15 C14 C6 C14 H14 +BOND C15 C16 C15 C3 C15 CC15 +BOND CC15 H151 CC15 H152 CC15 H153 +BOND C16 C17 C16 H16 C16 H16' +BOND C17 C1 C17 H17 C17 H17' +BOND C18 H181 C18 H182 C18 H183 + +!DONO HO1 O1 +!ACCE O1 + +IC O1 C1 C2 C3 1.4158 109.24 -176.17 111.80 1.5153 +IC C1 C2 C3 C4 1.5368 111.80 -123.48 121.41 1.3430 +IC C2 C3 C4 C5 1.5153 121.41 -178.76 123.84 1.5019 +IC C3 C4 C5 C6 1.3430 123.84 14.64 112.44 1.5504 +IC C4 C5 C6 C7 1.5019 112.44 -166.16 109.90 1.5192 +IC C5 C6 C7 C8 1.5504 109.90 -54.73 118.74 1.5447 +IC C6 C7 C8 C9 1.5192 118.74 -161.90 103.72 1.5418 +IC C7 C8 C9 C10 1.5447 103.72 5.69 105.45 1.5530 +IC C8 C9 C10 C11 1.5418 105.45 21.50 105.85 1.5300 +IC C9 C10 C11 C12 1.5530 105.85 -155.90 116.00 1.5351 +IC C7 C12 *C11 CC11 1.5194 108.58 -123.00 111.88 1.5530 +IC C10 C11 C12 C13 1.5300 116.00 167.75 110.42 1.5414 +IC C10 C11 C7 C8 1.5300 99.46 43.93 105.86 1.5447 +IC C11 C12 C13 C14 1.5351 110.42 -52.28 113.50 1.5626 +IC CC11 C11 C12 C13 1.5530 111.88 -66.16 110.42 1.5414 +IC CC11 C11 C7 C8 1.5530 111.12 -70.96 105.86 1.5447 +IC C12 C13 C14 C15 1.5414 113.50 179.43 114.52 1.5524 +IC C13 C14 C15 CC15 1.5626 114.52 -50.80 109.07 1.5522 +IC C13 C14 C15 C16 1.5626 114.52 69.29 108.64 1.5574 +IC C13 C14 C6 C7 1.5626 113.16 -48.42 109.31 1.5192 +IC CC15 C15 C16 C17 1.5522 110.15 -68.75 114.54 1.5383 +IC C14 C15 C16 C17 1.5524 108.64 171.83 114.54 1.5383 +IC C14 C15 C3 C4 1.5524 111.86 7.71 123.46 1.3430 +IC C15 C16 C17 C1 1.5574 114.54 -54.68 110.51 1.5312 +IC C11 C9 *C10 C18 1.5300 105.85 126.88 114.22 1.5413 +IC O1 C2 *C1 H1 1.4158 109.24 -119.02 109.53 1.1156 +IC C2 C1 O1 HO1 1.5368 109.24 62.69 105.39 0.9593 +IC C3 C1 *C2 H2 1.5153 111.80 121.88 109.11 1.1100 +IC C3 C1 *C2 H2' 1.5153 111.80 -123.05 107.36 1.1142 +IC C5 C3 *C4 H4 1.5019 123.84 177.13 119.55 1.1001 +IC C6 C4 *C5 H5 1.5504 112.44 122.17 110.88 1.1114 +IC C6 C4 *C5 H5' 1.5504 112.44 -119.69 109.16 1.1124 +IC C7 C5 *C6 H6 1.5192 109.90 -119.58 108.19 1.1122 +IC C8 C6 *C7 H7 1.5447 118.74 117.73 105.77 1.1205 +IC C9 C7 *C8 H8 1.5418 103.72 117.51 109.61 1.1108 +IC C9 C7 *C8 H8' 1.5418 103.72 -121.25 111.67 1.1078 +IC C10 C8 *C9 H9 1.5530 105.45 118.45 109.64 1.1105 +IC C10 C8 *C9 H9' 1.5530 105.45 -120.18 112.16 1.1085 +IC C18 C9 *C10 H10 1.5413 114.22 119.69 107.07 1.1162 +IC C7 C11 CC11 H111 1.5194 111.12 -178.60 110.01 1.1092 +IC H111 C11 *CC1 H112 1.1092 110.01 118.82 111.63 1.1068 +IC H111 C11 *CC1 H113 1.1092 110.01 -120.26 111.66 1.1075 +IC C13 C11 *C12 H12 1.5414 110.42 122.09 109.96 1.1102 +IC C13 C11 *C12 H12' 1.5414 110.42 -119.49 108.88 1.1120 +IC C14 C12 *C13 H13 1.5626 113.50 121.59 107.14 1.1091 +IC C14 C12 *C13 H13' 1.5626 113.50 -122.38 108.79 1.1098 +IC C13 C6 *C14 H14 1.5626 113.16 113.80 104.59 1.1184 +IC C3 C15 CC15 H151 1.5435 107.81 -172.81 110.68 1.1082 +IC H151 C15 *CC1 H152 1.1082 110.68 118.52 111.71 1.1081 +IC H151 C15 *CC1 H153 1.1082 110.68 -120.68 110.98 1.1094 +IC C17 C15 *C16 H16 1.5383 114.54 122.43 109.27 1.1104 +IC C17 C15 *C16 H16' 1.5383 114.54 -120.70 108.26 1.1134 +IC C16 C1 *C17 H17 1.5383 110.51 121.12 109.37 1.1120 +IC C16 C1 *C17 H17' 1.5383 110.51 -120.62 109.70 1.1111 +!use hbuild for c18 hydrogens + +RESI CHM1 0.00 !cholesterol analog with only rings 1 and 2 + !and the position 19 methyl +! atoms names after the comments correspond to the +! correct cholesterol nomenclature +! +!ring 1 +! +GROUP +ATOM C1 CRL1 0.14 !C3 +ATOM O1 OHL -0.66 +ATOM HO1 HOL 0.43 +ATOM H1 HGA1 0.09 + +ATOM C2 CRL2 -0.18 !c4 +ATOM H2 HGA2 0.09 +ATOM H2' HGA2 0.09 + +ATOM C3 CEL1 0.00 !c5 + +ATOM C15 CRL1 0.00 !c10 + +ATOM C16 CRL2 -0.18 !c1 +ATOM H16 HGA2 0.09 +ATOM H16' HGA2 0.09 + +ATOM C17 CRL2 -0.18 !c2 +ATOM H17 HGA2 0.09 +ATOM H17' HGA2 0.09 + +ATOM CC15 CTL3 -0.27 !c19, methyl at c10 +ATOM H151 HAL3 0.09 +ATOM H152 HAL3 0.09 +ATOM H153 HAL3 0.09 + +!ring 2 + +ATOM C4 CEL1 -0.15 !c6 +ATOM H4 HEL1 0.15 + +ATOM C5 CRL2 -0.18 !c7 +ATOM H5 HGA2 0.09 +ATOM H5' HGA2 0.09 + +ATOM C6 CRL2 -0.18 !c8 +ATOM H6 HGA2 0.09 +ATOM H6' HGA2 0.09 + +ATOM C14 CRL2 -0.18 !c9 +ATOM H14 HGA2 0.09 +ATOM H14' HGA2 0.09 + + +BOND C1 C2 C2 C3 C3 C15 C15 C16 C16 C17 C17 C1 +BOND C1 O1 O1 HO1 C1 H1 +BOND C2 H2 C2 H2' +BOND C15 CC15 CC15 H151 CC15 H152 CC15 H153 +BOND C16 H16 C16 H16' +BOND C17 H17 C17 H17' +DOUB C3 C4 +BOND C4 C5 C5 C6 C6 C14 C14 C15 +BOND C4 H4 +BOND C5 H5 C5 H5' +BOND C6 H6 C6 H6' +BOND C14 H14 C14 H14' + +IC C1 C2 C3 C15 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C15 C16 0.0000 0.00 0.00 0.00 0.0000 +IC C17 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C17 *C1 O1 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C17 *C1 H1 0.0000 0.00 -120.00 0.00 0.0000 +IC C17 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H2' 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 15.00 0.00 0.0000 +IC C4 C5 C6 C14 0.0000 0.00 -45.00 0.00 0.0000 +IC C14 C3 *C15 CC15 0.0000 0.00 -120.00 0.00 0.0000 +IC C17 C15 *C16 H16 0.0000 0.00 120.00 0.00 0.0000 +IC C17 C15 *C16 H16' 0.0000 0.00 -120.00 0.00 0.0000 +IC C16 C1 *C17 H17 0.0000 0.00 120.00 0.00 0.0000 +IC C16 C1 *C17 H17' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C15 CC15 H151 0.0000 0.00 180.00 0.00 0.0000 +IC H151 C15 *CC15 H152 0.0000 0.00 120.00 0.00 0.0000 +IC H151 C15 *CC15 H153 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C4 *C5 H5' 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C5 *C6 H6 0.0000 0.00 120.00 0.00 0.0000 +IC C14 C5 *C6 H6' 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C15 *C14 H14 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C15 *C14 H14' 0.0000 0.00 -120.00 0.00 0.0000 + +RESI ERG 0.0 ! Ergosterol +! Based off CHL1, Brent Rogaski (3/12) + +GROUP ! +ATOM C3 CRL1 0.14 ! +ATOM O3 OHL -0.66 ! +ATOM H3' HOL 0.43 ! +ATOM H3 HGA1 0.09 ! +GROUP ! +ATOM C4 CRL2 -0.18 ! H26B H26C H27C H27B +ATOM H4A HGA2 0.09 ! \ / \ / +ATOM H4B HGA2 0.09 ! C26 C27 +GROUP ! / \ / \ +ATOM C5 CEL1 0.00 ! H26A \ H25 / H27A +ATOM C6 CEL1 -0.15 ! \ | / +ATOM H6 HEL1 0.15 ! \ | / +GROUP ! \|/ +ATOM C7 CEL1 -0.15 ! C25 +ATOM C8 CEL1 0.00 ! | +ATOM H7 HEL1 0.15 ! | H28C +GROUP ! | | +ATOM C14 CRL1 -0.09 ! H24--C24-----C28--H28B +ATOM H14 HGA1 0.09 ! | | +GROUP ! | H28A +ATOM C15 CRL2 -0.18 ! | +ATOM H15A HGA2 0.09 ! C23--H23 +ATOM H15B HGA2 0.09 ! |! +GROUP ! |! (trans) +ATOM C16 CRL2 -0.18 ! |! +ATOM H16A HGA2 0.09 ! H22--C22 +ATOM H16B HGA2 0.09 ! | +GROUP ! H21A | +ATOM C17 CRL1 -0.09 ! | | +ATOM H17 HGA1 0.09 ! H21B--C21-----C20--H20 +GROUP ! | | +ATOM C13 CRL1 0.00 ! H21C | +GROUP ! | +ATOM C18 CTL3 -0.27 ! H18C | +ATOM H18A HAL3 0.09 ! | | H16B +ATOM H18B HAL3 0.09 ! H18B--C18 | | +ATOM H18C HAL3 0.09 ! / \ C17-----C16--H16A +GROUP ! H18A \ |\ | +ATOM C12 CRL2 -0.18 ! \ | H17 | +ATOM H12A HGA2 0.09 ! H12B \ | | H15B +ATOM H12B HGA2 0.09 ! \ \| |/ +GROUP ! H12A--C12-----C13 C15--H15A +ATOM C11 CRL2 -0.18 ! / \ / +ATOM H11A HGA2 0.09 ! H11B / \ / +ATOM H11B HGA2 0.09 ! \ / \ / +GROUP ! H11A--C11 C14--H14 +ATOM C9 CRL1 -0.09 ! \ / +ATOM H9 HGA1 0.09 ! H19C \ / +GROUP ! | \ / +ATOM C10 CRL1 0.00 ! H19A-C19-H19B C9------C8 +GROUP ! \ / \ \\ +ATOM C19 CTL3 -0.27 ! H1B \ / H9 \\ +ATOM H19A HAL3 0.09 ! | \ / \\ +ATOM H19B HAL3 0.09 ! H1A--C1------C10 C7--H7 +ATOM H19C HAL3 0.09 ! / \ / +GROUP ! H2A / \ / +ATOM C1 CRL2 -0.18 ! \ / \ ----- / +ATOM H1A HGA2 0.09 ! C2 C5------C6 +ATOM H1B HGA2 0.09 ! / \ / \ +GROUP ! H2B \ / H6 +ATOM C2 CRL2 -0.18 ! \ / +ATOM H2A HGA2 0.09 ! H3--C3------C4--H4A +ATOM H2B HGA2 0.09 ! | | +GROUP ! | H4B +ATOM C20 CTL1 -0.09 ! | +ATOM H20 HAL1 0.09 ! H3'--O3 +GROUP ! +ATOM C21 CTL3 -0.27 ! +ATOM H21A HAL3 0.09 ! +ATOM H21B HAL3 0.09 ! +ATOM H21C HAL3 0.09 ! +GROUP ! +ATOM C22 CEL1 -0.15 ! +ATOM C23 CEL1 -0.15 ! +ATOM H22 HEL1 0.15 ! +ATOM H23 HEL1 0.15 ! +GROUP ! +ATOM C24 CTL1 -0.09 ! +ATOM H24 HAL1 0.09 ! +GROUP ! +ATOM C25 CTL1 -0.09 ! +ATOM H25 HAL1 0.09 ! +GROUP ! +ATOM C26 CTL3 -0.27 ! +ATOM H26A HAL3 0.09 ! +ATOM H26B HAL3 0.09 ! +ATOM H26C HAL3 0.09 ! +GROUP ! +ATOM C27 CTL3 -0.27 ! +ATOM H27A HAL3 0.09 ! +ATOM H27B HAL3 0.09 ! +ATOM H27C HAL3 0.09 ! +GROUP ! +ATOM C28 CTL3 -0.27 ! +ATOM H28A HAL3 0.09 ! +ATOM H28B HAL3 0.09 ! +ATOM H28C HAL3 0.09 ! + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C2 C2 H2A C2 H2B +BOND C2 C1 C1 H1A C1 H1B +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 +BOND C5 C10 +BOND C10 C1 +BOND C10 C19 C19 H19A C19 H19B C19 H19C +DOUBLE C5 C6 +BOND C6 H6 +BOND C6 C7 C7 H7 +DOUBLE C7 C8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C13 C18 C18 H18A C18 H18B C18 H18C +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 +BOND C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22 +DOUBLE C22 C23 +BOND C23 H23 +BOND C23 C24 C24 H24 C24 C28 +BOND C24 C25 C25 H25 +BOND C25 C26 C26 H26A C26 H26B C26 H26C +BOND C25 C27 C27 H27A C27 H27B C27 H27C +BOND C28 H28A C28 H28B C28 H28C + +!ICs based on CHARMM optimized structure updated 3-2012 BJR +IC C4 C2 *C3 O3 1.5384 111.29 120.53 109.15 1.4152 +IC O3 C2 *C3 H3 1.4152 109.15 118.43 109.07 1.1161 +IC C2 C3 O3 H3' 1.534 109.15 -59.53 105.21 0.9594 +IC C2 C3 C4 C5 1.534 111.29 -55.64 110.68 1.5147 +IC C5 C3 *C4 H4A 1.5147 110.68 -122.49 107.48 1.114 +IC H4A C3 *C4 H4B 1.114 107.48 -115.4 109.39 1.1091 +IC C3 C4 C5 C10 1.5384 110.68 54.27 115.86 1.5508 +IC C10 C4 *C5 C6 1.5508 115.86 -176.59 122.84 1.3509 +IC C4 C5 C6 C7 1.5147 122.84 175.21 124.45 1.3514 +IC C7 C5 *C6 H6 1.3514 124.45 -178.72 117.51 1.0999 +IC C5 C6 C7 C8 1.3509 124.45 -2.28 123.72 1.349 +IC C8 C6 *C7 H7 1.349 123.72 -177.09 118.27 1.0989 +IC C6 C7 C8 C14 1.3514 123.72 -174.8 125.77 1.5158 +IC C14 C7 *C8 C9 1.5158 125.77 176.26 121.16 1.534 +IC C7 C8 C14 C13 1.349 125.77 -127.21 114.84 1.527 +IC C13 C8 *C14 C15 1.527 114.84 128.62 120.79 1.5474 +IC C13 C8 *C14 H14 1.527 114.84 -114.65 104.93 1.1181 +IC C8 C14 C15 C16 1.5158 120.79 -164.56 103.93 1.5364 +IC C16 C14 *C15 H15A 1.5364 103.93 -121.65 111.8 1.1083 +IC H15A C14 *C15 H15B 1.1083 111.8 -121.53 110.09 1.1118 +IC C14 C15 C16 C17 1.5474 103.93 8.48 106.75 1.5641 +IC C17 C15 *C16 H16A 1.5641 106.75 -120.41 111.79 1.1095 +IC H16A C15 *C16 H16B 1.1095 111.79 -120.41 109.03 1.1113 +IC C13 C16 *C17 C20 1.5483 105.1 131.23 112.64 1.5382 +IC C13 C16 *C17 H17 1.5483 105.1 -111.42 106.08 1.1169 +IC C17 C14 *C13 C12 1.5483 100.83 123.37 107.03 1.5453 +IC C12 C14 *C13 C18 1.5453 107.03 121.68 110 1.5503 +IC C14 C13 C18 H18A 1.527 110 64.09 111.53 1.1074 +IC H18A C13 *C18 H18B 1.1074 111.53 -120.53 111.19 1.1083 +IC H18A C13 *C18 H18C 1.1074 111.53 120 110.03 1.1088 +IC C14 C13 C12 C11 1.527 107.03 56.14 111.71 1.5474 +IC C11 C13 *C12 H12A 1.5474 111.71 -120.3 108.81 1.1114 +IC H12A C13 *C12 H12B 1.1114 108.81 -118.79 110.91 1.1064 +IC C9 C12 *C11 H11A 1.5641 114.35 -121.47 108.03 1.1115 +IC H11A C12 *C11 H11B 1.1115 108.03 -116.16 107.02 1.1107 +IC C10 C8 *C9 H9 1.5774 115.61 -115.28 104.59 1.1141 +IC C9 C5 *C10 C19 1.5774 113.62 -120.34 106.21 1.554 +IC C19 C5 *C10 C1 1.554 106.21 -117.85 108.65 1.5564 +IC C5 C10 C19 H19A 1.5508 106.21 63.88 110.62 1.1106 +IC H19A C10 *C19 H19B 1.1106 110.62 -120.12 112.1 1.1066 +IC H19A C10 *C19 H19C 1.1106 110.62 121.49 111.12 1.1081 +IC C2 C10 *C1 H1A 1.5411 114.47 -120.26 108.38 1.1136 +IC C2 C10 *C1 H1B 1.5411 114.47 123.02 108.74 1.1111 +IC C1 C3 *C2 H2A 1.5411 110.88 -121.14 109.65 1.1104 +IC H2A C3 *C2 H2B 1.1104 109.65 -117.79 109.12 1.1121 +IC C16 C17 C20 C22 1.5641 112.64 51.77 111.66 1.5187 +IC C22 C17 *C20 C21 1.5187 111.66 119.38 111.66 1.5443 +IC C21 C17 *C20 H20 1.5443 111.66 119.6 109.11 1.1139 +IC C17 C20 C21 H21A 1.5382 111.66 69.91 110.37 1.1067 +IC H21A C20 *C21 H21B 1.1067 110.37 -121 111.06 1.1104 +IC H21A C20 *C21 H21C 1.1067 110.37 117.94 111.09 1.1119 +IC C17 C20 C22 C23 1.5382 111.66 -127.81 124.83 1.3444 +IC C23 C20 *C22 H22 1.3444 124.83 -179.53 115.68 1.1005 +IC C20 C22 C23 C24 1.5187 124.83 -179.44 124.94 1.5151 +IC C24 C22 *C23 H23 1.5151 124.94 178.9 119.39 1.1007 +IC C22 C23 C24 C25 1.3444 124.94 74.2 112.31 1.5348 +IC C25 C23 *C24 C28 1.5348 112.31 125.07 109.12 1.5491 +IC C28 C23 *C24 H24 1.5491 109.12 116.8 108.77 1.1162 +IC C23 C24 C25 C26 1.5151 112.31 66.3 112.54 1.5424 +IC C26 C24 *C25 C27 1.5424 112.54 124.63 110.25 1.5415 +IC C26 C24 *C25 H25 1.5424 112.54 -118.78 107.84 1.1178 +IC C24 C25 C26 H26A 1.5348 112.54 66.53 111.05 1.1092 +IC H26A C25 *C26 H26B 1.1092 111.05 -121.38 111.05 1.1097 +IC H26A C25 *C26 H26C 1.1092 111.05 119.06 109.67 1.1108 +IC C24 C25 C27 H27A 1.5348 110.25 52.82 110.63 1.11 +IC H27A C25 *C27 H27B 1.11 110.63 -121 111.09 1.1092 +IC H27A C25 *C27 H27C 1.11 110.63 119.67 109.85 1.1108 +IC C23 C24 C28 H28A 1.5151 109.12 59.12 110.24 1.1113 +IC H28A C24 *C28 H28B 1.1113 110.24 -120.08 111.67 1.1097 +IC H28A C24 *C28 H28C 1.1113 110.24 118.88 111.07 1.1085 + + + +end + +read param card flex @app +* cholesterol parameters +* + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +! added from par_all35_lipid_jbl.prm by jbl +CEL1 CTL1 240.000 1.502 ! from CEL1 CTL2: sR12cc (c8-c39) +! added for new mixing rule for decalin/heptane by jbl +! CRL1 equivalent to CTL1, HGA1 equivalent to HAL1, etc. (jbl) +CTL1 CRL1 222.500 1.500 ! alkanes, 3/92 +CRL1 CRL1 222.500 1.500 ! alkanes, 3/92 +CRL1 CTL2 222.500 1.538 ! alkanes, 3/92 +CRL1 CRL2 222.500 1.538 ! alkanes, 3/92 +CTL1 CRL2 222.500 1.538 ! alkanes, 3/92 +CRL2 CRL2 222.500 1.530 ! alkanes, 3/92 +CTL2 CRL2 222.500 1.530 ! alkanes, 3/92 +CRL1 HGA1 309.00 1.111 ! alkanes, 3/92 +CRL2 HGA2 309.00 1.111 ! alkanes, 4/98 +OHL CRL1 428.0 1.420 ! glycerol +CRL1 CTL3 222.500 1.538 ! alkanes, 3/92 +CEL1 CRL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95 +CEL1 CRL1 240.000 1.502 ! from CEL1 CTL2: sR12cc (c8-c39) +! Added for ergosterol (bjr 3/12) +! CEL1 CTL1 240.000 1.502 ! butene, yin,adm jr., 12/95 + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +! +! Added from par_al35_lipid.prm by jbl + +CTL1 CTL2 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !all CEL1 containing terms will +CTL1 CEL1 CTL2 50.00 113.00 !guess FC, eq. angle to yield 360 deg sum +CEL1 CEL1 CTL1 48.00 123.50 ! from CEL1 CEL1 CTL1 +CTL1 CTL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 +CTL3 CTL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 +CTL2 CTL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !involve the dR1 and dR2 terms +OHL CTL1 CTL3 75.700 110.10 ! glycerol +! added for new mixing rule for decalin/heptane by jbl +! CRL1 equivalent to CTL1, HGA1 equivalent to HAL1, etc. (jbl) +HOL OHL CRL1 57.500 106.00 ! glycerol +OHL CRL1 CRL2 75.700 110.10 ! glycerol +OHL CRL1 HGA1 45.900 108.89 ! glycerol +HAL3 CTL3 CRL1 33.430 110.10 22.53 2.179 ! alkane, 4/98 +CRL1 CRL1 CTL3 53.350 108.50 8.00 2.561 ! alkane, 3/92 +CRL2 CRL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol +HEL1 CEL1 CRL2 40.00 116.00 ! 1-butene; from propene, yin,adm jr., 12/95 +HGA2 CRL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95 +HAL2 CRL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95 +HGA2 CTL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95 +CRL1 CRL2 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !all CEL1 containing terms will +CEL1 CEL1 CRL2 48.00 123.50 ! from 2-butene, yin,adm jr., 12/95 +CEL1 CEL1 CRL1 48.00 123.50 ! from CEL1 CEL1 CTL1 +CRL1 CRL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 +CTL1 CRL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 +CRL1 CTL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 +CTL3 CRL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 +CRL2 CRL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !involve the dR1 and dR2 terms +CTL2 CRL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !involve the dR1 and dR2 terms +CRL2 CTL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !involve the dR1 and dR2 terms +CRL2 CRL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol +CRL2 CRL1 CRL2 58.350 113.50 11.16 2.561 ! glycerol +HGA1 CRL1 CTL2 34.500 110.10 22.53 2.179 ! alkane, 3/92 +HGA1 CRL1 CRL2 34.500 110.10 22.53 2.179 ! alkane, 3/92 +CRL1 CRL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol +CRL1 CRL1 CRL2 58.350 113.50 11.16 2.561 ! glycerol +CRL1 CTL2 CTL3 58.350 113.50 11.16 2.561 ! glycerol +HAL2 CTL2 CRL1 26.500 110.10 22.53 2.179 ! alkane, 4/98 +HGA2 CRL2 CRL1 26.500 110.10 22.53 2.179 ! alkane, 4/98 +CRL1 CTL2 CTL2 58.350 113.50 11.16 2.561 ! glycerol +CRL1 CRL2 CRL2 58.350 113.50 11.16 2.561 ! glycerol +CRL1 CEL1 CRL2 50.00 113.00 !guess FC, eq. angle to yield 360 deg sum +CRL1 CRL1 CRL1 53.350 111.00 8.00 2.561 ! alkane, 3/92 +CTL1 CRL1 CRL2 58.350 113.50 11.16 2.561 ! glycerol +HGA1 CRL1 CTL1 34.500 110.10 22.53 2.179 ! alkane, 3/92 +HGA1 CRL1 CRL1 34.500 110.10 22.53 2.179 ! alkane, 3/92 +CTL1 CRL1 CRL1 53.350 111.00 8.00 2.561 ! alkane, 3/92 +HAL1 CTL1 CRL1 34.500 110.10 22.53 2.179 ! alkane, 3/92 +CRL1 CTL1 CTL3 53.350 108.50 8.00 2.561 ! alkane, 3/92 +CRL1 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol +CEL2 CEL1 CRL2 48.00 126.00 ! 1-butene; from propene, yin,adm jr., 12/95 +CEL1 CRL2 CRL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 +CEL1 CTL2 CRL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 +CEL1 CRL2 CTL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 +CEL1 CRL2 CTL3 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 +CEL1 CRL2 CEL1 30.0 114.0 ! 1,4-dipentene, adm jr., 2/00 +CTL1 CRL2 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !all CEL1 containing terms will +CRL1 CTL2 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !all CEL1 containing terms will +CTL1 CEL1 CRL2 50.00 113.00 !guess FC, eq. angle to yield 360 deg sum +CRL1 CEL1 CTL2 50.00 113.00 !guess FC, eq. angle to yield 360 deg sum +HGA2 CRL2 HGA2 35.500 109.00 5.40 1.80200 ! alkane, 3/92 +HGA2 CRL2 CRL2 26.500 110.10 22.53 2.179 ! alkane, 4/98 +HGA1 CRL1 CTL3 34.500 110.10 22.53 2.179 ! alkane, 3/92 +CRL2 CRL2 CRL2 58.350 113.60 11.16 2.561 ! alkane, 3/92 +!Angles appended for ergosterol (bjr) +CEL1 CEL1 CEL1 48.00 123.50 ! From CEL1 CEL1 CTL1 +CRL1 CEL1 CRL1 50.00 113.00 ! From CTL1 CEL1 CTL2 +CEL1 CRL1 HGA1 45.00 111.50 ! From HAL2 CTL2 CEL1 +HEL1 CEL1 CTL1 40.00 116.00 ! From HAL2 CTL2 CEL1 +CTL1 CEL1 CTL1 50.00 113.00 !guess from CTL1 CEL1 CTL2 +CEL1 CTL1 HAL1 45.00 111.50 !guess from HAL2 CTL2 CEL1 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +! added for new mixing rule for decalin/heptane by jbl +! CRL1 equivalent to CTL1, HGA1 equivalent to HAL1, etc. (jbl) +CRL1 CRL1 CTL1 CTL2 0.000 3 0.00 ! 6/10, jbk +CRL1 CTL1 CTL2 CTL3 0.1218 3 180.00 ! 6/10, jbk +CRL1 CTL1 CTL2 CTL3 0.2175 2 180.00 ! 6/10, jbk +CRL1 CTL1 CTL2 CTL3 0.2398 1 180.00 ! 6/10, jbk +CRL1 CTL1 CTL2 CTL2 0.1218 3 180.00 ! 6/10, jbk +CRL1 CTL1 CTL2 CTL2 0.2175 2 180.00 ! 6/10, jbk +CRL1 CTL1 CTL2 CTL2 0.2398 1 180.00 ! 6/10, jbk +CRL1 CRL2 CEL1 CRL1 0.30 3 180.0 ! torR1 +CTL1 CRL2 CEL1 CRL1 0.30 3 180.0 ! torR1 +CRL1 CTL2 CEL1 CRL1 0.30 3 180.0 ! torR1 +CRL1 CRL2 CEL1 CTL1 0.30 3 180.0 ! torR1 +CTL1 CTL2 CEL1 CRL1 0.30 3 180.0 ! torR1 +CTL1 CRL2 CEL1 CTL1 0.30 3 180.0 ! torR1 +CRL1 CTL2 CEL1 CTL1 0.30 3 180.0 ! torR1 +X CRL1 OHL X 0.14 3 0.00 ! glycerol +X CRL2 OHL X 0.14 3 0.00 ! glycerol +CRL2 CEL1 CRL1 CRL1 0.00 3 180.0 ! bR12 +CTL2 CEL1 CRL1 CRL1 0.00 3 180.0 ! bR12 +CRL2 CEL1 CTL1 CRL1 0.00 3 180.0 ! bR12 +CRL2 CEL1 CRL1 CTL1 0.00 3 180.0 ! bR12 +CTL2 CEL1 CTL1 CRL1 0.00 3 180.0 ! bR12 +CTL2 CEL1 CRL1 CTL1 0.00 3 180.0 ! bR12 +CRL2 CEL1 CTL1 CTL1 0.00 3 180.0 ! bR12 +CTL2 CEL1 CRL1 CTL3 0.00 3 180.0 ! bR12 +CRL2 CEL1 CTL1 CTL3 0.00 3 180.0 ! bR12 +CRL2 CEL1 CRL1 CRL2 0.30 3 180.0 ! torR1 +CRL2 CEL1 CRL1 CTL2 0.30 3 180.0 ! torR1 +CRL2 CEL1 CTL1 CRL2 0.30 3 180.0 ! torR1 +CTL2 CEL1 CRL1 CRL2 0.30 3 180.0 ! torR1 +CRL2 CEL1 CTL1 CTL2 0.30 3 180.0 ! torR1 +CTL2 CEL1 CRL1 CTL2 0.30 3 180.0 ! torR1 +CTL2 CEL1 CTL1 CRL2 0.30 3 180.0 ! torR1 +CEL1 CEL1 CRL2 HGA2 0.3000 3 180.00 !2-butene, adm jr., 4/04 +CEL1 CEL1 CRL2 HAL2 0.3000 3 180.00 !2-butene, adm jr., 4/04 +CEL1 CEL1 CTL2 HGA2 0.3000 3 180.00 !2-butene, adm jr., 4/04 +CEL1 CEL1 CRL2 CRL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CRL2 CRL1 1.3000 3 180.0 ! +CEL1 CEL1 CTL2 CRL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CTL2 CRL1 1.3000 3 180.0 ! +CEL1 CEL1 CRL2 CTL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CRL2 CTL1 1.3000 3 180.0 ! +CEL1 CEL1 CRL1 CRL2 0.5000 1 180.0 ! bR12, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CRL1 CRL2 1.3000 3 180.0 ! +CEL1 CEL1 CTL1 CRL2 0.5000 1 180.0 ! bR12, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CTL1 CRL2 1.3000 3 180.0 ! +CEL1 CEL1 CRL1 CTL2 0.5000 1 180.0 ! bR12, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CRL1 CTL2 1.3000 3 180.0 ! +CEL1 CEL1 CRL1 CTL3 0.5000 1 180.0 ! bR13, rCH3, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CRL1 CTL3 1.3000 3 180.0 ! +CEL1 CEL1 CRL2 CTL3 0.9000 1 180.00 !2-pentene and 3-heptene +CEL1 CEL1 CRL2 CTL3 0.2000 2 180.00 !2-pentene and 3-heptene +CEL1 CRL2 CRL2 CTL3 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CRL2 CTL3 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CRL2 CTL3 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CTL3 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CTL3 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CTL3 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CTL3 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CTL3 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CTL3 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CEL1 CRL2 CEL1 1.000 1 180.00 !2,5-diheptane +CEL1 CEL1 CRL2 CEL1 0.100 2 0.00 !2,5-diheptane +CEL1 CEL1 CRL2 CEL1 0.300 3 180.00 !2,5-diheptane +CEL1 CEL1 CRL2 CEL1 0.200 4 0.00 !2,5-diheptane +CEL1 CEL1 CRL1 CRL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CRL1 CRL1 1.3000 3 180.0 ! +CEL1 CEL1 CTL1 CRL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CTL1 CRL1 1.3000 3 180.0 ! +CEL1 CEL1 CRL1 CTL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CRL1 CTL1 1.3000 3 180.0 ! +CEL1 CEL1 CRL2 CRL2 0.9100 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CEL1 CRL2 CRL2 0.1800 2 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CEL1 CRL2 CRL2 0.1700 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CEL1 CRL2 CTL2 0.9100 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CEL1 CRL2 CTL2 0.1800 2 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CEL1 CRL2 CTL2 0.1700 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CEL1 CTL2 CRL2 0.9100 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CEL1 CTL2 CRL2 0.1800 2 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CEL1 CTL2 CRL2 0.1700 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda, 6/18) +CEL1 CRL2 CRL2 CRL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CRL2 CRL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CRL2 CRL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CTL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CTL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CTL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CTL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CTL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CTL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CTL2 CRL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CTL2 CRL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CTL2 CRL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CRL2 CTL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CRL2 CTL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CRL2 CTL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CRL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CRL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CRL2 CTL2 CRL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CRL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CRL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 (from jbklauda) +CEL1 CTL2 CRL2 CRL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 (from jbklauda) +X CRL1 CTL1 X 0.200 3 0.00 ! alkane, 3/92 +X CRL1 CRL1 X 0.200 3 0.00 ! alkane, 3/92 +X CRL1 CTL2 X 0.200 3 0.00 ! alkane, 3/92 +X CRL1 CRL2 X 0.200 3 0.00 ! alkane, 3/92 +X CTL1 CRL2 X 0.200 3 0.00 ! alkane, 3/92 +X CRL1 CTL3 X 0.200 3 0.00 ! alkane, 3/92 +X CTL2 CRL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell +X CRL2 CRL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell +X CRL2 CTL3 X 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell +CRL2 CEL1 CRL1 CTL3 0.00 3 180.0 ! bR12 +X CRL1 NH3L X 0.1000 3 0.00 ! for POPS +HEL1 CEL1 CRL2 CRL1 0.00 3 0.0 ! wC9H, HEL1 CEL1 CTL2 CTL2 +HEL1 CEL1 CTL2 CRL1 0.00 3 0.0 ! wC9H, HEL1 CEL1 CTL2 CTL2 +HEL1 CEL1 CRL2 CTL1 0.00 3 0.0 ! wC9H, HEL1 CEL1 CTL2 CTL2 +HEL1 CEL1 CRL2 CTL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 +HEL1 CEL1 CTL2 CRL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 +HEL1 CEL1 CRL2 CTL3 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 +HEL1 CEL1 CRL2 HGA2 0.0000 3 0.00 ! butene, adm jr., 2/00 update +HEL1 CEL1 CTL2 HGA2 0.0000 3 0.00 ! butene, adm jr., 2/00 update +HEL1 CEL1 CRL2 HAL2 0.0000 3 0.00 ! butene, adm jr., 2/00 update +CEL1 CRL2 CEL1 HEL1 0.000 2 0.00 !1,4-dipentene +CEL1 CRL2 CEL1 HEL1 0.000 3 0.00 !1,4-dipentene +CRL2 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 +CEL2 CEL1 CRL2 CRL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CRL2 CRL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CTL2 CRL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CTL2 CRL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CRL2 CTL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CRL2 CTL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CRL2 CTL3 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CRL2 CTL3 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update +CEL2 CEL1 CRL2 HGA2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95 +CEL2 CEL1 CTL2 HGA2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95 +CEL2 CEL1 CRL2 HAL2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95 +CEL2 CEL1 CRL2 CEL1 1.200 1 180.00 !1,4-dipentene +CEL2 CEL1 CRL2 CEL1 0.400 2 180.00 !1,4-dipentene +CEL2 CEL1 CRL2 CEL1 1.300 3 180.00 !1,4-dipentene +HGA2 CRL2 CEL1 CRL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +HAL2 CRL2 CEL1 CRL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +HGA2 CTL2 CEL1 CRL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +HGA2 CRL2 CEL1 CTL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +HGA2 CTL2 CEL1 CTL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +HAL2 CRL2 CEL1 CTL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +HAL2 CTL2 CEL1 CRL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +HEL1 CEL1 CRL2 CRL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 +!Dihedrals appended for ergosterol (bjr) +CEL1 CEL1 CTL1 HAL1 0.3000 3 180.00 ! From 2-butene +CEL1 CEL1 CRL1 HGA1 0.3000 3 180.00 ! From CEL1 CEL1 CRL2 HGA2 +X CEL1 CTL1 X 0.000 3 180.00 ! from br12 +HAL2 CTL2 CEL1 CTL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +CEL1 CEL1 CTL2 CTL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CTL2 CTL1 1.3000 3 180.0 ! +CTL1 CTL2 CEL1 CTL1 0.30 3 180.0 ! torR1 +X CEL1 CRL1 X 0.000 3 180.00 ! from br12 + + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +! added for new mixing rule for decalin and heptane by jbl + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +! +! added for new mixing rule for decalin/heptane by jbl +CRL1 HAL2 -0.0321 3.3500 +HGA1 HAL2 -0.0359 2.6800 +CRL2 HAL2 -0.0415 3.3600 +HGA2 HAL2 -0.0317 2.6800 +CRL1 HAL1 -0.0293 3.3500 +HGA1 HAL1 -0.0329 2.6800 +CRL2 HAL1 -0.0379 3.3600 +HGA2 HAL1 -0.0289 2.6800 +CRL1 CTL1 -0.0275 4.0100 +HGA1 CTL1 -0.0308 3.3400 +CRL2 CTL1 -0.0355 4.0200 +HGA2 CTL1 -0.0271 3.3400 + +end + +return + +endif + +! Original model of Suits et al., which is used on ANTON as well as +!being suitable for other systems (set chol_model 2 (or anything but 1....)) +! +!Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. "Molecular Level +!Organization of Saturated and Polyunsaturated Fatty Acids in a +!Phosphatidylcholine Bilayer Containing Cholesterol" Biochemistry, +!43(49):15318-28, 2004 +! + +read rtf card @app +* cholesterol residues +* +36 1 + +RESI CHL1 0.00 !cholesterol (name to avoid conflict with choline) +! atoms names correspond to the correct cholesterol nomenclature +GROUP +ATOM C3 CTL1 0.14 +ATOM O3 OHL -0.66 +ATOM H3' HOL 0.43 +ATOM H3 HAL1 0.09 +GROUP +ATOM C4 CTL2 -0.18 +ATOM H4A HAL2 0.09 +ATOM H4B HAL2 0.09 +GROUP +ATOM C5 CEL1 0.00 +ATOM C6 CEL1 -0.15 +ATOM H6 HEL1 0.15 +GROUP +ATOM C7 CTL2 -0.18 +ATOM H7A HAL2 0.09 +ATOM H7B HAL2 0.09 +GROUP +ATOM C8 CTL1 -0.09 +ATOM H8 HAL1 0.09 +GROUP +ATOM C14 CTL1 -0.09 +ATOM H14 HAL1 0.09 +GROUP +ATOM C15 CTL2 -0.18 +ATOM H15A HAL2 0.09 +ATOM H15B HAL2 0.09 +GROUP +ATOM C16 CTL2 -0.18 +ATOM H16A HAL2 0.09 +ATOM H16B HAL2 0.09 +GROUP +ATOM C17 CTL1 -0.09 +ATOM H17 HAL1 0.09 +GROUP +ATOM C13 CTL1 0.00 +GROUP +ATOM C18 CTL3 -0.27 !methyl at c13 +ATOM H18A HAL3 0.09 +ATOM H18B HAL3 0.09 +ATOM H18C HAL3 0.09 +GROUP +ATOM C12 CTL2 -0.18 +ATOM H12A HAL2 0.09 +ATOM H12B HAL2 0.09 +GROUP +ATOM C11 CTL2 -0.18 +ATOM H11A HAL2 0.09 +ATOM H11B HAL2 0.09 +GROUP +ATOM C9 CTL1 -0.09 +ATOM H9 HAL1 0.09 +GROUP +ATOM C10 CTL1 0.00 +GROUP +ATOM C19 CTL3 -0.27 !methyl at c10 +ATOM H19A HAL3 0.09 +ATOM H19B HAL3 0.09 +ATOM H19C HAL3 0.09 +GROUP +ATOM C1 CTL2 -0.18 +ATOM H1A HAL2 0.09 +ATOM H1B HAL2 0.09 +GROUP +ATOM C2 CTL2 -0.18 +ATOM H2A HAL2 0.09 +ATOM H2B HAL2 0.09 +GROUP +ATOM C20 CTL2 -0.09 +ATOM H20 HAL2 0.09 +GROUP +ATOM C21 CTL3 -0.27 +ATOM H21A HAL3 0.09 +ATOM H21B HAL3 0.09 +ATOM H21C HAL3 0.09 +GROUP +ATOM C22 CTL2 -0.18 +ATOM H22A HAL2 0.09 +ATOM H22B HAL2 0.09 +GROUP +ATOM C23 CTL2 -0.18 +ATOM H23A HAL2 0.09 +ATOM H23B HAL2 0.09 +GROUP +ATOM C24 CTL2 -0.18 !beyond this nomenclature may not be correct +ATOM H24A HAL2 0.09 +ATOM H24B HAL2 0.09 +GROUP +ATOM C25 CTL1 -0.09 !c25 +ATOM H25 HAL1 0.09 +GROUP +ATOM C26 CTL3 -0.27 !terminal methyl, c26 +ATOM H26A HAL3 0.09 +ATOM H26B HAL3 0.09 +ATOM H26C HAL3 0.09 +GROUP +ATOM C27 CTL3 -0.27 !terminal methyl, c27 +ATOM H27A HAL3 0.09 +ATOM H27B HAL3 0.09 +ATOM H27C HAL3 0.09 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C2 C2 H2A C2 H2B +BOND C2 C1 C1 H1A C1 H1B +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 +BOND C5 C10 +BOND C10 C1 +BOND C10 C19 C19 H19A C19 H19B C19 H19C +DOUBLE C5 C6 +BOND C6 H6 +BOND C6 C7 C7 H7A C7 H7B +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C13 C18 C18 H18A C18 H18B C18 H18C +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 +BOND C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 C24 C24 H24A C24 H24B +BOND C24 C25 C25 H25 +BOND C25 C26 C26 H26A C26 H26B C26 H26C +BOND C25 C27 C27 H27A C27 H27B C27 H27C +!ICs based on CHARMM optimized structure +IC C1 C2 C3 C4 1.5383 110.44 55.92 110.66 1.5367 +IC C4 C2 *C3 O3 1.5367 110.66 120.28 109.14 1.4158 +IC O3 C2 *C3 H3 1.4158 109.14 118.92 109.40 1.1155 +IC C2 C3 O3 H3' 1.5311 109.14 -58.51 105.39 0.9593 +IC C2 C3 C4 C5 1.5311 110.66 -55.96 111.70 1.5156 +IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 +IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 +IC C3 C4 C5 C10 1.5367 111.70 54.04 115.09 1.5304 +IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 +IC C4 C5 C6 C7 1.5156 121.28 -178.39 123.88 1.5018 +IC C7 C5 *C6 H6 1.5018 123.88 177.19 119.54 1.1001 +IC C5 C6 C7 C8 1.3432 123.88 14.50 112.36 1.5506 +IC C8 C6 *C7 H7A 1.5506 112.36 122.18 110.84 1.1114 +IC H7A C6 *C7 H7B 1.1114 110.84 118.17 109.17 1.1124 +IC C6 C7 C8 C14 1.5018 112.36 -165.89 110.02 1.5202 +IC C14 C7 *C8 C9 1.5202 110.02 121.07 110.84 1.5327 +IC C9 C7 *C8 H8 1.5327 110.84 119.34 108.18 1.1123 +IC C7 C8 C14 C13 1.5506 110.02 179.73 115.21 1.5247 +IC C13 C8 *C14 C15 1.5247 115.21 126.69 117.86 1.5382 +IC C13 C8 *C14 H14 1.5247 115.21 -116.05 105.83 1.1205 +IC C8 C14 C15 C16 1.5202 117.86 -163.10 103.40 1.5360 +IC C16 C14 *C15 H15A 1.5360 103.40 117.45 109.62 1.1113 +IC H15A C14 *C15 H15B 1.1113 109.62 121.32 111.94 1.1082 +IC C14 C15 C16 C17 1.5382 103.40 7.85 106.79 1.5620 +IC C17 C15 *C16 H16A 1.5620 106.79 118.96 109.25 1.1107 +IC H16A C15 *C16 H16B 1.1107 109.25 120.76 111.65 1.1090 +IC C13 C16 *C17 C20 1.5401 104.94 132.02 112.36 1.5633 +IC C13 C16 *C17 H17 1.5401 104.94 -111.76 106.42 1.1153 +IC C17 C14 *C13 C12 1.5401 100.27 122.68 106.98 1.5408 +IC C12 C14 *C13 C18 1.5408 106.98 122.91 110.83 1.5518 +IC C14 C13 C18 H18A 1.5247 110.83 60.33 111.48 1.1077 +IC H18A C13 *C18 H18B 1.1077 111.48 119.80 110.01 1.1086 +IC H18A C13 *C18 H18C 1.1077 111.48 -121.00 111.71 1.1067 +IC C14 C13 C12 C11 1.5247 106.98 56.78 111.10 1.5422 +IC C11 C13 *C12 H12A 1.5422 111.10 121.37 111.21 1.1067 +IC H12A C13 *C12 H12B 1.1067 111.21 118.82 108.68 1.1119 +IC C9 C12 *C11 H11A 1.5593 113.54 121.67 107.06 1.1093 +IC H11A C12 *C11 H11B 1.1093 107.06 115.98 108.75 1.1100 +IC C10 C8 *C9 H9 1.5531 112.73 -114.54 104.68 1.1185 +IC C9 C5 *C10 C19 1.5531 111.91 -120.04 108.03 1.5524 +IC C19 C5 *C10 C1 1.5524 108.03 -119.87 109.26 1.5579 +IC C5 C10 C19 H19A 1.5304 108.03 -172.88 110.67 1.1082 +IC H19A C10 *C19 H19B 1.1082 110.67 118.48 111.77 1.1080 +IC H19A C10 *C19 H19C 1.1082 110.67 -120.66 110.97 1.1095 +IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 +IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 +IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 +IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 +IC C16 C17 C20 C22 1.5620 112.36 55.21 110.55 1.5476 +IC C22 C17 *C20 C21 1.5476 110.55 125.88 113.32 1.5349 +IC C21 C17 *C20 H20 1.5349 113.32 118.87 107.27 1.1157 +IC C17 C20 C21 H21A 1.5633 113.32 64.90 110.93 1.1077 +IC H21A C20 *C21 H21B 1.1077 110.93 -121.00 110.41 1.1104 +IC H21A C20 *C21 H21C 1.1077 110.93 118.40 111.29 1.1085 +IC C17 C20 C22 C23 1.5633 110.55 -174.59 115.12 1.5394 +IC C23 C20 *C22 H22A 1.5394 115.12 120.23 109.35 1.1116 +IC H22A C20 *C22 H22B 1.1116 109.35 117.13 108.75 1.1121 +IC C20 C22 C23 C24 1.5476 115.12 172.50 112.25 1.5377 +IC C24 C22 *C23 H23A 1.5377 112.25 121.13 109.69 1.1108 +IC H23A C22 *C23 H23B 1.1108 109.69 118.14 108.99 1.1129 +IC C22 C23 C24 C25 1.5394 112.25 -176.23 114.06 1.5418 +IC C25 C23 *C24 H24A 1.5418 114.06 120.56 108.44 1.1132 +IC H24A C23 *C24 H24B 1.1132 108.44 117.11 109.39 1.1121 +IC C23 C24 C25 C26 1.5377 114.06 174.26 111.24 1.5378 +IC C26 C24 *C25 C27 1.5378 111.24 119.63 112.86 1.5381 +IC C26 C24 *C25 H25 1.5378 111.24 -119.50 108.47 1.1151 +IC C24 C25 C26 H26A 1.5418 111.24 -178.53 110.52 1.1105 +IC H26A C25 *C26 H26B 1.1105 110.52 120.00 110.36 1.1105 +IC H26A C25 *C26 H26C 1.1105 110.52 -120.09 110.33 1.1106 +IC C24 C25 C27 H27A 1.5418 112.86 -178.28 110.40 1.1105 +IC H27A C25 *C27 H27B 1.1105 110.40 119.95 110.31 1.1105 +IC H27A C25 *C27 H27C 1.1105 110.40 -119.82 110.77 1.1097 + +RESI CHNS 0.00 !cholesterol with sidechain beyond c18(c20) omitted +! atoms names after the comments correspond to the +! correct cholesterol nomenclature +GROUP +ATOM C1 CTL1 0.14 !c3 +ATOM O1 OHL -0.66 +ATOM HO1 HOL 0.43 +ATOM H1 HAL1 0.09 + +ATOM C2 CTL2 -0.18 !c4 +ATOM H2 HAL2 0.09 +ATOM H2' HAL2 0.09 + +ATOM C3 CEL1 0.00 !c5 +ATOM C4 CEL1 -0.15 !c6 +ATOM H4 HEL1 0.15 + +ATOM C5 CTL2 -0.18 !c7 +ATOM H5 HAL2 0.09 +ATOM H5' HAL2 0.09 + +ATOM C6 CTL1 -0.09 !c8 +ATOM H6 HAL1 0.09 + +ATOM C7 CTL1 -0.09 !c14 +ATOM H7 HAL1 0.09 + +ATOM C8 CTL2 -0.18 !c15 +ATOM H8 HAL2 0.09 +ATOM H8' HAL2 0.09 + +ATOM C9 CTL2 -0.18 !c16 +ATOM H9 HAL2 0.09 +ATOM H9' HAL2 0.09 + +ATOM C10 CTL1 -0.09 !c17 +ATOM H10 HAL1 0.09 + +ATOM C11 CTL1 0.00 !c13 + +ATOM CC11 CTL3 -0.27 !c18, methyl at c13 +ATOM H111 HAL3 0.09 +ATOM H112 HAL3 0.09 +ATOM H113 HAL3 0.09 + +ATOM C12 CTL2 -0.18 !c12 +ATOM H12 HAL2 0.09 +ATOM H12' HAL2 0.09 + +ATOM C13 CTL2 -0.18 !c11 +ATOM H13 HAL2 0.09 +ATOM H13' HAL2 0.09 + +ATOM C14 CTL1 -0.09 !c9 +ATOM H14 HAL1 0.09 + +ATOM C15 CTL1 0.00 !c10 + +ATOM CC15 CTL3 -0.27 !c19, methyl at c10 +ATOM H151 HAL3 0.09 +ATOM H152 HAL3 0.09 +ATOM H153 HAL3 0.09 + +ATOM C16 CTL2 -0.18 !c1 +ATOM H16 HAL2 0.09 +ATOM H16' HAL2 0.09 + +ATOM C17 CTL2 -0.18 !c2 +ATOM H17 HAL2 0.09 +ATOM H17' HAL2 0.09 + +ATOM C18 CTL3 -0.27 !c20 +ATOM H181 HAL3 0.09 +ATOM H182 HAL3 0.09 +ATOM H183 HAL3 0.09 + +BOND C1 O1 C1 H1 C1 C2 +BOND O1 HO1 +BOND C2 C3 C2 H2 C2 H2' +DOUBLE C3 C4 +BOND C4 C5 C4 H4 +BOND C5 C6 C5 H5 C5 H5' +BOND C6 C7 C6 H6 +BOND C7 C8 C7 H7 +BOND C8 C9 C8 H8 C8 H8' +BOND C9 C10 C9 H9 C9 H9' +BOND C10 C18 C10 C11 C10 H10 +BOND C11 CC11 C11 C7 C11 C12 +BOND CC11 H111 CC11 H112 CC11 H113 +BOND C12 C13 C12 H12 C12 H12' +BOND C13 C14 C13 H13 C13 H13' +BOND C14 C15 C14 C6 C14 H14 +BOND C15 C16 C15 C3 C15 CC15 +BOND CC15 H151 CC15 H152 CC15 H153 +BOND C16 C17 C16 H16 C16 H16' +BOND C17 C1 C17 H17 C17 H17' +BOND C18 H181 C18 H182 C18 H183 + +!DONO HO1 O1 +!ACCE O1 + +IC O1 C1 C2 C3 1.4158 109.24 -176.17 111.80 1.5153 +IC C1 C2 C3 C4 1.5368 111.80 -123.48 121.41 1.3430 +IC C2 C3 C4 C5 1.5153 121.41 -178.76 123.84 1.5019 +IC C3 C4 C5 C6 1.3430 123.84 14.64 112.44 1.5504 +IC C4 C5 C6 C7 1.5019 112.44 -166.16 109.90 1.5192 +IC C5 C6 C7 C8 1.5504 109.90 -54.73 118.74 1.5447 +IC C6 C7 C8 C9 1.5192 118.74 -161.90 103.72 1.5418 +IC C7 C8 C9 C10 1.5447 103.72 5.69 105.45 1.5530 +IC C8 C9 C10 C11 1.5418 105.45 21.50 105.85 1.5300 +IC C9 C10 C11 C12 1.5530 105.85 -155.90 116.00 1.5351 +IC C7 C12 *C11 CC11 1.5194 108.58 -123.00 111.88 1.5530 +IC C10 C11 C12 C13 1.5300 116.00 167.75 110.42 1.5414 +IC C10 C11 C7 C8 1.5300 99.46 43.93 105.86 1.5447 +IC C11 C12 C13 C14 1.5351 110.42 -52.28 113.50 1.5626 +IC CC11 C11 C12 C13 1.5530 111.88 -66.16 110.42 1.5414 +IC CC11 C11 C7 C8 1.5530 111.12 -70.96 105.86 1.5447 +IC C12 C13 C14 C15 1.5414 113.50 179.43 114.52 1.5524 +IC C13 C14 C15 CC15 1.5626 114.52 -50.80 109.07 1.5522 +IC C13 C14 C15 C16 1.5626 114.52 69.29 108.64 1.5574 +IC C13 C14 C6 C7 1.5626 113.16 -48.42 109.31 1.5192 +IC CC15 C15 C16 C17 1.5522 110.15 -68.75 114.54 1.5383 +IC C14 C15 C16 C17 1.5524 108.64 171.83 114.54 1.5383 +IC C14 C15 C3 C4 1.5524 111.86 7.71 123.46 1.3430 +IC C15 C16 C17 C1 1.5574 114.54 -54.68 110.51 1.5312 +IC C11 C9 *C10 C18 1.5300 105.85 126.88 114.22 1.5413 +IC O1 C2 *C1 H1 1.4158 109.24 -119.02 109.53 1.1156 +IC C2 C1 O1 HO1 1.5368 109.24 62.69 105.39 0.9593 +IC C3 C1 *C2 H2 1.5153 111.80 121.88 109.11 1.1100 +IC C3 C1 *C2 H2' 1.5153 111.80 -123.05 107.36 1.1142 +IC C5 C3 *C4 H4 1.5019 123.84 177.13 119.55 1.1001 +IC C6 C4 *C5 H5 1.5504 112.44 122.17 110.88 1.1114 +IC C6 C4 *C5 H5' 1.5504 112.44 -119.69 109.16 1.1124 +IC C7 C5 *C6 H6 1.5192 109.90 -119.58 108.19 1.1122 +IC C8 C6 *C7 H7 1.5447 118.74 117.73 105.77 1.1205 +IC C9 C7 *C8 H8 1.5418 103.72 117.51 109.61 1.1108 +IC C9 C7 *C8 H8' 1.5418 103.72 -121.25 111.67 1.1078 +IC C10 C8 *C9 H9 1.5530 105.45 118.45 109.64 1.1105 +IC C10 C8 *C9 H9' 1.5530 105.45 -120.18 112.16 1.1085 +IC C18 C9 *C10 H10 1.5413 114.22 119.69 107.07 1.1162 +IC C7 C11 CC11 H111 1.5194 111.12 -178.60 110.01 1.1092 +IC H111 C11 *CC1 H112 1.1092 110.01 118.82 111.63 1.1068 +IC H111 C11 *CC1 H113 1.1092 110.01 -120.26 111.66 1.1075 +IC C13 C11 *C12 H12 1.5414 110.42 122.09 109.96 1.1102 +IC C13 C11 *C12 H12' 1.5414 110.42 -119.49 108.88 1.1120 +IC C14 C12 *C13 H13 1.5626 113.50 121.59 107.14 1.1091 +IC C14 C12 *C13 H13' 1.5626 113.50 -122.38 108.79 1.1098 +IC C13 C6 *C14 H14 1.5626 113.16 113.80 104.59 1.1184 +IC C3 C15 CC15 H151 1.5435 107.81 -172.81 110.68 1.1082 +IC H151 C15 *CC1 H152 1.1082 110.68 118.52 111.71 1.1081 +IC H151 C15 *CC1 H153 1.1082 110.68 -120.68 110.98 1.1094 +IC C17 C15 *C16 H16 1.5383 114.54 122.43 109.27 1.1104 +IC C17 C15 *C16 H16' 1.5383 114.54 -120.70 108.26 1.1134 +IC C16 C1 *C17 H17 1.5383 110.51 121.12 109.37 1.1120 +IC C16 C1 *C17 H17' 1.5383 110.51 -120.62 109.70 1.1111 +!use hbuild for c18 hydrogens + +RESI CHM1 0.00 !cholesterol analog with only rings 1 and 2 + !and the position 19 methyl +! atoms names after the comments correspond to the +! correct cholesterol nomenclature +! +!ring 1 +! +GROUP +ATOM C1 CTL1 0.14 !c3 +ATOM O1 OHL -0.66 +ATOM HO1 HOL 0.43 +ATOM H1 HAL1 0.09 + +ATOM C2 CTL2 -0.18 !c4 +ATOM H2 HAL2 0.09 +ATOM H2' HAL2 0.09 + +ATOM C3 CEL1 0.00 !c5 + +ATOM C15 CTL1 0.00 !c10 + +ATOM C16 CTL2 -0.18 !c1 +ATOM H16 HAL2 0.09 +ATOM H16' HAL2 0.09 + +ATOM C17 CTL2 -0.18 !c2 +ATOM H17 HAL2 0.09 +ATOM H17' HAL2 0.09 + +ATOM CC15 CTL3 -0.27 !c19, methyl at c10 +ATOM H151 HAL3 0.09 +ATOM H152 HAL3 0.09 +ATOM H153 HAL3 0.09 + +!ring 2 +ATOM C4 CEL1 -0.15 !c6 +ATOM H4 HEL1 0.15 + +ATOM C5 CTL2 -0.18 !c7 +ATOM H5 HAL2 0.09 +ATOM H5' HAL2 0.09 + +ATOM C6 CTL2 -0.18 !c8 +ATOM H6 HAL2 0.09 +ATOM H6' HAL2 0.09 + +ATOM C14 CTL2 -0.18 !c9 +ATOM H14 HAL2 0.09 +ATOM H14' HAL2 0.09 + +BOND C1 C2 C2 C3 C3 C15 C15 C16 C16 C17 C17 C1 +BOND C1 O1 O1 HO1 C1 H1 +BOND C2 H2 C2 H2' +BOND C15 CC15 CC15 H151 CC15 H152 CC15 H153 +BOND C16 H16 C16 H16' +BOND C17 H17 C17 H17' +DOUB C3 C4 +BOND C4 C5 C5 C6 C6 C14 C14 C15 +BOND C4 H4 +BOND C5 H5 C5 H5' +BOND C6 H6 C6 H6' +BOND C14 H14 C14 H14' + +IC C1 C2 C3 C15 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C15 C16 0.0000 0.00 0.00 0.00 0.0000 +IC C17 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C17 *C1 O1 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C17 *C1 H1 0.0000 0.00 -120.00 0.00 0.0000 +IC C17 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H2' 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 15.00 0.00 0.0000 +IC C4 C5 C6 C14 0.0000 0.00 -45.00 0.00 0.0000 +IC C14 C3 *C15 CC15 0.0000 0.00 -120.00 0.00 0.0000 +IC C17 C15 *C16 H16 0.0000 0.00 120.00 0.00 0.0000 +IC C17 C15 *C16 H16' 0.0000 0.00 -120.00 0.00 0.0000 +IC C16 C1 *C17 H17 0.0000 0.00 120.00 0.00 0.0000 +IC C16 C1 *C17 H17' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C15 CC15 H151 0.0000 0.00 180.00 0.00 0.0000 +IC H151 C15 *CC15 H152 0.0000 0.00 120.00 0.00 0.0000 +IC H151 C15 *CC15 H153 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C4 *C5 H5' 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C5 *C6 H6 0.0000 0.00 120.00 0.00 0.0000 +IC C14 C5 *C6 H6' 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C15 *C14 H14 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C15 *C14 H14' 0.0000 0.00 -120.00 0.00 0.0000 +end + +read para card flex @app +* cholesterol parameters +* + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +CEL1 CTL1 240.000 1.502 ! from CEL1 CTL2: sR12cc (c8-c39) +! + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +CTL1 CTL2 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !all CEL1 containing terms will +CTL2 CTL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 !involve the dR1 and dR2 terms +CTL1 CTL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 +CTL3 CTL1 CEL1 32.00 112.20 !from CEL1 CTL2 CTL2 +CTL1 CEL1 CTL2 50.00 113.00 !guess FC, eq. angle to yield 360 deg sum +CEL1 CEL1 CTL1 48.00 123.50 ! from CEL1 CEL1 CTL1 +! +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +CTL1 CTL2 CEL1 CTL1 0.30 3 180.0 ! torR1 +CTL2 CEL1 CTL1 CTL1 0.00 3 180.0 ! bR12 +CTL2 CEL1 CTL1 CTL3 0.00 3 180.0 ! bR12 +CTL2 CEL1 CTL1 CTL2 0.30 3 180.0 ! torR1 +HAL2 CTL2 CEL1 CTL1 0.0300 3 0.0 ! CH2 wag and twist, from CEL1 CEL1 CTL2 HAL2 +CEL1 CEL1 CTL2 CTL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CTL2 CTL1 1.3000 3 180.0 ! +CEL1 CEL1 CTL1 CTL1 0.5000 1 180.0 ! torR2, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CTL1 CTL1 1.3000 3 180.0 ! +CEL1 CEL1 CTL1 CTL2 0.5000 1 180.0 ! bR12, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CTL1 CTL2 1.3000 3 180.0 ! +CEL1 CEL1 CTL1 CTL3 0.5000 1 180.0 ! bR13, rCH3, CEL1 CEL1 CTL2 CTL2 +CEL1 CEL1 CTL1 CTL3 1.3000 3 180.0 ! +HEL1 CEL1 CTL2 CTL1 0.00 3 0.0 ! wC9H, HEL1 CEL1 CTL2 CTL2 +CTL2 CTL1 OHL HOL 0.9 1 0.00 ! hydroxyl mp2/6-31g* surface +CTL2 CTL1 OHL HOL 0.3 3 0.00 ! possible conflict with protein + +end + +return diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_detergent.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_detergent.str new file mode 100644 index 00000000..c9d2419b --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_detergent.str @@ -0,0 +1,2336 @@ +* Toppar stream file for detergents. Stream following reading of +* top_all36_lipid.rtf +* and +* par_all36_lipid.rtf +* + +read rtf card append +* detergent residues +* +36 1 + +RESI SDS -1.00 ! Dodecylsulphate +GROUP +ATOM S SL 1.33 ! OS2(-1) +ATOM OS1 OSL -0.28 ! | +ATOM OS2 O2L -0.65 ! (-) OS3--S(+2)--OS4 (-) +ATOM OS3 O2L -0.65 ! | +ATOM OS4 O2L -0.65 ! OS1 +ATOM C1 CTL2 -0.28 ! \ +ATOM H11 HAL2 0.09 ! H11-C1-H12 +ATOM H12 HAL2 0.09 ! | +GROUP ! | +ATOM C2 CTL2 -0.18 ! H21-C2-H22 +ATOM H21 HAL2 0.09 ! | +ATOM H22 HAL2 0.09 ! | +GROUP ! | +ATOM C3 CTL2 -0.18 ! H31-C3-H32 +ATOM H31 HAL2 0.09 ! | +ATOM H32 HAL2 0.09 ! | +GROUP ! | +ATOM C4 CTL2 -0.18 ! H41-C4-H42 +ATOM H41 HAL2 0.09 ! | +ATOM H42 HAL2 0.09 ! | +GROUP ! | +ATOM C5 CTL2 -0.18 ! H51-C5-H52 +ATOM H51 HAL2 0.09 ! | +ATOM H52 HAL2 0.09 ! | +GROUP ! | +ATOM C6 CTL2 -0.18 ! H61-C6-H62 +ATOM H61 HAL2 0.09 ! | +ATOM H62 HAL2 0.09 ! | +GROUP ! | +ATOM C7 CTL2 -0.18 ! H71-C7-H72 +ATOM H71 HAL2 0.09 ! | +ATOM H72 HAL2 0.09 ! | +GROUP ! | +ATOM C8 CTL2 -0.18 ! H81-C8-H82 +ATOM H81 HAL2 0.09 ! | +ATOM H82 HAL2 0.09 ! | +GROUP ! | +ATOM C9 CTL2 -0.18 ! H91-C9-H92 +ATOM H91 HAL2 0.09 ! | +ATOM H92 HAL2 0.09 ! | +GROUP ! | +ATOM C10 CTL2 -0.18 ! H101-C10-H102 +ATOM H101 HAL2 0.09 ! | +ATOM H102 HAL2 0.09 ! | +GROUP ! | +ATOM C11 CTL2 -0.18 ! H111-C11-H112 +ATOM H111 HAL2 0.09 ! | +ATOM H112 HAL2 0.09 ! | +GROUP ! | +ATOM C12 CTL3 -0.27 ! H121-C12-H123 +ATOM H121 HAL3 0.09 ! | +ATOM H122 HAL3 0.09 ! H122 +ATOM H123 HAL3 0.09 ! + +BOND S OS1 S OS2 S OS3 S OS4 +BOND OS1 C1 C1 H11 C1 H12 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 C3 C3 H31 C3 H32 +BOND C3 C4 C4 H41 C4 H42 +BOND C4 C5 C5 H51 C5 H52 +BOND C5 C6 C6 H61 C6 H62 +BOND C6 C7 C7 H71 C7 H72 +BOND C7 C8 C8 H81 C8 H82 +BOND C8 C9 C9 H91 C9 H92 +BOND C9 C10 C10 H101 C10 H102 +BOND C10 C11 C11 H111 C11 H112 +BOND C11 C12 C12 H121 C12 H122 C12 H123 + +ACCE OS1 +ACCE OS2 +ACCE OS3 +ACCE OS4 + +!IC table from IC generate, minimized geometry +IC OS4 S OS1 C1 1.4528 105.54 60.48 114.12 1.4238 +IC OS2 OS1 *S OS3 1.4521 103.32 119.41 105.53 1.4528 +IC OS2 OS1 *S OS4 1.4521 103.32 -119.41 105.54 1.4528 +IC OS2 S OS1 C1 1.4521 103.32 179.90 114.12 1.4238 +IC S OS1 C1 C2 1.5670 114.12 179.86 108.48 1.5337 +IC C2 OS1 *C1 H11 1.5337 108.48 -119.30 111.15 1.1167 +IC H11 OS1 *C1 H12 1.1167 111.15 -121.39 111.13 1.1167 +IC OS1 C1 C2 C3 1.4238 108.48 -179.98 112.43 1.5340 +IC C3 C1 *C2 H21 1.5340 112.43 -121.50 108.71 1.1129 +IC H21 C1 *C2 H22 1.1129 108.71 -117.02 108.70 1.1129 +IC C1 C2 C3 C4 1.5337 112.43 179.90 112.76 1.5346 +IC C4 C2 *C3 H31 1.5346 112.76 -121.58 108.61 1.1129 +IC H31 C2 *C3 H32 1.1129 108.61 -116.82 108.62 1.1129 +IC C2 C3 C4 C5 1.5340 112.76 -179.96 112.67 1.5346 +IC C5 C3 *C4 H41 1.5346 112.67 -121.47 108.80 1.1130 +IC H41 C3 *C4 H42 1.1130 108.80 -117.09 108.78 1.1130 +IC C3 C4 C5 C6 1.5346 112.67 179.84 112.66 1.5346 +IC C6 C4 *C5 H51 1.5346 112.66 -121.41 108.87 1.1131 +IC H51 C4 *C5 H52 1.1131 108.87 -117.14 108.89 1.1131 +IC C4 C5 C6 C7 1.5346 112.66 -179.93 112.63 1.5346 +IC C7 C5 *C6 H61 1.5346 112.63 -121.40 108.95 1.1131 +IC H61 C5 *C6 H62 1.1131 108.95 -117.23 108.93 1.1131 +IC C5 C6 C7 C8 1.5346 112.63 179.86 112.65 1.5346 +IC C8 C6 *C7 H71 1.5346 112.65 -121.36 108.97 1.1132 +IC H71 C6 *C7 H72 1.1132 108.97 -117.25 108.98 1.1132 +IC C6 C7 C8 C9 1.5346 112.65 -179.96 112.62 1.5346 +IC C9 C7 *C8 H81 1.5346 112.62 -121.36 109.02 1.1132 +IC H81 C7 *C8 H82 1.1132 109.02 -117.30 109.00 1.1132 +IC C7 C8 C9 C10 1.5346 112.62 179.91 112.64 1.5347 +IC C10 C8 *C9 H91 1.5347 112.64 -121.34 109.01 1.1132 +IC H91 C8 *C9 H92 1.1132 109.01 -117.30 109.02 1.1132 +IC C8 C9 C10 C11 1.5346 112.64 -179.97 112.68 1.5339 +IC C11 C9 *C10 H101 1.5339 112.68 -121.35 109.07 1.1132 +IC H101 C9 *C10 H102 1.1132 109.07 -117.32 109.06 1.1132 +IC C9 C10 C11 C12 1.5347 112.68 179.95 113.31 1.5309 +IC C12 C10 *C11 H111 1.5309 113.31 -121.69 108.71 1.1141 +IC H111 C10 *C11 H112 1.1141 108.71 -116.61 108.71 1.1141 +IC C10 C11 C12 H121 1.5339 113.31 -59.91 110.42 1.1113 +IC H121 C11 *C12 H122 1.1113 110.42 119.82 110.42 1.1113 +IC H121 C11 *C12 H123 1.1113 110.42 -120.09 110.61 1.1111 + + +RESI TPC 0.00 ! tetradeocylphosphorylcholine +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A--C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 ! H13A-C13---N---C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12-H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! H11A--C11-H11B +ATOM P PL 1.50 ! | alpha4 +ATOM O13 O2L -0.78 ! (-)O13 O12 +ATOM O14 O2L -0.78 ! \ | alpha3 +ATOM O11 OSLP -0.57 ! P(+) +ATOM O12 OSLP -0.57 ! / | alpha2 +ATOM C1 CTL2 -0.08 ! (-)O14 O11 +ATOM HA HAL2 0.09 ! | alpha1 +ATOM HB HAL2 0.09 ! HA---C1---HB +GROUP ! | theta1 +ATOM C2 CTL2 -0.18 ! HR---C2---HS +ATOM HS HAL2 0.09 ! | +ATOM HR HAL2 0.09 ! | +GROUP ! | +ATOM C3 CTL2 -0.18 ! HX---C3---HY +ATOM HX HAL2 0.09 ! | +ATOM HY HAL2 0.09 ! | +GROUP ! | +ATOM C31 CTL2 -0.18 ! H1X--C31--H1Y +ATOM H1X HAL2 0.09 ! | +ATOM H1Y HAL2 0.09 ! | +GROUP ! | +ATOM C32 CTL2 -0.18 ! H2X--C32--H2Y +ATOM H2X HAL2 0.09 ! | +ATOM H2Y HAL2 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X--C33--H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X--C34--H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X--C35--H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X--C36--H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X--C37--H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X--C38--H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X--C39--H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X-C310-H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL3 -0.27 ! H11X-C311-H11Y +ATOM H11X HAL3 0.09 ! | +ATOM H11Y HAL3 0.09 ! | +ATOM H11Z HAL3 0.09 ! H11Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 HR C2 C3 +BOND C3 HX C3 HY C3 C31 +! Chain +BOND C31 H1X C31 H1Y C31 C32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 H11Z + +! Polar head +IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1 +IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2 +IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0 +IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0 +IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3 +IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0 +IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0 +IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4 +IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0 +IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0 +IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5 +IC C11 C12 N C13 0.0 0.0 180.0 0.0 0.0 !alpha6 +IC C12 C13 *N C14 0.0 0.0 120.0 0.0 0.0 +IC C12 C13 *N C15 0.0 0.0 240.0 0.0 0.0 +! Glycerol +IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1 +IC C1 C2 C3 C31 0.0 0.0 180.0 0.0 0.0 !theta2 +! Chain +IC C2 C3 C31 C32 0.0 0.0 180.0 0.0 0.0 !theta3 +IC C3 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !theta4 +IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 +IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 +IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 +IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 +IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 +IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 +IC C37 C38 C39 C310 0.0 0.0 180.0 0.0 0.0 +IC C38 C39 C310 C311 0.0 0.0 180.0 0.0 0.0 + + +RESI DPC 0.00 ! dodecylphosphocholine +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A--C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 ! H13A-C13---N---C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12-H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! H11A--C11-H11B +ATOM P PL 1.50 ! | alpha4 +ATOM O13 O2L -0.78 ! (-)O13 O12 +ATOM O14 O2L -0.78 ! \ | alpha3 +ATOM O11 OSLP -0.57 ! P(+) +ATOM O12 OSLP -0.57 ! / | alpha2 +ATOM C1 CTL2 -0.08 ! (-)O14 O11 +ATOM HA HAL2 0.09 ! | alpha1 +ATOM HB HAL2 0.09 ! HA---C1---HB +GROUP ! | theta1 +ATOM C2 CTL2 -0.18 ! HR---C2---HS +ATOM HS HAL2 0.09 ! | +ATOM HR HAL2 0.09 ! | +GROUP ! | +ATOM C3 CTL2 -0.18 ! HX---C3---HY +ATOM HX HAL2 0.09 ! | +ATOM HY HAL2 0.09 ! | +GROUP ! | +ATOM C31 CTL2 -0.18 ! H1X--C31--H1Y +ATOM H1X HAL2 0.09 ! | +ATOM H1Y HAL2 0.09 ! | +GROUP ! | +ATOM C32 CTL2 -0.18 ! H2X--C32--H2Y +ATOM H2X HAL2 0.09 ! | +ATOM H2Y HAL2 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X--C33--H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X--C34--H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X--C35--H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X--C36--H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X--C37--H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X--C38--H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL3 -0.27 ! H9X--C39--H9Y +ATOM H9X HAL3 0.09 ! | +ATOM H9Y HAL3 0.09 ! | +ATOM H9Z HAL3 0.09 ! H9Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 HR C2 C3 +BOND C3 HX C3 HY C3 C31 +! Chain +BOND C31 H1X C31 H1Y C31 C32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 H9Z + +! Polar head +IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1 +IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2 +IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0 +IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0 +IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3 +IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0 +IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0 +IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4 +IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0 +IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0 +IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5 +IC C11 C12 N C13 0.0 0.0 180.0 0.0 0.0 !alpha6 +IC C12 C13 *N C14 0.0 0.0 120.0 0.0 0.0 +IC C12 C13 *N C15 0.0 0.0 240.0 0.0 0.0 +! Glycerol +IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1 +IC C1 C2 C3 C31 0.0 0.0 180.0 0.0 0.0 !theta2 +! Chain +IC C2 C3 C31 C32 0.0 0.0 180.0 0.0 0.0 !theta3 +IC C3 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !theta4 +IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 +IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 +IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 +IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 +IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 +IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 + + +RESI DHPC 0.00 ! 1,2-diheptanoyl-sn-glycero-3-phosphocholine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - N(CH3)3 +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL3 -0.27 ! | | +ATOM H7R HAL3 0.09 ! H7R ---C27---H7S +ATOM H7S HAL3 0.09 ! | | +ATOM H7T HAL3 0.09 ! H7T +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL3 -0.27 ! | +ATOM H7X HAL3 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL3 0.09 ! | +ATOM H7Z HAL3 0.09 ! H7Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 H7T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 H7Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 N C12 C11 1.4955 110.64 57.27 116.86 1.5415 +IC C15 N C12 C11 1.4976 109.72 180.00 116.86 1.5415 +IC C13 C12 *N C14 1.4955 110.64 -119.74 108.01 1.5030 +IC C13 C12 *N C15 1.4955 110.64 122.73 109.72 1.4976 +IC C12 N C13 H13A 1.5224 110.64 -177.67 111.18 1.0813 +IC H13A N *C13 H13B 1.0813 111.18 119.03 109.35 1.0870 +IC H13A N *C13 H13C 1.0813 111.18 -122.04 111.32 1.0813 +IC C12 N C14 H14A 1.5224 108.01 56.08 111.03 1.0952 +IC H14A N *C14 H14B 1.0952 111.03 123.93 113.88 1.0740 +IC H14A N *C14 H14C 1.0952 111.03 -112.36 110.24 1.0938 +IC C12 N C15 H15A 1.5224 109.72 176.74 110.89 1.0821 +IC H15A N *C15 H15B 1.0821 110.89 121.45 111.48 1.0812 +IC H15A N *C15 H15C 1.0821 110.89 -118.76 109.68 1.0875 +IC C11 N *C12 H12A 1.5415 116.86 -126.38 111.91 1.0785 +IC H12A N *C12 H12B 1.0785 111.91 -116.30 108.18 1.0972 +IC N C12 C11 O12 1.5224 116.86 127.42 108.31 1.4234 +IC O12 C12 *C11 H11A 1.4234 108.31 -123.13 113.24 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.24 -118.65 109.16 1.1130 +IC C12 C11 O12 P 1.5415 108.31 -67.88 118.40 1.5875 +IC C11 O12 P O11 1.4234 118.40 -166.94 104.13 1.5782 +IC O11 O12 *P O13 1.5782 104.13 117.91 108.15 1.4793 +IC O11 O12 *P O14 1.5782 104.13 -117.27 106.75 1.4823 +IC O12 P O11 C1 1.5875 104.13 177.32 118.17 1.4318 +IC P O11 C1 C2 1.5782 118.17 167.65 110.87 1.5511 +IC C2 O11 *C1 HA 1.5511 110.87 -119.11 111.42 1.1172 +IC HA O11 *C1 HB 1.1172 111.42 -120.82 110.01 1.1145 +IC O11 C1 C2 C3 1.4318 110.87 177.69 110.63 1.5578 +IC C3 C1 *C2 O21 1.5578 110.63 120.78 108.07 1.4415 !defines S chirality +IC C3 C1 *C2 HS 1.5578 110.63 -118.30 106.69 1.1168 !defines S chirality +IC C1 C2 O21 C21 1.5511 108.07 147.89 115.06 1.3179 +IC C2 O21 C21 C22 1.4415 115.06 179.61 108.77 1.5289 +IC C22 O21 *C21 O22 1.5289 108.77 -179.08 126.52 1.2183 +IC O21 C21 C22 C23 1.3179 108.77 -173.00 112.01 1.5450 +IC C23 C21 *C22 H2R 1.5450 112.01 -121.50 107.73 1.1091 +IC H2R C21 *C22 H2S 1.1091 107.73 -117.24 107.85 1.1091 +IC C1 C2 C3 O31 1.5511 110.63 175.48 112.70 1.4436 +IC O31 C2 *C3 HX 1.4436 112.70 -118.48 106.61 1.1129 +IC HX C2 *C3 HY 1.1129 106.61 -115.12 109.44 1.1145 +IC C2 C3 O31 C31 1.5578 112.70 87.10 115.14 1.3313 +IC C3 O31 C31 C32 1.4436 115.14 -172.45 108.40 1.5287 +IC C32 O31 *C31 O32 1.5287 108.40 -178.98 125.63 1.2169 +IC O31 C31 C32 C33 1.3313 108.40 -169.89 113.40 1.5448 +IC C33 C31 *C32 H2X 1.5448 113.40 -121.09 107.19 1.1104 +IC H2X C31 *C32 H2Y 1.1104 107.19 -116.85 108.01 1.1089 +IC C21 C22 C23 C24 1.5289 112.01 177.45 112.54 1.5336 +IC C24 C22 *C23 H3R 1.5336 112.54 -120.79 109.48 1.1146 +IC H3R C22 *C23 H3S 1.1146 109.48 -117.62 109.70 1.1144 +IC C22 C23 C24 C25 1.5450 112.54 -177.78 112.24 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.24 -121.51 109.37 1.1130 +IC H4R C23 *C24 H4S 1.1130 109.37 -117.64 109.09 1.1133 +IC C23 C24 C25 C26 1.5336 112.24 178.33 112.83 1.5342 +IC C26 C24 *C25 H5R 1.5342 112.83 -121.07 108.90 1.1136 +IC H5R C24 *C25 H5S 1.1136 108.90 -117.22 109.21 1.1132 +IC C24 C25 C26 C27 1.5346 112.83 -177.92 112.39 1.5344 +IC C27 C25 *C26 H6R 1.5344 112.39 -121.57 109.28 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.28 -117.51 109.01 1.1133 +IC C25 C26 C27 H7R 1.5342 112.39 178.43 112.74 1.5342 +IC H7R C26 *C27 H7S 1.1113 110.43 119.85 110.46 1.1113 +IC H7R C26 *C27 H7T 1.1113 110.43 -120.04 110.62 1.1112 +IC C31 C32 C33 C34 1.5287 113.40 179.64 111.32 1.5341 +IC C34 C32 *C33 H3X 1.5341 111.32 -120.86 109.71 1.1137 +IC H3X C32 *C33 H3Y 1.1137 109.71 -118.09 109.81 1.1143 +IC C32 C33 C34 C35 1.5448 111.32 -176.82 113.37 1.5345 +IC C35 C33 *C34 H4X 1.5345 113.37 -121.80 109.05 1.1135 +IC H4X C33 *C34 H4Y 1.1135 109.05 -117.12 108.83 1.1136 +IC C33 C34 C35 C36 1.5341 113.37 178.26 111.94 1.5348 +IC C36 C34 *C35 H5X 1.5348 111.94 -120.83 109.02 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.02 -117.61 109.44 1.1129 +IC C34 C35 C36 C37 1.5346 112.68 179.81 113.29 1.5308 +IC C37 C35 *C36 H6X 1.5308 113.29 -121.66 108.73 1.1141 +IC H6X C35 *C36 H6Y 1.1141 108.73 -116.66 108.73 1.1141 +IC C35 C36 C37 H7X 1.5336 113.29 -59.97 110.46 1.1113 +IC H7X C36 *C37 H7Y 1.1113 110.46 119.87 110.46 1.1113 +IC H7X C36 *C37 H7Z 1.1113 110.46 -120.06 110.59 1.1112 + + +RESI LMPG -1.00 ! 2,3 dilauroyl-D-glycero-1-Phosphatidylglycerol +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.14 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OHL -0.65 ! O21 theta3 +ATOM H21 HOL 0.42 ! | beta2 | +GROUP ! H21 beta4 | +ATOM C3 CTL2 0.08 ! | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | +GROUP ! | gamma4 +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +BOND O21 H21 +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5571 112.39 -88.77 119.48 1.5876 +IC C11 O12 P O11 1.4344 119.48 -61.43 101.30 1.5863 +IC O11 O12 *P O13 1.5863 101.30 -115.24 108.56 1.4777 +IC O11 O12 *P O14 1.5863 101.30 114.96 107.76 1.4796 +IC O12 P O11 C1 1.5876 101.30 -76.29 119.38 1.4327 +IC P O11 C1 C2 1.5863 119.38 -98.06 111.23 1.5544 +IC C2 O11 *C1 HA 1.5544 111.23 -119.43 109.09 1.1120 +IC HA O11 *C1 HB 1.1120 109.09 -117.62 112.27 1.1163 +IC O11 C1 C2 C3 1.4327 111.23 155.08 111.33 1.5580 +IC C3 C1 *C2 O21 1.5580 111.33 121.74 107.47 1.4417 +IC C3 C1 *C2 HS 1.5580 111.33 -118.17 107.50 1.1176 +IC C1 C2 O21 H21 1.5544 107.47 164.23 115.49 1.3176 +IC C1 C2 C3 O31 1.5511 110.63 175.48 112.70 1.4436 +IC O31 C2 *C3 HX 1.4436 112.70 -118.48 106.61 1.1129 +IC HX C2 *C3 HY 1.1129 106.61 -115.12 109.44 1.1145 +IC C2 C3 O31 C31 1.5578 112.70 87.10 115.14 1.3313 +IC C3 O31 C31 C32 1.4436 115.14 -172.45 108.40 1.5287 +IC C32 O31 *C31 O32 1.5287 108.40 -178.98 125.63 1.2169 +IC O31 C31 C32 C33 1.3313 108.40 -169.89 113.40 1.5448 +IC C33 C31 *C32 H2X 1.5448 113.40 -121.09 107.19 1.1104 +IC H2X C31 *C32 H2Y 1.1104 107.19 -116.85 108.01 1.1089 +IC C31 C32 C33 C34 1.5287 113.40 179.64 111.32 1.5341 +IC C34 C32 *C33 H3X 1.5341 111.32 -120.86 109.71 1.1137 +IC H3X C32 *C33 H3Y 1.1137 109.71 -118.09 109.81 1.1143 +IC C32 C33 C34 C35 1.5448 111.32 -176.82 113.37 1.5345 +IC C35 C33 *C34 H4X 1.5345 113.37 -121.80 109.05 1.1135 +IC H4X C33 *C34 H4Y 1.1135 109.05 -117.12 108.83 1.1136 +IC C33 C34 C35 C36 1.5341 113.37 178.26 111.94 1.5348 +IC C36 C34 *C35 H5X 1.5348 111.94 -120.83 109.02 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.02 -117.61 109.44 1.1129 +IC C34 C35 C36 C37 1.5345 111.94 -176.79 113.19 1.5342 +IC C37 C35 *C36 H6X 1.5342 113.19 -121.90 109.15 1.1132 +IC H6X C35 *C36 H6Y 1.1132 109.15 -117.14 108.76 1.1136 +IC C35 C36 C37 C38 1.5348 113.19 177.72 112.13 1.5346 +IC C38 C36 *C37 H7X 1.5346 112.13 -120.80 109.00 1.1133 +IC H7X C36 *C37 H7Y 1.1133 109.00 -117.59 109.40 1.1128 +IC C36 C37 C38 C39 1.5342 112.13 -177.62 112.99 1.5342 +IC C39 C37 *C38 H8X 1.5342 112.99 -121.75 109.20 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.20 -117.24 108.86 1.1136 +IC C37 C38 C39 C310 1.5346 112.99 178.21 112.22 1.5344 +IC C310 C38 *C39 H9X 1.5344 112.22 -120.97 109.07 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.07 -117.54 109.30 1.1130 +IC C38 C39 C310 C311 1.5342 112.22 -178.81 112.83 1.5339 +IC C311 C39 *C310 H10X 1.5339 112.83 -121.55 109.12 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.12 -117.29 108.97 1.1134 +IC C39 C310 C311 C312 1.5344 112.83 179.12 112.41 1.5346 +IC C312 C310 *C311 H11X 1.5346 112.41 -121.13 109.11 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.11 -117.49 109.19 1.1130 +IC C310 C311 C312 C313 1.5339 112.41 -179.72 112.68 1.5336 +IC C313 C311 *C312 H12X 1.5336 112.68 -121.39 109.14 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.14 -117.34 109.09 1.1133 +IC C311 C312 C313 C314 1.5346 112.68 179.81 113.29 1.5308 +IC C314 C312 *C313 H13X 1.5308 113.29 -121.66 108.73 1.1141 +IC H13X C312 *C313 H13Y 1.1141 108.73 -116.66 108.73 1.1141 +IC C312 C313 C314 H14X 1.5336 113.29 -59.97 110.46 1.1113 +IC H14X C313 *C314 H14Y 1.1113 110.46 119.87 110.46 1.1113 +IC H14X C313 *C314 H14Z 1.1113 110.46 -120.06 110.59 1.1112 + + +RESI ADDG 0.000 ! dodecyl-alpha-D-glucoside +! +GROU ! AGLC +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.140 +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC311 -0.650 +ATOM 2HO4 HCP1 0.420 +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL2 -0.18 ! +ATOM 3H10P1 HAL2 0.09 ! +ATOM 3H10P2 HAL2 0.09 ! +GROUP +ATOM 3C11P CTL2 -0.18 ! +ATOM 3H11P1 HAL2 0.09 ! +ATOM 3H11P2 HAL2 0.09 ! +GROUP +ATOM 3C12P CTL3 -0.27 ! +ATOM 3H12P1 HAL3 0.09 ! +ATOM 3H12P2 HAL3 0.09 ! +ATOM 3H12P3 HAL3 0.09 ! +BOND 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 +BOND 2C3 2H3 2C3 2O3 2O3 2HO3 2C3 2C4 +BOND 2C4 2H4 2C4 2O4 2O4 2HO4 2C4 2C5 +BOND 2C5 2H5 2C5 2O5 2C5 2C6 +BOND 2C6 2H61 2C6 2H62 2C6 2O6 2O6 2HO6 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C10P 3C11P 3C11P 3C12P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 +BOND 3C11P 3H11P1 3C11P 3H11P2 +BOND 3C12P 3H12P1 3C12P 3H12P2 3C12P 3H12P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 2O1 2C2 *2C1 2H1 1.4077 108.33 -123.34 103.67 1.1200 +IC 2O1 2O5 *2C1 2C2 1.4077 108.39 -119.83 112.62 1.5516 +IC 2O2 2C3 *2C2 2H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 2O2 2C1 *2C2 2C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 2O3 2C4 *2C3 2H3 1.4122 110.86 120.36 107.49 1.1219 +IC 2O3 2C2 *2C3 2C4 1.4122 109.00 121.20 109.13 1.5315 +IC 2O4 2C5 *2C4 2H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 2O4 2C3 *2C4 2C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 2C6 2O5 *2C5 2H5 1.4718 112.19 113.05 108.36 1.1212 +IC 2C6 2C4 *2C5 2O5 1.4718 112.04 128.71 113.93 1.4175 +IC 2O6 2H62 *2C6 2H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 2O6 2C5 *2C6 2H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 2O5 2C1 2C2 2C3 1.4351 112.62 51.83 113.63 1.4880 +IC 2C1 2C2 2C3 2C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 2C2 2C3 2C4 2C5 1.4880 109.13 47.85 114.40 1.5087 +IC 2C3 2C4 2C5 2O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 2C4 2C5 2O5 2C1 1.5087 113.93 51.43 114.13 1.4351 +IC 2C5 2O5 2C1 2C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 2C4 2C5 2C6 2O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 2O5 2C1 2O1 2HO1 1.4351 108.39 47.62 101.41 0.9789 +IC 2C1 2C2 2O2 2HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 2C2 2C3 2O3 2HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC 2C3 2C4 2O4 2HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 2C5 2C6 2O6 2HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C11P 3C9P *3C10P 3H10P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C11P 3C9P *3C10P 3H10P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C12P 3C10P *3C11P 3H11P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C12P 3C10P *3C11P 3H11P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C11P 3C12P 3H12P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H12P1 3C11P *3C12P 3H12P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H12P1 3C11P *3C12P 3H12P3 1.0625 108.61 126.50 111.01 1.1613 + +PATC FIRS NONE LAST NONE + + +RESI BDDG 0.000 ! dodecyl-beta-D-glucoside +! +GROU ! BGLC +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.140 +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC311 -0.650 +ATOM 2HO4 HCP1 0.420 +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +! +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL2 -0.18 ! +ATOM 3H10P1 HAL2 0.09 ! +ATOM 3H10P2 HAL2 0.09 ! +GROUP +ATOM 3C11P CTL2 -0.18 ! +ATOM 3H11P1 HAL2 0.09 ! +ATOM 3H11P2 HAL2 0.09 ! +GROUP +ATOM 3C12P CTL3 -0.27 ! +ATOM 3H12P1 HAL3 0.09 ! +ATOM 3H12P2 HAL3 0.09 ! +ATOM 3H12P3 HAL3 0.09 ! +! +BOND 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 +BOND 2C3 2H3 2C3 2O3 2O3 2HO3 2C3 2C4 +BOND 2C4 2H4 2C4 2O4 2O4 2HO4 2C4 2C5 +BOND 2C5 2H5 2C5 2O5 2C5 2C6 +BOND 2C6 2H61 2C6 2H62 2C6 2O6 2O6 2HO6 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C10P 3C11P 3C11P 3C12P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 +BOND 3C11P 3H11P1 3C11P 3H11P2 +BOND 3C12P 3H12P1 3C12P 3H12P2 3C12P 3H12P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 2O1 2C2 *2C1 2H1 1.3899 110.90 120.10 104.58 1.0836 +IC 2O1 2O5 *2C1 2C2 1.3899 108.62 122.10 110.88 1.5316 +IC 2O2 2C3 *2C2 2H2 1.4594 108.12 -118.78 111.06 1.1375 +IC 2O2 2C1 *2C2 2C3 1.4594 115.65 -125.60 113.28 1.4983 +IC 2O3 2C4 *2C3 2H3 1.4071 113.48 122.06 103.39 1.0895 +IC 2O3 2C2 *2C3 2C4 1.4071 108.48 124.18 109.26 1.5497 +IC 2O4 2C5 *2C4 2H4 1.3940 111.12 -110.35 108.66 1.0857 +IC 2O4 2C3 *2C4 2C5 1.3940 112.77 -129.39 115.62 1.5530 +IC 2C6 2O5 *2C5 2H5 1.5597 111.17 120.85 110.98 1.1092 +IC 2C6 2C4 *2C5 2O5 1.5597 109.90 122.92 110.30 1.4512 +IC 2O6 2H62 *2C6 2H61 1.4589 116.11 -112.93 103.57 1.1467 +IC 2O6 2C5 *2C6 2H62 1.4589 109.41 -135.95 118.22 1.0853 +IC 2O5 2C1 2C2 2C3 1.4620 110.88 57.82 113.28 1.4983 +IC 2C1 2C2 2C3 2C4 1.5316 113.28 -48.40 109.26 1.5497 +IC 2C2 2C3 2C4 2C5 1.4983 109.26 45.07 115.62 1.5530 +IC 2C3 2C4 2C5 2O5 1.5497 115.62 -49.19 110.30 1.4512 +IC 2C4 2C5 2O5 2C1 1.5530 110.30 56.36 112.12 1.4620 +IC 2C5 2O5 2C1 2C2 1.4512 112.12 -61.39 110.88 1.5316 +IC 2C4 2C5 2C6 2O6 1.5530 109.90 -177.46 109.41 1.4589 +IC 2O5 2C1 2O1 2HO1 1.4620 108.62 72.25 106.48 0.9328 +IC 2C1 2C2 2O2 2HO2 1.5316 115.65 135.41 116.81 0.9527 +IC 2C2 2C3 2O3 2HO3 1.4983 108.48 -71.46 120.86 0.9441 +IC 2C3 2C4 2O4 2HO4 1.5497 112.77 47.45 109.31 0.9911 +IC 2C5 2C6 2O6 2HO6 1.5597 109.41 -54.60 118.82 0.95210 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C11P 3C9P *3C10P 3H10P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C11P 3C9P *3C10P 3H10P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C12P 3C10P *3C11P 3H11P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C12P 3C10P *3C11P 3H11P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C11P 3C12P 3H12P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H12P1 3C11P *3C12P 3H12P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H12P1 3C11P *3C12P 3H12P3 1.0625 108.61 126.50 111.01 1.1613 + +PATC FIRS NONE LAST NONE + + +RESI ADG 0.000 ! decyl-alpha-D-glucoside +! +GROU ! AGLC +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.140 +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC311 -0.650 +ATOM 2HO4 HCP1 0.420 +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL3 -0.27 ! +ATOM 3H10P1 HAL3 0.09 ! +ATOM 3H10P2 HAL3 0.09 ! +ATOM 3H10P3 HAL3 0.09 ! +BOND 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 +BOND 2C3 2H3 2C3 2O3 2O3 2HO3 2C3 2C4 +BOND 2C4 2H4 2C4 2O4 2O4 2HO4 2C4 2C5 +BOND 2C5 2H5 2C5 2O5 2C5 2C6 +BOND 2C6 2H61 2C6 2H62 2C6 2O6 2O6 2HO6 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 3C10P 3H10P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 2O1 2C2 *2C1 2H1 1.4077 108.33 -123.34 103.67 1.1200 +IC 2O1 2O5 *2C1 2C2 1.4077 108.39 -119.83 112.62 1.5516 +IC 2O2 2C3 *2C2 2H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 2O2 2C1 *2C2 2C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 2O3 2C4 *2C3 2H3 1.4122 110.86 120.36 107.49 1.1219 +IC 2O3 2C2 *2C3 2C4 1.4122 109.00 121.20 109.13 1.5315 +IC 2O4 2C5 *2C4 2H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 2O4 2C3 *2C4 2C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 2C6 2O5 *2C5 2H5 1.4718 112.19 113.05 108.36 1.1212 +IC 2C6 2C4 *2C5 2O5 1.4718 112.04 128.71 113.93 1.4175 +IC 2O6 2H62 *2C6 2H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 2O6 2C5 *2C6 2H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 2O5 2C1 2C2 2C3 1.4351 112.62 51.83 113.63 1.4880 +IC 2C1 2C2 2C3 2C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 2C2 2C3 2C4 2C5 1.4880 109.13 47.85 114.40 1.5087 +IC 2C3 2C4 2C5 2O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 2C4 2C5 2O5 2C1 1.5087 113.93 51.43 114.13 1.4351 +IC 2C5 2O5 2C1 2C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 2C4 2C5 2C6 2O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 2O5 2C1 2O1 2HO1 1.4351 108.39 47.62 101.41 0.9789 +IC 2C1 2C2 2O2 2HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 2C2 2C3 2O3 2HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC 2C3 2C4 2O4 2HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 2C5 2C6 2O6 2HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C8P 3C9P 3C10P 3H10P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H10P1 3C9P *3C10P 3H10P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H10P1 3C9P *3C10P 3H10P3 1.0625 108.61 126.50 111.01 1.1613 + +PATC FIRS NONE LAST NONE + + +RESI BDG 0.000 ! decyl-beta-D-glucoside +! +GROU ! BGLC +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.140 +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC311 -0.650 +ATOM 2HO4 HCP1 0.420 +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +! +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL3 -0.27 ! +ATOM 3H10P1 HAL3 0.09 ! +ATOM 3H10P2 HAL3 0.09 ! +ATOM 3H10P3 HAL3 0.09 ! +! +BOND 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 +BOND 2C3 2H3 2C3 2O3 2O3 2HO3 2C3 2C4 +BOND 2C4 2H4 2C4 2O4 2O4 2HO4 2C4 2C5 +BOND 2C5 2H5 2C5 2O5 2C5 2C6 +BOND 2C6 2H61 2C6 2H62 2C6 2O6 2O6 2HO6 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 3C10P 3H10P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 2O1 2C2 *2C1 2H1 1.3899 110.90 120.10 104.58 1.0836 +IC 2O1 2O5 *2C1 2C2 1.3899 108.62 122.10 110.88 1.5316 +IC 2O2 2C3 *2C2 2H2 1.4594 108.12 -118.78 111.06 1.1375 +IC 2O2 2C1 *2C2 2C3 1.4594 115.65 -125.60 113.28 1.4983 +IC 2O3 2C4 *2C3 2H3 1.4071 113.48 122.06 103.39 1.0895 +IC 2O3 2C2 *2C3 2C4 1.4071 108.48 124.18 109.26 1.5497 +IC 2O4 2C5 *2C4 2H4 1.3940 111.12 -110.35 108.66 1.0857 +IC 2O4 2C3 *2C4 2C5 1.3940 112.77 -129.39 115.62 1.5530 +IC 2C6 2O5 *2C5 2H5 1.5597 111.17 120.85 110.98 1.1092 +IC 2C6 2C4 *2C5 2O5 1.5597 109.90 122.92 110.30 1.4512 +IC 2O6 2H62 *2C6 2H61 1.4589 116.11 -112.93 103.57 1.1467 +IC 2O6 2C5 *2C6 2H62 1.4589 109.41 -135.95 118.22 1.0853 +IC 2O5 2C1 2C2 2C3 1.4620 110.88 57.82 113.28 1.4983 +IC 2C1 2C2 2C3 2C4 1.5316 113.28 -48.40 109.26 1.5497 +IC 2C2 2C3 2C4 2C5 1.4983 109.26 45.07 115.62 1.5530 +IC 2C3 2C4 2C5 2O5 1.5497 115.62 -49.19 110.30 1.4512 +IC 2C4 2C5 2O5 2C1 1.5530 110.30 56.36 112.12 1.4620 +IC 2C5 2O5 2C1 2C2 1.4512 112.12 -61.39 110.88 1.5316 +IC 2C4 2C5 2C6 2O6 1.5530 109.90 -177.46 109.41 1.4589 +IC 2O5 2C1 2O1 2HO1 1.4620 108.62 72.25 106.48 0.9328 +IC 2C1 2C2 2O2 2HO2 1.5316 115.65 135.41 116.81 0.9527 +IC 2C2 2C3 2O3 2HO3 1.4983 108.48 -71.46 120.86 0.9441 +IC 2C3 2C4 2O4 2HO4 1.5497 112.77 47.45 109.31 0.9911 +IC 2C5 2C6 2O6 2HO6 1.5597 109.41 -54.60 118.82 0.95210 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C8P 3C9P 3C10P 3H10P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H10P1 3C9P *3C10P 3H10P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H10P1 3C9P *3C10P 3H10P3 1.0625 108.61 126.50 111.01 1.1613 + +PATC FIRS NONE LAST NONE + + +RESI ADDM 0.000 ! dodecyl-alpha-D-maltoside +! +GROU ! +ATOM 1C1 CC3162 0.290 ! AGLC 4C1 alpha-D-glucose +ATOM 1H1 HCA1 0.090 ! +ATOM 1C5 CC3163 0.110 ! +ATOM 1H5 HCA1 0.090 ! +ATOM 1O5 OC3C61 -0.400 ! +GROU ! +ATOM 1C2 CC3161 0.140 ! +ATOM 1H2 HCA1 0.090 ! +ATOM 1O2 OC311 -0.650 ! +ATOM 1HO2 HCP1 0.420 ! +GROU ! +ATOM 1C3 CC3161 0.140 ! +ATOM 1H3 HCA1 0.090 ! +ATOM 1O3 OC311 -0.650 ! +ATOM 1HO3 HCP1 0.420 ! +GROU +ATOM 1C4 CC3161 0.140 +ATOM 1H4 HCA1 0.090 +ATOM 1O4 OC311 -0.650 +ATOM 1HO4 HCP1 0.420 +GROU +ATOM 1C6 CC321 0.050 +ATOM 1H61 HCA2 0.090 +ATOM 1H62 HCA2 0.090 +ATOM 1O6 OC311 -0.650 +ATOM 1HO6 HCP1 0.420 +GROU ! AGLC +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.090 ! +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC301 -0.360 ! +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL2 -0.18 ! +ATOM 3H10P1 HAL2 0.09 ! +ATOM 3H10P2 HAL2 0.09 ! +GROUP +ATOM 3C11P CTL2 -0.18 ! +ATOM 3H11P1 HAL2 0.09 ! +ATOM 3H11P2 HAL2 0.09 ! +GROUP +ATOM 3C12P CTL3 -0.27 ! +ATOM 3H12P1 HAL3 0.09 ! +ATOM 3H12P2 HAL3 0.09 ! +ATOM 3H12P3 HAL3 0.09 ! +BOND 1C1 1H1 1C1 1O5 1C1 1C2 +BOND 1C2 1H2 1C2 1O2 1O2 1HO2 1C2 1C3 1C3 1H3 +BOND 1C3 1O3 1O3 1HO3 1C3 1C4 1C4 1H4 1C4 1O4 +BOND 1O4 1HO4 1C4 1C5 1C5 1H5 1C5 1C6 1C6 1H61 +BOND 1C6 1H62 1C6 1O6 1O6 1HO6 1C5 1O5 +BOND 2O4 1C1 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 2C3 2H3 +BOND 2C3 2O3 2O3 2HO3 2C3 2C4 2C4 2H4 2C4 2O4 +BOND 2C4 2C5 2C5 2H5 2C5 2C6 2C6 2H61 +BOND 2C6 2H62 2C6 2O6 2O6 2HO6 2C5 2O5 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C10P 3C11P 3C11P 3C12P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 +BOND 3C11P 3H11P1 3C11P 3H11P2 +BOND 3C12P 3H12P1 3C12P 3H12P2 3C12P 3H12P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O2 1C3 *1C2 1H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 1O2 1C1 *1C2 1C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 1O3 1C4 *1C3 1H3 1.4122 110.86 120.36 107.49 1.1219 +IC 1O3 1C2 *1C3 1C4 1.4122 109.00 121.20 109.13 1.5315 +IC 1O4 1C5 *1C4 1H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 1O4 1C3 *1C4 1C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 1C6 1O5 *1C5 1H5 1.4718 112.19 113.05 108.36 1.1212 +IC 1C6 1C4 *1C5 1O5 1.4718 112.04 128.71 113.93 1.4175 +IC 1O6 1H62 *1C6 1H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 1O6 1C5 *1C6 1H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 1O5 1C1 1C2 1C3 1.4351 112.62 51.83 113.63 1.4880 +IC 1C1 1C2 1C3 1C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 1C2 1C3 1C4 1C5 1.4880 109.13 47.85 114.40 1.5087 +IC 1C3 1C4 1C5 1O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 1C4 1C5 1O5 1C1 1.5087 113.93 51.43 114.13 1.4351 +IC 1C5 1O5 1C1 1C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 1C4 1C5 1C6 1O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 1C1 1C2 1O2 1HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 1C2 1C3 1O3 1HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC 1C3 1C4 1O4 1HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 1C5 1C6 1O6 1HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2C3 2C4 2O4 1C1 1.5010 117.73 72.71 118.66 1.4036 ! psi +IC 2C4 2O4 1C1 1O5 1.4919 118.66 48.64 109.48 1.4570 ! phi +IC 1O5 2O4 *1C1 1C2 1.4570 109.48 124.57 110.72 1.5065 +IC 1O5 2O4 *1C1 1H1 1.4570 109.48 -116.61 107.55 1.1057 +IC 2O1 2C2 *2C1 2H1 1.4077 108.33 -123.34 103.67 1.1200 +IC 2O1 2O5 *2C1 2C2 1.4077 108.39 -119.83 112.62 1.5516 +IC 2O2 2C3 *2C2 2H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 2O2 2C1 *2C2 2C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 2O3 2C4 *2C3 2H3 1.4122 110.86 120.36 107.49 1.1219 +IC 2O3 2C2 *2C3 2C4 1.4122 109.00 121.20 109.13 1.5315 +IC 2O4 2C5 *2C4 2H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 2O4 2C3 *2C4 2C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 2C6 2O5 *2C5 2H5 1.4718 112.19 113.05 108.36 1.1212 +IC 2C6 2C4 *2C5 2O5 1.4718 112.04 128.71 113.93 1.4175 +IC 2O6 2H62 *2C6 2H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 2O6 2C5 *2C6 2H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 2O5 2C1 2C2 2C3 1.4351 112.62 51.83 113.63 1.4880 +IC 2C1 2C2 2C3 2C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 2C2 2C3 2C4 2C5 1.4880 109.13 47.85 114.40 1.5087 +IC 2C3 2C4 2C5 2O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 2C4 2C5 2O5 2C1 1.5087 113.93 51.43 114.13 1.4351 +IC 2C5 2O5 2C1 2C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 2C4 2C5 2C6 2O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 2O5 2C1 2O1 2HO1 1.4351 108.39 47.62 101.41 0.9789 +IC 2C1 2C2 2O2 2HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 2C2 2C3 2O3 2HO3 1.4880 109.00 -28.48 103.99 0.9971 +!IC 2C3 2C4 2O4 2HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 2C5 2C6 2O6 2HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C11P 3C9P *3C10P 3H10P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C11P 3C9P *3C10P 3H10P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C12P 3C10P *3C11P 3H11P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C12P 3C10P *3C11P 3H11P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C11P 3C12P 3H12P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H12P1 3C11P *3C12P 3H12P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H12P1 3C11P *3C12P 3H12P3 1.0625 108.61 126.50 111.01 1.1613 + +PATC FIRS NONE LAST NONE + + +RESI BDDM 0.000 ! dodecyl-beta-D-maltoside +! +GROU ! +ATOM 1C1 CC3162 0.290 ! AGLC 4C1 alpha-D-glucose +ATOM 1H1 HCA1 0.090 ! +ATOM 1C5 CC3163 0.110 ! +ATOM 1H5 HCA1 0.090 ! +ATOM 1O5 OC3C61 -0.400 ! +GROU ! +ATOM 1C2 CC3161 0.140 ! +ATOM 1H2 HCA1 0.090 ! +ATOM 1O2 OC311 -0.650 ! +ATOM 1HO2 HCP1 0.420 ! +GROU ! +ATOM 1C3 CC3161 0.140 ! +ATOM 1H3 HCA1 0.090 ! +ATOM 1O3 OC311 -0.650 ! +ATOM 1HO3 HCP1 0.420 ! +GROU +ATOM 1C4 CC3161 0.140 +ATOM 1H4 HCA1 0.090 +ATOM 1O4 OC311 -0.650 +ATOM 1HO4 HCP1 0.420 +GROU +ATOM 1C6 CC321 0.050 +ATOM 1H61 HCA2 0.090 +ATOM 1H62 HCA2 0.090 +ATOM 1O6 OC311 -0.650 +ATOM 1HO6 HCP1 0.420 +! ! +GROU ! BGLC +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.090 ! +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC301 -0.360 ! +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +! +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL2 -0.18 ! +ATOM 3H10P1 HAL2 0.09 ! +ATOM 3H10P2 HAL2 0.09 ! +GROUP +ATOM 3C11P CTL2 -0.18 ! +ATOM 3H11P1 HAL2 0.09 ! +ATOM 3H11P2 HAL2 0.09 ! +GROUP +ATOM 3C12P CTL3 -0.27 ! +ATOM 3H12P1 HAL3 0.09 ! +ATOM 3H12P2 HAL3 0.09 ! +ATOM 3H12P3 HAL3 0.09 ! +! +BOND 1C1 1H1 1C1 1O5 1C1 1C2 +BOND 1C2 1H2 1C2 1O2 1O2 1HO2 1C2 1C3 1C3 1H3 +BOND 1C3 1O3 1O3 1HO3 1C3 1C4 1C4 1H4 1C4 1O4 +BOND 1O4 1HO4 1C4 1C5 1C5 1H5 1C5 1C6 1C6 1H61 +BOND 1C6 1H62 1C6 1O6 1O6 1HO6 1C5 1O5 +BOND 2O4 1C1 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 2C3 2H3 +BOND 2C3 2O3 2O3 2HO3 2C3 2C4 2C4 2H4 2C4 2O4 +BOND 2C4 2C5 2C5 2H5 2C5 2C6 2C6 2H61 +BOND 2C6 2H62 2C6 2O6 2O6 2HO6 2C5 2O5 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C10P 3C11P 3C11P 3C12P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 +BOND 3C11P 3H11P1 3C11P 3H11P2 +BOND 3C12P 3H12P1 3C12P 3H12P2 3C12P 3H12P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O2 1C3 *1C2 1H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 1O2 1C1 *1C2 1C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 1O3 1C4 *1C3 1H3 1.4122 110.86 120.36 107.49 1.1219 +IC 1O3 1C2 *1C3 1C4 1.4122 109.00 121.20 109.13 1.5315 +IC 1O4 1C5 *1C4 1H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 1O4 1C3 *1C4 1C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 1C6 1O5 *1C5 1H5 1.4718 112.19 113.05 108.36 1.1212 +IC 1C6 1C4 *1C5 1O5 1.4718 112.04 128.71 113.93 1.4175 +IC 1O6 1H62 *1C6 1H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 1O6 1C5 *1C6 1H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 1O5 1C1 1C2 1C3 1.4351 112.62 51.83 113.63 1.4880 +IC 1C1 1C2 1C3 1C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 1C2 1C3 1C4 1C5 1.4880 109.13 47.85 114.40 1.5087 +IC 1C3 1C4 1C5 1O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 1C4 1C5 1O5 1C1 1.5087 113.93 51.43 114.13 1.4351 +IC 1C5 1O5 1C1 1C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 1C4 1C5 1C6 1O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 1C1 1C2 1O2 1HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 1C2 1C3 1O3 1HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC 1C3 1C4 1O4 1HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 1C5 1C6 1O6 1HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2C3 2C4 2O4 1C1 1.5010 117.73 72.71 118.66 1.4036 ! psi +IC 2C4 2O4 1C1 1O5 1.4919 118.66 48.64 109.48 1.4570 ! phi +IC 1O5 2O4 *1C1 1C2 1.4570 109.48 124.57 110.72 1.5065 +IC 1O5 2O4 *1C1 1H1 1.4570 109.48 -116.61 107.55 1.1057 +IC 2O1 2C2 *2C1 2H1 1.3899 110.90 120.10 104.58 1.0836 +IC 2O1 2O5 *2C1 2C2 1.3899 108.62 122.10 110.88 1.5316 +IC 2O2 2C3 *2C2 2H2 1.4594 108.12 -118.78 111.06 1.1375 +IC 2O2 2C1 *2C2 2C3 1.4594 115.65 -125.60 113.28 1.4983 +IC 2O3 2C4 *2C3 2H3 1.4071 113.48 122.06 103.39 1.0895 +IC 2O3 2C2 *2C3 2C4 1.4071 108.48 124.18 109.26 1.5497 +IC 2O4 2C5 *2C4 2H4 1.3940 111.12 -110.35 108.66 1.0857 +IC 2O4 2C3 *2C4 2C5 1.3940 112.77 -129.39 115.62 1.5530 +IC 2C6 2O5 *2C5 2H5 1.5597 111.17 120.85 110.98 1.1092 +IC 2C6 2C4 *2C5 2O5 1.5597 109.90 122.92 110.30 1.4512 +IC 2O6 2H62 *2C6 2H61 1.4589 116.11 -112.93 103.57 1.1467 +IC 2O6 2C5 *2C6 2H62 1.4589 109.41 -135.95 118.22 1.0853 +IC 2O5 2C1 2C2 2C3 1.4620 110.88 57.82 113.28 1.4983 +IC 2C1 2C2 2C3 2C4 1.5316 113.28 -48.40 109.26 1.5497 +IC 2C2 2C3 2C4 2C5 1.4983 109.26 45.07 115.62 1.5530 +IC 2C3 2C4 2C5 2O5 1.5497 115.62 -49.19 110.30 1.4512 +IC 2C4 2C5 2O5 2C1 1.5530 110.30 56.36 112.12 1.4620 +IC 2C5 2O5 2C1 2C2 1.4512 112.12 -61.39 110.88 1.5316 +IC 2C4 2C5 2C6 2O6 1.5530 109.90 -177.46 109.41 1.4589 +IC 2O5 2C1 2O1 2HO1 1.4620 108.62 72.25 106.48 0.9328 +IC 2C1 2C2 2O2 2HO2 1.5316 115.65 135.41 116.81 0.9527 +IC 2C2 2C3 2O3 2HO3 1.4983 108.48 -71.46 120.86 0.9441 +!IC 2C3 2C4 2O4 2HO4 1.5497 112.77 47.45 109.31 0.9911 +IC 2C5 2C6 2O6 2HO6 1.5597 109.41 -54.60 118.82 0.95210 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C11P 3C9P *3C10P 3H10P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C11P 3C9P *3C10P 3H10P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C12P 3C10P *3C11P 3H11P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C12P 3C10P *3C11P 3H11P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C11P 3C12P 3H12P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H12P1 3C11P *3C12P 3H12P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H12P1 3C11P *3C12P 3H12P3 1.0625 108.61 126.50 111.01 1.1613 + +PATC FIRS NONE LAST NONE + + +RESI ADM 0.000 ! decyl-alpha-D-maltoside +! +GROU ! +ATOM 1C1 CC3162 0.290 ! AGLC 4C1 alpha-D-glucose +ATOM 1H1 HCA1 0.090 ! +ATOM 1C5 CC3163 0.110 ! +ATOM 1H5 HCA1 0.090 ! +ATOM 1O5 OC3C61 -0.400 ! +GROU ! +ATOM 1C2 CC3161 0.140 ! +ATOM 1H2 HCA1 0.090 ! +ATOM 1O2 OC311 -0.650 ! +ATOM 1HO2 HCP1 0.420 ! +GROU ! +ATOM 1C3 CC3161 0.140 ! +ATOM 1H3 HCA1 0.090 ! +ATOM 1O3 OC311 -0.650 ! +ATOM 1HO3 HCP1 0.420 ! +GROU +ATOM 1C4 CC3161 0.140 +ATOM 1H4 HCA1 0.090 +ATOM 1O4 OC311 -0.650 +ATOM 1HO4 HCP1 0.420 +GROU +ATOM 1C6 CC321 0.050 +ATOM 1H61 HCA2 0.090 +ATOM 1H62 HCA2 0.090 +ATOM 1O6 OC311 -0.650 +ATOM 1HO6 HCP1 0.420 +GROU ! AGLC +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.090 ! +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC301 -0.360 ! +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL3 -0.27 ! +ATOM 3H10P1 HAL3 0.09 ! +ATOM 3H10P2 HAL3 0.09 ! +ATOM 3H10P3 HAL3 0.09 ! +BOND 1C1 1H1 1C1 1O5 1C1 1C2 +BOND 1C2 1H2 1C2 1O2 1O2 1HO2 1C2 1C3 1C3 1H3 +BOND 1C3 1O3 1O3 1HO3 1C3 1C4 1C4 1H4 1C4 1O4 +BOND 1O4 1HO4 1C4 1C5 1C5 1H5 1C5 1C6 1C6 1H61 +BOND 1C6 1H62 1C6 1O6 1O6 1HO6 1C5 1O5 +BOND 2O4 1C1 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 2C3 2H3 +BOND 2C3 2O3 2O3 2HO3 2C3 2C4 2C4 2H4 2C4 2O4 +BOND 2C4 2C5 2C5 2H5 2C5 2C6 2C6 2H61 +BOND 2C6 2H62 2C6 2O6 2O6 2HO6 2C5 2O5 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 3C10P 3H10P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O2 1C3 *1C2 1H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 1O2 1C1 *1C2 1C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 1O3 1C4 *1C3 1H3 1.4122 110.86 120.36 107.49 1.1219 +IC 1O3 1C2 *1C3 1C4 1.4122 109.00 121.20 109.13 1.5315 +IC 1O4 1C5 *1C4 1H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 1O4 1C3 *1C4 1C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 1C6 1O5 *1C5 1H5 1.4718 112.19 113.05 108.36 1.1212 +IC 1C6 1C4 *1C5 1O5 1.4718 112.04 128.71 113.93 1.4175 +IC 1O6 1H62 *1C6 1H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 1O6 1C5 *1C6 1H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 1O5 1C1 1C2 1C3 1.4351 112.62 51.83 113.63 1.4880 +IC 1C1 1C2 1C3 1C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 1C2 1C3 1C4 1C5 1.4880 109.13 47.85 114.40 1.5087 +IC 1C3 1C4 1C5 1O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 1C4 1C5 1O5 1C1 1.5087 113.93 51.43 114.13 1.4351 +IC 1C5 1O5 1C1 1C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 1C4 1C5 1C6 1O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 1C1 1C2 1O2 1HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 1C2 1C3 1O3 1HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC 1C3 1C4 1O4 1HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 1C5 1C6 1O6 1HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2C3 2C4 2O4 1C1 1.5010 117.73 72.71 118.66 1.4036 ! psi +IC 2C4 2O4 1C1 1O5 1.4919 118.66 48.64 109.48 1.4570 ! phi +IC 1O5 2O4 *1C1 1C2 1.4570 109.48 124.57 110.72 1.5065 +IC 1O5 2O4 *1C1 1H1 1.4570 109.48 -116.61 107.55 1.1057 +IC 2O1 2C2 *2C1 2H1 1.4077 108.33 -123.34 103.67 1.1200 +IC 2O1 2O5 *2C1 2C2 1.4077 108.39 -119.83 112.62 1.5516 +IC 2O2 2C3 *2C2 2H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 2O2 2C1 *2C2 2C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 2O3 2C4 *2C3 2H3 1.4122 110.86 120.36 107.49 1.1219 +IC 2O3 2C2 *2C3 2C4 1.4122 109.00 121.20 109.13 1.5315 +IC 2O4 2C5 *2C4 2H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 2O4 2C3 *2C4 2C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 2C6 2O5 *2C5 2H5 1.4718 112.19 113.05 108.36 1.1212 +IC 2C6 2C4 *2C5 2O5 1.4718 112.04 128.71 113.93 1.4175 +IC 2O6 2H62 *2C6 2H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 2O6 2C5 *2C6 2H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 2O5 2C1 2C2 2C3 1.4351 112.62 51.83 113.63 1.4880 +IC 2C1 2C2 2C3 2C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 2C2 2C3 2C4 2C5 1.4880 109.13 47.85 114.40 1.5087 +IC 2C3 2C4 2C5 2O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 2C4 2C5 2O5 2C1 1.5087 113.93 51.43 114.13 1.4351 +IC 2C5 2O5 2C1 2C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 2C4 2C5 2C6 2O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 2O5 2C1 2O1 2HO1 1.4351 108.39 47.62 101.41 0.9789 +IC 2C1 2C2 2O2 2HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 2C2 2C3 2O3 2HO3 1.4880 109.00 -28.48 103.99 0.9971 +!IC 2C3 2C4 2O4 2HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 2C5 2C6 2O6 2HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C8P 3C9P 3C10P 3H10P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H10P1 3C9P *3C10P 3H10P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H10P1 3C9P *3C10P 3H10P3 1.0625 108.61 126.50 111.01 1.1613 + +PATC FIRS NONE LAST NONE + + +RESI BDM 0.000 ! decyl-beta-D-maltoside +! +GROU ! +ATOM 1C1 CC3162 0.290 ! AGLC 4C1 alpha-D-glucose +ATOM 1H1 HCA1 0.090 ! +ATOM 1C5 CC3163 0.110 ! +ATOM 1H5 HCA1 0.090 ! +ATOM 1O5 OC3C61 -0.400 ! +GROU ! +ATOM 1C2 CC3161 0.140 ! +ATOM 1H2 HCA1 0.090 ! +ATOM 1O2 OC311 -0.650 ! +ATOM 1HO2 HCP1 0.420 ! +GROU ! +ATOM 1C3 CC3161 0.140 ! +ATOM 1H3 HCA1 0.090 ! +ATOM 1O3 OC311 -0.650 ! +ATOM 1HO3 HCP1 0.420 ! +GROU +ATOM 1C4 CC3161 0.140 +ATOM 1H4 HCA1 0.090 +ATOM 1O4 OC311 -0.650 +ATOM 1HO4 HCP1 0.420 +GROU +ATOM 1C6 CC321 0.050 +ATOM 1H61 HCA2 0.090 +ATOM 1H62 HCA2 0.090 +ATOM 1O6 OC311 -0.650 +ATOM 1HO6 HCP1 0.420 +! ! +GROU ! BGLC +ATOM 2C1 CC3162 0.290 ! +ATOM 2H1 HCA1 0.090 ! +ATOM 2O1 OC301 -0.360 ! +ATOM 2C5 CC3163 0.110 ! +ATOM 2H5 HCA1 0.090 ! +ATOM 2O5 OC3C61 -0.400 ! +GROU ! +ATOM 2C2 CC3161 0.140 ! +ATOM 2H2 HCA1 0.090 ! +ATOM 2O2 OC311 -0.650 ! +ATOM 2HO2 HCP1 0.420 ! +GROU ! +ATOM 2C3 CC3161 0.140 ! +ATOM 2H3 HCA1 0.090 ! +ATOM 2O3 OC311 -0.650 ! +ATOM 2HO3 HCP1 0.420 ! +GROU +ATOM 2C4 CC3161 0.090 ! +ATOM 2H4 HCA1 0.090 +ATOM 2O4 OC301 -0.360 ! +GROU +ATOM 2C6 CC321 0.050 +ATOM 2H61 HCA2 0.090 +ATOM 2H62 HCA2 0.090 +ATOM 2O6 OC311 -0.650 +ATOM 2HO6 HCP1 0.420 +! +GROUP +ATOM 3C1P CTL2 0.00 ! +ATOM 3H1P1 HAL2 0.09 ! +ATOM 3H1P2 HAL2 0.09 ! +GROUP +ATOM 3C2P CTL2 -0.18 ! +ATOM 3H2P1 HAL2 0.09 ! +ATOM 3H2P2 HAL2 0.09 ! +GROUP +ATOM 3C3P CTL2 -0.18 ! +ATOM 3H3P1 HAL2 0.09 ! +ATOM 3H3P2 HAL2 0.09 ! +GROUP +ATOM 3C4P CTL2 -0.18 ! +ATOM 3H4P1 HAL2 0.09 ! +ATOM 3H4P2 HAL2 0.09 ! +GROUP +ATOM 3C5P CTL2 -0.18 ! +ATOM 3H5P1 HAL2 0.09 ! +ATOM 3H5P2 HAL2 0.09 ! +GROUP +ATOM 3C6P CTL2 -0.18 ! +ATOM 3H6P1 HAL2 0.09 ! +ATOM 3H6P2 HAL2 0.09 ! +GROUP +ATOM 3C7P CTL2 -0.18 ! +ATOM 3H7P1 HAL2 0.09 ! +ATOM 3H7P2 HAL2 0.09 ! +GROUP +ATOM 3C8P CTL2 -0.18 ! +ATOM 3H8P1 HAL2 0.09 ! +ATOM 3H8P2 HAL2 0.09 ! +GROUP +ATOM 3C9P CTL2 -0.18 ! +ATOM 3H9P1 HAL2 0.09 ! +ATOM 3H9P2 HAL2 0.09 ! +GROUP +ATOM 3C10P CTL3 -0.27 ! +ATOM 3H10P1 HAL3 0.09 ! +ATOM 3H10P2 HAL3 0.09 ! +ATOM 3H10P3 HAL3 0.09 ! +! +BOND 1C1 1H1 1C1 1O5 1C1 1C2 +BOND 1C2 1H2 1C2 1O2 1O2 1HO2 1C2 1C3 1C3 1H3 +BOND 1C3 1O3 1O3 1HO3 1C3 1C4 1C4 1H4 1C4 1O4 +BOND 1O4 1HO4 1C4 1C5 1C5 1H5 1C5 1C6 1C6 1H61 +BOND 1C6 1H62 1C6 1O6 1O6 1HO6 1C5 1O5 +BOND 2O4 1C1 2C1 2O1 2C1 2H1 +BOND 2C1 2O5 2C1 2C2 +BOND 2C2 2H2 2C2 2O2 2O2 2HO2 2C2 2C3 2C3 2H3 +BOND 2C3 2O3 2O3 2HO3 2C3 2C4 2C4 2H4 2C4 2O4 +BOND 2C4 2C5 2C5 2H5 2C5 2C6 2C6 2H61 +BOND 2C6 2H62 2C6 2O6 2O6 2HO6 2C5 2O5 +BOND 2O1 3C1P 3C1P 3C2P +BOND 3C2P 3C3P 3C3P 3C4P +BOND 3C4P 3C5P 3C5P 3C6P +BOND 3C6P 3C7P 3C7P 3C8P +BOND 3C8P 3C9P 3C9P 3C10P +BOND 3C1P 3H1P1 3C1P 3H1P2 +BOND 3C2P 3H2P1 3C2P 3H2P2 +BOND 3C3P 3H3P1 3C3P 3H3P2 +BOND 3C4P 3H4P1 3C4P 3H4P2 +BOND 3C5P 3H5P1 3C5P 3H5P2 +BOND 3C6P 3H6P1 3C6P 3H6P2 +BOND 3C7P 3H7P1 3C7P 3H7P2 +BOND 3C8P 3H8P1 3C8P 3H8P2 +BOND 3C9P 3H9P1 3C9P 3H9P2 +BOND 3C10P 3H10P1 3C10P 3H10P2 3C10P 3H10P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O2 1C3 *1C2 1H2 1.4293 114.98 -108.39 100.80 1.0662 +IC 1O2 1C1 *1C2 1C3 1.4293 117.26 -138.07 113.63 1.4880 +IC 1O3 1C4 *1C3 1H3 1.4122 110.86 120.36 107.49 1.1219 +IC 1O3 1C2 *1C3 1C4 1.4122 109.00 121.20 109.13 1.5315 +IC 1O4 1C5 *1C4 1H4 1.4206 109.25 -124.20 109.65 1.1311 +IC 1O4 1C3 *1C4 1C5 1.4206 103.58 -118.81 114.40 1.5087 +IC 1C6 1O5 *1C5 1H5 1.4718 112.19 113.05 108.36 1.1212 +IC 1C6 1C4 *1C5 1O5 1.4718 112.04 128.71 113.93 1.4175 +IC 1O6 1H62 *1C6 1H61 1.3851 111.30 -112.76 100.96 1.1590 +IC 1O6 1C5 *1C6 1H62 1.3851 110.28 -128.49 116.95 1.1067 +IC 1O5 1C1 1C2 1C3 1.4351 112.62 51.83 113.63 1.4880 +IC 1C1 1C2 1C3 1C4 1.5516 113.63 -48.48 109.13 1.5315 +IC 1C2 1C3 1C4 1C5 1.4880 109.13 47.85 114.40 1.5087 +IC 1C3 1C4 1C5 1O5 1.5315 114.40 -49.84 113.93 1.4175 +IC 1C4 1C5 1O5 1C1 1.5087 113.93 51.43 114.13 1.4351 +IC 1C5 1O5 1C1 1C2 1.4175 114.13 -51.82 112.62 1.5516 +IC 1C4 1C5 1C6 1O6 1.5087 112.04 -173.06 110.28 1.3851 +IC 1C1 1C2 1O2 1HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC 1C2 1C3 1O3 1HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC 1C3 1C4 1O4 1HO4 1.5315 103.58 55.55 110.36 0.9685 +IC 1C5 1C6 1O6 1HO6 1.4718 110.28 -101.06 108.67 0.9667 +IC 2C3 2C4 2O4 1C1 1.5010 117.73 72.71 118.66 1.4036 ! psi +IC 2C4 2O4 1C1 1O5 1.4919 118.66 48.64 109.48 1.4570 ! phi +IC 1O5 2O4 *1C1 1C2 1.4570 109.48 124.57 110.72 1.5065 +IC 1O5 2O4 *1C1 1H1 1.4570 109.48 -116.61 107.55 1.1057 +IC 2O1 2C2 *2C1 2H1 1.3899 110.90 120.10 104.58 1.0836 +IC 2O1 2O5 *2C1 2C2 1.3899 108.62 122.10 110.88 1.5316 +IC 2O2 2C3 *2C2 2H2 1.4594 108.12 -118.78 111.06 1.1375 +IC 2O2 2C1 *2C2 2C3 1.4594 115.65 -125.60 113.28 1.4983 +IC 2O3 2C4 *2C3 2H3 1.4071 113.48 122.06 103.39 1.0895 +IC 2O3 2C2 *2C3 2C4 1.4071 108.48 124.18 109.26 1.5497 +IC 2O4 2C5 *2C4 2H4 1.3940 111.12 -110.35 108.66 1.0857 +IC 2O4 2C3 *2C4 2C5 1.3940 112.77 -129.39 115.62 1.5530 +IC 2C6 2O5 *2C5 2H5 1.5597 111.17 120.85 110.98 1.1092 +IC 2C6 2C4 *2C5 2O5 1.5597 109.90 122.92 110.30 1.4512 +IC 2O6 2H62 *2C6 2H61 1.4589 116.11 -112.93 103.57 1.1467 +IC 2O6 2C5 *2C6 2H62 1.4589 109.41 -135.95 118.22 1.0853 +IC 2O5 2C1 2C2 2C3 1.4620 110.88 57.82 113.28 1.4983 +IC 2C1 2C2 2C3 2C4 1.5316 113.28 -48.40 109.26 1.5497 +IC 2C2 2C3 2C4 2C5 1.4983 109.26 45.07 115.62 1.5530 +IC 2C3 2C4 2C5 2O5 1.5497 115.62 -49.19 110.30 1.4512 +IC 2C4 2C5 2O5 2C1 1.5530 110.30 56.36 112.12 1.4620 +IC 2C5 2O5 2C1 2C2 1.4512 112.12 -61.39 110.88 1.5316 +IC 2C4 2C5 2C6 2O6 1.5530 109.90 -177.46 109.41 1.4589 +IC 2O5 2C1 2O1 2HO1 1.4620 108.62 72.25 106.48 0.9328 +IC 2C1 2C2 2O2 2HO2 1.5316 115.65 135.41 116.81 0.9527 +IC 2C2 2C3 2O3 2HO3 1.4983 108.48 -71.46 120.86 0.9441 +!IC 2C3 2C4 2O4 2HO4 1.5497 112.77 47.45 109.31 0.9911 +IC 2C5 2C6 2O6 2HO6 1.5597 109.41 -54.60 118.82 0.95210 +IC 2O5 2C1 2O1 3C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC 2C1 2O1 3C1P 3C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC 2O1 3C1P 3C2P 3C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC 3C1P 3C2P 3C3P 3C4P 1.5408 111.72 174.29 118.38 1.4860 +IC 3C2P 3C3P 3C4P 3C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC 3C3P 3C4P 3C5P 3C6P 1.4860 117.15 176.92 116.91 1.5223 +IC 3C4P 3C5P 3C6P 3C7P 1.5882 116.91 166.99 109.72 1.5200 +IC 3C5P 3C6P 3C7P 3C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C6P 3C7P 3C8P 3C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C7P 3C8P 3C9P 3C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C8P 3C9P 3C10P 3C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C9P 3C10P 3C11P 3C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC 3C2P 2O1 *3C1P 3H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC 3C2P 2O1 *3C1P 3H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC 3C3P 3C1P *3C2P 3H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC 3C3P 3C1P *3C2P 3H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC 3C4P 3C2P *3C3P 3H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC 3C4P 3C2P *3C3P 3H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC 3C5P 3C3P *3C4P 3H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC 3C5P 3C3P *3C4P 3H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC 3C6P 3C4P *3C5P 3H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC 3C6P 3C4P *3C5P 3H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC 3C7P 3C5P *3C6P 3H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC 3C7P 3C5P *3C6P 3H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC 3C8P 3C6P *3C7P 3H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C8P 3C6P *3C7P 3H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C9P 3C7P *3C8P 3H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C9P 3C7P *3C8P 3H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C10P 3C8P *3C9P 3H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC 3C10P 3C8P *3C9P 3H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC 3C8P 3C9P 3C10P 3H10P1 1.5200 108.36 67.85 108.61 1.0625 +IC 3H10P1 3C9P *3C10P 3H10P2 1.0625 108.61 -118.96 114.90 1.1259 +IC 3H10P1 3C9P *3C10P 3H10P3 1.0625 108.61 126.50 111.01 1.1613 + +PATC FIRS NONE LAST NONE + +end +return + + diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_glycolipid.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_glycolipid.str new file mode 100644 index 00000000..c0ebefc6 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_glycolipid.str @@ -0,0 +1,380 @@ +read rtf card append +* Topology for inositol-based lipids +* +32 1 + + +PRES OCTA 0.11 ! og axial octyl patch to C1 +dele atom HO1 +GROUP +ATOM C1 CC3162 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM C1P CTL2 0.00 ! +ATOM H1P1 HAL2 0.09 ! +ATOM H1P2 HAL2 0.09 ! +GROUP +ATOM C2P CTL2 -0.18 ! +ATOM H2P1 HAL2 0.09 ! +ATOM H2P2 HAL2 0.09 ! +GROUP +ATOM C3P CTL2 -0.18 ! +ATOM H3P1 HAL2 0.09 ! +ATOM H3P2 HAL2 0.09 ! +GROUP +ATOM C4P CTL2 -0.18 ! +ATOM H4P1 HAL2 0.09 ! +ATOM H4P2 HAL2 0.09 ! +GROUP +ATOM C5P CTL2 -0.18 ! +ATOM H5P1 HAL2 0.09 ! +ATOM H5P2 HAL2 0.09 ! +GROUP +ATOM C6P CTL2 -0.18 ! +ATOM H6P1 HAL2 0.09 ! +ATOM H6P2 HAL2 0.09 ! +GROUP +ATOM C7P CTL2 -0.18 ! +ATOM H7P1 HAL2 0.09 ! +ATOM H7P2 HAL2 0.09 ! +GROUP +ATOM C8P CTL3 -0.27 ! +ATOM H8P1 HAL3 0.09 ! +ATOM H8P2 HAL3 0.09 ! +ATOM H8P3 HAL3 0.09 ! +BOND O1 C1P C1P C2P +BOND C2P C3P C3P C4P +BOND C4P C5P C5P C6P +BOND C6P C7P C7P C8P +BOND C1P H1P1 C1P H1P2 +BOND C2P H2P1 C2P H2P2 +BOND C3P H3P1 C3P H3P2 +BOND C4P H4P1 C4P H4P2 +BOND C5P H5P1 C5P H5P2 +BOND C6P H6P1 C6P H6P2 +BOND C7P H7P1 C7P H7P2 +BOND C8P H8P1 C8P H8P2 C8P H8P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C1 O1 C1P 1.4326 113.39 76.24 112.41 1.4390 +IC C1 O1 C1P C2P 1.3743 112.41 -174.48 113.71 1.5661 +IC O1 C1P C2P C3P 1.4390 113.71 171.35 116.60 1.5435 +IC C1P C2P C3P C4P 1.5661 116.60 167.78 109.45 1.5162 +IC C2P C3P C4P C5P 1.5435 109.45 176.22 113.48 1.5169 +IC C3P C4P C5P C6P 1.5162 113.48 -170.18 109.85 1.5192 +IC C4P C5P C6P C7P 1.5169 109.85 -178.66 113.31 1.5327 +IC C5P C6P C7P C8P 1.5192 113.31 168.96 112.74 1.5011 +IC C2P O1 *C1P H1P1 1.5661 113.71 -128.80 113.66 1.0672 +IC C2P O1 *C1P H1P2 1.5661 113.71 111.70 104.83 1.1576 +IC C3P C1P *C2P H2P1 1.5435 116.60 -122.44 111.35 1.1341 +IC C3P C1P *C2P H2P2 1.5435 116.60 120.83 104.33 1.0593 +IC C4P C2P *C3P H3P1 1.5162 109.45 -122.81 111.56 1.0873 +IC C4P C2P *C3P H3P2 1.5162 109.45 119.63 108.38 1.1453 +IC C5P C3P *C4P H4P1 1.5169 113.48 -113.66 106.44 1.1732 +IC C5P C3P *C4P H4P2 1.5169 113.48 127.08 117.15 1.0636 +IC C6P C4P *C5P H5P1 1.5192 109.85 -123.11 112.49 1.0773 +IC C6P C4P *C5P H5P2 1.5192 109.85 118.20 103.00 1.1136 +IC C7P C5P *C6P H6P1 1.5327 113.31 -120.77 104.09 1.1135 +IC C7P C5P *C6P H6P2 1.5327 113.31 121.24 102.96 1.1126 +IC C8P C6P *C7P H7P1 1.5011 112.74 -120.21 106.53 1.0732 +IC C8P C6P *C7P H7P2 1.5011 112.74 122.52 101.92 1.1138 +IC C6P C7P C8P H8P1 1.5327 112.74 68.12 110.42 1.0685 +IC H8P1 C7P *C8P H8P2 1.0685 110.42 -123.66 113.02 1.1341 +IC H8P1 C7P *C8P H8P3 1.0685 110.42 117.47 111.97 1.1299 + +PRES OCTB 0.11 ! og equatorial octyl patch to C1 +dele atom HO1 +GROUP +ATOM C1 CC3162 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM C1P CTL2 0.00 ! +ATOM H1P1 HAL2 0.09 ! +ATOM H1P2 HAL2 0.09 ! +GROUP +ATOM C2P CTL2 -0.18 ! +ATOM H2P1 HAL2 0.09 ! +ATOM H2P2 HAL2 0.09 ! +GROUP +ATOM C3P CTL2 -0.18 ! +ATOM H3P1 HAL2 0.09 ! +ATOM H3P2 HAL2 0.09 ! +GROUP +ATOM C4P CTL2 -0.18 ! +ATOM H4P1 HAL2 0.09 ! +ATOM H4P2 HAL2 0.09 ! +GROUP +ATOM C5P CTL2 -0.18 ! +ATOM H5P1 HAL2 0.09 ! +ATOM H5P2 HAL2 0.09 ! +GROUP +ATOM C6P CTL2 -0.18 ! +ATOM H6P1 HAL2 0.09 ! +ATOM H6P2 HAL2 0.09 ! +GROUP +ATOM C7P CTL2 -0.18 ! +ATOM H7P1 HAL2 0.09 ! +ATOM H7P2 HAL2 0.09 ! +GROUP +ATOM C8P CTL3 -0.27 ! +ATOM H8P1 HAL3 0.09 ! +ATOM H8P2 HAL3 0.09 ! +ATOM H8P3 HAL3 0.09 ! +BOND O1 C1P C1P C2P +BOND C2P C3P C3P C4P +BOND C4P C5P C5P C6P +BOND C6P C7P C7P C8P +BOND C1P H1P1 C1P H1P2 +BOND C2P H2P1 C2P H2P2 +BOND C3P H3P1 C3P H3P2 +BOND C4P H4P1 C4P H4P2 +BOND C5P H5P1 C5P H5P2 +BOND C6P H6P1 C6P H6P2 +BOND C7P H7P1 C7P H7P2 +BOND C8P H8P1 C8P H8P2 C8P H8P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C1 O1 C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC C1 O1 C1P C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC O1 C1P C2P C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC C1P C2P C3P C4P 1.5408 111.72 174.29 118.38 1.4860 +IC C2P C3P C4P C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC C3P C4P C5P C6P 1.4860 117.15 176.92 116.91 1.5223 +IC C4P C5P C6P C7P 1.5882 116.91 166.99 109.72 1.5200 +IC C5P C6P C7P C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC C2P O1 *C1P H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC C2P O1 *C1P H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC C3P C1P *C2P H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC C3P C1P *C2P H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC C4P C2P *C3P H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC C4P C2P *C3P H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC C5P C3P *C4P H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC C5P C3P *C4P H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC C6P C4P *C5P H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC C6P C4P *C5P H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC C7P C5P *C6P H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC C7P C5P *C6P H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC C8P C6P *C7P H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C8P C6P *C7P H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC C6P C7P C8P H8P1 1.5200 108.36 67.85 108.61 1.0625 +IC H8P1 C7P *C8P H8P2 1.0625 108.61 -118.96 114.90 1.1259 +IC H8P1 C7P *C8P H8P3 1.0625 108.61 126.50 111.01 1.1613 + +PRES DDMB 0.11 ! og equatorial dodecyl patch to C1 +dele atom HO1 +GROUP +ATOM C1 CC3162 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM C1P CTL2 0.00 ! +ATOM H1P1 HAL2 0.09 ! +ATOM H1P2 HAL2 0.09 ! +GROUP +ATOM C2P CTL2 -0.18 ! +ATOM H2P1 HAL2 0.09 ! +ATOM H2P2 HAL2 0.09 ! +GROUP +ATOM C3P CTL2 -0.18 ! +ATOM H3P1 HAL2 0.09 ! +ATOM H3P2 HAL2 0.09 ! +GROUP +ATOM C4P CTL2 -0.18 ! +ATOM H4P1 HAL2 0.09 ! +ATOM H4P2 HAL2 0.09 ! +GROUP +ATOM C5P CTL2 -0.18 ! +ATOM H5P1 HAL2 0.09 ! +ATOM H5P2 HAL2 0.09 ! +GROUP +ATOM C6P CTL2 -0.18 ! +ATOM H6P1 HAL2 0.09 ! +ATOM H6P2 HAL2 0.09 ! +GROUP +ATOM C7P CTL2 -0.18 ! +ATOM H7P1 HAL2 0.09 ! +ATOM H7P2 HAL2 0.09 ! +GROUP +ATOM C8P CTL2 -0.18 ! +ATOM H8P1 HAL2 0.09 ! +ATOM H8P2 HAL2 0.09 ! +GROUP +ATOM C9P CTL2 -0.18 ! +ATOM H9P1 HAL2 0.09 ! +ATOM H9P2 HAL2 0.09 ! +GROUP +ATOM C10P CTL2 -0.18 ! +ATOM H10P1 HAL2 0.09 ! +ATOM H10P2 HAL2 0.09 ! +GROUP +ATOM C11P CTL2 -0.18 ! +ATOM H11P1 HAL2 0.09 ! +ATOM H11P2 HAL2 0.09 ! +GROUP +ATOM C12P CTL3 -0.27 ! +ATOM H12P1 HAL3 0.09 ! +ATOM H12P2 HAL3 0.09 ! +ATOM H12P3 HAL3 0.09 ! +BOND O1 C1P C1P C2P +BOND C2P C3P C3P C4P +BOND C4P C5P C5P C6P +BOND C6P C7P C7P C8P +BOND C8P C9P C9P C10P +BOND C10P C11P C11P C12P +BOND C1P H1P1 C1P H1P2 +BOND C2P H2P1 C2P H2P2 +BOND C3P H3P1 C3P H3P2 +BOND C4P H4P1 C4P H4P2 +BOND C5P H5P1 C5P H5P2 +BOND C6P H6P1 C6P H6P2 +BOND C7P H7P1 C7P H7P2 +BOND C8P H8P1 C8P H8P2 +BOND C9P H9P1 C9P H9P2 +BOND C10P H10P1 C10P H10P2 +BOND C11P H11P1 C11P H11P2 +BOND C12P H12P1 C12P H12P2 C12P H12P3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C1 O1 C1P 1.4302 103.27 -83.30 111.36 1.4262 +IC C1 O1 C1P C2P 1.4465 111.36 -171.80 110.89 1.5408 +IC O1 C1P C2P C3P 1.4262 110.89 -178.19 111.72 1.5390 +IC C1P C2P C3P C4P 1.5408 111.72 174.29 118.38 1.4860 +IC C2P C3P C4P C5P 1.5390 118.38 -178.01 117.15 1.5882 +IC C3P C4P C5P C6P 1.4860 117.15 176.92 116.91 1.5223 +IC C4P C5P C6P C7P 1.5882 116.91 166.99 109.72 1.5200 +IC C5P C6P C7P C8P 1.5223 109.72 -162.31 108.36 1.5091 +IC C6P C7P C8P C9P 1.5223 109.72 -162.31 108.36 1.5091 +IC C7P C8P C9P C10P 1.5223 109.72 -162.31 108.36 1.5091 +IC C8P C9P C10P C11P 1.5223 109.72 -162.31 108.36 1.5091 +IC C9P C10P C11P C12P 1.5223 109.72 -162.31 108.36 1.5091 +IC C2P O1 *C1P H1P1 1.5408 110.89 -129.38 114.34 1.1088 +IC C2P O1 *C1P H1P2 1.5408 110.89 108.27 111.44 1.1435 +IC C3P C1P *C2P H2P1 1.5390 111.72 -123.94 112.56 1.1329 +IC C3P C1P *C2P H2P2 1.5390 111.72 116.28 109.75 1.1147 +IC C4P C2P *C3P H3P1 1.4860 118.38 -120.46 104.87 1.1356 +IC C4P C2P *C3P H3P2 1.4860 118.38 116.67 103.64 1.1033 +IC C5P C3P *C4P H4P1 1.5882 117.15 -116.87 110.32 1.1073 +IC C5P C3P *C4P H4P2 1.5882 117.15 122.70 106.80 1.0580 +IC C6P C4P *C5P H5P1 1.5223 116.91 -119.49 97.60 1.1005 +IC C6P C4P *C5P H5P2 1.5223 116.91 124.24 109.65 1.1031 +IC C7P C5P *C6P H6P1 1.5200 109.72 -119.08 113.08 1.1315 +IC C7P C5P *C6P H6P2 1.5200 109.72 120.58 116.49 1.1004 +IC C8P C6P *C7P H7P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C8P C6P *C7P H7P2 1.5091 108.36 126.14 108.14 1.1445 +IC C9P C7P *C8P H8P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C9P C7P *C8P H8P2 1.5091 108.36 126.14 108.14 1.1445 +IC C10P C8P *C9P H9P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C10P C8P *C9P H9P2 1.5091 108.36 126.14 108.14 1.1445 +IC C11P C9P *C10P H10P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C11P C9P *C10P H10P2 1.5091 108.36 126.14 108.14 1.1445 +IC C12P C10P *C11P H11P1 1.5091 108.36 -122.67 97.37 1.1727 +IC C12P C10P *C11P H11P2 1.5091 108.36 126.14 108.14 1.1445 +IC C10P C11P C12P H12P1 1.5200 108.36 67.85 108.61 1.0625 +IC H12P1 C11P *C12P H12P2 1.0625 108.61 -118.96 114.90 1.1259 +IC H12P1 C11P *C12P H12P3 1.0625 108.61 126.50 111.01 1.1613 + +PRES CERA 0.11 ! og axial patch of ceramide to C1 [based on PRES OCTA] + ! e.g., PRES CERA CARB CER +dele atom 1HO1 +dele atom 2HO1 +dele atom 2O1 + +GROUP +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC301 -0.36 ! + +ATOM 2C1S CTO2 0.00 ! +ATOM 2H1S HAL2 0.09 ! +ATOM 2H1T HAL2 0.09 ! + +BOND 1O1 2C1S + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C1S 1.4326 113.39 76.24 112.41 1.4390 +IC 1C1 1O1 2C1S 2C2S 1.3743 112.41 -174.48 113.71 1.5661 +IC 1O1 2C1S 2C2S 2C3S 1.4390 113.71 171.35 116.60 1.5435 +IC 2C2S 1O1 *2C1S 2H1S 1.5661 113.71 -128.80 113.66 1.0672 +IC 2C2S 1O1 *2C1S 2H1T 1.5661 113.71 111.70 104.83 1.1576 + +PRES CERB 0.11 ! og equatorial patch of ceramide to C1 [based on PRES OCTB] + ! e.g., PRES CERB CARB CER +dele atom 1HO1 +dele atom 2HO1 +dele atom 2O1 + +GROUP +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC301 -0.36 ! + +ATOM 2C1S CTO2 0.00 ! +ATOM 2H1S HAL2 0.09 ! +ATOM 2H1T HAL2 0.09 ! + +BOND 1O1 2C1S + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C1S 1.4302 103.27 -83.30 111.36 1.4262 +IC 1C1 1O1 2C1S 2C2S 1.4465 111.36 -171.80 110.89 1.5408 +IC 1O1 2C1S 2C2S 2C3S 1.4262 110.89 -178.19 111.72 1.5390 +IC 2C2S 1O1 *2C1S 2H1S 1.5661 113.71 -128.80 113.66 1.0672 +IC 2C2S 1O1 *2C1S 2H1T 1.5661 113.71 111.70 104.83 1.1576 + +END + + +read param card flex append +* PIP related parameters +* +! Parameters have been transferred from two FF +! sugar FF and lipid FF +! + +BONDS +!** sugar FF *** +CTL2 OC301 360.00 1.415 ! par35 CC32A OC30A +CTO2 OC301 360.00 1.415 ! par35 CC32A OC30A + +ANGLES +!** sugar FF *** +OC301 CTL2 CTL2 45.00 111.50 ! par35 OC30A CC32A CC32A +OC301 CTO2 CTL1 45.00 111.50 ! par35 OC30A CC32A CC32A +CC3162 OC301 CTL2 95.00 109.70 ! par35 CC33A OC30A CC32A +CC3162 OC301 CTO2 95.00 109.70 ! par35 CC33A OC30A CC32A +CC311D OC301 CTL2 95.00 109.70 ! pram, OMeTHP CC311D OC301 CC331 +CC311D OC301 CTO2 95.00 109.70 ! pram, OMeTHP CC311D OC301 CC331 +OC301 CTL2 HAL2 60.00 109.50 ! par34 HCA2 CC32A OC30A +OC301 CTO2 HAL2 60.00 109.50 ! par34 HCA2 CC32A OC30A + +DIHEDRALS +!** sugar FF *** +CTL2 CTL2 CTL2 OC301 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC3162 OC301 CTL2 CTL2 0.40 1 0.0 ! par35 +CC3162 OC301 CTL2 CTL2 0.49 3 0.0 ! " CC33A CC32A OC30A CC32A +CC3162 OC301 CTO2 CTL1 0.40 1 0.0 ! par35 +CC3162 OC301 CTO2 CTL1 0.49 3 0.0 ! " CC33A CC32A OC30A CC32A +CC3161 CC3162 OC301 CTL2 0.22 1 0.0 ! og OMeTHP compounds 2 and 3 +CC3161 CC3162 OC301 CTL2 0.28 2 180.0 ! " MCSA fit +CC3161 CC3162 OC301 CTL2 0.89 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CC3161 CC3162 OC301 CTO2 0.22 1 0.0 ! og OMeTHP compounds 2 and 3 +CC3161 CC3162 OC301 CTO2 0.28 2 180.0 ! " MCSA fit +CC3161 CC3162 OC301 CTO2 0.89 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +HAL2 CTL2 CTL2 OC301 0.19 3 0.0 ! par27 X CTL2 CTL2 X +CC3162 OC301 CTL2 HAL2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CC3162 OC301 CTO2 HAL2 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CTL2 OC301 CC3162 OC3C61 0.14 1 0.0 ! og OMeTHP compounds 2 and 3 +CTL2 OC301 CC3162 OC3C61 0.97 2 0.0 ! " MCSA fit +CTL2 OC301 CC3162 OC3C61 0.11 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CTO2 OC301 CC3162 OC3C61 0.14 1 0.0 ! og OMeTHP compounds 2 and 3 +CTO2 OC301 CC3162 OC3C61 0.97 2 0.0 ! " MCSA fit +CTO2 OC301 CC3162 OC3C61 0.11 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CTL2 OC301 CTL1 HAL1 0.284 3 0.0 ! OMeTHP CC331 OC301 CC311D HCA1 +OC301 CTL2 CTL3 HAL3 0.20 3 0.0 ! OC301 CTL2 CC3163 HCA1 +CTL2 OC301 CC311D OC3C61 0.36 1 180.0 ! pr, 1-ethoxy-THP2 QM phi-psi scan +CTL2 OC301 CC311D OC3C61 0.52 2 0.0 ! " MCSA fit " +CTL2 OC301 CC311D OC3C61 0.83 3 180.0 ! " MP2/cc-pVTZ//MP2/6-31G* +CTL2 OC301 CC311D CC321C 0.58 1 180.0 ! pr, 1-ethoxy-THP2 QM phi-psi scan +CTL2 OC301 CC311D CC321C 0.69 2 180.0 ! " MCSA fit " +CTL2 OC301 CC311D CC321C 1.16 3 0.0 ! " MP2/cc-pVTZ//MP2/6-31G* +HAL2 CTL2 OC301 CC3051 0.284 3 0.0 ! OMe-THF CC312D OC301 CC331 HCA3 +HAL2 CTL2 OC301 CC3152 0.284 3 0.0 ! OMe-THF CC312D OC301 CC331 HCA3 +HAL1 CC3152 OC301 CTL2 0.284 3 0.0 ! HCA1 CC3152 OC301 CC331 +CTL2 OC301 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A +CTO2 OC301 CC3162 HCA1 0.284 3 0.0 ! par35 HCA2 CC32A OC30A CC32A + +END + +RETURN + diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_inositol.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_inositol.str new file mode 100644 index 00000000..39de0c86 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_inositol.str @@ -0,0 +1,26045 @@ +read rtf card append +* Topology for inositol-based lipids +* +36 1 + +!!test_inositol.inp + +!*** Changes Made to this file by sairam *** +! Critical changes made to SAPI and DMPI +! POPI was also added +!1) OSLP has been changed to OC30P only at pos O12. +!3) Checked the charges on the phosphates. They are all consistent with the lipid FF. + +!************ +! Stream file to the following lipids. Additional residues and patches +! to extend the glycan or modify the sugar moieties (ie. PIPs etc.) are +! in the parent sugar topology file. +! RESI SAPI ! Phosphatidylinositol +! RESI DMPI ! Di-myristoyl-inositol +! RESI POPI ! 1-Palmitoyl-2-Oleoyl-inositol +! RESI DSPI ! For GPI-Emilia +!********************************* + +RESI SAPI -1.00 ! Phosphatidylinositol +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | +ATOM C12 CC3161 0.14 ! | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5-HO5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5867 122.31 180.00 111.45 1.5517 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5329 113.78 68.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 120.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 120.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 120.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 120.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 120.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 120.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SAPI13 -3.00 ! Phosphatidylinositol-(3)-phosphate (PIP1) +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 -0.09 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.40 ! | |\ | / +ATOM P3 PC 1.10 ! | | \ O2 / +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.14 ! | | OP32(-) +ATOM H4 HCA1 0.09 ! | H3 +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! \ +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! (-) O13 O12 +ATOM C11 CC3161 -0.08 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.59 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O12 OC30P -0.57 ! HA---C1---HB +ATOM O11 OSLP -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C26 CEL1 -0.15 ! | | +ATOM H6R HEL1 0.15 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H12R HEL1 0.15 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H16R---C216--H16S | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! H18R---C218--H18S | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! | | +ATOM H18S HAL2 0.09 ! H19R---C219--H19S | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! | | +ATOM H19S HAL2 0.09 ! H20R---C220--H20S | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! H20T | +ATOM H20R HAL3 0.09 ! | +ATOM H20S HAL3 0.09 ! | +ATOM H20T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! H15X---C315--H15Y +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! H16X---C316--H16Y +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! | +ATOM H16Y HAL2 0.09 ! H17X---C317--H17Y +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! | +ATOM H17Y HAL2 0.09 ! H18X---C318--H18Y +GROUP ! | +ATOM C318 CTL3 -0.27 ! H18Z +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5612 111.91 56.25 109.10 1.5917 +IC C12 C13 C14 C15 1.5674 109.10 -55.67 107.50 1.5949 +IC C13 C14 C15 C16 1.5917 107.50 58.53 114.15 1.5236 +IC C14 C15 C16 C11 1.5949 114.15 -57.38 109.31 1.5105 +IC C15 C16 C11 C12 1.5236 109.31 54.67 113.12 1.5612 +IC C16 C11 C12 C13 1.5105 113.12 -56.32 111.91 1.5674 +IC C16 C12 *C11 H1 1.5105 113.12 119.75 101.91 1.1392 +IC C16 C12 *C11 O12 1.5105 113.12 -126.20 107.76 1.4882 +IC C11 C13 *C12 H2 1.5612 111.91 114.21 103.64 1.1291 +IC C11 C13 *C12 O2 1.5612 111.91 -130.03 104.90 1.4097 +IC C12 C14 *C13 H3 1.5674 109.10 109.60 102.16 1.0541 +IC C12 C14 *C13 O3 1.5674 109.10 -134.10 112.67 1.4674 +IC C13 C15 *C14 H4 1.5917 107.50 -122.77 106.58 1.1398 +IC C13 C15 *C14 O4 1.5917 107.50 121.11 113.88 1.3934 +IC C14 C16 *C15 H5 1.5949 114.15 117.62 111.57 1.1817 +IC C14 C16 *C15 O5 1.5949 114.15 -125.54 99.96 1.4429 +IC C15 C11 *C16 H6 1.5236 109.31 -117.85 108.15 1.1464 +IC C15 C11 *C16 O6 1.5236 109.31 124.62 106.80 1.4905 +IC C13 C12 O2 HO2 1.5674 104.90 -41.95 99.63 0.9607 +IC C11 C16 O6 HO6 1.5105 106.80 -141.52 102.28 0.9438 +IC C12 C11 O12 P 1.5612 107.76 -97.72 122.87 1.6738 +IC C11 O12 P O11 1.4882 122.87 -170.14 101.78 1.5624 +IC O11 O12 *P O13 1.5624 101.78 -111.87 115.92 1.4812 +IC O11 O12 *P O14 1.5624 101.78 114.33 108.26 1.4737 +IC O12 P O11 C1 1.6738 101.78 93.71 119.03 1.4527 +IC P O11 C1 C2 1.5624 119.03 90.59 109.51 1.5472 +IC C2 O11 *C1 HA 1.5472 109.51 116.74 102.40 1.1035 +IC HA O11 *C1 HB 1.1035 102.40 119.29 118.20 1.0905 +IC O11 C1 C2 O21 1.4527 109.51 159.98 105.23 1.3918 +IC O21 C1 *C2 C3 1.3918 105.23 -122.31 113.46 1.5224 +IC C3 C1 *C2 HS 1.5224 113.46 -112.81 98.08 1.1373 +IC C1 C2 O21 C21 1.5472 105.23 121.03 107.61 1.3130 +IC C2 O21 C21 C22 1.3918 107.61 -143.71 110.27 1.5240 +IC C22 O21 *C21 O22 1.5240 110.27 -173.26 123.94 1.2252 +IC O21 C21 C22 C23 1.3130 110.27 -100.54 114.05 1.5966 +IC C23 C21 *C22 H2R 1.5966 114.05 136.83 117.96 1.1359 +IC H2R C21 *C22 H2S 1.1359 117.96 112.37 110.66 1.1750 +IC C1 C2 C3 O31 1.5472 113.46 -164.03 113.68 1.4560 +IC O31 C2 *C3 HX 1.4560 113.68 -124.81 109.24 1.1421 +IC HX C2 *C3 HY 1.1421 109.24 -119.37 107.12 1.0811 +IC C2 C3 O31 C31 1.5224 113.68 -78.97 117.94 1.3060 +IC C3 O31 C31 C32 1.4560 117.94 176.98 108.04 1.5067 +IC C32 O31 *C31 O32 1.5067 108.04 167.41 128.04 1.2105 +IC O31 C31 C32 C33 1.3060 108.04 -179.87 108.44 1.5479 +IC C33 C31 *C32 H2X 1.5479 108.44 -133.26 115.68 1.1387 +IC H2X C31 *C32 H2Y 1.1387 115.68 -113.16 105.10 1.0739 +IC C21 C22 C23 C24 1.5240 114.05 71.06 110.64 1.5734 +IC C24 C22 *C23 H3R 1.5734 110.64 -124.62 113.03 1.1251 +IC C24 C22 *C23 H3S 1.5734 110.64 116.69 108.70 1.1403 +IC C22 C23 C24 C25 1.5966 110.64 -179.26 119.38 1.4913 +IC C25 C23 *C24 H4R 1.4913 119.38 -124.49 104.52 1.0843 +IC C25 C23 *C24 H4S 1.4913 119.38 124.63 107.15 1.1030 +IC C23 C24 C25 C26 1.5734 119.38 104.26 129.10 1.3677 +IC C26 C24 *C25 H5R 1.3677 129.10 176.59 115.26 1.0369 +IC C24 C25 C26 C27 1.4913 129.10 -1.09 128.95 1.4965 +IC C27 C25 *C26 H6R 1.4965 128.95 178.57 115.14 1.0884 +IC C25 C26 C27 C28 1.3677 128.95 88.87 109.99 1.5103 +IC C28 C26 *C27 H7R 1.5103 109.99 -125.14 103.72 1.1240 +IC C28 C26 *C27 H7S 1.5103 109.99 127.07 117.61 1.1196 +IC C26 C27 C28 C29 1.4965 109.99 105.39 125.30 1.3756 +IC C29 C27 *C28 H8R 1.3756 125.30 -175.89 110.46 1.1394 +IC C27 C28 C29 C210 1.5103 125.30 2.05 126.72 1.4782 +IC C210 C28 *C29 H9R 1.4782 126.72 178.19 123.98 1.1037 +IC C28 C29 C210 C211 1.3756 126.72 79.40 107.42 1.5372 +IC C211 C29 *C210 H10R 1.5372 107.42 -128.93 115.37 1.0912 +IC C211 C29 *C210 H10S 1.5372 107.42 115.81 113.85 1.1327 +IC C29 C210 C211 C212 1.4782 107.42 -140.04 121.47 1.3393 +IC C212 C210 *C211 H11R 1.3393 121.47 171.74 116.92 1.1281 +IC C210 C211 C212 C213 1.5372 121.47 -3.78 130.85 1.4812 +IC C213 C211 *C212 H12R 1.4812 130.85 -177.60 118.38 1.1147 +IC C211 C212 C213 C214 1.3393 130.85 120.66 111.38 1.5172 +IC C214 C212 *C213 H13R 1.5172 111.38 -129.02 113.95 1.1050 +IC C214 C212 *C213 H13S 1.5172 111.38 124.92 106.34 1.1527 +IC C212 C213 C214 C215 1.4812 111.38 133.02 125.55 1.3475 +IC C215 C213 *C214 H14R 1.3475 125.55 174.69 112.15 1.0981 +IC C213 C214 C215 C216 1.5172 125.55 2.79 126.86 1.5362 +IC C216 C214 *C215 H15R 1.5362 126.86 171.96 115.71 1.0681 +IC C214 C215 C216 C217 1.3475 126.86 96.79 105.55 1.5511 +IC C217 C215 *C216 H16R 1.5511 105.55 -119.46 108.65 1.0747 +IC C217 C215 *C216 H16S 1.5511 105.55 122.04 103.41 1.1472 +IC C215 C216 C217 C218 1.5362 105.55 172.30 115.85 1.5069 +IC C218 C216 *C217 H17R 1.5069 115.85 -121.02 116.63 1.1722 +IC C218 C216 *C217 H17S 1.5069 115.85 125.49 104.11 1.0955 +IC C216 C217 C218 C219 1.5511 115.85 79.77 111.75 1.5857 +IC C219 C217 *C218 H18R 1.5857 111.75 -127.58 106.24 1.0653 +IC C219 C217 *C218 H18S 1.5857 111.75 115.12 103.25 1.0754 +IC C217 C218 C219 C220 1.5069 111.75 175.62 115.95 1.5698 +IC C220 C218 *C219 H19R 1.5698 115.95 -120.78 111.21 1.0990 +IC C220 C218 *C219 H19S 1.5698 115.95 119.60 107.38 1.0649 +IC C218 C219 C220 H20T 1.5857 115.95 -173.64 112.47 1.1184 +IC H20T C219 *C220 H20R 1.1184 112.47 -123.64 97.48 1.1035 +IC H20T C219 *C220 H20S 1.1184 112.47 120.77 108.48 1.1706 +IC C31 C32 C33 C34 1.5067 108.44 171.75 110.23 1.5436 +IC C34 C32 *C33 H3X 1.5436 110.23 -110.98 112.84 1.1615 +IC C34 C32 *C33 H3Y 1.5436 110.23 133.41 103.67 1.1558 +IC C32 C33 C34 C35 1.5479 110.23 164.84 111.18 1.4944 +IC C35 C33 *C34 H4X 1.4944 111.18 -117.20 104.87 1.1406 +IC C35 C33 *C34 H4Y 1.4944 111.18 124.00 116.82 1.0964 +IC C33 C34 C35 C36 1.5436 111.18 -170.14 117.36 1.5364 +IC C36 C34 *C35 H5X 1.5364 117.36 -125.86 108.55 1.1375 +IC C36 C34 *C35 H5Y 1.5364 117.36 126.84 113.36 1.0725 +IC C34 C35 C36 C37 1.4944 117.36 97.24 109.17 1.5562 +IC C37 C35 *C36 H6X 1.5562 109.17 -124.93 110.74 1.0531 +IC C37 C35 *C36 H6Y 1.5562 109.17 113.66 107.60 1.0487 +IC C35 C36 C37 C38 1.5364 109.17 178.96 106.99 1.5073 +IC C38 C36 *C37 H7X 1.5073 106.99 -124.94 117.90 1.1226 +IC C38 C36 *C37 H7Y 1.5073 106.99 122.45 105.50 1.1013 +IC C36 C37 C38 C39 1.5562 106.99 -83.54 109.71 1.5851 +IC C39 C37 *C38 H8X 1.5851 109.71 -109.22 104.16 1.0971 +IC C39 C37 *C38 H8Y 1.5851 109.71 134.34 112.52 1.1060 +IC C37 C38 C39 C310 1.5073 109.71 -174.64 116.30 1.5943 +IC C310 C38 *C39 H9X 1.5943 116.30 -114.65 100.74 1.1124 +IC C310 C38 *C39 H9Y 1.5943 116.30 134.06 112.85 1.1282 +IC C38 C39 C310 C311 1.5851 116.30 -169.44 109.43 1.4985 +IC C311 C39 *C310 H10X 1.4985 109.43 -130.21 105.72 1.1666 +IC C311 C39 *C310 H10Y 1.4985 109.43 119.53 108.62 1.1449 +IC C39 C310 C311 C312 1.5943 109.43 -170.56 117.91 1.4759 +IC C312 C310 *C311 H11X 1.4759 117.91 -122.37 116.45 1.1315 +IC C312 C310 *C311 H11Y 1.4759 117.91 116.61 108.69 1.1832 +IC C310 C311 C312 C313 1.4985 117.91 178.48 111.44 1.4766 +IC C313 C311 *C312 H12X 1.4766 111.44 -125.26 104.27 1.1090 +IC C313 C311 *C312 H12Y 1.4766 111.44 122.86 110.52 1.1546 +IC C311 C312 C313 C314 1.4759 111.44 -73.70 111.39 1.5502 +IC C314 C312 *C313 H13X 1.5502 111.39 -108.82 102.78 1.1224 +IC C314 C312 *C313 H13Y 1.5502 111.39 127.20 121.20 1.1985 +IC C312 C313 C314 C315 1.4766 111.39 -138.36 114.17 1.5711 +IC C315 C313 *C314 H14X 1.5711 114.17 -118.23 110.45 1.1197 +IC C315 C313 *C314 H14Y 1.5711 114.17 117.77 107.23 1.1239 +IC C313 C314 C315 C316 1.5502 114.17 -176.45 108.82 1.5409 +IC C316 C314 *C315 H15X 1.5409 108.82 -124.54 113.33 1.1526 +IC C316 C314 *C315 H15Y 1.5409 108.82 108.91 111.46 1.1320 +IC C314 C315 C316 C317 1.5711 108.82 -66.54 116.11 1.5091 +IC C317 C315 *C316 H16X 1.5091 116.11 -124.62 112.51 1.1029 +IC C317 C315 *C316 H16Y 1.5091 116.11 122.83 112.61 1.1144 +IC C315 C316 C317 C318 1.5409 116.11 169.13 111.73 1.5513 +IC C318 C316 *C317 H17X 1.5513 111.73 -123.95 110.47 1.1648 +IC C318 C316 *C317 H17Y 1.5513 111.73 117.32 106.84 1.0646 +IC C316 C317 C318 H18X 1.5091 111.73 158.37 114.50 1.1275 +IC H18X C317 *C318 H18Y 1.1275 114.50 -124.88 106.66 1.0485 +IC H18X C317 *C318 H18Z 1.1275 114.50 121.03 108.03 1.1519 +IC C13 C11 *C12 O2 1.5674 111.91 122.45 118.73 1.4097 +IC O2 C11 *C12 H2 1.4097 118.73 125.03 106.36 1.1291 +IC C11 C12 O2 HO2 1.5612 118.73 -167.83 99.63 0.9607 +IC C14 C12 *C13 O3 1.5917 109.10 130.92 118.74 1.4674 +IC O3 C12 *C13 H3 1.4674 118.74 120.68 103.94 1.0541 +IC C12 C13 O3 P3 1.5674 118.74 42.01 126.24 1.6871 +IC C13 O3 P3 OP32 1.4674 126.24 54.16 111.19 1.5345 +IC OP32 O3 *P3 OP33 1.5345 111.19 -124.96 106.37 1.5032 +IC OP32 O3 *P3 OP34 1.5345 111.19 121.46 106.41 1.5163 +IC C15 C13 *C14 O4 1.5949 107.50 -124.00 109.20 1.3934 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC O4 C13 *C14 H4 1.3934 109.20 -118.02 114.14 1.1398 +IC C13 C14 C15 O5 1.5917 107.50 174.60 116.85 1.4429 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC O5 C14 *C15 C16 1.4429 116.85 -116.07 114.15 1.5236 +IC C16 C14 *C15 H5 1.5236 114.15 -121.85 104.07 1.1817 +IC C11 C15 *C16 O6 1.5105 109.31 -119.88 114.69 1.4905 +IC C11 C15 *C16 H6 1.5105 109.31 117.69 108.42 1.1464 +IC C15 C16 O6 HO6 1.5236 114.69 -20.26 102.28 0.9438 + +RESI SAPI14 -3.00 ! Phosphatidylinositol-(4)-phosphate (PIP1) +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4---P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | | +ATOM OP42 OC2DP -0.90 ! | H3 +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5612 111.91 56.25 109.10 1.5917 +IC C12 C13 C14 C15 1.5674 109.10 -55.67 107.50 1.5949 +IC C13 C14 C15 C16 1.5917 107.50 58.53 114.15 1.5236 +IC C14 C15 C16 C11 1.5949 114.15 -57.38 109.31 1.5105 +IC C15 C16 C11 C12 1.5236 109.31 54.67 113.12 1.5612 +IC C16 C11 C12 C13 1.5105 113.12 -56.32 111.91 1.5674 +IC C16 C12 *C11 H1 1.5105 113.12 119.75 101.91 1.1392 +IC C16 C12 *C11 O12 1.5105 113.12 -126.20 107.76 1.4882 +IC C11 C13 *C12 H2 1.5612 111.91 114.21 103.64 1.1291 +IC C11 C13 *C12 O2 1.5612 111.91 -130.03 104.90 1.4097 +IC C12 C14 *C13 H3 1.5674 109.10 109.60 102.16 1.0541 +IC C12 C14 *C13 O3 1.5674 109.10 -134.10 112.67 1.4674 +IC C13 C15 *C14 H4 1.5917 107.50 -122.77 106.58 1.1398 +IC C13 C15 *C14 O4 1.5917 107.50 121.11 113.88 1.3934 +IC C14 C16 *C15 H5 1.5949 114.15 117.62 111.57 1.1817 +IC C14 C16 *C15 O5 1.5949 114.15 -125.54 99.96 1.4429 +IC C15 C11 *C16 H6 1.5236 109.31 -117.85 108.15 1.1464 +IC C15 C11 *C16 O6 1.5236 109.31 124.62 106.80 1.4905 +IC C13 C12 O2 HO2 1.5674 104.90 -41.95 99.63 0.9607 +IC C11 C16 O6 HO6 1.5105 106.80 -141.52 102.28 0.9438 +IC C12 C11 O12 P 1.5612 107.76 -97.72 122.87 1.6738 +IC C11 O12 P O11 1.4882 122.87 -170.14 101.78 1.5624 +IC O11 O12 *P O13 1.5624 101.78 -111.87 115.92 1.4812 +IC O11 O12 *P O14 1.5624 101.78 114.33 108.26 1.4737 +IC O12 P O11 C1 1.6738 101.78 93.71 119.03 1.4527 +IC P O11 C1 C2 1.5624 119.03 90.59 109.51 1.5472 +IC C2 O11 *C1 HA 1.5472 109.51 116.74 102.40 1.1035 +IC HA O11 *C1 HB 1.1035 102.40 119.29 118.20 1.0905 +IC O11 C1 C2 O21 1.4527 109.51 159.98 105.23 1.3918 +IC O21 C1 *C2 C3 1.3918 105.23 -122.31 113.46 1.5224 +IC C3 C1 *C2 HS 1.5224 113.46 -112.81 98.08 1.1373 +IC C1 C2 O21 C21 1.5472 105.23 121.03 107.61 1.3130 +IC C2 O21 C21 C22 1.3918 107.61 -143.71 110.27 1.5240 +IC C22 O21 *C21 O22 1.5240 110.27 -173.26 123.94 1.2252 +IC O21 C21 C22 C23 1.3130 110.27 -100.54 114.05 1.5966 +IC C23 C21 *C22 H2R 1.5966 114.05 136.83 117.96 1.1359 +IC H2R C21 *C22 H2S 1.1359 117.96 112.37 110.66 1.1750 +IC C1 C2 C3 O31 1.5472 113.46 -164.03 113.68 1.4560 +IC O31 C2 *C3 HX 1.4560 113.68 -124.81 109.24 1.1421 +IC HX C2 *C3 HY 1.1421 109.24 -119.37 107.12 1.0811 +IC C2 C3 O31 C31 1.5224 113.68 -78.97 117.94 1.3060 +IC C3 O31 C31 C32 1.4560 117.94 176.98 108.04 1.5067 +IC C32 O31 *C31 O32 1.5067 108.04 167.41 128.04 1.2105 +IC O31 C31 C32 C33 1.3060 108.04 -179.87 108.44 1.5479 +IC C33 C31 *C32 H2X 1.5479 108.44 -133.26 115.68 1.1387 +IC H2X C31 *C32 H2Y 1.1387 115.68 -113.16 105.10 1.0739 +IC C21 C22 C23 C24 1.5240 114.05 71.06 110.64 1.5734 +IC C24 C22 *C23 H3R 1.5734 110.64 -124.62 113.03 1.1251 +IC C24 C22 *C23 H3S 1.5734 110.64 116.69 108.70 1.1403 +IC C22 C23 C24 C25 1.5966 110.64 -179.26 119.38 1.4913 +IC C25 C23 *C24 H4R 1.4913 119.38 -124.49 104.52 1.0843 +IC C25 C23 *C24 H4S 1.4913 119.38 124.63 107.15 1.1030 +IC C23 C24 C25 C26 1.5734 119.38 104.26 129.10 1.3677 +IC C26 C24 *C25 H5R 1.3677 129.10 176.59 115.26 1.0369 +IC C24 C25 C26 C27 1.4913 129.10 -1.09 128.95 1.4965 +IC C27 C25 *C26 H6R 1.4965 128.95 178.57 115.14 1.0884 +IC C25 C26 C27 C28 1.3677 128.95 88.87 109.99 1.5103 +IC C28 C26 *C27 H7R 1.5103 109.99 -125.14 103.72 1.1240 +IC C28 C26 *C27 H7S 1.5103 109.99 127.07 117.61 1.1196 +IC C26 C27 C28 C29 1.4965 109.99 105.39 125.30 1.3756 +IC C29 C27 *C28 H8R 1.3756 125.30 -175.89 110.46 1.1394 +IC C27 C28 C29 C210 1.5103 125.30 2.05 126.72 1.4782 +IC C210 C28 *C29 H9R 1.4782 126.72 178.19 123.98 1.1037 +IC C28 C29 C210 C211 1.3756 126.72 79.40 107.42 1.5372 +IC C211 C29 *C210 H10R 1.5372 107.42 -128.93 115.37 1.0912 +IC C211 C29 *C210 H10S 1.5372 107.42 115.81 113.85 1.1327 +IC C29 C210 C211 C212 1.4782 107.42 -140.04 121.47 1.3393 +IC C212 C210 *C211 H11R 1.3393 121.47 171.74 116.92 1.1281 +IC C210 C211 C212 C213 1.5372 121.47 -3.78 130.85 1.4812 +IC C213 C211 *C212 H12R 1.4812 130.85 -177.60 118.38 1.1147 +IC C211 C212 C213 C214 1.3393 130.85 120.66 111.38 1.5172 +IC C214 C212 *C213 H13R 1.5172 111.38 -129.02 113.95 1.1050 +IC C214 C212 *C213 H13S 1.5172 111.38 124.92 106.34 1.1527 +IC C212 C213 C214 C215 1.4812 111.38 133.02 125.55 1.3475 +IC C215 C213 *C214 H14R 1.3475 125.55 174.69 112.15 1.0981 +IC C213 C214 C215 C216 1.5172 125.55 2.79 126.86 1.5362 +IC C216 C214 *C215 H15R 1.5362 126.86 171.96 115.71 1.0681 +IC C214 C215 C216 C217 1.3475 126.86 96.79 105.55 1.5511 +IC C217 C215 *C216 H16R 1.5511 105.55 -119.46 108.65 1.0747 +IC C217 C215 *C216 H16S 1.5511 105.55 122.04 103.41 1.1472 +IC C215 C216 C217 C218 1.5362 105.55 172.30 115.85 1.5069 +IC C218 C216 *C217 H17R 1.5069 115.85 -121.02 116.63 1.1722 +IC C218 C216 *C217 H17S 1.5069 115.85 125.49 104.11 1.0955 +IC C216 C217 C218 C219 1.5511 115.85 79.77 111.75 1.5857 +IC C219 C217 *C218 H18R 1.5857 111.75 -127.58 106.24 1.0653 +IC C219 C217 *C218 H18S 1.5857 111.75 115.12 103.25 1.0754 +IC C217 C218 C219 C220 1.5069 111.75 175.62 115.95 1.5698 +IC C220 C218 *C219 H19R 1.5698 115.95 -120.78 111.21 1.0990 +IC C220 C218 *C219 H19S 1.5698 115.95 119.60 107.38 1.0649 +IC C218 C219 C220 H20T 1.5857 115.95 -173.64 112.47 1.1184 +IC H20T C219 *C220 H20R 1.1184 112.47 -123.64 97.48 1.1035 +IC H20T C219 *C220 H20S 1.1184 112.47 120.77 108.48 1.1706 +IC C31 C32 C33 C34 1.5067 108.44 171.75 110.23 1.5436 +IC C34 C32 *C33 H3X 1.5436 110.23 -110.98 112.84 1.1615 +IC C34 C32 *C33 H3Y 1.5436 110.23 133.41 103.67 1.1558 +IC C32 C33 C34 C35 1.5479 110.23 164.84 111.18 1.4944 +IC C35 C33 *C34 H4X 1.4944 111.18 -117.20 104.87 1.1406 +IC C35 C33 *C34 H4Y 1.4944 111.18 124.00 116.82 1.0964 +IC C33 C34 C35 C36 1.5436 111.18 -170.14 117.36 1.5364 +IC C36 C34 *C35 H5X 1.5364 117.36 -125.86 108.55 1.1375 +IC C36 C34 *C35 H5Y 1.5364 117.36 126.84 113.36 1.0725 +IC C34 C35 C36 C37 1.4944 117.36 97.24 109.17 1.5562 +IC C37 C35 *C36 H6X 1.5562 109.17 -124.93 110.74 1.0531 +IC C37 C35 *C36 H6Y 1.5562 109.17 113.66 107.60 1.0487 +IC C35 C36 C37 C38 1.5364 109.17 178.96 106.99 1.5073 +IC C38 C36 *C37 H7X 1.5073 106.99 -124.94 117.90 1.1226 +IC C38 C36 *C37 H7Y 1.5073 106.99 122.45 105.50 1.1013 +IC C36 C37 C38 C39 1.5562 106.99 -83.54 109.71 1.5851 +IC C39 C37 *C38 H8X 1.5851 109.71 -109.22 104.16 1.0971 +IC C39 C37 *C38 H8Y 1.5851 109.71 134.34 112.52 1.1060 +IC C37 C38 C39 C310 1.5073 109.71 -174.64 116.30 1.5943 +IC C310 C38 *C39 H9X 1.5943 116.30 -114.65 100.74 1.1124 +IC C310 C38 *C39 H9Y 1.5943 116.30 134.06 112.85 1.1282 +IC C38 C39 C310 C311 1.5851 116.30 -169.44 109.43 1.4985 +IC C311 C39 *C310 H10X 1.4985 109.43 -130.21 105.72 1.1666 +IC C311 C39 *C310 H10Y 1.4985 109.43 119.53 108.62 1.1449 +IC C39 C310 C311 C312 1.5943 109.43 -170.56 117.91 1.4759 +IC C312 C310 *C311 H11X 1.4759 117.91 -122.37 116.45 1.1315 +IC C312 C310 *C311 H11Y 1.4759 117.91 116.61 108.69 1.1832 +IC C310 C311 C312 C313 1.4985 117.91 178.48 111.44 1.4766 +IC C313 C311 *C312 H12X 1.4766 111.44 -125.26 104.27 1.1090 +IC C313 C311 *C312 H12Y 1.4766 111.44 122.86 110.52 1.1546 +IC C311 C312 C313 C314 1.4759 111.44 -73.70 111.39 1.5502 +IC C314 C312 *C313 H13X 1.5502 111.39 -108.82 102.78 1.1224 +IC C314 C312 *C313 H13Y 1.5502 111.39 127.20 121.20 1.1985 +IC C312 C313 C314 C315 1.4766 111.39 -138.36 114.17 1.5711 +IC C315 C313 *C314 H14X 1.5711 114.17 -118.23 110.45 1.1197 +IC C315 C313 *C314 H14Y 1.5711 114.17 117.77 107.23 1.1239 +IC C313 C314 C315 C316 1.5502 114.17 -176.45 108.82 1.5409 +IC C316 C314 *C315 H15X 1.5409 108.82 -124.54 113.33 1.1526 +IC C316 C314 *C315 H15Y 1.5409 108.82 108.91 111.46 1.1320 +IC C314 C315 C316 C317 1.5711 108.82 -66.54 116.11 1.5091 +IC C317 C315 *C316 H16X 1.5091 116.11 -124.62 112.51 1.1029 +IC C317 C315 *C316 H16Y 1.5091 116.11 122.83 112.61 1.1144 +IC C315 C316 C317 C318 1.5409 116.11 169.13 111.73 1.5513 +IC C318 C316 *C317 H17X 1.5513 111.73 -123.95 110.47 1.1648 +IC C318 C316 *C317 H17Y 1.5513 111.73 117.32 106.84 1.0646 +IC C316 C317 C318 H18X 1.5091 111.73 158.37 114.50 1.1275 +IC H18X C317 *C318 H18Y 1.1275 114.50 -124.88 106.66 1.0485 +IC H18X C317 *C318 H18Z 1.1275 114.50 121.03 108.03 1.1519 +IC C13 C11 *C12 O2 1.5674 111.91 122.45 118.73 1.4097 +IC O2 C11 *C12 H2 1.4097 118.73 125.03 106.36 1.1291 +IC C11 C12 O2 HO2 1.5612 118.73 -167.83 99.63 0.9607 +IC C14 C12 *C13 O3 1.5917 109.10 130.92 118.74 1.4674 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC O3 C12 *C13 H3 1.4674 118.74 120.68 103.94 1.0541 +IC C15 C13 *C14 O4 1.5949 107.50 -124.00 109.20 1.3934 +IC C13 C14 O4 P4 1.5613 107.65 -87.92 128.14 1.7068 +IC C14 O4 P4 OP42 1.4338 128.14 -174.57 99.96 1.4982 +IC OP42 O4 *P4 OP43 1.4982 99.96 119.26 103.52 1.5184 +IC OP42 O4 *P4 OP44 1.4982 99.96 -119.87 108.84 1.5595 +IC O4 C13 *C14 H4 1.3934 109.20 -118.02 114.14 1.1398 +IC C13 C14 C15 O5 1.5917 107.50 174.60 116.85 1.4429 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC O5 C14 *C15 C16 1.4429 116.85 -116.07 114.15 1.5236 +IC C16 C14 *C15 H5 1.5236 114.15 -121.85 104.07 1.1817 +IC C11 C15 *C16 O6 1.5105 109.31 -119.88 114.69 1.4905 +IC C11 C15 *C16 H6 1.5105 109.31 117.69 108.42 1.1464 +IC C15 C16 O6 HO6 1.5236 114.69 -20.26 102.28 0.9438 + +RESI SAPI15 -3.00 ! Phosphatidylinositol-(5)-phosphate (PIP1) +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5612 111.91 56.25 109.10 1.5917 +IC C12 C13 C14 C15 1.5674 109.10 -55.67 107.50 1.5949 +IC C13 C14 C15 C16 1.5917 107.50 58.53 114.15 1.5236 +IC C14 C15 C16 C11 1.5949 114.15 -57.38 109.31 1.5105 +IC C15 C16 C11 C12 1.5236 109.31 54.67 113.12 1.5612 +IC C16 C11 C12 C13 1.5105 113.12 -56.32 111.91 1.5674 +IC C16 C12 *C11 H1 1.5105 113.12 119.75 101.91 1.1392 +IC C16 C12 *C11 O12 1.5105 113.12 -126.20 107.76 1.4882 +IC C11 C13 *C12 H2 1.5612 111.91 114.21 103.64 1.1291 +IC C11 C13 *C12 O2 1.5612 111.91 -130.03 104.90 1.4097 +IC C12 C14 *C13 H3 1.5674 109.10 109.60 102.16 1.0541 +IC C12 C14 *C13 O3 1.5674 109.10 -134.10 112.67 1.4674 +IC C13 C15 *C14 H4 1.5917 107.50 -122.77 106.58 1.1398 +IC C13 C15 *C14 O4 1.5917 107.50 121.11 113.88 1.3934 +IC C14 C16 *C15 H5 1.5949 114.15 117.62 111.57 1.1817 +IC C14 C16 *C15 O5 1.5949 114.15 -125.54 99.96 1.4429 +IC C15 C11 *C16 H6 1.5236 109.31 -117.85 108.15 1.1464 +IC C15 C11 *C16 O6 1.5236 109.31 124.62 106.80 1.4905 +IC C13 C12 O2 HO2 1.5674 104.90 -41.95 99.63 0.9607 +IC C11 C16 O6 HO6 1.5105 106.80 -141.52 102.28 0.9438 +IC C12 C11 O12 P 1.5612 107.76 -97.72 122.87 1.6738 +IC C11 O12 P O11 1.4882 122.87 -170.14 101.78 1.5624 +IC O11 O12 *P O13 1.5624 101.78 -111.87 115.92 1.4812 +IC O11 O12 *P O14 1.5624 101.78 114.33 108.26 1.4737 +IC O12 P O11 C1 1.6738 101.78 93.71 119.03 1.4527 +IC P O11 C1 C2 1.5624 119.03 90.59 109.51 1.5472 +IC C2 O11 *C1 HA 1.5472 109.51 116.74 102.40 1.1035 +IC HA O11 *C1 HB 1.1035 102.40 119.29 118.20 1.0905 +IC O11 C1 C2 O21 1.4527 109.51 159.98 105.23 1.3918 +IC O21 C1 *C2 C3 1.3918 105.23 -122.31 113.46 1.5224 +IC C3 C1 *C2 HS 1.5224 113.46 -112.81 98.08 1.1373 +IC C1 C2 O21 C21 1.5472 105.23 121.03 107.61 1.3130 +IC C2 O21 C21 C22 1.3918 107.61 -143.71 110.27 1.5240 +IC C22 O21 *C21 O22 1.5240 110.27 -173.26 123.94 1.2252 +IC O21 C21 C22 C23 1.3130 110.27 -100.54 114.05 1.5966 +IC C23 C21 *C22 H2R 1.5966 114.05 136.83 117.96 1.1359 +IC H2R C21 *C22 H2S 1.1359 117.96 112.37 110.66 1.1750 +IC C1 C2 C3 O31 1.5472 113.46 -164.03 113.68 1.4560 +IC O31 C2 *C3 HX 1.4560 113.68 -124.81 109.24 1.1421 +IC HX C2 *C3 HY 1.1421 109.24 -119.37 107.12 1.0811 +IC C2 C3 O31 C31 1.5224 113.68 -78.97 117.94 1.3060 +IC C3 O31 C31 C32 1.4560 117.94 176.98 108.04 1.5067 +IC C32 O31 *C31 O32 1.5067 108.04 167.41 128.04 1.2105 +IC O31 C31 C32 C33 1.3060 108.04 -179.87 108.44 1.5479 +IC C33 C31 *C32 H2X 1.5479 108.44 -133.26 115.68 1.1387 +IC H2X C31 *C32 H2Y 1.1387 115.68 -113.16 105.10 1.0739 +IC C21 C22 C23 C24 1.5240 114.05 71.06 110.64 1.5734 +IC C24 C22 *C23 H3R 1.5734 110.64 -124.62 113.03 1.1251 +IC C24 C22 *C23 H3S 1.5734 110.64 116.69 108.70 1.1403 +IC C22 C23 C24 C25 1.5966 110.64 -179.26 119.38 1.4913 +IC C25 C23 *C24 H4R 1.4913 119.38 -124.49 104.52 1.0843 +IC C25 C23 *C24 H4S 1.4913 119.38 124.63 107.15 1.1030 +IC C23 C24 C25 C26 1.5734 119.38 104.26 129.10 1.3677 +IC C26 C24 *C25 H5R 1.3677 129.10 176.59 115.26 1.0369 +IC C24 C25 C26 C27 1.4913 129.10 -1.09 128.95 1.4965 +IC C27 C25 *C26 H6R 1.4965 128.95 178.57 115.14 1.0884 +IC C25 C26 C27 C28 1.3677 128.95 88.87 109.99 1.5103 +IC C28 C26 *C27 H7R 1.5103 109.99 -125.14 103.72 1.1240 +IC C28 C26 *C27 H7S 1.5103 109.99 127.07 117.61 1.1196 +IC C26 C27 C28 C29 1.4965 109.99 105.39 125.30 1.3756 +IC C29 C27 *C28 H8R 1.3756 125.30 -175.89 110.46 1.1394 +IC C27 C28 C29 C210 1.5103 125.30 2.05 126.72 1.4782 +IC C210 C28 *C29 H9R 1.4782 126.72 178.19 123.98 1.1037 +IC C28 C29 C210 C211 1.3756 126.72 79.40 107.42 1.5372 +IC C211 C29 *C210 H10R 1.5372 107.42 -128.93 115.37 1.0912 +IC C211 C29 *C210 H10S 1.5372 107.42 115.81 113.85 1.1327 +IC C29 C210 C211 C212 1.4782 107.42 -140.04 121.47 1.3393 +IC C212 C210 *C211 H11R 1.3393 121.47 171.74 116.92 1.1281 +IC C210 C211 C212 C213 1.5372 121.47 -3.78 130.85 1.4812 +IC C213 C211 *C212 H12R 1.4812 130.85 -177.60 118.38 1.1147 +IC C211 C212 C213 C214 1.3393 130.85 120.66 111.38 1.5172 +IC C214 C212 *C213 H13R 1.5172 111.38 -129.02 113.95 1.1050 +IC C214 C212 *C213 H13S 1.5172 111.38 124.92 106.34 1.1527 +IC C212 C213 C214 C215 1.4812 111.38 133.02 125.55 1.3475 +IC C215 C213 *C214 H14R 1.3475 125.55 174.69 112.15 1.0981 +IC C213 C214 C215 C216 1.5172 125.55 2.79 126.86 1.5362 +IC C216 C214 *C215 H15R 1.5362 126.86 171.96 115.71 1.0681 +IC C214 C215 C216 C217 1.3475 126.86 96.79 105.55 1.5511 +IC C217 C215 *C216 H16R 1.5511 105.55 -119.46 108.65 1.0747 +IC C217 C215 *C216 H16S 1.5511 105.55 122.04 103.41 1.1472 +IC C215 C216 C217 C218 1.5362 105.55 172.30 115.85 1.5069 +IC C218 C216 *C217 H17R 1.5069 115.85 -121.02 116.63 1.1722 +IC C218 C216 *C217 H17S 1.5069 115.85 125.49 104.11 1.0955 +IC C216 C217 C218 C219 1.5511 115.85 79.77 111.75 1.5857 +IC C219 C217 *C218 H18R 1.5857 111.75 -127.58 106.24 1.0653 +IC C219 C217 *C218 H18S 1.5857 111.75 115.12 103.25 1.0754 +IC C217 C218 C219 C220 1.5069 111.75 175.62 115.95 1.5698 +IC C220 C218 *C219 H19R 1.5698 115.95 -120.78 111.21 1.0990 +IC C220 C218 *C219 H19S 1.5698 115.95 119.60 107.38 1.0649 +IC C218 C219 C220 H20T 1.5857 115.95 -173.64 112.47 1.1184 +IC H20T C219 *C220 H20R 1.1184 112.47 -123.64 97.48 1.1035 +IC H20T C219 *C220 H20S 1.1184 112.47 120.77 108.48 1.1706 +IC C31 C32 C33 C34 1.5067 108.44 171.75 110.23 1.5436 +IC C34 C32 *C33 H3X 1.5436 110.23 -110.98 112.84 1.1615 +IC C34 C32 *C33 H3Y 1.5436 110.23 133.41 103.67 1.1558 +IC C32 C33 C34 C35 1.5479 110.23 164.84 111.18 1.4944 +IC C35 C33 *C34 H4X 1.4944 111.18 -117.20 104.87 1.1406 +IC C35 C33 *C34 H4Y 1.4944 111.18 124.00 116.82 1.0964 +IC C33 C34 C35 C36 1.5436 111.18 -170.14 117.36 1.5364 +IC C36 C34 *C35 H5X 1.5364 117.36 -125.86 108.55 1.1375 +IC C36 C34 *C35 H5Y 1.5364 117.36 126.84 113.36 1.0725 +IC C34 C35 C36 C37 1.4944 117.36 97.24 109.17 1.5562 +IC C37 C35 *C36 H6X 1.5562 109.17 -124.93 110.74 1.0531 +IC C37 C35 *C36 H6Y 1.5562 109.17 113.66 107.60 1.0487 +IC C35 C36 C37 C38 1.5364 109.17 178.96 106.99 1.5073 +IC C38 C36 *C37 H7X 1.5073 106.99 -124.94 117.90 1.1226 +IC C38 C36 *C37 H7Y 1.5073 106.99 122.45 105.50 1.1013 +IC C36 C37 C38 C39 1.5562 106.99 -83.54 109.71 1.5851 +IC C39 C37 *C38 H8X 1.5851 109.71 -109.22 104.16 1.0971 +IC C39 C37 *C38 H8Y 1.5851 109.71 134.34 112.52 1.1060 +IC C37 C38 C39 C310 1.5073 109.71 -174.64 116.30 1.5943 +IC C310 C38 *C39 H9X 1.5943 116.30 -114.65 100.74 1.1124 +IC C310 C38 *C39 H9Y 1.5943 116.30 134.06 112.85 1.1282 +IC C38 C39 C310 C311 1.5851 116.30 -169.44 109.43 1.4985 +IC C311 C39 *C310 H10X 1.4985 109.43 -130.21 105.72 1.1666 +IC C311 C39 *C310 H10Y 1.4985 109.43 119.53 108.62 1.1449 +IC C39 C310 C311 C312 1.5943 109.43 -170.56 117.91 1.4759 +IC C312 C310 *C311 H11X 1.4759 117.91 -122.37 116.45 1.1315 +IC C312 C310 *C311 H11Y 1.4759 117.91 116.61 108.69 1.1832 +IC C310 C311 C312 C313 1.4985 117.91 178.48 111.44 1.4766 +IC C313 C311 *C312 H12X 1.4766 111.44 -125.26 104.27 1.1090 +IC C313 C311 *C312 H12Y 1.4766 111.44 122.86 110.52 1.1546 +IC C311 C312 C313 C314 1.4759 111.44 -73.70 111.39 1.5502 +IC C314 C312 *C313 H13X 1.5502 111.39 -108.82 102.78 1.1224 +IC C314 C312 *C313 H13Y 1.5502 111.39 127.20 121.20 1.1985 +IC C312 C313 C314 C315 1.4766 111.39 -138.36 114.17 1.5711 +IC C315 C313 *C314 H14X 1.5711 114.17 -118.23 110.45 1.1197 +IC C315 C313 *C314 H14Y 1.5711 114.17 117.77 107.23 1.1239 +IC C313 C314 C315 C316 1.5502 114.17 -176.45 108.82 1.5409 +IC C316 C314 *C315 H15X 1.5409 108.82 -124.54 113.33 1.1526 +IC C316 C314 *C315 H15Y 1.5409 108.82 108.91 111.46 1.1320 +IC C314 C315 C316 C317 1.5711 108.82 -66.54 116.11 1.5091 +IC C317 C315 *C316 H16X 1.5091 116.11 -124.62 112.51 1.1029 +IC C317 C315 *C316 H16Y 1.5091 116.11 122.83 112.61 1.1144 +IC C315 C316 C317 C318 1.5409 116.11 169.13 111.73 1.5513 +IC C318 C316 *C317 H17X 1.5513 111.73 -123.95 110.47 1.1648 +IC C318 C316 *C317 H17Y 1.5513 111.73 117.32 106.84 1.0646 +IC C316 C317 C318 H18X 1.5091 111.73 158.37 114.50 1.1275 +IC H18X C317 *C318 H18Y 1.1275 114.50 -124.88 106.66 1.0485 +IC H18X C317 *C318 H18Z 1.1275 114.50 121.03 108.03 1.1519 +IC C13 C11 *C12 O2 1.5674 111.91 122.45 118.73 1.4097 +IC O2 C11 *C12 H2 1.4097 118.73 125.03 106.36 1.1291 +IC C11 C12 O2 HO2 1.5612 118.73 -167.83 99.63 0.9607 +IC C14 C12 *C13 O3 1.5917 109.10 130.92 118.74 1.4674 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC O3 C12 *C13 H3 1.4674 118.74 120.68 103.94 1.0541 +IC C15 C13 *C14 O4 1.5949 107.50 -124.00 109.20 1.3934 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC O4 C13 *C14 H4 1.3934 109.20 -118.02 114.14 1.1398 +IC C13 C14 C15 O5 1.5917 107.50 174.60 116.85 1.4429 +IC C14 C15 O5 P5 1.5278 108.72 -81.32 122.97 1.6718 +IC C15 O5 P5 OP52 1.4226 122.97 47.02 110.21 1.5352 +IC OP52 O5 *P5 OP53 1.5352 110.21 -123.93 103.64 1.5006 +IC OP52 O5 *P5 OP54 1.5352 110.21 119.82 108.27 1.5123 +IC O5 C14 *C15 C16 1.4429 116.85 -116.07 114.15 1.5236 +IC C16 C14 *C15 H5 1.5236 114.15 -121.85 104.07 1.1817 +IC C11 C15 *C16 O6 1.5105 109.31 -119.88 114.69 1.4905 +IC C11 C15 *C16 H6 1.5105 109.31 117.69 108.42 1.1464 +IC C15 C16 O6 HO6 1.5236 114.69 -20.26 102.28 0.9438 + +RESI SAPI24 -4.00 ! Phosphatidylinositol-(4,5)-bisphosphate (PIP2) with protonation on P4 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42-HP42 +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.01 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC30P -0.62 ! | | +ATOM P4 PC 1.50 ! | | +ATOM OP42 OC312 -0.68 ! | H3 +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5621 110.54 60.89 111.34 1.5026 +IC C12 C13 C14 C15 1.5575 111.34 -59.52 107.22 1.5278 +IC C13 C14 C15 C16 1.5026 107.22 61.10 110.17 1.5378 +IC C14 C15 C16 C11 1.5278 110.17 -64.28 110.38 1.5496 +IC C15 C16 C11 C12 1.5378 110.38 60.62 105.21 1.5621 +IC C16 C11 C12 C13 1.5496 105.21 -58.42 110.54 1.5575 +IC C16 C12 *C11 H1 1.5496 105.21 110.05 107.53 1.1222 +IC C16 C12 *C11 O12 1.5496 105.21 -131.14 110.38 1.4427 +IC C11 C13 *C12 H2 1.5621 110.54 124.49 112.64 1.1206 +IC C11 C13 *C12 O2 1.5621 110.54 -115.66 111.96 1.4063 +IC C12 C14 *C13 H3 1.5575 111.34 120.42 109.88 1.1084 +IC C12 C14 *C13 O3 1.5575 111.34 -121.56 111.38 1.4241 +IC C13 C15 *C14 H4 1.5026 107.22 -125.49 108.61 1.1246 +IC C13 C15 *C14 O4 1.5026 107.22 115.67 116.82 1.4335 +IC C14 C16 *C15 H5 1.5278 110.17 109.49 104.68 1.0917 +IC C14 C16 *C15 O5 1.5278 110.17 -123.78 115.69 1.4226 +IC C15 C11 *C16 H6 1.5378 110.38 -121.60 116.27 1.0609 +IC C15 C11 *C16 O6 1.5378 110.38 113.66 107.00 1.4397 +IC C13 C12 O2 HO2 1.5575 111.96 71.63 106.48 0.9937 +IC C14 C13 O3 HO3 1.5026 111.38 -0.25 101.99 0.9558 +IC C11 C16 O6 HO6 1.5496 107.00 178.41 100.67 1.0033 +IC C12 C11 O12 P 1.5621 110.38 -72.66 125.01 1.7079 +IC C11 O12 P O11 1.4427 125.01 177.41 103.93 1.5953 +IC O11 O12 *P O13 1.5953 103.93 -111.03 115.50 1.4678 +IC O11 O12 *P O14 1.5953 103.93 116.43 108.67 1.5094 +IC O12 P O11 C1 1.7079 103.93 49.90 124.67 1.4019 +IC P O11 C1 C2 1.5953 124.67 130.15 106.62 1.5828 +IC C2 O11 *C1 HA 1.5828 106.62 118.12 110.07 1.0741 +IC HA O11 *C1 HB 1.0741 110.07 121.21 118.51 1.1604 +IC O11 C1 C2 O21 1.4019 106.62 -90.20 107.66 1.4562 +IC O21 C1 *C2 C3 1.4562 107.66 -121.90 117.11 1.5384 +IC C3 C1 *C2 HS 1.5384 117.11 -120.59 108.26 1.1131 +IC C1 C2 O21 C21 1.5828 107.66 114.28 116.54 1.3152 +IC C2 O21 C21 C22 1.4562 116.54 -153.73 108.34 1.5253 +IC C22 O21 *C21 O22 1.5253 108.34 -173.86 126.56 1.2073 +IC O21 C21 C22 C23 1.3152 108.34 -110.66 112.79 1.5574 +IC C23 C21 *C22 H2R 1.5574 112.79 120.32 117.08 1.1174 +IC H2R C21 *C22 H2S 1.1174 117.08 119.32 105.37 1.0660 +IC C1 C2 C3 O31 1.5828 117.11 -139.23 115.37 1.4341 +IC O31 C2 *C3 HX 1.4341 115.37 -139.06 112.02 1.0911 +IC HX C2 *C3 HY 1.0911 112.02 -102.02 99.46 1.0613 +IC C2 C3 O31 C31 1.5384 115.37 -99.01 112.79 1.3401 +IC C3 O31 C31 C32 1.4341 112.79 150.94 107.22 1.5034 +IC C32 O31 *C31 O32 1.5034 107.22 -178.35 125.71 1.2210 +IC O31 C31 C32 C33 1.3401 107.22 -146.21 115.84 1.5017 +IC C33 C31 *C32 H2X 1.5017 115.84 -113.16 94.73 1.1864 +IC H2X C31 *C32 H2Y 1.1864 94.73 -107.81 118.41 1.0511 +IC C21 C22 C23 C24 1.5253 112.79 80.29 115.55 1.5782 +IC C24 C22 *C23 H3R 1.5782 115.55 -121.96 109.62 1.0727 +IC C24 C22 *C23 H3S 1.5782 115.55 118.69 114.52 1.0904 +IC C22 C23 C24 C25 1.5574 115.55 174.18 115.63 1.4790 +IC C25 C23 *C24 H4R 1.4790 115.63 -124.17 105.06 1.1230 +IC C25 C23 *C24 H4S 1.4790 115.63 121.53 108.42 1.0666 +IC C23 C24 C25 C26 1.5782 115.63 82.19 124.76 1.3396 +IC C26 C24 *C25 H5R 1.3396 124.76 175.22 115.53 1.1243 +IC C24 C25 C26 C27 1.4790 124.76 0.02 125.25 1.4776 +IC C27 C25 *C26 H6R 1.4776 125.25 165.23 123.26 1.0949 +IC C25 C26 C27 C28 1.3396 125.25 99.05 117.40 1.5443 +IC C28 C26 *C27 H7R 1.5443 117.40 -117.82 111.59 1.1099 +IC C28 C26 *C27 H7S 1.5443 117.40 128.74 108.44 1.1508 +IC C26 C27 C28 C29 1.4776 117.40 81.16 127.22 1.3009 +IC C29 C27 *C28 H8R 1.3009 127.22 175.22 115.58 1.0818 +IC C27 C28 C29 C210 1.5443 127.22 0.73 126.65 1.5213 +IC C210 C28 *C29 H9R 1.5213 126.65 171.06 114.85 1.0944 +IC C28 C29 C210 C211 1.3009 126.65 68.67 118.88 1.4905 +IC C211 C29 *C210 H10R 1.4905 118.88 -126.37 102.66 1.1496 +IC C211 C29 *C210 H10S 1.4905 118.88 124.11 109.57 1.1538 +IC C29 C210 C211 C212 1.5213 118.88 106.01 126.63 1.4033 +IC C212 C210 *C211 H11R 1.4033 126.63 177.30 111.91 1.0901 +IC C210 C211 C212 C213 1.4905 126.63 -2.69 125.10 1.5295 +IC C213 C211 *C212 H12R 1.5295 125.10 -157.31 127.96 1.1366 +IC C211 C212 C213 C214 1.4033 125.10 111.12 102.98 1.5039 +IC C214 C212 *C213 H13R 1.5039 102.98 -112.30 115.34 1.1484 +IC C214 C212 *C213 H13S 1.5039 102.98 132.47 114.39 1.0404 +IC C212 C213 C214 C215 1.5295 102.98 90.83 127.96 1.3965 +IC C215 C213 *C214 H14R 1.3965 127.96 -177.48 103.56 1.1711 +IC C213 C214 C215 C216 1.5039 127.96 1.60 125.85 1.4965 +IC C216 C214 *C215 H15R 1.4965 125.85 178.97 120.01 1.1132 +IC C214 C215 C216 C217 1.3965 125.85 -125.06 114.03 1.5299 +IC C217 C215 *C216 H16R 1.5299 114.03 -120.00 110.46 1.1051 +IC C217 C215 *C216 H16S 1.5299 114.03 117.34 109.84 1.1492 +IC C215 C216 C217 C218 1.4965 114.03 167.86 112.49 1.4809 +IC C218 C216 *C217 H17R 1.4809 112.49 -117.68 115.56 1.0772 +IC C218 C216 *C217 H17S 1.4809 112.49 133.94 113.93 1.1399 +IC C216 C217 C218 C219 1.5299 112.49 161.61 109.15 1.5296 +IC C219 C217 *C218 H18R 1.5296 109.15 -117.15 107.59 1.1475 +IC C219 C217 *C218 H18S 1.5296 109.15 120.46 110.58 1.1275 +IC C217 C218 C219 C220 1.4809 109.15 174.23 117.25 1.5821 +IC C220 C218 *C219 H19R 1.5821 117.25 -130.32 118.69 1.1316 +IC C220 C218 *C219 H19S 1.5821 117.25 113.31 106.43 1.1601 +IC C218 C219 C220 H20T 1.5296 117.25 -178.06 122.04 1.0796 +IC H20T C219 *C220 H20R 1.0796 122.04 -126.88 103.33 1.1442 +IC H20T C219 *C220 H20S 1.0796 122.04 121.38 110.58 1.1006 +IC C31 C32 C33 C34 1.5034 115.84 155.51 111.41 1.4969 +IC C34 C32 *C33 H3X 1.4969 111.41 -118.76 109.35 1.0379 +IC C34 C32 *C33 H3Y 1.4969 111.41 125.97 113.42 1.1184 +IC C32 C33 C34 C35 1.5017 111.41 -179.15 117.86 1.5412 +IC C35 C33 *C34 H4X 1.5412 117.86 -124.97 116.58 1.0571 +IC C35 C33 *C34 H4Y 1.5412 117.86 113.91 108.16 1.1193 +IC C33 C34 C35 C36 1.4969 117.86 59.68 114.97 1.4860 +IC C36 C34 *C35 H5X 1.4860 114.97 -123.83 109.28 1.1334 +IC C36 C34 *C35 H5Y 1.4860 114.97 123.98 107.51 1.1200 +IC C34 C35 C36 C37 1.5412 114.97 -173.94 111.81 1.5579 +IC C37 C35 *C36 H6X 1.5579 111.81 -122.02 117.50 1.1304 +IC C37 C35 *C36 H6Y 1.5579 111.81 118.48 104.15 1.1010 +IC C35 C36 C37 C38 1.4860 111.81 178.74 118.84 1.5131 +IC C38 C36 *C37 H7X 1.5131 118.84 -125.11 105.14 1.0632 +IC C38 C36 *C37 H7Y 1.5131 118.84 122.55 107.62 1.1227 +IC C36 C37 C38 C39 1.5579 118.84 -156.61 117.80 1.5668 +IC C39 C37 *C38 H8X 1.5668 117.80 -129.03 108.04 1.1366 +IC C39 C37 *C38 H8Y 1.5668 117.80 117.46 100.28 1.1012 +IC C37 C38 C39 C310 1.5131 117.80 14.56 115.74 1.5951 +IC C310 C38 *C39 H9X 1.5951 115.74 -128.95 105.29 1.0894 +IC C310 C38 *C39 H9Y 1.5951 115.74 126.71 106.13 1.1090 +IC C38 C39 C310 C311 1.5668 115.74 173.18 111.49 1.5513 +IC C311 C39 *C310 H10X 1.5513 111.49 -112.83 105.99 1.1338 +IC C311 C39 *C310 H10Y 1.5513 111.49 127.19 110.24 1.1254 +IC C39 C310 C311 C312 1.5951 111.49 -176.24 112.83 1.4921 +IC C312 C310 *C311 H11X 1.4921 112.83 -120.87 107.48 1.1419 +IC C312 C310 *C311 H11Y 1.4921 112.83 126.83 104.06 1.0407 +IC C310 C311 C312 C313 1.5513 112.83 -164.13 108.99 1.5300 +IC C313 C311 *C312 H12X 1.5300 108.99 -112.11 110.47 1.1167 +IC C313 C311 *C312 H12Y 1.5300 108.99 122.24 115.04 1.1029 +IC C311 C312 C313 C314 1.4921 108.99 -176.26 116.22 1.5610 +IC C314 C312 *C313 H13X 1.5610 116.22 -133.05 122.39 1.0964 +IC C314 C312 *C313 H13Y 1.5610 116.22 100.49 103.86 1.1551 +IC C312 C313 C314 C315 1.5300 116.22 166.43 114.58 1.5220 +IC C315 C313 *C314 H14X 1.5220 114.58 -121.23 108.38 1.0669 +IC C315 C313 *C314 H14Y 1.5220 114.58 126.82 104.98 1.1244 +IC C313 C314 C315 C316 1.5610 114.58 171.99 114.00 1.5577 +IC C316 C314 *C315 H15X 1.5577 114.00 -114.77 106.08 1.1552 +IC C316 C314 *C315 H15Y 1.5577 114.00 126.72 111.77 1.1366 +IC C314 C315 C316 C317 1.5220 114.00 -175.28 115.52 1.5033 +IC C317 C315 *C316 H16X 1.5033 115.52 -123.82 108.57 1.0814 +IC C317 C315 *C316 H16Y 1.5033 115.52 117.19 110.73 1.1118 +IC C315 C316 C317 C318 1.5577 115.52 174.54 115.62 1.4605 +IC C318 C316 *C317 H17X 1.4605 115.62 -113.03 105.25 1.2030 +IC C318 C316 *C317 H17Y 1.4605 115.62 123.82 114.31 1.1172 +IC C316 C317 C318 H18X 1.5033 115.62 51.21 115.02 1.1137 +IC H18X C317 *C318 H18Y 1.1137 115.02 -110.42 108.27 1.1188 +IC H18X C317 *C318 H18Z 1.1137 115.02 126.90 112.70 1.1683 +IC C13 C11 *C12 O2 1.5575 110.54 120.43 104.17 1.4063 +IC O2 C11 *C12 H2 1.4063 104.17 114.00 110.75 1.1206 +IC C11 C12 O2 HO2 1.5621 104.17 -47.85 106.48 0.9937 +IC C14 C12 *C13 O3 1.5026 111.34 123.08 108.74 1.4241 +IC O3 C12 *C13 H3 1.4241 108.74 115.78 108.65 1.1084 +IC C12 C13 O3 HO3 1.5575 108.74 -123.31 101.99 0.9558 +IC C15 C13 *C14 O4 1.5278 107.22 -124.14 103.64 1.4335 +IC O4 C13 *C14 H4 1.4335 103.64 -114.64 115.54 1.1246 +IC C13 C14 O4 P4 1.5026 103.64 70.03 126.55 1.6493 +IC C14 O4 P4 OP42 1.4335 126.55 87.30 98.31 1.5023 +IC OP42 O4 *P4 OP43 1.5023 98.31 113.79 108.47 1.5285 +IC OP42 O4 *P4 OP44 1.5023 98.31 -115.52 115.36 1.4611 +IC O4 P4 OP42 HP42 1.6493 98.31 -26.86 111.79 0.9786 +IC C13 C14 C15 O5 1.5026 107.22 -171.16 108.72 1.4226 +IC O5 C14 *C15 C16 1.4226 108.72 -127.74 110.17 1.5378 +IC C16 C14 *C15 H5 1.5378 110.17 -110.95 102.45 1.0917 +IC C14 C15 O5 P5 1.5278 108.72 -81.32 122.97 1.6718 +IC C15 O5 P5 OP52 1.4226 122.97 47.02 110.21 1.5352 +IC OP52 O5 *P5 OP53 1.5352 110.21 -123.93 103.64 1.5006 +IC OP52 O5 *P5 OP54 1.5352 110.21 119.82 108.27 1.5123 +IC C11 C15 *C16 O6 1.5496 110.38 -114.96 104.94 1.4397 +IC C11 C15 *C16 H6 1.5496 110.38 127.14 106.64 1.0609 +IC C15 C16 O6 HO6 1.5378 104.94 -64.29 100.67 1.0033 + +RESI SAPI25 -4.00 ! Phosphatidylinositol-(4,5)-bisphosphate (PIP2) with protonation on P5 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! HP52--OP52 OP53(-) +! H6 \ / +GROUP ! | P5--OP54(-) +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4----P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | | +ATOM OP42 OC2DP -0.90 ! | | +ATOM OP43 OC2DP -0.90 ! | | +ATOM OP44 OC2DP -0.90 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5091 108.23 63.00 113.31 1.5613 +IC C12 C13 C14 C15 1.5181 113.31 -60.09 107.26 1.5940 +IC C13 C14 C15 C16 1.5613 107.26 54.30 107.51 1.5351 +IC C14 C15 C16 C11 1.5940 107.51 -57.76 114.34 1.5472 +IC C15 C16 C11 C12 1.5351 114.34 60.54 108.36 1.5091 +IC C16 C11 C12 C13 1.5472 108.36 -59.03 108.23 1.5181 +IC C16 C12 *C11 H1 1.5472 108.36 105.05 110.28 1.1197 +IC C16 C12 *C11 O12 1.5472 108.36 -132.89 112.00 1.4192 +IC C11 C13 *C12 H2 1.5091 108.23 117.68 102.86 1.1436 +IC C11 C13 *C12 O2 1.5091 108.23 -126.71 114.97 1.4276 +IC C12 C14 *C13 H3 1.5181 113.31 117.68 111.31 1.0967 +IC C12 C14 *C13 O3 1.5181 113.31 -124.31 110.00 1.4448 +IC C13 C15 *C14 H4 1.5613 107.26 -119.37 107.47 1.0849 +IC C13 C15 *C14 O4 1.5613 107.26 115.88 108.21 1.4338 +IC C14 C16 *C15 H5 1.5940 107.51 117.35 102.62 1.0967 +IC C14 C16 *C15 O5 1.5940 107.51 -121.01 115.87 1.4241 +IC C15 C11 *C16 H6 1.5351 114.34 -120.81 105.70 1.0300 +IC C15 C11 *C16 O6 1.5351 114.34 121.42 102.76 1.3943 +IC C13 C12 O2 HO2 1.5181 114.97 -1.53 99.23 0.9705 +IC C14 C13 O3 HO3 1.5613 110.00 -31.27 106.08 1.0656 +IC C11 C16 O6 HO6 1.5472 102.76 -137.19 110.06 0.9509 +IC C12 C11 O12 P 1.5091 112.00 -97.15 121.37 1.6616 +IC C11 O12 P O11 1.4192 121.37 179.79 105.33 1.5522 +IC O11 O12 *P O13 1.5522 105.33 -114.26 108.93 1.4813 +IC O11 O12 *P O14 1.5522 105.33 120.62 110.39 1.4697 +IC O12 P O11 C1 1.6616 105.33 53.54 117.11 1.4608 +IC P O11 C1 C2 1.5522 117.11 123.83 112.91 1.5765 +IC C2 O11 *C1 HA 1.5765 112.91 122.68 101.85 1.1325 +IC HA O11 *C1 HB 1.1325 101.85 109.49 113.01 1.1451 +IC O11 C1 C2 O21 1.4608 112.91 56.26 106.29 1.4604 +IC O21 C1 *C2 C3 1.4604 106.29 -117.55 107.82 1.5067 +IC C3 C1 *C2 HS 1.5067 107.82 -118.39 109.77 1.1046 +IC C1 C2 O21 C21 1.5765 106.29 121.50 120.14 1.3562 +IC C2 O21 C21 C22 1.4604 120.14 174.20 110.20 1.5683 +IC C22 O21 *C21 O22 1.5683 110.20 -170.80 125.23 1.2221 +IC O21 C21 C22 C23 1.3562 110.20 -146.08 112.69 1.5516 +IC C23 C21 *C22 H2R 1.5516 112.69 122.75 100.33 1.1152 +IC H2R C21 *C22 H2S 1.1152 100.33 114.45 113.03 1.0679 +IC C1 C2 C3 O31 1.5765 107.82 -171.01 109.92 1.4374 +IC O31 C2 *C3 HX 1.4374 109.92 -129.68 113.33 1.1661 +IC HX C2 *C3 HY 1.1661 113.33 -112.79 110.99 1.0462 +IC C2 C3 O31 C31 1.5067 109.92 -93.81 115.15 1.3166 +IC C3 O31 C31 C32 1.4374 115.15 -168.63 109.45 1.5266 +IC C32 O31 *C31 O32 1.5266 109.45 -178.04 129.17 1.1860 +IC O31 C31 C32 C33 1.3166 109.45 -179.35 106.62 1.5237 +IC C33 C31 *C32 H2X 1.5237 106.62 -124.93 104.84 1.1374 +IC H2X C31 *C32 H2Y 1.1374 104.84 -119.25 110.55 1.0721 +IC C21 C22 C23 C24 1.5683 112.69 63.73 115.84 1.5991 +IC C24 C22 *C23 H3R 1.5991 115.84 -125.43 111.48 1.1036 +IC C24 C22 *C23 H3S 1.5991 115.84 126.62 109.08 1.0335 +IC C22 C23 C24 C25 1.5516 115.84 -169.82 112.91 1.4673 +IC C25 C23 *C24 H4R 1.4673 112.91 -123.49 92.01 1.0820 +IC C25 C23 *C24 H4S 1.4673 112.91 116.11 109.41 1.1189 +IC C23 C24 C25 C26 1.5991 112.91 -115.44 127.14 1.3330 +IC C26 C24 *C25 H5R 1.3330 127.14 178.83 112.83 1.1262 +IC C24 C25 C26 C27 1.4673 127.14 -0.85 126.83 1.5153 +IC C27 C25 *C26 H6R 1.5153 126.83 173.46 116.71 1.1231 +IC C25 C26 C27 C28 1.3330 126.83 103.83 116.70 1.4988 +IC C28 C26 *C27 H7R 1.4988 116.70 -119.41 111.01 1.0812 +IC C28 C26 *C27 H7S 1.4988 116.70 130.19 110.64 1.0910 +IC C26 C27 C28 C29 1.5153 116.70 120.74 129.68 1.3374 +IC C29 C27 *C28 H8R 1.3374 129.68 -179.25 111.22 1.1305 +IC C27 C28 C29 C210 1.4988 129.68 0.06 126.95 1.4874 +IC C210 C28 *C29 H9R 1.4874 126.95 175.44 115.60 1.1108 +IC C28 C29 C210 C211 1.3374 126.95 124.90 111.33 1.4958 +IC C211 C29 *C210 H10R 1.4958 111.33 -117.39 116.61 1.1185 +IC C211 C29 *C210 H10S 1.4958 111.33 116.46 110.02 1.1315 +IC C29 C210 C211 C212 1.4874 111.33 130.78 126.57 1.3242 +IC C212 C210 *C211 H11R 1.3242 126.57 174.35 113.69 1.1246 +IC C210 C211 C212 C213 1.4958 126.57 -2.22 123.23 1.5012 +IC C213 C211 *C212 H12R 1.5012 123.23 178.62 118.94 1.1026 +IC C211 C212 C213 C214 1.3242 123.23 84.76 120.71 1.5043 +IC C214 C212 *C213 H13R 1.5043 120.71 -121.70 110.39 1.1159 +IC C214 C212 *C213 H13S 1.5043 120.71 121.96 101.00 1.0983 +IC C212 C213 C214 C215 1.5012 120.71 137.57 128.25 1.3486 +IC C215 C213 *C214 H14R 1.3486 128.25 178.58 110.38 1.0702 +IC C213 C214 C215 C216 1.5043 128.25 -0.01 129.31 1.5467 +IC C216 C214 *C215 H15R 1.5467 129.31 178.31 112.90 1.0947 +IC C214 C215 C216 C217 1.3486 129.31 113.67 113.23 1.5599 +IC C217 C215 *C216 H16R 1.5599 113.23 -126.72 111.88 1.1669 +IC C217 C215 *C216 H16S 1.5599 113.23 122.98 108.76 1.1125 +IC C215 C216 C217 C218 1.5467 113.23 148.50 113.29 1.5486 +IC C218 C216 *C217 H17R 1.5486 113.29 -122.10 104.39 1.0997 +IC C218 C216 *C217 H17S 1.5486 113.29 117.96 110.42 1.1415 +IC C216 C217 C218 C219 1.5599 113.29 -179.86 112.87 1.5706 +IC C219 C217 *C218 H18R 1.5706 112.87 -123.34 103.60 1.0678 +IC C219 C217 *C218 H18S 1.5706 112.87 118.77 103.73 1.0861 +IC C217 C218 C219 C220 1.5486 112.87 53.58 109.45 1.5724 +IC C220 C218 *C219 H19R 1.5724 109.45 -120.10 109.93 1.0438 +IC C220 C218 *C219 H19S 1.5724 109.45 120.64 109.83 1.1313 +IC C218 C219 C220 H20T 1.5706 109.45 151.17 115.41 1.1222 +IC H20T C219 *C220 H20R 1.1222 115.41 -115.18 110.13 1.1308 +IC H20T C219 *C220 H20S 1.1222 115.41 123.92 116.20 1.0684 +IC C31 C32 C33 C34 1.5266 106.62 174.58 115.64 1.5646 +IC C34 C32 *C33 H3X 1.5646 115.64 -120.04 104.58 1.1278 +IC C34 C32 *C33 H3Y 1.5646 115.64 121.42 110.93 1.1046 +IC C32 C33 C34 C35 1.5237 115.64 149.31 104.96 1.5534 +IC C35 C33 *C34 H4X 1.5534 104.96 -112.43 102.30 1.1435 +IC C35 C33 *C34 H4Y 1.5534 104.96 134.25 110.03 1.1269 +IC C33 C34 C35 C36 1.5646 104.96 166.42 111.23 1.4921 +IC C36 C34 *C35 H5X 1.4921 111.23 -122.52 107.61 1.0298 +IC C36 C34 *C35 H5Y 1.4921 111.23 117.82 107.95 1.1313 +IC C34 C35 C36 C37 1.5534 111.23 -160.56 116.93 1.5477 +IC C37 C35 *C36 H6X 1.5477 116.93 -125.57 112.49 1.1550 +IC C37 C35 *C36 H6Y 1.5477 116.93 110.51 114.75 1.0369 +IC C35 C36 C37 C38 1.4921 116.93 177.73 115.63 1.5486 +IC C38 C36 *C37 H7X 1.5486 115.63 -119.46 106.88 1.1082 +IC C38 C36 *C37 H7Y 1.5486 115.63 119.27 101.11 1.1222 +IC C36 C37 C38 C39 1.5477 115.63 180.00 111.72 1.5171 +IC C39 C37 *C38 H8X 1.5171 111.72 -122.52 103.36 1.1254 +IC C39 C37 *C38 H8Y 1.5171 111.72 123.65 111.01 1.1423 +IC C37 C38 C39 C310 1.5486 111.72 173.26 114.65 1.5053 +IC C310 C38 *C39 H9X 1.5053 114.65 -121.07 102.63 1.1017 +IC C310 C38 *C39 H9Y 1.5053 114.65 121.33 114.58 1.0952 +IC C38 C39 C310 C311 1.5171 114.65 -177.17 107.89 1.6115 +IC C311 C39 *C310 H10X 1.6115 107.89 -119.46 104.64 1.1386 +IC C311 C39 *C310 H10Y 1.6115 107.89 123.01 108.80 1.0412 +IC C39 C310 C311 C312 1.5053 107.89 177.10 104.90 1.5272 +IC C312 C310 *C311 H11X 1.5272 104.90 -112.24 105.70 1.0314 +IC C312 C310 *C311 H11Y 1.5272 104.90 124.10 107.36 1.1166 +IC C310 C311 C312 C313 1.6115 104.90 -170.17 118.78 1.5271 +IC C313 C311 *C312 H12X 1.5271 118.78 -122.05 111.94 1.1711 +IC C313 C311 *C312 H12Y 1.5271 118.78 120.16 112.39 1.0441 +IC C311 C312 C313 C314 1.5272 118.78 153.41 116.86 1.5784 +IC C314 C312 *C313 H13X 1.5784 116.86 -118.87 104.77 1.1613 +IC C314 C312 *C313 H13Y 1.5784 116.86 120.12 109.77 1.1247 +IC C312 C313 C314 C315 1.5271 116.86 -176.94 112.81 1.5528 +IC C315 C313 *C314 H14X 1.5528 112.81 -125.41 114.59 1.0495 +IC C315 C313 *C314 H14Y 1.5528 112.81 115.80 103.08 1.0679 +IC C313 C314 C315 C316 1.5784 112.81 -178.14 116.95 1.5043 +IC C316 C314 *C315 H15X 1.5043 116.95 -121.74 107.57 1.1315 +IC C316 C314 *C315 H15Y 1.5043 116.95 126.05 105.84 1.0774 +IC C314 C315 C316 C317 1.5528 116.95 61.44 114.64 1.4783 +IC C317 C315 *C316 H16X 1.4783 114.64 -131.12 109.50 1.1002 +IC C317 C315 *C316 H16Y 1.4783 114.64 110.61 107.72 1.1007 +IC C315 C316 C317 C318 1.5043 114.64 173.51 116.00 1.5109 +IC C318 C316 *C317 H17X 1.5109 116.00 -128.87 102.21 1.0970 +IC C318 C316 *C317 H17Y 1.5109 116.00 128.67 109.21 1.0585 +IC C316 C317 C318 H18X 1.4783 116.00 -160.60 106.46 1.1767 +IC H18X C317 *C318 H18Y 1.1767 106.46 -120.73 118.90 1.1441 +IC H18X C317 *C318 H18Z 1.1767 106.46 120.61 110.04 1.1273 +IC C13 C11 *C12 O2 1.5181 108.23 128.14 112.49 1.4276 +IC O2 C11 *C12 H2 1.4276 112.49 119.62 111.13 1.1436 +IC C11 C12 O2 HO2 1.5091 112.49 -126.03 99.23 0.9705 +IC C14 C12 *C13 O3 1.5613 113.31 124.01 110.55 1.4448 +IC O3 C12 *C13 H3 1.4448 110.55 114.52 104.69 1.0967 +IC C12 C13 O3 HO3 1.5181 110.55 -157.16 106.08 1.0656 +IC C12 C13 C14 C15 1.5181 113.31 -60.09 107.26 1.5940 +IC C15 C13 *C14 O4 1.5940 107.26 -116.25 107.65 1.4338 +IC O4 C13 *C14 H4 1.4338 107.65 -126.64 110.96 1.0849 +IC C13 C14 O4 P4 1.5613 107.65 -87.92 128.14 1.7068 +IC C14 O4 P4 OP42 1.4338 128.14 -174.57 99.96 1.4982 +IC OP42 O4 *P4 OP43 1.4982 99.96 119.26 103.52 1.5184 +IC OP42 O4 *P4 OP44 1.4982 99.96 -119.87 108.84 1.5595 +IC C13 C14 C15 O5 1.5613 107.26 -179.93 108.11 1.4241 +IC O5 C14 *C15 C16 1.4241 108.11 -125.77 107.51 1.5351 +IC C16 C14 *C15 H5 1.5351 107.51 -111.60 111.21 1.0967 +IC C14 C15 O5 P5 1.5940 108.11 177.95 132.56 1.6199 +IC C15 O5 P5 OP52 1.4241 132.56 108.15 100.81 1.5733 +IC OP52 O5 *P5 OP53 1.5733 100.81 -112.47 111.34 1.5025 +IC OP52 O5 *P5 OP54 1.5733 100.81 115.49 107.46 1.5072 +IC O5 P5 OP52 HP52 1.6199 100.81 16.08 101.23 1.0106 +IC C11 C15 *C16 O6 1.5472 114.34 -116.27 111.85 1.3943 +IC C11 C15 *C16 H6 1.5472 114.34 118.54 109.74 1.0300 +IC C15 C16 O6 HO6 1.5351 111.85 -14.09 110.06 0.9509 + +RESI SAPI2A -4.00 ! Phosphatidylinositol-(3,5)-bisphosphate (PIP2) with protonation on P3 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.01 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.62 ! | |\ | / +ATOM P3 PC 1.50 ! | | \ O2 / +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | | | +ATOM C14 CC3161 0.14 ! | H3 OP32--HP32 +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! \ +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! (-) O13 O12 +ATOM C11 CC3161 -0.08 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.59 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O12 OC30P -0.57 ! HA---C1---HB +ATOM O11 OSLP -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C26 CEL1 -0.15 ! | | +ATOM H6R HEL1 0.15 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H12R HEL1 0.15 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H16R---C216--H16S | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! H18R---C218--H18S | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! | | +ATOM H18S HAL2 0.09 ! H19R---C219--H19S | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! | | +ATOM H19S HAL2 0.09 ! H20R---C220--H20S | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! H20T | +ATOM H20R HAL3 0.09 ! | +ATOM H20S HAL3 0.09 ! | +ATOM H20T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! H15X---C315--H15Y +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! H16X---C316--H16Y +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! | +ATOM H16Y HAL2 0.09 ! H17X---C317--H17Y +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! | +ATOM H17Y HAL2 0.09 ! H18X---C318--H18Y +GROUP ! | +ATOM C318 CTL3 -0.27 ! H18Z +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.6085 107.54 60.79 111.19 1.5631 +IC C12 C13 C14 C15 1.5184 111.19 -56.12 111.39 1.5343 +IC C13 C14 C15 C16 1.5631 111.39 54.54 112.35 1.5007 +IC C14 C15 C16 C11 1.5343 112.35 -58.19 109.23 1.6111 +IC C15 C16 C11 C12 1.5007 109.23 61.82 106.81 1.6085 +IC C16 C11 C12 C13 1.6111 106.81 -62.97 107.54 1.5184 +IC C16 C12 *C11 H1 1.6111 106.81 113.72 110.66 1.0970 +IC C16 C12 *C11 O12 1.6111 106.81 -132.79 100.40 1.4976 +IC C11 C13 *C12 H2 1.6085 107.54 117.10 108.95 1.1104 +IC C11 C13 *C12 O2 1.6085 107.54 -120.52 112.68 1.4426 +IC C12 C14 *C13 H3 1.5184 111.19 124.74 110.89 1.1140 +IC C12 C14 *C13 O3 1.5184 111.19 -114.99 109.09 1.4274 +IC C13 C15 *C14 H4 1.5631 111.39 -116.94 108.09 1.0604 +IC C13 C15 *C14 O4 1.5631 111.39 127.19 109.18 1.4177 +IC C14 C16 *C15 H5 1.5343 112.35 115.94 109.59 1.1064 +IC C14 C16 *C15 O5 1.5343 112.35 -123.35 111.87 1.4270 +IC C15 C11 *C16 H6 1.5007 109.23 -123.77 106.40 1.1116 +IC C15 C11 *C16 O6 1.5007 109.23 117.85 102.04 1.4099 +IC C13 C12 O2 HO2 1.5184 112.68 4.26 92.34 1.0302 +IC C11 C16 O6 HO6 1.6111 102.04 174.01 103.78 1.0348 +IC C12 C11 O12 P 1.6085 100.40 173.02 130.40 1.6484 +IC C11 O12 P O11 1.4976 130.40 176.68 99.70 1.6050 +IC O11 O12 *P O13 1.6050 99.70 -109.02 115.70 1.4789 +IC O11 O12 *P O14 1.6050 99.70 106.84 115.04 1.4775 +IC O12 P O11 C1 1.6484 99.70 -86.90 122.81 1.4512 +IC P O11 C1 C2 1.6050 122.81 -117.13 113.54 1.6662 +IC C2 O11 *C1 HA 1.6662 113.54 120.82 117.60 1.0724 +IC HA O11 *C1 HB 1.0724 117.60 112.73 101.54 1.1034 +IC O11 C1 C2 O21 1.4512 113.54 67.81 112.32 1.4818 +IC O21 C1 *C2 C3 1.4818 112.32 -115.71 105.85 1.4850 +IC C3 C1 *C2 HS 1.4850 105.85 -116.46 112.45 1.1326 +IC C1 C2 O21 C21 1.6662 112.32 56.99 112.49 1.3635 +IC C2 O21 C21 C22 1.4818 112.49 -153.82 113.90 1.5495 +IC C22 O21 *C21 O22 1.5495 113.90 -166.45 122.48 1.2236 +IC O21 C21 C22 C23 1.3635 113.90 -97.47 110.04 1.5360 +IC C23 C21 *C22 H2R 1.5360 110.04 135.29 109.75 1.1450 +IC H2R C21 *C22 H2S 1.1450 109.75 112.05 103.31 1.1794 +IC C1 C2 C3 O31 1.6662 105.85 171.16 116.64 1.4438 +IC O31 C2 *C3 HX 1.4438 116.64 -118.85 101.17 1.0985 +IC HX C2 *C3 HY 1.0985 101.17 -104.81 106.46 1.1176 +IC C2 C3 O31 C31 1.4850 116.64 68.33 120.24 1.3520 +IC C3 O31 C31 C32 1.4438 120.24 -177.65 111.24 1.4875 +IC C32 O31 *C31 O32 1.4875 111.24 -178.84 125.40 1.2086 +IC O31 C31 C32 C33 1.3520 111.24 121.63 113.42 1.5621 +IC C33 C31 *C32 H2X 1.5621 113.42 -123.40 106.82 1.1474 +IC H2X C31 *C32 H2Y 1.1474 106.82 -105.11 113.46 1.1000 +IC C21 C22 C23 C24 1.5495 110.04 67.92 113.07 1.5546 +IC C24 C22 *C23 H3R 1.5546 113.07 -121.18 115.12 1.1189 +IC C24 C22 *C23 H3S 1.5546 113.07 116.77 109.69 1.1169 +IC C22 C23 C24 C25 1.5360 113.07 60.63 113.21 1.4448 +IC C25 C23 *C24 H4R 1.4448 113.21 -127.46 111.76 1.1049 +IC C25 C23 *C24 H4S 1.4448 113.21 119.78 99.62 1.1283 +IC C23 C24 C25 C26 1.5546 113.21 173.34 125.28 1.3364 +IC C26 C24 *C25 H5R 1.3364 125.28 179.03 114.79 1.0696 +IC C24 C25 C26 C27 1.4448 125.28 1.74 128.06 1.4490 +IC C27 C25 *C26 H6R 1.4490 128.06 178.88 115.21 1.1285 +IC C25 C26 C27 C28 1.3364 128.06 141.59 117.73 1.5109 +IC C28 C26 *C27 H7R 1.5109 117.73 -119.24 110.88 1.1468 +IC C28 C26 *C27 H7S 1.5109 117.73 121.92 107.89 1.1493 +IC C26 C27 C28 C29 1.4490 117.73 134.20 125.21 1.3700 +IC C29 C27 *C28 H8R 1.3700 125.21 175.16 118.29 1.1609 +IC C27 C28 C29 C210 1.5109 125.21 0.65 132.76 1.5304 +IC C210 C28 *C29 H9R 1.5304 132.76 -177.06 122.23 1.1088 +IC C28 C29 C210 C211 1.3700 132.76 108.32 105.00 1.4607 +IC C211 C29 *C210 H10R 1.4607 105.00 -119.86 118.79 1.1461 +IC C211 C29 *C210 H10S 1.4607 105.00 118.27 112.41 1.1989 +IC C29 C210 C211 C212 1.5304 105.00 126.46 126.50 1.3393 +IC C212 C210 *C211 H11R 1.3393 126.50 170.96 115.02 1.0788 +IC C210 C211 C212 C213 1.4607 126.50 1.45 129.47 1.5373 +IC C213 C211 *C212 H12R 1.5373 129.47 -177.03 116.04 1.0756 +IC C211 C212 C213 C214 1.3393 129.47 112.52 106.68 1.5525 +IC C214 C212 *C213 H13R 1.5525 106.68 -120.58 110.94 1.0956 +IC C214 C212 *C213 H13S 1.5525 106.68 121.63 104.28 1.0946 +IC C212 C213 C214 C215 1.5373 106.68 116.97 124.36 1.3427 +IC C215 C213 *C214 H14R 1.3427 124.36 -176.47 119.66 1.0003 +IC C213 C214 C215 C216 1.5525 124.36 0.36 129.37 1.4732 +IC C216 C214 *C215 H15R 1.4732 129.37 -178.58 114.71 1.1153 +IC C214 C215 C216 C217 1.3427 129.37 119.14 113.38 1.5511 +IC C217 C215 *C216 H16R 1.5511 113.38 -128.09 115.06 1.1150 +IC C217 C215 *C216 H16S 1.5511 113.38 112.67 106.11 1.1197 +IC C215 C216 C217 C218 1.4732 113.38 167.76 113.49 1.5199 +IC C218 C216 *C217 H17R 1.5199 113.49 -136.41 107.73 1.1215 +IC C218 C216 *C217 H17S 1.5199 113.49 109.14 104.66 1.0917 +IC C216 C217 C218 C219 1.5511 113.49 -69.66 113.45 1.4750 +IC C219 C217 *C218 H18R 1.4750 113.45 -121.18 111.39 1.1276 +IC C219 C217 *C218 H18S 1.4750 113.45 122.00 109.88 1.1394 +IC C217 C218 C219 C220 1.5199 113.45 -67.29 116.51 1.4859 +IC C220 C218 *C219 H19R 1.4859 116.51 -113.64 110.52 1.1479 +IC C220 C218 *C219 H19S 1.4859 116.51 123.31 116.84 1.1410 +IC C218 C219 C220 H20T 1.4750 116.51 -173.59 113.53 1.0826 +IC H20T C219 *C220 H20R 1.0826 113.53 -118.46 107.40 1.0844 +IC H20T C219 *C220 H20S 1.0826 113.53 122.07 111.06 1.1305 +IC C31 C32 C33 C34 1.4875 113.42 152.78 109.79 1.5203 +IC C34 C32 *C33 H3X 1.5203 109.79 -109.19 108.75 1.0857 +IC C34 C32 *C33 H3Y 1.5203 109.79 125.96 114.80 1.0550 +IC C32 C33 C34 C35 1.5621 109.79 -169.49 111.42 1.6128 +IC C35 C33 *C34 H4X 1.6128 111.42 -121.66 103.52 1.1288 +IC C35 C33 *C34 H4Y 1.6128 111.42 116.95 109.31 1.1475 +IC C33 C34 C35 C36 1.5203 111.42 -177.91 108.73 1.5691 +IC C36 C34 *C35 H5X 1.5691 108.73 -123.20 118.69 1.1198 +IC C36 C34 *C35 H5Y 1.5691 108.73 121.97 110.30 1.1238 +IC C34 C35 C36 C37 1.6128 108.73 156.40 108.50 1.4966 +IC C37 C35 *C36 H6X 1.4966 108.50 -114.88 106.92 1.0834 +IC C37 C35 *C36 H6Y 1.4966 108.50 124.70 107.92 1.1693 +IC C35 C36 C37 C38 1.5691 108.50 -176.11 115.37 1.5513 +IC C38 C36 *C37 H7X 1.5513 115.37 -132.10 117.12 1.1122 +IC C38 C36 *C37 H7Y 1.5513 115.37 117.93 103.69 1.1113 +IC C36 C37 C38 C39 1.4966 115.37 166.36 110.33 1.4980 +IC C39 C37 *C38 H8X 1.4980 110.33 -129.71 109.95 1.1296 +IC C39 C37 *C38 H8Y 1.4980 110.33 118.79 109.90 1.0764 +IC C37 C38 C39 C310 1.5513 110.33 -164.13 118.89 1.5943 +IC C310 C38 *C39 H9X 1.5943 118.89 -115.55 109.73 1.0952 +IC C310 C38 *C39 H9Y 1.5943 118.89 130.25 106.31 1.0929 +IC C38 C39 C310 C311 1.4980 118.89 -49.00 109.22 1.5137 +IC C311 C39 *C310 H10X 1.5137 109.22 -116.74 108.27 1.0813 +IC C311 C39 *C310 H10Y 1.5137 109.22 117.30 111.40 1.0636 +IC C39 C310 C311 C312 1.5943 109.22 170.95 112.95 1.5533 +IC C312 C310 *C311 H11X 1.5533 112.95 -123.43 111.51 1.1135 +IC C312 C310 *C311 H11Y 1.5533 112.95 112.52 99.10 1.0554 +IC C310 C311 C312 C313 1.5137 112.95 -164.15 106.89 1.5525 +IC C313 C311 *C312 H12X 1.5525 106.89 -115.76 102.65 1.0793 +IC C313 C311 *C312 H12Y 1.5525 106.89 116.44 125.17 1.1466 +IC C311 C312 C313 C314 1.5533 106.89 -140.81 107.79 1.5309 +IC C314 C312 *C313 H13X 1.5309 107.79 -112.37 108.50 1.0756 +IC C314 C312 *C313 H13Y 1.5309 107.79 124.74 113.42 1.0947 +IC C312 C313 C314 C315 1.5525 107.79 -67.74 114.85 1.4938 +IC C315 C313 *C314 H14X 1.4938 114.85 -119.60 107.21 1.0693 +IC C315 C313 *C314 H14Y 1.4938 114.85 116.01 108.14 1.0570 +IC C313 C314 C315 C316 1.5309 114.85 -178.97 111.64 1.5439 +IC C316 C314 *C315 H15X 1.5439 111.64 -125.57 110.73 1.1159 +IC C316 C314 *C315 H15Y 1.5439 111.64 124.77 114.52 1.0909 +IC C314 C315 C316 C317 1.4938 111.64 -177.93 107.20 1.5537 +IC C317 C315 *C316 H16X 1.5537 107.20 -113.34 106.47 1.0729 +IC C317 C315 *C316 H16Y 1.5537 107.20 116.58 112.07 1.1621 +IC C315 C316 C317 C318 1.5439 107.20 162.37 112.19 1.5610 +IC C318 C316 *C317 H17X 1.5610 112.19 -114.65 101.79 1.1260 +IC C318 C316 *C317 H17Y 1.5610 112.19 128.24 112.26 1.1118 +IC C316 C317 C318 H18X 1.5537 112.19 168.54 105.45 1.1437 +IC H18X C317 *C318 H18Y 1.1437 105.45 -112.51 114.99 1.1562 +IC H18X C317 *C318 H18Z 1.1437 105.45 132.44 116.32 1.1291 +IC C13 C11 *C12 O2 1.5184 107.54 122.63 109.30 1.4426 +IC O2 C11 *C12 H2 1.4426 109.30 119.81 108.24 1.1104 +IC C11 C12 O2 HO2 1.6085 109.30 -115.24 92.34 1.0302 +IC C14 C12 *C13 O3 1.5631 111.19 117.68 104.72 1.4274 +IC O3 C12 *C13 H3 1.4274 104.72 117.96 111.56 1.1140 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C15 C13 *C14 O4 1.5343 111.39 -124.35 114.32 1.4177 +IC O4 C13 *C14 H4 1.4177 114.32 -117.89 106.72 1.0604 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C13 C14 C15 O5 1.5631 111.39 179.33 109.28 1.4270 +IC O5 C14 *C15 C16 1.4270 109.28 -124.79 112.35 1.5007 +IC C16 C14 *C15 H5 1.5007 112.35 -118.86 104.70 1.1064 +IC C14 C15 O5 P5 1.5343 109.28 -123.53 132.73 1.6688 +IC C15 O5 P5 OP52 1.4270 132.73 64.99 107.56 1.5362 +IC OP52 O5 *P5 OP53 1.5362 107.56 -122.52 110.70 1.5140 +IC OP52 O5 *P5 OP54 1.5362 107.56 121.44 99.10 1.5259 +IC C11 C15 *C16 O6 1.6111 109.23 -111.89 111.27 1.4099 +IC C11 C15 *C16 H6 1.6111 109.23 119.01 114.23 1.1116 +IC C15 C16 O6 HO6 1.5007 111.27 -69.60 103.78 1.0348 + +RESI SAPI2B -4.00 ! Phosphatidylinositol-(3,5)-bisphosphate (PIP2) with protonation on P5 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 -0.09 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.40 ! | |\ | / +ATOM P3 PC 1.10 ! | | \ O2 / +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.14 ! | | OP32(-) +ATOM H4 HCA1 0.09 ! | H3 +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! \ +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! (-) O13 O12 +ATOM C11 CC3161 -0.08 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.59 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O12 OC30P -0.57 ! HA---C1---HB +ATOM O11 OSLP -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C26 CEL1 -0.15 ! | | +ATOM H6R HEL1 0.15 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H12R HEL1 0.15 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H16R---C216--H16S | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! H18R---C218--H18S | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! | | +ATOM H18S HAL2 0.09 ! H19R---C219--H19S | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! | | +ATOM H19S HAL2 0.09 ! H20R---C220--H20S | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! H20T | +ATOM H20R HAL3 0.09 ! | +ATOM H20S HAL3 0.09 ! | +ATOM H20T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! H15X---C315--H15Y +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! H16X---C316--H16Y +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! | +ATOM H16Y HAL2 0.09 ! H17X---C317--H17Y +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! | +ATOM H17Y HAL2 0.09 ! H18X---C318--H18Y +GROUP ! | +ATOM C318 CTL3 -0.27 ! H18Z +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.6085 107.54 60.79 111.19 1.5631 +IC C12 C13 C14 C15 1.5184 111.19 -56.12 111.39 1.5343 +IC C13 C14 C15 C16 1.5631 111.39 54.54 112.35 1.5007 +IC C14 C15 C16 C11 1.5343 112.35 -58.19 109.23 1.6111 +IC C15 C16 C11 C12 1.5007 109.23 61.82 106.81 1.6085 +IC C16 C11 C12 C13 1.6111 106.81 -62.97 107.54 1.5184 +IC C16 C12 *C11 H1 1.6111 106.81 113.72 110.66 1.0970 +IC C16 C12 *C11 O12 1.6111 106.81 -132.79 100.40 1.4976 +IC C11 C13 *C12 H2 1.6085 107.54 117.10 108.95 1.1104 +IC C11 C13 *C12 O2 1.6085 107.54 -120.52 112.68 1.4426 +IC C12 C14 *C13 H3 1.5184 111.19 124.74 110.89 1.1140 +IC C12 C14 *C13 O3 1.5184 111.19 -114.99 109.09 1.4274 +IC C13 C15 *C14 H4 1.5631 111.39 -116.94 108.09 1.0604 +IC C13 C15 *C14 O4 1.5631 111.39 127.19 109.18 1.4177 +IC C14 C16 *C15 H5 1.5343 112.35 115.94 109.59 1.1064 +IC C14 C16 *C15 O5 1.5343 112.35 -123.35 111.87 1.4270 +IC C15 C11 *C16 H6 1.5007 109.23 -123.77 106.40 1.1116 +IC C15 C11 *C16 O6 1.5007 109.23 117.85 102.04 1.4099 +IC C13 C12 O2 HO2 1.5184 112.68 4.26 92.34 1.0302 +IC C11 C16 O6 HO6 1.6111 102.04 174.01 103.78 1.0348 +IC C12 C11 O12 P 1.6085 100.40 173.02 130.40 1.6484 +IC C11 O12 P O11 1.4976 130.40 176.68 99.70 1.6050 +IC O11 O12 *P O13 1.6050 99.70 -109.02 115.70 1.4789 +IC O11 O12 *P O14 1.6050 99.70 106.84 115.04 1.4775 +IC O12 P O11 C1 1.6484 99.70 -86.90 122.81 1.4512 +IC P O11 C1 C2 1.6050 122.81 -117.13 113.54 1.6662 +IC C2 O11 *C1 HA 1.6662 113.54 120.82 117.60 1.0724 +IC HA O11 *C1 HB 1.0724 117.60 112.73 101.54 1.1034 +IC O11 C1 C2 O21 1.4512 113.54 67.81 112.32 1.4818 +IC O21 C1 *C2 C3 1.4818 112.32 -115.71 105.85 1.4850 +IC C3 C1 *C2 HS 1.4850 105.85 -116.46 112.45 1.1326 +IC C1 C2 O21 C21 1.6662 112.32 56.99 112.49 1.3635 +IC C2 O21 C21 C22 1.4818 112.49 -153.82 113.90 1.5495 +IC C22 O21 *C21 O22 1.5495 113.90 -166.45 122.48 1.2236 +IC O21 C21 C22 C23 1.3635 113.90 -97.47 110.04 1.5360 +IC C23 C21 *C22 H2R 1.5360 110.04 135.29 109.75 1.1450 +IC H2R C21 *C22 H2S 1.1450 109.75 112.05 103.31 1.1794 +IC C1 C2 C3 O31 1.6662 105.85 171.16 116.64 1.4438 +IC O31 C2 *C3 HX 1.4438 116.64 -118.85 101.17 1.0985 +IC HX C2 *C3 HY 1.0985 101.17 -104.81 106.46 1.1176 +IC C2 C3 O31 C31 1.4850 116.64 68.33 120.24 1.3520 +IC C3 O31 C31 C32 1.4438 120.24 -177.65 111.24 1.4875 +IC C32 O31 *C31 O32 1.4875 111.24 -178.84 125.40 1.2086 +IC O31 C31 C32 C33 1.3520 111.24 121.63 113.42 1.5621 +IC C33 C31 *C32 H2X 1.5621 113.42 -123.40 106.82 1.1474 +IC H2X C31 *C32 H2Y 1.1474 106.82 -105.11 113.46 1.1000 +IC C21 C22 C23 C24 1.5495 110.04 67.92 113.07 1.5546 +IC C24 C22 *C23 H3R 1.5546 113.07 -121.18 115.12 1.1189 +IC C24 C22 *C23 H3S 1.5546 113.07 116.77 109.69 1.1169 +IC C22 C23 C24 C25 1.5360 113.07 60.63 113.21 1.4448 +IC C25 C23 *C24 H4R 1.4448 113.21 -127.46 111.76 1.1049 +IC C25 C23 *C24 H4S 1.4448 113.21 119.78 99.62 1.1283 +IC C23 C24 C25 C26 1.5546 113.21 173.34 125.28 1.3364 +IC C26 C24 *C25 H5R 1.3364 125.28 179.03 114.79 1.0696 +IC C24 C25 C26 C27 1.4448 125.28 1.74 128.06 1.4490 +IC C27 C25 *C26 H6R 1.4490 128.06 178.88 115.21 1.1285 +IC C25 C26 C27 C28 1.3364 128.06 141.59 117.73 1.5109 +IC C28 C26 *C27 H7R 1.5109 117.73 -119.24 110.88 1.1468 +IC C28 C26 *C27 H7S 1.5109 117.73 121.92 107.89 1.1493 +IC C26 C27 C28 C29 1.4490 117.73 134.20 125.21 1.3700 +IC C29 C27 *C28 H8R 1.3700 125.21 175.16 118.29 1.1609 +IC C27 C28 C29 C210 1.5109 125.21 0.65 132.76 1.5304 +IC C210 C28 *C29 H9R 1.5304 132.76 -177.06 122.23 1.1088 +IC C28 C29 C210 C211 1.3700 132.76 108.32 105.00 1.4607 +IC C211 C29 *C210 H10R 1.4607 105.00 -119.86 118.79 1.1461 +IC C211 C29 *C210 H10S 1.4607 105.00 118.27 112.41 1.1989 +IC C29 C210 C211 C212 1.5304 105.00 126.46 126.50 1.3393 +IC C212 C210 *C211 H11R 1.3393 126.50 170.96 115.02 1.0788 +IC C210 C211 C212 C213 1.4607 126.50 1.45 129.47 1.5373 +IC C213 C211 *C212 H12R 1.5373 129.47 -177.03 116.04 1.0756 +IC C211 C212 C213 C214 1.3393 129.47 112.52 106.68 1.5525 +IC C214 C212 *C213 H13R 1.5525 106.68 -120.58 110.94 1.0956 +IC C214 C212 *C213 H13S 1.5525 106.68 121.63 104.28 1.0946 +IC C212 C213 C214 C215 1.5373 106.68 116.97 124.36 1.3427 +IC C215 C213 *C214 H14R 1.3427 124.36 -176.47 119.66 1.0003 +IC C213 C214 C215 C216 1.5525 124.36 0.36 129.37 1.4732 +IC C216 C214 *C215 H15R 1.4732 129.37 -178.58 114.71 1.1153 +IC C214 C215 C216 C217 1.3427 129.37 119.14 113.38 1.5511 +IC C217 C215 *C216 H16R 1.5511 113.38 -128.09 115.06 1.1150 +IC C217 C215 *C216 H16S 1.5511 113.38 112.67 106.11 1.1197 +IC C215 C216 C217 C218 1.4732 113.38 167.76 113.49 1.5199 +IC C218 C216 *C217 H17R 1.5199 113.49 -136.41 107.73 1.1215 +IC C218 C216 *C217 H17S 1.5199 113.49 109.14 104.66 1.0917 +IC C216 C217 C218 C219 1.5511 113.49 -69.66 113.45 1.4750 +IC C219 C217 *C218 H18R 1.4750 113.45 -121.18 111.39 1.1276 +IC C219 C217 *C218 H18S 1.4750 113.45 122.00 109.88 1.1394 +IC C217 C218 C219 C220 1.5199 113.45 -67.29 116.51 1.4859 +IC C220 C218 *C219 H19R 1.4859 116.51 -113.64 110.52 1.1479 +IC C220 C218 *C219 H19S 1.4859 116.51 123.31 116.84 1.1410 +IC C218 C219 C220 H20T 1.4750 116.51 -173.59 113.53 1.0826 +IC H20T C219 *C220 H20R 1.0826 113.53 -118.46 107.40 1.0844 +IC H20T C219 *C220 H20S 1.0826 113.53 122.07 111.06 1.1305 +IC C31 C32 C33 C34 1.4875 113.42 152.78 109.79 1.5203 +IC C34 C32 *C33 H3X 1.5203 109.79 -109.19 108.75 1.0857 +IC C34 C32 *C33 H3Y 1.5203 109.79 125.96 114.80 1.0550 +IC C32 C33 C34 C35 1.5621 109.79 -169.49 111.42 1.6128 +IC C35 C33 *C34 H4X 1.6128 111.42 -121.66 103.52 1.1288 +IC C35 C33 *C34 H4Y 1.6128 111.42 116.95 109.31 1.1475 +IC C33 C34 C35 C36 1.5203 111.42 -177.91 108.73 1.5691 +IC C36 C34 *C35 H5X 1.5691 108.73 -123.20 118.69 1.1198 +IC C36 C34 *C35 H5Y 1.5691 108.73 121.97 110.30 1.1238 +IC C34 C35 C36 C37 1.6128 108.73 156.40 108.50 1.4966 +IC C37 C35 *C36 H6X 1.4966 108.50 -114.88 106.92 1.0834 +IC C37 C35 *C36 H6Y 1.4966 108.50 124.70 107.92 1.1693 +IC C35 C36 C37 C38 1.5691 108.50 -176.11 115.37 1.5513 +IC C38 C36 *C37 H7X 1.5513 115.37 -132.10 117.12 1.1122 +IC C38 C36 *C37 H7Y 1.5513 115.37 117.93 103.69 1.1113 +IC C36 C37 C38 C39 1.4966 115.37 166.36 110.33 1.4980 +IC C39 C37 *C38 H8X 1.4980 110.33 -129.71 109.95 1.1296 +IC C39 C37 *C38 H8Y 1.4980 110.33 118.79 109.90 1.0764 +IC C37 C38 C39 C310 1.5513 110.33 -164.13 118.89 1.5943 +IC C310 C38 *C39 H9X 1.5943 118.89 -115.55 109.73 1.0952 +IC C310 C38 *C39 H9Y 1.5943 118.89 130.25 106.31 1.0929 +IC C38 C39 C310 C311 1.4980 118.89 -49.00 109.22 1.5137 +IC C311 C39 *C310 H10X 1.5137 109.22 -116.74 108.27 1.0813 +IC C311 C39 *C310 H10Y 1.5137 109.22 117.30 111.40 1.0636 +IC C39 C310 C311 C312 1.5943 109.22 170.95 112.95 1.5533 +IC C312 C310 *C311 H11X 1.5533 112.95 -123.43 111.51 1.1135 +IC C312 C310 *C311 H11Y 1.5533 112.95 112.52 99.10 1.0554 +IC C310 C311 C312 C313 1.5137 112.95 -164.15 106.89 1.5525 +IC C313 C311 *C312 H12X 1.5525 106.89 -115.76 102.65 1.0793 +IC C313 C311 *C312 H12Y 1.5525 106.89 116.44 125.17 1.1466 +IC C311 C312 C313 C314 1.5533 106.89 -140.81 107.79 1.5309 +IC C314 C312 *C313 H13X 1.5309 107.79 -112.37 108.50 1.0756 +IC C314 C312 *C313 H13Y 1.5309 107.79 124.74 113.42 1.0947 +IC C312 C313 C314 C315 1.5525 107.79 -67.74 114.85 1.4938 +IC C315 C313 *C314 H14X 1.4938 114.85 -119.60 107.21 1.0693 +IC C315 C313 *C314 H14Y 1.4938 114.85 116.01 108.14 1.0570 +IC C313 C314 C315 C316 1.5309 114.85 -178.97 111.64 1.5439 +IC C316 C314 *C315 H15X 1.5439 111.64 -125.57 110.73 1.1159 +IC C316 C314 *C315 H15Y 1.5439 111.64 124.77 114.52 1.0909 +IC C314 C315 C316 C317 1.4938 111.64 -177.93 107.20 1.5537 +IC C317 C315 *C316 H16X 1.5537 107.20 -113.34 106.47 1.0729 +IC C317 C315 *C316 H16Y 1.5537 107.20 116.58 112.07 1.1621 +IC C315 C316 C317 C318 1.5439 107.20 162.37 112.19 1.5610 +IC C318 C316 *C317 H17X 1.5610 112.19 -114.65 101.79 1.1260 +IC C318 C316 *C317 H17Y 1.5610 112.19 128.24 112.26 1.1118 +IC C316 C317 C318 H18X 1.5537 112.19 168.54 105.45 1.1437 +IC H18X C317 *C318 H18Y 1.1437 105.45 -112.51 114.99 1.1562 +IC H18X C317 *C318 H18Z 1.1437 105.45 132.44 116.32 1.1291 +IC C13 C11 *C12 O2 1.5184 107.54 122.63 109.30 1.4426 +IC O2 C11 *C12 H2 1.4426 109.30 119.81 108.24 1.1104 +IC C11 C12 O2 HO2 1.6085 109.30 -115.24 92.34 1.0302 +IC C14 C12 *C13 O3 1.5631 111.19 117.68 104.72 1.4274 +IC O3 C12 *C13 H3 1.4274 104.72 117.96 111.56 1.1140 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C15 C13 *C14 O4 1.5343 111.39 -124.35 114.32 1.4177 +IC O4 C13 *C14 H4 1.4177 114.32 -117.89 106.72 1.0604 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C13 C14 C15 O5 1.5631 111.39 179.33 109.28 1.4270 +IC O5 C14 *C15 C16 1.4270 109.28 -124.79 112.35 1.5007 +IC C16 C14 *C15 H5 1.5007 112.35 -118.86 104.70 1.1064 +IC C14 C15 O5 P5 1.5343 109.28 -123.53 132.73 1.6688 +IC C15 O5 P5 OP52 1.4270 132.73 64.99 107.56 1.5362 +IC OP52 O5 *P5 OP53 1.5362 107.56 -122.52 110.70 1.5140 +IC OP52 O5 *P5 OP54 1.5362 107.56 121.44 99.10 1.5259 +IC O5 P5 OP52 HP52 1.6329 100.88 14.07 107.21 0.9447 +IC C11 C15 *C16 O6 1.6111 109.23 -111.89 111.27 1.4099 +IC C11 C15 *C16 H6 1.6111 109.23 119.01 114.23 1.1116 +IC C15 C16 O6 HO6 1.5007 111.27 -69.60 103.78 1.0348 + +RESI SAPI2C -4.00 ! Phosphatidylinositol-(3,4)-bisphosphate (PIP2) with protonation on P3 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | | | +ATOM C14 CC3161 -0.09 ! | H3 OP32--HP32 +ATOM H4 HCA1 0.09 ! +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! \ +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! (-) O13 O12 +ATOM C11 CC3161 -0.08 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.59 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O12 OC30P -0.57 ! HA---C1---HB +ATOM O11 OSLP -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C26 CEL1 -0.15 ! | | +ATOM H6R HEL1 0.15 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H12R HEL1 0.15 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H16R---C216--H16S | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! H18R---C218--H18S | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! | | +ATOM H18S HAL2 0.09 ! H19R---C219--H19S | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! | | +ATOM H19S HAL2 0.09 ! H20R---C220--H20S | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! H20T | +ATOM H20R HAL3 0.09 ! | +ATOM H20S HAL3 0.09 ! | +ATOM H20T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! H15X---C315--H15Y +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! H16X---C316--H16Y +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! | +ATOM H16Y HAL2 0.09 ! H17X---C317--H17Y +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! | +ATOM H17Y HAL2 0.09 ! H18X---C318--H18Y +GROUP ! | +ATOM C318 CTL3 -0.27 ! H18Z +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.6085 107.54 60.79 111.19 1.5631 +IC C12 C13 C14 C15 1.5184 111.19 -56.12 111.39 1.5343 +IC C13 C14 C15 C16 1.5631 111.39 54.54 112.35 1.5007 +IC C14 C15 C16 C11 1.5343 112.35 -58.19 109.23 1.6111 +IC C15 C16 C11 C12 1.5007 109.23 61.82 106.81 1.6085 +IC C16 C11 C12 C13 1.6111 106.81 -62.97 107.54 1.5184 +IC C16 C12 *C11 H1 1.6111 106.81 113.72 110.66 1.0970 +IC C16 C12 *C11 O12 1.6111 106.81 -132.79 100.40 1.4976 +IC C11 C13 *C12 H2 1.6085 107.54 117.10 108.95 1.1104 +IC C11 C13 *C12 O2 1.6085 107.54 -120.52 112.68 1.4426 +IC C12 C14 *C13 H3 1.5184 111.19 124.74 110.89 1.1140 +IC C12 C14 *C13 O3 1.5184 111.19 -114.99 109.09 1.4274 +IC C13 C15 *C14 H4 1.5631 111.39 -116.94 108.09 1.0604 +IC C13 C15 *C14 O4 1.5631 111.39 127.19 109.18 1.4177 +IC C14 C16 *C15 H5 1.5343 112.35 115.94 109.59 1.1064 +IC C14 C16 *C15 O5 1.5343 112.35 -123.35 111.87 1.4270 +IC C15 C11 *C16 H6 1.5007 109.23 -123.77 106.40 1.1116 +IC C15 C11 *C16 O6 1.5007 109.23 117.85 102.04 1.4099 +IC C13 C12 O2 HO2 1.5184 112.68 4.26 92.34 1.0302 +IC C11 C16 O6 HO6 1.6111 102.04 174.01 103.78 1.0348 +IC C12 C11 O12 P 1.6085 100.40 173.02 130.40 1.6484 +IC C11 O12 P O11 1.4976 130.40 176.68 99.70 1.6050 +IC O11 O12 *P O13 1.6050 99.70 -109.02 115.70 1.4789 +IC O11 O12 *P O14 1.6050 99.70 106.84 115.04 1.4775 +IC O12 P O11 C1 1.6484 99.70 -86.90 122.81 1.4512 +IC P O11 C1 C2 1.6050 122.81 -117.13 113.54 1.6662 +IC C2 O11 *C1 HA 1.6662 113.54 120.82 117.60 1.0724 +IC HA O11 *C1 HB 1.0724 117.60 112.73 101.54 1.1034 +IC O11 C1 C2 O21 1.4512 113.54 67.81 112.32 1.4818 +IC O21 C1 *C2 C3 1.4818 112.32 -115.71 105.85 1.4850 +IC C3 C1 *C2 HS 1.4850 105.85 -116.46 112.45 1.1326 +IC C1 C2 O21 C21 1.6662 112.32 56.99 112.49 1.3635 +IC C2 O21 C21 C22 1.4818 112.49 -153.82 113.90 1.5495 +IC C22 O21 *C21 O22 1.5495 113.90 -166.45 122.48 1.2236 +IC O21 C21 C22 C23 1.3635 113.90 -97.47 110.04 1.5360 +IC C23 C21 *C22 H2R 1.5360 110.04 135.29 109.75 1.1450 +IC H2R C21 *C22 H2S 1.1450 109.75 112.05 103.31 1.1794 +IC C1 C2 C3 O31 1.6662 105.85 171.16 116.64 1.4438 +IC O31 C2 *C3 HX 1.4438 116.64 -118.85 101.17 1.0985 +IC HX C2 *C3 HY 1.0985 101.17 -104.81 106.46 1.1176 +IC C2 C3 O31 C31 1.4850 116.64 68.33 120.24 1.3520 +IC C3 O31 C31 C32 1.4438 120.24 -177.65 111.24 1.4875 +IC C32 O31 *C31 O32 1.4875 111.24 -178.84 125.40 1.2086 +IC O31 C31 C32 C33 1.3520 111.24 121.63 113.42 1.5621 +IC C33 C31 *C32 H2X 1.5621 113.42 -123.40 106.82 1.1474 +IC H2X C31 *C32 H2Y 1.1474 106.82 -105.11 113.46 1.1000 +IC C21 C22 C23 C24 1.5495 110.04 67.92 113.07 1.5546 +IC C24 C22 *C23 H3R 1.5546 113.07 -121.18 115.12 1.1189 +IC C24 C22 *C23 H3S 1.5546 113.07 116.77 109.69 1.1169 +IC C22 C23 C24 C25 1.5360 113.07 60.63 113.21 1.4448 +IC C25 C23 *C24 H4R 1.4448 113.21 -127.46 111.76 1.1049 +IC C25 C23 *C24 H4S 1.4448 113.21 119.78 99.62 1.1283 +IC C23 C24 C25 C26 1.5546 113.21 173.34 125.28 1.3364 +IC C26 C24 *C25 H5R 1.3364 125.28 179.03 114.79 1.0696 +IC C24 C25 C26 C27 1.4448 125.28 1.74 128.06 1.4490 +IC C27 C25 *C26 H6R 1.4490 128.06 178.88 115.21 1.1285 +IC C25 C26 C27 C28 1.3364 128.06 141.59 117.73 1.5109 +IC C28 C26 *C27 H7R 1.5109 117.73 -119.24 110.88 1.1468 +IC C28 C26 *C27 H7S 1.5109 117.73 121.92 107.89 1.1493 +IC C26 C27 C28 C29 1.4490 117.73 134.20 125.21 1.3700 +IC C29 C27 *C28 H8R 1.3700 125.21 175.16 118.29 1.1609 +IC C27 C28 C29 C210 1.5109 125.21 0.65 132.76 1.5304 +IC C210 C28 *C29 H9R 1.5304 132.76 -177.06 122.23 1.1088 +IC C28 C29 C210 C211 1.3700 132.76 108.32 105.00 1.4607 +IC C211 C29 *C210 H10R 1.4607 105.00 -119.86 118.79 1.1461 +IC C211 C29 *C210 H10S 1.4607 105.00 118.27 112.41 1.1989 +IC C29 C210 C211 C212 1.5304 105.00 126.46 126.50 1.3393 +IC C212 C210 *C211 H11R 1.3393 126.50 170.96 115.02 1.0788 +IC C210 C211 C212 C213 1.4607 126.50 1.45 129.47 1.5373 +IC C213 C211 *C212 H12R 1.5373 129.47 -177.03 116.04 1.0756 +IC C211 C212 C213 C214 1.3393 129.47 112.52 106.68 1.5525 +IC C214 C212 *C213 H13R 1.5525 106.68 -120.58 110.94 1.0956 +IC C214 C212 *C213 H13S 1.5525 106.68 121.63 104.28 1.0946 +IC C212 C213 C214 C215 1.5373 106.68 116.97 124.36 1.3427 +IC C215 C213 *C214 H14R 1.3427 124.36 -176.47 119.66 1.0003 +IC C213 C214 C215 C216 1.5525 124.36 0.36 129.37 1.4732 +IC C216 C214 *C215 H15R 1.4732 129.37 -178.58 114.71 1.1153 +IC C214 C215 C216 C217 1.3427 129.37 119.14 113.38 1.5511 +IC C217 C215 *C216 H16R 1.5511 113.38 -128.09 115.06 1.1150 +IC C217 C215 *C216 H16S 1.5511 113.38 112.67 106.11 1.1197 +IC C215 C216 C217 C218 1.4732 113.38 167.76 113.49 1.5199 +IC C218 C216 *C217 H17R 1.5199 113.49 -136.41 107.73 1.1215 +IC C218 C216 *C217 H17S 1.5199 113.49 109.14 104.66 1.0917 +IC C216 C217 C218 C219 1.5511 113.49 -69.66 113.45 1.4750 +IC C219 C217 *C218 H18R 1.4750 113.45 -121.18 111.39 1.1276 +IC C219 C217 *C218 H18S 1.4750 113.45 122.00 109.88 1.1394 +IC C217 C218 C219 C220 1.5199 113.45 -67.29 116.51 1.4859 +IC C220 C218 *C219 H19R 1.4859 116.51 -113.64 110.52 1.1479 +IC C220 C218 *C219 H19S 1.4859 116.51 123.31 116.84 1.1410 +IC C218 C219 C220 H20T 1.4750 116.51 -173.59 113.53 1.0826 +IC H20T C219 *C220 H20R 1.0826 113.53 -118.46 107.40 1.0844 +IC H20T C219 *C220 H20S 1.0826 113.53 122.07 111.06 1.1305 +IC C31 C32 C33 C34 1.4875 113.42 152.78 109.79 1.5203 +IC C34 C32 *C33 H3X 1.5203 109.79 -109.19 108.75 1.0857 +IC C34 C32 *C33 H3Y 1.5203 109.79 125.96 114.80 1.0550 +IC C32 C33 C34 C35 1.5621 109.79 -169.49 111.42 1.6128 +IC C35 C33 *C34 H4X 1.6128 111.42 -121.66 103.52 1.1288 +IC C35 C33 *C34 H4Y 1.6128 111.42 116.95 109.31 1.1475 +IC C33 C34 C35 C36 1.5203 111.42 -177.91 108.73 1.5691 +IC C36 C34 *C35 H5X 1.5691 108.73 -123.20 118.69 1.1198 +IC C36 C34 *C35 H5Y 1.5691 108.73 121.97 110.30 1.1238 +IC C34 C35 C36 C37 1.6128 108.73 156.40 108.50 1.4966 +IC C37 C35 *C36 H6X 1.4966 108.50 -114.88 106.92 1.0834 +IC C37 C35 *C36 H6Y 1.4966 108.50 124.70 107.92 1.1693 +IC C35 C36 C37 C38 1.5691 108.50 -176.11 115.37 1.5513 +IC C38 C36 *C37 H7X 1.5513 115.37 -132.10 117.12 1.1122 +IC C38 C36 *C37 H7Y 1.5513 115.37 117.93 103.69 1.1113 +IC C36 C37 C38 C39 1.4966 115.37 166.36 110.33 1.4980 +IC C39 C37 *C38 H8X 1.4980 110.33 -129.71 109.95 1.1296 +IC C39 C37 *C38 H8Y 1.4980 110.33 118.79 109.90 1.0764 +IC C37 C38 C39 C310 1.5513 110.33 -164.13 118.89 1.5943 +IC C310 C38 *C39 H9X 1.5943 118.89 -115.55 109.73 1.0952 +IC C310 C38 *C39 H9Y 1.5943 118.89 130.25 106.31 1.0929 +IC C38 C39 C310 C311 1.4980 118.89 -49.00 109.22 1.5137 +IC C311 C39 *C310 H10X 1.5137 109.22 -116.74 108.27 1.0813 +IC C311 C39 *C310 H10Y 1.5137 109.22 117.30 111.40 1.0636 +IC C39 C310 C311 C312 1.5943 109.22 170.95 112.95 1.5533 +IC C312 C310 *C311 H11X 1.5533 112.95 -123.43 111.51 1.1135 +IC C312 C310 *C311 H11Y 1.5533 112.95 112.52 99.10 1.0554 +IC C310 C311 C312 C313 1.5137 112.95 -164.15 106.89 1.5525 +IC C313 C311 *C312 H12X 1.5525 106.89 -115.76 102.65 1.0793 +IC C313 C311 *C312 H12Y 1.5525 106.89 116.44 125.17 1.1466 +IC C311 C312 C313 C314 1.5533 106.89 -140.81 107.79 1.5309 +IC C314 C312 *C313 H13X 1.5309 107.79 -112.37 108.50 1.0756 +IC C314 C312 *C313 H13Y 1.5309 107.79 124.74 113.42 1.0947 +IC C312 C313 C314 C315 1.5525 107.79 -67.74 114.85 1.4938 +IC C315 C313 *C314 H14X 1.4938 114.85 -119.60 107.21 1.0693 +IC C315 C313 *C314 H14Y 1.4938 114.85 116.01 108.14 1.0570 +IC C313 C314 C315 C316 1.5309 114.85 -178.97 111.64 1.5439 +IC C316 C314 *C315 H15X 1.5439 111.64 -125.57 110.73 1.1159 +IC C316 C314 *C315 H15Y 1.5439 111.64 124.77 114.52 1.0909 +IC C314 C315 C316 C317 1.4938 111.64 -177.93 107.20 1.5537 +IC C317 C315 *C316 H16X 1.5537 107.20 -113.34 106.47 1.0729 +IC C317 C315 *C316 H16Y 1.5537 107.20 116.58 112.07 1.1621 +IC C315 C316 C317 C318 1.5439 107.20 162.37 112.19 1.5610 +IC C318 C316 *C317 H17X 1.5610 112.19 -114.65 101.79 1.1260 +IC C318 C316 *C317 H17Y 1.5610 112.19 128.24 112.26 1.1118 +IC C316 C317 C318 H18X 1.5537 112.19 168.54 105.45 1.1437 +IC H18X C317 *C318 H18Y 1.1437 105.45 -112.51 114.99 1.1562 +IC H18X C317 *C318 H18Z 1.1437 105.45 132.44 116.32 1.1291 +IC C13 C11 *C12 O2 1.5184 107.54 122.63 109.30 1.4426 +IC O2 C11 *C12 H2 1.4426 109.30 119.81 108.24 1.1104 +IC C11 C12 O2 HO2 1.6085 109.30 -115.24 92.34 1.0302 +IC C14 C12 *C13 O3 1.5631 111.19 117.68 104.72 1.4274 +IC O3 C12 *C13 H3 1.4274 104.72 117.96 111.56 1.1140 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C15 C13 *C14 O4 1.5343 111.39 -124.35 114.32 1.4177 +IC O4 C13 *C14 H4 1.4177 114.32 -117.89 106.72 1.0604 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC C13 C14 C15 O5 1.5631 111.39 179.33 109.28 1.4270 +IC O5 C14 *C15 C16 1.4270 109.28 -124.79 112.35 1.5007 +IC C16 C14 *C15 H5 1.5007 112.35 -118.86 104.70 1.1064 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C15 *C16 O6 1.6111 109.23 -111.89 111.27 1.4099 +IC C11 C15 *C16 H6 1.6111 109.23 119.01 114.23 1.1116 +IC C15 C16 O6 HO6 1.5007 111.27 -69.60 103.78 1.0348 + +RESI SAPI2D -4.00 ! Phosphatidylinositol-(3,4)-bisphosphate (PIP2) with protonation on P4 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | | OP32(-) +ATOM H4 HCA1 0.09 ! | H3 +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! \ +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! (-) O13 O12 +ATOM C11 CC3161 -0.08 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.59 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O12 OC30P -0.57 ! HA---C1---HB +ATOM O11 OSLP -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C26 CEL1 -0.15 ! | | +ATOM H6R HEL1 0.15 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H12R HEL1 0.15 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H16R---C216--H16S | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! H18R---C218--H18S | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! | | +ATOM H18S HAL2 0.09 ! H19R---C219--H19S | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! | | +ATOM H19S HAL2 0.09 ! H20R---C220--H20S | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! H20T | +ATOM H20R HAL3 0.09 ! | +ATOM H20S HAL3 0.09 ! | +ATOM H20T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! H15X---C315--H15Y +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! H16X---C316--H16Y +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! | +ATOM H16Y HAL2 0.09 ! H17X---C317--H17Y +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! | +ATOM H17Y HAL2 0.09 ! H18X---C318--H18Y +GROUP ! | +ATOM C318 CTL3 -0.27 ! H18Z +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.6085 107.54 60.79 111.19 1.5631 +IC C12 C13 C14 C15 1.5184 111.19 -56.12 111.39 1.5343 +IC C13 C14 C15 C16 1.5631 111.39 54.54 112.35 1.5007 +IC C14 C15 C16 C11 1.5343 112.35 -58.19 109.23 1.6111 +IC C15 C16 C11 C12 1.5007 109.23 61.82 106.81 1.6085 +IC C16 C11 C12 C13 1.6111 106.81 -62.97 107.54 1.5184 +IC C16 C12 *C11 H1 1.6111 106.81 113.72 110.66 1.0970 +IC C16 C12 *C11 O12 1.6111 106.81 -132.79 100.40 1.4976 +IC C11 C13 *C12 H2 1.6085 107.54 117.10 108.95 1.1104 +IC C11 C13 *C12 O2 1.6085 107.54 -120.52 112.68 1.4426 +IC C12 C14 *C13 H3 1.5184 111.19 124.74 110.89 1.1140 +IC C12 C14 *C13 O3 1.5184 111.19 -114.99 109.09 1.4274 +IC C13 C15 *C14 H4 1.5631 111.39 -116.94 108.09 1.0604 +IC C13 C15 *C14 O4 1.5631 111.39 127.19 109.18 1.4177 +IC C14 C16 *C15 H5 1.5343 112.35 115.94 109.59 1.1064 +IC C14 C16 *C15 O5 1.5343 112.35 -123.35 111.87 1.4270 +IC C15 C11 *C16 H6 1.5007 109.23 -123.77 106.40 1.1116 +IC C15 C11 *C16 O6 1.5007 109.23 117.85 102.04 1.4099 +IC C13 C12 O2 HO2 1.5184 112.68 4.26 92.34 1.0302 +IC C11 C16 O6 HO6 1.6111 102.04 174.01 103.78 1.0348 +IC C12 C11 O12 P 1.6085 100.40 173.02 130.40 1.6484 +IC C11 O12 P O11 1.4976 130.40 176.68 99.70 1.6050 +IC O11 O12 *P O13 1.6050 99.70 -109.02 115.70 1.4789 +IC O11 O12 *P O14 1.6050 99.70 106.84 115.04 1.4775 +IC O12 P O11 C1 1.6484 99.70 -86.90 122.81 1.4512 +IC P O11 C1 C2 1.6050 122.81 -117.13 113.54 1.6662 +IC C2 O11 *C1 HA 1.6662 113.54 120.82 117.60 1.0724 +IC HA O11 *C1 HB 1.0724 117.60 112.73 101.54 1.1034 +IC O11 C1 C2 O21 1.4512 113.54 67.81 112.32 1.4818 +IC O21 C1 *C2 C3 1.4818 112.32 -115.71 105.85 1.4850 +IC C3 C1 *C2 HS 1.4850 105.85 -116.46 112.45 1.1326 +IC C1 C2 O21 C21 1.6662 112.32 56.99 112.49 1.3635 +IC C2 O21 C21 C22 1.4818 112.49 -153.82 113.90 1.5495 +IC C22 O21 *C21 O22 1.5495 113.90 -166.45 122.48 1.2236 +IC O21 C21 C22 C23 1.3635 113.90 -97.47 110.04 1.5360 +IC C23 C21 *C22 H2R 1.5360 110.04 135.29 109.75 1.1450 +IC H2R C21 *C22 H2S 1.1450 109.75 112.05 103.31 1.1794 +IC C1 C2 C3 O31 1.6662 105.85 171.16 116.64 1.4438 +IC O31 C2 *C3 HX 1.4438 116.64 -118.85 101.17 1.0985 +IC HX C2 *C3 HY 1.0985 101.17 -104.81 106.46 1.1176 +IC C2 C3 O31 C31 1.4850 116.64 68.33 120.24 1.3520 +IC C3 O31 C31 C32 1.4438 120.24 -177.65 111.24 1.4875 +IC C32 O31 *C31 O32 1.4875 111.24 -178.84 125.40 1.2086 +IC O31 C31 C32 C33 1.3520 111.24 121.63 113.42 1.5621 +IC C33 C31 *C32 H2X 1.5621 113.42 -123.40 106.82 1.1474 +IC H2X C31 *C32 H2Y 1.1474 106.82 -105.11 113.46 1.1000 +IC C21 C22 C23 C24 1.5495 110.04 67.92 113.07 1.5546 +IC C24 C22 *C23 H3R 1.5546 113.07 -121.18 115.12 1.1189 +IC C24 C22 *C23 H3S 1.5546 113.07 116.77 109.69 1.1169 +IC C22 C23 C24 C25 1.5360 113.07 60.63 113.21 1.4448 +IC C25 C23 *C24 H4R 1.4448 113.21 -127.46 111.76 1.1049 +IC C25 C23 *C24 H4S 1.4448 113.21 119.78 99.62 1.1283 +IC C23 C24 C25 C26 1.5546 113.21 173.34 125.28 1.3364 +IC C26 C24 *C25 H5R 1.3364 125.28 179.03 114.79 1.0696 +IC C24 C25 C26 C27 1.4448 125.28 1.74 128.06 1.4490 +IC C27 C25 *C26 H6R 1.4490 128.06 178.88 115.21 1.1285 +IC C25 C26 C27 C28 1.3364 128.06 141.59 117.73 1.5109 +IC C28 C26 *C27 H7R 1.5109 117.73 -119.24 110.88 1.1468 +IC C28 C26 *C27 H7S 1.5109 117.73 121.92 107.89 1.1493 +IC C26 C27 C28 C29 1.4490 117.73 134.20 125.21 1.3700 +IC C29 C27 *C28 H8R 1.3700 125.21 175.16 118.29 1.1609 +IC C27 C28 C29 C210 1.5109 125.21 0.65 132.76 1.5304 +IC C210 C28 *C29 H9R 1.5304 132.76 -177.06 122.23 1.1088 +IC C28 C29 C210 C211 1.3700 132.76 108.32 105.00 1.4607 +IC C211 C29 *C210 H10R 1.4607 105.00 -119.86 118.79 1.1461 +IC C211 C29 *C210 H10S 1.4607 105.00 118.27 112.41 1.1989 +IC C29 C210 C211 C212 1.5304 105.00 126.46 126.50 1.3393 +IC C212 C210 *C211 H11R 1.3393 126.50 170.96 115.02 1.0788 +IC C210 C211 C212 C213 1.4607 126.50 1.45 129.47 1.5373 +IC C213 C211 *C212 H12R 1.5373 129.47 -177.03 116.04 1.0756 +IC C211 C212 C213 C214 1.3393 129.47 112.52 106.68 1.5525 +IC C214 C212 *C213 H13R 1.5525 106.68 -120.58 110.94 1.0956 +IC C214 C212 *C213 H13S 1.5525 106.68 121.63 104.28 1.0946 +IC C212 C213 C214 C215 1.5373 106.68 116.97 124.36 1.3427 +IC C215 C213 *C214 H14R 1.3427 124.36 -176.47 119.66 1.0003 +IC C213 C214 C215 C216 1.5525 124.36 0.36 129.37 1.4732 +IC C216 C214 *C215 H15R 1.4732 129.37 -178.58 114.71 1.1153 +IC C214 C215 C216 C217 1.3427 129.37 119.14 113.38 1.5511 +IC C217 C215 *C216 H16R 1.5511 113.38 -128.09 115.06 1.1150 +IC C217 C215 *C216 H16S 1.5511 113.38 112.67 106.11 1.1197 +IC C215 C216 C217 C218 1.4732 113.38 167.76 113.49 1.5199 +IC C218 C216 *C217 H17R 1.5199 113.49 -136.41 107.73 1.1215 +IC C218 C216 *C217 H17S 1.5199 113.49 109.14 104.66 1.0917 +IC C216 C217 C218 C219 1.5511 113.49 -69.66 113.45 1.4750 +IC C219 C217 *C218 H18R 1.4750 113.45 -121.18 111.39 1.1276 +IC C219 C217 *C218 H18S 1.4750 113.45 122.00 109.88 1.1394 +IC C217 C218 C219 C220 1.5199 113.45 -67.29 116.51 1.4859 +IC C220 C218 *C219 H19R 1.4859 116.51 -113.64 110.52 1.1479 +IC C220 C218 *C219 H19S 1.4859 116.51 123.31 116.84 1.1410 +IC C218 C219 C220 H20T 1.4750 116.51 -173.59 113.53 1.0826 +IC H20T C219 *C220 H20R 1.0826 113.53 -118.46 107.40 1.0844 +IC H20T C219 *C220 H20S 1.0826 113.53 122.07 111.06 1.1305 +IC C31 C32 C33 C34 1.4875 113.42 152.78 109.79 1.5203 +IC C34 C32 *C33 H3X 1.5203 109.79 -109.19 108.75 1.0857 +IC C34 C32 *C33 H3Y 1.5203 109.79 125.96 114.80 1.0550 +IC C32 C33 C34 C35 1.5621 109.79 -169.49 111.42 1.6128 +IC C35 C33 *C34 H4X 1.6128 111.42 -121.66 103.52 1.1288 +IC C35 C33 *C34 H4Y 1.6128 111.42 116.95 109.31 1.1475 +IC C33 C34 C35 C36 1.5203 111.42 -177.91 108.73 1.5691 +IC C36 C34 *C35 H5X 1.5691 108.73 -123.20 118.69 1.1198 +IC C36 C34 *C35 H5Y 1.5691 108.73 121.97 110.30 1.1238 +IC C34 C35 C36 C37 1.6128 108.73 156.40 108.50 1.4966 +IC C37 C35 *C36 H6X 1.4966 108.50 -114.88 106.92 1.0834 +IC C37 C35 *C36 H6Y 1.4966 108.50 124.70 107.92 1.1693 +IC C35 C36 C37 C38 1.5691 108.50 -176.11 115.37 1.5513 +IC C38 C36 *C37 H7X 1.5513 115.37 -132.10 117.12 1.1122 +IC C38 C36 *C37 H7Y 1.5513 115.37 117.93 103.69 1.1113 +IC C36 C37 C38 C39 1.4966 115.37 166.36 110.33 1.4980 +IC C39 C37 *C38 H8X 1.4980 110.33 -129.71 109.95 1.1296 +IC C39 C37 *C38 H8Y 1.4980 110.33 118.79 109.90 1.0764 +IC C37 C38 C39 C310 1.5513 110.33 -164.13 118.89 1.5943 +IC C310 C38 *C39 H9X 1.5943 118.89 -115.55 109.73 1.0952 +IC C310 C38 *C39 H9Y 1.5943 118.89 130.25 106.31 1.0929 +IC C38 C39 C310 C311 1.4980 118.89 -49.00 109.22 1.5137 +IC C311 C39 *C310 H10X 1.5137 109.22 -116.74 108.27 1.0813 +IC C311 C39 *C310 H10Y 1.5137 109.22 117.30 111.40 1.0636 +IC C39 C310 C311 C312 1.5943 109.22 170.95 112.95 1.5533 +IC C312 C310 *C311 H11X 1.5533 112.95 -123.43 111.51 1.1135 +IC C312 C310 *C311 H11Y 1.5533 112.95 112.52 99.10 1.0554 +IC C310 C311 C312 C313 1.5137 112.95 -164.15 106.89 1.5525 +IC C313 C311 *C312 H12X 1.5525 106.89 -115.76 102.65 1.0793 +IC C313 C311 *C312 H12Y 1.5525 106.89 116.44 125.17 1.1466 +IC C311 C312 C313 C314 1.5533 106.89 -140.81 107.79 1.5309 +IC C314 C312 *C313 H13X 1.5309 107.79 -112.37 108.50 1.0756 +IC C314 C312 *C313 H13Y 1.5309 107.79 124.74 113.42 1.0947 +IC C312 C313 C314 C315 1.5525 107.79 -67.74 114.85 1.4938 +IC C315 C313 *C314 H14X 1.4938 114.85 -119.60 107.21 1.0693 +IC C315 C313 *C314 H14Y 1.4938 114.85 116.01 108.14 1.0570 +IC C313 C314 C315 C316 1.5309 114.85 -178.97 111.64 1.5439 +IC C316 C314 *C315 H15X 1.5439 111.64 -125.57 110.73 1.1159 +IC C316 C314 *C315 H15Y 1.5439 111.64 124.77 114.52 1.0909 +IC C314 C315 C316 C317 1.4938 111.64 -177.93 107.20 1.5537 +IC C317 C315 *C316 H16X 1.5537 107.20 -113.34 106.47 1.0729 +IC C317 C315 *C316 H16Y 1.5537 107.20 116.58 112.07 1.1621 +IC C315 C316 C317 C318 1.5439 107.20 162.37 112.19 1.5610 +IC C318 C316 *C317 H17X 1.5610 112.19 -114.65 101.79 1.1260 +IC C318 C316 *C317 H17Y 1.5610 112.19 128.24 112.26 1.1118 +IC C316 C317 C318 H18X 1.5537 112.19 168.54 105.45 1.1437 +IC H18X C317 *C318 H18Y 1.1437 105.45 -112.51 114.99 1.1562 +IC H18X C317 *C318 H18Z 1.1437 105.45 132.44 116.32 1.1291 +IC C13 C11 *C12 O2 1.5184 107.54 122.63 109.30 1.4426 +IC O2 C11 *C12 H2 1.4426 109.30 119.81 108.24 1.1104 +IC C11 C12 O2 HO2 1.6085 109.30 -115.24 92.34 1.0302 +IC C14 C12 *C13 O3 1.5631 111.19 117.68 104.72 1.4274 +IC O3 C12 *C13 H3 1.4274 104.72 117.96 111.56 1.1140 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C15 C13 *C14 O4 1.5343 111.39 -124.35 114.32 1.4177 +IC O4 C13 *C14 H4 1.4177 114.32 -117.89 106.72 1.0604 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC O4 P4 OP42 HP42 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 C15 O5 1.5631 111.39 179.33 109.28 1.4270 +IC O5 C14 *C15 C16 1.4270 109.28 -124.79 112.35 1.5007 +IC C16 C14 *C15 H5 1.5007 112.35 -118.86 104.70 1.1064 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C15 *C16 O6 1.6111 109.23 -111.89 111.27 1.4099 +IC C11 C15 *C16 H6 1.6111 109.23 119.01 114.23 1.1116 +IC C15 C16 O6 HO6 1.5007 111.27 -69.60 103.78 1.0348 + +RESI SAPI33 -6.00 ! Phosphatidylinositol-(3,4,5)-trisphosphate (PIP3) with protonation on P3 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | | | +ATOM C14 CC3161 -0.09 ! | H3 OP32--HP32 +ATOM H4 HCA1 0.09 ! +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! \ +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! (-) O13 O12 +ATOM C11 CC3161 -0.08 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.59 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O12 OC30P -0.57 ! HA---C1---HB +ATOM O11 OSLP -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C26 CEL1 -0.15 ! | | +ATOM H6R HEL1 0.15 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H12R HEL1 0.15 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H16R---C216--H16S | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! H18R---C218--H18S | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! | | +ATOM H18S HAL2 0.09 ! H19R---C219--H19S | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! | | +ATOM H19S HAL2 0.09 ! H20R---C220--H20S | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! H20T | +ATOM H20R HAL3 0.09 ! | +ATOM H20S HAL3 0.09 ! | +ATOM H20T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! H15X---C315--H15Y +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! H16X---C316--H16Y +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! | +ATOM H16Y HAL2 0.09 ! H17X---C317--H17Y +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! | +ATOM H17Y HAL2 0.09 ! H18X---C318--H18Y +GROUP ! | +ATOM C318 CTL3 -0.27 ! H18Z +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.6085 107.54 60.79 111.19 1.5631 +IC C12 C13 C14 C15 1.5184 111.19 -56.12 111.39 1.5343 +IC C13 C14 C15 C16 1.5631 111.39 54.54 112.35 1.5007 +IC C14 C15 C16 C11 1.5343 112.35 -58.19 109.23 1.6111 +IC C15 C16 C11 C12 1.5007 109.23 61.82 106.81 1.6085 +IC C16 C11 C12 C13 1.6111 106.81 -62.97 107.54 1.5184 +IC C16 C12 *C11 H1 1.6111 106.81 113.72 110.66 1.0970 +IC C16 C12 *C11 O12 1.6111 106.81 -132.79 100.40 1.4976 +IC C11 C13 *C12 H2 1.6085 107.54 117.10 108.95 1.1104 +IC C11 C13 *C12 O2 1.6085 107.54 -120.52 112.68 1.4426 +IC C12 C14 *C13 H3 1.5184 111.19 124.74 110.89 1.1140 +IC C12 C14 *C13 O3 1.5184 111.19 -114.99 109.09 1.4274 +IC C13 C15 *C14 H4 1.5631 111.39 -116.94 108.09 1.0604 +IC C13 C15 *C14 O4 1.5631 111.39 127.19 109.18 1.4177 +IC C14 C16 *C15 H5 1.5343 112.35 115.94 109.59 1.1064 +IC C14 C16 *C15 O5 1.5343 112.35 -123.35 111.87 1.4270 +IC C15 C11 *C16 H6 1.5007 109.23 -123.77 106.40 1.1116 +IC C15 C11 *C16 O6 1.5007 109.23 117.85 102.04 1.4099 +IC C13 C12 O2 HO2 1.5184 112.68 4.26 92.34 1.0302 +IC C11 C16 O6 HO6 1.6111 102.04 174.01 103.78 1.0348 +IC C12 C11 O12 P 1.6085 100.40 173.02 130.40 1.6484 +IC C11 O12 P O11 1.4976 130.40 176.68 99.70 1.6050 +IC O11 O12 *P O13 1.6050 99.70 -109.02 115.70 1.4789 +IC O11 O12 *P O14 1.6050 99.70 106.84 115.04 1.4775 +IC O12 P O11 C1 1.6484 99.70 -86.90 122.81 1.4512 +IC P O11 C1 C2 1.6050 122.81 -117.13 113.54 1.6662 +IC C2 O11 *C1 HA 1.6662 113.54 120.82 117.60 1.0724 +IC HA O11 *C1 HB 1.0724 117.60 112.73 101.54 1.1034 +IC O11 C1 C2 O21 1.4512 113.54 67.81 112.32 1.4818 +IC O21 C1 *C2 C3 1.4818 112.32 -115.71 105.85 1.4850 +IC C3 C1 *C2 HS 1.4850 105.85 -116.46 112.45 1.1326 +IC C1 C2 O21 C21 1.6662 112.32 56.99 112.49 1.3635 +IC C2 O21 C21 C22 1.4818 112.49 -153.82 113.90 1.5495 +IC C22 O21 *C21 O22 1.5495 113.90 -166.45 122.48 1.2236 +IC O21 C21 C22 C23 1.3635 113.90 -97.47 110.04 1.5360 +IC C23 C21 *C22 H2R 1.5360 110.04 135.29 109.75 1.1450 +IC H2R C21 *C22 H2S 1.1450 109.75 112.05 103.31 1.1794 +IC C1 C2 C3 O31 1.6662 105.85 171.16 116.64 1.4438 +IC O31 C2 *C3 HX 1.4438 116.64 -118.85 101.17 1.0985 +IC HX C2 *C3 HY 1.0985 101.17 -104.81 106.46 1.1176 +IC C2 C3 O31 C31 1.4850 116.64 68.33 120.24 1.3520 +IC C3 O31 C31 C32 1.4438 120.24 -177.65 111.24 1.4875 +IC C32 O31 *C31 O32 1.4875 111.24 -178.84 125.40 1.2086 +IC O31 C31 C32 C33 1.3520 111.24 121.63 113.42 1.5621 +IC C33 C31 *C32 H2X 1.5621 113.42 -123.40 106.82 1.1474 +IC H2X C31 *C32 H2Y 1.1474 106.82 -105.11 113.46 1.1000 +IC C21 C22 C23 C24 1.5495 110.04 67.92 113.07 1.5546 +IC C24 C22 *C23 H3R 1.5546 113.07 -121.18 115.12 1.1189 +IC C24 C22 *C23 H3S 1.5546 113.07 116.77 109.69 1.1169 +IC C22 C23 C24 C25 1.5360 113.07 60.63 113.21 1.4448 +IC C25 C23 *C24 H4R 1.4448 113.21 -127.46 111.76 1.1049 +IC C25 C23 *C24 H4S 1.4448 113.21 119.78 99.62 1.1283 +IC C23 C24 C25 C26 1.5546 113.21 173.34 125.28 1.3364 +IC C26 C24 *C25 H5R 1.3364 125.28 179.03 114.79 1.0696 +IC C24 C25 C26 C27 1.4448 125.28 1.74 128.06 1.4490 +IC C27 C25 *C26 H6R 1.4490 128.06 178.88 115.21 1.1285 +IC C25 C26 C27 C28 1.3364 128.06 141.59 117.73 1.5109 +IC C28 C26 *C27 H7R 1.5109 117.73 -119.24 110.88 1.1468 +IC C28 C26 *C27 H7S 1.5109 117.73 121.92 107.89 1.1493 +IC C26 C27 C28 C29 1.4490 117.73 134.20 125.21 1.3700 +IC C29 C27 *C28 H8R 1.3700 125.21 175.16 118.29 1.1609 +IC C27 C28 C29 C210 1.5109 125.21 0.65 132.76 1.5304 +IC C210 C28 *C29 H9R 1.5304 132.76 -177.06 122.23 1.1088 +IC C28 C29 C210 C211 1.3700 132.76 108.32 105.00 1.4607 +IC C211 C29 *C210 H10R 1.4607 105.00 -119.86 118.79 1.1461 +IC C211 C29 *C210 H10S 1.4607 105.00 118.27 112.41 1.1989 +IC C29 C210 C211 C212 1.5304 105.00 126.46 126.50 1.3393 +IC C212 C210 *C211 H11R 1.3393 126.50 170.96 115.02 1.0788 +IC C210 C211 C212 C213 1.4607 126.50 1.45 129.47 1.5373 +IC C213 C211 *C212 H12R 1.5373 129.47 -177.03 116.04 1.0756 +IC C211 C212 C213 C214 1.3393 129.47 112.52 106.68 1.5525 +IC C214 C212 *C213 H13R 1.5525 106.68 -120.58 110.94 1.0956 +IC C214 C212 *C213 H13S 1.5525 106.68 121.63 104.28 1.0946 +IC C212 C213 C214 C215 1.5373 106.68 116.97 124.36 1.3427 +IC C215 C213 *C214 H14R 1.3427 124.36 -176.47 119.66 1.0003 +IC C213 C214 C215 C216 1.5525 124.36 0.36 129.37 1.4732 +IC C216 C214 *C215 H15R 1.4732 129.37 -178.58 114.71 1.1153 +IC C214 C215 C216 C217 1.3427 129.37 119.14 113.38 1.5511 +IC C217 C215 *C216 H16R 1.5511 113.38 -128.09 115.06 1.1150 +IC C217 C215 *C216 H16S 1.5511 113.38 112.67 106.11 1.1197 +IC C215 C216 C217 C218 1.4732 113.38 167.76 113.49 1.5199 +IC C218 C216 *C217 H17R 1.5199 113.49 -136.41 107.73 1.1215 +IC C218 C216 *C217 H17S 1.5199 113.49 109.14 104.66 1.0917 +IC C216 C217 C218 C219 1.5511 113.49 -69.66 113.45 1.4750 +IC C219 C217 *C218 H18R 1.4750 113.45 -121.18 111.39 1.1276 +IC C219 C217 *C218 H18S 1.4750 113.45 122.00 109.88 1.1394 +IC C217 C218 C219 C220 1.5199 113.45 -67.29 116.51 1.4859 +IC C220 C218 *C219 H19R 1.4859 116.51 -113.64 110.52 1.1479 +IC C220 C218 *C219 H19S 1.4859 116.51 123.31 116.84 1.1410 +IC C218 C219 C220 H20T 1.4750 116.51 -173.59 113.53 1.0826 +IC H20T C219 *C220 H20R 1.0826 113.53 -118.46 107.40 1.0844 +IC H20T C219 *C220 H20S 1.0826 113.53 122.07 111.06 1.1305 +IC C31 C32 C33 C34 1.4875 113.42 152.78 109.79 1.5203 +IC C34 C32 *C33 H3X 1.5203 109.79 -109.19 108.75 1.0857 +IC C34 C32 *C33 H3Y 1.5203 109.79 125.96 114.80 1.0550 +IC C32 C33 C34 C35 1.5621 109.79 -169.49 111.42 1.6128 +IC C35 C33 *C34 H4X 1.6128 111.42 -121.66 103.52 1.1288 +IC C35 C33 *C34 H4Y 1.6128 111.42 116.95 109.31 1.1475 +IC C33 C34 C35 C36 1.5203 111.42 -177.91 108.73 1.5691 +IC C36 C34 *C35 H5X 1.5691 108.73 -123.20 118.69 1.1198 +IC C36 C34 *C35 H5Y 1.5691 108.73 121.97 110.30 1.1238 +IC C34 C35 C36 C37 1.6128 108.73 156.40 108.50 1.4966 +IC C37 C35 *C36 H6X 1.4966 108.50 -114.88 106.92 1.0834 +IC C37 C35 *C36 H6Y 1.4966 108.50 124.70 107.92 1.1693 +IC C35 C36 C37 C38 1.5691 108.50 -176.11 115.37 1.5513 +IC C38 C36 *C37 H7X 1.5513 115.37 -132.10 117.12 1.1122 +IC C38 C36 *C37 H7Y 1.5513 115.37 117.93 103.69 1.1113 +IC C36 C37 C38 C39 1.4966 115.37 166.36 110.33 1.4980 +IC C39 C37 *C38 H8X 1.4980 110.33 -129.71 109.95 1.1296 +IC C39 C37 *C38 H8Y 1.4980 110.33 118.79 109.90 1.0764 +IC C37 C38 C39 C310 1.5513 110.33 -164.13 118.89 1.5943 +IC C310 C38 *C39 H9X 1.5943 118.89 -115.55 109.73 1.0952 +IC C310 C38 *C39 H9Y 1.5943 118.89 130.25 106.31 1.0929 +IC C38 C39 C310 C311 1.4980 118.89 -49.00 109.22 1.5137 +IC C311 C39 *C310 H10X 1.5137 109.22 -116.74 108.27 1.0813 +IC C311 C39 *C310 H10Y 1.5137 109.22 117.30 111.40 1.0636 +IC C39 C310 C311 C312 1.5943 109.22 170.95 112.95 1.5533 +IC C312 C310 *C311 H11X 1.5533 112.95 -123.43 111.51 1.1135 +IC C312 C310 *C311 H11Y 1.5533 112.95 112.52 99.10 1.0554 +IC C310 C311 C312 C313 1.5137 112.95 -164.15 106.89 1.5525 +IC C313 C311 *C312 H12X 1.5525 106.89 -115.76 102.65 1.0793 +IC C313 C311 *C312 H12Y 1.5525 106.89 116.44 125.17 1.1466 +IC C311 C312 C313 C314 1.5533 106.89 -140.81 107.79 1.5309 +IC C314 C312 *C313 H13X 1.5309 107.79 -112.37 108.50 1.0756 +IC C314 C312 *C313 H13Y 1.5309 107.79 124.74 113.42 1.0947 +IC C312 C313 C314 C315 1.5525 107.79 -67.74 114.85 1.4938 +IC C315 C313 *C314 H14X 1.4938 114.85 -119.60 107.21 1.0693 +IC C315 C313 *C314 H14Y 1.4938 114.85 116.01 108.14 1.0570 +IC C313 C314 C315 C316 1.5309 114.85 -178.97 111.64 1.5439 +IC C316 C314 *C315 H15X 1.5439 111.64 -125.57 110.73 1.1159 +IC C316 C314 *C315 H15Y 1.5439 111.64 124.77 114.52 1.0909 +IC C314 C315 C316 C317 1.4938 111.64 -177.93 107.20 1.5537 +IC C317 C315 *C316 H16X 1.5537 107.20 -113.34 106.47 1.0729 +IC C317 C315 *C316 H16Y 1.5537 107.20 116.58 112.07 1.1621 +IC C315 C316 C317 C318 1.5439 107.20 162.37 112.19 1.5610 +IC C318 C316 *C317 H17X 1.5610 112.19 -114.65 101.79 1.1260 +IC C318 C316 *C317 H17Y 1.5610 112.19 128.24 112.26 1.1118 +IC C316 C317 C318 H18X 1.5537 112.19 168.54 105.45 1.1437 +IC H18X C317 *C318 H18Y 1.1437 105.45 -112.51 114.99 1.1562 +IC H18X C317 *C318 H18Z 1.1437 105.45 132.44 116.32 1.1291 +IC C13 C11 *C12 O2 1.5184 107.54 122.63 109.30 1.4426 +IC O2 C11 *C12 H2 1.4426 109.30 119.81 108.24 1.1104 +IC C11 C12 O2 HO2 1.6085 109.30 -115.24 92.34 1.0302 +IC C14 C12 *C13 O3 1.5631 111.19 117.68 104.72 1.4274 +IC O3 C12 *C13 H3 1.4274 104.72 117.96 111.56 1.1140 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C15 C13 *C14 O4 1.5343 111.39 -124.35 114.32 1.4177 +IC O4 C13 *C14 H4 1.4177 114.32 -117.89 106.72 1.0604 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC C13 C14 C15 O5 1.5631 111.39 179.33 109.28 1.4270 +IC O5 C14 *C15 C16 1.4270 109.28 -124.79 112.35 1.5007 +IC C16 C14 *C15 H5 1.5007 112.35 -118.86 104.70 1.1064 +IC C14 C15 O5 P5 1.5343 109.28 -123.53 132.73 1.6688 +IC C15 O5 P5 OP52 1.4270 132.73 64.99 107.56 1.5362 +IC OP52 O5 *P5 OP53 1.5362 107.56 -122.52 110.70 1.5140 +IC OP52 O5 *P5 OP54 1.5362 107.56 121.44 99.10 1.5259 +IC C11 C15 *C16 O6 1.6111 109.23 -111.89 111.27 1.4099 +IC C11 C15 *C16 H6 1.6111 109.23 119.01 114.23 1.1116 +IC C15 C16 O6 HO6 1.5007 111.27 -69.60 103.78 1.0348 + +RESI SAPI34 -6.00 ! Phosphatidylinositol-(3,4,5)-trisphosphate (PIP3) with protonation on P4 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | | OP32(-) +ATOM H4 HCA1 0.09 ! | H3 +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! \ +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! (-) O13 O12 +ATOM C11 CC3161 -0.08 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.59 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O12 OC30P -0.57 ! HA---C1---HB +ATOM O11 OSLP -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C26 CEL1 -0.15 ! | | +ATOM H6R HEL1 0.15 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H12R HEL1 0.15 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H16R---C216--H16S | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! H18R---C218--H18S | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! | | +ATOM H18S HAL2 0.09 ! H19R---C219--H19S | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! | | +ATOM H19S HAL2 0.09 ! H20R---C220--H20S | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! H20T | +ATOM H20R HAL3 0.09 ! | +ATOM H20S HAL3 0.09 ! | +ATOM H20T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! H15X---C315--H15Y +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! H16X---C316--H16Y +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! | +ATOM H16Y HAL2 0.09 ! H17X---C317--H17Y +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! | +ATOM H17Y HAL2 0.09 ! H18X---C318--H18Y +GROUP ! | +ATOM C318 CTL3 -0.27 ! H18Z +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5337 112.05 61.01 107.24 1.5404 +IC C12 C13 C14 C15 1.5780 107.24 -58.39 111.09 1.5901 +IC C13 C14 C15 C16 1.5404 111.09 58.47 107.90 1.5426 +IC C14 C15 C16 C11 1.5901 107.90 -59.25 112.21 1.5480 +IC C15 C16 C11 C12 1.5426 112.21 60.61 106.98 1.5337 +IC C16 C11 C12 C13 1.5480 106.98 -60.88 112.05 1.5780 +IC C16 C12 *C11 H1 1.5480 106.98 114.17 113.34 1.1241 +IC C16 C12 *C11 O12 1.5480 106.98 -126.05 111.12 1.4335 +IC C11 C13 *C12 H2 1.5337 112.05 115.87 102.54 1.1160 +IC C11 C13 *C12 O2 1.5337 112.05 -131.98 108.36 1.4473 +IC C12 C14 *C13 H3 1.5780 107.24 109.92 102.57 1.1088 +IC C12 C14 *C13 O3 1.5780 107.24 -129.18 117.53 1.4308 +IC C13 C15 *C14 H4 1.5404 111.09 -122.36 109.80 1.0685 +IC C13 C15 *C14 O4 1.5404 111.09 131.87 109.28 1.4360 +IC C14 C16 *C15 H5 1.5901 107.90 120.33 112.21 1.0974 +IC C14 C16 *C15 O5 1.5901 107.90 -116.65 106.67 1.4218 +IC C15 C11 *C16 H6 1.5426 112.21 -114.09 110.73 1.1358 +IC C15 C11 *C16 O6 1.5426 112.21 120.46 107.02 1.4251 +IC C13 C12 O2 HO2 1.5780 108.36 -58.45 100.94 1.0058 +IC C11 C16 O6 HO6 1.5480 107.02 -162.78 107.54 0.9775 +IC C12 C11 O12 P 1.5337 111.12 -79.76 128.73 1.6430 +IC C11 O12 P O11 1.4335 128.73 -173.52 98.46 1.6116 +IC O11 O12 *P O13 1.6116 98.46 -108.30 113.08 1.4875 +IC O11 O12 *P O14 1.6116 98.46 113.04 116.38 1.4745 +IC O12 P O11 C1 1.6430 98.46 -34.05 124.94 1.4195 +IC P O11 C1 C2 1.6116 124.94 -153.60 114.77 1.5911 +IC C2 O11 *C1 HA 1.5911 114.77 127.60 114.04 1.0787 +IC HA O11 *C1 HB 1.0787 114.04 122.25 101.87 1.0661 +IC O11 C1 C2 O21 1.4195 114.77 35.50 105.72 1.4330 +IC O21 C1 *C2 C3 1.4330 105.72 -122.90 114.85 1.5288 +IC C3 C1 *C2 HS 1.5288 114.85 -117.50 105.88 1.0697 +IC C1 C2 O21 C21 1.5911 105.72 124.06 114.80 1.3328 +IC C2 O21 C21 C22 1.4330 114.80 -162.05 109.65 1.5687 +IC C22 O21 *C21 O22 1.5687 109.65 -165.63 124.68 1.2190 +IC O21 C21 C22 C23 1.3328 109.65 -113.65 112.13 1.5120 +IC C23 C21 *C22 H2R 1.5120 112.13 126.18 111.98 1.1361 +IC H2R C21 *C22 H2S 1.1361 111.98 114.42 111.38 1.1292 +IC C1 C2 C3 O31 1.5911 114.85 -167.11 105.78 1.4467 +IC O31 C2 *C3 HX 1.4467 105.78 -124.34 112.58 1.1588 +IC HX C2 *C3 HY 1.1588 112.58 -116.88 112.65 1.0803 +IC C2 C3 O31 C31 1.5288 105.78 -119.54 122.35 1.3312 +IC C3 O31 C31 C32 1.4467 122.35 157.34 109.03 1.5378 +IC C32 O31 *C31 O32 1.5378 109.03 -171.40 125.93 1.1929 +IC O31 C31 C32 C33 1.3312 109.03 -173.91 111.34 1.5783 +IC C33 C31 *C32 H2X 1.5783 111.34 -136.59 112.83 1.0769 +IC H2X C31 *C32 H2Y 1.0769 112.83 -103.55 107.75 1.0939 +IC C21 C22 C23 C24 1.5687 112.13 83.44 116.74 1.5809 +IC C24 C22 *C23 H3R 1.5809 116.74 -123.15 105.55 1.1563 +IC C24 C22 *C23 H3S 1.5809 116.74 122.54 108.22 1.1259 +IC C22 C23 C24 C25 1.5120 116.74 156.79 120.71 1.5395 +IC C25 C23 *C24 H4R 1.5395 120.71 -125.88 105.48 1.1028 +IC C25 C23 *C24 H4S 1.5395 120.71 124.90 103.04 1.1449 +IC C23 C24 C25 C26 1.5809 120.71 138.09 130.55 1.3173 +IC C26 C24 *C25 H5R 1.3173 130.55 162.96 112.10 1.0959 +IC C24 C25 C26 C27 1.5395 130.55 -0.67 125.82 1.5535 +IC C27 C25 *C26 H6R 1.5535 125.82 173.80 111.49 1.1392 +IC C25 C26 C27 C28 1.3173 125.82 135.47 110.74 1.6144 +IC C28 C26 *C27 H7R 1.6144 110.74 -121.46 109.70 1.1527 +IC C28 C26 *C27 H7S 1.6144 110.74 125.88 116.24 1.0791 +IC C26 C27 C28 C29 1.5535 110.74 96.28 120.10 1.3603 +IC C29 C27 *C28 H8R 1.3603 120.10 174.46 117.59 1.1037 +IC C27 C28 C29 C210 1.6144 120.10 -0.69 128.51 1.4995 +IC C210 C28 *C29 H9R 1.4995 128.51 175.87 117.33 1.0881 +IC C28 C29 C210 C211 1.3603 128.51 108.88 108.27 1.5221 +IC C211 C29 *C210 H10R 1.5221 108.27 -117.04 112.54 1.1250 +IC C211 C29 *C210 H10S 1.5221 108.27 125.13 104.95 1.1485 +IC C29 C210 C211 C212 1.4995 108.27 129.20 125.32 1.3185 +IC C212 C210 *C211 H11R 1.3185 125.32 -178.68 115.88 1.1227 +IC C210 C211 C212 C213 1.5221 125.32 0.51 129.37 1.5474 +IC C213 C211 *C212 H12R 1.5474 129.37 -178.54 116.00 1.0952 +IC C211 C212 C213 C214 1.3185 129.37 94.71 109.41 1.4795 +IC C214 C212 *C213 H13R 1.4795 109.41 -122.97 113.66 1.0953 +IC C214 C212 *C213 H13S 1.4795 109.41 128.38 117.99 1.0607 +IC C212 C213 C214 C215 1.5474 109.41 149.14 127.34 1.3630 +IC C215 C213 *C214 H14R 1.3630 127.34 178.40 119.49 1.0921 +IC C213 C214 C215 C216 1.4795 127.34 1.31 126.39 1.5050 +IC C216 C214 *C215 H15R 1.5050 126.39 -175.20 116.00 1.1161 +IC C214 C215 C216 C217 1.3630 126.39 75.87 117.57 1.5416 +IC C217 C215 *C216 H16R 1.5416 117.57 -127.60 112.93 1.1486 +IC C217 C215 *C216 H16S 1.5416 117.57 116.47 103.98 1.1124 +IC C215 C216 C217 C218 1.5050 117.57 178.36 114.18 1.5317 +IC C218 C216 *C217 H17R 1.5317 114.18 -126.20 105.43 1.1718 +IC C218 C216 *C217 H17S 1.5317 114.18 124.77 109.31 1.1003 +IC C216 C217 C218 C219 1.5416 114.18 -173.99 112.02 1.5112 +IC C219 C217 *C218 H18R 1.5112 112.02 -127.51 108.48 1.0791 +IC C219 C217 *C218 H18S 1.5112 112.02 127.20 108.11 1.1293 +IC C217 C218 C219 C220 1.5317 112.02 -148.75 115.00 1.5876 +IC C220 C218 *C219 H19R 1.5876 115.00 -120.57 108.35 1.1447 +IC C220 C218 *C219 H19S 1.5876 115.00 120.98 102.86 1.0938 +IC C218 C219 C220 H20T 1.5112 115.00 -177.82 110.78 1.0359 +IC H20T C219 *C220 H20R 1.0359 110.78 -120.63 103.84 1.1351 +IC H20T C219 *C220 H20S 1.0359 110.78 129.99 110.11 1.1334 +IC C31 C32 C33 C34 1.5378 111.34 -134.58 116.92 1.5401 +IC C34 C32 *C33 H3X 1.5401 116.92 -114.82 104.91 1.0983 +IC C34 C32 *C33 H3Y 1.5401 116.92 128.41 116.14 1.1215 +IC C32 C33 C34 C35 1.5783 116.92 165.92 113.03 1.6057 +IC C35 C33 *C34 H4X 1.6057 113.03 -107.52 108.22 1.1343 +IC C35 C33 *C34 H4Y 1.6057 113.03 122.31 116.89 1.0832 +IC C33 C34 C35 C36 1.5401 113.03 -170.31 113.13 1.5409 +IC C36 C34 *C35 H5X 1.5409 113.13 -123.58 105.75 1.1293 +IC C36 C34 *C35 H5Y 1.5409 113.13 122.74 105.69 1.1577 +IC C34 C35 C36 C37 1.6057 113.13 -161.64 110.68 1.6226 +IC C37 C35 *C36 H6X 1.6226 110.68 -109.84 103.09 1.1342 +IC C37 C35 *C36 H6Y 1.6226 110.68 131.01 114.83 1.1589 +IC C35 C36 C37 C38 1.5409 110.68 167.05 107.36 1.5288 +IC C38 C36 *C37 H7X 1.5288 107.36 -122.93 107.03 1.0546 +IC C38 C36 *C37 H7Y 1.5288 107.36 122.84 109.22 1.1299 +IC C36 C37 C38 C39 1.6226 107.36 178.25 113.19 1.4897 +IC C39 C37 *C38 H8X 1.4897 113.19 -119.32 112.34 1.1212 +IC C39 C37 *C38 H8Y 1.4897 113.19 123.33 106.24 1.1212 +IC C37 C38 C39 C310 1.5288 113.19 156.38 114.15 1.5193 +IC C310 C38 *C39 H9X 1.5193 114.15 -122.68 111.64 1.0859 +IC C310 C38 *C39 H9Y 1.5193 114.15 123.51 107.50 1.1755 +IC C38 C39 C310 C311 1.4897 114.15 173.99 115.51 1.4854 +IC C311 C39 *C310 H10X 1.4854 115.51 -126.01 105.19 1.1180 +IC C311 C39 *C310 H10Y 1.4854 115.51 107.54 113.52 1.1467 +IC C39 C310 C311 C312 1.5193 115.51 169.29 118.19 1.5560 +IC C312 C310 *C311 H11X 1.5560 118.19 -117.11 101.43 1.1071 +IC C312 C310 *C311 H11Y 1.5560 118.19 127.93 111.57 1.0812 +IC C310 C311 C312 C313 1.4854 118.19 -145.39 109.57 1.5080 +IC C313 C311 *C312 H12X 1.5080 109.57 -126.72 103.24 1.0978 +IC C313 C311 *C312 H12Y 1.5080 109.57 118.63 108.89 1.1202 +IC C311 C312 C313 C314 1.5560 109.57 79.48 114.72 1.4930 +IC C314 C312 *C313 H13X 1.4930 114.72 -117.69 101.68 1.1245 +IC C314 C312 *C313 H13Y 1.4930 114.72 125.04 111.83 1.1370 +IC C312 C313 C314 C315 1.5080 114.72 -170.74 115.05 1.5280 +IC C315 C313 *C314 H14X 1.5280 115.05 -116.77 102.56 1.1520 +IC C315 C313 *C314 H14Y 1.5280 115.05 119.13 111.28 1.1122 +IC C313 C314 C315 C316 1.4930 115.05 -169.07 114.93 1.5157 +IC C316 C314 *C315 H15X 1.5157 114.93 -116.21 106.04 1.1302 +IC C316 C314 *C315 H15Y 1.5157 114.93 121.35 112.39 1.1098 +IC C314 C315 C316 C317 1.5280 114.93 -161.44 116.83 1.5318 +IC C317 C315 *C316 H16X 1.5318 116.83 -117.44 112.15 1.1349 +IC C317 C315 *C316 H16Y 1.5318 116.83 121.18 106.08 1.1349 +IC C315 C316 C317 C318 1.5157 116.83 -76.74 113.63 1.5293 +IC C318 C316 *C317 H17X 1.5293 113.63 -117.13 105.98 1.1227 +IC C318 C316 *C317 H17Y 1.5293 113.63 125.53 113.52 1.0461 +IC C316 C317 C318 H18X 1.5318 113.63 -170.91 114.68 1.0740 +IC H18X C317 *C318 H18Y 1.0740 114.68 -124.22 114.74 1.1352 +IC H18X C317 *C318 H18Z 1.0740 114.68 114.94 109.15 1.1019 +IC C13 C11 *C12 O2 1.5780 112.05 126.93 118.04 1.4473 +IC O2 C11 *C12 H2 1.4473 118.04 120.72 108.25 1.1160 +IC C11 C12 O2 HO2 1.5337 118.04 172.88 100.94 1.0058 +IC C14 C12 *C13 O3 1.5404 107.24 131.47 113.45 1.4308 +IC O3 C12 *C13 H3 1.4308 113.45 120.07 104.66 1.1088 +IC C12 C13 O3 P3 1.5780 113.45 11.27 138.66 1.6072 +IC C13 O3 P3 OP32 1.4308 138.66 -165.38 100.56 1.5545 +IC OP32 O3 *P3 OP33 1.5545 100.56 -121.96 105.49 1.5133 +IC OP32 O3 *P3 OP34 1.5545 100.56 114.72 107.68 1.5067 +IC C15 C13 *C14 O4 1.5901 111.09 -127.27 117.97 1.4360 +IC O4 C13 *C14 H4 1.4360 117.97 -110.70 110.36 1.0685 +IC C13 C14 O4 P4 1.5404 117.97 39.59 132.79 1.6528 +IC C14 O4 P4 OP42 1.4360 132.79 -84.43 93.71 1.6010 +IC OP42 O4 *P4 OP43 1.6010 93.71 106.21 113.85 1.5294 +IC OP42 O4 *P4 OP44 1.6010 93.71 -106.53 116.29 1.5406 +IC O4 P4 OP42 HP42 1.6528 93.71 41.40 108.58 1.0068 +IC C13 C14 C15 O5 1.5404 111.09 173.79 108.71 1.4218 +IC O5 C14 *C15 C16 1.4218 108.71 -115.32 107.90 1.5426 +IC C16 C14 *C15 H5 1.5426 107.90 -122.21 109.19 1.0974 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C15 *C16 O6 1.5480 112.21 -118.86 109.76 1.4251 +IC C11 C15 *C16 H6 1.5480 112.21 118.93 102.68 1.1358 +IC C15 C16 O6 HO6 1.5426 109.76 -40.77 107.54 0.9775 + +RESI SAPI35 -6.00 ! Phosphatidylinositol-(3,4,5)-trisphosphate (PIP3) with protonation on P5 +! +! Stearoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Arachidonyl - CH SAPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42(-) +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 -0.09 ! | | OP32(-) +ATOM H4 HCA1 0.09 ! | H3 +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! \ +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! (-) O13 O12 +ATOM C11 CC3161 -0.08 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.59 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O12 OC30P -0.57 ! HA---C1---HB +ATOM O11 OSLP -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C26 CEL1 -0.15 ! | | +ATOM H6R HEL1 0.15 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H12R HEL1 0.15 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H16R---C216--H16S | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! H18R---C218--H18S | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! | | +ATOM H18S HAL2 0.09 ! H19R---C219--H19S | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! | | +ATOM H19S HAL2 0.09 ! H20R---C220--H20S | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! H20T | +ATOM H20R HAL3 0.09 ! | +ATOM H20S HAL3 0.09 ! | +ATOM H20T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! H15X---C315--H15Y +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! H16X---C316--H16Y +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! | +ATOM H16Y HAL2 0.09 ! H17X---C317--H17Y +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! | +ATOM H17Y HAL2 0.09 ! H18X---C318--H18Y +GROUP ! | +ATOM C318 CTL3 -0.27 ! H18Z +ATOM H18X HAL3 0.09 ! +ATOM H18Y HAL3 0.09 ! +ATOM H18Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5612 111.91 56.25 109.10 1.5917 +IC C12 C13 C14 C15 1.5674 109.10 -55.67 107.50 1.5949 +IC C13 C14 C15 C16 1.5917 107.50 58.53 114.15 1.5236 +IC C14 C15 C16 C11 1.5949 114.15 -57.38 109.31 1.5105 +IC C15 C16 C11 C12 1.5236 109.31 54.67 113.12 1.5612 +IC C16 C11 C12 C13 1.5105 113.12 -56.32 111.91 1.5674 +IC C16 C12 *C11 H1 1.5105 113.12 119.75 101.91 1.1392 +IC C16 C12 *C11 O12 1.5105 113.12 -126.20 107.76 1.4882 +IC C11 C13 *C12 H2 1.5612 111.91 114.21 103.64 1.1291 +IC C11 C13 *C12 O2 1.5612 111.91 -130.03 104.90 1.4097 +IC C12 C14 *C13 H3 1.5674 109.10 109.60 102.16 1.0541 +IC C12 C14 *C13 O3 1.5674 109.10 -134.10 112.67 1.4674 +IC C13 C15 *C14 H4 1.5917 107.50 -122.77 106.58 1.1398 +IC C13 C15 *C14 O4 1.5917 107.50 121.11 113.88 1.3934 +IC C14 C16 *C15 H5 1.5949 114.15 117.62 111.57 1.1817 +IC C14 C16 *C15 O5 1.5949 114.15 -125.54 99.96 1.4429 +IC C15 C11 *C16 H6 1.5236 109.31 -117.85 108.15 1.1464 +IC C15 C11 *C16 O6 1.5236 109.31 124.62 106.80 1.4905 +IC C13 C12 O2 HO2 1.5674 104.90 -41.95 99.63 0.9607 +IC C11 C16 O6 HO6 1.5105 106.80 -141.52 102.28 0.9438 +IC C12 C11 O12 P 1.5612 107.76 -97.72 122.87 1.6738 +IC C11 O12 P O11 1.4882 122.87 -170.14 101.78 1.5624 +IC O11 O12 *P O13 1.5624 101.78 -111.87 115.92 1.4812 +IC O11 O12 *P O14 1.5624 101.78 114.33 108.26 1.4737 +IC O12 P O11 C1 1.6738 101.78 93.71 119.03 1.4527 +IC P O11 C1 C2 1.5624 119.03 90.59 109.51 1.5472 +IC C2 O11 *C1 HA 1.5472 109.51 116.74 102.40 1.1035 +IC HA O11 *C1 HB 1.1035 102.40 119.29 118.20 1.0905 +IC O11 C1 C2 O21 1.4527 109.51 159.98 105.23 1.3918 +IC O21 C1 *C2 C3 1.3918 105.23 -122.31 113.46 1.5224 +IC C3 C1 *C2 HS 1.5224 113.46 -112.81 98.08 1.1373 +IC C1 C2 O21 C21 1.5472 105.23 121.03 107.61 1.3130 +IC C2 O21 C21 C22 1.3918 107.61 -143.71 110.27 1.5240 +IC C22 O21 *C21 O22 1.5240 110.27 -173.26 123.94 1.2252 +IC O21 C21 C22 C23 1.3130 110.27 -100.54 114.05 1.5966 +IC C23 C21 *C22 H2R 1.5966 114.05 136.83 117.96 1.1359 +IC H2R C21 *C22 H2S 1.1359 117.96 112.37 110.66 1.1750 +IC C1 C2 C3 O31 1.5472 113.46 -164.03 113.68 1.4560 +IC O31 C2 *C3 HX 1.4560 113.68 -124.81 109.24 1.1421 +IC HX C2 *C3 HY 1.1421 109.24 -119.37 107.12 1.0811 +IC C2 C3 O31 C31 1.5224 113.68 -78.97 117.94 1.3060 +IC C3 O31 C31 C32 1.4560 117.94 176.98 108.04 1.5067 +IC C32 O31 *C31 O32 1.5067 108.04 167.41 128.04 1.2105 +IC O31 C31 C32 C33 1.3060 108.04 -179.87 108.44 1.5479 +IC C33 C31 *C32 H2X 1.5479 108.44 -133.26 115.68 1.1387 +IC H2X C31 *C32 H2Y 1.1387 115.68 -113.16 105.10 1.0739 +IC C21 C22 C23 C24 1.5240 114.05 71.06 110.64 1.5734 +IC C24 C22 *C23 H3R 1.5734 110.64 -124.62 113.03 1.1251 +IC C24 C22 *C23 H3S 1.5734 110.64 116.69 108.70 1.1403 +IC C22 C23 C24 C25 1.5966 110.64 -179.26 119.38 1.4913 +IC C25 C23 *C24 H4R 1.4913 119.38 -124.49 104.52 1.0843 +IC C25 C23 *C24 H4S 1.4913 119.38 124.63 107.15 1.1030 +IC C23 C24 C25 C26 1.5734 119.38 104.26 129.10 1.3677 +IC C26 C24 *C25 H5R 1.3677 129.10 176.59 115.26 1.0369 +IC C24 C25 C26 C27 1.4913 129.10 -1.09 128.95 1.4965 +IC C27 C25 *C26 H6R 1.4965 128.95 178.57 115.14 1.0884 +IC C25 C26 C27 C28 1.3677 128.95 88.87 109.99 1.5103 +IC C28 C26 *C27 H7R 1.5103 109.99 -125.14 103.72 1.1240 +IC C28 C26 *C27 H7S 1.5103 109.99 127.07 117.61 1.1196 +IC C26 C27 C28 C29 1.4965 109.99 105.39 125.30 1.3756 +IC C29 C27 *C28 H8R 1.3756 125.30 -175.89 110.46 1.1394 +IC C27 C28 C29 C210 1.5103 125.30 2.05 126.72 1.4782 +IC C210 C28 *C29 H9R 1.4782 126.72 178.19 123.98 1.1037 +IC C28 C29 C210 C211 1.3756 126.72 79.40 107.42 1.5372 +IC C211 C29 *C210 H10R 1.5372 107.42 -128.93 115.37 1.0912 +IC C211 C29 *C210 H10S 1.5372 107.42 115.81 113.85 1.1327 +IC C29 C210 C211 C212 1.4782 107.42 -140.04 121.47 1.3393 +IC C212 C210 *C211 H11R 1.3393 121.47 171.74 116.92 1.1281 +IC C210 C211 C212 C213 1.5372 121.47 -3.78 130.85 1.4812 +IC C213 C211 *C212 H12R 1.4812 130.85 -177.60 118.38 1.1147 +IC C211 C212 C213 C214 1.3393 130.85 120.66 111.38 1.5172 +IC C214 C212 *C213 H13R 1.5172 111.38 -129.02 113.95 1.1050 +IC C214 C212 *C213 H13S 1.5172 111.38 124.92 106.34 1.1527 +IC C212 C213 C214 C215 1.4812 111.38 133.02 125.55 1.3475 +IC C215 C213 *C214 H14R 1.3475 125.55 174.69 112.15 1.0981 +IC C213 C214 C215 C216 1.5172 125.55 2.79 126.86 1.5362 +IC C216 C214 *C215 H15R 1.5362 126.86 171.96 115.71 1.0681 +IC C214 C215 C216 C217 1.3475 126.86 96.79 105.55 1.5511 +IC C217 C215 *C216 H16R 1.5511 105.55 -119.46 108.65 1.0747 +IC C217 C215 *C216 H16S 1.5511 105.55 122.04 103.41 1.1472 +IC C215 C216 C217 C218 1.5362 105.55 172.30 115.85 1.5069 +IC C218 C216 *C217 H17R 1.5069 115.85 -121.02 116.63 1.1722 +IC C218 C216 *C217 H17S 1.5069 115.85 125.49 104.11 1.0955 +IC C216 C217 C218 C219 1.5511 115.85 79.77 111.75 1.5857 +IC C219 C217 *C218 H18R 1.5857 111.75 -127.58 106.24 1.0653 +IC C219 C217 *C218 H18S 1.5857 111.75 115.12 103.25 1.0754 +IC C217 C218 C219 C220 1.5069 111.75 175.62 115.95 1.5698 +IC C220 C218 *C219 H19R 1.5698 115.95 -120.78 111.21 1.0990 +IC C220 C218 *C219 H19S 1.5698 115.95 119.60 107.38 1.0649 +IC C218 C219 C220 H20T 1.5857 115.95 -173.64 112.47 1.1184 +IC H20T C219 *C220 H20R 1.1184 112.47 -123.64 97.48 1.1035 +IC H20T C219 *C220 H20S 1.1184 112.47 120.77 108.48 1.1706 +IC C31 C32 C33 C34 1.5067 108.44 171.75 110.23 1.5436 +IC C34 C32 *C33 H3X 1.5436 110.23 -110.98 112.84 1.1615 +IC C34 C32 *C33 H3Y 1.5436 110.23 133.41 103.67 1.1558 +IC C32 C33 C34 C35 1.5479 110.23 164.84 111.18 1.4944 +IC C35 C33 *C34 H4X 1.4944 111.18 -117.20 104.87 1.1406 +IC C35 C33 *C34 H4Y 1.4944 111.18 124.00 116.82 1.0964 +IC C33 C34 C35 C36 1.5436 111.18 -170.14 117.36 1.5364 +IC C36 C34 *C35 H5X 1.5364 117.36 -125.86 108.55 1.1375 +IC C36 C34 *C35 H5Y 1.5364 117.36 126.84 113.36 1.0725 +IC C34 C35 C36 C37 1.4944 117.36 97.24 109.17 1.5562 +IC C37 C35 *C36 H6X 1.5562 109.17 -124.93 110.74 1.0531 +IC C37 C35 *C36 H6Y 1.5562 109.17 113.66 107.60 1.0487 +IC C35 C36 C37 C38 1.5364 109.17 178.96 106.99 1.5073 +IC C38 C36 *C37 H7X 1.5073 106.99 -124.94 117.90 1.1226 +IC C38 C36 *C37 H7Y 1.5073 106.99 122.45 105.50 1.1013 +IC C36 C37 C38 C39 1.5562 106.99 -83.54 109.71 1.5851 +IC C39 C37 *C38 H8X 1.5851 109.71 -109.22 104.16 1.0971 +IC C39 C37 *C38 H8Y 1.5851 109.71 134.34 112.52 1.1060 +IC C37 C38 C39 C310 1.5073 109.71 -174.64 116.30 1.5943 +IC C310 C38 *C39 H9X 1.5943 116.30 -114.65 100.74 1.1124 +IC C310 C38 *C39 H9Y 1.5943 116.30 134.06 112.85 1.1282 +IC C38 C39 C310 C311 1.5851 116.30 -169.44 109.43 1.4985 +IC C311 C39 *C310 H10X 1.4985 109.43 -130.21 105.72 1.1666 +IC C311 C39 *C310 H10Y 1.4985 109.43 119.53 108.62 1.1449 +IC C39 C310 C311 C312 1.5943 109.43 -170.56 117.91 1.4759 +IC C312 C310 *C311 H11X 1.4759 117.91 -122.37 116.45 1.1315 +IC C312 C310 *C311 H11Y 1.4759 117.91 116.61 108.69 1.1832 +IC C310 C311 C312 C313 1.4985 117.91 178.48 111.44 1.4766 +IC C313 C311 *C312 H12X 1.4766 111.44 -125.26 104.27 1.1090 +IC C313 C311 *C312 H12Y 1.4766 111.44 122.86 110.52 1.1546 +IC C311 C312 C313 C314 1.4759 111.44 -73.70 111.39 1.5502 +IC C314 C312 *C313 H13X 1.5502 111.39 -108.82 102.78 1.1224 +IC C314 C312 *C313 H13Y 1.5502 111.39 127.20 121.20 1.1985 +IC C312 C313 C314 C315 1.4766 111.39 -138.36 114.17 1.5711 +IC C315 C313 *C314 H14X 1.5711 114.17 -118.23 110.45 1.1197 +IC C315 C313 *C314 H14Y 1.5711 114.17 117.77 107.23 1.1239 +IC C313 C314 C315 C316 1.5502 114.17 -176.45 108.82 1.5409 +IC C316 C314 *C315 H15X 1.5409 108.82 -124.54 113.33 1.1526 +IC C316 C314 *C315 H15Y 1.5409 108.82 108.91 111.46 1.1320 +IC C314 C315 C316 C317 1.5711 108.82 -66.54 116.11 1.5091 +IC C317 C315 *C316 H16X 1.5091 116.11 -124.62 112.51 1.1029 +IC C317 C315 *C316 H16Y 1.5091 116.11 122.83 112.61 1.1144 +IC C315 C316 C317 C318 1.5409 116.11 169.13 111.73 1.5513 +IC C318 C316 *C317 H17X 1.5513 111.73 -123.95 110.47 1.1648 +IC C318 C316 *C317 H17Y 1.5513 111.73 117.32 106.84 1.0646 +IC C316 C317 C318 H18X 1.5091 111.73 158.37 114.50 1.1275 +IC H18X C317 *C318 H18Y 1.1275 114.50 -124.88 106.66 1.0485 +IC H18X C317 *C318 H18Z 1.1275 114.50 121.03 108.03 1.1519 +IC C13 C11 *C12 O2 1.5674 111.91 122.45 118.73 1.4097 +IC O2 C11 *C12 H2 1.4097 118.73 125.03 106.36 1.1291 +IC C11 C12 O2 HO2 1.5612 118.73 -167.83 99.63 0.9607 +IC C14 C12 *C13 O3 1.5917 109.10 130.92 118.74 1.4674 +IC O3 C12 *C13 H3 1.4674 118.74 120.68 103.94 1.0541 +IC C12 C13 O3 P3 1.5674 118.74 42.01 126.24 1.6871 +IC C13 O3 P3 OP32 1.4674 126.24 54.16 111.19 1.5345 +IC OP32 O3 *P3 OP33 1.5345 111.19 -124.96 106.37 1.5032 +IC OP32 O3 *P3 OP34 1.5345 111.19 121.46 106.41 1.5163 +IC C15 C13 *C14 O4 1.5949 107.50 -124.00 109.20 1.3934 +IC O4 C13 *C14 H4 1.3934 109.20 -118.02 114.14 1.1398 +IC C13 C14 O4 P4 1.5917 109.20 -155.20 138.55 1.6696 +IC C14 O4 P4 OP42 1.3934 138.55 154.17 109.58 1.5432 +IC OP42 O4 *P4 OP43 1.5432 109.58 118.48 104.87 1.5206 +IC OP42 O4 *P4 OP44 1.5432 109.58 -119.95 107.99 1.5023 +IC C13 C14 C15 O5 1.5917 107.50 174.60 116.85 1.4429 +IC O5 C14 *C15 C16 1.4429 116.85 -116.07 114.15 1.5236 +IC C16 C14 *C15 H5 1.5236 114.15 -121.85 104.07 1.1817 +IC C14 C15 O5 P5 1.5949 116.85 124.14 124.04 1.6182 +IC C15 O5 P5 OP52 1.4429 124.04 -57.74 111.96 1.5508 +IC OP52 O5 *P5 OP53 1.5508 111.96 -124.84 110.33 1.5314 +IC OP52 O5 *P5 OP54 1.5508 111.96 117.58 105.32 1.5751 +IC O5 P5 OP52 HP52 1.6182 111.96 -28.06 104.86 1.0320 +IC C11 C15 *C16 O6 1.5105 109.31 -119.88 114.69 1.4905 +IC C11 C15 *C16 H6 1.5105 109.31 117.69 108.42 1.1464 +IC C15 C16 O6 HO6 1.5236 114.69 -20.26 102.28 0.9438 + +RESI DMPI -1.00 ! Di-myristoyl-inositol +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | +ATOM C12 CC3161 0.14 ! | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5-HO5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! / +ATOM C11 CC3161 0.01 ! | +ATOM H1 HCA1 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! | | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5181 110.46 56.87 111.43 1.5287 +IC C12 C13 C14 C15 1.5138 111.43 -43.19 114.99 1.5269 +IC C13 C14 C15 C16 1.5287 114.99 38.16 116.20 1.5230 +IC C14 C15 C16 C11 1.5269 116.20 -44.77 110.65 1.5227 +IC C15 C16 C11 C12 1.5230 110.65 57.48 109.67 1.5181 +IC C16 C11 C12 C13 1.5227 109.67 -65.04 110.46 1.5138 +IC C16 C12 *C11 H1 1.5227 109.67 114.66 106.65 1.1178 +IC C16 C12 *C11 O12 1.5227 109.67 -131.90 109.82 1.4318 +IC C11 C13 *C12 H2 1.5181 110.46 117.35 107.43 1.1194 +IC C11 C13 *C12 O2 1.5181 110.46 -125.85 110.80 1.4293 +IC C12 C14 *C13 H3 1.5138 111.43 117.88 107.19 1.1163 +IC C12 C14 *C13 O3 1.5138 111.43 -124.51 112.62 1.4286 +IC C13 C15 *C14 H4 1.5287 114.99 -115.87 105.68 1.1202 +IC C13 C15 *C14 O4 1.5287 114.99 128.81 110.03 1.4289 +IC C14 C16 *C15 H5 1.5269 116.20 115.42 104.85 1.1220 +IC C14 C16 *C15 O5 1.5269 116.20 -129.96 111.25 1.4291 +IC C15 C11 *C16 H6 1.5230 110.65 -118.36 109.53 1.1173 +IC C15 C11 *C16 O6 1.5230 110.65 121.93 111.61 1.4273 +IC C13 C12 O2 HO2 1.5138 110.80 164.69 108.61 0.9872 +IC C14 C13 O3 HO3 1.5287 112.62 83.09 104.55 0.9665 +IC C15 C14 O4 HO4 1.5269 110.03 53.65 105.76 0.9637 +IC C16 C15 O5 HO5 1.5230 111.25 -37.35 104.36 0.9679 +IC C11 C16 O6 HO6 1.5227 111.61 66.96 105.23 0.9850 +IC C12 C11 O12 P 1.5181 109.82 92.66 122.83 1.6352 +IC C11 O12 P O11 1.4318 122.83 -174.81 103.00 1.5798 +IC O11 O12 *P O13 1.5798 103.00 115.68 107.45 1.4772 +IC O11 O12 *P O14 1.5798 103.00 -116.53 107.95 1.4788 +IC O12 P O11 C1 1.6352 103.00 178.03 117.95 1.4319 +IC P O11 C1 C2 1.5798 117.95 170.93 110.60 1.5497 +IC C2 O11 *C1 HA 1.5497 110.60 -119.31 111.24 1.1171 +IC HA O11 *C1 HB 1.1171 111.24 -120.72 110.03 1.1147 +IC O11 C1 C2 C3 1.4319 110.60 175.22 110.94 1.5577 +IC C3 C1 *C2 O21 1.5577 110.94 120.67 108.06 1.4418 +IC C3 C1 *C2 HS 1.5577 110.94 -118.26 106.49 1.1172 +IC C1 C2 O21 C21 1.5497 108.06 146.83 114.79 1.3150 +IC C2 O21 C21 C22 1.4418 114.79 178.51 108.89 1.5323 +IC C22 O21 *C21 O22 1.5323 108.89 -178.54 126.44 1.2196 +IC O21 C21 C22 C23 1.3150 108.89 -159.89 112.28 1.5474 +IC C23 C21 *C22 H2R 1.5474 112.28 -120.54 106.46 1.1098 +IC H2R C21 *C22 H2S 1.1098 106.46 -116.86 108.65 1.1080 +IC C1 C2 C3 O31 1.5497 110.94 172.74 112.47 1.4452 +IC O31 C2 *C3 HX 1.4452 112.47 -118.24 106.38 1.1130 +IC HX C2 *C3 HY 1.1130 106.38 -115.02 109.30 1.1144 +IC C2 C3 O31 C31 1.5577 112.47 91.21 115.66 1.3288 +IC C3 O31 C31 C32 1.4452 115.66 -170.42 108.29 1.5295 +IC C32 O31 *C31 O32 1.5295 108.29 -178.72 125.90 1.2166 +IC O31 C31 C32 C33 1.3288 108.29 -164.93 113.87 1.5448 +IC C33 C31 *C32 H2X 1.5448 113.87 -120.70 106.91 1.1103 +IC H2X C31 *C32 H2Y 1.1103 106.91 -116.81 108.01 1.1086 +IC C21 C22 C23 C24 1.5323 112.28 71.93 112.64 1.5364 +IC C24 C22 *C23 H3R 1.5364 112.64 -122.11 109.42 1.1146 +IC H3R C22 *C23 H3S 1.1146 109.42 -117.17 109.35 1.1133 +IC C22 C23 C24 C25 1.5474 112.64 -166.38 112.54 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.54 -123.11 109.82 1.1120 +IC H4R C23 *C24 H4S 1.1120 109.82 -117.28 108.90 1.1131 +IC C23 C24 C25 C26 1.5364 112.54 174.23 112.75 1.5349 +IC C26 C24 *C25 H5R 1.5349 112.75 -120.04 108.36 1.1147 +IC H5R C24 *C25 H5S 1.1147 108.36 -117.32 109.68 1.1122 +IC C24 C25 C26 C27 1.5346 112.75 -174.85 112.38 1.5347 +IC C27 C25 *C26 H6R 1.5347 112.38 -121.97 109.42 1.1126 +IC H6R C25 *C26 H6S 1.1126 109.42 -117.44 108.85 1.1135 +IC C25 C26 C27 C28 1.5349 112.38 178.13 112.85 1.5344 +IC C28 C26 *C27 H7R 1.5344 112.85 -121.00 108.92 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.92 -117.29 109.16 1.1130 +IC C26 C27 C28 C29 1.5347 112.85 -179.77 112.39 1.5348 +IC C29 C27 *C28 H8R 1.5348 112.39 -121.37 109.24 1.1130 +IC H8R C27 *C28 H8S 1.1130 109.24 -117.46 109.06 1.1131 +IC C27 C28 C29 C210 1.5344 112.39 179.22 112.78 1.5344 +IC C210 C28 *C29 H9R 1.5344 112.78 -121.27 109.13 1.1135 +IC H9R C28 *C29 H9S 1.1135 109.13 -117.33 109.05 1.1132 +IC C28 C29 C210 C211 1.5348 112.78 178.81 112.48 1.5348 +IC C211 C29 *C210 H10R 1.5348 112.48 -121.30 109.24 1.1131 +IC H10R C29 *C210 H10S 1.1131 109.24 -117.39 109.04 1.1130 +IC C29 C210 C211 C212 1.5344 112.48 178.13 112.69 1.5344 +IC C212 C210 *C211 H11R 1.5344 112.69 -121.20 109.15 1.1132 +IC H11R C210 *C211 H11S 1.1132 109.15 -117.35 109.09 1.1132 +IC C210 C211 C212 C213 1.5348 112.69 179.05 112.61 1.5340 +IC C213 C211 *C212 H12R 1.5340 112.61 -121.36 109.28 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.28 -117.38 109.05 1.1132 +IC C211 C212 C213 C214 1.5344 112.61 177.87 113.24 1.5307 +IC C214 C212 *C213 H13R 1.5307 113.24 -121.58 108.85 1.1139 +IC H13R C212 *C213 H13S 1.1139 108.85 -116.60 108.81 1.1140 +IC C212 C213 C214 H14R 1.5340 113.24 -59.62 110.42 1.1115 +IC H14R C213 *C214 H14S 1.1115 110.42 119.89 110.51 1.1112 +IC H14R C213 *C214 H14T 1.1115 110.42 -119.95 110.61 1.1113 +IC C31 C32 C33 C34 1.5295 113.87 177.66 111.16 1.5336 +IC C34 C32 *C33 H3X 1.5336 111.16 -120.94 109.95 1.1136 +IC H3X C32 *C33 H3Y 1.1136 109.95 -118.08 109.56 1.1145 +IC C32 C33 C34 C35 1.5448 111.16 179.63 113.17 1.5335 +IC C35 C33 *C34 H4X 1.5335 113.17 -121.53 109.10 1.1140 +IC H4X C33 *C34 H4Y 1.1140 109.10 -117.11 108.97 1.1134 +IC C33 C34 C35 C36 1.5336 113.17 177.57 111.94 1.5339 +IC C36 C34 *C35 H5X 1.5339 111.94 -121.08 109.26 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.26 -117.59 109.20 1.1132 +IC C34 C35 C36 C37 1.5335 111.94 179.50 113.04 1.5337 +IC C37 C35 *C36 H6X 1.5337 113.04 -121.62 109.12 1.1135 +IC H6X C35 *C36 H6Y 1.1135 109.12 -117.10 108.94 1.1134 +IC C35 C36 C37 C38 1.5339 113.04 178.26 112.01 1.5337 +IC C38 C36 *C37 H7X 1.5337 112.01 -121.06 109.22 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.22 -117.62 109.23 1.1131 +IC C36 C37 C38 C39 1.5337 112.01 179.75 113.07 1.5337 +IC C39 C37 *C38 H8X 1.5337 113.07 -121.62 109.06 1.1133 +IC H8X C37 *C38 H8Y 1.1133 109.06 -117.09 108.95 1.1133 +IC C37 C38 C39 C310 1.5337 113.07 178.49 112.01 1.5338 +IC C310 C38 *C39 H9X 1.5338 112.01 -121.03 109.22 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.22 -117.65 109.26 1.1130 +IC C38 C39 C310 C311 1.5337 112.01 179.79 113.05 1.5336 +IC C311 C39 *C310 H10X 1.5336 113.05 -121.59 109.08 1.1133 +IC H10X C39 *C310 H10Y 1.1133 109.08 -117.16 108.94 1.1134 +IC C39 C310 C311 C312 1.5338 113.05 179.12 112.25 1.5346 +IC C312 C310 *C311 H11X 1.5346 112.25 -121.13 109.15 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.15 -117.54 109.20 1.1131 +IC C310 C311 C312 C313 1.5336 112.25 179.96 112.76 1.5333 +IC C313 C311 *C312 H12X 1.5333 112.76 -121.47 109.14 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.14 -117.23 109.07 1.1132 +IC C311 C312 C313 C314 1.5346 112.76 179.78 113.16 1.5308 +IC C314 C312 *C313 H13X 1.5308 113.16 -121.63 108.78 1.1142 +IC H13X C312 *C313 H13Y 1.1142 108.78 -116.69 108.79 1.1142 +IC C312 C313 C314 H14X 1.5333 113.16 -59.89 110.46 1.1114 +IC H14X C313 *C314 H14Y 1.1114 110.46 119.84 110.46 1.1114 +IC H14X C313 *C314 H14Z 1.1114 110.46 -120.08 110.64 1.1112 + +RESI DMPI13 -3.00 ! Di-myristoyl-inositol-(3)-phosphate (PIP1) +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 -0.09 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.40 ! | |\ | / +ATOM P3 PC 1.10 ! | | \ O2 / +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.14 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! / +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | alpha4 +GROUP ! (-) O13 O12 +ATOM C11 CC3161 0.01 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.50 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O11 OSLP -0.57 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25---H5S | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! H6R ---C26---H6S | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28---H8S | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29---H9S | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! | | +ATOM H9S HAL2 0.09 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211--H11S | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212--H12S | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! H14T | +ATOM H14R HAL3 0.09 ! | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL3 -0.27 ! H14Z +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5375 108.38 54.84 110.45 1.5169 +IC C12 C13 C14 C15 1.5595 110.45 -54.24 115.86 1.5883 +IC C13 C14 C15 C16 1.5169 115.86 55.00 105.73 1.4774 +IC C14 C15 C16 C11 1.5883 105.73 -58.00 112.17 1.5829 +IC C15 C16 C11 C12 1.4774 112.17 64.94 109.41 1.5375 +IC C16 C11 C12 C13 1.5829 109.41 -59.16 108.38 1.5595 +IC C16 C12 *C11 H1 1.5829 109.41 108.71 102.84 1.0943 +IC C16 C12 *C11 O12 1.5829 109.41 -129.71 116.30 1.4473 +IC C11 C13 *C12 H2 1.5375 108.38 115.85 113.36 1.1016 +IC C11 C13 *C12 O2 1.5375 108.38 -120.84 116.76 1.4546 +IC C12 C14 *C13 H3 1.5595 110.45 121.48 113.64 1.1002 +IC C12 C14 *C13 O3 1.5595 110.45 -117.61 114.44 1.4238 +IC C13 C15 *C14 H4 1.5169 115.86 -129.16 105.27 1.1566 +IC C13 C15 *C14 O4 1.5169 115.86 126.32 108.79 1.4490 +IC C14 C16 *C15 H5 1.5883 105.73 123.83 116.99 1.1187 +IC C14 C16 *C15 O5 1.5883 105.73 -114.26 106.96 1.4557 +IC C15 C11 *C16 H6 1.4774 112.17 -123.26 102.31 1.0627 +IC C15 C11 *C16 O6 1.4774 112.17 125.89 110.13 1.4549 +IC C13 C12 O2 HO2 1.5595 116.76 -64.05 100.17 0.9199 +IC C11 C16 O6 HO6 1.5829 110.13 -134.38 104.64 0.9790 +IC C12 C11 O12 P 1.5375 116.30 -133.08 114.89 1.6846 +IC C11 O12 P O11 1.4473 114.89 -175.83 90.36 1.6603 +IC O11 O12 *P O13 1.6603 90.36 108.26 119.96 1.4638 +IC O11 O12 *P O14 1.6603 90.36 -106.70 113.64 1.5096 +IC O12 P O11 C1 1.6846 90.36 68.94 113.03 1.4321 +IC P O11 C1 C2 1.6603 113.03 108.76 115.52 1.5654 +IC C2 O11 *C1 HA 1.5654 115.52 -126.74 112.90 1.0872 +IC HA O11 *C1 HB 1.0872 112.90 -115.13 107.51 1.1283 +IC O11 C1 C2 C3 1.4321 115.52 145.51 110.08 1.5824 +IC C3 C1 *C2 O21 1.5824 110.08 119.75 105.85 1.4458 +IC C3 C1 *C2 HS 1.5824 110.08 -118.40 109.97 1.0861 +IC C1 C2 O21 C21 1.5654 105.85 126.34 117.57 1.3565 +IC C2 O21 C21 C22 1.4458 117.57 -148.41 108.93 1.4868 +IC C22 O21 *C21 O22 1.4868 108.93 -176.29 121.28 1.2407 +IC O21 C21 C22 C23 1.3565 108.93 -159.14 111.38 1.5392 +IC C23 C21 *C22 H2R 1.5392 111.38 -113.74 113.69 1.0965 +IC H2R C21 *C22 H2S 1.0965 113.69 -115.13 111.14 1.1066 +IC C1 C2 C3 O31 1.5654 110.08 -161.94 110.67 1.4688 +IC O31 C2 *C3 HX 1.4688 110.67 -127.34 119.02 1.1407 +IC HX C2 *C3 HY 1.1407 119.02 -119.20 106.00 1.1348 +IC C2 C3 O31 C31 1.5824 110.67 -117.19 128.73 1.2684 +IC C3 O31 C31 C32 1.4688 128.73 27.42 114.39 1.5666 +IC C32 O31 *C31 O32 1.5666 114.39 177.83 125.23 1.2111 +IC O31 C31 C32 C33 1.2684 114.39 154.01 112.27 1.5652 +IC C33 C31 *C32 H2X 1.5652 112.27 -117.89 99.03 1.1075 +IC H2X C31 *C32 H2Y 1.1075 99.03 -117.51 103.35 1.0925 +IC C21 C22 C23 C24 1.4868 111.38 81.32 114.14 1.5525 +IC C24 C22 *C23 H3R 1.5525 114.14 -125.63 106.95 1.0878 +IC H3R C22 *C23 H3S 1.0878 106.95 -113.32 102.53 1.1178 +IC C22 C23 C24 C25 1.5392 114.14 162.88 112.82 1.6014 +IC C25 C23 *C24 H4R 1.6014 112.82 -119.10 109.69 1.0923 +IC H4R C23 *C24 H4S 1.0923 109.69 -116.04 116.08 1.1185 +IC C23 C24 C25 C26 1.5525 112.82 177.82 111.98 1.5380 +IC C26 C24 *C25 H5R 1.5380 111.98 -124.78 99.85 1.0853 +IC H5R C24 *C25 H5S 1.0853 99.85 -115.47 106.27 1.0788 +IC C24 C25 C26 C27 1.6014 111.98 82.68 113.25 1.5469 +IC C27 C25 *C26 H6R 1.5469 113.25 -123.30 108.12 1.1106 +IC H6R C25 *C26 H6S 1.1106 108.12 -114.44 105.98 1.1084 +IC C25 C26 C27 C28 1.5380 113.25 -170.73 115.78 1.5639 +IC C28 C26 *C27 H7R 1.5639 115.78 -127.52 116.09 1.0979 +IC H7R C26 *C27 H7S 1.0979 116.09 -115.87 100.08 1.1329 +IC C26 C27 C28 C29 1.5469 115.78 -54.96 109.26 1.5210 +IC C29 C27 *C28 H8R 1.5210 109.26 -122.98 107.91 1.1100 +IC H8R C27 *C28 H8S 1.1100 107.91 -119.35 119.20 1.1315 +IC C27 C28 C29 C210 1.5639 109.26 -162.61 118.78 1.4703 +IC C210 C28 *C29 H9R 1.4703 118.78 -112.76 106.50 1.1366 +IC H9R C28 *C29 H9S 1.1366 106.50 -114.55 109.06 1.1368 +IC C28 C29 C210 C211 1.5210 118.78 178.84 115.63 1.5103 +IC C211 C29 *C210 H10R 1.5103 115.63 -124.08 116.06 1.1727 +IC H10R C29 *C210 H10S 1.1727 116.06 -108.96 105.89 1.1221 +IC C29 C210 C211 C212 1.4703 115.63 150.90 114.03 1.5500 +IC C212 C210 *C211 H11R 1.5500 114.03 -112.68 109.58 1.1154 +IC H11R C210 *C211 H11S 1.1154 109.58 -117.56 115.94 1.1226 +IC C210 C211 C212 C213 1.5103 114.03 -162.62 117.22 1.4881 +IC C213 C211 *C212 H12R 1.4881 117.22 -126.85 109.33 1.0928 +IC H12R C211 *C212 H12S 1.0928 109.33 -118.62 103.32 1.1492 +IC C211 C212 C213 C214 1.5500 117.22 -176.13 108.38 1.5053 +IC C214 C212 *C213 H13R 1.5053 108.38 -124.92 114.07 1.1063 +IC H13R C212 *C213 H13S 1.1063 114.07 -114.96 102.28 1.1203 +IC C212 C213 C214 H14R 1.4881 108.38 -59.77 107.48 1.0746 +IC H14R C213 *C214 H14S 1.0746 107.48 123.17 114.73 1.1286 +IC H14R C213 *C214 H14T 1.0746 107.48 -113.91 109.44 1.1108 +IC C31 C32 C33 C34 1.5666 112.27 -173.77 110.28 1.5867 +IC C34 C32 *C33 H3X 1.5867 110.28 -119.98 108.48 1.1276 +IC H3X C32 *C33 H3Y 1.1276 108.48 -112.47 108.61 1.1020 +IC C32 C33 C34 C35 1.5652 110.28 -154.64 119.47 1.5506 +IC C35 C33 *C34 H4X 1.5506 119.47 -127.18 104.17 1.1385 +IC H4X C33 *C34 H4Y 1.1385 104.17 -105.92 104.64 1.1550 +IC C33 C34 C35 C36 1.5867 119.47 -53.83 110.36 1.5829 +IC C36 C34 *C35 H5X 1.5829 110.36 -117.38 116.09 1.0404 +IC H5X C34 *C35 H5Y 1.0404 116.09 -123.43 111.15 1.1180 +IC C34 C35 C36 C37 1.5506 110.36 174.95 112.64 1.5830 +IC C37 C35 *C36 H6X 1.5830 112.64 -130.83 110.06 1.1811 +IC H6X C35 *C36 H6Y 1.1811 110.06 -115.59 110.21 1.1094 +IC C35 C36 C37 C38 1.5829 112.64 163.81 108.50 1.5657 +IC C38 C36 *C37 H7X 1.5657 108.50 -111.62 110.36 1.1224 +IC H7X C36 *C37 H7Y 1.1224 110.36 -133.09 107.41 1.1305 +IC C36 C37 C38 C39 1.5830 108.50 168.44 117.45 1.5474 +IC C39 C37 *C38 H8X 1.5474 117.45 -111.09 107.24 1.0611 +IC H8X C37 *C38 H8Y 1.0611 107.24 -111.84 118.81 1.1205 +IC C37 C38 C39 C310 1.5657 117.45 -167.44 113.27 1.5573 +IC C310 C38 *C39 H9X 1.5573 113.27 -126.67 110.07 1.0794 +IC H9X C38 *C39 H9Y 1.0794 110.07 -110.89 106.28 1.1668 +IC C38 C39 C310 C311 1.5474 113.27 174.81 111.72 1.5598 +IC C311 C39 *C310 H10X 1.5598 111.72 -112.19 107.28 1.1045 +IC H10X C39 *C310 H10Y 1.1045 107.28 -122.87 108.40 1.0915 +IC C39 C310 C311 C312 1.5573 111.72 -170.92 112.30 1.5594 +IC C312 C310 *C311 H11X 1.5594 112.30 -123.00 101.20 1.1502 +IC H11X C310 *C311 H11Y 1.1502 101.20 -114.17 114.66 1.0598 +IC C310 C311 C312 C313 1.5598 112.30 173.51 115.80 1.5648 +IC C313 C311 *C312 H12X 1.5648 115.80 -124.24 109.98 1.1244 +IC H12X C311 *C312 H12Y 1.1244 109.98 -113.99 103.47 1.1235 +IC C311 C312 C313 C314 1.5594 115.80 147.84 117.42 1.5187 +IC C314 C312 *C313 H13X 1.5187 117.42 -122.11 104.87 1.1165 +IC H13X C312 *C313 H13Y 1.1165 104.87 -113.16 110.29 1.0768 +IC C312 C313 C314 H14X 1.5648 117.42 169.48 111.58 1.1295 +IC H14X C313 *C314 H14Y 1.1295 111.58 122.81 109.54 1.1053 +IC H14X C313 *C314 H14Z 1.1295 111.58 -127.85 114.95 1.0316 +IC C13 C11 *C12 O2 1.5595 108.38 126.71 107.01 1.4546 +IC O2 C11 *C12 H2 1.4546 107.01 111.99 104.77 1.1016 +IC C11 C12 O2 HO2 1.5375 107.01 174.39 100.17 0.9199 +IC C14 C12 *C13 O3 1.5169 110.45 123.55 104.52 1.4238 +IC O3 C12 *C13 H3 1.4238 104.52 111.66 107.94 1.1002 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C15 C13 *C14 O4 1.5883 115.86 -125.01 111.35 1.4490 +IC O4 C13 *C14 H4 1.4490 111.35 -111.09 115.68 1.1566 +IC C15 C14 O4 HO4 1.5269 110.03 53.65 105.76 0.9637 +IC C13 C14 C15 O5 1.5169 115.86 168.95 107.41 1.4557 +IC O5 C14 *C15 C16 1.4557 107.41 -113.95 105.73 1.4774 +IC C16 C14 *C15 H5 1.4774 105.73 -127.66 110.76 1.1187 +IC C16 C15 O5 HO5 1.5230 111.25 -37.35 104.36 0.9679 +IC C11 C15 *C16 O6 1.5829 112.17 -124.69 112.33 1.4549 +IC C11 C15 *C16 H6 1.5829 112.17 116.07 114.56 1.0627 +IC C15 C16 O6 HO6 1.4774 112.33 -8.57 104.64 0.9790 + +RESI DMPI14 -3.00 ! Di-myristoyl-inositol-(4)-phosphate (PIP1) +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! +! H6 +GROUP ! | O5---HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | H3 +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! / +ATOM C11 CC3161 0.01 ! | +ATOM H1 HCA1 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! | | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5375 108.38 54.84 110.45 1.5169 +IC C12 C13 C14 C15 1.5595 110.45 -54.24 115.86 1.5883 +IC C13 C14 C15 C16 1.5169 115.86 55.00 105.73 1.4774 +IC C14 C15 C16 C11 1.5883 105.73 -58.00 112.17 1.5829 +IC C15 C16 C11 C12 1.4774 112.17 64.94 109.41 1.5375 +IC C16 C11 C12 C13 1.5829 109.41 -59.16 108.38 1.5595 +IC C16 C12 *C11 H1 1.5829 109.41 108.71 102.84 1.0943 +IC C16 C12 *C11 O12 1.5829 109.41 -129.71 116.30 1.4473 +IC C11 C13 *C12 H2 1.5375 108.38 115.85 113.36 1.1016 +IC C11 C13 *C12 O2 1.5375 108.38 -120.84 116.76 1.4546 +IC C12 C14 *C13 H3 1.5595 110.45 121.48 113.64 1.1002 +IC C12 C14 *C13 O3 1.5595 110.45 -117.61 114.44 1.4238 +IC C13 C15 *C14 H4 1.5169 115.86 -129.16 105.27 1.1566 +IC C13 C15 *C14 O4 1.5169 115.86 126.32 108.79 1.4490 +IC C14 C16 *C15 H5 1.5883 105.73 123.83 116.99 1.1187 +IC C14 C16 *C15 O5 1.5883 105.73 -114.26 106.96 1.4557 +IC C15 C11 *C16 H6 1.4774 112.17 -123.26 102.31 1.0627 +IC C15 C11 *C16 O6 1.4774 112.17 125.89 110.13 1.4549 +IC C13 C12 O2 HO2 1.5595 116.76 -64.05 100.17 0.9199 +IC C11 C16 O6 HO6 1.5829 110.13 -134.38 104.64 0.9790 +IC C12 C11 O12 P 1.5375 116.30 -133.08 114.89 1.6846 +IC C11 O12 P O11 1.4473 114.89 -175.83 90.36 1.6603 +IC O11 O12 *P O13 1.6603 90.36 108.26 119.96 1.4638 +IC O11 O12 *P O14 1.6603 90.36 -106.70 113.64 1.5096 +IC O12 P O11 C1 1.6846 90.36 68.94 113.03 1.4321 +IC P O11 C1 C2 1.6603 113.03 108.76 115.52 1.5654 +IC C2 O11 *C1 HA 1.5654 115.52 -126.74 112.90 1.0872 +IC HA O11 *C1 HB 1.0872 112.90 -115.13 107.51 1.1283 +IC O11 C1 C2 C3 1.4321 115.52 145.51 110.08 1.5824 +IC C3 C1 *C2 O21 1.5824 110.08 119.75 105.85 1.4458 +IC C3 C1 *C2 HS 1.5824 110.08 -118.40 109.97 1.0861 +IC C1 C2 O21 C21 1.5654 105.85 126.34 117.57 1.3565 +IC C2 O21 C21 C22 1.4458 117.57 -148.41 108.93 1.4868 +IC C22 O21 *C21 O22 1.4868 108.93 -176.29 121.28 1.2407 +IC O21 C21 C22 C23 1.3565 108.93 -159.14 111.38 1.5392 +IC C23 C21 *C22 H2R 1.5392 111.38 -113.74 113.69 1.0965 +IC H2R C21 *C22 H2S 1.0965 113.69 -115.13 111.14 1.1066 +IC C1 C2 C3 O31 1.5654 110.08 -161.94 110.67 1.4688 +IC O31 C2 *C3 HX 1.4688 110.67 -127.34 119.02 1.1407 +IC HX C2 *C3 HY 1.1407 119.02 -119.20 106.00 1.1348 +IC C2 C3 O31 C31 1.5824 110.67 -117.19 128.73 1.2684 +IC C3 O31 C31 C32 1.4688 128.73 27.42 114.39 1.5666 +IC C32 O31 *C31 O32 1.5666 114.39 177.83 125.23 1.2111 +IC O31 C31 C32 C33 1.2684 114.39 154.01 112.27 1.5652 +IC C33 C31 *C32 H2X 1.5652 112.27 -117.89 99.03 1.1075 +IC H2X C31 *C32 H2Y 1.1075 99.03 -117.51 103.35 1.0925 +IC C21 C22 C23 C24 1.4868 111.38 81.32 114.14 1.5525 +IC C24 C22 *C23 H3R 1.5525 114.14 -125.63 106.95 1.0878 +IC H3R C22 *C23 H3S 1.0878 106.95 -113.32 102.53 1.1178 +IC C22 C23 C24 C25 1.5392 114.14 162.88 112.82 1.6014 +IC C25 C23 *C24 H4R 1.6014 112.82 -119.10 109.69 1.0923 +IC H4R C23 *C24 H4S 1.0923 109.69 -116.04 116.08 1.1185 +IC C23 C24 C25 C26 1.5525 112.82 177.82 111.98 1.5380 +IC C26 C24 *C25 H5R 1.5380 111.98 -124.78 99.85 1.0853 +IC H5R C24 *C25 H5S 1.0853 99.85 -115.47 106.27 1.0788 +IC C24 C25 C26 C27 1.6014 111.98 82.68 113.25 1.5469 +IC C27 C25 *C26 H6R 1.5469 113.25 -123.30 108.12 1.1106 +IC H6R C25 *C26 H6S 1.1106 108.12 -114.44 105.98 1.1084 +IC C25 C26 C27 C28 1.5380 113.25 -170.73 115.78 1.5639 +IC C28 C26 *C27 H7R 1.5639 115.78 -127.52 116.09 1.0979 +IC H7R C26 *C27 H7S 1.0979 116.09 -115.87 100.08 1.1329 +IC C26 C27 C28 C29 1.5469 115.78 -54.96 109.26 1.5210 +IC C29 C27 *C28 H8R 1.5210 109.26 -122.98 107.91 1.1100 +IC H8R C27 *C28 H8S 1.1100 107.91 -119.35 119.20 1.1315 +IC C27 C28 C29 C210 1.5639 109.26 -162.61 118.78 1.4703 +IC C210 C28 *C29 H9R 1.4703 118.78 -112.76 106.50 1.1366 +IC H9R C28 *C29 H9S 1.1366 106.50 -114.55 109.06 1.1368 +IC C28 C29 C210 C211 1.5210 118.78 178.84 115.63 1.5103 +IC C211 C29 *C210 H10R 1.5103 115.63 -124.08 116.06 1.1727 +IC H10R C29 *C210 H10S 1.1727 116.06 -108.96 105.89 1.1221 +IC C29 C210 C211 C212 1.4703 115.63 150.90 114.03 1.5500 +IC C212 C210 *C211 H11R 1.5500 114.03 -112.68 109.58 1.1154 +IC H11R C210 *C211 H11S 1.1154 109.58 -117.56 115.94 1.1226 +IC C210 C211 C212 C213 1.5103 114.03 -162.62 117.22 1.4881 +IC C213 C211 *C212 H12R 1.4881 117.22 -126.85 109.33 1.0928 +IC H12R C211 *C212 H12S 1.0928 109.33 -118.62 103.32 1.1492 +IC C211 C212 C213 C214 1.5500 117.22 -176.13 108.38 1.5053 +IC C214 C212 *C213 H13R 1.5053 108.38 -124.92 114.07 1.1063 +IC H13R C212 *C213 H13S 1.1063 114.07 -114.96 102.28 1.1203 +IC C212 C213 C214 H14R 1.4881 108.38 -59.77 107.48 1.0746 +IC H14R C213 *C214 H14S 1.0746 107.48 123.17 114.73 1.1286 +IC H14R C213 *C214 H14T 1.0746 107.48 -113.91 109.44 1.1108 +IC C31 C32 C33 C34 1.5666 112.27 -173.77 110.28 1.5867 +IC C34 C32 *C33 H3X 1.5867 110.28 -119.98 108.48 1.1276 +IC H3X C32 *C33 H3Y 1.1276 108.48 -112.47 108.61 1.1020 +IC C32 C33 C34 C35 1.5652 110.28 -154.64 119.47 1.5506 +IC C35 C33 *C34 H4X 1.5506 119.47 -127.18 104.17 1.1385 +IC H4X C33 *C34 H4Y 1.1385 104.17 -105.92 104.64 1.1550 +IC C33 C34 C35 C36 1.5867 119.47 -53.83 110.36 1.5829 +IC C36 C34 *C35 H5X 1.5829 110.36 -117.38 116.09 1.0404 +IC H5X C34 *C35 H5Y 1.0404 116.09 -123.43 111.15 1.1180 +IC C34 C35 C36 C37 1.5506 110.36 174.95 112.64 1.5830 +IC C37 C35 *C36 H6X 1.5830 112.64 -130.83 110.06 1.1811 +IC H6X C35 *C36 H6Y 1.1811 110.06 -115.59 110.21 1.1094 +IC C35 C36 C37 C38 1.5829 112.64 163.81 108.50 1.5657 +IC C38 C36 *C37 H7X 1.5657 108.50 -111.62 110.36 1.1224 +IC H7X C36 *C37 H7Y 1.1224 110.36 -133.09 107.41 1.1305 +IC C36 C37 C38 C39 1.5830 108.50 168.44 117.45 1.5474 +IC C39 C37 *C38 H8X 1.5474 117.45 -111.09 107.24 1.0611 +IC H8X C37 *C38 H8Y 1.0611 107.24 -111.84 118.81 1.1205 +IC C37 C38 C39 C310 1.5657 117.45 -167.44 113.27 1.5573 +IC C310 C38 *C39 H9X 1.5573 113.27 -126.67 110.07 1.0794 +IC H9X C38 *C39 H9Y 1.0794 110.07 -110.89 106.28 1.1668 +IC C38 C39 C310 C311 1.5474 113.27 174.81 111.72 1.5598 +IC C311 C39 *C310 H10X 1.5598 111.72 -112.19 107.28 1.1045 +IC H10X C39 *C310 H10Y 1.1045 107.28 -122.87 108.40 1.0915 +IC C39 C310 C311 C312 1.5573 111.72 -170.92 112.30 1.5594 +IC C312 C310 *C311 H11X 1.5594 112.30 -123.00 101.20 1.1502 +IC H11X C310 *C311 H11Y 1.1502 101.20 -114.17 114.66 1.0598 +IC C310 C311 C312 C313 1.5598 112.30 173.51 115.80 1.5648 +IC C313 C311 *C312 H12X 1.5648 115.80 -124.24 109.98 1.1244 +IC H12X C311 *C312 H12Y 1.1244 109.98 -113.99 103.47 1.1235 +IC C311 C312 C313 C314 1.5594 115.80 147.84 117.42 1.5187 +IC C314 C312 *C313 H13X 1.5187 117.42 -122.11 104.87 1.1165 +IC H13X C312 *C313 H13Y 1.1165 104.87 -113.16 110.29 1.0768 +IC C312 C313 C314 H14X 1.5648 117.42 169.48 111.58 1.1295 +IC H14X C313 *C314 H14Y 1.1295 111.58 122.81 109.54 1.1053 +IC H14X C313 *C314 H14Z 1.1295 111.58 -127.85 114.95 1.0316 +IC C13 C11 *C12 O2 1.5595 108.38 126.71 107.01 1.4546 +IC O2 C11 *C12 H2 1.4546 107.01 111.99 104.77 1.1016 +IC C11 C12 O2 HO2 1.5375 107.01 174.39 100.17 0.9199 +IC C14 C12 *C13 O3 1.5169 110.45 123.55 104.52 1.4238 +IC O3 C12 *C13 H3 1.4238 104.52 111.66 107.94 1.1002 +IC C14 C13 O3 HO3 1.5287 112.62 83.09 104.55 0.9665 +IC C15 C13 *C14 O4 1.5883 115.86 -125.01 111.35 1.4490 +IC O4 C13 *C14 H4 1.4490 111.35 -111.09 115.68 1.1566 +IC C13 C14 O4 P4 1.5169 111.35 77.64 137.88 1.6216 +IC C14 O4 P4 OP42 1.4490 137.88 -159.21 109.93 1.5413 +IC OP42 O4 *P4 OP43 1.5413 109.93 -118.30 102.38 1.5136 +IC OP42 O4 *P4 OP44 1.5413 109.93 123.01 110.00 1.4987 +IC C13 C14 C15 O5 1.5169 115.86 168.95 107.41 1.4557 +IC O5 C14 *C15 C16 1.4557 107.41 -113.95 105.73 1.4774 +IC C16 C15 O5 HO5 1.5230 111.25 -37.35 104.36 0.9679 +IC C16 C14 *C15 H5 1.4774 105.73 -127.66 110.76 1.1187 +IC C11 C15 *C16 O6 1.5829 112.17 -124.69 112.33 1.4549 +IC C11 C15 *C16 H6 1.5829 112.17 116.07 114.56 1.0627 +IC C15 C16 O6 HO6 1.4774 112.33 -8.57 104.64 0.9790 + +RESI DMPI15 -3.00 ! Di-myristoyl-inositol-(5)-phosphate (PIP1) +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! OP54(-) +! H6 | +GROUP ! | O5----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | H3 +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! / +ATOM C11 CC3161 0.01 ! | +ATOM H1 HCA1 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! | | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5375 108.38 54.84 110.45 1.5169 +IC C12 C13 C14 C15 1.5595 110.45 -54.24 115.86 1.5883 +IC C13 C14 C15 C16 1.5169 115.86 55.00 105.73 1.4774 +IC C14 C15 C16 C11 1.5883 105.73 -58.00 112.17 1.5829 +IC C15 C16 C11 C12 1.4774 112.17 64.94 109.41 1.5375 +IC C16 C11 C12 C13 1.5829 109.41 -59.16 108.38 1.5595 +IC C16 C12 *C11 H1 1.5829 109.41 108.71 102.84 1.0943 +IC C16 C12 *C11 O12 1.5829 109.41 -129.71 116.30 1.4473 +IC C11 C13 *C12 H2 1.5375 108.38 115.85 113.36 1.1016 +IC C11 C13 *C12 O2 1.5375 108.38 -120.84 116.76 1.4546 +IC C12 C14 *C13 H3 1.5595 110.45 121.48 113.64 1.1002 +IC C12 C14 *C13 O3 1.5595 110.45 -117.61 114.44 1.4238 +IC C13 C15 *C14 H4 1.5169 115.86 -129.16 105.27 1.1566 +IC C13 C15 *C14 O4 1.5169 115.86 126.32 108.79 1.4490 +IC C14 C16 *C15 H5 1.5883 105.73 123.83 116.99 1.1187 +IC C14 C16 *C15 O5 1.5883 105.73 -114.26 106.96 1.4557 +IC C15 C11 *C16 H6 1.4774 112.17 -123.26 102.31 1.0627 +IC C15 C11 *C16 O6 1.4774 112.17 125.89 110.13 1.4549 +IC C13 C12 O2 HO2 1.5595 116.76 -64.05 100.17 0.9199 +IC C11 C16 O6 HO6 1.5829 110.13 -134.38 104.64 0.9790 +IC C12 C11 O12 P 1.5375 116.30 -133.08 114.89 1.6846 +IC C11 O12 P O11 1.4473 114.89 -175.83 90.36 1.6603 +IC O11 O12 *P O13 1.6603 90.36 108.26 119.96 1.4638 +IC O11 O12 *P O14 1.6603 90.36 -106.70 113.64 1.5096 +IC O12 P O11 C1 1.6846 90.36 68.94 113.03 1.4321 +IC P O11 C1 C2 1.6603 113.03 108.76 115.52 1.5654 +IC C2 O11 *C1 HA 1.5654 115.52 -126.74 112.90 1.0872 +IC HA O11 *C1 HB 1.0872 112.90 -115.13 107.51 1.1283 +IC O11 C1 C2 C3 1.4321 115.52 145.51 110.08 1.5824 +IC C3 C1 *C2 O21 1.5824 110.08 119.75 105.85 1.4458 +IC C3 C1 *C2 HS 1.5824 110.08 -118.40 109.97 1.0861 +IC C1 C2 O21 C21 1.5654 105.85 126.34 117.57 1.3565 +IC C2 O21 C21 C22 1.4458 117.57 -148.41 108.93 1.4868 +IC C22 O21 *C21 O22 1.4868 108.93 -176.29 121.28 1.2407 +IC O21 C21 C22 C23 1.3565 108.93 -159.14 111.38 1.5392 +IC C23 C21 *C22 H2R 1.5392 111.38 -113.74 113.69 1.0965 +IC H2R C21 *C22 H2S 1.0965 113.69 -115.13 111.14 1.1066 +IC C1 C2 C3 O31 1.5654 110.08 -161.94 110.67 1.4688 +IC O31 C2 *C3 HX 1.4688 110.67 -127.34 119.02 1.1407 +IC HX C2 *C3 HY 1.1407 119.02 -119.20 106.00 1.1348 +IC C2 C3 O31 C31 1.5824 110.67 -117.19 128.73 1.2684 +IC C3 O31 C31 C32 1.4688 128.73 27.42 114.39 1.5666 +IC C32 O31 *C31 O32 1.5666 114.39 177.83 125.23 1.2111 +IC O31 C31 C32 C33 1.2684 114.39 154.01 112.27 1.5652 +IC C33 C31 *C32 H2X 1.5652 112.27 -117.89 99.03 1.1075 +IC H2X C31 *C32 H2Y 1.1075 99.03 -117.51 103.35 1.0925 +IC C21 C22 C23 C24 1.4868 111.38 81.32 114.14 1.5525 +IC C24 C22 *C23 H3R 1.5525 114.14 -125.63 106.95 1.0878 +IC H3R C22 *C23 H3S 1.0878 106.95 -113.32 102.53 1.1178 +IC C22 C23 C24 C25 1.5392 114.14 162.88 112.82 1.6014 +IC C25 C23 *C24 H4R 1.6014 112.82 -119.10 109.69 1.0923 +IC H4R C23 *C24 H4S 1.0923 109.69 -116.04 116.08 1.1185 +IC C23 C24 C25 C26 1.5525 112.82 177.82 111.98 1.5380 +IC C26 C24 *C25 H5R 1.5380 111.98 -124.78 99.85 1.0853 +IC H5R C24 *C25 H5S 1.0853 99.85 -115.47 106.27 1.0788 +IC C24 C25 C26 C27 1.6014 111.98 82.68 113.25 1.5469 +IC C27 C25 *C26 H6R 1.5469 113.25 -123.30 108.12 1.1106 +IC H6R C25 *C26 H6S 1.1106 108.12 -114.44 105.98 1.1084 +IC C25 C26 C27 C28 1.5380 113.25 -170.73 115.78 1.5639 +IC C28 C26 *C27 H7R 1.5639 115.78 -127.52 116.09 1.0979 +IC H7R C26 *C27 H7S 1.0979 116.09 -115.87 100.08 1.1329 +IC C26 C27 C28 C29 1.5469 115.78 -54.96 109.26 1.5210 +IC C29 C27 *C28 H8R 1.5210 109.26 -122.98 107.91 1.1100 +IC H8R C27 *C28 H8S 1.1100 107.91 -119.35 119.20 1.1315 +IC C27 C28 C29 C210 1.5639 109.26 -162.61 118.78 1.4703 +IC C210 C28 *C29 H9R 1.4703 118.78 -112.76 106.50 1.1366 +IC H9R C28 *C29 H9S 1.1366 106.50 -114.55 109.06 1.1368 +IC C28 C29 C210 C211 1.5210 118.78 178.84 115.63 1.5103 +IC C211 C29 *C210 H10R 1.5103 115.63 -124.08 116.06 1.1727 +IC H10R C29 *C210 H10S 1.1727 116.06 -108.96 105.89 1.1221 +IC C29 C210 C211 C212 1.4703 115.63 150.90 114.03 1.5500 +IC C212 C210 *C211 H11R 1.5500 114.03 -112.68 109.58 1.1154 +IC H11R C210 *C211 H11S 1.1154 109.58 -117.56 115.94 1.1226 +IC C210 C211 C212 C213 1.5103 114.03 -162.62 117.22 1.4881 +IC C213 C211 *C212 H12R 1.4881 117.22 -126.85 109.33 1.0928 +IC H12R C211 *C212 H12S 1.0928 109.33 -118.62 103.32 1.1492 +IC C211 C212 C213 C214 1.5500 117.22 -176.13 108.38 1.5053 +IC C214 C212 *C213 H13R 1.5053 108.38 -124.92 114.07 1.1063 +IC H13R C212 *C213 H13S 1.1063 114.07 -114.96 102.28 1.1203 +IC C212 C213 C214 H14R 1.4881 108.38 -59.77 107.48 1.0746 +IC H14R C213 *C214 H14S 1.0746 107.48 123.17 114.73 1.1286 +IC H14R C213 *C214 H14T 1.0746 107.48 -113.91 109.44 1.1108 +IC C31 C32 C33 C34 1.5666 112.27 -173.77 110.28 1.5867 +IC C34 C32 *C33 H3X 1.5867 110.28 -119.98 108.48 1.1276 +IC H3X C32 *C33 H3Y 1.1276 108.48 -112.47 108.61 1.1020 +IC C32 C33 C34 C35 1.5652 110.28 -154.64 119.47 1.5506 +IC C35 C33 *C34 H4X 1.5506 119.47 -127.18 104.17 1.1385 +IC H4X C33 *C34 H4Y 1.1385 104.17 -105.92 104.64 1.1550 +IC C33 C34 C35 C36 1.5867 119.47 -53.83 110.36 1.5829 +IC C36 C34 *C35 H5X 1.5829 110.36 -117.38 116.09 1.0404 +IC H5X C34 *C35 H5Y 1.0404 116.09 -123.43 111.15 1.1180 +IC C34 C35 C36 C37 1.5506 110.36 174.95 112.64 1.5830 +IC C37 C35 *C36 H6X 1.5830 112.64 -130.83 110.06 1.1811 +IC H6X C35 *C36 H6Y 1.1811 110.06 -115.59 110.21 1.1094 +IC C35 C36 C37 C38 1.5829 112.64 163.81 108.50 1.5657 +IC C38 C36 *C37 H7X 1.5657 108.50 -111.62 110.36 1.1224 +IC H7X C36 *C37 H7Y 1.1224 110.36 -133.09 107.41 1.1305 +IC C36 C37 C38 C39 1.5830 108.50 168.44 117.45 1.5474 +IC C39 C37 *C38 H8X 1.5474 117.45 -111.09 107.24 1.0611 +IC H8X C37 *C38 H8Y 1.0611 107.24 -111.84 118.81 1.1205 +IC C37 C38 C39 C310 1.5657 117.45 -167.44 113.27 1.5573 +IC C310 C38 *C39 H9X 1.5573 113.27 -126.67 110.07 1.0794 +IC H9X C38 *C39 H9Y 1.0794 110.07 -110.89 106.28 1.1668 +IC C38 C39 C310 C311 1.5474 113.27 174.81 111.72 1.5598 +IC C311 C39 *C310 H10X 1.5598 111.72 -112.19 107.28 1.1045 +IC H10X C39 *C310 H10Y 1.1045 107.28 -122.87 108.40 1.0915 +IC C39 C310 C311 C312 1.5573 111.72 -170.92 112.30 1.5594 +IC C312 C310 *C311 H11X 1.5594 112.30 -123.00 101.20 1.1502 +IC H11X C310 *C311 H11Y 1.1502 101.20 -114.17 114.66 1.0598 +IC C310 C311 C312 C313 1.5598 112.30 173.51 115.80 1.5648 +IC C313 C311 *C312 H12X 1.5648 115.80 -124.24 109.98 1.1244 +IC H12X C311 *C312 H12Y 1.1244 109.98 -113.99 103.47 1.1235 +IC C311 C312 C313 C314 1.5594 115.80 147.84 117.42 1.5187 +IC C314 C312 *C313 H13X 1.5187 117.42 -122.11 104.87 1.1165 +IC H13X C312 *C313 H13Y 1.1165 104.87 -113.16 110.29 1.0768 +IC C312 C313 C314 H14X 1.5648 117.42 169.48 111.58 1.1295 +IC H14X C313 *C314 H14Y 1.1295 111.58 122.81 109.54 1.1053 +IC H14X C313 *C314 H14Z 1.1295 111.58 -127.85 114.95 1.0316 +IC C13 C11 *C12 O2 1.5595 108.38 126.71 107.01 1.4546 +IC O2 C11 *C12 H2 1.4546 107.01 111.99 104.77 1.1016 +IC C11 C12 O2 HO2 1.5375 107.01 174.39 100.17 0.9199 +IC C14 C12 *C13 O3 1.5169 110.45 123.55 104.52 1.4238 +IC O3 C12 *C13 H3 1.4238 104.52 111.66 107.94 1.1002 +IC C14 C13 O3 HO3 1.5287 112.62 83.09 104.55 0.9665 +IC C15 C13 *C14 O4 1.5883 115.86 -125.01 111.35 1.4490 +IC O4 C13 *C14 H4 1.4490 111.35 -111.09 115.68 1.1566 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C13 C14 C15 O5 1.5169 115.86 168.95 107.41 1.4557 +IC O5 C14 *C15 C16 1.4557 107.41 -113.95 105.73 1.4774 +IC C14 C15 O5 P5 1.5757 107.44 145.73 126.35 1.6570 +IC C15 O5 P5 OP52 1.3813 126.35 -54.55 107.18 1.4982 +IC OP52 O5 *P5 OP53 1.4982 107.18 -122.47 104.74 1.5307 +IC OP52 O5 *P5 OP54 1.4982 107.18 117.86 108.41 1.4911 +IC C16 C14 *C15 H5 1.4774 105.73 -127.66 110.76 1.1187 +IC C11 C15 *C16 O6 1.5829 112.17 -124.69 112.33 1.4549 +IC C11 C15 *C16 H6 1.5829 112.17 116.07 114.56 1.0627 +IC C15 C16 O6 HO6 1.4774 112.33 -8.57 104.64 0.9790 + +RESI DMPI24 -4.00 ! Di-myristoyl-inositol-(4,5)-bisphosphate (PIP2) with protonation on P4 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42-HP42 +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.01 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC30P -0.62 ! | | +ATOM P4 PC 1.50 ! | | +ATOM OP42 OC312 -0.68 ! | H3 +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! / +ATOM C11 CC3161 0.01 ! | +ATOM H1 HCA1 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! | | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5570 107.98 66.59 109.06 1.4744 +IC C12 C13 C14 C15 1.6112 109.06 -63.59 109.98 1.5757 +IC C13 C14 C15 C16 1.4744 109.98 57.43 109.01 1.5490 +IC C14 C15 C16 C11 1.5757 109.01 -54.78 113.94 1.5753 +IC C15 C16 C11 C12 1.5490 113.94 57.46 106.42 1.5570 +IC C16 C11 C12 C13 1.5753 106.42 -59.89 107.98 1.6112 +IC C16 C12 *C11 H1 1.5753 106.42 114.51 104.71 1.1599 +IC C16 C12 *C11 O12 1.5753 106.42 -123.32 109.24 1.4142 +IC C11 C13 *C12 H2 1.5570 107.98 120.58 102.86 1.1543 +IC C11 C13 *C12 O2 1.5570 107.98 -120.35 111.75 1.4022 +IC C12 C14 *C13 H3 1.6112 109.06 119.70 119.97 1.0841 +IC C12 C14 *C13 O3 1.6112 109.06 -120.92 108.82 1.4512 +IC C13 C15 *C14 H4 1.4744 109.98 -118.41 102.18 1.1566 +IC C13 C15 *C14 O4 1.4744 109.98 126.88 114.44 1.4434 +IC C14 C16 *C15 H5 1.5757 109.01 118.19 107.20 1.1409 +IC C14 C16 *C15 O5 1.5757 109.01 -117.08 109.14 1.3813 +IC C15 C11 *C16 H6 1.5490 113.94 -123.80 114.69 1.1093 +IC C15 C11 *C16 O6 1.5490 113.94 121.41 108.98 1.3963 +IC C13 C12 O2 HO2 1.6112 111.75 103.21 103.24 0.9343 +IC C14 C13 O3 HO3 1.4744 108.82 -58.83 107.79 1.0156 +IC C11 C16 O6 HO6 1.5753 108.98 -155.83 108.26 1.0169 +IC C12 C11 O12 P 1.5570 109.24 -84.45 120.81 1.7100 +IC C11 O12 P O11 1.4142 120.81 178.95 106.31 1.6366 +IC O11 O12 *P O13 1.6366 106.31 114.34 109.52 1.4564 +IC O11 O12 *P O14 1.6366 106.31 -113.98 108.01 1.5127 +IC O12 P O11 C1 1.7100 106.31 56.88 121.04 1.4017 +IC P O11 C1 C2 1.6366 121.04 114.07 113.51 1.5871 +IC C2 O11 *C1 HA 1.5871 113.51 -134.65 109.53 1.0851 +IC HA O11 *C1 HB 1.0851 109.53 -112.39 107.17 1.1352 +IC O11 C1 C2 C3 1.4017 113.51 -166.25 116.43 1.5748 +IC C3 C1 *C2 O21 1.5748 116.43 117.48 104.95 1.4045 +IC C3 C1 *C2 HS 1.5748 116.43 -120.58 101.54 1.0869 +IC C1 C2 O21 C21 1.5871 104.95 105.20 118.71 1.3118 +IC C2 O21 C21 C22 1.4045 118.71 -159.74 105.57 1.5006 +IC C22 O21 *C21 O22 1.5006 105.57 179.90 125.11 1.2067 +IC O21 C21 C22 C23 1.3118 105.57 -123.95 107.22 1.5413 +IC C23 C21 *C22 H2R 1.5413 107.22 -117.77 103.88 1.0999 +IC H2R C21 *C22 H2S 1.0999 103.88 -122.82 108.44 1.1226 +IC C1 C2 C3 O31 1.5871 116.43 175.91 113.97 1.4437 +IC O31 C2 *C3 HX 1.4437 113.97 -113.55 106.39 1.1875 +IC HX C2 *C3 HY 1.1875 106.39 -118.23 108.55 1.1447 +IC C2 C3 O31 C31 1.5748 113.97 67.28 110.27 1.3661 +IC C3 O31 C31 C32 1.4437 110.27 -157.82 110.38 1.5427 +IC C32 O31 *C31 O32 1.5427 110.38 177.61 126.07 1.1956 +IC O31 C31 C32 C33 1.3661 110.38 -167.11 118.55 1.5340 +IC C33 C31 *C32 H2X 1.5340 118.55 -119.23 102.07 1.1331 +IC H2X C31 *C32 H2Y 1.1331 102.07 -116.38 102.69 1.1470 +IC C21 C22 C23 C24 1.5006 107.22 83.95 118.79 1.5552 +IC C24 C22 *C23 H3R 1.5552 118.79 -129.40 117.25 1.1792 +IC H3R C22 *C23 H3S 1.1792 117.25 -111.80 104.82 1.1045 +IC C22 C23 C24 C25 1.5413 118.79 -170.88 117.39 1.4989 +IC C25 C23 *C24 H4R 1.4989 117.39 -118.59 107.11 1.1088 +IC H4R C23 *C24 H4S 1.1088 107.11 -121.77 107.10 1.1232 +IC C23 C24 C25 C26 1.5552 117.39 58.67 116.44 1.5582 +IC C26 C24 *C25 H5R 1.5582 116.44 -122.40 107.95 1.0798 +IC H5R C24 *C25 H5S 1.0798 107.95 -112.11 106.85 1.1313 +IC C24 C25 C26 C27 1.4989 116.44 -173.47 113.03 1.5780 +IC C27 C25 *C26 H6R 1.5780 113.03 -131.71 110.02 1.0683 +IC H6R C25 *C26 H6S 1.0683 110.02 -118.03 111.19 1.1095 +IC C25 C26 C27 C28 1.5582 113.03 -168.32 113.79 1.5678 +IC C28 C26 *C27 H7R 1.5678 113.79 -111.29 111.14 1.1339 +IC H7R C26 *C27 H7S 1.1339 111.14 -127.77 110.17 1.1260 +IC C26 C27 C28 C29 1.5780 113.79 176.33 112.26 1.5373 +IC C29 C27 *C28 H8R 1.5373 112.26 -123.41 104.52 1.1551 +IC H8R C27 *C28 H8S 1.1551 104.52 -115.26 114.32 1.1472 +IC C27 C28 C29 C210 1.5678 112.26 -177.00 107.81 1.5458 +IC C210 C28 *C29 H9R 1.5458 107.81 -111.92 107.28 1.0452 +IC H9R C28 *C29 H9S 1.0452 107.28 -133.42 110.65 1.1324 +IC C28 C29 C210 C211 1.5373 107.81 178.77 112.46 1.5503 +IC C211 C29 *C210 H10R 1.5503 112.46 -118.84 108.73 1.0794 +IC H10R C29 *C210 H10S 1.0794 108.73 -111.94 106.48 1.1528 +IC C29 C210 C211 C212 1.5458 112.46 -162.58 112.67 1.5308 +IC C212 C210 *C211 H11R 1.5308 112.67 -121.69 114.32 1.1102 +IC H11R C210 *C211 H11S 1.1102 114.32 -119.60 104.27 1.0607 +IC C210 C211 C212 C213 1.5503 112.67 163.51 114.93 1.5174 +IC C213 C211 *C212 H12R 1.5174 114.93 -117.32 107.00 1.1552 +IC H12R C211 *C212 H12S 1.1552 107.00 -117.61 110.77 1.0937 +IC C211 C212 C213 C214 1.5308 114.93 -166.47 116.42 1.4950 +IC C214 C212 *C213 H13R 1.4950 116.42 -129.98 107.32 1.1654 +IC H13R C212 *C213 H13S 1.1654 107.32 -105.42 113.23 1.1189 +IC C212 C213 C214 H14R 1.5174 116.42 -58.93 109.44 1.0483 +IC H14R C213 *C214 H14S 1.0483 109.44 120.06 107.25 1.0967 +IC H14R C213 *C214 H14T 1.0483 109.44 -116.40 115.02 1.0913 +IC C31 C32 C33 C34 1.5427 118.55 175.70 111.50 1.5227 +IC C34 C32 *C33 H3X 1.5227 111.50 -120.45 109.67 1.0938 +IC H3X C32 *C33 H3Y 1.0938 109.67 -123.65 101.51 1.0689 +IC C32 C33 C34 C35 1.5340 111.50 150.56 106.07 1.6169 +IC C35 C33 *C34 H4X 1.6169 106.07 -121.42 112.94 1.0932 +IC H4X C33 *C34 H4Y 1.0932 112.94 -124.19 111.33 1.1370 +IC C33 C34 C35 C36 1.5227 106.07 168.82 115.69 1.4824 +IC C36 C34 *C35 H5X 1.4824 115.69 -125.26 107.86 1.1124 +IC H5X C34 *C35 H5Y 1.1124 107.86 -113.33 102.54 1.1736 +IC C34 C35 C36 C37 1.6169 115.69 177.92 117.08 1.4599 +IC C37 C35 *C36 H6X 1.4599 117.08 -114.72 107.52 1.1392 +IC H6X C35 *C36 H6Y 1.1392 107.52 -123.48 106.51 1.1103 +IC C35 C36 C37 C38 1.4824 117.08 -162.16 110.73 1.5426 +IC C38 C36 *C37 H7X 1.5426 110.73 -115.83 107.54 1.0899 +IC H7X C36 *C37 H7Y 1.0899 107.54 -128.28 107.66 1.0946 +IC C36 C37 C38 C39 1.4599 110.73 -162.68 111.09 1.5864 +IC C39 C37 *C38 H8X 1.5864 111.09 -131.74 113.27 1.1687 +IC H8X C37 *C38 H8Y 1.1687 113.27 -118.55 112.98 1.0916 +IC C37 C38 C39 C310 1.5426 111.09 167.97 109.40 1.6024 +IC C310 C38 *C39 H9X 1.6024 109.40 -113.67 108.23 1.1144 +IC H9X C38 *C39 H9Y 1.1144 108.23 -116.57 114.64 1.1022 +IC C38 C39 C310 C311 1.5864 109.40 -150.64 105.82 1.4868 +IC C311 C39 *C310 H10X 1.4868 105.82 -121.46 111.01 1.0572 +IC H10X C39 *C310 H10Y 1.0572 111.01 -127.18 113.86 1.0715 +IC C39 C310 C311 C312 1.6024 105.82 -167.17 110.80 1.5245 +IC C312 C310 *C311 H11X 1.5245 110.80 -115.60 105.89 1.1061 +IC H11X C310 *C311 H11Y 1.1061 105.89 -118.40 113.02 1.0567 +IC C310 C311 C312 C313 1.4868 110.80 -178.43 109.63 1.4957 +IC C313 C311 *C312 H12X 1.4957 109.63 -122.64 109.55 1.1032 +IC H12X C311 *C312 H12Y 1.1032 109.55 -117.86 107.82 1.1222 +IC C311 C312 C313 C314 1.5245 109.63 159.26 109.32 1.5137 +IC C314 C312 *C313 H13X 1.5137 109.32 -125.98 108.02 1.1217 +IC H13X C312 *C313 H13Y 1.1217 108.02 -110.25 107.13 1.0719 +IC C312 C313 C314 H14X 1.4957 109.32 -62.31 105.96 1.1006 +IC H14X C313 *C314 H14Y 1.1006 105.96 117.95 106.72 1.0752 +IC H14X C313 *C314 H14Z 1.1006 105.96 -124.80 112.49 1.0399 +IC C13 C11 *C12 O2 1.6112 107.98 121.83 109.39 1.4022 +IC O2 C11 *C12 H2 1.4022 109.39 124.68 113.76 1.1543 +IC C11 C12 O2 HO2 1.5570 109.39 -16.32 103.24 0.9343 +IC C14 C12 *C13 O3 1.4744 109.06 119.73 110.76 1.4512 +IC O3 C12 *C13 H3 1.4512 110.76 111.14 104.04 1.0841 +IC C12 C13 O3 HO3 1.6112 110.76 -178.70 107.79 1.0156 +IC C15 C13 *C14 O4 1.5757 109.98 -128.32 111.85 1.4434 +IC O4 C13 *C14 H4 1.4434 111.85 -119.12 111.40 1.1566 +IC C13 C14 O4 P4 1.4744 111.85 51.81 135.06 1.6400 +IC C14 O4 P4 OP42 1.4434 135.06 67.85 107.20 1.6040 +IC OP42 O4 *P4 OP43 1.6040 107.20 119.44 113.86 1.5421 +IC OP42 O4 *P4 OP44 1.6040 107.20 -118.73 104.86 1.5125 +IC O4 P4 OP42 HP42 1.6400 107.20 5.61 115.03 1.0080 +IC C13 C14 C15 O5 1.4744 109.98 175.58 107.44 1.3813 +IC O5 C14 *C15 C16 1.3813 107.44 -118.15 109.01 1.5490 +IC C16 C14 *C15 H5 1.5490 109.01 -116.87 109.29 1.1409 +IC C14 C15 O5 P5 1.5757 107.44 145.73 126.35 1.6570 +IC C15 O5 P5 OP52 1.3813 126.35 -54.55 107.18 1.4982 +IC OP52 O5 *P5 OP53 1.4982 107.18 -122.47 104.74 1.5307 +IC OP52 O5 *P5 OP54 1.4982 107.18 117.86 108.41 1.4911 +IC C11 C15 *C16 O6 1.5753 113.94 -121.64 108.57 1.3963 +IC C11 C15 *C16 H6 1.5753 113.94 127.86 107.00 1.1093 +IC C15 C16 O6 HO6 1.5490 108.57 -31.20 108.26 1.0169 + +RESI DMPI25 -4.00 ! Di-myristoyl-inositol-(4,5)-bisphosphate (PIP2) with protonation on P5 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! HP52--OP52 OP53(-) +! H6 \ / +GROUP ! | P5--OP54(-) +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4----P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | | +ATOM OP42 OC2DP -0.90 ! | H3 +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | +GROUP ! / +ATOM C11 CC3161 0.01 ! | +ATOM H1 HCA1 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! | | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND P4 OP42 P4 OP43 P4 OP44 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND P5 OP52 P5 OP53 P5 OP54 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.4733 108.89 61.32 109.25 1.5575 +IC C12 C13 C14 C15 1.5126 109.25 -60.78 109.82 1.5491 +IC C13 C14 C15 C16 1.5575 109.82 58.33 108.34 1.5481 +IC C14 C15 C16 C11 1.5491 108.34 -56.62 109.13 1.5490 +IC C15 C16 C11 C12 1.5481 109.13 59.89 111.92 1.4733 +IC C16 C11 C12 C13 1.5490 111.92 -61.68 108.89 1.5126 +IC C16 C12 *C11 H1 1.5490 111.92 115.47 106.14 1.1093 +IC C16 C12 *C11 O12 1.5490 111.92 -125.19 103.48 1.5019 +IC C11 C13 *C12 H2 1.4733 108.89 116.60 104.60 1.0748 +IC C11 C13 *C12 O2 1.4733 108.89 -126.55 108.46 1.4063 +IC C12 C14 *C13 H3 1.5126 109.25 122.56 101.33 1.1354 +IC C12 C14 *C13 O3 1.5126 109.25 -121.13 111.54 1.4352 +IC C13 C15 *C14 H4 1.5575 109.82 -124.14 114.13 1.1419 +IC C13 C15 *C14 O4 1.5575 109.82 119.42 111.14 1.4644 +IC C14 C16 *C15 H5 1.5491 108.34 118.39 102.76 1.1512 +IC C14 C16 *C15 O5 1.5491 108.34 -123.50 110.48 1.4278 +IC C15 C11 *C16 H6 1.5481 109.13 -123.50 106.95 1.1387 +IC C15 C11 *C16 O6 1.5481 109.13 121.01 110.21 1.4573 +IC C13 C12 O2 HO2 1.5126 108.46 -27.55 97.83 0.9348 +IC C14 C13 O3 HO3 1.5575 111.54 -20.86 107.59 0.9959 +IC C11 C16 O6 HO6 1.5490 110.21 -118.54 105.64 0.9930 +IC C12 C11 O12 P 1.4733 103.48 -106.76 123.22 1.5965 +IC C11 O12 P O11 1.5019 123.22 -177.01 103.47 1.6129 +IC O11 O12 *P O13 1.6129 103.47 113.16 112.38 1.4787 +IC O11 O12 *P O14 1.6129 103.47 -114.93 111.96 1.4920 +IC O12 P O11 C1 1.5965 103.47 51.93 119.68 1.4240 +IC P O11 C1 C2 1.6129 119.68 148.07 107.91 1.5600 +IC C2 O11 *C1 HA 1.5600 107.91 -107.63 111.87 1.1330 +IC HA O11 *C1 HB 1.1330 111.87 -123.58 111.86 1.1126 +IC O11 C1 C2 C3 1.4240 107.91 173.76 113.61 1.5573 +IC C3 C1 *C2 O21 1.5573 113.61 117.63 103.98 1.4585 +IC C3 C1 *C2 HS 1.5573 113.61 -122.30 108.88 1.1424 +IC C1 C2 O21 C21 1.5600 103.98 133.61 116.01 1.3034 +IC C2 O21 C21 C22 1.4585 116.01 -173.97 107.66 1.5444 +IC C22 O21 *C21 O22 1.5444 107.66 -169.71 127.31 1.2367 +IC O21 C21 C22 C23 1.3034 107.66 -179.46 113.54 1.5193 +IC C23 C21 *C22 H2R 1.5193 113.54 -125.84 107.25 1.1224 +IC H2R C21 *C22 H2S 1.1224 107.25 -113.54 105.46 1.1149 +IC C1 C2 C3 O31 1.5600 113.61 168.98 111.53 1.4710 +IC O31 C2 *C3 HX 1.4710 111.53 -121.38 115.78 1.0778 +IC HX C2 *C3 HY 1.0778 115.78 -115.64 102.73 1.1315 +IC C2 C3 O31 C31 1.5573 111.53 81.70 116.38 1.3626 +IC C3 O31 C31 C32 1.4710 116.38 -178.49 106.07 1.5691 +IC C32 O31 *C31 O32 1.5691 106.07 -175.13 125.27 1.2107 +IC O31 C31 C32 C33 1.3626 106.07 124.62 113.00 1.5686 +IC C33 C31 *C32 H2X 1.5686 113.00 -127.63 112.20 1.0741 +IC H2X C31 *C32 H2Y 1.0741 112.20 -112.54 106.76 1.1231 +IC C21 C22 C23 C24 1.5444 113.54 94.03 111.53 1.5777 +IC C24 C22 *C23 H3R 1.5777 111.53 -127.29 113.66 1.1090 +IC H3R C22 *C23 H3S 1.1090 113.66 -121.30 110.31 1.0962 +IC C22 C23 C24 C25 1.5193 111.53 175.61 111.98 1.5215 +IC C25 C23 *C24 H4R 1.5215 111.98 -117.50 114.10 1.0933 +IC H4R C23 *C24 H4S 1.0933 114.10 -118.04 104.22 1.1388 +IC C23 C24 C25 C26 1.5777 111.98 170.38 118.48 1.5106 +IC C26 C24 *C25 H5R 1.5106 118.48 -123.15 106.22 1.1335 +IC H5R C24 *C25 H5S 1.1335 106.22 -118.85 105.44 1.1235 +IC C24 C25 C26 C27 1.5215 118.48 -178.13 109.59 1.4659 +IC C27 C25 *C26 H6R 1.4659 109.59 -114.64 109.01 1.0913 +IC H6R C25 *C26 H6S 1.0913 109.01 -130.05 106.32 1.1231 +IC C25 C26 C27 C28 1.5106 109.59 -176.78 110.06 1.5917 +IC C28 C26 *C27 H7R 1.5917 110.06 -121.00 108.40 1.1294 +IC H7R C26 *C27 H7S 1.1294 108.40 -116.95 114.95 1.0692 +IC C26 C27 C28 C29 1.4659 110.06 -163.43 116.31 1.5341 +IC C29 C27 *C28 H8R 1.5341 116.31 -113.38 105.11 1.0734 +IC H8R C27 *C28 H8S 1.0734 105.11 -115.26 109.34 1.0944 +IC C27 C28 C29 C210 1.5917 116.31 173.97 116.34 1.5579 +IC C210 C28 *C29 H9R 1.5579 116.34 -110.50 99.92 1.1569 +IC H9R C28 *C29 H9S 1.1569 99.92 -115.55 113.13 1.0687 +IC C28 C29 C210 C211 1.5341 116.34 160.88 112.21 1.5221 +IC C211 C29 *C210 H10R 1.5221 112.21 -119.51 106.47 1.1418 +IC H10R C29 *C210 H10S 1.1418 106.47 -111.28 114.65 1.1188 +IC C29 C210 C211 C212 1.5579 112.21 167.04 111.52 1.5418 +IC C212 C210 *C211 H11R 1.5418 111.52 -123.67 109.84 1.0572 +IC H11R C210 *C211 H11S 1.0572 109.84 -115.42 110.37 1.1541 +IC C210 C211 C212 C213 1.5221 111.52 55.55 109.40 1.5340 +IC C213 C211 *C212 H12R 1.5340 109.40 -116.37 111.48 1.0939 +IC H12R C211 *C212 H12S 1.0939 111.48 -120.50 117.34 1.1785 +IC C211 C212 C213 C214 1.5418 109.40 166.27 111.06 1.5197 +IC C214 C212 *C213 H13R 1.5197 111.06 -122.52 107.52 1.1671 +IC H13R C212 *C213 H13S 1.1671 107.52 -114.28 103.14 1.1656 +IC C212 C213 C214 H14R 1.5340 111.06 -66.41 110.34 1.0344 +IC H14R C213 *C214 H14S 1.0344 110.34 119.59 112.23 1.1747 +IC H14R C213 *C214 H14T 1.0344 110.34 -116.52 109.15 1.1451 +IC C31 C32 C33 C34 1.5691 113.00 174.62 115.84 1.5149 +IC C34 C32 *C33 H3X 1.5149 115.84 -125.19 105.96 1.1389 +IC H3X C32 *C33 H3Y 1.1389 105.96 -113.85 108.63 1.0758 +IC C32 C33 C34 C35 1.5686 115.84 176.75 105.81 1.5312 +IC C35 C33 *C34 H4X 1.5312 105.81 -119.34 113.61 1.1665 +IC H4X C33 *C34 H4Y 1.1665 113.61 -121.89 106.24 1.0784 +IC C33 C34 C35 C36 1.5149 105.81 178.99 109.63 1.5074 +IC C36 C34 *C35 H5X 1.5074 109.63 -123.67 111.46 1.1550 +IC H5X C34 *C35 H5Y 1.1550 111.46 -116.56 111.19 1.1823 +IC C34 C35 C36 C37 1.5312 109.63 163.59 113.11 1.5675 +IC C37 C35 *C36 H6X 1.5675 113.11 -117.96 106.20 1.1294 +IC H6X C35 *C36 H6Y 1.1294 106.20 -123.07 111.30 1.0919 +IC C35 C36 C37 C38 1.5074 113.11 -166.68 117.15 1.5330 +IC C38 C36 *C37 H7X 1.5330 117.15 -133.41 111.29 1.0706 +IC H7X C36 *C37 H7Y 1.0706 111.29 -109.47 105.17 1.1338 +IC C36 C37 C38 C39 1.5675 117.15 -59.45 112.95 1.4790 +IC C39 C37 *C38 H8X 1.4790 112.95 -121.11 105.22 1.1019 +IC H8X C37 *C38 H8Y 1.1019 105.22 -116.48 110.85 1.0213 +IC C37 C38 C39 C310 1.5330 112.95 -171.02 106.98 1.5433 +IC C310 C38 *C39 H9X 1.5433 106.98 -109.57 103.00 1.1166 +IC H9X C38 *C39 H9Y 1.1166 103.00 -120.67 115.73 1.1257 +IC C38 C39 C310 C311 1.4790 106.98 172.67 114.17 1.5851 +IC C311 C39 *C310 H10X 1.5851 114.17 -127.37 113.08 1.1531 +IC H10X C39 *C310 H10Y 1.1531 113.08 -112.35 106.71 1.0754 +IC C39 C310 C311 C312 1.5433 114.17 160.19 108.45 1.5274 +IC C312 C310 *C311 H11X 1.5274 108.45 -113.49 106.27 1.1835 +IC H11X C310 *C311 H11Y 1.1835 106.27 -119.13 115.51 1.1454 +IC C310 C311 C312 C313 1.5851 108.45 177.71 116.83 1.5725 +IC C313 C311 *C312 H12X 1.5725 116.83 -127.40 109.78 1.1524 +IC H12X C311 *C312 H12Y 1.1524 109.78 -116.95 103.00 1.1433 +IC C311 C312 C313 C314 1.5274 116.83 75.72 111.36 1.5420 +IC C314 C312 *C313 H13X 1.5420 111.36 -121.11 112.79 1.1580 +IC H13X C312 *C313 H13Y 1.1580 112.79 -122.34 104.84 1.1147 +IC C312 C313 C314 H14X 1.5725 111.36 -65.17 107.59 1.1199 +IC H14X C313 *C314 H14Y 1.1199 107.59 124.02 107.15 1.1182 +IC H14X C313 *C314 H14Z 1.1199 107.59 -128.71 111.81 1.1024 +IC C13 C11 *C12 O2 1.5126 108.89 122.34 115.59 1.4063 +IC O2 C11 *C12 H2 1.4063 115.59 124.01 109.17 1.0748 +IC C11 C12 O2 HO2 1.4733 115.59 -150.12 97.83 0.9348 +IC C14 C12 *C13 O3 1.5575 109.25 122.39 109.45 1.4352 +IC O3 C12 *C13 H3 1.4352 109.45 124.09 115.69 1.1354 +IC C12 C13 O3 HO3 1.5126 109.45 -141.88 107.59 0.9959 +IC C15 C13 *C14 O4 1.5491 109.82 -121.34 107.99 1.4644 +IC O4 C13 *C14 H4 1.4644 107.99 -112.20 110.08 1.1419 +IC C13 C14 O4 P4 1.5575 107.99 -96.51 124.98 1.6460 +IC C14 O4 P4 OP42 1.4644 124.98 57.33 104.36 1.5147 +IC OP42 O4 *P4 OP43 1.5147 104.36 118.10 111.42 1.5305 +IC OP42 O4 *P4 OP44 1.5147 104.36 -115.29 105.93 1.5035 +IC C13 C14 C15 O5 1.5575 109.82 -179.32 112.38 1.4278 +IC O5 C14 *C15 C16 1.4278 112.38 -122.35 108.34 1.5481 +IC C16 C14 *C15 H5 1.5481 108.34 -112.51 111.76 1.1512 +IC C14 C15 O5 P5 1.5491 112.38 125.82 119.01 1.6460 +IC C15 O5 P5 OP52 1.4278 119.01 -55.25 101.61 1.6267 +IC OP52 O5 *P5 OP53 1.6267 101.61 -119.25 114.32 1.4862 +IC OP52 O5 *P5 OP54 1.6267 101.61 109.12 108.38 1.5202 +IC O5 P5 OP52 HP52 1.6460 101.61 -30.24 108.75 0.9932 +IC C11 C15 *C16 O6 1.5490 109.13 -121.08 110.09 1.4573 +IC C11 C15 *C16 H6 1.5490 109.13 119.34 113.78 1.1387 +IC C15 C16 O6 HO6 1.5481 110.09 1.89 105.64 0.9930 + +RESI DMPI2A -4.00 ! Di-myristoyl-inositol-(3,5)-trisphosphate (PIP2) with protonation on P3 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.01 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.62 ! | |\ | / +ATOM P3 PC 1.50 ! | | \ O2 / +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 0.14 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! / +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | alpha4 +GROUP ! (-) O13 O12 +ATOM C11 CC3161 0.01 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.50 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O11 OSLP -0.57 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25---H5S | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! H6R ---C26---H6S | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28---H8S | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29---H9S | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! | | +ATOM H9S HAL2 0.09 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211--H11S | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212--H12S | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! H14T | +ATOM H14R HAL3 0.09 ! | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL3 -0.27 ! H14Z +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5442 106.14 59.32 106.78 1.5841 +IC C12 C13 C14 C15 1.5708 106.78 -57.83 115.11 1.5730 +IC C13 C14 C15 C16 1.5841 115.11 54.25 109.27 1.5046 +IC C14 C15 C16 C11 1.5730 109.27 -52.19 110.06 1.5641 +IC C15 C16 C11 C12 1.5046 110.06 61.58 113.17 1.5442 +IC C16 C11 C12 C13 1.5641 113.17 -64.42 106.14 1.5708 +IC C16 C12 *C11 H1 1.5641 113.17 117.75 105.95 1.0987 +IC C16 C12 *C11 O12 1.5641 113.17 -122.14 111.38 1.3846 +IC C11 C13 *C12 H2 1.5442 106.14 121.72 108.53 1.1465 +IC C11 C13 *C12 O2 1.5442 106.14 -121.83 107.04 1.4150 +IC C12 C14 *C13 H3 1.5708 106.78 114.36 112.47 1.1369 +IC C12 C14 *C13 O3 1.5708 106.78 -132.88 116.18 1.4092 +IC C13 C15 *C14 H4 1.5841 115.11 -130.24 108.94 1.1087 +IC C13 C15 *C14 O4 1.5841 115.11 116.93 101.94 1.4518 +IC C14 C16 *C15 H5 1.5730 109.27 118.39 108.24 1.1376 +IC C14 C16 *C15 O5 1.5730 109.27 -124.57 106.62 1.4362 +IC C15 C11 *C16 H6 1.5046 110.06 -124.28 108.96 1.1243 +IC C15 C11 *C16 O6 1.5046 110.06 122.31 108.37 1.4260 +IC C13 C12 O2 HO2 1.5708 107.04 41.22 106.36 0.9565 +IC C11 C16 O6 HO6 1.5641 108.37 158.87 98.67 0.9784 +IC C12 C11 O12 P 1.5442 111.38 -104.68 133.31 1.6310 +IC C11 O12 P O11 1.3846 133.31 -172.98 103.94 1.6041 +IC O11 O12 *P O13 1.6041 103.94 110.78 117.61 1.4886 +IC O11 O12 *P O14 1.6041 103.94 -115.32 116.61 1.4838 +IC O12 P O11 C1 1.6310 103.94 66.47 119.43 1.4810 +IC P O11 C1 C2 1.6041 119.43 133.86 109.21 1.5153 +IC C2 O11 *C1 HA 1.5153 109.21 -123.10 109.59 1.1456 +IC HA O11 *C1 HB 1.1456 109.59 -118.35 105.08 1.0817 +IC O11 C1 C2 C3 1.4810 109.21 -171.32 112.91 1.5297 +IC C3 C1 *C2 O21 1.5297 112.91 120.95 111.94 1.4818 +IC C3 C1 *C2 HS 1.5297 112.91 -118.94 100.03 1.0896 +IC C1 C2 O21 C21 1.5153 111.94 90.14 108.73 1.3871 +IC C2 O21 C21 C22 1.4818 108.73 -143.21 113.50 1.4860 +IC C22 O21 *C21 O22 1.4860 113.50 179.03 122.55 1.2328 +IC O21 C21 C22 C23 1.3871 113.50 -116.27 109.75 1.5284 +IC C23 C21 *C22 H2R 1.5284 109.75 -125.63 105.23 1.1135 +IC H2R C21 *C22 H2S 1.1135 105.23 -121.57 101.80 1.0953 +IC C1 C2 C3 O31 1.5153 112.91 174.06 115.80 1.4575 +IC O31 C2 *C3 HX 1.4575 115.80 -121.96 108.65 1.1020 +IC HX C2 *C3 HY 1.1020 108.65 -110.12 109.43 1.1095 +IC C2 C3 O31 C31 1.5297 115.80 57.31 115.77 1.3332 +IC C3 O31 C31 C32 1.4575 115.77 -164.48 102.02 1.5114 +IC C32 O31 *C31 O32 1.5114 102.02 179.53 127.47 1.2224 +IC O31 C31 C32 C33 1.3332 102.02 152.48 109.81 1.5294 +IC C33 C31 *C32 H2X 1.5294 109.81 -128.88 109.12 1.1501 +IC H2X C31 *C32 H2Y 1.1501 109.12 -110.87 108.58 1.0447 +IC C21 C22 C23 C24 1.4860 109.75 69.79 106.95 1.6108 +IC C24 C22 *C23 H3R 1.6108 106.95 -118.04 115.42 1.1148 +IC H3R C22 *C23 H3S 1.1148 115.42 -119.53 110.62 1.1468 +IC C22 C23 C24 C25 1.5284 106.95 -174.91 114.14 1.5234 +IC C25 C23 *C24 H4R 1.5234 114.14 -117.03 105.03 1.1442 +IC H4R C23 *C24 H4S 1.1442 105.03 -121.06 111.89 1.1552 +IC C23 C24 C25 C26 1.6108 114.14 -178.39 112.90 1.5610 +IC C26 C24 *C25 H5R 1.5610 112.90 -119.18 106.43 1.1302 +IC H5R C24 *C25 H5S 1.1302 106.43 -120.20 114.27 1.1269 +IC C24 C25 C26 C27 1.5234 112.90 173.93 116.93 1.5749 +IC C27 C25 *C26 H6R 1.5749 116.93 -123.77 110.71 1.1380 +IC H6R C25 *C26 H6S 1.1380 110.71 -114.00 108.27 1.0516 +IC C25 C26 C27 C28 1.5610 116.93 179.60 107.32 1.5336 +IC C28 C26 *C27 H7R 1.5336 107.32 -134.31 119.96 1.0756 +IC H7R C26 *C27 H7S 1.0756 119.96 -106.56 100.63 1.1713 +IC C26 C27 C28 C29 1.5749 107.32 153.17 116.68 1.5432 +IC C29 C27 *C28 H8R 1.5432 116.68 -122.30 100.98 1.1350 +IC H8R C27 *C28 H8S 1.1350 100.98 -112.99 109.47 1.1307 +IC C27 C28 C29 C210 1.5336 116.68 63.69 110.59 1.5273 +IC C210 C28 *C29 H9R 1.5273 110.59 -116.56 112.28 1.1367 +IC H9R C28 *C29 H9S 1.1367 112.28 -119.18 114.55 1.0325 +IC C28 C29 C210 C211 1.5432 110.59 -170.23 109.85 1.5474 +IC C211 C29 *C210 H10R 1.5474 109.85 -119.37 106.67 1.0475 +IC H10R C29 *C210 H10S 1.0475 106.67 -118.25 107.97 1.0764 +IC C29 C210 C211 C212 1.5273 109.85 172.06 111.27 1.5174 +IC C212 C210 *C211 H11R 1.5174 111.27 -119.93 109.22 1.1497 +IC H11R C210 *C211 H11S 1.1497 109.22 -120.13 100.65 1.0827 +IC C210 C211 C212 C213 1.5474 111.27 63.97 110.82 1.5297 +IC C213 C211 *C212 H12R 1.5297 110.82 -130.89 112.91 1.1226 +IC H12R C211 *C212 H12S 1.1226 112.91 -109.38 109.64 1.1216 +IC C211 C212 C213 C214 1.5174 110.82 168.71 111.74 1.5361 +IC C214 C212 *C213 H13R 1.5361 111.74 -117.93 104.26 1.1347 +IC H13R C212 *C213 H13S 1.1347 104.26 -119.62 111.44 1.1482 +IC C212 C213 C214 H14R 1.5297 111.74 -39.20 110.09 1.0950 +IC H14R C213 *C214 H14S 1.0950 110.09 107.43 104.19 1.1057 +IC H14R C213 *C214 H14T 1.0950 110.09 -120.22 114.34 1.1194 +IC C31 C32 C33 C34 1.5114 109.81 179.96 117.19 1.5560 +IC C34 C32 *C33 H3X 1.5560 117.19 -113.66 110.93 1.1262 +IC H3X C32 *C33 H3Y 1.1262 110.93 -121.98 108.25 1.1504 +IC C32 C33 C34 C35 1.5294 117.19 164.05 117.10 1.5393 +IC C35 C33 *C34 H4X 1.5393 117.10 -114.92 98.62 1.1057 +IC H4X C33 *C34 H4Y 1.1057 98.62 -118.15 111.04 1.1078 +IC C33 C34 C35 C36 1.5560 117.10 -153.37 107.67 1.5261 +IC C36 C34 *C35 H5X 1.5261 107.67 -120.09 112.73 1.1621 +IC H5X C34 *C35 H5Y 1.1621 112.73 -127.23 107.73 1.1481 +IC C34 C35 C36 C37 1.5393 107.67 171.93 113.19 1.5114 +IC C37 C35 *C36 H6X 1.5114 113.19 -123.73 114.28 1.1620 +IC H6X C35 *C36 H6Y 1.1620 114.28 -111.11 108.36 1.1178 +IC C35 C36 C37 C38 1.5261 113.19 -173.39 121.74 1.5138 +IC C38 C36 *C37 H7X 1.5138 121.74 -122.08 109.25 1.0898 +IC H7X C36 *C37 H7Y 1.0898 109.25 -111.63 102.56 1.1507 +IC C36 C37 C38 C39 1.5114 121.74 151.94 111.71 1.5977 +IC C39 C37 *C38 H8X 1.5977 111.71 -123.00 114.04 1.1857 +IC H8X C37 *C38 H8Y 1.1857 114.04 -112.86 100.98 1.1035 +IC C37 C38 C39 C310 1.5138 111.71 140.12 111.23 1.5140 +IC C310 C38 *C39 H9X 1.5140 111.23 -127.65 116.95 1.1707 +IC H9X C38 *C39 H9Y 1.1707 116.95 -120.60 104.35 1.1378 +IC C38 C39 C310 C311 1.5977 111.23 170.37 108.36 1.5376 +IC C311 C39 *C310 H10X 1.5376 108.36 -121.04 108.75 1.1030 +IC H10X C39 *C310 H10Y 1.1030 108.75 -116.30 109.34 1.1331 +IC C39 C310 C311 C312 1.5140 108.36 176.60 119.17 1.5839 +IC C312 C310 *C311 H11X 1.5839 119.17 -120.41 102.78 1.0449 +IC H11X C310 *C311 H11Y 1.0449 102.78 -118.37 107.44 1.0542 +IC C310 C311 C312 C313 1.5376 119.17 57.83 108.63 1.5293 +IC C313 C311 *C312 H12X 1.5293 108.63 -129.82 108.08 1.0929 +IC H12X C311 *C312 H12Y 1.0929 108.08 -109.52 112.37 1.0998 +IC C311 C312 C313 C314 1.5839 108.63 173.91 107.75 1.4949 +IC C314 C312 *C313 H13X 1.4949 107.75 -121.60 114.51 1.1598 +IC H13X C312 *C313 H13Y 1.1598 114.51 -122.36 104.36 1.1109 +IC C312 C313 C314 H14X 1.5293 107.75 -66.12 110.43 1.0637 +IC H14X C313 *C314 H14Y 1.0637 110.43 130.07 116.47 1.1175 +IC H14X C313 *C314 H14Z 1.0637 110.43 -115.09 101.39 1.1251 +IC C13 C11 *C12 O2 1.5184 107.54 122.63 109.30 1.4426 +IC O2 C11 *C12 H2 1.4426 109.30 119.81 108.24 1.1104 +IC C11 C12 O2 HO2 1.6085 109.30 -115.24 92.34 1.0302 +IC C14 C12 *C13 O3 1.5631 111.19 117.68 104.72 1.4274 +IC O3 C12 *C13 H3 1.4274 104.72 117.96 111.56 1.1140 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C15 C13 *C14 O4 1.5343 111.39 -124.35 114.32 1.4177 +IC O4 C13 *C14 H4 1.4177 114.32 -117.89 106.72 1.0604 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C13 C14 C15 O5 1.5631 111.39 179.33 109.28 1.4270 +IC O5 C14 *C15 C16 1.4270 109.28 -124.79 112.35 1.5007 +IC C16 C14 *C15 H5 1.5007 112.35 -118.86 104.70 1.1064 +IC C14 C15 O5 P5 1.5343 109.28 -123.53 132.73 1.6688 +IC C15 O5 P5 OP52 1.4270 132.73 64.99 107.56 1.5362 +IC OP52 O5 *P5 OP53 1.5362 107.56 -122.52 110.70 1.5140 +IC OP52 O5 *P5 OP54 1.5362 107.56 121.44 99.10 1.5259 +IC C11 C15 *C16 O6 1.6111 109.23 -111.89 111.27 1.4099 +IC C11 C15 *C16 H6 1.6111 109.23 119.01 114.23 1.1116 +IC C15 C16 O6 HO6 1.5007 111.27 -69.60 103.78 1.0348 + +RESI DMPI2B -4.00 ! Di-myristoyl-inositol-(3,5)-bisphosphate (PIP2) with protonation on P5 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 -0.09 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.40 ! | |\ | / +ATOM P3 PC 1.10 ! | | \ O2 / +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.14 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! / +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | alpha4 +GROUP ! (-) O13 O12 +ATOM C11 CC3161 0.01 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.50 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O11 OSLP -0.57 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25---H5S | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! H6R ---C26---H6S | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28---H8S | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29---H9S | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! | | +ATOM H9S HAL2 0.09 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211--H11S | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212--H12S | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! H14T | +ATOM H14R HAL3 0.09 ! | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL3 -0.27 ! H14Z +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5442 106.14 59.32 106.78 1.5841 +IC C12 C13 C14 C15 1.5708 106.78 -57.83 115.11 1.5730 +IC C13 C14 C15 C16 1.5841 115.11 54.25 109.27 1.5046 +IC C14 C15 C16 C11 1.5730 109.27 -52.19 110.06 1.5641 +IC C15 C16 C11 C12 1.5046 110.06 61.58 113.17 1.5442 +IC C16 C11 C12 C13 1.5641 113.17 -64.42 106.14 1.5708 +IC C16 C12 *C11 H1 1.5641 113.17 117.75 105.95 1.0987 +IC C16 C12 *C11 O12 1.5641 113.17 -122.14 111.38 1.3846 +IC C11 C13 *C12 H2 1.5442 106.14 121.72 108.53 1.1465 +IC C11 C13 *C12 O2 1.5442 106.14 -121.83 107.04 1.4150 +IC C12 C14 *C13 H3 1.5708 106.78 114.36 112.47 1.1369 +IC C12 C14 *C13 O3 1.5708 106.78 -132.88 116.18 1.4092 +IC C13 C15 *C14 H4 1.5841 115.11 -130.24 108.94 1.1087 +IC C13 C15 *C14 O4 1.5841 115.11 116.93 101.94 1.4518 +IC C14 C16 *C15 H5 1.5730 109.27 118.39 108.24 1.1376 +IC C14 C16 *C15 O5 1.5730 109.27 -124.57 106.62 1.4362 +IC C15 C11 *C16 H6 1.5046 110.06 -124.28 108.96 1.1243 +IC C15 C11 *C16 O6 1.5046 110.06 122.31 108.37 1.4260 +IC C13 C12 O2 HO2 1.5708 107.04 41.22 106.36 0.9565 +IC C11 C16 O6 HO6 1.5641 108.37 158.87 98.67 0.9784 +IC C12 C11 O12 P 1.5442 111.38 -104.68 133.31 1.6310 +IC C11 O12 P O11 1.3846 133.31 -172.98 103.94 1.6041 +IC O11 O12 *P O13 1.6041 103.94 110.78 117.61 1.4886 +IC O11 O12 *P O14 1.6041 103.94 -115.32 116.61 1.4838 +IC O12 P O11 C1 1.6310 103.94 66.47 119.43 1.4810 +IC P O11 C1 C2 1.6041 119.43 133.86 109.21 1.5153 +IC C2 O11 *C1 HA 1.5153 109.21 -123.10 109.59 1.1456 +IC HA O11 *C1 HB 1.1456 109.59 -118.35 105.08 1.0817 +IC O11 C1 C2 C3 1.4810 109.21 -171.32 112.91 1.5297 +IC C3 C1 *C2 O21 1.5297 112.91 120.95 111.94 1.4818 +IC C3 C1 *C2 HS 1.5297 112.91 -118.94 100.03 1.0896 +IC C1 C2 O21 C21 1.5153 111.94 90.14 108.73 1.3871 +IC C2 O21 C21 C22 1.4818 108.73 -143.21 113.50 1.4860 +IC C22 O21 *C21 O22 1.4860 113.50 179.03 122.55 1.2328 +IC O21 C21 C22 C23 1.3871 113.50 -116.27 109.75 1.5284 +IC C23 C21 *C22 H2R 1.5284 109.75 -125.63 105.23 1.1135 +IC H2R C21 *C22 H2S 1.1135 105.23 -121.57 101.80 1.0953 +IC C1 C2 C3 O31 1.5153 112.91 174.06 115.80 1.4575 +IC O31 C2 *C3 HX 1.4575 115.80 -121.96 108.65 1.1020 +IC HX C2 *C3 HY 1.1020 108.65 -110.12 109.43 1.1095 +IC C2 C3 O31 C31 1.5297 115.80 57.31 115.77 1.3332 +IC C3 O31 C31 C32 1.4575 115.77 -164.48 102.02 1.5114 +IC C32 O31 *C31 O32 1.5114 102.02 179.53 127.47 1.2224 +IC O31 C31 C32 C33 1.3332 102.02 152.48 109.81 1.5294 +IC C33 C31 *C32 H2X 1.5294 109.81 -128.88 109.12 1.1501 +IC H2X C31 *C32 H2Y 1.1501 109.12 -110.87 108.58 1.0447 +IC C21 C22 C23 C24 1.4860 109.75 69.79 106.95 1.6108 +IC C24 C22 *C23 H3R 1.6108 106.95 -118.04 115.42 1.1148 +IC H3R C22 *C23 H3S 1.1148 115.42 -119.53 110.62 1.1468 +IC C22 C23 C24 C25 1.5284 106.95 -174.91 114.14 1.5234 +IC C25 C23 *C24 H4R 1.5234 114.14 -117.03 105.03 1.1442 +IC H4R C23 *C24 H4S 1.1442 105.03 -121.06 111.89 1.1552 +IC C23 C24 C25 C26 1.6108 114.14 -178.39 112.90 1.5610 +IC C26 C24 *C25 H5R 1.5610 112.90 -119.18 106.43 1.1302 +IC H5R C24 *C25 H5S 1.1302 106.43 -120.20 114.27 1.1269 +IC C24 C25 C26 C27 1.5234 112.90 173.93 116.93 1.5749 +IC C27 C25 *C26 H6R 1.5749 116.93 -123.77 110.71 1.1380 +IC H6R C25 *C26 H6S 1.1380 110.71 -114.00 108.27 1.0516 +IC C25 C26 C27 C28 1.5610 116.93 179.60 107.32 1.5336 +IC C28 C26 *C27 H7R 1.5336 107.32 -134.31 119.96 1.0756 +IC H7R C26 *C27 H7S 1.0756 119.96 -106.56 100.63 1.1713 +IC C26 C27 C28 C29 1.5749 107.32 153.17 116.68 1.5432 +IC C29 C27 *C28 H8R 1.5432 116.68 -122.30 100.98 1.1350 +IC H8R C27 *C28 H8S 1.1350 100.98 -112.99 109.47 1.1307 +IC C27 C28 C29 C210 1.5336 116.68 63.69 110.59 1.5273 +IC C210 C28 *C29 H9R 1.5273 110.59 -116.56 112.28 1.1367 +IC H9R C28 *C29 H9S 1.1367 112.28 -119.18 114.55 1.0325 +IC C28 C29 C210 C211 1.5432 110.59 -170.23 109.85 1.5474 +IC C211 C29 *C210 H10R 1.5474 109.85 -119.37 106.67 1.0475 +IC H10R C29 *C210 H10S 1.0475 106.67 -118.25 107.97 1.0764 +IC C29 C210 C211 C212 1.5273 109.85 172.06 111.27 1.5174 +IC C212 C210 *C211 H11R 1.5174 111.27 -119.93 109.22 1.1497 +IC H11R C210 *C211 H11S 1.1497 109.22 -120.13 100.65 1.0827 +IC C210 C211 C212 C213 1.5474 111.27 63.97 110.82 1.5297 +IC C213 C211 *C212 H12R 1.5297 110.82 -130.89 112.91 1.1226 +IC H12R C211 *C212 H12S 1.1226 112.91 -109.38 109.64 1.1216 +IC C211 C212 C213 C214 1.5174 110.82 168.71 111.74 1.5361 +IC C214 C212 *C213 H13R 1.5361 111.74 -117.93 104.26 1.1347 +IC H13R C212 *C213 H13S 1.1347 104.26 -119.62 111.44 1.1482 +IC C212 C213 C214 H14R 1.5297 111.74 -39.20 110.09 1.0950 +IC H14R C213 *C214 H14S 1.0950 110.09 107.43 104.19 1.1057 +IC H14R C213 *C214 H14T 1.0950 110.09 -120.22 114.34 1.1194 +IC C31 C32 C33 C34 1.5114 109.81 179.96 117.19 1.5560 +IC C34 C32 *C33 H3X 1.5560 117.19 -113.66 110.93 1.1262 +IC H3X C32 *C33 H3Y 1.1262 110.93 -121.98 108.25 1.1504 +IC C32 C33 C34 C35 1.5294 117.19 164.05 117.10 1.5393 +IC C35 C33 *C34 H4X 1.5393 117.10 -114.92 98.62 1.1057 +IC H4X C33 *C34 H4Y 1.1057 98.62 -118.15 111.04 1.1078 +IC C33 C34 C35 C36 1.5560 117.10 -153.37 107.67 1.5261 +IC C36 C34 *C35 H5X 1.5261 107.67 -120.09 112.73 1.1621 +IC H5X C34 *C35 H5Y 1.1621 112.73 -127.23 107.73 1.1481 +IC C34 C35 C36 C37 1.5393 107.67 171.93 113.19 1.5114 +IC C37 C35 *C36 H6X 1.5114 113.19 -123.73 114.28 1.1620 +IC H6X C35 *C36 H6Y 1.1620 114.28 -111.11 108.36 1.1178 +IC C35 C36 C37 C38 1.5261 113.19 -173.39 121.74 1.5138 +IC C38 C36 *C37 H7X 1.5138 121.74 -122.08 109.25 1.0898 +IC H7X C36 *C37 H7Y 1.0898 109.25 -111.63 102.56 1.1507 +IC C36 C37 C38 C39 1.5114 121.74 151.94 111.71 1.5977 +IC C39 C37 *C38 H8X 1.5977 111.71 -123.00 114.04 1.1857 +IC H8X C37 *C38 H8Y 1.1857 114.04 -112.86 100.98 1.1035 +IC C37 C38 C39 C310 1.5138 111.71 140.12 111.23 1.5140 +IC C310 C38 *C39 H9X 1.5140 111.23 -127.65 116.95 1.1707 +IC H9X C38 *C39 H9Y 1.1707 116.95 -120.60 104.35 1.1378 +IC C38 C39 C310 C311 1.5977 111.23 170.37 108.36 1.5376 +IC C311 C39 *C310 H10X 1.5376 108.36 -121.04 108.75 1.1030 +IC H10X C39 *C310 H10Y 1.1030 108.75 -116.30 109.34 1.1331 +IC C39 C310 C311 C312 1.5140 108.36 176.60 119.17 1.5839 +IC C312 C310 *C311 H11X 1.5839 119.17 -120.41 102.78 1.0449 +IC H11X C310 *C311 H11Y 1.0449 102.78 -118.37 107.44 1.0542 +IC C310 C311 C312 C313 1.5376 119.17 57.83 108.63 1.5293 +IC C313 C311 *C312 H12X 1.5293 108.63 -129.82 108.08 1.0929 +IC H12X C311 *C312 H12Y 1.0929 108.08 -109.52 112.37 1.0998 +IC C311 C312 C313 C314 1.5839 108.63 173.91 107.75 1.4949 +IC C314 C312 *C313 H13X 1.4949 107.75 -121.60 114.51 1.1598 +IC H13X C312 *C313 H13Y 1.1598 114.51 -122.36 104.36 1.1109 +IC C312 C313 C314 H14X 1.5293 107.75 -66.12 110.43 1.0637 +IC H14X C313 *C314 H14Y 1.0637 110.43 130.07 116.47 1.1175 +IC H14X C313 *C314 H14Z 1.0637 110.43 -115.09 101.39 1.1251 +IC C13 C11 *C12 O2 1.5184 107.54 122.63 109.30 1.4426 +IC O2 C11 *C12 H2 1.4426 109.30 119.81 108.24 1.1104 +IC C11 C12 O2 HO2 1.6085 109.30 -115.24 92.34 1.0302 +IC C14 C12 *C13 O3 1.5631 111.19 117.68 104.72 1.4274 +IC O3 C12 *C13 H3 1.4274 104.72 117.96 111.56 1.1140 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6072 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C15 C13 *C14 O4 1.5343 111.39 -124.35 114.32 1.4177 +IC O4 C13 *C14 H4 1.4177 114.32 -117.89 106.72 1.0604 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C13 C14 C15 O5 1.5631 111.39 179.33 109.28 1.4270 +IC O5 C14 *C15 C16 1.4270 109.28 -124.79 112.35 1.5007 +IC C16 C14 *C15 H5 1.5007 112.35 -118.86 104.70 1.1064 +IC C14 C15 O5 P5 1.5343 109.28 -123.53 132.73 1.6688 +IC C15 O5 P5 OP52 1.4270 132.73 64.99 107.56 1.5362 +IC OP52 O5 *P5 OP53 1.5362 107.56 -122.52 110.70 1.5140 +IC OP52 O5 *P5 OP54 1.5362 107.56 121.44 99.10 1.5259 +IC O5 P5 OP52 HP52 1.6329 100.88 14.07 107.21 0.9447 +IC C11 C15 *C16 O6 1.6111 109.23 -111.89 111.27 1.4099 +IC C11 C15 *C16 H6 1.6111 109.23 119.01 114.23 1.1116 +IC C15 C16 O6 HO6 1.5007 111.27 -69.60 103.78 1.0348 + +RESI DMPI2C -4.00 ! Di-myristoyl-inositol-(3,4)-bisphosphate (PIP2) with protonation on P3 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 -0.09 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! / +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | alpha4 +GROUP ! (-) O13 O12 +ATOM C11 CC3161 0.01 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.50 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O11 OSLP -0.57 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25---H5S | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! H6R ---C26---H6S | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28---H8S | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29---H9S | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! | | +ATOM H9S HAL2 0.09 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211--H11S | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212--H12S | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! H14T | +ATOM H14R HAL3 0.09 ! | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL3 -0.27 ! H14Z +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5442 106.14 59.32 106.78 1.5841 +IC C12 C13 C14 C15 1.5708 106.78 -57.83 115.11 1.5730 +IC C13 C14 C15 C16 1.5841 115.11 54.25 109.27 1.5046 +IC C14 C15 C16 C11 1.5730 109.27 -52.19 110.06 1.5641 +IC C15 C16 C11 C12 1.5046 110.06 61.58 113.17 1.5442 +IC C16 C11 C12 C13 1.5641 113.17 -64.42 106.14 1.5708 +IC C16 C12 *C11 H1 1.5641 113.17 117.75 105.95 1.0987 +IC C16 C12 *C11 O12 1.5641 113.17 -122.14 111.38 1.3846 +IC C11 C13 *C12 H2 1.5442 106.14 121.72 108.53 1.1465 +IC C11 C13 *C12 O2 1.5442 106.14 -121.83 107.04 1.4150 +IC C12 C14 *C13 H3 1.5708 106.78 114.36 112.47 1.1369 +IC C12 C14 *C13 O3 1.5708 106.78 -132.88 116.18 1.4092 +IC C13 C15 *C14 H4 1.5841 115.11 -130.24 108.94 1.1087 +IC C13 C15 *C14 O4 1.5841 115.11 116.93 101.94 1.4518 +IC C14 C16 *C15 H5 1.5730 109.27 118.39 108.24 1.1376 +IC C14 C16 *C15 O5 1.5730 109.27 -124.57 106.62 1.4362 +IC C15 C11 *C16 H6 1.5046 110.06 -124.28 108.96 1.1243 +IC C15 C11 *C16 O6 1.5046 110.06 122.31 108.37 1.4260 +IC C13 C12 O2 HO2 1.5708 107.04 41.22 106.36 0.9565 +IC C11 C16 O6 HO6 1.5641 108.37 158.87 98.67 0.9784 +IC C12 C11 O12 P 1.5442 111.38 -104.68 133.31 1.6310 +IC C11 O12 P O11 1.3846 133.31 -172.98 103.94 1.6041 +IC O11 O12 *P O13 1.6041 103.94 110.78 117.61 1.4886 +IC O11 O12 *P O14 1.6041 103.94 -115.32 116.61 1.4838 +IC O12 P O11 C1 1.6310 103.94 66.47 119.43 1.4810 +IC P O11 C1 C2 1.6041 119.43 133.86 109.21 1.5153 +IC C2 O11 *C1 HA 1.5153 109.21 -123.10 109.59 1.1456 +IC HA O11 *C1 HB 1.1456 109.59 -118.35 105.08 1.0817 +IC O11 C1 C2 C3 1.4810 109.21 -171.32 112.91 1.5297 +IC C3 C1 *C2 O21 1.5297 112.91 120.95 111.94 1.4818 +IC C3 C1 *C2 HS 1.5297 112.91 -118.94 100.03 1.0896 +IC C1 C2 O21 C21 1.5153 111.94 90.14 108.73 1.3871 +IC C2 O21 C21 C22 1.4818 108.73 -143.21 113.50 1.4860 +IC C22 O21 *C21 O22 1.4860 113.50 179.03 122.55 1.2328 +IC O21 C21 C22 C23 1.3871 113.50 -116.27 109.75 1.5284 +IC C23 C21 *C22 H2R 1.5284 109.75 -125.63 105.23 1.1135 +IC H2R C21 *C22 H2S 1.1135 105.23 -121.57 101.80 1.0953 +IC C1 C2 C3 O31 1.5153 112.91 174.06 115.80 1.4575 +IC O31 C2 *C3 HX 1.4575 115.80 -121.96 108.65 1.1020 +IC HX C2 *C3 HY 1.1020 108.65 -110.12 109.43 1.1095 +IC C2 C3 O31 C31 1.5297 115.80 57.31 115.77 1.3332 +IC C3 O31 C31 C32 1.4575 115.77 -164.48 102.02 1.5114 +IC C32 O31 *C31 O32 1.5114 102.02 179.53 127.47 1.2224 +IC O31 C31 C32 C33 1.3332 102.02 152.48 109.81 1.5294 +IC C33 C31 *C32 H2X 1.5294 109.81 -128.88 109.12 1.1501 +IC H2X C31 *C32 H2Y 1.1501 109.12 -110.87 108.58 1.0447 +IC C21 C22 C23 C24 1.4860 109.75 69.79 106.95 1.6108 +IC C24 C22 *C23 H3R 1.6108 106.95 -118.04 115.42 1.1148 +IC H3R C22 *C23 H3S 1.1148 115.42 -119.53 110.62 1.1468 +IC C22 C23 C24 C25 1.5284 106.95 -174.91 114.14 1.5234 +IC C25 C23 *C24 H4R 1.5234 114.14 -117.03 105.03 1.1442 +IC H4R C23 *C24 H4S 1.1442 105.03 -121.06 111.89 1.1552 +IC C23 C24 C25 C26 1.6108 114.14 -178.39 112.90 1.5610 +IC C26 C24 *C25 H5R 1.5610 112.90 -119.18 106.43 1.1302 +IC H5R C24 *C25 H5S 1.1302 106.43 -120.20 114.27 1.1269 +IC C24 C25 C26 C27 1.5234 112.90 173.93 116.93 1.5749 +IC C27 C25 *C26 H6R 1.5749 116.93 -123.77 110.71 1.1380 +IC H6R C25 *C26 H6S 1.1380 110.71 -114.00 108.27 1.0516 +IC C25 C26 C27 C28 1.5610 116.93 179.60 107.32 1.5336 +IC C28 C26 *C27 H7R 1.5336 107.32 -134.31 119.96 1.0756 +IC H7R C26 *C27 H7S 1.0756 119.96 -106.56 100.63 1.1713 +IC C26 C27 C28 C29 1.5749 107.32 153.17 116.68 1.5432 +IC C29 C27 *C28 H8R 1.5432 116.68 -122.30 100.98 1.1350 +IC H8R C27 *C28 H8S 1.1350 100.98 -112.99 109.47 1.1307 +IC C27 C28 C29 C210 1.5336 116.68 63.69 110.59 1.5273 +IC C210 C28 *C29 H9R 1.5273 110.59 -116.56 112.28 1.1367 +IC H9R C28 *C29 H9S 1.1367 112.28 -119.18 114.55 1.0325 +IC C28 C29 C210 C211 1.5432 110.59 -170.23 109.85 1.5474 +IC C211 C29 *C210 H10R 1.5474 109.85 -119.37 106.67 1.0475 +IC H10R C29 *C210 H10S 1.0475 106.67 -118.25 107.97 1.0764 +IC C29 C210 C211 C212 1.5273 109.85 172.06 111.27 1.5174 +IC C212 C210 *C211 H11R 1.5174 111.27 -119.93 109.22 1.1497 +IC H11R C210 *C211 H11S 1.1497 109.22 -120.13 100.65 1.0827 +IC C210 C211 C212 C213 1.5474 111.27 63.97 110.82 1.5297 +IC C213 C211 *C212 H12R 1.5297 110.82 -130.89 112.91 1.1226 +IC H12R C211 *C212 H12S 1.1226 112.91 -109.38 109.64 1.1216 +IC C211 C212 C213 C214 1.5174 110.82 168.71 111.74 1.5361 +IC C214 C212 *C213 H13R 1.5361 111.74 -117.93 104.26 1.1347 +IC H13R C212 *C213 H13S 1.1347 104.26 -119.62 111.44 1.1482 +IC C212 C213 C214 H14R 1.5297 111.74 -39.20 110.09 1.0950 +IC H14R C213 *C214 H14S 1.0950 110.09 107.43 104.19 1.1057 +IC H14R C213 *C214 H14T 1.0950 110.09 -120.22 114.34 1.1194 +IC C31 C32 C33 C34 1.5114 109.81 179.96 117.19 1.5560 +IC C34 C32 *C33 H3X 1.5560 117.19 -113.66 110.93 1.1262 +IC H3X C32 *C33 H3Y 1.1262 110.93 -121.98 108.25 1.1504 +IC C32 C33 C34 C35 1.5294 117.19 164.05 117.10 1.5393 +IC C35 C33 *C34 H4X 1.5393 117.10 -114.92 98.62 1.1057 +IC H4X C33 *C34 H4Y 1.1057 98.62 -118.15 111.04 1.1078 +IC C33 C34 C35 C36 1.5560 117.10 -153.37 107.67 1.5261 +IC C36 C34 *C35 H5X 1.5261 107.67 -120.09 112.73 1.1621 +IC H5X C34 *C35 H5Y 1.1621 112.73 -127.23 107.73 1.1481 +IC C34 C35 C36 C37 1.5393 107.67 171.93 113.19 1.5114 +IC C37 C35 *C36 H6X 1.5114 113.19 -123.73 114.28 1.1620 +IC H6X C35 *C36 H6Y 1.1620 114.28 -111.11 108.36 1.1178 +IC C35 C36 C37 C38 1.5261 113.19 -173.39 121.74 1.5138 +IC C38 C36 *C37 H7X 1.5138 121.74 -122.08 109.25 1.0898 +IC H7X C36 *C37 H7Y 1.0898 109.25 -111.63 102.56 1.1507 +IC C36 C37 C38 C39 1.5114 121.74 151.94 111.71 1.5977 +IC C39 C37 *C38 H8X 1.5977 111.71 -123.00 114.04 1.1857 +IC H8X C37 *C38 H8Y 1.1857 114.04 -112.86 100.98 1.1035 +IC C37 C38 C39 C310 1.5138 111.71 140.12 111.23 1.5140 +IC C310 C38 *C39 H9X 1.5140 111.23 -127.65 116.95 1.1707 +IC H9X C38 *C39 H9Y 1.1707 116.95 -120.60 104.35 1.1378 +IC C38 C39 C310 C311 1.5977 111.23 170.37 108.36 1.5376 +IC C311 C39 *C310 H10X 1.5376 108.36 -121.04 108.75 1.1030 +IC H10X C39 *C310 H10Y 1.1030 108.75 -116.30 109.34 1.1331 +IC C39 C310 C311 C312 1.5140 108.36 176.60 119.17 1.5839 +IC C312 C310 *C311 H11X 1.5839 119.17 -120.41 102.78 1.0449 +IC H11X C310 *C311 H11Y 1.0449 102.78 -118.37 107.44 1.0542 +IC C310 C311 C312 C313 1.5376 119.17 57.83 108.63 1.5293 +IC C313 C311 *C312 H12X 1.5293 108.63 -129.82 108.08 1.0929 +IC H12X C311 *C312 H12Y 1.0929 108.08 -109.52 112.37 1.0998 +IC C311 C312 C313 C314 1.5839 108.63 173.91 107.75 1.4949 +IC C314 C312 *C313 H13X 1.4949 107.75 -121.60 114.51 1.1598 +IC H13X C312 *C313 H13Y 1.1598 114.51 -122.36 104.36 1.1109 +IC C312 C313 C314 H14X 1.5293 107.75 -66.12 110.43 1.0637 +IC H14X C313 *C314 H14Y 1.0637 110.43 130.07 116.47 1.1175 +IC H14X C313 *C314 H14Z 1.0637 110.43 -115.09 101.39 1.1251 +IC C13 C11 *C12 O2 1.5708 106.14 117.43 113.76 1.4150 +IC O2 C11 *C12 H2 1.4150 113.76 123.74 112.98 1.1465 +IC C11 C12 O2 HO2 1.5442 113.76 -75.69 106.36 0.9565 +IC C14 C12 *C13 O3 1.5841 106.78 132.32 117.21 1.4092 +IC O3 C12 *C13 H3 1.4092 117.21 108.20 104.75 1.1369 +IC C12 C13 O3 P3 1.5708 117.21 -34.31 131.18 1.6546 +IC C13 O3 P3 OP32 1.4092 131.18 47.24 105.58 1.6228 +IC OP32 O3 *P3 OP33 1.6228 105.58 113.04 110.03 1.5116 +IC OP32 O3 *P3 OP34 1.6228 105.58 -115.15 116.85 1.5254 +IC O3 P3 OP32 HP32 1.6546 105.58 -45.76 105.91 0.9821 +IC C15 C13 *C14 O4 1.5730 115.11 -113.28 108.27 1.4518 +IC O4 C13 *C14 H4 1.4518 108.27 -119.25 114.55 1.1087 +IC C13 C14 O4 P4 1.5841 108.27 46.82 139.32 1.6408 +IC C14 O4 P4 OP42 1.4518 139.32 134.89 108.03 1.5340 +IC OP42 O4 *P4 OP43 1.5340 108.03 -120.17 108.03 1.5208 +IC OP42 O4 *P4 OP44 1.5340 108.03 119.44 112.37 1.4879 +IC C13 C14 C15 O5 1.5841 115.11 173.92 114.75 1.4362 +IC O5 C14 *C15 C16 1.4362 114.75 -119.67 109.27 1.5046 +IC C16 C14 *C15 H5 1.5046 109.27 -118.01 108.85 1.1376 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C15 *C16 O6 1.5641 110.06 -120.38 111.62 1.4260 +IC C11 C15 *C16 H6 1.5641 110.06 121.98 112.89 1.1243 +IC C15 C16 O6 HO6 1.5046 111.62 -79.77 98.67 0.9784 + +RESI DMPI2D -4.00 ! Di-myristoyl-inositol-(3,4)-bisphosphate (PIP2) with protonation on P4 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | | OP32(-) +ATOM H4 HCA1 0.09 ! | H3 +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! / +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | alpha4 +GROUP ! (-) O13 O12 +ATOM C11 CC3161 0.01 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.50 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O11 OSLP -0.57 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25---H5S | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! H6R ---C26---H6S | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28---H8S | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29---H9S | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! | | +ATOM H9S HAL2 0.09 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211--H11S | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212--H12S | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! H14T | +ATOM H14R HAL3 0.09 ! | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL3 -0.27 ! H14Z +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5442 106.14 59.32 106.78 1.5841 +IC C12 C13 C14 C15 1.5708 106.78 -57.83 115.11 1.5730 +IC C13 C14 C15 C16 1.5841 115.11 54.25 109.27 1.5046 +IC C14 C15 C16 C11 1.5730 109.27 -52.19 110.06 1.5641 +IC C15 C16 C11 C12 1.5046 110.06 61.58 113.17 1.5442 +IC C16 C11 C12 C13 1.5641 113.17 -64.42 106.14 1.5708 +IC C16 C12 *C11 H1 1.5641 113.17 117.75 105.95 1.0987 +IC C16 C12 *C11 O12 1.5641 113.17 -122.14 111.38 1.3846 +IC C11 C13 *C12 H2 1.5442 106.14 121.72 108.53 1.1465 +IC C11 C13 *C12 O2 1.5442 106.14 -121.83 107.04 1.4150 +IC C12 C14 *C13 H3 1.5708 106.78 114.36 112.47 1.1369 +IC C12 C14 *C13 O3 1.5708 106.78 -132.88 116.18 1.4092 +IC C13 C15 *C14 H4 1.5841 115.11 -130.24 108.94 1.1087 +IC C13 C15 *C14 O4 1.5841 115.11 116.93 101.94 1.4518 +IC C14 C16 *C15 H5 1.5730 109.27 118.39 108.24 1.1376 +IC C14 C16 *C15 O5 1.5730 109.27 -124.57 106.62 1.4362 +IC C15 C11 *C16 H6 1.5046 110.06 -124.28 108.96 1.1243 +IC C15 C11 *C16 O6 1.5046 110.06 122.31 108.37 1.4260 +IC C13 C12 O2 HO2 1.5708 107.04 41.22 106.36 0.9565 +IC C11 C16 O6 HO6 1.5641 108.37 158.87 98.67 0.9784 +IC C12 C11 O12 P 1.5442 111.38 -104.68 133.31 1.6310 +IC C11 O12 P O11 1.3846 133.31 -172.98 103.94 1.6041 +IC O11 O12 *P O13 1.6041 103.94 110.78 117.61 1.4886 +IC O11 O12 *P O14 1.6041 103.94 -115.32 116.61 1.4838 +IC O12 P O11 C1 1.6310 103.94 66.47 119.43 1.4810 +IC P O11 C1 C2 1.6041 119.43 133.86 109.21 1.5153 +IC C2 O11 *C1 HA 1.5153 109.21 -123.10 109.59 1.1456 +IC HA O11 *C1 HB 1.1456 109.59 -118.35 105.08 1.0817 +IC O11 C1 C2 C3 1.4810 109.21 -171.32 112.91 1.5297 +IC C3 C1 *C2 O21 1.5297 112.91 120.95 111.94 1.4818 +IC C3 C1 *C2 HS 1.5297 112.91 -118.94 100.03 1.0896 +IC C1 C2 O21 C21 1.5153 111.94 90.14 108.73 1.3871 +IC C2 O21 C21 C22 1.4818 108.73 -143.21 113.50 1.4860 +IC C22 O21 *C21 O22 1.4860 113.50 179.03 122.55 1.2328 +IC O21 C21 C22 C23 1.3871 113.50 -116.27 109.75 1.5284 +IC C23 C21 *C22 H2R 1.5284 109.75 -125.63 105.23 1.1135 +IC H2R C21 *C22 H2S 1.1135 105.23 -121.57 101.80 1.0953 +IC C1 C2 C3 O31 1.5153 112.91 174.06 115.80 1.4575 +IC O31 C2 *C3 HX 1.4575 115.80 -121.96 108.65 1.1020 +IC HX C2 *C3 HY 1.1020 108.65 -110.12 109.43 1.1095 +IC C2 C3 O31 C31 1.5297 115.80 57.31 115.77 1.3332 +IC C3 O31 C31 C32 1.4575 115.77 -164.48 102.02 1.5114 +IC C32 O31 *C31 O32 1.5114 102.02 179.53 127.47 1.2224 +IC O31 C31 C32 C33 1.3332 102.02 152.48 109.81 1.5294 +IC C33 C31 *C32 H2X 1.5294 109.81 -128.88 109.12 1.1501 +IC H2X C31 *C32 H2Y 1.1501 109.12 -110.87 108.58 1.0447 +IC C21 C22 C23 C24 1.4860 109.75 69.79 106.95 1.6108 +IC C24 C22 *C23 H3R 1.6108 106.95 -118.04 115.42 1.1148 +IC H3R C22 *C23 H3S 1.1148 115.42 -119.53 110.62 1.1468 +IC C22 C23 C24 C25 1.5284 106.95 -174.91 114.14 1.5234 +IC C25 C23 *C24 H4R 1.5234 114.14 -117.03 105.03 1.1442 +IC H4R C23 *C24 H4S 1.1442 105.03 -121.06 111.89 1.1552 +IC C23 C24 C25 C26 1.6108 114.14 -178.39 112.90 1.5610 +IC C26 C24 *C25 H5R 1.5610 112.90 -119.18 106.43 1.1302 +IC H5R C24 *C25 H5S 1.1302 106.43 -120.20 114.27 1.1269 +IC C24 C25 C26 C27 1.5234 112.90 173.93 116.93 1.5749 +IC C27 C25 *C26 H6R 1.5749 116.93 -123.77 110.71 1.1380 +IC H6R C25 *C26 H6S 1.1380 110.71 -114.00 108.27 1.0516 +IC C25 C26 C27 C28 1.5610 116.93 179.60 107.32 1.5336 +IC C28 C26 *C27 H7R 1.5336 107.32 -134.31 119.96 1.0756 +IC H7R C26 *C27 H7S 1.0756 119.96 -106.56 100.63 1.1713 +IC C26 C27 C28 C29 1.5749 107.32 153.17 116.68 1.5432 +IC C29 C27 *C28 H8R 1.5432 116.68 -122.30 100.98 1.1350 +IC H8R C27 *C28 H8S 1.1350 100.98 -112.99 109.47 1.1307 +IC C27 C28 C29 C210 1.5336 116.68 63.69 110.59 1.5273 +IC C210 C28 *C29 H9R 1.5273 110.59 -116.56 112.28 1.1367 +IC H9R C28 *C29 H9S 1.1367 112.28 -119.18 114.55 1.0325 +IC C28 C29 C210 C211 1.5432 110.59 -170.23 109.85 1.5474 +IC C211 C29 *C210 H10R 1.5474 109.85 -119.37 106.67 1.0475 +IC H10R C29 *C210 H10S 1.0475 106.67 -118.25 107.97 1.0764 +IC C29 C210 C211 C212 1.5273 109.85 172.06 111.27 1.5174 +IC C212 C210 *C211 H11R 1.5174 111.27 -119.93 109.22 1.1497 +IC H11R C210 *C211 H11S 1.1497 109.22 -120.13 100.65 1.0827 +IC C210 C211 C212 C213 1.5474 111.27 63.97 110.82 1.5297 +IC C213 C211 *C212 H12R 1.5297 110.82 -130.89 112.91 1.1226 +IC H12R C211 *C212 H12S 1.1226 112.91 -109.38 109.64 1.1216 +IC C211 C212 C213 C214 1.5174 110.82 168.71 111.74 1.5361 +IC C214 C212 *C213 H13R 1.5361 111.74 -117.93 104.26 1.1347 +IC H13R C212 *C213 H13S 1.1347 104.26 -119.62 111.44 1.1482 +IC C212 C213 C214 H14R 1.5297 111.74 -39.20 110.09 1.0950 +IC H14R C213 *C214 H14S 1.0950 110.09 107.43 104.19 1.1057 +IC H14R C213 *C214 H14T 1.0950 110.09 -120.22 114.34 1.1194 +IC C31 C32 C33 C34 1.5114 109.81 179.96 117.19 1.5560 +IC C34 C32 *C33 H3X 1.5560 117.19 -113.66 110.93 1.1262 +IC H3X C32 *C33 H3Y 1.1262 110.93 -121.98 108.25 1.1504 +IC C32 C33 C34 C35 1.5294 117.19 164.05 117.10 1.5393 +IC C35 C33 *C34 H4X 1.5393 117.10 -114.92 98.62 1.1057 +IC H4X C33 *C34 H4Y 1.1057 98.62 -118.15 111.04 1.1078 +IC C33 C34 C35 C36 1.5560 117.10 -153.37 107.67 1.5261 +IC C36 C34 *C35 H5X 1.5261 107.67 -120.09 112.73 1.1621 +IC H5X C34 *C35 H5Y 1.1621 112.73 -127.23 107.73 1.1481 +IC C34 C35 C36 C37 1.5393 107.67 171.93 113.19 1.5114 +IC C37 C35 *C36 H6X 1.5114 113.19 -123.73 114.28 1.1620 +IC H6X C35 *C36 H6Y 1.1620 114.28 -111.11 108.36 1.1178 +IC C35 C36 C37 C38 1.5261 113.19 -173.39 121.74 1.5138 +IC C38 C36 *C37 H7X 1.5138 121.74 -122.08 109.25 1.0898 +IC H7X C36 *C37 H7Y 1.0898 109.25 -111.63 102.56 1.1507 +IC C36 C37 C38 C39 1.5114 121.74 151.94 111.71 1.5977 +IC C39 C37 *C38 H8X 1.5977 111.71 -123.00 114.04 1.1857 +IC H8X C37 *C38 H8Y 1.1857 114.04 -112.86 100.98 1.1035 +IC C37 C38 C39 C310 1.5138 111.71 140.12 111.23 1.5140 +IC C310 C38 *C39 H9X 1.5140 111.23 -127.65 116.95 1.1707 +IC H9X C38 *C39 H9Y 1.1707 116.95 -120.60 104.35 1.1378 +IC C38 C39 C310 C311 1.5977 111.23 170.37 108.36 1.5376 +IC C311 C39 *C310 H10X 1.5376 108.36 -121.04 108.75 1.1030 +IC H10X C39 *C310 H10Y 1.1030 108.75 -116.30 109.34 1.1331 +IC C39 C310 C311 C312 1.5140 108.36 176.60 119.17 1.5839 +IC C312 C310 *C311 H11X 1.5839 119.17 -120.41 102.78 1.0449 +IC H11X C310 *C311 H11Y 1.0449 102.78 -118.37 107.44 1.0542 +IC C310 C311 C312 C313 1.5376 119.17 57.83 108.63 1.5293 +IC C313 C311 *C312 H12X 1.5293 108.63 -129.82 108.08 1.0929 +IC H12X C311 *C312 H12Y 1.0929 108.08 -109.52 112.37 1.0998 +IC C311 C312 C313 C314 1.5839 108.63 173.91 107.75 1.4949 +IC C314 C312 *C313 H13X 1.4949 107.75 -121.60 114.51 1.1598 +IC H13X C312 *C313 H13Y 1.1598 114.51 -122.36 104.36 1.1109 +IC C312 C313 C314 H14X 1.5293 107.75 -66.12 110.43 1.0637 +IC H14X C313 *C314 H14Y 1.0637 110.43 130.07 116.47 1.1175 +IC H14X C313 *C314 H14Z 1.0637 110.43 -115.09 101.39 1.1251 +IC C13 C11 *C12 O2 1.5708 106.14 117.43 113.76 1.4150 +IC O2 C11 *C12 H2 1.4150 113.76 123.74 112.98 1.1465 +IC C11 C12 O2 HO2 1.5442 113.76 -75.69 106.36 0.9565 +IC C14 C12 *C13 O3 1.5841 106.78 132.32 117.21 1.4092 +IC O3 C12 *C13 H3 1.4092 117.21 108.20 104.75 1.1369 +IC C12 C13 O3 P3 1.5708 117.21 -34.31 131.18 1.6546 +IC C13 O3 P3 OP32 1.4092 131.18 47.24 105.58 1.6228 +IC OP32 O3 *P3 OP33 1.6228 105.58 113.04 110.03 1.5116 +IC OP32 O3 *P3 OP34 1.6228 105.58 -115.15 116.85 1.5254 +IC C15 C13 *C14 O4 1.5730 115.11 -113.28 108.27 1.4518 +IC O4 C13 *C14 H4 1.4518 108.27 -119.25 114.55 1.1087 +IC C13 C14 O4 P4 1.5841 108.27 46.82 139.32 1.6408 +IC C14 O4 P4 OP42 1.4518 139.32 134.89 108.03 1.5340 +IC OP42 O4 *P4 OP43 1.5340 108.03 -120.17 108.03 1.5208 +IC OP42 O4 *P4 OP44 1.5340 108.03 119.44 112.37 1.4879 +IC O4 P4 OP42 HP42 1.6546 105.58 -45.76 105.91 0.9821 +IC C13 C14 C15 O5 1.5841 115.11 173.92 114.75 1.4362 +IC O5 C14 *C15 C16 1.4362 114.75 -119.67 109.27 1.5046 +IC C16 C14 *C15 H5 1.5046 109.27 -118.01 108.85 1.1376 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C15 *C16 O6 1.5641 110.06 -120.38 111.62 1.4260 +IC C11 C15 *C16 H6 1.5641 110.06 121.98 112.89 1.1243 +IC C15 C16 O6 HO6 1.5046 111.62 -79.77 98.67 0.9784 + +RESI DMPI33 -6.00 ! Di-myristoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P3 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 -0.09 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! / +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | alpha4 +GROUP ! (-) O13 O12 +ATOM C11 CC3161 0.01 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.50 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O11 OSLP -0.57 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25---H5S | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! H6R ---C26---H6S | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28---H8S | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29---H9S | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! | | +ATOM H9S HAL2 0.09 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211--H11S | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212--H12S | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! H14T | +ATOM H14R HAL3 0.09 ! | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL3 -0.27 ! H14Z +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5442 106.14 59.32 106.78 1.5841 +IC C12 C13 C14 C15 1.5708 106.78 -57.83 115.11 1.5730 +IC C13 C14 C15 C16 1.5841 115.11 54.25 109.27 1.5046 +IC C14 C15 C16 C11 1.5730 109.27 -52.19 110.06 1.5641 +IC C15 C16 C11 C12 1.5046 110.06 61.58 113.17 1.5442 +IC C16 C11 C12 C13 1.5641 113.17 -64.42 106.14 1.5708 +IC C16 C12 *C11 H1 1.5641 113.17 117.75 105.95 1.0987 +IC C16 C12 *C11 O12 1.5641 113.17 -122.14 111.38 1.3846 +IC C11 C13 *C12 H2 1.5442 106.14 121.72 108.53 1.1465 +IC C11 C13 *C12 O2 1.5442 106.14 -121.83 107.04 1.4150 +IC C12 C14 *C13 H3 1.5708 106.78 114.36 112.47 1.1369 +IC C12 C14 *C13 O3 1.5708 106.78 -132.88 116.18 1.4092 +IC C13 C15 *C14 H4 1.5841 115.11 -130.24 108.94 1.1087 +IC C13 C15 *C14 O4 1.5841 115.11 116.93 101.94 1.4518 +IC C14 C16 *C15 H5 1.5730 109.27 118.39 108.24 1.1376 +IC C14 C16 *C15 O5 1.5730 109.27 -124.57 106.62 1.4362 +IC C15 C11 *C16 H6 1.5046 110.06 -124.28 108.96 1.1243 +IC C15 C11 *C16 O6 1.5046 110.06 122.31 108.37 1.4260 +IC C13 C12 O2 HO2 1.5708 107.04 41.22 106.36 0.9565 +IC C11 C16 O6 HO6 1.5641 108.37 158.87 98.67 0.9784 +IC C12 C11 O12 P 1.5442 111.38 -104.68 133.31 1.6310 +IC C11 O12 P O11 1.3846 133.31 -172.98 103.94 1.6041 +IC O11 O12 *P O13 1.6041 103.94 110.78 117.61 1.4886 +IC O11 O12 *P O14 1.6041 103.94 -115.32 116.61 1.4838 +IC O12 P O11 C1 1.6310 103.94 66.47 119.43 1.4810 +IC P O11 C1 C2 1.6041 119.43 133.86 109.21 1.5153 +IC C2 O11 *C1 HA 1.5153 109.21 -123.10 109.59 1.1456 +IC HA O11 *C1 HB 1.1456 109.59 -118.35 105.08 1.0817 +IC O11 C1 C2 C3 1.4810 109.21 -171.32 112.91 1.5297 +IC C3 C1 *C2 O21 1.5297 112.91 120.95 111.94 1.4818 +IC C3 C1 *C2 HS 1.5297 112.91 -118.94 100.03 1.0896 +IC C1 C2 O21 C21 1.5153 111.94 90.14 108.73 1.3871 +IC C2 O21 C21 C22 1.4818 108.73 -143.21 113.50 1.4860 +IC C22 O21 *C21 O22 1.4860 113.50 179.03 122.55 1.2328 +IC O21 C21 C22 C23 1.3871 113.50 -116.27 109.75 1.5284 +IC C23 C21 *C22 H2R 1.5284 109.75 -125.63 105.23 1.1135 +IC H2R C21 *C22 H2S 1.1135 105.23 -121.57 101.80 1.0953 +IC C1 C2 C3 O31 1.5153 112.91 174.06 115.80 1.4575 +IC O31 C2 *C3 HX 1.4575 115.80 -121.96 108.65 1.1020 +IC HX C2 *C3 HY 1.1020 108.65 -110.12 109.43 1.1095 +IC C2 C3 O31 C31 1.5297 115.80 57.31 115.77 1.3332 +IC C3 O31 C31 C32 1.4575 115.77 -164.48 102.02 1.5114 +IC C32 O31 *C31 O32 1.5114 102.02 179.53 127.47 1.2224 +IC O31 C31 C32 C33 1.3332 102.02 152.48 109.81 1.5294 +IC C33 C31 *C32 H2X 1.5294 109.81 -128.88 109.12 1.1501 +IC H2X C31 *C32 H2Y 1.1501 109.12 -110.87 108.58 1.0447 +IC C21 C22 C23 C24 1.4860 109.75 69.79 106.95 1.6108 +IC C24 C22 *C23 H3R 1.6108 106.95 -118.04 115.42 1.1148 +IC H3R C22 *C23 H3S 1.1148 115.42 -119.53 110.62 1.1468 +IC C22 C23 C24 C25 1.5284 106.95 -174.91 114.14 1.5234 +IC C25 C23 *C24 H4R 1.5234 114.14 -117.03 105.03 1.1442 +IC H4R C23 *C24 H4S 1.1442 105.03 -121.06 111.89 1.1552 +IC C23 C24 C25 C26 1.6108 114.14 -178.39 112.90 1.5610 +IC C26 C24 *C25 H5R 1.5610 112.90 -119.18 106.43 1.1302 +IC H5R C24 *C25 H5S 1.1302 106.43 -120.20 114.27 1.1269 +IC C24 C25 C26 C27 1.5234 112.90 173.93 116.93 1.5749 +IC C27 C25 *C26 H6R 1.5749 116.93 -123.77 110.71 1.1380 +IC H6R C25 *C26 H6S 1.1380 110.71 -114.00 108.27 1.0516 +IC C25 C26 C27 C28 1.5610 116.93 179.60 107.32 1.5336 +IC C28 C26 *C27 H7R 1.5336 107.32 -134.31 119.96 1.0756 +IC H7R C26 *C27 H7S 1.0756 119.96 -106.56 100.63 1.1713 +IC C26 C27 C28 C29 1.5749 107.32 153.17 116.68 1.5432 +IC C29 C27 *C28 H8R 1.5432 116.68 -122.30 100.98 1.1350 +IC H8R C27 *C28 H8S 1.1350 100.98 -112.99 109.47 1.1307 +IC C27 C28 C29 C210 1.5336 116.68 63.69 110.59 1.5273 +IC C210 C28 *C29 H9R 1.5273 110.59 -116.56 112.28 1.1367 +IC H9R C28 *C29 H9S 1.1367 112.28 -119.18 114.55 1.0325 +IC C28 C29 C210 C211 1.5432 110.59 -170.23 109.85 1.5474 +IC C211 C29 *C210 H10R 1.5474 109.85 -119.37 106.67 1.0475 +IC H10R C29 *C210 H10S 1.0475 106.67 -118.25 107.97 1.0764 +IC C29 C210 C211 C212 1.5273 109.85 172.06 111.27 1.5174 +IC C212 C210 *C211 H11R 1.5174 111.27 -119.93 109.22 1.1497 +IC H11R C210 *C211 H11S 1.1497 109.22 -120.13 100.65 1.0827 +IC C210 C211 C212 C213 1.5474 111.27 63.97 110.82 1.5297 +IC C213 C211 *C212 H12R 1.5297 110.82 -130.89 112.91 1.1226 +IC H12R C211 *C212 H12S 1.1226 112.91 -109.38 109.64 1.1216 +IC C211 C212 C213 C214 1.5174 110.82 168.71 111.74 1.5361 +IC C214 C212 *C213 H13R 1.5361 111.74 -117.93 104.26 1.1347 +IC H13R C212 *C213 H13S 1.1347 104.26 -119.62 111.44 1.1482 +IC C212 C213 C214 H14R 1.5297 111.74 -39.20 110.09 1.0950 +IC H14R C213 *C214 H14S 1.0950 110.09 107.43 104.19 1.1057 +IC H14R C213 *C214 H14T 1.0950 110.09 -120.22 114.34 1.1194 +IC C31 C32 C33 C34 1.5114 109.81 179.96 117.19 1.5560 +IC C34 C32 *C33 H3X 1.5560 117.19 -113.66 110.93 1.1262 +IC H3X C32 *C33 H3Y 1.1262 110.93 -121.98 108.25 1.1504 +IC C32 C33 C34 C35 1.5294 117.19 164.05 117.10 1.5393 +IC C35 C33 *C34 H4X 1.5393 117.10 -114.92 98.62 1.1057 +IC H4X C33 *C34 H4Y 1.1057 98.62 -118.15 111.04 1.1078 +IC C33 C34 C35 C36 1.5560 117.10 -153.37 107.67 1.5261 +IC C36 C34 *C35 H5X 1.5261 107.67 -120.09 112.73 1.1621 +IC H5X C34 *C35 H5Y 1.1621 112.73 -127.23 107.73 1.1481 +IC C34 C35 C36 C37 1.5393 107.67 171.93 113.19 1.5114 +IC C37 C35 *C36 H6X 1.5114 113.19 -123.73 114.28 1.1620 +IC H6X C35 *C36 H6Y 1.1620 114.28 -111.11 108.36 1.1178 +IC C35 C36 C37 C38 1.5261 113.19 -173.39 121.74 1.5138 +IC C38 C36 *C37 H7X 1.5138 121.74 -122.08 109.25 1.0898 +IC H7X C36 *C37 H7Y 1.0898 109.25 -111.63 102.56 1.1507 +IC C36 C37 C38 C39 1.5114 121.74 151.94 111.71 1.5977 +IC C39 C37 *C38 H8X 1.5977 111.71 -123.00 114.04 1.1857 +IC H8X C37 *C38 H8Y 1.1857 114.04 -112.86 100.98 1.1035 +IC C37 C38 C39 C310 1.5138 111.71 140.12 111.23 1.5140 +IC C310 C38 *C39 H9X 1.5140 111.23 -127.65 116.95 1.1707 +IC H9X C38 *C39 H9Y 1.1707 116.95 -120.60 104.35 1.1378 +IC C38 C39 C310 C311 1.5977 111.23 170.37 108.36 1.5376 +IC C311 C39 *C310 H10X 1.5376 108.36 -121.04 108.75 1.1030 +IC H10X C39 *C310 H10Y 1.1030 108.75 -116.30 109.34 1.1331 +IC C39 C310 C311 C312 1.5140 108.36 176.60 119.17 1.5839 +IC C312 C310 *C311 H11X 1.5839 119.17 -120.41 102.78 1.0449 +IC H11X C310 *C311 H11Y 1.0449 102.78 -118.37 107.44 1.0542 +IC C310 C311 C312 C313 1.5376 119.17 57.83 108.63 1.5293 +IC C313 C311 *C312 H12X 1.5293 108.63 -129.82 108.08 1.0929 +IC H12X C311 *C312 H12Y 1.0929 108.08 -109.52 112.37 1.0998 +IC C311 C312 C313 C314 1.5839 108.63 173.91 107.75 1.4949 +IC C314 C312 *C313 H13X 1.4949 107.75 -121.60 114.51 1.1598 +IC H13X C312 *C313 H13Y 1.1598 114.51 -122.36 104.36 1.1109 +IC C312 C313 C314 H14X 1.5293 107.75 -66.12 110.43 1.0637 +IC H14X C313 *C314 H14Y 1.0637 110.43 130.07 116.47 1.1175 +IC H14X C313 *C314 H14Z 1.0637 110.43 -115.09 101.39 1.1251 +IC C13 C11 *C12 O2 1.5708 106.14 117.43 113.76 1.4150 +IC O2 C11 *C12 H2 1.4150 113.76 123.74 112.98 1.1465 +IC C11 C12 O2 HO2 1.5442 113.76 -75.69 106.36 0.9565 +IC C14 C12 *C13 O3 1.5841 106.78 132.32 117.21 1.4092 +IC O3 C12 *C13 H3 1.4092 117.21 108.20 104.75 1.1369 +IC C12 C13 O3 P3 1.5708 117.21 -34.31 131.18 1.6546 +IC C13 O3 P3 OP32 1.4092 131.18 47.24 105.58 1.6228 +IC OP32 O3 *P3 OP33 1.6228 105.58 113.04 110.03 1.5116 +IC OP32 O3 *P3 OP34 1.6228 105.58 -115.15 116.85 1.5254 +IC O3 P3 OP32 HP32 1.6546 105.58 -45.76 105.91 0.9821 +IC C15 C13 *C14 O4 1.5730 115.11 -113.28 108.27 1.4518 +IC O4 C13 *C14 H4 1.4518 108.27 -119.25 114.55 1.1087 +IC C13 C14 O4 P4 1.5841 108.27 46.82 139.32 1.6408 +IC C14 O4 P4 OP42 1.4518 139.32 134.89 108.03 1.5340 +IC OP42 O4 *P4 OP43 1.5340 108.03 -120.17 108.03 1.5208 +IC OP42 O4 *P4 OP44 1.5340 108.03 119.44 112.37 1.4879 +IC C13 C14 C15 O5 1.5841 115.11 173.92 114.75 1.4362 +IC O5 C14 *C15 C16 1.4362 114.75 -119.67 109.27 1.5046 +IC C16 C14 *C15 H5 1.5046 109.27 -118.01 108.85 1.1376 +IC C14 C15 O5 P5 1.5730 114.75 -94.83 133.81 1.6887 +IC C15 O5 P5 OP52 1.4362 133.81 165.90 112.10 1.5691 +IC OP52 O5 *P5 OP53 1.5691 112.10 121.63 109.09 1.4817 +IC OP52 O5 *P5 OP54 1.5691 112.10 -120.63 107.24 1.5331 +IC C11 C15 *C16 O6 1.5641 110.06 -120.38 111.62 1.4260 +IC C11 C15 *C16 H6 1.5641 110.06 121.98 112.89 1.1243 +IC C15 C16 O6 HO6 1.5046 111.62 -79.77 98.67 0.9784 + +RESI DMPI34 -6.00 ! Di-myristoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P4 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42-HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! / +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | alpha4 +GROUP ! (-) O13 O12 +ATOM C11 CC3161 0.01 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.50 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O11 OSLP -0.57 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25---H5S | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! H6R ---C26---H6S | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28---H8S | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29---H9S | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! | | +ATOM H9S HAL2 0.09 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211--H11S | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212--H12S | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! H14T | +ATOM H14R HAL3 0.09 ! | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL3 -0.27 ! H14Z +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5939 112.00 61.21 105.83 1.6580 +IC C12 C13 C14 C15 1.5417 105.83 -58.78 111.25 1.5619 +IC C13 C14 C15 C16 1.6580 111.25 54.68 108.46 1.5749 +IC C14 C15 C16 C11 1.5619 108.46 -56.58 115.34 1.4996 +IC C15 C16 C11 C12 1.5749 115.34 57.80 107.55 1.5939 +IC C16 C11 C12 C13 1.4996 107.55 -61.72 112.00 1.5417 +IC C16 C12 *C11 H1 1.4996 107.55 115.33 111.57 1.1455 +IC C16 C12 *C11 O12 1.4996 107.55 -126.25 108.83 1.4566 +IC C11 C13 *C12 H2 1.5939 112.00 108.76 101.02 1.1189 +IC C11 C13 *C12 O2 1.5939 112.00 -133.22 115.68 1.3870 +IC C12 C14 *C13 H3 1.5417 105.83 118.80 110.07 1.1473 +IC C12 C14 *C13 O3 1.5417 105.83 -123.17 110.83 1.4408 +IC C13 C15 *C14 H4 1.6580 111.25 -109.41 107.49 1.1376 +IC C13 C15 *C14 O4 1.6580 111.25 130.08 112.44 1.4507 +IC C14 C16 *C15 H5 1.5619 108.46 114.23 104.05 1.0854 +IC C14 C16 *C15 O5 1.5619 108.46 -125.99 108.94 1.4526 +IC C15 C11 *C16 H6 1.5749 115.34 -121.20 106.35 1.1280 +IC C15 C11 *C16 O6 1.5749 115.34 123.03 107.08 1.4357 +IC C13 C12 O2 HO2 1.5417 115.68 -59.28 108.15 0.9664 +IC C11 C16 O6 HO6 1.4996 107.08 -166.03 107.30 1.0446 +IC C12 C11 O12 P 1.5939 108.83 -106.29 131.31 1.6844 +IC C11 O12 P O11 1.4566 131.31 175.84 104.83 1.6529 +IC O11 O12 *P O13 1.6529 104.83 116.07 111.81 1.4275 +IC O11 O12 *P O14 1.6529 104.83 -114.74 113.72 1.5076 +IC O12 P O11 C1 1.6844 104.83 91.33 121.59 1.4499 +IC P O11 C1 C2 1.6529 121.59 107.02 113.09 1.5806 +IC C2 O11 *C1 HA 1.5806 113.09 -120.72 113.90 1.1057 +IC HA O11 *C1 HB 1.1057 113.90 -120.19 106.92 1.0736 +IC O11 C1 C2 C3 1.4499 113.09 -99.18 110.01 1.5836 +IC C3 C1 *C2 O21 1.5836 110.01 122.78 112.84 1.3859 +IC C3 C1 *C2 HS 1.5836 110.01 -112.82 107.10 1.1154 +IC C1 C2 O21 C21 1.5806 112.84 50.22 114.28 1.3350 +IC C2 O21 C21 C22 1.3859 114.28 -137.00 111.26 1.4993 +IC C22 O21 *C21 O22 1.4993 111.26 -171.30 125.33 1.2351 +IC O21 C21 C22 C23 1.3350 111.26 -83.30 114.24 1.5437 +IC C23 C21 *C22 H2R 1.5437 114.24 -118.13 102.62 1.1003 +IC H2R C21 *C22 H2S 1.1003 102.62 -115.22 103.01 1.0924 +IC C1 C2 C3 O31 1.5806 110.01 176.28 116.28 1.4408 +IC O31 C2 *C3 HX 1.4408 116.28 -120.92 101.73 1.0869 +IC HX C2 *C3 HY 1.0869 101.73 -115.68 112.24 1.0971 +IC C2 C3 O31 C31 1.5836 116.28 64.02 116.63 1.3069 +IC C3 O31 C31 C32 1.4408 116.63 -166.92 108.47 1.5784 +IC C32 O31 *C31 O32 1.5784 108.47 -176.50 130.30 1.2295 +IC O31 C31 C32 C33 1.3069 108.47 107.83 118.32 1.5768 +IC C33 C31 *C32 H2X 1.5768 118.32 -124.15 106.85 1.1407 +IC H2X C31 *C32 H2Y 1.1407 106.85 -107.83 114.61 1.1308 +IC C21 C22 C23 C24 1.4993 114.24 76.09 109.91 1.5400 +IC C24 C22 *C23 H3R 1.5400 109.91 -125.94 110.48 1.0688 +IC H3R C22 *C23 H3S 1.0688 110.48 -120.36 111.73 1.0830 +IC C22 C23 C24 C25 1.5437 109.91 -175.86 115.78 1.4965 +IC C25 C23 *C24 H4R 1.4965 115.78 -132.25 109.27 1.0822 +IC H4R C23 *C24 H4S 1.0822 109.27 -107.88 105.42 1.1482 +IC C23 C24 C25 C26 1.5400 115.78 175.14 109.07 1.5755 +IC C26 C24 *C25 H5R 1.5755 109.07 -127.64 111.95 1.1060 +IC H5R C24 *C25 H5S 1.1060 111.95 -117.21 110.19 1.1139 +IC C24 C25 C26 C27 1.4965 109.07 -175.35 109.62 1.6196 +IC C27 C25 *C26 H6R 1.6196 109.62 -128.20 108.33 1.1144 +IC H6R C25 *C26 H6S 1.1144 108.33 -123.99 110.36 1.0952 +IC C25 C26 C27 C28 1.5755 109.62 178.54 111.21 1.5045 +IC C28 C26 *C27 H7R 1.5045 111.21 -120.94 104.60 1.1212 +IC H7R C26 *C27 H7S 1.1212 104.60 -119.78 92.25 1.0810 +IC C26 C27 C28 C29 1.6196 111.21 173.16 111.47 1.5761 +IC C29 C27 *C28 H8R 1.5761 111.47 -117.54 104.69 1.1487 +IC H8R C27 *C28 H8S 1.1487 104.69 -120.17 115.31 1.0525 +IC C27 C28 C29 C210 1.5045 111.47 166.23 115.98 1.5294 +IC C210 C28 *C29 H9R 1.5294 115.98 -111.49 102.86 1.1035 +IC H9R C28 *C29 H9S 1.1035 102.86 -123.91 114.56 1.1047 +IC C28 C29 C210 C211 1.5761 115.98 -170.60 110.88 1.5831 +IC C211 C29 *C210 H10R 1.5831 110.88 -121.05 104.23 1.0889 +IC H10R C29 *C210 H10S 1.0889 104.23 -121.59 111.52 1.1497 +IC C29 C210 C211 C212 1.5294 110.88 -170.33 112.39 1.5443 +IC C212 C210 *C211 H11R 1.5443 112.39 -124.29 105.67 1.1426 +IC H11R C210 *C211 H11S 1.1426 105.67 -111.42 107.67 1.1155 +IC C210 C211 C212 C213 1.5831 112.39 -129.70 118.42 1.5893 +IC C213 C211 *C212 H12R 1.5893 118.42 -129.07 115.30 1.1041 +IC H12R C211 *C212 H12S 1.1041 115.30 -114.83 104.49 1.1224 +IC C211 C212 C213 C214 1.5443 118.42 -175.56 115.78 1.5032 +IC C214 C212 *C213 H13R 1.5032 115.78 -119.93 104.65 1.0929 +IC H13R C212 *C213 H13S 1.0929 104.65 -115.50 109.01 1.0670 +IC C212 C213 C214 H14R 1.5893 115.78 50.35 110.99 1.1548 +IC H14R C213 *C214 H14S 1.1548 110.99 120.50 117.44 1.0919 +IC H14R C213 *C214 H14T 1.1548 110.99 -116.20 102.12 1.0733 +IC C31 C32 C33 C34 1.5784 118.32 -166.02 107.78 1.5227 +IC C34 C32 *C33 H3X 1.5227 107.78 -121.35 98.80 1.1564 +IC H3X C32 *C33 H3Y 1.1564 98.80 -114.24 111.28 1.1627 +IC C32 C33 C34 C35 1.5768 107.78 156.76 113.76 1.5235 +IC C35 C33 *C34 H4X 1.5235 113.76 -118.80 109.18 1.0290 +IC H4X C33 *C34 H4Y 1.0290 109.18 -112.94 113.93 1.1551 +IC C33 C34 C35 C36 1.5227 113.76 -177.53 118.32 1.5520 +IC C36 C34 *C35 H5X 1.5520 118.32 -118.01 104.54 1.0687 +IC H5X C34 *C35 H5Y 1.0687 104.54 -118.43 109.60 1.1014 +IC C34 C35 C36 C37 1.5235 118.32 -73.55 112.23 1.5264 +IC C37 C35 *C36 H6X 1.5264 112.23 -125.60 113.47 1.1552 +IC H6X C35 *C36 H6Y 1.1552 113.47 -109.18 110.39 1.0938 +IC C35 C36 C37 C38 1.5520 112.23 170.39 103.55 1.5283 +IC C38 C36 *C37 H7X 1.5283 103.55 -118.75 112.16 1.0768 +IC H7X C36 *C37 H7Y 1.0768 112.16 -120.86 111.26 1.1631 +IC C36 C37 C38 C39 1.5264 103.55 167.53 113.33 1.5186 +IC C39 C37 *C38 H8X 1.5186 113.33 -116.58 107.57 1.0397 +IC H8X C37 *C38 H8Y 1.0397 107.57 -114.92 118.93 1.1352 +IC C37 C38 C39 C310 1.5283 113.33 -175.30 114.56 1.5399 +IC C310 C38 *C39 H9X 1.5399 114.56 -115.93 106.72 1.1580 +IC H9X C38 *C39 H9Y 1.1580 106.72 -110.43 110.75 1.1261 +IC C38 C39 C310 C311 1.5186 114.56 179.33 105.45 1.5666 +IC C311 C39 *C310 H10X 1.5666 105.45 -120.40 111.58 1.1557 +IC H10X C39 *C310 H10Y 1.1557 111.58 -122.56 113.58 1.0941 +IC C39 C310 C311 C312 1.5399 105.45 -173.75 112.42 1.5688 +IC C312 C310 *C311 H11X 1.5688 112.42 -124.62 110.77 1.1000 +IC H11X C310 *C311 H11Y 1.1000 110.77 -121.05 106.12 1.0954 +IC C310 C311 C312 C313 1.5666 112.42 -81.59 109.60 1.5128 +IC C313 C311 *C312 H12X 1.5128 109.60 -117.68 111.21 1.1256 +IC H12X C311 *C312 H12Y 1.1256 111.21 -123.86 110.57 1.1216 +IC C311 C312 C313 C314 1.5688 109.60 159.85 112.50 1.5672 +IC C314 C312 *C313 H13X 1.5672 112.50 -121.68 107.38 1.0647 +IC H13X C312 *C313 H13Y 1.0647 107.38 -122.19 111.82 1.1090 +IC C312 C313 C314 H14X 1.5128 112.50 -43.79 113.84 1.1411 +IC H14X C313 *C314 H14Y 1.1411 113.84 115.11 112.93 1.1066 +IC H14X C313 *C314 H14Z 1.1411 113.84 -128.80 109.59 1.1284 +IC C13 C11 *C12 O2 1.5417 112.00 133.95 114.20 1.3870 +IC O2 C11 *C12 H2 1.3870 114.20 118.42 102.77 1.1189 +IC C11 C12 O2 HO2 1.5939 114.20 168.51 108.15 0.9664 +IC C14 C12 *C13 O3 1.6580 105.83 121.62 113.26 1.4408 +IC O3 C12 *C13 H3 1.4408 113.26 119.52 109.98 1.1473 +IC C12 C13 O3 P3 1.5417 113.26 29.50 132.17 1.5993 +IC C13 O3 P3 OP32 1.4408 132.17 55.84 103.51 1.5378 +IC OP32 O3 *P3 OP33 1.5378 103.51 118.53 106.88 1.5281 +IC OP32 O3 *P3 OP34 1.5378 103.51 -122.37 105.71 1.5590 +IC C15 C13 *C14 O4 1.5619 111.25 -128.94 114.60 1.4507 +IC O4 C13 *C14 H4 1.4507 114.60 -117.36 100.75 1.1376 +IC C13 C14 O4 P4 1.6580 114.60 16.58 139.36 1.6303 +IC C14 O4 P4 OP42 1.4507 139.36 -73.63 95.84 1.5718 +IC OP42 O4 *P4 OP43 1.5718 95.84 -110.75 109.60 1.5652 +IC OP42 O4 *P4 OP44 1.5718 95.84 120.17 110.10 1.5316 +IC O4 P4 OP42 HP42 1.6303 95.84 37.35 106.77 0.9952 +IC C13 C14 C15 O5 1.6580 111.25 176.99 115.11 1.4526 +IC O5 C14 *C15 C16 1.4526 115.11 -122.31 108.46 1.5749 +IC C16 C14 *C15 H5 1.5749 108.46 -111.94 107.50 1.0854 +IC C14 C15 O5 P5 1.5619 115.11 161.80 138.90 1.6200 +IC C15 O5 P5 OP52 1.4526 138.90 166.46 102.32 1.5502 +IC OP52 O5 *P5 OP53 1.5502 102.32 -115.60 105.16 1.5014 +IC OP52 O5 *P5 OP54 1.5502 102.32 120.22 110.74 1.5305 +IC C11 C15 *C16 O6 1.4996 115.34 -121.36 110.19 1.4357 +IC C11 C15 *C16 H6 1.4996 115.34 119.65 109.20 1.1280 +IC C15 C16 O6 HO6 1.5749 110.19 -39.86 107.30 1.0446 + +RESI DMPI35 -6.00 ! Di-myristoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P5 +! +! myristoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! myristoyl - CH DMPC +! | (-) +! CH2 - PO4 - inositol +! +! OP54(-) +! H6 | +GROUP ! | O5-----P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4------P4---OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42(-) +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 -0.09 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! / +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! | alpha4 +GROUP ! (-) O13 O12 +ATOM C11 CC3161 0.01 ! \ / alpha3 +ATOM H1 HCA1 0.09 ! P (+) +ATOM P PL 1.50 ! / \ alpha2 +ATOM O13 O2L -0.78 ! (-) O14 O11 +ATOM O14 O2L -0.78 ! | alpha1 +ATOM O11 OSLP -0.57 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM C1 CTL2 -0.08 ! | +ATOM HA HAL2 0.09 ! HS---C2-------------- +ATOM HB HAL2 0.09 ! | beta1 | +GROUP ! O22 O21 theta3 +ATOM C2 CTL1 0.17 ! \\ / beta2 | +ATOM HS HAL1 0.09 ! C21 | +ATOM O21 OSL -0.49 ! | beta3 | +ATOM C21 CL 0.90 ! H2R---C22---H2S | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | beta4 | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | HX---C3---HY +GROUP ! | | gamma1 +ATOM C3 CTL2 0.08 ! | O32 O31 +ATOM HX HAL2 0.09 ! | \\ / gamma2 +ATOM HY HAL2 0.09 ! | C31 +ATOM O31 OSL -0.49 ! | | gamma3 +ATOM C31 CL 0.90 ! | H2X---C32---H2Y +ATOM O32 OBL -0.63 ! | | +ATOM C32 CTL2 -0.22 ! | | gamma4 +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! H3R ---C23---H3S | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! H4R ---C24---H4S | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! H5R ---C25---H5S | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! H6R ---C26---H6S | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! H7R ---C27---H7S | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! H8R ---C28---H8S | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29---H9S | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! | | +ATOM H9S HAL2 0.09 ! H10R---C210--H10S | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! | | +ATOM H10S HAL2 0.09 ! H11R---C211--H11S | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212--H12S | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! H13R---C213--H13S | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL3 -0.27 ! H14T | +ATOM H14R HAL3 0.09 ! | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H3X ---C33---H3Y +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! H4X ---C34---H4Y +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! H5X ---C35---H5Y +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! H6X ---C36---H6Y +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! H7X ---C37---H7Y +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! H8X ---C38---H8Y +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! H9X ---C39---H9Y +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H11X---C311--H11Y +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! H12X---C312--H12Y +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! H13X---C313--H13Y +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! H14X---C314--H14Y +GROUP ! | +ATOM C314 CTL3 -0.27 ! H14Z +ATOM H14X HAL3 0.09 ! +ATOM H14Y HAL3 0.09 ! +ATOM H14Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +! +IC C11 C12 C13 C14 1.5375 108.38 54.84 110.45 1.5169 +IC C12 C13 C14 C15 1.5595 110.45 -54.24 115.86 1.5883 +IC C13 C14 C15 C16 1.5169 115.86 55.00 105.73 1.4774 +IC C14 C15 C16 C11 1.5883 105.73 -58.00 112.17 1.5829 +IC C15 C16 C11 C12 1.4774 112.17 64.94 109.41 1.5375 +IC C16 C11 C12 C13 1.5829 109.41 -59.16 108.38 1.5595 +IC C16 C12 *C11 H1 1.5829 109.41 108.71 102.84 1.0943 +IC C16 C12 *C11 O12 1.5829 109.41 -129.71 116.30 1.4473 +IC C11 C13 *C12 H2 1.5375 108.38 115.85 113.36 1.1016 +IC C11 C13 *C12 O2 1.5375 108.38 -120.84 116.76 1.4546 +IC C12 C14 *C13 H3 1.5595 110.45 121.48 113.64 1.1002 +IC C12 C14 *C13 O3 1.5595 110.45 -117.61 114.44 1.4238 +IC C13 C15 *C14 H4 1.5169 115.86 -129.16 105.27 1.1566 +IC C13 C15 *C14 O4 1.5169 115.86 126.32 108.79 1.4490 +IC C14 C16 *C15 H5 1.5883 105.73 123.83 116.99 1.1187 +IC C14 C16 *C15 O5 1.5883 105.73 -114.26 106.96 1.4557 +IC C15 C11 *C16 H6 1.4774 112.17 -123.26 102.31 1.0627 +IC C15 C11 *C16 O6 1.4774 112.17 125.89 110.13 1.4549 +IC C13 C12 O2 HO2 1.5595 116.76 -64.05 100.17 0.9199 +IC C11 C16 O6 HO6 1.5829 110.13 -134.38 104.64 0.9790 +IC C12 C11 O12 P 1.5375 116.30 -133.08 114.89 1.6846 +IC C11 O12 P O11 1.4473 114.89 -175.83 90.36 1.6603 +IC O11 O12 *P O13 1.6603 90.36 108.26 119.96 1.4638 +IC O11 O12 *P O14 1.6603 90.36 -106.70 113.64 1.5096 +IC O12 P O11 C1 1.6846 90.36 68.94 113.03 1.4321 +IC P O11 C1 C2 1.6603 113.03 108.76 115.52 1.5654 +IC C2 O11 *C1 HA 1.5654 115.52 -126.74 112.90 1.0872 +IC HA O11 *C1 HB 1.0872 112.90 -115.13 107.51 1.1283 +IC O11 C1 C2 C3 1.4321 115.52 145.51 110.08 1.5824 +IC C3 C1 *C2 O21 1.5824 110.08 119.75 105.85 1.4458 +IC C3 C1 *C2 HS 1.5824 110.08 -118.40 109.97 1.0861 +IC C1 C2 O21 C21 1.5654 105.85 126.34 117.57 1.3565 +IC C2 O21 C21 C22 1.4458 117.57 -148.41 108.93 1.4868 +IC C22 O21 *C21 O22 1.4868 108.93 -176.29 121.28 1.2407 +IC O21 C21 C22 C23 1.3565 108.93 -159.14 111.38 1.5392 +IC C23 C21 *C22 H2R 1.5392 111.38 -113.74 113.69 1.0965 +IC H2R C21 *C22 H2S 1.0965 113.69 -115.13 111.14 1.1066 +IC C1 C2 C3 O31 1.5654 110.08 -161.94 110.67 1.4688 +IC O31 C2 *C3 HX 1.4688 110.67 -127.34 119.02 1.1407 +IC HX C2 *C3 HY 1.1407 119.02 -119.20 106.00 1.1348 +IC C2 C3 O31 C31 1.5824 110.67 -117.19 128.73 1.2684 +IC C3 O31 C31 C32 1.4688 128.73 27.42 114.39 1.5666 +IC C32 O31 *C31 O32 1.5666 114.39 177.83 125.23 1.2111 +IC O31 C31 C32 C33 1.2684 114.39 154.01 112.27 1.5652 +IC C33 C31 *C32 H2X 1.5652 112.27 -117.89 99.03 1.1075 +IC H2X C31 *C32 H2Y 1.1075 99.03 -117.51 103.35 1.0925 +IC C21 C22 C23 C24 1.4868 111.38 81.32 114.14 1.5525 +IC C24 C22 *C23 H3R 1.5525 114.14 -125.63 106.95 1.0878 +IC H3R C22 *C23 H3S 1.0878 106.95 -113.32 102.53 1.1178 +IC C22 C23 C24 C25 1.5392 114.14 162.88 112.82 1.6014 +IC C25 C23 *C24 H4R 1.6014 112.82 -119.10 109.69 1.0923 +IC H4R C23 *C24 H4S 1.0923 109.69 -116.04 116.08 1.1185 +IC C23 C24 C25 C26 1.5525 112.82 177.82 111.98 1.5380 +IC C26 C24 *C25 H5R 1.5380 111.98 -124.78 99.85 1.0853 +IC H5R C24 *C25 H5S 1.0853 99.85 -115.47 106.27 1.0788 +IC C24 C25 C26 C27 1.6014 111.98 82.68 113.25 1.5469 +IC C27 C25 *C26 H6R 1.5469 113.25 -123.30 108.12 1.1106 +IC H6R C25 *C26 H6S 1.1106 108.12 -114.44 105.98 1.1084 +IC C25 C26 C27 C28 1.5380 113.25 -170.73 115.78 1.5639 +IC C28 C26 *C27 H7R 1.5639 115.78 -127.52 116.09 1.0979 +IC H7R C26 *C27 H7S 1.0979 116.09 -115.87 100.08 1.1329 +IC C26 C27 C28 C29 1.5469 115.78 -54.96 109.26 1.5210 +IC C29 C27 *C28 H8R 1.5210 109.26 -122.98 107.91 1.1100 +IC H8R C27 *C28 H8S 1.1100 107.91 -119.35 119.20 1.1315 +IC C27 C28 C29 C210 1.5639 109.26 -162.61 118.78 1.4703 +IC C210 C28 *C29 H9R 1.4703 118.78 -112.76 106.50 1.1366 +IC H9R C28 *C29 H9S 1.1366 106.50 -114.55 109.06 1.1368 +IC C28 C29 C210 C211 1.5210 118.78 178.84 115.63 1.5103 +IC C211 C29 *C210 H10R 1.5103 115.63 -124.08 116.06 1.1727 +IC H10R C29 *C210 H10S 1.1727 116.06 -108.96 105.89 1.1221 +IC C29 C210 C211 C212 1.4703 115.63 150.90 114.03 1.5500 +IC C212 C210 *C211 H11R 1.5500 114.03 -112.68 109.58 1.1154 +IC H11R C210 *C211 H11S 1.1154 109.58 -117.56 115.94 1.1226 +IC C210 C211 C212 C213 1.5103 114.03 -162.62 117.22 1.4881 +IC C213 C211 *C212 H12R 1.4881 117.22 -126.85 109.33 1.0928 +IC H12R C211 *C212 H12S 1.0928 109.33 -118.62 103.32 1.1492 +IC C211 C212 C213 C214 1.5500 117.22 -176.13 108.38 1.5053 +IC C214 C212 *C213 H13R 1.5053 108.38 -124.92 114.07 1.1063 +IC H13R C212 *C213 H13S 1.1063 114.07 -114.96 102.28 1.1203 +IC C212 C213 C214 H14R 1.4881 108.38 -59.77 107.48 1.0746 +IC H14R C213 *C214 H14S 1.0746 107.48 123.17 114.73 1.1286 +IC H14R C213 *C214 H14T 1.0746 107.48 -113.91 109.44 1.1108 +IC C31 C32 C33 C34 1.5666 112.27 -173.77 110.28 1.5867 +IC C34 C32 *C33 H3X 1.5867 110.28 -119.98 108.48 1.1276 +IC H3X C32 *C33 H3Y 1.1276 108.48 -112.47 108.61 1.1020 +IC C32 C33 C34 C35 1.5652 110.28 -154.64 119.47 1.5506 +IC C35 C33 *C34 H4X 1.5506 119.47 -127.18 104.17 1.1385 +IC H4X C33 *C34 H4Y 1.1385 104.17 -105.92 104.64 1.1550 +IC C33 C34 C35 C36 1.5867 119.47 -53.83 110.36 1.5829 +IC C36 C34 *C35 H5X 1.5829 110.36 -117.38 116.09 1.0404 +IC H5X C34 *C35 H5Y 1.0404 116.09 -123.43 111.15 1.1180 +IC C34 C35 C36 C37 1.5506 110.36 174.95 112.64 1.5830 +IC C37 C35 *C36 H6X 1.5830 112.64 -130.83 110.06 1.1811 +IC H6X C35 *C36 H6Y 1.1811 110.06 -115.59 110.21 1.1094 +IC C35 C36 C37 C38 1.5829 112.64 163.81 108.50 1.5657 +IC C38 C36 *C37 H7X 1.5657 108.50 -111.62 110.36 1.1224 +IC H7X C36 *C37 H7Y 1.1224 110.36 -133.09 107.41 1.1305 +IC C36 C37 C38 C39 1.5830 108.50 168.44 117.45 1.5474 +IC C39 C37 *C38 H8X 1.5474 117.45 -111.09 107.24 1.0611 +IC H8X C37 *C38 H8Y 1.0611 107.24 -111.84 118.81 1.1205 +IC C37 C38 C39 C310 1.5657 117.45 -167.44 113.27 1.5573 +IC C310 C38 *C39 H9X 1.5573 113.27 -126.67 110.07 1.0794 +IC H9X C38 *C39 H9Y 1.0794 110.07 -110.89 106.28 1.1668 +IC C38 C39 C310 C311 1.5474 113.27 174.81 111.72 1.5598 +IC C311 C39 *C310 H10X 1.5598 111.72 -112.19 107.28 1.1045 +IC H10X C39 *C310 H10Y 1.1045 107.28 -122.87 108.40 1.0915 +IC C39 C310 C311 C312 1.5573 111.72 -170.92 112.30 1.5594 +IC C312 C310 *C311 H11X 1.5594 112.30 -123.00 101.20 1.1502 +IC H11X C310 *C311 H11Y 1.1502 101.20 -114.17 114.66 1.0598 +IC C310 C311 C312 C313 1.5598 112.30 173.51 115.80 1.5648 +IC C313 C311 *C312 H12X 1.5648 115.80 -124.24 109.98 1.1244 +IC H12X C311 *C312 H12Y 1.1244 109.98 -113.99 103.47 1.1235 +IC C311 C312 C313 C314 1.5594 115.80 147.84 117.42 1.5187 +IC C314 C312 *C313 H13X 1.5187 117.42 -122.11 104.87 1.1165 +IC H13X C312 *C313 H13Y 1.1165 104.87 -113.16 110.29 1.0768 +IC C312 C313 C314 H14X 1.5648 117.42 169.48 111.58 1.1295 +IC H14X C313 *C314 H14Y 1.1295 111.58 122.81 109.54 1.1053 +IC H14X C313 *C314 H14Z 1.1295 111.58 -127.85 114.95 1.0316 +IC C13 C11 *C12 O2 1.5595 108.38 126.71 107.01 1.4546 +IC O2 C11 *C12 H2 1.4546 107.01 111.99 104.77 1.1016 +IC C11 C12 O2 HO2 1.5375 107.01 174.39 100.17 0.9199 +IC C14 C12 *C13 O3 1.5169 110.45 123.55 104.52 1.4238 +IC O3 C12 *C13 H3 1.4238 104.52 111.66 107.94 1.1002 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C15 C13 *C14 O4 1.5883 115.86 -125.01 111.35 1.4490 +IC O4 C13 *C14 H4 1.4490 111.35 -111.09 115.68 1.1566 +IC C13 C14 O4 P4 1.5169 111.35 77.64 137.88 1.6216 +IC C14 O4 P4 OP42 1.4490 137.88 -159.21 109.93 1.5413 +IC OP42 O4 *P4 OP43 1.5413 109.93 -118.30 102.38 1.5136 +IC OP42 O4 *P4 OP44 1.5413 109.93 123.01 110.00 1.4987 +IC C13 C14 C15 O5 1.5169 115.86 168.95 107.41 1.4557 +IC O5 C14 *C15 C16 1.4557 107.41 -113.95 105.73 1.4774 +IC C16 C14 *C15 H5 1.4774 105.73 -127.66 110.76 1.1187 +IC C14 C15 O5 P5 1.5883 107.41 155.00 129.54 1.5582 +IC C15 O5 P5 OP52 1.4557 129.54 -76.83 106.63 1.6466 +IC OP52 O5 *P5 OP53 1.6466 106.63 112.12 108.77 1.5178 +IC OP52 O5 *P5 OP54 1.6466 106.63 -123.68 110.07 1.5402 +IC O5 P5 OP52 HP52 1.5582 106.63 11.41 112.02 0.9945 +IC C11 C15 *C16 O6 1.5829 112.17 -124.69 112.33 1.4549 +IC C11 C15 *C16 H6 1.5829 112.17 116.07 114.56 1.0627 +IC C15 C16 O6 HO6 1.4774 112.33 -8.57 104.64 0.9790 + +RESI POPI -1.00 ! 1-Palmitoyl-2-Oleoyl-inositol +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | +ATOM C12 CC3161 0.14 ! | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5-HO5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI13 -3.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(3)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42(-) +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | OP32(-) +ATOM C14 CC3161 0.14 ! | H3 +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H12R---C212--H12S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H13R---C213--H13S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H14R---C214--H14S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI14 -3.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(4)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | H3 +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! H12R---C212--H12S | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! H13R---C213--H13S | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! H15R---C215--H15S | +ATOM H15R HAL2 0.09 ! | | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! H16R---C216--H16S | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C13 C14 O4 P4 1.5169 111.35 77.64 137.88 1.6216 +IC C14 O4 P4 OP42 1.4490 137.88 -159.21 109.93 1.5413 +IC OP42 O4 *P4 OP43 1.5413 109.93 -118.30 102.38 1.5136 +IC OP42 O4 *P4 OP44 1.5413 109.93 123.01 110.00 1.4987 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI15 -3.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(5)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4---HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3---HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI24 -4.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(4,5)-bisphosphate (PIP2) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42--HP42 +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.01 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.62 ! | | +ATOM P4 PC 1.50 ! | H3 +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! H12R---C212--H12S | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! H13R---C213--H13S | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! H15R---C215--H15S | +ATOM H15R HAL2 0.09 ! | | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! H16R---C216--H16S | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5026 111.38 -0.25 101.99 0.9558 +IC C13 C14 O4 P4 1.5404 117.97 39.59 132.79 1.6528 +IC C14 O4 P4 OP42 1.4360 132.79 -84.43 93.71 1.6010 +IC OP42 O4 *P4 OP43 1.6010 93.71 106.21 113.85 1.5294 +IC OP42 O4 *P4 OP44 1.6010 93.71 -106.53 116.29 1.5406 +IC O4 P4 OP42 HP42 1.6528 93.71 41.40 108.58 1.0068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI25 -4.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(4,5)-bisphosphate (PIP2) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | H3 +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! H12R---C212--H12S | +ATOM H12R HAL2 0.09 ! | | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! H13R---C213--H13S | +ATOM H13R HAL2 0.09 ! | | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! H15R---C215--H15S | +ATOM H15R HAL2 0.09 ! | | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! H16R---C216--H16S | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5026 111.38 -0.25 101.99 0.9558 +IC C13 C14 O4 P4 1.5613 107.65 -87.92 128.14 1.7068 +IC C14 O4 P4 OP42 1.4338 128.14 -174.57 99.96 1.4982 +IC OP42 O4 *P4 OP43 1.4982 99.96 119.26 103.52 1.5184 +IC OP42 O4 *P4 OP44 1.4982 99.96 -119.87 108.84 1.5595 +IC C14 C15 O5 P5 1.5940 108.11 177.95 132.56 1.6199 +IC C15 O5 P5 OP52 1.4241 132.56 108.15 100.81 1.5733 +IC OP52 O5 *P5 OP53 1.5733 100.81 -112.47 111.34 1.5025 +IC OP52 O5 *P5 OP54 1.5733 100.81 115.49 107.46 1.5072 +IC O5 P5 OP52 HP52 1.6199 100.81 16.08 101.23 1.0106 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI2A -4.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(3,5)-bisphosphate (PIP2) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.01 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.62 ! | |\ | / +ATOM P3 PC 1.50 ! | | \ O2 / +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 0.14 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H12R---C212--H12S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H13R---C213--H13S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H14R---C214--H14S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI2B -4.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(3,5)-bisphosphate (PIP2) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 -0.09 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.40 ! | |\ | / +ATOM P3 PC 1.10 ! | | \ O2 / +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.14 ! | | OP32(-) +ATOM H4 HCA1 0.09 ! | H3 +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H12R---C212--H12S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H13R---C213--H13S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H14R---C214--H14S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC O5 P5 OP52 HP52 1.6329 100.88 14.07 107.21 0.9447 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI2D -4.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(3,4)-bisphosphate (PIP2) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5---HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H12R---C212--H12S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H13R---C213--H13S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H14R---C214--H14S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC O4 P4 OP42 HP42 1.6329 100.88 14.07 107.21 0.9447 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI2C -4.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(3,4)-bisphosphate (PIP2) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 -0.09 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H12R---C212--H12S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H13R---C213--H13S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H14R---C214--H14S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI33 -6.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 -0.09 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H12R---C212--H12S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H13R---C213--H13S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H14R---C214--H14S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI34 -6.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H12R---C212--H12S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H13R---C213--H13S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H14R---C214--H14S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C13 C14 O4 P4 1.5404 117.97 39.59 132.79 1.6528 +IC C14 O4 P4 OP42 1.4360 132.79 -84.43 93.71 1.6010 +IC OP42 O4 *P4 OP43 1.6010 93.71 106.21 113.85 1.5294 +IC OP42 O4 *P4 OP44 1.6010 93.71 -106.53 116.29 1.5406 +IC O4 P4 OP42 HP42 1.6528 93.71 41.40 108.58 1.0068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPI35 -6.00 ! 1-Palmitoyl-2-Oleoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Oleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42(-) +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 -0.09 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H12R---C212--H12S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H13R---C213--H13S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H14R---C214--H14S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C13 C14 O4 P4 1.5169 111.35 77.64 137.88 1.6216 +IC C14 O4 P4 OP42 1.4490 137.88 -159.21 109.93 1.5413 +IC OP42 O4 *P4 OP43 1.5413 109.93 -118.30 102.38 1.5136 +IC OP42 O4 *P4 OP44 1.5413 109.93 123.01 110.00 1.4987 +IC C14 C15 O5 P5 1.5883 107.41 155.00 129.54 1.5582 +IC C15 O5 P5 OP52 1.4557 129.54 -76.83 106.63 1.6466 +IC OP52 O5 *P5 OP53 1.6466 106.63 112.12 108.77 1.5178 +IC OP52 O5 *P5 OP54 1.6466 106.63 -123.68 110.07 1.5402 +IC O5 P5 OP52 HP52 1.5582 106.63 11.41 112.02 0.9945 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI -1.00 ! 1-Palmitoyl-2-Linolenoyl-inositol +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | +ATOM C12 CC3161 0.14 ! | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5-HO5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H121---C212 | +GROUP ! || | +ATOM C213 CEL1 -0.15 ! || | +ATOM H131 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H151 HEL1 0.15 ! H151---C215 | +GROUP ! || | +ATOM C216 CEL1 -0.15 ! || | +ATOM H161 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 178.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -178.40 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI13 -3.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(3)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42(-) +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | OP32(-) +ATOM C14 CC3161 0.14 ! | H3 +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! || | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H151---C215 | +ATOM H14S HAL2 0.09 ! || | +GROUP ! || | +ATOM C215 CEL1 -0.15 ! || | +ATOM H151 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H161 HEL1 0.15 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI14 -3.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(4)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | H3 +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! H121---C212 | +ATOM H121 HEL1 0.15 ! || | +GROUP ! || | +ATOM C213 CEL1 -0.15 ! H131---C213 | +ATOM H131 HEL1 0.15 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! H151---C215 | +ATOM H151 HEL1 0.15 ! || | +GROUP ! || | +ATOM C216 CEL1 -0.15 ! H161---C216 | +ATOM H161 HEL1 0.15 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C13 C14 O4 P4 1.5169 111.35 77.64 137.88 1.6216 +IC C14 O4 P4 OP42 1.4490 137.88 -159.21 109.93 1.5413 +IC OP42 O4 *P4 OP43 1.5413 109.93 -118.30 102.38 1.5136 +IC OP42 O4 *P4 OP44 1.5413 109.93 123.01 110.00 1.4987 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI15 -3.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(5)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4---HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3---HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H121---C212 | +GROUP ! || | +ATOM C213 CEL1 -0.15 ! || | +ATOM H131 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H151 HEL1 0.15 ! H151---C215 | +GROUP ! || | +ATOM C216 CEL1 -0.15 ! || | +ATOM H161 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI24 -4.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(4,5)-bisphosphate (PIP2) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42--HP42 +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.01 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.62 ! | | +ATOM P4 PC 1.50 ! | H3 +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! H121---C212 | +ATOM H121 HEL1 0.15 ! || | +GROUP ! || | +ATOM C213 CEL1 -0.15 ! H131---C213 | +ATOM H131 HEL1 0.15 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! H151---C215 | +ATOM H151 HEL1 0.15 ! || | +GROUP ! || | +ATOM C216 CEL1 -0.15 ! H161---C216 | +ATOM H161 HEL1 0.15 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5026 111.38 -0.25 101.99 0.9558 +IC C13 C14 O4 P4 1.5404 117.97 39.59 132.79 1.6528 +IC C14 O4 P4 OP42 1.4360 132.79 -84.43 93.71 1.6010 +IC OP42 O4 *P4 OP43 1.6010 93.71 106.21 113.85 1.5294 +IC OP42 O4 *P4 OP44 1.6010 93.71 -106.53 116.29 1.5406 +IC O4 P4 OP42 HP42 1.6528 93.71 41.40 108.58 1.0068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI25 -4.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(4,5)-bisphosphate (PIP2) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | H3 +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! H121---C212 | +ATOM H121 HEL1 0.15 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! H131---C213 | +ATOM H131 HEL1 0.15 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! H151---C215 | +ATOM H151 HEL1 0.15 ! | | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! H161---C216 | +ATOM H161 HEL1 0.15 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5026 111.38 -0.25 101.99 0.9558 +IC C13 C14 O4 P4 1.5613 107.65 -87.92 128.14 1.7068 +IC C14 O4 P4 OP42 1.4338 128.14 -174.57 99.96 1.4982 +IC OP42 O4 *P4 OP43 1.4982 99.96 119.26 103.52 1.5184 +IC OP42 O4 *P4 OP44 1.4982 99.96 -119.87 108.84 1.5595 +IC C14 C15 O5 P5 1.5940 108.11 177.95 132.56 1.6199 +IC C15 O5 P5 OP52 1.4241 132.56 108.15 100.81 1.5733 +IC OP52 O5 *P5 OP53 1.5733 100.81 -112.47 111.34 1.5025 +IC OP52 O5 *P5 OP54 1.5733 100.81 115.49 107.46 1.5072 +IC O5 P5 OP52 HP52 1.6199 100.81 16.08 101.23 1.0106 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI2A -4.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(3,5)-bisphosphate (PIP2) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.01 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.62 ! | |\ | / +ATOM P3 PC 1.50 ! | | \ O2 / +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | | OP32--HP32 +ATOM C14 CC3161 0.14 ! | H3 +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H151---C215 | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H151 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H161 HEL1 0.15 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI2B -4.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(3,5)-bisphosphate (PIP2) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 -0.09 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.40 ! | |\ | / +ATOM P3 PC 1.10 ! | | \ O2 / +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | OP32(-) +ATOM C14 CC3161 0.14 ! | H3 +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H151---C215 | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H151 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H161 HEL1 0.15 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC O5 P5 OP52 HP52 1.6329 100.88 14.07 107.21 0.9447 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI2C -4.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(3,4)-trisphosphate (PIP2) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 -0.09 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H151---C215 | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H151 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H161 HEL1 0.15 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI2D -4.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(3,4)-bisphosphate (PIP2) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | | OP32(-) +ATOM H4 HCA1 0.09 ! | H3 +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H151---C215 | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H151 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H161 HEL1 0.15 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC O4 P4 OP42 HP42 1.6329 100.88 14.07 107.21 0.9447 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI33 -6.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 -0.09 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H151---C215 | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H151 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H161 HEL1 0.15 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI34 -6.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! || | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H151---C215 | +ATOM H14S HAL2 0.09 ! || | +GROUP ! || | +ATOM C215 CEL1 -0.15 ! || | +ATOM H151 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H161 HEL1 0.15 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C13 C14 O4 P4 1.5404 117.97 39.59 132.79 1.6528 +IC C14 O4 P4 OP42 1.4360 132.79 -84.43 93.71 1.6010 +IC OP42 O4 *P4 OP43 1.6010 93.71 106.21 113.85 1.5294 +IC OP42 O4 *P4 OP44 1.6010 93.71 -106.53 116.29 1.5406 +IC O4 P4 OP42 HP42 1.6528 93.71 41.40 108.58 1.0068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PNPI35 -6.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42(-) +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 -0.09 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H151---C215 | +ATOM H14S HAL2 0.09 ! || | +GROUP ! || | +ATOM C215 CEL1 -0.15 ! || | +ATOM H151 HEL1 0.15 ! H161---C216 | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H161 HEL1 0.15 ! H17R---C217--H17S | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H151 +DOUBLE C215 C216 +BOND C216 H161 C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C13 C14 O4 P4 1.5169 111.35 77.64 137.88 1.6216 +IC C14 O4 P4 OP42 1.4490 137.88 -159.21 109.93 1.5413 +IC OP42 O4 *P4 OP43 1.5413 109.93 -118.30 102.38 1.5136 +IC OP42 O4 *P4 OP44 1.5413 109.93 123.01 110.00 1.4987 +IC C14 C15 O5 P5 1.5883 107.41 155.00 129.54 1.5582 +IC C15 O5 P5 OP52 1.4557 129.54 -76.83 106.63 1.6466 +IC OP52 O5 *P5 OP53 1.6466 106.63 112.12 108.77 1.5178 +IC OP52 O5 *P5 OP54 1.6466 106.63 -123.68 110.07 1.5402 +IC O5 P5 OP52 HP52 1.5582 106.63 11.41 112.02 0.9945 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H151 1.5347 112.71 -121.31 109.08 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H161 1.5341 112.62 -121.30 109.16 1.1132 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI -1.00 ! 1-Palmitoyl-2-Linoleoyl-inositol +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | +ATOM C12 CC3161 0.14 ! | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5-HO5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3-HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H121---C212 | +GROUP ! || | +ATOM C213 CEL1 -0.15 ! || | +ATOM H131 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16S---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 178.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -178.40 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI13 -3.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(3)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42(-) +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | OP32(-) +ATOM C14 CC3161 0.14 ! | H3 +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! || | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI14 -3.00 ! 1-Palmitoyl-2-Linolenoyl-inositol-(4)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linolenoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | H3 +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! H121---C212 | +ATOM H121 HEL1 0.15 ! || | +GROUP ! || | +ATOM C213 CEL1 -0.15 ! H131---C213 | +ATOM H131 HEL1 0.15 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! H15R---C215--H15S | +ATOM H15R HAL2 0.09 ! | | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! H16R---C216--H16S | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C13 C14 O4 P4 1.5169 111.35 77.64 137.88 1.6216 +IC C14 O4 P4 OP42 1.4490 137.88 -159.21 109.93 1.5413 +IC OP42 O4 *P4 OP43 1.5413 109.93 -118.30 102.38 1.5136 +IC OP42 O4 *P4 OP44 1.5413 109.93 123.01 110.00 1.4987 +IC C16 C15 O5 HO5 1.5166 110.91 -40.75 106.35 0.9600 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI15 -3.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(5)-phosphate (PIP1) +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4---HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3---HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H121---C212 | +GROUP ! || | +ATOM C213 CEL1 -0.15 ! || | +ATOM H131 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5159 110.94 -43.53 106.45 0.9600 +IC C15 C14 O4 HO4 1.5153 110.93 44.16 106.21 0.9600 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI24 -4.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(4,5)-bisphosphate (PIP2) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42--HP42 +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.01 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.62 ! | | +ATOM P4 PC 1.50 ! | H3 +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! H121---C212 | +ATOM H121 HEL1 0.15 ! || | +GROUP ! || | +ATOM C213 CEL1 -0.15 ! H131---C213 | +ATOM H131 HEL1 0.15 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! H15R---C215--H15S | +ATOM H15R HAL2 0.09 ! | | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! H16R---C216--H16S | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5026 111.38 -0.25 101.99 0.9558 +IC C13 C14 O4 P4 1.5404 117.97 39.59 132.79 1.6528 +IC C14 O4 P4 OP42 1.4360 132.79 -84.43 93.71 1.6010 +IC OP42 O4 *P4 OP43 1.6010 93.71 106.21 113.85 1.5294 +IC OP42 O4 *P4 OP44 1.6010 93.71 -106.53 116.29 1.5406 +IC O4 P4 OP42 HP42 1.6528 93.71 41.40 108.58 1.0068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI25 -4.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(4,5)-bisphosphate (PIP2) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.14 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC311 -0.65 ! | |\ | / | +ATOM HO3 HCP1 0.42 ! | | \ O2 / OP42(-) +GROUP ! | H1 \ | / +ATOM C14 CC3161 -0.09 ! | \| / +ATOM H4 HCA1 0.09 ! | H2--C12----------C13--O3--HO3 +ATOM O4 OC30P -0.40 ! | | +ATOM P4 PC 1.10 ! | H3 +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! \ +ATOM HO6 HCP1 0.42 ! \ +GROUP ! | +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! (-) O13 O12 +ATOM P PL 1.59 ! \ / alpha3 +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ alpha2 +ATOM O12 OC30P -0.57 ! (-) O14 O11 +ATOM O11 OSLP -0.57 ! | alpha1 +ATOM C1 CTL2 -0.08 ! HA---C1---HB +ATOM HA HAL2 0.09 ! | theta1 +ATOM HB HAL2 0.09 ! | +GROUP ! HS---C2-------------- +ATOM C2 CTL1 0.17 ! | beta1 | +ATOM HS HAL1 0.09 ! O22 O21 theta3 +ATOM O21 OSL -0.49 ! \\ / beta2 | +ATOM C21 CL 0.90 ! C21 | +ATOM O22 OBL -0.63 ! | beta3 | +ATOM C22 CTL2 -0.22 ! H2R---C22---H2S | +ATOM H2R HAL2 0.09 ! | | +ATOM H2S HAL2 0.09 ! | beta4 | +GROUP ! | | +ATOM C3 CTL2 0.08 ! | HX---C3---HY +ATOM HX HAL2 0.09 ! | | gamma1 +ATOM HY HAL2 0.09 ! | O32 O31 +ATOM O31 OSL -0.49 ! | \\ / gamma2 +ATOM C31 CL 0.90 ! | C31 +ATOM O32 OBL -0.63 ! | | gamma3 +ATOM C32 CTL2 -0.22 ! | H2X---C32---H2Y +ATOM H2X HAL2 0.09 ! | | +ATOM H2Y HAL2 0.09 ! | | gamma4 +GROUP ! | | +ATOM C23 CTL2 -0.18 ! H3R ---C23---H3S | +ATOM H3R HAL2 0.09 ! | | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! H4R ---C24---H4S | +ATOM H4R HAL2 0.09 ! | | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! H5R ---C25---H5S | +ATOM H5R HAL2 0.09 ! | | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! H7R ---C27---H7S | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! H8R ---C28---H8S | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! H91 ---C29 | +ATOM H91 HEL1 0.15 ! || (CIS) | +GROUP ! || | +ATOM C210 CEL1 -0.15 ! H101---C210 | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! H11R---C211--H11S | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! H121---C212 | +ATOM H121 HEL1 0.15 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! H131---C213 | +ATOM H131 HEL1 0.15 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! H14R---C214--H14S | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! H15R---C215--H15S | +ATOM H15R HAL2 0.09 ! | | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! H16R---C216--H16S | +ATOM H16R HAL2 0.09 ! | | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! H17R---C217--H17S | +ATOM H17R HAL2 0.09 ! | | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18R---C218--H18S | +ATOM H18R HAL3 0.09 ! | | +ATOM H18S HAL3 0.09 ! H18T | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! H3X ---C33---H3Y +ATOM H3X HAL2 0.09 ! | +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! H4X ---C34---H4Y +ATOM H4X HAL2 0.09 ! | +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! H5X ---C35---H5Y +ATOM H5X HAL2 0.09 ! | +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! H6X ---C36---H6Y +ATOM H6X HAL2 0.09 ! | +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! H7X ---C37---H7Y +ATOM H7X HAL2 0.09 ! | +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! H8X ---C38---H8Y +ATOM H8X HAL2 0.09 ! | +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! H9X ---C39---H9Y +ATOM H9X HAL2 0.09 ! | +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! H10X---C310--H10Y +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! H11X---C311--H11Y +ATOM H11X HAL2 0.09 ! | +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! H12X---C312--H12Y +ATOM H12X HAL2 0.09 ! | +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! H13X---C313--H13Y +ATOM H13X HAL2 0.09 ! | +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! H14X---C314--H14Y +ATOM H14X HAL2 0.09 ! | +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! H15X---C315--H15Y +ATOM H15X HAL2 0.09 ! | +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! H16X---C316--H16Y +ATOM H16X HAL3 0.09 ! | +ATOM H16Y HAL3 0.09 ! H16Z +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C14 C13 O3 HO3 1.5026 111.38 -0.25 101.99 0.9558 +IC C13 C14 O4 P4 1.5613 107.65 -87.92 128.14 1.7068 +IC C14 O4 P4 OP42 1.4338 128.14 -174.57 99.96 1.4982 +IC OP42 O4 *P4 OP43 1.4982 99.96 119.26 103.52 1.5184 +IC OP42 O4 *P4 OP44 1.4982 99.96 -119.87 108.84 1.5595 +IC C14 C15 O5 P5 1.5940 108.11 177.95 132.56 1.6199 +IC C15 O5 P5 OP52 1.4241 132.56 108.15 100.81 1.5733 +IC OP52 O5 *P5 OP53 1.5733 100.81 -112.47 111.34 1.5025 +IC OP52 O5 *P5 OP54 1.5733 100.81 115.49 107.46 1.5072 +IC O5 P5 OP52 HP52 1.6199 100.81 16.08 101.23 1.0106 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI2A -4.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(3,5)-bisphosphate (PIP2) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.01 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.62 ! | |\ | / +ATOM P3 PC 1.50 ! | | \ O2 / +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 0.14 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI2B -4.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(3,5)-bisphosphate (PIP2) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 -0.09 ! / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4--HO4 +ATOM O3 OC30P -0.40 ! | |\ | / +ATOM P3 PC 1.10 ! | | \ O2 / +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | OP32(-) +ATOM C14 CC3161 0.14 ! | H3 +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC311 -0.65 ! | +ATOM HO4 HCP1 0.42 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 HO4 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C13 C14 O4 HO4 1.5575 108.74 -123.31 101.99 0.9558 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC O5 P5 OP52 HP52 1.6329 100.88 14.07 107.21 0.9447 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI2C -4.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(3,4)-trisphosphate (PIP2) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 -0.09 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI2D -4.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(3,4)-bisphosphate (PIP2) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | O5--HO5 +ATOM C12 CC3161 0.14 ! | / +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 ! | +ATOM HO5 HCP1 0.42 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 +BOND O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC O4 P4 OP42 HP42 1.6329 100.88 14.07 107.21 0.9447 +IC C14 C15 O5 HO5 1.5575 108.74 -123.31 101.99 0.9558 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI33 -6.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P3 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 0.01 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.62 ! | |\ | / | +ATOM P3 PC 1.50 ! | | \ O2 / OP42(-) +ATOM OP32 OC312 -0.68 ! | H1 \ | / OP34(-) +ATOM HP32 HCP1 0.34 ! | \| / | +ATOM OP33 OC2DP -0.82 ! | H2--C12----------C13--O3--P3--OP33(-) +ATOM OP34 OC2DP -0.82 ! | | | +GROUP ! | H3 OP32--HP32 +ATOM C14 CC3161 -0.09 ! | +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 OP32 HP32 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5184 104.72 81.60 126.34 1.6329 +IC C13 O3 P3 OP32 1.4274 126.34 85.69 100.88 1.5510 +IC OP32 O3 *P3 OP33 1.5510 100.88 115.27 112.07 1.5156 +IC OP32 O3 *P3 OP34 1.5510 100.88 -117.12 113.58 1.5553 +IC O3 P3 OP32 HP32 1.6329 100.88 14.07 107.21 0.9447 +IC C13 C14 O4 P4 1.5631 114.32 6.89 138.58 1.6286 +IC C14 O4 P4 OP42 1.4177 138.58 167.59 107.65 1.5034 +IC OP42 O4 *P4 OP43 1.5034 107.65 -120.37 104.68 1.5368 +IC OP42 O4 *P4 OP44 1.5034 107.65 120.68 112.17 1.5068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI34 -6.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P4 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52(-) +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42--HP42 +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 0.01 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.62 ! | +ATOM P4 PC 1.50 ! | +ATOM OP42 OC312 -0.68 ! | +ATOM HP42 HCP1 0.34 ! | +ATOM OP43 OC2DP -0.82 ! | +ATOM OP44 OC2DP -0.82 ! | +GROUP ! | +ATOM C15 CC3161 -0.09 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.40 ! | +ATOM P5 PC 1.10 ! | +ATOM OP52 OC2DP -0.90 ! | +ATOM OP53 OC2DP -0.90 ! | +ATOM OP54 OC2DP -0.90 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! || | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 OP42 HP42 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C13 C14 O4 P4 1.5404 117.97 39.59 132.79 1.6528 +IC C14 O4 P4 OP42 1.4360 132.79 -84.43 93.71 1.6010 +IC OP42 O4 *P4 OP43 1.6010 93.71 106.21 113.85 1.5294 +IC OP42 O4 *P4 OP44 1.6010 93.71 -106.53 116.29 1.5406 +IC O4 P4 OP42 HP42 1.6528 93.71 41.40 108.58 1.0068 +IC C14 C15 O5 P5 1.5901 108.71 153.93 129.94 1.6464 +IC C15 O5 P5 OP52 1.4218 129.94 -51.31 111.77 1.5727 +IC OP52 O5 *P5 OP53 1.5727 111.77 124.13 101.17 1.5465 +IC OP52 O5 *P5 OP54 1.5727 111.77 -122.28 104.13 1.5321 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PLPI35 -6.00 ! 1-Palmitoyl-2-Linoleoyl-inositol-(3,4,5)-trisphosphate (PIP3) with protonation on P5 +! +! Palmitoyl - CH2 Uses INI1 - cyclic myi-inositol, +! | +! Linoleoyl - CH POPC +! | (-) +! CH2 - PO4 - inositol +! OP54(-) +! H6 | +GROUP ! | O5---P5--OP53(-) +ATOM C12 CC3161 0.14 ! | / | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15 OP52--HP52 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | OP44(-) +ATOM C13 CC3161 -0.09 ! / \| | +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-------P4--OP43(-) +ATOM O3 OC30P -0.40 ! | |\ | / | +ATOM P3 PC 1.10 ! | | \ O2 / OP42(-) +ATOM OP32 OC2DP -0.90 ! | H1 \ | / OP34(-) +ATOM OP33 OC2DP -0.90 ! | \| / | +ATOM OP34 OC2DP -0.90 ! | H2--C12----------C13--O3--P3--OP33(-) +GROUP ! | | | +ATOM C14 CC3161 -0.09 ! | H3 OP32(-) +ATOM H4 HCA1 0.09 ! | +ATOM O4 OC30P -0.40 ! | +ATOM P4 PC 1.10 ! | +ATOM OP42 OC2DP -0.90 ! | +ATOM OP43 OC2DP -0.90 ! | +ATOM OP44 OC2DP -0.90 ! | +GROUP ! | +ATOM C15 CC3161 0.01 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC30P -0.62 ! | +ATOM P5 PC 1.50 ! | +ATOM OP52 OC312 -0.68 ! | +ATOM HP52 HCP1 0.34 ! | +ATOM OP53 OC2DP -0.82 ! | +ATOM OP54 OC2DP -0.82 ! | +GROUP ! \ +ATOM C16 CC3161 0.14 ! \ +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 ! (-) O13 O12 +GROUP ! \ / alpha3 +ATOM C11 CC3161 -0.08 ! P (+) +ATOM H1 HCA1 0.09 ! / \ alpha2 +ATOM P PL 1.59 ! (-) O14 O11 +ATOM O13 O2L -0.78 ! | alpha1 +ATOM O14 O2L -0.78 ! HA---C1---HB +ATOM O12 OC30P -0.57 ! | theta1 +ATOM O11 OSLP -0.57 ! | +ATOM C1 CTL2 -0.08 ! HS---C2-------------- +ATOM HA HAL2 0.09 ! | beta1 | +ATOM HB HAL2 0.09 ! O22 O21 theta3 +GROUP ! \\ / beta2 | +ATOM C2 CTL1 0.17 ! C21 | +ATOM HS HAL1 0.09 ! | beta3 | +ATOM O21 OSL -0.49 ! H2R---C22---H2S | +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | beta4 | +ATOM C22 CTL2 -0.22 ! | | +ATOM H2R HAL2 0.09 ! | HX---C3---HY +ATOM H2S HAL2 0.09 ! | | gamma1 +GROUP ! | O32 O31 +ATOM C3 CTL2 0.08 ! | \\ / gamma2 +ATOM HX HAL2 0.09 ! | C31 +ATOM HY HAL2 0.09 ! | | gamma3 +ATOM O31 OSL -0.49 ! | H2X---C32---H2Y +ATOM C31 CL 0.90 ! | | +ATOM O32 OBL -0.63 ! | | gamma4 +ATOM C32 CTL2 -0.22 ! | | +ATOM H2X HAL2 0.09 ! H3R ---C23---H3S | +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H91 ---C29 | +ATOM H8S HAL2 0.09 ! || (CIS) | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! H101---C210 | +ATOM H91 HEL1 0.15 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! H11R---C211--H11S | +ATOM H101 HEL1 0.15 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H121---C212 | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CEL1 -0.15 ! | | +ATOM H121 HEL1 0.15 ! H131---C213 | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H131 HEL1 0.15 ! H14R---C214--H14S | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H15R---C215--H15S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! H18T | +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! H3X ---C33---H3Y +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H10X---C310--H10Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H11X---C311--H11Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H12X---C312--H12Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H13X---C313--H13Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H14X---C314--H14Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H15X---C315--H15Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H16X---C316--H16Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! H16Z +ATOM C316 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 P3 C13 C14 C14 H4 C14 O4 +BOND OP32 P3 OP33 P3 OP34 P3 +BOND O4 P4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND OP42 P4 OP43 P4 OP44 P4 +BOND C16 O6 O6 HO6 C15 O5 O5 P5 +BOND OP52 P5 OP53 P5 OP54 P5 OP52 HP52 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H121 +DOUBLE C212 C213 +BOND C213 H131 C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol Head Group +IC C11 C12 C13 C14 1.5159 111.29 55.49 111.37 1.5159 +IC C12 C13 C14 C15 1.5155 111.37 -54.85 111.58 1.5153 +IC C13 C14 C15 C16 1.5159 111.58 53.89 111.90 1.5166 +IC C14 C15 C16 C11 1.5153 111.90 -53.47 111.64 1.5179 +IC C15 C16 C11 C12 1.5166 111.64 54.07 111.55 1.5159 +IC C16 C11 C12 C13 1.5179 111.55 -55.13 111.29 1.5155 +IC C16 C12 *C11 H1 1.5179 111.55 117.98 107.87 1.1110 +IC C16 C12 *C11 O12 1.5179 111.55 -125.13 111.38 1.4267 +IC C11 C13 *C12 H2 1.5159 111.29 119.04 108.26 1.1110 +IC C11 C13 *C12 O2 1.5159 111.29 -123.57 110.51 1.4281 +IC C12 C14 *C13 H3 1.5155 111.37 118.49 107.91 1.1110 +IC C12 C14 *C13 O3 1.5155 111.37 -124.39 110.94 1.4291 +IC C13 C15 *C14 H4 1.5159 111.58 -118.58 107.71 1.1110 +IC C13 C15 *C14 O4 1.5159 111.58 124.53 110.93 1.4298 +IC C14 C16 *C15 H5 1.5153 111.90 118.26 107.62 1.1110 +IC C14 C16 *C15 O5 1.5153 111.90 -124.94 110.91 1.4288 +IC C15 C11 *C16 H6 1.5166 111.64 -118.18 107.79 1.1110 +IC C15 C11 *C16 O6 1.5166 111.64 124.63 110.89 1.4278 +IC C13 C12 O2 HO2 1.5155 110.51 -41.69 106.20 0.9600 +IC C12 C13 O3 P3 1.5595 104.52 20.95 136.94 1.6478 +IC C13 O3 P3 OP32 1.4238 136.94 173.49 111.23 1.5174 +IC OP32 O3 *P3 OP33 1.5174 111.23 -120.64 106.44 1.5455 +IC OP32 O3 *P3 OP34 1.5174 111.23 113.75 106.51 1.5409 +IC C13 C14 O4 P4 1.5169 111.35 77.64 137.88 1.6216 +IC C14 O4 P4 OP42 1.4490 137.88 -159.21 109.93 1.5413 +IC OP42 O4 *P4 OP43 1.5413 109.93 -118.30 102.38 1.5136 +IC OP42 O4 *P4 OP44 1.5413 109.93 123.01 110.00 1.4987 +IC C14 C15 O5 P5 1.5883 107.41 155.00 129.54 1.5582 +IC C15 O5 P5 OP52 1.4557 129.54 -76.83 106.63 1.6466 +IC OP52 O5 *P5 OP53 1.6466 106.63 112.12 108.77 1.5178 +IC OP52 O5 *P5 OP54 1.6466 106.63 -123.68 110.07 1.5402 +IC O5 P5 OP52 HP52 1.5582 106.63 11.41 112.02 0.9945 +IC C11 C16 O6 HO6 1.5179 110.89 38.63 106.79 0.9600 +IC C12 C11 O12 P 1.5159 111.38 60.99 122.31 1.5867 +IC C11 O12 P O11 1.3655 121.23 153.36 102.74 1.5058 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 180.00 122.31 1.4271 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H121 1.5354 112.31 -121.28 109.81 1.1134 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H131 1.5346 112.70 -121.26 109.08 1.1132 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1131 109.14 -117.39 109.08 1.1133 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.39 109.08 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI PYPI -1.00 ! 1-palmitoyl-2-palmitoleoyl-sn-glycero-3-phosphoinositol +! PI lipid in yeast membranes (added BJR 3/12) +! (16:0)- CH2 Uses INI1 - cyclic myi-inositol, +! | +! (16:1)- CH +! | (-) +! CH2 - PO4 - inositol +! +! H6 +GROUP ! | +ATOM C12 CC3161 0.14 ! | +ATOM H2 HCA1 0.09 ! HO6-O6--C16----------C15--O5-HO5 +ATOM O2 OC311 -0.65 ! / |\ +ATOM HO2 HCP1 0.42 ! / | \ H4 +GROUP ! / H5 \ | +ATOM C13 CC3161 0.14 !5 / \| +ATOM H3 HCA1 0.09 ! ----C11 H02 C14--O4-HO4 +ATOM O3 OC311 -0.65 ! | |\ | / +ATOM HO3 HCP1 0.42 ! | | \ O2 / +GROUP ! | H1 \ | / +ATOM C14 CC3161 0.14 ! | \| / +ATOM H4 HCA1 0.09 !10 | H2--C12----------C13--O3-HO3 +ATOM O4 OC311 -0.65 ! | | +ATOM HO4 HCP1 0.42 ! | | +GROUP ! | H3 +ATOM C15 CC3161 0.14 ! | +ATOM H5 HCA1 0.09 ! | +ATOM O5 OC311 -0.65 !15 | +ATOM HO5 HCP1 0.42 ! | +GROUP ! | +ATOM C16 CC3161 0.14 ! | +ATOM H6 HCA1 0.09 ! | +ATOM O6 OC311 -0.65 ! | +ATOM HO6 HCP1 0.42 !20 \ +GROUP ! \ +ATOM C11 CC3161 -0.08 ! | +ATOM H1 HCA1 0.09 ! | +ATOM P PL 1.59 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 !25 P (+) +ATOM O12 OC30P -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 !30 | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! |! (CIS) | +ATOM C210 CEL1 -0.15 ! |! | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15 | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + + +! Inositol Head Group +BOND C11 H1 C11 C16 C11 C12 C11 O12 +BOND C12 H2 C12 O2 O2 HO2 C12 C13 C13 H3 +BOND C13 O3 O3 HO3 C13 C14 C14 H4 C14 O4 +BOND O4 HO4 C14 C15 C15 H5 C15 C16 C16 H6 +BOND C16 O6 O6 HO6 C15 O5 O5 HO5 +BOND O12 P P O11 P O13 P O14 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Inositol head group +IC C13 C11 *C12 O2 1.5274 106.54 -125.12 110.86 1.4313 +IC O2 C11 *C12 H2 1.4313 110.86 -119.04 110.69 1.1227 +IC C11 C12 O2 HO2 1.522 110.86 -165.21 106.21 0.9796 +IC C11 C12 C13 C14 1.522 106.54 -54.02 110.39 1.5294 +IC C14 C12 *C13 O3 1.5294 110.39 -132.22 116.61 1.4393 +IC O3 C12 *C13 H3 1.4393 116.61 -114.59 103.83 1.1211 +IC C12 C13 O3 HO3 1.5274 116.61 37.19 107.1 0.992 +IC C12 C13 C14 C15 1.5274 110.39 54.97 113.34 1.5089 +IC C15 C13 *C14 O4 1.5089 113.34 122.19 109.49 1.4208 +IC O4 C13 *C14 H4 1.4208 109.49 120.4 108.02 1.1182 +IC C13 C14 O4 HO4 1.5294 109.49 47.81 101.56 0.9647 +IC C13 C14 C15 C16 1.5294 113.34 -61.56 107.21 1.5044 +IC C16 C14 *C15 O5 1.5044 107.21 -126.91 111.32 1.443 +IC C16 C14 *C15 H5 1.5044 107.21 115.55 109.82 1.1204 +IC C14 C15 O5 HO5 1.5089 111.32 -30.29 105.37 0.9616 +IC C11 C15 *C16 O6 1.5718 103.38 130.41 106.35 1.4269 +IC C11 C15 *C16 H6 1.5718 103.38 -115.3 114.94 1.1059 +IC C15 C16 O6 HO6 1.5044 106.35 -159.49 112.22 0.9578 +IC C16 C12 *C11 O12 1.5718 110.04 123.23 100.51 1.4051 +IC C16 C12 *C11 H1 1.5718 110.04 -122.17 105.33 1.1213 +IC C12 C11 O12 P 1.522 100.51 160.4 116.02 1.6006 +! Phosphate linker +IC C11 O12 P O11 1.4051 116.02 147.17 96.96 1.5611 +IC O11 O12 *P O13 1.5611 96.96 -109.96 112.13 1.4817 +IC O11 O12 *P O14 1.5611 96.96 117.4 111.01 1.468 +IC O12 P O11 C1 1.6006 96.96 -152.25 110.59 1.4229 +IC P O11 C1 C2 1.5611 110.59 -179.08 107.17 1.5129 +IC C2 O11 *C1 HA 1.5129 107.17 -119.89 113.01 1.121 +IC HA O11 *C1 HB 1.121 113.01 -121.45 108.33 1.1155 +! Backbone +IC O11 C1 C2 O21 1.4229 107.17 173.35 107.15 1.4362 +IC O21 C1 *C2 C3 1.4362 107.15 -120.49 108.76 1.5558 +IC C3 C1 *C2 HS 1.5558 108.76 -117.31 108.75 1.118 +IC C1 C2 O21 C21 1.5129 107.15 76.22 114.17 1.3245 +IC C2 O21 C21 C22 1.4362 114.17 -167.18 108.82 1.5297 +IC C22 O21 *C21 O22 1.5297 108.82 179.57 126.74 1.2182 +IC O21 C21 C22 C23 1.3245 108.82 -105.57 113.23 1.5485 +IC C23 C21 *C22 H2R 1.5485 113.23 -121.14 106.89 1.11 +IC H2R C21 *C22 H2S 1.11 106.89 -116.54 108.12 1.1089 +IC C1 C2 C3 O31 1.5129 108.76 -177.11 111.15 1.4483 +IC O31 C2 *C3 HX 1.4483 111.15 -123.13 106.46 1.1158 +IC HX C2 *C3 HY 1.1158 106.46 -115.26 108.52 1.117 +IC C2 C3 O31 C31 1.5558 111.15 -169.42 113.83 1.3301 +IC C3 O31 C31 C32 1.4483 113.83 -179.09 109.01 1.5527 +IC C32 O31 *C31 O32 1.5527 109.01 -179.05 125.74 1.2141 +IC O31 C31 C32 C33 1.3301 109.01 -179.15 116.85 1.606 +IC C33 C31 *C32 H2X 1.606 116.85 -121.96 105.89 1.1078 +IC H2X C31 *C32 H2Y 1.1078 105.89 -115.56 105.84 1.1076 +IC C21 C22 C23 C24 1.5297 113.23 179.57 111.35 1.5442 +IC C24 C22 *C23 H3R 1.5442 111.35 -120.94 108.83 1.114 +IC H3R C22 *C23 H3S 1.114 108.83 -117.8 109.11 1.1149 +! Acyl Chain 1 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5347 112.69 -179.93 113.30 1.5309 +IC C216 C214 *C215 H15R 1.5309 113.30 -121.70 108.75 1.1140 +IC H15R C214 *C215 H15S 1.1140 108.75 -116.65 108.73 1.1141 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5287 113.01 -179.36 111.84 1.5345 +IC C34 C32 *C33 H3X 1.5345 111.84 -121.48 110.04 1.1135 +IC H3X C32 *C33 H3Y 1.1135 110.04 -117.95 109.39 1.1149 +IC C32 C33 C34 C35 1.5453 111.84 178.35 112.93 1.5350 +IC C35 C33 *C34 H4X 1.5350 112.93 -121.06 108.92 1.1138 +IC H4X C33 *C34 H4Y 1.1138 108.92 -117.32 109.20 1.1130 +IC C33 C34 C35 C36 1.5345 112.93 -179.86 112.46 1.5352 +IC C36 C34 *C35 H5X 1.5352 112.46 -121.45 109.25 1.1129 +IC H5X C34 *C35 H5Y 1.1129 109.25 -117.43 109.01 1.1134 +IC C34 C35 C36 C37 1.5350 112.46 179.21 112.88 1.5352 +IC C37 C35 *C36 H6X 1.5352 112.88 -121.25 109.00 1.1134 +IC H6X C35 *C36 H6Y 1.1134 109.00 -117.27 109.08 1.1131 +IC C35 C36 C37 C38 1.5352 112.88 179.79 112.50 1.5352 +IC C38 C36 *C37 H7X 1.5352 112.50 -121.35 109.17 1.1130 +IC H7X C36 *C37 H7Y 1.1130 109.17 -117.42 109.08 1.1132 +IC C36 C37 C38 C39 1.5352 112.50 179.41 112.91 1.5352 +IC C39 C37 *C38 H8X 1.5352 112.91 -121.30 109.04 1.1133 +IC H8X C37 *C38 H8Y 1.1133 109.04 -117.27 109.05 1.1132 +IC C37 C38 C39 C310 1.5352 112.91 179.74 112.46 1.5353 +IC C310 C38 *C39 H9X 1.5353 112.46 -121.33 109.17 1.1131 +IC H9X C38 *C39 H9Y 1.1131 109.17 -117.42 109.10 1.1132 +IC C38 C39 C310 C311 1.5352 112.46 179.50 112.91 1.5350 +IC C311 C39 *C310 H10X 1.5350 112.91 -121.32 109.05 1.1133 +IC H10X C39 *C310 H10Y 1.1133 109.05 -117.29 109.05 1.1132 +IC C39 C310 C311 C312 1.5353 112.91 179.80 112.52 1.5354 +IC C312 C310 *C311 H11X 1.5354 112.52 -121.32 109.16 1.1131 +IC H11X C310 *C311 H11Y 1.1131 109.16 -117.41 109.11 1.1132 +IC C310 C311 C312 C313 1.5350 112.52 179.66 112.78 1.5349 +IC C313 C311 *C312 H12X 1.5349 112.78 -121.30 109.08 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.08 -117.35 109.09 1.1132 +IC C311 C312 C313 C314 1.5354 112.78 179.95 112.66 1.5353 +IC C314 C312 *C313 H13X 1.5353 112.66 -121.33 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.38 109.07 1.1132 +IC C312 C313 C314 C315 1.5349 112.66 179.95 112.69 1.5341 +IC C315 C313 *C314 H14X 1.5341 112.69 -121.30 109.17 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.17 -117.38 109.15 1.1132 +IC C313 C314 C315 C316 1.5353 112.69 179.98 113.37 1.5312 +IC C316 C314 *C315 H15X 1.5312 113.37 -121.71 108.74 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.74 -116.61 108.74 1.1141 +IC C314 C315 C316 H16X 1.5341 113.37 -59.94 110.51 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.51 119.91 110.52 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.51 -120.06 110.58 1.1112 + +END + +read param card flex append +* PIP related parameters +* +! Parameters have been transferred from two FF +! sugar FF and lipid FF +! +! Important atom def: +! Sugar FF phosphate : PC +! Lipid FF phosphate : PL +! NA FF phosphate : P +! +! phosphate =O , sug (OC2DP), lipid (O2L), NA (ON3) +! phosphate -O , sug (OC30P), lipid (OSLP), NA (ON2) +! phosphate -OH , sug (OC312), lipid (OHL), NA (ON4) +! + +BONDS +!** sugar FF *** +OC30P PL 270.0 1.675 ! +OC2DP PL 580.0 1.525 ! +OC312 PL 237.0 1.61 ! + +ANGLES +!** sugar FF *** +OC30P PL OC2DP 98.9 111.6 +OC2DP PL OC2DP 120.0 120.0 +OC30P PL OC30P 80.0 104.3 ! ON2 P ON2 !DMP, ADM Jr. +CC3161 OC30P PL 20.0 120.0 35.0 2.33 !CTL2 OSLP PL ! phosphate, PIP +!*** lipid FF *** +OC30P PL O2L 98.9 111.6 ! OSLP PL O2L ! phosphate +OC30P PL OSLP 80.0 104.3 ! OSLP PL OSLP ! phosphate + + +DIHEDRALS +!** sugar FF *** +CC3161 CC3161 OC30P PL 0.02 3 180.0 +CC3161 OC30P PL OC2DP 0.33 3 0.0 +HCA1 CC3161 OC30P PL 0.284 3 0.0 ! dmp,eps, H-C3'-O3'-P || from the par_all27_na.prm +CC3161 OC30P PL OSLP 1.45 2 0.0 !CC311D OC30P PC OC312 +CC3161 OC30P PL O2L 0.33 3 0.0 !CC311D OC30P PC OC2DP + +!*** lipid FF *** +OC30P PL OSLP CTL2 1.20 1 180.00 !OSLP PL OSLP CTL2 ! phosphate, new NA, 4/98, adm jr. +OC30P PL OSLP CTL2 0.10 2 180.00 ! +OC30P PL OSLP CTL2 0.10 3 180.00 ! + +IMPROPER + +END + +RETURN + diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_list.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_list.str new file mode 100644 index 00000000..acf89799 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_list.str @@ -0,0 +1,66 @@ +* stream file to read all the rtf, para and lipid stream files +* + +! read water +stream @water + +! lipid +! read the topology +open unit 9 read form name @a +read rtf card append unit 9 + +! read the parameters +open unit 9 read form name @b +read para card append flex unit 9 + +!protein +! append the topology +open unit 9 read form name @c +read rtf card append unit 9 + +! append the parameters +open unit 9 read form name @d +read para card flex append unit 9 + +! nucleic acid +! append the topology +open unit 9 read form name @e +read rtf card append unit 9 + +! append the parameters +open unit 9 read form name @f +read para card flex append unit 9 + +! carbohydrate +! append the topology +open unit 9 read form name @g +read rtf card append unit 9 + +! append the parameters +open unit 9 read form name @h +read para card flex append unit 9 + +! CGenFF +! append the topology +open unit 9 read form name @i +read rtf card append unit 9 + +! append the parameters +open unit 9 read form name @j +read para card flex append unit 9 + +stream @toppar/stream/lipid/toppar_all36_lipid_bacterial.str +stream @toppar/stream/lipid/toppar_all36_lipid_miscellaneous.str +stream @toppar/stream/lipid/toppar_all36_lipid_cholesterol.str +stream @toppar/stream/lipid/toppar_all36_lipid_detergent.str +stream @toppar/stream/lipid/toppar_all36_lipid_yeast.str +stream @toppar/stream/lipid/toppar_all36_lipid_sphingo.str +stream @toppar/stream/lipid/toppar_all36_lipid_inositol.str +stream @toppar/stream/lipid/toppar_all36_lipid_cardiolipin.str +stream @toppar/stream/lipid/toppar_all36_lipid_glycolipid.str +stream @toppar/stream/lipid/toppar_all36_lipid_model.str +stream @toppar/stream/lipid/toppar_all36_lipid_llo.str +stream @toppar/stream/lipid/toppar_all36_lipid_prot.str + +return + diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_llo.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_llo.str new file mode 100644 index 00000000..58393323 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_llo.str @@ -0,0 +1,2148 @@ +* Topology and parameters for lipid tail linkers to cysteine and glycine, +* for example, palmitoylation, maristoylation, fernasylation, geranylation +* + +read rtf card append +* Topology for LLO related compounds +* +36 1 + +RESI ABAC 0.000 ! 2,4-diacetamido-2,4,6-trideoxyglucose + ! (beta bacillosamine or Bac) +GROU ! +ATOM C1 CC3162 0.340 ! H63 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! HT41 ON4 C4 | C1 +ATOM C2 CC3161 0.070 ! | || / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HT41-CT4--CN4--N4 \| | / O1-HO1 +ATOM N NC2D1 -0.470 ! | | C3---C2 +ATOM HN HCP1 0.310 ! HT43 HN4 | | +GROU ! H3 N-HN +ATOM C CC2O1 0.510 ! / +ATOM O OC2D1 -0.510 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.070 ! +ATOM H4 HCA1 0.090 ! +ATOM N4 NC2D1 -0.470 ! +ATOM HN4 HCP1 0.310 ! +GROU ! +ATOM CN4 CC2O1 0.510 ! +ATOM ON4 OC2D1 -0.510 ! +GROU ! +ATOM CT4 CC331 -0.270 ! +ATOM HT41 HCA3 0.090 ! +ATOM HT42 HCA3 0.090 ! +ATOM HT43 HCA3 0.090 ! +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 N4 N4 HN4 C4 C5 +BOND C5 H5 C5 C6 C5 O5 +BOND C6 H61 C6 H62 C6 H63 +BOND N C C O C CT +BOND CT HT1 CT HT2 CT HT3 +BOND N4 CN4 CN4 ON4 CN4 CT4 +BOND CT4 HT41 CT4 HT42 CT4 HT43 +IMPR C CT N O +IMPR N C C2 HN +IMPR CN4 CT4 N4 ON4 +IMPR N4 CN4 C4 HN4 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.0000 120.00 -120.00 120.00 1.0000 +IC O1 O5 *C1 C2 1.3949 110.13 120.34 109.32 1.5156 +IC N C3 *C2 H2 1.4607 113.70 -119.19 107.08 1.1227 +IC N C1 *C2 C3 1.4607 112.62 -127.32 109.20 1.5149 +IC O3 C4 *C3 H3 1.4246 110.45 117.60 108.58 1.1171 +IC O3 C2 *C3 C4 1.4246 111.13 123.24 110.86 1.5168 +IC N4 C5 *C4 H4 1.4204 110.47 -117.94 108.07 1.1172 +IC N4 C3 *C4 C5 1.4204 110.88 -123.03 110.79 1.5206 +IC C6 O5 *C5 H5 1.5134 108.06 117.57 109.86 1.1171 +IC C6 C4 *C5 O5 1.5134 113.35 119.99 108.45 1.4386 +IC H63 H62 *C6 H61 1.4280 109.26 -117.58 107.87 1.1141 +IC H63 C5 *C6 H62 1.4280 111.18 -121.26 110.14 1.1132 +IC O5 C1 C2 C3 1.4220 109.32 58.90 109.20 1.5149 +IC C1 C2 C3 C4 1.5156 109.20 -52.68 110.86 1.5168 +IC C2 C3 C4 C5 1.5149 110.86 52.13 110.79 1.5206 +IC C3 C4 C5 O5 1.5168 110.79 -56.10 108.45 1.4386 +IC C4 C5 O5 C1 1.5206 108.45 64.09 111.47 1.4220 +IC C5 O5 C1 C2 1.4386 111.47 -66.18 109.32 1.5156 +IC C4 C5 C6 H63 1.5206 113.35 -179.21 111.18 1.4280 +IC O5 C1 O1 HO1 1.4220 110.13 53.79 107.03 0.9601 +IC C1 C2 N HN 1.5156 112.62 -21.73 117.18 0.9940 +IC C2 C3 O3 HO3 1.5149 111.13 0.20 109.43 0.9762 +IC C3 C4 N4 HN4 1.5156 112.62 -21.73 117.18 0.9940 +IC C N C2 C3 1.3365 123.04 -84.98 113.70 1.5149 +IC C C2 *N HN 1.3365 123.04 -171.85 117.18 0.9940 +IC CT C N C2 1.4798 117.02 -173.18 123.04 1.4607 +IC N CT *C O 1.3365 117.02 178.97 121.63 1.2235 +IC O C CT HT1 1.2235 121.63 116.39 110.28 1.1105 +IC O C CT HT2 1.2235 121.63 -3.06 109.29 1.1121 +IC O C CT HT3 1.2235 121.63 -122.59 110.33 1.1105 +IC CN4 N4 C4 C5 1.3365 123.04 -84.98 113.70 1.5149 +IC CN4 C2 *N4 HN4 1.3365 123.04 -171.85 117.18 0.9940 +IC CT4 CN4 N4 C4 1.4798 117.02 -173.18 123.04 1.4607 +IC N4 CT4 *CN4 ON4 1.3365 117.02 178.97 121.63 1.2235 +IC ON4 CN4 CT4 HT41 1.2235 121.63 116.39 110.28 1.1105 +IC ON4 CN4 CT4 HT42 1.2235 121.63 -3.06 109.29 1.1121 +IC ON4 CN4 CT4 HT43 1.2235 121.63 -122.59 110.33 1.1105 +PATC FIRS NONE LAST NONE + +RESI BBAC 0.000 ! 2,4-diacetamido-2,4,6-trideoxyglucose + ! (beta bacillosamine or Bac) +GROU ! +ATOM C1 CC3162 0.340 ! H63 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! HT41 ON4 C4 | C1 +ATOM C2 CC3161 0.070 ! | || / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HT41-CT4--CN4--N4 \| | / H1 +ATOM N NC2D1 -0.470 ! | | C3---C2 +ATOM HN HCP1 0.310 ! HT43 HN4 | | +GROU ! H3 N-HN +ATOM C CC2O1 0.510 ! / +ATOM O OC2D1 -0.510 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.070 ! +ATOM H4 HCA1 0.090 ! +ATOM N4 NC2D1 -0.470 ! +ATOM HN4 HCP1 0.310 ! +GROU ! +ATOM CN4 CC2O1 0.510 ! +ATOM ON4 OC2D1 -0.510 ! +GROU ! +ATOM CT4 CC331 -0.270 ! +ATOM HT41 HCA3 0.090 ! +ATOM HT42 HCA3 0.090 ! +ATOM HT43 HCA3 0.090 ! +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 N4 N4 HN4 C4 C5 +BOND C5 H5 C5 C6 C5 O5 +BOND C6 H61 C6 H62 C6 H63 +BOND N C C O C CT +BOND CT HT1 CT HT2 CT HT3 +BOND N4 CN4 CN4 ON4 CN4 CT4 +BOND CT4 HT41 CT4 HT42 CT4 HT43 +IMPR C CT N O +IMPR N C C2 HN +IMPR CN4 CT4 N4 ON4 +IMPR N4 CN4 C4 HN4 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 -120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 -118.92 111.32 1.5218 +IC N C3 *C2 H2 1.4607 113.70 -119.19 107.08 1.1227 +IC N C1 *C2 C3 1.4607 112.62 -127.32 109.20 1.5149 +IC O3 C4 *C3 H3 1.4246 110.45 117.60 108.58 1.1171 +IC O3 C2 *C3 C4 1.4246 111.13 123.24 110.86 1.5168 +IC N4 C5 *C4 H4 1.4204 110.47 -117.94 108.07 1.1172 +IC N4 C3 *C4 C5 1.4204 110.88 -123.03 110.79 1.5206 +IC C6 O5 *C5 H5 1.5134 108.06 117.57 109.86 1.1171 +IC C6 C4 *C5 O5 1.5134 113.35 119.99 108.45 1.4386 +IC H63 H62 *C6 H61 1.4280 109.26 -117.58 107.87 1.1141 +IC H63 C5 *C6 H62 1.4280 111.18 -121.26 110.14 1.1132 +IC O5 C1 C2 C3 1.4220 109.32 58.90 109.20 1.5149 +IC C1 C2 C3 C4 1.5156 109.20 -52.68 110.86 1.5168 +IC C2 C3 C4 C5 1.5149 110.86 52.13 110.79 1.5206 +IC C3 C4 C5 O5 1.5168 110.79 -56.10 108.45 1.4386 +IC C4 C5 O5 C1 1.5206 108.45 64.09 111.47 1.4220 +IC C5 O5 C1 C2 1.4386 111.47 -66.18 109.32 1.5156 +IC C4 C5 C6 H63 1.5206 113.35 -179.21 111.18 1.4280 +IC O5 C1 O1 HO1 1.4220 110.13 53.79 107.03 0.9601 +IC C1 C2 N HN 1.5156 112.62 -21.73 117.18 0.9940 +IC C2 C3 O3 HO3 1.5149 111.13 0.20 109.43 0.9762 +IC C3 C4 N4 HN4 1.5156 112.62 -21.73 117.18 0.9940 +IC C N C2 C3 1.3365 123.04 -84.98 113.70 1.5149 +IC C C2 *N HN 1.3365 123.04 -171.85 117.18 0.9940 +IC CT C N C2 1.4798 117.02 -173.18 123.04 1.4607 +IC N CT *C O 1.3365 117.02 178.97 121.63 1.2235 +IC O C CT HT1 1.2235 121.63 116.39 110.28 1.1105 +IC O C CT HT2 1.2235 121.63 -3.06 109.29 1.1121 +IC O C CT HT3 1.2235 121.63 -122.59 110.33 1.1105 +IC CN4 N4 C4 C5 1.3365 123.04 -84.98 113.70 1.5149 +IC CN4 C2 *N4 HN4 1.3365 123.04 -171.85 117.18 0.9940 +IC CT4 CN4 N4 C4 1.4798 117.02 -173.18 123.04 1.4607 +IC N4 CT4 *CN4 ON4 1.3365 117.02 178.97 121.63 1.2235 +IC ON4 CN4 CT4 HT41 1.2235 121.63 116.39 110.28 1.1105 +IC ON4 CN4 CT4 HT42 1.2235 121.63 -3.06 109.29 1.1121 +IC ON4 CN4 CT4 HT43 1.2235 121.63 -122.59 110.33 1.1105 +PATC FIRS NONE LAST NONE + +RESI DL16PP -2.00 ! [name] +GROUP +ATOM P2 PG1 1.34 ! HO22 +ATOM O22 OG311 -0.71 ! | +ATOM HO22 HGP1 0.44 ! O22 !! based on PPI2 +ATOM O23 OG2P1 -0.86 ! | +ATOM O24 OG2P1 -0.86 ! O23==P2==O24 (-) + ! | +ATOM P1 PG1 1.46 ! O12 +ATOM O12 OG304 -0.63 ! | +ATOM O13 OG2P1 -0.83 ! O13==P1==O14 (-) +ATOM O14 OG2P1 -0.83 ! | +ATOM O11 OG303 -0.62 ! O11 + ! | +ATOM C1 CG321 -0.08 ! H11--C1--H12 +ATOM H11 HGA2 0.09 ! | +ATOM H12 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C2 CG321 -0.18 ! H21--C2--H12 +ATOM H21 HGA2 0.09 ! ! +ATOM H22 HGA2 0.09 ! | H41 +GROUP 0.00 ! ! | +ATOM C3 CG311 -0.09 ! H3--C3---C4--H42 +ATOM H3 HGA1 0.09 ! | | +GROUP 0.00 ! | H43 +ATOM C4 CG331 -0.27 ! | +ATOM H41 HGA3 0.09 ! | +ATOM H42 HGA3 0.09 ! | +ATOM H43 HGA3 0.09 ! | +GROUP 0.00 ! | +ATOM C5 CG321 -0.18 ! H51--C5--H52 +ATOM H51 HGA2 0.09 ! | +ATOM H52 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C1A CG321 -0.18 ! H1A1--C1A--H1A2 +ATOM H1A1 HGA2 0.09 ! | +ATOM H1A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C1B CG2D1 -0.15 ! C1B--H1B (cis) +ATOM H1B HGA4 0.15 ! || +GROUP 0.00 ! || H1D1 +ATOM C1C CG2D1 0.00 ! || | +GROUP 0.00 ! C1C--C1D--H1D2 +ATOM C1D CG331 -0.27 ! | | +ATOM H1D1 HGA3 0.09 ! | H1D3 +ATOM H1D2 HGA3 0.09 ! ! +ATOM H1D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C1E CG321 -0.18 ! H1E1--C1E--H1E2 +ATOM H1E1 HGA2 0.09 ! ! +ATOM H1E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C2A CG321 -0.18 ! H2A1--C2A--H2A2 +ATOM H2A1 HGA2 0.09 ! | +ATOM H2A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C2B CG2D1 -0.15 ! C2B--H2B (cis) +ATOM H2B HGA4 0.15 ! || +GROUP 0.00 ! || H2D1 +ATOM C2C CG2D1 0.00 ! || | +GROUP 0.00 ! C2C--C2D--H2D2 +ATOM C2D CG331 -0.27 ! | | +ATOM H2D1 HGA3 0.09 ! | H2D3 +ATOM H2D2 HGA3 0.09 ! ! +ATOM H2D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C2E CG321 -0.18 ! H2E1--C2E--H2E2 +ATOM H2E1 HGA2 0.09 ! ! +ATOM H2E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C3A CG321 -0.18 ! H3A1--C3A--H3A2 +ATOM H3A1 HGA2 0.09 ! | +ATOM H3A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C3B CG2D1 -0.15 ! C3B--H3B (cis) +ATOM H3B HGA4 0.15 ! || +GROUP 0.00 ! || H3D1 +ATOM C3C CG2D1 0.00 ! || | +GROUP 0.00 ! C3C--C3D--H3D2 +ATOM C3D CG331 -0.27 ! | | +ATOM H3D1 HGA3 0.09 ! | H3D3 +ATOM H3D2 HGA3 0.09 ! ! +ATOM H3D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C3E CG321 -0.18 ! H3E1--C3E--H3E2 +ATOM H3E1 HGA2 0.09 ! ! +ATOM H3E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C4A CG321 -0.18 ! H4A1--C4A--H4A2 +ATOM H4A1 HGA2 0.09 ! | +ATOM H4A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C4B CG2D1 -0.15 ! C4B--H4B (cis) +ATOM H4B HGA4 0.15 ! || +GROUP 0.00 ! || H4D1 +ATOM C4C CG2D1 0.00 ! || | +GROUP 0.00 ! C4C--C4D--H4D2 +ATOM C4D CG331 -0.27 ! | | +ATOM H4D1 HGA3 0.09 ! | H4D3 +ATOM H4D2 HGA3 0.09 ! ! +ATOM H4D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C4E CG321 -0.18 ! H4E1--C4E--H4E2 +ATOM H4E1 HGA2 0.09 ! ! +ATOM H4E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C5A CG321 -0.18 ! H5A1--C5A--H5A2 +ATOM H5A1 HGA2 0.09 ! | +ATOM H5A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C5B CG2D1 -0.15 ! C5B--H5B (cis) +ATOM H5B HGA4 0.15 ! || +GROUP 0.00 ! || H5D1 +ATOM C5C CG2D1 0.00 ! || | +GROUP 0.00 ! C5C--C5D--H5D2 +ATOM C5D CG331 -0.27 ! | | +ATOM H5D1 HGA3 0.09 ! | H5D3 +ATOM H5D2 HGA3 0.09 ! ! +ATOM H5D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C5E CG321 -0.18 ! H5E1--C5E--H5E2 +ATOM H5E1 HGA2 0.09 ! ! +ATOM H5E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C6A CG321 -0.18 ! H6A1--C6A--H6A2 +ATOM H6A1 HGA2 0.09 ! | +ATOM H6A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C6B CG2D1 -0.15 ! C6B--H6B (cis) +ATOM H6B HGA4 0.15 ! || +GROUP 0.00 ! || H6D1 +ATOM C6C CG2D1 0.00 ! || | +GROUP 0.00 ! C6C--C6D--H6D2 +ATOM C6D CG331 -0.27 ! | | +ATOM H6D1 HGA3 0.09 ! | H6D3 +ATOM H6D2 HGA3 0.09 ! ! +ATOM H6D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C6E CG321 -0.18 ! H6E1-C6E--H6E2 +ATOM H6E1 HGA2 0.09 ! ! +ATOM H6E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C7A CG321 -0.18 ! H7A1--C7A--H7A2 +ATOM H7A1 HGA2 0.09 ! | +ATOM H7A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C7B CG2D1 -0.15 ! C7B--H7B (cis) +ATOM H7B HGA4 0.15 ! || +GROUP 0.00 ! || H7D1 +ATOM C7C CG2D1 0.00 ! || | +GROUP 0.00 ! C7C--C7D--H7D2 +ATOM C7D CG331 -0.27 ! | | +ATOM H7D1 HGA3 0.09 ! | H7D3 +ATOM H7D2 HGA3 0.09 ! ! +ATOM H7D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C7E CG321 -0.18 ! H7E1-C7E--H7E2 +ATOM H7E1 HGA2 0.09 ! ! +ATOM H7E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C8A CG321 -0.18 ! H8A1--C8A--H8A2 +ATOM H8A1 HGA2 0.09 ! | +ATOM H8A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C8B CG2D1 -0.15 ! C8B--H8B (cis) +ATOM H8B HGA4 0.15 ! || +GROUP 0.00 ! || H8D1 +ATOM C8C CG2D1 0.00 ! || | +GROUP 0.00 ! C8C--C8D--H8D2 +ATOM C8D CG331 -0.27 ! | | +ATOM H8D1 HGA3 0.09 ! | H8D3 +ATOM H8D2 HGA3 0.09 ! ! +ATOM H8D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C8E CG321 -0.18 ! H8E1-C8E--H8E2 +ATOM H8E1 HGA2 0.09 ! ! +ATOM H8E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C9A CG321 -0.18 ! H9A1--C9A--H9A2 +ATOM H9A1 HGA2 0.09 ! | +ATOM H9A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C9B CG2D1 -0.15 ! C9B--H9B (cis) +ATOM H9B HGA4 0.15 ! || +GROUP 0.00 ! || H9D1 +ATOM C9C CG2D1 0.00 ! || | +GROUP 0.00 ! C9C--C9D--H9D2 +ATOM C9D CG331 -0.27 ! | | +ATOM H9D1 HGA3 0.09 ! | H9D3 +ATOM H9D2 HGA3 0.09 ! ! +ATOM H9D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C9E CG321 -0.18 ! H9E1-C9E--H9E2 +ATOM H9E1 HGA2 0.09 ! ! +ATOM H9E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C10A CG321 -0.18 ! H10A1--C10A--H10A2 +ATOM H10A1 HGA2 0.09 ! | +ATOM H10A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C10B CG2D1 -0.15 ! C10B--H110B (cis) +ATOM H10B HGA4 0.15 ! || +GROUP 0.00 ! || H10D1 +ATOM C10C CG2D1 0.00 ! || | +GROUP 0.00 ! C10C-C10D--H10D2 +ATOM C10D CG331 -0.27 ! | | +ATOM H10D1 HGA3 0.09 ! | H10D3 +ATOM H10D2 HGA3 0.09 ! ! +ATOM H10D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C10E CG321 -0.18 ! H10E1-C10E--H10E2 +ATOM H10E1 HGA2 0.09 ! ! +ATOM H10E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C11A CG321 -0.18 ! H11A1--C11A--H11A2 +ATOM H11A1 HGA2 0.09 ! | +ATOM H11A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C11B CG2D1 -0.15 ! C11B--H11B (cis) +ATOM H11B HGA4 0.15 ! || +GROUP 0.00 ! || H11D1 +ATOM C11C CG2D1 0.00 ! || | +GROUP 0.00 ! C11C-C11D--H11D2 +ATOM C11D CG331 -0.27 ! | | +ATOM H11D1 HGA3 0.09 ! | H11D3 +ATOM H11D2 HGA3 0.09 ! ! +ATOM H11D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C11E CG321 -0.18 ! H11E1-C11E--H11E2 +ATOM H11E1 HGA2 0.09 ! ! +ATOM H11E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C12A CG321 -0.18 ! H12A1--C12A--H12A2 +ATOM H12A1 HGA2 0.09 ! | +ATOM H12A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C12B CG2D1 -0.15 ! C12B--H12B (cis) +ATOM H12B HGA4 0.15 ! || +GROUP 0.00 ! || H12D1 +ATOM C12C CG2D1 0.00 ! || | +GROUP 0.00 ! C12C-C12D--H12D2 +ATOM C12D CG331 -0.27 ! | | +ATOM H12D1 HGA3 0.09 ! | H12D3 +ATOM H12D2 HGA3 0.09 ! ! +ATOM H12D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C12E CG321 -0.18 ! H1E12-C12E--H12E2 +ATOM H12E1 HGA2 0.09 ! ! +ATOM H12E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C13A CG321 -0.18 ! H13A1--C13A--H13A2 +ATOM H13A1 HGA2 0.09 ! | +ATOM H13A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C13B CG2D1 -0.15 ! C13B--H13B (trans) +ATOM H13B HGA4 0.15 ! || +GROUP 0.00 ! || H13D1 +ATOM C13C CG2D1 0.00 ! || | +GROUP 0.00 ! C13C-C13D--H13D2 +ATOM C13D CG331 -0.27 ! | | +ATOM H13D1 HGA3 0.09 ! | H13D3 +ATOM H13D2 HGA3 0.09 ! ! +ATOM H13D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C13E CG321 -0.18 ! H13E1-C13E--H13E2 +ATOM H13E1 HGA2 0.09 ! ! +ATOM H13E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C14A CG321 -0.18 ! H14A1--C14A--H14A2 +ATOM H14A1 HGA2 0.09 ! | +ATOM H14A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C14B CG2D1 -0.15 ! C14B--H14B (trans) +ATOM H14B HGA4 0.15 ! || +GROUP 0.00 ! || H14D1 +ATOM C14C CG2D1 0.00 ! || | +GROUP 0.00 ! C14C-C14D--H14D2 +ATOM C14D CG331 -0.27 ! | | +ATOM H14D1 HGA3 0.09 ! | H14D3 +ATOM H14D2 HGA3 0.09 ! ! +ATOM H14D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C14E CG321 -0.18 ! H14E1-C14E--H14E2 +ATOM H14E1 HGA2 0.09 ! ! +ATOM H14E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C15A CG321 -0.18 ! H15A1--C15A--H15A2 +ATOM H15A1 HGA2 0.09 ! | +ATOM H15A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C15B CG2D1 -0.15 ! C15B--H15B +ATOM H15B HGA4 0.15 ! || +GROUP 0.00 ! || H15D1 +ATOM C15C CG2D1 0.00 ! || | +GROUP 0.00 ! C15C-C15D--H15D2 +ATOM C15D CG331 -0.27 ! | | +ATOM H15D1 HGA3 0.09 ! | H15D3 +ATOM H15D2 HGA3 0.09 ! ! +ATOM H15D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C15E CG331 -0.27 ! H15E1-C15E--H15E2 +ATOM H15E1 HGA3 0.09 ! ! +ATOM H15E2 HGA3 0.09 ! H15E3 +ATOM H15E3 HGA3 0.09 ! + +BOND O22 HO22 P2 O22 P2 O23 P2 O24 P2 O12 ! Phosphate group 2 +BOND P1 O12 P1 O13 P1 O14 P1 O11 O11 C1 ! Phosphate group 1 +BOND C1 C2 C2 C3 C3 C4 C3 C5 ! Alpha isoprene backbone carbons +BOND C1 H11 C1 H12 ! C1 hydrogens +BOND C2 H21 C2 H22 ! C2 hydrogens +BOND C3 H3 ! C3 hydrogen +BOND C4 H41 C4 H42 C4 H43 ! C4 hydrogens +BOND C5 H51 C5 H52 ! C5 hydrogens +BOND C5 C1A ! isoprene linking bond +BOND C1A C1B C1C C1D C1C C1E ! cis isoprene backbone carbons +DOUBLE C1B C1C ! cis double bond +BOND C1A H1A1 C1A H1A2 ! C1A hydrogens +BOND C1B H1B ! C1B hydrogen +BOND C1D H1D1 C1D H1D2 C1D H1D3 ! C1D hydrogens +BOND C1E H1E1 C1E H1E2 ! C1E hydrogens +BOND C1E C2A ! isoprene linking bond +BOND C2A C2B C2C C2D C2C C2E ! cis isoprene backbone carbons +DOUBLE C2B C2C ! cis double bond +BOND C2A H2A1 C2A H2A2 ! C2A hydrogens +BOND C2B H2B ! C2B hydrogen +BOND C2D H2D1 C2D H2D2 C2D H2D3 ! C2D hydrogens +BOND C2E H2E1 C2E H2E2 ! C2E hydrogens +BOND C2E C3A ! isoprene linking bond +BOND C3A C3B C3C C3D C3C C3E ! cis isoprene backbone carbons +DOUBLE C3B C3C ! cis double bond +BOND C3A H3A1 C3A H3A2 ! C3A hydrogens +BOND C3B H3B ! C3B hydrogen +BOND C3D H3D1 C3D H3D2 C3D H3D3 ! C3D hydrogens +BOND C3E H3E1 C3E H3E2 ! C3E hydrogens +BOND C3E C4A ! isoprene linking bond +BOND C4A C4B C4C C4D C4C C4E ! cis isoprene backbone carbons +DOUBLE C4B C4C ! cis double bond +BOND C4A H4A1 C4A H4A2 ! C4A hydrogens +BOND C4B H4B ! C4B hydrogen +BOND C4D H4D1 C4D H4D2 C4D H4D3 ! C4D hydrogens +BOND C4E H4E1 C4E H4E2 ! C4E hydrogens +BOND C4E C5A ! isoprene linking bond +BOND C5A C5B C5C C5D C5C C5E ! cis isoprene backbone carbons +DOUBLE C5B C5C ! cis double bond +BOND C5A H5A1 C5A H5A2 ! C5A hydrogens +BOND C5B H5B ! C5B hydrogen +BOND C5D H5D1 C5D H5D2 C5D H5D3 ! C5D hydrogens +BOND C5E H5E1 C5E H5E2 ! C5E hydrogens +BOND C5E C6A ! isoprene linking bond +BOND C6A C6B C6C C6D C6C C6E ! cis isoprene backbone carbons +DOUBLE C6B C6C ! cis double bond +BOND C6A H6A1 C6A H6A2 ! C6A hydrogens +BOND C6B H6B ! C6B hydrogen +BOND C6D H6D1 C6D H6D2 C6D H6D3 ! C6D hydrogens +BOND C6E H6E1 C6E H6E2 ! C6E hydrogens +BOND C6E C7A ! isoprene linking bond +BOND C7A C7B C7C C7D C7C C7E ! cis isoprene backbone carbons +DOUBLE C7B C7C ! cis double bond +BOND C7A H7A1 C7A H7A2 ! C7A hydrogens +BOND C7B H7B ! C7B hydrogen +BOND C7D H7D1 C7D H7D2 C7D H7D3 ! C7D hydrogens +BOND C7E H7E1 C7E H7E2 ! C7E hydrogens +BOND C7E C8A ! isoprene linking bond +BOND C8A C8B C8C C8D C8C C8E ! cis isoprene backbone carbons +DOUBLE C8B C8C ! cis double bond +BOND C8A H8A1 C8A H8A2 ! C8A hydrogens +BOND C8B H8B ! C8B hydrogen +BOND C8D H8D1 C8D H8D2 C8D H8D3 ! C8D hydrogens +BOND C8E H8E1 C8E H8E2 ! C8E hydrogens +BOND C8E C9A ! isoprene linking bond +BOND C9A C9B C9C C9D C9C C9E ! cis isoprene backbone carbons +DOUBLE C9B C9C ! cis double bond +BOND C9A H9A1 C9A H9A2 ! C9A hydrogens +BOND C9B H9B ! C9B hydrogen +BOND C9D H9D1 C9D H9D2 C9D H9D3 ! C9D hydrogens +BOND C9E H9E1 C9E H9E2 ! C9E hydrogens +BOND C9E C10A ! isoprene linking bond +BOND C10A C10B C10C C10D C10C C10E ! cis isoprene backbone carbons +DOUBLE C10B C10C ! cis double bond +BOND C10A H10A1 C10A H10A2 ! C10A hydrogens +BOND C10B H10B ! C10B hydrogen +BOND C10D H10D1 C10D H10D2 C10D H10D3 ! C10D hydrogens +BOND C10E H10E1 C10E H10E2 ! C10E hydrogens +BOND C10E C11A ! isoprene linking bond +BOND C11A C11B C11C C11D C11C C11E ! cis isoprene backbone carbons +DOUBLE C11B C11C ! cis double bond +BOND C11A H11A1 C11A H11A2 ! C11A hydrogens +BOND C11B H11B ! C11B hydrogen +BOND C11D H11D1 C11D H11D2 C11D H11D3 ! C11D hydrogens +BOND C11E H11E1 C11E H11E2 ! C11E hydrogens +BOND C11E C12A ! isoprene linking bond +BOND C12A C12B C12C C12D C12C C12E ! cis isoprene backbone carbons +DOUBLE C12B C12C ! cis double bond +BOND C12A H12A1 C12A H12A2 ! C12A hydrogens +BOND C12B H12B ! C12B hydrogen +BOND C12D H12D1 C12D H12D2 C12D H12D3 ! C12D hydrogens +BOND C12E H12E1 C12E H12E2 ! C12E hydrogens +BOND C12E C13A ! isoprene linking bond +BOND C13A C13B C13C C13D C13C C13E ! cis isoprene backbone carbons +DOUBLE C13B C13C ! cis double bond +BOND C13A H13A1 C13A H13A2 ! C13A hydrogens +BOND C13B H13B ! C13B hydrogen +BOND C13D H13D1 C13D H13D2 C13D H13D3 ! C13D hydrogens +BOND C13E H13E1 C13E H13E2 ! C13E hydrogens +BOND C13E C14A ! isoprene linking bond +BOND C14A C14B C14C C14D C14C C14E ! cis isoprene backbone carbons +DOUBLE C14B C14C ! cis double bond +BOND C14A H14A1 C14A H14A2 ! C14A hydrogens +BOND C14B H14B ! C14B hydrogen +BOND C14D H14D1 C14D H14D2 C14D H14D3 ! C14D hydrogens +BOND C14E H14E1 C14E H14E2 ! C14E hydrogens +BOND C14E C15A ! isoprene linking bond +BOND C15A C15B C15C C15D C15C C15E ! cis isoprene backbone carbons +DOUBLE C15B C15C ! cis double bond +BOND C15A H15A1 C15A H15A2 ! C15A hydrogens +BOND C15B H15B ! C15B hydrogen +BOND C15D H15D1 C15D H15D2 C15D H15D3 ! C15D hydrogens +BOND C15E H15E1 C15E H15E2 C15E H15E3 ! C15E hydrogens +IC O22 O12 *P2 O23 1.6100 111.00 120.00 111.60 1.5100 +IC O22 O12 *P2 O24 1.6100 111.00 -120.00 111.60 1.5100 +IC O12 P2 O22 HO22 1.6750 111.00 180.00 115.00 0.9600 +IC O22 P2 O12 P1 1.6100 111.00 180.00 143.00 1.6750 +IC P2 O12 P1 O11 1.6750 143.00 180.00 105.00 1.6500 +IC O11 O12 *P1 O13 1.6500 105.00 120.00 111.60 1.5100 +IC O11 O12 *P1 O14 1.5100 111.60 -120.00 111.60 1.5100 +IC O12 P1 O11 C1 1.6750 105.00 180.00 120.00 1.4400 +IC P1 O11 C1 C2 1.6500 120.00 180.00 110.10 1.5300 +IC C2 O11 *C1 H11 1.5300 110.10 120.00 109.50 1.1110 +IC C2 O11 *C1 H12 1.5300 110.10 -120.00 109.50 1.1110 +IC O11 C1 C2 C3 1.4400 110.10 180.00 113.50 1.5380 +IC C3 C1 *C2 H21 1.5380 113.50 120.00 110.10 1.1110 +IC C3 C1 *C2 H22 1.5380 113.50 -120.00 110.10 1.1110 +IC C1 C2 C3 C5 1.5280 113.50 180.00 113.50 1.5380 +IC C5 C2 *C3 C4 1.5380 113.50 120.00 114.00 1.5380 +IC C5 C2 *C3 H3 1.5380 114.00 -120.00 110.10 1.1110 +IC C2 C3 C4 H41 1.5380 114.00 180.00 110.10 1.1110 +IC H41 C3 *C4 H42 1.1110 110.10 120.00 110.10 1.1110 +IC H41 C3 *C4 H43 1.1110 110.10 -120.00 110.10 1.1110 +IC C2 C3 C5 C1A 1.5380 113.50 180.00 113.50 1.5300 +IC C1A C3 *C5 H51 1.5300 113.50 120.00 110.10 1.1110 +IC C1A C3 *C5 H52 1.1110 110.10 -120.00 110.10 1.1110 +IC C3 C5 C1A C1B 1.5380 113.50 180.00 112.20 1.5020 +IC C1B C5 *C1A H1A1 1.5020 112.20 120.00 110.10 1.1110 +IC C1B C5 *C1A H1A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C5 C1A C1B C1C 1.5300 112.20 180.00 123.50 1.3400 +IC C1C C1A *C1B H1B 1.3400 123.50 180.00 116.00 1.1000 +IC C1A C1B C1C C1D 1.5020 123.50 180.00 123.50 1.5020 +IC C1E C1B *C1C C1D 1.5020 123.50 180.00 123.50 1.5040 +IC C1B C1C C1D H1D1 1.3400 123.50 180.00 111.50 1.1110 +IC H1D1 C1C *C1D H1D2 1.1110 111.50 120.00 111.50 1.1110 +IC H1D1 C1C *C1D H1D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C1B C1C C1E C2A 1.3400 123.50 180.00 112.20 1.5300 +IC C2A C1C *C1E H1E1 1.5300 112.20 120.00 111.50 1.1110 +IC C2A C1C *C1E H1E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C1C C1E C2A C2B 1.5020 112.20 180.00 112.20 1.5020 +IC C2B C1E *C2A H2A1 1.5020 112.20 120.00 110.10 1.1110 +IC C2B C1E *C2A H2A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C1E C2A C2B C2C 1.5300 112.20 180.00 123.50 1.3400 +IC C2C C2A *C2B H2B 1.3400 123.50 180.00 116.00 1.1000 +IC C2A C2B C2C C2D 1.5020 123.50 180.00 123.50 1.5020 +IC C2E C2B *C2C C2D 1.5020 123.50 180.00 123.50 1.5040 +IC C2B C2C C2D H2D1 1.3400 123.50 180.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D2 1.1110 111.50 120.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C2B C2C C2E C3A 1.3400 123.50 180.00 112.20 1.5300 +IC C3A C2C *C2E H2E1 1.5300 112.20 120.00 111.50 1.1110 +IC C3A C2C *C2E H2E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C2C C2E C3A C3B 1.5020 112.20 180.00 112.20 1.5020 +IC C3B C2E *C3A H3A1 1.5020 112.20 120.00 110.10 1.1110 +IC C3B C2E *C3A H3A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C2E C3A C3B C3C 1.5300 112.20 180.00 123.50 1.3400 +IC C3C C3A *C3B H3B 1.3400 123.50 180.00 116.00 1.1000 +IC C3A C3B C3C C3D 1.5020 123.50 180.00 123.50 1.5020 +IC C3E C3B *C3C C3D 1.5020 123.50 180.00 123.50 1.5040 +IC C3B C3C C3D H3D1 1.3400 123.50 180.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D2 1.1110 111.50 120.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C3B C3C C3E C4A 1.3400 123.50 180.00 112.20 1.5300 +IC C4A C3C *C3E H3E1 1.5300 112.20 120.00 111.50 1.1110 +IC C4A C3C *C3E H3E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C3C C3E C4A C4B 1.5020 112.20 180.00 112.20 1.5020 +IC C4B C3E *C4A H4A1 1.5020 112.20 120.00 110.10 1.1110 +IC C4B C3E *C4A H4A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C3E C4A C4B C4C 1.5300 112.20 180.00 123.50 1.3400 +IC C4C C4A *C4B H4B 1.3400 123.50 180.00 116.00 1.1000 +IC C4A C4B C4C C4D 1.5020 123.50 180.00 123.50 1.5020 +IC C4E C4B *C4C C4D 1.5020 123.50 180.00 123.50 1.5040 +IC C4B C4C C4D H4D1 1.3400 123.50 180.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D2 1.1110 111.50 120.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C4B C4C C4E C5A 1.3400 123.50 180.00 112.20 1.5300 +IC C5A C4C *C4E H4E1 1.5300 112.20 120.00 111.50 1.1110 +IC C5A C4C *C4E H4E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C4C C4E C5A C5B 1.5020 112.20 180.00 112.20 1.5020 +IC C5B C4E *C5A H5A1 1.5020 112.20 120.00 110.10 1.1110 +IC C5B C4E *C5A H5A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C4E C5A C5B C5C 1.5300 112.20 180.00 123.50 1.3400 +IC C5C C5A *C5B H5B 1.3400 123.50 180.00 116.00 1.1000 +IC C5A C5B C5C C5D 1.5020 123.50 180.00 123.50 1.5020 +IC C5E C5B *C5C C5D 1.5020 123.50 180.00 123.50 1.5040 +IC C5B C5C C5D H5D1 1.3400 123.50 180.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D2 1.1110 111.50 120.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C5B C5C C5E C6A 1.3400 123.50 180.00 112.20 1.5300 +IC C6A C5C *C5E H5E1 1.5300 112.20 120.00 111.50 1.1110 +IC C6A C5C *C5E H5E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C5C C5E C6A C6B 1.5020 112.20 180.00 112.20 1.5020 +IC C6B C5E *C6A H6A1 1.5020 112.20 120.00 110.10 1.1110 +IC C6B C5E *C6A H6A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C5E C6A C6B C6C 1.5300 112.20 180.00 123.50 1.3400 +IC C6C C6A *C6B H6B 1.3400 123.50 180.00 116.00 1.1000 +IC C6A C6B C6C C6D 1.5020 123.50 180.00 123.50 1.5020 +IC C6E C6B *C6C C6D 1.5020 123.50 180.00 123.50 1.5040 +IC C6B C6C C6D H6D1 1.3400 123.50 180.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D2 1.1110 111.50 120.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C6B C6C C6E C7A 1.3400 123.50 180.00 112.20 1.5300 +IC C7A C6C *C6E H6E1 1.5300 112.20 120.00 111.50 1.1110 +IC C7A C6C *C6E H6E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C6C C6E C7A C7B 1.5020 112.20 180.00 112.20 1.5020 +IC C7B C6E *C7A H7A1 1.5020 112.20 120.00 110.10 1.1110 +IC C7B C6E *C7A H7A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C6E C7A C7B C7C 1.5300 112.20 180.00 123.50 1.3400 +IC C7C C7A *C7B H7B 1.3400 123.50 180.00 116.00 1.1000 +IC C7A C7B C7C C7D 1.5020 123.50 180.00 123.50 1.5020 +IC C7E C7B *C7C C7D 1.5020 123.50 180.00 123.50 1.5040 +IC C7B C7C C7D H7D1 1.3400 123.50 180.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D2 1.1110 111.50 120.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C7B C7C C7E C8A 1.3400 123.50 180.00 112.20 1.5300 +IC C8A C7C *C7E H7E1 1.5300 112.20 120.00 111.50 1.1110 +IC C8A C7C *C7E H7E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C7C C7E C8A C8B 1.5020 112.20 180.00 112.20 1.5020 +IC C8B C7E *C8A H8A1 1.5020 112.20 120.00 110.10 1.1110 +IC C8B C7E *C8A H8A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C7E C8A C8B C8C 1.5300 112.20 180.00 123.50 1.3400 +IC C8C C8A *C8B H8B 1.3400 123.50 180.00 116.00 1.1000 +IC C8A C8B C8C C8D 1.5020 123.50 180.00 123.50 1.5020 +IC C8E C8B *C8C C8D 1.5020 123.50 180.00 123.50 1.5040 +IC C8B C8C C8D H8D1 1.3400 123.50 180.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D2 1.1110 111.50 120.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C8B C8C C8E C9A 1.3400 123.50 180.00 112.20 1.5300 +IC C9A C8C *C8E H8E1 1.5300 112.20 120.00 111.50 1.1110 +IC C9A C8C *C8E H8E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C8C C8E C9A C9B 1.5020 112.20 180.00 112.20 1.5020 +IC C9B C8E *C9A H9A1 1.5020 112.20 120.00 110.10 1.1110 +IC C9B C8E *C9A H9A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C8E C9A C9B C9C 1.5300 112.20 180.00 123.50 1.3400 +IC C9C C9A *C9B H9B 1.3400 123.50 180.00 116.00 1.1000 +IC C9A C9B C9C C9D 1.5020 123.50 180.00 123.50 1.5020 +IC C9E C9B *C9C C9D 1.5020 123.50 180.00 123.50 1.5040 +IC C9B C9C C9D H9D1 1.3400 123.50 180.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D2 1.1110 111.50 120.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C9B C9C C9E C10A 1.3400 123.50 180.00 112.20 1.5300 +IC C10A C9C *C9E H9E1 1.5300 112.20 120.00 111.50 1.1110 +IC C10A C9C *C9E H9E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C9C C9E C10A C10B 1.5020 112.20 180.00 112.20 1.5020 +IC C10B C9E *C10A H10A1 1.5020 112.20 120.00 110.10 1.1110 +IC C10B C9E *C10A H10A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C9E C10A C10B C10C 1.5300 112.20 180.00 123.50 1.3400 +IC C10C C10A *C10B H10B 1.3400 123.50 180.00 116.00 1.1000 +IC C10A C10B C10C C10D 1.5020 123.50 180.00 123.50 1.5020 +IC C10E C10B *C10C C10D 1.5020 123.50 180.00 123.50 1.5040 +IC C10B C10C C10D H10D1 1.3400 123.50 180.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D2 1.1110 111.50 120.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C10B C10C C10E C11A 1.3400 123.50 180.00 112.20 1.5300 +IC C11A C10C *C10E H10E1 1.5300 112.20 120.00 111.50 1.1110 +IC C11A C10C *C10E H10E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C10C C10E C11A C11B 1.5020 112.20 180.00 112.20 1.5020 +IC C11B C10E *C11A H11A1 1.5020 112.20 120.00 110.10 1.1110 +IC C11B C10E *C11A H11A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C10E C11A C11B C11C 1.5300 112.20 180.00 123.50 1.3400 +IC C11C C11A *C11B H11B 1.3400 123.50 180.00 116.00 1.1000 +IC C11A C11B C11C C11D 1.5020 123.50 180.00 123.50 1.5020 +IC C11E C11B *C11C C11D 1.5020 123.50 180.00 123.50 1.5040 +IC C11B C11C C11D H11D1 1.3400 123.50 180.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D2 1.1110 111.50 120.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C11B C11C C11E C12A 1.3400 123.50 180.00 112.20 1.5300 +IC C12A C11C *C11E H11E1 1.5300 112.20 120.00 111.50 1.1110 +IC C12A C11C *C11E H11E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C11C C11E C12A C12B 1.5020 112.20 180.00 112.20 1.5020 +IC C12B C11E *C12A H12A1 1.5020 112.20 120.00 110.10 1.1110 +IC C12B C11E *C12A H12A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C11E C12A C12B C12C 1.5300 112.20 180.00 123.50 1.3400 +IC C12C C12A *C12B H12B 1.3400 123.50 180.00 116.00 1.1000 +IC C12A C12B C12C C12D 1.5020 123.50 180.00 123.50 1.5020 +IC C12E C12B *C12C C12D 1.5020 123.50 180.00 123.50 1.5040 +IC C12B C12C C12D H12D1 1.3400 123.50 180.00 111.50 1.1110 +IC H12D1 C12C *C12D H12D2 1.1110 111.50 120.00 111.50 1.1110 +IC H12D1 C12C *C12D H12D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C12B C12C C12E C13A 1.3400 123.50 180.00 112.20 1.5300 +IC C13A C12C *C12E H12E1 1.5300 112.20 120.00 111.50 1.1110 +IC C13A C12C *C12E H12E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C12C C12E C13A C13B 1.5020 112.20 180.00 112.20 1.5020 +IC C13B C12E *C13A H13A1 1.5020 112.20 120.00 110.10 1.1110 +IC C13B C12E *C13A H13A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C12E C13A C13B C13C 1.5300 112.20 180.00 123.50 1.3400 +IC C13C C13A *C13B H13B 1.3400 123.50 180.00 116.00 1.1000 +IC C13A C13B C13C C13E 1.5020 123.50 180.00 123.50 1.5040 +IC C13D C13B *C13C C13E 1.5040 123.50 180.00 123.50 1.5020 +IC C13B C13C C13D H13D1 1.3400 123.50 180.00 111.50 1.1110 +IC H13D1 C13C *C13D H13D2 1.1110 111.50 120.00 111.50 1.1110 +IC H13D1 C13C *C13D H13D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C13C C14A *C13E H13E1 1.3400 123.50 120.00 111.50 1.1110 +IC C13C C14A *C13E H13E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C13B C13C C13E C14A 1.3400 123.50 180.00 112.20 1.5300 +IC C13C C13E C14A C14B 1.5020 112.20 180.00 112.20 1.5020 +IC C14B C13E *C14A H14A1 1.5020 112.20 120.00 110.10 1.1110 +IC C14B C13E *C14A H14A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C13E C14A C14B C14C 1.5300 112.20 180.00 123.50 1.3400 +IC C14C C14A *C14B H14B 1.3400 123.50 180.00 116.00 1.1000 +IC C14A C14B C14C C14E 1.5020 123.50 180.00 123.50 1.5020 +IC C14E C14B *C14C C14D 1.5020 123.50 180.00 123.50 1.5040 +IC C14B C14C C14D H14D1 1.3400 123.50 180.00 111.50 1.1110 +IC H14D1 C14C *C14D H14D2 1.1110 111.50 120.00 111.50 1.1110 +IC H14D1 C14C *C14D H14D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C14B C14C C14E C15A 1.3400 123.50 180.00 112.20 1.5300 +IC C15A C14C *C14E H14E1 1.5300 112.20 120.00 111.50 1.1110 +IC C15A C14C *C14E H14E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C14C C14E C15A C15B 1.5020 112.20 180.00 112.20 1.5020 +IC C15B C14E *C15A H15A1 1.5020 112.20 120.00 110.10 1.1110 +IC C15B C14E *C15A H15A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C14E C15A C15B C15C 1.5300 112.20 180.00 123.50 1.3400 +IC C15C C15A *C15B H15B 1.3400 123.50 180.00 116.00 1.1000 +IC C15A C15B C15C C15E 1.5020 123.50 180.00 123.50 1.5040 +IC C15D C15B *C15C C15E 1.5040 123.50 180.00 123.50 1.5040 +IC C15B C15C C15D H15D1 1.3400 123.50 180.00 111.50 1.1110 +IC H15D1 C15C *C15D H15D2 1.1110 111.50 120.00 111.50 1.1110 +IC H15D1 C15C *C15D H15D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C15B C15C C15E H15E1 1.3400 123.50 180.00 111.50 1.1110 +IC H15E1 C15C *C15E H15E2 1.1110 111.50 120.00 111.50 1.1110 +IC H15E1 C15C *C15E H15E3 1.1110 111.50 -120.00 111.50 1.1110 + +RESI DL19PP -2.00 ! [name] +GROUP +ATOM P2 PG1 1.34 ! HO22 +ATOM O22 OG311 -0.71 ! | +ATOM HO22 HGP1 0.44 ! O22 !! based on PPI2 +ATOM O23 OG2P1 -0.86 ! | +ATOM O24 OG2P1 -0.86 ! O23==P2==O24 (-) + ! | +ATOM P1 PG1 1.46 ! O12 +ATOM O12 OG304 -0.63 ! | +ATOM O13 OG2P1 -0.83 ! O13==P1==O14 (-) +ATOM O14 OG2P1 -0.83 ! | +ATOM O11 OG303 -0.62 ! O11 + ! | +ATOM C1A CG321 -0.08 ! H1A1--C1A--H1A2 +ATOM H1A1 HGA2 0.09 ! | +ATOM H1A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C1B CG321 -0.18 ! H1B1--C1B--H1B2 +ATOM H1B1 HGA2 0.09 ! | +ATOM H1B2 HGA2 0.09 ! | H1D1 +GROUP 0.00 ! | | +ATOM C1C CG311 -0.09 ! H1C--C1C--C1D--H1D2 +ATOM H1C HGA1 0.09 ! | | +GROUP 0.00 ! | H1D3 +ATOM C1D CG331 -0.27 ! | +ATOM H1D1 HGA3 0.09 ! | +ATOM H1D2 HGA3 0.09 ! | +ATOM H1D3 HGA3 0.09 ! H1E1--C1E--H1E2 +GROUP 0.00 ! | +ATOM C1E CG321 -0.18 ! | +ATOM H1E1 HGA2 0.09 ! | +ATOM H1E2 HGA2 0.09 ! H2A1--C2A--H2A2 +GROUP 0.00 ! | +ATOM C2A CG321 -0.18 ! | +ATOM H2A1 HGA2 0.09 ! | +ATOM H2A2 HGA2 0.09 ! C2B--H2B (cis) +GROUP 0.00 ! || +ATOM C2B CG2D1 -0.15 ! || H2D1 +ATOM H2B HGA4 0.15 ! || | +GROUP 0.00 ! C2C--C2D--H2D2 +ATOM C2C CG2D1 0.00 ! | | +GROUP 0.00 ! | H2D3 +ATOM C2D CG331 -0.27 ! ! +ATOM H2D1 HGA3 0.09 ! ! +ATOM H2D2 HGA3 0.09 ! ! +ATOM H2D3 HGA3 0.09 ! H2E1--C2E--H2E2 +GROUP 0.00 ! ! +ATOM C2E CG321 -0.18 ! ! +ATOM H2E1 HGA2 0.09 ! | +ATOM H2E2 HGA2 0.09 ! H3A1--C3A--H3A2 +GROUP 0.00 ! | +ATOM C3A CG321 -0.18 ! | +ATOM H3A1 HGA2 0.09 ! | +ATOM H3A2 HGA2 0.09 ! C3B--H3B (cis) +GROUP 0.00 ! || +ATOM C3B CG2D1 -0.15 ! || H3D1 +ATOM H3B HGA4 0.15 ! || | +GROUP 0.00 ! C3C--C3D--H3D2 +ATOM C3C CG2D1 0.00 ! | | +GROUP 0.00 ! | H3D3 +ATOM C3D CG331 -0.27 ! ! +ATOM H3D1 HGA3 0.09 ! ! +ATOM H3D2 HGA3 0.09 ! ! +ATOM H3D3 HGA3 0.09 ! H3E1--C3E--H3E2 +GROUP 0.00 ! ! +ATOM C3E CG321 -0.18 ! ! +ATOM H3E1 HGA2 0.09 ! | +ATOM H3E2 HGA2 0.09 ! H4A1--C4A--H4A2 +GROUP 0.00 ! | +ATOM C4A CG321 -0.18 ! | +ATOM H4A1 HGA2 0.09 ! | +ATOM H4A2 HGA2 0.09 ! C4B--H4B (cis) +GROUP 0.00 ! || +ATOM C4B CG2D1 -0.15 ! || H4D1 +ATOM H4B HGA4 0.15 ! || | +GROUP 0.00 ! C4C--C4D--H4D2 +ATOM C4C CG2D1 0.00 ! | | +GROUP 0.00 ! | H4D3 +ATOM C4D CG331 -0.27 ! ! +ATOM H4D1 HGA3 0.09 ! ! +ATOM H4D2 HGA3 0.09 ! ! +ATOM H4D3 HGA3 0.09 ! H4E1--C4E--H4E2 +GROUP 0.00 ! ! +ATOM C4E CG321 -0.18 ! ! +ATOM H4E1 HGA2 0.09 ! | +ATOM H4E2 HGA2 0.09 ! H5A1--C5A--H5A2 +GROUP 0.00 ! | +ATOM C5A CG321 -0.18 ! | +ATOM H5A1 HGA2 0.09 ! | +ATOM H5A2 HGA2 0.09 ! C5B--H5B (cis) +GROUP 0.00 ! || +ATOM C5B CG2D1 -0.15 ! || H5D1 +ATOM H5B HGA4 0.15 ! || | +GROUP 0.00 ! C5C--C5D--H5D2 +ATOM C5C CG2D1 0.00 ! | | +GROUP 0.00 ! | H5D3 +ATOM C5D CG331 -0.27 ! ! +ATOM H5D1 HGA3 0.09 ! ! +ATOM H5D2 HGA3 0.09 ! ! +ATOM H5D3 HGA3 0.09 ! H5E1--C5E--H5E2 +GROUP 0.00 ! ! +ATOM C5E CG321 -0.18 ! ! +ATOM H5E1 HGA2 0.09 ! | +ATOM H5E2 HGA2 0.09 ! H6A1--C6A--H6A2 +GROUP 0.00 ! | +ATOM C6A CG321 -0.18 ! | +ATOM H6A1 HGA2 0.09 ! | +ATOM H6A2 HGA2 0.09 ! C6B--H6B (cis) +GROUP 0.00 ! || +ATOM C6B CG2D1 -0.15 ! || H6D1 +ATOM H6B HGA4 0.15 ! || | +GROUP 0.00 ! C6C--C6D--H6D2 +ATOM C6C CG2D1 0.00 ! | | +GROUP 0.00 ! | H6D3 +ATOM C6D CG331 -0.27 ! ! +ATOM H6D1 HGA3 0.09 ! ! +ATOM H6D2 HGA3 0.09 ! ! +ATOM H6D3 HGA3 0.09 ! H6E1-C6E--H6E2 +GROUP 0.00 ! ! +ATOM C6E CG321 -0.18 ! ! +ATOM H6E1 HGA2 0.09 ! | +ATOM H6E2 HGA2 0.09 ! H7A1--C7A--H7A2 +GROUP 0.00 ! | +ATOM C7A CG321 -0.18 ! | +ATOM H7A1 HGA2 0.09 ! | +ATOM H7A2 HGA2 0.09 ! C7B--H7B (cis) +GROUP 0.00 ! || +ATOM C7B CG2D1 -0.15 ! || H7D1 +ATOM H7B HGA4 0.15 ! || | +GROUP 0.00 ! C7C--C7D--H7D2 +ATOM C7C CG2D1 0.00 ! | | +GROUP 0.00 ! | H7D3 +ATOM C7D CG331 -0.27 ! ! +ATOM H7D1 HGA3 0.09 ! ! +ATOM H7D2 HGA3 0.09 ! ! +ATOM H7D3 HGA3 0.09 ! H7E1-C7E--H7E2 +GROUP 0.00 ! ! +ATOM C7E CG321 -0.18 ! ! +ATOM H7E1 HGA2 0.09 ! | +ATOM H7E2 HGA2 0.09 ! H8A1--C8A--H8A2 +GROUP 0.00 ! | +ATOM C8A CG321 -0.18 ! | +ATOM H8A1 HGA2 0.09 ! | +ATOM H8A2 HGA2 0.09 ! C8B--H8B (cis) +GROUP 0.00 ! || +ATOM C8B CG2D1 -0.15 ! || H8D1 +ATOM H8B HGA4 0.15 ! || | +GROUP 0.00 ! C8C--C8D--H8D2 +ATOM C8C CG2D1 0.00 ! | | +GROUP 0.00 ! | H8D3 +ATOM C8D CG331 -0.27 ! ! +ATOM H8D1 HGA3 0.09 ! ! +ATOM H8D2 HGA3 0.09 ! ! +ATOM H8D3 HGA3 0.09 ! H8E1-C8E--H8E2 +GROUP 0.00 ! ! +ATOM C8E CG321 -0.18 ! ! +ATOM H8E1 HGA2 0.09 ! | +ATOM H8E2 HGA2 0.09 ! H9A1--C9A--H9A2 +GROUP 0.00 ! | +ATOM C9A CG321 -0.18 ! | +ATOM H9A1 HGA2 0.09 ! | +ATOM H9A2 HGA2 0.09 ! C9B--H9B (cis) +GROUP 0.00 ! || +ATOM C9B CG2D1 -0.15 ! || H9D1 +ATOM H9B HGA4 0.15 ! || | +GROUP 0.00 ! C9C--C9D--H9D2 +ATOM C9C CG2D1 0.00 ! | | +GROUP 0.00 ! | H9D3 +ATOM C9D CG331 -0.27 ! ! +ATOM H9D1 HGA3 0.09 ! ! +ATOM H9D2 HGA3 0.09 ! ! +ATOM H9D3 HGA3 0.09 ! H9E1-C9E--H9E2 +GROUP 0.00 ! ! +ATOM C9E CG321 -0.18 ! ! +ATOM H9E1 HGA2 0.09 ! | +ATOM H9E2 HGA2 0.09 ! H10A1--C10A--H10A2 +GROUP 0.00 ! | +ATOM C10A CG321 -0.18 ! | +ATOM H10A1 HGA2 0.09 ! | +ATOM H10A2 HGA2 0.09 ! C10B--H110B (cis) +GROUP 0.00 ! || +ATOM C10B CG2D1 -0.15 ! || H10D1 +ATOM H10B HGA4 0.15 ! || | +GROUP 0.00 ! C10C-C10D--H10D2 +ATOM C10C CG2D1 0.00 ! | | +GROUP 0.00 ! | H10D3 +ATOM C10D CG331 -0.27 ! ! +ATOM H10D1 HGA3 0.09 ! ! +ATOM H10D2 HGA3 0.09 ! ! +ATOM H10D3 HGA3 0.09 ! H10E1-C10E--H10E2 +GROUP 0.00 ! ! +ATOM C10E CG321 -0.18 ! ! +ATOM H10E1 HGA2 0.09 ! | +ATOM H10E2 HGA2 0.09 ! H11A1--C11A--H11A2 +GROUP 0.00 ! | +ATOM C11A CG321 -0.18 ! | +ATOM H11A1 HGA2 0.09 ! | +ATOM H11A2 HGA2 0.09 ! C11B--H11B (cis) +GROUP 0.00 ! || +ATOM C11B CG2D1 -0.15 ! || H11D1 +ATOM H11B HGA4 0.15 ! || | +GROUP 0.00 ! C11C-C11D--H11D2 +ATOM C11C CG2D1 0.00 ! | | +GROUP 0.00 ! | H11D3 +ATOM C11D CG331 -0.27 ! ! +ATOM H11D1 HGA3 0.09 ! ! +ATOM H11D2 HGA3 0.09 ! ! +ATOM H11D3 HGA3 0.09 ! H11E1-C11E--H11E2 +GROUP 0.00 ! ! +ATOM C11E CG321 -0.18 ! ! +ATOM H11E1 HGA2 0.09 ! | +ATOM H11E2 HGA2 0.09 ! H12A1--C12A--H12A2 +GROUP 0.00 ! | +ATOM C12A CG321 -0.18 ! | +ATOM H12A1 HGA2 0.09 ! | +ATOM H12A2 HGA2 0.09 ! C12B--H12B (cis) +GROUP 0.00 ! || +ATOM C12B CG2D1 -0.15 ! || H12D1 +ATOM H12B HGA4 0.15 ! || | +GROUP 0.00 ! C12C-C12D--H12D2 +ATOM C12C CG2D1 0.00 ! | | +GROUP 0.00 ! | H12D3 +ATOM C12D CG331 -0.27 ! ! +ATOM H12D1 HGA3 0.09 ! ! +ATOM H12D2 HGA3 0.09 ! ! +ATOM H12D3 HGA3 0.09 ! H1E12-C12E--H12E2 +GROUP 0.00 ! ! +ATOM C12E CG321 -0.18 ! ! +ATOM H12E1 HGA2 0.09 ! | +ATOM H12E2 HGA2 0.09 ! H13A1--C13A--H13A2 +GROUP 0.00 ! | +ATOM C13A CG321 -0.18 ! | +ATOM H13A1 HGA2 0.09 ! | +ATOM H13A2 HGA2 0.09 ! C13B--H13B (cis) +GROUP 0.00 ! || +ATOM C13B CG2D1 -0.15 ! || H13D1 +ATOM H13B HGA4 0.15 ! || | +GROUP 0.00 ! C13C-C13D--H13D2 +ATOM C13C CG2D1 0.00 ! | | +GROUP 0.00 ! | H13D3 +ATOM C13D CG331 -0.27 ! ! +ATOM H13D1 HGA3 0.09 ! ! +ATOM H13D2 HGA3 0.09 ! ! +ATOM H13D3 HGA3 0.09 ! H13E1-C13E--H13E2 +GROUP 0.00 ! ! +ATOM C13E CG321 -0.18 ! ! +ATOM H13E1 HGA2 0.09 ! | +ATOM H13E2 HGA2 0.09 ! H14A1--C14A--H14A2 +GROUP 0.00 ! | +ATOM C14A CG321 -0.18 ! | +ATOM H14A1 HGA2 0.09 ! | +ATOM H14A2 HGA2 0.09 ! C14B--H14B (cis) +GROUP 0.00 ! || +ATOM C14B CG2D1 -0.15 ! || H14D1 +ATOM H14B HGA4 0.15 ! || | +GROUP 0.00 ! C14C-C14D--H14D2 +ATOM C14C CG2D1 0.00 ! | | +GROUP 0.00 ! | H14D3 +ATOM C14D CG331 -0.27 ! ! +ATOM H14D1 HGA3 0.09 ! ! +ATOM H14D2 HGA3 0.09 ! ! +ATOM H14D3 HGA3 0.09 ! H14E1-C14E--H14E2 +GROUP 0.00 ! | +ATOM C14E CG321 -0.18 ! | +ATOM H14E1 HGA2 0.09 ! | +ATOM H14E2 HGA2 0.09 ! H15A1--C15A--H15A2 +GROUP 0.00 ! | +ATOM C15A CG321 -0.18 ! | +ATOM H15A1 HGA2 0.09 ! | +ATOM H15A2 HGA2 0.09 ! C15B--H15B (cis) +GROUP 0.00 ! || +ATOM C15B CG2D1 -0.15 ! || H15D1 +ATOM H15B HGA4 0.15 ! || | +GROUP 0.00 ! C15C-C15D--H15D2 +ATOM C15C CG2D1 0.00 ! | | +GROUP 0.00 ! | H15D3 +ATOM C15D CG331 -0.27 ! | +ATOM H15D1 HGA3 0.09 ! | +ATOM H15D2 HGA3 0.09 ! | +ATOM H15D3 HGA3 0.09 ! H15E1-C15E--H15E2 +GROUP 0.00 ! | +ATOM C15E CG321 -0.18 ! | +ATOM H15E1 HGA2 0.09 ! | +ATOM H15E2 HGA2 0.09 ! H16A1--C16A--H16A2 +GROUP 0.00 ! | +ATOM C16A CG321 -0.18 ! | +ATOM H16A1 HGA2 0.09 ! | +ATOM H16A2 HGA2 0.09 ! C16B--H16B (cis) +GROUP 0.00 ! || +ATOM C16B CG2D1 -0.15 ! || H16D1 +ATOM H16B HGA4 0.15 ! || | +GROUP 0.00 ! C16C-C16D--H16D2 +ATOM C16C CG2D1 0.00 ! | | +GROUP 0.00 ! | H16D3 +ATOM C16D CG331 -0.27 ! | +ATOM H16D1 HGA3 0.09 ! | +ATOM H16D2 HGA3 0.09 ! | +ATOM H16D3 HGA3 0.09 ! H16E1-C16E--H16E2 +GROUP 0.00 ! | +ATOM C16E CG321 -0.18 ! | +ATOM H16E1 HGA2 0.09 ! | +ATOM H16E2 HGA2 0.09 ! H17A1--C17A--H17A2 +GROUP 0.00 ! | +ATOM C17A CG321 -0.18 ! | +ATOM H17A1 HGA2 0.09 ! | +ATOM H17A2 HGA2 0.09 ! C17B--H17B (trans) +GROUP 0.00 ! || +ATOM C17B CG2D1 -0.15 ! || H17D1 +ATOM H17B HGA4 0.15 ! || | +GROUP 0.00 ! C17C-C17D--H17D2 +ATOM C17C CG2D1 0.00 ! | | +GROUP 0.00 ! | H17D3 +ATOM C17D CG331 -0.27 ! | +ATOM H17D1 HGA3 0.09 ! | +ATOM H17D2 HGA3 0.09 ! | +ATOM H17D3 HGA3 0.09 ! H17E1-C17E--H17E2 +GROUP 0.00 ! | +ATOM C17E CG321 -0.18 ! | +ATOM H17E1 HGA2 0.09 ! | +ATOM H17E2 HGA2 0.09 ! H18A1--C18A--H18A2 +GROUP 0.00 ! | +ATOM C18A CG321 -0.18 ! | +ATOM H18A1 HGA2 0.09 ! | +ATOM H18A2 HGA2 0.09 ! C18B--H18B (trans) +GROUP 0.00 ! || +ATOM C18B CG2D1 -0.15 ! || H18D1 +ATOM H18B HGA4 0.15 ! || | +GROUP 0.00 ! C18C-C18D--H18D2 +ATOM C18C CG2D1 0.00 ! | | +GROUP 0.00 ! | H18D3 +ATOM C18D CG331 -0.27 ! | +ATOM H18D1 HGA3 0.09 ! | +ATOM H18D2 HGA3 0.09 ! | +ATOM H18D3 HGA3 0.09 ! H18E1-C18E--H18E2 +GROUP 0.00 ! | +ATOM C18E CG321 -0.18 ! | +ATOM H18E1 HGA2 0.09 ! | +ATOM H18E2 HGA2 0.09 ! H19A1--C19A--H19A2 +GROUP 0.00 ! | +ATOM C19A CG321 -0.18 ! | +ATOM H19A1 HGA2 0.09 ! | +ATOM H19A2 HGA2 0.09 ! C19B--H19B +GROUP 0.00 ! || +ATOM C19B CG2D1 -0.15 ! || H19D1 +ATOM H19B HGA4 0.15 ! || | +GROUP 0.00 ! C19C-C19D--H19D2 +ATOM C19C CG2D1 0.00 ! | | +GROUP 0.00 ! | H19D3 +ATOM C19D CG331 -0.27 ! | +ATOM H19D1 HGA3 0.09 ! | +ATOM H19D2 HGA3 0.09 ! | +ATOM H19D3 HGA3 0.09 ! H19E1-C19E--H19E2 +GROUP 0.00 ! +ATOM C19E CG331 -0.27 ! +ATOM H19E1 HGA3 0.09 ! +ATOM H19E2 HGA3 0.09 ! +ATOM H19E3 HGA3 0.09 ! + +BOND O22 HO22 P2 O22 P2 O23 P2 O24 P2 O12 ! Phosphate group 2 +BOND P1 O12 P1 O13 P1 O14 P1 O11 O11 C1A ! Phosphate group 1 +BOND C1A C1B C1B C1C C1C C1D C1C C1E ! alpha isoprene backbone carbons +BOND C1A H1A1 C1A H1A2 ! C1A hydrogens +BOND C1B H1B1 C1B H1B2 ! C1B hydrogens +BOND C1C H1C ! C1C hydrogen +BOND C1D H1D1 C1D H1D2 C1D H1D3 ! C1D hydrogens +BOND C1E H1E1 C1E H1E2 ! C1E hydrogens +BOND C1E C2A ! isoprene linking bond +BOND C2A C2B C2C C2D C2C C2E ! cis isoprene backbone carbons +DOUBLE C2B C2C ! cis double bond +BOND C2A H2A1 C2A H2A2 ! C2A hydrogens +BOND C2B H2B ! C2B hydrogen +BOND C2D H2D1 C2D H2D2 C2D H2D3 ! C2D hydrogens +BOND C2E H2E1 C2E H2E2 ! C2E hydrogens +BOND C2E C3A ! isoprene linking bond +BOND C3A C3B C3C C3D C3C C3E ! cis isoprene backbone carbons +DOUBLE C3B C3C ! cis double bond +BOND C3A H3A1 C3A H3A2 ! C3A hydrogens +BOND C3B H3B ! C3B hydrogen +BOND C3D H3D1 C3D H3D2 C3D H3D3 ! C3D hydrogens +BOND C3E H3E1 C3E H3E2 ! C3E hydrogens +BOND C3E C4A ! isoprene linking bond +BOND C4A C4B C4C C4D C4C C4E ! cis isoprene backbone carbons +DOUBLE C4B C4C ! cis double bond +BOND C4A H4A1 C4A H4A2 ! C4A hydrogens +BOND C4B H4B ! C4B hydrogen +BOND C4D H4D1 C4D H4D2 C4D H4D3 ! C4D hydrogens +BOND C4E H4E1 C4E H4E2 ! C4E hydrogens +BOND C4E C5A ! isoprene linking bond +BOND C5A C5B C5C C5D C5C C5E ! cis isoprene backbone carbons +DOUBLE C5B C5C ! cis double bond +BOND C5A H5A1 C5A H5A2 ! C5A hydrogens +BOND C5B H5B ! C5B hydrogen +BOND C5D H5D1 C5D H5D2 C5D H5D3 ! C5D hydrogens +BOND C5E H5E1 C5E H5E2 ! C5E hydrogens +BOND C5E C6A ! isoprene linking bond +BOND C6A C6B C6C C6D C6C C6E ! cis isoprene backbone carbons +DOUBLE C6B C6C ! cis double bond +BOND C6A H6A1 C6A H6A2 ! C6A hydrogens +BOND C6B H6B ! C6B hydrogen +BOND C6D H6D1 C6D H6D2 C6D H6D3 ! C6D hydrogens +BOND C6E H6E1 C6E H6E2 ! C6E hydrogens +BOND C6E C7A ! isoprene linking bond +BOND C7A C7B C7C C7D C7C C7E ! cis isoprene backbone carbons +DOUBLE C7B C7C ! cis double bond +BOND C7A H7A1 C7A H7A2 ! C7A hydrogens +BOND C7B H7B ! C7B hydrogen +BOND C7D H7D1 C7D H7D2 C7D H7D3 ! C7D hydrogens +BOND C7E H7E1 C7E H7E2 ! C7E hydrogens +BOND C7E C8A ! isoprene linking bond +BOND C8A C8B C8C C8D C8C C8E ! cis isoprene backbone carbons +DOUBLE C8B C8C ! cis double bond +BOND C8A H8A1 C8A H8A2 ! C8A hydrogens +BOND C8B H8B ! C8B hydrogen +BOND C8D H8D1 C8D H8D2 C8D H8D3 ! C8D hydrogens +BOND C8E H8E1 C8E H8E2 ! C8E hydrogens +BOND C8E C9A ! isoprene linking bond +BOND C9A C9B C9C C9D C9C C9E ! cis isoprene backbone carbons +DOUBLE C9B C9C ! cis double bond +BOND C9A H9A1 C9A H9A2 ! C9A hydrogens +BOND C9B H9B ! C9B hydrogen +BOND C9D H9D1 C9D H9D2 C9D H9D3 ! C9D hydrogens +BOND C9E H9E1 C9E H9E2 ! C9E hydrogens +BOND C9E C10A ! isoprene linking bond +BOND C10A C10B C10C C10D C10C C10E ! cis isoprene backbone carbons +DOUBLE C10B C10C ! cis double bond +BOND C10A H10A1 C10A H10A2 ! C10A hydrogens +BOND C10B H10B ! C10B hydrogen +BOND C10D H10D1 C10D H10D2 C10D H10D3 ! C10D hydrogens +BOND C10E H10E1 C10E H10E2 ! C10E hydrogens +BOND C10E C11A ! isoprene linking bond +BOND C11A C11B C11C C11D C11C C11E ! cis isoprene backbone carbons +DOUBLE C11B C11C ! cis double bond +BOND C11A H11A1 C11A H11A2 ! C11A hydrogens +BOND C11B H11B ! C11B hydrogen +BOND C11D H11D1 C11D H11D2 C11D H11D3 ! C11D hydrogens +BOND C11E H11E1 C11E H11E2 ! C11E hydrogens +BOND C11E C12A ! isoprene linking bond +BOND C12A C12B C12C C12D C12C C12E ! cis isoprene backbone carbons +DOUBLE C12B C12C ! cis double bond +BOND C12A H12A1 C12A H12A2 ! C12A hydrogens +BOND C12B H12B ! C12B hydrogen +BOND C12D H12D1 C12D H12D2 C12D H12D3 ! C12D hydrogens +BOND C12E H12E1 C12E H12E2 ! C12E hydrogens +BOND C12E C13A ! isoprene linking bond +BOND C13A C13B C13C C13D C13C C13E ! cis isoprene backbone carbons +DOUBLE C13B C13C ! cis double bond +BOND C13A H13A1 C13A H13A2 ! C13A hydrogens +BOND C13B H13B ! C13B hydrogen +BOND C13D H13D1 C13D H13D2 C13D H13D3 ! C13D hydrogens +BOND C13E H13E1 C13E H13E2 ! C13E hydrogens +BOND C13E C14A ! isoprene linking bond +BOND C14A C14B C14C C14D C14C C14E ! cis isoprene backbone carbons +DOUBLE C14B C14C ! cis double bond +BOND C14A H14A1 C14A H14A2 ! C14A hydrogens +BOND C14B H14B ! C14B hydrogen +BOND C14D H14D1 C14D H14D2 C14D H14D3 ! C14D hydrogens +BOND C14E H14E1 C14E H14E2 ! C14E hydrogens +BOND C14E C15A ! isoprene linking bond +BOND C15A C15B C15C C15D C15C C15E ! cis isoprene backbone carbons +DOUBLE C15B C15C ! cis double bond +BOND C15A H15A1 C15A H15A2 ! C15A hydrogens +BOND C15B H15B ! C15B hydrogen +BOND C15D H15D1 C15D H15D2 C15D H15D3 ! C15D hydrogens +BOND C15E H15E1 C15E H15E2 ! C15E hydrogens +BOND C15E C16A ! isoprene linking bond +BOND C16A C16B C16C C16D C16C C16E ! cis isoprene backbone carbons +DOUBLE C16B C16C ! cis double bond +BOND C16A H16A1 C16A H16A2 ! C16A hydrogens +BOND C16B H16B ! C16B hydrogen +BOND C16D H16D1 C16D H16D2 C16D H16D3 ! C16D hydrogens +BOND C16E H16E1 C16E H16E2 ! C16E hydrogens +BOND C16E C17A ! isoprene linking bond +BOND C17A C17B C17C C17D C17C C17E ! trans isoprene backbone carbons +DOUBLE C17B C17C ! trans double bond +BOND C17A H17A1 C17A H17A2 ! C17A hydrogens +BOND C17B H17B ! C17B hydrogen +BOND C17D H17D1 C17D H17D2 C17D H17D3 ! C17D hydrogens +BOND C17E H17E1 C17E H17E2 ! C17E hydrogens +BOND C17E C18A ! isoprene linking bond +BOND C18A C18B C18C C18D C18C C18E ! trans isoprene backbone carbons +DOUBLE C18B C18C ! trans double bond +BOND C18A H18A1 C18A H18A2 ! C18A hydrogens +BOND C18B H18B ! C18B hydrogen +BOND C18D H18D1 C18D H18D2 C18D H18D3 ! C18D hydrogens +BOND C18E H18E1 C18E H18E2 ! C18E hydrogens +BOND C18E C19A ! isoprene linking bond +BOND C19A C19B C19C C19D C19C C19E ! omega isoprene backbone carbons +DOUBLE C19B C19C ! omega double bond +BOND C19A H19A1 C19A H19A2 ! C19A hydrogens +BOND C19B H19B ! C19B hydrogen +BOND C19D H19D1 C19D H19D2 C19D H19D3 ! C19D hydrogens +BOND C19E H19E1 C19E H19E2 C19E H19E3 ! C19E hydrogens +IC O22 O12 *P2 O23 1.6100 111.00 120.00 111.60 1.5100 +IC O22 O12 *P2 O24 1.6100 111.00 -120.00 111.60 1.5100 +IC O12 P2 O22 HO22 1.6750 111.00 180.00 115.00 0.9600 +IC O22 P2 O12 P1 1.6100 111.00 180.00 143.00 1.6750 +IC P2 O12 P1 O11 1.6750 143.00 180.00 105.00 1.6500 +IC O11 O12 *P1 O13 1.6500 105.00 120.00 111.60 1.5100 +IC O11 O12 *P1 O14 1.5100 111.60 -120.00 111.60 1.5100 +IC O12 P1 O11 C1A 1.6750 105.00 180.00 120.00 1.4400 +IC P1 O11 C1A C1B 1.6500 120.00 180.00 110.10 1.5300 +IC C1B O11 *C1A H1A1 1.5300 110.10 120.00 109.50 1.1110 +IC C1B O11 *C1A H1A2 1.5300 110.10 -120.00 109.50 1.1110 +IC O11 C1A C1B C1C 1.4400 110.10 180.00 113.50 1.5380 +IC C1C C1A *C1B H1B1 1.5380 113.50 120.00 110.10 1.1110 +IC C1C C1A *C1B H1B2 1.5380 113.50 -120.00 110.10 1.1110 +IC C1A C1B C1C C1E 1.5300 113.50 180.00 113.50 1.5380 +IC C1E C1B *C1C C1D 1.5380 113.50 -120.00 114.00 1.5380 +IC C1E C1B *C1C H1C 1.5380 114.00 120.00 110.10 1.1110 +IC C1B C1C C1D H1D1 1.5380 114.00 180.00 110.10 1.1110 +IC H1D1 C1C *C1D H1D2 1.1110 110.10 120.00 110.10 1.1110 +IC H1D1 C1C *C1D H1D3 1.1110 110.10 -120.00 110.10 1.1110 +IC C1B C1C C1E C2A 1.5380 113.50 180.00 113.50 1.5300 +IC C2A C1C *C1E H1E1 1.5300 113.50 120.00 110.10 1.1110 +IC C2A C1C *C1E H1E2 1.1110 110.10 -120.00 110.10 1.1110 +IC C1C C1E C2A C2B 1.5380 113.50 180.00 112.20 1.5020 +IC C2B C1E *C2A H2A1 1.5020 112.20 120.00 110.10 1.1110 +IC C2B C1E *C2A H2A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C1E C2A C2B C2C 1.5300 112.20 180.00 123.50 1.3400 +IC C2C C2A *C2B H2B 1.3400 123.50 180.00 116.00 1.1000 +IC C2A C2B C2C C2D 1.5020 123.50 180.00 123.50 1.5020 +IC C2E C2B *C2C C2D 1.5020 123.50 180.00 123.50 1.5040 +IC C2B C2C C2D H2D1 1.3400 123.50 180.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D2 1.1110 111.50 120.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C2B C2C C2E C3A 1.3400 123.50 180.00 112.20 1.5300 +IC C3A C2C *C2E H2E1 1.5300 112.20 120.00 111.50 1.1110 +IC C3A C2C *C2E H2E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C2C C2E C3A C3B 1.5020 112.20 180.00 112.20 1.5020 +IC C3B C2E *C3A H3A1 1.5020 112.20 120.00 110.10 1.1110 +IC C3B C2E *C3A H3A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C2E C3A C3B C3C 1.5300 112.20 180.00 123.50 1.3400 +IC C3C C3A *C3B H3B 1.3400 123.50 180.00 116.00 1.1000 +IC C3A C3B C3C C3D 1.5020 123.50 180.00 123.50 1.5020 +IC C3E C3B *C3C C3D 1.5020 123.50 180.00 123.50 1.5040 +IC C3B C3C C3D H3D1 1.3400 123.50 180.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D2 1.1110 111.50 120.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C3B C3C C3E C4A 1.3400 123.50 180.00 112.20 1.5300 +IC C4A C3C *C3E H3E1 1.5300 112.20 120.00 111.50 1.1110 +IC C4A C3C *C3E H3E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C3C C3E C4A C4B 1.5020 112.20 180.00 112.20 1.5020 +IC C4B C3E *C4A H4A1 1.5020 112.20 120.00 110.10 1.1110 +IC C4B C3E *C4A H4A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C3E C4A C4B C4C 1.5300 112.20 180.00 123.50 1.3400 +IC C4C C4A *C4B H4B 1.3400 123.50 180.00 116.00 1.1000 +IC C4A C4B C4C C4D 1.5020 123.50 180.00 123.50 1.5020 +IC C4E C4B *C4C C4D 1.5020 123.50 180.00 123.50 1.5040 +IC C4B C4C C4D H4D1 1.3400 123.50 180.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D2 1.1110 111.50 120.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C4B C4C C4E C5A 1.3400 123.50 180.00 112.20 1.5300 +IC C5A C4C *C4E H4E1 1.5300 112.20 120.00 111.50 1.1110 +IC C5A C4C *C4E H4E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C4C C4E C5A C5B 1.5020 112.20 180.00 112.20 1.5020 +IC C5B C4E *C5A H5A1 1.5020 112.20 120.00 110.10 1.1110 +IC C5B C4E *C5A H5A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C4E C5A C5B C5C 1.5300 112.20 180.00 123.50 1.3400 +IC C5C C5A *C5B H5B 1.3400 123.50 180.00 116.00 1.1000 +IC C5A C5B C5C C5D 1.5020 123.50 180.00 123.50 1.5020 +IC C5E C5B *C5C C5D 1.5020 123.50 180.00 123.50 1.5040 +IC C5B C5C C5D H5D1 1.3400 123.50 180.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D2 1.1110 111.50 120.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C5B C5C C5E C6A 1.3400 123.50 180.00 112.20 1.5300 +IC C6A C5C *C5E H5E1 1.5300 112.20 120.00 111.50 1.1110 +IC C6A C5C *C5E H5E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C5C C5E C6A C6B 1.5020 112.20 180.00 112.20 1.5020 +IC C6B C5E *C6A H6A1 1.5020 112.20 120.00 110.10 1.1110 +IC C6B C5E *C6A H6A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C5E C6A C6B C6C 1.5300 112.20 180.00 123.50 1.3400 +IC C6C C6A *C6B H6B 1.3400 123.50 180.00 116.00 1.1000 +IC C6A C6B C6C C6D 1.5020 123.50 180.00 123.50 1.5020 +IC C6E C6B *C6C C6D 1.5020 123.50 180.00 123.50 1.5040 +IC C6B C6C C6D H6D1 1.3400 123.50 180.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D2 1.1110 111.50 120.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C6B C6C C6E C7A 1.3400 123.50 180.00 112.20 1.5300 +IC C7A C6C *C6E H6E1 1.5300 112.20 120.00 111.50 1.1110 +IC C7A C6C *C6E H6E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C6C C6E C7A C7B 1.5020 112.20 180.00 112.20 1.5020 +IC C7B C6E *C7A H7A1 1.5020 112.20 120.00 110.10 1.1110 +IC C7B C6E *C7A H7A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C6E C7A C7B C7C 1.5300 112.20 180.00 123.50 1.3400 +IC C7C C7A *C7B H7B 1.3400 123.50 180.00 116.00 1.1000 +IC C7A C7B C7C C7D 1.5020 123.50 180.00 123.50 1.5020 +IC C7E C7B *C7C C7D 1.5020 123.50 180.00 123.50 1.5040 +IC C7B C7C C7D H7D1 1.3400 123.50 180.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D2 1.1110 111.50 120.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C7B C7C C7E C8A 1.3400 123.50 180.00 112.20 1.5300 +IC C8A C7C *C7E H7E1 1.5300 112.20 120.00 111.50 1.1110 +IC C8A C7C *C7E H7E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C7C C7E C8A C8B 1.5020 112.20 180.00 112.20 1.5020 +IC C8B C7E *C8A H8A1 1.5020 112.20 120.00 110.10 1.1110 +IC C8B C7E *C8A H8A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C7E C8A C8B C8C 1.5300 112.20 180.00 123.50 1.3400 +IC C8C C8A *C8B H8B 1.3400 123.50 180.00 116.00 1.1000 +IC C8A C8B C8C C8D 1.5020 123.50 180.00 123.50 1.5020 +IC C8E C8B *C8C C8D 1.5020 123.50 180.00 123.50 1.5040 +IC C8B C8C C8D H8D1 1.3400 123.50 180.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D2 1.1110 111.50 120.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C8B C8C C8E C9A 1.3400 123.50 180.00 112.20 1.5300 +IC C9A C8C *C8E H8E1 1.5300 112.20 120.00 111.50 1.1110 +IC C9A C8C *C8E H8E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C8C C8E C9A C9B 1.5020 112.20 180.00 112.20 1.5020 +IC C9B C8E *C9A H9A1 1.5020 112.20 120.00 110.10 1.1110 +IC C9B C8E *C9A H9A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C8E C9A C9B C9C 1.5300 112.20 180.00 123.50 1.3400 +IC C9C C9A *C9B H9B 1.3400 123.50 180.00 116.00 1.1000 +IC C9A C9B C9C C9D 1.5020 123.50 180.00 123.50 1.5020 +IC C9E C9B *C9C C9D 1.5020 123.50 180.00 123.50 1.5040 +IC C9B C9C C9D H9D1 1.3400 123.50 180.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D2 1.1110 111.50 120.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C9B C9C C9E C10A 1.3400 123.50 180.00 112.20 1.5300 +IC C10A C9C *C9E H9E1 1.5300 112.20 120.00 111.50 1.1110 +IC C10A C9C *C9E H9E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C9C C9E C10A C10B 1.5020 112.20 180.00 112.20 1.5020 +IC C10B C9E *C10A H10A1 1.5020 112.20 120.00 110.10 1.1110 +IC C10B C9E *C10A H10A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C9E C10A C10B C10C 1.5300 112.20 180.00 123.50 1.3400 +IC C10C C10A *C10B H10B 1.3400 123.50 180.00 116.00 1.1000 +IC C10A C10B C10C C10D 1.5020 123.50 180.00 123.50 1.5020 +IC C10E C10B *C10C C10D 1.5020 123.50 180.00 123.50 1.5040 +IC C10B C10C C10D H10D1 1.3400 123.50 180.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D2 1.1110 111.50 120.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C10B C10C C10E C11A 1.3400 123.50 180.00 112.20 1.5300 +IC C11A C10C *C10E H10E1 1.5300 112.20 120.00 111.50 1.1110 +IC C11A C10C *C10E H10E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C10C C10E C11A C11B 1.5020 112.20 180.00 112.20 1.5020 +IC C11B C10E *C11A H11A1 1.5020 112.20 120.00 110.10 1.1110 +IC C11B C10E *C11A H11A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C10E C11A C11B C11C 1.5300 112.20 180.00 123.50 1.3400 +IC C11C C11A *C11B H11B 1.3400 123.50 180.00 116.00 1.1000 +IC C11A C11B C11C C11D 1.5020 123.50 180.00 123.50 1.5020 +IC C11E C11B *C11C C11D 1.5020 123.50 180.00 123.50 1.5040 +IC C11B C11C C11D H11D1 1.3400 123.50 180.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D2 1.1110 111.50 120.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C11B C11C C11E C12A 1.3400 123.50 180.00 112.20 1.5300 +IC C12A C11C *C11E H11E1 1.5300 112.20 120.00 111.50 1.1110 +IC C12A C11C *C11E H11E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C11C C11E C12A C12B 1.5020 112.20 180.00 112.20 1.5020 +IC C12B C11E *C12A H12A1 1.5020 112.20 120.00 110.10 1.1110 +IC C12B C11E *C12A H12A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C11E C12A C12B C12C 1.5300 112.20 180.00 123.50 1.3400 +IC C12C C12A *C12B H12B 1.3400 123.50 180.00 116.00 1.1000 +IC C12A C12B C12C C12D 1.5020 123.50 180.00 123.50 1.5020 +IC C12E C12B *C12C C12D 1.5020 123.50 180.00 123.50 1.5040 +IC C12B C12C C12D H12D1 1.3400 123.50 180.00 111.50 1.1110 +IC H12D1 C12C *C12D H12D2 1.1110 111.50 120.00 111.50 1.1110 +IC H12D1 C12C *C12D H12D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C12B C12C C12E C13A 1.3400 123.50 180.00 112.20 1.5300 +IC C13A C12C *C12E H12E1 1.5300 112.20 120.00 111.50 1.1110 +IC C13A C12C *C12E H12E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C12C C12E C13A C13B 1.5020 112.20 180.00 112.20 1.5020 +IC C13B C12E *C13A H13A1 1.5020 112.20 120.00 110.10 1.1110 +IC C13B C12E *C13A H13A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C12E C13A C13B C13C 1.5300 112.20 180.00 123.50 1.3400 +IC C13C C13A *C13B H13B 1.3400 123.50 180.00 116.00 1.1000 +IC C13A C13B C13C C13D 1.5020 123.50 180.00 123.50 1.5020 +IC C13E C13B *C13C C13D 1.5020 123.50 180.00 123.50 1.5040 +IC C13B C13C C13D H13D1 1.3400 123.50 180.00 111.50 1.1110 +IC H13D1 C13C *C13D H13D2 1.1110 111.50 120.00 111.50 1.1110 +IC H13D1 C13C *C13D H13D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C13B C13C C13E C14A 1.3400 123.50 180.00 112.20 1.5300 +IC C14A C13C *C13E H13E1 1.5300 112.20 120.00 111.50 1.1110 +IC C14A C13C *C13E H13E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C13C C13E C14A C14B 1.5020 112.20 180.00 112.20 1.5020 +IC C14B C13E *C14A H14A1 1.5020 112.20 120.00 110.10 1.1110 +IC C14B C13E *C14A H14A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C13E C14A C14B C14C 1.5300 112.20 180.00 123.50 1.3400 +IC C14C C14A *C14B H14B 1.3400 123.50 180.00 116.00 1.1000 +IC C14A C14B C14C C14D 1.5020 123.50 180.00 123.50 1.5020 +IC C14E C14B *C14C C14D 1.5020 123.50 180.00 123.50 1.5040 +IC C14B C14C C14D H14D1 1.3400 123.50 180.00 111.50 1.1110 +IC H14D1 C14C *C14D H14D2 1.1110 111.50 120.00 111.50 1.1110 +IC H14D1 C14C *C14D H14D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C14B C14C C14E C15A 1.3400 123.50 180.00 112.20 1.5300 +IC C15A C14C *C14E H14E1 1.5300 112.20 120.00 111.50 1.1110 +IC C15A C14C *C14E H14E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C14C C14E C15A C15B 1.5020 112.20 180.00 112.20 1.5020 +IC C15B C14E *C15A H15A1 1.5020 112.20 120.00 110.10 1.1110 +IC C15B C14E *C15A H15A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C14E C15A C15B C15C 1.5300 112.20 180.00 123.50 1.3400 +IC C15C C15A *C15B H15B 1.3400 123.50 180.00 116.00 1.1000 +IC C15A C15B C15C C15D 1.5020 123.50 180.00 123.50 1.5020 +IC C15E C15B *C15C C15D 1.5020 123.50 180.00 123.50 1.5040 +IC C15B C15C C15D H15D1 1.3400 123.50 180.00 111.50 1.1110 +IC H15D1 C15C *C15D H15D2 1.1110 111.50 120.00 111.50 1.1110 +IC H15D1 C15C *C15D H15D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C15B C15C C15E C16A 1.3400 123.50 180.00 112.20 1.5300 +IC C16A C15C *C15E H15E1 1.5300 112.20 120.00 111.50 1.1110 +IC C16A C15C *C15E H15E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C15C C15E C16A C16B 1.5020 112.20 180.00 112.20 1.5020 +IC C16B C15E *C16A H16A1 1.5020 112.20 120.00 110.10 1.1110 +IC C16B C15E *C16A H16A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C15E C16A C16B C16C 1.5300 112.20 180.00 123.50 1.3400 +IC C16C C16A *C16B H16B 1.3400 123.50 180.00 116.00 1.1000 +IC C16A C16B C16C C16D 1.5020 123.50 180.00 123.50 1.5020 +IC C16E C16B *C16C C16D 1.5020 123.50 180.00 123.50 1.5040 +IC C16B C16C C16D H16D1 1.3400 123.50 180.00 111.50 1.1110 +IC H16D1 C16C *C16D H16D2 1.1110 111.50 120.00 111.50 1.1110 +IC H16D1 C16C *C16D H16D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C16B C16C C16E C17A 1.3400 123.50 180.00 112.20 1.5300 +IC C17A C16C *C16E H16E1 1.5300 112.20 120.00 111.50 1.1110 +IC C17A C16C *C16E H16E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C16C C16E C17A C17B 1.5020 112.20 180.00 112.20 1.5020 +IC C17B C16E *C17A H17A1 1.5020 112.20 120.00 110.10 1.1110 +IC C17B C16E *C17A H17A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C16E C17A C17B C17C 1.5300 112.20 180.00 123.50 1.3400 +IC C17C C17A *C17B H17B 1.3400 123.50 180.00 116.00 1.1000 +IC C17A C17B C17C C17E 1.5020 123.50 180.00 123.50 1.5020 +IC C17E C17B *C17C C17D 1.5020 123.50 180.00 123.50 1.5040 +IC C17B C17C C17D H17D1 1.3400 123.50 180.00 111.50 1.1110 +IC H17D1 C17C *C17D H17D2 1.1110 111.50 120.00 111.50 1.1110 +IC H17D1 C17C *C17D H17D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C17B C17C C17E C18A 1.3400 123.50 180.00 112.20 1.5300 +IC C18A C17C *C17E H17E1 1.5300 112.20 120.00 111.50 1.1110 +IC C18A C17C *C17E H17E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C17C C17E C18A C18B 1.5020 112.20 180.00 112.20 1.5020 +IC C18B C17E *C18A H18A1 1.5020 112.20 120.00 110.10 1.1110 +IC C18B C17E *C18A H18A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C17E C18A C18B C18C 1.5300 112.20 180.00 123.50 1.3400 +IC C18C C18A *C18B H18B 1.3400 123.50 180.00 116.00 1.1000 +IC C18A C18B C18C C18E 1.5020 123.50 180.00 123.50 1.5020 +IC C18E C18B *C18C C18D 1.5020 123.50 180.00 123.50 1.5040 +IC C18B C18C C18D H18D1 1.3400 123.50 180.00 111.50 1.1110 +IC H18D1 C18C *C18D H18D2 1.1110 111.50 120.00 111.50 1.1110 +IC H18D1 C18C *C18D H18D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C18B C18C C18E C19A 1.3400 123.50 180.00 112.20 1.5300 +IC C19A C18C *C18E H18E1 1.5300 112.20 120.00 111.50 1.1110 +IC C19A C18C *C18E H18E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C18C C18E C19A C19B 1.5020 112.20 180.00 112.20 1.5020 +IC C19B C18E *C19A H19A1 1.5020 112.20 120.00 110.10 1.1110 +IC C19B C18E *C19A H19A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C18E C19A C19B C19C 1.5300 112.20 180.00 123.50 1.3400 +IC C19C C19A *C19B H19B 1.3400 123.50 180.00 116.00 1.1000 +IC C19A C19B C19C C19D 1.5020 123.50 180.00 123.50 1.5040 +IC C19D C19B *C19C C19E 1.5040 123.50 180.00 123.50 1.5040 +IC C19B C19C C19D H19D1 1.3400 123.50 180.00 111.50 1.1110 +IC H19D1 C19C *C19D H19D2 1.1110 111.50 120.00 111.50 1.1110 +IC H19D1 C19C *C19D H19D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C19B C19C C19E H19E1 1.3400 123.50 180.00 111.50 1.1110 +IC H19E1 C19C *C19E H19E2 1.1110 111.50 120.00 111.50 1.1110 +IC H19E1 C19C *C19E H19E3 1.1110 111.50 -120.00 111.50 1.1110 + +RESI UNDPP -2.00 ! [name] +GROUP +ATOM P2 PG1 1.34 ! HO22 +ATOM O22 OG311 -0.71 ! | +ATOM HO22 HGP1 0.44 ! O22 !! based on PPI2 +ATOM O23 OG2P1 -0.86 ! | +ATOM O24 OG2P1 -0.86 ! O23==P2==O24 (-) + ! | +ATOM P1 PG1 1.46 ! O12 +ATOM O12 OG304 -0.63 ! | +ATOM O13 OG2P1 -0.83 ! O13==P1==O14 (-) +ATOM O14 OG2P1 -0.83 ! | +ATOM O11 OG303 -0.62 ! O11 + ! | +ATOM C1A CG321 -0.08 ! H1A1--C1A--H1A2 +ATOM H1A1 HGA2 0.09 ! | +ATOM H1A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C1B CG2D1 -0.15 ! C1B--H1B (cis) +ATOM H1B HGA4 0.15 ! || +GROUP 0.00 ! || H1D1 +ATOM C1C CG2D1 0.00 ! || | +GROUP 0.00 ! C1C--C1D--H1D2 +ATOM C1D CG331 -0.27 ! | | +ATOM H1D1 HGA3 0.09 ! | H1D3 +ATOM H1D2 HGA3 0.09 ! ! +ATOM H1D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C1E CG321 -0.18 ! H1E1--C1E--H1E2 +ATOM H1E1 HGA2 0.09 ! ! +ATOM H1E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C2A CG321 -0.18 ! H2A1--C2A--H2A2 +ATOM H2A1 HGA2 0.09 ! | +ATOM H2A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C2B CG2D1 -0.15 ! C2B--H2B (cis) +ATOM H2B HGA4 0.15 ! || +GROUP 0.00 ! || H2D1 +ATOM C2C CG2D1 0.00 ! || | +GROUP 0.00 ! C2C--C2D--H2D2 +ATOM C2D CG331 -0.27 ! | | +ATOM H2D1 HGA3 0.09 ! | H2D3 +ATOM H2D2 HGA3 0.09 ! ! +ATOM H2D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C2E CG321 -0.18 ! H2E1--C2E--H2E2 +ATOM H2E1 HGA2 0.09 ! ! +ATOM H2E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C3A CG321 -0.18 ! H3A1--C3A--H3A2 +ATOM H3A1 HGA2 0.09 ! | +ATOM H3A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C3B CG2D1 -0.15 ! C3B--H3B (cis) +ATOM H3B HGA4 0.15 ! || +GROUP 0.00 ! || H3D1 +ATOM C3C CG2D1 0.00 ! || | +GROUP 0.00 ! C3C--C3D--H3D2 +ATOM C3D CG331 -0.27 ! | | +ATOM H3D1 HGA3 0.09 ! | H3D3 +ATOM H3D2 HGA3 0.09 ! ! +ATOM H3D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C3E CG321 -0.18 ! H3E1--C3E--H3E2 +ATOM H3E1 HGA2 0.09 ! ! +ATOM H3E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C4A CG321 -0.18 ! H4A1--C4A--H4A2 +ATOM H4A1 HGA2 0.09 ! | +ATOM H4A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C4B CG2D1 -0.15 ! C4B--H4B (cis) +ATOM H4B HGA4 0.15 ! || +GROUP 0.00 ! || H4D1 +ATOM C4C CG2D1 0.00 ! || | +GROUP 0.00 ! C4C--C4D--H4D2 +ATOM C4D CG331 -0.27 ! | | +ATOM H4D1 HGA3 0.09 ! | H4D3 +ATOM H4D2 HGA3 0.09 ! ! +ATOM H4D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C4E CG321 -0.18 ! H4E1--C4E--H4E2 +ATOM H4E1 HGA2 0.09 ! ! +ATOM H4E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C5A CG321 -0.18 ! H5A1--C5A--H5A2 +ATOM H5A1 HGA2 0.09 ! | +ATOM H5A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C5B CG2D1 -0.15 ! C5B--H5B (cis) +ATOM H5B HGA4 0.15 ! || +GROUP 0.00 ! || H5D1 +ATOM C5C CG2D1 0.00 ! || | +GROUP 0.00 ! C5C--C5D--H5D2 +ATOM C5D CG331 -0.27 ! | | +ATOM H5D1 HGA3 0.09 ! | H5D3 +ATOM H5D2 HGA3 0.09 ! ! +ATOM H5D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C5E CG321 -0.18 ! H5E1--C5E--H5E2 +ATOM H5E1 HGA2 0.09 ! ! +ATOM H5E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C6A CG321 -0.18 ! H6A1--C6A--H6A2 +ATOM H6A1 HGA2 0.09 ! | +ATOM H6A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C6B CG2D1 -0.15 ! C6B--H6B (cis) +ATOM H6B HGA4 0.15 ! || +GROUP 0.00 ! || H6D1 +ATOM C6C CG2D1 0.00 ! || | +GROUP 0.00 ! C6C--C6D--H6D2 +ATOM C6D CG331 -0.27 ! | | +ATOM H6D1 HGA3 0.09 ! | H6D3 +ATOM H6D2 HGA3 0.09 ! ! +ATOM H6D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C6E CG321 -0.18 ! H6E1-C6E--H6E2 +ATOM H6E1 HGA2 0.09 ! ! +ATOM H6E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C7A CG321 -0.18 ! H7A1--C7A--H7A2 +ATOM H7A1 HGA2 0.09 ! | +ATOM H7A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C7B CG2D1 -0.15 ! C7B--H7B (cis) +ATOM H7B HGA4 0.15 ! || +GROUP 0.00 ! || H7D1 +ATOM C7C CG2D1 0.00 ! || | +GROUP 0.00 ! C7C--C7D--H7D2 +ATOM C7D CG331 -0.27 ! | | +ATOM H7D1 HGA3 0.09 ! | H7D3 +ATOM H7D2 HGA3 0.09 ! ! +ATOM H7D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C7E CG321 -0.18 ! H7E1-C7E--H7E2 +ATOM H7E1 HGA2 0.09 ! ! +ATOM H7E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C8A CG321 -0.18 ! H8A1--C8A--H8A2 +ATOM H8A1 HGA2 0.09 ! | +ATOM H8A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C8B CG2D1 -0.15 ! C8B--H8B (trans) +ATOM H8B HGA4 0.15 ! || +GROUP 0.00 ! || H8D1 +ATOM C8C CG2D1 0.00 ! || | +GROUP 0.00 ! C8C--C8D--H8D2 +ATOM C8D CG331 -0.27 ! | | +ATOM H8D1 HGA3 0.09 ! | H8D3 +ATOM H8D2 HGA3 0.09 ! ! +ATOM H8D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C8E CG321 -0.18 ! H8E1-C8E--H8E2 +ATOM H8E1 HGA2 0.09 ! ! +ATOM H8E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C9A CG321 -0.18 ! H9A1--C9A--H9A2 +ATOM H9A1 HGA2 0.09 ! | +ATOM H9A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C9B CG2D1 -0.15 ! C9B--H9B (trans) +ATOM H9B HGA4 0.15 ! || +GROUP 0.00 ! || H9D1 +ATOM C9C CG2D1 0.00 ! || | +GROUP 0.00 ! C9C--C9D--H9D2 +ATOM C9D CG331 -0.27 ! | | +ATOM H9D1 HGA3 0.09 ! | H9D3 +ATOM H9D2 HGA3 0.09 ! ! +ATOM H9D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C9E CG321 -0.18 ! H9E1-C9E--H9E2 +ATOM H9E1 HGA2 0.09 ! ! +ATOM H9E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C10A CG321 -0.18 ! H10A1--C10A--H10A2 +ATOM H10A1 HGA2 0.09 ! | +ATOM H10A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C10B CG2D1 -0.15 ! C10B--H110B (trans) +ATOM H10B HGA4 0.15 ! || +GROUP 0.00 ! || H10D1 +ATOM C10C CG2D1 0.00 ! || | +GROUP 0.00 ! C10C-C10D--H10D2 +ATOM C10D CG331 -0.27 ! | | +ATOM H10D1 HGA3 0.09 ! | H10D3 +ATOM H10D2 HGA3 0.09 ! ! +ATOM H10D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C10E CG321 -0.18 ! H10E1-C10E--H10E2 +ATOM H10E1 HGA2 0.09 ! ! +ATOM H10E2 HGA2 0.09 ! ! +GROUP 0.00 ! | +ATOM C11A CG321 -0.18 ! H11A1--C11A--H11A2 +ATOM H11A1 HGA2 0.09 ! | +ATOM H11A2 HGA2 0.09 ! | +GROUP 0.00 ! | +ATOM C11B CG2D1 -0.15 ! C11B--H11B +ATOM H11B HGA4 0.15 ! || +GROUP 0.00 ! || H11D1 +ATOM C11C CG2D1 0.00 ! || | +GROUP 0.00 ! C11C-C11D--H11D2 +ATOM C11D CG331 -0.27 ! | | +ATOM H11D1 HGA3 0.09 ! | H11D3 +ATOM H11D2 HGA3 0.09 ! ! +ATOM H11D3 HGA3 0.09 ! ! +GROUP 0.00 ! ! +ATOM C11E CG331 -0.27 ! H11E1-C11E--H11E2 +ATOM H11E1 HGA3 0.09 ! ! +ATOM H11E2 HGA3 0.09 ! ! +ATOM H11E3 HGA3 0.09 ! H11E3 + +BOND O22 HO22 P2 O22 P2 O23 P2 O24 P2 O12 ! Phosphate group 2 +BOND P1 O12 P1 O13 P1 O14 P1 O11 O11 C1A ! Phosphate group 1 +BOND C1A C1B C1C C1D C1C C1E ! cis isoprene backbone carbons +DOUBLE C1B C1C ! cis double bond +BOND C1A H1A1 C1A H1A2 ! C1A hydrogens +BOND C1B H1B ! C1B hydrogen +BOND C1D H1D1 C1D H1D2 C1D H1D3 ! C1D hydrogens +BOND C1E H1E1 C1E H1E2 ! C1E hydrogens +BOND C1E C2A ! isoprene linking bond +BOND C2A C2B C2C C2D C2C C2E ! cis isoprene backbone carbons +DOUBLE C2B C2C ! cis double bond +BOND C2A H2A1 C2A H2A2 ! C2A hydrogens +BOND C2B H2B ! C2B hydrogen +BOND C2D H2D1 C2D H2D2 C2D H2D3 ! C2D hydrogens +BOND C2E H2E1 C2E H2E2 ! C2E hydrogens +BOND C2E C3A ! isoprene linking bond +BOND C3A C3B C3C C3D C3C C3E ! cis isoprene backbone carbons +DOUBLE C3B C3C ! cis double bond +BOND C3A H3A1 C3A H3A2 ! C3A hydrogens +BOND C3B H3B ! C3B hydrogen +BOND C3D H3D1 C3D H3D2 C3D H3D3 ! C3D hydrogens +BOND C3E H3E1 C3E H3E2 ! C3E hydrogens +BOND C3E C4A ! isoprene linking bond +BOND C4A C4B C4C C4D C4C C4E ! cis isoprene backbone carbons +DOUBLE C4B C4C ! cis double bond +BOND C4A H4A1 C4A H4A2 ! C4A hydrogens +BOND C4B H4B ! C4B hydrogen +BOND C4D H4D1 C4D H4D2 C4D H4D3 ! C4D hydrogens +BOND C4E H4E1 C4E H4E2 ! C4E hydrogens +BOND C4E C5A ! isoprene linking bond +BOND C5A C5B C5C C5D C5C C5E ! cis isoprene backbone carbons +DOUBLE C5B C5C ! cis double bond +BOND C5A H5A1 C5A H5A2 ! C5A hydrogens +BOND C5B H5B ! C5B hydrogen +BOND C5D H5D1 C5D H5D2 C5D H5D3 ! C5D hydrogens +BOND C5E H5E1 C5E H5E2 ! C5E hydrogens +BOND C5E C6A ! isoprene linking bond +BOND C6A C6B C6C C6D C6C C6E ! cis isoprene backbone carbons +DOUBLE C6B C6C ! cis double bond +BOND C6A H6A1 C6A H6A2 ! C6A hydrogens +BOND C6B H6B ! C6B hydrogen +BOND C6D H6D1 C6D H6D2 C6D H6D3 ! C6D hydrogens +BOND C6E H6E1 C6E H6E2 ! C6E hydrogens +BOND C6E C7A ! isoprene linking bond +BOND C7A C7B C7C C7D C7C C7E ! cis isoprene backbone carbons +DOUBLE C7B C7C ! cis double bond +BOND C7A H7A1 C7A H7A2 ! C7A hydrogens +BOND C7B H7B ! C7B hydrogen +BOND C7D H7D1 C7D H7D2 C7D H7D3 ! C7D hydrogens +BOND C7E H7E1 C7E H7E2 ! C7E hydrogens +BOND C7E C8A ! isoprene linking bond +BOND C8A C8B C8C C8D C8C C8E ! trans isoprene backbone carbons +DOUBLE C8B C8C ! trans double bond +BOND C8A H8A1 C8A H8A2 ! C8A hydrogens +BOND C8B H8B ! C8B hydrogen +BOND C8D H8D1 C8D H8D2 C8D H8D3 ! C8D hydrogens +BOND C8E H8E1 C8E H8E2 ! C8E hydrogens +BOND C8E C9A ! isoprene linking bond +BOND C9A C9B C9C C9D C9C C9E ! trans isoprene backbone carbons +DOUBLE C9B C9C ! trans double bond +BOND C9A H9A1 C9A H9A2 ! C9A hydrogens +BOND C9B H9B ! C9B hydrogen +BOND C9D H9D1 C9D H9D2 C9D H9D3 ! C9D hydrogens +BOND C9E H9E1 C9E H9E2 ! C9E hydrogens +BOND C9E C10A ! isoprene linking bond +BOND C10A C10B C10C C10D C10C C10E ! trans isoprene backbone carbons +DOUBLE C10B C10C ! trans double bond +BOND C10A H10A1 C10A H10A2 ! C10A hydrogens +BOND C10B H10B ! C10B hydrogen +BOND C10D H10D1 C10D H10D2 C10D H10D3 ! C10D hydrogens +BOND C10E H10E1 C10E H10E2 ! C10E hydrogens +BOND C10E C11A ! isoprene linking bond +BOND C11A C11B C11C C11D C11C C11E ! isoprene backbone carbons +DOUBLE C11B C11C ! double bond +BOND C11A H11A1 C11A H11A2 ! C11A hydrogens +BOND C11B H11B ! C11B hydrogen +BOND C11D H11D1 C11D H11D2 C11D H11D3 ! C11D hydrogens +BOND C11E H11E1 C11E H11E2 C11E H11E3 ! C11E hydrogens +IC O22 O12 *P2 O23 1.6100 111.00 120.00 111.60 1.5100 +IC O22 O12 *P2 O24 1.6100 111.00 -120.00 111.60 1.5100 +IC O12 P2 O22 HO22 1.6750 111.00 180.00 115.00 0.9600 +IC O22 P2 O12 P1 1.6100 111.00 180.00 143.00 1.6750 +IC P2 O12 P1 O11 1.6750 143.00 180.00 105.00 1.6500 +IC O11 O12 *P1 O13 1.6500 105.00 120.00 111.60 1.5100 +IC O11 O12 *P1 O14 1.5100 111.60 -120.00 111.60 1.5100 +IC O12 P1 O11 C1A 1.6750 105.00 180.00 120.00 1.4400 +IC P1 O11 C1A C1B 1.6500 120.00 180.00 110.10 1.5300 +IC C1B O11 *C1A H1A1 1.5300 110.10 120.00 109.50 1.1110 +IC C1B O11 *C1A H1A2 1.5300 110.10 -120.00 109.50 1.1110 +IC O11 C1A C1B C1C 1.4400 110.10 180.00 113.50 1.5380 +IC C1C C1A *C1B H1B 1.3400 123.50 180.00 116.00 1.1000 +IC C1A C1B C1C C1D 1.5020 123.50 180.00 123.50 1.5020 +IC C1E C1B *C1C C1D 1.5020 123.50 180.00 123.50 1.5040 +IC C1B C1C C1D H1D1 1.3400 123.50 180.00 111.50 1.1110 +IC H1D1 C1C *C1D H1D2 1.1110 111.50 120.00 111.50 1.1110 +IC H1D1 C1C *C1D H1D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C1B C1C C1E C2A 1.3400 123.50 180.00 112.20 1.5300 +IC C2A C1C *C1E H1E1 1.5300 112.20 120.00 111.50 1.1110 +IC C2A C1C *C1E H1E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C1C C1E C2A C2B 1.5020 112.20 180.00 112.20 1.5020 +IC C2B C1E *C2A H2A1 1.5020 112.20 120.00 110.10 1.1110 +IC C2B C1E *C2A H2A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C1E C2A C2B C2C 1.5300 112.20 180.00 123.50 1.3400 +IC C2C C2A *C2B H2B 1.3400 123.50 180.00 116.00 1.1000 +IC C2A C2B C2C C2D 1.5020 123.50 180.00 123.50 1.5020 +IC C2E C2B *C2C C2D 1.5020 123.50 180.00 123.50 1.5040 +IC C2B C2C C2D H2D1 1.3400 123.50 180.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D2 1.1110 111.50 120.00 111.50 1.1110 +IC H2D1 C2C *C2D H2D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C2B C2C C2E C3A 1.3400 123.50 180.00 112.20 1.5300 +IC C3A C2C *C2E H2E1 1.5300 112.20 120.00 111.50 1.1110 +IC C3A C2C *C2E H2E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C2C C2E C3A C3B 1.5020 112.20 180.00 112.20 1.5020 +IC C3B C2E *C3A H3A1 1.5020 112.20 120.00 110.10 1.1110 +IC C3B C2E *C3A H3A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C2E C3A C3B C3C 1.5300 112.20 180.00 123.50 1.3400 +IC C3C C3A *C3B H3B 1.3400 123.50 180.00 116.00 1.1000 +IC C3A C3B C3C C3D 1.5020 123.50 180.00 123.50 1.5020 +IC C3E C3B *C3C C3D 1.5020 123.50 180.00 123.50 1.5040 +IC C3B C3C C3D H3D1 1.3400 123.50 180.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D2 1.1110 111.50 120.00 111.50 1.1110 +IC H3D1 C3C *C3D H3D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C3B C3C C3E C4A 1.3400 123.50 180.00 112.20 1.5300 +IC C4A C3C *C3E H3E1 1.5300 112.20 120.00 111.50 1.1110 +IC C4A C3C *C3E H3E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C3C C3E C4A C4B 1.5020 112.20 180.00 112.20 1.5020 +IC C4B C3E *C4A H4A1 1.5020 112.20 120.00 110.10 1.1110 +IC C4B C3E *C4A H4A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C3E C4A C4B C4C 1.5300 112.20 180.00 123.50 1.3400 +IC C4C C4A *C4B H4B 1.3400 123.50 180.00 116.00 1.1000 +IC C4A C4B C4C C4D 1.5020 123.50 180.00 123.50 1.5020 +IC C4E C4B *C4C C4D 1.5020 123.50 180.00 123.50 1.5040 +IC C4B C4C C4D H4D1 1.3400 123.50 180.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D2 1.1110 111.50 120.00 111.50 1.1110 +IC H4D1 C4C *C4D H4D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C4B C4C C4E C5A 1.3400 123.50 180.00 112.20 1.5300 +IC C5A C4C *C4E H4E1 1.5300 112.20 120.00 111.50 1.1110 +IC C5A C4C *C4E H4E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C4C C4E C5A C5B 1.5020 112.20 180.00 112.20 1.5020 +IC C5B C4E *C5A H5A1 1.5020 112.20 120.00 110.10 1.1110 +IC C5B C4E *C5A H5A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C4E C5A C5B C5C 1.5300 112.20 180.00 123.50 1.3400 +IC C5C C5A *C5B H5B 1.3400 123.50 180.00 116.00 1.1000 +IC C5A C5B C5C C5D 1.5020 123.50 180.00 123.50 1.5020 +IC C5E C5B *C5C C5D 1.5020 123.50 180.00 123.50 1.5040 +IC C5B C5C C5D H5D1 1.3400 123.50 180.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D2 1.1110 111.50 120.00 111.50 1.1110 +IC H5D1 C5C *C5D H5D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C5B C5C C5E C6A 1.3400 123.50 180.00 112.20 1.5300 +IC C6A C5C *C5E H5E1 1.5300 112.20 120.00 111.50 1.1110 +IC C6A C5C *C5E H5E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C5C C5E C6A C6B 1.5020 112.20 180.00 112.20 1.5020 +IC C6B C5E *C6A H6A1 1.5020 112.20 120.00 110.10 1.1110 +IC C6B C5E *C6A H6A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C5E C6A C6B C6C 1.5300 112.20 180.00 123.50 1.3400 +IC C6C C6A *C6B H6B 1.3400 123.50 180.00 116.00 1.1000 +IC C6A C6B C6C C6D 1.5020 123.50 180.00 123.50 1.5020 +IC C6E C6B *C6C C6D 1.5020 123.50 180.00 123.50 1.5040 +IC C6B C6C C6D H6D1 1.3400 123.50 180.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D2 1.1110 111.50 120.00 111.50 1.1110 +IC H6D1 C6C *C6D H6D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C6B C6C C6E C7A 1.3400 123.50 180.00 112.20 1.5300 +IC C7A C6C *C6E H6E1 1.5300 112.20 120.00 111.50 1.1110 +IC C7A C6C *C6E H6E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C6C C6E C7A C7B 1.5020 112.20 180.00 112.20 1.5020 +IC C7B C6E *C7A H7A1 1.5020 112.20 120.00 110.10 1.1110 +IC C7B C6E *C7A H7A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C6E C7A C7B C7C 1.5300 112.20 180.00 123.50 1.3400 +IC C7C C7A *C7B H7B 1.3400 123.50 180.00 116.00 1.1000 +IC C7A C7B C7C C7D 1.5020 123.50 180.00 123.50 1.5020 +IC C7E C7B *C7C C7D 1.5020 123.50 180.00 123.50 1.5040 +IC C7B C7C C7D H7D1 1.3400 123.50 180.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D2 1.1110 111.50 120.00 111.50 1.1110 +IC H7D1 C7C *C7D H7D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C7B C7C C7E C8A 1.3400 123.50 180.00 112.20 1.5300 +IC C8A C7C *C7E H7E1 1.5300 112.20 120.00 111.50 1.1110 +IC C8A C7C *C7E H7E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C7C C7E C8A C8B 1.5020 112.20 180.00 112.20 1.5020 +IC C8B C7E *C8A H8A1 1.5020 112.20 120.00 110.10 1.1110 +IC C8B C7E *C8A H8A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C7E C8A C8B C8C 1.5300 112.20 180.00 123.50 1.3400 +IC C8C C8A *C8B H8B 1.3400 123.50 180.00 116.00 1.1000 +IC C8A C8B C8C C8D 1.5020 123.50 0.00 123.50 1.5020 +IC C8E C8B *C8C C8D 1.5020 123.50 180.00 123.50 1.5040 +IC C8B C8C C8D H8D1 1.3400 123.50 180.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D2 1.1110 111.50 120.00 111.50 1.1110 +IC H8D1 C8C *C8D H8D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C8B C8C C8E C9A 1.3400 123.50 180.00 112.20 1.5300 +IC C9A C8C *C8E H8E1 1.5300 112.20 120.00 111.50 1.1110 +IC C9A C8C *C8E H8E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C8C C8E C9A C9B 1.5020 112.20 180.00 112.20 1.5020 +IC C9B C8E *C9A H9A1 1.5020 112.20 120.00 110.10 1.1110 +IC C9B C8E *C9A H9A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C8E C9A C9B C9C 1.5300 112.20 180.00 123.50 1.3400 +IC C9C C9A *C9B H9B 1.3400 123.50 180.00 116.00 1.1000 +IC C9A C9B C9C C9D 1.5020 123.50 0.00 123.50 1.5020 +IC C9E C9B *C9C C9D 1.5020 123.50 180.00 123.50 1.5040 +IC C9B C9C C9D H9D1 1.3400 123.50 180.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D2 1.1110 111.50 120.00 111.50 1.1110 +IC H9D1 C9C *C9D H9D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C9B C9C C9E C10A 1.3400 123.50 180.00 112.20 1.5300 +IC C10A C9C *C9E H9E1 1.5300 112.20 120.00 111.50 1.1110 +IC C10A C9C *C9E H9E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C9C C9E C10A C10B 1.5020 112.20 180.00 112.20 1.5020 +IC C10B C9E *C10A H10A1 1.5020 112.20 120.00 110.10 1.1110 +IC C10B C9E *C10A H10A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C9E C10A C10B C10C 1.5300 112.20 180.00 123.50 1.3400 +IC C10C C10A *C10B H10B 1.3400 123.50 180.00 116.00 1.1000 +IC C10A C10B C10C C10D 1.5020 123.50 0.00 123.50 1.5020 +IC C10E C10B *C10C C10D 1.5020 123.50 180.00 123.50 1.5040 +IC C10B C10C C10D H10D1 1.3400 123.50 180.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D2 1.1110 111.50 120.00 111.50 1.1110 +IC H10D1 C10C *C10D H10D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C10B C10C C10E C11A 1.3400 123.50 180.00 112.20 1.5300 +IC C11A C10C *C10E H10E1 1.5300 112.20 120.00 111.50 1.1110 +IC C11A C10C *C10E H10E2 1.1110 111.50 -120.00 111.50 1.1110 +IC C10C C10E C11A C11B 1.5020 112.20 180.00 112.20 1.5020 +IC C11B C10E *C11A H11A1 1.5020 112.20 120.00 110.10 1.1110 +IC C11B C10E *C11A H11A2 1.5020 112.20 -120.00 110.10 1.1110 +IC C10E C11A C11B C11C 1.5300 112.20 180.00 123.50 1.3400 +IC C11C C11A *C11B H11B 1.3400 123.50 180.00 116.00 1.1000 +IC C11A C11B C11C C11D 1.5020 123.50 180.00 123.50 1.5020 +IC C11E C11B *C11C C11D 1.5020 123.50 180.00 123.50 1.5040 +IC C11B C11C C11D H11D1 1.3400 123.50 180.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D2 1.1110 111.50 120.00 111.50 1.1110 +IC H11D1 C11C *C11D H11D3 1.1110 111.50 -120.00 111.50 1.1110 +IC C11B C11C C11E H11E1 1.5300 112.20 180.00 111.50 1.1110 +IC C11B C11C *C11E H11E2 1.1110 111.50 120.00 111.50 1.1110 +IC C11B C11C *C11E H11E3 1.1110 111.50 -120.00 111.50 1.1110 + +PRES LLLO -2.10 ! linkage for dol-P-P and sugar +dele atom 1HO1 ! +dele atom 1O1 ! +dele atom 2HO22 ! +GROUP ! +ATOM 1C1 CC3162 0.30 ! adjust to make this section charge 0.1 (same as the dol part) +ATOM 1H1 HCA1 0.09 ! +ATOM 1C5 CC3163 0.02 ! H5 +ATOM 1H5 HCA1 0.09 ! \ +ATOM 1O5 OC3C61 -0.40 ! C5-------O5 + ! / \ H1 + ! / \ / + ! C4 C1 + ! \ / \ + ! \ / \ + ! C3------C2 \ + ! \ + ! \ + ! \ +ATOM 2P2 PG1 1.50 ! \ +ATOM 2O22 OG303 -0.62 ! O22 +ATOM 2O23 OG2P1 -0.82 ! | +ATOM 2O24 OG2P1 -0.82 ! O23==P2==O24 (-) + ! | +ATOM 2O12 OG304 -0.68 ! O12 +ATOM 2P1 PG1 1.50 ! | +ATOM 2O13 OG2P1 -0.82 ! O13==P1==O14 (-) +ATOM 2O14 OG2P1 -0.82 ! | +ATOM 2O11 OG303 -0.62 ! O11 + ! | +!ATOM 2C1 CG321 -0.08! H11--C1--H12 +!ATOM 2H11 HGA2 0.09! | +!ATOM 2H12 HGA2 0.09! | + +BOND 1C1 2O22 + +!Thermalized IC +!IC 1C3 1C2 1C1 2O22 1.5364 112.47 -174.92 109.44 1.4102 +!IC 1C2 2O22 *1C1 1H1 1.5323 109.44 -120.96 109.46 1.1223 +IC 1C3 1C2 1C1 1H1 1.5364 112.47 180.00 109.44 1.4102 +IC 1C2 1H1 *1C1 2O22 1.5323 109.44 -120.00 109.46 1.1223 +IC 1C2 1C1 2O22 2P2 1.5323 109.44 -84.54 127.66 1.5968 +IC 1C1 2O22 2P2 2O12 1.4102 127.66 -174.21 102.94 1.5071 +IC 2O22 2O12 *2P2 2O23 1.5968 102.94 113.03 118.81 1.5471 +IC 2O22 2O12 *2P2 2O24 1.5968 102.94 -113.60 109.37 1.4811 + +END + +read param card flex append +* LLO related parameters +* + +BONDS +!LLLO +CC3162 OG303 360.00 1.425 !! from CC3162 OC30P 360.00 1.425 ! + +ANGLES +!DOL-PP +CG331 CG2D1 CG331 48.00 123.50 !! from CG321 CG2D1 CG331 48.00 123.50 ! RETINOL TMCH +!LLLO +OG303 CC3162 HCA1 60.00 109.50 !! from OC30P CC3162 HCA1 60.00 109.50 ! par35 HCA2 CC32A OC30A +OG303 CC3162 OC3C61 90.00 110.00 !! from OC30P CC3162 OC3C61 90.00 110.00 +OG303 CC3162 CC3161 45.00 109.00 !! from OC30P CC3162 CC3161 45.00 109.00 +CC3162 OG303 PG1 20.00 120.00 35.0 2.33 !! from CC3162 OC30P PC 20.0 120.0 35.0 2.33 ! same in CGenFF (CG311 OG303 PG1 from CG321 OG303 PG1) +!UND-PP +CG2D1 CG321 OG303 75.70 110.10 !! from CG2D1 CG321 OG311 75.70 110.10 ! RETINOL PROL + +DIHEDRALS +!DOL-PP +CG311 CG321 CG321 OG303 0.1950 3 0.00 !! from CG321 CG321 CG321 OG303 0.1950 3 0.00 ! PROT alkane update, adm jr., 3/2/92 +CG2D1 CG321 CG321 CG311 0.1400 1 180.0 !! from CG2D1 CG321 CG321 CG321 0.1400 1 180.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG311 0.1700 2 0.0 !! from CG2D1 CG321 CG321 CG321 0.1700 2 0.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG311 0.0500 3 180.0 !! from CG2D1 CG321 CG321 CG321 0.0500 3 180.0 ! 2-hexene, adm jr., 11/09 +CG2D1 CG321 CG321 CG2D1 0.1400 1 180.0 !! from CG2D1 CG321 CG321 CG321 0.1400 1 180.0 ! 2-hexene, adm jr., 11/09 ; potential candidate for optimization -- kevo +CG2D1 CG321 CG321 CG2D1 0.1700 2 0.0 !! from CG2D1 CG321 CG321 CG321 0.1700 2 0.0 ! 2-hexene, adm jr., 11/09 ; potential candidate for optimization -- kevo +CG2D1 CG321 CG321 CG2D1 0.0500 3 180.0 !! from CG2D1 CG321 CG321 CG321 0.0500 3 180.0 ! 2-hexene, adm jr., 11/09 ; potential candidate for optimization -- kevo +CG331 CG2D1 CG331 HGA3 0.3000 3 0.00 !! from CG331 CG2DC1 CG331 HGA3 0.3000 3 0.00 ! RETINOL DMP1, 4-methyl-1,3-pentadiene ; alternative CG321 CG2D1 CG331 HGA3, RETINOL TMCH is cyclic so probably worse -- kevo +!LLLO +CC3162 OG303 PG1 OG2P1 0.33 3 0.0 !! from CC3162 OC30P PC OC2DP 0.33 3 0.0 ! probably better with the old phosphate charges in the topology (and the L-J haven't changed) -- kevo +CC3162 OG303 PG1 OG304 1.45 2 0.0 !! from CC3162 OC30P PC OC312 1.45 2 0.0 ! probably better with the old phosphate charges in the topology (and the L-J haven't changed) -- kevo +HCA1 CC3162 OG303 PG1 0.284 3 0.0 !! from HCA1 CC3162 OC30P PC 0.284 3 0.0 ! dmp,eps, H-C3'-O3'-P || from the par_all27_na.prm +OC3C61 CC3162 OG303 PG1 0.38 2 0.0 !! from OC3C61 CC3162 OC30P PC 0.38 2 0.0 +OC3C61 CC3162 OG303 PG1 0.41 3 180.0 !! from OC3C61 CC3162 OC30P PC 0.41 3 180.0 +CC3161 CC3162 OG303 PG1 0.02 3 180.0 !! from CC3161 CC3162 OC30P PC 0.02 3 180.0 +CC3163 OC3C61 CC3162 OG303 2.44 3 180.0 !! from CC3163 OC3C61 CC3162 OC30P 2.44 3 180.0 +HCA1 CC3161 CC3162 OG303 0.20 3 0.0 !! from HCA1 CC3161 CC3162 OC30P 0.20 3 0.0 ! par27 X CTL1 CTL2 X +CC3161 CC3161 CC3162 OG303 1.76 1 0.0 !! from CC3161 CC3161 CC3162 OC30P 1.76 1 0.0 +CC3161 CC3161 CC3162 OG303 2.56 2 0.0 !! from CC3161 CC3161 CC3162 OC30P 2.56 2 0.0 +CC3161 CC3161 CC3162 OG303 0.01 3 0.0 !! from CC3161 CC3161 CC3162 OC30P 0.01 3 0.0 +OG303 CC3162 CC3161 NC2D1 0.20 3 0.0 !! from OC301 CC3162 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +!BBAC +CC331 CC3163 CC3161 NC2D1 0.20 3 0.0 !! from CC312 CC3163 CC3161 NC2D1 0.20 3 0.0 ! par27 X CTL1 CTL1 X +!UND-PP +CG2D1 CG2D1 CG321 OG303 1.9000 1 180.00 !! from CG2D2 CG2D1 CG321 OG311 and CG2DC1 CG2DC1 CG321 OG311 , RETINOL PROL +CG2D1 CG2D1 CG321 OG303 0.4000 2 180.00 !! from CG2D2 CG2D1 CG321 OG311 and CG2DC1 CG2DC1 CG321 OG311 , RETINOL PROL +CG2D1 CG2D1 CG321 OG303 0.6000 3 180.00 !! from CG2D2 CG2D1 CG321 OG311 and CG2DC1 CG2DC1 CG321 OG311 , RETINOL PROL +HGA4 CG2D1 CG321 OG303 0.2000 3 0.00 !! from HGA4 CG2D1 CG321 OG311 and HGA4 CG2DC1 CG321 OG311 , RETINOL PROL +CG2D1 CG321 OG303 PG1 0.6000 1 180.00 !! from CG321 CG321 OG303 PG1 0.6000 1 180.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others ; potential candidate for optimization -- kevo +CG2D1 CG321 OG303 PG1 0.6500 2 0.00 !! from CG321 CG321 OG303 PG1 0.6500 2 0.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others ; potential candidate for optimization -- kevo +CG2D1 CG321 OG303 PG1 0.0500 3 0.00 !! from CG321 CG321 OG303 PG1 0.0500 3 0.00 ! EP_2 phospho-ser/thr !Reorganization: BPET and others ; potential candidate for optimization -- kevo + + +END + +RETURN + diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_miscellaneous.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_miscellaneous.str new file mode 100644 index 00000000..0421c924 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_miscellaneous.str @@ -0,0 +1,17105 @@ +read rtf card append flex +* Topology for miscellaneous lipids +* +32 1 + + +!* cardiolipin molecule assembly kit; append this file to the all36_lipid set +!* begun may 2010 rick venable, nih/nhlbi Lab of computational biology +!* venabler at nhlbi*nih*gov +!* + +RESI DXPC 0.00 ! di-palmitoleic-phosphatidylcholine (diC16:1) +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C15 N C12 C11 1.5031 108.03 -62.19 116.82 1.5409 +IC C13 C12 *N C14 1.4955 110.60 122.73 109.67 1.4976 +IC C13 C12 *N C15 1.4955 110.60 -119.76 108.04 1.5032 +IC C13 N C12 C11 1.4955 110.60 57.52 116.83 1.5412 +IC C11 N *C12 H12A 1.5412 116.83 -126.40 111.94 1.0787 +IC H12A N *C12 H12B 1.0787 111.94 -116.29 108.17 1.0974 +IC C14 N C13 H13A 1.4976 110.99 179.50 109.35 1.0869 +IC H13A N *C13 H13B 1.0869 109.35 118.93 111.32 1.0813 +IC H13A N *C13 H13C 1.0869 109.35 -119.04 111.19 1.0811 +IC C13 N C14 H14A 1.4955 110.99 -179.22 109.65 1.0877 +IC H14A N *C14 H14B 1.0877 109.65 118.74 110.91 1.0820 +IC H14A N *C14 H14C 1.0877 109.65 -119.76 111.49 1.0812 +IC C13 N C15 H15A 1.4955 109.44 -64.69 111.04 1.0951 +IC H15A N *C15 H15B 1.0951 111.04 123.93 113.87 1.0740 +IC H15A N *C15 H15C 1.0951 111.04 -112.38 110.25 1.0938 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DGPC 0.0 ! di-gadoleic-phosphatidylcholine (diC20:1) +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! || (CIS) | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.27 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || (CIS) +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X +DOUBLE C311 C312 +BOND C312 H12X C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 H20Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C15 N C12 C11 1.5031 108.03 -62.19 116.82 1.5409 +IC C13 C12 *N C14 1.4955 110.60 122.73 109.67 1.4976 +IC C13 C12 *N C15 1.4955 110.60 -119.76 108.04 1.5032 +IC C13 N C12 C11 1.4955 110.60 57.52 116.83 1.5412 +IC C11 N *C12 H12A 1.5412 116.83 -126.40 111.94 1.0787 +IC H12A N *C12 H12B 1.0787 111.94 -116.29 108.17 1.0974 +IC C14 N C13 H13A 1.4976 110.99 179.50 109.35 1.0869 +IC H13A N *C13 H13B 1.0869 109.35 118.93 111.32 1.0813 +IC H13A N *C13 H13C 1.0869 109.35 -119.04 111.19 1.0811 +IC C13 N C14 H14A 1.4955 110.99 -179.22 109.65 1.0877 +IC H14A N *C14 H14B 1.0877 109.65 118.74 110.91 1.0820 +IC H14A N *C14 H14C 1.0877 109.65 -119.76 111.49 1.0812 +IC C13 N C15 H15A 1.4955 109.44 -64.69 111.04 1.0951 +IC H15A N *C15 H15B 1.0951 111.04 123.93 113.87 1.0740 +IC H15A N *C15 H15C 1.0951 111.04 -112.38 110.25 1.0938 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5344 112.48 176.92 112.46 1.5398 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5356 112.46 -178.53 111.43 1.5097 +IC C211 C29 *C210 H10R 1.5097 111.43 -123.58 107.80 1.1132 +IC H10R C29 *C210 H10S 1.1132 107.80 -115.43 108.37 1.1128 +IC C29 C210 C211 C212 1.5398 111.43 -126.96 126.62 1.3465 +IC C212 C210 *C211 H11R 1.3465 126.62 178.41 114.65 1.1012 +IC C210 C211 C212 C213 1.5097 126.62 -1.69 126.32 1.5088 +IC C213 C211 *C212 H12R 1.5088 126.32 -179.55 118.79 1.1012 +IC C211 C212 C213 C214 1.3465 126.32 93.02 112.15 1.5392 +IC C214 C212 *C213 H13R 1.5392 112.15 -121.30 111.28 1.1133 +IC H13R C212 *C213 H13S 1.1133 111.28 -117.50 110.00 1.1126 +IC C212 C213 C214 C215 1.5088 112.15 -178.81 112.29 1.5354 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5345 112.59 -179.58 112.63 1.5347 +IC C218 C216 *C217 H17R 1.5347 112.63 -121.36 109.09 1.1132 +IC H17R C216 *C217 H17S 1.1132 109.09 -117.38 109.07 1.1132 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5347 112.69 -179.93 113.30 1.5309 +IC C220 C218 *C219 H19R 1.5309 113.30 -121.70 108.75 1.1140 +IC H19R C218 *C219 H19S 1.1140 108.75 -116.65 108.73 1.1141 +IC C218 C219 C220 H20R 1.5339 113.30 -59.98 110.46 1.1113 +IC H20R C219 *C220 H20S 1.1113 110.46 119.84 110.45 1.1114 +IC H20R C219 *C220 H20T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5345 112.42 -176.73 112.80 1.5356 +IC C39 C37 *C38 H8X 1.5356 112.80 -121.69 109.16 1.1130 +IC H8X C37 *C38 H8Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C37 C38 C39 C310 1.5349 112.80 178.92 112.27 1.5402 +IC C310 C38 *C39 H9X 1.5402 112.27 -121.37 108.23 1.1139 +IC H9X C38 *C39 H9Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C38 C39 C310 C311 1.5356 112.27 -174.92 111.69 1.5099 +IC C311 C39 *C310 H10X 1.5099 111.69 -124.14 107.77 1.1124 +IC H10X C39 *C310 H10Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C39 C310 C311 C312 1.5402 111.69 -121.39 127.35 1.3470 +IC C312 C310 *C311 H11X 1.3470 127.35 179.11 114.24 1.1012 +IC C310 C311 C312 C313 1.5099 127.35 -0.69 127.25 1.5096 +IC C313 C311 *C312 H12X 1.5096 127.25 179.82 118.43 1.1012 +IC C311 C312 C313 C314 1.3470 127.25 106.03 111.65 1.5393 +IC C314 C312 *C313 H13X 1.5393 111.65 -121.49 112.10 1.1123 +IC H13X C312 *C313 H13Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C312 C313 C314 C315 1.5096 111.65 179.63 112.41 1.5355 +IC C315 C313 *C314 H14X 1.5355 112.41 -121.09 109.75 1.1135 +IC H14X C313 *C314 H14Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5347 112.66 -179.12 112.61 1.5348 +IC C318 C316 *C317 H17X 1.5348 112.61 -121.34 109.09 1.1132 +IC H17X C316 *C317 H17Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5348 112.71 -179.67 113.30 1.5309 +IC C320 C318 *C319 H19X 1.5309 113.30 -121.68 108.77 1.1141 +IC H19X C318 *C319 H19Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C318 C319 C320 H20X 1.5340 113.30 -59.94 110.46 1.1113 +IC H20X C319 *C320 H20Y 1.1113 110.46 119.86 110.45 1.1113 +IC H20X C319 *C320 H20Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DEPC 0.0 !!! di-erucic-phosphatidylcholine (diC22:1) +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! || (CIS) | +ATOM C214 CEL1 -0.15 ! || | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CEL1 -0.15 ! | +ATOM H13X HEL1 0.15 ! H13X---C313 +GROUP ! || (CIS) +ATOM C314 CEL1 -0.15 ! || +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL3 -0.27 ! | +ATOM H22X HAL3 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL3 0.09 ! | +ATOM H22Z HAL3 0.09 ! H22Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X +DOUBLE C313 C314 +BOND C314 H14X C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 H22Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C15 N C12 C11 1.5031 108.03 -62.19 116.82 1.5409 +IC C13 C12 *N C14 1.4955 110.60 122.73 109.67 1.4976 +IC C13 C12 *N C15 1.4955 110.60 -119.76 108.04 1.5032 +IC C13 N C12 C11 1.4955 110.60 57.52 116.83 1.5412 +IC C11 N *C12 H12A 1.5412 116.83 -126.40 111.94 1.0787 +IC H12A N *C12 H12B 1.0787 111.94 -116.29 108.17 1.0974 +IC C14 N C13 H13A 1.4976 110.99 179.50 109.35 1.0869 +IC H13A N *C13 H13B 1.0869 109.35 118.93 111.32 1.0813 +IC H13A N *C13 H13C 1.0869 109.35 -119.04 111.19 1.0811 +IC C13 N C14 H14A 1.4955 110.99 -179.22 109.65 1.0877 +IC H14A N *C14 H14B 1.0877 109.65 118.74 110.91 1.0820 +IC H14A N *C14 H14C 1.0877 109.65 -119.76 111.49 1.0812 +IC C13 N C15 H15A 1.4955 109.44 -64.69 111.04 1.0951 +IC H15A N *C15 H15B 1.0951 111.04 123.93 113.87 1.0740 +IC H15A N *C15 H15C 1.0951 111.04 -112.38 110.25 1.0938 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5344 112.48 176.92 112.46 1.5398 +IC C211 C29 *C210 H10R 1.5398 112.46 -121.38 108.40 1.1139 +IC H10R C29 *C210 H10S 1.1139 108.40 -116.93 108.77 1.1139 +IC C29 C210 C211 C212 1.5344 112.48 176.92 112.46 1.5398 +IC C212 C210 *C211 H11R 1.5398 112.46 -121.38 108.40 1.1139 +IC H11R C210 *C211 H11S 1.1139 108.40 -116.93 108.77 1.1139 +IC C210 C211 C212 C213 1.5356 112.46 -178.53 111.43 1.5097 +IC C213 C211 *C212 H12R 1.5097 111.43 -123.58 107.80 1.1132 +IC H12R C211 *C212 H12S 1.1132 107.80 -115.43 108.37 1.1128 +IC C211 C212 C213 C214 1.5398 111.43 -126.96 126.62 1.3465 +IC C214 C212 *C213 H13R 1.3465 126.62 178.41 114.65 1.1012 +IC C212 C213 C214 C215 1.5097 126.62 -1.69 126.32 1.5088 +IC C215 C213 *C214 H14R 1.5088 126.32 -179.55 118.79 1.1012 +IC C213 C214 C215 C216 1.3465 126.32 93.02 112.15 1.5392 +IC C216 C214 *C215 H15R 1.5392 112.15 -121.30 111.28 1.1133 +IC H15R C214 *C215 H15S 1.1133 111.28 -117.50 110.00 1.1126 +IC C214 C215 C216 C217 1.5088 112.15 -178.81 112.29 1.5354 +IC C217 C215 *C216 H16R 1.5354 112.29 -121.34 109.78 1.1133 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5345 112.59 -179.58 112.63 1.5347 +IC C220 C218 *C219 H19R 1.5347 112.63 -121.36 109.09 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.09 -117.38 109.07 1.1132 +IC C218 C219 C220 C221 1.5347 112.63 179.65 112.69 1.5339 +IC C221 C219 *C220 H20R 1.5339 112.69 -121.27 109.11 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.11 -117.36 109.14 1.1132 +IC C219 C220 C221 C222 1.5347 112.69 -179.93 113.30 1.5309 +IC C222 C220 *C221 H21R 1.5309 113.30 -121.70 108.75 1.1140 +IC H21R C220 *C221 H21S 1.1140 108.75 -116.65 108.73 1.1141 +IC C220 C221 C222 H22R 1.5339 113.30 -59.98 110.46 1.1113 +IC H22R C221 *C222 H22S 1.1113 110.46 119.84 110.45 1.1114 +IC H22R C221 *C222 H22T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5447 111.73 -176.74 112.91 1.5345 +IC C39 C37 *C38 H8X 1.5345 112.91 -121.67 109.15 1.1134 +IC H8X C37 *C38 H8Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5345 112.91 -121.67 109.15 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C38 C39 C310 C311 1.5447 111.73 -176.74 112.91 1.5345 +IC C311 C39 *C310 H10X 1.5345 112.91 -121.67 109.15 1.1134 +IC H10X C39 *C310 H10Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5356 112.27 -174.92 111.69 1.5099 +IC C313 C311 *C312 H12X 1.5099 111.69 -124.14 107.77 1.1124 +IC H12X C311 *C312 H12Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C311 C312 C313 C314 1.5402 111.69 -121.39 127.35 1.3470 +IC C314 C312 *C313 H13X 1.3470 127.35 179.11 114.24 1.1012 +IC C312 C313 C314 C315 1.5099 127.35 -0.69 127.25 1.5096 +IC C315 C313 *C314 H14X 1.5096 127.25 179.82 118.43 1.1012 +IC C313 C314 C315 C316 1.3470 127.25 106.03 111.65 1.5393 +IC C316 C314 *C315 H15X 1.5393 111.65 -121.49 112.10 1.1123 +IC H15X C314 *C315 H15Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C314 C315 C316 C317 1.5096 111.65 179.63 112.41 1.5355 +IC C317 C315 *C316 H16X 1.5355 112.41 -121.09 109.75 1.1135 +IC H16X C315 *C316 H16Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5347 112.66 -179.12 112.61 1.5348 +IC C320 C318 *C319 H19X 1.5348 112.61 -121.34 109.09 1.1132 +IC H19X C318 *C319 H19Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C318 C319 C320 C321 1.5347 112.61 179.83 112.71 1.5340 +IC C321 C319 *C320 H20X 1.5340 112.71 -121.28 109.10 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C319 C320 C321 C322 1.5348 112.71 -179.67 113.30 1.5309 +IC C322 C320 *C321 H21X 1.5309 113.30 -121.68 108.77 1.1141 +IC H21X C320 *C321 H21Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C320 C321 C322 H22X 1.5340 113.30 -59.94 110.46 1.1113 +IC H22X C321 *C322 H22Y 1.1113 110.46 119.86 110.45 1.1113 +IC H22X C321 *C322 H22Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DNPC 0.0 ! di-nervonic-phosphatidylcholine (diC24:1) +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! || (CIS) | +ATOM C216 CEL1 -0.15 ! || | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL2 -0.18 ! | | +ATOM H22R HAL2 0.09 ! H22R---C222--H22S | +ATOM H22S HAL2 0.09 ! | | +GROUP ! | | +ATOM C223 CTL2 -0.18 ! | | +ATOM H23R HAL2 0.09 ! H23R---C223--H23S | +ATOM H23S HAL2 0.09 ! | | +GROUP ! | | +ATOM C224 CTL3 -0.27 ! | | +ATOM H24R HAL3 0.09 ! H24R---C224--H24S | +ATOM H24S HAL3 0.09 ! | | +ATOM H24T HAL3 0.09 ! H24T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CEL1 -0.15 ! | +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! || (CIS) +ATOM C316 CEL1 -0.15 ! || +ATOM H16X HEL1 0.15 ! H16X---C316 +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL2 -0.18 ! | +ATOM H22X HAL2 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL2 0.09 ! | +GROUP ! | +ATOM C323 CTL2 -0.18 ! | +ATOM H23X HAL2 0.09 ! H23X---C323--H23Y +ATOM H23Y HAL2 0.09 ! | +GROUP ! | +ATOM C324 CTL3 -0.27 ! | +ATOM H24X HAL3 0.09 ! H24X---C324--H24Y +ATOM H24Y HAL3 0.09 ! | +ATOM H24Z HAL3 0.09 ! H24Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R +DOUBLE C215 C216 +BOND C216 H16R C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 C223 +BOND C223 H23R C223 H23S C223 C224 +BOND C224 H24R C224 H24S C224 H24T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X +DOUBLE C315 C316 +BOND C316 H16X C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 C323 +BOND C323 H23X C323 H23Y C323 C324 +BOND C324 H24X C324 H24Y C324 H24Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C15 N C12 C11 1.5031 108.03 -62.19 116.82 1.5409 +IC C13 C12 *N C14 1.4955 110.60 122.73 109.67 1.4976 +IC C13 C12 *N C15 1.4955 110.60 -119.76 108.04 1.5032 +IC C13 N C12 C11 1.4955 110.60 57.52 116.83 1.5412 +IC C11 N *C12 H12A 1.5412 116.83 -126.40 111.94 1.0787 +IC H12A N *C12 H12B 1.0787 111.94 -116.29 108.17 1.0974 +IC C14 N C13 H13A 1.4976 110.99 179.50 109.35 1.0869 +IC H13A N *C13 H13B 1.0869 109.35 118.93 111.32 1.0813 +IC H13A N *C13 H13C 1.0869 109.35 -119.04 111.19 1.0811 +IC C13 N C14 H14A 1.4955 110.99 -179.22 109.65 1.0877 +IC H14A N *C14 H14B 1.0877 109.65 118.74 110.91 1.0820 +IC H14A N *C14 H14C 1.0877 109.65 -119.76 111.49 1.0812 +IC C13 N C15 H15A 1.4955 109.44 -64.69 111.04 1.0951 +IC H15A N *C15 H15B 1.0951 111.04 123.93 113.87 1.0740 +IC H15A N *C15 H15C 1.0951 111.04 -112.38 110.25 1.0938 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5339 112.69 -121.27 109.11 1.1132 +IC H9R C28 *C29 H9S 1.1132 109.11 -117.36 109.14 1.1132 +IC C28 C29 C210 C211 1.5345 112.59 -179.58 112.63 1.5347 +IC C211 C29 *C210 H10R 1.5347 112.63 -121.36 109.09 1.1132 +IC H10R C29 *C210 H10S 1.1132 109.09 -117.38 109.07 1.1132 +IC C29 C210 C211 C212 1.5345 112.59 -179.58 112.63 1.5347 +IC C212 C210 *C211 H11R 1.5347 112.63 -121.36 109.09 1.1132 +IC H11R C210 *C211 H11S 1.1132 109.09 -117.38 109.07 1.1132 +IC C210 C211 C212 C213 1.5345 112.59 -179.58 112.63 1.5347 +IC C213 C211 *C212 H12R 1.5347 112.63 -121.36 109.09 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.09 -117.38 109.07 1.1132 +IC C211 C212 C213 C214 1.5344 112.48 176.92 112.46 1.5398 +IC C214 C212 *C213 H13R 1.5398 112.46 -121.38 108.40 1.1139 +IC H13R C212 *C213 H13S 1.1139 108.40 -116.93 108.77 1.1139 +IC C212 C213 C214 C215 1.5356 112.46 -178.53 111.43 1.5097 +IC C215 C213 *C214 H14R 1.5097 111.43 -123.58 107.80 1.1132 +IC H14R C213 *C214 H14S 1.1132 107.80 -115.43 108.37 1.1128 +IC C213 C214 C215 C216 1.5398 111.43 -126.96 126.62 1.3465 +IC C216 C214 *C215 H15R 1.3465 126.62 178.41 114.65 1.1012 +IC C214 C215 C216 C217 1.5097 126.62 -1.69 126.32 1.5088 !!! +IC C217 C215 *C216 H16R 1.5088 126.32 -179.55 118.79 1.1012 +IC C215 C216 C217 C218 1.3465 126.32 93.02 112.15 1.5392 +IC C218 C216 *C217 H17R 1.5392 112.15 -121.30 111.28 1.1133 +IC H17R C216 *C217 H17S 1.1133 111.28 -117.50 110.00 1.1126 +IC C216 C217 C218 C219 1.5088 112.15 -178.81 112.29 1.5354 +IC C219 C217 *C218 H18R 1.5354 112.29 -121.34 109.78 1.1133 +IC H18R C217 *C218 H18S 1.1133 109.78 -118.01 109.42 1.1144 +IC C217 C218 C219 C220 1.5392 112.29 179.81 112.68 1.5345 +IC C220 C218 *C219 H19R 1.5345 112.68 -121.26 109.04 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.04 -117.39 109.10 1.1131 +IC C218 C219 C220 C221 1.5354 112.68 179.80 112.59 1.5347 +IC C221 C219 *C220 H20R 1.5347 112.59 -121.29 109.09 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.09 -117.37 109.11 1.1133 +IC C219 C220 C221 C222 1.5345 112.59 -179.58 112.63 1.5347 +IC C222 C220 *C221 H21R 1.5347 112.63 -121.36 109.09 1.1132 +IC H21R C220 *C221 H21S 1.1132 109.09 -117.38 109.07 1.1132 +IC C220 C221 C222 C223 1.5347 112.63 179.65 112.69 1.5339 +IC C223 C221 *C222 H22R 1.5339 112.69 -121.27 109.11 1.1132 +IC H22R C221 *C222 H22S 1.1132 109.11 -117.36 109.14 1.1132 +IC C221 C222 C223 C224 1.5347 112.69 -179.93 113.30 1.5309 +IC C224 C222 *C223 H23R 1.5309 113.30 -121.70 108.75 1.1140 +IC H23R C222 *C223 H23S 1.1140 108.75 -116.65 108.73 1.1141 +IC C222 C223 C224 H24R 1.5339 113.30 -59.98 110.46 1.1113 +IC H24R C223 *C224 H24S 1.1113 110.46 119.84 110.45 1.1114 +IC H24R C223 *C224 H24T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5349 112.80 178.92 112.27 1.5402 +IC C39 C37 *C38 H8X 1.5402 112.27 -121.37 108.23 1.1139 +IC H8X C37 *C38 H8Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5349 112.42 -120.99 108.94 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C38 C39 C310 C311 1.5345 112.42 -176.73 112.80 1.5356 +IC C311 C39 *C310 H10X 1.5356 112.80 -121.69 109.16 1.1130 +IC H10X C39 *C310 H10Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5345 112.42 -176.73 112.80 1.5356 +IC C313 C311 *C312 H12X 1.5349 112.42 -120.99 108.94 1.1133 +IC H12X C311 *C312 H12Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C311 C312 C313 C314 1.5349 112.80 178.92 112.27 1.5402 +IC C314 C312 *C313 H13X 1.5402 112.27 -121.37 108.23 1.1139 +IC H13X C312 *C313 H13Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C312 C313 C314 C315 1.5356 112.27 -174.92 111.69 1.5099 +IC C315 C313 *C314 H14X 1.5099 111.69 -124.14 107.77 1.1124 +IC H14X C313 *C314 H14Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C313 C314 C315 C316 1.5402 111.69 -121.39 127.35 1.3470 +IC C316 C314 *C315 H15X 1.3470 127.35 179.11 114.24 1.1012 +IC C314 C315 C316 C317 1.5099 127.35 -0.69 127.25 1.5096 +IC C317 C315 *C316 H16X 1.5096 127.25 179.82 118.43 1.1012 +IC C315 C316 C317 C318 1.3470 127.25 106.03 111.65 1.5393 +IC C318 C316 *C317 H17X 1.5393 111.65 -121.49 112.10 1.1123 +IC H17X C316 *C317 H17Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C316 C317 C318 C319 1.5096 111.65 179.63 112.41 1.5355 +IC C319 C317 *C318 H18X 1.5355 112.41 -121.09 109.75 1.1135 +IC H18X C317 *C318 H18Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C317 C318 C319 C320 1.5393 112.41 -178.89 112.60 1.5347 +IC C320 C318 *C319 H19X 1.5347 112.60 -121.37 109.10 1.1131 +IC H19X C318 *C319 H19Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C318 C319 C320 C321 1.5355 112.60 179.88 112.66 1.5347 +IC C321 C319 *C320 H20X 1.5347 112.66 -121.27 109.06 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C319 C320 C321 C322 1.5347 112.66 -179.12 112.61 1.5348 +IC C322 C320 *C321 H21X 1.5348 112.61 -121.34 109.09 1.1132 +IC H21X C320 *C321 H21Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C320 C321 C322 C323 1.5347 112.61 179.83 112.71 1.5340 +IC C323 C321 *C322 H22X 1.5340 112.71 -121.28 109.10 1.1132 +IC H22X C321 *C322 H22Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C321 C322 C323 C324 1.5348 112.71 -179.67 113.30 1.5309 +IC C324 C322 *C323 H23X 1.5309 113.30 -121.68 108.77 1.1141 +IC H23X C322 *C323 H23Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C322 C323 C324 H24X 1.5340 113.30 -59.94 110.46 1.1113 +IC H24X C323 *C324 H24Y 1.1113 110.46 119.86 110.45 1.1113 +IC H24X C323 *C324 H24Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DXPE 0.00 ! di-palmitoleic-phosphatidylethanolamine (diC16:1) +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DGPE 0.0 ! di-gadoleic-phosphatidylethanolamine (diC20:1) +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! || (CIS) | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.27 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || (CIS) +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X +DOUBLE C311 C312 +BOND C312 H12X C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 H20Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5344 112.48 176.92 112.46 1.5398 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5356 112.46 -178.53 111.43 1.5097 +IC C211 C29 *C210 H10R 1.5097 111.43 -123.58 107.80 1.1132 +IC H10R C29 *C210 H10S 1.1132 107.80 -115.43 108.37 1.1128 +IC C29 C210 C211 C212 1.5398 111.43 -126.96 126.62 1.3465 +IC C212 C210 *C211 H11R 1.3465 126.62 178.41 114.65 1.1012 +IC C210 C211 C212 C213 1.5097 126.62 -1.69 126.32 1.5088 +IC C213 C211 *C212 H12R 1.5088 126.32 -179.55 118.79 1.1012 +IC C211 C212 C213 C214 1.3465 126.32 93.02 112.15 1.5392 +IC C214 C212 *C213 H13R 1.5392 112.15 -121.30 111.28 1.1133 +IC H13R C212 *C213 H13S 1.1133 111.28 -117.50 110.00 1.1126 +IC C212 C213 C214 C215 1.5088 112.15 -178.81 112.29 1.5354 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5345 112.59 -179.58 112.63 1.5347 +IC C218 C216 *C217 H17R 1.5347 112.63 -121.36 109.09 1.1132 +IC H17R C216 *C217 H17S 1.1132 109.09 -117.38 109.07 1.1132 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5347 112.69 -179.93 113.30 1.5309 +IC C220 C218 *C219 H19R 1.5309 113.30 -121.70 108.75 1.1140 +IC H19R C218 *C219 H19S 1.1140 108.75 -116.65 108.73 1.1141 +IC C218 C219 C220 H20R 1.5339 113.30 -59.98 110.46 1.1113 +IC H20R C219 *C220 H20S 1.1113 110.46 119.84 110.45 1.1114 +IC H20R C219 *C220 H20T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5345 112.42 -176.73 112.80 1.5356 +IC C39 C37 *C38 H8X 1.5356 112.80 -121.69 109.16 1.1130 +IC H8X C37 *C38 H8Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C37 C38 C39 C310 1.5349 112.80 178.92 112.27 1.5402 +IC C310 C38 *C39 H9X 1.5402 112.27 -121.37 108.23 1.1139 +IC H9X C38 *C39 H9Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C38 C39 C310 C311 1.5356 112.27 -174.92 111.69 1.5099 +IC C311 C39 *C310 H10X 1.5099 111.69 -124.14 107.77 1.1124 +IC H10X C39 *C310 H10Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C39 C310 C311 C312 1.5402 111.69 -121.39 127.35 1.3470 +IC C312 C310 *C311 H11X 1.3470 127.35 179.11 114.24 1.1012 +IC C310 C311 C312 C313 1.5099 127.35 -0.69 127.25 1.5096 +IC C313 C311 *C312 H12X 1.5096 127.25 179.82 118.43 1.1012 +IC C311 C312 C313 C314 1.3470 127.25 106.03 111.65 1.5393 +IC C314 C312 *C313 H13X 1.5393 111.65 -121.49 112.10 1.1123 +IC H13X C312 *C313 H13Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C312 C313 C314 C315 1.5096 111.65 179.63 112.41 1.5355 +IC C315 C313 *C314 H14X 1.5355 112.41 -121.09 109.75 1.1135 +IC H14X C313 *C314 H14Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5347 112.66 -179.12 112.61 1.5348 +IC C318 C316 *C317 H17X 1.5348 112.61 -121.34 109.09 1.1132 +IC H17X C316 *C317 H17Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5348 112.71 -179.67 113.30 1.5309 +IC C320 C318 *C319 H19X 1.5309 113.30 -121.68 108.77 1.1141 +IC H19X C318 *C319 H19Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C318 C319 C320 H20X 1.5340 113.30 -59.94 110.46 1.1113 +IC H20X C319 *C320 H20Y 1.1113 110.46 119.86 110.45 1.1113 +IC H20X C319 *C320 H20Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DEPE 0.0 !!! di-erucic-phosphatidylethanolamine (diC22:1) +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! || (CIS) | +ATOM C214 CEL1 -0.15 ! || | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CEL1 -0.15 ! | +ATOM H13X HEL1 0.15 ! H13X---C313 +GROUP ! || (CIS) +ATOM C314 CEL1 -0.15 ! || +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL3 -0.27 ! | +ATOM H22X HAL3 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL3 0.09 ! | +ATOM H22Z HAL3 0.09 ! H22Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X +DOUBLE C313 C314 +BOND C314 H14X C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 H22Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5344 112.48 176.92 112.46 1.5398 +IC C211 C29 *C210 H10R 1.5398 112.46 -121.38 108.40 1.1139 +IC H10R C29 *C210 H10S 1.1139 108.40 -116.93 108.77 1.1139 +IC C29 C210 C211 C212 1.5344 112.48 176.92 112.46 1.5398 +IC C212 C210 *C211 H11R 1.5398 112.46 -121.38 108.40 1.1139 +IC H11R C210 *C211 H11S 1.1139 108.40 -116.93 108.77 1.1139 +IC C210 C211 C212 C213 1.5356 112.46 -178.53 111.43 1.5097 +IC C213 C211 *C212 H12R 1.5097 111.43 -123.58 107.80 1.1132 +IC H12R C211 *C212 H12S 1.1132 107.80 -115.43 108.37 1.1128 +IC C211 C212 C213 C214 1.5398 111.43 -126.96 126.62 1.3465 +IC C214 C212 *C213 H13R 1.3465 126.62 178.41 114.65 1.1012 +IC C212 C213 C214 C215 1.5097 126.62 -1.69 126.32 1.5088 +IC C215 C213 *C214 H14R 1.5088 126.32 -179.55 118.79 1.1012 +IC C213 C214 C215 C216 1.3465 126.32 93.02 112.15 1.5392 +IC C216 C214 *C215 H15R 1.5392 112.15 -121.30 111.28 1.1133 +IC H15R C214 *C215 H15S 1.1133 111.28 -117.50 110.00 1.1126 +IC C214 C215 C216 C217 1.5088 112.15 -178.81 112.29 1.5354 +IC C217 C215 *C216 H16R 1.5354 112.29 -121.34 109.78 1.1133 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5345 112.59 -179.58 112.63 1.5347 +IC C220 C218 *C219 H19R 1.5347 112.63 -121.36 109.09 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.09 -117.38 109.07 1.1132 +IC C218 C219 C220 C221 1.5347 112.63 179.65 112.69 1.5339 +IC C221 C219 *C220 H20R 1.5339 112.69 -121.27 109.11 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.11 -117.36 109.14 1.1132 +IC C219 C220 C221 C222 1.5347 112.69 -179.93 113.30 1.5309 +IC C222 C220 *C221 H21R 1.5309 113.30 -121.70 108.75 1.1140 +IC H21R C220 *C221 H21S 1.1140 108.75 -116.65 108.73 1.1141 +IC C220 C221 C222 H22R 1.5339 113.30 -59.98 110.46 1.1113 +IC H22R C221 *C222 H22S 1.1113 110.46 119.84 110.45 1.1114 +IC H22R C221 *C222 H22T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5447 111.73 -176.74 112.91 1.5345 +IC C39 C37 *C38 H8X 1.5345 112.91 -121.67 109.15 1.1134 +IC H8X C37 *C38 H8Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5345 112.91 -121.67 109.15 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C38 C39 C310 C311 1.5447 111.73 -176.74 112.91 1.5345 +IC C311 C39 *C310 H10X 1.5345 112.91 -121.67 109.15 1.1134 +IC H10X C39 *C310 H10Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5356 112.27 -174.92 111.69 1.5099 +IC C313 C311 *C312 H12X 1.5099 111.69 -124.14 107.77 1.1124 +IC H12X C311 *C312 H12Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C311 C312 C313 C314 1.5402 111.69 -121.39 127.35 1.3470 +IC C314 C312 *C313 H13X 1.3470 127.35 179.11 114.24 1.1012 +IC C312 C313 C314 C315 1.5099 127.35 -0.69 127.25 1.5096 +IC C315 C313 *C314 H14X 1.5096 127.25 179.82 118.43 1.1012 +IC C313 C314 C315 C316 1.3470 127.25 106.03 111.65 1.5393 +IC C316 C314 *C315 H15X 1.5393 111.65 -121.49 112.10 1.1123 +IC H15X C314 *C315 H15Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C314 C315 C316 C317 1.5096 111.65 179.63 112.41 1.5355 +IC C317 C315 *C316 H16X 1.5355 112.41 -121.09 109.75 1.1135 +IC H16X C315 *C316 H16Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5347 112.66 -179.12 112.61 1.5348 +IC C320 C318 *C319 H19X 1.5348 112.61 -121.34 109.09 1.1132 +IC H19X C318 *C319 H19Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C318 C319 C320 C321 1.5347 112.61 179.83 112.71 1.5340 +IC C321 C319 *C320 H20X 1.5340 112.71 -121.28 109.10 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C319 C320 C321 C322 1.5348 112.71 -179.67 113.30 1.5309 +IC C322 C320 *C321 H21X 1.5309 113.30 -121.68 108.77 1.1141 +IC H21X C320 *C321 H21Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C320 C321 C322 H22X 1.5340 113.30 -59.94 110.46 1.1113 +IC H22X C321 *C322 H22Y 1.1113 110.46 119.86 110.45 1.1113 +IC H22X C321 *C322 H22Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DNPE 0.0 ! di-nervonic-phosphatidylethanolamine (diC24:1) +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! || (CIS) | +ATOM C216 CEL1 -0.15 ! || | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL2 -0.18 ! | | +ATOM H22R HAL2 0.09 ! H22R---C222--H22S | +ATOM H22S HAL2 0.09 ! | | +GROUP ! | | +ATOM C223 CTL2 -0.18 ! | | +ATOM H23R HAL2 0.09 ! H23R---C223--H23S | +ATOM H23S HAL2 0.09 ! | | +GROUP ! | | +ATOM C224 CTL3 -0.27 ! | | +ATOM H24R HAL3 0.09 ! H24R---C224--H24S | +ATOM H24S HAL3 0.09 ! | | +ATOM H24T HAL3 0.09 ! H24T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CEL1 -0.15 ! | +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! || (CIS) +ATOM C316 CEL1 -0.15 ! || +ATOM H16X HEL1 0.15 ! H16X---C316 +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL2 -0.18 ! | +ATOM H22X HAL2 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL2 0.09 ! | +GROUP ! | +ATOM C323 CTL2 -0.18 ! | +ATOM H23X HAL2 0.09 ! H23X---C323--H23Y +ATOM H23Y HAL2 0.09 ! | +GROUP ! | +ATOM C324 CTL3 -0.27 ! | +ATOM H24X HAL3 0.09 ! H24X---C324--H24Y +ATOM H24Y HAL3 0.09 ! | +ATOM H24Z HAL3 0.09 ! H24Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R +DOUBLE C215 C216 +BOND C216 H16R C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 C223 +BOND C223 H23R C223 H23S C223 C224 +BOND C224 H24R C224 H24S C224 H24T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X +DOUBLE C315 C316 +BOND C316 H16X C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 C323 +BOND C323 H23X C323 H23Y C323 C324 +BOND C324 H24X C324 H24Y C324 H24Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5339 112.69 -121.27 109.11 1.1132 +IC H9R C28 *C29 H9S 1.1132 109.11 -117.36 109.14 1.1132 +IC C28 C29 C210 C211 1.5345 112.59 -179.58 112.63 1.5347 +IC C211 C29 *C210 H10R 1.5347 112.63 -121.36 109.09 1.1132 +IC H10R C29 *C210 H10S 1.1132 109.09 -117.38 109.07 1.1132 +IC C29 C210 C211 C212 1.5345 112.59 -179.58 112.63 1.5347 +IC C212 C210 *C211 H11R 1.5347 112.63 -121.36 109.09 1.1132 +IC H11R C210 *C211 H11S 1.1132 109.09 -117.38 109.07 1.1132 +IC C210 C211 C212 C213 1.5345 112.59 -179.58 112.63 1.5347 +IC C213 C211 *C212 H12R 1.5347 112.63 -121.36 109.09 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.09 -117.38 109.07 1.1132 +IC C211 C212 C213 C214 1.5344 112.48 176.92 112.46 1.5398 +IC C214 C212 *C213 H13R 1.5398 112.46 -121.38 108.40 1.1139 +IC H13R C212 *C213 H13S 1.1139 108.40 -116.93 108.77 1.1139 +IC C212 C213 C214 C215 1.5356 112.46 -178.53 111.43 1.5097 +IC C215 C213 *C214 H14R 1.5097 111.43 -123.58 107.80 1.1132 +IC H14R C213 *C214 H14S 1.1132 107.80 -115.43 108.37 1.1128 +IC C213 C214 C215 C216 1.5398 111.43 -126.96 126.62 1.3465 +IC C216 C214 *C215 H15R 1.3465 126.62 178.41 114.65 1.1012 +IC C214 C215 C216 C217 1.5097 126.62 -1.69 126.32 1.5088 !!! +IC C217 C215 *C216 H16R 1.5088 126.32 -179.55 118.79 1.1012 +IC C215 C216 C217 C218 1.3465 126.32 93.02 112.15 1.5392 +IC C218 C216 *C217 H17R 1.5392 112.15 -121.30 111.28 1.1133 +IC H17R C216 *C217 H17S 1.1133 111.28 -117.50 110.00 1.1126 +IC C216 C217 C218 C219 1.5088 112.15 -178.81 112.29 1.5354 +IC C219 C217 *C218 H18R 1.5354 112.29 -121.34 109.78 1.1133 +IC H18R C217 *C218 H18S 1.1133 109.78 -118.01 109.42 1.1144 +IC C217 C218 C219 C220 1.5392 112.29 179.81 112.68 1.5345 +IC C220 C218 *C219 H19R 1.5345 112.68 -121.26 109.04 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.04 -117.39 109.10 1.1131 +IC C218 C219 C220 C221 1.5354 112.68 179.80 112.59 1.5347 +IC C221 C219 *C220 H20R 1.5347 112.59 -121.29 109.09 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.09 -117.37 109.11 1.1133 +IC C219 C220 C221 C222 1.5345 112.59 -179.58 112.63 1.5347 +IC C222 C220 *C221 H21R 1.5347 112.63 -121.36 109.09 1.1132 +IC H21R C220 *C221 H21S 1.1132 109.09 -117.38 109.07 1.1132 +IC C220 C221 C222 C223 1.5347 112.63 179.65 112.69 1.5339 +IC C223 C221 *C222 H22R 1.5339 112.69 -121.27 109.11 1.1132 +IC H22R C221 *C222 H22S 1.1132 109.11 -117.36 109.14 1.1132 +IC C221 C222 C223 C224 1.5347 112.69 -179.93 113.30 1.5309 +IC C224 C222 *C223 H23R 1.5309 113.30 -121.70 108.75 1.1140 +IC H23R C222 *C223 H23S 1.1140 108.75 -116.65 108.73 1.1141 +IC C222 C223 C224 H24R 1.5339 113.30 -59.98 110.46 1.1113 +IC H24R C223 *C224 H24S 1.1113 110.46 119.84 110.45 1.1114 +IC H24R C223 *C224 H24T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5349 112.80 178.92 112.27 1.5402 +IC C39 C37 *C38 H8X 1.5402 112.27 -121.37 108.23 1.1139 +IC H8X C37 *C38 H8Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5349 112.42 -120.99 108.94 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C38 C39 C310 C311 1.5345 112.42 -176.73 112.80 1.5356 +IC C311 C39 *C310 H10X 1.5356 112.80 -121.69 109.16 1.1130 +IC H10X C39 *C310 H10Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5345 112.42 -176.73 112.80 1.5356 +IC C313 C311 *C312 H12X 1.5349 112.42 -120.99 108.94 1.1133 +IC H12X C311 *C312 H12Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C311 C312 C313 C314 1.5349 112.80 178.92 112.27 1.5402 +IC C314 C312 *C313 H13X 1.5402 112.27 -121.37 108.23 1.1139 +IC H13X C312 *C313 H13Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C312 C313 C314 C315 1.5356 112.27 -174.92 111.69 1.5099 +IC C315 C313 *C314 H14X 1.5099 111.69 -124.14 107.77 1.1124 +IC H14X C313 *C314 H14Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C313 C314 C315 C316 1.5402 111.69 -121.39 127.35 1.3470 +IC C316 C314 *C315 H15X 1.3470 127.35 179.11 114.24 1.1012 +IC C314 C315 C316 C317 1.5099 127.35 -0.69 127.25 1.5096 +IC C317 C315 *C316 H16X 1.5096 127.25 179.82 118.43 1.1012 +IC C315 C316 C317 C318 1.3470 127.25 106.03 111.65 1.5393 +IC C318 C316 *C317 H17X 1.5393 111.65 -121.49 112.10 1.1123 +IC H17X C316 *C317 H17Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C316 C317 C318 C319 1.5096 111.65 179.63 112.41 1.5355 +IC C319 C317 *C318 H18X 1.5355 112.41 -121.09 109.75 1.1135 +IC H18X C317 *C318 H18Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C317 C318 C319 C320 1.5393 112.41 -178.89 112.60 1.5347 +IC C320 C318 *C319 H19X 1.5347 112.60 -121.37 109.10 1.1131 +IC H19X C318 *C319 H19Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C318 C319 C320 C321 1.5355 112.60 179.88 112.66 1.5347 +IC C321 C319 *C320 H20X 1.5347 112.66 -121.27 109.06 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C319 C320 C321 C322 1.5347 112.66 -179.12 112.61 1.5348 +IC C322 C320 *C321 H21X 1.5348 112.61 -121.34 109.09 1.1132 +IC H21X C320 *C321 H21Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C320 C321 C322 C323 1.5347 112.61 179.83 112.71 1.5340 +IC C323 C321 *C322 H22X 1.5340 112.71 -121.28 109.10 1.1132 +IC H22X C321 *C322 H22Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C321 C322 C323 C324 1.5348 112.71 -179.67 113.30 1.5309 +IC C324 C322 *C323 H23X 1.5309 113.30 -121.68 108.77 1.1141 +IC H23X C322 *C323 H23Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C322 C323 C324 H24X 1.5340 113.30 -59.94 110.46 1.1113 +IC H24X C323 *C324 H24Y 1.1113 110.46 119.86 110.45 1.1113 +IC H24X C323 *C324 H24Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI SAPE 0.00 ! 1-Stearoyl-2-Arachidonyl-Phosphatidylethanolamine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5329 113.78 68.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 120.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 120.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 120.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 120.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 120.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 120.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SLPE 0.00 ! 1-Stearoyl-2-Linoleoyl-Phosphatidylethanolamine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI PLPE 0.00 ! 1-palmitoyl-2-linoleoyl-Phosphatidylethanolamine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4243 108.43 -123.15 113.04 1.1139 +IC H11A C12 *C11 H11B 1.1139 113.04 -118.48 109.10 1.1129 +IC C12 C11 O12 P 1.5420 108.43 -67.66 118.24 1.5905 +IC C11 O12 P O11 1.4243 118.24 -168.65 103.08 1.5759 +IC O11 O12 *P O13 1.5759 103.08 117.52 107.25 1.4784 +IC O11 O12 *P O14 1.5759 103.08 -117.26 106.69 1.4808 +IC O12 P O11 C1 1.5905 103.08 53.06 121.96 1.4290 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI SLPC 0.00 ! 1-Stearoyl-2-Linoleoyl-Phosphatidylcholine +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C15 N C12 C11 1.5031 108.03 -62.19 116.82 1.5409 +IC C13 C12 *N C14 1.4955 110.60 122.73 109.67 1.4976 +IC C13 C12 *N C15 1.4955 110.60 -119.76 108.04 1.5032 +IC C13 N C12 C11 1.4955 110.60 57.52 116.83 1.5412 +IC C11 N *C12 H12A 1.5412 116.83 -126.40 111.94 1.0787 +IC H12A N *C12 H12B 1.0787 111.94 -116.29 108.17 1.0974 +IC C14 N C13 H13A 1.4976 110.99 179.50 109.35 1.0869 +IC H13A N *C13 H13B 1.0869 109.35 118.93 111.32 1.0813 +IC H13A N *C13 H13C 1.0869 109.35 -119.04 111.19 1.0811 +IC C13 N C14 H14A 1.4955 110.99 -179.22 109.65 1.0877 +IC H14A N *C14 H14B 1.0877 109.65 118.74 110.91 1.0820 +IC H14A N *C14 H14C 1.0877 109.65 -119.76 111.49 1.0812 +IC C13 N C15 H15A 1.4955 109.44 -64.69 111.04 1.0951 +IC H15A N *C15 H15B 1.0951 111.04 123.93 113.87 1.0740 +IC H15A N *C15 H15C 1.0951 111.04 -112.38 110.25 1.0938 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI PLPC 0.00 ! 1-palmitoyl-2-linoleoyl-Phosphatidylcholine +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 N C12 C11 1.4950 110.81 58.46 117.00 1.5420 +IC C13 C12 *N C14 1.4950 110.81 122.75 109.46 1.4979 +IC C13 C12 *N C15 1.4950 110.81 -120.02 108.16 1.5034 +IC C11 N *C12 H12A 1.5420 117.00 -126.73 111.85 1.0787 +IC H12A N *C12 H12B 1.0787 111.85 -115.99 107.93 1.0977 +IC C14 N C13 H13A 1.4979 111.01 179.36 109.41 1.0866 +IC H13A N *C13 H13B 1.0866 109.41 119.11 111.31 1.0813 +IC H13A N *C13 H13C 1.0866 109.41 -119.02 111.10 1.0815 +IC C13 N C14 H14A 1.4950 111.01 -179.09 109.58 1.0882 +IC H14A N *C14 H14B 1.0882 109.58 118.63 110.95 1.0819 +IC H14A N *C14 H14C 1.0882 109.58 -119.72 111.56 1.0811 +IC C13 N C15 H15A 1.4950 109.49 -176.86 110.11 1.0949 +IC H15A N *C15 H15B 1.0949 110.11 112.40 111.19 1.0942 +IC H15A N *C15 H15C 1.0949 110.11 -123.40 113.89 1.0740 +IC N C12 C11 O12 1.5227 117.00 126.96 108.43 1.4243 +IC O12 C12 *C11 H11A 1.4243 108.43 -123.15 113.04 1.1139 +IC H11A C12 *C11 H11B 1.1139 113.04 -118.48 109.10 1.1129 +IC C12 C11 O12 P 1.5420 108.43 -67.66 118.24 1.5905 +IC C11 O12 P O11 1.4243 118.24 -168.65 103.08 1.5759 +IC O11 O12 *P O13 1.5759 103.08 117.52 107.25 1.4784 +IC O11 O12 *P O14 1.5759 103.08 -117.26 106.69 1.4808 +IC O12 P O11 C1 1.5905 103.08 53.06 121.96 1.4290 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI DXPS -1.00 ! di-palmitoleic-phosphatidylserine (diC16:1) +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DGPS -1.0 ! di-gadoleic-phosphatidylserine (diC20:1) +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! || (CIS) | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.27 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || (CIS) +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X +DOUBLE C311 C312 +BOND C312 H12X C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 H20Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5344 112.48 176.92 112.46 1.5398 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5356 112.46 -178.53 111.43 1.5097 +IC C211 C29 *C210 H10R 1.5097 111.43 -123.58 107.80 1.1132 +IC H10R C29 *C210 H10S 1.1132 107.80 -115.43 108.37 1.1128 +IC C29 C210 C211 C212 1.5398 111.43 -126.96 126.62 1.3465 +IC C212 C210 *C211 H11R 1.3465 126.62 178.41 114.65 1.1012 +IC C210 C211 C212 C213 1.5097 126.62 -1.69 126.32 1.5088 +IC C213 C211 *C212 H12R 1.5088 126.32 -179.55 118.79 1.1012 +IC C211 C212 C213 C214 1.3465 126.32 93.02 112.15 1.5392 +IC C214 C212 *C213 H13R 1.5392 112.15 -121.30 111.28 1.1133 +IC H13R C212 *C213 H13S 1.1133 111.28 -117.50 110.00 1.1126 +IC C212 C213 C214 C215 1.5088 112.15 -178.81 112.29 1.5354 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5345 112.59 -179.58 112.63 1.5347 +IC C218 C216 *C217 H17R 1.5347 112.63 -121.36 109.09 1.1132 +IC H17R C216 *C217 H17S 1.1132 109.09 -117.38 109.07 1.1132 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5347 112.69 -179.93 113.30 1.5309 +IC C220 C218 *C219 H19R 1.5309 113.30 -121.70 108.75 1.1140 +IC H19R C218 *C219 H19S 1.1140 108.75 -116.65 108.73 1.1141 +IC C218 C219 C220 H20R 1.5339 113.30 -59.98 110.46 1.1113 +IC H20R C219 *C220 H20S 1.1113 110.46 119.84 110.45 1.1114 +IC H20R C219 *C220 H20T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5345 112.42 -176.73 112.80 1.5356 +IC C39 C37 *C38 H8X 1.5356 112.80 -121.69 109.16 1.1130 +IC H8X C37 *C38 H8Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C37 C38 C39 C310 1.5349 112.80 178.92 112.27 1.5402 +IC C310 C38 *C39 H9X 1.5402 112.27 -121.37 108.23 1.1139 +IC H9X C38 *C39 H9Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C38 C39 C310 C311 1.5356 112.27 -174.92 111.69 1.5099 +IC C311 C39 *C310 H10X 1.5099 111.69 -124.14 107.77 1.1124 +IC H10X C39 *C310 H10Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C39 C310 C311 C312 1.5402 111.69 -121.39 127.35 1.3470 +IC C312 C310 *C311 H11X 1.3470 127.35 179.11 114.24 1.1012 +IC C310 C311 C312 C313 1.5099 127.35 -0.69 127.25 1.5096 +IC C313 C311 *C312 H12X 1.5096 127.25 179.82 118.43 1.1012 +IC C311 C312 C313 C314 1.3470 127.25 106.03 111.65 1.5393 +IC C314 C312 *C313 H13X 1.5393 111.65 -121.49 112.10 1.1123 +IC H13X C312 *C313 H13Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C312 C313 C314 C315 1.5096 111.65 179.63 112.41 1.5355 +IC C315 C313 *C314 H14X 1.5355 112.41 -121.09 109.75 1.1135 +IC H14X C313 *C314 H14Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5347 112.66 -179.12 112.61 1.5348 +IC C318 C316 *C317 H17X 1.5348 112.61 -121.34 109.09 1.1132 +IC H17X C316 *C317 H17Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5348 112.71 -179.67 113.30 1.5309 +IC C320 C318 *C319 H19X 1.5309 113.30 -121.68 108.77 1.1141 +IC H19X C318 *C319 H19Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C318 C319 C320 H20X 1.5340 113.30 -59.94 110.46 1.1113 +IC H20X C319 *C320 H20Y 1.1113 110.46 119.86 110.45 1.1113 +IC H20X C319 *C320 H20Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DEPS -1.0 !!! di-erucic-phosphatidylserine (diC22:1) +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! || (CIS) | +ATOM C214 CEL1 -0.15 ! || | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CEL1 -0.15 ! | +ATOM H13X HEL1 0.15 ! H13X---C313 +GROUP ! || (CIS) +ATOM C314 CEL1 -0.15 ! || +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL3 -0.27 ! | +ATOM H22X HAL3 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL3 0.09 ! | +ATOM H22Z HAL3 0.09 ! H22Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X +DOUBLE C313 C314 +BOND C314 H14X C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 H22Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5344 112.48 176.92 112.46 1.5398 +IC C211 C29 *C210 H10R 1.5398 112.46 -121.38 108.40 1.1139 +IC H10R C29 *C210 H10S 1.1139 108.40 -116.93 108.77 1.1139 +IC C29 C210 C211 C212 1.5344 112.48 176.92 112.46 1.5398 +IC C212 C210 *C211 H11R 1.5398 112.46 -121.38 108.40 1.1139 +IC H11R C210 *C211 H11S 1.1139 108.40 -116.93 108.77 1.1139 +IC C210 C211 C212 C213 1.5356 112.46 -178.53 111.43 1.5097 +IC C213 C211 *C212 H12R 1.5097 111.43 -123.58 107.80 1.1132 +IC H12R C211 *C212 H12S 1.1132 107.80 -115.43 108.37 1.1128 +IC C211 C212 C213 C214 1.5398 111.43 -126.96 126.62 1.3465 +IC C214 C212 *C213 H13R 1.3465 126.62 178.41 114.65 1.1012 +IC C212 C213 C214 C215 1.5097 126.62 -1.69 126.32 1.5088 +IC C215 C213 *C214 H14R 1.5088 126.32 -179.55 118.79 1.1012 +IC C213 C214 C215 C216 1.3465 126.32 93.02 112.15 1.5392 +IC C216 C214 *C215 H15R 1.5392 112.15 -121.30 111.28 1.1133 +IC H15R C214 *C215 H15S 1.1133 111.28 -117.50 110.00 1.1126 +IC C214 C215 C216 C217 1.5088 112.15 -178.81 112.29 1.5354 +IC C217 C215 *C216 H16R 1.5354 112.29 -121.34 109.78 1.1133 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5345 112.59 -179.58 112.63 1.5347 +IC C220 C218 *C219 H19R 1.5347 112.63 -121.36 109.09 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.09 -117.38 109.07 1.1132 +IC C218 C219 C220 C221 1.5347 112.63 179.65 112.69 1.5339 +IC C221 C219 *C220 H20R 1.5339 112.69 -121.27 109.11 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.11 -117.36 109.14 1.1132 +IC C219 C220 C221 C222 1.5347 112.69 -179.93 113.30 1.5309 +IC C222 C220 *C221 H21R 1.5309 113.30 -121.70 108.75 1.1140 +IC H21R C220 *C221 H21S 1.1140 108.75 -116.65 108.73 1.1141 +IC C220 C221 C222 H22R 1.5339 113.30 -59.98 110.46 1.1113 +IC H22R C221 *C222 H22S 1.1113 110.46 119.84 110.45 1.1114 +IC H22R C221 *C222 H22T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5447 111.73 -176.74 112.91 1.5345 +IC C39 C37 *C38 H8X 1.5345 112.91 -121.67 109.15 1.1134 +IC H8X C37 *C38 H8Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5345 112.91 -121.67 109.15 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C38 C39 C310 C311 1.5447 111.73 -176.74 112.91 1.5345 +IC C311 C39 *C310 H10X 1.5345 112.91 -121.67 109.15 1.1134 +IC H10X C39 *C310 H10Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5356 112.27 -174.92 111.69 1.5099 +IC C313 C311 *C312 H12X 1.5099 111.69 -124.14 107.77 1.1124 +IC H12X C311 *C312 H12Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C311 C312 C313 C314 1.5402 111.69 -121.39 127.35 1.3470 +IC C314 C312 *C313 H13X 1.3470 127.35 179.11 114.24 1.1012 +IC C312 C313 C314 C315 1.5099 127.35 -0.69 127.25 1.5096 +IC C315 C313 *C314 H14X 1.5096 127.25 179.82 118.43 1.1012 +IC C313 C314 C315 C316 1.3470 127.25 106.03 111.65 1.5393 +IC C316 C314 *C315 H15X 1.5393 111.65 -121.49 112.10 1.1123 +IC H15X C314 *C315 H15Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C314 C315 C316 C317 1.5096 111.65 179.63 112.41 1.5355 +IC C317 C315 *C316 H16X 1.5355 112.41 -121.09 109.75 1.1135 +IC H16X C315 *C316 H16Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5347 112.66 -179.12 112.61 1.5348 +IC C320 C318 *C319 H19X 1.5348 112.61 -121.34 109.09 1.1132 +IC H19X C318 *C319 H19Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C318 C319 C320 C321 1.5347 112.61 179.83 112.71 1.5340 +IC C321 C319 *C320 H20X 1.5340 112.71 -121.28 109.10 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C319 C320 C321 C322 1.5348 112.71 -179.67 113.30 1.5309 +IC C322 C320 *C321 H21X 1.5309 113.30 -121.68 108.77 1.1141 +IC H21X C320 *C321 H21Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C320 C321 C322 H22X 1.5340 113.30 -59.94 110.46 1.1113 +IC H22X C321 *C322 H22Y 1.1113 110.46 119.86 110.45 1.1113 +IC H22X C321 *C322 H22Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DNPS -1.0 ! di-nervonic-phosphatidylserine (diC24:1) +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! || (CIS) | +ATOM C216 CEL1 -0.15 ! || | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL2 -0.18 ! | | +ATOM H22R HAL2 0.09 ! H22R---C222--H22S | +ATOM H22S HAL2 0.09 ! | | +GROUP ! | | +ATOM C223 CTL2 -0.18 ! | | +ATOM H23R HAL2 0.09 ! H23R---C223--H23S | +ATOM H23S HAL2 0.09 ! | | +GROUP ! | | +ATOM C224 CTL3 -0.27 ! | | +ATOM H24R HAL3 0.09 ! H24R---C224--H24S | +ATOM H24S HAL3 0.09 ! | | +ATOM H24T HAL3 0.09 ! H24T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CEL1 -0.15 ! | +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! || (CIS) +ATOM C316 CEL1 -0.15 ! || +ATOM H16X HEL1 0.15 ! H16X---C316 +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL2 -0.18 ! | +ATOM H22X HAL2 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL2 0.09 ! | +GROUP ! | +ATOM C323 CTL2 -0.18 ! | +ATOM H23X HAL2 0.09 ! H23X---C323--H23Y +ATOM H23Y HAL2 0.09 ! | +GROUP ! | +ATOM C324 CTL3 -0.27 ! | +ATOM H24X HAL3 0.09 ! H24X---C324--H24Y +ATOM H24Y HAL3 0.09 ! | +ATOM H24Z HAL3 0.09 ! H24Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R +DOUBLE C215 C216 +BOND C216 H16R C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 C223 +BOND C223 H23R C223 H23S C223 C224 +BOND C224 H24R C224 H24S C224 H24T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X +DOUBLE C315 C316 +BOND C316 H16X C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 C323 +BOND C323 H23X C323 H23Y C323 C324 +BOND C324 H24X C324 H24Y C324 H24Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5339 112.69 -121.27 109.11 1.1132 +IC H9R C28 *C29 H9S 1.1132 109.11 -117.36 109.14 1.1132 +IC C28 C29 C210 C211 1.5345 112.59 -179.58 112.63 1.5347 +IC C211 C29 *C210 H10R 1.5347 112.63 -121.36 109.09 1.1132 +IC H10R C29 *C210 H10S 1.1132 109.09 -117.38 109.07 1.1132 +IC C29 C210 C211 C212 1.5345 112.59 -179.58 112.63 1.5347 +IC C212 C210 *C211 H11R 1.5347 112.63 -121.36 109.09 1.1132 +IC H11R C210 *C211 H11S 1.1132 109.09 -117.38 109.07 1.1132 +IC C210 C211 C212 C213 1.5345 112.59 -179.58 112.63 1.5347 +IC C213 C211 *C212 H12R 1.5347 112.63 -121.36 109.09 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.09 -117.38 109.07 1.1132 +IC C211 C212 C213 C214 1.5344 112.48 176.92 112.46 1.5398 +IC C214 C212 *C213 H13R 1.5398 112.46 -121.38 108.40 1.1139 +IC H13R C212 *C213 H13S 1.1139 108.40 -116.93 108.77 1.1139 +IC C212 C213 C214 C215 1.5356 112.46 -178.53 111.43 1.5097 +IC C215 C213 *C214 H14R 1.5097 111.43 -123.58 107.80 1.1132 +IC H14R C213 *C214 H14S 1.1132 107.80 -115.43 108.37 1.1128 +IC C213 C214 C215 C216 1.5398 111.43 -126.96 126.62 1.3465 +IC C216 C214 *C215 H15R 1.3465 126.62 178.41 114.65 1.1012 +IC C214 C215 C216 C217 1.5097 126.62 -1.69 126.32 1.5088 !!! +IC C217 C215 *C216 H16R 1.5088 126.32 -179.55 118.79 1.1012 +IC C215 C216 C217 C218 1.3465 126.32 93.02 112.15 1.5392 +IC C218 C216 *C217 H17R 1.5392 112.15 -121.30 111.28 1.1133 +IC H17R C216 *C217 H17S 1.1133 111.28 -117.50 110.00 1.1126 +IC C216 C217 C218 C219 1.5088 112.15 -178.81 112.29 1.5354 +IC C219 C217 *C218 H18R 1.5354 112.29 -121.34 109.78 1.1133 +IC H18R C217 *C218 H18S 1.1133 109.78 -118.01 109.42 1.1144 +IC C217 C218 C219 C220 1.5392 112.29 179.81 112.68 1.5345 +IC C220 C218 *C219 H19R 1.5345 112.68 -121.26 109.04 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.04 -117.39 109.10 1.1131 +IC C218 C219 C220 C221 1.5354 112.68 179.80 112.59 1.5347 +IC C221 C219 *C220 H20R 1.5347 112.59 -121.29 109.09 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.09 -117.37 109.11 1.1133 +IC C219 C220 C221 C222 1.5345 112.59 -179.58 112.63 1.5347 +IC C222 C220 *C221 H21R 1.5347 112.63 -121.36 109.09 1.1132 +IC H21R C220 *C221 H21S 1.1132 109.09 -117.38 109.07 1.1132 +IC C220 C221 C222 C223 1.5347 112.63 179.65 112.69 1.5339 +IC C223 C221 *C222 H22R 1.5339 112.69 -121.27 109.11 1.1132 +IC H22R C221 *C222 H22S 1.1132 109.11 -117.36 109.14 1.1132 +IC C221 C222 C223 C224 1.5347 112.69 -179.93 113.30 1.5309 +IC C224 C222 *C223 H23R 1.5309 113.30 -121.70 108.75 1.1140 +IC H23R C222 *C223 H23S 1.1140 108.75 -116.65 108.73 1.1141 +IC C222 C223 C224 H24R 1.5339 113.30 -59.98 110.46 1.1113 +IC H24R C223 *C224 H24S 1.1113 110.46 119.84 110.45 1.1114 +IC H24R C223 *C224 H24T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5349 112.80 178.92 112.27 1.5402 +IC C39 C37 *C38 H8X 1.5402 112.27 -121.37 108.23 1.1139 +IC H8X C37 *C38 H8Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5349 112.42 -120.99 108.94 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C38 C39 C310 C311 1.5345 112.42 -176.73 112.80 1.5356 +IC C311 C39 *C310 H10X 1.5356 112.80 -121.69 109.16 1.1130 +IC H10X C39 *C310 H10Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5345 112.42 -176.73 112.80 1.5356 +IC C313 C311 *C312 H12X 1.5349 112.42 -120.99 108.94 1.1133 +IC H12X C311 *C312 H12Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C311 C312 C313 C314 1.5349 112.80 178.92 112.27 1.5402 +IC C314 C312 *C313 H13X 1.5402 112.27 -121.37 108.23 1.1139 +IC H13X C312 *C313 H13Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C312 C313 C314 C315 1.5356 112.27 -174.92 111.69 1.5099 +IC C315 C313 *C314 H14X 1.5099 111.69 -124.14 107.77 1.1124 +IC H14X C313 *C314 H14Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C313 C314 C315 C316 1.5402 111.69 -121.39 127.35 1.3470 +IC C316 C314 *C315 H15X 1.3470 127.35 179.11 114.24 1.1012 +IC C314 C315 C316 C317 1.5099 127.35 -0.69 127.25 1.5096 +IC C317 C315 *C316 H16X 1.5096 127.25 179.82 118.43 1.1012 +IC C315 C316 C317 C318 1.3470 127.25 106.03 111.65 1.5393 +IC C318 C316 *C317 H17X 1.5393 111.65 -121.49 112.10 1.1123 +IC H17X C316 *C317 H17Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C316 C317 C318 C319 1.5096 111.65 179.63 112.41 1.5355 +IC C319 C317 *C318 H18X 1.5355 112.41 -121.09 109.75 1.1135 +IC H18X C317 *C318 H18Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C317 C318 C319 C320 1.5393 112.41 -178.89 112.60 1.5347 +IC C320 C318 *C319 H19X 1.5347 112.60 -121.37 109.10 1.1131 +IC H19X C318 *C319 H19Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C318 C319 C320 C321 1.5355 112.60 179.88 112.66 1.5347 +IC C321 C319 *C320 H20X 1.5347 112.66 -121.27 109.06 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C319 C320 C321 C322 1.5347 112.66 -179.12 112.61 1.5348 +IC C322 C320 *C321 H21X 1.5348 112.61 -121.34 109.09 1.1132 +IC H21X C320 *C321 H21Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C320 C321 C322 C323 1.5347 112.61 179.83 112.71 1.5340 +IC C323 C321 *C322 H22X 1.5340 112.71 -121.28 109.10 1.1132 +IC H22X C321 *C322 H22Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C321 C322 C323 C324 1.5348 112.71 -179.67 113.30 1.5309 +IC C324 C322 *C323 H23X 1.5309 113.30 -121.68 108.77 1.1141 +IC H23X C322 *C323 H23Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C322 C323 C324 H24X 1.5340 113.30 -59.94 110.46 1.1113 +IC H24X C323 *C324 H24Y 1.1113 110.46 119.86 110.45 1.1113 +IC H24X C323 *C324 H24Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI SAPS -1.00 ! 1-Stearoyl-2-Arachidonyl-Phosphatidylserine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5329 113.78 68.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 120.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 120.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 120.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 120.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 120.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 120.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SLPS -1.00 ! 1-Stearoyl-2-Linoleoyl-Phosphatidylserine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI PLPS -1.00 ! 1-palmitoyl-2-linoleoyl-Phosphatidylserine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4243 108.43 -123.15 113.04 1.1139 +IC H11A C12 *C11 H11B 1.1139 113.04 -118.48 109.10 1.1129 +IC C12 C11 O12 P 1.5420 108.43 -67.66 118.24 1.5905 +IC C11 O12 P O11 1.4243 118.24 -168.65 103.08 1.5759 +IC O11 O12 *P O13 1.5759 103.08 117.52 107.25 1.4784 +IC O11 O12 *P O14 1.5759 103.08 -117.26 106.69 1.4808 +IC O12 P O11 C1 1.5905 103.08 53.06 121.96 1.4290 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI DXPA -1.00 ! di-palmitoleic-phosphatidic acid (diC16:1) +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DGPA -1.00 ! di-gadoleic-phosphatidic acid (diC20:1) +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! || (CIS) | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.27 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || (CIS) +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X +DOUBLE C311 C312 +BOND C312 H12X C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 H20Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5344 112.48 176.92 112.46 1.5398 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5356 112.46 -178.53 111.43 1.5097 +IC C211 C29 *C210 H10R 1.5097 111.43 -123.58 107.80 1.1132 +IC H10R C29 *C210 H10S 1.1132 107.80 -115.43 108.37 1.1128 +IC C29 C210 C211 C212 1.5398 111.43 -126.96 126.62 1.3465 +IC C212 C210 *C211 H11R 1.3465 126.62 178.41 114.65 1.1012 +IC C210 C211 C212 C213 1.5097 126.62 -1.69 126.32 1.5088 +IC C213 C211 *C212 H12R 1.5088 126.32 -179.55 118.79 1.1012 +IC C211 C212 C213 C214 1.3465 126.32 93.02 112.15 1.5392 +IC C214 C212 *C213 H13R 1.5392 112.15 -121.30 111.28 1.1133 +IC H13R C212 *C213 H13S 1.1133 111.28 -117.50 110.00 1.1126 +IC C212 C213 C214 C215 1.5088 112.15 -178.81 112.29 1.5354 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5345 112.59 -179.58 112.63 1.5347 +IC C218 C216 *C217 H17R 1.5347 112.63 -121.36 109.09 1.1132 +IC H17R C216 *C217 H17S 1.1132 109.09 -117.38 109.07 1.1132 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5347 112.69 -179.93 113.30 1.5309 +IC C220 C218 *C219 H19R 1.5309 113.30 -121.70 108.75 1.1140 +IC H19R C218 *C219 H19S 1.1140 108.75 -116.65 108.73 1.1141 +IC C218 C219 C220 H20R 1.5339 113.30 -59.98 110.46 1.1113 +IC H20R C219 *C220 H20S 1.1113 110.46 119.84 110.45 1.1114 +IC H20R C219 *C220 H20T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5345 112.42 -176.73 112.80 1.5356 +IC C39 C37 *C38 H8X 1.5356 112.80 -121.69 109.16 1.1130 +IC H8X C37 *C38 H8Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C37 C38 C39 C310 1.5349 112.80 178.92 112.27 1.5402 +IC C310 C38 *C39 H9X 1.5402 112.27 -121.37 108.23 1.1139 +IC H9X C38 *C39 H9Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C38 C39 C310 C311 1.5356 112.27 -174.92 111.69 1.5099 +IC C311 C39 *C310 H10X 1.5099 111.69 -124.14 107.77 1.1124 +IC H10X C39 *C310 H10Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C39 C310 C311 C312 1.5402 111.69 -121.39 127.35 1.3470 +IC C312 C310 *C311 H11X 1.3470 127.35 179.11 114.24 1.1012 +IC C310 C311 C312 C313 1.5099 127.35 -0.69 127.25 1.5096 +IC C313 C311 *C312 H12X 1.5096 127.25 179.82 118.43 1.1012 +IC C311 C312 C313 C314 1.3470 127.25 106.03 111.65 1.5393 +IC C314 C312 *C313 H13X 1.5393 111.65 -121.49 112.10 1.1123 +IC H13X C312 *C313 H13Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C312 C313 C314 C315 1.5096 111.65 179.63 112.41 1.5355 +IC C315 C313 *C314 H14X 1.5355 112.41 -121.09 109.75 1.1135 +IC H14X C313 *C314 H14Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5347 112.66 -179.12 112.61 1.5348 +IC C318 C316 *C317 H17X 1.5348 112.61 -121.34 109.09 1.1132 +IC H17X C316 *C317 H17Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5348 112.71 -179.67 113.30 1.5309 +IC C320 C318 *C319 H19X 1.5309 113.30 -121.68 108.77 1.1141 +IC H19X C318 *C319 H19Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C318 C319 C320 H20X 1.5340 113.30 -59.94 110.46 1.1113 +IC H20X C319 *C320 H20Y 1.1113 110.46 119.86 110.45 1.1113 +IC H20X C319 *C320 H20Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DEPA -1.00 !!! di-erucic-phosphatidic acid (diC22:1) +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! || (CIS) | +ATOM C214 CEL1 -0.15 ! || | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CEL1 -0.15 ! | +ATOM H13X HEL1 0.15 ! H13X---C313 +GROUP ! || (CIS) +ATOM C314 CEL1 -0.15 ! || +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL3 -0.27 ! | +ATOM H22X HAL3 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL3 0.09 ! | +ATOM H22Z HAL3 0.09 ! H22Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X +DOUBLE C313 C314 +BOND C314 H14X C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 H22Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5344 112.48 176.92 112.46 1.5398 +IC C211 C29 *C210 H10R 1.5398 112.46 -121.38 108.40 1.1139 +IC H10R C29 *C210 H10S 1.1139 108.40 -116.93 108.77 1.1139 +IC C29 C210 C211 C212 1.5344 112.48 176.92 112.46 1.5398 +IC C212 C210 *C211 H11R 1.5398 112.46 -121.38 108.40 1.1139 +IC H11R C210 *C211 H11S 1.1139 108.40 -116.93 108.77 1.1139 +IC C210 C211 C212 C213 1.5356 112.46 -178.53 111.43 1.5097 +IC C213 C211 *C212 H12R 1.5097 111.43 -123.58 107.80 1.1132 +IC H12R C211 *C212 H12S 1.1132 107.80 -115.43 108.37 1.1128 +IC C211 C212 C213 C214 1.5398 111.43 -126.96 126.62 1.3465 +IC C214 C212 *C213 H13R 1.3465 126.62 178.41 114.65 1.1012 +IC C212 C213 C214 C215 1.5097 126.62 -1.69 126.32 1.5088 +IC C215 C213 *C214 H14R 1.5088 126.32 -179.55 118.79 1.1012 +IC C213 C214 C215 C216 1.3465 126.32 93.02 112.15 1.5392 +IC C216 C214 *C215 H15R 1.5392 112.15 -121.30 111.28 1.1133 +IC H15R C214 *C215 H15S 1.1133 111.28 -117.50 110.00 1.1126 +IC C214 C215 C216 C217 1.5088 112.15 -178.81 112.29 1.5354 +IC C217 C215 *C216 H16R 1.5354 112.29 -121.34 109.78 1.1133 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5345 112.59 -179.58 112.63 1.5347 +IC C220 C218 *C219 H19R 1.5347 112.63 -121.36 109.09 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.09 -117.38 109.07 1.1132 +IC C218 C219 C220 C221 1.5347 112.63 179.65 112.69 1.5339 +IC C221 C219 *C220 H20R 1.5339 112.69 -121.27 109.11 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.11 -117.36 109.14 1.1132 +IC C219 C220 C221 C222 1.5347 112.69 -179.93 113.30 1.5309 +IC C222 C220 *C221 H21R 1.5309 113.30 -121.70 108.75 1.1140 +IC H21R C220 *C221 H21S 1.1140 108.75 -116.65 108.73 1.1141 +IC C220 C221 C222 H22R 1.5339 113.30 -59.98 110.46 1.1113 +IC H22R C221 *C222 H22S 1.1113 110.46 119.84 110.45 1.1114 +IC H22R C221 *C222 H22T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5447 111.73 -176.74 112.91 1.5345 +IC C39 C37 *C38 H8X 1.5345 112.91 -121.67 109.15 1.1134 +IC H8X C37 *C38 H8Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5345 112.91 -121.67 109.15 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C38 C39 C310 C311 1.5447 111.73 -176.74 112.91 1.5345 +IC C311 C39 *C310 H10X 1.5345 112.91 -121.67 109.15 1.1134 +IC H10X C39 *C310 H10Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5356 112.27 -174.92 111.69 1.5099 +IC C313 C311 *C312 H12X 1.5099 111.69 -124.14 107.77 1.1124 +IC H12X C311 *C312 H12Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C311 C312 C313 C314 1.5402 111.69 -121.39 127.35 1.3470 +IC C314 C312 *C313 H13X 1.3470 127.35 179.11 114.24 1.1012 +IC C312 C313 C314 C315 1.5099 127.35 -0.69 127.25 1.5096 +IC C315 C313 *C314 H14X 1.5096 127.25 179.82 118.43 1.1012 +IC C313 C314 C315 C316 1.3470 127.25 106.03 111.65 1.5393 +IC C316 C314 *C315 H15X 1.5393 111.65 -121.49 112.10 1.1123 +IC H15X C314 *C315 H15Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C314 C315 C316 C317 1.5096 111.65 179.63 112.41 1.5355 +IC C317 C315 *C316 H16X 1.5355 112.41 -121.09 109.75 1.1135 +IC H16X C315 *C316 H16Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5347 112.66 -179.12 112.61 1.5348 +IC C320 C318 *C319 H19X 1.5348 112.61 -121.34 109.09 1.1132 +IC H19X C318 *C319 H19Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C318 C319 C320 C321 1.5347 112.61 179.83 112.71 1.5340 +IC C321 C319 *C320 H20X 1.5340 112.71 -121.28 109.10 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C319 C320 C321 C322 1.5348 112.71 -179.67 113.30 1.5309 +IC C322 C320 *C321 H21X 1.5309 113.30 -121.68 108.77 1.1141 +IC H21X C320 *C321 H21Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C320 C321 C322 H22X 1.5340 113.30 -59.94 110.46 1.1113 +IC H22X C321 *C322 H22Y 1.1113 110.46 119.86 110.45 1.1113 +IC H22X C321 *C322 H22Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DNPA -1.00 ! di-nervonic-phosphatidic acid (diC24:1) +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! || (CIS) | +ATOM C216 CEL1 -0.15 ! || | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL2 -0.18 ! | | +ATOM H22R HAL2 0.09 ! H22R---C222--H22S | +ATOM H22S HAL2 0.09 ! | | +GROUP ! | | +ATOM C223 CTL2 -0.18 ! | | +ATOM H23R HAL2 0.09 ! H23R---C223--H23S | +ATOM H23S HAL2 0.09 ! | | +GROUP ! | | +ATOM C224 CTL3 -0.27 ! | | +ATOM H24R HAL3 0.09 ! H24R---C224--H24S | +ATOM H24S HAL3 0.09 ! | | +ATOM H24T HAL3 0.09 ! H24T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CEL1 -0.15 ! | +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! || (CIS) +ATOM C316 CEL1 -0.15 ! || +ATOM H16X HEL1 0.15 ! H16X---C316 +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL2 -0.18 ! | +ATOM H22X HAL2 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL2 0.09 ! | +GROUP ! | +ATOM C323 CTL2 -0.18 ! | +ATOM H23X HAL2 0.09 ! H23X---C323--H23Y +ATOM H23Y HAL2 0.09 ! | +GROUP ! | +ATOM C324 CTL3 -0.27 ! | +ATOM H24X HAL3 0.09 ! H24X---C324--H24Y +ATOM H24Y HAL3 0.09 ! | +ATOM H24Z HAL3 0.09 ! H24Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R +DOUBLE C215 C216 +BOND C216 H16R C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 C223 +BOND C223 H23R C223 H23S C223 C224 +BOND C224 H24R C224 H24S C224 H24T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X +DOUBLE C315 C316 +BOND C316 H16X C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 C323 +BOND C323 H23X C323 H23Y C323 C324 +BOND C324 H24X C324 H24Y C324 H24Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5339 112.69 -121.27 109.11 1.1132 +IC H9R C28 *C29 H9S 1.1132 109.11 -117.36 109.14 1.1132 +IC C28 C29 C210 C211 1.5345 112.59 -179.58 112.63 1.5347 +IC C211 C29 *C210 H10R 1.5347 112.63 -121.36 109.09 1.1132 +IC H10R C29 *C210 H10S 1.1132 109.09 -117.38 109.07 1.1132 +IC C29 C210 C211 C212 1.5345 112.59 -179.58 112.63 1.5347 +IC C212 C210 *C211 H11R 1.5347 112.63 -121.36 109.09 1.1132 +IC H11R C210 *C211 H11S 1.1132 109.09 -117.38 109.07 1.1132 +IC C210 C211 C212 C213 1.5345 112.59 -179.58 112.63 1.5347 +IC C213 C211 *C212 H12R 1.5347 112.63 -121.36 109.09 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.09 -117.38 109.07 1.1132 +IC C211 C212 C213 C214 1.5344 112.48 176.92 112.46 1.5398 +IC C214 C212 *C213 H13R 1.5398 112.46 -121.38 108.40 1.1139 +IC H13R C212 *C213 H13S 1.1139 108.40 -116.93 108.77 1.1139 +IC C212 C213 C214 C215 1.5356 112.46 -178.53 111.43 1.5097 +IC C215 C213 *C214 H14R 1.5097 111.43 -123.58 107.80 1.1132 +IC H14R C213 *C214 H14S 1.1132 107.80 -115.43 108.37 1.1128 +IC C213 C214 C215 C216 1.5398 111.43 -126.96 126.62 1.3465 +IC C216 C214 *C215 H15R 1.3465 126.62 178.41 114.65 1.1012 +IC C214 C215 C216 C217 1.5097 126.62 -1.69 126.32 1.5088 !!! +IC C217 C215 *C216 H16R 1.5088 126.32 -179.55 118.79 1.1012 +IC C215 C216 C217 C218 1.3465 126.32 93.02 112.15 1.5392 +IC C218 C216 *C217 H17R 1.5392 112.15 -121.30 111.28 1.1133 +IC H17R C216 *C217 H17S 1.1133 111.28 -117.50 110.00 1.1126 +IC C216 C217 C218 C219 1.5088 112.15 -178.81 112.29 1.5354 +IC C219 C217 *C218 H18R 1.5354 112.29 -121.34 109.78 1.1133 +IC H18R C217 *C218 H18S 1.1133 109.78 -118.01 109.42 1.1144 +IC C217 C218 C219 C220 1.5392 112.29 179.81 112.68 1.5345 +IC C220 C218 *C219 H19R 1.5345 112.68 -121.26 109.04 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.04 -117.39 109.10 1.1131 +IC C218 C219 C220 C221 1.5354 112.68 179.80 112.59 1.5347 +IC C221 C219 *C220 H20R 1.5347 112.59 -121.29 109.09 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.09 -117.37 109.11 1.1133 +IC C219 C220 C221 C222 1.5345 112.59 -179.58 112.63 1.5347 +IC C222 C220 *C221 H21R 1.5347 112.63 -121.36 109.09 1.1132 +IC H21R C220 *C221 H21S 1.1132 109.09 -117.38 109.07 1.1132 +IC C220 C221 C222 C223 1.5347 112.63 179.65 112.69 1.5339 +IC C223 C221 *C222 H22R 1.5339 112.69 -121.27 109.11 1.1132 +IC H22R C221 *C222 H22S 1.1132 109.11 -117.36 109.14 1.1132 +IC C221 C222 C223 C224 1.5347 112.69 -179.93 113.30 1.5309 +IC C224 C222 *C223 H23R 1.5309 113.30 -121.70 108.75 1.1140 +IC H23R C222 *C223 H23S 1.1140 108.75 -116.65 108.73 1.1141 +IC C222 C223 C224 H24R 1.5339 113.30 -59.98 110.46 1.1113 +IC H24R C223 *C224 H24S 1.1113 110.46 119.84 110.45 1.1114 +IC H24R C223 *C224 H24T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5349 112.80 178.92 112.27 1.5402 +IC C39 C37 *C38 H8X 1.5402 112.27 -121.37 108.23 1.1139 +IC H8X C37 *C38 H8Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5349 112.42 -120.99 108.94 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C38 C39 C310 C311 1.5345 112.42 -176.73 112.80 1.5356 +IC C311 C39 *C310 H10X 1.5356 112.80 -121.69 109.16 1.1130 +IC H10X C39 *C310 H10Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5345 112.42 -176.73 112.80 1.5356 +IC C313 C311 *C312 H12X 1.5349 112.42 -120.99 108.94 1.1133 +IC H12X C311 *C312 H12Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C311 C312 C313 C314 1.5349 112.80 178.92 112.27 1.5402 +IC C314 C312 *C313 H13X 1.5402 112.27 -121.37 108.23 1.1139 +IC H13X C312 *C313 H13Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C312 C313 C314 C315 1.5356 112.27 -174.92 111.69 1.5099 +IC C315 C313 *C314 H14X 1.5099 111.69 -124.14 107.77 1.1124 +IC H14X C313 *C314 H14Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C313 C314 C315 C316 1.5402 111.69 -121.39 127.35 1.3470 +IC C316 C314 *C315 H15X 1.3470 127.35 179.11 114.24 1.1012 +IC C314 C315 C316 C317 1.5099 127.35 -0.69 127.25 1.5096 +IC C317 C315 *C316 H16X 1.5096 127.25 179.82 118.43 1.1012 +IC C315 C316 C317 C318 1.3470 127.25 106.03 111.65 1.5393 +IC C318 C316 *C317 H17X 1.5393 111.65 -121.49 112.10 1.1123 +IC H17X C316 *C317 H17Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C316 C317 C318 C319 1.5096 111.65 179.63 112.41 1.5355 +IC C319 C317 *C318 H18X 1.5355 112.41 -121.09 109.75 1.1135 +IC H18X C317 *C318 H18Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C317 C318 C319 C320 1.5393 112.41 -178.89 112.60 1.5347 +IC C320 C318 *C319 H19X 1.5347 112.60 -121.37 109.10 1.1131 +IC H19X C318 *C319 H19Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C318 C319 C320 C321 1.5355 112.60 179.88 112.66 1.5347 +IC C321 C319 *C320 H20X 1.5347 112.66 -121.27 109.06 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C319 C320 C321 C322 1.5347 112.66 -179.12 112.61 1.5348 +IC C322 C320 *C321 H21X 1.5348 112.61 -121.34 109.09 1.1132 +IC H21X C320 *C321 H21Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C320 C321 C322 C323 1.5347 112.61 179.83 112.71 1.5340 +IC C323 C321 *C322 H22X 1.5340 112.71 -121.28 109.10 1.1132 +IC H22X C321 *C322 H22Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C321 C322 C323 C324 1.5348 112.71 -179.67 113.30 1.5309 +IC C324 C322 *C323 H23X 1.5309 113.30 -121.68 108.77 1.1141 +IC H23X C322 *C323 H23Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C322 C323 C324 H24X 1.5340 113.30 -59.94 110.46 1.1113 +IC H24X C323 *C324 H24Y 1.1113 110.46 119.86 110.45 1.1113 +IC H24X C323 *C324 H24Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI SAPA -1.00 ! 1-Stearoyl-2-Arachidonyl-Phosphotidic acid +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O12 O11 *P O13 1.5648 107.12 112.86 111.62 1.4716 +IC O12 O11 *P O14 1.5648 107.12 -112.61 111.22 1.4723 +IC O12 P O11 C1 1.5648 107.12 177.80 116.98 1.4333 +IC P O11 C1 C2 1.5807 116.98 177.37 111.07 1.5515 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5329 113.78 68.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 120.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 120.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 120.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 120.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 120.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 120.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SLPA -1.00 ! 1-Stearoyl-2-Linoleoyl-Phosphotidic acid +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 +! +RESI PLPA -1.00 ! 1-palmitoyl-2-linoleoyl-Phosphatidic acid +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z +! +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5759 103.08 117.52 107.25 1.4784 +IC O11 O12 *P O14 1.5759 103.08 -117.26 106.69 1.4808 +IC O12 P O11 C1 1.5905 103.08 53.06 121.96 1.4290 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 +! +RESI DXPG -1.00 ! di-palmitoleic-phosphatidylglycerol (diC16:1) +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DGPG -1.00 ! di-gadoleic-phosphatidylglycerol (diC20:1) +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! || (CIS) | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.27 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || (CIS) +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X +DOUBLE C311 C312 +BOND C312 H12X C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 H20Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5344 112.48 176.92 112.46 1.5398 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5356 112.46 -178.53 111.43 1.5097 +IC C211 C29 *C210 H10R 1.5097 111.43 -123.58 107.80 1.1132 +IC H10R C29 *C210 H10S 1.1132 107.80 -115.43 108.37 1.1128 +IC C29 C210 C211 C212 1.5398 111.43 -126.96 126.62 1.3465 +IC C212 C210 *C211 H11R 1.3465 126.62 178.41 114.65 1.1012 +IC C210 C211 C212 C213 1.5097 126.62 -1.69 126.32 1.5088 +IC C213 C211 *C212 H12R 1.5088 126.32 -179.55 118.79 1.1012 +IC C211 C212 C213 C214 1.3465 126.32 93.02 112.15 1.5392 +IC C214 C212 *C213 H13R 1.5392 112.15 -121.30 111.28 1.1133 +IC H13R C212 *C213 H13S 1.1133 111.28 -117.50 110.00 1.1126 +IC C212 C213 C214 C215 1.5088 112.15 -178.81 112.29 1.5354 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5345 112.59 -179.58 112.63 1.5347 +IC C218 C216 *C217 H17R 1.5347 112.63 -121.36 109.09 1.1132 +IC H17R C216 *C217 H17S 1.1132 109.09 -117.38 109.07 1.1132 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5347 112.69 -179.93 113.30 1.5309 +IC C220 C218 *C219 H19R 1.5309 113.30 -121.70 108.75 1.1140 +IC H19R C218 *C219 H19S 1.1140 108.75 -116.65 108.73 1.1141 +IC C218 C219 C220 H20R 1.5339 113.30 -59.98 110.46 1.1113 +IC H20R C219 *C220 H20S 1.1113 110.46 119.84 110.45 1.1114 +IC H20R C219 *C220 H20T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5345 112.42 -176.73 112.80 1.5356 +IC C39 C37 *C38 H8X 1.5356 112.80 -121.69 109.16 1.1130 +IC H8X C37 *C38 H8Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C37 C38 C39 C310 1.5349 112.80 178.92 112.27 1.5402 +IC C310 C38 *C39 H9X 1.5402 112.27 -121.37 108.23 1.1139 +IC H9X C38 *C39 H9Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C38 C39 C310 C311 1.5356 112.27 -174.92 111.69 1.5099 +IC C311 C39 *C310 H10X 1.5099 111.69 -124.14 107.77 1.1124 +IC H10X C39 *C310 H10Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C39 C310 C311 C312 1.5402 111.69 -121.39 127.35 1.3470 +IC C312 C310 *C311 H11X 1.3470 127.35 179.11 114.24 1.1012 +IC C310 C311 C312 C313 1.5099 127.35 -0.69 127.25 1.5096 +IC C313 C311 *C312 H12X 1.5096 127.25 179.82 118.43 1.1012 +IC C311 C312 C313 C314 1.3470 127.25 106.03 111.65 1.5393 +IC C314 C312 *C313 H13X 1.5393 111.65 -121.49 112.10 1.1123 +IC H13X C312 *C313 H13Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C312 C313 C314 C315 1.5096 111.65 179.63 112.41 1.5355 +IC C315 C313 *C314 H14X 1.5355 112.41 -121.09 109.75 1.1135 +IC H14X C313 *C314 H14Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5347 112.66 -179.12 112.61 1.5348 +IC C318 C316 *C317 H17X 1.5348 112.61 -121.34 109.09 1.1132 +IC H17X C316 *C317 H17Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5348 112.71 -179.67 113.30 1.5309 +IC C320 C318 *C319 H19X 1.5309 113.30 -121.68 108.77 1.1141 +IC H19X C318 *C319 H19Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C318 C319 C320 H20X 1.5340 113.30 -59.94 110.46 1.1113 +IC H20X C319 *C320 H20Y 1.1113 110.46 119.86 110.45 1.1113 +IC H20X C319 *C320 H20Z 1.1113 110.46 -120.06 110.61 1.1112 +! +RESI DEPG -1.00 !!! di-erucic-phosphatidylglycerol (diC22:1) +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! || (CIS) | +ATOM C214 CEL1 -0.15 ! || | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CEL1 -0.15 ! | +ATOM H13X HEL1 0.15 ! H13X---C313 +GROUP ! || (CIS) +ATOM C314 CEL1 -0.15 ! || +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL3 -0.27 ! | +ATOM H22X HAL3 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL3 0.09 ! | +ATOM H22Z HAL3 0.09 ! H22Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X +DOUBLE C313 C314 +BOND C314 H14X C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 H22Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5398 112.46 -121.38 108.40 1.1139 +IC H9R C28 *C29 H9S 1.1139 108.40 -116.93 108.77 1.1139 +IC C28 C29 C210 C211 1.5344 112.48 176.92 112.46 1.5398 +IC C211 C29 *C210 H10R 1.5398 112.46 -121.38 108.40 1.1139 +IC H10R C29 *C210 H10S 1.1139 108.40 -116.93 108.77 1.1139 +IC C29 C210 C211 C212 1.5344 112.48 176.92 112.46 1.5398 +IC C212 C210 *C211 H11R 1.5398 112.46 -121.38 108.40 1.1139 +IC H11R C210 *C211 H11S 1.1139 108.40 -116.93 108.77 1.1139 +IC C210 C211 C212 C213 1.5356 112.46 -178.53 111.43 1.5097 +IC C213 C211 *C212 H12R 1.5097 111.43 -123.58 107.80 1.1132 +IC H12R C211 *C212 H12S 1.1132 107.80 -115.43 108.37 1.1128 +IC C211 C212 C213 C214 1.5398 111.43 -126.96 126.62 1.3465 +IC C214 C212 *C213 H13R 1.3465 126.62 178.41 114.65 1.1012 +IC C212 C213 C214 C215 1.5097 126.62 -1.69 126.32 1.5088 +IC C215 C213 *C214 H14R 1.5088 126.32 -179.55 118.79 1.1012 +IC C213 C214 C215 C216 1.3465 126.32 93.02 112.15 1.5392 +IC C216 C214 *C215 H15R 1.5392 112.15 -121.30 111.28 1.1133 +IC H15R C214 *C215 H15S 1.1133 111.28 -117.50 110.00 1.1126 +IC C214 C215 C216 C217 1.5088 112.15 -178.81 112.29 1.5354 +IC C217 C215 *C216 H16R 1.5354 112.29 -121.34 109.78 1.1133 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 C219 1.5347 112.63 179.65 112.69 1.5339 +IC C219 C217 *C218 H18R 1.5339 112.69 -121.27 109.11 1.1132 +IC H18R C217 *C218 H18S 1.1132 109.11 -117.36 109.14 1.1132 +IC C217 C218 C219 C220 1.5345 112.59 -179.58 112.63 1.5347 +IC C220 C218 *C219 H19R 1.5347 112.63 -121.36 109.09 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.09 -117.38 109.07 1.1132 +IC C218 C219 C220 C221 1.5347 112.63 179.65 112.69 1.5339 +IC C221 C219 *C220 H20R 1.5339 112.69 -121.27 109.11 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.11 -117.36 109.14 1.1132 +IC C219 C220 C221 C222 1.5347 112.69 -179.93 113.30 1.5309 +IC C222 C220 *C221 H21R 1.5309 113.30 -121.70 108.75 1.1140 +IC H21R C220 *C221 H21S 1.1140 108.75 -116.65 108.73 1.1141 +IC C220 C221 C222 H22R 1.5339 113.30 -59.98 110.46 1.1113 +IC H22R C221 *C222 H22S 1.1113 110.46 119.84 110.45 1.1114 +IC H22R C221 *C222 H22T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5447 111.73 -176.74 112.91 1.5345 +IC C39 C37 *C38 H8X 1.5345 112.91 -121.67 109.15 1.1134 +IC H8X C37 *C38 H8Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5345 112.91 -121.67 109.15 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C38 C39 C310 C311 1.5447 111.73 -176.74 112.91 1.5345 +IC C311 C39 *C310 H10X 1.5345 112.91 -121.67 109.15 1.1134 +IC H10X C39 *C310 H10Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5356 112.27 -174.92 111.69 1.5099 +IC C313 C311 *C312 H12X 1.5099 111.69 -124.14 107.77 1.1124 +IC H12X C311 *C312 H12Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C311 C312 C313 C314 1.5402 111.69 -121.39 127.35 1.3470 +IC C314 C312 *C313 H13X 1.3470 127.35 179.11 114.24 1.1012 +IC C312 C313 C314 C315 1.5099 127.35 -0.69 127.25 1.5096 +IC C315 C313 *C314 H14X 1.5096 127.25 179.82 118.43 1.1012 +IC C313 C314 C315 C316 1.3470 127.25 106.03 111.65 1.5393 +IC C316 C314 *C315 H15X 1.5393 111.65 -121.49 112.10 1.1123 +IC H15X C314 *C315 H15Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C314 C315 C316 C317 1.5096 111.65 179.63 112.41 1.5355 +IC C317 C315 *C316 H16X 1.5355 112.41 -121.09 109.75 1.1135 +IC H16X C315 *C316 H16Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 C319 1.5347 112.61 179.83 112.71 1.5340 +IC C319 C317 *C318 H18X 1.5340 112.71 -121.28 109.10 1.1132 +IC H18X C317 *C318 H18Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C317 C318 C319 C320 1.5347 112.66 -179.12 112.61 1.5348 +IC C320 C318 *C319 H19X 1.5348 112.61 -121.34 109.09 1.1132 +IC H19X C318 *C319 H19Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C318 C319 C320 C321 1.5347 112.61 179.83 112.71 1.5340 +IC C321 C319 *C320 H20X 1.5340 112.71 -121.28 109.10 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C319 C320 C321 C322 1.5348 112.71 -179.67 113.30 1.5309 +IC C322 C320 *C321 H21X 1.5309 113.30 -121.68 108.77 1.1141 +IC H21X C320 *C321 H21Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C320 C321 C322 H22X 1.5340 113.30 -59.94 110.46 1.1113 +IC H22X C321 *C322 H22Y 1.1113 110.46 119.86 110.45 1.1113 +IC H22X C321 *C322 H22Z 1.1113 110.46 -120.06 110.61 1.1112 +! +RESI DNPG -1.00 ! di-nervonic-phosphatidylglycerol (diC24:1) +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CEL1 -0.15 ! | | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! || (CIS) | +ATOM C216 CEL1 -0.15 ! || | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL2 -0.18 ! | | +ATOM H20R HAL2 0.09 ! H20R---C220--H20S | +ATOM H20S HAL2 0.09 ! | | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL2 -0.18 ! | | +ATOM H22R HAL2 0.09 ! H22R---C222--H22S | +ATOM H22S HAL2 0.09 ! | | +GROUP ! | | +ATOM C223 CTL2 -0.18 ! | | +ATOM H23R HAL2 0.09 ! H23R---C223--H23S | +ATOM H23S HAL2 0.09 ! | | +GROUP ! | | +ATOM C224 CTL3 -0.27 ! | | +ATOM H24R HAL3 0.09 ! H24R---C224--H24S | +ATOM H24S HAL3 0.09 ! | | +ATOM H24T HAL3 0.09 ! H24T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CEL1 -0.15 ! | +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! || (CIS) +ATOM C316 CEL1 -0.15 ! || +ATOM H16X HEL1 0.15 ! H16X---C316 +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL2 -0.18 ! | +ATOM H20X HAL2 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL2 0.09 ! | +GROUP ! | +ATOM C321 CTL2 -0.18 ! | +ATOM H21X HAL2 0.09 ! H21X---C321--H21Y +ATOM H21Y HAL2 0.09 ! | +GROUP ! | +ATOM C322 CTL2 -0.18 ! | +ATOM H22X HAL2 0.09 ! H22X---C322--H22Y +ATOM H22Y HAL2 0.09 ! | +GROUP ! | +ATOM C323 CTL2 -0.18 ! | +ATOM H23X HAL2 0.09 ! H23X---C323--H23Y +ATOM H23Y HAL2 0.09 ! | +GROUP ! | +ATOM C324 CTL3 -0.27 ! | +ATOM H24X HAL3 0.09 ! H24X---C324--H24Y +ATOM H24Y HAL3 0.09 ! | +ATOM H24Z HAL3 0.09 ! H24Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R +DOUBLE C215 C216 +BOND C216 H16R C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 C223 +BOND C223 H23R C223 H23S C223 C224 +BOND C224 H24R C224 H24S C224 H24T + +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X +DOUBLE C315 C316 +BOND C316 H16X C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 C319 +BOND C319 H19X C319 H19Y C319 C320 +BOND C320 H20X C320 H20Y C320 C321 +BOND C321 H21X C321 H21Y C321 C322 +BOND C322 H22X C322 H22Y C322 C323 +BOND C323 H23X C323 H23Y C323 C324 +BOND C324 H24X C324 H24Y C324 H24Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5345 112.59 -179.58 112.63 1.5347 +IC C29 C27 *C28 H8R 1.5347 112.63 -121.36 109.09 1.1132 +IC H8R C27 *C28 H8S 1.1132 109.09 -117.38 109.07 1.1132 +IC C27 C28 C29 C210 1.5347 112.63 179.65 112.69 1.5339 +IC C210 C28 *C29 H9R 1.5339 112.69 -121.27 109.11 1.1132 +IC H9R C28 *C29 H9S 1.1132 109.11 -117.36 109.14 1.1132 +IC C28 C29 C210 C211 1.5345 112.59 -179.58 112.63 1.5347 +IC C211 C29 *C210 H10R 1.5347 112.63 -121.36 109.09 1.1132 +IC H10R C29 *C210 H10S 1.1132 109.09 -117.38 109.07 1.1132 +IC C29 C210 C211 C212 1.5345 112.59 -179.58 112.63 1.5347 +IC C212 C210 *C211 H11R 1.5347 112.63 -121.36 109.09 1.1132 +IC H11R C210 *C211 H11S 1.1132 109.09 -117.38 109.07 1.1132 +IC C210 C211 C212 C213 1.5345 112.59 -179.58 112.63 1.5347 +IC C213 C211 *C212 H12R 1.5347 112.63 -121.36 109.09 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.09 -117.38 109.07 1.1132 +IC C211 C212 C213 C214 1.5344 112.48 176.92 112.46 1.5398 +IC C214 C212 *C213 H13R 1.5398 112.46 -121.38 108.40 1.1139 +IC H13R C212 *C213 H13S 1.1139 108.40 -116.93 108.77 1.1139 +IC C212 C213 C214 C215 1.5356 112.46 -178.53 111.43 1.5097 +IC C215 C213 *C214 H14R 1.5097 111.43 -123.58 107.80 1.1132 +IC H14R C213 *C214 H14S 1.1132 107.80 -115.43 108.37 1.1128 +IC C213 C214 C215 C216 1.5398 111.43 -126.96 126.62 1.3465 +IC C216 C214 *C215 H15R 1.3465 126.62 178.41 114.65 1.1012 +IC C214 C215 C216 C217 1.5097 126.62 -1.69 126.32 1.5088 !!! +IC C217 C215 *C216 H16R 1.5088 126.32 -179.55 118.79 1.1012 +IC C215 C216 C217 C218 1.3465 126.32 93.02 112.15 1.5392 +IC C218 C216 *C217 H17R 1.5392 112.15 -121.30 111.28 1.1133 +IC H17R C216 *C217 H17S 1.1133 111.28 -117.50 110.00 1.1126 +IC C216 C217 C218 C219 1.5088 112.15 -178.81 112.29 1.5354 +IC C219 C217 *C218 H18R 1.5354 112.29 -121.34 109.78 1.1133 +IC H18R C217 *C218 H18S 1.1133 109.78 -118.01 109.42 1.1144 +IC C217 C218 C219 C220 1.5392 112.29 179.81 112.68 1.5345 +IC C220 C218 *C219 H19R 1.5345 112.68 -121.26 109.04 1.1132 +IC H19R C218 *C219 H19S 1.1132 109.04 -117.39 109.10 1.1131 +IC C218 C219 C220 C221 1.5354 112.68 179.80 112.59 1.5347 +IC C221 C219 *C220 H20R 1.5347 112.59 -121.29 109.09 1.1132 +IC H20R C219 *C220 H20S 1.1132 109.09 -117.37 109.11 1.1133 +IC C219 C220 C221 C222 1.5345 112.59 -179.58 112.63 1.5347 +IC C222 C220 *C221 H21R 1.5347 112.63 -121.36 109.09 1.1132 +IC H21R C220 *C221 H21S 1.1132 109.09 -117.38 109.07 1.1132 +IC C220 C221 C222 C223 1.5347 112.63 179.65 112.69 1.5339 +IC C223 C221 *C222 H22R 1.5339 112.69 -121.27 109.11 1.1132 +IC H22R C221 *C222 H22S 1.1132 109.11 -117.36 109.14 1.1132 +IC C221 C222 C223 C224 1.5347 112.69 -179.93 113.30 1.5309 +IC C224 C222 *C223 H23R 1.5309 113.30 -121.70 108.75 1.1140 +IC H23R C222 *C223 H23S 1.1140 108.75 -116.65 108.73 1.1141 +IC C222 C223 C224 H24R 1.5339 113.30 -59.98 110.46 1.1113 +IC H24R C223 *C224 H24S 1.1113 110.46 119.84 110.45 1.1114 +IC H24R C223 *C224 H24T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5349 112.80 178.92 112.27 1.5402 +IC C39 C37 *C38 H8X 1.5402 112.27 -121.37 108.23 1.1139 +IC H8X C37 *C38 H8Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C37 C38 C39 C310 1.5343 112.91 178.63 112.42 1.5349 +IC C310 C38 *C39 H9X 1.5349 112.42 -120.99 108.94 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C38 C39 C310 C311 1.5345 112.42 -176.73 112.80 1.5356 +IC C311 C39 *C310 H10X 1.5356 112.80 -121.69 109.16 1.1130 +IC H10X C39 *C310 H10Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C39 C310 C311 C312 1.5349 112.80 178.92 112.27 1.5402 +IC C312 C310 *C311 H11X 1.5402 112.27 -121.37 108.23 1.1139 +IC H11X C310 *C311 H11Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C310 C311 C312 C313 1.5345 112.42 -176.73 112.80 1.5356 +IC C313 C311 *C312 H12X 1.5349 112.42 -120.99 108.94 1.1133 +IC H12X C311 *C312 H12Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C311 C312 C313 C314 1.5349 112.80 178.92 112.27 1.5402 +IC C314 C312 *C313 H13X 1.5402 112.27 -121.37 108.23 1.1139 +IC H13X C312 *C313 H13Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C312 C313 C314 C315 1.5356 112.27 -174.92 111.69 1.5099 +IC C315 C313 *C314 H14X 1.5099 111.69 -124.14 107.77 1.1124 +IC H14X C313 *C314 H14Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C313 C314 C315 C316 1.5402 111.69 -121.39 127.35 1.3470 +IC C316 C314 *C315 H15X 1.3470 127.35 179.11 114.24 1.1012 +IC C314 C315 C316 C317 1.5099 127.35 -0.69 127.25 1.5096 +IC C317 C315 *C316 H16X 1.5096 127.25 179.82 118.43 1.1012 +IC C315 C316 C317 C318 1.3470 127.25 106.03 111.65 1.5393 +IC C318 C316 *C317 H17X 1.5393 111.65 -121.49 112.10 1.1123 +IC H17X C316 *C317 H17Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C316 C317 C318 C319 1.5096 111.65 179.63 112.41 1.5355 +IC C319 C317 *C318 H18X 1.5355 112.41 -121.09 109.75 1.1135 +IC H18X C317 *C318 H18Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C317 C318 C319 C320 1.5393 112.41 -178.89 112.60 1.5347 +IC C320 C318 *C319 H19X 1.5347 112.60 -121.37 109.10 1.1131 +IC H19X C318 *C319 H19Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C318 C319 C320 C321 1.5355 112.60 179.88 112.66 1.5347 +IC C321 C319 *C320 H20X 1.5347 112.66 -121.27 109.06 1.1132 +IC H20X C319 *C320 H20Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C319 C320 C321 C322 1.5347 112.66 -179.12 112.61 1.5348 +IC C322 C320 *C321 H21X 1.5348 112.61 -121.34 109.09 1.1132 +IC H21X C320 *C321 H21Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C320 C321 C322 C323 1.5347 112.61 179.83 112.71 1.5340 +IC C323 C321 *C322 H22X 1.5340 112.71 -121.28 109.10 1.1132 +IC H22X C321 *C322 H22Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C321 C322 C323 C324 1.5348 112.71 -179.67 113.30 1.5309 +IC C324 C322 *C323 H23X 1.5309 113.30 -121.68 108.77 1.1141 +IC H23X C322 *C323 H23Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C322 C323 C324 H24X 1.5340 113.30 -59.94 110.46 1.1113 +IC H24X C323 *C324 H24Y 1.1113 110.46 119.86 110.45 1.1113 +IC H24X C323 *C324 H24Z 1.1113 110.46 -120.06 110.61 1.1112 +! +RESI SAPG -1.00 ! 1-Stearoyl-2-Arachidonyl-Phosphatidylglycerol +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5571 112.39 -88.77 119.48 1.5876 +IC C11 O12 P O11 1.4344 119.48 -61.43 101.30 1.5863 +IC O11 O12 *P O13 1.5863 101.30 -115.24 108.56 1.4777 +IC O11 O12 *P O14 1.5863 101.30 114.96 107.76 1.4796 +IC O12 P O11 C1 1.5876 101.30 -76.29 119.38 1.4327 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5329 113.78 68.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 120.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 120.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 120.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 120.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 120.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 120.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SLPG -1.00 ! 1-Stearoyl-2-Linoleoyl-Phosphatidylglycerol +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +!! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +!! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z +! +!IMPR C21 O21 C22 O22 C31 O31 C32 O32 +! +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5571 112.39 -88.77 119.48 1.5876 +IC C11 O12 P O11 1.4344 119.48 -61.43 101.30 1.5863 +IC O11 O12 *P O13 1.5863 101.30 -115.24 108.56 1.4777 +IC O11 O12 *P O14 1.5863 101.30 114.96 107.76 1.4796 +IC O12 P O11 C1 1.5876 101.30 -76.29 119.38 1.4327 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI PLPG -1.00 ! 1-palmitoyl-2-linoleoyl-Phosphatidylglycerol +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! H6R ---C26---H6S | +ATOM H6R HAL2 0.09 ! | | +ATOM H6S HAL2 0.09 ! | | +GROUP ! H7R ---C27---H7S | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! | | +ATOM H7S HAL2 0.09 ! | | +GROUP ! H8R ---C28---H8S | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! | | +ATOM H8S HAL2 0.09 ! H9R ---C29 | +GROUP ! || | +ATOM C29 CEL1 -0.15 ! || | +ATOM H9R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! | | +GROUP ! H11R---C211---H11S | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! | | +ATOM H11S HAL2 0.09 ! H12R---C212---H12S | +GROUP ! || | +ATOM C212 CEL1 -0.15 ! || | +ATOM H12R HEL1 0.15 ! H13R---C213---H13S | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! | | +GROUP ! H14R---C214---H14S | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! | | +ATOM H14S HAL2 0.09 ! H15R---C215---H15S | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H16R---C216--H16S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H17R---C217--H17S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H18R---C218--H18S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! H18T | +ATOM H18R HAL3 0.09 ! | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R +DOUBLE C212 C213 +BOND C213 H13R C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5571 112.39 -88.77 119.48 1.5876 +IC C11 O12 P O11 1.4344 119.48 -61.43 101.30 1.5863 +IC O11 O12 *P O13 1.5863 101.30 -115.24 108.56 1.4777 +IC O11 O12 *P O14 1.5863 101.30 114.96 107.76 1.4796 +IC O12 P O11 C1 1.5876 101.30 -76.29 119.38 1.4327 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5280 113.25 70.18 112.81 1.5346 +IC C24 C22 *C23 H3R 1.5346 112.81 -123.14 110.14 1.1142 +IC H3R C22 *C23 H3S 1.1142 110.14 -116.66 107.70 1.1125 +IC C22 C23 C24 C25 1.5456 112.81 172.40 112.79 1.5353 +IC C25 C23 *C24 H4R 1.5353 112.79 -122.05 109.90 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.90 -117.14 108.37 1.1150 +IC C23 C24 C25 C26 1.5346 112.79 167.30 112.42 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.42 -120.63 108.10 1.1132 +IC H5R C24 *C25 H5S 1.1132 108.10 -117.30 109.47 1.1120 +IC C24 C25 C26 C27 1.5353 112.42 177.91 114.45 1.5409 +IC C27 C25 *C26 H6R 1.5409 114.45 -121.60 108.84 1.1121 +IC H6R C25 *C26 H6S 1.1121 108.84 -116.16 108.48 1.1134 +IC C25 C26 C27 C28 1.5358 114.45 53.66 115.58 1.5440 +IC C28 C26 *C27 H7R 1.5440 115.58 -121.63 108.47 1.1138 +IC H7R C26 *C27 H7S 1.1138 108.47 -116.24 108.32 1.1141 +IC C26 C27 C28 C29 1.5409 115.58 55.01 112.73 1.5097 +IC C29 C27 *C28 H8R 1.5097 112.73 -121.48 108.57 1.1114 +IC H8R C27 *C28 H8S 1.1114 108.57 -114.55 107.55 1.1126 +IC C27 C28 C29 C210 1.5440 112.73 109.39 127.97 1.3474 +IC C210 C28 *C29 H9R 1.3474 127.97 -179.15 113.83 1.1025 +IC C28 C29 C210 C211 1.5097 127.97 0.64 127.89 1.5108 +IC C211 C29 *C210 H10R 1.5108 127.89 179.31 117.75 1.1014 +IC C29 C210 C211 C212 1.3474 127.89 -112.95 111.22 1.5114 +IC C212 C210 *C211 H11R 1.5114 111.22 -120.46 108.90 1.1119 +IC H11R C210 *C211 H11S 1.1119 108.90 -115.57 110.84 1.1112 +IC C210 C211 C212 C213 1.5108 111.22 134.57 126.37 1.3465 +IC C213 C211 *C212 H12R 1.3465 126.37 -177.01 115.27 1.1018 +IC C211 C212 C213 C214 1.5114 126.37 3.15 126.32 1.5077 +IC C214 C212 *C213 H13R 1.5077 126.32 178.37 118.79 1.1003 +IC C212 C213 C214 C215 1.3465 126.32 -92.58 113.47 1.5417 +IC C215 C213 *C214 H14R 1.5417 113.47 -122.01 110.01 1.1123 +IC H14R C213 *C214 H14S 1.1123 110.01 -116.77 110.38 1.1120 +IC C213 C214 C215 C216 1.5077 113.47 -63.55 113.58 1.5369 +IC C216 C214 *C215 H15R 1.5369 113.58 -120.33 108.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 108.08 -116.59 109.36 1.1132 +IC C214 C215 C216 C217 1.5417 113.58 -171.21 113.87 1.5374 +IC C217 C215 *C216 H16R 1.5374 113.87 -121.70 108.87 1.1122 +IC H16R C215 *C216 H16S 1.1122 108.87 -117.00 108.72 1.1132 +IC C215 C216 C217 C218 1.5369 113.87 -61.57 114.41 1.5314 +IC C218 C216 *C217 H17R 1.5314 114.41 -121.26 108.12 1.1148 +IC H17R C216 *C217 H17S 1.1148 108.12 -116.30 108.76 1.1136 +IC C216 C217 C218 H18R 1.5374 114.41 63.53 110.93 1.1107 +IC H18R C217 *C218 H18S 1.1107 110.93 -119.76 110.34 1.1109 +IC H18R C217 *C218 H18T 1.1107 110.93 120.37 110.77 1.1100 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI SDPE 0.00 ! 1-Stearoyl-2-Docosahexaenoyl-Phosphatidylethanolamine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CEL1 -0.15 ! | | +ATOM H4R HEL1 0.15 ! H4R ---C24 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H4R ---C25 | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CEL1 -0.15 ! | | +ATOM H7R HEL1 0.15 ! H7R ---C27 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R----C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! |! (CIS) | +ATOM C217 CEL1 -0.15 ! |! | +ATOM H17R HEL1 0.15 ! H17R---C217 | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CEL1 -0.15 ! | | +ATOM H19R HEL1 0.15 ! H19R---C219 | +GROUP ! |! (CIS) | +ATOM C220 CEL1 -0.15 ! |! | +ATOM H20R HEL1 0.15 ! H20R---C220 | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R +DOUBLE C24 C25 +BOND C25 H5R C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R +DOUBLE C27 C28 +BOND C28 H8R C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R +DOUBLE C210 C211 +BOND C211 H11R C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R +DOUBLE C216 C217 +BOND C217 H17R C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R +DOUBLE C219 C220 +BOND C220 H20R C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5261 119.27 61.50 111.44 1.4207 +IC O12 C12 *C11 H11A 1.4207 111.44 -127.11 110.31 1.1153 +IC O12 C12 *C11 H11B 1.5529 119.27 122.46 108.90 1.0813 +IC C12 C11 O12 P 1.5529 111.44 -110.28 123.53 1.5856 +IC C11 O12 P O11 1.4207 123.53 -117.07 102.54 1.5781 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5347 115.21 180.00 110.44 1.5096 +IC C24 C22 *C23 H3R 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C22 *C23 H3S 1.5192 121.35 123.34 106.97 1.1128 +IC C22 C23 C24 C25 1.5530 110.44 180.00 127.08 1.3487 +IC C25 C23 *C24 H4R 1.3487 127.08 180.00 114.44 1.1010 +IC C23 C24 C25 C26 1.5096 127.08 0.00 127.17 1.5116 !cis db +IC C26 C24 *C25 H5R 1.5116 127.17 179.68 118.27 1.1015 +IC C24 C25 C26 C27 1.3487 127.17 180.00 111.97 1.5099 +IC C27 C25 *C26 H6R 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C25 *C26 H6S 1.5192 121.35 123.34 106.97 1.1128 +IC C25 C26 C27 C28 1.5116 111.97 180.00 126.68 1.3492 +IC C28 C26 *C27 H7R 1.3492 126.68 178.47 114.82 1.1014 +IC C26 C27 C28 C29 1.5099 126.68 0.00 126.94 1.5099 !cis db +IC C29 C27 *C28 H8R 1.5099 126.94 -177.42 118.69 1.1018 +IC C27 C28 C29 C210 1.3492 126.94 180.00 111.95 1.5084 +IC C210 C28 *C29 H9R 1.5396 113.52 -123.43 110.53 1.1101 +IC C210 C28 *C29 H9S 1.5192 121.35 123.34 106.97 1.1128 +IC C28 C29 C210 C211 1.5099 111.95 180.00 126.47 1.3485 +IC C211 C29 *C210 H10R 1.3453 125.97 -176.85 115.39 1.1011 +IC C29 C210 C211 C212 1.5084 126.47 0.00 127.07 1.5122 !cis db +IC C212 C210 *C211 H11R 1.5097 125.28 178.19 119.65 1.1004 +IC C210 C211 C212 C213 1.3485 127.07 180.00 112.04 1.5115 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5192 121.35 123.34 106.97 1.1128 +IC C211 C212 C213 C214 1.5122 112.04 180.00 126.62 1.3479 +IC C214 C212 *C213 H13R 1.3453 125.97 -176.85 115.39 1.1011 +IC C212 C213 C214 C215 1.5115 126.62 0.00 127.02 1.5107 !cis db +IC C215 C213 *C214 H14R 1.5097 125.28 178.19 119.65 1.1004 +IC C213 C214 C215 C216 1.3479 127.02 180.00 112.92 1.5093 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5192 121.35 123.34 106.97 1.1128 +IC C214 C215 C216 C217 1.5107 112.92 180.00 124.28 1.3467 +IC C217 C215 *C216 H16R 1.3453 125.97 -176.85 115.39 1.1011 +IC C215 C216 C217 C218 1.5093 124.28 0.00 126.43 1.5125 !cis db +IC C218 C216 *C217 H17R 1.5097 125.28 178.19 119.65 1.1004 +IC C216 C217 C218 C219 1.3467 126.43 180.00 116.29 1.5121 +IC C219 C217 *C218 H18R 1.5396 113.52 -123.43 110.53 1.1101 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5125 116.29 180.00 124.57 1.3458 +IC C220 C218 *C219 H19R 1.3453 125.97 -176.85 115.39 1.1011 +IC C218 C219 C220 C221 1.5121 124.57 0.00 126.91 1.5106 !cis db +IC C221 C219 *C220 H20R 1.5097 125.28 178.19 119.65 1.1004 +IC C219 C220 C221 C222 1.3458 126.91 0.74 115.89 1.5382 +IC C222 C220 *C221 H21R 1.5396 113.52 -123.43 110.53 1.1101 +IC C222 C220 *C221 H21S 1.5192 121.35 123.34 106.97 1.1128 +IC C220 C221 C222 H22R 1.5106 115.89 -60.86 110.71 1.1115 +IC H22R C221 *C222 H22S 1.5396 113.52 -123.43 110.53 1.1101 +IC H22R C221 *C222 H22T 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SOPE 0.00 ! 1-Stearoyl-2-Oleoyl-Phosphatidylethanolamine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5261 119.27 61.50 111.44 1.4207 +IC O12 C12 *C11 H11A 1.4207 111.44 -127.11 110.31 1.1153 +IC O12 C12 *C11 H11B 1.5529 119.27 122.46 108.90 1.0813 +IC C12 C11 O12 P 1.5529 111.44 -110.28 123.53 1.5856 +IC C11 O12 P O11 1.4207 123.53 -117.07 102.54 1.5781 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5285 113.04 -70.28 113.21 1.5360 +IC C24 C22 *C23 H3R 1.5360 113.21 -119.83 108.42 1.1148 +IC C24 C22 *C23 H3S 1.5396 113.52 -123.43 110.53 1.1101 +IC C22 C23 C24 C25 1.5450 113.21 -172.34 113.68 1.5399 +IC C25 C23 *C24 H4R 1.5399 113.68 120.91 108.91 1.1136 +IC C25 C23 *C24 H4S 1.5396 113.52 -123.43 110.53 1.1101 +IC C23 C24 C25 C26 1.5360 113.68 -56.95 113.57 1.5353 +IC C26 C24 *C25 H5R 1.5353 113.57 121.41 108.70 1.1129 +IC C26 C24 *C25 H5S 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C25 C26 C27 1.5399 113.57 -173.39 113.79 1.5375 +IC C27 C25 *C26 H6R 1.5375 113.79 122.09 109.21 1.1127 +IC C27 C25 *C26 H6S 1.5396 113.52 -123.43 110.53 1.1101 +IC C25 C26 C27 C28 1.5353 113.79 177.45 113.35 1.5458 +IC C28 C26 *C27 H7R 1.5458 113.35 119.87 108.07 1.1139 +IC C28 C26 *C27 H7S 1.5396 113.52 -123.43 110.53 1.1101 +IC C26 C27 C28 C29 1.5375 113.35 67.78 114.46 1.5115 +IC C29 C27 *C28 H8R 1.5115 114.46 121.34 107.89 1.1131 +IC C29 C27 *C28 H8S 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C28 C29 C210 1.5458 114.46 180.00 126.91 1.3502 +IC C210 C28 *C29 H91 1.3502 126.91 -178.81 114.69 1.1010 +IC C28 C29 C210 C211 1.5115 126.91 0.00 126.69 1.5092 !cis db +IC C211 C29 *C210 H101 1.5099 126.94 -177.42 118.69 1.1018 +IC C29 C210 C211 C212 1.3502 126.69 180.00 111.86 1.5417 +IC C212 C210 *C211 H11R 1.5396 113.52 -123.43 110.53 1.1101 +IC C212 C210 *C211 H11S 1.5097 125.28 121.00 119.65 1.1004 +IC C210 C211 C212 C213 1.5092 111.86 180.00 113.99 1.5334 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5097 125.28 121.00 119.65 1.1004 +IC C211 C212 C213 C214 1.5417 113.99 180.00 111.46 1.5365 +IC C214 C212 *C213 H13R 1.5396 113.52 -123.43 110.53 1.1101 +IC C214 C212 *C213 H13S 1.5097 125.28 121.00 119.65 1.1004 +IC C212 C213 C214 C215 1.5334 111.46 180.00 114.22 1.5376 +IC C215 C213 *C214 H14R 1.5396 113.52 -123.43 110.53 1.1101 +IC C215 C213 *C214 H14S 1.5097 125.28 121.00 119.65 1.1004 +IC C213 C214 C215 C216 1.5365 114.22 180.00 114.97 1.5385 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5097 125.28 121.00 119.65 1.1004 +IC C214 C215 C216 C217 1.5376 114.97 180.00 113.95 1.5347 +IC C217 C215 *C216 H16R 1.5396 113.52 -123.43 110.53 1.1101 +IC C217 C215 *C216 H16S 1.5097 125.28 121.00 119.65 1.1004 +IC C215 C216 C217 C218 1.5385 113.95 180.00 113.05 1.5311 +IC C218 C216 *C217 H17R 1.5396 113.52 -123.43 110.53 1.1101 +IC C218 C216 *C217 H17S 1.5097 125.28 121.00 119.65 1.1004 +IC C216 C217 C218 H18R 1.5347 113.05 180.00 110.58 1.1110 +IC H18R C217 *C218 H18S 1.5396 113.52 -123.43 110.53 1.1101 +IC H18R C217 *C218 H18T 1.5097 125.28 121.00 119.65 1.1004 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 121.00 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 121.00 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI DAPE 0.00 ! 1,2-Diarachidonyl-Phosphatidylethanolamine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | ! +ATOM H3R HAL2 0.09 ! H3R---C23---H3S ! +ATOM H3S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C24 CTL2 -0.18 ! | ! +ATOM H4R HAL2 0.09 ! H4R---C24---H4S ! +ATOM H4S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C25 CEL1 -0.15 ! | ! +ATOM H5R HEL1 0.15 ! H5R---C25 ! +GROUP ! || ! +ATOM C26 CEL1 -0.15 ! || ! +ATOM H6R HEL1 0.15 ! H6R---C26 ! +GROUP ! | ! +ATOM C27 CTL2 -0.18 ! | ! +ATOM H7R HAL2 0.09 ! H7R---C27--H7S ! +ATOM H7S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C28 CEL1 -0.15 ! | ! +ATOM H8R HEL1 0.15 ! H8R---C28 ! +GROUP ! || ! +ATOM C29 CEL1 -0.15 ! || ! +ATOM H9R HEL1 0.15 ! H9R---C29 ! +GROUP ! | ! +ATOM C210 CTL2 -0.18 ! | ! +ATOM H10R HAL2 0.09 ! | ! +ATOM H10S HAL2 0.09 ! H10R---C210--H10S ! +GROUP ! | ! +ATOM C211 CEL1 -0.15 ! | ! +ATOM H11R HEL1 0.15 ! H11R---C211 ! +GROUP ! || ! +ATOM C212 CEL1 -0.15 ! || ! +ATOM H12R HEL1 0.15 ! H12R---C212 ! +GROUP ! | ! +ATOM C213 CTL2 -0.18 ! | ! +ATOM H13R HAL2 0.09 ! H13R---C213---H13S ! +ATOM H13S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C214 CEL1 -0.15 ! | ! +ATOM H14R HEL1 0.15 ! H14R---C214 ! +GROUP ! || ! +ATOM C215 CEL1 -0.15 ! || ! +ATOM H15R HEL1 0.15 ! H15R---C215 ! +GROUP ! | ! +ATOM C216 CTL2 -0.18 ! | ! +ATOM H16R HAL2 0.09 ! H16R---C216--H16S ! +ATOM H16S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C217 CTL2 -0.18 ! | ! +ATOM H17R HAL2 0.09 ! H17R---C217--H17S ! +ATOM H17S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C218 CTL2 -0.18 ! | ! +ATOM H18R HAL2 0.09 ! H18R---C218--H18S ! +ATOM H18S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C219 CTL2 -0.18 ! | ! +ATOM H19R HAL2 0.09 ! H19R---C219--H19S ! +ATOM H19S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C220 CTL3 -0.27 ! | ! +ATOM H20R HAL3 0.09 ! H20R---C220--H20S ! +ATOM H20S HAL3 0.09 ! | ! +ATOM H20T HAL3 0.09 ! H20T ! +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CEL1 -0.15 ! | +ATOM H5X HEL1 0.15 ! H5X---C35 +GROUP ! || +ATOM C36 CEL1 -0.15 ! || +ATOM H6X HEL1 0.15 ! H6X---C36 +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CEL1 -0.15 ! | +ATOM H8X HEL1 0.15 ! H8X---C38 +GROUP ! || +ATOM C39 CEL1 -0.15 ! || +ATOM H9X HEL1 0.15 ! H9X---C39 +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313---H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CEL1 -0.15 ! | +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! || +ATOM C315 CEL1 -0.15 ! || +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316---H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 C1 O11 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND C21 O21 C21 C22 +DOUBLE C21 O22 +BOND C22 C23 C22 H2R C22 H2S +BOND C23 C24 C23 H3R C23 H3S +BOND C24 C25 C24 H4R C24 H4S +DOUBLE C25 C26 +BOND C25 H5R +BOND C26 C27 C26 H6R +BOND C27 C28 C27 H7R C27 H7S +DOUBLE C28 C29 +BOND C28 H8R +BOND C29 C210 C29 H9R +BOND C210 C211 C210 H10R C210 H10S +DOUBLE C211 C212 +BOND C211 H11R +BOND C212 C213 C212 H12R +BOND C213 C214 C213 H13R C213 H13S +DOUBLE C214 C215 +BOND C214 H14R +BOND C215 C216 C215 H15R +BOND C216 C217 C216 H16R C216 H16S +BOND C217 C218 C217 H17R C217 H17S +BOND C218 C219 C218 H18R C218 H18S +BOND C219 C220 C219 H19R C219 H19S +BOND C220 H20T C220 H20R C220 H20S +! Chain From C3 +BOND C31 O31 C31 C32 +DOUBLE C31 O32 +BOND C32 C33 C32 H2X C32 H2Y +BOND C33 C34 C33 H3X C33 H3Y +BOND C34 C35 C34 H4X C34 H4Y +DOUBLE C35 C36 +BOND C35 H5X +BOND C36 C37 C36 H6X +BOND C37 C38 C37 H7X C37 H7Y +DOUBLE C38 C39 +BOND C38 H8X +BOND C39 C310 C39 H9X +BOND C310 C311 C310 H10X C310 H10Y +DOUBLE C311 C312 +BOND C311 H11X +BOND C312 C313 C312 H12X +BOND C313 C314 C313 H13X C313 H13Y +DOUBLE C314 C315 +BOND C314 H14X +BOND C315 C316 C315 H15X +BOND C316 C317 C316 H16X C316 H16Y +BOND C317 C318 C317 H17X C317 H17Y +BOND C318 C319 C318 H18X C318 H18Y +BOND C319 C320 C319 H19X C319 H19Y +BOND C320 H20Z C320 H20X C320 H20Y + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC HN1 C12 *N HN2 1.0400 113.54 121.34 115.64 1.0411 +IC HN1 C12 *N HN3 1.0400 113.54 -123.64 106.00 1.0397 +IC HN1 N C12 C11 1.0400 113.54 -163.97 108.03 1.6269 +IC C11 N *C12 H12A 1.6269 108.03 -116.99 110.74 1.1107 +IC H12A N *C12 H12B 1.1107 110.74 -123.08 109.49 1.1110 +IC N C12 C11 O12 1.5273 118.22 69.62 111.90 1.4262 +IC O12 C12 *C11 H11A 1.4262 111.90 -121.72 110.21 1.1107 +IC H11A C12 *C11 H11B 1.1107 110.21 -116.97 108.97 1.1164 +IC C12 C11 O12 P 1.5547 111.90 56.58 119.25 1.5954 +IC C11 O12 P O11 1.4262 119.25 125.38 103.46 1.5769 +IC O11 O12 *P O13 1.5769 103.46 -117.59 108.11 1.4797 +IC O11 O12 *P O14 1.5769 103.46 116.77 106.20 1.4775 +IC O12 P O11 C1 1.5954 103.46 33.43 121.47 1.4291 +IC P O11 C1 C2 1.5769 121.47 146.27 110.07 1.5526 +IC C2 O11 *C1 HA 1.5526 110.07 -121.29 113.08 1.1166 +IC HA O11 *C1 HB 1.1166 113.08 -120.24 108.73 1.1132 +IC O11 C1 C2 C3 1.4291 110.07 37.91 111.11 1.5544 +IC C3 C1 *C2 O21 1.5544 111.11 119.78 110.70 1.4395 +IC C3 C1 *C2 HS 1.5544 111.11 -117.46 108.81 1.1157 +IC C1 C2 O21 C21 1.5526 110.70 72.82 115.87 1.3174 +IC C2 O21 C21 C22 1.4395 115.87 179.18 109.41 1.5329 +IC C22 O21 *C21 O22 1.5329 109.41 -178.52 126.45 1.2180 +IC O21 C21 C22 C23 1.3174 109.41 180.00 113.78 1.5483 +IC C23 C21 *C22 H2R 1.5483 113.78 -121.17 107.02 1.1096 +IC C23 C21 *C22 H2S 1.5483 113.78 122.25 107.54 1.1088 +IC C1 C2 C3 O31 1.5526 111.11 179.84 110.78 1.4471 +IC O31 C2 *C3 HX 1.4471 110.78 -122.23 106.07 1.1170 +IC HX C2 *C3 HY 1.1170 106.07 -116.50 109.11 1.1127 +IC C2 C3 O31 C31 1.5544 110.78 -158.57 113.91 1.3265 +IC C3 O31 C31 C32 1.4471 113.91 178.20 108.97 1.5287 +IC C32 O31 *C31 O32 1.5287 108.97 178.94 125.84 1.2167 +IC O31 C31 C32 C33 1.3265 108.97 180.00 111.97 1.5453 +IC C33 C31 *C32 H2X 1.5453 111.97 -120.94 107.50 1.1090 +IC C33 C31 *C32 H2Y 1.5453 111.97 121.71 108.29 1.1085 +IC C21 C22 C23 C24 1.5329 113.78 180.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 !cis db +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 180.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 180.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 !cis db +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 180.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 180.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 !cis db +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 180.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 180.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 !cis db +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5287 111.97 180.00 112.58 1.5385 +IC C34 C32 *C33 H3X 1.5385 112.58 -122.10 109.10 1.1140 +IC C34 C32 *C33 H3Y 1.5385 112.58 121.05 109.26 1.1142 +IC C32 C33 C34 C35 1.5453 112.58 180.00 110.80 1.5074 +IC C35 C33 *C34 H4X 1.5074 110.80 -121.89 108.15 1.1141 +IC C35 C33 *C34 H4Y 1.5074 110.80 121.81 109.29 1.1125 +IC C33 C34 C35 C36 1.5385 110.80 180.00 124.10 1.3433 +IC C36 C34 *C35 H5X 1.3433 124.10 174.75 116.37 1.1008 +IC C34 C35 C36 C37 1.5074 124.10 0.00 125.00 1.5143 !cis db +IC C37 C35 *C36 H6X 1.5143 125.00 -174.44 119.05 1.1017 +IC C35 C36 C37 C38 1.3433 125.00 180.00 117.59 1.5177 +IC C38 C36 *C37 H7X 1.5177 117.59 -122.41 107.65 1.1123 +IC C38 C36 *C37 H7Y 1.5177 117.59 123.72 109.79 1.1133 +IC C36 C37 C38 C39 1.5143 117.59 180.00 126.89 1.3482 +IC C39 C37 *C38 H8X 1.3482 126.89 179.60 114.90 1.1010 +IC C37 C38 C39 C310 1.5177 126.89 0.00 126.25 1.5108 !cis db +IC C310 C38 *C39 H9X 1.5108 126.25 -179.63 118.76 1.1018 +IC C38 C39 C310 C311 1.3482 126.25 180.00 114.73 1.5131 +IC C311 C39 *C310 H10X 1.5177 117.59 -122.41 107.65 1.1123 +IC C311 C39 *C310 H10Y 1.5177 117.59 123.72 109.79 1.1133 +IC C39 C310 C311 C312 1.5108 114.73 180.00 127.49 1.3509 +IC C312 C310 *C311 H11X 1.3482 126.89 179.60 114.90 1.1010 +IC C310 C311 C312 C313 1.5131 127.49 0.00 126.92 1.5159 !cis db +IC C313 C311 *C312 H12X 1.5108 126.25 -179.63 118.76 1.1018 +IC C311 C312 C313 C314 1.3509 126.92 180.00 118.29 1.5170 +IC C314 C312 *C313 H13X 1.5177 117.59 -122.41 107.65 1.1123 +IC C314 C312 *C313 H13Y 1.5177 117.59 123.72 109.79 1.1133 +IC C312 C313 C314 C315 1.5159 118.29 180.00 127.41 1.3481 +IC C315 C313 *C314 H14X 1.3509 126.92 180.00 118.29 1.5170 +IC C313 C314 C315 C316 1.5170 127.41 0.00 125.25 1.5075 !cis db +IC C316 C314 *C315 H15X 1.5108 126.25 -179.63 118.76 1.1018 +IC C314 C315 C316 C317 1.3481 125.25 180.00 113.42 1.5450 +IC C317 C315 *C316 H16X 1.5177 117.59 -122.41 107.65 1.1123 +IC C317 C315 *C316 H16Y 1.5177 117.59 123.72 109.79 1.1133 +IC C315 C316 C317 C318 1.5075 113.42 180.00 116.08 1.5437 +IC C318 C316 *C317 H17X 1.5177 117.59 -122.41 107.65 1.1123 +IC C318 C316 *C317 H17Y 1.5177 117.59 123.72 109.79 1.1133 +IC C316 C317 C318 C319 1.5450 116.08 180.00 116.10 1.6007 +IC C319 C317 *C318 H18X 1.5177 117.59 -122.41 107.65 1.1123 +IC C319 C317 *C318 H18Y 1.5177 117.59 123.72 109.79 1.1133 +IC C317 C318 C319 C320 1.5437 116.10 180.00 132.00 1.5738 +IC C320 C318 *C319 H19X 1.5177 117.59 -122.41 107.65 1.1123 +IC C320 C318 *C319 H19Y 1.5177 117.59 123.72 109.79 1.1133 +IC C318 C319 C320 H20Z 1.6007 132.00 -119.54 110.70 1.1112 +IC H20Z C319 *C320 H20X 1.5177 117.59 -122.41 107.65 1.1123 +IC H20Z C319 *C320 H20Y 1.5177 117.59 123.72 109.79 1.1133 + +RESI SDPS -1.00 ! 1-Stearoyl-2-Docosahexaenoyl-Phosphatidylserine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CEL1 -0.15 ! | | +ATOM H4R HEL1 0.15 ! H4R ---C24 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H4R ---C25 | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CEL1 -0.15 ! | | +ATOM H7R HEL1 0.15 ! H7R ---C27 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R----C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! |! (CIS) | +ATOM C217 CEL1 -0.15 ! |! | +ATOM H17R HEL1 0.15 ! H17R---C217 | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CEL1 -0.15 ! | | +ATOM H19R HEL1 0.15 ! H19R---C219 | +GROUP ! |! (CIS) | +ATOM C220 CEL1 -0.15 ! |! | +ATOM H20R HEL1 0.15 ! H20R---C220 | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R +DOUBLE C24 C25 +BOND C25 H5R C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R +DOUBLE C27 C28 +BOND C28 H8R C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R +DOUBLE C210 C211 +BOND C211 H11R C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R +DOUBLE C216 C217 +BOND C217 H17R C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R +DOUBLE C219 C220 +BOND C220 H20R C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4207 111.44 -127.11 110.31 1.1153 +IC O12 C12 *C11 H11B 1.5529 119.27 122.46 108.90 1.0813 +IC C12 C11 O12 P 1.5529 111.44 -110.28 123.53 1.5856 +IC C11 O12 P O11 1.4207 123.53 -117.07 102.54 1.5781 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5347 115.21 180.00 110.44 1.5096 +IC C24 C22 *C23 H3R 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C22 *C23 H3S 1.5192 121.35 123.34 106.97 1.1128 +IC C22 C23 C24 C25 1.5530 110.44 180.00 127.08 1.3487 +IC C25 C23 *C24 H4R 1.3487 127.08 180.00 114.44 1.1010 +IC C23 C24 C25 C26 1.5096 127.08 0.00 127.17 1.5116 !cis db +IC C26 C24 *C25 H5R 1.5116 127.17 179.68 118.27 1.1015 +IC C24 C25 C26 C27 1.3487 127.17 180.00 111.97 1.5099 +IC C27 C25 *C26 H6R 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C25 *C26 H6S 1.5192 121.35 123.34 106.97 1.1128 +IC C25 C26 C27 C28 1.5116 111.97 180.00 126.68 1.3492 +IC C28 C26 *C27 H7R 1.3492 126.68 178.47 114.82 1.1014 +IC C26 C27 C28 C29 1.5099 126.68 0.00 126.94 1.5099 !cis db +IC C29 C27 *C28 H8R 1.5099 126.94 -177.42 118.69 1.1018 +IC C27 C28 C29 C210 1.3492 126.94 180.00 111.95 1.5084 +IC C210 C28 *C29 H9R 1.5396 113.52 -123.43 110.53 1.1101 +IC C210 C28 *C29 H9S 1.5192 121.35 123.34 106.97 1.1128 +IC C28 C29 C210 C211 1.5099 111.95 180.00 126.47 1.3485 +IC C211 C29 *C210 H10R 1.3453 125.97 -176.85 115.39 1.1011 +IC C29 C210 C211 C212 1.5084 126.47 0.00 127.07 1.5122 !cis db +IC C212 C210 *C211 H11R 1.5097 125.28 178.19 119.65 1.1004 +IC C210 C211 C212 C213 1.3485 127.07 180.00 112.04 1.5115 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5192 121.35 123.34 106.97 1.1128 +IC C211 C212 C213 C214 1.5122 112.04 180.00 126.62 1.3479 +IC C214 C212 *C213 H13R 1.3453 125.97 -176.85 115.39 1.1011 +IC C212 C213 C214 C215 1.5115 126.62 0.00 127.02 1.5107 !cis db +IC C215 C213 *C214 H14R 1.5097 125.28 178.19 119.65 1.1004 +IC C213 C214 C215 C216 1.3479 127.02 180.00 112.92 1.5093 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5192 121.35 123.34 106.97 1.1128 +IC C214 C215 C216 C217 1.5107 112.92 180.00 124.28 1.3467 +IC C217 C215 *C216 H16R 1.3453 125.97 -176.85 115.39 1.1011 +IC C215 C216 C217 C218 1.5093 124.28 0.00 126.43 1.5125 !cis db +IC C218 C216 *C217 H17R 1.5097 125.28 178.19 119.65 1.1004 +IC C216 C217 C218 C219 1.3467 126.43 180.00 116.29 1.5121 +IC C219 C217 *C218 H18R 1.5396 113.52 -123.43 110.53 1.1101 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5125 116.29 180.00 124.57 1.3458 +IC C220 C218 *C219 H19R 1.3453 125.97 -176.85 115.39 1.1011 +IC C218 C219 C220 C221 1.5121 124.57 0.00 126.91 1.5106 !cis db +IC C221 C219 *C220 H20R 1.5097 125.28 178.19 119.65 1.1004 +IC C219 C220 C221 C222 1.3458 126.91 0.74 115.89 1.5382 +IC C222 C220 *C221 H21R 1.5396 113.52 -123.43 110.53 1.1101 +IC C222 C220 *C221 H21S 1.5192 121.35 123.34 106.97 1.1128 +IC C220 C221 C222 H22R 1.5106 115.89 -60.86 110.71 1.1115 +IC H22R C221 *C222 H22S 1.5396 113.52 -123.43 110.53 1.1101 +IC H22R C221 *C222 H22T 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SOPS -1.00 ! 1-Stearoyl-2-Oleoyl-Phosphatidylserine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4207 111.44 -127.11 110.31 1.1153 +IC O12 C12 *C11 H11B 1.5529 119.27 122.46 108.90 1.0813 +IC C12 C11 O12 P 1.5529 111.44 -110.28 123.53 1.5856 +IC C11 O12 P O11 1.4207 123.53 -117.07 102.54 1.5781 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5285 113.04 -70.28 113.21 1.5360 +IC C24 C22 *C23 H3R 1.5360 113.21 -119.83 108.42 1.1148 +IC C24 C22 *C23 H3S 1.5396 113.52 -123.43 110.53 1.1101 +IC C22 C23 C24 C25 1.5450 113.21 -172.34 113.68 1.5399 +IC C25 C23 *C24 H4R 1.5399 113.68 120.91 108.91 1.1136 +IC C25 C23 *C24 H4S 1.5396 113.52 -123.43 110.53 1.1101 +IC C23 C24 C25 C26 1.5360 113.68 -56.95 113.57 1.5353 +IC C26 C24 *C25 H5R 1.5353 113.57 121.41 108.70 1.1129 +IC C26 C24 *C25 H5S 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C25 C26 C27 1.5399 113.57 -173.39 113.79 1.5375 +IC C27 C25 *C26 H6R 1.5375 113.79 122.09 109.21 1.1127 +IC C27 C25 *C26 H6S 1.5396 113.52 -123.43 110.53 1.1101 +IC C25 C26 C27 C28 1.5353 113.79 177.45 113.35 1.5458 +IC C28 C26 *C27 H7R 1.5458 113.35 119.87 108.07 1.1139 +IC C28 C26 *C27 H7S 1.5396 113.52 -123.43 110.53 1.1101 +IC C26 C27 C28 C29 1.5375 113.35 67.78 114.46 1.5115 +IC C29 C27 *C28 H8R 1.5115 114.46 121.34 107.89 1.1131 +IC C29 C27 *C28 H8S 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C28 C29 C210 1.5458 114.46 180.00 126.91 1.3502 +IC C210 C28 *C29 H91 1.3502 126.91 -178.81 114.69 1.1010 +IC C28 C29 C210 C211 1.5115 126.91 0.00 126.69 1.5092 !cis db +IC C211 C29 *C210 H101 1.5099 126.94 -177.42 118.69 1.1018 +IC C29 C210 C211 C212 1.3502 126.69 180.00 111.86 1.5417 +IC C212 C210 *C211 H11R 1.5396 113.52 -123.43 110.53 1.1101 +IC C212 C210 *C211 H11S 1.5097 125.28 121.00 119.65 1.1004 +IC C210 C211 C212 C213 1.5092 111.86 180.00 113.99 1.5334 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5097 125.28 121.00 119.65 1.1004 +IC C211 C212 C213 C214 1.5417 113.99 180.00 111.46 1.5365 +IC C214 C212 *C213 H13R 1.5396 113.52 -123.43 110.53 1.1101 +IC C214 C212 *C213 H13S 1.5097 125.28 121.00 119.65 1.1004 +IC C212 C213 C214 C215 1.5334 111.46 180.00 114.22 1.5376 +IC C215 C213 *C214 H14R 1.5396 113.52 -123.43 110.53 1.1101 +IC C215 C213 *C214 H14S 1.5097 125.28 121.00 119.65 1.1004 +IC C213 C214 C215 C216 1.5365 114.22 180.00 114.97 1.5385 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5097 125.28 121.00 119.65 1.1004 +IC C214 C215 C216 C217 1.5376 114.97 180.00 113.95 1.5347 +IC C217 C215 *C216 H16R 1.5396 113.52 -123.43 110.53 1.1101 +IC C217 C215 *C216 H16S 1.5097 125.28 121.00 119.65 1.1004 +IC C215 C216 C217 C218 1.5385 113.95 180.00 113.05 1.5311 +IC C218 C216 *C217 H17R 1.5396 113.52 -123.43 110.53 1.1101 +IC C218 C216 *C217 H17S 1.5097 125.28 121.00 119.65 1.1004 +IC C216 C217 C218 H18R 1.5347 113.05 180.00 110.58 1.1110 +IC H18R C217 *C218 H18S 1.5396 113.52 -123.43 110.53 1.1101 +IC H18R C217 *C218 H18T 1.5097 125.28 121.00 119.65 1.1004 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 121.00 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 121.00 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI DAPS -1.00 ! 1,2-Diarachidonyl-Phosphatidylserine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | ! +ATOM H3R HAL2 0.09 ! H3R---C23---H3S ! +ATOM H3S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C24 CTL2 -0.18 ! | ! +ATOM H4R HAL2 0.09 ! H4R---C24---H4S ! +ATOM H4S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C25 CEL1 -0.15 ! | ! +ATOM H5R HEL1 0.15 ! H5R---C25 ! +GROUP ! || ! +ATOM C26 CEL1 -0.15 ! || ! +ATOM H6R HEL1 0.15 ! H6R---C26 ! +GROUP ! | ! +ATOM C27 CTL2 -0.18 ! | ! +ATOM H7R HAL2 0.09 ! H7R---C27--H7S ! +ATOM H7S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C28 CEL1 -0.15 ! | ! +ATOM H8R HEL1 0.15 ! H8R---C28 ! +GROUP ! || ! +ATOM C29 CEL1 -0.15 ! || ! +ATOM H9R HEL1 0.15 ! H9R---C29 ! +GROUP ! | ! +ATOM C210 CTL2 -0.18 ! | ! +ATOM H10R HAL2 0.09 ! | ! +ATOM H10S HAL2 0.09 ! H10R---C210--H10S ! +GROUP ! | ! +ATOM C211 CEL1 -0.15 ! | ! +ATOM H11R HEL1 0.15 ! H11R---C211 ! +GROUP ! || ! +ATOM C212 CEL1 -0.15 ! || ! +ATOM H12R HEL1 0.15 ! H12R---C212 ! +GROUP ! | ! +ATOM C213 CTL2 -0.18 ! | ! +ATOM H13R HAL2 0.09 ! H13R---C213---H13S ! +ATOM H13S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C214 CEL1 -0.15 ! | ! +ATOM H14R HEL1 0.15 ! H14R---C214 ! +GROUP ! || ! +ATOM C215 CEL1 -0.15 ! || ! +ATOM H15R HEL1 0.15 ! H15R---C215 ! +GROUP ! | ! +ATOM C216 CTL2 -0.18 ! | ! +ATOM H16R HAL2 0.09 ! H16R---C216--H16S ! +ATOM H16S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C217 CTL2 -0.18 ! | ! +ATOM H17R HAL2 0.09 ! H17R---C217--H17S ! +ATOM H17S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C218 CTL2 -0.18 ! | ! +ATOM H18R HAL2 0.09 ! H18R---C218--H18S ! +ATOM H18S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C219 CTL2 -0.18 ! | ! +ATOM H19R HAL2 0.09 ! H19R---C219--H19S ! +ATOM H19S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C220 CTL3 -0.27 ! | ! +ATOM H20R HAL3 0.09 ! H20R---C220--H20S ! +ATOM H20S HAL3 0.09 ! | ! +ATOM H20T HAL3 0.09 ! H20T ! +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CEL1 -0.15 ! | +ATOM H5X HEL1 0.15 ! H5X---C35 +GROUP ! || +ATOM C36 CEL1 -0.15 ! || +ATOM H6X HEL1 0.15 ! H6X---C36 +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CEL1 -0.15 ! | +ATOM H8X HEL1 0.15 ! H8X---C38 +GROUP ! || +ATOM C39 CEL1 -0.15 ! || +ATOM H9X HEL1 0.15 ! H9X---C39 +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313---H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CEL1 -0.15 ! | +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! || +ATOM C315 CEL1 -0.15 ! || +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316---H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND C21 O21 C21 C22 +DOUBLE C21 O22 +BOND C22 C23 C22 H2R C22 H2S +BOND C23 C24 C23 H3R C23 H3S +BOND C24 C25 C24 H4R C24 H4S +DOUBLE C25 C26 +BOND C25 H5R +BOND C26 C27 C26 H6R +BOND C27 C28 C27 H7R C27 H7S +DOUBLE C28 C29 +BOND C28 H8R +BOND C29 C210 C29 H9R +BOND C210 C211 C210 H10R C210 H10S +DOUBLE C211 C212 +BOND C211 H11R +BOND C212 C213 C212 H12R +BOND C213 C214 C213 H13R C213 H13S +DOUBLE C214 C215 +BOND C214 H14R +BOND C215 C216 C215 H15R +BOND C216 C217 C216 H16R C216 H16S +BOND C217 C218 C217 H17R C217 H17S +BOND C218 C219 C218 H18R C218 H18S +BOND C219 C220 C219 H19R C219 H19S +BOND C220 H20T C220 H20R C220 H20S +! Chain From C3 +BOND C31 O31 C31 C32 +DOUBLE C31 O32 +BOND C32 C33 C32 H2X C32 H2Y +BOND C33 C34 C33 H3X C33 H3Y +BOND C34 C35 C34 H4X C34 H4Y +DOUBLE C35 C36 +BOND C35 H5X +BOND C36 C37 C36 H6X +BOND C37 C38 C37 H7X C37 H7Y +DOUBLE C38 C39 +BOND C38 H8X +BOND C39 C310 C39 H9X +BOND C310 C311 C310 H10X C310 H10Y +DOUBLE C311 C312 +BOND C311 H11X +BOND C312 C313 C312 H12X +BOND C313 C314 C313 H13X C313 H13Y +DOUBLE C314 C315 +BOND C314 H14X +BOND C315 C316 C315 H15X +BOND C316 C317 C316 H16X C316 H16Y +BOND C317 C318 C317 H17X C317 H17Y +BOND C318 C319 C318 H18X C318 H18Y +BOND C319 C320 C319 H19X C319 H19Y +BOND C320 H20Z C320 H20X C320 H20Y + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4262 111.90 -121.72 110.21 1.1107 +IC H11A C12 *C11 H11B 1.1107 110.21 -116.97 108.97 1.1164 +IC C12 C11 O12 P 1.5547 111.90 56.58 119.25 1.5954 +IC C11 O12 P O11 1.4262 119.25 125.38 103.46 1.5769 +IC O11 O12 *P O13 1.5769 103.46 -117.59 108.11 1.4797 +IC O11 O12 *P O14 1.5769 103.46 116.77 106.20 1.4775 +IC O12 P O11 C1 1.5954 103.46 33.43 121.47 1.4291 +IC P O11 C1 C2 1.5769 121.47 146.27 110.07 1.5526 +IC C2 O11 *C1 HA 1.5526 110.07 -121.29 113.08 1.1166 +IC HA O11 *C1 HB 1.1166 113.08 -120.24 108.73 1.1132 +IC O11 C1 C2 C3 1.4291 110.07 37.91 111.11 1.5544 +IC C3 C1 *C2 O21 1.5544 111.11 119.78 110.70 1.4395 +IC C3 C1 *C2 HS 1.5544 111.11 -117.46 108.81 1.1157 +IC C1 C2 O21 C21 1.5526 110.70 72.82 115.87 1.3174 +IC C2 O21 C21 C22 1.4395 115.87 179.18 109.41 1.5329 +IC C22 O21 *C21 O22 1.5329 109.41 -178.52 126.45 1.2180 +IC O21 C21 C22 C23 1.3174 109.41 180.00 113.78 1.5483 +IC C23 C21 *C22 H2R 1.5483 113.78 -121.17 107.02 1.1096 +IC C23 C21 *C22 H2S 1.5483 113.78 122.25 107.54 1.1088 +IC C1 C2 C3 O31 1.5526 111.11 179.84 110.78 1.4471 +IC O31 C2 *C3 HX 1.4471 110.78 -122.23 106.07 1.1170 +IC HX C2 *C3 HY 1.1170 106.07 -116.50 109.11 1.1127 +IC C2 C3 O31 C31 1.5544 110.78 -158.57 113.91 1.3265 +IC C3 O31 C31 C32 1.4471 113.91 178.20 108.97 1.5287 +IC C32 O31 *C31 O32 1.5287 108.97 178.94 125.84 1.2167 +IC O31 C31 C32 C33 1.3265 108.97 180.00 111.97 1.5453 +IC C33 C31 *C32 H2X 1.5453 111.97 -120.94 107.50 1.1090 +IC C33 C31 *C32 H2Y 1.5453 111.97 121.71 108.29 1.1085 +IC C21 C22 C23 C24 1.5329 113.78 180.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 !cis db +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 180.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 180.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 !cis db +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 180.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 180.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 !cis db +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 180.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 180.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 !cis db +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5287 111.97 180.00 112.58 1.5385 +IC C34 C32 *C33 H3X 1.5385 112.58 -122.10 109.10 1.1140 +IC C34 C32 *C33 H3Y 1.5385 112.58 121.05 109.26 1.1142 +IC C32 C33 C34 C35 1.5453 112.58 180.00 110.80 1.5074 +IC C35 C33 *C34 H4X 1.5074 110.80 -121.89 108.15 1.1141 +IC C35 C33 *C34 H4Y 1.5074 110.80 121.81 109.29 1.1125 +IC C33 C34 C35 C36 1.5385 110.80 180.00 124.10 1.3433 +IC C36 C34 *C35 H5X 1.3433 124.10 174.75 116.37 1.1008 +IC C34 C35 C36 C37 1.5074 124.10 0.00 125.00 1.5143 !cis db +IC C37 C35 *C36 H6X 1.5143 125.00 -174.44 119.05 1.1017 +IC C35 C36 C37 C38 1.3433 125.00 180.00 117.59 1.5177 +IC C38 C36 *C37 H7X 1.5177 117.59 -122.41 107.65 1.1123 +IC C38 C36 *C37 H7Y 1.5177 117.59 123.72 109.79 1.1133 +IC C36 C37 C38 C39 1.5143 117.59 180.00 126.89 1.3482 +IC C39 C37 *C38 H8X 1.3482 126.89 179.60 114.90 1.1010 +IC C37 C38 C39 C310 1.5177 126.89 0.00 126.25 1.5108 !cis db +IC C310 C38 *C39 H9X 1.5108 126.25 -179.63 118.76 1.1018 +IC C38 C39 C310 C311 1.3482 126.25 180.00 114.73 1.5131 +IC C311 C39 *C310 H10X 1.5177 117.59 -122.41 107.65 1.1123 +IC C311 C39 *C310 H10Y 1.5177 117.59 123.72 109.79 1.1133 +IC C39 C310 C311 C312 1.5108 114.73 180.00 127.49 1.3509 +IC C312 C310 *C311 H11X 1.3482 126.89 179.60 114.90 1.1010 +IC C310 C311 C312 C313 1.5131 127.49 0.00 126.92 1.5159 !cis db +IC C313 C311 *C312 H12X 1.5108 126.25 -179.63 118.76 1.1018 +IC C311 C312 C313 C314 1.3509 126.92 180.00 118.29 1.5170 +IC C314 C312 *C313 H13X 1.5177 117.59 -122.41 107.65 1.1123 +IC C314 C312 *C313 H13Y 1.5177 117.59 123.72 109.79 1.1133 +IC C312 C313 C314 C315 1.5159 118.29 180.00 127.41 1.3481 +IC C315 C313 *C314 H14X 1.3509 126.92 180.00 118.29 1.5170 +IC C313 C314 C315 C316 1.5170 127.41 0.00 125.25 1.5075 !cis db +IC C316 C314 *C315 H15X 1.5108 126.25 -179.63 118.76 1.1018 +IC C314 C315 C316 C317 1.3481 125.25 180.00 113.42 1.5450 +IC C317 C315 *C316 H16X 1.5177 117.59 -122.41 107.65 1.1123 +IC C317 C315 *C316 H16Y 1.5177 117.59 123.72 109.79 1.1133 +IC C315 C316 C317 C318 1.5075 113.42 180.00 116.08 1.5437 +IC C318 C316 *C317 H17X 1.5177 117.59 -122.41 107.65 1.1123 +IC C318 C316 *C317 H17Y 1.5177 117.59 123.72 109.79 1.1133 +IC C316 C317 C318 C319 1.5450 116.08 180.00 116.10 1.6007 +IC C319 C317 *C318 H18X 1.5177 117.59 -122.41 107.65 1.1123 +IC C319 C317 *C318 H18Y 1.5177 117.59 123.72 109.79 1.1133 +IC C317 C318 C319 C320 1.5437 116.10 180.00 132.00 1.5738 +IC C320 C318 *C319 H19X 1.5177 117.59 -122.41 107.65 1.1123 +IC C320 C318 *C319 H19Y 1.5177 117.59 123.72 109.79 1.1133 +IC C318 C319 C320 H20Z 1.6007 132.00 -119.54 110.70 1.1112 +IC H20Z C319 *C320 H20X 1.5177 117.59 -122.41 107.65 1.1123 +IC H20Z C319 *C320 H20Y 1.5177 117.59 123.72 109.79 1.1133 + +RESI SDPA -1.00 ! 1-Stearoyl-2-Docosahexaenoyl-Phosphatidic acid +GROUP ! H12 +ATOM P PL 1.50 ! | alpha4 +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CEL1 -0.15 ! | | +ATOM H4R HEL1 0.15 ! H4R ---C24 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H4R ---C25 | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CEL1 -0.15 ! | | +ATOM H7R HEL1 0.15 ! H7R ---C27 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R----C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! |! (CIS) | +ATOM C217 CEL1 -0.15 ! |! | +ATOM H17R HEL1 0.15 ! H17R---C217 | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CEL1 -0.15 ! | | +ATOM H19R HEL1 0.15 ! H19R---C219 | +GROUP ! |! (CIS) | +ATOM C220 CEL1 -0.15 ! |! | +ATOM H20R HEL1 0.15 ! H20R---C220 | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R +DOUBLE C24 C25 +BOND C25 H5R C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R +DOUBLE C27 C28 +BOND C28 H8R C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R +DOUBLE C210 C211 +BOND C211 H11R C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R +DOUBLE C216 C217 +BOND C217 H17R C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R +DOUBLE C219 C220 +BOND C220 H20R C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5347 115.21 180.00 110.44 1.5096 +IC C24 C22 *C23 H3R 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C22 *C23 H3S 1.5192 121.35 123.34 106.97 1.1128 +IC C22 C23 C24 C25 1.5530 110.44 180.00 127.08 1.3487 +IC C25 C23 *C24 H4R 1.3487 127.08 180.00 114.44 1.1010 +IC C23 C24 C25 C26 1.5096 127.08 0.00 127.17 1.5116 !cis db +IC C26 C24 *C25 H5R 1.5116 127.17 179.68 118.27 1.1015 +IC C24 C25 C26 C27 1.3487 127.17 180.00 111.97 1.5099 +IC C27 C25 *C26 H6R 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C25 *C26 H6S 1.5192 121.35 123.34 106.97 1.1128 +IC C25 C26 C27 C28 1.5116 111.97 180.00 126.68 1.3492 +IC C28 C26 *C27 H7R 1.3492 126.68 178.47 114.82 1.1014 +IC C26 C27 C28 C29 1.5099 126.68 0.00 126.94 1.5099 !cis db +IC C29 C27 *C28 H8R 1.5099 126.94 -177.42 118.69 1.1018 +IC C27 C28 C29 C210 1.3492 126.94 180.00 111.95 1.5084 +IC C210 C28 *C29 H9R 1.5396 113.52 -123.43 110.53 1.1101 +IC C210 C28 *C29 H9S 1.5192 121.35 123.34 106.97 1.1128 +IC C28 C29 C210 C211 1.5099 111.95 180.00 126.47 1.3485 +IC C211 C29 *C210 H10R 1.3453 125.97 -176.85 115.39 1.1011 +IC C29 C210 C211 C212 1.5084 126.47 0.00 127.07 1.5122 !cis db +IC C212 C210 *C211 H11R 1.5097 125.28 178.19 119.65 1.1004 +IC C210 C211 C212 C213 1.3485 127.07 180.00 112.04 1.5115 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5192 121.35 123.34 106.97 1.1128 +IC C211 C212 C213 C214 1.5122 112.04 180.00 126.62 1.3479 +IC C214 C212 *C213 H13R 1.3453 125.97 -176.85 115.39 1.1011 +IC C212 C213 C214 C215 1.5115 126.62 0.00 127.02 1.5107 !cis db +IC C215 C213 *C214 H14R 1.5097 125.28 178.19 119.65 1.1004 +IC C213 C214 C215 C216 1.3479 127.02 180.00 112.92 1.5093 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5192 121.35 123.34 106.97 1.1128 +IC C214 C215 C216 C217 1.5107 112.92 180.00 124.28 1.3467 +IC C217 C215 *C216 H16R 1.3453 125.97 -176.85 115.39 1.1011 +IC C215 C216 C217 C218 1.5093 124.28 0.00 126.43 1.5125 !cis db +IC C218 C216 *C217 H17R 1.5097 125.28 178.19 119.65 1.1004 +IC C216 C217 C218 C219 1.3467 126.43 180.00 116.29 1.5121 +IC C219 C217 *C218 H18R 1.5396 113.52 -123.43 110.53 1.1101 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5125 116.29 180.00 124.57 1.3458 +IC C220 C218 *C219 H19R 1.3453 125.97 -176.85 115.39 1.1011 +IC C218 C219 C220 C221 1.5121 124.57 0.00 126.91 1.5106 !cis db +IC C221 C219 *C220 H20R 1.5097 125.28 178.19 119.65 1.1004 +IC C219 C220 C221 C222 1.3458 126.91 0.74 115.89 1.5382 +IC C222 C220 *C221 H21R 1.5396 113.52 -123.43 110.53 1.1101 +IC C222 C220 *C221 H21S 1.5192 121.35 123.34 106.97 1.1128 +IC C220 C221 C222 H22R 1.5106 115.89 -60.86 110.71 1.1115 +IC H22R C221 *C222 H22S 1.5396 113.52 -123.43 110.53 1.1101 +IC H22R C221 *C222 H22T 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SOPA -1.00 ! 1-Stearoyl-2-Oleoyl-Phosphatidic acid +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5285 113.04 -70.28 113.21 1.5360 +IC C24 C22 *C23 H3R 1.5360 113.21 -119.83 108.42 1.1148 +IC C24 C22 *C23 H3S 1.5396 113.52 -123.43 110.53 1.1101 +IC C22 C23 C24 C25 1.5450 113.21 -172.34 113.68 1.5399 +IC C25 C23 *C24 H4R 1.5399 113.68 120.91 108.91 1.1136 +IC C25 C23 *C24 H4S 1.5396 113.52 -123.43 110.53 1.1101 +IC C23 C24 C25 C26 1.5360 113.68 -56.95 113.57 1.5353 +IC C26 C24 *C25 H5R 1.5353 113.57 121.41 108.70 1.1129 +IC C26 C24 *C25 H5S 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C25 C26 C27 1.5399 113.57 -173.39 113.79 1.5375 +IC C27 C25 *C26 H6R 1.5375 113.79 122.09 109.21 1.1127 +IC C27 C25 *C26 H6S 1.5396 113.52 -123.43 110.53 1.1101 +IC C25 C26 C27 C28 1.5353 113.79 177.45 113.35 1.5458 +IC C28 C26 *C27 H7R 1.5458 113.35 119.87 108.07 1.1139 +IC C28 C26 *C27 H7S 1.5396 113.52 -123.43 110.53 1.1101 +IC C26 C27 C28 C29 1.5375 113.35 67.78 114.46 1.5115 +IC C29 C27 *C28 H8R 1.5115 114.46 121.34 107.89 1.1131 +IC C29 C27 *C28 H8S 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C28 C29 C210 1.5458 114.46 180.00 126.91 1.3502 +IC C210 C28 *C29 H91 1.3502 126.91 -178.81 114.69 1.1010 +IC C28 C29 C210 C211 1.5115 126.91 0.00 126.69 1.5092 !cis db +IC C211 C29 *C210 H101 1.5099 126.94 -177.42 118.69 1.1018 +IC C29 C210 C211 C212 1.3502 126.69 180.00 111.86 1.5417 +IC C212 C210 *C211 H11R 1.5396 113.52 -123.43 110.53 1.1101 +IC C212 C210 *C211 H11S 1.5097 125.28 121.00 119.65 1.1004 +IC C210 C211 C212 C213 1.5092 111.86 180.00 113.99 1.5334 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5097 125.28 121.00 119.65 1.1004 +IC C211 C212 C213 C214 1.5417 113.99 180.00 111.46 1.5365 +IC C214 C212 *C213 H13R 1.5396 113.52 -123.43 110.53 1.1101 +IC C214 C212 *C213 H13S 1.5097 125.28 121.00 119.65 1.1004 +IC C212 C213 C214 C215 1.5334 111.46 180.00 114.22 1.5376 +IC C215 C213 *C214 H14R 1.5396 113.52 -123.43 110.53 1.1101 +IC C215 C213 *C214 H14S 1.5097 125.28 121.00 119.65 1.1004 +IC C213 C214 C215 C216 1.5365 114.22 180.00 114.97 1.5385 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5097 125.28 121.00 119.65 1.1004 +IC C214 C215 C216 C217 1.5376 114.97 180.00 113.95 1.5347 +IC C217 C215 *C216 H16R 1.5396 113.52 -123.43 110.53 1.1101 +IC C217 C215 *C216 H16S 1.5097 125.28 121.00 119.65 1.1004 +IC C215 C216 C217 C218 1.5385 113.95 180.00 113.05 1.5311 +IC C218 C216 *C217 H17R 1.5396 113.52 -123.43 110.53 1.1101 +IC C218 C216 *C217 H17S 1.5097 125.28 121.00 119.65 1.1004 +IC C216 C217 C218 H18R 1.5347 113.05 180.00 110.58 1.1110 +IC H18R C217 *C218 H18S 1.5396 113.52 -123.43 110.53 1.1101 +IC H18R C217 *C218 H18T 1.5097 125.28 121.00 119.65 1.1004 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 121.00 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 121.00 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI DAPA -1.00 ! 1,2-Diarachidonyl-Phosphatidic acid +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O13 O2L -0.82 ! (-) O13 O12 +ATOM O14 O2L -0.82 ! \ / alpha3 +ATOM O12 OHL -0.68 ! P (+) +ATOM H12 HOL 0.34 ! / \ alpha2 +ATOM O11 OSLP -0.62 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | ! +ATOM H3R HAL2 0.09 ! H3R---C23---H3S ! +ATOM H3S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C24 CTL2 -0.18 ! | ! +ATOM H4R HAL2 0.09 ! H4R---C24---H4S ! +ATOM H4S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C25 CEL1 -0.15 ! | ! +ATOM H5R HEL1 0.15 ! H5R---C25 ! +GROUP ! || ! +ATOM C26 CEL1 -0.15 ! || ! +ATOM H6R HEL1 0.15 ! H6R---C26 ! +GROUP ! | ! +ATOM C27 CTL2 -0.18 ! | ! +ATOM H7R HAL2 0.09 ! H7R---C27--H7S ! +ATOM H7S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C28 CEL1 -0.15 ! | ! +ATOM H8R HEL1 0.15 ! H8R---C28 ! +GROUP ! || ! +ATOM C29 CEL1 -0.15 ! || ! +ATOM H9R HEL1 0.15 ! H9R---C29 ! +GROUP ! | ! +ATOM C210 CTL2 -0.18 ! | ! +ATOM H10R HAL2 0.09 ! | ! +ATOM H10S HAL2 0.09 ! H10R---C210--H10S ! +GROUP ! | ! +ATOM C211 CEL1 -0.15 ! | ! +ATOM H11R HEL1 0.15 ! H11R---C211 ! +GROUP ! || ! +ATOM C212 CEL1 -0.15 ! || ! +ATOM H12R HEL1 0.15 ! H12R---C212 ! +GROUP ! | ! +ATOM C213 CTL2 -0.18 ! | ! +ATOM H13R HAL2 0.09 ! H13R---C213---H13S ! +ATOM H13S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C214 CEL1 -0.15 ! | ! +ATOM H14R HEL1 0.15 ! H14R---C214 ! +GROUP ! || ! +ATOM C215 CEL1 -0.15 ! || ! +ATOM H15R HEL1 0.15 ! H15R---C215 ! +GROUP ! | ! +ATOM C216 CTL2 -0.18 ! | ! +ATOM H16R HAL2 0.09 ! H16R---C216--H16S ! +ATOM H16S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C217 CTL2 -0.18 ! | ! +ATOM H17R HAL2 0.09 ! H17R---C217--H17S ! +ATOM H17S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C218 CTL2 -0.18 ! | ! +ATOM H18R HAL2 0.09 ! H18R---C218--H18S ! +ATOM H18S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C219 CTL2 -0.18 ! | ! +ATOM H19R HAL2 0.09 ! H19R---C219--H19S ! +ATOM H19S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C220 CTL3 -0.27 ! | ! +ATOM H20R HAL3 0.09 ! H20R---C220--H20S ! +ATOM H20S HAL3 0.09 ! | ! +ATOM H20T HAL3 0.09 ! H20T ! +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CEL1 -0.15 ! | +ATOM H5X HEL1 0.15 ! H5X---C35 +GROUP ! || +ATOM C36 CEL1 -0.15 ! || +ATOM H6X HEL1 0.15 ! H6X---C36 +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CEL1 -0.15 ! | +ATOM H8X HEL1 0.15 ! H8X---C38 +GROUP ! || +ATOM C39 CEL1 -0.15 ! || +ATOM H9X HEL1 0.15 ! H9X---C39 +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313---H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CEL1 -0.15 ! | +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! || +ATOM C315 CEL1 -0.15 ! || +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316---H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND C21 O21 C21 C22 +DOUBLE C21 O22 +BOND C22 C23 C22 H2R C22 H2S +BOND C23 C24 C23 H3R C23 H3S +BOND C24 C25 C24 H4R C24 H4S +DOUBLE C25 C26 +BOND C25 H5R +BOND C26 C27 C26 H6R +BOND C27 C28 C27 H7R C27 H7S +DOUBLE C28 C29 +BOND C28 H8R +BOND C29 C210 C29 H9R +BOND C210 C211 C210 H10R C210 H10S +DOUBLE C211 C212 +BOND C211 H11R +BOND C212 C213 C212 H12R +BOND C213 C214 C213 H13R C213 H13S +DOUBLE C214 C215 +BOND C214 H14R +BOND C215 C216 C215 H15R +BOND C216 C217 C216 H16R C216 H16S +BOND C217 C218 C217 H17R C217 H17S +BOND C218 C219 C218 H18R C218 H18S +BOND C219 C220 C219 H19R C219 H19S +BOND C220 H20T C220 H20R C220 H20S +! Chain From C3 +BOND C31 O31 C31 C32 +DOUBLE C31 O32 +BOND C32 C33 C32 H2X C32 H2Y +BOND C33 C34 C33 H3X C33 H3Y +BOND C34 C35 C34 H4X C34 H4Y +DOUBLE C35 C36 +BOND C35 H5X +BOND C36 C37 C36 H6X +BOND C37 C38 C37 H7X C37 H7Y +DOUBLE C38 C39 +BOND C38 H8X +BOND C39 C310 C39 H9X +BOND C310 C311 C310 H10X C310 H10Y +DOUBLE C311 C312 +BOND C311 H11X +BOND C312 C313 C312 H12X +BOND C313 C314 C313 H13X C313 H13Y +DOUBLE C314 C315 +BOND C314 H14X +BOND C315 C316 C315 H15X +BOND C316 C317 C316 H16X C316 H16Y +BOND C317 C318 C317 H17X C317 H17Y +BOND C318 C319 C318 H18X C318 H18Y +BOND C319 C320 C319 H19X C319 H19Y +BOND C320 H20Z C320 H20X C320 H20Y + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O11 O12 *P O13 1.5769 103.46 -117.59 108.11 1.4797 +IC O11 O12 *P O14 1.5769 103.46 116.77 106.20 1.4775 +IC O12 P O11 C1 1.5954 103.46 33.43 121.47 1.4291 +IC P O11 C1 C2 1.5769 121.47 146.27 110.07 1.5526 +IC C2 O11 *C1 HA 1.5526 110.07 -121.29 113.08 1.1166 +IC HA O11 *C1 HB 1.1166 113.08 -120.24 108.73 1.1132 +IC O11 C1 C2 C3 1.4291 110.07 37.91 111.11 1.5544 +IC C3 C1 *C2 O21 1.5544 111.11 119.78 110.70 1.4395 +IC C3 C1 *C2 HS 1.5544 111.11 -117.46 108.81 1.1157 +IC C1 C2 O21 C21 1.5526 110.70 72.82 115.87 1.3174 +IC C2 O21 C21 C22 1.4395 115.87 179.18 109.41 1.5329 +IC C22 O21 *C21 O22 1.5329 109.41 -178.52 126.45 1.2180 +IC O21 C21 C22 C23 1.3174 109.41 180.00 113.78 1.5483 +IC C23 C21 *C22 H2R 1.5483 113.78 -121.17 107.02 1.1096 +IC C23 C21 *C22 H2S 1.5483 113.78 122.25 107.54 1.1088 +IC C1 C2 C3 O31 1.5526 111.11 179.84 110.78 1.4471 +IC O31 C2 *C3 HX 1.4471 110.78 -122.23 106.07 1.1170 +IC HX C2 *C3 HY 1.1170 106.07 -116.50 109.11 1.1127 +IC C2 C3 O31 C31 1.5544 110.78 -158.57 113.91 1.3265 +IC C3 O31 C31 C32 1.4471 113.91 178.20 108.97 1.5287 +IC C32 O31 *C31 O32 1.5287 108.97 178.94 125.84 1.2167 +IC O31 C31 C32 C33 1.3265 108.97 180.00 111.97 1.5453 +IC C33 C31 *C32 H2X 1.5453 111.97 -120.94 107.50 1.1090 +IC C33 C31 *C32 H2Y 1.5453 111.97 121.71 108.29 1.1085 +IC C21 C22 C23 C24 1.5329 113.78 180.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 !cis db +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 180.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 180.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 !cis db +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 180.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 180.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 !cis db +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 180.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 180.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 !cis db +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5287 111.97 180.00 112.58 1.5385 +IC C34 C32 *C33 H3X 1.5385 112.58 -122.10 109.10 1.1140 +IC C34 C32 *C33 H3Y 1.5385 112.58 121.05 109.26 1.1142 +IC C32 C33 C34 C35 1.5453 112.58 180.00 110.80 1.5074 +IC C35 C33 *C34 H4X 1.5074 110.80 -121.89 108.15 1.1141 +IC C35 C33 *C34 H4Y 1.5074 110.80 121.81 109.29 1.1125 +IC C33 C34 C35 C36 1.5385 110.80 180.00 124.10 1.3433 +IC C36 C34 *C35 H5X 1.3433 124.10 174.75 116.37 1.1008 +IC C34 C35 C36 C37 1.5074 124.10 0.00 125.00 1.5143 !cis db +IC C37 C35 *C36 H6X 1.5143 125.00 -174.44 119.05 1.1017 +IC C35 C36 C37 C38 1.3433 125.00 180.00 117.59 1.5177 +IC C38 C36 *C37 H7X 1.5177 117.59 -122.41 107.65 1.1123 +IC C38 C36 *C37 H7Y 1.5177 117.59 123.72 109.79 1.1133 +IC C36 C37 C38 C39 1.5143 117.59 180.00 126.89 1.3482 +IC C39 C37 *C38 H8X 1.3482 126.89 179.60 114.90 1.1010 +IC C37 C38 C39 C310 1.5177 126.89 0.00 126.25 1.5108 !cis db +IC C310 C38 *C39 H9X 1.5108 126.25 -179.63 118.76 1.1018 +IC C38 C39 C310 C311 1.3482 126.25 180.00 114.73 1.5131 +IC C311 C39 *C310 H10X 1.5177 117.59 -122.41 107.65 1.1123 +IC C311 C39 *C310 H10Y 1.5177 117.59 123.72 109.79 1.1133 +IC C39 C310 C311 C312 1.5108 114.73 180.00 127.49 1.3509 +IC C312 C310 *C311 H11X 1.3482 126.89 179.60 114.90 1.1010 +IC C310 C311 C312 C313 1.5131 127.49 0.00 126.92 1.5159 !cis db +IC C313 C311 *C312 H12X 1.5108 126.25 -179.63 118.76 1.1018 +IC C311 C312 C313 C314 1.3509 126.92 180.00 118.29 1.5170 +IC C314 C312 *C313 H13X 1.5177 117.59 -122.41 107.65 1.1123 +IC C314 C312 *C313 H13Y 1.5177 117.59 123.72 109.79 1.1133 +IC C312 C313 C314 C315 1.5159 118.29 180.00 127.41 1.3481 +IC C315 C313 *C314 H14X 1.3509 126.92 180.00 118.29 1.5170 +IC C313 C314 C315 C316 1.5170 127.41 0.00 125.25 1.5075 !cis db +IC C316 C314 *C315 H15X 1.5108 126.25 -179.63 118.76 1.1018 +IC C314 C315 C316 C317 1.3481 125.25 180.00 113.42 1.5450 +IC C317 C315 *C316 H16X 1.5177 117.59 -122.41 107.65 1.1123 +IC C317 C315 *C316 H16Y 1.5177 117.59 123.72 109.79 1.1133 +IC C315 C316 C317 C318 1.5075 113.42 180.00 116.08 1.5437 +IC C318 C316 *C317 H17X 1.5177 117.59 -122.41 107.65 1.1123 +IC C318 C316 *C317 H17Y 1.5177 117.59 123.72 109.79 1.1133 +IC C316 C317 C318 C319 1.5450 116.08 180.00 116.10 1.6007 +IC C319 C317 *C318 H18X 1.5177 117.59 -122.41 107.65 1.1123 +IC C319 C317 *C318 H18Y 1.5177 117.59 123.72 109.79 1.1133 +IC C317 C318 C319 C320 1.5437 116.10 180.00 132.00 1.5738 +IC C320 C318 *C319 H19X 1.5177 117.59 -122.41 107.65 1.1123 +IC C320 C318 *C319 H19Y 1.5177 117.59 123.72 109.79 1.1133 +IC C318 C319 C320 H20Z 1.6007 132.00 -119.54 110.70 1.1112 +IC H20Z C319 *C320 H20X 1.5177 117.59 -122.41 107.65 1.1123 +IC H20Z C319 *C320 H20Y 1.5177 117.59 123.72 109.79 1.1133 + +RESI SDPG -1.00 ! 1-Stearoyl-2-Docosahexaenoyl-Phosphatidylglycerol +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CEL1 -0.15 ! | | +ATOM H4R HEL1 0.15 ! H4R ---C24 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H4R ---C25 | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CEL1 -0.15 ! | | +ATOM H7R HEL1 0.15 ! H7R ---C27 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R----C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! |! (CIS) | +ATOM C217 CEL1 -0.15 ! |! | +ATOM H17R HEL1 0.15 ! H17R---C217 | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CEL1 -0.15 ! | | +ATOM H19R HEL1 0.15 ! H19R---C219 | +GROUP ! |! (CIS) | +ATOM C220 CEL1 -0.15 ! |! | +ATOM H20R HEL1 0.15 ! H20R---C220 | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R +DOUBLE C24 C25 +BOND C25 H5R C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R +DOUBLE C27 C28 +BOND C28 H8R C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R +DOUBLE C210 C211 +BOND C211 H11R C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R +DOUBLE C216 C217 +BOND C217 H17R C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R +DOUBLE C219 C220 +BOND C220 H20R C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5529 111.44 -110.28 123.53 1.5856 +IC C11 O12 P O11 1.4207 123.53 -117.07 102.54 1.5781 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -139.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 -120.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5347 115.21 180.00 110.44 1.5096 +IC C24 C22 *C23 H3R 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C22 *C23 H3S 1.5192 121.35 123.34 106.97 1.1128 +IC C22 C23 C24 C25 1.5530 110.44 180.00 127.08 1.3487 +IC C25 C23 *C24 H4R 1.3487 127.08 180.00 114.44 1.1010 +IC C23 C24 C25 C26 1.5096 127.08 0.00 127.17 1.5116 !cis db +IC C26 C24 *C25 H5R 1.5116 127.17 179.68 118.27 1.1015 +IC C24 C25 C26 C27 1.3487 127.17 180.00 111.97 1.5099 +IC C27 C25 *C26 H6R 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C25 *C26 H6S 1.5192 121.35 123.34 106.97 1.1128 +IC C25 C26 C27 C28 1.5116 111.97 180.00 126.68 1.3492 +IC C28 C26 *C27 H7R 1.3492 126.68 178.47 114.82 1.1014 +IC C26 C27 C28 C29 1.5099 126.68 0.00 126.94 1.5099 !cis db +IC C29 C27 *C28 H8R 1.5099 126.94 -177.42 118.69 1.1018 +IC C27 C28 C29 C210 1.3492 126.94 180.00 111.95 1.5084 +IC C210 C28 *C29 H9R 1.5396 113.52 -123.43 110.53 1.1101 +IC C210 C28 *C29 H9S 1.5192 121.35 123.34 106.97 1.1128 +IC C28 C29 C210 C211 1.5099 111.95 180.00 126.47 1.3485 +IC C211 C29 *C210 H10R 1.3453 125.97 -176.85 115.39 1.1011 +IC C29 C210 C211 C212 1.5084 126.47 0.00 127.07 1.5122 !cis db +IC C212 C210 *C211 H11R 1.5097 125.28 178.19 119.65 1.1004 +IC C210 C211 C212 C213 1.3485 127.07 180.00 112.04 1.5115 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5192 121.35 123.34 106.97 1.1128 +IC C211 C212 C213 C214 1.5122 112.04 180.00 126.62 1.3479 +IC C214 C212 *C213 H13R 1.3453 125.97 -176.85 115.39 1.1011 +IC C212 C213 C214 C215 1.5115 126.62 0.00 127.02 1.5107 !cis db +IC C215 C213 *C214 H14R 1.5097 125.28 178.19 119.65 1.1004 +IC C213 C214 C215 C216 1.3479 127.02 180.00 112.92 1.5093 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5192 121.35 123.34 106.97 1.1128 +IC C214 C215 C216 C217 1.5107 112.92 180.00 124.28 1.3467 +IC C217 C215 *C216 H16R 1.3453 125.97 -176.85 115.39 1.1011 +IC C215 C216 C217 C218 1.5093 124.28 0.00 126.43 1.5125 !cis db +IC C218 C216 *C217 H17R 1.5097 125.28 178.19 119.65 1.1004 +IC C216 C217 C218 C219 1.3467 126.43 180.00 116.29 1.5121 +IC C219 C217 *C218 H18R 1.5396 113.52 -123.43 110.53 1.1101 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5125 116.29 180.00 124.57 1.3458 +IC C220 C218 *C219 H19R 1.3453 125.97 -176.85 115.39 1.1011 +IC C218 C219 C220 C221 1.5121 124.57 0.00 126.91 1.5106 !cis db +IC C221 C219 *C220 H20R 1.5097 125.28 178.19 119.65 1.1004 +IC C219 C220 C221 C222 1.3458 126.91 0.74 115.89 1.5382 +IC C222 C220 *C221 H21R 1.5396 113.52 -123.43 110.53 1.1101 +IC C222 C220 *C221 H21S 1.5192 121.35 123.34 106.97 1.1128 +IC C220 C221 C222 H22R 1.5106 115.89 -60.86 110.71 1.1115 +IC H22R C221 *C222 H22S 1.5396 113.52 -123.43 110.53 1.1101 +IC H22R C221 *C222 H22T 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SOPG -1.00 ! 1-Stearoyl-2-Oleoyl-Phosphatidylglycerol +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5529 111.44 -110.28 123.53 1.5856 +IC C11 O12 P O11 1.4207 123.53 -117.07 102.54 1.5781 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5285 113.04 -70.28 113.21 1.5360 +IC C24 C22 *C23 H3R 1.5360 113.21 -119.83 108.42 1.1148 +IC C24 C22 *C23 H3S 1.5396 113.52 -123.43 110.53 1.1101 +IC C22 C23 C24 C25 1.5450 113.21 -172.34 113.68 1.5399 +IC C25 C23 *C24 H4R 1.5399 113.68 120.91 108.91 1.1136 +IC C25 C23 *C24 H4S 1.5396 113.52 -123.43 110.53 1.1101 +IC C23 C24 C25 C26 1.5360 113.68 -56.95 113.57 1.5353 +IC C26 C24 *C25 H5R 1.5353 113.57 121.41 108.70 1.1129 +IC C26 C24 *C25 H5S 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C25 C26 C27 1.5399 113.57 -173.39 113.79 1.5375 +IC C27 C25 *C26 H6R 1.5375 113.79 122.09 109.21 1.1127 +IC C27 C25 *C26 H6S 1.5396 113.52 -123.43 110.53 1.1101 +IC C25 C26 C27 C28 1.5353 113.79 177.45 113.35 1.5458 +IC C28 C26 *C27 H7R 1.5458 113.35 119.87 108.07 1.1139 +IC C28 C26 *C27 H7S 1.5396 113.52 -123.43 110.53 1.1101 +IC C26 C27 C28 C29 1.5375 113.35 67.78 114.46 1.5115 +IC C29 C27 *C28 H8R 1.5115 114.46 121.34 107.89 1.1131 +IC C29 C27 *C28 H8S 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C28 C29 C210 1.5458 114.46 180.00 126.91 1.3502 +IC C210 C28 *C29 H91 1.3502 126.91 -178.81 114.69 1.1010 +IC C28 C29 C210 C211 1.5115 126.91 0.00 126.69 1.5092 !cis db +IC C211 C29 *C210 H101 1.5099 126.94 -177.42 118.69 1.1018 +IC C29 C210 C211 C212 1.3502 126.69 180.00 111.86 1.5417 +IC C212 C210 *C211 H11R 1.5396 113.52 -123.43 110.53 1.1101 +IC C212 C210 *C211 H11S 1.5097 125.28 121.00 119.65 1.1004 +IC C210 C211 C212 C213 1.5092 111.86 180.00 113.99 1.5334 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5097 125.28 121.00 119.65 1.1004 +IC C211 C212 C213 C214 1.5417 113.99 180.00 111.46 1.5365 +IC C214 C212 *C213 H13R 1.5396 113.52 -123.43 110.53 1.1101 +IC C214 C212 *C213 H13S 1.5097 125.28 121.00 119.65 1.1004 +IC C212 C213 C214 C215 1.5334 111.46 180.00 114.22 1.5376 +IC C215 C213 *C214 H14R 1.5396 113.52 -123.43 110.53 1.1101 +IC C215 C213 *C214 H14S 1.5097 125.28 121.00 119.65 1.1004 +IC C213 C214 C215 C216 1.5365 114.22 180.00 114.97 1.5385 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5097 125.28 121.00 119.65 1.1004 +IC C214 C215 C216 C217 1.5376 114.97 180.00 113.95 1.5347 +IC C217 C215 *C216 H16R 1.5396 113.52 -123.43 110.53 1.1101 +IC C217 C215 *C216 H16S 1.5097 125.28 121.00 119.65 1.1004 +IC C215 C216 C217 C218 1.5385 113.95 180.00 113.05 1.5311 +IC C218 C216 *C217 H17R 1.5396 113.52 -123.43 110.53 1.1101 +IC C218 C216 *C217 H17S 1.5097 125.28 121.00 119.65 1.1004 +IC C216 C217 C218 H18R 1.5347 113.05 180.00 110.58 1.1110 +IC H18R C217 *C218 H18S 1.5396 113.52 -123.43 110.53 1.1101 +IC H18R C217 *C218 H18T 1.5097 125.28 121.00 119.65 1.1004 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 121.00 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 121.00 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI DAPG -1.00 ! 1,2-Diarachidonyl-Phosphatidylglycerol +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | ! +ATOM H3R HAL2 0.09 ! H3R---C23---H3S ! +ATOM H3S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C24 CTL2 -0.18 ! | ! +ATOM H4R HAL2 0.09 ! H4R---C24---H4S ! +ATOM H4S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C25 CEL1 -0.15 ! | ! +ATOM H5R HEL1 0.15 ! H5R---C25 ! +GROUP ! || ! +ATOM C26 CEL1 -0.15 ! || ! +ATOM H6R HEL1 0.15 ! H6R---C26 ! +GROUP ! | ! +ATOM C27 CTL2 -0.18 ! | ! +ATOM H7R HAL2 0.09 ! H7R---C27--H7S ! +ATOM H7S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C28 CEL1 -0.15 ! | ! +ATOM H8R HEL1 0.15 ! H8R---C28 ! +GROUP ! || ! +ATOM C29 CEL1 -0.15 ! || ! +ATOM H9R HEL1 0.15 ! H9R---C29 ! +GROUP ! | ! +ATOM C210 CTL2 -0.18 ! | ! +ATOM H10R HAL2 0.09 ! | ! +ATOM H10S HAL2 0.09 ! H10R---C210--H10S ! +GROUP ! | ! +ATOM C211 CEL1 -0.15 ! | ! +ATOM H11R HEL1 0.15 ! H11R---C211 ! +GROUP ! || ! +ATOM C212 CEL1 -0.15 ! || ! +ATOM H12R HEL1 0.15 ! H12R---C212 ! +GROUP ! | ! +ATOM C213 CTL2 -0.18 ! | ! +ATOM H13R HAL2 0.09 ! H13R---C213---H13S ! +ATOM H13S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C214 CEL1 -0.15 ! | ! +ATOM H14R HEL1 0.15 ! H14R---C214 ! +GROUP ! || ! +ATOM C215 CEL1 -0.15 ! || ! +ATOM H15R HEL1 0.15 ! H15R---C215 ! +GROUP ! | ! +ATOM C216 CTL2 -0.18 ! | ! +ATOM H16R HAL2 0.09 ! H16R---C216--H16S ! +ATOM H16S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C217 CTL2 -0.18 ! | ! +ATOM H17R HAL2 0.09 ! H17R---C217--H17S ! +ATOM H17S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C218 CTL2 -0.18 ! | ! +ATOM H18R HAL2 0.09 ! H18R---C218--H18S ! +ATOM H18S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C219 CTL2 -0.18 ! | ! +ATOM H19R HAL2 0.09 ! H19R---C219--H19S ! +ATOM H19S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C220 CTL3 -0.27 ! | ! +ATOM H20R HAL3 0.09 ! H20R---C220--H20S ! +ATOM H20S HAL3 0.09 ! | ! +ATOM H20T HAL3 0.09 ! H20T ! +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CEL1 -0.15 ! | +ATOM H5X HEL1 0.15 ! H5X---C35 +GROUP ! || +ATOM C36 CEL1 -0.15 ! || +ATOM H6X HEL1 0.15 ! H6X---C36 +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CEL1 -0.15 ! | +ATOM H8X HEL1 0.15 ! H8X---C38 +GROUP ! || +ATOM C39 CEL1 -0.15 ! || +ATOM H9X HEL1 0.15 ! H9X---C39 +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313---H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CEL1 -0.15 ! | +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! || +ATOM C315 CEL1 -0.15 ! || +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316---H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND C21 O21 C21 C22 +DOUBLE C21 O22 +BOND C22 C23 C22 H2R C22 H2S +BOND C23 C24 C23 H3R C23 H3S +BOND C24 C25 C24 H4R C24 H4S +DOUBLE C25 C26 +BOND C25 H5R +BOND C26 C27 C26 H6R +BOND C27 C28 C27 H7R C27 H7S +DOUBLE C28 C29 +BOND C28 H8R +BOND C29 C210 C29 H9R +BOND C210 C211 C210 H10R C210 H10S +DOUBLE C211 C212 +BOND C211 H11R +BOND C212 C213 C212 H12R +BOND C213 C214 C213 H13R C213 H13S +DOUBLE C214 C215 +BOND C214 H14R +BOND C215 C216 C215 H15R +BOND C216 C217 C216 H16R C216 H16S +BOND C217 C218 C217 H17R C217 H17S +BOND C218 C219 C218 H18R C218 H18S +BOND C219 C220 C219 H19R C219 H19S +BOND C220 H20T C220 H20R C220 H20S +! Chain From C3 +BOND C31 O31 C31 C32 +DOUBLE C31 O32 +BOND C32 C33 C32 H2X C32 H2Y +BOND C33 C34 C33 H3X C33 H3Y +BOND C34 C35 C34 H4X C34 H4Y +DOUBLE C35 C36 +BOND C35 H5X +BOND C36 C37 C36 H6X +BOND C37 C38 C37 H7X C37 H7Y +DOUBLE C38 C39 +BOND C38 H8X +BOND C39 C310 C39 H9X +BOND C310 C311 C310 H10X C310 H10Y +DOUBLE C311 C312 +BOND C311 H11X +BOND C312 C313 C312 H12X +BOND C313 C314 C313 H13X C313 H13Y +DOUBLE C314 C315 +BOND C314 H14X +BOND C315 C316 C315 H15X +BOND C316 C317 C316 H16X C316 H16Y +BOND C317 C318 C317 H17X C317 H17Y +BOND C318 C319 C318 H18X C318 H18Y +BOND C319 C320 C319 H19X C319 H19Y +BOND C320 H20Z C320 H20X C320 H20Y + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C13 C12 C11 O12 1.5488 112.66 55.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5547 111.90 56.58 119.25 1.5954 +IC C11 O12 P O11 1.4262 119.25 125.38 103.46 1.5769 +IC O11 O12 *P O13 1.5769 103.46 -117.59 108.11 1.4797 +IC O11 O12 *P O14 1.5769 103.46 116.77 106.20 1.4775 +IC O12 P O11 C1 1.5954 103.46 33.43 121.47 1.4291 +IC P O11 C1 C2 1.5769 121.47 146.27 110.07 1.5526 +IC C2 O11 *C1 HA 1.5526 110.07 -121.29 113.08 1.1166 +IC HA O11 *C1 HB 1.1166 113.08 -120.24 108.73 1.1132 +IC O11 C1 C2 C3 1.4291 110.07 37.91 111.11 1.5544 +IC C3 C1 *C2 O21 1.5544 111.11 119.78 110.70 1.4395 +IC C3 C1 *C2 HS 1.5544 111.11 -117.46 108.81 1.1157 +IC C1 C2 O21 C21 1.5526 110.70 72.82 115.87 1.3174 +IC C2 O21 C21 C22 1.4395 115.87 179.18 109.41 1.5329 +IC C22 O21 *C21 O22 1.5329 109.41 -178.52 126.45 1.2180 +IC O21 C21 C22 C23 1.3174 109.41 180.00 113.78 1.5483 +IC C23 C21 *C22 H2R 1.5483 113.78 -121.17 107.02 1.1096 +IC C23 C21 *C22 H2S 1.5483 113.78 122.25 107.54 1.1088 +IC C1 C2 C3 O31 1.5526 111.11 179.84 110.78 1.4471 +IC O31 C2 *C3 HX 1.4471 110.78 -122.23 106.07 1.1170 +IC HX C2 *C3 HY 1.1170 106.07 -116.50 109.11 1.1127 +IC C2 C3 O31 C31 1.5544 110.78 -158.57 113.91 1.3265 +IC C3 O31 C31 C32 1.4471 113.91 178.20 108.97 1.5287 +IC C32 O31 *C31 O32 1.5287 108.97 178.94 125.84 1.2167 +IC O31 C31 C32 C33 1.3265 108.97 180.00 111.97 1.5453 +IC C33 C31 *C32 H2X 1.5453 111.97 -120.94 107.50 1.1090 +IC C33 C31 *C32 H2Y 1.5453 111.97 121.71 108.29 1.1085 +IC C21 C22 C23 C24 1.5329 113.78 180.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 !cis db +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 180.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 180.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 !cis db +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 180.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 180.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 !cis db +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 180.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 180.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 !cis db +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5287 111.97 180.00 112.58 1.5385 +IC C34 C32 *C33 H3X 1.5385 112.58 -122.10 109.10 1.1140 +IC C34 C32 *C33 H3Y 1.5385 112.58 121.05 109.26 1.1142 +IC C32 C33 C34 C35 1.5453 112.58 180.00 110.80 1.5074 +IC C35 C33 *C34 H4X 1.5074 110.80 -121.89 108.15 1.1141 +IC C35 C33 *C34 H4Y 1.5074 110.80 121.81 109.29 1.1125 +IC C33 C34 C35 C36 1.5385 110.80 180.00 124.10 1.3433 +IC C36 C34 *C35 H5X 1.3433 124.10 174.75 116.37 1.1008 +IC C34 C35 C36 C37 1.5074 124.10 0.00 125.00 1.5143 !cis db +IC C37 C35 *C36 H6X 1.5143 125.00 -174.44 119.05 1.1017 +IC C35 C36 C37 C38 1.3433 125.00 180.00 117.59 1.5177 +IC C38 C36 *C37 H7X 1.5177 117.59 -122.41 107.65 1.1123 +IC C38 C36 *C37 H7Y 1.5177 117.59 123.72 109.79 1.1133 +IC C36 C37 C38 C39 1.5143 117.59 180.00 126.89 1.3482 +IC C39 C37 *C38 H8X 1.3482 126.89 179.60 114.90 1.1010 +IC C37 C38 C39 C310 1.5177 126.89 0.00 126.25 1.5108 !cis db +IC C310 C38 *C39 H9X 1.5108 126.25 -179.63 118.76 1.1018 +IC C38 C39 C310 C311 1.3482 126.25 180.00 114.73 1.5131 +IC C311 C39 *C310 H10X 1.5177 117.59 -122.41 107.65 1.1123 +IC C311 C39 *C310 H10Y 1.5177 117.59 123.72 109.79 1.1133 +IC C39 C310 C311 C312 1.5108 114.73 180.00 127.49 1.3509 +IC C312 C310 *C311 H11X 1.3482 126.89 179.60 114.90 1.1010 +IC C310 C311 C312 C313 1.5131 127.49 0.00 126.92 1.5159 !cis db +IC C313 C311 *C312 H12X 1.5108 126.25 -179.63 118.76 1.1018 +IC C311 C312 C313 C314 1.3509 126.92 180.00 118.29 1.5170 +IC C314 C312 *C313 H13X 1.5177 117.59 -122.41 107.65 1.1123 +IC C314 C312 *C313 H13Y 1.5177 117.59 123.72 109.79 1.1133 +IC C312 C313 C314 C315 1.5159 118.29 180.00 127.41 1.3481 +IC C315 C313 *C314 H14X 1.3509 126.92 180.00 118.29 1.5170 +IC C313 C314 C315 C316 1.5170 127.41 0.00 125.25 1.5075 !cis db +IC C316 C314 *C315 H15X 1.5108 126.25 -179.63 118.76 1.1018 +IC C314 C315 C316 C317 1.3481 125.25 180.00 113.42 1.5450 +IC C317 C315 *C316 H16X 1.5177 117.59 -122.41 107.65 1.1123 +IC C317 C315 *C316 H16Y 1.5177 117.59 123.72 109.79 1.1133 +IC C315 C316 C317 C318 1.5075 113.42 180.00 116.08 1.5437 +IC C318 C316 *C317 H17X 1.5177 117.59 -122.41 107.65 1.1123 +IC C318 C316 *C317 H17Y 1.5177 117.59 123.72 109.79 1.1133 +IC C316 C317 C318 C319 1.5450 116.08 180.00 116.10 1.6007 +IC C319 C317 *C318 H18X 1.5177 117.59 -122.41 107.65 1.1123 +IC C319 C317 *C318 H18Y 1.5177 117.59 123.72 109.79 1.1133 +IC C317 C318 C319 C320 1.5437 116.10 180.00 132.00 1.5738 +IC C320 C318 *C319 H19X 1.5177 117.59 -122.41 107.65 1.1123 +IC C320 C318 *C319 H19Y 1.5177 117.59 123.72 109.79 1.1133 +IC C318 C319 C320 H20Z 1.6007 132.00 -119.54 110.70 1.1112 +IC H20Z C319 *C320 H20X 1.5177 117.59 -122.41 107.65 1.1123 +IC H20Z C319 *C320 H20Y 1.5177 117.59 123.72 109.79 1.1133 + +END + +return + diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_model.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_model.str new file mode 100644 index 00000000..5dca3fed --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_model.str @@ -0,0 +1,2392 @@ +* CHARMM36 All-Hydrogen Lipid Force Field Toppar Stream File +* Collection of residues and patches for model compounds used +* in the optimization the lipid force field. +* + +!Parent files that have to be read prior to streaming this file +!top_all36_lipid.rtf +!par_all36_lipid.prm + +!Testcase +!test_all36_lipid_model.inp + +read rtf card append +* c36 lipid model compounds +* +31 1 + +RESI MAS 0.00 ! methylacetate +GROUP ! +ATOM C1 CTL3 -0.31 ! H22 +ATOM C CL 0.90 ! | +ATOM OM OSL -0.49 ! H21-C2-H23 +ATOM C2 CTL3 -0.01 ! \ +ATOM O OBL -0.63 ! OM +ATOM H11 HAL3 0.09 ! / +ATOM H12 HAL3 0.09 ! O=C +ATOM H13 HAL3 0.09 ! | +ATOM H21 HAL3 0.09 ! H11-C1-H13 +ATOM H22 HAL3 0.09 ! | +ATOM H23 HAL3 0.09 ! H12 + +BOND C1 C C OM OM C2 +DOUBLE C O +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IMPR C OM C1 O +! internal coordinates from experiment for heavy atoms +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 + +RESI ETAC 0.00 ! Ethylacetate + ! H213 +GROUP ! | +ATOM C1 CTL3 -0.31 ! H211-C21-H212 +ATOM C CL 0.90 ! / +ATOM OM OSL -0.49 ! H22-C2-H23 +ATOM C2 CTL2 0.08 ! \ +ATOM O OBL -0.63 ! OM +ATOM H11 HAL3 0.09 ! / +ATOM H12 HAL3 0.09 ! O=C +ATOM H13 HAL3 0.09 ! \ +ATOM H22 HAL2 0.09 ! H11-C1-H13 +ATOM H23 HAL2 0.09 ! | +GROUP ! H12 +ATOM C21 CTL3 -0.27 +ATOM H211 HAL3 0.09 +ATOM H212 HAL3 0.09 +ATOM H213 HAL3 0.09 +BOND C1 C C OM OM C2 +DOUBLE C O +BOND C1 H11 C1 H12 C1 H13 +BOND C2 C21 C2 H22 C2 H23 +BOND C21 H211 C21 H212 C21 H213 +IMPR C OM C1 O +! internal coordinates from experiment for heavy atoms +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC C21 C2 OM C 1.520 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 +IC H211 C21 C2 OM 1.1 108.90 180.0 116.7 1.437 +IC H212 C21 C2 OM 1.1 108.90 60.0 116.7 1.437 +IC H213 C21 C2 OM 1.1 108.90 -60.0 116.7 1.437 + +RESI MPRO 0.00 ! Methylpropionate +GROUP ! +ATOM C1 CTL2 -0.22 ! H22 +ATOM C CL 0.90 ! | +ATOM OM OSL -0.49 ! H21-C2-H23 +ATOM C2 CTL3 -0.01 ! \ +ATOM O OBL -0.63 ! OM +ATOM H12 HAL2 0.09 ! / +ATOM H13 HAL2 0.09 ! O=C +ATOM H21 HAL3 0.09 ! \ +ATOM H22 HAL3 0.09 ! H12-C1-H13 +ATOM H23 HAL3 0.09 ! / +GROUP ! H112-C11-H111 +ATOM C11 CTL3 -0.27 ! | +ATOM H111 HAL3 0.09 ! H113 +ATOM H112 HAL3 0.09 ! +ATOM H113 HAL3 0.09 ! +BOND C1 C C OM C O OM C2 +BOND C1 C11 C1 H12 C1 H13 +BOND C11 H111 C11 H112 C11 H113 +BOND C2 H21 C2 H22 C2 H23 +IMPR C OM C1 O +! internal coordinates from experiment for heavy atoms +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC C11 C1 C OM 1.520 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 +IC H111 C11 C1 C 1.1 109.75 180.0 109.0 1.520 +IC H112 C11 C1 C 1.1 109.75 60.4 109.0 1.520 +IC H113 C11 C1 C 1.1 109.75 -60.4 109.0 1.520 + +RESI ACEH 0.00 ! acetic acid + ! atoms in proper order for molvib input +GROUP ! +ATOM C2 CTL3 -0.30 ! +ATOM C1 CL 0.75 ! H21 O2 +ATOM H21 HAL3 0.09 ! \ // +ATOM H22 HAL3 0.09 ! H22-C2--C1 +ATOM H23 HAL3 0.09 ! / \ +ATOM O2 OBL -0.55 ! H23 O1-HO1 +ATOM O1 OHL -0.61 ! +ATOM HO1 HOL 0.44 ! +BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23 +DOUBLE C1 O2 +IMPR C1 O1 C2 O2 +IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 +IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 + +RESI DMP -1.00 ! Dimethylphosphate +GROUP ! +ATOM P1 PL 1.50 ! +ATOM O3 O2L -0.78 ! +ATOM O4 O2L -0.78 ! H11 +ATOM O1 OSLP -0.57 ! | +ATOM O2 OSLP -0.57 ! H13- C1-H12 + ! \ +ATOM C1 CTL3 -0.17 ! (-) O3 O1 +ATOM H11 HAL3 0.09 ! \ / +ATOM H12 HAL3 0.09 ! P1 (+) +ATOM H13 HAL3 0.09 ! / \ + ! (-) O4 O2 +ATOM C2 CTL3 -0.17 ! / +ATOM H21 HAL3 0.09 ! H23-C2-H22 +ATOM H22 HAL3 0.09 ! | +ATOM H23 HAL3 0.09 ! H21 + ! +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 O2 C2 +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 + +! IC FOR THE g,g conformation (3-21G* opt. geometry) +IC O3 P1 O1 C1 1.4723 107.31 000.0 117.79 1.4356 +IC O4 P1 O2 C2 1.4722 000.0 000.0 117.79 1.4357 +IC O1 P1 O2 C2 1.6343 000.0 73.8 117.79 1.4357 +IC O2 P1 O1 C1 1.6344 000.0 73.7 117.79 1.4356 +IC H11 C1 O1 P1 1.0827 107.8 174.8 117.79 1.6343 +IC H12 C1 O1 P1 1.0800 110.4 54.1 117.79 1.6343 +IC H13 C1 O1 P1 1.0848 110.7 294.3 117.79 1.6343 +IC H21 C2 O2 P1 1.0827 107.9 174.7 117.79 1.6344 +IC H22 C2 O2 P1 1.0800 110.4 54.1 117.79 1.6344 +IC H23 C2 O2 P1 1.0848 110.7 294.2 117.79 1.6344 + +RESI MP_1 -1.00 ! Methylphosphate, anionic +GROUP ! +! atom order for molvib +ATOM C1 CTL3 -0.17 ! +ATOM O1 OSL -0.62 ! H11 +ATOM P1 PL 1.50 ! | +ATOM O2 OHL -0.68 ! H13--C1--H12 +ATOM O3 O2L -0.82 ! | +ATOM O4 O2L -0.82 ! O1 +ATOM H11 HAL3 0.09 ! | +ATOM H12 HAL3 0.09 ! O4==P1==O3 (-) +ATOM H13 HAL3 0.09 ! | +ATOM H2 HOL 0.34 ! O2 + ! \ + ! H2 + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 H13 O2 H2 + +IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H2 O2 P1 O1 0.0000 000.00 000.0 000.00 0.0000 + +RESI MP_2 -2.00 ! Methylphosphate, dianionic +GROUP ! +ATOM P1 PL 1.10 ! +ATOM O1 OSL -0.40 ! H11 +ATOM O2 O2L -0.90 ! | +ATOM O3 O2L -0.90 ! H13--C1--H12 +ATOM O4 O2L -0.90 ! | +GROUP ! O1 +ATOM C1 CTL3 -0.27 ! | +ATOM H11 HAL3 0.09 ! (-) O4--P1(+)--O3 (-) +ATOM H12 HAL3 0.09 ! | +ATOM H13 HAL3 0.09 ! O2 (-) + ! +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 H13 + +IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +! dummy to analyze cetain angles +IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 + +RESI MSO4 -1.00 ! Methylsulfate +GROUP ! +ATOM S SL 1.33 ! OS2(-1) +ATOM OS1 OSL -0.28 ! | +ATOM OS2 O2L -0.65 ! (-1) OS2--S(+2)--OS4 (-1) +ATOM OS3 O2L -0.65 ! | +ATOM OS4 O2L -0.65 ! OS1 +ATOM C1 CTL3 -0.37 ! \ +ATOM H11 HAL3 0.09 ! H11-C1-H13 +ATOM H12 HAL3 0.09 ! | +ATOM H13 HAL3 0.09 ! H12 + ! +BOND S OS1 S OS2 S OS3 S OS4 OS1 C1 +BOND C1 H11 C1 H12 C1 H13 +ACCE OS1 +ACCE OS2 +ACCE OS3 +ACCE OS4 + +IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS2 S OS2 OS3 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC OS3 S OS1 OS4 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS1 S OS3 OS2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C1 OS1 S OS2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC S OS1 C1 OS3 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS1 S OS4 OS2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OS1 S OS2 OS3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OS1 S OS3 OS2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS4 S OS3 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS3 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS4 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS2 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS3 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 + +RESI BUTA 0.00 ! BUTANE +Group +Atom h11 HAL3 0.09 ! H2 +Atom h12 HAL3 0.09 ! | +Atom h13 HAL3 0.09 ! H1-C1-H3 +Atom c1 CTL3 -0.27 ! | +Group ! | +Atom h21 HAL2 0.09 ! H4-C2-H5 +Atom h22 HAL2 0.09 ! | +Atom c2 CTL2 -0.18 ! | +Group ! | +Atom h31 HAL2 0.09 ! H6-C3-H7 +Atom h32 HAL2 0.09 ! | +atom c3 CTL2 -0.18 ! | +Group ! | +atom h41 HAL3 0.09 ! H8-C4-H10 +atom h42 HAL3 0.09 ! | +atom h43 HAL3 0.09 ! H9 +atom c4 CTL3 -0.27 ! +Bond h11 c1 h12 c1 h13 c1 c1 c2 +Bond h21 c2 h22 c2 c2 c3 +Bond h31 c3 h32 c3 c3 c4 +Bond h41 c4 h42 c4 h43 c4 +ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 +ic c2 c3 c4 h41 0.00 0.00 180.0 0.00 0.00 +ic c3 h41 *c4 h42 0.00 0.00 120.0 0.00 0.00 +ic c3 h41 *c4 h43 0.00 0.00 -120.0 0.00 0.00 +ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00 +ic c2 h11 *c1 h12 0.00 0.00 120.0 0.00 0.00 +ic c2 h11 *c1 h13 0.00 0.00 -120.0 0.00 0.00 +ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00 +ic c1 c3 *c2 h22 0.00 0.00 -120.0 0.00 0.00 +ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00 +ic c2 c4 *c3 h32 0.00 0.00 -120.0 0.00 0.00 + +RESI PENT 0.00 ! pentane +GROUP +ATOM H11 HAL3 0.09 ! H12 +ATOM H12 HAL3 0.09 ! | +ATOM H13 HAL3 0.09 ! H11-C1-H13 +ATOM C1 CTL3 -0.27 ! | +GROUP ! | +ATOM H21 HAL2 0.09 ! H21-C2-H22 +ATOM H22 HAL2 0.09 ! | +ATOM C2 CTL2 -0.18 ! | +GROUP ! | +ATOM H31 HAL2 0.09 ! H31-C3-H32 +ATOM H32 HAL2 0.09 ! | +ATOM C3 CTL2 -0.18 ! | +GROUP ! | +ATOM H41 HAL2 0.09 ! H41-C4-H42 +ATOM H42 HAL2 0.09 ! | +ATOM C4 CTL2 -0.18 ! | +GROUP ! | +ATOM H51 HAL3 0.09 ! H51-C4-H52 +ATOM H52 HAL3 0.09 ! | +ATOM H53 HAL3 0.09 ! H53 +ATOM C5 CTL3 -0.27 ! +Bond h11 c1 h12 c1 h13 c1 c1 c2 +Bond h21 c2 h22 c2 c2 c3 +Bond h31 c3 h32 c3 c3 c4 +Bond h41 c4 h42 c4 c4 c5 +Bond h51 c5 h52 c5 c5 h53 +ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 +ic c2 c3 c4 c5 0.00 0.00 180.0 0.00 0.00 +ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00 +ic h11 c2 *c1 h12 0.00 0.00 120.0 0.00 0.00 +ic h11 c2 *c1 h13 0.00 0.00 240.0 0.00 0.00 +ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00 +ic c1 c3 *c2 h22 0.00 0.00 240.0 0.00 0.00 +ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00 +ic c2 c4 *c3 h32 0.00 0.00 240.0 0.00 0.00 +ic c3 c5 *c4 h41 0.00 0.00 120.0 0.00 0.00 +ic c3 c5 *c4 h42 0.00 0.00 240.0 0.00 0.00 +ic c3 c4 c5 h51 0.00 0.00 180.0 0.00 0.00 +ic h51 c4 *c5 h52 0.00 0.00 120.0 0.00 0.00 +ic h51 c4 *c5 h53 0.00 0.00 240.0 0.00 0.00 + +RESI HEXA 0.00 ! hexane +Group +Atom h11 HAL3 0.09 ! H2 +Atom h12 HAL3 0.09 ! | +Atom h13 HAL3 0.09 ! H1-C1-H3 +Atom c1 CTL3 -0.27 ! | +Group ! | +Atom h21 HAL2 0.09 ! H4-C2-H5 +Atom h22 HAL2 0.09 ! | +Atom c2 CTL2 -0.18 ! | +Group ! | +Atom h31 HAL2 0.09 ! H6-C3-H7 +Atom h32 HAL2 0.09 ! | +atom c3 CTL2 -0.18 ! | +Group ! | +atom h41 HAL2 0.09 ! H8-C4-H10 +atom h42 HAL2 0.09 ! | +atom c4 CTL2 -0.18 ! | +Group ! | +atom h51 HAL2 0.09 ! H51-C5-H152 +atom h52 HAL2 0.09 ! | +atom c5 CTL2 -0.18 ! | +Group ! | +atom h61 HAL3 0.09 ! H61-C4-H62 +atom h62 HAL3 0.09 ! | +atom h63 HAL3 0.09 ! H63 +atom c6 CTL3 -0.27 ! +Bond h11 c1 h12 c1 h13 c1 c1 c2 +Bond h21 c2 h22 c2 c2 c3 +Bond h31 c3 h32 c3 c3 c4 +Bond h41 c4 h42 c4 c4 c5 +Bond h51 c5 h52 c5 c5 c6 +Bond h61 c6 h62 c6 c6 h63 +ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 +ic c2 c3 c4 c5 0.00 0.00 180.0 0.00 0.00 +ic c3 c4 c5 c6 0.00 0.00 180.0 0.00 0.00 +ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00 +ic h11 c2 *c1 h12 0.00 0.00 120.0 0.00 0.00 +ic h11 c2 *c1 h13 0.00 0.00 240.0 0.00 0.00 +ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00 +ic c1 c3 *c2 h22 0.00 0.00 240.0 0.00 0.00 +ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00 +ic c2 c4 *c3 h32 0.00 0.00 240.0 0.00 0.00 +ic c3 c5 *c4 h41 0.00 0.00 120.0 0.00 0.00 +ic c3 c5 *c4 h42 0.00 0.00 240.0 0.00 0.00 +ic c4 c6 *c5 h51 0.00 0.00 120.0 0.00 0.00 +ic c4 c6 *c5 h52 0.00 0.00 240.0 0.00 0.00 +ic c4 c5 c6 h61 0.00 0.00 180.0 0.00 0.00 +ic h61 c5 *c6 h62 0.00 0.00 120.0 0.00 0.00 +ic h61 c5 *c6 h63 0.00 0.00 240.0 0.00 0.00 + +RESI HEPT 0.00 ! heptane +Group +Atom h11 HAL3 0.09 ! H12 +Atom h12 HAL3 0.09 ! | +Atom h13 HAL3 0.09 ! H11-C1-H13 +Atom c1 CTL3 -0.27 ! | +Group ! | +Atom h21 HAL2 0.09 ! H21-C2-H22 +Atom h22 HAL2 0.09 ! | +Atom c2 CTL2 -0.18 ! | +Group ! | +Atom h31 HAL2 0.09 ! H31-C3-H32 +Atom h32 HAL2 0.09 ! | +atom c3 CTL2 -0.18 ! | +Group ! | +atom h41 HAL2 0.09 ! H41-C4-H42 +atom h42 HAL2 0.09 ! | +atom c4 CTL2 -0.18 ! | +Group ! | +atom h51 HAL2 0.09 ! H51-C5-H52 +atom h52 HAL2 0.09 ! | +atom c5 CTL2 -0.18 ! | +Group ! | +atom h61 HAL2 0.09 ! H61-C6-H62 +atom h62 HAL2 0.09 ! | +atom c6 CTL2 -0.18 ! | +Group ! | +atom h71 HAL3 0.09 ! H71-C7-H72 +atom h72 HAL3 0.09 ! | +atom h73 HAL3 0.09 ! H73 +atom c7 CTL3 -0.27 ! +Bond h11 c1 h12 c1 h13 c1 c1 c2 +Bond h21 c2 h22 c2 c2 c3 +Bond h31 c3 h32 c3 c3 c4 +Bond h41 c4 h42 c4 c4 c5 +Bond h51 c5 h52 c5 c5 c6 +Bond h61 c6 h62 c6 c6 c7 +Bond h71 c7 h72 c7 c7 h73 +ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 +ic c2 c3 c4 c5 0.00 0.00 180.0 0.00 0.00 +ic c3 c4 c5 c6 0.00 0.00 180.0 0.00 0.00 +ic c4 c5 c6 c7 0.00 0.00 180.0 0.00 0.00 +ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00 +ic h11 c2 *c1 h12 0.00 0.00 120.0 0.00 0.00 +ic h11 c2 *c1 h13 0.00 0.00 240.0 0.00 0.00 +ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00 +ic c1 c3 *c2 h22 0.00 0.00 240.0 0.00 0.00 +ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00 +ic c2 c4 *c3 h32 0.00 0.00 240.0 0.00 0.00 +ic c3 c5 *c4 h41 0.00 0.00 120.0 0.00 0.00 +ic c3 c5 *c4 h42 0.00 0.00 240.0 0.00 0.00 +ic c4 c6 *c5 h51 0.00 0.00 120.0 0.00 0.00 +ic c4 c6 *c5 h52 0.00 0.00 240.0 0.00 0.00 +ic c5 c7 *c6 h61 0.00 0.00 120.0 0.00 0.00 +ic c5 c7 *c6 h62 0.00 0.00 240.0 0.00 0.00 +ic c5 c6 c7 h71 0.00 0.00 180.0 0.00 0.00 +ic h71 c6 *c7 h72 0.00 0.00 120.0 0.00 0.00 +ic h71 c6 *c7 h73 0.00 0.00 240.0 0.00 0.00 + +RESI ETHE 0.00 ! ethylene, yin/adm jr. +Group + Atom c1 cel2 -0.42 ! + Atom h11 hel2 0.21 ! H11 H21 + Atom h12 hel2 0.21 ! \ / +Group ! C1=C2 + Atom c2 cel2 -0.42 ! / \ + Atom h21 hel2 0.21 ! H12 H22 + Atom h22 hel2 0.21 ! +Bond c1 h11 c1 h12 +Double c1 c2 +Bond c2 h21 c2 h22 +IMPR c1 c2 h12 h11 +IMPR c1 c2 h11 h12 +IMPR c2 c1 h22 h21 +IMPR c2 c1 h21 h22 +ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 +ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0 +ic h22 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0 +ic c1 c2 h21 h22 0.00 0.00 180.0 0.0 0.0 +patc firs none last none + +RESI PRPE 0.00 ! propene, yin/adm jr. +Group + Atom c1 cel2 -0.42 ! + Atom h11 hel2 0.21 ! H11 H21 + Atom h12 hel2 0.21 ! \ / +Group ! C1=C2 H31 + Atom c2 cel1 -0.15 ! / \ / + Atom h21 HEL1 0.15 ! H12 C3 +Group ! / \ + Atom c3 ctl3 -0.27 ! H33 H32 + Atom h31 HAL3 0.09 ! + Atom h32 HAL3 0.09 ! + Atom h33 HAL3 0.09 ! +Bond c1 h11 c1 h12 +Double c1 c2 +Bond c2 h21 +Bond c2 c3 +bond c3 h31 c3 h32 c3 h33 +ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 +ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0 +ic c3 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0 +ic h31 c3 c2 c1 0.00 0.00 0.0 0.0 0.0 +ic h32 c3 c2 c1 0.00 0.00 120.0 0.0 0.0 +ic h33 c3 c2 c1 0.00 0.00 -120.0 0.0 0.0 +patc firs none last none + +RESI BTE1 0.00 ! 1-Butene, yin/adm jr. +Group + Atom c1 cel2 -0.42 ! + Atom h11 hel2 0.21 ! H11 H21 H41 + Atom h12 hel2 0.21 ! \ / | +Group ! C1=C2 C4-H42 + Atom c2 cel1 -0.15 ! / \ / \ + Atom h21 HEL1 0.15 ! H12 C3 H43 +Group ! / \ + Atom c3 ctl2 -0.18 ! H31 H32 + Atom h31 HAL2 0.09 ! + Atom h32 HAL2 0.09 ! +Group + Atom c4 ctl3 -0.27 + Atom h41 HAL3 0.09 + Atom h42 HAL3 0.09 + Atom h43 HAL3 0.09 +BOND c1 h11 c1 h12 +Double c1 c2 +BOND c2 h21 +BOND c2 c3 +BOND c3 h31 c3 h32 +BOND c3 c4 +BOND c4 h41 c4 h42 c4 h43 +ic c1 c2 c3 c4 0.00 0.00 0.0 0.00 0.00 +ic h11 c1 c2 c3 0.00 0.00 180.0 0.00 0.00 +ic h12 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 +ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 +ic h31 c2 *c3 c4 0.00 0.00 120.0 0.00 0.00 +ic h32 c2 *c3 c4 0.00 0.00 -120.0 0.00 0.00 +ic h41 c4 c3 c2 0.00 0.00 180.0 0.00 0.00 +ic h42 c4 c3 c2 0.00 0.00 60.0 0.00 0.00 +ic h43 c4 c3 c2 0.00 0.00 -60.0 0.00 0.00 +patc firs none last none + +RESI BTE2 0.00 ! 2-Butene, yin/adm jr. +Group + Atom c1 ctl3 -0.27 ! H12 H13 + Atom h11 HAL3 0.09 ! \ | + Atom h12 HAL3 0.09 ! H13-C1 H31 + Atom h13 HAL3 0.09 ! \ / +Group ! C2=C3 + Atom c2 cel1 -0.15 ! / \ + Atom h21 HEL1 0.15 ! H21 C4-H41 +Group ! | \ + Atom c3 cel1 -0.15 ! H43 H42 + Atom h31 HEL1 0.15 ! +Group + Atom c4 ctl3 -0.27 + Atom h41 HAL3 0.09 + Atom h42 HAL3 0.09 + Atom h43 HAL3 0.09 +BOND c1 h11 c1 h12 c1 h13 +BOND c1 c2 +BOND c2 h21 +DOUBLE c2 c3 +BOND c3 h31 +BOND c3 c4 +BOND c4 h41 c4 h42 c4 h43 +ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 +ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 +ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00 +ic h13 c1 c2 c3 0.00 0.00 -120.0 0.00 0.00 +ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 +ic h31 c4 *c3 c2 0.00 0.00 120.0 0.00 0.00 +ic h41 c4 c3 c2 0.00 0.00 0.0 0.00 0.00 +ic h42 c4 c3 c2 0.00 0.00 120.0 0.00 0.00 +ic h43 c4 c3 c2 0.00 0.00 -120.0 0.00 0.00 +patc firs none last none + +RESI 2PTE 0.00 ! 2-pentene, adm jr. +Group + Atom c1 ctl3 -0.27 ! H12 H11 + Atom h11 HAL3 0.09 ! \ | + Atom h12 HAL3 0.09 ! H13-C1 H31 + Atom h13 HAL3 0.09 ! \ / +Group ! C2=C3 H51 + Atom c2 cel1 -0.15 ! / \ / + Atom h21 HEL1 0.15 ! H21 C4--C5-H52 +Group ! / \ \ + Atom c3 cel1 -0.15 ! H41 H42 H53 + Atom h31 HEL1 0.15 ! +Group + Atom c4 ctl2 -0.18 + Atom h41 HAL2 0.09 + Atom h42 HAL2 0.09 +Group + Atom c5 ctl3 -0.27 + Atom h51 HAL3 0.09 + Atom h52 HAL3 0.09 + Atom h53 HAL3 0.09 + +BOND c1 h11 c1 h12 c1 h13 +BOND c1 c2 +BOND c2 h21 +DOUBLE c2 c3 +BOND c3 h31 +BOND c3 c4 +BOND c4 h41 c4 h42 c4 c5 +BOND c5 H51 c5 h52 c5 h53 + +ic C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 !cis double bond +ic H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +ic H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +ic H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +ic C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +ic C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +ic C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +ic C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +ic H41 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +ic C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 +ic H51 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 +ic H51 C4 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +RESI DIPE 0.00 ! 1,4-dipentene, adm jr. +Group + Atom c1 cel2 -0.42 ! + Atom h11 hel2 0.21 ! H11 H21 H41 H51 + Atom h12 hel2 0.21 ! \ / | / +Group ! C1=C2 C4=C5 + Atom c2 cel1 -0.15 ! / \ / \ + Atom h21 HEL1 0.15 ! H12 C3 H52 +Group ! / \ + Atom c3 ctl2 -0.18 ! H31 H32 + Atom h31 HAL2 0.09 ! + Atom h32 HAL2 0.09 ! +Group + Atom c4 cel1 -0.15 + Atom h41 hel1 0.15 +Group + Atom c5 cel2 -0.42 + Atom h51 hel2 0.21 + Atom h52 hel2 0.21 +BOND c1 h11 c1 h12 +Double c1 c2 +BOND c2 h21 +BOND c2 c3 +BOND c3 h31 c3 h32 +BOND c3 c4 +BOND c4 h41 +Double c4 c5 +BOND c5 h51 c5 h52 +IC H11 C1 C2 H21 0.0000 0.00 0.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H51 C4 *C5 H52 0.0000 0.00 180.00 0.00 0.0000 +patc firs none last none + +RESI DIHE 0.00 ! 2,5-diheptene, adm jr. +Group + Atom c1 ctl3 -0.27 ! + Atom h11 hal3 0.09 ! + Atom h12 hal3 0.09 ! + Atom h13 hal3 0.09 ! +Group + Atom c2 cel1 -0.15 ! H21 H31 H51 H61 + Atom h21 hel1 0.15 ! \ / | / +Group ! C2=C3 C5=C6 + Atom c3 cel1 -0.15 ! / \ / \ + Atom h31 HEL1 0.15 ! H11-C1 C4 C7-H71 +Group ! / \ / \ / \ + Atom c4 ctl2 -0.18 ! H12 H13 H41 H42 H73 H72 + Atom h41 HAL2 0.09 ! + Atom h42 HAL2 0.09 ! +Group + Atom c5 cel1 -0.15 + Atom h51 hel1 0.15 +Group + Atom c6 cel1 -0.15 + Atom h61 hel1 0.15 +Group + Atom c7 ctl3 -0.27 + Atom h71 hal3 0.09 + Atom h72 hal3 0.09 + Atom h73 hal3 0.09 + +BOND c1 h11 c1 h12 c1 h13 +BOND c1 c2 c2 h21 +Double c2 c3 +BOND c3 h31 +BOND c3 c4 c4 h41 c4 h42 +BOND c4 c5 c5 h51 +Double c5 c6 +BOND c6 h61 +BOND c6 c7 c7 h71 c7 h72 c7 h73 +IC H11 C1 C2 H21 0.0000 0.00 0.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C5 *C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC H71 C6 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 +IC H71 C6 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +RESI 2HEX 0.00 ! 2-hexene, yin/adm jr. +Group + Atom c1 ctl3 -0.27 ! H12 H13 + Atom h11 HAL3 0.09 ! \ | + Atom h12 HAL3 0.09 ! H13-C1 H31 H51 H52 + Atom h13 HAL3 0.09 ! \ / \ / +Group ! C2=C3 C5 H61 + Atom c2 cel1 -0.15 ! / \ / \ / + Atom h21 HEL1 0.15 ! H21 C4 C6-H62 +Group ! / \ \ + Atom c3 cel1 -0.15 ! H41 H42 H63 + Atom h31 HEL1 0.15 ! +Group + Atom c4 ctl2 -0.18 + Atom h41 HAL2 0.09 + Atom h42 HAL2 0.09 +Group + Atom c5 ctl2 -0.18 + Atom h51 HAL2 0.09 + Atom h52 HAL2 0.09 +Group + Atom c6 ctl3 -0.27 + Atom h61 HAL3 0.09 + Atom h62 HAL3 0.09 + Atom h63 HAL3 0.09 + +BOND c1 h11 c1 h12 c1 h13 +BOND c1 c2 +BOND c2 h21 +DOUBLE c2 c3 +BOND c3 h31 +BOND c3 c4 +BOND c4 h41 c4 h42 +BOND c4 c5 c5 h51 c5 h52 +BOND c5 c6 c6 h61 c6 h62 c6 h63 + +ic C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 !cis double bond +ic C3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +ic H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +ic H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +ic H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +ic C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +ic C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +ic C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +ic C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +ic C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +ic H41 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +ic C6 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +ic H51 C4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +ic C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +ic H61 C5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 +ic H61 C5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +RESI 3HEX 0.00 ! 3-hexene, adm jr. +Group + Atom c1 ctl3 -0.27 ! H12 H21 H31 H41 H61 + Atom h11 HAL3 0.09 ! \ | \ / / + Atom h12 HAL3 0.09 ! H13-C1 C3=C4 C6-H62 + Atom h13 HAL3 0.09 ! \ / \ / \ +Group ! C2 C5 H63 + Atom c2 ctl2 -0.18 ! / \ / \ + Atom h21 HAL2 0.09 ! H21 H22 H51 H52 + Atom h22 HAL2 0.09 +Group + Atom c3 cel1 -0.15 + Atom h31 HEL1 0.15 +Group + Atom c4 cel1 -0.15 + Atom h41 HEL1 0.15 +Group + Atom c5 ctl2 -0.18 + Atom h51 HAL2 0.09 + Atom h52 HAL2 0.09 +Group + Atom c6 ctl3 -0.27 + Atom h61 HAL3 0.09 + Atom h62 HAL3 0.09 + Atom h63 HAL3 0.09 + +BOND c1 h11 c1 h12 c1 h13 c1 c2 +BOND c2 h21 c2 h22 c2 c3 +BOND c3 h31 +DOUBLE c3 c4 +BOND c4 h41 c4 c5 +BOND c5 H51 c5 h52 c5 c6 +BOND c6 H61 c6 h62 c6 h63 + +ic C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +ic C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 !cis double bond +ic C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +ic H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +ic H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +ic H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +ic C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +ic H21 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +ic C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +ic C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 +ic C6 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +ic H51 C4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +ic C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +ic H61 C5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 +ic H61 C5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +RESI NC4 1.00 ! tetramethylammonium +GROUP ! +ATOM N NTL -0.60 ! H32 +ATOM C1 CTL5 -0.35 ! | +ATOM C2 CTL5 -0.35 ! H31-C3-H33 +ATOM C3 CTL5 -0.35 ! H23 | H41 +ATOM C4 CTL5 -0.35 ! | | | +ATOM H11 HL 0.25 ! H22-C2------N------C4-H42 (+) +ATOM H12 HL 0.25 ! | | | +ATOM H13 HL 0.25 ! H21 | H43 +ATOM H21 HL 0.25 ! H11-C1-H13 +ATOM H22 HL 0.25 ! | +ATOM H23 HL 0.25 ! H12 +ATOM H31 HL 0.25 +ATOM H32 HL 0.25 +ATOM H33 HL 0.25 +ATOM H41 HL 0.25 +ATOM H42 HL 0.25 +ATOM H43 HL 0.25 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +! internal are wrong +IC C2 N C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N C1 H12 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC C2 N C1 H13 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C2 C1 *N C3 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2 C1 *N C4 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C3 N C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C3 N C2 H22 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C3 N C2 H23 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C4 N C3 H31 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4 N C3 H32 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C4 N C3 H33 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C1 N C4 H41 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C1 N C4 H42 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C1 N C4 H43 0.0000 0.0000 120.0000 0.0000 0.0000 + +RESI NC5 1.00 ! tetramethylammonium ethyl analog +GROUP +ATOM N NTL -0.60 ! +ATOM C1 CTL2 -0.10 ! | +ATOM C2 CTL5 -0.35 ! -C3- +ATOM C3 CTL5 -0.35 ! | +ATOM C4 CTL5 -0.35 ! | | | +ATOM H11 HL 0.25 ! -C2---N---C4- (+) +ATOM H12 HL 0.25 ! | | | +ATOM H21 HL 0.25 ! | +ATOM H22 HL 0.25 ! -C1- +ATOM H23 HL 0.25 ! | +ATOM H31 HL 0.25 ! | +ATOM H32 HL 0.25 ! -C5- +ATOM H33 HL 0.25 ! | +ATOM H41 HL 0.25 +ATOM H42 HL 0.25 +ATOM H43 HL 0.25 +GROUP +ATOM C5 CTL3 -0.27 +ATOM H51 HAL3 0.09 +ATOM H52 HAL3 0.09 +ATOM H53 HAL3 0.09 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 C5 H53 +! ab-initio HF/6-31G* structure +IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217 +IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950 +IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950 +IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809 +IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809 +IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795 +IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773 +IC C1 N C2 H23 1.5176 111.12 -54.79 109.07 1.0797 +IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795 +IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773 +IC C1 N C3 H33 1.5176 111.12 54.79 109.07 1.0797 +IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793 +IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793 +IC C1 N C4 H43 1.5176 107.80 -60.03 109.12 1.0793 +IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820 + +RESI CHOL 1.00 ! choline +GROUP ! +ATOM N NTL -0.60 ! +ATOM C1 CTL2 -0.10 ! | +ATOM C2 CTL5 -0.35 ! -C3- +ATOM C3 CTL5 -0.35 ! | +ATOM C4 CTL5 -0.35 ! | | | +ATOM H11 HL 0.25 ! -C2---N---C4- (+) +ATOM H12 HL 0.25 ! | | | +ATOM H21 HL 0.25 ! | +ATOM H22 HL 0.25 ! -C1- +ATOM H23 HL 0.25 ! | +ATOM H31 HL 0.25 ! | +ATOM H32 HL 0.25 ! | +ATOM H33 HL 0.25 ! | +ATOM H41 HL 0.25 ! | +ATOM H42 HL 0.25 ! | +ATOM H43 HL 0.25 ! | +GROUP ! | +ATOM C5 CTL2 0.05 ! | +ATOM H51 HAL2 0.09 ! -C5- +ATOM H52 HAL2 0.09 ! | +ATOM OH1 OHL -0.66 ! OH1---HO1 +ATOM HO1 HOL 0.43 ! +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND C5 OH1 OH1 HO1 +! ab-initio HF/6-31G* geometry of gauche conformer +IC C4 N C1 C5 1.4964 107.76 161.60 116.58 1.5208 +IC C5 C1 N C2 1.5208 116.58 -80.13 111.04 1.5031 +IC C5 C1 N C3 1.5208 116.58 42.05 111.71 1.4945 +IC N C1 C5 OH1 1.5158 116.58 56.02 109.57 1.3947 +IC C1 C5 OH1 HO1 1.5208 109.57 169.05 110.84 0.9491 +IC C2 N C1 H11 1.5031 111.04 158.76 106.72 1.0813 +IC C3 N C1 H12 1.4945 111.71 165.25 106.14 1.0802 +IC C1 N C2 H21 1.5158 111.04 -179.38 108.21 1.0796 +IC C3 N C2 H22 1.4945 109.20 -63.85 109.22 1.0746 +IC C4 N C2 H23 1.4964 108.15 57.69 108.56 1.0794 +IC C1 N C3 H31 1.5158 111.71 173.42 108.53 1.0794 +IC C2 N C3 H32 1.5031 109.20 177.22 109.23 1.0800 +IC C4 N C3 H33 1.4964 108.88 174.14 109.12 1.0773 +IC C1 N C4 H41 1.5158 107.76 175.04 109.01 1.0793 +IC C2 N C4 H42 1.5031 108.15 -64.86 109.05 1.0796 +IC C3 N C4 H43 1.4945 108.88 56.40 109.30 1.0794 +IC N C1 C5 H51 1.5158 116.58 176.61 105.66 1.0855 +IC N C1 C5 H52 1.5158 116.58 -67.32 110.89 1.0847 + +RESI ACHO 1.00 ! acetylcholine +GROUP ! +ATOM N NTL -0.60 ! +ATOM C1 CTL2 -0.10 ! | +ATOM C2 CTL5 -0.35 ! -C3- +ATOM C3 CTL5 -0.35 ! | +ATOM C4 CTL5 -0.35 ! | | | +ATOM H11 HL 0.25 ! -C2---N---C4- (+) +ATOM H12 HL 0.25 ! | | | +ATOM H21 HL 0.25 ! | +ATOM H22 HL 0.25 ! -C1- +ATOM H23 HL 0.25 ! | +ATOM H31 HL 0.25 ! | +ATOM H32 HL 0.25 ! | +ATOM H33 HL 0.25 ! | +ATOM H41 HL 0.25 ! | +ATOM H42 HL 0.25 ! | +ATOM H43 HL 0.25 ! | +GROUP ! | +ATOM C5 CTL2 0.08 ! -C5- +ATOM OM OSL -0.49 ! | +ATOM C CL 0.90 ! OM +ATOM C7 CTL3 -0.31 ! / +ATOM O OBL -0.63 ! O==C +ATOM H51 HAL2 0.09 ! | +ATOM H52 HAL2 0.09 ! --C7-- +ATOM H71 HAL3 0.09 ! | +ATOM H72 HAL3 0.09 ! +ATOM H73 HAL3 0.09 ! +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND C7 C C OM OM C5 +DOUBLE C O +BOND C7 H71 C7 H72 C7 H73 +IMPR C OM C7 O +IC C4 N C1 C5 0.0000 000.00 161.60 000.00 0.0000 +IC C5 C1 N C2 0.0000 000.00 -80.13 000.00 0.0000 +IC C5 C1 N C3 0.0000 000.00 42.05 000.00 0.0000 +IC C2 N C1 H11 0.0000 000.00 158.76 000.00 0.0000 +IC C3 N C1 H12 0.0000 000.00 165.25 000.00 0.0000 +IC C1 N C2 H21 0.0000 000.00 -179.38 000.00 0.0000 +IC C3 N C2 H22 0.0000 000.00 -63.85 000.00 0.0000 +IC C4 N C2 H23 0.0000 000.00 57.69 000.00 0.0000 +IC C1 N C3 H31 0.0000 000.00 173.42 000.00 0.0000 +IC C2 N C3 H32 0.0000 000.00 177.22 000.00 0.0000 +IC C4 N C3 H33 0.0000 000.00 174.14 000.00 0.0000 +IC C1 N C4 H41 0.0000 000.00 175.04 000.00 0.0000 +IC C2 N C4 H42 0.0000 000.00 -64.86 000.00 0.0000 +IC C3 N C4 H43 0.0000 000.00 56.40 000.00 0.0000 +IC N C1 C5 H51 0.0000 000.00 180.00 000.00 0.0000 +IC N C1 C5 H52 0.0000 000.00 -60.0 000.00 0.0000 +IC N C1 C5 OM 0.0000 000.00 72.0 000.00 0.0000 +IC C1 C5 OM C 0.0000 000.00 166.9 000.00 0.0000 +IC C7 C OM C5 0.0000 000.00 20.0 000.00 0.0000 +IC O C OM C5 0.0000 000.00 -160.0 000.00 0.0000 +IC H71 C7 C OM 0.0000 000.00 180.0 000.00 0.0000 +IC H72 C7 C OM 0.0000 000.00 60.4 000.00 0.0000 +IC H73 C7 C OM 0.0000 000.00 -60.4 000.00 0.0000 + +RESI PC 0.00 ! phosphatidylcholine +GROUP ! +ATOM N NTL -0.60 ! +ATOM C1 CTL2 -0.10 ! | +ATOM C2 CTL5 -0.35 ! -C3- +ATOM C3 CTL5 -0.35 ! | +ATOM C4 CTL5 -0.35 ! | | | +ATOM H11 HL 0.25 ! -C2---N---C4- (+) +ATOM H12 HL 0.25 ! | | | +ATOM H21 HL 0.25 ! | +ATOM H22 HL 0.25 ! -C1- +ATOM H23 HL 0.25 ! | +ATOM H31 HL 0.25 ! | +ATOM H32 HL 0.25 ! | +ATOM H33 HL 0.25 ! | +ATOM H41 HL 0.25 ! | +ATOM H42 HL 0.25 ! | +ATOM H43 HL 0.25 ! | +GROUP ! | +ATOM C5 CTL2 -0.08 ! | +ATOM H51 HAL2 0.09 ! H52---C5---H51 +ATOM H52 HAL2 0.09 ! | +GROUP ! | +ATOM P1 PL 1.50 ! (-) O3 O1 +ATOM O3 O2L -0.78 ! \ / +ATOM O4 O2L -0.78 ! P1 (+) +ATOM O1 OSLP -0.57 ! / \ +ATOM O2 OSLP -0.57 ! (-) O4 O2 +GROUP ! | +ATOM C6 CTL3 -0.17 ! | +ATOM H61 HAL3 0.09 ! H63-C6-H62 +ATOM H62 HAL3 0.09 ! | +ATOM H63 HAL3 0.09 ! H61 + ! +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C5 O2 C6 +BOND C6 H61 C6 H62 C6 H63 + +IC C4 N C1 C5 0.0000 000.00 112.00 000.00 0.0000 +IC C5 C1 N C2 0.0000 000.00 -121.00 000.00 0.0000 +IC C5 C1 N C3 0.0000 000.00 0.00 000.00 0.0000 +IC C2 N C1 H11 0.0000 000.00 120.00 000.00 0.0000 +IC C3 N C1 H12 0.0000 000.00 120.00 000.00 0.0000 +IC C1 N C2 H21 0.0000 000.00 180.00 000.00 0.0000 +IC C3 N C2 H22 0.0000 000.00 -60.00 000.00 0.0000 +IC C4 N C2 H23 0.0000 000.00 60.00 000.00 0.0000 +IC C1 N C3 H31 0.0000 000.00 180.00 000.00 0.0000 +IC C2 N C3 H32 0.0000 000.00 180.00 000.00 0.0000 +IC C4 N C3 H33 0.0000 000.00 180.00 000.00 0.0000 +IC C1 N C4 H41 0.0000 000.00 180.00 000.00 0.0000 +IC C2 N C4 H42 0.0000 000.00 -60.00 000.00 0.0000 +IC C3 N C4 H43 0.0000 000.00 60.00 000.00 0.0000 +IC N C1 C5 H51 0.0000 000.00 -150.00 000.00 0.0000 +IC N C1 C5 H52 0.0000 000.00 100.00 000.00 0.0000 +IC N C1 C5 O1 0.0000 000.00 -30.00 000.00 0.0000 +IC C1 C5 O1 P1 0.0000 000.00 130.00 000.00 0.0000 +IC C5 O1 P1 O2 0.0000 000.00 -160.0 000.00 0.0000 +IC O3 P1 O1 C5 0.0000 000.00 80.00 000.00 0.0000 +IC O4 P1 O1 C5 0.0000 000.00 -60.00 000.00 0.0000 +IC O1 P1 O2 C6 0.0000 000.00 180.00 000.00 0.0000 +IC H61 C6 O2 P1 0.0000 000.00 0.00 000.00 0.0000 +IC H62 C6 O2 P1 0.0000 000.00 120.00 000.00 0.0000 +IC H63 C6 O2 P1 0.0000 000.00 -120.00 000.00 0.0000 + +RESI GPC 0.00 ! glycerolphosphorylcholine +GROUP ! +ATOM N NTL -0.60 ! +ATOM C1 CTL2 -0.10 ! | +ATOM C2 CTL5 -0.35 ! -C3- +ATOM C3 CTL5 -0.35 ! | +ATOM C4 CTL5 -0.35 ! | | | +ATOM H11 HL 0.25 ! -C2---N---C4- (+) +ATOM H12 HL 0.25 ! | | | +ATOM H21 HL 0.25 ! | +ATOM H22 HL 0.25 ! -C1- +ATOM H23 HL 0.25 ! | +ATOM H31 HL 0.25 ! | +ATOM H32 HL 0.25 ! | +ATOM H33 HL 0.25 ! | +ATOM H41 HL 0.25 ! | +ATOM H42 HL 0.25 ! | +ATOM H43 HL 0.25 ! | +GROUP ! | +ATOM C5 CTL2 -0.08 ! | +ATOM H51 HAL2 0.09 ! H51---C5---H52 +ATOM H52 HAL2 0.09 ! | +ATOM P PL 1.50 ! (-) O3 O1 +ATOM O3 O2L -0.78 ! \ / +ATOM O4 O2L -0.78 ! P (+) +ATOM O1 OSLP -0.57 ! / \ +ATOM O2 OSLP -0.57 ! (-) O4 O2 +ATOM CG1 CTL2 -0.08 ! | +ATOM HG11 HAL2 0.09 ! HG11-CG1-HG12 +ATOM HG12 HAL2 0.09 ! | +GROUP ! | +ATOM CG2 CTL1 0.14 ! | +ATOM HG21 HAL1 0.09 ! HG21-CG2-OG2-HO2 +ATOM OG2 OHL -0.66 ! | +ATOM HO2 HOL 0.43 ! | +GROUP ! | +ATOM CG3 CTL2 0.05 ! | +ATOM HG31 HAL2 0.09 ! HG31-CG3-OG3-HO3 +ATOM HG32 HAL2 0.09 ! | +ATOM OG3 OHL -0.66 ! HG32 +ATOM HO3 HOL 0.43 ! +BOND CG1 O2 CG1 HG11 CG1 HG12 +BOND CG2 CG1 CG2 HG21 CG2 OG2 OG2 HO2 +BOND CG3 CG2 CG3 HG31 CG3 HG32 CG3 OG3 OG3 HO3 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND P O1 P O2 P O3 P O4 O1 C5 + +! internal coordinates for analysis +! see H.Hauser,I.Pascher,R.H.Pearson,S.Sundell, BBA 650, 21-51 (1981) +! glycerol backbone +IC O2 CG1 CG2 CG3 0. 0. 0. 0. 0. ! t1 +IC O2 CG1 CG2 OG2 0. 0. 0. 0. 0. ! t2 +IC CG1 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3 +IC OG2 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3 +! +! zwitterionic headgroup +IC P O2 CG1 CG2 0. 0. 0. 0. 0. ! a1 +IC O1 P O2 CG1 0. 0. 0. 0. 0. ! a2 +IC O2 P O1 C5 0. 0. 0. 0. 0. ! a3 +IC C1 C5 O1 P 0. 0. 0. 0. 0. ! a4 +IC N C1 C5 O1 0. 0. 0. 0. 0. ! a5 +IC C2 N C1 C5 0. 0. 0. 0. 0. ! a6 +IC C3 N C1 C5 0. 0. 0. 0. 0. ! a6 +IC C4 N C1 C5 0. 0. 0. 0. 0. ! a6 +IC O1 O2 *P O3 0. 0. 120. 0. 0. +IC O1 O2 *P O4 0. 0. -120. 0. 0. + +RESI TEA 1.00 ! tetra ethylammonium (TEA) + ! S. Crouzy, S. Berneche and B. Roux + ! calc F.E. solvation = -51 kcal/mol + ! versus experiment = -49 kcal/mol + ! + ! | +GROUP ! -C7- +ATOM N NTL -0.60 ! | +ATOM C1 CTL2 -0.10 ! | +ATOM C2 CTL2 -0.10 ! -C3- +ATOM C3 CTL2 -0.10 ! | +ATOM C4 CTL2 -0.10 ! | | | | | +ATOM H11 HL 0.25 ! -C6--C2---N---C4--C8- (+) +ATOM H12 HL 0.25 ! | | | | | +ATOM H21 HL 0.25 ! | +ATOM H22 HL 0.25 ! -C1- +ATOM H31 HL 0.25 ! | +ATOM H32 HL 0.25 ! -C5- +ATOM H41 HL 0.25 ! | +ATOM H42 HL 0.25 ! +! +! in the following methyl groups, the atom type HAL +! has been changed to HAL3. adm jr. +! +GROUP +ATOM C5 CTL3 -0.27 +ATOM H51 HAL3 0.09 +ATOM H52 HAL3 0.09 +ATOM H53 HAL3 0.09 +GROUP +ATOM C6 CTL3 -0.27 +ATOM H61 HAL3 0.09 +ATOM H62 HAL3 0.09 +ATOM H63 HAL3 0.09 +GROUP +ATOM C7 CTL3 -0.27 +ATOM H71 HAL3 0.09 +ATOM H72 HAL3 0.09 +ATOM H73 HAL3 0.09 +GROUP +ATOM C8 CTL3 -0.27 +ATOM H81 HAL3 0.09 +ATOM H82 HAL3 0.09 +ATOM H83 HAL3 0.09 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 C6 +BOND C3 H31 C3 H32 C3 C7 +BOND C4 H41 C4 H42 C4 C8 +BOND C5 H51 C5 H52 C5 H53 +BOND C6 H61 C6 H62 C6 H63 +BOND C7 H71 C7 H72 C7 H73 +BOND C8 H81 C8 H82 C8 H83 + +! ab-initio HF/6-31G* structure +IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217 +IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950 +IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950 +IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809 +IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809 +IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795 +IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773 +IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795 +IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773 +IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793 +IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793 +IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820 +IC C3 N C2 C6 1.4967 107.80 180.00 115.98 1.5217 +IC N C1 C6 H61 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C6 H62 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C6 H63 1.5176 115.98 -62.29 112.91 1.0820 +IC C2 N C3 C7 1.4967 107.80 180.00 115.98 1.5217 +IC N C1 C7 H71 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C7 H72 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C7 H73 1.5176 115.98 -62.29 112.91 1.0820 +IC C1 N C4 C8 1.4967 107.80 180.00 115.98 1.5217 +IC N C1 C8 H81 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C8 H82 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C8 H83 1.5176 115.98 -62.29 112.91 1.0820 + +RESI ETAM 1.00 ! ethanolamine +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C1 CTL2 0.13 ! | +ATOM H11 HAL2 0.09 ! H12---C1---H11 +ATOM H12 HAL2 0.09 ! | +GROUP ! | +ATOM C5 CTL2 0.05 ! | +ATOM H51 HAL2 0.09 ! H52---C5---H51 +ATOM H52 HAL2 0.09 ! | +ATOM OH1 OHL -0.66 ! OH1---HO1 +ATOM HO1 HOL 0.43 ! +BOND N HN1 N HN2 N HN3 N C1 +BOND C1 H11 C1 H12 C1 C5 +BOND C5 H51 C5 H52 +BOND C5 OH1 OH1 HO1 +! HF/6-31G* OPTIMIZED STRUCTURE: +IC N C1 C5 OH1 1.5084 107.86 48.44 104.92 1.3987 +IC C1 C5 OH1 HO1 1.5191 104.92 173.19 111.99 0.9495 +IC HN1 N C1 C5 1.0145 108.35 -49.03 107.86 1.5191 +IC HN2 N C1 C5 1.0107 112.05 69.23 107.86 1.5191 +IC HN3 N C1 C5 1.0102 112.39 -169.37 107.86 1.5191 +IC N C5 *C1 H11 0.0000 000.00 120.00 000.00 0.0000 +IC N C5 *C1 H12 0.0000 000.00 -120.00 000.00 0.0000 +IC OH1 C1 *C5 H51 0.0000 000.00 120.00 000.00 0.0000 +IC OH1 C1 *C5 H52 0.0000 000.00 -120.00 000.00 0.0000 + +RESI GLYC 0.00 ! Model compound for glycerol headgroup the + ! aliphatic tail linker region +GROUP ! +ATOM C3 CTL3 -0.27 ! +ATOM H31 HAL3 0.09 ! +ATOM H32 HAL3 0.09 ! +ATOM H33 HAL3 0.09 ! +GROUP ! +ATOM C1 CTL2 0.08 ! H12 H21 H31 +ATOM H11 HAL2 0.09 ! | | | +ATOM H12 HAL2 0.09 ! H11--C1--C2--C3--H32 +ATOM O4 OSL -0.49 ! / | | +ATOM C5 CL 0.90 ! O4 O8 H33 +ATOM O6 OBL -0.63 ! / \ +ATOM C7 CTL3 -0.31 ! O6=C5 C9=O10 +ATOM H71 HAL3 0.09 ! / \ +ATOM H72 HAL3 0.09 ! H71-C7-H73 H113-C11-H111 +ATOM H73 HAL3 0.09 ! | | +GROUP ! H72 H112 +ATOM C2 CTL1 0.17 ! +ATOM H21 HAL1 0.09 ! +ATOM O8 OSL -0.49 ! +ATOM C9 CL 0.90 ! +ATOM O10 OBL -0.63 ! +ATOM C11 CTL3 -0.31 ! +ATOM H111 HAL3 0.09 ! +ATOM H112 HAL3 0.09 ! +ATOM H113 HAL3 0.09 ! +BOND C1 C2 C2 C3 +BOND C1 O4 O4 C5 C5 C7 C5 O6 +BOND C2 O8 O8 C9 C9 C11 C9 O10 +BOND C1 H11 C1 H12 +BOND C2 H21 +BOND C3 H31 C3 H32 C3 H33 +BOND C7 H71 C7 H72 C7 H73 +BOND C11 H111 C11 H112 C11 H113 +! internal coordinates +IC C1 C2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 +IC H31 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 O8 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 C1 O4 0.0000 0.00 180.00 0.00 0.0000 +IC O4 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC O4 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C1 O4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O4 C5 O6 0.0000 0.00 0.00 0.00 0.0000 +IC O6 O4 *C5 C7 0.0000 0.00 180.00 0.00 0.0000 +IC O4 C5 C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC H71 C5 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 +IC H71 C5 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 O8 C9 0.0000 0.00 90.00 0.00 0.0000 +IC C2 O8 C9 O10 0.0000 0.00 0.00 0.00 0.0000 +IC O10 O8 *C9 C11 0.0000 0.00 180.00 0.00 0.0000 +IC O8 C9 C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC H111 C9 *C11 H112 0.0000 0.00 120.00 0.00 0.0000 +IC H111 C9 *C11 H113 0.0000 0.00 -120.00 0.00 0.0000 + +RESI GLYP -1.00 ! Model compound for glycerol headgroup the + ! aliphatic tail linker region, phosphorylated +GROUP ! +ATOM P1 PL 1.50 ! +ATOM OP3 O2L -0.78 ! +ATOM OP4 O2L -0.78 ! HP11 +ATOM OP1 OSL -0.57 ! | +ATOM OP2 OSL -0.57 ! HP13-CP1-HP12 + ! \ +ATOM CP1 CTL3 -0.17 ! (-)OP3 OP1 +ATOM HP11 HAL3 0.09 ! \ / +ATOM HP12 HAL3 0.09 ! P1 (+) +ATOM HP13 HAL3 0.09 ! / \ + ! (-)OP4 OP2 + ! \ +ATOM C3 CTL2 -0.08 ! \ Combining DMPA and GLYC lead to omission +ATOM H31 HAL2 0.09 ! \ of the C2 methylene group +ATOM H32 HAL2 0.09 ! \ +GROUP ! | +ATOM C1 CTL2 0.08 ! H12 H21 | +ATOM H11 HAL2 0.09 ! | | | +ATOM H12 HAL2 0.09 ! H11--C1--C2--C3--H31 +ATOM O4 OSL -0.49 ! / | | +ATOM C5 CL 0.90 ! O4 O8 H32 +ATOM O6 OBL -0.63 ! / \ +ATOM C7 CTL3 -0.31 ! O6=C5 C9=O10 +ATOM H71 HAL3 0.09 ! / \ +ATOM H72 HAL3 0.09 ! H71-C7-H73 H113-C11-H111 +ATOM H73 HAL3 0.09 ! | | +GROUP ! H72 H112 +ATOM C2 CTL1 0.17 ! +ATOM H21 HAL1 0.09 ! +ATOM O8 OSL -0.49 ! +ATOM C9 CL 0.90 ! +ATOM O10 OBL -0.63 ! +ATOM C11 CTL3 -0.31 ! +ATOM H111 HAL3 0.09 ! +ATOM H112 HAL3 0.09 ! +ATOM H113 HAL3 0.09 ! +BOND P1 OP1 P1 OP2 P1 OP3 P1 OP4 OP1 CP1 +BOND CP1 HP11 CP1 HP12 CP1 HP13 OP2 C3 +BOND C1 C2 C2 C3 +BOND C1 O4 O4 C5 C5 C7 C5 O6 +BOND C2 O8 O8 C9 C9 C11 C9 O10 +BOND C1 H11 C1 H12 C2 H21 C3 H31 C3 H32 +BOND C7 H71 C7 H72 C7 H73 +BOND C11 H111 C11 H112 C11 H113 +! internal coordinates from ic generate, dihedrals corrected +IC CP1 OP1 P1 OP2 0.0000 0.00 60.00 0.00 0.0000 +IC OP1 OP2 *P1 OP3 0.0000 0.00 120.00 0.00 0.0000 +IC OP1 OP2 *P1 OP4 0.0000 0.00 -120.00 0.00 0.0000 +IC OP2 P1 OP1 CP1 0.0000 0.00 60.00 0.00 0.0000 +IC P1 OP1 CP1 HP11 0.0000 0.00 180.00 0.00 0.0000 +IC HP11 OP1 *CP1 HP12 0.0000 0.00 120.00 0.00 0.0000 +IC HP11 OP1 *CP1 HP13 0.0000 0.00 -120.00 0.00 0.0000 +IC OP1 P1 OP2 C3 0.0000 0.00 -120.00 0.00 0.0000 +IC P1 OP2 C3 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 OP2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 OP2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC OP2 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 O8 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 C1 O4 0.0000 0.00 180.00 0.00 0.0000 +IC O4 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC O4 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C1 O4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O4 C5 O6 0.0000 0.00 180.00 0.00 0.0000 +IC O6 O4 *C5 C7 0.0000 0.00 180.00 0.00 0.0000 +IC O4 C5 C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC H71 C5 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 +IC H71 C5 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 O8 C9 0.0000 0.00 60.00 0.00 0.0000 +IC C2 O8 C9 O10 0.0000 0.00 180.00 0.00 0.0000 +IC O10 O8 *C9 C11 0.0000 0.00 180.00 0.00 0.0000 +IC O8 C9 C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC H111 C9 *C11 H112 0.0000 0.00 120.00 0.00 0.0000 +IC H111 C9 *C11 H113 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MBUT 0.00 ! methyl-butyrate +GROUP +ATOM C4 CTL3 -0.27 ! H42 +ATOM H41 HAL3 0.09 ! | +ATOM H42 HAL3 0.09 ! H41-C4-H43 +ATOM H43 HAL3 0.09 ! | +GROUP ! | +ATOM C3 CTL2 -0.18 ! H31-C3-H32 +ATOM H31 HAL2 0.09 ! | +ATOM H32 HAL2 0.09 ! | +GROUP ! H21-C2-H22 +ATOM C2 CTL2 -0.22 ! | +ATOM H21 HAL2 0.09 ! | +ATOM H22 HAL2 0.09 ! C1 HM1 +ATOM C1 CL 0.90 ! // \ / +ATOM O1 OBL -0.63 ! O1 OM-CM-HM2 +ATOM OM OSL -0.49 ! \ +ATOM CM CTL3 -0.01 ! HM3 +ATOM HM1 HAL3 0.09 ! +ATOM HM2 HAL3 0.09 +ATOM HM3 HAL3 0.09 +BOND C1 OM OM CM CM HM1 CM HM2 CM HM3 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 C3 C3 H31 C3 H32 +BOND C3 C4 C4 H41 C4 H42 C4 H43 +DOUBLE C1 O1 +IMPR C1 OM C2 O1 + +IC C1 C2 C3 C4 0.0000 0.00 60.00 0.00 0.0000 +IC C3 C2 C1 OM 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 +IC H41 C4 C3 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 C1 OM 0.0000 0.00 180.00 0.00 0.0000 +IC OM C2 *C1 O1 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C1 OM CM 0.0000 0.00 180.00 0.00 0.0000 +IC C1 OM CM HM1 0.0000 0.00 180.00 0.00 0.0000 +IC HM1 OM *CM HM2 0.0000 0.00 120.00 0.00 0.0000 +IC HM1 OM *CM HM3 0.0000 0.00 -120.00 0.00 0.0000 + +RESI IPAC 0.00 ! Isopropylacetate; glycerol C2 analog + ! H33 +GROUP ! | +ATOM C1 CTL3 -0.31 ! H31-C3-H32 H41 +ATOM C CL 0.90 ! / / +ATOM OM OSL -0.49 ! H2-C2------C4-H42 +ATOM C2 CTL1 0.17 ! \ \ +ATOM O OBL -0.63 ! OM H43 +ATOM H11 HAL3 0.09 ! / +ATOM H12 HAL3 0.09 ! O=C +ATOM H13 HAL3 0.09 ! \ +ATOM H2 HAL1 0.09 ! H11-C1-H13 +GROUP ! | +ATOM C3 CTL3 -0.27 ! H12 +ATOM H31 HAL3 0.09 +ATOM H32 HAL3 0.09 +ATOM H33 HAL3 0.09 +GROUP +ATOM C4 CTL3 -0.27 +ATOM H41 HAL3 0.09 +ATOM H42 HAL3 0.09 +ATOM H43 HAL3 0.09 +BOND C1 C C OM OM C2 +DOUBLE C O +BOND C1 H11 C1 H12 C1 H13 +BOND C2 C3 C2 H2 C2 C4 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +IMPR C OM C1 O +ACCE O C +ACCE OM +IC C1 C OM C2 0.0000 0.00 180.00 0.00 0.0000 +IC C OM C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC OM C1 *C O 0.0000 0.00 180.00 0.00 0.0000 +IC C3 OM *C2 C4 0.0000 0.00 120.00 0.00 0.0000 +IC OM C C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 OM *C2 H2 0.0000 0.00 -120.00 0.00 0.0000 +IC OM C2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 +IC OM C2 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C2 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C2 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +! TORSIONAL TEST RESIDUE; 1,2,3-TRIPROPIONYL-GLYCEROL +RESI TPG 0.0 +GROUP +ATOM C13 CTL3 -0.27 ! H13C +ATOM H13A HAL3 0.09 ! | +ATOM H13B HAL3 0.09 ! H13A-C13-H13B +ATOM H13C HAL3 0.09 ! | +GROUP ! | +ATOM C12 CTL2 -0.22 ! H12A-C12-H12B +ATOM H12A HAL2 0.09 ! | +ATOM H12B HAL2 0.09 ! | +ATOM C11 CL 0.90 ! C11==O12 +ATOM O12 OBL -0.63 ! | +ATOM O11 OSL -0.49 ! O11 +ATOM C1 CTL2 0.08 ! | +ATOM H1A HAL2 0.09 ! H1A-C1-H1B +ATOM H1B HAL2 0.09 ! | +GROUP ! | +ATOM C2 CTL1 0.17 ! H2A-C2------O21 +ATOM H2A HAL1 0.09 ! | | +ATOM O21 OSL -0.49 ! | C21==O22 +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | | +ATOM C22 CTL2 -0.22 ! | H22A-C22-H22B +ATOM H22A HAL2 0.09 ! | | +ATOM H22B HAL2 0.09 ! | | +GROUP ! | H23A-C23-H23B +ATOM C23 CTL3 -0.27 ! | | +ATOM H23A HAL3 0.09 ! | H23C +ATOM H23B HAL3 0.09 ! | +ATOM H23C HAL3 0.09 ! | +GROUP ! | +ATOM C3 CTL2 0.08 ! H3A-C3-H3B +ATOM H3A HAL2 0.09 ! | +ATOM H3B HAL2 0.09 ! | +ATOM O31 OSL -0.49 ! O31 +ATOM C31 CL 0.90 ! | +ATOM O32 OBL -0.63 ! C31==O32 +ATOM C32 CTL2 -0.22 ! | +ATOM H32A HAL2 0.09 ! H32A-C32-H32B +ATOM H32B HAL2 0.09 ! | +GROUP ! | +ATOM C33 CTL3 -0.27 ! H33A-C33-H33B +ATOM H33A HAL3 0.09 ! | +ATOM H33B HAL3 0.09 ! H33C +ATOM H33C HAL3 0.09 +BOND C13 H13A C13 H13B C13 H13C C13 C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 O12 C11 O11 O11 C1 +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 O21 C2 C3 +BOND O21 C21 C21 O22 C21 C22 +BOND C22 H22A C22 H22B C22 C23 +BOND C23 H23A C23 H23B C23 H23C +BOND C3 H3A C3 H3B C3 O31 +BOND O31 C31 C31 O32 C31 C32 +BOND C32 H32A C32 H32B C32 C33 +BOND C33 H33A C33 H33B C33 H33C +IMPR C11 O11 C12 O12 +IMPR C21 O21 C22 O22 +IMPR C31 O31 C32 O32 + +IC C13 C12 C11 O11 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C11 O11 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C11 O11 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC O11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 O31 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 O31 C31 0.0000 0.00 180.00 0.00 0.0000 +IC C3 O31 C31 C32 0.0000 0.00 180.00 0.00 0.0000 +IC O31 C31 C32 C33 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 O21 0.0000 0.00 120.00 0.00 0.0000 !chirality not checked +IC C1 C2 O21 C21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O21 C21 C22 0.0000 0.00 180.00 0.00 0.0000 +IC O21 C21 C22 C23 0.0000 0.00 180.00 0.00 0.0000 +IC C12 O11 *C11 O12 0.0000 0.00 180.00 0.00 0.0000 +IC C22 O21 *C21 O22 0.0000 0.00 180.00 0.00 0.0000 +IC C32 O31 *C31 O32 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C13 *C12 H12A 0.0000 0.00 120.00 0.00 0.0000 +IC H13A C12 *C13 H13B 0.0000 0.00 120.00 0.00 0.0000 +IC H13A C12 *C13 H13C 0.0000 0.00 -120.00 0.00 0.0000 +IC H13A C13 C12 C11 0.0000 0.00 180.00 0.00 0.0000 +IC H12A C13 *C12 H12B 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 O11 *C1 H1A 0.0000 0.00 120.00 0.00 0.0000 +IC H1A O11 *C1 H1B 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H2A 0.0000 0.00 -120.00 0.00 0.0000 !chirality not checked +IC C23 C21 *C22 H22A 0.0000 0.00 120.00 0.00 0.0000 +IC H22A C21 *C22 H22B 0.0000 0.00 -120.00 0.00 0.0000 +IC C21 C22 C23 H23A 0.0000 0.00 180.00 0.00 0.0000 +IC H23A C22 *C23 H23B 0.0000 0.00 120.00 0.00 0.0000 +IC H23A C22 *C23 H23C 0.0000 0.00 -120.00 0.00 0.0000 +IC O31 C2 *C3 H3A 0.0000 0.00 120.00 0.00 0.0000 +IC H3A C2 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000 +IC C33 C31 *C32 H32A 0.0000 0.00 120.00 0.00 0.0000 +IC H32A C31 *C32 H32B 0.0000 0.00 -120.00 0.00 0.0000 +IC C31 C32 C33 H33A 0.0000 0.00 180.00 0.00 0.0000 +IC H33A C32 *C33 H33B 0.0000 0.00 120.00 0.00 0.0000 +IC H33A C32 *C33 H33C 0.0000 0.00 -120.00 0.00 0.0000 + +! TORSIONAL TEST RESIDUE; 1,2,3-TRIACETYL-GLYCEROL +RESI TAG 0.0 +GROUP +ATOM C12 CTL3 -0.31 ! H12C +ATOM H12A HAL3 0.09 ! | +ATOM H12B HAL3 0.09 ! H12A-C12-H12B +ATOM H12C HAL3 0.09 ! | +ATOM C11 CL 0.90 ! C11==O12 +ATOM O12 OBL -0.63 ! | +ATOM O11 OSL -0.49 ! O11 +ATOM C1 CTL2 0.08 ! | +ATOM H1A HAL2 0.09 ! H1A-C1-H1B +ATOM H1B HAL2 0.09 ! | +GROUP ! | +ATOM C2 CTL1 0.17 ! H2A-C2------O21 +ATOM H2A HAL1 0.09 ! | | +ATOM O21 OSL -0.49 ! | C21==O22 +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | H22A-C22-H22B +ATOM C22 CTL3 -0.31 ! | | +ATOM H22A HAL3 0.09 ! | H22C +ATOM H22B HAL3 0.09 ! | +ATOM H22C HAL3 0.09 ! | +GROUP ! | +ATOM C3 CTL2 0.08 ! H3A-C3-H3B +ATOM H3A HAL2 0.09 ! | +ATOM H3B HAL2 0.09 ! O31 +ATOM O31 OSL -0.49 ! | +ATOM C31 CL 0.90 ! C31==O32 +ATOM O32 OBL -0.63 ! | +ATOM C32 CTL3 -0.31 ! H32A-C32-H32B +ATOM H32A HAL3 0.09 ! | +ATOM H32B HAL3 0.09 ! H32C +ATOM H32C HAL3 0.09 +BOND C12 H12A C12 H12B C12 C11 C12 H12C +BOND C11 O12 C11 O11 O11 C1 +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 O21 C2 C3 +BOND O21 C21 C21 O22 C21 C22 +BOND C22 H22A C22 H22B C22 H22C +BOND C3 H3A C3 H3B C3 O31 +BOND O31 C31 C31 O32 C31 C32 +BOND C32 H32A C32 H32B C32 H32C +IMPR C11 O11 C12 O12 +IMPR C21 O21 C22 O22 +IMPR C31 O31 C32 O32 +IC C12 C11 O11 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C11 O11 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC O11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 O31 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 O31 C31 0.0000 0.00 180.00 0.00 0.0000 +IC C3 O31 C31 C32 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 O21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C2 O21 C21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O21 C21 O22 0.0000 0.00 180.00 0.00 0.0000 +IC C12 O11 *C11 O12 0.0000 0.00 180.00 0.00 0.0000 +IC C22 O21 *C21 O22 0.0000 0.00 180.00 0.00 0.0000 +IC C32 O31 *C31 O32 0.0000 0.00 180.00 0.00 0.0000 +IC H12A C11 *C12 H12B 0.0000 0.00 120.00 0.00 0.0000 +IC H12A C11 *C12 H12C 0.0000 0.00 -120.00 0.00 0.0000 +IC H12A C12 C11 O11 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O11 *C1 H1A 0.0000 0.00 120.00 0.00 0.0000 +IC H1A O11 *C1 H1B 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H2A 0.0000 0.00 -120.00 0.00 0.0000 +IC O21 C21 C22 H22A 0.0000 0.00 180.00 0.00 0.0000 +IC H22A C21 *C22 H22B 0.0000 0.00 120.00 0.00 0.0000 +IC H22A C21 *C22 H22C 0.0000 0.00 -120.00 0.00 0.0000 +IC O31 C2 *C3 H3A 0.0000 0.00 120.00 0.00 0.0000 +IC H3A C2 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000 +IC O31 C31 C32 H32A 0.0000 0.00 180.00 0.00 0.0000 +IC H32A C31 *C32 H32B 0.0000 0.00 120.00 0.00 0.0000 +IC H32A C31 *C32 H32C 0.0000 0.00 -120.00 0.00 0.0000 + +! FROM MINIMZED XTAL COORDS +!IC C32 C31 O31 C3 1.5156 109.33 178.36 117.24 1.4441 +!IC C31 O31 C3 C2 1.3293 117.24 -102.52 111.66 1.5549 +!IC O31 C3 C2 C1 1.4441 111.66 -171.91 112.15 1.5522 +!IC O31 C3 C2 O21 1.4441 111.66 68.49 109.29 1.4404 +!IC O21 C2 C1 O11 1.4404 107.89 175.79 112.12 1.4409 +!IC C2 C1 O11 C11 1.5522 112.12 78.56 116.08 1.3296 +!IC C1 O11 C11 C12 1.4409 116.08 -175.52 109.44 1.5122 +!IC C3 C2 O21 C21 1.5549 109.29 -141.43 117.03 1.3231 +!IC C2 O21 C21 C22 1.4404 117.03 -175.67 108.99 1.5150 +!IC C1 O11 C11 O12 1.4409 116.08 4.06 126.35 1.2169 +!IC C2 O21 C21 O22 1.4404 117.03 3.30 126.74 1.2152 +!IC C3 O31 C31 O32 1.4441 117.24 -1.76 126.59 1.2152 + +! TORSIONAL TEST RESIDUE; 1-PHOSPHO-2,3-DIACETYL-GLYCEROL +RESI PDAG -1.0 +GROUP ! H12 +ATOM P PL 1.50 ! | +ATOM O12 OHL -0.68 ! O12 +ATOM O13 O2L -0.82 ! | +ATOM O14 O2L -0.82 ! O14==P==O13 (-) +ATOM H12 HOL 0.42 ! | +ATOM O11 OSL -0.62 ! O11 +ATOM C1 CTL2 -0.16 ! | +ATOM H1A HAL2 0.09 ! H1A-C1-H1B +ATOM H1B HAL2 0.09 ! | +GROUP ! | +ATOM C2 CTL1 0.17 ! H2A-C2------O21 +ATOM H2A HAL1 0.09 ! | | +ATOM O21 OSL -0.49 ! | C21==O22 +ATOM C21 CL 0.90 ! | | +ATOM O22 OBL -0.63 ! | H22A-C22-H22B +ATOM C22 CTL3 -0.31 ! | | +ATOM H22A HAL3 0.09 ! | H22C +ATOM H22B HAL3 0.09 ! | +ATOM H22C HAL3 0.09 ! | +GROUP ! | +ATOM C3 CTL2 0.08 ! H3A-C3-H3B +ATOM H3A HAL2 0.09 ! | +ATOM H3B HAL2 0.09 ! O31 +ATOM O31 OSL -0.49 ! | +ATOM C31 CL 0.90 ! C31==O32 +ATOM O32 OBL -0.63 ! | +ATOM C32 CTL3 -0.31 ! H32A-C32-H32B +ATOM H32A HAL3 0.09 ! | +ATOM H32B HAL3 0.09 ! H32C +ATOM H32C HAL3 0.09 +BOND C1 O11 O11 P P O12 +BOND P O13 P O14 O12 H12 +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 O21 C2 C3 +BOND O21 C21 C21 O22 C21 C22 +BOND C22 H22A C22 H22B C22 H22C +BOND C3 H3A C3 H3B C3 O31 +BOND O31 C31 C31 O32 C31 C32 +BOND C32 H32A C32 H32B C32 H32C +IMPR C21 O21 C22 O22 +IMPR C31 O31 C32 O32 +IC O12 P O11 C1 1.5534 107.77 177.99 118.67 1.4319 +IC P O11 C1 C2 1.5809 118.67 -177.01 110.95 1.5485 +IC O11 C1 C2 C3 1.4319 110.95 168.57 109.90 1.5535 +IC C1 C2 C3 O31 1.5485 109.90 179.24 111.92 1.4405 +IC C2 C3 O31 C31 1.5535 111.92 -177.52 121.11 1.3324 +IC C3 O31 C31 O32 1.4405 121.11 177.32 124.63 1.2174 +IC C3 C1 *C2 O21 1.5535 109.90 119.64 107.92 1.4387 +IC C1 C2 O21 C21 1.5485 107.92 133.85 115.39 1.3121 +IC C2 O21 C21 C22 1.4387 115.39 -174.42 108.32 1.5100 +IC C2 O21 *C21 O22 2.3259 33.97 5.97 127.59 1.2160 +IC O12 O11 *P O13 1.5534 107.77 109.09 112.45 1.4702 +IC O12 O11 *P O14 1.5534 107.77 -114.50 112.21 1.4707 +IC C32 O31 *C31 O32 1.5136 113.93 -179.83 124.63 1.2174 +IC O11 P O12 H12 1.5809 107.77 154.24 99.52 0.9625 +IC C2 O11 *C1 H1A 1.5485 110.95 120.00 110.10 1.1157 +IC H1A O11 *C1 H1B 1.1157 110.10 119.98 110.49 1.1155 +IC C3 C1 *C2 H2A 1.5535 109.90 -117.75 107.18 1.1167 +IC O21 C21 C22 H22A 1.3121 108.32 -179.18 108.78 1.1100 +IC H22A C21 *C22 H22B 1.1100 108.78 120.25 109.46 1.1092 +IC H22A C21 *C22 H22C 1.1100 108.78 -119.58 108.78 1.1107 +IC O31 C2 *C3 H3A 1.4405 111.92 -121.32 105.65 1.1147 +IC H3A C2 *C3 H3B 1.1147 105.65 -117.00 106.26 1.1141 +IC O31 C31 C32 H32A 1.3324 113.93 -178.42 107.36 1.1105 +IC H32A C31 *C32 H32B 1.1105 107.36 118.14 110.80 1.1075 +IC H32A C31 *C32 H32C 1.1105 107.36 -118.10 110.64 1.1074 + +RESI MEEF 0.00 !1-methylethyl Ester +GROUP +ATOM C1 CTL3 -0.27 ! HA +ATOM HA HAL3 0.09 ! | +ATOM HB HAL3 0.09 ! HB ---C1---HC +ATOM HC HAL3 0.09 ! | +GROUP | HY +ATOM C2 CTL1 0.17 ! | | +ATOM HS HAL1 0.09 ! HS---C2---C3-HX +! | HZ +ATOM O21 OSL -0.49 ! O22 O21 +ATOM C21 CL 0.90 ! \\ / gamma2 +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | gamma3 +ATOM H2R HAL2 0.09 ! H2S---C22--H2R +ATOM H2S HAL2 0.09 ! | +GROUP ! +ATOM C23 CTL2 -0.18 ! | +ATOM H3R HAL2 0.09 ! H3S ---C23---H3R +ATOM H3S HAL2 0.09 ! | +GROUP +ATOM C24 CTL3 -0.27 ! | +ATOM H4R HAL3 0.09 ! H4R ---C24---H4R +ATOM H4S HAL3 0.09 ! | +ATOM H4T HAL3 0.09 ! H4T +GROUP +ATOM C3 CTL3 -0.27 +ATOM HX HAL3 0.09 +ATOM HY HAL3 0.09 +ATOM HZ HAL3 0.09 + +BOND C1 HA C1 HB C1 HC +BOND C1 C2 C2 HS +BOND C2 C3 C3 HX C3 HY C3 HZ +BOND O21 C2 C21 O21 +DOUBLE C21 O22 +BOND C22 C21 C22 H2R C22 H2S +BOND C23 C22 C23 H3R C23 H3S +BOND C24 C23 C24 H4R C24 H4S C24 H4T + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 O21 C21 1.5365 111.08 -65.43 120.28 1.3196 +IC C2 O21 C21 C22 1.4255 120.28 178.70 108.49 1.5291 +IC HA C2 *C1 HB 1.1097 111.19 119.53 110.02 1.1098 +IC HA C2 *C1 HC 1.1097 111.19 -120.56 110.17 1.1099 +IC HA C1 C2 O21 1.1097 111.19 67.73 111.08 1.4255 +IC O21 C1 *C2 C3 1.4255 111.08 -125.84 112.70 1.5370 +IC C3 C1 *C2 HS 1.5370 112.70 -117.64 107.22 1.1178 +IC C22 O21 *C21 O22 1.5291 108.49 -175.86 127.74 1.2156 +IC O21 C21 C22 C23 1.3196 108.49 64.37 112.77 1.5447 +IC C23 C21 *C22 H2R 1.5447 112.77 -122.06 108.01 1.1091 +IC H2R C21 *C22 H2S 1.1091 108.01 -116.86 107.18 1.1095 +IC C21 C22 C23 C24 1.5291 112.77 178.22 112.66 1.5298 +IC C24 C22 *C23 H3R 1.5298 112.66 -121.18 109.40 1.1152 +IC H3R C22 *C23 H3S 1.1152 109.40 -117.48 109.43 1.1152 +IC C22 C23 C24 H4R 1.5447 112.66 -60.85 110.50 1.1113 +IC H4R C23 *C24 H4S 1.1113 110.50 119.93 110.59 1.1117 +IC H4R C23 *C24 H4T 1.1113 110.50 -119.99 110.61 1.1114 +IC C1 C2 C3 HX 1.5365 112.70 176.80 110.22 1.1100 +IC HX C2 *C3 HY 1.1100 110.22 119.90 109.98 1.1099 +IC HX C2 *C3 HZ 1.1100 110.22 -120.70 111.26 1.1092 + +RESI ACTF 0.00 !Acetate Section of DPPC +GROUP +ATOM C1 CTL3 -0.27 ! H1Y +ATOM H1X HAL3 0.09 ! | +ATOM H1Y HAL3 0.09 ! H1X---C1---H1Z +ATOM H1Z HAL3 0.09 ! | +GROUP +ATOM C2 CTL2 -0.18 ! | +ATOM H2A HAL2 0.09 ! H2A---C2---H2B +ATOM H2B HAL2 0.09 ! | +GROUP +ATOM C3 CTL2 0.08 ! | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP +ATOM C34 CTL3 -0.27 ! | +ATOM H4X HAL3 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL3 0.09 ! | +ATOM H4Z HAL3 0.09 ! H4Z + +BOND C1 H1X C1 H1Y C1 H1Z +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 C3 HX C3 HY +BOND O31 C3 C31 O31 +DOUBLE C31 O32 +BOND C32 C31 C32 H2X C32 H2Y +BOND C33 C32 C33 H3X C33 H3Y +BOND C34 C33 C34 H4X C34 H4Y C34 H4Z + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 O31 1.5330 113.63 180.00 109.20 1.4379 +IC C2 C3 O31 C31 1.5348 109.20 -180.00 114.10 1.3342 +IC H1X C2 *C1 H1Y 1.1114 110.51 119.92 110.51 1.1114 +IC H1X C2 *C1 H1Z 1.1114 110.51 -120.04 110.59 1.1113 +IC H1X C1 C2 C3 1.1114 110.51 -59.96 113.63 1.5348 +IC C3 C1 *C2 H2A 1.5348 113.63 -121.50 109.10 1.1143 +IC H2A C1 *C2 H2B 1.1143 109.10 -117.00 109.10 1.1143 +IC O31 C2 *C3 HX 1.4379 109.20 -120.98 108.95 1.1158 +IC HX C2 *C3 HY 1.1158 108.95 -118.04 108.95 1.1158 +IC C3 O31 C31 C32 1.4379 114.10 180.00 109.39 1.5307 +IC C32 O31 *C31 O32 1.5307 109.39 -180.00 125.50 1.2173 +IC O31 C31 C32 C33 1.3342 109.39 -180.00 111.93 1.5449 +IC C33 C31 *C32 H2X 1.5449 111.93 -121.02 108.43 1.1098 +IC H2X C31 *C32 H2Y 1.1098 108.43 -117.96 108.43 1.1098 +IC C31 C32 C33 C34 1.5307 111.93 180.00 113.31 1.5318 +IC C34 C32 *C33 H3X 1.5318 113.31 -121.65 109.15 1.1152 +IC H3X C32 *C33 H3Y 1.1152 109.15 -116.69 109.15 1.1152 +IC C32 C33 C34 H4X 1.5449 113.31 60.14 110.69 1.1115 +IC H4X C33 *C34 H4Y 1.1115 110.69 -120.28 110.69 1.1115 +IC H4X C33 *C34 H4Z 1.1115 110.69 119.86 110.45 1.1119 + +RESI PGHG -1.00 !Phosphate-Glycerol section of DPPC + +GROUP ! +ATOM C11 CTL3 -0.08 ! H11C +ATOM H11A HAL3 0.06 ! | +ATOM H11B HAL3 0.06 ! H11A--C11---H11B +ATOM H11C HAL3 0.06 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL2 -0.18 ! HS---C2 -- HR +ATOM HS HAL2 0.09 ! | +ATOM HR HAL2 0.09 ! | +GROUP ! | +ATOM C3 CTL3 -0.27 ! | +ATOM HX HAL3 0.09 ! HX---C3---HY +ATOM HY HAL3 0.09 ! | +ATOM HZ HAL3 0.09 ! HZ + +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 HR +BOND C3 HX C3 HY C3 HZ +BOND C11 H11A C11 H11B C11 O12 C11 H11C +BOND O12 P P O11 P O13 P O14 + + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C11 O12 P O11 1.4261 118.43 63.96 101.79 1.5891 +IC O12 P O11 C1 1.5925 101.79 63.93 121.00 1.4273 +IC H11A O12 *C11 H11B 1.1137 111.32 121.88 111.25 1.1146 +IC H11A O12 *C11 H11C 1.1137 111.32 -119.15 109.29 1.1109 +IC H11A C11 O12 P 1.1137 111.32 -63.03 118.43 1.5925 +IC O11 O12 *P O13 1.5891 101.79 115.15 108.73 1.4787 +IC O11 O12 *P O14 1.5891 101.79 -115.03 108.93 1.4790 +IC P O11 C1 C2 1.5891 121.00 103.88 110.10 1.5375 +IC C2 O11 *C1 HA 1.5375 110.10 -122.13 113.04 1.1177 +IC HA O11 *C1 HB 1.1177 113.04 -118.84 108.60 1.1119 +IC O11 C1 C2 C3 1.4273 110.10 178.10 113.89 1.5312 +IC C3 C1 *C2 HS 1.5312 113.89 -121.65 108.86 1.1130 +IC HS C1 *C2 HR 1.1130 108.86 -116.98 108.75 1.1135 +IC C1 C2 C3 HX 1.5375 113.89 59.92 110.21 1.1109 +IC HX C2 *C3 HY 1.1109 110.21 -120.00 110.33 1.1107 +IC HX C2 *C3 HZ 1.1109 110.21 119.92 110.29 1.1107 + +RESI GH2F 0.00 ! Glycerol section of DPPC +GROUP +ATOM C1 CTL3 -0.27 ! HC +ATOM HA HAL3 0.09 ! | +ATOM HB HAL3 0.09 ! HA---C1---HB +ATOM HC HAL3 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP +ATOM C23 CTL3 -0.27 ! | | +ATOM H3R HAL3 0.09 ! H3R ---C23---H3S +ATOM H3S HAL3 0.09 ! | | +ATOM H3T HAL3 0.09 ! H3T +GROUP ! +ATOM C3 CTL2 0.08 ! | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | +GROUP ! +ATOM C33 CTL3 -0.27 ! | +ATOM H3X HAL3 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL3 0.09 ! | +ATOM H3Z HAL3 0.09 ! H3Z + +BOND C1 HA C1 HB C1 C2 C1 HC +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 H3T +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 H3Z + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 O21 C21 1.5388 108.50 85.09 115.62 1.3282 +IC C2 O21 C21 C22 1.4372 115.62 -179.95 109.02 1.5363 +IC HA C2 *C1 HB 1.1104 110.51 120.01 110.21 1.1102 +IC HA C2 *C1 HC 1.1104 110.51 -120.45 110.59 1.1109 +IC HA C1 C2 C3 1.1104 110.51 -61.94 111.38 1.5506 +IC C3 C1 *C2 O21 1.5506 111.38 120.60 108.50 1.4372 +IC C3 C1 *C2 HS 1.5506 111.38 -117.82 108.87 1.1185 +IC C22 O21 *C21 O22 1.5363 109.02 -179.22 126.14 1.2175 +IC O21 C21 C22 C23 1.3282 109.02 -179.88 112.42 1.5447 +IC C23 C21 *C22 H2R 1.5447 112.42 121.29 108.09 1.1104 +IC H2R C21 *C22 H2S 1.1104 108.09 117.40 108.10 1.1104 +IC C21 C22 C23 H3R 1.5363 112.42 -59.89 110.66 1.1120 +IC H3R C22 *C23 H3S 1.1120 110.66 119.77 110.67 1.1120 +IC H3R C22 *C23 H3T 1.1120 110.66 -120.11 110.58 1.1108 +IC C1 C2 C3 O31 1.5388 111.38 -171.89 111.04 1.4434 +IC O31 C2 *C3 HX 1.4434 111.04 -122.29 108.59 1.1149 +IC HX C2 *C3 HY 1.1149 108.59 -117.06 107.86 1.1146 +IC C2 C3 O31 C31 1.5506 111.04 -179.26 114.11 1.3334 +IC C3 O31 C31 C32 1.4434 114.11 -179.87 109.31 1.5355 +IC C32 O31 *C31 O32 1.5355 109.31 179.41 125.49 1.2173 +IC O31 C31 C32 C33 1.3334 109.31 -179.58 112.45 1.5447 +IC C33 C31 *C32 H2X 1.5447 112.45 -121.29 108.07 1.1104 +IC H2X C31 *C32 H2Y 1.1104 108.07 -117.37 108.11 1.1103 +IC C31 C32 C33 H3X 1.5355 112.45 59.84 110.69 1.1120 +IC H3X C32 *C33 H3Y 1.1120 110.69 120.11 110.57 1.1108 +IC H3X C32 *C33 H3Z 1.1120 110.69 -119.81 110.67 1.1120 + +RESI NDEC 0.00 ! n-decane +GROUP +ATOM C1 CTL3 -0.27 ! H1X H2X H3X H4X H9X H10X +ATOM H1X HAL3 0.09 ! \ | | | | / +ATOM H1Y HAL3 0.09 ! H1Z-C1--C2--C3--C4--...--C9--C10-H10Z +ATOM H1Z HAL3 0.09 ! / | | | | \ +GROUP ! H1Y H2Y H3Y H4Y H9Y H10Y +ATOM C2 CTL2 -0.18 +ATOM H2X HAL2 0.09 +ATOM H2Y HAL2 0.09 +GROUP +ATOM C3 CTL2 -0.18 +ATOM H3X HAL2 0.09 +ATOM H3Y HAL2 0.09 +GROUP +ATOM C4 CTL2 -0.18 +ATOM H4X HAL2 0.09 +ATOM H4Y HAL2 0.09 +GROUP +ATOM C5 CTL2 -0.18 +ATOM H5X HAL2 0.09 +ATOM H5Y HAL2 0.09 +GROUP +ATOM C6 CTL2 -0.18 +ATOM H6X HAL2 0.09 +ATOM H6Y HAL2 0.09 +GROUP +ATOM C7 CTL2 -0.18 +ATOM H7X HAL2 0.09 +ATOM H7Y HAL2 0.09 +GROUP +ATOM C8 CTL2 -0.18 +ATOM H8X HAL2 0.09 +ATOM H8Y HAL2 0.09 +GROUP +ATOM C9 CTL2 -0.18 +ATOM H9X HAL2 0.09 +ATOM H9Y HAL2 0.09 +GROUP +ATOM C10 CTL3 -0.27 +ATOM H10X HAL3 0.09 +ATOM H10Y HAL3 0.09 +ATOM H10Z HAL3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C7 +BOND C7 C8 C8 C9 C9 C10 +BOND C1 H1X C1 H1Y C1 H1Z C2 H2X C2 H2Y +BOND C3 H3X C3 H3Y C4 H4X C4 H4Y +BOND C5 H5X C5 H5Y C6 H6X C6 H6Y +BOND C7 H7X C7 H7Y C8 H8X C8 H8Y +BOND C9 H9X C9 H9Y C10 H10X C10 H10Y C10 H10Z + +! work - taken from the tail of dopc +IC C1 C3 *C2 H2X 1.5309 113.30 -121.68 108.77 1.1141 +IC H2X C3 *C2 H2Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C3 C2 C1 H1X 1.5340 113.30 -59.94 110.46 1.1113 +IC H1X C2 *C1 H1Y 1.1113 110.46 119.86 110.45 1.1113 +IC H1X C2 *C1 H1Z 1.1113 110.46 -120.06 110.61 1.1112 +IC C1 C2 C3 C4 1.5393 112.41 -178.89 112.60 1.5347 +IC C4 C2 *C3 H3X 1.5347 112.60 -121.37 109.10 1.1131 +IC H3X C2 *C3 H3Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C2 C3 C4 C5 1.5393 112.41 -178.89 112.60 1.5347 +IC C5 C3 *C4 H4X 1.5347 112.60 -121.37 109.10 1.1131 +IC H4X C3 *C4 H4Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C3 C4 C5 C6 1.5393 112.41 -178.89 112.60 1.5347 +IC C6 C4 *C5 H5X 1.5347 112.60 -121.37 109.10 1.1131 +IC H5X C4 *C5 H5Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C4 C5 C6 C7 1.5393 112.41 -178.89 112.60 1.5347 +IC C7 C5 *C6 H6X 1.5347 112.60 -121.37 109.10 1.1131 +IC H6X C5 *C6 H6Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C5 C6 C7 C8 1.5393 112.41 -178.89 112.60 1.5347 +IC C8 C6 *C7 H7X 1.5347 112.60 -121.37 109.10 1.1131 +IC H7X C6 *C7 H7Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C6 C7 C8 C9 1.5393 112.41 -178.89 112.60 1.5347 +IC C9 C7 *C8 H8X 1.5347 112.60 -121.37 109.10 1.1131 +IC H8X C7 *C8 H8Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C7 C8 C9 C10 1.5355 112.60 179.88 112.66 1.5347 +IC C10 C8 *C9 H9X 1.5347 112.66 -121.27 109.06 1.1132 +IC H9X C8 *C9 H9Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C8 C9 C10 H10X 1.5340 113.30 -59.94 110.46 1.1113 +IC H10X C9 *C10 H10Y 1.1113 110.46 119.86 110.45 1.1113 +IC H10X C9 *C10 H10Z 1.1113 110.46 -120.06 110.61 1.1112 + + +RESI NHEX 0.00 ! n-hexadecane +GROUP +ATOM C1 CTL3 -0.27 ! H1X H2X H3X H4X H15X H16X +ATOM H1X HAL3 0.09 ! \ | | | | / +ATOM H1Y HAL3 0.09 ! H1Z-C1--C2--C3--C4--...--C15--C16-H16Z +ATOM H1Z HAL3 0.09 ! / | | | | \ +GROUP ! H1Y H2Y H3Y H4Y H15Y H16Y +ATOM C2 CTL2 -0.18 +ATOM H2X HAL2 0.09 +ATOM H2Y HAL2 0.09 +GROUP +ATOM C3 CTL2 -0.18 +ATOM H3X HAL2 0.09 +ATOM H3Y HAL2 0.09 +GROUP +ATOM C4 CTL2 -0.18 +ATOM H4X HAL2 0.09 +ATOM H4Y HAL2 0.09 +GROUP +ATOM C5 CTL2 -0.18 +ATOM H5X HAL2 0.09 +ATOM H5Y HAL2 0.09 +GROUP +ATOM C6 CTL2 -0.18 +ATOM H6X HAL2 0.09 +ATOM H6Y HAL2 0.09 +GROUP +ATOM C7 CTL2 -0.18 +ATOM H7X HAL2 0.09 +ATOM H7Y HAL2 0.09 +GROUP +ATOM C8 CTL2 -0.18 +ATOM H8X HAL2 0.09 +ATOM H8Y HAL2 0.09 +GROUP +ATOM C9 CTL2 -0.18 +ATOM H9X HAL2 0.09 +ATOM H9Y HAL2 0.09 +GROUP +ATOM C10 CTL2 -0.18 +ATOM H10X HAL2 0.09 +ATOM H10Y HAL2 0.09 +GROUP +ATOM C11 CTL2 -0.18 +ATOM H11X HAL2 0.09 +ATOM H11Y HAL2 0.09 +GROUP +ATOM C12 CTL2 -0.18 +ATOM H12X HAL2 0.09 +ATOM H12Y HAL2 0.09 +GROUP +ATOM C13 CTL2 -0.18 +ATOM H13X HAL2 0.09 +ATOM H13Y HAL2 0.09 +GROUP +ATOM C14 CTL2 -0.18 +ATOM H14X HAL2 0.09 +ATOM H14Y HAL2 0.09 +GROUP +ATOM C15 CTL2 -0.18 +ATOM H15X HAL2 0.09 +ATOM H15Y HAL2 0.09 +GROUP +ATOM C16 CTL3 -0.27 +ATOM H16X HAL3 0.09 +ATOM H16Y HAL3 0.09 +ATOM H16Z HAL3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C7 +BOND C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 C12 C13 +BOND C13 C14 C14 C15 C15 C16 +BOND C1 H1X C1 H1Y C1 H1Z C2 H2X C2 H2Y +BOND C3 H3X C3 H3Y C4 H4X C4 H4Y +BOND C5 H5X C5 H5Y C6 H6X C6 H6Y +BOND C7 H7X C7 H7Y C8 H8X C8 H8Y +BOND C9 H9X C9 H9Y C10 H10X C10 H10Y +BOND C11 H11X C11 H11Y C12 H12X C12 H12Y +BOND C13 H13X C13 H13Y C14 H14X C14 H14Y +BOND C15 H15X C15 H15Y C16 H16X C16 H16Y C16 H16Z + +! work - taken from the tail of dopc +IC C1 C3 *C2 H2X 1.5309 113.30 -121.68 108.77 1.1141 +IC H2X C3 *C2 H2Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C3 C2 C1 H1X 1.5340 113.30 -59.94 110.46 1.1113 +IC H1X C2 *C1 H1Y 1.1113 110.46 119.86 110.45 1.1113 +IC H1X C2 *C1 H1Z 1.1113 110.46 -120.06 110.61 1.1112 +IC C1 C2 C3 C4 1.5393 112.41 -178.89 112.60 1.5347 +IC C4 C2 *C3 H3X 1.5347 112.60 -121.37 109.10 1.1131 +IC H3X C2 *C3 H3Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C2 C3 C4 C5 1.5393 112.41 -178.89 112.60 1.5347 +IC C5 C3 *C4 H4X 1.5347 112.60 -121.37 109.10 1.1131 +IC H4X C3 *C4 H4Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C3 C4 C5 C6 1.5393 112.41 -178.89 112.60 1.5347 +IC C6 C4 *C5 H5X 1.5347 112.60 -121.37 109.10 1.1131 +IC H5X C4 *C5 H5Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C4 C5 C6 C7 1.5393 112.41 -178.89 112.60 1.5347 +IC C7 C5 *C6 H6X 1.5347 112.60 -121.37 109.10 1.1131 +IC H6X C5 *C6 H6Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C5 C6 C7 C8 1.5393 112.41 -178.89 112.60 1.5347 +IC C8 C6 *C7 H7X 1.5347 112.60 -121.37 109.10 1.1131 +IC H7X C6 *C7 H7Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C6 C7 C8 C9 1.5393 112.41 -178.89 112.60 1.5347 +IC C9 C7 *C8 H8X 1.5347 112.60 -121.37 109.10 1.1131 +IC H8X C7 *C8 H8Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C7 C8 C9 C10 1.5393 112.41 -178.89 112.60 1.5347 +IC C10 C8 *C9 H9X 1.5347 112.60 -121.37 109.10 1.1131 +IC H9X C8 *C9 H9Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C8 C9 C10 C11 1.5355 112.60 179.88 112.66 1.5347 +IC C11 C9 *C10 H10X 1.5347 112.66 -121.27 109.06 1.1132 +IC H10X C9 *C10 H10Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C9 C10 C11 C12 1.5347 112.66 -179.12 112.61 1.5348 +IC C12 C10 *C11 H11X 1.5348 112.61 -121.34 109.09 1.1132 +IC H11X C10 *C11 H11Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C10 C11 C12 C13 1.5347 112.61 179.83 112.71 1.5340 +IC C13 C11 *C12 H12X 1.5340 112.71 -121.28 109.10 1.1132 +IC H12X C11 *C12 H12Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C11 C12 C13 C14 1.5347 112.61 179.83 112.71 1.5340 +IC C14 C12 *C13 H13X 1.5340 112.71 -121.28 109.10 1.1132 +IC H13X C12 *C13 H13Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C12 C13 C14 C15 1.5347 112.61 179.83 112.71 1.5340 +IC C15 C13 *C14 H14X 1.5340 112.71 -121.28 109.10 1.1132 +IC H14X C13 *C14 H14Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C13 C14 C15 C16 1.5348 112.71 -179.67 113.30 1.5309 +IC C16 C14 *C15 H15X 1.5309 113.30 -121.68 108.77 1.1141 +IC H15X C14 *C15 H15Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C14 C15 C16 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C15 *C16 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C15 *C16 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI EPEN 0.00 ! ethylpentane +GROUP +ATOM C1 CTL3 -0.27 ! H1X H2X H3X H4X H5X +ATOM H1X HAL3 0.09 ! \ | | | / +ATOM H1Y HAL3 0.09 ! H1Z-C1--C2--C3--C4--C5-H5Z +ATOM H1Z HAL3 0.09 ! / | | | \ +GROUP ! H1Y H2Y | H4Y H5Y +ATOM C2 CTL2 -0.18 ! | +ATOM H2X HAL2 0.09 ! H6X-C6-H6Y +ATOM H2Y HAL2 0.09 ! | +GROUP ! H7X-C7-H7Y +ATOM C3 CTL1 -0.09 ! | +ATOM H3X HAL1 0.09 ! H7Z +GROUP +ATOM C4 CTL2 -0.18 +ATOM H4X HAL2 0.09 +ATOM H4Y HAL2 0.09 +GROUP +ATOM C5 CTL3 -0.27 +ATOM H5X HAL3 0.09 +ATOM H5Y HAL3 0.09 +ATOM H5Z HAL3 0.09 +GROUP +ATOM C6 CTL2 -0.18 +ATOM H6X HAL2 0.09 +ATOM H6Y HAL2 0.09 +GROUP +ATOM C7 CTL3 -0.27 +ATOM H7X HAL3 0.09 +ATOM H7Y HAL3 0.09 +ATOM H7Z HAL3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C3 C6 C4 C5 C6 C7 +BOND C1 H1X C1 H1Y C1 H1Z C2 H2X C2 H2Y +BOND C3 H3X C4 H4X C4 H4Y C5 H5X C5 H5Y C5 H5Z +BOND C6 H6X C6 H6Y C7 H7X C7 H7Y C7 H7Z + +! work - taken from the tail of dopc +IC C1 C3 *C2 H2X 1.5309 113.30 -121.68 108.77 1.1141 +IC H2X C3 *C2 H2Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C3 C2 C1 H1X 1.5340 113.30 -59.94 110.46 1.1113 +IC H1X C2 *C1 H1Y 1.1113 110.46 119.86 110.45 1.1113 +IC H1X C2 *C1 H1Z 1.1113 110.46 -120.06 110.61 1.1112 +IC C1 C2 C3 C4 1.5393 112.41 -178.89 112.60 1.5347 +IC C4 C2 *C3 H3X 1.5347 112.60 -121.37 109.10 1.1131 +IC H3X C2 *C3 C6 1.1131 109.10 -117.41 109.08 1.5347 +IC C2 C3 C4 C5 1.5393 112.41 -178.89 112.60 1.5347 +IC C5 C3 *C4 H4X 1.5347 112.60 -121.37 109.10 1.1131 +IC H4X C3 *C4 H4Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C5 C3 *C4 H4X 1.5309 113.30 -121.68 108.77 1.1141 +IC H4X C3 *C4 H4Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C3 C4 C5 H5X 1.5340 113.30 -59.94 110.46 1.1113 +IC H5X C4 *C5 H5Y 1.1113 110.46 119.86 110.45 1.1113 +IC H5X C4 *C5 H5Z 1.1113 110.46 -120.06 110.61 1.1112 +IC C7 C3 *C6 H6X 1.5309 113.30 -121.68 108.77 1.1141 +IC H6X C3 *C6 H6Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C3 C6 C7 H7X 1.5340 113.30 -59.94 110.46 1.1113 +IC H7X C6 *C7 H7Y 1.1113 110.46 119.86 110.45 1.1113 +IC H7X C6 *C7 H7Z 1.1113 110.46 -120.06 110.61 1.1112 +IC C2 C3 C6 C7 1.5340 113.30 90.00 108.77 1.5340 +IC C3 C6 C7 H7X 1.5340 113.30 -59.94 110.46 1.1113 + +RESI TETD 0.00 ! tetradecane +GROUP +ATOM C1 CTL3 -0.27 ! H1X H2X H3X H4X H14X H14X +ATOM H1X HAL3 0.09 ! \ | | | | / +ATOM H1Y HAL3 0.09 ! H1Z-C1--C2--C3--C4--...--C14--C14-H14Z +ATOM H1Z HAL3 0.09 ! / | | | | \ +GROUP ! H1Y H2Y H3Y H4Y H14Y H14Y +ATOM C2 CTL2 -0.18 +ATOM H2X HAL2 0.09 +ATOM H2Y HAL2 0.09 +GROUP +ATOM C3 CTL2 -0.18 +ATOM H3X HAL2 0.09 +ATOM H3Y HAL2 0.09 +GROUP +ATOM C4 CTL2 -0.18 +ATOM H4X HAL2 0.09 +ATOM H4Y HAL2 0.09 +GROUP +ATOM C5 CTL2 -0.18 +ATOM H5X HAL2 0.09 +ATOM H5Y HAL2 0.09 +GROUP +ATOM C6 CTL2 -0.18 +ATOM H6X HAL2 0.09 +ATOM H6Y HAL2 0.09 +GROUP +ATOM C7 CTL2 -0.18 +ATOM H7X HAL2 0.09 +ATOM H7Y HAL2 0.09 +GROUP +ATOM C8 CTL2 -0.18 +ATOM H8X HAL2 0.09 +ATOM H8Y HAL2 0.09 +GROUP +ATOM C9 CTL2 -0.18 +ATOM H9X HAL2 0.09 +ATOM H9Y HAL2 0.09 +GROUP +ATOM C10 CTL2 -0.18 +ATOM H10X HAL2 0.09 +ATOM H10Y HAL2 0.09 +GROUP +ATOM C11 CTL2 -0.18 +ATOM H11X HAL2 0.09 +ATOM H11Y HAL2 0.09 +GROUP +ATOM C12 CTL2 -0.18 +ATOM H12X HAL2 0.09 +ATOM H12Y HAL2 0.09 +GROUP +ATOM C13 CTL2 -0.18 +ATOM H13X HAL2 0.09 +ATOM H13Y HAL2 0.09 +GROUP +ATOM C14 CTL3 -0.27 +ATOM H14X HAL3 0.09 +ATOM H14Y HAL3 0.09 +ATOM H14Z HAL3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C7 +BOND C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 C12 C13 +BOND C13 C14 +BOND C1 H1X C1 H1Y C1 H1Z C2 H2X C2 H2Y +BOND C3 H3X C3 H3Y C4 H4X C4 H4Y +BOND C5 H5X C5 H5Y C6 H6X C6 H6Y +BOND C7 H7X C7 H7Y C8 H8X C8 H8Y +BOND C9 H9X C9 H9Y C10 H10X C10 H10Y +BOND C11 H11X C11 H11Y C12 H12X C12 H12Y +BOND C13 H13X C13 H13Y C14 H14X C14 H14Y C14 H14Z + +IC C1 C3 *C2 H2X 1.5309 113.30 -121.68 108.77 1.1141 +IC H2X C3 *C2 H2Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C3 C2 C1 H1X 1.5340 113.30 -59.94 110.46 1.1113 +IC H1X C2 *C1 H1Y 1.1113 110.46 119.86 110.45 1.1113 +IC H1X C2 *C1 H1Z 1.1113 110.46 -120.06 110.61 1.1112 +IC C1 C2 C3 C4 1.5393 112.41 -178.89 112.60 1.5347 +IC C4 C2 *C3 H3X 1.5347 112.60 -121.37 109.10 1.1131 +IC H3X C2 *C3 H3Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C2 C3 C4 C5 1.5393 112.41 -178.89 112.60 1.5347 +IC C5 C3 *C4 H4X 1.5347 112.60 -121.37 109.10 1.1131 +IC H4X C3 *C4 H4Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C3 C4 C5 C6 1.5393 112.41 -178.89 112.60 1.5347 +IC C6 C4 *C5 H5X 1.5347 112.60 -121.37 109.10 1.1131 +IC H5X C4 *C5 H5Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C4 C5 C6 C7 1.5393 112.41 -178.89 112.60 1.5347 +IC C7 C5 *C6 H6X 1.5347 112.60 -121.37 109.10 1.1131 +IC H6X C5 *C6 H6Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C5 C6 C7 C8 1.5393 112.41 -178.89 112.60 1.5347 +IC C8 C6 *C7 H7X 1.5347 112.60 -121.37 109.10 1.1131 +IC H7X C6 *C7 H7Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C6 C7 C8 C9 1.5393 112.41 -178.89 112.60 1.5347 +IC C9 C7 *C8 H8X 1.5347 112.60 -121.37 109.10 1.1131 +IC H8X C7 *C8 H8Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C7 C8 C9 C10 1.5393 112.41 -178.89 112.60 1.5347 +IC C10 C8 *C9 H9X 1.5347 112.60 -121.37 109.10 1.1131 +IC H9X C8 *C9 H9Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C8 C9 C10 C11 1.5355 112.60 179.88 112.66 1.5347 +IC C11 C9 *C10 H10X 1.5347 112.66 -121.27 109.06 1.1132 +IC H10X C9 *C10 H10Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C9 C10 C11 C12 1.5347 112.66 -179.12 112.61 1.5348 +IC C12 C10 *C11 H11X 1.5348 112.61 -121.34 109.09 1.1132 +IC H11X C10 *C11 H11Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C10 C11 C12 C13 1.5347 112.61 179.83 112.71 1.5340 +IC C13 C11 *C12 H12X 1.5340 112.71 -121.28 109.10 1.1132 +IC H12X C11 *C12 H12Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C11 C12 C13 C14 1.5348 112.71 -179.67 113.30 1.5309 +IC C14 C12 *C13 H13X 1.5309 113.30 -121.68 108.77 1.1141 +IC H13X C12 *C13 H13Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C12 C13 C14 H14X 1.5340 113.30 -59.94 110.46 1.1113 +IC H14X C13 *C14 H14Y 1.1113 110.46 119.86 110.45 1.1113 +IC H14X C13 *C14 H14Z 1.1113 110.46 -120.06 110.61 1.1112 + +end + +return diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_prot.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_prot.str new file mode 100644 index 00000000..04b73530 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_prot.str @@ -0,0 +1,1191 @@ +* Topology and parameters for lipid tail linkers to cysteine and glycine, +* for example, palmitoylation, maristoylation, fernasylation, geranylation +* + +read rtf card append +* Lipid-modified protein residues +* +36 1 + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +!DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI CYSP 0.00 ! Cystein-Palmitate +GROUP ! +ATOM N NH1 -0.47 ! +ATOM HN H 0.31 ! +ATOM CA CT1 0.07 ! +ATOM HA HB1 0.09 ! | +GROUP ! HN-N +ATOM C C 0.51 ! | HB1 +ATOM O O -0.51 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB CT2 -0.05 ! | | | +ATOM HB1 HA2 0.09 ! | HB2 | +ATOM HB2 HA2 0.09 ! O=C | +ATOM SG S -0.34 ! | | +ATOM C1 CL 0.63 ! O1=C1 +ATOM O1 OBL -0.52 ! | +ATOM C2 CTL2 -0.08 ! H2A-C2-H2B +ATOM H2A HAL2 0.09 ! | +ATOM H2B HAL2 0.09 ! | +GROUP ! | +ATOM C3 CTL2 -0.18 ! H3A-C3-H3B +ATOM H3A HAL2 0.09 ! | +ATOM H3B HAL2 0.09 ! | +GROUP ! | +ATOM C4 CTL2 -0.18 ! H4A-C4-H4B +ATOM H4A HAL2 0.09 ! | +ATOM H4B HAL2 0.09 ! | +GROUP ! | +ATOM C5 CTL2 -0.18 ! H5A-C5-H5B +ATOM H5A HAL2 0.09 ! | +ATOM H5B HAL2 0.09 ! | +GROUP ! | +ATOM C6 CTL2 -0.18 ! H6A-C6-H6B +ATOM H6A HAL2 0.09 ! | +ATOM H6B HAL2 0.09 ! | +GROUP ! | +ATOM C7 CTL2 -0.18 ! H7A-C7-H7B +ATOM H7A HAL2 0.09 ! | +ATOM H7B HAL2 0.09 ! | +GROUP ! | +ATOM C8 CTL2 -0.18 ! H8A-C8-H8B +ATOM H8A HAL2 0.09 ! | +ATOM H8B HAL2 0.09 ! | +GROUP ! | +ATOM C9 CTL2 -0.18 ! H9A-C9-H9B +ATOM H9A HAL2 0.09 ! | +ATOM H9B HAL2 0.09 ! | +GROUP ! | +ATOM C10 CTL2 -0.18 ! H10A-C10-H10B +ATOM H10A HAL2 0.09 ! | +ATOM H10B HAL2 0.09 ! | +GROUP ! | +ATOM C11 CTL2 -0.18 ! H11A-C11-H11B +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! | +GROUP ! | +ATOM C12 CTL2 -0.18 ! H12A-C12-H12B +ATOM H12A HAL2 0.09 ! | +ATOM H12B HAL2 0.09 ! | +GROUP ! | +ATOM C13 CTL2 -0.18 ! H13A-C13-H13B +ATOM H13A HAL2 0.09 ! | +ATOM H13B HAL2 0.09 ! | +GROUP ! | +ATOM C14 CTL2 -0.18 ! H14A-C14-H14B +ATOM H14A HAL2 0.09 ! | +ATOM H14B HAL2 0.09 ! | +GROUP ! | +ATOM C15 CTL2 -0.18 ! H15A-C15-H15B +ATOM H15A HAL2 0.09 ! | +ATOM H15B HAL2 0.09 ! | +GROUP ! | +ATOM C16 CTL3 -0.27 ! H16A-C16-H16B +ATOM H16A HAL3 0.09 ! | +ATOM H16B HAL3 0.09 ! H16C +ATOM H16C HAL3 0.09 ! + +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG C1 +DOUBLE O C + +DOUBLE C1 O1 +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 C3 H3A C3 H3B +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5A C5 H5B +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7A C7 H7B +BOND C7 C8 C8 H8A C8 H8B +BOND C8 C9 C9 H9A C9 H9B +BOND C9 C10 C10 H10A C10 H10B +BOND C10 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 C13 C13 H13A C13 H13B +BOND C13 C14 C14 H14A C14 H14B +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B C16 H16C +IMPR C1 O1 SG C2 +IMPR N -C CA HN C CA +N O + +DONOR HN N +ACCEPTOR O C +ACCEPTOR O1 C1 + +IC -C CA *N HN 1.3479 123.93 180.00 114.77 0.9982 +IC -C N CA C 1.3479 123.93 180.00 105.89 1.5202 +IC N CA C +N 1.4533 105.89 180.00 118.30 1.3498 +IC +N CA *C O 1.3498 118.30 180.00 120.59 1.2306 +IC CA C +N +CA 1.5202 118.30 180.00 124.50 1.4548 +IC HN N CA CB 0.9674 117.70 -36.00 110.95 1.5003 +IC CB N *CA C 1.5003 110.95 128.76 106.38 1.5291 +IC CB N *CA HA 1.5003 110.95 -121.31 107.62 1.1060 +IC N CA CB SG 1.3945 110.95 -174.62 111.79 1.8692 +IC SG CA *CB HB1 1.8692 111.79 114.87 107.79 1.1406 +IC SG CA *CB HB2 1.8692 111.79 -128.20 109.45 1.0949 +IC N CA C O 1.3945 106.38 5.30 121.98 1.2956 +IC CA CB SG C1 1.5003 111.79 -178.37 107.64 1.8012 +IC CB SG C1 C2 1.8692 107.64 158.80 115.77 1.5434 +IC C2 SG *C1 O1 1.5434 115.77 -174.68 119.62 1.2281 +IC SG C1 C2 C3 1.8012 115.77 152.55 111.56 1.5614 +IC C3 C1 *C2 H2A 1.5614 111.56 -126.88 116.60 1.0567 +IC H2A C1 *C2 H2B 1.0567 116.60 -120.46 107.56 1.0927 +IC C1 C2 C3 C4 1.5434 111.56 178.17 112.38 1.5543 +IC C4 C2 *C3 H3A 1.5543 112.38 -115.58 110.36 1.0691 +IC H3A C2 *C3 H3B 1.0691 110.36 -116.74 109.97 1.1344 +IC C2 C3 C4 C5 1.5614 112.38 174.26 114.93 1.5290 +IC C5 C3 *C4 H4A 1.5290 114.93 -117.82 107.19 1.0636 +IC H4A C3 *C4 H4B 1.0636 107.19 -118.11 109.41 1.1180 +IC C3 C4 C5 C6 1.5543 114.93 139.45 116.26 1.5437 +IC C6 C4 *C5 H5A 1.5437 116.26 -115.47 116.05 1.1088 +IC H5A C4 *C5 H5B 1.1088 116.05 -122.13 108.08 1.1320 +IC C4 C5 C6 C7 1.5290 116.26 159.28 113.90 1.5449 +IC C7 C5 *C6 H6A 1.5449 113.90 -120.21 112.43 1.0817 +IC H6A C5 *C6 H6B 1.0817 112.43 -112.42 110.24 1.0503 +IC C5 C6 C7 C8 1.5437 113.90 167.68 115.30 1.5615 +IC C8 C6 *C7 H7A 1.5615 115.30 -116.36 108.50 1.1480 +IC H7A C6 *C7 H7B 1.1480 108.50 -115.94 110.56 1.1231 +IC C6 C7 C8 C9 1.5449 115.30 165.37 111.83 1.5514 +IC C9 C7 *C8 H8A 1.5514 111.83 -113.43 111.91 1.1377 +IC H8A C7 *C8 H8B 1.1377 111.91 -118.34 108.18 1.0480 +IC C7 C8 C9 C10 1.5615 111.83 176.59 110.57 1.5526 +IC C10 C8 *C9 H9A 1.5526 110.57 -129.97 113.53 1.1310 +IC H9A C8 *C9 H9B 1.1310 113.53 -109.70 107.39 1.1594 +IC C8 C9 C10 C11 1.5514 110.57 -177.26 112.26 1.5783 +IC C11 C9 *C10 H10A 1.5783 112.26 -123.45 106.63 1.1533 +IC H10A C9 *C10 H10B 1.1533 106.63 -118.25 115.85 1.0771 +IC C9 C10 C11 C12 1.5526 112.26 -163.15 112.58 1.5528 +IC C12 C10 *C11 H11A 1.5528 112.58 -121.90 102.65 1.0764 +IC H11A C10 *C11 H11B 1.0764 102.65 -122.46 109.95 1.1248 +IC C10 C11 C12 C13 1.5783 112.58 -179.16 115.34 1.5375 +IC C13 C11 *C12 H12A 1.5375 115.34 -129.55 111.80 1.0856 +IC H12A C11 *C12 H12B 1.0856 111.80 -109.80 105.66 1.0741 +IC C11 C12 C13 C14 1.5528 115.34 -178.59 114.71 1.5546 +IC C14 C12 *C13 H13A 1.5546 114.71 -121.77 106.42 1.0758 +IC H13A C12 *C13 H13B 1.0758 106.42 -114.53 102.53 1.0909 +IC C12 C13 C14 C15 1.5375 114.71 179.82 117.78 1.5331 +IC C15 C13 *C14 H14A 1.5331 117.78 -126.75 106.30 1.1072 +IC H14A C13 *C14 H14B 1.1072 106.30 -108.90 106.38 1.0834 +IC C13 C14 C15 C16 1.5546 117.78 169.53 109.01 1.4928 +IC C16 C14 *C15 H15A 1.4928 109.01 -121.10 100.35 1.1439 +IC H15A C14 *C15 H15B 1.1439 100.35 -117.57 115.28 1.1080 +IC C14 C15 C16 H16A 1.5331 109.01 -61.78 119.36 1.0834 +IC H16A C15 *C16 H16B 1.0834 119.36 138.24 116.61 1.0932 +IC H16A C15 *C16 H16C 1.0834 119.36 -107.69 109.08 1.1555 + + +RESI GLYM 0.00 ! Glycin-myristate +GROUP +ATOM N NH1 -0.47 ! +ATOM HN H 0.31 ! HA1 +ATOM CA CT2 -0.02 ! | +ATOM HA1 HB2 0.09 ! O=C--CA---N-HN +ATOM HA2 HB2 0.09 ! | | | +GROUP ! HA2 | +ATOM C C 0.51 ! | +ATOM O O -0.51 ! | +GROUP ! O1=C1 +ATOM C1 C 0.55 ! | +ATOM O1 O -0.60 ! | +ATOM C2 CTL2 -0.07 ! H2A-C2-H2B +ATOM H2A HAL2 0.06 ! | +ATOM H2B HAL2 0.06 ! | +GROUP ! | +ATOM C3 CTL2 -0.18 ! H3A-C3-H3B +ATOM H3A HAL2 0.09 ! | +ATOM H3B HAL2 0.09 ! | +GROUP ! | +ATOM C4 CTL2 -0.18 ! H4A-C4-H4B +ATOM H4A HAL2 0.09 ! | +ATOM H4B HAL2 0.09 ! | +GROUP ! | +ATOM C5 CTL2 -0.18 ! H5A-C5-H5B +ATOM H5A HAL2 0.09 ! | +ATOM H5B HAL2 0.09 ! | +GROUP ! | +ATOM C6 CTL2 -0.18 ! H6A-C6-H6B +ATOM H6A HAL2 0.09 ! | +ATOM H6B HAL2 0.09 ! | +GROUP ! | +ATOM C7 CTL2 -0.18 ! H7A-C7-H7B +ATOM H7A HAL2 0.09 ! | +ATOM H7B HAL2 0.09 ! | +GROUP ! | +ATOM C8 CTL2 -0.18 ! H8A-C8-H8B +ATOM H8A HAL2 0.09 ! | +ATOM H8B HAL2 0.09 ! | +GROUP ! | +ATOM C9 CTL2 -0.18 ! H9A-C9-H9B +ATOM H9A HAL2 0.09 ! | +ATOM H9B HAL2 0.09 ! | +GROUP ! | +ATOM C10 CTL2 -0.18 ! H10A-C10-H10B +ATOM H10A HAL2 0.09 ! | +ATOM H10B HAL2 0.09 ! | +GROUP ! | +ATOM C11 CTL2 -0.18 ! H11A-C11-H11B +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! | +GROUP ! | +ATOM C12 CTL2 -0.18 ! H12A-C12-H12B +ATOM H12A HAL2 0.09 ! | +ATOM H12B HAL2 0.09 ! | +GROUP ! | +ATOM C13 CTL2 -0.18 ! H13A-C13-H13B +ATOM H13A HAL2 0.09 ! | +ATOM H13B HAL2 0.09 ! | +GROUP ! | +ATOM C14 CTL3 -0.27 ! H14A-C14-H14B +ATOM H14A HAL3 0.09 ! | +ATOM H14B HAL3 0.09 ! | +ATOM H14C HAL3 0.09 ! H14C + +BOND N HN N CA +BOND C CA C +N CA HA1 CA HA2 +BOND N C1 +DOUBLE O C + +DOUBLE C1 O1 +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 C3 H3A C3 H3B +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5A C5 H5B +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7A C7 H7B +BOND C7 C8 C8 H8A C8 H8B +BOND C8 C9 C9 H9A C9 H9B +BOND C9 C10 C10 H10A C10 H10B +BOND C10 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 C13 C13 H13A C13 H13B +BOND C13 C14 C14 H14A C14 H14B C14 H14C +IMPR C1 O1 N C2 +IMPR N C1 CA HN C CA +N O +!IMPR C CA +N O + +DONOR HN N +ACCEPTOR O C +ACCEPTOR O1 C1 + +IC C1 CA *N HN 1.3479 123.93 180.00 114.77 0.9982 +IC C1 N CA C 1.3479 123.93 180.00 105.89 1.5202 +IC N CA C +N 1.4533 105.89 180.00 118.30 1.3498 +IC +N CA *C O 1.3498 118.30 180.00 120.59 1.2306 +IC CA C +N +CA 1.5202 118.30 180.00 124.50 1.4548 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 + +IC N CA C O 1.3945 106.38 5.30 121.98 1.2956 +IC CA N C1 C2 1.4553 108.64 158.80 115.77 1.5434 +IC C2 N *C1 O1 1.4534 115.77 -174.68 119.62 1.2281 +IC N C1 C2 C3 1.4553 108.77 152.55 111.56 1.5614 +IC C3 C1 *C2 H2A 1.5614 111.56 -126.88 116.60 1.0567 +IC H2A C1 *C2 H2B 1.0567 116.60 -120.46 107.56 1.0927 +IC C1 C2 C3 C4 1.5434 111.56 178.17 112.38 1.5543 +IC C4 C2 *C3 H3A 1.5543 112.38 -115.58 110.36 1.0691 +IC H3A C2 *C3 H3B 1.0691 110.36 -116.74 109.97 1.1344 +IC C2 C3 C4 C5 1.5614 112.38 174.26 114.93 1.5290 +IC C5 C3 *C4 H4A 1.5290 114.93 -117.82 107.19 1.0636 +IC H4A C3 *C4 H4B 1.0636 107.19 -118.11 109.41 1.1180 +IC C3 C4 C5 C6 1.5543 114.93 139.45 116.26 1.5437 +IC C6 C4 *C5 H5A 1.5437 116.26 -115.47 116.05 1.1088 +IC H5A C4 *C5 H5B 1.1088 116.05 -122.13 108.08 1.1320 +IC C4 C5 C6 C7 1.5290 116.26 159.28 113.90 1.5449 +IC C7 C5 *C6 H6A 1.5449 113.90 -120.21 112.43 1.0817 +IC H6A C5 *C6 H6B 1.0817 112.43 -112.42 110.24 1.0503 +IC C5 C6 C7 C8 1.5437 113.90 167.68 115.30 1.5615 +IC C8 C6 *C7 H7A 1.5615 115.30 -116.36 108.50 1.1480 +IC H7A C6 *C7 H7B 1.1480 108.50 -115.94 110.56 1.1231 +IC C6 C7 C8 C9 1.5449 115.30 165.37 111.83 1.5514 +IC C9 C7 *C8 H8A 1.5514 111.83 -113.43 111.91 1.1377 +IC H8A C7 *C8 H8B 1.1377 111.91 -118.34 108.18 1.0480 +IC C7 C8 C9 C10 1.5615 111.83 176.59 110.57 1.5526 +IC C10 C8 *C9 H9A 1.5526 110.57 -129.97 113.53 1.1310 +IC H9A C8 *C9 H9B 1.1310 113.53 -109.70 107.39 1.1594 +IC C8 C9 C10 C11 1.5514 110.57 -177.26 112.26 1.5783 +IC C11 C9 *C10 H10A 1.5783 112.26 -123.45 106.63 1.1533 +IC H10A C9 *C10 H10B 1.1533 106.63 -118.25 115.85 1.0771 +IC C9 C10 C11 C12 1.5526 112.26 -163.15 112.58 1.5528 +IC C12 C10 *C11 H11A 1.5528 112.58 -121.90 102.65 1.0764 +IC H11A C10 *C11 H11B 1.0764 102.65 -122.46 109.95 1.1248 +IC C10 C11 C12 C13 1.5783 112.58 -179.16 115.34 1.5375 +IC C13 C11 *C12 H12A 1.5375 115.34 -129.55 111.80 1.0856 +IC H12A C11 *C12 H12B 1.0856 111.80 -109.80 105.66 1.0741 +IC C11 C12 C13 C14 1.5528 115.34 -178.59 114.71 1.5546 +IC C14 C12 *C13 H13A 1.5546 114.71 -121.77 106.42 1.0758 +IC H13A C12 *C13 H13B 1.0758 106.42 -114.53 102.53 1.0909 +IC C12 C13 C14 H14A 1.5331 109.01 -61.78 119.36 1.0834 +IC H14A C13 *C14 H14B 1.0834 119.36 138.24 116.61 1.0932 +IC H14A C13 *C14 H14C 1.0834 119.36 -107.69 109.08 1.1555 + + +RESI CYSF 0.00 ! Cystein-Farnesyl +GROUP ! +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | | +GROUP ! HA-CA--CB--SG +ATOM C C 0.51 ! | | | +ATOM O O -0.51 ! | HB2 | +GROUP ! O=C | +ATOM CB CT2 -0.13 ! | | +ATOM HB1 HA2 0.09 ! | +ATOM HB2 HA2 0.09 ! | +ATOM SG S -0.10 ! | +ATOM C1 CG321 -0.13 ! H1A--C1--H1B +ATOM H1A HGA2 0.09 ! | +ATOM H1B HGA2 0.09 ! | +GROUP ! | +ATOM C2 CG2D1 -0.15 ! C2--H2A (cis) +ATOM H2A HGA4 0.15 ! || +GROUP ! || H4A +ATOM C3 CG2D1 0.00 ! || | +GROUP ! C3--C4--H4B +ATOM C4 CG331 -0.27 ! | | +ATOM H4A HGA3 0.09 ! | H4C +ATOM H4B HGA3 0.09 ! ! +ATOM H4C HGA3 0.09 ! ! +GROUP ! ! +ATOM C5 CG321 -0.18 ! H5A--C5--H5B +ATOM H5A HGA2 0.09 ! ! +ATOM H5B HGA2 0.09 ! ! +GROUP ! | +ATOM C6 CG321 -0.18 ! H6A--C6--H6B +ATOM H6A HGA2 0.09 ! | +ATOM H6B HGA2 0.09 ! | +GROUP ! | +ATOM C7 CG2D1 -0.15 ! C7--H7A (cis) +ATOM H7A HGA4 0.15 ! || +GROUP ! || H9A +ATOM C8 CG2D1 0.00 ! || | +GROUP ! C8--C9--H9B +ATOM C9 CG331 -0.27 ! | | +ATOM H9A HGA3 0.09 ! | H9C +ATOM H9B HGA3 0.09 ! ! +ATOM H9C HGA3 0.09 ! ! +GROUP ! ! +ATOM C10 CG321 -0.18 ! H10A--C10--H10B +ATOM H10A HGA2 0.09 ! ! +ATOM H10B HGA2 0.09 ! ! +GROUP ! | +ATOM C11 CG321 -0.18 ! H11A--C11--H11B +ATOM H11A HGA2 0.09 ! | +ATOM H11B HGA2 0.09 ! | +GROUP ! | +ATOM C12 CG2D1 -0.15 ! C12--H12A (cis) +ATOM H12A HGA4 0.15 ! || +GROUP ! || H14A +ATOM C13 CG2D1 0.00 ! || | +GROUP ! C13--C14--H14B +ATOM C14 CG331 -0.27 ! | | +ATOM H14A HGA3 0.09 ! | H14C +ATOM H14B HGA3 0.09 ! ! +ATOM H14C HGA3 0.09 ! ! +GROUP ! ! +ATOM C15 CG331 -0.27 ! H15A--C15--H15B +ATOM H15A HGA3 0.09 ! | +ATOM H15B HGA3 0.09 ! | +ATOM H15C HGA3 0.09 ! H15C + +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG C1 +DOUBLE O C + +BOND C1 C2 C3 C4 C3 C5 ! cis isoprene backbone carbons +DOUBLE C2 C3 ! cis double bond +BOND C1 H1A C1 H1B ! C1 hydrogens +BOND C2 H2A ! C2 hydrogen +BOND C4 H4A C4 H4B C4 H4C ! C4 hydrogens +BOND C5 H5A C5 H5B ! C5 hydrogens +BOND C5 C6 ! isoprene linking bond +BOND C6 C7 C8 C9 C8 C10 ! cis isoprene backbone carbons +DOUBLE C7 C8 ! cis double bond +BOND C6 H6A C6 H6B ! C6 hydrogens +BOND C7 H7A ! C7 hydrogen +BOND C9 H9A C9 H9B C9 H9C ! C9 hydrogens +BOND C10 H10A C10 H10B ! C10 hydrogens +BOND C10 C11 ! isoprene linking bond +BOND C11 C12 C13 C14 C13 C15 ! cis isoprene backbone carbons +DOUBLE C12 C13 ! cis double bond +BOND C11 H11A C11 H11B ! C11 hydrogens +BOND C12 H12A ! C12 hydrogen +BOND C14 H14A C14 H14B C14 H14C ! C14 hydrogens +BOND C15 H15A C15 H15B C15 H15C ! C15 hydrogens + +IC -C CA *N HN 1.3479 123.93 180.00 114.77 0.9982 +IC -C N CA C 1.3479 123.93 180.00 105.89 1.5202 +IC N CA C +N 1.4533 105.89 180.00 118.30 1.3498 +IC +N CA *C O 1.3498 118.30 180.00 120.59 1.2306 +IC CA C +N +CA 1.5202 118.30 180.00 124.50 1.4548 +IC HN N CA CB 0.9674 117.70 -36.00 110.95 1.5003 +IC CB N *CA C 1.5003 110.95 128.76 106.38 1.5291 +IC CB N *CA HA 1.5003 110.95 -121.31 107.62 1.1060 +IC N CA CB SG 1.3945 110.95 -174.62 111.79 1.8692 +IC SG CA *CB HB1 1.8692 111.79 114.87 107.79 1.1406 +IC SG CA *CB HB2 1.8692 111.79 -128.20 109.45 1.0949 +IC N CA C O 1.3945 106.38 5.30 121.98 1.2956 +IC CA CB SG C1 1.5003 111.79 -178.37 107.64 1.8012 +IC CB SG C1 C2 1.8692 107.64 158.80 115.77 1.5434 +IC SG C1 C2 C3 1.8012 115.77 152.55 111.56 1.5614 +IC C2 SG *C1 H1A 1.5300 110.10 120.00 109.50 1.1110 +IC C2 SG *C1 H1B 1.5300 110.10 -120.00 109.50 1.1110 +IC C3 C1 *C2 H2A 1.3400 123.50 180.00 116.00 1.1000 +IC C1 C2 C3 C4 1.5020 123.50 180.00 123.50 1.5020 +IC C5 C2 *C3 C4 1.5020 123.50 180.00 123.50 1.5040 +IC C2 C3 C4 H4A 1.3400 123.50 180.00 111.50 1.1110 +IC H4A C3 *C4 H4B 1.1110 111.50 120.00 111.50 1.1110 +IC H4A C3 *C4 H4C 1.1110 111.50 -120.00 111.50 1.1110 +IC C2 C3 C5 C6 1.3400 123.50 180.00 112.20 1.5300 +IC C6 C3 *C5 H5A 1.5300 112.20 120.00 111.50 1.1110 +IC C6 C3 *C5 H5B 1.1110 111.50 -120.00 111.50 1.1110 +IC C3 C5 C6 C7 1.5020 112.20 180.00 112.20 1.5020 +IC C7 C5 *C6 H6A 1.5020 112.20 120.00 110.10 1.1110 +IC C7 C5 *C6 H6B 1.5020 112.20 -120.00 110.10 1.1110 +IC C5 C6 C7 C8 1.5300 112.20 180.00 123.50 1.3400 +IC C8 C6 *C7 H7A 1.3400 123.50 180.00 116.00 1.1000 +IC C6 C7 C8 C9 1.5020 123.50 180.00 123.50 1.5020 +IC C10 C7 *C8 C9 1.5020 123.50 180.00 123.50 1.5040 +IC C7 C8 C9 H9A 1.3400 123.50 180.00 111.50 1.1110 +IC H9A C8 *C9 H9B 1.1110 111.50 120.00 111.50 1.1110 +IC H9A C8 *C9 H9C 1.1110 111.50 -120.00 111.50 1.1110 +IC C7 C8 C10 C11 1.3400 123.50 180.00 112.20 1.5300 +IC C11 C8 *C10 H10A 1.5300 112.20 120.00 111.50 1.1110 +IC C11 C8 *C10 H10B 1.1110 111.50 -120.00 111.50 1.1110 +IC C8 C10 C11 C12 1.5020 112.20 180.00 112.20 1.5020 +IC C12 C10 *C11 H11A 1.5020 112.20 120.00 110.10 1.1110 +IC C12 C10 *C11 H11B 1.5020 112.20 -120.00 110.10 1.1110 +IC C10 C11 C12 C13 1.5300 112.20 180.00 123.50 1.3400 +IC C13 C11 *C12 H12A 1.3400 123.50 180.00 116.00 1.1000 +IC C11 C12 C13 C14 1.5020 123.50 180.00 123.50 1.5020 +IC C15 C12 *C13 C14 1.5020 123.50 180.00 123.50 1.5040 +IC C12 C13 C14 H14A 1.3400 123.50 180.00 111.50 1.1110 +IC H14A C13 *C14 H14B 1.1110 111.50 120.00 111.50 1.1110 +IC H14A C13 *C14 H14C 1.1110 111.50 -120.00 111.50 1.1110 +IC C12 C13 C15 H15C 1.3400 123.50 180.00 108.20 1.1110 +IC H15C C13 *C15 H15A 1.1110 108.20 120.00 111.50 1.1110 +IC H15C C13 *C15 H15B 1.1110 108.20 -120.00 111.50 1.1110 + +RESI CYSG 0.00 ! Cystein-Geranyl +GROUP ! +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | | +GROUP ! HA-CA--CB--SG +ATOM C C 0.51 ! | | | +ATOM O O -0.51 ! | HB2 | +GROUP ! O=C | +ATOM CB CT2 -0.13 ! | | +ATOM HB1 HA2 0.09 ! | +ATOM HB2 HA2 0.09 ! | +ATOM SG S -0.10 ! | +ATOM C1 CG321 -0.13 ! H1A--C1--H1B +ATOM H1A HGA2 0.09 ! | +ATOM H1B HGA2 0.09 ! | +GROUP ! | +ATOM C2 CG2D1 -0.15 ! C2--H2A (cis) +ATOM H2A HGA4 0.15 ! || +GROUP ! || H4A +ATOM C3 CG2D1 0.00 ! || | +GROUP ! C3--C4--H4B +ATOM C4 CG331 -0.27 ! | | +ATOM H4A HGA3 0.09 ! | H4C +ATOM H4B HGA3 0.09 ! ! +ATOM H4C HGA3 0.09 ! ! +GROUP ! ! +ATOM C5 CG321 -0.18 ! H5A--C5--H5B +ATOM H5A HGA2 0.09 ! ! +ATOM H5B HGA2 0.09 ! ! +GROUP ! | +ATOM C6 CG321 -0.18 ! H6A--C6--H6B +ATOM H6A HGA2 0.09 ! | +ATOM H6B HGA2 0.09 ! | +GROUP ! | +ATOM C7 CG2D1 -0.15 ! C7--H7A (cis) +ATOM H7A HGA4 0.15 ! || +GROUP ! || H9A +ATOM C8 CG2D1 0.00 ! || | +GROUP ! C8--C9--H9B +ATOM C9 CG331 -0.27 ! | | +ATOM H9A HGA3 0.09 ! | H9C +ATOM H9B HGA3 0.09 ! ! +ATOM H9C HGA3 0.09 ! ! +GROUP ! ! +ATOM C10 CG321 -0.18 ! H10A--C10--H10B +ATOM H10A HGA2 0.09 ! ! +ATOM H10B HGA2 0.09 ! ! +GROUP ! | +ATOM C11 CG321 -0.18 ! H11A--C11--H11B +ATOM H11A HGA2 0.09 ! | +ATOM H11B HGA2 0.09 ! | +GROUP ! | +ATOM C12 CG2D1 -0.15 ! C12--H12A (cis) +ATOM H12A HGA4 0.15 ! || +GROUP ! || H14A +ATOM C13 CG2D1 0.00 ! || | +GROUP ! C13--C14--H14B +ATOM C14 CG331 -0.27 ! | | +ATOM H14A HGA3 0.09 ! | H14C +ATOM H14B HGA3 0.09 ! ! +ATOM H14C HGA3 0.09 ! ! +GROUP ! ! +ATOM C15 CG321 -0.18 ! H15A--C15--H15B +ATOM H15A HGA2 0.09 ! | +ATOM H15B HGA2 0.09 ! | +GROUP ! | +ATOM C16 CG321 -0.18 ! H16A--C16--H16B +ATOM H16A HGA2 0.09 ! | +ATOM H16B HGA2 0.09 ! | +GROUP ! | +ATOM C17 CG2D1 -0.15 ! C17--H17A (cis) +ATOM H17A HGA4 0.15 ! || +GROUP ! || H19A +ATOM C18 CG2D1 0.00 ! || | +GROUP ! C18--C19--H19B +ATOM C19 CG331 -0.27 ! | | +ATOM H19A HGA3 0.09 ! | H19C +ATOM H19B HGA3 0.09 ! ! +ATOM H19C HGA3 0.09 ! ! +GROUP ! ! +ATOM C20 CG331 -0.27 ! H20A--C20--H20B +ATOM H20A HGA3 0.09 ! ! +ATOM H20B HGA3 0.09 ! ! +ATOM H20C HGA3 0.09 ! H20C + +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG C1 +DOUBLE O C + +BOND C1 C2 C3 C4 C3 C5 ! cis isoprene backbone carbons +DOUBLE C2 C3 ! cis double bond +BOND C1 H1A C1 H1B ! C1 hydrogens +BOND C2 H2A ! C2 hydrogen +BOND C4 H4A C4 H4B C4 H4C ! C4 hydrogens +BOND C5 H5A C5 H5B ! C5 hydrogens +BOND C5 C6 ! isoprene linking bond +BOND C6 C7 C8 C9 C8 C10 ! cis isoprene backbone carbons +DOUBLE C7 C8 ! cis double bond +BOND C6 H6A C6 H6B ! C6 hydrogens +BOND C7 H7A ! C7 hydrogen +BOND C9 H9A C9 H9B C9 H9C ! C9 hydrogens +BOND C10 H10A C10 H10B ! C10 hydrogens +BOND C10 C11 ! isoprene linking bond +BOND C11 C12 C13 C14 C13 C15 ! cis isoprene backbone carbons +DOUBLE C12 C13 ! cis double bond +BOND C11 H11A C11 H11B ! C11 hydrogens +BOND C12 H12A ! C312 hydrogen +BOND C14 H14A C14 H14B C14 H14C ! C14 hydrogens +BOND C15 H15A C15 H15B ! C15 hydrogens +BOND C15 C16 ! isoprene linking bond +BOND C16 C17 C18 C19 C18 C20 ! cis isoprene backbone carbons +DOUBLE C17 C18 ! cis double bond +BOND C16 H16A C16 H16B ! C16 hydrogens +BOND C17 H17A ! C17 hydrogen +BOND C19 H19A C19 H19B C19 H19C ! C19 hydrogens +BOND C20 H20A C20 H20B C20 H20C ! C20 hydrogens + +IC -C CA *N HN 1.3479 123.93 180.00 114.77 0.9982 +IC -C N CA C 1.3479 123.93 180.00 105.89 1.5202 +IC N CA C +N 1.4533 105.89 180.00 118.30 1.3498 +IC +N CA *C O 1.3498 118.30 180.00 120.59 1.2306 +IC CA C +N +CA 1.5202 118.30 180.00 124.50 1.4548 +IC HN N CA CB 0.9674 117.70 -36.00 110.95 1.5003 +IC CB N *CA C 1.5003 110.95 128.76 106.38 1.5291 +IC CB N *CA HA 1.5003 110.95 -121.31 107.62 1.1060 +IC N CA CB SG 1.3945 110.95 -174.62 111.79 1.8692 +IC SG CA *CB HB1 1.8692 111.79 114.87 107.79 1.1406 +IC SG CA *CB HB2 1.8692 111.79 -128.20 109.45 1.0949 +IC N CA C O 1.3945 106.38 5.30 121.98 1.2956 +IC CA CB SG C1 1.5003 111.79 -178.37 107.64 1.8012 +IC CB SG C1 C2 1.8692 107.64 158.80 115.77 1.5434 +IC SG C1 C2 C3 1.8012 115.77 152.55 111.56 1.5614 +IC C2 SG *C1 H1A 1.5300 110.10 120.00 109.50 1.1110 +IC C2 SG *C1 H1B 1.5300 110.10 -120.00 109.50 1.1110 +IC C3 C1 *C2 H2A 1.3400 123.50 180.00 116.00 1.1000 +IC C1 C2 C3 C4 1.5020 123.50 180.00 123.50 1.5020 +IC C5 C2 *C3 C4 1.5020 123.50 180.00 123.50 1.5040 +IC C2 C3 C4 H4A 1.3400 123.50 180.00 111.50 1.1110 +IC H4A C3 *C4 H4B 1.1110 111.50 120.00 111.50 1.1110 +IC H4A C3 *C4 H4C 1.1110 111.50 -120.00 111.50 1.1110 +IC C2 C3 C5 C6 1.3400 123.50 180.00 112.20 1.5300 +IC C6 C3 *C5 H5A 1.5300 112.20 120.00 111.50 1.1110 +IC C6 C3 *C5 H5B 1.1110 111.50 -120.00 111.50 1.1110 +IC C3 C5 C6 C7 1.5020 112.20 180.00 112.20 1.5020 +IC C7 C5 *C6 H6A 1.5020 112.20 120.00 110.10 1.1110 +IC C7 C5 *C6 H6B 1.5020 112.20 -120.00 110.10 1.1110 +IC C5 C6 C7 C8 1.5300 112.20 180.00 123.50 1.3400 +IC C8 C6 *C7 H7A 1.3400 123.50 180.00 116.00 1.1000 +IC C6 C7 C8 C9 1.5020 123.50 180.00 123.50 1.5020 +IC C10 C7 *C8 C9 1.5020 123.50 180.00 123.50 1.5040 +IC C7 C8 C9 H9A 1.3400 123.50 180.00 111.50 1.1110 +IC H9A C8 *C9 H9B 1.1110 111.50 120.00 111.50 1.1110 +IC H9A C8 *C9 H9C 1.1110 111.50 -120.00 111.50 1.1110 +IC C7 C8 C10 C11 1.3400 123.50 180.00 112.20 1.5300 +IC C11 C8 *C10 H10A 1.5300 112.20 120.00 111.50 1.1110 +IC C11 C8 *C10 H10B 1.1110 111.50 -120.00 111.50 1.1110 +IC C8 C10 C11 C12 1.5020 112.20 180.00 112.20 1.5020 +IC C12 C10 *C11 H11A 1.5020 112.20 120.00 110.10 1.1110 +IC C12 C10 *C11 H11B 1.5020 112.20 -120.00 110.10 1.1110 +IC C10 C11 C12 C13 1.5300 112.20 180.00 123.50 1.3400 +IC C13 C11 *C12 H12A 1.3400 123.50 180.00 116.00 1.1000 +IC C11 C12 C13 C14 1.5020 123.50 180.00 123.50 1.5020 +IC C15 C12 *C13 C14 1.5020 123.50 180.00 123.50 1.5040 +IC C12 C13 C14 H14A 1.3400 123.50 180.00 111.50 1.1110 +IC H14A C13 *C14 H14B 1.1110 111.50 120.00 111.50 1.1110 +IC H14A C13 *C14 H14C 1.1110 111.50 -120.00 111.50 1.1110 +IC C12 C13 C15 C16 1.3400 123.50 180.00 112.20 1.5300 +IC C16 C13 *C15 H15A 1.5300 112.20 120.00 111.50 1.1110 +IC C16 C13 *C15 H15B 1.5300 112.20 -120.00 111.50 1.1110 +IC C13 C15 C16 C17 1.5020 112.20 180.00 112.20 1.5020 +IC C17 C15 *C16 H16A 1.5020 112.20 120.00 110.10 1.1110 +IC C17 C15 *C16 H16B 1.5020 112.20 -120.00 110.10 1.1110 +IC C15 C16 C17 C18 1.5300 112.20 180.00 123.50 1.3400 +IC C18 C16 *C17 H17A 1.3400 123.50 180.00 116.00 1.1000 +IC C16 C17 C18 C19 1.5020 123.50 180.00 123.50 1.5020 +IC C20 C17 *C18 C19 1.5020 123.50 180.00 123.50 1.5040 +IC C17 C18 C19 H19A 1.3400 123.50 180.00 111.50 1.1110 +IC H19A C18 *C19 H19B 1.1110 111.50 120.00 111.50 1.1110 +IC H19A C18 *C19 H19C 1.1110 111.50 -120.00 111.50 1.1110 +IC C17 C18 C20 H20A 1.5300 112.20 180.00 111.50 1.1110 +IC C17 C18 *C20 H20B 1.1110 111.50 120.00 111.50 1.1110 +IC C17 C18 *C20 H20C 1.1110 111.50 -120.00 111.50 1.1110 + +RESI CYSL 0.00 ! cysteine-triacylhexadecane?? +GROUP +ATOM N NH1 -0.47 ! O HA +ATOM HN H 0.31 ! || | +ATOM CA CT1 0.07 ! --C---CA---N-HN +ATOM HA HB1 0.09 ! / \ +GROUP ! HB1--CB--HB2 \ +ATOM C C 0.51 ! H1A / \ +ATOM O O -0.51 ! | / \ +GROUP ! C1----SG OA1=CA1 +ATOM CB CT2 -0.13 ! / \ | +ATOM HB1 HA2 0.09 ! / H1B | +ATOM HB2 HA2 0.09 ! O11--------------C11--H11 H2A-CA2-H2B +ATOM SG S -0.10 ! / | | +ATOM C1 CG321 -0.13 ! / | | +ATOM H1A HGA2 0.09 ! OX1=CX1 H12R--C12--H12S | +ATOM H1B HGA2 0.09 ! | | H3A-CA3-H3B +GROUP ! | | | +ATOM CA1 C 0.55 ! H2X-CX2-H2Y O12 | +ATOM OA1 O -0.60 ! | | | +ATOM CA2 CTL2 -0.07 ! | CD1=OD1 H4A-CA4-H4B +ATOM H2A HAL2 0.06 ! | | | +ATOM H2B HAL2 0.06 ! H3X-CX3-H3Y | | +GROUP ! | H2D-CD2-H2E | +ATOM C11 CTL1 0.17 ! | | H5A-CA5-H5B +ATOM H11 HAL1 0.09 ! | | | +ATOM O11 OSL -0.49 ! H4X-CX4-H4Y | | +ATOM CX1 CL 0.90 ! | H3D-CD3-H3E | +ATOM OX1 OBL -0.63 ! | | H6A-CA6-H6B +ATOM CX2 CTL2 -0.22 ! | | | +ATOM H2X HAL2 0.09 ! H5X-CX5-H5Y | | +ATOM H2Y HAL2 0.09 ! | H4D-CD4-H4E | +GROUP ! | | H7A-CA7-H7B +ATOM C12 CTL2 0.08 ! | | | +ATOM H12R HAL2 0.09 ! H6X-CX6-H6Y | | +ATOM H12S HAL2 0.09 ! | H5D-CD5-H5E | +ATOM O12 OSL -0.49 ! | | H8A-CA8-H8B +ATOM CD1 CL 0.90 ! | | | +ATOM OD1 OBL -0.63 ! H7X-CX7-H7Y | | +ATOM CD2 CTL2 -0.22 ! | H6D-CD6-H6E | +ATOM H2D HAL2 0.09 ! | | H9A-CA9-H9B +ATOM H2E HAL2 0.09 ! | | | +GROUP ! H8X-CX8-H8Y | | +ATOM CA3 CTL2 -0.18 ! | H7D-CD7-H7E | +ATOM H3A HAL2 0.09 ! | | H10A-CA10-H10B +ATOM H3B HAL2 0.09 ! | | | +GROUP ! H9X-CX9-H9Y | | +ATOM CA4 CTL2 -0.18 ! | H8D-CD8-H8E | +ATOM H4A HAL2 0.09 ! | | H11A-CA11-H11B +ATOM H4B HAL2 0.09 ! | | | +GROUP ! H10X-CX10-H10Y | | +ATOM CA5 CTL2 -0.18 ! | H9D-CD9-H9E | +ATOM H5A HAL2 0.09 ! | | H12A-CA12-H12B +ATOM H5B HAL2 0.09 ! | | | +GROUP ! H11X-CX11-H11Y | | +ATOM CA6 CTL2 -0.18 ! | H10D-CD10-H10E | +ATOM H6A HAL2 0.09 ! | | H13A-CA13-H13B +ATOM H6B HAL2 0.09 ! | | | +GROUP ! H12X-CX12-H12Y | | +ATOM CA7 CTL2 -0.18 ! | H11D-CD11-H11E | +ATOM H7A HAL2 0.09 ! | | H14A-CA14-H14B +ATOM H7B HAL2 0.09 ! | | | +GROUP ! H13X-CX13-H13Y | | +ATOM CA8 CTL2 -0.18 ! | H12D-CD12-H12E | +ATOM H8A HAL2 0.09 ! | | H15A-CA15-H15B +ATOM H8B HAL2 0.09 ! | | | +GROUP ! H14X-CX14-H14Y | | +ATOM CA9 CTL2 -0.18 ! | H13D-CD13-H13E | +ATOM H9A HAL2 0.09 ! | | H16A-CA16-H16B +ATOM H9B HAL2 0.09 ! | | | +GROUP ! H15X-CX15-H15Y | | +ATOM CA10 CTL2 -0.18 ! | H14D-CD14-H14E H16C +ATOM H10A HAL2 0.09 ! | | +ATOM H10B HAL2 0.09 ! | | +GROUP ! H16X-CX16-H16Y | +ATOM CA11 CTL2 -0.18 ! | H15D-CD15-H15E +ATOM H11A HAL2 0.09 ! | | +ATOM H11B HAL2 0.09 ! H16Z | +GROUP ! | +ATOM CA12 CTL2 -0.18 ! H16D-CD16-H16E +ATOM H12A HAL2 0.09 ! | +ATOM H12B HAL2 0.09 ! | +GROUP ! H16F +ATOM CA13 CTL2 -0.18 ! +ATOM H13A HAL2 0.09 ! +ATOM H13B HAL2 0.09 ! +GROUP ! +ATOM CA14 CTL2 -0.18 ! +ATOM H14A HAL2 0.09 ! +ATOM H14B HAL2 0.09 ! +GROUP ! +ATOM CA15 CTL2 -0.18 ! +ATOM H15A HAL2 0.09 ! +ATOM H15B HAL2 0.09 ! +GROUP ! +ATOM CA16 CTL3 -0.27 ! +ATOM H16A HAL3 0.09 ! +ATOM H16B HAL3 0.09 ! +ATOM H16C HAL3 0.09 ! +GROUP ! +ATOM CD3 CTL2 -0.18 ! +ATOM H3D HAL2 0.09 ! +ATOM H3E HAL2 0.09 ! +GROUP ! +ATOM CD4 CTL2 -0.18 ! +ATOM H4D HAL2 0.09 ! +ATOM H4E HAL2 0.09 ! +GROUP ! +ATOM CD5 CTL2 -0.18 ! +ATOM H5D HAL2 0.09 ! +ATOM H5E HAL2 0.09 ! +GROUP ! +ATOM CD6 CTL2 -0.18 ! +ATOM H6D HAL2 0.09 ! +ATOM H6E HAL2 0.09 ! +GROUP ! +ATOM CD7 CTL2 -0.18 ! +ATOM H7D HAL2 0.09 ! +ATOM H7E HAL2 0.09 ! +GROUP ! +ATOM CD8 CTL2 -0.18 ! +ATOM H8D HAL2 0.09 ! +ATOM H8E HAL2 0.09 ! +GROUP ! +ATOM CD9 CTL2 -0.18 ! +ATOM H9D HAL2 0.09 ! +ATOM H9E HAL2 0.09 ! +GROUP ! +ATOM CD10 CTL2 -0.18 ! +ATOM H10D HAL2 0.09 ! +ATOM H10E HAL2 0.09 ! +GROUP ! +ATOM CD11 CTL2 -0.18 ! +ATOM H11D HAL2 0.09 ! +ATOM H11E HAL2 0.09 ! +GROUP ! +ATOM CD12 CTL2 -0.18 ! +ATOM H12D HAL2 0.09 ! +ATOM H12E HAL2 0.09 ! +GROUP ! +ATOM CD13 CTL2 -0.18 ! +ATOM H13D HAL2 0.09 ! +ATOM H13E HAL2 0.09 ! +GROUP ! +ATOM CD14 CTL2 -0.18 ! +ATOM H14D HAL2 0.09 ! +ATOM H14E HAL2 0.09 ! +GROUP ! +ATOM CD15 CTL2 -0.18 ! +ATOM H15D HAL2 0.09 ! +ATOM H15E HAL2 0.09 ! +GROUP ! +ATOM CD16 CTL3 -0.27 ! +ATOM H16D HAL3 0.09 ! +ATOM H16E HAL3 0.09 ! +ATOM H16F HAL3 0.09 ! +GROUP ! +ATOM CX3 CTL2 -0.18 ! +ATOM H3X HAL2 0.09 ! +ATOM H3Y HAL2 0.09 ! +GROUP ! +ATOM CX4 CTL2 -0.18 ! +ATOM H4X HAL2 0.09 ! +ATOM H4Y HAL2 0.09 ! +GROUP ! +ATOM CX5 CTL2 -0.18 ! +ATOM H5X HAL2 0.09 ! +ATOM H5Y HAL2 0.09 ! +GROUP ! +ATOM CX6 CTL2 -0.18 ! +ATOM H6X HAL2 0.09 ! +ATOM H6Y HAL2 0.09 ! +GROUP ! +ATOM CX7 CTL2 -0.18 ! +ATOM H7X HAL2 0.09 ! +ATOM H7Y HAL2 0.09 ! +GROUP ! +ATOM CX8 CTL2 -0.18 ! +ATOM H8X HAL2 0.09 ! +ATOM H8Y HAL2 0.09 ! +GROUP ! +ATOM CX9 CTL2 -0.18 ! +ATOM H9X HAL2 0.09 ! +ATOM H9Y HAL2 0.09 ! +GROUP ! +ATOM CX10 CTL2 -0.18 ! +ATOM H10X HAL2 0.09 ! +ATOM H10Y HAL2 0.09 ! +GROUP ! +ATOM CX11 CTL2 -0.18 ! +ATOM H11X HAL2 0.09 ! +ATOM H11Y HAL2 0.09 ! +GROUP ! +ATOM CX12 CTL2 -0.18 ! +ATOM H12X HAL2 0.09 ! +ATOM H12Y HAL2 0.09 ! +GROUP ! +ATOM CX13 CTL2 -0.18 ! +ATOM H13X HAL2 0.09 ! +ATOM H13Y HAL2 0.09 ! +GROUP ! +ATOM CX14 CTL2 -0.18 ! +ATOM H14X HAL2 0.09 ! +ATOM H14Y HAL2 0.09 ! +GROUP ! +ATOM CX15 CTL2 -0.18 ! +ATOM H15X HAL2 0.09 ! +ATOM H15Y HAL2 0.09 ! +GROUP ! +ATOM CX16 CTL3 -0.27 ! +ATOM H16X HAL3 0.09 ! +ATOM H16Y HAL3 0.09 ! +ATOM H16Z HAL3 0.09 ! + +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +DOUBLE O C +BOND CB HB2 SG C1 C1 C11 C1 H1A C1 H1B +BOND C11 C12 C11 H11 C11 O11 C12 O12 +BOND C12 H12R C12 H12S O12 CD1 O11 CX1 +BOND N CA1 +DOUBLE CA1 OA1 +BOND CA1 CA2 CA2 H2A CA2 H2B +BOND CA2 CA3 CA3 H3A CA3 H3B +BOND CA3 CA4 CA4 H4A CA4 H4B +BOND CA4 CA5 CA5 H5A CA5 H5B +BOND CA5 CA6 CA6 H6A CA6 H6B +BOND CA6 CA7 CA7 H7A CA7 H7B +BOND CA7 CA8 CA8 H8A CA8 H8B +BOND CA8 CA9 CA9 H9A CA9 H9B +BOND CA9 CA10 CA10 H10A CA10 H10B +BOND CA10 CA11 CA11 H11A CA11 H11B +BOND CA11 CA12 CA12 H12A CA12 H12B +BOND CA12 CA13 CA13 H13A CA13 H13B +BOND CA13 CA14 CA14 H14A CA14 H14B +BOND CA14 CA15 CA15 H15A CA15 H15B +BOND CA15 CA16 CA16 H16A CA16 H16B CA16 H16C +DOUBLE CD1 OD1 +BOND CD1 CD2 CD2 H2D CD2 H2E +BOND CD2 CD3 CD3 H3D CD3 H3E +BOND CD3 CD4 CD4 H4D CD4 H4E +BOND CD4 CD5 CD5 H5D CD5 H5E +BOND CD5 CD6 CD6 H6D CD6 H6E +BOND CD6 CD7 CD7 H7D CD7 H7E +BOND CD7 CD8 CD8 H8D CD8 H8E +BOND CD8 CD9 CD9 H9D CD9 H9E +BOND CD9 CD10 CD10 H10D CD10 H10E +BOND CD10 CD11 CD11 H11D CD11 H11E +BOND CD11 CD12 CD12 H12D CD12 H12E +BOND CD12 CD13 CD13 H13D CD13 H13E +BOND CD13 CD14 CD14 H14D CD14 H14E +BOND CD14 CD15 CD15 H15D CD15 H15E +BOND CD15 CD16 CD16 H16D CD16 H16E CD16 H16F +DOUBLE CX1 OX1 +BOND CX1 CX2 CX2 H2X CX2 H2Y +BOND CX2 CX3 CX3 H3X CX3 H3Y +BOND CX3 CX4 CX4 H4X CX4 H4Y +BOND CX4 CX5 CX5 H5X CX5 H5Y +BOND CX5 CX6 CX6 H6X CX6 H6Y +BOND CX6 CX7 CX7 H7X CX7 H7Y +BOND CX7 CX8 CX8 H8X CX8 H8Y +BOND CX8 CX9 CX9 H9X CX9 H9Y +BOND CX9 CX10 CX10 H10X CX10 H10Y +BOND CX10 CX11 CX11 H11X CX11 H11Y +BOND CX11 CX12 CX12 H12X CX12 H12Y +BOND CX12 CX13 CX13 H13X CX13 H13Y +BOND CX13 CX14 CX14 H14X CX14 H14Y +BOND CX14 CX15 CX15 H15X CX15 H15Y +BOND CX15 CX16 CX16 H16X CX16 H16Y CX16 H16Z + +IMPR CA1 OA1 N CA2 +IMPR N CA1 CA HN C CA +N O +!IMPR C CA +N O +IMPR CD1 O12 CD2 OD1 +IMPR CX1 O11 CX2 OX1 + +DONOR HN N +ACCEPTOR O C +ACCEPTOR OA1 CA1 +ACCEPTOR OD1 CD1 +ACCEPTOR OX1 CX1 +ACCEPTOR O11 C11 + +IC CA1 CA *N HN 1.3479 123.93 180.00 114.77 0.9982 +IC CA1 N CA C 1.3479 123.93 180.00 105.89 1.5202 +IC N CA C +N 1.4533 105.89 180.00 118.30 1.3498 +IC +N CA *C O 1.3498 118.30 180.00 120.59 1.2306 +IC CA C +N +CA 1.5202 118.30 180.00 124.50 1.4548 +IC HN N CA CB 0.9674 117.70 -36.00 110.95 1.5003 +IC CB N *CA C 1.5003 110.95 128.76 106.38 1.5291 +IC CB N *CA HA 1.5003 110.95 -121.31 107.62 1.1060 +IC N CA C O 1.3945 106.38 5.30 121.98 1.2956 +IC CA N CA1 CA2 1.4553 108.64 158.80 115.77 1.5434 +IC CA2 N *CA1 OA1 1.4534 115.77 -174.68 119.62 1.2281 +IC N CA1 CA2 CA3 1.4553 108.77 152.55 111.56 1.5614 +IC N CA CB SG 1.3945 110.95 -124.62 111.79 1.8692 +IC CA CB SG C1 1.5003 111.79 -178.37 107.64 1.8012 +IC SG CA *CB HB1 1.8692 111.79 114.87 107.79 1.1406 +IC SG CA *CB HB2 1.8692 111.79 -128.20 109.45 1.0949 +IC CB SG C1 C11 1.3945 116.90 -70.20 120.82 1.5785 +IC C11 SG *C1 H1A 1.5785 120.82 -121.59 102.98 1.1110 +IC H1A SG *C1 H1B 1.1110 102.98 -117.94 115.12 1.1109 +IC SG C1 C11 C12 1.3945 120.82 -120.44 110.14 1.4806 +IC C12 C1 *C11 O11 1.4806 110.14 123.75 104.19 1.4203 +IC O11 C1 *C11 H11 1.4203 104.19 -117.29 108.71 1.1108 +IC C1 C11 O11 CX1 1.5785 104.19 152.63 121.75 1.3357 +IC C11 O11 CX1 CX2 1.4203 121.75 -172.10 105.98 1.5689 +IC CX2 O11 *CX1 OX1 1.5689 105.98 172.32 128.82 1.2022 +IC O11 CX1 CX2 CX3 1.3357 105.98 -133.79 106.00 1.5485 +IC C1 C11 C12 O12 1.5785 110.14 52.09 108.48 1.4206 +IC O12 C11 *C12 H12R 1.4206 108.48 -117.15 111.73 1.1103 +IC H12R C11 *C12 H12S 1.1103 111.73 -117.14 109.17 1.1115 +IC C11 C12 O12 CD1 1.4806 108.48 100.89 115.21 1.3485 +IC C12 O12 CD1 CD2 1.4206 115.21 0.0 102.03 1.4979 +IC CD2 O12 *CD1 OD1 1.4979 102.03 172.46 124.90 1.2074 +IC O12 CD1 CD2 CD3 1.3485 102.03 145.94 108.15 1.5439 +!chain 1 +IC CA3 CA1 *CA2 H2A 1.5614 111.56 -126.88 116.60 1.0567 +IC H2A CA1 *CA2 H2B 1.0567 116.60 -120.46 107.56 1.0927 +IC CA1 CA2 CA3 CA4 1.5434 111.56 178.17 112.38 1.5543 +IC CA4 CA2 *CA3 H3A 1.5543 112.38 -115.58 110.36 1.0691 +IC H3A CA2 *CA3 H3B 1.0691 110.36 -116.74 109.97 1.1344 +IC CA2 CA3 CA4 CA5 1.5614 112.38 174.26 114.93 1.5290 +IC CA5 CA3 *CA4 H4A 1.5290 114.93 -117.82 107.19 1.0636 +IC H4A CA3 *CA4 H4B 1.0636 107.19 -118.11 109.41 1.1180 +IC CA3 CA4 CA5 CA6 1.5543 114.93 139.45 116.26 1.5437 +IC CA6 CA4 *CA5 H5A 1.5437 116.26 -115.47 116.05 1.1088 +IC H5A CA4 *CA5 H5B 1.1088 116.05 -122.13 108.08 1.1320 +IC CA4 CA5 CA6 CA7 1.5290 116.26 159.28 113.90 1.5449 +IC CA7 CA5 *CA6 H6A 1.5449 113.90 -120.21 112.43 1.0817 +IC H6A CA5 *CA6 H6B 1.0817 112.43 -112.42 110.24 1.0503 +IC CA5 CA6 CA7 CA8 1.5437 113.90 167.68 115.30 1.5615 +IC CA8 CA6 *CA7 H7A 1.5615 115.30 -116.36 108.50 1.1480 +IC H7A CA6 *CA7 H7B 1.1480 108.50 -115.94 110.56 1.1231 +IC CA6 CA7 CA8 CA9 1.5449 115.30 165.37 111.83 1.5514 +IC CA9 CA7 *CA8 H8A 1.5514 111.83 -113.43 111.91 1.1377 +IC H8A CA7 *CA8 H8B 1.1377 111.91 -118.34 108.18 1.0480 +IC CA7 CA8 CA9 CA10 1.5615 111.83 176.59 110.57 1.5526 +IC CA10 CA8 *CA9 H9A 1.5526 110.57 -129.97 113.53 1.1310 +IC H9A CA8 *CA9 H9B 1.1310 113.53 -109.70 107.39 1.1594 +IC CA8 CA9 CA10 CA11 1.5514 110.57 -177.26 112.26 1.5783 +IC CA11 CA9 *CA10 H10A 1.5783 112.26 -123.45 106.63 1.1533 +IC H10A CA9 *CA10 H10B 1.1533 106.63 -118.25 115.85 1.0771 +IC CA9 CA10 CA11 CA12 1.5526 112.26 -163.15 112.58 1.5528 +IC CA12 CA10 *CA11 H11A 1.5528 112.58 -121.90 102.65 1.0764 +IC H11A CA10 *CA11 H11B 1.0764 102.65 -122.46 109.95 1.1248 +IC CA10 CA11 CA12 CA13 1.5783 112.58 -179.16 115.34 1.5375 +IC CA13 CA11 *CA12 H12A 1.5375 115.34 -129.55 111.80 1.0856 +IC H12A CA11 *CA12 H12B 1.0856 111.80 -109.80 105.66 1.0741 +IC CA11 CA12 CA13 CA14 1.5528 115.34 -178.59 114.71 1.5546 +IC CA14 CA12 *CA13 H13A 1.5546 114.71 -121.77 106.42 1.0758 +IC H13A CA12 *CA13 H13B 1.0758 106.42 -114.53 102.53 1.0909 +IC CA12 CA13 CA14 CA15 1.5375 114.71 179.82 117.78 1.5331 +IC CA15 CA13 *CA14 H14A 1.5331 117.78 -126.75 106.30 1.1072 +IC H14A CA13 *CA14 H14B 1.1072 106.30 -108.90 106.38 1.0834 +IC CA13 CA14 CA15 CA16 1.5546 117.78 169.53 109.01 1.4928 +IC CA16 CA14 *CA15 H15A 1.4928 109.01 -121.10 100.35 1.1439 +IC H15A CA14 *CA15 H15B 1.1439 100.35 -117.57 115.28 1.1080 +IC CA14 CA15 CA16 H16A 1.5331 109.01 -61.78 119.36 1.0834 +IC H16A CA15 *CA16 H16B 1.0834 119.36 138.24 116.61 1.0932 +IC H16A CA15 *CA16 H16C 1.0834 119.36 -107.69 109.08 1.1555 +!chain 2 +IC CD3 CD1 *CD2 H2D 1.5614 111.56 -126.88 116.60 1.0567 +IC H2D CD1 *CD2 H2E 1.0567 116.60 -120.46 107.56 1.0927 +IC CD1 CD2 CD3 CD4 1.5434 111.56 178.17 112.38 1.5543 +IC CD4 CD2 *CD3 H3D 1.5543 112.38 -115.58 110.36 1.0691 +IC H3D CD2 *CD3 H3E 1.0691 110.36 -116.74 109.97 1.1344 +IC CD2 CD3 CD4 CD5 1.5614 112.38 174.26 114.93 1.5290 +IC CD5 CD3 *CD4 H4D 1.5290 114.93 -117.82 107.19 1.0636 +IC H4D CD3 *CD4 H4E 1.0636 107.19 -118.11 109.41 1.1180 +IC CD3 CD4 CD5 CD6 1.5543 114.93 139.45 116.26 1.5437 +IC CD6 CD4 *CD5 H5D 1.5437 116.26 -115.47 116.05 1.1088 +IC H5D CD4 *CD5 H5E 1.1088 116.05 -122.13 108.08 1.1320 +IC CD4 CD5 CD6 CD7 1.5290 116.26 159.28 113.90 1.5449 +IC CD7 CD5 *CD6 H6D 1.5449 113.90 -120.21 112.43 1.0817 +IC H6D CD5 *CD6 H6E 1.0817 112.43 -112.42 110.24 1.0503 +IC CD5 CD6 CD7 CD8 1.5437 113.90 167.68 115.30 1.5615 +IC CD8 CD6 *CD7 H7D 1.5615 115.30 -116.36 108.50 1.1480 +IC H7D CD6 *CD7 H7E 1.1480 108.50 -115.94 110.56 1.1231 +IC CD6 CD7 CD8 CD9 1.5449 115.30 165.37 111.83 1.5514 +IC CD9 CD7 *CD8 H8D 1.5514 111.83 -113.43 111.91 1.1377 +IC H8D CD7 *CD8 H8E 1.1377 111.91 -118.34 108.18 1.0480 +IC CD7 CD8 CD9 CD10 1.5615 111.83 176.59 110.57 1.5526 +IC CD10 CD8 *CD9 H9D 1.5526 110.57 -129.97 113.53 1.1310 +IC H9D CD8 *CD9 H9E 1.1310 113.53 -109.70 107.39 1.1594 +IC CD8 CD9 CD10 CD11 1.5514 110.57 -177.26 112.26 1.5783 +IC CD11 CD9 *CD10 H10D 1.5783 112.26 -123.45 106.63 1.1533 +IC H10D CD9 *CD10 H10E 1.1533 106.63 -118.25 115.85 1.0771 +IC CD9 CD10 CD11 CD12 1.5526 112.26 -163.15 112.58 1.5528 +IC CD12 CD10 *CD11 H11D 1.5528 112.58 -121.90 102.65 1.0764 +IC H11D CD10 *CD11 H11E 1.0764 102.65 -122.46 109.95 1.1248 +IC CD10 CD11 CD12 CD13 1.5783 112.58 -179.16 115.34 1.5375 +IC CD13 CD11 *CD12 H12D 1.5375 115.34 -129.55 111.80 1.0856 +IC H12D CD11 *CD12 H12E 1.0856 111.80 -109.80 105.66 1.0741 +IC CD11 CD12 CD13 CD14 1.5528 115.34 -178.59 114.71 1.5546 +IC CD14 CD12 *CD13 H13D 1.5546 114.71 -121.77 106.42 1.0758 +IC H13D CD12 *CD13 H13E 1.0758 106.42 -114.53 102.53 1.0909 +IC CD12 CD13 CD14 CD15 1.5375 114.71 179.82 117.78 1.5331 +IC CD15 CD13 *CD14 H14D 1.5331 117.78 -126.75 106.30 1.1072 +IC H14D CD13 *CD14 H14E 1.1072 106.30 -108.90 106.38 1.0834 +IC CD13 CD14 CD15 CD16 1.5546 117.78 169.53 109.01 1.4928 +IC CD16 CD14 *CD15 H15D 1.4928 109.01 -121.10 100.35 1.1439 +IC H15D CD14 *CD15 H15E 1.1439 100.35 -117.57 115.28 1.1080 +IC CD14 CD15 CD16 H16D 1.5331 109.01 -61.78 119.36 1.0834 +IC H16D CD15 *CD16 H16E 1.0834 119.36 138.24 116.61 1.0932 +IC H16D CD15 *CD16 H16F 1.0834 119.36 -107.69 109.08 1.1555 +!chain 3 +IC CX3 CX1 *CX2 H2X 1.5614 111.56 -126.88 116.60 1.0567 +IC H2X CX1 *CX2 H2Y 1.0567 116.60 -120.46 107.56 1.0927 +IC CX1 CX2 CX3 CX4 1.5434 111.56 178.17 112.38 1.5543 +IC CX4 CX2 *CX3 H3X 1.5543 112.38 -115.58 110.36 1.0691 +IC H3X CX2 *CX3 H3Y 1.0691 110.36 -116.74 109.97 1.1344 +IC CX2 CX3 CX4 CX5 1.5614 112.38 174.26 114.93 1.5290 +IC CX5 CX3 *CX4 H4X 1.5290 114.93 -117.82 107.19 1.0636 +IC H4X CX3 *CX4 H4Y 1.0636 107.19 -118.11 109.41 1.1180 +IC CX3 CX4 CX5 CX6 1.5543 114.93 139.45 116.26 1.5437 +IC CX6 CX4 *CX5 H5X 1.5437 116.26 -115.47 116.05 1.1088 +IC H5X CX4 *CX5 H5Y 1.1088 116.05 -122.13 108.08 1.1320 +IC CX4 CX5 CX6 CX7 1.5290 116.26 159.28 113.90 1.5449 +IC CX7 CX5 *CX6 H6X 1.5449 113.90 -120.21 112.43 1.0817 +IC H6X CX5 *CX6 H6Y 1.0817 112.43 -112.42 110.24 1.0503 +IC CX5 CX6 CX7 CX8 1.5437 113.90 167.68 115.30 1.5615 +IC CX8 CX6 *CX7 H7X 1.5615 115.30 -116.36 108.50 1.1480 +IC H7X CX6 *CX7 H7Y 1.1480 108.50 -115.94 110.56 1.1231 +IC CX6 CX7 CX8 CX9 1.5449 115.30 165.37 111.83 1.5514 +IC CX9 CX7 *CX8 H8X 1.5514 111.83 -113.43 111.91 1.1377 +IC H8X CX7 *CX8 H8Y 1.1377 111.91 -118.34 108.18 1.0480 +IC CX7 CX8 CX9 CX10 1.5615 111.83 176.59 110.57 1.5526 +IC CX10 CX8 *CX9 H9X 1.5526 110.57 -129.97 113.53 1.1310 +IC H9X CX8 *CX9 H9Y 1.1310 113.53 -109.70 107.39 1.1594 +IC CX8 CX9 CX10 CX11 1.5514 110.57 -177.26 112.26 1.5783 +IC CX11 CX9 *CX10 H10X 1.5783 112.26 -123.45 106.63 1.1533 +IC H10X CX9 *CX10 H10Y 1.1533 106.63 -118.25 115.85 1.0771 +IC CX9 CX10 CX11 CX12 1.5526 112.26 -163.15 112.58 1.5528 +IC CX12 CX10 *CX11 H11X 1.5528 112.58 -121.90 102.65 1.0764 +IC H11X CX10 *CX11 H11Y 1.0764 102.65 -122.46 109.95 1.1248 +IC CX10 CX11 CX12 CX13 1.5783 112.58 -179.16 115.34 1.5375 +IC CX13 CX11 *CX12 H12X 1.5375 115.34 -129.55 111.80 1.0856 +IC H12X CX11 *CX12 H12Y 1.0856 111.80 -109.80 105.66 1.0741 +IC CX11 CX12 CX13 CX14 1.5528 115.34 -178.59 114.71 1.5546 +IC CX14 CX12 *CX13 H13X 1.5546 114.71 -121.77 106.42 1.0758 +IC H13X CX12 *CX13 H13Y 1.0758 106.42 -114.53 102.53 1.0909 +IC CX12 CX13 CX14 CX15 1.5375 114.71 179.82 117.78 1.5331 +IC CX15 CX13 *CX14 H14X 1.5331 117.78 -126.75 106.30 1.1072 +IC H14X CX13 *CX14 H14Y 1.1072 106.30 -108.90 106.38 1.0834 +IC CX13 CX14 CX15 CX16 1.5546 117.78 169.53 109.01 1.4928 +IC CX16 CX14 *CX15 H15X 1.4928 109.01 -121.10 100.35 1.1439 +IC H15X CX14 *CX15 H15Y 1.1439 100.35 -117.57 115.28 1.1080 +IC CX14 CX15 CX16 H16X 1.5331 109.01 -61.78 119.36 1.0834 +IC H16X CX15 *CX16 H16Y 1.0834 119.36 138.24 116.61 1.0932 +IC H16X CX15 *CX16 H16Z 1.0834 119.36 -107.69 109.08 1.1555 + +end + +read para card append flex +* cystein-palmitate parameters +* + +BONDS + +S CL 240.000 1.8160 ! from, CG331 SG311 240.00 1.8160 ! PROT fitted to C-S s 9/26/92 (FL) +S CG321 198.000 1.8180 ! from, CG321 SG311, PROT fitted to C-S s 9/26/92 (FL) +CG321 CTL1 222.500 1.5380 ! from, CTL1 CTL2, alkanes, 3/92 + +ANGLES +!!CYSP +CT2 S CL 34.000 95.00 ! ALLOW ALI SUL ION +CTL2 CL S 58.000 114.50 ! from, S CT2 CT2, ALLOW ALI SUL ION +OBL CL S 75.000 122.20 ! ALLOW ALI SUL ION +!!GLYM +NH1 C CTL2 80.000 122.50 ! prot22; NMA Vib Modes (LK); O-C-NH1 +!!CYSF and CYSG +CT2 S CG321 34.000 95.00 ! from, CG321 SG311 CG321, PROTNA sahc +S CG321 HGA2 46.100 111.30 ! from, SG311 CG321 HGA2, PROT vib. freq. and HF/geo. (DTN) 8/24/90 +S CG321 CG2D1 58.000 112.50 ! from, CG311 CG321 SG311, PROT as in expt.MeEtS & DALC crystal, 5/15/92 +!!CYSLP1 +S CG321 CTL1 58.00 114.50 ! from, CG331 CG321 SG311, PROT expt. MeEtS, 3/26/92 (FL) +HGA2 CG321 CTL1 26.500 110.10 22.53 2.179 ! from, HAL2 CTL2 CTL1, alkane, 4/98 +CG321 CTL1 HAL1 34.500 110.10 22.53 2.179 ! from, HAL1 CTL1 CTL2, alkane, 3/92 +CG321 CTL1 OSL 75.700 110.10 ! from, OSL CTL1 CTL2, acetic acid +CG321 CTL1 CTL2 58.350 113.50 11.16 2.561 ! from, CTL2 CTL1 CTL2, glycerol + +DIHEDRALS + +!!CYSP +CL S CT2 CT1 0.240 1 180.00 ! from, CG321 CG321 SG311 CG331 +CL S CT2 CT1 0.370 3 0.00 ! " +HA2 CT2 S CL 0.280 3 0.00 ! from, HGA2 CG321 SG311 CG331 +CT2 S CL CTL2 0.240 1 180.00 ! from, CG321 CG321 SG311 CG331 +CT2 S CL CTL2 0.370 3 0.00 ! " +CT2 S CL OBL 2.050 2 180.00 ! +!!GLYM +NH1 C CTL2 HAL2 0.000 3 0.00 ! from, prot22; sp2-methyl, no dihedral potential; NH1 C CT2 HA +NH1 C CTL2 CTL2 1.990 1 0.00 ! from, CTL2 CTL2 C NHL +NH1 C CTL2 CTL2 0.640 2 180.00 ! +NH1 C CTL2 CTL2 0.280 3 180.00 ! +H NH1 C CTL2 2.500 2 180.00 ! prot22; H NH1 C CT2 +CT2 NH1 C CTL2 0.000 1 0.00 ! from, CTL1 NHL C CTL2 + +!!CYSF and CYSG +CT1 CT2 S CG321 0.240 1 180.00 ! from, CG321 CG321 SG311 CG321, PROT expt. MeEtS, 3/26/92 +CT1 CT2 S CG321 0.370 3 0.00 ! " +CT2 S CG321 HGA2 0.280 3 0.00 ! from, HGA2 CG321 SG311 CG321, PROT DTN 8/24/90 +CT2 S CG321 CG2D1 0.240 1 180.00 ! from, CG321 CG321 SG311 CG321, PROT expt. MeEtS, 3/26/92 +CT2 S CG321 CG2D1 0.370 3 0.00 ! " +HA2 CT2 S CG321 0.280 3 0.00 ! from, HGA2 CG321 SG311 CG321, PROT DTN 8/24/90 +S CG321 CG2D1 HGA4 0.200 3 0.0 ! from, par27 X CTL1 CTL2 X +S CG321 CG2D1 CG2D1 0.200 3 0.0 ! from, par27 X CTL1 CTL2 X +!!CYSLP1 +CT1 NH1 C CTL2 0.000 1 0.00 ! from, CTL1 NHL C CTL2 +CT2 S CG321 CTL1 0.240 1 180.00 ! from, CG321 CG321 SG311 CG321, PROT expt. MeEtS, 3/26/92 +CT2 S CG321 CTL1 0.370 3 0.00 ! " +S CG321 CTL1 HAL1 0.200 3 0.0 ! from, par27 X CTL1 CTL2 X +S CG321 CTL1 OSL 0.200 3 0.0 ! from, par27 X CTL1 CTL2 X +S CG321 CTL1 CTL2 0.200 3 0.0 ! from, par27 X CTL1 CTL2 X +HGA2 CG321 CTL1 HAL1 0.200 3 0.0 ! from, par27 X CTL1 CTL2 X +HGA2 CG321 CTL1 OSL 0.200 3 0.0 ! from, par27 X CTL1 CTL2 X +HGA2 CG321 CTL1 CTL2 0.200 3 0.0 ! from, par27 X CTL1 CTL2 X + + +IMPROPER + +CL X X CTL2 96.0000 0 0.0000 ! from, CC X X CT2 +C O NH1 CTL2 96.0000 0 0.0000 ! from, CC X X CT2 +end + +return diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_sphingo.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_sphingo.str new file mode 100644 index 00000000..db037a81 --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_sphingo.str @@ -0,0 +1,6247 @@ +* Toppar stream for ceramides and spingomyelins; requires flex format files +* top_all36_lipid.rtf and par_all36_lipid.prm +* + +! REFERENCES +! +! PSM and SSM Lipids +! +! Venable, R.M., B. Rogaski, H. Rui, A.D. MacKerell, Jr., R.W. Pastor, & J.B. Klauda. +! An Experimentally Validated All-atom Force Field for Sphingomyelin. In prep. (2013). +! +! Ceramide +! +! Submited by Sam Tonddast-Navaei of U. Cincinnati. Advised by Russell Devane +! + +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have proirity, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* cer/sm residues +* +36 1 + +! Ceramides + +MASS 165 NHL 14.00700 N ! +MASS 166 CTO1 12.01100 C ! +MASS 167 CEL3 12.01100 C ! +MASS 168 CTO2 12.01100 C ! + + +RESI PSM 0.00 ! sphingomyelin d18:1/16:0 +GROUP ! +ATOM N NTL -0.60 ! H15B +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H15A-C15-H15C +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | | | +ATOM H14A HL 0.25 ! H13A-C13---N--C14-H14A (+) +ATOM H14B HL 0.25 ! | | | +ATOM H14C HL 0.25 ! H13B | H14B +ATOM C13 CTL5 -0.35 ! | +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! | +ATOM H13C HL 0.25 ! H12A-C12-H12B +ATOM C12 CTL2 -0.10 ! | +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H11A-C11-H11B +GROUP ! | +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! (-) O13 O12 +ATOM P PL 1.50 ! \ / +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM O12 OSLP -0.57 ! | +ATOM C1S CTL2 -0.08 ! | +ATOM H1S HAL2 0.09 ! H1S---C1S---H1T +ATOM H1T HAL2 0.09 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C15F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H16F---C16F---H16G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H16H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL3 -0.27 ! +ATOM H16F HAL3 0.09 ! +ATOM H16G HAL3 0.09 ! +ATOM H16H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O11 +!PHOSLPHOCHOLINE +BOND O11 P O12 P O13 P O14 P +BOND O12 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 N N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F H16H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C13 C12 *N C14 1.4967 109.68 116.91 107.30 1.5040 + IC C13 C12 *N C15 1.4967 109.68 -123.42 110.88 1.4938 + IC C12 N C15 H15A 1.5212 110.88 -177.15 111.31 1.0816 + IC H15A N *C15 H15B 1.0816 111.31 118.98 109.44 1.0875 + IC H15A N *C15 H15C 1.0816 111.31 -122.11 111.46 1.0818 + IC C12 N C14 H14A 1.5212 107.30 -178.89 114.23 1.0739 + IC H14A N *C14 H14B 1.0739 114.23 123.44 110.21 1.0968 + IC H14A N *C14 H14C 1.0739 114.23 -124.43 111.41 1.0948 + IC C12 N C13 H13A 1.5212 109.68 176.44 111.15 1.0822 + IC H13A N *C13 H13B 1.0822 111.15 121.89 111.75 1.0814 + IC H13A N *C13 H13C 1.0822 111.15 -118.50 109.57 1.0892 + IC C13 N C12 C11 1.4967 109.68 -178.83 116.30 1.5392 + IC C11 N *C12 H12A 1.5392 116.30 117.04 108.30 1.0985 + IC C11 N *C12 H12B 1.5392 116.30 -126.61 112.36 1.0787 + IC N C12 C11 O12 1.5212 116.30 126.79 107.85 1.4239 + IC O12 C12 *C11 H11A 1.4239 107.85 118.10 109.30 1.1131 + IC O12 C12 *C11 H11B 1.4239 107.85 -123.12 113.16 1.1140 + IC C12 C11 O12 P 1.5392 107.85 -68.29 118.09 1.5886 + IC C11 O12 P O11 1.4239 118.09 -167.58 104.18 1.5725 + IC O11 O12 *P O13 1.5725 104.18 116.57 107.05 1.4823 + IC O11 O12 *P O14 1.5725 104.18 -118.73 106.98 1.4805 + IC O12 P O11 C1S 1.5886 104.18 51.85 121.69 1.4327 + IC P O11 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O11 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O11 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F H16F 1.5334 113.16 -59.91 110.49 1.1113 + IC H16F C15F *C16F H16G 1.1113 110.49 119.86 110.41 1.1115 + IC H16F C15F *C16F H16H 1.1113 110.49 -120.11 110.63 1.1112 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 ! OH chirality (ch + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 ! OH chirality (ch + IC O11 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 ! assume ok + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 ! assume ok +! IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009! assume redundent +! SWAPPED + IC C4S C3S C2S C1S 1.5009 110.14 160.94 114.25 1.5586 + IC C1S C2S NF C1F 1.5586 111.52 -70.50 124.85 1.3364 +! SWAPPED + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 +PATCH FIRST NONE LAST NONE + +RESI SSM 0.00 ! sphingomyelin d18:1/18:0 +GROUP ! +ATOM N NTL -0.60 ! H15B +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H15A-C15-H15C +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | | | +ATOM H14A HL 0.25 ! H13A-C13---N--C14-H14A (+) +ATOM H14B HL 0.25 ! | | | +ATOM H14C HL 0.25 ! H13B | H14B +ATOM C13 CTL5 -0.35 ! | +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! | +ATOM H13C HL 0.25 ! H12A-C12-H12B +ATOM C12 CTL2 -0.10 ! | +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H11A-C11-H11B +GROUP ! | +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! (-) O13 O12 +ATOM P PL 1.50 ! \ / +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM O12 OSLP -0.57 ! | +ATOM C1S CTL2 -0.08 ! | +ATOM H1S HAL2 0.09 ! H1S---C1S---H1T +ATOM H1T HAL2 0.09 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C17F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H18F---C18F---H18G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H18H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL3 -0.27 ! +ATOM H18F HAL3 0.09 ! +ATOM H18G HAL3 0.09 ! +ATOM H18H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O11 +!PHOSLPHOCHOLINE +BOND O11 P O12 P O13 P O14 P +BOND O12 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 N N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F H18H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C13 C12 *N C14 1.4967 109.68 116.91 107.30 1.5040 + IC C13 C12 *N C15 1.4967 109.68 -123.42 110.88 1.4938 + IC C12 N C15 H15A 1.5212 110.88 -177.15 111.31 1.0816 + IC H15A N *C15 H15B 1.0816 111.31 118.98 109.44 1.0875 + IC H15A N *C15 H15C 1.0816 111.31 -122.11 111.46 1.0818 + IC C12 N C14 H14A 1.5212 107.30 -178.89 114.23 1.0739 + IC H14A N *C14 H14B 1.0739 114.23 123.44 110.21 1.0968 + IC H14A N *C14 H14C 1.0739 114.23 -124.43 111.41 1.0948 + IC C12 N C13 H13A 1.5212 109.68 176.44 111.15 1.0822 + IC H13A N *C13 H13B 1.0822 111.15 121.89 111.75 1.0814 + IC H13A N *C13 H13C 1.0822 111.15 -118.50 109.57 1.0892 + IC C13 N C12 C11 1.4967 109.68 -178.83 116.30 1.5392 + IC C11 N *C12 H12A 1.5392 116.30 117.04 108.30 1.0985 + IC C11 N *C12 H12B 1.5392 116.30 -126.61 112.36 1.0787 + IC N C12 C11 O12 1.5212 116.30 126.79 107.85 1.4239 + IC O12 C12 *C11 H11A 1.4239 107.85 118.10 109.30 1.1131 + IC O12 C12 *C11 H11B 1.4239 107.85 -123.12 113.16 1.1140 + IC C12 C11 O12 P 1.5392 107.85 -68.29 118.09 1.5886 + IC C11 O12 P O11 1.4239 118.09 -167.58 104.18 1.5725 + IC O11 O12 *P O13 1.5725 104.18 116.57 107.05 1.4823 + IC O11 O12 *P O14 1.5725 104.18 -118.73 106.98 1.4805 + IC O12 P O11 C1S 1.5886 104.18 51.85 121.69 1.4327 + IC P O11 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O11 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O11 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O11 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 170.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 59.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F H18F 1.5334 113.16 -59.91 110.49 1.1113 + IC H18F C17F *C18F H18G 1.1113 110.49 119.86 110.41 1.1115 + IC H18F C17F *C18F H18H 1.1113 110.49 -120.11 110.63 1.1112 +PATCH FIRST NONE LAST NONE + +RESI OSM 0.00 ! sphingomyelin d18:1/18:1 (w/oleic acid) +GROUP ! +ATOM N NTL -0.60 ! H15B +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H15A-C15-H15C +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | | | +ATOM H14A HL 0.25 ! H13A-C13---N--C14-H14A (+) +ATOM H14B HL 0.25 ! | | | +ATOM H14C HL 0.25 ! H13B | H14B +ATOM C13 CTL5 -0.35 ! | +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! | +ATOM H13C HL 0.25 ! H12A-C12-H12B +ATOM C12 CTL2 -0.10 ! | +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H11A-C11-H11B +GROUP ! | +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! (-) O13 O12 +ATOM P PL 1.50 ! \ / +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM O12 OSLP -0.57 ! | +ATOM C1S CTL2 -0.08 ! | +ATOM H1S HAL2 0.09 ! H1S---C1S---H1T +ATOM H1T HAL2 0.09 ! | +GROUP ! H2S---C2S-----------------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C8F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | C9F +ATOM C5S CEL3 -0.15 ! | || +ATOM H5S HEL1 0.15 ! | C10F +GROUP ! H3S----C3S--O3--HO3 | +ATOM C6S CTL2 -0.18 ! | [(CH2)11F (C3F,C4F...C17F) +ATOM H6S HAL2 0.09 ! C4S--H4S | +ATOM H6T HAL2 0.09 ! || H18F---C18F---H18G +GROUP ! C5S--H5S | +ATOM C7S CTL2 -0.18 ! | H18H +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CEL1 -0.15 ! +ATOM H9F HEL1 0.15 ! +GROUP ! +ATOM C10F CEL1 -0.15 ! +ATOM H10F HEL1 0.15 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL3 -0.27 ! +ATOM H18F HAL3 0.09 ! +ATOM H18G HAL3 0.09 ! +ATOM H18H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O11 +!PHOSLPHOCHOLINE +BOND O11 P O12 P O13 P O14 P +BOND O12 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 N N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F +BOND C10F H10F +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F H18H + +DOUBLE C4S C5S +DOUBLE C9F C10F +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC C13 C12 *N C14 1.4967 109.68 116.91 107.30 1.5040 + IC C13 C12 *N C15 1.4967 109.68 -123.42 110.88 1.4938 + IC C12 N C15 H15A 1.5212 110.88 -177.15 111.31 1.0816 + IC H15A N *C15 H15B 1.0816 111.31 118.98 109.44 1.0875 + IC H15A N *C15 H15C 1.0816 111.31 -122.11 111.46 1.0818 + IC C12 N C14 H14A 1.5212 107.30 -178.89 114.23 1.0739 + IC H14A N *C14 H14B 1.0739 114.23 123.44 110.21 1.0968 + IC H14A N *C14 H14C 1.0739 114.23 -124.43 111.41 1.0948 + IC C12 N C13 H13A 1.5212 109.68 176.44 111.15 1.0822 + IC H13A N *C13 H13B 1.0822 111.15 121.89 111.75 1.0814 + IC H13A N *C13 H13C 1.0822 111.15 -118.50 109.57 1.0892 + IC C13 N C12 C11 1.4967 109.68 -178.83 116.30 1.5392 + IC C11 N *C12 H12A 1.5392 116.30 117.04 108.30 1.0985 + IC C11 N *C12 H12B 1.5392 116.30 -126.61 112.36 1.0787 + IC N C12 C11 O12 1.5212 116.30 126.79 107.85 1.4239 + IC O12 C12 *C11 H11A 1.4239 107.85 118.10 109.30 1.1131 + IC O12 C12 *C11 H11B 1.4239 107.85 -123.12 113.16 1.1140 + IC C12 C11 O12 P 1.5392 107.85 -68.29 118.09 1.5886 + IC C11 O12 P O11 1.4239 118.09 -167.58 104.18 1.5725 + IC O11 O12 *P O13 1.5725 104.18 116.57 107.05 1.4823 + IC O11 O12 *P O14 1.5725 104.18 -118.73 106.98 1.4805 + IC O12 P O11 C1S 1.5886 104.18 51.85 121.69 1.4327 + IC P O11 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O11 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O11 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O11 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC C8F C9F C10F C11F 1.5340 112.34 0.00 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC C9F C10F C11F C12F 1.5343 112.74 180.00 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 0.00 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F H18F 1.5334 113.16 -59.91 110.49 1.1113 + IC H18F C17F *C18F H18G 1.1113 110.49 119.86 110.41 1.1115 + IC H18F C17F *C18F H18H 1.1113 110.49 -120.11 110.63 1.1112 +PATCH FIRST NONE LAST NONE + +RESI ASM 0.00 ! sphingomyelin d18:1/20:0 +GROUP ! +ATOM N NTL -0.60 ! H15B +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H15A-C15-H15C +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | | | +ATOM H14A HL 0.25 ! H13A-C13---N--C14-H14A (+) +ATOM H14B HL 0.25 ! | | | +ATOM H14C HL 0.25 ! H13B | H14B +ATOM C13 CTL5 -0.35 ! | +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! | +ATOM H13C HL 0.25 ! H12A-C12-H12B +ATOM C12 CTL2 -0.10 ! | +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H11A-C11-H11B +GROUP ! | +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! (-) O13 O12 +ATOM P PL 1.50 ! \ / +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM O12 OSLP -0.57 ! | +ATOM C1S CTL2 -0.08 ! | +ATOM H1S HAL2 0.09 ! H1S---C1S---H1T +ATOM H1T HAL2 0.09 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C19F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H20F---C20F---H20G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H20H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL3 -0.27 ! +ATOM H20F HAL3 0.09 ! +ATOM H20G HAL3 0.09 ! +ATOM H20H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O11 +!PHOSLPHOCHOLINE +BOND O11 P O12 P O13 P O14 P +BOND O12 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 N N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F H20H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC C13 C12 *N C14 1.4967 109.68 116.91 107.30 1.5040 + IC C13 C12 *N C15 1.4967 109.68 -123.42 110.88 1.4938 + IC C12 N C15 H15A 1.5212 110.88 -177.15 111.31 1.0816 + IC H15A N *C15 H15B 1.0816 111.31 118.98 109.44 1.0875 + IC H15A N *C15 H15C 1.0816 111.31 -122.11 111.46 1.0818 + IC C12 N C14 H14A 1.5212 107.30 -178.89 114.23 1.0739 + IC H14A N *C14 H14B 1.0739 114.23 123.44 110.21 1.0968 + IC H14A N *C14 H14C 1.0739 114.23 -124.43 111.41 1.0948 + IC C12 N C13 H13A 1.5212 109.68 176.44 111.15 1.0822 + IC H13A N *C13 H13B 1.0822 111.15 121.89 111.75 1.0814 + IC H13A N *C13 H13C 1.0822 111.15 -118.50 109.57 1.0892 + IC C13 N C12 C11 1.4967 109.68 -178.83 116.30 1.5392 + IC C11 N *C12 H12A 1.5392 116.30 117.04 108.30 1.0985 + IC C11 N *C12 H12B 1.5392 116.30 -126.61 112.36 1.0787 + IC N C12 C11 O12 1.5212 116.30 126.79 107.85 1.4239 + IC O12 C12 *C11 H11A 1.4239 107.85 118.10 109.30 1.1131 + IC O12 C12 *C11 H11B 1.4239 107.85 -123.12 113.16 1.1140 + IC C12 C11 O12 P 1.5392 107.85 -68.29 118.09 1.5886 + IC C11 O12 P O11 1.4239 118.09 -167.58 104.18 1.5725 + IC O11 O12 *P O13 1.5725 104.18 116.57 107.05 1.4823 + IC O11 O12 *P O14 1.5725 104.18 -118.73 106.98 1.4805 + IC O12 P O11 C1S 1.5886 104.18 51.85 121.69 1.4327 + IC P O11 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O11 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O11 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O11 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 -178.23 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5345 112.68 -178.23 113.16 1.5306 + IC C20F C18F *C19F H19F 1.5306 113.16 -121.86 108.84 1.1140 + IC H19F C18F *C19F H19G 1.1140 108.84 -116.70 108.76 1.1144 + IC C18F C19F C20F H20F 1.5334 113.16 -59.91 110.49 1.1113 + IC H20F C19F *C20F H20G 1.1113 110.49 119.86 110.41 1.1115 + IC H20F C19F *C20F H20H 1.1113 110.49 -120.11 110.63 1.1112 +PATCH FIRST NONE LAST NONE + +RESI BSM 0.00 ! sphingomyelin d18:1/22:0 +GROUP ! +ATOM N NTL -0.60 ! H15B +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H15A-C15-H15C +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | | | +ATOM H14A HL 0.25 ! H13A-C13---N--C14-H14A (+) +ATOM H14B HL 0.25 ! | | | +ATOM H14C HL 0.25 ! H13B | H14B +ATOM C13 CTL5 -0.35 ! | +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! | +ATOM H13C HL 0.25 ! H12A-C12-H12B +ATOM C12 CTL2 -0.10 ! | +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H11A-C11-H11B +GROUP ! | +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! (-) O13 O12 +ATOM P PL 1.50 ! \ / +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM O12 OSLP -0.57 ! | +ATOM C1S CTL2 -0.08 ! | +ATOM H1S HAL2 0.09 ! H1S---C1S---H1T +ATOM H1T HAL2 0.09 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C21F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H22F---C22F---H22G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H22H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL2 -0.18 ! +ATOM H20F HAL2 0.09 ! +ATOM H20G HAL2 0.09 ! +GROUP ! +ATOM C21F CTL2 -0.18 ! +ATOM H21F HAL2 0.09 ! +ATOM H21G HAL2 0.09 ! +GROUP ! +ATOM C22F CTL3 -0.27 ! +ATOM H22F HAL3 0.09 ! +ATOM H22G HAL3 0.09 ! +ATOM H22H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O11 +!PHOSLPHOCHOLINE +BOND O11 P O12 P O13 P O14 P +BOND O12 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 N N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F C21F C21F H21F C21F H21G +BOND C21F C22F C22F H22F C22F H22G +BOND C22F H22H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC C13 C12 *N C14 1.4967 109.68 116.91 107.30 1.5040 + IC C13 C12 *N C15 1.4967 109.68 -123.42 110.88 1.4938 + IC C12 N C15 H15A 1.5212 110.88 -177.15 111.31 1.0816 + IC H15A N *C15 H15B 1.0816 111.31 118.98 109.44 1.0875 + IC H15A N *C15 H15C 1.0816 111.31 -122.11 111.46 1.0818 + IC C12 N C14 H14A 1.5212 107.30 -178.89 114.23 1.0739 + IC H14A N *C14 H14B 1.0739 114.23 123.44 110.21 1.0968 + IC H14A N *C14 H14C 1.0739 114.23 -124.43 111.41 1.0948 + IC C12 N C13 H13A 1.5212 109.68 176.44 111.15 1.0822 + IC H13A N *C13 H13B 1.0822 111.15 121.89 111.75 1.0814 + IC H13A N *C13 H13C 1.0822 111.15 -118.50 109.57 1.0892 + IC C13 N C12 C11 1.4967 109.68 -178.83 116.30 1.5392 + IC C11 N *C12 H12A 1.5392 116.30 117.04 108.30 1.0985 + IC C11 N *C12 H12B 1.5392 116.30 -126.61 112.36 1.0787 + IC N C12 C11 O12 1.5212 116.30 126.79 107.85 1.4239 + IC O12 C12 *C11 H11A 1.4239 107.85 118.10 109.30 1.1131 + IC O12 C12 *C11 H11B 1.4239 107.85 -123.12 113.16 1.1140 + IC C12 C11 O12 P 1.5392 107.85 -68.29 118.09 1.5886 + IC C11 O12 P O11 1.4239 118.09 -167.58 104.18 1.5725 + IC O11 O12 *P O13 1.5725 104.18 116.57 107.05 1.4823 + IC O11 O12 *P O14 1.5725 104.18 -118.73 106.98 1.4805 + IC O12 P O11 C1S 1.5886 104.18 51.85 121.69 1.4327 + IC P O11 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O11 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O11 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O11 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 -178.23 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5344 112.57 179.80 112.59 1.5346 + IC C20F C18F *C19F H19F 1.5346 112.59 -121.28 109.10 1.1133 + IC H19F C18F *C19F H19G 1.1133 109.10 -117.38 109.12 1.1133 + IC C18F C19F C20F C21F 1.5345 112.59 -179.89 112.63 1.5337 + IC C21F C19F *C20F H20F 1.5337 112.63 -121.33 109.16 1.1133 + IC H20F C19F *C20F H20G 1.1133 109.16 -117.38 109.14 1.1133 + IC C19F C20F C21F C22F 1.5346 112.63 179.93 113.24 1.5309 + IC C22F C20F *C21F H21F 1.5309 113.24 -121.66 108.77 1.1142 + IC H21F C20F *C21F H21G 1.1142 108.77 -116.65 108.78 1.1142 + IC C20F C21F C22F H22F 1.5337 113.24 -59.91 110.47 1.1114 + IC H22F C21F *C22F H22G 1.1114 110.47 119.87 110.48 1.1113 + IC H22F C21F *C22F H22H 1.1114 110.47 -120.06 110.63 1.1113 +PATCH FIRST NONE LAST NONE + +RESI 23SM 0.00 ! sphingomyelin d18:1/23:0 +GROUP ! +ATOM N NTL -0.60 ! H15B +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H15A-C15-H15C +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | | | +ATOM H14A HL 0.25 ! H13A-C13---N--C14-H14A (+) +ATOM H14B HL 0.25 ! | | | +ATOM H14C HL 0.25 ! H13B | H14B +ATOM C13 CTL5 -0.35 ! | +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! | +ATOM H13C HL 0.25 ! H12A-C12-H12B +ATOM C12 CTL2 -0.10 ! | +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H11A-C11-H11B +GROUP ! | +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! (-) O13 O12 +ATOM P PL 1.50 ! \ / +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM O12 OSLP -0.57 ! | +ATOM C1S CTL2 -0.08 ! | +ATOM H1S HAL2 0.09 ! H1S---C1S---H1T +ATOM H1T HAL2 0.09 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C22F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H23F---C23F---H23G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H23H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL2 -0.18 ! +ATOM H20F HAL2 0.09 ! +ATOM H20G HAL2 0.09 ! +GROUP ! +ATOM C21F CTL2 -0.18 ! +ATOM H21F HAL2 0.09 ! +ATOM H21G HAL2 0.09 ! +GROUP ! +ATOM C22F CTL2 -0.18 ! +ATOM H22F HAL2 0.09 ! +ATOM H22G HAL2 0.09 ! +GROUP ! +ATOM C23F CTL3 -0.27 ! +ATOM H23F HAL3 0.09 ! +ATOM H23G HAL3 0.09 ! +ATOM H23H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O11 +!PHOSLPHOCHOLINE +BOND O11 P O12 P O13 P O14 P +BOND O12 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 N N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F C21F C21F H21F C21F H21G +BOND C21F C22F C22F H22F C22F H22G +BOND C22F C23F C23F H23F C23F H23G +BOND C23F H23H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC C13 C12 *N C14 1.4967 109.68 116.91 107.30 1.5040 + IC C13 C12 *N C15 1.4967 109.68 -123.42 110.88 1.4938 + IC C12 N C15 H15A 1.5212 110.88 -177.15 111.31 1.0816 + IC H15A N *C15 H15B 1.0816 111.31 118.98 109.44 1.0875 + IC H15A N *C15 H15C 1.0816 111.31 -122.11 111.46 1.0818 + IC C12 N C14 H14A 1.5212 107.30 -178.89 114.23 1.0739 + IC H14A N *C14 H14B 1.0739 114.23 123.44 110.21 1.0968 + IC H14A N *C14 H14C 1.0739 114.23 -124.43 111.41 1.0948 + IC C12 N C13 H13A 1.5212 109.68 176.44 111.15 1.0822 + IC H13A N *C13 H13B 1.0822 111.15 121.89 111.75 1.0814 + IC H13A N *C13 H13C 1.0822 111.15 -118.50 109.57 1.0892 + IC C13 N C12 C11 1.4967 109.68 -178.83 116.30 1.5392 + IC C11 N *C12 H12A 1.5392 116.30 117.04 108.30 1.0985 + IC C11 N *C12 H12B 1.5392 116.30 -126.61 112.36 1.0787 + IC N C12 C11 O12 1.5212 116.30 126.79 107.85 1.4239 + IC O12 C12 *C11 H11A 1.4239 107.85 118.10 109.30 1.1131 + IC O12 C12 *C11 H11B 1.4239 107.85 -123.12 113.16 1.1140 + IC C12 C11 O12 P 1.5392 107.85 -68.29 118.09 1.5886 + IC C11 O12 P O11 1.4239 118.09 -167.58 104.18 1.5725 + IC O11 O12 *P O13 1.5725 104.18 116.57 107.05 1.4823 + IC O11 O12 *P O14 1.5725 104.18 -118.73 106.98 1.4805 + IC O12 P O11 C1S 1.5886 104.18 51.85 121.69 1.4327 + IC P O11 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O11 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O11 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O11 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 -178.23 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5344 112.57 179.80 112.59 1.5346 + IC C20F C18F *C19F H19F 1.5346 112.59 -121.28 109.10 1.1133 + IC H19F C18F *C19F H19G 1.1133 109.10 -117.38 109.12 1.1133 + IC C18F C19F C20F C21F 1.5345 112.59 -179.89 112.63 1.5337 + IC C21F C19F *C20F H20F 1.5337 112.63 -121.33 109.16 1.1133 + IC H20F C19F *C20F H20G 1.1133 109.16 -117.38 109.14 1.1133 + IC C19F C20F C21F C22F 1.5346 112.63 179.93 113.24 1.5309 + IC C22F C20F *C21F H21F 1.5309 113.24 -121.66 108.77 1.1142 + IC H21F C20F *C21F H21G 1.1142 108.77 -116.65 108.78 1.1142 + IC C20F C21F C22F C23F 1.5346 112.63 179.93 113.24 1.5309 + IC C23F C21F *C22F H22F 1.5309 113.24 -121.66 108.77 1.1142 + IC H22F C21F *C22F H22G 1.1142 108.77 -116.65 108.78 1.1142 + IC C21F C22F C23F H23F 1.5337 113.24 -59.91 110.47 1.1114 + IC H23F C22F *C23F H23G 1.1114 110.47 119.87 110.48 1.1113 + IC H23F C22F *C23F H23H 1.1114 110.47 -120.06 110.63 1.1113 +PATCH FIRST NONE LAST NONE + +RESI LSM 0.00 ! sphingomyelin d18:1/24:0 +GROUP ! +ATOM N NTL -0.60 ! H15B +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H15A-C15-H15C +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | | | +ATOM H14A HL 0.25 ! H13A-C13---N--C14-H14A (+) +ATOM H14B HL 0.25 ! | | | +ATOM H14C HL 0.25 ! H13B | H14B +ATOM C13 CTL5 -0.35 ! | +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! | +ATOM H13C HL 0.25 ! H12A-C12-H12B +ATOM C12 CTL2 -0.10 ! | +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H11A-C11-H11B +GROUP ! | +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! (-) O13 O12 +ATOM P PL 1.50 ! \ / +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM O12 OSLP -0.57 ! | +ATOM C1S CTL2 -0.08 ! | +ATOM H1S HAL2 0.09 ! H1S---C1S---H1T +ATOM H1T HAL2 0.09 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C23F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H24F---C24F---H24G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H24H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL2 -0.18 ! +ATOM H20F HAL2 0.09 ! +ATOM H20G HAL2 0.09 ! +GROUP ! +ATOM C21F CTL2 -0.18 ! +ATOM H21F HAL2 0.09 ! +ATOM H21G HAL2 0.09 ! +GROUP ! +ATOM C22F CTL2 -0.18 ! +ATOM H22F HAL2 0.09 ! +ATOM H22G HAL2 0.09 ! +GROUP ! +ATOM C23F CTL2 -0.18 ! +ATOM H23F HAL2 0.09 ! +ATOM H23G HAL2 0.09 ! +GROUP ! +ATOM C24F CTL3 -0.27 ! +ATOM H24F HAL3 0.09 ! +ATOM H24G HAL3 0.09 ! +ATOM H24H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O11 +!PHOSLPHOCHOLINE +BOND O11 P O12 P O13 P O14 P +BOND O12 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 N N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F C21F C21F H21F C21F H21G +BOND C21F C22F C22F H22F C22F H22G +BOND C22F C23F C23F H23F C23F H23G +BOND C23F C24F C24F H24F C24F H24G +BOND C24F H24H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC C13 C12 *N C14 1.4967 109.68 116.91 107.30 1.5040 + IC C13 C12 *N C15 1.4967 109.68 -123.42 110.88 1.4938 + IC C12 N C15 H15A 1.5212 110.88 -177.15 111.31 1.0816 + IC H15A N *C15 H15B 1.0816 111.31 118.98 109.44 1.0875 + IC H15A N *C15 H15C 1.0816 111.31 -122.11 111.46 1.0818 + IC C12 N C14 H14A 1.5212 107.30 -178.89 114.23 1.0739 + IC H14A N *C14 H14B 1.0739 114.23 123.44 110.21 1.0968 + IC H14A N *C14 H14C 1.0739 114.23 -124.43 111.41 1.0948 + IC C12 N C13 H13A 1.5212 109.68 176.44 111.15 1.0822 + IC H13A N *C13 H13B 1.0822 111.15 121.89 111.75 1.0814 + IC H13A N *C13 H13C 1.0822 111.15 -118.50 109.57 1.0892 + IC C13 N C12 C11 1.4967 109.68 -178.83 116.30 1.5392 + IC C11 N *C12 H12A 1.5392 116.30 117.04 108.30 1.0985 + IC C11 N *C12 H12B 1.5392 116.30 -126.61 112.36 1.0787 + IC N C12 C11 O12 1.5212 116.30 126.79 107.85 1.4239 + IC O12 C12 *C11 H11A 1.4239 107.85 118.10 109.30 1.1131 + IC O12 C12 *C11 H11B 1.4239 107.85 -123.12 113.16 1.1140 + IC C12 C11 O12 P 1.5392 107.85 -68.29 118.09 1.5886 + IC C11 O12 P O11 1.4239 118.09 -167.58 104.18 1.5725 + IC O11 O12 *P O13 1.5725 104.18 116.57 107.05 1.4823 + IC O11 O12 *P O14 1.5725 104.18 -118.73 106.98 1.4805 + IC O12 P O11 C1S 1.5886 104.18 51.85 121.69 1.4327 + IC P O11 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O11 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O11 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O11 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 -178.23 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5344 112.57 179.80 112.59 1.5346 + IC C20F C18F *C19F H19F 1.5346 112.59 -121.28 109.10 1.1133 + IC H19F C18F *C19F H19G 1.1133 109.10 -117.38 109.12 1.1133 + IC C18F C19F C20F C21F 1.5345 112.59 -179.89 112.63 1.5337 + IC C21F C19F *C20F H20F 1.5337 112.63 -121.33 109.16 1.1133 + IC H20F C19F *C20F H20G 1.1133 109.16 -117.38 109.14 1.1133 + IC C19F C20F C21F C22F 1.5346 112.63 179.93 113.24 1.5309 + IC C22F C20F *C21F H21F 1.5309 113.24 -121.66 108.77 1.1142 + IC H21F C20F *C21F H21G 1.1142 108.77 -116.65 108.78 1.1142 + IC C20F C21F C22F C23F 1.5346 112.63 179.93 113.24 1.5309 + IC C23F C21F *C22F H22F 1.5309 113.24 -121.66 108.77 1.1142 + IC H22F C21F *C22F H22G 1.1142 108.77 -116.65 108.78 1.1142 + IC C21F C22F C23F C24F 1.5346 112.63 179.93 113.24 1.5309 + IC C24F C22F *C23F H23F 1.5309 113.24 -121.66 108.77 1.1142 + IC H23F C22F *C23F H23G 1.1142 108.77 -116.65 108.78 1.1142 + IC C22F C23F C24F H24F 1.5337 113.24 -59.91 110.47 1.1114 + IC H24F C23F *C24F H24G 1.1114 110.47 119.87 110.48 1.1113 + IC H24F C23F *C24F H24H 1.1114 110.47 -120.06 110.63 1.1113 +PATCH FIRST NONE LAST NONE + +RESI NSM 0.00 ! sphingomyelin d18:1/24:1 (w/nervonic acid) +GROUP ! +ATOM N NTL -0.60 ! H15B +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H15A-C15-H15C +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | | | +ATOM H14A HL 0.25 ! H13A-C13---N--C14-H14A (+) +ATOM H14B HL 0.25 ! | | | +ATOM H14C HL 0.25 ! H13B | H14B +ATOM C13 CTL5 -0.35 ! | +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! | +ATOM H13C HL 0.25 ! H12A-C12-H12B +ATOM C12 CTL2 -0.10 ! | +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H11A-C11-H11B +GROUP ! | +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! | +ATOM H11B HAL2 0.09 ! (-) O13 O12 +ATOM P PL 1.50 ! \ / +ATOM O13 O2L -0.78 ! P (+) +ATOM O14 O2L -0.78 ! / \ +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM O12 OSLP -0.57 ! | +ATOM C1S CTL2 -0.08 ! | +ATOM H1S HAL2 0.09 ! H1S---C1S---H1T +ATOM H1T HAL2 0.09 ! | +GROUP ! H2S---C2S-------------------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C14F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H15F---C15F +ATOM C5S CEL3 -0.15 ! | || +ATOM H5S HEL1 0.15 ! | H16F---C16F +GROUP ! H3S----C3S--O3--HO3 | +ATOM C6S CTL2 -0.18 ! | [(CH2)17F (C17F,C4F...C23F) +ATOM H6S HAL2 0.09 ! C4S--H4S | +ATOM H6T HAL2 0.09 ! || H24F---C24F---H24H +GROUP ! C5S--H5S | +ATOM C7S CTL2 -0.18 ! | H24G +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CEL1 -0.15 ! +ATOM H15F HEL1 0.15 ! +GROUP ! +ATOM C16F CEL1 -0.15 ! +ATOM H16F HEL1 0.15 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL2 -0.18 ! +ATOM H20F HAL2 0.09 ! +ATOM H20G HAL2 0.09 ! +GROUP ! +ATOM C21F CTL2 -0.18 ! +ATOM H21F HAL2 0.09 ! +ATOM H21G HAL2 0.09 ! +GROUP ! +ATOM C22F CTL2 -0.18 ! +ATOM H22F HAL2 0.09 ! +ATOM H22G HAL2 0.09 ! +GROUP ! +ATOM C23F CTL2 -0.18 ! +ATOM H23F HAL2 0.09 ! +ATOM H23G HAL2 0.09 ! +GROUP ! +ATOM C24F CTL3 -0.27 ! +ATOM H24F HAL3 0.09 ! +ATOM H24G HAL3 0.09 ! +ATOM H24H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O11 +!PHOSLPHOCHOLINE +BOND O11 P O12 P O13 P O14 P +BOND O12 C11 C11 H11A C11 H11B +BOND C11 C12 C12 H12A C12 H12B +BOND C12 N N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F +BOND C16F H16F +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F C21F C21F H21F C21F H21G +BOND C21F C22F C22F H22F C22F H22G +BOND C22F C23F C23F H23F C23F H23G +BOND C23F C24F C24F H24F C24F H24G +BOND C24F H24H + +DOUBLE C4S C5S +DOUBLE C15F C16F +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC C13 C12 *N C14 1.4967 109.68 116.91 107.30 1.5040 + IC C13 C12 *N C15 1.4967 109.68 -123.42 110.88 1.4938 + IC C12 N C15 H15A 1.5212 110.88 -177.15 111.31 1.0816 + IC H15A N *C15 H15B 1.0816 111.31 118.98 109.44 1.0875 + IC H15A N *C15 H15C 1.0816 111.31 -122.11 111.46 1.0818 + IC C12 N C14 H14A 1.5212 107.30 -178.89 114.23 1.0739 + IC H14A N *C14 H14B 1.0739 114.23 123.44 110.21 1.0968 + IC H14A N *C14 H14C 1.0739 114.23 -124.43 111.41 1.0948 + IC C12 N C13 H13A 1.5212 109.68 176.44 111.15 1.0822 + IC H13A N *C13 H13B 1.0822 111.15 121.89 111.75 1.0814 + IC H13A N *C13 H13C 1.0822 111.15 -118.50 109.57 1.0892 + IC C13 N C12 C11 1.4967 109.68 -178.83 116.30 1.5392 + IC C11 N *C12 H12A 1.5392 116.30 117.04 108.30 1.0985 + IC C11 N *C12 H12B 1.5392 116.30 -126.61 112.36 1.0787 + IC N C12 C11 O12 1.5212 116.30 126.79 107.85 1.4239 + IC O12 C12 *C11 H11A 1.4239 107.85 118.10 109.30 1.1131 + IC O12 C12 *C11 H11B 1.4239 107.85 -123.12 113.16 1.1140 + IC C12 C11 O12 P 1.5392 107.85 -68.29 118.09 1.5886 + IC C11 O12 P O11 1.4239 118.09 -167.58 104.18 1.5725 + IC O11 O12 *P O13 1.5725 104.18 116.57 107.05 1.4823 + IC O11 O12 *P O14 1.5725 104.18 -118.73 106.98 1.4805 + IC O12 P O11 C1S 1.5886 104.18 51.85 121.69 1.4327 + IC P O11 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O11 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O11 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O11 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC C14F C15F C16F C17F 1.5345 112.68 0.00 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 0.00 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5344 112.57 180.00 112.59 1.5346 + IC C20F C18F *C19F H19F 1.5346 112.59 -121.28 109.10 1.1133 + IC H19F C18F *C19F H19G 1.1133 109.10 -117.38 109.12 1.1133 + IC C18F C19F C20F C21F 1.5345 112.59 -179.89 112.63 1.5337 + IC C21F C19F *C20F H20F 1.5337 112.63 -121.33 109.16 1.1133 + IC H20F C19F *C20F H20G 1.1133 109.16 -117.38 109.14 1.1133 + IC C19F C20F C21F C22F 1.5346 112.63 179.93 113.24 1.5309 + IC C22F C20F *C21F H21F 1.5309 113.24 -121.66 108.77 1.1142 + IC H21F C20F *C21F H21G 1.1142 108.77 -116.65 108.78 1.1142 + IC C20F C21F C22F C23F 1.5346 112.63 179.93 113.24 1.5309 + IC C23F C21F *C22F H22F 1.5309 113.24 -121.66 108.77 1.1142 + IC H22F C21F *C22F H22G 1.1142 108.77 -116.65 108.78 1.1142 + IC C21F C22F C23F C24F 1.5346 112.63 179.93 113.24 1.5309 + IC C24F C22F *C23F H23F 1.5309 113.24 -121.66 108.77 1.1142 + IC H23F C22F *C23F H23G 1.1142 108.77 -116.65 108.78 1.1142 + IC C22F C23F C24F H24F 1.5337 113.24 -59.91 110.47 1.1114 + IC H24F C23F *C24F H24G 1.1114 110.47 119.87 110.48 1.1113 + IC H24F C23F *C24F H24H 1.1114 110.47 -120.06 110.63 1.1113 +PATCH FIRST NONE LAST NONE + +RESI CER2 0.00 ! CERAMIDE by by Sam Tonddast-Navaei (U. Cin/Russel Lab) + ! +GROUP ! HO1 +ATOM O1 OHL -0.69 ! \ +ATOM HO1 HOL 0.30 ! O1 +ATOM C1S CTO2 0.49 ! | +ATOM H1S HAL2 -0.05 ! H1S---C1S---H1T +ATOM H1T HAL2 -0.05 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C23F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H24F---C24F---H24G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H24H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL2 -0.18 ! +ATOM H20F HAL2 0.09 ! +ATOM H20G HAL2 0.09 ! +GROUP ! +ATOM C21F CTL2 -0.18 ! +ATOM H21F HAL2 0.09 ! +ATOM H21G HAL2 0.09 ! +GROUP ! +ATOM C22F CTL2 -0.18 ! +ATOM H22F HAL2 0.09 ! +ATOM H22G HAL2 0.09 ! +GROUP ! +ATOM C23F CTL2 -0.18 ! +ATOM H23F HAL2 0.09 ! +ATOM H23G HAL2 0.09 ! +GROUP ! +ATOM C24F CTL3 -0.27 ! +ATOM H24F HAL3 0.09 ! +ATOM H24G HAL3 0.09 ! +ATOM H24H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O1 O1 HO1 + +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F C21F C21F H21F C21F H21G +BOND C21F C22F C22F H22F C22F H22G +BOND C22F C23F C23F H23F C23F H23G +BOND C23F C24F C24F H24F C24F H24G +BOND C24F H24H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC HO1 O1 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O1 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O1 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O1 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 -178.23 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5344 112.57 179.80 112.59 1.5346 + IC C20F C18F *C19F H19F 1.5346 112.59 -121.28 109.10 1.1133 + IC H19F C18F *C19F H19G 1.1133 109.10 -117.38 109.12 1.1133 + IC C18F C19F C20F C21F 1.5345 112.59 -179.89 112.63 1.5337 + IC C21F C19F *C20F H20F 1.5337 112.63 -121.33 109.16 1.1133 + IC H20F C19F *C20F H20G 1.1133 109.16 -117.38 109.14 1.1133 + IC C19F C20F C21F C22F 1.5346 112.63 179.93 113.24 1.5309 + IC C22F C20F *C21F H21F 1.5309 113.24 -121.66 108.77 1.1142 + IC H21F C20F *C21F H21G 1.1142 108.77 -116.65 108.78 1.1142 + IC C20F C21F C22F C23F 1.5346 112.63 179.93 113.24 1.5309 + IC C23F C21F *C22F H22F 1.5309 113.24 -121.66 108.77 1.1142 + IC H22F C21F *C22F H22G 1.1142 108.77 -116.65 108.78 1.1142 + IC C21F C22F C23F C24F 1.5346 112.63 179.93 113.24 1.5309 + IC C24F C22F *C23F H23F 1.5309 113.24 -121.66 108.77 1.1142 + IC H23F C22F *C23F H23G 1.1142 108.77 -116.65 108.78 1.1142 + IC C22F C23F C24F H24F 1.5337 113.24 -59.91 110.47 1.1114 + IC H24F C23F *C24F H24G 1.1114 110.47 119.87 110.48 1.1113 + IC H24F C23F *C24F H24H 1.1114 110.47 -120.06 110.63 1.1113 +PATCH FIRST NONE LAST NONE + +RESI CER160 0.00 ! CERAMIDE d18:1/16:0 + ! +GROUP ! HO1 +ATOM O1 OHL -0.69 ! \ +ATOM HO1 HOL 0.30 ! O1 +ATOM C1S CTO2 0.49 ! | +ATOM H1S HAL2 -0.05 ! H1S---C1S---H1T +ATOM H1T HAL2 -0.05 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C15F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H16F---C16F---H16G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H16H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL3 -0.27 ! +ATOM H16F HAL3 0.09 ! +ATOM H16G HAL3 0.09 ! +ATOM H16H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O1 O1 HO1 + +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F H16H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC HO1 O1 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O1 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O1 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O1 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F H16F 1.5334 113.16 -59.91 110.49 1.1113 + IC H16F C15F *C16F H16G 1.1113 110.49 119.86 110.41 1.1115 + IC H16F C15F *C16F H16H 1.1113 110.49 -120.11 110.63 1.1112 +PATCH FIRST NONE LAST NONE + +RESI CER180 0.00 ! CERAMIDE d18:1/18:0 + ! +GROUP ! HO1 +ATOM O1 OHL -0.69 ! \ +ATOM HO1 HOL 0.30 ! O1 +ATOM C1S CTO2 0.49 ! | +ATOM H1S HAL2 -0.05 ! H1S---C1S---H1T +ATOM H1T HAL2 -0.05 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C17F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H18F---C18F---H18G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H18H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL3 -0.27 ! +ATOM H18F HAL3 0.09 ! +ATOM H18G HAL3 0.09 ! +ATOM H18H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O1 O1 HO1 + +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F H18H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC HO1 O1 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O1 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O1 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O1 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 59.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F H18F 1.5334 113.16 -59.91 110.49 1.1113 + IC H18F C17F *C18F H18G 1.1113 110.49 119.86 110.41 1.1115 + IC H18F C17F *C18F H18H 1.1113 110.49 -120.11 110.63 1.1112 +PATCH FIRST NONE LAST NONE + +RESI CER181 0.00 ! CERAMIDE d18:1/18:1 (w/oleic acid) + ! +GROUP ! HO1 +ATOM O1 OHL -0.69 ! \ +ATOM HO1 HOL 0.30 ! O1 +ATOM C1S CTO2 0.49 ! | +ATOM H1S HAL2 -0.05 ! H1S---C1S---H1T +ATOM H1T HAL2 -0.05 ! | +GROUP ! H2S---C2S-----------------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C8F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | C9F +ATOM C5S CEL3 -0.15 ! | || +ATOM H5S HEL1 0.15 ! | C10F +GROUP ! H3S----C3S--O3--HO3 | +ATOM C6S CTL2 -0.18 ! | [(CH2)11F (C3F,C4F...C17F) +ATOM H6S HAL2 0.09 ! C4S--H4S | +ATOM H6T HAL2 0.09 ! || H18F---C18F---H18G +GROUP ! C5S--H5S | +ATOM C7S CTL2 -0.18 ! | H18H +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CEL1 -0.15 ! +ATOM H9F HEL1 0.15 ! +GROUP ! +ATOM C10F CEL1 -0.15 ! +ATOM H10F HEL1 0.15 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL3 -0.27 ! +ATOM H18F HAL3 0.09 ! +ATOM H18G HAL3 0.09 ! +ATOM H18H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O1 O1 HO1 + +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F +BOND C10F H10F +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F H18H + +DOUBLE C4S C5S +DOUBLE C9F C10F +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC HO1 O1 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O1 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O1 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O1 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC C8F C9F C10F C11F 1.5340 112.34 0.00 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC C9F C10F C11F C12F 1.5343 112.74 180.00 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 0.00 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F H18F 1.5334 113.16 -59.91 110.49 1.1113 + IC H18F C17F *C18F H18G 1.1113 110.49 119.86 110.41 1.1115 + IC H18F C17F *C18F H18H 1.1113 110.49 -120.11 110.63 1.1112 +PATCH FIRST NONE LAST NONE + +RESI CER200 0.00 ! CERAMIDE d18:1/20:0 + ! +GROUP ! HO1 +ATOM O1 OHL -0.69 ! \ +ATOM HO1 HOL 0.30 ! O1 +ATOM C1S CTO2 0.49 ! | +ATOM H1S HAL2 -0.05 ! H1S---C1S---H1T +ATOM H1T HAL2 -0.05 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C19F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H20F---C20F---H20G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H20H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL3 -0.27 ! +ATOM H20F HAL3 0.09 ! +ATOM H20G HAL3 0.09 ! +ATOM H20H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O1 O1 HO1 + +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F H20H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC HO1 O1 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O1 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O1 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O1 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 -178.23 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5345 112.68 -178.23 113.16 1.5306 + IC C20F C18F *C19F H19F 1.5306 113.16 -121.86 108.84 1.1140 + IC H19F C18F *C19F H19G 1.1140 108.84 -116.70 108.76 1.1144 + IC C18F C19F C20F H20F 1.5334 113.16 -59.91 110.49 1.1113 + IC H20F C19F *C20F H20G 1.1113 110.49 119.86 110.41 1.1115 + IC H20F C19F *C20F H20H 1.1113 110.49 -120.11 110.63 1.1112 +PATCH FIRST NONE LAST NONE + +RESI CER220 0.00 ! CERAMIDE d18:1/22:0 + ! +GROUP ! HO1 +ATOM O1 OHL -0.69 ! \ +ATOM HO1 HOL 0.30 ! O1 +ATOM C1S CTO2 0.49 ! | +ATOM H1S HAL2 -0.05 ! H1S---C1S---H1T +ATOM H1T HAL2 -0.05 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C21F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H22F---C22F---H22G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H22H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL2 -0.18 ! +ATOM H20F HAL2 0.09 ! +ATOM H20G HAL2 0.09 ! +GROUP ! +ATOM C21F CTL2 -0.18 ! +ATOM H21F HAL2 0.09 ! +ATOM H21G HAL2 0.09 ! +GROUP ! +ATOM C22F CTL3 -0.27 ! +ATOM H22F HAL3 0.09 ! +ATOM H22G HAL3 0.09 ! +ATOM H22H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O1 O1 HO1 + +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F C21F C21F H21F C21F H21G +BOND C21F C22F C22F H22F C22F H22G +BOND C22F H22H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC HO1 O1 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O1 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O1 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O1 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 -178.23 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5344 112.57 179.80 112.59 1.5346 + IC C20F C18F *C19F H19F 1.5346 112.59 -121.28 109.10 1.1133 + IC H19F C18F *C19F H19G 1.1133 109.10 -117.38 109.12 1.1133 + IC C18F C19F C20F C21F 1.5345 112.59 -179.89 112.63 1.5337 + IC C21F C19F *C20F H20F 1.5337 112.63 -121.33 109.16 1.1133 + IC H20F C19F *C20F H20G 1.1133 109.16 -117.38 109.14 1.1133 + IC C19F C20F C21F C22F 1.5346 112.63 179.93 113.24 1.5309 + IC C22F C20F *C21F H21F 1.5309 113.24 -121.66 108.77 1.1142 + IC H21F C20F *C21F H21G 1.1142 108.77 -116.65 108.78 1.1142 + IC C20F C21F C22F H22F 1.5337 113.24 -59.91 110.47 1.1114 + IC H22F C21F *C22F H22G 1.1114 110.47 119.87 110.48 1.1113 + IC H22F C21F *C22F H22H 1.1114 110.47 -120.06 110.63 1.1113 +PATCH FIRST NONE LAST NONE + +RESI CER240 0.00 ! CERAMIDE d18:1/24:0 + ! +GROUP ! HO1 +ATOM O1 OHL -0.69 ! \ +ATOM HO1 HOL 0.30 ! O1 +ATOM C1S CTO2 0.49 ! | +ATOM H1S HAL2 -0.05 ! H1S---C1S---H1T +ATOM H1T HAL2 -0.05 ! | +GROUP ! H2S---C2S-------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C23F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H24F---C24F---H24G +ATOM C5S CEL3 -0.15 ! | | +ATOM H5S HEL1 0.15 ! | H24H +GROUP ! H3S----C3S--O3--HO3 +ATOM C6S CTL2 -0.18 ! | +ATOM H6S HAL2 0.09 ! C4S--H4S +ATOM H6T HAL2 0.09 ! || +GROUP ! C5S--H5S +ATOM C7S CTL2 -0.18 ! | +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CTL2 -0.18 ! +ATOM H15F HAL2 0.09 ! +ATOM H15G HAL2 0.09 ! +GROUP ! +ATOM C16F CTL2 -0.18 ! +ATOM H16F HAL2 0.09 ! +ATOM H16G HAL2 0.09 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL2 -0.18 ! +ATOM H20F HAL2 0.09 ! +ATOM H20G HAL2 0.09 ! +GROUP ! +ATOM C21F CTL2 -0.18 ! +ATOM H21F HAL2 0.09 ! +ATOM H21G HAL2 0.09 ! +GROUP ! +ATOM C22F CTL2 -0.18 ! +ATOM H22F HAL2 0.09 ! +ATOM H22G HAL2 0.09 ! +GROUP ! +ATOM C23F CTL2 -0.18 ! +ATOM H23F HAL2 0.09 ! +ATOM H23G HAL2 0.09 ! +GROUP ! +ATOM C24F CTL3 -0.27 ! +ATOM H24F HAL3 0.09 ! +ATOM H24G HAL3 0.09 ! +ATOM H24H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O1 O1 HO1 + +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F C15F H15G +BOND C15F C16F C16F H16F C16F H16G +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F C21F C21F H21F C21F H21G +BOND C21F C22F C22F H22F C22F H22G +BOND C22F C23F C23F H23F C23F H23G +BOND C23F C24F C24F H24F C24F H24G +BOND C24F H24H + +DOUBLE C4S C5S +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC HO1 O1 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O1 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O1 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O1 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC H15F C14F *C15F H15G 1.1140 108.84 -116.70 108.76 1.1144 + IC C14F C15F C16F C17F 1.5345 112.68 -178.23 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC H16F C15F *C16F H16G 1.1140 108.84 -116.70 108.76 1.1144 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 -178.23 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5344 112.57 179.80 112.59 1.5346 + IC C20F C18F *C19F H19F 1.5346 112.59 -121.28 109.10 1.1133 + IC H19F C18F *C19F H19G 1.1133 109.10 -117.38 109.12 1.1133 + IC C18F C19F C20F C21F 1.5345 112.59 -179.89 112.63 1.5337 + IC C21F C19F *C20F H20F 1.5337 112.63 -121.33 109.16 1.1133 + IC H20F C19F *C20F H20G 1.1133 109.16 -117.38 109.14 1.1133 + IC C19F C20F C21F C22F 1.5346 112.63 179.93 113.24 1.5309 + IC C22F C20F *C21F H21F 1.5309 113.24 -121.66 108.77 1.1142 + IC H21F C20F *C21F H21G 1.1142 108.77 -116.65 108.78 1.1142 + IC C20F C21F C22F C23F 1.5346 112.63 179.93 113.24 1.5309 + IC C23F C21F *C22F H22F 1.5309 113.24 -121.66 108.77 1.1142 + IC H22F C21F *C22F H22G 1.1142 108.77 -116.65 108.78 1.1142 + IC C21F C22F C23F C24F 1.5346 112.63 179.93 113.24 1.5309 + IC C24F C22F *C23F H23F 1.5309 113.24 -121.66 108.77 1.1142 + IC H23F C22F *C23F H23G 1.1142 108.77 -116.65 108.78 1.1142 + IC C22F C23F C24F H24F 1.5337 113.24 -59.91 110.47 1.1114 + IC H24F C23F *C24F H24G 1.1114 110.47 119.87 110.48 1.1113 + IC H24F C23F *C24F H24H 1.1114 110.47 -120.06 110.63 1.1113 +PATCH FIRST NONE LAST NONE + +RESI CER241 0.00 ! CERAMIDE d18:1/24:1 (w/nervonic acid) + ! +GROUP ! HO1 +ATOM O1 OHL -0.69 ! \ +ATOM HO1 HOL 0.30 ! O1 +ATOM C1S CTO2 0.49 ! | +ATOM H1S HAL2 -0.05 ! H1S---C1S---H1T +ATOM H1T HAL2 -0.05 ! | +GROUP ! H2S---C2S-------------------------NF--HNF +ATOM NF NHL -0.70 ! | | +ATOM HNF H 0.35 ! | | +ATOM C2S CTL1 0.30 ! | | +ATOM H2S HAL1 0.05 ! | | +GROUP ! | | +ATOM C3S CTO1 0.50 ! | C1F=OF (FATTY ACID CHAIN) +ATOM H3S HAL1 -0.11 ! | | +ATOM O3 OHL -0.69 ! | | +ATOM HO3 HOL 0.30 ! | H2F----C2F---H2G +GROUP ! | | +ATOM C4S CEL3 -0.15 ! | [(CH2)3F (C3F,C4F...C14F) +ATOM H4S HEL1 0.15 ! | | +GROUP ! | H15F---C15F +ATOM C5S CEL3 -0.15 ! | || +ATOM H5S HEL1 0.15 ! | H16F---C16F +GROUP ! H3S----C3S--O3--HO3 | +ATOM C6S CTL2 -0.18 ! | [(CH2)17F (C17F,C4F...C23F) +ATOM H6S HAL2 0.09 ! C4S--H4S | +ATOM H6T HAL2 0.09 ! || H24F---C24F---H24H +GROUP ! C5S--H5S | +ATOM C7S CTL2 -0.18 ! | H24G +ATOM H7S HAL2 0.09 ! | +ATOM H7T HAL2 0.09 ! [(CH)2]6 (C6S, C7S....C17S) +GROUP ! | +ATOM C8S CTL2 -0.18 ! H18S---C18S---H18U +ATOM H8S HAL2 0.09 ! | +ATOM H8T HAL2 0.09 ! H18T +GROUP ! +ATOM C9S CTL2 -0.18 ! +ATOM H9S HAL2 0.09 ! +ATOM H9T HAL2 0.09 ! +GROUP ! +ATOM C10S CTL2 -0.18 ! +ATOM H10S HAL2 0.09 ! +ATOM H10T HAL2 0.09 ! +GROUP +ATOM C11S CTL2 -0.18 ! +ATOM H11S HAL2 0.09 ! +ATOM H11T HAL2 0.09 ! +GROUP +ATOM C12S CTL2 -0.18 ! +ATOM H12S HAL2 0.09 ! +ATOM H12T HAL2 0.09 ! +GROUP +ATOM C13S CTL2 -0.18 ! +ATOM H13S HAL2 0.09 ! +ATOM H13T HAL2 0.09 ! +GROUP +ATOM C14S CTL2 -0.18 ! +ATOM H14S HAL2 0.09 ! +ATOM H14T HAL2 0.09 ! +GROUP +ATOM C15S CTL2 -0.18 ! +ATOM H15S HAL2 0.09 ! +ATOM H15T HAL2 0.09 ! +GROUP +ATOM C16S CTL2 -0.18 ! +ATOM H16S HAL2 0.09 ! +ATOM H16T HAL2 0.09 ! +GROUP +ATOM C17S CTL2 -0.18 ! +ATOM H17S HAL2 0.09 ! +ATOM H17T HAL2 0.09 ! +GROUP ! +ATOM C18S CTL3 -0.27 ! +ATOM H18S HAL3 0.09 ! +ATOM H18T HAL3 0.09 ! +ATOM H18U HAL3 0.09 ! +GROUP !FATTY ACID CHAIN +ATOM C1F C 0.55 ! +ATOM OF O -0.60 ! +ATOM C2F CTL2 -0.07 ! +ATOM H2F HAL2 0.06 ! +ATOM H2G HAL2 0.06 ! +GROUP ! +ATOM C3F CTL2 -0.18 ! +ATOM H3F HAL2 0.09 ! +ATOM H3G HAL2 0.09 ! +GROUP ! +ATOM C4F CTL2 -0.18 ! +ATOM H4F HAL2 0.09 ! +ATOM H4G HAL2 0.09 ! +GROUP ! +ATOM C5F CTL2 -0.18 ! +ATOM H5F HAL2 0.09 ! +ATOM H5G HAL2 0.09 ! +GROUP ! +ATOM C6F CTL2 -0.18 ! +ATOM H6F HAL2 0.09 ! +ATOM H6G HAL2 0.09 ! +GROUP ! +ATOM C7F CTL2 -0.18 ! +ATOM H7F HAL2 0.09 ! +ATOM H7G HAL2 0.09 ! +GROUP ! +ATOM C8F CTL2 -0.18 ! +ATOM H8F HAL2 0.09 ! +ATOM H8G HAL2 0.09 ! +GROUP ! +ATOM C9F CTL2 -0.18 ! +ATOM H9F HAL2 0.09 ! +ATOM H9G HAL2 0.09 ! +GROUP ! +ATOM C10F CTL2 -0.18 ! +ATOM H10F HAL2 0.09 ! +ATOM H10G HAL2 0.09 ! +GROUP ! +ATOM C11F CTL2 -0.18 ! +ATOM H11F HAL2 0.09 ! +ATOM H11G HAL2 0.09 ! +GROUP ! +ATOM C12F CTL2 -0.18 ! +ATOM H12F HAL2 0.09 ! +ATOM H12G HAL2 0.09 ! +GROUP ! +ATOM C13F CTL2 -0.18 ! +ATOM H13F HAL2 0.09 ! +ATOM H13G HAL2 0.09 ! +GROUP ! +ATOM C14F CTL2 -0.18 ! +ATOM H14F HAL2 0.09 ! +ATOM H14G HAL2 0.09 ! +GROUP ! +ATOM C15F CEL1 -0.15 ! +ATOM H15F HEL1 0.15 ! +GROUP ! +ATOM C16F CEL1 -0.15 ! +ATOM H16F HEL1 0.15 ! +GROUP ! +ATOM C17F CTL2 -0.18 ! +ATOM H17F HAL2 0.09 ! +ATOM H17G HAL2 0.09 ! +GROUP ! +ATOM C18F CTL2 -0.18 ! +ATOM H18F HAL2 0.09 ! +ATOM H18G HAL2 0.09 ! +GROUP ! +ATOM C19F CTL2 -0.18 ! +ATOM H19F HAL2 0.09 ! +ATOM H19G HAL2 0.09 ! +GROUP ! +ATOM C20F CTL2 -0.18 ! +ATOM H20F HAL2 0.09 ! +ATOM H20G HAL2 0.09 ! +GROUP ! +ATOM C21F CTL2 -0.18 ! +ATOM H21F HAL2 0.09 ! +ATOM H21G HAL2 0.09 ! +GROUP ! +ATOM C22F CTL2 -0.18 ! +ATOM H22F HAL2 0.09 ! +ATOM H22G HAL2 0.09 ! +GROUP ! +ATOM C23F CTL2 -0.18 ! +ATOM H23F HAL2 0.09 ! +ATOM H23G HAL2 0.09 ! +GROUP ! +ATOM C24F CTL3 -0.27 ! +ATOM H24F HAL3 0.09 ! +ATOM H24G HAL3 0.09 ! +ATOM H24H HAL3 0.09 ! + +!SPHINGOSINE CHAIN +BOND C18S H18S C18S H18T C18S H18U +BOND C18S C17S C17S H17S C17S H17T +BOND C17S C16S C16S H16S C16S H16T +BOND C16S C15S C15S H15S C15S H15T +BOND C15S C14S C14S H14S C14S H14T +BOND C14S C13S C13S H13S C13S H13T +BOND C13S C12S C12S H12S C12S H12T +BOND C12S C11S C11S H11S C11S H11T +BOND C11S C10S C10S H10S C10S H10T +BOND C10S C9S C9S H9S C9S H9T +BOND C9S C8S C8S H8S C8S H8T +BOND C8S C7S C7S H7S C7S H7T +BOND C7S C6S C6S H6S C6S H6T +BOND C6S C5S C5S H5S C4S H4S +BOND C4S C3S C3S H3S C3S O3 +BOND O3 HO3 +BOND C3S C2S C2S H2S +BOND C2S C1S C1S H1S C1S H1T +BOND C1S O1 O1 HO1 + +!FATTY ACID CHAIN +BOND C2S NF NF HNF NF C1F +BOND C1F C2F C2F H2F C2F H2G +BOND C2F C3F C3F H3F C3F H3G +BOND C3F C4F C4F H4F C4F H4G +BOND C4F C5F C5F H5F C5F H5G +BOND C5F C6F C6F H6F C6F H6G +BOND C6F C7F C7F H7F C7F H7G +BOND C7F C8F C8F H8F C8F H8G +BOND C8F C9F C9F H9F C9F H9G +BOND C9F C10F C10F H10F C10F H10G +BOND C10F C11F C11F H11F C11F H11G +BOND C11F C12F C12F H12F C12F H12G +BOND C12F C13F C13F H13F C13F H13G +BOND C13F C14F C14F H14F C14F H14G +BOND C14F C15F C15F H15F +BOND C16F H16F +BOND C16F C17F C17F H17F C17F H17G +BOND C17F C18F C18F H18F C18F H18G +BOND C18F C19F C19F H19F C19F H19G +BOND C19F C20F C20F H20F C20F H20G +BOND C20F C21F C21F H21F C21F H21G +BOND C21F C22F C22F H22F C22F H22G +BOND C22F C23F C23F H23F C23F H23G +BOND C23F C24F C24F H24F C24F H24G +BOND C24F H24H + +DOUBLE C4S C5S +DOUBLE C15F C16F +DOUBLE C1F OF +IMPR C1F C2F NF OF NF C1F C2S HNF + + IC C18S C17S C16S C15S 1.5309 113.23 180.00 112.64 1.5346 + IC C17S C16S C15S C14S 1.5337 112.64 180.00 112.58 1.5345 + IC C16S C15S C14S C13S 1.5346 112.58 180.00 112.58 1.5345 + IC C15S C14S C13S C12S 1.5345 112.58 -179.99 112.58 1.5345 + IC C14S C13S C12S C11S 1.5345 112.58 179.97 112.58 1.5344 + IC C13S C12S C11S C10S 1.5345 112.58 -179.96 112.61 1.5345 + IC C12S C11S C10S C9S 1.5344 112.61 179.97 112.54 1.5344 + IC C11S C10S C9S C8S 1.5345 112.54 -179.87 112.66 1.5345 + IC C10S C9S C8S C7S 1.5344 112.66 -179.89 112.50 1.5354 + IC C9S C8S C7S C6S 1.5345 112.50 -179.79 112.41 1.5391 + IC C8S C7S C6S C5S 1.5354 112.41 -179.61 111.46 1.5077 + IC C7S C6S C5S C4S 1.5391 111.46 -117.13 124.77 1.3444 + IC C6S C5S C4S C3S 1.5077 124.77 179.01 124.28 1.5009 + IC C5S C4S C3S C2S 1.3444 124.28 -84.24 110.14 1.5343 + IC C5S C4S C3S O3 1.3444 124.28 156.07 107.64 1.4235 + IC C4S C3S C2S C1S 1.5009 110.14 -70.50 114.25 1.5586 + IC HO1 O1 C1S C2S 1.5725 121.69 103.66 111.21 1.5586 + IC C2S O1 *C1S H1S 1.5586 111.21 118.79 108.35 1.1121 + IC C2S O1 *C1S H1T 1.5586 111.21 -123.25 112.85 1.1152 + IC O1 C1S C2S C3S 1.4327 111.21 175.67 114.25 1.5343 + IC C3S C1S *C2S NF 1.5343 114.25 120.00 111.52 1.4406 + IC C3S C1S *C2S H2S 1.5343 114.25 -120.00 105.03 1.1194 + IC C1S C2S NF C1F 1.5586 111.52 160.94 124.85 1.3364 + IC C1F C2S *NF HNF 1.3364 124.85 -157.81 113.39 1.0062 + IC C1S C2S C3S C4S 1.5586 114.25 -70.50 110.14 1.5009 + IC C4S C2S *C3S O3 1.5009 110.14 118.36 109.80 1.4235 + IC C4S C2S *C3S H3S 1.5009 110.14 -121.14 110.10 1.1140 + IC C2S C3S O3 HO3 1.5343 109.80 46.50 104.54 0.9610 + IC C2S C3S C4S C5S 1.5343 110.14 -84.24 124.28 1.3444 + IC C5S C3S *C4S H4S 1.3444 124.28 178.79 115.93 1.1003 + IC C3S C4S C5S C6S 1.5009 124.28 179.01 124.77 1.5077 + IC C6S C4S *C5S H5S 1.5077 124.77 -178.18 119.00 1.1029 + IC C4S C5S C6S C7S 1.3444 124.77 -117.13 111.46 1.5391 + IC C7S C5S *C6S H6S 1.5391 111.46 120.98 111.41 1.1142 + IC C7S C5S *C6S H6T 1.5391 111.46 -120.60 109.91 1.1125 + IC C5S C6S C7S C8S 1.5077 111.46 -179.61 112.41 1.5354 + IC C8S C6S *C7S H7S 1.5354 112.41 121.26 109.74 1.1138 + IC C8S C6S *C7S H7T 1.5354 112.41 -120.99 109.40 1.1147 + IC C6S C7S C8S C9S 1.5391 112.41 -179.79 112.50 1.5345 + IC C9S C7S *C8S H8S 1.5345 112.50 121.20 108.97 1.1132 + IC C9S C7S *C8S H8T 1.5345 112.50 -121.38 109.07 1.1129 + IC C7S C8S C9S C10S 1.5354 112.50 -179.89 112.66 1.5344 + IC C10S C8S *C9S H9S 1.5344 112.66 121.49 109.05 1.1133 + IC C10S C8S *C9S H9T 1.5344 112.66 -121.38 108.96 1.1136 + IC C8S C9S C10S C11S 1.5345 112.66 -179.87 112.54 1.5345 + IC C11S C9S *C10S H10S 1.5345 112.54 121.27 109.07 1.1133 + IC C11S C9S *C10S H10T 1.5345 112.54 -121.34 109.11 1.1132 + IC C9S C10S C11S C12S 1.5344 112.54 179.97 112.61 1.5344 + IC C12S C10S *C11S H11S 1.5344 112.61 121.36 109.09 1.1133 + IC C12S C10S *C11S H11T 1.5344 112.61 -121.33 109.07 1.1134 + IC C10S C11S C12S C13S 1.5345 112.61 -179.96 112.58 1.5345 + IC C13S C11S *C12S H12S 1.5345 112.58 121.29 109.12 1.1133 + IC C13S C11S *C12S H12T 1.5345 112.58 -121.31 109.15 1.1133 + IC C11S C12S C13S C14S 1.5344 112.58 179.97 112.58 1.5345 + IC C14S C12S *C13S H13S 1.5345 112.58 121.30 109.13 1.1133 + IC C14S C12S *C13S H13T 1.5345 112.58 -121.30 109.13 1.1133 + IC C12S C13S C14S C15S 1.5345 112.58 -179.99 112.58 1.5345 + IC C15S C13S *C14S H14S 1.5345 112.58 121.30 109.12 1.1133 + IC C15S C13S *C14S H14T 1.5345 112.58 -121.31 109.12 1.1133 + IC C13S C14S C15S C16S 1.5345 112.58 180.00 112.58 1.5346 + IC C16S C14S *C15S H15S 1.5346 112.58 121.30 109.11 1.1133 + IC C16S C14S *C15S H15T 1.5346 112.58 -121.30 109.11 1.1133 + IC C14S C15S C16S C17S 1.5345 112.58 180.00 112.64 1.5337 + IC C17S C15S *C16S H16S 1.5337 112.64 121.32 109.14 1.1133 + IC C17S C15S *C16S H16T 1.5337 112.64 -121.32 109.14 1.1133 + IC C15S C16S C17S C18S 1.5346 112.64 180.00 113.23 1.5309 + IC C18S C16S *C17S H17S 1.5309 113.23 121.67 108.77 1.1142 + IC C18S C16S *C17S H17T 1.5309 113.23 -121.67 108.77 1.1142 + IC C16S C17S C18S H18S 1.5337 113.23 180.00 110.63 1.1113 + IC H18S C17S *C18S H18T 1.1113 110.63 120.07 110.47 1.1114 + IC H18S C17S *C18S H18U 1.1113 110.63 -120.07 110.47 1.1114 + IC C2S NF C1F C2F 1.4406 124.85 -156.83 114.97 1.4964 + IC C2F NF *C1F OF 1.4964 114.97 162.54 122.11 1.2268 + IC NF C1F C2F C3F 1.3364 114.97 -146.57 111.92 1.5432 + IC C3F C1F *C2F H2F 1.5432 111.92 -120.83 107.93 1.1115 + IC H2F C1F *C2F H2G 1.1115 107.93 -117.30 109.04 1.1113 + IC C1F C2F C3F C4F 1.4964 111.92 179.54 112.84 1.5310 + IC C4F C2F *C3F H3F 1.5310 112.84 -121.63 109.37 1.1145 + IC H3F C2F *C3F H3G 1.1145 109.37 -117.07 109.08 1.1157 + IC C2F C3F C4F C5F 1.5434 112.23 174.86 112.58 1.5342 + IC C5F C3F *C4F H4F 1.5342 112.58 -120.18 108.65 1.1140 + IC H4F C3F *C4F H4G 1.1140 108.65 -117.52 109.62 1.1127 + IC C3F C4F C5F C6F 1.5340 112.58 -174.06 112.39 1.5340 + IC C6F C4F *C5F H5F 1.5340 112.39 -122.01 109.38 1.1130 + IC H5F C4F *C5F H5G 1.1130 109.38 -117.34 108.92 1.1134 + IC C4F C5F C6F C7F 1.5342 112.39 178.27 112.75 1.5340 + IC C7F C5F *C6F H6F 1.5340 112.75 -120.93 108.96 1.1137 + IC H6F C5F *C6F H6G 1.1137 108.96 -117.41 109.22 1.1131 + IC C5F C6F C7F C8F 1.5340 112.75 -178.89 112.33 1.5342 + IC C8F C6F *C7F H7F 1.5342 112.33 -121.40 109.26 1.1132 + IC H7F C6F *C7F H7G 1.1132 109.26 -117.45 109.12 1.1130 + IC C6F C7F C8F C9F 1.5340 112.33 179.09 112.77 1.5340 + IC C9F C7F *C8F H8F 1.5340 112.77 -121.23 109.16 1.1134 + IC H8F C7F *C8F H8G 1.1134 109.16 -117.38 109.08 1.1133 + IC C7F C8F C9F C10F 1.5342 112.77 179.02 112.34 1.5343 + IC C10F C8F *C9F H9F 1.5343 112.34 -121.27 109.27 1.1132 + IC H9F C8F *C9F H9G 1.1132 109.27 -117.45 109.10 1.1130 + IC C8F C9F C10F C11F 1.5340 112.34 178.16 112.74 1.5340 + IC C11F C9F *C10F H10F 1.5340 112.74 -121.18 109.16 1.1134 + IC H10F C9F *C10F H10G 1.1134 109.16 -117.35 109.10 1.1132 + IC C9F C10F C11F C12F 1.5343 112.74 178.91 112.38 1.5343 + IC C12F C10F *C11F H11F 1.5343 112.38 -121.39 109.34 1.1131 + IC H11F C10F *C11F H11G 1.1131 109.34 -117.43 108.98 1.1132 + IC C10F C11F C12F C13F 1.5340 112.38 176.93 112.68 1.5340 + IC C13F C11F *C12F H12F 1.5340 112.68 -121.02 109.05 1.1134 + IC H12F C11F *C12F H12G 1.1134 109.05 -117.34 109.20 1.1131 + IC C11F C12F C13F C14F 1.5343 112.68 -179.93 112.45 1.5345 + IC C14F C12F *C13F H13F 1.5345 112.45 -121.60 109.42 1.1129 + IC H13F C12F *C13F H13G 1.1129 109.42 -117.40 108.85 1.1134 + IC C12F C13F C14F C15F 1.5340 112.45 175.93 112.68 1.5334 + IC C15F C13F *C14F H14F 1.5334 112.68 -121.00 109.06 1.1131 + IC H14F C13F *C14F H14G 1.1131 109.06 -117.24 109.28 1.1130 + IC C13F C14F C15F C16F 1.5345 112.68 -178.23 113.16 1.5306 + IC C16F C14F *C15F H15F 1.5306 113.16 -121.86 108.84 1.1140 + IC C14F C15F C16F C17F 1.5345 112.68 0.00 113.16 1.5306 + IC C17F C15F *C16F H16F 1.5306 113.16 -121.86 108.84 1.1140 + IC C15F C16F C17F C18F 1.5345 112.68 -178.23 113.16 1.5306 + IC C18F C16F *C17F H17F 1.5306 113.16 -121.86 108.84 1.1140 + IC H17F C16F *C17F H17G 1.1140 108.84 -116.70 108.76 1.1144 + IC C16F C17F C18F C19F 1.5345 112.68 0.00 113.16 1.5306 + IC C19F C17F *C18F H18F 1.5306 113.16 -121.86 108.84 1.1140 + IC H18F C17F *C18F H18G 1.1140 108.84 -116.70 108.76 1.1144 + IC C17F C18F C19F C20F 1.5344 112.57 180.00 112.59 1.5346 + IC C20F C18F *C19F H19F 1.5346 112.59 -121.28 109.10 1.1133 + IC H19F C18F *C19F H19G 1.1133 109.10 -117.38 109.12 1.1133 + IC C18F C19F C20F C21F 1.5345 112.59 -179.89 112.63 1.5337 + IC C21F C19F *C20F H20F 1.5337 112.63 -121.33 109.16 1.1133 + IC H20F C19F *C20F H20G 1.1133 109.16 -117.38 109.14 1.1133 + IC C19F C20F C21F C22F 1.5346 112.63 179.93 113.24 1.5309 + IC C22F C20F *C21F H21F 1.5309 113.24 -121.66 108.77 1.1142 + IC H21F C20F *C21F H21G 1.1142 108.77 -116.65 108.78 1.1142 + IC C20F C21F C22F C23F 1.5346 112.63 179.93 113.24 1.5309 + IC C23F C21F *C22F H22F 1.5309 113.24 -121.66 108.77 1.1142 + IC H22F C21F *C22F H22G 1.1142 108.77 -116.65 108.78 1.1142 + IC C21F C22F C23F C24F 1.5346 112.63 179.93 113.24 1.5309 + IC C24F C22F *C23F H23F 1.5309 113.24 -121.66 108.77 1.1142 + IC H23F C22F *C23F H23G 1.1142 108.77 -116.65 108.78 1.1142 + IC C22F C23F C24F H24F 1.5337 113.24 -59.91 110.47 1.1114 + IC H24F C23F *C24F H24G 1.1114 110.47 119.87 110.48 1.1113 + IC H24F C23F *C24F H24H 1.1114 110.47 -120.06 110.63 1.1113 +PATCH FIRST NONE LAST NONE + +end + +read para card flex @app +* new parameters +* + +ATOMS +MASS 165 NHL 14.00700 !N ! +MASS 166 CTO1 12.01100 !C ! +MASS 167 CEL3 12.01100 !C ! +MASS 168 CTO2 12.01100 !C ! + + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! Cyclopropane Moeity Addition +! + +! Ceramides +! CC +CTL1 CEL3 250.000 1.490 ! prot22; Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91); CT1-C +CTO1 CEL3 250.000 1.490 ! prot22; Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) ; CT1-C +CTO1 CTL1 222.500 1.500 ! lip36; alkanes, 3/92; CTL1-CTL1 +CTO1 CTL3 222.500 1.538 ! lip36; alkanes, 3/92; CTL1-CTL3 +CEL3 CTL2 365.000 1.502 ! lip36; butene; from propene, yin,adm jr., 12/95; CEL1-CTL2 +CEL3 CEL3 440.000 1.340 ! lip36; butene, yin,adm jr., 12/95; CEL1-CEL1 +CTL2 C 250.000 1.490 ! prot22; Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91); CT2-C +CTL3 C 250.000 1.490 ! prot22; Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91); CT3-C +CTO1 OHL 428.000 1.420 ! lip36; glycerol; OHL-CTL1 +CTO1 OSL 340.000 1.430 ! lipid ester; rmv nov 2009 +CTO1 HAL1 309.000 1.111 ! lip36; alkanes, 3/92; CTL1-HAL1 +HEL1 CEL3 360.500 1.100 ! lip36; propene, yin,adm jr., 12/95; HEL1-CEL1 +NHL H 440.000 0.997 ! prot22; Alanine Dipeptide ab initio calc's (LK); NH1-H +NHL CTL3 320.000 1.430 ! prot22; NMA Gas & Liquid Phase IR Spectra (LK); NH1-CT3 +NHL C 370.000 1.345 ! prot22; Alanine Dipeptide ab initio calc's (LK); NH1-C +NHL CTL1 320.000 1.430 ! prot22; NMA Gas & Liquid Phase IR Spectra (LK); NH1-CT1 +CTO2 HAL2 309.000 1.111 ! lip36; alkanes, 4/98 +CTO2 CTL1 222.500 1.538 ! lip36; alkanes, 3/92 +CTO2 OHL 428.000 1.420 ! glycerol + + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! Ceramides +!CCC +CTL3 CTL1 CEL3 52.000 108.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); CT3-CT1-C +CTL3 CTO1 CEL3 52.000 108.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); CT3-CT1-C +CTL1 CEL3 CEL3 48.00 123.50 ! lip36; 2-butene,from 2-butene, yin,adm jr., 12/95; CEL1-CEL1-CTL2 +CTO1 CEL3 CEL3 48.00 123.50 ! lip36; 2-butene,from 2-butene, yin,adm jr., 12/95; CEL1-CEL1-CTL2 +CTL1 CTL1 CEL3 52.000 108.00 ! prot22; Alanine Dipeptide ab inition calc's (LK); CT1 CT1 C +CTL1 CTO1 CEL3 52.000 108.00 ! prot22; Alanine Dipeptide ab inition calc's (LK); CT1 CT1 C +C CTL2 CTL2 52.000 108.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); CT3-CT1-C +CTL2 CTL1 CTO1 58.350 113.50 11.16 2.561 ! lip36; glycerol; CTL1-CTL1-CTL2 +CEL3 CEL3 CTL2 48.000 123.50 ! lip36; 2-butene,from 2-butene, yin,adm jr., 12/95; CEL1-CEL1-CTL2 +CEL3 CTL2 CTL3 32.00 112.20 ! lip36; 1-butene; from propene, yin,adm jr., 12/95; CEL1-CTL2-CTL3 +CEL3 CTL2 CTL2 32.00 112.20 ! lip36; 1-butene; from propene, yin,adm jr., 12/95; CEL1-CTL2-CTL2 +CTL3 CTL2 C 52.000 108.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); CT3-CT1-C +OHL CTL1 CEL3 75.700 110.10 ! prot22; MeOH, EMB, 10/10/89; OH1-CT1-CT1 +OHL CTO1 CEL3 75.700 110.10 ! prot22; MeOH, EMB, 10/10/89; OH1-CT1-CT1 +OHL CTO1 CTL3 75.700 110.10 ! prot22; MeOH, EMB, 10/10/89; OH1 CT1 CT3 +OHL CTO1 CTL1 75.700 110.10 ! prot22; MeOH, EMB, 10/10/89; OH1 CT1 CT1 +O C CTL2 80.000 121.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); O-C-CT2 +O C CTL3 80.000 121.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); O C CT3 +OSL CTO1 CTL1 75.700 110.10 ! analog for acetyl at sphingosine O3; rmv nov 2009 +OSL CTO1 CEL3 75.700 110.10 ! analog for acetyl at sphingosine O3; rmv nov 2009 +CL OSL CTO1 40.00 109.60 30.0 2.2651 ! analog for acetyl at sphingosine O3; rmv nov 2009 +CTL1 CEL3 HEL1 40.00 116.00 ! lip36; 1-butene, from propene,yin.adm jr.,12/95; HEL1-CEL1-CTL2 +CTO1 CEL3 HEL1 40.00 116.00 ! lip36; 1-butene, from propene,yin.adm jr.,12/95; HEL1-CEL1-CTL2 +HAL1 CTL1 CEL3 33.000 109.50 30.00 2.16300 ! prot22; alanine dipeptide, LK, replaced, adm jr., 5/09/91; HA-CT1-C (Protein) +HAL1 CTO1 CEL3 33.000 109.50 30.00 2.16300 ! prot22; alanine dipeptide, LK, replaced, adm jr., 5/09/91; HA-CT1-C (Protein) +HAL1 CTO1 CTL3 34.500 110.10 22.53 2.179 ! lip36; alkane, 3/92; HAL1-CTL1-CTL3 +HAL1 CTO1 CTL1 34.500 110.10 22.53 2.179 ! lip36; alkane, 3/92; HAL1-CTL1-CTL1 +HAL1 CTL1 CTO1 34.500 110.10 22.53 2.179 ! lip36; alkane, 3/92; HAL1-CTL1-CTL1 +HAL3 CTL3 CTO1 33.430 110.10 22.53 2.179 ! lip36; alkane, 4/98; HAL3-CTL3-CTL +HEL1 CEL3 CEL3 52.00 119.50 ! lip36; 2-butene, yin,adm jr., 12/95; HEL1-CEL1-CEL1 +HEL1 CEL3 CTL2 40.00 116.00 ! lip36; 1-butene; from propene, yin,adm jr., 12/95; HEL1-CEL1-CTL2 +CEL3 CTL2 HAL2 45.00 111.50 ! lip36; 1-butene; from propene, yin,adm jr., 12/95; HAL2-CTL2-CEL1 +HAL2 CTL2 C 33.000 109.50 30.00 2.16300 ! prot22; alanine dipeptide, LK, replaced, adm jr., 5/09/91; HA-CT2-C +HAL3 CTL3 C 33.000 109.50 30.00 2.16300 ! prot22; alanine dipeptide, LK, replaced, adm jr., 5/09/91; C CT3 HA +NHL CTL1 OSL 80.000 122.50 ! prot22; NMA Vib Modes (LK); O-C-NH1 +O C NHL 80.000 122.50 ! prot22; NMA Vib Modes (LK); O-C-NH1 +HOL OHL CTO1 57.500 106.00 ! lip36; glycerol; HOL-OHL-CTL1 +OHL CTO1 HAL1 45.900 108.89 ! lip36; glycerol; OHL-CTL1-HAL1 +OSL CTO1 HAL1 45.900 108.89 ! lip36; glycerol; OHL-CTL1-HAL1; rmv nov 2009 +NHL CTL1 CTO1 70.000 113.50 ! prot22; Alanine Dipeptide ab initio calc's (LK); NH1-CT1-CT1 +NHL C CTL2 80.000 116.50 ! prot22; NMA Vib Modes (LK); NH1-C-CT2 +NHL CTL1 CTL2 70.000 113.50 ! prot22; Alanine Dipeptide ab initio calc's (LK); NH1-CT1-CT2 +NHL CTL1 CTL3 70.000 113.50 ! prot22; +NHL CTL1 CTL1 70.000 113.50 ! prot22; Alanine Dipeptide ab initio calc's (LK); NH1-CT1-CT1 +NHL C CTL3 80.000 116.50 ! prot22; NMA Vib Modes (LK); NH1-C-CT3 +H NHL CTL3 35.000 117.00 ! prot22; NMA Vibrational Modes (LK); H-NH1-CT3 +H NHL C 34.000 123.00 ! prot22; NMA Vib Modes (LK); H-NH1-C +H NHL CTL1 35.000 117.00 ! prot22; NMA Vibrational Modes (LK); H-NH1-CT1 +CTL3 NHL C 50.000 120.00 ! prot22; NMA Vib Modes (LK); CT3-NH1-C +CTL1 NHL C 50.000 120.00 ! prot22; NMA Vib Modes (LK); CT1 NH1 C +NHL CTL3 HAL3 51.500 109.50 ! prot22; NMA crystal (JCS); NH1-CT3-HA +NHL CTL1 HAL1 48.000 108.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); NH1-CT1-HB +HOL OHL CTO2 57.500 106.00 ! lip36; glycerol; HOL-OHL-CTL2 +OHL CTO2 HAL2 45.900 108.89 ! lip36; glycerol; OHL-CTL2-HAL1 +HAL2 CTO2 CTL1 26.500 110.10 22.53 2.179 ! lip36; alkane, 4/98; HAL2-CTL2-CTL1 +HAL1 CTL1 CTO2 34.500 110.10 22.53 2.179 ! lip36; alkane, 3/92; HAL1-CTL1-CTL2 +NHL CTL1 CTO2 70.000 113.50 ! prot22; Alanine Dipeptide ab initio calc's(LK);NH1-CT1-CTO2 +CTO2 CTL1 CTO1 58.350 113.50 11.16 2.561 ! lip36; glycerol; CTL1-CTL1-CTL2 +HAL2 CTO2 HAL2 35.500 109.00 5.40 1.80200 ! alkane, 3/92 HAL2-CLT2-HAL2 +OHL CTO2 CTL1 75.700 110.10 ! prot22; MeOH, EMB, 10/10/89; OH1 CT2 CT2 + + +! +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta + +! Ceramides +!CCCC +CTL3 CTL1 CEL3 CEL3 0.9000 1 180.00 ! lip36; 2-pentene and 3-heptene; CEL1 CEL1 CTL2 CTL3 +CEL3 CEL3 CTL2 CTL3 0.9100 1 180.00 ! lip36; 2-hexene, adm jr., 11/09 +CEL3 CEL3 CTL2 CTL3 0.1800 2 180.00 ! +CEL3 CEL3 CTL2 CTL3 0.1700 3 180.00 ! "" +CEL3 CEL3 CTL2 CTL2 0.9100 1 180.00 ! lip36; 2-hexene, adm jr., 11/09 +CEL3 CEL3 CTL2 CTL2 0.1800 2 180.00 ! +CEL3 CEL3 CTL2 CTL2 0.1700 3 180.00 ! "" +CTL1 CEL3 CEL3 CTL2 0.4500 1 180.00 ! lip36; 2-butene, adm jr., 4/04; X CEL1 CEL1 X +CTL1 CEL3 CEL3 CTL2 8.5000 2 180.00 ! lip36; 2-butene, adm jr., 4/04; X CEL1 CEL1 X +CTO1 CEL3 CEL3 CTL2 0.1500 1 0.00 ! prot27; 2-butene, adm jr., 2/00 update; X CEL1 CEL1 X +CTO1 CEL3 CEL3 CTL2 8.5000 2 180.00 ! prot27; 2-butene, adm jr., 2/00 update; X CEL1 CEL1 X +CTL1 CTL1 CEL3 CEL3 0.6000 1 180.00 ! lip36; 2-hexene; CEL1 CEL1 CTL2 CTL2 +!CCCO +O C CTL2 CTL3 1.400 1 0.00 ! prot22; lactams, adm jr; O C CT2 CT2/O C CT1 CT3 +O C CTL2 CTL2 1.400 1 0.00 ! prot22; lactams, adm jr; O C CT2 CT2/O C CT1 CT3 +OHL CTL1 CEL3 CEL3 0.600 1 180.00 ! lip36; 2-hexene; CEL3 CEL3 CTL2 CTL2 +OSL CTO1 CEL3 CEL3 1.280 1 180.0 ! torsfit MP2/ccpVTZ, cer1 model, erh 8/09 +OSL CTO1 CEL3 CEL3 0.560 2 180.0 ! "" analogy fot TACSPH, rmv nov 2009 +OSL CTO1 CEL3 CEL3 0.860 3 0.0 ! "" +CTL2 CTL1 CTO1 OHL 0.200 3 0.00 ! lip36; alkane, 3/92, X CTL1 CTL1 X +CTO1 CTL1 CTL2 OSL 0.390 1 180.00 ! torsfit MP2/ccpVTZ, sph model, erh 8/09; transferred from cer4 +CTO1 CTL1 CTL2 OSL 0.510 2 180.00 ! "" +CTO1 CTL1 CTL2 OSL 0.870 3 180.00 ! "" +CTL2 CTL1 CTO1 OSL 0.390 1 180.00 ! torsfit MP2/ccpVTZ, sph model, erh 8/09; transferred from cer4 +CTL2 CTL1 CTO1 OSL 0.510 2 180.00 ! "" analogy for TACSPH, rmv nov 2009 +CTL2 CTL1 CTO1 OSL 0.870 3 180.00 ! "" +!HCOH +HAL1 CTO1 OHL HOL 0.140 3 0.00 ! lip36; glycerol, X CTL1 OHL X +!COCC +CL OSL CTO1 CTL1 0.000 4 0.00 ! glycerol, beta1 6/07; from lip36 for TACSPH, rmv nov 2009 +CL OSL CTO1 CTL1 0.150 3 180.00 ! glycerol, beta1 6/07 +CL OSL CTO1 CTL1 1.453 2 180.00 ! glycerol, beta1 6/07 +CL OSL CTO1 CTL1 0.837 1 180.00 ! glycerol, beta1 6/07 +CEL3 CTO1 OSL CL 0.220 1 0.00 ! og OMeTHP compounds 2 and 3; rmv nov 2009 +CEL3 CTO1 OSL CL 0.280 2 180.00 ! " MCSA fit +CEL3 CTO1 OSL CL 0.890 3 0.00 ! " MP2/cc-pVTZ//MP2/6-31G* +!COCH +HAL1 CTO1 OSL CL 0.00 3 0.00 ! lip36, X CT1 OSL X; TACCSPH, rmv nov 2009 +!CCCH +HEL1 CEL3 CTL1 CTL3 0.1200 3 0.00 ! prot22; for butene, yin/adm jr., 12/95; HE1 CE1 CT2 CT3 +HEL1 CEL3 CTO1 CTL3 0.1200 3 0.00 ! prot22; for butene, yin/adm jr., 12/95; HE1 CE1 CT2 CT3 +HEL1 CEL3 CTL2 CTL2 0.1200 3 0.00 ! prot22; for butene, yin/adm jr., 12/95; HE1 CE1 CT2 CT3 +HAL1 CTL1 CEL3 CEL3 0.0300 3 0.00 ! prot22;for butene, yin/adm jr., 12/95; CE1 CE1 CT3 HA +HAL1 CTO1 CEL3 CEL3 0.0300 3 0.00 ! prot22;for butene, yin/adm jr., 12/95; CE1 CE1 CT3 HA +CTL1 CTL1 CEL3 HEL1 0.1200 3 0.00 ! lip36; butene, yin, adm. jr; CTL2 CTL2 CEL1 HEL1 +HAL1 CTL3 CTO1 CEL3 0.2000 3 0.00 ! lip36; alkane, 3/92; X CTL1 CTL3 X +CTL2 CTL1 CTO1 HAL1 0.200 3 0.00 ! lip36; alkane, 3/92; X CTL1 CTL3 X +CTL1 CTO1 CEL3 HEL1 0.1200 3 0.00 ! lip36 butene, yin, adm. jr; CTL2 CTL2 CEL1 HEL1 +HAL1 CTL1 CTO1 CEL3 0.200 3 0.00 ! lip36; alkane, 3/92: X CTL1 CTL3 X +CTO1 CEL3 CEL3 HEL1 0.1500 1 180.00 ! lip36; 2-butene, adm jr., 2/00 update; X CEL1 CEL1 X +CTO1 CEL3 CEL3 HEL1 8.5000 2 180.00 ! lip36; 2-butene, adm jr., 2/00 update; X CEL1 CEL1 X +CEL3 CEL3 CTL2 HAL2 0.3000 3 180.00 ! lip36; 2-butene, adm jr., 4/04; CEL1 CEL1 CTL2 HAL2 +HEL1 CEL3 CEL3 CTL2 0.1500 1 180.00 ! lip36; 2-butene, adm jr., 2/00 update; X CEL1 CEL1 X +HEL1 CEL3 CEL3 CTL2 8.5000 2 180.00 ! lip36; 2-butene, adm jr., 2/00 update; X CEL1 CEL1 X +HEL1 CEL3 CTL2 CTL3 0.1200 3 0.00 ! lip36; butene, yin,adm jr., 12/95; HEL1 CEL1 CTL2 CTL3 +!HCCH +HEL1 CEL3 CTL1 HAL1 0.000 3 0.00 ! prot22; butene, adm jr., 2/00 update; HE1 CE1 CT2 HA +HEL1 CEL3 CTO1 HAL1 0.000 3 0.00 ! prot22; butene, adm jr., 2/00 update; HE1 CE1 CT2 HA +HAL3 CTL3 CTO1 HAL1 0.200 3 0.00 ! lip36; alkane, 3/92; X CTL1 CTL3 X +HAL1 CTL1 CTO1 HAL1 0.200 3 0.00 ! lip36; alkane, 3/92; X CTL1 CTL1 X +HEL1 CEL3 CEL3 HEL1 1.000 2 180.00 ! lip36; 2-butene, adm jr., 8/98 update; HEL1 CEL1 CEL1 HEL1 +HEL1 CEL3 CTL2 HAL2 0.000 3 0.00 ! lip36; butene, adm jr., 2/00 update; HEL1 CEL1 CTL2 HAL2 +!OCCH +OHL CTL1 CEL3 HEL1 0.120 3 180.00 ! lip36; butene, yin, adm jr., 12/95; HEL1 CEL1 CTL1 CTL3 +OHL CTO1 CEL3 HEL1 0.120 3 180.00 ! lip36; butene, yin, adm jr., 12/95; HEL1 CEL1 CTL1 CTL3 +OSL CTO1 CEL3 HEL1 0.120 3 180.00 ! lip36; butene, yin, adm jr., 12/95; HEL1 CEL1 CTL1 CTL3 rmv nov 2009 +O C CTL2 HAL2 0.000 3 180.00 ! prot22; adm jr., 8/13/90 acetamide geometry and vibrations; O C CT2 HA +O C CTL3 HAL3 0.000 3 180.00 ! prot22; adm jr., 8/13/90 acetamide geometry and vibrations; O C CT3 HA +HAL3 CTL3 CTO1 OHL 0.200 3 0.00 ! lip36; alkane, 3/92; X CTL1 CTL3 X +HAL1 CTL1 CTO1 OHL 0.200 3 0.00 ! lip36; alkane, 3/92; X CTL1 CTL1 X +HAL1 CTL1 CTO1 OSL 0.200 3 0.00 ! lip36; alkane, 3/92; X CTL1 CTL1 X; rmv nov 2009 +!NCCC +NHL CTL1 CTL1 CTL3 0.260 1 180.00 ! torsfit MP2/ccpVTZ, cer3 model, erh 8/09 +NHL CTL1 CTL1 CTL3 0.390 2 180.00 ! "" +NHL CTL1 CTL1 CTL3 0.120 3 180.00 ! "" +!NCCH +NHL C CTL2 HAL2 0.000 3 0.00 ! prot22; LK for autogenerate dihe, sp2-methyl, no dihedral potential; NH1 C CT2 HA +NHL C CTL3 HAL3 0.000 3 0.00 ! prot22; LK for autogenerate dihe, sp2-methyl, no dihedral potential; NH1 C CT3 HA +NHL CTL1 CTO1 HAL1 0.200 3 0.00 ! lip36; alkane, 3/92; X CTL1 CTL1 X +!HNCH +HAL3 CTL3 NHL H 0.000 3 0.00 ! prot22; LK for autogenerate dihe, sp2-methyl, no dihedral potential; HA CT3 NH1 H +HAL1 CTL1 NHL H 0.000 1 0.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); HB CT1 NH1 H +!OCNH HNCC for NMA/CERN cis/trans barrier +H NHL C O 0.530 1 0.00 ! fit to cern QM profile, jbk 10/12 +H NHL C O 1.270 2 180.00 ! fit to cern QM profile, jbk 10/12 +H NHL C O 0.140 3 0.00 ! fit to cern QM profile, jbk 10/12 +H NHL C O 0.780 4 0.00 ! fit to cern QM profile, jbk 10/12 +H NHL C CTL2 2.500 2 180.00 ! prot22;,Gives appropriate NMA cis/trans barrier. (LK); H NH1 C CT2 +H NHL CTL1 CTL2 0.000 1 0.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); H NH1 CT1 CT2 +H NHL CTL1 CTL1 0.000 1 0.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); H NH1 CT1 CT1 +H NHL C CTL3 2.500 2 180.00 ! prot22; Gives appropriate NMA cis/trans barrier. (LK); H NH1 C CT3 +H NHL CTL1 CTL3 2.500 2 180.00 ! prot22; +H NHL CTL1 CTO1 0.000 1 0.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); H NH1 CT1 CT1 +!OCNC +O C NHL CTL3 2.500 2 180.00 ! prot22; Gives appropriate NMA cis/trans barrier. (LK); O C NH1 CT3 +O C NHL CTL1 2.500 2 180.00 ! prot22; Gives appropriate NMA cis/trans barrier. (LK); O C NH1 CT1 +!CCNC +CTL1 NHL C CTL2 0.000 1 0.00 ! set to zero in fits +CTL1 NHL C CTL3 0.000 1 0.00 ! set to zero in fits +! torsion 4 and OH torsion +CTL2 C NHL CTL3 1.600 1 0.00 ! prot22; from CT2 C NH1 CT2, adm jr. 10/21/96; CT2 C NH1 CT3 +CTL3 C NHL CTL3 1.600 1 0.00 ! prot22; from CT2 C NH1 CT2, adm jr. 10/21/96; CT2 C NH1 CT3 +CTL1 CTL1 NHL C 0.000 1 0.00 ! set to zero in fit +CTL2 CTL1 NHL C 0.000 1 0.00 ! set to zero in fit +CTL3 CTL1 NHL C 0.000 1 0.00 ! set to zero in fit +C NHL CTL1 CTO1 4.080 1 0.00 ! torsion fit to cer6 qm, jbk 10/12 +C NHL CTL1 CTO1 1.560 2 180.00 ! torsion fit to cer6 qm, jbk 10/12 +C NHL CTL1 CTO1 1.800 3 0.00 ! torsion fit to cer6 qm, jbk 10/12 +CTL1 CTO1 OHL HOL 5.000 1 180.00 ! torsion fit to cer6 qm, jbk 10/12 +CTL1 CTO1 OHL HOL 0.220 2 0.00 ! torsion fit to cer6 qm, jbk 10/12 +CTL1 CTO1 OHL HOL 1.110 3 180.00 ! torsion fit to cer6 qm, jbk 10/12 +HOL OHL CTL1 CEL3 1.330 1 0.00 ! prot22; 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93; H OH1 CT1 CT1 +HOL OHL CTO1 CEL3 1.330 1 0.00 ! prot22; 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93; H OH1 CT1 CT1 +HOL OHL CTO1 CTL3 0.000 3 0.00 ! torsion fit to cer6 qm, jbk 9/12 +!HCNC +HAL3 CTL3 NHL C 0.000 3 0.00 ! prot22; LK for autogenerate dihe, sp2-methyl, no dihedral potential; HA CT3 NH1 C +HAL1 CTL1 NHL C 0.000 1 0.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); HB CT1 NH1 C +!NCCO +NHL CTL1 CTL2 OSL 1.630 1 180.00 ! torsfit MP2/ccpVTZ, cer3 model, erh 8/09; transferred +NHL CTL1 CTL2 OSL 0.490 2 0.00 ! "" +NHL CTL1 CTL2 OSL 0.570 3 0.00 ! "" +NHL CTL1 CTO1 OSL 1.630 1 180.00 ! torsfit MP2/ccpVTZ, cer3 model, erh 8/09; transferred +NHL CTL1 CTO1 OSL 0.490 2 0.00 ! "" analogy for TACSPH, rmv nov 2009 +NHL CTL1 CTO1 OSL 0.570 3 0.00 ! "" +!OPOC +OSL PL OSL CTL2 1.200 1 180.00 ! lip36; phosphate, new NA, 4/98, adm jr. +OSL PL OSL CTL2 0.100 2 180.00 ! lip36; phosphate, new NA, 4/98, adm jr. +OSL PL OSL CTL2 0.100 3 180.00 ! lip36; phosphate, new NA, 4/98, adm jr. +!torsion1 +CEL3 CTO1 CTL1 NHL 0.940 1 0.00 ! torfit to cer4 qm, jbk 5/13 +CEL3 CTO1 CTL1 NHL 0.880 2 180.00 ! torfit to cer4 qm, jbk 5/13 +CEL3 CTO1 CTL1 NHL 2.090 3 0.00 ! torfit to cer4 qm, jbk 5/13 +NHL CTL1 CTO1 OHL 0.420 1 0.00 ! torfit to cer4 qm, jbk 5/13 +NHL CTL1 CTO1 OHL 1.530 2 180.00 ! torfit to cer4 qm, jbk 5/13 +NHL CTL1 CTO1 OHL 1.580 3 180.00 ! torfit to cer4 qm, jbk 5/13 +CEL3 CTO1 CTL1 CTL2 0.000 1 0.00 ! torfit to cer4 qm, jbk 10/12 +!torsion2 +CEL3 CEL3 CTO1 CTL1 0.860 1 0.00 ! torfit to cer4 qm w/adj, jbk 5/13 +CEL3 CEL3 CTO1 CTL1 1.910 2 0.00 ! torfit to cer4 qm w/adj, jbk 5/13 +CEL3 CEL3 CTO1 CTL1 1.520 3 180.00 ! torfit to cer4 qm w/adj, jbk 5/13 +CEL3 CEL3 CTO1 OHL 1.380 1 180.00 ! torfit to cer4 qm w/adj, jbk 5/13 +CEL3 CEL3 CTO1 OHL 0.580 2 0.00 ! torfit to cer4 qm w/adj, jbk 5/13 +CEL3 CEL3 CTO1 OHL 1.030 3 0.00 ! torfit to cer4 qm w/adj, jbk 5/13 +!torsion3 +NHL CTL1 CTL2 OSLP 1.370 1 0.00 ! torfit to cer3 qm, jbk 5/13 +NHL CTL1 CTL2 OSLP 0.340 2 0.00 ! torfit to cer3 qm, jbk 5/13 +NHL CTL1 CTL2 OSLP 0.200 3 180.00 ! torfit to cer3 qm, jbk 5/13 +NHL CTL1 CTL2 OSLP 0.020 4 180.00 ! torfit to cer3 qm, jbk 5/13 +NHL CTL1 CTL2 OSLP 0.140 5 0.00 ! torfit to cer3 qm, jbk 5/13 +NHL CTL1 CTL2 OSLP 0.060 6 0.00 ! torfit to cer3 qm, jbk 5/13 +CTL1 CTL1 CTL2 OSLP 0.000 1 0.00 ! torfit to cer3 qm, jbk 5/13 +!torsion5 +CTL3 CTL2 C NHL 1.990 1 0.00 ! torfit to cer2 qm, jbk 10/12 +CTL3 CTL2 C NHL 0.640 2 180.00 ! torfit to cer2 qm, jbk 10/12 +CTL3 CTL2 C NHL 0.280 3 180.00 ! torfit to cer2 qm, jbk 10/12 +CTL2 CTL2 C NHL 1.990 1 0.00 ! torfit to cer2 qm, jbk 10/12 +CTL2 CTL2 C NHL 0.640 2 180.00 ! torfit to cer2 qm, jbk 10/12 +CTL2 CTL2 C NHL 0.280 3 180.00 ! torfit to cer2 qm, jbk 10/12 +X CTL1 CTO1 X 0.200 3 0.00 ! alkane, 3/92 +X CTO1 CTL3 X 0.200 3 0.00 ! alkane, 3/92 +!Added by STN for CER24, 3/13 +NHL CTL1 CTO2 OHL 0.550 1 0.00 ! jbk; NHL CTL1 CTO1 OHL +NHL CTL1 CTO2 OHL 1.630 2 180.00 ! jbk; NHL CTL1 CTO1 OHL +NHL CTL1 CTO2 OHL 1.430 3 180.00 ! jbk; NHL CTL1 CTO1 OHL +C NHL CTL1 CTO2 4.080 1 0.00 ! jbk; C NHL CTL1 CTO1 +C NHL CTL1 CTO2 1.560 2 180.00 ! jbk; C NHL CTL1 CTO1 +C NHL CTL1 CTO2 1.800 3 0.00 ! jbk; C NHL CTL1 CTO1 +X CTL1 CTO2 X 0.200 3 0.00 ! alkane, 3/92; X CTL1 CTL2 X +X CTO2 OHL X 0.140 3 0.00 ! glycerol; X CTL2 OHL X +CTO2 CTL1 CTO1 OHL 0.200 3 0.00 ! lip36; alkane, 3/92, X CTL1 CTL1 X +H NHL CTL1 CTO2 0.000 1 0.00 ! prot22; Alanine Dipeptide ab initio calc's (LK); H NH1 CT1 CT2 +CEL3 CTO1 CTL1 CTO2 0.000 1 0.00 ! torfit to cer4 qm, jbk 10/12 + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +! Ceramides +NHL X X H 20. 0 0.00 ! amide, from peptide; rmv nov 2009 + + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! Ceramides +NHL 0.0 -0.2000 1.850 0.0 -0.20 1.55 ! ALLOW PEP POL ARO + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) - TAKEN FROM NH1 +CTO1 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92 + ! Transferred from CTL1; lip36 +CEL3 0.0 -0.0680 2.090 ! alkene, yin,adm jr., 12/95 + ! Transferred from CEL1; lip36! Added my STN for CER24 +CTO2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! STN, 3/13 + + +end + +return + + diff --git a/charmm/toppar/stream/lipid/toppar_all36_lipid_yeast.str b/charmm/toppar/stream/lipid/toppar_all36_lipid_yeast.str new file mode 100644 index 00000000..079f65df --- /dev/null +++ b/charmm/toppar/stream/lipid/toppar_all36_lipid_yeast.str @@ -0,0 +1,2516 @@ +* Toppar stream file for Branched and Cyclic Chained lipids. Following reading of +* top_all36_lipid.rtf +* and +* par_all36_lipid.rtf +* + +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have proirity, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* cholesterol residues +* +36 1 + +RESI PYPE 0.00 ! 3-palmitoyl-2-palmitoleoyl-D-glycero-1-Phosphatidylethanolamine +! +! (16:0) - CH2 +! | +! (16:1) - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! |! (CIS) | +ATOM C210 CEL1 -0.15 ! |! | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15 | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Ethanolamine Head Group +IC N C12 C11 O12 1.5078 111.09 68.79 110.33 1.4254 +IC C11 N *C12 H12A 1.5400 111.09 -122.33 108.17 1.1079 +IC H12A N *C12 H12B 1.1079 108.17 -118.40 107.74 1.1112 +IC C11 C12 N HN1 1.5400 111.09 -35.27 106.06 1.0664 +IC HN1 C12 *N HN2 1.0664 106.06 114.05 112.10 1.0358 +IC HN1 C12 *N HN3 1.0664 106.06 -118.21 113.62 1.0353 +IC O12 C12 *C11 H11A 1.4254 110.33 -126.01 111.43 1.1173 +IC H11A C12 *C11 H11B 1.1173 111.43 -116.40 108.25 1.1146 +IC C12 C11 O12 P 1.5400 110.33 -98.67 122.01 1.5838 +! Phosphate linker +IC C11 O12 P O11 1.4390 120.96 147.32 102.15 1.5764 +IC O11 O12 *P O13 1.5764 102.15 117.22 109.94 1.4724 +IC O11 O12 *P O14 1.5764 102.15 -112.56 106.22 1.4823 +IC O12 P O11 C1 1.5875 102.15 37.44 124.60 1.4242 +IC P O11 C1 C2 1.5764 124.60 -116.16 109.98 1.5498 +IC C2 O11 *C1 HA 1.5498 109.98 -117.32 107.50 1.1131 +IC HA O11 *C1 HB 1.1131 107.50 -118.29 113.74 1.1147 +IC O11 C1 C2 O21 1.4242 109.98 -146.90 108.63 1.4417 +! Backbone +IC O21 C1 *C2 C3 1.4417 108.63 -122.13 111.53 1.5568 !defines S chirality +IC C3 C1 *C2 HS 1.5568 111.53 -118.09 105.71 1.1179 !defines S chirality +IC C1 C2 O21 C21 1.5498 108.63 151.73 114.74 1.3222 +IC C2 O21 C21 C22 1.4417 114.74 173.79 108.64 1.5288 +IC C22 O21 *C21 O22 1.5288 108.64 -179.69 126.47 1.2177 +IC O21 C21 C22 C23 1.3222 108.64 178.90 112.26 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.26 -121.78 108.06 1.1089 +IC H2R C21 *C22 H2S 1.1089 108.06 -117.20 107.52 1.1095 +IC C1 C2 C3 O31 1.5498 111.53 -171.28 112.79 1.4438 +IC O31 C2 *C3 HX 1.4438 112.79 125.24 109.10 1.1078 +IC HX C2 *C3 HY 1.1078 109.10 114.68 107.27 1.1126 +IC C2 C3 O31 C31 1.5568 112.79 83.27 115.09 1.3297 +IC C3 O31 C31 C32 1.4438 115.09 -171.75 108.79 1.5271 +IC C32 O31 *C31 O32 1.5271 108.79 -178.65 125.65 1.2211 +IC O31 C31 C32 C33 1.3297 108.79 161.87 112.85 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.85 -120.68 107.68 1.1109 +IC H2X C31 *C32 H2Y 1.1109 107.68 -117.29 107.91 1.1085 +IC C21 C22 C23 C24 1.5288 112.26 175.83 112.36 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.36 -120.78 109.67 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.67 -117.71 109.57 1.1142 +! Acyl Chain 1 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5347 112.69 -179.93 113.30 1.5309 +IC C216 C214 *C215 H15R 1.5309 113.30 -121.70 108.75 1.1140 +IC H15R C214 *C215 H15S 1.1140 108.75 -116.65 108.73 1.1141 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5287 113.01 -179.36 111.84 1.5345 +IC C34 C32 *C33 H3X 1.5345 111.84 -121.48 110.04 1.1135 +IC H3X C32 *C33 H3Y 1.1135 110.04 -117.95 109.39 1.1149 +IC C32 C33 C34 C35 1.5453 111.84 178.35 112.93 1.5350 +IC C35 C33 *C34 H4X 1.5350 112.93 -121.06 108.92 1.1138 +IC H4X C33 *C34 H4Y 1.1138 108.92 -117.32 109.20 1.1130 +IC C33 C34 C35 C36 1.5345 112.93 -179.86 112.46 1.5352 +IC C36 C34 *C35 H5X 1.5352 112.46 -121.45 109.25 1.1129 +IC H5X C34 *C35 H5Y 1.1129 109.25 -117.43 109.01 1.1134 +IC C34 C35 C36 C37 1.5350 112.46 179.21 112.88 1.5352 +IC C37 C35 *C36 H6X 1.5352 112.88 -121.25 109.00 1.1134 +IC H6X C35 *C36 H6Y 1.1134 109.00 -117.27 109.08 1.1131 +IC C35 C36 C37 C38 1.5352 112.88 179.79 112.50 1.5352 +IC C38 C36 *C37 H7X 1.5352 112.50 -121.35 109.17 1.1130 +IC H7X C36 *C37 H7Y 1.1130 109.17 -117.42 109.08 1.1132 +IC C36 C37 C38 C39 1.5352 112.50 179.41 112.91 1.5352 +IC C39 C37 *C38 H8X 1.5352 112.91 -121.30 109.04 1.1133 +IC H8X C37 *C38 H8Y 1.1133 109.04 -117.27 109.05 1.1132 +IC C37 C38 C39 C310 1.5352 112.91 179.74 112.46 1.5353 +IC C310 C38 *C39 H9X 1.5353 112.46 -121.33 109.17 1.1131 +IC H9X C38 *C39 H9Y 1.1131 109.17 -117.42 109.10 1.1132 +IC C38 C39 C310 C311 1.5352 112.46 179.50 112.91 1.5350 +IC C311 C39 *C310 H10X 1.5350 112.91 -121.32 109.05 1.1133 +IC H10X C39 *C310 H10Y 1.1133 109.05 -117.29 109.05 1.1132 +IC C39 C310 C311 C312 1.5353 112.91 179.80 112.52 1.5354 +IC C312 C310 *C311 H11X 1.5354 112.52 -121.32 109.16 1.1131 +IC H11X C310 *C311 H11Y 1.1131 109.16 -117.41 109.11 1.1132 +IC C310 C311 C312 C313 1.5350 112.52 179.66 112.78 1.5349 +IC C313 C311 *C312 H12X 1.5349 112.78 -121.30 109.08 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.08 -117.35 109.09 1.1132 +IC C311 C312 C313 C314 1.5354 112.78 179.95 112.66 1.5353 +IC C314 C312 *C313 H13X 1.5353 112.66 -121.33 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.38 109.07 1.1132 +IC C312 C313 C314 C315 1.5349 112.66 179.95 112.69 1.5341 +IC C315 C313 *C314 H14X 1.5341 112.69 -121.30 109.17 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.17 -117.38 109.15 1.1132 +IC C313 C314 C315 C316 1.5353 112.69 179.98 113.37 1.5312 +IC C316 C314 *C315 H15X 1.5312 113.37 -121.71 108.74 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.74 -116.61 108.74 1.1141 +IC C314 C315 C316 H16X 1.5341 113.37 -59.94 110.51 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.51 119.91 110.52 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.51 -120.06 110.58 1.1112 + +RESI YOPA -1.00 ! 3-palmitoleoyl-2-oleoyl-D-glycero-1-Phosphatidic acid +! +! (16:1) - CH2 +! | +! (18:1) - CH +! | (-) +! CH2 - PO4 - H +! +! Polar Head and glycerol backbone +GROUP ! H12 + ! | +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.82 ! \ / alpha3 +ATOM O14 O2L -0.82 ! P (+) +ATOM O12 OHL -0.68 ! / \ alpha2 +ATOM H12 HOL 0.34 ! (-) O14 O11 +ATOM O11 OSLP -0.62 ! | +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! |! (cis) | +ATOM C210 CEL1 -0.15 ! |! | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15 | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! |! (cis) +ATOM C310 CEL1 -0.15 ! |! +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Phosphate linker +IC H12 O12 P O11 0.9603 104.90 175.02 104.77 1.5790 +IC O12 O11 *P O13 1.5667 104.77 111.35 112.54 1.4699 +IC O12 O11 *P O14 1.5667 104.77 -111.29 111.81 1.4718 +IC O12 P O11 C1 1.5667 104.77 74.19 120.92 1.4311 +IC P O11 C1 C2 1.5790 120.92 -130.06 110.78 1.5478 +IC C2 O11 *C1 HA 1.5478 110.78 -120.11 109.49 1.1119 +IC HA O11 *C1 HB 1.1119 109.49 -119.44 112.98 1.1188 +IC O11 C1 C2 O21 1.4311 110.78 170.72 106.82 1.4423 +! Backbone +IC O21 C1 *C2 C3 1.4417 108.63 -122.13 111.53 1.5568 !defines S chirality +IC C3 C1 *C2 HS 1.5568 111.53 -118.09 105.71 1.1179 !defines S chirality +IC C1 C2 O21 C21 1.5498 108.63 151.73 114.74 1.3222 +IC C2 O21 C21 C22 1.4417 114.74 173.79 108.64 1.5288 +IC C22 O21 *C21 O22 1.5288 108.64 -179.69 126.47 1.2177 +IC O21 C21 C22 C23 1.3222 108.64 178.90 112.26 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.26 -121.78 108.06 1.1089 +IC H2R C21 *C22 H2S 1.1089 108.06 -117.20 107.52 1.1095 +IC C1 C2 C3 O31 1.5498 111.53 -171.28 112.79 1.4438 +IC O31 C2 *C3 HX 1.4438 112.79 125.24 109.10 1.1078 +IC HX C2 *C3 HY 1.1078 109.10 114.68 107.27 1.1126 +IC C2 C3 O31 C31 1.5568 112.79 83.27 115.09 1.3297 +IC C3 O31 C31 C32 1.4438 115.09 -171.75 108.79 1.5271 +IC C32 O31 *C31 O32 1.5271 108.79 -178.65 125.65 1.2211 +IC O31 C31 C32 C33 1.3297 108.79 161.87 112.85 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.85 -120.68 107.68 1.1109 +IC H2X C31 *C32 H2Y 1.1109 107.68 -117.29 107.91 1.1085 +IC C21 C22 C23 C24 1.5288 112.26 175.83 112.36 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.36 -120.78 109.67 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.67 -117.71 109.57 1.1142 +! Acyl Chain 1 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5344 112.29 -121.35 109.32 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.32 -117.49 109.04 1.1133 +IC C213 C214 C215 C216 1.5344 112.29 178.10 112.83 1.5343 +IC C216 C214 *C215 H15R 1.5343 112.83 -121.22 109.06 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.06 -117.27 109.05 1.1132 +IC C214 C215 C216 C217 1.5344 112.83 179.20 112.48 1.5338 +IC C217 C215 *C216 H16R 1.5338 112.48 -121.30 109.23 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.23 -117.48 109.17 1.1133 +IC C215 C216 C217 C218 1.5343 112.48 179.30 113.32 1.5307 +IC C218 C216 *C217 H17R 1.5307 113.32 -121.67 108.76 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.76 -116.60 108.71 1.1141 +IC C216 C217 C218 H18R 1.5338 113.32 -60.32 110.45 1.1114 +IC H18R C217 *C218 H18S 1.1114 110.45 119.86 110.49 1.1113 +IC H18R C217 *C218 H18T 1.1114 110.45 -120.04 110.58 1.1112 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5348 112.71 -179.67 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.77 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DYPC 0.00 ! 3-palmitoleoyl-2-palmitoleoyl-D-glycero-1-Phosphatidylcholine +! +! (16:1) - CH2 +! | +! (16:1) - CH +! | (-) (+) +! CH2 - PO4 - CH2 - CH2 - N-(CH3)3 +! +! Polar Head and glycerol backbone +! +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C12 CTL2 -0.10 ! H15A-C15-H15C +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H13B | H14A +ATOM C13 CTL5 -0.35 ! | | | +ATOM H13A HL 0.25 ! H13A-C13----N----C14-H14B (+) +ATOM H13B HL 0.25 ! | | | +ATOM H13C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | +ATOM H14A HL 0.25 ! | +ATOM H14B HL 0.25 ! | alpha6 +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H12A--C12---H12B +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! |! (CIS) | +ATOM C210 CEL1 -0.15 ! |! | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15 | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! |! (cis) +ATOM C310 CEL1 -0.15 ! |! +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Phosphocholine Head Group +IC C13 N C12 C11 1.4950 110.81 58.46 117.00 1.5420 +IC C13 C12 *N C14 1.4950 110.81 122.75 109.46 1.4979 +IC C13 C12 *N C15 1.4950 110.81 -120.02 108.16 1.5034 +IC C11 N *C12 H12A 1.5420 117.00 -126.73 111.85 1.0787 +IC H12A N *C12 H12B 1.0787 111.85 -115.99 107.93 1.0977 +IC C14 N C13 H13A 1.4979 111.01 179.36 109.41 1.0866 +IC H13A N *C13 H13B 1.0866 109.41 119.11 111.31 1.0813 +IC H13A N *C13 H13C 1.0866 109.41 -119.02 111.10 1.0815 +IC C13 N C14 H14A 1.4950 111.01 -179.09 109.58 1.0882 +IC H14A N *C14 H14B 1.0882 109.58 118.63 110.95 1.0819 +IC H14A N *C14 H14C 1.0882 109.58 -119.72 111.56 1.0811 +IC C13 N C15 H15A 1.4950 109.49 -176.86 110.11 1.0949 +IC H15A N *C15 H15B 1.0949 110.11 112.40 111.19 1.0942 +IC H15A N *C15 H15C 1.0949 110.11 -123.40 113.89 1.0740 +IC N C12 C11 O12 1.5227 117.00 126.96 108.43 1.4243 +IC O12 C12 *C11 H11A 1.4243 108.43 -123.15 113.04 1.1139 +IC H11A C12 *C11 H11B 1.1139 113.04 -118.48 109.10 1.1129 +IC C12 C11 O12 P 1.5420 108.43 -67.66 118.24 1.5905 +! Phosphate linker +IC C11 O12 P O11 1.4390 120.96 147.32 102.15 1.5764 +IC O11 O12 *P O13 1.5764 102.15 117.22 109.94 1.4724 +IC O11 O12 *P O14 1.5764 102.15 -112.56 106.22 1.4823 +IC O12 P O11 C1 1.5875 102.15 37.44 124.60 1.4242 +IC P O11 C1 C2 1.5764 124.60 -116.16 109.98 1.5498 +IC C2 O11 *C1 HA 1.5498 109.98 -117.32 107.50 1.1131 +IC HA O11 *C1 HB 1.1131 107.50 -118.29 113.74 1.1147 +IC O11 C1 C2 O21 1.4242 109.98 -146.90 108.63 1.4417 +! Backbone +IC O21 C1 *C2 C3 1.4417 108.63 -122.13 111.53 1.5568 !defines S chirality +IC C3 C1 *C2 HS 1.5568 111.53 -118.09 105.71 1.1179 !defines S chirality +IC C1 C2 O21 C21 1.5498 108.63 151.73 114.74 1.3222 +IC C2 O21 C21 C22 1.4417 114.74 173.79 108.64 1.5288 +IC C22 O21 *C21 O22 1.5288 108.64 -179.69 126.47 1.2177 +IC O21 C21 C22 C23 1.3222 108.64 178.90 112.26 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.26 -121.78 108.06 1.1089 +IC H2R C21 *C22 H2S 1.1089 108.06 -117.20 107.52 1.1095 +IC C1 C2 C3 O31 1.5498 111.53 -171.28 112.79 1.4438 +IC O31 C2 *C3 HX 1.4438 112.79 125.24 109.10 1.1078 +IC HX C2 *C3 HY 1.1078 109.10 114.68 107.27 1.1126 +IC C2 C3 O31 C31 1.5568 112.79 83.27 115.09 1.3297 +IC C3 O31 C31 C32 1.4438 115.09 -171.75 108.79 1.5271 +IC C32 O31 *C31 O32 1.5271 108.79 -178.65 125.65 1.2211 +IC O31 C31 C32 C33 1.3297 108.79 161.87 112.85 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.85 -120.68 107.68 1.1109 +IC H2X C31 *C32 H2Y 1.1109 107.68 -117.29 107.91 1.1085 +IC C21 C22 C23 C24 1.5288 112.26 175.83 112.36 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.36 -120.78 109.67 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.67 -117.71 109.57 1.1142 +! Acyl Chain 1 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5347 112.69 -179.93 113.30 1.5309 +IC C216 C214 *C215 H15R 1.5309 113.30 -121.70 108.75 1.1140 +IC H15R C214 *C215 H15S 1.1140 108.75 -116.65 108.73 1.1141 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5348 112.71 -179.67 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.77 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI YOPC 0.00 ! 3-palmitoleoyl-2-oleoyl-D-glycero-1-Phosphatidylcholine +! +! (16:1) - CH2 +! | +! (18:1) - CH +! | (-) (+) +! CH2 - PO4 - CH2 - CH2 - N-(CH3)3 +! +! Polar Head and glycerol backbone +! +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C12 CTL2 -0.10 ! H15A-C15-H15C +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H13B | H14A +ATOM C13 CTL5 -0.35 ! | | | +ATOM H13A HL 0.25 ! H13A-C13----N----C14-H14B (+) +ATOM H13B HL 0.25 ! | | | +ATOM H13C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | +ATOM H14A HL 0.25 ! | +ATOM H14B HL 0.25 ! | alpha6 +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H12A--C12---H12B +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! |! (cis) | +ATOM C210 CEL1 -0.15 ! |! | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15 | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! |! (cis) +ATOM C310 CEL1 -0.15 ! |! +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Phosphocholine Head Group +IC C13 N C12 C11 1.4950 110.81 58.46 117.00 1.5420 +IC C13 C12 *N C14 1.4950 110.81 122.75 109.46 1.4979 +IC C13 C12 *N C15 1.4950 110.81 -120.02 108.16 1.5034 +IC C11 N *C12 H12A 1.5420 117.00 -126.73 111.85 1.0787 +IC H12A N *C12 H12B 1.0787 111.85 -115.99 107.93 1.0977 +IC C14 N C13 H13A 1.4979 111.01 179.36 109.41 1.0866 +IC H13A N *C13 H13B 1.0866 109.41 119.11 111.31 1.0813 +IC H13A N *C13 H13C 1.0866 109.41 -119.02 111.10 1.0815 +IC C13 N C14 H14A 1.4950 111.01 -179.09 109.58 1.0882 +IC H14A N *C14 H14B 1.0882 109.58 118.63 110.95 1.0819 +IC H14A N *C14 H14C 1.0882 109.58 -119.72 111.56 1.0811 +IC C13 N C15 H15A 1.4950 109.49 -176.86 110.11 1.0949 +IC H15A N *C15 H15B 1.0949 110.11 112.40 111.19 1.0942 +IC H15A N *C15 H15C 1.0949 110.11 -123.40 113.89 1.0740 +IC N C12 C11 O12 1.5227 117.00 126.96 108.43 1.4243 +IC O12 C12 *C11 H11A 1.4243 108.43 -123.15 113.04 1.1139 +IC H11A C12 *C11 H11B 1.1139 113.04 -118.48 109.10 1.1129 +IC C12 C11 O12 P 1.5420 108.43 -67.66 118.24 1.5905 +! Phosphate linker +IC C11 O12 P O11 1.4390 120.96 147.32 102.15 1.5764 +IC O11 O12 *P O13 1.5764 102.15 117.22 109.94 1.4724 +IC O11 O12 *P O14 1.5764 102.15 -112.56 106.22 1.4823 +IC O12 P O11 C1 1.5875 102.15 37.44 124.60 1.4242 +IC P O11 C1 C2 1.5764 124.60 -116.16 109.98 1.5498 +IC C2 O11 *C1 HA 1.5498 109.98 -117.32 107.50 1.1131 +IC HA O11 *C1 HB 1.1131 107.50 -118.29 113.74 1.1147 +IC O11 C1 C2 O21 1.4242 109.98 -146.90 108.63 1.4417 +! Backbone +IC O21 C1 *C2 C3 1.4417 108.63 -122.13 111.53 1.5568 !defines S chirality +IC C3 C1 *C2 HS 1.5568 111.53 -118.09 105.71 1.1179 !defines S chirality +IC C1 C2 O21 C21 1.5498 108.63 151.73 114.74 1.3222 +IC C2 O21 C21 C22 1.4417 114.74 173.79 108.64 1.5288 +IC C22 O21 *C21 O22 1.5288 108.64 -179.69 126.47 1.2177 +IC O21 C21 C22 C23 1.3222 108.64 178.90 112.26 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.26 -121.78 108.06 1.1089 +IC H2R C21 *C22 H2S 1.1089 108.06 -117.20 107.52 1.1095 +IC C1 C2 C3 O31 1.5498 111.53 -171.28 112.79 1.4438 +IC O31 C2 *C3 HX 1.4438 112.79 125.24 109.10 1.1078 +IC HX C2 *C3 HY 1.1078 109.10 114.68 107.27 1.1126 +IC C2 C3 O31 C31 1.5568 112.79 83.27 115.09 1.3297 +IC C3 O31 C31 C32 1.4438 115.09 -171.75 108.79 1.5271 +IC C32 O31 *C31 O32 1.5271 108.79 -178.65 125.65 1.2211 +IC O31 C31 C32 C33 1.3297 108.79 161.87 112.85 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.85 -120.68 107.68 1.1109 +IC H2X C31 *C32 H2Y 1.1109 107.68 -117.29 107.91 1.1085 +IC C21 C22 C23 C24 1.5288 112.26 175.83 112.36 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.36 -120.78 109.67 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.67 -117.71 109.57 1.1142 +! Acyl Chain 1 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5344 112.29 -121.35 109.32 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.32 -117.49 109.04 1.1133 +IC C213 C214 C215 C216 1.5344 112.29 178.10 112.83 1.5343 +IC C216 C214 *C215 H15R 1.5343 112.83 -121.22 109.06 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.06 -117.27 109.05 1.1132 +IC C214 C215 C216 C217 1.5344 112.83 179.20 112.48 1.5338 +IC C217 C215 *C216 H16R 1.5338 112.48 -121.30 109.23 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.23 -117.48 109.17 1.1133 +IC C215 C216 C217 C218 1.5343 112.48 179.30 113.32 1.5307 +IC C218 C216 *C217 H17R 1.5307 113.32 -121.67 108.76 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.76 -116.60 108.71 1.1141 +IC C216 C217 C218 H18R 1.5338 113.32 -60.32 110.45 1.1114 +IC H18R C217 *C218 H18S 1.1114 110.45 119.86 110.49 1.1113 +IC H18R C217 *C218 H18T 1.1114 110.45 -120.04 110.58 1.1112 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5348 112.71 -179.67 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.77 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DYPE 0.00 ! 3-palmitoleoyl-2-palmitoleoyl-D-glycero-1-Phosphatidylethanolamine +! +! (16:1) - CH2 +! | +! (16:1) - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! |! (CIS) | +ATOM C210 CEL1 -0.15 ! |! | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15 | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL3 -0.27 ! | | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! |! (cis) +ATOM C310 CEL1 -0.15 ! |! +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Ethanolamine Head Group +IC N C12 C11 O12 1.5078 111.09 68.79 110.33 1.4254 +IC C11 N *C12 H12A 1.5400 111.09 -122.33 108.17 1.1079 +IC H12A N *C12 H12B 1.1079 108.17 -118.40 107.74 1.1112 +IC C11 C12 N HN1 1.5400 111.09 -35.27 106.06 1.0664 +IC HN1 C12 *N HN2 1.0664 106.06 114.05 112.10 1.0358 +IC HN1 C12 *N HN3 1.0664 106.06 -118.21 113.62 1.0353 +IC O12 C12 *C11 H11A 1.4254 110.33 -126.01 111.43 1.1173 +IC H11A C12 *C11 H11B 1.1173 111.43 -116.40 108.25 1.1146 +IC C12 C11 O12 P 1.5400 110.33 -98.67 122.01 1.5838 +! Phosphate linker +IC C11 O12 P O11 1.4390 120.96 147.32 102.15 1.5764 +IC O11 O12 *P O13 1.5764 102.15 117.22 109.94 1.4724 +IC O11 O12 *P O14 1.5764 102.15 -112.56 106.22 1.4823 +IC O12 P O11 C1 1.5875 102.15 37.44 124.60 1.4242 +IC P O11 C1 C2 1.5764 124.60 -116.16 109.98 1.5498 +IC C2 O11 *C1 HA 1.5498 109.98 -117.32 107.50 1.1131 +IC HA O11 *C1 HB 1.1131 107.50 -118.29 113.74 1.1147 +IC O11 C1 C2 O21 1.4242 109.98 -146.90 108.63 1.4417 +! Backbone +IC O21 C1 *C2 C3 1.4417 108.63 -122.13 111.53 1.5568 !defines S chirality +IC C3 C1 *C2 HS 1.5568 111.53 -118.09 105.71 1.1179 !defines S chirality +IC C1 C2 O21 C21 1.5498 108.63 151.73 114.74 1.3222 +IC C2 O21 C21 C22 1.4417 114.74 173.79 108.64 1.5288 +IC C22 O21 *C21 O22 1.5288 108.64 -179.69 126.47 1.2177 +IC O21 C21 C22 C23 1.3222 108.64 178.90 112.26 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.26 -121.78 108.06 1.1089 +IC H2R C21 *C22 H2S 1.1089 108.06 -117.20 107.52 1.1095 +IC C1 C2 C3 O31 1.5498 111.53 -171.28 112.79 1.4438 +IC O31 C2 *C3 HX 1.4438 112.79 125.24 109.10 1.1078 +IC HX C2 *C3 HY 1.1078 109.10 114.68 107.27 1.1126 +IC C2 C3 O31 C31 1.5568 112.79 83.27 115.09 1.3297 +IC C3 O31 C31 C32 1.4438 115.09 -171.75 108.79 1.5271 +IC C32 O31 *C31 O32 1.5271 108.79 -178.65 125.65 1.2211 +IC O31 C31 C32 C33 1.3297 108.79 161.87 112.85 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.85 -120.68 107.68 1.1109 +IC H2X C31 *C32 H2Y 1.1109 107.68 -117.29 107.91 1.1085 +IC C21 C22 C23 C24 1.5288 112.26 175.83 112.36 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.36 -120.78 109.67 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.67 -117.71 109.57 1.1142 +! Acyl Chain 1 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5347 112.69 -179.93 113.30 1.5309 +IC C216 C214 *C215 H15R 1.5309 113.30 -121.70 108.75 1.1140 +IC H15R C214 *C215 H15S 1.1140 108.75 -116.65 108.73 1.1141 +IC C214 C215 C216 H16R 1.5339 113.30 -59.98 110.46 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.46 119.84 110.45 1.1114 +IC H16R C215 *C216 H16T 1.1113 110.46 -120.09 110.62 1.1112 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5348 112.71 -179.67 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.77 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + + +RESI YOPE 0.00 ! 3-palmitoleoyl-2-oleoyl-D-glycero-1-Phosphatidylethanolamine +! +! (16:1) - CH2 +! | +! (18:1) - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! |! (cis) | +ATOM C210 CEL1 -0.15 ! |! | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15 | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! |! (cis) +ATOM C310 CEL1 -0.15 ! |! +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Ethanolamine Head Group +IC N C12 C11 O12 1.5078 111.09 68.79 110.33 1.4254 +IC C11 N *C12 H12A 1.5400 111.09 -122.33 108.17 1.1079 +IC H12A N *C12 H12B 1.1079 108.17 -118.40 107.74 1.1112 +IC C11 C12 N HN1 1.5400 111.09 -35.27 106.06 1.0664 +IC HN1 C12 *N HN2 1.0664 106.06 114.05 112.10 1.0358 +IC HN1 C12 *N HN3 1.0664 106.06 -118.21 113.62 1.0353 +IC O12 C12 *C11 H11A 1.4254 110.33 -126.01 111.43 1.1173 +IC H11A C12 *C11 H11B 1.1173 111.43 -116.40 108.25 1.1146 +IC C12 C11 O12 P 1.5400 110.33 -98.67 122.01 1.5838 +! Phosphate linker +IC C11 O12 P O11 1.4390 120.96 147.32 102.15 1.5764 +IC O11 O12 *P O13 1.5764 102.15 117.22 109.94 1.4724 +IC O11 O12 *P O14 1.5764 102.15 -112.56 106.22 1.4823 +IC O12 P O11 C1 1.5875 102.15 37.44 124.60 1.4242 +IC P O11 C1 C2 1.5764 124.60 -116.16 109.98 1.5498 +IC C2 O11 *C1 HA 1.5498 109.98 -117.32 107.50 1.1131 +IC HA O11 *C1 HB 1.1131 107.50 -118.29 113.74 1.1147 +IC O11 C1 C2 O21 1.4242 109.98 -146.90 108.63 1.4417 +! Backbone +IC O21 C1 *C2 C3 1.4417 108.63 -122.13 111.53 1.5568 !defines S chirality +IC C3 C1 *C2 HS 1.5568 111.53 -118.09 105.71 1.1179 !defines S chirality +IC C1 C2 O21 C21 1.5498 108.63 151.73 114.74 1.3222 +IC C2 O21 C21 C22 1.4417 114.74 173.79 108.64 1.5288 +IC C22 O21 *C21 O22 1.5288 108.64 -179.69 126.47 1.2177 +IC O21 C21 C22 C23 1.3222 108.64 178.90 112.26 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.26 -121.78 108.06 1.1089 +IC H2R C21 *C22 H2S 1.1089 108.06 -117.20 107.52 1.1095 +IC C1 C2 C3 O31 1.5498 111.53 -171.28 112.79 1.4438 +IC O31 C2 *C3 HX 1.4438 112.79 125.24 109.10 1.1078 +IC HX C2 *C3 HY 1.1078 109.10 114.68 107.27 1.1126 +IC C2 C3 O31 C31 1.5568 112.79 83.27 115.09 1.3297 +IC C3 O31 C31 C32 1.4438 115.09 -171.75 108.79 1.5271 +IC C32 O31 *C31 O32 1.5271 108.79 -178.65 125.65 1.2211 +IC O31 C31 C32 C33 1.3297 108.79 161.87 112.85 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.85 -120.68 107.68 1.1109 +IC H2X C31 *C32 H2Y 1.1109 107.68 -117.29 107.91 1.1085 +IC C21 C22 C23 C24 1.5288 112.26 175.83 112.36 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.36 -120.78 109.67 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.67 -117.71 109.57 1.1142 +! Acyl Chain 1 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5344 112.29 -121.35 109.32 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.32 -117.49 109.04 1.1133 +IC C213 C214 C215 C216 1.5344 112.29 178.10 112.83 1.5343 +IC C216 C214 *C215 H15R 1.5343 112.83 -121.22 109.06 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.06 -117.27 109.05 1.1132 +IC C214 C215 C216 C217 1.5344 112.83 179.20 112.48 1.5338 +IC C217 C215 *C216 H16R 1.5338 112.48 -121.30 109.23 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.23 -117.48 109.17 1.1133 +IC C215 C216 C217 C218 1.5343 112.48 179.30 113.32 1.5307 +IC C218 C216 *C217 H17R 1.5307 113.32 -121.67 108.76 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.76 -116.60 108.71 1.1141 +IC C216 C217 C218 H18R 1.5338 113.32 -60.32 110.45 1.1114 +IC H18R C217 *C218 H18S 1.1114 110.45 119.86 110.49 1.1113 +IC H18R C217 *C218 H18T 1.1114 110.45 -120.04 110.58 1.1112 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5348 112.71 -179.67 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.77 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + + +RESI YOPS -1.00 ! 3-palmitoleoyl-2-oleoyl-D-glycero-1-Phosphatidylserine +! +! (16:1) - CH2 +! | (-) +! (18:1) - CH CO2 +! | (-) | (+) +! CH2 - PO4 - CH2 - CH - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! |! (cis) | +ATOM C210 CEL1 -0.15 ! |! | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15 | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! |! (cis) +ATOM C310 CEL1 -0.15 ! |! +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 C13 C12 O13B O13A + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +! Serine Head Group +IC N C12 C11 O12 1.4892 110.33 60.56 112.04 1.4390 +IC N C12 C13 O13B 1.4892 109.53 -177.41 117.87 1.2553 +IC C11 N *C12 C13 1.5611 110.33 123.90 109.53 1.5407 +IC C13 N *C12 H12A 1.5407 109.53 116.02 108.38 1.0781 +IC HN1 N C12 C11 1.0454 110.41 -117.56 110.33 1.5611 +IC HN1 C12 *N HN2 1.0454 110.41 121.15 108.26 1.0580 +IC HN1 C12 *N HN3 1.0454 110.41 -120.80 103.02 1.0474 +IC O13B C12 *C13 O13A 1.2553 117.87 177.95 118.17 1.2648 +IC O12 C12 *C11 H11A 1.4390 112.04 -126.32 109.67 1.1172 +IC H11A C12 *C11 H11B 1.1172 109.67 -114.74 107.27 1.1147 +IC C12 C11 O12 P 1.5611 112.04 -98.86 120.96 1.5875 +! Phosphate linker +IC C11 O12 P O11 1.4390 120.96 147.32 102.15 1.5764 +IC O11 O12 *P O13 1.5764 102.15 117.22 109.94 1.4724 +IC O11 O12 *P O14 1.5764 102.15 -112.56 106.22 1.4823 +IC O12 P O11 C1 1.5875 102.15 37.44 124.60 1.4242 +IC P O11 C1 C2 1.5764 124.60 -116.16 109.98 1.5498 +IC C2 O11 *C1 HA 1.5498 109.98 -117.32 107.50 1.1131 +IC HA O11 *C1 HB 1.1131 107.50 -118.29 113.74 1.1147 +IC O11 C1 C2 O21 1.4242 109.98 -146.90 108.63 1.4417 +! Backbone +IC O21 C1 *C2 C3 1.4417 108.63 -122.13 111.53 1.5568 !defines S chirality +IC C3 C1 *C2 HS 1.5568 111.53 -118.09 105.71 1.1179 !defines S chirality +IC C1 C2 O21 C21 1.5498 108.63 151.73 114.74 1.3222 +IC C2 O21 C21 C22 1.4417 114.74 173.79 108.64 1.5288 +IC C22 O21 *C21 O22 1.5288 108.64 -179.69 126.47 1.2177 +IC O21 C21 C22 C23 1.3222 108.64 178.90 112.26 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.26 -121.78 108.06 1.1089 +IC H2R C21 *C22 H2S 1.1089 108.06 -117.20 107.52 1.1095 +IC C1 C2 C3 O31 1.5498 111.53 -171.28 112.79 1.4438 +IC O31 C2 *C3 HX 1.4438 112.79 125.24 109.10 1.1078 +IC HX C2 *C3 HY 1.1078 109.10 114.68 107.27 1.1126 +IC C2 C3 O31 C31 1.5568 112.79 83.27 115.09 1.3297 +IC C3 O31 C31 C32 1.4438 115.09 -171.75 108.79 1.5271 +IC C32 O31 *C31 O32 1.5271 108.79 -178.65 125.65 1.2211 +IC O31 C31 C32 C33 1.3297 108.79 161.87 112.85 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.85 -120.68 107.68 1.1109 +IC H2X C31 *C32 H2Y 1.1109 107.68 -117.29 107.91 1.1085 +IC C21 C22 C23 C24 1.5288 112.26 175.83 112.36 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.36 -120.78 109.67 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.67 -117.71 109.57 1.1142 +! Acyl Chain 1 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5344 112.29 -121.35 109.32 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.32 -117.49 109.04 1.1133 +IC C213 C214 C215 C216 1.5344 112.29 178.10 112.83 1.5343 +IC C216 C214 *C215 H15R 1.5343 112.83 -121.22 109.06 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.06 -117.27 109.05 1.1132 +IC C214 C215 C216 C217 1.5344 112.83 179.20 112.48 1.5338 +IC C217 C215 *C216 H16R 1.5338 112.48 -121.30 109.23 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.23 -117.48 109.17 1.1133 +IC C215 C216 C217 C218 1.5343 112.48 179.30 113.32 1.5307 +IC C218 C216 *C217 H17R 1.5307 113.32 -121.67 108.76 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.76 -116.60 108.71 1.1141 +IC C216 C217 C218 H18R 1.5338 113.32 -60.32 110.45 1.1114 +IC H18R C217 *C218 H18S 1.1114 110.45 119.86 110.49 1.1113 +IC H18R C217 *C218 H18T 1.1114 110.45 -120.04 110.58 1.1112 +! Acyl Chain 2 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5348 112.71 -179.67 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.77 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C314 C315 C316 H16X 1.5340 113.30 -59.94 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.86 110.45 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.06 110.61 1.1112 + + +end + +read para card flex @app +* new parameters +* + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +!Neutral N terminus + + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! + + +END + +return diff --git a/charmm/toppar/stream/misc/toppar_amines.str b/charmm/toppar/stream/misc/toppar_amines.str new file mode 100644 index 00000000..b1e22688 --- /dev/null +++ b/charmm/toppar/stream/misc/toppar_amines.str @@ -0,0 +1,231 @@ +* Topology and parameters for neutral, aliphatic amines. +* + +!Testcase +!test_amines.inp + +!Reference +!Chen, I.-J., Yin, D. and MacKerell, Jr., A.D., "Combined Ab +!initio/Empirical Approach for Optimization of Lennard-Jones Parameters +!for Polar-Neutral Compounds," Journal of Computational Chemistry, +!2002, 23:199-213. +! +!Note that these parameters are higly optimized to reproduce the +!corresponding condensed phase properties and have not been incorporated +!into the CHARMM22 or CHARMM27 biomolecular force fields + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have proirity, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for amines +* +31 1 + +MASS 446 HNT0 1.00800 H ! N-ter H (ammonia) +MASS 447 HNT1 1.00800 H ! N-ter H (methylamine) +MASS 448 HNT2 1.00800 H ! N-ter H (dimethylamine) +MASS 449 HNA1 1.00800 H ! Aliphatic H +MASS 450 HNA2 1.00800 H ! Aliphatic H +MASS 451 HNA3 1.00800 H ! Aliphatic H +MASS 452 N0 14.00700 N ! ammonia nitrogen +MASS 453 N1 14.00700 N ! methylamine nitrogen +MASS 454 N2 14.00700 N ! dimethylamine nitrogen +MASS 455 N3 14.00700 N ! trimethylamine nitrogen +MASS 456 CNT1 12.01100 C ! methylamine methyl carbon +MASS 457 CNT2 12.01100 C ! dimethylamine methyl carbon +MASS 458 CNT3 12.01100 C ! trimethylamine methyl carbon + +default first none last none + +autogenerate angles dihedrals ! 2/05 update + +RESI AMM1 0.00 ! Ammonia +GROUP +ATOM N1 N0 -1.125 +ATOM H11 HNT0 0.375 +ATOM H12 HNT0 0.375 +ATOM H13 HNT0 0.375 +BOND N1 H11 N1 H12 N1 H13 +IC H13 H11 N1 H12 0.0 0.0 180. 0.0 0.0 +IC H11 H12 N1 H13 0.0 0.0 180. 0.0 0.0 +IC H12 H13 N1 H11 0.0 0.0 180. 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI MAM1 0.00 ! +GROUP +ATOM N1 N1 -0.99 ! +ATOM C1 CNT1 -0.06 ! HC1 HN1 +ATOM HN1 HNT1 0.39 ! \ / +ATOM HN2 HNT1 0.39 ! HC2-C1---N1 +ATOM HC1 HNA1 0.09 ! / \ +ATOM HC2 HNA1 0.09 ! HC3 HN2 +ATOM HC3 HNA1 0.09 ! +BOND N1 C1 N1 HN1 N1 HN2 +BOND C1 HC1 C1 HC2 C1 HC3 +IMPH N1 HN2 HN1 C1 +IC BLNK HN1 N1 C1 0.0 0.0 180. 0.0 0.0 +IC HN1 N1 C1 HC1 0.0 0.0 180. 0.0 0.0 +IC HN1 N1 C1 HC2 0.0 0.0 60. 0.0 0.0 +IC HN1 N1 C1 HC3 0.0 0.0 300. 0.0 0.0 +IC HC1 C1 N1 HN2 0.0 0.0 0. 0.0 0.0 +PATCHING FIRS NONE LAST NONE + +RESI DMAM 0.00 ! +GROUP +ATOM N1 N2 -0.82 ! +ATOM HN1 HNT2 0.40 ! +ATOM C1 CNT2 -0.06 ! H11 HN1 +ATOM C2 CNT2 -0.06 ! \ / +ATOM H11 HNA2 0.09 ! H12-C1---N1 +ATOM H12 HNA2 0.09 ! / \ +ATOM H13 HNA2 0.09 ! H13 C2-H23 +ATOM H21 HNA2 0.09 ! / \ +ATOM H22 HNA2 0.09 ! H21 H22 +ATOM H23 HNA2 0.09 ! +BOND N1 HN1 N1 C1 N1 C2 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IC BLNK HN1 N1 C1 0.0 0.0 180. 0.0 0.0 +IC HN1 N1 C1 H11 0.0 0.0 180. 0.0 0.0 +IC HN1 N1 C1 H12 0.0 0.0 60. 0.0 0.0 +IC HN1 N1 C1 H13 0.0 0.0 300. 0.0 0.0 +IC C2 *N1 HN1 C1 0.0 0.0 120. 0.0 0.0 +IC H11 C1 N1 C2 0.0 0.0 180. 0.0 0.0 +IC HN1 N1 C2 H21 0.0 0.0 180. 0.0 0.0 +IC HN1 N1 C2 H22 0.0 0.0 60. 0.0 0.0 +IC HN1 N1 C2 H23 0.0 0.0 300. 0.0 0.0 +PATCHING FIRS NONE LAST NONE + +RESI TMAM 0.00 ! trimethylamine, adm jr. +GROUP ! H31 H32 +ATOM N1 N3 -0.63 ! \ / +ATOM C1 CNT3 -0.06 ! H11 C3-H33 +ATOM C2 CNT3 -0.06 ! \ / +ATOM C3 CNT3 -0.06 ! H12-C1---N1 +ATOM H11 HNA3 0.09 ! / \ +ATOM H12 HNA3 0.09 ! H13 C2-H23 +ATOM H13 HNA3 0.09 ! / \ +ATOM H21 HNA3 0.09 ! H21 H22 +ATOM H22 HNA3 0.09 ! +ATOM H23 HNA3 0.09 ! +ATOM H31 HNA3 0.09 ! +ATOM H32 HNA3 0.09 ! +ATOM H33 HNA3 0.09 ! +BOND N1 C1 N1 C2 N1 C3 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +IC BLNK C3 N1 C1 0.0 0.0 180. 0.0 0.0 +IC C3 N1 C1 H11 0.0 0.0 180. 0.0 0.0 +IC C3 N1 C1 H12 0.0 0.0 60. 0.0 0.0 +IC C3 N1 C1 H13 0.0 0.0 300. 0.0 0.0 +IC H11 C1 N1 C2 0.0 0.0 0. 0.0 0.0 +IC C3 N1 C2 H21 0.0 0.0 180. 0.0 0.0 +IC C3 N1 C2 H22 0.0 0.0 60. 0.0 0.0 +IC C3 N1 C2 H23 0.0 0.0 300. 0.0 0.0 +IC C2 N1 C3 H31 0.0 0.0 180. 0.0 0.0 +IC C2 N1 C3 H32 0.0 0.0 60. 0.0 0.0 +IC C2 N1 C3 H33 0.0 0.0 300. 0.0 0.0 +PATCHING FIRS NONE LAST NONE + +end + +read para card flex @app +* All-Atom Amine Parameters +* Ammonia, Methylamine, Dimethylamine and Trimethylamine +* + +ATOMS +MASS 446 HNT0 1.00800 ! N-ter H (ammonia) +MASS 447 HNT1 1.00800 ! N-ter H (methylamine) +MASS 448 HNT2 1.00800 ! N-ter H (dimethylamine) +MASS 449 HNA1 1.00800 ! Aliphatic H +MASS 450 HNA2 1.00800 ! Aliphatic H +MASS 451 HNA3 1.00800 ! Aliphatic H +MASS 452 N0 14.00700 ! ammonia nitrogen +MASS 453 N1 14.00700 ! methylamine nitrogen +MASS 454 N2 14.00700 ! dimethylamine nitrogen +MASS 455 N3 14.00700 ! trimethylamine nitrogen +MASS 456 CNT1 12.01100 ! methylamine methyl carbon +MASS 457 CNT2 12.01100 ! dimethylamine methyl carbon +MASS 458 CNT3 12.01100 ! trimethylamine methyl carbon + +BONDS +!atom type Kb b0 +!============================================ +N0 HNT0 455.500 1.0140 +N1 HNT1 453.100 1.0140 +N2 HNT2 447.800 1.0190 +N1 CNT1 263.000 1.4740 +N2 CNT2 255.000 1.4630 +N3 CNT3 235.000 1.4540 +HNA1 CNT1 314.500 1.0930 +HNA2 CNT2 313.800 1.0980 +HNA3 CNT3 311.000 1.1110 +!dum HNT1 100.000 1.0000 + +ANGLES +!atom types Ktheta Theta0 Kub S0 +!================================================== +HNT0 N0 HNT0 29.000 107.10 +HNT1 N1 HNT1 29.500 105.85 +HNA1 CNT1 HNA1 35.000 109.47 5.40 1.80200 +HNA2 CNT2 HNA2 35.800 109.00 5.40 1.80200 +HNA3 CNT3 HNA3 35.500 108.40 5.40 1.80200 +HNT1 N1 CNT1 41.000 112.10 +HNT2 N2 CNT2 42.100 108.90 5.00 2.0292 +N1 CNT1 HNA1 32.400 109.50 50.00 2.14000 +N2 CNT2 HNA2 30.500 109.70 50.00 2.14000 +N3 CNT3 HNA3 35.000 109.50 50.00 2.14000 +CNT2 N2 CNT2 40.500 112.20 5.00 2.42170 +CNT3 N3 CNT3 53.000 110.90 +!CNT3 N3 CNT3 65.000 110.90 ! 2/05 update +!dum HNT1 N1 100.000 90.00 + +DIHEDRALS +!atom types Kchi n delta +!================================================== +HNA1 CNT1 N1 HNT1 0.1600 3 0.00 !fitting to exptl data +HNA2 CNT2 N2 HNT2 0.4200 3 0.0000 !fitting to exptl data +HNA2 CNT2 N2 CNT2 0.0800 3 0.0000 !fitting to HF/6-31G(d) surface +HNA3 CNT3 N3 CNT3 0.3150 3 0.00 !fitting to exptl data + +IMPROPER +!atom types Kpsi 0 psi0 +!================================================== +N1 HNT1 HNT1 CNT1 34.8000 0 0.0000 !methylamine + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!NOTE: the omission of the 1,4 LJ terms for the different +!types of methyl groups is essential, adm. jr, april 2005 + +N0 0.000000 -0.070000 1.980000 +N1 0.000000 -0.060000 1.990000 +N2 0.000000 -0.045000 2.000000 !correction, 1/09 +N3 0.000000 -0.035000 2.000000 +HNT0 0.000000 -0.012000 0.870000 +HNT1 0.000000 -0.010000 0.875000 +HNT2 0.000000 -0.009000 0.875000 +CNT1 0.000000 -0.080000 1.990000 ! 0.00 -0.01 1.90 +CNT2 0.000000 -0.078000 1.980000 ! 0.00 -0.01 1.90 +CNT3 0.000000 -0.070000 1.970000 ! 0.00 -0.01 1.90 +HNA1 0.000000 -0.040000 1.260000 +HNA2 0.000000 -0.028000 1.280000 +HNA3 0.000000 -0.028000 1.280000 + +END + +return + + + + diff --git a/charmm/toppar/stream/misc/toppar_dum_noble_gases.str b/charmm/toppar/stream/misc/toppar_dum_noble_gases.str new file mode 100644 index 00000000..ac9a4f7e --- /dev/null +++ b/charmm/toppar/stream/misc/toppar_dum_noble_gases.str @@ -0,0 +1,62 @@ +* Toplogy and parameter information for helium, neon and a dummy atom. +* + +!Testcase +!test_dum_nobel_gases.inp + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have proirity, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for helium, neon and a dummy atom. +* +31 1 + +MASS 495 HE 4.00260 ! helium +MASS 496 NE 20.17970 ! neon +MASS 497 DUM 0.00000 ! dummy atom + +RESI HE1 0.00 ! helium +GROUP +ATOM HE01 HE 0.00 +PATCHING FIRST NONE LAST NONE + +RESI NE1 0.00 ! neon +GROUP +ATOM NE01 NE 0.00 +PATCHING FIRST NONE LAST NONE + +RESI DUM 0.00 ! DUMMY ATOM +GROUP +ATOM DUM DUM 0.00 +PATCHING FIRST NONE LAST NONE + +end + +read para card flex @app +* Parameters for helium, neon and a dummy atom. +* + +ATOMS +MASS 495 HE 4.00260 ! helium +MASS 496 NE 20.17970 ! neon +MASS 497 DUM 0.00000 ! dummy atom + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +DUM 0.000000 -0.000000 0.000000 +HE 0.000000 -0.021270 1.480000 +NE 0.000000 -0.085450 1.530000 + +end + +return + + diff --git a/charmm/toppar/stream/misc/toppar_hbond.str b/charmm/toppar/stream/misc/toppar_hbond.str new file mode 100644 index 00000000..bdb1e018 --- /dev/null +++ b/charmm/toppar/stream/misc/toppar_hbond.str @@ -0,0 +1,38 @@ +* This stream file is for hydrogen bond analysis ONLY. +* It WILL change your energy function (not for the better) +* by adding an HBOND energy term. Use at your own risk. +* NOTE: The charmm potential energy function is designed NOT +* to include an explicit hydrogen bond term. Therefore, use +* of the following hydrogen bond parameters will lead to incorrect +* results. +* + +!Parent files that have to be read prior to streaming this file +!top_all36_na.rtf or the protein or lipid top file +!par_all36_na.prm or the protein or lipid par file + +!Testcase +!test_hbond.inp + +read para card flex append +* hbond parameters for analysis only +* + +EQUIVALENCE +NALL 10 N* +OALL 10 O* +SALL 10 S* + +HBOND AEXP 4 REXP 6 HAEX 2 AAEX 2 NOACCEPTORS HBNOEXCLUSIONS ALL - +CUTHB 6.0 CTOFHB 5.0 CTONHB 4.0 CUTHA 100.0 CTOFHA 90.0 CTONHA 90.0 +NALL NALL -5.000 3.0000 +NALL OALL -4.900 2.9000 +OALL NALL -4.850 2.8500 +OALL OALL -4.750 2.7500 +SALL NALL -3.500 3.0000 +SALL OALL -3.500 2.9000 + +END + +return + diff --git a/charmm/toppar/stream/misc/toppar_ions_won.str b/charmm/toppar/stream/misc/toppar_ions_won.str new file mode 100644 index 00000000..2bb85e05 --- /dev/null +++ b/charmm/toppar/stream/misc/toppar_ions_won.str @@ -0,0 +1,575 @@ +* top_ions_won.str: general model for mono-, di-, and trivalent cations +* + +!This is a comprehensive set of ions developed using stochastic boundary +!conditions. It is strongly recommended that ion parameters in +!toppar_water_ions.str be used if available, as they are more highly +!optimized. Accordingly, those ions have been commented in this +!file. +! +!reference +!Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations +!Developed under the Solvent Boundary Potential," Journal of Physical +!Chemistry A., 116: 11763-11767, 2012. + + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +37 1 + +! J. Phys. Chem. B Supporting Information, October 12, 2012 +!Mass 301 Li1p 6.940 Li ! Lithium +!Mass 302 Na1p 22.990 Na ! Sodium +!Mass 303 K1p 39.098 K ! Potassium +!Mass 304 Rb1p 85.468 Rb ! Rubidium +!Mass 305 Cs1p 132.91 Cs ! Cesium +Mass 306 Cu1p 63.546 Cu ! Copper +Mass 307 Ag1p 107.87 Ag ! Silver +Mass 308 Au1p 196.97 Au ! Gold +Mass 309 Ti1p 47.867 Ti ! Titanium +Mass 321 Be2p 9.0122 Be ! Beryllium +!Mass 322 Mg2p 24.305 Mg ! Magnesium +!Mass 323 Ca2p 40.078 Ca ! Calcium +Mass 324 Sr2p 87.62 Sr ! Strontium +!Mass 325 Ba2p 137.33 Ba ! Barium +Mass 326 Ra2p 226.03 Ra ! Radium +Mass 327 V2p 50.942 V ! Vanadium +Mass 328 Cr2p 51.996 Cr ! Chromium +Mass 329 Mn2p 54.938 Mn ! Manganese +Mass 330 Fe2p 55.854 Fe ! Iron +Mass 331 Co2p 58.933 Co ! Cobalt +Mass 332 Ni2p 58.693 Ni ! Nickel +Mass 333 Cu2p 63.546 Cu ! Copper +!Mass 334 Zn2p 65.38 Zn ! Zinc +Mass 335 Pd2p 106.42 Pd ! Palladium +Mass 336 Ag2p 107.87 Ag ! Silver +!Mass 337 Cd2p 112.41 Cd ! Cadmium +Mass 338 Sn2p 118.71 Sn ! Tin +Mass 339 Pt2p 195.08 Pt ! Platinum +Mass 340 Hg2p 200.59 Hg ! Mercury +Mass 341 Pb2p 207.20 Pb ! Lead +Mass 342 Sm2p 150.36 Sm ! Samarium +Mass 343 Eu2p 151.96 Eu ! Europium +Mass 344 Yb2p 173.05 Yb ! Ytterbium +Mass 351 Al3p 26.982 Al ! Aluminum +Mass 352 Sc3p 44.956 Sc ! Scandium +Mass 353 Y3p 88.906 Y ! Yttrium +Mass 354 La3p 138.91 La ! Lanthanum +Mass 355 Ce3p 140.12 Ce ! Cerium +Mass 356 Pr3p 140.91 Pr ! Praseodynium +Mass 357 Nd3p 144.24 Nd ! Neodynium +Mass 358 Pm3p 144.91 Pm ! Promethium +Mass 359 Sm3p 150.36 Sm ! Samarium +Mass 360 Eu3p 151.96 Eu ! Europium +Mass 361 Gd3p 157.25 Gd ! Gadolinium +Mass 362 Tb3p 158.93 Tb ! Terbium +Mass 363 Dy3p 162.50 Dy ! Dysprosium +Mass 364 Ho3p 164.93 Ho ! Holmium +Mass 365 Er3p 167.28 Er ! Erbium +Mass 366 Tm3p 168.93 Tm ! Thulium +Mass 367 Yb3p 173.05 Yb ! Ytterbium +Mass 368 Lu3p 174.97 Lu ! Lutetium +Mass 369 U3p 238.03 U ! Uranium +Mass 370 Pu3p 244.06 Pu ! Plutonium +Mass 371 Ti3p 47.867 Ti ! Titanium +Mass 372 V3p 50.942 V ! Vanadium +Mass 373 Cr3p 51.996 Cr ! Chromium +Mass 374 Mn3p 54.938 Mn ! Manganese +Mass 375 Fe3p 55.854 Fe ! Iron +Mass 376 Co3p 58.933 Co ! Cobalt +Mass 377 Ga3p 69.723 Ga ! Gallium +Mass 378 Rh3p 102.91 Rh ! Rhodium +Mass 379 In3p 114.82 In ! Indium +Mass 380 Au3p 196.97 Au ! Gold +Mass 381 Tl3p 204.38 Tl ! Thallium +Mass 382 Bi3p 208.98 Bi ! Bismuth + +default first none last none + +!RESI Li1p 1.00 ! Lithium +1 ion +!GROUP +!ATOM Li1p Li1p 1.00 +!PATCH FIRST NONE LAST NONE + +!RESI Na1p 1.00 ! Sodium +1 ion +!GROUP +!ATOM Na1p Na1p 1.00 +!PATCH FIRST NONE LAST NONE + +!RESI K1p 1.00 ! Potassium +1 ion +!GROUP +!ATOM K1p K1p 1.00 +!PATCH FIRST NONE LAST NONE + +!RESI Rb1p 1.00 ! Rubidium +1 ion +!GROUP +!ATOM Rb1p Rb1p 1.00 +!PATCH FIRST NONE LAST NONE + +!RESI Cs1p 1.00 ! Cesium +1 ion +!GROUP +!ATOM Cs1p Cs1p 1.00 +!PATCH FIRST NONE LAST NONE + +RESI Cu1p 1.00 ! Copper +1 ion +GROUP +ATOM Cu1p Cu1p 1.00 +PATCH FIRST NONE LAST NONE + +RESI Ag1p 1.00 ! Silver +1 ion +GROUP +ATOM Ag1p Ag1p 1.00 +PATCH FIRST NONE LAST NONE + +RESI Au1p 1.00 ! Gold +1 ion +GROUP +ATOM Au1p Au1p 1.00 +PATCH FIRST NONE LAST NONE + +RESI Ti1p 1.00 ! Titanium +1 ion +GROUP +ATOM Ti1p Ti1p 1.00 +PATCH FIRST NONE LAST NONE + +RESI Be2P 2.00 ! Beryllium +2 ion +GROUP +ATOM Be2p Be2p 2.00 +PATCH FIRST NONE LAST NONE + +!RESI Mg2P 2.00 ! Magnesium +2 ion +!GROUP +!ATOM Mg2p Mg2p 2.00 +!PATCH FIRST NONE LAST NONE + +!RESI Ca2p 2.00 ! Calcium +2 ion +!GROUP +!ATOM Ca2p Ca2p 2.00 +!PATCH FIRST NONE LAST NONE + +RESI Sr2p 2.00 ! Strontium +2 ion +GROUP +ATOM Sr2p Sr2p 2.00 +PATCH FIRST NONE LAST NONE + +!RESI Ba2p 2.00 ! Barium +2 ion +!GROUP +!ATOM Ba2p Ba2p 2.00 +!PATCH FIRST NONE LAST NONE + +RESI Ra2p 2.00 ! Radium +2 ion +GROUP +ATOM Ra2p Ra2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI V2p 2.00 ! Vanadium +2 ion +GROUP +ATOM V2p V2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Cr2p 2.00 ! Chromium +2 ion +GROUP +ATOM Cr2p Cr2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Mn2p 2.00 ! Manganese +2 ion +GROUP +ATOM Mn2p Mn2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Fe2p 2.00 ! Iron +2 ion +GROUP +ATOM Fe2p Fe2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Co2p 2.00 ! Cobalt +2 ion +GROUP +ATOM Co2p Co2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Ni2p 2.00 ! Nickel +2 ion +GROUP +ATOM Ni2p Ni2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Cu2p 2.00 ! Copper +2 ion +GROUP +ATOM Cu2p Cu2p 2.00 +PATCH FIRST NONE LAST NONE + +!RESI Zn2p 2.00 ! Zinc +2 ion +!GROUP +!ATOM Zn2p Zn2p 2.00 +!PATCH FIRST NONE LAST NONE + +RESI Pd2p 2.00 ! Palladium +2 ion +GROUP +ATOM Pd2p Pd2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Ag2p 2.00 ! Silver +2 ion +GROUP +ATOM Ag2p Ag2p 2.00 +PATCH FIRST NONE LAST NONE + +!RESI Cd2p 2.00 ! Cadmium +2 ion +!GROUP +!ATOM Cd2p Cd2p 2.00 +!PATCH FIRST NONE LAST NONE + +RESI Sn2p 2.00 ! Tin +2 ion +GROUP +ATOM Sn2p Sn2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Pt2p 2.00 ! Platinum +2 ion +GROUP +ATOM Pt2p Pt2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Hg2p 2.00 ! Mercury +2 ion +GROUP +ATOM Hg2p Hg2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Pb2p 2.00 ! Lead +2 ion +GROUP +ATOM Pb2p Pb2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Sm2p 2.00 ! Samarium +2 ion +GROUP +ATOM Sm2p Sm2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Eu2p 2.00 ! Europium +2 ion +GROUP +ATOM Eu2p Eu2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Yb2p 2.00 ! Ytterbium +2 ion +GROUP +ATOM Yb2p Yb2p 2.00 +PATCH FIRST NONE LAST NONE + +RESI Al3p 3.00 ! Aluminum +3 ion +GROUP +ATOM Al3p Al3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Sc3p 3.00 ! Scandium +3 ion +GROUP +ATOM Sc3p Sc3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Y3p 3.00 ! Yttrium +3 ion +GROUP +ATOM Y3p Y3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI La3p 3.00 ! Lanthanum +3 ion +GROUP +ATOM La3p La3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Ce3p 3.00 ! Cerium +3 ion +GROUP +ATOM Ce3p Ce3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Pr3p 3.00 ! Praseodynium +3 ion +GROUP +ATOM Pr3p Pr3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Nd3p 3.00 ! Neodynium +3 ion +GROUP +ATOM Nd3p Nd3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Pm3p 3.00 ! Promethium +3 ion +GROUP +ATOM Pm3p Pm3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Sm3p 3.00 ! Samarium +3 ion +GROUP +ATOM Sm3p Sm3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Eu3p 3.00 ! Europium +3 ion +GROUP +ATOM Eu3p Eu3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Gd3p 3.00 ! Gadolinium +3 ion +GROUP +ATOM Gd3p Gd3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Tb3p 3.00 ! Terbium +3 ion +GROUP +ATOM Tb3p Tb3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Dy3p 3.00 ! Dysprosium +3 ion +GROUP +ATOM Dy3p Dy3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Ho3p 3.00 ! Holmium +3 ion +GROUP +ATOM Ho3p Ho3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Er3p 3.00 ! Erbium +3 ion +GROUP +ATOM Er3p Er3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Tm3p 3.00 ! Thulium +3 ion +GROUP +ATOM Tm3p Tm3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Yb3p 3.00 ! Ytterbium +3 ion +GROUP +ATOM Yb3p Yb3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Lu3p 3.00 ! Lutetium +3 ion +GROUP +ATOM Lu3p Lu3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI U3p 3.00 ! Uranium +3 ion +GROUP +ATOM U3p U3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Pu3p 3.00 ! Plutonium +3 ion +GROUP +ATOM Pu3p Pu3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Ti3p 3.00 ! Titanium +3 ion +GROUP +ATOM Ti3p Ti3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI V3p 3.00 ! Vanadium +3 ion +GROUP +ATOM V3p V3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Cr3p 3.00 ! Chromium +3 ion +GROUP +ATOM Cr3p Cr3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Mn3p 3.00 ! Manganese +3 ion +GROUP +ATOM Mn3p Mn3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Fe3p 3.00 ! Iron +3 ion +GROUP +ATOM Fe3p Fe3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Co3p 3.00 ! Cobalt +3 ion +GROUP +ATOM Co3p Co3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Ga3p 3.00 ! Gallium +3 ion +GROUP +ATOM Ga3p Ga3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Rh3p 3.00 ! Rhodium +3 ion +GROUP +ATOM Rh3p Rh3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI In3p 3.00 ! Indium +3 ion +GROUP +ATOM In3p In3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Au3p 3.00 ! Gold +3 ion +GROUP +ATOM Au3p Au3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Tl3p 3.00 ! Thallium +3 ion +GROUP +ATOM Tl3p Tl3p 3.00 +PATCH FIRST NONE LAST NONE + +RESI Bi3p 3.00 ! Bismuth +3 ion +GROUP +ATOM Bi3p Bi3p 3.00 +PATCH FIRST NONE LAST NONE + +END + +read para card flex @app +* par_cation.prm for mono-, di-, and trivalent cations +* + +ATOMS +!Mass 301 Li1p 6.940 ! Lithium +!Mass 302 Na1p 22.990 ! Sodium +!Mass 303 K1p 39.098 ! Potassium +!Mass 304 Rb1p 85.468 ! Rubidium +!Mass 305 Cs1p 132.91 ! Cesium +Mass 306 Cu1p 63.546 ! Copper +Mass 307 Ag1p 107.87 ! Silver +Mass 308 Au1p 196.97 ! Gold +Mass 309 Ti1p 47.867 ! Titanium +Mass 321 Be2p 9.0122 ! Beryllium +!Mass 322 Mg2p 24.305 ! Magnesium +!Mass 323 Ca2p 40.078 ! Calcium +Mass 324 Sr2p 87.62 ! Strontium +!Mass 325 Ba2p 137.33 ! Barium +Mass 326 Ra2p 226.03 ! Radium +Mass 327 V2p 50.942 ! Vanadium +Mass 328 Cr2p 51.996 ! Chromium +Mass 329 Mn2p 54.938 ! Manganese +Mass 330 Fe2p 55.854 ! Iron +Mass 331 Co2p 58.933 ! Cobalt +Mass 332 Ni2p 58.693 ! Nickel +Mass 333 Cu2p 63.546 ! Copper +!Mass 334 Zn2p 65.38 ! Zinc +Mass 335 Pd2p 106.42 ! Palladium +Mass 336 Ag2p 107.87 ! Silver +!Mass 337 Cd2p 112.41 ! Cadmium +Mass 338 Sn2p 118.71 ! Tin +Mass 339 Pt2p 195.08 ! Platinum +Mass 340 Hg2p 200.59 ! Mercury +Mass 341 Pb2p 207.20 ! Lead +Mass 342 Sm2p 150.36 ! Samarium +Mass 343 Eu2p 151.96 ! Europium +Mass 344 Yb2p 173.05 ! Ytterbium +Mass 351 Al3p 26.982 ! Aluminum +Mass 352 Sc3p 44.956 ! Scandium +Mass 353 Y3p 88.906 ! Yttrium +Mass 354 La3p 138.91 ! Lanthanum +Mass 355 Ce3p 140.12 ! Cerium +Mass 356 Pr3p 140.91 ! Praseodynium +Mass 357 Nd3p 144.24 ! Neodynium +Mass 358 Pm3p 144.91 ! Promethium +Mass 359 Sm3p 150.36 ! Samarium +Mass 360 Eu3p 151.96 ! Europium +Mass 361 Gd3p 157.25 ! Gadolinium +Mass 362 Tb3p 158.93 ! Terbium +Mass 363 Dy3p 162.50 ! Dysprosium +Mass 364 Ho3p 164.93 ! Holmium +Mass 365 Er3p 167.28 ! Erbium +Mass 366 Tm3p 168.93 ! Thulium +Mass 367 Yb3p 173.05 ! Ytterbium +Mass 368 Lu3p 174.97 ! Lutetium +Mass 369 U3p 238.03 ! Uranium +Mass 370 Pu3p 244.06 ! Plutonium +Mass 371 Ti3p 47.867 ! Titanium +Mass 372 V3p 50.942 ! Vanadium +Mass 373 Cr3p 51.996 ! Chromium +Mass 374 Mn3p 54.938 ! Manganese +Mass 375 Fe3p 55.854 ! Iron +Mass 376 Co3p 58.933 ! Cobalt +Mass 377 Ga3p 69.723 ! Gallium +Mass 378 Rh3p 102.91 ! Rhodium +Mass 379 In3p 114.82 ! Indium +Mass 380 Au3p 196.97 ! Gold +Mass 381 Tl3p 204.38 ! Thallium +Mass 382 Bi3p 208.98 ! Bismuth + +!standard C36 additive truncation +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!truncation scheme used in JPCA 2012 paper under stochastic +!boundary conditions. +!NONBONDED nbxmod 5 atom cdiel switch vatom vdistance vswitch - +!cutnb 22.0 ctofnb 20.0 ctonnb 18.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!---- Monovalent cations +!Li1p 0.0 -0.1670 1.0767 ! dA = -475 kJ/mol +!Na1p 0.0 -0.2007 1.6076 ! dA = -365 kJ/mol +!K1p 0.0 -0.3600 1.9881 ! dA = -295 kJ/mol +!Rb1p 0.0 -0.4022 2.1315 ! dA = -275 kJ/mol +!Cs1p 0.0 -0.4910 2.3324 ! dA = -250 kJ/mol +Cu1p 0.0 -0.1852 0.8620 ! dA = -525 kJ/mol +Ag1p 0.0 -0.2870 1.2143 ! dA = -430 kJ/mol +Au1p 0.0 -0.3563 0.6314 ! dA = -575 kJ/mol +Ti1p 0.0 -0.4067 1.9307 ! dA = -300 kJ/mol +!---- Divalent cations +Be2p 0.0 -0.1016 0.04 ! dA = -2395 kJ/mol +!Mg2p 0.0 -0.1485 1.1050 ! dA = -1830 kJ/mol +!Ca2p 0.0 -0.2016 1.6206 ! dA = -1505 kJ/mol +Sr2p 0.0 -0.2288 1.8559 ! dA = -1380 kJ/mol +!Ba2p 0.0 -0.2830 2.0986 ! dA = -1250 kJ/mol +Ra2p 0.0 -0.3019 2.0899 ! dA = -1250 kJ/mol +V2p 0.0 -0.1609 1.1037 ! dA = -1825 kJ/mol +Cr2p 0.0 -0.1667 1.0592 ! dA = -1850 kJ/mol +Mn2p 0.0 -0.1685 1.2037 ! dA = -1760 kJ/mol +Fe2p 0.0 -0.1595 1.0801 ! dA = -1840 kJ/mol +Co2p 0.0 -0.1539 0.9276 ! dA = -1915 kJ/mol +Ni2p 0.0 -0.1434 0.7803 ! dA = -1980 kJ/mol +Cu2p 0.0 -0.1505 0.7251 ! dA = -2010 kJ/mol +!Zn2p 0.0 -0.1539 0.8144 ! dA = -1955 kJ/mol +Pd2p 0.0 -0.1742 0.9271 ! dA = -1910 kJ/mol +Ag2p 0.0 -0.1853 1.0490 ! dA = -1850 kJ/mol +!Cd2p 0.0 -0.1926 1.1962 ! dA = -1755 kJ/mol +Sn2p 0.0 -0.1879 1.6580 ! dA = -1490 kJ/mol +Pt2p 0.0 -0.1631 0.7971 ! dA = -1960 kJ/mol +Hg2p 0.0 -0.2054 1.1818 ! dA = -1760 kJ/mol +Pb2p 0.0 -0.2394 1.7580 ! dA = -1425 kJ/mol +Sm2p 0.0 -0.2448 1.8565 ! dA = -1375 kJ/mol +Eu2p 0.0 -0.2368 1.8404 ! dA = -1385 kJ/mol +Yb2p 0.0 -0.2054 1.6090 ! dA = -1510 kJ/mol +!---- Trivalent cations +Al3p 0.0 -0.1066 0.2210 ! dA = -4525 kJ/mol +Sc3p 0.0 -0.1410 1.0969 ! dA = -3795 kJ/mol +Y3p 0.0 -0.1656 1.4134 ! dA = -3450 kJ/mol +La3p 0.0 -0.1896 1.7727 ! dA = -3145 kJ/mol +Ce3p 0.0 -0.1841 1.7115 ! dA = -3200 kJ/mol +Pr3p 0.0 -0.1823 1.6591 ! dA = -3245 kJ/mol +Nd3p 0.0 -0.1792 1.6199 ! dA = -3280 kJ/mol +Pm3p 0.0 -0.1775 1.6572 ! dA = -3250 kJ/mol +Sm3p 0.0 -0.1757 1.5667 ! dA = -3325 kJ/mol +Eu3p 0.0 -0.1740 1.5230 ! dA = -3360 kJ/mol +Gd3p 0.0 -0.1723 1.5050 ! dA = -3375 kJ/mol +Tb3p 0.0 -0.1693 1.4750 ! dA = -3400 kJ/mol +Dy3p 0.0 -0.1673 1.4444 ! dA = -3425 kJ/mol +Ho3p 0.0 -0.1656 1.3907 ! dA = -3470 kJ/mol +Er3p 0.0 -0.1636 1.3673 ! dA = -3495 kJ/mol +Tm3p 0.0 -0.1620 1.3486 ! dA = -3515 kJ/mol +Yb3p 0.0 -0.1604 1.2952 ! dA = -3570 kJ/mol +Lu3p 0.0 -0.1588 1.3512 ! dA = -3515 kJ/mol +U3p 0.0 -0.1896 1.7012 ! dA = -3205 kJ/mol +Pu3p 0.0 -0.1841 1.6697 ! dA = -3235 kJ/mol +Ti3p 0.0 -0.1285 0.8289 ! dA = -4015 kJ/mol +V3p 0.0 -0.1236 0.6142 ! dA = -4220 kJ/mol +Cr3p 0.0 -0.1206 0.8431 ! dA = -4010 kJ/mol +Mn3p 0.0 -0.1252 0.3844 ! dA = -4410 kJ/mol +Fe3p 0.0 -0.1252 0.5663 ! dA = -4265 kJ/mol +Co3p 0.0 -0.1191 0.2581 ! dA = -4495 kJ/mol +Ga3p 0.0 -0.1206 0.2269 ! dA = -4515 kJ/mol +Rh3p 0.0 -0.1285 0.4613 ! dA = -4350 kJ/mol +In3p 0.0 -0.1473 0.8663 ! dA = -3980 kJ/mol +Au3p 0.0 -0.1330 0.3654 ! dA = -4420 kJ/mol +Tl3p 0.0 -0.1629 0.8693 ! dA = -3970 kJ/mol +Bi3p 0.0 -0.1850 1.3682 ! dA = -3480 kJ/mol + +END diff --git a/charmm/toppar/stream/na/toppar_all36_na_model.str b/charmm/toppar/stream/na/toppar_all36_na_model.str new file mode 100644 index 00000000..f03c934b --- /dev/null +++ b/charmm/toppar/stream/na/toppar_all36_na_model.str @@ -0,0 +1,3438 @@ +* CHARMM27 All-Hydrogen Nucleic Acid Force Toppar Stream File +* Collection of residues and patches for model compounds used +* in the optimization the Charmm27 all-atom nucleic acid +* force field. +* N. Foloppe and A.D. MacKerell, Jr., July 2001 +* + +!new residues: +!RESI TBP1 -2.00 ! 3',5'-bis-methylphosphate-tetrahydrofuran +!RESI RBP1 -2.00 ! 3',5'-bis-methylphosphate-tetrahydrofuran RNA alalog +!RESI T3PS -1.00 ! 3'phosphate-tetrahydrofuran (phosphate -1) +!RESI R3PS -1.00 ! 3'phosphate-tetrahydrofuran (phosphate -1): ribo ana< RESI NUTA -1.00 ! deoxy-nucleotide with adenine +!RESI NUTC 0.00 ! nucleotide with cytosine + +!Parent files that have to be read prior to streaming this file +!top_all36_na.rtf +!par_all36_na.prm + +!Testcase +!test_all36_na_model.inp + +read rtf card append +* c36 na model compounds +* +31 1 + +MASS 466 CN7C 12.011000 C ! C2' in arabinose +MASS 467 CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives +MASS 468 FN1 18.998400 F ! Fluorine for sugar derivatives (NF) + +RESI TBP1 -2.00 ! 3',5'-bis-methylphosphate-tetrahydrofuran + ! capped with a methyl groups on 3' and 5' phosphates + ! C3T is defined as CN8B to mimick DNA +GROUP ! +ATOM C5M CN9 -0.17 ! +ATOM H5M1 HN9 0.09 ! +ATOM H5M2 HN9 0.09 ! +ATOM H5M3 HN9 0.09 ! H5M2 +ATOM O3A ON2 -0.57 ! | +ATOM PA P 1.50 ! H5M1--C5M--H5M3 +ATOM O1PA ON3 -0.78 ! / +ATOM O2PA ON3 -0.78 ! O3A +ATOM O5' ON2 -0.57 ! | +ATOM C5' CN8B -0.08 ! O1PA==PA==O2PA (-1) +ATOM H51' HN8 0.09 ! | +ATOM H52' HN8 0.09 ! O5' +GROUP ! H52' | +ATOM O4' ON6 -0.50 ! \ | +ATOM C1' CN7B 0.07 ! H51'-C5' O4' H11' +ATOM H11' HN7 0.09 ! \ / \ / +ATOM H12' HN7 0.09 ! H41'--C4' C1'--H12' +ATOM C4' CN7 0.16 ! | | +ATOM H41' HN7 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C2' CN8 -0.18 ! O3' H22' +ATOM H21' HN8 0.09 ! | +ATOM H22' HN8 0.09 ! O1P==P==O2P +GROUP ! | +ATOM C3' CN7 0.01 ! O5b (-1) +ATOM H31' HN7 0.09 ! \ + ! C5b--H5b3 +ATOM O3' ON2 -0.57 ! / \ +ATOM P P 1.50 ! H5b1 H5b2 +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 +ATOM O5b ON2 -0.57 +ATOM C5b CN9 -0.17 +ATOM H5b1 HN9 0.09 +ATOM H5b2 HN9 0.09 +ATOM H5b3 HN9 0.09 + +BOND C5M O3A O3A PA PA O1PA PA O2PA PA O5' O5' C5' +BOND C5M H5M1 C5M H5M2 C5M H5M3 C5' H51' C5' H52' +BOND C5' C4' C4' C3' C4' O4' C3' C2' C2' C1' C1' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND O3' P P O1P P O2P P O5b O5b C5b +BOND C5B H5B1 C5B H5B2 C5B H5B3 + +IC C5M O3A PA O5' 0.0000 0.00 -90.00 0.00 0.0000 !zeta-1,A:287,bi:-89.68,bii:159.19,Z:74/296,RNA:287(-73) +IC O3A PA O5' C5' 0.0000 0.00 180.00 0.00 0.0000 !alpha,A:291, B:298, Z:70/200, RNA:291 +IC PA O3A C5M h5M1 0.0000 0.00 180.00 0.00 0.0000 +IC H5M1 O3A *C5M H5M2 0.0000 0.00 120.00 0.00 0.0000 +IC H5M1 O3A *C5M H5M3 0.0000 0.00 -120.00 0.00 0.0000 +IC O5' O3A *PA O1PA 0.0000 0.00 120.00 0.00 0.0000 +IC O5' O3A *PA O2PA 0.0000 0.00 -120.00 0.00 0.0000 +IC PA O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 !beta,A:175, B:168, Z:185, RNA:174 +IC C4' O5' *C5' H51' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' O5' *C5' H52' 0.0000 0.00 -120.00 0.00 0.0000 +IC O5' C5' C4' C3' 0.0000 0.00 180.00 0.00 0.0000 !gamma,A:57, B:51, Z:54/179, RNA:57 +!IC C5' C4' C3' O3' 0.0000 0.00 180.00 0.00 0.0000 !delta (not used, sugar defined below) +IC C5' C4' C3' C2' 0.0000 0.00 -108.00 0.00 0.0000 !-155:c3'endo(north) -108:c2'endo(south) +IC C4' C3' C2' C1' 0.0000 0.00 -40.00 0.00 0.0000 !40:c3'endo(north) -40:c2'endo(south) +IC C3' C2' C1' O4' 0.0000 0.00 40.00 0.00 0.0000 !-40:c3'endo(north) 40:c2'endo(south) +IC C3' C4' O4' C1' 0.0000 0.00 0.00 0.00 0.0000 ! define c2'endo = 0 +IC C4' O4' C1' C2' 0.0000 0.00 0.00 0.00 0.0000 ! define c3'endo = 0 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC C3' C5' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' C3' O3' P 0.0000 0.00 180.00 0.00 0.0000 !epsilon,A:205,bi:-164.29,bii:-92.78,Z:265,RNA:211(-149) +IC C3' O3' P O5B 0.0000 0.00 180.00 0.00 0.0000 !zeta,A:287,bi:-89.68,bii:159.19,Z:74/296,RNA:287(-73) +IC O5B O3' *P O1P 0.0000 0.00 120.00 0.00 0.0000 +IC O5B O3' *P O2P 0.0000 0.00 -120.00 0.00 0.0000 +IC O3' P O5B C5B 0.0000 0.00 180.00 0.00 0.0000 !alpha+1,A:291, B:298, Z:70/200, RNA:291 +IC P O5B C5B H5B1 0.0000 0.00 180.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B2 0.0000 0.00 120.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B3 0.0000 0.00 -120.00 0.00 0.0000 + +RESI RBP1 -2.00 ! 3',5'-bis-methylphosphate-tetrahydrofuran RNA alalog + ! capped with a methyl groups on 3' and 5' phosphates + ! C3T is defined as CN8B to mimick DNA +GROUP ! +ATOM C5M CN9 -0.17 ! +ATOM H5M1 HN9 0.09 ! +ATOM H5M2 HN9 0.09 ! +ATOM H5M3 HN9 0.09 ! H5M2 +ATOM O3A ON2 -0.57 ! | +ATOM PA P 1.50 ! H5M1--C5M--H5M3 +ATOM O1PA ON3 -0.78 ! / +ATOM O2PA ON3 -0.78 ! O3A +ATOM O5' ON2 -0.57 ! | +ATOM C5' CN8B -0.08 ! O1PA==PA==O2PA (-1) +ATOM H51' HN8 0.09 ! | +ATOM H52' HN8 0.09 ! O5' +GROUP ! H52' | +ATOM O4' ON6B -0.50 ! \ | +ATOM C1' CN7B 0.07 ! H51'-C5' O4' H11' +ATOM H11' HN7 0.09 ! \ / \ / +ATOM H12' HN7 0.09 ! H41'--C4' C1'--H12' +ATOM C4' CN7 0.16 ! | | +ATOM H41' HN7 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C2' CN7B 0.14 ! O3' O2T-H2T +ATOM H21' HN7 0.09 ! | +ATOM O2T ON5 -0.66 ! O1P==P==O2P +ATOM H2T HN5 0.43 ! +GROUP ! | +ATOM C3' CN7 0.01 ! O5b (-1) +ATOM H31' HN7 0.09 ! \ + ! C5b--H5b3 +ATOM O3' ON2 -0.57 ! / \ +ATOM P P 1.50 ! H5b1 H5b2 +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 +ATOM O5b ON2 -0.57 +ATOM C5b CN9 -0.17 +ATOM H5b1 HN9 0.09 +ATOM H5b2 HN9 0.09 +ATOM H5b3 HN9 0.09 + +BOND C5M O3A O3A PA PA O1PA PA O2PA PA O5' O5' C5' +BOND C5M H5M1 C5M H5M2 C5M H5M3 C5' H51' C5' H52' +BOND C5' C4' C4' C3' C4' O4' C3' C2' C2' C1' C1' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' O2T O2T H2T C3' H31' C4' H41' +BOND O3' P P O1P P O2P P O5b O5b C5b +BOND C5B H5B1 C5B H5B2 C5B H5B3 + +IC C5M O3A PA O5' 0.0000 0.00 -90.00 0.00 0.0000 !zeta-1,A:287,bi:-89.68,bii:159.19,Z:74/296,RNA:287(-73) +IC O3A PA O5' C5' 0.0000 0.00 180.00 0.00 0.0000 !alpha,A:291, B:298, Z:70/200, RNA:291 +IC PA O3A C5M h5M1 0.0000 0.00 180.00 0.00 0.0000 +IC H5M1 O3A *C5M H5M2 0.0000 0.00 120.00 0.00 0.0000 +IC H5M1 O3A *C5M H5M3 0.0000 0.00 -120.00 0.00 0.0000 +IC O5' O3A *PA O1PA 0.0000 0.00 120.00 0.00 0.0000 +IC O5' O3A *PA O2PA 0.0000 0.00 -120.00 0.00 0.0000 +IC PA O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 !beta,A:175, B:168, Z:185, RNA:174 +IC C4' O5' *C5' H51' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' O5' *C5' H52' 0.0000 0.00 -120.00 0.00 0.0000 +IC O5' C5' C4' C3' 0.0000 0.00 180.00 0.00 0.0000 !gamma,A:57, B:51, Z:54/179, RNA:57 +!IC C5' C4' C3' O3' 0.0000 0.00 180.00 0.00 0.0000 !delta (not used, sugar defined below) +IC C5' C4' C3' C2' 0.0000 0.00 -108.00 0.00 0.0000 !-155:c3'endo(north) -108:c2'endo(south) +IC C4' C3' C2' C1' 0.0000 0.00 -40.00 0.00 0.0000 !40:c3'endo(north) -40:c2'endo(south) +IC C3' C2' C1' O4' 0.0000 0.00 40.00 0.00 0.0000 !-40:c3'endo(north) 40:c2'endo(south) +IC C3' C4' O4' C1' 0.0000 0.00 0.00 0.00 0.0000 ! define c2'endo = 0 +IC C4' O4' C1' C2' 0.0000 0.00 0.00 0.00 0.0000 ! define c3'endo = 0 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC C3' C5' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' O2T 0.0000 0.00 120.00 0.00 0.0000 +IC C1' C2' O2T H2T 0.0000 0.00 180.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' C3' O3' P 0.0000 0.00 180.00 0.00 0.0000 !epsilon,A:205,bi:-164.29,bii:-92.78,Z:265,RNA:211(-149) +IC C3' O3' P O5B 0.0000 0.00 180.00 0.00 0.0000 !zeta,A:287,bi:-89.68,bii:159.19,Z:74/296,RNA:287(-73) +IC O5B O3' *P O1P 0.0000 0.00 120.00 0.00 0.0000 +IC O5B O3' *P O2P 0.0000 0.00 -120.00 0.00 0.0000 +IC O3' P O5B C5B 0.0000 0.00 180.00 0.00 0.0000 !alpha+1,A:291, B:298, Z:70/200, RNA:291 +IC P O5B C5B H5B1 0.0000 0.00 180.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B2 0.0000 0.00 120.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B3 0.0000 0.00 -120.00 0.00 0.0000 + +RESI T3PS -1.00 ! 3'phosphate-tetrahydrofuran (phosphate -1) + ! capped with a 5' methyl furan + ! This is to investigate the differences + ! between BI and BII forms of DNA + ! C3T is defined as CN8B to mimick DNA +GROUP +ATOM O4' ON6 -0.50 ! +ATOM C1' CN7B 0.07 ! H41' O4' H11' +ATOM H11' HN7 0.09 ! \ / \ / +ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C4' CN7 0.07 ! | | +ATOM H41' HN7 0.09 ! H31'--C3'--C2'--H21' +ATOM H42' HN7 0.09 ! / \ +GROUP ! O3' H22' +ATOM C2' CN8 -0.18 ! | +ATOM H21' HN8 0.09 ! O1P==P==O2P +ATOM H22' HN8 0.09 ! | +GROUP ! O5b (-1) H4b1 O4b H1b1 +ATOM C3' CN7 0.01 ! \ \ / \ / +ATOM H31' HN7 0.09 ! C5b-------C4b C1b-H1b2 + ! / \ | | +ATOM O3' ON2 -0.57 ! H5b1 H5b2 C3b----C2b-H2b2 +ATOM P P2 1.50 ! / | \ +ATOM O1P ON3 -0.78 H3b1 H3b2 H2b1 +ATOM O2P ON3 -0.78 +ATOM O5b ON2 -0.57 +ATOM C5b CN8B -0.08 +ATOM H5b1 HN8 0.09 +ATOM H5b2 HN8 0.09 +GROUP +ATOM C4B CN7 0.16 +ATOM H4b1 HN7 0.09 +ATOM O4b ON6 -0.50 +ATOM C1b CN7B 0.07 +ATOM H1b1 HN7 0.09 +ATOM H1b2 HN7 0.09 +GROUP +ATOM C2b CN8 -0.18 +ATOM H2b1 HN8 0.09 +ATOM H2b2 HN8 0.09 +GROUP +ATOM C3b CN7 -0.18 ! use CN7 atom type for consistancy with full DNA +ATOM H3b1 HN7 0.09 +ATOM H3b2 HN7 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O5b O5b C5b +BOND C5b H5b1 C5b H5b2 C5b C4b C4b O4b O4b C1b C1b C2b +BOND C2b C3b C3b C4b C4b H4b1 C1b H1b1 C1b H1b2 C2b H2b1 +BOND C2b H2b2 C3b H3b1 C3b H3b2 + +IC C4' O4' C1' C2' 1.4055 108.09 -21.00 106.18 1.5457 !0.0 for c3'endo (north) pucker +IC O4' C1' C2' C3' 1.4127 106.18 30.00 103.11 1.5346 ! +IC C1' C2' C3' C4' 1.5457 103.11 -30.00 100.86 1.5211 !0.0 for o4'endo barrier +IC C2' C3' C4' O4' 1.5346 100.86 20.00 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 0.00 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC C4' C3' O3' P 0.0000 000.00 -164.29 000.00 0.0000 !epsilon bi:-164.29,bii:-92.78 +IC C3' O3' P O5b 0.0000 000.00 -89.68 000.00 0.0000 !zeta bi:-89.68,bii:159.19 +IC O5b O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 +IC O5b O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000 +IC O3' P O5b C5b 0.0000 000.00 -46.90 000.00 0.0000 !alpha+1:A:291, B:298 +IC P O5B C5B C4B 0.0000 0.00 180.00 0.00 0.0000 !beta+1:A:175, B:168 +IC H5b1 C5b O5b P 0.0000 000.00 180.00 000.00 0.0000 +IC H5b2 C5b O5b P 0.0000 000.00 60.00 000.00 0.0000 +IC O3' P O5B C5B 0.0000 0.00 180.00 0.00 0.0000 +IC C4B O5B *C5B H5B1 0.0000 0.00 120.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B2 0.0000 0.00 -120.00 0.00 0.0000 +IC O5B C5B C4B C3B 0.0000 0.00 180.00 0.00 0.0000 !gamma+1,A:57, B:51 +!IC C3B C5B *C4B O4B 0.0000 0.00 -120.00 0.00 0.0000 +!IC C5B C4B O4B C1B 0.0000 0.00 180.00 0.00 0.0000 +IC C5B C4B C3B C2B 0.0000 0.00 -108.00 0.00 0.0000 !-155:c3'endo(north) -108:c2'endo(south) +IC C4B C3B C2B C1B 0.0000 0.00 -40.00 0.00 0.0000 !40:c3'endo(north) -40:c2'endo(south) +IC C3B C2B C1B O4B 0.0000 0.00 40.00 0.00 0.0000 !-40:c3'endo(north) 40:c2'endo(south) +!following IC is used to define C3'endo in surfaces, but commented due to redundancy +!IC C4B O4B C1B C2B 0.0000 0.00 25.00 0.00 0.0000 !0.0: c3'endo(north) 25:c2'endo(south) +IC O4B C5B *C4B H4B1 0.0000 0.00 -120.00 0.00 0.0000 +IC C2B O4B *C1B H1B1 0.0000 0.00 120.00 0.00 0.0000 +IC C2B O4B *C1B H1B2 0.0000 0.00 -120.00 0.00 0.0000 +IC C3B C1B *C2B H2B1 0.0000 0.00 -120.00 0.00 0.0000 +IC C3B C1B *C2B H2B2 0.0000 0.00 120.00 0.00 0.0000 +IC C2B C4B *C3B H3B1 0.0000 0.00 120.00 0.00 0.0000 +IC C2B C4B *C3B H3B2 0.0000 0.00 -120.00 0.00 0.0000 + +PATC FIRS NONE LAST NONE + +RESI R3PS -1.00 ! 3'phosphate-tetrahydrofuran (phosphate -1): ribo analog + ! capped with a 5' methyl furan + ! This is to investigate the differences + ! between BI and BII forms of DNA + ! C3T is defined as CN8B to mimick DNA +GROUP +ATOM O4' ON6B -0.50 ! +ATOM C1' CN7B 0.07 ! H41' O4' H11' +ATOM H11' HN7 0.09 ! \ / \ / +ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C4' CN7 0.07 ! | | +ATOM H41' HN7 0.09 ! H31'--C3'--C2'--H21' +ATOM H42' HN7 0.09 ! / \ +GROUP ! O3' O2T-H2T +ATOM C2' CN7B 0.14 ! | +ATOM H21' HN7 0.09 ! O1P==P==O2P +ATOM O2T ON5 -0.66 ! | +ATOM H2T HN5 0.43 ! | +GROUP ! O5b (-1) H4b1 O4b H1b1 +ATOM C3' CN7 0.01 ! \ \ / \ / +ATOM H31' HN7 0.09 ! C5b-------C4b C1b-H1b2 + ! / \ | | +ATOM O3' ON2 -0.57 ! H5b1 H5b2 C3b----C2b-H2b1 +ATOM P P 1.50 ! / | \ +ATOM O1P ON3 -0.78 ! H3b1 H3b2 O2Tb-H2Tb +ATOM O2P ON3 -0.78 +ATOM O5b ON2 -0.57 +ATOM C5b CN8B -0.08 +ATOM H5b1 HN8 0.09 +ATOM H5b2 HN8 0.09 +GROUP +ATOM C4B CN7 0.16 +ATOM H4b1 HN7 0.09 +ATOM O4b ON6B -0.50 +ATOM C1b CN7B 0.07 +ATOM H1b1 HN7 0.09 +ATOM H1b2 HN7 0.09 +GROUP +ATOM C2b CN7B 0.14 +ATOM H2b1 HN7 0.09 +ATOM O2Tb ON5 -0.66 +ATOM H2Tb HN5 0.43 +GROUP +ATOM C3b CN7 -0.18 ! use CN7 atom type for consistancy with full DNA +ATOM H3b1 HN7 0.09 +ATOM H3b2 HN7 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' O2T C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O5b O5b C5b +BOND C5b H5b1 C5b H5b2 C5b C4b C4b O4b O4b C1b C1b C2b +BOND C2b C3b C3b C4b C4b H4b1 C1b H1b1 C1b H1b2 C2b H2b1 +BOND C2b O2Tb C3b H3b1 C3b H3b2 +BOND O2T H2T O2Tb H2Tb + +IC C4' O4' C1' C2' 1.4055 108.09 0.00 106.18 1.5457 !0.0 for c3'endo (south) pucker +IC O4' C1' C2' C3' 1.4127 106.18 -30.00 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 45.00 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 -45.00 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 30.00 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC O2T C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC C1' C2' O2T H2T 0.0000 0.00 180.00 0.00 0.0000 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC C4' C3' O3' P 0.0000 000.00 -164.29 000.00 0.0000 !epsilon bi:-164.29,bii:-92.78 +IC C3' O3' P O5b 0.0000 000.00 -89.68 000.00 0.0000 !zeta bi:-89.68,bii:159.19 +IC O5b O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 +IC O5b O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000 +IC O3' P O5b C5b 0.0000 000.00 -46.90 000.00 0.0000 !alpha+1:A:291, B:298 +IC P O5B C5B C4B 0.0000 0.00 180.00 0.00 0.0000 !beta+1:A:175, B:168 +IC H5b1 C5b O5b P 0.0000 000.00 180.00 000.00 0.0000 +IC H5b2 C5b O5b P 0.0000 000.00 60.00 000.00 0.0000 +IC O3' P O5B C5B 0.0000 0.00 180.00 0.00 0.0000 +IC C4B O5B *C5B H5B1 0.0000 0.00 120.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B2 0.0000 0.00 -120.00 0.00 0.0000 +IC O5B C5B C4B C3B 0.0000 0.00 180.00 0.00 0.0000 !gamma+1,A:57, B:51 +!IC C3B C5B *C4B O4B 0.0000 0.00 -120.00 0.00 0.0000 +!IC C5B C4B O4B C1B 0.0000 0.00 180.00 0.00 0.0000 +IC C5B C4B C3B C2B 0.0000 0.00 -155.00 0.00 0.0000 !-155:c3'endo(north) -108:c2'endo(south) +IC C4B C3B C2B C1B 0.0000 0.00 40.00 0.00 0.0000 !40:c3'endo(north) -40:c2'endo(south) +IC C3B C2B C1B O4B 0.0000 0.00 -40.00 0.00 0.0000 !-40:c3'endo(north) 40:c2'endo(south) +!following IC is used to define C3'endo in surfaces, but commented due to redundancy +!IC C4B O4B C1B C2B 0.0000 0.00 25.00 0.00 0.0000 !0.0: c3'endo(north) 25:c2'endo(south) +IC O4B C5B *C4B H4B1 0.0000 0.00 -120.00 0.00 0.0000 +IC C2B O4B *C1B H1B1 0.0000 0.00 120.00 0.00 0.0000 +IC C2B O4B *C1B H1B2 0.0000 0.00 -120.00 0.00 0.0000 +IC C3B C1B *C2B H2B1 0.0000 0.00 -120.00 0.00 0.0000 +IC C3B C1B *C2B O2Tb 0.0000 0.00 120.00 0.00 0.0000 +IC C1B C2B O2Tb H2Tb 0.0000 0.00 180.00 0.00 0.0000 +IC C2B C4B *C3B H3B1 0.0000 0.00 120.00 0.00 0.0000 +IC C2B C4B *C3B H3B2 0.0000 0.00 -120.00 0.00 0.0000 + +PATC FIRS NONE LAST NONE + +RESI NUTA -1.00 ! deoxy-nucleotide with adenine +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Adenine +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HN8 0.09 ! | | +ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' +! Adenine atoms ! / \ +GROUP ! O3' H22' +ATOM C5 CN5 0.28 ! | +ATOM N7 NN4 -0.71 ! O1P==P==O2P +ATOM C8 CN4 0.34 ! | +ATOM H8 HN3 0.12 ! O5b +ATOM N9 NN2 -0.05 ! \ +ATOM N1 NN3A -0.74 ! C5b--H5b3 +ATOM C2 CN4 0.50 ! / \ +ATOM H2 HN3 0.13 ! H5b1 H5b2 +ATOM N3 NN3A -0.75 +ATOM C4 CN5 0.43 +ATOM C6 CN2 0.46 +ATOM N6 NN1 -0.77 +ATOM H61 HN1 0.38 +ATOM H62 HN1 0.38 +GROUP +ATOM C3' CN7 0.01 +ATOM H31' HN7 0.09 +ATOM O3' ON2 -0.57 ! +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 +ATOM O5b ON2 -0.57 +ATOM C5b CN9 -0.17 +ATOM H5b1 HN9 0.09 +ATOM H5b2 HN9 0.09 +ATOM H5b3 HN9 0.09 +GROUP ! Methyl group on C4' +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' P P O1P P O2P P O5b O5b C5b +BOND C5B H5B1 C5B H5B2 C5B H5B3 +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 + +IC C4' O4' C1' C2' 1.4055 108.09 -21.00 106.18 1.5457 !0.0 for c3'endo (north) pucker +IC O4' C1' C2' C3' 1.4127 106.18 30.00 103.11 1.5346 ! +IC C1' C2' C3' C4' 1.5457 103.11 -30.00 100.86 1.5211 !0.0 for o4'endo barrier +IC C2' C3' C4' O4' 1.5346 100.86 20.00 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 0.00 108.09 1.4127 +IC C3' O4' *C4' C5' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' O4' *C1' N9 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 120.00 0.00 0.0000 +IC O4' C1' N9 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C1' C4 *N9 C8 0.0000 0.00 -180.00 0.00 0.0000 +IC C1' N9 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N9 *C4 N3 0.0000 0.00 180.00 0.00 0.0000 +IC N9 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 N7 0.0000 0.00 180.00 0.00 0.0000 +IC N7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C6 N6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 N6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC H61 C6 *N6 H62 0.0000 0.00 180.00 0.00 0.0000 +IC C2' C4' *C3' O3' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' C3' O3' P 0.0000 0.00 180.00 0.00 0.0000 !epsilon +IC C3' O3' P O5B 0.0000 0.00 180.00 0.00 0.0000 !zeta +IC O5B O3' *P O1P 0.0000 0.00 120.00 0.00 0.0000 +IC O5B O3' *P O2P 0.0000 0.00 -120.00 0.00 0.0000 +IC O3' P O5B C5B 0.0000 0.00 180.00 0.00 0.0000 !alpha +IC P O5B C5B H5B1 0.0000 0.00 180.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B2 0.0000 0.00 120.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B3 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C4' C5' O5' 0.0000 0.00 60.00 0.00 0.0000 !gamma +IC C4' C5' O5' H5T 0.0000 0.00 180.00 0.00 0.0000 !beta +IC H5T C4' *C5' H51' 1.9450 142.80 120.00 0.00 0.0000 +IC H5T C4' *C5' H52' 1.9450 142.80 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI NUTC -1.00 ! nucleotide with cytosine +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Cytosine +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HN8 0.09 ! | | +ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' +! Cytosine atoms ! / \ +GROUP ! O3' H22' +ATOM N1 NN2 -0.13 ! | +ATOM C6 CN3 0.05 ! O1P==P==O2P +ATOM H6 HN3 0.17 ! | +ATOM C2 CN1 0.52 ! O5b +ATOM O2 ON1C -0.49 ! \ +ATOM N3 NN3 -0.66 ! C5b--H5b3 +ATOM C4 CN2 0.65 ! / \ +ATOM N4 NN1 -0.75 ! H5b1 H5b2 +ATOM H41 HN1 0.37 +ATOM H42 HN1 0.33 +ATOM C5 CN3 -0.13 +ATOM H5 HN3 0.07 +GROUP +ATOM C3' CN7 0.01 +ATOM H31' HN7 0.09 +ATOM O3' ON2 -0.57 ! +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 +ATOM O5b ON2 -0.57 +ATOM C5b CN9 -0.17 +ATOM H5b1 HN9 0.09 +ATOM H5b2 HN9 0.09 +ATOM H5b3 HN9 0.09 +GROUP ! Methyl group on C4' +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' P P O1P P O2P P O5b O5b C5b +BOND C5B H5B1 C5B H5B2 C5B H5B3 +BOND C1' N1 +BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 +BOND C2 N3 C4 C5 C5 H5 C6 H6 +DOUB C2 O2 C5 C6 N3 C4 +IMPR N4 C4 H41 H42 C2 N1 N3 O2 C4 N3 C5 N4 + +! This IC table is only an initial guess: +!IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C4' O4' C1' C2' 1.4055 108.09 -21.00 106.18 1.5457 !0.0 for c3'endo (north) pucker +IC O4' C1' C2' C3' 1.4127 106.18 30.00 103.11 1.5346 ! +IC C1' C2' C3' C4' 1.5457 103.11 -30.00 100.86 1.5211 !0.0 for o4'endo barrier +IC C2' C3' C4' O4' 1.5346 100.86 20.00 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 0.00 108.09 1.4127 +IC C3' O4' *C4' C5' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' O4' *C1' N1 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 120.00 0.00 0.0000 +IC O4' C1' N1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C1' C2 *N1 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C1' N1 C6 C5 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C6 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C1' N1 C2 N3 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C5 *C4 N4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C4 N4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C4 *N4 H42 0.0000 0.00 180.00 0.00 0.0000 +IC C2' C4' *C3' O3' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' C3' O3' P 0.0000 0.00 180.00 0.00 0.0000 !epsilon +IC C3' O3' P O5B 0.0000 0.00 180.00 0.00 0.0000 !zeta +IC O5B O3' *P O1P 0.0000 0.00 120.00 0.00 0.0000 +IC O5B O3' *P O2P 0.0000 0.00 -120.00 0.00 0.0000 +IC O3' P O5B C5B 0.0000 0.00 180.00 0.00 0.0000 !alpha +IC P O5B C5B H5B1 0.0000 0.00 180.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B2 0.0000 0.00 120.00 0.00 0.0000 +IC H5B1 O5B *C5B H5B3 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C4' C5' O5' 0.0000 0.00 60.00 0.00 0.0000 !gamma +IC C4' C5' O5' H5T 0.0000 0.00 180.00 0.00 0.0000 !beta +IC H5T C4' *C5' H51' 1.9450 142.80 120.00 0.00 0.0000 +IC H5T C4' *C5' H52' 1.9450 142.80 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + + +PRES PYRC 0.00 ! Patch to generate CYTOSINE (pyrimidine) + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +! following atom order to maintain +! compatibility with previous topology files +GROUP +ATOM N1 NN2 -0.50 !charge changed by patch +ATOM H1 HN2 0.37 !charge changed by patch +ATOM C6 CN3 0.05 !charge changed by patch +ATOM H6 HN3 0.17 !charge changed by patch +ATOM C2 CN1 0.52 !unchanged +ATOM O2 ON1C -0.49 !unchanged +ATOM N3 NN3 -0.66 !unchanged +ATOM C4 CN2 0.65 !unchanged +ATOM N4 NN1 -0.75 !unchanged +ATOM H41 HN1 0.37 !unchanged +ATOM H42 HN1 0.33 !unchanged +ATOM C5 CN3 -0.13 !charge changed by patch +ATOM H5 HN3 0.07 !charge changed by patch +BOND N1 H1 +IMPR N1 C6 C2 H1 +BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 + +PRES PYRU 0.00 ! Patch to generate URACIL (pyrimidine) + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +GROUP +ATOM N1 NN2B -0.82 ! +ATOM H1 HN2 0.48 ! +ATOM C6 CN3 0.20 ! +ATOM H6 HN3 0.14 ! +BOND N1 H1 +BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 + +PRES PYRT 0.00 ! Patch to generate THYMINE (pyrimidine) + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +GROUP +ATOM N1 NN2B -0.80 ! +ATOM H1 HN2 0.46 ! +ATOM C6 CN3 0.17 ! +ATOM H6 HN3 0.17 ! +BOND N1 H1 +BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 + +PRES PURG 0.00 ! Patch to generate GUANINE (purine) + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +! following atom order to maintain +! compatibility with previous topology files +GROUP +ATOM N9 NN2B -0.38 !charge changed by patch +ATOM C4 CN5 0.26 !charge changed by patch +ATOM H9 HN2 0.36 !charge changed by patch +ATOM N3 NN3G -0.74 !unchanged +ATOM C2 CN2 0.75 !unchanged +ATOM N1 NN2G -0.34 !unchanged +ATOM H1 HN2 0.26 !unchanged +ATOM N2 NN1 -0.68 !unchanged +ATOM H21 HN1 0.32 !unchanged +ATOM H22 HN1 0.35 !unchanged +ATOM C6 CN1 0.54 !unchanged +ATOM O6 ON1 -0.51 !unchanged +ATOM C5 CN5G 0.00 !unchanged +ATOM N7 NN4 -0.60 !charge changed by patch +ATOM C8 CN4 0.25 !charge changed by patch +ATOM H8 HN3 0.16 !charge changed by patch +BOND N9 H9 +IMPR N9 C8 C4 H9 +BILD C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0 + +PRES PURA 0.00 ! Patch to generate ADENINE (purine) + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +GROUP +ATOM C5 CN5 0.28 +ATOM N7 NN4 -0.71 +ATOM C8 CN4 0.34 +ATOM H8 HN3 0.12 +ATOM N9 NN2 -0.37 +ATOM H9 HN2 0.32 +ATOM N1 NN3A -0.74 +ATOM C2 CN4 0.50 +ATOM H2 HN3 0.13 +ATOM N3 NN3A -0.75 +ATOM C4 CN5 0.43 +ATOM C6 CN2 0.46 +ATOM N6 NN1 -0.77 +ATOM H61 HN1 0.38 +ATOM H62 HN1 0.38 +BOND N9 H9 +BILD C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0 + +PRES 9MG 0.000 ! 9-Methyl guanine patch + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +GROUP +ATOM N9 NN2B -0.02 !unchanged +ATOM C4 CN5 0.26 !unchanged +ATOM C9 CN9 -0.27 !replaces H9 in pres purg +ATOM N3 NN3G -0.74 !unchanged +ATOM C2 CN2 0.75 !unchanged +ATOM N1 NN2G -0.34 !unchanged +ATOM H1 HN2 0.26 !unchanged +ATOM N2 NN1 -0.68 !unchanged +ATOM H21 HN1 0.32 !unchanged +ATOM H22 HN1 0.35 !unchanged +ATOM C6 CN1 0.54 !unchanged +ATOM O6 ON1 -0.51 !unchanged +ATOM C5 CN5G 0.00 !unchanged +ATOM N7 NN4 -0.60 !charge changed by patch +ATOM C8 CN4 0.25 !charge changed by patch +ATOM H8 HN3 0.16 !charge changed by patch +ATOM H91 HN9 0.09 +ATOM H92 HN9 0.09 +ATOM H93 HN9 0.09 +BOND N9 C9 C9 H91 C9 H92 C9 H93 +BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 +BILD C8 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 +BILD N9 H91 *C9 H92 0.0 0.0 -115.0 0.0 0.0 +BILD H91 H92 *C9 H93 0.0 0.0 115.0 0.0 0.0 + +PRES 9EG 0.000 ! 9-Ethyl guanine patch + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +GROUP +ATOM C9 CN8 -0.18 +ATOM H91 HN8 0.09 +ATOM H92 HN8 0.09 +GROUP +ATOM C9B CN9 -0.27 +ATOM H9B1 HN9 0.09 +ATOM H9B2 HN9 0.09 +ATOM H9B3 HN9 0.09 +BOND N9 C9 C9 H91 C9 H92 C9 H93 +BOND C9 C9B C9B H9B1 C9B H9B2 C9B H9B3 +BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 +BILD C8 N9 C9 C9B 0.0 0.0 0.0 0.0 0.0 +BILD N9 C9B *C9 H91 0.0 0.0 -115.0 0.0 0.0 +BILD C9B H91 *C9 H92 0.0 0.0 115.0 0.0 0.0 +BILD N9 C9 C9B H9B1 0.0 0.0 180.0 0.0 0.0 +BILD C9 H9B1 *C9B H9B2 0.0 0.0 -115.0 0.0 0.0 +BILD H9B1 H9B2 *C9B H9B3 0.0 0.0 115.0 0.0 0.0 + +PRES 9MA 0.00 ! 9-Methyl adenine patch + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +! all atoms included in patch to get correct atom +! order to simplify analysis +GROUP +ATOM C5 CN5 0.28 !no change +ATOM N7 NN4 -0.71 !no change +ATOM C8 CN4 0.34 !no change +ATOM H8 HN3 0.12 !no change +ATOM N9 NN2 -0.05 !no change +ATOM C9 CN9 -0.27 !new charge, replaces h9 +ATOM N1 NN3A -0.74 !no change +ATOM C2 CN4 0.50 !no change +ATOM H2 HN3 0.13 !no change +ATOM N3 NN3A -0.75 !no change +ATOM C4 CN5 0.43 !no change +ATOM C6 CN2 0.46 !no change +ATOM N6 NN1 -0.77 !no change +ATOM H61 HN1 0.38 !no change +ATOM H62 HN1 0.38 !no change +ATOM H91 HN9 0.09 !new charge +ATOM H92 HN9 0.09 !new charge +ATOM H93 HN9 0.09 !new charge +BOND N9 C9 C9 H91 C9 H92 C9 H93 +BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 +BILD C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 +BILD N9 H91 *C9 H92 0.0 0.0 -115.0 0.0 0.0 +BILD H91 H92 *C9 H93 0.0 0.0 115.0 0.0 0.0 + +PRES 1MC 0.000 ! 1-Methyl Cytosine patch + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +GROUP +ATOM N1 NN2 -0.13 !no change +ATOM C1 CN9 -0.27 !replaces h1 in pres pyrc +ATOM C6 CN3 0.05 !no change +ATOM H6 HN3 0.17 !no change +ATOM C2 CN1 0.52 !no change +ATOM O2 ON1C -0.49 !no change +ATOM N3 NN3 -0.66 !no change +ATOM C4 CN2 0.65 !no change +ATOM N4 NN1 -0.75 !no change +ATOM H41 HN1 0.37 !no change +ATOM H42 HN1 0.33 !no change +ATOM C5 CN3 -0.13 !no change +ATOM H5 HN3 0.07 !no change +ATOM H11 HN9 0.09 +ATOM H12 HN9 0.09 +ATOM H13 HN9 0.09 +BOND N1 C1 C1 H11 C1 H12 C1 H13 +BILD C6 C2 *N1 C1 0.0 0.0 180.0 0.0 0.0 +BILD C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +BILD N1 H11 *C1 H12 0.0 0.0 -115.0 0.0 0.0 +BILD H11 H12 *C1 H13 0.0 0.0 115.0 0.0 0.0 + +PRES 1MT 0.00 ! 1-Methyl Thymine patch + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +GROUP +ATOM N1 NN2B -0.34 !no change +ATOM C1 CN9 -0.27 !replaces h1 in pres pyrt +ATOM C6 CN3 0.17 !no change +ATOM H6 HN3 0.17 !no change +ATOM C2 CN1T 0.51 !no change +ATOM O2 ON1 -0.41 !no change +ATOM N3 NN2U -0.46 !no change +ATOM H3 HN2 0.36 !no change +ATOM C4 CN1 0.50 !no change +ATOM O4 ON1 -0.45 !no change +ATOM C5 CN3T -0.15 !no change +ATOM C5M CN9 -0.11 !no change +ATOM H51 HN9 0.07 !no change +ATOM H52 HN9 0.07 !no change +ATOM H53 HN9 0.07 !no change +ATOM H11 HN9 0.09 +ATOM H12 HN9 0.09 +ATOM H13 HN9 0.09 +BOND N1 C1 C1 H11 C1 H12 C1 H13 +BILD C6 C2 *N1 C1 0.0 0.0 180.0 0.0 0.0 +BILD C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +BILD N1 H11 *C1 H12 0.0 0.0 -115.0 0.0 0.0 +BILD H11 H12 *C1 H13 0.0 0.0 115.0 0.0 0.0 + +PRES 1MU 0.00 ! 1-Methyl Uracil patch + ! use in generate statement +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +GROUP +ATOM N1 NN2B -0.34 !unchanged +ATOM C1 CN9 -0.27 !replaces H1 in pres pyru +ATOM C6 CN3 0.20 !unchanged +ATOM H6 HN3 0.14 !unchanged +ATOM C2 CN1T 0.55 !unchanged +ATOM O2 ON1 -0.45 !unchanged +ATOM N3 NN2U -0.46 !unchanged +ATOM H3 HN2 0.36 !unchanged +ATOM C4 CN1 0.53 !unchanged +ATOM O4 ON1 -0.48 !unchanged +ATOM C5 CN3 -0.15 !unchanged +ATOM H5 HN3 0.10 !unchanged +ATOM H11 HN9 0.09 +ATOM H12 HN9 0.09 +ATOM H13 HN9 0.09 +BOND N1 C1 C1 H11 C1 H12 C1 H13 +BILD C6 C2 *N1 C1 0.0 0.0 180.0 0.0 0.0 +BILD C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +BILD N1 H11 *C1 H12 0.0 0.0 -115.0 0.0 0.0 +BILD H11 H12 *C1 H13 0.0 0.0 115.0 0.0 0.0 + +RESI DMP -1.00 ! Dimethylphosphate +GROUP ! +ATOM P1 P 1.500 ! H11! +ATOM O3 ON3 -0.780 ! | +ATOM O4 ON3 -0.780 ! H13- C1-H12 +ATOM O1 ON2 -0.570 ! \ +ATOM O2 ON2 -0.570 ! O3 O1 +ATOM C1 CN9 -0.170 ! \\ / +ATOM H11 HN9 0.090 ! (-) P1 +ATOM H12 HN9 0.090 ! // \ +ATOM H13 HN9 0.090 ! O4 O2 +ATOM C2 CN9 -0.170 ! / +ATOM H21 HN9 0.090 ! H23-C2-H22 +ATOM H22 HN9 0.090 ! | +ATOM H23 HN9 0.090 ! H21 + ! +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 O2 C2 +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 +! IC FOR THE g,g conformation (3-21G* opt. structure) +IC O3 P1 O1 C1 1.4723 107.31 000.0 117.79 1.4356 +IC O4 P1 O2 C2 1.4722 000.0 000.0 117.79 1.4357 +IC O1 P1 O2 C2 1.6343 000.0 73.8 117.79 1.4357 +IC O2 P1 O1 C1 1.6344 000.0 73.7 117.79 1.4356 +IC H11 C1 O1 P1 1.0827 107.8 174.8 117.79 1.6343 +IC H12 C1 O1 P1 1.0800 110.4 54.1 117.79 1.6343 +IC H13 C1 O1 P1 1.0848 110.7 294.3 117.79 1.6343 +IC H21 C2 O2 P1 1.0827 107.9 174.7 117.79 1.6344 +IC H22 C2 O2 P1 1.0800 110.4 54.1 117.79 1.6344 +IC H23 C2 O2 P1 1.0848 110.7 294.2 117.79 1.6344 + +RESI MP_0 0.00 ! Methylphosphate, neutral +GROUP ! +! atom order for molvib +ATOM C1 CN9 -0.17 ! +ATOM O1 ON2 -0.56 ! H11 +ATOM P1 P 1.50 ! | +ATOM O2 ON4 -0.63 ! H13--C1--H12 +ATOM O3 ON4 -0.63 ! | +ATOM O4 ON3 -0.64 ! O1 +ATOM H11 HN9 0.09 ! | +ATOM H12 HN9 0.09 ! O4==P1--O3 +ATOM H13 HN9 0.09 ! | \ +ATOM H2 HN4 0.43 ! O2 H3 +ATOM H3 HN4 0.43 ! \ + ! H2 + ! +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 H13 O2 H2 O3 H3 +IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H2 O2 P1 O1 0.0000 000.00 180.0 000.00 0.0000 +IC H3 O3 P1 O1 0.0000 000.00 180.0 000.00 0.0000 +! dummies to analyze cetain angles +IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 + +RESI MP_1 -1.00 ! Methylphosphate, anionic +GROUP ! +! atom order for molvib +ATOM C1 CN9 -0.170 ! +ATOM O1 ON2 -0.620 ! H11 +ATOM P1 P 1.500 ! | +ATOM O2 ON4 -0.680 ! H13--C1--H12 +ATOM O3 ON3 -0.820 ! | +ATOM O4 ON3 -0.820 ! O1 +ATOM H11 HN9 0.090 ! | +ATOM H12 HN9 0.090 ! O4==P1==O3 (-) +ATOM H13 HN9 0.090 ! | +ATOM H2 HN4 0.340 ! O2 + ! \ + ! H2 + ! +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 H13 O2 H2 +! IC +IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H2 O2 P1 O1 0.0000 000.00 000.0 000.00 0.0000 +! dummies to analyze cetain angles +IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 + +RESI MP_2 -2.00 ! Methylphosphate, dianionic +GROUP ! +ATOM P1 P 1.100 ! +ATOM O1 ON2 -0.400 ! H11 +ATOM O2 ON3 -0.900 ! | +ATOM O3 ON3 -0.900 ! H13--C1--H12 +ATOM O4 ON3 -0.900 ! | +GROUP ! O1 +ATOM C1 CN9 -0.270 ! | +ATOM H11 HN9 0.090 ! (-) O4==P1==O3 (-) +ATOM H12 HN9 0.090 ! || +ATOM H13 HN9 0.090 ! O2 + ! +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 H13 +! IC +IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 +IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 +! dummies to analyze cetain angles +IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 + +! below are residues and patches added for the 97/98 optimization +! and extension of the na all-atom parameters + +RESI THF 0.00 ! tetrahydrofuran, for MOLVIB +! +GROUP +ATOM O4' ON6 -0.50 ! H41' O4' H11' +ATOM C4' CN8 0.07 ! \ / \ / +ATOM C3' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM C2' CN8 -0.18 ! | | +ATOM C1' CN8 0.07 ! H31'--C3'--C2'--H21' +ATOM H11' HN8 0.09 ! / \ +ATOM H12' HN8 0.09 ! H32' H22' +ATOM H21' HN8 0.09 ! +ATOM H22' HN8 0.09 ! +ATOM H31' HN8 0.09 ! +ATOM H32' HN8 0.09 ! +ATOM H41' HN8 0.09 ! +ATOM H42' HN8 0.09 ! + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +PATC FIRS NONE LAST NONE + +RESI THFO 0.00 ! 3'-hydroxyl-tetrahydrofuran + ! Atom types for aliphatic hydrogens based on nucleotide +GROUP +ATOM O4' ON6 -0.50 ! H41' O4' H11' +ATOM C1' CN7B 0.07 ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM C4' CN7 0.07 ! | | +ATOM H11' HN7 0.09 ! H31'--C3'--C2'--H21' +ATOM H12' HN7 0.09 ! / \ +ATOM H21' HN8 0.09 ! O3' H22' +ATOM H22' HN8 0.09 ! | +ATOM H41' HN7 0.09 ! H32' +ATOM H42' HN7 0.09 +GROUP +ATOM C3' CN7 0.14 +ATOM H31' HN7 0.09 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' H32' +!Nicolas: the following IC are for thf-oh as optimized via ab initio calculations +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 +PATC FIRS NONE LAST NONE + +RESI THFC 0.00 ! THF-3'-OH-4'-CH3 + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' ON6 -0.50 ! H52' H53' +ATOM C1' CN8 0.07 ! \ / +ATOM H11' HN8 0.09 ! H51'-C5' O4' H11' +ATOM H12' HN8 0.09 ! \ / \ / +ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' +ATOM H42' HN7 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CN8 -0.18 ! / \ +ATOM H21' HN8 0.09 ! O3' H22' +ATOM H22' HN8 0.09 ! | +GROUP ! H32' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP +ATOM C5' CN9 -0.27 +ATOM H51' HN9 0.09 +ATOM H52' HN9 0.09 +ATOM H53' HN9 0.09 +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' +BOND C1' H11' C1' H12' +BOND C2' H21' C2' H22' +BOND C3' H31' +BOND C4' H42' +BOND C5' H51' C5' H52' C5' H53' +BOND O3' H32' +PATC FIRS NONE LAST NONE + +RESI TH5P -2.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -2) + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP ! O1P (-2) +ATOM O4' ON6 -0.50 ! || +ATOM C1' CN7B 0.07 ! O2P==P==O2P +ATOM H1' HN7 0.09 ! | +ATOM H1'' HN7 0.09 ! H5'' | +ATOM C4' CN7 0.16 ! \ | +ATOM H4'' HN7 0.09 ! H5'--C5' O4' H1' +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H4'--C4' C1'--H1'' +ATOM H2' HN8 0.09 ! | | +ATOM H2'' HN8 0.09 ! H3'--C3'--C2'--H2' +GROUP ! / \ +ATOM C3' CN7 -0.18 ! H3'' H2'' +ATOM H3' HN7 0.09 ! +ATOM H3'' HN7 0.09 +GROUP +ATOM C5' CN8B -0.18 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +GROUP +ATOM O5' ON2 -0.40 +ATOM P P 1.10 +ATOM O1P ON3 -0.90 +ATOM O2P ON3 -0.90 +ATOM O3P ON3 -0.90 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' +BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P P O3P +IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 +IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 +IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 +IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 +IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 +IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 +IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 +IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 +IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 +IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 +IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 +IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 +IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 +IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 +IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 +IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 +IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 +IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TH5H 0.00 ! 5'-hydroxy-methyl-tetrahydrofuran (phosphate -2) + +! Atom types for aliphatic hydrogens based on nucleotide + + ! H5T +GROUP ! / +ATOM O4' ON6 -0.50 ! H5'' O5' +ATOM C1' CN7B 0.07 ! \ | +ATOM H1' HN7 0.09 ! H5'--C5' O4' H1' +ATOM H1'' HN7 0.09 ! \ / \ / +ATOM C4' CN7 0.16 ! H4'--C4' C1'--H1'' +ATOM H4'' HN7 0.09 ! | | +GROUP ! H3'--C3'--C2'--H2' +ATOM C2' CN8 -0.18 ! / \ +ATOM H2' HN8 0.09 ! H3'' H2'' +ATOM H2'' HN8 0.09 +GROUP +ATOM C3' CN7 -0.18 +ATOM H3' HN7 0.09 +ATOM H3'' HN7 0.09 +GROUP +ATOM C5' CN8B 0.05 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' +BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' H5T + +IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 +IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 +IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 +IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 +IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 +IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 +IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 +IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 +IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 +IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 +IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 +IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 +IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 +IC H5' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 +IC H5'' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 +IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 +IC C4' C5' O5' H5T 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI T5PH -1.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -1) + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM C5' CN8B -0.08 ! +ATOM H5' HN8 0.09 ! O1P H5T +ATOM H5'' HN8 0.09 ! || / +ATOM O5' ON2 -0.62 ! O2P==P==O3P +ATOM P P 1.50 ! | +ATOM O1P ON3 -0.82 ! O5' +ATOM O2P ON3 -0.82 ! | +ATOM O3P ON4 -0.68 ! H5'' | +ATOM H5T HN4 0.34 ! \ | +GROUP ! H5'--C5' O4' H1' +ATOM O4' ON6 -0.50 ! \ / \ / +ATOM C1' CN7B 0.07 ! H4'--C4' C1'--H1'' +ATOM H1' HN7 0.09 ! | | +ATOM H1'' HN7 0.09 ! H3'--C3'--C2'--H2' +ATOM C4' CN7 0.16 ! / \ +ATOM H4'' HN7 0.09 ! H3'' H2'' +GROUP ! +ATOM C2' CN8 -0.18 +ATOM H2' HN8 0.09 +ATOM H2'' HN8 0.09 +GROUP +ATOM C3' CN7 -0.18 +ATOM H3' HN7 0.09 +ATOM H3'' HN7 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' +BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P P O3P O3P H5T +IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 +IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 +IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 +IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 +IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 +IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 +IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 +IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 +IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 +IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 +IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 +IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 +IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 +IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 +IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 +IC O4' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 +IC O4' C4' C5' H5' 0.0 0.0 180.0 0.0 0.0 +IC O4' C4' C5' H5'' 0.0 0.0 -60.0 0.0 0.0 +IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 +IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 +IC O5' P O3P H5T 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TH3P -2.00 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -2) + ! used to fit epsilon + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' ON6 -0.50 ! H52' H53' +ATOM C1' CN7B 0.07 ! \ / +ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' +ATOM H12' HN7 0.09 ! \ / \ / +ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' +ATOM H41' HN7 0.09 ! | | +ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C2' CN8 -0.18 ! O3' H22' +ATOM H21' HN8 0.09 ! | +ATOM H22' HN8 0.09 ! O1P==P==O2P +GROUP ! || +ATOM C3' CN7 -0.09 ! O3P (-2) +ATOM H31' HN7 0.09 ! +GROUP +ATOM O3' ON2 -0.40 +ATOM P P 1.10 +ATOM O1P ON3 -0.90 +ATOM O2P ON3 -0.90 +ATOM O3P ON3 -0.90 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3P +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI T3PH -1.00 ! monoanionic 3'phosphate-tetrahydrofuran + ! used to fit epsilon + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' ON6 -0.50 ! +ATOM C1' CN7B 0.07 ! +ATOM H11' HN7 0.09 ! H41' O4' H11' +ATOM H12' HN7 0.09 ! \ / \ / +ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' +ATOM H41' HN7 0.09 ! | | +ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C2' CN8 -0.18 ! O3' H22' +ATOM H21' HN8 0.09 ! | +ATOM H22' HN8 0.09 ! O1P==P==O2P +GROUP ! | +ATOM C3' CN7 0.01 ! O3T (-1) +ATOM H31' HN7 0.09 ! \ +ATOM O3' ON2 -0.62 ! H3T +ATOM P P 1.50 ! +ATOM O1P ON3 -0.82 +ATOM O2P ON3 -0.82 +ATOM O3T ON4 -0.68 +ATOM H3T HN4 0.34 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI R3PH -1.00 ! monoanionic 3'phosphate-tetrahydrofuran + ! with O2' hydroxyl. Used to fit C2'-O2' torsion in RNA + +! Atom types for aliphatic hydrogens based on RNA nucleotide + +GROUP +ATOM O4' ON6B -0.50 ! +ATOM C1' CN7B 0.07 ! +ATOM H11' HN7 0.09 ! H41' O4' H11' +ATOM H12' HN7 0.09 ! \ / \ / +ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' +ATOM H41' HN7 0.09 ! | | +ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C2' CN7B 0.14 ! O3' O2' +ATOM H21' HN7 0.09 ! | | +ATOM O2' ON5 -0.66 ! O1P==P==O2P H22' +ATOM H22' HN5 0.43 ! | +GROUP ! O3T (-1) +ATOM C3' CN7 0.01 ! \ +ATOM H31' HN7 0.09 ! H3T +ATOM O3' ON2 -0.62 ! +ATOM P P 1.50 +ATOM O1P ON3 -0.82 +ATOM O2P ON3 -0.82 +ATOM O3T ON4 -0.68 +ATOM H3T HN4 0.34 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC O2' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 +IC H22' O2' C2' C3' 1.0822 110.88 0.00 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI A3PH -1.00 ! monoanionic 3'phosphate-tetrahydrofuran + ! with O2' hydroxyl in an arabinose (beta) conformation. + +! The furanose ring contains atom type CN7C, specific of arabinose + +GROUP +ATOM O4' ON6 -0.50 ! +ATOM C1' CN7B 0.07 ! +ATOM H11' HN7 0.09 ! H41' O4' H11' +ATOM H12' HN7 0.09 ! \ / \ / +ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' +ATOM H41' HN7 0.09 ! | | +ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C2' CN7C 0.14 ! O3' O2' O2' is beta +ATOM H22' HN7 0.09 ! | | +ATOM O2' ON5 -0.66 ! O1P==P==O2P H22' +ATOM H21' HN5 0.43 ! | +GROUP ! O3T (-1) +ATOM C3' CN7 0.01 ! \ +ATOM H31' HN7 0.09 ! H3T +ATOM O3' ON2 -0.62 ! +ATOM P P 1.50 +ATOM O1P ON3 -0.82 +ATOM O2P ON3 -0.82 +ATOM O3T ON4 -0.68 +ATOM H3T HN4 0.34 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H22' C2' O2' O2' H21' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H22' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 +IC O2' C2' C3' C4' 1.0846 110.65 120.00 100.86 1.5211 +IC H21' O2' C2' C3' 1.0822 110.88 120.00 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI T3PM -1.00 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1) + ! capped with a methyl group. This is to investigate the differences + ! between BI and BII forms of DNA + ! C3T is defined as CN8B to miminck DNA +GROUP +ATOM O4' ON6 -0.50 ! +ATOM C1' CN7B 0.07 ! H41' O4' H11' +ATOM H11' HN7 0.09 ! \ / \ / +ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C4' CN7 0.07 ! | | +ATOM H41' HN7 0.09 ! H31'--C3'--C2'--H21' +ATOM H42' HN7 0.09 ! / \ +GROUP ! O3' H22' +ATOM C2' CN8 -0.18 ! | +ATOM H21' HN8 0.09 ! O1P==P==O2P +ATOM H22' HN8 0.09 ! | +GROUP ! O3T (-1) +ATOM C3' CN7 0.01 ! \ +ATOM H31' HN7 0.09 ! C3T--H3T3 +GROUP ! / \ +ATOM O3' ON2 -0.57 ! H3T1 H3T2 +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 +ATOM O2P ON3 -0.78 +ATOM O3T ON2 -0.57 +ATOM C3T CN8B -0.17 +ATOM H3T1 HN8 0.09 +ATOM H3T2 HN8 0.09 +ATOM H3T3 HN8 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T C3T +BOND C3T H3T1 C3T H3T2 C3T H3T3 +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000 +IC C3' O3' P O3T 0.0000 000.00 -95.22 000.00 0.0000 +IC O3T O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 +IC O3T O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000 +IC C3T O3T P O3' 0.0000 000.00 -46.90 000.00 0.0000 +IC H3T1 C3T O3T P 0.0000 000.00 180.00 000.00 0.0000 +IC H3T2 C3T O3T P 0.0000 000.00 60.00 000.00 0.0000 +IC H3T3 C3T O3T P 0.0000 000.00 -60.00 000.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI TM3P -2.00 ! 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) + +! This is the DNA version (the RNA version is RM3P, see below) + +GROUP +ATOM O4' ON6 -0.50 ! H52' H53' +ATOM C1' CN7B 0.07 ! \ / +ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' +ATOM H12' HN7 0.09 ! \ / \ / +ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' +ATOM H42' HN7 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CN8 -0.18 ! / \ +ATOM H21' HN8 0.09 ! O3' H22' +ATOM H22' HN8 0.09 ! | +GROUP ! O1P==P==O2P +ATOM C3' CN7 -0.09 ! || +ATOM H31' HN7 0.09 ! O3P (-2) +GROUP ! +ATOM O3' ON2 -0.40 +ATOM P P 1.10 +ATOM O1P ON3 -0.90 +ATOM O2P ON3 -0.90 +ATOM O3P ON3 -0.90 +GROUP +ATOM C5' CN8B -0.27 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM H53' HN8 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND C4' C5' C5' H51' C5' H52' C5' H53' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RM3P -2.00 ! 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) + +! This is the RNA version of TM3P: NOTE that it does NOT have a 2'hydroxyl to +! allow for the determination of the influence of the ring dihedrals on the +! sugar puckering energetics in the absence of the 2' hydroxyl + +GROUP +ATOM O4' ON6B -0.50 +ATOM C1' CN7B 0.07 +ATOM H11' HN7 0.09 +ATOM H12' HN7 0.09 +ATOM C4' CN7 0.16 +ATOM H42' HN7 0.09 +GROUP +ATOM C2' CN7B -0.18 +ATOM H21' HN7 0.09 +ATOM H22' HN7 0.09 +GROUP +ATOM C3' CN7 -0.09 +ATOM H31' HN7 0.09 +GROUP +ATOM O3' ON2 -0.40 +ATOM P P 1.10 +ATOM O1P ON3 -0.90 +ATOM O2P ON3 -0.90 +ATOM O3P ON3 -0.90 +GROUP +ATOM C5' CN8B -0.27 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM H53' HN8 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND C4' C5' C5' H51' C5' H52' C5' H53' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI T35P -4.00 ! 5'-phosphate-3'-phosphate- + ! methyl-tetrahydrofuran (phosphate -2) +GROUP +ATOM O4' ON6 -0.50 ! +ATOM C1' CN7B 0.07 ! O1P (-2) +ATOM H1' HN7 0.09 ! || +ATOM H1'' HN7 0.09 ! O2P==P==O2P +ATOM C4' CN7 0.16 ! | +ATOM H4'' HN7 0.09 ! H5'' O5' +GROUP ! \ | +ATOM C2' CN8 -0.18 ! H5'--C5' O4' H1' +ATOM H2' HN8 0.09 ! \ / \ / +ATOM H2'' HN8 0.09 ! H4'--C4' C1'--H1'' +GROUP ! | | +ATOM C3' CN7 -0.09 ! H3'--C3'--C2'--H2' +ATOM H3' HN7 0.09 ! / \ +GROUP ! O3' H22' +ATOM O3' ON2 -0.40 ! | +ATOM P3 P 1.10 ! O31P==P==O32P +ATOM O31P ON3 -0.90 ! || +ATOM O32P ON3 -0.90 ! O33P (-2) +ATOM O33P ON3 -0.90 +GROUP +ATOM C5' CN8B -0.18 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +GROUP +ATOM O5' ON2 -0.40 +ATOM P P 1.10 +ATOM O1P ON3 -0.90 +ATOM O2P ON3 -0.90 +ATOM O3P ON3 -0.90 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' O3' +BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P P O3P O3' P3 P3 O31P P3 O32P P3 O33P +IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 +IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 +IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 +IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 +IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 +IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 +IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 +IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 +IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 +IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 +IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 +IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 +IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 +IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 +IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 +IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 +IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 +IC P3 C3' C4' O4' 1.5 112.41 -156.66 105.43 1.4416 +IC C5' C4' C3' O3' 0.0 0.0 180.0 0.0 0.0 +IC C4' C3' O3' P3 0.0 0.0 180.0 0.0 0.0 +IC C3' O3' P3 O31P 0.0 0.0 -60.0 0.0 0.0 +IC C3' O3' P3 O32P 0.0 0.0 180.0 0.0 0.0 +IC C3' O3' P3 O33P 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TMPM -1.00 ! 4'-methyl,3'-methylphosphate tetrahydrofuran (phosphate -1) + !charges corrected by adm jr. 9/98 + +GROUP +ATOM O4' ON6 -0.50 ! H52' H53' +ATOM C1' CN7B 0.07 ! \ / !c1' atom type to match full nucleotide +ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' !h11' "" +ATOM H12' HN7 0.09 ! \ / \ / !h12' "" +ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' +ATOM H42' HN7 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CN8 -0.18 ! / \ +ATOM H21' HN8 0.09 ! O3' H22' +ATOM H22' HN8 0.09 ! | +GROUP ! O1P==P==O2P +ATOM C3' CN7 0.01 ! | +ATOM H31' HN7 0.09 ! O3P (-1) +GROUP ! \ +ATOM O3' ON2 -0.57 ! C3T--H3T3 +ATOM P P 1.50 ! / \ +ATOM O1P ON3 -0.78 ! H3T1 H3T2 +ATOM O2P ON3 -0.78 ! +ATOM O3P ON2 -0.57 +ATOM C3T CN9 -0.17 +ATOM H3T1 HN9 0.09 +ATOM H3T2 HN9 0.09 +ATOM H3T3 HN9 0.09 +GROUP +ATOM C5' CN8B -0.27 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM H53' HN8 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' C5' C5' H51' C5' H52' C5' H53' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TADE 0.00 ! thf with adenine + ! Atom types for aliphatic atoms based on nucleotide + ! atom order consistent with 9-m-ade +GROUP +ATOM C5 CN5 0.28 ! H61 H62! +ATOM N7 NN4 -0.71 ! \ / +ATOM C8 CN4 0.34 ! N6 +ATOM H8 HN3 0.12 ! | +ATOM N9 NN2 -0.05 ! C6 +ATOM C1' CN7B 0.16 ! // \ +ATOM N1 NN3A -0.74 ! N1 C5--N7\\ +ATOM C2 CN4 0.50 ! | || C8-H8 +ATOM H2 HN3 0.13 ! C2 C4--N9/ +ATOM N3 NN3A -0.75 ! / \\ / \ +ATOM C4 CN5 0.43 ! H2 N3 \ +ATOM C6 CN2 0.46 ! \ +ATOM N6 NN1 -0.77 ! \ +ATOM H61 HN1 0.38 ! \ +ATOM H62 HN1 0.38 ! H42' O4' \ +ATOM O4' ON6 -0.50 ! \ / \ \ +ATOM H12' HN7 0.09 ! H41'-C4' C1' +ATOM C4' CN7 0.07 ! \ / \ +ATOM H41' HN7 0.09 ! H31'--C3'--C2' H12' +ATOM H42' HN7 0.09 ! / / \ +GROUP ! H32' H21' H22' +ATOM C2' CN8 -0.18 ! +ATOM H21' HN8 0.09 +ATOM H22' HN8 0.09 +GROUP +ATOM C3' CN7 -0.18 +ATOM H31' HN7 0.09 +ATOM H32' HN7 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TCYT 0.00 ! THF with cytosine + ! Atom types for aliphatic atoms based on nucleotide + !atom order to be consistent with 1-m-cyt +GROUP +ATOM N1 NN2 -0.13 ! +ATOM C1' CN7B 0.16 ! H42 H41 +ATOM C6 CN3 0.05 ! \ / +ATOM H6 HN3 0.17 ! N4 +ATOM C2 CN1 0.52 ! | +ATOM O2 ON1C -0.49 ! C4 +ATOM N3 NN3 -0.66 ! / \\ +ATOM C4 CN2 0.65 ! H5-C5 N3 +ATOM N4 NN1 -0.75 ! || | +ATOM H41 HN1 0.37 ! H6-C6 C2 +ATOM H42 HN1 0.33 ! \ / \\ +ATOM C5 CN3 -0.13 ! N1 O2 +ATOM H5 HN3 0.07 ! \ +ATOM O4' ON6 -0.50 ! \ +ATOM H12' HN7 0.09 ! \ +ATOM C4' CN7 0.07 ! H42' O4' \ +ATOM H41' HN7 0.09 ! \ / \ \ +ATOM H42' HN7 0.09 ! H41'-C4' C1' +GROUP ! \ / \ +ATOM C2' CN8 -0.18 ! H31'--C3'--C2' H12' +ATOM H21' HN8 0.09 ! / / \ +ATOM H22' HN8 0.09 ! H32' H21' H22' +GROUP +ATOM C3' CN7 -0.18 +ATOM H31' HN7 0.09 +ATOM H32' HN7 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N1 +BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 +BOND C2 N3 C4 C5 C5 H5 C6 H6 +DOUBLE C2 O2 C5 C6 N3 C4 +IMPR C2 N1 N3 O2 C4 N3 C5 N4 +IMPR N4 C4 H41 H42 +BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TGUA 0.00 ! thf with guanine + ! Atom types for aliphatic atoms based on nucleotide + ! atom order consistent with 9-m-gua +GROUP +ATOM N9 NN2B -0.02 ! O6 +ATOM C4 CN5 0.26 ! || +ATOM C1' CN7B 0.16 ! C6 +ATOM N3 NN3G -0.74 ! / \ +ATOM C2 CN2 0.75 ! H1-N1 C5--N7\\ +ATOM N1 NN2G -0.34 ! | || C8-H8 +ATOM H1 HN2 0.26 ! C2 C4--N9/ +ATOM N2 NN1 -0.68 ! / \\ / \ +ATOM H21 HN1 0.32 ! H21-N2 N3 \ +ATOM H22 HN1 0.35 ! | \ +ATOM C6 CN1 0.54 ! H22 \ +ATOM O6 ON1 -0.51 ! \ +ATOM C5 CN5G 0.00 ! H42' O4' \ +ATOM N7 NN4 -0.60 ! \ / \ \ +ATOM C8 CN4 0.25 ! H41'-C4' C1' +ATOM H8 HN3 0.16 ! \ / \ +ATOM O4' ON6 -0.50 ! H31'--C3'--C2' H12' +ATOM H12' HN7 0.09 ! / / \ +ATOM C4' CN7 0.07 ! H32' H21' H22' +ATOM H41' HN7 0.09 +ATOM H42' HN7 0.09 +GROUP +ATOM C2' CN8 -0.18 +ATOM H21' HN8 0.09 +ATOM H22' HN8 0.09 +GROUP +ATOM C3' CN7 -0.18 +ATOM H31' HN7 0.09 +ATOM H32' HN7 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 +DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 +IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TTHY 0.00 ! THF with thymine on C1' + ! Atom type for N1 changed from NN2 to NN2B, to adjust + ! chi in thymine independantly of cytosine. + ! Atom types for aliphatic atoms based on nucleotide + ! atom order consistent with 1-m-thy +GROUP +ATOM N1 NN2B -0.34 ! H51 O4 +ATOM C1' CN7B 0.16 ! | || +ATOM C6 CN3 0.17 ! H52-C5M C4 H3 +ATOM H6 HN3 0.17 ! | \ / \ / +ATOM C2 CN1T 0.51 ! H53 C5 N3 +ATOM O2 ON1 -0.41 ! || | +ATOM N3 NN2U -0.46 ! H6-C6 C2 +ATOM H3 HN2 0.36 ! \ / \\ +ATOM C4 CN1 0.50 ! N1 O2 +ATOM O4 ON1 -0.45 ! \ +ATOM C5 CN3T -0.15 ! \ +ATOM C5M CN9 -0.11 ! \ +ATOM H51 HN9 0.07 ! H42' O4' \ +ATOM H52 HN9 0.07 ! \ / \ \ +ATOM H53 HN9 0.07 ! H41'-C4' C1' +ATOM O4' ON6 -0.50 ! \ / \ +ATOM H12' HN7 0.09 ! H31'--C3'--C2' H12' +ATOM C4' CN7 0.07 ! / / \ +ATOM H41' HN7 0.09 ! H32' H21' H22' +ATOM H42' HN7 0.09 +GROUP +ATOM C2' CN8 -0.18 +ATOM H21' HN8 0.09 +ATOM H22' HN8 0.09 +GROUP +ATOM C3' CN7 -0.18 +ATOM H31' HN7 0.09 +ATOM H32' HN7 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N1 +BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TURA 0.00 ! THF with uracil on C1' + ! Atom type for N1 changed from NN2 to NN2B, in order to adjust + ! chi in uracil/thymine independantly of cytosine. + ! Atom types for aliphatic atoms based on nucleotide + ! atom order consistent with 1-m-thy +GROUP +ATOM N1 NN2B -0.34 ! O4 +ATOM C1' CN7B 0.16 ! || +ATOM C6 CN3 0.20 ! C4 H3 +ATOM H6 HN3 0.14 ! / \ / +ATOM C2 CN1T 0.55 ! H5-C5 N3 +ATOM O2 ON1 -0.45 ! || | +ATOM N3 NN2U -0.46 ! H6-C6 C2 +ATOM H3 HN2 0.36 ! \ / \\ +ATOM C4 CN1 0.53 ! N1 O2 +ATOM O4 ON1 -0.48 ! \ +ATOM C5 CN3 -0.15 ! \ +ATOM H5 HN3 0.10 ! \ +ATOM O4' ON6 -0.50 ! H42' O4' \ +ATOM H12' HN7 0.09 ! \ / \ \ +ATOM C4' CN7 0.07 ! H41'-C4' C1' +ATOM H41' HN7 0.09 ! \ / \ +ATOM H42' HN7 0.09 ! H31'--C3'--C2' H12' +GROUP ! / / \ +ATOM C2' CN8 -0.18 ! H32' H21' H22' +ATOM H21' HN8 0.09 +ATOM H22' HN8 0.09 +GROUP +ATOM C3' CN7 -0.18 +ATOM H31' HN7 0.09 +ATOM H32' HN7 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N1 +BOND N1 C2 N1 C6 +BOND C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 H5 C6 H6 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUSA 0.00 ! deoxy-nucleoside with adenine +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Adenine +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HN8 0.09 ! | | +ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' +! Adenine atoms ! / \ +GROUP ! O3' H22' +ATOM C5 CN5 0.28 ! | +ATOM N7 NN4 -0.71 ! H32' +ATOM C8 CN4 0.34 +ATOM H8 HN3 0.12 +ATOM N9 NN2 -0.05 +ATOM N1 NN3A -0.74 +ATOM C2 CN4 0.50 +ATOM H2 HN3 0.13 +ATOM N3 NN3A -0.75 +ATOM C4 CN5 0.43 +ATOM C6 CN2 0.46 +ATOM N6 NN1 -0.77 +ATOM H61 HN1 0.38 +ATOM H62 HN1 0.38 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! Methyl group on C4' +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +! This IC table is only an initial guess: +IC C4' O4' C1' C2' 1.4055 108.09 -21.00 106.18 1.5457 !0.0 for c3'endo (north) pucker +IC O4' C1' C2' C3' 1.4127 106.18 30.00 103.11 1.5346 ! +IC C1' C2' C3' C4' 1.5457 103.11 -30.00 100.86 1.5211 !0.0 for o4'endo barrier +IC C2' C3' C4' O4' 1.5346 100.86 20.00 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 0.00 108.09 1.4127 +IC C3' O4' *C4' C5' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' O4' *C1' N9 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 120.00 0.00 0.0000 +IC O4' C1' N9 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C1' C4 *N9 C8 0.0000 0.00 -180.00 0.00 0.0000 +IC C1' N9 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N9 *C4 N3 0.0000 0.00 180.00 0.00 0.0000 +IC N9 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 N7 0.0000 0.00 180.00 0.00 0.0000 +IC N7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C6 N6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 N6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC H61 C6 *N6 H62 0.0000 0.00 180.00 0.00 0.0000 +IC C2' C4' *C3' O3' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' C3' O3' H32' 0.0000 0.00 180.00 0.00 0.0000 !epsilon +IC C3' C4' C5' O5' 0.0000 0.00 60.00 0.00 0.0000 !gamma +IC C4' C5' O5' H5T 0.0000 0.00 180.00 0.00 0.0000 !beta +IC H5T C4' *C5' H51' 1.9450 142.80 120.00 0.00 0.0000 +IC H5T C4' *C5' H52' 1.9450 142.80 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI NUSG 0.00 ! nucleoside with guanine +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Guanine +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HN8 0.09 ! | | +ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' +! Guanine atoms ! / \ +GROUP ! O3' H22' +ATOM N9 NN2B -0.02 ! | +ATOM C4 CN5 0.26 ! H32' +ATOM N3 NN3G -0.74 +ATOM C2 CN2 0.75 +ATOM N1 NN2G -0.34 +ATOM H1 HN2 0.26 +ATOM N2 NN1 -0.68 +ATOM H21 HN1 0.32 +ATOM H22 HN1 0.35 +ATOM C6 CN1 0.54 +ATOM O6 ON1 -0.51 +ATOM C5 CN5G 0.00 +ATOM N7 NN4 -0.60 +ATOM C8 CN4 0.25 +ATOM H8 HN3 0.16 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! C5' hydroxyl +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 +DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 +IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUSC 0.00 ! nucleoside with cytosine +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Cytosine +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HN8 0.09 ! | | +ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' +! Cytosine atoms ! / \ +GROUP ! O3' H22' +ATOM N1 NN2 -0.13 ! | +ATOM C6 CN3 0.05 ! H32' +ATOM H6 HN3 0.17 +ATOM C2 CN1 0.52 +ATOM O2 ON1C -0.49 +ATOM N3 NN3 -0.66 +ATOM C4 CN2 0.65 +ATOM N4 NN1 -0.75 +ATOM H41 HN1 0.37 +ATOM H42 HN1 0.33 +ATOM C5 CN3 -0.13 +ATOM H5 HN3 0.07 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! C5' hydroxyl +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N1 +BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 +BOND C2 N3 C4 C5 C5 H5 C6 H6 +DOUBLE C2 O2 C5 C6 N3 C4 +IMPR N4 C4 H41 H42 C2 N1 N3 O2 C4 N3 C5 N4 +! +IC C4' O4' C1' C2' 1.4055 108.09 -21.00 106.18 1.5457 !0.0 for c3'endo (north) pucker +IC O4' C1' C2' C3' 1.4127 106.18 30.00 103.11 1.5346 ! +IC C1' C2' C3' C4' 1.5457 103.11 -30.00 100.86 1.5211 !0.0 for o4'endo barrier +IC C2' C3' C4' O4' 1.5346 100.86 20.00 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 0.00 108.09 1.4127 +IC C3' O4' *C4' C5' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' O4' *C1' N1 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 120.00 0.00 0.0000 +IC O4' C1' N1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C1' C2 *N1 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C1' N1 C6 C5 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C6 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C1' N1 C2 N3 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C5 *C4 N4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C4 N4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C4 *N4 H42 0.0000 0.00 180.00 0.00 0.0000 +IC C2' C4' *C3' O3' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' C3' O3' H32' 0.0000 0.00 180.00 0.00 0.0000 !epsilon +IC C3' C4' C5' O5' 0.0000 0.00 60.00 0.00 0.0000 !gamma +IC C4' C5' O5' H5T 0.0000 0.00 180.00 0.00 0.0000 !beta +IC H5T C4' *C5' H51' 1.9450 142.80 120.00 0.00 0.0000 +IC H5T C4' *C5' H52' 1.9450 142.80 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI NUST 0.00 ! nucleoside with thymine +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Thymine +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HN8 0.09 ! | | +ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' +! Atoms for thymine ! / \ +GROUP ! O3' H22' +ATOM N1 NN2B -0.34 ! | +ATOM C6 CN3 0.17 ! H32' +ATOM H6 HN3 0.17 +ATOM C2 CN1T 0.51 +ATOM O2 ON1 -0.41 +ATOM N3 NN2U -0.46 +ATOM H3 HN2 0.36 +ATOM C4 CN1 0.50 +ATOM O4 ON1 -0.45 +ATOM C5 CN3T -0.15 +ATOM C5M CN9 -0.11 +ATOM H51 HN9 0.07 +ATOM H52 HN9 0.07 +ATOM H53 HN9 0.07 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! C5' hydroxyl +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N1 +BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUSU 0.00 ! nucleoside with uracil +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Uracil +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HN8 0.09 ! | | +ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' +! Atoms for uracil ! / \ +GROUP ! O3' H22' +ATOM N1 NN2B -0.34 ! | +ATOM C6 CN3 0.20 ! H32' +ATOM H6 HN3 0.14 +ATOM C2 CN1T 0.55 +ATOM O2 ON1 -0.45 +ATOM N3 NN2U -0.46 +ATOM H3 HN2 0.36 +ATOM C4 CN1 0.53 +ATOM O4 ON1 -0.48 +ATOM C5 CN3 -0.15 +ATOM H5 HN3 0.10 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! C5' hydroxyl +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N1 N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C6 C5 H5 C6 H6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +BILD O4' C1' N1 C2 1.5251 113.71 180.0 117.06 1.3746 +BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 +BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 +BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 +BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 +BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 +BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 +BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 +BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUA 0.00 ! ribo-nucleoside with adenine +GROUP +ATOM O4' ON6B -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Adenine +GROUP ! \ / \ / +ATOM H21' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CN7B 0.14 ! | | +ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' +ATOM H22' HN5 0.43 ! / \ +! Adenine atoms ! O3' O2' +GROUP ! | | +ATOM C5 CN5 0.28 ! H32' H22' +ATOM N7 NN4 -0.71 +ATOM C8 CN4 0.34 +ATOM H8 HN3 0.12 +ATOM N9 NN2 -0.05 +ATOM N1 NN3A -0.74 +ATOM C2 CN4 0.50 +ATOM H2 HN3 0.13 +ATOM N3 NN3A -0.75 +ATOM C4 CN5 0.43 +ATOM C6 CN2 0.46 +ATOM N6 NN1 -0.77 +ATOM H61 HN1 0.38 +ATOM H62 HN1 0.38 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! C5' hydroxyl +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O2' H22' O3' H32' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 +IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 150.8 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 108.6 180.0 125.5 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUG 0.00 ! ribo-nucleoside with guanine +GROUP +ATOM O4' ON6B -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Guanine +GROUP ! \ / \ / +ATOM H21' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CN7B 0.14 ! | | +ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' +ATOM H22' HN5 0.43 ! / \ +! Guanine atoms ! O3' O2' +GROUP ! | | +ATOM N9 NN2B -0.02 ! H32' H22' +ATOM C4 CN5 0.26 +ATOM N3 NN3G -0.74 +ATOM C2 CN2 0.75 +ATOM N1 NN2G -0.34 +ATOM H1 HN2 0.26 +ATOM N2 NN1 -0.68 +ATOM H21 HN1 0.32 +ATOM H22 HN1 0.35 +ATOM C6 CN1 0.54 +ATOM O6 ON1 -0.51 +ATOM C5 CN5G 0.00 +ATOM N7 NN4 -0.60 +ATOM C8 CN4 0.25 +ATOM H8 HN3 0.16 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! C5' hydroxyl +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O2' H22' O3' H32' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 +DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 +IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 +IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +BILD O4' C1' N9 C4 1.5251 113.71 180.0 125.59 1.3783 !chi +BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 +BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUC 0.00 ! ribo-nucleoside with cytosine +GROUP +ATOM O4' ON6B -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Cytosine +GROUP ! \ / \ / +ATOM H21' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CN7B 0.14 ! | | +ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' +ATOM H22' HN5 0.43 ! / \ +! Cytosine atoms ! O3' O2' +GROUP ! | | +ATOM N1 NN2 -0.13 ! H32' H22' +ATOM C6 CN3 0.05 +ATOM H6 HN3 0.17 +ATOM C2 CN1 0.52 +ATOM O2 ON1C -0.49 +ATOM N3 NN3 -0.66 +ATOM C4 CN2 0.65 +ATOM N4 NN1 -0.75 +ATOM H41 HN1 0.37 +ATOM H42 HN1 0.33 +ATOM C5 CN3 -0.13 +ATOM H5 HN3 0.07 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! Methyl group on C4' +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O2' H22' O3' H32' +BOND C1' N1 +BOND N1 C2 N1 C6 +BOND C2 N3 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 H5 C6 H6 +DOUBLE C2 O2 C5 C6 N3 C4 +IMPR N4 C4 H41 H42 C2 N1 N3 O2 C4 N3 C5 N4 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 +IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUU 0.00 ! ribo-nucleoside with uracil +GROUP +ATOM O4' ON6B -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Uracil +GROUP ! \ / \ / +ATOM H21' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CN7B 0.14 ! | | +ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' +ATOM H22' HN5 0.43 ! / \ +! Uracil atoms ! O3' O2' +GROUP ! | | +ATOM N1 NN2B -0.34 ! H32' H22' +ATOM C6 CN3 0.20 +ATOM H6 HN3 0.14 +ATOM C2 CN1T 0.55 +ATOM O2 ON1 -0.45 +ATOM N3 NN2U -0.46 +ATOM H3 HN2 0.36 +ATOM C4 CN1 0.53 +ATOM O4 ON1 -0.48 +ATOM C5 CN3 -0.15 +ATOM H5 HN3 0.10 + +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! Methyl group on C4' +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O2' H22' O3' H32' +BOND C1' N1 N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C6 C5 H5 C6 H6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 +IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 117.06 1.3746 +IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 +IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 +IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 +IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 +IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 +IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 +IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUT 0.00 ! ribo-nucleoside with thymine +GROUP +ATOM O4' ON6B -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Thymine +GROUP ! \ / \ / +ATOM H21' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CN7B 0.14 ! | | +ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' +ATOM H22' HN5 0.43 ! / \ +! Thymine atoms ! O3' O2' +GROUP ! | | +ATOM N1 NN2B -0.34 ! H32' H22' +ATOM C6 CN3 0.17 +ATOM H6 HN3 0.17 +ATOM C2 CN1T 0.51 +ATOM O2 ON1 -0.41 +ATOM N3 NN2U -0.46 +ATOM H3 HN2 0.36 +ATOM C4 CN1 0.50 +ATOM O4 ON1 -0.45 +ATOM C5 CN3T -0.15 +ATOM C5M CN9 -0.11 +ATOM H51 HN9 0.07 +ATOM H52 HN9 0.07 +ATOM H53 HN9 0.07 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP ! Methyl group on C4' +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O2' H22' O3' H32' +BOND C1' N1 +BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 +IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NADE -1.00 ! +! NADE is a nucleotide analogue similar to NUCL, except that the imidazole +! has been replaced by an adenine +! - The charge distribution on the sugar is identical to what +! it is in the DNA. +! - The charge' on the 3' end of the "backbone" is identical to +! what it is in the DNA, except for the terminal methyl group for which +! there is no DNA equivalent. +! - The charges on the 5' extremity of the backbone is as in the +! 5TER patch used for the DNA. An alternative to that would be to use +! charges more similar to what is actuallly in non-terminal residues in the +! DNA. +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C1' CN7B 0.16 ! | +ATOM H12' HN7 0.09 ! H52' O5' +ATOM C4' CN7 0.16 ! \ / +ATOM H42' HN7 0.09 ! H51'-C5' O4' Adenine +GROUP ! \ / \ / +ATOM C5 CN5 0.30 ! H42'--C4' C1'--H12' +ATOM N7 NN4 -0.69 ! | | +ATOM C8 CN4 0.34 ! H31'--C3'--C2'--H21' +ATOM H8 HN3 0.10 ! / \ +ATOM N9 NN2 -0.06 ! O3' H22' +ATOM N1 NN3A -0.74 ! | +ATOM C2 CN4 0.50 ! O1P==P==O2P +ATOM H2 HN3 0.13 ! | +ATOM N3 NN3A -0.75 ! O3P (-1) +ATOM C4 CN5 0.43 ! \ +ATOM C6 CN2 0.44 ! C3T--H3T3 +ATOM N6 NN1 -0.75 ! / \ +ATOM H61 HN1 0.38 ! H3T1 H3T2 +ATOM H62 HN1 0.37 +GROUP +ATOM C2' CN8 -0.18 +ATOM H21' HN8 0.09 +ATOM H22' HN8 0.09 +GROUP +ATOM C3' CN7 0.01 +ATOM H31' HN7 0.09 +ATOM O3' ON2 -0.57 +ATOM P P 1.50 +ATOM O1P ON3 -0.78 +ATOM O2P ON3 -0.78 +ATOM O3P ON2 -0.57 +ATOM C3T CN8B -0.17 +ATOM H3T1 HN8 0.09 +ATOM H3T2 HN8 0.09 +ATOM H3T3 HN8 0.09 +GROUP +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM H5T HN5 0.43 +ATOM O5' ON5 -0.66 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' C5' C5' H51' C5' H52' +BOND C5' O5' O5' H5T +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NTHY -1.00 ! +! NTHY is a nucleotide analogue similar to NUCL, except that the imidazole +! has been replaced by a thymine +! - The charge distribution on the sugar is identical to what +! it is in the DNA. +! - The charge' on the 3' end of the "backbone" is identical to +! what it is in the DNA, except for the terminal methyl group for which +! there is no DNA equivalent. +! - The charges on the 5' extremity of the backbone is as in the +! 5TER patch used for the DNA. An alternative to that would be to use +! charges more similar to what is actuallly in non-terminal residues in the +! DNA. +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C1' CN7B 0.16 ! | +ATOM H12' HN7 0.09 ! H52' O5' +ATOM C4' CN7 0.16 ! \ / +ATOM H42' HN7 0.09 ! H51'-C5' O4' Thymine +GROUP ! \ / \ / +ATOM N1 NN2B -0.34 ! H42'--C4' C1'--H12' +ATOM C6 CN3 0.17 ! | | +ATOM H6 HN3 0.17 ! H31'--C3'--C2'--H21' +ATOM C2 CN1T 0.51 ! / \ +ATOM O2 ON1 -0.41 ! O3' H22' +ATOM N3 NN2U -0.46 ! | +ATOM H3 HN2 0.36 ! O1P==P==O2P +ATOM C4 CN1 0.50 ! | +ATOM O4 ON1 -0.45 ! O3P (-1) +ATOM C5 CN3T -0.15 ! \ +ATOM C5M CN9 -0.11 ! C3T--H3T3 +ATOM H51 HN9 0.07 ! / \ +ATOM H52 HN9 0.07 ! H3T1 H3T2 +ATOM H53 HN9 0.07 +GROUP +ATOM C2' CN8 -0.18 +ATOM H21' HN8 0.09 +ATOM H22' HN8 0.09 +GROUP +ATOM C3' CN7 0.01 +ATOM H31' HN7 0.09 +ATOM O3' ON2 -0.57 +ATOM P P 1.50 +ATOM O1P ON3 -0.78 +ATOM O2P ON3 -0.78 +ATOM O3P ON2 -0.57 +ATOM C3T CN8B -0.17 +ATOM H3T1 HN8 0.09 +ATOM H3T2 HN8 0.09 +ATOM H3T3 HN8 0.09 +GROUP +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM H5T HN5 0.43 +ATOM O5' ON5 -0.66 +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' C5' C5' H51' C5' H52' +BOND C5' O5' O5' H5T +BOND C1' N1 +BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +PRES FEX1 0.000 ! Patch to make C2'-fluoro +DELETE ATOM O2' ! with fluorine cis to O3' (EXo or alpha). +DELETE ATOM H2' ! follow with AUTOgenerate ANGLes DIHEdrals command + ! +GROUP +ATOM C2' CN7D 0.19 +ATOM F2' FN1 -0.28 +ATOM H2'' HN7 0.09 +BOND C2' F2' +BILD C1' C3' *C2' F2' 0.0 0.0 -115.0 0.0 0.0 + +PRES FEN1 0.000 ! Patch to make C2'-fluoro + ! with fluorine trans to O3' (ENdo or beta). + ! follow with AUTOgenerate ANGLes DIHEdrals command +DELETE ATOM O2' +DELETE ATOM H2'' +GROUP +ATOM C2' CN7D 0.19 +ATOM F2' FN1 -0.28 +ATOM H2' HN7 0.09 +BOND C2' F C2' H2' +BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 +BILD C3' C1' *C2' F2' 0.0 0.0 -115.0 0.0 0.0 + +end + +read para card flex append +* c27 na parameters +* + +ATOMS +MASS 466 CN7C 12.011000 ! C2' in arabinose +MASS 467 CN7D 12.011000 ! C2' in nucleic acids fluorine derivatives +MASS 468 FN1 18.998400 ! Fluorine for sugar derivatives (NF) + +!Bonded parameters for FN1 seem to be missing... +BONDS +!@@@@@@@@@ Begining of endocyclic bonds for arabinose @@@@@@@@@ +! Transfered from DNA +CN7B CN7C 200.0 1.518 ! For arabinose, from CN7B CN8 +CN7 CN7C 222.5 1.516 ! For arabinose, from CN7 CN8 +CN7C HN7 309.0 1.111 ! From CN8 HN7 +!@@@@@@@@@ End of endocyclic bonds for arabinose @@@@@@@@@ + +!@@@@@@@@@ Begining of exocyclic bonds for arabinose @@@@@@@@@ +!CN7C ON5 250.0 1.400 ! From CN7 ON5 +CN7C ON5 428.0 1.400 ! check adm jr., +!FC should be 428.000 based on Meoh +!@@@@@@@@@ End of exocyclic bonds for arabinose @@@@@@@@@ + +ANGLES +CN7C CN7B NN2 110.0 111.0 !C/A, Arabinose (NF) +CN7C CN7B NN2B 110.0 111.0 !T/U/G, Arabinose (NF) + +!@@@@@@@@@ Beginning of endocyclic valence angles for arabinose @@@@@@@ +ON6 CN7B CN7C 90.0 102.0 ! NF, 11/97, C4'O4'C1' +CN7B CN7C CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3' +CN7C CN7 CN7 60.00 102.0 8.00 2.561 !NF, 11/97, C2'C3'C4' +CN7B CN7C HN7 33.4 110.10 22.53 2.179 ! following terms directly +CN7C CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes +HN7 CN7 CN7C 34.5 110.1 22.53 2.179 ! +HN7 CN7C CN7 34.53 110.10 22.53 2.179 ! +HN7 CN7C HN7 35.5 109.00 5.40 1.802 ! +!@@@@@@@@@ End of endocyclic valence angles for arabinose @@@@@@@ + +!@@@@@@@@@ Beginning of exocyclic valence angles for arabinose @@@@@@@ +CN7C CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3' +!===== For 3ter patch: +!From DNA: +ON5 CN7 CN7C 75.7 110.0 ! from CHARMM22 +!From RNA: +ON5 CN7C CN7B 80.0 108.4 ! From ON5 CN7B CN7B +!O2'-C2'-C3' +ON5 CN7C CN7 90.0 108.0 ! From ON5 CN7B CN7 +HN7 CN7C ON5 60.0 109.5 ! +HN5 ON5 CN7C 57.5 109.0 ! 032598 +!@@@@@@@@@ End of exocyclic valence angles for arabinose @@@@@@@ + +DIHEDRALS + !Arabinose: +CN7C CN7B NN2 CN5 0.3 3 0.0 ! +CN7C CN7B NN2 CN4 0.0 3 180.0 ! + !Arabinose: +CN7C CN7B NN2 CN1 1.0 3 0.0 ! +CN7C CN7B NN2 CN3 0.0 3 180.0 ! + !Arabinose: +CN7C CN7B NN2B CN1T 0.2 3 180.0 ! +CN7C CN7B NN2B CN3 0.0 3 180.0 ! + !Arabinose: +CN7C CN7B NN2B CN5 0.0 3 0.0 ! +CN7C CN7B NN2B CN4 0.0 3 180.0 ! + !Arabinose: +CN7 CN7C CN7B NN2 0.0 3 0.0 +CN7 CN7C CN7B NN2B 0.0 3 0.0 + !Arabinose: +HN7 CN7C CN7B NN2 0.0 3 0.0 +HN7 CN7C CN7B NN2B 0.0 3 0.0 + +CN7C CN7 CN7 CN8B 0.5 4 180.0 !del, arabinose +ON2 CN7 CN7C CN7B 0.8 6 0.0 ! Arabinose (from DNA) +ON2 CN7 CN7C CN7B 0.4 5 0.0 ! +ON2 CN7 CN7C CN7B 2.0 3 180.0 ! +ON5 CN7 CN7C CN7B 0.8 6 0.0 ! Arabinose (from DNA) +ON5 CN7 CN7C CN7B 0.4 5 0.0 ! Arabinose (from DNA) +ON5 CN7 CN7C CN7B 2.0 3 180.0 ! Arabinose (from DNA) +ON2 CN7 CN7C HN7 0.195 3 0.0 ! Arabinose (from DNA) +ON5 CN7 CN7C HN7 0.195 3 180.0 ! Arabinose (from DNA) +CN7C CN7 ON2 P 2.5 1 180.0 !eps, Arabinose (from DNA) +CN7C CN7 ON5 HN5 0.8 3 0.0 ! Arabinose (from DNA) +CN7C CN7 ON5 HN5 0.5 1 0.0 ! Arabinose (from DNA) +CN7C CN7B ON6 CN7 0.6 6 180.0 ! Arabinose (from DNA) +CN7C CN7 CN7 ON6 0.0 3 0.0 ! Arabinose (from DNA) +CN7 CN7C CN7B ON6 0.6 6 0.0 ! Arabinose (from DNA) +CN7B CN7C CN7 CN7 0.4 6 0.0 ! Arabinose (from DNA) +HN7 CN7 CN7 CN7C 0.0 3 0.0 ! Arabinose (from DNA) +HN7 CN7 CN7C CN7B 0.195 3 0.0 !Arabinose (from DNA), H-C3'-C2'-C1' +HN7 CN7B CN7C CN7 0.195 3 0.0 !Arabinose (from DNA), H-C1'-C2'-C3' +HN7 CN7C CN7B ON6 0.195 3 0.0 !Arabinose (from DNA), H-C2'-C1'-O4' +HN7 CN7B CN7C HN7 0.195 3 0.0 !Arabinose (from DNA), H-C1'-C2'-H +HN7 CN7 CN7C HN7 0.195 3 0.0 !Arabinose (from DNA), H-C3'-C2'-H +HN7 CN7C CN7 CN7 0.195 3 0.0 !Arabinose (from DNA), useful *cccc* + +!@@@@@@ Begining of torsions specifically defined for arabinose @@@@@@ +ON6 CN7B CN7C ON5 0.000 3 0.0 +! the following differ significantly from the protein based +! alcohol parameters (based on ethanol, see above) +CN7B CN7C ON5 HN5 0.000 3 0.0 +CN7 CN7C ON5 HN5 0.000 3 0.0 +HN7 CN7B CN7C ON5 0.000 3 0.0 +CN7 CN7 CN7C ON5 0.000 3 0.0 +HN7 CN7C ON5 HN5 0.000 3 0.0 +ON5 CN7C CN7 HN7 0.000 3 0.0 +ON5 CN7C CN7 ON2 0.000 3 0.0 +!@@@@@@ End of torsions specifically defined for arabinose @@@@@@ + +NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 +CN7C 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 +CN7D 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 +FN1 0.0 -0.09 1.70 !aliphatic F preliminary from Yin Thesis + !see toppar_all22_prot_fluoro_alkane.str for better parameters +END diff --git a/charmm/toppar/stream/na/toppar_all36_na_modifications.str b/charmm/toppar/stream/na/toppar_all36_na_modifications.str new file mode 100644 index 00000000..a9c92da4 --- /dev/null +++ b/charmm/toppar/stream/na/toppar_all36_na_modifications.str @@ -0,0 +1,4959 @@ +* CHARMM27 All-Hydrogen Nucleic Acid Force Toppar Stream File +* Collection of residues and patches for various NA modifications +* A.D. MacKerell, Jr., July 2011 +* + +!includes all residues/patches formally in +!toppar_all36_na_base_modifications.str +!toppar_all36_na_bkb_modifications.str +!toppar_all36_na_carbocyclic.str + +!Parent files that have to be read prior to streaming this file +!top_all36_na.rtf +!par_all36_na.prm + +!Testcase +!test_all36_na_modifications.inp + +!References +! +!CHARMM nucleic acid 27 Foloppe and MacKerell JCC paper +! +!backbone parameters +!PNA +!Boel Nystrom, Karolinska Institutet, 2005. Based on origina implementation: +!Sen S, Nilsson L. 1998. Molecular dynamics of duplex systems involving PNA: +!Structural and dynamical consequences of the nucleic acid backbone. +!J. Am. Chem. Soc. 120(4):619-631. +! +!carbocyclic sugar parameters +! +!Wang, P., Nicklaus, M.C., Marquez, V.E., Brank, A.S., +!Christman, J., Banavali, N.K. and MacKerell, Jr., A.D., "Use of +!Oligodeoxyribonucleotides with Conformationally Constrained +!Abasic Sugar Targets to Probe the Mechanism of Base Flipping by +!HhaI DNA (Cytosine C5)-Methyltransferase" Journal of the +!American Chemical Society, 2000, 122:12422-12434 +! + +read rtf card append +* residues and patches associated with base modifications +* +31 1 + +MASS 416 CN6 12.011000 C ! carbocylic NA modifications (numbering is correct) +MASS 417 CN7E 12.011000 C ! cabocyclic NA modifications +MASS 469 HNP 1.008000 H ! pure aromatic H +MASS 470 HNE1 1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha) +MASS 471 HNE2 1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha) +MASS 472 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC +MASS 473 CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha) +MASS 474 CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha) +MASS 475 CNA 12.011000 C ! pure aromatic carbon +MASS 476 CNA2 12.011000 C ! pure aromatic carbon bound to F +MASS 477 CNG 12.011000 C ! guanidinium type carbon +MASS 478 NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha) +MASS 479 NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha) +MASS 480 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 +MASS 481 NNG 14.007000 N ! guanidinium type nitrogen +MASS 482 FNA 18.998400 F ! Aromatic fluorine +MASS 483 ON2M 15.999400 O ! ether oxygen for methylated C2' of ribose + +!DECL -C !common to proteins +DECL -O1' +!DECL +N !common to proteins +DECL -C2' +DECL -C6' +DECL -C5' +DECL -H2' +DECL -H2'' +DECL +H1' +DECL +C6' +!need to reassign declare statements for PNA residues +!proteins +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +!!nucleic acid section +DECL +P +DECL +O1P +DECL +O2P +DECL +O5' +DECL -O3' + +!base section + +PRES 5MC1 0.03 ! Patch to generate 5-methylcytosine (base only) + ! use in generate statement + ! checked for consistency with new NA params, adm jr., 9/98 +! DELETE PHOSPHATE AND RIBOSE ATOMS +DELE ATOM P +DELE ATOM O1P +DELE ATOM O2P +DELE ATOM O5' +DELE ATOM C5' +DELE ATOM H5' +DELE ATOM H5'' +DELE ATOM C4' +DELE ATOM H4' +DELE ATOM O4' +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM H2' +DELE ATOM C3' +DELE ATOM O3' +DELE ATOM H3' +DELE ATOM H5 +ATOM N1 NN2 -0.50 +ATOM H1 HN2 0.37 +ATOM C6 CN3 0.05 +ATOM H6 HN3 0.17 +ATOM C5 CN3D -0.11 +ATOM C5M CN9 -0.22 +ATOM H5M1 HN9 0.09 +ATOM H5M2 HN9 0.09 +ATOM H5M3 HN9 0.09 +BOND N1 H1 +BOND C5 C5M C5M H5M1 C5M H5M2 C5M H5M3 +IMPR N1 C6 C2 H1 +BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 +BILD C6 C4 *C5 C5M 0.0 0.0 180.0 0.0 0.0 +BILD C4 C5 C5M H5M1 0.0 0.0 180.0 0.0 0.0 +BILD C5 H5M1 *C5M H5M2 0.0 0.0 -115.0 0.0 0.0 +BILD H5M1 H5M2 *C5M H5M3 0.0 0.0 115.0 0.0 0.0 + +PRES 5MC2 -0.06 ! Patch to convert cytosine in DNA to 5-methylcytosine + ! use in PATCH statement followed by AUTOgenerate ANGLes DIHE +DELE ATOM H5 +GROUP +ATOM C5 CN3D -0.11 +ATOM C5M CN9 -0.22 +ATOM H5M1 HN9 0.09 +ATOM H5M2 HN9 0.09 +ATOM H5M3 HN9 0.09 +BOND C5 C5M C5M H5M1 C5M H5M2 C5M H5M3 +BILD C6 C4 *C5 C5M 0.0 0.0 180.0 0.0 0.0 +BILD C4 C5 C5M H5M1 0.0 0.0 180.0 0.0 0.0 +BILD C5 H5M1 *C5M H5M2 0.0 0.0 -115.0 0.0 0.0 +BILD H5M1 H5M2 *C5M H5M3 0.0 0.0 115.0 0.0 0.0 + +PRES INO1 -0.08 ! patch to convert guanine to inosine + ! use in patch statement followed by AUTOgenerate ANGLes DIHE + +!reference: Pastor, N., MacKerell, A.D., Jr., and Weinstein, H. "TIT +!for TAT: The Properties of Inosine and Adenosine in TATA Box DNA" +!Journal of Biomolecular Structure & Design, 1999, 16: 787-810. + +DELE ATOM N2 +DELE ATOM H21 +DELE ATOM H22 +! charges updated to be consistent with new NA set, adm jr., 9/98 +ATOM N3 NN3I -0.61 +ATOM C2 CN4 0.50 +ATOM H2 HN3 0.08 +ATOM N1 NN2G -0.32 +ATOM H1 HN2 0.27 +BOND C2 H2 +IMPR C2 N1 N3 H2 +BILD N1 N3 *C2 H2 1.375 124.0 180.0 119.7 1.341 + +PRES GUT1 0.00 ! guanine tautomer patch to convert guanine + ! in DNA or RNA + ! adm jr. w/Daniel Barsky + ! + ! use patch statement, followed by AUTOgenerate + ! angles dihedrals in c25 and later versions + ! not MMFF compatible +! Delete guanine H1 atom ! +DELE ATOM H1 ! --> H6 +GROUP ! | \ +ATOM C6 CN1 0.58 ! proton O6 +ATOM O6 ON5 -0.58 ! shifted | +ATOM H6 HN5 0.48 ! | C6 +ATOM C5 CN5G 0.08 ! | // \ +ATOM N3 NN3G -0.69 ! -< N1 C5--N7\\ +ATOM C2 CN2 0.78 ! | || C8-H8 +ATOM N1 NN3G -0.72 ! C2 C4--N9/ +ATOM N2 NN1 -0.65 ! / \\ / \ +ATOM H21 HN1 0.30 ! H21-N2 N3 \ +ATOM H22 HN1 0.31 ! | \ +ATOM N9 NN2B 0.00 ! H22 R +ATOM C4 CN5 0.32 ! +ATOM N7 NN4 -0.62 ! atom order consistent with 9-m-gua +ATOM C8 CN4 0.26 ! +ATOM H8 HN3 0.15 ! + +BOND O6 H6 + +BILD N1 C6 O6 H6 0.0 0.0 0.0 0.0 0.0 + +PRES CYT1 0.00 ! cytosine tautomer patch to convert cytosine + ! in DNA or RNA + ! adm jr. w/Daniel Barsky + ! + ! use in patch statement, followed by AUTOgenerate + ! angles dihedrals in c25 and later versions + ! not MMFF compatible + ! ____________ + ! | | +! Delete cytosine H41 atom ! | proton +DELE ATOM H42 ! | shifted +GROUP ! | | +ATOM N1 NN2 -0.14 ! | H41 | +ATOM H3 HN2 0.31 ! | \ >- +ATOM C6 CN3 0.15 ! | N4 +ATOM H6 HN3 0.13 ! | || +ATOM C2 CN1 0.52 ! | C4 +ATOM O2 ON1C -0.46 ! | / \ +ATOM N3 NN2C -0.35 ! -->H3-N3 C5-H5 +ATOM C4 CN2 0.30 ! | || +ATOM N4 NN1C -0.76 ! C2 C6 +ATOM H41 HN1 0.35 ! //\ / \ +ATOM C5 CN3 -0.22 ! O2 N1 H6 +ATOM H5 HN3 0.17 ! | + ! H1 +BOND N3 H3 + +BILD N4 C4 N3 H3 0.0 0.0 0.0 0.0 0.0 + +PRES 1EG 0.00 ! 1-Ethyl guanine patch + ! adm jr. w/Daniel Barsky + ! + ! use in patch statement, followed by AUTOgenerate + ! angles dihedrals in c25 and later versions +! Delete guanine H1 atom ! +DELE ATOM H1 ! +GROUP ! H1B1 H1A1 O6 +ATOM C6 CN1 0.54 ! \ | || +ATOM O6 ON1 -0.51 ! H1B2--C1B-C1A C6 +ATOM C5 CN5G 0.00 ! / | \ / \ +ATOM N3 NN3G -0.74 ! H1B3 H1A2 N1 C5--N7\\ +ATOM C2 CN2 0.75 ! | || C8-H8 +ATOM N1 NN2G -0.08 ! C2 C4--N9/ +ATOM N2 NN1 -0.68 ! / \\ / \ +ATOM H21 HN1 0.32 ! H21-N2 N3 \ +ATOM H22 HN1 0.35 ! | \ +ATOM C4 CN5 0.26 ! H22 R +ATOM N9 NN2B -0.02 ! +!ATOM N9 NN2B -0.38 ! use these charges for the base alone +!ATOM H9 HN2 0.36 ! +ATOM N7 NN4 -0.60 ! +ATOM C8 CN4 0.25 ! +ATOM H8 HN3 0.16 ! +ATOM C1A CN8 -0.18 ! +ATOM H1A1 HN8 0.09 ! +ATOM H1A2 HN8 0.09 ! +ATOM C1B CN9 -0.27 ! +ATOM H1B1 HN9 0.09 ! +ATOM H1B2 HN9 0.09 ! +ATOM H1B3 HN9 0.09 ! + +BOND N1 C1A C1A C1B C1A H1A1 C1A H1A2 C1B H1B1 C1B H1B2 C1B H1B3 + +BILD N3 C2 N1 C1A 0.0 0.0 180.0 0.0 0.0 +BILD C2 N1 C1A C1B 0.0 0.0 90.0 0.0 0.0 +BILD C1B N1 *C1A H1A1 0.0 0.0 120.0 0.0 0.0 +BILD C1B N1 *C1A H1A2 0.0 0.0 240.0 0.0 0.0 +BILD N1 C1A C1B H1B1 0.0 0.0 180.0 0.0 0.0 +BILD C1A H1B1 *C1B H1B2 0.0 0.0 120.0 0.0 0.0 +BILD C1A H1B1 *C1B H1B3 0.0 0.0 240.0 0.0 0.0 + +PRES 3EC 1.00 ! 3-Ethyl cytosine patch + ! adm jr. w/Daniel Barsky + ! + ! use in patch statement, followed by AUTOgenerate + ! angles dihedrals in c25 and later versions + ! not MMFF compatible + ! +GROUP ! +ATOM N1 NN2 -0.12 ! comment this line and uncomment the following 2 atoms for the base alone +!ATOM N1 NN2 -0.50 ! H41 H42 +!ATOM H1 HN2 0.38 ! \ / +ATOM C6 CN3 0.14 ! H3B1 H3A1 N4 +ATOM H6 HN3 0.20 ! \ | | +ATOM C2 CN1 0.38 ! H3B2--C3B--C3A C4 +ATOM O2 ON1C -0.20 ! / | \ / \ +ATOM N3 NN3 -0.16 ! H3B3 H3A2 N3 C5-H5 +ATOM C4 CN2 0.64 ! | || +ATOM N4 NN1 -0.78 ! C2 C6 +ATOM H41 HN1 0.48 ! //\ / \ +ATOM H42 HN1 0.37 ! O2 N1 H6 +ATOM C5 CN3 -0.02 ! | +ATOM H5 HN3 0.07 ! H1 +ATOM C3A CN8 -0.18 ! +ATOM H3A1 HN8 0.09 ! +ATOM H3A2 HN8 0.09 ! +ATOM C3B CN9 -0.27 ! +ATOM H3B1 HN9 0.09 ! +ATOM H3B2 HN9 0.09 ! +ATOM H3B3 HN9 0.09 ! + +BOND N3 C3A C3A H3A1 C3A H3A2 C3A C3B C3B H3B1 C3B H3B2 C3B H3B3 +BILD N1 C2 N3 C3A 0.0 0.0 180.0 0.0 0.0 +BILD C2 N3 C3A C3B 0.0 0.0 90.0 0.0 0.0 +BILD N3 C3B *C3A H3A1 0.0 0.0 120.0 0.0 0.0 +BILD N3 C3B *C3A H3A2 0.0 0.0 240.0 0.0 0.0 +BILD N3 C3A C3B H3B1 0.0 0.0 180.0 0.0 0.0 +BILD C3A H3B1 *C3B H3B2 0.0 0.0 120.0 0.0 0.0 +BILD C3A H3B1 *C3B H3B3 0.0 0.0 240.0 0.0 0.0 + +PRES CetG 0.92 ! Create ethyl link between CYT N3 and GUA N1 + ! adm jr. w/Daniel Barsky + ! + ! residue 1: cyt, residue 2 gua + ! PATCh CETG dna1 1 dna2 1 setup warn + ! use in patch statement, followed by AUTOgenerate + ! angles dihedrals in c25 and later versions +! Delete guanine H1 atom ! +DELE ATOM 2H1 ! +! +GROUP ! H41 H42 +ATOM 1N1 NN2 -0.12 ! \ / +ATOM 1C6 CN3 0.14 ! H3B1 H3A1 N4 +ATOM 1H6 HN3 0.20 ! \ | | +ATOM 1C2 CN1 0.38 ! H3B2--C3B--C3A C4 +ATOM 1O2 ON1C -0.20 ! / | \ / \ +ATOM 1N3 NN3 -0.16 ! H3B3 H3A2 N3 C5-H5 +ATOM 1C4 CN2 0.64 ! | || +ATOM 1N4 NN1 -0.78 ! C2 C6 +ATOM 1H41 HN1 0.48 ! //\ / \ +ATOM 1H42 HN1 0.37 ! O2 N1 H6 +ATOM 1C5 CN3 -0.02 ! | +ATOM 1H5 HN3 0.07 ! H1 +GROUP +ATOM 1C3A CN8 -0.18 ! +ATOM 1H3A1 HN8 0.09 ! +ATOM 1H3A2 HN8 0.09 ! +ATOM 1C3B CN8 -0.18 ! +ATOM 1H3B1 HN8 0.09 ! +ATOM 1H3B2 HN8 0.09 ! +GROUP +ATOM 2N1 NN2G -0.08 + +BOND 1N3 1C3A 1C3A 1C3B 1C3B 2N1 +BOND 1C3A 1H3A1 1C3A 1H3A2 1C3B 1H3B1 1C3B 1H3B2 + +!ic build from the cytosine +BILD 1N1 1C2 1N3 1C3A 0.0 0.0 180.0 0.0 0.0 +BILD 1C2 1N3 1C3A 1C3B 0.0 0.0 90.0 0.0 0.0 +BILD 1N3 1C3B *1C3A 1H3A1 0.0 0.0 120.0 0.0 0.0 +BILD 1N3 1C3B *1C3A 1H3A2 0.0 0.0 240.0 0.0 0.0 +BILD 1N3 1C3A 1C3B 1H3B1 0.0 0.0 180.0 0.0 0.0 +BILD 1C3A 1H3B1 *1C3B 1H3B2 0.0 0.0 120.0 0.0 0.0 + +RESI CYTP 1.00 ! To Protonate C5-Me CYT at N3, edarian 2009-03 +GROUP +ATOM N1 NN2 -0.13 ! H42 H41 +ATOM C6 CN3 0.10 ! \ / +ATOM H6 HN3 0.24 ! HM51 N4 +ATOM C2 CN1 0.64 ! \ | +ATOM O2 ON1C -0.34 !HM52--C5M C4 H3 +ATOM N3 NN2G -0.72 ! / \ / \\ / +ATOM H3 HN2 0.42 ! HM53 C5 N3 (Change NN3 to NN3C to adjust C2-N3 bond)? +ATOM C4 CN2 0.90 ! || | +ATOM N4 NN1 -0.75 ! H6-C6 C2 +ATOM H41 HN1 0.37 ! \ / \\ +ATOM H42 HN1 0.33 ! N1 O2 +ATOM C5 CN3D -0.11 ! | +ATOM C5M CN9 -0.22 ! CM1 +ATOM HM51 HN9 0.09 ! / | \ +ATOM HM52 HN9 0.09 ! HM11 HM12 HM13 +ATOM HM53 HN9 0.09 +GROUP +ATOM CM1 CN9 -0.27 +ATOM HM11 HN9 0.09 +ATOM HM12 HN9 0.09 +ATOM HM13 HN9 0.09 +BOND N1 C2 N1 C6 C2 N3 N3 C4 C4 C5 +BOND C5 C6 N1 CM1 C2 O2 C4 N4 C5 C5M +BOND CM1 HM11 CM1 HM12 CM1 HM13 +BOND N3 H3 +BOND N4 H41 N4 H42 +BOND C5M HM51 C5M HM52 C5M HM53 +BOND C6 H6 +IMPR C2 N1 N3 O2 C4 N3 C5 N4 +IMPR N4 C4 H41 H42 +BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +BILD C4 C2 *N3 H3 0.0 0.0 180.0 0.0 0.0 +BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +BILD C6 C4 *C5 C5M 0.0 0.0 180.0 0.0 0.0 +BILD C4 C5 C5M HM51 0.0 0.0 180.0 0.0 0.0 +BILD C5 HM51 *C5M HM52 0.0 0.0 115.0 0.0 0.0 +BILD HM51 HM52 *C5M HM53 0.0 0.0 -115.0 0.0 0.0 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +BILD C6 C2 *N1 C1M 0.0 0.0 180.0 0.0 0.0 +BILD C6 N1 C1M HM11 0.0 0.0 180.0 0.0 0.0 +BILD N1 HM11 *C1M HM12 0.0 0.0 115.0 0.0 0.0 +BILD HM11 HM12 *C1M HM13 0.0 0.0 -115.0 0.0 0.0 + +PRES CNH3 1.24 ! Patch to convert methylated cytosine CYTP to protonated + ! cytosine at N3. Need to change some atom types and charges +GROUP +ATOM C6 CN3 0.10 ! change charge +ATOM H6 HN3 0.24 ! change charge +ATOM C2 CN1 0.64 ! change charge +ATOM O2 ON1C -0.34 ! change charge +ATOM N3 NN2G -0.72 ! change charge, atom type +ATOM H3 HN2 0.42 ! new +ATOM C4 CN2 0.90 ! change charge + +BOND N3 H3 +BILD C4 C2 *N3 H3 0.0 0.0 180.0 0.0 0.0 + +RESI CYTH 1.00 ! To Protonate CYT at N3, edarian 2009-03 +GROUP +ATOM N1 NN2 -0.08 ! H42 H41 +ATOM C6 CN3 0.03 ! \ / +ATOM H6 HN3 0.27 ! N4 +ATOM C5 CN3 -0.19 ! | +ATOM H5 HN3 0.09 ! C4 H3 +ATOM C2 CN1 0.48 ! / \\ / +ATOM O2 ON1C -0.30 ! H5--C5 N3 (Change NN3 to NN3C to adjust C2-N3 bond)? +ATOM N3 NN2G -0.62 ! || | +ATOM H3 HN2 0.42 ! H6--C6 C2 +ATOM C4 CN2 0.85 ! \ / \\ +ATOM N4 NN1 -0.65 ! N1 O2 +ATOM H41 HN1 0.37 ! | +ATOM H42 HN1 0.33 ! C1M +GROUP ! / | \ +ATOM C1M CN9 -0.27 ! HM11 HM12 HM13 +ATOM H11M HN9 0.09 ! +ATOM H12M HN9 0.09 ! +ATOM H13M HN9 0.09 +BOND N1 C2 N1 C6 C2 N3 N3 C4 C4 C5 +BOND C5 C6 N1 C1M C2 O2 C4 N4 +BOND C1M H11M C1M H12M C1M H13M +BOND N3 H3 +BOND N4 H41 N4 H42 +BOND C5 H5 +BOND C6 H6 +IMPR C2 N1 N3 O2 C4 N3 C5 N4 +IMPR N4 C4 H41 H42 +BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +BILD C4 C2 *N3 H3 0.0 0.0 180.0 0.0 0.0 +BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +BILD C6 C2 *N1 C1M 0.0 0.0 180.0 0.0 0.0 +BILD C6 N1 C1M H11M 0.0 0.0 180.0 0.0 0.0 +BILD N1 H11M *C1M H12M 0.0 0.0 115.0 0.0 0.0 +BILD H11M H12M *C1M H13M 0.0 0.0 -115.0 0.0 0.0 + +RESI N4EM 0.00 ! C5-Me CYT with N4-Ethyl-Methyl, edarian 2009-06 +GROUP ! model compound for CYT-EtGUA +ATOM N1 NN2 -0.13 ! +ATOM C6 CN3 -0.09 ! +ATOM H6 HN3 0.18 ! H411 H412 +ATOM C2 CN1 0.77 ! \ / +ATOM O2 ON1C -0.57 ! H42 C41 H421 +ATOM N3 NN3 -0.65 ! \ / \ / +ATOM C4 CN2 0.52 ! HM51 N4 C42 -- H422 +ATOM N4 NN1 -0.52 ! \ | \ +ATOM H42 HN1 0.33 ! HM52--C5M C4 H423 +ATOM C5 CN3D -0.11 ! / \ / \\ +ATOM C5M CN9 -0.22 ! HM53 C5 N3 +ATOM HM51 HN9 0.09 ! || | +ATOM HM52 HN9 0.09 ! H6-C6 C2 +ATOM HM53 HN9 0.09 ! \ / \\ +GROUP ! N1 O2 +ATOM CM1 CN9 -0.27 ! | +ATOM HM11 HN9 0.09 ! CM1 +ATOM HM12 HN9 0.09 ! / | \ +ATOM HM13 HN9 0.09 ! HM11 HM12 HM13 +GROUP +ATOM C41 CN8 0.04 +ATOM H411 HN8 0.09 +ATOM H412 HN8 0.09 +ATOM C42 CN9 -0.27 +ATOM H421 HN9 0.09 +ATOM H422 HN9 0.09 +ATOM H423 HN9 0.09 +BOND N1 C2 N1 C6 C2 N3 N3 C4 C4 C5 +BOND C5 C6 N1 CM1 C2 O2 C4 N4 C5 C5M +BOND N4 C41 C41 C42 +BOND CM1 HM11 CM1 HM12 CM1 HM13 +BOND C5M HM51 C5M HM52 C5M HM53 +BOND C6 H6 +BOND N4 H42 +BOND C41 H411 C41 H412 +BOND C42 H421 C42 H422 C42 H423 +!DOUBLE C5 C6 N3 C4 C2 O2 +IMPR C2 N1 N3 O2 C4 N3 C5 N4 +IMPR N4 C4 C41 H42 +BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +BILD C5 N3 *C4 N4 1.426 121.8 180.0 118.9 1.337 +BILD N3 C4 N4 C41 0.0 0.0 0.0 0.0 0.0 +BILD C41 C4 *N4 H42 0.0 0.0 150.0 0.0 0.0 +BILD C4 N4 C41 C42 0.0 0.0 -160.0 0.0 0.0 +BILD C42 N4 *C41 H411 0.0 0.0 120.0 0.0 0.0 +BILD C42 N4 *C41 H412 0.0 0.0 -120.0 0.0 0.0 +BILD N4 C41 C42 H423 0.0 0.0 -180.0 0.0 0.0 +BILD H423 C41 *C42 H421 0.0 0.0 120.0 0.0 0.0 +BILD H423 C41 *C42 H422 0.0 0.0 -120.0 0.0 0.0 +BILD C6 C4 *C5 C5M 0.0 0.0 180.0 0.0 0.0 +BILD C4 C5 C5M HM51 0.0 0.0 180.0 0.0 0.0 +BILD C5 HM51 *C5M HM52 0.0 0.0 115.0 0.0 0.0 +BILD HM51 HM52 *C5M HM53 0.0 0.0 -115.0 0.0 0.0 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +BILD C6 C2 *N1 C1M 0.0 0.0 180.0 0.0 0.0 +BILD C6 N1 C1M HM11 0.0 0.0 180.0 0.0 0.0 +BILD N1 HM11 *C1M HM12 0.0 0.0 115.0 0.0 0.0 +BILD HM11 HM12 *C1M HM13 0.0 0.0 -115.0 0.0 0.0 + +PRES 4EG1 0.86 ! Patch to add Ethyl-Guanidinium tail to CYT at N4, edarian 2009-06 + ! Need to change some atom types (stream toppar_pres_4eg.str for parameters) + ! Addjust charge accordingly +DELE ATOM H41 +GROUP +ATOM C41 CN8 0.04 +ATOM H411 HN8 0.09 +ATOM H412 HN8 0.09 +ATOM C42 CN8 0.20 +ATOM H421 HN8 0.09 +ATOM H422 HN8 0.09 +ATOM N43 NNG -0.70 ! NEW atom type +ATOM H43 HN1 0.44 +ATOM C44 CNG 0.64 ! NEW atom type +ATOM N44 NNG -0.80 ! NEW atom type +ATOM H441 HN1 0.46 +ATOM H442 HN1 0.46 +ATOM N45 NNG -0.80 ! NEW atom type +ATOM H451 HN1 0.46 +ATOM H452 HN1 0.46 +ATOM C6 CN3 -0.09 ! change charge +ATOM H6 HN3 0.18 ! change charge +ATOM C2 CN1 0.77 ! change charge +ATOM O2 ON1C -0.57 ! change charge +ATOM N3 NN3 -0.65 ! change charge +ATOM C4 CN2 0.52 ! change charge +ATOM N4 NN1 -0.52 ! change charge +BOND N4 C41 C41 C42 C42 N43 N43 C44 C44 N44 +BOND C44 N45 +BOND C41 H411 C41 H412 +BOND C42 H421 C42 H422 +BOND N43 H43 +BOND N44 H441 N44 H442 +BOND N45 H451 N45 H452 +!DOUBLE C44 N44 +IMPR N4 C4 C41 H42 +BILD N3 C4 N4 C41 0.0 0.0 0.0 0.0 0.0 +BILD C41 C4 *N4 H42 0.0 0.0 150.0 0.0 0.0 +BILD C4 N4 C41 C42 0.0 0.0 -160.0 0.0 0.0 +BILD C42 N4 *C41 H411 0.0 0.0 120.0 0.0 0.0 +BILD C42 N4 *C41 H412 0.0 0.0 -120.0 0.0 0.0 +BILD N4 C41 C42 N43 0.0 0.0 -180.0 0.0 0.0 +BILD N43 C41 *C42 H421 0.0 0.0 120.0 0.0 0.0 +BILD N43 C41 *C42 H422 0.0 0.0 -120.0 0.0 0.0 +BILD C41 C42 N43 C44 0.0 0.0 109.0 0.0 0.0 +BILD C44 C42 *N43 H43 0.0 0.0 140.0 0.0 0.0 +BILD C42 N43 C44 N44 0.0 0.0 180.0 0.0 0.0 +BILD N43 C44 N44 H441 0.0 0.0 -178.0 0.0 0.0 +BILD H441 C44 *N44 H442 0.0 0.0 171.0 0.0 0.0 +BILD N44 N43 *C44 N45 0.0 0.0 178.0 0.0 0.0 +BILD N44 C44 N45 H451 0.0 0.0 -174.0 0.0 0.0 +BILD H451 C44 *N45 H452 0.0 0.0 166.0 0.0 0.0 +!BILD C42 N43 C44 N45 0.0 0.0 -40.0 0.0 0.0 +!BILD N43 C44 N45 H451 0.0 0.0 -175.0 0.0 0.0 +!BILD N45 C44 N44 H441 0.0 0.0 170.0 0.0 0.0 +!BILD H441 C44 *N44 H442 0.0 0.0 180.0 0.0 0.0 +!BILD H451 C44 *N45 H452 0.0 0.0 125.0 0.0 0.0 + +PRES G8AP 0.41 ! N-[deoxy-guanosin-8-yl]-p-AminoPhenyl + ! Use 9MG patch to add Methyl group at N9 (or PURG to add H9) +GROUP ! +ATOM C8 CN4 0.45 !charge changed by patch G8AP +ATOM N8 NN1 -0.42 !replaces H8 +ATOM H81 HN2 0.33 ! H14 +ATOM C82 CN3 0.05 ! | +GROUP ! C14 +ATOM C10 CN3 -0.115 ! // \ +ATOM H10 HN3 0.115 ! H12-C12 C13-H13 +GROUP ! O6 | || +ATOM C11 CN3 -0.115 ! || H10-C10 C11-H11 +ATOM H11 HN3 0.115 ! C6 \\ / +GROUP ! / \ C82 +ATOM C12 CN3 -0.115 ! H1-N1 C5--N7\\ / +ATOM H12 HN3 0.115 ! | || C8--N8 +GROUP ! C2 C4--N9/ \ +ATOM C13 CN3 -0.115 ! / \\ / \ H81 +ATOM H13 HN3 0.115 ! H21-N2 N3 C9 +GROUP ! | / | \ +ATOM C14 CN3 -0.115 ! H22 H91 H92 H93 +ATOM H14 HN3 0.115 ! + +DELE ATOM H8 + +BOND C8 N8 N8 C82 C82 C10 C10 C12 +BOND C12 C14 C14 C13 C13 C11 C11 C82 +BOND N8 H81 C10 H10 C11 H11 C12 H12 C13 H13 C14 H14 + +IC N9 N7 *C8 N8 0.0000 0.00 180.00 0.00 0.0000 +IC N9 C8 N8 C82 0.0000 0.00 180.00 0.00 0.0000 +IC C82 C8 *N8 H81 0.0000 0.00 130.00 0.00 0.0000 +IC C8 N8 C82 C11 0.0000 0.00 180.00 0.00 0.0000 +IC N8 C82 C11 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C82 C11 C13 C14 0.0000 0.00 0.00 0.00 0.0000 +IC N8 C11 *C82 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C82 C10 C12 0.0000 0.00 0.00 0.00 0.0000 +IC C13 C82 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C11 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C14 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C82 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 *C14 H14 0.0000 0.00 180.00 0.00 0.0000 + +RESI DFT 0.00 ! Difluorotoluene + ! adm jr. w/Daniel Barsky + ! +GROUP ! +ATOM C1 CNA -0.24 ! F4 +ATOM C2 CNA2 0.28 ! | +ATOM C3 CNA -0.24 ! H51 C4 H3 +ATOM C4 CNA2 0.22 ! \ / \\ / +ATOM C5 CNA 0.10 ! H52--C5M-C5 C3 +ATOM C6 CNA -0.28 ! / || | +ATOM H1 HNP 0.21 ! H52 C6 C2 +ATOM F2 FNA -0.21 ! / \ // \ +ATOM H3 HN3 0.19 ! H6 C1 F2 +ATOM F4 FNA -0.21 ! | +ATOM C5M CN9 -0.24 ! H1 +ATOM H51 HN9 0.07 ! +ATOM H52 HN9 0.07 ! +ATOM H53 HN9 0.07 ! +ATOM H6 HNP 0.21 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C1 H1 C2 F2 C3 H3 C4 F4 C5 C5M C6 H6 +BOND C5M H51 C5M H52 C5M H53 +BILD C1 C2 C3 C4 0.00 0.00 0.00 0.00 0.00 +BILD C2 C3 C4 C5 0.00 0.00 0.00 0.00 0.00 +BILD C3 C4 C5 C6 0.00 0.00 0.00 0.00 0.00 +BILD C4 C5 C6 C1 0.00 0.00 0.00 0.00 0.00 +BILD C5 C6 C1 C2 0.00 0.00 0.00 0.00 0.00 +BILD C6 C1 C2 C3 0.00 0.00 0.00 0.00 0.00 +BILD C3 C2 C1 H1 0.00 0.00 180.00 0.00 0.00 +BILD C4 C3 C2 F2 0.00 0.00 180.00 0.00 0.00 +BILD C5 C4 C3 H3 0.00 0.00 180.00 0.00 0.00 +BILD C6 C5 C4 F4 0.00 0.00 180.00 0.00 0.00 +BILD C3 C4 C5 C5M 0.00 0.00 180.00 0.00 0.00 +BILD C4 C5 C6 H6 0.00 0.00 180.00 0.00 0.00 +BILD C4 C5 C5M H51 0.00 0.00 180.00 0.00 0.00 +BILD H51 C5 *C5M H52 0.00 0.00 60.00 0.00 0.00 +BILD H51 C5 *C5M H53 0.00 0.00 240.00 0.00 0.00 + +PRES DFTO 0.00 ! patch to convert THY to Difluorotoluene + ! adm jr. w/Daniel Barsky + ! + ! use in patch statement, followed by AUTOgenerate + ! angles dihedrals in c25 and later versions + ! atom ordering to match ab initio + ! not MMFF compatible + ! +! prior to invoking this patch the following atom RENAME +! must be performed where segid and residue are changed +! to the name and number corresponding to the THY being +! converted +!rename atom f2 sele atom segid residue o2 end +!rename atom f4 sele atom segid residue o4 end +!rename atom c1 sele atom segid residue n1 end +!rename atom c3 sele atom segid residue n3 end +! The next RENAME command can be used to change +! the residue name from THY to DFT +!rename resn DFT sele segid "segid" .and. resi "residue" end +! +GROUP ! +ATOM C1 CNA -0.03 ! F4 +ATOM C2 CNA2 0.28 ! | +ATOM C3 CNA -0.24 ! H51 C4 H3 +ATOM C4 CNA2 0.22 ! \ / \\ / +ATOM C5 CNA 0.10 ! H52--C5M-C5 C3 +ATOM C6 CNA -0.28 ! / || | +ATOM F2 FNA -0.21 ! H52 C6 C2 +ATOM H3 HN3 0.19 ! / \ // \ +ATOM F4 FNA -0.21 ! H6 C1 F2 +ATOM C5M CN9 -0.24 ! | +ATOM H51 HN9 0.07 ! R +ATOM H52 HN9 0.07 ! +ATOM H53 HN9 0.07 ! +ATOM H6 HNP 0.21 ! +! delete impropers leftover from THY due to use of rename atom +DELE IMPR C5 C4 C6 C5M +DELE IMPR C4 C3 C5 F4 +DELE IMPR C2 C1 C3 F2 + +RESI DFB 0.00 ! Difluorobenzene + ! adm jr. w/Daniel Barsky + ! + ! atom numbering based in difluorotoluene + ! not MMFF compatible +GROUP ! +ATOM C1 CNA -0.26 ! F4 +ATOM H1 HNP 0.23 ! | +ATOM C2 CNA2 0.27 ! H5 C4 H3 +ATOM F2 FNA -0.19 ! \ / \\ / +ATOM C3 CNA -0.23 ! C5 C3 +ATOM H3 HN3 0.19 ! || | +ATOM C4 CNA2 0.27 ! C6 C2 +ATOM F4 FNA -0.19 ! / \ // \ +ATOM C5 CNA -0.26 ! H6 C1 F2 +ATOM H5 HNP 0.23 ! | +ATOM C6 CNA -0.32 ! H1 +ATOM H6 HNP 0.26 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C1 H1 C2 F2 C3 H3 C4 F4 C5 H5 C6 H6 + +BILD C1 C2 C3 C4 0.00 0.00 0.00 0.00 0.00 +BILD C2 C3 C4 C5 0.00 0.00 0.00 0.00 0.00 +BILD C3 C4 C5 C6 0.00 0.00 0.00 0.00 0.00 +BILD C4 C5 C6 C1 0.00 0.00 0.00 0.00 0.00 +BILD C5 C6 C1 C2 0.00 0.00 0.00 0.00 0.00 +BILD C6 C1 C2 C3 0.00 0.00 0.00 0.00 0.00 +BILD C3 C2 C1 H1 0.00 0.00 180.00 0.00 0.00 +BILD C4 C3 C2 F2 0.00 0.00 180.00 0.00 0.00 +BILD C5 C4 C3 H3 0.00 0.00 180.00 0.00 0.00 +BILD C6 C5 C4 F4 0.00 0.00 180.00 0.00 0.00 +BILD C3 C4 C5 H5 0.00 0.00 180.00 0.00 0.00 +BILD C4 C5 C6 H6 0.00 0.00 180.00 0.00 0.00 + +! modified thymine patches for DNA strand separation calculations + +PRES THYM 0.00 ! Modified thymine with ethylene on C5 + ! adm jr. + ! + ! patch to create the isolated base + ! use in patch statement, followed by AUTOgenerate + ! angles dihedrals in c25 and later versions + ! +! Delete thymine C5M, H51, H52, H53 atoms +DELE ATOM C5M ! +DELE ATOM H51 ! +DELE ATOM H52 ! +DELE ATOM H53 ! +GROUP ! +ATOM N1 NN2B -0.80 ! +ATOM C6 CN3 0.17 ! +ATOM C5 CN3T -0.10 ! O4 +ATOM C4 CN1 0.50 ! || +ATOM N3 NN2U -0.46 ! C4 H5A1 H5B1 +ATOM C2 CN1T 0.51 ! / \ / / +ATOM O2 ON1 -0.41 ! H3-N3 C5-C5A==C5B +ATOM H3 HN2 0.36 ! | || \ +ATOM O4 ON1 -0.45 ! C2 C6 H5B2 +ATOM H6 HN3 0.17 ! //\ / \ +ATOM H1 HN2 0.46 ! O2 N1 H6 +ATOM C5A CNE1 -0.06 ! | +ATOM C5B CNE2 -0.32 ! H1 +ATOM H5A1 HNE1 0.14 ! +ATOM H5B1 HNE2 0.16 ! +ATOM H5B2 HNE2 0.13 ! + +BOND C5 C5A C5A H5A1 C5B H5B1 C5B H5B2 +DOUBLE C5A C5B + +BILD N3 C4 C5 C5A 0.0 0.0 180.0 0.0 0.0 +BILD C6 C5 C5A C5B 0.0 0.0 0.0 0.0 0.0 +BILD C5B C5 *C5A H5A1 0.0 0.0 180.0 0.0 0.0 +BILD C5 C5A C5B H5B1 0.0 0.0 180.0 0.0 0.0 +BILD H5B1 C5A *C5B H5B2 0.0 0.0 180.0 0.0 0.0 + +PRES THYE 0.00 ! patch to convert thymine to c5-ethylene + ! thymine in DNA + ! adm jr. + ! + ! use in patch statement, followed by AUTOgenerate + ! angles dihedrals in c25 and later versions + ! +! Delete thymine C5M, H51, H52, H53 atoms +DELE ATOM C5M ! +DELE ATOM H51 ! +DELE ATOM H52 ! +DELE ATOM H53 ! +GROUP ! +ATOM N1 NN2B -0.34 ! +ATOM C6 CN3 0.17 ! +ATOM C5 CN3T -0.10 ! O4 +ATOM C4 CN1 0.50 ! || +ATOM N3 NN2U -0.46 ! C4 H5A1 H5B1 +ATOM C2 CN1T 0.51 ! / \ / / +ATOM O2 ON1 -0.41 ! H3-N3 C5-C5A==C5B +ATOM H3 HN2 0.36 ! | || \ +ATOM O4 ON1 -0.45 ! C2 C6 H5B2 +ATOM H6 HN3 0.17 ! //\ / \ +ATOM C5A CNE1 -0.06 ! O2 N1 H6 +ATOM C5B CNE2 -0.32 ! | +ATOM H5A1 HNE1 0.14 ! R +ATOM H5B1 HNE2 0.16 ! +ATOM H5B2 HNE2 0.13 ! + +BOND C5 C5A C5A H5A1 C5B H5B1 C5B H5B2 +DOUBLE C5A C5B + +BILD N3 C4 C5 C5A 0.0 0.0 180.0 0.0 0.0 +BILD C6 C5 C5A C5B 0.0 0.0 0.0 0.0 0.0 +BILD C5B C5 *C5A H5A1 0.0 0.0 180.0 0.0 0.0 +BILD C5 C5A C5B H5B1 0.0 0.0 180.0 0.0 0.0 +BILD H5B1 C5A *C5B H5B2 0.0 0.0 180.0 0.0 0.0 + +!backbone section + +!PNA calculations + +PRES 25P1 -1.00 ! patch to convert a 3'-5' phosphodiester RNA + ! linkage to a 2'-5' phosphodiester linkage + ! Note that this can be used for DNA, just don't convert + ! the 5' base to RNA (via PRES DEO1) prior to invoking + ! this patch + ! Use AUTOgenerate ANGLes DIHEdrals following application +DELE ATOM 1O3' +DELE ATOM 1H2' ! previous O2' hydroxyl H +GROUP +ATOM 1C3' CN8 -0.18 +ATOM 1H3' HN8 0.09 +ATOM 1H3'' HN8 0.09 +GROUP +ATOM 1C2' CN7B 0.01 +ATOM 1H2'' HN7 0.09 +ATOM 1O2' ON2 -0.57 +ATOM 2P P 1.50 +ATOM 2O1P ON3 -0.78 +ATOM 2O2P ON3 -0.78 +ATOM 2O5' ON2 -0.57 +ATOM 2C5' CN8B -0.08 +ATOM 2H5' HN8 0.09 +ATOM 2H5'' HN8 0.09 + +bond 1c3' 1h3'' +bond 1o2' 2p + +ic 1C2' 1C4' *1C3' H3'' 0.0000 000.00 -124.08 000.00 0.0000 + +RESI BPET -2.00 ! Bis-methylphosphate-ethane + ! adm jr., w/Daniel Barsky +GROUP ! +ATOM C1 CN9 -0.17 ! H11 +ATOM H11 HN9 0.09 ! | +ATOM H12 HN9 0.09 ! H13-C1-H12 +ATOM H13 HN9 0.09 ! \ +ATOM O2 ON2 -0.57 ! O31 O2 +ATOM P3 P 1.50 ! \\ / +ATOM O31 ON3 -0.78 ! (-) P3 +ATOM O32 ON3 -0.78 ! // \ +ATOM O4 ON2 -0.57 ! O32 O4 +ATOM C5 CN8 -0.08 ! / +ATOM H51 HN8 0.09 ! H51-C5-H52 +ATOM H52 HN8 0.09 ! | +ATOM C6 CN8 -0.08 ! H51-C6-H52 +ATOM H61 HN8 0.09 ! \ +ATOM H62 HN8 0.09 ! O81 O7 +ATOM O7 ON2 -0.57 ! \\ / +ATOM P8 P 1.50 ! (-) P8 +ATOM O81 ON3 -0.78 ! // \ +ATOM O82 ON3 -0.78 ! O82 O9 +ATOM O9 ON2 -0.57 ! / +ATOM C10 CN9 -0.17 ! H101-C10-H102 +ATOM H101 HN9 0.09 ! | +ATOM H102 HN9 0.09 ! H103 +ATOM H103 HN9 0.09 ! + +BOND C1 O2 O2 P3 P3 O4 O4 C5 C5 C6 C6 O7 +BOND O7 P8 P8 O9 O9 C10 P3 O31 P3 O32 +BOND P8 O81 P8 O82 +BOND C1 H11 C1 H12 C1 H13 C5 H51 C5 H52 +BOND C6 H61 C6 H62 C10 H101 C10 H102 C10 H103 +!from IC generate +IC H11 C1 O2 P3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O2 P3 O4 0.0000 0.00 180.00 0.00 0.0000 +IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC O4 O2 *P3 O31 0.0000 0.00 120.00 0.00 0.0000 +IC O4 O2 *P3 O32 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 P3 O4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC P3 O4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 O4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C6 O4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC O4 C5 C6 O7 0.0000 0.00 180.00 0.00 0.0000 +IC O7 C5 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC O7 C5 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C6 O7 P8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 O7 P8 O9 0.0000 0.00 180.00 0.00 0.0000 +IC O9 O7 *P8 O81 0.0000 0.00 120.00 0.00 0.0000 +IC O9 O7 *P8 O82 0.0000 0.00 -120.00 0.00 0.0000 +IC O7 P8 O9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC P8 O9 C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC H101 O9 *C10 H102 0.0000 0.00 120.00 0.00 0.0000 +IC H101 O9 *C10 H103 0.0000 0.00 -120.00 0.00 0.0000 + +RESI ABNS 0.00 ! abasic deoxyribose nucleoside (susil) + ! adm jr., w/Daniel Barsky +GROUP ! +ATOM H5T HN5 0.43 ! +ATOM O5' ON5 -0.66 ! +ATOM C5' CN8B 0.05 ! H5T +ATOM H51' HN8 0.09 ! \ +ATOM H52' HN8 0.09 ! H51' O5' +ATOM C4' CN7 0.16 ! \ / +ATOM H42' HN7 0.09 ! H52'--C5' O4' H11' +ATOM O4' ON6 -0.50 ! \ / \ / +ATOM C1' CN8B 0.07 ! H42'-C4' C1'-H12' +ATOM H11' HN8 0.09 ! | | +ATOM H12' HN8 0.09 ! C3'---C2'-H21' +ATOM C2' CN8 -0.18 ! / | \ +ATOM H21' HN8 0.09 ! O3' H31' H22' +ATOM H22' HN8 0.09 ! | +ATOM C3' CN7 0.14 ! H32' +ATOM H31' HN7 0.09 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 + +BOND O4' C4' O4' C1' C4' C5' C4' H42' C4' C3' +BOND C1' H11' C1' H12' C1' C2' C2' H21' C2' H22' +BOND C3' H31' C3' O3' O3' H32' C5' O5' C5' H51' +BOND C5' H52' O5' H5T C2' C3' + +BILD O4' C1' C2' C3' 1.433 104.1 41.2 100.9 1.525 +BILD C1' C2' C3' C4' 1.521 100.9 325.1 102.6 1.533 +BILD C2' C3' C4' C5' 1.525 102.6 257.8 113.7 1.513 +BILD C3' C4' C5' O5' 1.534 113.7 46.5 108.2 1.428 +BILD C4' C5' O5' H5T 1.513 108.2 170.4 107.7 0.971 +BILD C3' C4' C5' H52' 1.534 113.7 167.5 108.4 1.098 +BILD C3' C4' C5' H51' 1.534 113.7 285.5 109.1 1.101 +BILD C2' C3' C4' H42' 1.525 102.6 135.9 108.6 1.099 +BILD C1' C2' C3' H31' 1.521 100.9 204.2 113.0 1.097 +BILD C1' C2' C3' O3' 1.521 100.9 78.3 111.7 1.434 +BILD C2' C3' O3' H32' 1.525 111.7 65.4 107.1 0.973 +BILD O4' C1' C2' H22' 1.433 104.1 162.1 113.9 1.096 +BILD O4' C1' C2' H21' 1.433 104.1 285.5 110.1 1.093 +BILD O4' C1' C2' H11' 1.433 104.1 243.2 26.8 2.209 +BILD O4' C1' C2' H12' 1.433 104.1 119.0 28.2 2.173 + +RESi THF2 0.000 ! THF-2'OME, delete H22'->OM neutral, edarian, 2009-07 + ! Change C2' and H21' type +GROUP +ATOM O4' ON6B -0.40 ! H41' O4' H11' +ATOM C4' CN7 0.02 ! \ / \ / +ATOM C3' CN7 -0.18 ! H42'--C4' C1'--H12' +ATOM C1' CN7B 0.02 ! | | +ATOM H11' HN7 0.09 ! H31'--C3'--C2'--H21' +ATOM H12' HN7 0.09 ! / | +ATOM H31' HN7 0.09 ! H32' O2' (changed OM to O2') +ATOM H32' HN7 0.09 ! | +ATOM H41' HN7 0.09 ! CM +ATOM H42' HN7 0.09 ! / | \ +GROUP ! HM1 HM2 HM3 +ATOM C2' CN7B 0.12 ! +ATOM H21' HN7 0.09 ! +ATOM O2' ON2M -0.36 ! +ATOM CM CN9 -0.12 ! +ATOM HM1 HN9 0.09 ! +ATOM HM2 HN9 0.09 ! +ATOM HM3 HN9 0.09 ! + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H11' C1' H12' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C2' H21' O2' C2' O2' CM +BOND CM HM1 CM HM2 CM HM3 +! IC table print from thf2om_mp2.pdb optimized +IC C1' O4' C4' C3' 0.0000 0.00 36.00 0.00 0.0000 +IC C3' O4' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC C4' O4' C1' C2' 0.0000 0.00 -19.00 0.00 0.0000 +IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' O2' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' C4' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 +ic O2' C2' C1' O4' 0.0000 0.00 105.00 0.00 0.0000 +ic C1' C2' O2' CM 0.0000 0.00 165.00 0.00 0.0000 +ic C2' O2' CM HM1 0.0000 0.00 55.00 0.00 0.0000 +ic C1' O2' *C2' H21' 0.0000 0.00 -120.00 0.00 0.0000 +ic HM1 O2' *CM HM2 0.0000 0.00 118.00 0.00 0.0000 +ic HM3 O2' *CM HM2 0.0000 0.00 -120.00 0.00 0.0000 + +PRES MEO 0.000 ! Patch to make 2'-OMe in deoxyribose for Nucleic Acids +DELETE ATOM H2' + +GROUP +ATOM C2' CN7B 0.12 ! changed from CN7B to CN7 to use in URA +ATOM H2'' HN7 0.09 +ATOM O2' ON2M -0.36 +ATOM CM CN9 -0.12 +ATOM HM1 HN9 0.09 +ATOM HM2 HN9 0.09 +ATOM HM3 HN9 0.09 + +BOND O2' CM +BOND CM HM1 CM HM2 CM HM3 +! Minimized IC of 2-OMe with THF in cgenff +!IC O2' C2' C1' O4' 1.4225 108.81 105.92 107.60 1.4342 +IC C1' C2' O2' CM 1.5299 108.81 171.56 113.00 1.4247 +IC C2' O2' CM HM1 1.4225 113.00 116.79 109.58 1.1114 +IC C1' O2' *C2' H2'' 1.5299 108.81 -125.32 112.51 1.0998 +IC HM1 O2' *CM HM2 1.1114 109.58 120.34 109.40 1.1114 +IC HM3 O2' *CM HM2 1.1120 111.89 -119.52 109.40 1.1114 + + +PRES ABNP 0.00 ! patch to convert a standard base into an abasic furanose + ! adm jr., w/Daniel Barsky + ! + ! Note 1) apply patch PRES DELB prior to this patch +GROUP +ATOM C4' CN7 0.16 +ATOM H4' HN7 0.09 +ATOM O4' ON6 -0.50 +ATOM C1' CN8B 0.07 +ATOM H1' HN8 0.09 +ATOM H1'' HN8 0.09 +BOND C1' H1'' +!BILD H1'' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.9 !orig +!BILD H1'' *C1' C2' H1' 0.0 0.0 -115.0 0.0 0.9 !<-new db(3/11/99) +BILD H1'' C2' *C1' H1' 0.0 0.0 115.0 0.0 0.9 !adm attempt + + +PRES ABPQ 0.00 ! patch to substitute 2-(aminobutyl)-1,3-propanediol + ! for a standard base + ! adm jr., w/Daniel Barsky + ! + ! Note 1) apply patch PRES DELB prior to this patch + ! + ! Note 2) apply patch and ic build after reading unmodified + ! DNA/RNA coordinates otherwise positions of deleted base atoms + ! will be assigned to the amino-alkane chain +!delete unneeded sugar atoms +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM O4' +ATOM P P 1.50 +ATOM O1P ON3 -0.78 +ATOM O2P ON3 -0.78 +ATOM O5' ON2 -0.57 +ATOM C5' CN8 -0.08 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 ! H11 H12 H31 H32 H51 +GROUP ! \ / \ / / +ATOM C4' CN7 -0.09 ! O1P H5' H4' C1 C3 N5-H52 (+) +ATOM H4' HN7 0.09 ! | | \ / \ / \ / \ +GROUP ! -P-O5'-C5'---C4' C2 C4 H53 +ATOM C1 CN8 -0.18 ! | | | / \ / \ +ATOM H11 HN8 0.09 ! O2P H5'' | H21 H22 H41 H42 +ATOM H12 HN8 0.09 ! | +GROUP ! H3'-C3'-H3'' +ATOM C2 CN8 -0.18 ! | +ATOM H21 HN8 0.09 ! O3' +ATOM H22 HN8 0.09 ! | +GROUP +ATOM C3 CN8 -0.18 +ATOM H31 HN8 0.09 +ATOM H32 HN8 0.09 +GROUP +ATOM C4 CN8 0.21 +ATOM H41 HN8 0.05 +ATOM H42 HN8 0.05 +ATOM N5 NN6 -0.30 +ATOM H51 HN1 0.33 +ATOM H52 HN1 0.33 +ATOM H53 HN1 0.33 +GROUP +ATOM C3' CN8 -0.08 +ATOM H3' HN8 0.09 +ATOM H3'' HN8 0.09 +ATOM O3' ON2 -0.57 + +BOND C3' H3'' C4' C1 C1 C2 C2 C3 C3 C4 C4 N5 +BOND C1 H11 C1 H12 C2 H21 C2 H22 C3 H31 C3 H32 +BOND C4 H41 C4 H42 N5 H51 N5 H52 N5 H53 + +IC O3' C4' *C3' H3' 0.0000 0.00 -120.00 0.00 0.0000 +IC O3' C4' *C3' H3'' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C5' *C4' C1 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C5' *C4' H4' 0.0000 0.00 120.00 0.00 0.0000 +IC C5' C4' C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4' *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4' *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C4' C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C4 N5 0.0000 0.00 180.00 0.00 0.0000 +IC N5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC N5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C4 N5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H51 C4 *N5 H52 0.0000 0.00 120.00 0.00 0.0000 +IC H51 C4 *N5 H53 0.0000 0.00 -120.00 0.00 0.0000 + +PRES ABQU 0.00 ! patch to substitute 2-(aminobutyl)-1,3-propanediol + ! for a standard base in the "Up" position -db(12/1/98) + ! adm jr., w/Daniel Barsky + ! + ! Note 1) apply patch PRES DELB prior to this patch + ! + ! Note 2) apply patch and ic build after reading unmodified + ! DNA/RNA coordinates otherwise positions of deleted base atoms + ! will be assigned to the amino-alkane chain +!delete unneeded sugar atoms +DELE ATOM C1' ! +DELE ATOM H1' ! +DELE ATOM C2' ! +DELE ATOM H2' ! +DELE ATOM H2'' ! +DELE ATOM O2' ! +DELE ATOM O4' ! +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 ! +ATOM O5' ON2 -0.57 ! H11 H12 H31 H32 H51 +ATOM C5' CN8 -0.08 ! \ / \ / / +ATOM H5' HN8 0.09 ! C1 C3 N5-H52 (+) +ATOM H5'' HN8 0.09 ! / \ / \ / \ +GROUP ! / C2 C4 H53 +ATOM C4' CN7 -0.09 ! O1P H5' / / \ / \ +ATOM H4' HN7 0.09 ! | | / H21 H22 H41 H42 +GROUP ! -P-O5'-C5'---C4' +ATOM C1 CN8 -0.18 ! | | |\ +ATOM H11 HN8 0.09 ! O2P H5'' | H4' +ATOM H12 HN8 0.09 ! | +GROUP ! H3'-C3'-H3'' +ATOM C2 CN8 -0.18 ! | +ATOM H21 HN8 0.09 ! O3' +ATOM H22 HN8 0.09 ! | +GROUP +ATOM C3 CN8 -0.18 +ATOM H31 HN8 0.09 +ATOM H32 HN8 0.09 +GROUP +ATOM C4 CN8 0.21 +ATOM H41 HN8 0.05 +ATOM H42 HN8 0.05 +ATOM N5 NN6 -0.30 +ATOM H51 HN1 0.33 +ATOM H52 HN1 0.33 +ATOM H53 HN1 0.33 +GROUP +ATOM C3' CN8 -0.08 +ATOM H3' HN8 0.09 +ATOM H3'' HN8 0.09 +ATOM O3' ON2 -0.57 + +BOND C3' H3'' C4' C1 C1 C2 C2 C3 C3 C4 C4 N5 +BOND C1 H11 C1 H12 C2 H21 C2 H22 C3 H31 C3 H32 +BOND C4 H41 C4 H42 N5 H51 N5 H52 N5 H53 + +IC O3' C4' *C3' H3' 0.0000 0.00 -120.00 0.00 0.0000 +IC O3' C4' *C3' H3'' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C5' *C4' C1 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C5' *C4' H4' 0.0000 0.00 120.00 0.00 0.0000 +IC C5' C4' C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4' *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4' *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C4' C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C4 N5 0.0000 0.00 180.00 0.00 0.0000 +IC N5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC N5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C4 N5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H51 C4 *N5 H52 0.0000 0.00 120.00 0.00 0.0000 +IC H51 C4 *N5 H53 0.0000 0.00 -120.00 0.00 0.0000 + +PRES ABPR -1.00 ! patch to substitute an abasic propyl linkage + ! for a standard base + ! adm jr., w/Daniel Barsky + ! + ! Note 1) apply patch PRES DELB prior to this patch + ! + ! Note 2) apply patch and ic build after reading unmodified + ! DNA/RNA coordinates otherwise positions of deleted base atoms + ! will be assigned to the amino-alkane chain +!delete unneeded sugar atoms +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM O4' +ATOM P P 1.50 +ATOM O1P ON3 -0.78 +ATOM O2P ON3 -0.78 +ATOM O5' ON2 -0.57 +ATOM C5' CN8 -0.08 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +GROUP ! O1P H5' H4' H3' +ATOM C4' CN8 -0.18 ! | | | | +ATOM H4' HN8 0.09 ! -P-O5'-C5'---C4'---C3'---O3'- +ATOM H4'' HN8 0.09 ! | | | | +GROUP ! O2P H5'' H4'' H3'' +ATOM C3' CN8 -0.08 ! +ATOM H3' HN8 0.09 ! +ATOM H3'' HN8 0.09 ! +ATOM O3' ON2 -0.57 ! + +BOND C4' H4'' C3' H3'' +IC C3' C5' *C4' H4' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C5' *C4' H4'' 0.0000 0.00 -120.00 0.00 0.0000 +IC O3' C4' *C3' H3'' 0.0000 0.00 120.00 0.00 0.0000 +IC O3' C4' *C3' H3' 0.0000 0.00 -120.00 0.00 0.0000 + + +PRES ABET -1.00 ! patch to substitute an abasic ethyl linkage + ! for a standard base + ! adm jr., w/Daniel Barsky + ! + ! Note 1) apply patch PRES DELB prior to this patch + ! + ! Note 2) apply patch and ic build after reading unmodified + ! DNA/RNA coordinates otherwise positions of deleted base atoms + ! will be assigned to the amino-alkane chain +!delete unneeded sugar atoms +DELE ATOM C1' +DELE ATOM H1' +DELE ATOM C2' +DELE ATOM H2' +DELE ATOM H2'' +DELE ATOM O2' +DELE ATOM O4' +DELE ATOM C4' +DELE ATOM H4' +ATOM P P 1.50 ! O1P H5' H3' +ATOM O1P ON3 -0.78 ! | | | +ATOM O2P ON3 -0.78 ! -P-O5'-C5'---C3'---O3'- +ATOM O5' ON2 -0.57 ! | | | +ATOM C5' CN8 -0.08 ! O2P H5'' H3'' +ATOM H5' HN8 0.09 ! +ATOM H5'' HN8 0.09 +GROUP +ATOM C3' CN8 -0.08 +ATOM H3' HN8 0.09 +ATOM H3'' HN8 0.09 +ATOM O3' ON2 -0.57 + +BOND C3' C5' C3' H3'' +IC C3' O5' *C5' H5' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O5' *C5' H5'' 0.0000 0.00 -120.00 0.00 0.0000 +IC O3' C5' *C3' H3'' 0.0000 0.00 120.00 0.00 0.0000 !<- swapped H3' and +IC O3' C5' *C3' H3' 0.0000 0.00 -120.00 0.00 0.0000 ! H3'' --db(3/8/99) + +!phosphoramidate related model compounds and patches +!reference +!Banavali, N.B. and MacKerell, Jr., A.D. "Reexamination of the +!Intrinsic, Dynamic, and Hydration Properties of Phosphoramidate DNA," +!Nucleic Acids Research, 2001, 29:3219-3230. +RESI PHA -1.00 ! Phosphoramidate (backbone for DNA) +GROUP ! +ATOM P1 P 1.570 ! +ATOM O3 ON3 -0.820 ! +ATOM O4 ON3 -0.820 ! +ATOM O2 ON2 -0.560 ! H11 +ATOM N1 NN1 -0.860 ! | +ATOM H1 HN2 0.330 ! H13- C1-H12 + ! \ +ATOM C1 CN8B -0.190 ! (-)O3 N1-H1 +ATOM H11 HN8 0.090 ! \ / +ATOM H12 HN8 0.090 ! P1(+1) +ATOM H13 HN8 0.090 ! / \ + ! (-)O4 O2 +ATOM C2 CN7 -0.190 ! / +ATOM H21 HN7 0.090 ! H23-C2-H22 +ATOM H22 HN7 0.090 ! | +ATOM H23 HN7 0.090 ! H21 + +BOND P1 N1 P1 O2 P1 O3 P1 O4 N1 C2 N1 H1 O2 C1 +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 +! IC FOR THE g,g crystal conformation (6-31G* opt. structure) +IC O3 P1 N1 C2 1.4816 107.70 342.80 123.13 1.4559 +IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 +IC O4 P1 O2 C1 1.4812 105.80 43.90 118.08 1.4331 +IC N1 P1 O2 C1 1.6728 99.90 158.10 118.08 1.4331 +IC O2 P1 N1 C2 1.6480 99.90 96.20 123.13 1.4559 +IC H11 C1 O2 P1 1.0913 113.30 253.00 123.13 1.6728 +IC H12 C1 O2 P1 1.0790 106.20 12.40 123.13 1.6728 +IC H13 C1 O2 P1 1.0898 111.90 131.00 123.13 1.6728 +IC H21 C2 N1 P1 1.0841 108.20 196.00 118.08 1.6480 +IC H22 C2 N1 P1 1.0805 109.90 316.40 118.08 1.6480 +IC H23 C2 N1 P1 1.0862 111.20 76.70 118.08 1.6480 +patc firs none last none + +RESI TPHC -1.00 ! monoanionic 3'phosphoramidate-tetrahydrofuran +! used to fit epsilon +! Charges and atom types for the monoanionic phosphate groups were +! transfered from residue PHA + +! Atom types for aliphatic hydrogens are a mess + +GROUP +ATOM O4' ON6 -0.50 ! H41' O4' H11' +ATOM C1' CN7B 0.07 ! \ / \ / +ATOM H11' HN7 0.09 ! H42'-C4' C1'-H12' +ATOM H12' HN7 0.09 ! | | +ATOM C4' CN7 0.07 ! H31'-C3'-C2'-H21' +ATOM H41' HN7 0.09 ! / \ +ATOM H42' HN7 0.09 ! H1-N1 O3 H22' +GROUP ! \ / +ATOM C2' CN8 -0.18 ! P1 +ATOM H21' HN8 0.09 ! / \ +ATOM H22' HN8 0.09 ! O2 O4 +GROUP ! | +ATOM C3' CN7 -0.01 ! H51'-C5-H52' +ATOM H31' HN7 0.09 ! | +ATOM N1 NN1 -0.86 ! H53' +ATOM H1 HN2 0.33 ! +ATOM P1 P 1.57 +ATOM O3 ON3 -0.82 +ATOM O4 ON3 -0.82 +ATOM O2 ON2 -0.56 +ATOM C5' CN8B -0.19 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM H53' HN8 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' N1 +BOND N1 H1 C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' +BOND C4' H41' C4' H42' N1 P1 P1 O3 P1 O4 P1 O2 +BOND O2 C5' C5' H51' C5' H52' C5' H53' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC O4' C2' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC O4' C2' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC C1' C3' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C1' C3' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC N1 C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 +IC P1 N1 C3' C4' 1.7190 119.98 185.77 110.95 1.5332 +IC O3 P1 N1 C3' 1.4771 109.35 14.75 120.00 1.4525 +IC O4 P1 N1 C3' 1.4818 105.19 150.42 120.00 1.4525 +IC O2 P1 N1 C3' 1.6379 101.65 263.47 120.00 1.4525 +IC C5' O2 P1 N1 1.3955 119.61 286.08 101.65 1.7190 +IC H51' C5' O2 P1 1.0859 107.43 179.85 119.61 1.6379 +IC H52' C5' O2 P1 1.0835 111.18 299.56 119.61 1.6379 +IC H53' C5' O2 P1 1.0868 111.29 60.84 119.61 1.6379 + +PATC FIRS NONE LAST NONE + +RESI THNI 0.00 ! tetrahydrofuran with 3'-NH2, 5'-CH2OH, 1'-imidazole +GROUP ! +ATOM O4' ON6 -0.50 +ATOM C4' CN7 0.16 +ATOM H42' HN7 0.09 +ATOM C1' CN7B 0.16 +ATOM H12' HN7 0.09 +GROUP +ATOM C2' CN8 -0.18 +ATOM H21' HN8 0.09 +ATOM H22' HN8 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CPH1 -0.05 ! HE1 +ATOM HG HR3 0.09 ! / +ATOM CD2 CPH1 0.22 ! ND1---CE1 +ATOM HD2 HR3 0.10 ! / | +ATOM ND1 NR1 -0.04 ! HG-CG | +ATOM CE1 CPH2 0.25 ! \ | +ATOM HE1 HR1 0.13 ! CD2---NE2 +ATOM NE2 NR2 -0.70 ! | + ! HD2 +GROUP ! Hydroxyl group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM N1 NN1 -0.91 +ATOM H1 HN2 0.34 +ATOM H2 HN2 0.34 +GROUP ! Methyl group on C4' +ATOM C5' CN8B -0.17 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON2 -0.10 +ATOM H5' HN8 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' N1 N1 H1 N1 H2 C1' H12' C2' H21' C2' H22' +BOND C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5' +BOND C1' ND1 ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC N1 C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H1 N1 C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H2 N1 C3' C2' 0.0 0.0 60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 +IC H5' O5' C5' C4' 0.0 0.0 59.68 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THNP -1.00 ! Tetrahydrofuran with 3'-NH-PO2-OCH3, 5'-CH2OH, 1'-imidazole +GROUP ! +ATOM O4' ON6 -0.50 +ATOM C4' CN7 0.16 +ATOM H42' HN7 0.09 +ATOM C1' CN7B 0.16 +ATOM H12' HN7 0.09 +GROUP +ATOM C2' CN8 -0.18 +ATOM H21' HN8 0.09 +ATOM H22' HN8 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CPH1 -0.05 ! HE1 +ATOM HG HR3 0.09 ! / +ATOM CD2 CPH1 0.22 ! ND1---CE1 +ATOM HD2 HR3 0.10 ! / | +ATOM ND1 NR1 -0.04 ! HG-CG | +ATOM CE1 CPH2 0.25 ! \ | +ATOM HE1 HR1 0.13 ! CD2---NE2 +ATOM NE2 NR2 -0.70 ! | + ! HD2 +GROUP ! phosphoramidate group on C3' +ATOM H31' HN7 0.09 +ATOM C3' CN7 0.14 +ATOM N1 NN1 -0.86 +ATOM P1 P 1.570 ! +ATOM H1 HN2 0.33 + +GROUP ! Methyl group on C4' +ATOM C5' CN8B -0.17 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON2 -0.59 +ATOM H5' HN8 0.43 + +ATOM O3 ON3 -0.820 ! +ATOM O4 ON3 -0.820 ! +ATOM O5 ON2 -0.560 ! +ATOM C5 CN8B -0.190 ! +ATOM H51 HN8 0.090 ! +ATOM H52 HN8 0.090 ! +ATOM H53 HN8 0.090 ! + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' N1 N1 H1 C1' H12' C2' H21' C2' H22' +BOND C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5' +BOND C1' ND1 ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +BOND P1 N1 P1 O5 P1 O3 P1 O4 O5 C5 +BOND C5 H51 C5 H52 C5 H53 +! This IC table is only an initial guess: +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC ND1 C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC N1 C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P1 N1 C3' C4' 0.0000 000.00 180.00 000.00 0.0000 +IC C3' N1 P1 O5 0.0000 000.00 -95.22 000.00 0.0000 +IC O5 N1 *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O5 N1 *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 +IC C5 O5 P1 N1 0.0000 000.00 -46.90 000.00 0.0000 +IC H51 C5 O5 P1 0.0000 000.00 180.00 000.00 0.0000 +IC H52 C5 O5 P1 0.0000 000.00 60.00 000.00 0.0000 +IC H53 C5 O5 P1 0.0000 000.00 -60.00 000.00 0.0000 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 +IC H5' O5' C5' C4' 0.0 0.0 59.68 0.0 0.0 +PATC FIRS NONE LAST NONE + +! patches for phosphoramidate + +PRES N5TR 0.00 ! 5'-terminal phosphoramidate patch + ! use in generate statement + ! thni charges used for NH2 +DELETE ATOM O5' +DELETE ATOM H5T +! +GROUP +ATOM H5T1 HN2 0.34 +ATOM H5T2 HN2 0.34 +ATOM N5' NN1 -0.91 +ATOM C5' CN8B 0.05 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +! +BOND H5T1 N5' H5T2 N5' N5' C5' +DONO H5T1 N5' +DONO H5T2 N5' +BILD N5' C5' C4' C3' 0.0000 000.00 51.00 000.00 0.0000 +BILD H5T1 N5' C5' C4' 0.9600 114.97 148.63 111.92 1.5284 +BILD H5T2 N5' C5' C4' 0.9600 114.97 260.00 111.92 1.5284 + +PRES N3TR 0.00 ! 3'terminal phosphoramidate patch + ! use in generate statement + ! thni charges used for NH2 +DELETE ATOM O3' +DELETE ATOM H3T + +GROUP +ATOM C3' CN7 0.14 +ATOM H3' HN7 0.09 +ATOM N3' NN1 -0.91 +ATOM H3T1 HN2 0.34 +ATOM H3T2 HN2 0.34 +! +BOND N3' C3' N3' H3T1 N3' H3T2 +DONO H3T1 N3' +DONO H3T2 N3' +BILD N3' C3' C4' C5' 1.4582 109.38 139.71 114.90 1.5185 +BILD N3' C3' C4' O4' 1.4582 109.38 258.76 106.51 1.4149 +BILD H3T1 N3' C3' C4' 1.0257 109.42 165.51 115.52 1.5470 +BILD H3T2 N3' C3' C4' 1.0260 109.82 284.55 115.52 1.5470 +BILD H3T1 N3' C3' C2' 1.0257 109.42 47.49 110.08 1.5071 +BILD H3T2 N3' C3' C2' 1.0260 109.82 166.53 110.08 1.5071 + +PRES TN3T 0.00 ! 3'-NH2 patch to generate thymine nucleoside analog + ! to be applied to NUST + +DELETE ATOM O3' +DELETE ATOM H32' + +GROUP +ATOM C3' CN7 0.14 +ATOM H31' HN7 0.09 +ATOM N3' NN1 -0.91 +ATOM H3T1 HN2 0.34 +ATOM H3T2 HN2 0.34 +! +BOND N3' C3' N3' H3T1 N3' H3T2 +DONO H3T1 N3' +DONO H3T2 N3' +BILD N3' C3' C4' C5' 1.4582 109.38 139.71 114.90 1.5185 +BILD N3' C3' C4' O4' 1.4582 109.38 258.76 106.51 1.4149 +BILD H3T1 N3' C3' C4' 1.0257 109.42 165.51 115.52 1.5470 +BILD H3T2 N3' C3' C4' 1.0260 109.82 284.55 115.52 1.5470 +BILD H3T1 N3' C3' C2' 1.0257 109.42 47.49 110.08 1.5071 +BILD H3T2 N3' C3' C2' 1.0260 109.82 166.53 110.08 1.5071 + +PRES N3PA -1.00 ! 3' phosphoramidate patch +DELETE ATOM 1O3' ! necessary due to auto-generate dihedrals + +! use the following statement to apply this patch to O3' of resid1 +! also changes charges of C5',O5' of resid2, so resid2 HAS TO BE +! immediately 3' to resid1 : +! patch n3pa segid resid1 segid resid2 setup warn + +GROUP ! To correct backbone charges near NH, total charge -0.53 +ATOM 2P P 1.570 ! +ATOM 2O1P ON3 -0.820 ! +ATOM 2O2P ON3 -0.820 ! +ATOM 2O5' ON2 -0.560 ! +ATOM 2C5' CN8B -0.08 ! +ATOM 2H5' HN8 0.09 ! +ATOM 2H5'' HN8 0.09 ! + +GROUP ! Total charge -0.47 +ATOM 1C3' CN7 -0.03 +ATOM 1H3' HN7 0.09 +ATOM 1N3' NN1 -0.860 ! Atom added in patch +ATOM 1HN3' HN2 0.330 ! Atom added in patch + +BOND 1N3' 1HN3' 1N3' 2P 1N3' 1C3' +DONO HN3' N3' +! +BILD 1C5' 1C4' 1C3' 1N3' 0.0000 000.00 80.00 000.00 0.0000 +BILD 2C4' 2C3' 1N3' 1HN3' 0.0000 000.00 80.00 000.00 0.0000 +BILD 2O1P 2P 1N3' 1C3' 0.0000 000.00 60.00 000.00 0.0000 +BILD 2O1P 2P 1N3' 1HN3' 0.0000 000.00 180.00 000.00 0.0000 +BILD 1N3' 2P 2O5' 2C5' 0.0000 000.00 100.00 000.00 0.0000 +BILD 2O5' 2P 1N3' 1C3' 0.0000 000.00 60.00 000.00 0.0000 +BILD 1H3' 1C3' 1N3' 2P 0.0000 000.00 40.00 000.00 0.0000 + +PRES N5PA -1.00 ! 5' phosphoramidate patch +DELETE ATOM 2O5' ! necessary due to auto-generate dihedrals + +! use the following statement to apply this patch to O5' of resid2 +! also changes charges of C3',O3' of resid1, so resid1 HAS TO BE +! immediately 5' to resid2 : +! patch n5pa segid resid1 segid resid2 setup warn + +GROUP ! To correct backbone charges near NH, total charge -0.53 +ATOM 2P P 1.570 ! +ATOM 2O1P ON3 -0.820 ! +ATOM 2O2P ON3 -0.820 ! +ATOM 2N5' NN1 -0.860 ! Atom added in patch +ATOM 2H5N' HN2 0.330 ! Atom added in patch +ATOM 2C5' CN8B -0.11 ! +ATOM 2H5' HN8 0.09 ! +ATOM 2H5'' HN8 0.09 ! +GROUP +ATOM 1C3' CN7 0.00 +ATOM 1H3' HN7 0.09 +ATOM 1O3' ON2 -0.56 + +BOND 2N5' 2H5N' 2N5' 2P 2N5' 2C5' +DONO 2H5N' 2N5' +! +BILD 2C3' 2C4' 2C5' 2N5' 0.0000 000.00 50.00 000.00 0.0000 +BILD 2C4' 2C5' 2N5' 2H5N' 0.0000 000.00 60.00 000.00 0.0000 +BILD 2O1P 2P 2N5' 2C5' 0.0000 000.00 180.00 000.00 0.0000 +BILD 2O2P 2P 2N5' 2H5N' 0.0000 000.00 60.00 000.00 0.0000 +BILD 2N5' 2P 1O3' 1C3' 0.0000 000.00 70.00 000.00 0.0000 +BILD 1O3' 2P 2N5' 2C5' 0.0000 000.00 60.00 000.00 0.0000 +BILD 2H5' 2C5' 2N5' 2P 0.0000 000.00 60.00 000.00 0.0000 +BILD 2H5'' 2C5' 2N5' 2P 0.0000 000.00 130.00 000.00 0.0000 + + +!Residues and Patches for PNA +!end +!goto skip_pna + +RESI GPN 0.00 +!THE FOLLOWING ATOMS ARE ON THE PNA BACKBONE. THE CHARGES HAVE BEEN COMPUTED +GROUP !BY THE MOPAC PACKAGE AND HAVE BEEN ROUNDED TO MAKE +ATOM C C 0.33 !THE BACKBONE ELECTRICALLY NEUTRAL.(SEE NOTES) +ATOM O1' O -0.25 +GROUP +ATOM C2' CT2 -0.35 +ATOM H2' HB2 0.18 +ATOM H2'' HB2 0.18 +GROUP +ATOM N2' NC2 -0.09 +GROUP +ATOM C5' CT2 -0.33 +ATOM H5' HB2 0.17 +ATOM H5'' HB2 0.17 +GROUP +ATOM C6' CT2 -0.06 +ATOM H6' HB2 0.10 +ATOM H6'' HB2 0.10 +GROUP +ATOM N NH1 -0.37 +ATOM H1' H 0.24 +GROUP +ATOM C3' CD 0.25 +ATOM O3' O -0.27 +GROUP +ATOM C4' CT2 -0.34 +ATOM H4' HB2 0.17 +ATOM H4'' HB2 0.17 +!BASE ATOMS STARTS HERE.! WE HAVE TAKEN THE CHARGES FOR THESE ATOMS +GROUP ! FROM THOSE OF THE DNA TOPOLOGY FILE TO KEEP +ATOM N9 NN2B -0.02 ! THESE BASE PARTS IDENTICAL WITH THE +ATOM C4 CN5 0.26 ! CORRESPONDING DNA PART. THIS FACILITATE THE +GROUP ! STUDY OF THE BACKBONE EFFECT, THE BASES +ATOM N3 NN3G -0.74 ! BEING SIMILAR. THE NET CHARGE OF THIS BASE +ATOM C2 CN2 0.75 ! PART IS ALSO 0.00. +ATOM N1 NN2G -0.34 ! That is, both the BACKBONE and the BASE are +ATOM H1 HN2 0.26 ! separately ELECTRONEUTRAL. +GROUP +ATOM N2 NN1 -0.68 +ATOM H21 HN1 0.32 +ATOM H22 HN2 0.35 +GROUP +ATOM C6 CN1 0.54 +ATOM O6 ON1 -0.51 +ATOM C5 CN5G 0.00 +GROUP +ATOM N7 NN4 -0.60 +ATOM C8 CN4 0.25 +ATOM H8 HN3 0.16 + +BOND +N C C O1' C C2' C2' H2' C2' H2'' C2' N2' +BOND N2' C5' C5' H5' C5' H5'' C6' C5' C6' H6' C6' H6'' +BOND C6' N N H1' +BOND N2' C3' C3' O3' C3' C4' C4' H4' C4' H4'' +BOND C4' N9 N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 C8 H8 +IMPH N2 N3 N1 C2 H1 C2 C6 N1 O6 N1 C5 C6 +IMPH H8 N7 N9 C8 H22 H21 C2 N2 +!impropers for PNA backbone. +IMPH C6' H1' -C N +IMPH N -O1' -C2' -C +IMPH N2' O3' C4' C3' +IMPH C2' O1' +N C +IMPH C +H1' +C6' +N +IMPH C4' C4 C8 N9 !PNA-BASE linkage + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +DONO H1' N1 +ACCE O6 C6 +ACCE N3 +ACCE N7 +ACCE O1' C +ACCE O3' C3' +BILD C6' N -C -C2' 1.4500 120.00 0.0000 120.00 1.5300 +BILD C6' N -C -O1' 1.4500 120.00 0.0000 121.00 1.2300 +BILD N -C -C2' -H2' 1.3450 117.50 0.0000 109.50 1.0900 +BILD N -C -C2' -H2'' 1.3450 117.50 0.0000 109.50 1.0900 +BILD O1' C C2' H2'' 1.2170 120.50 20.000 107.00 1.090 +BILD +N C C2' N2' 1.3450 117.50 0.0000 120.00 1.4500 +BILD C C2' N2' C3' 1.5300 111.50 0.0000 110.00 1.4500 +BILD H2' C2' N2' C3' 1.0900 109.50 0.0000 120.00 1.4500 +BILD C2' N2' C3' C4' 1.4500 120.00 0.0000 109.50 1.5300 +BILD C2' N2' C3' O3' 0.0 0.00 0.0000 0.00 0.00 +BILD O3' C3' C4' H4' 1.2 120.00 127.5 108.00 1.1 +BILD O3' C3' C4' H4'' 1.2 120.00 -116.3 108.00 1.1 +BILD C3' C4' N9 C4 1.5251 113.71 -96.0 125.59 1.3783 +BILD C4' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +BILD C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N C6' C5' N2' 0.0 0.0 180.0 0.0 0.0 +IC C5' N2' C2' C 1.5 112.00 101.00 109.00 1.5 +IC N2' C2' C O1' 1.5 109.00 180.0 101.00 1.3 +IC N3' C C2' N2' 1.2 124.00 -32.00 109.00 1.5 +PATCHING FIRST NT LAST CT + +RESI CPN 0.00 +!THE FOLLOWING ATOMS ARE ON THE PNA BACKBONE. THE CHARGES HAVE BEEN COMPUTED +GROUP !BY THE MOPAC PACKAGE AND HAVE BEEN ROUNDED TO MAKE +ATOM C C 0.33 !THE BACKBONE ELECTRICALLY NEUTRAL.(SEE NOTES) +ATOM O1' O -0.25 +GROUP +ATOM C2' CT2 -0.35 +ATOM H2' HB2 0.18 +ATOM H2'' HB2 0.18 +GROUP +ATOM N2' NC2 -0.09 +GROUP +ATOM C5' CT2 -0.33 +ATOM H5' HB2 0.17 +ATOM H5'' HB2 0.17 +GROUP +ATOM C6' CT2 -0.06 +ATOM H6' HB2 0.10 +ATOM H6'' HB2 0.10 +GROUP +ATOM N NH1 -0.37 +ATOM H1' H 0.24 +GROUP +ATOM C3' CD 0.25 +ATOM O3' O -0.27 +GROUP +ATOM C4' CT2 -0.34 +ATOM H4' HB2 0.17 +ATOM H4'' HB2 0.17 +!BASE ATOMS STARTS HERE. +GROUP +ATOM N1 NN2 -0.16 +ATOM C6 CN3 0.11 +ATOM H6 HN3 0.05 +GROUP +ATOM C2 CN1 0.53 +ATOM O2 ON1C -0.48 +ATOM N3 NN3 -0.67 +ATOM C4 CN2 0.62 +GROUP +ATOM N4 NN1 -0.58 +ATOM H41 HN1 0.31 +ATOM H42 HN1 0.27 +GROUP +ATOM C5 CN3 -0.10 +ATOM H5 HN3 0.10 + +BOND +N C C O1' C C2' C2' H2' C2' H2'' C2' N2' +BOND N2' C5' C5' H5' C5' H5'' C6' C5' C6' H6' C6' H6'' +BOND C6' N N H1' +BOND N2' C3' C3' O3' C3' C4' C4' H4' C4' H4'' +BOND C4' N1 N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C5 H5 C6 H6 + +IMPH O2 N1 N3 C2 N4 N3 C5 C4 +IMPH H5 C4 C6 C5 H6 C5 N1 C6 +IMPH H42 C4 H41 N4 +!impropers for PNA backbone. +IMPH C6' H1' -C N +IMPH N -O1' -C2' -C +IMPH N2' O3' C4' C3' +IMPH C2' O1' +N C +IMPH C +H1' +C6' +N +IMPH C4' C2 C6 N1 !PNA-BASE linkage + +DONO H42 N4 +DONO H41 N4 +DONO H1' N +ACCE O1' C +ACCE O3' C3' + +BILD C6' N -C -C2' 1.4500 120.00 0.0000 120.00 1.5300 +BILD C6' N -C -O1' 1.4500 120.00 0.0000 121.00 1.2300 +BILD N -C -C2' -H2' 1.3450 117.50 0.0000 109.50 1.0900 +BILD N -C -C2' -H2'' 1.3450 117.50 0.0000 109.50 1.0900 +BILD O1' C C2' H2'' 1.2300 121.00 0.0000 109.50 1.0900 +BILD +N C C2' N2' 1.3450 117.50 0.0000 120.00 1.4500 +BILD C C2' N2' C3' 1.5300 111.50 0.0000 110.00 1.4500 +BILD H2' C2' N2' C3' 1.0900 109.50 0.0000 120.00 1.4500 +BILD C2' N2' C3' C4' 1.4500 120.00 0.0000 109.50 1.5300 +BILD C2' N2' C3' O3' 1.4500 120.00 0.0000 120.00 1.2300 +BILD O3' C3' C4' H4' 1.2300 121.00 0.0000 109.50 1.0900 +BILD O3' C3' C4' H4'' 1.2300 121.00 0.0000 109.50 1.4500 +BILD C3' C4' N1 C2 1.5251 113.71 -96.0 117.79 1.399 +BILD C4' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC N C6' C5' N2' 0.0 0.0 180.0 0.0 0.0 +IC C5' N2' C2' C 1.5 112.00 101.00 109.00 1.5 +IC N2' C2' C O1' 1.5 109.00 180.0 101.00 1.3 +IC N3' C C2' N2' 1.2 124.00 -32.00 109.00 1.5 +PATCHING FIRST NT LAST CT + + +RESI TPN 0.00 +!THE FOLLOWING ATOMS ARE ON THE PNA BACKBONE. THE CHARGES HAVE BEEN COMPUTED +GROUP !BY THE MOPAC PACKAGE AND HAVE BEEN ROUNDED TO MAKE +ATOM C C 0.33 !THE BACKBONE ELECTRICALLY NEUTRAL.(SEE NOTES) +ATOM O1' O -0.25 +GROUP +ATOM C2' CT2 -0.35 +ATOM H2' HB2 0.18 +ATOM H2'' HB2 0.18 +GROUP +ATOM N2' NC2 -0.09 +GROUP +ATOM C5' CT2 -0.33 +ATOM H5' HB2 0.17 +ATOM H5'' HB2 0.17 +GROUP +ATOM C6' CT2 -0.06 +ATOM H6' HB2 0.10 +ATOM H6'' HB2 0.10 +GROUP +ATOM N NH1 -0.37 +ATOM H1' H 0.24 +GROUP +ATOM C3' CD 0.25 +ATOM O3' O -0.27 +GROUP +ATOM C4' CT2 -0.34 +ATOM H4' HB2 0.17 +ATOM H4'' HB2 0.17 +!BASE ATOMS STARTS HERE. +GROUP +ATOM N1 NN2B -0.30 +ATOM C6 CN3 0.17 +ATOM H6 HN3 0.13 +GROUP +ATOM C2 CN1T 0.57 +ATOM O2 ON1 -0.47 +ATOM N3 NN2U -0.46 +ATOM H3 HN2 0.36 +GROUP +ATOM C4 CN1 0.54 +ATOM O4 ON1 -0.49 +ATOM C5 CN3T -0.15 +ATOM C5M CN9 -0.11 +ATOM H51 HN9 0.07 +ATOM H52 HN9 0.07 +ATOM H53 HN9 0.07 + +BOND +N C C O1' C C2' C2' H2' C2' H2'' C2' N2' +BOND N2' C5' C5' H5' C5' H5'' C6' C5' C6' H6' C6' H6'' +BOND C6' N N H1' +BOND N2' C3' C3' O3' C3' C4' C4' H4' C4' H4'' +BOND C4' N1 N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C5M C5 C6 C6 H6 C5M H51 C5M H52 +BOND C5M H53 +IMPH O2 N1 N3 C2 H3 C2 C4 N3 +IMPH O4 N3 C5 C4 H6 N1 C5 C6 +IMPH C5M C4 C6 C5 +!impropers for PNA backbone. +IMPH C6' H1' -C N +IMPH N -O1' -C2' -C +IMPH N2' O3' C4' C3' +IMPH C2' O1' +N C +IMPH C +H1' +C6' +N +IMPH C4' C2 C6 N1 !PNA-BASE linkage +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 +DONO H1' N +ACCE O1' C +ACCE O3' C3' + +BILD C6' N -C -C2' 1.4500 120.00 0.0000 120.00 1.5300 +BILD C6' N -C -O1' 1.4500 120.00 0.0000 121.00 1.2300 +BILD N -C -C2' -H2' 1.3450 117.50 0.0000 109.50 1.0900 +BILD N -C -C2' -H2'' 1.3450 117.50 0.0000 109.50 1.0900 +BILD O1' C C2' H2'' 1.2300 121.00 0.0000 109.50 1.0900 +BILD +N C C2' N2' 1.3450 117.50 0.0000 120.00 1.4500 +BILD C C2' N2' C3' 1.5300 111.50 0.0000 110.00 1.4500 +BILD H2' C2' N2' C3' 1.0900 109.50 0.0000 120.00 1.4500 +BILD C2' N2' C3' C4' 1.4500 120.00 0.0000 109.50 1.5300 +BILD C2' N2' C3' O3' 1.4500 120.00 0.0000 120.00 1.2300 +BILD O3' C3' C4' H4' 1.2300 121.00 0.0000 109.50 1.0900 +BILD O3' C3' C4' H4'' 1.2300 121.00 0.0000 109.50 1.4500 +BILD C3' C4' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 +BILD C4' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +IC N C6' C5' N2' 0.0 0.0 180.0 0.0 0.0 +IC C5' N2' C2' C 1.5 112.00 101.00 109.00 1.5 +IC N2' C2' C O1' 1.5 109.00 180.0 101.00 1.3 +IC N3' C C2' N2' 1.2 124.00 -32.00 109.00 1.5 +PATCHING FIRST NT LAST CT + +RESI APN 0.00 +!THE FOLLOWING ATOMS ARE ON THE PNA BACKBONE. THE CHARGES HAVE BEEN COMPUTED +GROUP !BY THE MOPAC PACKAGE AND HAVE BEEN ROUNDED TO MAKE +ATOM C C 0.33 !THE BACKBONE ELECTRICALLY NEUTRAL.(SEE NOTES) +ATOM O1' O -0.25 +GROUP +ATOM C2' CT2 -0.35 +ATOM H2' HB2 0.18 +ATOM H2'' HB2 0.18 +GROUP +ATOM N2' NC2 -0.09 +GROUP +ATOM C5' CT2 -0.33 +ATOM H5' HB2 0.17 +ATOM H5'' HB2 0.17 +GROUP +ATOM C6' CT2 -0.06 +ATOM H6' HB2 0.10 +ATOM H6'' HB2 0.10 +GROUP +ATOM N NH1 -0.37 +ATOM H1' H 0.24 +GROUP +ATOM C3' CD 0.25 +ATOM O3' O -0.27 +GROUP +ATOM C4' CT2 -0.34 +ATOM H4' HB2 0.17 +ATOM H4'' HB2 0.17 +!BASE ATOMS STARTS HERE. +GROUP +ATOM C5 CN5 0.23 +ATOM N7 NN4 -0.63 +ATOM C8 CN4 0.38 +ATOM H8 HN3 0.18 +ATOM N9 NN2 -0.16 +GROUP +ATOM N1 NN3A -0.74 +ATOM C2 CN4 0.53 +ATOM H2 HN3 0.16 +ATOM N3 NN3A -0.69 +ATOM C4 CN5 0.31 +ATOM C6 CN2 0.43 +GROUP +ATOM N6 NN1 -0.80 +ATOM H61 HN1 0.40 +ATOM H62 HN1 0.40 + +BOND +N C C O1' C C2' C2' H2' C2' H2'' C2' N2' +BOND N2' C5' C5' H5' C5' H5'' C6' C5' C6' H6' C6' H6'' +BOND C6' N N H1' +BOND N2' C3' C3' O3' C3' C4' C4' H4' C4' H4'' +BOND C4' N9 N9 C4 N9 C8 C4 N3 +BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 +BOND C8 H8 C2 H2 + +IMPH H62 C6 H61 N6 N6 N1 C5 C6 H2 N1 N3 C2 +IMPH H8 N7 N9 C8 +!impropers for PNA backbone. +IMPH C6' H1' -C N +IMPH N -O1' -C2' -C +IMPH N2' O3' C4' C3' +IMPH C2' O1' +N C +IMPH C +H1' +C6' +N +IMPH C4' C4 C8 N9 !PNA-BASE linkage + +DONO H61 N6 +DONO H62 N6 +ACCE N3 +ACCE N7 +ACCE N1 +DONO H1' N +ACCE O1' C +ACCE O3' C3' + +BILD C6' N -C -C2' 1.4500 120.00 0.0000 120.00 1.5300 +BILD C6' N -C -O1' 1.4500 120.00 0.0000 121.00 1.2300 +BILD N -C -C2' -H2' 1.3450 117.50 0.0000 109.50 1.0900 +BILD N -C -C2' -H2'' 1.3450 117.50 0.0000 109.50 1.0900 +BILD O1' C C2' H2'' 1.2300 121.00 0.0000 109.50 1.0900 +BILD +N C C2' N2' 1.3450 117.50 0.0000 120.00 1.4500 +BILD C C2' N2' C3' 1.5300 111.50 0.0000 110.00 1.4500 +BILD H2' C2' N2' C3' 1.0900 109.50 0.0000 120.00 1.4500 +BILD C2' N2' C3' C4' 1.4500 120.00 0.0000 109.50 1.5300 +BILD C2' N2' C3' O3' 1.4500 120.00 0.0000 120.00 1.2300 +BILD O3' C3' C4' H4' 1.2300 121.00 0.0000 109.50 1.0900 +BILD O3' C3' C4' H4'' 1.2300 121.00 0.0000 109.50 1.4500 +BILD C3' C4' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 +BILD C4' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC N C6' C5' N2' 0.0 0.0 180.0 0.0 0.0 +IC C5' N2' C2' C 1.5 112.00 101.00 109.00 1.5 +IC N2' C2' C O1' 1.5 109.00 180.0 101.00 1.3 +IC N3' C C2' N2' 1.2 124.00 -32.00 109.00 1.5 + +PATCHING FIRST NT LAST CT + +!PRES for adding TERMINAL CAPs to a PNA strand. +!--------------------------------------------- +PRES NT -0.14 +GROU +DELETE ATOM H1' +ATOM N NH1 -0.39 !Changed by Boel from N4' NH2 -0.39 +ATOM HT1 HN1 0.17 +ATOM HT2 HN1 0.17 +ATOM C6' CT2 -0.09 +BOND HT1 N HT2 N +DONO HT1 N +DONO HT2 N +!IC HT1 N CA C 0.0000 0.00 180.00 0.00 0.0000 +!IC HT2 CA *N HT1 0.0000 0.00 120.00 0.00 0.0000 +!IC HT3 CA *N HT2 0.0000 0.00 120.00 0.00 0.0000 + +PRES CT 0.28 +GROU +ATOM C C 0.33 +ATOM HT3 HN1 0.17 +ATOM HT4 HN1 0.17 +ATOM N3' NH2 -0.39 +BOND C N3' N3' HT3 N3' HT4 +DONO HT3 N3' +DONO HT4 N3' +PATCH FIRST NONE LAST NONE + +!carbocyclic section +! model compounds for carbocyclic sugars +! CPEN,CPES,BPNP,BPSP,CSAD,CSGU,CSTH,CSCY,CNAD,CNGU,CNTH,CNCY, +! B5NP,B5SP + +RESI CPEN 0.00 ! cyclopentane, adm jr. + ! with north atom types +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C1 CN8 -0.18 ! H51 H52 +ATOM H11 HN8 0.09 ! \ / +ATOM H12 HN8 0.09 ! C5 +GROUP ! H41 / \ H11 +ATOM C2 CN7 -0.18 ! \ / \ / +ATOM H21 HN7 0.09 ! H42-C4 C1-H12 +ATOM H22 HN7 0.09 ! | | +GROUP ! H31-C3------C2-H21 +ATOM C3 CN8 -0.18 ! | | +ATOM H31 HN8 0.09 ! H32 H22 +ATOM H32 HN8 0.09 +GROUP +ATOM C4 CN7 -0.18 +ATOM H41 HN7 0.09 +ATOM H42 HN7 0.09 +GROUP +ATOM C5 CN8 -0.18 +ATOM H51 HN8 0.09 +ATOM H52 HN8 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C1 +BOND C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 +BOND C5 H51 C5 H52 +! internal coordinates from parameter file, note initial planar geometry +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C2 *C1 H12 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI CPES 0.00 ! cyclopentane, adm jr. + ! with south atom types +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C1 CN6 -0.18 ! H51 H52 +ATOM H11 HN7 0.09 ! \ / +ATOM H12 HN7 0.09 ! C5 +GROUP ! H41 / \ H11 +ATOM C2 CN8B -0.18 ! \ / \ / +ATOM H21 HN8 0.09 ! H42-C4 C1-H12 +ATOM H22 HN8 0.09 ! | | +GROUP ! H31-C3------C2-H21 +ATOM C3 CN7 -0.18 ! | | +ATOM H31 HN7 0.09 ! H32 H22 +ATOM H32 HN7 0.09 +GROUP +ATOM C4 CN7E -0.18 +ATOM H41 HN7 0.09 +ATOM H42 HN7 0.09 +GROUP +ATOM C5 CN8 -0.18 +ATOM H51 HN8 0.09 +ATOM H52 HN8 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C1 +BOND C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 +BOND C5 H51 C5 H52 +! internal coordinates from parameter file, note initial planar geometry +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C2 *C1 H12 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI BPNP -1.00 ! North carbocyclic sugar with 3'-OPOCH3 + ! used to parameterize epsilon +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C2 CN7 0.01 ! This charge changed from -0.09 to make it +ATOM H21 HN7 0.09 ! compatible with -OPOCH3 +ATOM O3' ON2 -0.57 ! +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 ! +ATOM O5' ON2 -0.57 ! +ATOM C5' CN8B -0.17 ! +ATOM H51' HN8 0.09 ! +ATOM H52' HN8 0.09 ! +ATOM H53' HN8 0.09 ! + ! H61 H62 + ! \ / + ! C6 +GROUP ! / \ H11 +ATOM C4 CN7 -0.18 ! / \ / +ATOM H41 HN7 0.09 ! H51-C5-----C1 H51' +ATOM H42 HN7 0.09 ! | | / +GROUP ! H41-C4 C2--O3'--P--O5'-C5'-H52' +ATOM C3 CN8 -0.18 ! / \ / \ // \ _ \ +ATOM H31 HN8 0.09 ! H42 \ / H21 O1P O2P H53' +ATOM H32 HN8 0.09 ! C3 +GROUP ! / \ +ATOM C1 CN6 -0.09 ! H31 H32 +ATOM H11 HN7 0.09 +GROUP +ATOM C5 CN7E -0.09 ! +ATOM H51 HN7 0.09 ! +GROUP +ATOM C6 CN8 -0.18 ! +ATOM H61 HN8 0.09 ! +ATOM H62 HN8 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C5 C6 C6 C1 C5 H51 +BOND C2 H21 C4 H42 C3 H31 C3 H32 +BOND C4 H41 C6 H61 C1 H11 +BOND C6 H62 C2 O3' O3' P P O1P +BOND P O2P P O5' O5' C5' C5' H51' +BOND C5' H52' C5' H53' +! internal coordinates from parameter file, note initial planar geometry +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 O3' 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C4 *C5 C6 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 +IC O3' C2 C1 C5 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C2 C1 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C2 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C2 0.0 0.0 60.0 0.0 0.0 +IC O5' P O3' C2 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 +IC H51' C5' O5' P 0.0 0.0 60.0 0.0 0.0 +IC H52' C5' O5' P 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' O5' P 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI BPSP -1.00 ! south carbcyclic sugar with 3'-OPOCH3 +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C1 CN7E -0.09 ! H31 H32 +ATOM H11 HN7 0.09 ! \ / + ! C6 +GROUP ! / \ +ATOM C2 CN7E -0.18 ! / \ +ATOM H21 HN7 0.09 ! H51-C5------C1-H11 +ATOM H22 HN7 0.09 ! | | +GROUP ! H41-C4 C2-H22 +ATOM C6 CN8 -0.18 ! / \ / \ +ATOM H61 HN8 0.09 ! H42 \ / H21 +ATOM H62 HN8 0.09 ! C3-H31 +GROUP ! | +ATOM C4 CN8B -0.18 ! O3' H51' +ATOM H41 HN8 0.09 ! \ / +ATOM H42 HN8 0.09 ! P--O5'-C5'-H52' + ! // \ _ \ +GROUP ! O1P O2P H53' +ATOM C5 CN6 -0.09 +ATOM H51 HN7 0.09 +GROUP +ATOM C3 CN7 0.01 ! This charge changed from -0.09 to make it +ATOM H31 HN7 0.09 ! compatible with -OPOCH3 +ATOM O3' ON2 -0.57 ! +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 ! +ATOM O5' ON2 -0.57 ! +ATOM C5' CN8B -0.17 ! +ATOM H51' HN8 0.09 ! +ATOM H52' HN8 0.09 ! +ATOM H53' HN8 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C5 C6 C6 C1 C4 H42 +BOND C1 H11 C2 H21 C2 H22 +BOND C6 H61 C6 H62 C4 H41 +BOND C5 H51 C3 H31 C3 O3' O3' P +BOND P O1P P O2P P O5' O5' C5' +BOND C5' H51' C5' H52' C5' H53' +! internal coordinates +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C2 *C1 C6 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 O3' 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 +IC O3' C3 C4 C5 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3 C4 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3 0.0 0.0 60.0 0.0 0.0 +IC O5' P O3' C3 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 +IC H51' C5' O5' P 0.0 0.0 60.0 0.0 0.0 +IC H52' C5' O5' P 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' O5' P 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI CSAD 0.00 ! carbocyclic sugar with adenine base, south + ! base attached to C1 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7E -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN8B -0.18 ! / \ +ATOM H21S HN8 0.09 ! H51S-C5S----C1S-----------* +ATOM H22S HN8 0.09 ! | | +GROUP ! H41S-C4S C2S-H22S +ATOM C3S CN7 -0.18 ! / \ / \ +ATOM H31S HN7 0.09 ! H42S \ / H21S +ATOM H32S HN7 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN7E -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN6 0.00 ! +ATOM C5 CN5 0.28 ! H61 H62 +ATOM N7 NN4 -0.71 ! \ / +ATOM C8 CN4 0.34 ! N6 +ATOM H8 HN3 0.12 ! | +ATOM N9 NN2 -0.05 ! C6 + ! // \ +ATOM N1 NN3A -0.74 ! N1 C5--N7\\ +ATOM C2 CN4 0.50 ! | || C8-H8 +ATOM H2 HN3 0.13 ! C2 C4--N9/ +ATOM N3 NN3A -0.75 ! / \\ / \ +ATOM C4 CN5 0.43 ! H2 N3 \ +ATOM C6 CN2 0.46 ! \ +ATOM N6 NN1 -0.77 ! \ +ATOM H61 HN1 0.38 ! \ +ATOM H62 HN1 0.38 ! * + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C2S H21S C2S H22S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C1S N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 +BOND C6 N6 N6 H61 N6 H62 C6 C5 +BOND C5 N7 C8 H8 C2 H2 +DOUB N1 C6 C2 N3 C4 C5 N7 C8 + +IMPH H62 C6 H61 N6 N6 N1 C5 C6 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S N9 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C2S C1S N9 1.5284 101.97 147.80 113.71 1.4896 +IC C5S C1S N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C1S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI CSGU 0.00 ! carbocyclic sugar with guanine base, south + ! base attached to C1 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7E -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN8B -0.18 ! / \ +ATOM H21S HN8 0.09 ! H51S-C5S----C1S-----------* +ATOM H22S HN8 0.09 ! | | +GROUP ! H41S-C4S C2S-H22S +ATOM C3S CN7 -0.18 ! / \ / \ +ATOM H31S HN7 0.09 ! H42S \ / H21S +ATOM H32S HN7 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN7E -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN6 0.00 ! +ATOM N9 NN2B -0.14 ! O6 +ATOM C4 CN5 0.14 ! || +GROUP ! C6 +ATOM N3 NN3G -0.66 ! / \ +ATOM C2 CN2 0.76 ! H1-N1 C5--N7\\ +ATOM N1 NN2G -0.38 ! | || C8-H8 +ATOM H1 HN2 0.28 ! C2 C4--N9/ +GROUP ! / \\ / \ +ATOM N2 NN1 -0.64 ! H21-N2 N3 \ +ATOM H21 HN1 0.31 ! | \ +ATOM H22 HN1 0.33 ! H22 \ +GROUP ! * +ATOM C6 CN1 0.55 ! +ATOM O6 ON1 -0.47 ! +ATOM C5 CN5G -0.08 +GROUP +ATOM N7 NN4 -0.69 +ATOM C8 CN4 0.41 +ATOM H8 HN3 0.28 + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C2S H21S C2S H22S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C1S N9 +BOND N9 C4 N9 C8 C4 N3 C8 H8 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 + +IMPH N2 N3 N1 C2 O6 N1 C5 C6 H22 H21 C2 N2 + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +ACCE O6 C6 +ACCE N3 +ACCE N7 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S N9 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C2S C1S N9 1.5284 101.97 147.80 113.71 1.4896 +IC C5S C1S N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C1S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI CSTH 0.00 ! carbocyclic sugar with thymine base, south + ! base attached to C1 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7E -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN8B -0.18 ! / \ +ATOM H21S HN8 0.09 ! H51S-C5S----C1S-----------* +ATOM H22S HN8 0.09 ! | | +GROUP ! H41S-C4S C2S-H22S +ATOM C3S CN7 -0.18 ! / \ / \ +ATOM H31S HN7 0.09 ! H42S \ / H21S +ATOM H32S HN7 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN7E -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN6 0.00 ! +ATOM N1 NN2B -0.30 ! H51 O4 +ATOM C6 CN3 0.17 ! | || +ATOM H6 HN3 0.13 ! H52-C5M C4 H3 +GROUP ! | \ / \ / +ATOM C2 CN1T 0.57 ! H53 C5 N3 +ATOM O2 ON1 -0.47 ! || | +ATOM N3 NN2U -0.46 ! H6-C6 C2 +ATOM H3 HN2 0.36 ! \ / \\ +GROUP ! N1 O2 +ATOM C4 CN1 0.54 ! \ +ATOM O4 ON1 -0.49 ! \ +ATOM C5 CN3T -0.15 ! \ +ATOM C5M CN9 -0.11 ! * +ATOM H51 HN9 0.07 ! +ATOM H52 HN9 0.07 ! +ATOM H53 HN9 0.07 + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C2S H21S C2S H22S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C1S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPH O2 N1 N3 C2 O4 N3 C5 C4 C5M C4 C6 C5 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C2S C1S N1 1.5284 101.97 147.80 113.71 1.4896 +IC C5S C1S N1 C2 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C1S C2 *N1 C6 1.4896 125.97 -180.00 106.0 1.367 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI CSCY 0.00 ! carbocyclic sugar with cytosine base, south + ! base attached to C1 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7E -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN8B -0.18 ! / \ +ATOM H21S HN8 0.09 ! H51S-C5S----C1S-----------* +ATOM H22S HN8 0.09 ! | | +GROUP ! H41S-C4S C2S-H22S +ATOM C3S CN7 -0.18 ! / \ / \ +ATOM H31S HN7 0.09 ! H42S \ / H21S +ATOM H32S HN7 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN7E -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN6 0.00 ! +GROUP ! H42 H41 +ATOM N1 NN2 -0.16 ! \ / +ATOM C6 CN3 0.11 ! N4 +ATOM H6 HN3 0.05 ! | +GROUP ! C4 +ATOM C2 CN1 0.53 ! / \\ +ATOM O2 ON1C -0.48 ! H5-C5 N3 +ATOM N3 NN3 -0.67 ! || | +ATOM C4 CN2 0.62 ! H6-C6 C2 +GROUP ! \ / \\ +ATOM N4 NN1 -0.58 ! N1 O2 +ATOM H41 HN1 0.31 ! \ +ATOM H42 HN1 0.27 ! \ +GROUP ! * +ATOM C5 CN3 -0.10 ! +ATOM H5 HN3 0.10 ! + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C2S H21S C2S H22S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C1S N1 +BOND N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C5 H5 C6 H6 + +IMPH O2 N1 N3 C2 N4 N3 C5 C4 +IMPH H42 C4 H41 N4 + +DONO H42 N4 +DONO H41 N4 +ACCE O2 C2 +ACCE N3 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C2S C1S N1 1.5284 101.97 147.80 113.71 1.4896 +IC C5S C1S N1 C2 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C1S C2 *N1 C6 1.4896 125.97 -180.00 106.0 1.367 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI CNAD 0.00 ! carbocyclic sugar with adenine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7 -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN7 -0.09 ! / \ +ATOM H21S HN7 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CN8 -0.18 ! / \ / \ +ATOM H31S HN8 0.09 ! H42S \ / H21S +ATOM H32S HN8 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN6 -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN7E -0.09 ! +ATOM H11S HN7 0.09 ! +GROUP +ATOM C5 CN5 0.28 ! H61 H62 +ATOM N7 NN4 -0.71 ! \ / +ATOM C8 CN4 0.34 ! N6 +ATOM H8 HN3 0.12 ! | +ATOM N9 NN2 -0.05 ! C6 + ! // \ +ATOM N1 NN3A -0.74 ! N1 C5--N7\\ +ATOM C2 CN4 0.50 ! | || C8-H8 +ATOM H2 HN3 0.13 ! C2 C4--N9/ +ATOM N3 NN3A -0.75 ! / \\ / \ +ATOM C4 CN5 0.43 ! H2 N3 \ +ATOM C6 CN2 0.46 ! \ +ATOM N6 NN1 -0.77 ! \ +ATOM H61 HN1 0.38 ! \ +ATOM H62 HN1 0.38 ! * + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUB N1 C6 C2 N3 C4 C5 N7 C8 + +IMPH H62 C6 H61 N6 N6 N1 C5 C6 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N9 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C4S C3S C2S N9 1.5284 101.97 147.80 113.71 1.4896 +IC C1S C2S N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C2S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +PATCH FIRST NONE LAST NONE + +RESI CNGU 0.00 ! carbocyclic sugar with guanine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7 -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN7 -0.09 ! / \ +ATOM H21S HN7 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CN8 -0.18 ! / \ / \ +ATOM H31S HN8 0.09 ! H42S \ / H21S +ATOM H32S HN8 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN6 -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN7E -0.09 ! +ATOM H11S HN7 0.09 ! +GROUP +ATOM N9 NN2B -0.14 ! O6 +ATOM C4 CN5 0.14 ! || +GROUP ! C6 +ATOM N3 NN3G -0.66 ! / \ +ATOM C2 CN2 0.76 ! H1-N1 C5--N7\\ +ATOM N1 NN2G -0.38 ! | || C8-H8 +ATOM H1 HN2 0.28 ! C2 C4--N9/ +GROUP ! / \\ / \ +ATOM N2 NN1 -0.64 ! H21-N2 N3 \ +ATOM H21 HN1 0.31 ! | \ +ATOM H22 HN1 0.33 ! H22 \ +GROUP ! * +ATOM C6 CN1 0.55 ! +ATOM O6 ON1 -0.47 ! +ATOM C5 CN5G -0.08 +GROUP +ATOM N7 NN4 -0.69 +ATOM C8 CN4 0.41 +ATOM H8 HN3 0.28 + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N9 +BOND N9 C4 N9 C8 C4 N3 C8 H8 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 + +IMPH N2 N3 N1 C2 O6 N1 C5 C6 H22 H21 C2 N2 + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +ACCE O6 C6 +ACCE N3 +ACCE N7 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N9 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C4S C3S C2S N9 1.5284 101.97 147.80 113.71 1.4896 +IC C1S C2S N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C2S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI CNTH 0.00 ! carbocyclic sugar with thymine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7 -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN7 -0.09 ! / \ +ATOM H21S HN7 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CN8 -0.18 ! / \ / \ +ATOM H31S HN8 0.09 ! H42S \ / H21S +ATOM H32S HN8 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN6 -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN7E -0.09 ! +ATOM H11S HN7 0.09 ! +GROUP ! +ATOM N1 NN2B -0.30 ! H51 O4 +ATOM C6 CN3 0.17 ! | || +ATOM H6 HN3 0.13 ! H52-C5M C4 H3 +GROUP ! | \ / \ / +ATOM C2 CN1T 0.57 ! H53 C5 N3 +ATOM O2 ON1 -0.47 ! || | +ATOM N3 NN2U -0.46 ! H6-C6 C2 +ATOM H3 HN2 0.36 ! \ / \\ +GROUP ! N1 O2 +ATOM C4 CN1 0.54 ! \ +ATOM O4 ON1 -0.49 ! \ +ATOM C5 CN3T -0.15 ! \ +ATOM C5M CN9 -0.11 ! * +ATOM H51 HN9 0.07 ! +ATOM H52 HN9 0.07 ! +ATOM H53 HN9 0.07 + + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPH O2 N1 N3 C2 O4 N3 C5 C4 C5M C4 C6 C5 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 +IC C1S C2S N1 C2 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C2S C2 *N1 C6 1.4896 125.97 -180.00 106.0 1.367 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI CNT1 0.00 ! carbocyclic sugar with thymine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7 -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN7 -0.09 ! / \ +ATOM H21S HN7 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CN8 -0.18 ! / \ / \ +ATOM H31S HN8 0.09 ! H42S \ / H21S +ATOM H32S HN8 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN6 -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN7E -0.09 ! +ATOM H11S HN7 0.09 ! +GROUP ! +ATOM N1 NN2B -0.30 ! H51 O4 +ATOM C6 CN3 0.17 ! | || +ATOM H6 HN3 0.13 ! H52-C5M C4 H3 +GROUP ! | \ / \ / +ATOM C2 CN1T 0.57 ! H53 C5 N3 +ATOM O2 ON1 -0.47 ! || | +ATOM N3 NN2U -0.46 ! H6-C6 C2 +ATOM H3 HN2 0.36 ! \ / \\ +GROUP ! N1 O2 +ATOM C4 CN1 0.54 ! \ +ATOM O4 ON1 -0.49 ! \ +ATOM C5 CN3T -0.15 ! \ +ATOM C5M CN9 -0.11 ! * +ATOM H51 HN9 0.07 ! +ATOM H52 HN9 0.07 ! +ATOM H53 HN9 0.07 + + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPH O2 N1 N3 C2 O4 N3 C5 C4 C5M C4 C6 C5 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 +IC C1S C2S N1 C2 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C2S C2 *N1 C6 1.4896 125.97 -180.00 106.0 1.367 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI CNT2 0.00 ! carbocyclic sugar with thymine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7 -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN7 -0.09 ! / \ +ATOM H21S HN7 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CN8 -0.18 ! / \ / \ +ATOM H31S HN8 0.09 ! H42S \ / H21S +ATOM H32S HN8 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN6 -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN7E -0.09 ! +ATOM H11S HN7 0.09 ! +GROUP ! +ATOM N1 NN2B -0.30 ! H51 O4 +ATOM C6 CN3 0.17 ! | || +ATOM H6 HN3 0.13 ! H52-C5M C4 H3 +GROUP ! | \ / \ / +ATOM C2 CN1T 0.57 ! H53 C5 N3 +ATOM O2 ON1 -0.47 ! || | +ATOM N3 NN2U -0.46 ! H6-C6 C2 +ATOM H3 HN2 0.36 ! \ / \\ +GROUP ! N1 O2 +ATOM C4 CN1 0.54 ! \ +ATOM O4 ON1 -0.49 ! \ +ATOM C5 CN3T -0.15 ! \ +ATOM C5M CN9 -0.11 ! * +ATOM H51 HN9 0.07 ! +ATOM H52 HN9 0.07 ! +ATOM H53 HN9 0.07 + + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPH O2 N1 N3 C2 O4 N3 C5 C4 C5M C4 C6 C5 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 +IC C1S C2S N1 C2 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C2S C2 *N1 C6 1.4896 125.97 -180.00 106.0 1.367 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI CNT3 0.00 ! carbocyclic sugar with thymine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7 -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN7 -0.09 ! / \ +ATOM H21S HN7 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CN8 -0.18 ! / \ / \ +ATOM H31S HN8 0.09 ! H42S \ / H21S +ATOM H32S HN8 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN6 -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN7E -0.09 ! +ATOM H11S HN7 0.09 ! +GROUP ! +ATOM N1 NN2B -0.30 ! H51 O4 +ATOM C6 CN3 0.17 ! | || +ATOM H6 HN3 0.13 ! H52-C5M C4 H3 +GROUP ! | \ / \ / +ATOM C2 CN1T 0.57 ! H53 C5 N3 +ATOM O2 ON1 -0.47 ! || | +ATOM N3 NN2U -0.46 ! H6-C6 C2 +ATOM H3 HN2 0.36 ! \ / \\ +GROUP ! N1 O2 +ATOM C4 CN1 0.54 ! \ +ATOM O4 ON1 -0.49 ! \ +ATOM C5 CN3T -0.15 ! \ +ATOM C5M CN9 -0.11 ! * +ATOM H51 HN9 0.07 ! +ATOM H52 HN9 0.07 ! +ATOM H53 HN9 0.07 + + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPH O2 N1 N3 C2 O4 N3 C5 C4 C5M C4 C6 C5 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 +IC C1S C2S N1 C2 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C2S C2 *N1 C6 1.4896 125.97 -180.00 106.0 1.367 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + + +RESI CNCY 0.00 ! carbocyclic sugar with cytosine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi +! +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties +! +GROUP ! +ATOM C4S CN7 -0.18 ! H61S H62S +ATOM H41S HN7 0.09 ! \ / +ATOM H42S HN7 0.09 ! C6S +GROUP ! / \ +ATOM C2S CN7 -0.09 ! / \ +ATOM H21S HN7 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CN8 -0.18 ! / \ / \ +ATOM H31S HN8 0.09 ! H42S \ / H21S +ATOM H32S HN8 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CN6 -0.09 ! +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 ! +ATOM H61S HN8 0.09 ! +ATOM H62S HN8 0.09 ! +GROUP +ATOM C1S CN7E -0.09 ! +ATOM H11S HN7 0.09 ! +GROUP ! H42 H41 +ATOM N1 NN2 -0.16 ! \ / +ATOM C6 CN3 0.11 ! N4 +ATOM H6 HN3 0.05 ! | +GROUP ! C4 +ATOM C2 CN1 0.53 ! / \\ +ATOM O2 ON1C -0.48 ! H5-C5 N3 +ATOM N3 NN3 -0.67 ! || | +ATOM C4 CN2 0.62 ! H6-C6 C2 +GROUP ! \ / \\ +ATOM N4 NN1 -0.58 ! N1 O2 +ATOM H41 HN1 0.31 ! \ +ATOM H42 HN1 0.27 ! \ +GROUP ! * +ATOM C5 CN3 -0.10 ! +ATOM H5 HN3 0.10 ! + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C5 H5 C6 H6 + +IMPH O2 N1 N3 C2 N4 N3 C5 C4 +IMPH H42 C4 H41 N4 + +DONO H42 N4 +DONO H41 N4 +ACCE O2 C2 +ACCE N3 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 +IC C1S C2S N1 C2 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C2S C2 *N1 C6 1.4896 125.97 -180.00 106.0 1.367 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI B5NP -1.00 ! carbocyclic sugar with 5' OPOCH3 + ! north conformation + ! used to parameterize gamma + ! +GROUP ! Note : C1 charge changed from -0.09 to 0.00 to +ATOM C5' CN8B -0.08 ! accomodate the CH2-OPOCH3 +ATOM H51' HN8 0.09 ! +ATOM H52' HN8 0.09 ! +ATOM O5' ON2 -0.57 ! +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 ! +ATOM O3' ON2 -0.57 ! +ATOM C3' CN8B -0.17 ! +ATOM H31' HN8 0.09 ! H31' +ATOM H32' HN8 0.09 ! H61 H62 / +ATOM H33' HN8 0.09 ! \ / H51' O1P C3'-H32' + ! C6 | | / \ +GROUP ! / \ C5'-O5'-P-O3' H33' +ATOM C4 CN7 -0.18 ! / \ / \ | +ATOM H41 HN7 0.09 ! H51-C5-----C1 H52' O2P +ATOM H42 HN7 0.09 ! | | +GROUP ! H41-C4 C2--H21 +ATOM C3 CN8 -0.18 ! / \ / \ +ATOM H31 HN8 0.09 ! H42 \ / O3T-H3T +ATOM H32 HN8 0.09 ! C3 +GROUP ! / \ +ATOM C1 CN6 0.00 ! H31 H32 +GROUP +ATOM C2 CN7 0.14 ! changed from -0.18 to accomodate O3'-H +ATOM H21 HN7 0.09 ! +ATOM O3T ON5 -0.66 ! +ATOM H3T HN5 0.43 ! +GROUP +ATOM C5 CN7E -0.09 ! +ATOM H51 HN7 0.09 ! +GROUP +ATOM C6 CN8 -0.18 ! +ATOM H61 HN8 0.09 ! +ATOM H62 HN8 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C5 C6 C6 C1 C5 H51 +BOND C2 H21 C4 H42 C3 H31 C3 H32 +BOND C4 H41 C6 H61 C1 C5' C2 O3T +BOND C6 H62 C5' O5' O5' P P O1P +BOND P O2P P O3' O3' C3' C3' H31' +BOND C3' H32' C3' H33' C5' H51' C5' H52' +BOND O3T H3T + +! internal coordinates from parameter file, note initial planar geometry +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 C5' 0.0000 0.00 240.0 0.00 0.0000 +IC C1 O5' *C5' H51' 0.0000 0.00 120.0 0.00 0.0000 +IC C1 O5' *C5' H52' 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C2 O3T 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C2 O3T H3T 0.0000 0.00 180.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C4 *C5 C6 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 +IC C5' C1 C2 O3T 0.0000 0.00 70.0 0.00 0.0000 +IC O5' C5' C1 C2 0.0000 0.00 60.0 0.00 0.0000 +IC P O5' C5' C1 0.0 0.0 180.00 0.0 0.0 +IC O1P P O5' C5' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O5' C5' 0.0 0.0 60.0 0.0 0.0 +IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 +IC O5' P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H31' C3' O3' P 0.0 0.0 60.0 0.0 0.0 +IC H32' C3' O3' P 0.0 0.0 -60.0 0.0 0.0 +IC H33' C3' O3' P 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI B5SP -1.00 ! south carbcyclic sugar with C5'-OPOCH3 + +GROUP ! +ATOM C1 CN7E -0.09 ! +ATOM H11 HN7 0.09 ! H61 H62 +GROUP ! \ / +ATOM C3 CN7 0.14 ! C6 +ATOM H31 HN7 0.09 ! / \ +ATOM O3T ON5 -0.66 ! H51-C5------C1-H11 H51' O1P H31' +ATOM H3T HN5 0.43 ! | | / | / +GROUP ! H41-C4 C2-----C5'-O5'-P-O3'-C3'-H32' +ATOM C6 CN8 -0.18 ! / \ / \ \ | \ +ATOM H61 HN8 0.09 ! H42 \ / H21 H52' O2P H33' +ATOM H62 HN8 0.09 ! C3-H31 +GROUP ! | +ATOM C4 CN8B -0.18 ! O3T +ATOM H41 HN8 0.09 ! \ +ATOM H42 HN8 0.09 ! H3T +GROUP ! +ATOM C5 CN6 -0.09 ! +ATOM H51 HN7 0.09 ! +GROUP +ATOM C2 CN7E -0.09 ! This charge changed from -0.18 to make it +ATOM H21 HN7 0.09 ! compatible with C5'-OPOCH3 +ATOM C5' CN8B -0.08 ! +ATOM H51' HN8 0.09 ! +ATOM H52' HN8 0.09 ! +ATOM O5' ON2 -0.57 ! +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 ! +ATOM O3' ON2 -0.57 ! +ATOM C3' CN8B -0.17 ! +ATOM H31' HN8 0.09 ! +ATOM H32' HN8 0.09 ! +ATOM H33' HN8 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C5 C6 C6 C1 C2 C5' +BOND C4 H41 C4 H42 C5' H51' C1 H11 +BOND C5' H52' C6 H61 C6 H62 C2 H21 +BOND C5 H51 C3 H31 C3 O3T C5' O5' +BOND O5' P O3T H3T +BOND P O1P P O2P P O3' O3' C3' +BOND C3' H31' C3' H32' C3' H33' + +! internal coordinates +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C3 O3T H3T 0.0000 0.00 270.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 O3T 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C1 *C2 C5' 0.0000 0.00 120.0 0.00 0.0000 +IC C2 O5' *C5' H51' 0.0000 0.00 120.0 0.00 0.0000 +IC C2 O5' *C5' H52' 0.0000 0.00 240.0 0.00 0.0000 +IC C5 C3 *C2 H21 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C4 *C5 C6 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 +IC C5' C2 C3 O3T 0.0000 0.00 150.0 0.00 0.0000 +IC O5' C5' C2 C3 0.0000 0.00 60.0 0.00 0.0000 +IC P O5' C5' C2 0.0 0.0 180.00 0.0 0.0 +IC O1P P O5' C5' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O5' C5' 0.0 0.0 60.0 0.0 0.0 +IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 +IC O5' P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H31' C3' O3' P 0.0 0.0 60.0 0.0 0.0 +IC H32' C3' O3' P 0.0 0.0 -60.0 0.0 0.0 +IC H33' C3' O3' P 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +! patches for carbocyclic sugars + +PRES BCPE 0.00 ! patch for RESI CPEN + ! to create Bicyclo[3.1.0]hexane, adm jr., + ! north atom types +! +! avoids problems with a residue due to the 3-membered ring of +! the cyclopropane ring +! +DELE ATOM H12 +DELE ATOM H52 +GROUP +ATOM C1 CN7E -0.09 +ATOM H11 HN7 0.09 +GROUP +ATOM C5 CN6 -0.09 +ATOM H51 HN7 0.09 +GROUP +ATOM C6 CN8 -0.18 +ATOM H61 HN8 0.09 +ATOM H62 HN8 0.09 + +BOND C1 C6 C5 C6 +BOND C6 H61 C6 H62 + +! internal coordinates to build additional atoms +IC C5 C2 *C1 C6 0.0000 0.00 300.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 + +PRES BCPF 0.00 ! patch for RESI CPEN + ! to create Bicyclo[3.1.0]hexane, adm jr. + ! south atom types +! +! avoids problems with a residue due to the 3-membered ring of +! the cyclopropane ring +! +DELE ATOM H12 +DELE ATOM H52 +GROUP +ATOM C1 CN6 -0.09 +ATOM H11 HN7 0.09 +GROUP +ATOM C5 CN7E -0.09 +ATOM H51 HN7 0.09 +GROUP +ATOM C6 CN8 -0.18 +ATOM H61 HN8 0.09 +ATOM H62 HN8 0.09 + +BOND C1 C6 C5 C6 +BOND C6 H61 C6 H62 + +! internal coordinates to build additional atoms +IC C5 C2 *C1 C6 0.0000 0.00 300.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 + +PRES PSTH 0.10 ! patch to convert NA furanose ring + ! to a Bicyclo[3.1.0]hexane, for thymine + ! 1,6 methano compound (SOUTH conformation) +! N.B. +! 1) Rename certain atoms to make patch work +! Perform the following prior to invoking this patch +!rename atom C5S sele type O4' end +!rename atom C4S sele type C4' end +!rename atom C3S sele type C3' end +!rename atom C2S sele type C2' end +!rename atom C1S sele type C1' end +!rename atom H41S sele type H4' end +!rename atom H21S sele type H2' end +!rename atom H22S sele type H2'' end +!rename atom H31S sele type H3' end + +DELE ATOM H1' +GROUP +ATOM C4S CN7E -0.09 ! This charge changed from -0.18 to make it +ATOM H41S HN7 0.09 ! compatible with C5'-OPO +GROUP +ATOM C2S CN8B -0.18 +ATOM H21S HN8 0.09 +ATOM H22S HN8 0.09 +GROUP +ATOM C3S CN7 0.01 ! This charge changed from -0.09 to make it +ATOM H31S HN7 0.09 ! compatible with -OPOCH2 +GROUP +ATOM C5S CN7E -0.09 +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 +ATOM H61S HN8 0.09 +ATOM H62S HN8 0.09 +GROUP +ATOM C1S CN6 0.00 + +BOND C5S C6S C6S C1S +BOND C5S H51S C6S H61S +BOND C6S H62S + +! internal coordinates +IC P O5' C5' C4S 0.0000 0.00 160.0 0.00 0.0000 +IC O5' C5' C4S C3S 0.0000 0.00 50.0 0.00 0.0000 +IC O5' P O3' C3S 0.0000 0.00 300.0 0.00 0.0000 +IC P O3' C3S C4S 0.0000 0.00 190.0 0.00 0.0000 +IC C3S C2S C1S C5S 0.0000 0.00 330.0 0.00 0.0000 +IC C2S C1S C5S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C2S C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C2S C1S C5S C6S 0.0000 0.00 100.0 0.00 0.0000 +IC C4S C5S C1S C6S 0.0000 0.00 100.0 0.00 0.0000 +IC C2S C1S C6S H61S 0.0000 0.00 170.0 0.00 0.0000 +IC C2S C1S C6S H62S 0.0000 0.00 20.0 0.00 0.0000 +IC N1 C1S C5S C6S 0.0000 0.00 130.0 0.00 0.0000 +IC C2 N1 C1S C6S 0.0000 0.00 20.0 0.00 0.0000 +IC C2S C1S C5S H51S 0.0000 0.00 170.0 0.00 0.0000 + +PRES PNTH 0.10 ! patch to convert NA furanose ring + ! to a Bicyclo[3.1.0]hexane, thymine + ! 4,6 methano compound (NORTH conformation) + +! N.B. +! 1) Rename certain atoms to make patch work +! Perform the following prior to invoking this patch +!rename atom C1S sele type O4' end +!rename atom C5S sele type C4' end +!rename atom C4S sele type C3' end +!rename atom C3S sele type C2' end +!rename atom C2S sele type C1' end +!rename atom H21S sele type H1' end +!rename atom H31S sele type H2' end +!rename atom H32S sele type H2'' end +!rename atom H41S sele type H3' end +!rename atom C6S sele type C6' end + +DELE ATOM H4' +GROUP +ATOM C4S CN7 0.01 ! This charge changed from -0.18 to make it +ATOM H41S HN7 0.09 ! compatible with -OPOCH2 +GROUP +ATOM C2S CN7 -0.09 +ATOM H21S HN7 0.09 +GROUP +ATOM C3S CN8 -0.18 +ATOM H31S HN8 0.09 +ATOM H32S HN8 0.09 +GROUP +ATOM C5S CN6 0.00 ! This charge changed from -0.09 to make it +GROUP ! compatible with C5'-OPO +ATOM C6S CN8 -0.18 +ATOM H61S HN8 0.09 +ATOM H62S HN8 0.09 +GROUP +ATOM C1S CN7E -0.09 +ATOM H11S HN7 0.09 + +BOND C5S C6S C6S C1S +BOND C1S H11S C6S H61S C6S H62S + +! internal coordinates +IC P O5' C5' C4S 0.0000 0.00 160.0 0.00 0.0000 +IC O5' C5' C4S C3S 0.0000 0.00 50.0 0.00 0.0000 +IC O5' P O3' C3S 0.0000 0.00 300.0 0.00 0.0000 +IC P O3' C3S C4S 0.0000 0.00 190.0 0.00 0.0000 +IC C2S C1S C5S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 330.0 0.00 0.0000 +IC C3S C2S C1S H11S 0.0000 0.00 162.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5' C1S *C5S C6S 0.0000 0.00 108.0 60.00 0.0000 + +PRES PSAD 0.10 ! patch to convert NA furanose ring + ! to a Bicyclo[3.1.0]hexane, for adenine + ! 1,6 methano compound (SOUTH conformation) + +! N.B. +! 1) Rename certain atoms to make patch work +! Perform the following prior to invoking this patch +!rename atom C5S sele type O4' end +!rename atom C4S sele type C4' end +!rename atom C3S sele type C3' end +!rename atom C2S sele type C2' end +!rename atom C1S sele type C1' end +!rename atom H41S sele type H4' end +!rename atom H21S sele type H2' end +!rename atom H22S sele type H2'' end +!rename atom H31S sele type H3' end + +DELE ATOM H1' +GROUP +ATOM C4S CN7E -0.09 ! This charge changed from -0.18 to make it +ATOM H41S HN7 0.09 ! compatible with C5'-OPO +GROUP +ATOM C2S CN8B -0.18 +ATOM H21S HN8 0.09 +ATOM H22S HN8 0.09 +GROUP +ATOM C3S CN7 0.01 ! This charge changed from -0.09 to make it +ATOM H31S HN7 0.09 ! compatible with -OPOCH2 +GROUP +ATOM C5S CN7E -0.09 +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 +ATOM H61S HN8 0.09 +ATOM H62S HN8 0.09 +GROUP +ATOM C1S CN6 0.00 + +BOND C5S C6S C6S C1S +BOND C5S H51S C6S H61S +BOND C6S H62S + +! internal coordinates +IC C3S C2S C1S C6S 0.0000 0.00 311.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC N9 C5S *C1S C6S 0.0000 0.00 254.0 60.00 0.0000 +IC C2S C1S C5S H51S 0.0000 0.00 170.0 0.00 0.0000 + +PRES PNAD 0.10 ! patch to convert NA furanose ring + ! to a Bicyclo[3.1.0]hexane, adenine + ! 4,6 methano compound (NORTH conformation) + +! N.B. +! 1) Rename certain atoms to make patch work +! Perform the following prior to invoking this patch +!rename atom C1S sele type O4' end +!rename atom C5S sele type C4' end +!rename atom C4S sele type C3' end +!rename atom C3S sele type C2' end +!rename atom C2S sele type C1' end +!rename atom H21S sele type H1' end +!rename atom H31S sele type H2' end +!rename atom H32S sele type H2'' end +!rename atom H41S sele type H3' end +!rename atom C6S sele type C6' end + +DELE ATOM H4' +GROUP +ATOM C4S CN7 0.01 ! This charge changed from -0.18 to make it +ATOM H41S HN7 0.09 ! compatible with -OPOCH2 +GROUP +ATOM C2S CN7 -0.09 +ATOM H21S HN7 0.09 +GROUP +ATOM C3S CN8 -0.18 +ATOM H31S HN8 0.09 +ATOM H32S HN8 0.09 +GROUP +ATOM C5S CN6 0.00 ! This charge changed from -0.09 to make it +GROUP ! compatible with C5'-OPO +ATOM C6S CN8 -0.18 +ATOM H61S HN8 0.09 +ATOM H62S HN8 0.09 +GROUP +ATOM C1S CN7E -0.09 +ATOM H11S HN7 0.09 + +BOND C5S C6S C6S C1S +BOND C1S H11S C6S H61S C6S H62S + +! internal coordinates +IC P O5' C5' C4S 0.0000 0.00 160.0 0.00 0.0000 +IC O5' C5' C4S C3S 0.0000 0.00 50.0 0.00 0.0000 +IC O5' P O3' C3S 0.0000 0.00 300.0 0.00 0.0000 +IC P O3' C3S C4S 0.0000 0.00 190.0 0.00 0.0000 +IC C2S C1S C5S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 330.0 0.00 0.0000 +IC C3S C2S C1S H11S 0.0000 0.00 162.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5' C1S *C5S C6S 0.0000 0.00 108.0 60.00 0.0000 + +PRES PSNB 0.10 ! patch to convert NA furanose ring without base + ! to a Bicyclo[3.1.0]hexane, for thymine + ! 1,6 methano compound (SOUTH conformation) +! N.B. +! 1) Apply patch DELB before this patch +! 2) Rename certain atoms to make patch work +! Perform the following prior to invoking this patch +!rename atom C5S sele type O4' end +!rename atom C4S sele type C4' end +!rename atom C3S sele type C3' end +!rename atom C2S sele type C2' end +!rename atom C1S sele type C1' end +!rename atom H41S sele type H4' end +!rename atom H21S sele type H2' end +!rename atom H22S sele type H2'' end +!rename atom H31S sele type H3' end + +DELE ATOM H1' + +GROUP +ATOM C4S CN7E -0.09 ! This charge changed from -0.18 to make it +ATOM H41S HN7 0.09 ! compatible with C5'-OPO +GROUP +ATOM C2S CN8B -0.18 +ATOM H21S HN8 0.09 +ATOM H22S HN8 0.09 +GROUP +ATOM C3S CN7 0.01 ! This charge changed from -0.09 to make it +ATOM H31S HN7 0.09 ! compatible with -OPOCH2 +GROUP +ATOM C5S CN7E -0.09 +ATOM H51S HN7 0.09 +GROUP +ATOM C6S CN8 -0.18 +ATOM H61S HN8 0.09 +ATOM H62S HN8 0.09 +GROUP +ATOM C1S CN6 -0.09 ! the charge was changed from 0.00 to accomodate absence of base +ATOM H11S HN7 0.09 + +BOND C5S C6S C6S C1S C1S H11S +BOND C5S H51S C6S H61S +BOND C6S H62S + +! internal coordinates +IC C3S C2S C1S C6S 0.0000 0.00 311.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC H11S C5S *C1S C6S 0.0000 0.00 254.0 60.00 0.0000 +IC H51S C5S C1S C6S 0.0000 0.00 180.0 60.00 0.0000 + +PRES PNNB 0.10 ! patch to convert NA furanose ring without base + ! to a Bicyclo[3.1.0]hexane, for adenine + ! 4,6 methano compound (NORTH conformation) + ! NOTE: Apply patch delb before applying this patch + +! N.B. +! 1) Apply patch DELB before this patch +! 2) Rename certain atoms to make patch work +! Perform the following prior to invoking this patch +!rename atom C1S sele type O4' end +!rename atom C5S sele type C4' end +!rename atom C4S sele type C3' end +!rename atom C3S sele type C2' end +!rename atom C2S sele type C1' end +!rename atom H21S sele type H1' end +!rename atom H31S sele type H2' end +!rename atom H32S sele type H2'' end +!rename atom H41S sele type H3' end +!rename atom C6S sele type C6' end + +DELE ATOM H4' +GROUP +ATOM C4S CN7 0.01 ! This charge changed from -0.18 to make it +ATOM H41S HN7 0.09 ! compatible with -OPOCH2 +GROUP +ATOM C2S CN7 -0.18 ! This charge was changed from -0.09 to +ATOM H21S HN7 0.09 ! accomodate the absence of base +ATOM H22S HN7 0.09 +GROUP +ATOM C3S CN8 -0.18 +ATOM H31S HN8 0.09 +ATOM H32S HN8 0.09 +GROUP +ATOM C5S CN6 0.00 ! This charge changed from -0.09 to make it +GROUP ! compatible with C5'-OPO +ATOM C6S CN8 -0.18 +ATOM H61S HN8 0.09 +ATOM H62S HN8 0.09 +GROUP +ATOM C1S CN7E -0.09 +ATOM H11S HN7 0.09 + +BOND C5S C6S C6S C1S C2S H22S +BOND C1S H11S C6S H61S C6S H62S + +! internal coordinates +IC C3S C2S C1S C6S 0.0000 0.00 311.0 0.00 0.0000 +IC C3S C2S C1S H11S 0.0000 0.00 162.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5' C1S *C5S C6S 0.0000 0.00 108.0 60.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 120.0 0.00 0.0000 + +PRES ABCF 0.00 ! patch to convert a standard base into an + ! abasic carbocyclic furanose + ! o4' replaced by c42 + +! N.B. +! 1) Apply patch PRES DELB prior to this patch +! 2) Rename certain atoms to make patch work +! Perform the following prior to invoking this patch +!rename atom C42 sele type O4' end + +GROUP +ATOM C4' CN7 -0.09 +ATOM H4' HN7 0.09 +ATOM C42 CN8 -0.18 +ATOM H41' HN8 0.09 +ATOM H42' HN8 0.09 +ATOM C1' CN8B -0.18 +ATOM H1' HN8 0.09 +ATOM H1'' HN8 0.09 + +BOND C1' H1'' C42 H41' C42 H42' + +BILD H1'' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' C1' *C42 H41' 0.0 0.0 240.0 0.0 0.0 +BILD C4' C1' *C42 H42' 0.0 0.0 60.0 0.0 0.0 + +END + +read para card flex append +* parameters developed in collaboration with Daniel Barsky +* + +ATOMS +!carbocyclic section +MASS 416 CN6 12.011000 +MASS 417 CN7E 12.011000 +!base section +MASS 469 HNP 1.008000 ! pure aromatic H +MASS 470 HNE1 1.008000 ! for alkene; RHC=CR (modified thy patch Sasha) +MASS 471 HNE2 1.008000 ! for alkene; H2C=CR (modified thy patch Sasha) +MASS 472 CN3D 12.011000 ! Nucleic acid aromatic carbon for 5MC +MASS 473 CNE1 12.011000 ! for alkene; RHC=CR (modified thy patch Sasha) +MASS 474 CNE2 12.011000 ! for alkene; H2C=CR (modified thy patch Sasha) +MASS 475 CNA 12.011000 ! pure aromatic carbon +MASS 476 CNA2 12.011000 ! pure aromatic carbon bound to F +MASS 477 CNG 12.011000 ! guanidinium type carbon +MASS 478 NN1C 14.007000 ! Nucleic acid imino nitrogen (cyt taut Sasha) +MASS 479 NN2C 14.007000 ! Nucleic acid protonated ring nitrogen (cyt taut Sasha) +MASS 480 NN3I 14.007000 ! Nucleic acid unprotonated ring nitrogen, inosine N3 +MASS 481 NNG 14.007000 ! guanidinium type nitrogen +MASS 482 FNA 18.998400 ! Aromatic fluorine +!backbone section +MASS 483 ON2M 15.999400 ! ether oxygen for methylated C2' of ribose + +BONDS +! +!atom types Kb b0 +! +CN4 NN2G 350.0 1.365 !Inosine, adm jr. 2/94 +CN4 NN3I 450.0 1.295 !Inosine, adm jr. 2/94 +CN5 NN3I 350.0 1.332 !Inosine, adm jr. 9/98 +CN2 CN3D 260.0 1.405 !5mc, adm jr. 9/9/93, from cn2 cn3 +CN3D CN3 560.0 1.335 !5mc, adm jr. 9/9/93, from cn3 cn3 +CN3D CN9 230.0 1.480 !5mc, adm jr. 9/9/93, from cn3 cn9 +!guanine tautomer terms +CN1 NN3G 480.0 1.310 !from CN1 NN3 (of cyt), db 6/97 +CN1 ON5 450.0 1.330 !from CN6 ON5 (RIBOSE), db 6/97 +!cytosine tautomer terms +CN1 NN2C 400.0 1.383 !c2-n3 +CN2 NN2C 400.0 1.389 !c4-n3 +CN2 NN1C 555.0 1.343 !c4-n4 +NN1C HN1 488.0 1.00 +NN2C HN2 474.0 1.01 +!1-Ethyl Guanine +NN2G CN8 400.0 1.340 ! (Sasha) +!3-Ethyl Cytosine +NN3 CN8 400.0 1.340 ! (Sasha) +!difluorotoluene, adm jr. +CNA CNA 305.000 1.3750 !benzene, JES 8/25/89 +CN9 CNA 230.000 1.4900 !phe,tyr, JES 8/25/89 +CN8 CNA 230.000 1.4900 !phe,tyr, JES 8/25/89 +CN7B CNA 230.000 1.4900 !phe,tyr, JES 8/25/89 +HNP CNA 340.000 1.0800 !phe,tyr JES 8/25/89 +CNA2 CNA 305.000 1.3700 !benzene, JES 8/25/89 +HN3 CNA 340.000 1.0800 !dft, adm jr. +CNA2 FNA 400.0 1.3580 !dft, adm jr. +!5-ethylene-thymine +CN3T CNE1 365.0 1.475 ! (modified thy, Sasha) +CNE2 HNE2 365.0 1.100 ! (modified thy, Sasha) +CNE2 CNE1 500.0 1.342 ! (modified thy, Sasha) +CNE1 HNE1 360.5 1.100 ! (modified thy, Sasha) +!C5-Me CYT with N4-Ethyl-Methyl, N4EM, edarian 2009-06 +NN1 CN8 430.00 1.450 ! +!C8-Amino-Phenyl-Guanine, G8AP, edarian, 2009-11 +CN4 NN1 300.0 1.378 !G, adm jr. 11/97 CN4 NN2B +NN1 HN2 474.0 1.010 !G, adm jr. 11/97 HN2 NN2B. DIFFERENT COPY OF SAME PARAMETER IN toppar_all27_na_bkb_modifications.str +NN1 CN3 305.00 1.414 ! RETINOL PACP ! CG2R61 NG2S1 +!params for GUANIDINIUM tail patch at N4 of CYT, 4EG1, edarian, 2009-11 +NNG CN8 261.000 1.490 !NC2 CT2 261.000 1.4900 ! ALLOW ALI POL +NNG CNG 463.000 1.365 !NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO, NA param 360.0 1.366 +NNG HN1 455.000 1.000 !NC2 HC 455.000 1.0000 ! ALLOW POL , NA param 488.0 1.00 + +!backbone section +NN1 CN8B 360.0 1.462 ! +NN1 P 180.0 1.792 ! +NN1 HN2 432.5 1.025 ! +NN1 CN7 360.0 1.462 ! +ON2 HN8 545.0 0.960 !copied from RIBOSE, MeOH for thni +ON5 HN7 545.0 0.960 !copied from RIBOSE, MeOH for n5ph +!PNA related terms +!HN2 NN1 488.0 1.000 +NC2 CD 200.0 1.480 +CT2 NN2 300.0 1.480 +CT2 NN2B 300.0 1.480 +O CD 620.0 1.230 ! DIFFERENT COPY OF SAME PARAMETER IN par_all22_prot.prm generates "Error: Repeated BOND" +NH2 C 430.0 1.360 +NH2 HN1 405.0 0.980 +NH1 HN1 405.0 0.980 +! THF2 - 2'-OMe ribose model compound, edarian, 2009-07 +CN7B ON2M 334.3 1.411 ! CG2R61 OG311 -- PROT MeOH, EMB 10/10/89, +CN9 ON2M 360.0 1.415 ! diethylether, alex + +!carbocyclic section +CN8 CN6 400.0 1.500 ! south/north, C6-C1/C5 +CN7 CN6 222.5 1.538 ! north, C2-C1 +CN7E CN8B 222.5 1.516 ! south, C4-C5' +CN6 CN8B 222.5 1.532 ! south, C1-C2 +CN6 HN7 309.0 1.111 ! south/north, only model compd, C1/C5-H +CN7E HN7 309.0 1.105 ! south/north, C5-H51/C1-H11 +CN7E CN6 400.0 1.535 ! south/north, C1-C5 +CN7E CN8 400.0 1.500 ! south/north, C1/C5-C6 +CN7E CN7E 222.5 1.512 ! south, C4-C5 +CN7 CN7E 222.5 1.510 ! north, C1-C2, and south, C4-C3 +! C1'-N9 (purines)/C1'-N1 (pyrimidines) +CN6 NN2 220.0 1.456 ! C1-N1/N9, A/C +CN7 NN2 220.0 1.456 ! C1-N1/N9, A/C +CN6 NN2B 220.0 1.458 ! C1-N1/N9, G/T/U +CN7 NN2B 220.0 1.458 ! C1-N1/N9, G/T/U + +ANGLES +! +!atom types Ktheta Theta0 Kub S0 +! +! Inosine, adm jr., 9/98 update +HN3 CN4 NN3I 35.0 116.75 !c2 +HN3 CN4 NN2G 35.0 115.75 !c2 +NN3I CN4 NN2G 80.0 127.5 !c2 +CN5G CN5 NN3I 100.0 127.0 !c4, r6 +NN2B CN5 NN3I 140.0 128.4 !c4, r5 +CN1 NN2G CN4 125.0 129.7 !n1 +CN4 NN2G HN2 40.5 117.0 !n1 +CN4 NN3I CN5 90.0 108.4 !n3 +CN3D CN2 NN1 110.0 116.4 !5mc, adm jr. 9/9/93 +CN3D CN2 NN3 30.0 121.3 !5mc, adm jr. 9/9/93 +CN2 CN3D CN3 100.0 117.8 !5mc, adm jr. 9/9/93 +CN2 CN3D CN9 40.0 118.0 !5mc, adm jr. 9/9/93 +CN3 CN3D CN9 40.0 124.2 !5mc, adm jr. 9/9/93 +CN3D CN3 HN3 30.0 122.0 !5mc, adm jr. 9/9/93 +CN3D CN3 NN2 100.0 124.2 !5mc, adm jr. 9/9/93 +CN3D CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred +!guanine tautomer terms +CN1 NN3G CN2 125.0 122.3 !n1, Sasha +NN3G CN2 NN3G 70.0 115.2 !c2, Sasha +NN3G CN1 CN5G 67.0 123.6 !c6, Sasah +NN3G CN1 ON5 75.7 121.6 !o6 +ON5 CN1 CN5G 75.7 114.8 !o6 +CN1 ON5 HN5 60.0 114.7 !h5 +!cytosine tautomer terms +NN2C CN1 NN2 35.0 115.5 !c2, ring +CN2 NN2C CN1 35.0 130.2 !n3, ring +NN2C CN2 CN3 35.0 109.5 !c4, ring +CN2 NN2C HN2 40.5 116.1 !h3 +CN1 NN2C HN2 40.5 113.7 !h3 +NN2C CN1 ON1C 70.0 125.1 !o2 +NN2C CN2 NN1C 90.0 126.8 !n4 +CN3 CN2 NN1C 90.0 123.7 !n4 +CN2 NN1C HN1 51.0 113.0 !h4 +!1-Ethyl Guanine +CN2 NN2G CN8 70.0 117.3 !c2-n1-c1a +CN1 NN2G CN8 70.0 111.6 !c6-n1-c1a +NN2G CN8 CN9 70.0 119.9 !n1-c1a-c1b +NN2G CN8 HN8 33.43 110.10 22.53 2.179 !from alkanes +!3-Ethyl Cytosine, Sasha +CN1 NN3 CN8 70.0 116.0 !c2-n3-c3a +CN2 NN3 CN8 70.0 124.9 !c4-n3-c3a +CN9 CN8 NN3 70.0 114.5 !n3-c3a-c3b +NN3 CN8 HN8 33.43 110.10 22.53 2.179 !from alkanes +!CetG patch; from 1-ethyl-G and 2-ethyl-C +CN8 CN8 NN3 70.0 114.5 !n3-c3a-c3b +NN2G CN8 CN8 70.0 119.9 !n1-c1a-c1b +!difluorotoluene, adm jr. +CNA CNA CNA 40.0 120.00 35.00 2.41620 ! JES 8/25/89 +CNA CNA2 CNA 40.0 122.50 35.00 2.41620 !dft, adm jr. +CNA2 CNA CNA 40.0 119.00 35.00 2.41620 !dft, adm jr. +CNA2 CNA CNA2 40.0 117.00 35.00 2.41620 !dft, adm jr. +CN7B CNA CNA 45.8 121.00 !dft, adm jr., changed from toluene +CN7B CNA CNA2 45.8 120.00 !dft, adm jr. +CN9 CNA CNA 45.8 121.00 !dft, adm jr., changed from toluene +CN9 CNA CNA2 45.8 120.00 !dft, adm jr. +CN8 CN7B CNA 51.8 107.50 !ethylbenzene, adm jr., 3/7/92 +ON6 CN7B CNA 51.8 107.50 !ethylbenzene, adm jr., 3/7/92 +HN7 CN7B CNA 43.0 111.00 !From HN7 CN7B NN2 +HN9 CN9 CNA 49.3 107.50 ! toluene, adm jr. 3/7/92 +HNP CNA CNA 30.0 120.00 22.00 2.15250 !JES 8/25/89 benzene +HNP CNA CNA2 30.0 121.00 22.00 2.15250 !dft, adm jr. +HN3 CNA CNA2 30.0 121.50 22.00 2.15250 !dft, adm jr. +FNA CNA2 CNA 60.0 118.75 !dft, adm jr. +!5-ethylene-thymine terms +CN1 CN3T CNE1 38.0 117.0 !c4-c5-c5a +CN3 CN3T CNE1 38.0 126.3 !c6-c5-c5a +CN3T CNE1 CNE2 48.0 122.4 !c5-c5a-c5b +CN3T CNE1 HNE1 40.0 119.6 !c5-c5a-h5a1 +CNE2 CNE1 HNE1 42.0 118.0 !fixed, alkene +HNE2 CNE2 CNE1 45.0 120.5 !fixed, alkene +HNE2 CNE2 HNE2 19.0 119.0 !fixed, alkene +!N3-protonated CYT(CYTH) and 5Me-CYT(CYTP), edarian 2009-03 +NN2G CN1 NN2 70.0 107.8 ! CYTH +NN2G CN1 ON1C 50.0 125.5 ! CYTH +NN2G CN2 CN3 70.0 122.2 ! CYTH +NN2G CN2 CN3D 70.0 122.2 ! for CYTP +!C5-Me CYT with N4-Ethyl-Methyl, N4EM, edarian 2009-06 +NN1 CN8 HN8 48.0 108.0 +NN1 CN8 CN9 70.0 113.5 +CN8 NN1 HN1 35.0 117.0 +CN2 NN1 CN8 40.0 121.5 +!C8-Amino-Phenyl-Guanine, G8AP, edarian, 2009-11 +CN1 NN3 HN2 37.0 121.2 !C, h1 cn1 nn2 hn2 +CN2 NN3 HN2 40.5 115.4 !U cn1 nn2u hn2 +NN2B CN4 NN1 70.0 113.0 !NG321 CG2N1 NG321 ! MGU1, methylguanidine kevo: +NN4 CN4 NN1 70.0 125.0 !NG2D1 CG2N1 NG321 ! MGU1, methylguanidine; +CN4 NN1 CN3 50.0 120.0 !CG2O1 NG2S1 CG2R61 ! RETINOL TMCH/MECH +NN1 CN3 CN3 40.0 120.0 35.00 2.4162 !CG2R61 CG2R61 NG2S1 ! RETINOL TMCH/MECH +CN3 CN3 CN3 40.0 120.0 35.00 2.4162 !CG2R61 CG2R61 CG2R61 ! PROT JES 8/25/89 +CN4 NN1 HN2 34.0 117.0 !CG2R61 NG2S1 HGP1 ! RETINOL TMCH/MECH +HN2 NN1 CN3 34.0 117.0 !CG2R61 NG2S1 HGP1 ! RETINOL TMCH/MECH +!params for GUANIDINIUM tail patch at N4 of CYT, 4EG1, edarian, 2009-11 +CN8 NNG CNG 62.30 120.0 !CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO guanid +NNG CNG NNG 52.00 120.0 90.00 2.36420 !NG2P1 CG2N1 NG2P1 (NC2 C NC2 aa param) guanid +HN1 NNG HN1 25.00 120.0 ! ALLOW POL ! NA param HN1 NN1 HN1 31.0 117.0 !C,A,G +NNG CN8 HN8 51.50 107.5 !NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL guanid +NNG CN8 CN8 67.70 107.5 !NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL guanid +CNG NNG HN1 49.00 120.0 ! ALLOW POL PEP ARO ! NA param CN2 NN1 HN1 40.0 121.5 +NN1 CN8 CN8 70.00 113.5 !NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO +CN8 NNG HN1 40.40 120.0 !HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI + +!backbone section +HN2 NN1 CN8B 35.000 109.00 ! +NN1 CN8B HN8 48.000 110.00 ! +CN8B NN1 P 110.0 118.3 35.0 2.33 ! +HN2 NN1 P 30.0 123.6 40.0 2.35 ! +NN1 P ON2 60.0 103.2 ! +NN1 P ON3 140.0 110.6 ! +NN1 CN8B CN7B 43.70 110.00 ! +NN1 P ON4 60.0 103.2 ! +HN7 CN7 NN1 48.00 110.00 ! +CN7 NN1 P 110.0 118.3 35.0 2.33 ! +HN2 NN1 CN7 35.00 109.00 ! +NN1 CN7 CN7 43.70 110.00 ! +NN1 CN7 CN7B 43.70 110.00 ! +NN1 CN7 CN8 43.70 110.00 ! +NN1 CN8B CN7 43.70 110.00 ! +HN2 NN1 HN2 39.0 106.00 ! thni. DIFFERENT COPY OF SAME PARAMETER IN toppar_all27_na_base_modifications.str +CN8B ON2 HN8 60.0 114.70 !thni +CN7 ON5 HN7 60.0 114.70 !n5ph +!included in NA param file due to use in multiple toppar stream files +!ON5 CN7 CN8B 90.0 108.20 !n5ph +!PNA related terms +NC2 CT2 C 43.70 110.00 +NC2 CT2 HB2 51.50 107.50 +HN1 NN1 HN2 31.00 117.00 +O CD CT2 45.20 107.24 ! DIFFERENT COPY OF SAME PARAMETER IN toppar_all22_prot_aldehydes.str +CT2 NC2 CT2 35.00 117.00 +CT2 NC2 CD 50.00 120.00 +HB2 CT2 CT2 50.00 109.50 +O CD NC2 80.00 122.50 +NC2 CD CT2 50.00 116.50 +NN2 CT2 HB2 48.00 108.00 +NN2B CT2 HB2 48.00 108.00 +NN2B CT2 CD 43.70 110.00 +NN2 CT2 CD 43.70 110.00 +CN1 NN2 CT2 70.00 117.70 +CN1T NN2B CT2 70.00 117.70 +CN3 NN2 CT2 70.00 121.70 +CN3 NN2B CT2 70.00 121.70 +CN4 NN2 CT2 70.00 128.40 +CN5 NN2 CT2 70.00 126.00 +CN4 NN2B CT2 70.00 128.40 +CN5 NN2B CT2 70.00 126.00 +CN2 NN1 HN2 40.00 121.50 +HN1 NH2 C 49.00 120.00 +O C NH2 80.00 122.50 +NH2 C CT2 80.00 116.50 +HN1 NH2 HN1 23.00 120.00 +HN1 NH1 CT2 35.00 117.00 +HN1 NH1 HN1 23.00 120.00 +! THF2 - 2'-OMe ribose model compound, edarian, 2009-07 +CN7 CN7B ON2M 58.00 108.67 ! 8.00 2.561 ! c3'-c2'-om +CN7B CN7B ON2M 58.00 106.67 ! 8.00 2.561 ! c1'-c2'-om +CN7B ON2M CN9 65.00 108.00 ! c2'-om-cm +HN7 CN7B ON2M 45.90 109.00 ! h2''-c2'-om +ON2M CN9 HN9 45.90 108.89 ! from cgenff OG301 CG331 HN7 + +!25P1 tests +CN7 CN7B NN2 110.0 111.0 !C/A, RNA, 25P1 +CN7 CN7B NN2B 110.0 111.0 !T/U/G, RNA, 25P1 +CN8 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4', 25P1 +CN8 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6, 25P1 +CN7B CN7B CN8 110.0 96.0 ! 25P1 +!CN7 CN8 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4', 25P1 +CN8 CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3', 25P1 +!CPH2 NR1 CPH1 130.0 107.5000 ! From imidazole (NF). Standard param from par_all22_prot.prm . Generates "Error: Repeated ANGLE". + +!carbocyclic setion +!cyclopropane ring angles +CN6 CN7E CN8 53.35 62.5 ! C1-C5-C6 +CN7E CN6 CN8 53.35 60.5 ! C1-C5-C6 +CN7E CN8 CN6 53.35 58.5 ! C5-C1-C6 +!other ring angles +HN7 CN7 CN7E 34.5 110.1 22.53 2.179 ! +HN7 CN7E CN7 34.53 110.10 22.53 2.179 ! +HN7 CN7E HN7 35.5 109.00 5.40 1.802 ! +CN7E CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3' +ON5 CN7 CN7E 75.7 110.0 ! from CHARMM22 +CN8 CN7 CN7E 80.00 101.9 ! north, C3-C2-C1, (from NF, 11/97, C1'C2'C3') +CN7 CN8 CN7 80.00 100.0 ! north, C4-C3-C2, (from NF, 11/97, C1'C2'C3') +CN6 CN7 CN8 53.35 103.7 8.0 2.561 ! north, C5-C4-C3 +CN7E CN6 CN7 53.35 113.7 8.0 2.561 ! north, C1-C5-C4 +CN8 CN6 CN7 53.35 108.7 8.0 2.561 ! north, C6-C5-C4 +CN8 CN7E CN7 53.35 111.0 8.0 2.561 ! north, C6-C1-C2 +CN6 CN7E CN7 53.35 111.0 8.0 2.561 ! north, C5-C1-C2 +HN7 CN7 CN6 34.5 110.1 22.53 2.179 ! north, H41-C4-C5 +CN6 CN8B CN7 80.00 105.5 8.0 2.561 ! south, C1-C2-C3 +CN8B CN7 CN7E 80.00 101.0 ! south, C2-C3-C4, (from NF, 11/97, C1'C2'C3') +CN7E CN7E CN7 53.35 102.0 8.0 2.561 ! south, C5-C4-C3 +CN6 CN7E CN7E 53.35 116.0 8.0 2.561 ! south, C1-C5-C4 +CN7E CN7E CN8 53.35 108.0 8.0 2.561 ! south, C4-C5-C6 +CN8B CN6 CN7E 53.35 117.0 8.0 2.561 ! north, C5'-C5-C1 and south, C2-C1-C5 +CN7E CN7E CN8B 53.35 111.0 8.0 2.561 ! south, C5-C4-C5' +CN7E CN7E HN7 34.5 110.1 22.53 2.179 ! south, C5-C4-H41 +HN7 CN7E CN6 34.5 110.1 22.53 2.179 ! north, H11-C1-C5, and south, H51-C5-C1 +HN8 CN8 CN6 34.5 110.1 22.53 2.179 ! north, H6*-C6-C5, and south, H6*-C6-C1 +HN7 CN6 CN7 34.5 110.1 22.53 2.179 ! north,south,model compd only +HN7 CN6 CN7E 34.5 110.1 22.53 2.179 ! north,south,model compd only +HN7 CN6 CN8 34.5 110.1 22.53 2.179 ! north,south,model compd only +HN7 CN6 CN8B 34.5 110.1 22.53 2.179 ! north,south,model compd only +HN7 CN7E CN8 34.5 110.1 22.53 2.179 ! north, H51-C5-C6, and south, H11-C1-C6 +HN8 CN8 CN7E 34.5 110.1 22.53 2.179 ! north, H6*-C6-C1, and south, H6*-C6-C5 +HN7 CN6 HN7 35.5 109.0 5.40 1.802 ! north,south,model compd only +!chi related angles +CN8 CN6 NN2 70.0 113.7 ! south, C6-C1-N1/N9, C/A DNA +CN8B CN6 NN2 70.0 113.7 ! south, C6-C1-N1/N9, C/A DNA +CN8 CN7 NN2 110.0 113.7 ! north, C3-C2-N1/N9, (from ON6 CN7B NN2, C/A DNA) +CN1 NN2 CN7 45.0 118.4 ! north, from CN1T NN2B CN7B, U/T, FC from A +CN1 NN2 CN6 45.0 120.0 ! south, from CN1 NN2 CN7B, C, FC from A +CN3 NN2 CN6 45.0 115.9 ! south, from CN3 NN2 CN7B, C +CN5 NN2 CN6 45.0 126.1 ! south, from CN5 NN2 CN7B, A +CN4 NN2 CN6 45.0 127.6 ! south, from CN4 NN2 CN7B, A +CN1T NN2 CN7 45.0 118.4 ! north, from CN1T NN2B CN7B, U/T, FC from A +CN3 NN2 CN7 45.0 118.4 ! north, from CN1T NN2B CN7B, U/T, FC from A +CN5 NN2 CN7 45.0 126.5 ! north, from CN5 NN2B CN7B, G +CN4 NN2 CN7 45.0 126.3 ! north, from CN4 NN2B CN7B, G +HN7 CN7 NN2 43.0 111.0 ! north, From HN7 CN7B NN2 +CN7 CN6 NN2B 70.0 113.7 ! south, from CN6 CN6B NN2 +CN7E CN6 NN2B 70.0 113.7 ! south, from CN6 CN6B NN2 +CN7E CN6 NN2 70.0 113.7 ! south, from CN6 CN6B NN2 +CN8 CN6 NN2B 70.0 113.7 ! south, from CN6 CN6B NN2 +CN8B CN6 NN2B 70.0 113.7 ! south, from CN6 CN6B NN2 +CN7 CN7 NN2B 110.0 108.0 ! north, from ON6 CN7B NN2, C/A DNA +CN8 CN7 NN2B 110.0 113.7 ! north, from ON6 CN7B NN2, C/A DNA +CN7E CN7 NN2B 110.0 108.0 ! north, from ON6 CN7B NN2, C/A DNA +CN7E CN7 NN2 110.0 108.0 ! north, from ON6 CN7B NN2, C/A DNA +CN1T NN2B CN6 45.0 118.4 ! south, from CN1T NN2B CN7B, U/T, FC from A +CN3 NN2B CN6 45.0 119.6 ! south, from CN3 NN2B CN7B, U/T +CN5 NN2B CN6 45.0 126.5 ! south, from CN5 NN2B CN7B, G +CN4 NN2B CN6 45.0 126.3 ! south, from CN4 NN2B CN7B, G +CN1T NN2B CN7 45.0 118.4 ! north, from CN1T NN2B CN7B, U/T, FC from A +CN3 NN2B CN7 45.0 118.4 ! north, from CN1T NN2B CN7B, U/T, FC from A +CN5 NN2B CN7 45.0 126.5 ! north, from CN5 NN2B CN7B, G +CN4 NN2B CN7 45.0 126.3 ! north, from CN4 NN2B CN7B, G +HN7 CN7 NN2B 43.0 111.0 ! north, from HN7 CN7B NN2 +!parameters related to gamma +CN7 CN6 CN8B 53.35 111.0 8.0 2.561 ! north, C4-C5-C5' +CN7 CN7E CN8B 45.0 110.0 ! south, C3-C4-C5', (from NF, 11/97, C3'C4'C5') +CN8 CN6 CN8B 53.35 111.0 8.0 2.561 ! north, C6-C5-C5', and south, C6-C1-C2 +CN6 CN8B ON2 75.7 110.10 ! north, C5-C5'-O5', From CN7 CN8B ON5 +CN6 CN8B ON5 75.7 110.10 ! north, C5-C5'-O5', From CN7 CN8B ON5 +CN7E CN8B ON2 75.7 110.10 ! south, C4-C5'-O5', From CN7 CN8B ON5 +CN7E CN8B ON5 75.7 110.10 ! south, C4-C5'-O5', From CN7 CN8B ON5, model cmpd only +HN7 CN7E CN8B 34.5 110.1 22.53 2.179 ! south, H41-C4-C5' +HN8 CN8B CN7E 34.5 110.1 22.53 2.179 ! south, H5'-C5'-C4 +HN8 CN8B CN6 34.5 110.1 22.53 2.179 ! north, H5'-C5'-C5 +!parameters related to epsilon +CN6 CN7 ON2 75.7 110.1 !north, C5-C4-O3', from CN6 CN6 ON2 +CN8B CN7 ON2 75.7 110.1 !south, C2-C3-O3', from CN6 CN6 ON2 +CN6 CN7 ON5 75.7 110.1 !north, C5-C4-O3', from CN6 CN6 ON2 +! parameters unique to abasic carbo-furanose +CN8 CN8B CN8 58.35 113.60 11.16 2.561 ! from alkane, Nilesh + +DIHEDRALS +! +!atom types Kchi n delta +! +! inosine, adm jr. 2/94 +CN5 CN5 NN3I CN4 6.0 2 180.0 +NN2G CN4 NN3I CN5 6.0 2 180.0 +NN3I CN4 NN2G HN2 1.5 2 180.0 +NN3I CN4 NN2G CN1 1.5 2 180.0 +HN3 CN4 NN2G HN2 1.5 2 180.0 +HN3 CN4 NN2G CN1 1.5 2 180.0 +! Wild cards for inosine +X CN4 NN3I X 3.5 2 180.0 +X CN5 NN3I X 1.0 2 180.0 +! 5-methylcytosine +NN2 CN3 CN3D CN2 3.0 2 180.0 !5mc, adm jr. 9/9/93 +CN3 CN3D CN2 NN3 1.0 2 180.0 !5mc, adm jr. 9/9/93 +CN3D CN2 NN3 CN1 10.0 2 180.0 !5mc, adm jr. 9/9/93 +CN3D CN3 NN2 CN1 1.0 2 180.0 !5mc, adm jr. 9/9/93 +CN3D CN2 NN1 HN1 2.0 2 180.0 !5mc, adm jr. 9/9/93 +NN1 CN2 CN3D CN3 0.0 2 180.0 !5mc, adm jr. 9/9/93 +NN1 CN2 CN3D CN9 0.0 2 180.0 !5mc, adm jr. 9/9/93 +NN2 CN3 CN3D CN9 4.0 2 180.0 !5mc, adm jr. 9/9/93 +NN3 CN2 CN3D CN9 0.0 2 180.0 !5mc, adm jr. 9/9/93 +CN3 CN3D CN9 HN9 0.0 3 0.0 !5mc, adm jr. 9/9/93 +CN2 CN3D CN9 HN9 0.35 3 0.0 !5mc, adm jr. 9/9/93 +CN2 CN3D CN3 HN3 4.0 2 180.0 !5mc, adm jr. 9/9/93 +CN9 CN3D CN3 HN3 4.0 2 180.0 !5mc, adm jr. 9/9/93 +!guanine tautomer terms +ON5 CN1 NN3G CN2 1.0 2 180.0 !to o6 +CN5G CN1 NN3G CN2 2.0 2 180.0 !ring +CN1 NN3G CN2 NN3G 2.0 2 180.0 !ring +NN3G CN1 CN5G CN5 8.0 2 180.0 !ring +NN3G CN2 NN3G CN5 2.0 2 180.0 !ring +NN3G CN1 CN5G NN4 5.0 2 180.0 !bfly +NN3G CN1 ON5 HN5 1.5 2 180.0 !to h6 +CN5G CN1 ON5 HN5 1.8 2 180.0 !to h6 +!cytosine tautomer terms +HN1 NN1C CN2 CN3 8.0 2 180.0 +HN1 NN1C CN2 NN2C 0.7 1 0.0 +HN1 NN1C CN2 NN2C 6.0 2 180.0 +NN1C CN2 NN2C CN1 1.0 2 180.0 !to N4 +CN3 CN2 NN2C CN1 0.5 2 180.0 !ring +NN2 CN1 NN2C CN2 0.5 2 180.0 !ring +NN2 CN1 NN2C HN2 3.3 2 180.0 !h3 +HN2 NN2C CN1 ON1C 0.0 2 180.0 !h3 +HN2 NN2C CN2 NN1C 0.0 2 180.0 !h3 +HN2 NN2C CN2 CN3 3.3 2 180.0 !h3 +ON1C CN1 NN2C CN2 1.6 2 180.0 !to O2 +!1-Ethyl Guanine, sasha +CN5G CN1 NN2G CN8 2.0 2 180.0 !to C1A +ON1 CN1 NN2G CN8 2.0 2 180.0 !to C1A +CN2 NN2G CN8 CN9 1.5 1 0.0 !to C1B +CN2 NN2G CN8 CN9 1.0 2 0.0 !to C1B +CN2 NN2G CN8 CN9 0.2 3 180.0 !to C1B +CN1 NN2G CN8 CN9 1.0 2 0.0 !to C1B +CN2 NN2G CN8 HN8 0.15 3 0.0 !alkanes +CN1 NN2G CN8 HN8 0.15 3 0.0 !alkanes +NN2G CN8 CN9 HN9 0.15 3 0.0 !alkanes +!3-Ethyl Cytosine, sasha +NN2 CN1 NN3 CN8 2.0 2 180.0 !to C3A +CN8 NN3 CN1 ON1C 2.0 2 180.0 !to C3A +CN8 NN3 CN2 NN1 2.0 2 180.0 !to C3A +CN8 NN3 CN2 CN3 2.0 2 180.0 !to C3A +CN2 NN3 CN8 CN9 2.0 1 0.0 !to C3B +CN2 NN3 CN8 CN9 0.30 3 0.0 !to C3B +CN1 NN3 CN8 CN9 0.50 3 180.0 !to C3B +CN2 NN3 CN8 HN8 0.15 3 0.0 !alkanes +CN1 NN3 CN8 HN8 0.15 3 0.0 !alkanes +NN3 CN8 CN9 HN9 0.15 3 0.0 !alkanes +!CetG patch; from 1-ethyl-G and 2-ethyl-C +CN2 NN2G CN8 CN8 1.0 2 0.0 !to C1B +CN2 NN2G CN8 CN8 0.2 3 180.0 !to C1B +CN1 NN2G CN8 CN8 1.0 2 0.0 !to C1B +CN2 NN3 CN8 CN8 2.0 1 0.0 !to C3B +CN2 NN3 CN8 CN8 0.30 3 0.0 !to C3B +CN1 NN3 CN8 CN8 0.50 3 180.0 !to C3B +NN2G CN8 CN8 NN3 0.15 3 0.0 !alkanes +NN2G CN8 CN8 HN8 0.15 3 0.0 !alkanes +NN3 CN8 CN8 HN8 0.15 3 0.0 !alkanes +!difluorotoluene, adm jr. +CNA CNA CNA CNA 3.10 2 180.0 ! JES 8/25/89 +CNA2 CNA CNA CNA 3.10 2 180.0 ! dft, adm jr. +CNA2 CNA CNA2 CNA 3.10 2 180.0 ! dft, adm jr. +CNA CNA2 CNA CNA 3.10 2 180.0 ! dft, adm jr. +CNA CN7B CN7 CN7 0.04 3 0.0 ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HN7 CN7B CNA CNA 0.10 6 180.0 ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HN8 CN8 CN7B CNA 0.00 3 0.0 ! from HN8 CN8 CN7B NN2 +HN7 CN7B CNA CNA2 0.10 6 180.0 ! dft, adm jr. +HN9 CN9 CNA CNA 0.10 6 180.0 ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HN9 CN9 CNA CNA2 0.10 6 180.0 ! dft, adm jr. +CN7 CN7B CNA CNA 0.23 2 180.0 ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CN8 CN7B CNA CNA 0.23 2 180.0 ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CN8 CN7B CNA CNA2 0.23 2 180.0 ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CN7B CNA CNA2 CNA 3.10 2 180.0 ! JES 8/25/89 toluene and ethylbenzene +CN7B CNA CNA CNA 3.10 2 180.0 ! JES 8/25/89 toluene and ethylbenzene +CN9 CNA CNA CNA 3.10 2 180.0 ! JES 8/25/89 toluene and ethylbenzene +CN9 CNA CNA2 CNA 3.10 2 180.0 ! dft, adm jr. +HN7 CN7 CN7B CNA 0.04 3 0.0 ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +HNP CNA CNA CNA 4.20 2 180.0 ! JES 8/25/89 benzene +HNP CNA CNA2 CNA 4.20 2 180.0 ! dft, adm jr. +HN3 CNA CNA2 CNA 4.20 2 180.0 ! dft, adm jr. +HNP CNA CNA CNA2 4.20 2 180.0 ! dft, adm jr. +HNP CNA CNA CN9 4.20 2 180.0 ! JES 8/25/89 toluene and ethylbenzene +HNP CNA CNA CN7B 4.20 2 180.0 ! JES 8/25/89 toluene and ethylbenzene +HNP CNA CNA HNP 2.40 2 180.0 ! JES 8/25/89 benzene +HNP CNA CNA2 FNA 2.40 2 180.0 ! dft, adm jr. +HN3 CNA CNA2 FNA 2.40 2 180.0 ! dft, adm jr. +FNA CNA2 CNA CNA 4.50 2 180.0 ! dft, adm jr. +FNA CNA2 CNA CNA2 4.50 2 180.0 ! dft, adm jr. +FNA CNA2 CNA CN9 4.50 2 180.0 ! dft, adm jr. +FNA CNA2 CNA CN7B 4.50 2 180.0 ! dft, adm jr. +ON6 CN7B CNA CNA 0.00 3 0.0 ! from ON6 CN7B NN2 CN3C +ON6 CN7B CNA CNA2 0.00 3 0.0 ! from ON6 CN7B NN2 CN3C +CN7 ON6 CN7B CNA 0.0 3 0.0 ! from CN7 ON6 CN7B NN2 +CN7 CN8 CN7B CNA 0.0 3 0.0 ! from CN8 CN8 CN7B NR1 +! 5-ethylene-thymine terms +ON1 CN1 CN3T CNE1 6.0 2 180.0 +HN3 CN3 CN3T CNE1 3.0 2 180.0 +CN1 CN3T CNE1 HNE1 1.0 2 180.0 +CN3 CN3T CNE1 HNE1 1.0 2 180.0 +CNE2 CNE1 CN3T CN3 0.85 1 0.0 !to c5a +CNE2 CNE1 CN3T CN3 0.5 2 180.0 !to c5a +CNE2 CNE1 CN3T CN1 0.5 2 180.0 !to c5a +CNE2 CNE1 CN3T CN1 1.1 3 180.0 !to c5a +HNE2 CNE2 CNE1 HNE1 5.2 2 180.0 +HNE2 CNE2 CNE1 CN3T 5.2 2 180.0 +!N3-protonated CYT(CYTH) and 5Me-CYT(CYTP), edarian 2009-03 +ON1C CN1 NN2G HN2 2.5 2 180.0 +NN2 CN1 NN2G HN2 3.8 2 180.0 +CN3 CN2 NN2G HN2 4.8 2 180.0 +CN3 CN3D CN2 NN2G 2.0 2 180.0 +NN2G CN2 CN3D CN9 1.8 2 180.0 +!C5-Me CYT with N4-Ethyl-Methyl, edarian, N4EM, 2009-06 +HN1 NN1 CN8 HN8 0.02 2 180.0 +HN1 NN1 CN8 CN9 0.05 1 0.0 +CN2 NN1 CN8 HN8 0.09 3 0.0 +CN2 NN1 CN8 CN9 0.53 1 180.0 +CN2 NN1 CN8 CN9 0.80 2 0.0 +CN2 NN1 CN8 CN9 0.09 3 0.0 +NN3 CN2 NN1 CN8 1.45 2 180.0 !NN3 CN2 NN1 HN1 +CN3 CN2 NN1 CN8 2.25 2 180.0 !CN3 CN2 NN1 HN1 +CN3 CN2 NN1 CN8 1.30 3 0.0 !CN3 CN2 NN1 HN1 +CN3D CN2 NN1 CN8 2.25 2 180.0 !CN3 CN2 NN1 HN1 +CN3D CN2 NN1 CN8 1.30 3 0.0 !CN3 CN2 NN1 HN1 +NN1 CN8 CN9 HN9 1.00 1 0.0 +!C8-Amino-Phenyl-Guanine, G8AP, edarian, 2009-11 +NN4 CN4 NN1 CN3 0.23 1 0.0 ! RETINOL PACP ! OG2D1 CG2O1 NG2S1 CG2R61 +NN4 CN4 NN1 CN3 0.70 2 180.0 ! RETINOL PACP ! OG2D1 CG2O1 NG2S1 CG2R61 +NN2B CN4 NN1 CN3 0.50 1 0.0 +NN2B CN4 NN1 CN3 0.70 2 180.0 ! RETINOL PACP ! CG331 CG2O1 NG2S1 CG2R61 +NN2B CN4 NN1 CN3 0.45 3 0.0 ! RETINOL PACP ! CG331 CG2O1 NG2S1 CG2R61 +NN2B CN4 NN1 HN2 0.40 2 180.0 +NN4 CN4 NN1 HN2 0.41 3 0.0 +CN4 NN1 CN3 CN3 0.90 2 180.0 ! RETINOL PACP ! CG2R61 CG2R61 NG2S1 CG2O1 +CN4 NN1 CN3 CN3 0.75 3 0.0 ! RETINOL PACP ! CG2R61 CG2R61 NG2S1 CG2O1 +HN2 NN1 CN3 CN3 0.25 2 180.0 ! RETINOL PACP ! CG2R61 CG2R61 NG2S1 HGP1 +HN2 NN1 CN3 CN3 0.05 3 0.0 ! RETINOL PACP ! CG2R61 CG2R61 NG2S1 HGP1 +!params for GUANIDINIUM tail patch at N4 of CYT, 4EG1, edarian, 2009-11 +HN1 NN1 CN8 CN8 0.05 1 0.0 !H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP +CN2 NN1 CN8 CN8 0.53 1 180.0 +CN2 NN1 CN8 CN8 0.80 2 0.0 +CN2 NN1 CN8 CN8 0.07 3 0.0 +NN1 CN8 CN8 HN8 1.00 2 180.0 +! guanidinium tail parameters +CN8 CN8 NNG CNG 0.10 3 0.0 !CG321 CG321 NG2D1 CG2D1 +CN8 CN8 NNG HN1 0.00 6 180.0 !X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL +HN8 CN8 NNG CNG 0.00 6 180.0 !X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL +CN8 NNG CNG NNG 2.25 2 180.0 !NG2P1 CG2N1 NG2P1 CG334/CG324 MGUA +HN8 CN8 NNG HN1 0.19 3 0.0 !CN1 NN2 CN9 HN9 ?? +NNG CNG NNG HN1 2.25 2 180.0 !NG2P1 CG2N1 NG2P1 HGP2 MGUA + +!backbone section +P NN1 CN7 HN7 0.15 3 0.0 !DMP, ADM Jr. (P ON2 CN7 HN7) +P NN1 CN8B HN8 0.15 3 0.0 !DMP, ADM Jr. (P ON2 CN7 HN7) +!N-P-Oes-C +NN1 P ON2 CN7 0.40 1 0.0 ! +NN1 P ON2 CN7 0.40 2 50.0 ! +NN1 P ON2 CN7 0.35 3 0.0 ! +NN1 P ON2 CN8B 0.40 1 0.0 ! +NN1 P ON2 CN8B 0.40 2 50.0 ! +NN1 P ON2 CN8B 0.35 3 0.0 ! +!Oes-P-N-C +ON3 P NN1 CN7 0.40 3 0.0 ! +ON3 P NN1 CN7 0.80 2 120.0 ! +ON3 P NN1 CN7 0.50 4 0.0 ! +ON2 P NN1 CN7 1.50 2 0.0 ! +ON3 P NN1 CN8B 0.40 3 0.0 ! for 5' phosphoramidate +ON3 P NN1 CN8B 0.80 2 120.0 ! for 5' phosphoramidate +ON3 P NN1 CN8B 0.50 4 0.0 ! for 5' phosphoramidate +ON2 P NN1 CN8B 1.50 2 0.0 ! for 5' phosphoramidate + +HN2 NN1 CN7 HN7 0.01 3 0.0 ! +HN2 NN1 CN8B HN8 0.01 3 0.0 ! +HN2 NN1 P ON2 0.05 3 0.0 ! +HN2 NN1 P ON3 0.05 3 0.0 ! + +HN2 NN1 CN7 CN7 0.30 1 0.00 !tphc +HN2 NN1 CN7 CN7B 0.30 1 0.00 !tphc +HN2 NN1 CN7 CN8 0.30 1 0.00 !tphc +HN7 CN7 CN7 NN1 0.195 3 0.0 !tphc +HN7 CN7B CN7 NN1 0.195 3 0.0 !tphc +HN8 CN8 CN7 NN1 0.195 3 0.0 !for dna +ON6B CN7 CN7 NN1 0.20 3 0.0 !tphc +ON6 CN7 CN7 NN1 0.20 3 0.0 !for dna +HN2 NN1 P ON4 0.05 3 0.0 !tphc +!epsilon tphc parameters, Nilesh +P NN1 CN7 CN7 0.65 2 180.0 ! +P NN1 CN7 CN7 1.5 1 180.0 ! +P NN1 CN7 CN7 1.0 3 0.0 ! +P NN1 CN7 CN7B 1.4 1 220.0 ! +P NN1 CN7 CN7B 0.4 5 180.0 ! +P NN1 CN7 CN8 1.4 1 220.0 ! +P NN1 CN7 CN8 0.4 5 180.0 ! +CN7 CN8B ON2 HN8 0.5 3 0.0 !thni +CN7 CN8B ON2 HN8 1.0 1 0.0 !thni +HN8 CN8B ON2 HN8 0.1 3 0.0 !thni +! Sugar pucker parameters for phosphoramidate +NN1 CN7 CN7B CN7B 1.5 1 180.0 ! for rna +NN1 CN7 CN7B CN7B 1.5 2 0.0 ! for rna +NN1 CN7 CN7B CN7B 1.1 3 180.0 ! for rna +NN1 CN7 CN8 CN7B 1.35 1 180.0 ! for dna +NN1 CN7 CN8 CN7B 1.0 2 0.0 ! for dna +NN1 CN7 CN8 CN7B 0.2 3 180.0 ! for dna +NN1 CN7 CN7 CN8B 0.5 2 180.0 ! +! Parameters for n5' phosphoramidate +P NN1 CN8B CN7 0.245 1 120.0 !bet C4'-C5'-O5'-P, adm jr. +CN7 CN7 CN8B NN1 0.20 4 180.0 !gam adm jr. +CN7 CN7 CN8B NN1 0.80 3 180.0 !gam C3'-C4'-C5'-O5' +CN7 CN7 CN8B NN1 0.40 2 0.0 !gam +CN7 CN7 CN8B NN1 2.50 1 180.0 !gam +HN7 CN7 CN8B NN1 0.195 3 0.0 !gam H-C4'-C5'-O5' +HN2 NN1 CN8B CN7 0.26 1 0.0 !tphc +ON6B CN7 CN8B NN1 3.4 1 180.0 !gam, N5' RNA +ON6 CN7 CN8B NN1 3.4 1 180.0 !gam , for dna +CN7 CN7 ON5 HN7 0.5 3 0.0 !n5ph +CN7 CN7 ON5 HN7 1.0 1 0.0 !n5ph +CN8B CN7 ON5 HN7 0.5 3 0.0 !n5ph +CN8B CN7 ON5 HN7 1.0 1 0.0 !n5ph +HN7 CN7 ON5 HN7 0.1 3 0.0 !n5ph +ON5 CN7 CN8B NN1 3.4 1 180.0 !n5ph +!PNA related terms +NN3G CN2 NN1 HN2 1.00 2 180.0 +NN2G CN2 NN1 HN2 1.20 2 180.0 +X CT2 C X 0.05 6 180.0 +O CD NC2 CT2 1.40 2 180.0 +CT2 C NH3 CT2 1.40 2 180.0 +CT2 CD NC2 CT2 1.40 2 180.0 +X CT2 NN2 X 0.00 3 0.0 +X CT2 NN2B X 0.00 3 0.0 +HN1 NH2 CT2 CT2 0.00 1 0.0 +HN1 NH1 CT2 CT2 0.00 1 0.0 +HB2 CT2 NH2 HN1 0.11 3 0.0 +HB2 CT2 NH1 HN1 0.11 3 0.0 +HN1 NH2 C CT2 1.40 2 180.0 +O C NH2 HN1 1.40 2 180.0 +! THF2 - 2'-OMe ribose model compound, edarian, 2009-07 +CN7 CN7B ON2M CN9 0.200 1 180.0 ! c-C2'-OM-cm For THF-2'O2M +CN7 CN7B ON2M CN9 1.850 2 180.0 +CN7 CN7B ON2M CN9 1.000 3 0.0 +HN7 CN7B ON2M CN9 1.000 1 0.0 ! h-C2'-OM-cm +HN7 CN7B ON2M CN9 1.900 2 180.0 +HN7 CN7B ON2M CN9 0.380 3 0.0 +CN7B ON2M CN9 HN9 0.100 3 180.0 ! C2'-OM-CM-H OK +CN7B ON2M CN9 HN9 1.200 2 0.0 +CN7B CN7B ON2M CN9 2.000 2 180.0 +NN2B CN7B CN7B ON2M 0.000 3 0.0 +ON2M CN7B CN7 ON2 0.195 3 0.0 ! from HN7 CN7 CN7 ON2 +NN2 CN7B CN7B ON2M 0.000 3 0.0 +ON2M CN7B CN7 ON5 0.195 3 0.0 +ON6B CN7B CN7B ON2M 0.000 3 0.0 +CN7 CN7 CN7B ON2M 0.000 3 0.0 +HN7 CN7B CN7B ON2M 0.095 3 180.0 ! OG311 CN7B CN7 HN7 -- NA, sugar +HN7 CN7 CN7B ON2M 0.195 3 0.0 ! from HN7 CN7 CN7 ON5 +HN8 CN8 CN7B ON2 0.195 3 0.0 ! 25P1 +ON2 CN7B CN7B NN2B 0.0 3 0.0 ! 25P1 + +!25P1 tests +ON2 P ON2 CN7B 1.20 1 180.0 !10/97, DMP, adm jr., 25P1 +ON2 P ON2 CN7B 0.10 2 180.0 !10/97, DMP, adm jr., 25P1 +ON2 P ON2 CN7B 0.10 3 180.0 !10/97, DMP, adm jr., 25P1 +ON2 P ON2 CN7B 0.00 6 0.0 !10/97, DMP, adm jr., 25P1 +CN8 CN7 CN7B ON6 0.6 6 0.0 ! 25P1 +! 25P1 +ON2 CN7B CN8 CN7 0.8 6 0.0 ! +ON2 CN7B CN8 CN7 0.4 5 0.0 ! Moves the barrier right +ON2 CN7B CN8 CN7 2.0 3 180.0 ! +CN7 CN7B NN2 CN1 1.0 3 0.0 ! 25P1 +CN7 CN7B NN2 CN3 0.0 3 180.0 ! NF 030697, 25P1 +CN8 CN7B CN7B NN2 0.0 3 0.0 ! 25P1 +CN8 CN7B CN7B NN2B 0.0 3 0.0 ! 25P1 +HN7 CN7B CN7 CN8 0.195 3 0.0 !cn8 -> cn9, 25P1 +CN7B ON6B CN7 CN8 2.0 3 0.0 ! To lower barrier in RNA, 25P1 +CN8 CN7B ON2 P 2.5 1 180.0 !eps, 25P1 +CN8 CN7B CN7B ON6B 0.4 6 0.0 ! RNA, 25P1 +CN7B CN7B CN8 CN7 0.0 6 0.0 ! RNA, 25P1 +HN8 CN8 CN7B CN7B 0.195 3 0.0 ! RNA, H-C3'-C2'-C1', 25P1 +HN7 CN7B CN7B CN8 0.195 3 0.0 ! RNA, H-C1'-C2'-C3', 25P1 + +!carbocyclic section +! cyclopropane and BCPE +CN7E CN7 CN8 CN7 0.15 3 0.0 ! north, C1-C2-C3-C4 +CN7 CN7E CN6 CN8 0.15 3 0.0 ! north, C2-C1-C5-C6 +CN7 CN7E CN6 CN7 0.15 3 0.0 ! north, C2-C1-C5-C4 +CN8 CN7E CN6 CN7 0.15 3 0.0 ! north, C6-C1-C5-C4 +CN6 CN8 CN7E CN7 0.15 3 0.0 ! north, C5-C6-C1-C2 +CN7E CN8 CN6 CN7 0.15 3 0.0 ! north, C1-C6-C5-C4 +CN7E CN7E CN8 CN6 0.15 3 0.0 ! south, C4-C5-C6-C1 +CN7E CN7E CN6 CN8 0.15 3 0.0 ! south, C4-C5-C1-C6 +CN8B CN6 CN7E CN7 0.15 3 0.0 ! north, C5'-C5-C1-C2 +CN8B CN6 CN7E CN8 0.15 3 0.0 ! north, C5'-C5-C1-C6 +CN8B CN6 CN8 CN7E 0.15 3 0.0 ! north, C5'-C5-C6-C1 +CN8 CN7E CN7E CN8B 0.15 3 0.0 ! south, C5'-C4-C5-C6 +CN6 CN7E CN7E CN8B 0.15 3 0.0 ! south, C1-C5-C4-C5' +CN6 CN8B CN7 HN7 0.15 3 0.0 ! south, C1-C2-C3-H31 +HN7 CN6 CN8B HN8 0.15 3 0.0 ! south, H11-C1-C2-H2*, model compd only +HN7 CN6 CN8B CN7 0.15 3 0.0 ! south, H11-C1-C2-C3, model compd only +HN8 CN8B CN7 CN7E 0.15 3 0.0 ! south, H2*-C2-C3-C4 +CN6 CN8B CN7 CN7E 0.15 3 0.0 ! south, C1-C2-C3-C4 +CN8B CN7 CN7E HN7 0.15 3 0.0 ! south, C2-C3-C4-H41 +CN8B CN7 CN7E CN7E 0.15 3 0.0 ! south, C2-C3-C4-C5 +CN7E CN7E CN8B HN8 0.15 3 0.0 ! south, C5-C4-C5'-H5' +HN7 CN7E CN7E CN8B 0.15 3 0.0 ! south, H51-C5-C4-C5' +CN8B CN6 CN7E HN7 0.15 3 0.0 ! north, C5'-C5-C1-H11 +HN8 CN8B CN6 CN7E 0.15 3 0.0 ! north, H5'-C5'-C5-C1 +HN7 CN7E CN7 HN7 0.15 3 0.0 ! north, H11-C1-C2-H21, and south, H41-C4-C3-H31 +CN7E CN6 CN8 HN8 0.15 3 0.0 ! north, C1-C5-C6-H6*, and south, C5-C1-C6-H6* +CN7E CN6 CN7 HN7 0.15 3 0.0 ! north, C1-C5-C4-H41 +CN7E CN7E CN8 HN8 0.15 3 0.0 ! south, C4-C5-C6-H6* +CN7 CN7E CN6 HN7 0.15 3 0.0 ! north, model compd only +CN7E CN8 CN6 HN7 0.15 3 0.0 ! north,south, model cmpd only +CN7E CN7E CN6 HN7 0.15 3 0.0 ! south, model cmpd only +CN7E CN7E CN7 HN7 0.15 3 0.0 ! south, C5-C4-C3-H31 +HN7 CN7 CN7E CN6 0.15 3 0.0 ! north, H21-C2-C1-C5 +HN7 CN7 CN6 CN8 0.15 3 0.0 ! north, H41-C4-C5-C6 +HN7 CN7E CN6 CN8 0.15 3 0.0 ! north, H11-C1-C5-C6, and south, H51-C5-C1-C6 +HN7 CN7E CN8 CN6 0.15 3 0.0 ! north, H11-C1-C6-C5, and south, H51-C5-C6-C1 +HN8 CN8 CN7E CN6 0.15 3 0.0 ! north, H6*-C6-C1-C5, and south, H6*-C6-C5-C1 +HN7 CN7E CN6 HN7 0.15 3 0.0 ! north,south, model cmpd only +HN7 CN6 CN7E CN8 0.15 3 0.0 ! north,south, model compd only +HN7 CN7E CN8 HN8 0.15 3 0.0 ! north, H11-C1-C6-H6*, and south, H51-C5-C6-H6* +HN8 CN8 CN6 CN7 0.15 3 0.0 ! north, H6*-C6-C5-C4 +HN7 CN7E CN6 CN7 0.15 3 0.0 ! north, H11-C1-C5-C4 +HN7 CN7E CN7E CN7 0.15 3 0.0 ! south, H51-C5-C4-C3 +HN7 CN7E CN7E CN8 0.15 3 0.0 ! south, H41-C4-C5-C6 +HN7 CN7E CN7E CN6 0.15 3 0.0 ! south, H41-C4-C5-C1 +HN7 CN7E CN7E HN7 0.15 3 0.0 ! south, H41-C4-C5-H51 +CN6 CN7 CN8 CN7 0.40 6 0.0 ! C4'-C3'-C2'-C1', north, C5-C4-C3-C2 +CN6 CN7E CN7E CN7 1.75 3 0.0 ! Nilesh, south, boat-chair energy, C1-C5-C4-C3 +CN7E CN6 CN8B CN7 1.75 3 0.0 ! Nilesh, south, boat-chair energy, C5-C1-C2-C3 +CN8 CN7E CN7E CN7 4.00 3 0.0 ! Nilesh, south, boat-chair energy, C6-C5-C4-C3 +CN8 CN6 CN8B CN7 4.00 3 0.0 ! Nilesh, south, boat-chair energy, C6-C1-C2-C3 +CN6 CN7E CN7 CN8 0.50 3 0.0 ! Nilesh, north, boat-chair energy, C5-C1-C2-C3 +CN7E CN6 CN7 CN8 0.50 3 0.0 ! Nilesh, north, boat-chair energy, C1-C5-C4-C3 +CN8 CN6 CN7 CN8 4.00 3 0.0 ! Nilesh, north, boat-chair energy, C6-C5-C4-C3 +CN8 CN7E CN7 CN8 4.00 3 0.0 ! Nilesh, north, boat-chair energy, C6-C1-C2-C3 +CN8B CN6 CN7E CN7E 0.25 3 0.0 ! south, C2-C1-C5-C4, to get C2-C1-C5-C4 planar +! epsilon parameters +CN8 CN6 CN7 ON2 0.45 2 0.0 ! north sugar C6'-C4'-C3'-O3', C6-C5-C4-O3' +CN7E CN6 CN7 ON2 0.45 2 0.0 ! north sugar C6'-C4'-C3'-O3', C1-C5-C4-O3' +CN7E CN7E CN8B ON2 0.45 2 0.0 ! south sugar C3'-C4'-C5'-O5', C5-C4-C5'-O5' +! The following six parameters used to optimize boat-chair surface in bpsp, and bpnp +CN6 CN8B CN7 ON2 1.90 2 0.0 ! south sugar C1'-C2'-C3'-O3', C1-C2-C3-O3' +CN6 CN8B CN7 ON5 1.90 2 0.0 ! south sugar C1'-C2'-C3'-O3', model compd only +CN7E CN7E CN7 ON2 0.90 6 0.0 ! south sugar O4'-C4'-C3'-O3', C5-C4-C3-O3' +CN7E CN7E CN7 ON5 0.90 6 0.0 ! south sugar O4'-C4'-C3'-O3', model cmpd only +ON2 CN7 CN8 CN7 0.70 2 0.0 ! north sugar O3'-C4-C3-C2 +ON5 CN7 CN8 CN7 0.70 2 0.0 ! north sugar O3'-C4-C3-C2, model cmpd only +HN8 CN8B CN7 ON2 0.195 3 0.0 ! south sugar H2'-C2'-C3'-O3', H2*-C2-C3-O3' +HN7 CN7E CN7 ON2 0.195 3 0.0 ! south sugar H4'-C4'-C3'-O3', H41-C4-C3-O3' +HN7 CN7E CN7 ON5 0.195 3 0.0 ! south sugar H4'-C4'-C3'-O3', model cmpd only +CN7E CN7 ON5 HN5 0.5 3 0.0 ! south, model cmpd only +CN7E CN7 ON5 HN5 0.3 2 180.0 ! south, model cmpd only +CN7E CN7 ON5 HN5 1.5 1 0.0 ! south, model cmpd only +CN8B CN7 ON5 HN5 0.5 3 0.0 ! south, model cmpd only +CN8B CN7 ON5 HN5 1.0 2 180.0 ! south, model cmpd only +CN8B CN7 ON5 HN5 0.3 1 0.0 ! south, model cmpd only +CN8 CN6 CN7 ON5 0.45 2 0.0 ! north sugar C6'-C4'-C3'-O3', model cmpd only +CN7E CN6 CN7 ON5 0.45 2 0.0 ! north sugar O4'-C4'-C3'-O3', model cmpd only +CN6 CN7 ON2 P 2.40 1 180.0 ! eps, north only, C5-C4-O3'-P +CN6 CN7 ON2 P 0.40 2 180.0 ! eps, north only, C5-C4-O3'-P +CN6 CN7 ON2 P 1.50 3 240.0 ! eps, north only, C5-C4-O3'-P +CN6 CN7 ON2 P2 2.40 1 180.0 ! eps, north only, C5-C4-O3'-P, adm, 2011 DNA update +CN6 CN7 ON2 P2 0.40 2 180.0 ! eps, north only, C5-C4-O3'-P, adm, 2011 DNA update +CN6 CN7 ON2 P2 1.50 3 240.0 ! eps, north only, C5-C4-O3'-P, adm, 2011 DNA update +CN7E CN7 ON2 P 0.45 4 180.0 ! eps, south only, C4-C3-O3'-P +CN7E CN7 ON2 P 0.45 3 180.0 ! eps, south only, C4-C3-O3'-P +CN7E CN7 ON2 P 0.25 5 180.0 ! eps, south only, C4-C3-O3'-P +CN7E CN7 ON2 P 0.50 1 0.0 ! eps, south only, C4-C3-O3'-P +CN7E CN7 ON2 P2 0.45 4 180.0 ! eps, south only, C4-C3-O3'-P, adm, 2011 DNA update +CN7E CN7 ON2 P2 0.45 3 180.0 ! eps, south only, C4-C3-O3'-P, adm, 2011 DNA update +CN7E CN7 ON2 P2 0.25 5 180.0 ! eps, south only, C4-C3-O3'-P, adm, 2011 DNA update +CN7E CN7 ON2 P2 0.50 1 0.0 ! eps, south only, C4-C3-O3'-P, adm, 2011 DNA update +CN8B CN7 ON2 P 2.00 1 180.0 ! eps, south only, C2-C3-O3'-P +CN8B CN7 ON2 P2 2.00 1 180.0 ! eps, south only, C2-C3-O3'-P, adm, 2011 DNA update +HN7 CN7 CN6 HN7 0.15 3 0.0 ! north, model cmpd only +ON2 CN7 CN6 HN7 0.15 3 0.0 ! north, model cmpd only +CN8 CN7 CN6 HN7 0.15 3 0.0 ! north, model cmpd only +HN7 CN6 CN8 HN8 0.15 3 0.0 ! north, south, model cmpd only +CN8 CN7 CN7E HN7 0.15 3 0.0 ! north, C3-C2-C1-H11 +!chi parameters for bicyclo sugars +!next two parameters used to control boat-chair in cnth, csth +CN7 CN8 CN7 NN2B 1.00 1 180.0 ! north, C4-C3-C2-N1/N9 +CN7 CN8 CN7 NN2B 0.80 3 180.0 ! north, C4-C3-C2-N1/N9 +CN7 CN8B CN6 NN2B 0.70 3 0.0 ! south, C3-C2-C1-N1/N9 +CN7 CN8 CN6 NN2 0.70 3 0.0 ! south, C3-C2-C1-N1/N9 +CN7 CN8B CN6 NN2 0.70 3 0.0 ! south, C3-C2-C1-N1/N9 +CN7E CN8 CN6 NN2 0.70 3 0.0 ! south, C3-C2-C1-N1/N9 +CN7E CN7E CN6 NN2B 0.15 3 0.0 ! south, C4-C5-C1-N1/N9 +CN7E CN7E CN6 NN2 0.15 3 0.0 ! south, C4-C5-C1-N1/N9 +CN6 CN7E CN7 NN2B 0.15 3 0.0 ! north, C5-C1-C2-N1/N9 +CN6 CN7E CN7 NN2 0.15 3 0.0 ! north, C5-C1-C2-N1/N9 +CN8 CN7E CN7 NN2B 0.15 3 0.0 ! north, C6-C1-C2-N1/N9 +CN8 CN7E CN7 NN2 0.15 3 0.0 ! north, C6-C1-C2-N1/N9 +CN7E CN8 CN6 NN2B 0.15 3 0.0 ! south, C5-C6-C1-N1/N9 +CN8 CN7E CN6 NN2B 0.15 3 0.0 ! south, C6-C5-C1-N1/N9 +CN8 CN7E CN6 NN2 0.15 3 0.0 ! south, C6-C5-C1-N1/N9 +HN8 CN8 CN6 NN2B 0.15 3 0.0 ! south, H6*-C6-C1-N1/N9 +HN8 CN8B CN6 NN2B 0.15 3 0.0 ! south, H2*-C2-C1-N1/N9 +HN8 CN8B CN6 NN2 0.15 3 0.0 ! south, H2*-C2-C1-N1/N9 +HN8 CN8 CN6 NN2 0.15 3 0.0 ! south, H6*-C6-C1-N1/N9 +HN7 CN7E CN6 NN2B 0.15 3 0.0 ! H51-C5-C1-N1/N9 +HN7 CN7E CN6 NN2 0.15 3 0.0 ! H51-C5-C1-N1/N9 +HN7 CN7E CN7 NN2B 0.15 3 0.0 ! H51-C5-C1-N1/N9 +HN7 CN7E CN7 NN2 0.15 3 0.0 ! H51-C5-C1-N1/N9 +! exclusive chi parameters +CN7 CN7 NN2 CN4 0.5 1 180.0 ! adenine, north +CN7 CN7 NN2 CN5 1.1 1 180.0 ! adenine, north +CN7E CN7 NN2 CN4 0.5 1 180.0 ! adenine, north +CN7E CN7 NN2 CN5 1.1 1 180.0 ! adenine, north +CN8 CN7 NN2 CN4 0.5 1 180.0 ! adenine, north +CN8 CN7 NN2 CN5 1.1 1 180.0 ! adenine, north +CN8B CN6 NN2 CN5 0.3 3 0.0 ! adenine, south +CN8 CN6 NN2 CN5 0.3 3 0.0 ! adenine, south +CN8B CN6 NN2 CN4 0.1 3 0.0 ! adenine, south +CN8 CN6 NN2 CN4 0.1 3 0.0 ! adenine, south +CN7E CN6 NN2 CN5 1.1 1 180.0 ! adenine, south +CN7E CN6 NN2 CN4 1.1 1 180.0 ! adenine, south +CN7 CN7 NN2B CN4 0.5 1 180.0 ! guanine, north +CN7 CN7 NN2B CN5 1.1 1 180.0 ! guanine, north +CN7E CN7 NN2B CN4 0.5 1 180.0 ! guanine, north +CN7E CN7 NN2B CN5 1.1 1 180.0 ! guanine, north +CN8 CN7 NN2B CN4 0.5 1 180.0 ! guanine, north +CN8 CN7 NN2B CN5 1.1 1 180.0 ! guanine, north +CN8B CN6 NN2B CN5 0.3 3 0.0 ! guanine, south +CN8 CN6 NN2B CN5 0.3 3 0.0 ! adenine, south +CN8B CN6 NN2B CN4 0.1 3 0.0 ! guanine, south +CN8 CN6 NN2B CN4 0.1 3 0.0 ! adenine, south +CN7E CN6 NN2B CN5 1.1 1 180.0 ! guanine, south +CN7E CN6 NN2B CN4 1.1 1 180.0 ! guanine, south +CN8 CN6 NN2B CN3 0.0 3 180.0 ! thymine, south +CN8 CN6 NN2B CN1T 0.3 3 0.0 ! thymine, south +CN8B CN6 NN2B CN3 0.0 3 180.0 ! thymine, south +CN8B CN6 NN2B CN1T 0.3 3 0.0 ! thymine, south +CN7E CN6 NN2B CN3 0.0 3 180.0 ! thymine, south +CN7E CN6 NN2B CN1T 0.3 3 0.0 ! thymine, south +CN8 CN7 NN2B CN3 0.0 3 180.0 ! thymine, north +CN8 CN7 NN2B CN1T 0.0 3 180.0 ! thymine, north +CN7E CN7 NN2B CN3 0.4 4 0.0 ! thymine, north +CN7E CN7 NN2B CN1T 1.0 3 0.0 ! thymine, north +CN8 CN7 NN2 CN3 0.0 3 180.0 ! cytosine, north +CN8 CN7 NN2 CN1 0.0 3 180.0 ! cytosine, north +CN7E CN7 NN2 CN3 0.4 4 0.0 ! cytosine, north +CN7E CN7 NN2 CN1 1.0 3 0.0 ! cytosine, north +CN8 CN6 NN2 CN3 0.0 3 180.0 ! cytosine, south +CN8 CN6 NN2 CN1 0.3 3 0.0 ! cytosine, south +CN8B CN6 NN2 CN3 0.0 3 180.0 ! cytosine, south +CN8B CN6 NN2 CN1 0.2 3 180.0 ! cytosine, south +CN7E CN6 NN2 CN3 0.0 3 180.0 ! cytosine, south +CN7E CN6 NN2 CN1 0.2 3 180.0 ! cytosine, south +HN7 CN7 NN2B CN3 0.195 3 0.0 ! north, H21-C2-N1/N9-C, (from HN7 CN7B NN2 CN3) +HN7 CN7 NN2 CN3 0.195 3 0.0 ! north, H21-C2-N1/N9-C, (from HN7 CN7B NN2 CN3) +HN7 CN7 NN2B CN1T 0.195 3 0.0 ! north, H21-C2-N1/N9-C, (from HN7 CN7B NN2 CN3) +HN7 CN7 NN2 CN1 0.195 3 0.0 ! north, H21-C2-N1/N9-C, (from HN7 CN7B NN2 CN3) +HN7 CN7 NN2 CN4 0.195 3 0.0 ! north, H21-C2-N1/N9-C, (from HN7 CN7B NN2 CN3) +HN7 CN7 NN2B CN4 0.195 3 0.0 ! north, H21-C2-N1/N9-C, (from HN7 CN7B NN2 CN3) +HN7 CN7 NN2 CN5 0.195 3 0.0 ! north, H21-C2-N1/N9-C, (from HN7 CN7B NN2 CN3) +HN7 CN7 NN2B CN5 0.195 3 0.0 ! north, H21-C2-N1/N9-C, (from HN7 CN7B NN2 CN3) +CN8 CN7E CN7 HN7 0.15 3 0.0 ! north, C6-C1-C2-H21 +HN8 CN8 CN7E CN7 0.15 3 0.0 ! north, H6*-C6-C1-C2 +! gamma parameters +CN7 CN7E CN8B ON2 0.15 3 180.0 ! gamma, south, C3-C4-C5'-O5' +CN7 CN7E CN8B ON2 0.10 2 0.0 ! gamma, south, C3-C4-C5'-O5' +CN7 CN7E CN8B ON2 1.25 1 180.0 ! gamma, south, C3-C4-C5'-O5' +! The next parameter used for boat-chair in b5sp +CN8B CN7 CN7E CN8B 1.80 3 0.0 ! south, C2'-C3'-C4'-C5', C2-C3-C4-C5' +HN7 CN7E CN8B ON2 0.195 3 0.0 ! gamma, south, H41-C4-C5'-O5' +HN7 CN7E CN8B HN8 0.15 3 0.0 ! gamma, south, H41-C4-C5'-H5' +CN7 CN7E CN8B HN8 0.195 3 0.0 ! gamma, south, C3-C4-C5'-H5' +HN8 CN8B CN6 CN7 0.195 3 0.0 ! gamma, north, H5'-C5'-C5-C4 +HN8 CN8B CN6 CN8 0.195 3 0.0 ! gamma, north, H5'-C5'-C5-C6 +CN8 CN6 CN8B ON2 0.15 1 180.0 ! gamma, north, C6-C5-C5'-O5' +CN7E CN6 CN8B ON2 0.60 1 0.0 ! gamma, north, C1-C5-C5'-O5' +CN7E CN6 CN8B ON2 0.70 3 0.0 ! gamma, north, C1-C5-C5'-O5' +CN7E CN6 CN8B ON5 0.60 1 0.0 ! gamma, north, C1-C5-C5'-O5' +CN7E CN6 CN8B ON5 0.70 3 0.0 ! gamma, north, C1-C5-C5'-O5' +CN7 CN6 CN8B ON2 0.50 2 0.0 ! gamma, north, C4-C5-C5'-O5' +CN7 CN6 CN8B ON5 0.50 2 0.0 ! gamma, north, C4-C5-C5'-O5' +! delta dihedral parameters +ON2 CN7 CN7E CN8B 0.2 4 0.0 !delta, south, O3'-C3-C4-C5' +ON2 CN7 CN7E CN8B 0.8 3 180.0 !delta, south, O3'-C3-C4-C5', decreases P [100,250] +ON5 CN7 CN7E CN8B 0.2 4 0.0 !delta, south, model cmpd only +ON5 CN7 CN7E CN8B 0.8 3 180.0 !delta, south, model cmpd only, decreases P [100,250] +ON5 CN7 CN6 CN8B 0.2 4 0.0 !delta, north, model cmpd only +ON5 CN7 CN6 CN8B 0.8 3 180.0 !delta, north, model cmpd only, decreases P [100,250] +ON2 CN7 CN6 CN8B 0.2 4 0.0 !delta, north, O3'-C4-C5-C5' +ON2 CN7 CN6 CN8B 0.8 3 180.0 !delta, north, O3'-C4-C5-C5', decreases P [100,250] +! other miscellaneous parameters +! next parameter used for b5np boat-chair energy +CN8B CN6 CN7 CN8 2.20 2 180.0 !north, C5'-C4'-C3'-C2', C5'-C5-C4-C3 +CN8B CN6 CN7 CN8 0.55 6 180.0 !north, C5'-C4'-C3'-C2', C5'-C5-C4-C3 +CN8B CN6 CN7 HN7 0.195 3 0.0 !north, C5'-C4'-C3'-H3', C5'-C5-C4-H41 +CN8B CN6 CN8 HN8 0.195 3 0.0 !north, C5'-C5-C6-H6*, and south, C2-C1-C6-H6* +P ON2 CN8B CN6 0.2 1 120.0 !north, beta, C5-C5'-O5'-P +P2 ON2 CN8B CN6 0.2 1 120.0 !north, beta, C5-C5'-O5'-P, adm, 2011 DNA update +HN5 ON5 CN8B CN6 0.2 1 120.0 !north, beta, C5-C5'-O5'-P +P ON2 CN8B CN7E 0.2 1 120.0 !south, beta, C4-C5'-O5'-P +P2 ON2 CN8B CN7E 0.2 1 120.0 !south, beta, C4-C5'-O5'-P, adm, 2011 DNA update +HN5 ON5 CN8B CN7E 0.2 1 120.0 !south, beta, C4-C5'-O5'-P +CN6 CN7 ON5 HN5 0.5 3 0.0 !north, C4'-C3'-O3'-H3'', model cmpd only +HN7 CN7 CN7E CN8B 0.195 3 0.0 !south, H4'-C4'-C3'-O3', H31-C3-C4-C5' +! parameters unique to carbo-furanose +!------------------------------------------------------------------------------- +CN8 CN7 CN8B ON5 0.2 3 180.0 ! from gam +CN8 CN8B CN8 HN8 0.195 1 0.0 ! Nilesh, newly assigned +! endocyclic +ON5 CN7 CN7 CN8 0.5 6 180.0 ! corresponds to ON5 CN7 CN7 ON6 +ON5 CN7 CN7 CN8 0.5 5 0.0 ! +ON5 CN7 CN7 CN8 0.2 4 0.0 ! +ON5 CN7 CN7 CN8 0.2 3 0.0 ! +ON2 CN7 CN7 CN8 0.5 6 180.0 ! corresponds to ON5 CN7 CN7 ON6 +ON2 CN7 CN7 CN8 0.5 5 0.0 ! +ON2 CN7 CN7 CN8 0.2 4 0.0 ! +ON2 CN7 CN7 CN8 0.2 3 0.0 ! +CN8 CN7 CN7 CN8 0.0 3 0.0 ! from C2'-C3'-C4'-O4' +CN8 CN8B CN8 CN7 0.5 6 180.0 ! from c4'-o4'-c1'-c2', tau0 +CN8 CN8B CN8 CN7 0.5 3 0.0 ! +HN8 CN8B CN7 ON5 0.195 1 0.0 ! phosphoramidate and carbocyclic sugars + +IMPROPER +! +!atom types Kpsi psi0 +! +NN2G CN4 CN1 HN2 0.8 0 0.0 !Inosine, adm jr. 2/94 +CN4 NN2G NN3I HN3 39.0 0 0.0 !Inosine, adm jr. 2/94 +!guanine tautomer terms +CN1 NN3G CN5G ON5 55.0 0 0.0 !sasha, 2/98 +!cytosine tautomer terms +CN2 NN2C CN3 NN1C 90.0 0 0.0 !sasha, 2/98 +!N3-protonated CYT(CYTH) and 5Me-CYT(CYTP), edarian 2009-03 +NN2G CN1 CN2 HN2 0.0 1 180.0 +!params for GUANIDINIUM tail patch at N4 of CYT, 4EG1, edarian, 2009-11 +NNG X X CNG 40.0 0 0.0 ! NC2 X X C ALLOW PEP POL ARO + +!backbone section +!PNA related terms +HN2 X X NN2G 1.0 0 0.0 +HN2 X X NN2U 1.0 0 0.0 +NN1 CN2 HN1 HN2 6.0 0 0.0 +CT2 CN5 CN4 NN2 7.0 0 0.0 +CT2 CN5 CN4 NN2B 7.0 0 0.0 +CT2 CN1 CN3 NN2 18.0 0 0.0 +CT2 CN1T CN3 NN2B 18.0 0 0.0 +CT2 H C NH1 20.0 0 0.0 +NH1 O CT2 C 20.0 0 0.0 +NH3 O CT2 C 20.0 0 0.0 +NC2 O CT2 CD 20.0 0 0.0 +CT2 O NH1 C 20.0 0 0.0 +NH1 CT2 H C 20.0 0 0.0 +HN3 X X CN4 20.0 0 0.0 +HN3 X X CN3 15.0 0 0.0 + +NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 + +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +HNP 0.0 -0.03 1.3582 !JES 8/25/89 values from Jorgensen fit to hydration energy +HNE1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95 +HNE2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95 +CN3D 0.0 -0.09 1.9000 ! 5mc, adm jr. +CNE1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95 +CNE2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95 +CNA 0.0 -0.07 1.9924 !benzene (JES) +CNA2 0.0 -0.07 1.90 !dft, adm jr. +CNG 0.0 -0.1100 2.0000 ! guanidinium type carbon +NN1C 0.0 -0.20 1.85 +NN2C 0.0 -0.20 1.85 ! +NN3I 0.0 -0.20 1.85 +NNG 0.0 -0.20 1.85 ! guanidinium type nitroge +FNA 0.0 -0.12 1.70 !aromatic F, 1,3-difluorobenzene pure solvent +!backbone section +ON2M 0.0 -0.1000 1.65 ! ether O, from OC30A ether params +!carbocyclic section +CN6 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 +CN7E 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 + +END + +return diff --git a/charmm/toppar/stream/na/toppar_all36_na_nad_ppi.str b/charmm/toppar/stream/na/toppar_all36_na_nad_ppi.str new file mode 100644 index 00000000..12ee757c --- /dev/null +++ b/charmm/toppar/stream/na/toppar_all36_na_nad_ppi.str @@ -0,0 +1,2602 @@ +* CHARMM36 All-Hydrogen Nucleic Acid Force Toppar Stream File +* NAD+, NADH, ADP, ATP, PPI and related analogs +* A.D. MacKerell, Jr., July 2001 +* stream following RTF and PARAM read of +* + +!Update, 2015/1, nomenclature for NAD+ etc. consistent with PDB + +!Parent files that have to be read prior to streaming this file +!top_all36_na.rtf +!par_all36_na.prm + +!Testcase +!test_all36_na_nad_ppi.inp + +!Reference +!Pavelites, J.J., Bash, P.A., Gao, J., and MacKerell, Jr., +!A.D. A Molecular Mechanics Force Field for NAD+, NADH and the +!Pyrophosphate Groups of Nucleotides, Journal of Computational +!Chemistry, 1997, 18: 221-239. + +read rtf card append +* NAD, PPI topology +* +31 1 + +MASS 459 HN3B 1.008000 H ! NAD+ aromatic hydrogen +MASS 460 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon +MASS 461 CN3A 12.011000 C ! NAD+ aromatic carbon +MASS 462 CN3B 12.011000 C ! NAD+ aromatic carbon +MASS 463 CN3C 12.011000 C ! NADH aromatic carbon +MASS 464 P3 30.974000 P ! pyrophosphate phosphorus +MASS 465 P4 30.974000 P ! protonated pyrophosphate phosphorus + +RESI NIC 1.00 ! oxidized nicotinamide, jjp1/adm jr. + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! + ! H15 +GROUP ! \ +ATOM H1 HN2 0.45 ! H16-N14 H8 +ATOM N2 NN2 -0.52 ! \ | +ATOM C3 CN3B 0.16 ! C12 C7 +ATOM H4 HN3B 0.19 ! // \ / \\ +ATOM C5 CN3 -0.10 ! O13 C9 C5-H6 +ATOM H6 HN3B 0.16 ! || | +ATOM C7 CN3A -0.05 ! H11-C10 C3-H4 +ATOM H8 HN3B 0.16 ! \+ // +ATOM C9 CN3 0.05 ! N2 +ATOM C10 CN3B 0.18 ! | +ATOM H11 HN3B 0.16 ! H1 +ATOM C12 CN1A 0.68 ! +ATOM O13 ON1 -0.40 ! +ATOM N14 NN1 -0.82 ! +ATOM H15 HN1 0.34 ! trans to O13 +ATOM H16 HN1 0.36 ! cis to O13 +BOND N2 H1 C3 H4 C3 C5 C5 H6 +BOND C7 H8 C7 C9 N2 C10 +BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16 +DOUBLE C12 O13 C9 C10 C5 C7 N2 C3 +! amide impropers +IMPR C12 N14 C9 O13 C12 C9 N14 O13 +IMPR N14 C12 H16 H15 N14 C12 H15 H16 +! ring hydrogen impropers +IMPR N2 C10 C3 H1 C3 N2 C5 H4 C5 C3 C7 H6 +IMPR C7 C5 C9 H8 C10 C9 N2 H11 +! ic table for analysis +IC N2 C3 C5 C7 0.0000 000.00 000.00 000.00 0.000 +IC C3 C5 C7 C9 0.0000 000.00 000.00 000.00 0.000 +IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C10 N2 0.0000 000.00 000.00 000.00 0.000 +IC C9 C10 N2 C3 0.0000 000.00 000.00 000.00 0.000 +IC C10 N2 C3 C5 0.0000 000.00 000.00 000.00 0.000 +IC C9 C10 N2 H1 0.0000 000.00 000.00 000.00 0.000 +IC C10 N2 C3 H4 0.0000 000.00 000.00 000.00 0.000 +IC N2 C3 C5 H6 0.0000 000.00 000.00 000.00 0.000 +IC C3 C5 C7 H8 0.0000 000.00 000.00 000.00 0.000 +IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000 +IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000 +IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000 +IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000 +patch first none last none + +RESI NICH 0.00 ! reduced nicotinamide, jjp1/adm jr. + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! HN3 to HN6 atom type switch to maintain proper vdw params, 9/98 + ! + ! H15 +GROUP ! \ +ATOM H1 HN2 0.42 ! H16-N14 H8 H17 +ATOM N2 NN2 -0.69 ! \ \ / +ATOM C3 CN3C -0.06 ! C12 C7 +ATOM H4 HN6 0.17 ! / \ / \ +ATOM C5 CN3 -0.18 ! O13 C9 C5-H6 +ATOM H6 HN6 0.14 ! || || +ATOM C7 CN8 -0.28 ! H11-C10 C3-H4 +ATOM H8 HN8 0.09 ! \ / +ATOM H17 HN8 0.09 ! N2 +ATOM C10 CN3C -0.10 ! | +ATOM H11 HN6 0.14 ! H1 +ATOM C9 CN3 0.36 ! +ATOM C12 CN1A 0.55 ! +ATOM O13 ON1 -0.51 ! +ATOM N14 NN1 -0.72 ! +ATOM H15 HN1 0.26 ! trans to O13 +ATOM H16 HN1 0.32 ! cis to O13 + +BOND N2 H1 N2 C3 C3 H4 C5 H6 +BOND C5 C7 C7 H8 C7 H17 C7 C9 N2 C10 +BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16 +DOUBLE C12 O13 C9 C10 C3 C5 +! amide impropers +IMPR C12 N14 C9 O13 C12 C9 N14 O13 +IMPR N14 C12 H16 H15 N14 C12 H15 H16 +! ring hydrogen impropers +IMPR N2 C10 C3 H1 C3 N2 C5 H4 C5 C3 C7 H6 +IMPR C10 C9 N2 H11 +! ic table for analysis +IC N2 C3 C5 C7 0.0000 000.00 000.00 000.00 0.000 +IC C3 C5 C7 C9 0.0000 000.00 000.00 000.00 0.000 +IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C10 N2 0.0000 000.00 000.00 000.00 0.000 +IC C9 C10 N2 C3 0.0000 000.00 000.00 000.00 0.000 +IC C10 N2 C3 C5 0.0000 000.00 000.00 000.00 0.000 +IC C9 C10 N2 H1 0.0000 000.00 000.00 000.00 0.000 +IC C10 N2 C3 H4 0.0000 000.00 000.00 000.00 0.000 +IC N2 C3 C5 H6 0.0000 000.00 000.00 000.00 0.000 +IC C3 C5 C7 H8 0.0000 000.00 000.00 000.00 0.000 +IC C3 C5 C7 H17 0.0000 000.00 000.00 000.00 0.000 +IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000 +IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000 +IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000 +IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000 +patch first none last none + +RESI PPI1 -3.00 ! Inorganic phosphate, jjp1/adm jr. +GROUP ! +ATOM C1 CN9 -0.17 ! +ATOM O11 ON2 -0.62 ! +ATOM P1 P 1.50 ! H11 +ATOM O12 ON2 -0.74 ! | +ATOM O13 ON3 -0.82 ! H13--C1--H12 +ATOM O14 ON3 -0.82 ! | + ! O11 +ATOM P2 P3 1.10 ! | +ATOM O22 ON3 -0.90 ! O14==P1==O13 (-) +ATOM O23 ON3 -0.90 ! | +ATOM O24 ON3 -0.90 ! O12 + ! | +ATOM H11 HN9 0.09 ! (-) O24==P2==O23 (-) +ATOM H12 HN9 0.09 ! || +ATOM H13 HN9 0.09 ! O22 + +BOND P1 O11 P1 O12 P1 O13 P1 O14 O11 C1 +BOND C1 H11 C1 H12 C1 H13 +BOND O12 P2 P2 O22 P2 O23 P2 O24 +! IC Table +IC C1 O11 P1 O12 0.0000 000.00 180.0 000.00 0.0000 +IC O11 P1 O12 P2 0.0000 000.00 180.0 000.00 0.0000 +IC P1 O12 P2 O22 0.0000 000.00 180.0 000.00 0.0000 +IC C1 O11 P1 O13 0.0000 000.00 60.0 000.00 0.0000 +IC C1 O11 P1 O14 0.0000 000.00 -60.0 000.00 0.0000 +IC P1 O12 P2 O23 0.0000 000.00 60.0 000.00 0.0000 +IC P1 O12 P2 O24 0.0000 000.00 -60.0 000.00 0.0000 +IC P1 O11 C1 H11 0.0000 000.00 180.0 000.00 0.0000 +IC P1 O11 C1 H12 0.0000 000.00 60.0 000.00 0.0000 +IC P1 O11 C1 H13 0.0000 000.00 -60.0 000.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI PPI2 -2.00 ! Inorganic phosphate, protonated, adm jr. + ! terminal P charges based on neutral +GROUP ! methylphosphate +ATOM C1 CN9 -0.17 ! +ATOM O11 ON2 -0.62 ! +ATOM P1 P 1.46 ! H11 +ATOM O12 ON2 -0.63 ! | +ATOM O13 ON3 -0.83 ! H13--C1--H12 +ATOM O14 ON3 -0.83 ! | + ! O11 +ATOM P2 P4 1.34 ! | +ATOM O22 ON4 -0.72 ! O14==P1==O13 (-) +ATOM H22 HN4 0.45 ! | +ATOM O23 ON3 -0.86 ! | +ATOM O24 ON3 -0.86 ! O12 + ! | +ATOM H11 HN9 0.09 ! (-) O24==P2==O23 (-) +ATOM H12 HN9 0.09 ! | +ATOM H13 HN9 0.09 ! O22 + ! \ + ! H22 + +BOND P1 O11 P1 O12 P1 O13 P1 O14 O11 C1 +BOND C1 H11 C1 H12 C1 H13 +BOND O12 P2 P2 O22 P2 O23 P2 O24 O22 H22 +! IC Table +IC C1 O11 P1 O12 0.0000 000.00 180.0 000.00 0.0000 +IC O11 P1 O12 P2 0.0000 000.00 180.0 000.00 0.0000 +IC P1 O12 P2 O22 0.0000 000.00 180.0 000.00 0.0000 +IC C1 O11 P1 O13 0.0000 000.00 60.0 000.00 0.0000 +IC C1 O11 P1 O14 0.0000 000.00 -60.0 000.00 0.0000 +IC P1 O12 P2 O23 0.0000 000.00 60.0 000.00 0.0000 +IC P1 O12 P2 O24 0.0000 000.00 -60.0 000.00 0.0000 +IC P1 O11 C1 H11 0.0000 000.00 180.0 000.00 0.0000 +IC P1 O11 C1 H12 0.0000 000.00 60.0 000.00 0.0000 +IC P1 O11 C1 H13 0.0000 000.00 -60.0 000.00 0.0000 +IC O12 P2 O22 H22 0.0000 000.00 180.0 000.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI AMP -2.00 ! adenosine monophosphate, jjp1/adm jr. + ! atom names correspond to pdb nomenclature +GROUP +ATOM C4' CN7 0.16 ! H61 H62 +ATOM H4' HN7 0.09 ! \ / +ATOM O4' ON6B -0.50 ! N6 +ATOM C1' CN7B 0.16 ! | +ATOM H1' HN7 0.09 ! C6 +GROUP ! // \ +ATOM C5 CN5 0.28 ! N1 C5--N7\\ +ATOM N7 NN4 -0.71 ! | || C8-H8 +ATOM C8 CN4 0.34 ! C2 C4--N9/ +ATOM H8 HN3 0.12 ! / \\ / \ +ATOM N9 NN2 -0.05 ! H2 N3 \ + ! \ +ATOM N1 NN3A -0.74 ! \ +ATOM C2 CN4 0.50 ! \ +ATOM H2 HN3 0.13 ! O1A H5' H4' O4' \ +ATOM N3 NN3A -0.75 ! | | \ / \ \ +ATOM C4 CN5 0.43 ! O3A=PA-O5'-C5'---C4' C1' +ATOM C6 CN2 0.46 ! | | \ / \ + ! O2A H5'' C3'--C2' H1' +ATOM N6 NN1 -0.77 ! / \ / \ +ATOM H61 HN1 0.38 ! O3' H3' O2' H2'' +ATOM H62 HN1 0.38 ! | | +GROUP ! H3T H2' +ATOM C2' CN7B 0.14 ! +ATOM H2'' HN7 0.09 +ATOM O2' ON5 -0.66 +ATOM H2' HN5 0.43 +GROUP +ATOM C3' CN7 0.14 +ATOM H3' HN7 0.09 +ATOM O3' ON5 -0.66 +ATOM H3T HN5 0.43 +GROUP +ATOM C5' CN8B -0.18 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +GROUP +ATOM O5' ON2 -0.40 +ATOM PA P 1.10 +ATOM O1A ON3 -0.90 +ATOM O2A ON3 -0.90 +ATOM O3A ON3 -0.90 + +BOND PA O1A PA O2A PA O3A PA O5' O3' H3T +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C2' C3' C2' O2' O2' H2' C3' O3' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1A PA +ACCE O2A PA +ACCE O3A PA +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +IC C5' O5' PA O1A 0.0000 000.00 60.0 000.00 0.0000 +IC C5' O5' PA O2A 0.0000 000.00 -60.0 000.00 0.0000 +IC O1A O2A *PA O3A 0.0000 000.00 120.0 000.00 0.0000 +IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + + +RESI ADP -3.00 ! adenosine diphosphate, jjp1/adm jr. + ! atom names correspond to pdb nomenclature +GROUP +ATOM C4' CN7 0.16 ! H61 H62 +ATOM H4' HN7 0.09 ! \ / +ATOM O4' ON6B -0.50 ! N6 +ATOM C1' CN7B 0.16 ! | +ATOM H1' HN7 0.09 ! C6 +GROUP ! // \ +ATOM C5 CN5 0.28 ! N1 C5--N7\\ +ATOM N7 NN4 -0.71 ! | || C8-H8 +ATOM C8 CN4 0.34 ! C2 C4--N9/ +ATOM H8 HN3 0.12 ! / \\ / \ +ATOM N9 NN2 -0.05 ! H2 N3 \ + ! \ +ATOM N1 NN3A -0.74 ! \ +ATOM C2 CN4 0.50 ! \ +ATOM H2 HN3 0.13 ! O3B O1A H5' H4' O4' \ +ATOM N3 NN3A -0.75 ! | | | \ / \ \ +ATOM C4 CN5 0.43 ! O1B=PB-O3A--PA-O5'-C5'---C4' C1' +ATOM C6 CN2 0.46 ! | | | \ / \ + ! O2B O2A H5'' C3'--C2' H1' +ATOM N6 NN1 -0.77 ! / \ / \ +ATOM H61 HN1 0.38 ! O3' H3' O2' H2'' +ATOM H62 HN1 0.38 ! | | +GROUP ! H3T H2' +ATOM C2' CN7B 0.14 ! +ATOM H2'' HN7 0.09 +ATOM O2' ON5 -0.66 +ATOM H2' HN5 0.43 +GROUP +ATOM C3' CN7 0.14 +ATOM H3' HN7 0.09 +ATOM O3' ON5 -0.66 +ATOM H3T HN5 0.43 +GROUP +ATOM C5' CN8B -0.08 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +ATOM O5' ON2 -0.62 +ATOM PA P 1.50 +ATOM O1A ON3 -0.82 +ATOM O2A ON3 -0.82 +ATOM O3A ON2 -0.74 +ATOM PB P3 1.10 +ATOM O1B ON3 -0.90 +ATOM O2B ON3 -0.90 +ATOM O3B ON3 -0.90 + +BOND PB O3A PB O1B PB O2B PB O3B O3A PA +BOND PA O1A PA O2A PA O5' O3' H3T +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C2' C3' C2' O2' O2' H2' C3' O3' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1A PA +ACCE O2A PA +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +ACCE O3A +ACCE O3B +ACCE O2B +ACCE O1B +IC PA O3A PB O1B 0.0000 000.00 180.0 000.00 0.0000 +IC C5' O5' PA O1A 0.0000 000.00 60.0 000.00 0.0000 +IC C5' O5' PA O2A 0.0000 000.00 -60.0 000.00 0.0000 +IC PA O3A PB O2B 0.0000 000.00 60.0 000.00 0.0000 +IC PA O3A PB O3B 0.0000 000.00 -60.0 000.00 0.0000 +IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI ATP -4.00 !adenosine triphosphate , jjp1/adm jr. + !atom names correspond to pdb nomenclature + ! +GROUP +ATOM C4' CN7 0.16 ! H61 H62 +ATOM H4' HN7 0.09 ! \ / +ATOM O4' ON6B -0.50 ! N6 +ATOM C1' CN7B 0.16 ! | +ATOM H1' HN7 0.09 ! C6 +GROUP ! // \ +ATOM C5 CN5 0.28 ! N1 C5--N7\\ +ATOM N7 NN4 -0.71 ! | || C8-H8 +ATOM C8 CN4 0.34 ! C2 C4--N9/ +ATOM H8 HN3 0.12 ! / \\ / \ +ATOM N9 NN2 -0.05 ! H2 N3 \ + ! \ +ATOM N1 NN3A -0.74 ! \ +ATOM C2 CN4 0.50 ! \ +ATOM H2 HN3 0.13 ! (-)O3G O2B O1A H5' H4' O4' \ +ATOM N3 NN3A -0.75 ! | | | | \ / \ \ +ATOM C4 CN5 0.43 !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4' C1' +ATOM C6 CN2 0.46 ! | | | | \ / \ + ! (-)O2G (-)O1B (-)O2A H5'' C3'--C2' H1' +ATOM N6 NN1 -0.77 ! / \ / \ +ATOM H61 HN1 0.38 ! O3' H3' O2' H2'' +ATOM H62 HN1 0.38 ! | | +GROUP ! H3T H2' +ATOM C2' CN7B 0.14 ! +ATOM H2'' HN7 0.09 +ATOM O2' ON5 -0.66 +ATOM H2' HN5 0.43 +GROUP +ATOM C3' CN7 0.14 +ATOM H3' HN7 0.09 +ATOM O3' ON5 -0.66 +ATOM H3T HN5 0.43 +GROUP +ATOM C5' CN8B -0.08 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +ATOM O5' ON2 -0.62 +ATOM PA P 1.50 +ATOM O1A ON3 -0.82 +ATOM O2A ON3 -0.82 +ATOM O3A ON2 -0.74 +ATOM PB P3 1.50 +ATOM O1B ON3 -0.82 +ATOM O2B ON3 -0.82 +ATOM O3B ON2 -0.86 ! charge adjusted to yield total triP of -4.0 +ATOM PG P3 1.10 +ATOM O1G ON3 -0.90 +ATOM O2G ON3 -0.90 +ATOM O3G ON3 -0.90 + +BOND O5' C5' O5' PA PA O1A PA O2A PA O3A +BOND O3A PB PB O1B PB O2B PB O3B O3B PG +BOND PG O1G PG O2G PG O3G +BOND C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' H3T +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1A PA +ACCE O2A PA +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +ACCE O3A +ACCE O2B +ACCE O1B +ACCE O3B +ACCE O3G +ACCE O2G +ACCE O2G +IC PA O3A PB O3B 0.0000 000.00 180.0 000.00 0.0000 +IC O3A PB O3B PG 0.0000 000.00 180.0 000.00 0.0000 +IC PB O3B PG O1G 0.0000 000.00 180.0 000.00 0.0000 +IC C5' O5' PA O1A 0.0000 000.00 60.0 000.00 0.0000 +IC C5' O5' PA O2A 0.0000 000.00 -60.0 000.00 0.0000 +IC PA O3A PB O1B 0.0000 000.00 60.0 000.00 0.0000 +IC PA O3A PB O2B 0.0000 000.00 -60.0 000.00 0.0000 +IC PB O3B PG O2G 0.0000 000.00 60.0 000.00 0.0000 +IC PB O3B PG O3G 0.0000 000.00 -60.0 000.00 0.0000 +IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +PRES 5DP -3.00 ! patch to create 5' diphosphate on nucleotides, jjp1/adm jr. + ! as in ADP, use in generate statement +GROUP +ATOM C5' CN8 -0.08 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +ATOM O5' ON2 -0.62 +ATOM P P 1.50 +ATOM O1P ON3 -0.82 +ATOM O2P ON3 -0.82 +ATOM O13 ON2 -0.74 +ATOM P2 P3 1.10 +ATOM O21 ON3 -0.90 +ATOM O22 ON3 -0.90 +ATOM O23 ON3 -0.90 + +BOND P O13 O13 P2 +BOND P2 O21 P2 O22 P2 O23 +ACCE O13 +ACCE O21 +ACCE O22 +ACCE O23 +IC C5' O5' P O13 0.0000 000.00 180.0 000.00 0.0000 +IC O5' P O13 P2 0.0000 000.00 180.0 000.00 0.0000 +IC P O13 P2 O21 0.0000 000.00 180.0 000.00 0.0000 +IC P O13 P2 O22 0.0000 000.00 60.0 000.00 0.0000 +IC P O13 P2 O23 0.0000 000.00 -60.0 000.00 0.0000 +PATC FIRS NONE LAST NONE + +!atom nomenclature consisent with PDB, 2015 + +RESI NAD -1.00 ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr. + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params +GROUP ! +ATOM C4B CN7 0.16 ! H61A H62A +ATOM H4B HN7 0.09 ! \ / +ATOM O4B ON6B -0.50 ! N6A +ATOM C1B CN7B 0.16 ! | +ATOM H1B HN7 0.09 ! C6A +GROUP ! // \ +ATOM C5A CN5 0.28 ! N1A C5A--N7A\\ +ATOM N7A NN4 -0.71 ! | || C8A-H8A +ATOM C8A CN4 0.34 ! C2A C4A--N9A/ +ATOM H8A HN3 0.12 ! / \\ / \ +ATOM N9A NN2 -0.05 ! H2A N3A \ + ! \ +ATOM N1A NN3A -0.74 ! \ +ATOM C2A CN4 0.50 ! \ +ATOM H2A HN3 0.13 ! O1N O1A H52AH4B O4B \ +ATOM N3A NN3A -0.75 ! | | | \ / \ \ +ATOM C4A CN5 0.43 ! O5D PN-O3--PA-O5B -C5B -C4B C1B +ATOM C6A CN2 0.46 ! \ | | | \ / \ + ! \ O2N O2A H51A C3B -C2B H1B +ATOM N6A NN1 -0.77 ! \ / \ / \ +ATOM H61A HN1 0.38 ! \ O3B H3B O2B H2B +ATOM H62A HN1 0.38 ! \ | | +GROUP ! \ HO3A HO2A +ATOM C2B CN7B 0.14 ! \ N71N +ATOM H2B HN7 0.09 ! \ \ +ATOM O2B ON5 -0.66 ! \ H72N-N7N N41N +ATOM HO2A HN5 0.43 ! \ \ | +GROUP ! \ C7N C4N +ATOM C3B CN7 0.14 ! \ / \ / \ +ATOM H3B HN7 0.09 ! \ O7N C3N C5N-H5N +ATOM O3B ON5 -0.66 ! \ | | +ATOM HO3A HN5 0.43 ! \ H51N H4D O4D H2N-C2N C6N-HN6 +GROUP ! \ | \ / \ \+ / +ATOM C5B CN8B -0.08 ! C5D --C4D C1D ---------N1N +ATOM H51A HN8 0.09 ! | \ / \ +ATOM H52A HN8 0.09 ! H52N C3D -C2D H1D +ATOM PA P 1.50 ! / \ / \ +ATOM O1A ON3 -0.82 ! O3D H3D O2D H2D +ATOM O2A ON3 -0.82 ! | | +ATOM O5B ON2 -0.62 ! HO3N HO2N +ATOM O3 ON2 -0.68 +ATOM PN P 1.50 +ATOM O1N ON3 -0.82 +ATOM O2N ON3 -0.82 +ATOM O5D ON2 -0.62 +ATOM C5D CN8B -0.08 +ATOM H51N HN8 0.09 +ATOM H52N HN8 0.09 +GROUP +ATOM C2D CN7B 0.14 +ATOM H2D HN7 0.09 +ATOM O2D ON5 -0.66 +ATOM HO2N HN5 0.43 +GROUP +ATOM C3D CN7 0.14 +ATOM H3D HN7 0.09 +ATOM O3D ON5 -0.66 +ATOM HO3N HN5 0.43 +GROUP +ATOM C1D CN7B 0.16 +ATOM H1D HN7 0.09 +ATOM C4D CN7 0.16 +ATOM H4D HN7 0.09 +ATOM O4D ON6B -0.50 +GROUP +ATOM N1N NN2 -0.07 +ATOM C6N CN3B 0.16 +ATOM HN6 HN3B 0.19 +ATOM C5N CN3 -0.10 +ATOM H5N HN3B 0.16 +ATOM C4N CN3A -0.05 +ATOM H41N HN3B 0.16 !H4N in official nomenclature +ATOM C3N CN3 0.05 +ATOM C2N CN3B 0.18 +ATOM H2N HN3B 0.16 +ATOM C7N CN1A 0.68 +ATOM O7N ON1 -0.40 +ATOM N7N NN1 -0.82 +ATOM N71N HN1 0.34 ! trans to amide O +ATOM H72N HN1 0.36 ! cis to amide O + +BOND N1A C2A N3A C4A C5A C6A +BOND C6A N6A C5A N7A C8A N9A +BOND N9A C4A C2A H2A N6A H61A N6A H62A C8A H8A +DOUBLE C6A N1A C2A N3A C4A C5A N7A C8A +BOND N9A C1B C1B C2B C2B C3B C3B C4B C4B O4B +BOND O4B C1B C1B H1B C2B O2B O2B HO2A C2B H2B +BOND C3B H3B C3B O3B O3B HO3A C4B H4B C4B C5B +BOND C5B H52A C5B H51A C5B O5B O5B PA PA O1A +BOND PA O2A PA O3 O3 PN PN O1N PN O2N +BOND PN O5D O5D C5D C5D H51N C5D H52N C5D C4D +BOND C4D O4D O4D C1D C1D C2D C2D C3D C3D C4D +BOND C1D H1D C2D H2D C2D O2D O2D HO2N C3D H3D +BOND C3D O3D O3D HO3N C4D H4D C1D N1N N1N C2N +BOND C3N C4N C5N C6N +BOND C2N H2N C3N C7N C7N O7N C7N N7N N7N N71N +BOND N7N H72N C4N H41N C5N H5N C6N HN6 +DOUBLE C2N C3N C4N C5N C6N N1N +! adenine impropers +IMPR N6A C6A H61A H62A C6A N1A C5A N6A +! amide impropers +IMPR C7N N7N C3N O7N C7N C3N N7N O7N +IMPR N7N C7N N71N H72N N7N C7N H72N N71N +! ring hydrogen impropers +IMPR C6N N1N C5N HN6 C5N C6N C4N H5N +IMPR C4N C5N C3N H41N C2N C3N N1N H2N +DONO H61A N6A +DONO H62A N6A +DONO HO2A O2B +DONO HO3A O3B +ACCE N1A +ACCE N3A +ACCE N7A +ACCE O4B +ACCE O2B +ACCE O3B +ACCE O5B +ACCE O1A PA +ACCE O2A PA +ACCE O3 +ACCE O1N PN +ACCE O2N PN +ACCE O5D +ACCE O4D +ACCE O3D +ACCE O2D +ACCE O7N +DONO HO2N O2D +DONO HO3N O3D +DONO N71N N7N +DONO H72N N7N + +IC O4B C4B C5B O5B 1.4602 109.06 141.71 112.09 1.4439 +IC O4B C5B *C4B C3B 1.4602 109.06 -116.95 116.13 1.5393 +IC C3B C5B *C4B H4B 1.5393 116.13 -123.66 110.37 1.1118 +IC C5B C4B O4B C1B 1.5373 109.06 -136.33 109.65 1.4148 +IC C4B O4B C1B N9A 1.4602 109.65 -135.81 111.11 1.4598 +IC N9A O4B *C1B C2B 1.4598 111.11 122.68 107.19 1.5091 +IC N9A O4B *C1B H1B 1.4598 111.11 -120.43 106.09 1.1157 +IC O4B C1B N9A C4A 1.4148 111.11 -132.21 126.91 1.3718 +IC C4A C1B *N9A C8A 1.3718 126.91 -179.77 127.02 1.3735 +IC C1B N9A C4A C5A 1.4598 126.91 -179.47 105.60 1.3834 +IC C5A N9A *C4A N3A 1.3834 105.60 -179.98 127.70 1.3425 +IC N9A C4A C5A C6A 1.3718 105.60 179.90 116.93 1.4100 +IC C6A C4A *C5A N7A 1.4100 116.93 -179.96 110.88 1.3888 +IC N7A N9A *C8A H8A 1.3106 113.69 179.35 121.11 1.0928 +IC C4A C5A C6A N1A 1.3834 116.93 -0.07 117.90 1.3546 +IC N1A C5A *C6A N6A 1.3546 117.90 179.83 123.29 1.3450 +IC C5A C6A N1A C2A 1.4100 117.90 0.12 118.20 1.3359 +IC N3A N1A *C2A H2A 1.3354 129.50 179.91 115.36 1.0937 +IC C5A C6A N6A H61A 1.4100 123.29 -178.42 117.49 0.9946 +IC H61A C6A *N6A H62A 0.9946 117.49 176.18 120.81 0.9965 +IC C3B C1B *C2B O2B 1.5071 101.20 117.08 111.89 1.4144 +IC C3B C1B *C2B H2B 1.5071 101.20 -117.38 111.86 1.1141 +IC C1B C2B O2B HO2A 1.5091 111.89 178.91 108.27 0.9632 +IC C2B C4B *C3B O3B 1.5071 102.42 118.21 111.98 1.4364 +IC C2B C4B *C3B H3B 1.5071 102.42 -117.88 107.58 1.1121 +IC C4B C3B O3B HO3A 1.5393 111.98 53.77 108.82 0.9987 +IC C3B C4B C5B O5B 1.5393 116.13 24.76 112.09 1.4439 +IC O5B C4B *C5B H52A 1.4439 112.09 -118.16 109.00 1.1133 +IC H52A C4B *C5B H51A 1.1133 109.00 -114.98 109.51 1.1161 +IC C4B C5B O5B PA 1.5373 112.09 94.39 121.28 1.5826 +IC C5B O5B PA O3 1.4439 121.28 148.70 94.54 1.4969 +IC O3 O5B *PA O1A 1.4969 94.54 -121.80 106.23 1.4772 +IC O1A O5B *PA O2A 1.4772 106.23 -125.48 100.49 1.4822 +IC O5B PA O3 PN 1.5826 94.54 -171.26 103.25 1.5079 +IC PA O3 PN O5D 1.4969 103.25 -156.08 92.59 1.5791 +IC O5D O3 *PN O1N 1.5791 92.59 -108.10 112.08 1.4709 +IC O1N O3 *PN O2N 1.4709 112.08 -147.35 119.96 1.4872 +IC O3 PN O5D C5D 1.5079 92.59 169.85 121.25 1.4424 +IC PN O5D C5D C4D 1.5791 121.25 -120.85 113.63 1.5461 +IC C4D O5D *C5D H51N 1.5461 113.63 -118.98 107.36 1.1130 +IC H51N O5D *C5D H52N 1.1130 107.36 -116.76 113.02 1.1173 +IC O5D C5D C4D O4D 1.4424 113.63 -49.73 112.77 1.4709 +IC O4D C5D *C4D C3D 1.4709 112.77 124.54 119.31 1.5563 +IC O4D C5D *C4D H4D 1.4709 112.77 -115.70 107.56 1.1116 +IC C5D C4D C3D C2D 1.5461 119.31 -156.53 99.76 1.5184 +IC C2D C4D *C3D O3D 1.5184 99.76 119.65 119.67 1.4380 +IC C2D C4D *C3D H3D 1.5184 99.76 -115.32 107.95 1.1119 +IC C4D C3D C2D C1D 1.5563 99.76 43.53 100.45 1.5351 +IC C1D C3D *C2D O2D 1.5351 100.45 123.80 111.51 1.4145 +IC C1D C3D *C2D H2D 1.5351 100.45 -114.84 109.59 1.1136 +IC C3D C2D O2D HO2N 1.5184 111.51 -13.38 103.51 0.9747 +IC C4D C3D O3D HO3N 1.5563 119.67 42.59 111.67 0.9972 +IC O4D C2D *C1D N1N 1.4197 103.46 122.07 115.99 1.5110 +IC O4D C2D *C1D H1D 1.4197 103.46 -113.32 108.74 1.1122 +IC C2D C1D N1N C2N 1.5351 115.99 48.31 121.57 1.3422 +IC C2N C1D *N1N C6N 1.3422 121.57 -175.31 121.05 1.3474 +IC C1D N1N C6N C5N 1.5110 121.05 177.97 122.74 1.3691 +IC C5N N1N *C6N HN6 1.3691 122.74 -171.45 116.89 1.0961 +IC N1N C6N C5N C4N 1.3474 122.74 -3.94 119.48 1.3753 +IC C4N C6N *C5N H5N 1.3753 119.48 -170.98 120.63 1.0956 +IC C6N C5N C4N C3N 1.3691 119.48 1.56 118.55 1.3864 +IC C3N C5N *C4N H41N 1.3864 118.55 -175.37 120.26 1.0910 +IC C3N N1N *C2N H2N 1.3745 123.21 178.08 117.05 1.0911 +IC C2N C4N *C3N C7N 1.3745 118.63 -178.85 118.88 1.5091 +IC C4N C3N C7N N7N 1.3864 118.88 23.83 117.95 1.3519 +IC N7N C3N *C7N O7N 1.3519 117.95 175.54 118.43 1.2254 +IC C3N C7N N7N N71N 1.5091 117.95 160.64 114.22 0.9962 +IC N71N C7N *N7N H72N 0.9962 114.22 -140.75 118.52 1.0129 +PATCH FIRST NONE LAST NONE + +RESI NAI -2.00 ! reduced nicotinamide adenine dinucleotide, NADH, jjp1/adm jr. + ! some PDB files use NAD for NADH + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! +GROUP ! +ATOM C4B CN7 0.16 ! H61A H62A +ATOM H4B HN7 0.09 ! \ / +ATOM O4B ON6B -0.50 ! N6A +ATOM C1B CN7B 0.16 ! | +ATOM H1B HN7 0.09 ! C6A +GROUP ! // \ +ATOM C5A CN5 0.28 ! N1A C5A--N7A\\ +ATOM N7A NN4 -0.71 ! | || C8A-H8A +ATOM C8A CN4 0.34 ! C2A C4A--N9A/ +ATOM H8A HN3 0.12 ! / \\ / \ +ATOM N9A NN2 -0.05 ! H2A N3A \ + ! \ +ATOM N1A NN3A -0.74 ! \ +ATOM C2A CN4 0.50 ! \ +ATOM H2A HN3 0.13 ! O1N O1A H52AH4B O4B \ +ATOM N3A NN3A -0.75 ! | | | \ / \ \ +ATOM C4A CN5 0.43 ! O5D PN-O3--PA-O5B -C5B -C4B C1B +ATOM C6A CN2 0.46 ! \ | | | \ / \ + ! \ O2N O2A H51A C3B -C2B H1B +ATOM N6A NN1 -0.77 ! \ / \ / \ +ATOM H61A HN1 0.38 ! \ O3B H3B O2B H2B +ATOM H62A HN1 0.38 ! \ | | +GROUP ! \ HO3A HO2A +ATOM C2B CN7B 0.14 ! \ N71N +ATOM H2B HN7 0.09 ! \ \ +ATOM O2B ON5 -0.66 ! \ H72N-N7N H41NH42N +ATOM HO2A HN5 0.43 ! \ \ \ / +GROUP ! \ C7N C4N +ATOM C3B CN7 0.14 ! \ / \ / \ +ATOM H3B HN7 0.09 ! \ O7N C3N C5N-H5N +ATOM O3B ON5 -0.66 ! \ | | +ATOM HO3A HN5 0.43 ! \ H51N H4D O4D H2N-C2N C6N-HN6 +GROUP ! \ | \ / \ \ / +ATOM C5B CN8B -0.08 ! C5D --C4D C1D ---------N1N +ATOM H51A HN8 0.09 ! | \ / \ +ATOM H52A HN8 0.09 ! H52N C3D -C2D H1D +ATOM PA P 1.50 ! / \ / \ +ATOM O1A ON3 -0.82 ! O3D H3D O2D H2D +ATOM O2A ON3 -0.82 ! | | +ATOM O5B ON2 -0.62 ! HO3N HO2N +ATOM O3 ON2 -0.68 +ATOM PN P 1.50 +ATOM O1N ON3 -0.82 +ATOM O2N ON3 -0.82 +ATOM O5D ON2 -0.62 +ATOM C5D CN8B -0.08 +ATOM H51N HN8 0.09 +ATOM H52N HN8 0.09 +GROUP +ATOM C2D CN7B 0.14 +ATOM H2D HN7 0.09 +ATOM O2D ON5 -0.66 +ATOM HO2N HN5 0.43 +GROUP +ATOM C3D CN7 0.14 +ATOM H3D HN7 0.09 +ATOM O3D ON5 -0.66 +ATOM HO3N HN5 0.43 +GROUP +ATOM C1D CN7B 0.16 +ATOM H1D HN7 0.09 +ATOM C4D CN7 0.16 +ATOM H4D HN7 0.09 +ATOM O4D ON6B -0.50 +GROUP +ATOM N1N NN2 -0.27 !N2 +ATOM C6N CN3C -0.06 !C3 +ATOM HN6 HN6 0.17 !H4 +ATOM C5N CN3 -0.18 !C5 +ATOM H5N HN6 0.14 !H6 +ATOM C4N CN8 -0.28 !C7 +ATOM H41N HN8 0.09 !H8 +ATOM H42N HN8 0.09 !H17 +ATOM C3N CN3 0.36 !C9 +ATOM C2N CN3C -0.10 !C10 +ATOM H2N HN6 0.14 !H11 +ATOM C7N CN1A 0.55 !C12 +ATOM O7N ON1 -0.51 !O13 +ATOM N7N NN1 -0.72 !N14 +ATOM N71N HN1 0.26 !H15 ! trans to amide O +ATOM H72N HN1 0.32 !H16 ! cis to amide O + +BOND N1A C2A N3A C4A C5A C6A +BOND C6A N6A C5A N7A C8A N9A +BOND N9A C4A C2A H2A N6A H61A N6A H62A C8A H8A +DOUBLE C6A N1A C2A N3A C4A C5A N7A C8A +BOND N9A C1B C1B C2B C2B C3B C3B C4B C4B O4B +BOND O4B C1B C1B H1B C2B O2B O2B HO2A C2B H2B +BOND C3B H3B C3B O3B O3B HO3A C4B H4B C4B C5B +BOND C5B H52A C5B H51A C5B O5B O5B PA PA O1A +BOND PA O2A PA O3 O3 PN PN O1N PN O2N +BOND PN O5D O5D C5D C5D H51N C5D H52N C5D C4D +BOND C4D O4D O4D C1D C1D C2D C2D C3D C3D C4D +BOND C1D H1D C2D H2D C2D O2D O2D HO2N C3D H3D +BOND C3D O3D O3D HO3N C4D H4D C1D N1N N1N C2N +BOND C3N C4N C4N C5N C6N N1N +BOND C2N H2N C3N C7N C7N O7N C7N N7N N7N N71N +BOND N7N H72N C4N H41N C4N H42N C5N H5N C6N HN6 +DOUBLE C2N C3N C5N C6N +! adenine impropers +IMPR N6A C6A H61A H62A C6A N1A C5A N6A +! amide impropers +IMPR C7N N7N C3N O7N C7N C3N N7N O7N +IMPR N7N C7N N71N H72N N7N C7N H72N N71N +! ring hydrogen impropers +IMPR C6N N1N C5N HN6 C5N C6N C4N H5N +IMPR C4N C5N C3N H41N C2N C3N N1N H2N +DONO H61A N6A +DONO H62A N6A +DONO HO2A O2B +DONO HO3A O3B +ACCE N1A +ACCE N3A +ACCE N7A +ACCE O4B +ACCE O2B +ACCE O3B +ACCE O5B +ACCE O1A PA +ACCE O2A PA +ACCE O3 +ACCE O1N PN +ACCE O2N PN +ACCE O5D +ACCE O4D +ACCE O3D +ACCE O2D +ACCE O7N +DONO HO2N O2D +DONO HO3N O3D +DONO N71N N7N +DONO H72N N7N + +IC O4B C4B C5B O5B 1.4592 109.88 127.15 112.06 1.4436 +IC O4B C5B *C4B C3B 1.4592 109.88 -119.04 118.31 1.5383 +IC C3B C5B *C4B H4B 1.5383 118.31 -123.09 109.39 1.1113 +IC C5B C4B O4B C1B 1.5404 109.88 -146.22 109.49 1.4139 +IC C4B O4B C1B N9A 1.4592 109.49 -127.93 110.13 1.4603 +IC N9A O4B *C1B C2B 1.4603 110.13 122.48 107.68 1.5154 +IC N9A O4B *C1B H1B 1.4603 110.13 -120.39 106.05 1.1153 +IC O4B C1B N9A C4A 1.4139 110.13 -117.96 127.68 1.3725 +IC C4A C1B *N9A C8A 1.3725 127.68 177.86 126.28 1.3734 +IC C1B N9A C4A C5A 1.4603 127.68 178.99 105.54 1.3840 +IC C5A N9A *C4A N3A 1.3840 105.54 179.70 127.97 1.3431 +IC N9A C4A C5A C6A 1.3725 105.54 -179.81 117.00 1.4096 +IC C6A C4A *C5A N7A 1.4096 117.00 179.47 111.00 1.3884 +IC N7A N9A *C8A H8A 1.3113 113.83 179.81 121.02 1.0926 +IC C4A C5A C6A N1A 1.3840 117.00 -0.40 118.02 1.3545 +IC N1A C5A *C6A N6A 1.3545 118.02 179.70 123.12 1.3454 +IC C5A C6A N1A C2A 1.4096 118.02 0.07 118.03 1.3365 +IC N3A N1A *C2A H2A 1.3345 129.58 179.79 115.39 1.0936 +IC C5A C6A N6A H61A 1.4096 123.12 -178.46 117.57 0.9939 +IC H61A C6A *N6A H62A 0.9939 117.57 176.57 120.42 0.9965 +IC C3B C1B *C2B O2B 1.5103 102.02 117.99 111.67 1.4134 +IC C3B C1B *C2B H2B 1.5103 102.02 -117.32 112.17 1.1132 +IC C1B C2B O2B HO2A 1.5154 111.67 -163.97 107.58 0.9678 +IC C2B C4B *C3B O3B 1.5103 101.80 116.77 110.83 1.4344 +IC C2B C4B *C3B H3B 1.5103 101.80 -119.13 108.74 1.1128 +IC C4B C3B O3B HO3A 1.5383 110.83 54.91 107.95 0.9983 +IC C3B C4B C5B O5B 1.5383 118.31 8.12 112.06 1.4436 +IC O5B C4B *C5B H52A 1.4436 112.06 -118.83 109.45 1.1125 +IC H52A C4B *C5B H51A 1.1125 109.45 -115.45 109.09 1.1167 +IC C4B C5B O5B PA 1.5404 112.06 103.36 120.31 1.5832 +IC C5B O5B PA O3 1.4436 120.31 176.42 94.39 1.5047 +IC O3 O5B *PA O1A 1.5047 94.39 -120.03 104.05 1.4804 +IC O1A O5B *PA O2A 1.4804 104.05 -123.95 100.78 1.4839 +IC O5B PA O3 PN 1.5832 94.39 -178.56 100.47 1.5104 +IC PA O3 PN O5D 1.5047 100.47 -170.27 94.47 1.5770 +IC O5D O3 *PN O1N 1.5770 94.47 -107.91 114.74 1.4790 +IC O1N O3 *PN O2N 1.4790 114.74 -147.43 117.97 1.4863 +IC O3 PN O5D C5D 1.5104 94.47 -177.92 120.58 1.4431 +IC PN O5D C5D C4D 1.5770 120.58 -122.07 113.80 1.5459 +IC C4D O5D *C5D H51N 1.5459 113.80 -119.75 107.60 1.1121 +IC H51N O5D *C5D H52N 1.1121 107.60 -117.14 112.75 1.1171 +IC O5D C5D C4D O4D 1.4431 113.80 -64.50 112.96 1.4660 +IC O4D C5D *C4D C3D 1.4660 112.96 127.07 120.95 1.5529 +IC O4D C5D *C4D H4D 1.4660 112.96 -113.76 106.56 1.1112 +IC C5D C4D C3D C2D 1.5459 120.95 -160.75 99.47 1.5206 +IC C2D C4D *C3D O3D 1.5206 99.47 121.69 119.59 1.4385 +IC C2D C4D *C3D H3D 1.5206 99.47 -114.49 107.55 1.1109 +IC C4D C3D C2D C1D 1.5529 99.47 42.83 101.15 1.5416 +IC C1D C3D *C2D O2D 1.5416 101.15 126.12 112.03 1.4127 +IC C1D C3D *C2D H2D 1.5416 101.15 -113.62 108.86 1.1129 +IC C3D C2D O2D HO2N 1.5206 112.03 -33.33 102.61 0.9714 +IC C4D C3D O3D HO3N 1.5529 119.59 46.10 109.78 0.9937 +IC O4D C2D *C1D N1N 1.4246 103.98 123.05 117.48 1.5125 +IC O4D C2D *C1D H1D 1.4246 103.98 -113.06 108.45 1.1101 +IC C2D C1D N1N C2N 1.5416 117.48 21.65 124.87 1.3754 +IC C2N C1D *N1N C6N 1.3754 124.87 -167.67 121.17 1.3759 +IC C1D N1N C6N C5N 1.5125 121.17 126.10 120.49 1.3282 +IC C5N N1N *C6N HN6 1.3282 120.49 -173.51 119.76 1.0882 +IC N1N C6N C5N C4N 1.3759 120.49 26.68 121.42 1.5170 +IC C4N C6N *C5N H5N 1.5170 121.42 -140.43 114.25 1.0930 +IC C6N C5N C4N C3N 1.3282 121.42 -4.55 109.89 1.5374 +IC C3N C5N *C4N H41N 1.5374 109.89 127.11 113.12 1.1052 +IC C3N C5N *C4N H42N 1.5374 109.89 -116.77 106.76 1.1126 +IC C3N N1N *C2N H2N 1.3514 121.98 -179.23 117.66 1.0902 +IC C2N C4N *C3N C7N 1.3514 119.70 156.64 121.99 1.5300 +IC C4N C3N C7N N7N 1.5374 121.99 23.57 115.90 1.3567 +IC N7N C3N *C7N O7N 1.3567 115.90 178.78 122.04 1.2305 +IC C3N C7N N7N N71N 1.5300 115.90 162.43 114.68 0.9962 +IC N71N C7N *N7N H72N 0.9962 114.68 -141.25 117.82 1.0104 +PATCH FIRST NONE LAST NONE + +RESI NAP -2.00 ! oxidized nicotinamide adenine dinucleotide, NADP+, adm jr. + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! +GROUP ! +ATOM C4B CN7 0.16 ! H61A H62A +ATOM H4B HN7 0.09 ! \ / +ATOM O4B ON6B -0.50 ! N6A +ATOM C1B CN7B 0.16 ! | +ATOM H1B HN7 0.09 ! C6A +GROUP ! // \ +ATOM C5A CN5 0.28 ! N1A C5A--N7A\\ +ATOM N7A NN4 -0.71 ! | || C8A-H8A +ATOM C8A CN4 0.34 ! C2A C4A--N9A/ +ATOM H8A HN3 0.12 ! / \\ / \ +ATOM N9A NN2 -0.05 ! H2A N3A \ + ! \ +ATOM N1A NN3A -0.74 ! \ +ATOM C2A CN4 0.50 ! \ +ATOM H2A HN3 0.13 ! O1N O1A H52AH4B O4B \ +ATOM N3A NN3A -0.75 ! | | | \ / \ \ +ATOM C4A CN5 0.43 !O5D PN-O3--PA-O5B -C5B -C4B C1B +ATOM C6A CN2 0.46 ! \ | | | \ / \ + ! \ O2N O2A H51A C3B -C2B H1B +ATOM N6A NN1 -0.77 ! \ / \ / \ +ATOM H61A HN1 0.38 ! \ O3B H3B O2B H2B +ATOM H62A HN1 0.38 ! \ | | +GROUP ! \ HO3A O1X =P2B==O2X (-) +ATOM C2B CN7B 0.01 ! \ | N71N +ATOM H2B HN7 0.09 ! \ HO2A-O3X / +ATOM O2B ON2 -0.62 ! \ H72N-N7N H41N +ATOM P2B P 1.50 ! \ \ | +ATOM O1X ON3 -0.82 ! \ C7N C4N +ATOM O2X ON3 -0.82 ! \ / \ / \ +ATOM O3X ON4 -0.68 ! \ O7N C3N C5N-H5N +ATOM HO2A HN4 0.34 ! \ | | +GROUP ! \ | | +ATOM C3B CN7 0.14 ! \ H51N H4D O4D H2N-C2N C6N-HN6 +ATOM H3B HN7 0.09 ! \ | \ / \ \ / +ATOM O3B ON5 -0.66 ! C5D --C4D C1D --------N1N +ATOM HO3A HN5 0.43 ! | \ / \ +GROUP ! H52N C3D--C2D H1D +ATOM C5B CN8B -0.08 ! / \ / \ +ATOM H51A HN8 0.09 ! O3D H3D O2D H2D +ATOM H52A HN8 0.09 ! | | +ATOM PA P 1.50 ! HO3N HO2N +ATOM O1A ON3 -0.82 ! +ATOM O2A ON3 -0.82 ! +ATOM O5B ON2 -0.62 ! +ATOM O3 ON2 -0.68 +ATOM PN P 1.50 +ATOM O1N ON3 -0.82 +ATOM O2N ON3 -0.82 +ATOM O5D ON2 -0.62 +ATOM C5D CN8B -0.08 +ATOM H51N HN8 0.09 +ATOM H52N HN8 0.09 +GROUP +ATOM C2D CN7B 0.14 +ATOM H2D HN7 0.09 +ATOM O2D ON5 -0.66 +ATOM HO2N HN5 0.43 +GROUP +ATOM C3D CN7 0.14 +ATOM H3D HN7 0.09 +ATOM O3D ON5 -0.66 +ATOM HO3N HN5 0.43 +GROUP +ATOM C1D CN7B 0.16 +ATOM H1D HN7 0.09 +ATOM C4D CN7 0.16 +ATOM H4D HN7 0.09 +ATOM O4D ON6B -0.50 +GROUP +ATOM N1N NN2 -0.07 +ATOM C6N CN3B 0.16 +ATOM HN6 HN3B 0.19 +ATOM C5N CN3 -0.10 +ATOM H5N HN3B 0.16 +ATOM C4N CN3A -0.05 +ATOM H41N HN3B 0.16 !H4N in official nomenclature +ATOM C3N CN3 0.05 +ATOM C2N CN3B 0.18 +ATOM H2N HN3B 0.16 +ATOM C7N CN1A 0.68 +ATOM O7N ON1 -0.40 +ATOM N7N NN1 -0.82 +ATOM N71N HN1 0.34 ! trans to amide O +ATOM H72N HN1 0.36 ! cis to amide O + +BOND N1A C2A N3A C4A C5A C6A +BOND C6A N6A C5A N7A C8A N9A +BOND N9A C4A C2A H2A N6A H61A N6A H62A C8A H8A +DOUBLE C6A N1A C2A N3A C4A C5A N7A C8A +BOND N9A C1B C1B C2B C2B C3B C3B C4B C4B O4B +BOND O4B C1B C1B H1B C2B O2B O2B P2B C2B H2B +BOND C3B H3B C3B O3B O3B HO3A C4B H4B C4B C5B +BOND C5B H52A C5B H51A C5B O5B O5B PA PA O1A +BOND PA O2A PA O3 O3 PN PN O1N PN O2N +BOND PN O5D O5D C5D C5D H51N C5D H52N C5D C4D +BOND C4D O4D O4D C1D C1D C2D C2D C3D C3D C4D +BOND C1D H1D C2D H2D C2D O2D O2D HO2N C3D H3D +BOND C3D O3D O3D HO3N C4D H4D C1D N1N N1N C2N +BOND C3N C4N C5N C6N +BOND C2N H2N C3N C7N C7N O7N C7N N7N N7N N71N +BOND N7N H72N C4N H41N C5N H5N C6N HN6 +BOND P2B O1X P2B O2X P2B O3X O3X HO2A +DOUBLE C2N C3N C4N C5N C6N N1N +! adenine impropers +IMPR N6A C6A H61A H62A C6A N1A C5A N6A +! amide impropers +IMPR C7N N7N C3N O7N C7N C3N N7N O7N +IMPR N7N C7N N71N H72N N7N C7N H72N N71N +! ring hydrogen impropers +IMPR C6N N1N C5N HN6 C5N C6N C4N H5N +IMPR C4N C5N C3N H41N C2N C3N N1N H2N +DONO H61A N6A +DONO H62A N6A +DONO HO2A O2B +DONO HO3A O3B +ACCE N1A +ACCE N3A +ACCE N7A +ACCE O4B +ACCE O2B +ACCE O3B +ACCE O5B +ACCE O1A PA +ACCE O2A PA +ACCE O3 +ACCE O1N PN +ACCE O2N PN +ACCE O5D +ACCE O4D +ACCE O3D +ACCE O2D +ACCE O7N +DONO HO2N O2D +DONO HO3N O3D +DONO N71N N7N +DONO H72N N7N +DONO HO2A O3X +ACCE O3X +ACCE O1X +ACCE O2X +ACCE O2B + +IC O4B C4B C5B O5B 1.4585 109.71 159.30 112.46 1.4473 +IC O4B C5B *C4B C3B 1.4585 109.71 -116.16 111.85 1.5464 +IC C3B C5B *C4B H4B 1.5464 111.85 -123.40 110.92 1.1115 +IC C5B C4B O4B C1B 1.5376 109.71 -108.48 108.78 1.4075 +IC C4B O4B C1B N9A 1.4585 108.78 -152.38 111.04 1.4568 +IC N9A O4B *C1B C2B 1.4568 111.04 121.73 107.16 1.5067 +IC N9A O4B *C1B H1B 1.4568 111.04 -121.01 106.15 1.1159 +IC O4B C1B N9A C4A 1.4075 111.04 -116.40 127.62 1.3704 +IC C4A C1B *N9A C8A 1.3704 127.62 -179.20 126.23 1.3719 +IC C1B N9A C4A C5A 1.4568 127.62 -179.21 105.46 1.3840 +IC C5A N9A *C4A N3A 1.3840 105.46 -179.98 128.09 1.3448 +IC N9A C4A C5A C6A 1.3704 105.46 179.01 116.94 1.4094 +IC C6A C4A *C5A N7A 1.4094 116.94 -179.45 111.14 1.3881 +IC N7A N9A *C8A H8A 1.3133 113.83 179.37 120.83 1.0924 +IC C4A C5A C6A N1A 1.3840 116.94 -0.02 118.16 1.3545 +IC N1A C5A *C6A N6A 1.3545 118.16 -179.37 122.98 1.3453 +IC C5A C6A N1A C2A 1.4094 118.16 -0.02 117.86 1.3367 +IC N3A N1A *C2A H2A 1.3332 129.71 178.74 115.38 1.0931 +IC C5A C6A N6A H61A 1.4094 122.98 174.65 117.36 0.9937 +IC H61A C6A *N6A H62A 0.9937 117.36 -169.69 119.66 0.9963 +IC C3B C1B *C2B O2B 1.5188 101.16 119.53 108.66 1.4398 +IC C3B C1B *C2B H2B 1.5188 101.16 -116.17 111.47 1.1163 +IC C1B C2B O2B P2B 1.5067 108.66 164.95 121.64 1.5624 +IC C2B O2B P2B O3X 1.4398 121.64 -145.91 106.75 1.5575 +IC O3X O2B *P2B O1X 1.5575 106.75 112.52 112.63 1.4723 +IC O1X O2B *P2B O2X 1.4723 112.63 135.09 111.70 1.4730 +IC O2B P2B O3X HO2A 1.5624 106.75 179.79 107.64 0.9606 +IC C1B C2B O2B HO2A 1.5067 108.66 140.65 141.83 3.3318 +IC C2B C4B *C3B O3B 1.5188 105.43 121.35 109.34 1.4348 +IC C2B C4B *C3B H3B 1.5188 105.43 -117.32 108.06 1.1126 +IC C4B C3B O3B HO3A 1.5464 109.34 51.56 106.53 0.9936 +IC C3B C4B C5B O5B 1.5464 111.85 43.14 112.46 1.4473 +IC O5B C4B *C5B H52A 1.4473 112.46 -119.04 108.58 1.1125 +IC H52A C4B *C5B H51A 1.1125 108.58 -116.00 109.43 1.1155 +IC C4B C5B O5B PA 1.5376 112.46 78.42 120.97 1.5816 +IC C5B O5B PA O3 1.4473 120.97 163.89 94.51 1.5036 +IC O3 O5B *PA O1A 1.5036 94.51 -121.21 105.58 1.4802 +IC O1A O5B *PA O2A 1.4802 105.58 -126.12 102.35 1.4824 +IC O5B PA O3 PN 1.5816 94.51 -169.65 103.13 1.5074 +IC PA O3 PN O5D 1.5036 103.13 -158.88 92.67 1.5783 +IC O5D O3 *PN O1N 1.5783 92.67 -107.59 112.84 1.4735 +IC O1N O3 *PN O2N 1.4735 112.84 -147.96 119.72 1.4863 +IC O3 PN O5D C5D 1.5074 92.67 167.85 121.64 1.4408 +IC PN O5D C5D C4D 1.5783 121.64 -119.99 113.59 1.5457 +IC C4D O5D *C5D H51N 1.5457 113.59 -118.85 107.20 1.1125 +IC H51N O5D *C5D H52N 1.1125 107.20 -116.81 112.97 1.1169 +IC O5D C5D C4D O4D 1.4408 113.59 -47.57 113.01 1.4697 +IC O4D C5D *C4D C3D 1.4697 113.01 124.91 119.42 1.5538 +IC O4D C5D *C4D H4D 1.4697 113.01 -115.69 107.46 1.1114 +IC C5D C4D C3D C2D 1.5457 119.42 -158.23 99.73 1.5185 +IC C2D C4D *C3D O3D 1.5185 99.73 119.79 119.52 1.4371 +IC C2D C4D *C3D H3D 1.5185 99.73 -115.26 108.09 1.1115 +IC C4D C3D C2D C1D 1.5538 99.73 43.62 100.48 1.5339 +IC C1D C3D *C2D O2D 1.5339 100.48 123.65 111.48 1.4144 +IC C1D C3D *C2D H2D 1.5339 100.48 -114.85 109.66 1.1132 +IC C3D C2D O2D HO2N 1.5185 111.48 -19.41 103.55 0.9759 +IC C4D C3D O3D HO3N 1.5538 119.52 41.07 112.08 0.9969 +IC O4D C2D *C1D N1N 1.4209 103.89 122.79 115.51 1.5069 +IC O4D C2D *C1D H1D 1.4209 103.89 -113.36 108.85 1.1120 +IC C2D C1D N1N C2N 1.5339 115.51 54.88 121.01 1.3424 +IC C2N C1D *N1N C6N 1.3424 121.01 -177.68 121.58 1.3487 +IC C1D N1N C6N C5N 1.5069 121.58 -178.88 122.67 1.3689 +IC C5N N1N *C6N HN6 1.3689 122.67 -174.63 117.18 1.0940 +IC N1N C6N C5N C4N 1.3487 122.67 -2.95 119.09 1.3746 +IC C4N C6N *C5N H5N 1.3746 119.09 -173.56 121.44 1.0955 +IC C6N C5N C4N C3N 1.3689 119.09 -1.00 119.02 1.3830 +IC C3N C5N *C4N H41N 1.3830 119.02 -178.05 120.48 1.0937 +IC C3N N1N *C2N H2N 1.3696 123.10 177.36 117.15 1.0905 +IC C2N C4N *C3N C7N 1.3696 118.55 -179.48 116.96 1.5065 +IC C4N C3N C7N N7N 1.3830 116.96 49.86 116.48 1.3522 +IC N7N C3N *C7N O7N 1.3522 116.48 169.66 118.17 1.2276 +IC C3N C7N N7N N71N 1.5065 116.48 -148.55 113.04 1.0028 +IC N71N C7N *N7N H72N 1.0028 113.04 127.16 116.64 1.0104 +PATCH FIRST NONE LAST NONE + +RESI NDP -3.00 ! reduced nicotinamide adenine dinucleotide, NADPH, VARNAI/adm jr. + ! from NADH and 3PHO + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! +GROUP ! +ATOM C4B CN7 0.16 ! H61A H62A +ATOM H4B HN7 0.09 ! \ / +ATOM O4B ON6B -0.50 ! N6A +ATOM C1B CN7B 0.16 ! | +ATOM H1B HN7 0.09 ! C6A +GROUP ! // \ +ATOM C5A CN5 0.28 ! N1A C5A--N7A\\ +ATOM N7A NN4 -0.71 ! | || C8A-H8A +ATOM C8A CN4 0.34 ! C2A C4A--N9A/ +ATOM H8A HN3 0.12 ! / \\ / \ +ATOM N9A NN2 -0.05 ! H2A N3A \ + ! \ +ATOM N1A NN3A -0.74 ! \ +ATOM C2A CN4 0.50 ! \ +ATOM H2A HN3 0.13 ! O1N O1A H52AH4B O4B \ +ATOM N3A NN3A -0.75 ! | | | \ / \ \ +ATOM C4A CN5 0.43 ! O5D PN-O3--PA-O5B -C5B -C4B C1B +ATOM C6A CN2 0.46 ! \ | | | \ / \ + ! \ O2N O2A H51A C3B -C2B H1B +ATOM N6A NN1 -0.77 ! \ / \ / \ +ATOM H61A HN1 0.38 ! \ O3B H3B O2B H2B +ATOM H62A HN1 0.38 ! \ | | +GROUP ! \ HO3A O1X =P2B==O2X (-) +ATOM C2B CN7B 0.01 ! \ | N71N +ATOM H2B HN7 0.09 ! \ HO2A-O3X / +ATOM O2B ON2 -0.62 ! \ H72N-N7N H41NH42N +ATOM P2B P 1.50 ! \ \ \ / +ATOM O1X ON3 -0.82 ! \ C7N C4N +ATOM O2X ON3 -0.82 ! \ / \ / \ +ATOM O3X ON4 -0.68 ! \ O7N C3N C5N-H5N +ATOM HO2A HN4 0.34 ! \ | | +GROUP ! \ | | +ATOM C3B CN7 0.14 ! \ H51N H4D O4D H2N-C2N C6N-HN6 +ATOM H3B HN7 0.09 ! \ | \ / \ \ / +ATOM O3B ON5 -0.66 ! C5D --C4D C1D --------N1N +ATOM HO3A HN5 0.43 ! | \ / \ +GROUP ! H52N C3D -C2D H1D +ATOM C5B CN8B -0.08 ! / \ / \ +ATOM H51A HN8 0.09 ! O3D H3D O2D H2D +ATOM H52A HN8 0.09 ! | | +ATOM PA P 1.50 ! HO3N HO2N +ATOM O1A ON3 -0.82 ! +ATOM O2A ON3 -0.82 ! +ATOM O5B ON2 -0.62 ! +ATOM O3 ON2 -0.68 +ATOM PN P 1.50 +ATOM O1N ON3 -0.82 +ATOM O2N ON3 -0.82 +ATOM O5D ON2 -0.62 +ATOM C5D CN8B -0.08 +ATOM H51N HN8 0.09 +ATOM H52N HN8 0.09 +GROUP +ATOM C2D CN7B 0.14 +ATOM H2D HN7 0.09 +ATOM O2D ON5 -0.66 +ATOM HO2N HN5 0.43 +GROUP +ATOM C3D CN7 0.14 +ATOM H3D HN7 0.09 +ATOM O3D ON5 -0.66 +ATOM HO3N HN5 0.43 +GROUP +ATOM C1D CN7B 0.16 +ATOM H1D HN7 0.09 +ATOM C4D CN7 0.16 +ATOM H4D HN7 0.09 +ATOM O4D ON6B -0.50 +GROUP +ATOM N1N NN2 -0.27 !N2 +ATOM C6N CN3C -0.06 !C3 +ATOM HN6 HN6 0.17 !H4 +ATOM C5N CN3 -0.18 !C5 +ATOM H5N HN6 0.14 !H6 +ATOM C4N CN8 -0.28 !C7 +ATOM H41N HN8 0.09 !H8 +ATOM H42N HN8 0.09 !H17 +ATOM C3N CN3 0.36 !C9 +ATOM C2N CN3C -0.10 !C10 +ATOM H2N HN6 0.14 !H11 +ATOM C7N CN1A 0.55 !C12 +ATOM O7N ON1 -0.51 !O13 +ATOM N7N NN1 -0.72 !N14 +ATOM N71N HN1 0.26 !H15 ! trans to amide O +ATOM H72N HN1 0.32 !H16 ! cis to amide O +BOND N1A C2A N3A C4A C5A C6A +BOND C6A N6A C5A N7A C8A N9A +BOND N9A C4A C2A H2A N6A H61A N6A H62A C8A H8A +DOUBLE C6A N1A C2A N3A C4A C5A N7A C8A +BOND N9A C1B C1B C2B C2B C3B C3B C4B C4B O4B +BOND O4B C1B C1B H1B C2B O2B O2B P2B C2B H2B +BOND C3B H3B C3B O3B O3B HO3A C4B H4B C4B C5B +BOND C5B H52A C5B H51A C5B O5B O5B PA PA O1A +BOND PA O2A PA O3 O3 PN PN O1N PN O1N +BOND PN O5D O5D C5D C5D H51N C5D H52N C5D C4D +BOND C4D O4D O4D C1D C1D C2D C2D C3D C3D C4D +BOND C1D H1D C2D H2D C2D O2D O2D HO2N C3D H3D +BOND C3D O3D O3D HO3N C4D H4D C1D N1N N1N C2N +BOND C3N C4N C5N C6N +BOND C2N H2N C3N C7N C7N O7N C7N N7N N7N N71N +BOND N7N H72N C4N H41N C4N H42N C5N H5N C6N HN6 +BOND P2B O1X P2B O2X P2B O3X O3X HO2A +DOUBLE C2N C3N C4N C5N C6N N1N +! adenine impropers +IMPR N6A C6A H61A H62A C6A N1A C5A N6A +! amide impropers +IMPR C7N N7N C3N O7N C7N C3N N7N O7N +IMPR N7N C7N N71N H72N N7N C7N H72N N71N +! ring hydrogen impropers +IMPR C6N N1N C5N HN6 C5N C6N C4N H5N +IMPR C4N C5N C3N H41N C2N C3N N1N H2N +DONO H61A N6A +DONO H62A N6A +DONO HO3A O3B +ACCE N1A +ACCE N3A +ACCE N7A +ACCE O4B +ACCE O3B +ACCE O5B +ACCE O1A PA +ACCE O2A PA +ACCE O3 +ACCE O1N PN +ACCE O2N PN +ACCE O5D +ACCE O4D +ACCE O3D +ACCE O2D +ACCE O7N +DONO HO2N O2D +DONO HO3N O3D +DONO N71N N7N +DONO H72N N7N +DONO HO2A O3X +ACCE O3X +ACCE O1X +ACCE O2X +ACCE O2B + +IC O4B C4B C5B O5B 1.4582 108.69 147.29 113.38 1.4416 +IC O4B C5B *C4B C3B 1.4582 108.69 -118.37 116.42 1.5453 +IC C3B C5B *C4B H4B 1.5453 116.42 -123.26 110.26 1.1108 +IC C5B C4B O4B C1B 1.5423 108.69 -124.93 109.48 1.4122 +IC C4B O4B C1B N9A 1.4582 109.48 -147.01 110.04 1.4652 +IC N9A O4B *C1B C2B 1.4652 110.04 124.33 107.34 1.5182 +IC N9A O4B *C1B H1B 1.4652 110.04 -119.42 105.83 1.1152 +IC O4B C1B N9A C4A 1.4122 110.04 -86.61 125.65 1.3733 +IC C4A C1B *N9A C8A 1.3733 125.65 178.34 128.52 1.3773 +IC C1B N9A C4A C5A 1.4652 125.65 178.57 105.62 1.3829 +IC C5A N9A *C4A N3A 1.3829 105.62 179.51 128.22 1.3485 +IC N9A C4A C5A C6A 1.3733 105.62 178.87 117.03 1.4089 +IC C6A C4A *C5A N7A 1.4089 117.03 -179.61 111.33 1.3844 +IC N7A N9A *C8A H8A 1.3165 113.76 -178.62 121.49 1.0929 +IC C4A C5A C6A N1A 1.3829 117.03 0.17 118.37 1.3553 +IC N1A C5A *C6A N6A 1.3553 118.37 -179.13 122.76 1.3455 +IC C5A C6A N1A C2A 1.4089 118.37 -0.08 117.58 1.3367 +IC N3A N1A *C2A H2A 1.3316 129.88 179.50 115.45 1.0928 +IC C5A C6A N6A H61A 1.4089 122.76 172.71 117.17 0.9924 +IC H61A C6A *N6A H62A 0.9924 117.17 -165.83 118.92 0.9969 +IC C3B C1B *C2B O2B 1.5172 100.70 117.95 111.52 1.4469 +IC C3B C1B *C2B H2B 1.5172 100.70 -114.49 112.15 1.1158 +IC C1B C2B O2B P2B 1.5182 111.52 88.87 120.26 1.5695 +IC C2B O2B P2B O3X 1.4469 120.26 -89.09 105.16 1.5592 +IC O3X O2B *P2B O1X 1.5592 105.16 112.49 112.19 1.4735 +IC O1X O2B *P2B O2X 1.4735 112.19 138.98 113.24 1.4714 +IC O2B P2B O3X HO2A 1.5695 105.16 -143.03 105.24 0.9629 +IC C1B C2B O2B HO2A 1.5182 111.52 52.38 125.15 3.2167 +IC C2B C4B *C3B O3B 1.5172 104.21 119.99 110.36 1.4348 +IC C2B C4B *C3B H3B 1.5172 104.21 -117.77 107.81 1.1123 +IC C4B C3B O3B HO3A 1.5453 110.36 61.04 107.59 0.9899 +IC C3B C4B C5B O5B 1.5453 116.42 28.91 113.38 1.4416 +IC O5B C4B *C5B H52A 1.4416 113.38 -118.10 108.23 1.1129 +IC H52A C4B *C5B H51A 1.1129 108.23 -115.04 109.34 1.1144 +IC C4B C5B O5B PA 1.5423 113.38 90.70 124.02 1.5733 +IC C5B O5B PA O3 1.4416 124.02 151.99 89.67 1.5604 +IC O3 O5B *PA O1A 1.5604 89.67 -118.40 102.31 1.4957 +IC O1A O5B *PA O2A 1.4957 102.31 -121.55 98.60 1.4978 +IC O5B PA O3 PN 1.5733 89.67 175.92 82.07 1.5171 +IC PA O3 PN O5D 1.5604 82.07 -130.29 100.52 1.5806 +IC O5D O3 *PN O1N 1.5806 100.52 -112.12 108.73 1.4864 +IC O1N O3 *PN O2N 1.4864 108.73 147.44 159.68 5.2397 +IC O3 PN O5D C5D 1.5171 100.52 -156.02 122.16 1.4407 +IC PN O5D C5D C4D 1.5806 122.16 -155.55 113.98 1.5556 +IC C4D O5D *C5D H51N 1.5556 113.98 -119.58 108.24 1.1127 +IC H51N O5D *C5D H52N 1.1127 108.24 -117.86 112.23 1.1172 +IC O5D C5D C4D O4D 1.4407 113.98 -39.97 113.27 1.4728 +IC O4D C5D *C4D C3D 1.4728 113.27 123.24 116.41 1.5466 +IC O4D C5D *C4D H4D 1.4728 113.27 -117.97 108.11 1.1097 +IC C5D C4D C3D C2D 1.5556 116.41 -137.48 104.59 1.5300 +IC C2D C4D *C3D O3D 1.5300 104.59 128.04 115.55 1.4371 +IC C2D C4D *C3D H3D 1.5300 104.59 -114.00 106.10 1.1131 +IC C4D C3D C2D C1D 1.5466 104.59 26.25 103.50 1.5376 +IC C1D C3D *C2D O2D 1.5376 103.50 127.18 111.43 1.4128 +IC C1D C3D *C2D H2D 1.5376 103.50 -113.70 107.89 1.1128 +IC C3D C2D O2D HO2N 1.5300 111.43 -33.45 103.13 0.9733 +IC C4D C3D O3D HO3N 1.5466 115.55 84.57 105.43 0.9941 +IC O4D C2D *C1D N1N 1.4276 105.00 128.25 117.48 1.5144 +IC O4D C2D *C1D H1D 1.4276 105.00 -111.04 107.28 1.1120 +IC C2D C1D N1N C2N 1.5376 117.48 57.37 120.71 1.3843 +IC C2N C1D *N1N C6N 1.3843 120.71 160.76 120.55 1.3815 +IC C1D N1N C6N C5N 1.5144 120.55 -170.31 124.26 1.3287 +IC C5N N1N *C6N HN6 1.3287 124.26 -178.43 118.52 1.0918 +IC N1N C6N C5N C4N 1.3815 124.26 9.43 123.21 1.5077 +IC C4N C6N *C5N H5N 1.5077 123.21 -145.56 114.70 1.0925 +IC C6N C5N C4N C3N 1.3287 123.21 -9.51 109.08 1.5286 +IC C3N C5N *C4N H41N 1.5286 109.08 123.86 111.86 1.1053 +IC C3N C5N *C4N H42N 1.5286 109.08 -119.79 109.00 1.1069 +IC C3N N1N *C2N H2N 1.3470 124.38 -176.93 117.74 1.0900 +IC C2N C4N *C3N C7N 1.3470 121.40 -164.55 123.17 1.5301 +IC C4N C3N C7N N7N 1.5286 123.17 17.57 116.23 1.3547 +IC N7N C3N *C7N O7N 1.3547 116.23 -179.04 120.83 1.2310 +IC C3N C7N N7N N71N 1.5301 116.23 173.93 118.74 0.9953 +IC N71N C7N *N7N H72N 0.9953 118.74 -160.46 121.30 1.0065 + +PATCH FIRST NONE LAST NONE + +!old NAD/NADP nomenclature for both residue and atom names. maintained +!for back compatibility. residue names differ from current nomenclature + +!following was NAD in old nomenclature; change to NAD1 to avoid conflict with +!new nomenclature +! +RESI NAD1 -1.00 ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr. + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params +GROUP ! +ATOM AC4' CN7 0.16 ! AH61 AH62 +ATOM AH4' HN7 0.09 ! \ / +ATOM AO4' ON6B -0.50 ! AN6 +ATOM AC1' CN7B 0.16 ! | +ATOM AH1' HN7 0.09 ! AC6 +GROUP ! // \ +ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\ +ATOM AN7 NN4 -0.71 ! | || AC8-AH8 +ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/ +ATOM AH8 HN3 0.12 ! / \\ / \ +ATOM AN9 NN2 -0.05 ! AH2 AN3 \ + ! \ +ATOM AN1 NN3A -0.74 ! \ +ATOM AC2 CN4 0.50 ! \ +ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \ +ATOM AN3 NN3A -0.75 ! | | | \ / \ \ +ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' +ATOM AC6 CN2 0.46 ! \ | | | \ / \ + ! \ NO2 AO2 AH5' AC3'-AC2' AH1' +ATOM AN6 NN1 -0.77 ! \ / \ / \ +ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2' +ATOM AH62 HN1 0.38 ! \ | | +GROUP ! \ AH3T AH2T +ATOM AC2' CN7B 0.14 ! \ NH71 +ATOM AH2' HN7 0.09 ! \ \ +ATOM AO2' ON5 -0.66 ! \ NH72-NN7 NH4 +ATOM AH2T HN5 0.43 ! \ \ | +GROUP ! \ NC7 NC4 +ATOM AC3' CN7 0.14 ! \ / \ / \ +ATOM AH3' HN7 0.09 ! \ NO7 NC3 NC5-NH5 +ATOM AO3' ON5 -0.66 ! \ | | +ATOM AH3T HN5 0.43 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 +GROUP ! \ | \ / \ \+ / +ATOM AC5' CN8B -0.08 ! NC5'--NC4' NC1'---------NN1 +ATOM AH5' HN8 0.09 ! | \ / \ +ATOM AH5s HN8 0.09 ! NH5' NC3'-NC2'NH1' +ATOM AP P 1.50 ! / \ / \ +ATOM AO1 ON3 -0.82 ! NO3' NH3'NO2'NH2' +ATOM AO2 ON3 -0.82 ! | | +ATOM AO5' ON2 -0.62 ! NH3T NH2T +ATOM O3 ON2 -0.68 +ATOM NP P 1.50 +ATOM NO1 ON3 -0.82 +ATOM NO2 ON3 -0.82 +ATOM NO5' ON2 -0.62 +ATOM NC5' CN8B -0.08 +ATOM NH5s HN8 0.09 +ATOM NH5' HN8 0.09 +GROUP +ATOM NC2' CN7B 0.14 +ATOM NH2' HN7 0.09 +ATOM NO2' ON5 -0.66 +ATOM NH2T HN5 0.43 +GROUP +ATOM NC3' CN7 0.14 +ATOM NH3' HN7 0.09 +ATOM NO3' ON5 -0.66 +ATOM NH3T HN5 0.43 +GROUP +ATOM NC1' CN7B 0.16 +ATOM NH1' HN7 0.09 +ATOM NC4' CN7 0.16 +ATOM NH4' HN7 0.09 +ATOM NO4' ON6B -0.50 +GROUP +ATOM NN1 NN2 -0.07 +ATOM NC6 CN3B 0.16 +ATOM NH6 HN3B 0.19 +ATOM NC5 CN3 -0.10 +ATOM NH5 HN3B 0.16 +ATOM NC4 CN3A -0.05 +ATOM NH4 HN3B 0.16 +ATOM NC3 CN3 0.05 +ATOM NC2 CN3B 0.18 +ATOM NH2 HN3B 0.16 +ATOM NC7 CN1A 0.68 +ATOM NO7 ON1 -0.40 +ATOM NN7 NN1 -0.82 +ATOM NH71 HN1 0.34 ! trans to amide O +ATOM NH72 HN1 0.36 ! cis to amide O + +BOND AN1 AC2 AN3 AC4 AC5 AC6 +BOND AC6 AN6 AC5 AN7 AC8 AN9 +BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 +DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 +BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' +BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AH2T AC2' AH2' +BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' +BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP AP AO1 +BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 +BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4' +BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' +BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' +BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 +BOND NC3 NC4 NC5 NC6 +BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 +BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6 +DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 +! adenine impropers +IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6 +! amide impropers +IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7 +IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71 +! ring hydrogen impropers +IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5 +IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2 +DONO AH61 AN6 +DONO AH62 AN6 +DONO AH2T AO2' +DONO AH3T AO3' +ACCE AN1 +ACCE AN3 +ACCE AN7 +ACCE AO4' +ACCE AO2' +ACCE AO3' +ACCE AO5' +ACCE AO1 AP +ACCE AO2 AP +ACCE O3 +ACCE NO1 NP +ACCE NO2 NP +ACCE NO5' +ACCE NO4' +ACCE NO3' +ACCE NO2' +ACCE NO7 +DONO NH2T NO2' +DONO NH3T NO3' +DONO NH71 NN7 +DONO NH72 NN7 +IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977 +IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863 +IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836 +IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942 +IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756 +IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636 +IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491 +IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232 +IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942 +IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337 +IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942 +IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491 +IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337 +IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415 +IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847 +IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013 +IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777 +IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282 +IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782 +IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146 +IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482 +IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300 +IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648 +IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 +IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 +IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 +IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 +IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 +IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 +IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962 +IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928 +IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294 +IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097 +IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097 +IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105 +IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999 +IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110 +IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000 +IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 +IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 +IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636 +IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977 +IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977 +IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160 +IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160 +IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160 +IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270 +IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100 +IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712 +IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100 +IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270 +IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110 +IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110 +IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110 +IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110 +IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110 +IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110 +IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800 +IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270 +IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160 +IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150 +IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500 +IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600 +IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600 +IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500 +IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199 +IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150 +IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800 +IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300 +IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600 +IC NO7 NC7 NN7 NH71 1.2300 0.00 180.00 120.00 1.0000 +IC NO7 NC7 NN7 NH72 1.2300 0.00 0.00 120.00 1.0000 +IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900 +IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900 +IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900 +IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900 +PATCH FIRST NONE LAST NONE + +RESI NADH -2.00 ! reduced nicotinamide adenine dinucleotide, jjp1/adm jr. + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! +GROUP ! +ATOM AC4' CN7 0.16 ! AH61 AH62 +ATOM AH4' HN7 0.09 ! \ / +ATOM AO4' ON6B -0.50 ! AN6 +ATOM AC1' CN7B 0.16 ! | +ATOM AH1' HN7 0.09 ! AC6 +GROUP ! // \ +ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\ +ATOM AN7 NN4 -0.71 ! | || AC8-AH8 +ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/ +ATOM AH8 HN3 0.12 ! / \\ / \ +ATOM AN9 NN2 -0.05 ! AH2 AN3 \ + ! \ +ATOM AN1 NN3A -0.74 ! \ +ATOM AC2 CN4 0.50 ! \ +ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \ +ATOM AN3 NN3A -0.75 ! | | | \ / \ \ +ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' +ATOM AC6 CN2 0.46 ! \ | | | \ / \ + ! \ NO2 AO2 AH5' AC3'-AC2' AH1' +ATOM AN6 NN1 -0.77 ! \ / \ / \ +ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2' +ATOM AH62 HN1 0.38 ! \ | | +GROUP ! \ AH3T AH2T +ATOM AC2' CN7B 0.14 ! \ NH71 +ATOM AH2' HN7 0.09 ! \ \ +ATOM AO2' ON5 -0.66 ! \ NH72-NN7 NH4 NH42 +ATOM AH2T HN5 0.43 ! \ \ \ / +GROUP ! \ NC7 NC4 +ATOM AC3' CN7 0.14 ! \ / \ / \ +ATOM AH3' HN7 0.09 ! \ NO7 NC3 NC5-NH5 +ATOM AO3' ON5 -0.66 ! \ | | +ATOM AH3T HN5 0.43 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 +GROUP ! \ | \ / \ \ / +ATOM AC5' CN8B -0.08 ! NC5'--NC4' NC1'---------NN1 +ATOM AH5' HN8 0.09 ! | \ / \ +ATOM AH5s HN8 0.09 ! NH5' NC3'-NC2'NH1' +ATOM AP P 1.50 ! / \ / \ +ATOM AO1 ON3 -0.82 ! NO3' NH3'NO2'NH2' +ATOM AO2 ON3 -0.82 ! | | +ATOM AO5' ON2 -0.62 ! NH3T NH2T +ATOM O3 ON2 -0.68 +ATOM NP P 1.50 +ATOM NO1 ON3 -0.82 +ATOM NO2 ON3 -0.82 +ATOM NO5' ON2 -0.62 +ATOM NC5' CN8B -0.08 +ATOM NH5s HN8 0.09 +ATOM NH5' HN8 0.09 +GROUP +ATOM NC2' CN7B 0.14 +ATOM NH2' HN7 0.09 +ATOM NO2' ON5 -0.66 +ATOM NH2T HN5 0.43 +GROUP +ATOM NC3' CN7 0.14 +ATOM NH3' HN7 0.09 +ATOM NO3' ON5 -0.66 +ATOM NH3T HN5 0.43 +GROUP +ATOM NC1' CN7B 0.16 +ATOM NH1' HN7 0.09 +ATOM NC4' CN7 0.16 +ATOM NH4' HN7 0.09 +ATOM NO4' ON6B -0.50 +GROUP +ATOM NN1 NN2 -0.27 !N2 +ATOM NC6 CN3C -0.06 !C3 +ATOM NH6 HN6 0.17 !H4 +ATOM NC5 CN3 -0.18 !C5 +ATOM NH5 HN6 0.14 !H6 +ATOM NC4 CN8 -0.28 !C7 +ATOM NH4 HN8 0.09 !H8 +ATOM NH42 HN8 0.09 !H17 +ATOM NC3 CN3 0.36 !C9 +ATOM NC2 CN3C -0.10 !C10 +ATOM NH2 HN6 0.14 !H11 +ATOM NC7 CN1A 0.55 !C12 +ATOM NO7 ON1 -0.51 !O13 +ATOM NN7 NN1 -0.72 !N14 +ATOM NH71 HN1 0.26 !H15 ! trans to amide O +ATOM NH72 HN1 0.32 !H16 ! cis to amide O + +BOND AN1 AC2 AN3 AC4 AC5 AC6 +BOND AC6 AN6 AC5 AN7 AC8 AN9 +BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 +DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 +BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' +BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AH2T AC2' AH2' +BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' +BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP AP AO1 +BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 +BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4' +BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' +BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' +BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 +BOND NC3 NC4 NC4 NC5 NC6 NN1 +BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 +BOND NN7 NH72 NC4 NH4 NC4 NH42 NC5 NH5 NC6 NH6 +DOUBLE NC2 NC3 NC5 NC6 +! adenine impropers +IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6 +! amide impropers +IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7 +IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71 +! ring hydrogen impropers +IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5 +IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2 +DONO AH61 AN6 +DONO AH62 AN6 +DONO AH2T AO2' +DONO AH3T AO3' +ACCE AN1 +ACCE AN3 +ACCE AN7 +ACCE AO4' +ACCE AO2' +ACCE AO3' +ACCE AO5' +ACCE AO1 AP +ACCE AO2 AP +ACCE O3 +ACCE NO1 NP +ACCE NO2 NP +ACCE NO5' +ACCE NO4' +ACCE NO3' +ACCE NO2' +ACCE NO7 +DONO NH2T NO2' +DONO NH3T NO3' +DONO NH71 NN7 +DONO NH72 NN7 +IC AP O3 NP NO5' 1.5477 110.11 175.47 98.59 1.5945 +IC AC5' AO5' AP O3 1.4379 124.23 -120.69 96.29 1.5477 +IC AC5' AO5' AP AO2 1.4379 124.23 -4.20 104.25 1.4838 +IC AH5S AC5' AC4' AC3' 1.1127 107.45 -172.00 111.64 1.5309 +IC AP O3 NP NO1 1.5477 110.11 63.14 114.14 1.4739 +IC AP O3 NP NO2 1.5477 110.11 -73.96 111.08 1.4835 +IC AP AO5' AC5' AC4' 1.5968 124.23 104.17 111.45 1.5366 +IC AO1 AP AO5' AC5' 1.4736 106.06 122.59 124.23 1.4379 +IC AO5' AC5' AC4' AC3' 1.4379 111.45 -54.02 111.64 1.5309 +IC AC5' AC4' AC3' AO3' 1.5366 111.64 117.91 108.23 1.4176 +IC AH3T AO3' AC3' AC4' 0.9780 101.86 -77.83 108.23 1.5309 +IC AO4' AC3' *AC4 AC5' 3.7210 30.68 12.44 22.46 6.0953 +IC AC2' AC4' *AC3' AO3' 1.5171 107.22 -123.00 108.23 1.4176 +IC AC4' AC3' AC2' AC1' 1.5309 107.22 -27.93 98.01 1.5397 +IC AC3' AC2' AC1' AN9 1.5171 98.01 168.03 114.25 1.4756 +IC AO4' AC1' AN9 AC4 1.4308 112.85 -160.05 123.87 1.3958 +IC AC1' AC4 *AN9 AC8 1.4756 123.87 160.62 105.30 1.3614 +IC AC4 AN9 AC8 AN7 1.3958 105.30 2.73 114.72 1.3222 +IC AC8 AN9 AC4 AC5 1.3614 105.30 -0.85 105.33 1.3777 +IC AC8 AN7 AC5 AC6 1.3222 102.89 -175.73 131.43 1.4163 +IC AN7 AC5 AC6 AN1 1.3877 131.43 177.76 117.35 1.3499 +IC AC5 AC6 AN1 AC2 1.4163 117.35 0.19 119.36 1.3330 +IC AN9 AC5 *AC4 AN3 1.3958 105.33 -177.76 126.56 1.3567 +IC AC5 AN1 *AC6 AN6 1.4163 117.35 178.91 119.82 1.3439 +IC AN1 AC6 AN6 AH61 1.3499 119.82 -2.82 115.89 0.9932 +IC AH61 AC6 *AN6 AH62 0.9932 115.89 -173.48 118.52 0.9961 +IC AC5 AN1 *AC6 AN6 1.4163 117.35 178.91 119.82 1.3439 +IC AN1 AC6 AN6 AH61 1.3499 119.82 -2.82 115.89 0.9932 +IC AH61 AC6 *AN6 AH62 0.9932 115.89 -173.48 118.52 0.9961 +IC AN9 AN7 *AC8 AH8 1.3614 114.72 173.63 127.58 1.0942 +IC AN1 AN3 *AC2 AH2 1.3330 128.86 179.26 114.95 1.0940 +IC AC1' AC3' *AC2 AO2' 4.3577 16.73 79.16 23.49 5.5426 +IC AH2' AO2' AC2' AC3' 2.0992 29.77 125.89 110.79 1.5171 +IC AH2T AO2' AC2' AC3' 0.9759 105.90 7.59 110.79 1.5171 +IC AO4' AC2' *AC1' AH1' 1.4308 104.32 -114.05 107.95 1.1153 +IC AC1' AC3' *AC2 AH2' 4.3577 16.73 138.52 14.56 4.3331 +IC AC2' AC4' *AC3' AH3' 1.5171 107.22 118.77 114.33 1.1023 +IC AC3' AO4' *AC4 AH4' 4.6236 30.68 55.38 18.92 5.2267 +IC AC4' AO5' *AC5 AH5' 5.8410 8.40 125.34 12.50 6.6777 +IC AC4' AO5' *AC5 AH5' 5.8410 8.40 125.34 12.50 6.6777 +IC NC5' NO5' NP NO2 1.4351 125.31 34.31 105.69 1.4835 +IC NH5S NC5' NO5' NP 1.1087 111.20 -6.79 125.31 1.5945 +IC NH5' NC5' NO5' NP 1.1115 107.95 108.24 125.31 1.5945 +IC NP NO5' NC5' NC4' 1.5945 125.31 -133.06 113.61 1.5644 +IC NO5' NC5' NC4' NC3' 1.4351 113.61 37.01 114.92 1.5111 +IC NC5' NC4' NC3' NC2' 1.5644 114.92 71.49 99.06 1.5369 +IC NC4' NC3' NC2' NC1' 1.5111 99.06 54.76 97.08 1.5500 +IC NC3' NC2' NC1' NO4' 1.5369 97.08 -39.12 103.14 1.4628 +IC NC2' NC1' NO4' NC4' 1.5500 103.14 9.47 109.09 1.4960 +IC NO2' NC2' NC1' NO4' 1.4207 114.02 -166.39 103.14 1.4628 +IC NH2T NO2' NC2' NC1' 0.9638 100.52 -89.37 114.02 1.5500 +IC NO4' NC2' *NC1' NH1' 1.4628 103.14 -111.22 105.40 1.1096 +IC NC1' NC3' *NC2 NH2' 2.4663 46.96 -41.97 34.01 3.9460 +IC NC2' NC4' *NC3 NH3' 3.9136 23.54 -115.76 16.12 3.6674 +IC NC3' NO4' *NC4 NH4' 5.4003 24.61 -39.21 14.97 6.7904 +IC NC4' NO5' *NC5 NH5' 5.9665 13.65 -41.47 15.17 7.7670 +IC NC4' NO5' *NC5 NH5S 5.9665 13.65 -87.41 13.92 6.7251 +IC NC3' NC2' NC1' NN1 1.5369 97.08 88.64 116.58 1.5502 +IC NO3' NC3' NC2' NC1' 1.4176 119.76 -172.52 97.08 1.5500 +IC NH3T NO3' NC3' NC2' 0.9717 103.61 17.81 119.76 1.5369 +IC NC2' NC1' NN1 NC2 1.5500 116.58 -19.65 116.34 1.3499 +IC NC1' NN1 NC2 NC3 1.5502 116.34 134.66 130.57 1.3607 +IC NN1 NC2 NC3 NC4 1.3499 130.57 5.82 111.74 1.5356 +IC NC2 NC3 NC4 NC5 1.3607 111.74 -1.05 119.26 1.5319 +IC NC3 NC4 NC5 NC6 1.5356 119.26 -1.26 113.69 1.3745 +IC NC4 NC5 NC6 NN1 1.5319 113.69 -0.29 128.15 1.3388 +IC NC5 NC6 NN1 NC2 1.3745 128.15 4.14 116.26 1.3499 +IC NN1 NC2 NC3 NC7 1.3499 130.57 -147.46 122.72 1.5282 +IC NC2 NC3 NC7 NO7 1.3607 122.72 -140.47 119.41 1.2169 +IC NC2 NC3 NC7 NN7 1.3607 122.72 46.61 116.68 1.3621 +IC NO7 NC7 NN7 NH71 1.2169 123.49 -177.07 120.21 1.0093 +IC NO7 NC7 NN7 NH72 1.2169 123.49 -4.94 119.16 1.0014 +IC NC2 NC3 NC4 NH4 1.3607 111.74 -135.39 112.16 1.1099 +IC NC2 NC3 NC4 NH42 1.3607 111.74 114.48 103.52 1.1129 +IC NC3 NC4 NC5 NH5 1.5356 119.26 -171.18 122.65 1.0912 +IC NC4 NC5 NC6 NH6 1.5319 113.69 179.92 118.00 1.0878 +IC NC6 NN1 NC2 NH2 1.3388 116.26 162.03 117.47 1.0731 +PATCH FIRST NONE LAST NONE + +RESI NADP -2.00 ! oxidized nicotinamide adenine dinucleotide, + ! NADP+, adm jr. + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! +GROUP ! +ATOM AC4' CN7 0.16 ! AH61 AH62 +ATOM AH4' HN7 0.09 ! \ / +ATOM AO4' ON6B -0.50 ! AN6 +ATOM AC1' CN7B 0.16 ! | +ATOM AH1' HN7 0.09 ! AC6 +GROUP ! // \ +ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\ +ATOM AN7 NN4 -0.71 ! | || AC8-AH8 +ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/ +ATOM AH8 HN3 0.12 ! / \\ / \ +ATOM AN9 NN2 -0.05 ! AH2 AN3 \ + ! \ +ATOM AN1 NN3A -0.74 ! \ +ATOM AC2 CN4 0.50 ! \ +ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \ +ATOM AN3 NN3A -0.75 ! | | | \ / \ \ +ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' +ATOM AC6 CN2 0.46 ! \ | | | \ / \ + ! \ NO2 AO2 AH5' AC3'-AC2' AH1' +ATOM AN6 NN1 -0.77 ! \ / \ / \ +ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2' +ATOM AH62 HN1 0.38 ! \ | | +GROUP ! \ AH3T AO1P=AP2==AO2P (-) +ATOM AC2' CN7B 0.01 ! \ | NH71 +ATOM AH2' HN7 0.09 ! \ AH2T-AO2T / +ATOM AO2' ON2 -0.62 ! \ NH72-NN7 NH4 NH42 +ATOM AP2 P 1.50 ! \ \ \ / +ATOM AO1P ON3 -0.82 ! \ NC7 NC4 +ATOM AO2P ON3 -0.82 ! \ / \ / \ +ATOM AO2T ON4 -0.68 ! \ NO7 NC3 NC5-NH5 +ATOM AH2T HN4 0.34 ! \ | | +GROUP ! \ | | +ATOM AC3' CN7 0.14 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 +ATOM AH3' HN7 0.09 ! \ | \ / \ \ / +ATOM AO3' ON5 -0.66 ! NC5'--NC4' NC1'--------NN1 +ATOM AH3T HN5 0.43 ! | \ / \ +GROUP ! NH5' NC3'-NC2'NH1' +ATOM AC5' CN8B -0.08 ! / \ / \ +ATOM AH5' HN8 0.09 ! NO3' NH3'NO2'NH2' +ATOM AH5s HN8 0.09 ! | | +ATOM AP P 1.50 ! NH3T NH2T +ATOM AO1 ON3 -0.82 ! +ATOM AO2 ON3 -0.82 ! +ATOM AO5' ON2 -0.62 ! +ATOM O3 ON2 -0.68 +ATOM NP P 1.50 +ATOM NO1 ON3 -0.82 +ATOM NO2 ON3 -0.82 +ATOM NO5' ON2 -0.62 +ATOM NC5' CN8B -0.08 +ATOM NH5s HN8 0.09 +ATOM NH5' HN8 0.09 +GROUP +ATOM NC2' CN7B 0.14 +ATOM NH2' HN7 0.09 +ATOM NO2' ON5 -0.66 +ATOM NH2T HN5 0.43 +GROUP +ATOM NC3' CN7 0.14 +ATOM NH3' HN7 0.09 +ATOM NO3' ON5 -0.66 +ATOM NH3T HN5 0.43 +GROUP +ATOM NC1' CN7B 0.16 +ATOM NH1' HN7 0.09 +ATOM NC4' CN7 0.16 +ATOM NH4' HN7 0.09 +ATOM NO4' ON6B -0.50 +GROUP +ATOM NN1 NN2 -0.07 +ATOM NC6 CN3B 0.16 +ATOM NH6 HN3B 0.19 +ATOM NC5 CN3 -0.10 +ATOM NH5 HN3B 0.16 +ATOM NC4 CN3A -0.05 +ATOM NH4 HN3B 0.16 +ATOM NC3 CN3 0.05 +ATOM NC2 CN3B 0.18 +ATOM NH2 HN3B 0.16 +ATOM NC7 CN1A 0.68 +ATOM NO7 ON1 -0.40 +ATOM NN7 NN1 -0.82 +ATOM NH71 HN1 0.34 ! trans to amide O +ATOM NH72 HN1 0.36 ! cis to amide O + +BOND AN1 AC2 AN3 AC4 AC5 AC6 +BOND AC6 AN6 AC5 AN7 AC8 AN9 +BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 +DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 +BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' +BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2' +BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' +BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP AP AO1 +BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 +BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4' +BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' +BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' +BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 +BOND NC3 NC4 NC5 NC6 +BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 +BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6 +BOND AP2 AO1P AP2 AO2P AP2 AO2T AO2T AH2T +DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 +! adenine impropers +IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6 +! amide impropers +IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7 +IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71 +! ring hydrogen impropers +IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5 +IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2 +DONO AH61 AN6 +DONO AH62 AN6 +DONO AH2T AO2' +DONO AH3T AO3' +ACCE AN1 +ACCE AN3 +ACCE AN7 +ACCE AO4' +ACCE AO2' +ACCE AO3' +ACCE AO5' +ACCE AO1 AP +ACCE AO2 AP +ACCE O3 +ACCE NO1 NP +ACCE NO2 NP +ACCE NO5' +ACCE NO4' +ACCE NO3' +ACCE NO2' +ACCE NO7 +DONO NH2T NO2' +DONO NH3T NO3' +DONO NH71 NN7 +DONO NH72 NN7 +DONO AH2T AO2T +ACCE AO2T +ACCE AO1P +ACCE AO2P +ACCE AO2' +IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977 +IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863 +IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836 +IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942 +IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756 +IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636 +IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491 +IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232 +IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942 +IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337 +IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942 +IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491 +IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337 +IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415 +IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847 +IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013 +IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777 +IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282 +IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782 +IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146 +IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482 +IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300 +IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648 +IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 +IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 +IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 +IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 +IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 +IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 +IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962 +IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928 +IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294 +IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097 +IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097 +IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105 +IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999 +IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110 +IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000 +IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 +IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 +IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636 +IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977 +IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977 +IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160 +IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160 +IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160 +IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270 +IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100 +IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712 +IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100 +IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270 +IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110 +IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110 +IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110 +IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110 +IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110 +IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110 +IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800 +IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270 +IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160 +IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150 +IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500 +IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600 +IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600 +IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500 +IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199 +IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150 +IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800 +IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300 +IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600 +IC NO7 NC7 NN7 NH71 1.2300 0.00 180.00 120.00 1.0000 +IC NO7 NC7 NN7 NH72 1.2300 0.00 0.00 120.00 1.0000 +IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900 +IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900 +IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900 +IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900 +IC AC3' AC2' AO2' AP2 0.0000 000.00 180.00 000.00 0.0000 +IC AC2' AO2' AP2 AO2T 0.0000 000.00 -39.52 000.00 0.0000 +IC AO2T AO2' *AP2 AO1P 0.0000 000.00 -115.82 000.00 0.0000 +IC AO2T AO2' *AP2 AO2P 0.0000 000.00 115.90 000.00 0.0000 +IC AH2T AO2T AP2 AO2' 0.0000 000.00 180.00 000.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI NDPH -3.00 ! reduced nicotinamide adenine dinucleotide + ! NADPH, VARNAI/adm jr. + ! from NADH and 3PHO + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! +GROUP ! +ATOM AC4' CN7 0.16 ! AH61 AH62 +ATOM AH4' HN7 0.09 ! \ / +ATOM AO4' ON6B -0.50 ! AN6 +ATOM AC1' CN7B 0.16 ! | +ATOM AH1' HN7 0.09 ! AC6 +GROUP ! // \ +ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\ +ATOM AN7 NN4 -0.71 ! | || AC8-AH8 +ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/ +ATOM AH8 HN3 0.12 ! / \\ / \ +ATOM AN9 NN2 -0.05 ! AH2 AN3 \ + ! \ +ATOM AN1 NN3A -0.74 ! \ +ATOM AC2 CN4 0.50 ! \ +ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \ +ATOM AN3 NN3A -0.75 ! | | | \ / \ \ +ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' +ATOM AC6 CN2 0.46 ! \ | | | \ / \ + ! \ NO2 AO2 AH5' AC3'-AC2' AH1' +ATOM AN6 NN1 -0.77 ! \ / \ / \ +ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2' +ATOM AH62 HN1 0.38 ! \ | | +GROUP ! \ AH3T AO1P=AP2==AO2P (-) +ATOM AC2' CN7B 0.01 ! \ | NH71 +ATOM AH2' HN7 0.09 ! \ AH2T-AO2T / +ATOM AO2' ON2 -0.62 ! \ NH72-NN7 NH4 NH42 +ATOM AP2 P 1.50 ! \ \ \ / +ATOM AO1P ON3 -0.82 ! \ NC7 NC4 +ATOM AO2P ON3 -0.82 ! \ / \ / \ +ATOM AO2T ON4 -0.68 ! \ NO7 NC3 NC5-NH5 +ATOM AH2T HN4 0.34 ! \ | | +GROUP ! \ | | +ATOM AC3' CN7 0.14 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 +ATOM AH3' HN7 0.09 ! \ | \ / \ \ / +ATOM AO3' ON5 -0.66 ! NC5'--NC4' NC1'--------NN1 +ATOM AH3T HN5 0.43 ! | \ / \ +GROUP ! NH5' NC3'-NC2'NH1' +ATOM AC5' CN8B -0.08 ! / \ / \ +ATOM AH5' HN8 0.09 ! NO3' NH3'NO2'NH2' +ATOM AH5s HN8 0.09 ! | | +ATOM AP P 1.50 ! NH3T NH2T +ATOM AO1 ON3 -0.82 ! +ATOM AO2 ON3 -0.82 ! +ATOM AO5' ON2 -0.62 ! +ATOM O3 ON2 -0.68 +ATOM NP P 1.50 +ATOM NO1 ON3 -0.82 +ATOM NO2 ON3 -0.82 +ATOM NO5' ON2 -0.62 +ATOM NC5' CN8B -0.08 +ATOM NH5s HN8 0.09 +ATOM NH5' HN8 0.09 +GROUP +ATOM NC2' CN7B 0.14 +ATOM NH2' HN7 0.09 +ATOM NO2' ON5 -0.66 +ATOM NH2T HN5 0.43 +GROUP +ATOM NC3' CN7 0.14 +ATOM NH3' HN7 0.09 +ATOM NO3' ON5 -0.66 +ATOM NH3T HN5 0.43 +GROUP +ATOM NC1' CN7B 0.16 +ATOM NH1' HN7 0.09 +ATOM NC4' CN7 0.16 +ATOM NH4' HN7 0.09 +ATOM NO4' ON6B -0.50 +GROUP +ATOM NN1 NN2 -0.27 !N2 +ATOM NC6 CN3C -0.06 !C3 +ATOM NH6 HN6 0.17 !H4 +ATOM NC5 CN3 -0.18 !C5 +ATOM NH5 HN6 0.14 !H6 +ATOM NC4 CN8 -0.28 !C7 +ATOM NH4 HN8 0.09 !H8 +ATOM NH42 HN8 0.09 !H17 +ATOM NC3 CN3 0.36 !C9 +ATOM NC2 CN3C -0.10 !C10 +ATOM NH2 HN6 0.14 !H11 +ATOM NC7 CN1A 0.55 !C12 +ATOM NO7 ON1 -0.51 !O13 +ATOM NN7 NN1 -0.72 !N14 +ATOM NH71 HN1 0.26 !H15 ! trans to amide O +ATOM NH72 HN1 0.32 !H16 ! cis to amide O +BOND AN1 AC2 AN3 AC4 AC5 AC6 +BOND AC6 AN6 AC5 AN7 AC8 AN9 +BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 +DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 +BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' +BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2' +BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' +BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP AP AO1 +BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 +BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4' +BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' +BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' +BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 +BOND NC3 NC4 NC5 NC6 +BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 +BOND NN7 NH72 NC4 NH4 NC4 NH42 NC5 NH5 NC6 NH6 +BOND AP2 AO1P AP2 AO2P AP2 AO2T AO2T AH2T +DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 +! adenine impropers +IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6 +! amide impropers +IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7 +IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71 +! ring hydrogen impropers +IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5 +IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2 +DONO AH61 AN6 +DONO AH62 AN6 +DONO AH3T AO3' +ACCE AN1 +ACCE AN3 +ACCE AN7 +ACCE AO4' +ACCE AO3' +ACCE AO5' +ACCE AO1 AP +ACCE AO2 AP +ACCE O3 +ACCE NO1 NP +ACCE NO2 NP +ACCE NO5' +ACCE NO4' +ACCE NO3' +ACCE NO2' +ACCE NO7 +DONO NH2T NO2' +DONO NH3T NO3' +DONO NH71 NN7 +DONO NH72 NN7 +DONO AH2T AO2T +ACCE AO2T +ACCE AO1P +ACCE AO2P +ACCE AO2' +! the following ICs will not totally IC BUILD NADPH +IC AP O3 NP NO5' 1.5477 110.11 175.47 98.59 1.5945 +IC AC5' AO5' AP O3 1.4379 124.23 -120.69 96.29 1.5477 +IC AC5' AO5' AP AO2 1.4379 124.23 -4.20 104.25 1.4838 +IC AH5S AC5' AC4' AC3' 1.1127 107.45 -172.00 111.64 1.5309 +IC AP O3 NP NO1 1.5477 110.11 63.14 114.14 1.4739 +IC AP O3 NP NO2 1.5477 110.11 -73.96 111.08 1.4835 +IC AP AO5' AC5' AC4' 1.5968 124.23 104.17 111.45 1.5366 +IC AO1 AP AO5' AC5' 1.4736 106.06 122.59 124.23 1.4379 +IC AO5' AC5' AC4' AC3' 1.4379 111.45 -54.02 111.64 1.5309 +IC AC5' AC4' AC3' AO3' 1.5366 111.64 117.91 108.23 1.4176 +IC AH3T AO3' AC3' AC4' 0.9780 101.86 -77.83 108.23 1.5309 +IC AO4' AC3' *AC4 AC5' 3.7210 30.68 12.44 22.46 6.0953 +IC AC2' AC4' *AC3' AO3' 1.5171 107.22 -123.00 108.23 1.4176 +IC AC4' AC3' AC2' AC1' 1.5309 107.22 -27.93 98.01 1.5397 +IC AC3' AC2' AC1' AN9 1.5171 98.01 168.03 114.25 1.4756 +IC AO4' AC1' AN9 AC4 1.4308 112.85 -160.05 123.87 1.3958 +IC AC1' AC4 *AN9 AC8 1.4756 123.87 160.62 105.30 1.3614 +IC AC4 AN9 AC8 AN7 1.3958 105.30 2.73 114.72 1.3222 +IC AC8 AN9 AC4 AC5 1.3614 105.30 -0.85 105.33 1.3777 +IC AC8 AN7 AC5 AC6 1.3222 102.89 -175.73 131.43 1.4163 +IC AN7 AC5 AC6 AN1 1.3877 131.43 177.76 117.35 1.3499 +IC AC5 AC6 AN1 AC2 1.4163 117.35 0.19 119.36 1.3330 +IC AN9 AC5 *AC4 AN3 1.3958 105.33 -177.76 126.56 1.3567 +IC AC5 AN1 *AC6 AN6 1.4163 117.35 178.91 119.82 1.3439 +IC AN1 AC6 AN6 AH61 1.3499 119.82 -2.82 115.89 0.9932 +IC AH61 AC6 *AN6 AH62 0.9932 115.89 -173.48 118.52 0.9961 +IC AC5 AN1 *AC6 AN6 1.4163 117.35 178.91 119.82 1.3439 +IC AN1 AC6 AN6 AH61 1.3499 119.82 -2.82 115.89 0.9932 +IC AH61 AC6 *AN6 AH62 0.9932 115.89 -173.48 118.52 0.9961 +IC AN9 AN7 *AC8 AH8 1.3614 114.72 173.63 127.58 1.0942 +IC AN1 AN3 *AC2 AH2 1.3330 128.86 179.26 114.95 1.0940 +IC AO4' AC2' *AC1' AH1' 1.4308 104.32 -114.05 107.95 1.1153 +IC AC1' AC3' *AC2 AH2' 4.3577 16.73 138.52 14.56 4.3331 +IC AC2' AC4' *AC3' AH3' 1.5171 107.22 118.77 114.33 1.1023 +IC AC3' AO4' *AC4 AH4' 4.6236 30.68 55.38 18.92 5.2267 +IC AC4' AO5' *AC5 AH5' 5.8410 8.40 125.34 12.50 6.6777 +IC AC4' AO5' *AC5 AH5' 5.8410 8.40 125.34 12.50 6.6777 +IC NC5' NO5' NP NO2 1.4351 125.31 34.31 105.69 1.4835 +IC NH5S NC5' NO5' NP 1.1087 111.20 -6.79 125.31 1.5945 +IC NH5' NC5' NO5' NP 1.1115 107.95 108.24 125.31 1.5945 +IC NP NO5' NC5' NC4' 1.5945 125.31 -133.06 113.61 1.5644 +IC NO5' NC5' NC4' NC3' 1.4351 113.61 37.01 114.92 1.5111 +IC NC5' NC4' NC3' NC2' 1.5644 114.92 71.49 99.06 1.5369 +IC NC4' NC3' NC2' NC1' 1.5111 99.06 54.76 97.08 1.5500 +IC NC3' NC2' NC1' NO4' 1.5369 97.08 -39.12 103.14 1.4628 +IC NC2' NC1' NO4' NC4' 1.5500 103.14 9.47 109.09 1.4960 +IC NO2' NC2' NC1' NO4' 1.4207 114.02 -166.39 103.14 1.4628 +IC NH2T NO2' NC2' NC1' 0.9638 100.52 -89.37 114.02 1.5500 +IC NO4' NC2' *NC1' NH1' 1.4628 103.14 -111.22 105.40 1.1096 +IC NC1' NC3' *NC2 NH2' 2.4663 46.96 -41.97 34.01 3.9460 +IC NC2' NC4' *NC3 NH3' 3.9136 23.54 -115.76 16.12 3.6674 +IC NC3' NO4' *NC4 NH4' 5.4003 24.61 -39.21 14.97 6.7904 +IC NC4' NO5' *NC5 NH5' 5.9665 13.65 -41.47 15.17 7.7670 +IC NC4' NO5' *NC5 NH5S 5.9665 13.65 -87.41 13.92 6.7251 +IC NC3' NC2' NC1' NN1 1.5369 97.08 88.64 116.58 1.5502 +IC NO3' NC3' NC2' NC1' 1.4176 119.76 -172.52 97.08 1.5500 +IC NH3T NO3' NC3' NC2' 0.9717 103.61 17.81 119.76 1.5369 +IC NC2' NC1' NN1 NC2 1.5500 116.58 -19.65 116.34 1.3499 +IC NC1' NN1 NC2 NC3 1.5502 116.34 134.66 130.57 1.3607 +IC NN1 NC2 NC3 NC4 1.3499 130.57 5.82 111.74 1.5356 +IC NC2 NC3 NC4 NC5 1.3607 111.74 -1.05 119.26 1.5319 +IC NC3 NC4 NC5 NC6 1.5356 119.26 -1.26 113.69 1.3745 +IC NC4 NC5 NC6 NN1 1.5319 113.69 -0.29 128.15 1.3388 +IC NC5 NC6 NN1 NC2 1.3745 128.15 4.14 116.26 1.3499 +IC NN1 NC2 NC3 NC7 1.3499 130.57 -147.46 122.72 1.5282 +IC NC2 NC3 NC7 NO7 1.3607 122.72 -140.47 119.41 1.2169 +IC NC2 NC3 NC7 NN7 1.3607 122.72 46.61 116.68 1.3621 +IC NO7 NC7 NN7 NH71 1.2169 123.49 -177.07 120.21 1.0093 +IC NO7 NC7 NN7 NH72 1.2169 123.49 -4.94 119.16 1.0014 +IC NC2 NC3 NC4 NH4 1.3607 111.74 -135.39 112.16 1.1099 +IC NC2 NC3 NC4 NH42 1.3607 111.74 114.48 103.52 1.1129 +IC NC3 NC4 NC5 NH5 1.5356 119.26 -171.18 122.65 1.0912 +IC NC4 NC5 NC6 NH6 1.5319 113.69 179.92 118.00 1.0878 +IC NC6 NN1 NC2 NH2 1.3388 116.26 162.03 117.47 1.0731 +IC AC3' AC2' AO2' AP2 0.0000 000.00 180.00 000.00 0.0000 +IC AC2' AO2' AP2 AO2T 0.0000 000.00 -39.52 000.00 0.0000 +IC AO2T AO2' *AP2 AO1P 0.0000 000.00 -115.82 000.00 0.0000 +IC AO2T AO2' *AP2 AO2P 0.0000 000.00 115.90 000.00 0.0000 +IC AH2T AO2T AP2 AO2' 0.0000 000.00 180.00 000.00 0.0000 +PATCH FIRST NONE LAST NONE + +end + +read para card flex append +* NAD, PPI parameters +* + +ATOMS +MASS 459 HN3B 1.008000 ! NAD+ aromatic hydrogen +MASS 460 CN1A 12.011000 ! NAD+/NADH amide carbonyl carbon +MASS 461 CN3A 12.011000 ! NAD+ aromatic carbon +MASS 462 CN3B 12.011000 ! NAD+ aromatic carbon +MASS 463 CN3C 12.011000 ! NADH aromatic carbon +MASS 464 P3 30.974000 ! pyrophosphate phosphorus +MASS 465 P4 30.974000 ! protonated pyrophosphate phosphorus + +BONDS +! +!atom types Kb b0 +! +!NICH parameters to maintain back compatibility following +!atom type switch from HN3 to HN6 +CN3C HN6 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95 +CN3 HN6 350.0 1.09 !nadh, adm jr., 8/98 +! +CN1A CN3 302.0 1.480 !nad/ppi, jjp1/adm jr. 7/95 +CN1A NN1 560.0 1.360 !nad/ppi, jjp1/adm jr. 7/95 +CN1A ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95 +CN3A CN3 450.0 1.360 !nad/ppi, jjp1/adm jr. 7/95 +CN3B CN3 420.0 1.350 !nad/ppi, jjp1/adm jr. 7/95 +CN3C CN3 420.0 1.320 !nadh/ppi, jjp1/adm jr. 7/95 +CN3 CN8 222.5 1.490 !nadh/ppi, jjp1/adm jr. 7/95 +CN3 HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 +CN3A HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 +CN3B HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 +CN3C HN3 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95 +CN3B NN2 420.0 1.315 !nad/ppi, jjp1/adm jr. 7/95 +CN3C NN2 420.0 1.355 !nadh/ppi, jjp1/adm jr. 7/95 +ON2 P3 300.0 1.68 !nad/ppi, jjp1/adm jr. 7/95 +ON3 P3 480.0 1.53 !nad/ppi, jjp1/adm jr. 7/95 +ON2 P4 300.0 1.68 !PPI2, from nad/ppi, adm jr. 7/01 +ON3 P4 480.0 1.53 !PPI2, from nad/ppi, adm jr. 7/01 +ON4 P4 237.0 1.58 !PPI2, from MP_1, ADM Jr. + +ANGLES +! +!atom types Ktheta Theta0 Kub S0 +! +!NICH parameters to maintain back compatibility following +!atom type switch from HN3 to HN6 +CN3 CN1A NN1 85.0 113.0 80.0 2.46 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN1A ON1 85.0 118.5 20.0 2.43 !nad/ppi, jjp1/adm jr. 7/95 +NN1 CN1A ON1 85.0 128.5 20.0 2.17 !nad/ppi, jjp1/adm jr. 7/95 +NN2 CN3C HN6 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 +HN6 CN3C CN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 +HN6 CN3 CN8 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95 +CN3C CN3 HN6 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 +CN1A CN3 CN3C 5.0 107.8 !nad/ppi, jjp1/adm jr. 7/95 +CN1A CN3 CN8 125.0 124.2 !nadh/ppi, jjp1/adm jr. 7/95 +CN3A CN3 CN1A 40.0 110.2 !nad/ppi, jjp1/adm jr. 7/95 +CN3B CN3 CN1A 10.0 131.8 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3A CN3 50.0 118.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3A CN3 CN3B 40.0 118.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3 CN8 53.5 108.5 !nadh/ppi, jjp1/adm jr. 7/95 +CN3B CN3 CN8 53.5 108.5 !nad/ppi, jjp1/adm jr. 7/95 +CN3C CN3 CN8 43.5 128.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3B CN3 HN3B 30.0 122.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3A CN3 HN3B 30.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3C HN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 +CN3C CN3 HN3 42.0 116.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3A HN3B 80.0 121.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3B HN3B 80.0 120.5 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3B NN2 120.0 122.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3C NN2 60.0 122.0 !nadh/ppi, jjp1/adm jr. 7/95 +CN8 CN3 HN3 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95 +HN3B CN3B NN2 80.0 117.5 !nad/ppi, jjp1/adm jr. 7/95 +HN3 CN3C NN2 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN8 CN3 125.0 108.0 !nadh/ppi, jjp1/adm jr. 7/95 +CN3 CN8 HN8 55.0 110.10 !nadh/ppi, jjp1/adm jr. 7/95 +CN1A NN1 HN1 35.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3B NN2 CN3B 30.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3C NN2 CN3C 20.0 114.0 !nadh/ppi, jjp1/adm jr. 7/95 +CN3B NN2 CN7B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95 +CN3C NN2 CN7B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95 +CN3B NN2 HN2 32.0 117.4 !nad/ppi, jjp1/adm jr. 7/95 +CN3C NN2 HN2 39.0 123.0 !nad/ppi, jjp1/adm jr. 7/95 +CN9 ON2 P3 20.0 120.0 35. 2.33 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 +P3 ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 +P4 ON2 P 45.0 140.0 40.0 3.15 !PPI2, from nad/ppi, adm jr., 7/01 +P3 ON2 P3 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 +HN4 ON4 P4 30.0 120.0 40.0 2.35 !PPI2, from MP_1, adm jr., 7/01 +CN7 CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH +ON2 P4 ON4 48.1 100.0 !PPI2, from MP_1, adm jr., 7/01 +ON3 P4 ON4 98.9 108.23 !PPI2, from MP_1, adm jr., 7/01 +ON2 P3 ON2 80.0 104.3 !nad/ppi, jjp1/adm jr. 7/95 +ON2 P3 ON3 88.9 111.6 !nad/ppi, jjp1/adm jr. 7/95 +ON2 P4 ON3 88.9 105.0 !PPI2, from nad/ppi, adm jr., 7/01 +ON3 P3 ON3 104.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 +ON3 P4 ON3 104.0 120.0 !PPI2, from nad/ppi, adm jr., 7/01 + +DIHEDRALS +! +!atom types Kchi n delta +! +ON4 P ON2 CN7B 0.95 2 0.0 !for NADPH +ON4 P ON2 CN7B 0.50 3 0.0 !for NADPH +! nicotinamide adenine dinucleotide +CN3 NN2 CN3B HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +HN2 NN2 CN3B HN3B 3.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +HN3B CN3 CN3A HN3B 2.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +HN3B CN3 CN3B HN3B 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +NN2 CN3B CN3 HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN1A CN3 HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN1A CN3 CN3B HN3B 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN1A CN3 CN3A HN3B 5.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN1A CN3 HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN1A CN3 CN3 HN3 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3A CN3 CN1A ON1 2.38 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3B CN3 CN1A ON1 2.38 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3A CN3 CN1A NN1 0.35 1 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3A CN3 CN1A NN1 0.62 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3B CN3 CN1A NN1 0.35 1 0.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3B CN3 CN1A NN1 0.62 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3A CN3 CN1A 3.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 CN3A CN3 CN3B 6.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +NN2 CN3B CN3 CN3A 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3B NN2 CN3B CN3 4.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +X CN3 CN3A X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +X CN3 CN3B X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +X CN3 CN8 X 1.0 3 180.0 !nad/ppi, jjp1/adm jr. 7/95 +X NN1 CN1A X 2.5 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +X NN2 CN3B X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +! nicotinamide adenine dinucleotide hydride, nadh +CN8 CN3 CN1A ON1 1.00 2 180.0 !nadh, jjp1,adm jr. 4/95 +CN8 CN3 CN1A ON1 1.00 3 0.0 !nadh, jjp1,adm jr. 4/95 +CN8 CN3 CN1A ON1 0.40 6 0.0 !nadh, jjp1,adm jr. 4/95 +CN8 CN3 CN1A NN1 0.50 2 180.0 !nadh, jjp1,adm jr. 4/95 +CN8 CN3 CN1A NN1 0.35 3 180.0 !nadh, jjp1,adm jr. 4/95 +CN8 CN3 CN1A NN1 0.40 6 0.0 !nadh, jjp1,adm jr. 4/95 +CN3C CN3 CN1A ON1 0.30 1 0.0 !nadh, jjp1,adm jr. 4/95 +CN3C CN3 CN1A ON1 1.95 2 180.0 !nadh, jjp1,adm jr. 4/95 +CN3C CN3 CN1A NN1 1.10 1 180.0 !nadh, jjp1,adm jr. 4/95 +CN3C CN3 CN1A NN1 1.95 2 180.0 !nadh, jjp1,adm jr. 4/95 +HN2 NN2 CN3C HN3 4.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3 NN2 CN3C HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +NN2 CN3C CN3 HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN8 CN3 CN3C NN2 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3C CN3 CN8 CN3 4.0 3 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN1A CN3 CN3C NN2 2.5 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +X CN3 CN3C X 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +X NN2 CN3C X 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +CN3C NN2 CN3C CN3 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 +! pyrophosphate (ppi) +P3 ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P3 ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P3 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P3 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P3 ON2 P3 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P3 ON2 P3 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P3 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P ON2 P3 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P3 ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P3 ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P3 ON2 P3 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 +P3 ON2 P3 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 +! protonated pyrophosphate (ppi2) +P ON2 P4 ON2 0.03 2 0.0 !from P ON2 P2 ON2, adm jr. 7/01 +P ON2 P4 ON2 0.03 3 0.0 !from P ON2 P2 ON2, adm jr. 7/01 +P4 ON2 P ON2 0.03 2 0.0 !from P ON2 P2 ON2, adm jr. 7/01 +P4 ON2 P ON2 0.03 3 0.0 !from P ON2 P2 ON2, adm jr. 7/01 +P ON2 P4 ON3 0.10 2 0.0 !from P ON2 P2 ON3, adm jr. 7/01 +P ON2 P4 ON3 0.03 3 0.0 !from P ON2 P2 ON3, adm jr. 7/01 +P4 ON2 P ON3 0.10 2 0.0 !from P ON2 P2 ON3, adm jr. 7/01 +P4 ON2 P ON3 0.03 3 0.0 !from P ON2 P2 ON3, adm jr. 7/01 +P ON2 P4 ON4 0.10 2 0.0 !from P ON2 P2 ON4, adm jr. 7/01 +P ON2 P4 ON4 0.03 3 0.0 !from P ON2 P2 ON4, adm jr. 7/01 +X ON4 P4 X 0.30 3 0.0 !from MP_1, adm jr. +!for nadp/nadph (?), adm jr. +HN7 CN7 CN7 CN7 0.195 3 0.0 +HN7 CN7B NN2 CN3B 0.195 3 0.0 +HN7 CN7B NN2 CN3C 0.195 3 0.0 +HN7 CN7 CN7B ON6 0.195 3 0.0 +HN7 CN7 CN7B ON2 0.195 3 0.0 +HN7 CN7 CN7B NN2 0.195 3 0.0 +! +ON6 CN7B CN7 ON5 3.4 1 180.0 !gam +CN7 CN7B NN2 CN3B 0.0 3 0.0 +CN8 CN7B NN2 CN3B 0.0 3 0.0 ! 25P1 +CN7B CN7B NN2 CN3B 0.0 3 0.0 ! for NADPH +ON6 CN7B NN2 CN3B 0.0 3 0.0 ! +ON6B CN7B NN2 CN3B 0.0 3 0.0 ! for NADPH +CN7 CN7B NN2 CN3C 0.0 3 0.0 +CN7B CN7B NN2 CN3C 0.0 3 0.0 ! for NADPH +ON6 CN7B NN2 CN3C 0.0 3 0.0 ! +ON6B CN7B NN2 CN3C 0.0 3 0.0 ! for NADPH +CN7 CN7 CN7B NN2 0.0 3 0.0 +CN8 CN7 CN7B NN2 0.0 3 0.0 ! 25P1 +CN7 CN7B NN2 CN5 0.3 3 0.0 ! NF +CN7 CN7B NN2 CN4 0.0 3 180.0 ! NF +ON2 CN7 CN7B NN2 0.0 3 0.0 +ON5 CN7 CN7B NN2 0.0 3 0.0 + +IMPROPER +! +!atom types Kpsi psi0 +! +! nicotinamide adenine dinucleotide +CN3 CN3C CN8 HN6 15.0 0 0.0 !nich, jjp1/adm jr. +HN3B X X CN3 15.0 0 0.0 !nad/ppi, jjp1/adm jr. +HN3B X X CN3A 13.0 0 0.0 !nad/ppi, jjp1/adm jr. +HN3B X X CN3B 13.0 0 0.0 !nad/ppi, jjp1/adm jr. +HN2 CN3 CN3B NN2 50.0 0 0.0 !nad/ppi, jjp1/adm jr. +HN1 HN1 CN1A NN1 -5.0 0 0.0 !nad/ppi, jjp1/adm jr. +ON1 X X CN1A 40.0 0 0.0 !nad/ppi, jjp1/adm jr. +HN3 X X CN3C 53.0 0 0.0 !nad/ppi, jjp1/adm jr. +HN6 X X CN3C 53.0 0 0.0 !nich, adm jr. +HN8 CN3 CN3 CN8 18.0 0 0.0 !nad/ppi, jjp1/adm jr. + +NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +HN3B 0.0 -0.046 0.9000 !nad/ppi, jjp1/adm jr. +CN1A 0.0 -0.07 2.0000 ! nad/ppi, jjp1/adm jr. (protein CC) +CN3A 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. +CN3B 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. +CN3C 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. +P3 0.0 -0.585 2.15 ! nad/ppi, jjp1/adm jr. +P4 0.0 -0.585 2.15 ! for PPI2, adm jr. + +end + + diff --git a/charmm/toppar/stream/na/toppar_all36_na_reactive_rna.str b/charmm/toppar/stream/na/toppar_all36_na_reactive_rna.str new file mode 100644 index 00000000..ae8d17be --- /dev/null +++ b/charmm/toppar/stream/na/toppar_all36_na_reactive_rna.str @@ -0,0 +1,1066 @@ +* CHARMM36 All-Hydrogen Nucleic Acid Toppar Stream File +* Reactive RNA residues and patches +* All comments to the CHARMM web site: www.charmm.org +* parameter set discussion forum +* + +!Note: This stream file included atom type PC, which is also present +!in the parent carbohydrate toppar files. Thus, if the carbohydrate +!files are read prior to this stream file an repeated atom error will +!be returned. Alternatively, the toppar carbohydrate files could be +!read prior to this stream, but this has not been implemented. + +!parent toppar files +!top_all36_na.rtf +!par_all36_na.prm +! + +!Reference +!Mayaan E, Moser A, MacKerell AD Jr, York DM. "CHARMM force field +!parameters for simulation of reactive intermediates in native and +!thio-substituted ribozymes." J Comput Chem. 2007 Jan 30;28(2):495-507. +! + +read rtf card append +* residues and patches associated with reactive RNA FF +* +31 1 + +!note that these mass numbers overlap with those in +! toppar_all36_na_modifications.str, such that the two toppar files +! cannot be used simultaneously without changing the mass numbers in +! one of the files (and also below in the parameter section. + +MASS 510 OW 15.999400 O ! HDRX OXYGEN +MASS 511 PX 30.974000 P ! TS PHOSPHOROUS +MASS 512 PC 30.974000 P ! CYCP PHOSPHOROUS +MASS 513 ONX 15.999400 O ! TS 2' OXYGEN +MASS 514 ONY 15.999400 O ! TS 5' OXYGEN +MASS 515 SO 32.064000 S ! mono-thio phosphate sulfur +MASS 516 SS1 32.064000 S ! di-thio phosphate sulfur +MASS 517 SX 32.064000 S ! phosphorane sulfur +MASS 518 ONS 15.999400 O ! mono-thio phosphate oxygen +MASS 519 ONC 15.999400 O ! DEPROTONATED OXYGEN +MASS 520 OX1 15.999400 O ! TS non-bridging OXYGEN +MASS 521 CN2D 12.011000 C ! for DAP? + +RESI TMPP -1.00 ! Modified for RNA from T3PM + +GROUP +ATOM O4' ON6 -0.50 ! +ATOM C1' CN7 0.07 ! +ATOM H11' HN7 0.09 ! +ATOM H12' HN7 0.09 ! H41' O4' H11' +ATOM C4' CN7 0.07 ! \ / \ / +ATOM H41' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM H42' HN7 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CN7 0.14 ! / \ +ATOM H21' HN7 0.09 ! O3' O2'--H22' +ATOM H22' HN5 0.43 ! | +ATOM O2' ON5 -0.66 ! O1P==P==O2P (-1) +GROUP ! | +ATOM C3' CN7 0.01 ! O3P +ATOM H31' HN7 0.09 ! \ +GROUP ! C3T--H3T3 +ATOM O3' ON2 -0.57 ! / \ +ATOM P P 1.50 ! H3T1 H3T2 +ATOM O1P ON3 -0.78 ! +ATOM O2P ON3 -0.78 ! +ATOM O3P ON2 -0.57 ! +ATOM C3T CN9 -0.17 ! +ATOM H3T1 HN9 0.09 ! +ATOM H3T2 HN9 0.09 ! +ATOM H3T3 HN9 0.09 ! + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P O2' H22' +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' H41' +DONO H22' O2' +ACCE O1P +ACCE O2P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O3P +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' O2' C2' C3' 1.7846 110.65 180.00 100.88 1.5211 +IC O2' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + + +RESI TMPD -2.00 ! + +GROUP +ATOM O4' ON6 -0.53 ! +ATOM C1' CN7 -0.12 ! +ATOM H11' HN7 0.09 ! +ATOM H12' HN7 0.09 ! H41' O4' H11' +ATOM C4' CN7 -0.11 ! \ / \ / +ATOM H41' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM H42' HN7 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CN7 0.23 ! / \ +ATOM H21' HN7 0.09 ! O3' O2' (-1) +ATOM O2' ONC -0.91 ! | +GROUP ! O1P==P==O2P +ATOM C3' CN7 0.18 ! | +ATOM H31' HN7 0.09 ! O3P (-1) +GROUP ! \ +ATOM O3' ON2 -0.63 ! C3T--H3T3 +ATOM P P 1.64 ! / \ +ATOM O1P ON3 -0.84 ! H3T1 H3T2 +ATOM O2P ON3 -0.84 ! +ATOM O3P ON2 -0.65 ! +ATOM C3T CN9 -0.23 ! +ATOM H3T1 HN9 0.09 ! +ATOM H3T2 HN9 0.09 ! +ATOM H3T3 HN9 0.09 ! +ACCE O1P +ACCE O2P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O3P +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' H41' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC O2' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + + +PRES DEPR -2.46 ! Patch to deprotonate 2'O in an RNA sugar +GROUP +ATOM 1O4' ON6B -0.53 ! +ATOM 1C1' CN7B -0.12 ! +ATOM 1C4' CN7 -0.11 ! +ATOM 1C2' CN7B 0.23 ! +ATOM 1O2' ONC -0.91 ! +ATOM 1C3' CN7 0.18 ! +ATOM 1O3' ON2 -0.63 ! +ATOM 2P P 1.64 ! +ATOM 2O1P ON3 -0.84 ! +ATOM 2O2P ON3 -0.84 ! +ATOM 2O5' ON2 -0.53 ! + +DELETE ATOM 1H2' + + +RESI PTS -2.00 ! phosphorane transition state residue +GROUP +ATOM O4' ON6 -0.51 ! H41' O4' H11' +ATOM C1' CN7 -0.02 ! \ / \ / +ATOM H11' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM H12' HN7 0.09 ! | | +ATOM C4' CN7 -0.13 ! H31'--C3'--C2'--H21' +ATOM H41' HN7 0.09 ! / \ +ATOM H42' HN7 0.09 ! O3' O2' +ATOM C2' CN7 0.10 ! \ / +ATOM H21' HN7 0.09 ! O1X--PX--O2X (-2) +ATOM O2' ONX -0.68 ! | +ATOM C3' CN7 0.10 ! O3X +ATOM H31' HN7 0.09 ! | +!GROUP ! C3T--H3T3 +ATOM O3' ON2 -0.62 ! / \ +ATOM PX PX 1.81 ! H3T1 H3T2 +ATOM O1X OX1 -0.915! +ATOM O2X OX1 -0.915! +ATOM O3X ONY -0.75 ! +ATOM C3T CN9 -0.28 ! +ATOM H3T1 HN9 0.09 ! +ATOM H3T2 HN9 0.09 ! +ATOM H3T3 HN9 0.09 ! + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' O2' C3' H31' C4' H41' +BOND O3' PX PX O1X PX O2X PX O3X O2' PX C4' H42' +BOND O3X C3T C3T H3T1 C3T H3T2 C3T H3T3 +IMPR PX O1X O2X O3' +ACCE O1X PX +ACCE O2X PX +IC C4' C3' O3' PX 1.5284 115.12 147.89 110.68 1.7500 +IC C1' C2' O2' PX 1.5284 115.12 -147.89 110.68 1.7500 +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC O2' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC PX O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC C3' O3' PX O1X 1.4212 108.00 105.00 109.74 1.4802 +IC C2' O2' PX O2X 1.4212 108.00 105.00 109.74 1.4802 +IC O3X PX O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3X PX O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3X PX 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3X PX 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3X PX 0.0 0.0 180.0 0.0 0.0 +!PATC FIRS NONE LAST NONE + + +PRES PXTS -2.46 ! Patch to create a phosphorane from phosphate backbone + ! +GROUP +ATOM 1O4' ON6B -0.51 ! +ATOM 1C1' CN7B -0.02 ! +ATOM 1C4' CN7 -0.13 ! +ATOM 1C2' CN7B 0.10 ! +ATOM 1O2' ONX -0.68 ! +ATOM 1C3' CN7 0.10 ! +ATOM 1O3' ON2 -0.62 ! +ATOM 1PX PX 1.81 ! +ATOM 1O1X OX1 -0.915! +ATOM 1O2X OX1 -0.915! +ATOM 2O5' ONY -0.68 ! + +DELETE ATOM 1H2' +DELETE ATOM 2P +DELETE ATOM 2O1P +DELETE ATOM 2O2P + +BOND 1O3' 1PX 1O2' 1PX 1PX 1O1X 1PX 1O2X +BOND 1PX 2O5' 1O2' 2O5' +ANGLE 1C3' 1O3' 1PX 1O3' 1PX 1O1X 1O1X 1PX 1O2X 1O2X 1PX 1O2' +ANGLE 1PX 1O2' 1C2' 1O3' 1PX 1O2X 1O2' 1PX 1O1X 1O2' 1PX 1O3' +ANGLE 2O5' 1PX 1O1X 2O5' 1PX 1O2X 2O5' 1PX 1O3' 1O2' 1PX 2O5' +ANGLE 2C5' 2O5' 1PX +DIHE 1C3' 1O3' 1PX 1O1X 1C3' 1O3' 1PX 1O2X 1C3' 1O3' 1PX 1O2' +DIHE 1C3' 1O3' 1PX 2O5' +DIHE 1C2' 1O2' 1PX 1O1X 1C2' 1O2' 1PX 1O2X 1C2' 1O2' 1PX 1O3' +DIHE 1C2' 1O2' 1PX 2O5' +DIHE 2C5' 2O5' 1PX 1O1X 2C5' 2O5' 1PX 1O2X 2C5' 2O5' 1PX 1O3' +DIHE 2C5' 2O5' 1PX 1O2' +DIHE 2O5' 1PX 1O2' 1C2' 2O5' 1PX 1O3' 1C3' +DIHE 1O2' 1PX 2O5' 2C5' 1O2' 1PX 1O3' 1C3' +DIHE 1C2' 1C3' 1O3' 1PX 1C3' 1C2' 1O2' 1PX +DIHE 1H3' 1C3' 1O3' 1PX 1H2'' 1C2' 1O2' 1PX +DIHE 1C4' 1C3' 1O3' 1PX 1C1' 1C2' 1O2' 1PX +IMPR 1PX 1O1X 1O2X 1O3' +ACCE 1O1X 1PX +ACCE 1O2X 1PX +BILD 1C3' 1O3' 1PX 1O1X 1.3890 117.50 63.50 115.30 1.5210 +BILD 1C2' 1O2' 1PX 1O2X 1.3610 109.30 157.70 91.40 1.5210 +BILD 1C4' 1C3' 1O3' 1PX 1.5374 113.06 123.61 117.49 1.7859 +BILD 1C1' 1C2' 1O2' 1PX 1.5534 113.51 -151.84 109.33 1.9860 + + +RESI CCC -1.00 ! +GROUP ! +ATOM C4' CN7 0.00 ! H4' O4' H1' +ATOM H41' HN7 0.09 ! \ / \ / +ATOM H42' HN7 0.09 ! H4''--C4' C1'--H1'' +ATOM O4' ON6 -0.50 ! | | +ATOM C1' CN7 0.00 ! H3'--C3'--C2'--H2' +ATOM H11' HN7 0.09 ! / \ +ATOM H12' HN7 0.09 ! O3' O2' +GROUP ! \ / +ATOM C2' CN7 0.20 ! PC +ATOM H21' HN7 0.09 ! / \ +ATOM O2' ON2 -0.61 ! O1C O2C(1-) +ATOM C3' CN7 0.20 +ATOM H31' HN7 0.09 +ATOM O3' ON2 -0.61 +ATOM PC PC 1.40 +ATOM O1C ON3 -0.81 +ATOM O2C ON3 -0.81 +BOND C4' O4' O4' C1' +BOND C4' C3' C1' C2' C2' C3' +BOND C3' O3' O3' PC PC O1C +BOND C2' O2' O2' PC PC O2C +BOND C1' H11' C2' H21' C3' H31' C4' H41' +BOND C1' H12' C4' H42' +ACCE O1C PC +ACCE O2C PC +ACCE O2' +ACCE O3' +ACCE O4' + +BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 +BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +BILD H21' C2' O2' PC 1.1200 107.73 -134.70 110.68 1.7500 +BILD H31' C3' O3' PC 1.1200 107.73 134.70 110.68 1.7500 +BILD O4' C2' *C1' H11' 0.0 0.0 -115.0 0.0 0.0 +BILD C2' C4' *C3' H31' 0.0 0.0 115.0 0.0 0.0 +BILD C3' O4' *C4' H41' 0.0 0.0 -115.0 0.0 0.0 +BILD C3' C1' *C2' H31' 0.0 0.0 -115.0 0.0 0.0 +BILD C3' O3' PC O1C 1.4212 108.00 105.00 109.74 1.4802 +BILD C2' O2' PC O2C 1.4212 108.00 105.00 109.74 1.4802 +BILD C4' C3' O3' PC 1.5284 115.12 147.89 110.68 1.7500 +BILD C1' C2' O2' PC 1.5284 115.12 -147.89 110.68 1.7500 + + +PRES CYCP -1.18 !Patch to create 2',3'-cyclic phosphate from RNA sugar + ! H5' H5'' +GROUP ! \ / +ATOM 1O2' ON2 -0.61 ! -O5'-C5' O4' base +ATOM 1C3' CN7 0.20 ! \ / \ / +ATOM 1O3' ON2 -0.61 ! H4'--C4' C1'--H1' +ATOM 1PC PC 1.40 ! | | +ATOM 1O1C ON3 -0.81 ! H3'--C3'--C2'--H2'' H5' +ATOM 1O2C ON3 -0.81 ! / \ | +ATOM 1C2' CN7B 0.20 ! O3' O2' + -C5'-O5'-H5T (1-) +GROUP ! \ / | +ATOM 2H5T HN5 0.43 ! PC H5'' +ATOM 2O5' ON5 -0.67 ! // \ +ATOM 2C5' CN8B -0.08 ! O1C O2C(1-) +ATOM 2H5' HN8 0.09 ! +ATOM 2H5'' HN8 0.09 ! + +DELETE ATOM 1H2' +DELETE ATOM 2P +DELETE ATOM 2O1P +DELETE ATOM 2O2P + +BOND 1O3' 1PC 1O2' 1PC 1PC 1O1C 1PC 1O2C +BOND 2H5T 2O5' +ANGLE 1C3' 1O3' 1PC 1O3' 1PC 1O1C 1O1C 1PC 1O2C 1O2C 1PC 1O2' +ANGLE 1PC 1O2' 1C2' 1O3' 1PC 1O2C 1O2' 1PC 1O1C 1O2' 1PC 1O3' +ANGLE 2H5T 2O5' 2C5' +DIHE 1C3' 1O3' 1PC 1O1C 1C3' 1O3' 1PC 1O2C 1C3' 1O3' 1PC 1O2' +DIHE 1C2' 1O2' 1PC 1O1C 1C2' 1O2' 1PC 1O2C 1C2' 1O2' 1PC 1O3' +DIHE 1C2' 1C3' 1O3' 1PC 1C3' 1C2' 1O2' 1PC +DIHE 1H3' 1C3' 1O3' 1PC 1H2'' 1C2' 1O2' 1PC +DIHE 1C4' 1C3' 1O3' 1PC 1C1' 1C2' 1O2' 1PC +ACCE 1O1C 1PC +ACCE 1O2C 1PC +DONO 2H5T 2O5' +BILD 1C3' 1O3' 1PC 1O1C 1.4212 108.00 105.00 109.74 1.4802 +BILD 1C2' 1O2' 1PC 1O2C 1.4212 108.00 105.00 109.74 1.4802 +BILD 1C4' 1C3' 1O3' 1PC 1.5284 115.12 147.89 110.68 1.7500 +BILD 1C1' 1C2' 1O2' 1PC 1.5284 115.12 -147.89 110.68 1.7500 +BILD 2H5T 2O5' 2C5' 2C4' 0.0000 0.00 180.00 0.00 0.0000 + + +PRES DMPR -1.54 ! thio substitution of DMPA +GROUP + +ATOM C1 CN9 -0.20 ! +ATOM O1 ON2 -0.49 ! +ATOM P1 P 1.41 ! +ATOM S1 SO -0.80 ! +ATOM O3 ONS -0.80 ! +ATOM O2 ON2 -0.54 ! +ATOM C2 CN9 -0.12 ! + +DELETE ATOM O4 + +BOND P1 S1 +ANGLE S1 P1 O1 S1 P1 O3 S1 P1 O2 +DIHE S1 P1 O1 C1 S1 P1 O2 C2 +ACCE S1 +BILD S1 P1 O1 C1 2.0 109.6 69.0 120.0 1.5 + +PRES DMPD -1.54 ! di-thio substitution of DMPA +GROUP + +ATOM C1 CN9 -0.14 ! +ATOM O1 ON2 -0.48 ! +ATOM P1 P 1.30 ! +ATOM S1 SS1 -0.80 ! +ATOM S2 SS1 -0.80 ! +ATOM O2 ON2 -0.48 ! +ATOM C2 CN9 -0.14 ! + +DELETE ATOM O4 +DELETE ATOM O3 + +BOND P1 S2 P1 S1 +ANGLE S2 P1 S1 S1 P1 O1 S2 P1 O1 S1 P1 O2 S2 P1 O2 +DIHE S1 P1 O1 C1 S1 P1 O2 C2 S2 P1 O1 C1 S2 P1 O2 C2 +ACCE S2 +ACCE S1 +BILD S2 P1 O1 C1 0.0 109.0 180.0 0.0 0.0 +BILD S1 P1 O1 C1 0.0 109.0 0.0 0.0 0.0 + + +PRES PROR -1.27 ! O2P thio substitution of DNA/RNA phosphate +GROUP + +ATOM 1C3' CN7 -0.065! +ATOM 1O3' ON2 -0.49 ! +ATOM 2P P 1.41 ! +ATOM 2O1P ONS -0.80 ! +ATOM 2S2 SO -0.80 ! +ATOM 2O5' ON2 -0.54 ! +ATOM 2C5' CN8B 0.015! + +DELETE ATOM 2O2P + +BOND 2P 2S2 +ANGLE 2S2 2P 2O5' 1O3' 2P 2S2 2S2 2P 2O1P +DIHE 2S2 2P 2O5' 2C5' 2S2 2P 1O3' 1C3' +ACCE 2S2 +BILD 2S2 2P 2O5' 2C5' 0.0 109.0 120.0 0.0 0.0 + +PRES PROS -1.27 ! O1P thio substitution of DNA/RNA phosphate +GROUP + +ATOM 1C3' CN7 -0.065! +ATOM 1O3' ON2 -0.54 ! +ATOM 2P P 1.41 ! +ATOM 2O2P ONS -0.80 ! +ATOM 2S1 SO -0.80 ! +ATOM 2O5' ON2 -0.49 ! +ATOM 2C5' CN8B 0.015! + +DELETE ATOM 2O1P + +BOND 2P 2S1 +ANGLE 2S1 2P 2O5' 1O3' 2P 2S1 2S1 2P 2O2P +DIHE 2S1 2P 2O5' 2C5' 2S1 2P 1O3' 1C3' +ACCE 2S1 +BILD 2S1 2P 2O5' 2C5' 0.0 109.0 120.0 0.0 0.0 + + +PRES PROD -1.27 ! Di-thio substitution of DNA/RNA phosphate +GROUP + +ATOM 1C3' CN7 -0.005! +ATOM 1O3' ON2 -0.48 ! +ATOM 2P P 1.30 ! +ATOM 2S1 SS1 -0.80 ! +ATOM 2S2 SS1 -0.80 ! +ATOM 2O5' ON2 -0.48 ! +ATOM 2C5' CN8B -0.005! + +DELETE ATOM 2O1P +DELETE ATOM 2O2P + +BOND 2P 2S1 +BOND 2P 2S2 +ANGLE 2S1 2P 2O5' 1O3' 2P 2S1 +ANGLE 2S2 2P 2O5' 1O3' 2P 2S2 2S1 2P 2S2 +DIHE 2S1 2P 2O5' 2C5' 2S1 2P 1O3' 1C3' +DIHE 2S2 2P 2O5' 2C5' 2S2 2P 1O3' 1C3' +ACCE 2S1 +ACCE 2S2 +BILD 2S1 2P 2O5' 2C5' 0.0 109.0 120.0 0.0 0.0 +BILD 2S2 2P 2O5' 2C5' 0.0 109.0 0.0 0.0 0.0 + + +PRES PTSR -2.81 ! O2P thio substitution of PTS phosphorane +GROUP + +ATOM O4' ON6 -0.51 ! +ATOM C4' CN7 -0.10 ! +ATOM C1' CN7 0.02 ! +ATOM C3' CN7 0.06 ! +ATOM O3' ON2 -0.59 ! +ATOM C2' CN7 0.09 ! +ATOM O2' ONX -0.63 ! +ATOM PX PX 1.73 ! +ATOM O1X OX1 -0.935! +ATOM S2X SX -0.955! +ATOM O3X ONY -0.72 ! +ATOM C3T CN9 -0.27 ! + +DELETE ATOM O2X + +BOND PX S2X +ANGLE S2X PX O3X O3' PX S2X S2X PX O1X S2X PX O2' +DIHE S2X PX O3X C3T S2X PX O3' C3' S2X PX O2' C2' +IMPR PX O1X S2X O3' +ACCE S2X +BILD S2X PX O3X C3T 0.0 95.4 54.4 0.0 0.0 + + +PRES PTSS -2.81 ! O1P thio substitution of PTS phosphorane +GROUP + +ATOM O4' ON6 -0.51 ! +ATOM C4' CN7 -0.10 ! +ATOM C1' CN7 0.02 ! +ATOM C3' CN7 0.06 ! +ATOM O3' ON2 -0.59 ! +ATOM C2' CN7 0.09 ! +ATOM O2' ONX -0.63 ! +ATOM PX PX 1.73 ! +ATOM O2X OX1 -0.935! +ATOM S1X SX -0.955! +ATOM O3X ONY -0.72 ! +ATOM C3T CN9 -0.27 ! + +DELETE ATOM O1X + +BOND PX S1X +ANGLE S1X PX O3X O3' PX S1X S1X PX O1X S1X PX O2' +DIHE S1X PX O3X C3T S1X PX O3' C3' S1X PX O2' C2' +IMPR PX S1X O2X O3' +ACCE S1X +BILD S1X PX O3TX C3T 0.0 94.5 -179.8 0.0 0.0 + + +PRES PTSD -2.81 ! Di-thio substitution of PTS phosphorane +GROUP + +ATOM O4' ON6 -0.54 ! +ATOM C4' CN7 -0.05 ! +ATOM C1' CN7 0.05 ! +ATOM C3' CN7 -0.01 ! +ATOM O3' ON2 -0.53 ! +ATOM C2' CN7 0.09 ! +ATOM O2' ONX -0.58 ! +ATOM PX PX 1.51 ! +ATOM S1X SX -0.915! +ATOM S2X SX -0.915! +ATOM O3X ONY -0.68 ! +ATOM C3T CN9 -0.24 ! + +DELETE ATOM O1X +DELETE ATOM O2X + +BOND PX S1X +BOND PX S2X +ANGLE S1X PX O3X O3' PX S1X S1X PX O2' +ANGLE S2X PX O3X O3' PX S2X S2X PX O2' S1X PX S2X +DIHE S1X PX O3X C3T S1X PX O3' C3' S1X PX O2' C2' +DIHE S2X PX O3X C3T S2X PX O3' C3' S2X PX O2' C2' +IMPR PX S1X S2X O3' +ACCE S1X +ACCE S2X +BILD S2X PX O3X C3T 0.0 94.5 54.4 0.0 0.0 +BILD S1X PX O3X C3T 0.0 94.5 -179.8 0.0 0.0 + + +PRES PXR -2.54 ! O2P thio substitution of RNA phosphorane +GROUP ! must be used after the PXTS patch +ATOM 1O4' ON6B -0.51 ! +ATOM 1C4' CN7 -0.10 ! +ATOM 1C1' CN7B 0.02 ! +ATOM 1C2' CN7B 0.09 ! +ATOM 1O2' ONX -0.63 ! +ATOM 1C3' CN7 0.06 ! +ATOM 1O3' ON2 -0.59 ! +GROUP +ATOM 1PX PX 1.73 ! +ATOM 1O1X OX1 -0.935! +ATOM 1S2X SX -0.955! +ATOM 2O5' ONY -0.72 ! +ATOM 2C5' CN8B -0.00 ! + +DELETE ATOM 1O2X + +BOND 1PX 1S2X +ANGLE 1S2X 1PX 2O5' 1O3' 1PX 1S2X 1S2X 1PX 1O1X 1S2X 1PX 1O2' +DIHE 1S2X 1PX 2O5' 2C5' 1S2X 1PX 1O3' 1C3' 1S2X 1PX 1O2' 1C2' +IMPR 1PX 1O1X 1S2X 1O3' +ACCE 1S2X +BILD 1S2X 1PX 2O5' 1C5' 0.0 94.5 40.0 0.0 0.0 + +PRES PXS -2.54 ! O1P thio substitution of RNA phosphorane +GROUP ! must be used after the PXTS patch +ATOM 1O4' ON6B -0.51 ! +ATOM 1C4' CN7 -0.10 ! +ATOM 1C1' CN7B 0.02 ! +ATOM 1C2' CN7B 0.09 ! +ATOM 1O2' ONX -0.63 ! +ATOM 1C3' CN7 0.06 ! +ATOM 1O3' ON2 -0.59 ! +GROUP +ATOM 1PX PX 1.73 ! +ATOM 1O2X OX1 -0.935! +ATOM 1S1X SX -0.955! +ATOM 2O5' ONY -0.72 ! +ATOM 2C5' CN8B -0.00 ! + +DELETE ATOM 1O1X + +BOND 1PX 1S1X +ANGLE 1S1X 1PX 2O5' 1O3' 1PX 1S1X 1S1X 1PX 1O2X 1S1X 1PX 1O2' +DIHE 1S1X 1PX 2O5' 2C5' 1S1X 1PX 1O3' 1C3' 1S1X 1PX 1O2' 1C2' +IMPR 1PX 1S1X 1O2X 1O3' +ACCE 1S1X +BILD 1S1X 1PX 2O5' 1C5' 0.0 94.5 100.0 0.0 0.0 + +PRES PXD -2.54 ! Di-thio substitution of RNA phosphorane +GROUP ! must be used after the PXTS patch +ATOM 1O4' ON6B -0.54 ! +ATOM 1C4' CN7 -0.05 ! +ATOM 1C1' CN7B 0.05 ! +ATOM 1C2' CN7B 0.09 ! +ATOM 1O2' ONX -0.58 ! +ATOM 1C3' CN7 0.01 ! +ATOM 1O3' ON2 -0.53 ! +GROUP +ATOM 1PX PX 1.51 ! +ATOM 1S1X SX -0.915! +ATOM 1S2X SX -0.915! +ATOM 2O5' ONY -0.68 ! +ATOM 2C5' CN8B 0.01 ! + +DELETE ATOM 1O1X +DELETE ATOM 1O2X + +BOND 1PX 1S1X +BOND 1PX 1S2X +ANGLE 1S1X 1PX 2O5' 1O3' 1PX 1S1X 1S1X 1PX 1O2' +ANGLE 1S2X 1PX 2O5' 1O3' 1PX 1S2X 1S2X 1PX 1O2' 1S1X 1PX 1S2X +DIHE 1S1X 1PX 2O5' 2C5' 1S1X 1PX 1O3' 1C3' 1S1X 1PX 1O2' 1C2' +DIHE 1S2X 1PX 2O5' 2C5' 1S2X 1PX 1O3' 1C3' 1S2X 1PX 1O2' 1C2' +IMPR 1PX 1S1X 1S2X 1O3' +ACCE 1S1X +ACCE 1S2X +BILD 1S1X 1PX 2O5' 1C5' 0.0 94.5 40.0 0.0 0.0 +BILD 1S2X 1PX 2O5' 1C5' 0.0 94.0 100.0 0.0 0.0 + +end + +read para card flex append +* reactive RNA parameters +* + +!>>>>>>>>>>>>>>> Additional Parameter File for <<<<<<<<<<<<<<<<< +!>>>>>>>>>>>>>>>>>>>>>> RNA Catalysis <<<<<<<<<<<<<<<<<<<<<<<<<< +!>>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<< +!>>>>>>>>>>>>>>>>>>>>>>> Sept 2005 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< +!>>>>>>>>>>>>>>>>>>>>>Evelyn A. Mayaan <<<<<<<<<<<<<<<<<<<<<<<<< +!>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +ATOM +MASS 510 OW 15.999400 ! HDRX OXYGEN +MASS 511 PX 30.974000 ! TS PHOSPHOROUS +MASS 512 PC 30.974000 ! CYCP PHOSPHOROUS +MASS 513 ONX 15.999400 ! TS 2' OXYGEN +MASS 514 ONY 15.999400 ! TS 5' OXYGEN +MASS 515 SO 32.064000 ! mono-thio phosphate sulfur +MASS 516 SS1 32.064000 ! di-thio phosphate sulfur +MASS 517 SX 32.064000 ! phosphorane sulfur +MASS 518 ONS 15.999400 ! mono-thio phosphate oxygen +MASS 519 ONC 15.999400 ! DEPROTONATED OXYGEN +MASS 520 OX1 15.999400 ! TS non-bridging OXYGEN +MASS 521 CN2D 12.011000 ! for DAP? + +BONDS +! For HDRX +HT OW 663.2 0.9575 ! + +! For DEPR/TMPD +CN7B ONC 488.0 1.310 ! +CN7 ONC 488.0 1.320 ! + +!For PTS +CN7 ONX 387.2 1.3475 ! +CN9 ONY 398.3 1.364 ! + +! For PXTS/PTS +ON2 PX 183.9 1.81 ! +! Early TS +!ONX PX 142.9 2.01 ! +!ONY PX 130.1 1.85 ! +! late TS +ONX PX 130.1 1.856 ! +ONY PX 142.9 2.382 ! +OX1 PX 637.9 1.53 ! +ONX ONY 77.3 3.75 ! + +! For PXTS +CN7B ONX 387.2 1.342 ! +CN8B ONY 320.0 1.44 !From ON2 CN8B + +!For CCC/CYCP +ON2 PC 229.5 1.71 ! +ON3 PC 720.0 1.51 ! + +! For PROR/PROS/DMPR/DMPD +ONS P 578.0 1.4770 ! +SO P 260.4 1.9953 ! +SS1 P 258.9 1.9953 ! + +! For PTSR/PTSS +SX PX 225.1 2.11 ! + +! for DAP +CN2D NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91 +CN2D NN3A 400.0 1.342 !A, adm jr. 11/97 + +!for TAP +HN3 CN2 500.0 1.090 + +!=============================================== + +ANGLES + +! For DEPR/TMPD +HN7 CN7B ONC 73.6 125.0 ! +HN7 CN7 ONC 73.6 121.3 ! +ONC CN7B CN7B 91.2 120.2 ! +ONC CN7B CN7 82.4 116.7 ! +ONC CN7 CN7 86.8 118.45 ! + +! For PTS +HN9 CN9 ONY 66.2 111.5 ! +HN7 CN7 ONX 70.6 111.6 ! +CN7 ON6 CN7 99.0 113.1 ! +CN7 ONX PX 73.6 107.2 ! +CN9 ONY PX 63.3 105.9 ! +CN7 CN7 ONX 95.6 106.1 ! + +! For PTS/PXTS +CN7 ON2 PX 107.4 121.6 ! + +OX1 PX OX1 251.5 127.4 ! +ON2 PX ONX 219.2 82.0 ! +ON2 PX ONY 136.8 85.2 ! + +ON2 PX OX1 55.9 115.0 ! +ONX PX OX1 89.8 89.3 ! +ONY PX OX1 70.0 97.6 ! + +ONY PX ONX 61.8 159.4 ! + +! For PXTS +HN7 CN7B ONX 70.6 114.9 ! +HN8 CN8B ONY 60.0 109.5 !From HN8 CN8B ON2 + +CN7B CN7B ONX 95.6 110.4 ! +CN7 CN7B ONX 119.2 104.8 ! +CN7B ONX PX 73.6 107.0 ! +CN8B ONY PX 20.0 120.0 35.00 2.33 !From CN8B ON2 P +CN7 CN8B ONY 70.0 109.7 !From CN7 CN8B ON2 + +!For CYCP +CN7B ON2 PC 70.6 120.0 ! +CN7 ON2 PC 70.6 112.85 ! +ON2 PC ON2 194.2 90.1 ! +ON2 PC ON3 91.2 111.7 ! +ON3 PC ON3 100.1 124.6 ! + +!For CCC +CN7 CN7 CN7 60.0 100.0 !From CN7B CN7 CN7 + +! For DMPR/DMPS/DMPD/PROR/PROS/PROD +ON3 P SO 75.0 131.03 ! +ONS P SO 75.0 131.03 ! +ON2 P SO 96.8 112.84 ! +ON2 P SS1 96.8 112.84 ! +ON2 P ONS 96.8 112.84 ! +SS1 P SS1 92.4 128.47 ! + +! For PTSR/PTSS +OX1 PX SX 35.8 113.4 ! +ON2 PX SX 43.4 105.3 ! +ONX PX SX 99.2 87.7 ! +ONY PX SX 82.9 97.5 ! + +SX PX SX 35.8 110.0 ! + +! For DAP +CN2 NN3A CN2D 90.0 117.8 !6R) adm jr. 11/97 +NN3A CN2D NN3A 60.0 133.0 !6R) +CN2D NN3A CN5 90.0 110.1 !6R) +CN2D NN1 HN1 40.0 121.5 !h61,h62, C,A,G +NN3A CN2D NN1 50.0 130.7 !n6 + +!For TAP +NN3A CN2 HN3 50.0 120.0 +CN5 CN2 HN3 50.0 120.0 + +!============================================ + +DIHEDRALS + +! For DEPR/TMPD +ONC CN7 CN7 CN7 0.6 6 0.0 !From ON2 CN7 CN7B CN7B +ONC CN7 CN7 CN7 0.0 5 0.0 ! +ONC CN7 CN7 CN7 1.6 3 180.0 ! +! +ONC CN7 CN7 ON6 0.5 6 0.0 !From ON2 CN7 CN7 ON6 +ONC CN7 CN7 ON6 0.3 5 0.0 ! +ONC CN7 CN7 ON6 0.6 4 180.0 ! +ONC CN7 CN7 ON6 0.2 3 0.0 ! +! +HN7 CN7 CN7B ONC 0.195 3 0.0 !From HN7 CN7 CN7B ON2 +HN7 CN7 CN7 ONC 0.195 3 0.0 ! +ONC CN7B CN7B HN7 0.000 3 0.0 ! +ON6B CN7B CN7B ONC 0.000 3 0.0 ! +NN2 CN7B CN7B ONC 0.000 3 0.0 ! +NN2B CN7B CN7B ONC 0.000 3 0.0 ! +ONC CN7B CN7 ON2 0.000 3 0.0 ! +ONC CN7 CN7 ON2 0.000 3 0.0 ! +CN7 CN7 CN7B ONC 0.000 3 0.0 ! + +! For CYCP sugar +ON2 CN7 CN7B ON2 0.0 3 0.0 ! +!CYCP phosphate +ON2 PC ON2 CN7 0.0 6 180.0 ! +! +ON2 PC ON2 CN7B 0.0 3 180.0 ! +! +CN7B CN7B ON2 PC 0.6 5 0.0 !From CN7 CN7 ON2 P +CN7B CN7B ON2 PC 0.2 4 0.0 ! +CN7B CN7B ON2 PC 0.4 2 0.0 ! +CN7B CN7B ON2 PC 1.9 1 180.0 ! +! +CN7B CN7 ON2 PC 0.0 6 180.0 ! +! +PC ON2 CN7 HN7 0.000 3 0.0 !From P ON2 CN7 HN7 +PC ON2 CN7B HN7 0.000 3 0.0 !From P ON2 CN7 HN7 +ON3 PC ON2 CN7 0.0 3 0.0 ! +ON3 PC ON2 CN7B 0.0 3 0.0 ! +CN7 CN7 ON2 PC 2.5 1 180.0 !From CN7B CN7 ON2 P +CN7 CN7B ON2 PC 2.5 1 180.0 !From CN7B CN7 ON2 P + +! For CCC sugar +ON2 CN7 CN7 ON2 0.0 3 0.0 !From ON5 CN7 CN7B ON2? + +!PXTS +!base terms +ONX CN7B CN7B NN2 0.0 3 0.0 ! +ONX CN7B CN7B NN2B 0.0 3 0.0 ! +!sugar terms +HN7 CN7 CN7B ONX 0.195 3 0.0 !From HN7 CN7 CN7B ON2 +HN7 CN7B CN7B ONX 0.195 3 0.0 !From HN7 CN7 CN7 ON2 +HN7 CN7 CN8B ONY 0.195 3 0.0 !From HN7 CN7 CN8B ON2 +! +ON6B CN7 CN8B ONY 3.4 1 180.0 !From ON6B CN7 CN8B ON2 + +ONX CN7B CN7B ON6B 0.4 6 0.0 !From ON2 CN7 CN7 ON6B +ONX CN7B CN7B ON6B 0.0 5 0.0 ! +ONX CN7B CN7B ON6B 0.0 4 180.0 ! +ONX CN7B CN7B ON6B 1.6 3 0.0 ! +! +ONX CN7B CN7 CN7 0.6 6 0.0 !From ON2 CN7 CN7B CN7B +ONX CN7B CN7 CN7 0.0 5 0.0 ! +ONX CN7B CN7 CN7 1.6 3 180.0 ! +! +CN7 CN7 CN8B ONY 0.2 4 180.0 !From CN7 CN7 CN8B ON +CN7 CN7 CN8B ONY 0.8 3 180.0 ! +CN7 CN7 CN8B ONY 0.4 2 0.0 ! +CN7 CN7 CN8B ONY 2.5 1 180.0 ! +! +ONX CN7B CN7 ON2 0.0 3 0.0 ! +! +!phosphorane terms +PX ONY CN8B HN8 0.000 3 0.0 !From P ON2 CN8B HN8 +PX ON2 CN7 HN7 0.000 3 0.0 !From P ON2 CN7 HN7 +PX ONX CN7B HN7 0.000 3 0.0 !From P ON2 CN7B HN7 +! +CN7 CN7 ON2 PX 0.6 5 0.0 !From CN7 CN7 ON2 P +CN7 CN7 ON2 PX 0.2 4 0.0 ! +CN7 CN7 ON2 PX 0.4 2 0.0 ! +CN7 CN7 ON2 PX 1.9 1 180.0 ! +! +CN7B CN7B ONX PX 0.6 5 0.0 !From CN7 CN7 ON2 P +CN7B CN7B ONX PX 0.2 4 0.0 ! +CN7B CN7B ONX PX 0.4 2 0.0 ! +CN7B CN7B ONX PX 1.9 1 180.0 ! +! +CN7 CN7 ONX PX 0.6 5 0.0 !From CN7 CN7 ON2 P +CN7 CN7 ONX PX 0.2 4 0.0 ! +CN7 CN7 ONX PX 0.4 2 0.0 ! +CN7 CN7 ONX PX 1.9 1 180.0 ! +! +CN7B CN7 ON2 PX 2.5 1 180.0 !From CN7B CN7 ON2 P +CN7 CN7B ONX PX 2.5 1 180.0 !From CN7B CN7 ON2 P +! +CN7 CN8B ONY PX 0.2 1 120.0 !From CN7 CN8B ON2 P +! +ON2 PX ONX CN7B 1.20 1 180.0 !From ON2 P ON2 CN7 +ON2 PX ONX CN7B 0.10 2 180.0 ! +ON2 PX ONX CN7B 0.10 3 180.0 ! +ON2 PX ONX CN7B 0.00 6 0.0 ! +! +ONY PX ONX CN7B 1.20 1 180.0 !From ON2 P ON2 CN7 +ONY PX ONX CN7B 0.10 2 180.0 ! +ONY PX ONX CN7B 0.10 3 180.0 ! +ONY PX ONX CN7B 0.00 6 0.0 ! +! +!ON2 PX ONY CN8B 1.20 1 180.0 !From ON2 P ON2 CN8B +!ON2 PX ONY CN8B 0.10 2 180.0 ! +!ON2 PX ONY CN8B 0.10 3 180.0 ! +!ON2 PX ONY CN8B 0.00 6 0.0 ! +! +!OX1 PX ON2 CN7 0.10 3 0.0 !From ON3 P ON2 CN7 +!OX1 PX ONX CN7B 0.10 3 0.0 !From ON3 P ON2 CN7 +!OX1 PX ONY CN8B 0.10 3 0.0 !From ON3 P ON2 CN8B +! +ONX PX ONY CN8B 1.20 1 180.0 !From ON2 P ON2 CN8B +ONX PX ONY CN8B 0.10 2 180.0 ! +ONX PX ONY CN8B 0.10 3 180.0 ! +ONX PX ONY CN8B 0.00 6 0.0 ! +! +ONX PX ON2 CN7 1.20 1 0.0 ! +ONX PX ON2 CN7 0.10 2 0.0 ! +ONX PX ON2 CN7 0.10 3 0.0 ! +! +ONY PX ON2 CN7 1.20 1 180.0 !From ON2 P ON2 CN7 +ONY PX ON2 CN7 0.10 2 180.0 ! +ONY PX ON2 CN7 0.10 3 180.0 ! +ONY PX ON2 CN7 0.00 6 0.0 ! + + +!For PTS +HN7 CN7 CN7 ONX 0.195 3 0.0 !From HN7 CN7 CN7 ON2 +! +HN7 CN7 ON6 CN7 0.000 3 0.0 !From HN7 CN7B ON6 CN7 +! +CN7 CN7 ON6 CN7 0.0 6 180.0 !From CN7 CN7 ON6B CN7B +! +CN7 CN7 CN7 CN7 0.0 6 0.0 !From CN7B CN7B CN7 CN7 +! +PX ONX CN7 HN7 0.000 3 0.0 !From P ON2 CN7 HN7 +! +PX ONY CN9 HN9 0.000 3 0.0 !From P ON2 CN8B HN8 +! +!OX1 PX ONX CN7 0.10 3 0.0 !From ON3 P ON2 CN7 +!OX1 PX ONY CN9 0.10 3 0.0 !From ON3 P ON2 CN8B +! +ONY PX ONX CN7 1.20 1 180.0 !From ON2 P ON2 CN7 +ONY PX ONX CN7 0.10 2 180.0 ! +ONY PX ONX CN7 0.10 3 180.0 ! +ONY PX ONX CN7 0.00 6 0.0 ! +! +ONX CN7 CN7 ON2 0.0 3 0.0 ! +! +ON2 PX ONX CN7 1.20 1 180.0 !From ON2 P ON2 CN7 +ON2 PX ONX CN7 0.10 2 180.0 ! +ON2 PX ONX CN7 0.10 3 180.0 ! +ON2 PX ONX CN7 0.00 6 0.0 ! +! +ONX CN7 CN7 CN7 0.6 6 0.0 !From ON2 CN7 CN7B CN7B +ONX CN7 CN7 CN7 0.0 5 0.0 ! +ONX CN7 CN7 CN7 1.6 3 180.0 ! +! +ONX PX ONY CN9 1.20 1 180.0 !From ON2 P ON2 CN8B +ONX PX ONY CN9 0.10 2 180.0 ! +ONX PX ONY CN9 0.10 3 180.0 ! +ONX PX ONY CN9 0.00 6 0.0 ! +! +ON2 PX ONY CN9 1.20 1 180.0 !From ON2 P ON2 CN8B +ON2 PX ONY CN9 0.10 2 180.0 ! +ON2 PX ONY CN9 0.10 3 180.0 ! +ON2 PX ONY CN9 0.00 6 0.0 ! +! +ONX CN7 CN7 ON6 0.5 6 0.0 !From ON2 CN7 CN7 ON6 +ONX CN7 CN7 ON6 0.3 5 0.0 ! +ONX CN7 CN7 ON6 0.6 4 180.0 ! +ONX CN7 CN7 ON6 0.2 3 0.0 ! + +!For DMPR/DMPS/DMPD +CN9 ON2 P SO 0.40 1 0.0 ! +CN9 ON2 P SO 0.10 3 0.0 ! +! +CN9 ON2 P SS1 0.45 1 180.0 ! +CN9 ON2 P SS1 0.20 2 0.0 ! +CN9 ON2 P SS1 0.10 3 0.0 ! +! +CN9 ON2 P ONS 0.20 2 0.0 ! +CN9 ON2 P ONS 0.20 3 0.0 ! +!For PROR/PROS/PROD +CN8B ON2 P SO 0.40 1 0.0 ! +CN8B ON2 P SO 0.10 3 0.0 ! +! +CN8B ON2 P SS1 0.45 1 180.0 ! +CN8B ON2 P SS1 0.20 2 0.0 ! +CN8B ON2 P SS1 0.10 3 0.0 ! +! +CN8B ON2 P ONS 0.20 2 0.0 ! +CN8B ON2 P ONS 0.20 3 0.0 ! +! +CN7 ON2 P ONS 0.10 3 0.0 !From ON3 P ON2 CN7 +CN7 ON2 P SO 0.10 3 0.0 !From ON3 P ON2 CN7 +CN7 ON2 P SS1 0.10 3 0.0 !From ON3 P ON2 CN7 +! For PTSR/PTSS +CN9 ONY PX SX 0.10 3 0.0 ! +CN7 ONY PX SX 0.10 3 0.0 ! +CN7 ON2 PX SX 0.10 3 0.0 ! +SX PX ONX CN7 0.10 3 0.0 !From ON3 P ON2 CN7 +SX PX ONY CN8B 0.10 3 0.0 !From ON3 P ON2 CN8B +SX PX ONX CN7B 0.10 3 0.0 !From ON3 P ON2 CN7 +!DAP +NN1 NN3A NN3A CN2D 8.5 2 180.0 ! +CN2 NN3A CN2D NN3A 1.8 2 180.0 ! adm jr. 11/97, 6-mem +NN3A CN2D NN3A CN5 2.0 2 180.0 ! +CN2D NN3A CN5 CN5 1.8 2 180.0 ! +CN5 CN2 NN3A CN2D 10.0 2 180.0 ! +CN5 CN5 NN4 CN2D 6.0 2 180.0 ! 5-mem +CN2D NN2 CN5 CN5 6.0 2 180.0 ! +CN2 NN3A CN2D NN1 8.5 2 180.0 ! H2 +CN5 NN3A CN2D NN1 8.5 2 180.0 ! H2 +NN3A CN2D NN1 HN1 2.0 2 180.0 ! + +!================================================================ + +IMPROPER +PX OX1 OX1 ON2 80.0 0 0.0000 ! Keep non-bridging O's planar +PX OX1 SX ON2 80.0 0 0.0000 ! Keep non-bridging S/O's planar +PX SX OX1 ON2 80.0 0 0.0000 ! Keep non-bridging S/O's planar +PX SX SX ON2 80.0 0 0.0000 ! Keep non-bridging S's planar +!DAP +NN3A CN2D NN3A CN2 80.0 0 0.000 +NN3A CN2D NN3A CN5 80.0 0 0.000 +CN5 CN2 NN3A CN2D 80.0 0 0.000 + +NONBONDED +!MG 0.0 -0.0140 1.4647 ! +OW 0.0 -0.2385 1.7513 ! +PC 0.0 -0.585 2.15 ! +PX 0.0 -0.585 2.15 ! +ONC 0.0 -0.3236 1.7513 ! +ONS 0.0 -0.1423 1.6796 ! +ONX 0.0 -0.2378 1.76 ! +ONY 0.0 -0.2378 1.76 ! +SO 0.0 -0.6308 2.0937 ! +SS1 0.0 -0.6199 2.0546 ! +SX 0.0 -0.6540 2.2872 ! +OX1 0.0 -0.1407 1.7430 ! +CN2D 0.0 -0.10 1.9000 + +NBFIX +MG SO -0.2063 2.8213 +MG SS1 -0.2011 2.8308 + +END + +return + diff --git a/charmm/toppar/stream/prot/.toppar_all36_prot_na_combined.str.swp b/charmm/toppar/stream/prot/.toppar_all36_prot_na_combined.str.swp new file mode 100644 index 0000000000000000000000000000000000000000..d895c2fd5d1171d216d4b3a7cef115c00530abdc GIT binary patch literal 16384 zcmeHOTZ|(|6)j#_1`>iu6y*!9iNww27B;s|b)lNJJokB0hM05RgF12SNz=;tNCqio{O@A4sr2D9cL_5?%=j%emFne(mHT zBqXGCOQ)y1?yXz5PTeYZ-R{}XoT)cxUCRj^?-t^hCmucXi(mgxlpYhp4=m5=>MVKH zW8hz~^?YIdRh1z8s4|%Ly>7bHH;+ssNV_A;84lAu>%qWv2Y&j%^}5!9Z4G*Uy4yEB z$kd;}9gR#c?FXJ^4$~vg4boxJo;eug*7mq$&oTG9?r`6BteytV*K#SA#|*rI7`Q>? zvU-L)eB1jIbkloIzk&K5cQs}pW*}xDW*}xDW*}xDW*}xDW*`{dEItMr-mIuF)!#QQ z{JpA{6!^yK*`gp zLy`R#lzdOgzq%m*r;@jo{OW@IA4(qWm_G8BP%*OqcO}1D)&ItV{BKGg@pE-S{#PY$ zsru*MI&c4ZC6D}jd_n%4lJBbeFD=ObqU0Y|@}0NM+kaNc?^W_g7UX|c@`jRMS&;up z$s_;s*Uj5k-4(a0`kz>ktK#@i%s|XQ%s|XQ%s|XQ%s|XQ%s|XQ%s|Y*|A+w-8|ss= z{UmQ>@&4ab?fm#gAwCV91x^DU;ATJoe|#6d699e!8~_$@4%h?=z>7Bs@dEH$;2GfS zz&YS1;Ahw49{3vYS)dD;z&YR^;L1CN_zLi4zy|t22Ke1Og!nda5qJ<70-L~%z~v<& zz7Ko~I1i+OTY#6}F2rwur-1JOUj#l5Yyr0d&z?XZfX9GKfB__d>w!ODfBJjiali-e z0X_g+2Rwtl@ArUD0tRp!a25OQr-5$*mw*O9!1LJnJ^_3Q7y?_sEx;Az7k&VI4(I^| z;0EA%jKgyPkH-_h>pa>OqfVV#qfX(G(J~oaB`D}0q`LiF${yN1^O8HTgxD>1N<`Iq z+n{EvS)rYx(UDi8UZSODB}+@Ca(1b-O-nTZrih`hZ)o{dd5K%-E|n@et4r-#8P%q$ z1#KfYqY6vVozb7s-NmF018cb-{3s4d*5mW(=>d%^PNAwtSqjzPhRv3iB>!+49u-jO9#T%gobO z%d+L;lsB^4>Y~p&D^4rSSYF%Ea`VwPYZGiwb#pl_SC}Vb#wHUuqnpiZh3uqz39`Es znEL~Z@Zk~97JHba1J4~&)9$(h)87>J#%`MsheVhbLL zoDsr5(w71*3k_9tRe^1X#$*M)l}Fepmq{rmT38`$Q@X__(PLF16v#3u)lZ59-C3#Z z8dSTx+-_}Gng-RI)UG$TX?LgCtca~vvrL$F%F(bVkwfT`l+W0m_Cfk3H6wNQ5~|83 zxF-%{;!(g=_M{T9yEP0yAy#mOsEMw)EXQSt(dcTf8V`QhUs*RiaSd5bHY86|J@!W^ zdKUg9!h5E**l9IL4p+0y?5E^>R0{NPD3>EyYs=xxXnGE7tUSP3DwRU*P)(9q+O4sj zjFw%E)Xs<6ku}L_Q(8l7nLN~L+bKEFQZZ_j$*r|>T!uz7k+t-^H92l*l$}GP*+`AY z1J1!G)rV~;Ow45p6TQg0wCV)wh4$FHs1wsr0~unw-8#Lyl%RU_3$saqXFC3Y<#|>w zoJ+QksTAOD@-sxs^+vt8qWraGW3<>97V|(>G8{$o zXG*9a2Ktn>^~o@z+QZyP6g@o6=2>LJa11upT!LX}DZ}uCO3n2xwgGb2riKw9@S4w| zs+?l2<{E2)qt!`d$~jL`JPC}+2nms(Vt_R^I2u{LTzSobJ?fhQR^$Fr&vOqg$ESVM zN65GiIpglYas#_(p<>Xt$R8h?9(7G`A5wE_$@DC8+<-j$(DmH0KRBYUi!kg4sAzDd zV}cWl{)cGHP4Q2FI|>k_m*5Iay9dYgFYU~ zs&K|RM2`{g<>Ec9oeCA3#huo+LDe?ao9QR4*>(PUb?El2LHOxvqi7i5HNUY+#x66A zAN|Z)2G1S_Mr7prc3?kfp58@wVK&2 z()mZekcX)jOf{KbP;Yka9*z30&qHC6#oz0a`_K_agO*1ghAJ58>0p!vBl2V1z2L~( z^DS>L=zDvUitPQ05IHPEx;Q0HQO6y*pyWsr9ICnAQMe+QL)&p>%f7&ey*=^*kZyWC zGDr9{xCiD+eQRiU%>fy1*S3PABzYUy_HYclJa(qjqiM~) zeGpK|9CVe~*XRy+>|v;QkU6G`L(4-ej!4w(!+xrGa9}%ja73noMZD||P1{NBN^bDU zGJ>RMQOO;S2G&Ege?$#DTC;7B%0~|R)b-&^;ElV%*h3rm+SxO^pmQd&xKU*gG-5O{ zT3fc$L%2}eI#lszibU0N4wKZ-QZ+4!8aAfN2#k&guFu7Q*}W41Iv6DB4iEQ5t*puZ z@9@)13A~8JZmneiox9sDqmG|^k-%5eG%|y3ALBY4`vL9qL(pL0Uc^*Dmx`x5{H#!E z7dsrY+dCD5%Jo{M+%E1Is2?CcUg^_o+Zl;O2MS%xVd$!lwx_`!eXo5m7-Ocw%mvf2 ze2yH%--<74 z$ug<8i*>{a=)fLu$YU;0-^4@BzJBanYr)V?1P-ac~e-gp7H)W<_%fu7neS zgL2XzvK_1`Lm94^C35Cty;5D00~n2ubi%V97~5Fk_Fb$j?5$9@Bc4jf6e=E-v3AMXMc)){*%BLfJcGP19jj8@LlZjP2fJ@ zy}-}0uYVf&4DbkW7Dxi8fXlG^E8tteeZU?N?e$;h-ZoZ?8HgE(8HgE(8HgE(8HgE( z8HgG9|7SpM-owNNau-OsaS8(m@cr__MwC1O^<6@Bi|k%Js^)Zk`HN4(M}a0PwJ_BD5p?? z3j~aXcbim9NU8%iNMpr`V(9 z{VQz$%<_)qILLjZ?r^aiUV(8{=iD;4&9&1WPAjKQ=~+rq_L}0gdtr$9D4p&!k?6q- z8eDf;RlY&~NZvI0Msmn+1#~X0==o}~6keZg;Pn7rhzYzOeUXNkws_9b)!>kmMV0nYMiZiN;OIeA(PuO5iS$S)3o9mk9>HjD>%gY z!z#ahnWod0o7I&hT|i{;mKABbiAkMv)7hC!<$rH7f%N!s2Niogl^C3Qbey6{+|1sHhE-qlzN@xf78)y_;O2G$T+4c~7J$I9VYxq*m8O bDgdvr#zUFMbjHJdPN6JkRtSj-74YIeTeX`1 literal 0 HcmV?d00001 diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_aldehydes.str b/charmm/toppar/stream/prot/toppar_all36_prot_aldehydes.str new file mode 100644 index 00000000..3b0a4b29 --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_aldehydes.str @@ -0,0 +1,242 @@ +* Topology and Parameter Stream File for aldehydes +* + +!Parent files that have to be read prior to streaming this file +!top_all36_prot.rtf +!par_all36_prot.prm +! +!Testcase +!test_all36_prot_aldehydes.inp + +!reference +!Wymore, T., Hempel, J., Cho, S.S., MacKerell, Jr., A.D. +!Nicholas, Jr., H.B., Deerfield, II, D.W. Molecular +!Recognition of Aldehydes by Aldehyde Dehydrogenase and +!Mechanism of Nucleophile Activation, Submitted for +!publication. + +read rtf card append +* Topology for aldehydes +* +31 1 + +MASS 418 CLAL 35.453000 CL ! Chlorine Atom + +!acetaldehyde additions, ssc & adm, jr., 2/01 +RESI AALD 0.00 ! Acetaldehyde +GROUP ! +ATOM HA HR1 0.06 ! HB3 +ATOM C CD 0.12 ! | +ATOM O O -0.32 !HB1-CB-HB2 +ATOM CB CT3 -0.13 ! | +ATOM HB1 HA3 0.09 ! O=C +ATOM HB2 HA3 0.09 ! | +ATOM HB3 HA3 0.09 ! HA +BOND HA C C CB CB HB1 CB HB2 +BOND CB HB3 +DOUBLE C O +IMPH CB C O HA +ACCE O +IC o c cb hb1 0.0 0.0 0.0 0.0 0.0 +IC hb2 cb c o 0.0 0.0 120.0 0.0 0.0 +IC hb3 cb c o 0.0 0.0 -120.0 0.0 0.0 +IC ha o *c cb 0.0 0.0 180.0 0.0 0.0 +PATCHING FIRST NONE LAST NONE + +RESI PALD 0.00 ! Propionaldehyde +GROUP ! +ATOM O O -0.32 ! HG3 +ATOM C CD 0.12 ! | +ATOM CB CT2 -0.04 !HG1-CG-HG2 +ATOM HB1 HA2 0.09 ! | +ATOM HB2 HA2 0.09 !HB1-CB-HB2 +ATOM HA HR1 0.06 ! | +GROUP ! O=C +ATOM CG CT3 -0.27 ! | +ATOM HG1 HA3 0.09 ! HA +ATOM HG2 HA3 0.09 ! +ATOM HG3 HA3 0.09 +BOND HA C C CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG3 CG HG2 +DOUBLE C O +IMPH CB C O HA +ACCE O +IC o c cb cg 0.0 0.0 0.0 0.0 0.0 +IC cg cb c ha 0.0 0.0 180.0 0.0 0.0 +IC hb1 cb c o 0.0 0.0 120.0 0.0 0.0 +IC hb2 cb c o 0.0 0.0 -120.0 0.0 0.0 +IC c cb cg hg1 0.0 0.0 180.0 0.0 0.0 +IC c cb cg hg2 0.0 0.0 60.0 0.0 0.0 +IC c cb cg hg3 0.0 0.0 -60.0 0.0 0.0 +PATCHING FIRST NONE LAST NONE + +RESI CALD 0.00 ! Chloroacetaldehyde +GROUP ! CL +ATOM O O -0.34 ! | +ATOM C CD 0.19 !HB1-CB-HB2 +ATOM CB CT2 -0.08 ! | +ATOM HB1 HA2 0.09 ! O=C +ATOM HB2 HA2 0.09 ! | +ATOM CL CLAL -0.04 ! HA +ATOM HA HR1 0.09 +BOND HA C C CB CB HB1 CB HB2 +BOND CB CL +DOUBLE C O +IMPH CB C O HA +ACCE O +IC o c cb cl 0.0 0.0 180.0 0.0 0.0 +IC cl cb c ha 0.0 0.0 0.0 0.0 0.0 +IC ha o *c cb 0.0 0.0 0.0 0.0 0.0 +IC cl c *cb hb1 0.0 0.0 120.0 0.0 0.0 +IC hb1 c *cb hb2 0.0 0.0 120.0 0.0 0.0 +PATCHING FIRST NONE LAST NONE + +!benzaldehyde additions, ssc & adm, jr., 2/01 +RESI BALD 0.00 ! Benzaldehyde +GROUP ! +ATOM HA HR1 0.05 ! HZ +ATOM C CD 0.16 ! | +ATOM O O -0.33 ! CZ +ATOM CG CA 0.12 ! // \ +GROUP !HE1-CE1 CE2-HE2 +ATOM CD1 CA -0.115 ! | || +ATOM HD1 HP 0.115 !HD1-CD1 CD2-HD2 +GROUP ! \\ / +ATOM CE1 CA -0.115 ! CG +ATOM HE1 HP 0.115 ! | +GROUP ! O=C +ATOM CZ CA -0.115 ! | +ATOM HZ HP 0.115 ! HA +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +BOND HA C C CG CG CD1 CG CD2 +BOND CD1 HD1 CD2 HD2 CD1 CE1 CD2 CE2 +BOND CE1 HE1 CE2 HE2 CE1 CZ CE2 CZ +BOND CZ HZ +DOUBLE C O +IMPH CG C O HA +ACCE O +IC O C CG CD1 0.0 0.0 0.0 0.0 0.0 +IC HA O *C CG 0.0 0.0 180.0 0.0 0.0 +IC CD1 C *CG CD2 0.0 0.0 -177.9600 0.0 0.0 +IC C CG CD1 CE1 0.0 0.0 -177.3700 0.0 0.0 +IC CE1 CG *CD1 HD1 0.0 0.0 179.7000 0.0 0.0 +IC C CG CD2 CE2 0.0 0.0 177.2000 0.0 0.0 +IC CE2 CG *CD2 HD2 0.0 0.0 -178.6900 0.0 0.0 +IC CG CD1 CE1 CZ 0.0 0.0 -0.1200 0.0 0.0 +IC CZ CD1 *CE1 HE1 0.0 0.0 -179.6900 0.0 0.0 +IC CZ CD2 *CE2 HE2 0.0 0.0 -179.9300 0.0 0.0 +IC CE1 CE2 *CZ HZ 0.0 0.0 179.5100 0.0 0.0 +PATCHING FIRST NONE LAST NONE + +end + +read para card flex append +* additional parameters for aldehydes +* + +ATOMS +MASS 418 CLAL 35.453000 ! Chlorine Atom + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +!benzaldehyde and model compounds, the RESI names on each line indicate the +!model compound that should be used to parametrize the particular term +!NOTE: only change terms in the benzaldehyde section. DO NOT change any other +!terms. +! +CD CA 300.000 1.4798 ! benzaldehyde +CT2 CLAL 220.000 1.7768 ! chloroacetaldehyde +!******************************** + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HR1 CD CT3 20.000 116.0000 ! acetaldehyde +O CD CT3 140.000 123.0000 ! acetaldehyde +CT3 CT2 CD 60.000 113.8000 ! propionaldehyde +O CD CT2 140.000 125.0000 ! propionaldehyde. DIFFERENT COPY OF SAME PARAMETER IN toppar_all27_na_bkb_modifications.str +HR1 CD CT2 35.000 115.0000 ! propionaldehyde +CD CT2 CLAL 65.000 111.8215 ! chloroacetaldehyde +HA2 CT2 CLAL 35.000 108.9905 ! chloroacetaldehyde +HR1 CD CA 15.000 115.0000 ! benzaldehyde +O CD CA 75.000 124.0000 ! benzaldehyde +CD CA CA 45.000 119.8000 ! benzaldehyde +!******************************************** + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +O CD CT2 CT3 1.050 1 180.00 ! propionaldehyde +O CD CT2 CT3 0.400 2 180.00 ! +O CD CT2 CT3 0.600 3 180.00 ! +O CD CT2 CT3 0.100 4 180.00 ! +O CD CT2 CLAL 0.100 1 0.00 ! chloracetaldehyde +O CD CT2 CLAL 1.000 2 180.00 ! +O CD CT2 CLAL 0.550 3 180.00 ! +O CD CA CA 1.000 2 0.00 ! benzaldehyde +HR1 CD CA CA 3.2000 2 180.00 ! benzaldehyde +CD CA CA HP 4.2000 2 180.00 ! benzaldehyde +CD CA CA CA 3.1000 2 180.00 ! benzaldehyde +!******************************************** + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +CT3 CD O HR1 28.0000 0 180.0000 ! acetaldehyde +CT2 CD O HR1 28.0000 0 180.0000 ! propionaldehyde +CA CD O HR1 14.0000 0 180.0000 ! benzaldehyde +!***************************** + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +CLAL 0.000000 -0.030000 1.908200 ! from Jorgensen/BOSS + ! for choroacetaldehyde + +end + +return diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_arg0.str b/charmm/toppar/stream/prot/toppar_all36_prot_arg0.str new file mode 100644 index 00000000..6023473d --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_arg0.str @@ -0,0 +1,446 @@ +*>>>>>> All-hydrogen topology for neutral Arg <<<<<<<<<<<<<<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>>> 2007 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< +*>>>>>>>>>>>>>>> Parameter forum, www.charmm.org <<<<<<<<<<<<<<<<< +* + +! Atom names include "R" (for Arg) as the second letter. The +! only other atom types in the additive FF with this second +! letter are histidine [HN]R[123] in the protein FF and CRL[12] +! in toppar_all36_lipid_cholesterol.str , so no more conflicts. + +!Parent files that have to be read prior to streaming this file +!top_all36_prot.rtf +!par_all36_prot.rtf +! +!Testcase +!test_all36_prot_arg0.inp + +!Li, L., Vorobyov, I.V., MacKerell, Jr., A.D., Allen, T.W., "Is +!arginine charged in a membrane?" Biophysical Journal, 94: L11-L13, +!2008, PMCID: PMC2157258 + +read rtf card append +* Topology for protein related model compounds +* +31 1 + +! use flexible toplogy/parameter reader +!!atom for methylguanidine compounds +!!atoms renamed to 4 letter code +MASS 501 HRA3 1.00800 ! alphatic proton, CH3 +MASS 502 HRP2 1.00800 ! polar H, +ve charge +MASS 503 HRM1 1.00800 ! polar H, dimethylamine +MASS 504 HRM2 1.00800 ! polar H, methylamine +MASS 505 CRN1 12.01100 ! conjugated C in Arg/guanidinium +MASS 506 CR33 12.01100 ! aliphatic C for methyl group (-CH3) +MASS 507 NRC4 14.00700 ! N for deprotonated Schiff's base +MASS 508 NRN1 14.00700 ! dimethylamine nitrogen +MASS 509 NRN2 14.00700 ! methylamine nitrogen + + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!! original topology from Alex +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + +!methylguanidine model compounds +RESI MGU1 0.00 ! deprotonated methyl-guanidinium + ! Ne deprotonated +GROUP +ATOM C CRN1 0.66 ! H11 H12 +ATOM N1 NRN2 -0.60 ! \ / +ATOM H11 HRM2 0.29 ! N1 +ATOM H12 HRM2 0.29 ! | +ATOM N2 NRN2 -0.60 ! C H41 +ATOM H21 HRM2 0.29 ! / \\ / +ATOM H22 HRM2 0.29 ! H21-N2 N3--C4-H42 +ATOM N3 NRC4 -0.86 ! | \ +ATOM C4 CR33 -0.03 ! H22 H43 !extra charge on C4 to neutralize +ATOM H41 HRA3 0.09 +ATOM H42 HRA3 0.09 +ATOM H43 HRA3 0.09 +BOND C N1 C N2 C N3 N3 C4 +BOND N1 H11 N1 H12 N2 H21 N2 H22 +BOND C4 H41 C4 H42 C4 H43 +IMPH C N2 N1 N3 +IMPH N1 H11 H12 C N2 H21 H22 C + +IC C4 N3 C N1 0.0000 0.00 180.00 0.00 0.0000 +IC N1 N3 *C N2 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C N1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C *N1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C N2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC H21 C *N2 H22 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C N3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C N3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 N3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 N3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +RESI MGU2 0.00 ! deprotonated methyl-guanidinium + ! NH1-H12 (outer) deprotonated +GROUP +ATOM C CRN1 0.59 ! +ATOM N1 NRC4 -0.91 ! H11 +ATOM H11 HRP2 0.37 ! \ +ATOM N2 NRN2 -0.60 ! N1 +ATOM H21 HRM2 0.33 ! || +ATOM H22 HRM2 0.33 ! C H41 +ATOM N3 NRN1 -0.54 ! / \ / +ATOM H31 HRM1 0.36 ! H21-N2 N3--C4-H42 +ATOM C4 CR33 -0.20 ! | | \ !carbon charge to neutralize +ATOM H41 HRA3 0.09 ! H22 H31 H43 +ATOM H42 HRA3 0.09 +ATOM H43 HRA3 0.09 +BOND C N1 C N2 C N3 N3 C4 +BOND N1 H11 N2 H21 N2 H22 N3 H31 +BOND C4 H41 C4 H42 C4 H43 +IMPH C N2 N1 N3 +IMPH N3 C4 C H31 N2 H21 H22 C + +IC C4 N3 C N1 0.0000 0.00 180.00 0.00 0.0000 +IC N1 N3 *C N2 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C N1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C N2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC H21 C *N2 H22 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C N3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C C4 *N3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C N3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 N3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 N3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +patc firs none last none + +RESI MGU3 0.00 ! deprotonated methyl-guanidinium + ! NH1-H11 (inner) deprotonated +! +!MGU3 parameters obtained directly from MGU2 optimization +!charges readjust to improve interactions with water +!Two charge models determined with and without IMPRoper +!on H31 atom, which has a large effect on the pyramidalization +!and the overall dipole moment +! +!charges with !IMPH N3 C4 C H31 commented out +GROUP +ATOM C CRN1 0.59 ! +ATOM N1 NRC4 -0.95 ! H12 +ATOM H12 HRP2 0.33 ! / +ATOM N2 NRN2 -0.60 ! N1 +ATOM H21 HRM2 0.33 ! || +ATOM H22 HRM2 0.33 ! C H41 +ATOM N3 NRN1 -0.54 ! / \ / +ATOM H31 HRM1 0.44 ! H21-N2 N3--C4-H42 +ATOM C4 CR33 -0.20 ! | | \ +ATOM H41 HRA3 0.09 ! H22 H31 H43 +ATOM H42 HRA3 0.09 +ATOM H43 HRA3 0.09 + +!charges with !IMPH N3 C4 C H31 included +!GROUP +!ATOM C CRN1 0.59 ! +!ATOM N1 NRC4 -1.01 ! H12 +!ATOM H12 HRP2 0.39 ! / +!ATOM N2 NRN2 -0.56 ! N1 +!ATOM H21 HRM2 0.33 ! || +!ATOM H22 HRM2 0.33 ! C H41 +!ATOM N3 NRN1 -0.55 ! / \ / +!ATOM H31 HRM1 0.41 ! H21-N2 N3--C4-H42 +!ATOM C4 CR33 -0.20 ! | | \ +!ATOM H41 HRA3 0.09 ! H22 H31 H43 +!ATOM H42 HRA3 0.09 +!ATOM H43 HRA3 0.09 +BOND C N1 C N2 C N3 N3 C4 +BOND N1 H12 N2 H21 N2 H22 N3 H31 +BOND C4 H41 C4 H42 C4 H43 +IMPH C N2 N1 N3 +!IMPH N3 C4 C H31 +IMPH N2 H21 H22 C + +IC C4 N3 C N1 0.0000 0.00 180.00 0.00 0.0000 +IC N1 N3 *C N2 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C N1 H12 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C N2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC H21 C *N2 H22 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C N3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C C4 *N3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C N3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 N3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 N3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +!patches to convert arginine to neutral species based on the +!methylguanidine model compounds +PRES RN1 0.00 !patch for neutral arginine: He delete +DELE ATOM HE !from RESI MGU1 +GROUP +ATOM CD CT2 0.06 !-0.03 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +ATOM NE NRC4 -0.86 +ATOM CZ CRN1 0.66 +ATOM NH1 NRN2 -0.60 +ATOM HH11 HRM2 0.29 +ATOM HH12 HRM2 0.29 +ATOM NH2 NRN2 -0.60 +ATOM HH21 HRM2 0.29 +ATOM HH22 HRM2 0.29 +!IMPH C N2 N1 N3 !present in RESI ARG +IMPH NH1 HH11 HH12 CZ +IMPH NH2 HH21 HH22 CZ + +PRES RN2 0.00 !patch for neutral arginine: HH12 deleted (proton removed from NH2) +DELE ATOM HH12 !from RESI MGU2 +GROUP +ATOM CD CT2 -0.11 ! -0.20 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +ATOM NE NRN1 -0.54 +ATOM HE HRM1 0.36 +ATOM CZ CRN1 0.59 +ATOM NH1 NRC4 -0.91 +ATOM HH11 HRP2 0.37 +ATOM NH2 NRN2 -0.60 +ATOM HH21 HRM2 0.33 +ATOM HH22 HRM2 0.33 +IMPH NE CD CZ HE +IMPH NH2 HH21 HH22 CZ + +PRES RN3 0.00 !patch for neutral arginine: HH12 deleted (proton adjacent to NH2) +DELE ATOM HH11 !from RESI MGU3 (see comments on MGU3 residue above) +GROUP +ATOM CD CT2 -0.11 ! -0.20 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +ATOM NE NRN1 -0.54 +ATOM HE HRM1 0.44 +ATOM CZ CRN1 0.59 +ATOM NH1 NRC4 -0.95 +ATOM HH12 HRP2 0.33 +ATOM NH2 NRN2 -0.60 +ATOM HH21 HRM2 0.33 +ATOM HH22 HRM2 0.33 +!IMPH NE CD CZ HE !removed based on MGU3, see above +IMPH NH2 HH21 HH22 CZ + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!! The topology below is from +!!!! the group of Toby Allen +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +!! propyl guanidine +!! based on MGU1 and RN1 +!! note different atom naming +!! and numbering + +!reset default patches + +DEFA FIRS NONE LAST NONE + +!following not tested + +RESI PGUN 0.00 +GROUP +ATOM CB CT3 -0.27 ! +ATOM HB1 HA3 0.09 ! +ATOM HB2 HA3 0.09 ! +ATOM HB3 HA3 0.09 +GROUP ! +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CT2 0.06 !-0.03 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +ATOM NE NRC4 -0.86 +!ATOM HE DUM 0.00 +ATOM CZ CRN1 0.66 +ATOM NH1 NRN2 -0.60 +ATOM HH11 HRM2 0.29 +ATOM HH12 HRM2 0.29 +ATOM NH2 NRN2 -0.60 +ATOM HH21 HRM2 0.29 +ATOM HH22 HRM2 0.29 + +BOND CG CB CD CG NE CD CZ NE +BOND NH2 CZ +BOND CB HB3 CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE CZ NH1 +IMPH CZ NH1 NH2 NE +IMPH NH1 HH11 HH12 CZ +IMPH NH2 HH21 HH22 CZ +ACCEPTOR NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 + +!! Methyl guanidine residue +!! based on MGU1 and RN1 +!! note different atom naming +!! and numbering + +RESI MGUN 0.00 +GROUP +ATOM CD CT2 -0.03 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +ATOM HD3 HA2 0.09 +ATOM NE NRC4 -0.86 +!ATOM HE DUM 0.00 +ATOM CZ CRN1 0.66 +ATOM NH1 NRN2 -0.60 +ATOM HH11 HRM2 0.29 +ATOM HH12 HRM2 0.29 +ATOM NH2 NRN2 -0.60 +ATOM HH21 HRM2 0.29 +ATOM HH22 HRM2 0.29 + +BOND NE CD CZ NE +BOND NH2 CZ +BOND CD HD1 CD HD2 CD HD3 +BOND NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE CZ NH1 +IMPH CZ NH1 NH2 NE +IMPH NH1 HH11 HH12 CZ +IMPH NH2 HH21 HH22 CZ +ACCEPTOR NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 + + +PATCHING FIRST NONE LAST NONE + +END + +read param card flex append + +ATOMS +MASS 501 HRA3 1.00800 ! alphatic proton, CH3 +MASS 502 HRP2 1.00800 ! polar H, +ve charge +MASS 503 HRM1 1.00800 ! polar H, dimethylamine +MASS 504 HRM2 1.00800 ! polar H, methylamine +MASS 505 CRN1 12.01100 ! conjugated C in Arg/guanidinium +MASS 506 CR33 12.01100 ! aliphatic C for methyl group (-CH3) +MASS 507 NRC4 14.00700 ! N for deprotonated Schiff's base +MASS 508 NRN1 14.00700 ! dimethylamine nitrogen +MASS 509 NRN2 14.00700 ! methylamine nitrogen + +BONDS +!atom type Kb b0 +!methylguanidine +!new parameters +CRN1 NRC4 500.00 1.3100 ! MGU1, methylguanidine +CRN1 NRN2 450.00 1.4400 ! MGU1, methylguanidine +! +CRN1 NRN1 500.00 1.4400 ! MGU2, methylguanidine2 +CR33 NRN1 255.00 1.4630 ! MGU2, methylguanidine2 +NRC4 HRP2 455.00 1.0000 ! MGU2, methylguanidine2 +!transferred parameters +CR33 NRC4 310.00 1.4400 ! RETINOL SCH1, Schiff's base, deprotonated +CR33 HRA3 322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 +NRN1 HRM1 447.80 1.0190 ! AMINE aliphatic amines +NRN2 HRM2 453.10 1.0140 ! AMINE aliphatic amines +NRN1 CT2 255.00 1.4630 ! MGU2, methylguanidine2 +NRC4 CT2 310.00 1.4400 ! RETINOL SCH1, Schiff's base, deprotonated +!end methylguanidine + + +ANGLES +!atom types Ktheta Theta0 Kub S0 +!methylguanidine +!new parameters +NRN2 CRN1 NRN2 75.00 113.00 ! MGU1, methylguanidine +NRN2 CRN1 NRC4 100.00 125.00 ! MGU1, methylguanidine +CRN1 NRC4 CR33 50.00 108.00 ! MGU1, methylguanidine +CRN1 NRN2 HRM2 55.00 108.00 ! MGU1, methylguanidine +! +NRC4 CRN1 NRN1 50.00 125.00 ! MGU2, methylguanidine2 +NRN2 CRN1 NRN1 50.00 110.00 ! MGU2, methylguanidine2 +CRN1 NRN1 CR33 43.00 106.00 ! MGU2, methylguanidine2 +CRN1 NRN1 HRM1 45.00 104.00 ! MGU2, methylguanidine2 +CR33 NRN1 HRM1 45.00 104.00 ! MGU2, methylguanidine2 +NRN1 CR33 HRA3 30.50 109.70 50.00 2.1400 ! MGU2, methylguanidine2 +CRN1 NRC4 HRP2 49.00 113.00 ! MGU2, methylguanidine2 +!transferred parameters +NRC4 CR33 HRA3 42.00 113.50 ! RETINOL SCH1, Schiff's base, deprotonated +HRM2 NRN2 HRM2 29.50 105.85 ! AMINE aliphatic amines +HRA3 CR33 HRA3 35.50 108.40 5.40 1.80200 ! PROT alkane update +CT2 CT2 NRC4 67.70 110.00 ! RETINOL SCK0, deprotonated Schiff's base +HA2 CT2 NRC4 42.00 113.50 ! RETINOL SCK0, deprotonated Schiff's base +CT2 NRC4 CRN1 50.00 108.00 ! MGU1, methylguanidine +CT2 CT2 NRN1 67.70 107.50 ! PROT arg, (DS) +HA2 CT2 NRN1 30.50 109.70 50.00 2.1400 ! MGU2, methylguanidine2 +CT2 NRN1 HRM1 45.00 104.00 ! MGU2, methylguanidine2 +CT2 NRN1 CRN1 43.00 106.00 ! MGU2, methylguanidine +!end methylguanidine + +DIHEDRALS +!atom types Kchi n delta +! +!methylguanidine +!new parameters +CRN1 NRC4 CR33 HRA3 0.1100 3 180.00 ! MGU1, methylguanidine +NRN2 CRN1 NRC4 CR33 6.5000 2 180.00 ! MGU1, methylguanidine +NRC4 CRN1 NRN2 HRM2 1.3000 3 180.00 ! MGU1, methylguanidine +NRN2 CRN1 NRN2 HRM2 1.3000 3 180.00 ! MGU1, methylguanidine +! +NRC4 CRN1 NRN1 CR33 0.5000 2 180.00 ! MGU2, methylguanidine2 +NRN2 CRN1 NRN1 CR33 0.5000 2 180.00 ! MGU2, methylguanidine2 +HRP2 NRC4 CRN1 NRN2 5.2000 2 180.00 ! MGU2, methylguanidine2 +HRP2 NRC4 CRN1 NRN1 5.2000 2 180.00 ! MGU2, methylguanidine2 +HRM2 NRN2 CRN1 NRN1 1.3000 3 180.00 ! MGU2, methylguanidine2 +NRC4 CRN1 NRN1 HRM1 2.8000 3 180.00 ! MGU2, methylguanidine2 +NRN2 CRN1 NRN1 HRM1 2.8000 3 180.00 ! MGU2, methylguanidine2 +CRN1 NRN1 CR33 HRA3 0.0000 3 180.00 ! MGU2, methylguanidine2 +HRM1 NRN1 CR33 HRA3 0.4200 3 0.00 ! MGU2, methylguanidine2 +!transferred parameters +CT2 CT2 NRC4 CRN1 0.1000 3 0.00 ! RETINOL SCH1, Schiff's base, deprotonated +CT2 NRC4 CRN1 NRN2 6.5000 2 180.00 ! MGU1, methylguanidine +HA2 CT2 NRC4 CRN1 0.1100 3 180.00 ! MGU1, methylguanidine +CT2 CT2 NRN1 HRM1 0.3000 3 180.00 ! amines +CT2 CT2 NRN1 CRN1 0.3000 3 180.00 ! amines +CT2 NRN1 CRN1 NRC4 0.5000 2 180.00 ! MGU2, methylguanidine2 +HA2 CT2 NRN1 HRM1 0.4200 3 0.00 ! MGU2, methylguanidine2 +HA2 CT2 NRN1 CRN1 0.0000 3 180.00 ! MGU2, methylguanidine2 +CT2 NRN1 CRN1 NRN2 0.5000 2 180.00 ! MGU2, methylguanidine2 +!end methylguanidine + +IMPROPER +!atom types Kpsi psi0 +!methylguanidine +CRN1 NRN2 NRN2 NRC4 170.0000 1 180.00 ! MGU1, methylguanidine +NRN2 HRM2 HRM2 CRN1 40.0000 1 180.00 ! MGU1, methylguanidine +! +CRN1 NRN2 NRC4 NRN1 170.0000 1 180.00 ! MGU2, methylguanidine2 +NRN1 CR33 CRN1 HRM1 60.0000 1 180.00 ! MGU2, methylguanidine2 +!transferred parameters +CRN1 NRC4 NRN2 NRN1 170.0000 1 180.00 ! MGU1, methylguanidine +NRN1 CT2 CRN1 HRM1 60.0000 1 180.00 ! MGU2, methylguanidine2 +!end methylguanidine + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +!methylguanidine parameters +HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 +HRP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged systems +HRM1 0.0 -0.0090 0.8750 ! aliphatic amines +HRM2 0.0 -0.0100 0.8750 ! aliphatic amines +! +CRN1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93 +CR33 0.0 -0.0780 2.0500 0.0 -0.01 1.9 ! alkane (CT3), 4/98, yin, adm jr +! +NRC4 0.0 -0.2000 1.8500 ! deprotonated Schiff's base +NRN1 0.0 -0.4500 2.0000 ! aliphatic amines +NRN2 0.0 -0.0600 1.9900 ! aliphatic amines +!end methylguanidine + +end + +return diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_d_aminoacids.str b/charmm/toppar/stream/prot/toppar_all36_prot_d_aminoacids.str new file mode 100644 index 00000000..e11ea4d1 --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_d_aminoacids.str @@ -0,0 +1,2541 @@ +*>>>>>>CHARMM36 All-Hydrogen Toppar File for D-Proteins <<<<<<< +*>>>>>>>>>>>>>>>>>>>>>>>>>> Feb 2012 <<<<<<<<<<<<<<<<<<<<<<<<<<<< +* All comments to the CHARMM web site: www.charmm.org +* parameter set discussion forum +* + +!toppar stream file for D-amino acids. Includes new residue +!names, inverted CMAP and additional parameters. + +!Parent files that have to be read prior to streaming this file +!top_all36_prot.rtf +!par_all36_prot.prm +! +!Testcase +!test_all36_d_amino_acid.inp + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for D- aminoacids +* +36 1 + +MASS 438 CTD1 12.01100 ! added for D-amino acids +MASS 439 CPD1 12.01100 ! added for D-proline + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI ALDD 0.00 ! D-Alanine dipeptide, with CMAP term + ! AMG 2/27/08 -- changed alpha carbon type + ! and flipped the cmap term +GROUP +ATOM CL CT3 -0.27 +ATOM HL1 HA3 0.09 +ATOM HL2 HA3 0.09 +ATOM HL3 HA3 0.09 +GROUP +ATOM CLP C 0.51 +ATOM OL O -0.51 +GROUP +ATOM NL NH1 -0.47 +ATOM HL H 0.31 +ATOM CA CTD1 0.07 ! THIS IS THE ONLY CHANGE +ATOM HA HB1 0.09 +GROUP +ATOM CB CT3 -0.27 ! HL1 OL OR HR1 +ATOM HB1 HA3 0.09 ! \ || HL HA || HR / +ATOM HB2 HA3 0.09 ! \ || | | || | / +ATOM HB3 HA3 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 +GROUP ! / | \ +ATOM CRP C 0.51 ! / HB1--CB--HB3 \ +ATOM OR O -0.51 ! HL3 | HR3 +GROUP ! HB2 +ATOM NR NH1 -0.47 +ATOM HR H 0.31 +ATOM CR CT3 -0.11 +ATOM HR1 HA3 0.09 +ATOM HR2 HA3 0.09 +ATOM HR3 HA3 0.09 + +BOND CL CLP CLP NL NL CA +BOND CA CRP CRP NR NR CR +DOUBLE CLP OL CRP OR +BOND NL HL NR HR +BOND CA HA CA CB +BOND CL HL1 CL HL2 CL HL3 +BOND CB HB1 CB HB2 CB HB3 +BOND CR HR1 CR HR2 CR HR3 +IMPR CLP CL NL OL NL CLP CA HL +IMPR CRP CA NR OR NR CRP CR HR + +CMAP CLP NL CA CRP NL CA CRP NR + +ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0 +ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic nl ca crp or 0.0 0.0 0.0 0.0 0.0 +ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left +ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0 +ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0 +ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right +ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0 +ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0 +ic nl crp *ca ha 0.0 0.0 120.0 0.0 0.0 +ic nl crp *ca cb 0.0 0.0 -120.0 0.0 0.0 +ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0 +ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0 +ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0 +ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0 +ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0 +ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0 +ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0 +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0 +ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0 +ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0 +ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0 +patch first none last none + +RESI DALA 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | / +GROUP ! HA-CA--CB-HB2 +ATOM CB CT3 -0.27 ! | \ +ATOM HB1 HA3 0.09 ! | HB3 +ATOM HB2 HA3 0.09 ! O=C +ATOM HB3 HA3 0.09 ! | +GROUP ! +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA N HN N CA +BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 !phi +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 !psi +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 -123.2300 111.0900 1.5461 !D form +IC N C *CA HA 1.4592 114.4400 120.4500 106.3900 1.0840 !D form +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +RESI DARG 1.00 +GROUP +ATOM N NH1 -0.47 ! | HH11 +ATOM HN H 0.31 ! HN-N | +ATOM CA CTD1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA HB1 0.09 ! | | | | | //(+) +GROUP ! HA-CA--CB--CG--CD--NE--CZ +ATOM CB CT2 -0.18 ! | | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HB2 HA2 0.09 ! O=C | +GROUP ! | HH21 +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CT2 0.20 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +ATOM NE NC2 -0.70 +ATOM HE HC 0.44 +ATOM CZ C 0.64 +ATOM NH1 NC2 -0.80 +ATOM HH11 HC 0.46 +ATOM HH12 HC 0.46 +ATOM NH2 NC2 -0.80 +ATOM HH21 HC 0.46 +ATOM HH22 HC 0.46 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE O C CZ NH1 +IMPR N -C CA HN C CA +N O +IMPR CZ NH1 NH2 NE +IMPR NH1 HH11 HH12 CZ +IMPR NH2 HH21 HH22 CZ +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 -123.6400 112.2600 1.5552 !D form +IC N C *CA HA 1.4544 109.8600 117.9300 106.6100 1.0836 !D form +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +RESI DASN 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA HB1 0.09 ! | | || / +GROUP ! HA-CA--CB--CG--ND2 +ATOM CB CT2 -0.18 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 HD22 (trans to OD1) +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CC 0.55 +ATOM OD1 O -0.55 +GROUP +ATOM ND2 NH2 -0.62 +ATOM HD21 H 0.32 +ATOM HD22 H 0.30 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +DOUBLE C O CG OD1 +IMPR N -C CA HN C CA +N O +IMPR CG ND2 CB OD1 CG CB ND2 OD1 +IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 -121.1800 113.0400 1.5627 !D form +IC N C *CA HA 1.4510 105.2300 115.5200 107.6300 1.0848 !D form +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +RESI DASP -1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 OD1 +ATOM HA HB1 0.09 ! | | // +GROUP ! HA-CA--CB--CG +ATOM CB CT2 -0.28 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 OD2(-) +ATOM HB2 HA2 0.09 ! O=C +ATOM CG CC 0.62 ! | +ATOM OD1 OC -0.76 +ATOM OD2 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +DOUBLE O C CG OD1 +IMPR N -C CA HN C CA +N O +IMPR CG CB OD2 OD1 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 -122.3300 114.1000 1.5619 !D form +IC N C *CA HA 1.4490 105.6300 116.4000 106.7700 1.0841 !D form +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +RESI DCYS 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB CT2 -0.11 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG1 +ATOM HB2 HA2 0.09 ! O=C +ATOM SG S -0.23 ! | +ATOM HG1 HS 0.16 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 -121.7900 111.9800 1.5584 !D form +IC N C *CA HA 1.4533 105.8900 116.3400 107.7100 1.0837 !D form +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +RESI DGLN 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA HB1 0.09 ! | | | || / +GROUP ! HA-CA--CB--CG--CD--NE2 +ATOM CB CT2 -0.18 ! | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 HE22 (trans to OE1) +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CC 0.55 +ATOM OE1 O -0.55 +GROUP +ATOM NE2 NH2 -0.62 +ATOM HE21 H 0.32 +ATOM HE22 H 0.30 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD NE2 CG OE1 CD CG NE2 OE1 +IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 -121.9100 111.6800 1.5538 !D form +IC N C *CA HA 1.4506 106.5700 116.8200 107.5300 1.0832 !D form +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +RESI DGLU -1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 HG1 OE1 +ATOM HA HB1 0.09 ! | | | // +GROUP ! HA-CA--CB--CG--CD +ATOM CB CT2A -0.18 ! | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 OE2(-) +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.28 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +ATOM CD CC 0.62 +ATOM OE1 OC -0.76 +ATOM OE2 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD CG OE2 OE1 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 -121.9000 111.7100 1.5516 !D form +IC N C *CA HA 1.4512 107.2700 118.0600 107.2600 1.0828 !D form +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI DGLY 0.00 +!GROUP +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! N-H +ATOM CA CT2 -0.02 ! | +ATOM HA1 HB2 0.09 ! | +ATOM HA2 HB2 0.09 ! HA1-CA-HA2 +GROUP ! | +ATOM C C 0.51 ! | +ATOM O O -0.51 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 +PATCHING FIRS GLYP + +RESI DHSD 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CTD1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB1 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 -0.09 ! | | \\ || +ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA2 0.09 ! O=C | +ATOM ND1 NR1 -0.36 ! | HD2 +ATOM HD1 H 0.32 +ATOM CG CPH1 -0.05 +GROUP +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +ATOM NE2 NR2 -0.70 +ATOM CD2 CPH1 0.22 +ATOM HD2 HR3 0.10 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 -122.4600 109.9900 1.5519 !D form +IC N C *CA HA 1.4521 107.7000 117.4900 107.3700 1.0830 !D form +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +RESI DHSE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N NH1 -0.47 ! | HE1 +ATOM HN H 0.31 ! HN-N __ / +ATOM CA CTD1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB1 0.09 ! | | / | +GROUP ! HA-CA--CB--CG | +ATOM CB CT2 -0.08 ! | | \\ | +ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA2 0.09 ! O=C | \ +ATOM ND1 NR2 -0.70 ! | HD2 HE2 +ATOM CG CPH1 0.22 +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +GROUP +ATOM NE2 NR1 -0.36 +ATOM HE2 H 0.32 +ATOM CD2 CPH1 -0.05 +ATOM HD2 HR3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG CE1 ND1 +IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 -123.5200 111.6700 1.5578 !D form +IC N C *CA HA 1.4532 106.4300 116.4900 107.0800 1.0833 !D form +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +RESI DHSP 1.00 ! Protonated His +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CTD1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB1 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2A -0.05 ! | | \\ || +ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2(+) +ATOM HB2 HA2 0.09 ! O=C | \ +ATOM CD2 CPH1 0.19 ! | HD2 HE2 +ATOM HD2 HR1 0.13 +ATOM CG CPH1 0.19 +GROUP +ATOM NE2 NR3 -0.51 +ATOM HE2 H 0.44 +ATOM ND1 NR3 -0.51 +ATOM HD1 H 0.44 +ATOM CE1 CPH2 0.32 +ATOM HE1 HR2 0.18 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG NE2 CE1 +IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 -125.1300 109.3800 1.5533 !D form +IC N C *CA HA 1.4548 112.0300 119.2000 106.7200 1.0832 !D form +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +RESI DILE 0.00 +GROUP +ATOM N NH1 -0.47 ! | HG21 HG22 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CTD1 0.07 ! | CG2--HG23 +ATOM HA HB1 0.09 ! | / +GROUP ! HA-CA--CB-HB HD1 +ATOM CB CT1 -0.09 ! | \ / +ATOM HB HA1 0.09 ! | CG1--CD--HD2 +GROUP ! O=C / \ \ +ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3 +ATOM HG21 HA3 0.09 +ATOM HG22 HA3 0.09 +ATOM HG23 HA3 0.09 +GROUP +ATOM CG1 CT2 -0.18 +ATOM HG11 HA2 0.09 +ATOM HG12 HA2 0.09 +GROUP +ATOM CD CT3 -0.27 +ATOM HD1 HA3 0.09 +ATOM HD2 HA3 0.09 +ATOM HD3 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 -124.2200 112.9300 1.5681 !D form +IC N C *CA HA 1.4542 106.3500 115.6300 106.8100 1.0826 !D form +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + +RESI DLEU 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD11 HD12 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CTD1 0.07 ! | HB1 CD1--HD13 +ATOM HA HB1 0.09 ! | | / +GROUP ! HA-CA--CB--CG-HG +ATOM CB CT2 -0.18 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 CD2--HD23 +ATOM HB2 HA2 0.09 ! O=C | \ +GROUP ! | HD21 HD22 +ATOM CG CT1 -0.09 +ATOM HG HA1 0.09 +GROUP +ATOM CD1 CT3 -0.27 +ATOM HD11 HA3 0.09 +ATOM HD12 HA3 0.09 +ATOM HD13 HA3 0.09 +GROUP +ATOM CD2 CT3 -0.27 +ATOM HD21 HA3 0.09 +ATOM HD22 HA3 0.09 +ATOM HD23 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 -121.5200 112.1200 1.5543 !D form +IC N C *CA HA 1.4508 106.0500 116.5000 107.5700 1.0824 !D form +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +RESI DLYS 1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA HB1 0.09 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM CB CT2 -0.18 ! | | | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CT2 -0.18 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +GROUP +ATOM CE CT2 0.21 +ATOM HE1 HA2 0.05 +ATOM HE2 HA2 0.05 +ATOM NZ NH3 -0.30 +ATOM HZ1 HC 0.33 +ATOM HZ2 HC 0.33 +ATOM HZ3 HC 0.33 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUBLE O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 -122.2300 111.3600 1.5568 !D form +IC N C *CA HA 1.4504 107.2900 116.8800 107.3600 1.0833 !D form +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI DMET 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 HG1 HE1 +ATOM HA HB1 0.09 ! | | | | +GROUP ! HA-CA--CB--CG--SD--CE--HE3 +ATOM CB CT2 -0.18 ! | | | | +ATOM HB1 HA2 0.09 ! | HB2 HG2 HE2 +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.14 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +ATOM SD S -0.09 +ATOM CE CT3 -0.22 +ATOM HE1 HA3 0.09 +ATOM HE2 HA3 0.09 +ATOM HE3 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 -121.6200 111.8800 1.5546 !D form +IC N C *CA HA 1.4510 106.3100 116.9800 107.5700 1.0832 !D form +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +RESI DPHE 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | | +ATOM CA CTD1 0.07 ! | HB1 CD1--CE1 +ATOM HA HB1 0.09 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--HZ +ATOM CB CT2 -0.18 ! | | \ __ / +ATOM HB1 HA2 0.09 ! | HB2 CD2--CE2 +ATOM HB2 HA2 0.09 ! O=C | | +GROUP ! | HD2 HE2 +ATOM CG CA 0.00 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA -0.115 +ATOM HZ HP 0.115 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 -122.4900 112.4500 1.5594 !D form +IC N C *CA HA 1.4504 106.3800 115.6300 107.0500 1.0832 !D form +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +RESI DPRO 0.00 +GROUP ! HD1 HD2 +ATOM N N -0.29 ! | \ / +ATOM CD CP3 0.00 ! N---CD HG1 +ATOM HD1 HA2 0.09 ! | \ / +ATOM HD2 HA2 0.09 ! | CG +ATOM CA CPD1 0.02 ! | / \ +ATOM HA HB1 0.09 ! HA-CA--CB HG2 +GROUP ! | / \ +ATOM CB CP2 -0.18 ! | HB1 HB2 +ATOM HB1 HA2 0.09 ! O=C +ATOM HB2 HA2 0.09 ! | +GROUP +ATOM CG CP2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +DOUBLE O C +IMPR N -C CA CD +IMPR C CA +N O +CMAP -C N CA C N CA C +N +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 -113.7400 111.7400 1.5399 !D form +IC N C *CA HA 1.4585 110.8600 122.4000 109.0900 1.0837 !D form +!IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +!IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB CG 1.4585 102.5600 -31.6100 104.3900 1.5322 !D form +IC CA CB CG CD 1.5399 104.3900 34.5900 103.2100 1.5317 !D form +IC CA CG *CB HB1 1.4585 102.5600 120.0000 109.0200 1.1131 +IC CA CG *CB HB2 1.4585 102.5600 -120.0000 109.0200 1.1131 +IC CB CD *CG HG1 1.5399 104.3900 120.0000 112.9500 1.1077 +IC CB CD *CG HG2 1.5399 104.3900 -120.0000 109.2200 1.1143 +IC N CG *CD HD1 1.5322 103.2100 120.0000 110.0300 1.1137 +IC N CG *CD HD2 1.5322 103.2100 -120.0000 110.0000 1.1144 +PATCHING FIRS PROP + +RESI DSER 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | | +GROUP ! HA-CA--CB--OG +ATOM CB CT2 0.05 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG1 +ATOM HB2 HA2 0.09 ! O=C +ATOM OG OH1 -0.66 ! | +ATOM HG1 H 0.43 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 -124.7500 111.4000 1.5585 !D form +IC N C *CA HA 1.4579 105.8100 115.5600 107.3000 1.0821 !D form +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +RESI DTHR 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CTD1 0.07 ! | OG1--HG1 +ATOM HA HB1 0.09 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 0.14 ! | \ +ATOM HB HA1 0.09 ! | CG2--HG21 +ATOM OG1 OH1 -0.66 ! O=C / \ +ATOM HG1 H 0.43 ! | HG21 HG22 +GROUP +ATOM CG2 CT3 -0.27 +ATOM HG21 HA3 0.09 +ATOM HG22 HA3 0.09 +ATOM HG23 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 -126.4600 112.7400 1.5693 !D form +IC N C *CA HA 1.4607 106.0900 114.9200 106.5300 1.0817 !D form +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +RESI DTRP 0.00 +GROUP +ATOM N NH1 -0.47 ! | HE3 +ATOM HN H 0.31 ! HN-N | +ATOM CA CTD1 0.07 ! | HB1 CE3 +ATOM HA HB1 0.09 ! | | / \\ +GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM CB CT2 -0.18 ! | | || || | +ATOM HB1 HA2 0.09 ! | HB2 CD1 CE2 CH2-HH2 +ATOM HB2 HA2 0.09 ! O=C / \ / \ // +GROUP ! | HD1 NE1 CZ2 +ATOM CG CY -0.03 ! | | +ATOM CD1 CA -0.15 ! HE1 HZ2 +ATOM HD1 HP 0.22 +ATOM NE1 NY -0.51 +ATOM HE1 H 0.37 +ATOM CE2 CPT 0.24 +ATOM CD2 CPT 0.11 +ATOM CE3 CAI -0.25 +ATOM HE3 HP 0.17 +ATOM CZ3 CA -0.20 +ATOM HZ3 HP 0.14 +ATOM CZ2 CAI -0.27 +ATOM HZ2 HP 0.16 +ATOM CH2 CA -0.14 +ATOM HH2 HP 0.14 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 -122.6800 111.2300 1.5560 !D form +IC N C *CA HA 1.4507 107.6900 117.0200 106.9200 1.0835 !D form +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI DTYR 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | | +ATOM CA CTD1 0.07 ! | HB1 CD1--CE1 +ATOM HA HB1 0.09 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--OH +ATOM CB CT2 -0.18 ! | | \ __ / \ +ATOM HB1 HA2 0.09 ! | HB2 CD2--CE2 HH +ATOM HB2 HA2 0.09 ! O=C | | +GROUP ! | HD2 HE2 +ATOM CG CA 0.00 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA 0.11 +ATOM OH OH1 -0.54 +ATOM HH H 0.43 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +DOUBLE O C CD1 CG CE1 CZ CE2 CD2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 -122.2700 112.3400 1.5606 !D form +IC N C *CA HA 1.4501 106.5200 116.0400 107.1500 1.0833 !D form +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +RESI DVAL 0.00 +GROUP +ATOM N NH1 -0.47 ! | HG11 HG12 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CTD1 0.07 ! | CG1--HG13 +ATOM HA HB1 0.09 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 -0.09 ! | \ +ATOM HB HA1 0.09 ! | CG2--HG21 +GROUP ! O=C / \ +ATOM CG1 CT3 -0.27 ! | HG21 HG22 +ATOM HG11 HA3 0.09 +ATOM HG12 HA3 0.09 +ATOM HG13 HA3 0.09 +GROUP +ATOM CG2 CT3 -0.27 +ATOM HG21 HA3 0.09 +ATOM HG22 HA3 0.09 +ATOM HG23 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 -122.9500 111.2300 1.5660 !D form +IC N C *CA HA 1.4570 105.5400 117.2400 107.4600 1.0828 !D form +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +!PRES LTOD 0.00 ! patch to convert l amino acid to d +! ! needed for CMAP, AMG 2/27/2008 +! ! follow with AUTOgen +! ! DOESN'T WORK AT THE MOMENT!!!!!!! +!GROUP +!ATOM CA CTD1 0.07 +!CMAP -C N CA C N CA C +N + +END + +read para card flex @app +* Parameters for D- aminoacids +* + +ATOMS +MASS 438 CTD1 12.01100 ! added for D-amino acids +MASS 439 CPD1 12.01100 ! added for D-proline + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! + +! Added CTD1 -- new atom type for alpha carbon for d-amino acid, necessary +! for CMAP. Just duplicated the CT1 parameters. + +CTD1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO +CTD1 CC 200.000 1.5220 ! ALLOW POL +CTD1 CD 200.000 1.5220 ! ALLOW POL +CT1 CTD1 222.500 1.5000 ! ALLOW ALI +CT2 CTD1 222.500 1.5380 ! ALLOW ALI +CT3 CTD1 222.500 1.5380 ! ALLOW ALI +CT2A CTD1 222.500 1.5380 ! from CT2 CT1, Zhu +HA CTD1 309.000 1.1110 ! ALLOW ALI +HB1 CTD1 330.000 1.0800 ! ALLOW PEP +NH1 CTD1 320.000 1.4300 ! ALLOW ALI PEP POL ARO +NH3 CTD1 200.000 1.4800 ! ALLOW ALI POL +OH1 CTD1 428.000 1.4200 ! ALLOW ALI ALC ARO +CPD1 C 250.000 1.4900 ! ALLOW PRO +CP2 CPD1 222.500 1.5270 ! ALLOW PRO +HB1 CPD1 330.000 1.0800 ! ALLOW PRO +N CPD1 320.000 1.4340 ! ALLOW PRO + + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! + +! Added CTD1 -- new atom type for alpha carbon for d-amino acid, necessary +! for CMAP. Just duplicated the CT1 parameters. AMG 2/27/08 + +HA3 CT3 CTD1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) + +CT1 CTD1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CTD1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO +CTD1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CTD1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CTD1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO +CTD1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI +CTD1 CD OH1 55.000 110.50 ! From ASPP CT2-CD-OH1 +CTD1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO +CT2 CTD1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT2 CTD1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT2 CTD1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT2 CT1 CTD1 53.350 111.00 8.00 2.56100 ! ALLOW ALI +CT2 CT2 CTD1 58.350 113.50 11.16 2.56100 ! ALLOW ALI +CT2 CT3 CTD1 58.350 113.50 11.16 2.56100 ! ALLOW ALI +CT2A CTD1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT3 CTD1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT3 CTD1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT3 CTD1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI +CT3 CTD1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI +CT3 CTD1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI +CT3 CT2 CTD1 58.350 113.50 11.16 2.56100 ! ALLOW ALI +CT3 CT1 CTD1 53.350 108.50 8.00 2.56100 ! ALLOW ALI +CY CT2 CTD1 58.350 114.0000 ! ALLOW ARO +H NH1 CTD1 35.000 117.0000 ! ALLOW PEP POL ARO ALI +H OH1 CTD1 57.500 106.0000 ! ALLOW ALC ARO ALI +HA CTD1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO +HA CTD1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO +HA CTD1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI +HA CTD1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI +HA CTD1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI +HA CTD1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd +HA CT2 CTD1 33.430 110.10 22.53 2.17900 ! ALLOW ALI +HA CT3 CTD1 33.430 110.10 22.53 2.17900 ! ALLOW ALI +HA1 CT1 CTD1 34.500 110.10 22.53 2.17900 ! ALLOW ALI +HA2 CT2 CTD1 26.500 110.10 22.53 2.17900 ! ALLOW ALI +HB1 CTD1 C 50.000 109.5000 ! ALLOW PEP +HB1 CTD1 CC 50.000 109.5000 ! ALLOW PEP POL +HB1 CTD1 CD 50.000 109.5000 ! ALLOW PEP POL +HB1 CTD1 CT1 35.000 111.0000 ! ALLOW PEP +HB1 CTD1 CT2 35.000 111.0000 ! ALLOW PEP +HB1 CTD1 CT3 35.000 111.0000 ! ALLOW PEP +HC NH3 CTD1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI +N C CTD1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO +NH1 C CTD1 80.000 116.5000 ! ALLOW ALI PEP POL ARO +NH1 CTD1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI +NH1 CTD1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI +NH1 CTD1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI +NH1 CTD1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO +NH1 CTD1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO +NH1 CTD1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO +NH1 CTD1 HB1 48.000 108.0000 ! ALLOW PEP +NH2 CC CTD1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO +NH3 CTD1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI +NH3 CTD1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI +NH3 CTD1 CT1 67.700 110.0000 ! ALLOW ALI POL +NH3 CTD1 CT2 67.700 110.0000 ! ALLOW ALI POL +NH3 CTD1 CT3 67.700 110.0000 ! ALLOW ALI POL +NH3 CTD1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP +O C CTD1 80.000 121.0000 ! ALLOW ALI PEP POL ARO +O CC CTD1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO +OB CD CTD1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO +OC CC CTD1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION +OH1 CT1 CTD1 75.700 110.1000 ! ALLOW ALI ALC ARO +OH1 CT2 CTD1 75.700 110.1000 ! ALLOW ALI ALC ARO + +OS CD CTD1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP +S CT2 CTD1 58.000 112.5000 ! ALLOW ALI SUL ION +SM CT2 CTD1 58.000 112.5000 ! ALLOW ALI SUL ION + +!For GLU/HSP, Zhu transfer to D-FORM +NH1 CTD1 CT2A 70.000 113.5000 ! from NH1 CT1 CT2 +HB1 CTD1 CT2A 35.000 111.0000 ! from HB1 CT1 CT2 +CT2A CTD1 C 52.000 108.0000 ! from CT2 CT1 C +CTD1 CT2A HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT1 +CTD1 CT2A CT2 58.350 113.5000 11.16 2.56100 ! from CT2 CT2 CT1 +CTD1 CT2A CPH1 58.350 113.0000 ! from CT1 CT2 CPH1 + +!D-Proline +C N CPD1 60.000 117.0000 +N C CPD1 20.000 112.5000 +N CPD1 HB1 48.000 112.0000 +N CPD1 CP2 70.000 110.8000 +N CPD1 C 50.000 108.2000 +N CPD1 CC 50.000 108.2000 +N CPD1 CD 50.000 108.2000 +NH1 C CPD1 80.000 116.5000 +NH2 CC CPD1 80.000 112.5000 +NP CPD1 C 50.000 106.0000 +NP CPD1 CC 50.000 106.0000 +NP CPD1 CD 50.000 106.0000 +NP CPD1 CP2 70.000 108.5000 +NP CPD1 HB1 51.500 107.5000 +HB1 CPD1 CP2 35.000 118.0000 +HB1 CPD1 C 50.000 112.0000 +HB1 CPD1 CC 50.000 112.0000 +HB1 CPD1 CD 50.000 112.0000 +HC NP CPD1 33.000 109.50 4.00 2.05600 +CP2 CPD1 C 52.000 112.3000 +CP2 CPD1 CC 52.000 112.3000 +CP2 CPD1 CD 50.000 112.3000 +CP2 CP2 CPD1 70.000 108.5000 +CPD1 CP2 HA2 33.430 110.10 22.53 2.17900 +CPD1 C O 80.000 118.0000 +CPD1 CC O 80.000 118.0000 +CP3 N CPD1 100.000 114.2000 +CP3 NP CPD1 100.000 111.0000 +OB CD CPD1 70.000 125.00 20.00 2.44200 +OC CC CPD1 40.000 118.00 50.00 2.38800 +OS CD CPD1 55.000 109.00 20.00 2.32600 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + +! Added CTD1 -- new atom type for alpha carbon for d-amino acid, necessary +C CTD1 NH1 C 0.2000 1 180.00 ! ALLOW PEP +CC CTD1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO +CC CTD1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL +CD CTD1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL +CTD1 C N CP1 2.7500 2 180.00 ! ALLOW PRO +CTD1 C N CP1 0.3000 4 0.00 ! ALLOW PRO +CTD1 C N CP3 2.7500 2 180.00 ! ALLOW PRO +CTD1 C N CP3 0.3000 4 0.00 ! ALLOW PRO +CTD1 C NH1 CTD1 1.6000 1 0.00 ! ALLOW PEP +CTD1 C NH1 CTD1 2.5000 2 180.00 ! ALLOW PEP +CTD1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP +CTD1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP +CT1 C NH1 CTD1 1.6000 1 0.00 ! ALLOW PEP ! mix L and D +CT1 C NH1 CTD1 2.5000 2 180.00 ! ALLOW PEP ! mix L and D +CT1 CTD1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! mix L and D +CTD1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! mix L and D +CTD1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO +CTD1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO +CT2 C NH1 CTD1 1.6000 1 0.00 ! ALLOW PEP +CT2 C NH1 CTD1 2.5000 2 180.00 ! ALLOW PEP +CT2 CTD1 NH1 C 1.8000 1 0.00 ! ALLOW PEP +CT2 NH1 C CTD1 1.6000 1 0.00 ! ALLOW PEP +CT2 NH1 C CTD1 2.5000 2 180.00 ! ALLOW PEP +CT3 C NH1 CTD1 1.6000 1 0.00 ! ALLOW PEP +CT3 C NH1 CTD1 2.5000 2 180.00 ! ALLOW PEP +CT3 CTD1 NH1 C 1.8000 1 0.00 ! ALLOW PEP +CT3 NH1 C CTD1 1.6000 1 0.00 ! ALLOW PEP +CT3 NH1 C CTD1 2.5000 2 180.00 ! ALLOW PEP +H NH1 C CTD1 2.5000 2 180.00 ! ALLOW PEP +H NH1 CTD1 C 0.0000 1 0.00 ! ALLOW PEP +H NH1 CTD1 CC 0.0000 1 0.00 ! ALLOW PEP POL +H NH1 CTD1 CD 0.0000 1 0.00 ! ALLOW PEP POL +H NH1 CTD1 CTD1 0.0000 1 0.00 ! ALLOW PEP +H NH1 CT1 CTD1 0.0000 1 0.00 ! ALLOW PEP ! mix L and D +H NH1 CTD1 CT1 0.0000 1 0.00 ! ALLOW PEP +H NH1 CTD1 CT2 0.0000 1 0.00 ! ALLOW PEP +H NH1 CTD1 CT3 0.0000 1 0.00 ! ALLOW PEP +H NH2 CC CTD1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO +H OH1 CTD1 CT1 1.3300 1 0.00 ! ALLOW ALC ! mix L and D +H OH1 CTD1 CT1 0.1800 2 0.00 ! ALLOW ALC ! mix L and D +H OH1 CTD1 CT1 0.3200 3 0.00 ! ALLOW ALC ! mix L and D +H OH1 CTD1 CT3 1.3300 1 0.00 ! ALLOW ALC +H OH1 CTD1 CT3 0.1800 2 0.00 ! ALLOW ALC +H OH1 CTD1 CT3 0.3200 3 0.00 ! ALLOW ALC +HA CTD1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO +HB1 CTD1 NH1 C 0.0000 1 0.00 ! ALLOW PEP +HB1 CTD1 NH1 H 0.0000 1 0.00 ! ALLOW PEP +N C CT1 CTD1 0.0000 1 0.00 ! ALLOW PEP PRO ! mix L and D +N C CTD1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO ! mix L and D +N C CTD1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO +N C CTD1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO +N C CTD1 HB1 0.0000 1 0.00 ! ALLOW PEP PRO +N CTD1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO +NH1 C CT1 CTD1 0.0000 1 0.00 ! ALLOW PEP ! mix L and D +NH1 C CTD1 CT1 0.0000 1 0.00 ! ALLOW PEP ! mix L and D +NH1 C CTD1 CT2 0.0000 1 0.00 ! ALLOW PEP +NH1 C CTD1 CT3 0.0000 1 0.00 ! ALLOW PEP +NH1 C CTD1 HB1 0.0000 1 0.00 ! ALLOW PEP +NH1 C CTD1 NH1 0.6000 1 0.00 ! ALLOW PEP +NH1 CTD1 C N 0.4000 1 0.00 ! ALLOW PEP PRO +NH3 CTD1 C N 0.4000 1 0.00 ! ALLOW PEP PRO +NH3 CTD1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO +NH3 CTD1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO +NR3 CPH1 CT2 CTD1 0.1900 3 0.00 ! ALLOW ARO +!!!!O C CTD1 CTD1 1.4000 1 0.00 ! ALLOW PEP +O C CT1 CTD1 1.4000 1 0.00 ! ALLOW PEP ! mix L and D +O C CTD1 CT1 1.4000 1 0.00 ! ALLOW PEP ! mix L and D +O C CTD1 CT2 1.4000 1 0.00 ! ALLOW PEP +O C CTD1 CT3 1.4000 1 0.00 ! ALLOW PEP +O C CTD1 HB1 0.0000 1 0.00 ! ALLOW PEP +O C CTD1 NH1 0.0000 1 0.00 ! ALLOW PEP +O C CTD1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO +O C NH1 CTD1 2.5000 2 180.00 ! ALLOW PEP +OC CC CTD1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO +SM SM CT2 CTD1 0.3100 3 0.00 ! ALLOW SUL ALI + +X CTD1 CT2 X 0.2000 3 0.00 ! ALLOW ALI +X CTD1 CT3 X 0.2000 3 0.00 ! ALLOW ALI +X CTD1 CD X 0.0000 6 180.00 ! ALLOW POL PEP +X CTD1 CC X 0.0500 6 180.00 ! ALLOW POL PEP + +!D-amino acid side chain parameters +!chi1/chi2 fitting, Zhu, 2011 for D-FORM +!directly transferred parameters +NH1 CTD1 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT1 X +HB1 CTD1 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT1 X +HB1 CTD1 CT1 CT3 0.2000 3 0.00 ! From X CT1 CT1 X +HA1 CT1 CTD1 C 0.2000 3 0.00 ! From X CT1 CT1 X +NH1 CTD1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CTD1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CTD1 CT2 OH1 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CTD1 CT2 CT2 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2 CTD1 C 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CTD1 CT2 S 0.2000 3 0.00 ! From X CT1 CT2 X +!Asn +HB1 CTD1 CT2 CC 0.2000 3 0.00 ! From X CT1 CT2 X +!Trp +HB1 CTD1 CT2 CY 0.2000 3 0.00 ! From X CT1 CT2 X +!Hsd/Hse +HB1 CTD1 CT2 CPH1 0.2000 3 0.00 ! From X CT1 CT2 X +!Ile,Leu,Val +HB1 CTD1 CT1 CT2 0.2000 3 0.00 ! From X CT1 CT1 X +HB1 CTD1 CT2 CT1 0.2000 3 0.00 ! From X CT1 CT2 X +!Tyr/Phe +HB1 CTD1 CT2 CA 0.2000 3 0.00 ! From X CT1 CT2 X +!Thr +HB1 CTD1 CT1 OH1 0.2000 3 0.00 ! From X CT1 CT1 X +!Glu/Hsp +NH1 CTD1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X +CTD1 CT2A CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HB1 CTD1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CTD1 CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2A CTD1 C 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2A CTD1 CC 0.2000 3 0.00 ! RB: added for C-ter Glu +HB1 CTD1 CT2A CPH1 0.2000 3 0.00 ! From X CT1 CT2 X +C NH1 CTD1 CT2A 1.8000 1 0.00 ! from CT2 CT1 NH1 C +H NH1 CTD1 CT2A 0.0000 1 0.00 ! from H NH1 CT1 CT2 +CT2A CTD1 C O 1.4000 1 0.00 ! from O C CT1 CT2 +CT2A CTD1 C NH1 0.0000 1 0.00 ! NH1 C CT1 CT2 +CT2A CTD1 C N 0.0000 1 0.00 ! RB: added for GLU-PRO in UBQ +! Glup +CTD1 CT2A CT2 CD 0.1900 3 0.00 ! From X CT2 CT2 X +! Sidechain dihedrals: PEML transfered from L- to D- form +! Group-fitted for Lys/Arg/Gln/Met +C CTD1 CT2 CT2 0.3500 1 180.00 ! -180, +60 +C CTD1 CT2 CT2 0.4200 2 180.00 ! -180, +60 +C CTD1 CT2 CT2 1.9100 3 180.00 +CT2 CT2 CTD1 NH1 0.8800 1 180.00 +CT2 CT2 CTD1 NH1 0.0000 2 180.00 ! (-180), +60 +CT2 CT2 CTD1 NH1 1.9000 3 0.00 +CC CT2 CT2 CTD1 1.8400 1 180.00 ! (-180), -60, +60 +CC CT2 CT2 CTD1 0.8400 2 180.00 +CC CT2 CT2 CTD1 0.3900 3 180.00 +CTD1 CT2 CT2 CT2 0.6300 1 180.00 +CTD1 CT2 CT2 CT2 0.0100 2 0.00 +CTD1 CT2 CT2 CT2 0.1500 3 0.00 +CTD1 CT2 CT2 S 0.1400 1 180.00 +CTD1 CT2 CT2 S 0.5400 2 0.00 +CTD1 CT2 CT2 S 0.6900 3 0.00 +! Group-fitted for Asn/Asp +C CTD1 CT2 CC 1.4100 1 180.00 ! | +C CTD1 CT2 CC 1.2900 2 180.00 ! HN-N +C CTD1 CT2 CC 0.5900 3 180.00 ! | HB1 OD1 HD21 (cis to OD1) +CC CT2 CTD1 NH1 0.2800 1 180.00 ! | | || / +CC CT2 CTD1 NH1 0.5000 2 180.00 ! HA-CA--CB--CG--ND2 +CC CT2 CTD1 NH1 0.3800 3 0.00 ! | | \ +CTD1 CT2 CC NH2 0.6200 1 180.00 ! | HB2 HD22 (trans to OD1) +CTD1 CT2 CC NH2 0.6600 2 180.00 ! O=C +CTD1 CT2 CC NH2 0.7200 3 180.00 ! | +CTD1 CT2 CC O 0.4200 1 180.00 +CTD1 CT2 CC O 0.1500 2 180.00 +CTD1 CT2 CC O 0.9500 3 180.00 +CTD1 CT2 CC OC 0.8400 1 0.00 +CTD1 CT2 CC OC 0.9800 2 180.00 +CTD1 CT2 CC OC 1.4600 3 0.00 +! Fitted Cys +CTD1 CT2 S HS 0.2000 1 0.00 ! | +CTD1 CT2 S HS 0.6500 2 0.00 ! HN-N +CTD1 CT2 S HS 0.2200 3 0.00 ! | HB1 +C CTD1 CT2 S 0.2400 1 180.00 ! | | +C CTD1 CT2 S 0.7500 2 180.00 ! HA-CA--CB--SG +C CTD1 CT2 S 1.3500 3 180.00 ! | | \ +NH1 CTD1 CT2 S 0.3400 1 0.00 ! | HB2 HG1 +NH1 CTD1 CT2 S 0.5000 2 180.00 ! O=C +NH1 CTD1 CT2 S 1.4300 3 0.00 ! | +! Fitted Glu, 1/12 adjustment +CC CT2 CT2A CTD1 0.0000 1 180.00 ! | +CC CT2 CT2A CTD1 0.3800 2 180.00 ! HN-N +CC CT2 CT2A CTD1 0.5900 3 180.00 ! | HB1 HG1 OE1 +C CTD1 CT2A CT2 0.1100 1 0.00 ! | | | // +C CTD1 CT2A CT2 0.9800 2 180.00 ! HA-CA--CB--CG--CD +C CTD1 CT2A CT2 1.6000 3 180.00 ! | | | \ +CC CTD1 CT2A CT2 1.6000 3 180.00 ! | HB2 HG2 OE2(-) +CT2 CT2A CTD1 NH1 0.3000 1 0.00 ! (-180), (-60) ! O=C +CT2 CT2A CTD1 NH1 0.3500 2 0.00 ! -180 ! | +CT2 CT2A CTD1 NH1 1.7600 3 0.00 +! Group-fitted for Hsd/Hse +CPH1 CPH1 CT2 CTD1 1.7400 1 0.00 ! | HD1 HE1 +CPH1 CPH1 CT2 CTD1 0.1500 2 0.00 ! HN-N | / +CPH1 CPH1 CT2 CTD1 0.7700 3 180.00 ! | HB1 ND1--CE1 +CTD1 CT2 CPH1 NR1 1.4900 1 0.00 ! | | / || +CTD1 CT2 CPH1 NR1 0.0900 2 180.00 ! HA-CA--CB--CG || +CTD1 CT2 CPH1 NR1 0.7900 3 180.00 ! | | \\ || +CTD1 CT2 CPH1 NR2 1.0900 1 0.00 ! | HB2 CD2--NE2 +CTD1 CT2 CPH1 NR2 0.0900 2 0.00 ! O=C | +CTD1 CT2 CPH1 NR2 0.6700 3 180.00 ! | HD2 +C CTD1 CT2 CPH1 0.1800 1 180.00 +C CTD1 CT2 CPH1 0.6400 2 180.00 +C CTD1 CT2 CPH1 0.8700 3 180.00 +CPH1 CT2 CTD1 NH1 0.0000 1 0.00 +CPH1 CT2 CTD1 NH1 0.0000 2 180.00 +CPH1 CT2 CTD1 NH1 0.9000 3 0.00 +! Group-fitted for Hsp +CPH1 CPH1 CT2A CTD1 2.0400 1 0.00 +CPH1 CPH1 CT2A CTD1 0.4400 2 0.00 ! | HD1 HE1 +CPH1 CPH1 CT2A CTD1 0.1300 3 180.00 ! HN-N | / +CTD1 CT2A CPH1 NR3 0.5300 1 180.00 ! | HB1 ND1--CE1 +CTD1 CT2A CPH1 NR3 0.4200 2 180.00 ! | | / || +CTD1 CT2A CPH1 NR3 0.3000 3 180.00 ! HA-CA--CB--CG || +C CTD1 CT2A CPH1 1.7500 1 180.00 ! | | \\ || +C CTD1 CT2A CPH1 0.1300 2 0.00 ! | HB2 CD2--NE2(+) +C CTD1 CT2A CPH1 1.8600 3 180.00 ! O=C | \ +CPH1 CT2A CTD1 NH1 1.0900 1 180.00 ! | HD2 HE2 +CPH1 CT2A CTD1 NH1 0.2200 2 180.00 +CPH1 CT2A CTD1 NH1 2.3200 3 0.00 +! Group-fitted for Ile/Thr +CTD1 CT1 CT2 CT3 0.3800 1 180.00 ! | HG21 HG22 +CTD1 CT1 CT2 CT3 0.1300 2 180.00 ! HN-N | / +CTD1 CT1 CT2 CT3 0.2900 3 180.00 ! | CG2--HG23 +C CTD1 CT1 CT2 0.1000 1 180.00 ! -180,-,+60 ! | / +C CTD1 CT1 CT2 0.5200 2 180.00 ! HA-CA--CB-HB HD1 +C CTD1 CT1 CT2 0.2900 3 180.00 ! | \ / +CT2 CT1 CTD1 NH1 0.1200 1 180.00 ! | CG1--CD--HD2 +CT2 CT1 CTD1 NH1 0.3600 2 180.00 ! -180,-,- ! O=C / \ \ +CT2 CT1 CTD1 NH1 0.4100 3 0.00 ! | HG11 HG12 HD3 +! Fitted Leu +CTD1 CT2 CT1 CT3 0.0500 1 0.00 ! | HD11 HD12 +CTD1 CT2 CT1 CT3 0.1000 2 180.00 ! HN-N | / +CTD1 CT2 CT1 CT3 0.0100 3 180.00 ! | HB1 CD1--HD13 +C CTD1 CT2 CT1 0.3200 1 180.00 ! | | / +C CTD1 CT2 CT1 0.6100 2 180.00 ! -60 ! HA-CA--CB--CG-HG +C CTD1 CT2 CT1 0.7200 3 180.00 ! | | \ +CT1 CT2 CTD1 NH1 0.4800 1 180.00 ! | HB2 CD2--HD23 +CT1 CT2 CTD1 NH1 0.4200 2 180.00 ! O=C | \ +CT1 CT2 CTD1 NH1 0.6500 3 0.00 ! | HD21 HD22 +! Group-fitted for Phe/Tyr +CA CA CT2 CTD1 1.0700 1 0.00 +CA CA CT2 CTD1 0.2400 2 180.00 +CA CA CT2 CTD1 0.1700 3 180.00 +C CTD1 CT2 CA 1.2800 1 180.00 ! (-180),-60,+60 +C CTD1 CT2 CA 0.9400 2 180.00 ! -60 +C CTD1 CT2 CA 1.5700 3 180.00 ! all +CA CT2 CTD1 NH1 0.5200 1 180.00 ! -60,+60 +CA CT2 CTD1 NH1 0.6200 2 180.00 ! -60,+60 +CA CT2 CTD1 NH1 1.5800 3 0.00 ! none +! Fitted Ser +CTD1 CT2 OH1 H 0.0200 1 0.00 ! | +CTD1 CT2 OH1 H 0.5600 2 0.00 ! HN-N +CTD1 CT2 OH1 H 0.4900 3 0.00 ! | HB1 +C CTD1 CT2 OH1 0.6500 1 180.00 ! | | +C CTD1 CT2 OH1 0.2500 2 180.00 ! HA-CA--CB--OG +C CTD1 CT2 OH1 1.1700 3 180.00 ! | | \ +NH1 CTD1 CT2 OH1 0.1800 1 180.00 ! | HB2 HG1 +NH1 CTD1 CT2 OH1 0.1900 2 180.00 ! O=C +NH1 CTD1 CT2 OH1 1.4600 3 0.00 ! | +! Group-fitted for Ile/Thr +CTD1 CT1 OH1 H 0.1800 1 0.00 ! | +CTD1 CT1 OH1 H 0.0600 2 0.00 ! HN-N +CTD1 CT1 OH1 H 0.2500 3 0.00 ! | OG1--HG1 +C CTD1 CT1 OH1 0.7900 1 180.00 ! raise ! | / +C CTD1 CT1 OH1 0.3900 2 180.00 !lower this value if needed ! HA-CA--CB-HB +C CTD1 CT1 OH1 0.9900 3 180.00 ! | \ +NH1 CTD1 CT1 OH1 0.0900 1 0.00 ! raise to lower -180 ! | CG2--HG21 +NH1 CTD1 CT1 OH1 0.1900 2 180.00 ! O=C / \ +NH1 CTD1 CT1 OH1 0.1700 3 0.00 ! | HG21 HG22 +! Fitted Trp side-chain +CA CY CT2 CTD1 0.0300 1 0.00 +CA CY CT2 CTD1 0.5500 2 0.00 ! | HE3 +CA CY CT2 CTD1 0.3900 3 180.00 ! HN-N | +CPT CY CT2 CTD1 0.3600 1 180.00 ! | HB1 CE3 +CPT CY CT2 CTD1 0.0500 2 0.00 ! | | / \\ +CPT CY CT2 CTD1 0.1900 3 180.00 ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +C CTD1 CT2 CY 1.0900 1 180.00 ! modulates -180, +60 ! | | || || | +C CTD1 CT2 CY 0.5000 2 180.00 ! modulates -180, +60 ! | HB2 CD1 CE2 CH2-HH2 +C CTD1 CT2 CY 1.1700 3 180.00 ! O=C / \ / \ // +CY CT2 CTD1 NH1 0.2900 1 180.00 ! modulates -180 ! | HD1 NE1 CZ2 +CY CT2 CTD1 NH1 0.6600 2 180.00 ! modulates -60,60 ! | | +CY CT2 CTD1 NH1 1.1700 3 0.00 ! HE1 HZ2 +! Fitted Val +C CTD1 CT1 CT3 0.1400 1 180.00 ! | HG11 HG12 +C CTD1 CT1 CT3 0.2600 2 180.00 ! HN-N | / +C CTD1 CT1 CT3 0.3300 3 180.00 ! | CG1--HG13 +CT3 CT1 CTD1 NH1 0.1800 1 0.00 ! | / +CT3 CT1 CTD1 NH1 0.0600 2 0.00 ! HA-CA--CB-HB +CT3 CT1 CTD1 NH1 0.5900 3 0.00 ! | \ +! ! | CG2--HG21 +!D-proline +C N CPD1 C 0.8000 3 0.00 +CC CPD1 N C 0.8000 3 0.00 +CD CPD1 N C 0.0000 1 180.00 +CP1 C N CPD1 2.7500 2 180.00 +CP1 C N CPD1 0.3000 4 0.00 +CPD1 C N CPD1 2.7500 2 180.00 +CPD1 C N CPD1 0.3000 4 0.00 +CP2 CPD1 N C 0.8000 3 0.00 +CP2 CP3 N CPD1 0.1000 3 0.00 +CP2 CP3 NP CPD1 0.0800 3 0.00 +CP3 N C CPD1 2.7500 2 180.00 +CP3 N C CPD1 0.3000 4 0.00 +CP3 N CPD1 C 0.1000 3 0.00 +CP3 N CPD1 CC 0.1000 3 0.00 +CP3 N CPD1 CP2 0.1000 3 0.00 +CP3 NP CPD1 C 0.0800 3 0.00 +CP3 NP CPD1 CC 0.0800 3 0.00 +CP3 NP CPD1 CD 0.0800 3 0.00 +CP3 NP CPD1 CP2 0.0800 3 0.00 +CT1 C N CPD1 2.7500 2 180.00 +CT1 C N CPD1 0.3000 4 0.00 +CTD1 C N CPD1 2.7500 2 180.00 +CTD1 C N CPD1 0.3000 4 0.00 +CT1 NH1 C CPD1 1.6000 1 0.00 +CT1 NH1 C CPD1 2.5000 2 180.00 +CTD1 NH1 C CPD1 1.6000 1 0.00 +CTD1 NH1 C CPD1 2.5000 2 180.00 +CT2 C N CPD1 2.7500 2 180.00 +CT2 C N CPD1 0.3000 4 0.00 +CT2 NH1 C CPD1 1.6000 1 0.00 +CT2 NH1 C CPD1 2.5000 2 180.00 +CT3 C N CPD1 2.7500 2 180.00 +CT3 C N CPD1 0.3000 4 0.00 +CT3 NH1 C CPD1 1.6000 1 0.00 +CT3 NH1 C CPD1 2.5000 2 180.00 +H NH1 C CPD1 2.5000 2 180.00 +H NH2 CC CPD1 2.5000 2 180.00 +HA2 CP3 N CPD1 0.1000 3 0.00 +HA2 CP3 NP CPD1 0.0800 3 0.00 +HB1 CPD1 N C 0.8000 3 0.00 +HB1 CPD1 N CP3 0.1000 3 0.00 +HB1 CPD1 NP CP3 0.0800 3 0.00 +HC NP CPD1 C 0.0800 3 0.00 +HC NP CPD1 CC 0.0800 3 0.00 +HC NP CPD1 CD 0.0800 3 0.00 +HC NP CPD1 CP2 0.0800 3 0.00 +HC NP CPD1 HB1 0.0800 3 0.00 +N C CPD1 CP2 0.4000 1 0.00 +N C CPD1 CP2 0.6000 2 0.00 +N C CPD1 HB1 0.4000 1 180.00 +N C CPD1 HB1 0.6000 2 0.00 +N C CPD1 N 0.3000 1 0.00 +N C CPD1 N -0.3000 4 0.00 +NH1 C CPD1 CP2 0.4000 1 0.00 +NH1 C CPD1 CP2 0.6000 2 0.00 +NH1 C CPD1 HB1 0.4000 1 180.00 +NH1 C CPD1 HB1 0.6000 2 0.00 +NH1 C CPD1 N 0.3000 1 0.00 +NH1 C CPD1 N -0.3000 4 0.00 +NH2 CC CPD1 CP2 0.4000 1 0.00 +NH2 CC CPD1 CP2 0.6000 2 0.00 +NH2 CC CPD1 HB1 0.4000 1 180.00 +NH2 CC CPD1 HB1 0.6000 2 0.00 +NH2 CC CPD1 N 0.3000 1 0.00 +NH2 CC CPD1 N -0.3000 4 0.00 +NP CPD1 C N 0.3000 1 0.00 +NP CPD1 C NH1 0.3000 1 0.00 +NP CPD1 CC NH2 0.3000 1 0.00 +O C CPD1 CP2 0.4000 1 180.00 +O C CPD1 CP2 0.6000 2 0.00 +O C CPD1 HB1 0.4000 1 0.00 +O C CPD1 HB1 0.6000 2 0.00 +O C CPD1 N -0.3000 4 0.00 +O C N CPD1 2.7500 2 180.00 +O C N CPD1 0.3000 4 0.00 +O CC CPD1 CP2 0.4000 1 180.00 +O CC CPD1 CP2 0.6000 2 0.00 +O CC CPD1 HB1 0.4000 1 0.00 +O CC CPD1 HB1 0.6000 2 0.00 +O CC CPD1 N -0.3000 4 0.00 +OC CC CPD1 CP2 0.1600 3 0.00 +OC CC CPD1 HB1 0.1600 3 0.00 +OC CC CPD1 N 0.1600 3 0.00 +OC CC CPD1 NP 0.1600 3 0.00 +X CPD1 C X 0.0000 6 180.00 +X CPD1 CC X 0.0000 6 180.00 +X CPD1 CD X 0.0000 6 180.00 +X CPD1 CP2 X 0.1400 3 0.00 + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +! Added CTD1 -- new atom type for alpha carbon for d-amino acid, necessary +CC X X CTD1 96.0000 0 0.0000 +O CTD1 NH2 CC 45.0000 0 0.0000 +O NH2 CTD1 CC 45.0000 0 0.0000 +!D-proline +N C CPD1 CP3 0.0000 0 0.0000 +O CPD1 NH2 CC 45.0000 0 0.0000 +O NH2 CPD1 CC 45.0000 0 0.0000 + +CMAP +! 2D grid correction data. +! Finalfix3, Feig/Best/MacKerell 2010 + +!The following D CMAPs have been generated by calculating the L alanine dipeptide +!or L-proline dipeptide 2D surfaces, inverting those surfaces to create the +!corresponding D surfaces, calculating the D-alanine dipeptide or D-proline dipeptide +!2D surfaces without CMAP and then taking the differences between those surfaces +!and the target 2D surfaces to obtain the D CMAPs included below. This is due to +!the presence of some dihedral parameters that are chiral specific such that +!simple inversion of the L CMAP does not yield the target 2D surfaces. + +!CMAPS needed for D-proline +!C N CPD1 C N CPD1 C NH1 24 +!C N CPD1 C N CPD1 C N 24 + +! D-alanine map-- +! note the new type for the alpha carbon +C NH1 CTD1 C NH1 CTD1 C NH1 24 + +!-180 + 0.310000 0.146800 -0.765900 -1.335400 -2.148300 + -2.160810 -2.267870 -2.598220 -2.580830 -3.404490 + -4.725700 -4.634360 -4.642900 -2.019850 1.185000 + -0.506550 0.962840 1.972890 2.272970 2.903840 + 2.303100 1.434000 1.155000 0.952300 + +!-165 + -0.625300 -1.626900 -2.562900 -3.059740 -3.363110 + -3.369180 -3.658050 -3.481580 -4.008160 -4.954840 + -5.702850 -6.222600 -4.395030 -0.566050 -2.557530 + -0.905700 0.815560 1.703550 1.882100 1.825080 + 1.460990 0.726400 0.562500 0.112000 + +!-150 + -1.573410 -2.752750 -3.840310 -3.843910 -3.941180 + -3.858850 -3.931510 -4.005960 -4.599800 -5.206800 + -5.569900 -4.928200 -1.583900 2.007100 -2.982380 + -1.301530 0.109760 1.131600 1.544510 1.447380 + 0.817370 0.545310 0.207220 -0.219950 + +!-135 + -1.928130 -3.000390 -3.981520 -4.259580 -4.312100 + -4.116730 -4.702500 -4.659100 -4.814000 -4.817600 + -3.869800 -1.741200 -5.950460 -4.778710 -3.285200 + -1.647090 0.016510 0.808120 1.121900 1.268740 + 0.498800 0.176030 -0.139660 -0.985460 + +!-120 + -1.786080 -2.568620 -3.232880 -3.821130 -4.261120 + -4.664200 -5.178700 -5.003200 -4.330800 -3.519500 + -6.554900 -6.867890 -5.939310 -4.822740 -3.181440 + -1.688890 -0.151100 0.495340 0.940770 1.221510 + 0.945970 0.032380 -0.357300 -0.933600 + +!-105 + -1.667230 -2.227460 -3.090890 -3.903200 -4.417500 + -4.533100 -4.851800 -4.620100 -3.730800 -5.554900 + -6.688200 -6.679400 -5.868360 -4.295520 -2.829080 + -1.497990 -0.675160 -0.037500 0.667700 1.066940 + 1.188250 0.311660 -0.261780 -0.909050 + +!-90 + -1.537340 -2.468080 -2.974040 -3.586520 -3.916200 + -4.290500 -3.975500 -3.728500 -4.893330 -5.581720 + -6.433700 -6.109550 -5.025400 -3.641890 -2.606990 + -1.590500 -0.603900 -0.154300 0.664300 0.985700 + 0.990600 0.461020 -0.245250 -0.994560 + +!-75 + -2.065760 -2.436560 -3.552960 -3.542900 -3.987800 + -3.969000 -3.502300 -3.637400 -4.559880 -5.545520 + -5.417180 -5.412800 -4.299920 -3.235850 -2.120400 + -1.009000 -0.189300 0.169500 0.699100 1.006300 + 0.818600 0.222200 -0.828030 -1.458240 + +!-60 + -3.168670 -3.158360 -3.268800 -3.457100 -3.575500 + -3.328300 -2.658500 -3.598610 -4.825150 -5.344130 + -4.913630 -4.385710 -3.731190 -3.036880 -1.860800 + 1.809200 2.575000 0.619700 0.849600 0.906100 + -0.074100 -1.056100 -2.132610 -2.799340 + +!-45 + -3.840570 -3.414100 -3.485300 -3.243700 -2.681600 + -2.185900 -2.685300 -3.859600 -4.965010 -5.105430 + -4.429480 -3.696680 -3.108310 -0.240270 0.945060 + 2.085400 0.687300 0.935100 0.996000 0.545500 + -0.800500 -2.148880 -3.179090 -3.651610 + +!-30 + -2.792100 -2.282900 -1.446000 -0.889700 -1.785100 + -2.780900 -3.585400 -4.315070 -4.527310 -3.981470 + -3.438700 -1.305240 -0.228490 0.736810 1.705860 + 2.643640 1.148840 1.573550 1.609320 0.519540 + -0.940730 -2.216020 -3.260840 -3.309000 + +!-15 + -0.625600 0.489500 1.929300 -2.617500 -3.277500 + -3.728700 -4.086240 -4.011710 -3.071050 -2.002500 + -0.611300 -0.352880 -0.053690 0.861790 1.619750 + 2.630720 1.540220 2.405800 1.865840 0.366370 + -0.865770 -1.669500 -1.879400 -1.742900 + +!0 + 3.014700 -0.768400 -2.522000 -3.436500 -3.752600 + -3.606780 -2.558970 -1.663820 -1.029810 -1.386800 + 0.304110 0.253110 0.302940 0.959290 1.789360 + 2.702090 1.827350 1.854590 1.422100 1.156660 + 0.803300 0.650700 0.488800 0.929000 + +!15 + 0.424300 -1.576500 -2.975500 -3.626390 -3.601470 + -2.372160 -0.428870 0.366920 -0.158800 1.802290 + 1.205890 0.925440 0.695070 1.026880 1.797480 + 0.831650 1.037850 1.564000 1.769580 2.691460 + 3.442800 3.386500 3.901300 5.767700 + +!30 + -1.004100 -2.478530 -3.092900 -3.362600 -2.661700 + -1.410650 0.514510 0.715820 0.376320 2.397690 + 2.094840 1.701890 1.492380 -0.526880 0.456830 + 0.174590 0.947880 1.501990 2.957710 4.981370 + 6.248700 6.927100 4.349400 1.199300 + +!45 + -1.001170 -1.811860 -1.794070 -1.768200 -1.396500 + -0.707200 0.429800 0.561500 0.136900 0.447400 + 0.259700 -0.406400 -0.619250 0.034980 0.189600 + 0.288000 1.304750 2.639510 4.558270 5.569990 + 5.552690 4.374600 2.513200 0.258400 + +!60 + 0.424150 -0.019600 -1.296600 -1.349500 -0.764200 + -0.481900 0.493400 0.504500 0.451500 0.323600 + 0.010100 -0.639500 -0.174100 0.142600 -0.224500 + -0.302300 2.447550 3.854930 4.456530 4.570800 + 4.387830 3.348500 1.899320 1.418240 + +!75 + 1.556500 0.651200 -0.070000 -0.007000 -0.070300 + 0.375100 0.734600 0.485000 0.606000 0.409600 + -0.415400 -0.246400 0.058000 -0.499900 0.275700 + 1.870300 3.716330 4.395340 3.761880 3.881870 + 3.995780 3.244770 2.537360 3.529830 + +!90 + 1.632400 0.931100 0.463300 0.200200 0.111700 + 0.328800 0.641900 1.090400 0.598400 0.162700 + -0.779000 -1.438300 -1.329900 -0.425400 1.092300 + 2.621950 3.516850 4.080640 3.362660 3.526760 + 3.632110 3.339060 2.921140 2.928700 + +!105 + 2.225900 0.915200 0.496800 0.018100 -0.133800 + 0.057900 1.221900 0.954800 0.265200 0.389500 + -1.273400 -2.058300 -1.908700 -0.643700 1.087400 + 2.307110 3.139350 3.086180 3.255960 3.734380 + 3.553270 3.271080 3.000500 2.726600 + +!120 + 1.538400 0.630500 -0.067800 -0.674100 -0.785300 + -0.365800 1.093700 0.622200 0.121400 -0.242100 + -1.620400 -2.445900 -1.937400 -0.605300 0.888090 + 1.810940 2.902470 2.956230 2.821830 3.740670 + 3.881230 3.219850 2.880700 2.140100 + +!135 + 1.108400 -0.261000 -0.384100 -0.800400 -0.970500 + -0.336500 0.496400 0.205100 -0.749500 -1.156900 + -1.775800 -2.095600 -1.813400 -1.001570 0.298350 + 2.035200 2.240490 2.370360 2.643460 3.100740 + 3.293120 2.727800 2.423400 1.703000 + +!150 + 0.264300 -0.634000 -1.110300 -1.102000 -0.584700 + -0.043100 0.252100 -0.543700 -1.170600 -1.707200 + -2.368220 -2.822210 -2.400180 -1.632680 -0.043000 + 2.646740 1.738700 2.168300 2.504200 2.899100 + 2.836100 2.228900 1.806800 1.601800 + +!165 + 0.053200 -0.940700 -0.896100 -0.025800 -0.455600 + -0.676900 -0.917000 -1.316700 -2.115050 -2.417720 + -3.234770 -3.950500 -3.824950 -2.618000 0.441310 + 0.824250 1.269700 2.111910 2.619590 2.669100 + 2.581400 2.054500 1.759900 1.558700 + + +! alanine before proline map +! D-alanine map-- +! note the new type for the alpha carbon +C NH1 CTD1 C NH1 CTD1 C N 24 + +!-180 + 0.310000 0.146800 -0.765900 -1.335400 -2.148300 + -2.160810 -2.267870 -2.598220 -2.580830 -3.404490 + -4.725700 -4.634360 -4.642900 -2.019850 1.185000 + -0.506550 0.962840 1.972890 2.272970 2.903840 + 2.303100 1.434000 1.155000 0.952300 + +!-165 + -0.625300 -1.626900 -2.562900 -3.059740 -3.363110 + -3.369180 -3.658050 -3.481580 -4.008160 -4.954840 + -5.702850 -6.222600 -4.395030 -0.566050 -2.557530 + -0.905700 0.815560 1.703550 1.882100 1.825080 + 1.460990 0.726400 0.562500 0.112000 + +!-150 + -1.573410 -2.752750 -3.840310 -3.843910 -3.941180 + -3.858850 -3.931510 -4.005960 -4.599800 -5.206800 + -5.569900 -4.928200 -1.583900 2.007100 -2.982380 + -1.301530 0.109760 1.131600 1.544510 1.447380 + 0.817370 0.545310 0.207220 -0.219950 + +!-135 + -1.928130 -3.000390 -3.981520 -4.259580 -4.312100 + -4.116730 -4.702500 -4.659100 -4.814000 -4.817600 + -3.869800 -1.741200 -5.950460 -4.778710 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-45.00 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 + +!-30 + 1.792800 2.239800 -3.278800 -3.391000 -3.519700 + -3.665500 -4.200100 -4.906500 -4.744100 -3.234400 + -2.611900 -2.515300 -2.459200 -2.785100 -3.328900 + -3.572700 -3.159800 -2.502000 -2.989900 -4.402700 + -5.277500 -4.772500 -2.990600 -0.650500 + +!-15 + 0.918300 -1.233800 -2.695000 -3.174500 -3.681500 + -4.098600 -4.400900 -4.161300 -3.159500 -2.804600 + -3.060400 -2.927300 -2.902500 -3.327000 -3.944600 + -4.144100 -3.544500 -3.283500 -4.217800 -4.832800 + -4.646800 -3.775000 -2.473700 -0.558300 + +!0 + 2.331500 -0.875500 -2.927700 -4.233600 -4.931600 + -4.758100 -3.631500 -2.100800 -1.646400 -2.243700 + -2.340400 -2.172100 -2.249400 -2.796200 -3.529500 + -3.772900 -3.681400 -4.264800 -4.155300 -3.532600 + -2.890400 -2.278500 -0.743100 2.322800 + +!15 + 1.327300 3.224600 1.412700 -0.091200 -0.374000 + 0.883400 3.229500 4.961800 5.052500 -0.071900 + -0.018500 0.015000 -0.377200 -1.271600 -2.153400 + -2.573600 -3.429500 -3.258400 -2.017700 -0.897900 + -0.396300 0.533600 6.471000 -0.194500 + +!30 + 3.146400 1.208100 -0.786800 -1.675500 -1.010800 + 1.025000 3.225100 4.369300 4.722600 4.845600 + 4.899500 4.801600 4.245700 3.161200 1.895800 + 0.185400 -0.361900 1.011400 2.954500 4.572000 + 5.958500 7.467700 7.858100 5.419300 + +!45 + 2.611300 0.891700 -0.341600 -0.637000 0.275100 + 1.887000 3.213100 3.878700 4.162600 4.264900 + 4.303000 4.243300 3.910600 3.213200 1.730200 + 0.593300 1.164800 2.771800 4.153500 4.899400 + 5.379500 5.883700 5.305600 4.164600 + +!60 + 2.116700 1.410500 0.649000 0.415900 0.881800 + 1.571700 2.019600 2.275100 2.490300 2.670400 + 2.931600 3.250400 3.393900 2.782600 1.645000 + 1.258500 2.049200 3.363700 5.105400 4.364500 + 3.792600 3.332100 2.821200 2.500700 + +!75 + 3.387800 2.478100 1.402000 0.860500 1.265800 + 2.022300 2.201700 1.407200 0.353800 -0.159600 + -0.149800 0.306600 1.192500 1.143300 -0.313700 + -1.397200 -1.297900 -0.209800 1.390800 1.705600 + 1.865600 2.687100 3.698500 3.940100 + +!90 + 0.851400 0.276700 -0.551600 -0.976800 -0.989300 + -1.166400 -1.696100 -2.157500 -2.207200 -1.764100 + -0.784600 0.084000 0.008800 -0.558300 -1.168000 + -1.143100 -0.329300 0.334700 -0.228700 -1.516100 + -1.793200 -1.116800 -0.118100 0.670800 + +!105 + 3.528100 2.472500 0.933000 -0.136000 -0.007300 + 0.906900 1.473600 0.927800 -0.180300 -0.470600 + 0.122500 1.167100 0.821000 -0.612200 -2.245500 + -3.073100 -2.398100 -0.432300 1.104700 1.115900 + 1.283800 -2.898100 -1.136700 0.090800 + +!120 + 2.394900 1.212200 -0.433200 -1.623500 -1.650900 + -0.844200 0.000600 0.102200 -0.210400 0.000600 + 0.494300 0.335600 -0.698000 -2.351600 -3.942500 + -4.461000 -3.390000 -1.302300 -0.791000 -0.755400 + -0.181200 0.866900 2.036600 2.757600 + +!135 + 1.906100 0.591400 -1.101900 -2.270900 -2.225300 + -1.428300 -0.802700 -0.510000 -0.132300 0.268400 + 0.110800 -0.444300 -1.784500 -3.565300 -4.934200 + -4.954000 -3.505900 -1.277400 -1.170100 -1.287800 + -0.921300 0.174600 1.624200 2.432900 + +!150 + 1.033700 -0.093000 -1.657100 -2.686900 -2.619600 + -1.868900 -1.170000 -0.882700 -1.017200 -1.172300 + -1.114400 -1.353900 -1.937600 -2.557200 -2.888100 + -2.718300 -2.418200 -2.275000 -1.885900 -1.673900 + -1.281100 -0.328600 0.726400 1.254400 + +!165 + -0.033900 -1.362700 -3.181500 -4.276800 -4.053400 + -3.154400 -2.470200 -2.374600 -2.687200 -2.834600 + -2.713100 -2.899100 -3.581000 -4.255500 -4.552600 + -4.226900 -4.035800 -3.392600 -2.858000 -2.697800 + -2.315700 -1.240400 -0.146600 0.301300 + + + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 2013 correction +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!carbons + +! Added CTD1 -- new atom type for alpha carbon for d-amino acid, necessary +! for CMAP. Just duplicated the CT1 parameters. AMG 2/27/08 + +CTD1 0.000000 -0.032000 2.000000 0.000000 -0.010000 1.900000 ! alkane, 4/07, viv +CPD1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_fluoro_alkanes.str b/charmm/toppar/stream/prot/toppar_all36_prot_fluoro_alkanes.str new file mode 100644 index 00000000..eb3f0991 --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_fluoro_alkanes.str @@ -0,0 +1,285 @@ +* Topology and parameters for fluorinated alkanes. +* + +!Parent files that have to be read prior to streaming this file +!top_all36_prot.rtf +!par_all36_prot.prm + +!Testcase +!test_all36_prot_fluoro_alkanes.inp + +!Reference +!Chen, I.-J., Yin, D. and MacKerell, Jr., A.D., "Combined Ab +!initio/Empirical Approach for Optimization of Lennard-Jones Parameters +!for Polar-Neutral Compounds," Journal of Computational Chemistry, +!2002, 23:199-213. +! +!Note that these parameters are higly optimized to reproduce the +!corresponding condensed phase properties and have not been incorporated +!into the CHARMM22 or CHARMM27 biomolecular force fields + +read rtf card append +* topology for fluoroalkanes +* +31 1 + +MASS 430 HF1 1.00800 H ! Aliphatic H on fluorinated C +MASS 431 HF2 1.00800 H ! Aliphatic H on fluorinated C +MASS 432 CF1 12.01100 C ! monofluoromethyl +MASS 433 CF2 12.01100 C ! difluoromethyl +MASS 434 CF3 12.01100 C ! trifluoromethyl +MASS 435 F1 18.99800 F ! Fluorine, monofluoro +MASS 436 F2 18.99800 F ! Fluorine, difluoro +MASS 437 F3 18.99800 F ! Fluorine, trifluoro + +Auto angle dihedral +Default First None Last None ! ### No default patching. + +Resi ETHA 0.0 ! ethane +Group + Atom h13 ha3 0.09 + Atom c1 ct3 -0.27 + Atom c2 ct3 -0.27 + Atom h21 ha3 0.09 + Atom h22 ha3 0.09 + Atom h23 ha3 0.09 + Atom h11 ha3 0.09 + Atom h12 ha3 0.09 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 +Bond c2 h21 c2 h22 c2 h23 +ic h21 c2 c1 h13 0.00 0.00 180.0 0.0 0.0 +ic h22 c2 c1 h13 0.00 0.00 60.0 0.0 0.0 +ic h23 c2 c1 h13 0.00 0.00 -60.0 0.0 0.0 +ic h11 c1 c2 h21 0.00 0.00 60.0 0.0 0.0 +ic h12 c1 c2 h21 0.00 0.00 -60.0 0.0 0.0 +ic c1 c2 h21 h22 0.00 0.00 0.0 0.0 0.0 +patc firs none last none + +Resi FETH 0.0 ! fluoroethane, adm jr., 4/99 +Group + Atom h13 ha3 0.09 + Atom c1 ct3 -0.21 + Atom c2 cf1 -0.06 + Atom f21 f1 -0.22 + Atom h22 hf1 0.11 + Atom h23 hf1 0.11 + Atom h11 ha3 0.09 + Atom h12 ha3 0.09 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 +Bond c2 f21 c2 h22 c2 h23 +ic h13 c1 c2 f21 1.1111 110.55 180.00 109.78 1.3721 +ic h13 c1 c2 h22 1.1111 110.55 60.02 111.56 1.0839 +ic h13 c1 c2 h23 1.1111 110.55 -60.02 111.56 1.0839 +ic c1 c2 h22 h23 1.5188 111.56 -122.50 36.33 1.7464 +ic h13 c2 *c1 h11 1.1111 110.55 -120.29 110.55 1.1111 +ic h13 c2 *c1 h12 1.1111 110.55 120.29 110.55 1.1111 +patc firs none last none + +Resi DFET 0.0 ! difluoroethane, adm jr., 4/99 +Group + Atom h13 ha3 0.09 + Atom c1 ct3 -0.23 + Atom c2 cf2 0.24 + Atom h21 hf2 0.10 + Atom f22 f2 -0.19 + Atom f23 f2 -0.19 + Atom h11 ha3 0.09 + Atom h12 ha3 0.09 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 +Bond c2 f23 c2 f22 c2 h21 +ic h13 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 +ic c1 c2 f23 f22 0.00 0.00 0.0 0.0 0.0 +ic h13 c1 c2 f22 0.00 0.00 60.0 0.0 0.0 +ic h13 c1 c2 f23 0.00 0.00 -60.0 0.0 0.0 +ic h12 c1 c2 h21 0.00 0.00 -60.0 0.0 0.0 +ic h11 c1 c2 h21 0.00 0.00 60.0 0.0 0.0 +patc firs none last none + +Resi TFET 0.0 ! trifluoroethane +Group + Atom h11 ha3 0.09 + Atom h12 ha3 0.09 + Atom h13 ha3 0.09 + Atom c1 ct3 -0.20 + Atom f21 f3 -0.15 + Atom f22 f3 -0.15 + Atom f23 f3 -0.15 + Atom c2 cf3 0.38 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 f21 c2 f22 c2 f23 +ic h13 c1 c2 f21 0.00 0.00 180.0 0.0 0.0 +ic c1 c2 f22 f23 0.00 0.00 0.0 0.0 0.0 +ic h13 c1 c2 f22 0.00 0.00 60.0 0.0 0.0 +ic h13 c1 c2 f23 0.00 0.00 -60.0 0.0 0.0 +ic h11 c1 c2 f21 0.00 0.00 60.0 0.0 0.0 +ic h12 c1 c2 f21 0.00 0.00 -60.0 0.0 0.0 +patc firs none last none + +Resi TFE 0.0 ! trifluoroethanol, adm jr., 1/04 +Group ! + Atom o1 oh1 -0.60 + Atom ho1 H 0.42 + Atom h11 HA2 0.09 + Atom h12 HA2 0.09 + Atom c1 CT2 0.08 + Atom f21 f3 -0.14 + Atom f22 f3 -0.14 + Atom f23 f3 -0.14 + Atom c2 cf3 0.34 + +Bond c1 h11 c1 h12 c1 o1 o1 ho1 +Bond c1 c2 c2 f21 c2 f22 c2 f23 + +IC HO1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C2 F21 0.0000 0.00 180.00 0.00 0.0000 +IC F21 C1 *C2 F22 0.0000 0.00 120.00 0.00 0.0000 +IC F21 C1 *C2 F23 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +resi fe1a -0.27 ! residue for fluoroethane to ethane + ! perturbation. use with PATCH fe1b +atom c1 ct3 -0.27 +group +atom c2 ct3 -0.27 +atom h21 ha3 0.09 +atom h22 ha3 0.09 +atom h23 ha3 0.09 +bond c1 c2 c2 h21 c2 h22 c2 h23 + +pres fe1b 0.00 ! connect fe1a to fluoroethane + ! 1 fluoroethane + ! 2 fe1a +bond 1h11 2c1 +bond 1h12 2c1 +bond 1h13 2c1 +ic 1h11 2c1 2c2 2h21 0.0 0.0 0.0 0.0 0.0 +ic 1h11 2c1 2c2 2h22 0.0 0.0 0.0 0.0 0.0 +ic 2c1 2c2 2h21 2h22 0.0 0.0 0.0 0.0 0.0 + +end + +read para card flex append +* fluoroalkane parameters +* + +ATOMS +MASS 430 HF1 1.00800 ! Aliphatic H on fluorinated C +MASS 431 HF2 1.00800 ! Aliphatic H on fluorinated C +MASS 432 CF1 12.01100 ! monofluoromethyl +MASS 433 CF2 12.01100 ! difluoromethyl +MASS 434 CF3 12.01100 ! trifluoromethyl +MASS 435 F1 18.99800 ! Fluorine, monofluoro +MASS 436 F2 18.99800 ! Fluorine, difluoro +MASS 437 F3 18.99800 ! Fluorine, trifluoro + +BONDS + +CF3 CT2 250.00 1.5200 !from CF3 CT3 for TFE +!stanard alkane/hydroxyl parameters +!CT2 CT1 222.500 1.5380 +!CT3 CT1 222.500 1.5380 +!CT3 CT2 222.500 1.5280 +!HA1 CT1 309.000 1.1110 +!HA2 CT2 309.000 1.1110 +!HA3 CT3 322.000 1.1110 +!OH1 CT1x 428.000 1.4200 +!OH1 CT3x 428.000 1.4200 +!OH1 H 545.000 0.9600 +! new fluoroalkane parameters +F1 CF1 420.000 1.3740 +F2 CF2 349.000 1.3530 +F3 CF3 265.000 1.3400 +CF1 CT3 170.00 1.5200 +CF2 CT3 198.00 1.5200 +CF3 CT3 250.00 1.5200 +CF1 HF1 342.000 1.0828 ! from: HA CT3x!From CF1 HA +CF2 HF2 346.000 1.0828 ! from: HA CT3x!From CF2 HA + +ANGLES +HA2 CT2 CF3 34.600 110.10 22.53 2.179 !from HA2 CT2 CT3 for TFE +F3 CF3 CT2 42.0 112.00 30.00 2.357 !from F3 CF3 CT3 for TFE +!stanard alkane/hydroxyl parameters +!CT2x CT3x CT1x 58.350 113.50 11.16 2.561 +!CT3x CT1x CT2x 53.350 114.00 8.00 2.561 +!CT3x CT1x CT3x 53.350 114.00 8.00 2.561 +!CT3x CT2x CT3x 53.350 114.00 8.00 2.561 +!H OH1 CT1x 57.500 106.00 +!H OH1 CT3x 57.500 106.00 +!HA1 CT1x HA1 35.500 109.00 5.40 1.802 +!OH1 CT1x CT1x 75.700 110.10 +!OH1 CT1x CT3x 75.700 110.10 +!OH1 CT1x HA1 45.900 108.89 +!OH1 CT2x CT1x 75.700 110.10 +!OH1 CT2x CT3x 75.700 110.10 +!OH1 CT3x HA3 45.900 108.89 +! new fluoroalkane parameters +F2 CF2 F2 150.0 107.00 10.00 2.170 +F3 CF3 F3 118.0 107.00 30.00 2.155 +F1 CF1 CT3 44.0 112.00 30.00 2.369 +F2 CF2 CT3 50.0 112.00 30.00 2.357 +F3 CF3 CT3 42.0 112.00 30.00 2.357 +HA3 CT3 CF1 33.00 110.50 38.00 2.181 +HA3 CT3 CF2 33.000 110.50 37.00 2.168 +HA3 CT3 CF3 33.000 110.50 39.00 2.155 +CT3 CF1 HF1 31.000 112.00 3.00 2.168 !from: CT3 CF1 HA +CT3 CF2 HF2 32.000 112.00 3.00 2.168 !from: CT3 CF2 HA +F1 CF1 HF1 57.500 108.89 5.00 1.997 !from: F1 CF1 HA +F2 CF2 HF2 41.900 108.89 5.00 1.980 !from: F1 CF2 HA +HF1 CF1 HF1 35.500 108.40 10.40 1.746 !from: HA CF1 HA +! FOR FLUOROMETHANE AND FLUORO +!OH1 CT2 CF1 75.700 110.10 +!OH1 CT2 CF2 75.700 110.10 +OH1 CT2 CF3 75.700 110.10 !for TFE +F1 CF3 HA 45.900 108.89 !for TFE +!HA CF2 HA 37.500 108.40 5.40 1.802 !from: HA CT3 HA FOR CH2F2 + +DIHEDRALS +!TFE +H OH1 CT2 CF3 0.4000 1 0.00 !triflouroethanol +H OH1 CT2 CF3 0.9000 2 0.00 ! +H OH1 CT2 CF3 0.7000 3 0.00 ! +H OH1 CT2 CF3 0.1200 4 0.00 ! +!H OH1 CT2 HA2 0.0000 3 0.00 ! DIFFERENT COPY OF SAME PARAMETER IN toppar_all22_prot_pyridines.str +!HA2 CT2 OH1 H 0.1400 3 0.00 ! From X CT2 OH1 X; equivalent to parameter in protein set +HA2 CT2 CF3 F3 0.1580 3 0.00 ! +OH1 CT2 CF3 F3 0.2500 3 0.00 ! +!standard alkane/hydroxyl terms +!H OH1 CT1x CT1x 1.3300 1 0.00 ! triflouroethanol parameters +!H OH1 CT1x CT1x 0.1800 2 0.00 ! not available +!H OH1 CT1x CT1x 0.3200 3 0.00 ! +!H OH1 CT1x CT3x 1.3300 1 0.00 ! +!H OH1 CT1x CT3x 0.1800 2 0.00 ! +!H OH1 CT2x CT1x 1.3000 1 0.00 ! +!H OH1 CT2x CT1x 0.3000 2 0.00 ! +!H OH1 CT2x CT1x 0.4200 3 0.00 ! +!H OH1 CT2x CT3x 1.3000 1 0.00 ! +!H OH1 CT2x CT3x 0.3000 2 0.00 ! +!H OH1 CT2x CT3x 0.4200 3 0.00 ! +! new fluoroalkane parameters +X CT3 CF1 X 0.1850 3 0.00 +X CT3 CF2 X 0.1780 3 0.00 +X CT3 CF3 X 0.1580 3 0.00 + +IMPROPER + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +CF1 0.000000 -0.060000 1.900000 +CF2 0.000000 -0.042000 2.050000 +CF3 0.000000 -0.020000 2.300000 +HF1 0.000000 -0.028000 1.3200 +HF2 0.000000 -0.030000 1.3000 +F1 0.0 -0.135 1.63 +F2 0.0 -0.105 1.63 +F3 0.0 -0.097 1.60 + +END + +return + diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_heme.str b/charmm/toppar/stream/prot/toppar_all36_prot_heme.str new file mode 100644 index 00000000..15241164 --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_heme.str @@ -0,0 +1,602 @@ +* Topology and Parameter Stream File for heme and related +* ligands and patches. +* + +!Parent files that have to be read prior to streaming this file +!top_all36_prot.rtf +!par_all36_prot.prm + +!Testcase +!test_all36_prot_heme.inp + +read rtf card append +* Topology for heme and related compounds and patches +* +31 1 + +MASS 486 CPA 12.01100 C ! heme alpha-C +MASS 487 CPB 12.01100 C ! heme beta-C +MASS 488 CPM 12.01100 C ! heme meso-C +MASS 489 CM 12.01100 C ! heme CO carbon +MASS 490 CST 12.01100 C ! CO2 carbon +MASS 491 NPH 14.00700 N ! heme pyrrole N +MASS 492 OM 15.99900 O ! heme CO/O2 oxygen +MASS 493 OST 15.99900 O ! CO2 oxygen +MASS 494 FE 55.84700 Fe ! heme iron 56 + +RESI HEME -2.00 ! 6-liganded planar heme +GROUP +ATOM FE FE 0.24 ! O2A O1A O2D O1D +ATOM NA NPH -0.18 ! \\ // \\ // +ATOM NB NPH -0.18 ! CGA CGD +ATOM NC NPH -0.18 ! | | +ATOM ND NPH -0.18 ! HBA1--CBA--HBA2 HA HBD1--CBD--HBD2 +ATOM C1A CPA 0.12 ! | | | +ATOM C2A CPB -0.06 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2 +ATOM C3A CPB -0.06 ! | / \ | +ATOM C4A CPA 0.12 ! C2A---C1A C4D---C3D +ATOM C1B CPA 0.12 ! | | | | +ATOM C2B CPB -0.06 !HMA1\ | | | | /HMD1 +ATOM C3B CPB -0.06 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2 +ATOM C4B CPA 0.12 !HMA3/ \ / \ / \ / \HMD3 +ATOM C1C CPA 0.12 ! C4A \ / C1D +ATOM C2C CPB -0.06 ! / \ / \ +ATOM C3C CPB -0.06 ! HB--CHB FE CHD--HD +ATOM C4C CPA 0.12 ! \ / \ / +ATOM C1D CPA 0.12 ! C1B / \ C4C HAC +ATOM C2D CPB -0.06 !HMB1\ / \ / \ / \ / +ATOM C3D CPB -0.06 !HMB2-CMB--C2B NB NC C3C--CAC +ATOM C4D CPA 0.12 !HMB3/ | | | | \\ /HBC1 +GROUP ! | | | | CBC +ATOM CHA CPM -0.10 ! C3B---C4B C1C---C2C \HBC2 +ATOM HA HA 0.10 ! | \_CHC_/ | +GROUP ! CAB | CMC--HMC3 +ATOM CHB CPM -0.10 ! // \ HC / | +ATOM HB HA 0.10 ! CBB HAB HMC1 HMC2 +GROUP ! / \ +ATOM CHC CPM -0.10 ! HBB1 HBB2 +ATOM HC HA 0.10 ! +GROUP +ATOM CHD CPM -0.10 +ATOM HD HA 0.10 +GROUP +ATOM CMA CT3 -0.27 +ATOM HMA1 HA3 0.09 +ATOM HMA2 HA3 0.09 +ATOM HMA3 HA3 0.09 +GROUP +ATOM CAA CT2 -0.18 +ATOM HAA1 HA2 0.09 +ATOM HAA2 HA2 0.09 +GROUP +ATOM CBA CT2 -0.28 +ATOM HBA1 HA2 0.09 +ATOM HBA2 HA2 0.09 +ATOM CGA CC 0.62 +ATOM O1A OC -0.76 +ATOM O2A OC -0.76 +GROUP +ATOM CMB CT3 -0.27 +ATOM HMB1 HA3 0.09 +ATOM HMB2 HA3 0.09 +ATOM HMB3 HA3 0.09 +GROUP +ATOM CAB CE1 -0.15 !vinyl parameters updated, adm jr., May 2002 +ATOM HAB HE1 0.15 +GROUP +ATOM CBB CE2 -0.42 +ATOM HBB1 HE2 0.21 +ATOM HBB2 HE2 0.21 +GROUP +ATOM CMC CT3 -0.27 +ATOM HMC1 HA3 0.09 +ATOM HMC2 HA3 0.09 +ATOM HMC3 HA3 0.09 +GROUP +ATOM CAC CE1 -0.15 +ATOM HAC HE1 0.15 +GROUP +ATOM CBC CE2 -0.42 +ATOM HBC1 HE2 0.21 +ATOM HBC2 HE2 0.21 +GROUP +ATOM CMD CT3 -0.27 +ATOM HMD1 HA3 0.09 +ATOM HMD2 HA3 0.09 +ATOM HMD3 HA3 0.09 +GROUP +ATOM CAD CT2 -0.18 +ATOM HAD1 HA2 0.09 +ATOM HAD2 HA2 0.09 +GROUP +ATOM CBD CT2 -0.28 +ATOM HBD1 HA2 0.09 +ATOM HBD2 HA2 0.09 +ATOM CGD CC 0.62 +ATOM O1D OC -0.76 +ATOM O2D OC -0.76 +BOND FE NA FE NB FE NC FE ND NA C1A +BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA +BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA +BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B +BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB +BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C +BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC +BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D +BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD +BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A +BOND CHA HA CHB HB CHC HC CHD HD +BOND CAA HAA1 CAA HAA2 CBA HBA1 CBA HBA2 +BOND CMA HMA1 CMA HMA2 CMA HMA3 +BOND CMB HMB1 CMB HMB2 CMB HMB3 +BOND CAB HAB CBB HBB1 CBB HBB2 +BOND CMC HMC1 CMC HMC2 CMC HMC3 +BOND CAC HAC CBC HBC1 CBC HBC2 +BOND CMD HMD1 CMD HMD2 CMD HMD3 +BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2 +IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB +IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC +IMPR C2D C1D C3D CMD C3D C2D C4D CAD +IMPR CGA CBA O2A O1A CGD CBD O2D O1D +IMPR C4A NA C1A C2A C1A NA C4A C3A +IMPR C4B NB C1B C2B C1B NB C4B C3B +IMPR C4C NC C1C C2C C1C NC C4C C3C +IMPR C4D ND C1D C2D C1D ND C4D C3D +IMPR NA C1A C2A C3A NA C4A C3A C2A +IMPR NB C1B C2B C3B NB C4B C3B C2B +IMPR NC C1C C2C C3C NC C4C C3C C2C +IMPR ND C1D C2D C3D ND C4D C3D C2D +IMPR NA C1A CHA C4D NA C4A CHB C1B +IMPR NB C1B CHB C4A NB C4B CHC C1C +IMPR NC C1C CHC C4B NC C4C CHD C1D +IMPR ND C1D CHD C4C ND C4D CHA C1A +IMPR CHA C1A C4D HA +IMPR CHB C1B C4A HB +IMPR CHC C1C C4B HC +IMPR CHD C1D C4C HD +IMPR C1A C2A CHA NA C4A C3A CHB NA +IMPR C1B C2B CHB NB C4B C3B CHC NB +IMPR C1C C2C CHC NC C4C C3C CHD NC +IMPR C1D C2D CHD ND C4D C3D CHA ND +IMPR NA C1A C4A FE +IMPR NB C1B C4B FE +IMPR NC C1C C4C FE +IMPR ND C1D C4D FE +!No vinyl impropers in update +!IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1 +!IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1 +ACCEPTOR NA +ACCEPTOR O1A ! CGA +ACCEPTOR O2A ! CGA +ACCEPTOR NB +ACCEPTOR NC +ACCEPTOR ND +ACCEPTOR O1D ! CGD +ACCEPTOR O2D ! CGD +IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NA FE CHB HB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NB FE CHC HC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NC FE CHD HD 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC ND FE CHA HA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION +IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION +IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 +PATCHING FIRS NONE LAST NONE + +RESI O2 0.00 ! O2 ligand for heme +GROUP +ATOM O1 OM 0.021 +ATOM O2 OM -0.021 +BOND O1 O2 +PATCHING FIRS NONE LAST NONE + +RESI CO 0.00 ! CO ligand for heme +GROUP +ATOM C CM 0.021 +ATOM O OM -0.021 +TRIPLE C O +PATCHING FIRS NONE LAST NONE + +RESI CO2 0.00 ! Carbon Dioxide, John Straub +GROUP ! requires AUTOgenerate ANGLes +ATOM C CST 0.596 +ATOM OC1 OST -0.298 +ATOM OC2 OST -0.298 +BOND OC1 C OC2 C +!ANGLE OC1 C OC2 +PATCHING FIRS NONE LAST NONE + +PRES FHEM 0.00 ! FIX UP THE HEME BY DELETING UNWANTED AUTOGENERATED ANGLES + ! unliganded heme patch + ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch +DELETE ANGLE 1NA 1FE 1NC 1NB 1FE 1ND + +PRES PHEM 0.00 ! Patch for HEME to His link. + ! Patch residues must be 1-HIS, and 2-HEME. + ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch +DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND +BOND 1NE2 2FE +ANGLE 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB +ANGLE 1NE2 2FE 2NC 1NE2 2FE 2ND +DIHE 1CD2 1NE2 2FE 2NA +IC 1CD2 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CE1 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES PLOH 0.00 ! Patch residue for Heme ligand. Residues must be + ! 1-Tyr , 2-HEME , and 3-HIS + ! OH of the Tyr is bonded to the iron. + ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch +BOND 1OH 2FE +ANGLE 1HH 1OH 2FE +ANGLE 1OH 2FE 2NA 1OH 2FE 2NB !1CZ 1OH 2FE +ANGLE 1OH 2FE 2NC 1OH 2FE 2ND +!DIHE 1CZ 1OH 2FE 2NA +IC 1CZ 1OH 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CZ 1OH 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES PLO2 0.00 ! Patch residue for Heme ligand. Residues must be + ! 1-O2 , 2-HEME , and 3-HIS + ! O1 of the oxygen is bonded to the iron. + ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch +BOND 1O1 2FE +ANGLE 1O2 1O1 2FE 1O1 2FE 2NA 1O1 2FE 2NB +ANGLE 1O1 2FE 2NC 1O1 2FE 2ND +DIHE 1O2 1O1 2FE 2NA +IC 1O2 1O1 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1O2 1O1 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES PLIG 0.00 ! Patch residue for Heme ligand. Residues must be, + ! 1-CO , 2-HEME , and 3-HIS + ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch +BOND 1C 2FE +ANGLE 1C 2FE 3NE2 +ANGLE 1O 1C 2FE +ANGLE 1C 2FE 2NA 1C 2FE 2NB +ANGLE 1C 2FE 2NC 1C 2FE 2ND +DIHE 1O 1C 2FE 2NA +IC 1O 1C 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1O 1C 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 + +!added from top_all22_model_b5i.inp for heme-S-CH3 patch +RESI MES1 -1.00 ! methylthiolate, adm jr. +GROUP +ATOM S SS -0.80 ! H11 +ATOM C1 CS -0.47 ! \ +ATOM H11 HA 0.09 ! H12--C1--S (-) +ATOM H12 HA 0.09 ! / +ATOM H13 HA 0.09 ! H13 + ! +BOND S C1 C1 H11 C1 H12 C1 H13 +IC BLNK H11 C1 S 0.0000 0.0000 60.0000 0.0000 0.0000 +IC S H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC H12 H13 *C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +patch first none last none + +PRES PSUL 0.00 ! Patch for HEME to thiolate (MES1) link + ! Patch residues must be 1-MES1, and 2-HEME. + ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch +DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND +BOND 1S 2FE +ANGLE 1C1 1S 2FE 1C1 1S 2FE +ANGLE 1S 2FE 2NA 1S 2FE 2NB 1S 2FE 2NC 1S 2FE 2ND +IC 1C1 1S 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1C1 1S 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1C1 1S 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1C1 1S 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 + +end + +read para card flex append +* additional parameters for heme +* + +ATOMS +MASS 486 CPA 12.01100 ! heme alpha-C +MASS 487 CPB 12.01100 ! heme beta-C +MASS 488 CPM 12.01100 ! heme meso-C +MASS 489 CM 12.01100 ! heme CO carbon +MASS 490 CST 12.01100 ! CO2 carbon +MASS 491 NPH 14.00700 ! heme pyrrole N +MASS 492 OM 15.99900 ! heme CO/O2 oxygen +MASS 493 OST 15.99900 ! CO2 oxygen +MASS 494 FE 55.84700 ! heme iron 56 + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +C C 600.000 1.3350 ! ALLOW ARO HEM??? + ! Heme vinyl substituent (KK, from propene (JCS)) +!HA C 330.000 1.1000 ! ALLOW ARO HEM??? + ! Heme vinyl substituent (KK, from propene (JCS)) +!Carbon Dioxide +CST OST 937.96 1.1600 ! JES +!Heme to Sulfate (PSUL) link +SS FE 250.0 2.3200 !force constant a guess + !equilbrium bond length optimized to reproduce + !CSD survey values of + !2.341pm0.01 (mean, standard error) + !adm jr., 7/01 +CPB CE1 450.000 1.3800 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPA 299.800 1.4432 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB CPB 340.700 1.3464 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPM CPA 360.000 1.3716 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CT2 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +FE CM 258.000 1.9000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +FE CPM 0.000 3.3814 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +HA CPM 367.600 1.0900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA 377.200 1.3757 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE 270.200 1.9580 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR2 FE 65.000 2.2000 ! ALLOW HEM + ! Heme (6-liganded): His ligand (KK 05/13/91) +OM CM 1115.000 1.1280 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +OM FE 250.000 1.8000 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OM OM 600.000 1.2300 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OH1 FE 250.000 2.0000 ! patch PLOH + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +!HA C C 50.000 120.5000 ! ALLOW PEP POL ARO??? + ! Heme vinyl substituent (KK from propene (JCS)) +!HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO??? + ! Heme vinyl substituent (KK from propene (JCS)) +!Carbon Dioxide, JES +OST CST OST 3000.00 180.0000 ! CO2, JES +!Heme to Sulfate (PSUL) link +CS SS FE 50.0 100.6 !force constant a guess + !equilibrium angle optimized to reproduce + !CSD survey values + !107.5pm0.6 (mean, standard error) + !adm jr., 7/01 +SS FE NPH 100.0 90.0 !force constant a guess + !adm jr., 7/01 +CPA CPB CE1 70.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPA CPM CPA 94.200 125.1200 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPA NPH CPA 139.300 103.9000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB CE1 CE2 70.000 121.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB CE1 70.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB CPA 30.800 106.5100 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPM CPA CPB 61.600 124.0700 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +FE NPH CPA 96.150 128.0500 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +!HA C CPB 50.000 120.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA CPM CPA 12.700 117.4400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CPM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +HA2 CT2 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA3 CT3 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HE1 CE1 CPB 50.000 120.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +NPH CPA CPB 122.000 111.5400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM 88.000 124.3900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE CM 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NPH FE CPM 0.000 45.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +NPH FE NPH 14.390 90.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR2 FE CM 50.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR2 FE NPH 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM CM FE 35.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM FE NPH 5.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM OM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +H OH1 FE 65.000 108.0000 ! patch PLOH +OH1 FE NPH 5.000 90.0000 ! patch PLOH + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +!HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO??? + ! Heme vinyl substituent (KK, from propene (JCS)) +!HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO??? + ! Heme vinyl substituent (KK, from propene (JCS)) +HE2 CE2 CE1 CPB 5.2000 2 180.00 ! + ! for vinyl, from butene, yin/adm jr., 12/95 +!Heme to Sulfate (PSUL) link +X FE SS X 0.0000 4 0.00 ! guess + !adm jr., 7/01 +!X CS SS X 0.0000 3 0.20 ! guess + !from methanethiol, HS S CT3 HA + !adm jr., 7/01 +!X C C X 4.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB CE1 X 3.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X FE CM X 0.0500 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X FE NPH X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +X FE NR2 X 0.0500 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): from param19.inp +X FE OM X 0.0000 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB X X CE1 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +!HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO + ! Heme (6-liganded): substituents (KK 05/13/91) +NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CM 0.000000 -0.110000 2.100000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand carbon (KK 05/13/91) +CST 0.000000 -0.058000 1.563000 ! + ! carbon dioxide, JES +NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +OM 0.000000 -0.120000 1.700000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91) +OST 0.000000 -0.165000 1.692000 ! + ! carbon dioxide, JES +FE 0.010000 0.000000 0.650000 ! ALLOW HEM + ! Heme (6-liganded): Iron atom (KK 05/13/91) + +end + +return diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_model.str b/charmm/toppar/stream/prot/toppar_all36_prot_model.str new file mode 100644 index 00000000..f34985a8 --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_model.str @@ -0,0 +1,2338 @@ +*>> All-hydrogen topology for small model compounds used in the << +*>> development of the CHARMM22 protein all-hydrogen parameters << +*>>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< +*>>>>>>>>>>>>>>> Parameter forum, www.charmm.org <<<<<<<<<<<<<<<<< +*Converted to stream format, December 2003 +*Converted to CHARMM36 protein atom types, May 2011 +* + +!Parent files that have to be read prior to streaming this file +!top_all36_prot.rtf +!par_all36_prot.prm +! +!Testcase +!test_all36_prot_model.inp + +!changes after 9/98 +! +!change alkene HA1 and HA2 to HE1 and HE2 +! +!improper atom ordering corrected +! +!version b5i to be consistent with protein toppar files +! +!Heme vinyl groups upgraded based on new butene parameters +! + +! references +! +!PROTEINS +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. + +read rtf card append +* Topology for protein related model compounds +* +31 1 +MASS 445 C3 12.01100 ! cyclopropane carbon + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +!reset default patches +DEFA FIRS NONE LAST NONE +AUTO ANGLES DIHE + + +RESI ACET -1.00 ! acetate, K. Kuczera +GROUP +ATOM C1 CT3 -0.37 ! +ATOM C2 CC 0.62 ! H1 O1 (-) +ATOM H1 HA3 0.09 ! | / +ATOM H2 HA3 0.09 ! H2--C1--C2 +ATOM H3 HA3 0.09 ! | \\ +ATOM O1 OC -0.76 ! H3 O2 +ATOM O2 OC -0.76 ! +Bond c1 h1 c1 h2 c1 h3 +Bond c1 c2 c2 o1 +Double c2 o2 +impr c2 c1 o2 o1 +IC O1 C2 C1 H1 0.00 0.00 0.0 0.00 0.00 +IC C2 H1 *C1 H2 0.00 0.00 120.0 0.00 0.00 +IC C2 H1 *C1 H3 0.00 0.00 -120.0 0.00 0.00 +IC C1 O1 *C2 O2 0.00 0.00 180.0 0.00 0.00 +patc firs none last none + +RESI PROA -1.00 ! propionic acid +GROUP +ATOM C1 CT2 -0.28 ! +ATOM C2 CC 0.62 ! H1 O1 (-) +ATOM H1 HA2 0.09 ! | / +ATOM H2 HA2 0.09 ! H2--C1--C2 + ! | \\ +ATOM O1 OC -0.76 ! | O2 +ATOM O2 OC -0.76 !H01--C0 +GROUP ! | \ +ATOM C0 CT3 -0.27 ! H02 H03 +ATOM H01 HA3 0.09 +ATOM H02 HA3 0.09 +ATOM H03 HA3 0.09 +Bond c1 h1 c1 h2 c1 c0 +Bond c1 c2 c2 o1 +Bond c0 h01 c0 h02 c0 h03 +Double c2 o2 +impr c2 c1 o2 o1 +ic h1 c1 c2 o1 0.00 0.00 0.0 0.0 0.0 +ic h2 c1 c2 o1 0.00 0.00 0.0 0.0 0.0 +ic h3 c1 c2 o1 0.00 0.00 0.0 0.0 0.0 +ic h1 c1 c2 o2 0.00 0.00 0.0 0.0 0.0 +ic h2 c1 c2 o2 0.00 0.00 0.0 0.0 0.0 +ic h3 c1 c2 o2 0.00 0.00 0.0 0.0 0.0 +ic h1 c1 h2 h3 0.00 0.00 0.0 0.00 0.00 +ic h2 c1 h3 h1 0.00 0.00 0.0 0.00 0.00 +ic h3 c1 h1 h2 0.00 0.00 0.0 0.00 0.00 +ic o1 o2 *c2 c1 0.00 0.00 0.0 0.00 0.00 +!proa ics +ic c2 c1 c0 h01 0.00 0.00 180.0 0.00 0.00 +ic c2 c1 c0 h02 0.00 0.00 60.0 0.00 0.00 +ic c2 c1 c0 h03 0.00 0.00 300.0 0.00 0.00 +patc firs none last none + +RESI GUAN 1.00 ! guandinium, K. Kuczera +GROUP +ATOM C C 0.64 ! H11 H12 +ATOM N1 NC2 -0.80 ! \ / +ATOM H11 HC 0.46 ! N1 (+) +ATOM H12 HC 0.46 ! || +ATOM N2 NC2 -0.80 ! C +ATOM H21 HC 0.46 ! / \ +ATOM H22 HC 0.46 ! H21-N2 N3-H31 +ATOM N3 NC2 -0.80 ! | | +ATOM H31 HC 0.46 ! H22 H32 +ATOM H32 HC 0.46 ! +BOND C N2 C N3 +DOUBLE C N1 +BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 H32 +IMPH C N2 N1 N3 +IC H11 N1 C N2 0.00 0.00 0.0 0.00 0.00 +IC H11 N1 C N3 0.00 0.00 180.0 0.00 0.00 +IC H12 N1 C N3 0.00 0.00 0.0 0.00 0.00 +IC H21 N2 C N1 0.00 0.00 0.0 0.00 0.00 +IC H22 N2 C N3 0.00 0.00 0.0 0.00 0.00 +IC H31 N3 C N1 0.00 0.00 0.0 0.00 0.00 +IC H32 N3 C N2 0.00 0.00 0.0 0.00 0.00 +patc firs none last none + +RESI MGUA 1.00 ! methyl-guanidinium +GROUP +ATOM C C 0.64 ! H11 H12 +ATOM N1 NC2 -0.80 ! \ / +ATOM H11 HC 0.46 ! N1 (+) +ATOM H12 HC 0.46 ! || +ATOM N2 NC2 -0.80 ! C HC1 +ATOM H21 HC 0.46 ! / \ / +ATOM H22 HC 0.46 ! H21-N2 N3--C2-HC2 +ATOM N3 NC2 -0.70 ! | | \ +ATOM H31 HC 0.44 ! H22 H31 HC3 +ATOM C2 CT3 0.11 ! +ATOM HC1 HA3 0.09 +ATOM HC2 HA3 0.09 +ATOM HC3 HA3 0.09 +BOND C N2 C N3 +DOUBLE C N1 +BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 C2 +BOND C2 HC1 C2 HC2 C2 HC3 +IMPH C N2 N1 N3 +IC H11 N1 C N2 0.00 0.00 0.0 0.00 0.00 +IC H11 N1 C N3 0.00 0.00 180.0 0.00 0.00 +IC H12 N1 C N3 0.00 0.00 0.0 0.00 0.00 +IC H21 N2 C N1 0.00 0.00 0.0 0.00 0.00 +IC H22 N2 C N3 0.00 0.00 0.0 0.00 0.00 +IC H31 N3 C N1 0.00 0.00 0.0 0.00 0.00 +IC C2 N3 C N1 0.00 0.00 180.0 0.00 0.00 +IC C N3 C2 HC1 0.00 0.00 0.0 0.00 0.00 +IC C N3 C2 HC2 0.00 0.00 120.0 0.00 0.00 +IC C N3 C2 HC3 0.00 0.00 240.0 0.00 0.00 +patc firs none last none + +RESI GLYN 0.00 ! neutral glycine +GROUP ! +ATOM N NH2 -0.96 ! +ATOM HT1 HC 0.34 ! HT1 HT2 +ATOM HT2 HC 0.34 ! \ / +ATOM CA CT2 0.18 ! N +ATOM HA1 HB2 0.05 ! | +ATOM HA2 HB2 0.05 ! HA1-CA-HA2 +GROUP ! | +ATOM C CD 0.75 ! C +ATOM OT1 OB -0.55 ! // \ +ATOM OT2 OH1 -0.64 ! OT1 OT2 +ATOM HO2 H 0.44 ! | + ! HO2 + ! +BOND N CA CA C C OT2 OT2 HO2 +BOND N HT1 N HT2 CA HA1 CA HA2 +DOUBLE OT1 C +DONO HT1 N +DONO HT2 N +DONO HO2 OT2 +IC N CA C OT1 1.5010 119.00 88.76 126.10 1.2218 +IC N CA C OT2 1.5010 119.00 -111.57 113.44 1.3958 +IC OT1 OT2 *C CA 1.2218 117.44 -161.57 113.44 1.5780 +IC CA C OT2 HO2 1.5780 113.44 -168.97 107.16 0.9565 +IC C CA N HT1 1.5780 119.00 164.86 110.99 1.0023 +IC C CA N HT2 1.5780 119.00 -77.98 111.22 1.0030 +IC N C *CA HA1 1.5010 119.00 120.0 110.0 1.1 +IC N C *CA HA2 1.5010 119.00 -120.0 110.0 1.1 +PATCHING FIRS NONE LAST NONE + +RESI MAMM 1.00 ! methylammonium, K. Kuczera +GROUP +Atom ce ct3 0.16 ! +Atom nz nh3 -0.30 ! HE1 HZ1 +Atom he1 ha3 0.05 ! \ (+) | +Atom he2 ha3 0.05 !HE2-CE---NZ--HZ2 +Atom he3 ha3 0.05 ! / | +Atom hz1 hc 0.33 ! HE3 HZ3 +Atom hz2 hc 0.33 ! +Atom hz3 hc 0.33 ! +Bond ce he1 ce he2 ce he3 +Bond ce nz nz hz1 nz hz2 nz hz3 +ic he1 ce nz hz1 0.00 0.00 0.0 0.0 0.0 +ic he1 ce nz hz2 0.00 0.00 120.0 0.0 0.0 +ic he1 ce nz hz3 0.00 0.00 240.0 0.0 0.0 +ic he2 ce nz hz1 0.00 0.00 120.0 0.0 0.0 +ic he2 ce nz hz2 0.00 0.00 0.0 0.0 0.0 +ic he2 ce nz hz3 0.00 0.00 240.0 0.0 0.0 +ic he3 ce nz hz1 0.00 0.00 240.0 0.0 0.0 +ic he3 ce nz hz2 0.00 0.00 120.0 0.0 0.0 +ic he3 ce nz hz3 0.00 0.00 0.0 0.0 0.0 +ic ce nz hz1 hz3 0.00 0.00 0.0 0.0 0.0 +patc firs none last none + +RESI EAMM 1.00 ! ethylammonium, adm jr. +GROUP +Atom ce ct2 0.21 ! +Atom nz nh3 -0.30 ! HE1 HZ1 +Atom he1 ha2 0.05 ! \ (+) | +Atom he2 ha2 0.05 !HE2-CE---NZ--HZ2 + ! / | +Atom hz1 hc 0.33 ! / HZ3 +Atom hz2 hc 0.33 ! C1-H13 +Atom hz3 hc 0.33 ! / \ +Group !H11 H12 +atom c1 ct3 -0.27 ! +atom h11 ha3 0.09 ! +atom h12 ha3 0.09 ! +atom h13 ha3 0.09 ! +Bond ce he1 ce he2 ce c1 +Bond ce nz nz hz1 nz hz2 nz hz3 +Bond c1 h11 c1 h12 c1 h13 +ic he1 ce nz hz1 0.00 0.00 0.0 0.0 0.0 +ic he1 ce nz hz2 0.00 0.00 120.0 0.0 0.0 +ic he1 ce nz hz3 0.00 0.00 240.0 0.0 0.0 +ic he2 ce nz hz1 0.00 0.00 120.0 0.0 0.0 +ic he2 ce nz hz2 0.00 0.00 0.0 0.0 0.0 +ic he2 ce nz hz3 0.00 0.00 240.0 0.0 0.0 +ic he3 ce nz hz1 0.00 0.00 240.0 0.0 0.0 +ic he3 ce nz hz2 0.00 0.00 120.0 0.0 0.0 +ic he3 ce nz hz3 0.00 0.00 0.0 0.0 0.0 +ic ce nz hz1 hz3 0.00 0.00 0.0 0.0 0.0 +!ics for eamm +ic nz ce c1 h11 0.00 0.00 180.0 0.0 0.0 +ic nz ce c1 h12 0.00 0.00 60.0 0.0 0.0 +ic nz ce c1 h13 0.00 0.00 300.0 0.0 0.0 + +patc firs none last none + +RESI MAMI 0.00 ! methylamine, adm jr. +GROUP +ATOM N1 NH2 -0.96 ! +ATOM C1 CT3 0.13 ! HC1 HN1 +ATOM HN1 HC 0.34 ! \ / +ATOM HC1 HA3 0.05 ! HC2-C1---NZ +ATOM HC2 HA3 0.05 ! / \ +ATOM HC3 HA3 0.05 ! HC3 HN2 +ATOM HN2 HC 0.34 ! +BOND N1 C1 N1 HN1 N1 HN2 +BOND C1 HC1 C1 HC2 C1 HC3 +IC BLNK HN1 N1 C1 0.0 0.0 180. 0.0 0.0 +IC HN1 N1 C1 HC1 0.0 0.0 180. 0.0 0.0 +IC HN1 N1 C1 HC2 0.0 0.0 60. 0.0 0.0 +IC HN1 N1 C1 HC3 0.0 0.0 300. 0.0 0.0 +IC HC1 C1 N1 HN2 0.0 0.0 0. 0.0 0.0 + +RESI ACEH 0.00 ! acetic acid, ADM jr. +GROUP +ATOM C2 CT3 -0.30 ! +ATOM C1 CD 0.75 ! H21 O2 +ATOM H21 HA3 0.09 ! \ // +ATOM H22 HA3 0.09 ! H22-C2--C1 +ATOM H23 HA3 0.09 ! / \ +ATOM O2 OB -0.55 ! H23 O1-HO1 +ATOM O1 OH1 -0.61 ! +ATOM HO1 H 0.44 ! +BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23 +DOUBLE C1 O2 +IMPR C1 C2 O1 O2 +DONO BLNK HO1 ! O1 +ACCE O1 +ACCE O2 +IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 +IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 + +RESI MAS 0.00 ! methylacetate +GROUP ! +ATOM C1 CT3 -0.17 ! H22 +ATOM C CD 0.63 ! | +ATOM OM OS -0.34 ! H21-C2-H23 +ATOM C2 CT3 -0.14 ! \ +ATOM O OB -0.52 ! OM +ATOM H11 HA3 0.09 ! / +ATOM H12 HA3 0.09 ! O=C +ATOM H13 HA3 0.09 ! | +ATOM H21 HA3 0.09 ! H11-C1-H13 +ATOM H22 HA3 0.09 ! | +ATOM H23 HA3 0.09 ! H12 + +BOND C1 C C OM OM C2 +DOUBLE C O +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IMPR C C1 OM O +! internal coordinates from experiment for heavy atoms +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 + +RESI MEOH 0.00 ! methanol, adm jr. +GROUP ! order of atoms to match that used in ab initio +ATOM CB CT3 -0.04 ! H11 +ATOM OG OH1 -0.66 ! \ +ATOM HG1 H 0.43 ! H12--C1--O1 +ATOM HB1 HA3 0.09 ! / \ +ATOM HB2 HA3 0.09 ! H13 HO1 +ATOM HB3 HA3 0.09 ! +BOND CB OG OG HG1 +BOND CB HB1 CB HB2 CB HB3 +DONO HG1 OG +ACCE OG +! only for analysis +IC HG1 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HG1 OG CB HB2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HG1 OG CB HB3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG CB HB1 HB2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HG1 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI METO -1.00 ! methoxide, adm jr. +GROUP ! order of atoms to match that used in ab initio +ATOM CB CT3 -0.41 ! HB1 +ATOM OG OC -0.92 ! \ + ! HB2--CB--OG (-) +ATOM HB1 HA3 0.11 ! / +ATOM HB2 HA3 0.11 ! HB3 +ATOM HB3 HA3 0.11 ! +BOND CB OG +BOND CB HB1 CB HB2 CB HB3 +ACCE OG +! only for analysis +IC HB2 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG HB2 *CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG CB HB1 HB2 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI ETOH 0.00 ! Ethanol, adm jr. +GROUP +ATOM C1 CT2 0.05 ! H21 H11 H12 +ATOM O1 OH1 -0.66 ! \ \ / +ATOM HO1 H 0.43 ! H22--C2--C1 +ATOM H11 HA2 0.09 ! / \ +ATOM H12 HA2 0.09 ! H23 O1--HO1 +GROUP +ATOM C2 CT3 -0.27 +ATOM H21 HA3 0.09 +ATOM H22 HA3 0.09 +ATOM H23 HA3 0.09 +BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 H21 C2 H22 C2 H23 +DONO HO1 O1 +ACCE O1 +! for ic build +IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 +IC O1 C1 C2 H23 0.0000 0.0000 300.0000 0.0000 0.0000 +IC H21 C2 C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC H21 C2 C1 H12 0.0000 0.0000 240.0000 0.0000 0.0000 +IC C2 C1 O1 HO1 0.0000 0.0000 180.0000 0.0000 0.0000 +! only for analysis +!IC HO1 O1 C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC HO1 O1 C1 H12 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC HO1 O1 C1 H13 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC O1 C1 H11 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI ETO -1.00 ! Ethoxide, adm jr. +GROUP +ATOM OG OC -0.92 ! HA1 HB1 HB2 +ATOM CB CT2 -0.30 ! \ \ / +ATOM CA CT3 -0.27 ! HA2--CA--CB +ATOM HB1 HA2 0.11 ! / \ +ATOM HB2 HA2 0.11 ! HA3 OG (-) +!GROUP +ATOM HA1 HA3 0.09 +ATOM HA2 HA3 0.09 +ATOM HA3 HA3 0.09 +BOND CA CB CB OG CB HB1 CB HB2 +BOND CA HA1 CA HA2 CA HA3 +ACCE OG +! for ic build +ic cb ca Ha1 ha2 0.0000 0.0000 180.0000 0.0000 0.0000 +ic ca og cb hb1 0.0000 0.0000 180.0000 0.0000 0.0000 +ic ca og cb hb2 0.0000 0.0000 180.0000 0.0000 0.0000 +ic ca og cb hb3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 +IC HA1 CA CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HA1 CA CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 + +RESI PRO2 0.00 ! 2-propanol, adm jr. +GROUP +ATOM C2 CT1 0.14 ! H12 H13 H33 H32 +ATOM O2 OH1 -0.66 ! \ / \ / +ATOM HO2 H 0.43 ! H11--C1 C3--H31 +ATOM H21 HA1 0.09 ! \ / +GROUP ! C2 +ATOM C1 CT3 -0.27 ! / \ +ATOM H11 HA3 0.09 ! O2 H21 +ATOM H12 HA3 0.09 ! | +ATOM H13 HA3 0.09 ! HO2 +GROUP ! +ATOM C3 CT3 -0.27 ! +ATOM H31 HA3 0.09 +ATOM H32 HA3 0.09 +ATOM H33 HA3 0.09 +BOND C1 C2 C2 C3 C2 O2 C2 H21 O2 HO2 +BOND C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 C3 H33 +DONO HO2 O2 +ACCE O2 +! for ic build +IC C1 C2 C3 H31 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C1 C2 C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C1 C2 C3 H33 0.0000 0.0000 240.0000 0.0000 0.0000 +IC C3 C2 C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3 C2 C1 H12 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C3 C2 C1 H13 0.0000 0.0000 300.0000 0.0000 0.0000 +IC H31 C3 C2 O2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC H31 C3 C2 H21 0.0000 0.0000 240.0000 0.0000 0.0000 +IC C3 C2 O2 HO2 0.0000 0.0000 180.0000 0.0000 0.0000 +! only for analysis +!IC HO1 O1 C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC HO1 O1 C1 H12 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC HO1 O1 C1 H13 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC O1 C1 H11 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI FORM 0.00 ! formamide, adm jr. +ATOM HA HA1 0.08 ! +ATOM C CC 0.42 ! O Hc +ATOM N NH2 -0.69 ! \\ / +ATOM Hc H 0.35 ! C--N +ATOM Ht H 0.35 ! / \ +ATOM O O -0.51 ! HA Ht + ! +BOND C HA C N N Hc N Ht +DOUBLE C O +!BOND O DUM +IMPR C HA N O c n ha o +! GAS PHASE GEOMETRY +!IC DUM O C N 1.00 90.0 0. 124.70 1.352 +IC O C N HC 1.2190 124.70 0. 118.50 1.0016 ! variable 1 +IC HC N C HA 1.0016 118.50 180. 112.70 1.0980 ! variable 2 +IC O C N HT 1.2190 124.70 180. 120.00 1.0015 ! variable 3 + +RESI ACEM 0.00 ! acetamide, adm jr. +! the amide charges listed below are used in asparagine and glutamine +! if Hc and Ht are made equivalent use N = -0.64, Hc = Ht = 0.32 +GROUP +ATOM CC CT3 -0.27 ! +ATOM C CC 0.55 ! HC1 Ht +ATOM N NH2 -0.62 ! \ / +ATOM Hc H 0.32 ! HC2--CC--C---N +ATOM Ht H 0.30 ! / || \ +ATOM O O -0.55 ! HC3 O Hc +ATOM HC1 HA3 0.09 ! +ATOM HC2 HA3 0.09 ! +ATOM HC3 HA3 0.09 ! +!atom dum dum 0.0 ! dummy for ic build +BOND C N N Hc N Ht +DOUBLE C O +BOND C CC CC HC1 CC HC2 CC HC3 +!BOND O DUM +IMPR C CC N O C N CC O +IMPR N C HC HT N C HT HC +! GAS PHASE GEOMETRY +IC HC1 CC C N 1.0832 113.80 180. 124.70 1.3523 +IC O C N HC 1.2012 124.70 0. 118.63 0.9929 ! variable 1 +IC O C N HT 1.2012 124.70 180. 120.92 0.9960 ! variable 3 +IC HC N C CC 1.0016 118.63 180. 115.65 1.5150 ! variable 2 +IC O C CC HC1 1.2012 123.27 0. 113.80 1.0832 +IC O C CC HC2 1.2012 123.27 120. 108.52 1.0836 +IC O C CC HC3 1.2012 123.27 300. 108.52 1.0836 + +RESI MACE 0.00 ! methyl-acetamide, adm jr. +! the amide charges listed below are used in asparagine and glutamine +! if Hc and Ht are made equivalent use N = -0.64, Hc = Ht = 0.32 +GROUP +ATOM CC CT2 -0.18 ! +ATOM C CC 0.55 ! HC1 Ht +ATOM N NH2 -0.62 ! \ / +ATOM Hc H 0.32 ! HC2--CC--C---N +ATOM Ht H 0.30 ! / || \ +ATOM O O -0.55 ! / O Hc +ATOM HC1 HA2 0.09 ! C1-H13 +ATOM HC2 HA2 0.09 ! / \ +GROUP !H11 H12 +ATOM C1 CT3 -0.27 +ATOM H11 HA3 0.09 +ATOM H12 HA3 0.09 +ATOM H13 HA3 0.09 +!atom dum dum 0.0 ! dummy for ic build +BOND C N N Hc N Ht +DOUBLE C O +BOND C CC CC HC1 CC HC2 CC C1 +BOND C1 H11 C1 H12 C1 H13 +!BOND O DUM +IMPR C CC N O C N CC O +IMPR N C HC HT N C HT HC +! GAS PHASE GEOMETRY +IC HC1 CC C N 1.0832 113.80 180. 124.70 1.3523 +IC O C N HC 1.2012 124.70 0. 118.63 0.9929 ! variable 1 +IC O C N HT 1.2012 124.70 180. 120.92 0.9960 ! variable 3 +IC HC N C CC 1.0016 118.63 180. 115.65 1.5150 ! variable 2 +IC O C CC HC1 1.2012 123.27 60. 113.80 1.0832 +IC O C CC HC2 1.2012 123.27 300. 108.52 1.0836 +IC O C CC C1 1.2012 123.27 180. 108.52 1.5000 +IC C CC C1 H11 0.0 0.0 180. 0.0 0.0 +IC C CC C1 H12 0.0 0.0 60. 0.0 0.0 +IC C CC C1 H13 0.0 0.0 300. 0.0 0.0 + +RESI NMA 0.00 ! N-methylacetamide, Louis Kuchnir +GROUP +ATOM CL CT3 -0.27 +ATOM HL1 HA3 0.09 +ATOM HL2 HA3 0.09 +ATOM HL3 HA3 0.09 +ATOM C C 0.51 +ATOM O O -0.51 +ATOM N NH1 -0.47 +ATOM H H 0.31 +ATOM CR CT3 -0.11 +ATOM HR1 HA3 0.09 +ATOM HR2 HA3 0.09 +ATOM HR3 HA3 0.09 +BOND HL1 CL HL2 CL HL3 CL ! N-Methylacetamide: +BOND CL C C N N CR ! HL1\ O /HR1 +BOND N H ! HL2-- CL -- C -- N -- CR --HR2 +BOND HR1 CR HR2 CR HR3 CR ! HL3/ H \HR3 +DOUBLE C O +IMPR N C CR H +IMPR C CL N O + +ic o c n h 1.2233 122.84 180. 119.23 0.9933 ! variable 1 +ic h n c cl 0.9933 119.23 0. 116.25 1.5118 ! variable 8 +ic o c n cr 1.2233 122.84 0. 122.57 1.4488 ! variable 8 +ic n c cl hl1 1.3418 116.25 180. 109.3 1.109 ! variable 2 +ic n c cl hl2 1.3418 116.25 60. 109.3 1.109 ! variable 3 +ic n c cl hl3 1.3418 116.25 300. 109.3 1.109 ! variable 4 +ic c n cr hr1 1.3418 122.57 180. 110.7 1.113 ! variable 5 +ic c n cr hr2 1.3418 122.57 60. 110.7 1.113 ! variable 6 +ic c n cr hr3 1.3418 122.57 300. 110.7 1.113 ! variable 7 + +RESI ALAD 0.00 ! Alanine dipeptide, Louis Kuchnir +GROUP ! NO Cross term! see following residue, ALAC +ATOM CL CT3 -0.27 +ATOM HL1 HA3 0.09 +ATOM HL2 HA3 0.09 +ATOM HL3 HA3 0.09 +GROUP +ATOM CLP C 0.51 +ATOM OL O -0.51 +GROUP +ATOM NL NH1 -0.47 +ATOM HL H 0.31 +ATOM CA CT1 0.07 +ATOM HA HB1 0.09 +GROUP +ATOM CB CT3 -0.27 ! HL1 OL OR HR1 +ATOM HB1 HA3 0.09 ! \ || HL HA3 || HR / +ATOM HB2 HA3 0.09 ! \ || | | || | / +ATOM HB3 HA3 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 +GROUP ! / | \ +ATOM CRP C 0.51 ! / HB1--CB--HB3 \ +ATOM OR O -0.51 ! HL3 | HR3 +GROUP ! HB2 +ATOM NR NH1 -0.47 +ATOM HR H 0.31 +ATOM CR CT3 -0.11 +ATOM HR1 HA3 0.09 +ATOM HR2 HA3 0.09 +ATOM HR3 HA3 0.09 + +BOND CL CLP CLP NL NL CA +BOND CA CRP CRP NR NR CR +DOUBLE CLP OL CRP OR +BOND NL HL NR HR +BOND CA HA CA CB +BOND CL HL1 CL HL2 CL HL3 +BOND CB HB1 CB HB2 CB HB3 +BOND CR HR1 CR HR2 CR HR3 +IMPR CLP CL NL OL NL CLP CA HL +IMPR CRP CA NR OR NR CRP CR HR + +ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0 +ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic nl ca crp or 0.0 0.0 0.0 0.0 0.0 +ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left +ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0 +ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0 +ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right +ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0 +ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0 +ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0 +ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0 +ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0 +ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0 +ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0 +ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0 +ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0 +ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0 +ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0 +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0 +ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0 +ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0 +ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0 + +RESI ALAC 0.00 ! Alanine dipeptide, with CMAP term +GROUP +ATOM CL CT3 -0.27 +ATOM HL1 HA3 0.09 +ATOM HL2 HA3 0.09 +ATOM HL3 HA3 0.09 +GROUP +ATOM CLP C 0.51 +ATOM OL O -0.51 +GROUP +ATOM NL NH1 -0.47 +ATOM HL H 0.31 +ATOM CA CT1 0.07 +ATOM HA HB1 0.09 +GROUP +ATOM CB CT3 -0.27 ! HL1 OL OR HR1 +ATOM HB1 HA3 0.09 ! \ || HL HA3 || HR / +ATOM HB2 HA3 0.09 ! \ || | | || | / +ATOM HB3 HA3 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 +GROUP ! / | \ +ATOM CRP C 0.51 ! / HB1--CB--HB3 \ +ATOM OR O -0.51 ! HL3 | HR3 +GROUP ! HB2 +ATOM NR NH1 -0.47 +ATOM HR H 0.31 +ATOM CR CT3 -0.11 +ATOM HR1 HA3 0.09 +ATOM HR2 HA3 0.09 +ATOM HR3 HA3 0.09 + +BOND CL CLP CLP NL NL CA +BOND CA CRP CRP NR NR CR +DOUBLE CLP OL CRP OR +BOND NL HL NR HR +BOND CA HA CA CB +BOND CL HL1 CL HL2 CL HL3 +BOND CB HB1 CB HB2 CB HB3 +BOND CR HR1 CR HR2 CR HR3 +IMPR CLP CL NL OL NL CLP CA HL +IMPR CRP CA NR OR NR CRP CR HR + +CMAP CLP NL CA CRP NL CA CRP NR + +ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0 +ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic nl ca crp or 0.0 0.0 0.0 0.0 0.0 +ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left +ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0 +ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0 +ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right +ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0 +ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0 +ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0 +ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0 +ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0 +ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0 +ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0 +ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0 +ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0 +ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0 +ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0 +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0 +ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0 +ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0 +ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0 +patch first none last none + +RESI MESH 0.00 ! methanethiol, DZUNG NGUYEN +GROUP +ATOM H1 HA3 0.09 ! H1 +ATOM H2 HA3 0.09 ! \ +ATOM H3 HA3 0.09 ! H2--CM--S +ATOM CM CT3 -0.20 ! / \ +ATOM S S -0.23 ! H3 H4 +ATOM H4 HS 0.16 ! +Bond cm h1 cm h2 cm h3 +Bond cm s s h4 +ic h1 cm s h4 0.00 0.00 0.0 0.00 0.00 +ic h2 cm s h4 0.00 0.00 120.0 0.00 0.00 +ic h3 cm s h4 0.00 0.00 240.0 0.00 0.00 +ic cm s h4 h1 0.00 0.00 0.0 0.00 0.00 +patc firs none last none + +RESI MES1 -1.00 ! methylthiolate, adm jr. +GROUP +ATOM S SS -0.80 ! H11 +ATOM C1 CS -0.47 ! \ +ATOM H11 HA3 0.09 ! H12--C1--S (-) +ATOM H12 HA3 0.09 ! / +ATOM H13 HA3 0.09 ! H13 + ! +BOND S C1 C1 H11 C1 H12 C1 H13 +IC BLNK H11 C1 S 0.0000 0.0000 60.0000 0.0000 0.0000 +IC S H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC H12 H13 *C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +patch first none last none + +RESI ETSH 0.00 ! ethanethiol, Dzung Nguyen +GROUP +Atom h1 ha3 0.09 ! H1 H4 H5 +Atom h2 ha3 0.09 ! \ \ / +Atom h3 ha3 0.09 ! H2-CM1--CM2 +Atom cm1 ct3 -0.27 ! / \ +GROUP ! H3 S3--H6 +Atom h4 ha2 0.09 +Atom h5 ha2 0.09 +Atom cm2 ct2 -0.11 +Atom s3 s -0.23 +Atom h6 hs 0.16 +Bond cm1 h1 cm1 h2 cm1 h3 +Bond cm1 cm2 cm2 h4 cm2 h5 +bond cm2 s3 s3 h6 +ic h1 cm1 cm2 s3 0.00 0.00 60.0 0.0 0.0 +ic h2 cm1 cm2 s3 0.00 0.00 180.0 0.0 0.0 +ic h3 cm1 cm2 s3 0.00 0.00 300.0 0.0 0.0 +ic h1 cm1 cm2 h4 0.00 0.00 180.0 0.0 0.0 +ic h2 cm1 cm2 h4 0.00 0.00 300.0 0.0 0.0 +ic h3 cm1 cm2 h4 0.00 0.00 60.0 0.0 0.0 +ic h1 cm1 cm2 h5 0.00 0.00 300.0 0.0 0.0 +ic h2 cm1 cm2 h5 0.00 0.00 60.0 0.0 0.0 +ic h3 cm1 cm2 h5 0.00 0.00 180.0 0.0 0.0 +ic cm1 cm2 s3 h6 0.00 0.00 60.0 0.0 0.0 +ic h4 cm2 s3 h6 0.00 0.00 180.0 0.0 0.0 +ic h5 cm2 s3 h6 0.00 0.00 300.0 0.0 0.0 + +RESI ES1 -1.00 ! ethylthiolate, adm jr. +GROUP +ATOM S SS -0.80 ! H21 H11 H12 +ATOM C1 CS -0.38 ! \ \ / +ATOM C2 CT3 -0.27 ! H22--C2--C1 +ATOM H21 HA3 0.09 ! / \ +ATOM H22 HA3 0.09 ! H23 S (-) +ATOM H23 HA3 0.09 +ATOM H11 HA2 0.09 +ATOM H12 HA2 0.09 +BOND S C1 C1 H11 C1 H12 C1 C2 +BOND C2 H21 C2 H22 C2 H23 +IC BLNK H11 C1 S 0.0000 0.0000 60.0000 0.0000 0.0000 +IC S H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S H11 *C1 C2 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC H12 C2 *C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC S C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 +IC S C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 +patch first none last none + +RESI DMDS 0.00 ! dimethyldisulfide, Dzung Nguyen +GROUP +atom h1 ha3 0.09 ! +atom h2 ha3 0.09 ! H1 +atom h3 ha3 0.09 ! \ +atom cm1 ct3 -0.19 ! H2-CM1 +atom s2 sm -0.08 ! / \ +GROUP ! H3 S2--S3 H4 +atom s3 sm -0.08 ! \ / +atom cm4 ct3 -0.19 ! CM4-H5 +atom h4 ha3 0.09 ! \ +atom h5 ha3 0.09 ! H6 +atom h6 ha3 0.09 ! +bond h1 cm1 h2 cm1 h3 cm1 cm1 s2 +bond s2 s3 s3 cm4 cm4 h4 cm4 h5 +bond cm4 h6 +ic h1 cm1 s2 s3 0.00 0.00 60.0 0.0 0.0 +ic h2 cm1 s2 s3 0.00 0.00 180.0 0.0 0.0 +ic h3 cm1 s2 s3 0.00 0.00 300.0 0.0 0.0 +ic cm1 s2 s3 cm4 0.00 0.00 90.0 0.0 0.0 +ic s2 s3 cm4 h4 0.00 0.00 60.0 0.0 0.0 +ic s2 s3 cm4 h5 0.00 0.00 180.0 0.0 0.0 +ic s2 s3 cm4 h6 0.00 0.00 300.0 0.0 0.0 +patc firs none last none + +RESI DEDS 0.00 ! diethyldisulfide, adm jr. +GROUP +atom h1 ha2 0.09 ! +atom h2 ha2 0.09 ! H1 + ! \ +atom cm1 ct2 -0.10 ! H2-CM1 +atom s2 sm -0.08 ! / \ +GROUP ! CM0 S2--S3 H4 +atom s3 sm -0.08 ! / | \ \ / +atom cm4 ct2 -0.10 !H01| H03 CM4-H5 +atom h4 ha2 0.09 ! H02 \ +atom h5 ha2 0.09 ! CM5-H53 +GROUP ! / \ +atom CM0 ct3 -0.27 ! H51 H52 +atom h01 ha3 0.09 ! +atom h02 ha3 0.09 +atom h03 ha3 0.09 +GROUP +atom CM5 ct3 -0.27 +atom h51 ha3 0.09 +atom h52 ha3 0.09 +atom h53 ha3 0.09 + +bond h1 cm1 h2 cm1 cm1 cm0 cm1 s2 +bond s2 s3 s3 cm4 cm4 h4 cm4 h5 +bond cm4 cm5 +bond cm0 h01 cm0 h02 cm0 h03 +bond cm5 h51 cm5 h52 cm5 h53 + +ic h1 cm1 s2 s3 0.00 0.00 60.0 0.0 0.0 +ic h2 cm1 s2 s3 0.00 0.00 300.0 0.0 0.0 +ic cm0 cm1 s2 s3 0.00 0.00 180.0 0.0 0.0 +ic s2 cm1 cm0 h01 0.00 0.00 180.0 0.0 0.0 +ic s2 cm1 cm0 h02 0.00 0.00 60.0 0.0 0.0 +ic s2 cm1 cm0 h03 0.00 0.00 300.0 0.0 0.0 +ic cm1 s2 s3 cm4 0.00 0.00 90.0 0.0 0.0 +ic s2 s3 cm4 h4 0.00 0.00 60.0 0.0 0.0 +ic s2 s3 cm4 h5 0.00 0.00 300.0 0.0 0.0 +ic s2 s3 cm4 cm5 0.00 0.00 180.0 0.0 0.0 +ic s3 cm4 cm5 h51 0.00 0.00 180.0 0.0 0.0 +ic s3 cm4 cm5 h52 0.00 0.00 60.0 0.0 0.0 +ic s3 cm4 cm5 h53 0.00 0.00 300.0 0.0 0.0 +patc firs none last none + +RESI EMS 0.00 ! ethylmethylsulfide, Dzung Nguyen +group +Atom h1 ha3 0.09 ! +Atom h2 ha3 0.09 ! H1 H4 H5 +Atom h3 ha3 0.09 ! \ \ / +Atom cm1 ct3 -0.27 ! H2-CM1--CM2 H6 +group ! \ / +Atom h4 ha2 0.09 ! S3--CM4-H7 +Atom h5 ha2 0.09 ! \ +Atom cm2 ct2 -0.14 ! H8 +Atom s3 s -0.09 ! +atom cm4 ct3 -0.22 ! +atom h6 ha3 0.09 ! +atom h7 ha3 0.09 ! +atom h8 ha3 0.09 ! +Bond cm1 h1 cm1 h2 cm1 h3 +Bond cm1 cm2 cm2 h4 cm2 h5 +bond cm2 s3 s3 cm4 +bond cm4 h6 cm4 h7 cm4 h8 +ic h1 cm1 cm2 s3 0.00 0.00 60.0 0.0 0.0 +ic h2 cm1 cm2 s3 0.00 0.00 180.0 0.0 0.0 +ic h3 cm1 cm2 s3 0.00 0.00 300.0 0.0 0.0 +ic h1 cm1 cm2 h4 0.00 0.00 180.0 0.0 0.0 +ic h2 cm1 cm2 h4 0.00 0.00 300.0 0.0 0.0 +ic h3 cm1 cm2 h4 0.00 0.00 60.0 0.0 0.0 +ic h1 cm1 cm2 h5 0.00 0.00 300.0 0.0 0.0 +ic h2 cm1 cm2 h5 0.00 0.00 60.0 0.0 0.0 +ic h3 cm1 cm2 h5 0.00 0.00 180.0 0.0 0.0 +ic cm1 cm2 s3 cm4 0.00 0.00 60.0 0.0 0.0 +ic h4 cm2 s3 cm4 0.00 0.00 180.0 0.0 0.0 +ic h5 cm2 s3 cm4 0.00 0.00 300.0 0.0 0.0 +ic cm2 s3 cm4 h6 0.00 0.00 60.0 0.0 0.0 +ic cm2 s3 cm4 h7 0.00 0.00 180.0 0.0 0.0 +ic cm2 s3 cm4 h8 0.00 0.00 300.0 0.0 0.0 +patch first none last none + +RESI IMIA 0.00 ! Imidazole, adm jr. +GROUP +ATOM CG CPH1 -0.05 ! HD1 HE1 +ATOM HG HR3 0.09 ! | / +ATOM CD2 CPH1 0.22 ! ND1--CE1 +ATOM HD2 HR3 0.10 ! / || +ATOM ND1 NR1 -0.36 ! HG-CG || +ATOM HD1 H 0.32 ! \\ || +ATOM CE1 CPH2 0.25 ! CD2--NE2 +ATOM HE1 HR1 0.13 ! | +ATOM NE2 NR2 -0.70 ! HD2 + ! +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG HG +DOUBLE NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 +! KEEPS HYDROGENS IN RING PLANE +IMPH ND1 CG CE1 HD1 ND1 CE1 CG HD1 +IMPH CD2 CG NE2 HD2 CD2 NE2 CG HD2 +IMPH CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 +IMPH CG CD2 ND1 HG CG ND1 CD2 HG +DONO HD1 ND1 +ACCE NE2 +! for analysis +dono he1 ce1 +dono hg cg +acce ce1 +acce nd1 +acce cd2 +IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 +IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 + +RESI MIMI 0.00 ! 4-methylimidazole, adm jr. +GROUP +ATOM ND1 NR1 -0.36 ! HD1 HE1 +ATOM HD1 H 0.32 ! | / +ATOM CG CPH1 -0.05 ! HB1 ND1--CE1 +ATOM CB CT3 -0.18 ! | / || +ATOM HB1 HA3 0.09 ! HB2-CB-CG || +ATOM HB2 HA3 0.09 ! | \\ || +ATOM HB3 HA3 0.09 ! HB3 CD2--NE2 +GROUP ! | +ATOM NE2 NR2 -0.70 ! HD2 +ATOM CD2 CPH1 0.22 ! +ATOM HD2 HR3 0.10 ! +ATOM CE1 CPH2 0.25 ! +ATOM HE1 HR1 0.13 ! +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG CB +DOUBLE NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 +BOND CB HB1 CB HB2 CB HB3 +! KEEPS HYDROGENS IN RING PLANE +IMPH ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +DONO HD1 ND1 +ACCE NE2 +IC CB CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 +IC CB CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 +IC CD2 CG CB HB1 0.0 0.0 0.0 0.0 0.0 +IC CD2 CG CB HB2 0.0 0.0 120.0 0.0 0.0 +IC CD2 CG CB HB3 0.0 0.0 240.0 0.0 0.0 + +RESI EIMI 0.00 ! 4-ethylimidazole, adm jr. +GROUP +ATOM CA CT3 -0.27 ! Optimized charges to minimize group size +ATOM HA1 HA3 0.09 +ATOM HA2 HA3 0.09 +ATOM HA3 HA3 0.09 +GROUP +ATOM ND1 NR1 -0.36 ! HD1 HE1 +ATOM HD1 H 0.32 ! | / +ATOM CG CPH1 -0.05 ! HA1 HB1 ND1--CE1 +ATOM CB CT2 -0.09 ! \ | / || +ATOM HB1 HA2 0.09 ! HA2-CA--CB-CG || +ATOM HB2 HA2 0.09 ! / | \\ || +GROUP ! HA3 HB2 CD2--NE2 +ATOM NE2 NR2 -0.70 ! | +ATOM CD2 CPH1 0.22 ! HD2 +ATOM HD2 HR3 0.10 ! +ATOM CE1 CPH2 0.25 ! +ATOM HE1 HR1 0.13 ! +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG CB +DOUBLE NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 +! KEEPS HYDROGENS IN RING PLANE +IMPH ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +DONO HD1 ND1 +ACCE NE2 +IC CB CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 +IC CB CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 +IC CD2 CG CB HB1 0.0 0.0 0.0 0.0 0.0 +IC CD2 CG CB HB2 0.0 0.0 120.0 0.0 0.0 +IC CD2 CG CB CA 0.0 0.0 240.0 0.0 0.0 +IC CG CB CA HA1 0.0 0.0 -180.0 0.0 0.0 +IC CG CB CA HA2 0.0 0.0 -60.0 0.0 0.0 +IC CG CB CA HA3 0.0 0.0 60.0 0.0 0.0 + +RESI IMIM 1.00 ! Imidazolium, adm jr. +GROUP +ATOM CG CPH1 0.19 ! HD1 HE1 +ATOM HG HR1 0.13 ! | / +ATOM CD2 CPH1 0.19 ! ND1--CE1 +ATOM HD2 HR1 0.13 ! / || +GROUP ! HG-CG || +ATOM ND1 NR3 -0.51 ! \\ || +ATOM HD1 H 0.44 ! CD2--NE2 (+) +ATOM NE2 NR3 -0.51 ! | \ +ATOM HE2 H 0.44 ! HD2 HE2 +ATOM CE1 CPH2 0.32 +ATOM HE1 HR2 0.18 +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG HG +DOUBLE NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 NE2 HE2 +! KEEPS HYDROGENS IN RING PLANE +IMPH ND1 CG CE1 HD1 NE2 CD2 CE1 HE2 +IMPH ND1 CE1 CG HD1 NE2 CE1 CD2 HE2 +DONO HD1 ND1 +DONO HE2 NE2 +IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 +IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 +IC HE1 CE1 NE2 HE2 1.0879 125.00 0.00 125.00 1.0000 + +RESI EIMM 1.00 ! Ethyl-Imidazolium, adm jr. +GROUP +ATOM CA CT3 -0.27 +ATOM HA1 HA3 0.09 +ATOM HA2 HA3 0.09 +ATOM HA3 HA3 0.09 +GROUP ! +ATOM CB CT2 -0.05 ! HD1 HE1 +ATOM HB1 HA2 0.09 ! | / +ATOM HB2 HA2 0.09 ! HA1 HB1 ND1--CE1 +ATOM CG CPH1 0.19 ! \ | / || +ATOM CD2 CPH1 0.19 ! HA2-CA--CB-CG || +ATOM HD2 HR1 0.13 ! / | \\ || +GROUP ! HA3 HB2 CD2--NE2(+) +ATOM ND1 NR3 -0.51 ! | \ +ATOM HD1 H 0.44 ! HD2 HE2 +ATOM NE2 NR3 -0.51 ! +ATOM HE2 H 0.44 +ATOM CE1 CPH2 0.32 +ATOM HE1 HR2 0.18 +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG CB NE2 HE2 +DOUBLE CD2 CG NE2 CE1 +BOND ND1 HD1 CD2 HD2 CE1 HE1 +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 +! KEEPS HYDROGENS IN RING PLANE +IMPH ND1 CG CE1 HD1 NE2 CD2 CE1 HE2 +IMPH ND1 CE1 CG HD1 NE2 CE1 CD2 HE2 +DONO HD1 ND1 +ACCE NE2 +IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 +IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 +IC CD2 CG CB HB1 0.0 0.0 0.0 0.0 0.0 +IC CD2 CG CB HB2 0.0 0.0 120.0 0.0 0.0 +IC CD2 CG CB CA 0.0 0.0 240.0 0.0 0.0 +IC CG CB CA HA1 0.0 0.0 -180.0 0.0 0.0 +IC CG CB CA HA2 0.0 0.0 -60.0 0.0 0.0 +IC CG CB CA HA3 0.0 0.0 60.0 0.0 0.0 + +RESI BENZ 0.00 ! benzene, adm jr. +GROUP +ATOM CG CA -0.115 ! +ATOM HG HP 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CA -0.115 ! CD1--CE1 +ATOM HD1 HP 0.115 ! / \ +GROUP ! HG--CG CZ--HZ +ATOM CD2 CA -0.115 ! \ / +ATOM HD2 HP 0.115 ! CD2--CE2 +GROUP ! | | +ATOM CE1 CA -0.115 ! HD2 HE2 +ATOM HE1 HP 0.115 ! +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM CZ CA -0.115 +ATOM HZ HP 0.115 +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI EBEN 0.00 ! ethylbenzene, adm jr. +GROUP +ATOM CG CA 0.000 ! + ! HD1 HE1 +GROUP ! | | +ATOM CD1 CA -0.115 !HA1 HB1 CD1--CE1 +ATOM HD1 HP 0.115 ! \ | / \ +GROUP !HA2-CA--CB--CG CZ--HZ +ATOM CD2 CA -0.115 ! / | \ / +ATOM HD2 HP 0.115 !HA3 HB2 CD2--CE2 +GROUP ! | | +ATOM CE1 CA -0.115 ! HD2 HE2 +ATOM HE1 HP 0.115 ! +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM CZ CA -0.115 +ATOM HZ HP 0.115 +GROUP +ATOM CB CT2 -0.18 +ATOM HB1 HA2 0.09 +ATOM HB2 HA2 0.09 +GROUP +ATOM CA CT3 -0.27 +ATOM HA1 HA3 0.09 +ATOM HA2 HA3 0.09 +ATOM HA3 HA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG CB CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 + +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG CB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD2 CG CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD2 CG CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 +IC CD2 CG CB CA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC CG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 + +RESI PHEN 0.00 ! phenol, adm jr. +GROUP +ATOM CG CA -0.115 ! +ATOM HG HP 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CA -0.115 ! CD1--CE1 +ATOM HD1 HP 0.115 ! // \\ +GROUP ! HG--CG CZ--OH +ATOM CD2 CA -0.115 ! \ / \ +ATOM HD2 HP 0.115 ! CD2==CE2 HH +GROUP ! | | +ATOM CE1 CA -0.115 ! HD2 HE2 +ATOM HE1 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM CZ CA 0.11 +ATOM OH OH1 -0.54 +ATOM HH H 0.43 +BOND CD2 CG CE1 CD1 +BOND CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH OH HH +DOUBLE CD1 CG CE2 CD2 CZ CE1 +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CZ OH HH 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI EPHE 0.00 ! p-ethylphenol, adm jr. +GROUP +ATOM CG CA 0.00 ! + ! HD1 HE1 +GROUP ! | | +ATOM CD1 CA -0.115 !HA1 HB1 CD1--CE1 +ATOM HD1 HP 0.115 ! \ | / \ +GROUP !HA2-CA--CB--CG CZ--OH +ATOM CD2 CA -0.115 ! / | \ / \ +ATOM HD2 HP 0.115 !HA3 HB2 CD2--CE2 HH +GROUP ! | | +ATOM CE1 CA -0.115 ! HD2 HE2 +ATOM HE1 HP 0.115 ! +GROUP ! +ATOM CE2 CA -0.115 ! +ATOM HE2 HP 0.115 ! +GROUP +ATOM CZ CA 0.11 +ATOM OH OH1 -0.54 +ATOM HH H 0.43 +GROUP +ATOM CB CT2 -0.18 +ATOM HB1 HA2 0.09 +ATOM HB2 HA2 0.09 +GROUP +ATOM CA CT3 -0.27 +ATOM HA1 HA3 0.09 +ATOM HA2 HA3 0.09 +ATOM HA3 HA3 0.09 + +BOND CD2 CG CE1 CD1 +BOND CZ CE2 +BOND CG CB CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH OH HH +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 +DOUBLE CD1 CG CE2 CD2 CZ CE1 + +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG CB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CZ OH HH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD2 CG CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD2 CG CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 +IC CD2 CG CB CA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC CG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 + +RESI PHEO -1.00 ! phenoxide, adm jr. +GROUP +ATOM CG CA -0.115 ! +ATOM HG HP 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CA -0.115 ! CD1--CE1 +ATOM HD1 HP 0.115 ! / \ +GROUP ! HG--CG CZ--OH +ATOM CD2 CA -0.115 ! \ / +ATOM HD2 HP 0.115 ! CD2--CE2 +GROUP ! | | +ATOM CE1 CA -0.60 ! HD2 HE2 +ATOM HE1 HP 0.28 +ATOM CE2 CA -0.60 +ATOM HE2 HP 0.28 +ATOM CZ CA 0.40 +ATOM OH OC -0.76 +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI INDO 0.00 ! indole, adm jr. +GROUP +ATOM HG HP 0.115 ! HE3 +ATOM CG CY -0.145 ! | +ATOM CD2 CPT -0.020 ! HG CE3 +ATOM CD1 CA 0.035 ! \ / \\ +ATOM HD1 HP 0.115 ! CG-----CD2 CZ3-HZ3 +ATOM NE1 NY -0.610 ! || || | +ATOM HE1 H 0.380 ! CD1 CE2 CH2-HH2 +ATOM CE2 CPT 0.130 ! / \ / \ // +GROUP ! HD1 NE1 CZ2 +ATOM CE3 CA -0.115 ! | | +ATOM HE3 HP 0.115 ! HE1 HZ2 +GROUP +ATOM CZ2 CA -0.115 +ATOM HZ2 HP 0.115 +GROUP +ATOM CZ3 CA -0.115 +ATOM HZ3 HP 0.115 +GROUP +ATOM CH2 CA -0.115 +ATOM HH2 HP 0.115 +BOND CG HG CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND CZ3 CH2 CD2 CE3 NE1 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 +BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 +DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 +DONOR HE1 NE1 +IC CG CD1 NE1 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CB *CG CD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CG CD1 NE1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 CG *CD2 CE3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CD2 CE3 CZ3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CE3 CZ3 CH2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE3 CZ3 CH2 CZ2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CZ3 CD2 *CE3 HE3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CH2 CE3 *CZ3 HZ3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ2 CZ3 *CH2 HH2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CH2 *CZ2 HZ2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CE2 *NE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG NE1 *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI EIND 0.00 ! ethylindole, adm jr. + + ! HA2 + ! | +GROUP ! HA1-CA-HA3 HE3 +ATOM CG CY -0.030 ! | | +ATOM CD2 CPT -0.020 ! HB1-CB-HB2 CE3 +ATOM CD1 CA 0.035 ! \ / \\ +ATOM HD1 HP 0.115 ! CG-----CD2 CZ3-HZ3 +ATOM NE1 NY -0.610 ! || || | +ATOM HE1 H 0.380 ! CD1 CE2 CH2-HH2 +ATOM CE2 CPT 0.130 ! / \ / \ // +GROUP ! HD1 NE1 CZ2 +ATOM CE3 CA -0.115 ! | | +ATOM HE3 HP 0.115 ! HE1 HZ2 +GROUP +ATOM CZ2 CA -0.115 +ATOM HZ2 HP 0.115 +GROUP +ATOM CZ3 CA -0.115 +ATOM HZ3 HP 0.115 +GROUP +ATOM CH2 CA -0.115 +ATOM HH2 HP 0.115 +GROUP +ATOM CB CT2 -0.18 +ATOM HB1 HA2 0.09 +ATOM HB2 HA2 0.09 +GROUP +ATOM CA CT3 -0.27 +ATOM HA1 HA3 0.09 +ATOM HA2 HA3 0.09 +ATOM HA3 HA3 0.09 + +BOND CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND CZ3 CH2 CD2 CE3 NE1 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 +BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 +DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 +DONOR HE1 NE1 + +IC CG CD1 NE1 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CB *CG CD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CG CD1 NE1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 CG *CD2 CE3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CD2 CE3 CZ3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CE3 CZ3 CH2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE3 CZ3 CH2 CZ2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CZ3 CD2 *CE3 HE3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CH2 CE3 *CZ3 HZ3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ2 CZ3 *CH2 HH2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CH2 *CZ2 HZ2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CE2 *NE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG NE1 *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CD2 *CG CB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD2 CG CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD2 CG CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 +IC CD2 CG CB CA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC CG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 + +RESI AP2 0.00 ! acetyl-prolineamide, R. Dunbrack + ! No Cross Term + ! + !HY1 HY2 HY3 +ATOM N N -0.29 ! \ | / +ATOM CA CP1 0.02 ! CAY +ATOM CB CP2 -0.18 ! | +ATOM CG CP2 -0.18 ! OY=CY HD1 HD2 +ATOM CD CP3 0.00 ! \ \ / +ATOM CY C 0.51 ! N---CD HG1 +ATOM OY O -0.51 ! | \ / +ATOM C CC 0.51 ! | CG +ATOM HA HB1 0.09 ! | / \ +ATOM HB1 HA2 0.09 ! HA-CA--CB HG2 +ATOM HB2 HA2 0.09 ! | / \ +ATOM HG1 HA2 0.09 ! | HB1 HB2 +ATOM HG2 HA2 0.09 ! O=C +ATOM HD1 HA2 0.09 ! | +ATOM HD2 HA2 0.09 ! NT +ATOM CAY CT3 -0.27 ! / \ +ATOM HY1 HA3 0.09 ! HT1 HT2 +ATOM HY2 HA3 0.09 +ATOM HY3 HA3 0.09 +ATOM O O -0.51 +ATOM NT NH2 -0.62 +ATOM HT1 H 0.31 +ATOM HT2 H 0.31 +BOND CY N CAY HY1 CAY HY2 CAY HY3 +BOND CY CAY N CA CA CB CB CG CG CD CD N +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +BOND C CA C NT NT HT1 NT HT2 +DOUBLE C O CY OY +IMPR CY CAY N OY +IMPR C CA NT O +IMPR C NT CA O +IMPR N CY CA CD +IMPR NT C HT2 HT1 +DONOR HT1 NT +DONOR HT2 NT +ACCEPTOR OY CY +ACCEPTOR O C +! Improper ICs +IC CY CA *N CD 0.00 0.00 180.00 0.00 0.00 +IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 +IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 +IC N CAY *CY OY 0.00 0.00 180.00 0.00 0.00 +! Backbone + Peptide bond IC's +IC OY CY N CA 0.00 0.00 0.00 0.00 0.00 !Omega +IC CAY CY N CA 0.00 0.00 180.00 0.00 0.00 !Omega +IC CY N CA C 0.00 120.64 -60.00 0.00 0.00 !Psi +IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi +IC CAY CY N CD 0.00 0.00 0.00 120.64 0.00 +IC CY N CD CG 0.00 0.00 168.60 103.28 0.00 +IC CY N CA CB 0.00 0.00 168.64 103.34 0.00 +! Ring IC's +IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 +IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 +IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 +IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 +IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 +! Carbonyl IC's +IC CD N CA C 0.00 112.90 120.00 108.00 0.00 +! Hydrogen IC's +IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 +IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 +IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 +IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 +IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 +IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 +IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 +IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 +IC CA C NT HT2 0.00 0.00 180.00 0.00 0.00 +IC C HT2 *NT HT1 0.00 0.00 180.00 0.00 0.00 + +RESI PDIP 0.00 ! proline dipeptide + ! No Cross Term + ! + !HY1 HY2 HY3 +ATOM N N -0.29 ! \ | / +ATOM CA CP1 0.02 ! CAY +ATOM CB CP2 -0.18 ! | +ATOM CG CP2 -0.18 ! OY=CY HD1 HD2 +ATOM CD CP3 0.00 ! \ \ / +ATOM CY C 0.51 ! N---CD HG1 +ATOM OY O -0.51 ! | \ / +ATOM C C 0.51 ! | CG +ATOM HA HB1 0.09 ! | / \ +ATOM HB1 HA2 0.09 ! HA-CA--CB HG2 +ATOM HB2 HA2 0.09 ! | / \ +ATOM HG1 HA2 0.09 ! | HB1 HB2 +ATOM HG2 HA2 0.09 ! O=C +ATOM HD1 HA2 0.09 ! | +ATOM HD2 HA2 0.09 ! NT +ATOM CAY CT3 -0.27 ! / \ +ATOM HY1 HA3 0.09 ! HT1 CR-HR3 +ATOM HY2 HA3 0.09 ! / \ +ATOM HY3 HA3 0.09 ! HR1 HR2 +ATOM O O -0.51 +ATOM NT NH1 -0.47 +ATOM HT1 H 0.31 +ATOM CR CT3 -0.11 +ATOM HR1 HA3 0.09 +ATOM HR2 HA3 0.09 +ATOM HR3 HA3 0.09 + +BOND CY N CAY HY1 CAY HY2 CAY HY3 +BOND CY CAY N CA CA CB CB CG CG CD CD N +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +BOND C CA C NT NT HT1 NT CR +BOND CR HR1 CR HR2 CR HR3 +DOUBLE C O CY OY +IMPR CY CAY N OY +IMPR C CA NT O +IMPR C NT CA O +IMPR N CY CA CD +DONOR HT1 NT +ACCEPTOR OY CY +ACCEPTOR O C +! Improper ICs +IC CY CA *N CD 0.00 0.00 180.00 0.00 0.00 +IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 +IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 +IC N CAY *CY OY 0.00 0.00 180.00 0.00 0.00 +! Backbone + Peptide bond IC's +IC OY CY N CA 0.00 0.00 0.00 0.00 0.00 !Omega +IC CAY CY N CA 0.00 0.00 180.00 0.00 0.00 !Omega +IC CY N CA C 0.00 120.64 -60.00 0.00 0.00 !Psi +IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi +IC CAY CY N CD 0.00 0.00 0.00 120.64 0.00 +IC CY N CD CG 0.00 0.00 168.60 103.28 0.00 +IC CY N CA CB 0.00 0.00 168.64 103.34 0.00 +! Ring IC's +IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 +IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 +IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 +IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 +IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 +! Carbonyl IC's +IC CD N CA C 0.00 112.90 120.00 108.00 0.00 +! Hydrogen IC's +IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 +IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 +IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 +IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 +IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 +IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 +IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 +IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 +IC CA C NT HT1 0.00 0.00 180.00 0.00 0.00 +!C-terminal methyl +IC C HT1 *NT CR 0.00 0.00 180.00 0.00 0.00 +IC C NT CR HR1 0.00 0.00 180.00 0.00 0.00 +IC C NT CR HR2 0.00 0.00 60.00 0.00 0.00 +IC C NT CR HR3 0.00 0.00 300.00 0.00 0.00 + +RESI TP2 1.00 ! prolineamide, R. Dunbrack +ATOM N NP -0.07 ! +ATOM HN1 HC 0.24 ! +ATOM HN2 HC 0.24 ! +ATOM CD CP3 0.16 ! +ATOM CB CP2 -0.18 ! HN1 HD1 HD2 +ATOM CG CP2 -0.18 ! \ \ / +ATOM CA CP1 0.16 ! HN2--N---CD HG1 +ATOM C CC 0.51 ! | \ / +ATOM O O -0.51 ! | CG +ATOM HA HB1 0.09 ! | / \ +ATOM HB1 HA2 0.09 ! HA-CA--CB HG2 +ATOM HB2 HA2 0.09 ! | / \ +ATOM HG1 HA2 0.09 ! | HB1 HB2 +ATOM HG2 HA2 0.09 ! O=C +ATOM HD1 HA2 0.09 ! | +ATOM HD2 HA2 0.09 ! NT +ATOM NT NH2 -0.62 ! / \ +ATOM HT1 H 0.31 ! HT1 HT2 +ATOM HT2 H 0.31 ! +BOND HN1 N HN2 N N CA CA CB CB CG CG CD CD N +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +BOND C CA C NT NT HT1 NT HT2 +DOUBLE C O +IMPR C CA NT O +IMPR C NT CA O +IMPR NT C HT2 HT1 +DONOR HT1 NT +DONOR HT2 NT +DONOR HN1 N +DONOR HN2 N +ACCEPTOR O C +! Improper ICs +IC HN1 CA *N CD 0.00 0.00 120.00 0.00 0.00 +IC HN2 CA *N HN1 0.00 0.00 120.00 0.00 0.00 +IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 +IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 +! Backbone + Peptide bond IC's +IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi +! Ring IC's +IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 +IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 +IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 +IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 +IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 +! Carbonyl IC's +IC CD N CA C 0.00 112.90 120.00 108.00 0.00 +! Hydrogen IC's +IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 +IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 +IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 +IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 +IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 +IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 +IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 +IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 +IC CA C NT HT2 0.00 0.00 180.00 0.00 0.00 +IC C HT2 *NT HT1 0.00 0.00 180.00 0.00 0.00 + +Resi ETHA 0.00 ! ethane, S. Fischer +Group +Group + Atom h11 ha3 0.09 ! H11 H21 + Atom h12 ha3 0.09 ! \ / + Atom h13 ha3 0.09 ! H12-C1--C2-H22 + Atom c1 ct3 -0.27 ! / \ +Group ! H13 H23 + Atom h21 ha3 0.09 + Atom h22 ha3 0.09 + Atom h23 ha3 0.09 + Atom c2 ct3 -0.27 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 h21 c2 h22 c2 h23 +ic h11 c1 c2 h21 0.00 0.00 0.0 0.0 0.0 +ic h11 c1 c2 h22 0.00 0.00 120.0 0.0 0.0 +ic h11 c1 c2 h23 0.00 0.00 240.0 0.0 0.0 +ic h12 c1 c2 h23 0.00 0.00 120.0 0.0 0.0 +ic h13 c1 c2 h23 0.00 0.00 240.0 0.0 0.0 + +Resi PRPA 0.00 ! propane, adm jr. +Group ! + Atom h11 ha3 0.09 ! H11 H21 H31 + Atom h12 ha3 0.09 ! \ | / + Atom h13 ha3 0.09 ! H12-C1--C2--C3-H32 + Atom c1 ct3 -0.27 ! / | \ +Group ! H13 H22 H33 + Atom c2 ct2 -0.18 ! + Atom h21 ha2 0.09 ! + Atom H22 ha2 0.09 +Group + Atom h31 ha3 0.09 + Atom h32 ha3 0.09 + Atom h33 ha3 0.09 + Atom c3 ct3 -0.27 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 h21 c2 h22 +bond c2 c3 c3 h31 c3 h32 c3 h33 +ic h11 c1 c2 c3 0.00 0.00 0.0 0.0 0.0 +ic h11 c1 c2 h21 0.00 0.00 120.0 0.0 0.0 +ic h11 c1 c2 h22 0.00 0.00 240.0 0.0 0.0 +ic c1 c2 c3 h31 0.00 0.00 0.0 0.0 0.0 +ic c1 c2 c3 h32 0.00 0.00 120.0 0.0 0.0 +ic c1 c2 c3 h33 0.00 0.00 240.0 0.0 0.0 +ic c3 c2 c1 h12 0.00 0.00 120.0 0.0 0.0 +ic c3 c2 c1 h13 0.00 0.00 120.0 0.0 0.0 + +Resi BUTA 0.00 ! butane, S. Fischer +Group +Atom h11 ha3 0.09 ! H11 H21 H31 H41 +Atom h12 ha3 0.09 ! \ | | / +Atom h13 ha3 0.09 ! H12-C1--C2--C3--C4-H42 +Atom c1 ct3 -0.27 ! / | | \ +Group ! H13 H22 H33 H43 +Atom h21 ha2 0.09 +Atom h22 ha2 0.09 +Atom c2 ct2 -0.18 +Group +Atom h31 ha2 0.09 +Atom h32 ha2 0.09 +atom c3 ct2 -0.18 +Group +atom h41 ha3 0.09 +atom h42 ha3 0.09 +atom h43 ha3 0.09 +atom c4 ct3 -0.27 +Bond h11 c1 h12 c1 h13 c1 c1 c2 +Bond h21 c2 h22 c2 c2 c3 +Bond h31 c3 h32 c3 c3 c4 +Bond h41 c4 h42 c4 h43 c4 +ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 +ic h11 c1 c2 h21 0.00 0.00 120.0 0.00 0.00 +ic h11 c1 c2 h22 0.00 0.00 240.0 0.00 0.00 +ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00 +ic h13 c1 c2 c3 0.00 0.00 240.0 0.00 0.00 +ic c1 c2 c3 c4 0.00 0.00 0.0 0.00 0.00 +ic c1 c2 c3 h31 0.00 0.00 120.0 0.00 0.00 +ic c1 c2 c3 h32 0.00 0.00 240.0 0.00 0.00 +ic h21 c2 c3 c4 0.00 0.00 120.0 0.00 0.00 +ic h22 c2 c3 c4 0.00 0.00 240.0 0.00 0.00 +ic c2 c3 c4 h41 0.00 0.00 0.0 0.00 0.00 +ic c2 c3 c4 h42 0.00 0.00 120.0 0.00 0.00 +ic c2 c3 c4 h43 0.00 0.00 240.0 0.00 0.00 +ic h31 c3 c4 h43 0.00 0.00 120.0 0.00 0.00 +ic h32 c3 c4 h43 0.00 0.00 240.0 0.00 0.00 + +Resi IBUT 0.00 ! Iso-butane, S. Fischer +Group +atom ct ct1 -0.09 ! H12 +atom ht ha1 0.09 ! | +Group ! H11-C1-H13 +Atom c1 ct3 -0.27 ! | +Atom h11 ha3 0.09 ! CT-HT +Atom h12 ha3 0.09 ! / \ +Atom h13 ha3 0.09 ! / \ +Group ! H21-C2 C3-H31 +Atom c2 ct3 -0.27 ! / | | \ +Atom h21 ha3 0.09 ! H22 H23 H33 H32 +Atom h22 ha3 0.09 ! +Atom h23 ha3 0.09 ! +Group +atom c3 ct3 -0.27 +Atom h31 ha3 0.09 +atom h32 ha3 0.09 +atom h33 ha3 0.09 +Bond ct c1 ct c2 ct c3 ct ht +Bond c1 h11 c1 h12 c1 h13 +Bond c2 h21 c2 h22 c2 h23 +Bond c3 h31 c3 h32 c3 h33 +ic ht ct c1 h11 0.00 0.00 60.0 0.00 0.00 +ic ct c1 h11 h12 0.00 0.00 0.0 0.00 0.00 +ic ht ct c1 h12 0.00 0.00 180.0 0.00 0.00 +ic ht ct c1 h13 0.00 0.00 300.0 0.00 0.00 +ic h12 c1 ct c2 0.00 0.00 60.0 0.00 0.00 +ic h12 c1 ct c3 0.00 0.00 -60.0 0.00 0.00 +ic ht ct c2 h21 0.00 0.00 60.0 0.00 0.00 +ic ht ct c2 h22 0.00 0.00 180.0 0.00 0.00 +ic ht ct c2 h23 0.00 0.00 300.0 0.00 0.00 +ic ht ct c3 h31 0.00 0.00 60.0 0.00 0.00 +ic ht ct c3 h32 0.00 0.00 180.0 0.00 0.00 +ic ht ct c3 h33 0.00 0.00 300.0 0.00 0.00 + +Resi PENT 0.00 ! pentane, adm jr. +Group + Atom C1 CT3 -0.27 ! H11 H21 H31 H41 H51 + Atom H11 HA3 0.09 ! \ | | | / + Atom H12 HA3 0.09 ! H12-C1--C2--C3--C4--C5-H52 + Atom H13 HA3 0.09 ! / | | | \ +Group ! H13 H22 H33 H42 H53 + Atom C2 CT2 -0.18 + Atom H21 HA2 0.09 + Atom H22 HA2 0.09 +Group + Atom C3 CT2 -0.18 + Atom H31 HA2 0.09 + Atom H32 HA2 0.09 +Group + Atom C4 CT2 -0.18 + Atom H41 HA2 0.09 + Atom H42 HA2 0.09 +Group + Atom C5 CT3 -0.27 + Atom H51 HA3 0.09 + Atom H52 HA3 0.09 + Atom H53 HA3 0.09 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C5 H53 + +Ic H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +Ic C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +Ic C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +Ic C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 + +Ic H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +Ic H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +Ic C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +Ic C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +Ic C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +Ic C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +Ic C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +Ic C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +Ic C4 H51 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 +Ic C4 H51 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +!RESI TIP3 0.00 ! TIPS3P WATER MODEL, adm jr. +!GROUP ! Generate noangle nodihedral +!ATOM OH2 OT -0.834 +!ATOM H1 HT 0.417 +!ATOM H2 HT 0.417 +!BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +!ANGLE H1 OH2 H2 +!ACCE OH2 + +!RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p +!GROUP +!ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup +!ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup +!ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup +!BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p +!ANGLE H1 OH2 H2 ! required +!ACCEPTOR OH2 +!PATCHING FIRS NONE LAST NONE + +RESI OCOH 0.0 ! OCTANOL +GROUP + ATOM C1 CT2 0.05 + ATOM H11 HA2 0.09 + ATOM H12 HA2 0.09 + ATOM O1 OH1 -0.66 + ATOM HO1 H 0.43 +GROUP + ATOM C2 CT2 -0.180 + ATOM H21 HA2 0.090 + ATOM H22 HA2 0.090 +GROUP + ATOM C3 CT2 -0.180 + ATOM H31 HA2 0.090 + ATOM H32 HA2 0.090 +GROUP + ATOM C4 CT2 -0.180 + ATOM H41 HA2 0.090 + ATOM H42 HA2 0.090 +GROUP + ATOM C5 CT2 -0.180 + ATOM H51 HA2 0.090 + ATOM H52 HA2 0.090 +GROUP + ATOM C6 CT2 -0.180 + ATOM H61 HA2 0.090 + ATOM H62 HA2 0.090 +GROUP + ATOM C7 CT2 -0.180 + ATOM H71 HA2 0.090 + ATOM H72 HA2 0.090 +GROUP + ATOM C8 CT3 -0.270 + ATOM H81 HA3 0.090 + ATOM H82 HA3 0.090 + ATOM H83 HA3 0.090 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C1 O1 O1 HO1 +BOND C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +BOND C5 H52 C6 H61 C6 H62 C7 H71 C7 H72 +BOND C8 H81 C8 H82 C8 H83 + +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 H83 0.0000 0.00 180.00 0.00 0.0000 + +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 O1 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C8 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C8 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 +IC C7 H83 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 +IC C7 H83 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +Resi ETHE 0.00 ! ethylene, yin/adm jr. +Group + Atom c1 ce2 -0.42 + Atom h11 HE2 0.21 + Atom h12 HE2 0.21 +Group + Atom c2 ce2 -0.42 + Atom h21 HE2 0.21 + Atom h22 HE2 0.21 +Bond c1 h11 c1 h12 +Double c1 c2 +Bond c2 h21 c2 h22 +IMPR c1 c2 h12 h11 +IMPR c1 c2 h11 h12 +IMPR c2 c1 h22 h21 +IMPR c2 c1 h21 h22 +ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 +ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0 +ic h22 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0 +ic c1 c2 h21 h22 0.00 0.00 180.0 0.0 0.0 +patc firs none last none + +Resi PRPE 0.00 ! propene, yin/adm jr. +Group + Atom c1 ce2 -0.42 + Atom h11 HE2 0.21 + Atom h12 HE2 0.21 +Group + Atom c2 ce1 -0.15 + Atom h21 HE1 0.15 +Group + Atom c3 ct3 -0.27 + Atom h31 ha3 0.09 + Atom h32 ha3 0.09 + Atom h33 ha3 0.09 +Bond c1 h11 c1 h12 +Double c1 c2 +Bond c2 h21 +Bond c2 c3 +bond c3 h31 c3 h32 c3 h33 +ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 +ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0 +ic c3 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0 +ic h31 c3 c2 c1 0.00 0.00 0.0 0.0 0.0 +ic h32 c3 c2 c1 0.00 0.00 120.0 0.0 0.0 +ic h33 c3 c2 c1 0.00 0.00 -120.0 0.0 0.0 +patc firs none last none + +Resi BTE1 0.00 ! 1-Butene, yin/adm jr. +Group + Atom c1 ce2 -0.42 + Atom h11 HE2 0.21 + Atom h12 HE2 0.21 +Group + Atom c2 ce1 -0.15 + Atom h21 HE1 0.15 +Group + Atom c3 ct2 -0.18 + Atom h31 ha2 0.09 + Atom h32 ha2 0.09 +Group + Atom c4 ct3 -0.27 + Atom h41 ha3 0.09 + Atom h42 ha3 0.09 + Atom h43 ha3 0.09 +BOND c1 h11 c1 h12 +DOUBLE c1 c2 +BOND c2 h21 +BOND c2 c3 +BOND c3 h31 c3 h32 +BOND c3 c4 +BOND c4 h41 c4 h42 c4 h43 +ic c1 c2 c3 c4 0.00 0.00 0.0 0.00 0.00 +ic h11 c1 c2 c3 0.00 0.00 180.0 0.00 0.00 +ic h12 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 +ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 +ic h31 c2 *c3 c4 0.00 0.00 120.0 0.00 0.00 +ic h32 c2 *c3 c4 0.00 0.00 -120.0 0.00 0.00 +ic h41 c4 c3 c2 0.00 0.00 180.0 0.00 0.00 +ic h42 c4 c3 c2 0.00 0.00 60.0 0.00 0.00 +ic h43 c4 c3 c2 0.00 0.00 -60.0 0.00 0.00 +patc firs none last none + +Resi BTE2 0.00 ! 2-Butene, yin/adm jr. +Group + Atom c1 ct3 -0.27 + Atom h11 ha3 0.09 + Atom h12 ha3 0.09 + Atom h13 ha3 0.09 +Group + Atom c2 ce1 -0.15 + Atom h21 HE1 0.15 +Group + Atom c3 ce1 -0.15 + Atom h31 HE1 0.15 +Group + Atom c4 ct3 -0.27 + Atom h41 ha3 0.09 + Atom h42 ha3 0.09 + Atom h43 ha3 0.09 +BOND c1 h11 c1 h12 c1 h13 +BOND c1 c2 +BOND c2 h21 +DOUBLE c2 c3 +BOND c3 h31 +BOND c3 c4 +BOND c4 h41 c4 h42 c4 h43 +ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 +ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 +ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00 +ic h13 c1 c2 c3 0.00 0.00 -120.0 0.00 0.00 +ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 +ic h31 c4 *c3 c2 0.00 0.00 180.0 0.00 0.00 +ic h41 c4 c3 c2 0.00 0.00 0.0 0.00 0.00 +ic h42 c4 c3 c2 0.00 0.00 120.0 0.00 0.00 +ic h43 c4 c3 c2 0.00 0.00 -120.0 0.00 0.00 +patc firs none last none + +resi co3 -2.0 !ionized carbonate, adm jr., aug 2001 +group +ATOM C1 CD 1.42 +ATOM O1 OC -1.14 +ATOM O2 OC -1.14 +ATOM O3 OC -1.14 + +bond c1 o1 c1 o2 c1 o3 +! required for out-of-plane vibrations +impr c1 o1 o2 o3 +IC O2 O1 *C1 O3 0.0000 0.00 180.00 0.00 0.0000 + +RESI C3 0.00 ! Cyclopropane Model Compound +GROUP ! JMW and CBP 16 April 2004 +ATOM C1 C3 -0.18 ! +ATOM H11 HB2 0.09 ! H11 H12 +ATOM H12 HB2 0.09 ! \ / +GROUP ! C1 +ATOM C2 C3 -0.18 ! / \ +ATOM H21 HB2 0.09 ! H21--C2----C3--H31 +ATOM H22 HB2 0.09 ! | | +GROUP ! H22 H32 +ATOM C3 C3 -0.18 ! +ATOM H31 HB2 0.09 ! +ATOM H32 HB2 0.09 ! +BOND C1 C2 C2 C3 C3 C1 +BOND C1 H11 C1 H12 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 + +IC C1 C2 C3 H31 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C1 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C1 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 + +PATCHING FIRST NONE LAST NONE + +RESI MLYS 1.00 !methylated lysine, C.Varna and adm jr. +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA HB1 0.09 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM CB CT2 -0.18 ! | | | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CT2 -0.18 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +GROUP +ATOM CE CT2 0.21 +ATOM HE1 HA2 0.05 +ATOM HE2 HA2 0.05 +ATOM NZ NH3 -0.40 +ATOM HZ1 HC 0.32 +ATOM HZ2 HC 0.32 +ATOM CZ CT3 0.18 +ATOM HC1 HA3 0.09 +ATOM HC2 HA3 0.09 +ATOM HC3 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +BOND NZ HZ1 NZ HZ2 +BOND NZ CZ CZ HC1 CZ HC2 CZ HC3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HE1 CE NZ CZ 0.0 0.0 180. 0.0 0.0 +IC HZ1 N1 CZ HZ1 0.0 0.0 180. 0.0 0.0 +IC HZ1 N1 CZ HZ2 0.0 0.0 60. 0.0 0.0 +IC HZ1 N1 CZ HZ3 0.0 0.0 300. 0.0 0.0 + +RESI CME 0.00 ! S-methyl cysteine +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HD1 +ATOM HA HB1 0.09 ! | | | +GROUP ! HA-CA--CB--SG--CD-HD2 +ATOM CB CT2 -0.11 ! | | | +ATOM HB1 HA2 0.09 ! | HB2 HD3 +ATOM HB2 HA2 0.09 ! O=C +ATOM SG S -0.23 ! | +ATOM CD CT3 -0.11 ! +ATOM HD1 HA3 0.09 ! +ATOM HD2 HA3 0.09 ! +ATOM HD3 HA3 0.09 ! +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG CD CD HD1 CD HD2 +BOND CD HD3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CB SG CD HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HD1 SG *CD HD2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HD1 SG *CD HD3 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI CGU -2.00 !gamma carboxyglutamic aicd +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 OE11 +ATOM HA HB1 0.09 ! | | // +GROUP ! HA-CA--CB--CG--CD1 +ATOM CB CT2A -0.18 ! | | || \ +ATOM HB1 HA2 0.09 ! | HB2 CD2 OE12(-) +ATOM HB2 HA2 0.09 ! O=C || \ +GROUP ! | OE21 OE22(-) +ATOM CG CT1 -0.29 ! +ATOM HG HA1 0.09 ! +GROUP +ATOM CD1 CC 0.62 +ATOM OE11 OC -0.76 +ATOM OE12 OC -0.76 +GROUP +ATOM CD2 CC 0.62 +ATOM OE21 OC -0.76 +ATOM OE22 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD1 CG CD2 CG CG HG +BOND OE11 CD1 OE12 CD1 OE21 CD2 OE22 CD2 +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 +DOUBLE O C CD1 OE11 CD2 OE21 CG CD2 +IMPR N -C CA HN C CA +N O +IMPR CD1 CG OE11 OE12 CD2 CG OE21 OE22 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OE11 CD1 +ACCEPTOR OE21 CD2 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 60.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD1 1.5516 120.0000 120.0000 115.7300 1.5307 +IC CD1 CB *CG CD2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD1 CB *CG HG 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD1 OE11 1.5557 120.0000 -60.0000 120.0000 1.2590 +IC CB CG CD2 OE21 1.5557 120.0000 -60.0000 120.0000 1.2590 +IC OE11 CG *CD1 OE12 1.2590 114.9900 -179.1000 120.0800 1.2532 +IC OE21 CG *CD2 OE22 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI CGUP -1.00 !gamma carboxyglutamic acid, with one acid group protonated +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 OE11 +ATOM HA HB1 0.09 ! | | // +GROUP ! HA-CA--CB--CG--CD1 +ATOM CB CT2A -0.18 ! | | || \ +ATOM HB1 HA2 0.09 ! | HB2 CD2 OE12-HE12 +ATOM HB2 HA2 0.09 ! O=C || \ +GROUP ! | OE21 OE22(-) +ATOM CG CT1 -0.22 ! +ATOM HG HA1 0.09 ! +GROUP +ATOM CD1 CD 0.75 +ATOM OE11 OB -0.55 +ATOM OE12 OH1 -0.61 +ATOM HE12 H 0.44 +GROUP +ATOM CD2 CC 0.62 +ATOM OE21 OC -0.76 +ATOM OE22 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD1 CG CD2 CG CG HG +BOND OE11 CD1 OE12 CD1 OE21 CD2 OE22 CD2 +BOND OE12 HE12 +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 +DOUBLE O C CD1 OE11 CD2 OE21 CG CD2 +IMPR N -C CA HN C CA +N O +IMPR CD1 CG OE12 OE11 CD2 CG OE21 OE22 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OE11 CD1 +ACCEPTOR OE21 CD2 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 60.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD1 1.5516 120.0000 120.0000 115.7300 1.5307 +IC CD1 CB *CG CD2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD1 CB *CG HG 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD1 OE11 1.5557 120.0000 -60.0000 120.0000 1.2590 +IC CB CG CD2 OE21 1.5557 120.0000 -60.0000 120.0000 1.2590 +IC OE11 CG *CD1 OE12 1.2590 114.9900 -179.1000 120.0800 1.2532 +IC OE21 CG *CD2 OE22 1.2590 114.9900 -179.1000 120.0800 1.2532 +IC CG CD1 OE12 HE12 0.0000 0.0000 180.0000 0.00000 0.0000 + +END + +read para card flex append + +ATOMS +MASS 445 C3 12.01100 ! cyclopropane carbon + +BONDS +!atom type Kb b0 +OC CD 314.500 1.2940 ! carbonate +C3 C3 240.000 1.5010 ! cyclopropane +C3 HB2 340.000 1.0830 ! cyclopropane + +ANGLES +!atom types Ktheta Theta0 Kub S0 +OC CD OC 40.000 120.00 99.5 2.24127 ! carbonate +C3 C3 C3 77.350 111.00 8.00 2.56100 ! cyclopropane +C3 C3 HB2 23.000 117.10 22.53 2.17900 ! cyclopropane +HB2 C3 HB2 23.000 117.00 5.40 1.80200 ! cyclopropane +!gamma carboxy glutamic acid (CGU) +CC CT1 CC 52.000 108.0000 ! from CT3 CT1 CC, for CGU +HA1 CT1 CC 33.000 109.5000 30.00 2.16300 ! from HA2 CT2 CC, for CGU +CT1 CT2A CT1 58.350 113.5000 11.16 2.56100 ! from CT2 CT2 CT1, for CGU +HA1 CT1 CT2A 34.500 110.1000 22.53 2.17900 ! from HA1 CT1 CT2, for CGU +CC CT1 CD 52.000 108.0000 ! from CT3 CT1 CC, for CGUP + +DIHEDRALS +!atom types Kchi n delta +! +C3 C3 C3 HB2 0.1000 6 0.00 ! hf/6-31g* cyclopropane +HB2 C3 C3 HB2 0.2000 5 180.00 ! hf/6-31g* cyclopropane +! +CT3 S CT2 CT1 0.2400 1 180.00 ! ALOW ALI SUL ION +CT3 S CT2 CT1 0.3700 3 0.00 ! ALOW ALI SUL ION + ! For S-methylated Cysteine (RB) 2012 +!gamma carboxy glutamic acid (CGU) +CT1 CT2A CT1 NH3 0.1900 3 0.00 ! From X CT2 CT2 X !temporary RJP +HA1 CT1 CT2A CT1 0.2000 3 0.00 ! From X CT1 CT2 X !temporary RJP +CC CT1 CT2A CT1 0.2000 3 0.00 ! From X CT1 CT2 X !temporary RJP +CD CT1 CT2A CT1 0.2000 3 0.00 ! From X CT1 CT2 X !temporary RJP +HB1 CT1 CT2A CT1 0.2000 3 0.00 ! From X CT1 CT2 X !temporary RJP +HA1 CT1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X !temporary RJP +C CT1 CT2A CT1 0.1100 1 0.00 ! from fitted GLU !temporary RJP +C CT1 CT2A CT1 0.9800 2 180.00 ! from fitted GLU !temporary RJP +C CT1 CT2A CT1 1.6000 3 180.00 ! from fitted GLU !temporary RJP +CT1 CT2A CT1 NH1 0.8800 1 180.00 ! from fitted GLU !temporary RJP +CT1 CT2A CT1 NH1 0.0000 2 180.00 ! from fitted GLU !temporary RJP +CT1 CT2A CT1 NH1 1.9000 3 0.00 ! from fitted GLU !temporary RJP + +IMPROPER +!atom types Kpsi psi0 +! +CD OC OC OC 107.00 0 0.0000 ! carbonate + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +C3 0.000000 -0.020000 2.275000 ! cyclopropane JMW 16 april 04 + +end + +return diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_modify_res.str b/charmm/toppar/stream/prot/toppar_all36_prot_modify_res.str new file mode 100644 index 00000000..d9f74a37 --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_modify_res.str @@ -0,0 +1,1575 @@ +* Toppar file for various modified residues and patches, including +* patches to covalently link residues to ions to work the the +* additive C36 protein force field +* + +!Acetyllysine (ALY) +!Norleucine (NLE) and +! residues and patches for Zn-protein interactions modeled using +! bond and angles between the protein and Zn. + +read rtf card append +* Toppar file protein modifications +* +36 1 + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI ALY 0.00 !acetylated Lysine +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA HB1 0.09 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ CT-(HT1,HT2,HT3) +ATOM CB CT2 -0.18 ! | | | | | \ / +ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 HE2 CH +ATOM HB2 HA2 0.09 ! O=C || +GROUP ! | OT +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CT2 -0.18 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +GROUP +ATOM CE CT2 -0.02 +ATOM HE1 HA2 0.09 +ATOM HE2 HA2 0.09 +ATOM NZ NH1 -0.47 +ATOM HZ1 H 0.31 +GROUP +ATOM CH C 0.51 +ATOM OH O -0.51 +GROUP +ATOM CH3 CT3 -0.27 +ATOM HH31 HA3 0.09 +ATOM HH32 HA3 0.09 +ATOM HH33 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 + +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUB O C +BOND NZ HZ1 NZ CH CH OH CH CH3 +BOND CH3 HH31 CH3 HH32 CH3 HH33 + +IMPR N -C CA HN C CA +N O +IMPR NZ CH CE HZ1 CH CH3 NZ OH + +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HZ1 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ CH 1.0404 110.0200 180.0000 109.5000 1.35 +IC CE NZ CH CH3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CH3 NZ *CH OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CH CH3 HH31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HH31 CH *CH3 HH32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HH31 CH *CH3 HH33 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI DORN 1.00 ! "(delta)ornithine" (chemical name formally incorrect) + ! based on LYS with atoms mass-renamed, kevo +GROUP ! Copy-pasted from NTER +ATOM NT NH3 -0.30 +ATOM HT1 HC 0.33 +ATOM HT2 HC 0.33 ! HT2 +ATOM HT3 HC 0.33 ! | +ATOM CD CT1 0.21 ! HT1-NT-HT3 +ATOM HD HB1 0.10 ! | +GROUP ! | HG1 HB1 HA1 H +ATOM CG CT2 -0.18 ! | | | | | +ATOM HG1 HA2 0.09 ! HD-CD--CG--CB--CA--N-- +ATOM HG2 HA2 0.09 ! | | | | +GROUP ! | HG2 HB2 HA2 +ATOM CB CT2 -0.18 ! O=C +ATOM HB1 HA2 0.09 ! | +ATOM HB2 HA2 0.09 +GROUP ! Copy-pasted from GLY +ATOM CA CT2 -0.02 +ATOM HA1 HA2 0.09 ! Changed HB2 to HA2 because it's not backbone. LJ is different but +ATOM HA2 HA2 0.09 ! default charge is 0.09 in both cases; it's probably an improvement. +ATOM N NH1 -0.47 +ATOM HN H 0.31 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 + +BOND CG CD CB CG CA CB N CA +BOND N HN NT CD C CD +BOND C +N CD HD CG HG1 CG HG2 CB HB1 +BOND CB HB2 CA HA1 CA HA2 +DOUBLE O C +BOND NT HT1 NT HT2 NT HT3 +IMPR N -C CA HN C CD +N O +DONOR HN N +DONOR HT1 NT +DONOR HT2 NT +DONOR HT3 NT +ACCEPTOR O C +IC HT1 NT CD C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 CD *NT HT2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HT1 CD *NT HT3 1.0404 110.0200 -120.1300 109.4000 1.0401 +IC NT CD C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CD *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CD C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC C NT *CD CG 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C NT *CD HD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC NT CD CG CB 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CB CD *CG HG1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CB CD *CG HG2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CD CG CB CA 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CA CG *CB HB1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CA CG *CB HB2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CG CB CA N 1.5435 113.2800 180.0000 112.3300 1.5350 +IC N CB *CA HA1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC N CB *CA HA2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA CB 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI NLE 0.00 !Nor-leucine +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 +ATOM HA HB1 0.09 ! | | | | | +GROUP ! HA-CA--CB--CG--CD--CE--HE3 +ATOM CB CT2 -0.18 ! | | | | | +ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 HE2 +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CT2 -0.18 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +GROUP +ATOM CE CT3 -0.27 +ATOM HE1 HA3 0.09 +ATOM HE2 HA3 0.09 +ATOM HE3 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 + +BOND CB CA CG CB CD CG CE CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 CE HE3 +DOUBLE O C + +IMPR N -C CA HN C CA +N O + +CMAP -C N CA C N CA C +N +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE HE1 1.5397 112.3300 180.0000 110.4600 1.11 +IC HE1 CD *CE HE2 1.4604 110.4600 119.9100 110.5100 1.1128 +IC HE1 CD *CE HE3 1.4604 110.4600 -120.0200 110.5700 1.1123 + +PRES KAC 0.00 ! patch for Lys (K) acetylation, kevo +DELETE ATOM HZ2 ! follow with AUTOgenerate ANGLes DIHEdrals command +DELETE ATOM HZ3 +GROUP +ATOM CE CT2 -0.02 ! Transfered from NMA by summing +ATOM HE1 HA2 0.09 ! deleted hydrogen charge into parent. +ATOM HE2 HA2 0.09 ! Apply standard charges to now-nonpolar hydrogens. +ATOM NZ NH1 -0.47 ! From NMA +ATOM HZ1 H 0.31 +GROUP +ATOM CH C 0.51 ! from NMA / patch ACE +ATOM OH O -0.51 +GROUP +ATOM CH3 CT3 -0.27 ! standard CH3 as found in NMA / patch ACE +ATOM HH31 HA3 0.09 +ATOM HH32 HA3 0.09 +ATOM HH33 HA3 0.09 + +BOND NZ CH CH OH CH CH3 +BOND CH3 HH31 CH3 HH32 CH3 HH33 +IMPR NZ CH CE HZ1 +IMPR CH CH3 NZ OH +IC CD CE NZ CH 0.0000 0.00 180.00 0.00 0.0000 +IC CE CH *NZ HZ1 0.0000 0.00 180.00 0.00 0.0000 +IC CE NZ CH CH3 0.0000 0.00 180.00 0.00 0.0000 +IC NZ CH3 *CH OH 0.0000 0.00 180.00 0.00 0.0000 +IC NZ CH CH3 HH31 0.0000 0.00 180.00 0.00 0.0000 +IC HH31 CH *CH3 HH32 0.0000 0.00 120.00 0.00 0.0000 +IC HH32 CH *CH3 HH33 0.0000 0.00 -120.00 0.00 0.0000 + +PRES DKAM -0.18 ! Patch to create AMide bond between Asp (D) and Lys (K), kevo +DELETE ATOM 1OD2 ! follow with AUTOgenerate ANGLes DIHEdrals command +DELETE ATOM 2HZ2 +DELETE ATOM 2HZ3 +ATOM 1CB CT2 -0.18 ! Neutralize CB. This causes total -0.18 charge above. +GROUP +ATOM 1CG C 0.51 ! from NMA +ATOM 1OD1 O -0.51 +GROUP +ATOM 2NZ NH1 -0.47 ! From NMA +ATOM 2HZ1 H 0.31 +ATOM 2CE CT2 -0.02 ! Transfered from NMA by summing +ATOM 2HE1 HA2 0.09 ! deleted hydrogen charge into parent. +ATOM 2HE2 HA2 0.09 ! Apply standard charges to now-nonpolar hydrogens. + +BOND 1CG 2NZ +IMPR 2NZ 1CG 2CE 2HZ1 +IMPR 1CG 1CB 2NZ 1OD1 +IC 1CA 1CB 1CG 2NZ 0.0000 0.00 180.00 0.00 0.0000 +IC 1CB 2NZ *1CG 1OD1 0.0000 0.00 180.00 0.00 0.0000 +IC 2CD 2CE 2NZ 1CG 0.0000 0.00 180.00 0.00 0.0000 +IC 2CE 1CG *2NZ 2HZ1 0.0000 0.00 180.00 0.00 0.0000 +IC 1CB 1CG 2NZ 2CE 0.0000 0.00 180.00 0.00 0.0000 + +! 2-Aminoisobutyric acid (AIB), compatible with CHARMM36 +! by Kenno Vanommeslaeghe (kevo) +! IMPORTANT: depends on stream/toppar_all36_prot_retinol.str + +RESI AIBD 0.00 ! 2-Aminoisobutyric acid (AIB) dipeptide, kevo +GROUP +ATOM C1 CT3 -0.27 +ATOM H11 HA3 0.09 +ATOM H12 HA3 0.09 +ATOM H13 HA3 0.09 +GROUP +ATOM C2 C 0.51 +ATOM O2 O -0.51 +GROUP +ATOM N3 NH1 -0.47 +ATOM H3 H 0.31 +ATOM C4 CT 0.16 +GROUP +ATOM C41 CT3 -0.27 +ATOM H411 HA3 0.09 +ATOM H412 HA3 0.09 +ATOM H413 HA3 0.09 +GROUP +ATOM C42 CT3 -0.27 ! H12 H11 H71 H72 +ATOM H421 HA3 0.09 ! \ / \ / +ATOM H422 HA3 0.09 ! H13--C1 H3 O5 C7--H73 +ATOM H423 HA3 0.09 ! \ / \\ / +GROUP ! C2--N3 C5--N6 +ATOM C5 C 0.51 ! // \ / \ +ATOM O5 O -0.51 ! O2 C4 H6 +GROUP ! / \ +ATOM N6 NH1 -0.47 ! H411--C41 C42--H421 +ATOM H6 H 0.31 ! / | | \ +ATOM C7 CT3 -0.11 ! H412 H413 H423 H422 +ATOM H71 HA3 0.09 +ATOM H72 HA3 0.09 +ATOM H73 HA3 0.09 + +BOND C1 C2 C1 H11 C1 H12 C1 H13 C2 N3 C2 O2 +BOND N3 C4 N3 H3 C4 C5 C4 C41 C4 C42 C5 O5 +BOND C41 H411 C41 H412 C41 H413 C42 H421 C42 H422 C42 H423 +BOND C5 N6 N6 C7 N6 H6 C7 H71 C7 H72 C7 H73 +IMPR C2 C1 N3 O2 N3 C2 C4 H3 +IMPR C5 C4 N6 O5 N6 C5 C7 H6 +CMAP C2 N3 C4 C5 N3 C4 C5 N6 +IC N3 C4 C5 N6 0.0000 0.00 70.00 0.00 0.0000 ! Psi ! +IC C5 C4 N3 C2 0.0000 0.00 -130.00 0.00 0.0000 ! Phi ! +IC C4 N3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 ! Omega(N) +IC C4 C5 N6 C7 0.0000 0.00 180.00 0.00 0.0000 ! Omega(C) +IC N3 C5 *C4 C41 0.0000 0.00 120.00 0.00 0.0000 +IC N3 C5 *C4 C42 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 N3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 N6 *C5 O5 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C2 C1 H13 0.0000 0.00 180.00 0.00 0.0000 +IC C2 H13 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 H13 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 N6 C7 H73 0.0000 0.00 0.00 0.00 0.0000 +IC N6 H73 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 +IC N6 H73 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 +IC N3 C4 C41 H413 0.0000 0.00 180.00 0.00 0.0000 +IC C4 H413 *C41 H411 0.0000 0.00 120.00 0.00 0.0000 +IC C4 H413 *C41 H412 0.0000 0.00 -120.00 0.00 0.0000 +IC N3 C4 C42 H423 0.0000 0.00 180.00 0.00 0.0000 +IC C4 H423 *C42 H421 0.0000 0.00 120.00 0.00 0.0000 +IC C4 H423 *C42 H422 0.0000 0.00 -120.00 0.00 0.0000 + +RESI AIB 0.00 ! 2-Aminoisobutyric acid (AIB), kevo +GROUP +ATOM N NH1 -0.47 +ATOM HN H 0.31 +ATOM CA CT 0.16 +GROUP +ATOM CB1 CT3 -0.27 ! HN O +ATOM HB11 HA3 0.09 ! | \\ +ATOM HB12 HA3 0.09 ! _-N C-- +ATOM HB13 HA3 0.09 ! \ / +GROUP ! CA +ATOM CB2 CT3 -0.27 ! / \ +ATOM HB21 HA3 0.09 ! HB11--CB1 CB2--HB21 +ATOM HB22 HA3 0.09 ! / | | \ +ATOM HB23 HA3 0.09 ! HB12 HB13 HB23 HB22 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND N HN N CA CA C C +N +BOND CA CB1 CB1 HB11 CB1 HB12 CB1 HB13 +BOND CA CB2 CB2 HB21 CB2 HB22 CB2 HB23 +DOUBLE C O +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB1 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA CB2 1.4592 114.4400 -123.2300 111.0900 1.5461 +IC C CA CB1 HB11 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB11 CA *CB1 HB12 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB11 CA *CB1 HB13 1.1109 109.6000 -119.5800 111.6100 1.1114 +IC C CA CB2 HB21 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB21 CA *CB2 HB22 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB21 CA *CB2 HB23 1.1109 109.6000 -119.5800 111.6100 1.1114 +!PATCH FIRST QCNT LAST CTER + +PRES QCNT 1.00 ! Quaternary C N-terminus (AIB,...), kevo +GROUP ! use in generate statement +ATOM N NH3 -0.30 ! R HT1 +ATOM HT1 HC 0.33 ! | (+)/ +ATOM HT2 HC 0.33 ! --CA--N--HT2 +ATOM HT3 HC 0.33 ! | \ +ATOM CA CT 0.31 ! R' HT3 +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + + +PRES K7CS 0.32 ! K (lysine) to 7-Carbon Staple +DELETE ATOM 1HA ! ^ ^ ^ ^ +DELETE ATOM 1NZ +!DELETE ATOM 1HZ1 ! CHARMM doesn't like creating atoms with the same +!DELETE ATOM 1HZ2 ! name as deleted ones, so we transmute them instead. +DELETE ATOM 1HZ3 +DELETE ATOM 2HA +DELETE ATOM 2NZ +!DELETE ATOM 2HZ1 +!DELETE ATOM 2HZ2 +DELETE ATOM 2HZ3 +ATOM 1CA CT 0.16 ! sum deleted hydrogen charge into parent. This +ATOM 2CA CT 0.16 ! is the source of the total +0.32 charge above. +GROUP +ATOM 1CB' CT3 -0.27 +ATOM 1HB1' HA3 0.09 +ATOM 1HB2' HA3 0.09 +ATOM 1HB3' HA3 0.09 +GROUP ! adjusts charges +ATOM 1CE CT2 -0.18 +ATOM 1HE1 HA2 0.09 +ATOM 1HE2 HA2 0.09 +GROUP +ATOM 1CZ CT2 -0.18 +ATOM 1HZ1 HA2 0.09 +ATOM 1HZ2 HA2 0.09 +GROUP +ATOM 1CH CC1A -0.15 +ATOM 1HH HE1 0.15 +GROUP +ATOM 2CB' CT3 -0.27 +ATOM 2HB1' HA3 0.09 +ATOM 2HB2' HA3 0.09 +ATOM 2HB3' HA3 0.09 +GROUP ! adjusts charges +ATOM 2CE CT2 -0.18 +ATOM 2HE1 HA2 0.09 +ATOM 2HE2 HA2 0.09 +GROUP +ATOM 2CZ CT2 -0.18 +ATOM 2HZ1 HA2 0.09 +ATOM 2HZ2 HA2 0.09 +GROUP +ATOM 2CH CC1A -0.15 +ATOM 2HH HE1 0.15 + +BOND 1CA 1CB' 1CB' 1HB1' 1CB' 1HB2' 1CB' 1HB3' +BOND 1CE 1CZ 1CZ 1HZ1 1CZ 1HZ2 1CZ 1CH 1CH 1HH +BOND 2CA 2CB' 2CB' 2HB1' 2CB' 2HB2' 2CB' 2HB3' +BOND 2CE 2CZ 2CZ 2HZ1 2CZ 2HZ2 2CZ 2CH 2CH 2HH +BOND 1CH 2CH +IC 1N 1C *1CA 1CB' 0.0000 0.00 -120.00 0.00 0.0000 ! do not change +IC 1N 1CA 1CB' 1HB3' 0.0000 0.00 180.00 0.00 0.0000 +IC 1CA 1HB3' *1CB' 1HB1' 0.0000 0.00 120.00 0.00 0.0000 +IC 1CA 1HB3' *1CB' 1HB2' 0.0000 0.00 -120.00 0.00 0.0000 +IC 1CG 1CD 1CE 1CZ 0.0000 0.00 180.00 0.00 0.0000 +IC 1CD 1CZ *1CE 1HE1 0.0000 0.00 120.00 0.00 0.0000 +IC 1CD 1CZ *1CE 1HE2 0.0000 0.00 -120.00 0.00 0.0000 +IC 1CD 1CE 1CZ 1CH 0.0000 0.00 180.00 0.00 0.0000 +IC 1CE 1CH *1CZ 1HZ1 0.0000 0.00 120.00 0.00 0.0000 +IC 1CE 1CH *1CZ 1HZ2 0.0000 0.00 -120.00 0.00 0.0000 +IC 1CE 1CZ 1CH 2CH 0.0000 0.00 180.00 0.00 0.0000 +IC 1CZ 2CH *1CH 1HH 0.0000 0.00 180.00 0.00 0.0000 +IC 2N 2C *2CA 2CB' 0.0000 0.00 -120.00 0.00 0.0000 ! do not change +IC 2N 2CA 2CB' 2HB3' 0.0000 0.00 180.00 0.00 0.0000 +IC 2CA 2HB3' *2CB' 2HB1' 0.0000 0.00 120.00 0.00 0.0000 +IC 2CA 2HB3' *2CB' 2HB2' 0.0000 0.00 -120.00 0.00 0.0000 +IC 2CG 2CD 2CE 2CZ 0.0000 0.00 180.00 0.00 0.0000 +IC 2CD 2CZ *2CE 2HE1 0.0000 0.00 120.00 0.00 0.0000 +IC 2CD 2CZ *2CE 2HE2 0.0000 0.00 -120.00 0.00 0.0000 +IC 2CD 2CE 2CZ 2CH 0.0000 0.00 180.00 0.00 0.0000 +IC 2CE 2CH *2CZ 2HZ1 0.0000 0.00 120.00 0.00 0.0000 +IC 2CE 2CH *2CZ 2HZ2 0.0000 0.00 -120.00 0.00 0.0000 +IC 2CE 2CZ 2CH 1CH 0.0000 0.00 180.00 0.00 0.0000 +IC 2CZ 1CH *2CH 2HH 0.0000 0.00 180.00 0.00 0.0000 +IC 1CZ 1CH 2CH 2CZ 0.0000 0.00 180.00 0.00 0.0000 ! trans + +!toppar_nmgly +! N-Methylated Glycine, compatible with CHARMM36 +! Kenno Vanommeslaeghe (kevo) based on DMA by Wenbo Yu (xxwy) + +RESI NMGLYD 0.00 ! N-methylglycine dipeptide, kevo +GROUP +ATOM C1 CT3 -0.19 +ATOM H11 HA3 0.09 +ATOM H12 HA3 0.09 +ATOM H13 HA3 0.09 +ATOM C2 C 0.43 +ATOM O2 O -0.52 +ATOM N3 N -0.35 +ATOM C3 CT3 -0.09 ! H32 H33 +ATOM H31 HA3 0.09 ! \ / +ATOM H32 HA3 0.09 ! H11 H31--C3 O5 H71 +ATOM H33 HA3 0.09 ! \ | || | +ATOM C4 CT2 0.08 ! H12--C1 N3 C5 C7--H72 +ATOM H41 HB2 0.09 ! / \ / \ / \ / \ +ATOM H42 HB2 0.09 ! H13 C2 C4 N6 H73 +ATOM C5 C 0.43 ! || / \ | +ATOM O5 O -0.52 ! O2 H41 H42 C6--H63 +ATOM N6 N -0.35 ! / \ +ATOM C6 CT3 -0.09 ! H61 H62 +ATOM H61 HA3 0.09 +ATOM H62 HA3 0.09 +ATOM H63 HA3 0.09 +ATOM C7 CT3 -0.09 +ATOM H71 HA3 0.09 +ATOM H72 HA3 0.09 +ATOM H73 HA3 0.09 + +BOND C1 C2 C1 H11 C1 H12 C1 H13 C2 N3 C2 O2 +BOND N3 C4 N3 C3 C3 H31 C3 H32 C3 H33 C4 C5 +BOND C4 H41 C4 H42 C5 O5 C5 N6 N6 C7 N6 C6 +BOND C6 H61 C6 H62 C6 H63 C7 H71 C7 H72 C7 H73 +IMPR C2 C1 N3 O2 +IMPR C5 C4 N6 O5 +CMAP C2 N3 C4 C5 N3 C4 C5 N6 +IC N3 C4 C5 N6 0.0000 0.00 70.00 0.00 0.0000 ! Psi ! +IC C5 C4 N3 C2 0.0000 0.00 -130.00 0.00 0.0000 ! Phi ! +IC C4 N3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 ! Omega(N) +IC C4 C5 N6 C7 0.0000 0.00 180.00 0.00 0.0000 ! Omega(C) +IC C2 C4 *N3 C3 0.0000 0.00 180.00 0.00 0.0000 ! OOP(left) +IC C5 C7 *N6 C6 0.0000 0.00 180.00 0.00 0.0000 ! OOP(right) +IC N3 C2 C1 H13 0.0000 0.00 180.00 0.00 0.0000 +IC C2 H13 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 H13 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 N3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 N3 C3 H33 0.0000 0.00 -90.00 0.00 0.0000 +IC N3 H33 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC N3 H33 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC N3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC N3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 N6 *C5 O5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N6 C6 H63 0.0000 0.00 90.00 0.00 0.0000 ! 104.2 +IC N6 H63 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC N6 H63 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 N6 C7 H73 0.0000 0.00 0.00 0.00 0.0000 ! 13.5 +IC N6 H73 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 +IC N6 H73 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MGY 0.00 ! N-methylglycine, kevo + ! Currently only of utility for polyglycine with + ! AMGY and DMCT termini +GROUP +ATOM N N -0.35 ! HN2 HN3 +ATOM CN CT3 -0.09 ! \ / +ATOM HN1 HA3 0.09 ! HN1--CN O +ATOM HN2 HA3 0.09 ! | || +ATOM HN3 HA3 0.09 ! N C +ATOM CA CT2 0.08 ! / \ / \ +ATOM HA1 HB2 0.09 ! CA +ATOM HA2 HB2 0.09 ! / \ +ATOM C C 0.43 ! HA1 HA2 +ATOM O O -0.52 + +BOND -C N N CN CN HN1 CN HN2 CN HN3 +BOND N CA CA C CA HA1 CA HA2 C +N +DOUBLE C O +IMPR C CA +N O +CMAP -C N CA C N CA C +N +ACCEPTOR O C +IC N CA C +N 0.0000 0.00 70.00 0.00 0.0000 ! Psi ! +IC C CA N -C 0.0000 0.00 -130.00 0.00 0.0000 ! Phi ! +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 ! Omega(C) +IC -C CA *N CN 0.0000 0.00 180.00 0.00 0.0000 ! OOP(left) +IC CA N CN HN3 0.0000 0.00 -90.00 0.00 0.0000 +IC N HN3 *CN HN1 0.0000 0.00 120.00 0.00 0.0000 +IC N HN3 *CN HN2 0.0000 0.00 -120.00 0.00 0.0000 +IC N C *CA HA1 0.0000 0.00 120.00 0.00 0.0000 +IC N C *CA HA2 0.0000 0.00 -120.00 0.00 0.0000 +IC CA +N *C O 0.0000 0.00 180.00 0.00 0.0000 +PATCH FIRST AMGY LAST DMCT + +PRES AMGY -0.01 ! acetylated N-terminus for N-methylglycine, kevo +ATOM CAY CT3 -0.19 ! do NOT use to create dipeptides; see NMGLYD +ATOM HY1 HA3 0.09 ! HY1 +ATOM HY2 HA3 0.09 ! | / +ATOM HY3 HA3 0.09 ! HY2--CAY--CY +ATOM CY C 0.43 ! | \\ +ATOM OY O -0.52 ! HY3 OY + +BOND CAY CY CAY HY1 CAY HY2 CAY HY3 CY N +DOUBLE CY OY +IMPR CY CAY N OY +CMAP CY N CA C N CA C +N +ACCEPTOR OY CY +IC C CA N CY 0.0000 0.00 -130.00 0.00 0.0000 ! Phi ! +IC CA N CY CAY 0.0000 0.00 180.00 0.00 0.0000 ! Omega(N) +IC CY CA *N CN 0.0000 0.00 180.00 0.00 0.0000 ! OOP(left) +IC N CY CAY HY3 0.0000 0.00 180.00 0.00 0.0000 +IC CY HY3 *CAY HY1 0.0000 0.00 120.00 0.00 0.0000 +IC CY HY3 *CAY HY2 0.0000 0.00 -120.00 0.00 0.0000 +IC CAY N *CY OY 0.0000 0.00 180.00 0.00 0.0000 + +PRES DMCT 0.01 ! dimethylamine C-terminus for N-methylglycine, kevo +ATOM NT N -0.35 ! HT1 +ATOM CNT CT3 -0.09 ! | +ATOM H91 HA3 0.09 ! CAT--HT2 +ATOM H92 HA3 0.09 ! \ / \ +ATOM H93 HA3 0.09 ! NT HT3 +ATOM CAT CT3 -0.09 ! | +ATOM HT1 HA3 0.09 ! CNT--H93 +ATOM HT2 HA3 0.09 ! / \ +ATOM HT3 HA3 0.09 ! H91 H92 + +BOND C NT NT CAT CAT HT1 CAT HT2 CAT HT3 +BOND NT CNT CNT H91 CNT H92 CNT H93 +IMPR C CA NT O +CMAP -C N CA C N CA C NT +IC N CA C NT 0.0000 0.00 70.00 0.00 0.0000 ! Psi ! +IC CA C NT CAT 0.0000 0.00 180.00 0.00 0.0000 ! Omega(C) +IC C CAT *NT CNT 0.0000 0.00 180.00 0.00 0.0000 ! OOP(right) +IC CA NT *C O 0.0000 0.00 180.00 0.00 0.0000 +IC C NT CNT H93 0.0000 0.00 90.00 0.00 0.0000 ! 104.2 +IC NT H93 *CNT H91 0.0000 0.00 120.00 0.00 0.0000 +IC NT H93 *CNT H92 0.0000 0.00 -120.00 0.00 0.0000 +IC C NT CAT HT3 0.0000 0.00 0.00 0.00 0.0000 ! 13.5 +IC NT HT3 *CAT HT1 0.0000 0.00 120.00 0.00 0.0000 +IC NT HT3 *CAT HT2 0.0000 0.00 -120.00 0.00 0.0000 + +! Link lysine and histidine (HSE) with a triazole staple +! +! follow with AUTOgenerate ANGLes DIHEdrals command +PRES KHTZ -0.10 ! K (lysine) to HSE (histidine) TriaZole staple, kevo +DELETE ATOM 1NZ ! previous line: HSE CB-H2 has a +0.10 charge... +DELETE ATOM 1HZ1 +DELETE ATOM 1HZ2 +DELETE ATOM 1HZ3 +DELETE ATOM 2CE1 +DELETE ATOM 2HE1 +DELETE ATOM 2HE2 +DELETE IMPR 2CD2 2CG 2NE2 2HD2 +DELETE IMPR 2CD2 2NE2 2CG 2HD2 +ATOM 1CE CT2 0.11 ! net charge from TRZ3 H5 +ATOM 1HE1 HA2 0.09 +ATOM 1HE2 HA2 0.09 +! transmute prot indole to TRZ3 from CGenFF +ATOM 2CG CG2R51 0.26 ! TRZ3 C2 slightly polar ==> sum H into parent, then substact HSE CB-H2 +ATOM 2ND1 NG2R50 -0.41 ! TRZ3 N3 +ATOM 2CD2 CG2R51 -0.35 ! TRZ3 C1 +ATOM 2HD2 HGR52 0.20 ! TRZ3 H1 +ATOM 2NE1 NG2R50 -0.37 ! TRZ3 N4 +ATOM 2NE2 NG2R51 0.28 ! TRZ3 N5 polar ==> sum H into substituent + +! establish link and repair damage done by deleting 2CE1 +BOND 1CE 2NE2 2NE2 2NE1 2NE1 2ND1 +! no new impropers because the ring is CGenFF +IC 1CG 1CD 1CE 2NE2 0.0000 0.00 180.00 0.00 0.0000 +IC 1CD 2NE2 *1CE 1HE1 0.0000 0.00 120.00 0.00 0.0000 +IC 1CD 2NE2 *1CE 1HE2 0.0000 0.00 -120.00 0.00 0.0000 +IC 2CB 2CG 2ND1 2NE1 0.0000 0.00 180.00 0.00 0.0000 +IC 2CD2 2NE1 *2NE2 1CE 0.0000 0.00 180.00 0.00 0.0000 +IC 1CD 1CE 2NE2 2CD2 0.0000 0.00 90.00 0.00 0.0000 + +!Patches to create covalent bonds to from Cys or His to Zn2+ +!Zn-Cys and Zn-His equilibrium parameters based on PDB survey by Lei Fang, 2015 +!of 180+ structures in the PDB. +!FCs are estimates to allow for flexibility of the artificial bonds/angles + +PRES CSN -1.00 ! patch for anionic Cys: identical to patch CYSD in top_all36_prot.rtf + ! use in a patch statement + ! Doesn't require AUTOgenerate +!delete atom and reassign charges +DELETE ATOM HG1 +GROUP +ATOM CB CS -0.38 +ATOM HB1 HA2 0.09 +ATOM HB2 HA2 0.09 +ATOM SG SS -0.80 + +!S-Zn distances in SIRT3 xtal: 2.37, 2.32, 2.31, 2.21 +PRES ZN_C 0.00 ! patch to covalently link anionic Cys to Zn + ! Patch is 1-Cys and 2-Zn +! Use AUTOgenerate ANGLes DIHEdrals after invoking the patch to create +! the angles and dihedrals. The angle and dihedral parameter force constants +! are set below. Currently, there are angles parameters being used, but the +! diherdral force constants are set to zero. +BOND 1SG 2ZN + +PRES ZNHD 0.00 ! patch to covalently link HSD to Zn + ! Patch is 1-HSD and 2-Zn +BOND 1NE2 2ZN + +PRES ZNHE 0.00 ! patch to covalently link HSE to Zn + ! Patch is 1-Hse and 2-Zn +BOND 1ND1 2ZN + +!Following is an example to create covalent bonds between 4 Cys residues and +!a Zn ion. The Cys residues are initially converted to the anionic ionization +!state and then the bonds to the zn are created followed by autogenerate + +!Need to patch Cys 256, 259, 280, 283 to make them anionic +!as required to be ligands of the Zn+2 +!patch csn proa 256 setup warn +!patch csn proa 259 setup warn +!patch csn proa 280 setup warn +!patch csn proa 283 setup warn + +!Patch to create covalent bond between Cys residues and Zn +!patch zn_c proa 256 hetc 405 setup warn +!patch zn_c proa 259 hetc 405 setup warn +!patch zn_c proa 280 hetc 405 setup warn +!patch zn_c proa 283 hetc 405 setup warn + +!Patch to create covalent bond between Hse residues and Zn +!patch znhe proa 179 heta 301 setup warn + +!Following is important +!autogenerate angles dihedrals + +RESI HYP 0.00 ! hydroxyproline +! +!Domene, C., Jorgensen, C., Vanommeslaeghe, K., Schofield, C., +!MacKerell, A.D., Jr., “Quantifying the binding interaction between the +!hypoxia-inducible transcription factor and the von Hippel Lindau +!suppressor,” Journal of Chemical Theory and Computation, In Press, +!2015, DOI: 10.1021/acs.jctc.5b00411 +! +GROUP ! HD1 HD2 +ATOM N N -0.29 ! | \ / +ATOM CD CP3 0.00 ! N---CD HG +ATOM HD1 HA2 0.09 ! | \ / +ATOM HD2 HA2 0.09 ! | CG +ATOM CA CP1 0.02 ! | / \ +ATOM HA HB1 0.09 ! HA-CA--CB OE-HE +GROUP ! | / \ +ATOM CB CP2 -0.18 ! | HB1 HB2 +ATOM HB1 HA2 0.09 ! 0=C +ATOM HB2 HA2 0.09 ! | +GROUP +ATOM CG CP2 0.14 !note use of CP2 +ATOM HG HA1 0.09 +ATOM OE OH1 -0.66 +ATOM HE H 0.43 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND C CA C +N +BOND N CA +BOND CA CB +BOND CG CB +BOND CG CD +BOND CD N +BOND HA CA +BOND CG HG +BOND CG OE +BOND OE HE +BOND CD HD1 +BOND CD HD2 +BOND CB HB1 +BOND CB HB2 +DOUBLE O C +IMPR N -C CA CD +IMPR C CA +N O +CMAP -C N CA C N CA C +N +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CG *CB HB1 0.00 0.00 120.00 0.00 0.00 +IC CA CG *CB HB2 0.00 0.00 240.00 0.00 0.00 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC CA CB CG HG 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG OE 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG OE HE 0.00 0.00 240.00 0.00 0.00 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 +PATCHING FIRS PROP + +END + +read para card append flex + +BOND +SS ZN 20.000 2.32 ! Anionic Cys-Zn bond to maintain coordination +! HSE (HSD) - Zn +NR2 ZN 20.000 2.07 ! Neutral His-Zn bond to maintain coordination +!! For AIB and longer residues +CT C 250.000 1.4900 ! ALLOW ALI PEP POL ARO +CT3 CT 222.500 1.5380 ! ALLOW ALI +NH1 CT 320.000 1.4300 ! ALLOW ALI PEP POL ARO +CT2A CT 222.500 1.5380 ! from CT2 CT1, Zhu +! For termini +NH2 CT 240.000 1.4550 ! From LSN NH2-CT2 +CT CC 200.000 1.5220 ! ALLOW POL +CT CD 200.000 1.5220 ! ALLOW POL +NH3 CT 200.000 1.4800 ! ALLOW ALI POL +!! for NMGLY +CT3 N 315.000 1.4340 ! DMA, Dimethylacetamide, xxwy +CT2 N 315.000 1.4340 ! NMGLYD; from CT3 N, DMA; kevo +!! triazole staple +CT2 NG2R51 400.00 1.4580 ! protrz, from CG331 NG2R51, penalty= 6 +CT2 CG2R51 229.63 1.5000 ! from CT2 CPH1, kevo +!! hydroxyproline +CP2 OH1 428.000 1.4300 +HA1 CP2 309.000 1.1110 + +ANGLE +CT1 CT2 C 52.000 108.0000 ! DKAM, from CT1 CT2 CC , kevo +SS ZN SS 100.000 111.7700 ! Anionic Cys-Zn bond, equilibrium value based on PDB survey data +CS SS ZN 20.000 95.0000 ! Anionic Cys-Zn bond, Ao from ethylmethylsulfide CT2-S-CT3, FC guess +! HSE (HSD) - Zn +! Equilibrium value is the average value of 40 PDB p53 structures +CPH2 NR2 ZN 20.000 120.6500 +CPH1 NR2 ZN 20.000 125.9800 +SS ZN NR2 100.000 108.1100 ! Cys-Zn-His, equilibrium value based on PDB survey data +! Equilibrium value is the average value of 98.00 +NR2 ZN NR2 100.000 107.85 ! His-Zn-His, equilibrium value based on PDB survey data but + ! but standard deviation is large (SD = 10.32) +!! For AIB +CT NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO +CT3 CT C 52.000 108.0000 ! ALLOW ALI PEP POL ARO +H NH1 CT 35.000 117.0000 ! ALLOW PEP POL ARO ALI +NH1 C CT 80.000 116.5000 ! ALLOW ALI PEP POL ARO +NH1 CT C 50.000 107.0000 ! ALLOW PEP POL ARO ALI +NH1 CT CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO +O C CT 80.000 121.0000 ! ALLOW ALI PEP POL ARO +!! AIB, for longer residues +CY CT2 CT 58.350 114.00 ! from TRP crystal, JWK +CT CT2 CA 51.800 107.5000 ! ALLOW ALI ARO +CT CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT CT2 CPH1 58.350 113.0000 ! ALLOW ARO +CT2 CT C 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT3 CT2 CT 58.350 113.5000 11.16 2.56100 ! ALLOW ALI +NH1 CT CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO +OH1 CT2 CT 75.700 110.1000 ! ALLOW ALI ALC ARO +S CT2 CT 58.000 112.5000 ! ALLOW ALI SUL ION +SM CT2 CT 58.000 112.5000 ! ALLOW ALI SUL ION +NH1 CT CT2A 70.000 113.5000 ! from NH1 CT1 CT2 +CT2A CT C 52.000 108.0000 ! from CT2 CT1 C +CT CT2A HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT1 +CT CT2A CT2 58.350 113.5000 11.16 2.56100 ! from CT2 CT2 CT1 +CT CT2A CPH1 58.350 113.0000 ! from CT1 CT2 CPH1 +CT CT2A CC 52.000 108.0000 ! from CT1 CT2 CC +CT1 CT2 CT 58.350 113.50 11.16 2.56100 ! ALLOW ALI +!! AIB, for longer residues with termini +NH2 CT CT2 67.700 110.0000 ! From LSN NH2-CT2-CT2 +CT2 CT CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT2A CT CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +CT2 CT CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO +NH3 CT CT2 67.700 110.0000 ! ALLOW ALI POL +NH3 CT CT2A 67.700 110.0000 ! from NH3 CT1 CT2 +CT2A CT CD 52.000 108.0000 ! from CT2 CT1 CD +!! For termini +H NH2 CT 50.000 111.0000 ! From LSN HC-NH2-CT2 +NH2 CT CT3 67.700 110.0000 ! From LSN NH2-CT2-CT2 +CT CD OH1 55.000 110.5000 ! From ASPP CT2-CD-OH1 +CT3 CT CD 52.000 108.0000 ! Ala cter +NH2 CT C 50.000 107.0000 ! From ALA Dipep. NH1-CT2-C +CT3 CT CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO +HC NH3 CT 30.000 109.5000 20.00 2.07400 ! ALLOW POL ALI +NH1 CT CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI +NH1 CT CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI +NH2 CC CT 50.000 116.5000 50.00 2.45000 ! ALLOW ALI PEP POL ARO +NH3 CT C 43.700 110.0000 ! ALLOW PEP POL ARO ALI +NH3 CT CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI +NH3 CT CT3 67.700 110.0000 ! ALLOW ALI POL +O CC CT 15.000 121.0000 50.00 2.44000 ! ALLOW ALI PEP POL ARO +OB CD CT 70.000 125.0000 20.00 2.44200 ! ALLOW ALI PEP POL ARO +OC CC CT 40.000 118.0000 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION +OS CD CT 55.000 109.0000 20.00 2.32600 ! ALLOW POL PEP +N C CT 20.000 112.5000 ! From N C CT For attachment to Pro +!! for NMGLY +C N CT3 42.00 119.50 ! DMA, dimethylacetamide, xxwy +C N CT2 42.00 119.50 ! NMGLYD; from C N CT3, DMA (and angsum); kevo +CT3 N CT3 45.00 121.00 ! DMA, dimethylacetamide, xxwy +CT2 N CT3 45.00 121.00 ! NMGLYD; from CT3 N CT3, DMA (and angsum); kevo +N CT3 HA3 50.00 105.00 ! DMA, dimethylacetamide, xxwy +N CT2 HB2 48.00 108.00 ! NMGLYD; from NH1 CT2 HB2 (and closer to DMA); kevo +N CT2 C 50.00 107.00 ! NMGLYD; from CG2O1 CG321 NG2S1 & NH1 CT2 C; kevo +!! triazole staple +CT2 CT2 NG2R51 70.00 113.50 ! protrz, from CG321 CG321 NG2S1, penalty= 11 +NG2R51 CT2 HA2 33.43 110.10 ! protrz, from NG2R51 CG331 HGA3, penalty= 6 +CG2R51 NG2R51 CT2 70.00 127.10 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT2 NG2R51 NG2R50 70.00 117.90 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT1 CT2 CG2R51 58.350 113.00 ! from CT1 CT2 CPH1, kevo +CT2 CG2R51 CG2R51 45.800 130.00 ! from CT2 CPH1 CPH1, kevo +HA2 CT2 CG2R51 33.430 109.50 ! from HA2 CT2 CPH1, kevo +NG2R50 CG2R51 CT2 45.800 120.00 ! from NR2 CPH1 CT2 , kevo +!! hydroxyproline +CP3 CP2 OH1 50.000 112.2000 +CP2 CP2 OH1 50.000 112.5000 +CP2 OH1 H 65.900 109.5000 +HA1 CP2 OH1 45.900 111.0000 +HA1 CP2 CP3 26.500 110.1000 22.53 2.17900 ! +HA1 CP2 CP2 26.500 110.1000 22.53 2.17900 ! + +DIHE +CT1 CT2 C NH1 0.0500 6 180.00 ! DKAM, from CT2 CT2 CC NH2 , kevo +CT1 CT2 C O 0.0500 6 180.00 ! DKAM, from CT2 CT2 CC O , kevo +! Cys (CSN) - Zn +X CT1 CS X 0.2000 3 0.00 ! From X CT1 CT2 X +!terminal CS +!CS CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP +!H NH1 CT1 CS 0.0000 1 0.00 ! ALLOW PEP +!O C CT1 CS 1.4000 1 0.00 ! ALLOW PEP +!NH1 C CT1 CS 0.0000 1 0.00 ! ALLOW PEP +!N C CT1 CS 0.0000 1 0.00 ! ALLOW PEP +CS SS ZN SS 0.0000 3 0.00 ! Dummy for Anionic Cys-Zn bond +HA2 CS SS ZN 0.0000 3 0.00 ! Dummy for Anionic Cys-Zn bond +CT1 CS SS ZN 0.0000 3 0.00 ! Dummy for Anionic Cys-Zn bond +! HSE (HSD) - Zn +SS ZN NR2 CPH1 0.0000 3 0.00 +SS ZN NR2 CPH2 0.0000 3 0.00 +CT2 SS ZN NR2 0.0000 3 0.00 +ZN NR2 CPH2 NR1 0.0000 3 0.00 +ZN NR2 CPH1 CPH1 0.0000 3 0.00 +ZN NR2 CPH1 CT2 0.0000 3 0.00 +ZN NR2 CPH2 HR1 0.0000 3 0.00 +CS SS ZN NR2 0.0000 3 0.00 +! HSE(HSD) - Zn - HSE(HSD) (2 His ligands) +NR2 ZN NR2 CPH1 0.0000 3 0.00 +NR2 ZN NR2 CPH2 0.0000 3 0.00 +HR3 CPH1 NR2 ZN 0.0000 3 0.00 +!! For AIB +C CT NH1 C 1.0900 1 180.00 ! RMSE = 1.10565 +C CT NH1 C 0.3200 2 180.00 ! RMSE = 1.10565 +C CT NH1 C 0.1000 3 0.00 ! RMSE = 1.10565 +NH1 C CT NH1 0.0400 1 0.00 ! RMSE = 1.10565 +NH1 C CT NH1 1.0700 2 180.00 ! RMSE = 1.10565 +NH1 C CT NH1 0.2500 3 180.00 ! RMSE = 1.10565 +CT3 CT NH1 C 0.0000 1 0.00 ! decided to set these to zero in RMSE = 1.10565 fit +O C CT CT3 0.0000 1 0.00 ! decided to set these to zero in RMSE = 1.10565 fit +NH1 C CT CT3 0.0000 1 0.00 ! decided to set these to zero in RMSE = 1.10565 fit +O C CT NH1 0.0000 1 0.00 ! decided to set these to zero in RMSE = 1.10565 fit +H NH1 CT C 0.0000 1 0.00 ! ALLOW PEP +H NH1 CT CT3 0.0000 1 0.00 ! ALLOW PEP +H NH1 C CT 2.5000 2 180.00 ! ALLOW PEP +O C NH1 CT 2.5000 2 180.00 ! ALLOW PEP +NH1 CT CT3 HA3 0.2000 3 0.00 ! ALLOW ALI +C CT CT3 HA3 0.2000 3 0.00 ! ALLOW ALI +!! For dipeptide +CT3 C NH1 CT 1.6000 1 0.00 ! ALLOW PEP +CT3 C NH1 CT 2.5000 2 180.00 ! ALLOW PEP +CT3 NH1 C CT 1.6000 1 0.00 ! ALLOW PEP +CT3 NH1 C CT 2.5000 2 180.00 ! ALLOW PEP +!! For polypeptide +CT1 C NH1 CT 1.6000 1 0.00 ! ALLOW PEP +CT1 C NH1 CT 2.5000 2 180.00 ! ALLOW PEP +CT C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP +CT C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP +CT C NH1 CT 1.6000 1 0.00 ! ALLOW PEP +CT C NH1 CT 2.5000 2 180.00 ! ALLOW PEP +!! For longer residues +CT2 CT NH1 C 0.0000 1 0.00 ! Set to 0 because same as CT3 CT NH1 C 1.8 1 0 ; kevo +C NH1 CT CT2A 0.0000 1 0.00 ! Set to 0 because same as CT3 CT NH1 C 1.8 1 0 ; kevo +O C CT CT2 0.0000 1 0.00 ! Set to 0 because same as O C CT CT3 1.4 1 0 ; kevo +CT2A CT C O 0.0000 1 0.00 ! Set to 0 because same as O C CT CT3 1.4 1 0 ; kevo +N C CT CT2 0.0000 1 0.00 ! Same as NH1 C CT CT3 ; kevo +NH1 C CT CT2 0.0000 1 0.00 ! Same as NH1 C CT CT3 ; kevo +CT2A CT C NH1 0.0000 1 0.00 ! Same as NH1 C CT CT3 ; kevo +CT2A CT C N 0.0000 1 0.00 ! Same as NH1 C CT CT3 ; kevo +H NH1 CT CT2 0.0000 1 0.00 ! Same as H NH1 CT CT3 ; kevo +H NH1 CT CT2A 0.0000 1 0.00 ! Same as H NH1 CT CT3 ; kevo +NH1 CT CT2 HA2 0.2000 3 0.00 ! Same as NH1 CT CT3 HA3 ; kevo +NH1 CT CT2A HA2 0.2000 3 0.00 ! Same as NH1 CT CT3 HA3 ; kevo +HA2 CT2 CT C 0.2000 3 0.00 ! Same as C CT CT3 HA3 ; kevo +HA2 CT2A CT C 0.2000 3 0.00 ! Same as C CT CT3 HA3 ; kevo +SM SM CT2 CT 0.3100 3 0.00 ! Terminal CA ==> ALLOW SUL ALI +CT CT2 CT2 HA2 0.1900 3 0.00 ! Terminal CA ==> From X CT2 CT2 X +CT CT2A CT2 HA2 0.1900 3 0.00 ! Terminal CA ==> From X CT2 CT2 X +CT CT2A CT2 CD 0.1900 3 0.00 ! Terminal CA ==> From X CT2 CT2 X +! Group-fitted for Lys/Arg/Gln/Met +C CT CT2 CT2 0.3500 1 180.00 ! Beyond CH3 +C CT CT2 CT2 0.4200 2 180.00 ! Beyond CH3 +C CT CT2 CT2 1.9100 3 180.00 ! Beyond CH3 +CT2 CT2 CT NH1 0.8800 1 180.00 ! Beyond CH3 +CT2 CT2 CT NH1 0.0000 2 180.00 ! Beyond CH3 +CT2 CT2 CT NH1 1.9000 3 0.00 ! Beyond CH3 +CC CT2 CT2 CT 1.8400 1 180.00 ! Terminal CA +CC CT2 CT2 CT 0.8400 2 180.00 ! Terminal CA +CC CT2 CT2 CT 0.3900 3 180.00 ! Terminal CA +CT CT2 CT2 CT2 0.6300 1 180.00 ! Terminal CA +CT CT2 CT2 CT2 0.0100 2 0.00 ! Terminal CA +CT CT2 CT2 CT2 0.1500 3 0.00 ! Terminal CA +CT CT2 CT2 S 0.1400 1 180.00 ! Terminal CA +CT CT2 CT2 S 0.5400 2 0.00 ! Terminal CA +CT CT2 CT2 S 0.6900 3 0.00 ! Terminal CA +! Fitted Asn +C CT CT2 CC 1.4100 1 180.00 ! Beyond CH3 +C CT CT2 CC 1.2900 2 180.00 ! Beyond CH3 +C CT CT2 CC 0.5900 3 180.00 ! Beyond CH3 +CC CT2 CT NH1 0.2800 1 180.00 ! Beyond CH3 +CC CT2 CT NH1 0.5000 2 180.00 ! Beyond CH3 +CC CT2 CT NH1 0.3800 3 0.00 ! Beyond CH3 +CT CT2 CC NH2 0.6200 1 180.00 ! Terminal CA +CT CT2 CC NH2 0.6600 2 180.00 ! Terminal CA +CT CT2 CC NH2 0.7200 3 180.00 ! Terminal CA +CT CT2 CC O 0.4200 1 180.00 ! Terminal CA +CT CT2 CC O 0.1500 2 180.00 ! Terminal CA +CT CT2 CC O 0.9500 3 180.00 ! Terminal CA +! Fitted Asp +C CT CT2A CC 1.6100 1 180.00 ! Beyond CH3 +C CT CT2A CC 1.2900 2 180.00 ! Beyond CH3 +C CT CT2A CC 0.5900 3 180.00 ! Beyond CH3 +CC CT2A CT NH1 0.6800 1 180.00 ! Beyond CH3 +CC CT2A CT NH1 0.1000 2 180.00 ! Beyond CH3 +CC CT2A CT NH1 0.3800 3 0.00 ! Beyond CH3 +CT CT2A CC OC 0.8400 1 0.00 ! Terminal CA +CT CT2A CC OC 0.9800 2 180.00 ! Terminal CA +CT CT2A CC OC 1.4600 3 0.00 ! Terminal CA +! Fitted Cys +CT CT2 S HS 0.2000 1 0.00 ! Terminal CA +CT CT2 S HS 0.6500 2 0.00 ! Terminal CA +CT CT2 S HS 0.2200 3 0.00 ! Terminal CA +C CT CT2 S 0.2400 1 180.00 ! Beyond CH3 +C CT CT2 S 0.7500 2 180.00 ! Beyond CH3 +C CT CT2 S 1.3500 3 180.00 ! Beyond CH3 +NH1 CT CT2 S 0.3400 1 0.00 ! Beyond CH3 +NH1 CT CT2 S 0.5000 2 180.00 ! Beyond CH3 +NH1 CT CT2 S 1.4300 3 0.00 ! Beyond CH3 +! Fitted Glu +CC CT2 CT2A CT 0.0000 1 180.00 ! Terminal CA +CC CT2 CT2A CT 0.3800 2 180.00 ! Terminal CA +CC CT2 CT2A CT 0.5900 3 180.00 ! Terminal CA +C CT CT2A CT2 0.1100 1 0.00 ! Beyond CH3 +C CT CT2A CT2 0.9800 2 180.00 ! Beyond CH3 +C CT CT2A CT2 1.6000 3 180.00 ! Beyond CH3 +CC CT CT2A CT2 1.6000 3 180.00 ! Beyond CH3 +CT2 CT2A CT NH1 0.3000 1 0.00 ! Beyond CH3 +CT2 CT2A CT NH1 0.3500 2 0.00 ! Beyond CH3 +CT2 CT2A CT NH1 1.7600 3 0.00 ! Beyond CH3 +! Group-fitted for Hsd/Hse +CPH1 CPH1 CT2 CT 1.7400 1 0.00 ! Terminal CA +CPH1 CPH1 CT2 CT 0.1500 2 0.00 ! Terminal CA +CPH1 CPH1 CT2 CT 0.7700 3 180.00 ! Terminal CA +CT CT2 CPH1 NR1 1.4900 1 0.00 ! Terminal CA +CT CT2 CPH1 NR1 0.0900 2 180.00 ! Terminal CA +CT CT2 CPH1 NR1 0.7900 3 180.00 ! Terminal CA +CT CT2 CPH1 NR2 1.0900 1 0.00 ! Terminal CA +CT CT2 CPH1 NR2 0.0900 2 0.00 ! Terminal CA +CT CT2 CPH1 NR2 0.6700 3 180.00 ! Terminal CA +C CT CT2 CPH1 0.1800 1 180.00 ! Beyond CH3 +C CT CT2 CPH1 0.6400 2 180.00 ! Beyond CH3 +C CT CT2 CPH1 0.8700 3 180.00 ! Beyond CH3 +CPH1 CT2 CT NH1 0.0000 1 0.00 ! Beyond CH3 +CPH1 CT2 CT NH1 0.0000 2 180.00 ! Beyond CH3 +CPH1 CT2 CT NH1 0.9000 3 0.00 ! Beyond CH3 +! Fitted Hsp +CPH1 CPH1 CT2A CT 2.0400 1 0.00 ! Terminal CA +CPH1 CPH1 CT2A CT 0.4400 2 0.00 ! Terminal CA +CPH1 CPH1 CT2A CT 0.1300 3 180.00 ! Terminal CA +CT CT2A CPH1 NR3 0.5300 1 180.00 ! Terminal CA +CT CT2A CPH1 NR3 0.4200 2 180.00 ! Terminal CA +CT CT2A CPH1 NR3 0.3000 3 180.00 ! Terminal CA +C CT CT2A CPH1 1.7500 1 180.00 ! Beyond CH3 +C CT CT2A CPH1 0.1300 2 0.00 ! Beyond CH3 +C CT CT2A CPH1 1.8600 3 180.00 ! Beyond CH3 +CPH1 CT2A CT NH1 1.0900 1 180.00 ! Beyond CH3 +CPH1 CT2A CT NH1 0.2200 2 180.00 ! Beyond CH3 +CPH1 CT2A CT NH1 2.3200 3 0.00 ! Beyond CH3 +! Group-fitted for Phe/Tyr +CA CA CT2 CT 1.0700 1 0.00 ! Terminal CA +CA CA CT2 CT 0.2400 2 180.00 ! Terminal CA +CA CA CT2 CT 0.1700 3 180.00 ! Terminal CA +C CT CT2 CA 1.2800 1 180.00 ! Beyond CH3 +C CT CT2 CA 0.9400 2 180.00 ! Beyond CH3 +C CT CT2 CA 1.5700 3 180.00 ! Beyond CH3 +CA CT2 CT NH1 0.5200 1 180.00 ! Beyond CH3 +CA CT2 CT NH1 0.6200 2 180.00 ! Beyond CH3 +CA CT2 CT NH1 1.5800 3 0.00 ! Beyond CH3 +! Fitted Ser +CT CT2 OH1 H 0.0200 1 0.00 ! Terminal CA +CT CT2 OH1 H 0.5600 2 0.00 ! Terminal CA +CT CT2 OH1 H 0.4900 3 0.00 ! Terminal CA +C CT CT2 OH1 0.6500 1 180.00 ! Beyond CH3 +C CT CT2 OH1 0.2500 2 180.00 ! Beyond CH3 +C CT CT2 OH1 1.1700 3 180.00 ! Beyond CH3 +NH1 CT CT2 OH1 0.1800 1 180.00 ! Beyond CH3 +NH1 CT CT2 OH1 0.1900 2 180.00 ! Beyond CH3 +NH1 CT CT2 OH1 1.4600 3 0.00 ! Beyond CH3 +! Fitted Trp +CA CY CT2 CT 0.0300 1 0.00 ! Terminal CA +CA CY CT2 CT 0.5500 2 0.00 ! Terminal CA +CA CY CT2 CT 0.3900 3 180.00 ! Terminal CA +CPT CY CT2 CT 0.3600 1 180.00 ! Terminal CA +CPT CY CT2 CT 0.0500 2 0.00 ! Terminal CA +CPT CY CT2 CT 0.1900 3 180.00 ! Terminal CA +C CT CT2 CY 1.0900 1 180.00 ! Beyond CH3 +C CT CT2 CY 0.5000 2 180.00 ! Beyond CH3 +C CT CT2 CY 1.1700 3 180.00 ! Beyond CH3 +CY CT2 CT NH1 0.2900 1 180.00 ! Beyond CH3 +CY CT2 CT NH1 0.6600 2 180.00 ! Beyond CH3 +CY CT2 CT NH1 1.1700 3 0.00 ! Beyond CH3 +!! For longer residues with termini +H NH2 CT CT2 0.1100 3 0.00 ! From LSN HC-NH2-CT2-CT2; didn't change H NH1 CT CT3 so won't change this; kevo +CC CT CT2 CA 0.0400 3 0.00 ! ALLOW ARO; beyond CH3; kevo +NH3 CT CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X !N terminus ; beyond CH3; kevo +HA2 CT2A CT CC 0.2000 3 0.00 ! RB: added for C-ter Glu; same as C CT CT3 HA3; kevo +HA2 CT2A CT CD 0.2000 3 0.00 ! Same as C CT CT3 HA3 ; kevo +NH3 CT CT2A HA2 0.2000 3 0.00 ! Same as NH1 CT CT3 HA3 ; kevo +NH3 CT CT2A CC 0.2000 3 0.00 ! Beyond CH3 +CC CT2A CT CC 0.2000 3 0.00 ! Beyond CH3 +CPH1 CT2A CT CC 0.2000 3 0.00 ! Beyond CH3 +CPH1 CT2A CT NH3 0.2000 3 0.00 ! Beyond CH3 +CPH1 CT2A CT CD 0.2000 3 0.00 ! Beyond CH3 +CT2 CT2A CT CD 0.2000 3 0.00 ! Beyond CH3 +!! For termini +CC CT NH1 C 0.2000 1 180.00 ! ALLOW PEP POL; would benefit from refitting; kevo +CD CT NH1 C 0.2000 1 180.00 ! ALLOW PEP POL; would benefit from refitting; kevo +H NH1 CT CC 0.0000 1 0.00 ! ALLOW PEP POL; same as H NH1 CT C; kevo +H NH1 CT CD 0.0000 1 0.00 ! ALLOW PEP POL; same as H NH1 CT C; kevo +H NH2 CC CT 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO; terminal CA; just as transferable as H NH1 C CT ; kevo +NH3 CT C N 0.4000 1 0.00 ! ALLOW PEP PRO; would benefit from refitting; kevo +NH3 CT C NH1 0.6000 1 0.00 ! ALLOW PEP PRO; would benefit from refitting; kevo +O C CT NH3 0.0000 1 0.00 ! ALLOW PEP PRO; would benefit from refitting; kevo +NH3 CT CT3 HA3 0.2000 3 0.00 +CC CT CT3 HA3 0.2000 3 0.00 +CT3 CT CC OC 0.0500 6 180.00 +NH1 CT CC OC 0.0500 6 180.00 +CT3 CT NH3 HC 0.1000 3 0.00 +C CT NH3 HC 0.1000 3 0.00 +! for the free AA, which we only generated as a sanity check and don't actually support. +NH3 CT CC OC 0.0500 6 180.00 +CC CT NH3 HC 0.1000 3 0.00 +!! For attachment to Pro, Gly +CT C N CP1 2.7500 2 180.00 ! ALLOW PRO; terminal CA; just as transferable as CT3 C NH1 CT ; kevo +CT C N CP1 0.3000 4 0.00 ! ALLOW PRO; terminal CA; just as transferable as CT3 C NH1 CT ; kevo +CT C N CP3 2.7500 2 180.00 ! ALLOW PRO; terminal CA; just as transferable as CT3 C NH1 CT ; kevo +CT C N CP3 0.3000 4 0.00 ! ALLOW PRO; terminal CA; just as transferable as CT3 C NH1 CT ; kevo +CT NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO; terminal CA; kevo +CT NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO; terminal CA; kevo +CT2 C NH1 CT 1.6000 1 0.00 ! ALLOW PEP; terminal CA; same as CT3 C NH1 CT ; kevo +CT2 C NH1 CT 2.5000 2 180.00 ! ALLOW PEP; terminal CA; same as CT3 C NH1 CT ; kevo +CT2 NH1 C CT 1.6000 1 0.00 ! ALLOW PEP; terminal CA; same as CT3 NH1 C CT ; kevo +CT2 NH1 C CT 2.5000 2 180.00 ! ALLOW PEP; terminal CA; same as CT3 NH1 C CT ; kevo +N C CT CT3 0.0000 1 0.00 ! ALLOW PEP PRO; same as NH1 C CT CT3; kevo +N C CT NH1 0.1600 1 180.00 ! Optimized by kevo with -0.2 offset +N C CT NH1 1.0700 2 180.00 ! Optimized by kevo +N C CT NH1 0.2500 3 180.00 ! Optimized by kevo +!! Leu side chain +CT CT2 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT2 X +CT CT2 CT1 CT3 0.0500 1 0.00 ! Beyond CH3 +CT CT2 CT1 CT3 0.1000 2 180.00 ! Beyond CH3 +CT CT2 CT1 CT3 0.0100 3 180.00 ! Beyond CH3 +C CT CT2 CT1 0.3200 1 180.00 ! Terminal CA +C CT CT2 CT1 0.6100 2 180.00 ! Terminal CA +C CT CT2 CT1 0.7200 3 180.00 ! Terminal CA +CT1 CT2 CT NH1 0.4800 1 180.00 ! Terminal CA +CT1 CT2 CT NH1 0.4200 2 180.00 ! Terminal CA +CT1 CT2 CT NH1 0.6500 3 0.00 ! Terminal CA +!!! for side chain of patch K7CS , (S)-alpha-(2'-heptenyl)alanine based hydrocarbon staple +CT2 CC1A CC1A CT2 10.0000 2 180.00 ! from CT3 CC1A CC1A CT3 (double bond) +CT2 CC1A CC1A HE1 5.2000 2 180.00 ! from CT3 CC1A CC1A HE1 (double bond) +HE1 CC1A CT2 CT2 0.1200 3 0.00 ! from lipid HEL1 CEL1 CTL2 CTL2 (same in CGenFF) + +!! for NMGLY +CT3 C N CT3 2.6000 2 180.00 ! DMA, dimethylacetamide, xxwy +CT2 C N CT2 2.6000 2 180.00 ! MGY; from CT3 C N CT3, DMA; kevo +CT2 C N CT3 2.6000 2 180.00 ! NMGLYD; from CT3 C N CT3, DMA; kevo +CT3 C N CT2 2.6000 2 180.00 ! NMGLYD; from CT3 C N CT3, DMA; kevo +O C N CT3 2.6000 2 180.00 ! DMA, dimethylacetamide, xxwy +O C N CT2 2.6000 2 180.00 ! NMGLYD; from CT3 C N CT3, DMA; kevo +HA3 CT3 N CT3 0.4200 3 0.00 ! DMA, dimethylacetamide, xxwy +HA3 CT3 N CT2 0.4200 3 0.00 ! NMGLYD; from CT3 C N CT3, DMA; kevo +HA3 CT3 N C 0.0000 3 0.00 ! DMA, dimethylacetamide; sp2-methyl, no torsion potential; xxwy & jhs +HB2 CT2 N C 0.0000 3 0.00 ! NMGLYD; from HA3 CT3 N C, DMA and HB2 CT2 NH1 C; kevo +HB2 CT2 N CT3 0.4200 3 0.00 ! NMGLYD; from HA3 CT3 N CT3, DMA; kevo +C CT2 N C 1.2000 1 180.00 ! NMGLYD, N-methylglycine dipeptide, kevo +C CT2 N C 0.4600 2 180.00 ! NMGLYD, N-methylglycine dipeptide, kevo +C CT2 N C 0.0500 3 180.00 ! NMGLYD, N-methylglycine dipeptide, kevo +C CT2 N CT3 1.5000 1 0.00 ! NMGLYD, N-methylglycine dipeptide, kevo +N C CT2 N 0.1100 1 180.00 ! NMGLYD, N-methylglycine dipeptide, kevo +N C CT2 N 0.9500 2 180.00 ! NMGLYD, N-methylglycine dipeptide, kevo +N C CT2 N 0.2900 3 180.00 ! NMGLYD, N-methylglycine dipeptide, kevo +O C CT2 N 0.2100 1 0.00 ! NMGLYD, N-methylglycine dipeptide, kevo +O C CT2 N 1.0800 2 180.00 ! NMGLYD, N-methylglycine dipeptide, kevo +O C CT2 N 0.3000 3 0.00 ! NMGLYD, N-methylglycine dipeptide, kevo +!! triazole staple +CG2R51 CG2R51 NG2R51 CT2 0.0000 1 0.00 ! protrz, from CG2R51 CG2R51 NG2R51 CG3C51, penalty= 31.4 +HGR52 CG2R51 NG2R51 CT2 0.0000 2 180.00 ! protrz, from HGR52 CG2R53 NG2R51 CG331, penalty= 28.9 +CT2 CT2 CT2 NG2R51 0.2000 3 0.00 ! protrz, from CG321 CG321 CG321 NG2S1, penalty= 11.9 +NG2R51 CT2 CT2 HA2 0.1950 3 0.00 ! protrz, from NG2S1 CG321 CG321 HGA2, penalty= 11 +NG2R50 NG2R50 NG2R51 CT2 2.5000 2 180.00 ! protrz, from NG2R50 NG2R50 NG2R51 HGP1, kevo +CT2 CT2 NG2R51 CG2R51 0.3850 1 0.00 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT2 CT2 NG2R51 CG2R51 0.4200 2 0.00 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT2 CT2 NG2R51 CG2R51 0.0800 3 0.00 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT2 CT2 NG2R51 CG2R51 0.0550 4 0.00 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT2 CT2 NG2R51 NG2R50 0.3850 1 180.00 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT2 CT2 NG2R51 NG2R50 0.4200 2 0.00 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT2 CT2 NG2R51 NG2R50 0.0800 3 180.00 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +CT2 CT2 NG2R51 NG2R50 0.0550 4 0.00 ! ETRZ, 1-Ethyl-1,2,3-trizaole, kevo +HA2 CT2 NG2R51 CG2R51 0.0000 3 0.00 ! protrz, from HGA3 CG331 NG2R51 CG2R53, penalty= 9 +HA2 CT2 NG2R51 NG2R50 0.0000 3 0.00 ! protrz, from HGA3 CG331 NG2R51 CG2R53, kevo +CT2 CG2R51 NG2R50 NG2R50 3.0000 2 180.00 ! from CT2 CPH1 NR2 _CPH2_, kevo +HA2 CT2 CG2R51 CG2R51 0.0000 3 0.00 ! from HA2 CT2 CPH1 CPH1, kevo +HGR52 CG2R51 CG2R51 CT2 2.0000 2 180.00 ! from HR3 CPH1 CPH1 CT2 , kevo +NG2R51 CG2R51 CG2R51 CT2 3.0000 2 180.00 ! from NR1 CPH1 CPH1 CT2 , kevo +NG2R50 CG2R51 CT2 HA2 0.1900 3 0.00 ! from NR2 CPH1 CT2 HA2 , kevo +CG2R51 CG2R51 CT2 CT1 1.7400 1 0.00 ! from CPH1 CPH1 CT2 CT1 , kevo +CG2R51 CG2R51 CT2 CT1 0.1500 2 0.00 ! from CPH1 CPH1 CT2 CT1 , kevo +CG2R51 CG2R51 CT2 CT1 0.7700 3 180.00 ! from CPH1 CPH1 CT2 CT1 , kevo +CT1 CT2 CG2R51 NG2R50 1.0900 1 0.00 ! from CT1 CT2 CPH1 NR2 , kevo +CT1 CT2 CG2R51 NG2R50 0.0900 2 0.00 ! from CT1 CT2 CPH1 NR2 , kevo +CT1 CT2 CG2R51 NG2R50 0.6700 3 180.00 ! from CT1 CT2 CPH1 NR2 , kevo +! Use specific parameters from CHARMM36 side chain parametrization project +HB1 CT1 CT2 CG2R51 0.2000 3 0.00 ! from HB1 CT1 CT2 CPH1, kevo +C CT1 CT2 CG2R51 0.1800 1 180.00 ! from C CT1 CT2 CPH1, kevo +C CT1 CT2 CG2R51 0.6400 2 180.00 ! from C CT1 CT2 CPH1, kevo +C CT1 CT2 CG2R51 0.8700 3 180.00 ! from C CT1 CT2 CPH1, kevo +CG2R51 CT2 CT1 NH1 0.0000 1 0.00 ! from CPH1 CT2 CT1 NH1 , kevo +CG2R51 CT2 CT1 NH1 0.0000 2 180.00 ! from CPH1 CT2 CT1 NH1 , kevo +CG2R51 CT2 CT1 NH1 0.9000 3 0.00 ! from CPH1 CT2 CT1 NH1 , kevo +!! hydroxyproline +HA1 CP2 OH1 H 0.1400 3 0.00 ! 0.14 3 0 +N CP3 CP2 OH1 2.0100 1 180.00 +N CP3 CP2 OH1 2.5600 2 0.00 +N CP3 CP2 OH1 2.3900 3 0.00 +CP3 CP2 OH1 H 0.5700 1 0.00 +CP3 CP2 OH1 H 0.1500 2 180.00 +CP3 CP2 OH1 H 0.1100 3 180.00 +CP2 CP2 OH1 H 1.0200 1 0.00 +CP2 CP2 OH1 H 0.4300 2 180.00 +CP2 CP2 OH1 H 0.8500 3 0.00 +CP1 CP2 CP2 OH1 0.9800 1 0.00 +CP1 CP2 CP2 OH1 0.9700 2 180.00 +CP1 CP2 CP2 OH1 0.0600 3 180.00 + +IMPROPERS +!! for NMGLY +C CT3 N O 71.0000 0 0.00 ! DMA, Dimethylacetamide, xxwy +C CT2 N O 71.0000 0 0.00 ! NMGLYD; from C CT3 N O, DMA; kevo + + +CMAP + +! 2-Aminoisobutyric acid (AIB) map, kevo 2014 +C NH1 CT C NH1 CT C NH1 24 + +! phi = -180.0 + 0.615200 0.428100 -0.010900 -0.364800 -0.521900 + -0.406200 -0.075000 0.050300 -0.413200 -1.158300 + -1.803200 -2.219100 -1.693100 -2.219100 -1.803200 + -1.158300 -0.413200 0.050300 -0.075000 -0.406200 + -0.521900 -0.364800 -0.010900 0.428100 + +! phi = -165.0 + 0.370000 -0.157200 -0.778100 -1.155300 -1.221100 + -0.993500 -0.618900 -0.542600 -0.962400 -1.684500 + -2.273800 -2.377000 -2.089200 -1.937500 -1.485600 + -0.884900 -0.217000 0.244400 0.146800 -0.105100 + -0.150400 0.041600 0.323700 0.545400 + +! phi = -150.0 + 0.028200 -0.675900 -1.349900 -1.653300 -1.571500 + -1.263500 -1.000300 -1.135100 -1.494700 -1.926000 + -2.102000 -2.058800 -2.219100 -1.770000 -1.311300 + -0.776800 -0.180200 0.222400 0.096700 -0.135600 + -0.129200 0.069200 0.280900 0.351600 + +! phi = -135.0 + -0.094600 -0.634400 -1.147900 -1.322900 -1.219900 + -1.149500 -1.405300 -1.682500 -1.655900 -1.338200 + -0.169900 -2.481100 -2.136400 -1.570800 -1.061000 + -0.542400 -0.036600 0.212100 0.043800 -0.173400 + -0.172000 -0.041300 0.081500 0.132600 + +! phi = -120.0 + 0.019300 -0.160600 -0.469000 -0.738700 -1.006700 + -1.424500 -1.840600 -1.886000 -1.285400 -1.472500 + -2.435200 -2.440900 -1.875100 -1.250700 -0.707800 + -0.231800 -0.015900 0.066500 0.071000 -0.079100 + -0.114000 -0.076000 -0.055700 0.006000 + +! phi = -105.0 + 0.265600 0.267200 -0.069800 -0.579900 -1.092400 + -1.582000 -1.843500 -1.520900 -0.416400 -2.244400 + -2.625700 -2.228400 -1.462000 -0.728100 -0.240500 + -0.426700 -0.770500 -0.747400 -0.066500 0.188900 + 0.147800 0.102900 0.039600 0.093300 + +! phi = -90.0 + 0.255100 0.212700 -0.116200 -0.585400 -1.009800 + -1.341700 -1.351300 -0.973700 -1.878800 -2.622100 + -2.641400 -1.913400 -0.862100 -0.158600 -0.403000 + -0.698900 -0.986200 -1.174700 -0.481500 0.289100 + 0.418500 0.333100 0.181800 0.154300 + +! phi = -75.0 + -0.358500 -0.406300 -0.528900 -0.676700 -0.771600 + -0.802400 -0.570000 -1.033800 -2.255800 -2.883500 + -2.521700 -1.343600 -0.115300 0.036600 0.005900 + -0.052900 -0.317100 -0.688800 -0.574500 -0.076600 + 0.084600 0.008800 -0.205800 -0.341100 + +! phi = -60.0 + -1.685200 -1.514900 -1.178600 -0.766800 -0.372900 + -0.082400 0.192600 -1.158300 -2.647100 -3.048400 + -2.054900 -0.363900 0.289400 0.545700 0.661000 + 0.613700 0.185100 -0.215700 -0.467400 -0.503600 + -0.843900 -1.248800 -1.561200 -1.712000 + +! phi = -45.0 + -2.865400 -2.172000 -1.192100 -0.176300 0.593300 + 0.879100 0.385400 -1.611200 -3.020600 -2.747000 + -1.013800 0.268500 0.738700 1.122100 1.187500 + 0.950500 0.460500 -0.031700 -0.337600 -0.993300 + -2.071700 -2.883600 -3.247300 -3.227300 + +! phi = -30.0 + -2.466200 -1.100100 0.452100 1.766100 1.716800 + 0.746500 -0.672500 -2.239400 -2.778400 -1.529500 + 0.180800 0.621600 1.177300 1.473700 1.392600 + 1.040500 0.606900 0.366100 -0.025700 -1.458900 + -3.003700 -3.790600 -3.875200 -3.423600 + +! phi = -15.0 + -0.407300 1.606600 1.873200 -0.150900 -0.659300 + -1.209600 -1.785700 -2.102800 -1.409400 0.209000 + 0.357200 0.784400 1.223300 1.301300 1.056500 + 0.747700 0.697900 0.731400 -0.500400 -2.152600 + -3.213600 -3.427800 -3.065200 -2.103000 + +! phi = 0.0 + 1.776300 0.025300 -1.484300 -2.108300 -2.399100 + -2.302600 -1.679000 -0.775000 0.509400 0.419100 + 0.554200 0.946700 1.149700 0.946700 0.554200 + 0.419100 0.509400 -0.775000 -1.679000 -2.302600 + -2.399100 -2.108300 -1.484300 0.025300 + +! phi = 15.0 + -0.407300 -2.103000 -3.065200 -3.427800 -3.213600 + -2.152600 -0.500400 0.731400 0.697900 0.747700 + 1.056500 1.301300 1.223300 0.784400 0.357200 + 0.209000 -1.409400 -2.102800 -1.785700 -1.209600 + -0.659300 -0.150900 1.873200 1.606600 + +! phi = 30.0 + -2.466200 -3.423600 -3.875200 -3.790600 -3.003700 + -1.458900 -0.025700 0.366100 0.606900 1.040500 + 1.392600 1.473700 1.177300 0.621600 0.180800 + -1.529500 -2.778400 -2.239400 -0.672500 0.746500 + 1.716800 1.766100 0.452100 -1.100100 + +! phi = 45.0 + -2.865400 -3.227300 -3.247300 -2.883600 -2.071700 + -0.993300 -0.337600 -0.031700 0.460500 0.950500 + 1.187500 1.122100 0.738700 0.268500 -1.013800 + -2.747000 -3.020600 -1.611200 0.385400 0.879100 + 0.593300 -0.176300 -1.192100 -2.172000 + +! phi = 60.0 + -1.685200 -1.712000 -1.561200 -1.248800 -0.843900 + -0.503600 -0.467400 -0.215700 0.185100 0.613700 + 0.661000 0.545700 0.289400 -0.363900 -2.054900 + -3.048400 -2.647100 -1.158300 0.192600 -0.082400 + -0.372900 -0.766800 -1.178600 -1.514900 + +! phi = 75.0 + -0.358500 -0.341100 -0.205800 0.008800 0.084600 + -0.076600 -0.574500 -0.688800 -0.317100 -0.052900 + 0.005900 0.036600 -0.115300 -1.343600 -2.521700 + -2.883500 -2.255800 -1.033800 -0.570000 -0.802400 + -0.771600 -0.676700 -0.528900 -0.406300 + +! phi = 90.0 + 0.255100 0.154300 0.181800 0.333100 0.418500 + 0.289100 -0.481500 -1.174700 -0.986200 -0.698900 + -0.403000 -0.158600 -0.862100 -1.913400 -2.641400 + -2.622100 -1.878800 -0.973700 -1.351300 -1.341700 + -1.009800 -0.585400 -0.116200 0.212700 + +! phi = 105.0 + 0.265600 0.093300 0.039600 0.102900 0.147800 + 0.188900 -0.066500 -0.747400 -0.770500 -0.426700 + -0.240500 -0.728100 -1.462000 -2.228400 -2.625700 + -2.244400 -0.416400 -1.520900 -1.843500 -1.582000 + -1.092400 -0.579900 -0.069800 0.267200 + +! phi = 120.0 + 0.019300 0.006000 -0.055700 -0.076000 -0.114000 + -0.079100 0.071000 0.066500 -0.015900 -0.231800 + -0.707800 -1.250700 -1.875100 -2.440900 -2.435200 + -1.472500 -1.285400 -1.886000 -1.840600 -1.424500 + -1.006700 -0.738700 -0.469000 -0.160600 + +! phi = 135.0 + -0.094600 0.132600 0.081500 -0.041300 -0.172000 + -0.173400 0.043800 0.212100 -0.036600 -0.542400 + -1.061000 -1.570800 -2.136400 -2.481100 -0.169900 + -1.338200 -1.655900 -1.682500 -1.405300 -1.149500 + -1.219900 -1.322900 -1.147900 -0.634400 + +! phi = 150.0 + 0.028200 0.351600 0.280900 0.069200 -0.129200 + -0.135600 0.096700 0.222400 -0.180200 -0.776800 + -1.311300 -1.770000 -2.219100 -2.058800 -2.102000 + -1.926000 -1.494700 -1.135100 -1.000300 -1.263500 + -1.571500 -1.653300 -1.349900 -0.675900 + +! phi = 165.0 + 0.370000 0.545400 0.323700 0.041600 -0.150400 + -0.105100 0.146800 0.244400 -0.217000 -0.884900 + -1.485600 -1.937500 -2.089200 -2.377000 -2.273800 + -1.684500 -0.962400 -0.542600 -0.618900 -0.993500 + -1.221100 -1.155300 -0.778100 -0.157200 + +!! for NMGLY +! n-methylglycine map, kevo 2014 +C N CT2 C N CT2 C N 24 + +! phi = -180.0 + 2.625600 2.072300 1.975000 1.264000 1.598000 + 1.354900 0.720200 -0.021400 -0.588000 -1.063100 + -1.713200 -2.669400 -3.847900 -2.669400 -1.713200 + -1.063100 -0.588000 -0.021400 0.720200 1.354900 + 1.598000 1.264000 1.975000 2.072300 + +! phi = -165.0 + 0.848700 0.910300 1.269000 0.915600 1.228900 + 1.136700 0.391200 -0.580300 -1.530100 -2.457900 + -3.315300 -4.027400 -2.511800 -1.197400 -0.417400 + -0.206500 -0.061100 0.339700 0.988300 1.484900 + 1.581000 1.821000 2.061500 1.626000 + +! phi = -150.0 + 0.082300 0.767500 0.957000 1.315800 0.967100 + 1.076100 0.409300 -0.689000 -1.682600 -2.118000 + -4.379400 -2.887600 -1.256300 -0.072100 0.111400 + -0.144000 -0.172300 0.091100 0.536400 0.834600 + 0.741500 0.557500 0.901400 0.606000 + +! phi = -135.0 + 0.269800 0.540900 0.923700 0.997300 0.600500 + 0.724500 0.543000 -0.041900 -0.610400 -0.672200 + -3.282700 -1.656500 -0.130200 0.367800 -0.025100 + -0.369200 -0.414400 -0.317600 -0.000400 0.206600 + 0.027200 -0.442700 0.356900 0.258200 + +! phi = -120.0 + 0.349900 0.465000 0.634800 0.560200 0.281400 + 0.324600 0.149500 -0.476200 -0.993200 -2.930700 + -1.847200 -0.388300 0.538600 0.288000 -0.128100 + -0.313600 -0.164400 0.062600 0.033800 0.096500 + -0.107900 -0.609600 0.470400 0.406100 + +! phi = -105.0 + 0.496800 0.335900 0.257700 0.045100 -0.208600 + 0.059600 0.113300 -0.380000 -0.709800 -0.746500 + -0.269100 0.769800 0.597600 0.351200 0.077200 + 0.132300 0.352900 0.596800 0.613300 0.233500 + 0.096700 -0.156500 0.798700 0.711400 + +! phi = -90.0 + 0.267900 -0.177600 -0.437200 -0.649100 -0.676300 + 0.003900 0.195600 -0.029600 -0.307300 0.035500 + 1.607100 1.482100 1.396000 1.224200 1.036700 + 0.838900 0.635300 0.573000 0.560900 0.393700 + 0.081400 -0.025000 0.975600 0.770600 + +! phi = -75.0 + -0.802100 -1.346400 -1.524800 -1.383300 -0.839500 + 0.281100 0.520100 -0.142800 -0.244300 0.216100 + 1.139000 2.171100 2.068500 1.347200 2.921400 + 0.984600 0.439000 0.143500 0.166100 0.182200 + -0.280200 -0.678200 0.218500 -0.105400 + +! phi = -60.0 + -2.242500 -2.445000 -2.055900 -1.170400 0.242800 + 1.167600 0.499600 -0.157000 -0.309300 0.108700 + 1.130600 1.869400 1.603200 0.633400 1.865800 + 1.267200 0.732100 0.380100 0.226500 -0.050500 + -1.030800 -1.602100 -1.446700 -1.683200 + +! phi = -45.0 + -2.153000 -1.615300 -0.441900 0.936200 1.911200 + 1.490300 0.295700 -0.524500 -0.650700 0.024900 + 1.102900 1.807700 1.624500 0.996100 3.298700 + 2.646700 2.152000 1.958700 1.575800 0.267300 + -1.613300 -2.780600 -2.390400 -2.163300 + +! phi = -30.0 + 0.398200 1.536200 3.062400 1.351900 0.832200 + -0.010500 -1.122200 -1.482000 -0.770400 0.307800 + 1.794800 2.656300 2.827700 2.688700 3.260900 + 2.673300 2.324200 1.782300 1.166400 -0.312100 + -2.246200 -2.491200 -1.212500 -0.253300 + +! phi = -15.0 + 3.317800 6.837300 5.812700 0.585000 -0.371700 + -1.518700 -2.115200 -1.334400 -0.300600 1.425400 + 2.864800 3.605500 3.919700 4.023100 3.418500 + 2.717100 1.860300 0.575200 -0.293300 -1.683600 + -2.535800 -1.544100 0.606400 2.365600 + +! phi = 0.0 + 4.812400 4.069300 2.073500 -0.550600 -1.744000 + -2.289700 -1.617300 -0.493100 0.905900 2.379300 + 3.350700 4.670900 4.422300 4.670900 3.350700 + 2.379300 0.905900 -0.493100 -1.617300 -2.289700 + -1.744000 -0.550600 2.073500 4.069300 + +! phi = 15.0 + 3.317800 2.365600 0.606400 -1.544100 -2.535800 + -1.683600 -0.293300 0.575200 1.860300 2.717100 + 3.418500 4.023100 3.919700 3.605500 2.864800 + 1.425400 -0.300600 -1.334400 -2.115200 -1.518700 + -0.371700 0.585000 5.812700 6.837300 + +! phi = 30.0 + 0.398200 -0.253300 -1.212500 -2.491200 -2.246200 + -0.312100 1.166400 1.782300 2.324200 2.673300 + 3.260900 2.688700 2.827700 2.656300 1.794800 + 0.307800 -0.770400 -1.482000 -1.122200 -0.010500 + 0.832200 1.351900 3.062400 1.536200 + +! phi = 45.0 + -2.153000 -2.163300 -2.390400 -2.780600 -1.613300 + 0.267300 1.575800 1.958700 2.152000 2.646700 + 3.298700 0.996100 1.624500 1.807700 1.102900 + 0.024900 -0.650700 -0.524500 0.295700 1.490300 + 1.911200 0.936200 -0.441900 -1.615300 + +! phi = 60.0 + -2.242500 -1.683200 -1.446700 -1.602100 -1.030800 + -0.050500 0.226500 0.380100 0.732100 1.267200 + 1.865800 0.633400 1.603200 1.869400 1.130600 + 0.108700 -0.309300 -0.157000 0.499600 1.167600 + 0.242800 -1.170400 -2.055900 -2.445000 + +! phi = 75.0 + -0.802100 -0.105400 0.218500 -0.678200 -0.280200 + 0.182200 0.166100 0.143500 0.439000 0.984600 + 2.921400 1.347200 2.068500 2.171100 1.139000 + 0.216100 -0.244300 -0.142800 0.520100 0.281100 + -0.839500 -1.383300 -1.524800 -1.346400 + +! phi = 90.0 + 0.267900 0.770600 0.975600 -0.025000 0.081400 + 0.393700 0.560900 0.573000 0.635300 0.838900 + 1.036700 1.224200 1.396000 1.482100 1.607100 + 0.035500 -0.307300 -0.029600 0.195600 0.003900 + -0.676300 -0.649100 -0.437200 -0.177600 + +! phi = 105.0 + 0.496800 0.711400 0.798700 -0.156500 0.096700 + 0.233500 0.613300 0.596800 0.352900 0.132300 + 0.077200 0.351200 0.597600 0.769800 -0.269100 + -0.746500 -0.709800 -0.380000 0.113300 0.059600 + -0.208600 0.045100 0.257700 0.335900 + +! phi = 120.0 + 0.349900 0.406100 0.470400 -0.609600 -0.107900 + 0.096500 0.033800 0.062600 -0.164400 -0.313600 + -0.128100 0.288000 0.538600 -0.388300 -1.847200 + -2.930700 -0.993200 -0.476200 0.149500 0.324600 + 0.281400 0.560200 0.634800 0.465000 + +! phi = 135.0 + 0.269800 0.258200 0.356900 -0.442700 0.027200 + 0.206600 -0.000400 -0.317600 -0.414400 -0.369200 + -0.025100 0.367800 -0.130200 -1.656500 -3.282700 + -0.672200 -0.610400 -0.041900 0.543000 0.724500 + 0.600500 0.997300 0.923700 0.540900 + +! phi = 150.0 + 0.082300 0.606000 0.901400 0.557500 0.741500 + 0.834600 0.536400 0.091100 -0.172300 -0.144000 + 0.111400 -0.072100 -1.256300 -2.887600 -4.379400 + -2.118000 -1.682600 -0.689000 0.409300 1.076100 + 0.967100 1.315800 0.957000 0.767500 + +! phi = 165.0 + 0.848700 1.626000 2.061500 1.821000 1.581000 + 1.484900 0.988300 0.339700 -0.061100 -0.206500 + -0.417400 -1.197400 -2.511800 -4.027400 -3.315300 + -2.457900 -1.530100 -0.580300 0.391200 1.136700 + 1.228900 0.915600 1.269000 0.910300 + +end + +return diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_na_combined.str b/charmm/toppar/stream/prot/toppar_all36_prot_na_combined.str new file mode 100644 index 00000000..20064e95 --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_na_combined.str @@ -0,0 +1,1690 @@ +* Topology and Parameter Stream File for patches to create +* model compounds and patches that require both protein and +* nucleic acid topology and parameter information +* + +!Parent files that have to be read prior to streaming this file +!top_all36_prot.rtf +!par_all36_prot.prm +!top_all36_na.rtf +!par_all36_na.prm +!stream/toppar_all36_prot_fluoro_alkanes.str ! atom types an parameters for fluorinated compounds + +!Testcase +!test_all36_prot_na_combined.inp + +!all patches must be followed by AUTOGENERATE ANGLES DIHEDRALS + +!PHOSPHOTYROSINE +! +!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. +!Structural Characterization of the Phosphotyrosine Binding Region of a +!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics +!Simulation and Chemical Shift Calculations. Journal of the American +!Chemical Society, 1996, 118: 11265-11277. + +read rtf card append +* Topology for phosphorylated amino acids +* +31 1 + +MASS 484 ON2B 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str) +MASS 485 SP 32.06000 S ! positive Sulphur, S-adenosylmethionine (SAM) + +!IMIDAZOLE ANALOGS FROM toppar_all27_na_model.str + +RESI THFI 0.00 ! imidazole analog with THF ring +! Sugar: transferred from thf; used for optimization of chi, therefore +! the sugar carbon atom types are not rigorously correct +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' ON6 -0.50 ! H41' O4' Imidazole +ATOM C1' CN7B 0.16 ! \ / \ / +ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' +ATOM C4' CN7 0.07 ! | | +ATOM H41' HN7 0.09 ! H31'--C3'--C2'--H21' +ATOM H42' HN7 0.09 ! / \ +GROUP ! H32' H22' +ATOM C2' CN8 -0.18 ! +ATOM H21' HN8 0.09 ! +ATOM H22' HN8 0.09 ! +GROUP ! +ATOM C3' CN7 -0.18 ! +ATOM H31' HN7 0.09 ! +ATOM H32' HN7 0.09 ! +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CPH1 -0.05 ! C1' HE1 +ATOM HG HR3 0.09 ! \ / +ATOM CD2 CPH1 0.22 ! ND1---CE1 +ATOM HD2 HR3 0.10 ! / | +ATOM ND1 NR1 -0.04 ! HG-CG | +ATOM CE1 CPH2 0.25 ! \ | +ATOM HE1 HR1 0.13 ! CD2---NE2 +ATOM NE2 NR2 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +! KEEPS HYDROGENS IN RING PLANE +IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' +IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 +IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 +IMPR CG CD2 ND1 HG CG ND1 CD2 HG +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THMI 0.00 ! thf-ch3-imidazole +! C5' has been declared as CN8, and C3' as CN7, for compatibility +! with DNA, but these carbons are rigorously CN9 and CN8 respectively + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP ! Sugar: transferred from thf +ATOM O4' ON6 -0.50 ! H52' H53' +ATOM C1' CN7B 0.16 ! \ / +ATOM H12' HN7 0.09 ! H51'-C5' O4' Imidazole +ATOM C4' CN7 0.16 ! \ / \ / +ATOM H42' HN7 0.09 ! H42'--C4' C1'--H12' +GROUP ! | | +ATOM C2' CN8 -0.18 ! H31'--C3'--C2'--H21' +ATOM H21' HN8 0.09 ! / \ +ATOM H22' HN8 0.09 ! H32' H22' +GROUP +ATOM C3' CN7 -0.18 +ATOM H31' HN7 0.09 +ATOM H32' HN7 0.09 +GROUP +ATOM C5' CN8B -0.27 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM H53' HN8 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CPH1 -0.05 ! C1' HE1 +ATOM HG HR3 0.09 ! \ / +ATOM CD2 CPH1 0.22 ! ND1---CE1 +ATOM HD2 HR3 0.10 ! / || +ATOM ND1 NR1 -0.04 ! HG-CG || +ATOM CE1 CPH2 0.25 ! \\ || +ATOM HE1 HR1 0.13 ! CD2---NE2 +ATOM NE2 NR2 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H42' C4' C5' C5' H51' C5' H52' C5' H53' +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 + +! KEEPS HYDROGENS IN RING PLANE +IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' +IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 +IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 +IMPR CG CD2 ND1 HG CG ND1 CD2 HG +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THFA 0.00 ! THF-OH-CH3-IM +GROUP +ATOM O4' ON6 -0.50 ! H52' H53' +ATOM C4' CN7 0.16 ! \ / +ATOM H42' HN7 0.09 ! H51'-C5' O4' Imidazole +ATOM C1' CN7B 0.16 ! \ / \ / +ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' +GROUP ! | | +ATOM C2' CN8 -0.18 ! H31'--C3'--C2'--H21' +ATOM H21' HN8 0.09 ! / \ +ATOM H22' HN8 0.09 ! O3' H22' +GROUP ! | +ATOM H31' HN7 0.09 ! H32' +ATOM C3' CN7 0.14 +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP +ATOM C5' CN8B -0.27 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM H53' HN8 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CPH1 -0.05 ! C1' HE1 +ATOM HG HR3 0.09 ! \ / +ATOM CD2 CPH1 0.22 ! ND1---CE1 +ATOM HD2 HR3 0.10 ! / || +ATOM ND1 NR1 -0.04 ! HG-CG || +ATOM CE1 CPH2 0.25 ! \\ || +ATOM HE1 HR1 0.13 ! CD2---NE2 +ATOM NE2 NR2 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' H53' +BOND O3' H32' +BOND C1' ND1 ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THAO 0.00 ! Nucleoside analogue with imidazole +GROUP +ATOM O4' ON6 -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Imidazole +GROUP ! \ / \ / +ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HN8 0.09 ! | | +ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM H31' HN7 0.09 ! O3' H22' +ATOM C3' CN7 0.14 ! | +ATOM O3' ON5 -0.66 ! H32' +ATOM H32' HN5 0.43 ! +GROUP +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CPH1 -0.05 ! C1' HE1 +ATOM HG HR3 0.09 ! \ / +ATOM CD2 CPH1 0.22 ! ND1---CE1 +ATOM HD2 HR3 0.10 ! / || +ATOM ND1 NR1 -0.04 ! HG-CG || +ATOM CE1 CPH2 0.25 ! \\ || +ATOM HE1 HR1 0.13 ! CD2---NE2 +ATOM NE2 NR2 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' ND1 +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +! KEEPS HYDROGENS IN RING PLANE +IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' +IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 +IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 +IMPR CG CD2 ND1 HG CG ND1 CD2 HG +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CG 0.0 0.0 90.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUS 0.00 ! Ribonucleoside analogue with imidazole +GROUP +ATOM O4' ON6B -0.50 ! H5T +ATOM C4' CN7 0.16 ! / +ATOM H42' HN7 0.09 ! H51' O5' +ATOM C1' CN7B 0.16 ! \ | +ATOM H12' HN7 0.09 !H52'--C5' O4' Imidazole +GROUP ! \ / \ / +ATOM C2' CN7B 0.14 ! H42'--C4' C1'--H12' +ATOM H21' HN7 0.09 ! | | +ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' +ATOM H22' HN5 0.43 ! / \ +GROUP ! O3' O2' +ATOM H31' HN7 0.09 ! | | +ATOM C3' CN7 0.14 ! H32' H22' +ATOM O3' ON5 -0.66 +ATOM H32' HN5 0.43 +GROUP +ATOM C5' CN8B 0.05 +ATOM H51' HN8 0.09 +ATOM H52' HN8 0.09 +ATOM O5' ON5 -0.66 +ATOM H5T HN5 0.43 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CPH1 -0.05 ! C1' HE1 +ATOM HG HR3 0.09 ! \ / +ATOM CD2 CPH1 0.22 ! ND1---CE1 +ATOM HD2 HR3 0.10 ! / || +ATOM ND1 NR1 -0.04 ! HG-CG || +ATOM CE1 CPH2 0.25 ! \\ || +ATOM HE1 HR1 0.13 ! CD2---NE2 +ATOM NE2 NR2 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' +BOND C4' H42' C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' ND1 +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +! KEEPS HYDROGENS IN RING PLANE +IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' +IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 +IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 +IMPR CG CD2 ND1 HG CG ND1 CD2 HG +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H22' O2' C2' C3' 0.0 0.0 -60.00 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUCL -1.00 ! +!WARNING: - The charge distribution on the imidazole is identical +! to the charge distribution on the imidazole in THFI, which is +! different from the charge distribution on the equivalent moiety +! in adenine. +! - The charge distribution on the sugar is identical to what +! it is in the DNA. +! - The charge' on the 3' end of the "backbone" is identical to +! what it is in the DNA, except for the terminal methyl group for which +! there is no DNA equivalent. +! - The charges on the 5' extremity of the backbone is as in the +! 5TER patch used for the DNA. An alternative to that would be to use +! charges more similar to what is in non-terminal residues in DNA. +GROUP +ATOM O4' ON6 -0.50 +ATOM C1' CN7B 0.16 +ATOM H12' HN7 0.09 +ATOM C4' CN7 0.16 +ATOM H42' HN7 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +! The following atom types use the parameters specifically developed +! for the imidazole +! Atom types for aliphatic atoms based on nucleotide +ATOM CG CPH1 -0.05 ! C1' HE1 +ATOM HG HR3 0.09 ! \ / +ATOM CD2 CPH1 0.22 ! ND1---CE1 +ATOM HD2 HR3 0.10 ! / || +ATOM ND1 NR1 -0.04 ! HG-CG || +ATOM CE1 CPH2 0.25 ! \\ || +ATOM HE1 HR1 0.13 ! CD2---NE2 +ATOM NE2 NR2 -0.70 ! | + ! HD2 +GROUP ! +ATOM C2' CN8 -0.18 ! +ATOM H21' HN8 0.09 ! H5T +ATOM H22' HN8 0.09 ! | +GROUP ! H52' O5' +ATOM C3' CN7 0.01 ! \ / +ATOM H31' HN7 0.09 ! H51'-C5' O4' Imidazole +ATOM O3' ON2 -0.57 ! \ / \ / +ATOM P P 1.50 ! H42'--C4' C1'--H12' +ATOM O1P ON3 -0.78 ! | | +ATOM O2P ON3 -0.78 ! H31'--C3'--C2'--H21' +ATOM O3P ON2 -0.57 ! / \ +ATOM C3T CN8B -0.17 ! O3' H22' +ATOM H3T1 HN8 0.09 ! | +ATOM H3T2 HN8 0.09 ! O1P==P==O2P +ATOM H3T3 HN8 0.09 ! | +GROUP ! O3P (-1) +ATOM C5' CN8B 0.05 ! \ +ATOM H51' HN8 0.09 ! C3T--H3T3 +ATOM H52' HN8 0.09 ! / \ +ATOM H5T HN5 0.43 ! H3T1 H3T2 +ATOM O5' ON5 -0.66 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' C5' C5' H51' C5' H52' +BOND C5' O5' O5' H5T +BOND C1' ND1 +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +! KEEPS HYDROGENS IN RING PLANE +IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' +IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 +IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 +IMPR CG CD2 ND1 HG CG ND1 CD2 HG +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 90.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +!PHOSPHOTYROSINE + +PRES TP1 -1.00 ! convert tyrosine to monoanionic phosphotyrosine + ! +!patch to convert tyrosine to phenolphosphate +!PATCH TP1 TYR 1 SETUP WARN +! +DELE ATOM 1HH + +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.21 +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.16 +ATOM OH ON2b -0.36 ! NA ATOM TYPE +ATOM P1 P 1.40 ! NA ATOM TYPE +ATOM O2 ON4 -0.76 ! NA ATOM TYPE +ATOM H2 HN4 0.40 ! NA ATOM TYPE +ATOM O3 ON3 -0.76 ! NA ATOM TYPE +ATOM O4 ON3 -0.76 ! NA ATOM TYPE +BOND P1 OH P1 O2 P1 O3 P1 O4 +BOND O2 H2 +BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 +BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +BILD H2 O2 P1 OH 0.0000 000.00 180.00 000.00 0.0000 + +PRES TP1A -1.00 ! patch to convert tyrosine to + ! monoanionic phenol-phosphate model compound + ! when generating tyr, use first none last none for terminal patches +DELE ATOM N +DELE ATOM HN +DELE ATOM CA +DELE ATOM HA +DELE ATOM CB +DELE ATOM HB1 +DELE ATOM HB2 +DELE ATOM C +DELE ATOM O + +DELE ATOM 1HH + +GROUP +ATOM CG CA -0.115 +ATOM HG HP 0.115 +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.21 +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.16 +ATOM OH ON2B -0.36 ! NA ATOM TYPE +ATOM P1 P 1.40 ! NA ATOM TYPE +ATOM O2 ON4 -0.76 ! NA ATOM TYPE +ATOM H2 HN4 0.40 ! NA ATOM TYPE +ATOM O3 ON3 -0.76 ! NA ATOM TYPE +ATOM O4 ON3 -0.76 ! NA ATOM TYPE +BOND P1 OH P1 O2 P1 O3 P1 O4 +BOND O2 H2 +BOND CG HG +BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 +BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +BILD H2 O2 P1 OH 0.0000 000.00 180.00 000.00 0.0000 +BILD CD1 CD2 *CG HG 1.3978 120.09 179.64 120.58 1.0799 + +PRES TP2 -2.00 ! patch to convert tyrosine to + ! dianionic phosphotyrosine +DELE ATOM 1HH +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.21 +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.28 +ATOM OH ON2B -0.28 ! NA ATOM TYPE +ATOM P1 P 1.44 ! NA ATOM TYPE +ATOM O2 ON3 -0.96 ! NA ATOM TYPE +ATOM O3 ON3 -0.96 ! NA ATOM TYPE +ATOM O4 ON3 -0.96 ! NA ATOM TYPE +BOND P1 OH P1 O2 P1 O3 P1 O4 +BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 +BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 + +PRES TP2A -2.00 ! patch to convert tyrosine to + ! dianionic phosphotyrosine + ! when generating tyr, use first none last none for terminal patches +! this converts a single tyrosine to a phenol phosphate + +DELE ATOM N +DELE ATOM HN +DELE ATOM CA +DELE ATOM HA +DELE ATOM CB +DELE ATOM HB1 +DELE ATOM HB2 +DELE ATOM C +DELE ATOM O + +DELE ATOM 1HH + +GROUP +ATOM CG CA -0.115 +ATOM HG HP 0.115 +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.21 +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.28 +ATOM OH ON2B -0.28 ! NA ATOM TYPE +ATOM P1 P 1.44 ! NA ATOM TYPE +ATOM O2 ON3 -0.96 ! NA ATOM TYPE +ATOM O3 ON3 -0.96 ! NA ATOM TYPE +ATOM O4 ON3 -0.96 ! NA ATOM TYPE +BOND P1 OH P1 O2 P1 O3 P1 O4 +BOND CG HG +BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 +BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +BILD CD1 CD2 *CG HG 1.3978 120.09 179.64 120.58 1.0799 + +PRES TMP1 -1.00 ! patch to convert tyrosine to monoanionic phosphonate + ! ester O -> methylene (see RESI BMPH) + ! +DELE ATOM 1OH +DELE ATOM 1HH +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.24 +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.24 +ATOM CZ CA -0.44 +ATOM CH CT2 -0.18 +ATOM HH1 HA2 0.09 +ATOM HH2 HA2 0.09 +ATOM P1 P 1.53 ! NA ATOM TYPE +ATOM O2 ON4 -0.80 ! NA ATOM TYPE +ATOM H2 HN4 0.37 ! NA ATOM TYPE +ATOM O3 ON3 -0.86 ! NA ATOM TYPE +ATOM O4 ON3 -0.86 ! NA ATOM TYPE + +BOND CZ CH CH P1 P1 O2 P1 O3 P1 O4 +BOND CH HH1 CH HH2 O2 H2 + +IC CE1 CE2 *CZ CH 0.0000 000.00 180.00 000.00 0.0000 +IC CE1 CZ CH P1 0.0000 000.00 90.00 000.00 0.0000 +IC CZ CH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O2 CH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +IC CZ P1 *CH HH1 0.0000 000.00 120.00 000.00 0.0000 +IC CZ P1 *CH HH2 0.0000 000.00 -120.00 000.00 0.0000 +IC CH P1 O2 H2 0.0000 000.00 180.00 000.00 0.0000 + +PRES TMP2 -2.00 ! patch to convert tyrosine to dianionic phosphonate + ! ester O -> methylene (see RESI BMPD) + ! +! see PRES TP1 for proper preparation of the topology and +! parameter files +! +DELE ATOM 1OH +DELE ATOM 1HH +GROUP +ATOM CE1 CA -0.24 +ATOM HE1 HP 0.26 +ATOM CE2 CA -0.24 +ATOM HE2 HP 0.26 +ATOM CZ CA -0.45 +ATOM CH CT2 -0.28 +ATOM HH1 HA2 0.09 +ATOM HH2 HA2 0.09 +ATOM P1 P 1.90 ! NA ATOM TYPE +ATOM O2 ON3 -1.13 ! NA ATOM TYPE +ATOM O3 ON3 -1.13 ! NA ATOM TYPE +ATOM O4 ON3 -1.13 ! NA ATOM TYPE + +BOND CZ CH CH P1 P1 O2 P1 O3 P1 O4 +BOND CH HH1 CH HH2 + +IC CE1 CE2 *CZ CH 0.0000 000.00 180.00 000.00 0.0000 +IC CE1 CZ CH P1 0.0000 000.00 90.00 000.00 0.0000 +IC CZ CH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O2 CH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +IC CZ P1 *CH HH1 0.0000 000.00 120.00 000.00 0.0000 +IC CZ P1 *CH HH2 0.0000 000.00 -120.00 000.00 0.0000 + +PRES TDF1 -1.00 ! patch to convert tyrosine to monoanionic difluoro phosphonate + ! ester O -> methylene (see RESI BDFH) + ! +DELE ATOM 1OH +DELE ATOM 1HH +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.24 +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.24 +ATOM CZ CA -0.40 +ATOM CH CF2 0.21 +ATOM FH1 F2 -0.17 +ATOM FH2 F2 -0.17 +ATOM P1 P 1.43 ! NA ATOM TYPE +ATOM O2 ON4 -0.73 ! NA ATOM TYPE +ATOM H2 HN4 0.37 ! NA ATOM TYPE +ATOM O3 ON3 -0.80 ! NA ATOM TYPE +ATOM O4 ON3 -0.80 ! NA ATOM TYPE + +BOND CZ CH CH P1 P1 O2 P1 O3 P1 O4 +BOND CH FH1 CH FH2 O2 H2 + +IC CE1 CE2 *CZ CH 0.0000 000.00 180.00 000.00 0.0000 +IC CE1 CZ CH P1 0.0000 000.00 90.00 000.00 0.0000 +IC CZ CH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O2 CH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +IC CZ P1 *CH FH1 0.0000 000.00 120.00 000.00 0.0000 +IC CZ P1 *CH FH2 0.0000 000.00 -120.00 000.00 0.0000 +IC CH P1 O2 H2 0.0000 000.00 180.00 000.00 0.0000 + +PRES TDF2 -2.00 ! patch to convert tyrosine to dianionic difluoro phosphonate + ! ester O -> methylene (see RESI BDFD) + ! +DELE ATOM 1OH +DELE ATOM 1HH +GROUP +ATOM CE1 CA -0.24 +ATOM HE1 HP 0.26 +ATOM CE2 CA -0.24 +ATOM HE2 HP 0.26 +ATOM CZ CA -0.36 +ATOM CH CF2 0.24 +ATOM FH1 F2 -0.28 +ATOM FH2 F2 -0.28 +ATOM P1 P 2.00 ! NA ATOM TYPE +ATOM O2 ON3 -1.12 ! NA ATOM TYPE +ATOM O3 ON3 -1.12 ! NA ATOM TYPE +ATOM O4 ON3 -1.12 ! NA ATOM TYPE + +BOND CZ CH CH P1 P1 O2 P1 O3 P1 O4 +BOND CH FH1 CH FH2 + +IC CE1 CE2 *CZ CH 0.0000 000.00 180.00 000.00 0.0000 +IC CE1 CZ CH P1 0.0000 000.00 90.00 000.00 0.0000 +IC CZ CH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O2 CH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +IC CZ P1 *CH FH1 0.0000 000.00 120.00 000.00 0.0000 +IC CZ P1 *CH FH2 0.0000 000.00 -120.00 000.00 0.0000 + +RESI PPH1 -1.00 ! phenol-phosphate residue +GROUP +ATOM CG CA -0.115 ! +ATOM HG HP 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CA -0.115 ! CD1--CE1 +ATOM HD1 HP 0.115 ! // \\ +GROUP ! HG--CG CZ--OH O2-H2 +ATOM CD2 CA -0.115 ! \ __ / \ / +ATOM HD2 HP 0.115 ! CD2--CE2 P1 (-) +GROUP ! | | // \\ +ATOM CE1 CA -0.21 ! HD2 HE2 O4 O3 +ATOM HE1 HP 0.21 ! +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.16 +ATOM OH ON2B -0.36 ! NA ATOM TYPE +ATOM P1 P 1.40 ! NA ATOM TYPE +ATOM O2 ON4 -0.76 ! NA ATOM TYPE +ATOM H2 HN4 0.40 ! NA ATOM TYPE +ATOM O3 ON3 -0.76 ! NA ATOM TYPE +ATOM O4 ON3 -0.76 ! NA ATOM TYPE + +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ OH +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND P1 OH P1 O2 P1 O3 P1 O4 +BOND O2 H2 + +! IC table +IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 +IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CE1 *CZ OH 1.3750 120.00 180.00 120.00 1.3800 +IC CE1 CZ OH P1 1.3750 120.00 90.00 120.00 1.6100 +IC CZ OH P1 O2 1.3800 120.00 300.00 108.00 1.5800 +IC O2 OH *P1 O3 1.5800 108.00 120.00 103.00 1.4800 +IC O2 OH *P1 O4 1.5800 108.00 -120.00 103.00 1.4800 +IC OH P1 O2 H2 1.6100 108.00 180.00 115.00 0.9600 + +RESI BMPH -1.00 ! Benz.methylene phosphate +GROUP +ATOM CG CA -0.115 ! HD1 HE1 +ATOM HG HP 0.115 ! | | +GROUP ! CD1--CE1 HH1 O2-H2 +ATOM CD1 CA -0.115 ! // \\ \ / +ATOM HD1 HP 0.115 ! HG--CG CZ---CH---P1 (-) +GROUP ! \ __ / / //\\ +ATOM CD2 CA -0.115 ! CD2--CE2 HH2 O4 O3 +ATOM HD2 HP 0.115 ! | | +GROUP ! HD2 HE2 +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.24 +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.24 +ATOM CZ CA -0.44 +ATOM CH CT2 -0.18 +ATOM HH1 HA2 0.09 +ATOM HH2 HA2 0.09 +ATOM P1 P 1.53 ! NA ATOM TYPE +ATOM O2 ON4 -0.80 ! NA ATOM TYPE +ATOM H2 HN4 0.37 ! NA ATOM TYPE +ATOM O3 ON3 -0.86 ! NA ATOM TYPE +ATOM O4 ON3 -0.86 + ! NA ATOM TYPE +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ CH +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CH HH1 CH HH2 CH P1 P1 O2 P1 O3 +BOND P1 O4 O2 H2 +! IC table +IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 +IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 +IC CE2 CE1 *CZ CH 1.3750 120.00 180.00 122.30 1.4900 +IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CZ CH P1 1.3750 122.30 270.00 111.00 1.8800 +IC P1 CZ *CH HH1 1.8800 111.00 120.00 107.50 1.1110 +IC HH1 CZ *CH HH2 1.1110 107.50 -120.00 107.50 1.1110 +IC CZ CH P1 O2 1.4900 111.00 180.00 93.00 1.5800 +IC O2 CH *P1 O3 1.5800 93.00 120.00 103.00 1.4800 +IC O2 CH *P1 O4 1.5800 93.00 -120.00 103.00 1.4800 +IC CH P1 O2 H2 1.8800 93.00 120.00 115.00 0.9600 + +RESI BMPD -2.00 ! Benz.methyl phosphate dianionic +GROUP +ATOM CG CA -0.115 ! HD1 HE1 +ATOM HG HP 0.115 ! | | +GROUP ! CD1--CE1 HH1 O2 +ATOM CD1 CA -0.115 ! // \\ \ / +ATOM HD1 HP 0.115 ! HG--CG CZ---CH---P1 (-2) +GROUP ! \ __ / / //\\ +ATOM CD2 CA -0.115 ! CD2--CE2 HH2 O4 O3 +ATOM HD2 HP 0.115 ! | | +GROUP HD2 HE2 +ATOM CE1 CA -0.24 +ATOM HE1 HP 0.26 +ATOM CE2 CA -0.24 +ATOM HE2 HP 0.26 +ATOM CZ CA -0.45 +ATOM CH CT2 -0.28 +ATOM HH1 HA2 0.09 +ATOM HH2 HA2 0.09 +ATOM P1 P 1.90 ! NA ATOM TYPE +ATOM O2 ON3 -1.13 ! NA ATOM TYPE +ATOM O3 ON3 -1.13 ! NA ATOM TYPE +ATOM O4 ON3 -1.13 ! NA ATOM TYPE +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ CH +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CH HH1 CH HH2 CH P1 P1 O2 P1 O3 +BOND P1 O4 +! IC table + +IC CE1 CZ CH P1 0.0000 000.00 90.00 000.00 0.0000 +IC CZ CH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O2 CH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +IC CD1 CE1 CZ CH 0.0000 000.00 180.00 000.00 0.0000 +IC HD1 CD1 CG CD2 0.0000 000.00 180.00 000.00 0.0000 +IC CG CD1 CE1 CZ 0.0000 000.00 0.00 000.00 0.0000 +IC HG CG CD1 CE1 0.0000 000.00 180.00 000.00 0.0000 +IC CD2 CG CD1 CE1 0.0000 000.00 0.00 000.00 0.0000 +IC HD2 CD2 CG HG 0.0000 000.00 0.00 000.00 0.0000 +IC CE2 CD2 CG CD1 0.0000 000.00 0.00 000.00 0.0000 +IC HH1 CH P1 O3 0.0000 000.00 180.00 000.00 0.0000 +IC HH2 CH P1 O3 0.0000 000.00 0.00 000.00 0.0000 +IC HE1 CE1 CD1 HD1 0.0000 000.00 0.00 000.00 0.0000 +IC HE2 CE2 CD2 HD2 0.0000 000.00 0.00 000.00 0.0000 + +! +!parameters for the following have not been optimized +! +!RESI BFPH -1.00 ! Benz.fluor.phosphate +! parameters never optimized for this compound +!GROUP +!ATOM CG CA -0.115 ! HD1 HE1 +!ATOM HG HP 0.115 ! | | +!GROUP CD1--CE1 F O2-H2 +!ATOM CD1 CA -0.115 ! // \\ \ / +!ATOM HD1 HP 0.115 ! HG--CG CZ---C2'---P1 (-) +!GROUP \ __ / / //\\ +!ATOM CD2 CA -0.115 ! CD2--CE2 H2' O4 O3 +!ATOM HD2 HP 0.115 ! | | +!GROUP HD2 HE2 +!ATOM CE1 CA -0.21 ! +!ATOM HE1 HP 0.21 ! +!GROUP +!ATOM CE2 CA -0.21 +!ATOM HE2 HP 0.21 +!GROUP +!ATOM CZ CA -0.16 +!ATOM C2' CN7D -0.17 +!ATOM H2' HN7 0.09 +!ATOM F F -0.28 +!ATOM P1 P 1.40 ! NA ATOM TYPE +!ATOM O2 ON4 -0.76 ! NA ATOM TYPE +!ATOM H2 HN4 0.40 ! NA ATOM TYPE +!ATOM O3 ON3 -0.76 ! NA ATOM TYPE +!ATOM O4 ON3 -0.76 ! NA ATOM TYPE +!BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +!BOND CE1 CZ CE2 CZ CZ C2' +!BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +!BOND C2' H2' C2' F2' C2' P1 P1 O2 P1 O3 +!BOND P1 O4 O2 H2 +!! IC table +!IC CE1 CZ C2' P1 0.0000 000.00 0.00 000.00 0.0000 +!IC CZ C2' P1 O2 0.0000 000.00 180.00 000.00 0.0000 +!IC O2 C2' *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +!IC O2 C2' *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +!IC H2 O2 P1 C2' 0.0000 000.00 180.00 000.00 0.0000 +!IC CD1 CE1 CZ C2' 0.0000 000.00 180.00 000.00 0.0000 +!IC HD1 CD1 CG CD2 0.0000 000.00 180.00 000.00 0.0000 +!IC CG CD1 CE1 CZ 0.0000 000.00 0.00 000.00 0.0000 +!IC HG CG CD1 CE1 0.0000 000.00 180.00 000.00 0.0000 +!IC CD2 CG CD1 CE1 0.0000 000.00 0.00 000.00 0.0000 +!IC HD2 CD2 CG HG 0.0000 000.00 0.00 000.00 0.0000 +!IC CE2 CD2 CG CD1 0.0000 000.00 0.00 000.00 0.0000 +!IC F C2' P1 O3 0.0000 000.00 180.00 000.00 0.0000 +!IC H2' C2' P1 O3 0.0000 000.00 0.00 000.00 0.0000 +!IC HE1 CE1 CD1 HD1 0.0000 000.00 0.00 000.00 0.0000 +!IC HE2 CE2 CD2 HD2 0.0000 000.00 0.00 000.00 0.0000 + + +RESI BDFP -1.00 ! Benz.difluor.phosphate +GROUP +ATOM CG CA -0.115 ! HD1 HE1 +ATOM HG HP 0.115 ! | | +GROUP CD1--CE1 F1 O2-H2 +ATOM CD1 CA -0.115 ! // \\ \ / +ATOM HD1 HP 0.115 ! HG--CG CZ---CF---P1 (-) +GROUP \ __ / / //\\ +ATOM CD2 CA -0.115 ! CD2--CE2 F2 O4 O3 +ATOM HD2 HP 0.115 ! | | +GROUP HD2 HE2 +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.24 +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.24 +ATOM CZ CA -0.40 +ATOM CF CF2 0.21 +ATOM F1 F2 -0.17 +ATOM F2 F2 -0.17 +ATOM P1 P 1.43 ! NA ATOM TYPE +ATOM O2 ON4 -0.73 ! NA ATOM TYPE +ATOM H2 HN4 0.37 ! NA ATOM TYPE +ATOM O3 ON3 -0.80 ! NA ATOM TYPE +ATOM O4 ON3 -0.80 + +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ CF +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CF F1 CF F2 CF P1 P1 O2 P1 O3 +BOND P1 O4 O2 H2 +! IC table +IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 +IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 +IC CE2 CE1 *CZ CF 1.3750 120.00 180.00 120.00 1.4500 +IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CZ CF P1 1.3750 120.00 270.00 115.00 1.8800 +IC P1 CZ *CF F1 1.8800 115.00 120.00 118.00 1.3530 +IC F1 CZ *CF F2 1.3530 118.00 -120.00 118.00 1.3530 +IC CZ CF P1 O2 1.4500 115.00 180.00 86.00 1.5800 +IC O2 CF *P1 O3 1.5800 86.00 120.00 95.00 1.4800 +IC O2 CF *P1 O4 1.5800 86.00 -120.00 95.00 1.4800 +IC CF P1 O2 H2 1.8800 86.00 180.00 115.00 0.9600 + +RESI BDFD -2.00 ! Benz.difluor.phosphate dianionic, chris +GROUP +ATOM CG CA -0.115 ! HD1 HE1 +ATOM HG HP 0.115 ! | | +GROUP CD1--CE1 F1 O2 +ATOM CD1 CA -0.115 ! // \\ \ / +ATOM HD1 HP 0.115 ! HG--CG CZ---CF---P1 (-2) +GROUP \ __ / / //\\ +ATOM CD2 CA -0.115 ! CD2--CE2 F2 O4 O3 +ATOM HD2 HP 0.115 ! | | +GROUP HD2 HE2 +ATOM CE1 CA -0.24 +ATOM HE1 HP 0.26 +ATOM CE2 CA -0.24 +ATOM HE2 HP 0.26 +ATOM CZ CA -0.36 +ATOM CF CF2 0.24 +ATOM F1 F2 -0.28 +ATOM F2 F2 -0.28 +ATOM P1 P 2.00 ! NA ATOM TYPE +ATOM O2 ON3 -1.12 ! NA ATOM TYPE +ATOM O3 ON3 -1.12 ! NA ATOM TYPE +ATOM O4 ON3 -1.12 ! NA ATOM TYPE + +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ CF +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CF F1 CF F2 CF P1 P1 O2 P1 O3 +BOND P1 O4 + +! IC table +IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 +IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 +IC CE2 CE1 *CZ CF 1.3750 120.00 180.00 120.00 1.4500 +IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CZ CF P1 1.3750 120.00 90.00 115.00 1.8800 +IC P1 CZ *CF F1 1.8800 115.00 120.00 118.00 1.3530 +IC F1 CZ *CF F2 1.3530 118.00 -120.00 118.00 1.3530 +IC CZ CF P1 O2 1.4500 115.00 180.00 95.00 1.4800 +IC O2 CF *P1 O3 1.4800 95.00 120.00 95.00 1.4800 +IC O2 CF *P1 O4 1.4800 95.00 -120.00 95.00 1.4800 + +PRES SP1 -1.00 ! convert serine to monoanionic phosphoserine + ! use in a patch statement as follows +! patch to convert serine to phosphoserine +!PATCH SP1 segid resnum SETUP WARN +! +DELE ATOM 1HG1 +GROUP +ATOM CB CT2 -0.08 ! +ATOM HB1 HA2 0.09 ! +ATOM HB2 HA2 0.09 ! +ATOM OG ON2 -0.62 !maintain NA atom type +ATOM P P 1.50 +ATOM O1P ON3 -0.82 +ATOM O2P ON3 -0.82 +ATOM OT ON4 -0.68 +ATOM HT HN4 0.34 +BOND OG P P OT OT HT +BOND P O1P P O2P +BILD CA CB OG P 0.0000 000.00 180.00 000.00 0.0000 +BILD CB OG P OT 0.0000 000.00 180.00 000.00 0.0000 +BILD OG P OT HT 0.0000 000.00 180.00 000.00 0.0000 +BILD OG OT *P O1P 0.0000 000.00 -120.00 000.00 0.0000 +BILD OG OT *P O2P 0.0000 000.00 120.00 000.00 0.0000 + +PRES SP2 -2.00 ! convert serine to dianionic phosphoserine + ! use in a patch statement +DELE ATOM 1HG1 +GROUP +ATOM CB CT2 -0.18 ! +ATOM HB1 HA2 0.09 ! +ATOM HB2 HA2 0.09 ! +ATOM OG ON2 -0.40 !maintain NA atom type +ATOM P P 1.10 +ATOM O1P ON3 -0.90 +ATOM O2P ON3 -0.90 +ATOM OT ON3 -0.90 +BOND OG P P OT +BOND P O1P P O2P +BILD CA CB OG P 0.0000 000.00 180.00 000.00 0.0000 +BILD CB OG P OT 0.0000 000.00 180.00 000.00 0.0000 +BILD OG OT *P O1P 0.0000 000.00 -120.00 000.00 0.0000 +BILD OG OT *P O2P 0.0000 000.00 120.00 000.00 0.0000 + +PRES THP1 -1.00 ! convert threonine to monoanionic phosphothreonine + ! use in a patch statement +DELE ATOM 1HG1 +GROUP +ATOM CB CT1 0.01 ! +ATOM HB HA1 0.09 ! +ATOM OG1 ON2 -0.62 !maintain NA atom type +ATOM P P 1.50 +ATOM O1P ON3 -0.82 +ATOM O2P ON3 -0.82 +ATOM OT ON4 -0.68 +ATOM HT HN4 0.34 +BOND OG1 P P OT OT HT +BOND P O1P P O2P +BILD CA CB OG1 P 0.0000 000.00 180.00 000.00 0.0000 +BILD CB OG1 P OT 0.0000 000.00 180.00 000.00 0.0000 +BILD OG1 P OT HT 0.0000 000.00 180.00 000.00 0.0000 +BILD OG1 OT *P O1P 0.0000 000.00 -120.00 000.00 0.0000 +BILD OG1 OT *P O2P 0.0000 000.00 120.00 000.00 0.0000 + +PRES THP2 -2.00 ! convert threonine to dianionic phosphothreonine + ! use in a patch statement +DELE ATOM 1HG1 +GROUP +ATOM CB CT1 -0.09 ! +ATOM HB HA1 0.09 ! +ATOM OG1 ON2 -0.40 !maintain NA atom type +ATOM P P 1.10 +ATOM O1P ON3 -0.90 +ATOM O2P ON3 -0.90 +ATOM OT ON3 -0.90 +BOND OG1 P P OT +BOND P O1P P O2P +BILD CA CB OG1 P 0.0000 000.00 180.00 000.00 0.0000 +BILD CB OG1 P OT 0.0000 000.00 180.00 000.00 0.0000 +BILD OG1 OT *P O1P 0.0000 000.00 -120.00 000.00 0.0000 +BILD OG1 OT *P O2P 0.0000 000.00 120.00 000.00 0.0000 + +RESI EP_2 -2.00 ! Ethylphosphate, dianionic +!test CT3-CT2-ON2-P dihedral without complications from phosphate proton +GROUP ! H21 +ATOM P1 P 1.100 ! | +ATOM O1 ON2 -0.400 ! H23--C2--H22 +ATOM O2 ON3 -0.900 ! | +ATOM O3 ON3 -0.900 ! H11--C1--H12 +ATOM O4 ON3 -0.900 ! | +GROUP ! O1 +ATOM C1 CN8 -0.180 ! | +ATOM H11 HN8 0.090 ! (-) O4==P1==O3 (-) +ATOM H12 HN8 0.090 ! || +GROUP ! O2 +ATOM C2 CN9 -0.270 ! +ATOM H21 HN9 0.090 ! +ATOM H22 HN9 0.090 ! +ATOM H23 HN9 0.090 ! + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 C2 +BOND C2 H21 C2 H22 C2 H23 +! +IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 +IC O2 O1 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 +IC O2 O1 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 P1 O1 C1 0.0000 0.00 180.00 0.00 0.0000 +IC P1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 + +RESI IP_2 -2.00 ! isopropylphosphate, dianionic +!test CT3-CT1-ON2-P dihedral without complications from phosphate proton +GROUP ! H21 +ATOM P1 P 1.100 ! | +ATOM O1 ON2 -0.400 ! H23--C2--H22 H31 +ATOM O2 ON3 -0.900 ! | / +ATOM O3 ON3 -0.900 ! H11--C1----C3--H32 +ATOM O4 ON3 -0.900 ! | \ +GROUP ! O1 H33 +ATOM C1 CN7 -0.090 ! | +ATOM H11 HN7 0.090 ! (-) O4==P1==O3 (-) +! || +GROUP ! O2 +ATOM C2 CN9 -0.270 ! +ATOM H21 HN9 0.090 ! +ATOM H22 HN9 0.090 ! +ATOM H23 HN9 0.090 ! +GROUP ! +ATOM C3 CN9 -0.270 ! +ATOM H31 HN9 0.090 ! +ATOM H32 HN9 0.090 ! +ATOM H33 HN9 0.090 ! + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 C2 C1 C3 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +! +IC C1 O1 P1 O2 0.0000 0.00 60.00 0.00 0.0000 +IC O2 O1 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 +IC O2 O1 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 P1 O1 C1 0.0000 0.00 60.00 0.00 0.0000 +IC P1 O1 C1 C2 0.0000 0.00 220.00 0.00 0.0000 +IC C2 O1 *C1 C3 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 O1 *C1 H11 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C2 H21 0.0000 0.00 -60.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H31 C1 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C1 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 + +PRES SAHC 0.00 ! Patch for ade to get S-adenosyl-homocysteine + ! ade has to be generated prior to application of + ! this patch in a separate patch command +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P +DELETE ATOM O5' + +GROUP +ATOM N NH3 -0.30 ! +ATOM HT1 HC 0.33 ! (2) HT1 +ATOM HT2 HC 0.33 ! | / +ATOM HT3 HC 0.33 !(1)--CA--N--HT2 (+) +ATOM CA CT1 0.21 ! | \ +ATOM HA HB1 0.10 ! HA HT3 +GROUP ! +ATOM CB CT2 -0.18 ! +ATOM HB1 HA2 0.09 ! +ATOM HB2 HA2 0.09 ! HB1 HG1 H5' H4' O4' Adenine +GROUP ! | | | \ / \ / +ATOM CG CT2 -0.14 ! (1)--CB--CG--SD--C5'----C4' C1'-H1' +ATOM HG1 HA2 0.09 ! | | | | | +ATOM HG2 HA2 0.09 ! HB2 HG2 H5'' H3'-C3'--C2'-H21' +ATOM SD S -0.09 ! | | +ATOM C5' CN8B -0.13 ! H3T--O3' O2'-H2' +ATOM H5' HN8 0.09 ! +ATOM H5'' HN8 0.09 ! +GROUP +ATOM C CC 0.34 ! OT2(-) +ATOM OT1 OC -0.67 ! / +ATOM OT2 OC -0.67 !(2)-C + ! \\ + ! OT1 +GROUP +ATOM C3' CN7 0.14 +ATOM H3' HN7 0.09 +ATOM O3' ON5 -0.66 +ATOM H3T HN5 0.43 + +DOUB C OT1 +BOND N CA O3' H3T +BOND CB CA CG CB SD CG C5' SD C CA +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND HT1 N HT2 N HT3 N OT2 C +IMPR OT1 CA OT2 C + +!DONOR HT1 N +!DONOR HT2 N +!DONOR HT3 N +!ACCEPTOR OT1 C +!ACCEPTOR OT2 C + +IC N CA CB CG 1.4863 111.52 -68.05 114.80 1.5438 +IC CA CB CG SD 1.5495 114.80 -169.85 111.97 1.8249 +IC HT1 CA *N HT2 1.0633 98.00 113.14 109.99 1.0338 +IC HT1 CA *N HT3 1.0633 98.00 -117.28 113.48 1.0305 +IC HT1 N CA CB 1.0633 98.00 -136.27 111.52 1.5495 +IC CB N *CA C 1.5495 111.52 123.39 106.34 1.5395 +IC CB N *CA HA 1.5495 111.52 -122.64 109.49 1.0806 +IC CG CA *CB HB1 1.5438 114.80 125.78 110.22 1.1112 +IC CG CA *CB HB2 1.5438 114.80 -119.31 106.97 1.1179 +IC SD CB *CG HG1 1.8249 111.97 120.25 107.22 1.1112 +IC SD CB *CG HG2 1.8249 111.97 -122.78 110.68 1.1101 +IC CB CG SD C5' 1.5438 111.97 149.65 104.32 1.8303 +IC CG SD C5' C4' 1.8249 104.32 -59.34 117.91 1.5403 +IC C4' SD *C5' H5' 1.5403 117.91 122.31 108.22 1.1127 +IC C4' SD *C5' H5'' 1.5403 117.91 -122.71 108.62 1.1118 +IC N CA C OT1 1.4863 106.34 -166.34 117.88 1.2492 +IC OT1 CA *C OT2 1.2492 117.88 -178.37 117.42 1.2654 +IC SD C5' C4' O4' 1.8303 117.91 169.12 108.69 1.4591 +IC O4' C5' *C4' C3' 1.4591 108.69 118.83 122.55 1.5499 +IC O4' C5' *C4' H4' 1.4591 108.69 -116.07 109.38 1.1099 +IC C5' C4' O4' C1' 1.5403 108.69 133.30 108.22 1.4240 +IC C4' O4' C1' N9 1.4591 108.22 -159.13 111.15 1.4614 +IC N9 O4' *C1' C2' 1.4614 111.15 124.24 102.39 1.5135 +IC N9 O4' *C1' H1' 1.4614 111.15 -119.53 107.46 1.1156 +IC C4 C1' *N9 C8 1.3837 126.86 175.00 127.05 1.3697 +IC C1' N9 C4 C5 1.4614 126.86 176.84 105.37 1.3831 +IC C5 N9 *C4 N3 1.3831 105.37 179.25 128.02 1.3472 +IC N9 C4 C5 C6 1.3837 105.37 179.94 116.97 1.4115 +IC C6 C4 *C5 N7 1.4115 116.97 179.52 110.80 1.3914 +IC N7 N9 *C8 H8 1.3073 113.91 -179.74 121.60 1.0918 +IC C4 C5 C6 N1 1.3831 116.97 -0.21 118.01 1.3524 +IC N1 C5 *C6 N6 1.3524 118.01 -179.35 123.62 1.3438 +IC N3 N1 *C2 H2 1.3403 129.44 -179.97 115.20 1.0945 +IC C5 C6 N6 H61 1.4115 123.62 179.97 117.15 0.9949 +IC C3' C1' *C2' O2' 1.5132 95.49 115.41 113.17 1.4151 +IC C3' C1' *C2' H2'' 1.5132 95.49 -116.10 112.79 1.1120 +IC C1' C2' O2' H2' 1.5135 113.17 177.31 109.89 0.9633 +IC C4' C3' O3' H3T 1.5499 116.35 167.44 110.25 0.9629 + +PRES SAM 1.00 ! Patch for ade to get S-adenosyl-methionine + ! ade has to be generated prior to application of + ! this patch in a separate patch command +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P +DELETE ATOM O5' + +GROUP +ATOM N NH3 -0.30 ! +ATOM HT1 HC 0.33 ! (2) HT1 +ATOM HT2 HC 0.33 ! | / +ATOM HT3 HC 0.33 !(1)--CA--N--HT2 (+) +ATOM CA CT1 0.21 ! | \ +ATOM HA HB1 0.10 ! HA HT3 +GROUP ! HGP2 +ATOM CB CT2 -0.18 ! HGP1 | HGP3 +ATOM HB1 HA2 0.09 ! \ | / +ATOM HB2 HA2 0.09 ! HB1 HG1 CGP H5' H4' O4' Adenine +GROUP ! | | | | \ / \ / +ATOM CG CT2 0.03 ! (1)--CB--CG--SDP--C5'----C4' C1'-H1' +ATOM HG1 HA2 0.09 ! | | | | | +ATOM HG2 HA2 0.09 ! HB2 HG2 H5'' H3'-C3'--C2'-H21' +ATOM SDP SP 0.36 ! | | +ATOM C5' CN8B 0.03 ! H3T--O3' O2'-H2' +ATOM H5' HN8 0.09 ! +ATOM H5'' HN8 0.09 ! +ATOM CGP CT3 -0.05 +ATOM HGP1 HA3 0.09 +ATOM HGP2 HA3 0.09 +ATOM HGP3 HA3 0.09 +GROUP +ATOM C CC 0.34 ! OT2(-) +ATOM OT1 OC -0.67 ! / +ATOM OT2 OC -0.67 !(2)-C + ! \\ + ! OT1 +GROUP +ATOM C3' CN7 0.14 +ATOM H3' HN7 0.09 +ATOM O3' ON5 -0.66 +ATOM H3T HN5 0.43 + +DOUB C OT1 +BOND N CA O3' H3T +BOND CB CA CG CB SDP CG C5' SDP C CA +BOND SDP CGP CGP HGP1 CGP HGP2 CGP HGP3 +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND HT1 N HT2 N HT3 N OT2 C +IMPR OT1 CA OT2 C + +IC C5' C4' C3' O3' 1.5234 115.91 79.93 110.37 1.4304 +IC O4' C3' *C4' C5' 1.4346 102.61 -120.58 115.91 1.5234 +IC C2' C4' *C3' O3' 1.5424 104.09 -125.57 110.37 1.4304 +IC C4' C3' C2' C1' 1.5226 104.09 14.37 102.90 1.5288 +IC C3' C2' C1' N9 1.5424 102.90 133.87 112.82 1.4650 +IC O4' C1' N9 C4 1.4153 111.80 -107.70 125.37 1.3732 +IC C1' C4 *N9 C8 1.4650 125.37 -179.62 105.88 1.3752 +IC C4 N9 C8 N7 1.3732 105.88 -0.81 113.71 1.3064 +IC C8 N9 C4 C5 1.3752 105.88 0.94 105.77 1.3832 +IC C8 N7 C5 C6 1.3064 104.03 -179.04 132.57 1.4111 +IC N7 C5 C6 N1 1.3896 132.57 179.89 117.63 1.3541 +IC C5 C6 N1 C2 1.4111 117.63 -0.28 118.64 1.3350 +IC N9 C5 *C4 N3 1.3732 105.77 -179.43 127.11 1.3405 +IC C5 N1 *C6 N6 1.4111 117.63 179.31 118.77 1.3451 +IC N1 C6 N6 H61 1.3541 118.77 -176.12 121.71 0.9960 +IC H61 C6 *N6 H62 0.9960 121.71 174.12 117.26 0.9963 +IC C5 N1 *C6 N6 1.4111 117.63 179.31 118.77 1.3451 +IC N1 C6 N6 H61 1.3541 118.77 -176.12 121.71 0.9960 +IC H61 C6 *N6 H62 0.9960 121.71 174.12 117.26 0.9963 +IC N9 N7 *C8 H8 1.3752 113.71 179.99 124.30 1.0920 +IC N1 N3 *C2 H2 1.3350 129.24 -179.89 115.49 1.0944 +IC C1' C3' *C2' O2' 1.5288 102.90 -120.08 112.64 1.4131 +IC H2' O2' C2' C3' 0.9653 110.72 44.95 112.64 1.5424 +IC O4' C2' *C1' H1' 1.4153 107.09 -114.14 109.33 1.1164 +IC C1' C3' *C2' H2'' 1.5288 102.90 119.13 108.86 1.1116 +IC C2' C4' *C3' H3' 1.5424 104.09 114.80 107.09 1.1125 +IC C3' O4' *C4' H4' 1.5226 102.61 -113.93 106.25 1.1143 +IC HT1 CA *N HT2 1.0601 99.87 -113.55 111.45 1.0368 +IC HT1 CA *N HT3 1.0601 99.87 117.42 113.82 1.0324 +IC HT1 N CA CB 1.0601 99.87 -104.71 109.96 1.5670 +IC CB N *CA C 1.5670 109.96 118.39 106.87 1.5345 +IC CB N *CA HA 1.5670 109.96 -124.81 109.65 1.0831 +IC N CA CB CG 1.4972 109.96 169.87 116.31 1.5650 +IC CG CA *CB HB1 1.5650 116.31 -123.65 109.54 1.1114 +IC CG CA *CB HB2 1.5650 116.31 120.05 107.16 1.1129 +IC CA CB CG SDP 1.5670 116.31 -86.15 117.87 1.8507 +IC SDP CB *CG HG1 1.8507 117.87 -122.43 107.08 1.1125 +IC SDP CB *CG HG2 1.8507 117.87 123.34 107.23 1.1142 +IC CB CG SDP C5' 1.5650 117.87 -174.35 99.89 1.8255 +IC C5' CG *SDP CGP 1.8255 99.89 102.18 99.84 1.8185 +IC CG SDP C5' C4' 1.8507 99.89 -93.23 113.36 1.5234 +IC C4' SDP *C5' H5' 1.5234 113.36 -120.73 109.93 1.1118 +IC C4' SDP *C5' H5'' 1.5234 113.36 122.28 109.47 1.1127 +IC CG SDP CGP HGP1 1.8507 99.84 71.44 110.85 1.1114 +IC HGP1 SDP *CGP HGP2 1.1114 110.85 -120.86 111.89 1.1101 +IC HGP1 SDP *CGP HGP3 1.1114 110.85 118.89 110.59 1.1120 +IC N CA C OT1 1.4972 106.87 -17.54 117.69 1.2603 +IC OT1 CA *C OT2 1.2603 117.69 -177.96 117.51 1.2519 +IC SDP C5' C4' O4' 1.8255 113.36 153.27 110.56 1.4346 +IC O4' C5' *C4' C3' 1.4346 110.56 116.19 115.91 1.5226 +IC O4' C5' *C4' H4' 1.4346 110.56 -118.35 112.11 1.1143 +IC C5' C4' O4' C1' 1.5234 110.56 166.29 106.58 1.4153 +IC C4' O4' C1' N9 1.4346 106.58 -157.41 111.80 1.4650 +IC N9 O4' *C1' C2' 1.4650 111.80 124.06 107.09 1.5288 +IC N9 O4' *C1' H1' 1.4650 111.80 -119.42 105.76 1.1164 +IC O4' C1' N9 C4 1.4153 111.80 -107.70 125.37 1.3732 +IC C4 C1' *N9 C8 1.3732 125.37 179.53 128.76 1.3752 +IC C1' N9 C4 C5 1.4650 125.37 -179.45 105.77 1.3832 +IC C5 N9 *C4 N3 1.3832 105.77 179.43 127.12 1.3405 +IC N9 C4 C5 C6 1.3732 105.77 178.67 116.82 1.4111 +IC C6 C4 *C5 N7 1.4111 116.82 -179.47 110.61 1.3896 +IC N7 N9 *C8 H8 1.3064 113.71 -179.99 121.99 1.0920 +IC C4 C5 C6 N1 1.3832 116.82 0.56 117.63 1.3541 +IC N1 C5 *C6 N6 1.3541 117.63 -179.27 123.61 1.3451 +IC C5 C6 N1 C2 1.4111 117.63 -0.28 118.64 1.3350 +IC N3 N1 *C2 H2 1.3387 129.24 179.89 115.26 1.0944 +IC C5 C6 N6 H61 1.4111 123.61 3.15 121.71 0.9960 +IC H61 C6 *N6 H62 0.9960 121.71 174.12 117.26 0.9963 +IC C3' C1' *C2' O2' 1.5424 102.90 120.94 111.41 1.4131 +IC C3' C1' *C2' H2'' 1.5424 102.90 -116.83 112.14 1.1116 +IC C1' C2' O2' H2' 1.5288 111.41 -70.10 110.72 0.9653 +IC C2' C4' *C3' O3' 1.5424 104.09 -125.57 110.37 1.4304 +IC C2' C4' *C3' H3' 1.5424 104.09 114.80 107.09 1.1125 +IC C4' C3' O3' H3T 1.5226 110.37 165.88 110.05 0.9672 + + +end + +read para card flex append +* additional parameters for phosphorylated amino acids +* + +ATOMS +MASS 484 ON2B 15.999400 ! Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str) +MASS 485 SP 32.06000 ! positive Sulphur, S-adenosylmethionine (SAM) + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +CA ON2b 340.0 1.38 !phenol phosphate, 6/94, adm jr. +ON2b P 270.0 1.61 !phenol phosphate, 6/94, adm jr. +CT2 P 270.0 1.890 !Benz.Meth.Phosphate, Sasha +CF2 CA 198.0 1.450 !Benz.Difl.Phosphate +CF2 P 270.0 1.880 !Benz.Difl.Phosphate +!terms for serine/threonine phosphate +CT1 ON2 310.0 1.433 !from CN7 ON2 +CT2 ON2 320.0 1.44 !from CN8B ON2 +!CN7 CN9 222.5 1.516 !from CN7 CN8 +!sahc +CN8B S 240.000 1.8160 ! sahc +!sam +CN8B SP 198.000 1.8160 +CT2 SP 198.000 1.8160 +CT3 SP 240.000 1.8160 + +! C1'-ND1 in imidazole model compound +CN7B NR1 220.000 1.4620 ! From crystal nucleosides A/G (NF) + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +CA CA ON2b 75.0 120.0 !phenol phosphate, 6/94, adm jr. +CA ON2b P 90.0 120.0 20. 2.30 !phenol phosphate, 6/94, adm jr. +ON4 P ON2b 48.1 108.0 !phenol phosphate, 6/94, adm jr. +ON3 P ON2b 98.9 103.0 !phenol phosphate, 6/94, adm jr. +! Benz.Meth.Phos, Sasha, Chris, adm jr. +HA2 CT2 P 90.0 110.00 5.40 1.802 ! +CA CT2 P 90.0 111.0 20.0 2.30 ! +CT2 P ON4 90.1 94.0 ! +CT2 P ON3 98.9 103.0 ! +! Benz.Difl.Phos +CA CA CF2 100.0 120.00 ! +CA CF2 F2 50.0 115.00 30.0 2.357 ! +CA CF2 P 90.0 117.0 20.0 2.30 ! +F2 CF2 P 50.0 122.00 30.0 2.357 ! +CF2 P ON4 90.1 90.0 ! +CF2 P ON3 98.9 94.0 ! +!terms for serine/threonine phosphates +CT1 CT1 ON2 115.0 109.7 !Ser-Phos, from CN7 CN7 ON2 +CT3 CT1 ON2 115.0 109.7 !Ser-Phos, from CN8 CN7 ON2 +CT1 CT2 ON2 70.0 108.4 !Ser-Phos, from CN7 CN8B ON2 +CT3 CT2 ON2 70.0 108.4 !Thr-Phos, from CN7 CN8B ON2 +CN9 CN8 ON2 70.0 108.4 !Thr-Phos, from CN7 CN8B ON2 +CT1 ON2 P 20.0 120.0 35.00 2.33 ! from CN7 ON2 P +CT2 ON2 P 20.0 120.0 35.00 2.33 ! from CN8B ON2 P +HA1 CT1 ON2 60.0 109.5 ! from HN7 CN7 ON2 +HA2 CT2 ON2 60.0 109.5 ! from HN8 CN8B ON2 +CN9 CN7 CN9 58.35 113.60 11.16 2.561 !alkane, from CN8 CN7 CN8 +ON2 CN7 CN9 115.0 109.7 ! from CN7 CN8 ON2 +!CN7 CN9 HN9 34.53 110.10 22.53 2.179 !alkane, from HN8 CN8 CN7 +!CN9 CN7 HN7 34.53 110.10 22.53 2.179 !alkane, from HN8 CN8 CN7 +!sahc +S CN8B CN7 58.000 114.5000 +CN8B S CT2 34.000 95.0000 +S CN8B HN8 46.100 111.3000 +!sam +SP CT2 HA2 46.100 111.3000 +SP CT2 CT2 58.000 114.5000 +CT2 SP CT3 34.000 95.0000 +CT2 SP CN8B 34.000 95.0000 +SP CT3 HA3 46.100 111.3000 +CT3 SP CN8B 34.000 95.0000 +SP CN8B CN7 58.000 114.5000 +SP CN8B HN8 46.100 111.3000 +!-- For imidazole, from imidazole alone: +!-- and for link between sugar and imidazole +ON6 CN7B NR1 140.0 108.00 ! k guessed, theta from ribo./desox. xtal (NF) +ON6B CN7B NR1 140.0 108.00 ! RNUS +CN8 CN7B NR1 140.0 113.70 ! k guessed, theta from ribo./desox. xtal (NF) +CN7B CN7B NR1 140.0 113.70 ! RNUS +CN7B NR1 CPH2 130.0 127.00 ! k guessed, theta from A/G xtal (NF) +CN7B NR1 CPH1 130.0 126.00 ! k guessed, theta from A/G xtal (NF) +HN7 CN7B NR1 30.0 106.3 ! k guessed, theta from ai (NF) +!CPH2 NR1 CPH1 130.0 107.0000 ! From imidazole (NF). Nonstandard; modified for 360 deg. condition. Generates "Error: Repeated ANGLE". + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +CA CA CA ON2b 3.10 2 180.0 !phenol phosphate, 6/94, adm jr. +HP CA CA ON2b 4.20 2 180.0 !phenol phosphate, 6/94, adm jr. +CA CA ON2b P 1.40 2 180.0 !phenol phosphate, 6/94, adm jr. +CA CA ON2b P 0.20 3 180.0 !phenol phosphate, 6/94, adm jr. +CA ON2b P ON4 0.95 2 0.0 !phenol phosphate, 6/94, adm jr. +CA ON2b P ON4 0.50 3 0.0 !phenol phosphate, 6/94, adm jr. +CA ON2b P ON3 0.10 3 0.0 !phenol phosphate, 6/94, adm jr. +! Phenolphosphate, 10/02 fix, adm jr. +ON2B P ON4 HN4 1.60 1 180.0 ! +ON2B P ON4 HN4 0.90 2 0.0 ! +! Benz.Meth.Phosphate, Sasha, Chris, adm jr. +CA CA CT2 P 0.20 2 180.0 ! +CA CT2 P ON4 0.50 2 0.0 ! +CA CT2 P ON4 1.65 1 180.0 ! +HA2 CT2 P ON4 0.10 3 0.0 ! +CA CT2 P ON3 0.05 3 0.0 ! +HA2 CT2 P ON3 0.10 3 0.0 ! +CT2 P ON4 HN4 0.60 1 180.0 ! +CT2 P ON4 HN4 1.10 2 0.0 ! +! Benz.Difl.Phosphate +CA CA CA CF2 3.10 2 180.0 ! +HP CA CA CF2 4.20 2 180.0 ! +CA CA CF2 F2 0.40 3 0.0 ! +CA CA CF2 F2 0.30 2 0.0 ! +CA CA CF2 P 0.15 2 180.0 ! +CA CF2 P ON4 0.10 2 0.0 ! +CA CF2 P ON4 0.40 3 0.0 ! +F2 CF2 P ON4 0.10 3 0.0 ! +CA CF2 P ON3 0.00 3 0.0 ! +F2 CF2 P ON3 0.00 3 0.0 ! +CF2 P ON4 HN4 0.20 1 180.0 ! 10/02 fix, adm jr. +CF2 P ON4 HN4 1.60 2 0.0 ! 10/02 fix, adm jr. + +!terms for serine/threonine phosphates +CT1 CT1 ON2 P 0.40 1 180.0 !phosphothreonine, from dianionic isopropylphosphate +CT1 CT1 ON2 P 0.30 2 0.0 ! +CT1 CT1 ON2 P 0.10 3 0.0 ! +CT3 CT1 ON2 P 0.40 1 180.0 !phosphothreonine, from dianionic isopropylphosphate +CT3 CT1 ON2 P 0.30 2 0.0 ! +CT3 CT1 ON2 P 0.10 3 0.0 ! +CN9 CN7 ON2 P 0.40 1 180.0 !dianionic isopropylphosphate +CN9 CN7 ON2 P 0.30 2 0.0 ! +CN9 CN7 ON2 P 0.10 3 0.0 ! +CT1 CT2 ON2 P 0.60 1 180.0 !phosphoserine, from dianionic ethylphosphate +CT1 CT2 ON2 P 0.65 2 0.0 ! +CT1 CT2 ON2 P 0.05 3 0.0 ! +CN9 CN8 ON2 P 0.60 1 180.0 !dianionic ethylphosphate +CN9 CN8 ON2 P 0.65 2 0.0 ! +CN9 CN8 ON2 P 0.05 3 0.0 ! +! +CT1 ON2 P ON3 0.10 3 0.0 !from ON3 P ON2 CN7 +CT2 ON2 P ON3 0.10 3 0.0 !from ON3 P ON2 CN8B +CT1 ON2 P ON4 0.95 2 0.0 !from ON4 P ON2 CN8B +CT1 ON2 P ON4 0.50 3 0.0 !from ON4 P ON2 CN8B +CT2 ON2 P ON4 0.95 2 0.0 !from ON4 P ON2 CN8B +CT2 ON2 P ON4 0.50 3 0.0 !from ON4 P ON2 CN8B +HA1 CT1 ON2 P 0.00 3 0.0 !from P ON2 CN7 HN7 +HA2 CT2 ON2 P 0.00 3 0.0 !from P ON2 CN8B HN8 +!HN7 CN7 CN9 HN9 0.195 3 0.0 !from HN7 CN7 CN7B HN7 +CN9 CN7 CN9 HN9 0.195 3 0.0 +ON2 CN7 CN9 HN9 0.195 3 0.0 +!sahc +CN8B S CT2 CT2 0.2400 1 180.0 ! sahc, nilesh, from ALOW ALI SUL ION +CN7 CN8B S CT2 0.2 1 120.0 ! sahc, nilesh, from bet C4'-C5'-O5'-P, adm jr. +ON6B CN7 CN8B S 3.4 1 180.0 ! sahc, nilesh, from gam, RNA +CN7 CN7 CN8B S 0.20 4 180.0 ! sahc, nilesh, from gam adm jr. +CN7 CN7 CN8B S 0.80 3 180.0 ! sahc, nilesh, from gam C3'-C4'-C5'-O5' +CN7 CN7 CN8B S 0.40 2 0.0 ! sahc, nilesh, from gam +CN7 CN7 CN8B S 2.50 1 180.0 ! sahc, nilesh, from gam +HN7 CN7 CN8B S 0.195 3 0.0 ! sahc, nilesh, from gam H-C4'-C5'-O5' +CT2 S CN8B HN8 0.28 3 0.0 ! sahc, nilesh, from ALLOW ALI SUL ION +HA2 CT2 S CN8B 0.28 3 0.0 ! sahc, nilesh, from ALLOW ALI SUL ION +!sam +CT3 SP CN8B CN7 0.391 1 180.0 +CT3 SP CN8B CN7 0.373 3 0.0 +CT3 SP CT2 CT2 0.391 1 180.0 +CT3 SP CT2 CT2 0.373 3 0.0 +CN8B SP CT2 CT2 0.391 1 180.0 +CN8B SP CT2 CT2 0.373 3 0.0 +CN7 CN8B SP CT2 0.391 1 180.0 +CN7 CN8B SP CT2 0.373 3 0.0 +CT2 SP CT3 HA3 0.28 3 0.0 +HA2 CT2 SP CT3 0.28 3 0.0 +CN8B SP CT3 HA3 0.28 3 0.0 +HN8 CN8B SP CT3 0.28 3 0.0 +ON6B CN7 CN8B SP 3.4 1 180.0 ! sahc, nilesh, from gam, RNA +CN7 CN7 CN8B SP 0.20 4 180.0 ! sahc, nilesh, from gam adm jr. +CN7 CN7 CN8B SP 0.80 3 180.0 ! sahc, nilesh, from gam C3'-C4'-C5'-O5' +CN7 CN7 CN8B SP 0.40 2 0.0 ! sahc, nilesh, from gam +CN7 CN7 CN8B SP 2.50 1 180.0 ! sahc, nilesh, from gam +HN7 CN7 CN8B SP 0.195 3 0.0 ! sahc, nilesh, from gam H-C4'-C5'-O5' +CT2 SP CN8B HN8 0.28 3 0.0 ! sahc, nilesh, from ALLOW ALI SUL ION +HA2 CT2 SP CN8B 0.28 3 0.0 ! sahc, nilesh, from ALLOW ALI SUL ION + +!============ new parameters for sugar model compounds =============== +!---------------- added for thf-imidazole ------------------ +!-- For link between base and sugar: +CN7B NR1 CPH1 HR3 0.0 2 180.0 !NF +CN7B NR1 CPH1 CPH1 0.0 1 0.0 ! +CN7B NR1 CPH2 HR1 0.0 2 180.0 ! +CN7B NR1 CPH2 NR2 0.0 2 180.0 ! +!-- For chi: +ON6 CN7B NR1 CPH1 0.2 3 0.0 ! +ON6 CN7B NR1 CPH1 0.5 2 -70.0 ! +ON6 CN7B NR1 CPH1 0.6 1 180.0 ! +ON6 CN7B NR1 CPH2 0.3 1 0.0 ! + +ON6B CN7B NR1 CPH1 0.2 3 0.0 ! RNUS +ON6B CN7B NR1 CPH1 0.5 2 -70.0 ! RNUS +ON6B CN7B NR1 CPH1 0.6 1 180.0 ! RNUS +ON6B CN7B NR1 CPH2 0.3 1 0.0 ! RNUS + +CN8 CN7B NR1 CPH1 0.2 4 0.0 ! +CN8 CN7B NR1 CPH2 0.1 3 180.0 ! +CN8 CN7B NR1 CPH2 0.3 2 0.0 ! +CN8 CN7B NR1 CPH2 0.0 1 180.0 ! + +CN7B CN7B NR1 CPH1 0.2 4 0.0 ! RNUS +CN7B CN7B NR1 CPH2 0.1 3 180.0 ! RNUS +CN7B CN7B NR1 CPH2 0.3 2 0.0 ! RNUS +CN7B CN7B NR1 CPH2 0.0 1 180.0 ! RNUS + +HN7 CN7B NR1 CPH1 0.0 3 0.0 ! +HN7 CN7B NR1 CPH2 0.195 3 0.0 ! +CN8 CN8 CN7B NR1 0.0 3 0.0 +CN7 CN7B CN7B NR1 0.0 3 0.0 ! RNUS +CN8 ON6 CN7B NR1 0.0 3 0.0 +HN8 CN8 CN7B NR1 0.0 3 0.0 +HN7 CN7B CN7B NR1 0.0 3 0.0 ! RNUS +NR1 CN7B CN7B ON5 0.0 3 0.0 ! RNUS + +!------------------- added for thf-oh-ch3-im --------------------- +CN7B ON6 CN7 CN8 0.0 3 0.0 ! 25P1 +CN7 ON6 CN7B NR1 0.0 3 0.0 +CN7 ON6B CN7B NR1 0.0 3 0.0 ! RNUS +NR1 CN7B CN8 CN7 0.0 3 0.0 + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +! +!================== new terms added for sugar model compounds ========= +!----------------------- Added for imidazole -------------------- +NR1 CPH1 CPH2 CN7B 0.60 0 0.00 ! From imidazole (NF), k increased +NR1 CPH2 CPH1 CN7B 0.60 0 0.00 ! From imidazole (NF), k increased + +NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH - + CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +ON2B 0.0 -0.1521 1.77 !from ON2 +SP 0.0 -0.4500 2.20 !charged S in S-adenosylmethionine (SAM) + +end diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_pyridines.str b/charmm/toppar/stream/prot/toppar_all36_prot_pyridines.str new file mode 100644 index 00000000..f41c2c2c --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_pyridines.str @@ -0,0 +1,1166 @@ +* Toppar stream file for pyridines +* + +!Parent files that have to be read prior to streaming this file +!top_all36_prot.rtf +!par_all36_prot.prm + +!Testcase +!test_all36_prot_pyridines.inp + +!Reference +!Yin, D., Ph.D. Thesis, "Parameterization for Empirical Force +!Field Calculations and A Theoretical Study of Membrane +!Permeability of Pyridine Derivative," Department of Pharmaceutical +!Sciences, School of Pharmacy, University of Maryland, 1997 +! +!Note that some corrections have been made to the parameters +!since 1997. adm jr. + +read rtf card append +* Topology for substituted pyridines +* +31 1 + +MASS 419 CN 12.01100 C ! C for cyano group (see toppar_pyridines.str) +MASS 420 CAP 12.01100 C ! aromatic C for pyrimidines (see toppar_pyridines.str) +MASS 421 COA 12.01100 C ! carbonyl C for pyrimidines (see toppar_pyridines.str) +MASS 422 NC 14.00700 N ! N for cyano group (see toppar_pyridines.str) +MASS 423 OCA 15.99900 O ! carbonyl O for pyrimidines (see toppar_pyridines.str) +MASS 424 FA 18.99800 F ! flourine (see toppar_pyridines.str) + +RESI PYR1 0.00 ! pyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP -0.115 +ATOM CG CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM CD2 CAP -0.115 +ATOM HE1 HP 0.150 +ATOM HD1 HP 0.115 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 + +IMPH HE1 NZ CD1 CE1 HD1 CE1 CG CD1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +patch first none last none + +RESI 4AP2 0.00 ! 4-aminopyridine +GROUP +ATOM NZ NR2 -0.680 ! using the HIS nitrogen +ATOM CE1 CAP 0.190 +ATOM CD1 CAP -0.115 +ATOM CG CAP 0.050 +ATOM CE2 CAP 0.190 +ATOM CD2 CAP -0.115 +ATOM NG NH2 -0.850 +ATOM HE1 HP 0.150 +ATOM HD1 HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM HG11 H 0.400 +ATOM HG12 H 0.400 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CG NG NG HG11 NG HG12 + +IMPH HE1 NZ CD1 CE1 HD1 CE1 CG CD1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH NG CD1 CD2 CG +IMPH HG11 CG HG12 NG + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG NG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CG NG HG11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HG11 CG *NG HG12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +patch first none last none + +RESI 3APY 0.00 ! 3-aminopyridine + ! +GROUP !HD11 HD12 +ATOM CG CAP -0.115 ! \ / +ATOM HG HP 0.115 ! ND1 HE1 +GROUP ! \ | +ATOM CD1 CAP 0.090 ! CD1--CE1 +ATOM ND1 NH2 -0.840 ! / \ +ATOM HD11 H 0.370 ! HG--CG NZ +ATOM HD12 H 0.380 ! \ / +GROUP ! CD2--CE2 +ATOM CD2 CAP -0.115 ! | | +ATOM HD2 HP 0.115 ! HD2 HE2 +GROUP +ATOM CE1 CAP 0.170 +ATOM HE1 HP 0.150 +ATOM CE2 CAP 0.170 +ATOM HE2 HP 0.150 +ATOM NZ NR2 -0.640 ! using the HIS nitrogen + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 ND1 ND1 HD11 ND1 HD12 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH ND1 CG CE1 CD1 +IMPH HD11 CD1 HD12 ND1 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 ND1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 ND1 HD11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HD11 CD1 *ND1 HD12 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +RESI 3AP2 0.00 ! 3-aminopyridine +!repeat of 3APY for vibrational analysis +GROUP +ATOM NZ NR2 -0.640 ! +ATOM CE1 CAP 0.170 ! +ATOM CD1 CAP 0.090 ! +ATOM CG CAP -0.115 ! +ATOM CE2 CAP 0.170 ! +ATOM CD2 CAP -0.115 ! +ATOM ND1 NH2 -0.840 ! +ATOM HE1 HP 0.150 ! +ATOM HG HP 0.115 ! +ATOM HD2 HP 0.115 ! +ATOM HE2 HP 0.150 ! +ATOM HD11 H 0.370 ! +ATOM HD12 H 0.380 ! + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 ND1 ND1 HD11 ND1 HD12 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH ND1 CG CE1 CD1 +IMPH HD11 HD12 ND1 CD1 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 ND1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 ND1 HD11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HD11 CD1 *ND1 HD12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HD11 HD12 *ND1 CD1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +patch first none last none + +RESI 34AP 0.00 ! 3,4-diaminopyridine, adm jr. +GROUP ! +ATOM NZ NR2 -0.680 +ATOM CE1 CAP 0.190 +ATOM CD1 CAP 0.120 +ATOM CG CAP 0.070 +ATOM CE2 CAP 0.190 +ATOM CD2 CAP -0.115 +ATOM ND1 NH2 -0.850 +ATOM NG NH2 -0.850 +ATOM HE1 HP 0.150 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM HD11 H 0.350 +ATOM HD12 H 0.380 +ATOM HG11 H 0.390 +ATOM HG12 H 0.390 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 ND1 ND1 HD11 ND1 HD12 +BOND CG NG NG HG11 NG HG12 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH ND1 CG CE1 CD1 +IMPH HD11 CD1 HD12 ND1 +IMPH NG CD1 CD2 CG +IMPH HG11 CG HG12 NG + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG NG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 ND1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CG NG HG11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HG11 CG *NG HG12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CE1 CD1 ND1 HD11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HD11 CD1 *ND1 HD12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +patch first none last none + +RESI 3CPY -1.00 ! 3-carboxypyridine, anion + ! +GROUP +ATOM NZ NR2 -0.640 ! using the HIS nitrogen +ATOM CE1 CAP 0.170 ! +ATOM CD1 CAP -0.10 ! +ATOM CG CAP -0.155 ! +ATOM CE2 CAP 0.170 ! +ATOM CD2 CAP -0.115 ! +ATOM HE1 HP 0.150 ! +ATOM HG HP 0.155 ! +ATOM HD2 HP 0.115 ! +ATOM HE2 HP 0.150 ! +ATOM CD3 CC 0.62 ! +ATOM O1 OC -0.76 ! +ATOM O2 OC -0.76 ! + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 CD3 CD3 O1 +DOUB CD3 O2 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC O1 CD1 *CD3 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +RESI 3CB -1.00 ! benzoic acid, anion +GROUP +ATOM CZ CAP -0.115 ! +ATOM CE1 CAP -0.115 ! +ATOM CD1 CAP -0.100 ! +ATOM CG CAP -0.115 ! +ATOM CE2 CAP -0.115 ! +ATOM CD2 CAP -0.115 ! +ATOM HE1 HP 0.115 ! +ATOM HG HP 0.115 ! +ATOM HD2 HP 0.115 ! +ATOM HE2 HP 0.115 ! +ATOM HZ HP 0.115 ! +ATOM CD3 CC 0.620 ! +ATOM O1 OC -0.760 ! +ATOM O2 OC -0.760 ! + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 CD3 CD3 O1 +BOND CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +DOUB CD3 O2 + +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC O1 CD1 *CD3 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +RESI 3FLP 0.00 ! 3-fluoropyridine +GROUP +ATOM NZ NR2 -0.580 +ATOM CE1 CAP 0.130 +ATOM CD1 CAP 0.175 +ATOM CG CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM CD2 CAP -0.115 +ATOM HE1 HP 0.170 +ATOM F1 FA -0.215 !charge similar to difluorotoluene +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 F1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 + +IMPH HE1 NZ CD1 CE1 F1 CE1 CG CD1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 F1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +patch first none last none + +RESI 3ALP 0.00 ! 3-aldehyde pyridine + ! +GROUP +ATOM NZ NR2 -0.640 ! +ATOM CE1 CAP 0.170 ! +ATOM CD1 CAP 0.12 ! +ATOM CG CAP -0.115 ! +ATOM CD2 CAP -0.115 ! +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.150 ! +ATOM HG HP 0.115 ! +ATOM HD2 HP 0.115 ! +ATOM HE2 HP 0.150 +ATOM CD3 CD 0.16 !benzaldehyde, parameter corrections will be needed +ATOM O1 O -0.33 !benzaldehyde +ATOM H3 HR1 0.05 !benzaldehyde + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 CD3 CD3 H3 +DOUB CD3 O1 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CD3 O1 H3 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC O1 CD1 *CD3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +RESI 3HOP 0.000 ! 3-hydroxypyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CG CAP -0.115 +ATOM CD2 CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.150 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM CD1 CAP 0.11 !phenol +ATOM OH OH1 -0.54 !phenol +ATOM HO1 H 0.43 !phenol + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 OH CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HO1 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 OH CD2 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 +patch first none last none + +RESI 3MEP 0.00 ! 3-methylpyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP 0.000 +ATOM CG CAP -0.115 +ATOM CD2 CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.150 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM CD3 CT3 -0.27 !aliphatic, corresponds to new CT3, HA3 +ATOM H31 HA3 0.09 ! +ATOM H32 HA3 0.09 ! +ATOM H33 HA3 0.09 ! + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 CD3 CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD3 H31 CD3 H32 CD3 H33 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 +IMPH HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CE1 CG CD3 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CD1 CD3 H31 0.0000 0.0000 60.0000 0.0000 0.0000 +IC CE1 CD1 CD3 H32 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 H33 0.0000 0.0000 300.0000 0.0000 0.0000 +patch first none last none + +RESI 3ETP 0.00 ! ethylpyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP 0.000 +ATOM CG CAP -0.115 +ATOM CD2 CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.150 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM CD3 CT2 -0.18 !aliphatic, corresponds to new CT2, HA2 +ATOM H11 HA2 0.09 ! +ATOM H12 HA2 0.09 ! +ATOM C2 CT3 -0.27 !aliphatic, corresponds to new CT3, HA3 +ATOM H21 HA3 0.09 ! +ATOM H22 HA3 0.09 ! +ATOM H23 HA3 0.09 ! + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 CD3 CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD3 H11 CD3 H12 CD3 C2 +BOND H21 C2 H22 C2 H23 C2 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 +IMPH HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CE1 CG CD3 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 C2 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CD1 C2 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD1 C2 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CD1 CD3 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD3 H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD3 H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 +patch first none last none + +RESI 3BPY 0.00 ! butylpyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP -0.000 +ATOM CG CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM CD2 CAP -0.115 +ATOM HE1 HP 0.150 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM CD3 CT2 -0.18 !aliphatic, corresponds to new CT3 etc. +ATOM H11 HA2 0.09 +ATOM H12 HA2 0.09 +ATOM C2 CT2 -0.18 +ATOM H21 HA2 0.09 +ATOM H22 HA2 0.09 +ATOM C3 CT2 -0.18 +ATOM H31 HA2 0.09 +ATOM H32 HA2 0.09 +ATOM C4 CT3 -0.27 +ATOM H41 HA3 0.09 +ATOM H42 HA3 0.09 +ATOM H43 HA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 CE2 HE2 +BOND CD1 CD3 CD3 H11 CD3 H12 +BOND CD3 C2 C2 C3 C3 C4 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 +BOND C4 H41 C4 H42 C4 H43 + +IMPH HE1 NZ CD1 CE1 HG CD1 CD2 CG +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH CD1 CE1 CG CD3 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 C2 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CD1 C2 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD1 C2 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CD1 CD3 C2 C3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD3 C3 *C2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD3 C3 *C2 H22 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CD3 C2 C3 C4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H31 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2 C4 *C3 H32 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C2 C3 C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3 H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 +patch first none last none + +RESI 3CYP 0.00 !3-Cyanopyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP -0.010 +ATOM CG CAP -0.115 +ATOM CD2 CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.220 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.220 +ATOM C3N CN 0.400 +ATOM N3C NC -0.530 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 C3N +BOND C3N N3C + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CE1 CG C3N + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C3N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3C C3N CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 +patch first none last none + +RESI 3ACP 0.00 !3-acetylpyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP -0.100 +ATOM CG CAP -0.115 +ATOM CD2 CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.150 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM C COA 0.450 +ATOM O OCA -0.350 +ATOM CH3 CT3 -0.270 !aliphatic, corresponds to new CT3, HA3 +ATOM HC1 HA3 0.090 ! +ATOM HC2 HA3 0.090 ! +ATOM HC3 HA3 0.090 ! + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 C C CH3 +BOND HC1 CH3 HC2 CH3 HC3 CH3 +DOUB C O + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CE1 CG C +IMPH C CD1 CH3 O + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CH3 C CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CH3 CD1 *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HC1 CH3 C CD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HC2 CH3 C HC1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HC3 CH3 C HC1 0.0000 0.0000 -120.000 0.0000 0.0000 +patch first none last none + +RESI 3NAP 0.00 !3-nicotinamide-pyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP -0.020 +ATOM CG CAP -0.115 +ATOM CD2 CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.150 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM C COA 0.630 +ATOM O OCA -0.460 +ATOM N NH2 -0.900 +ATOM Hc H 0.390 +ATOM Ht H 0.360 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 C C N +BOND Hc N Ht N +DOUB C O + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CE1 CG C +IMPH C CD1 N O + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N C CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N CD1 *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC Hc N C O 0.0000 0.0000 0.0000 0.0000 0.0000 +IC Ht N C O 0.0000 0.0000 180.0000 0.0000 0.0000 +patch first none last none + +RESI 3CAP 0.00 !carbinol-pyridine, by daxu +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP 0.000 +ATOM CG CAP -0.115 +ATOM CD2 CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.150 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +GROUP +ATOM CD3 CT2 0.05 !aliphatic, corresponds to new CT2, HA2 +ATOM H11 HA2 0.09 +ATOM H12 HA2 0.09 +ATOM OH OH1 -0.66 +ATOM HO H 0.43 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 CD3 CD3 OH OH HO +BOND CD3 H11 CD3 H12 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CE1 CG CD3 !adm + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NZ CE1 CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CD3 OH HO 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OH CD1 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC OH CD1 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 + +patch first none last none + +RESI 3PHP 0.00 !3-phenyl-pyridine +GROUP +ATOM NZ NR2 -0.640 +ATOM CE1 CAP 0.170 +ATOM CD1 CAP 0.000 +ATOM CG CAP -0.115 +ATOM CD2 CAP -0.115 +ATOM CE2 CAP 0.170 +ATOM HE1 HP 0.150 +ATOM HG HP 0.115 +ATOM HD2 HP 0.115 +ATOM HE2 HP 0.150 +ATOM CA1 CA 0.000 +ATOM CA2 CA -0.115 +ATOM CA3 CA -0.115 +ATOM CA4 CA -0.115 +ATOM CA5 CA -0.115 +ATOM CA6 CA -0.115 +ATOM HA2 HP 0.115 +ATOM HA3 HP 0.115 +ATOM HA4 HP 0.115 +ATOM HA5 HP 0.115 +ATOM HA6 HP 0.115 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 CA1 CA1 CA2 CA2 CA3 +BOND CA3 CA4 CA4 CA5 CA6 CA5 +BOND CA6 CA1 +BOND CA2 HA2 CA3 HA3 CA4 HA4 +BOND CA5 HA5 CA6 HA6 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CE1 CG CA1 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA2 CA1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA3 CA2 CA1 CD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA4 CA3 CA2 CA1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA5 CA4 CA3 CA2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA6 CA5 CA4 CA3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA1 CA3 *CA2 HA2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA2 CA4 *CA3 HA3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA3 CA5 *CA4 HA4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA4 CA6 *CA5 HA5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA5 CA1 *CA6 HA6 0.0000 0.0000 180.0000 0.0000 0.0000 +patch first none last none + +RESI 3BNP 0.00 !3-benzyl-pyridine +GROUP !methylene between rings +ATOM NZ NR2 -0.640 !1 +ATOM CE1 CAP 0.170 !2 +ATOM CD1 CAP 0.000 !3 +ATOM CG CAP -0.115 !4 +ATOM CD2 CAP -0.115 !5 +ATOM CE2 CAP 0.170 !6 +ATOM HE1 HP 0.150 !7 +ATOM HG HP 0.115 !8 +ATOM HD2 HP 0.115 !9 +ATOM HE2 HP 0.150 !10 +ATOM C CT2 -0.180 !11 aliphatic, corresponds to new CT2, HA2 +ATOM HC1 HA2 0.090 !12 +ATOM HC2 HA2 0.090 !13 +ATOM CA1 CA 0.000 !14 +ATOM CA2 CA -0.115 !15 +ATOM CA3 CA -0.115 !16 +ATOM CA4 CA -0.115 !17 +ATOM CA5 CA -0.115 !18 +ATOM CA6 CA -0.115 !19 +ATOM HA2 HP 0.115 !20 +ATOM HA3 HP 0.115 !21 +ATOM HA4 HP 0.115 !22 +ATOM HA5 HP 0.115 !23 +ATOM HA6 HP 0.115 !24 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 C C CA1 +BOND C HC1 C HC2 +BOND CA1 CA2 CA2 CA3 +BOND CA3 CA4 CA4 CA5 CA6 CA5 +BOND CA6 CA1 +BOND CA2 HA2 CA3 HA3 CA4 HA4 +BOND CA5 HA5 CA6 HA6 + +IMPH HE1 NZ CD1 CE1 +IMPH HE2 NZ CD2 CE2 HD2 CE2 CG CD2 +IMPH HG CD1 CD2 CG +IMPH CD1 CE1 CG C + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CD1 C CA1 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CD1 C CA1 CA2 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CA1 CD1 *C HC1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CA1 CD1 *C HC2 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C CA1 CA2 CA3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA1 CA2 CA3 CA4 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA2 CA3 CA4 CA5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA3 CA4 CA5 CA6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA1 CA3 *CA2 HA2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA2 CA4 *CA3 HA3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA3 CA5 *CA4 HA4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA4 CA6 *CA5 HA5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA5 CA1 *CA6 HA6 0.0000 0.0000 180.0000 0.0000 0.0000 +patch first none last none + +end + +read para card flex append +* Parameters for substituted pyridines +* + +ATOMS +MASS 419 CN 12.01100 ! C for cyano group (see toppar_pyridines.str) +MASS 420 CAP 12.01100 ! aromatic C for pyrimidines (see toppar_pyridines.str) +MASS 421 COA 12.01100 ! carbonyl C for pyrimidines (see toppar_pyridines.str) +MASS 422 NC 14.00700 ! N for cyano group (see toppar_pyridines.str) +MASS 423 OCA 15.99900 ! carbonyl O for pyrimidines (see toppar_pyridines.str) +MASS 424 FA 18.99800 ! flourine (see toppar_pyridines.str) + +BONDS +! new pyridine parameters +CAP CAP 370.000 1.3600 ! pyridines +CAP NR2 420.000 1.3050 ! pyridine, adm jr., 7/94 +CAP C 305.000 1.3750 ! acetylpyridine +CAP CC 200.000 1.5000 ! nicotinic acid (pyridine carboxylate) +CT2 CAP 230.000 1.4900 ! phe,tyr, JES 8/25/89 +CT3 CAP 230.000 1.4900 ! toluene, adm jr. 3/7/92 +CAP NH2 400.000 1.3900 ! aminopyridine, adm jr., 7/94 +OH1 CAP 334.300 1.3512 ! MeOH, EMB 10/10/89, +CAP FA 349.000 1.3330 ! fluoropyridine +HP CAP 340.000 1.0800 ! benzene +! bond parameters for pyr-aldehyde +CD CAP 300.000 1.4798 ! benzaldehyde, for 3ALP +! bond parameter for pyr-CN +CN NC 1380.000 1.158 ! first guess by daxu +CN CAP 345.000 1.45 ! first guess by daxu +CT3 CN 250.00 1.50 ! guess daxu for cyano +! bond parameter for pyr-COCH3 +CT3 COA 200.000 1.522 ! guess by daxu from CHARMM94 +OCA COA 750.000 1.220 ! guess by daxu from CHARMM94 +COA CAP 300.000 1.450 ! guess by daxu +! bond parameter for NA_pyr +NH2 COA 430.000 1.3600 ! guessed by daxu "NH2 CC" +!bond parameters for ph_pyr +CAP CA 305.000 1.3750 ! +OC H 545.000 0.9600 ! + +ANGLES +! new pyridine parameters +CAP CAP CAP 90.00 122.00 30.00 2.3880 ! pyridine +CAP CAP NR2 10.00 129.00 ! pyridine +CAP NR2 CAP 10.00 96.00 55.00 2.28000 ! pyridine +HP CAP CAP 30.00 119.00 22.00 2.15250 ! pyridine +HP CAP NR2 30.00 112.00 35.00 2.05000 ! pyridine +C CAP CAP 40.00 119.00 ! 3-acetylpyridine +CAP CAP FA 50.00 112.00 30.00 2.357 ! fluoropyridine +CAP CAP NH2 60.00 121.00 ! aminopyridine, adm jr., 7/94 +CC CAP CAP 40.00 119.00 35.00 2.41620 ! nicotinic acid (pyridine carboxylate) +CAP CC OC 40.00 118.00 50.00 2.3880 !! nicotinic acid (pyridine carboxylate) +CAP NH2 H 60.00 120.00 ! aminopyridine, adm jr., 7/94 +CT2 CAP CAP 45.80 119.00 ! "old 45.800 122.3000" changed by daxu +CT3 CAP CAP 45.80 122.30 ! toluene +HA2 CT2 CAP 49.30 107.50 ! toluene +HA3 CT3 CAP 49.30 107.50 ! toluene +CT2 CT2 CAP 51.80 107.50 ! butylpyridine +CT3 CT2 CAP 51.80 107.50 ! ethylbenzene +H OH1 CAP 65.00 108.00 ! phenol +CD CAP CAP 45.00 119.80 ! benzaldehyde, for 3ALP +O CD CAP 75.00 124.00 ! benzaldehyde, for 3ALP +HR1 CD CAP 15.00 115.00 ! benzaldehyde, for 3ALP +O C CAP 80.00 118.00 ! acetylpyridine +O CC CAP 80.00 124.00 ! aldehydepyridine +OH1 CAP CAP 45.20 120.00 ! phenol +! angle parameter for pyr-CN +CN CAP CAP 35.00 119.00 ! +NC CN CAP 40.00 180.00 ! +HA3 CT3 CN 10.00 110.00 ! +! angle parameter for pyr-COCH3 +COA CAP CAP 45.00 119.00 ! +CAP COA CT3 30.00 111.00 ! +OCA COA CAP 30.00 124.50 ! +OCA COA CT3 30.00 124.50 ! +HA3 CT3 COA 33.00 109.50 ! +! angle parameter for pyr-CONH2 +OCA COA NH2 75.00 125.27 ! +CAP COA NH2 50.00 110.23 ! +COA NH2 H 50.00 121.00 ! +! angle parameter for pyr_CH2OH +CAP CT2 OH1 75.70 115.10 ! from "OH1 CT2 CT3" +! angle parameter for pyr_C6H5 +CAP CAP CA 40.00 119.00 ! from "ca ca ca" +CAP CA CA 40.00 120.00 ! from "ca ca ca" +! angle parameter for pyr_CH2C6H5 +CAP CT2 CA 51.80 107.50 ! from CA CT2 CT3 +! angle parameter for CBPN +CC OC H 55.00 115.00 ! +!CT2x, CT3x alkane alternate nomenclature parameters +!CT2x CA CA 45.80 120.00 ! +!CT2x CT2x CT2x 58.35 113.60 11.16 2.56100 ! +!CT3x CT2x CT2x 58.00 115.00 8.00 2.56100 ! +!HA2 CT2x CA 49.30 107.50 ! +!HA2 CT2x CT2x 26.50 110.10 22.53 2.17900 ! +!HA2 CT2x CT3x 34.60 110.10 22.53 2.17900 ! +!HA2 CT2x HA2 35.50 109.00 5.40 1.80200 ! +!HA3 CT3x CT2x 34.60 110.10 22.53 2.17900 ! +!HA3 CT3x CT3x 37.50 110.10 22.53 2.17900 ! +!HA3 CT3x HA3 35.50 108.40 5.40 1.80200 ! +!HE1 CE1 CT3x 22.00 117.00 ! for propene +!CE2 CE1 CT3x 47.00 125.20 ! for propene +!HA3 CT3x CE1 42.00 111.50 ! for 2-butene +!HE1 CE1 CT2x 40.00 116.00 ! for 1-butene; from propene +!HA2 CT2x CE1 45.00 111.50 ! for 1-butene; from propene +!CE2 CE1 CT2x 48.00 126.00 ! for 1-butene; from propene +!CE1 CT2x CT3x 32.00 112.20 ! for 1-butene; from propene +!CE1 CT2x CT2x 32.00 112.20 ! for 2-heptene from "CE1 CT2 CT3" +!CE1 CE1 CT3x 48.00 123.50 ! for 2-butene +!CE1 CE1 CT2x 48.00 123.50 ! for 2-heptene from "CE1 CE1 CT3" + +DIHEDRALS +! new pyridine parameters +HP CAP CAP CAP 4.20 2 180.00 ! pyridines +HP CAP CAP HP 1.90 2 180.00 ! pyridines +CAP CAP CAP CAP 1.20 2 180.00 ! pyridines +CAP CAP CAP NR2 0.80 2 180.00 ! pyridine +CAP CAP NR2 CAP 1.20 2 180.00 ! pyridine +CAP CAP CAP C 3.10 2 180.00 ! acetylpyridine +CAP CAP CAP NH2 5.00 2 180.00 ! aminopyridine +CAP CAP CAP NH3 5.00 2 180.00 ! aminopyridine +CAP CAP NH2 H 1.80 2 180.00 ! aminopyridine +CAP CAP CAP FA 3.10 2 180.00 ! fluoropyridine +CC CAP CAP NR2 1.00 2 180.00 ! pyridine +CC CAP CAP CAP 3.10 2 180.00 ! pyridines +CT2 CAP CAP NR2 1.00 2 180.00 ! 3-ethylpyridine +CT2 CAP CAP CAP 3.10 2 180.00 ! toluene and ethylbenzene +CT3 CAP CAP CAP 3.10 2 180.00 ! toluene +CT3 CAP CAP NR2 1.00 2 180.00 ! 3-methylpyridine +CT3 C CAP CAP 3.10 2 180.00 ! 3-acetylpyridine +H OH1 CAP CAP 0.99 2 180.00 ! phenol OH rot bar +HA CC CAP CAP 3.50 2 180.00 ! carboxaldehyde pyridine +HA3 CT3 C CAP 0.04 3 0.00 ! acetylpyridine +HC NH3 CAP CAP 0.00 3 180.00 ! aminopyridine +HP CAP CAP CC 4.20 2 180.00 ! aminopyridine +HP CAP CAP C 4.20 2 180.00 ! acetylpyridine +HP CAP CAP CT2 4.20 2 180.00 ! toluene and ethylbenzene +HP CAP CAP CT3 4.20 2 180.00 ! toluene +HP CAP CAP FA 3.10 2 180.00 ! fluoropyridine +HP CAP CAP NH2 4.20 2 180.00 ! aminopyridine +HP CAP CAP NR2 2.80 2 180.00 ! pyridine +OH1 CAP CAP CAP 3.10 2 180.00 ! phenol +OH1 CAP CAP HP 4.20 2 180.00 ! phenol +HP CAP NR2 CAP 5.80 2 180.00 ! pyridine +NH2 CAP CAP NH2 3.10 2 180.00 ! diaminopyridine +NR2 CAP CAP C 5.00 2 180.00 ! 3-acetylpyridine +NR2 CAP CAP NH2 5.00 2 180.00 ! aminopyridine +NR2 CAP CAP FA 3.10 2 180.00 ! fluoropyridine +OH1 CAP CAP NR2 0.00 1 0.00 ! 3-hydroxypyridine +OC CC CAP CAP 3.10 2 180.00 ! nicotinic acid (pyridine carboxylate) +O C CAP CAP 3.10 2 180.00 ! 3-acetylpyridine +O CC CAP CAP 3.10 2 180.00 ! nicotinic acid (pyridine carboxylate) +X CT2 CAP X 0.005 6 0.00 ! toluene +HA3 CT3 CAP CAP 0.003 6 180.00 ! toluene +! parameters for pyr-aldehyde +O CD CAP CAP 1.00 2 0.00 ! +HR1 CD CAP CAP 3.20 2 180.00 ! +CD CAP CAP HP 4.20 2 180.00 ! +CD CAP CAP CAP 3.10 2 180.00 ! +CD CAP CAP NR2 1.00 2 180.00 ! +! parameters for pyr-CN +CAP CAP CN NC 0.00 2 0.00 ! +NR2 CAP CAP CN 1.00 2 180.00 ! +CAP CAP CAP CN 2.00 2 180.00 ! +HP CAP CAP CN 2.40 2 180.00 ! correction, 1/09 +! parameters for pyr-COCH3 +NR2 CAP CAP COA 1.00 2 180.00 ! +CAP CAP CAP COA 1.00 2 180.00 ! +OCA COA CAP CAP 1.00 2 180.00 ! +HA CT3 COA CAP 0.50 3 180.00 ! +HA CT3 COA OCA 0.50 3 180.00 ! +CT3 COA CAP CAP 1.00 2 180.00 ! +HA3 CT3 COA CAP 0.00 3 180.00 ! +HA3 CT3 COA OCA 0.00 3 180.00 ! +HP CAP CAP COA 0.50 2 0.00 ! +! parameter for pyr-CONH2 +NH2 COA CAP CAP 1.00 2 180.00 ! +H NH2 COA CAP 1.00 2 180.00 ! +H NH2 COA OCA 0.50 2 180.00 ! +! parameter for pyr-CH2OH +HA2 CT2 CAP CAP 0.00 3 0.00 ! +OH1 CT2 CAP CAP 0.00 3 0.00 ! +CAP CT2 OH1 H 1.10 3 0.00 ! +CAP CT2 OH1 H 1.40 2 0.00 ! +CAP CT2 OH1 H 2.10 1 0.00 ! +!parameter for pyr-C6H5 +CAP CAP CAP CA 1.00 2 180.00 ! +CAP CAP CA CA 1.00 2 180.00 ! +CAP CA CA CA 1.00 2 180.00 ! +CAP CA CA HP 1.00 2 180.00 ! +NR2 CAP CAP CA 1.00 2 180.00 ! +HP CAP CAP CA 1.00 2 180.00 ! +! parameter for pyr-CH2C6H5 +CAP CAP CT2 CA 0.23 2 180.00 ! "CT3 CT2 CA CA", new param, daxu +CAP CT2 CA CA 0.23 2 180.00 ! "CT3 CT2 CA CA", new param, daxu +X CC OC X 0.00 6 180.00 ! +!CT2x, CT3x alkane nomenclature parameters +!CT2x CA CA CA 3.10 2 180.00 ! ALLOW ARO +!CT2x CT2x CT2x CT2x 0.13 1 0.00 ! ALLOW ALI, new param, daxu +!CT3x CT2x CT2x CT2x 0.13 1 0.00 ! ALLOW ALI, new param, daxu +!CT3x CT2x CT2x CT3x 0.13 1 0.00 ! ALLOW ALI, new param, daxu +!H OH1 CT2x CT2x 1.30 1 0.00 ! ethanol +!H OH1 CT2x CT2x 0.30 2 0.00 ! +!H OH1 CT2x CT2x 0.42 3 0.00 ! +!HP CA CA CT2x 4.20 2 180.00 ! ALLOW ARO +!X CT2x CA X 0.00 6 0.00 ! ALLOW ALI ARO +!X CT2x CT2x X 0.19 3 0.00 ! ALLOW ALI, new param, daxu +!X CT2x CT3x X 0.16 3 0.00 ! ALLOW ALI, new param, daxu +!X CT2x OH1 X 0.14 3 0.00 ! ALLOW ALI ALC ARO +!X CT3x CT3x X 0.155 3 0.00 ! ALLOW ALI, new param, daxu +!alkene +!CT3x CE1 CE2 HE2 5.20 2 180.00 ! for propene +!CE2 CE1 CT3x HA3 0.05 3 180.00 ! for propene +!HE2 CE2 CE1 CT2x 5.20 2 180.00 ! FOR BUTENE +!HE1 CE1 CT2x HA2 0.87 3 0.00 ! FOR BUTENE +!HE1 CE1 CT2x CT3x 0.12 3 0.00 ! FOR BUTENE +!HE1 CE1 CT2x CT2x 0.12 3 0.00 ! from "HA1 CE1 CT2 CT3" +!CE2 CE1 CT2x CT3x 0.50 3 0.00 ! FOR BUTENE +!CE1 CE1 CT2x CT2x 0.50 3 0.00 ! "CE2 CE1 CT2 CT3" +!CE2 CE1 CT2x HA2 0.12 3 0.00 ! FOR BUTENE +!CE1 CE1 CT2x HA2 0.03 3 0.00 ! from "CE1 CE1 CT3 HA" +!CE1 CE1 CT3x HA3 0.03 3 0.00 ! FOR BUTENE +!HE1 CE1 CT3x HA3 0.34 3 0.00 ! FOR BUTENE + +IMPROPER +! new pyridine parameters +CAP X X NH2 10.00 0 0.00 ! aminopyridine +H H NH2 CAP 1.90 0 180.00 ! aminopyridine +HP X X CAP 15.00 0 0.00 ! pyridine +FA CAP CAP CAP 1.90 0 0.00 ! fluoropyridine +CT3 CAP CAP CAP 1.90 0 0.00 ! methylpyridine +CT2 CAP CAP CAP 1.90 0 0.00 ! ethylpyridine +CAP CD O HR1 14.00 0 180.00 ! benzaldehyde +COA CAP CT3 OCA 30.00 0 0.00 ! 3acp +COA CAP NH2 OCA 30.00 0 0.00 ! 3nap +CAP CAP CAP COA 30.00 0 0.00 ! 3nap +CAP CAP CAP CA 30.00 0 0.00 ! 3php +CAP CAP CAP CN 30.00 0 0.00 ! 3cyp + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +CAP 0.000000 -0.070000 1.992400 ! +FA 0.000000 -0.12000 1.700000 + ! from 1,3-difluorobenzene pure solvent +CN 0.000000 -0.200000 1.750000 ! cyanopyridine +NC 0.000000 -0.600000 1.850000 ! cyanopyridine +OCA 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! 3acp +COA 0.000000 -0.110000 2.000000 ! 3acp + +end + +return diff --git a/charmm/toppar/stream/prot/toppar_all36_prot_retinol.str b/charmm/toppar/stream/prot/toppar_all36_prot_retinol.str new file mode 100644 index 00000000..46523897 --- /dev/null +++ b/charmm/toppar/stream/prot/toppar_all36_prot_retinol.str @@ -0,0 +1,1872 @@ +* Toppar stream file for retinol and retinal parameters +* A. Loccisano, A.M.W., J. Evanseck and A.D. MacKerell, Jr. +* April, 2005 +* + +!use with c36 protein force fields +!top_all36_prot.rtf +!par_all36_prot.prm + +read rtf card append +* retinal/retinol and related model compounds +* +32 1 + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +!DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +MASS 425 CC1A 12.01100 C ! alkene conjugation +MASS 426 CC1B 12.01100 C ! alkene conjugation +MASS 427 CC2 12.01100 C ! alkene conjugation +MASS 428 NS1 14.00700 N ! N for deprotonated Schiff's base +MASS 429 NS2 14.00700 N ! N for protonated Schiff's base + +RESI BTE2 0.00 ! 2-Butene, adm jr. +GROUP +ATOM C1 CT3 -0.27 ! H12 H13 +ATOM H11 HA3 0.09 ! \ | +ATOM H12 HA3 0.09 ! H13-C1 H31 +ATOM H13 HA3 0.09 ! \ / +GROUP ! C2=C3 +ATOM C2 CC1A -0.15 ! / \ +ATOM H21 HE1 0.15 ! H21 C4-H41 +GROUP ! | \ +ATOM C3 CC1A -0.15 ! H43 H42 +ATOM H31 HE1 0.15 ! +GROUP +ATOM C4 CT3 -0.27 +ATOM H41 HA3 0.09 +ATOM H42 HA3 0.09 +ATOM H43 HA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 H21 +DOUBLE C2 C3 +BOND C3 H31 C3 C4 C4 H41 C4 H42 C4 H43 + +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +PATC FIRS NONE LAST NONE + +RESI HEP3 0.00 ! 1,3,5-heptatriene +! +GROUP +ATOM C1 CC2 -0.42 ! +ATOM H11 HE2 0.21 ! H11 H21 +ATOM H12 HE2 0.21 ! \ / +ATOM C2 CC1A -0.15 ! C1=C2 H41 +ATOM H21 HE1 0.15 ! / \ / +GROUP ! H12 C3=C4 H61 +ATOM C3 CC1B -0.15 ! / \ / +ATOM H31 HE1 0.15 ! H31 C5=C6 +ATOM C4 CC1B -0.15 ! / \ +ATOM H41 HE1 0.15 ! H51 H62 +GROUP ! +ATOM C5 CC1A -0.15 +ATOM H51 HE1 0.15 +GROUP +ATOM C6 CC2 -0.42 +ATOM H61 HE2 0.21 +ATOM H62 HE2 0.21 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 H11 C1 H12 C2 H21 C3 H31 +BOND C4 H41 C5 H51 C6 H61 C6 H62 + +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI 13DB 0.00 ! 1,3-dibutene +! +GROUP +ATOM C1 CC2 -0.42 ! H11 H21 +ATOM H11 HE2 0.21 ! \ / +ATOM H12 HE2 0.21 ! C1=C2 H41 +GROUP ! / \ / +ATOM C2 CC1A -0.15 ! H12 C3=C4 +ATOM H21 HE1 0.15 ! / \ +ATOM C3 CC1B -0.15 ! H31 H42 +ATOM H31 HE1 0.15 ! +GROUP ! +ATOM C4 CC2 -0.42 ! +ATOM H41 HE2 0.21 ! +ATOM H42 HE2 0.21 ! + +BOND C1 C2 C2 C3 C3 C4 +BOND C1 H11 C1 H12 C2 H21 C3 H31 +BOND C4 H41 C4 H42 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 H41 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C3 H41 *C4 H42 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI 13DP 0.00 ! 1,3-dipentene +! +GROUP +ATOM C1 CC2 -0.42 ! +ATOM H11 HE2 0.21 ! H11 H21 +ATOM H12 HE2 0.21 ! \ / +ATOM C2 CC1A -0.15 ! C1=C2 H41 +ATOM H21 HE1 0.15 ! / \ / +GROUP ! H12 C3=C4 H51 +ATOM C3 CC1B -0.15 ! / \ / +ATOM H31 HE1 0.15 ! H31 C5-H52 +ATOM C4 CC1B -0.15 ! \ +ATOM H41 HE1 0.15 ! H53 +GROUP ! +ATOM C5 CT3 -0.27 ! +ATOM H51 HA3 0.09 ! +ATOM H52 HA3 0.09 ! +ATOM H53 HA3 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C1 H11 C1 H12 C2 H21 C3 H31 +BOND C4 H41 C5 H51 C5 H52 C5 H53 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C5 H51 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 180.0 0.00 0.00 +IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 +IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI DMB1 0.00 ! 2-methyl-1,3-butadiene +! +GROUP +ATOM C1 CC2 -0.42 ! +ATOM H11 HE2 0.21 ! H2M1 H2M2 +ATOM H12 HE2 0.21 ! \ / +GROUP ! H11 C2M-H2M3 +ATOM C2 CC1A 0.00 ! \ / +ATOM C2M CT3 -0.27 ! C1=C2 H41 +ATOM H2M1 HA3 0.09 ! / \ / +ATOM H2M2 HA3 0.09 ! H12 C3=C4 +ATOM H2M3 HA3 0.09 ! / \ +GROUP ! H31 H42 +ATOM C3 CC1B -0.15 ! +ATOM H31 HE1 0.15 ! +GROUP ! +ATOM C4 CC2 -0.42 ! +ATOM H41 HE2 0.21 ! +ATOM H42 HE2 0.21 ! + +BOND C1 C2 C2 C3 C3 C4 C2 C2M +BOND C1 H11 C1 H12 C3 H31 C4 H41 C4 H42 +BOND C2M H2M1 C2M H2M2 C2M H2M3 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 H41 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 C2M 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +IC C3 H41 *C4 H42 0.00 0.00 180.0 0.00 0.00 +IC C1 C2 C2M H2M1 0.00 0.00 180.0 0.00 0.00 +IC C2 H2M1 *C2M H2M2 0.00 0.00 120.0 0.00 0.00 +IC C2 H2M1 *C2M H2M3 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI DMP1 0.00 ! 4-methyl-1,3-pentadiene +! +GROUP +ATOM C1 CC2 -0.42 ! +ATOM H11 HE2 0.21 ! H11 H21 H4M1 H4M2 +ATOM H12 HE2 0.21 ! \ / \ / +GROUP ! C1=C2 C4M-H4M3 +ATOM C2 CC1A -0.15 ! / \ / +ATOM H21 HE1 0.15 ! H12 C3=C4 H51 +ATOM C3 CC1B -0.15 ! / \ / +ATOM H31 HE1 0.15 ! H31 C5-H52 +GROUP ! \ +ATOM C4 CC1B 0.00 ! H53 +ATOM C4M CT3 -0.27 ! +ATOM H4M1 HA3 0.09 ! +ATOM H4M2 HA3 0.09 ! +ATOM H4M3 HA3 0.09 ! +GROUP +ATOM C5 CT3 -0.27 ! +ATOM H51 HA3 0.09 ! +ATOM H52 HA3 0.09 ! +ATOM H53 HA3 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C4 C4M +BOND C1 H11 C1 H12 C2 H21 C3 H31 +BOND C4M H4M1 C4M H4M2 C4M H4M3 +BOND C5 H51 C5 H52 C5 H53 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C5 H51 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +IC C3 C5 *C4 C4M 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C4M H4M1 0.00 0.00 180.0 0.00 0.00 +IC C4 H4M1 *C4M H4M2 0.00 0.00 120.0 0.00 0.00 +IC C4 H4M1 *C4M H4M3 0.00 0.00 -120.0 0.00 0.00 +IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 +IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + + +RESI DMP2 0.00 ! 2-methyl-1,3-pentadiene +! +GROUP ! H2M1 H2M2 +ATOM C1 CC2 -0.42 ! \ / +ATOM H11 HE2 0.21 ! H11 C2M-H2M3 +ATOM H12 HE2 0.21 ! \ / +GROUP ! C1=C2 H41 +ATOM C2 CC1A 0.00 ! / \ / +ATOM C2M CT3 -0.27 ! H12 C3=C4 H51 +ATOM H2M1 HA3 0.09 ! / \ / +ATOM H2M2 HA3 0.09 ! H31 C5-H52 +ATOM H2M3 HA3 0.09 ! \ +ATOM C3 CC1B -0.15 ! H53 +ATOM H31 HE1 0.15 ! +GROUP ! +ATOM C4 CC1B -0.15 ! +ATOM H41 HE1 0.15 ! +ATOM C5 CT3 -0.27 ! +ATOM H51 HA3 0.09 ! +ATOM H52 HA3 0.09 ! +ATOM H53 HA3 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C2 C2M +BOND C1 H11 C1 H12 C3 H31 C4 H41 +BOND C2M H2M1 C2M H2M2 C2M H2M3 +BOND C5 H51 C5 H52 C5 H53 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C5 H51 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 C2M 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 180.0 0.00 0.00 +IC C1 C2 C2M H2M1 0.00 0.00 180.0 0.00 0.00 +IC C2 H2M1 *C2M H2M2 0.00 0.00 120.0 0.00 0.00 +IC C2 H2M1 *C2M H2M3 0.00 0.00 -120.0 0.00 0.00 +IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 +IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI CROT 0.00 ! 2-buteneamide,N,3-dimethyl (crotonamide) + ! numbering as in fennretinide +! note different atom types for N21 and C15: this is consistent +! with differences in NMA and acetamide +GROUP +ATOM C12 CT3 -0.27 ! +ATOM H121 HA3 0.09 ! H202 H203 +ATOM H122 HA3 0.09 ! \ / +ATOM H123 HA3 0.09 ! H201-C20 +GROUP ! | +ATOM C13 CC1A 0.00 !H121-C12--C13 O29 +ATOM C14 CC1A -0.15 ! / | \\ || +ATOM H141 HE1 0.15 !H122 H123 C14--C15 +GROUP ! / \ +ATOM C15 C 0.51 ! H141 N21-H211 (cis) +ATOM O29 O -0.51 ! | +GROUP ! H132-C16-H131 +ATOM N21 NH1 -0.47 ! | +ATOM H211 H 0.28 ! H133 +ATOM C16 CT3 -0.08 +ATOM H131 HA3 0.09 +ATOM H132 HA3 0.09 +ATOM H133 HA3 0.09 +GROUP ! +ATOM C20 CT3 -0.27 ! +ATOM H201 HA3 0.09 ! +ATOM H202 HA3 0.09 ! +ATOM H203 HA3 0.09 ! + +BOND C12 C13 C13 C14 C14 C15 C15 N21 N21 C16 +BOND C13 C20 C15 O29 C14 H141 N21 H211 +BOND C16 H131 C16 H132 C16 H133 +BOND C12 H121 C12 H122 C12 H123 +BOND C20 H201 C20 H202 C20 H203 + +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C15 N21 C16 0.0000 0.00 180.00 0.00 0.0000 +IC H121 C13 *C12 H122 0.0000 0.00 120.00 0.00 0.0000 +IC H121 C13 *C12 H123 0.0000 0.00 -120.00 0.00 0.0000 +IC H121 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 +IC C16 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 +IC C15 N21 C16 H131 0.0000 0.00 180.00 0.00 0.0000 +IC H131 N21 *C16 H132 0.0000 0.00 120.00 0.00 0.0000 +IC H131 N21 *C16 H133 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI PACP 0.00 ! p-acetamide-phenol + ! numbering as in fennretinide + ! +ATOM C14 CT3 -0.27 ! H142 +ATOM H141 HA3 0.09 ! | +ATOM H142 HA3 0.09 ! H141-C14-H143 +ATOM H143 HA3 0.09 ! | +GROUP ! C15=O29 +ATOM C15 C 0.52 ! | +ATOM O29 O -0.52 ! N21-H211 +GROUP ! | +ATOM N21 NH1 -0.47 ! C22 +ATOM H211 H 0.33 ! // \ +ATOM C22 CA 0.14 ! H231-C23 C27-H271 +GROUP ! | || +ATOM C23 CA -0.115! H241-C24 C26-H261 +ATOM H231 HP 0.115! \\ / +GROUP ! C25 +ATOM C24 CA -0.115! | +ATOM H241 HP 0.115! O28 +GROUP ! \ +ATOM C26 CA -0.115! H281 +ATOM H261 HP 0.115 +GROUP +ATOM C27 CA -0.115 +ATOM H271 HP 0.115 +GROUP +ATOM C25 CA 0.11 +ATOM O28 OH1 -0.54 +ATOM H281 H 0.43 + +BOND C14 C15 C15 N21 N21 C22 C22 C23 C15 O29 +BOND C23 C24 C24 C25 C25 C26 C26 C27 C27 C22 +BOND C25 O28 O28 H281 N21 H211 +BOND C14 H141 C14 H142 C14 H143 +BOND C23 H231 C24 H241 C26 H261 C27 H271 + +IC C14 C15 N21 C22 0.0000 0.00 180.00 0.00 0.0000 +IC C15 N21 C22 C27 0.0000 0.00 0.00 0.00 0.0000 +IC N21 C22 C23 C24 0.0000 0.00 180.00 0.00 0.0000 +IC C22 C23 C24 C25 0.0000 0.00 0.00 0.00 0.0000 +IC C23 C24 C25 O28 0.0000 0.00 180.00 0.00 0.0000 +IC H141 C15 *C14 H142 0.0000 0.00 120.00 0.00 0.0000 +IC H141 C15 *C14 H143 0.0000 0.00 -120.00 0.00 0.0000 +IC H141 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 +IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 +IC C22 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 +IC C27 N21 *C22 C23 0.0000 0.00 180.00 0.00 0.0000 +IC C24 C22 *C23 H231 0.0000 0.00 180.00 0.00 0.0000 +IC C25 C23 *C24 H241 0.0000 0.00 180.00 0.00 0.0000 +IC O28 C24 *C25 C26 0.0000 0.00 180.00 0.00 0.0000 +IC C27 C25 *C26 H261 0.0000 0.00 180.00 0.00 0.0000 +IC C26 C22 *C27 H271 0.0000 0.00 180.00 0.00 0.0000 +IC C24 C25 O28 H281 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI MECH 0.00 ! 1,6,6-trimethyl-2-ethene-cyclhexene + ! using retinol numbering +GROUP +ATOM C1 CT 0.00 !H162 H163 H171 H172 +ATOM C2 CT2 -0.18 ! \ | | / +ATOM H21 HA2 0.09 !H161-C16 C17-H173 H81 +ATOM H22 HA2 0.09 ! \ / | +ATOM C3 CT2 -0.18 ! H21 C1 C8-H82 +ATOM H31 HA2 0.09 ! \ / \ // +ATOM H32 HA2 0.09 ! H22-C2 C6------C7 +ATOM C4 CT2 -0.18 ! | || \ +ATOM H41 HA2 0.09 ! H31-C3 C5 H181 H71 +ATOM H42 HA2 0.09 ! / \ / \ / +ATOM C5 CC1A 0.00 ! H32 C4 C18-H18 +ATOM C6 CC1A 0.00 ! / \ \ +GROUP ! H41 H42 H183 +ATOM C7 CC1B -0.15 ! +ATOM H71 HE1 0.15 ! +ATOM C8 CC2 -0.42 ! +ATOM H81 HE2 0.21 ! +ATOM H82 HE2 0.21 ! +GROUP ! +ATOM C16 CT3 -0.27 ! +ATOM H161 HA3 0.09 ! +ATOM H162 HA3 0.09 ! +ATOM H163 HA3 0.09 ! +GROUP ! +ATOM C17 CT3 -0.27 ! +ATOM H171 HA3 0.09 ! +ATOM H172 HA3 0.09 ! +ATOM H173 HA3 0.09 ! +GROUP ! +ATOM C18 CT3 -0.27 ! +ATOM H181 HA3 0.09 ! +ATOM H182 HA3 0.09 ! +ATOM H183 HA3 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C1 C16 C1 C17 C5 C18 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C7 H71 C8 H81 C8 H82 C18 H181 C18 H182 C18 H183 + +!initial ring geometry is planar +IC C1 C2 C3 C4 0.00 0.00 63.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 -46.0 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 15.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 +IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 +IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 +IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 +IC C1 C5 *C6 C7 0.00 0.00 180.0 0.00 0.00 +IC C5 C6 C7 C8 0.00 0.00 60.0 0.00 0.00 +IC C6 C8 *C7 H71 0.00 0.00 180.0 0.00 0.00 +IC C6 C7 C8 H81 0.00 0.00 180.0 0.00 0.00 +IC C7 H81 *C8 H82 0.00 0.00 180.0 0.00 0.00 +IC C6 C2 *C1 C16 0.00 0.00 120.0 0.00 0.00 +IC C6 C2 *C1 C17 0.00 0.00 -120.0 0.00 0.00 +IC C2 C1 C16 H161 0.00 0.00 180.0 0.00 0.00 +IC C1 H161 *C16 H162 0.00 0.00 120.0 0.00 0.00 +IC C1 H161 *C16 H163 0.00 0.00 -120.0 0.00 0.00 +IC C2 C1 C17 H171 0.00 0.00 180.0 0.00 0.00 +IC C1 H171 *C17 H172 0.00 0.00 120.0 0.00 0.00 +IC C1 H171 *C17 H173 0.00 0.00 -120.0 0.00 0.00 +IC C4 C6 *C5 C18 0.00 0.00 180.0 0.00 0.00 +IC C4 C5 C18 H181 0.00 0.00 180.0 0.00 0.00 +IC C5 H181 *C18 H182 0.00 0.00 120.0 0.00 0.00 +IC C5 H181 *C18 H183 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI TMCH 0.00 ! 1,2,6,6-tetramethylcyclohexene + ! using retinol numbering +GROUP +ATOM C1 CT 0.00 !H162 H163 H171 H172 +ATOM C2 CT2 -0.18 ! \ | | / +ATOM H21 HA2 0.09 !H161-C16 C17-H173 +ATOM H22 HA2 0.09 ! \ / +ATOM C3 CT2 -0.18 ! H21 C1 H71 H72 +ATOM H31 HA2 0.09 ! \ / \ | / +ATOM H32 HA2 0.09 ! H22-C2 C6------C7-H73 +ATOM C4 CT2 -0.18 ! | || +ATOM H41 HA2 0.09 ! H31-C3 C5 H181 +ATOM H42 HA2 0.09 ! / \ / \ / +ATOM C5 CC1A 0.00 ! H32 C4 C18-H18 +ATOM C6 CC1A 0.00 ! / \ \ +GROUP ! H41 H42 H183 +ATOM C7 CT3 -0.27 ! +ATOM H71 HA3 0.09 ! +ATOM H72 HA3 0.09 ! +ATOM H73 HA3 0.09 ! +GROUP ! +ATOM C16 CT3 -0.27 ! +ATOM H161 HA3 0.09 ! +ATOM H162 HA3 0.09 ! +ATOM H163 HA3 0.09 ! +GROUP ! +ATOM C17 CT3 -0.27 ! +ATOM H171 HA3 0.09 ! +ATOM H172 HA3 0.09 ! +ATOM H173 HA3 0.09 ! +GROUP ! +ATOM C18 CT3 -0.27 ! +ATOM H181 HA3 0.09 ! +ATOM H182 HA3 0.09 ! +ATOM H183 HA3 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C1 C16 C1 C17 C5 C18 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C7 H71 C7 H72 C7 H73 C18 H181 C18 H182 C18 H183 + +!initial geometry is planar +IC C1 C2 C3 C4 0.00 0.00 -63.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 46.0 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 -13.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 +IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 +IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 +IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 +IC C1 C5 *C6 C7 0.00 0.00 180.0 0.00 0.00 +IC C5 C6 C7 H71 0.00 0.00 180.0 0.00 0.00 +IC C6 H71 *C7 H72 0.00 0.00 120.0 0.00 0.00 +IC C6 H71 *C7 H73 0.00 0.00 -120.0 0.00 0.00 +IC C6 C2 *C1 C16 0.00 0.00 120.0 0.00 0.00 +IC C6 C2 *C1 C17 0.00 0.00 -120.0 0.00 0.00 +IC C2 C1 C16 H161 0.00 0.00 180.0 0.00 0.00 +IC C1 H161 *C16 H162 0.00 0.00 120.0 0.00 0.00 +IC C1 H161 *C16 H163 0.00 0.00 -120.0 0.00 0.00 +IC C2 C1 C17 H171 0.00 0.00 180.0 0.00 0.00 +IC C1 H171 *C17 H172 0.00 0.00 120.0 0.00 0.00 +IC C1 H171 *C17 H173 0.00 0.00 -120.0 0.00 0.00 +IC C4 C6 *C5 C18 0.00 0.00 180.0 0.00 0.00 +IC C4 C5 C18 H181 0.00 0.00 180.0 0.00 0.00 +IC C5 H181 *C18 H182 0.00 0.00 120.0 0.00 0.00 +IC C5 H181 *C18 H183 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI FRET 0.00 ! fennretinide, nomenclature consistent with retinol +! +! +! +GROUP +ATOM C1 CT 0.00 +ATOM C2 CT2 -0.18 +ATOM H21 HA2 0.09 +ATOM H22 HA2 0.09 +ATOM C3 CT2 -0.18 +ATOM H31 HA2 0.09 +ATOM H32 HA2 0.09 +ATOM C4 CT2 -0.18 +ATOM H41 HA2 0.09 +ATOM H42 HA2 0.09 +ATOM C5 CC1A 0.00 +ATOM C6 CC1A 0.00 +GROUP +ATOM C7 CC1B -0.15 +ATOM H71 HE1 0.15 +ATOM C8 CC1B -0.15 +ATOM H81 HE1 0.15 +ATOM C9 CC1A 0.00 +ATOM C10 CC1A -0.15 +ATOM H101 HE1 0.15 +GROUP +ATOM C11 CC1B -0.15 !H162 H163 H171 H172 +ATOM H111 HE1 0.15 ! \ | | / +ATOM C12 CC1B -0.15 !H161-C16 C17-H173 H191 H192 +ATOM H121 HE1 0.15 ! \ / \ / +ATOM C13 CC1A 0.00 ! H21 C1 H71 H81 C19 +ATOM C14 CC1A -0.15 ! \ / \ | | / \ +ATOM H141 HE1 0.15 ! H22-C2 C6------C7=====C8----C9 H193 +GROUP ! | || || +ATOM C16 CT3 -0.27 ! H31-C3 C5 H181 C10-H101 +ATOM H161 HA3 0.09 ! / \ / \ / | +ATOM H162 HA3 0.09 ! H32 C4 C18-H182 C11-H111 +ATOM H163 HA3 0.09 ! / \ \ || +GROUP ! H41 H42 H183 C12-H121 H201 +ATOM C17 CT3 -0.27 ! | / +ATOM H171 HA3 0.09 ! C13---C20-H202 +ATOM H172 HA3 0.09 ! || \ +ATOM H173 HA3 0.09 ! C14-H141 H203 +GROUP ! | +ATOM C18 CT3 -0.27 ! C15=O29 +ATOM H181 HA3 0.09 ! | +ATOM H182 HA3 0.09 ! N21-H211 +ATOM H183 HA3 0.09 ! | +GROUP ! C22 +ATOM C19 CT3 -0.27 ! // \ +ATOM H191 HA3 0.09 ! H231-C23 C27-H271 +ATOM H192 HA3 0.09 ! | || +ATOM H193 HA3 0.09 ! H241-C24 C26-H261 +GROUP ! \\ / +ATOM C20 CT3 -0.27 ! C25 +ATOM H201 HA3 0.09 ! | +ATOM H202 HA3 0.09 ! O28 +ATOM H203 HA3 0.09 ! \ +GROUP ! H281 +ATOM C15 C 0.51 ! charges from CROT +ATOM O29 O -0.51 ! +GROUP +ATOM N21 NH1 -0.47 ! +ATOM H211 H 0.33 ! charges from PACP +ATOM C22 CA 0.14 ! +GROUP +ATOM C23 CA -0.115 +ATOM H231 HP 0.115 +GROUP +ATOM C24 CA -0.115 +ATOM H241 HP 0.115 +GROUP +ATOM C26 CA -0.115 +ATOM H261 HP 0.115 +GROUP +ATOM C27 CA -0.115 +ATOM H271 HP 0.115 +GROUP +ATOM C25 CA 0.11 +ATOM O28 OH1 -0.54 +ATOM H281 H 0.43 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 C13 C13 C14 C14 C15 C15 N21 N21 C22 C22 C23 +BOND C23 C24 C24 C25 C25 C26 C26 C27 C27 C22 +BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 C15 O29 +BOND C25 O28 O28 H281 N21 H211 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 +BOND C20 H201 C20 H202 C20 H203 +BOND C23 H231 C24 H241 C26 H261 C27 H271 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 +IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 +IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 +IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 +IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 +IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 +IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 +IC C13 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 +IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C15 N21 C22 0.0000 0.00 180.00 0.00 0.0000 +IC C22 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 +IC C15 N21 C22 C27 0.0000 0.00 180.00 0.00 0.0000 +IC C27 N21 *C22 C23 0.0000 0.00 180.00 0.00 0.0000 +IC N21 C22 C23 C24 0.0000 0.00 180.00 0.00 0.0000 +IC C24 C22 *C23 H231 0.0000 0.00 180.00 0.00 0.0000 +IC C22 C23 C24 C25 0.0000 0.00 0.00 0.00 0.0000 +IC C25 C23 *C24 H241 0.0000 0.00 180.00 0.00 0.0000 +IC C23 C24 C25 O28 0.0000 0.00 180.00 0.00 0.0000 +IC O28 C24 *C25 C26 0.0000 0.00 180.00 0.00 0.0000 +IC C27 C25 *C26 H261 0.0000 0.00 180.00 0.00 0.0000 +IC C26 C22 *C27 H271 0.0000 0.00 180.00 0.00 0.0000 +IC C24 C25 O28 H281 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI RTOL 0.00 ! retinol, nomenclature from PDB +! +GROUP +ATOM C1 CT 0.00 +ATOM C2 CT2 -0.18 +ATOM H21 HA2 0.09 +ATOM H22 HA2 0.09 +GROUP +ATOM C3 CT2 -0.18 +ATOM H31 HA2 0.09 +ATOM H32 HA2 0.09 +GROUP +ATOM C4 CT2 -0.18 +ATOM H41 HA2 0.09 +ATOM H42 HA2 0.09 +ATOM C5 CC1A 0.00 +ATOM C6 CC1A 0.00 +GROUP +ATOM C7 CC1B -0.15 +ATOM H71 HE1 0.15 +ATOM C8 CC1B -0.15 +ATOM H81 HE1 0.15 +GROUP +ATOM C9 CC1A 0.00 +ATOM C10 CC1A -0.15 +ATOM H101 HE1 0.15 +GROUP +ATOM C11 CC1B -0.15 +ATOM H111 HE1 0.15 +GROUP +ATOM C12 CC1B -0.15 +ATOM H121 HE1 0.15 +GROUP +ATOM C13 CC1A 0.00 +ATOM C14 CC1A -0.15 ! +ATOM H141 HE1 0.15 !H162 H163 H171 H172 +GROUP ! \ | | / +ATOM C15 CT2 0.05 !H161-C16 C17-H173 H191 H192 +ATOM H151 HA2 0.09 ! \ / \ / +ATOM H152 HA2 0.09 ! H21 C1 H71 H81 C19 +ATOM OR OH1 -0.66 ! \ / \ | | / \ +ATOM HR H 0.43 ! H22-C2 C6------C7=====C8----C9 H193 +GROUP ! | || || +ATOM C16 CT3 -0.27 ! H31-C3 C5 H181 C10-H101 +ATOM H161 HA3 0.09 ! / \ / \ / | +ATOM H162 HA3 0.09 ! H32 C4 C18-H182 C11-H111 +ATOM H163 HA3 0.09 ! / \ \ || +GROUP ! H41 H42 H183 C12-H121 H201 +ATOM C17 CT3 -0.27 ! | / +ATOM H171 HA3 0.09 ! C13---C20-H202 +ATOM H172 HA3 0.09 ! || \ +ATOM H173 HA3 0.09 ! C14-H141 H203 +GROUP ! | +ATOM C18 CT3 -0.27 ! H151-C15-H152 +ATOM H181 HA3 0.09 ! | +ATOM H182 HA3 0.09 ! OR +ATOM H183 HA3 0.09 ! \ +GROUP ! HR +ATOM C19 CT3 -0.27 ! +ATOM H191 HA3 0.09 ! +ATOM H192 HA3 0.09 ! +ATOM H193 HA3 0.09 ! +GROUP ! +ATOM C20 CT3 -0.27 ! +ATOM H201 HA3 0.09 ! +ATOM H202 HA3 0.09 ! +ATOM H203 HA3 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 C13 C13 C14 C14 C15 C15 OR +BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 +BOND C15 H151 C15 H152 OR HR +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 +BOND C20 H201 C20 H202 C20 H203 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 OR 0.0000 0.00 180.00 0.00 0.0000 +IC OR C14 *C15 H151 0.0000 0.00 120.00 0.00 0.0000 +IC OR C14 *C15 H152 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C15 OR HR 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 +IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 +IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 +IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 +IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 +IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 +IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI RTAL 0.00 ! retinal, nomenclature from PDB based on retinol +! +GROUP +ATOM C1 CT 0.00 +ATOM C2 CT2 -0.18 +ATOM H21 HA2 0.09 +ATOM H22 HA2 0.09 +ATOM C3 CT2 -0.18 +ATOM H31 HA2 0.09 +ATOM H32 HA2 0.09 +ATOM C4 CT2 -0.18 +ATOM H41 HA2 0.09 +ATOM H42 HA2 0.09 +ATOM C5 CC1A 0.00 +ATOM C6 CC1A 0.00 +GROUP +ATOM C7 CC1B -0.15 +ATOM H71 HE1 0.15 +ATOM C8 CC1B -0.15 +ATOM H81 HE1 0.15 +ATOM C9 CC1A 0.00 +ATOM C10 CC1A -0.15 +ATOM H101 HE1 0.15 +GROUP +ATOM C11 CC1B -0.15 +ATOM H111 HE1 0.15 +ATOM C12 CC1B -0.15 +ATOM H121 HE1 0.15 ! +ATOM C13 CC1A 0.00 !H162 H163 H171 H172 +GROUP ! \ | | / +ATOM C14 CC1A -0.01 !H161-C16 C17-H173 H191 H192 +ATOM H141 HE1 0.15 ! \ / \ / +ATOM C15 CD 0.19 ! H21 C1 H71 H81 C19 +ATOM O15 O -0.43 ! \ / \ | | / \ +ATOM H15 HR1 0.10 ! H22-C2 C6------C7=====C8----C9 H193 +GROUP ! | || || +ATOM C16 CT3 -0.27 ! H31-C3 C5 H181 C10-H101 +ATOM H161 HA3 0.09 ! / \ / \ / | +ATOM H162 HA3 0.09 ! H32 C4 C18-H182 C11-H111 +ATOM H163 HA3 0.09 ! / \ \ || +GROUP ! H41 H42 H183 C12-H121 H201 +ATOM C17 CT3 -0.27 ! | / +ATOM H171 HA3 0.09 ! C13---C20-H202 +ATOM H172 HA3 0.09 ! || \ +ATOM H173 HA3 0.09 ! C14-H141 H203 +GROUP ! | +ATOM C18 CT3 -0.27 ! C15 +ATOM H181 HA3 0.09 ! / \\ +ATOM H182 HA3 0.09 ! H15 O15 +ATOM H183 HA3 0.09 ! +GROUP ! +ATOM C19 CT3 -0.27 ! +ATOM H191 HA3 0.09 ! +ATOM H192 HA3 0.09 ! +ATOM H193 HA3 0.09 ! +GROUP ! +ATOM C20 CT3 -0.27 ! +ATOM H201 HA3 0.09 ! +ATOM H202 HA3 0.09 ! +ATOM H203 HA3 0.09 ! + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 C13 C13 C14 C14 C15 C15 O15 C15 H15 +BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 +BOND C20 H201 C20 H202 C20 H203 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 O15 0.0000 0.00 180.00 0.00 0.0000 +IC O15 C14 *C15 H15 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 +IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 +IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 +IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 +IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 +IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 +IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI RTAC -1.00 ! all-trans-retinoic acid, nomenclature from PDB +! +GROUP +ATOM C1 CT 0.00 +ATOM C16 CT3 -0.27 +ATOM H161 HA3 0.09 +ATOM H162 HA3 0.09 +ATOM H163 HA3 0.09 +ATOM C17 CT3 -0.27 +ATOM H171 HA3 0.09 +ATOM H172 HA3 0.09 +ATOM H173 HA3 0.09 +GROUP +ATOM C2 CT2 -0.18 +ATOM H21 HA2 0.09 +ATOM H22 HA2 0.09 +ATOM C3 CT2 -0.18 +ATOM H31 HA2 0.09 +ATOM H32 HA2 0.09 +ATOM C4 CT2 -0.18 +ATOM H41 HA2 0.09 +ATOM H42 HA2 0.09 +GROUP +ATOM C5 CC1A 0.00 +ATOM C6 CC1A 0.00 +GROUP +ATOM C18 CT3 -0.27 +ATOM H181 HA3 0.09 +ATOM H182 HA3 0.09 +ATOM H183 HA3 0.09 +GROUP +ATOM C7 CC1B -0.15 +ATOM H71 HE1 0.15 +ATOM C8 CC1B -0.15 +ATOM H81 HE1 0.15 +GROUP +ATOM C9 CC1A 0.00 +ATOM C19 CT3 -0.27 !H162 H163 H171 H172 +ATOM H191 HA3 0.09 ! \ | | / +ATOM H192 HA3 0.09 !H161-C16 C17-H173 H191 H192 +ATOM H193 HA3 0.09 ! \ / \ / +ATOM C10 CC1A -0.15 ! H21 C1 H71 H81 C19 +ATOM H101 HE1 0.15 ! \ / \ | | / \ +GROUP ! H22-C2 C6------C7=====C8----C9 H193 +ATOM C11 CC1B -0.15 ! | || || +ATOM H111 HE1 0.15 ! H31-C3 C5 H181 C10-H101 +ATOM C12 CC1B -0.15 ! / \ / \ / | +ATOM H121 HE1 0.15 ! H32 C4 C18-H182 C11-H111 +GROUP ! / \ \ || +ATOM C13 CC1A 0.00 ! H41 H42 H183 C12-H121 H201 +ATOM C20 CT3 -0.27 ! | / +ATOM H201 HA3 0.09 ! C13---C20-H202 +ATOM H202 HA3 0.09 ! || \ +ATOM H203 HA3 0.09 ! C14-H141 H203 +GROUP ! | +ATOM C14 CC1A -0.25 ! C15=O29 +ATOM H141 HE1 0.15 ! | (-) +ATOM C15 CC 0.62 ! O29B +ATOM O29 OC -0.76 ! +ATOM O29B OC -0.76 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 C13 C13 C14 C14 C15 C15 O29 C15 O29B +BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 +BOND C20 H201 C20 H202 C20 H203 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 +IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 +IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 +IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 +IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 +IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 +IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 O29 0.0000 0.00 180.00 0.00 0.0000 +IC O29 C14 *C15 O29B 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI PRAC -1.00 ! 2-propenoic acid +! +GROUP +ATOM C1 CC2 -0.42 ! +ATOM H11 HE2 0.21 ! +ATOM H12 HE2 0.21 ! H11 OD1 +GROUP ! \ || +ATOM C2 CC1A -0.25 ! C1 CG +ATOM H21 HE1 0.15 ! / \\ / \ +ATOM CG CC 0.62 ! H12 C2 OD2 (-) +ATOM OD1 OC -0.76 ! | +ATOM OD2 OC -0.76 ! H21 + +BOND C1 H11 C1 H12 C1 C2 C2 H21 +BOND C2 CG CG OD1 CG OD2 + +IC C1 C2 CG OD1 0.0000 0.00 180.00 0.00 0.0000 +IC OD1 C2 *CG OD2 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 CG 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC CG C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI PROL 0.00 ! 3-propenol (1-hydroxy-2-propene) +! +GROUP +ATOM C1 CC2 -0.42 ! +ATOM H11 HE2 0.21 ! H11 H31 +ATOM H12 HE2 0.21 ! \ | +ATOM C2 CC1A -0.15 ! C1 C3-OR +ATOM H21 HE1 0.15 ! / \\ / | \ +GROUP ! H12 C2 H32 HR +ATOM C3 CT2 0.05 ! | +ATOM H31 HA2 0.09 ! H21 +ATOM H32 HA2 0.09 +ATOM OR OH1 -0.66 +ATOM HR H 0.43 +BOND C1 C2 C2 C3 C3 OR OR HR +BOND H11 C1 H12 C1 H21 C2 H31 C3 +BOND H32 C3 + +IC C1 C2 C3 OR 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 OR HR 0.0000 0.00 60.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC OR C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC OR C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI PRAL 0.00 ! 1-propenal +GROUP +ATOM C1 CC2 -0.42 ! +ATOM H11 HE2 0.21 ! H11 OD1 +ATOM H12 HE2 0.21 ! \ || +ATOM C2 CC1A -0.01 ! C1 CG +ATOM H21 HE1 0.15 ! / \\ / \ +ATOM CG CD 0.19 ! H12 C2 H +ATOM OD1 O -0.43 ! | +ATOM H HR1 0.10 ! H21 + +BOND C1 H11 C1 H12 C1 C2 C2 H21 +BOND C2 CG CG OD1 CG H +IMPR CG C2 OD1 H + +IC C1 C2 CG OD1 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 CG 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC CG C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC OD1 C2 *CG H 0.0000 0.00 180.00 0.00 0.0000 + +RESI SCH1 0.00 ! Schiff's base model compound 1, deprotonated +! ! new atom type NS1 +GROUP +ATOM C1 CT3 -0.05 ! H11 H31 +ATOM H11 HA3 0.09 ! \ / +ATOM H12 HA3 0.09 ! H12--C1-N2=C3 H41 +ATOM H13 HA3 0.09 ! / \ / +ATOM N2 NS1 -0.60 ! H13 C4--H42 +ATOM C3 CC1B 0.23 ! \ +ATOM H31 HE1 0.15 ! H43 +GROUP ! +ATOM C4 CT3 -0.27 ! +ATOM H41 HA3 0.09 ! +ATOM H42 HA3 0.09 +ATOM H43 HA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 N2 N2 C3 C3 H31 +BOND C3 C4 C4 H41 C4 H42 C4 H43 + +IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C3 N2 C1 H11 0.0000 0.00 0.00 0.00 0.0000 +IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +RESI SCH2 1.00 ! Schiff's base model compound 2, protonated +! ! new atom type, NS2 +GROUP +ATOM C1 CT3 0.18 ! H11 H21 H31 +ATOM H11 HA3 0.09 ! \ | / +ATOM H12 HA3 0.09 ! H12--C1-N2=C3 H41 +ATOM H13 HA3 0.09 ! / \ / +ATOM N2 NS2 -0.40 ! H13 C4--H42 +ATOM H21 HC 0.38 ! \ +ATOM C3 CC1B 0.37 ! H43 +ATOM H31 HR1 0.20 ! hydrogen with intermediate VDW radius +GROUP ! +ATOM C4 CT3 -0.27 ! +ATOM H41 HA3 0.09 ! +ATOM H42 HA3 0.09 +ATOM H43 HA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 N2 N2 H21 N2 C3 C3 H31 +BOND C3 C4 C4 H41 C4 H42 C4 H43 + +IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *N2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C3 N2 C1 H11 0.0000 0.00 0.00 0.00 0.0000 +IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +RESI SCH3 1.00 ! Schiff's base model compound 3, protonated +! ! new atom type, NS2 +GROUP +ATOM C1 CT3 0.18 ! H11 H21 H31 +ATOM H11 HA3 0.09 ! \ | / +ATOM H12 HA3 0.09 ! H12--C1-N2=C3 H51 +ATOM H13 HA3 0.09 ! / \ / +ATOM N2 NS2 -0.40 ! H13 C4=C5 +ATOM H21 HC 0.38 ! / \ +ATOM C3 CC1B 0.37 ! H41 H52 +ATOM H31 HR1 0.20 ! hydrogen with intermediate VDW radius +GROUP ! +ATOM C4 CC1A -0.15 +ATOM H41 HE1 0.15 +ATOM C5 CC2 -0.42 +ATOM H51 HE2 0.21 +ATOM H52 HE2 0.21 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 N2 N2 H21 N2 C3 C3 H31 +BOND C3 C4 C4 H41 +BOND C4 C5 C5 H51 C5 H52 + +IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 N2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *N2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H51 C4 *C5 H52 0.0000 0.00 180.00 0.00 0.0000 + +PRES SCK0 0.00 ! patch to link lysine with retinal to form a + ! deprotonated schiff's base + ! follow with AUTOgenerate ANGLes DIHEdrals command +! residue 1: lysine +! residue 2: retinal +! +DELETE ATOM 1HZ1 +DELETE ATOM 1HZ2 +DELETE ATOM 1HZ3 +DELETE ATOM 2O15 +GROUP ! HE1 HE2 +ATOM 1CE CT2 0.04 ! \ / +ATOM 1HE1 HA2 0.09 ! --1CE1 2H15 +ATOM 1HE2 HA2 0.09 ! \ / +ATOM 1NZ NS1 -0.60 ! 1NZ=2C15 +ATOM 2C15 CC1B 0.23 ! / \ +ATOM 2H15 HE1 0.15 ! 2HZ1 2C14== +GROUP ! / +ATOM 2C14 CC1A -0.15 ! 2HE14 +ATOM 2H141 HE1 0.15 + +BOND 1NZ 2C15 + +IC 1CD 1CE 1NZ 2C15 0.0000 0.00 180.00 0.00 0.0000 +IC 1CE 1NZ 2C15 2C14 0.0000 0.00 180.00 0.00 0.0000 +IC 1NZ 2C15 2C14 2C13 0.0000 0.00 180.00 0.00 0.0000 +IC 2C14 1NZ *2C15 2H15 0.0000 0.00 180.00 0.00 0.0000 +IC 2C5 2C6 2C1 2C2 0.0000 0.00 0.00 0.00 0.0000 ! required to build retinal + + +PRES SCK1 1.00 ! patch to link lysine with retinal to form a + ! protonated schiff's base + ! follow with AUTOgenerate ANGLes DIHEdrals command +! residue 1: lysine +! residue 2: retinal +! +DELETE ATOM 1HZ2 +DELETE ATOM 1HZ3 +DELETE ATOM 2O15 +GROUP ! HE1 HE2 +ATOM 1CE CT2 0.27 ! \ / +ATOM 1HE1 HA2 0.09 ! --1CE1 2H15 +ATOM 1HE2 HA2 0.09 ! \ / +ATOM 1NZ NS2 -0.40 ! 1NZ=2C15 +ATOM HZ1 HC 0.38 ! / \ +ATOM 2C15 CC1B 0.37 ! 2HZ1 2C14== +ATOM 2H15 HR1 0.20 ! / +GROUP ! 2HE14 +ATOM 2C14 CC1A -0.15 +ATOM 2H141 HE1 0.15 + +BOND 1NZ 2C15 + +IC 1CD 1CE 1NZ 2C15 0.0000 0.00 180.00 0.00 0.0000 +IC 1CE 1NZ 2C15 2C14 0.0000 0.00 180.00 0.00 0.0000 +IC 1NZ 2C15 2C14 2C13 0.0000 0.00 180.00 0.00 0.0000 +IC 2C15 1CE *1NZ 1HZ1 0.0000 0.00 180.00 0.00 0.0000 +IC 2C14 1NZ *2C15 2H15 0.0000 0.00 180.00 0.00 0.0000 +IC 2C5 2C6 2C1 2C2 0.0000 0.00 0.00 0.00 0.0000 ! required to build retinal + +RESI LYR 1.00 ! PROTONATED SCHIFF BASE (modified Lysine with retinoic acid (RTAL)) + ! +GROUP ! +ATOM N NH1 -0.47 ! +ATOM HN H 0.31 ! +ATOM CA CT1 0.07 ! +ATOM HA HB1 0.09 ! +GROUP ! +ATOM C C 0.51 ! O HA H +ATOM O O -0.51 ! || | | +GROUP ! --C---CA----N-- +ATOM CB CT2 -0.18 ! | +ATOM HB2 HA2 0.09 ! HB3-CB-HB2 +ATOM HB3 HA2 0.09 ! | +GROUP ! | +ATOM CG CT2 -0.18 ! | +ATOM HG2 HA2 0.09 ! HG3-CG-HG2 +ATOM HG3 HA2 0.09 ! | +GROUP ! | +ATOM CD CT2 -0.18 ! | +ATOM HD2 HA2 0.09 ! HD3-CD-HD2 +ATOM HD3 HA2 0.09 ! | +GROUP ! | +ATOM CE CT2 0.27 ! | +ATOM HE2 HA2 0.09 ! HE3-CE-HE2 +ATOM HE3 HA2 0.09 ! | +ATOM NZ NS2 -0.40 ! HZ1-NZ+ +ATOM HZ1 HC 0.38 ! \\ +ATOM C1 CC1B 0.37 ! C1-H11 +ATOM H11 HR1 0.20 ! | +ATOM C2 CC1A -0.15 ! H42 C2-HC2 +ATOM HC2 HE1 0.15 ! | // +ATOM C3 CC1A 0.00 ! H41-C4-----C3 +ATOM C4 CT3 -0.27 ! | | +ATOM H41 HA3 0.09 ! H43 C5-H5 +ATOM H42 HA3 0.09 ! \\ +ATOM H43 HA3 0.09 ! H6--C6 +ATOM C5 CC1B -0.15 ! | +ATOM H5 HE1 0.15 ! H82 C7-H7 +ATOM C6 CC1B -0.15 ! | // +ATOM H6 HE1 0.15 ! H81-C8----C80 +GROUP ! | | +ATOM C7 CC1A -0.15 ! H83 C9--H9 +ATOM H7 HE1 0.15 ! || +ATOM C80 CC1A 0.00 ! C10--H10 +ATOM C8 CT3 -0.27 ! | +ATOM H81 HA3 0.09 ! | +ATOM H82 HA3 0.09 ! | +ATOM H83 HA3 0.09 ! | +GROUP ! | +ATOM C9 CC1B -0.15 ! | +ATOM H9 HE1 0.15 ! | +ATOM C10 CC1B -0.15 ! | +ATOM H10 HE1 0.15 ! C11 H191 H192 +GROUP ! // \ \ / +ATOM C11 CC1A 0.00 ! H132 // \ C19-H193 +GROUP ! | // \/ +ATOM C12 CC1A 0.00 ! H131-C13 -- C12 C17 -- C18-H181 +ATOM C13 CT3 -0.27 ! | | | / \ +ATOM H131 HA3 0.09 ! H133 | | H183 H182 +ATOM H132 HA3 0.09 ! H141-C14 C16-H161 +ATOM H133 HA3 0.09 ! / \ / \ +GROUP ! H142 \ / H162 +ATOM C14 CT2 -0.18 ! \ / +ATOM H141 HA2 0.09 ! C15 +ATOM H142 HA2 0.09 ! / \ +ATOM C15 CT2 -0.18 ! H151 H152 +ATOM H151 HA2 0.09 ! +ATOM H152 HA2 0.09 ! +ATOM C16 CT2 -0.18 ! +ATOM H161 HA2 0.09 ! +ATOM H162 HA2 0.09 ! +GROUP +ATOM C17 CT 0.00 ! +ATOM C18 CT3 -0.27 ! +ATOM H181 HA3 0.09 ! +ATOM H182 HA3 0.09 ! +ATOM H183 HA3 0.09 ! +ATOM C19 CT3 -0.27 ! +ATOM H191 HA3 0.09 ! +ATOM H192 HA3 0.09 ! +ATOM H193 HA3 0.09 ! + +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB2 CB HB3 CG HG2 +BOND CG HG3 CD HD2 CD HD3 CE HE2 CE HE3 +DOUBLE O C +BOND NZ HZ1 NZ C1 +BOND C1 C2 C1 H11 C2 C3 C2 HC2 +BOND C3 C4 C3 C5 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H5 C5 C6 C6 H6 +BOND C6 C7 C7 H7 +BOND C7 C80 +BOND C80 C9 C80 C8 +BOND C8 H81 C8 H82 C8 H83 +BOND C9 C10 C9 H9 +BOND C10 C11 C10 H10 +BOND C11 C12 C11 C17 +BOND C12 C13 C12 C14 +BOND C13 H131 C13 H132 C13 H133 +BOND C14 C15 C14 H141 C14 H142 +BOND C15 C16 C15 H151 C15 H152 +BOND C16 C17 C16 H161 C16 H162 +BOND C17 C18 C17 C19 +BOND C18 H181 C18 H182 C18 H183 +BOND C19 H191 C19 H192 C19 H193 +IMPR N -C CA HN C CA +N O +!IMPR C1 C2 NZ H11 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HZ1 NZ +ACCEPTOR O C + +IC -C CA *N HN 1.3482 123.57 180.00 115.11 0.9988 +IC -C N CA C 1.3482 123.57 180.00 107.29 1.5187 +IC N CA C +N 1.4504 107.29 180.00 117.27 1.3478 +IC +N CA *C O 1.3478 117.27 180.00 120.79 1.2277 +IC CA C +N +CA 1.5187 117.27 180.00 124.91 1.4487 +IC H N CA CB 1.0324 112.92 142.43 101.17 1.5618 +IC CB N *CA C 1.5618 101.17 117.80 107.69 1.5262 +IC CB N *CA HA 1.5618 101.17 -122.25 112.37 1.0467 +IC N CA C O 1.4066 107.69 169.60 118.27 1.2329 +IC N CA CB CG 1.4066 101.17 -169.06 112.88 1.5547 +IC CG CA *CB HB2 1.5547 112.88 126.21 108.43 1.0751 +IC CG CA *CB HB3 1.5547 112.88 -130.02 106.34 1.0839 +IC CA CB CG CD 1.5618 112.88 174.79 116.20 1.5139 +IC CD CB *CG HG2 1.5139 116.20 120.63 108.82 1.1282 +IC CD CB *CG HG3 1.5139 116.20 -132.72 108.50 1.1196 +IC CB CG CD CE 1.5547 116.20 175.39 111.29 1.5392 +IC CE CG *CD HD2 1.5392 111.29 125.53 102.68 1.1194 +IC CE CG *CD HD3 1.5392 111.29 -125.66 112.29 1.1189 +IC CG CD CE NZ 1.5139 111.29 174.26 105.61 1.4410 +IC NZ CD *CE HE2 1.4410 105.61 123.94 110.33 1.1625 +IC NZ CD *CE HE3 1.4410 105.61 -109.92 106.40 1.1132 +IC CD CE NZ C1 1.5392 105.61 -173.60 119.52 1.3271 +IC C1 CE *NZ HZ1 1.3271 119.52 -174.42 120.20 1.0043 +IC CE NZ C1 C2 1.4410 119.52 -168.80 116.63 1.4576 +IC C2 NZ *C1 H11 1.4576 116.63 171.69 119.09 1.1531 +IC NZ C1 C2 C3 1.3271 116.63 177.00 124.67 1.3994 +IC C3 C1 *C2 HC2 1.3994 124.67 -169.17 113.77 1.1613 +IC C1 C2 C3 C5 1.4576 124.67 -177.59 121.54 1.4600 +IC C5 C2 *C3 C4 1.4600 121.54 -179.13 122.30 1.5138 +IC C2 C3 C4 H41 1.3994 122.30 -126.30 117.92 1.0593 +IC H41 C3 *C4 H42 1.0593 117.92 125.50 111.68 1.0843 +IC H41 C3 *C4 H43 1.0593 117.92 -122.89 110.24 1.0565 +IC C2 C3 C5 C6 1.3994 121.54 -144.41 126.13 1.3528 +IC C6 C3 *C5 H5 1.3528 126.13 178.20 115.08 1.0691 +IC C3 C5 C6 C7 1.4600 126.13 -170.38 129.81 1.4627 +IC C7 C5 *C6 H6 1.4627 129.81 160.66 117.13 1.1130 +IC C5 C6 C7 C80 1.3528 129.81 149.05 126.38 1.3715 +IC C80 C6 *C7 H7 1.3715 126.38 -178.79 116.07 1.0867 +IC C6 C7 C80 C9 1.4627 126.38 -175.24 124.63 1.4493 +IC C9 C7 *C80 C8 1.4493 124.63 174.01 123.87 1.5042 +IC C7 C80 C8 H81 1.3715 123.87 -134.94 108.15 1.1456 +IC H81 C80 *C8 H82 1.1456 108.15 115.44 112.77 1.1215 +IC H81 C80 *C8 H83 1.1456 108.15 -122.35 113.48 1.1120 +IC C7 C80 C9 C10 1.3715 124.63 -146.54 126.66 1.3362 +IC C10 C80 *C9 H9 1.3362 126.66 164.41 111.19 1.1266 +IC C80 C9 C10 C11 1.4493 126.66 157.81 124.53 1.4870 +IC C11 C9 *C10 H10 1.4870 124.53 -167.09 126.78 1.1319 +IC C9 C10 C11 C17 1.3362 124.53 137.85 113.43 1.5273 +IC C17 C10 *C11 C12 1.5273 113.43 166.46 122.35 1.3683 +IC C10 C11 C12 C14 1.4870 122.35 -179.02 118.60 1.5230 +IC C14 C11 *C12 C13 1.5230 118.60 179.88 123.69 1.5824 +IC C11 C12 C13 H131 1.3683 123.69 -153.00 111.62 1.0407 +IC H131 C12 *C13 H132 1.0407 111.62 105.56 116.94 1.0845 +IC H131 C12 *C13 H133 1.0407 111.62 -125.41 115.89 1.1306 +IC C11 C12 C14 C15 1.3683 118.60 23.14 115.46 1.5309 +IC C15 C12 *C14 H141 1.5309 115.46 -121.05 111.64 1.1634 +IC C15 C12 *C14 H142 1.5309 115.46 120.98 110.16 1.1143 +IC C12 C14 C15 C16 1.5230 115.46 -49.13 109.56 1.5340 +IC C16 C14 *C15 H151 1.5340 109.56 121.30 103.64 1.0652 +IC C16 C14 *C15 H152 1.5340 109.56 -121.68 117.50 1.1269 +IC C17 C15 *C16 H161 1.5627 106.90 119.01 111.98 1.1082 +IC C17 C15 *C16 H162 1.5627 106.90 -118.27 114.51 1.1242 +IC C16 C11 *C17 C18 1.5627 111.91 117.06 109.86 1.6036 +IC C16 C11 *C17 C19 1.5627 111.91 -125.37 107.71 1.5933 +IC C11 C17 C18 H181 1.5273 109.86 -164.48 105.21 1.0701 +IC H181 C17 *C18 H182 1.0701 105.21 113.55 119.15 1.0744 +IC H181 C17 *C18 H183 1.0701 105.21 -120.08 114.03 1.1066 +IC C11 C17 C19 H191 1.5273 107.71 157.89 106.35 1.1223 +IC H191 C17 *C19 H192 1.1223 106.35 112.92 110.92 1.1415 +IC H191 C17 *C19 H193 1.1223 106.35 -116.85 111.31 1.1313 + +end + +read para card flex append +* retinal/retinol and related parameters +* + +ATOMS +MASS 425 CC1A 12.01100 ! alkene conjugation +MASS 426 CC1B 12.01100 ! alkene conjugation +MASS 427 CC2 12.01100 ! alkene conjugation +MASS 428 NS1 14.00700 ! N for deprotonated Schiff's base +MASS 429 NS2 14.00700 ! N for protonated Schiff's base + +BONDS +! +!atom types Kb b0 +! +!BTE2, 2-butene +HE1 CC1A 360.500 1.100 +HE1 CC1B 360.500 1.100 +HE2 CC2 365.000 1.100 +CC1A CC1A 440.000 1.340 +CC1B CC1B 440.000 1.340 +!13DB, Butadiene +CC1A CC2 500.000 1.342 +CC1B CC2 500.000 1.342 +CC1A CC1B 300.000 1.470 +!13DP, 1,3-Pentadiene +CC1B CT3 383.000 1.504 +!MECH +CC1A CT2 365.000 1.502 +CC1A CT 365.000 1.502 +CC1A CT3 383.000 1.504 +!TMCH/MECH +CT CT2 222.500 1.538 +CT CT3 222.500 1.538 +!PACP +CA NH1 305.000 1.414 +!PRAL +CC1A CD 300.000 1.4798 +CD HR1 330.000 1.110 +!PRAC +CC1A CC 440.000 1.489 +!CROT +CC1A C 440.000 1.489 +!SCH1, Schiff's base model compound 1, deprotonated +CT3 NS1 310.000 1.440 +NS1 CC1B 500.000 1.276 +!SCH2, Schiff's base model compound 2, protonated +HR1 CC1B 360.500 1.100 +CT3 NS2 300.000 1.453 +NS2 CC1B 470.000 1.283 +NS2 HC 455.000 1.000 +!SCK0, deprotonated Schiff's base, lysine retinal patch +CT2 NS1 310.000 1.440 +!SCK1, , Schiff's base, lysine retinal patch +CT2 NS2 300.000 1.453 + +ANGLES +! +!atom types Ktheta Theta0 Kub S0 +! +!BTE2, 2-butene +CC1A CC1A CT3 48.00 123.50 +HA2 CT2 CC1A 45.00 111.50 +HA3 CT3 CC1A 42.00 111.50 +HA3 CT3 CC1B 42.00 111.50 +HE1 CC1A CC1A 42.00 119.00 +HE1 CC1B CC1B 42.00 119.00 +HE1 CC1A CT3 42.00 117.50 +HE1 CC1B CT3 22.00 117.50 +!13DB, 1,3-Butadiene +HE1 CC1A CC2 42.00 118.00 +HE1 CC1B CC2 42.00 118.00 +HE2 CC2 CC1A 45.00 120.50 +HE2 CC2 CC1B 45.00 120.50 +HE1 CC1B CC1A 42.00 118.00 +HE1 CC1A CC1B 42.00 118.00 +CC1B CC1A CC2 48.00 123.50 +CC1A CC1B CC2 48.00 123.50 +HE2 CC2 HE2 19.00 119.00 +!13DP, Pentadiene +CC1A CC1B CC1B 48.00 123.50 +CC1B CC1B CT3 48.00 123.50 +!MECH +CC1A CT CT3 32.00 112.20 +CC1A CT CT2 32.00 112.20 +CC1A CT2 CT2 32.00 112.20 +CC1A CC1A CC1B 48.00 123.50 +CC1A CC1A CT 48.00 123.50 +CC1A CC1A CT2 48.00 123.50 +CC1B CC1A CT 48.00 123.50 +CT2 CC1A CT3 48.00 123.50 +!DMB1, 2-methyl-1,3-butadiene +CC2 CC1A CT3 48.00 123.50 +CC1B CC1A CT3 48.00 113.00 +!DMP1, 4-methyl-1,3-pentadiene +CT3 CC1B CT3 47.00 113.00 +!TMCH/MECH +CT2 CT CT3 58.35 113.50 11.16 2.561 +CT3 CT CT3 58.35 113.50 11.16 2.561 +CT CT2 CT2 58.35 113.50 11.16 2.561 +CT CT2 HA2 26.50 110.10 22.53 2.179 +CT CT3 HA3 33.43 110.10 22.53 2.179 +CT CC1A CT3 48.00 123.50 +!PACP +CA NH1 C 50.00 120.00 +H NH1 CA 34.00 117.00 +NH1 CA CA 40.00 120.00 35.00 2.4162 +!CROT +CT3 CC1A CT3 47.00 125.20 +CC1A CC1A C 48.00 123.50 +HE1 CC1A C 52.00 119.50 +O C CC1A 80.00 122.50 +NH1 C CC1A 80.00 116.50 +! PROL +HE1 CC1A CT2 40.00 116.00 +OH1 CT2 CC1A 75.70 110.10 +CT2 CC1A CC2 28.00 126.00 +!PRAL +CC2 CC1A CD 60.00 120.00 +CC1A CC1A CD 60.00 120.00 +HE1 CC1A CD 32.00 122.00 ! sum=242 +CC1A CD O 75.00 124.00 +CC1A CD HR1 15.00 115.00 +!PRAC +HE1 CC1A CC 52.00 119.50 ! +CC2 CC1A CC 40.00 119.00 35.00 2.5267 +CC1A CC OC 40.00 118.00 50.00 2.3880 +CC1A CC1A CC 48.00 123.50 ! +!SCH1, Schiff's base model compound 1, deprotonated +CT3 NS1 CC1B 67.00 111.00 +NS1 CC1B CT3 52.00 123.00 !sum=242.5 +NS1 CC1B HE1 38.00 119.50 ! +HA3 CT3 NS1 42.00 113.50 +!SCH2, Schiff's base model compound 2, protonated +CT3 NS2 CC1B 67.00 123.60 +CT3 NS2 HC 38.00 117.40 +CC1B NS2 HC 38.00 118.80 +NS2 CC1B CT3 40.00 125.60 +NS2 CC1B HR1 38.00 114.00 +CT3 CC1B HR1 42.00 120.40 +HA3 CT3 NS2 42.00 110.10 +!SCH3, Schiff's base model compound 3, protonated +NS2 CC1B CC1A 40.00 125.60 +HR1 CC1B CC1A 42.00 120.40 +!SCK0, deprotonated Schiff's base, lysine retinal patch +CT2 CT2 NS1 67.70 110.00 !from lysine +HA2 CT2 NS1 42.00 113.50 +CT2 NS1 CC1B 67.00 111.00 +NS1 CC1B CC1A 40.00 123.00 +!SCK1, protonated Schiff's base, lysine retinal patch +CT2 NS2 CC1B 67.00 123.60 +CT2 NS2 HC 38.00 117.40 +CT2 CT2 NS2 67.70 110.00 !from lysine +HA2 CT2 NS2 42.00 110.10 + +DIHEDRALS +! +!atom types Kchi n delta +! +!BTE2, 2-butene +HE1 CC1A CC1A HE1 5.2000 2 180.00 +CT3 CC1A CC1A HE1 5.2000 2 180.00 +CT3 CC1B CC1B HE1 5.2000 2 180.00 +CC1A CC1A CT3 HA3 0.3000 3 180.00 !Feller, 2008 +HE1 CC1A CT3 HA3 0.3000 3 0.00 +HE1 CC1B CT3 HA3 0.3000 3 0.00 +CT3 CC1A CC1A CT3 10.0000 2 180.00 !double bond +CT2 CC1A CC1A CT3 10.0000 2 180.00 !double bond +!13DB, 1,3-Butadiene +CC2 CC1A CC1B CC2 0.4000 1 180.00 ! +CC2 CC1A CC1B CC2 0.4000 2 180.00 ! +CC2 CC1A CC1B CC2 1.3000 3 0.00 ! +CC2 CC1A CC1B HE1 1.0000 2 180.00 ! +HE1 CC1A CC1B CC2 1.0000 2 180.00 ! +HE1 CC1A CC1B CC1B 1.0000 2 180.00 ! +HE2 CC2 CC1A CC1B 5.0000 2 180.00 !double bond +HE2 CC2 CC1B CC1A 5.0000 2 180.00 !double bond +HE1 CC1B CC1B CC1A 5.2000 2 180.00 !double bond +HE1 CC1B CC1A HE1 0.0000 2 180.00 ! +!HEP3, 1,3,5-heptatriene +CC1A CC1A CC1B CC2 0.5000 1 180.00 ! +CC1A CC1A CC1B CC2 2.0000 2 0.00 ! +CC1A CC1A CC1B CC2 1.0000 3 0.00 ! +CC1A CC1A CC1B CC1B 0.5000 1 180.00 ! +CC1A CC1A CC1B CC1B 2.0000 2 0.00 ! +CC1A CC1A CC1B CC1B 1.0000 3 0.00 ! +CC1A CC1B CC1B CC1A 0.5600 1 180.00 !double bond +CC1A CC1B CC1B CC1A 7.0000 2 180.00 !double bond +CC1B CC1A CC1A CC1B 0.5600 1 180.00 !double bond +CC1B CC1A CC1A CC1B 7.0000 2 180.00 !double bond +HE1 CC1A CC2 HE2 5.2000 2 180.00 !double bond +HE1 CC1B CC2 HE2 5.2000 2 180.00 !double bond +HE1 CC1A CC1A CC1B 1.0000 2 180.00 !double bond +!13DP, 1,3-Pentadiene +CC1B CC1B CT3 HA3 0.3000 3 0.00 +HE1 CC1B CC1B HE1 0.0000 2 180.00 ! +CC1A CC1B CC1B CT3 0.5600 1 180.00 !double bond +CC1A CC1B CC1B CT3 7.0000 2 180.00 !double bond +CC2 CC1A CC1B CC1B 0.6000 1 180.00 ! also in DMB1, DMP1, DMP2 +CC2 CC1A CC1B CC1B 0.5000 2 180.00 ! comprise values obtained +CC2 CC1A CC1B CC1B 1.0000 3 0.00 ! +!DMB1, 2-methyl-1,3-butadiene +CC1B CC1A CT3 HA3 0.3000 3 0.00 !Feller, 2008 +CT3 CC1A CC2 HE2 1.0000 2 180.00 +CT3 CC1A CC1B HE1 1.0000 2 180.00 +CT3 CC1A CC1B CC2 1.1000 1 180.00 !see DMP1 +CT3 CC1A CC1B CC2 0.7000 2 180.00 +!DMP1, 4-methyl-1,3-pentadiene, no additional terms versus 13DP +CT3 CC1B CT3 HA3 0.3000 3 0.00 +!DMP2, 2-methyl-1,3-pentadiene +CT3 CC1A CC1B CC1B 1.1000 1 180.00 !see DMP1 +CT3 CC1A CC1B CC1B 0.7000 2 180.00 +CC2 CC1A CT3 HA3 0.3000 3 0.00 +!TMCH +CT CC1A CC1A CT2 10.0000 2 180.00 ! double bond +CT CC1A CC1A CT3 10.0000 2 180.00 ! double bond +CC1A CC1A CT CT2 0.5000 2 0.00 ! c2-c1-c6=c5 +CC1A CC1A CT CT2 0.3000 3 0.00 ! c2-c1-c6=c5 +CC1A CC1A CT CT3 0.5000 2 0.00 ! c16/c17-c1-c6=c5 +CC1A CC1A CT CT3 0.4000 3 0.00 ! c16/c17-c1-c6=c5 +CC1A CC1A CT2 CT2 0.5000 2 0.00 ! c3-c4-c5=c6 +CC1A CC1A CT2 CT2 0.3000 3 0.00 ! c3-c4-c5=c6 +CT2 CT2 CC1A CT3 0.1900 3 0.00 ! c3-c4-c5-c18 +CT2 CT CC1A CT3 0.4000 3 0.00 ! c2-c1-c6-c7 +CT3 CT CC1A CT3 0.4000 3 0.00 ! c16/c17-c1-c6-c7 +CC1A CT2 CT2 CT2 0.1900 3 0.00 ! +CT2 CT2 CT CC1A 0.2000 3 0.00 ! +CT2 CT2 CT CT3 0.2000 3 0.00 ! +CT3 CC1A CT2 HA2 0.1900 3 0.00 +CC1A CT CT2 HA2 0.1900 3 0.00 +CT3 CT CT2 HA2 0.1900 3 0.00 +CC1A CT2 CT2 HA2 0.1900 3 0.00 +CT2 CC1A CT3 HA3 0.1600 3 0.00 +CT CC1A CT3 HA3 0.1600 3 0.00 +CT2 CT CT3 HA3 0.1600 3 0.00 +CC1A CT CT3 HA3 0.1600 3 0.00 +CT3 CT CT3 HA3 0.1600 3 0.00 +!MECH +CT CC1A CC1B CC2 0.9000 1 0.00 +CT CC1A CC1B CC2 2.1000 2 180.00 +CT CC1A CC1B CC2 0.2200 3 0.00 +CT CC1A CC1B CC2 0.2500 5 180.00 +CT CC1A CC1B CC2 0.1000 6 0.00 +CT CC1A CC1B CC1B 0.9000 1 0.00 +CT CC1A CC1B CC1B 2.1000 2 180.00 +CT CC1A CC1B CC1B 0.2200 3 0.00 +CT CC1A CC1B CC1B 0.2500 5 180.00 +CT CC1A CC1B CC1B 0.1000 6 0.00 +CC1B CC1A CT CT2 0.3000 3 0.00 +CC1B CC1A CT CT3 0.3000 3 0.00 +CC1B CC1A CC1A CT2 0.5600 1 180.00 ! double bond +CC1B CC1A CC1A CT2 7.0000 2 180.00 ! double bond +CC1B CC1A CC1A CT3 0.5600 1 180.00 ! double bond +CC1B CC1A CC1A CT3 7.0000 2 180.00 ! double bond +CT CC1A CC1B HE1 1.0000 2 180.00 +CC1A CC1A CC1B HE1 1.0000 2 180.00 +!PACP +O C NH1 CA 2.5000 2 180.00 ! +HP CA CA NH1 4.2000 2 180.00 ! +CA CA CA NH1 3.1000 2 180.00 ! +C NH1 CA CA 1.2000 2 180.00 ! +C NH1 CA CA 1.0000 3 180.00 ! +H NH1 CA CA 0.5000 2 180.00 ! +CA NH1 C CT3 2.5000 2 180.00 ! +!CROT +CT3 CC1A CT3 HA3 0.3000 3 0.00 ! +CC1B CC1A CC1A C 0.5600 1 180.00 !double bond +CC1B CC1A CC1A C 7.0000 2 180.00 !double bond +O C CC1A CC1A 0.7000 1 180.00 ! +O C CC1A CC1A 1.2000 2 180.00 ! +O C CC1A CC1A 0.1000 3 180.00 ! +O C CC1A CC1A 0.2000 4 0.00 ! +NH1 C CC1A CC1A 0.7000 1 0.00 ! +NH1 C CC1A CC1A 1.2000 2 180.00 ! +NH1 C CC1A CC1A 0.1000 3 0.00 ! +NH1 C CC1A CC1A 0.1500 4 0.00 ! +HE1 CC1A C NH1 0.3000 3 180.00 ! +HE1 CC1A C O 0.3000 3 180.00 ! +CC1A C NH1 H 2.5000 2 180.00 +CC1A C NH1 CT3 1.6000 1 0.00 +CC1A C NH1 CT3 2.5000 2 180.00 +CC1A C NH1 CA 1.6000 1 0.00 !FRET +CC1A C NH1 CA 2.5000 2 180.00 !FRET +C CC1A CC1A CT3 0.5600 1 180.00 !double bond +C CC1A CC1A CT3 7.0000 2 180.00 !double bond +!PROL +CC2 CC1A CT2 OH1 1.9000 1 180.00 +CC2 CC1A CT2 OH1 0.4000 2 180.00 +CC2 CC1A CT2 OH1 0.6000 3 180.00 +CC1A CC1A CT2 OH1 1.9000 1 180.00 +CC1A CC1A CT2 OH1 0.4000 2 180.00 +CC1A CC1A CT2 OH1 0.6000 3 180.00 +CC1A CT2 OH1 H 1.3000 1 0.00 +CC1A CT2 OH1 H 0.7000 2 0.00 +CC1A CT2 OH1 H 0.5000 3 0.00 +HE1 CC1A CT2 OH1 0.2000 3 0.00 +HE1 CC1A CT2 HA2 0.2000 3 0.00 +CC2 CC1A CT2 HA2 0.0300 3 0.00 +CC1A CC1A CT2 HA2 0.0300 3 0.00 +HE2 CC2 CC1A CT2 5.2000 2 180.00 +!PRAL +CC2 CC1A CD O 1.0000 2 180.00 ! +CC1A CC1A CD O 1.0000 2 180.00 ! +CC2 CC1A CD HR1 3.2000 2 180.00 +CC1A CC1A CD HR1 3.2000 2 180.00 +HE1 CC1A CD O 0.0000 2 180.00 +HE1 CC1A CD HR1 0.0000 2 180.00 +HE2 CC2 CC1A CD 3.2000 2 180.00 +CT3 CC1A CC1A CD 0.5600 1 180.00 ! double bond +CT3 CC1A CC1A CD 0.5000 2 180.00 ! db +CC1B CC1A CC1A CD 0.5600 1 180.00 ! db +CC1B CC1A CC1A CD 7.0000 2 180.00 ! db +!PRAC +CC2 CC1A CC OC 1.3000 2 180.00 +CC1A CC1A CC OC 1.3000 2 180.00 +HE2 CC2 CC1A CC 4.2000 2 180.00 +HE1 CC1A CC OC 0.0000 2 180.00 +CC1B CC1A CC1A CC 0.5600 1 180.00 !double bond +CC1B CC1A CC1A CC 7.0000 2 180.00 !double bond +CC CC1A CC1A CT3 0.5600 1 180.00 !double bond, rtac +CC CC1A CC1A CT3 7.0000 2 180.00 !double bond, rtac +!SCH1, Schiff's base model compound 1, deprotonated +CT3 NS1 CC1B HE1 8.5000 2 180.00 +CT3 NS1 CC1B CT3 12.0000 2 180.00 +NS1 CC1B CT3 HA3 0.1000 3 180.00 +CC1B NS1 CT3 HA3 0.3500 3 180.00 +!SCH2, Schiff's base model compound 2, protonated +CT3 NS2 CC1B HR1 8.5000 2 180.00 +CT3 NS2 CC1B CT3 7.0000 2 180.00 +NS2 CC1B CT3 HA3 0.1500 3 180.00 +HR1 CC1B CT3 HA3 0.1500 3 0.00 +CC1B NS2 CT3 HA3 0.1500 3 180.00 +HA3 CT3 NS2 HC 0.1100 3 0.00 +HC NS2 CC1B HR1 5.0000 2 180.00 +HC NS2 CC1B CT3 5.0000 2 180.00 +!SCH3, Schiff's base model compound 3, protonated +CT3 NS2 CC1B CC1A 7.0000 2 180.00 +HC NS2 CC1B CC1A 5.0000 2 180.00 +NS2 CC1B CC1A HE1 1.0000 2 180.00 +NS2 CC1B CC1A CC2 0.5000 1 0.00 !opt +NS2 CC1B CC1A CC2 2.2000 2 180.00 !opt +NS2 CC1B CC1A CC2 1.1000 3 0.00 !opt +NS2 CC1B CC1A CC2 0.6000 4 0.00 !opt +HR1 CC1B CC1A HE1 0.0000 2 180.00 +HR1 CC1B CC1A CC2 1.0000 2 180.00 +!SCK0, deprotonated Schiff's base, lysine retinal patch +CT2 CT2 NS1 CC1B 0.1000 3 0.00 +CT2 NS1 CC1B CC1A 12.0000 2 180.00 !from CT3 NS1 CC1B CT3 +CT2 NS1 CC1B HE1 8.5000 2 180.00 !from CT3 NS1 CC1B HE1 +HA2 CT2 NS1 CC1B 0.1000 3 0.00 +NS1 CC1B CC1A CC1A 0.5000 1 0.00 !from NS2 CC1B CC1A CC2 +NS1 CC1B CC1A CC1A 2.2000 2 180.00 !N=C-C=C dihedral not explicitly optimized +NS1 CC1B CC1A CC1A 1.1000 3 0.00 ! +NS1 CC1B CC1A CC1A 0.6000 4 0.00 ! +NS1 CC1B CC1A HE1 1.0000 2 180.00 +!SCK1, Schiff's base, lysine retinal patch +NS2 CC1B CC1A CC1A 0.5000 1 0.00 !from NS2 CC1B CC1A CC2 +NS2 CC1B CC1A CC1A 2.2000 2 180.00 ! +NS2 CC1B CC1A CC1A 1.1000 3 0.00 ! +NS2 CC1B CC1A CC1A 0.6000 4 0.00 ! +HR1 CC1B CC1A CC1A 1.0000 2 180.00 +CT2 CT2 NS2 CC1B 0.1000 3 0.00 +CT2 NS2 CC1B CC1A 7.0000 2 180.00 +CT2 NS2 CC1B HR1 8.5000 2 180.00 +HA2 CT2 NS2 CC1B 0.1000 3 0.00 +CT2 CT2 NS2 HC 0.1000 3 0.00 +HA2 CT2 NS2 HC 0.1000 3 0.00 + +IMPROPER +!atom types Kpsi psi0 +!PRAL +CD CC1A O HR1 14.0000 0 0.00 ! + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!Butadiene +CC1A 0.0 -0.0680 2.0900 ! +CC1B 0.0 -0.0680 2.0900 ! +CC2 0.0 -0.0640 2.0800 ! +!SCH1, SCH2 +NS1 0.000000 -0.200000 1.850000 !N for deprotonated Schiff's base +NS2 0.000000 -0.200000 1.850000 !N for protonated Schiff's base + +end + diff --git a/charmm/toppar/tamdfff/par_all22_prot_tadcmap.ahbb4.inp b/charmm/toppar/tamdfff/par_all22_prot_tadcmap.ahbb4.inp new file mode 100755 index 00000000..dbc75ff9 --- /dev/null +++ b/charmm/toppar/tamdfff/par_all22_prot_tadcmap.ahbb4.inp @@ -0,0 +1,4970 @@ +*>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< +*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< +*>>>>>> cmap replaced by tad correction (ahbb4) <<<<<<<<< +* + +! references +! +!PROTEINS +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. +! +!PHOSPHOTYROSINE +! +!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. +!Structural Characterization of the Phosphotyrosine Binding Region of a +!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics +!Simulation and Chemical Shift Calculations. Journal of the American +!Chemical Society, 1996, 118: 11265-11277. +! +!IONS (see lipid and nucleic acid topology and parameter files for +!additional ions +! +!ZINC +! +!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) +! + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +C C 600.000 1.3350 ! ALLOW ARO HEM + ! Heme vinyl substituent (KK, from propene (JCS)) +CA CA 305.000 1.3750 ! ALLOW ARO + ! benzene, JES 8/25/89 +CE1 CE1 440.000 1.3400 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CE2 500.000 1.3420 ! + ! for propene, yin/adm jr., 12/95 +CE1 CT2 365.000 1.5020 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CT3 383.000 1.5040 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE2 510.000 1.3300 ! + ! for ethene, yin/adm jr., 12/95 +CP1 C 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CC 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CD 200.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 222.500 1.5270 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPB C 450.000 1.3800 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPA 299.800 1.4432 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB CPB 340.700 1.3464 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH1 CPH1 410.000 1.3600 ! ALLOW ARO + ! histidine, adm jr., 6/27/90 +CPM CPA 360.000 1.3716 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT CA 305.000 1.3680 ! ALLOW ARO + ! adm jr., 12/30/91, for jwk +CPT CPT 360.000 1.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT1 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT1 222.500 1.5000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT2 CA 230.000 1.4900 ! ALLOW ALI ARO + ! phe,tyr, JES 8/25/89 +CT2 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT2 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT3 CA 230.000 1.4900 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +CT3 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CPB 230.000 1.4900 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT3 CS 190.000 1.5310 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CT3 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 222.500 1.5280 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT3 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CY CA 350.000 1.3650 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CY CPT 350.000 1.4400 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 230.000 1.5100 ! ALLOW ARO + !JWK Kb from alkane freq.. b0 from TRP crystal +FE CM 258.000 1.9000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +FE CPM 0.000 3.3814 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +H CD 330.000 1.1100 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA C 330.000 1.1000 ! ALLOW ARO HEM + ! Heme vinyl substituent (KK, from propene (JCS)) +HA CA 340.000 1.0830 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA CC 317.130 1.1000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +HA CP2 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CPM 367.600 1.0900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT1 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 322.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CY 330.000 1.0800 ! ALLOW ARO + ! JWK 05/14/91 new r0 from indole +HE1 CE1 360.500 1.1000 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 365.000 1.1000 ! + ! for ethene, yin/adm jr., 12/95 +HB CP1 330.000 1.0800 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HP CA 340.000 1.0800 ! ALLOW ARO + ! phe,tyr JES 8/25/89 +HP CY 350.000 1.0800 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HR1 CPH1 375.000 1.0830 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 340.000 1.0900 ! ALLOW ARO + ! his, adm jr., 6/28/29 +HR2 CPH2 333.000 1.0700 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR3 CPH1 365.000 1.0830 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HT HT 0.000 1.5139 ! ALLOW WAT + ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) +N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 320.000 1.4340 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 320.000 1.4550 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO + ! 403.0->463.0, 1.305->1.365 guanidinium (KK) +NC2 CT2 261.000 1.4900 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 261.000 1.4900 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NC2 HC 455.000 1.0000 ! ALLOW POL + ! 405.0->455.0 GUANIDINIUM (KK) +NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO + ! (DS) +NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +NH2 CT2 240.000 1.4550 + ! from NH2 CT3, neutral glycine, adm jr. +NH2 CT3 240.000 1.4550 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH2 H 480.000 1.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 HC 460.000 1.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT3 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 HC 403.000 1.0400 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 320.000 1.4850 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 320.000 1.5020 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP HC 460.000 1.0060 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NPH CPA 377.200 1.3757 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE 270.200 1.9580 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH2 400.000 1.3600 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 H 466.000 1.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 400.000 1.3200 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 FE 65.000 2.2000 ! ALLOW HEM + ! Heme (6-liganded): His ligand (KK 05/13/91) +NR3 CPH1 380.000 1.3700 ! ALLOW ARO + ! his, adm jr., 6/28/90 +NR3 CPH2 380.000 1.3200 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 H 453.000 1.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA 270.000 1.3700 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT 270.000 1.3750 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY H 465.000 0.9760 ! ALLOW ARO + ! indole JWK 08/28/89 +O C 620.000 1.2300 ! ALLOW PEP POL ARO + ! Peptide geometry, condensed phase (LK) +O CC 650.000 1.2300 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +OB CC 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid vibrations and geom. +OB CD 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 8/27/91, phenoxide +OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 7/23/91, acetic acid +OC CT2 450.000 1.3300 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 450.000 1.3300 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA 334.300 1.4110 ! ALLOW ARO ALC + ! MeOH, EMB 10/10/89, +OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC + ! adm jr. 5/02/91, acetic acid pure solvent +OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 H 545.000 0.9600 ! ALLOW ALC ARO + ! EMB 11/21/89 methanol vib fit +OM CM 1115.000 1.1280 ! ALLOW HEM + ! Heme (6-liganded): CO ligand (KK 05/13/91) +OM FE 250.000 1.8000 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OM OM 600.000 1.2300 ! ALLOW HEM + ! Heme (6-liganded): O2 ligand (KK 05/13/91) +OS CD 150.000 1.3340 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +OS CT3 340.000 1.4300 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OT HT 450.000 0.9572 ! ALLOW WAT + ! FROM TIPS3P GEOM +S CT2 198.000 1.8180 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S CT3 240.000 1.8160 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S HS 275.000 1.3250 ! ALLOW SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +S ZN 275.000 2.350 ! artifical zinc-sulfur bond + +SM CT2 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM CT3 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SM SM 173.000 2.0290 ! ALLOW SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +SS CS 205.000 1.8360 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO + ! JES 8/25/89 +CE1 CE1 CT3 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CT2 CT3 32.00 112.20 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT2 48.00 126.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT3 47.00 125.20 ! + ! for propene, yin/adm jr., 12/95 +CP1 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 C 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 100.000 114.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 100.000 111.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPA CPB C 70.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPA CPM CPA 94.200 125.1200 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPA NPH CPA 139.300 103.9000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB C C 70.000 121.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB C 70.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CPB CPB CPA 30.800 106.5100 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPM CPA CPB 61.600 124.0700 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT CA CA 60.000 118.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CPT CA 60.000 122.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CPT NY CA 110.000 108.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! from CT2 CT1 C, for lactams, adm jr. +CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CY CA 45.800 129.4000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 CY CPT 45.800 124.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! 107.5->120.0 to make planar Arg (KK) +CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/09/92, for ALA cter +CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! methylguanidinium, adm jr., 3/26/92 +CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +CY CT2 CT1 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +CY CT2 CT3 58.350 114.0000 ! ALLOW ARO + ! from TRP crystal, JWK +FE NPH CPA 96.150 128.0500 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO + ! his, adm jr. 8/13/90 acetamide geometry and vibrations +H NH2 H 23.000 120.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NY CA 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT 28.000 126.0000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO + ! JES 8/25/89 phenol +H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +HA C C 50.000 120.5000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK from propene (JCS)) +HA C CPB 50.000 120.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK from propene (JCS)) +HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO + ! trp, adm jr., 10/02/89 +HA CA CPT 41.000 122.0000 ! ALLOW ARO + !adm jr., 5/08/91, indole CCDB structure search +HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CPM CPA 12.700 117.4400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CPM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd + ! based on HA CT2 HA +HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT2 CE1 45.00 111.50 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HA CT2 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT2 CY 33.430 109.5000 ! ALLOW ARO + ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA +HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA CT3 CE1 42.00 111.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HA CT3 CPB 50.000 109.5000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HE1 CE1 CE1 52.00 119.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HE1 CE1 CE2 42.00 118.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 40.00 116.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HE1 CE1 CT3 22.00 117.00 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE1 45.00 120.50 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE2 55.50 120.50 ! + ! for ethene, yin/adm jr., 12/95 +HE2 CE2 HE2 19.00 119.00 ! + ! for propene, yin/adm jr., 12/95 +HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB CT1 CT1 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CT2 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 CT3 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB CT2 HB 36.000 115.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO + ! 35.3->49.0 GUANIDINIUM (KK) +HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI + ! 107.5->120.0 to make planar Arg (KK) +HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI + ! methylguanidinium, adm jr., 3/26/92 +HC NC2 HC 25.000 120.0000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH2 CT2 50.000 111.0000 ! ALLOW POL + ! from HC NH2 CT3, neutral glycine, adm jr. +HC NH2 CT3 50.000 111.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +HC NH2 HC 39.000 106.5000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 HC 44.000 109.5000 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP HC 51.000 107.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +ZN S CT2 1.00 109.5000 ! artificial C-S-Zn angle + +HT OT HT 55.000 104.5200 ! ALLOW WAT + ! TIP3P GEOMETRY, ADM JR. +N C CP1 20.000 112.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 C 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CC 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CP2 70.000 110.8000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 CP2 70.000 110.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO + ! changed from 60.0/120.3 for guanidinium (KK) +NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/20/92, for asn,asp,gln,glu and cters +NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT1 CT2, for lactams, adm jr. +NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT3 HA, for lactams, adm jr. +NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! NMA crystal (JCS) +NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +NH2 CT2 HB 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral glycine, adm jr. +NH2 CT2 CD 52.000 108.0000 + !from CT2 CT2 CD, neutral glycine, adm jr. +NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP + ! new aliphatics, adm jr., 2/3/92 +NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! alanine (JCS) +NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + ! alanine (JCS) +NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP + ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) +NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 C 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NPH CPA CPB 122.000 111.5400 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM 88.000 124.3900 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH FE CM 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NPH FE CPM 0.000 45.0000 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +NPH FE NPH 14.390 90.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 FE CM 50.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR2 FE NPH 50.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO + ! JWK 05/14/91 new theta0 and r0UB from indole +NY CPT CA 160.000 130.6000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +NY CPT CPT 110.000 107.4000 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +O C CP1 80.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C H 50.000 121.7000 ! ALLOW PEP POL ARO + ! acetaldehyde (JCS) +O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC HA 44.000 122.0000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO + ! adm jr. 4/10/91, acetamide update +OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA CA 40.000 120.0000 ! ALLOW POL ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CT2 CT3 65.000 122.0000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT2 HA 65.000 118.3000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 HA 65.000 118.3000 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC + ! PARALLH19 WITH [122.3] (JES) +OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OM CM FE 35.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM FE NPH 5.000 90.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OM OM FE 0.000 180.0000 ! ALLOW HEM + ! Heme (6-liganded): ligand links (KK 05/13/91) +OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 55.000 118.0000 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 +CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c +CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c +CE1 CE1 CT3 HA 0.0300 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 CT3 0.5000 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 HA 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT3 HA 0.0500 3 180.00 ! + ! for propene, yin/adm jr., 12/95 +CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 +CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 +CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! from CT2 CT1 NH1 C, for lactams, adm jr. +CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK +CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + !JWK +CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +CT3 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92, butane trans/gauche +CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO + ! from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION + ! DTN 8/24/90 +CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from H NH1 CT2 CT3, for lactams, adm jr. +H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/20/89 +H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NY CA CY 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC + ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO + ! adm jr., 10/02/89 +HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO + ! ADM JR., 10/02/89 +HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! TRP (JES) +HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK +HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK +HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CA NY H 1.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL + ! adm jr. 4/10/91, acetamide update +HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO + ! JWK +HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +HE1 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 HA 0.8700 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT2 CT3 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT3 HA 0.3400 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE2 CE2 CE1 CT2 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NH2 CT2 HB 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CD 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO + !adm jr., 12/30/91, for jwk +HP CA NY H 0.4000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, his +HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, YES, 0.0 +HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +ZN S CT2 CT1 0.0001 1 0.00 ! ALLOW ALI SUL ION +ZN S CT2 HA 0.0001 3 0.00 ! ALLOW ALI SUL ION + +HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from NH1 C CT1 CT2, for lactams, adm jr. +NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO + ! adm jr. 3/24/92, for PRES GLYP +NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO + ! JWK +NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO + ! JWK 09/05/89 +NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO + ! JWK 05/14/91 fit to indole +O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP + ! from O C CT1 CT2, for lactams, adm jr. +O C CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT3 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 H 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +X C C X 4.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO + ! 9.0->2.25 GUANIDINIUM (KK) +X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier +X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CE1 CE1 X 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +X CE2 CE2 X 4.9000 2 180.00 ! + ! for ethene, yin/adm jr., 12/95 +X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP + ! changed to 0.0 RLD 5/19/92 +X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB C X 3.0000 2 180.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) +X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO + ! JWK indole 05/14/91 +X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI + ! rotation barrier in Ethane (SF) +X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL + ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 +X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X FE CM X 0.0500 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X FE NPH X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): for "ic para" only (KK 05/13/91) +X FE OM X 0.0000 4 0.00 ! ALLOW HEM + ! Heme (6-liganded): ligands (KK 05/13/91) +X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM + ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB X X C 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): substituents (KK 05/13/91) +HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK, from propene (JCS)) +HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO + ! Heme (6-liganded): substituents (KK 05/13/91) +HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO + ! Heme vinyl substituent (KK, from propene (JCS)) +HE2 HE2 CE2 CE2 3.0 0 0.00 ! + ! for ethene, yin/adm jr., 12/95 +HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO + ! 5.75->40.0 GUANIDINIUM (KK) +NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +NH2 X X H 4.0000 0 0.0000 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO + ! his, adm jr., 7/05/90 +NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO + !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf. +O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! adm jr., 5/13/91, formamide geometry and vibrations +O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 +O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO + ! NMA Vibrational Modes (LK) +OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL + ! adm jr., 10/17/90, acetic acid vibrations +OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) +CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION + ! 90.0->96.0 acetate, single impr (KK) + + +CMAP + +! alanine map +! new map computed as: CMD - TAD, cdie, soft=0.2, ahbb4 + +C CT1 NH1 C NH1 C CT1 NH1 72 +! new map computed as: CMAP + CMD - TAD + + -0.4290 -0.1667 0.1046 0.3321 0.4786 ! -180 + 0.5634 0.6210 0.6846 0.7880 0.9649 + 1.2352 1.5590 1.8850 2.1650 2.3769 + 2.4974 2.5188 2.4698 2.3934 2.3153 + 2.2272 2.1098 1.9310 1.6229 1.1069 + 0.3784 -0.2484 -0.3875 0.1705 0.9236 + 1.1931 0.4917 -0.8917 -2.4695 -3.8386 + -4.9144 -5.7096 -6.2259 -6.4885 -6.5434 + -6.4577 -6.2412 -5.8939 -5.4250 -4.8927 + -4.3636 -3.8983 -3.5452 -3.3516 -3.3359 + -3.4214 -3.5032 -3.5043 -3.4547 -3.4091 + -3.4071 -3.4229 -3.4191 -3.3622 -3.2659 + -3.1514 -3.0377 -2.9343 -2.8444 -2.7642 + -2.6380 -2.4050 -2.0288 -1.5838 -1.1747 + -0.8760 -0.6498 + + -0.2829 -0.0375 0.2310 0.4525 0.5765 ! -175 + 0.6337 0.6733 0.7396 0.8516 1.0252 + 1.2652 1.5461 1.8349 2.1001 2.3204 + 2.4768 2.5528 2.5625 2.5268 2.4592 + 2.3491 2.1757 1.9208 1.5547 1.0442 + 0.4130 -0.0741 -0.0987 0.4902 1.1873 + 1.3158 0.4108 -1.1569 -2.8226 -4.1255 + -5.0622 -5.7236 -6.1412 -6.3183 -6.2961 + -6.1297 -5.8439 -5.4565 -4.9849 -4.4830 + -4.0064 -3.6050 -3.3071 -3.1381 -3.1023 + -3.1387 -3.1668 -3.1293 -3.0573 -3.0057 + -3.0077 -3.0360 -3.0412 -2.9890 -2.8902 + -2.7706 -2.6494 -2.5342 -2.4272 -2.3216 + -2.1790 -1.9449 -1.5945 -1.1985 -0.8527 + -0.6230 -0.4597 + + -0.1449 0.0797 0.3216 0.5196 0.6310 ! -170 + 0.6846 0.7289 0.8028 0.9173 1.0760 + 1.2780 1.5096 1.7496 1.9832 2.1976 + 2.3812 2.5211 2.6110 2.6409 2.6029 + 2.4777 2.2401 1.8831 1.4446 0.9790 + 0.5537 0.2876 0.3198 0.6802 1.0032 + 0.8179 -0.1830 -1.6744 -3.1827 -4.3414 + -5.1697 -5.7317 -6.0475 -6.1288 -6.0112 + -5.7475 -5.3858 -4.9676 -4.5273 -4.1014 + -3.7198 -3.4055 -3.1644 -2.9958 -2.8904 + -2.8233 -2.7624 -2.6849 -2.6123 -2.5747 + -2.5925 -2.6318 -2.6493 -2.6125 -2.5311 + -2.4257 -2.3124 -2.1916 -2.0549 -1.8969 + -1.7053 -1.4673 -1.1813 -0.8868 -0.6336 + -0.4545 -0.3104 + + -0.0109 0.1719 0.3599 0.5191 0.6267 ! -165 + 0.7008 0.7711 0.8620 0.9794 1.1273 + 1.3044 1.5025 1.7110 1.9193 2.1223 + 2.3156 2.4921 2.6328 2.7138 2.7094 + 2.5825 2.2931 1.8353 1.3351 0.9455 + 0.7862 0.7962 0.8744 0.9068 0.7275 + 0.1577 -0.8964 -2.2066 -3.4734 -4.4744 + -5.2037 -5.6785 -5.9084 -5.9095 -5.7223 + -5.3943 -4.9848 -4.5540 -4.1414 -3.7690 + -3.4512 -3.1912 -2.9812 -2.8003 -2.6385 + -2.4922 -2.3622 -2.2553 -2.1836 -2.1608 + -2.1950 -2.2511 -2.2843 -2.2586 -2.1867 + -2.0918 -1.9884 -1.8681 -1.7111 -1.5073 + -1.2770 -1.0392 -0.8183 -0.6205 -0.4491 + -0.3033 -0.1650 + + 0.1185 0.2301 0.3388 0.4483 0.5601 ! -160 + 0.6745 0.7903 0.9084 1.0362 1.1865 + 1.3652 1.5646 1.7724 1.9789 2.1755 + 2.3576 2.5184 2.6457 2.7335 2.7477 + 2.6363 2.3258 1.7996 1.2622 0.9723 + 1.0924 1.3908 1.5367 1.2735 0.6256 + -0.3064 -1.4190 -2.5746 -3.6427 -4.5051 + -5.1371 -5.5312 -5.6977 -5.6613 -5.4553 + -5.1290 -4.7271 -4.2999 -3.8822 -3.4976 + -3.1620 -2.8853 -2.6614 -2.4713 -2.3038 + -2.1548 -2.0204 -1.9031 -1.8221 -1.8004 + -1.8502 -1.9274 -1.9732 -1.9434 -1.8590 + -1.7539 -1.6513 -1.5364 -1.3827 -1.1729 + -0.9349 -0.7098 -0.5257 -0.3762 -0.2455 + -0.1199 0.0017 + + 0.2290 0.2628 0.2944 0.3594 0.4814 ! -155 + 0.6402 0.8040 0.9505 1.0936 1.2552 + 1.4480 1.6660 1.8911 2.1090 2.3066 + 2.4666 2.5815 2.6597 2.7143 2.7398 + 2.6526 2.3475 1.7970 1.2593 1.0683 + 1.4140 1.9377 2.1349 1.6417 0.6331 + -0.5805 -1.7428 -2.7926 -3.7114 -4.4515 + -4.9855 -5.3061 -5.4268 -5.3735 -5.1843 + -4.8974 -4.5389 -4.1324 -3.6954 -3.2619 + -2.8658 -2.5281 -2.2696 -2.0698 -1.9262 + -1.8167 -1.7151 -1.6044 -1.5158 -1.4880 + -1.5468 -1.6370 -1.6888 -1.6489 -1.5475 + -1.4266 -1.3213 -1.2144 -1.0749 -0.8838 + -0.6669 -0.4594 -0.2897 -0.1529 -0.0349 + 0.0732 0.1648 + + 0.3023 0.2833 0.2710 0.3172 0.4512 ! -150 + 0.6403 0.8374 1.0067 1.1611 1.3292 + 1.5312 1.7584 1.9969 2.2271 2.4277 + 2.5734 2.6492 2.6787 2.6984 2.7170 + 2.6454 2.3694 1.8500 1.3572 1.2389 + 1.6857 2.2839 2.4633 1.8133 0.5986 + -0.7635 -1.9385 -2.9093 -3.7096 -4.3415 + -4.7849 -5.0353 -5.1103 -5.0410 -4.8648 + -4.6177 -4.3082 -3.9324 -3.4924 -3.0291 + -2.5881 -2.2105 -1.9099 -1.6932 -1.5603 + -1.4781 -1.4064 -1.3158 -1.2361 -1.2119 + -1.2637 -1.3472 -1.3921 -1.3523 -1.2522 + -1.1353 -1.0310 -0.9283 -0.8001 -0.6308 + -0.4389 -0.2492 -0.0865 0.0472 0.1541 + 0.2361 0.2871 + + 0.3283 0.3040 0.3061 0.3675 0.5124 ! -145 + 0.7082 0.9091 1.0845 1.2439 1.4119 + 1.6028 1.8150 2.0435 2.2760 2.4823 + 2.6294 2.6958 2.7080 2.7049 2.7041 + 2.6333 2.4000 1.9719 1.5711 1.4830 + 1.8602 2.3279 2.3757 1.6504 0.4096 + -0.9358 -2.0609 -2.9552 -3.6633 -4.2034 + -4.5664 -4.7488 -4.7658 -4.6579 -4.4701 + -4.2366 -3.9554 -3.6170 -3.2103 -2.7724 + -2.3459 -1.9698 -1.6570 -1.4173 -1.2513 + -1.1431 -1.0674 -1.0060 -0.9660 -0.9598 + -0.9910 -1.0356 -1.0572 -1.0346 -0.9738 + -0.8914 -0.8011 -0.6965 -0.5663 -0.4048 + -0.2256 -0.0515 0.0999 0.2192 0.2995 + 0.3390 0.3441 + + 0.3315 0.3364 0.3857 0.4859 0.6416 ! -140 + 0.8269 1.0142 1.1812 1.3389 1.4998 + 1.6781 1.8742 2.0865 2.3070 2.5082 + 2.6564 2.7273 2.7420 2.7273 2.7004 + 2.6218 2.4419 2.1461 1.8707 1.7860 + 1.9778 2.1747 2.0177 1.2612 0.1129 + -1.1057 -2.1321 -2.9466 -3.5783 -4.0417 + -4.3305 -4.4482 -4.4094 -4.2587 -4.0451 + -3.8079 -3.5437 -3.2394 -2.8828 -2.5011 + -2.1231 -1.7756 -1.4684 -1.2039 -0.9910 + -0.8334 -0.7401 -0.7122 -0.7253 -0.7459 + -0.7500 -0.7407 -0.7311 -0.7269 -0.7163 + -0.6839 -0.6149 -0.5099 -0.3740 -0.2128 + -0.0433 0.1172 0.2533 0.3490 0.3982 + 0.3929 0.3595 + + 0.3490 0.3909 0.4900 0.6304 0.7965 ! -135 + 0.9715 1.1414 1.2931 1.4414 1.6030 + 1.7899 1.9942 2.2025 2.3995 2.5702 + 2.6954 2.7631 2.7775 2.7548 2.6988 + 2.6138 2.4950 2.3507 2.2138 2.1275 + 2.0977 1.9806 1.5951 0.8220 -0.1955 + -1.2516 -2.1620 -2.8977 -3.4599 -3.8513 + -4.0702 -4.1311 -4.0527 -3.8782 -3.6543 + -3.4159 -3.1627 -2.8824 -2.5671 -2.2301 + -1.8910 -1.5659 -1.2639 -0.9889 -0.7492 + -0.5700 -0.4782 -0.4851 -0.5436 -0.5868 + -0.5674 -0.5131 -0.4709 -0.4700 -0.4902 + -0.4892 -0.4409 -0.3480 -0.2203 -0.0698 + 0.0866 0.2318 0.3485 0.4259 0.4500 + 0.4195 0.3708 + + 0.4072 0.4765 0.6030 0.7666 0.9454 ! -130 + 1.1236 1.2829 1.4161 1.5503 1.7218 + 1.9525 2.2075 2.4377 2.6055 2.7135 + 2.7788 2.8131 2.8136 2.7749 2.6979 + 2.6139 2.5624 2.5615 2.5574 2.4797 + 2.2601 1.8675 1.2776 0.4825 -0.4327 + -1.3476 -2.1536 -2.8141 -3.3063 -3.6239 + -3.7777 -3.7927 -3.7024 -3.5389 -3.3357 + -3.1147 -2.8740 -2.6040 -2.2976 -1.9668 + -1.6292 -1.3014 -0.9962 -0.7284 -0.5145 + -0.3715 -0.3179 -0.3575 -0.4363 -0.4865 + -0.4588 -0.3849 -0.3160 -0.2905 -0.2920 + -0.2883 -0.2579 -0.1920 -0.0975 0.0238 + 0.1547 0.2788 0.3776 0.4424 0.4622 + 0.4398 0.4051 + + 0.4961 0.5820 0.7160 0.8878 1.0821 ! -125 + 1.2738 1.4339 1.5487 1.6651 1.8439 + 2.1220 2.4341 2.6947 2.8371 2.8845 + 2.8838 2.8733 2.8476 2.7896 2.6993 + 2.6256 2.6324 2.7472 2.8483 2.7775 + 2.4183 1.8177 1.0675 0.2462 -0.5917 + -1.3942 -2.1065 -2.6891 -3.1137 -3.3631 + -3.4637 -3.4526 -3.3716 -3.2384 -3.0648 + -2.8624 -2.6271 -2.3541 -2.0414 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alanine for now + +C CP1 N C NH1 C CP1 N 24 + +-0.37321 0.26870 0.47126 0.75097 1.62101 !-180 +2.19543 2.06444 1.76479 0.75587 -0.71347 +0.97613 -2.47552 -5.45565 -5.89645 -5.30585 +-3.97563 -3.08858 -3.28420 -3.17712 -3.14606 +-2.83535 -2.51044 -2.10804 -0.98225 + +-0.10229 0.37709 0.57702 0.87229 1.39899 !-165 +1.96163 2.33384 1.90407 0.56146 0.51840 +-0.11632 -3.57544 -5.28448 -5.16031 -4.19601 +-3.27621 -2.71534 -2.30620 -2.10178 -2.21032 +-2.00881 -1.63710 -1.00336 -0.47687 + +0.16519 0.15621 0.62435 1.04720 1.65391 !-150 +2.19141 2.29642 1.96045 0.82493 2.03829 +-1.15151 -3.74861 -4.65828 -4.53185 -3.79637 +-2.57209 -1.72725 -1.46141 -1.28291 -1.47912 +-1.23934 -0.91806 -0.37546 0.02364 + +0.26400 0.52137 0.97744 1.37795 1.92947 !-135 +2.39341 2.43581 2.16297 1.76150 1.19009 +-1.51861 -3.30890 -3.77610 -3.40534 -2.76844 +-1.83603 -0.95795 -0.47821 -0.63276 -0.56588 +-0.62117 -0.36232 0.10683 0.35296 + +0.57395 0.95916 1.50899 1.84110 2.69896 !-120 +2.80933 2.61430 2.48172 2.69466 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-3.59265 -4.25857 +-4.23741 -3.73516 -3.68858 -3.00991 -2.11294 +-1.45540 -0.92549 -1.12184 -1.56190 -2.75137 +-4.09486 -5.20753 -6.12853 -6.61303 + +-5.71625 -4.43406 -2.78860 -0.97440 -0.72920 +-0.90494 -1.83354 -3.01770 -3.31345 -3.33601 +-3.18164 -3.59472 -1.23137 -0.60379 0.12881 +-1.22261 -0.90915 -0.83770 -1.34682 -3.04088 +-4.73111 -5.84486 -6.42846 -6.42488 + +-3.99111 -2.04600 0.08255 -2.67611 -2.82850 +-2.59664 -2.84333 -3.01148 -2.31264 -2.40598 +-3.08621 -1.16462 -1.23166 -0.87190 -0.34898 +-1.73590 -0.91415 -0.48452 -1.81804 -3.60255 +-5.33032 -5.99227 -5.58808 -5.40836 + +-1.14706 -3.31773 -4.30510 -4.61520 -4.53378 +-3.62295 -2.83280 -1.87281 -1.14430 -1.99407 +-0.74198 -1.11501 -1.22925 -1.10368 -0.74243 +-1.97397 -1.07002 -1.80222 -2.71277 -3.62413 +-4.53710 -4.61997 -4.31089 -3.31829 + +-3.99771 -5.40836 -5.58808 -5.99227 -5.33032 +-3.60255 -1.81804 -0.48452 -0.91415 -1.73590 +-0.34898 -0.87190 -1.23166 -1.16462 -3.08621 +-2.40598 -2.31264 -3.01148 -2.84333 -2.59664 +-2.82850 -2.67611 0.08255 -2.04600 + +-5.71085 -6.42488 -6.42846 -5.84486 -4.73111 +-3.04088 -1.34682 -0.83770 -0.90915 -1.22261 +0.12881 -0.60379 -1.23137 -3.59472 -3.18164 +-3.33601 -3.31345 -3.01770 -1.83354 -0.90494 +-0.72920 -0.97440 -2.78860 -4.43406 + +-6.75494 -6.61303 -6.12853 -5.20753 -4.09486 +-2.75137 -1.56190 -1.12184 -0.92549 -1.45540 +-2.11294 -3.00991 -3.68858 -3.73516 -4.23741 +-4.25857 -3.59265 -2.03717 -0.53670 -0.52666 +-1.70871 -2.71409 -4.36219 -5.85003 + +-6.18807 -5.56581 -4.82104 -4.00810 -2.94814 +-2.43136 -1.33731 -1.00293 -0.87756 -1.45399 +-2.49543 -3.37414 -3.79628 -4.36626 -4.69334 +-4.28783 -2.96291 -1.11979 -1.09485 -2.06752 +-2.68323 -4.00082 -4.87894 -5.45608 + +-4.98608 -3.97060 -3.34795 -2.65940 -1.89251 +-1.60744 -1.31273 -1.26993 -1.25662 -1.85941 +-2.78666 -3.37541 -3.90850 -4.43617 -4.49214 +-3.71553 -2.24551 -1.10550 -1.66416 -2.34536 +-3.22863 -3.89255 -4.48531 -4.99521 + +-3.87919 -2.93999 -2.42097 -1.79448 -1.14135 +-1.02068 -1.06555 -0.97134 -1.13909 -2.09851 +-2.56439 -3.25990 -4.04689 -4.68143 -4.18116 +-3.10817 -0.97186 -1.45204 -1.97525 -2.40646 +-3.04085 -3.61137 -3.90211 -3.71361 + +-2.79328 -2.41268 -1.95997 -1.40150 -0.95019 +-0.54054 -0.46732 -0.63381 -0.89314 -1.39549 +-2.27676 -3.45519 -4.46285 -4.74821 -3.93280 +-2.56768 -1.19539 -1.68185 -1.95149 -2.26668 +-2.62663 -3.01371 -3.17815 -3.07957 + +-2.33019 -1.91485 -1.60180 -1.06833 -0.66122 +-0.29795 -0.17383 -0.15890 -0.55391 -1.45532 +-2.69443 -4.01519 -4.77582 -4.88321 -4.11439 +-0.97557 -1.35817 -1.28922 -1.43554 -1.70586 +-1.97007 -2.36407 -2.59614 -2.59379 + +-1.79612 -1.46553 -1.26745 -0.88061 -0.28837 +-0.05565 0.10091 -0.20756 -0.75895 -1.71806 +-3.02071 -4.33589 -4.97231 0.33801 -1.06257 +-1.33736 -1.02063 -0.85159 -0.80135 -0.88688 +-1.56716 -1.80372 -2.14302 -2.11775 + +-1.26361 -0.71076 -0.79498 -0.56333 -0.33905 +-0.09282 0.03316 0.00049 -0.62899 -1.66416 +-3.02563 -4.34918 0.75340 -1.54650 -2.16544 +-1.62626 -0.88708 -0.29067 -0.05422 -1.64254 +-1.11978 -1.65677 -1.66590 -1.48243 + +-0.68466 -0.47766 -0.34875 -0.46250 -0.27189 +-0.00043 0.19671 0.18086 -0.41068 -1.81012 +-3.17564 1.32269 -1.63602 -3.15335 -2.78032 +-1.71570 -0.53491 0.25810 0.32918 -0.12616 +-0.94026 -1.31924 -0.99085 -0.89670 + + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO + ! NMA pure solvent, adm jr., 3/3/93 +CA 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! benzene (JES) +CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO + ! adm jr. 3/3/92, acetic acid heat of solvation +CD 0.000000 -0.070000 2.000000 ! ALLOW POL + ! adm jr. 3/19/92, acetate a.i. and dH of solvation +CE1 0.000000 -0.068000 2.090000 ! + ! for propene, yin/adm jr., 12/95 +CE2 0.000000 -0.064000 2.080000 ! + ! for ethene, yin/adm jr., 12/95 +CM 0.000000 -0.110000 2.100000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand carbon (KK 05/13/91) +CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO + ! benzene (JES) +CS 0.000000 -0.110000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! isobutane pure solvent properties, adm jr, 2/3/92 +CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! propane pure solvent properties, adm jr, 2/3/92 +CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +CY 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! TRP, JWK 08/29/89 +! carbon wildcards, following atom order is essential for accurate results +!C* 0.000000 -0.070000 2.000000 +!CP% 0.000000 -0.090000 1.800000 +!C%1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 +!C%2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 +!C%3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 +!CPH+ 0.000000 -0.050000 1.800000 +!C 0.000000 -0.110000 2.000000 +!CA 0.000000 -0.070000 1.992400 +!CE1 0.000000 -0.068000 2.090000 +!CE2 0.000000 -0.064000 2.080000 +!CM 0.000000 -0.110000 2.100000 +!CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI +!CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 +!CS 0.000000 -0.110000 2.200000 +!CY 0.000000 -0.070000 1.992400 + +H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 +HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HE1 0.000000 -0.031000 1.250000 ! + ! for propene, yin/adm jr., 12/95 +HE2 0.000000 -0.026000 1.260000 ! + ! for ethene, yin/adm jr., 12/95 +HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HC 0.000000 -0.046000 0.224500 ! ALLOW POL + ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 +HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO + ! JES 8/25/89 values from Jorgensen fit to hydration energy +HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS 0.000000 -0.100000 0.450000 ! ALLOW SUL + ! methanethiol pure solvent, adm jr., 6/22/92 +HT 0.000000 -0.046000 0.224500 ! ALLOW WAT + !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete +! hydrogen wildcards +!H* 0.000000 -0.046000 0.224500 +!HA 0.000000 -0.022000 1.320000 +!HE1 0.000000 -0.031000 1.250000 +!HE2 0.000000 -0.026000 1.260000 +!HB 0.000000 -0.022000 1.320000 +!HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 +!HR1 0.000000 -0.046000 0.900000 +!HR2 0.000000 -0.046000 0.700000 +!HR3 0.000000 -0.007800 1.468000 +!HS 0.000000 -0.100000 0.450000 +! +N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! JG 8/27/89; note: NH1 in ARG was changed to NC2. +NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +NH2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NH3 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NP 0.000000 -0.200000 1.850000 ! ALLOW PRO + ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 +NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM + ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) +NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NY 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! trp, JWK +! nitrogen wildcards +!N* 0.000000 -0.200000 1.850000 +!N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 +!NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 +! +O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid carbonyl O +OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) +OM 0.000000 -0.120000 1.700000 ! ALLOW HEM + ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91) +OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 9/17/90, avoid O* wildcard +OT 0.000000 -0.152100 1.768200 ! ALLOW WAT + !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete +! oxygen wildcards +!O* 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 +!OC 0.000000 -0.120000 1.700000 +!OH1 0.000000 -0.152100 1.770000 +!OM 0.000000 -0.120000 1.700000 +!OS 0.000000 -0.152100 1.770000 +!OT 0.000000 -0.152100 1.768200 + +CAL 0.000000 -0.120000 1.710000 ! ALLOW ION + !Calcium (BP) +FE 0.010000 0.000000 0.650000 ! ALLOW HEM + ! Heme (6-liganded): Iron atom (KK 05/13/91) +S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION + ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent +SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION + ! adm jr., 3/3/92, dimethyldisulphide pure solvent +SS 0.000000 -0.470000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +ZN 0.000000 -0.250000 1.090000 ! ALLOW ION + ! RHS March 18, 1990 +DUM 0.000000 -0.000000 0.000000 ! + ! dummy atom +HE 0.000000 -0.021270 1.4800 ! + ! helium, experimental pot. energy surface, adm jr., 12/95 +NE 0.000000 -0.086000 1.5300 + ! neon, semiempirical pot. energy surface, adm jr., 12/95 + +HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use + ! READ PARAM APPEND CARD + ! to append hbond parameters from the file: par_hbond.inp + +END diff --git a/charmm/toppar/tamdfff/par_tadmap.chi1.ahbb4.inp b/charmm/toppar/tamdfff/par_tadmap.chi1.ahbb4.inp new file mode 100755 index 00000000..7fe505b6 --- /dev/null +++ b/charmm/toppar/tamdfff/par_tadmap.chi1.ahbb4.inp @@ -0,0 +1,25518 @@ +* TAD correction maps for psi-chi1 and phi-chi1 cross terms +* based on backbone topology: ahbb4, soft=0.2, cdie, charge rebalanced +* + +! using CMAP correction based on local chi1 segments: +! +! topology: -C N CA CB N CA CB R1 (phi' chi1) +! CB CA C +N C CA CB R1 (psi' chi1') +! +! parmeter: X3 CT1 NH1 C X4 X3 CT1 NH1 (reverse of topology file) +! NH1 C CT1 X3 X4 X3 CT1 C (reverse of topology file +! +! where X3 X4 are: +! +! 1) ... CT1 CT3 : VAL, ILE +! 2) ... CT2 CT1 : LEU +! 3) ... CT2 CT2 : MET, GLU, GLN, LYS, ARG +! 4) ... CT2 CA : PHE, TYR +! 5) ... CT2 CC : ASN +! 6) ... CT2 CPH1 : HIS +! 7) ... CT3 HA : ALA +! 8) ... CT2 OH1 : SER +! 9) ... CT1 OH1 : THR +! 10) ... CT2 CY : TRP +! 11) ... CT2 S : CYS +! 12) none : GLY, PRO + +CMAP + +! flat cmap for proline neighbors +N C CT1 CT1 CT3 CT1 CT1 C 3 ! 1) +1 1 1 +1 1 1 +1 1 1 +N C CT1 CT2 CT1 CT2 CT1 C 3 ! 2) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT2 CT2 CT2 CT1 C 3 ! 3) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT2 CA CT2 CT1 C 3 ! 4) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT2 CC CT2 CT1 C 3 ! 5) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT2 CPH1 CT2 CT1 C 3 ! 6) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT3 HA CT3 CT1 C 3 ! 7) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT2 OH1 CT2 CT1 C 3 ! 8) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT1 OH1 CT1 CT1 C 3 ! 9) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT2 CY CT2 CT1 C 3 ! 10) +1 1 1 +1 1 1 +1 1 1 + +N C CT1 CT2 CS CT2 CT1 C 3 ! 11) +1 1 1 +1 1 1 +1 1 1 + +! type 1: VAL, ILE + +CT1 CT1 NH1 C CT3 CT1 CT1 NH1 72 +! new map computed as: CMD - TAD + + -0.1014 -0.0820 -0.0647 -0.0500 -0.0389 ! -180 + -0.0328 -0.0320 -0.0390 -0.0500 -0.0630 + -0.0750 -0.0800 -0.0790 -0.0710 -0.0560 + -0.0420 -0.0270 -0.0160 -0.0100 -0.0071 + -0.0070 -0.0076 -0.0076 -0.0055 0.0000 + 0.0095 0.0232 0.0408 0.0608 0.0813 + 0.1003 0.1150 0.1260 0.1310 0.1330 + 0.1330 0.1320 0.1330 0.1340 0.1320 + 0.1270 0.1150 0.0965 0.0732 0.0451 + 0.0145 -0.0172 -0.0493 -0.0809 -0.1118 + -0.1420 -0.1715 -0.1999 -0.2272 -0.2510 + -0.2740 -0.2930 -0.3070 -0.3160 -0.3220 + -0.3210 -0.3160 -0.3070 -0.2940 -0.2770 + -0.2580 -0.2360 -0.2137 -0.1901 -0.1668 + -0.1440 -0.1220 + + -0.0965 -0.0776 -0.0605 -0.0464 -0.0359 ! 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155 + 0.0360 0.0270 0.0000 -0.0500 -0.1200 + -0.2110 -0.3090 -0.4030 -0.4770 -0.5150 + -0.5090 -0.4590 -0.3720 -0.2590 -0.1330 + -0.0080 0.1100 0.2090 0.2700 0.2650 + 0.1490 -0.1460 -0.7100 -1.6580 -3.0470 + -4.6030 -6.0080 -7.2500 -8.3240 -9.2030 + -9.8960 -10.3780 -10.6480 -10.7010 -10.5240 + -10.1410 -9.5420 -8.7390 -7.7550 -6.5960 + -5.3170 -4.0330 -2.7430 -1.4470 -0.5260 + -0.0430 0.1720 0.2430 0.2470 0.2300 + 0.2070 0.1820 0.1530 0.1140 0.0670 + 0.0110 -0.0450 -0.0960 -0.1330 -0.1530 + -0.1550 -0.1400 -0.1180 -0.0920 -0.0702 + -0.0522 -0.0376 + + -0.0181 -0.0007 0.0177 0.0349 0.0468 ! 160 + 0.0470 0.0310 -0.0100 -0.0800 -0.1760 + -0.2940 -0.4190 -0.5330 -0.6160 -0.6510 + -0.6300 -0.5580 -0.4450 -0.3080 -0.1630 + -0.0230 0.1040 0.2060 0.2630 0.2370 + 0.0710 -0.3230 -1.0640 -2.3090 -3.9310 + -5.4320 -6.7870 -7.9880 -8.9990 -9.8340 + -10.4610 -10.8850 -11.1040 -11.0910 -10.8640 + -10.4250 -9.7710 -8.9250 -7.8950 -6.6880 + -5.3760 -4.0490 -2.7230 -1.4000 -0.5020 + -0.0400 0.1640 0.2330 0.2410 0.2270 + 0.2060 0.1790 0.1400 0.0900 0.0250 + -0.0470 -0.1170 -0.1740 -0.2120 -0.2240 + -0.2120 -0.1840 -0.1470 -0.1110 -0.0790 + -0.0546 -0.0353 + + -0.0124 0.0084 0.0295 0.0479 0.0585 ! 165 + 0.0530 0.0240 -0.0360 -0.1310 -0.2580 + -0.4060 -0.5570 -0.6870 -0.7700 -0.7920 + -0.7490 -0.6470 -0.5060 -0.3460 -0.1830 + -0.0310 0.1030 0.2040 0.2480 0.1890 + -0.0510 -0.5820 -1.5640 -3.1260 -4.7200 + -6.1800 -7.4850 -8.6250 -9.5940 -10.3640 + -10.9460 -11.3110 -11.4700 -11.3970 -11.1160 + -10.6240 -9.9180 -9.0270 -7.9510 -6.7010 + -5.3400 -3.9760 -2.6070 -1.2790 -0.4440 + -0.0220 0.1630 0.2250 0.2350 0.2240 + 0.2010 0.1670 0.1150 0.0460 -0.0380 + -0.1260 -0.2070 -0.2690 -0.3000 -0.2990 + -0.2710 -0.2260 -0.1740 -0.1260 -0.0874 + -0.0570 -0.0333 + + -0.0066 0.0178 0.0406 0.0588 0.0650 ! 170 + 0.0510 0.0040 -0.0800 -0.2040 -0.3630 + -0.5390 -0.7100 -0.8440 -0.9190 -0.9180 + -0.8440 -0.7120 -0.5450 -0.3650 -0.1890 + -0.0290 0.1060 0.2020 0.2250 0.1150 + -0.2270 -0.9430 -2.2370 -3.8720 -5.4250 + -6.8260 -8.0810 -9.1800 -10.0870 -10.8140 + -11.3400 -11.6500 -11.7400 -11.6300 -11.2890 + -10.7360 -9.9870 -9.0400 -7.9110 -6.6230 + -5.2160 -3.8070 -2.3930 -1.1050 -0.3620 + 0.0070 0.1670 0.2220 0.2300 0.2180 + 0.1900 0.1440 0.0750 -0.0130 -0.1160 + -0.2180 -0.3050 -0.3640 -0.3830 -0.3650 + -0.3190 -0.2570 -0.1930 -0.1360 -0.0920 + -0.0579 -0.0308 + + -0.0006 0.0256 0.0497 0.0660 0.0660 ! 175 + 0.0380 -0.0290 -0.1390 -0.2930 -0.4790 + -0.6780 -0.8560 -0.9830 -1.0370 -1.0060 + -0.9000 -0.7400 -0.5540 -0.3610 -0.1790 + -0.0180 0.1140 0.1970 0.1870 0.0060 + -0.4700 -1.4210 -2.9360 -4.5250 -6.0330 + -7.3960 -8.6030 -9.6410 -10.5060 -11.1790 + -11.6400 -11.9100 -11.9400 -11.7700 -11.3690 + -10.7640 -9.9580 -8.9690 -7.7920 -6.4470 + -4.9940 -3.5380 -2.0770 -0.9030 -0.2680 + 0.0420 0.1760 0.2210 0.2260 0.2090 + 0.1710 0.1100 0.0240 -0.0840 -0.2010 + -0.3120 -0.3960 -0.4430 -0.4460 -0.4090 + -0.3460 -0.2710 -0.2000 -0.1400 -0.0925 + -0.0567 -0.0274 + +END diff --git a/charmm/toppar/tamdfff/top_all22_prot_cmap.ahbb4.inp b/charmm/toppar/tamdfff/top_all22_prot_cmap.ahbb4.inp new file mode 100755 index 00000000..6aa41769 --- /dev/null +++ b/charmm/toppar/tamdfff/top_all22_prot_cmap.ahbb4.inp @@ -0,0 +1,2232 @@ +*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<< +*>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< +*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< +*>>> CMAP entries for psi-chi1 TAD correction (ahbb4) <<<< +* +27 1 + +! +! references +! +!PROTEINS +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. +! +!PHOSPHOTYROSINE +! +!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. +!Structural Characterization of the Phosphotyrosine Binding Region of a +!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics +!Simulation and Chemical Shift Calculations. Journal of the American +!Chemical Society, 1996, 118: 11265-11277. +! +!IONS (see lipid and nucleic acid topology and parameter files for +!additional ions +! +!ZINC +! +!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) +! + +MASS 1 H 1.00800 H ! polar H +MASS 2 HC 1.00800 H ! N-ter H +MASS 3 HA 1.00800 H ! nonpolar H +MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 5 HP 1.00800 H ! aromatic H +MASS 6 HB 1.00800 H ! backbone H +MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 +MASS 8 HR2 1.00800 H ! (+) his HE1 +MASS 9 HR3 1.00800 H ! neutral his HG, HD2 +MASS 10 HS 1.00800 H ! thiol hydrogen +MASS 11 HE1 1.00800 H ! for alkene; RHC=CR +MASS 12 HE2 1.00800 H ! for alkene; H2C=CR +MASS 20 C 12.01100 C ! carbonyl C, peptide backbone +MASS 21 CA 12.01100 C ! aromatic C +MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH +MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 +MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 +MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons +MASS 26 CPH2 12.01100 C ! his CE1 carbon +MASS 27 CPT 12.01100 C ! trp C between rings +MASS 28 CY 12.01100 C ! TRP C in pyrrole ring +MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) +MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) +MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) +MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 +MASS 34 CPA 12.01100 C ! heme alpha-C +MASS 35 CPB 12.01100 C ! heme beta-C +MASS 36 CPM 12.01100 C ! heme meso-C +MASS 37 CM 12.01100 C ! heme CO carbon +MASS 38 CS 12.01100 C ! thiolate carbon +MASS 39 CE1 12.01100 C ! for alkene; RHC=CR +MASS 40 CE2 12.01100 C ! for alkene; H2C=CR +MASS 50 N 14.00700 N ! proline N +MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen +MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen +MASS 53 NR3 14.00700 N ! charged his ring nitrogen +MASS 54 NH1 14.00700 N ! peptide nitrogen +MASS 55 NH2 14.00700 N ! amide nitrogen +MASS 56 NH3 14.00700 N ! ammonium nitrogen +MASS 57 NC2 14.00700 N ! guanidinium nitroogen +MASS 58 NY 14.00700 N ! TRP N in pyrrole ring +MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) +MASS 60 NPH 14.00700 N ! heme pyrrole N +MASS 70 O 15.99900 O ! carbonyl oxygen +MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid +MASS 72 OC 15.99900 O ! carboxylate oxygen +MASS 73 OH1 15.99900 O ! hydroxyl oxygen +MASS 74 OS 15.99940 O ! ester oxygen +MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN +MASS 76 OM 15.99900 O ! heme CO/O2 oxygen +MASS 81 S 32.06000 S ! sulphur +MASS 82 SM 32.06000 S ! sulfur C-S-S-C type +MASS 83 SS 32.06000 S ! thiolate sulfur +MASS 85 HE 4.00260 HE ! helium +MASS 86 NE 20.17970 NE ! neon +MASS 90 CAL 40.08000 CA ! calcium 2+ +MASS 91 ZN 65.37000 ZN ! zinc (II) cation +MASS 92 FE 55.84700 Fe ! heme iron 56 +MASS 99 DUM 0.00000 H ! dummy atom + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DECL CY +DECL NT +DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI ALA 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB 0.09 ! | / +GROUP ! HA-CA--CB-HB2 +ATOM CB CT3 -0.27 ! | \ +ATOM HB1 HA 0.09 ! | HB3 +ATOM HB2 HA 0.09 ! O=C +ATOM HB3 HA 0.09 ! | +GROUP ! +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA N HN N CA +BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB HB1 +CMAP CB CA C +N C CA CB HB1 +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 123.23 111.09 1.5461 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC C CA CB HB1 1.5233 111.09 177.25 109.60 1.1109 +IC HB1 CA *CB HB2 1.1109 109.60 119.13 111.05 1.1119 +IC HB1 CA *CB HB3 1.1109 109.60 -119.58 111.61 1.1114 + +RESI ARG 1.00 +GROUP +ATOM N NH1 -0.47 ! | HH11 +ATOM HN H 0.31 ! HN-N | +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA HB 0.09 ! | | | | | //(+) +GROUP ! HA-CA--CB--CG--CD--NE--CZ +ATOM CB CT2 -0.18 ! | | | | \ +ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HB2 HA 0.09 ! O=C | +GROUP ! | HH21 +ATOM CG CT2 -0.18 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +GROUP +ATOM CD CT2 0.20 +ATOM HD1 HA 0.09 +ATOM HD2 HA 0.09 +ATOM NE NC2 -0.70 +ATOM HE HC 0.44 +ATOM CZ C 0.64 +ATOM NH1 NC2 -0.80 +ATOM HH11 HC 0.46 +ATOM HH12 HC 0.46 +ATOM NH2 NC2 -0.80 +ATOM HH21 HC 0.46 +ATOM HH22 HC 0.46 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE O C CZ NH1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +IMPR CZ NH1 NH2 NE +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.62 111.88 1.5546 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 107.70 -180.00 115.92 1.5460 +IC CG CA *CB HB1 1.5460 115.92 120.56 106.90 1.1153 +IC CG CA *CB HB2 1.5460 115.92 -124.80 109.38 1.1129 +IC CA CB CG CD 1.5546 115.92 180.00 114.01 1.5384 +IC CD CB *CG HG1 1.5384 114.01 125.20 108.55 1.1121 +IC CD CB *CG HG2 1.5384 114.01 -120.30 108.96 1.1143 +IC CB CG CD NE 1.5460 114.01 -180.00 107.09 1.5034 +IC NE CG *CD HD1 1.5034 107.09 120.69 109.41 1.1143 +IC NE CG *CD HD2 1.5034 107.09 -119.04 111.52 1.1150 +IC CG CD NE CZ 1.5384 107.09 -180.00 123.05 1.3401 +IC CZ CD *NE HE 1.3401 123.05 180.00 113.14 1.0065 +IC CD NE CZ NH1 1.5034 123.05 180.00 118.06 1.3311 +IC NE CZ NH1 HH11 1.3401 118.06 -178.28 120.61 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.61 171.19 116.29 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.06 178.64 122.14 1.3292 +IC NE CZ NH2 HH21 1.3401 122.14 -174.14 119.91 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.91 166.16 116.88 0.9914 + +RESI ASN 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA HB 0.09 ! | | || / +GROUP ! HA-CA--CB--CG--ND2 +ATOM CB CT2 -0.18 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 HD22 (trans to OD1) +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CC 0.55 +ATOM OD1 O -0.55 +GROUP +ATOM ND2 NH2 -0.62 +ATOM HD21 H 0.32 +ATOM HD22 H 0.30 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +DOUBLE C O CG OD1 +IMPR N -C CA HN C CA +N O +IMPR CG ND2 CB OD1 CG CB ND2 OD1 +IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.18 113.04 1.5627 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 106.71 180.00 114.30 1.5319 +IC CG CA *CB HB1 1.5319 114.30 119.17 107.82 1.1120 +IC CG CA *CB HB2 1.5319 114.30 -123.74 110.34 1.1091 +IC CA CB CG OD1 1.5627 114.30 -180.00 122.56 1.2323 +IC OD1 CB *CG ND2 1.2323 122.56 -179.19 116.15 1.3521 +IC CB CG ND2 HD21 1.5319 116.15 -179.26 117.35 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.35 178.02 120.05 0.9951 + +RESI ASP -1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 OD1 +ATOM HA HB 0.09 ! | | // +GROUP ! HA-CA--CB--CG +ATOM CB CT2 -0.28 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 OD2(-) +ATOM HB2 HA 0.09 ! O=C +ATOM CG CC 0.62 ! | +ATOM OD1 OC -0.76 +ATOM OD2 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +DOUBLE O C CG OD1 +IMPR N -C CA HN C CA +N O +!IMPR OD1 CB OD2 CG +IMPR CG CB OD2 OD1 +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.18 113.04 1.5627 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 106.71 180.00 114.30 1.5319 +IC CG CA *CB HB1 1.5319 114.30 119.22 109.23 1.1086 +IC CG CA *CB HB2 1.5319 114.30 -121.61 110.64 1.1080 +IC CA CB CG OD1 1.5627 114.30 180.00 117.99 1.2565 +IC OD1 CB *CG OD2 1.2565 117.99 -170.23 117.70 1.2541 + +RESI CYS 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB 0.09 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB CT2 -0.11 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 HG1 +ATOM HB2 HA 0.09 ! O=C +ATOM SG S -0.23 ! | +ATOM HG1 HS 0.16 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB SG +CMAP CB CA C +N C CA CB SG +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.79 111.98 1.5584 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB SG 1.4519 107.78 180.00 113.87 1.8359 +IC SG CA *CB HB1 1.8359 113.87 119.91 107.24 1.1134 +IC SG CA *CB HB2 1.8359 113.87 -125.32 109.82 1.1124 +IC CA CB SG HG1 1.5584 113.87 176.96 97.15 1.3341 + +RESI CYSS 0.00 ! along with CYSZ: for refining Zn binding proteins +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB 0.09 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB CT2 -0.11 ! | | +ATOM HB1 HA 0.09 ! | HB2 +ATOM HB2 HA 0.09 ! O=C +ATOM SG S -0.07 ! | +!ATOM HG1 HS 0.16 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.79 111.98 1.5584 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB SG 1.4519 107.78 180.00 113.87 1.8359 +IC SG CA *CB HB1 1.8359 113.87 119.91 107.24 1.1134 +IC SG CA *CB HB2 1.8359 113.87 -125.32 109.82 1.1124 + +RESI CYSZ 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB 0.09 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB CT2 -0.11 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 ZN +ATOM HB2 HA 0.09 ! O=C +ATOM SG S -0.23 ! | +ATOM ZN ZN 0.16 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG ZN +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB SG +CMAP CB CA C +N C CA CB SG +DONOR HN N +!DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.79 111.98 1.5584 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB SG 1.4519 107.78 180.00 113.87 1.8359 +IC SG CA *CB HB1 1.8359 113.87 119.91 107.24 1.1134 +IC SG CA *CB HB2 1.8359 113.87 -125.32 109.82 1.1124 +IC CA CB SG ZN 1.5584 113.87 176.96 97.15 2.3500 + +RESI GLN 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA HB 0.09 ! | | | || / +GROUP ! HA-CA--CB--CG--CD--NE2 +ATOM CB CT2 -0.18 ! | | | \ +ATOM HB1 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1) +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +GROUP +ATOM CD CC 0.55 +ATOM OE1 O -0.55 +GROUP +ATOM NE2 NH2 -0.62 +ATOM HE21 H 0.32 +ATOM HE22 H 0.30 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD NE2 CG OE1 CD CG NE2 OE1 +IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.62 111.88 1.5546 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 107.70 -180.00 115.92 1.5460 +IC CG CA *CB HB1 1.5460 115.92 120.56 106.90 1.1153 +IC CG CA *CB HB2 1.5460 115.92 -124.80 109.38 1.1129 +IC CA CB CG CD 1.5546 115.92 180.00 112.50 1.5320 +IC CD CB *CG HG1 1.5320 112.50 118.69 110.41 1.1112 +IC CD CB *CG HG2 1.5320 112.50 -121.91 110.74 1.1094 +IC CB CG CD OE1 1.5460 112.50 180.00 121.52 1.2294 +IC OE1 CG *CD NE2 1.2294 121.52 179.57 116.84 1.3530 +IC CG CD NE2 HE21 1.5320 116.84 -179.72 116.86 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.86 -178.91 119.83 0.9943 + +RESI GLU -1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 OE1 +ATOM HA HB 0.09 ! | | | // +GROUP ! HA-CA--CB--CG--CD +ATOM CB CT2 -0.18 ! | | | \ +ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-) +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.28 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +ATOM CD CC 0.62 +ATOM OE1 OC -0.76 +ATOM OE2 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +!IMPR OE1 CG OE2 CD +IMPR CD CG OE2 OE1 +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.62 111.88 1.5546 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 107.70 -180.00 115.92 1.5460 +IC CG CA *CB HB1 1.5460 115.92 120.56 106.90 1.1153 +IC CG CA *CB HB2 1.5460 115.92 -124.80 109.38 1.1129 +IC CA CB CG CD 1.5546 115.92 -180.00 115.73 1.5307 +IC CD CB *CG HG1 1.5307 115.73 117.38 109.50 1.1053 +IC CD CB *CG HG2 1.5307 115.73 -121.96 111.00 1.1081 +IC CB CG CD OE1 1.5460 115.73 -180.00 114.99 1.2590 +IC OE1 CG *CD OE2 1.2590 114.99 -179.10 120.08 1.2532 + +RESI GLY 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! N-H +ATOM CA CT2 -0.02 ! | +ATOM HA1 HB 0.09 ! | +ATOM HA2 HB 0.09 ! HA1-CA-HA2 +GROUP ! | +ATOM C C 0.51 ! | +ATOM O O -0.51 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA HA1 1.4519 112.80 117.86 108.03 1.0814 +IC N C *CA HA2 1.4519 112.80 -118.12 107.95 1.0817 +PATCHING FIRS GLYP + +RESI HSD 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 -0.09 ! | | \\ || +ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA 0.09 ! O=C | +ATOM ND1 NR1 -0.36 ! | HD2 +ATOM HD1 H 0.32 +ATOM CG CPH1 -0.05 +GROUP +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +ATOM NE2 NR2 -0.70 +ATOM CD2 CPH1 0.22 +ATOM HD2 HR3 0.10 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 122.46 109.99 1.5519 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 109.42 180.00 114.05 1.5041 +IC CG CA *CB HB1 1.5041 114.05 121.17 109.01 1.1118 +IC CG CA *CB HB2 1.5041 114.05 -122.36 109.53 1.1121 +IC CA CB CG ND1 1.5519 114.05 90.00 124.10 1.3783 +IC ND1 CB *CG CD2 1.3783 124.10 -171.29 129.60 1.3597 +IC CB CG ND1 CE1 1.5041 124.10 -173.21 107.03 1.3549 +IC CB CG CD2 NE2 1.5041 129.60 171.99 110.03 1.3817 +IC NE2 ND1 *CE1 HE1 1.3162 111.64 -179.63 123.89 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.03 -174.65 126.26 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.03 -177.85 129.63 1.0834 + +!!!! copy of HSD +RESI HIS 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 -0.09 ! | | \\ || +ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA 0.09 ! O=C | +ATOM ND1 NR1 -0.36 ! | HD2 +ATOM HD1 H 0.32 +ATOM CG CPH1 -0.05 +GROUP +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +ATOM NE2 NR2 -0.70 +ATOM CD2 CPH1 0.22 +ATOM HD2 HR3 0.10 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 122.46 109.99 1.5519 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 109.42 180.00 114.05 1.5041 +IC CG CA *CB HB1 1.5041 114.05 121.17 109.01 1.1118 +IC CG CA *CB HB2 1.5041 114.05 -122.36 109.53 1.1121 +IC CA CB CG ND1 1.5519 114.05 90.00 124.10 1.3783 +IC ND1 CB *CG CD2 1.3783 124.10 -171.29 129.60 1.3597 +IC CB CG ND1 CE1 1.5041 124.10 -173.21 107.03 1.3549 +IC CB CG CD2 NE2 1.5041 129.60 171.99 110.03 1.3817 +IC NE2 ND1 *CE1 HE1 1.3162 111.64 -179.63 123.89 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.03 -174.65 126.26 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.03 -177.85 129.63 1.0834 + +RESI HSE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N NH1 -0.47 ! | HE1 +ATOM HN H 0.31 ! HN-N __ / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB 0.09 ! | | / | +GROUP ! HA-CA--CB--CG | +ATOM CB CT2 -0.08 ! | | \\ | +ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA 0.09 ! O=C | \ +ATOM ND1 NR2 -0.70 ! | HD2 HE2 +ATOM CG CPH1 0.22 +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +GROUP +ATOM NE2 NR1 -0.36 +ATOM HE2 H 0.32 +ATOM CD2 CPH1 -0.05 +ATOM HD2 HR3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG CE1 ND1 +IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 123.52 111.67 1.5578 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 109.27 180.00 116.94 1.5109 +IC CG CA *CB HB1 1.5109 116.94 119.80 107.91 1.1114 +IC CG CA *CB HB2 1.5109 116.94 -124.04 109.50 1.1101 +IC CA CB CG ND1 1.5578 116.94 90.00 120.17 1.3859 +IC ND1 CB *CG CD2 1.3859 120.17 -178.26 129.71 1.3596 +IC CB CG ND1 CE1 1.5109 120.17 -179.20 105.20 1.3170 +IC CB CG CD2 NE2 1.5109 129.71 178.66 105.80 1.3782 +IC NE2 ND1 *CE1 HE1 1.3542 111.75 179.69 124.58 1.0929 +IC CE1 CD2 *NE2 HE2 1.3542 107.14 -178.69 125.86 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.80 -179.35 129.89 1.0809 + +RESI HSP 1.00 ! Protonated His +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 -0.05 ! | | \\ || +ATOM HB1 HA 0.09 ! | HB2 CD2--NE2(+) +ATOM HB2 HA 0.09 ! O=C | \ +ATOM CD2 CPH1 0.19 ! | HD2 HE2 +ATOM HD2 HR1 0.13 +ATOM CG CPH1 0.19 +GROUP +ATOM NE2 NR3 -0.51 +ATOM HE2 H 0.44 +ATOM ND1 NR3 -0.51 +ATOM HD1 H 0.44 +ATOM CE1 CPH2 0.32 +ATOM HE1 HR2 0.18 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG NE2 CE1 +IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 125.13 109.38 1.5533 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 111.83 180.00 114.18 1.5168 +IC CG CA *CB HB1 1.5168 114.18 122.50 108.99 1.1116 +IC CG CA *CB HB2 1.5168 114.18 -121.51 108.97 1.1132 +IC CA CB CG ND1 1.5533 114.18 90.00 122.94 1.3718 +IC ND1 CB *CG CD2 1.3718 122.94 -165.26 128.93 1.3549 +IC CB CG ND1 CE1 1.5168 122.94 -167.62 108.90 1.3262 +IC CB CG CD2 NE2 1.5168 128.93 167.13 106.93 1.3727 +IC NE2 ND1 *CE1 HE1 1.3254 108.50 178.39 125.76 1.0799 +IC CE1 CD2 *NE2 HE2 1.3254 108.82 -172.94 125.52 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.90 171.49 126.09 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.93 -174.49 128.41 1.0867 + +RESI ILE 0.00 +GROUP +ATOM N NH1 -0.47 ! | HG21 HG22 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | CG2--HG23 +ATOM HA HB 0.09 ! | / +GROUP ! HA-CA--CB-HB HD1 +ATOM CB CT1 -0.09 ! | \ / +ATOM HB HA 0.09 ! | CG1--CD--HD2 +GROUP ! O=C / \ \ +ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3 +ATOM HG21 HA 0.09 +ATOM HG22 HA 0.09 +ATOM HG23 HA 0.09 +GROUP +ATOM CG1 CT2 -0.18 +ATOM HG11 HA 0.09 +ATOM HG12 HA 0.09 +GROUP +ATOM CD CT3 -0.27 +ATOM HD1 HA 0.09 +ATOM HD2 HA 0.09 +ATOM HD3 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N ! **** NOTE: +CMAP -C N CA CB N CA CB CG2 ! CG2 of ILE actually corresponds to +CMAP CB CA C +N C CA CB CG2 ! CG1 of VAL by chirality +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 122.95 111.23 1.5660 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG2 1.4519 109.09 -180.00 113.97 1.5441 +IC CG2 CA *CB CG1 1.5441 113.97 123.99 112.17 1.5414 +IC CG2 CA *CB HB 1.5441 113.97 -119.17 107.57 1.1178 +IC CA CB CG2 HG21 1.5660 113.97 -171.30 110.61 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.61 119.35 110.90 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.61 -120.09 110.97 1.1105 +IC CA CB CG1 CD 1.5660 112.17 180.00 114.09 1.5381 +IC CD CB *CG1 HG11 1.5381 114.09 122.36 109.78 1.1130 +IC CD CB *CG1 HG12 1.5381 114.09 -120.59 108.89 1.1141 +IC CB CG1 CD HD1 1.5414 114.09 -176.78 110.31 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.31 119.75 110.65 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.31 -119.70 111.02 1.1103 + +RESI LEU 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD11 HD12 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 CD1--HD13 +ATOM HA HB 0.09 ! | | / +GROUP ! HA-CA--CB--CG-HG +ATOM CB CT2 -0.18 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 CD2--HD23 +ATOM HB2 HA 0.09 ! O=C | \ +GROUP ! | HD21 HD22 +ATOM CG CT1 -0.09 +ATOM HG HA 0.09 +GROUP +ATOM CD1 CT3 -0.27 +ATOM HD11 HA 0.09 +ATOM HD12 HA 0.09 +ATOM HD13 HA 0.09 +GROUP +ATOM CD2 CT3 -0.27 +ATOM HD21 HA 0.09 +ATOM HD22 HA 0.09 +ATOM HD23 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.52 112.12 1.5543 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 107.49 180.00 117.46 1.5472 +IC CG CA *CB HB1 1.5472 117.46 120.98 107.17 1.1145 +IC CG CA *CB HB2 1.5472 117.46 -124.67 108.98 1.1126 +IC CA CB CG CD1 1.5543 117.46 180.00 110.48 1.5361 +IC CD1 CB *CG CD2 1.5361 110.48 -123.75 112.57 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.26 -116.63 108.02 1.1168 +IC CB CG CD1 HD11 1.5472 110.48 177.33 110.54 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.54 119.96 110.62 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.54 -119.85 110.69 1.1108 +IC CB CG CD2 HD21 1.5472 112.57 178.96 110.32 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.32 119.71 111.69 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.32 -119.61 110.49 1.1115 + +RESI LYS 1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA HB 0.09 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM CB CT2 -0.18 ! | | | | | \ +ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +GROUP +ATOM CD CT2 -0.18 +ATOM HD1 HA 0.09 +ATOM HD2 HA 0.09 +GROUP +ATOM CE CT2 0.21 +ATOM HE1 HA 0.05 +ATOM HE2 HA 0.05 +ATOM NZ NH3 -0.30 +ATOM HZ1 HC 0.33 +ATOM HZ2 HC 0.33 +ATOM HZ3 HC 0.33 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUBLE O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.62 111.88 1.5546 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 107.70 -180.00 115.92 1.5460 +IC CG CA *CB HB1 1.5460 115.92 120.56 106.90 1.1153 +IC CG CA *CB HB2 1.5460 115.92 -124.80 109.38 1.1129 +IC CA CB CG CD 1.5546 115.92 -180.00 113.28 1.5397 +IC CD CB *CG HG1 1.5397 113.28 120.74 109.10 1.1138 +IC CD CB *CG HG2 1.5397 113.28 -122.34 108.99 1.1143 +IC CB CG CD CE 1.5460 113.28 180.00 112.33 1.5350 +IC CE CG *CD HD1 1.5350 112.33 122.25 108.41 1.1141 +IC CE CG *CD HD2 1.5350 112.33 -121.59 108.13 1.1146 +IC CG CD CE NZ 1.5397 112.33 -180.00 110.46 1.4604 +IC NZ CD *CE HE1 1.4604 110.46 119.91 110.51 1.1128 +IC NZ CD *CE HE2 1.4604 110.46 -120.02 110.57 1.1123 +IC CD CE NZ HZ1 1.5350 110.46 179.92 110.02 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.02 120.27 109.50 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.02 -120.13 109.40 1.0401 + +RESI MET 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HE1 +ATOM HA HB 0.09 ! | | | | +GROUP ! HA-CA--CB--CG--SD--CE--HE3 +ATOM CB CT2 -0.18 ! | | | | +ATOM HB1 HA 0.09 ! | HB2 HG2 HE2 +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.14 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +ATOM SD S -0.09 +ATOM CE CT3 -0.22 +ATOM HE1 HA 0.09 +ATOM HE2 HA 0.09 +ATOM HE3 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 121.62 111.88 1.5546 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 107.70 -180.00 115.92 1.5460 +IC CG CA *CB HB1 1.5460 115.92 120.56 106.90 1.1153 +IC CG CA *CB HB2 1.5460 115.92 -124.80 109.38 1.1129 +IC CA CB CG SD 1.5546 115.92 180.00 110.28 1.8219 +IC SD CB *CG HG1 1.8219 110.28 120.50 110.34 1.1106 +IC SD CB *CG HG2 1.8219 110.28 -121.16 109.64 1.1119 +IC CB CG SD CE 1.5460 110.28 180.00 98.94 1.8206 +IC CG SD CE HE1 1.8219 98.94 -179.42 110.91 1.1111 +IC HE1 SD *CE HE2 1.1111 110.91 119.95 111.03 1.1115 +IC HE1 SD *CE HE3 1.1111 110.91 -119.95 111.09 1.1112 + +RESI PHE 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | | +ATOM CA CT1 0.07 ! | HB1 CD1--CE1 +ATOM HA HB 0.09 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--HZ +ATOM CB CT2 -0.18 ! | | \ __ / +ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 +ATOM HB2 HA 0.09 ! O=C | | +GROUP ! | HD2 HE2 +ATOM CG CA 0.00 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA -0.115 +ATOM HZ HP 0.115 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 122.49 112.45 1.5594 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 108.04 180.00 112.76 1.5109 +IC CG CA *CB HB1 1.5109 112.76 118.27 109.10 1.1119 +IC CG CA *CB HB2 1.5109 112.76 -123.83 111.11 1.1113 +IC CA CB CG CD1 1.5594 112.76 90.00 120.32 1.4059 +IC CD1 CB *CG CD2 1.4059 120.32 -177.96 120.76 1.4062 +IC CB CG CD1 CE1 1.5109 120.32 -177.37 120.63 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.63 179.70 119.65 1.0814 +IC CB CG CD2 CE2 1.5109 120.76 177.20 120.62 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.62 -178.69 119.99 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.63 -0.12 119.93 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.93 -179.69 120.01 1.0808 +IC CZ CD2 *CE2 HE2 1.4003 119.95 -179.93 119.87 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.97 179.51 119.97 1.0807 + +RESI PRO 0.00 +GROUP ! HD1 HD2 +ATOM N N -0.29 ! | \ / +ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02 +ATOM HD1 HA 0.09 ! | \ / +ATOM HD2 HA 0.09 ! | CG +ATOM CA CP1 0.02 ! | / \ +ATOM HA HB 0.09 ! HA-CA--CB HG2 +GROUP ! | / \ +ATOM CB CP2 -0.18 ! | HB1 HB2 +ATOM HB1 HA 0.09 ! O=C +ATOM HB2 HA 0.09 ! | +GROUP +ATOM CG CP2 -0.18 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +DOUBLE O C +IMPR N -C CA CD +IMPR C CA +N O +!CMAP -C N CA C N CA C +N +ACCEPTOR O C +IC -C CA *N CD 1.3473 123.24 178.51 112.75 1.4624 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 113.74 111.74 1.5399 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 101.61 31.61 104.39 1.5322 +IC CA CB CG CD 1.5399 104.39 0.37 88.39 3.0887 +IC N CA CB HB1 1.4519 101.61 -84.94 109.02 1.1131 +IC N CA CB HB2 1.4519 101.61 153.93 112.74 1.1088 +IC CA CB CG HG1 1.5399 104.39 -156.72 112.95 1.1077 +IC CA CB CG HG2 1.5399 104.39 81.26 109.22 1.1143 +IC CB CG CD HD1 1.5322 88.39 -93.55 110.03 1.1137 +IC CB CG CD HD2 1.5322 88.39 144.52 110.00 1.1144 +PATCHING FIRS PROP + +RESI SER 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB 0.09 ! | | +GROUP ! HA-CA--CB--OG +ATOM CB CT2 0.05 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 HG1 +ATOM HB2 HA 0.09 ! O=C +ATOM OG OH1 -0.66 ! | +ATOM HG1 H 0.43 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB OG +CMAP CB CA C +N C CA CB OG +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 124.75 111.40 1.5585 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB OG 1.4519 110.36 180.00 112.45 1.4341 +IC OG CA *CB HB1 1.4341 112.45 119.32 108.10 1.1140 +IC OG CA *CB HB2 1.4341 112.45 -123.86 110.38 1.1136 +IC CA CB OG HG1 1.5585 112.45 165.96 107.08 0.9655 + +RESI THR 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | OG1--HG1 +ATOM HA HB 0.09 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 0.14 ! | \ +ATOM HB HA 0.09 ! | CG2--HG21 +ATOM OG1 OH1 -0.66 ! O=C / \ +ATOM HG1 H 0.43 ! | HG21 HG22 +GROUP +ATOM CG2 CT3 -0.27 +ATOM HG21 HA 0.09 +ATOM HG22 HA 0.09 +ATOM HG23 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB OG1 +CMAP CB CA C +N C CA CB OG1 +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 126.46 112.74 1.5693 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB OG1 1.4519 110.82 180.00 112.16 1.4252 +IC OG1 CA *CB HB 1.4252 112.16 116.39 106.11 1.1174 +IC OG1 CA *CB CG2 1.4252 112.16 -124.13 115.91 1.5324 +IC CA CB OG1 HG1 1.5693 112.16 -179.28 105.45 0.9633 +IC CA CB CG2 HG21 1.5693 115.91 -173.65 110.85 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.85 119.51 110.41 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.85 -120.39 111.11 1.1113 + +RESI TRP 0.00 +GROUP +ATOM N NH1 -0.47 ! | HE3 +ATOM HN H 0.31 ! HN-N | +ATOM CA CT1 0.07 ! | HB1 CE3 +ATOM HA HB 0.09 ! | | / \\ +GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM CB CT2 -0.18 ! | | || || | +ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2 +ATOM HB2 HA 0.09 ! O=C / \ / \ // +GROUP ! | HD1 NE1 CZ2 +ATOM CG CY -0.03 ! | | +ATOM CD1 CA 0.035 ! HE1 HZ2 +ATOM HD1 HP 0.115 +ATOM NE1 NY -0.61 +ATOM HE1 H 0.38 +ATOM CE2 CPT 0.13 +ATOM CD2 CPT -0.02 +GROUP +ATOM CE3 CA -0.115 +ATOM HE3 HP 0.115 +GROUP +ATOM CZ3 CA -0.115 +ATOM HZ3 HP 0.115 +GROUP +ATOM CZ2 CA -0.115 +ATOM HZ2 HP 0.115 +GROUP +ATOM CH2 CA -0.115 +ATOM HH2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 122.68 111.23 1.5560 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 108.88 -180.00 115.14 1.5233 +IC CG CA *CB HB1 1.5233 115.14 119.17 107.84 1.1127 +IC CG CA *CB HB2 1.5233 115.14 -124.73 109.87 1.1118 +IC CA CB CG CD2 1.5560 115.14 90.00 123.95 1.4407 +IC CD2 CB *CG CD1 1.4407 123.95 -172.81 129.18 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.57 -0.08 106.65 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.65 0.14 107.87 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.65 179.21 132.54 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.81 -0.20 118.16 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.16 0.10 120.97 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.97 0.01 120.87 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.16 -179.62 121.84 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.97 -179.82 119.45 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.87 -179.92 119.57 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3940 118.43 179.87 120.08 1.0790 +IC CD1 CE2 *NE1 HE1 1.3751 108.81 177.78 124.68 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.10 178.10 125.43 1.0820 + +RESI TYR 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | | +ATOM CA CT1 0.07 ! | HB1 CD1--CE1 +ATOM HA HB 0.09 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--OH +ATOM CB CT2 -0.18 ! | | \ __ / \ +ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 HH +ATOM HB2 HA 0.09 ! O=C | | +GROUP ! | HD2 HE2 +ATOM CG CA 0.00 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA 0.11 +ATOM OH OH1 -0.54 +ATOM HH H 0.43 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +DOUBLE O C CD1 CG CE1 CZ CE2 CD2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG +CMAP CB CA C +N C CA CB CG +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 122.49 112.45 1.5594 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG 1.4519 108.04 180.00 112.76 1.5109 +IC CG CA *CB HB1 1.5109 112.76 118.27 109.10 1.1119 +IC CG CA *CB HB2 1.5109 112.76 -123.83 111.11 1.1113 +IC CA CB CG CD1 1.5594 112.76 90.00 120.49 1.4064 +IC CD1 CB *CG CD2 1.4064 120.49 -176.46 120.46 1.4068 +IC CB CG CD1 CE1 1.5109 120.49 -175.49 120.40 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.40 178.94 119.80 1.0814 +IC CB CG CD2 CE2 1.5109 120.46 175.32 120.56 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.56 -177.57 119.98 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.40 -0.19 120.09 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.09 179.64 120.58 1.0799 +IC CZ CD2 *CE2 HE2 1.3978 119.94 -178.69 119.76 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.04 -178.98 120.25 1.4063 +IC CE1 CZ OH HH 1.3978 119.70 175.45 107.47 0.9594 + +RESI VAL 0.00 +GROUP +ATOM N NH1 -0.47 ! | HG11 HG12 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | CG1--HG13 +ATOM HA HB 0.09 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 -0.09 ! | \ +ATOM HB HA 0.09 ! | CG2--HG21 +GROUP ! O=C / \ +ATOM CG1 CT3 -0.27 ! | HG21 HG22 +ATOM HG11 HA 0.09 +ATOM HG12 HA 0.09 +ATOM HG13 HA 0.09 +GROUP +ATOM CG2 CT3 -0.27 +ATOM HG21 HA 0.09 +ATOM HG22 HA 0.09 +ATOM HG23 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +CMAP -C N CA CB N CA CB CG1 +CMAP CB CA C +N C CA CB CG1 +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3473 123.24 -179.32 116.77 0.9937 +IC -C N CA C 1.3473 123.24 180.00 112.80 1.5233 +IC N CA C +N 1.4519 112.80 180.00 118.41 1.3473 +IC +N CA *C O 1.3473 118.41 176.54 120.89 1.2245 +IC CA C +N +CA 1.5233 118.41 174.48 123.24 1.4519 +IC N C *CA CB 1.4519 112.80 122.95 111.23 1.5660 +IC N C *CA HA 1.4519 112.80 -118.27 106.28 1.0753 +IC N CA CB CG1 1.4519 109.09 -180.00 113.97 1.5441 +IC CG1 CA *CB CG2 1.5441 113.97 123.99 112.17 1.5414 +IC CG1 CA *CB HB 1.5441 113.97 -119.17 107.57 1.1178 +IC CA CB CG1 HG11 1.5660 113.97 177.83 110.30 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.30 119.25 111.67 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.30 -119.49 110.70 1.1110 +IC CA CB CG2 HG21 1.5660 112.17 -177.78 110.71 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.71 120.08 110.56 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.71 -119.55 111.23 1.1098 + +RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p +GROUP +ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup +ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup +ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup +BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p +ANGLE H1 OH2 H2 ! required +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI CAL 2.00 ! Calcium ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc ion +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI HEME -2.00 ! 6-liganded planar heme +GROUP +ATOM FE FE 0.24 ! O2A O1A O2D O1D +ATOM NA NPH -0.18 ! \\ // \\ // +ATOM NB NPH -0.18 ! CGA CGD +ATOM NC NPH -0.18 ! | | +ATOM ND NPH -0.18 ! HBA1--CBA--HBA2 HA HBD1--CBD--HBD2 +ATOM C1A CPA 0.12 ! | | | +ATOM C2A CPB -0.06 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2 +ATOM C3A CPB -0.06 ! | / \ | +ATOM C4A CPA 0.12 ! C2A---C1A C4D---C3D +ATOM C1B CPA 0.12 ! | | | | +ATOM C2B CPB -0.06 !HMA1\ | | | | /HMD1 +ATOM C3B CPB -0.06 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2 +ATOM C4B CPA 0.12 !HMA3/ \ / \ / \ / \HMD3 +ATOM C1C CPA 0.12 ! C4A \ / C1D +ATOM C2C CPB -0.06 ! / \ / \ +ATOM C3C CPB -0.06 ! HB--CHB FE CHD--HD +ATOM C4C CPA 0.12 ! \ / \ / +ATOM C1D CPA 0.12 ! C1B / \ C4C HAC +ATOM C2D CPB -0.06 !HMB1\ / \ / \ / \ / +ATOM C3D CPB -0.06 !HMB2-CMB--C2B NB NC C3C--CAC +ATOM C4D CPA 0.12 !HMB3/ | | | | \\ /HBC1 +GROUP ! | | | | CBC +ATOM CHA CPM -0.10 ! C3B---C4B C1C---C2C \HBC2 +ATOM HA HA 0.10 ! | \_CHC_/ | +GROUP ! CAB | CMC--HMC3 +ATOM CHB CPM -0.10 ! // \ HC / | +ATOM HB HA 0.10 ! CBB HAB HMC1 HMC2 +GROUP ! / \ +ATOM CHC CPM -0.10 ! HBB1 HBB2 +ATOM HC HA 0.10 ! +GROUP +ATOM CHD CPM -0.10 +ATOM HD HA 0.10 +GROUP +ATOM CMA CT3 -0.27 +ATOM HMA1 HA 0.09 +ATOM HMA2 HA 0.09 +ATOM HMA3 HA 0.09 +GROUP +ATOM CAA CT2 -0.18 +ATOM HAA1 HA 0.09 +ATOM HAA2 HA 0.09 +GROUP +ATOM CBA CT2 -0.28 +ATOM HBA1 HA 0.09 +ATOM HBA2 HA 0.09 +ATOM CGA CC 0.62 +ATOM O1A OC -0.76 +ATOM O2A OC -0.76 +GROUP +ATOM CMB CT3 -0.27 +ATOM HMB1 HA 0.09 +ATOM HMB2 HA 0.09 +ATOM HMB3 HA 0.09 +GROUP +ATOM CAB C -0.20 +ATOM HAB HA 0.20 +GROUP +ATOM CBB C -0.20 +ATOM HBB1 HA 0.10 +ATOM HBB2 HA 0.10 +GROUP +ATOM CMC CT3 -0.27 +ATOM HMC1 HA 0.09 +ATOM HMC2 HA 0.09 +ATOM HMC3 HA 0.09 +GROUP +ATOM CAC C -0.20 +ATOM HAC HA 0.20 +GROUP +ATOM CBC C -0.20 +ATOM HBC1 HA 0.10 +ATOM HBC2 HA 0.10 +GROUP +ATOM CMD CT3 -0.27 +ATOM HMD1 HA 0.09 +ATOM HMD2 HA 0.09 +ATOM HMD3 HA 0.09 +GROUP +ATOM CAD CT2 -0.18 +ATOM HAD1 HA 0.09 +ATOM HAD2 HA 0.09 +GROUP +ATOM CBD CT2 -0.28 +ATOM HBD1 HA 0.09 +ATOM HBD2 HA 0.09 +ATOM CGD CC 0.62 +ATOM O1D OC -0.76 +ATOM O2D OC -0.76 +BOND FE NA FE NB FE NC FE ND NA C1A +BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA +BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA +BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B +BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB +BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C +BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC +BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D +BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD +BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A +BOND CHA HA CHB HB CHC HC CHD HD +BOND CAA HAA1 CAA HAA2 CBA HBA1 CBA HBA2 +BOND CMA HMA1 CMA HMA2 CMA HMA3 +BOND CMB HMB1 CMB HMB2 CMB HMB3 +BOND CAB HAB CBB HBB1 CBB HBB2 +BOND CMC HMC1 CMC HMC2 CMC HMC3 +BOND CAC HAC CBC HBC1 CBC HBC2 +BOND CMD HMD1 CMD HMD2 CMD HMD3 +BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2 +IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB +IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC +IMPR C2D C1D C3D CMD C3D C2D C4D CAD +IMPR CGA CBA O2A O1A CGD CBD O2D O1D +IMPR C4A NA C1A C2A C1A NA C4A C3A +IMPR C4B NB C1B C2B C1B NB C4B C3B +IMPR C4C NC C1C C2C C1C NC C4C C3C +IMPR C4D ND C1D C2D C1D ND C4D C3D +IMPR NA C1A C2A C3A NA C4A C3A C2A +IMPR NB C1B C2B C3B NB C4B C3B C2B +IMPR NC C1C C2C C3C NC C4C C3C C2C +IMPR ND C1D C2D C3D ND C4D C3D C2D +IMPR NA C1A CHA C4D NA C4A CHB C1B +IMPR NB C1B CHB C4A NB C4B CHC C1C +IMPR NC C1C CHC C4B NC C4C CHD C1D +IMPR ND C1D CHD C4C ND C4D CHA C1A +IMPR CHA C1A C4D HA +IMPR CHB C1B C4A HB +IMPR CHC C1C C4B HC +IMPR CHD C1D C4C HD +IMPR C1A C2A CHA NA C4A C3A CHB NA +IMPR C1B C2B CHB NB C4B C3B CHC NB +IMPR C1C C2C CHC NC C4C C3C CHD NC +IMPR C1D C2D CHD ND C4D C3D CHA ND +IMPR NA C1A C4A FE +IMPR NB C1B C4B FE +IMPR NC C1C C4C FE +IMPR ND C1D C4D FE +IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1 +IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1 +ACCEPTOR NA +ACCEPTOR O1A ! CGA +ACCEPTOR O2A ! CGA +ACCEPTOR NB +ACCEPTOR NC +ACCEPTOR ND +ACCEPTOR O1D ! CGD +ACCEPTOR O2D ! CGD +IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NA FE CHB HB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NB FE CHC HC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NC FE CHD HD 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC ND FE CHA HA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION +IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION +IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 +PATCHING FIRS NONE LAST NONE + +PRES NTER 1.00 ! standard N-terminus +GROUP ! use in generate statement +ATOM N NH3 -0.30 ! +ATOM HT1 HC 0.33 ! HT1 +ATOM HT2 HC 0.33 ! (+)/ +ATOM HT3 HC 0.33 ! --CA--N--HT2 +ATOM CA CT1 0.21 ! | \ +ATOM HA HB 0.10 ! HA HT3 +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES GLYP 1.00 ! Glycine N-terminus +GROUP ! use in generate statement +ATOM N NH3 -0.30 ! +ATOM HT1 HC 0.33 ! HA1 HT1 +ATOM HT2 HC 0.33 ! | (+)/ +ATOM HT3 HC 0.33 ! --CA--N--HT2 +ATOM CA CT2 0.13 ! | \ +ATOM HA1 HB 0.09 ! HA2 HT3 +ATOM HA2 HB 0.09 ! +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES PROP 1.00 ! Proline N-Terminal +GROUP ! use in generate statement +ATOM N NP -0.07 ! HA +ATOM HN1 HC 0.24 ! | +ATOM HN2 HC 0.24 ! -CA HN1 +ATOM CD CP3 0.16 ! / \ / +ATOM HD1 HA 0.09 ! N(+) +ATOM HD2 HA 0.09 ! / \ +ATOM CA CP1 0.16 ! -CD HN2 +ATOM HA HB 0.09 ! | \ +BOND HN1 N HN2 N ! HD1 HD2 +DONOR HN1 N +DONOR HN2 N +IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES ACE 0.00 ! acetylated N-terminus +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA 0.09 ! \ | / +ATOM HY3 HA 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA HN +CMAP CY N CA C N CA C +N +ACCEPTOR OY CY +IC CY N CA C 1.3473 123.21 -65.33 112.79 1.5234 ! edit +IC CY CA *N HN 1.3473 123.21 -179.26 116.79 0.9935 ! edit +IC CAY CY N CA 1.5183 116.50 180.00 123.21 1.4518 ! edit +IC N CAY *CY OY 1.3473 116.50 -177.91 122.81 1.2248 ! edit +IC OY CY CAY HY1 1.2248 122.81 180.00 109.50 1.1110 ! edit +IC OY CY CAY HY2 1.2248 122.81 60.00 109.50 1.1110 ! edit +IC OY CY CAY HY3 1.2248 122.81 -60.00 109.50 1.1110 ! edit + +PRES ACP 0.00 ! acetylated N-terminus for proline +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA 0.09 ! \ | / +ATOM HY3 HA 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA CD +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES CTER -1.00 ! standard C-terminus +GROUP ! use in generate statement +ATOM C CC 0.34 ! OT2(-) +ATOM OT1 OC -0.67 ! / +ATOM OT2 OC -0.67 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +!IMPR OT1 CA OT2 C +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT1 0.00 ! methylated C-terminus from methyl acetate +GROUP ! use in generate statement +ATOM N NH1 -0.47 ! +ATOM HN H 0.31 ! OT1 +ATOM CA CT1 0.17 ! | // +ATOM HA HB 0.09 ! -N--CA--C HT1 +ATOM C CD 0.63 ! | | \ / +ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2 +ATOM OT2 OS -0.34 ! \ +ATOM CT CT3 -0.14 ! HT3 +ATOM HT1 HA 0.09 ! +ATOM HT2 HA 0.09 ! +ATOM HT3 HA 0.09 ! +DELETE ATOM O +BOND C OT2 OT2 CT +BOND CT HT1 CT HT2 CT HT3 +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 + +PRES CT2 0.00 ! amidated C-terminus +GROUP ! use in generate statement +ATOM C CC 0.55 ! +ATOM O O -0.55 ! | +GROUP ! O=C +ATOM NT NH2 -0.62 ! | +ATOM HT1 H 0.32 ! NT +ATOM HT2 H 0.30 ! / \ +BOND C NT ! HT1 HT2 +BOND NT HT1 NT HT2 ! +DIHE CA C NT HT2 ! (HT1 is cis to O) +IMPR C NT CA O C CA NT O +IMPR NT C HT1 HT2 NT C HT2 HT1 +DONOR HT1 NT +DONOR HT2 NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT3 0.00 ! N-Methylamide C-terminus +GROUP ! use in generate statement +ATOM C C 0.51 ! +ATOM O O -0.51 ! | +GROUP ! C=O +ATOM NT NH1 -0.47 ! | +ATOM HNT H 0.31 ! NT-HNT +ATOM CAT CT3 -0.11 ! | +ATOM HT1 HA 0.09 ! HT1-CAT-HT3 +ATOM HT2 HA 0.09 ! | +ATOM HT3 HA 0.09 ! HT2 + ! +BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 +!DIHE CA C NT CAT +IMPR NT C CAT HNT C CA NT O +CMAP -C N CA C N CA C NT +CMAP CY N CA C N CA C NT +DONOR HNT NT +IC N CA C O 1.4518 112.79 137.23 120.92 1.2247 ! edit +IC NT CA *C O 1.3479 118.41 176.60 120.92 1.2247 ! edit +IC C CAT *NT HNT 1.3479 120.00 -173.87 119.75 0.9941 ! edit +IC CA C NT CAT 1.5234 118.41 180.00 120.00 1.4300 ! edit +IC C NT CAT HT1 1.3479 120.00 60.00 109.50 1.1110 +IC C NT CAT HT2 1.3479 120.00 180.00 109.50 1.1110 +IC C NT CAT HT3 1.3479 120.00 -60.00 109.50 1.1110 + +PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 +GROUP ! via acetic acid, use in a patch statement +ATOM CB CT2 -0.21 ! +ATOM HB1 HA 0.09 ! HB1 OD1 +ATOM HB2 HA 0.09 ! | // +ATOM CG CD 0.75 ! -CB--CG +ATOM OD1 OB -0.55 ! | \ +ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2 +ATOM HD2 H 0.44 ! +BOND OD2 HD2 +ANGLE HD2 OD2 CG +DIHE HD2 OD2 CG OD1 HD2 OD2 CG CB +DONOR HD2 OD2 +IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 +GROUP ! via acetic acid, use in a patch statement +ATOM CG CT2 -0.21 ! +ATOM HG1 HA 0.09 ! HG1 OE1 +ATOM HG2 HA 0.09 ! | // +ATOM CD CD 0.75 ! -CG--CD +ATOM OE1 OB -0.55 ! | \ +ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2 +ATOM HE2 H 0.44 ! +BOND OE2 HE2 +ANGLE HE2 OE2 CD +DIHE HE2 OE2 CD OE1 HE2 OE2 CD CG +DONOR HE2 OE2 +IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES LINK 0.00 ! linkage for IMAGES or for joining segments + ! 1 refers to previous (N terminal) + ! 2 refers to next (C terminal) + ! use in a patch statement +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. +GROUP ! use in a patch statement +ATOM 1CB CT2 -0.10 ! +ATOM 1SG SM -0.08 ! 2SG--2CB-- +GROUP ! / +ATOM 2SG SM -0.08 ! -1CB--1SG +ATOM 2CB CT2 -0.10 ! +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +ANGLE 1CB 1SG 2SG 1SG 2SG 2CB +DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG +DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG +DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA +DIHE 1CB 1SG 2SG 2CB +!DIHE 1CB 1SG 2SG 2CB +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 +GROUP ! use in a patch statement +ATOM CE1 CPH2 0.25 ! HE1 +ATOM HE1 HR1 0.13 ! / +ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1 +ATOM CG CPH1 0.22 ! | / | +ATOM CB CT2 -0.08 ! -CB--CG | +ATOM HB1 HA 0.09 ! | \ | +ATOM HB2 HA 0.09 ! HB2 CD2--NE2 +GROUP ! | \ +ATOM NE2 NR1 -0.36 ! HD2 HE2 +ATOM HE2 H 0.32 +ATOM CD2 CPH1 -0.05 +ATOM HD2 HR3 0.09 +DELETE ATOM HD1 +DELETE ACCE NE2 +BOND NE2 HE2 +ANGLE CD2 NE2 HE2 CE1 NE2 HE2 +DIHE HE2 NE2 CE1 HE1 HE2 NE2 CE1 ND1 HE2 NE2 CD2 HD2 +DIHE HE2 NE2 CD2 CG +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +DONOR HE2 NE2 +ACCEPTOR ND1 +IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI O2 0.00 ! O2 ligand for heme +GROUP +ATOM O1 OM 0.021 +ATOM O2 OM -0.021 +BOND O1 O2 +PATCHING FIRS NONE LAST NONE + +RESI CO 0.00 ! CO ligand for heme +GROUP +ATOM C CM 0.021 +ATOM O OM -0.021 +TRIPLE C O +PATCHING FIRS NONE LAST NONE + +PRES FHEM 0.00 ! FIX UP THE HEME BY DELETING UNWANTED AUTOGENERATED ANGLES + ! unliganded heme patch +DELETE ANGLE 1NA 1FE 1NC 1NB 1FE 1ND + +PRES PHEM 0.00 ! Patch for HEME to His link. + ! Patch residues must be 1-HIS, and 2-HEME. +DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND +BOND 1NE2 2FE +ANGLE 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB +ANGLE 1NE2 2FE 2NC 1NE2 2FE 2ND +IC 1CD2 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1CE1 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES PLO2 0.00 ! Patch residue for Heme ligand. Residues must be + ! 1-O2 , 2-HEME , and 3-HIS + ! O1 of the oxygen is bonded to the iron. +BOND 1O1 2FE +ANGLE 1O2 1O1 2FE 1O1 2FE 2NA 1O1 2FE 2NB +ANGLE 1O1 2FE 2NC 1O1 2FE 2ND +DIHE 1O2 1O1 2FE 2NA +IC 1O2 1O1 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1O2 1O1 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES PLIG 0.00 ! Patch residue for Heme ligand. Residues must be, + ! 1-CO , 2-HEME , and 3-HIS +BOND 1C 2FE +ANGLE 1C 2FE 3NE2 +ANGLE 1O 1C 2FE 1C 2FE 2NA 1C 2FE 2NB +ANGLE 1C 2FE 2NC 1C 2FE 2ND +IC 1O 1C 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC 1O 1C 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 + +! patches for cyclic peptides +PRES LIG1 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG2 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 +DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG3 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE +BOND 1C 2N +ANGLE 1C 2N 2CA 1CA 1C 2N +ANGLE 1O 1C 2N 1C 2N 2HN +DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 +DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N +DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +DIHE 1CA 1C 2N 2CA +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI DUM 0.00 ! DUMMY ATOM +GROUP +ATOM DUM DUM 0.00 +PATCHING FIRST NONE LAST NONE + +END + +! The following patches for phosphotyrosine must be used with a +! parameter file containing both the protein and nucleic acid parameters. +! In addition, the commented parameters listed below must be included +! in the combined parameter file +! +PRES TP1 -1.00 ! convert tyrosine to monoanionic phosphotyrosine + ! use in a patch statement as follows +! +! patch to convert tyrosine to phenolphosphate +!PATCH TP1 TYR 1 SETUP WARN +! +! this patch requires that the use of the following +! +!1) protein topology file that contains mass list of atoms in both +! the protein and nucleic acid topology files and +! +! add to the topology file +!MASS 179 ON2b 15.999400 ! Nucleic acid phosphate ester oxygen (pres tp1/tp2) +! +!2) parameter file that contains both the protein and nucleic acid +! parameters plus the parameters listed below +! +! parameters to be added to the protein/nucleic acid parameter file +! +!bonds +!CA ON2b 340.0 1.38 !phenol phosphate, 6/94, adm jr. +!ON2b P 270.0 1.61 !phenol phosphate, 6/94, adm jr. +!angles +!CA CA ON2b 75.0 120.0 !phenol phosphate, 6/94, adm jr. +!CA ON2b P 90.0 120.0 20. 2.30 !phenol phosphate, 6/94, adm jr. +!ON4 P ON2b 48.1 108.0 !phenol phosphate, 6/94, adm jr. +!ON3 P ON2b 98.9 103.0 !phenol phosphate, 6/94, adm jr. +!dihedrals +!CA CA CA ON2b 3.10 2 180.0 !phenol phosphate, 6/94, adm jr. +!HP CA CA ON2b 4.20 2 180.0 !phenol phosphate, 6/94, adm jr. +!CA CA ON2b P 1.40 2 180.0 !phenol phosphate, 6/94, adm jr. +!CA CA ON2b P 0.20 3 180.0 !phenol phosphate, 6/94, adm jr. +!CA ON2b P ON4 0.95 2 0.0 !phenol phosphate, 6/94, adm jr. +!CA ON2b P ON4 0.50 3 0.0 !phenol phosphate, 6/94, adm jr. +!CA ON2b P ON3 0.10 3 0.0 !phenol phosphate, 6/94, adm jr. +!nonbonded +!ON2b 0.0 -0.1521 1.77 +! +! end of parameters to be added + +DELE ATOM 1HH + +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.21 +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.16 +ATOM OH ON2b -0.36 ! NA ATOM TYPE +ATOM P1 P 1.40 ! NA ATOM TYPE +ATOM O2 ON4 -0.76 ! NA ATOM TYPE +ATOM H2 HN4 0.40 ! NA ATOM TYPE +ATOM O3 ON3 -0.76 ! NA ATOM TYPE +ATOM O4 ON3 -0.76 ! NA ATOM TYPE +BOND P1 OH P1 O2 P1 O3 P1 O4 +BOND O2 H2 +ANGL CZ OH P1 +ANGL OH P1 O2 OH P1 O3 OH P1 O4 +ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 +ANGL P1 O2 H2 +DIHE CE1 CZ OH P1 CE2 CZ OH P1 +DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 +DIHE OH P1 O2 H2 O3 P1 O2 H2 O4 P1 O2 H2 +BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 +BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +BILD H2 O2 P1 OH 0.0000 000.00 180.00 000.00 0.0000 + +PRES TP1A -1.00 ! patch to convert tyrosine to + ! monoanionic phenol-phosphate model compound + ! use in patch statement +DELE ATOM N +DELE ATOM HN +DELE ATOM CA +DELE ATOM HA +DELE ATOM CB +DELE ATOM HB1 +DELE ATOM HB2 +DELE ATOM C +DELE ATOM O + +DELE ATOM 1HH + +GROUP +ATOM CG CA -0.115 +ATOM HG HP 0.115 +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.21 +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.16 +ATOM OH ON2B -0.36 ! NA ATOM TYPE +ATOM P1 P 1.40 ! NA ATOM TYPE +ATOM O2 ON4 -0.76 ! NA ATOM TYPE +ATOM H2 HN4 0.40 ! NA ATOM TYPE +ATOM O3 ON3 -0.76 ! NA ATOM TYPE +ATOM O4 ON3 -0.76 ! NA ATOM TYPE +BOND P1 OH P1 O2 P1 O3 P1 O4 +BOND O2 H2 +BOND CG HG +ANGL CZ OH P1 +ANGL OH P1 O2 OH P1 O3 OH P1 O4 +ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 +ANGL P1 O2 H2 +ANGL HG CG CD1 HG CG CD2 +DIHE CE1 CZ OH P1 CE2 CZ OH P1 +DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 +DIHE OH P1 O2 H2 O3 P1 O2 H2 O4 P1 O2 H2 +DIHE HG CG CD1 CE1 HG CG CD1 HD1 +DIHE HG CG CD2 CE2 HG CG CD2 HD2 +BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 +BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +BILD H2 O2 P1 OH 0.0000 000.00 180.00 000.00 0.0000 +BILD CD1 CD2 *CG HG 1.3978 120.09 179.64 120.58 1.0799 + +PRES TP2 -2.00 ! patch to convert tyrosine to + ! dianionic phosphotyrosine + ! use in patch statement + ! +! see PRES TP1 for proper preparation of the topology and +! parameter files +! +DELE ATOM 1HH +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.21 +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.28 +ATOM OH ON2B -0.28 ! NA ATOM TYPE +ATOM P1 P 1.44 ! NA ATOM TYPE +ATOM O2 ON3 -0.96 ! NA ATOM TYPE +ATOM O3 ON3 -0.96 ! NA ATOM TYPE +ATOM O4 ON3 -0.96 ! NA ATOM TYPE +BOND P1 OH P1 O2 P1 O3 P1 O4 +ANGL CZ OH P1 +ANGL OH P1 O2 OH P1 O3 OH P1 O4 +ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 +DIHE CE1 CZ OH P1 CE2 CZ OH P1 +DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 +BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 +BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 + +PRES TP2A -2.00 ! patch to convert tyrosine to + ! dianionic phosphotyrosine + ! use in patch statement + ! +! this converts a single tyrosine to a phenol phosphate +! see PRES TP1 for proper preparation of the topology and +! parameter files + +DELE ATOM N +DELE ATOM HN +DELE ATOM CA +DELE ATOM HA +DELE ATOM CB +DELE ATOM HB1 +DELE ATOM HB2 +DELE ATOM C +DELE ATOM O + +DELE ATOM 1HH + +GROUP +ATOM CG CA -0.115 +ATOM HG HP 0.115 +GROUP +ATOM CE1 CA -0.21 +ATOM HE1 HP 0.21 +GROUP +ATOM CE2 CA -0.21 +ATOM HE2 HP 0.21 +GROUP +ATOM CZ CA -0.28 +ATOM OH ON2B -0.28 ! NA ATOM TYPE +ATOM P1 P 1.44 ! NA ATOM TYPE +ATOM O2 ON3 -0.96 ! NA ATOM TYPE +ATOM O3 ON3 -0.96 ! NA ATOM TYPE +ATOM O4 ON3 -0.96 ! NA ATOM TYPE +BOND P1 OH P1 O2 P1 O3 P1 O4 +BOND CG HG +ANGL CZ OH P1 +ANGL OH P1 O2 OH P1 O3 OH P1 O4 +ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 +ANGL HG CG CD1 HG CG CD2 +DIHE CE1 CZ OH P1 CE2 CZ OH P1 +DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 +DIHE HG CG CD1 CE1 HG CG CD1 HD1 +DIHE HG CG CD2 CE2 HG CG CD2 HD2 +BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 +BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +BILD CD1 CD2 *CG HG 1.3978 120.09 179.64 120.58 1.0799 + +END + + diff --git a/charmm/toppar/top_all22_prot.rtf b/charmm/toppar/top_all22_prot.rtf new file mode 100644 index 00000000..b22e7e54 --- /dev/null +++ b/charmm/toppar/top_all22_prot.rtf @@ -0,0 +1,1682 @@ +*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<< +*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< +*>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<< +* All comments to ADM jr. via the CHARMM web site: www.charmm.org +* parameter set discussion forum +* +31 1 + +! references +! +!MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the +!treatment of backbone energetics in protein force fields: limitations +!of gas-phase quantum mechanics in reproducing protein conformational +!distributions in molecular dynamics simulations, Journal of +!Computational Chemistry, 25: 1400-1415, 2004. +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. + +MASS 41 H 1.00800 H ! polar H +MASS 42 HC 1.00800 H ! N-ter H +MASS 43 HA 1.00800 H ! nonpolar H +MASS 44 HP 1.00800 H ! aromatic H +MASS 45 HB 1.00800 H ! backbone H +MASS 46 HR1 1.00800 H ! his he1, (+) his HG,HD2 +MASS 47 HR2 1.00800 H ! (+) his HE1 +MASS 48 HR3 1.00800 H ! neutral his HG, HD2 +MASS 49 HS 1.00800 H ! thiol hydrogen +MASS 50 HE1 1.00800 H ! for alkene; RHC=CR +MASS 51 HE2 1.00800 H ! for alkene; H2C=CR +MASS 52 C 12.01100 C ! carbonyl C, peptide backbone +MASS 53 CA 12.01100 C ! aromatic C +MASS 54 CT1 12.01100 C ! aliphatic sp3 C for CH +MASS 55 CT2 12.01100 C ! aliphatic sp3 C for CH2 +MASS 56 CT3 12.01100 C ! aliphatic sp3 C for CH3 +MASS 57 CPH1 12.01100 C ! his CG and CD2 carbons +MASS 58 CPH2 12.01100 C ! his CE1 carbon +MASS 59 CPT 12.01100 C ! trp C between rings +MASS 60 CY 12.01100 C ! TRP C in pyrrole ring +MASS 61 CP1 12.01100 C ! tetrahedral C (proline CA) +MASS 62 CP2 12.01100 C ! tetrahedral C (proline CB/CG) +MASS 63 CP3 12.01100 C ! tetrahedral C (proline CD) +MASS 64 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS 65 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 +MASS 66 CS 12.01100 C ! thiolate carbon +MASS 67 CE1 12.01100 C ! for alkene; RHC=CR +MASS 68 CE2 12.01100 C ! for alkene; H2C=CR +MASS 69 C3 12.01100 C ! cyclopropyl carbon +MASS 70 N 14.00700 N ! proline N +MASS 71 NR1 14.00700 N ! neutral his protonated ring nitrogen +MASS 72 NR2 14.00700 N ! neutral his unprotonated ring nitrogen +MASS 73 NR3 14.00700 N ! charged his ring nitrogen +MASS 74 NH1 14.00700 N ! peptide nitrogen +MASS 75 NH2 14.00700 N ! amide nitrogen +MASS 76 NH3 14.00700 N ! ammonium nitrogen +MASS 77 NC2 14.00700 N ! guanidinium nitroogen +MASS 78 NY 14.00700 N ! TRP N in pyrrole ring +MASS 79 NP 14.00700 N ! Proline ring NH2+ (N-terminal) +MASS 80 O 15.99900 O ! carbonyl oxygen +MASS 81 OB 15.99900 O ! carbonyl oxygen in acetic acid +MASS 82 OC 15.99900 O ! carboxylate oxygen +MASS 83 OH1 15.99900 O ! hydroxyl oxygen +MASS 84 OS 15.99940 O ! ester oxygen +MASS 85 S 32.06000 S ! sulphur +MASS 86 SM 32.06000 S ! sulfur C-S-S-C type +MASS 87 SS 32.06000 S ! thiolate sulfur + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI ALA 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB 0.09 ! | / +GROUP ! HA-CA--CB-HB2 +ATOM CB CT3 -0.27 ! | \ +ATOM HB1 HA 0.09 ! | HB3 +ATOM HB2 HA 0.09 ! O=C +ATOM HB3 HA 0.09 ! | +GROUP ! +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA N HN N CA +BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +RESI ARG 1.00 +GROUP +ATOM N NH1 -0.47 ! | HH11 +ATOM HN H 0.31 ! HN-N | +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA HB 0.09 ! | | | | | //(+) +GROUP ! HA-CA--CB--CG--CD--NE--CZ +ATOM CB CT2 -0.18 ! | | | | \ +ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HB2 HA 0.09 ! O=C | +GROUP ! | HH21 +ATOM CG CT2 -0.18 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +GROUP +ATOM CD CT2 0.20 +ATOM HD1 HA 0.09 +ATOM HD2 HA 0.09 +ATOM NE NC2 -0.70 +ATOM HE HC 0.44 +ATOM CZ C 0.64 +ATOM NH1 NC2 -0.80 +ATOM HH11 HC 0.46 +ATOM HH12 HC 0.46 +ATOM NH2 NC2 -0.80 +ATOM HH21 HC 0.46 +ATOM HH22 HC 0.46 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE O C CZ NH1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +IMPR CZ NH1 NH2 NE +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +RESI ASN 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA HB 0.09 ! | | || / +GROUP ! HA-CA--CB--CG--ND2 +ATOM CB CT2 -0.18 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 HD22 (trans to OD1) +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CC 0.55 +ATOM OD1 O -0.55 +GROUP +ATOM ND2 NH2 -0.62 +ATOM HD21 H 0.32 +ATOM HD22 H 0.30 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +DOUBLE C O CG OD1 +IMPR N -C CA HN C CA +N O +IMPR CG ND2 CB OD1 CG CB ND2 OD1 +IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +RESI ASP -1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 OD1 +ATOM HA HB 0.09 ! | | // +GROUP ! HA-CA--CB--CG +ATOM CB CT2 -0.28 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 OD2(-) +ATOM HB2 HA 0.09 ! O=C +ATOM CG CC 0.62 ! | +ATOM OD1 OC -0.76 +ATOM OD2 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +DOUBLE O C CG OD1 +IMPR N -C CA HN C CA +N O +!IMPR OD1 CB OD2 CG +IMPR CG CB OD2 OD1 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +RESI CYS 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB 0.09 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB CT2 -0.11 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 HG1 +ATOM HB2 HA 0.09 ! O=C +ATOM SG S -0.23 ! | +ATOM HG1 HS 0.16 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +RESI GLN 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA HB 0.09 ! | | | || / +GROUP ! HA-CA--CB--CG--CD--NE2 +ATOM CB CT2 -0.18 ! | | | \ +ATOM HB1 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1) +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +GROUP +ATOM CD CC 0.55 +ATOM OE1 O -0.55 +GROUP +ATOM NE2 NH2 -0.62 +ATOM HE21 H 0.32 +ATOM HE22 H 0.30 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD NE2 CG OE1 CD CG NE2 OE1 +IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +RESI GLU -1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 OE1 +ATOM HA HB 0.09 ! | | | // +GROUP ! HA-CA--CB--CG--CD +ATOM CB CT2 -0.18 ! | | | \ +ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-) +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.28 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +ATOM CD CC 0.62 +ATOM OE1 OC -0.76 +ATOM OE2 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD CG OE2 OE1 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI GLY 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! N-H +ATOM CA CT2 -0.02 ! | +ATOM HA1 HB 0.09 ! | +ATOM HA2 HB 0.09 ! HA1-CA-HA2 +GROUP ! | +ATOM C C 0.51 ! | +ATOM O O -0.51 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 +PATCHING FIRS GLYP + +RESI HSD 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 -0.09 ! | | \\ || +ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA 0.09 ! O=C | +ATOM ND1 NR1 -0.36 ! | HD2 +ATOM HD1 H 0.32 +ATOM CG CPH1 -0.05 +GROUP +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +ATOM NE2 NR2 -0.70 +ATOM CD2 CPH1 0.22 +ATOM HD2 HR3 0.10 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +RESI HSE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N NH1 -0.47 ! | HE1 +ATOM HN H 0.31 ! HN-N __ / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB 0.09 ! | | / | +GROUP ! HA-CA--CB--CG | +ATOM CB CT2 -0.08 ! | | \\ | +ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA 0.09 ! O=C | \ +ATOM ND1 NR2 -0.70 ! | HD2 HE2 +ATOM CG CPH1 0.22 +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +GROUP +ATOM NE2 NR1 -0.36 +ATOM HE2 H 0.32 +ATOM CD2 CPH1 -0.05 +ATOM HD2 HR3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG CE1 ND1 +IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +RESI HSP 1.00 ! Protonated His +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 -0.05 ! | | \\ || +ATOM HB1 HA 0.09 ! | HB2 CD2--NE2(+) +ATOM HB2 HA 0.09 ! O=C | \ +ATOM CD2 CPH1 0.19 ! | HD2 HE2 +ATOM HD2 HR1 0.13 +ATOM CG CPH1 0.19 +GROUP +ATOM NE2 NR3 -0.51 +ATOM HE2 H 0.44 +ATOM ND1 NR3 -0.51 +ATOM HD1 H 0.44 +ATOM CE1 CPH2 0.32 +ATOM HE1 HR2 0.18 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG NE2 CE1 +IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +RESI ILE 0.00 +GROUP +ATOM N NH1 -0.47 ! | HG21 HG22 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | CG2--HG23 +ATOM HA HB 0.09 ! | / +GROUP ! HA-CA--CB-HB HD1 +ATOM CB CT1 -0.09 ! | \ / +ATOM HB HA 0.09 ! | CG1--CD--HD2 +GROUP ! O=C / \ \ +ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3 +ATOM HG21 HA 0.09 +ATOM HG22 HA 0.09 +ATOM HG23 HA 0.09 +GROUP +ATOM CG1 CT2 -0.18 +ATOM HG11 HA 0.09 +ATOM HG12 HA 0.09 +GROUP +ATOM CD CT3 -0.27 +ATOM HD1 HA 0.09 +ATOM HD2 HA 0.09 +ATOM HD3 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + +RESI LEU 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD11 HD12 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 CD1--HD13 +ATOM HA HB 0.09 ! | | / +GROUP ! HA-CA--CB--CG-HG +ATOM CB CT2 -0.18 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 CD2--HD23 +ATOM HB2 HA 0.09 ! O=C | \ +GROUP ! | HD21 HD22 +ATOM CG CT1 -0.09 +ATOM HG HA 0.09 +GROUP +ATOM CD1 CT3 -0.27 +ATOM HD11 HA 0.09 +ATOM HD12 HA 0.09 +ATOM HD13 HA 0.09 +GROUP +ATOM CD2 CT3 -0.27 +ATOM HD21 HA 0.09 +ATOM HD22 HA 0.09 +ATOM HD23 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +RESI LYS 1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA HB 0.09 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM CB CT2 -0.18 ! | | | | | \ +ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +GROUP +ATOM CD CT2 -0.18 +ATOM HD1 HA 0.09 +ATOM HD2 HA 0.09 +GROUP +ATOM CE CT2 0.21 +ATOM HE1 HA 0.05 +ATOM HE2 HA 0.05 +ATOM NZ NH3 -0.30 +ATOM HZ1 HC 0.33 +ATOM HZ2 HC 0.33 +ATOM HZ3 HC 0.33 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUBLE O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI MET 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HE1 +ATOM HA HB 0.09 ! | | | | +GROUP ! HA-CA--CB--CG--SD--CE--HE3 +ATOM CB CT2 -0.18 ! | | | | +ATOM HB1 HA 0.09 ! | HB2 HG2 HE2 +ATOM HB2 HA 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.14 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +ATOM SD S -0.09 +ATOM CE CT3 -0.22 +ATOM HE1 HA 0.09 +ATOM HE2 HA 0.09 +ATOM HE3 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +RESI PHE 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | | +ATOM CA CT1 0.07 ! | HB1 CD1--CE1 +ATOM HA HB 0.09 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--HZ +ATOM CB CT2 -0.18 ! | | \ __ / +ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 +ATOM HB2 HA 0.09 ! O=C | | +GROUP ! | HD2 HE2 +ATOM CG CA 0.00 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA -0.115 +ATOM HZ HP 0.115 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +RESI PRO 0.00 +GROUP ! HD1 HD2 +ATOM N N -0.29 ! | \ / +ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02 +ATOM HD1 HA 0.09 ! | \ / +ATOM HD2 HA 0.09 ! | CG +ATOM CA CP1 0.02 ! | / \ +ATOM HA HB 0.09 ! HA-CA--CB HG2 +GROUP ! | / \ +ATOM CB CP2 -0.18 ! | HB1 HB2 +ATOM HB1 HA 0.09 ! O=C +ATOM HB2 HA 0.09 ! | +GROUP +ATOM CG CP2 -0.18 +ATOM HG1 HA 0.09 +ATOM HG2 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +DOUBLE O C +IMPR N -C CA CD +IMPR C CA +N O +CMAP -C N CA C N CA C +N +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 +PATCHING FIRS PROP + +RESI SER 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB 0.09 ! | | +GROUP ! HA-CA--CB--OG +ATOM CB CT2 0.05 ! | | \ +ATOM HB1 HA 0.09 ! | HB2 HG1 +ATOM HB2 HA 0.09 ! O=C +ATOM OG OH1 -0.66 ! | +ATOM HG1 H 0.43 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +RESI THR 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | OG1--HG1 +ATOM HA HB 0.09 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 0.14 ! | \ +ATOM HB HA 0.09 ! | CG2--HG21 +ATOM OG1 OH1 -0.66 ! O=C / \ +ATOM HG1 H 0.43 ! | HG21 HG22 +GROUP +ATOM CG2 CT3 -0.27 +ATOM HG21 HA 0.09 +ATOM HG22 HA 0.09 +ATOM HG23 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +RESI TRP 0.00 +GROUP +ATOM N NH1 -0.47 ! | HE3 +ATOM HN H 0.31 ! HN-N | +ATOM CA CT1 0.07 ! | HB1 CE3 +ATOM HA HB 0.09 ! | | / \\ +GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM CB CT2 -0.18 ! | | || || | +ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2 +ATOM HB2 HA 0.09 ! O=C / \ / \ // +GROUP ! | HD1 NE1 CZ2 +ATOM CG CY -0.03 ! | | +ATOM CD1 CA 0.035 ! HE1 HZ2 +ATOM HD1 HP 0.115 +ATOM NE1 NY -0.61 +ATOM HE1 H 0.38 +ATOM CE2 CPT 0.13 +ATOM CD2 CPT -0.02 +GROUP +ATOM CE3 CA -0.115 +ATOM HE3 HP 0.115 +GROUP +ATOM CZ3 CA -0.115 +ATOM HZ3 HP 0.115 +GROUP +ATOM CZ2 CA -0.115 +ATOM HZ2 HP 0.115 +GROUP +ATOM CH2 CA -0.115 +ATOM HH2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI TYR 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | | +ATOM CA CT1 0.07 ! | HB1 CD1--CE1 +ATOM HA HB 0.09 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--OH +ATOM CB CT2 -0.18 ! | | \ __ / \ +ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 HH +ATOM HB2 HA 0.09 ! O=C | | +GROUP ! | HD2 HE2 +ATOM CG CA 0.00 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA 0.11 +ATOM OH OH1 -0.54 +ATOM HH H 0.43 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +DOUBLE O C CD1 CG CE1 CZ CE2 CD2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +RESI VAL 0.00 +GROUP +ATOM N NH1 -0.47 ! | HG11 HG12 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | CG1--HG13 +ATOM HA HB 0.09 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 -0.09 ! | \ +ATOM HB HA 0.09 ! | CG2--HG21 +GROUP ! O=C / \ +ATOM CG1 CT3 -0.27 ! | HG21 HG22 +ATOM HG11 HA 0.09 +ATOM HG12 HA 0.09 +ATOM HG13 HA 0.09 +GROUP +ATOM CG2 CT3 -0.27 +ATOM HG21 HA 0.09 +ATOM HG22 HA 0.09 +ATOM HG23 HA 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +RESI ALAD 0.00 ! Alanine dipeptide, with CMAP term +GROUP +ATOM CL CT3 -0.27 +ATOM HL1 HA 0.09 +ATOM HL2 HA 0.09 +ATOM HL3 HA 0.09 +GROUP +ATOM CLP C 0.51 +ATOM OL O -0.51 +GROUP +ATOM NL NH1 -0.47 +ATOM HL H 0.31 +ATOM CA CT1 0.07 +ATOM HA HB 0.09 +GROUP +ATOM CB CT3 -0.27 ! HL1 OL OR HR1 +ATOM HB1 HA 0.09 ! \ || HL HA || HR / +ATOM HB2 HA 0.09 ! \ || | | || | / +ATOM HB3 HA 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 +GROUP ! / | \ +ATOM CRP C 0.51 ! / HB1--CB--HB3 \ +ATOM OR O -0.51 ! HL3 | HR3 +GROUP ! HB2 +ATOM NR NH1 -0.47 +ATOM HR H 0.31 +ATOM CR CT3 -0.11 +ATOM HR1 HA 0.09 +ATOM HR2 HA 0.09 +ATOM HR3 HA 0.09 + +BOND CL CLP CLP NL NL CA +BOND CA CRP CRP NR NR CR +DOUBLE CLP OL CRP OR +BOND NL HL NR HR +BOND CA HA CA CB +BOND CL HL1 CL HL2 CL HL3 +BOND CB HB1 CB HB2 CB HB3 +BOND CR HR1 CR HR2 CR HR3 +IMPR CLP CL NL OL NL CLP CA HL +IMPR CRP CA NR OR NR CRP CR HR + +CMAP CLP NL CA CRP NL CA CRP NR + +ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0 +ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic nl ca crp or 0.0 0.0 0.0 0.0 0.0 +ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left +ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0 +ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0 +ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right +ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0 +ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0 +ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0 +ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0 +ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0 +ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0 +ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0 +ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0 +ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0 +ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0 +ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0 +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0 +ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0 +ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0 +ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0 +patch first none last none + +PRES NTER 1.00 ! standard N-terminus +GROUP ! use in generate statement +ATOM N NH3 -0.30 ! +ATOM HT1 HC 0.33 ! HT1 +ATOM HT2 HC 0.33 ! (+)/ +ATOM HT3 HC 0.33 ! --CA--N--HT2 +ATOM CA CT1 0.21 ! | \ +ATOM HA HB 0.10 ! HA HT3 +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES GLYP 1.00 ! Glycine N-terminus +GROUP ! use in generate statement +ATOM N NH3 -0.30 ! +ATOM HT1 HC 0.33 ! HA1 HT1 +ATOM HT2 HC 0.33 ! | (+)/ +ATOM HT3 HC 0.33 ! --CA--N--HT2 +ATOM CA CT2 0.13 ! | \ +ATOM HA1 HB 0.09 ! HA2 HT3 +ATOM HA2 HB 0.09 ! +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES PROP 1.00 ! Proline N-Terminal +GROUP ! use in generate statement +ATOM N NP -0.07 ! HA +ATOM HN1 HC 0.24 ! | +ATOM HN2 HC 0.24 ! -CA HN1 +ATOM CD CP3 0.16 ! / \ / +ATOM HD1 HA 0.09 ! N(+) +ATOM HD2 HA 0.09 ! / \ +ATOM CA CP1 0.16 ! -CD HN2 +ATOM HA HB 0.09 ! | \ +BOND HN1 N HN2 N ! HD1 HD2 +DONOR HN1 N +DONOR HN2 N +IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES ACE 0.00 ! acetylated N-terminus + ! do NOT use to create dipeptides, see ACED +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA 0.09 ! \ | / +ATOM HY3 HA 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA HN +CMAP CY N CA C N CA C +N +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACED 0.00 ! acetylated N-terminus (to create dipeptide) +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA 0.09 ! \ | / +ATOM HY3 HA 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA HN +CMAP CY N CA C N CA C NT +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACP 0.00 ! acetylated N-terminus + ! NOT for proline dipeptide, see ACPD +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA 0.09 ! \ | / +ATOM HY3 HA 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA CD +CMAP CY N CA C N CA C +N +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACPD 0.00 ! acetylated N-terminus (for proline dipeptide) +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA 0.09 ! \ | / +ATOM HY3 HA 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA CD +CMAP CY N CA C N CA C NT +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES NNEU 0.00 ! neutral N-terminus; charges from LSN +GROUP ! use in generate statement +ATOM N NH2 -0.96 ! +ATOM HT1 H 0.34 ! HT1 +ATOM HT2 H 0.34 ! / + ! --CA--N--HT2 +ATOM CA CT1 0.19 ! | ! change to CT2 for neutral N terminal glycine +ATOM HA HB 0.09 ! HA ! change to HA1 and HB2 and add HA2 atom for N terminal glycine +DELETE ATOM HN +BOND HT1 N HT2 N +DONOR HT1 N +DONOR HT2 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CTER -1.00 ! standard C-terminus +GROUP ! use in generate statement +ATOM C CC 0.34 ! OT2(-) +ATOM OT1 OC -0.67 ! / +ATOM OT2 OC -0.67 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT1 0.00 ! methylated C-terminus from methyl acetate +GROUP ! use in generate statement +ATOM N NH1 -0.47 ! +ATOM HN H 0.31 ! OT1 +ATOM CA CT1 0.17 ! | // +ATOM HA HB 0.09 ! -N--CA--C HT1 +ATOM C CD 0.63 ! | | \ / +ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2 +ATOM OT2 OS -0.34 ! \ +ATOM CT CT3 -0.14 ! HT3 +ATOM HT1 HA 0.09 ! +ATOM HT2 HA 0.09 ! +ATOM HT3 HA 0.09 ! +DELETE ATOM O +BOND C OT2 OT2 CT +BOND CT HT1 CT HT2 CT HT3 +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 + +PRES CT2 0.00 ! amidated C-terminus +GROUP ! use in generate statement +ATOM C CC 0.55 ! +ATOM O O -0.55 ! | +GROUP ! O=C +ATOM NT NH2 -0.62 ! | +ATOM HT1 H 0.32 ! NT +ATOM HT2 H 0.30 ! / \ +BOND C NT ! HT1 HT2 (HT1 is cis to O) +BOND NT HT1 NT HT2 ! +IMPR C NT CA O C CA NT O +IMPR NT C HT1 HT2 NT C HT2 HT1 +DONOR HT1 NT +DONOR HT2 NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT3 0.00 ! N-Methylamide C-terminus +GROUP ! use in generate statement +ATOM C C 0.51 ! +ATOM O O -0.51 ! | +GROUP ! C=O +ATOM NT NH1 -0.47 ! | +ATOM HNT H 0.31 ! NT-HNT +ATOM CAT CT3 -0.11 ! | +ATOM HT1 HA 0.09 ! HT1-CAT-HT3 +ATOM HT2 HA 0.09 ! | +ATOM HT3 HA 0.09 ! HT2 + ! +BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 +IMPR NT C CAT HNT C CA NT O +CMAP -C N CA C N CA C NT +DONOR HNT NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + + +PRES CNEU 0.00 ! neutral C-terminus; charges from ASPP +GROUP ! use in generate statement; C reduced to balance +ATOM C CD 0.72 ! OT2-HT2 +ATOM OT1 OB -0.55 ! / +ATOM OT2 OH1 -0.61 ! -C +ATOM HT2 H 0.44 ! \\ +DELETE ATOM O ! OT1 +BOND C OT2 ! +BOND OT2 HT2 +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 +GROUP ! via acetic acid, use in a patch statementand + ! follow with AUTOgenerate ANGLes DIHEdrals command +ATOM CB CT2 -0.21 ! +ATOM HB1 HA 0.09 ! HB1 OD1 +ATOM HB2 HA 0.09 ! | // +ATOM CG CD 0.75 ! -CB--CG +ATOM OD1 OB -0.55 ! | \ +ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2 +ATOM HD2 H 0.44 ! +BOND OD2 HD2 +DONOR HD2 OD2 +IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 +GROUP ! via acetic acid, use in a patch statement and + ! follow with AUTOgenerate ANGLes DIHEdrals command +ATOM CG CT2 -0.21 ! +ATOM HG1 HA 0.09 ! HG1 OE1 +ATOM HG2 HA 0.09 ! | // +ATOM CD CD 0.75 ! -CG--CD +ATOM OE1 OB -0.55 ! | \ +ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2 +ATOM HE2 H 0.44 ! +BOND OE2 HE2 +DONOR HE2 OE2 +IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES LSN 0.00 ! patch for neutral lysine based on methylamine + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +!delete atom and reassign charges +DELETE ATOM HZ3 +GROUP +ATOM CE CT2 0.13 +ATOM HE1 HA 0.075 +ATOM HE2 HA 0.075 +ATOM NZ NH2 -0.96 +ATOM HZ1 HC 0.34 +ATOM HZ2 HC 0.34 + +PRES LINK 0.00 ! linkage for IMAGES or for joining segments + ! 1 refers to previous (N terminal) + ! 2 refers to next (C terminal) + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +!the need for the explicit specification of angles and dihedrals in +!patches linking images has not been tested +!ANGLE 1C 2N 2CA 1CA 1C 2N +!ANGLE 1O 1C 2N 1C 2N 2HN +!DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +!DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +!DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +!DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM 1CB CT2 -0.10 ! +ATOM 1SG SM -0.08 ! 2SG--2CB-- +GROUP ! / +ATOM 2SG SM -0.08 ! -1CB--1SG +ATOM 2CB CT2 -0.10 ! +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM CE1 CPH2 0.25 ! HE1 +ATOM HE1 HR1 0.13 ! / +ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1 +ATOM CG CPH1 0.22 ! | / | +ATOM CB CT2 -0.08 ! -CB--CG | +ATOM HB1 HA 0.09 ! | \ | +ATOM HB2 HA 0.09 ! HB2 CD2--NE2 +GROUP ! | \ +ATOM NE2 NR1 -0.36 ! HD2 HE2 +ATOM HE2 H 0.32 +ATOM CD2 CPH1 -0.05 +ATOM HD2 HR3 0.09 +DELETE ATOM HD1 +DELETE ACCE NE2 +BOND NE2 HE2 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +DONOR HE2 NE2 +ACCEPTOR ND1 +IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 + +! patches for cyclic peptides +PRES LIG1 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus + ! use in a patch statement, perform initial + ! generation using first NONE last NONE + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG2 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG3 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +END + diff --git a/charmm/toppar/top_all35_ethers.rtf b/charmm/toppar/top_all35_ethers.rtf new file mode 100644 index 00000000..398d2622 --- /dev/null +++ b/charmm/toppar/top_all35_ethers.rtf @@ -0,0 +1,1213 @@ +*>>>>>>>>>>>>>>>>>>> All-hydrogen topology <<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>>>>>>>>>>> CHARMM32 ether force field <<<<<<<<<<<<<<<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>> December 2006 <<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< +*>>>>>>>>>>>> via the CHARMM forum: www.charmm.org <<<<<<<<<<<<<<< +* +34 + +!Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., +!Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude +!Polarizable Force Fields for Linear and Cyclic Ethers," Journal of +!Chemical Theory and Computing, 3: 1120-1133, 2007 +! +! O-C-C-O torsion modified; HK Lee, RM Venable, RW Pastor August 2007 +! +!Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor +!Molecular dynamics studies of polyethylene oxide and polyethylene glycol: +!Hydrodynamic radius and shape anisotropy +!Biophysical J., 95: 1590-1599, 2008 + +MASS 241 HCA1A 1.00800 H ! Alkane H attached to C(sp3)H (eq. HA1) +MASS 242 HCA2A 1.00800 H ! Alkane H attached to C(sp3)H2 (eq. HA2) +MASS 243 HCA3A 1.00800 H ! Alkane H attached to C(sp3)H3 (eq. HA3) +MASS 244 HCA25A 1.00800 H ! Alkane H attached to C(sp3)H2 in 5-membered ring +MASS 245 CC30A 12.01100 C ! -C(sp3) Carbon (eq. CT) +MASS 246 CC31A 12.01100 C ! -C(sp3)H Carbon (eq. CT1) +MASS 247 CC32A 12.01100 C ! -C(sp3)H2 Carbon (eq. CT2) +MASS 248 CC33A 12.01100 C ! -C(sp3)H3 Carbon (eq. CT3) +MASS 249 CC325A 12.01100 C ! -C(sp3)H2 Carbon in 5-membered ring +MASS 250 CC325B 12.01100 C ! -C(sp3)H2 Carbon in THF (tetrahydrofuran) +MASS 251 CC326A 12.01100 C ! -C(sp3)H2 Carbon in THP (tetrahydropyran) +MASS 252 OC30A 15.99940 O ! Ether Oxygen +MASS 253 OC305A 15.99940 O ! Ether Oxygen in THF + +DECL -C2 +DECL -O1 +DECL +C1 + +AUTOGENERATE angle dihe +DEFAULT FIRST HYD1 LAST HYD2 + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!! Linear alkanes from top_all27_alka.inp !!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +Resi ETHA 0.00 ! ethane +Group + Atom H11 HCA3A 0.09 ! H11 H21 + Atom H12 HCA3A 0.09 ! \ / + Atom H13 HCA3A 0.09 ! H12--C1--C2--H22 + Atom C1 CC33A -0.27 ! / \ +Group ! H13 H23 + Atom H21 HCA3A 0.09 + Atom H22 HCA3A 0.09 + Atom H23 HCA3A 0.09 + Atom C2 CC33A -0.27 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 h21 c2 h22 c2 h23 +! IC for ETHA staggered conformer MP2/6-31G* optimized +IC H11 C1 C2 H21 1.0932 111.18 180.00 111.18 1.0932 +IC H11 C1 C2 H22 1.0932 111.18 -60.00 111.18 1.0932 +IC H11 C1 C2 H23 1.0932 111.18 60.00 111.18 1.0932 +IC H12 C1 C2 H23 1.0932 111.18 180.00 111.18 1.0932 +IC H13 C1 C2 H23 1.0932 111.18 -60.00 111.18 1.0932 +IC C1 C2 H21 BLNK 1.5261 111.18 0.00 0.00 0.0000 +patc firs none last none + +Resi PROP 0.00 ! propane, adm jr. +Group ! + Atom H11 HCA3A 0.09 ! H11 H21 H31 + Atom H12 HCA3A 0.09 ! \ | / + Atom H13 HCA3A 0.09 ! H12-C1--C2--C3-H32 + Atom C1 CC33A -0.27 ! / | \ +Group ! H13 H22 H33 + Atom C2 CC32A -0.18 ! + Atom H21 HCA2A 0.09 ! + Atom H22 HCA2A 0.09 +Group + Atom H31 HCA3A 0.09 + Atom H32 HCA3A 0.09 + Atom H33 HCA3A 0.09 + Atom C3 CC33A -0.27 +Bond c1 h11 c1 h12 c1 h13 +Bond c1 c2 c2 h21 c2 h22 +bond c2 c3 c3 h31 c3 h32 c3 h33 +! IC for PROP staggered conformer MP2/6-31G* optimized +IC C1 C2 C3 H31 1.5260 112.39 59.77 110.82 1.0946 +IC C1 C2 C3 H32 1.5260 112.39 180.00 111.49 1.0938 +IC C1 C2 C3 H33 1.5260 112.39 -59.77 110.82 1.0946 +IC H11 C1 C2 C3 1.0946 110.82 -59.77 112.39 1.5260 +IC H11 C1 C2 H21 1.0946 110.82 62.14 109.48 1.0960 +IC H11 C1 C2 H22 1.0946 110.82 178.32 109.48 1.0960 +IC C3 C2 C1 H12 1.5260 112.39 59.77 110.82 1.0946 +IC C3 C2 C1 H13 1.5260 112.39 180.00 111.49 1.0938 +patc firs none last none + +Resi BUTA 0.00 ! butane +Group +Atom H11 HCA3A 0.09 ! H11 H21 H31 H41 +Atom H12 HCA3A 0.09 ! \ | | / +Atom H13 HCA3A 0.09 ! H12-C1--C2--C3--C4-H42 +Atom C1 CC33A -0.27 ! / | | \ +Group ! H13 H22 H33 H43 +Atom H21 HCA2A 0.09 +Atom H22 HCA2A 0.09 +Atom C2 CC32A -0.18 +Group +Atom H31 HCA2A 0.09 +Atom H32 HCA2A 0.09 +atom C3 CC32A -0.18 +Group +atom H41 HCA3A 0.09 +atom H42 HCA3A 0.09 +atom H43 HCA3A 0.09 +atom C4 CC33A -0.27 +Bond h11 c1 h12 c1 h13 c1 c1 c2 +Bond h21 c2 h22 c2 c2 c3 +Bond h31 c3 h32 c3 c3 c4 +Bond h41 c4 h42 c4 h43 c4 +! IC for BUTA trans conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5263 112.90 180.00 112.90 1.5263 +IC C1 C2 C3 H31 1.5263 112.90 57.85 109.11 1.0973 +IC C1 C2 C3 H32 1.5263 112.90 -57.85 109.11 1.0973 +IC C2 C3 C4 H41 1.5268 112.90 -59.80 110.84 1.0944 +IC C2 C3 C4 H42 1.5268 112.90 59.80 110.84 1.0944 +IC C2 C3 C4 H43 1.5268 112.90 180.00 111.48 1.0940 +IC H11 C1 C2 C3 1.0944 110.84 59.80 112.90 1.5268 +IC H11 C1 C2 H21 1.0944 110.84 -178.34 109.62 1.0973 +IC H11 C1 C2 H22 1.0944 110.84 -62.06 109.62 1.0973 +IC H12 C1 C2 C3 1.0940 111.48 -180.00 112.90 1.5268 +IC H13 C1 C2 C3 1.0944 110.84 -59.80 112.90 1.5268 +IC H21 C2 C3 C4 1.0973 109.11 57.85 112.90 1.5263 +IC H22 C2 C3 C4 1.0973 109.11 -57.85 112.90 1.5263 +IC H31 C3 C4 H43 1.0973 109.62 -58.14 111.48 1.0940 +IC H32 C3 C4 H43 1.0973 109.62 58.14 111.48 1.0940 +patc firs none last none + +Resi PENT 0.00 ! pentane, adm jr. +Group + Atom C1 CC33A -0.27 ! H11 H21 H31 H41 H51 + Atom H11 HCA3A 0.09 ! \ | | | / + Atom H12 HCA3A 0.09 ! H12-C1--C2--C3--C4--C5-H52 + Atom H13 HCA3A 0.09 ! / | | | \ +Group ! H13 H22 H33 H42 H53 + Atom C2 CC32A -0.18 + Atom H21 HCA2A 0.09 + Atom H22 HCA2A 0.09 +Group + Atom C3 CC32A -0.18 + Atom H31 HCA2A 0.09 + Atom H32 HCA2A 0.09 +Group + Atom C4 CC32A -0.18 + Atom H41 HCA2A 0.09 + Atom H42 HCA2A 0.09 +Group + Atom C5 CC33A -0.27 + Atom H51 HCA3A 0.09 + Atom H52 HCA3A 0.09 + Atom H53 HCA3A 0.09 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C5 H53 +! IC for PENT tt conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5264 112.83 180.00 113.35 1.5266 +IC C2 C3 C4 C5 1.5266 113.35 180.00 112.83 1.5264 +IC C3 C4 C5 H51 1.5266 112.83 180.00 111.50 1.0940 +IC H11 C1 C2 C3 1.0940 111.50 180.00 112.83 1.5266 +IC H11 C2 *C1 H12 1.0940 111.50 120.20 110.82 1.0945 +IC H11 C2 *C1 H13 1.0940 111.50 -120.20 110.82 1.0945 +IC C1 C3 *C2 H21 1.5264 112.83 122.12 109.12 1.0973 +IC C1 C3 *C2 H22 1.5264 112.83 -122.12 109.12 1.0973 +IC C2 C4 *C3 H31 1.5266 113.35 122.09 109.25 1.0986 +IC C2 C4 *C3 H32 1.5266 113.35 -122.09 109.25 1.0986 +IC C3 C5 *C4 H41 1.5266 112.83 121.83 109.63 1.0973 +IC C3 C5 *C4 H42 1.5266 112.83 -121.83 109.63 1.0973 +IC C4 H51 *C5 H52 1.5264 111.50 121.91 107.89 1.0945 +IC C4 H51 *C5 H53 1.5264 111.50 -121.91 107.89 1.0945 +patc firs none last none + +Resi HEXA 0.00 ! hexane, adm jr. +Group + Atom C1 CC33A -0.27 ! H11 H21 H31 H41 H51 H61 + Atom H11 HCA3A 0.09 ! \ | | | | / + Atom H12 HCA3A 0.09 ! H12-C1--C2--C3--C4--C5--C6-H62 + Atom H13 HCA3A 0.09 ! / | | | | \ +Group ! H13 H22 H33 H42 H52 H63 + Atom C2 CC32A -0.18 + Atom H21 HCA2A 0.09 + Atom H22 HCA2A 0.09 +Group + Atom C3 CC32A -0.18 + Atom H31 HCA2A 0.09 + Atom H32 HCA2A 0.09 +Group + Atom C4 CC32A -0.18 + Atom H41 HCA2A 0.09 + Atom H42 HCA2A 0.09 +Group + Atom C5 CC32A -0.18 + Atom H51 HCA2A 0.09 + Atom H52 HCA2A 0.09 +Group + Atom C6 CC33A -0.27 + Atom H61 HCA3A 0.09 + Atom H62 HCA3A 0.09 + Atom H63 HCA3A 0.09 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C6 H61 C6 H62 C6 H63 +! IC for HEXA ttt conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5263 112.85 180.00 113.27 1.5274 +IC C2 C3 C4 C5 1.5267 113.27 180.00 113.27 1.5267 +IC C3 C4 C5 C6 1.5274 113.27 180.00 112.85 1.5263 +IC C4 C5 C6 H61 1.5267 112.85 180.00 111.48 1.0941 +IC H11 C1 C2 C3 1.0941 111.48 180.00 112.85 1.5267 +IC H11 C2 *C1 H12 1.0941 111.48 120.20 110.84 1.0945 +IC H11 C2 *C1 H13 1.0941 111.48 -120.20 110.84 1.0945 +IC C3 C1 *C2 H21 1.5267 112.85 121.86 109.61 1.0973 +IC C3 C1 *C2 H22 1.5267 112.85 -121.86 109.61 1.0973 +IC C4 C2 *C3 H31 1.5274 113.27 122.07 109.25 1.0985 +IC C4 C2 *C3 H32 1.5274 113.27 -122.07 109.25 1.0985 +IC C5 C3 *C4 H41 1.5267 113.27 -122.06 109.28 1.0985 +IC C5 C3 *C4 H42 1.5267 113.27 122.06 109.28 1.0985 +IC C6 C4 *C5 H51 1.5263 112.85 122.12 109.14 1.0973 +IC C6 C4 *C5 H52 1.5263 112.85 -122.12 109.14 1.0973 +IC H61 C5 *C6 H62 1.0941 111.48 120.20 110.84 1.0945 +IC H61 C5 *C6 H63 1.0941 111.48 -120.20 110.84 1.0945 +patc firs none last none + +Resi HEPT 0.00 ! heptane, adm jr. +Group + Atom C1 CC33A -0.27 ! H11 H21 H31 H41 H51 + Atom H11 HCA3A 0.09 ! \ | | | / + Atom H12 HCA3A 0.09 ! H12-C1--C2--C3--C4--C5-H52 + Atom H13 HCA3A 0.09 ! / | | | \ +Group ! H13 H22 H33 H42 H53 + Atom C2 CC32A -0.18 + Atom H21 HCA2A 0.09 + Atom H22 HCA2A 0.09 +Group + Atom C3 CC32A -0.18 + Atom H31 HCA2A 0.09 + Atom H32 HCA2A 0.09 +Group + Atom C4 CC32A -0.18 + Atom H41 HCA2A 0.09 + Atom H42 HCA2A 0.09 +Group + Atom C5 CC32A -0.18 + Atom H51 HCA2A 0.09 + Atom H52 HCA2A 0.09 +Group + Atom C6 CC32A -0.18 + Atom H61 HCA2A 0.09 + Atom H62 HCA2A 0.09 +Group + Atom C7 CC33A -0.27 + Atom H71 HCA3A 0.09 + Atom H72 HCA3A 0.09 + Atom H73 HCA3A 0.09 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +Bond C6 C7 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C6 H61 C6 H62 C7 H71 C7 H72 +Bond C7 H73 +! IC for HEPT tttt conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5265 112.82 180.00 113.31 1.5271 +IC C2 C3 C4 C5 1.5270 113.31 180.00 113.24 1.5271 +IC C3 C4 C5 C6 1.5271 113.24 180.00 113.32 1.5270 +IC C4 C5 C6 C7 1.5271 113.32 180.00 112.81 1.5264 +IC C5 C6 C7 H71 1.5270 112.81 59.80 110.84 1.0945 +IC H11 C1 C2 C3 1.0940 111.50 180.00 112.82 1.5270 +IC H11 C2 *C1 H12 1.0940 111.50 120.20 110.84 1.0945 +IC H11 C2 *C1 H13 1.0940 111.50 -120.20 110.84 1.0945 +IC C3 C1 *C2 H21 1.5270 112.82 121.84 109.62 1.0973 +IC C3 C1 *C2 H22 1.5270 112.82 -121.84 109.62 1.0973 +IC C4 C2 *C3 H31 1.5271 113.31 122.09 109.23 1.0986 +IC C4 C2 *C3 H32 1.5271 113.31 -122.09 109.23 1.0986 +IC C5 C3 *C4 H41 1.5271 113.24 -122.06 109.27 1.0985 +IC C5 C3 *C4 H42 1.5271 113.24 122.06 109.27 1.0985 +IC C6 C4 *C5 H51 1.5270 113.32 122.06 109.29 1.0986 +IC C6 C4 *C5 H52 1.5270 113.32 -122.06 109.29 1.0986 +IC C7 C5 *C6 H61 1.5264 112.81 122.11 109.13 1.0973 +IC C7 C5 *C6 H62 1.5264 112.81 -122.11 109.13 1.0973 +IC H71 C6 *C7 H72 1.0945 110.84 120.20 111.51 1.0940 +IC H71 C6 *C7 H73 1.0945 110.84 -119.60 110.84 1.0945 +patc firs none last none + +Resi OCT 0.00 ! octane, adm jr. +GROUP + Atom C1 CC33A -0.27 ! H11 H21 H31 H41 H81 + Atom H11 HCA3A 0.09 ! \ | | | / + Atom H12 HCA3A 0.09 ! H12-C1--C2--C3--C4....C8-H82 + Atom H13 HCA3A 0.09 ! / | | | \ +GROUP ! H13 H22 H33 H42 H83 + Atom C2 CC32A -0.18 + Atom H21 HCA2A 0.09 + Atom H22 HCA2A 0.09 +GROUP + Atom C3 CC32A -0.18 + Atom H31 HCA2A 0.09 + Atom H32 HCA2A 0.09 +GROUP + Atom C4 CC32A -0.18 + Atom H41 HCA2A 0.09 + Atom H42 HCA2A 0.09 +GROUP + Atom C5 CC32A -0.18 + Atom H51 HCA2A 0.09 + Atom H52 HCA2A 0.09 +GROUP + Atom C6 CC32A -0.18 + Atom H61 HCA2A 0.09 + Atom H62 HCA2A 0.09 +GROUP + Atom C7 CC32A -0.18 + Atom H71 HCA2A 0.09 + Atom H72 HCA2A 0.09 +GROUP + Atom C8 CC33A -0.27 + Atom H81 HCA3A 0.09 + Atom H82 HCA3A 0.09 + Atom H83 HCA3A 0.09 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +Bond C6 C7 C7 C8 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +Bond C5 H52 C6 H61 C6 H62 C7 H71 C7 H72 +Bond C8 H81 C8 H82 C8 H83 +patc firs none last none + +Resi OCT2 0.00 ! octane, adm jr. +! half-octane for crystal calculations (see xtloct1.inp) +GROUP + Atom C1 CC33A -0.27 ! H11 H21 H31 H41 H81 + Atom H11 HCA3A 0.09 ! \ | | | / + Atom H12 HCA3A 0.09 ! H12-C1--C2--C3--C4....C8-H82 + Atom H13 HCA3A 0.09 ! / | | | \ +GROUP ! H13 H22 H33 H42 H83 + Atom C2 CC32A -0.18 + Atom H21 HCA2A 0.09 + Atom H22 HCA2A 0.09 +GROUP + Atom C3 CC32A -0.18 + Atom H31 HCA2A 0.09 + Atom H32 HCA2A 0.09 +GROUP + Atom C4 CC32A -0.18 + Atom H41 HCA2A 0.09 + Atom H42 HCA2A 0.09 + +Bond C1 C2 C2 C3 C3 C4 +Bond C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +Bond C3 H31 C3 H32 C4 H41 C4 H42 + +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 H41 0.0000 0.00 60.00 0.00 0.0000 +IC C2 C3 C4 H42 0.0000 0.00 -60.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +Resi deca 0.00 ! decane, Igor Vorobyov +GROUP + Atom C1 CC33A -0.27 ! H1A H2A H3A H4A H10A + Atom H1A HCA3A 0.09 ! \ | | | / + Atom H1B HCA3A 0.09 ! H1B-C1--C2--C3--C4...--C10-H10B + Atom H1C HCA3A 0.09 ! / | | | \ +GROUP ! H1C H2B H3B H4B H10C + Atom C2 CC32A -0.18 + Atom H2A HCA2A 0.09 + Atom H2B HCA2A 0.09 +GROUP + Atom C3 CC32A -0.18 + Atom H3A HCA2A 0.09 + Atom H3B HCA2A 0.09 +GROUP + Atom C4 CC32A -0.18 + Atom H4A HCA2A 0.09 + Atom H4B HCA2A 0.09 +GROUP + Atom C5 CC32A -0.18 + Atom H5A HCA2A 0.09 + Atom H5B HCA2A 0.09 +GROUP + Atom C6 CC32A -0.18 + Atom H6A HCA2A 0.09 + Atom H6B HCA2A 0.09 +GROUP + Atom C7 CC32A -0.18 + Atom H7A HCA2A 0.09 + Atom H7B HCA2A 0.09 +GROUP + Atom C8 CC32A -0.18 + Atom H8A HCA2A 0.09 + Atom H8B HCA2A 0.09 +GROUP + Atom C9 CC32A -0.18 + Atom H9A HCA2A 0.09 + Atom H9B HCA2A 0.09 +GROUP + Atom C10 CC33A -0.27 + Atom H10A HCA3A 0.09 + Atom H10B HCA3A 0.09 + Atom H10C HCA3A 0.09 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C5 C6 C6 C7 C7 C8 C8 C9 C9 C10 +Bond C1 H1A C1 H1B C1 H1C C2 H2A C2 H2B +Bond C3 H3A C3 H3B C4 H4A C4 H4B +Bond C5 H5A C5 H5B C6 H6A C6 H6B +Bond C7 H7A C7 H7B C8 H8A C8 H8B +Bond C9 H9A C9 H9B C10 H10A C10 H10B C10 H10C +patc firs none last none + +RESI PEND 0.00 ! pentadecane, Igor Vorobyov +GROUP + Atom C1 CC33A -0.27 ! H1A H2A H3A H4A H15A + Atom H1A HCA3A 0.09 ! \ | | | / + Atom H1B HCA3A 0.09 ! H1B-C1--C2--C3--C4..--C15-H15B + Atom H1C HCA3A 0.09 ! / | | | \ +GROUP ! H1C H2B H3B H4B H15C + Atom C2 CC32A -0.18 + Atom H2A HCA2A 0.09 + Atom H2B HCA2A 0.09 +GROUP + Atom C3 CC32A -0.18 + Atom H3A HCA2A 0.09 + Atom H3B HCA2A 0.09 +GROUP + Atom C4 CC32A -0.18 + Atom H4A HCA2A 0.09 + Atom H4B HCA2A 0.09 +GROUP + Atom C5 CC32A -0.18 + Atom H5A HCA2A 0.09 + Atom H5B HCA2A 0.09 +GROUP + Atom C6 CC32A -0.18 + Atom H6A HCA2A 0.09 + Atom H6B HCA2A 0.09 +GROUP + Atom C7 CC32A -0.18 + Atom H7A HCA2A 0.09 + Atom H7B HCA2A 0.09 +GROUP + Atom C8 CC32A -0.18 + Atom H8A HCA2A 0.09 + Atom H8B HCA2A 0.09 +GROUP + Atom C9 CC32A -0.18 + Atom H9A HCA2A 0.09 + Atom H9B HCA2A 0.09 +GROUP + Atom C10 CC32A -0.18 + Atom H10A HCA2A 0.09 + Atom H10B HCA2A 0.09 +GROUP + Atom C11 CC32A -0.18 + Atom H11A HCA2A 0.09 + Atom H11B HCA2A 0.09 +GROUP + Atom C12 CC32A -0.18 + Atom H12A HCA2A 0.09 + Atom H12B HCA2A 0.09 +GROUP + Atom C13 CC32A -0.18 + Atom H13A HCA2A 0.09 + Atom H13B HCA2A 0.09 +GROUP + Atom C14 CC32A -0.18 + Atom H14A HCA2A 0.09 + Atom H14B HCA2A 0.09 +GROUP + Atom C15 CC33A -0.27 + Atom H15A HCA3A 0.09 + Atom H15B HCA3A 0.09 + Atom H15C HCA3A 0.09 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C5 C6 C6 C7 C7 C8 C8 C9 C9 C10 +Bond C10 C11 C11 C12 C12 C13 C13 C14 C14 C15 +Bond C1 H1A C1 H1B C1 H1C C2 H2A C2 H2B +Bond C3 H3A C3 H3B C4 H4A C4 H4B +Bond C5 H5A C5 H5B C6 H6A C6 H6B +Bond C7 H7A C7 H7B C8 H8A C8 H8B +Bond C9 H9A C9 H9B C10 H10A C10 H10B +Bond C11 H11A C11 H11B C12 H12A C12 H12B +Bond C13 H13A C13 H13B +Bond C14 H14A C14 H14B C15 H15A C15 H15B C15 H15C +patc firs none last none + +RESI OCTD 0.00 ! octadecane, Igor Vorobyov +GROUP + Atom C1 CC33A -0.27 ! H1A H2A H3A H4A H18A + Atom H1A HCA3A 0.09 ! \ | | | / + Atom H1B HCA3A 0.09 ! H1B-C1--C2--C3--C4..--C18-H18B + Atom H1C HCA3A 0.09 ! / | | | \ +GROUP ! H1C H2C H3B H4B H18C + Atom C2 CC32A -0.18 + Atom H2A HCA2A 0.09 + Atom H2B HCA2A 0.09 +GROUP + Atom C3 CC32A -0.18 + Atom H3A HCA2A 0.09 + Atom H3B HCA2A 0.09 +GROUP + Atom C4 CC32A -0.18 + Atom H4A HCA2A 0.09 + Atom H4B HCA2A 0.09 +GROUP + Atom C5 CC32A -0.18 + Atom H5A HCA2A 0.09 + Atom H5B HCA2A 0.09 +GROUP + Atom C6 CC32A -0.18 + Atom H6A HCA2A 0.09 + Atom H6B HCA2A 0.09 +GROUP + Atom C7 CC32A -0.18 + Atom H7A HCA2A 0.09 + Atom H7B HCA2A 0.09 +GROUP + Atom C8 CC32A -0.18 + Atom H8A HCA2A 0.09 + Atom H8B HCA2A 0.09 +GROUP + Atom C9 CC32A -0.18 + Atom H9A HCA2A 0.09 + Atom H9B HCA2A 0.09 +GROUP + Atom C10 CC32A -0.18 + Atom H10A HCA2A 0.09 + Atom H10B HCA2A 0.09 +GROUP + Atom C11 CC32A -0.18 + Atom H11A HCA2A 0.09 + Atom H11B HCA2A 0.09 +GROUP + Atom C12 CC32A -0.18 + Atom H12A HCA2A 0.09 + Atom H12B HCA2A 0.09 +GROUP + Atom C13 CC32A -0.18 + Atom H13A HCA2A 0.09 + Atom H13B HCA2A 0.09 +GROUP + Atom C14 CC32A -0.18 + Atom H14A HCA2A 0.09 + Atom H14B HCA2A 0.09 +GROUP + Atom C15 CC32A -0.18 + Atom H15A HCA2A 0.09 + Atom H15B HCA2A 0.09 +GROUP + Atom C16 CC32A -0.18 + Atom H16A HCA2A 0.09 + Atom H16B HCA2A 0.09 +GROUP + Atom C17 CC32A -0.18 + Atom H17A HCA2A 0.09 + Atom H17B HCA2A 0.09 +GROUP + Atom C18 CC33A -0.27 + Atom H18A HCA3A 0.09 + Atom H18B HCA3A 0.09 + Atom H18C HCA3A 0.09 + +Bond C1 C2 C2 C3 C3 C4 C4 C5 +Bond C5 C6 C6 C7 C7 C8 C8 C9 C9 C10 +Bond C10 C11 C11 C12 C12 C13 C13 C14 C14 C15 +Bond C15 C16 C16 C17 C17 C18 +Bond C1 H1A C1 H1B C1 H1C C2 H2A C2 H2B +Bond C3 H3A C3 H3B C4 H4A C4 H4B +Bond C5 H5A C5 H5B C6 H6A C6 H6B +Bond C7 H7A C7 H7B C8 H8A C8 H8B +Bond C9 H9A C9 H9B C10 H10A C10 H10B +Bond C11 H11A C11 H11B C12 H12A C12 H12B +Bond C13 H13A C13 H13B C14 H14A C14 H14B +Bond C15 H15A C15 H15B C16 H16A C16 H16B +Bond C17 H17A C17 H17B C18 H18A C18 H18B C18 H18C +patc firs none last none + +!!!!!!!!!!!!!!!!!!!! +!! Branched alkanes +!!!!!!!!!!!!!!!!!!!! + +Resi IBUT 0.00 ! Iso-butane +Group +atom CT CC31A -0.09 ! H12 +atom HT HCA1A 0.09 ! | +Group ! H11-C1-H13 +Atom C1 CC33A -0.27 ! | +Atom H11 HCA3A 0.09 ! CT-HT +Atom H12 HCA3A 0.09 ! / \ +Atom H13 HCA3A 0.09 ! / \ +Group ! H21-C2 C3-H31 +Atom C2 CC33A -0.27 ! / | | \ +Atom H21 HCA3A 0.09 ! H22 H23 H33 H32 +Atom H22 HCA3A 0.09 ! +Atom H23 HCA3A 0.09 ! +Group +atom C3 CC33A -0.27 +Atom H31 HCA3A 0.09 +atom H32 HCA3A 0.09 +atom H33 HCA3A 0.09 + +Bond ct c1 ct c2 ct c3 ct ht +Bond c1 h11 c1 h12 c1 h13 +Bond c2 h21 c2 h22 c2 h23 +Bond c3 h31 c3 h32 c3 h33 +!! IC for IBUT staggered conformer MP2/6-31G* optimized +IC C1 CT C2 H21 1.5272 110.84 178.49 111.23 1.0946 +IC C2 CT C1 H11 1.5272 110.84 -57.98 111.23 1.0946 +IC C1 CT C3 H31 1.5272 110.84 -57.98 111.23 1.0946 +IC C2 C1 *CT C3 1.5272 110.84 -123.53 110.84 1.5272 +IC C2 C1 *CT HT 1.5272 110.84 118.24 108.06 1.0986 +IC H11 CT *C1 H12 1.0946 111.23 119.74 110.37 1.0958 +IC H11 CT *C1 H13 1.0946 111.23 -120.51 111.23 1.0946 +IC H21 CT *C2 H22 1.0946 111.23 119.74 110.37 1.0958 +IC H21 CT *C2 H23 1.0946 111.23 -120.51 111.23 1.0946 +IC H31 CT *C3 H32 1.0946 111.23 119.74 110.37 1.0958 +IC H31 CT *C3 H33 1.0946 111.23 -120.51 111.23 1.0946 +patc firs none last none + +Resi NEOP 0.00 ! Neo-pentane, I. Vorobyov +Group ! +atom CT CC30A 0.00 ! H11 H12 H13 +Group ! \ | / +Atom c1 CC33A -0.27 ! C1 +Atom h11 HCA3A 0.09 ! H43 | H21 +Atom h12 HCA3A 0.09 ! \ | / +Atom h13 HCA3A 0.09 ! H42-C4--CT--C2-H22 +Group ! / | \ +Atom c2 CC33A -0.27 ! H41 | H23 +Atom h21 HCA3A 0.09 ! C3 +Atom h22 HCA3A 0.09 ! / | \ +Atom h23 HCA3A 0.09 ! H31 H32 H33 +Group +atom c3 CC33A -0.27 +Atom h31 HCA3A 0.09 +atom h32 HCA3A 0.09 +atom h33 HCA3A 0.09 +Group +atom c4 CC33A -0.27 +Atom h41 HCA3A 0.09 +atom h42 HCA3A 0.09 +atom h43 HCA3A 0.09 + +Bond ct c1 ct c2 ct c3 ct c4 +Bond c1 h11 c1 h12 c1 h13 +Bond c2 h21 c2 h22 c2 h23 +Bond c3 h31 c3 h32 c3 h33 +Bond c4 h41 c4 h42 c4 h43 +patc firs none last none + +!!!!!!!!!!!!!!!! +!! Cycloalkanes +!!!!!!!!!!!!!!!! + +RESI CPEN 0.00 ! cyclopentane, viv +GROUP +ATOM C1 CC325A -0.18 +ATOM H1A HCA25A 0.09 +ATOM H1B HCA25A 0.09 +GROUP +ATOM C2 CC325A -0.18 +ATOM H2A HCA25A 0.09 +ATOM H2B HCA25A 0.09 +GROUP +ATOM C3 CC325A -0.18 +ATOM H3A HCA25A 0.09 +ATOM H3B HCA25A 0.09 +GROUP +ATOM C4 CC325A -0.18 +ATOM H4A HCA25A 0.09 +ATOM H4B HCA25A 0.09 +GROUP +ATOM C5 CC325A -0.18 +ATOM H5A HCA25A 0.09 +ATOM H5B HCA25A 0.09 + +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C1 +!! IC for CPEN C2 conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5485 105.88 -13.32 105.00 1.5334 +IC H1A C1 C2 C3 1.0958 110.05 104.06 105.88 1.5485 +IC C5 C2 *C1 H1A 1.5334 105.00 117.38 110.05 1.0958 +IC H1A C2 *C1 H1B 1.0958 110.05 119.30 112.68 1.0944 +IC C3 C1 *C2 H2A 1.5485 105.88 -120.88 110.89 1.0943 +IC H2A C1 *C2 H2B 1.0943 110.89 -118.52 111.32 1.0943 +IC C4 C2 *C3 H3A 1.5334 105.00 -123.32 112.68 1.0944 +IC H3A C2 *C3 H3B 1.0944 112.68 -119.30 110.05 1.0958 +IC C5 C3 *C4 H4A 1.5288 102.87 -116.68 110.22 1.0972 +IC H4A C3 *C4 H4B 1.0972 110.22 -120.38 113.00 1.0949 +IC C4 C1 *C5 H5A 1.5288 102.87 122.95 113.00 1.0949 +IC C4 C1 *C5 H5B 1.5288 102.87 -116.68 110.22 1.0972 +patc firs none last none + +RESI CHEX 0.00 ! cyclohexane, viv +GROUP +ATOM C1 CC32A -0.18 +ATOM H1A HCA2A 0.09 +ATOM H1B HCA2A 0.09 +GROUP +ATOM C2 CC32A -0.18 +ATOM H2A HCA2A 0.09 +ATOM H2B HCA2A 0.09 +GROUP +ATOM C3 CC32A -0.18 +ATOM H3A HCA2A 0.09 +ATOM H3B HCA2A 0.09 +GROUP +ATOM C4 CC32A -0.18 +ATOM H4A HCA2A 0.09 +ATOM H4B HCA2A 0.09 +GROUP +ATOM C5 CC32A -0.18 +ATOM H5A HCA2A 0.09 +ATOM H5B HCA2A 0.09 +GROUP +ATOM C6 CC32A -0.18 +ATOM H6A HCA2A 0.09 +ATOM H6B HCA2A 0.09 + +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C6 +BOND C6 H6A C6 H6B C6 C1 +!! IC for CHEX chair conformer MP2/6-31G* optimized +IC C1 C2 C3 C4 1.5294 111.17 -55.59 111.17 1.5294 +IC C2 C3 C4 C5 1.5294 111.17 55.59 111.17 1.5294 +IC C6 C1 C2 C3 1.5294 111.17 55.59 111.17 1.5294 +IC C2 C6 *C1 H1A 1.5294 111.17 -122.75 110.33 1.0967 +IC H1A C6 *C1 H1B 1.0967 110.33 -116.87 109.11 1.0988 +IC C3 C1 *C2 H2A 1.5294 111.17 -120.39 109.11 1.0988 +IC H2A C1 *C2 H2B 1.0988 109.11 -116.87 110.33 1.0967 +IC C4 C2 *C3 H3A 1.5294 111.17 -122.75 110.34 1.0967 +IC H3A C2 *C3 H3B 1.0967 110.34 -116.87 109.11 1.0988 +IC C5 C3 *C4 H4A 1.5294 111.17 -120.39 109.11 1.0988 +IC H4A C3 *C4 H4B 1.0988 109.11 -116.87 110.33 1.0967 +IC C6 C4 *C5 H5A 1.5294 111.17 -122.75 110.33 1.0967 +IC H5A C4 *C5 H5B 1.0967 110.33 -116.87 109.11 1.0988 +IC C5 C1 *C6 H6A 1.5294 111.17 120.39 109.11 1.0988 +IC C5 C1 *C6 H6B 1.5294 111.17 -122.75 110.33 1.0967 +patc firs none last none + +!!!!!!!!!!!!!!!!! +!! Cyclic ethers +!!!!!!!!!!!!!!!!! + +RESI THF 0.00 ! Tetrahydrofuran, viv +GROUP +ATOM O1 OC305A -0.40 +ATOM C1 CC325B 0.02 +ATOM H1A HCA25A 0.09 +ATOM H1B HCA25A 0.09 +ATOM C2 CC325B -0.18 +ATOM H2A HCA25A 0.09 +ATOM H2B HCA25A 0.09 +ATOM C3 CC325B -0.18 +ATOM H3A HCA25A 0.09 +ATOM H3B HCA25A 0.09 +ATOM C4 CC325B 0.02 +ATOM H4A HCA25A 0.09 +ATOM H4B HCA25A 0.09 +BOND O1 C1 C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 O1 +!! IC for THF C2 conformer MP2/6-31G* optimized +IC O1 C1 C2 C3 1.4368 106.09 32.94 101.18 1.5273 +IC C1 C2 C3 C4 1.5252 101.18 -39.14 101.18 1.5252 +IC C2 C3 C4 O1 1.5273 101.18 32.94 106.09 1.4368 +IC C3 C4 O1 C1 1.5252 106.09 -12.88 109.31 1.4368 +IC C4 O1 C1 C2 1.4368 109.31 -12.88 106.09 1.5252 +IC O1 C2 *C1 H1A 1.4368 106.09 118.91 113.61 1.0945 +IC O1 C2 *C1 H1B 1.4368 106.09 -118.66 111.00 1.0989 +IC C1 C3 *C2 H2A 1.5252 101.18 116.76 110.18 1.0949 +IC C1 C3 *C2 H2B 1.5252 101.18 -121.33 113.76 1.0935 +IC C2 C4 *C3 H3A 1.5273 101.18 121.95 112.88 1.0935 +IC C2 C4 *C3 H3B 1.5273 101.18 -116.64 110.35 1.0949 +IC C3 O1 *C4 H4A 1.5252 106.09 119.76 109.32 1.0989 +IC C3 O1 *C4 H4B 1.5252 106.09 -122.32 108.34 1.0945 +patc firs none last none + +RESI TF2M 0.00 ! 2-methyl-THF, viv +GROUP +ATOM O1 OC305A -0.40 +ATOM C1 CC325B 0.11 +ATOM H1A HCA25A 0.09 +ATOM C2 CC325B -0.18 +ATOM H2A HCA25A 0.09 +ATOM H2B HCA25A 0.09 +ATOM C3 CC325B -0.18 +ATOM H3A HCA25A 0.09 +ATOM H3B HCA25A 0.09 +ATOM C4 CC325B 0.02 +ATOM H4A HCA25A 0.09 +ATOM H4B HCA25A 0.09 +ATOM C5 CC33A -0.27 +ATOM H5A HCA3A 0.09 +ATOM H5B HCA3A 0.09 +ATOM H5C HCA3A 0.09 + +BOND O1 C1 C1 H1A C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 O1 +BOND C1 C5 C5 H5A C5 H5B C5 H5C +!! IC for TF2M C2 conformer MP2/6-31G* optimized +IC O1 C1 C2 C3 1.4443 106.24 14.28 103.29 1.5304 +IC C4 O1 C1 C2 1.4284 108.41 12.12 106.24 1.5435 +IC O1 C1 C5 H5A 1.4443 107.53 53.68 110.10 1.0928 +IC C2 O1 *C1 C5 1.5435 106.24 122.57 107.53 1.5167 +IC C2 O1 *C1 H1A 1.5435 106.24 -118.83 108.34 1.0993 +IC C3 C1 *C2 H2A 1.5304 103.29 122.32 112.09 1.0941 +IC H2A C1 *C2 H2B 1.0941 112.09 120.11 110.49 1.0949 +IC C4 C2 *C3 H3A 1.5208 100.72 115.91 110.89 1.0944 +IC H3A C2 *C3 H3B 1.0944 110.89 122.35 113.36 1.0940 +IC C3 O1 *C4 H4A 1.5208 104.28 -122.07 107.42 1.0931 +IC C3 O1 *C4 H4B 1.5208 104.28 119.33 110.91 1.1016 +IC H5A C1 *C5 H5B 1.0928 110.10 120.29 110.81 1.0947 +IC H5A C1 *C5 H5C 1.0928 110.10 -119.30 109.89 1.0938 +patc firs none last none + +RESI THP 0.00 ! Tetrahydro-2H-pyran, viv +GROUP +ATOM O1 OC30A -0.40 +ATOM C1 CC326A 0.02 +ATOM H1A HCA2A 0.09 +ATOM H1B HCA2A 0.09 +ATOM C2 CC326A -0.18 +ATOM H2A HCA2A 0.09 +ATOM H2B HCA2A 0.09 +ATOM C3 CC326A -0.18 +ATOM H3A HCA2A 0.09 +ATOM H3B HCA2A 0.09 +ATOM C4 CC326A -0.18 +ATOM H4A HCA2A 0.09 +ATOM H4B HCA2A 0.09 +ATOM C5 CC326A 0.02 +ATOM H5A HCA2A 0.09 +ATOM H5B HCA2A 0.09 +BOND O1 C1 C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 O1 +!! IC for THP chair conformer MP2/6-31G* optimized +IC O1 C1 C2 C3 1.4266 111.33 57.16 109.96 1.5293 +IC C1 C2 C3 C4 1.5230 109.96 -52.34 109.87 1.5293 +IC C5 O1 C1 C2 1.4266 110.87 -61.89 111.33 1.5230 +IC C2 O1 *C1 H1A 1.5230 111.33 -121.53 105.76 1.0934 +IC H1A O1 *C1 H1B 1.0934 105.76 -116.45 109.72 1.1033 +IC C3 C1 *C2 H2A 1.5293 109.96 122.65 109.93 1.0971 +IC H2A C1 *C2 H2B 1.0971 109.93 117.29 108.46 1.0963 +IC C4 C2 *C3 H3A 1.5293 109.87 -122.83 110.84 1.0956 +IC H3A C2 *C3 H3B 1.0956 110.84 -117.43 109.20 1.0986 +IC C5 C3 *C4 H4A 1.5230 109.96 -119.25 109.78 1.0963 +IC H4A C3 *C4 H4B 1.0963 109.78 -118.81 111.12 1.0971 +IC C4 O1 *C5 H5A 1.5230 111.33 121.53 105.76 1.0934 +IC C4 O1 *C5 H5B 1.5230 111.33 -122.02 109.72 1.1033 +patc firs none last none + +!!!!!!!!!!!!!!!!!! +!! Acyclic ethers +!!!!!!!!!!!!!!!!!! + +RESI DMET 0.00 ! Dimethylether, viv +GROUP +ATOM C1 CC33A -0.10 ! H1A H3A +ATOM H11 HCA3A 0.09 ! | | +ATOM H12 HCA3A 0.09 ! H1C - C1 - O2 - C3 - H3C +ATOM H13 HCA3A 0.09 ! | | +ATOM O2 OC30A -0.34 ! H1B H3B +ATOM C3 CC33A -0.10 +ATOM H31 HCA3A 0.09 +ATOM H32 HCA3A 0.09 +ATOM H33 HCA3A 0.09 +BOND C1 O2 O2 C3 +BOND C1 H11 C1 H12 C1 H13 +BOND C3 H31 C3 H32 C3 H33 +!! IC for DMET staggered (C2v) conformer MP2/6-31G* optimized +IC C1 O2 C3 H31 1.4156 111.05 -60.70 111.47 1.0993 +IC H11 C1 O2 C3 1.0993 111.47 -60.70 111.05 1.4156 +IC H11 O2 *C1 H12 1.0993 111.47 -119.30 106.89 1.0906 +IC H11 O2 *C1 H13 1.0993 111.47 121.39 111.47 1.0993 +IC H31 O2 *C3 H32 1.0993 111.47 -119.30 106.89 1.0906 +IC H31 O2 *C3 H33 1.0993 111.47 121.39 111.47 1.0993 +patc firs none last none + +RESI MEET 0.00 ! Methylethylether, viv +GROUP +ATOM C1 CC33A -0.27 ! H1A H2A H4A +ATOM H11 HCA3A 0.09 ! | | | +ATOM H12 HCA3A 0.09 ! H1C - C1 - C2 - O3 - C4 - H4C +ATOM H13 HCA3A 0.09 ! | | | +GROUP ! H1B H2B H4B +ATOM C2 CC32A -0.01 ! +ATOM H21 HCA2A 0.09 +ATOM H22 HCA2A 0.09 +ATOM O3 OC30A -0.34 +ATOM C4 CC33A -0.10 +ATOM H41 HCA3A 0.09 +ATOM H42 HCA3A 0.09 +ATOM H43 HCA3A 0.09 +BOND C1 C2 C2 O3 O3 C4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 C4 H43 +!! IC for MEET trans (t) conformer MP2/6-31G* optimized +IC C1 C2 O3 C4 1.5296 110.11 -180.00 111.05 1.4190 +IC C2 O3 C4 H41 1.4183 111.05 60.36 110.32 1.1113 +IC H11 C1 C2 O3 1.1106 110.47 180.00 110.11 1.4183 +IC H11 C2 *C1 H12 1.1106 110.47 120.09 110.34 1.1111 +IC H11 C2 *C1 H13 1.1106 110.47 -120.09 110.34 1.1111 +IC O3 C1 *C2 H21 1.4183 110.11 -120.56 109.50 1.1125 +IC O3 C1 *C2 H22 1.4183 110.11 120.56 109.50 1.1125 +IC H41 O3 *C4 H42 1.1113 110.32 -120.72 110.32 1.1113 +IC H41 O3 *C4 H43 1.1113 110.32 119.64 109.66 1.1110 +patc firs none last none + +RESI DEET 0.00 ! Diethylether, adm jr. +GROUP +ATOM C1 CC33A -0.27 ! H1A H2A H4A H5A +ATOM H11 HCA3A 0.09 ! | | | | +ATOM H12 HCA3A 0.09 ! H1C - C1 - C2 - O3 - C4 - C5 - H5C +ATOM H13 HCA3A 0.09 ! | | | | +GROUP ! H1B H2B H4B H5B +ATOM C2 CC32A -0.01 ! +ATOM H21 HCA2A 0.09 +ATOM H22 HCA2A 0.09 +ATOM O3 OC30A -0.34 +ATOM C4 CC32A -0.01 +ATOM H41 HCA2A 0.09 +ATOM H42 HCA2A 0.09 +GROUP +ATOM C5 CC33A -0.27 +ATOM H51 HCA3A 0.09 +ATOM H52 HCA3A 0.09 +ATOM H53 HCA3A 0.09 +BOND C1 C2 C2 O3 O3 C4 C4 C5 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 +BOND C5 H51 C5 H52 C5 H53 +!! IC for DEET tt conformer MP2/6-31G* optimized +IC C1 C2 O3 C4 1.5296 110.07 180.00 111.30 1.4188 +IC C2 O3 C4 C5 1.4188 111.30 180.00 110.07 1.5296 +IC H11 C1 C2 O3 1.1107 110.48 -180.00 110.07 1.4188 +IC O3 C4 C5 H51 1.4188 110.07 180.00 110.48 1.1107 +IC H11 C2 *C1 H12 1.1107 110.48 120.09 110.35 1.1111 +IC H11 C2 *C1 H13 1.1107 110.48 -120.09 110.35 1.1111 +IC O3 C1 *C2 H21 1.4188 110.07 120.56 109.49 1.1125 +IC O3 C1 *C2 H22 1.4188 110.07 -120.56 109.49 1.1125 +IC C5 O3 *C4 H41 1.5296 110.07 120.48 109.62 1.1125 +IC C5 O3 *C4 H42 1.5296 110.07 -120.48 109.62 1.1125 +IC H51 C4 *C5 H52 1.1107 110.48 120.09 110.35 1.1111 +IC H51 C4 *C5 H53 1.1107 110.48 -120.09 110.35 1.1111 +patc firs none last none + +RESI DME 0.00 ! Dimethoxyethane, adm jr. +GROUP +ATOM C1 CC33A -0.10 ! H12 H11 +ATOM H11 HCA3A 0.09 ! \ / +ATOM H12 HCA3A 0.09 ! H13-C1 H31 H32 H61 H62 +ATOM H13 HCA3A 0.09 ! \ \ / \ / +ATOM O2 OC30A -0.34 ! O2--C3 C6-H63 +ATOM C3 CC32A -0.01 ! \ / +ATOM H31 HCA2A 0.09 ! H41-C4-O5 +ATOM H32 HCA2A 0.09 ! | +GROUP ! H42 +ATOM C4 CC32A -0.01 ! +ATOM H41 HCA2A 0.09 +ATOM H42 HCA2A 0.09 +ATOM O5 OC30A -0.34 +ATOM C6 CC33A -0.10 +ATOM H61 HCA3A 0.09 +ATOM H62 HCA3A 0.09 +ATOM H63 HCA3A 0.09 +BOND C1 H11 C1 H12 C1 H13 +BOND C1 O2 O2 C3 +BOND C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 +BOND C4 O5 O5 C6 +BOND C6 H61 C6 H62 C6 H63 +!! IC for DME ttt conformer MP2/6-31G(d) opt. +IC C1 O2 C3 C4 1.4177 111.45 -180.00 106.95 1.5133 +IC H11 C1 O2 C3 1.0906 106.80 180.00 111.45 1.4180 +IC O2 C3 C4 O5 1.4180 106.95 180.00 106.95 1.4180 +IC C3 C4 O5 C6 1.5133 106.95 -180.00 111.45 1.4177 +IC C4 O5 C6 H61 1.4180 111.45 180.00 106.80 1.0906 +IC H11 O2 *C1 H12 1.0906 106.80 119.29 111.35 1.0986 +IC H11 O2 *C1 H13 1.0906 106.80 -119.29 111.35 1.0986 +IC C4 O2 *C3 H31 1.5133 106.95 -119.86 111.19 1.1001 +IC H31 O2 *C3 H32 1.1001 111.19 -120.27 111.19 1.1001 +IC O5 C3 *C4 H41 1.4180 106.95 -120.75 109.80 1.1001 +IC H41 C3 *C4 H42 1.1001 109.80 -118.49 109.80 1.1001 +IC H61 O5 *C6 H62 1.0906 106.80 119.29 111.35 1.0986 +IC H61 O5 *C6 H63 1.0906 106.80 -119.29 111.35 1.0986 +patc firs none last none + +RESI MPET 0.00 ! Methyl Propyl Ether, viv +GROUP ! +ATOM C1 CC33A -0.10 ! H11 H31 H41 H51 +ATOM H11 HCA3A 0.09 ! | | | | +ATOM H12 HCA3A 0.09 ! H11 - C1 - O2 - C3 - C4 - C5 - H53 +ATOM H13 HCA3A 0.09 ! | | | | +ATOM O2 OC30A -0.34 ! H12 H32 H42 H52 +ATOM C3 CC32A -0.01 +ATOM H31 HCA2A 0.09 +ATOM H32 HCA2A 0.09 +GROUP +ATOM C4 CC32A -0.18 +ATOM H41 HCA2A 0.09 +ATOM H42 HCA2A 0.09 +GROUP +ATOM C5 CC33A -0.27 +ATOM H51 HCA3A 0.09 +ATOM H52 HCA3A 0.09 +ATOM H53 HCA3A 0.09 +BOND C1 H11 C1 H12 C1 H13 C1 O2 +BOND O2 C3 C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 C4 C5 +BOND C5 H51 C5 H52 C5 H53 +!! IC for MPET tt conformer MP2/6-31G(d) opt. +IC C1 O2 C3 C4 1.4167 111.53 180.00 108.22 1.5159 +IC O2 C3 C4 C5 1.4196 108.22 180.00 112.12 1.5264 +IC H11 C1 O2 C3 1.0991 111.47 -60.71 111.53 1.4196 +IC C3 C4 C5 H51 1.5159 112.12 60.05 111.12 1.0944 +IC H11 O2 *C1 H12 1.0991 111.47 -119.29 106.86 1.0908 +IC H11 O2 *C1 H13 1.0991 111.47 121.42 111.47 1.0991 +IC C4 O2 *C3 H31 1.5159 108.22 -120.91 110.25 1.1031 +IC H31 O2 *C3 H32 1.1031 110.25 -118.17 110.25 1.1031 +IC C5 C3 *C4 H41 1.5264 112.12 -122.18 108.33 1.0947 +IC H41 C3 *C4 H42 1.0947 108.33 -115.64 108.33 1.0947 +IC H51 C4 *C5 H52 1.0944 111.12 -120.11 111.12 1.0944 +IC H51 C4 *C5 H53 1.0944 111.12 119.95 111.05 1.0931 +patc firs none last none + +RESI MBET 0.00 ! Methylbutylether, viv +GROUP ! +ATOM C1 CC33A -0.10 ! H11 H31 H41 H51 H6A +ATOM H11 HCA3A 0.09 ! | | | | | +ATOM H12 HCA3A 0.09 ! H11 - C1 - O2 - C3 - C4 - C5 - C6 - H6C +ATOM H13 HCA3A 0.09 ! | | | | | +ATOM O2 OC30A -0.34 ! H12 H32 H42 H52 H6B +ATOM C3 CC32A -0.01 +ATOM H31 HCA2A 0.09 +ATOM H32 HCA2A 0.09 +GROUP +ATOM C4 CC32A -0.18 +ATOM H41 HCA2A 0.09 +ATOM H42 HCA2A 0.09 +GROUP +ATOM C5 CC32A -0.18 +ATOM H51 HCA2A 0.09 +ATOM H52 HCA2A 0.09 +GROUP +ATOM C6 CC33A -0.27 +ATOM H61 HCA3A 0.09 +ATOM H62 HCA3A 0.09 +ATOM H63 HCA3A 0.09 +BOND C1 H11 C1 H12 C1 H13 C1 O2 +BOND O2 C3 C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 C4 C5 +BOND C5 H51 C5 H52 C5 C6 +BOND C6 H61 C6 H62 C6 H63 +!! IC for MBET ttt conformer MP2/6-31G(d) opt. +IC C1 O2 C3 C4 1.4167 111.49 -180.00 108.17 1.5161 +IC H11 C1 O2 C3 1.0908 106.86 -180.00 111.49 1.4201 +IC O2 C3 C4 C5 1.4201 108.17 -180.00 112.65 1.5270 +IC C3 C4 C5 C6 1.5161 112.65 -180.00 112.43 1.5265 +IC C4 C5 C6 H61 1.5270 112.43 -59.80 110.80 1.0942 +IC H11 O2 *C1 H12 1.0908 106.86 -119.29 111.47 1.0991 +IC H11 O2 *C1 H13 1.0908 106.86 119.29 111.47 1.0992 +IC C4 O2 *C3 H31 1.5161 108.17 -120.93 110.21 1.1030 +IC H31 O2 *C3 H32 1.1030 110.21 -118.13 110.21 1.1030 +IC C5 C3 *C4 H41 1.5270 112.65 -122.13 108.47 1.0960 +IC H41 C3 *C4 H42 1.0960 108.47 -115.75 108.47 1.0960 +IC C6 C4 *C5 H51 1.5265 112.43 -121.91 109.41 1.0972 +IC H51 C4 *C5 H52 1.0972 109.41 -116.18 109.41 1.0972 +IC H61 C5 *C6 H62 1.0942 110.80 -120.20 111.41 1.0938 +IC H61 C5 *C6 H63 1.0942 110.80 119.61 110.80 1.0942 +patc firs none last none + +RESI EPET 0.00 ! Ethylpropylether, viv +GROUP +ATOM C1 CC33A -0.27 ! H11 H21 H41 H51 H61 +ATOM H11 HCA3A 0.09 ! | | | | | +ATOM H12 HCA3A 0.09 ! H13 - C1 - C2 - O3 - C4 - C5 - C6 - H63 +ATOM H13 HCA3A 0.09 ! | | | | | +GROUP ! H12 H22 H42 H52 H62 +ATOM C2 CC32A -0.01 ! +ATOM H21 HCA2A 0.09 +ATOM H22 HCA2A 0.09 +ATOM O3 OC30A -0.34 +ATOM C4 CC32A -0.01 +ATOM H41 HCA2A 0.09 +ATOM H42 HCA2A 0.09 +GROUP +ATOM C5 CC32A -0.18 +ATOM H51 HCA2A 0.09 +ATOM H52 HCA2A 0.09 +GROUP +ATOM C6 CC33A -0.27 +ATOM H61 HCA3A 0.09 +ATOM H62 HCA3A 0.09 +ATOM H63 HCA3A 0.09 +BOND C1 C2 C2 O3 O3 C4 +BOND C4 C5 C5 C6 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 +BOND C5 H51 C5 H52 +BOND C6 H61 C6 H62 C6 H63 +!! IC for EPET ttt conformer MP2/6-31G(d) opt. +IC C1 C2 O3 C4 1.5140 107.70 180.00 112.04 1.4204 +IC H11 C1 C2 O3 1.0938 110.62 180.00 107.70 1.4216 +IC C2 O3 C4 C5 1.4216 112.04 180.00 108.18 1.5162 +IC O3 C4 C5 C6 1.4204 108.18 180.00 112.13 1.5264 +IC C4 C5 C6 H61 1.5162 112.13 -60.05 111.11 1.0944 +IC H11 C2 *C1 H12 1.0938 110.62 -120.23 110.08 1.0920 +IC H11 C2 *C1 H13 1.0938 110.62 120.23 110.08 1.0920 +IC O3 C1 *C2 H21 1.4216 107.70 120.47 110.86 1.1015 +IC O3 C1 *C2 H22 1.4216 107.70 -120.47 110.86 1.1015 +IC C5 O3 *C4 H41 1.5162 108.18 -120.89 110.26 1.1029 +IC C5 O3 *C4 H42 1.5162 108.18 120.89 110.26 1.1029 +IC C6 C4 *C5 H51 1.5264 112.13 -122.18 108.33 1.0948 +IC C6 C4 *C5 H52 1.5264 112.13 122.18 108.33 1.0948 +IC H61 C5 *C6 H62 1.0944 111.11 -119.95 111.06 1.0931 +IC H61 C5 *C6 H63 1.0944 111.11 120.10 111.11 1.0944 +patc firs none last none + +! The following have not be rigorously tested +! +RESI PEGM 0.00 ! Peg monomer for polymer construction + ! +GROUP ! H1A H2A +ATOM C1 CC32A -0.01 ! | | +ATOM H1B HCA2A 0.09 ! (-C2) - C1 - O1 - C2 - +ATOM H1A HCA2A 0.09 ! | | +ATOM O1 OC30A -0.34 ! H1B H2B +ATOM C2 CC32A -0.01 ! +ATOM H2A HCA2A 0.09 ! +ATOM H2B HCA2A 0.09 ! +BOND C1 H1A C1 H1B C1 O1 ! +BOND O1 C2 C2 H2A C2 H2B ! +BOND C1 -C2 +! +IC -O1 -C2 C1 O1 0.000 0.000 180.0 0.000 0.000 +IC -C2 C1 O1 C2 0.000 0.000 180.0 0.000 0.000 +IC C1 O1 C2 +C1 0.000 0.000 180.0 0.000 0.000 + +PRES HYD1 0.17 ! Complete terminal methyl group adjacent to ether O + ! H1C - +ATOM H1C HCA3A 0.09 ! +ATOM C1 CC33A -0.10 ! +ATOM H1A HCA3A 0.09 ! +ATOM H1B HCA3A 0.09 ! +BOND H1C C1 + +PRES HYD2 0.17 ! Complete terminal methyl group adjacent to ether O + ! H2C - +ATOM H2C HCA3A 0.09 ! +ATOM C2 CC33A -0.10 ! +ATOM H2A HCA3A 0.09 ! +ATOM H2B HCA3A 0.09 ! +BOND H2C C2 + +PRES MET1 0.00 ! Append terminal methyl group adjacent to CH2 + ! HE2 + ! | +ATOM CE CC33A -0.27 ! HE3 - CE - +ATOM HE1 HCA3A 0.09 ! | +ATOM HE2 HCA3A 0.09 ! HE1 +ATOM HE3 HCA3A 0.09 ! +BOND CE C1 CE HE1 CE HE2 CE HE3 +IC CE C1 O1 C2 0.00 0.00 180.00 0.00 0.00 + +PRES MET2 0.00 ! Append terminal methyl group adjacent to CH2 + ! HA3 + ! | +ATOM CA CC33A -0.27 ! HA2 - CA - +ATOM HA1 HCA3A 0.09 ! | +ATOM HA2 HCA3A 0.09 ! HA1 +ATOM HA3 HCA3A 0.09 ! +BOND CA C2 CA HA1 CA HA2 CA HA3 +IC CA C2 O1 C1 0.00 0.00 180.00 0.00 0.00 + +DEFAULT FIRST NONE LAST NONE + +END + diff --git a/charmm/toppar/top_all36_carb.rtf b/charmm/toppar/top_all36_carb.rtf new file mode 100644 index 00000000..a65d89b5 --- /dev/null +++ b/charmm/toppar/top_all36_carb.rtf @@ -0,0 +1,6028 @@ +* $Id: top_allxx_sugar.inp,v 1.106 2014/08/19 19:07:43 alex Exp $ +*>>>>>>>>>>>> All-hydrogen topologies used in the <<<<<<<<<<<<<<<< +*>>>>> development of the CHARMM carbohydrate force field<<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>>>>> June 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< +*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< +*>>>>>>>>>> via the CHARMM web site: www.charmm.org <<<<<<<<<<<<<< +*>>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<< +* +32 1 + +! please reference the following: + +! pyranose monosaccharides +!Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M., +!Pastor, R.W., MacKerell, Jr., A.D. "Additive empirical force field for +!hexopyranose monosaccharides," Journal of Computational Chemistry, 29: +!2543-2564, 2008. PMID: 18470966 + +! linear sugars, sugar alcohols, and inositol +!Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. "CHARMM Additive +!All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates +!and Inositol," Journal of Chemical Theory and Computation, 5: +!1315-1327, 2009, DOI: 10.1021/ct9000608. + +! hexopyranose glycosidic linkages +!Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell, Jr., +!A. D. "Additive Empirical CHARMM Force Field for glycosyl linked +!hexopyranoses," Journal of Chemical Theory and Computation, 5, +!2353-2370, 2009, DOI: 10.1021/ct900242e + +! furanose monosaccharides +!Hatcher, E. R.; Guvench, O. and MacKerell, Jr., A.D. +!"CHARMM Additive All-Atom Force Field for Aldopentofuranose +! Carbohydrates and Fructofuranose." Journal of Physical Chemistry B. +! 113:12466-76, 2009, PMID: 19694450 + +! glycosidic linkages involving furanoses +!Raman, E. P., Guvench, O., MacKerell, Jr., A.D., "CHARMM Additive All-Atom +!Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses," +!Journal of Physical Chemistry B, 114: 12981-12994, 2010, PMID: 20845956 + +! carbohydrate derivatives and glycosidic linkages for glycoproteins +!Guvench, O.; Mallajosyula, S. S.; Raman, E. P.; Hatcher, E. R.; +!Vanommeslaeghe, K.; Foster, T. J.; Jamison, F. W. and MacKerell, Jr., A.D., +!"CHARMM additive all-atom force field for carbohydrate derivatives and its +!utility in polysaccharide and carbohydrate-protein modeling," +!Journal of Chemical Theory and Computation 2011 7 (10), 3162-3180 + +!O-glycan linkages +!Mallajosyula, S. S. and MacKerell, Jr., A.D., "Influence of Solvent and +!Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked +!Glycopeptides," +!The Journal of Physical Chemistry B 2011 115 (38), 11215-11229. + +! Phosphates and sulfates +! Mallajosyula, S. S.; Guvench, O; Hatcher E. R. and MacKerell, Jr., A.D., +! "CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates" +! Journal of Chemical Theory and Computation 2012 8 (2), 759-776. + + +! adm: Alex MacKerell +! sng: Shannon Greene +! og: Olgun Guvench +! erh: Elizabeth Hatcher +! pram: E. Prabhu Raman +! sai: Sairam S. Mallajosyula +! my: Mingjun Yang + +! tip3p water +!MASS 1 HCTIP3 1.00800 H ! TIP3P water hydrogen +!MASS 2 OCTIP3 15.99940 O ! TIP3P water oxygen +! C6H12O6 pyranose monosaccharide atom types +MASS 171 CC301 12.01100 C ! aliphatic C, no H's +MASS 172 CC311 12.01100 C ! generic acyclic CH carbon +MASS 173 CC312 12.01100 C ! CH carbon in linear polyols +MASS 174 CC3161 12.01100 C ! C2, C3, C4 CH bound to OH +MASS 175 CC3162 12.01100 C ! C1 (anomeric) CH bound to OH +MASS 176 CC3163 12.01100 C ! C5 CH bound to exocylic CH2OH +MASS 177 CC321 12.01100 C ! generic acyclic CH2 carbon (hexopyranose C6) +MASS 178 CC322 12.01100 C ! CH2 carbon in linear polyols erh +MASS 179 CC3263 12.01100 C ! C5 in xylose +MASS 180 CC331 12.01100 C ! generic acyclic CH3 carbon (xyl C6, glcna/galna CT) +MASS 181 CC2O1 12.01100 C ! sp2 carbon in amides, aldoses +MASS 182 CC2O2 12.01100 C ! sp2 carbon in carboxylates +MASS 183 CC2O3 12.01100 C ! sp2 carbon in acetone, ketoses +MASS 184 CC2O4 12.01100 C ! c22 CD +MASS 185 HCA1 1.00800 H ! aliphatic proton, CH +MASS 186 HCA2 1.00800 H ! aliphatic proton, CH2 +MASS 187 HCA3 1.00800 H ! aliphatic proton, CH3 +MASS 188 HCP1 1.00800 H ! polar H +MASS 189 HCR1 1.00800 H ! c22 HR1 +MASS 191 OC311 15.99940 O ! hydroxyl oxygen +MASS 192 OC3C61 15.99940 O ! ether in six membered ring +MASS 193 OC301 15.99940 O ! generic linear ether +MASS 194 OC302 15.99940 O ! linear ether in 1-1 glycosidic linkage +MASS 195 OC2D1 15.99940 O ! sp2 oxygen in amides, aldoses +MASS 196 OC2D2 15.99940 O ! sp2 oxygen in carboxylates +MASS 197 OC2D3 15.99940 O ! sp2 oxygen in acetone, ketoses +MASS 198 OC2D4 15.99940 O ! par22 O +MASS 200 NC2D1 14.00700 N ! peptide, NMA, IPAA nitrogen (C=NHR) +! model compound atom types +MASS 201 CC321C 12.01100 C ! cyclohexane, thp CH2 +MASS 202 HCA3M 1.00800 H ! alcohol aliphatic proton, CH3 +MASS 203 HCP1M 1.00800 H ! EGLY hydroxyl H +MASS 204 OC311M 15.99940 O ! MEOH, ETOH, PRO2, EGLY hydroxyl O +MASS 205 CC321D 12.01100 C ! cyclohexane, thp CH2 model for 1-1 linkage +MASS 206 CC311C 12.01100 C ! patch C1 in model compound +MASS 207 CC311D 12.01100 C ! patch C1 in model compound +! THF atom types +MASS 208 OC3C5M 15.99940 O ! thf ring oxygen +MASS 209 CC322C 12.01100 C ! cyclopentane, thf CH2 +MASS 210 HCA2C2 1.00800 H ! cyclopentane, thp aliphatic proton, CH2 +MASS 211 CC312C 12.01100 C ! tf2m CH1 +MASS 212 HCA1C2 1.00800 H ! tf2m aliphatic proton, CH1 +! Furanose atom types; erh 10/24/07 +MASS 213 OC3C51 15.99940 O ! furan ring oxygen +MASS 214 CC3152 12.01100 C ! furan ring carbon +MASS 215 CC3153 12.01100 C ! furan ring carbon +MASS 216 CC3251 12.01100 C ! furan ring carbon; C2 deoxy +MASS 217 CC3151 12.01100 C ! furan ring carbon +MASS 218 CC3051 12.01100 C ! furan ring carbon; C2 fructose +! pyranose derivatives +MASS 219 CC3062 12.01100 C ! C2 on NE5AC +MASS 220 CC3261 12.01100 C ! C3 on NE5AC +!Added by sai for modelling phosphate +MASS 221 OC312 15.99940 O ! OH in PO3H (phosphate) || OHL in top_all27_lipid.rtf +MASS 222 OC30P 15.99940 O ! ester O in PO3H (phosphate) || OSL in top_all27_lipid.rtf +MASS 223 OC2DP 15.99940 O ! =0 in P03H (phosphate) || O2L in top_all27_lipid.rtf +MASS 224 PC 30.974000 P ! phosphorus || PL in top_all27_lipid.rtf +MASS 225 SC 32.060000 S ! Sulfate sulfur +!pram, furanosyl linkages +MASS 226 CC312D 12.01100 C ! from CC322C; THF anomeric carbon +MASS 227 OC303 15.99940 O ! from OC301; linear ether in P1->F3 pyranose-furanose glycosidic linkage +!o-acetyl on ABEQ and ARHM, Mingjun +MASS 228 CC2O5 12.01100 C ! carbonyl C on acetyl + +AUTOGENERATE angles dihedrals +! DEFAults for patching FIRSt and LAST residues +DEFA FIRS NONE LAST NONE + +RESI AGLC 0.000 ! 4C1 alpha-D-glucose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4077 108.33 -123.34 103.67 1.1200 +IC O1 O5 *C1 C2 1.4077 108.39 -119.83 112.62 1.5516 +IC O2 C3 *C2 H2 1.4293 114.98 -108.39 100.80 1.0662 +IC O2 C1 *C2 C3 1.4293 117.26 -138.07 113.63 1.4880 +IC O3 C4 *C3 H3 1.4122 110.86 120.36 107.49 1.1219 +IC O3 C2 *C3 C4 1.4122 109.00 121.20 109.13 1.5315 +IC O4 C5 *C4 H4 1.4206 109.25 -124.20 109.65 1.1311 +IC O4 C3 *C4 C5 1.4206 103.58 -118.81 114.40 1.5087 +IC C6 O5 *C5 H5 1.4718 112.19 113.05 108.36 1.1212 +IC C6 C4 *C5 O5 1.4718 112.04 128.71 113.93 1.4175 +IC O6 H62 *C6 H61 1.3851 111.30 -112.76 100.96 1.1590 +IC O6 C5 *C6 H62 1.3851 110.28 -128.49 116.95 1.1067 +IC O5 C1 C2 C3 1.4351 112.62 51.83 113.63 1.4880 +IC C1 C2 C3 C4 1.5516 113.63 -48.48 109.13 1.5315 +IC C2 C3 C4 C5 1.4880 109.13 47.85 114.40 1.5087 +IC C3 C4 C5 O5 1.5315 114.40 -49.84 113.93 1.4175 +IC C4 C5 O5 C1 1.5087 113.93 51.43 114.13 1.4351 +IC C5 O5 C1 C2 1.4175 114.13 -51.82 112.62 1.5516 +IC C4 C5 C6 O6 1.5087 112.04 -173.06 110.28 1.3851 +IC O5 C1 O1 HO1 1.4351 108.39 47.62 101.41 0.9789 +IC C1 C2 O2 HO2 1.5516 117.26 -50.05 114.32 0.9181 +IC C2 C3 O3 HO3 1.4880 109.00 -28.48 103.99 0.9971 +IC C3 C4 O4 HO4 1.5315 103.58 55.55 110.36 0.9685 +IC C5 C6 O6 HO6 1.4718 110.28 -101.06 108.67 0.9667 +PATC FIRS NONE LAST NONE + +RESI BGLC 0.000 ! 4C1 beta-D-glucose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3899 110.90 120.10 104.58 1.0836 +IC O1 O5 *C1 C2 1.3899 108.62 122.10 110.88 1.5316 +IC O2 C3 *C2 H2 1.4594 108.12 -118.78 111.06 1.1375 +IC O2 C1 *C2 C3 1.4594 115.65 -125.60 113.28 1.4983 +IC O3 C4 *C3 H3 1.4071 113.48 122.06 103.39 1.0895 +IC O3 C2 *C3 C4 1.4071 108.48 124.18 109.26 1.5497 +IC O4 C5 *C4 H4 1.3940 111.12 -110.35 108.66 1.0857 +IC O4 C3 *C4 C5 1.3940 112.77 -129.39 115.62 1.5530 +IC C6 O5 *C5 H5 1.5597 111.17 120.85 110.98 1.1092 +IC C6 C4 *C5 O5 1.5597 109.90 122.92 110.30 1.4512 +IC O6 H62 *C6 H61 1.4589 116.11 -112.93 103.57 1.1467 +IC O6 C5 *C6 H62 1.4589 109.41 -135.95 118.22 1.0853 +IC O5 C1 C2 C3 1.4620 110.88 57.82 113.28 1.4983 +IC C1 C2 C3 C4 1.5316 113.28 -48.40 109.26 1.5497 +IC C2 C3 C4 C5 1.4983 109.26 45.07 115.62 1.5530 +IC C3 C4 C5 O5 1.5497 115.62 -49.19 110.30 1.4512 +IC C4 C5 O5 C1 1.5530 110.30 56.36 112.12 1.4620 +IC C5 O5 C1 C2 1.4512 112.12 -61.39 110.88 1.5316 +IC C4 C5 C6 O6 1.5530 109.90 -177.46 109.41 1.4589 +IC O5 C1 O1 HO1 1.4620 108.62 72.25 106.48 0.9328 +IC C1 C2 O2 HO2 1.5316 115.65 135.41 116.81 0.9527 +IC C2 C3 O3 HO3 1.4983 108.48 -71.46 120.86 0.9441 +IC C3 C4 O4 HO4 1.5497 112.77 47.45 109.31 0.9911 +IC C5 C6 O6 HO6 1.5597 109.41 -54.60 118.82 0.95210 +PATC FIRS NONE LAST NONE + +RESI AALT 0.000 ! 4C1 alpha-D-altrose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO2 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ H3 O2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4059 109.84 -116.86 107.03 1.0749 +IC O1 O5 *C1 C2 1.4059 106.65 -124.27 118.28 1.5314 +IC O2 C3 *C2 H2 1.4540 106.08 123.94 116.41 1.0734 +IC O2 C1 *C2 C3 1.4540 108.11 116.16 111.37 1.4724 +IC O3 C4 *C3 H3 1.4262 116.38 -115.23 108.33 1.1702 +IC O3 C2 *C3 C4 1.4262 108.86 -129.67 111.42 1.4998 +IC O4 C5 *C4 H4 1.4250 108.92 -122.02 114.73 1.1508 +IC O4 C3 *C4 C5 1.4250 103.39 -116.89 111.54 1.4873 +IC C6 O5 *C5 H5 1.5191 108.29 117.76 108.02 1.1275 +IC C6 C4 *C5 O5 1.5191 112.49 120.64 109.76 1.4455 +IC O6 H62 *C6 H61 1.3863 101.25 -112.12 102.65 1.1299 +IC O6 C5 *C6 H62 1.3863 110.53 -110.40 108.93 1.1288 +IC O5 C1 C2 C3 1.4181 118.28 41.70 111.37 1.4724 +IC C1 C2 C3 C4 1.5314 111.37 -43.82 111.42 1.4998 +IC C2 C3 C4 C5 1.4724 111.42 56.21 111.54 1.4873 +IC C3 C4 C5 O5 1.4998 111.54 -61.84 109.76 1.4455 +IC C4 C5 O5 C1 1.4873 109.76 56.28 111.65 1.4181 +IC C5 O5 C1 C2 1.4455 111.65 -47.85 118.28 1.5314 +IC C4 C5 C6 O6 1.4873 112.49 178.99 110.53 1.3863 +IC O5 C1 O1 HO1 1.4181 106.65 56.46 100.91 0.9422 +IC C1 C2 O2 HO2 1.5314 108.11 -153.83 113.21 1.0131 +IC C2 C3 O3 HO3 1.4724 108.86 164.64 101.47 0.9893 +IC C3 C4 O4 HO4 1.4998 103.39 -131.59 111.45 0.9477 +IC C5 C6 O6 HO6 1.5191 110.53 -85.80 108.22 0.9698 +PATC FIRS NONE LAST NONE + +RESI BALT 0.000 ! 4C1 beta-D-altrose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO2 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ H3 O2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4318 113.28 122.84 113.44 1.1912 +IC O1 O5 *C1 C2 1.4318 98.01 118.50 110.22 1.4937 +IC O2 C3 *C2 H2 1.4452 105.69 112.57 107.58 1.1287 +IC O2 C1 *C2 C3 1.4452 118.30 118.45 106.22 1.4707 +IC O3 C4 *C3 H3 1.4161 116.67 -116.77 107.70 1.1602 +IC O3 C2 *C3 C4 1.4161 109.34 -129.39 110.06 1.5310 +IC O4 C5 *C4 H4 1.4041 109.84 -121.00 103.00 1.1380 +IC O4 C3 *C4 C5 1.4041 106.00 -121.86 115.49 1.5108 +IC C6 O5 *C5 H5 1.4772 112.24 122.31 107.27 1.0848 +IC C6 C4 *C5 O5 1.4772 110.66 124.06 109.24 1.4004 +IC O6 H62 *C6 H61 1.4160 113.83 -126.41 115.87 1.1685 +IC O6 C5 *C6 H62 1.4160 108.88 -122.00 104.54 1.1002 +IC O5 C1 C2 C3 1.4644 110.22 65.02 106.22 1.4707 +IC C1 C2 C3 C4 1.4937 106.22 -56.25 110.06 1.5310 +IC C2 C3 C4 C5 1.4707 110.06 49.69 115.49 1.5108 +IC C3 C4 C5 O5 1.5310 115.49 -46.27 109.24 1.4004 +IC C4 C5 O5 C1 1.5108 109.24 53.35 112.97 1.4644 +IC C5 O5 C1 C2 1.4004 112.97 -65.99 110.22 1.4937 +IC C4 C5 C6 O6 1.5108 110.66 -172.71 108.88 1.4160 +IC O5 C1 O1 HO1 1.4644 98.01 -48.09 108.23 0.9538 +IC C1 C2 O2 HO2 1.4937 118.30 -74.78 103.83 0.9777 +IC C2 C3 O3 HO3 1.4707 109.34 106.07 116.48 0.9998 +IC C3 C4 O4 HO4 1.5310 106.00 -43.64 106.03 0.9690 +IC C5 C6 O6 HO6 1.4772 108.88 -129.43 110.69 0.9739 +PATC FIRS NONE LAST NONE + +RESI AALL 0.000 ! 4C1 alpha-D-allose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / \ / +GROU ! C4 C1 +ATOM C2 CC3161 0.140 ! / \ H3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4098 110.83 -123.55 103.31 1.1208 +IC O1 O5 *C1 C2 1.4098 109.08 -122.35 110.92 1.5564 +IC O2 C3 *C2 H2 1.4479 114.09 -105.38 102.92 1.0648 +IC O2 C1 *C2 C3 1.4479 116.87 -135.18 112.80 1.4510 +IC O3 C4 *C3 H3 1.4756 113.82 -112.82 103.37 1.1328 +IC O3 C2 *C3 C4 1.4756 109.58 -126.87 111.42 1.5452 +IC O4 C5 *C4 H4 1.4147 111.32 -125.80 108.92 1.1328 +IC O4 C3 *C4 C5 1.4147 105.29 -121.63 112.88 1.5179 +IC C6 O5 *C5 H5 1.4813 111.46 111.89 106.04 1.1158 +IC C6 C4 *C5 O5 1.4813 113.62 129.33 114.16 1.4217 +IC O6 H62 *C6 H61 1.4254 104.77 -121.62 104.03 1.1216 +IC O6 C5 *C6 H62 1.4254 111.38 -121.22 118.00 1.1175 +IC O5 C1 C2 C3 1.4402 110.92 54.57 112.80 1.4510 +IC C1 C2 C3 C4 1.5564 112.80 -50.62 111.42 1.5452 +IC C2 C3 C4 C5 1.4510 111.42 46.53 112.88 1.5179 +IC C3 C4 C5 O5 1.5452 112.88 -46.19 114.16 1.4217 +IC C4 C5 O5 C1 1.5179 114.16 51.39 114.72 1.4402 +IC C5 O5 C1 C2 1.4217 114.72 -54.00 110.92 1.5564 +IC C4 C5 C6 O6 1.5179 113.62 -59.78 111.38 1.4254 +IC O5 C1 O1 HO1 1.4402 109.08 58.48 102.60 0.9806 +IC C1 C2 O2 HO2 1.5564 116.87 -119.27 106.08 0.9438 +IC C2 C3 O3 HO3 1.4510 109.58 -29.18 102.05 0.9525 +IC C3 C4 O4 HO4 1.5452 105.29 -22.81 109.42 0.9570 +IC C5 C6 O6 HO6 1.4813 111.38 63.12 111.98 0.9972 +PATC FIRS NONE LAST NONE + +RESI BALL 0.000 ! 4C1 beta-D-allose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / \ / +GROU ! C4 C1 +ATOM C2 CC3161 0.140 ! / \ H3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4195 111.04 124.25 111.51 1.1174 +IC O1 O5 *C1 C2 1.4195 102.62 117.00 107.12 1.4947 +IC O2 C3 *C2 H2 1.4041 113.70 -121.08 106.92 1.2090 +IC O2 C1 *C2 C3 1.4041 113.52 -125.56 106.07 1.5053 +IC O3 C4 *C3 H3 1.3756 114.59 -114.99 112.58 1.0991 +IC O3 C2 *C3 C4 1.3756 110.80 -130.25 113.12 1.4926 +IC O4 C5 *C4 H4 1.4086 116.22 -115.71 106.93 1.0762 +IC O4 C3 *C4 C5 1.4086 108.71 -128.79 110.69 1.5002 +IC C6 O5 *C5 H5 1.4986 113.17 117.77 109.71 1.1598 +IC C6 C4 *C5 O5 1.4986 111.00 125.30 108.99 1.4520 +IC O6 H62 *C6 H61 1.3973 108.34 -115.37 109.69 1.0887 +IC O6 C5 *C6 H62 1.3973 111.64 -118.40 107.03 1.1034 +IC O5 C1 C2 C3 1.3963 107.12 63.98 106.07 1.5053 +IC C1 C2 C3 C4 1.4947 106.07 -56.87 113.12 1.4926 +IC C2 C3 C4 C5 1.5053 113.12 50.62 110.69 1.5002 +IC C3 C4 C5 O5 1.4926 110.69 -49.08 108.99 1.4520 +IC C4 C5 O5 C1 1.5002 108.99 61.15 112.84 1.3963 +IC C5 O5 C1 C2 1.4520 112.84 -69.50 107.12 1.4947 +IC C4 C5 C6 O6 1.5002 111.00 -67.09 111.64 1.3973 +IC O5 C1 O1 HO1 1.3963 102.62 -59.81 110.50 0.9588 +IC C1 C2 O2 HO2 1.4947 113.52 75.20 110.55 0.9684 +IC C2 C3 O3 HO3 1.5053 110.80 54.33 102.92 0.9436 +IC C3 C4 O4 HO4 1.4926 108.71 -37.98 105.06 0.9792 +IC C5 C6 O6 HO6 1.4986 111.64 43.65 106.81 0.9783 +PATC FIRS NONE LAST NONE + +RESI AGAL 0.000 ! 4C1 alpha-D-galactose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3865 108.93 -123.99 104.38 1.1081 +IC O1 O5 *C1 C2 1.3865 108.96 -118.67 108.85 1.5226 +IC O2 C3 *C2 H2 1.4411 111.34 -110.11 102.47 1.1187 +IC O2 C1 *C2 C3 1.4411 115.23 -135.16 118.19 1.4969 +IC O3 C4 *C3 H3 1.4266 109.02 118.09 104.61 1.1300 +IC O3 C2 *C3 C4 1.4266 116.32 123.96 109.32 1.5156 +IC O4 C5 *C4 H4 1.4233 107.75 119.05 111.86 1.0818 +IC O4 C3 *C4 C5 1.4233 111.62 121.16 112.36 1.4931 +IC C6 O5 *C5 H5 1.5325 113.82 109.66 108.87 1.1501 +IC C6 C4 *C5 O5 1.5325 115.44 135.15 114.56 1.4252 +IC O6 H62 *C6 H61 1.4421 111.00 -121.63 104.24 1.1078 +IC O6 C5 *C6 H62 1.4421 112.98 -123.79 108.85 1.1420 +IC O5 C1 C2 C3 1.4134 108.85 48.90 118.19 1.4969 +IC C1 C2 C3 C4 1.5226 118.19 -46.22 109.32 1.5156 +IC C2 C3 C4 C5 1.4969 109.32 44.65 112.36 1.4931 +IC C3 C4 C5 O5 1.5156 112.36 -50.65 114.56 1.4252 +IC C4 C5 O5 C1 1.4931 114.56 55.65 115.64 1.4134 +IC C5 O5 C1 C2 1.4252 115.64 -51.39 108.85 1.5226 +IC C4 C5 C6 O6 1.4931 115.44 65.25 112.98 1.4421 +IC O5 C1 O1 HO1 1.4134 108.96 63.08 109.87 0.9758 +IC C1 C2 O2 HO2 1.5226 115.23 -42.41 115.36 0.9113 +IC C2 C3 O3 HO3 1.4969 116.32 -21.70 115.24 0.9926 +IC C3 C4 O4 HO4 1.5156 111.62 -23.31 104.57 0.9949 +IC C5 C6 O6 HO6 1.5325 112.98 -45.14 110.63 0.9762 +PATC FIRS NONE LAST NONE + +RESI BGAL 0.000 ! 4C1 beta-D-galactose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3474 106.42 116.51 115.09 1.1438 +IC O1 O5 *C1 C2 1.3474 104.56 115.77 113.93 1.5410 +IC O2 C3 *C2 H2 1.4631 108.10 -121.28 108.50 1.1329 +IC O2 C1 *C2 C3 1.4631 114.38 -122.04 110.23 1.4726 +IC O3 C4 *C3 H3 1.4614 112.11 123.20 113.19 1.1731 +IC O3 C2 *C3 C4 1.4614 110.41 123.80 109.34 1.5276 +IC O4 C5 *C4 H4 1.4408 117.10 124.69 105.11 1.1036 +IC O4 C3 *C4 C5 1.4408 108.63 126.45 105.69 1.5707 +IC C6 O5 *C5 H5 1.5525 105.55 121.59 108.44 1.0948 +IC C6 C4 *C5 O5 1.5525 109.96 114.62 107.87 1.4748 +IC O6 H62 *C6 H61 1.4039 115.08 -121.25 107.51 1.1562 +IC O6 C5 *C6 H62 1.4039 111.39 -123.55 102.46 1.1003 +IC O5 C1 C2 C3 1.3914 113.93 52.67 110.23 1.4726 +IC C1 C2 C3 C4 1.5410 110.23 -56.55 109.34 1.5276 +IC C2 C3 C4 C5 1.4726 109.34 62.95 105.69 1.5707 +IC C3 C4 C5 O5 1.5276 105.69 -63.57 107.87 1.4748 +IC C4 C5 O5 C1 1.5707 107.87 61.04 112.05 1.3914 +IC C5 O5 C1 C2 1.4748 112.05 -55.18 113.93 1.5410 +IC C4 C5 C6 O6 1.5707 109.96 47.46 111.39 1.4039 +IC O5 C1 O1 HO1 1.3914 104.56 47.03 104.25 0.9837 +IC C1 C2 O2 HO2 1.5410 114.38 86.78 105.57 0.9458 +IC C2 C3 O3 HO3 1.4726 110.41 -41.42 104.34 0.9789 +IC C3 C4 O4 HO4 1.5276 108.63 -53.94 107.01 0.9519 +IC C5 C6 O6 HO6 1.5525 111.39 -11.52 102.88 0.9548 +PATC FIRS NONE LAST NONE + +RESI AGUL 0.000 ! 4C1 alpha-D-gulose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / \ / +GROU ! C4 C1 +ATOM C2 CC3161 0.140 ! / \ H3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / OH1-H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3730 109.13 -114.32 110.17 1.0759 +IC O1 O5 *C1 C2 1.3730 110.11 -124.26 115.65 1.5446 +IC O2 C3 *C2 H2 1.4253 116.11 -117.13 110.47 1.1056 +IC O2 C1 *C2 C3 1.4253 116.42 -134.99 110.24 1.4821 +IC O3 C4 *C3 H3 1.4366 112.23 -118.25 111.07 1.1689 +IC O3 C2 *C3 C4 1.4366 110.15 -125.94 112.38 1.4818 +IC O4 C5 *C4 H4 1.4291 112.18 115.14 108.47 1.1681 +IC O4 C3 *C4 C5 1.4291 107.17 123.89 112.71 1.4952 +IC C6 O5 *C5 H5 1.5584 110.62 116.21 108.29 1.1257 +IC C6 C4 *C5 O5 1.5584 110.85 124.27 112.26 1.4186 +IC O6 H62 *C6 H61 1.3799 102.93 -113.47 106.66 1.1307 +IC O6 C5 *C6 H62 1.3799 111.99 -112.02 106.89 1.1210 +IC O5 C1 C2 C3 1.4591 115.65 47.62 110.24 1.4821 +IC C1 C2 C3 C4 1.5446 110.24 -46.69 112.38 1.4818 +IC C2 C3 C4 C5 1.4821 112.38 52.71 112.71 1.4952 +IC C3 C4 C5 O5 1.4818 112.71 -57.13 112.26 1.4186 +IC C4 C5 O5 C1 1.4952 112.26 55.40 110.94 1.4591 +IC C5 O5 C1 C2 1.4186 110.94 -52.14 115.65 1.5446 +IC C4 C5 C6 O6 1.4952 110.85 -166.43 111.99 1.3799 +IC O5 C1 O1 HO1 1.4591 110.11 -74.56 109.17 0.9540 +IC C1 C2 O2 HO2 1.5446 116.42 -66.49 108.06 0.9292 +IC C2 C3 O3 HO3 1.4821 110.15 105.79 106.12 0.9949 +IC C3 C4 O4 HO4 1.4818 107.17 79.28 112.61 0.9495 +IC C5 C6 O6 HO6 1.5584 111.99 -91.22 109.74 0.9787 +PATC FIRS NONE LAST NONE + +RESI BGUL 0.000 ! 4C1 beta-D-gulose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / \ / +GROU ! C4 C1 +ATOM C2 CC3161 0.140 ! / \ H3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3825 109.34 125.34 110.63 1.1765 +IC O1 O5 *C1 C2 1.3825 105.20 119.53 113.55 1.5176 +IC O2 C3 *C2 H2 1.4360 113.17 -113.77 111.02 1.1213 +IC O2 C1 *C2 C3 1.4360 116.61 -130.62 110.04 1.5067 +IC O3 C4 *C3 H3 1.4253 112.90 -120.39 107.67 1.1673 +IC O3 C2 *C3 C4 1.4253 109.69 -125.40 110.93 1.5032 +IC O4 C5 *C4 H4 1.3908 113.46 123.34 110.19 1.1566 +IC O4 C3 *C4 C5 1.3908 108.13 124.77 110.57 1.4791 +IC C6 O5 *C5 H5 1.5276 112.58 118.28 105.66 1.1232 +IC C6 C4 *C5 O5 1.5276 110.58 124.45 109.25 1.4518 +IC O6 H62 *C6 H61 1.3660 102.24 -115.00 103.17 1.1275 +IC O6 C5 *C6 H62 1.3660 111.24 -112.09 109.18 1.1265 +IC O5 C1 C2 C3 1.4490 113.55 50.27 110.04 1.5067 +IC C1 C2 C3 C4 1.5176 110.04 -50.09 110.93 1.5032 +IC C2 C3 C4 C5 1.5067 110.93 57.08 110.57 1.4791 +IC C3 C4 C5 O5 1.5032 110.57 -61.38 109.25 1.4518 +IC C4 C5 O5 C1 1.4791 109.25 60.60 111.35 1.4490 +IC C5 O5 C1 C2 1.4518 111.35 -56.04 113.55 1.5176 +IC C4 C5 C6 O6 1.4791 110.58 -176.59 111.24 1.3660 +IC O5 C1 O1 HO1 1.4490 105.20 171.60 108.75 0.9716 +IC C1 C2 O2 HO2 1.5176 116.61 -127.96 107.98 0.9472 +IC C2 C3 O3 HO3 1.5067 109.69 130.39 105.07 1.0055 +IC C3 C4 O4 HO4 1.5032 108.13 82.45 111.30 0.9602 +IC C5 C6 O6 HO6 1.5276 111.24 -97.14 109.20 0.9823 +PATC FIRS NONE LAST NONE + +RESI AIDO 0.000 ! 4C1 alpha-D-idose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO2 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ H3 O2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4030 110.70 -118.01 108.88 1.1054 +IC O1 O5 *C1 C2 1.4030 109.49 -123.53 112.49 1.5064 +IC O2 C3 *C2 H2 1.4727 106.55 115.47 118.67 1.1042 +IC O2 C1 *C2 C3 1.4727 114.02 119.04 109.20 1.5200 +IC O3 C4 *C3 H3 1.3943 115.01 -112.29 105.01 1.1238 +IC O3 C2 *C3 C4 1.3943 110.14 -129.45 112.14 1.4804 +IC O4 C5 *C4 H4 1.3892 107.94 119.64 111.65 1.0936 +IC O4 C3 *C4 C5 1.3892 112.33 120.17 109.88 1.5085 +IC C6 O5 *C5 H5 1.4888 112.14 120.03 112.38 1.1256 +IC C6 C4 *C5 O5 1.4888 110.66 126.55 112.81 1.4342 +IC O6 H62 *C6 H61 1.4374 107.23 -124.60 117.65 1.1136 +IC O6 C5 *C6 H62 1.4374 109.49 -113.02 101.29 1.1194 +IC O5 C1 C2 C3 1.3559 112.49 54.93 109.20 1.5200 +IC C1 C2 C3 C4 1.5064 109.20 -52.86 112.14 1.4804 +IC C2 C3 C4 C5 1.5200 112.14 51.12 109.88 1.5085 +IC C3 C4 C5 O5 1.4804 109.88 -50.48 112.81 1.4342 +IC C4 C5 O5 C1 1.5085 112.81 54.91 114.73 1.3559 +IC C5 O5 C1 C2 1.4342 114.73 -57.05 112.49 1.5064 +IC C4 C5 C6 O6 1.5085 110.66 -162.82 109.49 1.4374 +IC O5 C1 O1 HO1 1.3559 109.49 56.20 106.74 0.9610 +IC C1 C2 O2 HO2 1.5064 114.02 -149.77 114.21 1.0133 +IC C2 C3 O3 HO3 1.5200 110.14 -41.24 109.63 0.9224 +IC C3 C4 O4 HO4 1.4804 112.33 55.76 112.56 0.9964 +IC C5 C6 O6 HO6 1.4888 109.49 -121.61 102.80 0.9533 +PATC FIRS NONE LAST NONE + + +RESI BIDO 0.000 ! 4C1 beta-D-idose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO2 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ H3 O2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3628 112.08 120.79 108.00 1.1750 +IC O1 O5 *C1 C2 1.3628 106.67 125.22 115.43 1.5202 +IC O2 C3 *C2 H2 1.4093 107.12 113.85 108.43 1.1113 +IC O2 C1 *C2 C3 1.4093 114.99 119.35 107.74 1.5055 +IC O3 C4 *C3 H3 1.4194 112.06 -119.21 105.92 1.1298 +IC O3 C2 *C3 C4 1.4194 109.82 -123.13 109.02 1.5258 +IC O4 C5 *C4 H4 1.3936 112.11 114.28 108.15 1.0879 +IC O4 C3 *C4 C5 1.3936 107.61 126.57 116.15 1.4852 +IC C6 O5 *C5 H5 1.4598 110.36 116.44 107.74 1.1268 +IC C6 C4 *C5 O5 1.4598 114.14 127.04 112.82 1.4371 +IC O6 H62 *C6 H61 1.3728 112.75 -114.37 102.31 1.1593 +IC O6 C5 *C6 H62 1.3728 111.22 -129.49 114.76 1.1023 +IC O5 C1 C2 C3 1.4409 115.43 58.58 107.74 1.5055 +IC C1 C2 C3 C4 1.5202 107.74 -52.96 109.02 1.5258 +IC C2 C3 C4 C5 1.5055 109.02 51.16 116.15 1.4852 +IC C3 C4 C5 O5 1.5258 116.15 -47.54 112.82 1.4371 +IC C4 C5 O5 C1 1.4852 112.82 47.40 112.38 1.4409 +IC C5 O5 C1 C2 1.4371 112.38 -55.49 115.43 1.5202 +IC C4 C5 C6 O6 1.4852 114.14 -162.57 111.22 1.3728 +IC O5 C1 O1 HO1 1.4409 106.67 -44.97 112.65 0.9677 +IC C1 C2 O2 HO2 1.5202 114.99 -80.74 113.28 0.9808 +IC C2 C3 O3 HO3 1.5055 109.82 106.91 109.96 0.9958 +IC C3 C4 O4 HO4 1.5258 107.61 51.84 98.03 0.9995 +IC C5 C6 O6 HO6 1.4598 111.22 -138.12 110.40 0.9879 +PATC FIRS NONE LAST NONE + + +RESI AMAN 0.000 ! 4C1 alpha-D-mannose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 HO2 \ / +GROU ! C4 | | C1 +ATOM C2 CC3161 0.140 ! / \ O3 O2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3975 110.50 -118.09 109.89 1.1050 +IC O1 O5 *C1 C2 1.3975 108.93 -123.71 113.70 1.4876 +IC O2 C3 *C2 H2 1.4750 107.62 114.46 115.21 1.1022 +IC O2 C1 *C2 C3 1.4750 114.83 120.80 109.00 1.5586 +IC O3 C4 *C3 H3 1.4261 109.30 119.59 108.95 1.1150 +IC O3 C2 *C3 C4 1.4261 109.19 118.55 107.65 1.5049 +IC O4 C5 *C4 H4 1.3887 107.72 -127.19 110.85 1.1254 +IC O4 C3 *C4 C5 1.3887 108.42 -117.81 110.46 1.5035 +IC C6 O5 *C5 H5 1.4825 112.02 117.79 109.03 1.1288 +IC C6 C4 *C5 O5 1.4825 112.70 127.52 112.13 1.4375 +IC O6 H62 *C6 H61 1.4292 107.96 -123.56 113.24 1.1140 +IC O6 C5 *C6 H62 1.4292 109.39 -114.45 102.63 1.1098 +IC O5 C1 C2 C3 1.3632 113.70 56.64 109.00 1.5586 +IC C1 C2 C3 C4 1.4876 109.00 -56.11 107.65 1.5049 +IC C2 C3 C4 C5 1.5586 107.65 55.76 110.46 1.5035 +IC C3 C4 C5 O5 1.5049 110.46 -54.16 112.13 1.4375 +IC C4 C5 O5 C1 1.5035 112.13 53.40 114.61 1.3632 +IC C5 O5 C1 C2 1.4375 114.61 -55.52 113.70 1.4876 +IC C4 C5 C6 O6 1.5035 112.70 -173.75 109.39 1.4292 +IC O5 C1 O1 HO1 1.3632 108.93 53.42 107.62 0.9615 +IC C1 C2 O2 HO2 1.4876 114.83 -137.09 114.41 1.0113 +IC C2 C3 O3 HO3 1.5586 109.19 60.11 113.74 0.9944 +IC C3 C4 O4 HO4 1.5049 108.42 42.16 103.57 0.9552 +IC C5 C6 O6 HO6 1.4825 109.39 -84.75 103.86 0.9396 +PATC FIRS NONE LAST NONE + + +RESI BMAN 0.000 ! 4C1 beta-D-mannose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 HO2 \ / +GROU ! C4 | | C1 +ATOM C2 CC3161 0.140 ! / \ O3 O2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4147 114.01 123.87 115.47 1.1241 +IC O1 O5 *C1 C2 1.4147 102.76 121.94 110.36 1.5194 +IC O2 C3 *C2 H2 1.4714 110.16 123.24 108.47 1.1051 +IC O2 C1 *C2 C3 1.4714 114.57 122.69 107.36 1.5071 +IC O3 C4 *C3 H3 1.3878 111.68 114.99 113.62 1.1108 +IC O3 C2 *C3 C4 1.3878 109.74 124.46 111.76 1.5071 +IC O4 C5 *C4 H4 1.3992 108.74 -119.41 104.60 1.1086 +IC O4 C3 *C4 C5 1.3992 114.29 -123.16 110.67 1.5450 +IC C6 O5 *C5 H5 1.5345 108.55 116.69 108.96 1.0801 +IC C6 C4 *C5 O5 1.5345 111.73 122.98 113.28 1.4134 +IC O6 H62 *C6 H61 1.4228 107.34 -116.56 114.05 1.1041 +IC O6 C5 *C6 H62 1.4228 116.50 -120.25 107.28 1.1156 +IC O5 C1 C2 C3 1.4381 110.36 63.05 107.36 1.5071 +IC C1 C2 C3 C4 1.5194 107.36 -55.99 111.76 1.5071 +IC C2 C3 C4 C5 1.5071 111.76 49.25 110.67 1.5450 +IC C3 C4 C5 O5 1.5071 110.67 -49.18 113.28 1.4134 +IC C4 C5 O5 C1 1.5450 113.28 56.65 110.70 1.4381 +IC C5 O5 C1 C2 1.4134 110.70 -64.29 110.36 1.5194 +IC C4 C5 C6 O6 1.5450 111.73 -168.80 116.50 1.4228 +IC O5 C1 O1 HO1 1.4381 102.76 -14.89 110.00 0.9891 +IC C1 C2 O2 HO2 1.5194 114.57 -31.81 104.69 0.9864 +IC C2 C3 O3 HO3 1.5071 109.74 46.67 101.47 0.9688 +IC C3 C4 O4 HO4 1.5071 114.29 42.72 117.62 0.9726 +IC C5 C6 O6 HO6 1.5345 116.50 -62.83 105.97 0.9733 +PATC FIRS NONE LAST NONE + + +RESI ATAL 0.000 ! 4C1 alpha-D-talose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 HO2 \ / +GROU ! C4 | | C1 +ATOM C2 CC3161 0.140 ! / \ O3 O2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4221 107.55 -121.04 103.18 1.1260 +IC O1 O5 *C1 C2 1.4221 108.10 -120.96 116.21 1.5424 +IC O2 C3 *C2 H2 1.4492 108.99 111.12 111.71 1.1130 +IC O2 C1 *C2 C3 1.4492 110.19 121.38 111.84 1.4843 +IC O3 C4 *C3 H3 1.4110 114.05 118.54 103.93 1.1185 +IC O3 C2 *C3 C4 1.4110 111.20 126.43 108.81 1.5416 +IC O4 C5 *C4 H4 1.3621 111.29 117.93 107.00 1.0823 +IC O4 C3 *C4 C5 1.3621 110.03 125.60 113.70 1.5072 +IC C6 O5 *C5 H5 1.5017 109.27 111.35 106.33 1.1114 +IC C6 C4 *C5 O5 1.5017 116.34 129.67 115.09 1.4356 +IC O6 H62 *C6 H61 1.4386 106.14 -124.99 106.59 1.1207 +IC O6 C5 *C6 H62 1.4386 110.98 -119.80 114.03 1.1369 +IC O5 C1 C2 C3 1.4303 116.21 51.66 111.84 1.4843 +IC C1 C2 C3 C4 1.5424 111.84 -50.94 108.81 1.5416 +IC C2 C3 C4 C5 1.4843 108.81 51.41 113.70 1.5072 +IC C3 C4 C5 O5 1.5416 113.70 -49.51 115.09 1.4356 +IC C4 C5 O5 C1 1.5072 115.09 46.15 113.29 1.4303 +IC C5 O5 C1 C2 1.4356 113.29 -47.30 116.21 1.5424 +IC C4 C5 C6 O6 1.5072 116.34 63.06 110.98 1.4386 +IC O5 C1 O1 HO1 1.4303 108.10 62.34 103.18 0.9787 +IC C1 C2 O2 HO2 1.5424 110.19 97.32 103.39 0.9815 +IC C2 C3 O3 HO3 1.4843 111.20 60.87 105.69 0.9861 +IC C3 C4 O4 HO4 1.5416 110.03 150.82 103.42 0.9772 +IC C5 C6 O6 HO6 1.5017 110.98 78.75 112.42 0.9516 +PATC FIRS NONE LAST NONE + + +RESI BTAL 0.000 ! 4C1 beta-D-talose + ! +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 HO2 \ / +GROU ! C4 | | C1 +ATOM C2 CC3161 0.140 ! / \ O3 O2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3889 106.87 117.83 101.80 1.1309 +IC O1 O5 *C1 C2 1.3889 112.84 124.25 116.58 1.5618 +IC O2 C3 *C2 H2 1.4489 109.20 113.88 114.91 1.1114 +IC O2 C1 *C2 C3 1.4489 112.96 121.77 109.28 1.5591 +IC O3 C4 *C3 H3 1.4529 113.77 116.04 109.93 1.1125 +IC O3 C2 *C3 C4 1.4529 112.93 125.64 106.60 1.5550 +IC O4 C5 *C4 H4 1.4470 115.26 126.65 112.14 1.0859 +IC O4 C3 *C4 C5 1.4470 108.47 129.11 113.03 1.6431 +IC C6 O5 *C5 H5 1.5283 109.17 120.52 109.23 1.1154 +IC C6 C4 *C5 O5 1.5283 113.70 121.95 108.88 1.4584 +IC O6 H62 *C6 H61 1.4345 107.01 -118.66 112.81 1.1184 +IC O6 C5 *C6 H62 1.4345 113.18 -117.75 107.19 1.0553 +IC O5 C1 C2 C3 1.4104 116.58 57.36 109.28 1.5591 +IC C1 C2 C3 C4 1.5618 109.28 -53.96 106.60 1.5550 +IC C2 C3 C4 C5 1.5591 106.60 55.67 113.03 1.6431 +IC C3 C4 C5 O5 1.5550 113.03 -54.67 108.88 1.4584 +IC C4 C5 O5 C1 1.6431 108.88 52.47 113.48 1.4104 +IC C5 O5 C1 C2 1.4584 113.48 -57.26 116.58 1.5618 +IC C4 C5 C6 O6 1.6431 113.70 53.91 113.18 1.4345 +IC O5 C1 O1 HO1 1.4104 112.84 72.22 102.95 0.9977 +IC C1 C2 O2 HO2 1.5618 112.96 75.45 111.93 0.9813 +IC C2 C3 O3 HO3 1.5591 112.93 50.13 113.60 0.9452 +IC C3 C4 O4 HO4 1.5550 108.47 171.51 110.20 0.9652 +IC C5 C6 O6 HO6 1.5283 113.18 80.67 113.04 0.9869 +PATC FIRS NONE LAST NONE + +! hexopyranose analogs + +RESI AXYL 0.000 ! alpha-D-xylose (a-glucose w/o exocyclic moiety) og + ! +GROU ! +ATOM C1 CC3162 0.340 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! H52 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3263 0.020 ! H51-C5---O5 +ATOM H51 HCA2 0.090 ! H4 / \ H1 +ATOM H52 HCA2 0.090 ! \ / HO3 \ / +ATOM O5 OC3C61 -0.400 ! C4 | C1 +GROU ! / \ O3 H2 / \ +ATOM C2 CC3161 0.140 ! HO4-O4 \| | / O1-HO1 +ATOM H2 HCA1 0.090 ! C3---C2 +ATOM O2 OC311 -0.650 ! | | +ATOM HO2 HCP1 0.420 ! H3 O2-HO2 +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H51 C5 H52 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 -120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 -118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 110.99 -116.97 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 -123.77 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 107.51 119.38 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 119.03 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 107.94 -120.61 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -118.91 108.83 1.5171 +IC H52 O5 *C5 H51 1.0900 105.42 117.88 109.66 1.0926 +IC H52 C4 *C5 O5 1.0900 112.84 117.26 109.77 1.4384 +IC O5 C1 C2 C3 1.4059 111.32 53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 -54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 -58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 59.83 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 -57.30 111.32 1.5218 +IC O5 C1 O1 HO1 1.4059 113.00 67.18 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 -44.11 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 -51.80 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 47.58 105.89 0.9645 +PATC FIRS NONE LAST NONE + +RESI BXYL 0.000 ! beta-D-xylose (b-glucose w/o exocyclic moiety) og + ! +GROU ! +ATOM C1 CC3162 0.340 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! H52 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3263 0.020 ! H51-C5---O5 +ATOM H51 HCA2 0.090 ! H4 / \ O1-HO1 +ATOM H52 HCA2 0.090 ! \ / HO3 \ / +ATOM O5 OC3C61 -0.400 ! C4 | C1 +GROU ! / \ O3 H2 / \ +ATOM C2 CC3161 0.140 ! HO4-O4 \| | / H1 +ATOM H2 HCA1 0.090 ! C3---C2 +ATOM O2 OC311 -0.650 ! | | +ATOM HO2 HCP1 0.420 ! H3 O2-HO2 +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H51 C5 H52 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 110.99 -116.97 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 -123.77 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 107.51 119.38 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 119.03 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 107.94 -120.61 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -118.91 108.83 1.5171 +IC H52 O5 *C5 H51 1.0900 105.42 117.88 109.66 1.0926 +IC H52 C4 *C5 O5 1.0900 112.84 117.26 109.77 1.4384 +IC O5 C1 C2 C3 1.4059 111.32 53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 -54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 -58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 59.83 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 -57.30 111.32 1.5218 +IC O5 C1 O1 HO1 1.4059 113.00 67.18 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 -44.11 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 -51.80 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 47.58 105.89 0.9645 +PATC FIRS NONE LAST NONE + +RESI AFUC 0.000 ! alpha-L-fucose + ! +GROU ! +ATOM C1 CC3162 0.340 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! H5 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! C5---O5 +ATOM H5 HCA1 0.090 ! H4 /| \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / C6 HO2 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ H3 O2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! n.b.: H61, H62, and H63 are attached to C6 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 H63 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 110.99 116.97 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 123.77 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 108.29 -120.00 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 -120.00 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 108.82 -120.00 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -120.00 108.83 1.5171 +IC C6 O5 *C5 H5 1.5099 105.42 -117.88 109.66 1.0926 +IC C6 C4 *C5 O5 1.5099 112.84 -117.26 109.77 1.4384 +IC H63 H62 *C6 H61 1.0900 111.42 118.10 108.62 1.0873 +IC H63 C5 *C6 H62 1.0900 111.44 123.18 108.72 1.0943 +IC O5 C1 C2 C3 1.4059 111.32 -53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 -57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 -59.84 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 57.30 111.32 1.5218 +IC C4 C5 C6 H63 1.5171 112.84 -60.00 111.44 1.0900 +IC O5 C1 O1 HO1 1.4059 113.00 -60.00 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 60.00 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 60.00 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 60.00 105.89 0.9645 +PATC FIRS NONE LAST NONE + +RESI BFUC 0.000 ! beta-L-fucose + ! +GROU ! +ATOM C1 CC3162 0.340 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! H5 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! C5---O5 +ATOM H5 HCA1 0.090 ! H4 /| \ H1 +ATOM O5 OC3C61 -0.400 ! \ / C6 HO2 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ H3 O2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 H2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! n.b.: H61, H62, and H63 are attached to C6 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 H63 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 -120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 -118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 110.99 116.97 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 123.77 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 108.29 -120.00 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 -120.00 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 108.82 -120.00 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -120.00 108.83 1.5171 +IC C6 O5 *C5 H5 1.5099 105.42 -117.88 109.66 1.0926 +IC C6 C4 *C5 O5 1.5099 112.84 -117.26 109.77 1.4384 +IC H63 H62 *C6 H61 1.0900 111.42 118.10 108.62 1.0873 +IC H63 C5 *C6 H62 1.0900 111.44 123.18 108.72 1.0943 +IC O5 C1 C2 C3 1.4059 111.32 -53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 -57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 -59.84 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 57.30 111.32 1.5218 +IC C4 C5 C6 H63 1.5171 112.84 -60.00 111.44 1.0900 +IC O5 C1 O1 HO1 1.4059 113.00 -60.00 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 60.00 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 60.00 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 60.00 105.89 0.9645 +PATC FIRS NONE LAST NONE + + +RESI ARHM 0.000 ! alpha-L-rhamnose + ! +GROU ! +ATOM C1 CC3162 0.340 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! H5 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 /| \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / C6 \ / +GROU ! C4 C1 +ATOM C2 CC3161 0.140 ! / \ H3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! n.b.: H61, H62, and H63 are attached to C6 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 H63 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3944 113.12 113.32 113.54 1.0931 +IC O1 O5 *C1 C2 1.3944 105.17 121.89 109.59 1.4844 +IC O2 C3 *C2 H2 1.4612 106.71 -126.02 112.57 1.1816 +IC O2 C1 *C2 C3 1.4612 109.67 -117.56 110.83 1.4609 +IC O3 C4 *C3 H3 1.4249 115.14 -115.25 103.02 1.1148 +IC O3 C2 *C3 C4 1.4249 110.80 -128.44 109.99 1.5307 +IC O4 C5 *C4 H4 1.4184 113.92 119.20 107.62 1.0892 +IC O4 C3 *C4 C5 1.4184 109.75 125.32 108.89 1.5190 +IC C6 O5 *C5 H5 1.4678 111.82 -109.89 114.96 1.1578 +IC C6 C4 *C5 O5 1.4678 113.08 -124.54 108.34 1.3672 +IC H63 H62 *C6 H61 1.1174 112.38 -117.89 109.34 1.1241 +IC H63 C5 *C6 H62 1.1174 108.33 -126.36 114.61 1.1464 +IC O5 C1 C2 C3 1.4059 109.59 -55.45 110.83 1.4609 +IC C1 C2 C3 C4 1.4844 110.83 54.11 109.99 1.5307 +IC C2 C3 C4 C5 1.4609 109.99 -54.46 108.89 1.5190 +IC C3 C4 C5 O5 1.5307 108.89 56.69 108.34 1.3672 +IC C4 C5 O5 C1 1.5190 108.34 -62.43 115.13 1.4059 +IC C5 O5 C1 C2 1.3672 115.13 61.67 109.59 1.4844 +IC C4 C5 C6 H63 1.5190 113.08 52.76 108.33 1.1174 +IC O5 C1 O1 HO1 1.4059 105.17 -30.22 102.74 0.9773 +IC C1 C2 O2 HO2 1.4844 109.67 157.83 107.43 0.9550 +IC C2 C3 O3 HO3 1.4609 110.80 116.12 106.91 0.9395 +IC C3 C4 O4 HO4 1.5307 109.75 -60.70 104.02 0.9983 +PATC FIRS NONE LAST NONE + + +RESI BRHM 0.000 ! beta-L-rhamnose + ! +GROU ! +ATOM C1 CC3162 0.340 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! H5 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 /| \ H1 +ATOM O5 OC3C61 -0.400 ! \ / C6 \ / +GROU ! C4 C1 +ATOM C2 CC3161 0.140 ! / \ H3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! HO3-O3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! n.b.: H61, H62, and H63 are attached to C6 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 H63 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3714 115.44 -130.32 115.66 1.0650 +IC O1 O5 *C1 C2 1.3714 97.71 -119.30 105.93 1.5102 +IC O2 C3 *C2 H2 1.3856 108.96 -112.88 106.64 1.1412 +IC O2 C1 *C2 C3 1.3856 116.70 -120.64 104.85 1.4969 +IC O3 C4 *C3 H3 1.4067 117.08 -121.23 112.45 1.1256 +IC O3 C2 *C3 C4 1.4067 105.81 -126.39 108.46 1.5378 +IC O4 C5 *C4 H4 1.4328 108.73 117.09 110.37 1.0977 +IC O4 C3 *C4 C5 1.4328 110.49 118.94 108.23 1.5255 +IC C6 O5 *C5 H5 1.4958 114.03 -119.66 110.58 1.1663 +IC C6 C4 *C5 O5 1.4958 112.76 -124.39 104.52 1.4571 +IC H63 H62 *C6 H61 1.0742 103.31 -117.49 107.00 1.1261 +IC H63 C5 *C6 H62 1.0742 116.58 -112.26 102.92 1.1600 +IC O5 C1 C2 C3 1.3759 105.93 -67.20 104.85 1.4969 +IC C1 C2 C3 C4 1.5102 104.85 62.91 108.46 1.5378 +IC C2 C3 C4 C5 1.4969 108.46 -60.49 108.23 1.5255 +IC C3 C4 C5 O5 1.5378 108.23 57.27 104.52 1.4571 +IC C4 C5 O5 C1 1.5255 104.52 -66.65 112.86 1.3759 +IC C5 O5 C1 C2 1.4571 112.86 72.37 105.93 1.5102 +IC C4 C5 C6 H63 1.5255 112.76 44.47 116.58 1.0742 +IC O5 C1 O1 HO1 1.3759 97.71 -50.57 98.55 0.9672 +IC C1 C2 O2 HO2 1.5102 116.70 155.81 109.09 0.9625 +IC C2 C3 O3 HO3 1.4969 105.81 -154.73 110.78 0.9646 +IC C3 C4 O4 HO4 1.5378 110.49 -122.40 103.96 0.9808 +PATC FIRS NONE LAST NONE + + +RESI AGLCA -1.000 ! 4C1 alpha-D-glucoronic acid + ! +GROU ! +ATOM C1 CC3162 0.340 ! O61(-) +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! O62=C6 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC2O2 0.520 ! +ATOM O61 OC2D2 -0.760 ! +ATOM O62 OC2D2 -0.760 ! +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 O61 +BOND C6 O62 C5 O5 +IMPR C6 C5 O62 O61 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 -120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 -118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 110.99 -116.97 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 -123.77 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 107.51 119.38 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 119.03 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 107.94 -120.61 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -118.91 108.83 1.5171 +IC C6 O5 *C5 H5 1.5099 105.42 117.88 109.66 1.0926 +IC C6 C4 *C5 O5 1.5099 112.84 117.26 109.77 1.4384 +IC O61 C5 *C6 O62 1.4163 111.44 180.00 108.72 1.0943 +IC O5 C1 C2 C3 1.4059 111.32 53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 -54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 -58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 59.83 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 -57.30 111.32 1.5218 +IC C4 C5 C6 O61 1.5171 112.84 -120.00 111.44 1.4163 +IC O5 C1 O1 HO1 1.4059 113.00 67.18 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 -44.11 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 -51.80 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 47.58 105.89 0.9645 +PATC FIRS NONE LAST NONE + +RESI BGLCA -1.000 ! 4C1 beta-D-glucoronic acid + ! +GROU ! +ATOM C1 CC3162 0.340 ! O61(-) +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! O62=C6 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC2O2 0.520 ! +ATOM O61 OC2D2 -0.760 ! +ATOM O62 OC2D2 -0.760 ! +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 O61 +BOND C6 O62 C5 O5 +IMPR C6 C5 O62 O61 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 110.99 -116.97 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 -123.77 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 107.51 119.38 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 119.03 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 107.94 -120.61 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -118.91 108.83 1.5171 +IC C6 O5 *C5 H5 1.5099 105.42 120.00 109.66 1.0926 +IC C6 C4 *C5 O5 1.5099 112.84 120.00 109.77 1.4384 +IC O61 C5 *C6 O62 1.4163 111.44 180.00 108.72 1.0943 +IC O5 C1 C2 C3 1.4059 111.32 53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 -54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 -58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 59.83 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 -57.30 111.32 1.5218 +IC C4 C5 C6 O61 1.5171 112.84 -120.00 111.44 1.4163 +IC O5 C1 O1 HO1 1.4059 113.00 67.18 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 -44.11 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 -51.80 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 47.58 105.89 0.9645 +PATC FIRS NONE LAST NONE + +RESI BGLCA0 0.000 ! 4C1 beta-D-glucoronic acid + ! with alchemical 0 partial charges on COO group +GROU ! +ATOM C1 CC3162 0.340 ! O61(-) +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! O62=C6 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.140 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H3 O2-HO2 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC2O2 0.0 ! +ATOM O61 OC2D2 0.0 ! +ATOM O62 OC2D2 0.0 ! +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 O61 +BOND C6 O62 C5 O5 +IMPR C6 C5 O62 O61 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 110.99 -116.97 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 -123.77 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 107.51 119.38 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 119.03 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 107.94 -120.61 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -118.91 108.83 1.5171 +IC C6 O5 *C5 H5 1.5099 105.42 120.00 109.66 1.0926 +IC C6 C4 *C5 O5 1.5099 112.84 120.00 109.77 1.4384 +IC O61 C5 *C6 O62 1.4163 111.44 180.00 108.72 1.0943 +IC O5 C1 C2 C3 1.4059 111.32 53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 -54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 -58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 59.83 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 -57.30 111.32 1.5218 +IC C4 C5 C6 O61 1.5171 112.84 -120.00 111.44 1.4163 +IC O5 C1 O1 HO1 1.4059 113.00 67.18 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 -44.11 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 -51.80 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 47.58 105.89 0.9645 +PATC FIRS NONE LAST NONE + + +RESI AIDOA -1.000 ! alpha-L-iduronic acid + ! +GROU ! +ATOM C1 CC3162 0.340 ! H5 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! C5---O5 +ATOM HO1 HCP1 0.420 ! H4 /| \ O1-HO1 +ATOM C5 CC3163 0.110 ! \ / C6 HO3 \ / +ATOM H5 HCA1 0.090 ! C4 / C1 +ATOM O5 OC3C61 -0.400 ! / \ O3 H2 / \ +GROU ! HO4-O4 \| | / H1 +ATOM C2 CC3161 0.140 ! C3---C2 +ATOM H2 HCA1 0.090 ! | | +ATOM O2 OC311 -0.650 ! H3 O2-HO2 +ATOM HO2 HCP1 0.420 ! +GROU ! n.b.: O61 and O62 are attached to C6 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! | +ATOM O3 OC311 -0.650 ! O62=C6 +ATOM HO3 HCP1 0.420 ! | +GROU ! O61(-) +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC2O2 0.520 ! +ATOM O61 OC2D2 -0.760 ! +ATOM O62 OC2D2 -0.760 ! +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 O61 +BOND C6 O62 C5 O5 +IMPR C6 C5 O62 O61 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 108.02 -120.00 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 -120.00 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 108.29 120.00 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 120.00 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 108.82 -120.00 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -120.00 108.83 1.5171 +IC C6 O5 *C5 H5 1.5099 105.42 -117.88 109.66 1.0926 +IC C6 C4 *C5 O5 1.5099 112.84 -117.26 109.77 1.4384 +IC O61 C5 *C6 O62 1.4163 111.44 180.00 108.72 1.0943 +IC O5 C1 C2 C3 1.4059 111.32 -53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 -57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 -59.84 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 57.30 111.32 1.5218 +IC C4 C5 C6 O61 1.5171 112.84 120.00 111.44 1.4163 +IC O5 C1 O1 HO1 1.4059 113.00 -60.00 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 60.00 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 60.00 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 -60.00 105.89 0.9645 +PATC FIRS NONE LAST NONE + +RESI BIDOA -1.000 ! beta-L-iduronic acid + ! +GROU ! +ATOM C1 CC3162 0.340 ! H5 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! C5---O5 +ATOM HO1 HCP1 0.420 ! H4 /| \ H1 +ATOM C5 CC3163 0.110 ! \ / C6 HO3 \ / +ATOM H5 HCA1 0.090 ! C4 / C1 +ATOM O5 OC3C61 -0.400 ! / \ O3 H2 / \ +GROU ! HO4-O4 \| | / O1-HO1 +ATOM C2 CC3161 0.140 ! C3---C2 +ATOM H2 HCA1 0.090 ! | | +ATOM O2 OC311 -0.650 ! H3 O2-HO2 +ATOM HO2 HCP1 0.420 ! +GROU ! n.b.: O61 and O62 are attached to C6 +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! | +ATOM O3 OC311 -0.650 ! O62=C6 +ATOM HO3 HCP1 0.420 ! | +GROU ! O61(-) +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC2O2 0.520 ! +ATOM O61 OC2D2 -0.760 ! +ATOM O62 OC2D2 -0.760 ! +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 O61 +BOND C6 O62 C5 O5 +IMPR C6 C5 O62 O61 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 -120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 -118.92 111.32 1.5218 +IC O2 C3 *C2 H2 1.4190 108.02 -120.00 108.77 1.0892 +IC O2 C1 *C2 C3 1.4190 111.74 -120.00 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 108.29 120.00 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 120.00 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 108.82 -120.00 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -120.00 108.83 1.5171 +IC C6 O5 *C5 H5 1.5099 105.42 -117.88 109.66 1.0926 +IC C6 C4 *C5 O5 1.5099 112.84 -117.26 109.77 1.4384 +IC O61 C5 *C6 O62 1.4163 111.44 180.00 108.72 1.0943 +IC O5 C1 C2 C3 1.4059 111.32 -53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 -57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 -59.84 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 57.30 111.32 1.5218 +IC C4 C5 C6 O61 1.5171 112.84 120.00 111.44 1.4163 +IC O5 C1 O1 HO1 1.4059 113.00 -60.00 108.04 0.9634 +IC C1 C2 O2 HO2 1.5218 111.74 60.00 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 60.00 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 -60.00 105.89 0.9645 +PATC FIRS NONE LAST NONE + +RESI AGLCNA 0.000 ! 2-acetyl-2-deoxy-alpha-D-glucosamine + ! (alpha N-acetylglucosamine or GlcNAc) +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.070 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / O1-HO1 +ATOM N NC2D1 -0.470 ! C3---C2 +ATOM HN HCP1 0.310 ! | | +GROU ! H3 N-HN +ATOM C CC2O1 0.510 ! / +ATOM O OC2D1 -0.510 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.140 ! +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 N C +BOND C O C CT CT HT1 CT HT2 CT HT3 +IMPR C CT N O +IMPR N C C2 HN +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4115 105.82 -120.26 110.81 1.0905 +IC O1 O5 *C1 C2 1.4115 113.00 -118.92 111.32 1.5218 +IC N C3 *C2 H2 1.4190 110.99 -116.97 108.77 1.0892 +IC N C1 *C2 C3 1.4190 111.74 -123.77 110.04 1.5167 +IC O3 C4 *C3 H3 1.4198 107.51 119.38 108.28 1.0957 +IC O3 C2 *C3 C4 1.4198 111.19 119.03 110.08 1.5102 +IC O4 C5 *C4 H4 1.4163 107.94 -120.61 109.07 1.0972 +IC O4 C3 *C4 C5 1.4163 111.43 -118.91 108.83 1.5171 +IC C6 O5 *C5 H5 1.5099 105.42 117.88 109.66 1.0926 +IC C6 C4 *C5 O5 1.5099 112.84 117.26 109.77 1.4384 +IC O6 H62 *C6 H61 1.4163 111.41 -118.10 108.62 1.0873 +IC O6 C5 *C6 H62 1.4163 111.44 -123.18 108.72 1.0943 +IC O5 C1 C2 C3 1.4059 111.32 53.56 110.04 1.5167 +IC C1 C2 C3 C4 1.5218 110.04 -54.55 110.08 1.5102 +IC C2 C3 C4 C5 1.5167 110.08 57.15 108.83 1.5171 +IC C3 C4 C5 O5 1.5102 108.83 -58.25 109.77 1.4384 +IC C4 C5 O5 C1 1.5171 109.77 59.83 114.27 1.4059 +IC C5 O5 C1 C2 1.4384 114.27 -57.30 111.32 1.5218 +IC C4 C5 C6 O6 1.5171 112.84 -179.74 111.44 1.4163 +IC O5 C1 O1 HO1 1.4059 113.00 67.18 108.04 0.9634 +IC C1 C2 N HN 1.5218 111.74 -44.11 105.37 0.9665 +IC C2 C3 O3 HO3 1.5167 111.19 -51.80 106.26 0.9641 +IC C3 C4 O4 HO4 1.5102 111.43 47.58 105.89 0.9645 +IC C5 C6 O6 HO6 1.5099 111.44 -54.79 105.51 0.9630 +IC C N C2 C3 1.0000 120.00 -60.00 120.00 1.0000 +IC C C2 *N HN 1.0000 120.00 180.00 120.00 1.0000 +IC CT C N C2 1.0000 120.00 180.00 120.00 1.0000 +IC N CT *C O 1.0000 120.00 180.00 120.00 1.0000 +IC O C CT HT1 1.0000 120.00 180.00 120.00 1.0000 +IC O C CT HT2 1.0000 120.00 60.00 120.00 1.0000 +IC O C CT HT3 1.0000 120.00 -60.00 120.00 1.0000 +PATC FIRS NONE LAST NONE + +RESI BGLCNA 0.000 ! 2-acetyl-2-deoxy-beta-D-glucosamine + ! (beta N-acetylglucosamine or GlcNAc) +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.070 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM N NC2D1 -0.470 ! C3---C2 +ATOM HN HCP1 0.310 ! | | +GROU ! H3 N-HN +ATOM C CC2O1 0.510 ! / +ATOM O OC2D1 -0.510 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.140 ! +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 N C +BOND C O C CT CT HT1 CT HT2 CT HT3 +IMPR C CT N O +IMPR N C C2 HN +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3949 109.50 118.29 110.11 1.1152 +IC O1 O5 *C1 C2 1.3949 110.13 120.34 109.32 1.5156 +IC N C3 *C2 H2 1.4607 113.70 -119.19 107.08 1.1227 +IC N C1 *C2 C3 1.4607 112.62 -127.32 109.20 1.5149 +IC O3 C4 *C3 H3 1.4246 110.45 117.60 108.58 1.1171 +IC O3 C2 *C3 C4 1.4246 111.13 123.24 110.86 1.5168 +IC O4 C5 *C4 H4 1.4204 110.47 -117.94 108.07 1.1172 +IC O4 C3 *C4 C5 1.4204 110.88 -123.03 110.79 1.5206 +IC C6 O5 *C5 H5 1.5134 108.06 117.57 109.86 1.1171 +IC C6 C4 *C5 O5 1.5134 113.35 119.99 108.45 1.4386 +IC O6 H62 *C6 H61 1.4280 109.26 -117.58 107.87 1.1141 +IC O6 C5 *C6 H62 1.4280 111.18 -121.26 110.14 1.1132 +IC O5 C1 C2 C3 1.4220 109.32 58.90 109.20 1.5149 +IC C1 C2 C3 C4 1.5156 109.20 -52.68 110.86 1.5168 +IC C2 C3 C4 C5 1.5149 110.86 52.13 110.79 1.5206 +IC C3 C4 C5 O5 1.5168 110.79 -56.10 108.45 1.4386 +IC C4 C5 O5 C1 1.5206 108.45 64.09 111.47 1.4220 +IC C5 O5 C1 C2 1.4386 111.47 -66.18 109.32 1.5156 +IC C4 C5 C6 O6 1.5206 113.35 -179.21 111.18 1.4280 +IC O5 C1 O1 HO1 1.4220 110.13 53.79 107.03 0.9601 +IC C1 C2 N HN 1.5156 112.62 -21.73 117.18 0.9940 +IC C2 C3 O3 HO3 1.5149 111.13 0.20 109.43 0.9762 +IC C3 C4 O4 HO4 1.5168 110.88 45.93 106.90 0.9672 +IC C5 C6 O6 HO6 1.5134 111.18 -58.35 108.74 0.9641 +IC C N C2 C3 1.3365 123.04 -84.98 113.70 1.5149 +IC C C2 *N HN 1.3365 123.04 -171.85 117.18 0.9940 +IC CT C N C2 1.4798 117.02 -173.18 123.04 1.4607 +IC N CT *C O 1.3365 117.02 178.97 121.63 1.2235 +IC O C CT HT1 1.2235 121.63 116.39 110.28 1.1105 +IC O C CT HT2 1.2235 121.63 -3.06 109.29 1.1121 +IC O C CT HT3 1.2235 121.63 -122.59 110.33 1.1105 +PATC FIRS NONE LAST NONE + +RESI BGLCN0 0.000 ! 2-acetyl-2-deoxy-beta-D-glucosamine + ! (beta N-acetylglucosamine or GlcNAc) + ! with alchemical 0 partial charges on CONH +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 -0.090 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 +ATOM N NC2D1 0.0 ! C3---C2 +ATOM HN HCP1 0.0 ! | | +GROU ! H3 N-HN +ATOM C CC2O1 0.0 ! / +ATOM O OC2D1 0.0 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.140 ! +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 N C +BOND C O C CT CT HT1 CT HT2 CT HT3 +IMPR C CT N O +IMPR N C C2 HN +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3949 109.50 118.29 110.11 1.1152 +IC O1 O5 *C1 C2 1.3949 110.13 120.34 109.32 1.5156 +IC N C3 *C2 H2 1.4607 113.70 -119.19 107.08 1.1227 +IC N C1 *C2 C3 1.4607 112.62 -127.32 109.20 1.5149 +IC O3 C4 *C3 H3 1.4246 110.45 117.60 108.58 1.1171 +IC O3 C2 *C3 C4 1.4246 111.13 123.24 110.86 1.5168 +IC O4 C5 *C4 H4 1.4204 110.47 -117.94 108.07 1.1172 +IC O4 C3 *C4 C5 1.4204 110.88 -123.03 110.79 1.5206 +IC C6 O5 *C5 H5 1.5134 108.06 117.57 109.86 1.1171 +IC C6 C4 *C5 O5 1.5134 113.35 119.99 108.45 1.4386 +IC O6 H62 *C6 H61 1.4280 109.26 -117.58 107.87 1.1141 +IC O6 C5 *C6 H62 1.4280 111.18 -121.26 110.14 1.1132 +IC O5 C1 C2 C3 1.4220 109.32 58.90 109.20 1.5149 +IC C1 C2 C3 C4 1.5156 109.20 -52.68 110.86 1.5168 +IC C2 C3 C4 C5 1.5149 110.86 52.13 110.79 1.5206 +IC C3 C4 C5 O5 1.5168 110.79 -56.10 108.45 1.4386 +IC C4 C5 O5 C1 1.5206 108.45 64.09 111.47 1.4220 +IC C5 O5 C1 C2 1.4386 111.47 -66.18 109.32 1.5156 +IC C4 C5 C6 O6 1.5206 113.35 -179.21 111.18 1.4280 +IC O5 C1 O1 HO1 1.4220 110.13 53.79 107.03 0.9601 +IC C1 C2 N HN 1.5156 112.62 -21.73 117.18 0.9940 +IC C2 C3 O3 HO3 1.5149 111.13 0.20 109.43 0.9762 +IC C3 C4 O4 HO4 1.5168 110.88 45.93 106.90 0.9672 +IC C5 C6 O6 HO6 1.5134 111.18 -58.35 108.74 0.9641 +IC C N C2 C3 1.3365 123.04 -84.98 113.70 1.5149 +IC C C2 *N HN 1.3365 123.04 -171.85 117.18 0.9940 +IC CT C N C2 1.4798 117.02 -173.18 123.04 1.4607 +IC N CT *C O 1.3365 117.02 178.97 121.63 1.2235 +IC O C CT HT1 1.2235 121.63 116.39 110.28 1.1105 +IC O C CT HT2 1.2235 121.63 -3.06 109.29 1.1121 +IC O C CT HT3 1.2235 121.63 -122.59 110.33 1.1105 +PATC FIRS NONE LAST NONE + +RESI AGALNA 0.000 ! 2-acetyl-2-deoxy-alpha-D-galactosamine + ! (alpha N-acetylgalactosamine or GalNAc) +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.070 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / O1-HO1 +ATOM N NC2D1 -0.470 ! C3---C2 +ATOM HN HCP1 0.310 ! | | +GROU ! H3 N-HN +ATOM C CC2O1 0.510 ! / +ATOM O OC2D1 -0.510 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.140 ! +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 N C +BOND C O C CT CT HT1 CT HT2 CT HT3 +IMPR C CT N O +IMPR N C C2 HN +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4006 109.41 -118.16 109.00 1.1146 +IC O1 O5 *C1 C2 1.4006 112.45 -122.23 110.03 1.5235 +IC N C3 *C2 H2 1.4542 111.59 -115.73 107.43 1.1188 +IC N C1 *C2 C3 1.4542 115.05 -126.93 109.87 1.5127 +IC O3 C4 *C3 H3 1.4221 111.39 117.56 108.59 1.1168 +IC O3 C2 *C3 C4 1.4221 110.78 124.12 110.75 1.5146 +IC O4 C5 *C4 H4 1.4265 110.79 117.97 108.77 1.1167 +IC O4 C3 *C4 C5 1.4265 111.93 123.14 109.33 1.5203 +IC C6 O5 *C5 H5 1.5146 108.49 117.15 110.05 1.1177 +IC C6 C4 *C5 O5 1.5146 113.21 121.21 109.51 1.4431 +IC O6 H62 *C6 H61 1.4272 109.21 -117.35 107.74 1.1138 +IC O6 C5 *C6 H62 1.4272 111.21 -121.61 110.72 1.1131 +IC O5 C1 C2 C3 1.4328 110.03 55.96 109.87 1.5127 +IC C1 C2 C3 C4 1.5235 109.87 -54.38 110.75 1.5146 +IC C2 C3 C4 C5 1.5127 110.75 55.35 109.33 1.5203 +IC C3 C4 C5 O5 1.5146 109.33 -57.71 109.51 1.4431 +IC C4 C5 O5 C1 1.5203 109.51 61.91 112.69 1.4328 +IC C5 O5 C1 C2 1.4431 112.69 -60.89 110.03 1.5235 +IC C4 C5 C6 O6 1.5203 113.21 -172.44 111.21 1.4272 +IC O5 C1 O1 HO1 1.4328 112.45 72.07 107.32 0.9601 +IC C1 C2 N HN 1.5235 115.05 -118.24 115.62 0.9937 +IC C2 C3 O3 HO3 1.5127 110.78 86.08 107.29 0.9662 +IC C3 C4 O4 HO4 1.5146 111.93 81.54 108.79 0.9647 +IC C5 C6 O6 HO6 1.5146 111.21 -63.87 109.07 0.9637 +IC C N C2 C3 1.3354 123.56 -169.15 111.59 1.5127 +IC C C2 *N HN 1.3354 123.56 176.96 115.62 0.9937 +IC CT C N C2 1.4804 116.54 179.29 123.56 1.4542 +IC N CT *C O 1.3354 116.54 179.78 121.19 1.2233 +IC O C CT HT1 1.2233 121.19 119.84 110.19 1.1104 +IC O C CT HT2 1.2233 121.19 0.28 109.29 1.1117 +IC O C CT HT3 1.2233 121.19 -119.29 110.17 1.1104 +PATC FIRS NONE LAST NONE + +RESI BGALNA 0.000 ! 2-acetyl-2-deoxy-beta-D-galactosamine + ! (beta N-acetylgalactosamine or GalNAc) +GROU ! +ATOM C1 CC3162 0.340 ! O6-HO6 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / +GROU ! C4 | C1 +ATOM C2 CC3161 0.070 ! / \ O3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / H1 +ATOM N NC2D1 -0.470 ! C3---C2 +ATOM HN HCP1 0.310 ! | | +GROU ! H3 N-HN +ATOM C CC2O1 0.510 ! / +ATOM O OC2D1 -0.510 ! O=C HT1 +GROU ! \ / +ATOM CT CC331 -0.270 ! HT2-CT +ATOM HT1 HCA3 0.090 ! \ +ATOM HT2 HCA3 0.090 ! HT3 +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC3161 0.140 ! +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC321 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 N N HN C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 N C +BOND C O C CT CT HT1 CT HT2 CT HT3 +IMPR C CT N O +IMPR N C C2 HN +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.4006 109.41 118.16 109.00 1.1146 +IC O1 O5 *C1 C2 1.4006 112.45 122.23 110.03 1.5235 +IC N C3 *C2 H2 1.4542 111.59 -115.73 107.43 1.1188 +IC N C1 *C2 C3 1.4542 115.05 -126.93 109.87 1.5127 +IC O3 C4 *C3 H3 1.4221 111.39 117.56 108.59 1.1168 +IC O3 C2 *C3 C4 1.4221 110.78 124.12 110.75 1.5146 +IC O4 C5 *C4 H4 1.4265 110.79 117.97 108.77 1.1167 +IC O4 C3 *C4 C5 1.4265 111.93 123.14 109.33 1.5203 +IC C6 O5 *C5 H5 1.5146 108.49 117.15 110.05 1.1177 +IC C6 C4 *C5 O5 1.5146 113.21 121.21 109.51 1.4431 +IC O6 H62 *C6 H61 1.4272 109.21 -117.35 107.74 1.1138 +IC O6 C5 *C6 H62 1.4272 111.21 -121.61 110.72 1.1131 +IC O5 C1 C2 C3 1.4328 110.03 55.96 109.87 1.5127 +IC C1 C2 C3 C4 1.5235 109.87 -54.38 110.75 1.5146 +IC C2 C3 C4 C5 1.5127 110.75 55.35 109.33 1.5203 +IC C3 C4 C5 O5 1.5146 109.33 -57.71 109.51 1.4431 +IC C4 C5 O5 C1 1.5203 109.51 61.91 112.69 1.4328 +IC C5 O5 C1 C2 1.4431 112.69 -60.89 110.03 1.5235 +IC C4 C5 C6 O6 1.5203 113.21 -172.44 111.21 1.4272 +IC O5 C1 O1 HO1 1.4328 112.45 125.25 107.32 0.9601 +IC C1 C2 N HN 1.5235 115.05 -118.24 115.62 0.9937 +IC C2 C3 O3 HO3 1.5127 110.78 86.08 107.29 0.9662 +IC C3 C4 O4 HO4 1.5146 111.93 81.54 108.79 0.9647 +IC C5 C6 O6 HO6 1.5146 111.21 -63.87 109.07 0.9637 +IC C N C2 C3 1.3354 123.56 -169.15 111.59 1.5127 +IC C C2 *N HN 1.3354 123.56 176.96 115.62 0.9937 +IC CT C N C2 1.4804 116.54 179.29 123.56 1.4542 +IC N CT *C O 1.3354 116.54 179.78 121.19 1.2233 +IC O C CT HT1 1.2233 121.19 119.84 110.19 1.1104 +IC O C CT HT2 1.2233 121.19 0.28 109.29 1.1117 +IC O C CT HT3 1.2233 121.19 -119.29 110.17 1.1104 +PATC FIRS NONE LAST NONE + +RESI ANE5AC -1.000 ! alpha-Neu5Ac (N-acetyl-alpha-D-neuraminic acid) +GROU ! +ATOM C1 CC2O2 0.300 ! +ATOM O11 OC2D2 -0.600 ! +ATOM O12 OC2D2 -0.600 ! +ATOM C2 CC3062 0.330 ! +ATOM O2 OC311 -0.650 ! H6 +ATOM HO2 HCP1 0.420 ! HT2 HT1 HN | O12 (-) +ATOM C6 CC3163 0.110 ! \ | | C6---O6 | +ATOM H6 HCA1 0.090 ! HT3- CT N /| \ C1=O11 +ATOM O6 OC3C61 -0.400 ! \ / \ / R \ / +GROU ! C C5 C2 +ATOM C3 CC3261 -0.180 ! // / \ H4 H31/ \ +ATOM H31 HCA2 0.090 ! O H5 \| | / O2-HO2 +ATOM H32 HCA2 0.090 ! C4---C3 +GROU ! | | +ATOM C4 CC3161 0.140 ! HO4-O4 H32 +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! | +ATOM HO4 HCP1 0.420 ! R = H7-C7-O7-HO7 (Fischer projection) +GROU ! | +ATOM C5 CC3161 0.070 ! H8-C8-O8-HO8 +ATOM H5 HCA1 0.090 ! | +ATOM N NC2D1 -0.470 ! H91-C9-O9-HO9 +ATOM HN HCP1 0.310 ! | +GROU ! H92 +ATOM C CC2O1 0.510 ! +ATOM O OC2D1 -0.510 ! +GROU ! +ATOM CT CC331 -0.270 ! +ATOM HT1 HCA3 0.090 ! +ATOM HT2 HCA3 0.090 ! +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C7 CC312 0.14 ! +ATOM H7 HCA1 0.09 ! +ATOM O7 OC311 -0.65 ! +ATOM HO7 HCP1 0.42 ! +GROU ! +ATOM C8 CC312 0.14 ! +ATOM H8 HCA1 0.09 ! +ATOM O8 OC311 -0.65 ! +ATOM HO8 HCP1 0.42 ! +GROU ! +ATOM C9 CC322 0.05 ! +ATOM H91 HCA2 0.09 ! +ATOM H92 HCA2 0.09 ! +ATOM O9 OC311 -0.65 ! +ATOM HO9 HCP1 0.42 ! +! +BOND C1 O11 C1 O12 +BOND C2 O2 C2 C1 O2 HO2 C2 O6 C2 C3 +BOND C3 H31 C3 H32 C3 C4 C4 H4 +BOND C4 O4 O4 HO4 C4 C5 C5 H5 C5 N +BOND N HN N C C O +BOND C CT CT HT1 CT HT2 CT HT3 +BOND C5 C6 C6 H6 C6 C7 C7 O7 +BOND C7 H7 C6 O6 O7 HO7 +BOND C7 C8 C8 H8 C8 O8 O8 HO8 +BOND C8 C9 C9 H91 C9 H92 C9 O9 O9 HO9 +IMPR C CT N O +IMPR N C C5 HN +IMPR C1 C2 O12 O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C3 C2 C1 O11 1.5332 115.08 127.85 118.90 1.2820 +IC O11 C2 *C1 O12 1.2820 118.90 -169.86 118.69 1.2783 +IC C1 O6 *C2 O2 1.5873 111.40 -119.25 95.89 1.4562 +IC C1 C3 *C2 O6 1.5873 115.08 -128.11 111.50 1.3586 +IC O2 C3 *C2 C1 1.4562 106.83 -128.34 115.08 1.5873 +IC O2 O6 *C2 C3 1.4562 95.89 -110.70 111.50 1.5332 +IC H32 C4 *C3 H31 1.1226 116.01 -129.75 106.47 1.1243 +IC H32 C2 *C3 C4 1.1226 100.88 -123.87 111.72 1.4993 +IC O4 C5 *C4 H4 1.4174 113.48 -116.68 104.84 1.1566 +IC O4 C3 *C4 C5 1.4174 108.73 -124.65 109.75 1.5196 +IC N C6 *C5 H5 1.4631 118.23 117.11 99.10 1.1160 +IC N C4 *C5 C6 1.4631 109.06 135.62 115.11 1.5738 +IC C7 O6 *C6 H6 1.5481 106.77 -114.68 102.14 1.1151 +IC C7 C5 *C6 O6 1.5481 115.83 -118.93 107.06 1.4656 +IC O7 C6 *C7 H7 1.4154 107.73 111.23 109.47 1.0540 +IC O6 C2 C3 C4 1.3586 111.50 -55.13 111.72 1.4993 +IC C2 C3 C4 C5 1.5332 111.72 51.36 109.75 1.5196 +IC C3 C4 C5 C6 1.4993 109.75 -49.56 115.11 1.5738 +IC C4 C5 C6 O6 1.5196 115.11 46.38 107.06 1.4656 +IC C5 C6 O6 C2 1.5738 107.06 -51.86 119.33 1.3586 +IC C6 O6 C2 C3 1.4656 119.33 57.53 111.50 1.5332 +IC C5 C6 C7 O7 1.5738 115.83 -165.72 107.73 1.4154 +IC O6 C2 O2 HO2 1.3586 95.89 117.77 102.20 1.0031 +IC C3 C4 O4 HO4 1.4993 108.73 -23.17 106.80 0.9484 +IC C4 C5 N HN 1.5196 109.06 -64.34 114.94 1.0352 +IC C6 C7 O7 HO7 1.5481 107.73 11.90 109.66 0.9682 +IC C5 C6 C7 C8 1.5738 115.83 71.52 121.29 1.5518 +IC C6 C7 C8 C9 1.5481 121.29 162.62 114.25 1.5144 +IC O8 C9 *C8 C7 1.4615 103.93 122.46 114.25 1.5518 +IC O8 C8 C9 O9 1.4615 103.93 66.22 110.46 1.4595 +IC O8 C9 *C8 H8 1.4615 103.93 -118.33 109.54 1.1365 +IC C9 C8 O8 HO8 1.5144 103.93 -121.82 108.98 0.9926 +IC O9 C8 *C9 H91 1.4595 110.46 120.73 111.11 1.0852 +IC O9 C8 *C9 H92 1.4595 110.46 -116.97 113.31 1.0924 +IC C8 C9 O9 HO9 1.5144 110.46 -46.25 102.96 0.9306 +IC C N C5 C6 1.3423 128.82 -42.25 118.23 1.5738 +IC C C5 *N HN 1.3423 128.82 -156.13 114.94 1.0352 +IC CT C N C5 1.5224 116.69 -175.16 128.82 1.4631 +IC N CT *C O 1.3423 116.69 171.36 120.91 1.2175 +IC O C CT HT1 1.2175 120.91 -94.56 112.22 1.1162 +IC O C CT HT2 1.2175 120.91 153.01 105.52 1.0865 +IC O C CT HT3 1.2175 120.91 26.75 116.77 1.0960 +PATC FIRS NONE LAST NONE + +RESI BNE5AC -1.000 ! beta-Neu5Ac (N-acetyl-alpha-D-neuraminic acid) +GROU ! +ATOM C1 CC2O2 0.300 ! +ATOM O11 OC2D2 -0.600 ! +ATOM O12 OC2D2 -0.600 ! +ATOM C2 CC3062 0.330 ! +ATOM O2 OC311 -0.650 ! H6 +ATOM HO2 HCP1 0.420 ! HT2 HT1 HN | +ATOM C6 CC3163 0.110 ! \ | | C6---O6 +ATOM H6 HCA1 0.090 ! HT3- CT N /| \ O2-HO2 +ATOM O6 OC3C61 -0.400 ! \ / \ / R \ / +GROU ! C C5 C2 +ATOM C3 CC3261 -0.180 ! // / \ H4 H31/ \ +ATOM H31 HCA2 0.090 ! O H5 \| | / C1=O11 +ATOM H32 HCA2 0.090 ! C4---C3 | +GROU ! | | O12 (-) +ATOM C4 CC3161 0.140 ! HO4-O4 H32 +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! | +ATOM HO4 HCP1 0.420 ! R = H7-C7-O7-HO7 (Fischer projection) +GROU ! | +ATOM C5 CC3161 0.070 ! H8-C8-O8-HO8 +ATOM H5 HCA1 0.090 ! | +ATOM N NC2D1 -0.470 ! H91-C9-O9-HO9 +ATOM HN HCP1 0.310 ! | +GROU ! H92 +ATOM C CC2O1 0.510 ! +ATOM O OC2D1 -0.510 ! +GROU ! +ATOM CT CC331 -0.270 ! +ATOM HT1 HCA3 0.090 ! +ATOM HT2 HCA3 0.090 ! +ATOM HT3 HCA3 0.090 ! +GROU ! +ATOM C7 CC312 0.14 ! +ATOM H7 HCA1 0.09 ! +ATOM O7 OC311 -0.65 ! +ATOM HO7 HCP1 0.42 ! +GROU ! +ATOM C8 CC312 0.14 ! +ATOM H8 HCA1 0.09 ! +ATOM O8 OC311 -0.65 ! +ATOM HO8 HCP1 0.42 ! +GROU ! +ATOM C9 CC322 0.05 ! +ATOM H91 HCA2 0.09 ! +ATOM H92 HCA2 0.09 ! +ATOM O9 OC311 -0.65 ! +ATOM HO9 HCP1 0.42 ! +! +BOND C1 O11 C1 O12 +BOND C2 O2 C2 C1 O2 HO2 C2 O6 C2 C3 +BOND C3 H31 C3 H32 C3 C4 C4 H4 +BOND C4 O4 O4 HO4 C4 C5 C5 H5 C5 N +BOND N HN N C C O +BOND C CT CT HT1 CT HT2 CT HT3 +BOND C5 C6 C6 H6 C6 C7 C7 O7 +BOND C7 H7 C6 O6 O7 HO7 +BOND C7 C8 C8 H8 C8 O8 O8 HO8 +BOND C8 C9 C9 H91 C9 H92 C9 O9 O9 HO9 +IMPR C CT N O +IMPR N C C5 HN +IMPR C1 C2 O12 O11 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C3 C2 C1 O11 1.5619 111.05 72.33 119.02 1.2616 +IC O11 C2 *C1 O12 1.2616 119.02 -169.14 121.11 1.2984 +IC C1 O6 *C2 O2 1.5186 109.23 124.03 109.17 1.4161 +IC C1 C3 *C2 O6 1.5186 111.05 118.74 106.37 1.4582 +IC O2 C3 *C2 C1 1.4161 107.78 124.29 111.05 1.5186 +IC O2 O6 *C2 C3 1.4161 109.17 116.04 106.37 1.5619 +IC H32 C4 *C3 H31 1.1518 105.79 -113.53 113.61 1.0664 +IC H32 C2 *C3 C4 1.1518 107.90 -115.20 110.46 1.5015 +IC O4 C5 *C4 H4 1.4388 112.26 -110.36 104.46 1.0747 +IC O4 C3 *C4 C5 1.4388 108.53 -127.63 116.23 1.5290 +IC N C6 *C5 H5 1.4945 116.86 114.37 105.31 1.1203 +IC N C4 *C5 C6 1.4945 114.54 134.26 110.25 1.5662 +IC C7 O6 *C6 H6 1.5469 98.17 -114.48 110.29 1.1144 +IC C7 C5 *C6 O6 1.5469 117.84 -112.88 112.18 1.4591 +IC O7 C6 *C7 H7 1.4547 112.17 115.43 107.29 1.0967 +IC O6 C2 C3 C4 1.4582 106.37 -56.29 110.46 1.5015 +IC C2 C3 C4 C5 1.5619 110.46 54.01 116.23 1.5290 +IC C3 C4 C5 C6 1.5015 116.23 -45.40 110.25 1.5662 +IC C4 C5 C6 O6 1.5290 110.25 41.71 112.18 1.4591 +IC C5 C6 O6 C2 1.5662 112.18 -53.68 118.46 1.4582 +IC C6 O6 C2 C3 1.4591 118.46 59.57 106.37 1.5619 +IC C5 C6 C7 O7 1.5662 117.84 -171.22 112.17 1.4547 +IC O6 C2 O2 HO2 1.4582 109.17 -127.77 93.37 0.9583 +IC C3 C4 O4 HO4 1.5015 108.53 -15.40 104.02 0.9570 +IC C4 C5 N HN 1.5290 114.54 -82.41 108.18 1.0666 +IC C6 C7 O7 HO7 1.5469 112.17 40.70 107.40 0.9933 +IC C5 C6 C7 C8 1.5662 117.84 64.38 112.77 1.5048 +IC C6 C7 C8 C9 1.5469 112.77 158.80 112.05 1.5476 +IC O8 C9 *C8 C7 1.4013 101.88 119.12 112.05 1.5048 +IC O8 C8 C9 O9 1.4013 101.88 51.37 111.96 1.4627 +IC O8 C9 *C8 H8 1.4013 101.88 -116.00 110.59 1.1012 +IC C9 C8 O8 HO8 1.5476 101.88 -15.62 104.31 0.9826 +IC O9 C8 *C9 H91 1.4627 111.96 118.36 111.56 1.0985 +IC O9 C8 *C9 H92 1.4627 111.96 -119.14 103.21 1.1787 +IC C8 C9 O9 HO9 1.5476 111.96 169.63 111.06 0.9538 +IC C N C5 C6 1.3624 132.88 -43.95 116.86 1.5662 +IC C C5 *N HN 1.3624 132.88 -169.59 108.18 1.0666 +IC CT C N C5 1.4906 115.06 -173.29 132.88 1.4945 +IC N CT *C O 1.3624 115.06 -172.59 119.81 1.2308 +IC O C CT HT1 1.2308 119.81 -48.65 108.61 1.1307 +IC O C CT HT2 1.2308 119.81 -175.64 103.95 1.0804 +IC O C CT HT3 1.2308 119.81 70.35 108.08 1.1250 +PATC FIRS NONE LAST NONE + +RESI ABEQ 0.000 ! abequose, 3,6-didexoxy-alpha-D-xylo-hexose + ! adapted from AGAL + ! +GROU ! +ATOM C1 CC3162 0.340 ! H63 +ATOM H1 HCA1 0.090 ! | +ATOM O1 OC311 -0.650 ! H61-C6-H62 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! H5-C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 / \ H1 +ATOM O5 OC3C61 -0.400 ! \ / \ / +GROU ! C4 C1 +ATOM C2 CC3161 0.140 ! / \H32 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / O1-HO1 +ATOM O2 OC311 -0.650 ! C3---C2 +ATOM HO2 HCP1 0.420 ! | | +GROU ! H31 O2-HO2 +ATOM C3 CC3261 -0.180 ! +ATOM H31 HCA2 0.090 ! +ATOM H32 HCA2 0.090 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H31 +BOND C3 H32 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 H63 C5 O5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3865 108.93 -123.99 104.38 1.1081 +IC O1 O5 *C1 C2 1.3865 108.96 -118.67 108.85 1.5226 +IC O2 C3 *C2 H2 1.4411 111.34 -110.11 102.47 1.1187 +IC O2 C1 *C2 C3 1.4411 115.23 -135.16 118.19 1.4969 +IC H32 C4 *C3 H31 1.4266 109.02 118.09 104.61 1.1300 +IC H32 C2 *C3 C4 1.4266 116.32 123.96 109.32 1.5156 +IC O4 C5 *C4 H4 1.4233 107.75 119.05 111.86 1.0818 +IC O4 C3 *C4 C5 1.4233 111.62 121.16 112.36 1.4931 +IC C6 O5 *C5 H5 1.5325 113.82 109.66 108.87 1.1501 +IC C6 C4 *C5 O5 1.5325 115.44 135.15 114.56 1.4252 +IC H63 H62 *C6 H61 1.4421 111.00 -121.63 104.24 1.1078 +IC H63 C5 *C6 H62 1.4421 112.98 -123.79 108.85 1.1420 +IC O5 C1 C2 C3 1.4134 108.85 48.90 118.19 1.4969 +IC C1 C2 C3 C4 1.5226 118.19 -46.22 109.32 1.5156 +IC C2 C3 C4 C5 1.4969 109.32 44.65 112.36 1.4931 +IC C3 C4 C5 O5 1.5156 112.36 -50.65 114.56 1.4252 +IC C4 C5 O5 C1 1.4931 114.56 55.65 115.64 1.4134 +IC C5 O5 C1 C2 1.4252 115.64 -51.39 108.85 1.5226 +IC C4 C5 C6 H63 1.4931 115.44 65.25 112.98 1.4421 +IC O5 C1 O1 HO1 1.4134 108.96 63.08 109.87 0.9758 +IC C1 C2 O2 HO2 1.5226 115.23 -42.41 115.36 0.9113 +IC C3 C4 O4 HO4 1.5156 111.62 -23.31 104.57 0.9949 +PATC FIRS NONE LAST NONE + +RESI ARHMOA 0.000 ! 2-O-Acetyl-alpha-L-rhamnose (alpha-6-Deoxy-L-mannose) + ! Can be created from rhamnose and pres or2ac +GROU ! +ATOM C1 CC3162 0.340 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! H5 +ATOM HO1 HCP1 0.420 ! | +ATOM C5 CC3163 0.110 ! C5---O5 +ATOM H5 HCA1 0.090 ! HO4-O4 /| \ O1-HO1 +ATOM O5 OC3C61 -0.400 ! \ / C6 \ / +GROU ! C4 C1 +ATOM C2 CC3161 0.170 ! / \ H3 H2 / \ +ATOM H2 HCA1 0.090 ! H4 \| | / H1 +ATOM O2 OC301 -0.490 ! C3---C2 +ATOM CA2 CC2O5 0.900 ! | | +ATOM OA2 OC2D1 -0.630 ! H31 O2 +ATOM CB2 CC331 -0.310 ! | +ATOM HB1 HCA3 0.090 ! CA2=OA2 +ATOM HB2 HCA3 0.090 ! | +ATOM HB3 HCA3 0.090 ! HB2-CB2-HB1 +GROU ! | +ATOM C3 CC3161 0.140 ! HB3 +ATOM H3 HCA1 0.090 ! n.b.: H61, H62, and H63 are attached to C6 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC331 -0.270 +ATOM H61 HCA3 0.090 +ATOM H62 HCA3 0.090 +ATOM H63 HCA3 0.090 +! +BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 +BOND C2 H2 C2 O2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 H63 C5 O5 +BOND O2 CA2 CA2 OA2 CA2 CB2 CB2 HB1 CB2 HB2 +BOND CB2 HB3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C2 *C1 H1 1.3944 113.12 113.32 113.54 1.0931 +IC O1 O5 *C1 C2 1.3944 105.17 121.89 109.59 1.4844 +IC O2 C3 *C2 H2 1.4612 106.71 -126.02 112.57 1.1816 +IC O2 C1 *C2 C3 1.4612 109.67 -117.56 110.83 1.4609 +IC O3 C4 *C3 H3 1.4249 115.14 -115.25 103.02 1.1148 +IC O3 C2 *C3 C4 1.4249 110.80 -128.44 109.99 1.5307 +IC O4 C5 *C4 H4 1.4184 113.92 119.20 107.62 1.0892 +IC O4 C3 *C4 C5 1.4184 109.75 125.32 108.89 1.5190 +IC C6 O5 *C5 H5 1.4678 111.82 -109.89 114.96 1.1578 +IC C6 C4 *C5 O5 1.4678 113.08 -124.54 108.34 1.3672 +IC H63 H62 *C6 H61 1.1174 112.38 -117.89 109.34 1.1241 +IC H63 C5 *C6 H62 1.1174 108.33 -126.36 114.61 1.1464 +IC O5 C1 C2 C3 1.4059 109.59 -55.45 110.83 1.4609 +IC C1 C2 C3 C4 1.4844 110.83 54.11 109.99 1.5307 +IC C2 C3 C4 C5 1.4609 109.99 -54.46 108.89 1.5190 +IC C3 C4 C5 O5 1.5307 108.89 56.69 108.34 1.3672 +IC C4 C5 O5 C1 1.5190 108.34 -62.43 115.13 1.4059 +IC C5 O5 C1 C2 1.3672 115.13 61.67 109.59 1.4844 +IC C4 C5 C6 H63 1.5190 113.08 52.76 108.33 1.1174 +IC O5 C1 O1 HO1 1.4059 105.17 -30.22 102.74 0.9773 +IC C1 C2 O2 CA2 1.4844 109.67 157.83 107.43 1.4300 +IC C2 C3 O3 HO3 1.4609 110.80 116.12 106.91 0.9395 +IC C3 C4 O4 HO4 1.5307 109.75 -60.70 104.02 0.9983 +IC C3 C2 O2 CA2 1.4987 113.76 52.52 122.34 1.4300 +IC C2 O2 CA2 OA2 1.4235 122.34 -8.29 128.77 1.2584 +IC C2 O2 CA2 CB2 1.4235 122.34 179.59 107.44 1.5400 +IC O2 CA2 CB2 HB1 1.4300 107.44 75.77 109.47 1.0700 +IC O2 CA2 CB2 HB2 1.4300 107.44 -164.22 109.47 1.0700 +IC O2 CA2 CB2 HB3 1.4300 107.44 -44.22 109.47 1.0700 +PATC FIRS NONE LAST NONE + +!RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral +!GROUP +!ATOM OH2 OCTIP3 -0.834 +!ATOM H1 HCTIP3 0.417 +!ATOM H2 HCTIP3 0.417 +!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +!ANGLE H1 OH2 H2 ! required +!PATCHING FIRS NONE LAST NONE + + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!! linear sugars, sugar alcohols, and inositol +!! erh and og +!! see Fig 1.24 "Monosaccharide Wheel" Conformation of Carbohydrates, +!! Rao, Qasba, Balaji, and Chandrasekaran, p. 20. +!! Fischer projections for all linear compounds +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +RESI MGLYOL 0.000 ! Meso-GLYcerOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! H31-C3-H32 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! O3-HO3 +ATOM HO2 HCP1 0.420 ! +GROU ! +ATOM C3 CC322 0.050 ! +ATOM H31 HCA2 0.090 ! +ATOM H32 HCA2 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H31 +BOND C3 O3 O3 HO3 C3 H32 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 O3 1.5614 104.35 -179.21 109.84 1.3948 +IC O1 C2 *C1 H11 1.4314 107.79 134.95 116.24 1.0888 +IC O1 C2 *C1 H12 1.4314 107.79 -110.15 104.20 1.0930 +IC C2 C1 O1 HO1 1.5614 107.79 -44.46 96.37 1.0016 +IC O1 C1 C2 C3 1.4314 107.79 -179.55 104.35 1.5671 +IC C3 C1 *C2 O2 1.5671 104.35 -114.63 106.58 1.4526 +IC O2 C1 *C2 H2 1.4526 106.58 -127.27 107.70 1.0874 +IC C1 C2 O2 HO2 1.5614 106.58 -179.25 99.24 0.9726 +IC O3 C2 *C3 H31 1.3948 109.84 -124.08 111.99 1.1041 +IC H31 C2 *C3 H32 1.1041 111.99 -118.34 109.12 1.1120 +IC C2 C3 O3 HO3 1.5671 109.84 168.92 113.91 1.0009 +PATC FIRS NONE LAST NONE + +RESI MERYOL 0.000 ! Meso-ERYthritOL (mertitol) +GROUP ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROUP ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H41-C4-H42 +ATOM HO2 HCP1 0.420 ! | +GROUP ! O4-HO4 +ATOM C3 CC312 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROUP ! +ATOM C4 CC322 0.050 ! +ATOM H41 HCA2 0.090 ! +ATOM H42 HCA2 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H41 C4 O4 +BOND O4 HO4 C4 H42 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6259 108.86 -172.77 113.90 1.5743 +IC O1 C2 *C1 H11 1.4014 112.12 115.55 103.98 1.1662 +IC O1 C2 *C1 H12 1.4014 112.12 -120.90 108.56 1.1365 +IC C2 C1 O1 HO1 1.6259 112.12 -83.41 109.87 0.9573 +IC O1 C1 C2 C3 1.4014 112.12 -40.11 108.86 1.5519 +IC C3 C1 *C2 O2 1.5519 108.86 120.00 117.26 1.4093 +IC O2 C1 *C2 H2 1.4093 117.26 125.89 103.86 1.0853 +IC C1 C2 O2 HO2 1.6259 117.26 161.24 110.44 0.9565 +IC C4 C2 *C3 O3 1.5743 113.90 122.82 112.99 1.4151 +IC O3 C2 *C3 H3 1.4151 112.99 119.44 108.28 1.0882 +IC C2 C3 O3 HO3 1.5519 112.99 59.23 107.97 0.9870 +IC C2 C3 C4 O4 1.5519 113.90 64.75 112.09 1.4267 +IC O4 C3 *C4 H41 1.4267 112.09 -125.03 113.11 1.1073 +IC H41 C3 *C4 H42 1.1073 113.11 -120.20 111.82 1.1551 +IC C3 C4 O4 HO4 1.5743 112.09 41.58 105.29 0.9507 +PATC FIRS NONE LAST NONE + +RESI DTHROL 0.000 ! D-THReitOL +GROUP ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROUP ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H41-C4-H42 +ATOM HO2 HCP1 0.420 ! | +GROUP ! O4-HO4 +ATOM C3 CC312 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROUP ! +ATOM C4 CC322 0.050 ! +ATOM H41 HCA2 0.090 ! +ATOM H42 HCA2 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H41 C4 O4 +BOND O4 HO4 C4 H42 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6133 109.49 -179.64 112.66 1.6033 +IC O1 C2 *C1 H11 1.4339 111.79 116.55 111.17 1.1673 +IC O1 C2 *C1 H12 1.4339 111.79 -133.85 118.71 1.1020 +IC C2 C1 O1 HO1 1.6133 111.79 74.41 100.55 0.9809 +IC O1 C1 C2 C3 1.4339 111.79 -36.33 109.49 1.5493 +IC C3 C1 *C2 O2 1.5493 109.49 -123.45 111.59 1.4118 +IC O2 C1 *C2 H2 1.4118 111.59 -107.72 103.84 1.1268 +IC C1 C2 O2 HO2 1.6133 111.59 -49.02 104.62 0.9492 +IC C4 C2 *C3 O3 1.6033 112.66 116.79 110.78 1.4657 +IC O3 C2 *C3 H3 1.4657 110.78 123.28 108.04 1.1153 +IC C2 C3 O3 HO3 1.5493 110.78 -45.76 93.49 0.9392 +IC C2 C3 C4 O4 1.5493 112.66 -71.77 113.16 1.3868 +IC O4 C3 *C4 H41 1.3868 113.16 -124.93 107.98 1.1179 +IC H41 C3 *C4 H42 1.1179 107.98 -112.45 102.71 1.1552 +IC C3 C4 O4 HO4 1.6033 113.16 61.41 112.22 0.9955 +PATC FIRS NONE LAST NONE + +RESI LTHROL 0.000 ! L-THReitOL +GROUP ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROUP ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H41-C4-H42 +ATOM HO2 HCP1 0.420 ! | +GROUP ! O4-HO4 +ATOM C3 CC312 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROUP ! +ATOM C4 CC322 0.050 ! +ATOM H41 HCA2 0.090 ! +ATOM H42 HCA2 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H41 C4 O4 +BOND O4 HO4 C4 H42 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6051 108.42 -178.14 117.74 1.4808 +IC O1 C2 *C1 H11 1.3860 112.31 116.93 101.78 1.0899 +IC O1 C2 *C1 H12 1.3860 112.31 -117.34 102.31 1.1502 +IC C2 C1 O1 HO1 1.6051 112.31 -79.47 99.92 0.9436 +IC O1 C1 C2 C3 1.3860 112.31 59.93 108.42 1.6250 +IC C3 C1 *C2 O2 1.6250 108.42 126.18 114.04 1.4167 +IC O2 C1 *C2 H2 1.4167 114.04 127.02 110.02 1.1273 +IC C1 C2 O2 HO2 1.6051 114.04 58.65 114.59 0.9324 +IC C4 C2 *C3 O3 1.4808 117.74 -120.55 109.09 1.4175 +IC O3 C2 *C3 H3 1.4175 109.09 -120.37 108.92 1.1156 +IC C2 C3 O3 HO3 1.6250 109.09 59.06 103.30 0.9300 +IC C2 C3 C4 O4 1.6250 117.74 62.09 112.92 1.4559 +IC O4 C3 *C4 H42 1.4559 112.92 114.71 113.36 1.1171 +IC H42 C3 *C4 H41 1.1171 113.36 120.10 117.05 1.0813 +IC C3 C4 O4 HO4 1.4808 112.92 -64.44 109.22 0.9634 +PATC FIRS NONE LAST NONE + +RESI MRIBOL 0.000 ! Meso-RIBitOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H51-C5-H52 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! O5-HO5 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC322 0.050 ! +ATOM H51 HCA2 0.090 ! +ATOM H52 HCA2 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H51 +BOND C5 O5 O5 HO5 C5 H52 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5589 110.56 -163.15 113.22 1.6303 +IC O1 C2 *C1 H11 1.4222 116.80 124.61 105.66 1.1281 +IC O1 C2 *C1 H12 1.4222 116.80 -117.60 105.48 1.1051 +IC C2 C1 O1 HO1 1.5589 116.80 -164.04 112.13 0.9841 +IC O1 C1 C2 C3 1.4222 116.80 66.64 110.56 1.5250 +IC C3 C1 *C2 O2 1.5250 110.56 -113.04 103.83 1.4235 +IC O2 C1 *C2 H2 1.4235 103.83 -118.87 113.85 1.0963 +IC C1 C2 O2 HO2 1.5589 103.83 20.73 96.42 0.9656 +IC C4 C2 *C3 O3 1.6303 113.22 -126.84 108.09 1.4090 +IC O3 C2 *C3 H3 1.4090 108.09 -113.93 107.34 1.1051 +IC C2 C3 O3 HO3 1.5250 108.09 174.85 107.58 0.9853 +IC C2 C3 C4 C5 1.5250 113.22 -55.42 109.40 1.5351 +IC C5 C3 *C4 O4 1.5351 109.40 -125.27 107.97 1.4431 +IC O4 C3 *C4 H4 1.4431 107.97 -115.10 109.87 1.1304 +IC C3 C4 O4 HO4 1.6303 107.97 164.00 99.47 0.9714 +IC C3 C4 C5 O5 1.6303 109.40 177.89 110.44 1.4060 +IC O5 C4 *C5 H51 1.4060 110.44 -120.82 110.24 1.1278 +IC H51 C4 *C5 H52 1.1278 110.24 -118.19 116.45 1.1298 +IC C4 C5 O5 HO5 1.5351 110.44 -149.39 107.20 0.9880 +PATC FIRS NONE LAST NONE + +RESI DARAOL 0.000 ! D-ARAbitOL (same as lyxitol) +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H4-C4-O4-HO4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H51-C5-H52 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! O5-HO5 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC322 0.050 ! +ATOM H51 HCA2 0.090 ! +ATOM H52 HCA2 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H51 +BOND C5 O5 O5 HO5 C5 H52 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6056 112.65 173.24 109.58 1.5414 +IC O1 C2 *C1 H11 1.3851 114.18 118.96 103.71 1.1026 +IC O1 C2 *C1 H12 1.3851 114.18 -120.67 108.43 1.0860 +IC C2 C1 O1 HO1 1.6056 114.18 -73.78 112.70 1.0086 +IC O1 C1 C2 C3 1.3851 114.18 -47.65 112.65 1.5013 +IC C3 C1 *C2 O2 1.5013 112.65 -123.92 110.69 1.4462 +IC O2 C1 *C2 H2 1.4462 110.69 -125.35 104.98 1.1102 +IC C1 C2 O2 HO2 1.6056 110.69 69.62 100.22 0.9866 +IC C4 C2 *C3 O3 1.5414 109.58 126.30 111.67 1.4412 +IC O3 C2 *C3 H3 1.4412 111.67 115.35 108.34 1.1263 +IC C2 C3 O3 HO3 1.5013 111.67 76.22 94.88 0.9539 +IC C2 C3 C4 C5 1.5013 109.58 170.70 112.68 1.5413 +IC C5 C3 *C4 O4 1.5413 112.68 123.00 105.68 1.4531 +IC O4 C3 *C4 H4 1.4531 105.68 114.88 109.48 1.1137 +IC C3 C4 O4 HO4 1.5414 105.68 -118.03 102.41 0.9501 +IC C3 C4 C5 O5 1.5414 112.68 65.14 110.15 1.4606 +IC O5 C4 *C5 H51 1.4606 110.15 -131.01 117.80 1.0534 +IC H51 C4 *C5 H52 1.0534 117.80 -114.28 114.07 1.1820 +IC C4 C5 O5 HO5 1.5413 110.15 -62.35 106.12 0.9490 +PATC FIRS NONE LAST NONE + +RESI LARAOL 0.000 ! L-ARAbitOL (same as lyxitol) +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROU ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H51-C5-H52 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! O5-HO5 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC322 0.050 ! +ATOM H51 HCA2 0.090 ! +ATOM H52 HCA2 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H51 +BOND C5 O5 O5 HO5 C5 H52 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5163 110.17 -159.68 111.55 1.5270 +IC O1 C2 *C1 H11 1.4216 114.98 124.75 113.88 1.1363 +IC O1 C2 *C1 H12 1.4216 114.98 -117.51 109.99 1.1097 +IC C2 C1 O1 HO1 1.5163 114.98 78.09 105.93 0.9211 +IC O1 C1 C2 C3 1.4216 114.98 56.30 110.17 1.5404 +IC C3 C1 *C2 O2 1.5404 110.17 128.22 116.71 1.4565 +IC O2 C1 *C2 H2 1.4565 116.71 116.82 102.32 1.1457 +IC C1 C2 O2 HO2 1.5163 116.71 -80.57 96.32 0.9470 +IC C4 C2 *C3 O3 1.5270 111.55 -126.83 106.30 1.4622 +IC O3 C2 *C3 H3 1.4622 106.30 -117.91 108.12 1.1110 +IC C2 C3 O3 HO3 1.5404 106.30 -77.10 112.46 0.9927 +IC C2 C3 C4 C5 1.5404 111.55 -174.48 110.50 1.5672 +IC C5 C3 *C4 O4 1.5672 110.50 -127.64 113.29 1.4485 +IC O4 C3 *C4 H4 1.4485 113.29 -114.25 108.64 1.0962 +IC C3 C4 O4 HO4 1.5270 113.29 110.84 102.74 0.9758 +IC C3 C4 C5 O5 1.5270 110.50 -77.67 107.30 1.4592 +IC O5 C4 *C5 H52 1.4592 107.30 129.47 106.02 1.1807 +IC H52 C4 *C5 H51 1.1807 106.02 119.78 106.58 1.0953 +IC C4 C5 O5 HO5 1.5672 107.30 78.68 108.32 0.9484 +PATC FIRS NONE LAST NONE + +RESI MXYLOL 0.000 ! Meso-XYLitOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H51-C5-H52 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! O5-HO5 +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC322 0.050 ! +ATOM H51 HCA2 0.090 ! +ATOM H52 HCA2 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H51 +BOND C5 O5 O5 HO5 C5 H52 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5323 110.65 166.89 113.05 1.5788 +IC O1 C2 *C1 H11 1.4361 108.54 115.14 108.79 1.0730 +IC O1 C2 *C1 H12 1.4361 108.54 -124.47 109.06 1.1440 +IC C2 C1 O1 HO1 1.5323 108.54 -164.41 109.20 0.9440 +IC O1 C1 C2 C3 1.4361 108.54 -169.12 110.65 1.5607 +IC C3 C1 *C2 O2 1.5607 110.65 -123.52 110.46 1.4429 +IC O2 C1 *C2 H2 1.4429 110.46 -115.49 104.71 1.1635 +IC C1 C2 O2 HO2 1.5323 110.46 -48.09 111.45 0.9664 +IC C4 C2 *C3 O3 1.5788 113.05 130.70 109.20 1.4492 +IC O3 C2 *C3 H3 1.4492 109.20 111.37 108.76 1.1324 +IC C2 C3 O3 HO3 1.5607 109.20 -48.82 103.09 1.0049 +IC C2 C3 C4 C5 1.5607 113.05 -77.67 110.05 1.5698 +IC C5 C3 *C4 O4 1.5698 110.05 -119.84 110.05 1.4236 +IC O4 C3 *C4 H4 1.4236 110.05 -118.04 111.71 1.1318 +IC C3 C4 O4 HO4 1.5788 110.05 -33.69 112.14 0.9528 +IC C3 C4 C5 O5 1.5788 110.05 -177.74 113.29 1.4361 +IC O5 C4 *C5 H51 1.4361 113.29 -114.53 106.11 1.1050 +IC H51 C4 *C5 H52 1.1050 106.11 -122.72 106.53 1.1383 +IC C4 C5 O5 HO5 1.5698 113.29 32.43 104.43 1.0021 +PATC FIRS NONE LAST NONE + +RESI MALLOL 0.000 ! Meso-ALLitOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROU ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H4-C4-O4-HO4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H5-C5-O5-HO5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU ! +ATOM C6 CC322 0.050 ! +ATOM H61 HCA2 0.090 ! +ATOM H62 HCA2 0.090 ! +ATOM O6 OC311 -0.650 ! +ATOM HO6 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI DALTOL 0.000 ! D-ALTritOL (same as talitol) +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H4-C4-O4-HO4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H5-C5-O5-HO5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI LALTOL 0.000 ! L-ALTritOL (same as talitol) +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROU ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! HO5-O5-C5-H5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI DGLUOL 0.000 ! D-GLUcitOL (sorbitol) +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROU ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H4-C4-O4-HO4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H5-C5-O5-HO5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI LGLUOL 0.000 ! L-GLUcitOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! HO5-O5-C5-H5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI DMANOL 0.000 ! D-MANnitOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H4-C4-O4-HO4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H5-C5-O5-HO5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI LMANOL 0.000 ! L-MANnitOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROU ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! HO5-O5-C5-H5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI DGULOL 0.000 ! D-GULitOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROU ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H5-C5-O5-HO5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI LGULOL 0.000 ! L-GULitOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H4-C4-O4-HO4 +ATOM HO2 HCP1 0.420 ! | +GROU ! HO5-O5-C5-H5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI DIDIOL 0.000 ! D-IDItOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! HO2-O2-C2-H2 +GROU ! | +ATOM C2 CC312 0.140 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H5-C5-O5-HO5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 -120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI LIDIOL 0.000 ! L-IDItOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROU ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H4-C4-O4-HO4 +ATOM HO2 HCP1 0.420 ! | +GROU ! HO5-O5-C5-H5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 -120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI MGALOL 0.000 ! Meso-GALacticOL +GROU ! +ATOM C1 CC322 0.050 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! H2-C2-O2-HO2 +GROU ! | +ATOM C2 CC312 0.140 ! HO3-O3-C3-H3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! HO4-O4-C4-H4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H5-C5-O5-HO5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU +ATOM C6 CC322 0.050 +ATOM H61 HCA2 0.090 +ATOM H62 HCA2 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5600 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5300 112.00 180.00 112.00 1.4300 +IC C2 C1 O1 HO1 1.5300 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1100 !-120 for D +IC C1 C2 O2 HO2 1.5600 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 -120.00 111.02 1.4276 ! 120 for D +IC C4 C2 *C3 H3 1.4276 111.02 120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 -120.00 112.07 1.3955 ! 120 for D +IC C5 C3 *C4 H4 1.3955 112.07 120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.4300 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9600 +PATC FIRS NONE LAST NONE + +RESI ALLOSE 0.000 ! D-Allose, open, free aldehdye +GROU ! + ! H1 O1 + ! \ // +ATOM C1 CC2O4 0.200 ! C1 !transferred from acetaldehyde, erh 1/09 +ATOM O1 OC2D4 -0.400 ! | +ATOM H1 HCR1 0.060 ! H2-C2-O2-HO2 + ! | +ATOM C2 CC312 0.280 ! H3-C3-O3-HO3 +ATOM H2 HCA1 0.090 ! | +ATOM O2 OC311 -0.650 ! H4-C4-O4-HO4 +ATOM HO2 HCP1 0.420 ! | +GROU ! H5-C5-O5-HO5 +ATOM C3 CC312 0.140 ! | +ATOM H3 HCA1 0.090 ! H61-C6-H62 +ATOM O3 OC311 -0.650 ! | +ATOM HO3 HCP1 0.420 ! O6-HO6 +GROU ! +ATOM C4 CC312 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU ! +ATOM C6 CC322 0.050 ! +ATOM H61 HCA2 0.090 ! +ATOM H62 HCA2 0.090 ! +ATOM O6 OC311 -0.650 ! +ATOM HO6 HCP1 0.420 ! +! +BOND C1 O1 C1 H1 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +!IMPR C2 C1 O1 H1 old definition +IMPR C1 C2 O1 H1 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6170 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5000 113.80 180.00 124.00 1.2050 +IC O1 C2 *C1 H1 1.4350 108.07 180.00 105.35 1.0997 +IC C3 C1 *C2 O2 1.5300 111.59 120.00 109.42 1.4226 ! 120 for D (in aldoses/ketoses) +IC C3 C1 *C2 H2 1.4226 109.42 -120.00 109.09 1.1814 !-120 for D +IC C1 C2 O2 HO2 1.6170 109.42 -60.00 99.72 0.9669 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D (in aldoses/ketoses) +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D (in aldoses/ketoses) +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D (in aldoses/ketoses) +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.0511 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9350 +PATC FIRS NONE LAST NONE + +RESI PSICOS 0.000 ! D-Psicose, open, free ketose +GROU ! +ATOM C1 CC322 0.090 ! O1-HO1 +ATOM H11 HCA2 0.090 ! | +ATOM H12 HCA2 0.090 ! H11-C1-H12 +ATOM O1 OC311 -0.650 ! | +ATOM HO1 HCP1 0.420 ! C2=O2 !Charges similar to acetone, erh 1/09 +ATOM C2 CC2O3 0.400 ! | +ATOM O2 OC2D3 -0.480 ! H3-C3-O3-HO3 + ! | +ATOM C3 CC312 0.180 ! H4-C4-O4-HO4 +ATOM H3 HCA1 0.090 ! | +ATOM O3 OC311 -0.650 ! H5-C5-O5-HO5 +ATOM HO3 HCP1 0.420 ! | +GROU ! H61-C6-H62 +ATOM C4 CC312 0.140 ! | +ATOM H4 HCA1 0.090 ! O6-HO6 +ATOM O4 OC311 -0.650 ! +ATOM HO4 HCP1 0.420 ! +GROU ! +ATOM C5 CC312 0.140 ! +ATOM H5 HCA1 0.090 ! +ATOM O5 OC311 -0.650 ! +ATOM HO5 HCP1 0.420 ! +GROU ! +ATOM C6 CC322 0.050 ! +ATOM H61 HCA2 0.090 ! +ATOM H62 HCA2 0.090 ! +ATOM O6 OC311 -0.650 ! +ATOM HO6 HCP1 0.420 ! +! +BOND C1 O1 C1 H11 O1 HO1 C1 H12 C1 C2 +BOND C2 O2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 +BOND C6 H62 C6 O6 O6 HO6 C5 O5 O5 HO5 +IMPR C2 C1 C3 O2 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.6170 111.59 180.00 110.42 1.5369 +IC C2 C3 C4 C5 1.5300 110.42 180.00 110.20 1.5320 +IC C3 C4 C5 C6 1.5369 110.20 180.00 108.72 1.5316 +IC C3 C2 C1 O1 1.5000 116.00 180.00 108.89 1.4200 +IC C2 C1 O1 HO1 1.6170 108.07 180.00 109.97 0.9462 +IC O1 C2 *C1 H11 1.4350 108.07 120.00 105.35 1.0997 +IC O1 C2 *C1 H12 1.4350 108.07 -120.00 109.50 1.1112 +IC O1 C2 *C1 H1 1.4350 108.07 180.00 105.35 1.0997 +IC C3 C1 *C2 O2 1.5300 111.59 180.00 109.42 1.4226 +IC C4 C2 *C3 O3 1.5369 110.42 120.00 111.02 1.4276 ! 120 for D (in aldoses/ketoses) +IC C4 C2 *C3 H3 1.4276 111.02 -120.00 106.54 1.1878 !-120 for D +IC C2 C3 O3 HO3 1.5300 111.02 -60.00 98.73 0.9915 +IC C5 C3 *C4 O4 1.5320 110.20 120.00 112.07 1.3955 ! 120 for D (in aldoses/ketoses) +IC C5 C3 *C4 H4 1.3955 112.07 -120.00 113.60 1.0969 !-120 for D +IC C3 C4 O4 HO4 1.5369 112.07 -60.00 103.63 0.9940 +IC C6 C4 *C5 O5 1.5316 108.72 120.00 111.89 1.3976 ! 120 for D (in aldoses/ketoses) +IC C6 C4 *C5 H5 1.5316 108.72 -120.00 105.82 1.1468 !-120 for D +IC C4 C5 O5 HO5 1.5320 111.89 -60.00 105.13 0.9258 +IC C4 C5 C6 O6 1.5320 108.72 180.00 105.74 1.4909 +IC O6 C5 *C6 H61 1.4909 105.74 120.00 106.59 1.0511 +IC O6 C5 *C6 H62 1.0511 106.59 -120.00 106.23 1.0677 +IC C5 C6 O6 HO6 1.5316 105.74 180.00 115.02 0.9350 + +RESI INI1 0.000 ! cyclic myi-inositol + ! +GROU ! +ATOM C1 CC3161 0.140 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! O5-HO5 O6-HO6 +ATOM HO1 HCP1 0.420 ! | / +GROU ! H5-C5----C6 +ATOM C2 CC3161 0.140 ! / /\ +ATOM H2 HCA1 0.090 ! H4 / H6 \ H1 +ATOM O2 OC311 -0.650 ! \/ HO3 \ / +ATOM HO2 HCP1 0.420 ! C4 | C1 +GROU ! / \ O3 H2 / \ +ATOM C3 CC3161 0.140 ! HO4-O4 \| | / O1-HO1 +ATOM H3 HCA1 0.090 ! C3---C2 +ATOM O3 OC311 -0.650 ! | | +ATOM HO3 HCP1 0.420 ! H3 O2-HO2 +GROU ! +ATOM C4 CC3161 0.140 ! +ATOM H4 HCA1 0.090 ! +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C5 CC3161 0.140 +ATOM H5 HCA1 0.090 +ATOM O5 OC311 -0.650 +ATOM HO5 HCP1 0.420 +GROU +ATOM C6 CC3161 0.140 +ATOM H6 HCA1 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 C6 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H6 +BOND C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5530 107.31 -59.93 109.11 1.5612 +IC C2 C3 C4 C5 1.4341 109.11 59.27 114.44 1.4654 +IC C3 C2 C1 O1 1.4341 107.31 -175.79 117.69 1.4086 +IC C3 C4 C5 C6 1.5612 114.44 -55.48 109.80 1.5350 +IC C4 C5 C6 C1 1.4654 109.80 55.05 107.18 1.5598 +IC C2 C3 C4 O4 1.4341 109.11 -177.27 106.06 1.4595 +IC C3 C4 C5 O5 1.5612 114.44 171.27 114.28 1.4386 +IC C2 C3 C4 H4 1.4341 109.11 -64.25 106.39 1.1684 +IC O1 C1 C2 O2 1.4086 117.69 51.01 111.79 1.4490 +IC O1 C1 C2 H2 1.4086 117.69 -61.28 98.22 1.1105 +IC C3 C4 C5 H5 1.5612 114.44 52.34 110.34 1.0922 +IC O1 C2 *C1 H1 1.4086 117.69 121.05 110.98 1.1834 +IC O2 C1 *C2 C3 1.4490 111.79 133.20 107.31 1.4341 +IC O3 C4 *C3 H3 1.4537 110.99 114.31 113.73 1.1394 +IC O3 C2 *C3 C4 1.4537 105.59 119.36 109.11 1.5612 +IC O4 C3 *C4 C5 1.4595 106.06 -123.46 114.44 1.4654 +IC C6 C4 *C5 O5 1.5350 109.80 -133.25 114.28 1.4386 +IC C4 C5 O5 HO5 1.4654 114.28 -73.20 108.55 0.9726 +IC C4 C5 C6 O6 1.4654 109.80 -179.24 110.87 1.4043 +IC C2 C1 O1 HO1 1.5530 117.69 -165.05 114.27 0.9451 +IC C1 C2 O2 HO2 1.5530 111.79 -31.80 115.65 0.9404 +IC C2 C3 O3 HO3 1.4341 105.59 37.19 107.10 0.9920 +IC C3 C4 O4 HO4 1.5612 106.06 35.00 105.15 0.9686 +IC C5 C6 O6 HO6 1.5350 110.87 51.35 112.65 0.9879 +IC C4 C5 C6 H6 1.4654 109.80 -58.40 111.34 1.0796 +PATC FIRS NONE LAST NONE + + +RESI INI2 0.000 ! cyclic epi-inositol + ! +GROU ! +ATOM C1 CC3161 0.140 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! O5-HO5 O6-HO6 +ATOM HO1 HCP1 0.420 ! | / +GROU ! H5-C5----C6 +ATOM C5 CC3161 0.140 ! / /\ +ATOM H5 HCA1 0.090 ! H4 / H6 \ H1 +ATOM O5 OC311 -0.650 ! \/ HO3 \ / +ATOM HO5 HCP1 0.420 ! C4 | C1 +GROU ! / \ O3 H2 / \ +ATOM C2 CC3161 0.140 ! HO4-O4 \| | / O1-HO1 +ATOM H2 HCA1 0.090 ! C3---C2 +ATOM O2 OC311 -0.650 ! | | +ATOM HO2 HCP1 0.420 ! H3 O2-HO2 +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC3161 0.140 +ATOM H6 HCA1 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 C6 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H6 +BOND C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5857 105.54 -52.21 116.84 1.4863 +IC C2 C3 C4 C5 1.5491 116.84 53.10 109.72 1.4862 +IC C3 C2 C1 O1 1.5491 105.54 178.07 111.80 1.4160 +IC C3 C4 C5 C6 1.4863 109.72 -55.09 112.05 1.5150 +IC C4 C5 C6 C1 1.4862 112.05 61.73 109.25 1.4866 +IC C2 C3 C4 O4 1.5491 116.84 173.26 112.79 1.4481 +IC C3 C4 C5 O5 1.4863 109.72 -177.93 114.90 1.4564 +IC C2 C3 C4 H4 1.5491 116.84 -66.87 112.11 1.0857 +IC O1 C1 C2 O2 1.4160 111.80 61.23 107.20 1.3789 +IC O1 C1 C2 H2 1.4160 111.80 -61.61 111.15 1.0970 +IC C3 C4 C5 H5 1.4863 109.72 61.83 105.37 1.1096 +IC O1 C2 *C1 H1 1.4160 111.80 111.42 103.32 1.1097 +IC O2 C1 *C2 C3 1.3789 107.20 116.84 105.54 1.5491 +IC O3 C4 *C3 H3 1.4319 107.22 119.50 102.96 1.1864 +IC O3 C2 *C3 C4 1.4319 107.38 120.40 116.84 1.4863 +IC O4 C3 *C4 C5 1.4481 112.79 -120.16 109.72 1.4862 +IC C6 C4 *C5 O5 1.5150 112.05 -122.84 114.90 1.4564 +IC C4 C5 O5 HO5 1.4862 114.90 -35.31 106.98 0.9716 +IC C4 C5 C6 O6 1.4862 112.05 -67.61 111.78 1.4447 +IC C2 C1 O1 HO1 1.5857 111.80 -81.89 102.48 0.9902 +IC C1 C2 O2 HO2 1.5857 107.20 21.01 116.73 0.9638 +IC C2 C3 O3 HO3 1.5491 107.38 22.82 110.10 0.9389 +IC C3 C4 O4 HO4 1.4863 112.79 65.14 100.89 0.9815 +IC C5 C6 O6 HO6 1.5150 111.78 -69.76 108.04 0.9678 +IC C4 C5 C6 H6 1.4862 112.05 179.59 105.14 1.1218 +PATC FIRS NONE LAST NONE + +RESI INI3 0.000 ! cyclic allo-inositol + ! +GROU ! +ATOM C1 CC3161 0.140 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! O5-HO5 O6-HO6 +ATOM HO1 HCP1 0.420 ! | / +GROU ! H5-C5----C6 +ATOM C5 CC3161 0.140 ! / /\ +ATOM H5 HCA1 0.090 ! H4 / H6 \ H1 +ATOM O5 OC311 -0.650 ! \/ HO3 \ / +ATOM HO5 HCP1 0.420 ! C4 | C1 +GROU ! / \ O3 H2 / \ +ATOM C2 CC3161 0.140 ! HO4-O4 \| | / O1-HO1 +ATOM H2 HCA1 0.090 ! C3---C2 +ATOM O2 OC311 -0.650 ! | | +ATOM HO2 HCP1 0.420 ! H3 O2-HO2 +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC3161 0.140 +ATOM H6 HCA1 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 C6 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H6 +BOND C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5975 112.20 52.30 109.96 1.5735 +IC C2 C3 C4 C5 1.5893 109.96 -50.28 112.65 1.5205 +IC C3 C2 C1 O1 1.5893 112.20 62.08 109.30 1.4095 +IC C3 C4 C5 C6 1.5735 112.65 52.32 114.65 1.5455 +IC C4 C5 C6 C1 1.5205 114.65 -54.93 111.58 1.5167 +IC C2 C3 C4 O4 1.5893 109.96 72.50 110.08 1.4172 +IC C3 C4 C5 O5 1.5735 112.65 177.95 112.67 1.4182 +IC C2 C3 C4 H4 1.5893 109.96 -171.59 106.26 1.0989 +IC C1 C2 C3 H3 1.5975 112.20 -65.52 111.91 1.0875 +IC O1 C1 C2 O2 1.4095 109.30 -69.67 112.98 1.3843 +IC C1 C2 C3 O3 1.5975 112.20 174.94 109.61 1.4280 +IC O1 C1 C2 H2 1.4095 109.30 173.79 101.66 1.0913 +IC C3 C4 C5 H5 1.5735 112.65 -70.51 113.19 1.0991 +IC O1 C2 *C1 H1 1.4095 109.30 124.45 105.27 1.0988 +IC O2 C1 *C2 C3 1.3843 112.98 131.75 112.20 1.5893 +IC O3 C4 *C3 H3 1.4280 111.28 -117.07 106.24 1.0875 +IC O3 C2 *C3 C4 1.4280 109.61 -122.64 109.96 1.5735 +IC O4 C3 *C4 C5 1.4172 110.08 -122.78 112.65 1.5205 +IC C6 C4 *C5 O5 1.5455 114.65 125.63 112.67 1.4182 +IC C4 C5 O5 HO5 1.5205 112.67 -63.56 98.13 0.9831 +IC C4 C5 C6 O6 1.5205 114.65 68.97 107.64 1.4395 +IC C2 C1 O1 HO1 1.5975 109.30 83.42 109.23 0.9576 +IC C1 C2 O2 HO2 1.5975 112.98 -136.65 106.93 0.9786 +IC C2 C3 O3 HO3 1.5893 109.61 86.54 109.26 0.9444 +IC C3 C4 O4 HO4 1.5735 110.08 51.12 110.65 0.9693 +IC C5 C6 O6 HO6 1.5455 107.64 -32.04 106.51 0.9912 +IC C4 C5 C6 H6 1.5205 114.65 -170.89 104.65 1.0958 +PATC FIRS NONE LAST NONE + +RESI INI4 0.000 ! cyclic l-chiro-inositol + ! +GROU ! +ATOM C1 CC3161 0.140 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! O5-HO5 O6-HO6 +ATOM HO1 HCP1 0.420 ! | / +GROU ! H5-C5----C6 +ATOM C5 CC3161 0.140 ! / /\ +ATOM H5 HCA1 0.090 ! H4 / H6 \ H1 +ATOM O5 OC311 -0.650 ! \/ HO3 \ / +ATOM HO5 HCP1 0.420 ! C4 | C1 +GROU ! / \ O3 H2 / \ +ATOM C2 CC3161 0.140 ! HO4-O4 \| | / O1-HO1 +ATOM H2 HCA1 0.090 ! C3---C2 +ATOM O2 OC311 -0.650 ! | | +ATOM HO2 HCP1 0.420 ! H3 O2-HO2 +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC3161 0.140 +ATOM H6 HCA1 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 C6 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H6 +BOND C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.5740 105.16 58.42 113.42 1.4855 +IC C2 C3 C4 C5 1.4644 113.42 -53.08 113.80 1.5305 +IC C3 C2 C1 O1 1.4644 105.16 63.40 115.79 1.3814 +IC C3 C4 C5 C6 1.4855 113.80 46.77 109.75 1.5215 +IC C4 C5 C6 C1 1.5305 109.75 -53.36 110.80 1.4416 +IC C2 C3 C4 O4 1.4644 113.42 178.17 113.65 1.4325 +IC C3 C4 C5 O5 1.4855 113.80 169.65 113.09 1.4286 +IC C2 C3 C4 H4 1.4644 113.42 59.58 110.61 1.1498 +IC C1 C2 C3 H3 1.5740 105.16 -57.64 110.94 1.1157 +IC O1 C1 C2 O2 1.3814 115.79 -59.46 109.52 1.3913 +IC C1 C2 C3 O3 1.5740 105.16 179.81 108.46 1.4338 +IC O1 C1 C2 H2 1.3814 115.79 -179.44 103.85 1.0993 +IC C3 C4 C5 H5 1.4855 113.80 -71.41 107.97 1.1124 +IC O1 C2 *C1 H1 1.3814 115.79 115.70 104.48 1.1174 +IC O2 C1 *C2 C3 1.3913 109.52 122.85 105.16 1.4644 +IC O3 C4 *C3 H3 1.4338 109.12 -118.63 103.56 1.1157 +IC O3 C2 *C3 C4 1.4338 108.46 -121.39 113.42 1.4855 +IC O4 C3 *C4 C5 1.4325 113.65 128.74 113.80 1.5305 +IC C6 C4 *C5 O5 1.5215 109.75 122.89 113.09 1.4286 +IC C4 C5 O5 HO5 1.5305 113.09 -85.28 109.66 0.9400 +IC C4 C5 C6 O6 1.5305 109.75 68.97 109.31 1.4497 +IC C2 C1 O1 HO1 1.5740 115.79 69.79 102.92 0.9892 +IC C1 C2 O2 HO2 1.5740 109.52 139.42 115.26 0.9357 +IC C2 C3 O3 HO3 1.4644 108.46 -162.07 107.98 0.9637 +IC C3 C4 O4 HO4 1.4855 113.65 166.02 99.93 0.9451 +IC C5 C6 O6 HO6 1.5215 109.31 152.41 113.08 0.9748 +IC C4 C5 C6 H6 1.5305 109.75 -168.18 103.15 1.1311 +PATC FIRS NONE LAST NONE + +RESI INI5 0.000 ! cyclic muco-inositol + ! +GROU ! +ATOM C1 CC3161 0.140 ! +ATOM H1 HCA1 0.090 ! +ATOM O1 OC311 -0.650 ! O5-HO5 O6-HO6 +ATOM HO1 HCP1 0.420 ! | / +GROU ! H5-C5----C6 +ATOM C5 CC3161 0.140 ! / /\ +ATOM H5 HCA1 0.090 ! H4 / H6 \ H1 +ATOM O5 OC311 -0.650 ! \/ HO3 \ / +ATOM HO5 HCP1 0.420 ! C4 | C1 +GROU ! / \ O3 H2 / \ +ATOM C2 CC3161 0.140 ! HO4-O4 \| | / O1-HO1 +ATOM H2 HCA1 0.090 ! C3---C2 +ATOM O2 OC311 -0.650 ! | | +ATOM HO2 HCP1 0.420 ! H3 O2-HO2 +GROU ! +ATOM C3 CC3161 0.140 ! +ATOM H3 HCA1 0.090 ! +ATOM O3 OC311 -0.650 ! +ATOM HO3 HCP1 0.420 ! +GROU +ATOM C4 CC3161 0.140 +ATOM H4 HCA1 0.090 +ATOM O4 OC311 -0.650 +ATOM HO4 HCP1 0.420 +GROU +ATOM C6 CC3161 0.140 +ATOM H6 HCA1 0.090 +ATOM O6 OC311 -0.650 +ATOM HO6 HCP1 0.420 +! +BOND C1 O1 C1 H1 O1 HO1 C1 C6 C1 C2 +BOND C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 +BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 +BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H6 +BOND C6 O6 O6 HO6 C5 O5 O5 HO5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 C3 C4 1.4979 109.56 52.88 109.76 1.4642 +IC C2 C3 C4 C5 1.5120 109.76 -61.62 111.99 1.4932 +IC C3 C2 C1 O1 1.5120 109.56 175.45 111.65 1.4353 +IC C3 C4 C5 C6 1.4642 111.99 64.66 106.41 1.5193 +IC C4 C5 C6 C1 1.4932 106.41 -59.87 108.52 1.4864 +IC C2 C3 C4 O4 1.5120 109.76 70.28 114.33 1.4063 +IC C3 C4 C5 O5 1.4642 111.99 -172.02 111.44 1.4489 +IC C2 C3 C4 H4 1.5120 109.76 -179.72 112.06 1.1357 +IC C1 C2 C3 H3 1.4979 109.56 169.46 107.46 1.1292 +IC O1 C1 C2 O2 1.4353 111.65 -52.78 120.83 1.4150 +IC C1 C2 C3 O3 1.4979 109.56 -77.37 115.42 1.4650 +IC O1 C1 C2 H2 1.4353 111.65 62.49 105.79 1.1543 +IC C3 C4 C5 H5 1.4642 111.99 -50.16 105.18 1.1938 +IC O1 C2 *C1 H1 1.4353 111.65 -105.08 101.84 1.1025 +IC O2 C1 *C2 C3 1.4150 120.83 -131.78 109.56 1.5120 +IC O3 C4 *C3 H3 1.4650 113.83 112.33 107.48 1.1292 +IC O3 C2 *C3 C4 1.4650 115.42 130.25 109.76 1.4642 +IC O4 C3 *C4 C5 1.4063 114.33 -131.90 111.99 1.4932 +IC C6 C4 *C5 O5 1.5193 106.41 123.31 111.44 1.4489 +IC C4 C5 O5 HO5 1.4932 111.44 -170.85 112.60 0.9756 +IC C4 C5 C6 O6 1.4932 106.41 179.19 112.32 1.3870 +IC C2 C1 O1 HO1 1.4979 111.65 -13.46 112.02 0.9797 +IC C1 C2 O2 HO2 1.4979 120.83 -83.39 101.92 0.9639 +IC C2 C3 O3 HO3 1.5120 115.42 -54.05 119.02 0.9777 +IC C3 C4 O4 HO4 1.4642 114.33 -173.03 102.19 0.9893 +IC C5 C6 O6 HO6 1.5193 112.32 154.66 104.77 0.9679 +IC C4 C5 C6 H6 1.4932 106.41 59.35 113.49 1.0572 +PATC FIRS NONE LAST NONE + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!! Furanose monosaccharides; erh 10/24/07!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +RESI ADEO 0.00 ! alpha-Deoxy-Ribose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ H1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / O1--HO1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! HO3--O3 H3 H21 H22 +ATOM HO5 HCP1 0.42 ! +GROUP ! +ATOM C2 CC3251 -0.18 ! +ATOM H21 HCA2 0.09 ! +ATOM H22 HCA2 0.09 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H21 C2 H22 C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 O4 C4 C5 C5 H51 +BOND C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry +IC C4 O4 C1 C2 1.4309 108.67 -19.01 106.25 1.5278 +IC O4 C1 C2 C3 1.4258 106.25 -8.82 103.23 1.5178 +IC C1 C2 C3 C4 1.5278 103.23 31.05 101.83 1.5232 +IC C3 O4 *C4 C5 1.5232 101.44 124.05 113.01 1.5448 +IC C3 O4 *C4 H4 1.5232 101.44 -115.42 106.74 1.1134 +IC O4 C4 C5 O5 1.4309 113.01 -178.27 111.12 1.4304 +IC C4 C5 O5 HO5 1.5448 111.12 -87.73 110.40 0.9643 +IC O4 C4 *C5 H51 2.4824 32.04 59.71 109.84 1.1020 +IC O4 C4 *C5 H52 2.4824 32.04 -58.37 108.86 1.1027 +IC C2 O4 *C1 O1 1.5278 106.25 119.87 110.66 1.3905 +IC O4 C1 O1 HO1 1.4258 110.66 60.11 106.63 0.9584 +IC C2 O4 *C1 H1 1.5278 106.25 -119.86 107.45 1.1137 +IC C3 C1 *C2 H21 1.5178 103.23 118.42 111.24 1.1030 +IC C3 C1 *C2 H22 1.5178 103.23 -122.05 112.95 1.0962 +IC C2 C4 *C3 O3 1.5178 101.83 -120.07 112.49 1.4116 +IC C4 C3 O3 HO3 1.5232 112.49 -53.93 107.21 0.9673 +IC C2 C4 *C3 H3 1.5178 101.83 117.41 109.93 1.1144 + +RESI BDEO 0.00 ! beta-Deoxy-Ribose +GROUP ! +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ O1--HO1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / H1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! HO3--O3 H3 H21 H22 +ATOM HO5 HCP1 0.42 ! +GROUP ! +ATOM C2 CC3251 -0.18 ! +ATOM H21 HCA2 0.09 ! +ATOM H22 HCA2 0.09 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H21 C2 H22 C2 C3 +BOND C3 H3 C3 O3 O3 HO3 C3 C4 +BOND C4 H4 C4 O4 C4 C5 C5 H51 +BOND C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4309 108.67 -19.01 106.25 1.5278 +IC O4 C1 C2 C3 1.4258 106.25 -8.82 103.23 1.5178 +IC C1 C2 C3 C4 1.5278 103.23 31.05 101.83 1.5232 +IC C3 O4 *C4 C5 1.5232 101.44 124.05 113.01 1.5448 +IC C3 O4 *C4 H4 1.5232 101.44 -115.42 106.74 1.1134 +IC O4 C4 C5 O5 1.4309 113.01 -178.27 111.12 1.4304 +IC C4 C5 O5 HO5 1.5448 111.12 -87.73 110.40 0.9643 +IC O4 C4 *C5 H51 2.4824 32.04 59.71 109.84 1.1020 +IC O4 C4 *C5 H52 2.4824 32.04 -58.37 108.86 1.1027 +IC C2 O4 *C1 O1 1.5278 106.25 -119.87 110.66 1.3905 +IC O4 C1 O1 HO1 1.4258 110.66 60.11 106.63 0.9584 +IC C2 O4 *C1 H1 1.5278 106.25 119.86 107.45 1.1137 +IC C3 C1 *C2 H21 1.5178 103.23 118.42 111.24 1.1030 +IC C3 C1 *C2 H22 1.5178 103.23 -122.05 112.95 1.0962 +IC C2 C4 *C3 O3 1.5178 101.83 -120.07 112.49 1.4116 +IC C4 C3 O3 HO3 1.5232 112.49 -53.93 107.21 0.9673 +IC C2 C4 *C3 H3 1.5178 101.83 117.41 109.93 1.1144 + + +RESI ARIB 0.00 ! alpha-Ribose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ H1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / O1--HO1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! HO3--O3 H3 O2 H2 +ATOM HO5 HCP1 0.42 ! | +GROUP ! HO2 +ATOM C2 CC3151 0.14 ! +ATOM H2 HCA1 0.09 ! +ATOM O2 OC311 -0.65 ! +ATOM HO2 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4343 107.06 -43.51 102.91 1.5564 +IC O4 C1 C2 C3 1.4227 102.91 29.68 103.27 1.5615 +IC C1 C2 C3 C4 1.5564 103.27 -6.90 103.97 1.5386 +IC C3 O4 *C4 C5 1.5386 104.85 125.17 112.30 1.5446 +IC C3 O4 *C4 H4 1.5386 104.85 -116.42 106.12 1.1143 +IC O4 C4 C5 O5 1.4343 112.30 -178.59 110.88 1.4293 +IC C4 C5 O5 HO5 1.5446 110.88 -86.85 110.49 0.9639 +IC O5 C4 *C5 H51 1.4293 110.88 119.78 108.95 1.1027 +IC O5 C4 *C5 H52 1.4293 110.88 -122.02 109.96 1.1020 +IC C2 O4 *C1 O1 1.5564 102.91 122.54 109.76 1.4025 +IC O4 C1 O1 HO1 1.4227 109.76 66.79 107.33 0.9584 +IC C2 O4 *C1 H1 1.5564 102.91 -117.68 108.69 1.1117 +IC C3 C1 *C2 H2 1.5615 103.27 -113.35 106.87 1.1124 +IC C3 C1 *C2 O2 1.5615 103.27 127.46 116.16 1.4278 +IC C1 C2 O2 HO2 1.5564 116.16 -81.77 106.00 0.9665 +IC C2 C4 *C3 O3 1.5615 103.97 -125.04 111.07 1.4263 +IC C2 C4 *C3 H3 1.5615 103.97 115.28 109.94 1.1126 +IC C4 C3 O3 HO3 1.5386 111.07 -77.15 108.40 0.9644 +IC C2 C4 *C3 H4 1.5615 103.97 -95.69 28.61 2.1867 + +RESI BRIB 0.00 ! beta-Ribose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ O1--HO1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / H1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! HO3--O3 H3 O2 H2 +ATOM HO5 HCP1 0.42 ! | +GROUP ! HO2 +ATOM C2 CC3151 0.14 ! +ATOM H2 HCA1 0.09 ! +ATOM O2 OC311 -0.65 ! +ATOM HO2 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4343 107.06 -43.51 102.91 1.5564 +IC O4 C1 C2 C3 1.4227 102.91 29.68 103.27 1.5615 +IC C1 C2 C3 C4 1.5564 103.27 -6.90 103.97 1.5386 +IC C3 O4 *C4 C5 1.5386 104.85 125.17 112.30 1.5446 +IC C3 O4 *C4 H4 1.5386 104.85 -116.42 106.12 1.1143 +IC O4 C4 C5 O5 1.4343 112.30 -178.59 110.88 1.4293 +IC C4 C5 O5 HO5 1.5446 110.88 -86.85 110.49 0.9639 +IC O5 C4 *C5 H51 1.4293 110.88 119.78 108.95 1.1027 +IC O5 C4 *C5 H52 1.4293 110.88 -122.02 109.96 1.1020 +IC C2 O4 *C1 O1 1.5564 102.91 -122.54 109.76 1.4025 +IC O4 C1 O1 HO1 1.4227 109.76 66.79 107.33 0.9584 +IC C2 O4 *C1 H1 1.5564 102.91 117.68 108.69 1.1117 +IC C3 C1 *C2 H2 1.5615 103.27 -113.35 106.87 1.1124 +IC C3 C1 *C2 O2 1.5615 103.27 127.46 116.16 1.4278 +IC C1 C2 O2 HO2 1.5564 116.16 -81.77 106.00 0.9665 +IC C2 C4 *C3 O3 1.5615 103.97 -125.04 111.07 1.4263 +IC C2 C4 *C3 H3 1.5615 103.97 115.28 109.94 1.1126 +IC C4 C3 O3 HO3 1.5386 111.07 -77.15 108.40 0.9644 +IC C2 C4 *C3 H4 1.5615 103.97 -95.69 28.61 2.1867 + +RESI AARB 0.00 ! alpha-Arabinose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ H1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / O1--HO1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! HO3--O3 H3 H2 O2 +ATOM HO5 HCP1 0.42 ! | +GROUP ! HO2 +ATOM C2 CC3151 0.14 ! +ATOM H2 HCA1 0.09 ! +ATOM O2 OC311 -0.65 ! +ATOM HO2 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4319 108.67 -17.05 106.71 1.5578 +IC O4 C1 C2 C3 1.4302 106.71 -10.12 102.15 1.5355 +IC C1 C2 C3 C4 1.5578 102.15 31.25 101.91 1.5267 +IC C3 O4 *C4 C5 1.5267 102.62 124.20 112.49 1.5454 +IC C3 O4 *C4 H4 1.5267 102.62 -115.89 106.69 1.1135 +IC O4 C4 C5 O5 1.4319 112.49 -179.23 111.10 1.4305 +IC C4 C5 O5 HO5 1.5454 111.10 -93.06 110.47 0.9646 +IC O5 C4 *C5 H51 1.4305 111.10 119.95 108.87 1.1029 +IC O5 C4 *C5 H52 1.4305 111.10 -122.01 109.82 1.1021 +IC C2 O4 *C1 O1 1.5578 106.71 122.01 110.02 1.3992 +IC O4 C1 O1 HO1 1.4302 110.02 65.19 106.88 0.9590 +IC C2 O4 *C1 H1 1.5578 106.71 -118.66 107.16 1.1129 +IC C3 C1 *C2 H2 1.5355 102.15 115.71 109.19 1.1138 +IC C3 C1 *C2 O2 1.5355 102.15 -121.95 114.37 1.4285 +IC C1 C2 O2 HO2 1.5578 114.37 -171.75 108.32 0.9638 +IC C2 C4 *C3 O3 1.5355 101.91 -122.00 112.32 1.4206 +IC C2 C4 *C3 H3 1.5355 101.91 116.42 109.37 1.1143 +IC C4 C3 O3 HO3 1.5267 112.32 -53.24 107.21 0.9692 +IC C2 C4 *C3 H4 1.5355 101.91 -71.04 28.67 2.1783 + +RESI BARB 0.00 ! beta-Arabinose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ H1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / O1--HO1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! HO3--O3 H3 H2 O2 +ATOM HO5 HCP1 0.42 ! | +GROUP ! HO2 +ATOM C2 CC3151 0.14 ! +ATOM H2 HCA1 0.09 ! +ATOM O2 OC311 -0.65 ! +ATOM HO2 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4319 108.67 -17.05 106.71 1.5578 +IC O4 C1 C2 C3 1.4302 106.71 -10.12 102.15 1.5355 +IC C1 C2 C3 C4 1.5578 102.15 31.25 101.91 1.5267 +IC C3 O4 *C4 C5 1.5267 102.62 124.20 112.49 1.5454 +IC C3 O4 *C4 H4 1.5267 102.62 -115.89 106.69 1.1135 +IC O4 C4 C5 O5 1.4319 112.49 -179.23 111.10 1.4305 +IC C4 C5 O5 HO5 1.5454 111.10 -93.06 110.47 0.9646 +IC O5 C4 *C5 H51 1.4305 111.10 119.95 108.87 1.1029 +IC O5 C4 *C5 H52 1.4305 111.10 -122.01 109.82 1.1021 +IC C2 O4 *C1 O1 1.5578 106.71 -122.01 110.02 1.3992 +IC O4 C1 O1 HO1 1.4302 110.02 65.19 106.88 0.9590 +IC C2 O4 *C1 H1 1.5578 106.71 118.66 107.16 1.1129 +IC C3 C1 *C2 H2 1.5355 102.15 115.71 109.19 1.1138 +IC C3 C1 *C2 O2 1.5355 102.15 -121.95 114.37 1.4285 +IC C1 C2 O2 HO2 1.5578 114.37 -171.75 108.32 0.9638 +IC C2 C4 *C3 O3 1.5355 101.91 -122.00 112.32 1.4206 +IC C2 C4 *C3 H3 1.5355 101.91 116.42 109.37 1.1143 +IC C4 C3 O3 HO3 1.5267 112.32 -53.24 107.21 0.9692 +IC C2 C4 *C3 H4 1.5355 101.91 -71.04 28.67 2.1783 + +RESI ALYF 0.00 ! alpha-Lyxofuranose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ H1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / O1--HO1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! H3 O3 H2 O2 +ATOM HO5 HCP1 0.42 ! | | +GROUP ! HO3 HO2 +ATOM C2 CC3151 0.14 ! +ATOM H2 HCA1 0.09 ! +ATOM O2 OC311 -0.65 ! +ATOM HO2 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4315 107.76 -22.45 106.42 1.5606 +IC O4 C1 C2 C3 1.4298 106.42 -6.06 102.41 1.5494 +IC C1 C2 C3 C4 1.5606 102.41 29.67 101.01 1.5315 +IC C3 O4 *C4 C5 1.5315 102.23 127.07 113.37 1.5469 +IC C3 O4 *C4 H4 1.5315 102.23 -114.55 106.16 1.1145 +IC O4 C4 C5 O5 1.4315 113.37 172.78 110.88 1.4279 +IC C4 C5 O5 HO5 1.5469 110.88 -89.23 111.11 0.9627 +IC O5 C4 *C5 H51 1.4279 110.88 120.67 109.96 1.1012 +IC O5 C4 *C5 H52 1.4279 110.88 -120.92 109.55 1.1021 +IC C2 O4 *C1 O1 1.5606 106.42 121.62 109.95 1.3992 +IC O4 C1 O1 HO1 1.4298 109.95 66.51 107.28 0.9594 +IC C2 O4 *C1 H1 1.5606 106.42 -119.08 107.39 1.1123 +IC C3 C1 *C2 H2 1.5494 102.41 115.35 109.45 1.1122 +IC C3 C1 *C2 O2 1.5494 102.41 -123.37 114.05 1.4282 +IC C1 C2 O2 HO2 1.5606 114.05 104.03 106.69 0.9675 +IC C2 C4 *C3 O3 1.5494 101.01 118.58 111.21 1.4279 +IC C2 C4 *C3 H3 1.5494 101.01 -119.18 112.30 1.1095 +IC C4 C3 O3 HO3 1.5315 111.21 -32.26 108.53 0.9635 +IC C2 C4 *C3 H4 1.5494 101.01 -68.34 28.96 2.1721 + +RESI BLYF 0.00 ! beta-Lyxofuranose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ H1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / O1--HO1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! H3 O3 H2 O2 +ATOM HO5 HCP1 0.42 ! | | +GROUP ! HO3 HO2 +ATOM C2 CC3151 0.14 ! +ATOM H2 HCA1 0.09 ! +ATOM O2 OC311 -0.65 ! +ATOM HO2 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4315 107.76 -22.45 106.42 1.5606 +IC O4 C1 C2 C3 1.4298 106.42 -6.06 102.41 1.5494 +IC C1 C2 C3 C4 1.5606 102.41 29.67 101.01 1.5315 +IC C3 O4 *C4 C5 1.5315 102.23 127.07 113.37 1.5469 +IC C3 O4 *C4 H4 1.5315 102.23 -114.55 106.16 1.1145 +IC O4 C4 C5 O5 1.4315 113.37 172.78 110.88 1.4279 +IC C4 C5 O5 HO5 1.5469 110.88 -89.23 111.11 0.9627 +IC O5 C4 *C5 H51 1.4279 110.88 120.67 109.96 1.1012 +IC O5 C4 *C5 H52 1.4279 110.88 -120.92 109.55 1.1021 +IC C2 O4 *C1 O1 1.5606 106.42 -121.62 109.95 1.3992 +IC O4 C1 O1 HO1 1.4298 109.95 66.51 107.28 0.9594 +IC C2 O4 *C1 H1 1.5606 106.42 119.08 107.39 1.1123 +IC C3 C1 *C2 H2 1.5494 102.41 115.35 109.45 1.1122 +IC C3 C1 *C2 O2 1.5494 102.41 -123.37 114.05 1.4282 +IC C1 C2 O2 HO2 1.5606 114.05 104.03 106.69 0.9675 +IC C2 C4 *C3 O3 1.5494 101.01 118.58 111.21 1.4279 +IC C2 C4 *C3 H3 1.5494 101.01 -119.18 112.30 1.1095 +IC C4 C3 O3 HO3 1.5315 111.21 -32.26 108.53 0.9635 +IC C2 C4 *C3 H4 1.5494 101.01 -68.34 28.96 2.1721 + + +RESI AXYF 0.00 ! alpha-Xylofuranose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ H1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / O1--HO1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! H3 O3 O2 H2 +ATOM HO5 HCP1 0.42 ! | | +GROUP ! HO3 HO2 +ATOM C2 CC3151 0.14 ! +ATOM H2 HCA1 0.09 ! +ATOM O2 OC311 -0.65 ! +ATOM HO2 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4368 109.21 7.17 106.92 1.5609 +IC O4 C1 C2 C3 1.4288 106.92 -29.31 100.61 1.5256 +IC C1 C2 C3 C4 1.5609 100.61 38.33 101.22 1.5366 +IC C3 O4 *C4 C5 1.5366 105.95 126.07 111.10 1.5466 +IC C3 O4 *C4 H4 1.5366 105.95 -115.62 106.41 1.1129 +IC O4 C4 C5 O5 1.4368 111.10 -170.12 111.17 1.4292 +IC C4 C5 O5 HO5 1.5466 111.17 -86.81 110.69 0.9637 +IC O5 C4 *C5 H51 1.4292 111.17 119.44 108.73 1.1031 +IC O5 C4 *C5 H52 1.4292 111.17 -122.76 110.12 1.1017 +IC C2 O4 *C1 O1 1.5609 106.92 123.12 110.19 1.4024 +IC O4 C1 O1 HO1 1.4288 110.19 60.16 106.38 0.9603 +IC C2 O4 *C1 H1 1.5609 106.92 -117.24 106.84 1.1130 +IC C3 C1 *C2 H2 1.5256 100.61 -119.80 111.22 1.1086 +IC C3 C1 *C2 O2 1.5256 100.61 116.99 113.84 1.4299 +IC C1 C2 O2 HO2 1.5609 113.84 25.15 106.11 0.9678 +IC C2 C4 *C3 O3 1.5256 101.22 116.82 111.32 1.4223 +IC C2 C4 *C3 H3 1.5256 101.22 -120.45 112.39 1.1104 +IC C4 C3 O3 HO3 1.5366 111.32 68.17 107.50 0.9664 +IC C2 C4 *C3 H4 1.5256 101.22 -77.82 29.09 2.1676 + +RESI BXYF 0.00 ! beta-Xylofuranose +GROUP +ATOM O4 OC3C51 -0.40 ! +ATOM C1 CC3152 0.34 ! +ATOM H1 HCA1 0.09 ! HO5--O5 +ATOM O1 OC311 -0.65 ! \ O4 +ATOM HO1 HCP1 0.42 ! H51--C5 / \ H1 +ATOM C4 CC3153 0.11 ! / \ / \ / +ATOM H4 HCA1 0.09 ! H52 C4 C1 +GROUP ! / \ / \ +ATOM C5 CC321 0.05 ! H4 \ / O1--HO1 +ATOM H51 HCA2 0.09 ! C3----C2 +ATOM H52 HCA2 0.09 ! / \ / \ +ATOM O5 OC311 -0.65 ! H3 O3 O2 H2 +ATOM HO5 HCP1 0.42 ! | | +GROUP ! HO3 HO2 +ATOM C2 CC3151 0.14 ! +ATOM H2 HCA1 0.09 ! +ATOM O2 OC311 -0.65 ! +ATOM HO2 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +BOND O4 C1 C1 H1 C1 O1 O1 HO1 +BOND C1 C2 C2 H2 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 C5 C4 O4 +BOND C5 H51 C5 H52 C5 O5 O5 HO5 +! IC table; from minimized geometry* +IC C4 O4 C1 C2 1.4368 109.21 7.17 106.92 1.5609 +IC O4 C1 C2 C3 1.4288 106.92 -29.31 100.61 1.5256 +IC C1 C2 C3 C4 1.5609 100.61 38.33 101.22 1.5366 +IC C3 O4 *C4 C5 1.5366 105.95 126.07 111.10 1.5466 +IC C3 O4 *C4 H4 1.5366 105.95 -115.62 106.41 1.1129 +IC O4 C4 C5 O5 1.4368 111.10 -170.12 111.17 1.4292 +IC C4 C5 O5 HO5 1.5466 111.17 -86.81 110.69 0.9637 +IC O5 C4 *C5 H51 1.4292 111.17 119.44 108.73 1.1031 +IC O5 C4 *C5 H52 1.4292 111.17 -122.76 110.12 1.1017 +IC C2 O4 *C1 O1 1.5609 106.92 -123.12 110.19 1.4024 +IC O4 C1 O1 HO1 1.4288 110.19 60.16 106.38 0.9603 +IC C2 O4 *C1 H1 1.5609 106.92 117.24 106.84 1.1130 +IC C3 C1 *C2 H2 1.5256 100.61 -119.80 111.22 1.1086 +IC C3 C1 *C2 O2 1.5256 100.61 116.99 113.84 1.4299 +IC C1 C2 O2 HO2 1.5609 113.84 25.15 106.11 0.9678 +IC C2 C4 *C3 O3 1.5256 101.22 116.82 111.32 1.4223 +IC C2 C4 *C3 H3 1.5256 101.22 -120.45 112.39 1.1104 +IC C4 C3 O3 HO3 1.5366 111.32 68.17 107.50 0.9664 +IC C2 C4 *C3 H4 1.5256 101.22 -77.82 29.09 2.1676 + +!erh 3/19/08 +RESI AFRU 0.00 ! alpha-Fructofuranose +GROUP +ATOM O5 OC3C51 -0.40 ! +ATOM C2 CC3051 0.43 ! H61 H62 H11 H12 +ATOM O2 OC311 -0.65 ! \ / O5 \ / +ATOM HO2 HCP1 0.42 ! HO6-O6--C6 / \ C1--O1-HO1 +ATOM C5 CC3153 0.11 ! \ / \ / +ATOM H5 HCA1 0.09 ! C5 C2 +GROUP ! / \ / \ +ATOM C6 CC321 0.05 ! H5 \ / O2--HO2 +ATOM H61 HCA2 0.09 ! C4----C3 +ATOM H62 HCA2 0.09 ! / \ / \ +ATOM O6 OC311 -0.65 ! H4 O4 O3 H3 +ATOM HO6 HCP1 0.42 ! | | +GROUP ! HO4 HO3 +ATOM C1 CC321 0.05 ! +ATOM H11 HCA2 0.09 ! +ATOM H12 HCA2 0.09 ! +ATOM O1 OC311 -0.65 ! +ATOM HO1 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +GROUP ! +ATOM C4 CC3151 0.14 ! +ATOM H4 HCA1 0.09 ! +ATOM O4 OC311 -0.65 ! +ATOM HO4 HCP1 0.42 ! +BOND O5 C2 C2 C1 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 O4 O4 HO4 +BOND C4 C5 C5 H5 C5 C6 C5 O5 +BOND C6 H61 C6 H62 C6 O6 O6 HO6 +BOND C1 H11 C1 H12 C1 O1 O1 HO1 +! IC table; from minimized geometry* +IC C5 O5 C2 C3 1.4395 110.18 -3.87 105.48 1.5648 +IC O5 C2 C3 C4 1.4336 105.48 -22.42 101.84 1.5306 +IC C2 C3 C4 C5 1.5648 101.84 38.32 100.70 1.5279 +IC C4 O5 *C5 C6 1.5279 103.59 125.05 112.69 1.5464 +IC C4 O5 *C5 H5 1.5279 103.59 -115.88 106.71 1.1148 +IC O5 C5 C6 O6 1.4395 112.69 61.06 111.04 1.4266 +IC C5 C6 O6 HO6 1.5464 111.04 -54.34 109.23 0.9640 +IC O6 C5 *C6 H61 1.4266 111.04 120.13 109.35 1.1026 +IC O6 C5 *C6 H62 1.4266 111.04 -121.07 109.82 1.1014 +IC C3 O5 *C2 O2 1.5648 105.48 118.28 109.92 1.4008 +IC O5 C2 O2 HO2 1.4336 109.92 74.40 106.34 0.9587 +IC C4 C2 *C3 H3 1.5306 101.84 113.46 108.58 1.1157 +IC C4 C2 *C3 O3 1.5306 101.84 -124.07 116.26 1.4342 +IC C2 C3 O3 HO3 1.5648 116.26 -110.77 108.92 0.9651 +IC C3 C5 *C4 O4 1.5306 100.70 -121.44 112.56 1.4204 +IC C3 C5 *C4 H4 1.5306 100.70 116.39 109.75 1.1135 +IC C5 C4 O4 HO4 1.5279 112.56 -173.27 109.31 0.9636 +IC C3 C5 *C4 H5 1.5306 100.70 -71.96 28.83 2.1752 +IC C5 O5 C2 C1 1.4395 110.18 -125.10 106.36 1.5716 +IC O5 C2 C1 H11 1.4336 106.36 64.27 108.72 1.1000 +IC O5 C2 C1 H12 1.4336 106.36 -52.00 108.02 1.1012 +IC O5 C2 C1 O1 1.4336 106.36 -172.81 115.31 1.4354 +IC C2 C1 O1 HO1 1.5716 115.31 -62.37 108.51 0.9672 +IC O1 C2 *C1 H11 1.4354 115.31 -122.91 108.72 1.1000 +IC O1 C2 *C1 H12 1.4354 115.31 120.81 108.02 1.1012 + + +RESI BFRU 0.00 ! beta-Fructofuranose +GROUP +ATOM O5 OC3C51 -0.40 ! +ATOM C2 CC3051 0.43 ! H61 H62 H11 H12 +ATOM O2 OC311 -0.65 ! \ / O5 \ / +ATOM HO2 HCP1 0.42 ! HO6-O6--C6 / \ C1--O1-HO1 +ATOM C5 CC3153 0.11 ! \ / \ / +ATOM H5 HCA1 0.09 ! C5 C2 +GROUP ! / \ / \ +ATOM C6 CC321 0.05 ! H5 \ / O2--HO2 +ATOM H61 HCA2 0.09 ! C4----C3 +ATOM H62 HCA2 0.09 ! / \ / \ +ATOM O6 OC311 -0.65 ! H4 O4 O3 H3 +ATOM HO6 HCP1 0.42 ! | | +GROUP ! HO4 HO3 +ATOM C1 CC321 0.05 ! +ATOM H11 HCA2 0.09 ! +ATOM H12 HCA2 0.09 ! +ATOM O1 OC311 -0.65 ! +ATOM HO1 HCP1 0.42 ! +GROUP ! +ATOM C3 CC3151 0.14 ! +ATOM H3 HCA1 0.09 ! +ATOM O3 OC311 -0.65 ! +ATOM HO3 HCP1 0.42 ! +GROUP ! +ATOM C4 CC3151 0.14 ! +ATOM H4 HCA1 0.09 ! +ATOM O4 OC311 -0.65 ! +ATOM HO4 HCP1 0.42 ! +BOND O5 C2 C2 C1 C2 O2 O2 HO2 +BOND C2 C3 C3 H3 C3 O3 O3 HO3 +BOND C3 C4 C4 H4 C4 O4 O4 HO4 +BOND C4 C5 C5 H5 C5 C6 C5 O5 +BOND C6 H61 C6 H62 C6 O6 O6 HO6 +BOND C1 H11 C1 H12 C1 O1 O1 HO1 +! IC table; from minimized geometry* +IC C5 O5 C2 C3 1.4445 110.17 24.54 103.90 1.5535 +IC O5 C2 C3 C4 1.4287 103.90 -39.46 100.37 1.5308 +IC C2 C3 C4 C5 1.5535 100.37 38.82 101.99 1.5367 +IC C4 O5 *C5 C6 1.5367 106.18 125.52 112.09 1.5470 +IC C4 O5 *C5 H5 1.5367 106.18 -116.60 106.00 1.1142 +IC O5 C5 C6 O6 1.4445 112.09 59.25 111.08 1.4266 +IC C5 C6 O6 HO6 1.5470 111.08 -58.47 108.57 0.9643 +IC O6 C5 *C6 H61 1.4266 111.08 120.33 109.39 1.1023 +IC O6 C5 *C6 H62 1.4266 111.08 -120.82 109.55 1.1021 +IC C3 O5 *C2 O2 1.5535 103.90 -118.22 109.18 1.4035 +IC O5 C2 O2 HO2 1.4287 109.18 159.12 104.91 0.9617 +IC C4 C2 *C3 H3 1.5308 100.37 114.40 108.58 1.1131 +IC C4 C2 *C3 O3 1.5308 100.37 -122.50 115.94 1.4351 +IC C2 C3 O3 HO3 1.5535 115.94 -76.65 108.79 0.9673 +IC C3 C5 *C4 O4 1.5308 101.99 -122.06 112.87 1.4204 +IC C3 C5 *C4 H4 1.5308 101.99 116.11 109.34 1.1142 +IC C5 C4 O4 HO4 1.5367 112.87 -177.81 108.59 0.9641 +IC C3 C5 *C4 H5 1.5308 101.99 -88.31 28.76 2.1807 +IC C5 O5 C2 C1 1.4445 110.17 145.62 109.90 1.5622 +IC O5 C2 C1 H11 1.4287 109.90 62.33 108.75 1.1018 +IC O5 C2 C1 H12 1.4287 109.90 -54.09 107.90 1.1015 +IC O5 C2 C1 O1 1.4287 109.90 -174.69 113.93 1.4392 +IC C2 C1 O1 HO1 1.5622 113.93 -99.33 109.99 0.9653 +IC O1 C2 *C1 H11 1.4392 113.93 -122.98 108.75 1.1018 +IC O1 C2 *C1 H12 1.4392 113.93 120.60 107.90 1.1015 + + +!! PATCHES for the disaccharides !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +! diaxial 1<->1 linkage use for alpha,alpha(1<->1) trehalose +! crystals used for TREHAL03, YOXFOG, YOXFUM +PRES 11aa 0.22 ! axial to C1 and axial to C1' 1<->1 +dele atom 1HO1 +dele atom 2O1 +dele atom 2HO1 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O1 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C1 1.4759 106.06 103.46 121.25 1.4128 +IC 1C1 1O1 2C1 2O5 1.3408 121.25 103.54 107.68 1.4504 +IC 1O1 2C1 2O5 2C5 1.4128 107.68 64.56 108.29 1.4499 +IC 2O5 1O1 *2C1 2H1 1.4504 107.68 -109.80 112.98 1.0897 + +!axial-equatorial 1<->1 linkage for alpha,beta(1<->1) trehalose +! crystal used for TIQDUS +PRES 11ab 0.22 ! axial to C1 and equat to C1' 1<->1 +dele atom 1HO1 +dele atom 2O1 +dele atom 2HO1 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O1 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C1 1.4879 109.36 121.75 114.93 1.3543 +IC 1C1 1O1 2C1 2O5 1.4072 114.93 51.80 105.04 1.4974 +IC 1O1 2C1 2O5 2C5 1.3543 105.04 167.51 110.75 1.4328 +IC 2O5 1O1 *2C1 2H1 1.4974 105.04 111.19 99.50 1.1284 + +! equatorial-equatorial 1<->1 linkage for beta,beta (1<->) trehalose +! crystal disaccharide used for WACHOX +PRES 11bb 0.22 ! equat to C1 and equat to C1' 1<->1 +dele atom 1HO1 +dele atom 2O1 +dele atom 2HO1 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O1 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C1 1.4568 111.54 -56.58 115.54 1.3686 +IC 1C1 1O1 2C1 2O5 1.3693 115.54 -79.64 103.31 1.4023 +IC 1O1 2C1 2O5 2C5 1.3686 103.31 172.18 110.20 1.4519 +IC 2O5 1O1 *2C1 2H1 1.4023 103.31 127.53 109.38 1.0973 + +! axial-axial 1->2 linkage +! use for FABYOW axial mannopyranose +PRES 12aa 0.02 ! (i)1->2(i-1) axial at C1 and axial at C2 +dele atom 1HO2 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C2 CC3161 0.09 ! +ATOM 1O2 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O2 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C1 1C2 1O2 2C1 1.4748 111.74 -132.81 112.92 1.4036 ! psi +IC 1C2 1O2 2C1 2O5 1.4675 112.92 47.16 109.48 1.4290 ! phi +IC 2O5 1O2 *2C1 2C2 1.4290 109.48 124.60 110.70 1.5068 +IC 2O5 1O2 *2C1 2H1 1.4290 109.48 -116.61 107.55 1.1057 + +! axial-equatorial 1->2 linkage +! use for RESMOR alpha mannose (1->2) beta glucose +PRES 12ab 0.02 ! (i)1->2(i-1) axial at C1 and equatorial at C2 +dele atom 1HO2 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C2 CC3161 0.09 ! +ATOM 1O2 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O2 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C1 1C2 1O2 2C1 1.5772 113.82 115.32 117.71 1.4039 ! psi +IC 1C2 1O2 2C1 2O5 1.4740 117.71 86.93 109.52 1.3790 ! phi +IC 2O5 1O2 *2C1 2C2 1.3790 109.52 124.61 110.68 1.5068 +IC 2O5 1O2 *2C1 2H1 1.3790 109.52 -116.62 107.54 1.1057 + +! equatorial-axial 1->2 linkage +PRES 12ba 0.02 ! (i)1->2(i-1) equatorial at C1 and axial at C2 +dele atom 1HO2 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C2 CC3161 0.09 ! +ATOM 1O2 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O2 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C1 1C2 1O2 2C1 1.4742 111.77 -132.78 118.52 1.3902 ! psi +IC 1C2 1O2 2C1 2O5 1.5137 118.52 -168.07 108.63 1.4500 ! phi +IC 2O5 1O2 *2C1 2C2 1.4500 108.63 -122.09 110.89 1.5316 +IC 2O5 1O2 *2C1 2H1 1.4500 108.63 121.92 111.32 1.0837 + +! equatorial-equatorial 1->2 linkage +PRES 12bb 0.02 ! (i)1->2(i-1) equatorial at C1 and equatorial at C2 +dele atom 1HO2 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C2 CC3161 0.09 ! +ATOM 1O2 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O2 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C1 1C2 1O2 2C1 1.5351 110.95 117.14 118.52 1.3902 ! psi +IC 1C2 1O2 2C1 2O5 1.5137 118.52 -168.07 108.63 1.4500 ! phi +IC 2O5 1O2 *2C1 2C2 1.4500 108.63 -122.09 110.89 1.5316 +IC 2O5 1O2 *2C1 2H1 1.4500 108.63 121.92 111.32 1.0837 + +! axial-axial 1->3 linkage +PRES 13aa 0.02 ! (i)1->3(i-1) axial at C1 and axial at C3 +dele atom 1HO3 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C3 CC3161 0.09 ! +ATOM 1O3 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O3 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1C3 1O3 2C1 1.5128 108.83 113.29 116.91 1.4039 ! psi +IC 1C3 1O3 2C1 2O5 1.5110 116.91 65.46 109.52 1.4630 ! phi +IC 2O5 1O3 *2C1 2C2 1.4630 109.52 124.61 110.68 1.5068 +IC 2O5 1O3 *2C1 2H1 1.4630 109.52 -116.62 107.54 1.1057 + +!axial-equatorial 1->3 linkage +! nigerose MOGLPR +PRES 13ab 0.02 ! (i)1->3(i-1) axial at C1 and equatorial at C3 +dele atom 1HO3 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C3 CC3161 0.09 ! +ATOM 1O3 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O3 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1C3 1O3 2C1 1.5353 112.07 -141.32 116.91 1.4039 ! psi +IC 1C3 1O3 2C1 2O5 1.5110 116.91 65.46 109.52 1.4630 ! phi +IC 2O5 1O3 *2C1 2C2 1.4630 109.52 124.61 110.68 1.5068 +IC 2O5 1O3 *2C1 2H1 1.4630 109.52 -116.62 107.54 1.1057 + +!equatorial-axial 1->3 linkage +PRES 13ba 0.02 ! (i)1->3(i-1) equatorial at C1 and axial at C3 +dele atom 1HO3 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C3 CC3161 0.09 ! +ATOM 1O3 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O3 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1C3 1O3 2C1 1.4976 117.50 -131.68 120.58 1.3902 ! psi +IC 1C3 1O3 2C1 2O5 1.4319 120.58 -100.16 108.63 1.4470 ! phi +IC 2O5 1O3 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316 +IC 2O5 1O3 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837 + +! equatorial (1->3) linkage +! LAMBIO3 beta glucose (1->3) beta glucose +PRES 13bb 0.02 ! (i)1->3(i-1) equatorial at C1 and equatorial at C3 +dele atom 1HO3 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C3 CC3161 0.09 ! +ATOM 1O3 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O3 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1C3 1O3 2C1 1.5129 108.83 -131.68 123.77 1.3902 ! psi +IC 1C3 1O3 2C1 2O5 1.4801 123.77 -130.16 108.63 1.4780 ! phi +IC 2O5 1O3 *2C1 2C2 1.4780 108.63 -122.09 110.89 1.5316 +IC 2O5 1O3 *2C1 2H1 1.4780 108.63 121.92 111.32 1.0837 + +! axial-axial 1->4 linkage +! use when both units are galactose +! CITSIH10 +PRES 14aa 0.02 ! (i)1->4(i-1) axial at C1 and axial at C4 +dele atom 1HO4 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C4 CC3161 0.09 ! +ATOM 1O4 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O4 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C3 1C4 1O4 2C1 1.5075 110.40 -86.29 119.44 1.4036 ! psi +IC 1C4 1O4 2C1 2O5 1.4716 119.44 133.57 109.48 1.4490 ! phi +IC 2O5 1O4 *2C1 2C2 1.4490 109.48 124.57 110.72 1.5065 +IC 2O5 1O4 *2C1 2H1 1.4490 109.48 -116.61 107.55 1.1057 + + +! axial-equatorial 1->4 linkage +! use for MALTOS11 +PRES 14ab 0.02 ! (i)1->4(i-1) axial at C1 and equatorial at C4 +dele atom 1HO4 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C4 CC3161 0.09 ! +ATOM 1O4 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O4 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C3 1C4 1O4 2C1 1.5010 117.73 72.71 118.66 1.4036 ! psi +IC 1C4 1O4 2C1 2O5 1.4919 118.66 48.64 109.48 1.4570 ! phi +IC 2O5 1O4 *2C1 2C2 1.4570 109.48 124.57 110.72 1.5065 +IC 2O5 1O4 *2C1 2H1 1.4570 109.48 -116.61 107.55 1.1057 + +! equatorial-axial 1->4 linkage +PRES 14ba 0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4 +dele atom 1HO4 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C4 CC3161 0.09 ! +ATOM 1O4 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O4 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C3 1C4 1O4 2C1 1.5071 110.40 -86.30 121.00 1.3902 ! psi +IC 1C4 1O4 2C1 2O5 1.4560 121.00 -130.97 108.63 1.4470 ! phi +IC 2O5 1O4 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316 +IC 2O5 1O4 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837 + +! equatorial-equatorial 1->4 linkage +! LACTOS03, EYOCUQ01, CELLOB01 +PRES 14bb 0.02 ! (i)1->4(i-1) equatorial at C1 and equatorial at C4 +dele atom 1HO4 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C4 CC3161 0.09 ! +ATOM 1O4 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O4 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C3 1C4 1O4 2C1 1.5009 110.76 81.86 121.00 1.3902 ! psi +IC 1C4 1O4 2C1 2O5 1.4560 121.00 -130.97 108.63 1.4470 ! phi +IC 2O5 1O4 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316 +IC 2O5 1O4 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837 + +! axial-equatorial 1->6 linkage +! MELBM01 +! galactose and glucose +! alpha,beta mellibiose hydrate +PRES 16ab -0.07 ! (i)1->6(i-1) axial at C1 and equatorial at C6 +dele atom 1HO6 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C6 CC321 0.00 ! +ATOM 1O6 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O6 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C5 1C6 1O6 2C1 1.5266 104.41 178.98 111.56 1.4036 ! PSI +IC 1C6 1O6 2C1 2O5 1.4492 111.56 71.24 109.48 1.4270 ! PHI +IC 2O5 1O6 *2C1 2C2 1.4270 109.48 124.57 110.72 1.5065 +IC 2O5 1O6 *2C1 2H1 1.4270 109.48 -116.57 107.58 1.1054 +!IC 1O6 2C1 2O5 2C5 1.4036 109.48 66.50 112.10 1.4061 +!IC 1O6 2C1 2C2 2C3 1.4036 110.72 -67.90 109.19 1.5200 + +! equatorial-equatorial 1->6 linkage +! GENTBSO1 +PRES 16bb -0.07 ! (i)1->6(i-1) equatorial at C1 and equatorial at C6 +dele atom 1HO6 +dele atom 2HO1 +dele atom 2O1 +ATOM 1C6 CC321 0.00 ! +ATOM 1O6 OC301 -0.36 ! +ATOM 2C1 CC3162 0.29 ! +BOND 1O6 2C1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C5 1C6 1O6 2C1 1.5616 105.37 172.71 113.93 1.3902 ! PSI +IC 1C6 1O6 2C1 2O5 1.4311 113.93 -63.49 108.63 1.4110 ! PHI +IC 2O5 1O6 *2C1 2C2 1.4110 108.63 -122.09 110.89 1.5316 +IC 2O5 1O6 *2C1 2H1 1.4110 108.63 121.92 111.32 1.0837 +IC 1O6 2C1 2O5 2C5 1.3902 108.63 176.53 113.95 1.4709 +IC 1O6 2C1 2C2 2C3 1.3902 110.89 178.57 113.29 1.4987 + +!!!!!!!!!!!!!!!!!!! +! O-alkyl patches ! +!!!!!!!!!!!!!!!!!!! +PRES OMEA 0.11 ! og adding axial O-methyl to C1 on pyranose +dele atom HO1 +ATOM C1 CC3162 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +BOND O1 CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C1 O1 CM 1.4477 109.89 66.08 108.74 1.4244 +IC C1 O1 CM HM1 1.4355 108.74 59.11 111.44 1.0883 +IC HM1 O1 *CM HM2 1.0883 111.44 119.69 113.64 1.0586 +IC HM3 O1 *CM HM2 1.1131 110.64 -122.99 113.64 1.0586 + +PRES OMEB 0.11 ! og add equatorial O-methyl to C1 on pyranose +dele atom HO1 +ATOM C1 CC3162 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +BOND O1 CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O5 C1 O1 CM 1.4138 114.30 -66.36 108.55 1.4077 +IC C1 O1 CM HM1 1.4353 108.55 41.11 109.39 1.0734 +IC HM1 O1 *CM HM2 1.0734 109.39 129.90 119.45 1.0441 +IC HM3 O1 *CM HM2 1.1148 107.24 -121.74 119.45 1.0441 + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +! O-alkyl patches for furanose ! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +PRES OMEF 0.20 ! erh adding an O-methyl to C1 on THF +dele atom H1A +ATOM C1 CC312C 0.29 ! +ATOM H1B HCA1C2 0.09 ! +ATOM OM OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +BOND C1 OM OM CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O1 C1 OM CM 1.4477 109.89 66.08 108.74 1.4244 +IC C1 OM CM HM1 1.4355 108.74 59.11 111.44 1.0883 +IC HM1 OM *CM HM2 1.0883 111.44 119.69 113.64 1.0586 +IC HM3 OM *CM HM2 1.1131 110.64 -122.99 113.64 1.0586 + + +PRES FOMEA 0.11 ! erh adding alpha O-methyl to C1 on aldopentose +dele atom HO1 +ATOM C1 CC3152 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +BOND O1 CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O4 C1 O1 CM 1.4477 109.89 66.08 108.74 1.4244 +IC C1 O1 CM HM1 1.4355 108.74 59.11 111.44 1.0883 +IC HM1 O1 *CM HM2 1.0883 111.44 119.69 113.64 1.0586 +IC HM3 O1 *CM HM2 1.1131 110.64 -122.99 113.64 1.0586 + +PRES FOMEB 0.11 ! erh add beta O-methyl to C1 on aldopentose +dele atom HO1 +ATOM C1 CC3152 0.29 ! +ATOM O1 OC301 -0.36 ! +ATOM CM CC331 -0.09 ! +ATOM HM1 HCA3 0.09 ! +ATOM HM2 HCA3 0.09 ! +ATOM HM3 HCA3 0.09 ! +BOND O1 CM +BOND CM HM1 CM HM2 CM HM3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O4 C1 O1 CM 1.4138 114.30 -66.36 108.55 1.4077 +IC C1 O1 CM HM1 1.4353 108.55 41.11 109.39 1.0734 +IC HM1 O1 *CM HM2 1.0734 109.39 129.90 119.45 1.0441 +IC HM3 O1 *CM HM2 1.1148 107.24 -121.74 119.45 1.0441 + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!PATCHES for the pyranose-furanose mixed di/polysaccharides !! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +PRES SUCR 0.00 ! pram; make sucrose, apply to AGLC,BFRU +dele atom 1HO1 +dele atom 2O2 +dele atom 2HO2 +GROU +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C2 CC3051 0.38 ! +ATOM 1H1 HCA1 0.09 ! +ATOM 1C5 CC3163 0.11 ! +ATOM 1H5 HCA1 0.09 ! +ATOM 1O5 OC3C61 -0.40 ! +ATOM 2O5 OC3C51 -0.40 ! +ATOM 2C5 CC3153 0.11 ! +ATOM 2H5 HCA1 0.09 ! +BOND 1O1 2C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C2 1.4300 108.97 106.13 115.17 1.4632 +IC 1C1 1O1 2C2 2O5 1.4159 115.17 -47.60 114.57 1.3880 +IC 1O1 2C2 2O5 2C5 1.4632 114.57 -100.55 109.86 1.4233 +IC 2O5 1O1 *2C2 2C1 1.3880 114.57 121.04 106.87 1.5052 + +PRES LCTL 0.02 ! pram; make lactulose, apply to BGAL,BFRU +dele atom 1HO1 +dele atom 2O4 +dele atom 2HO4 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC303 -0.36 ! +ATOM 2C4 CC3151 0.09 ! +BOND 1O1 2C4 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C4 1.4515 114.15 -92.26 115.45 1.4008 +IC 1C1 1O1 2C4 2C5 1.4006 115.45 176.86 109.78 1.5389 +IC 1O1 2C4 2C5 2O5 1.4008 109.78 -135.17 108.07 1.4194 +IC 2C5 1O1 *2C4 2H4 1.5389 109.78 128.08 113.16 1.1120 + +PRES MELZ 0.33 ! pram; make melezitose, apply to AGLC,BFRU,AGLC +dele atom 1HO1 +dele atom 2O2 +dele atom 2HO2 +dele atom 3HO1 +dele atom 2O3 +dele atom 2HO3 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C2 CC3051 0.38 ! +ATOM 3C1 CC3162 0.29 ! +ATOM 3O1 OC303 -0.36 ! +ATOM 2C3 CC3151 0.09 ! +BOND 1O1 2C2 3O1 2C3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C2 1.4864 115.30 91.81 110.86 1.4247 +IC 1C1 1O1 2C2 2O5 1.3862 110.86 -33.24 115.81 1.4155 +IC 1O1 2C2 2O5 2C5 1.4247 115.81 -114.00 113.57 1.4046 +IC 2O5 1O1 *2C2 2C1 1.4155 115.81 122.86 110.13 1.5127 +IC 3O5 3C1 3O1 2C3 1.4242 109.54 96.75 115.32 1.4214 +IC 3C1 3O1 2C3 2C2 1.3627 115.32 -102.67 124.93 1.5043 +IC 3O1 2C3 2C4 2C5 1.4214 104.97 169.79 101.69 1.5772 +IC 2C4 3O1 *2C3 2H3 1.5070 104.97 -120.20 108.70 1.1059 + +PRES RAFF 0.24 ! pram; make raffinose, apply to AGLC,BFRU,AGAL +dele atom 1HO1 +dele atom 1O6 +dele atom 1HO6 +dele atom 2O2 +dele atom 2HO2 +dele atom 3HO1 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C2 CC3051 0.38 ! +ATOM 1C6 CC321 0.00 ! +ATOM 3O1 OC301 -0.36 ! +ATOM 3C1 CC3162 0.29 ! +BOND 1O1 2C2 3O1 1C6 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C2 1.4330 109.61 95.81 116.11 1.4566 +IC 1C1 1O1 2C2 2O5 1.4462 116.11 -7.56 118.83 1.4392 +IC 1O1 2C2 2O5 2C5 1.4566 118.83 -122.51 107.48 1.4250 +IC 2O5 1O1 *2C2 2C1 1.4392 118.83 114.24 111.93 1.5251 +IC 3O1 1H62 *1C6 1H61 1.4658 106.63 -109.22 114.93 1.0580 +IC 3O1 1C5 *1C6 1H62 1.4658 110.09 -115.22 106.51 1.1198 +IC 1C4 1C5 1C6 3O1 1.5349 110.61 64.23 110.09 1.4658 +IC 1C5 1C6 3O1 3C1 1.5047 110.09 -175.22 104.45 1.4109 +IC 1C6 3O1 3C1 3O5 1.4658 104.45 63.16 116.89 1.4028 +IC 3O5 3O1 *3C1 3C2 1.4028 116.89 119.18 104.50 1.5720 +IC 3O5 3O1 *3C1 3H1 1.4028 116.89 -127.41 115.53 1.1554 +IC 3O1 3C1 3O5 3C5 1.4109 116.89 52.69 110.57 1.4526 +IC 3O1 3C1 3C2 3C3 1.4109 104.50 -59.33 109.43 1.4788 + +PRES KES 0.33 ! pram; make Kestose, apply to AGLC,BFRU,BFRU +dele atom 1HO1 +dele atom 2O2 +dele atom 2HO2 +dele atom 2HO1 +dele atom 3O2 +dele atom 3HO2 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C2 CC3051 0.38 ! +ATOM 2C1 CC321 0.00 ! +ATOM 2O1 OC301 -0.36 ! +ATOM 3C2 CC3051 0.38 ! +BOND 1O1 2C2 2O1 3C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C2 1.4008 113.50 51.54 123.30 1.4618 +IC 1C1 1O1 2C2 2O5 1.4074 123.30 -54.14 116.69 1.4213 +IC 1O1 2C2 2O5 2C5 1.4618 116.69 -109.67 107.68 1.4768 +IC 2O5 1O1 *2C2 2C1 1.4213 116.69 130.90 107.46 1.4777 +IC 2O5 2C2 2C1 2O1 1.4213 115.04 -169.03 107.87 1.4427 +IC 2C2 2C1 2O1 3C2 1.4777 107.87 179.88 117.21 1.4349 +IC 2C1 2O1 3C2 3O5 1.4427 117.21 -39.67 121.12 1.4697 +IC 3O5 2O1 *3C2 3C1 1.4697 121.12 128.11 106.14 1.5693 + +PRES 6KES 0.33 ! pram; make 6-Kestose, apply to AGLC,BFRU,BFRU +dele atom 1HO1 +dele atom 2O2 +dele atom 2HO2 +dele atom 2HO6 +dele atom 3O2 +dele atom 3HO2 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C2 CC3051 0.38 ! +ATOM 2C6 CC321 0.00 ! +ATOM 2O6 OC301 -0.36 ! +ATOM 3C2 CC3051 0.38 ! +BOND 1O1 2C2 2O6 3C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C2 1.4445 117.22 61.40 115.79 1.4090 +IC 1C1 1O1 2C2 2O5 1.3966 115.79 -64.84 114.77 1.4404 +IC 1O1 2C2 2O5 2C5 1.4090 114.77 -124.86 109.61 1.4501 +IC 2O5 1O1 *2C2 2C1 1.4404 114.77 117.26 113.37 1.4838 +IC 2O5 2C5 2C6 2O6 1.4501 109.89 62.56 105.75 1.3648 +IC 2C5 2C6 2O6 3C2 1.5298 105.75 153.21 114.75 1.3764 +IC 2C6 2O6 3C2 3O5 1.3648 114.75 -57.88 109.92 1.4329 +IC 3O5 2O6 *3C2 3C1 1.4329 109.92 120.58 116.21 1.5692 + +PRES IMAL -0.07 ! pram; make isomaltulose, apply to AGLC,BFRU +dele atom 1HO1 +dele atom 2O6 +dele atom 2HO6 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC301 -0.36 ! +ATOM 2C6 CC321 0.00 ! +BOND 1O1 2C6 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C6 1.4274 113.06 68.37 118.23 1.4620 +IC 1C1 1O1 2C6 2C5 1.3693 118.23 161.18 106.41 1.459 +IC 1O1 2C6 2C5 2O5 1.4620 106.41 -63.39 106.10 1.4004 +IC 1O1 2C5 *2C6 2H61 1.4620 106.41 120.34 105.02 1.1560 +IC 1O1 2C5 *2C6 2H62 1.4620 106.41 -121.07 110.94 1.1468 + +PRES PLAN 0.24 ! pram; make PLANTE, apply to AGLC,BFRU,AGAL +dele atom 1HO1 +dele atom 2O2 +dele atom 2HO2 +dele atom 2O6 +dele atom 2HO6 +dele atom 3HO1 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C2 CC3051 0.38 ! +ATOM 2C6 CC321 0.00 ! +ATOM 3O1 OC301 -0.36 ! +ATOM 3C1 CC3162 0.29 ! +BOND 1O1 2C2 2C6 3O1 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C2 1.3822 114.36 80.45 120.43 1.4309 +IC 1C1 1O1 2C2 2O5 1.4567 120.43 5.53 119.11 1.4042 +IC 1O1 2C2 2O5 2C5 1.4309 119.11 -113.52 105.95 1.4748 +IC 2O5 1O1 *2C2 2C1 1.4042 119.11 108.56 105.90 1.5178 +IC 3O5 3C1 3O1 2C6 1.4274 111.54 61.62 112.57 1.4221 +IC 3C1 3O1 2C6 2C5 1.4012 112.57 176.39 106.00 1.5319 +IC 3O1 2C6 2C5 2O5 1.4221 106.00 45.34 112.96 1.4748 +IC 2O5 2C6 *2C5 2C4 1.4748 112.96 124.92 112.86 1.5581 +IC 3O1 2C5 *2C6 2H61 1.4221 106.00 -118.01 104.37 1.1089 +IC 3O1 2C5 *2C6 2H62 1.4221 106.00 126.30 110.67 1.0701 + +PRES PEKH 0.35 ! pram; make nystose, apply to AGLC,BFRU,BFRU,BFRU +dele atom 1HO1 +dele atom 2O2 +dele atom 2HO2 +dele atom 2HO1 +dele atom 3O2 +dele atom 3HO2 +dele atom 3HO1 +dele atom 4O2 +dele atom 4HO2 +ATOM 1C1 CC3162 0.29 ! +ATOM 1O1 OC302 -0.36 ! +ATOM 2C2 CC3051 0.38 ! +ATOM 2C1 CC321 0.00 ! +ATOM 2O1 OC301 -0.36 ! +ATOM 3C2 CC3051 0.38 ! +ATOM 3C1 CC321 0.00 ! +ATOM 3O1 OC301 -0.36 ! +ATOM 4C2 CC3051 0.38 ! +BOND 1O1 2C2 2O1 3C2 3O1 4C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O5 1C1 1O1 2C2 1.4165 109.15 106.82 122.56 1.4247 +IC 1C1 1O1 2C2 2O5 1.4014 122.56 -34.45 110.08 1.4075 +IC 1O1 2C2 2O5 2C5 1.4247 110.08 -98.88 111.59 1.4556 +IC 2O5 1O1 *2C2 2C1 1.4075 110.08 118.32 105.91 1.4725 +IC 2O5 2C2 2C1 2O1 1.4075 109.54 -83.81 110.44 1.4230 +IC 2C2 2C1 2O1 3C2 1.4725 110.44 -118.43 114.35 1.4027 +IC 2C1 2O1 3C2 3O5 1.4230 114.35 60.09 106.32 1.3911 +IC 3O5 2O1 *3C2 3C1 1.3911 106.32 111.99 105.47 1.4987 +IC 3O5 3C2 3C1 3O1 1.3911 105.74 176.59 108.46 1.4315 +IC 3C2 3C1 3O1 4C2 1.4987 108.46 -155.94 114.02 1.3926 +IC 3C1 3O1 4C2 4O5 1.4315 114.02 -48.90 115.91 1.3891 +IC 4O5 3O1 *4C2 4C1 1.3891 115.91 127.06 108.05 1.5197 + +PRES AR15 0.04 ! pram; make 1->5 arabinose disac, apply to AARB,AARB +dele atom 1HO1 ! angl and dihe params associated in this linkage have not been explicitly validated +dele atom 2O5 ! using crystals. crystal validation was done on fructofuranose based di/poly-saccharides +dele atom 2HO5 +dele atom 2HO1 +ATOM 1C1 CC3152 0.29 ! +ATOM 1O1 OC301 -0.36 ! +ATOM 2C5 CC321 0.00 ! +ATOM 2C1 CC3152 0.29 ! +ATOM 2O1 OC301 -0.36 ! +ATOM 2CM CC331 -0.09 ! +ATOM 2HM1 HCA3 0.09 ! +ATOM 2HM2 HCA3 0.09 ! +ATOM 2HM3 HCA3 0.09 ! +BOND 2O1 2CM +BOND 2CM 2HM1 2CM 2HM2 2CM 2HM3 +BOND 1O1 2C5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O4 1C1 1O1 2C5 1.4560 110.35 75.44 112.98 1.4384 +IC 1C1 1O1 2C5 2C4 1.3759 112.98 148.61 111.00 1.4291 +IC 1O1 2C5 2C4 2O4 1.4384 111.00 -56.56 107.21 1.4617 +IC 1O1 2C4 *2C5 2H51 1.4384 111.00 113.48 107.52 1.1042 +IC 1O1 2C4 *2C5 2H52 1.4384 111.00 -131.84 115.17 1.1078 +IC 2O4 2C1 2O1 2CM 1.3550 111.42 63.88 112.58 1.4052 +IC 2C1 2O1 2CM 2HM1 1.4614 112.58 56.64 111.38 1.1703 +IC 2HM1 2O1 *2CM 2HM2 1.1703 111.38 121.40 109.42 1.0655 +IC 2HM3 2O1 *2CM 2HM2 1.1108 108.98 -117.32 109.42 1.0655 + +PRES AB15 -0.07 ! pram; make 1->5 arabinose disac without methylation, apply to AARB,AARB +dele atom 1HO1 ! angl and dihe params associated in this linkage have not been explicitly validated +dele atom 2O5 ! using crystals. crystal validation was done on fructofuranose based di/poly-saccharides +dele atom 2HO5 +ATOM 1C1 CC3152 0.29 ! +ATOM 1O1 OC301 -0.36 ! +ATOM 2C5 CC321 0.00 ! +BOND 1O1 2C5 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1O4 1C1 1O1 2C5 1.4560 110.35 75.44 112.98 1.4384 +IC 1C1 1O1 2C5 2C4 1.3759 112.98 148.61 111.00 1.4291 +IC 1O1 2C5 2C4 2O4 1.4384 111.00 -56.56 107.21 1.4617 +IC 1O1 2C4 *2C5 2H51 1.4384 111.00 113.48 107.52 1.1042 +IC 1O1 2C4 *2C5 2H52 1.4384 111.00 -131.84 115.17 1.1078 + + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!! PATCHES for sialic acid-containing saccharides !!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + +PRES sa23e 0.01 ! og sialic acid alpha 2->3 equatorial +dele atom 1HO3 +dele atom 2HO2 +dele atom 2O2 +ATOM 1C3 CC3161 0.09 ! +ATOM 1O3 OC301 -0.36 ! +ATOM 2C2 CC3062 0.28 ! +BOND 1O3 2C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C2 1C3 1O3 2C2 1.5353 112.07 -141.32 116.91 1.4039 ! psi +IC 1C3 1O3 2C2 2O6 1.5110 116.91 -65.46 109.52 1.4630 ! phi +IC 2O6 1O3 *2C2 2C3 1.4630 109.52 124.61 110.68 1.5068 +IC 2O6 1O3 *2C2 2C1 1.4630 109.52 -116.62 107.54 1.1057 + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!! PATCHES for phosphorylated inositols (the PIPs) !!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +! patches to make PIP2 and PIP3 charge variants; PO4 or PO4H at inositol C3,C4,C5 +! charges and chemical types based on patches from sairam in toppar_allxx_sugar_model.str + +PRES I3P1 -1.00 ! add PO4H at C3 of inositol +DELE ATOM HO3 +GROUP +ATOM C13 CC3161 0.01 ! +ATOM H3 HCA1 0.09 ! axial Hydrogen +ATOM O3 OC30P -0.62 ! +ATOM P3 PC 1.50 ! +ATOM OP32 OC312 -0.68 ! +ATOM OP33 OC2DP -0.82 ! C15 +ATOM OP34 OC2DP -0.82 ! \ +ATOM H32 HCP1 0.34 ! C14 + ! / + ! / + ! C12------C13 + ! /\ + ! H3 O3 + ! | + ! (-)OP34--P3--OP33(-) + ! | + ! OP32--H32 +BOND O3 P3 OP32 P3 OP33 P3 OP34 P3 OP32 H32 +!Thermalized IC +IC C15 C14 C13 O3 1.5364 112.47 -174.92 109.44 1.4102 +IC C14 O3 *C13 H3 1.5323 109.44 -120.96 109.46 1.1223 +IC C14 C13 O3 P3 1.5323 109.44 -84.54 127.66 1.5968 +IC C13 O3 P3 OP32 1.4102 127.66 -174.21 102.94 1.5071 +IC O3 OP32 *P3 OP33 1.5968 102.94 113.03 118.81 1.5471 +IC O3 OP32 *P3 OP34 1.5968 102.94 -113.60 109.37 1.4811 +IC O3 P3 OP32 H32 1.6634 92.04 17.38 110.00 0.9486 + +PRES I3P2 -2.00 ! add PO4 at C3 of inositol +DELE ATOM HO3 +GROUP +ATOM C13 CC3161 -0.09 ! +ATOM H3 HCA1 0.09 ! axial Hydrogen +ATOM O3 OC30P -0.40 ! +ATOM P3 PC 1.10 ! +ATOM OP32 OC2DP -0.90 ! +ATOM OP33 OC2DP -0.90 ! C15 +ATOM OP34 OC2DP -0.90 ! \ + ! C14 + ! / + ! / + ! C12------C13 + ! /\ + ! H3 O3 + ! | + ! (-)OP34--P3--OP33(-) + ! | + ! OP32(-) +BOND O3 P3 OP32 P3 OP33 P3 OP34 P3 +!Thermalized IC +IC C15 C14 C13 O3 1.5364 112.47 -174.92 109.44 1.4102 +IC C14 O3 *C13 H3 1.5323 109.44 -120.96 109.46 1.1223 +IC C14 C13 O3 P3 1.5323 109.44 -84.54 127.66 1.5968 +IC C13 O3 P3 OP32 1.4102 127.66 -174.21 102.94 1.5071 +IC O3 OP32 *P3 OP33 1.5968 102.94 113.03 118.81 1.5471 +IC O3 OP32 *P3 OP34 1.5968 102.94 -113.60 109.37 1.4811 + +PRES I4P1 -1.00 ! add PO4H at C4 of inositol +DELE ATOM HO4 +GROUP +ATOM C14 CC3161 0.01 ! +ATOM H4 HCA1 0.09 ! axial Hydrogen +ATOM O4 OC30P -0.62 ! +ATOM P4 PC 1.50 ! +ATOM OP42 OC312 -0.68 ! +ATOM OP43 OC2DP -0.82 ! C16 +ATOM OP44 OC2DP -0.82 ! \ +ATOM H42 HCP1 0.34 ! C15 + ! / + ! / + ! C13-----C14 + ! /\ + ! H4 O4 + ! | + ! (-)O44--P4--O43(-) + ! | + ! O42--H42 +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 OP42 H42 +!Thermalized IC +IC C16 C15 C14 O4 1.5364 112.47 -174.92 109.44 1.4102 +IC C15 O4 *C14 H4 1.5323 109.44 -120.96 109.46 1.1223 +IC C15 C14 O4 P4 1.5323 109.44 -84.54 127.66 1.5968 +IC C14 O4 P4 OP42 1.4102 127.66 -174.21 102.94 1.5071 +IC O4 OP42 *P4 OP43 1.5968 102.94 113.03 118.81 1.5471 +IC O4 OP42 *P4 OP44 1.5968 102.94 -113.60 109.37 1.4811 +IC O4 P4 OP42 H42 1.6634 92.04 17.38 110.00 0.9486 + +PRES I4P2 -2.00 ! add PO4 at C4 of inositol +DELE ATOM HO4 +GROUP +ATOM C14 CC3161 -0.09 ! +ATOM H4 HCA1 0.09 ! axial Hydrogen +ATOM O4 OC30P -0.40 ! +ATOM P4 PC 1.10 ! +ATOM OP42 OC2DP -0.90 ! +ATOM OP43 OC2DP -0.90 ! C16 +ATOM OP44 OC2DP -0.90 ! \ + ! C15 + ! / + ! / + ! C13-----C14 + ! /\ + ! H4 O4 + ! | + ! (-)O44--P4--O43(-) + ! | + ! O42(-) +BOND O4 P4 OP42 P4 OP43 P4 OP44 P4 +!Thermalized IC +IC C16 C15 C14 O4 1.5364 112.47 -174.92 109.44 1.4102 +IC C15 O4 *C14 H4 1.5323 109.44 -120.96 109.46 1.1223 +IC C15 C14 O4 P4 1.5323 109.44 -84.54 127.66 1.5968 +IC C14 O4 P4 OP42 1.4102 127.66 -174.21 102.94 1.5071 +IC O4 OP42 *P4 OP43 1.5968 102.94 113.03 118.81 1.5471 +IC O4 OP42 *P4 OP44 1.5968 102.94 -113.60 109.37 1.4811 + +PRES I5P1 -1.00 ! add PO4H at C5 of inositol +DELE ATOM HO5 +GROUP +ATOM C15 CC3161 0.01 ! +ATOM H5 HCA1 0.09 ! axial Hydrogen +ATOM O5 OC30P -0.62 ! +ATOM P5 PC 1.50 ! +ATOM OP52 OC312 -0.68 ! +ATOM OP53 OC2DP -0.82 ! C11 +ATOM OP54 OC2DP -0.82 ! \ +ATOM H52 HCP1 0.34 ! C16 + ! / + ! / + ! C14-----C15 + ! /\ + ! H5 O5 + ! | + ! (-)OP54--P5--OP53(-) + ! | + ! OP52--H52 +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 OP52 H52 +!Thermalized IC +IC C11 C16 C16 O5 1.5364 112.47 -174.92 109.44 1.4102 +IC C16 O5 *C15 H5 1.5323 109.44 -120.96 109.46 1.1223 +IC C16 C15 O5 P5 1.5323 109.44 -84.54 127.66 1.5968 +IC C14 O5 P5 OP52 1.4102 127.66 -174.21 102.94 1.5071 +IC O5 OP52 *P5 OP53 1.5968 102.94 113.03 118.81 1.5471 +IC O5 OP52 *P5 OP54 1.5968 102.94 -113.60 109.37 1.4811 +IC O5 P5 OP52 H52 1.6634 92.04 17.38 110.00 0.9486 + +PRES I5P2 -2.00 ! add PO4 at C5 of inositol +DELE ATOM HO5 +GROUP +ATOM C15 CC3161 -0.09 ! +ATOM H5 HCA1 0.09 ! axial Hydrogen +ATOM O5 OC30P -0.40 ! +ATOM P5 PC 1.10 ! +ATOM OP52 OC2DP -0.90 ! +ATOM OP53 OC2DP -0.90 ! C11 +ATOM OP54 OC2DP -0.90 ! \ + ! C16 + ! / + ! / + ! C14-----C15 + ! /\ + ! H5 O5 + ! | + ! (-)OP54--P5--OP53(-) + ! | + ! OP52(-) +BOND O5 P5 OP52 P5 OP53 P5 OP54 P5 +!Thermalized IC +IC C11 C16 C16 O5 1.5364 112.47 -174.92 109.44 1.4102 +IC C16 O5 *C15 H5 1.5323 109.44 -120.96 109.46 1.1223 +IC C16 C15 O5 P5 1.5323 109.44 -84.54 127.66 1.5968 +IC C14 O5 P5 OP52 1.4102 127.66 -174.21 102.94 1.5071 +IC O5 OP52 *P5 OP53 1.5968 102.94 113.03 118.81 1.5471 +IC O5 OP52 *P5 OP54 1.5968 102.94 -113.60 109.37 1.4811 + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!! PATCHES for Sulphates by Sairam !!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +PRES SUF1A -0.80 ! Sulfate at alpha C1 position +dele atom HO1 + +GROUP +ATOM C1 CC3162 0.01 +ATOM H1 HCA1 0.09 +ATOM O1 OC30P -0.28 +ATOM S1 SC 1.33 +ATOM OS12 OC2DP -0.65 +ATOM OS13 OC2DP -0.65 +ATOM OS14 OC2DP -0.65 + +BOND O1 S1 OS12 S1 OS13 S1 OS14 S1 + +IC C5 O5 C1 O1 1.4305 111.50 63.93 108.22 1.4352 +IC O5 O1 *C1 H1 1.5613 108.22 -116.76 114.09 1.1193 +IC O5 C1 O1 S1 1.5613 108.22 131.56 117.57 1.5527 +IC C1 O1 S1 OS12 1.4352 117.57 177.25 104.11 1.4504 +IC O1 OS12 *S1 OS13 1.5527 104.11 112.40 113.72 1.4529 +IC O1 OS12 *S1 OS14 1.5527 104.11 -114.18 114.03 1.4500 + +PRES SUF1B -0.80 ! Sulfate at beta C1 position +dele atom HO1 + +GROUP +ATOM C1 CC3162 0.01 +ATOM H1 HCA1 0.09 +ATOM O1 OC30P -0.28 +ATOM S1 SC 1.33 +ATOM OS12 OC2DP -0.65 +ATOM OS13 OC2DP -0.65 +ATOM OS14 OC2DP -0.65 + +BOND O1 S1 OS12 S1 OS13 S1 OS14 S1 + +IC C5 O5 C1 O1 1.4305 111.50 174.93 108.22 1.4352 +IC O5 O1 *C1 H1 1.5613 108.22 116.76 114.09 1.1193 +IC O5 C1 O1 S1 1.5613 108.22 131.56 117.57 1.5527 +IC C1 O1 S1 OS12 1.4352 117.57 177.25 104.11 1.4504 +IC O1 OS12 *S1 OS13 1.5527 104.11 112.40 113.72 1.4529 +IC O1 OS12 *S1 OS14 1.5527 104.11 -114.18 114.03 1.4500 + +PRES SUF2A -1.00 ! Sulfate at axial C2 position +dele atom HO2 + +GROUP +ATOM C2 CC3161 -0.19 +ATOM H2 HCA1 0.09 +ATOM O2 OC30P -0.28 +ATOM S2 SC 1.33 +ATOM OS22 OC2DP -0.65 +ATOM OS23 OC2DP -0.65 +ATOM OS24 OC2DP -0.65 + +BOND O2 S2 OS22 S2 OS23 S2 OS24 S2 + +IC O5 C1 C2 O2 1.4305 111.50 -60.93 108.22 1.4352 +IC C1 O2 *C2 H2 1.5613 108.22 116.76 114.09 1.1193 +IC C1 C2 O2 S2 1.5613 108.22 131.56 117.57 1.5527 +IC C2 O2 S2 OS22 1.4352 117.57 177.25 104.11 1.4504 +IC O2 OS22 *S2 OS23 1.5527 104.11 112.40 113.72 1.4529 +IC O2 OS22 *S2 OS24 1.5527 104.11 -114.18 114.03 1.4500 + +PRES SUF2B -1.00 ! Sulfate at equitorial C2 position +dele atom HO2 + +GROUP +ATOM C2 CC3161 -0.19 +ATOM H2 HCA1 0.09 +ATOM O2 OC30P -0.28 +ATOM S2 SC 1.33 +ATOM OS22 OC2DP -0.65 +ATOM OS23 OC2DP -0.65 +ATOM OS24 OC2DP -0.65 + +BOND O2 S2 OS22 S2 OS23 S2 OS24 S2 + +IC O5 C1 C2 O2 1.4305 111.50 -170.93 108.22 1.4352 +IC C1 O2 *C2 H2 1.5613 108.22 -116.76 114.09 1.1193 +IC C1 C2 O2 S2 1.5613 108.22 131.56 117.57 1.5527 +IC C2 O2 S2 OS22 1.4352 117.57 177.25 104.11 1.4504 +IC O2 OS22 *S2 OS23 1.5527 104.11 112.40 113.72 1.4529 +IC O2 OS22 *S2 OS24 1.5527 104.11 -114.18 114.03 1.4500 + +PRES SUF3A -1.00 ! Sulfate at axial C3 position +dele atom HO3 + +GROUP +ATOM C3 CC3161 -0.19 +ATOM H3 HCA1 0.09 +ATOM O3 OC30P -0.28 +ATOM S3 SC 1.33 +ATOM OS32 OC2DP -0.65 +ATOM OS33 OC2DP -0.65 +ATOM OS34 OC2DP -0.65 + +BOND O3 S3 OS32 S3 OS33 S3 OS34 S3 + +IC C1 C2 C3 O3 1.5413 114.47 71.07 109.68 1.4364 +IC C2 O3 *C3 H3 1.5146 109.68 -119.48 114.05 1.1261 +IC C2 C3 O3 S3 1.5146 109.68 125.46 115.96 1.5805 +IC C3 O3 S3 OS32 1.4364 115.96 176.98 104.32 1.4471 +IC O3 OS32 *S3 OS33 1.5805 104.32 111.57 114.64 1.4516 +IC O3 OS32 *S3 OS34 1.5805 104.32 -111.89 114.79 1.4496 + +PRES SUF3B -1.00 ! Sulfate at equitorial C3 position +dele atom HO3 + +GROUP +ATOM C3 CC3161 -0.19 +ATOM H3 HCA1 0.09 +ATOM O3 OC30P -0.28 +ATOM S3 SC 1.33 +ATOM OS32 OC2DP -0.65 +ATOM OS33 OC2DP -0.65 +ATOM OS34 OC2DP -0.65 + +BOND O3 S3 OS32 S3 OS33 S3 OS34 S3 + +IC C1 C2 C3 O3 1.5397 112.35 179.14 111.07 1.4293 +IC C2 O3 *C3 H3 1.5217 111.07 115.81 106.51 1.1190 +IC C2 C3 O3 S3 1.5217 111.07 88.75 123.02 1.5789 +IC C3 O3 S3 OS32 1.4293 123.02 -165.25 103.14 1.4482 +IC O3 OS32 *S3 OS33 1.5789 103.14 111.60 114.04 1.4527 +IC O3 OS32 *S3 OS34 1.5789 103.14 -114.44 114.19 1.4494 + + +PRES SUF4A -1.00 ! Sulfate at axial C4 position +dele atom HO4 + +GROUP +ATOM C4 CC3161 -0.19 +ATOM H4 HCA1 0.09 +ATOM O4 OC30P -0.28 +ATOM S4 SC 1.33 +ATOM OS42 OC2DP -0.65 +ATOM OS43 OC2DP -0.65 +ATOM OS44 OC2DP -0.65 + +BOND O4 S4 OS42 S4 OS43 S4 OS44 S4 + +IC C2 C3 C4 O4 1.5156 110.32 -64.72 111.35 1.4312 +IC C3 O4 *C4 H4 1.5118 111.35 122.25 113.81 1.1233 +IC C3 C4 O4 S4 1.5118 111.35 -108.94 116.63 1.5860 +IC C4 O4 S4 OS42 1.4312 116.63 -179.91 103.62 1.4478 +IC O4 OS42 *S4 OS43 1.5860 103.62 111.53 114.38 1.4512 +IC O4 OS42 *S4 OS44 1.5860 103.62 -113.15 114.60 1.4494 + + +PRES SUF4B -1.00 ! Sulfate at equitorial C4 position +dele atom HO4 + +GROUP +ATOM C4 CC3161 -0.19 +ATOM H4 HCA1 0.09 +ATOM O4 OC30P -0.28 +ATOM S4 SC 1.33 +ATOM OS42 OC2DP -0.65 +ATOM OS43 OC2DP -0.65 +ATOM OS44 OC2DP -0.65 + +BOND O4 S4 OS42 S4 OS43 S4 OS44 S4 + +IC C2 C3 C4 O4 1.5146 109.17 170.97 110.74 1.4309 +IC C3 O4 *C4 H4 1.5121 110.74 -123.52 114.80 1.1229 +IC C3 C4 O4 S4 1.5121 110.74 110.03 115.71 1.5894 +IC C4 O4 S4 OS42 1.4309 115.71 -178.78 103.74 1.4477 +IC O4 OS42 *S4 OS43 1.5894 103.74 113.11 114.55 1.4496 +IC O4 OS42 *S4 OS44 1.5894 103.74 -111.86 114.39 1.4516 + +PRES SUF6 -1.00 ! Sulfate at C6 +dele atom HO6 + +GROUP +ATOM C6 CC321 -0.28 +ATOM H61 HCA2 0.09 +ATOM H62 HCA2 0.09 +ATOM O6 OC30P -0.28 +ATOM S6 SC 1.33 +ATOM OS62 OC2DP -0.65 +ATOM OS63 OC2DP -0.65 +ATOM OS64 OC2DP -0.65 + +BOND O6 S6 OS62 S6 OS63 S6 OS64 S6 + +IC O5 C5 C6 O6 1.4383 108.81 76.01 109.30 1.4275 +IC C5 O6 *C6 H61 1.5222 109.30 120.33 111.18 1.1156 +IC C5 O6 *C6 H62 1.5222 109.30 -118.94 111.25 1.1168 +IC C5 C6 O6 S6 1.5222 109.30 169.79 115.83 1.5647 +IC C6 O6 S6 OS62 1.4275 115.83 177.39 103.52 1.4539 +IC O6 OS62 *S6 OS63 1.5647 103.52 114.97 113.22 1.4527 +IC O6 OS62 *S6 OS64 1.5647 103.52 -113.66 112.94 1.4539 + + +!adapted from 16bb; used for linkage btw A-sialic acid and other carbohydrate; mjyang +PRES SA26E -0.08 ! (i)2->6(i-1) equatorial at C2 and equatorial at C6 +dele atom 1HO6 +dele atom 2HO2 +dele atom 2O2 +ATOM 1C6 CC321 0.00 ! +ATOM 1O6 OC301 -0.36 ! +ATOM 2C2 CC3062 0.28 ! +BOND 1O6 2C2 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C5 1C6 1O6 2C2 1.5616 106.87 168.41 113.93 1.3902 ! PSI +IC 1C6 1O6 2C2 2O6 1.4311 113.73 51.33 111.43 1.4110 ! PHI +IC 2O6 1O6 *2C2 2C3 1.4110 111.40 115.09 99.69 1.5316 +IC 2O6 1O6 *2C2 2C1 1.4110 111.43 -123.72 109.62 1.0837 +IC 1O6 2C2 2O6 2C6 1.3902 111.43 166.53 113.95 1.4709 +IC 1O6 2C2 2C3 2C4 1.3902 99.89 -170.57 112.29 1.4987 + +PRES SA28E 0.01 ! disialic acid, (i)2->8(i-1) equatorial at C2 and equatorial at C8 +dele atom 1HO8 +dele atom 2HO2 +dele atom 2O2 + +ATOM 1C8 CC312 -0.04 ! +ATOM 1O8 OC301 -0.40 ! +ATOM 2C2 CC3062 0.45 ! + +BOND 1O8 2C2 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C7 1C8 1O8 2C2 1.5545 108.16 -172.28 117.34 1.4706 +IC 1C8 1O8 2C2 2O6 1.4260 117.34 61.49 115.50 1.4426 +IC 1O8 2C2 2O6 2C6 1.4706 115.50 170.73 113.07 1.4760 +IC 1O8 2C2 2C3 2C4 1.4706 96.37 -174.49 111.38 1.5178 +IC 1O8 1C8 1C9 1O9 1.4617 103.92 113.45 110.43 1.4594 + +PRES SA29E -0.08 ! disialic acid, (i)2->9(i-1) equatorial at C2 and equatorial at C9 +dele atom 1HO9 +dele atom 2HO2 +dele atom 2O2 + +ATOM 1C9 CC322 -0.01 ! +ATOM 1O9 OC301 -0.31 ! +ATOM 2C2 CC3062 0.24 ! + +BOND 1O9 2C2 + +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC 1C8 1C9 1O9 2C2 1.5545 107.23 140.02 114.75 1.4706 +IC 1C9 1O9 2C2 2O6 1.4260 114.75 65.13 104.87 1.4426 +IC 1O9 2C2 2O6 2C6 1.4706 104.87 166.10 116.35 1.4760 +IC 1O9 2C2 2C3 2C4 1.4706 105.38 -165.42 111.54 1.5178 +IC 1O9 1C9 1C8 1O8 1.4617 107.23 -66.86 112.03 1.4594 + +PRES OB2AC -0.09 ! patch for O-acetyl on ABEQ-like residue at C2 +delete ATOM HO2 + ! +ATOM C2 CC3161 0.17 ! +ATOM O2 OC301 -0.49 ! +ATOM CA2 CC2O5 0.90 ! +ATOM OA2 OC2D1 -0.63 ! +ATOM CB2 CC331 -0.31 ! +ATOM HB1 HCA3 0.09 ! +ATOM HB2 HCA3 0.09 ! +ATOM HB3 HCA3 0.09 ! +! +BOND O2 CA2 CA2 OA2 CA2 CB2 CB2 HB1 CB2 HB2 +BOND CB2 HB3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 O2 CA2 1.5226 115.23 -42.41 115.36 1.4300 +IC C3 C2 O2 CA2 1.4987 113.76 52.52 122.34 1.4300 +IC C2 O2 CA2 OA2 1.4235 122.34 -8.29 128.77 1.2584 +IC C2 O2 CA2 CB2 1.4235 122.34 179.59 107.44 1.5400 +IC O2 CA2 CB2 HB1 1.4300 107.44 75.77 109.47 1.0700 +IC O2 CA2 CB2 HB2 1.4300 107.44 -164.22 109.47 1.0700 +IC O2 CA2 CB2 HB3 1.4300 107.44 -44.22 109.47 1.0700 +PATC FIRS NONE LAST NONE + +PRES OR2AC -0.09 ! patch for O-acetyl for ARHM-like residue at C2 +delete ATOM HO2 + ! +ATOM C2 CC3161 0.17 ! +ATOM O2 OC301 -0.49 ! +ATOM CA2 CC2O5 0.90 ! +ATOM OA2 OC2D1 -0.63 ! +ATOM CB2 CC331 -0.31 ! +ATOM HB1 HCA3 0.09 ! +ATOM HB2 HCA3 0.09 ! +ATOM HB3 HCA3 0.09 ! +! +BOND O2 CA2 CA2 OA2 CA2 CB2 CB2 HB1 CB2 HB2 +BOND CB2 HB3 +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC C1 C2 O2 CA2 1.4844 109.67 157.83 107.43 1.4300 +IC C3 C2 O2 CA2 1.4987 113.76 52.52 122.34 1.4300 +IC C2 O2 CA2 OA2 1.4235 122.34 -8.29 128.77 1.2584 +IC C2 O2 CA2 CB2 1.4235 122.34 179.59 107.44 1.5400 +IC O2 CA2 CB2 HB1 1.4300 107.44 75.77 109.47 1.0700 +IC O2 CA2 CB2 HB2 1.4300 107.44 -164.22 109.47 1.0700 +IC O2 CA2 CB2 HB3 1.4300 107.44 -44.22 109.47 1.0700 +PATC FIRS NONE LAST NONE + + +END + diff --git a/charmm/toppar/top_all36_cgenff.rtf b/charmm/toppar/top_all36_cgenff.rtf new file mode 100644 index 00000000..0edcb104 --- /dev/null +++ b/charmm/toppar/top_all36_cgenff.rtf @@ -0,0 +1,30726 @@ +* -------------------------------------------------------------------------- * +* CGenFF: Topology for the Charmm General Force Field v. 3.1 * +* for Small Molecule Drug Design * +* -------------------------------------------------------------------------- * +* +36 1 + +! -------------------------------------------------------------------------- ! +! References: - K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, ! +! J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov and ! +! A. D. Mackerell Jr., J. Comput. Chem. 2010, 31, 671-690. ! +! - W. Yu, X. He, K. Vanommeslaeghe, A. D. MacKerell Jr., ! +! J. Comput. Chem. 2012, 33, 2451-2468. ! +! -------------------------------------------------------------------------- ! +! Notes: - CGenFF is an ongoing project that is updated regularly. Please ! +! check http://mackerell.umaryland.edu/~kenno/cgenff/download.html ! +! and/or http://mackerell.umaryland.edu/ for updates! ! +! - As more functional groups will be introduced, small changes in ! +! existing parameters and/or charges may occur. ! +! - Comments in this file may be misleading. ! +! -------------------------------------------------------------------------- ! +! Contributors: abar = Arghya Barman ! +! adm = Alexander D. MacKerell Jr. ! +! alr = Ashley L. Ringer ! +! cacha = Chayan Acharya ! +! ctsai = Cheng-Chieh Tsai ! +! ed = Eva Darian ! +! ejd = Elizabeth J. Denning ! +! erh = Elizabeth R. Hatcher Frush ! +! fylin = Fang-Yu Lin ! +! isg = Ignacio Soteras Gutiérrez ! +! jal = Justin A. Lemkul ! +! jhs = JiHyun Shim ! +! kevo = Kenno VanOmmeslaeghe ! +! kundu = Sibsankar Kundu ! +! lf = Lei Fang ! +! lsk = Lakkaraju Sirish Kaushik ! +! mcs = Meagan C. Small ! +! mnoon = Muhammad Noon ! +! my = Mingjun Yang ! +! oashi = Taiji Oashi ! +! og = Olgun Guvench ! +! peml = Pedro Lopes ! +! pram = E. Prabhu Raman ! +! rima = Madhurima Jana ! +! rting = Ting Ran ! +! sc = Sherry (Hua) Chen ! +! sna = Shanthi Nagarajan ! +! sz = Shijun Zhong ! +! viv = Igor Vorobyov ! +! xhe = Xibing He ! +! xxwy = Wenbo Yu ! +! yapol = Iakov Polyak ! +! yin = Daxu Yin ! +! yxu = You Xu ! +! -------------------------------------------------------------------------- ! +! All comments to ADM jr. via the CHARMM web site: www.charmm.org ! +! parameter set discussion forum ! +! -------------------------------------------------------------------------- ! + +!hydrogens +MASS 256 HGA1 1.00800 ! alphatic proton, CH +MASS 257 HGA2 1.00800 ! alphatic proton, CH2 +MASS 258 HGA3 1.00800 ! alphatic proton, CH3 +MASS 259 HGA4 1.00800 ! alkene proton; RHC= +MASS 260 HGA5 1.00800 ! alkene proton; H2C=CR +MASS 261 HGA6 1.00800 ! aliphatic H on fluorinated C, monofluoro +MASS 262 HGA7 1.00800 ! aliphatic H on fluorinated C, difluoro +MASS 263 HGAAM0 1.00800 ! aliphatic H, NEUTRAL trimethylamine (#) +MASS 264 HGAAM1 1.00800 ! aliphatic H, NEUTRAL dimethylamine (#) +MASS 265 HGAAM2 1.00800 ! aliphatic H, NEUTRAL methylamine (#) +!(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY +!on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens +MASS 266 HGP1 1.00800 ! polar H +MASS 267 HGP2 1.00800 ! polar H, +ve charge +MASS 268 HGP3 1.00800 ! polar H, thiol +MASS 269 HGP4 1.00800 ! polar H, neutral conjugated -NH2 group (NA bases) +MASS 270 HGP5 1.00800 ! polar H on quarternary ammonium salt (choline) +MASS 271 HGPAM1 1.00800 ! polar H, NEUTRAL dimethylamine (#), terminal alkyne H +MASS 272 HGPAM2 1.00800 ! polar H, NEUTRAL methylamine (#) +MASS 273 HGPAM3 1.00800 ! polar H, NEUTRAL ammonia (#) +!(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY +!on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens +MASS 274 HGR51 1.00800 ! nonpolar H, neutral 5-mem planar ring C, LJ based on benzene +MASS 275 HGR52 1.00800 ! Aldehyde H, formamide H (RCOH); nonpolar H, neutral 5-mem planar ring C adjacent to heteroatom or + charge +MASS 276 HGR53 1.00800 ! nonpolar H, +ve charge HIS he1(+1) +MASS 277 HGR61 1.00800 ! aromatic H +MASS 278 HGR62 1.00800 ! nonpolar H, neutral 6-mem planar ring C adjacent to heteroatom +MASS 279 HGR63 1.00800 ! nonpolar H, NAD+ nicotineamide all ring CH hydrogens +MASS 280 HGR71 1.00800 ! nonpolar H, neutral 7-mem arom ring, AZUL, azulene, kevo +!carbons +MASS 281 CG1T1 12.01100 ! internal alkyne R-C#C +MASS 282 CG1T2 12.01100 ! terminal alkyne H-C#C +MASS 283 CG1N1 12.01100 ! C for cyano group +MASS 284 CG2D1 12.01100 ! alkene; RHC= ; imine C +MASS 285 CG2D2 12.01100 ! alkene; H2C= +MASS 286 CG2D1O 12.01100 ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC1. +MASS 287 CG2D2O 12.01100 ! double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC2. +MASS 288 CG2DC1 12.01100 ! conjugated alkenes, R2C=CR2 +MASS 289 CG2DC2 12.01100 ! conjugated alkenes, R2C=CR2 +MASS 290 CG2DC3 12.01100 ! conjugated alkenes, H2C= +MASS 291 CG2N1 12.01100 ! conjugated C in guanidine/guanidinium +MASS 292 CG2N2 12.01100 ! conjugated C in amidinium cation +MASS 293 CG2O1 12.01100 ! carbonyl C: amides +MASS 294 CG2O2 12.01100 ! carbonyl C: esters, [neutral] carboxylic acids +MASS 295 CG2O3 12.01100 ! carbonyl C: [negative] carboxylates +MASS 296 CG2O4 12.01100 ! carbonyl C: aldehydes +MASS 297 CG2O5 12.01100 ! carbonyl C: ketones +MASS 298 CG2O6 12.01100 ! carbonyl C: urea, carbonate +MASS 299 CG2O7 12.01100 ! CO2 carbon +MASS 300 CG2R51 12.01100 ! 5-mem ring, his CG, CD2(0), trp +MASS 301 CG2R52 12.01100 ! 5-mem ring, double bound to N, PYRZ, pyrazole +MASS 302 CG2R53 12.01100 ! 5-mem ring, double bound to N and adjacent to another heteroatom, purine C8, his CE1 (0,+1), 2PDO, kevo +MASS 303 CG2R57 12.01100 ! 5-mem ring, bipyrroles +MASS 304 CG25C1 12.01100 ! same as CG2DC1 but in 5-membered ring with exocyclic double bond +MASS 305 CG25C2 12.01100 ! same as CG2DC2 but in 5-membered ring with exocyclic double bond +MASS 306 CG251O 12.01100 ! same as CG2D1O but in 5-membered ring with exocyclic double bond +MASS 307 CG252O 12.01100 ! same as CG2D2O but in 5-membered ring with exocyclic double bond +MASS 308 CG2R61 12.01100 ! 6-mem aromatic C +MASS 309 CG2R62 12.01100 ! 6-mem aromatic C for protonated pyridine (NIC) and rings containing carbonyls (see CG2R63) (NA) +MASS 310 CG2R63 12.01100 ! 6-mem aromatic amide carbon (NA) (and other 6-mem aromatic carbonyls?) +MASS 311 CG2R64 12.01100 ! 6-mem aromatic amidine and guanidine carbon (between 2 or 3 Ns and double-bound to one of them), NA, PYRM +MASS 312 CG2R66 12.01100 ! 6-mem aromatic carbon bound to F +MASS 313 CG2R67 12.01100 ! 6-mem aromatic carbon of biphenyl +MASS 314 CG2RC0 12.01100 ! 6/5-mem ring bridging C, guanine C4,C5, trp +MASS 315 CG2R71 12.01100 ! 7-mem ring arom C, AZUL, azulene, kevo +MASS 316 CG2RC7 12.01100 ! sp2 ring connection with single bond(!), AZUL, azulene, kevo +MASS 317 CG301 12.01100 ! aliphatic C, no hydrogens, neopentane +MASS 318 CG302 12.01100 ! aliphatic C, no hydrogens, trifluoromethyl +MASS 319 CG311 12.01100 ! aliphatic C with 1 H, CH +MASS 320 CG312 12.01100 ! aliphatic C with 1 H, difluoromethyl +MASS 321 CG314 12.01100 ! aliphatic C with 1 H, adjacent to positive N (PROT NTER) (+) +MASS 322 CG321 12.01100 ! aliphatic C for CH2 +MASS 323 CG322 12.01100 ! aliphatic C for CH2, monofluoromethyl +MASS 324 CG323 12.01100 ! aliphatic C for CH2, thiolate carbon +MASS 325 CG324 12.01100 ! aliphatic C for CH2, adjacent to positive N (piperidine) (+) +MASS 326 CG331 12.01100 ! aliphatic C for methyl group (-CH3) +MASS 327 CG334 12.01100 ! aliphatic C for methyl group (-CH3), adjacent to positive N (PROT NTER) (+) +MASS 328 CG3AM0 12.01100 ! aliphatic C for CH3, NEUTRAL trimethylamine methyl carbon (#) +MASS 329 CG3AM1 12.01100 ! aliphatic C for CH3, NEUTRAL dimethylamine methyl carbon (#) +MASS 330 CG3AM2 12.01100 ! aliphatic C for CH3, NEUTRAL methylamine methyl carbon (#) +!(#) EXTREME care is required when doing atom typing on compounds that look like this. Use ONLY +!on NEUTRAL METHYLAMINE groups, NOT ETHYL, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens +MASS 331 CG3C31 12.01100 ! cyclopropyl carbon +MASS 332 CG3C41 12.01100 ! cyclobutyl carbon +MASS 333 CG3C50 12.01100 ! 5-mem ring aliphatic quaternary C (cholesterol, bile acids) +MASS 334 CG3C51 12.01100 ! 5-mem ring aliphatic CH (proline CA, furanoses) +MASS 335 CG3C52 12.01100 ! 5-mem ring aliphatic CH2 (proline CB/CG/CD, THF, deoxyribose) +MASS 336 CG3C53 12.01100 ! 5-mem ring aliphatic CH adjacent to positive N (proline.H+ CA) (+) +MASS 337 CG3C54 12.01100 ! 5-mem ring aliphatic CH2 adjacent to positive N (proline.H+ CD) (+) +MASS 338 CG3RC1 12.01100 ! bridgehead in bicyclic systems containing at least one 5-membered or smaller ring +!(+) Includes protonated Shiff base (NG3D5, NG2R52 in 2HPP) but NOT amidinium (NG2R52 in IMIM), guanidinium +!nitrogens +MASS 339 NG1T1 14.00700 ! N for cyano group +!MASS 340 NG1D1 14.00700 ! terminal N in azides, lsk +MASS 341 NG2D1 14.00700 ! N for neutral imine/Schiff's base (C=N-R, acyclic amidine, gunaidine) +MASS 342 NG2S0 14.00700 ! N,N-disubstituted amide, proline N (CO=NRR') +MASS 343 NG2S1 14.00700 ! peptide nitrogen (CO=NHR) +MASS 344 NG2S2 14.00700 ! terminal amide nitrogen (CO=NH2) +MASS 345 NG2S3 14.00700 ! external amine ring nitrogen (planar/aniline), phosphoramidate +!MASS 346 NG2S4 14.00700 ! neutral hydroxamic acid +MASS 347 NG2O1 14.00700 ! NITB, nitrobenzene +MASS 348 NG2P1 14.00700 ! N for protonated imine/Schiff's base (C=N(+)H-R, acyclic amidinium, guanidinium) +MASS 349 NG2R43 14.00700 ! amide in 4-memebered ring (planar), AZDO, lsk +MASS 350 NG2R50 14.00700 ! double bound neutral 5-mem planar ring, purine N7 +MASS 351 NG2R51 14.00700 ! single bound neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused) +MASS 352 NG2R52 14.00700 ! protonated schiff base, amidinium, guanidinium in 5-membered ring, HIS, 2HPP, kevo +MASS 353 NG2R53 14.00700 ! amide in 5-memebered NON-SP2 ring (slightly pyramidized), 2PDO, kevo +MASS 354 NG2R57 14.00700 ! 5-mem ring, bipyrroles +MASS 355 NG2R60 14.00700 ! double bound neutral 6-mem planar ring, pyr1, pyzn +MASS 356 NG2R61 14.00700 ! single bound neutral 6-mem planar ring imino nitrogen; glycosyl linkage +MASS 357 NG2R62 14.00700 ! double bound 6-mem planar ring with heteroatoms in o or m, pyrd, pyrm +MASS 358 NG2R67 14.00700 ! 6-mem planar ring substituted with 6-mem planar ring (N-phenyl pyridinones etc.) +MASS 359 NG2RC0 14.00700 ! 6/5-mem ring bridging N, indolizine, INDZ, kevo +MASS 360 NG301 14.00700 ! neutral trimethylamine nitrogen +MASS 361 NG311 14.00700 ! neutral dimethylamine nitrogen +MASS 362 NG321 14.00700 ! neutral methylamine nitrogen +MASS 363 NG331 14.00700 ! neutral ammonia nitrogen +MASS 364 NG3C51 14.00700 ! secondary sp3 amine in 5-membered ring +MASS 365 NG3N1 14.00700 ! N in hydrazine, HDZN +MASS 366 NG3P0 14.00700 ! quarternary N+, choline +MASS 367 NG3P1 14.00700 ! tertiary NH+ (PIP) +MASS 368 NG3P2 14.00700 ! secondary NH2+ (proline) +MASS 369 NG3P3 14.00700 ! primary NH3+, phosphatidylethanolamine +!oxygens +MASS 370 OG2D1 15.99940 ! carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera +MASS 371 OG2D2 15.99940 ! carbonyl O: negative groups: carboxylates, carbonate +MASS 372 OG2D3 15.99940 ! carbonyl O: ketones +MASS 373 OG2D4 15.99940 ! 6-mem aromatic carbonyl oxygen (nucleic bases) +MASS 374 OG2D5 15.99940 ! CO2 oxygen +MASS 375 OG2N1 15.99940 ! NITB, nitrobenzene +MASS 376 OG2P1 15.99940 ! =O in phosphate or sulfate +MASS 377 OG2R50 15.99940 ! FURA, furan +MASS 378 OG3R60 15.99940 ! O in 6-mem cyclic enol ether (PY01, PY02) or ester +MASS 379 OG301 15.99940 ! ether -O- !SHOULD WE HAVE A SEPARATE ENOL ETHER??? IF YES, SHOULD WE MERGE IT WITH OG3R60??? +MASS 380 OG302 15.99940 ! ester -O- +MASS 381 OG303 15.99940 ! phosphate/sulfate ester oxygen +MASS 382 OG304 15.99940 ! linkage oxygen in pyrophosphate/pyrosulphate +MASS 383 OG311 15.99940 ! hydroxyl oxygen +MASS 384 OG312 15.99940 ! ionized alcohol oxygen +MASS 385 OG3C31 15.99940 ! epoxide oxygen, 1EOX, 1BOX, sc +MASS 386 OG3C51 15.99940 ! 5-mem furanose ring oxygen (ether) +MASS 387 OG3C61 15.99940 ! DIOX, dioxane, ether in 6-membered ring !SHOULD WE MERGE THIS WITH OG3R60??? +!sulphurs +MASS 388 SG2D1 32.06000 ! thiocarbonyl S +MASS 389 SG2R50 32.06000 ! THIP, thiophene +MASS 390 SG311 32.06000 ! sulphur, SH, -S- +MASS 391 SG301 32.06000 ! sulfur C-S-S-C type +MASS 392 SG302 32.06000 ! thiolate sulfur (-1) +MASS 393 SG3O1 32.06000 ! sulfate -1 sulfur +MASS 394 SG3O2 32.06000 ! neutral sulfone/sulfonamide sulfur +MASS 395 SG3O3 32.06000 ! neutral sulfoxide sulfur +!halogens +MASS 396 CLGA1 35.45300 ! CLET, DCLE, chloroethane, 1,1-dichloroethane +MASS 397 CLGA3 35.45300 ! TCLE, 1,1,1-trichloroethane +MASS 398 CLGR1 35.45300 ! CHLB, chlorobenzene +MASS 399 BRGA1 79.90400 ! BRET, bromoethane +MASS 400 BRGA2 79.90400 ! DBRE, 1,1-dibromoethane +MASS 401 BRGA3 79.90400 ! TBRE, 1,1,1-dibromoethane +MASS 402 BRGR1 79.90400 ! BROB, bromobenzene +MASS 403 IGR1 126.90447 ! IODB, iodobenzene +MASS 404 FGA1 18.99800 ! aliphatic fluorine, monofluoro +MASS 405 FGA2 18.99800 ! aliphatic fluorine, difluoro +MASS 406 FGA3 18.99800 ! aliphatic fluorine, trifluoro +MASS 407 FGP1 18.99800 ! anionic F, for ALF4 AlF4- +MASS 408 FGR1 18.99800 ! aromatic flourine +!miscellaneous +MASS 409 PG0 30.97380 ! neutral phosphate +MASS 410 PG1 30.97380 ! phosphate -1 +MASS 411 PG2 30.97380 ! phosphate -2 +MASS 412 ALG1 26.98154 ! Aluminum, for ALF4, AlF4- +!MASS 414 HGTIP3 1.00800 ! polar H, TIPS3P WATER HYDROGEN +!MASS 415 OGTIP3 15.99940 ! TIPS3P WATER OXYGEN +!MASS 416 DUM 0.00000 ! dummy atom +!MASS 417 HE 4.00260 ! helium +!MASS 418 NE 20.17970 ! neon + +DEFA FIRS NONE LAST NONE +AUTO ANGLES DIHE + +!RESI TIP3 0.00 ! tip3p water model, generate using noangle nodihedral +!GROUP +!ATOM OH2 OGTIP3 -0.834 +!ATOM H1 HGTIP3 0.417 +!ATOM H2 HGTIP3 0.417 +!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +!ANGLE H1 OH2 H2 ! required +!ACCEPTOR OH2 +!PATCHING FIRS NONE LAST NONE + +!protein model compounds +!toppar_all22_model_aliphatic.str +RESI ACET -1.00 ! C2H3O2 acetate, K. Kuczera +GROUP +ATOM C1 CG331 -0.37 +ATOM C2 CG2O3 0.62 ! H1 O1 (-) +ATOM H1 HGA3 0.09 ! | / +ATOM H2 HGA3 0.09 ! H2--C1--C2 +ATOM H3 HGA3 0.09 ! | \\ +ATOM O1 OG2D2 -0.76 ! H3 O2 +ATOM O2 OG2D2 -0.76 +BOND C1 H1 C1 H2 C1 H3 +BOND C1 C2 C2 O1 +DOUBLE C2 O2 +IMPR C2 O2 O1 C1 +IC O1 C2 C1 H1 0.00 0.00 0.0 0.00 0.00 +IC C2 H1 *C1 H2 0.00 0.00 120.0 0.00 0.00 +IC C2 H1 *C1 H3 0.00 0.00 -120.0 0.00 0.00 +IC C1 O1 *C2 O2 0.00 0.00 180.0 0.00 0.00 +PATC FIRS NONE LAST NONE + +RESI PROA -1.00 ! C3H5O2 propionic acid +GROUP +ATOM C2 CG321 -0.28 +ATOM C1 CG2O3 0.62 ! H21 O1 (-) +ATOM H21 HGA2 0.09 ! | / +ATOM H22 HGA2 0.09 ! H22-C2--C1 + ! | \\ +ATOM O1 OG2D2 -0.76 ! | O2 +ATOM O2 OG2D2 -0.76 !H31--C3 +GROUP ! | \ +ATOM C3 CG331 -0.27 ! H32 H33 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND C1 C2 C2 C3 C1 O1 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 C3 H33 +DOUBLE C1 O2 +IMPR C1 O2 O1 C2 + +IC O1 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 O2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 C1 O1 0.0000 0.00 180.00 0.00 0.0000 +IC O1 C2 *C1 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI GUAN 1.00 ! CH6N3 guandinium, K. Kuczera +GROUP +ATOM C CG2N1 0.64 ! H11 H12 +ATOM N1 NG2P1 -0.80 ! \ / +ATOM H11 HGP2 0.46 ! N1 (+) +ATOM H12 HGP2 0.46 ! || +ATOM N2 NG2P1 -0.80 ! C +ATOM H21 HGP2 0.46 ! / \ +ATOM H22 HGP2 0.46 ! H21-N2 N3-H31 +ATOM N3 NG2P1 -0.80 ! | | +ATOM H31 HGP2 0.46 ! H22 H32 +ATOM H32 HGP2 0.46 +BOND C N2 C N3 +DOUBLE C N1 +BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 H32 +IMPR C N2 N1 N3 +IC H11 N1 C N2 0.00 0.00 0.0 0.00 0.00 +IC H11 N1 C N3 0.00 0.00 180.0 0.00 0.00 +IC H12 N1 C N3 0.00 0.00 0.0 0.00 0.00 +IC H21 N2 C N1 0.00 0.00 0.0 0.00 0.00 +IC H22 N2 C N3 0.00 0.00 0.0 0.00 0.00 +IC H31 N3 C N1 0.00 0.00 0.0 0.00 0.00 +IC H32 N3 C N2 0.00 0.00 0.0 0.00 0.00 +PATC FIRS NONE LAST NONE + +RESI MGUA 1.00 ! C2H8N3 methyl-guanidinium +GROUP +ATOM C CG2N1 0.64 ! H11 H12 +ATOM N1 NG2P1 -0.80 ! \ / +ATOM H11 HGP2 0.46 ! N1 (+) +ATOM H12 HGP2 0.46 ! || +ATOM N2 NG2P1 -0.80 ! C HC1 +ATOM H21 HGP2 0.46 ! / \ / +ATOM H22 HGP2 0.46 ! H21-N2 N3--C2-HC2 +ATOM N3 NG2P1 -0.70 ! | | \ +ATOM H31 HGP2 0.44 ! H22 H31 HC3 +ATOM C2 CG334 0.11 +ATOM HC1 HGA3 0.09 +ATOM HC2 HGA3 0.09 +ATOM HC3 HGA3 0.09 +BOND C N2 C N3 +DOUBLE C N1 +BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 C2 +BOND C2 HC1 C2 HC2 C2 HC3 +IMPR C N2 N1 N3 +IC H11 N1 C N2 0.00 0.00 0.0 0.00 0.00 +IC H11 N1 C N3 0.00 0.00 180.0 0.00 0.00 +IC H12 N1 C N3 0.00 0.00 0.0 0.00 0.00 +IC H21 N2 C N1 0.00 0.00 0.0 0.00 0.00 +IC H22 N2 C N3 0.00 0.00 0.0 0.00 0.00 +IC H31 N3 C N1 0.00 0.00 0.0 0.00 0.00 +IC C2 N3 C N1 0.00 0.00 180.0 0.00 0.00 +IC C N3 C2 HC1 0.00 0.00 0.0 0.00 0.00 +IC C N3 C2 HC2 0.00 0.00 120.0 0.00 0.00 +IC C N3 C2 HC3 0.00 0.00 240.0 0.00 0.00 +PATC FIRS NONE LAST NONE + +RESI GLYN 0.00 ! C2H5NO2 neutral glycine +GROUP +ATOM N NG321 -0.96 +ATOM HT1 HGPAM2 0.34 ! HT1 HT2 +ATOM HT2 HGPAM2 0.34 ! \ / +ATOM CA CG321 0.18 ! N +ATOM HA1 HGA2 0.05 ! | +ATOM HA2 HGA2 0.05 ! HA1-CA-HA2 +GROUP ! | +ATOM C CG2O2 0.75 ! C +ATOM OT1 OG2D1 -0.55 ! // \ +ATOM OT2 OG311 -0.63 ! OT1 OT2 +ATOM HO2 HGP1 0.43 ! | + ! HO2 + +BOND N CA CA C C OT2 OT2 HO2 +BOND N HT1 N HT2 CA HA1 CA HA2 +DOUBLE OT1 C +DONO HT1 N +DONO HT2 N +DONO HO2 OT2 +IMPR C CA OT1 OT2 +IC N CA C OT1 1.5010 119.00 88.76 126.10 1.2218 +IC N CA C OT2 1.5010 119.00 -111.57 113.44 1.3958 +IC OT1 OT2 *C CA 1.2218 117.44 -161.57 113.44 1.5780 +IC CA C OT2 HO2 1.5780 113.44 -168.97 107.16 0.9565 +IC C CA N HT1 1.5780 119.00 164.86 110.99 1.0023 +IC C CA N HT2 1.5780 119.00 -77.98 111.22 1.0030 +IC N C *CA HA1 1.5010 119.00 120.0 110.0 1.1 +IC N C *CA HA2 1.5010 119.00 -120.0 110.0 1.1 +PATCHING FIRS NONE LAST NONE + +RESI MAMM 1.00 ! CH6N methylammonium, K. Kuczera +GROUP +ATOM CE CG334 0.16 +ATOM NZ NG3P3 -0.30 ! HE1 HZ1 +ATOM HE1 HGA3 0.05 ! \ (+) | +ATOM HE2 HGA3 0.05 !HE2-CE---NZ--HZ2 +ATOM HE3 HGA3 0.05 ! / | +ATOM HZ1 HGP2 0.33 ! HE3 HZ3 +ATOM HZ2 HGP2 0.33 +ATOM HZ3 HGP2 0.33 + +BOND CE HE1 CE HE2 CE HE3 +BOND CE NZ NZ HZ1 NZ HZ2 NZ HZ3 +IC NZ HE3 *CE HE1 0.0000 0.00 120.00 0.00 0.0000 +IC NZ HE3 *CE HE2 0.0000 0.00 -120.00 0.00 0.0000 +IC HE3 CE NZ HZ3 0.0000 0.00 180.00 0.00 0.0000 +IC CE HZ3 *NZ HZ1 0.0000 0.00 120.00 0.00 0.0000 +IC CE HZ3 *NZ HZ2 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI EAMM 1.00 ! C2H8N ethylammonium, adm jr. +GROUP +ATOM CE CG324 0.21 +ATOM NZ NG3P3 -0.30 ! HE1 HZ1 +ATOM HE1 HGA2 0.05 ! \ (+) | +ATOM HE2 HGA2 0.05 !HE2-CE---NZ--HZ2 + ! / | +ATOM HZ1 HGP2 0.33 ! / HZ3 +ATOM HZ2 HGP2 0.33 ! C1-H13 +ATOM HZ3 HGP2 0.33 ! / \ +GROUP !H11 H12 +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +BOND CE HE1 CE HE2 CE C1 +BOND CE NZ NZ HZ1 NZ HZ2 NZ HZ3 +BOND C1 H11 C1 H12 C1 H13 + +IC H11 C1 CE NZ 0.0000 0.00 180.00 0.00 0.0000 +IC C1 NZ *CE HE1 0.0000 0.00 120.00 0.00 0.0000 +IC HE1 NZ *CE HE2 0.0000 0.00 -120.00 0.00 0.0000 +IC HE1 CE NZ HZ1 0.0000 0.00 180.00 0.00 0.0000 +IC HZ1 CE *NZ HZ2 0.0000 0.00 120.00 0.00 0.0000 +IC HZ1 CE *NZ HZ3 0.0000 0.00 -120.00 0.00 0.0000 +IC HE1 CE C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 CE *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 CE *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI ACEH 0.00 ! C2H4O2 acetic acid, ADM jr. +GROUP +ATOM C2 CG331 -0.30 +ATOM C1 CG2O2 0.75 ! H21 O2 +ATOM H21 HGA3 0.09 ! \ // +ATOM H22 HGA3 0.09 ! H22-C2--C1 +ATOM H23 HGA3 0.09 ! / \ +ATOM O2 OG2D1 -0.55 ! H23 O1-HO1 +ATOM O1 OG311 -0.60 +ATOM HO1 HGP1 0.43 +BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23 +DOUBLE C1 O2 +IMPR C1 C2 O2 O1 +DONO BLNK HO1 ! O1 +ACCE O1 +ACCE O2 +IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 +IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 + +RESI MEOH 0.00 ! CH4O methanol, adm jr. +GROUP +ATOM CB CG331 -0.04 ! H11 +ATOM OG OG311 -0.65 ! \ +ATOM HG1 HGP1 0.42 ! H12--C1--O1 +ATOM HB1 HGA3 0.09 ! / \ +ATOM HB2 HGA3 0.09 ! H13 HO1 +ATOM HB3 HGA3 0.09 +BOND CB OG OG HG1 +BOND CB HB1 CB HB2 CB HB3 +DONO HG1 OG +ACCE OG +! only for analysis +IC HG1 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG HB1 *CB HB2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC OG HB1 *CB HB3 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI METO -1.00 ! CH3O methoxide, adm jr. +GROUP ! order of atoms to match that used in ab initio +ATOM CB CG331 -0.41 ! HB1 +ATOM OG OG312 -0.92 ! \ + ! HB2--CB--OG (-) +ATOM HB1 HGA3 0.11 ! / +ATOM HB2 HGA3 0.11 ! HB3 +ATOM HB3 HGA3 0.11 +BOND CB OG +BOND CB HB1 CB HB2 CB HB3 +ACCE OG +! only for analysis +IC HB2 OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG HB2 *CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG CB HB1 HB2 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI ETOH 0.00 ! C2H6O Ethanol, adm jr. +GROUP +ATOM C1 CG321 0.05 ! H21 H11 H12 +ATOM O1 OG311 -0.65 ! \ \ / +ATOM HO1 HGP1 0.42 ! H22--C2--C1 +ATOM H11 HGA2 0.09 ! / \ +ATOM H12 HGA2 0.09 ! H23 O1--HO1 +GROUP +ATOM C2 CG331 -0.27 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 +BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 +BOND C2 H21 C2 H22 C2 H23 +DONO HO1 O1 +ACCE O1 +! for ic build +IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C1 H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C1 H21 *C2 H23 0.0000 0.0000 240.0000 0.0000 0.0000 +IC O1 C2 *C1 H11 0.0000 0.0000 240.0000 0.0000 0.0000 +IC O1 C2 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2 C1 O1 HO1 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI ETO -1.00 ! C2H5O Ethoxide, adm jr. +GROUP +ATOM OG OG312 -0.92 ! HA1 HB1 HB2 +ATOM CB CG321 -0.30 ! \ \ / +ATOM CA CG331 -0.27 ! HA2--CA--CB +ATOM HB1 HGA2 0.11 ! / \ +ATOM HB2 HGA2 0.11 ! HA3 OG (-) +ATOM HA1 HGA3 0.09 +ATOM HA2 HGA3 0.09 +ATOM HA3 HGA3 0.09 +BOND CA CB CB OG CB HB1 CB HB2 +BOND CA HA1 CA HA2 CA HA3 +ACCE OG +! for ic build +IC CB CA HA1 HA2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA OG CB HB1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA OG CB HB2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA OG CB HB3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 +IC HA1 CA CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HA1 CA CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 + +RESI PRO2 0.00 ! C3H8O 2-propanol, adm jr. +GROUP +ATOM C2 CG311 0.14 ! H12 H13 H33 H32 +ATOM O2 OG311 -0.65 ! \ / \ / +ATOM HO2 HGP1 0.42 ! H11--C1 C3--H31 +ATOM H21 HGA1 0.09 ! \ / +GROUP ! C2 +ATOM C1 CG331 -0.27 ! / \ +ATOM H11 HGA3 0.09 ! O2 H21 +ATOM H12 HGA3 0.09 ! | +ATOM H13 HGA3 0.09 ! HO2 +GROUP +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 +BOND C1 C2 C2 C3 C2 O2 C2 H21 O2 HO2 +BOND C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 C3 H33 +DONO HO2 O2 +ACCE O2 +IC C1 C2 C3 H31 0.0000 0.000 180.0000 0.000 0.0000 +IC C2 H31 *C3 H32 0.0000 0.000 120.0000 0.000 0.0000 +IC C2 H31 *C3 H33 0.0000 0.000 -120.0000 0.000 0.0000 +IC C3 C2 C1 H11 0.0000 0.000 180.0000 0.000 0.0000 +IC C2 H11 *C1 H12 0.0000 0.000 120.0000 0.000 0.0000 +IC C2 H11 *C1 H13 0.0000 0.000 -120.0000 0.000 0.0000 +IC C1 C3 *C2 O2 0.0000 0.000 120.0000 0.000 0.0000 +IC C1 C3 *C2 H21 0.0000 0.000 -120.0000 0.000 0.0000 +IC C3 C2 O2 HO2 0.0000 0.000 180.0000 0.000 0.0000 + +RESI FORM 0.00 ! CH3NO formamide, adm jr. +GROUP +ATOM HA HGR52 0.08 +ATOM C CG2O1 0.42 ! O Hc +ATOM N NG2S2 -0.69 ! \\ / +ATOM HC HGP1 0.35 ! C--N +ATOM HT HGP1 0.35 ! / \ +ATOM O OG2D1 -0.51 ! HA Ht + +BOND C HA C N N HC N HT +DOUBLE C O +!BOND O DUM +IMPR C N O HA +! GAS PHASE GEOMETRY +!IC DUM O C N 1.00 90.0 0. 124.70 1.352 +!Gives strange error: +!IC O C N HC 1.2190 124.70 0. 118.50 1.0016 ! variable 1 +!IC HC N C HA 1.0016 118.50 180. 112.70 1.0980 ! variable 2 +!IC O C N HT 1.2190 124.70 180. 120.00 1.0015 ! variable 3 +!Works with IC param: +IC O C N HT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O N *C HA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C HT *N HC 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI ACEM 0.00 ! C2H5NO acetamide, adm jr. +! the amide charges listed below are used in asparagine and glutamine +! if Hc and HT are made equivalent use N = -0.64, Hc = HT = 0.32 +GROUP +ATOM CC CG331 -0.27 +ATOM C CG2O1 0.55 ! HC1 Ht +ATOM N NG2S2 -0.62 ! \ / +ATOM HC HGP1 0.32 ! HC2--CC--C---N +ATOM HT HGP1 0.30 ! / || \ +ATOM O OG2D1 -0.55 ! HC3 O Hc +ATOM HC1 HGA3 0.09 +ATOM HC2 HGA3 0.09 +ATOM HC3 HGA3 0.09 +!atom dum dum 0.0 ! dummy for ic build +BOND C N N HC N HT +DOUBLE C O +BOND C CC CC HC1 CC HC2 CC HC3 +!BOND O DUM +IMPR C CC N O +! GAS PHASE GEOMETRY +IC HC1 CC C N 1.0832 113.80 180. 124.70 1.3523 +IC O C N HC 1.2012 124.70 0. 118.63 0.9929 ! variable 1 +IC O C N HT 1.2012 124.70 180. 120.92 0.9960 ! variable 3 +IC HC N C CC 1.0016 118.63 180. 115.65 1.5150 ! variable 2 +IC O C CC HC1 1.2012 123.27 0. 113.80 1.0832 +IC O C CC HC2 1.2012 123.27 120. 108.52 1.0836 +IC O C CC HC3 1.2012 123.27 300. 108.52 1.0836 + +RESI PRAM 0.00 ! C3H7NO propionamide, adm jr. +! the amide charges listed below are used in asparagine and glutamine +! if Hc and HT are made equivalent use N = -0.64, Hc = HT = 0.32 +GROUP +ATOM CC CG321 -0.18 +ATOM C CG2O1 0.55 ! HC1 Ht +ATOM N NG2S2 -0.62 ! \ / +ATOM HC HGP1 0.32 ! HC2--CC--C---N +ATOM HT HGP1 0.30 ! / || \ +ATOM O OG2D1 -0.55 ! / O Hc +ATOM HC1 HGA2 0.09 ! C1-H13 +ATOM HC2 HGA2 0.09 ! / \ +GROUP !H11 H12 +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +!atom dum dum 0.0 ! dummy for ic build +BOND C N N HC N HT +DOUBLE C O +BOND C CC CC HC1 CC HC2 CC C1 +BOND C1 H11 C1 H12 C1 H13 +!BOND O DUM +IMPR C CC N O +! GAS PHASE GEOMETRY +IC HC1 CC C N 1.0832 113.80 180. 124.70 1.3523 +IC O C N HC 1.2012 124.70 0. 118.63 0.9929 ! variable 1 +IC O C N HT 1.2012 124.70 180. 120.92 0.9960 ! variable 3 +IC HC N C CC 1.0016 118.63 180. 115.65 1.5150 ! variable 2 +IC O C CC HC1 1.2012 123.27 60. 113.80 1.0832 +IC O C CC HC2 1.2012 123.27 300. 108.52 1.0836 +IC O C CC C1 1.2012 123.27 180. 108.52 1.5000 +IC C CC C1 H11 0.0 0.0 180. 0.0 0.0 +IC C CC C1 H12 0.0 0.0 60. 0.0 0.0 +IC C CC C1 H13 0.0 0.0 300. 0.0 0.0 + + +RESI NMA 0.00 ! C3H7NO N-methylacetamide, Louis Kuchnir +GROUP +ATOM CL CG331 -0.27 +ATOM HL1 HGA3 0.09 +ATOM HL2 HGA3 0.09 +ATOM HL3 HGA3 0.09 +ATOM C CG2O1 0.51 +ATOM O OG2D1 -0.51 +ATOM N NG2S1 -0.47 +ATOM H HGP1 0.31 +ATOM CR CG331 -0.11 +ATOM HR1 HGA3 0.09 +ATOM HR2 HGA3 0.09 +ATOM HR3 HGA3 0.09 +BOND HL1 CL HL2 CL HL3 CL ! N-Methylacetamide: +BOND CL C C N N CR ! HL1\ O /HR1 +BOND N H ! HL2-- CL -- C -- N -- CR --HR2 +BOND HR1 CR HR2 CR HR3 CR ! HL3/ H \HR3 +DOUBLE C O +IMPR C CL N O + +IC O C N H 1.2233 122.84 180. 119.23 0.9933 ! variable 1 +IC H N C CL 0.9933 119.23 0. 116.25 1.5118 ! variable 8 +IC O C N CR 1.2233 122.84 0. 122.57 1.4488 ! variable 8 +IC N C CL HL1 1.3418 116.25 180. 109.3 1.109 ! variable 2 +IC N C CL HL2 1.3418 116.25 60. 109.3 1.109 ! variable 3 +IC N C CL HL3 1.3418 116.25 300. 109.3 1.109 ! variable 4 +IC C N CR HR1 1.3418 122.57 180. 110.7 1.113 ! variable 5 +IC C N CR HR2 1.3418 122.57 60. 110.7 1.113 ! variable 6 +IC C N CR HR3 1.3418 122.57 300. 110.7 1.113 ! variable 7 + +RESI AANM 0.00 ! C6H12N2O2 Ac-Ala-NMe, aka. alanine dipeptide +GROUP +ATOM CL CG331 -0.27 +ATOM HL1 HGA3 0.09 +ATOM HL2 HGA3 0.09 +ATOM HL3 HGA3 0.09 +GROUP +ATOM CLP CG2O1 0.51 +ATOM OL OG2D1 -0.51 +GROUP +ATOM NL NG2S1 -0.47 +ATOM HL HGP1 0.31 +ATOM CA CG311 0.07 +ATOM HA HGA1 0.09 +GROUP +ATOM CB CG331 -0.27 ! HL1 OL OR HR1 +ATOM HB1 HGA3 0.09 ! \ || HL HA || HR / +ATOM HB2 HGA3 0.09 ! \ || | | || | / +ATOM HB3 HGA3 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 +GROUP ! / | \ +ATOM CRP CG2O1 0.51 ! / HB1--CB--HB3 \ +ATOM OR OG2D1 -0.51 ! HL3 | HR3 +GROUP ! HB2 +ATOM NR NG2S1 -0.47 +ATOM HR HGP1 0.31 +ATOM CR CG331 -0.11 +ATOM HR1 HGA3 0.09 +ATOM HR2 HGA3 0.09 +ATOM HR3 HGA3 0.09 + +BOND CL CLP CLP NL NL CA +BOND CA CRP CRP NR NR CR +DOUBLE CLP OL CRP OR +BOND NL HL NR HR +BOND CA HA CA CB +BOND CL HL1 CL HL2 CL HL3 +BOND CB HB1 CB HB2 CB HB3 +BOND CR HR1 CR HR2 CR HR3 +IMPR CLP CL NL OL +IMPR CRP CA NR OR + +IC CLP NL CA CRP 0.0 0.0 180.0 0.0 0.0 ! Phi +IC CA CLP *NL HL 0.0 0.0 180.0 0.0 0.0 +IC HL NL CA CRP 0.0 0.0 0.0 0.0 0.0 +IC NL CA CRP NR 0.0 0.0 180.0 0.0 0.0 ! Psi +IC CA NR *CRP OR 0.0 0.0 180.0 0.0 0.0 +IC NL CA CRP OR 0.0 0.0 0.0 0.0 0.0 +IC CL CLP NL CA 0.0 0.0 180.0 0.0 0.0 ! Omega Left +IC NL CL *CLP OL 0.0 0.0 180.0 0.0 0.0 +IC OL CLP NL CA 0.0 0.0 0.0 0.0 0.0 +IC CA CRP NR CR 0.0 0.0 180.0 0.0 0.0 ! Omega Right +IC CRP CR *NR HR 0.0 0.0 180.0 0.0 0.0 +IC NL CRP *CA HA 0.0 0.0 240.0 0.0 0.0 +IC NL CRP *CA CB 0.0 0.0 120.0 0.0 0.0 +IC HL1 CL CLP NL 0.0 0.0 180.0 0.0 0.0 +IC HL2 CL CLP NL 0.0 0.0 60.0 0.0 0.0 +IC HL3 CL CLP OL 0.0 0.0 120.0 0.0 0.0 +IC HA CA CB HB1 0.0 0.0 180.0 0.0 0.0 +IC NL CA CB HB2 0.0 0.0 180.0 0.0 0.0 +IC CRP CA CB HB3 0.0 0.0 180.0 0.0 0.0 +IC CRP NR CR HR1 0.0 0.0 180.0 0.0 0.0 +IC CRP NR CR HR2 0.0 0.0 60.0 0.0 0.0 +IC HR NR CR HR3 0.0 0.0 120.0 0.0 0.0 +IC CA CLP *NL HL 0.0 0.0 180.0 0.0 0.0 +IC CA NR *CRP OR 0.0 0.0 180.0 0.0 0.0 +IC HB1 HB2 *CB HB3 0.0 0.0 120.0 0.0 0.0 +IC HL1 HL2 *CL HL3 0.0 0.0 240.0 0.0 0.0 +IC HR1 HR2 *CR HR3 0.0 0.0 240.0 0.0 0.0 +IC HA CA NL HL 0.0 0.0 240.0 0.0 0.0 + +RESI MESH 0.00 ! CH4S methanethiol, DZUNG NGUYEN +GROUP +ATOM H1 HGA3 0.09 ! H1 +ATOM H2 HGA3 0.09 ! \ +ATOM H3 HGA3 0.09 ! H2--CM--S +ATOM CM CG331 -0.20 ! / \ +ATOM S SG311 -0.23 ! H3 H4 +ATOM H4 HGP3 0.16 +BOND CM H1 CM H2 CM H3 +BOND CM S S H4 +IC H1 CM S H4 0.00 0.00 0.0 0.00 0.00 +IC H2 CM S H4 0.00 0.00 120.0 0.00 0.00 +IC H3 CM S H4 0.00 0.00 240.0 0.00 0.00 +IC CM S H4 H1 0.00 0.00 0.0 0.00 0.00 +PATC FIRS NONE LAST NONE + +RESI MES1 -1.00 ! CH3S methylthiolate, adm jr. +GROUP +ATOM S SG302 -0.80 ! H11 +ATOM C1 CG323 -0.47 ! \ +ATOM H11 HGA3 0.09 ! H12--C1--S (-) +ATOM H12 HGA3 0.09 ! / +ATOM H13 HGA3 0.09 ! H13 + +BOND S C1 C1 H11 C1 H12 C1 H13 +IC BLNK H11 C1 S 0.0000 0.0000 60.0000 0.0000 0.0000 +IC S H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC H12 H13 *C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI ETSH 0.00 ! C2H6S ethanethiol, Dzung Nguyen +GROUP +ATOM H1 HGA3 0.09 ! H1 H4 H5 +ATOM H2 HGA3 0.09 ! \ \ / +ATOM H3 HGA3 0.09 ! H2-CM1--CM2 +ATOM CM1 CG331 -0.27 ! / \ +GROUP ! H3 S3--H6 +ATOM H4 HGA2 0.09 +ATOM H5 HGA2 0.09 +ATOM CM2 CG321 -0.11 +ATOM S3 SG311 -0.23 +ATOM H6 HGP3 0.16 +BOND CM1 H1 CM1 H2 CM1 H3 +BOND CM1 CM2 CM2 H4 CM2 H5 +BOND CM2 S3 S3 H6 +IC H1 CM1 CM2 S3 0.00 0.00 60.0 0.0 0.0 +IC H2 CM1 CM2 S3 0.00 0.00 180.0 0.0 0.0 +IC H3 CM1 CM2 S3 0.00 0.00 300.0 0.0 0.0 +IC H1 CM1 CM2 H4 0.00 0.00 180.0 0.0 0.0 +IC H2 CM1 CM2 H4 0.00 0.00 300.0 0.0 0.0 +IC H3 CM1 CM2 H4 0.00 0.00 60.0 0.0 0.0 +IC H1 CM1 CM2 H5 0.00 0.00 300.0 0.0 0.0 +IC H2 CM1 CM2 H5 0.00 0.00 60.0 0.0 0.0 +IC H3 CM1 CM2 H5 0.00 0.00 180.0 0.0 0.0 +IC CM1 CM2 S3 H6 0.00 0.00 60.0 0.0 0.0 +IC H4 CM2 S3 H6 0.00 0.00 180.0 0.0 0.0 +IC H5 CM2 S3 H6 0.00 0.00 300.0 0.0 0.0 +PATCH FIRST NONE LAST NONE + +RESI ES1 -1.00 ! C2H5S ethylthiolate, adm jr. +GROUP +ATOM S SG302 -0.80 ! H21 H11 H12 +ATOM C1 CG323 -0.38 ! \ \ / +ATOM C2 CG331 -0.27 ! H22--C2--C1 +ATOM H21 HGA3 0.09 ! / \ +ATOM H22 HGA3 0.09 ! H23 S (-) +ATOM H23 HGA3 0.09 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +BOND S C1 C1 H11 C1 H12 C1 C2 +BOND C2 H21 C2 H22 C2 H23 +IC BLNK H11 C1 S 0.0000 0.00 0.00 109.72 1.8281 +IC S H11 *C1 H12 1.8281 109.72 118.35 105.91 1.1131 +IC S H11 *C1 C2 1.8281 109.72 -125.21 108.57 1.5315 +IC H12 C2 *C1 H11 1.1131 108.57 -114.71 108.57 1.1131 +IC S C1 C2 H21 1.8281 114.02 -180.00 110.65 1.1089 +IC S C1 C2 H22 1.8281 114.02 59.57 109.98 1.1111 +IC S C1 C2 H23 1.8281 114.02 -59.57 109.98 1.1111 +PATCH FIRST NONE LAST NONE + +RESI DMDS 0.00 ! C2H6S2 dimethyldisulfide, Dzung Nguyen +GROUP +ATOM H1 HGA3 0.09 +ATOM H2 HGA3 0.09 ! H1 +ATOM H3 HGA3 0.09 ! \ +ATOM CM1 CG331 -0.19 ! H2-CM1 +ATOM S2 SG301 -0.08 ! / \ +GROUP ! H3 S2--S3 H4 +ATOM S3 SG301 -0.08 ! \ / +ATOM CM4 CG331 -0.19 ! CM4-H5 +ATOM H4 HGA3 0.09 ! \ +ATOM H5 HGA3 0.09 ! H6 +ATOM H6 HGA3 0.09 +BOND H1 CM1 H2 CM1 H3 CM1 CM1 S2 +BOND S2 S3 S3 CM4 CM4 H4 CM4 H5 +BOND CM4 H6 +IC H1 CM1 S2 S3 0.00 0.00 60.0 0.0 0.0 +IC H2 CM1 S2 S3 0.00 0.00 180.0 0.0 0.0 +IC H3 CM1 S2 S3 0.00 0.00 300.0 0.0 0.0 +IC CM1 S2 S3 CM4 0.00 0.00 90.0 0.0 0.0 +IC S2 S3 CM4 H4 0.00 0.00 60.0 0.0 0.0 +IC S2 S3 CM4 H5 0.00 0.00 180.0 0.0 0.0 +IC S2 S3 CM4 H6 0.00 0.00 300.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI DEDS 0.00 ! C4H10S2 diethyldisulfide, adm jr. +GROUP +ATOM H1 HGA2 0.09 +ATOM H2 HGA2 0.09 ! H1 + ! \ +ATOM CM1 CG321 -0.10 ! H2-CM1 +ATOM S2 SG301 -0.08 ! / \ +GROUP ! CM0 S2--S3 H4 +ATOM S3 SG301 -0.08 ! / | \ \ / +ATOM CM4 CG321 -0.10 !H01| H03 CM4-H5 +ATOM H4 HGA2 0.09 ! H02 \ +ATOM H5 HGA2 0.09 ! CM5-H53 +GROUP ! / \ +ATOM CM0 CG331 -0.27 ! H51 H52 +ATOM H01 HGA3 0.09 +ATOM H02 HGA3 0.09 +ATOM H03 HGA3 0.09 +GROUP +ATOM CM5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 + +BOND H1 CM1 H2 CM1 CM1 CM0 CM1 S2 +BOND S2 S3 S3 CM4 CM4 H4 CM4 H5 +BOND CM4 CM5 +BOND CM0 H01 CM0 H02 CM0 H03 +BOND CM5 H51 CM5 H52 CM5 H53 + +IC CM0 CM1 S2 S3 0.00 0.00 60.0 0.0 0.0 +IC H1 CM1 S2 S3 0.00 0.00 60.0 0.0 0.0 +IC H2 CM1 S2 S3 0.00 0.00 300.0 0.0 0.0 +IC CM0 CM1 S2 S3 0.00 0.00 180.0 0.0 0.0 +IC S2 CM1 CM0 H01 0.00 0.00 180.0 0.0 0.0 +IC S2 CM1 CM0 H02 0.00 0.00 60.0 0.0 0.0 +IC S2 CM1 CM0 H03 0.00 0.00 300.0 0.0 0.0 +IC CM1 S2 S3 CM4 0.00 0.00 90.0 0.0 0.0 +IC S2 S3 CM4 H4 0.00 0.00 60.0 0.0 0.0 +IC S2 S3 CM4 H5 0.00 0.00 300.0 0.0 0.0 +IC S2 S3 CM4 CM5 0.00 0.00 180.0 0.0 0.0 +IC S3 CM4 CM5 H51 0.00 0.00 180.0 0.0 0.0 +IC S3 CM4 CM5 H52 0.00 0.00 60.0 0.0 0.0 +IC S3 CM4 CM5 H53 0.00 0.00 300.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI EMS 0.00 ! C3H8S ethylmethylsulfide, Dzung Nguyen +GROUP +ATOM H1 HGA3 0.09 +ATOM H2 HGA3 0.09 ! H1 H4 H5 +ATOM H3 HGA3 0.09 ! \ \ / +ATOM CM1 CG331 -0.27 ! H2-CM1--CM2 H6 +GROUP ! \ / +ATOM H4 HGA2 0.09 ! S3--CM4-H7 +ATOM H5 HGA2 0.09 ! \ +ATOM CM2 CG321 -0.13 ! kevo: symmetrized H8 +ATOM S3 SG311 -0.10 ! kevo: symmetrized +ATOM CM4 CG331 -0.22 +ATOM H6 HGA3 0.09 +ATOM H7 HGA3 0.09 +ATOM H8 HGA3 0.09 +BOND CM1 H1 CM1 H2 CM1 H3 +BOND CM1 CM2 CM2 H4 CM2 H5 +BOND CM2 S3 S3 CM4 +BOND CM4 H6 CM4 H7 CM4 H8 +IC H1 CM1 CM2 S3 0.00 0.00 60.0 0.0 0.0 +IC H2 CM1 CM2 S3 0.00 0.00 180.0 0.0 0.0 +IC H3 CM1 CM2 S3 0.00 0.00 300.0 0.0 0.0 +IC H1 CM1 CM2 H4 0.00 0.00 180.0 0.0 0.0 +IC H2 CM1 CM2 H4 0.00 0.00 300.0 0.0 0.0 +IC H3 CM1 CM2 H4 0.00 0.00 60.0 0.0 0.0 +IC H1 CM1 CM2 H5 0.00 0.00 300.0 0.0 0.0 +IC H2 CM1 CM2 H5 0.00 0.00 60.0 0.0 0.0 +IC H3 CM1 CM2 H5 0.00 0.00 180.0 0.0 0.0 +IC CM1 CM2 S3 CM4 0.00 0.00 60.0 0.0 0.0 +IC H4 CM2 S3 CM4 0.00 0.00 180.0 0.0 0.0 +IC H5 CM2 S3 CM4 0.00 0.00 300.0 0.0 0.0 +IC CM2 S3 CM4 H6 0.00 0.00 60.0 0.0 0.0 +IC CM2 S3 CM4 H7 0.00 0.00 180.0 0.0 0.0 +IC CM2 S3 CM4 H8 0.00 0.00 300.0 0.0 0.0 +PATCH FIRST NONE LAST NONE + +RESI IMIA 0.00 ! C3H4N2 Imidazole, adm jr. +GROUP +ATOM CG CG2R51 -0.05 ! HD1 HE1 +ATOM HG HGR52 0.09 ! | / +ATOM CD2 CG2R51 0.22 ! ND1--CE1 +ATOM HD2 HGR52 0.10 ! / || +ATOM ND1 NG2R51 -0.36 ! HG-CG || +ATOM HD1 HGP1 0.32 ! \\ || +ATOM CE1 CG2R53 0.25 ! CD2--NE2 +ATOM HE1 HGR52 0.13 ! | +ATOM NE2 NG2R50 -0.70 ! HD2 + +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG HG +DOUBLE NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 +DONO HD1 ND1 +ACCE NE2 +! for analysis +DONO HE1 CE1 +DONO HG CG +ACCE CE1 +ACCE ND1 +ACCE CD2 +IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 +IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 + +RESI MIMI 0.00 ! C4H6N2 4-methylimidazole, adm jr. +GROUP +ATOM ND1 NG2R51 -0.36 ! HD1 HE1 +ATOM HD1 HGP1 0.32 ! | / +ATOM CG CG2R51 -0.05 ! HB1 ND1--CE1 +ATOM CB CG331 -0.18 ! | / || +ATOM HB1 HGA3 0.09 ! HB2-CB-CG || +ATOM HB2 HGA3 0.09 ! | \\ || +ATOM HB3 HGA3 0.09 ! HB3 CD2--NE2 +GROUP ! | +ATOM NE2 NG2R50 -0.70 ! HD2 +ATOM CD2 CG2R51 0.22 +ATOM HD2 HGR52 0.10 +ATOM CE1 CG2R53 0.25 +ATOM HE1 HGR52 0.13 +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG CB +DOUBLE NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 +BOND CB HB1 CB HB2 CB HB3 +DONO HD1 ND1 +ACCE NE2 +IC CB CG ND1 CE1 1.5421 122.67 180.0 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CD2 NE2 CE1 HE1 1.3165 105.82 180.0 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 180.0 123.39 0.9770 +IC CB CG CD2 HD2 1.5421 131.52 0.0 118.30 1.0902 +IC CD2 CG CB HB1 0.0 0.0 0.0 0.0 0.0 +IC CD2 CG CB HB2 0.0 0.0 120.0 0.0 0.0 +IC CD2 CG CB HB3 0.0 0.0 240.0 0.0 0.0 +!IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +!IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +!IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +!IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +!Multiple errors corrected. + +RESI EIMI 0.00 ! C5H8N2 4-ethylimidazole, adm jr. +GROUP +ATOM CA CG331 -0.27 ! Optimized charges to minimize group size +ATOM HA1 HGA3 0.09 +ATOM HA2 HGA3 0.09 +ATOM HA3 HGA3 0.09 +GROUP +ATOM ND1 NG2R51 -0.36 ! HD1 HE1 +ATOM HD1 HGP1 0.32 ! | / +ATOM CG CG2R51 -0.05 ! HA1 HB1 ND1--CE1 +ATOM CB CG321 -0.09 ! \ | / || +ATOM HB1 HGA2 0.09 ! HA2-CA--CB-CG || +ATOM HB2 HGA2 0.09 ! / | \\ || +GROUP ! HA3 HB2 CD2--NE2 +ATOM NE2 NG2R50 -0.70 ! | +ATOM CD2 CG2R51 0.22 ! HD2 +ATOM HD2 HGR52 0.10 +ATOM CE1 CG2R53 0.25 +ATOM HE1 HGR52 0.13 +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG CB +DOUBLE NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 +DONO HD1 ND1 +ACCE NE2 +IC CB CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 +IC CG NE2 *CD2 HD2 0.0 0.0 180.0 0.0 0.0 +IC ND1 CD2 *CG CB 0.0 0.0 180.0 0.0 0.0 +IC CD2 CG CB CA 0.0 0.0 240.0 0.0 0.0 +IC CA CG *CB HB1 0.0 0.0 120.0 0.0 0.0 +IC CA CG *CB HB2 0.0 0.0 -120.0 0.0 0.0 +IC CG CB CA HA1 0.0 0.0 180.0 0.0 0.0 +IC HA1 CB *CA HA2 0.0 0.0 120.0 0.0 0.0 +IC HA1 CB *CA HA3 0.0 0.0 -120.0 0.0 0.0 + +RESI IMIM 1.00 ! C3H5N2 Imidazolium, adm jr. +GROUP +ATOM CG CG2R51 0.19 ! HD1 HE1 +ATOM HG HGR52 0.13 ! | / +ATOM CD2 CG2R51 0.19 ! ND1--CE1 +ATOM HD2 HGR52 0.13 ! / || +GROUP ! HG-CG || +ATOM ND1 NG2R52 -0.51 ! \\ || +ATOM HD1 HGP2 0.44 ! CD2--NE2 (+) +ATOM NE2 NG2R52 -0.51 ! | \ +ATOM HE2 HGP2 0.44 ! HD2 HE2 +ATOM CE1 CG2R53 0.32 +ATOM HE1 HGR53 0.18 +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG HG +DOUBLE NE2 CE1 CD2 CG +BOND ND1 HD1 CD2 HD2 CE1 HE1 NE2 HE2 +DONO HD1 ND1 +DONO HE2 NE2 +IC HG CG ND1 CE1 1.5421 122.67 -173.67 109.79 1.2987 +IC CG ND1 CE1 NE2 1.2854 109.79 0.21 110.31 1.3071 +IC ND1 CE1 NE2 CD2 1.2987 110.31 0.03 105.82 1.3165 +IC CE1 NE2 CD2 CG 1.3071 105.82 -0.23 108.68 1.3758 +IC NE2 CD2 CG ND1 1.3165 108.68 0.35 105.39 1.2854 +IC NE2 CD2 CG HG 1.3165 108.68 172.86 131.52 1.5421 +IC CD2 CG ND1 CE1 1.3758 105.39 -0.34 109.79 1.2987 +IC CD2 NE2 CE1 HE1 1.3165 105.82 149.51 119.57 1.0879 +IC NE2 CE1 ND1 HD1 1.3071 110.31 157.04 123.39 0.9770 +IC HG CG CD2 HD2 1.5421 131.52 -48.16 118.30 1.0902 +IC HE1 CE1 NE2 HE2 1.0879 125.00 0.00 125.00 1.0000 + +RESI EIMM 1.00 ! C5H9N2 Ethyl-Imidazolium, adm jr. +GROUP +ATOM CA CG331 -0.27 +ATOM HA1 HGA3 0.09 +ATOM HA2 HGA3 0.09 +ATOM HA3 HGA3 0.09 +GROUP +ATOM CB CG321 -0.05 ! HD1 HE1 +ATOM HB1 HGA2 0.09 ! | / +ATOM HB2 HGA2 0.09 ! HA1 HB1 ND1--CE1 +ATOM CG CG2R51 0.19 ! \ | / || +ATOM CD2 CG2R51 0.19 ! HA2-CA--CB-CG || +ATOM HD2 HGR52 0.13 ! / | \\ || +GROUP ! HA3 HB2 CD2--NE2(+) +ATOM ND1 NG2R52 -0.51 ! | \ +ATOM HD1 HGP2 0.44 ! HD2 HE2 +ATOM NE2 NG2R52 -0.51 +ATOM HE2 HGP2 0.44 +ATOM CE1 CG2R53 0.32 +ATOM HE1 HGR53 0.18 +BOND NE2 CD2 ND1 CG CE1 ND1 +BOND CG CB NE2 HE2 +DOUBLE CD2 CG NE2 CE1 +BOND ND1 HD1 CD2 HD2 CE1 HE1 +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 +DONO HD1 ND1 +ACCE NE2 + +IC CA CB CG ND1 0.0000 0.00 180.00 0.00 0.0000 +IC HA1 CB *CA HA2 0.0000 0.00 120.00 0.00 0.0000 +IC HA1 CB *CA HA3 0.0000 0.00 -120.00 0.00 0.0000 +IC HA1 CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CG CA *CB HB1 0.0000 0.00 120.00 0.00 0.0000 +IC CG CA *CB HB2 0.0000 0.00 -120.00 0.00 0.0000 +IC CA CB CG ND1 0.0000 0.00 180.00 0.00 0.0000 +IC ND1 CB *CG CD2 0.0000 0.00 180.00 0.00 0.0000 +IC CB CG CD2 NE2 0.0000 0.00 180.00 0.00 0.0000 +IC NE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC CB CG ND1 CE1 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CD2 *NE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC NE2 ND1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 + +RESI BENZ 0.00 ! C6H6 benzene, adm jr. +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 ! HD1 HE1 +ATOM CD1 CG2R61 -0.115 ! | | +ATOM HD1 HGR61 0.115 ! CD1--CE1 +ATOM CD2 CG2R61 -0.115 ! / \ +ATOM HD2 HGR61 0.115 ! HG--CG CZ--HZ +ATOM CE1 CG2R61 -0.115 ! \ / +ATOM HE1 HGR61 0.115 ! CD2--CE2 +ATOM CE2 CG2R61 -0.115 ! | | +ATOM HE2 HGR61 0.115 ! HD2 HE2 +ATOM CZ CG2R61 -0.115 +ATOM HZ HGR61 0.115 +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI EBEN 0.00 ! C8H10 ethylbenzene, adm jr. +GROUP +ATOM CG CG2R61 0.000 + ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 !HA1 HB1 CD1--CE1 +ATOM HD1 HGR61 0.115 ! \ | / \ +GROUP !HA2-CA--CB--CG CZ--HZ +ATOM CD2 CG2R61 -0.115 ! / | \ / +ATOM HD2 HGR61 0.115 !HA3 HB2 CD2--CE2 +GROUP ! | | +ATOM CE1 CG2R61 -0.115 ! HD2 HE2 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CZ CG2R61 -0.115 +ATOM HZ HGR61 0.115 +GROUP +ATOM CB CG321 -0.18 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CA CG331 -0.27 +ATOM HA1 HGA3 0.09 +ATOM HA2 HGA3 0.09 +ATOM HA3 HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG CB CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 + +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG CB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD2 CG CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD2 CG CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 +IC CD2 CG CB CA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC CG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 + +RESI PHEN 0.00 ! C6H6O phenol, adm jr. +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 ! CD1--CE1 +ATOM HD1 HGR61 0.115 ! // \\ +GROUP ! HG--CG CZ--OH +ATOM CD2 CG2R61 -0.115 ! \ / \ +ATOM HD2 HGR61 0.115 ! CD2==CE2 HH +GROUP ! | | +ATOM CE1 CG2R61 -0.115 ! HD2 HE2 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CZ CG2R61 0.11 +ATOM OH OG311 -0.53 +ATOM HH HGP1 0.42 +BOND CD2 CG CE1 CD1 +BOND CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH OH HH +DOUBLE CD1 CG CE2 CD2 CZ CE1 +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CZ OH HH 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI EPHE 0.00 ! C8H10O p-ethylphenol, adm jr. +GROUP +ATOM CG CG2R61 0.00 + ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 !HA1 HB1 CD1--CE1 +ATOM HD1 HGR61 0.115 ! \ | / \ +GROUP !HA2-CA--CB--CG CZ--OH +ATOM CD2 CG2R61 -0.115 ! / | \ / \ +ATOM HD2 HGR61 0.115 !HA3 HB2 CD2--CE2 HH +GROUP ! | | +ATOM CE1 CG2R61 -0.115 ! HD2 HE2 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CZ CG2R61 0.11 +ATOM OH OG311 -0.53 +ATOM HH HGP1 0.42 +GROUP +ATOM CB CG321 -0.18 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CA CG331 -0.27 +ATOM HA1 HGA3 0.09 +ATOM HA2 HGA3 0.09 +ATOM HA3 HGA3 0.09 + +BOND CD2 CG CE1 CD1 +BOND CZ CE2 +BOND CG CB CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH OH HH +BOND CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA HA3 +DOUBLE CD1 CG CE2 CD2 CZ CE1 + +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG CB 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CZ OH HH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD2 CG CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD2 CG CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 +IC CD2 CG CB CA 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG CB CA HA2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC CG CB CA HA3 0.0000 0.0000 300.0000 0.0000 0.0000 + +RESI PHEO -1.00 ! C6H5O phenoxide, adm jr. +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 ! CD1--CE1 +ATOM HD1 HGR61 0.115 ! / \ +GROUP ! HG--CG CZ--OH (-) +ATOM CD2 CG2R61 -0.115 ! \ / +ATOM HD2 HGR61 0.115 ! CD2--CE2 +GROUP ! | | +ATOM CE1 CG2R61 -0.60 ! HD2 HE2 +ATOM HE1 HGR61 0.28 +ATOM CE2 CG2R61 -0.60 +ATOM HE2 HGR61 0.28 +ATOM CZ CG2R61 0.40 +ATOM OH OG312 -0.76 +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ OH 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI APNH 0.00 ! C7H12N2O2 acetyl-prolineamide (aka AP2, APAM), R. Dunbrack + + !HY1 HY2 HY3 +ATOM N NG2S0 -0.29 ! \ | / +ATOM CA CG3C51 0.02 ! CAY +ATOM CB CG3C52 -0.18 ! | +ATOM CG CG3C52 -0.18 ! OY=CY HD1 HD2 +ATOM CD CG3C52 0.00 ! \ \ / +ATOM CY CG2O1 0.51 ! N---CD HG1 +ATOM OY OG2D1 -0.51 ! | \ / +ATOM C CG2O1 0.51 ! | CG +ATOM HA HGA1 0.09 ! | / \ +ATOM HB1 HGA2 0.09 ! HA-CA--CB HG2 +ATOM HB2 HGA2 0.09 ! | / \ +ATOM HG1 HGA2 0.09 ! | HB1 HB2 +ATOM HG2 HGA2 0.09 ! O=C +ATOM HD1 HGA2 0.09 ! | +ATOM HD2 HGA2 0.09 ! NT +ATOM CAY CG331 -0.27 ! / \ +ATOM HY1 HGA3 0.09 ! HT1 HT2 +ATOM HY2 HGA3 0.09 +ATOM HY3 HGA3 0.09 +ATOM O OG2D1 -0.51 +ATOM NT NG2S2 -0.62 +ATOM HT1 HGP1 0.31 +ATOM HT2 HGP1 0.31 +BOND CY N CAY HY1 CAY HY2 CAY HY3 +BOND CY CAY N CA CA CB CB CG CG CD CD N +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +BOND C CA C NT NT HT1 NT HT2 +DOUBLE C O CY OY +IMPR CY CAY N OY +IMPR C CA NT O +DONOR HT1 NT +DONOR HT2 NT +ACCEPTOR OY CY +ACCEPTOR O C +! Improper ICs +IC CY CA *N CD 0.00 0.00 180.00 0.00 0.00 +IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 +IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 +IC N CAY *CY OY 0.00 0.00 180.00 0.00 0.00 +! Backbone + Peptide bond IC's +IC OY CY N CA 0.00 0.00 0.00 0.00 0.00 !Omega +IC CAY CY N CA 0.00 0.00 180.00 0.00 0.00 !Omega +IC CY N CA C 0.00 120.64 -60.00 0.00 0.00 !Psi +IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi +IC CAY CY N CD 0.00 0.00 0.00 120.64 0.00 +IC CY N CD CG 0.00 0.00 168.60 103.28 0.00 +IC CY N CA CB 0.00 0.00 168.64 103.34 0.00 +! Ring IC's +IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 +IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 +IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 +IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 +IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 +! Carbonyl IC's +IC CD N CA C 0.00 112.90 120.00 108.00 0.00 +! Hydrogen IC's +IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 +IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 +IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 +IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 +IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 +IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 +IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 +IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 +IC CA C NT HT2 0.00 0.00 180.00 0.00 0.00 +IC C HT2 *NT HT1 0.00 0.00 180.00 0.00 0.00 +IC OY CY CAY HY1 0.00 0.00 90.00 0.00 0.00 +IC CY HY1 *CAY HY2 0.00 0.00 120.00 0.00 0.00 +IC CY HY1 *CAY HY3 0.00 0.00 -120.00 0.00 0.00 + +RESI PDIP 0.00 ! C8H14N2O2 proline dipeptide + + !HY1 HY2 HY3 +ATOM N NG2S0 -0.29 ! \ | / +ATOM CA CG3C51 0.02 ! CAY +ATOM CB CG3C52 -0.18 ! | +ATOM CG CG3C52 -0.18 ! OY=CY HD1 HD2 +ATOM CD CG3C52 0.00 ! \ \ / +ATOM CY CG2O1 0.51 ! N---CD HG1 +ATOM OY OG2D1 -0.51 ! | \ / +ATOM C CG2O1 0.51 ! | CG +ATOM HA HGA1 0.09 ! | / \ +ATOM HB1 HGA2 0.09 ! HA-CA--CB HG2 +ATOM HB2 HGA2 0.09 ! | / \ +ATOM HG1 HGA2 0.09 ! | HB1 HB2 +ATOM HG2 HGA2 0.09 ! O=C +ATOM HD1 HGA2 0.09 ! | +ATOM HD2 HGA2 0.09 ! NT +ATOM CAY CG331 -0.27 ! / \ +ATOM HY1 HGA3 0.09 ! HT1 CR-HR3 +ATOM HY2 HGA3 0.09 ! / \ +ATOM HY3 HGA3 0.09 ! HR1 HR2 +ATOM O OG2D1 -0.51 +ATOM NT NG2S1 -0.47 +ATOM HT1 HGP1 0.31 +ATOM CR CG331 -0.11 +ATOM HR1 HGA3 0.09 +ATOM HR2 HGA3 0.09 +ATOM HR3 HGA3 0.09 + +BOND CY N CAY HY1 CAY HY2 CAY HY3 +BOND CY CAY N CA CA CB CB CG CG CD CD N +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +BOND C CA C NT NT HT1 NT CR +BOND CR HR1 CR HR2 CR HR3 +DOUBLE C O CY OY +IMPR CY CAY N OY +IMPR C CA NT O +DONOR HT1 NT +ACCEPTOR OY CY +ACCEPTOR O C + +IC CAY CY N CA 1.4871 118.91 174.70 123.38 1.4590 +IC CY N CA C 1.3234 123.38 -72.54 111.46 1.5357 +IC N CA C NT 1.4590 111.46 117.46 121.78 1.3479 +IC CY CA *N CD 1.3234 123.38 176.71 112.56 1.4667 +IC N C *CA CB 1.4590 111.46 114.78 112.03 1.5409 +IC N C *CA HA 1.4590 111.46 -122.11 109.86 1.0785 +IC N CAY *CY OY 1.3234 118.91 -179.24 119.14 1.2260 +IC OY CY N CA 1.2260 121.95 -6.08 123.38 1.4590 +IC CAY CY N CA 1.4871 118.91 174.70 123.38 1.4590 +IC CY N CA C 1.3234 123.38 -72.54 111.46 1.5357 +IC N CA C NT 1.4590 111.46 117.46 121.78 1.3479 +IC CAY CY N CD 1.4871 118.91 -1.63 123.97 1.4667 +IC CY N CD CG 1.3234 123.97 171.81 105.08 1.5319 +IC CY N CA CB 1.3234 123.38 167.19 102.97 1.5409 +IC N CA CB CG 1.4590 102.97 30.57 104.52 1.5340 +IC CA CB CG CD 1.5409 104.52 -33.72 103.37 1.5319 +IC CB CG CD N 1.5340 103.37 23.86 105.08 1.4667 +IC CG CD N CA 1.5319 105.08 -4.88 112.56 1.4590 +IC CD N CA CB 1.4667 112.56 -16.10 102.97 1.5409 +IC CD N CA C 1.4667 112.56 104.17 111.46 1.5357 +IC CD N CA HA 1.4667 112.56 -133.77 109.94 1.0785 +IC N CA CB HB1 1.4590 102.97 153.44 113.27 1.1091 +IC N CA CB HB2 1.4590 102.97 -85.51 108.72 1.1129 +IC CA CB CG HG1 1.5409 104.52 82.51 109.30 1.1137 +IC CA CB CG HG2 1.5409 104.52 -155.89 112.80 1.1079 +IC CB CG CD HD1 1.5340 103.37 144.10 110.20 1.1134 +IC CB CG CD HD2 1.5340 103.37 -93.57 110.40 1.1126 +IC NT CA *C O 1.3479 121.78 179.58 119.57 1.2276 +IC CA C NT HT1 1.5357 121.78 -178.24 114.38 0.9952 +IC N CY CAY HY1 1.3234 118.91 177.72 108.99 1.1118 +IC HY1 CY *CAY HY2 1.1118 108.99 119.00 110.21 1.1099 +IC HY1 CY *CAY HY3 1.1118 108.99 -119.34 110.53 1.1094 +IC C HT1 *NT CR 1.3479 114.38 -176.13 117.94 1.4463 +IC C NT CR HR1 1.3479 127.54 -178.11 110.27 1.1125 +IC C NT CR HR2 1.3479 127.54 62.09 110.97 1.1130 +IC C NT CR HR3 1.3479 127.54 -58.81 110.79 1.1141 + +RESI PNH2 1.00 ! C5H11N2O prolineamide (aka TP2, PAMD), R. Dunbrack +ATOM N NG3P2 -0.07 +ATOM HN1 HGP2 0.24 +ATOM HN2 HGP2 0.24 +ATOM CD CG3C54 0.16 +ATOM CB CG3C52 -0.18 ! HN1 HD1 HD2 +ATOM CG CG3C52 -0.18 ! \ \ / +ATOM CA CG3C53 0.16 ! HN2--N---CD HG1 +ATOM C CG2O1 0.51 ! |(+) \ / +ATOM O OG2D1 -0.51 ! | CG +ATOM HA HGA1 0.09 ! | / \ +ATOM HB1 HGA2 0.09 ! HA-CA--CB HG2 +ATOM HB2 HGA2 0.09 ! | / \ +ATOM HG1 HGA2 0.09 ! | HB1 HB2 +ATOM HG2 HGA2 0.09 ! O=C +ATOM HD1 HGA2 0.09 ! | +ATOM HD2 HGA2 0.09 ! NT +ATOM NT NG2S2 -0.62 ! / \ +ATOM HT1 HGP1 0.31 ! HT1 HT2 +ATOM HT2 HGP1 0.31 +BOND HN1 N HN2 N N CA CA CB CB CG CG CD CD N +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +BOND C CA C NT NT HT1 NT HT2 +DOUBLE C O +IMPR C CA NT O +DONOR HT1 NT +DONOR HT2 NT +DONOR HN1 N +DONOR HN2 N +ACCEPTOR O C +! Improper ICs +IC HN1 CA *N CD 0.00 0.00 120.00 0.00 0.00 +IC HN2 CA *N HN1 0.00 0.00 120.00 0.00 0.00 +IC N C *CA CB 0.00 0.00 120.00 0.00 0.00 +IC N C *CA HA 0.00 0.00 -120.00 0.00 0.00 +! Backbone + Peptide bond IC's +IC N CA C NT 0.00 0.00 180.0 0.00 0.00 !Phi +! Ring IC's +IC N CA CB CG 0.00 103.34 29.25 103.67 0.00 +IC CA CB CG CD 0.00 103.67 -36.72 103.63 0.00 +IC CB CG CD N 0.00 103.63 29.50 103.28 0.00 +IC CG CD N CA 0.00 103.28 -11.61 112.90 0.00 +IC CD N CA CB 0.00 112.90 -11.17 103.34 0.00 +! Carbonyl IC's +IC CD N CA C 0.00 112.90 120.00 108.00 0.00 +! Hydrogen IC's +IC CD N CA HA 0.00 0.00 -120.00 108.00 0.00 +IC N CA CB HB1 0.00 0.00 120.00 108.00 0.00 +IC N CA CB HB2 0.00 0.00 -120.00 108.00 0.00 +IC CA CB CG HG1 0.00 0.00 120.00 108.00 0.00 +IC CA CB CG HG2 0.00 0.00 -120.00 108.00 0.00 +IC CB CG CD HD1 0.00 0.00 120.00 108.00 0.00 +IC CB CG CD HD2 0.00 0.00 -120.00 108.00 0.00 +IC NT CA *C O 0.00 0.00 180.00 0.00 0.00 +IC CA C NT HT2 0.00 0.00 180.00 0.00 0.00 +IC C HT2 *NT HT1 0.00 0.00 180.00 0.00 0.00 + +RESI ETHA 0.00 ! C2H6 ethane +GROUP +ATOM H11 HGA3 0.09 ! H11 H21 +ATOM H12 HGA3 0.09 ! \ / +ATOM H13 HGA3 0.09 ! H12-C1--C2-H22 +ATOM C1 CG331 -0.27 ! / \ +GROUP ! H13 H23 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 +ATOM C2 CG331 -0.27 +BOND C1 H11 C1 H12 C1 H13 +BOND C1 C2 C2 H21 C2 H22 C2 H23 +IC C2 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 +IC C2 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 +IC H11 C1 C2 H21 0.00 0.00 180.0 0.0 0.0 +IC C1 H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 +IC C1 H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 + +RESI PRPA 0.00 ! C3H8 propane, adm jr. +GROUP +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM C1 CG331 -0.27 ! H11 H21 H31 +ATOM C2 CG321 -0.18 ! \ | / +ATOM H21 HGA2 0.09 ! H12-C1--C2--C3-H32 +ATOM H22 HGA2 0.09 ! / | \ +ATOM H31 HGA3 0.09 ! H13 H22 H33 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 +ATOM C3 CG331 -0.27 +BOND C1 H11 C1 H12 C1 H13 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 C3 C3 H31 C3 H32 C3 H33 +IC C1 C2 C3 H31 0.00 0.00 180.0 0.0 0.0 +IC C2 H31 *C3 H32 0.00 0.00 120.0 0.0 0.0 +IC C2 H31 *C3 H33 0.00 0.00 -120.0 0.0 0.0 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.0 0.0 +IC C2 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 +IC C2 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.0 0.0 +IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.0 0.0 + +RESI BUTA 0.00 ! C4H10 butane +GROUP +ATOM H11 HGA3 0.09 ! H11 H21 H31 H41 +ATOM H12 HGA3 0.09 ! \ | | / +ATOM H13 HGA3 0.09 ! H12-C1--C2--C3--C4-H42 +ATOM C1 CG331 -0.27 ! / | | \ +GROUP ! H13 H22 H33 H43 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C2 CG321 -0.18 +GROUP +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C3 CG321 -0.18 +GROUP +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 +ATOM C4 CG331 -0.27 +BOND H11 C1 H12 C1 H13 C1 C1 C2 +BOND H21 C2 H22 C2 C2 C3 +BOND H31 C3 H32 C3 C3 C4 +BOND H41 C4 H42 C4 H43 C4 +IC C1 C2 C3 C4 0.00 0.00 180.0 0.0 0.0 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.0 0.0 +IC C2 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 +IC C2 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.0 0.0 +IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.0 0.0 +IC C2 C4 *C3 H31 0.00 0.00 120.0 0.0 0.0 +IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.0 0.0 +IC C2 C3 C4 H41 0.00 0.00 180.0 0.0 0.0 +IC C3 H41 *C4 H42 0.00 0.00 120.0 0.0 0.0 +IC C3 H41 *C4 H43 0.00 0.00 -120.0 0.0 0.0 + +RESI IBUT 0.00 ! C4H10 Iso-butane, S. Fischer +GROUP +ATOM CT CG311 -0.09 ! H12 +ATOM HT HGA1 0.09 ! | +GROUP ! H11-C1-H13 +ATOM C1 CG331 -0.27 ! | +ATOM H11 HGA3 0.09 ! CT-HT +ATOM H12 HGA3 0.09 ! / \ +ATOM H13 HGA3 0.09 ! / \ +GROUP ! H21-C2 C3-H31 +ATOM C2 CG331 -0.27 ! / | | \ +ATOM H21 HGA3 0.09 ! H22 H23 H33 H32 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 +GROUP +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 +BOND CT C1 CT C2 CT C3 CT HT +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +IC C1 C2 *CT C3 0.00 0.00 120.0 0.0 0.0 +IC C1 C2 *CT HT 0.00 0.00 -120.0 0.0 0.0 +IC C2 CT C1 H11 0.00 0.00 180.0 0.0 0.0 +IC CT H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 +IC CT H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 +IC C1 CT C2 H21 0.00 0.00 180.0 0.0 0.0 +IC CT H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 +IC CT H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 +IC C1 CT C3 H31 0.00 0.00 180.0 0.0 0.0 +IC CT H31 *C3 H32 0.00 0.00 120.0 0.0 0.0 +IC CT H31 *C3 H33 0.00 0.00 -120.0 0.0 0.0 + +RESI PENT 0.00 ! C5H12 pentane, adm jr. +GROUP +ATOM C1 CG331 -0.27 ! H11 H21 H31 H41 H51 +ATOM H11 HGA3 0.09 ! \ | | | / +ATOM H12 HGA3 0.09 ! H12-C1--C2--C3--C4--C5-H52 +ATOM H13 HGA3 0.09 ! / | | | \ +GROUP ! H13 H22 H33 H42 H53 +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +GROUP +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +BOND C5 H52 C5 H53 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 H51 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 +IC C4 H51 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI OCOH 0.00 ! C8H18O OCTANOL +GROUP +ATOM C1 CG321 0.05 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM O1 OG311 -0.65 +ATOM HO1 HGP1 0.42 +GROUP +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +GROUP +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG321 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +GROUP +ATOM C6 CG321 -0.18 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 +GROUP +ATOM C7 CG321 -0.18 +ATOM H71 HGA2 0.09 +ATOM H72 HGA2 0.09 +GROUP +ATOM C8 CG331 -0.27 +ATOM H81 HGA3 0.09 +ATOM H82 HGA3 0.09 +ATOM H83 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C1 O1 O1 HO1 +BOND C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 C5 H51 +BOND C5 H52 C6 H61 C6 H62 C7 H71 C7 H72 +BOND C8 H81 C8 H82 C8 H83 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 H83 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 O1 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C8 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C8 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 +IC C7 H83 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 +IC C7 H83 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI CO2 0.00 ! CO2 Carbon Dioxide, John Straub +GROUP +ATOM C CG2O7 0.60 +ATOM OC1 OG2D5 -0.30 +ATOM OC2 OG2D5 -0.30 +BOND OC1 C OC2 C + +RESI CO3 -2.00 ! CO3 ionized carbonate, adm jr., aug 2001 +!As organic carbonates and carbamates are uncharged, we definitely want to use +!other (ester respectively amide?) atom typing for those. This leaves the atom +!typing for their (-1) counterparts undefined, but these are unstable anyway... +GROUP +ATOM C1 CG2O6 1.42 +ATOM O1 OG2D2 -1.14 +ATOM O2 OG2D2 -1.14 +ATOM O3 OG2D2 -1.14 + +BOND C1 O1 C1 O2 C1 O3 +! required for out-of-plane vibrations +IMPR C1 O1 O2 O3 +IC O2 O1 *C1 O3 0.0000 0.00 180.00 0.00 0.0000 +IC O3 O2 *C1 O1 0.0000 0.00 180.00 0.00 0.0000 !redundant definition needed to enable seeding. + +RESI C3 0.00 ! C3H6 Cyclopropane Model Compound +GROUP ! JMW and CBP 16 April 2004 +ATOM C1 CG3C31 -0.18 +ATOM H11 HGA2 0.09 ! H11 H12 +ATOM H12 HGA2 0.09 ! \ / +GROUP ! C1 +ATOM C2 CG3C31 -0.18 ! / \ +ATOM H21 HGA2 0.09 ! H21--C2----C3--H31 +ATOM H22 HGA2 0.09 ! | | +GROUP ! H22 H32 +ATOM C3 CG3C31 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +BOND C1 C2 C2 C3 C3 C1 +BOND C1 H11 C1 H12 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 + +IC C1 C2 C3 H31 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C1 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C1 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 + +PATCHING FIRST NONE LAST NONE + +!toppar_all22_prot_aldehydes.str +!acetaldehyde additions, ssc & adm, jr., 2/01 +RESI AALD 0.00 ! C2H4O Acetaldehyde, adm, Oct 2008 +GROUP +ATOM HA HGR52 0.09 ! HB3 +ATOM C CG2O4 0.20 ! | +ATOM O OG2D1 -0.40 !HB1-CB-HB2 +ATOM CB CG331 -0.16 ! | +ATOM HB1 HGA3 0.09 ! O=C +ATOM HB2 HGA3 0.09 ! | +ATOM HB3 HGA3 0.09 ! HA + +BOND HA C C CB CB HB1 CB HB2 CB HB3 +DOUB C O +IMPR C CB O HA +ACCE O +IC O C CB HB1 1.2074 123.73 -0.46 108.58 1.1053 +IC HB2 CB C O 1.0625 110.65 118.23 123.73 1.2074 +IC HB3 CB C O 1.0898 105.98 -126.83 123.73 1.2074 +IC HA O *C CB 1.1347 126.86 -176.51 123.73 1.5462 +PATCHING FIRST NONE LAST NONE + +RESI PALD 0.00 ! C3H6O Propionaldehyde +GROUP +ATOM O OG2D1 -0.40 ! HG3 +ATOM C CG2O4 0.20 ! | +ATOM CB CG321 -0.07 !HG1-CG-HG2 +ATOM HB1 HGA2 0.09 ! | +ATOM HB2 HGA2 0.09 !HB1-CB-HB2 +ATOM HA HGR52 0.09 ! | +GROUP ! O=C +ATOM CG CG331 -0.27 ! | +ATOM HG1 HGA3 0.09 ! HA +ATOM HG2 HGA3 0.09 +ATOM HG3 HGA3 0.09 +BOND HA C C CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG3 CG HG2 +DOUBLE C O +IMPR C CB O HA +ACCE O +IC O C CB CG 0.0 0.0 0.0 0.0 0.0 +IC CG CB C HA 0.0 0.0 180.0 0.0 0.0 +IC HB1 CB C O 0.0 0.0 120.0 0.0 0.0 +IC HB2 CB C O 0.0 0.0 -120.0 0.0 0.0 +IC C CB CG HG1 0.0 0.0 180.0 0.0 0.0 +IC C CB CG HG2 0.0 0.0 60.0 0.0 0.0 +IC C CB CG HG3 0.0 0.0 -60.0 0.0 0.0 +PATCHING FIRST NONE LAST NONE + +RESI CALD 0.00 ! C2H3ClO Chloroacetaldehyde +!KEVO: charges adjusted to reflect updated aldehyde AND aliphatic chlorine L-J. +!==> RE-OPTIMIZE!!! +GROUP ! CL +ATOM O OG2D1 -0.40 ! | +ATOM C CG2O4 0.20 !HB1-CB-HB2 +ATOM CB CG321 -0.03 ! | +ATOM HB1 HGA2 0.09 ! O=C +ATOM HB2 HGA2 0.09 ! | +ATOM CL CLGA1 -0.04 ! HA +ATOM HA HGR52 0.09 +BOND HA C C CB CB HB1 CB HB2 +BOND CB CL +DOUBLE C O +IMPR C CB O HA +ACCE O +IC O C CB CL 0.0 0.0 180.0 0.0 0.0 +IC CL CB C HA 0.0 0.0 0.0 0.0 0.0 +IC HA O *C CB 0.0 0.0 0.0 0.0 0.0 +IC CL C *CB HB1 0.0 0.0 120.0 0.0 0.0 +IC HB1 C *CB HB2 0.0 0.0 120.0 0.0 0.0 +PATCHING FIRST NONE LAST NONE + +!benzaldehyde additions, ssc & adm, jr., 2/01 +RESI BALD 0.00 ! C7H6O Benzaldehyde +GROUP +ATOM HA HGR52 0.08 ! HZ +ATOM C CG2O4 0.24 ! | +ATOM O OG2D1 -0.41 ! CZ +ATOM CG CG2R61 0.09 ! // \ +GROUP !HE1-CE1 CE2-HE2 +ATOM CD1 CG2R61 -0.115 ! | || +ATOM HD1 HGR61 0.115 !HD1-CD1 CD2-HD2 +GROUP ! \\ / +ATOM CE1 CG2R61 -0.115 ! CG +ATOM HE1 HGR61 0.115 ! | +GROUP ! O=C +ATOM CZ CG2R61 -0.115 ! | +ATOM HZ HGR61 0.115 ! HA +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +BOND HA C C CG CG CD1 CG CD2 +BOND CD1 HD1 CD2 HD2 CD1 CE1 CD2 CE2 +BOND CE1 HE1 CE2 HE2 CE1 CZ CE2 CZ +BOND CZ HZ +DOUBLE C O +IMPR C CG O HA +ACCE O +IC O C CG CD1 0.0 0.0 0.0 0.0 0.0 +IC HA O *C CG 0.0 0.0 180.0 0.0 0.0 +IC CD1 C *CG CD2 0.0 0.0 -177.9600 0.0 0.0 +IC C CG CD1 CE1 0.0 0.0 -177.3700 0.0 0.0 +IC CE1 CG *CD1 HD1 0.0 0.0 179.7000 0.0 0.0 +IC C CG CD2 CE2 0.0 0.0 177.2000 0.0 0.0 +IC CE2 CG *CD2 HD2 0.0 0.0 -178.6900 0.0 0.0 +IC CG CD1 CE1 CZ 0.0 0.0 -0.1200 0.0 0.0 +IC CZ CD1 *CE1 HE1 0.0 0.0 -179.6900 0.0 0.0 +IC CZ CD2 *CE2 HE2 0.0 0.0 -179.9300 0.0 0.0 +IC CE1 CE2 *CZ HZ 0.0 0.0 179.5100 0.0 0.0 +PATCHING FIRST NONE LAST NONE + +!toppar_all22_prot_fluoro_alkanes.str +RESI FETH 0.00 ! C2H5F fluoroethane, adm jr., 4/99 +GROUP +ATOM H13 HGA3 0.09 +ATOM C1 CG331 -0.21 +ATOM C2 CG322 -0.06 +ATOM F21 FGA1 -0.22 +ATOM H22 HGA6 0.11 +ATOM H23 HGA6 0.11 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +BOND C1 H11 C1 H12 C1 H13 +BOND C1 C2 +BOND C2 F21 C2 H22 C2 H23 +IC H13 C1 C2 F21 1.1111 110.55 180.00 109.78 1.3721 +IC H13 C1 C2 H22 1.1111 110.55 60.02 111.56 1.0839 +IC H13 C1 C2 H23 1.1111 110.55 -60.02 111.56 1.0839 +IC C1 C2 H22 H23 1.5188 111.56 -122.50 36.33 1.7464 +IC H13 C2 *C1 H11 1.1111 110.55 -120.29 110.55 1.1111 +IC H13 C2 *C1 H12 1.1111 110.55 120.29 110.55 1.1111 +PATC FIRS NONE LAST NONE + +RESI DFET 0.00 ! C2H4F2 difluoroethane, adm jr., 4/99 +GROUP +ATOM H13 HGA3 0.09 +ATOM C1 CG331 -0.23 +ATOM C2 CG312 0.24 +ATOM H21 HGA7 0.10 +ATOM F22 FGA2 -0.19 +ATOM F23 FGA2 -0.19 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +BOND C1 H11 C1 H12 C1 H13 +BOND C1 C2 +BOND C2 F23 C2 F22 C2 H21 +IC H13 C1 C2 H21 0.00 0.00 180.0 0.0 0.0 +IC C1 C2 F23 F22 0.00 0.00 0.0 0.0 0.0 +IC H13 C1 C2 F22 0.00 0.00 60.0 0.0 0.0 +IC H13 C1 C2 F23 0.00 0.00 -60.0 0.0 0.0 +IC H12 C1 C2 H21 0.00 0.00 -60.0 0.0 0.0 +IC H11 C1 C2 H21 0.00 0.00 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TFET 0.00 ! C2H3F3 trifluoroethane +GROUP +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM C1 CG331 -0.20 +ATOM F21 FGA3 -0.15 +ATOM F22 FGA3 -0.15 +ATOM F23 FGA3 -0.15 +ATOM C2 CG302 0.38 +BOND C1 H11 C1 H12 C1 H13 +BOND C1 C2 C2 F21 C2 F22 C2 F23 +IC H13 C1 C2 F21 0.00 0.00 180.0 0.0 0.0 +IC C1 C2 F22 F23 0.00 0.00 0.0 0.0 0.0 +IC H13 C1 C2 F22 0.00 0.00 60.0 0.0 0.0 +IC H13 C1 C2 F23 0.00 0.00 -60.0 0.0 0.0 +IC H11 C1 C2 F21 0.00 0.00 60.0 0.0 0.0 +IC H12 C1 C2 F21 0.00 0.00 -60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TFE 0.00 ! C2H3F3O trifluoroethanol +GROUP +ATOM O1 OG311 -0.59 +ATOM HO1 HGP1 0.41 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM C1 CG321 0.08 +ATOM F21 FGA3 -0.14 +ATOM F22 FGA3 -0.14 +ATOM F23 FGA3 -0.14 +ATOM C2 CG302 0.34 +BOND C1 H11 C1 H12 C1 O1 O1 HO1 +BOND C1 C2 C2 F21 C2 F22 C2 F23 +IC HO1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C2 F21 0.0000 0.00 180.00 0.00 0.0000 +IC F21 C1 *C2 F22 0.0000 0.00 120.00 0.00 0.0000 +IC F21 C1 *C2 F23 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +!toppar_all22_prot_pyridines.str +RESI PYR1 0.00 ! C5H5N pyridine, yin +GROUP +ATOM N1 NG2R60 -0.600 +ATOM C2 CG2R61 0.180 +ATOM C3 CG2R61 -0.115 +ATOM C4 CG2R61 -0.115 +ATOM C5 CG2R61 -0.115 +ATOM C6 CG2R61 0.180 +ATOM H2 HGR62 0.120 +ATOM H3 HGR61 0.115 +ATOM H4 HGR61 0.115 +ATOM H5 HGR61 0.115 +ATOM H6 HGR62 0.120 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 N1 +BOND C2 H2 C3 H3 C4 H4 C5 H5 C6 H6 + +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 N1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 4AP2 0.00 ! C5H6N2 4-aminopyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 -0.115 +ATOM CG CG2R61 0.050 +ATOM CE2 CG2R61 0.180 +ATOM CD2 CG2R61 -0.115 +ATOM NG NG2S3 -0.850 +ATOM HE1 HGR62 0.120 +ATOM HD1 HGR61 0.115 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR62 0.120 +ATOM HG11 HGP4 0.400 +ATOM HG12 HGP4 0.400 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CG NG NG HG11 NG HG12 + +IMPR NG HG12 HG11 CG + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG NG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CG NG HG11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HG11 CG *NG HG12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3APY 0.00 ! C5H6N2 3-aminopyridine, yin + +GROUP ! HD11 HD12 +ATOM CG CG2R61 -0.115 ! \ / +ATOM HG HGR61 0.115 ! ND1 HE1 +GROUP ! \ | +ATOM CD1 CG2R61 0.090 ! CD1--CE1 +ATOM ND1 NG2S3 -0.840 ! / \ +ATOM HD11 HGP4 0.370 ! HG--CG NZ +ATOM HD12 HGP4 0.380 ! \ / +GROUP ! CD2--CE2 +ATOM CD2 CG2R61 -0.115 ! | | +ATOM HD2 HGR61 0.115 ! HD2 HE2 +GROUP +ATOM CE1 CG2R61 0.180 +ATOM HE1 HGR62 0.120 +ATOM CE2 CG2R61 0.180 +ATOM HE2 HGR62 0.120 +ATOM NZ NG2R60 -0.600 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 ND1 ND1 HD11 ND1 HD12 + +IMPR ND1 HD12 HD11 CD1 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 ND1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 ND1 HD11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HD11 CD1 *ND1 HD12 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +RESI 34AP 0.00 ! C5H7N3 3,4-diaminopyridine, adm jr. +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 0.120 +ATOM CG CG2R61 0.070 +ATOM CE2 CG2R61 0.180 +ATOM CD2 CG2R61 -0.115 +ATOM ND1 NG2S3 -0.850 +ATOM NG NG2S3 -0.850 +ATOM HE1 HGR62 0.120 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR62 0.120 +ATOM HD11 HGP4 0.350 +ATOM HD12 HGP4 0.380 +ATOM HG11 HGP4 0.390 +ATOM HG12 HGP4 0.390 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 ND1 ND1 HD11 ND1 HD12 +BOND CG NG NG HG11 NG HG12 + +IMPR ND1 HD12 HD11 CD1 +IMPR NG HG12 HG11 CG + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG NG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 ND1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CG NG HG11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HG11 CG *NG HG12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CE1 CD1 ND1 HD11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HD11 CD1 *ND1 HD12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI 3CPY -1.00 ! C6H4NO2 pyridine-3-carboxylate (niacinate), yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 -0.10 +ATOM CG CG2R61 -0.155 +ATOM CE2 CG2R61 0.180 ! O1 HG +ATOM CD2 CG2R61 -0.115 ! \ | +ATOM HE1 HGR62 0.120 ! (-) ) CD3 CG +ATOM HG HGR61 0.155 ! / \ / \\ +ATOM HD2 HGR61 0.115 ! O2 CD1 CD2--HD2 +ATOM HE2 HGR62 0.120 ! || | +ATOM CD3 CG2O3 0.62 ! HE1--CE1 CE2--HE2 +ATOM O1 OG2D2 -0.76 ! \ // +ATOM O2 OG2D2 -0.76 ! NZ + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 CD3 CD3 O1 +DOUB CD3 O2 +IMPR CD3 O2 O1 CD1 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC O1 CD1 *CD3 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +RESI 3CB -1.00 ! C7H5O2 benzoate +GROUP +ATOM CZ CG2R61 -0.115 +ATOM CE1 CG2R61 -0.115 +ATOM CD1 CG2R61 -0.100 +ATOM CG CG2R61 -0.115 +ATOM CE2 CG2R61 -0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM HG HGR61 0.115 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR61 0.115 +ATOM HZ HGR61 0.115 +ATOM CD3 CG2O3 0.620 +ATOM O1 OG2D2 -0.760 +ATOM O2 OG2D2 -0.760 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 CD3 CD3 O1 +BOND CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +DOUB CD3 O2 +IMPR CD3 O2 O1 CD1 + +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC O1 CD1 *CD3 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +RESI 3FLP 0.00 ! C5H4FN 3-fluoropyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.220 +ATOM CD1 CG2R66 0.170 +ATOM CG CG2R61 -0.115 +ATOM CE2 CG2R61 0.180 +ATOM CD2 CG2R61 -0.115 +ATOM HE1 HGR62 0.120 +ATOM F1 FGR1 -0.210 !charge similar to difluorotoluene +ATOM HG HGR62 0.115 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR62 0.120 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 F1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 F1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3ALP 0.00 ! C6H5NO 3-pyridinecarboxaldehyde, 3-formylpyridine, nicotinaldehyde, yin +GROUP +ATOM NZ NG2R60 -0.600 ! H3 HG +ATOM CE1 CG2R61 0.180 ! \ | +ATOM CD1 CG2R61 0.09 ! CD3 CG +ATOM CG CG2R61 -0.115 ! // \ / \\ +ATOM CD2 CG2R61 -0.115 ! O1 CD1 CD2--HD2 +ATOM CE2 CG2R61 0.180 ! || | +ATOM HE1 HGR62 0.120 ! HE1--CE1 CE2--HE2 +ATOM HG HGR61 0.115 ! \ // +ATOM HD2 HGR61 0.115 ! NZ +ATOM HE2 HGR62 0.120 +ATOM CD3 CG2O4 0.24 !benzaldehyde +ATOM O1 OG2D1 -0.41 !benzaldehyde +ATOM H3 HGR52 0.08 !benzaldehyde + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 +BOND CE2 HE2 +BOND CD1 CD3 CD3 H3 +DOUB CD3 O1 + +IMPR CD3 CD1 O1 H3 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 O1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC O1 CD1 *CD3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +RESI 3HOP 0.000 ! C5H5NO 3-hydroxypyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CG CG2R61 -0.115 +ATOM CD2 CG2R61 -0.115 +ATOM CE2 CG2R61 0.180 +ATOM HE1 HGR62 0.120 +ATOM HG HGR61 0.115 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR62 0.120 +ATOM CD1 CG2R61 0.11 !phenol +ATOM OH OG311 -0.53 !phenol +ATOM HO1 HGP1 0.42 !phenol + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 OH CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HO1 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HO1 OH CD2 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3MEP 0.00 ! C6H7N 3-methylpyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 0.000 ! H32 H33 +ATOM CG CG2R61 -0.115 ! \ / +ATOM CD2 CG2R61 -0.115 ! H31--CD3 HE1 +ATOM CE2 CG2R61 0.180 ! \ | +ATOM HE1 HGR62 0.120 ! CD1--CE1 +ATOM HG HGR61 0.115 ! / \ +ATOM HD2 HGR61 0.115 ! HG--CG NZ +ATOM HE2 HGR62 0.120 ! \ / +ATOM CD3 CG331 -0.27 ! CD2--CE2 +ATOM H31 HGA3 0.09 ! | | +ATOM H32 HGA3 0.09 ! HD2 HE2 +ATOM H33 HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 CD3 CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD3 H31 CD3 H32 CD3 H33 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CD1 CD3 H31 0.0000 0.0000 60.0000 0.0000 0.0000 +IC CE1 CD1 CD3 H32 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 H33 0.0000 0.0000 300.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3ETP 0.00 ! C7H9N ethylpyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 0.000 +ATOM CG CG2R61 -0.115 +ATOM CD2 CG2R61 -0.115 +ATOM CE2 CG2R61 0.180 +ATOM HE1 HGR62 0.120 +ATOM HG HGR61 0.115 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR62 0.120 +ATOM CD3 CG321 -0.18 !aliphatic, corresponds to new CT2, HA2 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM C2 CG331 -0.27 !aliphatic, corresponds to new CT3, HA3 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD1 CD3 CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD3 H11 CD3 H12 CD3 C2 +BOND H21 C2 H22 C2 H23 C2 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 C2 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CD1 C2 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD1 C2 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CD1 CD3 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD3 H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD3 H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3BPY 0.00 ! C9H13N butylpyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 0.000 +ATOM CG CG2R61 -0.115 +ATOM CE2 CG2R61 0.180 +ATOM CD2 CG2R61 -0.115 +ATOM HE1 HGR62 0.120 +ATOM HG HGR61 0.115 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR62 0.120 +ATOM CD3 CG321 -0.18 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 CE1 HE1 CE2 HE2 +BOND CD1 CD3 CD3 H11 CD3 H12 +BOND CD3 C2 C2 C3 C3 C4 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 +BOND C4 H41 C4 H42 C4 H43 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CG *CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 C2 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CD1 C2 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD1 C2 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CD1 CD3 C2 C3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD3 C3 *C2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CD3 C3 *C2 H22 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CD3 C2 C3 C4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H31 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2 C4 *C3 H32 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C2 C3 C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3 H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3CYP 0.00 ! C6H4N2 3-Cyanopyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 ! N3C +ATOM CD1 CG2R61 0.100 ! \\\ +ATOM CG CG2R61 -0.115 ! C3N HE1 +ATOM CD2 CG2R61 -0.115 ! \ | +ATOM CE2 CG2R61 0.180 ! CD1--CE1 +ATOM HE1 HGR62 0.120 ! / \ +ATOM HG HGR61 0.115 ! HG--CG NZ +ATOM HD2 HGR61 0.115 ! \ / +ATOM HE2 HGR62 0.120 ! CD2--CE2 +ATOM C3N CG1N1 0.360 ! | | +ATOM N3C NG1T1 -0.460 ! HD2 HE2 +! Original charges after bringing HE1 and HE2 in line with the other pyridines. + +!ATOM NZ NG2R60 -0.600 +!ATOM CE1 CG2R61 0.180 ! N3C +!ATOM CD1 CG2R61 0.080 ! \\\ +!ATOM CG CG2R61 -0.120 ! C3N HE1 +!ATOM CD2 CG2R61 -0.115 ! \ | +!ATOM CE2 CG2R61 0.180 ! CD1--CE1 +!ATOM HE1 HGR62 0.120 ! / \ +!ATOM HG HGR61 0.140 ! HG--CG NZ +!ATOM HD2 HGR61 0.115 ! \ / +!ATOM HE2 HGR62 0.120 ! CD2--CE2 +!ATOM C3N CG1N1 0.360 ! | | +!ATOM N3C NG1T1 -0.460 ! HD2 HE2 +!! Partially optimized charges with +!! - Dipoles and H2O interactions substantially better +!! - DHvap slightly worse (but not really significant) +!! - Not transferable + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 C3N +BOND C3N N3C + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C3N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3C C3N CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3ACP 0.00 ! C7H7NO 3-acetylpyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 ! HC2 HC3 +ATOM CE1 CG2R61 0.180 ! \ / +ATOM CD1 CG2R61 0.070 ! HC1--CH3 HG +ATOM CG CG2R61 -0.115 ! \ | +ATOM CD2 CG2R61 -0.115 ! C CG +ATOM CE2 CG2R61 0.180 ! //\ / \\ +ATOM HE1 HGR62 0.120 ! O CD1 CD2--HD2 +ATOM HG HGR61 0.115 ! || | +ATOM HD2 HGR61 0.115 ! HE1--CE1 CE2--HE2 +ATOM HE2 HGR62 0.120 ! \ // +ATOM C CG2O5 0.360 ! NZ +ATOM O OG2D3 -0.470 +ATOM CH3 CG331 -0.230 !aliphatic, corresponds to new CT3, HA3 +ATOM HC1 HGA3 0.090 +ATOM HC2 HGA3 0.090 +ATOM HC3 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 C C CH3 +BOND HC1 CH3 HC2 CH3 HC3 CH3 +DOUB C O + +IMPR C CD1 CH3 O + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CH3 C CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CH3 CD1 *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O C CH3 HC1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O C CH3 HC2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC O C CH3 HC3 0.0000 0.0000 -60.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3NAP 0.00 ! C6H6N2O Really just unprotonated oxidized nicotinamide, +GROUP ! aka. "nicotinamide". Other correct names include: +ATOM NZ NG2R60 -0.600 ! 3-pyridinecarboxamide, 3-amidopyridine, +ATOM CE1 CG2R61 0.180 ! 3-(aminocarbonyl)pyridine, yin +ATOM CD1 CG2R61 -0.020 +ATOM CG CG2R61 -0.115 +ATOM CD2 CG2R61 -0.115 ! HT +ATOM CE2 CG2R61 0.180 ! / +ATOM HE1 HGR62 0.120 ! Hc--N HG +ATOM HG HGR61 0.115 ! \ | +ATOM HD2 HGR61 0.115 ! C CG +ATOM HE2 HGR62 0.120 ! //\ / \\ +ATOM C CG2O1 0.630 ! O CD1 CD2--HD2 +ATOM O OG2D1 -0.460 ! || | +ATOM N NG2S2 -0.900 ! HE1--CE1 CE2--HE2 +ATOM HC HGP1 0.390 ! \ // +ATOM HT HGP1 0.360 ! NZ + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 C C N +BOND HC N HT N +DOUB C O + +IMPR C CD1 N O + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N C CD1 CE1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N CD1 *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HC N C O 0.0000 0.0000 0.0000 0.0000 0.0000 +IC HT N C O 0.0000 0.0000 180.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3CAP 0.00 ! C6H7NO carbinol-pyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 0.000 +ATOM CG CG2R61 -0.115 +ATOM CD2 CG2R61 -0.115 +ATOM CE2 CG2R61 0.180 +ATOM HE1 HGR62 0.120 +ATOM HG HGR61 0.115 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR62 0.120 +GROUP +ATOM CD3 CG321 0.05 !aliphatic, corresponds to new CT2, HA2 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM OH OG311 -0.65 +ATOM HO HGP1 0.42 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 CD3 CD3 OH OH HO +BOND CD3 H11 CD3 H12 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC NZ CE1 CD1 CD3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CD1 CD3 OH 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CD3 OH HO 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OH CD1 *CD3 H11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC OH CD1 *CD3 H12 0.0000 0.0000 -120.0000 0.0000 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI 3PHP 0.00 ! C11H9N 3-phenyl-pyridine, yin +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R67 0.000 +ATOM CG CG2R61 -0.115 +ATOM CD2 CG2R61 -0.115 +ATOM CE2 CG2R61 0.180 +ATOM HE1 HGR62 0.120 +ATOM HG HGR61 0.115 +ATOM HD2 HGR61 0.115 +ATOM HE2 HGR62 0.120 +ATOM CA1 CG2R67 0.000 +ATOM CA2 CG2R61 -0.115 +ATOM CA3 CG2R61 -0.115 +ATOM CA4 CG2R61 -0.115 +ATOM CA5 CG2R61 -0.115 +ATOM CA6 CG2R61 -0.115 +ATOM HA2 HGR61 0.115 +ATOM HA3 HGR61 0.115 +ATOM HA4 HGR61 0.115 +ATOM HA5 HGR61 0.115 +ATOM HA6 HGR61 0.115 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 CA1 CA1 CA2 CA2 CA3 +BOND CA3 CA4 CA4 CA5 CA6 CA5 +BOND CA6 CA1 +BOND CA2 HA2 CA3 HA3 CA4 HA4 +BOND CA5 HA5 CA6 HA6 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 CA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA2 CA1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA3 CA2 CA1 CD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA4 CA3 CA2 CA1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA5 CA4 CA3 CA2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA6 CA5 CA4 CA3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA1 CA3 *CA2 HA2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA2 CA4 *CA3 HA3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA3 CA5 *CA4 HA4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA4 CA6 *CA5 HA5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA5 CA1 *CA6 HA6 0.0000 0.0000 180.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 3BNP 0.00 ! C12H11N 3-benzyl-pyridine, yin +GROUP !methylene between rings +ATOM NZ NG2R60 -0.600 !1 +ATOM CE1 CG2R61 0.180 !2 +ATOM CD1 CG2R61 0.000 !3 +ATOM CG CG2R61 -0.115 !4 +ATOM CD2 CG2R61 -0.115 !5 +ATOM CE2 CG2R61 0.180 !6 +ATOM HE1 HGR62 0.120 !7 +ATOM HG HGR61 0.115 !8 +ATOM HD2 HGR61 0.115 !9 +ATOM HE2 HGR62 0.120 !10 +ATOM C CG321 -0.180 !11 +ATOM HC1 HGA2 0.090 !12 +ATOM HC2 HGA2 0.090 !13 +ATOM CA1 CG2R61 0.000 !14 +ATOM CA2 CG2R61 -0.115 !15 +ATOM CA3 CG2R61 -0.115 !16 +ATOM CA4 CG2R61 -0.115 !17 +ATOM CA5 CG2R61 -0.115 !18 +ATOM CA6 CG2R61 -0.115 !19 +ATOM HA2 HGR61 0.115 !20 +ATOM HA3 HGR61 0.115 !21 +ATOM HA4 HGR61 0.115 !22 +ATOM HA5 HGR61 0.115 !23 +ATOM HA6 HGR61 0.115 !24 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG HG CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND CD1 C C CA1 +BOND C HC1 C HC2 +BOND CA1 CA2 CA2 CA3 +BOND CA3 CA4 CA4 CA5 CA6 CA5 +BOND CA6 CA1 +BOND CA2 HA2 CA3 HA3 CA4 HA4 +BOND CA5 HA5 CA6 HA6 + +IC CG CD1 CE1 NZ 0.0000 0.0000 0.000 0.0000 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NZ CE1 CD1 CG 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 NZ CE1 CD1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CD1 C CA1 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CD1 C CA1 CA2 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CA1 CD1 *C HC1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CA1 CD1 *C HC2 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C CA1 CA2 CA3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA1 CA2 CA3 CA4 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA2 CA3 CA4 CA5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA3 CA4 CA5 CA6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CA1 CA3 *CA2 HA2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA2 CA4 *CA3 HA3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA3 CA5 *CA4 HA4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA4 CA6 *CA5 HA5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA5 CA1 *CA6 HA6 0.0000 0.0000 180.0000 0.0000 0.0000 +PATCH FIRST NONE LAST NONE + +!toppar_all27_lipid_cholesterol.str +RESI CLOL 0.00 ! C27H46O cholesterol (name to avoid conflict with choline) +! atoms names correspond to the correct cholesterol nomenclature +GROUP +ATOM C3 CG311 0.14 +ATOM O3 OG311 -0.65 +ATOM H3' HGP1 0.42 +ATOM H3 HGA1 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H4A HGA2 0.09 +ATOM H4B HGA2 0.09 +GROUP +ATOM C5 CG2D1 0.00 +ATOM C6 CG2D1 -0.15 +ATOM H6 HGA4 0.15 +GROUP +ATOM C7 CG321 -0.18 +ATOM H7A HGA2 0.09 +ATOM H7B HGA2 0.09 +GROUP +ATOM C8 CG311 -0.09 +ATOM H8 HGA1 0.09 +GROUP +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 ! no hydrogen +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 ! OH Me21 C22 C24 Me26 +ATOM H2A HGA2 0.09 ! | \ / \ / \ / +ATOM H2B HGA2 0.09 ! C12 Me18 C20 C23 C25--Me27 +GROUP ! / \ | / +ATOM C20 CG311 -0.09 ! C11 C13---C17 +ATOM H20 HGA1 0.09 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM C21 CG331 -0.27 ! / \|/ \ / \ / +ATOM H21A HGA3 0.09 ! C2 C10 C8 C15 +ATOM H21B HGA3 0.09 ! | | | +ATOM H21C HGA3 0.09 ! C3 C5 C7 +GROUP ! / \ / \\ / +ATOM C22 CG321 -0.18 ! HO C4 C6 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 ! Cholesterol (CHL1) +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM C24 CG321 -0.18 !beyond this nomenclature may not be correct +ATOM H24A HGA2 0.09 +ATOM H24B HGA2 0.09 +GROUP +ATOM C25 CG311 -0.09 !c25 +ATOM H25 HGA1 0.09 +GROUP +ATOM C26 CG331 -0.27 !terminal methyl, c26 +ATOM H26A HGA3 0.09 +ATOM H26B HGA3 0.09 +ATOM H26C HGA3 0.09 +GROUP +ATOM C27 CG331 -0.27 !terminal methyl, c27 +ATOM H27A HGA3 0.09 +ATOM H27B HGA3 0.09 +ATOM H27C HGA3 0.09 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C2 C2 H2A C2 H2B +BOND C2 C1 C1 H1A C1 H1B +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 +BOND C5 C10 +BOND C10 C1 +BOND C10 C19 C19 H19A C19 H19B C19 H19C +DOUBLE C5 C6 +BOND C6 H6 +BOND C6 C7 C7 H7A C7 H7B +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C13 C18 C18 H18A C18 H18B C18 H18C +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 +BOND C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 C24 C24 H24A C24 H24B +BOND C24 C25 C25 H25 +BOND C25 C26 C26 H26A C26 H26B C26 H26C +BOND C25 C27 C27 H27A C27 H27B C27 H27C +!ICs based on CHARMM optimized structure +IC C1 C2 C3 C4 1.5383 110.44 55.92 110.66 1.5367 +IC C4 C2 *C3 O3 1.5367 110.66 120.28 109.14 1.4158 +IC O3 C2 *C3 H3 1.4158 109.14 118.92 109.40 1.1155 +IC C2 C3 O3 H3' 1.5311 109.14 -58.51 105.39 0.9593 +IC C2 C3 C4 C5 1.5311 110.66 -55.96 111.70 1.5156 +IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 +IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 +IC C3 C4 C5 C10 1.5367 111.70 54.04 115.09 1.5304 +IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 +IC C4 C5 C6 C7 1.5156 121.28 -178.39 123.88 1.5018 +IC C7 C5 *C6 H6 1.5018 123.88 177.19 119.54 1.1001 +IC C5 C6 C7 C8 1.3432 123.88 14.50 112.36 1.5506 +IC C8 C6 *C7 H7A 1.5506 112.36 122.18 110.84 1.1114 +IC H7A C6 *C7 H7B 1.1114 110.84 118.17 109.17 1.1124 +IC C6 C7 C8 C14 1.5018 112.36 -165.89 110.02 1.5202 +IC C14 C7 *C8 C9 1.5202 110.02 121.07 110.84 1.5327 +IC C9 C7 *C8 H8 1.5327 110.84 119.34 108.18 1.1123 +IC C7 C8 C14 C13 1.5506 110.02 179.73 115.21 1.5247 +IC C13 C8 *C14 C15 1.5247 115.21 126.69 117.86 1.5382 +IC C13 C8 *C14 H14 1.5247 115.21 -116.05 105.83 1.1205 +IC C8 C14 C15 C16 1.5202 117.86 -163.10 103.40 1.5360 +IC C16 C14 *C15 H15A 1.5360 103.40 117.45 109.62 1.1113 +IC H15A C14 *C15 H15B 1.1113 109.62 121.32 111.94 1.1082 +IC C14 C15 C16 C17 1.5382 103.40 7.85 106.79 1.5620 +IC C17 C15 *C16 H16A 1.5620 106.79 118.96 109.25 1.1107 +IC H16A C15 *C16 H16B 1.1107 109.25 120.76 111.65 1.1090 +IC C13 C16 *C17 C20 1.5401 104.94 132.02 112.36 1.5633 +IC C13 C16 *C17 H17 1.5401 104.94 -111.76 106.42 1.1153 +IC C17 C14 *C13 C12 1.5401 100.27 122.68 106.98 1.5408 +IC C12 C14 *C13 C18 1.5408 106.98 122.91 110.83 1.5518 +IC C14 C13 C18 H18A 1.5247 110.83 60.33 111.48 1.1077 +IC H18A C13 *C18 H18B 1.1077 111.48 119.80 110.01 1.1086 +IC H18A C13 *C18 H18C 1.1077 111.48 -121.00 111.71 1.1067 +IC C14 C13 C12 C11 1.5247 106.98 56.78 111.10 1.5422 +IC C11 C13 *C12 H12A 1.5422 111.10 121.37 111.21 1.1067 +IC H12A C13 *C12 H12B 1.1067 111.21 118.82 108.68 1.1119 +IC C9 C12 *C11 H11A 1.5593 113.54 121.67 107.06 1.1093 +IC H11A C12 *C11 H11B 1.1093 107.06 115.98 108.75 1.1100 +IC C10 C8 *C9 H9 1.5531 112.73 -114.54 104.68 1.1185 +IC C9 C5 *C10 C19 1.5531 111.91 -120.04 108.03 1.5524 +IC C19 C5 *C10 C1 1.5524 108.03 -119.87 109.26 1.5579 +IC C5 C10 C19 H19A 1.5304 108.03 -172.88 110.67 1.1082 +IC H19A C10 *C19 H19B 1.1082 110.67 118.48 111.77 1.1080 +IC H19A C10 *C19 H19C 1.1082 110.67 -120.66 110.97 1.1095 +IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 +IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 +IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 +IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 +IC C16 C17 C20 C22 1.5620 112.36 55.21 110.55 1.5476 +IC C22 C17 *C20 C21 1.5476 110.55 125.88 113.32 1.5349 +IC C21 C17 *C20 H20 1.5349 113.32 118.87 107.27 1.1157 +IC C17 C20 C21 H21A 1.5633 113.32 64.90 110.93 1.1077 +IC H21A C20 *C21 H21B 1.1077 110.93 -121.00 110.41 1.1104 +IC H21A C20 *C21 H21C 1.1077 110.93 118.40 111.29 1.1085 +IC C17 C20 C22 C23 1.5633 110.55 -174.59 115.12 1.5394 +IC C23 C20 *C22 H22A 1.5394 115.12 120.23 109.35 1.1116 +IC H22A C20 *C22 H22B 1.1116 109.35 117.13 108.75 1.1121 +IC C20 C22 C23 C24 1.5476 115.12 172.50 112.25 1.5377 +IC C24 C22 *C23 H23A 1.5377 112.25 121.13 109.69 1.1108 +IC H23A C22 *C23 H23B 1.1108 109.69 118.14 108.99 1.1129 +IC C22 C23 C24 C25 1.5394 112.25 -176.23 114.06 1.5418 +IC C25 C23 *C24 H24A 1.5418 114.06 120.56 108.44 1.1132 +IC H24A C23 *C24 H24B 1.1132 108.44 117.11 109.39 1.1121 +IC C23 C24 C25 C26 1.5377 114.06 174.26 111.24 1.5378 +IC C26 C24 *C25 C27 1.5378 111.24 119.63 112.86 1.5381 +IC C26 C24 *C25 H25 1.5378 111.24 -119.50 108.47 1.1151 +IC C24 C25 C26 H26A 1.5418 111.24 -178.53 110.52 1.1105 +IC H26A C25 *C26 H26B 1.1105 110.52 120.00 110.36 1.1105 +IC H26A C25 *C26 H26C 1.1105 110.52 -120.09 110.33 1.1106 +IC C24 C25 C27 H27A 1.5418 112.86 -178.28 110.40 1.1105 +IC H27A C25 *C27 H27B 1.1105 110.40 119.95 110.31 1.1105 +IC H27A C25 *C27 H27C 1.1105 110.40 -119.82 110.77 1.1097 + +RESI CLNS 0.00 ! C20H32O cholesterol with sidechain beyond c18(c20) omitted +! atoms names after the comments correspond to the +! correct cholesterol nomenclature +GROUP +ATOM C1 CG311 0.14 !c3 +ATOM O1 OG311 -0.65 +ATOM HO1 HGP1 0.42 +ATOM H1 HGA1 0.09 + +ATOM C2 CG321 -0.18 !c4 +ATOM H2 HGA2 0.09 +ATOM H2' HGA2 0.09 + +ATOM C3 CG2D1 0.00 !c5 +ATOM C4 CG2D1 -0.15 !c6 +ATOM H4 HGA4 0.15 + +ATOM C5 CG321 -0.18 !c7 +ATOM H5 HGA2 0.09 +ATOM H5' HGA2 0.09 + +ATOM C6 CG311 -0.09 !c8 +ATOM H6 HGA1 0.09 +GROUP +ATOM C7 CG3RC1 -0.09 !c14 +ATOM H7 HGA1 0.09 + +ATOM C8 CG3C52 -0.18 !c15 +ATOM H8 HGA2 0.09 +ATOM H8' HGA2 0.09 + +ATOM C9 CG3C52 -0.18 !c16 +ATOM H9 HGA2 0.09 +ATOM H9' HGA2 0.09 + +ATOM C10 CG3C51 -0.09 !c17 +ATOM H10 HGA1 0.09 + +ATOM C11 CG3RC1 0.00 !c13 +GROUP +ATOM CC11 CG331 -0.27 !c18, methyl at c13 +ATOM H111 HGA3 0.09 +ATOM H112 HGA3 0.09 +ATOM H113 HGA3 0.09 + +ATOM C12 CG321 -0.18 !c12 +ATOM H12 HGA2 0.09 +ATOM H12' HGA2 0.09 + +ATOM C13 CG321 -0.18 !c11 +ATOM H13 HGA2 0.09 +ATOM H13' HGA2 0.09 + +ATOM C14 CG311 -0.09 !c9 +ATOM H14 HGA1 0.09 + +ATOM C15 CG301 0.00 !c10: no hydrogen +GROUP +ATOM CC15 CG331 -0.27 !c19, methyl at c10 +ATOM H151 HGA3 0.09 +ATOM H152 HGA3 0.09 +ATOM H153 HGA3 0.09 + +ATOM C16 CG321 -0.18 !c1 +ATOM H16 HGA2 0.09 +ATOM H16' HGA2 0.09 + +ATOM C17 CG321 -0.18 !c2 +ATOM H17 HGA2 0.09 +ATOM H17' HGA2 0.09 + +ATOM C18 CG331 -0.27 !c20 +ATOM H181 HGA3 0.09 +ATOM H182 HGA3 0.09 +ATOM H183 HGA3 0.09 + +BOND C1 O1 C1 H1 C1 C2 +BOND O1 HO1 +BOND C2 C3 C2 H2 C2 H2' +DOUBLE C3 C4 +BOND C4 C5 C4 H4 +BOND C5 C6 C5 H5 C5 H5' +BOND C6 C7 C6 H6 +BOND C7 C8 C7 H7 +BOND C8 C9 C8 H8 C8 H8' +BOND C9 C10 C9 H9 C9 H9' +BOND C10 C18 C10 C11 C10 H10 +BOND C11 CC11 C11 C7 C11 C12 +BOND CC11 H111 CC11 H112 CC11 H113 +BOND C12 C13 C12 H12 C12 H12' +BOND C13 C14 C13 H13 C13 H13' +BOND C14 C15 C14 C6 C14 H14 +BOND C15 C16 C15 C3 C15 CC15 +BOND CC15 H151 CC15 H152 CC15 H153 +BOND C16 C17 C16 H16 C16 H16' +BOND C17 C1 C17 H17 C17 H17' +BOND C18 H181 C18 H182 C18 H183 + +!DONO HO1 O1 +!ACCE O1 + +IC O1 C1 C2 C3 1.4158 109.24 -176.17 111.80 1.5153 +IC C1 C2 C3 C4 1.5368 111.80 -123.48 121.41 1.3430 +IC C2 C3 C4 C5 1.5153 121.41 -178.76 123.84 1.5019 +IC C3 C4 C5 C6 1.3430 123.84 14.64 112.44 1.5504 +IC C4 C5 C6 C7 1.5019 112.44 -166.16 109.90 1.5192 +IC C5 C6 C7 C8 1.5504 109.90 -54.73 118.74 1.5447 +IC C6 C7 C8 C9 1.5192 118.74 -161.90 103.72 1.5418 +IC C7 C8 C9 C10 1.5447 103.72 5.69 105.45 1.5530 +IC C8 C9 C10 C11 1.5418 105.45 21.50 105.85 1.5300 +IC C9 C10 C11 C12 1.5530 105.85 -155.90 116.00 1.5351 +IC C7 C12 *C11 CC11 1.5194 108.58 -123.00 111.88 1.5530 +IC C10 C11 C12 C13 1.5300 116.00 167.75 110.42 1.5414 +IC C10 C11 C7 C8 1.5300 99.46 43.93 105.86 1.5447 +IC C11 C12 C13 C14 1.5351 110.42 -52.28 113.50 1.5626 +IC CC11 C11 C12 C13 1.5530 111.88 -66.16 110.42 1.5414 +IC CC11 C11 C7 C8 1.5530 111.12 -70.96 105.86 1.5447 +IC C12 C13 C14 C15 1.5414 113.50 179.43 114.52 1.5524 +IC C13 C14 C15 CC15 1.5626 114.52 -50.80 109.07 1.5522 +IC C13 C14 C15 C16 1.5626 114.52 69.29 108.64 1.5574 +IC C13 C14 C6 C7 1.5626 113.16 -48.42 109.31 1.5192 +IC CC15 C15 C16 C17 1.5522 110.15 -68.75 114.54 1.5383 +IC C14 C15 C16 C17 1.5524 108.64 171.83 114.54 1.5383 +IC C14 C15 C3 C4 1.5524 111.86 7.71 123.46 1.3430 +IC C15 C16 C17 C1 1.5574 114.54 -54.68 110.51 1.5312 +IC C11 C9 *C10 C18 1.5300 105.85 126.88 114.22 1.5413 +IC O1 C2 *C1 H1 1.4158 109.24 -119.02 109.53 1.1156 +IC C2 C1 O1 HO1 1.5368 109.24 62.69 105.39 0.9593 +IC C3 C1 *C2 H2 1.5153 111.80 121.88 109.11 1.1100 +IC C3 C1 *C2 H2' 1.5153 111.80 -123.05 107.36 1.1142 +IC C5 C3 *C4 H4 1.5019 123.84 177.13 119.55 1.1001 +IC C6 C4 *C5 H5 1.5504 112.44 122.17 110.88 1.1114 +IC C6 C4 *C5 H5' 1.5504 112.44 -119.69 109.16 1.1124 +IC C7 C5 *C6 H6 1.5192 109.90 -119.58 108.19 1.1122 +IC C8 C6 *C7 H7 1.5447 118.74 117.73 105.77 1.1205 +IC C9 C7 *C8 H8 1.5418 103.72 117.51 109.61 1.1108 +IC C9 C7 *C8 H8' 1.5418 103.72 -121.25 111.67 1.1078 +IC C10 C8 *C9 H9 1.5530 105.45 118.45 109.64 1.1105 +IC C10 C8 *C9 H9' 1.5530 105.45 -120.18 112.16 1.1085 +IC C18 C9 *C10 H10 1.5413 114.22 119.69 107.07 1.1162 +IC C7 C11 CC11 H111 1.5194 111.12 -178.60 110.01 1.1092 +IC H111 C11 *CC11 H112 1.1092 110.01 118.82 111.63 1.1068 +IC H111 C11 *CC11 H113 1.1092 110.01 -120.26 111.66 1.1075 +IC C13 C11 *C12 H12 1.5414 110.42 122.09 109.96 1.1102 +IC C13 C11 *C12 H12' 1.5414 110.42 -119.49 108.88 1.1120 +IC C14 C12 *C13 H13 1.5626 113.50 121.59 107.14 1.1091 +IC C14 C12 *C13 H13' 1.5626 113.50 -122.38 108.79 1.1098 +IC C13 C6 *C14 H14 1.5626 113.16 113.80 104.59 1.1184 +IC C3 C15 CC15 H151 1.5435 107.81 -172.81 110.68 1.1082 +IC H151 C15 *CC15 H152 1.1082 110.68 118.52 111.71 1.1081 +IC H151 C15 *CC15 H153 1.1082 110.68 -120.68 110.98 1.1094 +IC C17 C15 *C16 H16 1.5383 114.54 122.43 109.27 1.1104 +IC C17 C15 *C16 H16' 1.5383 114.54 -120.70 108.26 1.1134 +IC C16 C1 *C17 H17 1.5383 110.51 121.12 109.37 1.1120 +IC C16 C1 *C17 H17' 1.5383 110.51 -120.62 109.70 1.1111 +IC C9 C10 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC C10 H181 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC C10 H181 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 + +RESI CLM1 0.00 ! C11H18O cholesterol analog with only rings 1 and 2 + !and the position 19 methyl +! atoms names after the comments correspond to the +! correct cholesterol nomenclature + +! ring 1 + +GROUP +ATOM C1 CG311 0.14 !c3 +ATOM O1 OG311 -0.65 +ATOM HO1 HGP1 0.42 +ATOM H1 HGA1 0.09 + +ATOM C2 CG321 -0.18 !c4 +ATOM H2 HGA2 0.09 +ATOM H2' HGA2 0.09 + +ATOM C3 CG2D1 0.00 !c5 +ATOM C15 CG301 0.00 !c10: no hydrogen + +ATOM C16 CG321 -0.18 !c1 +ATOM H16 HGA2 0.09 +ATOM H16' HGA2 0.09 + +ATOM C17 CG321 -0.18 !c2 +ATOM H17 HGA2 0.09 +ATOM H17' HGA2 0.09 + +ATOM CC15 CG331 -0.27 !c19, methyl at c10 +ATOM H151 HGA3 0.09 +ATOM H152 HGA3 0.09 +ATOM H153 HGA3 0.09 +! ring 2 +GROUP +ATOM C4 CG2D1 -0.15 !c6 +ATOM H4 HGA4 0.15 + +ATOM C5 CG321 -0.18 !c7 +ATOM H5 HGA2 0.09 +ATOM H5' HGA2 0.09 + +ATOM C6 CG321 -0.18 !c8 +ATOM H6 HGA2 0.09 +ATOM H6' HGA2 0.09 + +ATOM C14 CG321 -0.18 !c9 +ATOM H14 HGA2 0.09 +ATOM H14' HGA2 0.09 + +BOND C1 C2 C2 C3 C3 C15 C15 C16 C16 C17 C17 C1 +BOND C1 O1 O1 HO1 C1 H1 +BOND C2 H2 C2 H2' +BOND C15 CC15 CC15 H151 CC15 H152 CC15 H153 +BOND C16 H16 C16 H16' +BOND C17 H17 C17 H17' +DOUB C3 C4 +BOND C4 C5 C5 C6 C6 C14 C14 C15 +BOND C4 H4 +BOND C5 H5 C5 H5' +BOND C6 H6 C6 H6' +BOND C14 H14 C14 H14' + +IC C1 C2 C3 C15 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C15 C16 0.0000 0.00 0.00 0.00 0.0000 +IC C17 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C17 *C1 O1 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C17 *C1 H1 0.0000 0.00 -120.00 0.00 0.0000 +IC C17 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H2' 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 15.00 0.00 0.0000 +IC C4 C5 C6 C14 0.0000 0.00 -45.00 0.00 0.0000 +IC C14 C3 *C15 CC15 0.0000 0.00 -120.00 0.00 0.0000 +IC C17 C15 *C16 H16 0.0000 0.00 120.00 0.00 0.0000 +IC C17 C15 *C16 H16' 0.0000 0.00 -120.00 0.00 0.0000 +IC C16 C1 *C17 H17 0.0000 0.00 120.00 0.00 0.0000 +IC C16 C1 *C17 H17' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C15 CC15 H151 0.0000 0.00 180.00 0.00 0.0000 +IC H151 C15 *CC15 H152 0.0000 0.00 120.00 0.00 0.0000 +IC H151 C15 *CC15 H153 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C4 *C5 H5' 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C5 *C6 H6 0.0000 0.00 120.00 0.00 0.0000 +IC C14 C5 *C6 H6' 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C15 *C14 H14 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C15 *C14 H14' 0.0000 0.00 -120.00 0.00 0.0000 + +!toppar_all27_lipid_model.str +RESI MAS 0.00 ! C3H6O2 methylacetate +GROUP +ATOM C1 CG331 -0.31 ! H22 +ATOM C CG2O2 0.90 ! | +ATOM OM OG302 -0.49 ! H21-C2-H23 +ATOM C2 CG331 -0.01 ! \ +ATOM O OG2D1 -0.63 ! OM +ATOM H11 HGA3 0.09 ! / +ATOM H12 HGA3 0.09 ! O=C +ATOM H13 HGA3 0.09 ! | +ATOM H21 HGA3 0.09 ! H11-C1-H13 +ATOM H22 HGA3 0.09 ! | +ATOM H23 HGA3 0.09 ! H12 + +BOND C1 C C OM OM C2 +DOUBLE C O +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IMPR C C1 O OM +! internal coordinates from experiment for heavy atoms +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 + +RESI ETAC 0.00 ! C4H8O2 Ethylacetate +! ! H213 +GROUP ! | +ATOM C1 CG331 -0.31 ! H211-C21-H212 +ATOM C CG2O2 0.90 ! / +ATOM OM OG302 -0.49 ! H22-C2-H23 +ATOM C2 CG321 0.08 ! \ +ATOM O OG2D1 -0.63 ! OM +ATOM H11 HGA3 0.09 ! / +ATOM H12 HGA3 0.09 ! O=C +ATOM H13 HGA3 0.09 ! \ +ATOM H22 HGA2 0.09 ! H11-C1-H13 +ATOM H23 HGA2 0.09 ! | +GROUP ! H12 +ATOM C21 CG331 -0.27 +ATOM H211 HGA3 0.09 +ATOM H212 HGA3 0.09 +ATOM H213 HGA3 0.09 +BOND C1 C C OM OM C2 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 C21 C2 H22 C2 H23 +BOND C21 H211 C21 H212 C21 H213 +DOUBLE C O +IMPR C C1 O OM +! internal coordinates from experiment for heavy atoms +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC C21 C2 OM C 1.520 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 +IC H211 C21 C2 OM 1.1 108.90 180.0 116.7 1.437 +IC H212 C21 C2 OM 1.1 108.90 60.0 116.7 1.437 +IC H213 C21 C2 OM 1.1 108.90 -60.0 116.7 1.437 + +RESI MPRO 0.00 ! C4H8O2 Methylpropionate +GROUP +ATOM C1 CG321 -0.22 ! H22 +ATOM C CG2O2 0.90 ! | +ATOM OM OG302 -0.49 ! H21-C2-H23 +ATOM C2 CG331 -0.01 ! \ +ATOM O OG2D1 -0.63 ! OM +ATOM H12 HGA2 0.09 ! / +ATOM H13 HGA2 0.09 ! O=C +ATOM H21 HGA3 0.09 ! \ +ATOM H22 HGA3 0.09 ! H12-C1-H13 +ATOM H23 HGA3 0.09 ! / +GROUP ! H112-C11-H111 +ATOM C11 CG331 -0.27 ! | +ATOM H111 HGA3 0.09 ! H113 +ATOM H112 HGA3 0.09 +ATOM H113 HGA3 0.09 +BOND C1 C C OM C O OM C2 +BOND C1 C11 C1 H12 C1 H13 +BOND C11 H111 C11 H112 C11 H113 +BOND C2 H21 C2 H22 C2 H23 +IMPR C C1 O OM +! internal coordinates from experiment for heavy atoms +IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 +IC O C OM C2 1.200 125.9 0.0 114.8 1.437 +IC C11 C1 C OM 1.520 108.9 180.0 109.0 1.334 +IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 +IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 +IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 +IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 +IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 +IC H111 C11 C1 C 1.1 109.75 180.0 109.0 1.520 +IC H112 C11 C1 C 1.1 109.75 60.4 109.0 1.520 +IC H113 C11 C1 C 1.1 109.75 -60.4 109.0 1.520 + +RESI MSO4 -1.00 ! CH3O4S Methylsulfate +GROUP +ATOM S SG3O1 1.33 ! OS2(-1) +ATOM OS1 OG303 -0.28 ! | +ATOM OS2 OG2P1 -0.65 ! (-1) OS2--S(+2)--OS4 (-1) +ATOM OS3 OG2P1 -0.65 ! | +ATOM OS4 OG2P1 -0.65 ! OS1 +ATOM C1 CG331 -0.37 ! \ +ATOM H11 HGA3 0.09 ! H11-C1-H13 +ATOM H12 HGA3 0.09 ! | +ATOM H13 HGA3 0.09 ! H12 + +BOND S OS1 S OS2 S OS3 S OS4 OS1 C1 +BOND C1 H11 C1 H12 C1 H13 +ACCE OS1 +ACCE OS2 +ACCE OS3 +ACCE OS4 + +IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS2 S OS2 OS3 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC OS3 S OS1 OS4 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS1 S OS3 OS2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C1 OS1 S OS2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC S OS1 C1 OS3 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS1 S OS4 OS2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OS1 S OS2 OS3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OS1 S OS3 OS2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS4 S OS3 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS3 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS4 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS2 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OS3 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 + +RESI HEXA 0.00 ! C6H14 hexane +GROUP +ATOM H11 HGA3 0.09 ! H2 +ATOM H12 HGA3 0.09 ! | +ATOM H13 HGA3 0.09 ! H1-C1-H3 +ATOM C1 CG331 -0.27 ! | +GROUP ! | +ATOM H21 HGA2 0.09 ! H4-C2-H5 +ATOM H22 HGA2 0.09 ! | +ATOM C2 CG321 -0.18 ! | +GROUP ! | +ATOM H31 HGA2 0.09 ! H6-C3-H7 +ATOM H32 HGA2 0.09 ! | +ATOM C3 CG321 -0.18 ! | +GROUP ! | +ATOM H41 HGA2 0.09 ! H8-C4-H10 +ATOM H42 HGA2 0.09 ! | +ATOM C4 CG321 -0.18 ! | +GROUP ! | +ATOM H51 HGA2 0.09 ! H51-C5-H152 +ATOM H52 HGA2 0.09 ! | +ATOM C5 CG321 -0.18 ! | +GROUP ! | +ATOM H61 HGA3 0.09 ! H61-C4-H62 +ATOM H62 HGA3 0.09 ! | +ATOM H63 HGA3 0.09 ! H63 +ATOM C6 CG331 -0.27 +BOND H11 C1 H12 C1 H13 C1 C1 C2 +BOND H21 C2 H22 C2 C2 C3 +BOND H31 C3 H32 C3 C3 C4 +BOND H41 C4 H42 C4 C4 C5 +BOND H51 C5 H52 C5 C5 C6 +BOND H61 C6 H62 C6 C6 H63 +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC H11 C2 *C1 H12 0.00 0.00 120.0 0.00 0.00 +IC H11 C2 *C1 H13 0.00 0.00 240.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 +IC C1 C3 *C2 H22 0.00 0.00 240.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 +IC C2 C4 *C3 H32 0.00 0.00 240.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 +IC C3 C5 *C4 H42 0.00 0.00 240.0 0.00 0.00 +IC C4 C6 *C5 H51 0.00 0.00 120.0 0.00 0.00 +IC C4 C6 *C5 H52 0.00 0.00 240.0 0.00 0.00 +IC C4 C5 C6 H61 0.00 0.00 180.0 0.00 0.00 +IC H61 C5 *C6 H62 0.00 0.00 120.0 0.00 0.00 +IC H61 C5 *C6 H63 0.00 0.00 240.0 0.00 0.00 + +RESI ETHE 0.00 ! C2H4 ethylene, yin/adm jr. +GROUP +ATOM C1 CG2D2 -0.42 +ATOM H11 HGA5 0.21 ! H11 H21 +ATOM H12 HGA5 0.21 ! \ / +GROUP ! C1=C2 +ATOM C2 CG2D2 -0.42 ! / \ +ATOM H21 HGA5 0.21 ! H12 H22 +ATOM H22 HGA5 0.21 +BOND C1 H11 C1 H12 +DOUBLE C1 C2 +BOND C2 H21 C2 H22 +IC H11 C1 C2 H21 1.1036 121.37 180.00 121.37 1.1036 +IC H12 C2 *C1 H11 1.1036 121.37 180.00 121.37 1.1036 +IC H22 C1 *C2 H21 1.1036 121.37 180.00 121.37 1.1036 +IC C1 C2 H21 H22 1.3370 121.37 -180.00 31.37 1.8845 +PATC FIRS NONE LAST NONE + +RESI PRPE 0.00 ! C3H6 propene, yin/adm jr. +GROUP +ATOM C1 CG2D2 -0.42 +ATOM H11 HGA5 0.21 ! H11 H21 +ATOM H12 HGA5 0.21 ! \ / +GROUP ! C1=C2 H31 +ATOM C2 CG2D1 -0.15 ! / \ / +ATOM H21 HGA4 0.15 ! H12 C3 +GROUP ! / \ +ATOM C3 CG331 -0.27 ! H33 H32 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 +BOND C1 H11 C1 H12 +DOUBLE C1 C2 +BOND C2 H21 +BOND C2 C3 +BOND C3 H31 C3 H32 C3 H33 +IC H11 C1 C2 H21 0.00 0.00 180.0 0.0 0.0 +IC H12 C2 *C1 H11 0.00 0.00 180.0 0.0 0.0 +IC C3 C1 *C2 H21 0.00 0.00 180.0 0.0 0.0 +IC H31 C3 C2 C1 0.00 0.00 0.0 0.0 0.0 +IC H32 C3 C2 C1 0.00 0.00 120.0 0.0 0.0 +IC H33 C3 C2 C1 0.00 0.00 -120.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI BTE1 0.00 ! C4H8 1-Butene, yin/adm jr. +GROUP +ATOM C1 CG2D2 -0.42 +ATOM H11 HGA5 0.21 ! H11 H21 H41 +ATOM H12 HGA5 0.21 ! \ / | +GROUP ! C1=C2 C4-H42 +ATOM C2 CG2D1 -0.15 ! / \ / \ +ATOM H21 HGA4 0.15 ! H12 C3 H43 +GROUP ! / \ +ATOM C3 CG321 -0.18 ! H31 H32 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 +BOND C1 H11 C1 H12 +DOUBLE C1 C2 +BOND C2 H21 +BOND C2 C3 +BOND C3 H31 C3 H32 +BOND C3 C4 +BOND C4 H41 C4 H42 C4 H43 +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC H11 C1 C2 C3 0.00 0.00 180.0 0.00 0.00 +IC H12 C1 C2 C3 0.00 0.00 0.0 0.00 0.00 +IC H21 C1 *C2 C3 0.00 0.00 180.0 0.00 0.00 +IC H31 C2 *C3 C4 0.00 0.00 120.0 0.00 0.00 +IC H32 C2 *C3 C4 0.00 0.00 -120.0 0.00 0.00 +IC H41 C4 C3 C2 0.00 0.00 180.0 0.00 0.00 +IC H42 C4 C3 C2 0.00 0.00 60.0 0.00 0.00 +IC H43 C4 C3 C2 0.00 0.00 -60.0 0.00 0.00 +PATC FIRS NONE LAST NONE + +RESI BTE2 0.00 ! C4H8 2-Butene, yin/adm jr. +GROUP +ATOM C1 CG331 -0.27 ! H12 H13 +ATOM H11 HGA3 0.09 ! \ | +ATOM H12 HGA3 0.09 ! H13-C1 H31 +ATOM H13 HGA3 0.09 ! \ / +GROUP ! C2=C3 +ATOM C2 CG2D1 -0.15 ! / \ +ATOM H21 HGA4 0.15 ! H21 C4-H41 +GROUP ! | \ +ATOM C3 CG2D1 -0.15 ! H43 H42 +ATOM H31 HGA4 0.15 +GROUP +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 +BOND C1 H11 C1 H12 C1 H13 +BOND C1 C2 +BOND C2 H21 +DOUBLE C2 C3 +BOND C3 H31 +BOND C3 C4 +BOND C4 H41 C4 H42 C4 H43 +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC H11 C1 C2 C3 0.00 0.00 0.0 0.00 0.00 +IC H12 C1 C2 C3 0.00 0.00 120.0 0.00 0.00 +IC H13 C1 C2 C3 0.00 0.00 -120.0 0.00 0.00 +IC H21 C1 *C2 C3 0.00 0.00 180.0 0.00 0.00 +IC H31 C4 *C3 C2 0.00 0.00 180.0 0.00 0.00 +IC H41 C4 C3 C2 0.00 0.00 0.0 0.00 0.00 +IC H42 C4 C3 C2 0.00 0.00 120.0 0.00 0.00 +IC H43 C4 C3 C2 0.00 0.00 -120.0 0.00 0.00 +PATC FIRS NONE LAST NONE + +RESI DIPE 0.00 ! C5H8 1,4-dipentene, adm jr. +GROUP +ATOM C1 CG2D2 -0.42 +ATOM H11 HGA5 0.21 ! H11 H21 H41 H51 +ATOM H12 HGA5 0.21 ! \ / | / +GROUP ! C1=C2 C4=C5 +ATOM C2 CG2D1 -0.15 ! / \ / \ +ATOM H21 HGA4 0.15 ! H12 C3 H52 +GROUP ! / \ +ATOM C3 CG321 -0.18 ! H31 H32 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG2D1 -0.15 +ATOM H41 HGA4 0.15 +GROUP +ATOM C5 CG2D2 -0.42 +ATOM H51 HGA5 0.21 +ATOM H52 HGA5 0.21 +BOND C1 H11 C1 H12 +DOUBLE C1 C2 +BOND C2 H21 +BOND C2 C3 +BOND C3 H31 C3 H32 +BOND C3 C4 +BOND C4 H41 +DOUBLE C4 C5 +BOND C5 H51 C5 H52 +IC H11 C1 C2 H21 0.0000 0.00 0.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H51 C4 *C5 H52 0.0000 0.00 180.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI DIHE 0.00 ! C7H12 2,5-diheptene, adm jr. + +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +GROUP +ATOM C2 CG2D1 -0.15 ! H21 H31 H51 H61 +ATOM H21 HGA4 0.15 ! \ / | / +GROUP ! C2=C3 C5=C6 +ATOM C3 CG2D1 -0.15 ! / \ / \ +ATOM H31 HGA4 0.15 ! H11-C1 C4 C7-H71 +GROUP ! / \ / \ / \ +ATOM C4 CG321 -0.18 ! H12 H13 H41 H42 H73 H72 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG2D1 -0.15 +ATOM H51 HGA4 0.15 +GROUP +ATOM C6 CG2D1 -0.15 +ATOM H61 HGA4 0.15 +GROUP +ATOM C7 CG331 -0.27 +ATOM H71 HGA3 0.09 +ATOM H72 HGA3 0.09 +ATOM H73 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 C2 C2 H21 +DOUBLE C2 C3 +BOND C3 H31 +BOND C3 C4 C4 H41 C4 H42 +BOND C4 C5 C5 H51 +DOUBLE C5 C6 +BOND C6 H61 +BOND C6 C7 C7 H71 C7 H72 C7 H73 +IC H11 C1 C2 H21 0.0000 0.00 0.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C5 *C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC H71 C6 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 +IC H71 C6 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI HXE2 0.00 ! C6H12 2-hexene, yin/adm jr. +GROUP +ATOM C1 CG331 -0.27 ! H12 H13 +ATOM H11 HGA3 0.09 ! \ | +ATOM H12 HGA3 0.09 ! H13-C1 H31 H51 H52 +ATOM H13 HGA3 0.09 ! \ / \ / +GROUP ! C2=C3 C5 H61 +ATOM C2 CG2D1 -0.15 ! / \ / \ / +ATOM H21 HGA4 0.15 ! H21 C4 C6-H62 +GROUP ! / \ \ +ATOM C3 CG2D1 -0.15 ! H41 H42 H63 +ATOM H31 HGA4 0.15 +GROUP +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG321 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +GROUP +ATOM C6 CG331 -0.27 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 C2 +BOND C2 H21 +DOUBLE C2 C3 +BOND C3 H31 +BOND C3 C4 +BOND C4 H41 C4 H42 +BOND C4 C5 C5 H51 C5 H52 +BOND C5 C6 C6 H61 C6 H62 C6 H63 +! all trans +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC H11 C1 C2 C3 0.00 0.00 0.0 0.00 0.00 +IC H12 C1 C2 C3 0.00 0.00 120.0 0.00 0.00 +IC H13 C1 C2 C3 0.00 0.00 -120.0 0.00 0.00 +IC H21 C1 *C2 C3 0.00 0.00 180.0 0.00 0.00 +IC H31 C4 *C3 C2 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 +IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 180.0 0.00 0.00 +IC C4 C6 *C5 H51 0.00 0.00 120.0 0.00 0.00 +IC C4 C6 *C5 H52 0.00 0.00 -120.0 0.00 0.00 +IC H61 C6 C5 C4 0.00 0.00 180.0 0.00 0.00 +IC H62 C6 C5 C4 0.00 0.00 60.0 0.00 0.00 +IC H63 C6 C5 C4 0.00 0.00 300.0 0.00 0.00 +PATC FIRS NONE LAST NONE + +RESI NC4 1.00 ! C4H12N tetramethylammonium +GROUP +ATOM N NG3P0 -0.60 ! H32 +ATOM C1 CG334 -0.35 ! | +ATOM C2 CG334 -0.35 ! H31-C3-H33 +ATOM C3 CG334 -0.35 ! H23 | H41 +ATOM C4 CG334 -0.35 ! | | | +ATOM H11 HGP5 0.25 ! H22-C2------N------C4-H42 (+) +ATOM H12 HGP5 0.25 ! | | | +ATOM H13 HGP5 0.25 ! H21 | H43 +ATOM H21 HGP5 0.25 ! H11-C1-H13 +ATOM H22 HGP5 0.25 ! | +ATOM H23 HGP5 0.25 ! H12 +ATOM H31 HGP5 0.25 +ATOM H32 HGP5 0.25 +ATOM H33 HGP5 0.25 +ATOM H41 HGP5 0.25 +ATOM H42 HGP5 0.25 +ATOM H43 HGP5 0.25 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +IC C2 N C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C2 C1 *N C3 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2 C1 *N C4 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C3 N C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C4 N C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C1 N C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI NC5 1.00 ! C5H14N tetramethylammonium ethyl analog +GROUP +ATOM N NG3P0 -0.60 +ATOM C1 CG324 -0.10 ! | +ATOM C2 CG334 -0.35 ! -C3- +ATOM C3 CG334 -0.35 ! | +ATOM C4 CG334 -0.35 ! | | | +ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) +ATOM H12 HGP5 0.25 ! | | | +ATOM H21 HGP5 0.25 ! | +ATOM H22 HGP5 0.25 ! -C1- +ATOM H23 HGP5 0.25 ! | +ATOM H31 HGP5 0.25 ! | +ATOM H32 HGP5 0.25 ! -C5- +ATOM H33 HGP5 0.25 ! | +ATOM H41 HGP5 0.25 +ATOM H42 HGP5 0.25 +ATOM H43 HGP5 0.25 +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 C5 H53 +! ab-initio HF/6-31G* structure +IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217 +IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950 +IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950 +IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809 +IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809 +IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795 +IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773 +IC C1 N C2 H23 1.5176 111.12 -54.79 109.07 1.0797 +IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795 +IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773 +IC C1 N C3 H33 1.5176 111.12 54.79 109.07 1.0797 +IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793 +IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793 +IC C1 N C4 H43 1.5176 107.80 -60.03 109.12 1.0793 +IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820 + +RESI CHOL 1.00 ! C5H14NO choline +GROUP +ATOM N NG3P0 -0.60 +ATOM C1 CG324 -0.10 ! | +ATOM C2 CG334 -0.35 ! -C3- +ATOM C3 CG334 -0.35 ! | +ATOM C4 CG334 -0.35 ! | | | +ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) +ATOM H12 HGP5 0.25 ! | | | +ATOM H21 HGP5 0.25 ! | +ATOM H22 HGP5 0.25 ! -C1- +ATOM H23 HGP5 0.25 ! | +ATOM H31 HGP5 0.25 ! | +ATOM H32 HGP5 0.25 ! | +ATOM H33 HGP5 0.25 ! | +ATOM H41 HGP5 0.25 ! | +ATOM H42 HGP5 0.25 ! | +ATOM H43 HGP5 0.25 ! | +GROUP ! | +ATOM C5 CG321 0.05 ! | +ATOM H51 HGA2 0.09 ! -C5- +ATOM H52 HGA2 0.09 ! | +ATOM OH1 OG311 -0.65 ! OH1---HO1 +ATOM HO1 HGP1 0.42 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND C5 OH1 OH1 HO1 +! ab-initio HF/6-31G* geometry of gauche conformer +IC C4 N C1 C5 1.4964 107.76 161.60 116.58 1.5208 +IC C5 C1 N C2 1.5208 116.58 -80.13 111.04 1.5031 +IC C5 C1 N C3 1.5208 116.58 42.05 111.71 1.4945 +IC N C1 C5 OH1 1.5158 116.58 56.02 109.57 1.3947 +IC C1 C5 OH1 HO1 1.5208 109.57 169.05 110.84 0.9491 +IC C2 N C1 H11 1.5031 111.04 158.76 106.72 1.0813 +IC C3 N C1 H12 1.4945 111.71 165.25 106.14 1.0802 +IC C1 N C2 H21 1.5158 111.04 -179.38 108.21 1.0796 +IC C3 N C2 H22 1.4945 109.20 -63.85 109.22 1.0746 +IC C4 N C2 H23 1.4964 108.15 57.69 108.56 1.0794 +IC C1 N C3 H31 1.5158 111.71 173.42 108.53 1.0794 +IC C2 N C3 H32 1.5031 109.20 177.22 109.23 1.0800 +IC C4 N C3 H33 1.4964 108.88 174.14 109.12 1.0773 +IC C1 N C4 H41 1.5158 107.76 175.04 109.01 1.0793 +IC C2 N C4 H42 1.5031 108.15 -64.86 109.05 1.0796 +IC C3 N C4 H43 1.4945 108.88 56.40 109.30 1.0794 +IC N C1 C5 H51 1.5158 116.58 176.61 105.66 1.0855 +IC N C1 C5 H52 1.5158 116.58 -67.32 110.89 1.0847 + +RESI ACHO 1.00 ! C7H16NO2 acetylcholine +GROUP +ATOM N NG3P0 -0.60 +ATOM C1 CG324 -0.10 ! | +ATOM C2 CG334 -0.35 ! -C3- +ATOM C3 CG334 -0.35 ! | +ATOM C4 CG334 -0.35 ! | | | +ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) +ATOM H12 HGP5 0.25 ! | | | +ATOM H21 HGP5 0.25 ! | +ATOM H22 HGP5 0.25 ! -C1- +ATOM H23 HGP5 0.25 ! | +ATOM H31 HGP5 0.25 ! | +ATOM H32 HGP5 0.25 ! | +ATOM H33 HGP5 0.25 ! | +ATOM H41 HGP5 0.25 ! | +ATOM H42 HGP5 0.25 ! | +ATOM H43 HGP5 0.25 ! | +GROUP ! | +ATOM C5 CG321 0.08 ! -C5- +ATOM OM OG302 -0.49 ! | +ATOM C CG2O2 0.90 ! OM +ATOM C7 CG331 -0.31 ! / +ATOM O OG2D1 -0.63 ! O==C +ATOM H51 HGA2 0.09 ! | +ATOM H52 HGA2 0.09 ! --C7-- +ATOM H71 HGA3 0.09 ! | +ATOM H72 HGA3 0.09 +ATOM H73 HGA3 0.09 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND C7 C C OM OM C5 +DOUBLE C O +BOND C7 H71 C7 H72 C7 H73 +IMPR C C7 O OM +IC C4 N C1 C5 0.0000 000.00 161.60 000.00 0.0000 +IC C5 C1 N C2 0.0000 000.00 -80.13 000.00 0.0000 +IC C5 C1 N C3 0.0000 000.00 42.05 000.00 0.0000 +IC C2 N C1 H11 0.0000 000.00 158.76 000.00 0.0000 +IC C3 N C1 H12 0.0000 000.00 165.25 000.00 0.0000 +IC C1 N C2 H21 0.0000 000.00 -179.38 000.00 0.0000 +IC C3 N C2 H22 0.0000 000.00 -63.85 000.00 0.0000 +IC C4 N C2 H23 0.0000 000.00 57.69 000.00 0.0000 +IC C1 N C3 H31 0.0000 000.00 173.42 000.00 0.0000 +IC C2 N C3 H32 0.0000 000.00 177.22 000.00 0.0000 +IC C4 N C3 H33 0.0000 000.00 174.14 000.00 0.0000 +IC C1 N C4 H41 0.0000 000.00 175.04 000.00 0.0000 +IC C2 N C4 H42 0.0000 000.00 -64.86 000.00 0.0000 +IC C3 N C4 H43 0.0000 000.00 56.40 000.00 0.0000 +IC N C1 C5 H51 0.0000 000.00 180.00 000.00 0.0000 +IC N C1 C5 H52 0.0000 000.00 -60.0 000.00 0.0000 +IC N C1 C5 OM 0.0000 000.00 72.0 000.00 0.0000 +IC C1 C5 OM C 0.0000 000.00 166.9 000.00 0.0000 +IC C7 C OM C5 0.0000 000.00 20.0 000.00 0.0000 +IC O C OM C5 0.0000 000.00 -160.0 000.00 0.0000 +IC H71 C7 C OM 0.0000 000.00 180.0 000.00 0.0000 +IC H72 C7 C OM 0.0000 000.00 60.4 000.00 0.0000 +IC H73 C7 C OM 0.0000 000.00 -60.4 000.00 0.0000 + +RESI PC 0.00 ! C6H16NO4P phosphatidylcholine +GROUP +ATOM N NG3P0 -0.60 +ATOM C1 CG324 -0.10 ! | +ATOM C2 CG334 -0.35 ! -C3- +ATOM C3 CG334 -0.35 ! | +ATOM C4 CG334 -0.35 ! | | | +ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) +ATOM H12 HGP5 0.25 ! | | | +ATOM H21 HGP5 0.25 ! | +ATOM H22 HGP5 0.25 ! -C1- +ATOM H23 HGP5 0.25 ! | +ATOM H31 HGP5 0.25 ! | +ATOM H32 HGP5 0.25 ! | +ATOM H33 HGP5 0.25 ! | +ATOM H41 HGP5 0.25 ! | +ATOM H42 HGP5 0.25 ! | +ATOM H43 HGP5 0.25 ! | +GROUP ! | +ATOM C5 CG321 -0.08 ! | +ATOM H51 HGA2 0.09 ! H52---C5---H51 +ATOM H52 HGA2 0.09 ! | +GROUP ! | +ATOM P1 PG1 1.50 ! (-) O3 O1 +ATOM O3 OG2P1 -0.78 ! \ / +ATOM O4 OG2P1 -0.78 ! P1 (+) +ATOM O1 OG303 -0.57 ! / \ +ATOM O2 OG303 -0.57 ! (-) O4 O2 +GROUP ! | +ATOM C6 CG331 -0.17 ! | +ATOM H61 HGA3 0.09 ! H63-C6-H62 +ATOM H62 HGA3 0.09 ! | +ATOM H63 HGA3 0.09 ! H61 + +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C5 O2 C6 +BOND C6 H61 C6 H62 C6 H63 + +IC C4 N C1 C5 0.0000 000.00 112.00 000.00 0.0000 +IC C5 C1 N C2 0.0000 000.00 -121.00 000.00 0.0000 +IC C5 C1 N C3 0.0000 000.00 0.00 000.00 0.0000 +IC C2 N C1 H11 0.0000 000.00 120.00 000.00 0.0000 +IC C3 N C1 H12 0.0000 000.00 120.00 000.00 0.0000 +IC C1 N C2 H21 0.0000 000.00 180.00 000.00 0.0000 +IC C3 N C2 H22 0.0000 000.00 -60.00 000.00 0.0000 +IC C4 N C2 H23 0.0000 000.00 60.00 000.00 0.0000 +IC C1 N C3 H31 0.0000 000.00 180.00 000.00 0.0000 +IC C2 N C3 H32 0.0000 000.00 180.00 000.00 0.0000 +IC C4 N C3 H33 0.0000 000.00 180.00 000.00 0.0000 +IC C1 N C4 H41 0.0000 000.00 180.00 000.00 0.0000 +IC C2 N C4 H42 0.0000 000.00 -60.00 000.00 0.0000 +IC C3 N C4 H43 0.0000 000.00 60.00 000.00 0.0000 +IC N C1 C5 H51 0.0000 000.00 -150.00 000.00 0.0000 +IC N C1 C5 H52 0.0000 000.00 100.00 000.00 0.0000 +IC N C1 C5 O1 0.0000 000.00 -30.00 000.00 0.0000 +IC C1 C5 O1 P1 0.0000 000.00 130.00 000.00 0.0000 +IC C5 O1 P1 O2 0.0000 000.00 -160.0 000.00 0.0000 +IC O3 P1 O1 C5 0.0000 000.00 80.00 000.00 0.0000 +IC O4 P1 O1 C5 0.0000 000.00 -60.00 000.00 0.0000 +IC O1 P1 O2 C6 0.0000 000.00 180.00 000.00 0.0000 +IC H61 C6 O2 P1 0.0000 000.00 0.00 000.00 0.0000 +IC H62 C6 O2 P1 0.0000 000.00 120.00 000.00 0.0000 +IC H63 C6 O2 P1 0.0000 000.00 -120.00 000.00 0.0000 + +RESI GPC 0.00 ! C8H20NO6P glycerolphosphorylcholine +GROUP +ATOM N NG3P0 -0.60 +ATOM C1 CG324 -0.10 ! | +ATOM C2 CG334 -0.35 ! -C3- +ATOM C3 CG334 -0.35 ! | +ATOM C4 CG334 -0.35 ! | | | +ATOM H11 HGP5 0.25 ! -C2---N---C4- (+) +ATOM H12 HGP5 0.25 ! | | | +ATOM H21 HGP5 0.25 ! | +ATOM H22 HGP5 0.25 ! -C1- +ATOM H23 HGP5 0.25 ! | +ATOM H31 HGP5 0.25 ! | +ATOM H32 HGP5 0.25 ! | +ATOM H33 HGP5 0.25 ! | +ATOM H41 HGP5 0.25 ! | +ATOM H42 HGP5 0.25 ! | +ATOM H43 HGP5 0.25 ! | +GROUP ! | +ATOM C5 CG321 -0.08 ! | +ATOM H51 HGA2 0.09 ! H51---C5---H52 +ATOM H52 HGA2 0.09 ! | +ATOM P PG1 1.50 ! (-) O3 O1 +ATOM O3 OG2P1 -0.78 ! \ / +ATOM O4 OG2P1 -0.78 ! P (+) +ATOM O1 OG303 -0.57 ! / \ +ATOM O2 OG303 -0.57 ! (-) O4 O2 +ATOM CG1 CG321 -0.08 ! | +ATOM HG11 HGA2 0.09 ! HG11-CG1-HG12 +ATOM HG12 HGA2 0.09 ! | +GROUP ! | +ATOM CG2 CG311 0.14 ! | +ATOM HG21 HGA1 0.09 ! HG21-CG2-OG2-HO2 +ATOM OG2 OG311 -0.65 ! | +ATOM HO2 HGP1 0.42 ! | +GROUP ! | +ATOM CG3 CG321 0.05 ! | +ATOM HG31 HGA2 0.09 ! HG31-CG3-OG3-HO3 +ATOM HG32 HGA2 0.09 ! | +ATOM OG3 OG311 -0.65 ! HG32 +ATOM HO3 HGP1 0.42 +BOND CG1 O2 CG1 HG11 CG1 HG12 +BOND CG2 CG1 CG2 HG21 CG2 OG2 OG2 HO2 +BOND CG3 CG2 CG3 HG31 CG3 HG32 CG3 OG3 OG3 HO3 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +BOND C5 H51 C5 H52 +BOND P O1 P O2 P O3 P O4 O1 C5 + +! internal coordinates for analysis +! see H.Hauser,I.Pascher,R.H.Pearson,S.Sundell, BBA 650, 21-51 (1981) +! glycerol backbone +IC O2 CG1 CG2 CG3 0. 0. 0. 0. 0. ! t1 +IC O2 CG1 CG2 OG2 0. 0. 0. 0. 0. ! t2 +IC CG1 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3 +IC OG2 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3 + +! zwitterionic headgroup +IC P O2 CG1 CG2 0. 0. 0. 0. 0. ! a1 +IC O1 P O2 CG1 0. 0. 0. 0. 0. ! a2 +IC O2 P O1 C5 0. 0. 0. 0. 0. ! a3 +IC C1 C5 O1 P 0. 0. 0. 0. 0. ! a4 +IC N C1 C5 O1 0. 0. 0. 0. 0. ! a5 +IC C2 N C1 C5 0. 0. 0. 0. 0. ! a6 +IC C3 N C1 C5 0. 0. 0. 0. 0. ! a6 +IC C4 N C1 C5 0. 0. 0. 0. 0. ! a6 +IC O1 O2 *P O3 0. 0. 120. 0. 0. +IC O1 O2 *P O4 0. 0. -120. 0. 0. +PATCH FIRST NONE LAST NONE + +RESI TEA 1.00 ! C8H20N tetra ethylammonium (TEA) + ! S. Crouzy, S. Berneche and B. Roux + ! calc F.E. solvation = -51 kcal/mol + ! versus experiment = -49 kcal/mol + + ! | +GROUP ! -C7- +ATOM N NG3P0 -0.60 ! | +ATOM C1 CG324 -0.10 ! | +ATOM C2 CG324 -0.10 ! -C3- +ATOM C3 CG324 -0.10 ! | +ATOM C4 CG324 -0.10 ! | | | | | +ATOM H11 HGP5 0.25 ! -C6--C2---N---C4--C8- (+) +ATOM H12 HGP5 0.25 ! | | | | | +ATOM H21 HGP5 0.25 ! | +ATOM H22 HGP5 0.25 ! -C1- +ATOM H31 HGP5 0.25 ! | +ATOM H32 HGP5 0.25 ! -C5- +ATOM H41 HGP5 0.25 ! | +ATOM H42 HGP5 0.25 + +! in the following methyl groups, the atom type HAL +! has been changed to HGA3 . adm jr. + +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 +GROUP +ATOM C6 CG331 -0.27 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 +GROUP +ATOM C7 CG331 -0.27 +ATOM H71 HGA3 0.09 +ATOM H72 HGA3 0.09 +ATOM H73 HGA3 0.09 +GROUP +ATOM C8 CG331 -0.27 +ATOM H81 HGA3 0.09 +ATOM H82 HGA3 0.09 +ATOM H83 HGA3 0.09 +BOND N C1 N C2 N C3 N C4 +BOND C1 H11 C1 H12 C1 C5 +BOND C2 H21 C2 H22 C2 C6 +BOND C3 H31 C3 H32 C3 C7 +BOND C4 H41 C4 H42 C4 C8 +BOND C5 H51 C5 H52 C5 H53 +BOND C6 H61 C6 H62 C6 H63 +BOND C7 H71 C7 H72 C7 H73 +BOND C8 H81 C8 H82 C8 H83 + +! ab-initio HF/6-31G* structure +IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217 +IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950 +IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950 +IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809 +IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809 +IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795 +IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773 +IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795 +IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773 +IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793 +IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793 +IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820 +IC C3 N C2 C6 1.4967 107.80 180.00 115.98 1.5217 +IC N C1 C6 H61 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C6 H62 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C6 H63 1.5176 115.98 -62.29 112.91 1.0820 +IC C2 N C3 C7 1.4967 107.80 180.00 115.98 1.5217 +IC N C1 C7 H71 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C7 H72 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C7 H73 1.5176 115.98 -62.29 112.91 1.0820 +IC C1 N C4 C8 1.4967 107.80 180.00 115.98 1.5217 +IC N C1 C8 H81 1.5176 115.98 180.00 107.05 1.0836 +IC N C1 C8 H82 1.5176 115.98 62.29 112.91 1.0820 +IC N C1 C8 H83 1.5176 115.98 -62.29 112.91 1.0820 + +RESI ETAM 1.00 ! C2H8NO ethanolamine +GROUP +ATOM N NG3P3 -0.30 ! HN2 +ATOM HN1 HGP2 0.33 ! | +ATOM HN2 HGP2 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HGP2 0.33 ! | +ATOM C1 CG324 0.13 ! | +ATOM H11 HGA2 0.09 ! H12---C1---H11 +ATOM H12 HGA2 0.09 ! | +GROUP ! | +ATOM C5 CG321 0.05 ! | +ATOM H51 HGA2 0.09 ! H52---C5---H51 +ATOM H52 HGA2 0.09 ! | +ATOM OH1 OG311 -0.65 ! OH1---HO1 +ATOM HO1 HGP1 0.42 +BOND N HN1 N HN2 N HN3 N C1 +BOND C1 H11 C1 H12 C1 C5 +BOND C5 H51 C5 H52 +BOND C5 OH1 OH1 HO1 +! HF/6-31G* OPTIMIZED STRUCTURE: +IC N C1 C5 OH1 1.5084 107.86 48.44 104.92 1.3987 +IC C1 C5 OH1 HO1 1.5191 104.92 173.19 111.99 0.9495 +IC HN1 N C1 C5 1.0145 108.35 -49.03 107.86 1.5191 +IC HN2 N C1 C5 1.0107 112.05 69.23 107.86 1.5191 +IC HN3 N C1 C5 1.0102 112.39 -169.37 107.86 1.5191 +IC N C5 *C1 H11 0.0000 000.00 120.00 000.00 0.0000 +IC N C5 *C1 H12 0.0000 000.00 -120.00 000.00 0.0000 +IC OH1 C1 *C5 H51 0.0000 000.00 120.00 000.00 0.0000 +IC OH1 C1 *C5 H52 0.0000 000.00 -120.00 000.00 0.0000 + +RESI GLYC 0.00 ! C7H12O4 Model compound for glycerol headgroup the + ! aliphatic tail linker region +GROUP +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 +GROUP +ATOM C1 CG321 0.08 ! H12 H21 H31 +ATOM H11 HGA2 0.09 ! | | | +ATOM H12 HGA2 0.09 ! H11--C1--C2--C3--H32 +ATOM O4 OG302 -0.49 ! / | | +ATOM C5 CG2O2 0.90 ! O4 O8 H33 +ATOM O6 OG2D1 -0.63 ! / \ +ATOM C7 CG331 -0.31 ! O6=C5 C9=O10 +ATOM H71 HGA3 0.09 ! / \ +ATOM H72 HGA3 0.09 ! H71-C7-H73 H113-C11-H111 +ATOM H73 HGA3 0.09 ! | | +GROUP ! H72 H112 +ATOM C2 CG311 0.17 +ATOM H21 HGA1 0.09 +ATOM O8 OG302 -0.49 +ATOM C9 CG2O2 0.90 +ATOM O10 OG2D1 -0.63 +ATOM C11 CG331 -0.31 +ATOM H111 HGA3 0.09 +ATOM H112 HGA3 0.09 +ATOM H113 HGA3 0.09 +BOND C1 C2 C2 C3 +BOND C1 O4 O4 C5 C5 C7 C5 O6 +BOND C2 O8 O8 C9 C9 C11 C9 O10 +BOND C1 H11 C1 H12 +BOND C2 H21 +BOND C3 H31 C3 H32 C3 H33 +BOND C7 H71 C7 H72 C7 H73 +BOND C11 H111 C11 H112 C11 H113 +IMPR C5 C7 O6 O4 +IMPR C9 C11 O10 O8 +! internal coordinates +IC C1 C2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 +IC H31 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 O8 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 C1 O4 0.0000 0.00 180.00 0.00 0.0000 +IC O4 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC O4 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C1 O4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O4 C5 O6 0.0000 0.00 0.00 0.00 0.0000 +IC O6 O4 *C5 C7 0.0000 0.00 180.00 0.00 0.0000 +IC O4 C5 C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC H71 C5 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 +IC H71 C5 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 O8 C9 0.0000 0.00 90.00 0.00 0.0000 +IC C2 O8 C9 O10 0.0000 0.00 0.00 0.00 0.0000 +IC O10 O8 *C9 C11 0.0000 0.00 180.00 0.00 0.0000 +IC O8 C9 C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC H111 C9 *C11 H112 0.0000 0.00 120.00 0.00 0.0000 +IC H111 C9 *C11 H113 0.0000 0.00 -120.00 0.00 0.0000 + +RESI AAPM -1.00 ! C8H14O8P acetyl,acetyl-phosphatidylmethanol +GROUP ! Model compound for glycerol headgroup the +ATOM P1 PG1 1.50 ! aliphatic tail linker region, phosphorylated +ATOM OP3 OG2P1 -0.78 +ATOM OP4 OG2P1 -0.78 ! HP11 +ATOM OP1 OG303 -0.57 ! | +ATOM OP2 OG303 -0.57 ! HP13-CP1-HP12 + ! \ +ATOM CP1 CG331 -0.17 ! (-)OP3 OP1 +ATOM HP11 HGA3 0.09 ! \ / +ATOM HP12 HGA3 0.09 ! P1 (+) +ATOM HP13 HGA3 0.09 ! / \ + ! (-)OP4 OP2 + ! \ +ATOM C3 CG321 -0.08 ! \ Combining DMEP and GLYC lead to omission +ATOM H31 HGA2 0.09 ! \ of the C2 methylene group +ATOM H32 HGA2 0.09 ! \ +GROUP ! | +ATOM C1 CG321 0.08 ! H12 H21 | +ATOM H11 HGA2 0.09 ! | | | +ATOM H12 HGA2 0.09 ! H11--C1--C2--C3--H31 +ATOM O4 OG302 -0.49 ! / | | +ATOM C5 CG2O2 0.90 ! O4 O8 H32 +ATOM O6 OG2D1 -0.63 ! / \ +ATOM C7 CG331 -0.31 ! O6=C5 C9=O10 +ATOM H71 HGA3 0.09 ! / \ +ATOM H72 HGA3 0.09 ! H71-C7-H73 H113-C11-H111 +ATOM H73 HGA3 0.09 ! | | +GROUP ! H72 H112 +ATOM C2 CG311 0.17 +ATOM H21 HGA1 0.09 +ATOM O8 OG302 -0.49 +ATOM C9 CG2O2 0.90 +ATOM O10 OG2D1 -0.63 +ATOM C11 CG331 -0.31 +ATOM H111 HGA3 0.09 +ATOM H112 HGA3 0.09 +ATOM H113 HGA3 0.09 +BOND P1 OP1 P1 OP2 P1 OP3 P1 OP4 OP1 CP1 +BOND CP1 HP11 CP1 HP12 CP1 HP13 OP2 C3 +BOND C1 C2 C2 C3 +BOND C1 O4 O4 C5 C5 C7 C5 O6 +BOND C2 O8 O8 C9 C9 C11 C9 O10 +BOND C1 H11 C1 H12 C2 H21 C3 H31 C3 H32 +BOND C7 H71 C7 H72 C7 H73 +BOND C11 H111 C11 H112 C11 H113 +IMPR C5 C7 O6 O4 +IMPR C9 C11 O10 O8 +! internal coordinates from ic generate, dihedrals corrected +IC CP1 OP1 P1 OP2 0.0000 0.00 60.00 0.00 0.0000 +IC OP1 OP2 *P1 OP3 0.0000 0.00 120.00 0.00 0.0000 +IC OP1 OP2 *P1 OP4 0.0000 0.00 -120.00 0.00 0.0000 +IC OP2 P1 OP1 CP1 0.0000 0.00 60.00 0.00 0.0000 +IC P1 OP1 CP1 HP11 0.0000 0.00 180.00 0.00 0.0000 +IC HP11 OP1 *CP1 HP12 0.0000 0.00 120.00 0.00 0.0000 +IC HP11 OP1 *CP1 HP13 0.0000 0.00 -120.00 0.00 0.0000 +IC OP1 P1 OP2 C3 0.0000 0.00 -120.00 0.00 0.0000 +IC P1 OP2 C3 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 OP2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 OP2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC OP2 C3 C2 C1 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 O8 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 C1 O4 0.0000 0.00 180.00 0.00 0.0000 +IC O4 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC O4 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C1 O4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O4 C5 O6 0.0000 0.00 180.00 0.00 0.0000 +IC O6 O4 *C5 C7 0.0000 0.00 180.00 0.00 0.0000 +IC O4 C5 C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC H71 C5 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 +IC H71 C5 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 O8 C9 0.0000 0.00 60.00 0.00 0.0000 +IC C2 O8 C9 O10 0.0000 0.00 180.00 0.00 0.0000 +IC O10 O8 *C9 C11 0.0000 0.00 180.00 0.00 0.0000 +IC O8 C9 C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC H111 C9 *C11 H112 0.0000 0.00 120.00 0.00 0.0000 +IC H111 C9 *C11 H113 0.0000 0.00 -120.00 0.00 0.0000 +!Small corrections + +RESI MBUT 0.00 ! C5H10O2 methyl-butyrate +GROUP +ATOM C4 CG331 -0.27 ! H42 +ATOM H41 HGA3 0.09 ! | +ATOM H42 HGA3 0.09 ! H41-C4-H43 +ATOM H43 HGA3 0.09 ! | +GROUP ! | +ATOM C3 CG321 -0.18 ! H31-C3-H32 +ATOM H31 HGA2 0.09 ! | +ATOM H32 HGA2 0.09 ! | +GROUP ! H21-C2-H22 +ATOM C2 CG321 -0.22 ! | +ATOM H21 HGA2 0.09 ! | +ATOM H22 HGA2 0.09 ! C1 HM1 +ATOM C1 CG2O2 0.90 ! // \ / +ATOM O1 OG2D1 -0.63 ! O1 OM-CM-HM2 +ATOM OM OG302 -0.49 ! \ +ATOM CM CG331 -0.01 ! HM3 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 +BOND C1 OM OM CM CM HM1 CM HM2 CM HM3 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 C3 C3 H31 C3 H32 +BOND C3 C4 C4 H41 C4 H42 C4 H43 +DOUBLE C1 O1 +IMPR C1 C2 O1 OM + +IC C1 C2 C3 C4 0.0000 0.00 60.00 0.00 0.0000 +IC C3 C2 C1 OM 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 +IC H41 C4 C3 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 C1 OM 0.0000 0.00 180.00 0.00 0.0000 +IC OM C2 *C1 O1 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C1 OM CM 0.0000 0.00 180.00 0.00 0.0000 +IC C1 OM CM HM1 0.0000 0.00 180.00 0.00 0.0000 +IC HM1 OM *CM HM2 0.0000 0.00 120.00 0.00 0.0000 +IC HM1 OM *CM HM3 0.0000 0.00 -120.00 0.00 0.0000 + +!toppar_all27_na_base_modifications.str + +RESI DFT 0.00 ! C7H6F2 2,4-difluorotoluene +GROUP ! adm jr. w/Daniel Barsky +ATOM C1 CG2R61 -0.24 +ATOM C2 CG2R66 0.28 +ATOM C3 CG2R61 -0.24 ! F4 +ATOM C4 CG2R66 0.22 ! | +ATOM C5 CG2R61 0.10 ! H51 C4 H3 +ATOM C6 CG2R61 -0.28 ! \ / \\ / +ATOM H1 HGR62 0.21 ! H52--C5M-C5 C3 +ATOM F2 FGR1 -0.21 ! / || | +ATOM H3 HGR62 0.19 ! H52 C6 C2 +ATOM F4 FGR1 -0.21 ! / \ // \ +ATOM C5M CG331 -0.24 ! H6 C1 F2 +ATOM H51 HGA3 0.07 ! | +ATOM H52 HGA3 0.07 ! H1 +ATOM H53 HGA3 0.07 +ATOM H6 HGR61 0.21 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C1 H1 C2 F2 C3 H3 C4 F4 C5 C5M C6 H6 +BOND C5M H51 C5M H52 C5M H53 +IC C1 C2 C3 C4 0.00 0.00 0.00 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 0.00 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 0.00 0.00 0.00 +IC C4 C5 C6 C1 0.00 0.00 0.00 0.00 0.00 +IC C5 C6 C1 C2 0.00 0.00 0.00 0.00 0.00 +IC C6 C1 C2 C3 0.00 0.00 0.00 0.00 0.00 +IC C3 C2 C1 H1 0.00 0.00 180.00 0.00 0.00 +IC C4 C3 C2 F2 0.00 0.00 180.00 0.00 0.00 +IC C5 C4 C3 H3 0.00 0.00 180.00 0.00 0.00 +IC C6 C5 C4 F4 0.00 0.00 180.00 0.00 0.00 +IC C3 C4 C5 C5M 0.00 0.00 180.00 0.00 0.00 +IC C4 C5 C6 H6 0.00 0.00 180.00 0.00 0.00 +IC C4 C5 C5M H51 0.00 0.00 180.00 0.00 0.00 +IC H51 C5 *C5M H52 0.00 0.00 60.00 0.00 0.00 +IC H51 C5 *C5M H53 0.00 0.00 240.00 0.00 0.00 + +RESI DFB 0.00 ! C6H4F2 1,3-difluorobenzene aka m-difluorobenzene + ! adm jr. w/Daniel Barsky +GROUP ! atom numbering based in difluorotoluene +ATOM C1 CG2R61 -0.26 +ATOM H1 HGR62 0.23 ! F4 +ATOM C2 CG2R66 0.27 ! | +ATOM F2 FGR1 -0.19 ! H5 C4 H3 +ATOM C3 CG2R61 -0.23 ! \ / \\ / +ATOM H3 HGR62 0.19 ! C5 C3 +ATOM C4 CG2R66 0.27 ! || | +ATOM F4 FGR1 -0.19 ! C6 C2 +ATOM C5 CG2R61 -0.26 ! / \ // \ +ATOM H5 HGR62 0.23 ! H6 C1 F2 +ATOM C6 CG2R61 -0.32 ! | +ATOM H6 HGR61 0.26 ! H1 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C1 H1 C2 F2 C3 H3 C4 F4 C5 H5 C6 H6 + +IC C1 C2 C3 C4 0.00 0.00 0.00 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 0.00 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 0.00 0.00 0.00 +IC C4 C5 C6 C1 0.00 0.00 0.00 0.00 0.00 +IC C5 C6 C1 C2 0.00 0.00 0.00 0.00 0.00 +IC C6 C1 C2 C3 0.00 0.00 0.00 0.00 0.00 +IC C3 C2 C1 H1 0.00 0.00 180.00 0.00 0.00 +IC C4 C3 C2 F2 0.00 0.00 180.00 0.00 0.00 +IC C5 C4 C3 H3 0.00 0.00 180.00 0.00 0.00 +IC C6 C5 C4 F4 0.00 0.00 180.00 0.00 0.00 +IC C3 C4 C5 H5 0.00 0.00 180.00 0.00 0.00 +IC C4 C5 C6 H6 0.00 0.00 180.00 0.00 0.00 + +!toppar_all27_na_bkb_modifications.str +RESI BPET -2.00 ! C4H10O8P2 Bis-methylphosphate-ethane + ! adm jr., w/Daniel Barsky +GROUP +ATOM C1 CG331 -0.17 ! H11 +ATOM H11 HGA3 0.09 ! | +ATOM H12 HGA3 0.09 ! H13-C1-H12 +ATOM H13 HGA3 0.09 ! \ +ATOM O2 OG303 -0.57 ! O31 O2 +ATOM P3 PG1 1.50 ! \\ / +ATOM O31 OG2P1 -0.78 ! (-) P3 +ATOM O32 OG2P1 -0.78 ! // \ +ATOM O4 OG303 -0.57 ! O32 O4 +ATOM C5 CG321 -0.08 ! / +ATOM H51 HGA2 0.09 ! H51-C5-H52 +ATOM H52 HGA2 0.09 ! | +ATOM C6 CG321 -0.08 ! H51-C6-H52 +ATOM H61 HGA2 0.09 ! \ +ATOM H62 HGA2 0.09 ! O81 O7 +ATOM O7 OG303 -0.57 ! \\ / +ATOM P8 PG1 1.50 ! (-) P8 +ATOM O81 OG2P1 -0.78 ! // \ +ATOM O82 OG2P1 -0.78 ! O82 O9 +ATOM O9 OG303 -0.57 ! / +ATOM C10 CG331 -0.17 ! H101-C10-H102 +ATOM H101 HGA3 0.09 ! | +ATOM H102 HGA3 0.09 ! H103 +ATOM H103 HGA3 0.09 + +BOND C1 O2 O2 P3 P3 O4 O4 C5 C5 C6 C6 O7 +BOND O7 P8 P8 O9 O9 C10 P3 O31 P3 O32 +BOND P8 O81 P8 O82 +BOND C1 H11 C1 H12 C1 H13 C5 H51 C5 H52 +BOND C6 H61 C6 H62 C10 H101 C10 H102 C10 H103 +!from IC generate +IC H11 C1 O2 P3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O2 P3 O4 0.0000 0.00 180.00 0.00 0.0000 +IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC O4 O2 *P3 O31 0.0000 0.00 120.00 0.00 0.0000 +IC O4 O2 *P3 O32 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 P3 O4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC P3 O4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 O4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C6 O4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC O4 C5 C6 O7 0.0000 0.00 180.00 0.00 0.0000 +IC O7 C5 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC O7 C5 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C6 O7 P8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 O7 P8 O9 0.0000 0.00 180.00 0.00 0.0000 +IC O9 O7 *P8 O81 0.0000 0.00 120.00 0.00 0.0000 +IC O9 O7 *P8 O82 0.0000 0.00 -120.00 0.00 0.0000 +IC O7 P8 O9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC P8 O9 C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC H101 O9 *C10 H102 0.0000 0.00 120.00 0.00 0.0000 +IC H101 O9 *C10 H103 0.0000 0.00 -120.00 0.00 0.0000 + +RESI ABNS 0.00 ! C5H10O3 abasic deoxyribose nucleoside (susil) + ! adm jr., w/Daniel Barsky +GROUP +ATOM H5T HGP1 0.42 +ATOM O5' OG311 -0.65 +ATOM C5' CG321 0.05 ! H5T +ATOM H51' HGA2 0.09 ! \ +ATOM H52' HGA2 0.09 ! H51' O5' +ATOM C4' CG3C51 0.11 ! \ / +ATOM H42' HGA1 0.09 ! H52'--C5' O4' H11' +ATOM O4' OG3C51 -0.40 ! \ / \ / +ATOM C1' CG3C52 0.02 ! H42'-C4' C1'-H12' +ATOM H11' HGA2 0.09 ! | | +ATOM H12' HGA2 0.09 ! C3'---C2'-H21' +ATOM C2' CG3C52 -0.18 ! / | \ +ATOM H21' HGA2 0.09 ! O3' H31' H22' +ATOM H22' HGA2 0.09 ! | +ATOM C3' CG3C51 0.14 ! H32' +ATOM H31' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 + +BOND O4' C4' O4' C1' C4' C5' C4' H42' C4' C3' +BOND C1' H11' C1' H12' C1' C2' C2' H21' C2' H22' +BOND C3' H31' C3' O3' O3' H32' C5' O5' C5' H51' +BOND C5' H52' O5' H5T C2' C3' + +IC O4' C1' C2' C3' 1.433 104.1 41.2 100.9 1.525 +IC C1' C2' C3' C4' 1.521 100.9 325.1 102.6 1.533 +IC C2' C3' C4' C5' 1.525 102.6 257.8 113.7 1.513 +IC C3' C4' C5' O5' 1.534 113.7 46.5 108.2 1.428 +IC C4' C5' O5' H5T 1.513 108.2 170.4 107.7 0.971 +IC C3' C4' C5' H52' 1.534 113.7 167.5 108.4 1.098 +IC C3' C4' C5' H51' 1.534 113.7 285.5 109.1 1.101 +IC C2' C3' C4' H42' 1.525 102.6 135.9 108.6 1.099 +IC C1' C2' C3' H31' 1.521 100.9 204.2 113.0 1.097 +IC C1' C2' C3' O3' 1.521 100.9 78.3 111.7 1.434 +IC C2' C3' O3' H32' 1.525 111.7 65.4 107.1 0.973 +IC O4' C1' C2' H22' 1.433 104.1 162.1 113.9 1.096 +IC O4' C1' C2' H21' 1.433 104.1 285.5 110.1 1.093 +IC O4' C1' C2' H11' 1.433 104.1 243.2 26.8 2.209 +IC O4' C1' C2' H12' 1.433 104.1 119.0 28.2 2.173 + +! May need to revisit the phosphoramidates when we get to the anionic sulfamates and try an aromatic one. -- Kenno +RESI PHA -1.00 ! C2H7NO3P Phosphoramidate (backbone for DNA) +GROUP +ATOM P1 PG1 1.57 +ATOM O3 OG2P1 -0.82 +ATOM O4 OG2P1 -0.82 +ATOM O2 OG303 -0.56 ! H11 +ATOM N1 NG2S3 -0.86 ! | +ATOM H1 HGP1 0.33 ! H13- C1-H12 + ! \ +ATOM C1 CG331 -0.19 ! (-)O3 N1-H1 +ATOM H11 HGA3 0.09 ! \ / +ATOM H12 HGA3 0.09 ! P1(+1) +ATOM H13 HGA3 0.09 ! / \ + ! (-)O4 O2 +ATOM C2 CG331 -0.19 ! / +ATOM H21 HGA3 0.09 ! H23-C2-H22 +ATOM H22 HGA3 0.09 ! | +ATOM H23 HGA3 0.09 ! H21 + +BOND P1 N1 P1 O2 P1 O3 P1 O4 N1 C2 N1 H1 O2 C1 +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 +! IC FOR THE g,g crystal conformation (6-31G* opt. structure) +IC O3 P1 N1 C2 1.4816 107.70 342.80 123.13 1.4559 +IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 +IC O4 P1 O2 C1 1.4812 105.80 43.90 118.08 1.4331 +IC N1 P1 O2 C1 1.6728 99.90 158.10 118.08 1.4331 +IC O2 P1 N1 C2 1.6480 99.90 96.20 123.13 1.4559 +IC H11 C1 O2 P1 1.0913 113.30 253.00 123.13 1.6728 +IC H12 C1 O2 P1 1.0790 106.20 12.40 123.13 1.6728 +IC H13 C1 O2 P1 1.0898 111.90 131.00 123.13 1.6728 +IC H21 C2 N1 P1 1.0841 108.20 196.00 118.08 1.6480 +IC H22 C2 N1 P1 1.0805 109.90 316.40 118.08 1.6480 +IC H23 C2 N1 P1 1.0862 111.20 76.70 118.08 1.6480 +PATC FIRS NONE LAST NONE + +RESI TPHC -1.00 ! C5H11NO4P monoanionic 3'phosphoramidate-tetrahydrofuran +! used to fit epsilon +! Charges and atom types for the monoanionic phosphate groups were +! transfered from residue PHA +! Atom types for aliphatic hydrogens are a mess + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H41' O4' H11' +ATOM C4' CG3C52 0.02 ! \ / \ / +ATOM H41' HGA2 0.09 ! H42'-C4' C1'-H12' +ATOM H42' HGA2 0.09 ! | | +GROUP ! H31'-C3'-C2'-H21' +ATOM C2' CG3C52 -0.18 ! / \ +ATOM H21' HGA2 0.09 ! H1-N1 O3 H22' +ATOM H22' HGA2 0.09 ! \ / +GROUP ! P1 +ATOM C3' CG3C51 -0.01 ! / \ +ATOM H31' HGA1 0.09 ! O2 O4 +ATOM N1 NG2S3 -0.86 ! | +ATOM H1 HGP1 0.33 ! H51'-C5-H52' +ATOM P1 PG1 1.57 ! | +ATOM O3 OG2P1 -0.82 ! H53' +ATOM O4 OG2P1 -0.82 +ATOM O2 OG303 -0.56 +ATOM C5' CG331 -0.19 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' N1 +BOND N1 H1 C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' +BOND C4' H41' C4' H42' N1 P1 P1 O3 P1 O4 P1 O2 +BOND O2 C5' C5' H51' C5' H52' C5' H53' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC O4' C2' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC O4' C2' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC C1' C3' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C1' C3' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC N1 C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 +IC P1 N1 C3' C4' 1.7190 119.98 185.77 110.95 1.5332 +IC O3 P1 N1 C3' 1.4771 109.35 14.75 120.00 1.4525 +IC O4 P1 N1 C3' 1.4818 105.19 150.42 120.00 1.4525 +IC O2 P1 N1 C3' 1.6379 101.65 263.47 120.00 1.4525 +IC C5' O2 P1 N1 1.3955 119.61 286.08 101.65 1.7190 +IC H51' C5' O2 P1 1.0859 107.43 179.85 119.61 1.6379 +IC H52' C5' O2 P1 1.0835 111.18 299.56 119.61 1.6379 +IC H53' C5' O2 P1 1.0868 111.29 60.84 119.61 1.6379 + +PATC FIRS NONE LAST NONE + +RESI THNI 0.00 ! C8H13N3O2 tetrahydrofuran with 3'-NH2, 5'-CH2OH, 1'-imidazole +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 3 asymmetric carbons. +ATOM C4' CG3C51 0.11 ! Abs. config is arbitrary. +ATOM H42' HGA1 0.09 +ATOM C1' CG3C51 0.11 +ATOM H12' HGA1 0.09 +GROUP +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CG2R51 -0.05 ! HE1 +ATOM HG HGR52 0.09 ! / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / | +ATOM ND1 NG2R51 -0.04 ! HG-CG | +ATOM CE1 CG2R53 0.25 ! \ | +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM N1 NG321 -0.91 +ATOM H1 HGPAM2 0.34 +ATOM H2 HGPAM2 0.34 +GROUP ! Methyl group on C4' +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5' HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' N1 N1 H1 N1 H2 C1' H12' C2' H21' C2' H22' +BOND C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5' +BOND C1' ND1 ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC N1 C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H1 N1 C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H2 N1 C3' C2' 0.0 0.0 60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 +IC H5' O5' C5' C4' 0.0 0.0 59.68 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THNP -1.00 ! C9H15N3O5P Tetrahydrofuran with 3'-NH-PO2-OCH3, 5'-CH2OH, 1'-imidazole +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 3 asymmetric carbons. +ATOM C4' CG3C51 0.11 ! Abs. config is arbitrary. +ATOM H42' HGA1 0.09 +ATOM C1' CG3C51 0.11 +ATOM H12' HGA1 0.09 +GROUP +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CG2R51 -0.05 ! HE1 +ATOM HG HGR52 0.09 ! / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / | +ATOM ND1 NG2R51 -0.04 ! HG-CG | +ATOM CE1 CG2R53 0.25 ! \ | +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 +GROUP ! Methyl group on C4' +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5' HGP1 0.42 + +GROUP ! phosphoramidate group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 -0.01 +ATOM N1 NG2S3 -0.86 +ATOM H1 HGP1 0.33 +ATOM P1 PG1 1.57 +ATOM O3 OG2P1 -0.82 +ATOM O4 OG2P1 -0.82 +ATOM O5 OG303 -0.56 +ATOM C5 CG331 -0.19 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' N1 N1 H1 C1' H12' C2' H21' C2' H22' +BOND C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5' +BOND C1' ND1 ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +BOND P1 N1 P1 O5 P1 O3 P1 O4 O5 C5 +BOND C5 H51 C5 H52 C5 H53 +! This IC table is only an initial guess: +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC ND1 C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC N1 C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P1 N1 C3' C4' 0.0000 000.00 180.00 000.00 0.0000 +IC C3' N1 P1 O5 0.0000 000.00 -95.22 000.00 0.0000 +IC O5 N1 *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O5 N1 *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +IC O3 P1 N1 H1 1.4816 107.70 171.10 119.02 0.9986 +IC C5 O5 P1 N1 0.0000 000.00 -46.90 000.00 0.0000 +IC H51 C5 O5 P1 0.0000 000.00 180.00 000.00 0.0000 +IC H52 C5 O5 P1 0.0000 000.00 60.00 000.00 0.0000 +IC H53 C5 O5 P1 0.0000 000.00 -60.00 000.00 0.0000 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 +IC H5' O5' C5' C4' 0.0 0.0 59.68 0.0 0.0 +PATC FIRS NONE LAST NONE + +!toppar_all27_na_carbocyclic.str +RESI CPEN 0.00 ! C5H10 cyclopentane, adm jr. + ! with north atom types + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C1 CG3C52 -0.18 ! H51 H52 +ATOM H11 HGA2 0.09 ! \ / +ATOM H12 HGA2 0.09 ! C5 +GROUP ! H41 / \ H11 +ATOM C2 CG3C52 -0.18 ! \ / \ / +ATOM H21 HGA2 0.09 ! H42-C4 C1-H12 +ATOM H22 HGA2 0.09 ! | | +GROUP ! H31-C3------C2-H21 +ATOM C3 CG3C52 -0.18 ! | | +ATOM H31 HGA2 0.09 ! H32 H22 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG3C52 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG3C52 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C1 +BOND C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 +BOND C5 H51 C5 H52 +! internal coordinates from parameter file, note initial planar geometry +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C2 *C1 H12 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI CPES 0.00 ! C5H10 cyclopentane, adm jr. + ! with south atom types + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C1 CG3C52 -0.18 ! H51 H52 +ATOM H11 HGA2 0.09 ! \ / +ATOM H12 HGA2 0.09 ! C5 +GROUP ! H41 / \ H11 +ATOM C2 CG3C52 -0.18 ! \ / \ / +ATOM H21 HGA2 0.09 ! H42-C4 C1-H12 +ATOM H22 HGA2 0.09 ! | | +GROUP ! H31-C3------C2-H21 +ATOM C3 CG3C52 -0.18 ! | | +ATOM H31 HGA2 0.09 ! H32 H22 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG3C52 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG3C52 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C1 +BOND C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 +BOND C5 H51 C5 H52 +! internal coordinates from parameter file, note initial planar geometry +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C2 *C1 H12 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI BPNP -1.00 ! C7H12O4P North carbocyclic sugar with 3'-OPOCH3 + ! used to parameterize epsilon + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C2 CG3C51 0.01 ! This charge changed from -0.09 to make it +ATOM H21 HGA1 0.09 ! compatible with -OPOCH3 +ATOM O3' OG303 -0.57 +ATOM P PG1 1.50 +ATOM O1P OG2P1 -0.78 +ATOM O2P OG2P1 -0.78 +ATOM O5' OG303 -0.57 +ATOM C5' CG331 -0.17 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + ! H61 H62 + ! \ / + ! C6 +GROUP ! / \ H11 +ATOM C4 CG3C52 -0.18 ! / \ / +ATOM H41 HGA2 0.09 ! H51-C5-----C1 H51' +ATOM H42 HGA2 0.09 ! | | / +GROUP ! H41-C4 C2--O3'--P--O5'-C5'-H52' +ATOM C3 CG3C52 -0.18 ! / \ / \ // \ _ \ +ATOM H31 HGA2 0.09 ! H42 \ / H21 O1P O2P H53' +ATOM H32 HGA2 0.09 ! C3 +GROUP ! / \ +ATOM C1 CG3RC1 -0.09 ! H31 H32 +ATOM H11 HGA1 0.09 +GROUP +ATOM C5 CG3RC1 -0.09 +ATOM H51 HGA1 0.09 +GROUP +ATOM C6 CG3C31 -0.18 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C5 C6 C6 C1 C5 H51 +BOND C2 H21 C4 H42 C3 H31 C3 H32 +BOND C4 H41 C6 H61 C1 H11 +BOND C6 H62 C2 O3' O3' P P O1P +BOND P O2P P O5' O5' C5' C5' H51' +BOND C5' H52' C5' H53' +! internal coordinates from parameter file, note initial planar geometry +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C5 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 O3' 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C4 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 C6 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 +IC O3' C2 C1 C5 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C2 C1 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C2 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C2 0.0 0.0 60.0 0.0 0.0 +IC O5' P O3' C2 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 +IC H51' C5' O5' P 0.0 0.0 60.0 0.0 0.0 +IC H52' C5' O5' P 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' O5' P 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI BPSP -1.00 ! C7H12O4P south carbcyclic sugar with 3'-OPOCH3 + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C1 CG3RC1 -0.09 ! H31 H32 +ATOM H11 HGA1 0.09 ! \ / + ! C6 +GROUP ! / \ +ATOM C2 CG3C52 -0.18 ! / \ +ATOM H21 HGA2 0.09 ! H51-C5------C1-H11 +ATOM H22 HGA2 0.09 ! | | +GROUP ! H41-C4 C2-H22 +ATOM C6 CG3C31 -0.18 ! / \ / \ +ATOM H61 HGA2 0.09 ! H42 \ / H21 +ATOM H62 HGA2 0.09 ! C3-H31 +GROUP ! | +ATOM C4 CG3C52 -0.18 ! O3' H51' +ATOM H41 HGA2 0.09 ! \ / +ATOM H42 HGA2 0.09 ! P--O5'-C5'-H52' + ! // \ _ \ +GROUP ! O1P O2P H53' +ATOM C5 CG3RC1 -0.09 +ATOM H51 HGA1 0.09 +GROUP +ATOM C3 CG3C51 0.01 ! This charge changed from -0.09 to make it +ATOM H31 HGA1 0.09 ! compatible with -OPOCH3 +ATOM O3' OG303 -0.57 +ATOM P PG1 1.50 +ATOM O1P OG2P1 -0.78 +ATOM O2P OG2P1 -0.78 +ATOM O5' OG303 -0.57 +ATOM C5' CG331 -0.17 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C5 C6 C6 C1 C4 H42 +BOND C1 H11 C2 H21 C2 H22 +BOND C6 H61 C6 H62 C4 H41 +BOND C5 H51 C3 H31 C3 O3' O3' P +BOND P O1P P O2P P O5' O5' C5' +BOND C5' H51' C5' H52' C5' H53' +! internal coordinates +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C5 *C1 C6 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 O3' 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 H52 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 +IC O3' C3 C4 C5 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3 C4 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3 0.0 0.0 60.0 0.0 0.0 +IC O5' P O3' C3 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 +IC H51' C5' O5' P 0.0 0.0 60.0 0.0 0.0 +IC H52' C5' O5' P 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' O5' P 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI CSAD 0.00 ! C11H13N5 carbocyclic sugar with adenine base, south + ! base attached to C1 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C52 -0.18 ! / \ +ATOM H21S HGA2 0.09 ! H51S-C5S----C1S-----------* +ATOM H22S HGA2 0.09 ! | | +GROUP ! H41S-C4S C2S-H22S +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 0.00 +ATOM C5 CG2RC0 0.28 ! H61 H62 +ATOM N7 NG2R50 -0.71 ! \ / +ATOM C8 CG2R53 0.34 ! N6 +ATOM H8 HGR52 0.12 ! | +ATOM N9 NG2R51 -0.05 ! C6 + ! // \ +ATOM N1 NG2R62 -0.74 ! N1 C5--N7\\ +ATOM C2 CG2R64 0.50 ! | || C8-H8 +ATOM H2 HGR62 0.13 ! C2 C4--N9/ +ATOM N3 NG2R62 -0.75 ! / \\ / \ +ATOM C4 CG2RC0 0.43 ! H2 N3 \ +ATOM C6 CG2R64 0.46 ! \ +ATOM N6 NG2S3 -0.77 ! \ +ATOM H61 HGP4 0.38 ! \ +ATOM H62 HGP4 0.38 ! * + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C2S H21S C2S H22S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C1S N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 +BOND C6 N6 N6 H61 N6 H62 C6 C5 +BOND C5 N7 C8 H8 C2 H2 +DOUB N1 C6 C2 N3 C4 C5 N7 C8 + +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S N9 0.0000 108.00 140.0 120.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C3S C2S C1S N9 1.5284 101.97 147.80 120.00 1.4896 !N9 is already defined +IC C5S C1S N9 C4 1.5251 120.00 -150.0 125.59 1.3783 !chi +IC C1S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI CSGU 0.00 ! C11H13N5O carbocyclic sugar with guanine base, south + ! base attached to C1 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C52 -0.18 ! / \ +ATOM H21S HGA2 0.09 ! H51S-C5S----C1S-----------* +ATOM H22S HGA2 0.09 ! | | +GROUP ! H41S-C4S C2S-H22S +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 0.00 +GROUP +ATOM N9 NG2R51 -0.02 ! O6 +ATOM C4 CG2RC0 0.26 ! || +ATOM N3 NG2R62 -0.74 ! C6 +ATOM C2 CG2R64 0.75 ! / \ +ATOM N1 NG2R61 -0.34 ! H1-N1 C5--N7\\ +ATOM H1 HGP1 0.26 ! | || C8-H8 +ATOM N2 NG2S3 -0.68 ! C2 C4--N9/ +ATOM H21 HGP4 0.32 ! / \\ / \ +ATOM H22 HGP4 0.35 ! H21-N2 N3 \ +ATOM C6 CG2R63 0.54 ! | \ +ATOM O6 OG2D4 -0.51 ! H22 \ +ATOM C5 CG2RC0 0.00 ! * +ATOM N7 NG2R50 -0.60 +ATOM C8 CG2R53 0.25 +ATOM H8 HGR52 0.16 + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C2S H21S C2S H22S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C1S N9 +BOND N9 C4 N9 C8 C4 N3 C8 H8 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 + +IMPR C2 N1 N3 N2 +IMPR N2 H22 H21 C2 +IMPR C6 C5 N1 O6 + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +ACCE O6 C6 +ACCE N3 +ACCE N7 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S N9 0.0000 108.00 140.0 120.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C3S C2S C1S N9 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C5S C1S N9 C4 1.5251 120.00 -150.0 125.59 1.3783 !chi +IC C1S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI CSTH 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, south + ! base attached to C1 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C52 -0.18 ! / \ +ATOM H21S HGA2 0.09 ! H51S-C5S----C1S-----------* +ATOM H22S HGA2 0.09 ! | | +GROUP ! H41S-C4S C2S-H22S +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 0.00 +GROUP +ATOM N1 NG2R61 -0.34 ! H51 O4 +ATOM C6 CG2R62 0.17 ! | || +ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 +ATOM C2 CG2R63 0.51 ! | \ / \ / +ATOM O2 OG2D4 -0.41 ! H53 C5 N3 +ATOM N3 NG2R61 -0.46 ! || | +ATOM H3 HGP1 0.36 ! H6-C6 C2 +ATOM C4 CG2R63 0.50 ! \ / \\ +ATOM O4 OG2D4 -0.45 ! N1 O2 +ATOM C5 CG2R62 -0.15 ! \ +ATOM C5M CG331 -0.11 ! \ +ATOM H51 HGA3 0.07 ! \ +ATOM H52 HGA3 0.07 ! * +ATOM H53 HGA3 0.07 + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C2S H21S C2S H22S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C1S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S N1 0.0000 108.00 140.0 120.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C3S C2S C1S N1 1.5284 101.97 147.80 120.00 1.4896 !N9 is already defined +IC C5S C1S N1 C2 0.0000 120.00 -130.0 125.59 1.3783 !chi +IC C1S C2 *N1 C6 0.0000 0.0 -180.00 0.0 0.0 +IC C2 N1 C6 C5 0.0000 0.0 -0.02 0.0 0.0 +IC C6 N1 C2 N3 0.0000 0.0 0.06 0.0 0.0 +IC N1 N3 *C2 O2 0.0000 0.0 -179.95 0.0 0.0 +IC N1 C2 N3 C4 0.0000 0.0 -0.07 0.0 0.0 +IC C5 N3 *C4 O4 0.0000 0.0 179.98 0.0 0.0 +IC C2 C4 *N3 H3 0.0000 0.0 180.00 0.0 0.0 +IC C4 C6 *C5 C5M 0.0000 0.0 -179.94 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 90.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI CSCY 0.00 ! C10H13N3O carbocyclic sugar with cytosine base, south + ! base attached to C1 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C52 -0.18 ! / \ +ATOM H21S HGA2 0.09 ! H51S-C5S----C1S-----------* +ATOM H22S HGA2 0.09 ! | | +GROUP ! H41S-C4S C2S-H22S +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 0.00 ! H42 H41 +GROUP ! \ / +ATOM N1 NG2R61 -0.13 ! N4 +ATOM C6 CG2R62 0.05 ! | +ATOM H6 HGR62 0.17 ! C4 +ATOM C2 CG2R63 0.52 ! / \\ +ATOM O2 OG2D4 -0.49 ! H5-C5 N3 +ATOM N3 NG2R62 -0.66 ! || | +ATOM C4 CG2R64 0.65 ! H6-C6 C2 +ATOM N4 NG2S3 -0.75 ! \ / \\ +ATOM H41 HGP4 0.37 ! N1 O2 +ATOM H42 HGP4 0.33 ! \ +ATOM C5 CG2R62 -0.13 ! \ +ATOM H5 HGR62 0.07 ! * + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C2S H21S C2S H22S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C1S N1 +BOND N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C5 H5 C6 H6 + +IMPR C4 C5 N3 N4 +IMPR C2 N1 N3 O2 +IMPR N4 H42 H41 C4 + +DONO H42 N4 +DONO H41 N4 +ACCE O2 C2 +ACCE N3 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S N1 0.0000 108.00 140.0 120.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H22S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C3S C2S C1S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C5S C1S N1 C2 0.0000 120.00 -130.0 125.59 1.3783 !chi +IC C1S C2 *N1 C6 0.0000 0.00 -180.00 0.00 0.0000 +IC C2 N1 C6 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C6 N1 C2 N3 0.0000 0.00 0.0 0.00 0.0000 +IC N1 N3 *C2 O2 0.0000 0.00 180.0 0.00 0.0000 +IC N1 C2 N3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C5 N3 *C4 N4 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C4 N4 H41 0.0000 0.00 0.00 0.00 0.0000 +IC H41 C4 *N4 H42 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI CNAD 0.00 ! C11H13N5 carbocyclic sugar with adenine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C51 -0.09 ! / \ +ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 -0.09 +ATOM H11S HGA1 0.09 +GROUP +ATOM C5 CG2RC0 0.28 ! H61 H62 +ATOM N7 NG2R50 -0.71 ! \ / +ATOM C8 CG2R53 0.34 ! N6 +ATOM H8 HGR52 0.12 ! | +ATOM N9 NG2R51 -0.05 ! C6 + ! // \ +ATOM N1 NG2R62 -0.74 ! N1 C5--N7\\ +ATOM C2 CG2R64 0.50 ! | || C8-H8 +ATOM H2 HGR62 0.13 ! C2 C4--N9/ +ATOM N3 NG2R62 -0.75 ! / \\ / \ +ATOM C4 CG2RC0 0.43 ! H2 N3 \ +ATOM C6 CG2R64 0.46 ! \ +ATOM N6 NG2S3 -0.77 ! \ +ATOM H61 HGP4 0.38 ! \ +ATOM H62 HGP4 0.38 ! * + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUB N1 C6 C2 N3 C4 C5 N7 C8 + +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N9 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C4S C3S C2S N9 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C1S C2S N9 C4 1.5251 113.71 -120.0 125.59 1.3783 !chi +IC C2S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +PATCH FIRST NONE LAST NONE + +RESI CNGU 0.00 ! C11H13N5O carbocyclic sugar with guanine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C51 -0.09 ! / \ +ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 -0.09 +ATOM H11S HGA1 0.09 +GROUP +ATOM N9 NG2R51 -0.02 ! O6 +ATOM C4 CG2RC0 0.26 ! || +ATOM N3 NG2R62 -0.74 ! C6 +ATOM C2 CG2R64 0.75 ! / \ +ATOM N1 NG2R61 -0.34 ! H1-N1 C5--N7\\ +ATOM H1 HGP1 0.26 ! | || C8-H8 +ATOM N2 NG2S3 -0.68 ! C2 C4--N9/ +ATOM H21 HGP4 0.32 ! / \\ / \ +ATOM H22 HGP4 0.35 ! H21-N2 N3 \ +ATOM C6 CG2R63 0.54 ! | \ +ATOM O6 OG2D4 -0.51 ! H22 \ +ATOM C5 CG2RC0 0.00 ! * +ATOM N7 NG2R50 -0.60 +ATOM C8 CG2R53 0.25 +ATOM H8 HGR52 0.16 + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N9 +BOND N9 C4 N9 C8 C4 N3 C8 H8 +BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 +BOND C5 N7 N7 C8 + +IMPR C2 N1 N3 N2 +IMPR N2 H22 H21 C2 +IMPR C6 C5 N1 O6 + +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +ACCE O6 C6 +ACCE N3 +ACCE N7 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N9 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C4S C3S C2S N9 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C1S C2S N9 C4 1.5251 113.71 -120.00 125.59 1.3783 !chi +IC C2S C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI CNTH 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C51 -0.09 ! / \ +ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 -0.09 +ATOM H11S HGA1 0.09 +GROUP +ATOM N1 NG2R61 -0.34 ! H51 O4 +ATOM C6 CG2R62 0.17 ! | || +ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 +ATOM C2 CG2R63 0.51 ! | \ / \ / +ATOM O2 OG2D4 -0.41 ! H53 C5 N3 +ATOM N3 NG2R61 -0.46 ! || | +ATOM H3 HGP1 0.36 ! H6-C6 C2 +ATOM C4 CG2R63 0.50 ! \ / \\ +ATOM O4 OG2D4 -0.45 ! N1 O2 +ATOM C5 CG2R62 -0.15 ! \ +ATOM C5M CG331 -0.11 ! \ +ATOM H51 HGA3 0.07 ! \ +ATOM H52 HGA3 0.07 ! * +ATOM H53 HGA3 0.07 + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C1S C2S N1 C2 0.0 0.0 -160.0 0.0 0.0 !chi +IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 +IC C2 N1 C6 C5 0.0 0.0 -0.02 0.0 0.0 +IC C6 N1 C2 N3 0.0 0.0 0.06 0.0 0.0 +IC N1 N3 *C2 O2 0.0 0.0 -179.95 0.0 0.0 +IC N1 C2 N3 C4 0.0 0.0 -0.07 0.0 0.0 +IC C5 N3 *C4 O4 0.0 0.0 179.98 0.0 0.0 +IC C2 C4 *N3 H3 0.0 0.0 180.00 0.0 0.0 +IC C4 C6 *C5 C5M 0.0 0.0 -179.94 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 -90.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI CNT1 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C51 -0.09 ! / \ +ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 -0.09 +ATOM H11S HGA1 0.09 +GROUP +ATOM N1 NG2R61 -0.34 ! H51 O4 +ATOM C6 CG2R62 0.17 ! | || +ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 +ATOM C2 CG2R63 0.51 ! | \ / \ / +ATOM O2 OG2D4 -0.41 ! H53 C5 N3 +ATOM N3 NG2R61 -0.46 ! || | +ATOM H3 HGP1 0.36 ! H6-C6 C2 +ATOM C4 CG2R63 0.50 ! \ / \\ +ATOM O4 OG2D4 -0.45 ! N1 O2 +ATOM C5 CG2R62 -0.15 ! \ +ATOM C5M CG331 -0.11 ! \ +ATOM H51 HGA3 0.07 ! \ +ATOM H52 HGA3 0.07 ! * +ATOM H53 HGA3 0.07 + + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C1S C2S N1 C2 0.0 0.0 -160.00 0.0 0.0 !chi +IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 +IC C2 N1 C6 C5 0.0 0.0 -0.02 0.0 0.0 +IC C6 N1 C2 N3 0.0 0.0 0.06 0.0 0.0 +IC N1 N3 *C2 O2 0.0 0.0 -179.95 0.0 0.0 +IC N1 C2 N3 C4 0.0 0.0 -0.07 0.0 0.0 +IC C5 N3 *C4 O4 0.0 0.0 179.98 0.0 0.0 +IC C2 C4 *N3 H3 0.0 0.0 180.00 0.0 0.0 +IC C4 C6 *C5 C5M 0.0 0.0 -179.94 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 -90.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI CNT2 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C51 -0.09 ! / \ +ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 -0.09 +ATOM H11S HGA1 0.09 +GROUP +ATOM N1 NG2R61 -0.34 ! H51 O4 +ATOM C6 CG2R62 0.17 ! | || +ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 +ATOM C2 CG2R63 0.51 ! | \ / \ / +ATOM O2 OG2D4 -0.41 ! H53 C5 N3 +ATOM N3 NG2R61 -0.46 ! || | +ATOM H3 HGP1 0.36 ! H6-C6 C2 +ATOM C4 CG2R63 0.50 ! \ / \\ +ATOM O4 OG2D4 -0.45 ! N1 O2 +ATOM C5 CG2R62 -0.15 ! \ +ATOM C5M CG331 -0.11 ! \ +ATOM H51 HGA3 0.07 ! \ +ATOM H52 HGA3 0.07 ! * +ATOM H53 HGA3 0.07 + + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C1S C2S N1 C2 0.0 0.0 -160.00 0.0 0.0 !chi +IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 +IC C2 N1 C6 C5 0.0 0.0 -0.02 0.0 0.0 +IC C6 N1 C2 N3 0.0 0.0 0.06 0.0 0.0 +IC N1 N3 *C2 O2 0.0 0.0 -179.95 0.0 0.0 +IC N1 C2 N3 C4 0.0 0.0 -0.07 0.0 0.0 +IC C5 N3 *C4 O4 0.0 0.0 179.98 0.0 0.0 +IC C2 C4 *N3 H3 0.0 0.0 180.00 0.0 0.0 +IC C4 C6 *C5 C5M 0.0 0.0 -179.94 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 -90.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI CNT3 0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C51 -0.09 ! / \ +ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 -0.09 +ATOM H11S HGA1 0.09 +GROUP +ATOM N1 NG2R61 -0.34 ! H51 O4 +ATOM C6 CG2R62 0.17 ! | || +ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 +ATOM C2 CG2R63 0.51 ! | \ / \ / +ATOM O2 OG2D4 -0.41 ! H53 C5 N3 +ATOM N3 NG2R61 -0.46 ! || | +ATOM H3 HGP1 0.36 ! H6-C6 C2 +ATOM C4 CG2R63 0.50 ! \ / \\ +ATOM O4 OG2D4 -0.45 ! N1 O2 +ATOM C5 CG2R62 -0.15 ! \ +ATOM C5M CG331 -0.11 ! \ +ATOM H51 HGA3 0.07 ! \ +ATOM H52 HGA3 0.07 ! * +ATOM H53 HGA3 0.07 + + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 C4 C5 +BOND C2 N3 N3 H3 N3 C4 C4 O4 +BOND C5 C5M C5 C6 C6 H6 C5M H51 +BOND C5M H52 C5M H53 + +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 + +DONO H3 N3 +ACCE O2 C2 +ACCE O4 C4 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C1S C2S N1 C2 0.0 0.0 -160.00 0.0 0.0 !chi +IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 +IC C2 N1 C6 C5 0.0 0.0 -0.02 0.0 0.0 +IC C6 N1 C2 N3 0.0 0.0 0.06 0.0 0.0 +IC N1 N3 *C2 O2 0.0 0.0 -179.95 0.0 0.0 +IC N1 C2 N3 C4 0.0 0.0 -0.07 0.0 0.0 +IC C5 N3 *C4 O4 0.0 0.0 179.98 0.0 0.0 +IC C2 C4 *N3 H3 0.0 0.0 180.00 0.0 0.0 +IC C4 C6 *C5 C5M 0.0 0.0 -179.94 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 -90.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + + +RESI CNCY 0.00 ! C10H13N3O carbocyclic sugar with cytosine base, north + ! base attached to C2 of carbocyclic sugar + ! used to parameterize chi + +! the atom types used correspond to those used in the NA +! ribose/deoxyribose moieties + +GROUP +ATOM C4S CG3C52 -0.18 ! H61S H62S +ATOM H41S HGA2 0.09 ! \ / +ATOM H42S HGA2 0.09 ! C6S +GROUP ! / \ +ATOM C2S CG3C51 -0.09 ! / \ +ATOM H21S HGA1 0.09 ! H51S-C5S----C1S-H11S + ! | | +GROUP ! H41S-C4S C2S---------* +ATOM C3S CG3C52 -0.18 ! / \ / \ +ATOM H31S HGA2 0.09 ! H42S \ / H21S +ATOM H32S HGA2 0.09 ! C3S + ! / \ +GROUP ! H31S H32S +ATOM C5S CG3RC1 -0.09 +ATOM H51S HGA1 0.09 +GROUP +ATOM C6S CG3C31 -0.18 +ATOM H61S HGA2 0.09 +ATOM H62S HGA2 0.09 +GROUP +ATOM C1S CG3RC1 -0.09 +ATOM H11S HGA1 0.09 ! H42 H41 +GROUP ! \ / +ATOM N1 NG2R61 -0.13 ! N4 +ATOM C6 CG2R62 0.05 ! | +ATOM H6 HGR62 0.17 ! C4 +ATOM C2 CG2R63 0.52 ! / \\ +ATOM O2 OG2D4 -0.49 ! H5-C5 N3 +ATOM N3 NG2R62 -0.66 ! || | +ATOM C4 CG2R64 0.65 ! H6-C6 C2 +ATOM N4 NG2S3 -0.75 ! \ / \\ +ATOM H41 HGP4 0.37 ! N1 O2 +ATOM H42 HGP4 0.33 ! \ +ATOM C5 CG2R62 -0.13 ! \ +ATOM H5 HGR62 0.07 ! * + +BOND C1S C2S C2S C3S C3S C4S C4S C5S +BOND C5S C1S C5S C6S C6S C1S +BOND C1S H11S C2S H21S C3S H31S C3S H32S +BOND C4S H41S C4S H42S C5S H51S C6S H61S +BOND C6S H62S C2S N1 +BOND N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 C6 C5 H5 C6 H6 + +IMPR C4 C5 N3 N4 +IMPR C2 N1 N3 O2 +IMPR N4 H42 H41 C4 + +DONO H42 N4 +DONO H41 N4 +ACCE O2 C2 +ACCE N3 + +! internal coordinates +IC C1S C2S C3S C4S 0.0000 0.00 0.0 0.00 0.0000 +IC C2S C3S C4S C5S 0.0000 0.00 0.0 0.00 0.0000 +IC C3S C4S C5S C1S 0.0000 0.00 0.0 0.00 0.0000 +IC C5S C2S *C1S C6S 0.0000 0.00 300.0 0.00 0.0000 +IC C1S C5S *C6S H61S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C5S *C6S H62S 0.0000 0.00 240.0 0.00 0.0000 +IC C5S C2S *C1S H11S 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S N1 0.0000 0.00 120.0 0.00 0.0000 +IC C1S C3S *C2S H21S 0.0000 0.00 240.0 0.00 0.0000 +IC C2S C4S *C3S H31S 0.0000 0.00 120.0 0.00 0.0000 +IC C2S C4S *C3S H32S 0.0000 0.00 240.0 0.00 0.0000 +IC C3S C5S *C4S H41S 0.0000 0.00 120.0 0.00 0.0000 +IC C3S C5S *C4S H42S 0.0000 0.00 240.0 0.00 0.0000 +IC C4S C1S *C5S H51S 0.0000 0.00 120.0 0.00 0.0000 +!IC C4S C3S C2S N1 1.5284 101.97 147.80 113.71 1.4896 !N9 is already defined +IC C1S C2S N1 C2 0.0 0.0 -160.00 0.0 0.0 !chi +IC C2S C2 *N1 C6 0.0 0.0 -180.00 0.0 0.0 +IC C2 N1 C6 C5 0.0 0.0 0.0 0.0 0.0 +IC C6 N1 C2 N3 0.0 0.0 0.0 0.0 0.0 +IC N1 N3 *C2 O2 0.0 0.0 180.0 0.0 0.0 +IC N1 C2 N3 C4 0.0 0.0 0.0 0.0 0.0 +IC C5 N3 *C4 N4 0.0 0.0 180.00 0.0 0.0 +IC N3 C4 N4 H41 0.0 0.0 0.00 0.0 0.0 +IC H41 C4 *N4 H42 0.0 0.0 180.00 0.0 0.0 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 + +PATCH FIRST NONE LAST NONE + +RESI B5NP -1.00 ! C8H14O5P carbocyclic sugar with 5' OPOCH3 + ! north conformation + ! used to parameterize gamma +GROUP ! Note : C1 charge changed from -0.09 to 0.00 to +ATOM C5' CG321 -0.08 ! accomodate the CH2-OPOCH3 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG303 -0.57 +ATOM P PG1 1.50 +ATOM O1P OG2P1 -0.78 +ATOM O2P OG2P1 -0.78 +ATOM O3' OG303 -0.57 +ATOM C3' CG331 -0.17 +ATOM H31' HGA3 0.09 ! H31' +ATOM H32' HGA3 0.09 ! H61 H62 / +ATOM H33' HGA3 0.09 ! \ / H51' O1P C3'-H32' + ! C6 | | / \ +GROUP ! / \ C5'-O5'-P-O3' H33' +ATOM C4 CG3C52 -0.18 ! / \ / \ | +ATOM H41 HGA2 0.09 ! H51-C5-----C1 H52' O2P +ATOM H42 HGA2 0.09 ! | | +GROUP ! H41-C4 C2--H21 +ATOM C3 CG3C52 -0.18 ! / \ / \ +ATOM H31 HGA2 0.09 ! H42 \ / O3T-H3T +ATOM H32 HGA2 0.09 ! C3 +GROUP ! / \ +ATOM C1 CG3RC1 0.00 ! H31 H32 +GROUP +ATOM C2 CG3C51 0.14 ! changed from -0.18 to accomodate O3'-H +ATOM H21 HGA1 0.09 +ATOM O3T OG311 -0.65 +ATOM H3T HGP1 0.42 +GROUP +ATOM C5 CG3RC1 -0.09 +ATOM H51 HGA1 0.09 +GROUP +ATOM C6 CG3C31 -0.18 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C5 C6 C6 C1 C5 H51 +BOND C2 H21 C4 H42 C3 H31 C3 H32 +BOND C4 H41 C6 H61 C1 C5' C2 O3T +BOND C6 H62 C5' O5' O5' P P O1P +BOND P O2P P O3' O3' C3' C3' H31' +BOND C3' H32' C3' H33' C5' H51' C5' H52' +BOND O3T H3T + +! internal coordinates from parameter file, note initial planar geometry +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 C5' 0.0000 0.00 240.0 0.00 0.0000 +IC C1 O5' *C5' H51' 0.0000 0.00 120.0 0.00 0.0000 +IC C1 O5' *C5' H52' 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C2 O3T 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C2 O3T H3T 0.0000 0.00 -60.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C4 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 C6 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 +IC C5' C1 C2 O3T 0.0000 0.00 70.0 0.00 0.0000 +IC O5' C5' C1 C2 0.0000 0.00 50.0 0.00 0.0000 +IC P O5' C5' C1 0.0 0.0 -105.0 0.0 0.0 +IC C5' O5' P O3' 0.0 0.0 140.0 0.0 0.0 +IC O5' O3' *P O1P 0.0 0.0 120.0 0.0 0.0 +IC O5' O3' *P O2P 0.0 0.0 240.0 0.0 0.0 +IC O5' P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H31' C3' O3' P 0.0 0.0 60.0 0.0 0.0 +IC H32' C3' O3' P 0.0 0.0 -60.0 0.0 0.0 +IC H33' C3' O3' P 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI B5SP -1.00 ! C8H14O5P south carbcyclic sugar with C5'-OPOCH3 + +GROUP +ATOM C1 CG3RC1 -0.09 +ATOM H11 HGA1 0.09 ! H61 H62 +GROUP ! \ / +ATOM C3 CG3C51 0.14 ! C6 +ATOM H31 HGA1 0.09 ! / \ +ATOM O3T OG311 -0.65 ! H51-C5------C1-H11 H51' O1P H31' +ATOM H3T HGP1 0.42 ! | | / | / +GROUP ! H41-C4 C2-----C5'-O5'-P-O3'-C3'-H32' +ATOM C6 CG3C31 -0.18 ! / \ / \ \ | \ +ATOM H61 HGA2 0.09 ! H42 \ / H21 H52' O2P H33' +ATOM H62 HGA2 0.09 ! C3-H31 +GROUP ! | +ATOM C4 CG3C52 -0.18 ! O3T +ATOM H41 HGA2 0.09 ! \ +ATOM H42 HGA2 0.09 ! H3T +GROUP +ATOM C5 CG3RC1 -0.09 +ATOM H51 HGA1 0.09 +GROUP +ATOM C2 CG3C51 -0.09 ! This charge changed from -0.18 to make it +ATOM H21 HGA1 0.09 ! compatible with C5'-OPOCH3 +ATOM C5' CG321 -0.08 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG303 -0.57 +ATOM P PG1 1.50 +ATOM O1P OG2P1 -0.78 +ATOM O2P OG2P1 -0.78 +ATOM O3' OG303 -0.57 +ATOM C3' CG331 -0.17 +ATOM H31' HGA3 0.09 +ATOM H32' HGA3 0.09 +ATOM H33' HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C5 C6 C6 C1 C2 C5' +BOND C4 H41 C4 H42 C5' H51' C1 H11 +BOND C5' H52' C6 H61 C6 H62 C2 H21 +BOND C5 H51 C3 H31 C3 O3T C5' O5' +BOND O5' P O3T H3T +BOND P O1P P O2P P O3' O3' C3' +BOND C3' H31' C3' H32' C3' H33' + +! internal coordinates +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C3 C4 C5 C1 0.0000 0.00 0.0 0.00 0.0000 +IC C4 C5 C1 C6 1.5000 60.00 120.0 60.00 1.5000 +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C3 O3T H3T 0.0000 0.00 270.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 O3T 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C1 *C2 C5' 0.0000 0.00 120.0 0.00 0.0000 +IC C2 O5' *C5' H51' 0.0000 0.00 120.0 0.00 0.0000 +IC C2 O5' *C5' H52' 0.0000 0.00 240.0 0.00 0.0000 +IC C5 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C4 *C5 C6 1.5000 0.00 120.0 60.00 1.5000 +IC C1 C5 *C6 H61 0.0000 60.00 120.0 0.00 0.0000 +IC C1 C5 *C6 H62 0.0000 60.00 240.0 0.00 0.0000 +IC C5' C2 C3 O3T 0.0000 0.00 150.0 0.00 0.0000 +IC O5' C5' C2 C3 0.0000 0.00 60.0 0.00 0.0000 +IC P O5' C5' C2 0.0 0.0 180.00 0.0 0.0 +IC O1P P O5' C5' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O5' C5' 0.0 0.0 60.0 0.0 0.0 +IC C5' O5' P O3' 0.0 0.0 180.0 0.0 0.0 +IC O5' P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H31' C3' O3' P 0.0 0.0 60.0 0.0 0.0 +IC H32' C3' O3' P 0.0 0.0 -60.0 0.0 0.0 +IC H33' C3' O3' P 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +!toppar_all27_na_model.str + +RESI DMEP -1.00 ! C2H6O4P Dimethylphosphate +GROUP +ATOM P1 PG1 1.50 ! H11 +ATOM O3 OG2P1 -0.78 ! | +ATOM O4 OG2P1 -0.78 ! H13- C1-H12 +ATOM O1 OG303 -0.57 ! \ +ATOM O2 OG303 -0.57 ! O3 O1 +ATOM C1 CG331 -0.17 ! \\ / +ATOM H11 HGA3 0.09 ! (-) P1 +ATOM H12 HGA3 0.09 ! // \ +ATOM H13 HGA3 0.09 ! O4 O2 +ATOM C2 CG331 -0.17 ! / +ATOM H21 HGA3 0.09 ! H23-C2-H22 +ATOM H22 HGA3 0.09 ! | +ATOM H23 HGA3 0.09 ! H21 + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 O2 C2 +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 +! IC FOR THE g,g conformation (3-21G* opt. structure) +IC O3 P1 O1 C1 1.4723 107.31 000.0 117.79 1.4356 +IC O4 P1 O2 C2 1.4722 000.0 000.0 117.79 1.4357 +IC O1 P1 O2 C2 1.6343 000.0 73.8 117.79 1.4357 +IC O2 P1 O1 C1 1.6344 000.0 73.7 117.79 1.4356 +IC H11 C1 O1 P1 1.0827 107.8 174.8 117.79 1.6343 +IC H12 C1 O1 P1 1.0800 110.4 54.1 117.79 1.6343 +IC H13 C1 O1 P1 1.0848 110.7 294.3 117.79 1.6343 +IC H21 C2 O2 P1 1.0827 107.9 174.7 117.79 1.6344 +IC H22 C2 O2 P1 1.0800 110.4 54.1 117.79 1.6344 +IC H23 C2 O2 P1 1.0848 110.7 294.2 117.79 1.6344 + +RESI MP_0 0.00 ! CH5O4P Methylphosphate, neutral +GROUP +! atom order for molvib +ATOM C1 CG331 -0.17 +ATOM O1 OG303 -0.56 ! H11 +ATOM P1 PG0 1.50 ! | +ATOM O2 OG311 -0.62 ! H13--C1--H12 +ATOM O3 OG311 -0.62 ! | +ATOM O4 OG2P1 -0.64 ! O1 +ATOM H11 HGA3 0.09 ! | +ATOM H12 HGA3 0.09 ! O4==P1--O3 +ATOM H13 HGA3 0.09 ! | \ +ATOM H2 HGP1 0.42 ! O2 H3 +ATOM H3 HGP1 0.42 ! \ + ! H2 + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 H13 O2 H2 O3 H3 + +IC H11 C1 O1 P1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 +IC H11 O1 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O1 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 O1 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 +IC O2 O1 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 P1 O2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC O1 P1 O3 H3 0.0000 0.00 180.00 0.00 0.0000 + +RESI MP_1 -1.00 ! CH4O4P Methylphosphate, anionic +GROUP +ATOM C1 CG331 -0.170 ! H11 +ATOM O1 OG303 -0.620 ! | +ATOM P1 PG1 1.500 ! H13--C1--H12 +ATOM O2 OG311 -0.670 ! | +ATOM O3 OG2P1 -0.820 ! O1 +ATOM O4 OG2P1 -0.820 ! | +ATOM H11 HGA3 0.090 ! O4==P1==O3 (-) +ATOM H12 HGA3 0.090 ! | +ATOM H13 HGA3 0.090 ! O2 +ATOM H2 HGP1 0.330 ! \ + ! H2 + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 H13 O2 H2 +IC P1 O1 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC O1 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC O1 H11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 +IC O1 O2 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 +IC O1 O2 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 P1 O2 H2 0.0000 0.00 90.00 0.00 0.0000 ! asymm + +RESI MP_2 -2.00 ! CH3O4P Methylphosphate, dianionic +GROUP +ATOM P1 PG2 1.100 +ATOM O1 OG303 -0.400 ! H11 +ATOM O2 OG2P1 -0.900 ! | +ATOM O3 OG2P1 -0.900 ! H13--C1--H12 +ATOM O4 OG2P1 -0.900 ! | +GROUP ! O1 +ATOM C1 CG331 -0.270 ! | +ATOM H11 HGA3 0.090 ! (-) O4==P1==O3 (-) +ATOM H12 HGA3 0.090 ! || +ATOM H13 HGA3 0.090 ! O2 + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 H13 +IC P1 O1 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC O1 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC O1 H11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 +IC O1 O2 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 +IC O1 O2 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 + +! below are residues and patches added for the 97/98 optimization +! and extension of the na all-atom parameters + +RESI THF 0.00 ! C4H8O tetrahydrofuran, for MOLVIB + +GROUP +ATOM O4' OG3C51 -0.40 ! H41' O4' H11' +ATOM C4' CG3C52 0.02 ! \ / \ / +ATOM C3' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM C2' CG3C52 -0.18 ! | | +ATOM C1' CG3C52 0.02 ! H31'--C3'--C2'--H21' +ATOM H11' HGA2 0.09 ! / \ +ATOM H12' HGA2 0.09 ! H32' H22' +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +ATOM H31' HGA2 0.09 +ATOM H32' HGA2 0.09 +ATOM H41' HGA2 0.09 +ATOM H42' HGA2 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' + +IC C1' O4' C4' C3' 0.0000 0.00 45.00 0.00 0.0000 +IC C3' O4' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC C4' O4' C1' C2' 0.0000 0.00 -45.00 0.00 0.0000 +IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' C4' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI THFM 0.00 ! C5H10O Methyl-tetrahydrofuran +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM C2' CG3C52 -0.18 +ATOM C3' CG3C52 -0.18 ! H52' H53' +ATOM C4' CG3C51 0.11 ! \ / +ATOM H11' HGA2 0.09 ! H51'-C5' O4' H11' +ATOM H12' HGA2 0.09 ! \ / \ / +ATOM H21' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM H22' HGA2 0.09 ! | | +ATOM H31' HGA2 0.09 ! H31'--C3'--C2'--H21' +ATOM H32' HGA2 0.09 ! / \ +ATOM H42' HGA1 0.09 ! H32' H22' +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H42' C5' H51' C5' H52' C5' H53' + +IC C4' O4' C1' C2' 0.0000 0.00 45.00 0.00 0.0000 +IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC O4' C1' C2' C3' 0.0000 0.00 -25.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C4' C2' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' C2' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' O4' *C4' C5' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC O4' C4' C5' H51' 0.0000 0.00 180.00 0.00 0.0000 +IC H51' C4' *C5' H52' 0.0000 0.00 120.00 0.00 0.0000 +IC H51' C4' *C5' H53' 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI THFO 0.00 ! C4H8O2 3'-hydroxyl-tetrahydrofuran + ! Atom types for aliphatic hydrogens based on nucleotide +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM C2' CG3C52 -0.18 +ATOM C4' CG3C52 0.02 ! H41' O4' H11' +ATOM H11' HGA2 0.09 ! \ / \ / +ATOM H12' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +ATOM H41' HGA2 0.09 ! / \ +ATOM H42' HGA2 0.09 ! O3' H22' +GROUP ! | +ATOM C3' CG3C51 0.14 ! H32' +ATOM H31' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' H32' +!Nicolas: the following IC are for thf-oh as optimized via ab initio calculations +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 +PATC FIRS NONE LAST NONE + +RESI THFI 0.00 ! C7H10N2O imidazole analog with THF ring +! Sugar: transferred from thf; used for optimization of chi, therefore +! the sugar carbon atom types are not rigorously correct +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C51 0.11 ! Abs. config is arbitrary. +ATOM H12' HGA1 0.09 +ATOM C4' CG3C52 0.02 ! H41' O4' Imidazole +ATOM H41' HGA2 0.09 ! \ / \ / +ATOM H42' HGA2 0.09 ! H42'--C4' C1'--H12' +GROUP ! | | +ATOM C2' CG3C52 -0.18 ! H31'--C3'--C2'--H21' +ATOM H21' HGA2 0.09 ! / \ +ATOM H22' HGA2 0.09 ! H32' H22' +GROUP +ATOM C3' CG3C52 -0.18 +ATOM H31' HGA2 0.09 +ATOM H32' HGA2 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CG2R51 -0.05 ! C1' HE1 +ATOM HG HGR52 0.09 ! \ / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / | +ATOM ND1 NG2R51 -0.04 ! HG-CG | +ATOM CE1 CG2R53 0.25 ! \ | +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THMI 0.00 ! C8H12N2O thf-ch3-imidazole +! C5' has been declared as CN8, and C3' as CN7, for compatibility +! with DNA, but these carbons are rigorously CG331 and CG321 respectively + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP ! Sugar: transferred from thf +ATOM O4' OG3C51 -0.40 ! Note: has 2 asymmetric carbons. +ATOM C1' CG3C51 0.11 ! Abs. config is arbitrary. +ATOM H12' HGA1 0.09 +ATOM C4' CG3C51 0.11 ! H52' H53' +ATOM H42' HGA1 0.09 ! \ / +GROUP ! H51'-C5' O4' Imidazole +ATOM C2' CG3C52 -0.18 ! \ / \ / +ATOM H21' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM H22' HGA2 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C3' CG3C52 -0.18 ! / \ +ATOM H31' HGA2 0.09 ! H32' H22' +ATOM H32' HGA2 0.09 +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CG2R51 -0.05 ! C1' HE1 +ATOM HG HGR52 0.09 ! \ / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / || +ATOM ND1 NG2R51 -0.04 ! HG-CG || +ATOM CE1 CG2R53 0.25 ! \\ || +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H42' C4' C5' C5' H51' C5' H52' C5' H53' +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 + +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THFC 0.00 ! C5H10O2 THF-3'-OH-4'-CH3 + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 2 asymmetric carbons. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H52' H53' +ATOM C4' CG3C51 0.11 ! \ / +ATOM H42' HGA1 0.09 ! H51'-C5' O4' H11' +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM H31' HGA1 0.09 ! O3' H22' +ATOM C3' CG3C51 0.14 ! | +ATOM O3' OG311 -0.65 ! H32' +ATOM H32' HGP1 0.42 +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' +BOND C1' H11' C1' H12' +BOND C2' H21' C2' H22' +BOND C3' H31' +BOND C4' H42' +BOND C5' H51' C5' H52' C5' H53' +BOND O3' H32' + +IC C4' O4' C1' C2' 0.0000 0.00 180.00 0.00 0.0000 +IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC C1' O4' C4' C3' 0.0000 0.00 180.00 0.00 0.0000 +IC C3' O4' *C4' C5' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C2' C4' *C3' O3' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 -120.00 0.00 0.0000 +IC C4' C3' O3' H32' 0.0000 0.00 180.00 0.00 0.0000 +IC O4' C4' C5' H51' 0.0000 0.00 180.00 0.00 0.0000 +IC H51' C4' *C5' H52' 0.0000 0.00 120.00 0.00 0.0000 +IC H51' C4' *C5' H53' 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI TH5P -2.00 ! C5H9O5P 5'-phosphate-methyl-tetrahydrofuran (phosphate -2) + ! Atom types for aliphatic hydrogens based on nucleotide +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H1' HGA2 0.09 +ATOM H1'' HGA2 0.09 ! O1P (-2) +ATOM C4' CG3C51 0.11 ! || +ATOM H4'' HGA1 0.09 ! O2P==P==O2P +GROUP ! | +ATOM C2' CG3C52 -0.18 ! H5'' O5' +ATOM H2' HGA2 0.09 ! \ | +ATOM H2'' HGA2 0.09 ! H5'--C5' O4' H1' +GROUP ! \ / \ / +ATOM C3' CG3C52 -0.18 ! H4'--C4' C1'--H1'' +ATOM H3' HGA2 0.09 ! | | +ATOM H3'' HGA2 0.09 ! H3'--C3'--C2'--H2' +GROUP ! / \ +ATOM C5' CG321 -0.18 ! H3'' H2'' +ATOM H5' HGA2 0.09 +ATOM H5'' HGA2 0.09 +GROUP +ATOM O5' OG303 -0.40 +ATOM P PG2 1.10 +ATOM O1P OG2P1 -0.90 +ATOM O2P OG2P1 -0.90 +ATOM O3P OG2P1 -0.90 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' +BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P P O3P +IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 +IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 +IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 +IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 +IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 +IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 +IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 +IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 +IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 +IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 +IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 +IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 +IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 +IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 +IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 +IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 +IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 +IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TH5H 0.00 ! C5H10O2 5'-hydroxy-methyl-tetrahydrofuran (phosphate -2) + ! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H1' HGA2 0.09 +ATOM H1'' HGA2 0.09 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H4'' HGA1 0.09 ! H5'' O5' +GROUP ! \ | +ATOM C2' CG3C52 -0.18 ! H5'--C5' O4' H1' +ATOM H2' HGA2 0.09 ! \ / \ / +ATOM H2'' HGA2 0.09 ! H4'--C4' C1'--H1'' +GROUP ! | | +ATOM C3' CG3C52 -0.18 ! H3'--C3'--C2'--H2' +ATOM H3' HGA2 0.09 ! / \ +ATOM H3'' HGA2 0.09 ! H3'' H2'' +GROUP +ATOM C5' CG321 0.05 +ATOM H5' HGA2 0.09 +ATOM H5'' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' +BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' H5T + +IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 +IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 +IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 +IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 +IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 +IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 +IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 +IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 +IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 +IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 +IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 +IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 +IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 +IC H5' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 +IC H5'' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 +IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 +IC C4' C5' O5' H5T 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI T5PH -1.00 ! C5H10O5P 5'-phosphate-methyl-tetrahydrofuran (phosphate -1) + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM C5' CG321 -0.08 ! Note: has 1 asymmetric carbon. +ATOM H5' HGA2 0.09 ! Abs. config is arbitrary. +ATOM H5'' HGA2 0.09 +ATOM O5' OG303 -0.62 ! O1P H5T +ATOM P PG1 1.50 ! || / +ATOM O1P OG2P1 -0.82 ! O2P==P==O3P +ATOM O2P OG2P1 -0.82 ! | +ATOM O3P OG311 -0.67 ! O5' +ATOM H5T HGP1 0.33 ! | +GROUP ! H5'' | +ATOM O4' OG3C51 -0.40 ! \ | +ATOM C1' CG3C52 0.02 ! H5'--C5' O4' H1' +ATOM H1' HGA2 0.09 ! \ / \ / +ATOM H1'' HGA2 0.09 ! H4'--C4' C1'--H1'' +ATOM C4' CG3C51 0.11 ! | | +ATOM H4'' HGA1 0.09 ! H3'--C3'--C2'--H2' +GROUP ! / \ +ATOM C2' CG3C52 -0.18 ! H3'' H2'' +ATOM H2' HGA2 0.09 +ATOM H2'' HGA2 0.09 +GROUP +ATOM C3' CG3C52 -0.18 +ATOM H3' HGA2 0.09 +ATOM H3'' HGA2 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' +BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P +BOND P O2P P O3P O3P H5T +IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 +IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 +IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 +IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 +IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 +IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 +IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 +IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 +IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 +IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 +IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 +IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 +IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 +IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 +IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 +IC O4' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 +IC O4' C4' C5' H5' 0.0 0.0 180.0 0.0 0.0 +IC O4' C4' C5' H5'' 0.0 0.0 -60.0 0.0 0.0 +IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 +IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 +IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 +IC O5' P O3P H5T 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TH3P -2.00 ! C4H7O5P 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -2) + ! used to fit epsilon + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H41' O4' H11' +ATOM C4' CG3C52 0.02 ! \ / \ / +ATOM H41' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM H42' HGA2 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CG3C52 -0.18 ! / \ +ATOM H21' HGA2 0.09 ! O3' H22' +ATOM H22' HGA2 0.09 ! | +GROUP ! O1P==P==O2P +ATOM C3' CG3C51 -0.09 ! || +ATOM H31' HGA1 0.09 ! O3P (-2) +GROUP +ATOM O3' OG303 -0.40 +ATOM P PG2 1.10 +ATOM O1P OG2P1 -0.90 +ATOM O2P OG2P1 -0.90 +ATOM O3P OG2P1 -0.90 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3P +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI T3PH -1.00 ! C4H8O5P monoanionic 3'phosphate-tetrahydrofuran + ! used to fit epsilon + +! Atom types for aliphatic hydrogens based on nucleotide + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H41' O4' H11' +ATOM C4' CG3C52 0.02 ! \ / \ / +ATOM H41' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM H42' HGA2 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CG3C52 -0.18 ! / \ +ATOM H21' HGA2 0.09 ! O3' H22' +ATOM H22' HGA2 0.09 ! | +GROUP ! O1P==P==O2P +ATOM C3' CG3C51 0.01 ! | +ATOM H31' HGA1 0.09 ! O3T (-1) +ATOM O3' OG303 -0.62 ! \ +ATOM P PG1 1.50 ! H3T +ATOM O1P OG2P1 -0.82 +ATOM O2P OG2P1 -0.82 +ATOM O3T OG311 -0.67 +ATOM H3T HGP1 0.33 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI R3PH -1.00 ! C4H8O6P monoanionic 3'phosphate-tetrahydrofuran + ! with O2' hydroxyl. Used to fit C2'-O2' torsion in RNA + +! Atom types for aliphatic hydrogens based on RNA nucleotide + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H41' O4' H11' +ATOM C4' CG3C52 0.02 ! \ / \ / +ATOM H41' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM H42' HGA2 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CG3C51 0.14 ! / \ +ATOM H21' HGA1 0.09 ! O3' O2' +ATOM O2' OG311 -0.65 ! | | +ATOM H22' HGP1 0.42 ! O1P==P==O2P H22' +GROUP ! | +ATOM C3' CG3C51 0.01 ! O3T (-1) +ATOM H31' HGA1 0.09 ! \ +ATOM O3' OG303 -0.62 ! H3T +ATOM P PG1 1.50 +ATOM O1P OG2P1 -0.82 +ATOM O2P OG2P1 -0.82 +ATOM O3T OG311 -0.67 +ATOM H3T HGP1 0.33 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC O2' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 +IC H22' O2' C2' C3' 1.0822 110.88 0.00 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI A3PH -1.00 ! C4H8O6P monoanionic 3'phosphate-tetrahydrofuran + ! with O2' hydroxyl in an arabinose (beta) conformation. + +! The furanose ring contains atom type CG311 , specific of arabinose + +GROUP +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C52 0.02 +ATOM H11' HGA2 0.09 ! H41' O4' H11' +ATOM H12' HGA2 0.09 ! \ / \ / +ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' +ATOM H41' HGA2 0.09 ! | | +ATOM H42' HGA2 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C2' CG3C51 0.14 ! O3' O2' O2' is beta +ATOM H22' HGA1 0.09 ! | | +ATOM O2' OG311 -0.65 ! O1P==P==O2P H22' +ATOM H21' HGP1 0.42 ! | +GROUP ! O3T (-1) +ATOM C3' CG3C51 0.01 ! \ +ATOM H31' HGA1 0.09 ! H3T +ATOM O3' OG303 -0.62 +ATOM P PG1 1.50 +ATOM O1P OG2P1 -0.82 +ATOM O2P OG2P1 -0.82 +ATOM O3T OG311 -0.67 +ATOM H3T HGP1 0.33 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H22' C2' O2' O2' H21' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H22' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 +IC O2' C2' C3' C4' 1.0846 110.65 120.00 100.86 1.5211 +IC H21' O2' C2' C3' 1.0822 110.88 120.00 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI T3PM -1.00 ! C5H10O5P 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1) + ! capped with a methyl group. This is to investigate the differences + ! between BI and BII forms of DNA + ! C3T is defined as CG321 to miminck DNA +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 1 asymmetric carbon. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H41' O4' H11' +ATOM C4' CG3C52 0.02 ! \ / \ / +ATOM H41' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM H42' HGA2 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CG3C52 -0.18 ! / \ +ATOM H21' HGA2 0.09 ! O3' H22' +ATOM H22' HGA2 0.09 ! | +GROUP ! O1P==P==O2P +ATOM C3' CG3C51 0.01 ! | +ATOM H31' HGA1 0.09 ! O3T (-1) +GROUP ! \ +ATOM O3' OG303 -0.57 ! C3T--H3T3 +ATOM P PG1 1.50 ! / \ +ATOM O1P OG2P1 -0.78 ! H3T1 H3T2 +ATOM O2P OG2P1 -0.78 +ATOM O3T OG303 -0.57 +ATOM C3T CG331 -0.17 +ATOM H3T1 HGA3 0.09 +ATOM H3T2 HGA3 0.09 +ATOM H3T3 HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3T O3T C3T +BOND C3T H3T1 C3T H3T2 C3T H3T3 +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000 +IC C3' O3' P O3T 0.0000 000.00 -95.22 000.00 0.0000 +IC O3T O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 +IC O3T O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000 +IC C3T O3T P O3' 0.0000 000.00 -46.90 000.00 0.0000 +IC H3T1 C3T O3T P 0.0000 000.00 180.00 000.00 0.0000 +IC H3T2 C3T O3T P 0.0000 000.00 60.00 000.00 0.0000 +IC H3T3 C3T O3T P 0.0000 000.00 -60.00 000.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI TM3P -2.00 ! C5H9O5P 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) + +! This is the DNA version (the RNA version is RM3P, see below) + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 2 asymmetric carbons. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H52' H53' +ATOM C4' CG3C51 0.11 ! \ / +ATOM H42' HGA1 0.09 ! H51'-C5' O4' H11' +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C3' CG3C51 -0.09 ! O3' H22' +ATOM H31' HGA1 0.09 ! | +GROUP ! O1P==P==O2P +ATOM O3' OG303 -0.40 ! || +ATOM P PG2 1.10 ! O3P (-2) +ATOM O1P OG2P1 -0.90 +ATOM O2P OG2P1 -0.90 +ATOM O3P OG2P1 -0.90 +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND C4' C5' C5' H51' C5' H52' C5' H53' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RM3P -2.00 ! C5H9O5P 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) + +! This is the RNA version of TM3P: NOTE that it does NOT have a 2'hydroxyl to +! allow for the determination of the influence of the ring dihedrals on the +! sugar puckering energetics in the absence of the 2' hydroxyl + +GROUP +ATOM O4' OG3C51 -0.40 ! Note: has 2 asymmetric carbons. +ATOM C1' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 +ATOM C4' CG3C51 0.11 +ATOM H42' HGA1 0.09 +GROUP +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP +ATOM C3' CG3C51 -0.09 +ATOM H31' HGA1 0.09 +GROUP +ATOM O3' OG303 -0.40 +ATOM P PG2 1.10 +ATOM O1P OG2P1 -0.90 +ATOM O2P OG2P1 -0.90 +ATOM O3P OG2P1 -0.90 +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND C4' C5' C5' H51' C5' H52' C5' H53' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI T2FU -2.00 ! C4H6FO5P THF with PO3 on c3, F (beta, up) on c2 +GROUP ! Charges by analogy +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C52 0.05 ! Note: has 2 asymmetric carbons. +ATOM C4' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H41' O4' H11' +ATOM H41' HGA2 0.09 ! \ / \ / +ATOM H42' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CG3C51 0.05 ! | | +ATOM H22' HGA6 0.11 ! H31'--C3'--C2'--F2' (beta) +ATOM F2' FGA1 -0.22 ! / \ +ATOM C3' CG3C51 -0.06 ! O3' H22' +ATOM H31' HGA1 0.09 ! | +GROUP ! O1P==P==O2P +ATOM O3' OG303 -0.40 ! || +ATOM P PG2 1.10 ! O3P (-2) +ATOM O1P OG2P1 -0.90 +ATOM O2P OG2P1 -0.90 +ATOM O3P OG2P1 -0.90 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' F2' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3P +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC F2' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TMFU -2.00 ! C5H8FO5P THF with ch3 on c4', opo3 on c3', F (beta, up) on c2' +GROUP ! Charges by analogy +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C52 0.05 ! Note: has 3 asymmetric carbons. +ATOM H11' HGA2 0.09 ! Abs. config is arbitrary. +ATOM H12' HGA2 0.09 +ATOM C4' CG3C51 0.11 ! H52' H53' +ATOM H42' HGA1 0.09 ! \ / +ATOM C2' CG3C51 0.05 ! H51'-C5' O4' H11' +ATOM H22' HGA6 0.11 ! \ / \ / +ATOM F2' FGA1 -0.22 ! H42'--C4' C1'--H12' +ATOM C3' CG3C51 -0.06 ! | | +ATOM H31' HGA1 0.09 ! H31'--C3'--C2'--F2' (beta) +GROUP ! / \ +ATOM O3' OG303 -0.40 ! O3' H22' +ATOM P PG2 1.10 ! | +ATOM O1P OG2P1 -0.90 ! O1P==P==O2P +ATOM O2P OG2P1 -0.90 ! || +ATOM O3P OG2P1 -0.90 ! O3P (-2) +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H11' C1' H12' +BOND C2' H22' C2' F2' +BOND C3' O3' C3' H31' +BOND O3' P P O1P P O2P P O3P +BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' +! The following IC table is a guess from thfohch3 (Nicolas): +IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 +IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 +IC F2' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 180.00 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.00 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 -60.00 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 + +PATC FIRS NONE LAST NONE + +RESI T2FD -2.00 ! C4H6FO5P THF with PO3 on c3, F (alpha, down) on c2 +GROUP ! Charges by analogy +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C52 0.05 ! Note: has 2 asymmetric carbons. +ATOM C4' CG3C52 0.02 ! Abs. config is arbitrary. +ATOM H11' HGA2 0.09 +ATOM H12' HGA2 0.09 ! H41' O4' H11' +ATOM H41' HGA2 0.09 ! \ / \ / +ATOM H42' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CG3C51 0.05 ! | | +ATOM H21' HGA6 0.11 ! H31'--C3'--C2'--F2' (beta) +ATOM F2' FGA1 -0.22 ! / \ +ATOM C3' CG3C51 -0.06 ! O3' H22' +ATOM H31' HGA1 0.09 ! | +GROUP ! O1P==P==O2P +ATOM O3' OG303 -0.40 ! || +ATOM P PG2 1.10 ! O3P (-2) +ATOM O1P OG2P1 -0.90 +ATOM O2P OG2P1 -0.90 +ATOM O3P OG2P1 -0.90 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' F2' C2' H21' C3' H31' C4' H41' +BOND C4' H42' O3' P P O1P P O2P P O3P +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC F2' C2' C3' C4' 1.0846 110.65 -148.45 100.86 1.5211 +IC H21' C2' C3' C4' 1.0822 110.88 91.68 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TMFD -2.00 ! C5H8FO5P Flourine on C2' (alpha, down) with ch3 on c4', opo3 on c3', oh on c2' +GROUP ! Charges by analogy +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C52 0.05 ! Note: has 3 asymmetric carbons. +ATOM H11' HGA2 0.09 ! Abs. config is arbitrary. +ATOM H12' HGA2 0.09 +ATOM C4' CG3C51 0.11 ! H52' H53' +ATOM H42' HGA1 0.09 ! \ / +ATOM C2' CG3C51 0.05 ! H51'-C5' O4' H11' +ATOM H21' HGA6 0.11 ! \ / \ / +ATOM F2' FGA1 -0.22 ! H42'--C4' C1'--H12' +ATOM C3' CG3C51 -0.06 ! | | +ATOM H31' HGA1 0.09 ! H31'--C3'--C2'--F2' (beta) +GROUP ! / \ +ATOM O3' OG303 -0.40 ! O3' H22' +ATOM P PG2 1.10 ! | +ATOM O1P OG2P1 -0.90 ! O1P==P==O2P +ATOM O2P OG2P1 -0.90 ! || +ATOM O3P OG2P1 -0.90 ! O3P (-2) +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H11' C1' H12' +BOND C2' F2' C2' H21' +BOND C3' O3' C3' H31' +BOND O3' P P O1P P O2P P O3P +BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' +! The following IC table is a guess from thfohch3 (Nicolas): +IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 +IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 +IC F2' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 180.00 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.00 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 -60.00 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI ARMO 0.00 ! C5H10O3 ribose, thfch3ohoh, with the c2' hydroxyl in the beta configuration +GROUP +ATOM O4' OG3C51 -0.40 ! H52' H53' +ATOM C1' CG3C52 0.02 ! \ / +ATOM H11' HGA2 0.09 ! H51'-C5' O4' H11' +ATOM H12' HGA2 0.09 ! \ / \ / +ATOM C4' CG3C51 0.11 ! H42'--C4' C1'--H12' +ATOM H42' HGA1 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CG3C51 0.14 ! / \ +ATOM H22' HGA1 0.09 ! O3' O2' +ATOM O2' OG311 -0.65 ! | | (beta) +ATOM H21' HGP1 0.42 ! H32' H22' +GROUP +ATOM C3' CG3C51 0.14 +ATOM H31' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H11' C1' H12' +BOND C2' O2' C2' H22' O2' H21' +BOND C3' O3' O3' H32' C3' H31' +BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' + +! The following IC table is a guess from thfohch3 (Nicolas): +IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 +IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 +IC O2' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 +IC H21' O2' C2' C3' 0.0 0.0 90.00 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 +IC H32' O3' C3' C4' 0.0 0.0 44.72 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THFA 0.00 ! C8H12N2O2 THF-OH-CH3-IM +GROUP ! Note: has 3 asymmetric carbons. +ATOM O4' OG3C51 -0.40 ! Abs. config is arbitrary. +ATOM C4' CG3C51 0.11 +ATOM H42' HGA1 0.09 ! H52' H53' +ATOM C1' CG3C51 0.11 ! \ / +ATOM H12' HGA1 0.09 ! H51'-C5' O4' Imidazole +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM H31' HGA1 0.09 ! O3' H22' +ATOM C3' CG3C51 0.14 ! | +ATOM O3' OG311 -0.65 ! H32' +ATOM H32' HGP1 0.42 +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CG2R51 -0.05 ! C1' HE1 +ATOM HG HGR52 0.09 ! \ / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / || +ATOM ND1 NG2R51 -0.04 ! HG-CG || +ATOM CE1 CG2R53 0.25 ! \\ || +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' H53' +BOND O3' H32' +BOND C1' ND1 ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI ARAO 0.00 ! C4H8O3 arabinose sugar, oh alpha on c3', oh beta on c2' +GROUP +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C52 0.02 +ATOM H11' HGA2 0.09 ! H41' O4' H11' +ATOM H12' HGA2 0.09 ! \ / \ / +ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' +ATOM H41' HGA2 0.09 ! | | +ATOM H42' HGA2 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C2' CG3C51 0.14 ! O3' O2' +ATOM H22' HGA1 0.09 ! | | (beta) +ATOM O2' OG311 -0.65 ! H32' H22' +ATOM H21' HGP1 0.42 +GROUP +ATOM C3' CG3C51 0.14 +ATOM H31' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' O2' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O2' H21' O3' H32' +!Nicolas: the following IC are for thf-oh as optimized via ab initio calculations +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC O2' C2' C3' C4' 0.0000 0.00 91.68 0.0000 0.0000 +IC H21' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 +PATC FIRS NONE LAST NONE + +RESI ARIM 0.00 ! C7H10N2O2 arabinose sugar with imidazole + ! transferred from thf +GROUP +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C51 0.11 ! H41' O4' Imidazole +ATOM H12' HGA1 0.09 ! \ / \ / +ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' +ATOM H41' HGA2 0.09 ! | | +ATOM H42' HGA2 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM C3' CG3C52 -0.18 ! H32' O2' +ATOM H31' HGA2 0.09 ! | (beta) +ATOM H32' HGA2 0.09 ! H22' +GROUP +ATOM C2' CG3C51 0.14 +ATOM H22' HGA1 0.09 +ATOM O2' OG311 -0.65 +ATOM H21' HGP1 0.42 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CG2R51 -0.05 ! C1' HE1 +ATOM HG HGR52 0.09 ! \ / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / || +ATOM ND1 NG2R51 -0.04 ! HG-CG || +ATOM CE1 CG2R53 0.25 ! \\ || +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 +BOND C2' O2' C1' H12' C2' H22' C3' H31' C3' H32' O2' H21' +BOND C4' H41' C4' H42' +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 1.532 101.886 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC O2' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H21' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI AR3P -2.00 ! C4H7O6P arabinose sugar with phosphate on 3' (phosphate -2) +GROUP +ATOM O4' OG3C51 -0.40 ! H41' O4' H11' +ATOM C1' CG3C52 0.02 ! \ / \ / +ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' +ATOM H11' HGA2 0.09 ! | | +ATOM H12' HGA2 0.09 ! H31'--C3'--C2'--H22' (alpha) +ATOM H41' HGA2 0.09 ! / \ +ATOM H42' HGA2 0.09 ! O3' O2' +GROUP ! | | +ATOM C2' CG3C51 0.14 ! O1P==P==O2P H21' +ATOM H22' HGA1 0.09 ! || +ATOM O2' OG311 -0.65 ! O3P (-2) +ATOM H21' HGP1 0.42 +GROUP +ATOM C3' CG3C51 -0.09 +ATOM H31' HGA1 0.09 +GROUP +ATOM O3' OG303 -0.40 +ATOM P PG2 1.10 +ATOM O1P OG2P1 -0.90 +ATOM O2P OG2P1 -0.90 +ATOM O3P OG2P1 -0.90 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' O2' C2' H22' C3' H31' C4' H41' +BOND C4' H42' O2' H21' O3' P P O1P P O2P P O3P +IC C4' O4' C1' C2' 1.4055 108.09 6.07 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 -25.13 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 33.40 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 -30.20 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 14.98 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 91.77 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -144.31 103.11 1.5346 +IC O2' C2' C3' C4' 1.0846 110.65 152.51 100.86 1.5211 +IC H21' O2' C2' C3' 0.0 0.0 60.0 0.0 0.0 +IC H22' C2' C3' C4' 1.0822 110.88 -84.13 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 87.99 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 136.35 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -102.74 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -151.73 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RIBO 0.00 ! C4H8O3 ribose, both c2' and c3' hydroxyls are alpha +GROUP +ATOM O4' OG3C51 -0.40 ! H41' O4' H11' +ATOM C1' CG3C52 0.02 ! \ / \ / +ATOM C4' CG3C52 0.02 ! H42'--C4' C1'--H12' +ATOM H11' HGA2 0.09 ! | | +ATOM H12' HGA2 0.09 ! H31'--C3'--C2'--H22' +ATOM H41' HGA2 0.09 ! / \ +ATOM H42' HGA2 0.09 ! O3' O2' +GROUP ! | | +ATOM C2' CG3C51 0.14 ! H32' H21' +ATOM H21' HGA1 0.09 +ATOM O2' OG311 -0.65 +ATOM H22' HGP1 0.42 +GROUP +ATOM C3' CG3C51 0.14 +ATOM H31' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' O2' C2' H21' C3' H31' C4' H41' +BOND C4' H42' O2' H22' O3' H32' +!Nicolas: the following IC are for thf-oh as optimized via ab initio calculations +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC O2' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H22' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 +PATC FIRS NONE LAST NONE + +RESI TMPM -1.00 ! C6H12O5P 4'-methyl,3'-methylphosphate tetrahydrofuran (phosphate -1) + !charges corrected by adm jr. 9/98 +GROUP +ATOM O4' OG3C51 -0.40 ! H52' H53' +ATOM C1' CG3C52 0.02 ! \ / +ATOM H11' HGA2 0.09 ! H51'-C5' O4' H11' +ATOM H12' HGA2 0.09 ! \ / \ / +ATOM C4' CG3C51 0.11 ! H42'--C4' C1'--H12' +ATOM H42' HGA1 0.09 ! | | +GROUP ! H31'--C3'--C2'--H21' +ATOM C2' CG3C52 -0.18 ! / \ +ATOM H21' HGA2 0.09 ! O3' H22' +ATOM H22' HGA2 0.09 ! | +GROUP ! O1P==P==O2P +ATOM C3' CG3C51 0.01 ! | +ATOM H31' HGA1 0.09 ! O3P (-1) +GROUP ! \ +ATOM O3' OG303 -0.57 ! C3T--H3T3 +ATOM P PG1 1.50 ! / \ +ATOM O1P OG2P1 -0.78 ! H3T1 H3T2 +ATOM O2P OG2P1 -0.78 +ATOM O3P OG303 -0.57 +ATOM C3T CG331 -0.17 +ATOM H3T1 HGA3 0.09 +ATOM H3T2 HGA3 0.09 +ATOM H3T3 HGA3 0.09 +GROUP +ATOM C5' CG331 -0.27 +ATOM H51' HGA3 0.09 +ATOM H52' HGA3 0.09 +ATOM H53' HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' C5' C5' H51' C5' H52' C5' H53' +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TADE 0.00 ! C9H11N5O thf with adenine + ! Atom types for aliphatic atoms based on nucleotide + ! atom order consistent with 9-m-ade +GROUP +ATOM C5 CG2RC0 0.28 ! H61 H62 +ATOM N7 NG2R50 -0.71 ! \ / +ATOM C8 CG2R53 0.34 ! N6 +ATOM H8 HGR52 0.12 ! | +ATOM N9 NG2R51 -0.05 ! C6 +ATOM N1 NG2R62 -0.74 ! // \ +ATOM C2 CG2R64 0.50 ! N1 C5--N7\\ +ATOM H2 HGR62 0.13 ! | || C8-H8 +ATOM N3 NG2R62 -0.75 ! C2 C4--N9/ +ATOM C4 CG2RC0 0.43 ! / \\ / \ +ATOM C6 CG2R64 0.46 ! H2 N3 \ +ATOM N6 NG2S3 -0.77 ! \ +ATOM H61 HGP4 0.38 ! \ +ATOM H62 HGP4 0.38 ! \ +ATOM O4' OG3C51 -0.40 ! H42' O4' \ +ATOM C1' CG3C51 0.11 ! \ / \ \ +ATOM H12' HGA1 0.09 ! H41'-C4' C1' +ATOM C4' CG3C52 0.02 ! \ / \ +ATOM H41' HGA2 0.09 ! H31'--C3'--C2' H12' +ATOM H42' HGA2 0.09 ! / / \ +GROUP ! H32' H21' H22' +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP +ATOM C3' CG3C52 -0.18 +ATOM H31' HGA2 0.09 +ATOM H32' HGA2 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TCYT 0.00 ! C8H11N3O2 THF with cytosine + ! Atom types for aliphatic atoms based on nucleotide + !atom order to be consistent with 1-m-cyt +GROUP +ATOM N1 NG2R61 -0.13 +ATOM C6 CG2R62 0.05 ! H42 H41 +ATOM H6 HGR62 0.17 ! \ / +ATOM C2 CG2R63 0.52 ! N4 +ATOM O2 OG2D4 -0.49 ! | +ATOM N3 NG2R62 -0.66 ! C4 +ATOM C4 CG2R64 0.65 ! / \\ +ATOM N4 NG2S3 -0.75 ! H5-C5 N3 +ATOM H41 HGP4 0.37 ! || | +ATOM H42 HGP4 0.33 ! H6-C6 C2 +ATOM C5 CG2R62 -0.13 ! \ / \\ +ATOM H5 HGR62 0.07 ! N1 O2 +ATOM O4' OG3C51 -0.40 ! \ +ATOM C1' CG3C51 0.11 ! \ +ATOM H12' HGA1 0.09 ! \ +ATOM C4' CG3C52 0.02 ! H42' O4' \ +ATOM H41' HGA2 0.09 ! \ / \ \ +ATOM H42' HGA2 0.09 ! H41'-C4' C1' +GROUP ! \ / \ +ATOM C2' CG3C52 -0.18 ! H31'--C3'--C2' H12' +ATOM H21' HGA2 0.09 ! / / \ +ATOM H22' HGA2 0.09 ! H32' H21' H22' +GROUP +ATOM C3' CG3C52 -0.18 +ATOM H31' HGA2 0.09 +ATOM H32' HGA2 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N1 +BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 +BOND C2 N3 C4 C5 C5 H5 C6 H6 +DOUBLE C2 O2 C5 C6 N3 C4 +IMPR C4 C5 N3 N4 +IMPR C2 N1 N3 O2 +IMPR N4 H42 H41 C4 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TGUA 0.00 ! C9H11N5O2 thf with guanine + ! Atom types for aliphatic atoms based on nucleotide + ! atom order consistent with 9-m-gua +GROUP +ATOM N9 NG2R51 -0.02 ! O6 +ATOM C4 CG2RC0 0.26 ! || +ATOM N3 NG2R62 -0.74 ! C6 +ATOM C2 CG2R64 0.75 ! / \ +ATOM N1 NG2R61 -0.34 ! H1-N1 C5--N7\\ +ATOM H1 HGP1 0.26 ! | || C8-H8 +ATOM N2 NG2S3 -0.68 ! C2 C4--N9/ +ATOM H21 HGP4 0.32 ! / \\ / \ +ATOM H22 HGP4 0.35 ! H21-N2 N3 \ +ATOM C6 CG2R63 0.54 ! | \ +ATOM O6 OG2D4 -0.51 ! H22 \ +ATOM C5 CG2RC0 0.00 ! \ +ATOM N7 NG2R50 -0.60 ! H42' O4' \ +ATOM C8 CG2R53 0.25 ! \ / \ \ +ATOM H8 HGR52 0.16 ! H41'-C4' C1' +ATOM O4' OG3C51 -0.40 ! \ / \ +ATOM C1' CG3C51 0.11 ! H31'--C3'--C2' H12' +ATOM H12' HGA1 0.09 ! / / \ +ATOM C4' CG3C52 0.02 ! H32' H21' H22' +ATOM H41' HGA2 0.09 +ATOM H42' HGA2 0.09 +GROUP +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP +ATOM C3' CG3C52 -0.18 +ATOM H31' HGA2 0.09 +ATOM H32' HGA2 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 +DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 +IMPR C2 N1 N3 N2 +IMPR N2 H22 H21 C2 +IMPR C6 C5 N1 O6 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TTHY 0.00 ! C9H12N2O3 THF with thymine on C1' + ! Atom type for N1 changed from NN2 to NN2B, to adjust + ! chi in thymine independantly of cytosine. + ! Atom types for aliphatic atoms based on nucleotide + ! atom order consistent with 1-m-thy +GROUP +ATOM N1 NG2R61 -0.34 ! H51 O4 +ATOM C6 CG2R62 0.17 ! | || +ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 +ATOM C2 CG2R63 0.51 ! | \ / \ / +ATOM O2 OG2D4 -0.41 ! H53 C5 N3 +ATOM N3 NG2R61 -0.46 ! || | +ATOM H3 HGP1 0.36 ! H6-C6 C2 +ATOM C4 CG2R63 0.50 ! \ / \\ +ATOM O4 OG2D4 -0.45 ! N1 O2 +ATOM C5 CG2R62 -0.15 ! \ +ATOM C5M CG331 -0.11 ! \ +ATOM H51 HGA3 0.07 ! \ +ATOM H52 HGA3 0.07 ! H42' O4' \ +ATOM H53 HGA3 0.07 ! \ / \ \ +ATOM O4' OG3C51 -0.40 ! H41'-C4' C1' +ATOM C1' CG3C51 0.11 ! \ / \ +ATOM H12' HGA1 0.09 ! H31'--C3'--C2' H12' +ATOM C4' CG3C52 0.02 ! / / \ +ATOM H41' HGA2 0.09 ! H32' H21' H22' +ATOM H42' HGA2 0.09 +GROUP +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP +ATOM C3' CG3C52 -0.18 +ATOM H31' HGA2 0.09 +ATOM H32' HGA2 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N1 +BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI TURA 0.00 ! C8H10N2O3 THF with uracil on C1' + ! Atom type for N1 changed from NN2 to NN2B, in order to adjust + ! chi in uracil/thymine independantly of cytosine. + ! Atom types for aliphatic atoms based on nucleotide + ! atom order consistent with 1-m-thy +GROUP +ATOM N1 NG2R61 -0.34 ! O4 +ATOM C6 CG2R62 0.20 ! || +ATOM H6 HGR62 0.14 ! C4 H3 +ATOM C2 CG2R63 0.55 ! / \ / +ATOM O2 OG2D4 -0.45 ! H5-C5 N3 +ATOM N3 NG2R61 -0.46 ! || | +ATOM H3 HGP1 0.36 ! H6-C6 C2 +ATOM C4 CG2R63 0.53 ! \ / \\ +ATOM O4 OG2D4 -0.48 ! N1 O2 +ATOM C5 CG2R62 -0.15 ! \ +ATOM H5 HGR62 0.10 ! \ +ATOM O4' OG3C51 -0.40 ! \ +ATOM C1' CG3C51 0.11 ! H42' O4' \ +ATOM H12' HGA1 0.09 ! \ / \ \ +ATOM C4' CG3C52 0.02 ! H41'-C4' C1' +ATOM H41' HGA2 0.09 ! \ / \ +ATOM H42' HGA2 0.09 ! H31'--C3'--C2' H12' +GROUP ! / / \ +ATOM C2' CG3C52 -0.18 ! H32' H21' H22' +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP +ATOM C3' CG3C52 -0.18 +ATOM H31' HGA2 0.09 +ATOM H32' HGA2 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C1' N1 +BOND N1 C2 N1 C6 +BOND C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 H5 C6 H6 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 +! ic table for thfim, from Nicolas: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 +IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC C4 C6 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI THAO 0.00 ! C8H12N2O3 Nucleoside analogue with imidazole +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Imidazole +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +GROUP ! / \ +ATOM H31' HGA1 0.09 ! O3' H22' +ATOM C3' CG3C51 0.14 ! | +ATOM O3' OG311 -0.65 ! H32' +ATOM H32' HGP1 0.42 +GROUP +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CG2R51 -0.05 ! C1' HE1 +ATOM HG HGR52 0.09 ! \ / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / || +ATOM ND1 NG2R51 -0.04 ! HG-CG || +ATOM CE1 CG2R53 0.25 ! \\ || +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' ND1 +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CG 0.0 0.0 90.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUSA 0.00 ! C10H13N5O3 deoxy-nucleoside with adenine +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Adenine +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +! Adenine atoms ! / \ +GROUP ! O3' H22' +ATOM C5 CG2RC0 0.28 ! | +ATOM N7 NG2R50 -0.71 ! H32' +ATOM C8 CG2R53 0.34 +ATOM H8 HGR52 0.12 +ATOM N9 NG2R51 -0.05 +ATOM N1 NG2R62 -0.74 +ATOM C2 CG2R64 0.50 +ATOM H2 HGR62 0.13 +ATOM N3 NG2R62 -0.75 +ATOM C4 CG2RC0 0.43 +ATOM C6 CG2R64 0.46 +ATOM N6 NG2S3 -0.77 +ATOM H61 HGP4 0.38 +ATOM H62 HGP4 0.38 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP ! Methyl group on C4' +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUSG 0.00 ! C10H13N5O4 nucleoside with guanine +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Guanine +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +!Guanine atoms ! / \ +GROUP ! O3' H22' +ATOM N9 NG2R51 -0.02 ! | +ATOM C4 CG2RC0 0.26 ! H32' +ATOM N3 NG2R62 -0.74 +ATOM C2 CG2R64 0.75 +ATOM N1 NG2R61 -0.34 +ATOM H1 HGP1 0.26 +ATOM N2 NG2S3 -0.68 +ATOM H21 HGP4 0.32 +ATOM H22 HGP4 0.35 +ATOM C6 CG2R63 0.54 +ATOM O6 OG2D4 -0.51 +ATOM C5 CG2RC0 0.00 +ATOM N7 NG2R50 -0.60 +ATOM C8 CG2R53 0.25 +ATOM H8 HGR52 0.16 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP ! C5' hydroxyl +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 +DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 +IMPR C2 N1 N3 N2 +IMPR N2 H22 H21 C2 +IMPR C6 C5 N1 O6 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUSC 0.00 ! C9H13N3O4 nucleoside with cytosine +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Cytosine +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +! Cytosine atoms ! / \ +GROUP ! O3' H22' +ATOM N1 NG2R61 -0.13 ! | +ATOM C6 CG2R62 0.05 ! H32' +ATOM H6 HGR62 0.17 +ATOM C2 CG2R63 0.52 +ATOM O2 OG2D4 -0.49 +ATOM N3 NG2R62 -0.66 +ATOM C4 CG2R64 0.65 +ATOM N4 NG2S3 -0.75 +ATOM H41 HGP4 0.37 +ATOM H42 HGP4 0.33 +ATOM C5 CG2R62 -0.13 +ATOM H5 HGR62 0.07 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP ! C5' hydroxyl +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N1 +BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 +BOND C2 N3 C4 C5 C5 H5 C6 H6 +DOUBLE C2 O2 C5 C6 N3 C4 +IMPR C4 C5 N3 N4 +IMPR C2 N1 N3 O2 +IMPR N4 H42 H41 C4 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUST 0.00 ! C10H14N2O5 nucleoside with thymine +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Thymine +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +! Atoms for thymine ! / \ +GROUP ! O3' H22' +ATOM N1 NG2R61 -0.34 ! | +ATOM C6 CG2R62 0.17 ! H32' +ATOM H6 HGR62 0.17 +ATOM C2 CG2R63 0.51 +ATOM O2 OG2D4 -0.41 +ATOM N3 NG2R61 -0.46 +ATOM H3 HGP1 0.36 +ATOM C4 CG2R63 0.50 +ATOM O4 OG2D4 -0.45 +ATOM C5 CG2R62 -0.15 +ATOM C5M CG331 -0.11 +ATOM H51 HGA3 0.07 +ATOM H52 HGA3 0.07 +ATOM H53 HGA3 0.07 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP ! C5' hydroxyl +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N1 +BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUSU 0.00 ! C9H12N2O5 nucleoside with uracil +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Uracil +GROUP ! \ / \ / +ATOM C2' CG3C52 -0.18 ! H42'--C4' C1'--H12' +ATOM H21' HGA2 0.09 ! | | +ATOM H22' HGA2 0.09 ! H31'--C3'--C2'--H21' +! Atoms for uracil ! / \ +GROUP ! O3' H22' +ATOM N1 NG2R61 -0.34 ! | +ATOM C6 CG2R62 0.20 ! H32' +ATOM H6 HGR62 0.14 +ATOM C2 CG2R63 0.55 +ATOM O2 OG2D4 -0.45 +ATOM N3 NG2R61 -0.46 +ATOM H3 HGP1 0.36 +ATOM C4 CG2R63 0.53 +ATOM O4 OG2D4 -0.48 +ATOM C5 CG2R62 -0.15 +ATOM H5 HGR62 0.10 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP ! C5' hydroxyl +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' N1 N1 C2 N1 C6 C2 O2 +BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 C6 C5 H5 C6 H6 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 +IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 +IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 +IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 +IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 +IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 +IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 +IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUS 0.00 ! C8H12N2O4 Ribonucleoside analogue with imidazole +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Imidazole +GROUP ! \ / \ / +ATOM C2' CG3C51 0.14 ! H42'--C4' C1'--H12' +ATOM H21' HGA1 0.09 ! | | +ATOM O2' OG311 -0.65 ! H31'--C3'--C2'--H21' +ATOM H22' HGP1 0.42 ! / \ +GROUP ! O3' O2' +ATOM H31' HGA1 0.09 ! | | +ATOM C3' CG3C51 0.14 ! H32' H22' +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +ATOM CG CG2R51 -0.05 ! C1' HE1 +ATOM HG HGR52 0.09 ! \ / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / || +ATOM ND1 NG2R51 -0.04 ! HG-CG || +ATOM CE1 CG2R53 0.25 ! \\ || +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' +BOND C4' H42' C5' H51' C5' H52' C5' O5' O5' H5T +BOND O3' H32' +BOND C1' ND1 +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 +IC H22' O2' C2' C3' 0.0 0.0 -60.00 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUA 0.00 ! C10H13N5O4 ribo-nucleoside with adenine +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Adenine +GROUP ! \ / \ / +ATOM H21' HGA1 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CG3C51 0.14 ! | | +ATOM O2' OG311 -0.65 ! H31'--C3'--C2'--H21' +ATOM H22' HGP1 0.42 ! / \ +! Adenine atoms ! O3' O2' +GROUP ! | | +ATOM C5 CG2RC0 0.28 ! H32' H22' +ATOM N7 NG2R50 -0.71 +ATOM C8 CG2R53 0.34 +ATOM H8 HGR52 0.12 +ATOM N9 NG2R51 -0.05 +ATOM N1 NG2R62 -0.74 +ATOM C2 CG2R64 0.50 +ATOM H2 HGR62 0.13 +ATOM N3 NG2R62 -0.75 +ATOM C4 CG2RC0 0.43 +ATOM C6 CG2R64 0.46 +ATOM N6 NG2S3 -0.77 +ATOM H61 HGP4 0.38 +ATOM H62 HGP4 0.38 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP ! C5' hydroxyl +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O2' H22' O3' H32' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 +IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 150.8 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 108.6 229.5 125.5 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUG 0.00 ! C10H13N5O5 ribo-nucleoside with guanine +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Guanine +GROUP ! \ / \ / +ATOM H21' HGA1 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CG3C51 0.14 ! | | +ATOM O2' OG311 -0.65 ! H31'--C3'--C2'--H21' +ATOM H22' HGP1 0.42 ! / \ +! Guanine atoms ! O3' O2' +GROUP ! | | +ATOM N9 NG2R51 -0.02 ! H32' H22' +ATOM C4 CG2RC0 0.26 +ATOM N3 NG2R62 -0.74 +ATOM C2 CG2R64 0.75 +ATOM N1 NG2R61 -0.34 +ATOM H1 HGP1 0.26 +ATOM N2 NG2S3 -0.68 +ATOM H21 HGP4 0.32 +ATOM H22 HGP4 0.35 +ATOM C6 CG2R63 0.54 +ATOM O6 OG2D4 -0.51 +ATOM C5 CG2RC0 0.00 +ATOM N7 NG2R50 -0.60 +ATOM C8 CG2R53 0.25 +ATOM H8 HGR52 0.16 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP ! C5' hydroxyl +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O2' H22' O3' H32' +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 +DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 +IMPR C2 N1 N3 N2 +IMPR N2 H22 H21 C2 +IMPR C6 C5 N1 O6 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 +IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 +IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI RNUC 0.00 ! C9H13N3O5 ribo-nucleoside with cytosine +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C4' CG3C51 0.11 ! / +ATOM H42' HGA1 0.09 ! H51' O5' +ATOM C1' CG3C51 0.11 ! \ | +ATOM H12' HGA1 0.09 !H52'--C5' O4' Cytosine +GROUP ! \ / \ / +ATOM H21' HGA1 0.09 ! H42'--C4' C1'--H12' +ATOM C2' CG3C51 0.14 ! | | +ATOM O2' OG311 -0.65 ! H31'--C3'--C2'--H21' +ATOM H22' HGP1 0.42 ! / \ +! Cytosine atoms ! O3' O2' +GROUP ! | | +ATOM N1 NG2R61 -0.13 ! H32' H22' +ATOM C6 CG2R62 0.05 +ATOM H6 HGR62 0.17 +ATOM C2 CG2R63 0.52 +ATOM O2 OG2D4 -0.49 +ATOM N3 NG2R62 -0.66 +ATOM C4 CG2R64 0.65 +ATOM N4 NG2S3 -0.75 +ATOM H41 HGP4 0.37 +ATOM H42 HGP4 0.33 +ATOM C5 CG2R62 -0.13 +ATOM H5 HGR62 0.07 +GROUP ! Hydroxyl group on C3' +ATOM H31' HGA1 0.09 +ATOM C3' CG3C51 0.14 +ATOM O3' OG311 -0.65 +ATOM H32' HGP1 0.42 +GROUP ! Methyl group on C4' +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM O5' OG311 -0.65 +ATOM H5T HGP1 0.42 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' +BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' +BOND C5' H51' C5' H52' C5' O5' O5' H5T +BOND O2' H22' O3' H32' +BOND C1' N1 +BOND N1 C2 N1 C6 +BOND C2 N3 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C5 H5 C6 H6 +DOUBLE C2 O2 C5 C6 N3 C4 +IMPR C4 C5 N3 N4 +IMPR C2 N1 N3 O2 +IMPR N4 H42 H41 C4 +! This IC table is only an initial guess: +IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 +IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 +IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 +IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 +IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 +IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 +IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 +IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 +IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 +IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 +IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 +IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 +IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NUCL -1.00 ! C9H14N2O6P +!WARNING: - The charge distribution on the imidazole is identical +! to the charge distribution on the imidazole in THFI, which is +! different from the charge distribution on the equivalent moiety +! in adenine. +! - The charge distribution on the sugar is identical to what +! it is in the DNA. +! - The charge' on the 3' end of the "backbone" is identical to +! what it is in the DNA, except for the terminal methyl group for which +! there is no DNA equivalent. +! - The charges on the 5' extremity of the backbone is as in the +! 5TER patch used for the DNA. An alternative to that would be to use +! charges more similar to what is in non-terminal residues in DNA. +GROUP +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C51 0.11 +ATOM H12' HGA1 0.09 +ATOM C4' CG3C51 0.11 +ATOM H42' HGA1 0.09 +GROUP ! Imidazole: transferred from isolated imidazole (IMIA) +! The following atom types use the parameters specifically developed +! for the imidazole +! Atom types for aliphatic atoms based on nucleotide +ATOM CG CG2R51 -0.05 ! C1' HE1 +ATOM HG HGR52 0.09 ! \ / +ATOM CD2 CG2R51 0.22 ! ND1---CE1 +ATOM HD2 HGR52 0.10 ! / || +ATOM ND1 NG2R51 -0.04 ! HG-CG || +ATOM CE1 CG2R53 0.25 ! \\ || +ATOM HE1 HGR52 0.13 ! CD2---NE2 +ATOM NE2 NG2R50 -0.70 ! | + ! HD2 +GROUP +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 ! H5T +ATOM H22' HGA2 0.09 ! | +GROUP ! H52' O5' +ATOM C3' CG3C51 0.01 ! \ / +ATOM H31' HGA1 0.09 ! H51'-C5' O4' Imidazole +ATOM O3' OG303 -0.57 ! \ / \ / +ATOM P PG1 1.50 ! H42'--C4' C1'--H12' +ATOM O1P OG2P1 -0.78 ! | | +ATOM O2P OG2P1 -0.78 ! H31'--C3'--C2'--H21' +ATOM O3P OG303 -0.57 ! / \ +ATOM C3T CG331 -0.17 ! O3' H22' +ATOM H3T1 HGA3 0.09 ! | +ATOM H3T2 HGA3 0.09 ! O1P==P==O2P +ATOM H3T3 HGA3 0.09 ! | +GROUP ! O3P (-1) +ATOM C5' CG321 0.05 ! \ +ATOM H51' HGA2 0.09 ! C3T--H3T3 +ATOM H52' HGA2 0.09 ! / \ +ATOM H5T HGP1 0.42 ! H3T1 H3T2 +ATOM O5' OG311 -0.65 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' C5' C5' H51' C5' H52' +BOND C5' O5' O5' H5T +BOND C1' ND1 +BOND ND1 CE1 NE2 CD2 CG ND1 +BOND CE1 HE1 CD2 HD2 CG HG +DOUBLE CG CD2 CE1 NE2 +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 +IC O4' C1' ND1 CE1 0.0 0.0 90.00 0.0 0.0 +IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 +IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 +IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 +IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 +IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 +IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 +IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI NADE -1.00 ! C11H15N5O6P +! NADE is a nucleotide analogue similar to NUCL, except that the imidazole +! has been replaced by an adenine +! - The charge distribution on the sugar is identical to what +! it is in the DNA. +! - The charge' on the 3' end of the "backbone" is identical to +! what it is in the DNA, except for the terminal methyl group for which +! there is no DNA equivalent. +! - The charges on the 5' extremity of the backbone is as in the +! 5TER patch used for the DNA. An alternative to that would be to use +! charges more similar to what is actuallly in non-terminal residues in the +! DNA. +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C1' CG3C51 0.11 ! | +ATOM H12' HGA1 0.09 ! H52' O5' +ATOM C4' CG3C51 0.11 ! \ / +ATOM H42' HGA1 0.09 ! H51'-C5' O4' Adenine +GROUP ! \ / \ / +ATOM C5 CG2RC0 0.30 ! H42'--C4' C1'--H12' +ATOM N7 NG2R50 -0.69 ! | | +ATOM C8 CG2R53 0.34 ! H31'--C3'--C2'--H21' +ATOM H8 HGR52 0.10 ! / \ +ATOM N9 NG2R51 -0.06 ! O3' H22' +ATOM N1 NG2R62 -0.74 ! | +ATOM C2 CG2R64 0.50 ! O1P==P==O2P +ATOM H2 HGR62 0.13 ! | +ATOM N3 NG2R62 -0.75 ! O3P (-1) +ATOM C4 CG2RC0 0.43 ! \ +ATOM C6 CG2R64 0.44 ! C3T--H3T3 +ATOM N6 NG2S3 -0.75 ! / \ +ATOM H61 HGP4 0.38 ! H3T1 H3T2 +ATOM H62 HGP4 0.37 +GROUP +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP +ATOM C3' CG3C51 0.01 +ATOM H31' HGA1 0.09 +ATOM O3' OG303 -0.57 +ATOM P PG1 1.50 +ATOM O1P OG2P1 -0.78 +ATOM O2P OG2P1 -0.78 +ATOM O3P OG303 -0.57 +ATOM C3T CG331 -0.17 +ATOM H3T1 HGA3 0.09 +ATOM H3T2 HGA3 0.09 +ATOM H3T3 HGA3 0.09 +GROUP +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM H5T HGP1 0.42 +ATOM O5' OG311 -0.65 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' C5' C5' H51' C5' H52' +BOND C5' O5' O5' H5T +BOND C1' N9 +BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 +IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI NTHY -1.00 ! C11H16N2O8P +! NTHY is a nucleotide analogue similar to NUCL, except that the imidazole +! has been replaced by a thymine +! - The charge distribution on the sugar is identical to what +! it is in the DNA. +! - The charge' on the 3' end of the "backbone" is identical to +! what it is in the DNA, except for the terminal methyl group for which +! there is no DNA equivalent. +! - The charges on the 5' extremity of the backbone is as in the +! 5TER patch used for the DNA. An alternative to that would be to use +! charges more similar to what is actuallly in non-terminal residues in the +! DNA. +GROUP +ATOM O4' OG3C51 -0.40 ! H5T +ATOM C1' CG3C51 0.11 ! | +ATOM H12' HGA1 0.09 ! H52' O5' +ATOM C4' CG3C51 0.11 ! \ / +ATOM H42' HGA1 0.09 ! H51'-C5' O4' Thymine +GROUP ! \ / \ / +ATOM N1 NG2R61 -0.34 ! H42'--C4' C1'--H12' +ATOM C6 CG2R62 0.17 ! | | +ATOM H6 HGR62 0.17 ! H31'--C3'--C2'--H21' +ATOM C2 CG2R63 0.51 ! / \ +ATOM O2 OG2D4 -0.41 ! O3' H22' +ATOM N3 NG2R61 -0.46 ! | +ATOM H3 HGP1 0.36 ! O1P==P==O2P +ATOM C4 CG2R63 0.50 ! | +ATOM O4 OG2D4 -0.45 ! O3P (-1) +ATOM C5 CG2R62 -0.15 ! \ +ATOM C5M CG331 -0.11 ! C3T--H3T3 +ATOM H51 HGA3 0.07 ! / \ +ATOM H52 HGA3 0.07 ! H3T1 H3T2 +ATOM H53 HGA3 0.07 +GROUP +ATOM C2' CG3C52 -0.18 +ATOM H21' HGA2 0.09 +ATOM H22' HGA2 0.09 +GROUP +ATOM C3' CG3C51 0.01 +ATOM H31' HGA1 0.09 +ATOM O3' OG303 -0.57 +ATOM P PG1 1.50 +ATOM O1P OG2P1 -0.78 +ATOM O2P OG2P1 -0.78 +ATOM O3P OG303 -0.57 +ATOM C3T CG331 -0.17 +ATOM H3T1 HGA3 0.09 +ATOM H3T2 HGA3 0.09 +ATOM H3T3 HGA3 0.09 +GROUP +ATOM C5' CG321 0.05 +ATOM H51' HGA2 0.09 +ATOM H52' HGA2 0.09 +ATOM H5T HGP1 0.42 +ATOM O5' OG311 -0.65 +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' +BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' +BOND O3' P P O1P P O2P P O3P +BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 +BOND C4' C5' C5' H51' C5' H52' +BOND C5' O5' O5' H5T +BOND C1' N1 +BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 +IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 +IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 +IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 +IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 +IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 +IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 +IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 +IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 +IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 +IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 +IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 +IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 +IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 +IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 +IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 +IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 +IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 +IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 +IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 +IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 +IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 +IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 +IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 +IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi +IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +!toppar_all27_na_nad_ppi.str +RESI NIC 1.00 ! C6H7N2O oxidized nicotinamide (protonated), jjp1/adm jr. + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + + ! H15 +GROUP ! \ +ATOM H1 HGP2 0.45 ! H16-N14 H8 +ATOM N2 NG2R61 -0.52 ! \ | +ATOM C3 CG2R62 0.16 ! C12 C7 +ATOM H4 HGR63 0.19 ! // \ / \\ +ATOM C5 CG2R62 -0.10 ! O13 C9 C5-H6 +ATOM H6 HGR63 0.16 ! || | +ATOM C7 CG2R62 -0.05 ! H11-C10 C3-H4 +ATOM H8 HGR63 0.16 ! \+ // +ATOM C9 CG2R62 0.05 ! N2 +ATOM C10 CG2R62 0.18 ! | +ATOM H11 HGR63 0.16 ! H1 +ATOM C12 CG2O1 0.68 +ATOM O13 OG2D1 -0.40 +ATOM N14 NG2S2 -0.82 +ATOM H15 HGP1 0.34 ! trans to O13 +ATOM H16 HGP1 0.36 ! cis to O13 +BOND N2 H1 C3 H4 C3 C5 C5 H6 +BOND C7 H8 C7 C9 N2 C10 +BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16 +DOUBLE C12 O13 C9 C10 C5 C7 N2 C3 +IMPR C12 C9 N14 O13 +! ic table for analysis +IC N2 C3 C5 C7 0.0000 000.00 000.00 000.00 0.000 +IC C3 C5 C7 C9 0.0000 000.00 000.00 000.00 0.000 +IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C10 N2 0.0000 000.00 000.00 000.00 0.000 +IC C9 C10 N2 C3 0.0000 000.00 000.00 000.00 0.000 +IC C10 N2 C3 C5 0.0000 000.00 000.00 000.00 0.000 +IC C9 C10 N2 H1 0.0000 000.00 000.00 000.00 0.000 +IC C10 N2 C3 H4 0.0000 000.00 000.00 000.00 0.000 +IC N2 C3 C5 H6 0.0000 000.00 000.00 000.00 0.000 +IC C3 C5 C7 H8 0.0000 000.00 000.00 000.00 0.000 +IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000 +IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000 +IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000 +IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000 +IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000 +PATCH FIRST NONE LAST NONE + +RESI NICH 0.00 ! C6H8N2O reduced nicotinamide, jjp1/adm jr. + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + ! HN3 to HN6 atom type switch to maintain proper vdw params, 9/98 + + ! H15 +GROUP ! \ +ATOM H1 HGPAM1 0.42 ! H16-N14 H8 H17 +ATOM N2 NG311 -0.69 ! \ \ / +ATOM C3 CG2D1O -0.06 ! C12 C7 +ATOM H4 HGA4 0.17 ! / \ / \ +ATOM C5 CG2D1 -0.18 ! O13 C9 C5-H6 +ATOM H6 HGA4 0.14 ! || || +ATOM C7 CG321 -0.28 ! H11-C10 C3-H4 +ATOM H8 HGA2 0.09 ! \ / +ATOM H17 HGA2 0.09 ! N2 +ATOM C10 CG2D1O -0.10 ! | +ATOM H11 HGA4 0.14 ! H1 +ATOM C9 CG2DC1 0.36 +ATOM C12 CG2O1 0.55 +ATOM O13 OG2D1 -0.51 +ATOM N14 NG2S2 -0.72 +ATOM H15 HGP1 0.26 ! trans to O13 +ATOM H16 HGP1 0.32 ! cis to O13 + +BOND N2 H1 N2 C3 C3 H4 C5 H6 +BOND C5 C7 C7 H8 C7 H17 C7 C9 N2 C10 +BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16 +DOUBLE C12 O13 C9 C10 C3 C5 +IMPR C3 C5 N2 H4 +IMPR C10 C9 N2 H11 +IMPR C12 C9 N14 O13 +! new IC table by kevo. Deliberately slightly distorted. +IC C10 C9 C7 C5 0.0000 0.00 10.00 0.00 0.0000 +IC C7 C9 C10 N2 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C7 *C9 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 C5 C3 0.0000 0.00 -10.00 0.00 0.0000 +IC C10 C9 C12 N14 0.0000 0.00 180.00 0.00 0.0000 +IC C9 N14 *C12 O13 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C12 N14 H15 0.0000 0.00 0.00 0.00 0.0000 +IC C12 H15 *N14 H16 0.0000 0.00 180.00 0.00 0.0000 +IC C9 N2 *C10 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C3 *N2 H1 0.0000 0.00 175.00 0.00 0.0000 +IC N2 C5 *C3 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C7 *C5 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C9 *C7 H8 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C9 *C7 H17 0.0000 0.00 -120.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI PPI1 -3.00 ! CH3O7P2 Inorganic phosphate, jjp1/adm jr. +GROUP +ATOM C1 CG331 -0.17 +ATOM O11 OG303 -0.62 +ATOM P1 PG1 1.50 ! H11 +ATOM O12 OG304 -0.74 ! | +ATOM O13 OG2P1 -0.82 ! H13--C1--H12 +ATOM O14 OG2P1 -0.82 ! | + ! O11 +ATOM P2 PG2 1.10 ! | +ATOM O22 OG2P1 -0.90 ! O14==P1==O13 (-) +ATOM O23 OG2P1 -0.90 ! | +ATOM O24 OG2P1 -0.90 ! O12 + ! | +ATOM H11 HGA3 0.09 ! (-) O24==P2==O23 (-) +ATOM H12 HGA3 0.09 ! || +ATOM H13 HGA3 0.09 ! O22 + +BOND P1 O11 P1 O12 P1 O13 P1 O14 O11 C1 +BOND C1 H11 C1 H12 C1 H13 +BOND O12 P2 P2 O22 P2 O23 P2 O24 +IC C1 O11 P1 O12 0.0000 000.00 180.0 000.00 0.0000 +IC O11 O12 *P1 O13 0.0000 000.00 120.0 000.00 0.0000 +IC O11 O12 *P1 O14 0.0000 000.00 -120.0 000.00 0.0000 +IC O11 P1 O12 P2 0.0000 000.00 180.0 000.00 0.0000 +IC P1 O12 P2 O22 0.0000 000.00 0.0 000.00 0.0000 +IC O12 O22 *P2 O23 0.0000 000.00 120.0 000.00 0.0000 +IC O12 O22 *P2 O24 0.0000 000.00 -120.0 000.00 0.0000 +IC P1 O11 C1 H11 0.0000 000.00 180.0 000.00 0.0000 +IC O11 H11 *C1 H12 0.0000 000.00 120.0 000.00 0.0000 +IC O11 H11 *C1 H13 0.0000 000.00 -120.0 000.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI PPI2 -2.00 ! CH4O7P2 Inorganic phosphate, protonated, adm jr. + ! terminal P charges based on neutral +GROUP ! methylphosphate +ATOM C1 CG331 -0.17 +ATOM O11 OG303 -0.62 +ATOM P1 PG1 1.46 ! H11 +ATOM O12 OG304 -0.63 ! | +ATOM O13 OG2P1 -0.83 ! H13--C1--H12 +ATOM O14 OG2P1 -0.83 ! | + ! O11 +ATOM P2 PG1 1.34 ! | +ATOM O22 OG311 -0.71 ! -0.60 , kevo O14==P1==O13 (-) +ATOM H22 HGP1 0.44 ! 0.33 , kevo | +ATOM O23 OG2P1 -0.86 ! | +ATOM O24 OG2P1 -0.86 ! O12 + ! | +ATOM H11 HGA3 0.09 ! O24==P2==O23 (-) +ATOM H12 HGA3 0.09 ! | +ATOM H13 HGA3 0.09 ! O22 + ! \ + ! H22 + +BOND P1 O11 P1 O12 P1 O13 P1 O14 O11 C1 +BOND C1 H11 C1 H12 C1 H13 +BOND O12 P2 P2 O22 P2 O23 P2 O24 O22 H22 +! IC Table +IC C1 O11 P1 O12 0.0000 000.00 180.0 000.00 0.0000 +IC O11 P1 O12 P2 0.0000 000.00 180.0 000.00 0.0000 +IC P1 O12 P2 O22 0.0000 000.00 180.0 000.00 0.0000 +IC C1 O11 P1 O13 0.0000 000.00 60.0 000.00 0.0000 +IC C1 O11 P1 O14 0.0000 000.00 -60.0 000.00 0.0000 +IC P1 O12 P2 O23 0.0000 000.00 60.0 000.00 0.0000 +IC P1 O12 P2 O24 0.0000 000.00 -60.0 000.00 0.0000 +IC P1 O11 C1 H11 0.0000 000.00 180.0 000.00 0.0000 +IC P1 O11 C1 H12 0.0000 000.00 60.0 000.00 0.0000 +IC P1 O11 C1 H13 0.0000 000.00 -60.0 000.00 0.0000 +IC O12 P2 O22 H22 0.0000 000.00 180.0 000.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI AMP -2.00 ! C10H12N5O7P adenosine monophosphate, jjp1/adm jr. + ! atom names correspond to pdb nomenclature +GROUP +ATOM C4' CG3C51 0.11 ! H61 H62 +ATOM H4' HGA1 0.09 ! \ / +ATOM O4' OG3C51 -0.40 ! N6 +ATOM C1' CG3C51 0.11 ! | +ATOM H1' HGA1 0.09 ! C6 +GROUP ! // \ +ATOM C5 CG2RC0 0.28 ! N1 C5--N7\\ +ATOM N7 NG2R50 -0.71 ! | || C8-H8 +ATOM C8 CG2R53 0.34 ! C2 C4--N9/ +ATOM H8 HGR52 0.12 ! / \\ / \ +ATOM N9 NG2R51 -0.05 ! H2 N3 \ + ! \ +ATOM N1 NG2R62 -0.74 ! \ +ATOM C2 CG2R64 0.50 ! \ +ATOM H2 HGR62 0.13 ! O1A H5' H4' O4' \ +ATOM N3 NG2R62 -0.75 ! | | \ / \ \ +ATOM C4 CG2RC0 0.43 ! O3A=PA-O5'-C5'---C4' C1' +ATOM C6 CG2R64 0.46 ! | | \ / \ + ! O2A H5'' C3'--C2' H1' +ATOM N6 NG2S3 -0.77 ! / \ / \ +ATOM H61 HGP4 0.38 ! O3' H3' O2' H2'' +ATOM H62 HGP4 0.38 ! | | +GROUP ! H3T H2' +ATOM C2' CG3C51 0.14 +ATOM H2'' HGA1 0.09 +ATOM O2' OG311 -0.65 +ATOM H2' HGP1 0.42 +GROUP +ATOM C3' CG3C51 0.14 +ATOM H3' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H3T HGP1 0.42 +GROUP +ATOM C5' CG321 -0.18 +ATOM H5' HGA2 0.09 +ATOM H5'' HGA2 0.09 +GROUP +ATOM O5' OG303 -0.40 +ATOM PA PG2 1.10 +ATOM O1A OG2P1 -0.90 +ATOM O2A OG2P1 -0.90 +ATOM O3A OG2P1 -0.90 + +BOND PA O1A PA O2A PA O3A PA O5' O3' H3T +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C2' C3' C2' O2' O2' H2' C3' O3' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1A PA +ACCE O2A PA +ACCE O3A PA +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +IC O5' O3A *PA O1A 0.0000 000.00 120.0 000.00 0.0000 +IC O5' O3A *PA O2A 0.0000 000.00 -120.0 000.00 0.0000 +IC O3A PA O5' C5' 0.0000 000.00 -30.0 000.00 0.0000 +!IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 !Not-so-stable minimum +IC PA O5' C5' C4' 0.0000 000.00 -110.0 000.00 0.0000 +!IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 !Not-so-stable minimum +IC O5' C5' C4' C3' 0.0000 000.00 70.0 000.00 0.0000 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +!IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 !144.39 can't be right +IC O4' C2' *C1' N9 0.0 0.0 120.0 0.0 0.0 +!IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 !clash after fixing N9 +IC O4' C1' N9 C4 0.0 0.0 -150.0 0.0 0.0 +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + + +RESI ADP -3.00 ! C10H12N5O10P2 adenosine diphosphate, jjp1/adm jr. + ! atom names correspond to pdb nomenclature +GROUP +ATOM C4' CG3C51 0.11 ! H61 H62 +ATOM H4' HGA1 0.09 ! \ / +ATOM O4' OG3C51 -0.40 ! N6 +ATOM C1' CG3C51 0.11 ! | +ATOM H1' HGA1 0.09 ! C6 +GROUP ! // \ +ATOM C5 CG2RC0 0.28 ! N1 C5--N7\\ +ATOM N7 NG2R50 -0.71 ! | || C8-H8 +ATOM C8 CG2R53 0.34 ! C2 C4--N9/ +ATOM H8 HGR52 0.12 ! / \\ / \ +ATOM N9 NG2R51 -0.05 ! H2 N3 \ + ! \ +ATOM N1 NG2R62 -0.74 ! \ +ATOM C2 CG2R64 0.50 ! \ +ATOM H2 HGR62 0.13 ! O3B O1A H5' H4' O4' \ +ATOM N3 NG2R62 -0.75 ! | | | \ / \ \ +ATOM C4 CG2RC0 0.43 ! O1B=PB-O3A--PA-O5'-C5'---C4' C1' +ATOM C6 CG2R64 0.46 ! | | | \ / \ + ! O2B O2A H5'' C3'--C2' H1' +ATOM N6 NG2S3 -0.77 ! / \ / \ +ATOM H61 HGP4 0.38 ! O3' H3' O2' H2'' +ATOM H62 HGP4 0.38 ! | | +GROUP ! H3T H2' +ATOM C2' CG3C51 0.14 +ATOM H2'' HGA1 0.09 +ATOM O2' OG311 -0.65 +ATOM H2' HGP1 0.42 +GROUP +ATOM C3' CG3C51 0.14 +ATOM H3' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H3T HGP1 0.42 +GROUP +ATOM C5' CG321 -0.08 +ATOM H5' HGA2 0.09 +ATOM H5'' HGA2 0.09 +ATOM O5' OG303 -0.62 +ATOM PA PG1 1.50 +ATOM O1A OG2P1 -0.82 +ATOM O2A OG2P1 -0.82 +ATOM O3A OG304 -0.74 +ATOM PB PG2 1.10 +ATOM O1B OG2P1 -0.90 +ATOM O2B OG2P1 -0.90 +ATOM O3B OG2P1 -0.90 + +BOND PB O3A PB O1B PB O2B PB O3B O3A PA +BOND PA O1A PA O2A PA O5' O3' H3T +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C2' C3' C2' O2' O2' H2' C3' O3' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1A PA +ACCE O2A PA +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +ACCE O3A +ACCE O3B +ACCE O2B +ACCE O1B +IC PA O3A PB O3B 0.0000 000.00 180.0 000.00 0.0000 +IC PB O3A PA O5' 0.0000 000.00 120.0 000.00 0.0000 +IC O5' O3A *PA O1A 0.0000 000.00 120.0 000.00 0.0000 +IC O5' O3A *PA O2A 0.0000 000.00 -120.0 000.00 0.0000 +IC O3A O3B *PB O1B 0.0000 000.00 120.0 000.00 0.0000 +IC O3A O3B *PB O2B 0.0000 000.00 -120.0 000.00 0.0000 +IC O3A PA O5' C5' 0.0000 000.00 -30.0 000.00 0.0000 +!IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 !Not-so-stable minimum +IC PA O5' C5' C4' 0.0000 000.00 -110.0 000.00 0.0000 +!IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 !Not-so-stable minimum +IC O5' C5' C4' C3' 0.0000 000.00 70.0 000.00 0.0000 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +!IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 !144.39 can't be right +IC O4' C2' *C1' N9 0.0 0.0 120.0 0.0 0.0 +!IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 !clash after fixing N9 +IC O4' C1' N9 C4 0.0 0.0 -150.0 0.0 0.0 +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + +RESI ATP -4.00 ! C10H12N5O13P3 adenosine triphosphate , jjp1/adm jr. + !atom names correspond to pdb nomenclature + +GROUP +ATOM C4' CG3C51 0.11 ! H61 H62 +ATOM H4' HGA1 0.09 ! \ / +ATOM O4' OG3C51 -0.40 ! N6 +ATOM C1' CG3C51 0.11 ! | +ATOM H1' HGA1 0.09 ! C6 +GROUP ! // \ +ATOM C5 CG2RC0 0.28 ! N1 C5--N7\\ +ATOM N7 NG2R50 -0.71 ! | || C8-H8 +ATOM C8 CG2R53 0.34 ! C2 C4--N9/ +ATOM H8 HGR52 0.12 ! / \\ / \ +ATOM N9 NG2R51 -0.05 ! H2 N3 \ + ! \ +ATOM N1 NG2R62 -0.74 ! \ +ATOM C2 CG2R64 0.50 ! \ +ATOM H2 HGR62 0.13 ! (-)O3G O2B O1A H5' H4' O4' \ +ATOM N3 NG2R62 -0.75 ! | | | | \ / \ \ +ATOM C4 CG2RC0 0.43 !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4' C1' +ATOM C6 CG2R64 0.46 ! | | | | \ / \ + ! (-)O2G (-)O1B (-)O2A H5'' C3'--C2' H1' +ATOM N6 NG2S3 -0.77 ! / \ / \ +ATOM H61 HGP4 0.38 ! O3' H3' O2' H2'' +ATOM H62 HGP4 0.38 ! | | +GROUP ! H3T H2' +ATOM C2' CG3C51 0.14 +ATOM H2'' HGA1 0.09 +ATOM O2' OG311 -0.65 +ATOM H2' HGP1 0.42 +GROUP +ATOM C3' CG3C51 0.14 +ATOM H3' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H3T HGP1 0.42 +GROUP +ATOM C5' CG321 -0.08 +ATOM H5' HGA2 0.09 +ATOM H5'' HGA2 0.09 +ATOM O5' OG303 -0.62 +ATOM PA PG1 1.50 +ATOM O1A OG2P1 -0.82 +ATOM O2A OG2P1 -0.82 +ATOM O3A OG304 -0.74 +ATOM PB PG1 1.50 +ATOM O1B OG2P1 -0.82 +ATOM O2B OG2P1 -0.82 +ATOM O3B OG304 -0.86 ! charge adjusted to yield total triP of -4.0 +ATOM PG PG2 1.10 +ATOM O1G OG2P1 -0.90 +ATOM O2G OG2P1 -0.90 +ATOM O3G OG2P1 -0.90 + +BOND O5' C5' O5' PA PA O1A PA O2A PA O3A +BOND O3A PB PB O1B PB O2B PB O3B O3B PG +BOND PG O1G PG O2G PG O3G +BOND C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' H3T +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1A PA +ACCE O2A PA +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +ACCE O3A +ACCE O2B +ACCE O1B +ACCE O3B +ACCE O3G +ACCE O1G +ACCE O2G +IC PA O3A PB O3B 0.0000 000.00 180.0 000.00 0.0000 +IC PB O3A PA O5' 0.0000 000.00 120.0 000.00 0.0000 +IC O5' O3A *PA O1A 0.0000 000.00 120.0 000.00 0.0000 +IC O5' O3A *PA O2A 0.0000 000.00 -120.0 000.00 0.0000 +IC O3A O3B *PB O1B 0.0000 000.00 120.0 000.00 0.0000 +IC O3A O3B *PB O2B 0.0000 000.00 -120.0 000.00 0.0000 +IC O3A PB O3B PG 0.0000 000.00 150.0 000.00 0.0000 +IC PB O3B PG O1G 0.0000 000.00 150.0 000.00 0.0000 +IC O3B O1G *PG O2G 0.0000 000.00 120.0 000.00 0.0000 +IC O3B O1G *PG O3G 0.0000 000.00 -120.0 000.00 0.0000 +IC O3A PA O5' C5' 0.0000 000.00 -30.0 000.00 0.0000 +!IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 !Not-so-stable minimum +IC PA O5' C5' C4' 0.0000 000.00 -110.0 000.00 0.0000 +!IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 !Not-so-stable minimum +IC O5' C5' C4' C3' 0.0000 000.00 70.0 000.00 0.0000 +IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +!IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 !144.39 can't be right +IC O4' C2' *C1' N9 0.0 0.0 120.0 0.0 0.0 +!IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 !clash after fixing N9 +IC O4' C1' N9 C4 0.0 0.0 -150.0 0.0 0.0 +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 +PATC FIRS NONE LAST NONE + + +RESI NAD -1.00 ! C21H26N7O14P2 oxidized nicotinamide adenine dinucleotide, jjp1/adm jr. + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params +GROUP +ATOM AC4' CG3C51 0.11 ! AH61 AH62 +ATOM AH4' HGA1 0.09 ! \ / +ATOM AO4' OG3C51 -0.40 ! AN6 +ATOM AC1' CG3C51 0.11 ! | +ATOM AH1' HGA1 0.09 ! AC6 +GROUP ! // \ +ATOM AC5 CG2RC0 0.28 ! AN1 AC5--AN7\\ +ATOM AN7 NG2R50 -0.71 ! | || AC8-AH8 +ATOM AC8 CG2R53 0.34 ! AC2 AC4--AN9/ +ATOM AH8 HGR52 0.12 ! / \\ / \ +ATOM AN9 NG2R51 -0.05 ! AH2 AN3 \ + ! \ +ATOM AN1 NG2R62 -0.74 ! \ +ATOM AC2 CG2R64 0.50 ! \ +ATOM AH2 HGR62 0.13 ! NO1 AO1 AH5sAH4' AO4' \ +ATOM AN3 NG2R62 -0.75 ! | | | \ / \ \ +ATOM AC4 CG2RC0 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' +ATOM AC6 CG2R64 0.46 ! \ | | | \ / \ + ! \ NO2 AO2 AH5' AC3'-AC2' AH1' +ATOM AN6 NG2S3 -0.77 ! \ / \ / \ +ATOM AH61 HGP4 0.38 ! \ AO3' AH3'AO2'AH2' +ATOM AH62 HGP4 0.38 ! \ | | +GROUP ! \ AH3T AH2T +ATOM AC2' CG3C51 0.14 ! \ NH71 +ATOM AH2' HGA1 0.09 ! \ \ +ATOM AO2' OG311 -0.65 ! \ NH72-NN7 NH4 +ATOM AH2T HGP1 0.42 ! \ \ | +GROUP ! \ NC7 NC4 +ATOM AC3' CG3C51 0.14 ! \ // \ / \\ +ATOM AH3' HGA1 0.09 ! \ NO7 NC3 NC5-NH5 +ATOM AO3' OG311 -0.65 ! \ || | +ATOM AH3T HGP1 0.42 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 +GROUP ! \ | \ / \ \+// +ATOM AC5' CG321 -0.08 ! NC5'--NC4' NC1'---------NN1 +ATOM AH5' HGA2 0.09 ! | \ / \ +ATOM AH5S HGA2 0.09 ! NH5' NC3'-NC2'NH1' +ATOM AP PG1 1.50 ! / \ / \ +ATOM AO1 OG2P1 -0.82 ! NO3' NH3'NO2'NH2' +ATOM AO2 OG2P1 -0.82 ! | | +ATOM AO5' OG303 -0.62 ! NH3T NH2T +ATOM O3 OG304 -0.68 +ATOM NP PG1 1.50 +ATOM NO1 OG2P1 -0.82 +ATOM NO2 OG2P1 -0.82 +ATOM NO5' OG303 -0.62 +ATOM NC5' CG321 -0.08 +ATOM NH5S HGA2 0.09 +ATOM NH5' HGA2 0.09 +GROUP +ATOM NC2' CG3C51 0.14 +ATOM NH2' HGA1 0.09 +ATOM NO2' OG311 -0.65 +ATOM NH2T HGP1 0.42 +GROUP +ATOM NC3' CG3C51 0.14 +ATOM NH3' HGA1 0.09 +ATOM NO3' OG311 -0.65 +ATOM NH3T HGP1 0.42 +GROUP +ATOM NC1' CG3C53 0.11 +ATOM NH1' HGA1 0.09 +ATOM NC4' CG3C51 0.11 +ATOM NH4' HGA1 0.09 +ATOM NO4' OG3C51 -0.40 +GROUP +ATOM NN1 NG2R61 -0.07 +ATOM NC6 CG2R62 0.16 +ATOM NH6 HGR63 0.19 +ATOM NC5 CG2R62 -0.10 +ATOM NH5 HGR63 0.16 +ATOM NC4 CG2R62 -0.05 +ATOM NH4 HGR63 0.16 +ATOM NC3 CG2R62 0.05 +ATOM NC2 CG2R62 0.18 +ATOM NH2 HGR63 0.16 +ATOM NC7 CG2O1 0.68 +ATOM NO7 OG2D1 -0.40 +ATOM NN7 NG2S2 -0.82 +ATOM NH71 HGP1 0.34 ! trans to amide O +ATOM NH72 HGP1 0.36 ! cis to amide O + +BOND AN1 AC2 AN3 AC4 AC5 AC6 +BOND AC6 AN6 AC5 AN7 AC8 AN9 +BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 +DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 +BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' +BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AH2T AC2' AH2' +BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' +BOND AC5' AH5S AC5' AH5' AC5' AO5' AO5' AP AP AO1 +BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 +BOND NP NO5' NO5' NC5' NC5' NH5S NC5' NH5' NC5' NC4' +BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' +BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' +BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 +BOND NC3 NC4 NC5 NC6 +BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 +BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6 +DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 +IMPR AC6 AC5 AN1 AN6 +IMPR AN6 AH62 AH61 AC6 +IMPR NC7 NC3 NN7 NO7 +DONO AH61 AN6 +DONO AH62 AN6 +DONO AH2T AO2' +DONO AH3T AO3' +ACCE AN1 +ACCE AN3 +ACCE AN7 +ACCE AO4' +ACCE AO2' +ACCE AO3' +ACCE AO5' +ACCE AO1 AP +ACCE AO2 AP +ACCE O3 +ACCE NO1 NP +ACCE NO2 NP +ACCE NO5' +ACCE NO4' +ACCE NO3' +ACCE NO2' +ACCE NO7 +DONO NH2T NO2' +DONO NH3T NO3' +DONO NH71 NN7 +DONO NH72 NN7 +IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977 +IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863 +IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836 +IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942 +IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756 +IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636 +IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491 +IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232 +IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942 +IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337 +IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942 +IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491 +IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337 +IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415 +IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847 +IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013 +IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777 +IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282 +IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782 +IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146 +IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482 +IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300 +IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648 +IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 +IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 +IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 +IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 +IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 +IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 +IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962 +IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928 +IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294 +IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097 +IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097 +IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105 +IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999 +IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110 +IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000 +IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 +IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 +IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636 +IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977 +IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977 +IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160 +IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160 +IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160 +IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270 +IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100 +IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712 +IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100 +IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270 +IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110 +IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110 +IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110 +IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110 +IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110 +IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110 +IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800 +IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270 +IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160 +IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150 +IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500 +IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600 +IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600 +IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500 +IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199 +IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150 +IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800 +IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300 +IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600 +IC NO7 NC7 NN7 NH71 1.2300 120.00 180.00 120.00 1.0000 +IC NO7 NC7 NN7 NH72 1.2300 120.00 0.00 120.00 1.0000 +IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900 +IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900 +IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900 +IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900 +PATCH FIRST NONE LAST NONE + +RESI NADH -2.00 ! C21H27N7O14P2 reduced nicotinamide adenine dinucleotide, jjp1/adm jr. + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + +GROUP +ATOM AC4' CG3C51 0.11 ! AH61 AH62 +ATOM AH4' HGA1 0.09 ! \ / +ATOM AO4' OG3C51 -0.40 ! AN6 +ATOM AC1' CG3C51 0.11 ! | +ATOM AH1' HGA1 0.09 ! AC6 +GROUP ! // \ +ATOM AC5 CG2RC0 0.28 ! AN1 AC5--AN7\\ +ATOM AN7 NG2R50 -0.71 ! | || AC8-AH8 +ATOM AC8 CG2R53 0.34 ! AC2 AC4--AN9/ +ATOM AH8 HGR52 0.12 ! / \\ / \ +ATOM AN9 NG2R51 -0.05 ! AH2 AN3 \ + ! \ +ATOM AN1 NG2R62 -0.74 ! \ +ATOM AC2 CG2R64 0.50 ! \ +ATOM AH2 HGR62 0.13 ! NO1 AO1 AH5sAH4' AO4' \ +ATOM AN3 NG2R62 -0.75 ! | | | \ / \ \ +ATOM AC4 CG2RC0 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' +ATOM AC6 CG2R64 0.46 ! \ | | | \ / \ + ! \ NO2 AO2 AH5' AC3'-AC2' AH1' +ATOM AN6 NG2S3 -0.77 ! \ / \ / \ +ATOM AH61 HGP4 0.38 ! \ AO3' AH3'AO2'AH2' +ATOM AH62 HGP4 0.38 ! \ | | +GROUP ! \ AH3T AH2T +ATOM AC2' CG3C51 0.14 ! \ NH71 +ATOM AH2' HGA1 0.09 ! \ \ +ATOM AO2' OG311 -0.65 ! \ NH72-NN7 NH4 NH42 +ATOM AH2T HGP1 0.42 ! \ \ \ / +GROUP ! \ NC7 NC4 +ATOM AC3' CG3C51 0.14 ! \ / \ / \ +ATOM AH3' HGA1 0.09 ! \ NO7 NC3 NC5-NH5 +ATOM AO3' OG311 -0.65 ! \ || || +ATOM AH3T HGP1 0.42 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 +GROUP ! \ | \ / \ \ / +ATOM AC5' CG321 -0.08 ! NC5'--NC4' NC1'---------NN1 +ATOM AH5' HGA2 0.09 ! | \ / \ +ATOM AH5S HGA2 0.09 ! NH5' NC3'-NC2'NH1' +ATOM AP PG1 1.50 ! / \ / \ +ATOM AO1 OG2P1 -0.82 ! NO3' NH3'NO2'NH2' +ATOM AO2 OG2P1 -0.82 ! | | +ATOM AO5' OG303 -0.62 ! NH3T NH2T +ATOM O3 OG304 -0.68 +ATOM NP PG1 1.50 +ATOM NO1 OG2P1 -0.82 +ATOM NO2 OG2P1 -0.82 +ATOM NO5' OG303 -0.62 +ATOM NC5' CG321 -0.08 +ATOM NH5S HGA2 0.09 +ATOM NH5' HGA2 0.09 +GROUP +ATOM NC2' CG3C51 0.14 +ATOM NH2' HGA1 0.09 +ATOM NO2' OG311 -0.65 +ATOM NH2T HGP1 0.42 +GROUP +ATOM NC3' CG3C51 0.14 +ATOM NH3' HGA1 0.09 +ATOM NO3' OG311 -0.65 +ATOM NH3T HGP1 0.42 +GROUP +ATOM NC1' CG3C51 0.11 +ATOM NH1' HGA1 0.09 +ATOM NC4' CG3C51 0.11 +ATOM NH4' HGA1 0.09 +ATOM NO4' OG3C51 -0.40 +GROUP +ATOM NN1 NG301 -0.27 !N2 +ATOM NC6 CG2D1O -0.06 !C3 +ATOM NH6 HGA4 0.17 !H4 +ATOM NC5 CG2D1 -0.18 !C5 +ATOM NH5 HGA4 0.14 !H6 +ATOM NC4 CG321 -0.28 !C7 +ATOM NH4 HGA2 0.09 !H8 +ATOM NH42 HGA2 0.09 !H17 +ATOM NC3 CG2DC1 0.36 !C9 +ATOM NC2 CG2D1O -0.10 !C10 +ATOM NH2 HGA4 0.14 !H11 +ATOM NC7 CG2O1 0.55 !C12 +ATOM NO7 OG2D1 -0.51 !O13 +ATOM NN7 NG2S2 -0.72 !N14 +ATOM NH71 HGP1 0.26 !H15 ! trans to amide O +ATOM NH72 HGP1 0.32 !H16 ! cis to amide O + +BOND AN1 AC2 AN3 AC4 AC5 AC6 +BOND AC6 AN6 AC5 AN7 AC8 AN9 +BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 +DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 +BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' +BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AH2T AC2' AH2' +BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' +BOND AC5' AH5S AC5' AH5' AC5' AO5' AO5' AP AP AO1 +BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 +BOND NP NO5' NO5' NC5' NC5' NH5S NC5' NH5' NC5' NC4' +BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' +BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' +BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 +BOND NC3 NC4 NC4 NC5 NC6 NN1 +BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 +BOND NN7 NH72 NC4 NH4 NC4 NH42 NC5 NH5 NC6 NH6 +DOUBLE NC2 NC3 NC5 NC6 +IMPR AC6 AC5 AN1 AN6 +IMPR AN6 AH62 AH61 AC6 +IMPR NC6 NC5 NN1 NH6 +IMPR NC2 NC3 NN1 NH2 +IMPR NC7 NC3 NN7 NO7 +DONO AH61 AN6 +DONO AH62 AN6 +DONO AH2T AO2' +DONO AH3T AO3' +ACCE AN1 +ACCE AN3 +ACCE AN7 +ACCE AO4' +ACCE AO2' +ACCE AO3' +ACCE AO5' +ACCE AO1 AP +ACCE AO2 AP +ACCE O3 +ACCE NO1 NP +ACCE NO2 NP +ACCE NO5' +ACCE NO4' +ACCE NO3' +ACCE NO2' +ACCE NO7 +DONO NH2T NO2' +DONO NH3T NO3' +DONO NH71 NN7 +DONO NH72 NN7 +! IC table was beyond repair ==> replaced (kevo) +IC AP O3 NP NO5' 1.6011 92.88 167.64 96.12 1.6600 +IC AP O3 NP NO1 1.6011 92.88 62.12 118.93 1.5360 +IC AP O3 NP NO2 1.6011 92.88 -85.34 112.47 1.5263 +IC NP O3 AP AO5' 1.6074 92.88 169.27 93.16 1.6636 +IC O3 AO5' *AP AO1 1.6011 93.16 -115.15 102.32 1.5255 +IC O3 AO5' *AP AO2 1.6011 93.16 120.82 100.53 1.5378 +IC O3 AP AO5' AC5' 1.6011 93.16 -65.25 117.89 1.4434 +IC AP AO5' AC5' AC4' 1.6636 117.89 -111.08 111.72 1.5437 +IC AC4' AO5' *AC5' AH5' 1.5437 111.72 121.91 113.03 1.1186 +IC AC4' AO5' *AC5' AH5S 1.5437 111.72 -120.24 108.95 1.1118 +IC AO5' AC5' AC4' AC3' 1.4434 111.72 32.23 115.30 1.5403 +IC AC5' AC4' AC3' AO3' 1.5437 115.30 82.44 113.07 1.4340 +IC AH3T AO3' AC3' AC4' 0.9956 102.19 -78.33 113.07 1.5403 +IC AO4' AC3' *AC4' AC5' 1.4436 105.34 -122.02 115.30 1.5437 +IC AC2' AC4' *AC3' AO3' 1.5312 103.02 -124.10 113.07 1.4340 +IC AC4' AC3' AC2' AC1' 1.5403 103.02 34.98 101.18 1.5414 +IC AC3' AC2' AC1' AN9 1.5312 101.18 88.32 111.78 1.4609 +IC AO4' AC1' AN9 AC4 1.4336 105.95 -149.10 127.35 1.3682 +IC AC1' AC4 *AN9 AC8 1.4609 127.35 179.89 106.85 1.3818 +IC AC4 AN9 AC8 AN7 1.3682 106.85 0.34 112.92 1.3338 +IC AC8 AN9 AC4 AC5 1.3818 106.85 -0.12 105.55 1.3970 +IC AC8 AN7 AC5 AC6 1.3338 103.64 -179.39 132.41 1.4083 +IC AN7 AC5 AC6 AN1 1.3924 132.41 179.90 118.87 1.3616 +IC AC5 AC6 AN1 AC2 1.4083 118.87 -0.29 119.53 1.3626 +IC AN9 AC5 *AC4 AN3 1.3682 105.55 -179.81 125.91 1.3450 +IC AC5 AN1 *AC6 AN6 1.4083 118.87 179.60 117.11 1.3448 +IC AN1 AC6 AN6 AH61 1.3616 117.11 -176.96 119.87 0.9980 +IC AH61 AC6 *AN6 AH62 0.9980 119.87 174.83 117.95 0.9930 +IC AN9 AN7 *AC8 AH8 1.3818 112.92 -179.84 125.33 1.0978 +IC AN1 AN3 *AC2 AH2 1.3626 125.37 -179.78 117.21 1.0932 +IC AO4' AC2' *AC1' AH1' 1.4336 107.49 -118.51 111.70 1.1012 +IC AC1' AC3' *AC2' AH2' 1.5414 101.18 120.60 111.56 1.0994 +IC AC2' AC4' *AC3' AH3' 1.5312 103.02 114.75 109.97 1.1020 +IC AC3' AO4' *AC4' AH4' 1.5403 105.34 -116.63 105.95 1.1009 +IC NC5' NO5' NP NO2 1.4353 125.45 -110.33 103.18 1.5263 +IC NP NO5' NC5' NC4' 1.6600 125.45 -100.01 114.36 1.5573 +IC NO5' NC5' NC4' NC3' 1.4353 114.36 42.03 115.36 1.5403 +IC NC5' NC4' NC3' NC2' 1.5573 115.36 -91.03 101.62 1.5376 +IC NC4' NC3' NC2' NC1' 1.5403 101.62 -39.21 100.72 1.5399 +IC NC3' NC2' NC1' NO4' 1.5376 100.72 35.40 105.65 1.4395 +IC NO2' NC2' NC1' NO4' 1.4392 115.62 158.69 105.65 1.4395 +IC NH2T NO2' NC2' NC1' 0.9686 102.30 157.15 115.62 1.5399 +IC NO4' NC2' *NC1' NH1' 1.4395 105.65 -114.11 109.56 1.1015 +IC NC1' NC3' *NC2 NH2' 2.4605 9.08 131.65 26.20 3.7695 +IC NC2' NC4' *NC3 NH3' 4.7247 22.53 -7.48 17.99 6.8615 +IC NC3' NO4' *NC4 NH4' 6.4634 19.31 -56.73 2.93 7.0769 +IC NC4' NO5' *NC5 NH5' 5.1412 29.29 35.30 14.10 6.2151 +IC NC4' NO5' *NC5 NH5S 5.1412 29.29 55.33 24.87 4.9161 +IC NC3' NC2' NC1' NN1 1.5376 100.72 153.61 113.06 1.4871 +IC NO3' NC3' NC2' NC1' 1.4390 111.69 79.56 100.72 1.5399 +IC NH3T NO3' NC3' NC2' 0.9633 102.31 55.04 111.69 1.5376 +IC NC2' NC1' NN1 NC2 1.5399 113.06 115.33 119.55 1.3595 +IC NC1' NN1 NC2 NC3 1.4871 119.55 179.60 123.83 1.3763 +IC NN1 NC2 NC3 NC4 1.3595 123.83 5.03 118.94 1.5428 +IC NC2 NC3 NC4 NC5 1.3763 118.94 -6.70 111.53 1.5189 +IC NC3 NC4 NC5 NC6 1.5428 111.53 5.08 122.32 1.3550 +IC NN1 NC2 NC3 NC7 1.3595 123.83 -158.70 118.33 1.5212 +IC NC2 NC3 NC7 NO7 1.3763 118.33 -160.59 120.47 1.2354 +IC NC2 NC3 NC7 NN7 1.3763 118.33 20.47 119.04 1.3683 +IC NO7 NC7 NN7 NH71 1.2354 120.48 -176.29 120.56 0.9982 +IC NO7 NC7 NN7 NH72 1.2354 120.48 0.52 116.91 0.9963 +IC NC2 NC3 NC4 NH4 1.3763 118.94 -136.51 113.66 1.1068 +IC NC2 NC3 NC4 NH42 1.3763 118.94 108.33 105.96 1.1115 +IC NC3 NC4 NC5 NH5 1.5428 111.53 -149.76 116.93 1.0907 +IC NC4 NC5 NC6 NH6 1.5189 122.32 179.97 119.29 1.0969 +IC NC6 NN1 NC2 NH2 1.3589 121.05 177.95 116.69 1.0900 +IC AC1' AC3' *AC2' AO2' 1.5414 101.18 -118.90 110.89 1.4319 +IC AC3' AC2' AO2' AH2T 1.5312 110.89 -28.83 100.98 0.9715 +PATCH FIRST NONE LAST NONE + +RESI NADP -2.00 ! C21H26N7O17P3 oxidized nicotinamide adenine dinucleotide, + ! NADP+, adm jr. + ! atom names correspond to pdb nomenclature + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + +GROUP +ATOM AC4' CG3C51 0.11 ! AH61 AH62 +ATOM AH4' HGA1 0.09 ! \ / +ATOM AO4' OG3C51 -0.40 ! AN6 +ATOM AC1' CG3C51 0.11 ! | +ATOM AH1' HGA1 0.09 ! AC6 +GROUP ! // \ +ATOM AC5 CG2RC0 0.28 ! AN1 AC5--AN7\\ +ATOM AN7 NG2R50 -0.71 ! | || AC8-AH8 +ATOM AC8 CG2R53 0.34 ! AC2 AC4--AN9/ +ATOM AH8 HGR52 0.12 ! / \\ / \ +ATOM AN9 NG2R51 -0.05 ! AH2 AN3 \ + ! \ +ATOM AN1 NG2R62 -0.74 ! \ +ATOM AC2 CG2R64 0.50 ! \ +ATOM AH2 HGR62 0.13 ! NO1 AO1 AH5sAH4' AO4' \ +ATOM AN3 NG2R62 -0.75 ! | | | \ / \ \ +ATOM AC4 CG2RC0 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' +ATOM AC6 CG2R64 0.46 ! \ | | | \ / \ + ! \ NO2 AO2 AH5' AC3'-AC2' AH1' +ATOM AN6 NG2S3 -0.77 ! \ / \ / \ +ATOM AH61 HGP4 0.38 ! \ AO3' AH3'AO2'AH2' +ATOM AH62 HGP4 0.38 ! \ | | +GROUP ! \ AH3T AO1P=AP2==AO2P (-) +ATOM AC2' CG3C51 0.01 ! \ | NH71 +ATOM AH2' HGA1 0.09 ! \ AH2T-AO2T / +ATOM AO2' OG303 -0.62 ! \ NH72-NN7 NH4 +ATOM AP2 PG1 1.50 ! \ \ | +ATOM AO1P OG2P1 -0.82 ! \ NC7 NC4 +ATOM AO2P OG2P1 -0.82 ! \ / \ / \\ +ATOM AO2T OG311 -0.67 ! \ NO7 NC3 NC5-NH5 +ATOM AH2T HGP1 0.33 ! \ || | +GROUP ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 +ATOM AC3' CG3C51 0.14 ! \ | \ / \ \+ // +ATOM AH3' HGA1 0.09 ! NC5'--NC4' NC1'---------NN1 +ATOM AO3' OG311 -0.65 ! | \ / \ +ATOM AH3T HGP1 0.42 ! NH5' NC3'-NC2'NH1' +GROUP ! / \ / \ +ATOM AC5' CG321 -0.08 ! NO3' NH3'NO2'NH2' +ATOM AH5' HGA2 0.09 ! | | +ATOM AH5S HGA2 0.09 ! NH3T NH2T +ATOM AP PG1 1.50 +ATOM AO1 OG2P1 -0.82 +ATOM AO2 OG2P1 -0.82 +ATOM AO5' OG303 -0.62 +ATOM O3 OG304 -0.68 +ATOM NP PG1 1.50 +ATOM NO1 OG2P1 -0.82 +ATOM NO2 OG2P1 -0.82 +ATOM NO5' OG303 -0.62 +ATOM NC5' CG321 -0.08 +ATOM NH5S HGA2 0.09 +ATOM NH5' HGA2 0.09 +GROUP +ATOM NC2' CG3C51 0.14 +ATOM NH2' HGA1 0.09 +ATOM NO2' OG311 -0.65 +ATOM NH2T HGP1 0.42 +GROUP +ATOM NC3' CG3C51 0.14 +ATOM NH3' HGA1 0.09 +ATOM NO3' OG311 -0.65 +ATOM NH3T HGP1 0.42 +GROUP +ATOM NC1' CG3C53 0.11 +ATOM NH1' HGA1 0.09 +ATOM NC4' CG3C51 0.11 +ATOM NH4' HGA1 0.09 +ATOM NO4' OG3C51 -0.40 +GROUP +ATOM NN1 NG2R61 -0.07 +ATOM NC6 CG2R62 0.16 +ATOM NH6 HGR63 0.19 +ATOM NC5 CG2R62 -0.10 +ATOM NH5 HGR63 0.16 +ATOM NC4 CG2R62 -0.05 +ATOM NH4 HGR63 0.16 +ATOM NC3 CG2R62 0.05 +ATOM NC2 CG2R62 0.18 +ATOM NH2 HGR63 0.16 +ATOM NC7 CG2O1 0.68 +ATOM NO7 OG2D1 -0.40 +ATOM NN7 NG2S2 -0.82 +ATOM NH71 HGP1 0.34 ! trans to amide O +ATOM NH72 HGP1 0.36 ! cis to amide O + +BOND AN1 AC2 AN3 AC4 AC5 AC6 +BOND AC6 AN6 AC5 AN7 AC8 AN9 +BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 +DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 +BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' +BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2' +BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' +BOND AC5' AH5S AC5' AH5' AC5' AO5' AO5' AP AP AO1 +BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 +BOND NP NO5' NO5' NC5' NC5' NH5S NC5' NH5' NC5' NC4' +BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' +BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' +BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 +BOND NC3 NC4 NC5 NC6 +BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 +BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6 +BOND AP2 AO1P AP2 AO2P AP2 AO2T AO2T AH2T +DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 +IMPR AC6 AC5 AN1 AN6 +IMPR AN6 AH62 AH61 AC6 +IMPR NC7 NC3 NN7 NO7 +DONO AH61 AN6 +DONO AH62 AN6 +DONO AH3T AO3' +ACCE AN1 +ACCE AN3 +ACCE AN7 +ACCE AO4' +ACCE AO2' +ACCE AO3' +ACCE AO5' +ACCE AO1 AP +ACCE AO2 AP +ACCE O3 +ACCE NO1 NP +ACCE NO2 NP +ACCE NO5' +ACCE NO4' +ACCE NO3' +ACCE NO2' +ACCE NO7 +DONO NH2T NO2' +DONO NH3T NO3' +DONO NH71 NN7 +DONO NH72 NN7 +DONO AH2T AO2T +ACCE AO2T +ACCE AO1P +ACCE AO2P +ACCE AO2' +IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977 +IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863 +IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836 +IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942 +IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756 +IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636 +IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491 +IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232 +IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942 +IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337 +IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942 +IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491 +IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337 +IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415 +IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847 +IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013 +IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777 +IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282 +IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782 +IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146 +IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482 +IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300 +IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648 +IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 +IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 +IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 +IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 +IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 +IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 +IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962 +IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928 +IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294 +IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097 +!IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097 +IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105 +IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999 +IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110 +IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000 +IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 +IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 +IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636 +IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977 +IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977 +IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160 +IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160 +IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160 +IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270 +IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100 +IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712 +IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100 +IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270 +IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110 +IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110 +IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110 +IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110 +IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110 +IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110 +IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800 +IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270 +IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160 +IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150 +IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500 +IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600 +IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600 +IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500 +IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199 +IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150 +IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800 +IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300 +IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600 +IC NO7 NC7 NN7 NH71 1.2300 0.00 180.00 120.00 1.0000 +IC NO7 NC7 NN7 NH72 1.2300 0.00 0.00 120.00 1.0000 +IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900 +IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900 +IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900 +IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900 +IC AC3' AC2' AO2' AP2 0.0000 000.00 180.00 000.00 0.0000 +IC AC2' AO2' AP2 AO2T 0.0000 000.00 -39.52 000.00 0.0000 +IC AO2T AO2' *AP2 AO1P 0.0000 000.00 -115.82 000.00 0.0000 +IC AO2T AO2' *AP2 AO2P 0.0000 000.00 115.90 000.00 0.0000 +IC AH2T AO2T AP2 AO2' 0.0000 000.00 180.00 000.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI NDPH -3.00 ! C21H27N7O17P3 reduced nicotinamide adenine dinucleotide + ! NADPH, VARNAI/adm jr. + ! from RESI NADH and 3PHO + ! checked for consistency with new NA params, adm jr., 9/98 + ! note that differences with respect to published results exist + ! due to new NA params + +GROUP +ATOM AC4' CG3C51 0.11 ! AH61 AH62 +ATOM AH4' HGA1 0.09 ! \ / +ATOM AO4' OG3C51 -0.40 ! AN6 +ATOM AC1' CG3C51 0.11 ! | +ATOM AH1' HGA1 0.09 ! AC6 +GROUP ! // \ +ATOM AC5 CG2RC0 0.28 ! AN1 AC5--AN7\\ +ATOM AN7 NG2R50 -0.71 ! | || AC8-AH8 +ATOM AC8 CG2R53 0.34 ! AC2 AC4--AN9/ +ATOM AH8 HGR52 0.12 ! / \\ / \ +ATOM AN9 NG2R51 -0.05 ! AH2 AN3 \ + ! \ +ATOM AN1 NG2R62 -0.74 ! \ +ATOM AC2 CG2R64 0.50 ! \ +ATOM AH2 HGR62 0.13 ! NO1 AO1 AH5sAH4' AO4' \ +ATOM AN3 NG2R62 -0.75 ! | | | \ / \ \ +ATOM AC4 CG2RC0 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' +ATOM AC6 CG2R64 0.46 ! \ | | | \ / \ + ! \ NO2 AO2 AH5' AC3'-AC2' AH1' +ATOM AN6 NG2S3 -0.77 ! \ / \ / \ +ATOM AH61 HGP4 0.38 ! \ AO3' AH3'AO2'AH2' +ATOM AH62 HGP4 0.38 ! \ | | +GROUP ! \ AH3T AO1P=AP2==AO2P (-) +ATOM AC2' CG3C51 0.01 ! \ | NH71 +ATOM AH2' HGA1 0.09 ! \ AH2T-AO2T / +ATOM AO2' OG303 -0.62 ! \ NH72-NN7 NH4 NH42 +ATOM AP2 PG1 1.50 ! \ \ \ / +ATOM AO1P OG2P1 -0.82 ! \ NC7 NC4 +ATOM AO2P OG2P1 -0.82 ! \ / \ / \ +ATOM AO2T OG311 -0.67 ! \ NO7 NC3 NC5-NH5 +ATOM AH2T HGP1 0.33 ! \ || || +GROUP ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 +ATOM AC3' CG3C51 0.14 ! \ | \ / \ \ / +ATOM AH3' HGA1 0.09 ! NC5'--NC4' NC1'---------NN1 +ATOM AO3' OG311 -0.65 ! | \ / \ +ATOM AH3T HGP1 0.42 ! NH5' NC3'-NC2'NH1' +GROUP ! / \ / \ +ATOM AC5' CG321 -0.08 ! NO3' NH3'NO2'NH2' +ATOM AH5' HGA2 0.09 ! | | +ATOM AH5S HGA2 0.09 ! NH3T NH2T +ATOM AP PG1 1.50 +ATOM AO1 OG2P1 -0.82 +ATOM AO2 OG2P1 -0.82 +ATOM AO5' OG303 -0.62 +ATOM O3 OG304 -0.68 +ATOM NP PG1 1.50 +ATOM NO1 OG2P1 -0.82 +ATOM NO2 OG2P1 -0.82 +ATOM NO5' OG303 -0.62 +ATOM NC5' CG321 -0.08 +ATOM NH5S HGA2 0.09 +ATOM NH5' HGA2 0.09 +GROUP +ATOM NC2' CG3C51 0.14 +ATOM NH2' HGA1 0.09 +ATOM NO2' OG311 -0.65 +ATOM NH2T HGP1 0.42 +GROUP +ATOM NC3' CG3C51 0.14 +ATOM NH3' HGA1 0.09 +ATOM NO3' OG311 -0.65 +ATOM NH3T HGP1 0.42 +GROUP +ATOM NC1' CG3C51 0.11 +ATOM NH1' HGA1 0.09 +ATOM NC4' CG3C51 0.11 +ATOM NH4' HGA1 0.09 +ATOM NO4' OG3C51 -0.40 +GROUP +ATOM NN1 NG301 -0.27 !N2 +ATOM NC6 CG2D1O -0.06 !C3 +ATOM NH6 HGA4 0.17 !H4 +ATOM NC5 CG2D1 -0.18 !C5 +ATOM NH5 HGA4 0.14 !H6 +ATOM NC4 CG321 -0.28 !C7 +ATOM NH4 HGA2 0.09 !H8 +ATOM NH42 HGA2 0.09 !H17 +ATOM NC3 CG2DC1 0.36 !C9 +ATOM NC2 CG2D1O -0.10 !C10 +ATOM NH2 HGA4 0.14 !H11 +ATOM NC7 CG2O1 0.55 !C12 +ATOM NO7 OG2D1 -0.51 !O13 +ATOM NN7 NG2S2 -0.72 !N14 +ATOM NH71 HGP1 0.26 !H15 ! trans to amide O +ATOM NH72 HGP1 0.32 !H16 ! cis to amide O +BOND AN1 AC2 AN3 AC4 AC5 AC6 +BOND AC6 AN6 AC5 AN7 AC8 AN9 +BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 +DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 +BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' +BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2' +BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' +BOND AC5' AH5S AC5' AH5' AC5' AO5' AO5' AP AP AO1 +BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 +BOND NP NO5' NO5' NC5' NC5' NH5S NC5' NH5' NC5' NC4' +BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' +BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' +BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 +BOND NC3 NC4 NC4 NC5 NC6 NN1 +BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 +BOND NN7 NH72 NC4 NH4 NC4 NH42 NC5 NH5 NC6 NH6 +BOND AP2 AO1P AP2 AO2P AP2 AO2T AO2T AH2T +DOUBLE NC2 NC3 NC5 NC6 +IMPR AC6 AC5 AN1 AN6 +IMPR AN6 AH62 AH61 AC6 +IMPR NC6 NC5 NN1 NH6 +IMPR NC2 NC3 NN1 NH2 +IMPR NC7 NC3 NN7 NO7 +DONO AH61 AN6 +DONO AH62 AN6 +DONO AH3T AO3' +ACCE AN1 +ACCE AN3 +ACCE AN7 +ACCE AO4' +ACCE AO3' +ACCE AO5' +ACCE AO1 AP +ACCE AO2 AP +ACCE O3 +ACCE NO1 NP +ACCE NO2 NP +ACCE NO5' +ACCE NO4' +ACCE NO3' +ACCE NO2' +ACCE NO7 +DONO NH2T NO2' +DONO NH3T NO3' +DONO NH71 NN7 +DONO NH72 NN7 +DONO AH2T AO2T +ACCE AO2T +ACCE AO1P +ACCE AO2P +ACCE AO2' +! IC table was beyond repair ==> replaced (kevo) +IC AP O3 NP NO5' 1.5954 101.60 146.76 97.71 1.6612 +IC AP O3 NP NO1 1.5954 101.60 37.78 120.83 1.5331 +IC AP O3 NP NO2 1.5954 101.60 -103.74 108.35 1.5264 +IC NP O3 AP AO5' 1.6061 101.60 164.74 96.46 1.6655 +IC O3 AO5' *AP AO1 1.5954 96.46 -112.08 103.67 1.5327 +IC O3 AO5' *AP AO2 1.5954 96.46 120.37 104.32 1.5300 +IC O3 AP AO5' AC5' 1.5954 96.46 -55.54 115.61 1.4409 +IC AP AO5' AC5' AC4' 1.6655 115.61 -176.43 112.56 1.5479 +IC AC4' AO5' *AC5' AH5' 1.5479 112.56 120.22 110.27 1.1161 +IC AC4' AO5' *AC5' AH5S 1.5479 112.56 -120.20 110.70 1.1158 +IC AO5' AC5' AC4' AC3' 1.4409 112.56 51.86 114.73 1.5409 +IC AC5' AC4' AC3' AO3' 1.5479 114.73 138.72 111.81 1.4297 +IC AH3T AO3' AC3' AC4' 0.9769 98.08 131.19 111.81 1.5409 +IC AO4' AC3' *AC4' AC5' 1.4383 107.54 -123.87 114.73 1.5479 +IC AC2' AC4' *AC3' AO3' 1.5457 105.32 -117.01 111.81 1.4297 +IC AC4' AC3' AC2' AC1' 1.5409 105.32 -20.11 102.83 1.5465 +IC AC3' AC2' AC1' AN9 1.5457 102.83 133.28 112.16 1.4587 +IC AO4' AC1' AN9 AC4 1.4312 106.95 -116.73 127.46 1.3677 +IC AC1' AC4 *AN9 AC8 1.4587 127.46 -179.84 106.79 1.3782 +IC AC4 AN9 AC8 AN7 1.3677 106.79 0.68 113.34 1.3348 +IC AC8 AN9 AC4 AC5 1.3782 106.79 -0.37 105.46 1.3976 +IC AC8 AN7 AC5 AC6 1.3348 103.19 179.17 132.19 1.4074 +IC AN7 AC5 AC6 AN1 1.3939 132.19 -179.58 119.12 1.3630 +IC AC5 AC6 AN1 AC2 1.4074 119.12 -0.76 119.15 1.3635 +IC AN9 AC5 *AC4 AN3 1.3677 105.46 179.47 125.74 1.3491 +IC AC5 AN1 *AC6 AN6 1.4074 119.12 -178.70 117.19 1.3459 +IC AN1 AC6 AN6 AH61 1.3630 117.19 175.38 119.41 0.9983 +IC AH61 AC6 *AN6 AH62 0.9983 119.41 -173.82 118.04 0.9911 +IC AN9 AN7 *AC8 AH8 1.3782 113.34 -179.89 124.72 1.0924 +IC AN1 AN3 *AC2 AH2 1.3635 125.66 -177.12 116.89 1.0924 +IC AO4' AC2' *AC1' AH1' 1.4312 109.65 -115.54 110.14 1.1011 +IC AC1' AC3' *AC2' AH2' 1.5465 102.83 118.17 107.40 1.1056 +IC AC2' AC4' *AC3' AH3' 1.5457 105.32 120.87 111.10 1.0996 +IC AC3' AO4' *AC4' AH4' 1.5409 107.54 -117.93 106.34 1.1019 +IC NC5' NO5' NP NO2 1.4347 124.65 -95.76 105.77 1.5264 +IC NP NO5' NC5' NC4' 1.6612 124.65 -102.77 115.34 1.5645 +IC NO5' NC5' NC4' NC3' 1.4347 115.34 72.35 114.08 1.5406 +IC NC5' NC4' NC3' NC2' 1.5645 114.08 -96.03 100.78 1.5383 +IC NC4' NC3' NC2' NC1' 1.5406 100.78 -41.51 100.30 1.5383 +IC NC3' NC2' NC1' NO4' 1.5383 100.30 39.58 104.62 1.4444 +IC NO2' NC2' NC1' NO4' 1.4360 117.19 163.91 104.62 1.4444 +IC NH2T NO2' NC2' NC1' 0.9842 100.86 159.27 117.19 1.5383 +IC NO4' NC2' *NC1' NH1' 1.4444 104.62 -113.82 109.33 1.1012 +IC NC1' NC3' *NC2 NH2' 2.4561 9.02 118.36 26.48 3.8155 +IC NC2' NC4' *NC3 NH3' 4.7358 22.19 -3.45 17.84 6.8914 +IC NC3' NO4' *NC4 NH4' 6.4975 19.19 -28.86 1.80 7.1052 +IC NC4' NO5' *NC5 NH5' 5.2257 29.02 -4.03 10.68 6.4109 +IC NC4' NO5' *NC5 NH5S 5.2257 29.02 51.20 19.04 5.7156 +IC NC3' NC2' NC1' NN1 1.5383 100.30 157.86 113.54 1.4868 +IC NO3' NC3' NC2' NC1' 1.4402 112.92 77.43 100.30 1.5383 +IC NH3T NO3' NC3' NC2' 0.9765 102.62 77.94 112.92 1.5383 +IC NC2' NC1' NN1 NC2 1.5383 113.54 116.11 119.27 1.3589 +IC NC1' NN1 NC2 NC3 1.4868 119.27 179.46 123.90 1.3767 +IC NN1 NC2 NC3 NC4 1.3589 123.90 5.63 118.97 1.5415 +IC NC2 NC3 NC4 NC5 1.3767 118.97 -6.62 111.44 1.5185 +IC NC3 NC4 NC5 NC6 1.5415 111.44 4.92 122.41 1.3553 +IC NN1 NC2 NC3 NC7 1.3589 123.90 -157.15 117.98 1.5220 +IC NC2 NC3 NC7 NO7 1.3767 117.98 -162.23 120.57 1.2364 +IC NC2 NC3 NC7 NN7 1.3767 117.98 18.92 119.12 1.3682 +IC NO7 NC7 NN7 NH71 1.2364 120.30 -176.87 120.26 0.9992 +IC NO7 NC7 NN7 NH72 1.2364 120.30 1.04 117.08 0.9956 +IC NC2 NC3 NC4 NH4 1.3767 118.97 -136.44 113.82 1.1070 +IC NC2 NC3 NC4 NH42 1.3767 118.97 108.13 105.93 1.1113 +IC NC3 NC4 NC5 NH5 1.5415 111.44 -151.27 117.50 1.0907 +IC NC4 NC5 NC6 NH6 1.5185 122.41 178.77 119.10 1.0963 +IC NC6 NN1 NC2 NH2 1.3587 120.94 176.28 116.55 1.0900 +IC AC1' AC3' *AC2' AO2' 1.5465 102.83 -119.62 111.15 1.4465 +IC AC3' AC2' AO2' AP2 1.5457 111.15 -174.33 121.36 1.5853 +IC AC2' AO2' AP2 AO2T 1.4465 121.36 -92.28 103.37 1.5606 +IC AO2T AO2' *AP2 AO1P 1.5606 103.37 -113.56 111.24 1.4737 +IC AO2T AO2' *AP2 AO2P 1.5606 103.37 109.47 111.16 1.4708 +IC AO2' AP2 AO2T AH2T 1.5853 103.37 81.16 108.83 0.9674 +PATCH FIRST NONE LAST NONE + +!toppar_amines.str + +RESI AMM1 0.00 ! NH3 Ammonia +GROUP +ATOM N1 NG331 -1.125 +ATOM H11 HGPAM3 0.375 +ATOM H12 HGPAM3 0.375 +ATOM H13 HGPAM3 0.375 +BOND N1 H11 N1 H12 N1 H13 +IC H11 H12 *N1 H13 0.0 0.0 120. 0.0 0.0 +IC H13 H11 *N1 H12 0.0 0.0 120. 0.0 0.0 !redundant definition needed to enable seeding. + +RESI MAM1 0.00 ! CH5N methylamine +GROUP +ATOM N1 NG321 -0.99 +ATOM C1 CG3AM2 -0.06 ! HC1 HN1 +ATOM HN1 HGPAM2 0.39 ! \ / +ATOM HN2 HGPAM2 0.39 ! HC2-C1---N1 +ATOM HC1 HGAAM2 0.09 ! / \ +ATOM HC2 HGAAM2 0.09 ! HC3 HN2 +ATOM HC3 HGAAM2 0.09 +BOND N1 C1 N1 HN1 N1 HN2 +BOND C1 HC1 C1 HC2 C1 HC3 +IC N1 HC1 *C1 HC2 0.00 0.00 120.0 0.0 0.0 +IC N1 HC1 *C1 HC3 0.00 0.00 -120.0 0.0 0.0 +IC HC1 C1 N1 HN1 0.00 0.00 180.0 0.0 0.0 +IC C1 HN1 *N1 HN2 0.00 0.00 120.0 0.0 0.0 + +RESI DMAM 0.00 ! C2H7N dimethylamine +GROUP +ATOM N1 NG311 -0.82 +ATOM HN1 HGPAM1 0.40 +ATOM C1 CG3AM1 -0.06 ! H11 HN1 +ATOM C2 CG3AM1 -0.06 ! \ / +ATOM H11 HGAAM1 0.09 ! H12-C1---N1 +ATOM H12 HGAAM1 0.09 ! / \ +ATOM H13 HGAAM1 0.09 ! H13 C2-H23 +ATOM H21 HGAAM1 0.09 ! / \ +ATOM H22 HGAAM1 0.09 ! H21 H22 +ATOM H23 HGAAM1 0.09 +BOND N1 HN1 N1 C1 N1 C2 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IC C1 N1 C2 H21 0.00 0.00 180.0 0.0 0.0 +IC N1 H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 +IC N1 H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 +IC C1 C2 *N1 HN1 0.00 0.00 120.0 0.0 0.0 +IC C2 N1 C1 H11 0.00 0.00 180.0 0.0 0.0 +IC N1 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 +IC N1 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 + +RESI TMAM 0.00 ! C3H9N trimethylamine, adm jr. +GROUP ! H31 H32 +ATOM N1 NG301 -0.63 ! \ / +ATOM C1 CG3AM0 -0.06 ! H11 C3-H33 +ATOM C2 CG3AM0 -0.06 ! \ / +ATOM C3 CG3AM0 -0.06 ! H12-C1---N1 +ATOM H11 HGAAM0 0.09 ! / \ +ATOM H12 HGAAM0 0.09 ! H13 C2-H23 +ATOM H13 HGAAM0 0.09 ! / \ +ATOM H21 HGAAM0 0.09 ! H21 H22 +ATOM H22 HGAAM0 0.09 +ATOM H23 HGAAM0 0.09 +ATOM H31 HGAAM0 0.09 +ATOM H32 HGAAM0 0.09 +ATOM H33 HGAAM0 0.09 +BOND N1 C1 N1 C2 N1 C3 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +IC C1 C2 *N1 C3 0.00 0.00 120.0 0.0 0.0 +IC C2 N1 C1 H11 0.00 0.00 180.0 0.0 0.0 +IC N1 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 +IC N1 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 +IC C1 N1 C2 H21 0.00 0.00 180.0 0.0 0.0 +IC N1 H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 +IC N1 H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 +IC C1 N1 C3 H31 0.00 0.00 180.0 0.0 0.0 +IC N1 H31 *C3 H32 0.00 0.00 120.0 0.0 0.0 +IC N1 H31 *C3 H33 0.00 0.00 -120.0 0.0 0.0 + +!toppar_prot_na_all.str +RESI PPH1 -1.00 ! C6H6O4P phenol phosphate residue +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 ! CD1--CE1 +ATOM HD1 HGR61 0.115 ! // \\ +GROUP ! HG--CG CZ--OH O2-H2 +ATOM CD2 CG2R61 -0.115 ! \ __ / \ / +ATOM HD2 HGR61 0.115 ! CD2--CE2 P1 (-) +GROUP ! | | // \\ +ATOM CE1 CG2R61 -0.21 ! HD2 HE2 O4 O3 +ATOM HE1 HGR61 0.21 +GROUP +ATOM CE2 CG2R61 -0.21 +ATOM HE2 HGR61 0.21 +GROUP +ATOM CZ CG2R61 -0.16 +ATOM OH OG303 -0.36 +ATOM P1 PG1 1.40 +ATOM O2 OG311 -0.75 +ATOM H2 HGP1 0.39 +ATOM O3 OG2P1 -0.76 +ATOM O4 OG2P1 -0.76 + +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ OH +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND P1 OH P1 O2 P1 O3 P1 O4 +BOND O2 H2 + +! IC table +IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 +IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CE1 *CZ OH 1.3750 120.00 180.00 120.00 1.3800 +IC CE1 CZ OH P1 1.3750 120.00 90.00 120.00 1.6100 +IC CZ OH P1 O2 1.3800 120.00 300.00 108.00 1.5800 +IC O2 OH *P1 O3 1.5800 108.00 120.00 103.00 1.4800 +IC O2 OH *P1 O4 1.5800 108.00 -120.00 103.00 1.4800 +IC OH P1 O2 H2 1.6100 108.00 180.00 115.00 0.9600 + +RESI BMPH -1.00 ! C7H8O3P Benzylphosphonate +GROUP +ATOM CG CG2R61 -0.115 ! HD1 HE1 +ATOM HG HGR61 0.115 ! | | +GROUP ! CD1--CE1 HH1 O2-H2 +ATOM CD1 CG2R61 -0.115 ! // \\ \ / +ATOM HD1 HGR61 0.115 ! HG--CG CZ---CH---P1 (-) +GROUP ! \ __ / / //\\ +ATOM CD2 CG2R61 -0.115 ! CD2--CE2 HH2 O4 O3 +ATOM HD2 HGR61 0.115 ! | | +GROUP ! HD2 HE2 +ATOM CE1 CG2R61 -0.21 +ATOM HE1 HGR61 0.24 +ATOM CE2 CG2R61 -0.21 +ATOM HE2 HGR61 0.24 +ATOM CZ CG2R61 -0.44 +ATOM CH CG321 -0.18 +ATOM HH1 HGA2 0.09 +ATOM HH2 HGA2 0.09 +ATOM P1 PG1 1.53 +ATOM O2 OG311 -0.79 +ATOM H2 HGP1 0.36 +ATOM O3 OG2P1 -0.86 +ATOM O4 OG2P1 -0.86 + ! NA ATOM TYPE +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ CH +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CH HH1 CH HH2 CH P1 P1 O2 P1 O3 +BOND P1 O4 O2 H2 +! IC table +IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 +IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 +IC CE2 CE1 *CZ CH 1.3750 120.00 180.00 122.30 1.4900 +IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CZ CH P1 1.3750 122.30 270.00 111.00 1.8800 +IC P1 CZ *CH HH1 1.8800 111.00 120.00 107.50 1.1110 +IC HH1 CZ *CH HH2 1.1110 107.50 -120.00 107.50 1.1110 +IC CZ CH P1 O2 1.4900 111.00 180.00 93.00 1.5800 +IC O2 CH *P1 O3 1.5800 93.00 120.00 103.00 1.4800 +IC O2 CH *P1 O4 1.5800 93.00 -120.00 103.00 1.4800 +IC CH P1 O2 H2 1.8800 93.00 120.00 115.00 0.9600 + +RESI BMPD -2.00 ! C7H7O3P Benzylphosphonate dianionic +GROUP +ATOM CG CG2R61 -0.115 ! HD1 HE1 +ATOM HG HGR61 0.115 ! | | +GROUP ! CD1--CE1 HH1 O2 +ATOM CD1 CG2R61 -0.115 ! // \\ \ / +ATOM HD1 HGR61 0.115 ! HG--CG CZ---CH---P1 (-2) +GROUP ! \ __ / / //\\ +ATOM CD2 CG2R61 -0.115 ! CD2--CE2 HH2 O4 O3 +ATOM HD2 HGR61 0.115 ! | | +GROUP HD2 HE2 +ATOM CE1 CG2R61 -0.24 +ATOM HE1 HGR61 0.26 +ATOM CE2 CG2R61 -0.24 +ATOM HE2 HGR61 0.26 +ATOM CZ CG2R61 -0.45 +ATOM CH CG321 -0.28 +ATOM HH1 HGA2 0.09 +ATOM HH2 HGA2 0.09 +ATOM P1 PG2 1.90 +ATOM O2 OG2P1 -1.13 +ATOM O3 OG2P1 -1.13 +ATOM O4 OG2P1 -1.13 +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ CH +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CH HH1 CH HH2 CH P1 P1 O2 P1 O3 +BOND P1 O4 +! IC table + +IC CE1 CZ CH P1 0.0000 000.00 90.00 000.00 0.0000 +IC CZ CH P1 O2 0.0000 000.00 180.00 000.00 0.0000 +IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O2 CH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 +IC O2 CH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 +IC CD1 CE1 CZ CH 0.0000 000.00 180.00 000.00 0.0000 +IC HD1 CD1 CG CD2 0.0000 000.00 180.00 000.00 0.0000 +IC CG CD1 CE1 CZ 0.0000 000.00 0.00 000.00 0.0000 +IC HG CG CD1 CE1 0.0000 000.00 180.00 000.00 0.0000 +IC CD2 CG CD1 CE1 0.0000 000.00 0.00 000.00 0.0000 +IC HD2 CD2 CG HG 0.0000 000.00 0.00 000.00 0.0000 +IC CE2 CD2 CG CD1 0.0000 000.00 0.00 000.00 0.0000 +IC HH1 CH P1 O3 0.0000 000.00 180.00 000.00 0.0000 +IC HH2 CH P1 O3 0.0000 000.00 0.00 000.00 0.0000 +IC HE1 CE1 CD1 HD1 0.0000 000.00 0.00 000.00 0.0000 +IC HE2 CE2 CD2 HD2 0.0000 000.00 0.00 000.00 0.0000 + +RESI BDFP -1.00 ! C7H6F2O3P Difuorobenzylphosphonate +GROUP +ATOM CG CG2R61 -0.115 ! HD1 HE1 +ATOM HG HGR61 0.115 ! | | +GROUP CD1--CE1 F1 O2-H2 +ATOM CD1 CG2R61 -0.115 ! // \\ \ / +ATOM HD1 HGR61 0.115 ! HG--CG CZ---CF---P1 (-) +GROUP \ __ / / //\\ +ATOM CD2 CG2R61 -0.115 ! CD2--CE2 F2 O4 O3 +ATOM HD2 HGR61 0.115 ! | | +GROUP HD2 HE2 +ATOM CE1 CG2R61 -0.21 +ATOM HE1 HGR61 0.24 +ATOM CE2 CG2R61 -0.21 +ATOM HE2 HGR61 0.24 +ATOM CZ CG2R61 -0.40 +ATOM CF CG312 0.21 +ATOM F1 FGA2 -0.17 +ATOM F2 FGA2 -0.17 +ATOM P1 PG1 1.43 +ATOM O2 OG311 -0.72 +ATOM H2 HGP1 0.36 +ATOM O3 OG2P1 -0.80 +ATOM O4 OG2P1 -0.80 + +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ CF +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CF F1 CF F2 CF P1 P1 O2 P1 O3 +BOND P1 O4 O2 H2 +! IC table +IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 +IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 +IC CE2 CE1 *CZ CF 1.3750 120.00 180.00 120.00 1.4500 +IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CZ CF P1 1.3750 120.00 270.00 115.00 1.8800 +IC P1 CZ *CF F1 1.8800 115.00 120.00 118.00 1.3530 +IC F1 CZ *CF F2 1.3530 118.00 -120.00 118.00 1.3530 +IC CZ CF P1 O2 1.4500 115.00 180.00 86.00 1.5800 +IC O2 CF *P1 O3 1.5800 86.00 120.00 95.00 1.4800 +IC O2 CF *P1 O4 1.5800 86.00 -120.00 95.00 1.4800 +IC CF P1 O2 H2 1.8800 86.00 180.00 115.00 0.9600 + +RESI BDFD -2.00 ! C7H5F2O3P Difuorobenzylphosphonate dianionic, chris +GROUP +ATOM CG CG2R61 -0.115 ! HD1 HE1 +ATOM HG HGR61 0.115 ! | | +GROUP CD1--CE1 F1 O2 +ATOM CD1 CG2R61 -0.115 ! // \\ \ / +ATOM HD1 HGR61 0.115 ! HG--CG CZ---CF---P1 (-2) +GROUP \ __ / / //\\ +ATOM CD2 CG2R61 -0.115 ! CD2--CE2 F2 O4 O3 +ATOM HD2 HGR61 0.115 ! | | +GROUP HD2 HE2 +ATOM CE1 CG2R61 -0.24 +ATOM HE1 HGR61 0.26 +ATOM CE2 CG2R61 -0.24 +ATOM HE2 HGR61 0.26 +ATOM CZ CG2R61 -0.36 +ATOM CF CG312 0.24 +ATOM F1 FGA2 -0.28 +ATOM F2 FGA2 -0.28 +ATOM P1 PG2 2.00 +ATOM O2 OG2P1 -1.12 +ATOM O3 OG2P1 -1.12 +ATOM O4 OG2P1 -1.12 + +BOND CG CD1 CG CD2 CD1 CE1 CD2 CE2 +BOND CE1 CZ CE2 CZ CZ CF +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CF F1 CF F2 CF P1 P1 O2 P1 O3 +BOND P1 O4 + +! IC table +IC CD2 CG CD1 CE1 1.3750 120.00 0.00 120.00 1.3750 +IC CD1 CG CD2 CE2 1.3750 120.00 0.00 120.00 1.3750 +IC CG CD1 CE1 CZ 1.3750 120.00 0.00 120.00 1.3750 +IC CE2 CE1 *CZ CF 1.3750 120.00 180.00 120.00 1.4500 +IC CD1 CD2 *CG HG 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.3750 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.3750 120.00 180.00 120.00 1.0800 +IC CE1 CZ CF P1 1.3750 120.00 90.00 115.00 1.8800 +IC P1 CZ *CF F1 1.8800 115.00 120.00 118.00 1.3530 +IC F1 CZ *CF F2 1.3530 118.00 -120.00 118.00 1.3530 +IC CZ CF P1 O2 1.4500 115.00 180.00 95.00 1.4800 +IC O2 CF *P1 O3 1.4800 95.00 120.00 95.00 1.4800 +IC O2 CF *P1 O4 1.4800 95.00 -120.00 95.00 1.4800 + +RESI EP_2 -2.00 ! C2H5O4P Ethylphosphate, dianionic +!test CT3-CT2-ON2-P dihedral without complications from phosphate proton +GROUP ! H21 +ATOM P1 PG2 1.10 ! | +ATOM O1 OG303 -0.40 ! H23--C2--H22 +ATOM O2 OG2P1 -0.90 ! | +ATOM O3 OG2P1 -0.90 ! H11--C1--H12 +ATOM O4 OG2P1 -0.90 ! | +GROUP ! O1 +ATOM C1 CG321 -0.18 ! | +ATOM H11 HGA2 0.09 ! (-) O4==P1==O3 (-) +ATOM H12 HGA2 0.09 ! || +GROUP ! O2 +ATOM C2 CG331 -0.27 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 H12 C1 C2 +BOND C2 H21 C2 H22 C2 H23 + +IC C1 O1 P1 O2 0.0000 0.00 180.00 0.00 0.0000 +IC O2 O1 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 +IC O2 O1 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 P1 O1 C1 0.0000 0.00 180.00 0.00 0.0000 +IC P1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 + +RESI IP_2 -2.00 ! C3H7O4P isopropylphosphate, dianionic +!test CT3-CT1-ON2-P dihedral without complications from phosphate proton +GROUP ! H21 +ATOM P1 PG2 1.10 ! | +ATOM O1 OG303 -0.40 ! H23--C2--H22 H31 +ATOM O2 OG2P1 -0.90 ! | / +ATOM O3 OG2P1 -0.90 ! H11--C1----C3--H32 +ATOM O4 OG2P1 -0.90 ! | \ +GROUP ! O1 H33 +ATOM C1 CG311 -0.09 ! | +ATOM H11 HGA1 0.09 ! (-) O4==P1==O3 (-) +! || +GROUP ! O2 +ATOM C2 CG331 -0.27 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 +GROUP +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 +BOND C1 H11 C1 C2 C1 C3 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 + +IC C1 O1 P1 O2 0.0000 0.00 60.00 0.00 0.0000 +IC O2 O1 *P1 O3 0.0000 0.00 120.00 0.00 0.0000 +IC O2 O1 *P1 O4 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 P1 O1 C1 0.0000 0.00 60.00 0.00 0.0000 +IC P1 O1 C1 C2 0.0000 0.00 220.00 0.00 0.0000 +IC C2 O1 *C1 C3 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 O1 *C1 H11 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C2 H21 0.0000 0.00 -60.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H31 C1 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C1 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 + +RESI SAH 0.00 ! C14H20N6O5S S-adenosyl-homocysteine +GROUP +ATOM N NG3P3 -0.30 +ATOM HT1 HGP2 0.33 ! (2) HT1 +ATOM HT2 HGP2 0.33 ! | / +ATOM HT3 HGP2 0.33 !(1)--CA--N--HT2 (+) +ATOM CA CG314 0.21 ! | \ +ATOM HA HGA1 0.10 ! HA HT3 +GROUP +ATOM CB CG321 -0.18 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 ! HB1 HG1 H5' H4' O4' Adenine +GROUP ! | | | \ / \ / +ATOM CG CG321 -0.13 ! (1)--CB--CG--SD--C5'----C4' C1'-H1' +ATOM HG1 HGA2 0.09 ! | | | | | +ATOM HG2 HGA2 0.09 ! HB2 HG2 H5'' H3'-C3'--C2'-H21' +ATOM SD SG311 -0.10 ! kevo: symmetrized | | +ATOM C5' CG321 -0.13 ! H3T--O3' O2'-H2' +ATOM H5' HGA2 0.09 +ATOM H5'' HGA2 0.09 ! OT2(-) +GROUP ! / +ATOM C CG2O3 0.34 !(2)-C +ATOM OT1 OG2D2 -0.67 ! \\ +ATOM OT2 OG2D2 -0.67 ! OT1 +GROUP +ATOM C4' CG3C51 0.16 +ATOM H4' HGA1 0.09 +ATOM O4' OG3C51 -0.50 +ATOM C1' CG3C51 0.16 +ATOM H1' HGA1 0.09 +GROUP +ATOM N9 NG2R51 -0.05 +ATOM C5 CG2RC0 0.28 +ATOM N7 NG2R50 -0.71 +ATOM C8 CG2R53 0.34 +ATOM H8 HGR52 0.12 +ATOM N1 NG2R62 -0.74 +ATOM C2 CG2R64 0.50 +ATOM H2 HGR62 0.13 +ATOM N3 NG2R62 -0.75 +ATOM C4 CG2RC0 0.43 +ATOM C6 CG2R64 0.46 +ATOM N6 NG2S3 -0.77 +ATOM H61 HGP4 0.38 +ATOM H62 HGP4 0.38 +GROUP +ATOM C2' CG3C51 0.14 +ATOM H2'' HGA1 0.09 +ATOM O2' OG311 -0.65 +ATOM H2' HGP1 0.42 +GROUP +ATOM C3' CG3C51 0.14 +ATOM H3' HGA1 0.09 +ATOM O3' OG311 -0.65 +ATOM H3T HGP1 0.42 + +BOND C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C2' C3' C2' O2' O2' H2' C3' O3' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +BOND N CA O3' H3T +BOND CB CA CG CB SD CG C5' SD C CA +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND HT1 N HT2 N HT3 N OT2 C +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +DOUBLE C OT1 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +IMPR OT1 CA OT2 C + +IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck +IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +IC N CA CB CG 1.4863 111.52 -68.05 114.80 1.5438 +IC CA CB CG SD 1.5495 114.80 -169.85 111.97 1.8249 +IC HT1 CA *N HT2 1.0633 98.00 113.14 109.99 1.0338 +IC HT1 CA *N HT3 1.0633 98.00 -117.28 113.48 1.0305 +IC HT1 N CA CB 1.0633 98.00 -136.27 111.52 1.5495 +IC CB N *CA C 1.5495 111.52 123.39 106.34 1.5395 +IC CB N *CA HA 1.5495 111.52 -122.64 109.49 1.0806 +IC CG CA *CB HB1 1.5438 114.80 125.78 110.22 1.1112 +IC CG CA *CB HB2 1.5438 114.80 -119.31 106.97 1.1179 +IC SD CB *CG HG1 1.8249 111.97 120.25 107.22 1.1112 +IC SD CB *CG HG2 1.8249 111.97 -122.78 110.68 1.1101 +IC CB CG SD C5' 1.5438 111.97 149.65 104.32 1.8303 +IC CG SD C5' C4' 1.8249 104.32 -59.34 117.91 1.5403 +IC C4' SD *C5' H5' 1.5403 117.91 122.31 108.22 1.1127 +IC C4' SD *C5' H5'' 1.5403 117.91 -122.71 108.62 1.1118 +IC N CA C OT1 1.4863 106.34 -166.34 117.88 1.2492 +IC OT1 CA *C OT2 1.2492 117.88 -178.37 117.42 1.2654 +IC SD C5' C4' O4' 1.8303 117.91 169.12 108.69 1.4591 +IC O4' C5' *C4' C3' 1.4591 108.69 118.83 122.55 1.5499 +IC O4' C5' *C4' H4' 1.4591 108.69 -116.07 109.38 1.1099 +IC C5' C4' O4' C1' 1.5403 108.69 133.30 108.22 1.4240 +IC C4' O4' C1' N9 1.4591 108.22 -159.13 111.15 1.4614 +IC N9 O4' *C1' C2' 1.4614 111.15 124.24 102.39 1.5135 +IC N9 O4' *C1' H1' 1.4614 111.15 -119.53 107.46 1.1156 +IC C4 C1' *N9 C8 1.3837 126.86 175.00 127.05 1.3697 +IC C1' N9 C4 C5 1.4614 126.86 176.84 105.37 1.3831 +IC C5 N9 *C4 N3 1.3831 105.37 179.25 128.02 1.3472 +IC N9 C4 C5 C6 1.3837 105.37 179.94 116.97 1.4115 +IC C6 C4 *C5 N7 1.4115 116.97 179.52 110.80 1.3914 +IC N7 N9 *C8 H8 1.3073 113.91 -179.74 121.60 1.0918 +IC C4 C5 C6 N1 1.3831 116.97 -0.21 118.01 1.3524 +IC N1 C5 *C6 N6 1.3524 118.01 -179.35 123.62 1.3438 +IC N3 N1 *C2 H2 1.3403 129.44 -179.97 115.20 1.0945 +IC C5 C6 N6 H61 1.4115 123.62 179.97 117.15 0.9949 +IC C3' C1' *C2' O2' 1.5132 95.49 115.41 113.17 1.4151 +IC C3' C1' *C2' H2'' 1.5132 95.49 -116.10 112.79 1.1120 +IC C1' C2' O2' H2' 1.5135 113.17 177.31 109.89 0.9633 +IC C4' C3' O3' H3T 1.5499 116.35 167.44 110.25 0.9629 + +RESI INDO 0.00 ! C8H7N indole, adm jr., atm +GROUP +ATOM HG HGR51 0.14 ! HE3 +ATOM CG CG2R51 -0.17 ! | +ATOM CD2 CG2RC0 0.11 ! HG CE3 +ATOM CD1 CG2R51 -0.15 ! \ / \\ +ATOM HD1 HGR52 0.22 ! CG-----CD2 CZ3-HZ3 +ATOM NE1 NG2R51 -0.51 ! || || | +ATOM HE1 HGP1 0.37 ! CD1 CE2 CH2-HH2 +ATOM CE2 CG2RC0 0.24 ! / \ / \ // +ATOM CE3 CG2R61 -0.25 ! HD1 NE1 CZ2 +ATOM HE3 HGR61 0.17 ! | | +ATOM CZ2 CG2R61 -0.27 ! HE1 HZ2 +ATOM HZ2 HGR61 0.16 +ATOM CZ3 CG2R61 -0.20 +ATOM HZ3 HGR61 0.14 +ATOM CH2 CG2R61 -0.14 +ATOM HH2 HGR61 0.14 +BOND CG HG CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND CZ3 CH2 CD2 CE3 NE1 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 +BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 +DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 +DONOR HE1 NE1 +IC CG CD1 NE1 CE2 1.3650 110.50 0.00 112.00 1.3700 +IC CD1 CG CD2 CE2 1.3650 106.40 0.00 108.00 1.3850 +IC CD2 CG CD1 NE1 1.4300 106.40 0.00 110.50 1.3700 +IC CE2 CG *CD2 CE3 1.3850 108.00 180.00 133.50 1.3600 +IC CE2 CD2 CE3 CZ3 1.3850 110.00 0.00 113.20 1.3750 +IC CD2 CE3 CZ3 CH2 1.3600 113.20 0.00 120.00 1.3750 +IC CE3 CZ3 CH2 CZ2 1.3750 120.00 0.00 120.00 1.3750 +IC CZ3 CD2 *CE3 HE3 1.3750 113.20 180.00 122.00 1.0800 +IC CH2 CE3 *CZ3 HZ3 1.3750 120.00 180.00 120.00 1.0800 +IC CZ2 CZ3 *CH2 HH2 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CH2 *CZ2 HZ2 1.3600 113.20 180.00 120.00 1.0800 +IC CD1 CE2 *NE1 HE1 1.3700 112.00 180.00 126.00 0.9760 +IC CG NE1 *CD1 HD1 1.3650 110.50 180.00 125.00 1.0800 +IC CD1 CD2 *CG HG 1.3650 106.40 180.00 126.40 1.0800 +PATCH FIRST NONE LAST NONE + +RESI MIND 0.00 ! C9H9N 3-methylindole, adm jr., atm +GROUP +ATOM CB CG331 -0.27 +ATOM HB1 HGA3 0.09 +ATOM HB2 HGA3 0.09 +ATOM HB3 HGA3 0.09 +GROUP +ATOM CG CG2R51 -0.03 +ATOM CD2 CG2RC0 0.11 +ATOM CD1 CG2R51 -0.15 +ATOM HD1 HGR52 0.22 +ATOM NE1 NG2R51 -0.51 +ATOM HE1 HGP1 0.37 +ATOM CE2 CG2RC0 0.24 +ATOM CE3 CG2R61 -0.25 +ATOM HE3 HGR61 0.17 +ATOM CZ2 CG2R61 -0.27 +ATOM HZ2 HGR61 0.16 +ATOM CZ3 CG2R61 -0.20 +ATOM HZ3 HGR61 0.14 +ATOM CH2 CG2R61 -0.14 +ATOM HH2 HGR61 0.14 +BOND CB HB1 CB HB2 CB HB3 +BOND CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND CZ3 CH2 CD2 CE3 NE1 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 +BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 +DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 +DONOR HE1 NE1 +IC CB CG CD1 NE1 1.4920 127.00 180.00 110.50 1.3700 +IC CG CD1 NE1 CE2 1.3650 110.50 0.00 112.00 1.3700 +IC CD1 CG CD2 CE2 1.3650 106.40 0.00 108.00 1.3850 +IC CD2 CB *CG CD1 1.4300 126.70 180.00 127.00 1.3650 +IC HB1 CB CG CD1 1.1110 109.50 0.00 127.00 1.3650 +IC HB2 CB CG CD1 1.1110 109.50 120.00 127.00 1.3650 +IC HB3 CB CG CD1 1.1110 109.50 240.00 127.00 1.3650 +IC CD2 CG CD1 NE1 1.4300 106.40 0.00 110.50 1.3700 +IC CE2 CG *CD2 CE3 1.3850 108.00 180.00 133.50 1.3600 +IC CE2 CD2 CE3 CZ3 1.3850 110.00 0.00 113.20 1.3750 +IC CD2 CE3 CZ3 CH2 1.3600 113.20 0.00 120.00 1.3750 +IC CE3 CZ3 CH2 CZ2 1.3750 120.00 0.00 120.00 1.3750 +IC CZ3 CD2 *CE3 HE3 1.3750 113.20 180.00 122.00 1.0800 +IC CH2 CE3 *CZ3 HZ3 1.3750 120.00 180.00 120.00 1.0800 +IC CZ2 CZ3 *CH2 HH2 1.3750 120.00 180.00 120.00 1.0800 +IC CE2 CH2 *CZ2 HZ2 1.3600 113.20 180.00 120.00 1.0800 +IC CD1 CE2 *NE1 HE1 1.3700 112.00 180.00 126.00 0.9760 +IC CG NE1 *CD1 HD1 1.3650 110.50 180.00 125.00 1.0800 + + +RESI EIND 0.00 ! C10H11N ethylindole, adm jr., atm +GROUP +ATOM CA CG331 -0.27 ! HA2 +ATOM HA1 HGA3 0.09 ! | +ATOM HA2 HGA3 0.09 ! HA1-CA-HA3 HE3 +ATOM HA3 HGA3 0.09 ! | | +GROUP ! HB1-CB-HB2 CE3 +ATOM CB CG321 -0.18 ! \ / \\ +ATOM HB1 HGA2 0.09 ! CG-----CD2 CZ3-HZ3 +ATOM HB2 HGA2 0.09 ! || || | +GROUP ! CD1 CE2 CH2-HH2 +ATOM CG CG2R51 -0.03 ! / \ / \ // +ATOM CD2 CG2RC0 0.11 ! HD1 NE1 CZ2 +ATOM CD1 CG2R51 -0.15 ! | | +ATOM HD1 HGR52 0.22 ! HE1 HZ2 +ATOM NE1 NG2R51 -0.51 +ATOM HE1 HGP1 0.37 +ATOM CE2 CG2RC0 0.24 +ATOM CE3 CG2R61 -0.25 +ATOM HE3 HGR61 0.17 +ATOM CZ2 CG2R61 -0.27 +ATOM HZ2 HGR61 0.16 +ATOM CZ3 CG2R61 -0.20 +ATOM HZ3 HGR61 0.14 +ATOM CH2 CG2R61 -0.14 +ATOM HH2 HGR61 0.14 +BOND CA HA1 CA HA2 CA HA3 +BOND CA CB CB HB1 CB HB2 +BOND CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND CZ3 CH2 CD2 CE3 NE1 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 +BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2 +DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 +DONOR HE1 NE1 +IC CA CB CG CD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CB CG CD1 NE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HA1 CB *CA HA2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HA1 CB *CA HA3 0.0000 0.0000 240.0000 0.0000 0.0000 +IC CA CG *CB HB1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CA CG *CB HB2 0.0000 0.0000 240.0000 0.0000 0.0000 +IC CG CD1 NE1 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CB *CG CD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CG CD1 NE1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE2 CG *CD2 CE3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CD2 CE3 CZ3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD2 CE3 CZ3 CH2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE3 CZ3 CH2 CZ2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CZ3 CD2 *CE3 HE3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CH2 CE3 *CZ3 HZ3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ2 CZ3 *CH2 HH2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CH2 *CZ2 HZ2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CD1 CE2 *NE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CG NE1 *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +!reset default patches +DEFA FIRS NONE LAST NONE + +RESI BFL 0.00 ! C12H10 biphenyl, peml. +GROUP +ATOM CG1 CG2R67 0.000 +ATOM CG2 CG2R67 0.000 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 ! HE1 HD1 HD3 HE3 +ATOM CE2 CG2R61 -0.115 ! \ / \ / +ATOM HE2 HGR61 0.115 ! CE1--CD1 CD3--CE3 +ATOM CZ1 CG2R61 -0.115 ! / \ / \ +ATOM HZ1 HGR61 0.115 ! HZ1--CZ1 CG1---CG2 CZ2--HZ2 +ATOM CD3 CG2R61 -0.115 ! \ / \ / +ATOM HD3 HGR61 0.115 ! CE2--CD2 CD4--CE4 +ATOM CD4 CG2R61 -0.115 ! / \ / \ +ATOM HD4 HGR61 0.115 ! HE2 HD2 HD4 HE4 +ATOM CE3 CG2R61 -0.115 +ATOM HE3 HGR61 0.115 +ATOM CE4 CG2R61 -0.115 +ATOM HE4 HGR61 0.115 +ATOM CZ2 CG2R61 -0.115 +ATOM HZ2 HGR61 0.115 + +BOND CD1 CG1 CG1 CD2 CG1 CG2 +BOND CD2 CE2 CE2 CZ1 CZ1 CE1 +BOND CE1 CD1 CG2 CD3 CD3 CE3 +BOND CE3 CZ2 CZ2 CE4 CE4 CD4 +BOND CD4 CG2 +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CD3 HD3 +BOND CD4 HD4 CE3 HE3 CE4 HE4 +BOND CZ1 HZ1 CZ2 HZ2 + +IC CG2 CG1 CD1 CE1 0.0000 0.00 180.00 0.00 0.0000 +IC CD1 CG2 *CG1 CD2 0.0000 0.00 180.00 0.00 0.0000 +IC CG2 CG1 CD1 CE1 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CG1 *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CG2 CG1 CD2 CE2 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CG1 *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC CG1 CD1 CE1 CZ1 0.0000 0.00 180.00 0.00 0.0000 +IC CZ1 CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC CZ1 CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CE1 *CZ1 HZ1 0.0000 0.00 180.00 0.00 0.0000 +IC CD1 CG1 CG2 CD4 0.0000 0.00 180.00 0.00 0.0000 +IC CD4 CG1 *CG2 CD3 0.0000 0.00 180.00 0.00 0.0000 +IC CG1 CG2 CD3 CE3 0.0000 0.00 180.00 0.00 0.0000 +IC CE3 CG2 *CD3 HD3 0.0000 0.00 180.00 0.00 0.0000 +IC CG1 CG2 CD4 CE4 0.0000 0.00 180.00 0.00 0.0000 +IC CE4 CG2 *CD4 HD4 0.0000 0.00 180.00 0.00 0.0000 +IC CG2 CD3 CE3 CZ2 0.0000 0.00 180.00 0.00 0.0000 +IC CZ2 CD3 *CE3 HE3 0.0000 0.00 180.00 0.00 0.0000 +IC CZ2 CD4 *CE4 HE4 0.0000 0.00 180.00 0.00 0.0000 +IC CE4 CE3 *CZ2 HZ2 0.0000 0.00 180.00 0.00 0.0000 + +RESI BF6 -2.00 ! C16H12O6 biphenyl analog, peml. +!KEVO: charges adjusted to reflect updated acetone L-J. +!Resulting charges are unlikey to be good ==> re-optimize? +GROUP +ATOM CG1 CG2R67 0.000 +ATOM CG2 CG2R67 0.000 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 ! HE1 HD1 HD3 HE3 +ATOM HE1 HGR61 0.115 ! \ / \ / +ATOM CE2 CG2R61 -0.115 ! CE1--CD1 CD3--CE3 +ATOM HE2 HGR61 0.115 ! / \ / \ +ATOM CZ1 CG2R61 0.000 ! SUBS--CZ1 CG1---CG2 CZ2--SUBS +ATOM CD3 CG2R61 -0.115 ! \ / \ / +ATOM HD3 HGR61 0.115 ! CE2--CD2 CD4--CE4 +ATOM CD4 CG2R61 -0.115 ! / \ / \ +ATOM HD4 HGR61 0.115 ! HE2 HD2 HD4 HE4 +ATOM CE3 CG2R61 -0.115 +ATOM HE3 HGR61 0.115 +ATOM CE4 CG2R61 -0.115 +ATOM HE4 HGR61 0.115 +ATOM CZ2 CG2R61 0.000 + +GROUP +ATOM C1 CG2O5 0.38 +ATOM O1 OG2D3 -0.48 ! O1 +ATOM C2 CG311 0.17 ! // +ATOM H2 HGA1 0.09 !Ring--C1 H2 +ATOM O2A OG311 -0.60 ! \ / +ATOM H2A HGP1 0.32 ! C2--O2A--H2A +ATOM O2B OG312 -0.88 ! \ + ! O2B (-) +GROUP +ATOM C3 CG2O5 0.38 +ATOM O3 OG2D3 -0.48 +ATOM C4 CG311 0.17 +ATOM H4 HGA1 0.09 +ATOM O4A OG311 -0.60 +ATOM H4A HGP1 0.32 +ATOM O4B OG312 -0.88 + +BOND CD1 CG1 CG1 CD2 CG1 CG2 +BOND CD2 CE2 CE2 CZ1 CZ1 CE1 +BOND CE1 CD1 CG2 CD3 CD3 CE3 +BOND CE3 CZ2 CZ2 CE4 CE4 CD4 +BOND CD4 CG2 + +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CD3 HD3 +BOND CD4 HD4 CE3 HE3 CE4 HE4 + +BOND CZ1 C1 C1 O1 C1 C2 +BOND C2 H2 C2 O2A O2A H2A +BOND C2 O2B +BOND CZ2 C3 C3 O3 C3 C4 +BOND C4 H4 C4 O4A O4A H4A +BOND C4 O4B + +IMPR C1 CZ1 C2 O1 +IMPR C3 CZ2 C4 O3 + +IC CD1 CG2 *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 +IC CG2 CG1 CD1 CE1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CG1 CD2 CE2 1.4000 120.00 180.00 120.00 1.4000 +IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 +IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 +IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 +IC CD1 CG1 CG2 CD4 1.4000 120.00 180.00 120.00 1.4000 +IC CD4 CG1 *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 +IC CG1 CG2 CD3 CE3 1.4000 120.00 180.00 120.00 1.4000 +IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CG2 CD4 CE4 1.4000 120.00 180.00 120.00 1.4000 +IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 +IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 +IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 +IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CZ1 C1 C2 1.4000 120.00 180.00 120.00 1.4000 +IC C2 CZ1 *C1 O1 1.4000 120.00 180.00 120.00 1.2000 +IC CZ1 C1 C2 O2A 1.4000 120.00 -60.00 110.00 1.4000 +IC O2A C1 *C2 O2B 1.4000 110.00 120.00 110.00 1.4000 +IC O2A C1 *C2 H2 1.4000 110.00 -120.00 110.00 1.1000 +IC C1 C2 O2A H2A 1.4000 110.00 180.00 110.00 0.9000 +IC CE4 CE3 *CZ2 C3 1.4000 120.00 180.00 120.00 1.0900 +IC CE3 CZ2 C3 C4 1.4000 120.00 180.00 120.00 1.4000 +IC C4 CZ2 *C3 O3 1.4000 120.00 180.00 120.00 1.2000 +IC CZ2 C3 C4 O4A 1.4000 120.00 -60.00 110.00 1.4000 +IC O4A C3 *C4 O4B 1.4000 110.00 120.00 110.00 1.4000 +IC O4A C3 *C4 H4 1.4000 110.00 -120.00 110.00 1.1000 +IC C3 C4 O4A H4A 1.4000 110.00 180.00 110.00 0.9000 + +RESI BF7 -2.00 ! C16H8O6 biphenyl analog, peml. +!KEVO: charges adjusted to reflect updated acetone L-J. +!Resulting charges are probably not that bad. +GROUP +ATOM CG1 CG2R67 0.00 +ATOM CG2 CG2R67 0.00 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 ! HE1 HD1 HD3 HE3 +GROUP ! \ / \ / +ATOM CZ1 CG2R61 0.000 ! CE1--CD1 CD3--CE3 +GROUP ! / \ / \ +ATOM CD3 CG2R61 -0.115 ! SUBS--CZ1 CG1---CG2 CZ2--SUBS +ATOM HD3 HGR61 0.115 ! \ / \ / +GROUP ! CE2--CD2 CD4--CE4 +ATOM CD4 CG2R61 -0.115 ! / \ / \ +ATOM HD4 HGR61 0.115 ! HE2 HD2 HD4 HE4 +GROUP +ATOM CE3 CG2R61 -0.115 +ATOM HE3 HGR61 0.115 +GROUP +ATOM CE4 CG2R61 -0.115 +ATOM HE4 HGR61 0.115 +GROUP +ATOM CZ2 CG2R61 0.000 +GROUP +ATOM C1 CG2O5 0.38 ! O +ATOM O1 OG2D3 -0.48 ! // +ATOM C2 CG2O3 0.62 ! Ring-C +ATOM O2A OG2D2 -0.76 ! \ +ATOM O2B OG2D2 -0.76 ! C==O +GROUP ! | +ATOM C3 CG2O5 0.38 ! O (-) +ATOM O3 OG2D3 -0.48 +ATOM C4 CG2O3 0.62 +ATOM O4A OG2D2 -0.76 +ATOM O4B OG2D2 -0.76 + +BOND CD1 CG1 CG1 CD2 CG1 CG2 +BOND CD2 CE2 CE2 CZ1 CZ1 CE1 +BOND CE1 CD1 CG2 CD3 CD3 CE3 +BOND CE3 CZ2 CZ2 CE4 CE4 CD4 +BOND CD4 CG2 +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CD3 HD3 +BOND CD4 HD4 CE3 HE3 CE4 HE4 +BOND CZ1 C1 CZ2 C3 +BOND C1 O1 C1 C2 C2 O2A +BOND C2 O2B +BOND C3 O3 C3 C4 C4 O4A +BOND C4 O4B +IMPR C1 C2 CZ1 O1 +IMPR C2 O2B O2A C1 +IMPR C3 C4 CZ2 O3 +IMPR C4 O4B O4A C3 + +IC CD1 CG2 *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 +IC CG2 CG1 CD1 CE1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CG1 CD2 CE2 1.4000 120.00 180.00 120.00 1.4000 +IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 +IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 +IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 +IC CD1 CG1 CG2 CD4 1.4000 120.00 180.00 120.00 1.4000 +IC CD4 CG1 *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 +IC CG1 CG2 CD3 CE3 1.4000 120.00 180.00 120.00 1.4000 +IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CG2 CD4 CE4 1.4000 120.00 180.00 120.00 1.4000 +IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 +IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 +IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 +IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CZ1 C1 C2 1.4000 120.00 180.00 120.00 1.4000 +IC C2 CZ1 *C1 O1 1.4000 120.00 180.00 120.00 1.2000 +IC CZ1 C1 C2 O2A 1.4000 120.00 -60.00 110.00 1.4000 +IC O2A C1 *C2 O2B 1.4000 110.00 120.00 110.00 1.4000 +IC CE4 CE3 *CZ2 C3 1.4000 120.00 180.00 120.00 1.0900 +IC CE3 CZ2 C3 C4 1.4000 120.00 180.00 120.00 1.4000 +IC C4 CZ2 *C3 O3 1.4000 120.00 180.00 120.00 1.2000 +IC CZ2 C3 C4 O4A 1.4000 120.00 -60.00 110.00 1.4000 +IC O4A C3 *C4 O4B 1.4000 110.00 120.00 110.00 1.4000 + +RESI BCA -2.00 ! C14H8O4 biphenyl analog, peml., acid analog +GROUP +ATOM CG1 CG2R67 0.000 +ATOM CG2 CG2R67 0.000 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP ! HE1 HD1 HD3 HE3 +ATOM CE1 CG2R61 -0.115 ! \ / \ / +ATOM HE1 HGR61 0.115 ! CE1--CD1 CD3--CE3 +GROUP ! / \ / \ +ATOM CE2 CG2R61 -0.115 ! SUBS--CZ1 CG1---CG2 CZ2--SUBS +ATOM HE2 HGR61 0.115 ! \ / \ / +GROUP ! CE2--CD2 CD4--CE4 +ATOM CD3 CG2R61 -0.115 ! / \ / \ +ATOM HD3 HGR61 0.115 ! HE2 HD2 HD4 HE4 +GROUP +ATOM CD4 CG2R61 -0.115 +ATOM HD4 HGR61 0.115 +GROUP +ATOM CE3 CG2R61 -0.115 +ATOM HE3 HGR61 0.115 +GROUP +ATOM CE4 CG2R61 -0.115 +ATOM HE4 HGR61 0.115 +GROUP +ATOM CZ1 CG2R61 -0.10 ! O +ATOM C1 CG2O3 0.62 ! // +ATOM O1A OG2D2 -0.76 ! Ring-C (-) +ATOM O1B OG2D2 -0.76 ! \ +GROUP ! O +ATOM CZ2 CG2R61 -0.10 +ATOM C2 CG2O3 0.62 +ATOM O2A OG2D2 -0.76 +ATOM O2B OG2D2 -0.76 + +BOND CD1 CG1 CG1 CD2 CG1 CG2 +BOND CD2 CE2 CE2 CZ1 CZ1 CE1 +BOND CE1 CD1 CG2 CD3 CD3 CE3 +BOND CE3 CZ2 CZ2 CE4 CE4 CD4 +BOND CD4 CG2 +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CD3 HD3 +BOND CD4 HD4 CE3 HE3 CE4 HE4 +BOND CZ1 C1 C1 O1A C1 O1B +BOND CZ2 C2 C2 O2A C2 O2B +IMPR C1 O1B O1A CZ1 +IMPR C2 O2B O2A CZ2 + +IC CD1 CG2 *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 +IC CG2 CG1 CD1 CE1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CG1 CD2 CE2 1.4000 120.00 180.00 120.00 1.4000 +IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 +IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 +IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 +IC CD1 CG1 CG2 CD4 1.4000 120.00 180.00 120.00 1.4000 +IC CD4 CG1 *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 +IC CG1 CG2 CD3 CE3 1.4000 120.00 180.00 120.00 1.4000 +IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CG2 CD4 CE4 1.4000 120.00 180.00 120.00 1.4000 +IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 +IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 +IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 +IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CZ1 C1 O1A 1.4000 120.00 180.00 120.00 1.4000 +IC O1A CZ1 *C1 O1B 1.4000 120.00 180.00 120.00 1.4000 +IC CE4 CE3 *CZ2 C2 1.4000 120.00 180.00 120.00 1.4000 +IC CE3 CZ2 C2 O2A 1.4000 120.00 180.00 120.00 1.4000 +IC O2A CZ2 *C2 O2B 1.4000 120.00 180.00 120.00 1.4000 + + +RESI C36 -2.00 ! C16H12O7 biphenyl with bridging O analog, peml. +!KEVO: charges adjusted to reflect updated acetone L-J. +!Resulting charges are unlikey to be good ==> re-optimize? +GROUP ! hydrated aldehyde analog (ionized) +ATOM CG1 CG2R61 0.215 +ATOM O OG301 -0.430 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 ! HE3 +ATOM CD2 CG2R61 -0.115 ! \ / +ATOM HD2 HGR61 0.115 ! CD3--CE3 +ATOM CE1 CG2R61 -0.115 ! / \ +ATOM HE1 HGR61 0.115 ! HD1 O ---CG2 CZ2--SUBS +ATOM CE2 CG2R61 -0.115 ! \ / \ / +ATOM HE2 HGR61 0.115 ! CD1--CG1 CD4--CE4 +ATOM CZ1 CG2R61 0.000 ! / \ / \ +ATOM CG2 CG2R61 0.215 ! HE1--CE1 CD2--HD2 HD4 HE4 +ATOM CD3 CG2R61 -0.115 ! \ / +ATOM HD3 HGR61 0.115 ! CZ1--CE2 +ATOM CD4 CG2R61 -0.115 ! / \ +ATOM HD4 HGR61 0.115 ! SUBS HE2 +ATOM CE3 CG2R61 -0.115 +ATOM HE3 HGR61 0.115 +ATOM CE4 CG2R61 -0.115 +ATOM HE4 HGR61 0.115 +ATOM CZ2 CG2R61 0.000 +GROUP +ATOM C1 CG2O5 0.38 ! O1 +ATOM O1 OG2D3 -0.48 ! // +ATOM C2 CG311 0.17 !Ring--C1 H2 +ATOM H2 HGA1 0.09 ! \ / +ATOM O2A OG311 -0.60 ! C2--OH +ATOM H2A HGP1 0.32 ! \ +ATOM O2B OG312 -0.88 ! O (-) +GROUP +ATOM C3 CG2O5 0.38 +ATOM O3 OG2D3 -0.48 +ATOM C4 CG311 0.17 +ATOM H4 HGA1 0.09 +ATOM O4A OG311 -0.60 +ATOM H4A HGP1 0.32 +ATOM O4B OG312 -0.88 + +BOND CD1 CG1 CG1 CD2 CG1 O +BOND CD2 CE2 CE2 CZ1 CZ1 CE1 +BOND CE1 CD1 CG2 CD3 CD3 CE3 +BOND CE3 CZ2 CZ2 CE4 CE4 CD4 +BOND CD4 CG2 CG2 O +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CD3 HD3 +BOND CD4 HD4 CE3 HE3 CE4 HE4 +BOND CZ1 C1 C1 O1 C1 C2 +BOND C2 H2 C2 O2A O2A H2A +BOND C2 O2B +BOND CZ2 C3 C3 O3 C3 C4 +BOND C4 H4 C4 O4A O4A H4A +BOND C4 O4B + +IMPR C1 CZ1 C2 O1 +IMPR C3 CZ2 C4 O3 + +IC CD1 O *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 +IC O CG1 CD1 CE1 1.3820 120.00 180.00 120.00 1.4000 +IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 +IC O CG1 CD2 CE2 1.3820 120.00 180.00 120.00 1.4000 +IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 +IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 +IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 +IC CD1 CG1 O CG2 1.4000 120.00 -144.00 120.00 1.3820 +IC CG1 O CG2 CD4 1.3820 120.00 40.00 120.00 1.4000 +IC CD4 O *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 +IC O CG2 CD3 CE3 1.3820 120.00 180.00 120.00 1.4000 +IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 +IC O CG2 CD4 CE4 1.3820 120.00 180.00 120.00 1.4000 +IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 +IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 +IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 +IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CZ1 C1 C2 1.4000 120.00 180.00 120.00 1.4000 +IC C2 CZ1 *C1 O1 1.4000 120.00 180.00 120.00 1.2000 +IC CZ1 C1 C2 O2A 1.4000 120.00 -60.00 110.00 1.4000 +IC O2A C1 *C2 O2B 1.4000 110.00 120.00 110.00 1.4000 +IC O2A C1 *C2 H2 1.4000 110.00 -120.00 110.00 1.1000 +IC C1 C2 O2A H2A 1.4000 110.00 180.00 110.00 0.9000 +IC CE4 CE3 *CZ2 C3 1.4000 120.00 180.00 120.00 1.0900 +IC CE3 CZ2 C3 C4 1.4000 120.00 180.00 120.00 1.4000 +IC C4 CZ2 *C3 O3 1.4000 120.00 180.00 120.00 1.2000 +IC CZ2 C3 C4 O4A 1.4000 120.00 -60.00 110.00 1.4000 +IC O4A C3 *C4 O4B 1.4000 110.00 120.00 110.00 1.4000 +IC O4A C3 *C4 H4 1.4000 110.00 -120.00 110.00 1.1000 +IC C3 C4 O4A H4A 1.4000 110.00 180.00 110.00 0.9000 + +RESI C37 -2.00 ! C16H8O7 biphenyl analog, peml. +!KEVO: charges adjusted to reflect updated acetone L-J. +!Resulting charges are probably not that bad. +GROUP +ATOM CG1 CG2R61 0.215 +ATOM O OG301 -0.430 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 ! HE3 +ATOM CD2 CG2R61 -0.115 ! \ / +ATOM HD2 HGR61 0.115 ! CD3--CE3 +ATOM CE1 CG2R61 -0.115 ! / \ +ATOM HE1 HGR61 0.115 ! HD1 O ---CG2 CZ2--SUBS +ATOM CE2 CG2R61 -0.115 ! \ / \ / +ATOM HE2 HGR61 0.115 ! CD1--CG1 CD4--CE4 +ATOM CZ1 CG2R61 0.000 ! / \ / \ +ATOM CG2 CG2R61 0.215 ! HE1--CE1 CD2--HD2 HD4 HE4 +ATOM CD3 CG2R61 -0.115 ! \ / +ATOM HD3 HGR61 0.115 ! CZ1--CE2 +ATOM CD4 CG2R61 -0.115 ! / \ +ATOM HD4 HGR61 0.115 ! SUBS HE2 +ATOM CE3 CG2R61 -0.115 +ATOM HE3 HGR61 0.115 +ATOM CE4 CG2R61 -0.115 +ATOM HE4 HGR61 0.115 +ATOM CZ2 CG2R61 0.000 +GROUP +ATOM C1 CG2O5 0.38 +ATOM O1 OG2D3 -0.48 ! O +ATOM C2 CG2O3 0.62 ! // +ATOM O2A OG2D2 -0.76 ! Ring--C +ATOM O2B OG2D2 -0.76 ! \ +GROUP ! C--O (-) +ATOM C3 CG2O5 0.38 ! // +ATOM O3 OG2D3 -0.48 ! O +ATOM C4 CG2O3 0.62 +ATOM O4A OG2D2 -0.76 +ATOM O4B OG2D2 -0.76 + +BOND CD1 CG1 CG1 CD2 CG1 O +BOND CD2 CE2 CE2 CZ1 CZ1 CE1 +BOND CE1 CD1 CG2 CD3 CD3 CE3 +BOND CE3 CZ2 CZ2 CE4 CE4 CD4 +BOND CD4 CG2 CG2 O +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CD3 HD3 +BOND CD4 HD4 CE3 HE3 CE4 HE4 +BOND CZ1 C1 C1 O1 C1 C2 +BOND C2 O2A +BOND C2 O2B +BOND CZ2 C3 C3 O3 C3 C4 +BOND C4 O4A +BOND C4 O4B +IMPR C1 C2 CZ1 O1 +IMPR C2 O2B O2A C1 +IMPR C3 C4 CZ2 O3 +IMPR C4 O4B O4A C3 + +IC CD1 O *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 +IC O CG1 CD1 CE1 1.3820 120.00 180.00 120.00 1.4000 +IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 +IC O CG1 CD2 CE2 1.3820 120.00 180.00 120.00 1.4000 +IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 +IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 +IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 +IC CD1 CG1 O CG2 1.4000 120.00 -144.00 120.00 1.3820 +IC CG1 O CG2 CD4 1.3820 120.00 40.00 120.00 1.4000 +IC CD4 O *CG2 CD3 1.4000 120.00 180.00 120.00 1.4000 +IC O CG2 CD3 CE3 1.3820 120.00 180.00 120.00 1.4000 +IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 +IC O CG2 CD4 CE4 1.3820 120.00 180.00 120.00 1.4000 +IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 +IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 +IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 +IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CZ1 C1 C2 1.4000 120.00 180.00 120.00 1.4000 +IC C2 CZ1 *C1 O1 1.4000 120.00 180.00 120.00 1.2000 +IC CZ1 C1 C2 O2A 1.4000 120.00 180.00 120.00 1.4000 +IC O2A C1 *C2 O2B 1.4000 120.00 180.00 120.00 1.4000 +IC CE4 CE3 *CZ2 C3 1.4000 120.00 180.00 120.00 1.0900 +IC CE3 CZ2 C3 C4 1.4000 120.00 180.00 120.00 1.4000 +IC C4 CZ2 *C3 O3 1.4000 120.00 180.00 120.00 1.2000 +IC CZ2 C3 C4 O4A 1.4000 120.00 180.00 120.00 1.4000 +IC O4A C3 *C4 O4B 1.4000 120.00 180.00 120.00 1.4000 + +RESI C3C -2.00 ! C14H8O5 +GROUP +ATOM CG1 CG2R61 0.215 +ATOM O OG301 -0.430 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 ! HE3 +ATOM HD2 HGR61 0.115 ! \ / +ATOM CE1 CG2R61 -0.115 ! CD3--CE3 +ATOM HE1 HGR61 0.115 ! / \ +ATOM CE2 CG2R61 -0.115 ! HD1 O ---CG2 CZ2--SUBS +ATOM HE2 HGR61 0.115 ! \ / \ / +ATOM CZ1 CG2R61 -0.100 ! CD1--CG1 CD4--CE4 +ATOM CG2 CG2R61 0.215 ! / \ / \ +ATOM CD3 CG2R61 -0.115 ! HE1--CE1 CD2--HD2 HD4 HE4 +ATOM HD3 HGR61 0.115 ! \ / +ATOM CD4 CG2R61 -0.115 ! CZ1--CE2 +ATOM HD4 HGR61 0.115 ! / \ +ATOM CE3 CG2R61 -0.115 ! SUBS HE2 +ATOM HE3 HGR61 0.115 +ATOM CE4 CG2R61 -0.115 +ATOM HE4 HGR61 0.115 +ATOM CZ2 CG2R61 -0.100 +GROUP +ATOM C1 CG2O3 0.62 +ATOM O1A OG2D2 -0.76 ! O +ATOM O1B OG2D2 -0.76 ! // +GROUP ! Ring-C (-) +ATOM C2 CG2O3 0.62 ! \ +ATOM O2A OG2D2 -0.76 ! O +ATOM O2B OG2D2 -0.76 + +BOND CD1 CG1 CG1 CD2 CG1 O +BOND CD2 CE2 CE2 CZ1 CZ1 CE1 +BOND CE1 CD1 CG2 CD3 CD3 CE3 +BOND CE3 CZ2 CZ2 CE4 CE4 CD4 +BOND CD4 CG2 CG2 O +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CD3 HD3 +BOND CD4 HD4 CE3 HE3 CE4 HE4 +BOND CZ1 C1 C1 O1A C1 O1B +BOND CZ2 C2 C2 O2A C2 O2B + +IMPR C1 O1B O1A CZ1 +IMPR C2 O2B O2A CZ2 + +IC CD1 O *CG1 CD2 1.4000 120.00 180.00 120.00 1.4000 +IC O CG1 CD1 CE1 1.3820 120.00 180.00 120.00 1.4000 +IC CE1 CG1 *CD1 HD1 1.4000 120.00 180.00 120.00 1.0900 +IC O CG1 CD2 CE2 1.3820 120.00 180.00 120.00 1.4000 +IC CE2 CG1 *CD2 HD2 1.4000 120.00 180.00 120.00 1.0900 +IC CG1 CD1 CE1 CZ1 1.4000 120.00 0.00 120.00 1.4000 +IC CZ1 CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0900 +IC CZ1 CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0900 +IC CD1 CG1 O CG2 1.4000 120.00 -144.00 120.00 1.3820 +IC CG1 O CG2 CD3 1.3820 120.00 0.00 120.00 1.4000 +IC CD3 O *CG2 CD4 1.4000 120.00 180.00 120.00 1.4000 +IC O CG2 CD3 CE3 1.3820 120.00 180.00 120.00 1.4000 +IC CE3 CG2 *CD3 HD3 1.4000 120.00 180.00 120.00 1.0900 +IC O CG2 CD4 CE4 1.3820 120.00 180.00 120.00 1.4000 +IC CE4 CG2 *CD4 HD4 1.4000 120.00 180.00 120.00 1.0900 +IC CG2 CD3 CE3 CZ2 1.4000 120.00 0.00 120.00 1.4000 +IC CZ2 CD3 *CE3 HE3 1.4000 120.00 180.00 120.00 1.0900 +IC CZ2 CD4 *CE4 HE4 1.4000 120.00 180.00 120.00 1.0900 +IC CE2 CE1 *CZ1 C1 1.4000 120.00 180.00 120.00 1.4000 +IC CE1 CZ1 C1 O1A 1.4000 120.00 180.00 120.00 1.4000 +IC O1A CZ1 *C1 O1B 1.4000 120.00 180.00 120.00 1.4000 +IC CE4 CE3 *CZ2 C2 1.4000 120.00 180.00 120.00 1.4000 +IC CE3 CZ2 C2 O2A 1.4000 120.00 180.00 120.00 1.4000 +IC O2A CZ2 *C2 O2B 1.4000 120.00 180.00 120.00 1.4000 +PATCHING FIRST NONE LAST NONE + +!toppar_retinol_2.str +RESI HEX3 0.00 ! C6H8 1,3,5-hexatriene + +GROUP +ATOM C1 CG2DC3 -0.42 +ATOM H11 HGA5 0.21 ! H11 H21 +ATOM H12 HGA5 0.21 ! \ / +ATOM C2 CG2DC2 -0.15 ! C1=C2 H41 +ATOM H21 HGA4 0.15 ! / \ / +GROUP ! H12 C3=C4 H61 +ATOM C3 CG2DC1 -0.15 ! / \ / +ATOM H31 HGA4 0.15 ! H31 C5=C6 +ATOM C4 CG2DC1 -0.15 ! / \ +ATOM H41 HGA4 0.15 ! H51 H62 +GROUP +ATOM C5 CG2DC2 -0.15 +ATOM H51 HGA4 0.15 +GROUP +ATOM C6 CG2DC3 -0.42 +ATOM H61 HGA5 0.21 +ATOM H62 HGA5 0.21 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C1 H11 C1 H12 C2 H21 C3 H31 +BOND C4 H41 C5 H51 C6 H61 C6 H62 + +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI 13DB 0.00 ! C4H6 1,3-dibutene + +GROUP +ATOM C1 CG2DC3 -0.42 ! H11 H21 +ATOM H11 HGA5 0.21 ! \ / +ATOM H12 HGA5 0.21 ! C1=C2 H41 +GROUP ! / \ / +ATOM C2 CG2DC2 -0.15 ! H12 C3=C4 +ATOM H21 HGA4 0.15 ! / \ +ATOM C3 CG2DC1 -0.15 ! H31 H42 +ATOM H31 HGA4 0.15 +GROUP +ATOM C4 CG2DC3 -0.42 +ATOM H41 HGA5 0.21 +ATOM H42 HGA5 0.21 + +BOND C1 C2 C2 C3 C3 C4 +BOND C1 H11 C1 H12 C2 H21 C3 H31 +BOND C4 H41 C4 H42 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 H41 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C3 H41 *C4 H42 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI 13DP 0.00 ! C5H8 1,3-dipentene + +GROUP +ATOM C1 CG2DC3 -0.42 +ATOM H11 HGA5 0.21 ! H11 H21 +ATOM H12 HGA5 0.21 ! \ / +ATOM C2 CG2DC2 -0.15 ! C1=C2 H41 +ATOM H21 HGA4 0.15 ! / \ / +GROUP ! H12 C3=C4 H51 +ATOM C3 CG2DC1 -0.15 ! / \ / +ATOM H31 HGA4 0.15 ! H31 C5-H52 +ATOM C4 CG2DC1 -0.15 ! \ +ATOM H41 HGA4 0.15 ! H53 +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C1 H11 C1 H12 C2 H21 C3 H31 +BOND C4 H41 C5 H51 C5 H52 C5 H53 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C5 H51 0.00 0.00 0.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 180.0 0.00 0.00 +IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 +IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI DMB1 0.00 ! C5H8 2-methyl-1,3-butadiene + +GROUP +ATOM C1 CG2DC3 -0.42 +ATOM H11 HGA5 0.21 ! H2M1 H2M2 +ATOM H12 HGA5 0.21 ! \ / +GROUP ! H11 C2M-H2M3 +ATOM C2 CG2DC2 0.00 ! \ / +ATOM C2M CG331 -0.27 ! C1=C2 H41 +ATOM H2M1 HGA3 0.09 ! / \ / +ATOM H2M2 HGA3 0.09 ! H12 C3=C4 +ATOM H2M3 HGA3 0.09 ! / \ +GROUP ! H31 H42 +ATOM C3 CG2DC1 -0.15 +ATOM H31 HGA4 0.15 +GROUP +ATOM C4 CG2DC3 -0.42 +ATOM H41 HGA5 0.21 +ATOM H42 HGA5 0.21 + +BOND C1 C2 C2 C3 C3 C4 C2 C2M +BOND C1 H11 C1 H12 C3 H31 C4 H41 C4 H42 +BOND C2M H2M1 C2M H2M2 C2M H2M3 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 H41 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 C2M 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +IC C3 H41 *C4 H42 0.00 0.00 180.0 0.00 0.00 +IC C1 C2 C2M H2M1 0.00 0.00 180.0 0.00 0.00 +IC C2 H2M1 *C2M H2M2 0.00 0.00 120.0 0.00 0.00 +IC C2 H2M1 *C2M H2M3 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI DMP1 0.00 ! C6H10 4-methyl-1,3-pentadiene + +GROUP +ATOM C1 CG2DC3 -0.42 +ATOM H11 HGA5 0.21 ! H11 H21 H4M1 H4M2 +ATOM H12 HGA5 0.21 ! \ / \ / +GROUP ! C1=C2 C4M-H4M3 +ATOM C2 CG2DC2 -0.15 ! / \ / +ATOM H21 HGA4 0.15 ! H12 C3=C4 H51 +ATOM C3 CG2DC1 -0.15 ! / \ / +ATOM H31 HGA4 0.15 ! H31 C5-H52 +GROUP ! \ +ATOM C4 CG2DC1 0.00 ! H53 +ATOM C4M CG331 -0.27 +ATOM H4M1 HGA3 0.09 +ATOM H4M2 HGA3 0.09 +ATOM H4M3 HGA3 0.09 +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C4 C4M +BOND C1 H11 C1 H12 C2 H21 C3 H31 +BOND C4M H4M1 C4M H4M2 C4M H4M3 +BOND C5 H51 C5 H52 C5 H53 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C5 H51 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +IC C3 C5 *C4 C4M 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C4M H4M1 0.00 0.00 180.0 0.00 0.00 +IC C4 H4M1 *C4M H4M2 0.00 0.00 120.0 0.00 0.00 +IC C4 H4M1 *C4M H4M3 0.00 0.00 -120.0 0.00 0.00 +IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 +IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + + +RESI DMP2 0.00 ! C6H10 2-methyl-1,3-pentadiene + +GROUP ! H2M1 H2M2 +ATOM C1 CG2DC3 -0.42 ! \ / +ATOM H11 HGA5 0.21 ! H11 C2M-H2M3 +ATOM H12 HGA5 0.21 ! \ / +GROUP ! C1=C2 H41 +ATOM C2 CG2DC2 0.00 ! / \ / +ATOM C2M CG331 -0.27 ! H12 C3=C4 H51 +ATOM H2M1 HGA3 0.09 ! / \ / +ATOM H2M2 HGA3 0.09 ! H31 C5-H52 +ATOM H2M3 HGA3 0.09 ! \ +ATOM C3 CG2DC1 -0.15 ! H53 +ATOM H31 HGA4 0.15 +GROUP +ATOM C4 CG2DC1 -0.15 +ATOM H41 HGA4 0.15 +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C2 C2M +BOND C1 H11 C1 H12 C3 H31 C4 H41 +BOND C2M H2M1 C2M H2M2 C2M H2M3 +BOND C5 H51 C5 H52 C5 H53 + +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C5 H51 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 H11 0.00 0.00 180.0 0.00 0.00 +IC C2 H11 *C1 H12 0.00 0.00 180.0 0.00 0.00 +IC C1 C3 *C2 C2M 0.00 0.00 180.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 180.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 180.0 0.00 0.00 +IC C1 C2 C2M H2M1 0.00 0.00 180.0 0.00 0.00 +IC C2 H2M1 *C2M H2M2 0.00 0.00 120.0 0.00 0.00 +IC C2 H2M1 *C2M H2M3 0.00 0.00 -120.0 0.00 0.00 +IC C4 H51 *C5 H52 0.00 0.00 120.0 0.00 0.00 +IC C4 H51 *C5 H53 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI CROT 0.00 ! C6H11NO N,3-dimethyl-2-buteneamide, (N,3-dimethylcrotonamide) + ! numbering as in fennretinide +! note different atom types for N21 and C15: this is consistent +! with differences in NMA and acetamide +GROUP +ATOM C12 CG331 -0.27 +ATOM H121 HGA3 0.09 ! H202 H203 +ATOM H122 HGA3 0.09 ! \ / +ATOM H123 HGA3 0.09 ! H201-C20 +GROUP ! | +ATOM C13 CG2DC2 0.00 !H121-C12--C13 O29 +ATOM C14 CG2DC2 -0.15 ! / | \\ || +ATOM H141 HGA4 0.15 !H122 H123 C14--C15 +GROUP ! / \ +ATOM C15 CG2O1 0.51 ! H141 N21-H211 (cis) +ATOM O29 OG2D1 -0.51 ! | +GROUP ! H132-C16-H131 +ATOM N21 NG2S1 -0.47 ! | +ATOM H211 HGP1 0.28 ! H133 +ATOM C16 CG331 -0.08 +ATOM H131 HGA3 0.09 +ATOM H132 HGA3 0.09 +ATOM H133 HGA3 0.09 +GROUP +ATOM C20 CG331 -0.27 +ATOM H201 HGA3 0.09 +ATOM H202 HGA3 0.09 +ATOM H203 HGA3 0.09 + +BOND C12 C13 C13 C14 C14 C15 C15 N21 N21 C16 +BOND C13 C20 C15 O29 C14 H141 N21 H211 +BOND C16 H131 C16 H132 C16 H133 +BOND C12 H121 C12 H122 C12 H123 +BOND C20 H201 C20 H202 C20 H203 +IMPR C15 C14 N21 O29 + +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C15 N21 C16 0.0000 0.00 180.00 0.00 0.0000 +IC H121 C13 *C12 H122 0.0000 0.00 120.00 0.00 0.0000 +IC H121 C13 *C12 H123 0.0000 0.00 -120.00 0.00 0.0000 +IC H121 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 +IC C16 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 +IC C15 N21 C16 H131 0.0000 0.00 180.00 0.00 0.0000 +IC H131 N21 *C16 H132 0.0000 0.00 120.00 0.00 0.0000 +IC H131 N21 *C16 H133 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI PACP 0.00 ! C8H9NO2 p-acetamide-phenol + ! numbering as in fennretinide + +ATOM C14 CG331 -0.27 ! H142 +ATOM H141 HGA3 0.09 ! | +ATOM H142 HGA3 0.09 ! H141-C14-H143 +ATOM H143 HGA3 0.09 ! | +GROUP ! C15=O29 +ATOM C15 CG2O1 0.52 ! | +ATOM O29 OG2D1 -0.52 ! N21-H211 +GROUP ! | +ATOM N21 NG2S1 -0.47 ! C22 +ATOM H211 HGP1 0.33 ! // \ +ATOM C22 CG2R61 0.14 ! H231-C23 C27-H271 +GROUP ! | || +ATOM C23 CG2R61 -0.115 ! H241-C24 C26-H261 +ATOM H231 HGR61 0.115 ! \\ / +GROUP ! C25 +ATOM C24 CG2R61 -0.115 ! | +ATOM H241 HGR61 0.115 ! O28 +GROUP ! \ +ATOM C26 CG2R61 -0.115 ! H281 +ATOM H261 HGR61 0.115 +GROUP +ATOM C27 CG2R61 -0.115 +ATOM H271 HGR61 0.115 +GROUP +ATOM C25 CG2R61 0.11 +ATOM O28 OG311 -0.53 +ATOM H281 HGP1 0.42 + +BOND C14 C15 C15 N21 N21 C22 C22 C23 C15 O29 +BOND C23 C24 C24 C25 C25 C26 C26 C27 C27 C22 +BOND C25 O28 O28 H281 N21 H211 +BOND C14 H141 C14 H142 C14 H143 +BOND C23 H231 C24 H241 C26 H261 C27 H271 +IMPR C15 C14 N21 O29 + +IC C14 C15 N21 C22 0.0000 0.00 180.00 0.00 0.0000 +IC C15 N21 C22 C27 0.0000 0.00 0.00 0.00 0.0000 +IC N21 C22 C23 C24 0.0000 0.00 180.00 0.00 0.0000 +IC C22 C23 C24 C25 0.0000 0.00 0.00 0.00 0.0000 +IC C23 C24 C25 O28 0.0000 0.00 180.00 0.00 0.0000 +IC H141 C15 *C14 H142 0.0000 0.00 120.00 0.00 0.0000 +IC H141 C15 *C14 H143 0.0000 0.00 -120.00 0.00 0.0000 +IC H141 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 +IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 +IC C22 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 +IC C27 N21 *C22 C23 0.0000 0.00 180.00 0.00 0.0000 +IC C24 C22 *C23 H231 0.0000 0.00 180.00 0.00 0.0000 +IC C25 C23 *C24 H241 0.0000 0.00 180.00 0.00 0.0000 +IC O28 C24 *C25 C26 0.0000 0.00 180.00 0.00 0.0000 +IC C27 C25 *C26 H261 0.0000 0.00 180.00 0.00 0.0000 +IC C26 C22 *C27 H271 0.0000 0.00 180.00 0.00 0.0000 +IC C24 C25 O28 H281 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI MECH 0.00 ! C11H18 1,6,6-trimethyl-2-ethenyl-cyclohexene + ! using retinol numbering +GROUP +ATOM C1 CG301 0.00 !H162 H163 H171 H172 +ATOM C2 CG321 -0.18 ! \ | | / +ATOM H21 HGA2 0.09 !H161-C16 C17-H173 H81 +ATOM H22 HGA2 0.09 ! \ / | +ATOM C3 CG321 -0.18 ! H21 C1 C8-H82 +ATOM H31 HGA2 0.09 ! \ / \ // +ATOM H32 HGA2 0.09 ! H22-C2 C6------C7 +ATOM C4 CG321 -0.18 ! | || \ +ATOM H41 HGA2 0.09 ! H31-C3 C5 H181 H71 +ATOM H42 HGA2 0.09 ! / \ / \ / +ATOM C5 CG2DC2 0.00 ! H32 C4 C18-H18 +ATOM C6 CG2DC2 0.00 ! / \ \ +GROUP ! H41 H42 H183 +ATOM C7 CG2DC1 -0.15 +ATOM H71 HGA4 0.15 +ATOM C8 CG2DC3 -0.42 +ATOM H81 HGA5 0.21 +ATOM H82 HGA5 0.21 +GROUP +ATOM C16 CG331 -0.27 +ATOM H161 HGA3 0.09 +ATOM H162 HGA3 0.09 +ATOM H163 HGA3 0.09 +GROUP +ATOM C17 CG331 -0.27 +ATOM H171 HGA3 0.09 +ATOM H172 HGA3 0.09 +ATOM H173 HGA3 0.09 +GROUP +ATOM C18 CG331 -0.27 +ATOM H181 HGA3 0.09 +ATOM H182 HGA3 0.09 +ATOM H183 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C1 C16 C1 C17 C5 C18 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C7 H71 C8 H81 C8 H82 C18 H181 C18 H182 C18 H183 + +!initial ring geometry is planar +IC C1 C2 C3 C4 0.00 0.00 63.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 -46.0 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 15.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 +IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 +IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 +IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 +IC C1 C5 *C6 C7 0.00 0.00 180.0 0.00 0.00 +IC C5 C6 C7 C8 0.00 0.00 60.0 0.00 0.00 +IC C6 C8 *C7 H71 0.00 0.00 180.0 0.00 0.00 +IC C6 C7 C8 H81 0.00 0.00 180.0 0.00 0.00 +IC C7 H81 *C8 H82 0.00 0.00 180.0 0.00 0.00 +IC C6 C2 *C1 C16 0.00 0.00 120.0 0.00 0.00 +IC C6 C2 *C1 C17 0.00 0.00 -120.0 0.00 0.00 +IC C2 C1 C16 H161 0.00 0.00 180.0 0.00 0.00 +IC C1 H161 *C16 H162 0.00 0.00 120.0 0.00 0.00 +IC C1 H161 *C16 H163 0.00 0.00 -120.0 0.00 0.00 +IC C2 C1 C17 H171 0.00 0.00 180.0 0.00 0.00 +IC C1 H171 *C17 H172 0.00 0.00 120.0 0.00 0.00 +IC C1 H171 *C17 H173 0.00 0.00 -120.0 0.00 0.00 +IC C4 C6 *C5 C18 0.00 0.00 180.0 0.00 0.00 +IC C4 C5 C18 H181 0.00 0.00 180.0 0.00 0.00 +IC C5 H181 *C18 H182 0.00 0.00 120.0 0.00 0.00 +IC C5 H181 *C18 H183 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI TMCH 0.00 ! C10H18 1,2,6,6-tetramethylcyclohexene + ! using retinol numbering +GROUP +ATOM C1 CG301 0.00 !H162 H163 H171 H172 +ATOM C2 CG321 -0.18 ! \ | | / +ATOM H21 HGA2 0.09 !H161-C16 C17-H173 +ATOM H22 HGA2 0.09 ! \ / +ATOM C3 CG321 -0.18 ! H21 C1 H71 H72 +ATOM H31 HGA2 0.09 ! \ / \ | / +ATOM H32 HGA2 0.09 ! H22-C2 C6------C7-H73 +ATOM C4 CG321 -0.18 ! | || +ATOM H41 HGA2 0.09 ! H31-C3 C5 H181 +ATOM H42 HGA2 0.09 ! / \ / \ / +ATOM C5 CG2D1 0.00 ! H32 C4 C18-H18 +ATOM C6 CG2D1 0.00 ! / \ \ +GROUP ! H41 H42 H183 +ATOM C7 CG331 -0.27 +ATOM H71 HGA3 0.09 +ATOM H72 HGA3 0.09 +ATOM H73 HGA3 0.09 +GROUP +ATOM C16 CG331 -0.27 +ATOM H161 HGA3 0.09 +ATOM H162 HGA3 0.09 +ATOM H163 HGA3 0.09 +GROUP +ATOM C17 CG331 -0.27 +ATOM H171 HGA3 0.09 +ATOM H172 HGA3 0.09 +ATOM H173 HGA3 0.09 +GROUP +ATOM C18 CG331 -0.27 +ATOM H181 HGA3 0.09 +ATOM H182 HGA3 0.09 +ATOM H183 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C1 C16 C1 C17 C5 C18 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C7 H71 C7 H72 C7 H73 C18 H181 C18 H182 C18 H183 + +!initial geometry is planar +IC C1 C2 C3 C4 0.00 0.00 -63.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 46.0 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 -13.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 +IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 +IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 +IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 +IC C1 C5 *C6 C7 0.00 0.00 180.0 0.00 0.00 +IC C5 C6 C7 H71 0.00 0.00 180.0 0.00 0.00 +IC C6 H71 *C7 H72 0.00 0.00 120.0 0.00 0.00 +IC C6 H71 *C7 H73 0.00 0.00 -120.0 0.00 0.00 +IC C6 C2 *C1 C16 0.00 0.00 120.0 0.00 0.00 +IC C6 C2 *C1 C17 0.00 0.00 -120.0 0.00 0.00 +IC C2 C1 C16 H161 0.00 0.00 180.0 0.00 0.00 +IC C1 H161 *C16 H162 0.00 0.00 120.0 0.00 0.00 +IC C1 H161 *C16 H163 0.00 0.00 -120.0 0.00 0.00 +IC C2 C1 C17 H171 0.00 0.00 180.0 0.00 0.00 +IC C1 H171 *C17 H172 0.00 0.00 120.0 0.00 0.00 +IC C1 H171 *C17 H173 0.00 0.00 -120.0 0.00 0.00 +IC C4 C6 *C5 C18 0.00 0.00 180.0 0.00 0.00 +IC C4 C5 C18 H181 0.00 0.00 180.0 0.00 0.00 +IC C5 H181 *C18 H182 0.00 0.00 120.0 0.00 0.00 +IC C5 H181 *C18 H183 0.00 0.00 -120.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI FRET 0.00 ! C26H33NO2 fennretinide, nomenclature consistent with retinol +GROUP +ATOM C1 CG301 0.00 +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +ATOM C5 CG2DC2 0.00 +ATOM C6 CG2DC2 0.00 +GROUP +ATOM C7 CG2DC1 -0.15 +ATOM H71 HGA4 0.15 +ATOM C8 CG2DC1 -0.15 +ATOM H81 HGA4 0.15 +ATOM C9 CG2DC2 0.00 +ATOM C10 CG2DC2 -0.15 +ATOM H101 HGA4 0.15 +GROUP +ATOM C11 CG2DC1 -0.15 !H162 H163 H171 H172 +ATOM H111 HGA4 0.15 ! \ | | / +ATOM C12 CG2DC1 -0.15 !H161-C16 C17-H173 H191 H192 +ATOM H121 HGA4 0.15 ! \ / \ / +ATOM C13 CG2DC2 0.00 ! H21 C1 H71 H81 C19 +ATOM C14 CG2DC2 -0.15 ! \ / \ | | / \ +ATOM H141 HGA4 0.15 ! H22-C2 C6------C7=====C8----C9 H193 +GROUP ! | || || +ATOM C16 CG331 -0.27 ! H31-C3 C5 H181 C10-H101 +ATOM H161 HGA3 0.09 ! / \ / \ / | +ATOM H162 HGA3 0.09 ! H32 C4 C18-H182 C11-H111 +ATOM H163 HGA3 0.09 ! / \ \ || +GROUP ! H41 H42 H183 C12-H121 H201 +ATOM C17 CG331 -0.27 ! | / +ATOM H171 HGA3 0.09 ! C13---C20-H202 +ATOM H172 HGA3 0.09 ! || \ +ATOM H173 HGA3 0.09 ! C14-H141 H203 +GROUP ! | +ATOM C18 CG331 -0.27 ! C15=O29 +ATOM H181 HGA3 0.09 ! | +ATOM H182 HGA3 0.09 ! N21-H211 +ATOM H183 HGA3 0.09 ! | +GROUP ! C22 +ATOM C19 CG331 -0.27 ! // \ +ATOM H191 HGA3 0.09 ! H231-C23 C27-H271 +ATOM H192 HGA3 0.09 ! | || +ATOM H193 HGA3 0.09 ! H241-C24 C26-H261 +GROUP ! \\ / +ATOM C20 CG331 -0.27 ! C25 +ATOM H201 HGA3 0.09 ! | +ATOM H202 HGA3 0.09 ! O28 +ATOM H203 HGA3 0.09 ! \ +GROUP ! H281 +ATOM C15 CG2O1 0.51 ! charges from CROT +ATOM O29 OG2D1 -0.51 +GROUP +ATOM N21 NG2S1 -0.47 +ATOM H211 HGP1 0.33 ! charges from PACP +ATOM C22 CG2R61 0.14 +GROUP +ATOM C23 CG2R61 -0.115 +ATOM H231 HGR61 0.115 +GROUP +ATOM C24 CG2R61 -0.115 +ATOM H241 HGR61 0.115 +GROUP +ATOM C26 CG2R61 -0.115 +ATOM H261 HGR61 0.115 +GROUP +ATOM C27 CG2R61 -0.115 +ATOM H271 HGR61 0.115 +GROUP +ATOM C25 CG2R61 0.11 +ATOM O28 OG311 -0.53 +ATOM H281 HGP1 0.42 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 C13 C13 C14 C14 C15 C15 N21 N21 C22 C22 C23 +BOND C23 C24 C24 C25 C25 C26 C26 C27 C27 C22 +BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 C15 O29 +BOND C25 O28 O28 H281 N21 H211 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 +BOND C20 H201 C20 H202 C20 H203 +BOND C23 H231 C24 H241 C26 H261 C27 H271 +IMPR C15 C14 N21 O29 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 +IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 +IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 +IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 +IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 +IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 +IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 +IC C13 C14 C15 N21 0.0000 0.00 180.00 0.00 0.0000 +IC N21 C14 *C15 O29 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C15 N21 C22 0.0000 0.00 180.00 0.00 0.0000 +IC C22 C15 *N21 H211 0.0000 0.00 180.00 0.00 0.0000 +IC C15 N21 C22 C27 0.0000 0.00 180.00 0.00 0.0000 +IC C27 N21 *C22 C23 0.0000 0.00 180.00 0.00 0.0000 +IC N21 C22 C23 C24 0.0000 0.00 180.00 0.00 0.0000 +IC C24 C22 *C23 H231 0.0000 0.00 180.00 0.00 0.0000 +IC C22 C23 C24 C25 0.0000 0.00 0.00 0.00 0.0000 +IC C25 C23 *C24 H241 0.0000 0.00 180.00 0.00 0.0000 +IC C23 C24 C25 O28 0.0000 0.00 180.00 0.00 0.0000 +IC O28 C24 *C25 C26 0.0000 0.00 180.00 0.00 0.0000 +IC C27 C25 *C26 H261 0.0000 0.00 180.00 0.00 0.0000 +IC C26 C22 *C27 H271 0.0000 0.00 180.00 0.00 0.0000 +IC C24 C25 O28 H281 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI RTOL 0.00 ! C20H30O retinol, nomenclature from PDB + +GROUP +ATOM C1 CG301 0.00 +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +GROUP +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +ATOM C5 CG2DC2 0.00 +ATOM C6 CG2DC2 0.00 +GROUP +ATOM C7 CG2DC1 -0.15 +ATOM H71 HGA4 0.15 +ATOM C8 CG2DC1 -0.15 +ATOM H81 HGA4 0.15 +GROUP +ATOM C9 CG2DC2 0.00 +ATOM C10 CG2DC2 -0.15 +ATOM H101 HGA4 0.15 +GROUP +ATOM C11 CG2DC1 -0.15 +ATOM H111 HGA4 0.15 +GROUP +ATOM C12 CG2DC1 -0.15 +ATOM H121 HGA4 0.15 +GROUP +ATOM C13 CG2DC2 0.00 +ATOM C14 CG2DC2 -0.15 +ATOM H141 HGA4 0.15 !H162 H163 H171 H172 +GROUP ! \ | | / +ATOM C15 CG321 0.05 !H161-C16 C17-H173 H191 H192 +ATOM H151 HGA2 0.09 ! \ / \ / +ATOM H152 HGA2 0.09 ! H21 C1 H71 H81 C19 +ATOM OR OG311 -0.65 ! \ / \ | | / \ +ATOM HR HGP1 0.42 ! H22-C2 C6------C7=====C8----C9 H193 +GROUP ! | || || +ATOM C16 CG331 -0.27 ! H31-C3 C5 H181 C10-H101 +ATOM H161 HGA3 0.09 ! / \ / \ / | +ATOM H162 HGA3 0.09 ! H32 C4 C18-H182 C11-H111 +ATOM H163 HGA3 0.09 ! / \ \ || +GROUP ! H41 H42 H183 C12-H121 H201 +ATOM C17 CG331 -0.27 ! | / +ATOM H171 HGA3 0.09 ! C13---C20-H202 +ATOM H172 HGA3 0.09 ! || \ +ATOM H173 HGA3 0.09 ! C14-H141 H203 +GROUP ! | +ATOM C18 CG331 -0.27 ! H151-C15-H152 +ATOM H181 HGA3 0.09 ! | +ATOM H182 HGA3 0.09 ! OR +ATOM H183 HGA3 0.09 ! \ +GROUP ! HR +ATOM C19 CG331 -0.27 +ATOM H191 HGA3 0.09 +ATOM H192 HGA3 0.09 +ATOM H193 HGA3 0.09 +GROUP +ATOM C20 CG331 -0.27 +ATOM H201 HGA3 0.09 +ATOM H202 HGA3 0.09 +ATOM H203 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 C13 C13 C14 C14 C15 C15 OR +BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 +BOND C15 H151 C15 H152 OR HR +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 +BOND C20 H201 C20 H202 C20 H203 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 OR 0.0000 0.00 180.00 0.00 0.0000 +IC OR C14 *C15 H151 0.0000 0.00 120.00 0.00 0.0000 +IC OR C14 *C15 H152 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C15 OR HR 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 +IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 +IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 +IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 +IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 +IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 +IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI RTAL 0.00 ! C20H28O retinal, nomenclature from PDB based on retinol + +GROUP +ATOM C1 CG301 0.00 +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +ATOM C5 CG2DC2 0.00 +ATOM C6 CG2DC2 0.00 +GROUP +ATOM C7 CG2DC1 -0.15 +ATOM H71 HGA4 0.15 +ATOM C8 CG2DC1 -0.15 +ATOM H81 HGA4 0.15 +ATOM C9 CG2DC2 0.00 +ATOM C10 CG2DC2 -0.15 +ATOM H101 HGA4 0.15 +GROUP +ATOM C11 CG2DC1 -0.15 +ATOM H111 HGA4 0.15 +ATOM C12 CG2DC1 -0.15 +ATOM H121 HGA4 0.15 +ATOM C13 CG2DC2 0.00 !H162 H163 H171 H172 +GROUP ! \ | | / +ATOM C14 CG2DC2 -0.04 !H161-C16 C17-H173 H191 H192 +ATOM H141 HGA4 0.15 ! \ / \ / +ATOM C15 CG2O4 0.27 ! H21 C1 H71 H81 C19 +ATOM O15 OG2D1 -0.51 ! \ / \ | | / \ +ATOM H15 HGR52 0.13 ! H22-C2 C6------C7=====C8----C9 H193 +GROUP ! | || || +ATOM C16 CG331 -0.27 ! H31-C3 C5 H181 C10-H101 +ATOM H161 HGA3 0.09 ! / \ / \ / | +ATOM H162 HGA3 0.09 ! H32 C4 C18-H182 C11-H111 +ATOM H163 HGA3 0.09 ! / \ \ || +GROUP ! H41 H42 H183 C12-H121 H201 +ATOM C17 CG331 -0.27 ! | / +ATOM H171 HGA3 0.09 ! C13---C20-H202 +ATOM H172 HGA3 0.09 ! || \ +ATOM H173 HGA3 0.09 ! C14-H141 H203 +GROUP ! | +ATOM C18 CG331 -0.27 ! C15 +ATOM H181 HGA3 0.09 ! / \\ +ATOM H182 HGA3 0.09 ! H15 O15 +ATOM H183 HGA3 0.09 +GROUP +ATOM C19 CG331 -0.27 +ATOM H191 HGA3 0.09 +ATOM H192 HGA3 0.09 +ATOM H193 HGA3 0.09 +GROUP +ATOM C20 CG331 -0.27 +ATOM H201 HGA3 0.09 +ATOM H202 HGA3 0.09 +ATOM H203 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 C13 C13 C14 C14 C15 C15 O15 C15 H15 +BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 +BOND C20 H201 C20 H202 C20 H203 +IMPR C15 C14 O15 H15 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 O15 0.0000 0.00 180.00 0.00 0.0000 +IC O15 C14 *C15 H15 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 +IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 +IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 +IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 +IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 +IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 +IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI RTAC -1.00 ! C20H27O2 all-trans-retinoic acid, nomenclature from PDB + +GROUP +ATOM C1 CG301 0.00 +ATOM C16 CG331 -0.27 +ATOM H161 HGA3 0.09 +ATOM H162 HGA3 0.09 +ATOM H163 HGA3 0.09 +ATOM C17 CG331 -0.27 +ATOM H171 HGA3 0.09 +ATOM H172 HGA3 0.09 +ATOM H173 HGA3 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG2DC2 0.00 +ATOM C6 CG2DC2 0.00 +GROUP +ATOM C18 CG331 -0.27 +ATOM H181 HGA3 0.09 +ATOM H182 HGA3 0.09 +ATOM H183 HGA3 0.09 +GROUP +ATOM C7 CG2DC1 -0.15 +ATOM H71 HGA4 0.15 +ATOM C8 CG2DC1 -0.15 +ATOM H81 HGA4 0.15 +GROUP +ATOM C9 CG2DC2 0.00 +ATOM C19 CG331 -0.27 !H162 H163 H171 H172 +ATOM H191 HGA3 0.09 ! \ | | / +ATOM H192 HGA3 0.09 !H161-C16 C17-H173 H191 H192 +ATOM H193 HGA3 0.09 ! \ / \ / +ATOM C10 CG2DC2 -0.15 ! H21 C1 H71 H81 C19 +ATOM H101 HGA4 0.15 ! \ / \ | | / \ +GROUP ! H22-C2 C6------C7=====C8----C9 H193 +ATOM C11 CG2DC1 -0.15 ! | || || +ATOM H111 HGA4 0.15 ! H31-C3 C5 H181 C10-H101 +ATOM C12 CG2DC1 -0.15 ! / \ / \ / | +ATOM H121 HGA4 0.15 ! H32 C4 C18-H182 C11-H111 +GROUP ! / \ \ || +ATOM C13 CG2DC2 0.00 ! H41 H42 H183 C12-H121 H201 +ATOM C20 CG331 -0.27 ! | / +ATOM H201 HGA3 0.09 ! C13---C20-H202 +ATOM H202 HGA3 0.09 ! || \ +ATOM H203 HGA3 0.09 ! C14-H141 H203 +GROUP ! | +ATOM C14 CG2DC2 -0.25 ! C15=O29 +ATOM H141 HGA4 0.15 ! | (-) +ATOM C15 CG2O3 0.62 ! O29B +ATOM O29 OG2D2 -0.76 +ATOM O29B OG2D2 -0.76 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 C13 C13 C14 C14 C15 C15 O29 C15 O29B +BOND C1 C16 C1 C17 C5 C18 C9 C19 C13 C20 +BOND C2 H21 C2 H22 C3 H31 C3 H32 C4 H41 C4 H42 +BOND C7 H71 C8 H81 C10 H101 C11 H111 C12 H121 C14 H141 +BOND C16 H161 C16 H162 C16 H163 C17 H171 C17 H172 C17 H173 +BOND C18 H181 C18 H182 C18 H183 C19 H191 C19 H192 C19 H193 +BOND C20 H201 C20 H202 C20 H203 +IMPR C15 O29B O29 C14 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 C16 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 C17 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C16 H161 0.0000 0.00 180.00 0.00 0.0000 +IC H161 C1 *C16 H162 0.0000 0.00 120.00 0.00 0.0000 +IC H161 C1 *C16 H163 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 C17 H171 0.0000 0.00 180.00 0.00 0.0000 +IC H171 C1 *C17 H172 0.0000 0.00 120.00 0.00 0.0000 +IC H171 C1 *C17 H173 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 C18 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C18 H181 0.0000 0.00 180.00 0.00 0.0000 +IC H181 C5 *C18 H182 0.0000 0.00 120.00 0.00 0.0000 +IC H181 C5 *C18 H183 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 C19 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C19 H191 0.0000 0.00 180.00 0.00 0.0000 +IC H191 C9 *C19 H192 0.0000 0.00 120.00 0.00 0.0000 +IC H191 C9 *C19 H193 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H101 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H121 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 C20 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C13 C20 H201 0.0000 0.00 180.00 0.00 0.0000 +IC H201 C13 *C20 H202 0.0000 0.00 120.00 0.00 0.0000 +IC H201 C13 *C20 H203 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C13 *C14 H141 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C14 C15 O29 0.0000 0.00 180.00 0.00 0.0000 +IC O29 C14 *C15 O29B 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI PRAC -1.00 ! C3H3O2 2-propenoic acid +GROUP +ATOM C1 CG2DC3 -0.42 +ATOM H11 HGA5 0.21 +ATOM H12 HGA5 0.21 ! H11 OD1 +GROUP ! \ || +ATOM C2 CG2DC1 -0.25 ! C1 CG +ATOM H21 HGA4 0.15 ! / \\ / \ +ATOM CG CG2O3 0.62 ! H12 C2 OD2 (-) +ATOM OD1 OG2D2 -0.76 ! | +ATOM OD2 OG2D2 -0.76 ! H21 + +BOND C1 H11 C1 H12 C1 C2 C2 H21 +BOND C2 CG CG OD1 CG OD2 +IMPR CG OD2 OD1 C2 + +IC C1 C2 CG OD1 0.0000 0.00 180.00 0.00 0.0000 +IC OD1 C2 *CG OD2 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 CG 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC CG C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI PROL 0.00 ! C3H6O 3-propenol (1-hydroxy-2-propene) + +GROUP +ATOM C1 CG2D2 -0.42 +ATOM H11 HGA5 0.21 ! H11 H31 +ATOM H12 HGA5 0.21 ! \ | +ATOM C2 CG2D1 -0.15 ! C1 C3-OR +ATOM H21 HGA4 0.15 ! / \\ / | \ +GROUP ! H12 C2 H32 HR +ATOM C3 CG321 0.05 ! | +ATOM H31 HGA2 0.09 ! H21 +ATOM H32 HGA2 0.09 +ATOM OR OG311 -0.65 +ATOM HR HGP1 0.42 +BOND C1 C2 C2 C3 C3 OR OR HR +BOND H11 C1 H12 C1 H21 C2 H31 C3 +BOND H32 C3 + +IC C1 C2 C3 OR 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 OR HR 0.0000 0.00 60.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC OR C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC OR C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + +RESI PRAL 0.00 ! C3H4O 2-propenal (acrolein) +GROUP +ATOM C1 CG2DC3 -0.42 +ATOM H11 HGA5 0.21 ! H11 OD1 +ATOM H12 HGA5 0.21 ! \ || +ATOM C2 CG2DC1 -0.04 ! C1 CG +ATOM H21 HGA4 0.15 ! / \\ / \ +ATOM CG CG2O4 0.27 ! H12 C2 H +ATOM OD1 OG2D1 -0.51 ! | +ATOM H HGR52 0.13 ! H21 + +BOND C1 H11 C1 H12 C1 C2 C2 H21 +BOND C2 CG CG OD1 CG H +IMPR CG C2 OD1 H + +IC C1 C2 CG OD1 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 CG 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC CG C1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC OD1 C2 *CG H 0.0000 0.00 180.00 0.00 0.0000 + +RESI SCH1 0.00 ! C3H7N Schiff's base model compound 1, deprotonated +GROUP +ATOM C1 CG331 -0.05 ! H11 H31 +ATOM H11 HGA3 0.09 ! \ / +ATOM H12 HGA3 0.09 ! H12--C1-N2=C3 H41 +ATOM H13 HGA3 0.09 ! / \ / +ATOM N2 NG2D1 -0.60 ! H13 C4--H42 +ATOM C3 CG2D1 0.23 ! \ +ATOM H31 HGA4 0.15 ! H43 +GROUP +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 N2 N2 C3 C3 H31 +BOND C3 C4 C4 H41 C4 H42 C4 H43 +IMPR C3 C4 N2 H31 + +IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C3 N2 C1 H11 0.0000 0.00 0.00 0.00 0.0000 +IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +RESI SCH2 1.00 ! C3H8N Schiff's base model compound 2, protonated +GROUP +ATOM C1 CG334 0.18 ! H11 H21 H31 +ATOM H11 HGA3 0.09 ! \ | / +ATOM H12 HGA3 0.09 ! H12--C1-N2=C3 H41 +ATOM H13 HGA3 0.09 ! / (+) \ / +ATOM N2 NG2P1 -0.40 ! H13 C4--H42 +ATOM H21 HGP2 0.38 ! \ +ATOM C3 CG2D1 0.37 ! H43 +ATOM H31 HGR52 0.20 ! hydrogen with intermediate VDW radius +GROUP +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 N2 N2 H21 N2 C3 C3 H31 +BOND C3 C4 C4 H41 C4 H42 C4 H43 +IMPR C3 C4 N2 H31 + +IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *N2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C3 N2 C1 H11 0.0000 0.00 0.00 0.00 0.0000 +IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +RESI SCH3 1.00 ! C4H8N Schiff's base model compound 3, protonated +GROUP +ATOM C1 CG334 0.18 ! H11 H21 H31 +ATOM H11 HGA3 0.09 ! \ | / +ATOM H12 HGA3 0.09 ! H12--C1-N2=C3 H51 +ATOM H13 HGA3 0.09 ! / (+) \ / +ATOM N2 NG2P1 -0.40 ! H13 C4=C5 +ATOM H21 HGP2 0.38 ! / \ +ATOM C3 CG2DC1 0.37 ! H41 H52 +ATOM H31 HGR52 0.20 ! hydrogen with intermediate VDW radius +GROUP +ATOM C4 CG2DC2 -0.15 +ATOM H41 HGA4 0.15 +ATOM C5 CG2DC3 -0.42 +ATOM H51 HGA5 0.21 +ATOM H52 HGA5 0.21 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 N2 N2 H21 N2 C3 C3 H31 +BOND C3 C4 C4 H41 +BOND C4 C5 C5 H51 C5 H52 +IMPR C3 C4 N2 H31 + +IC C1 N2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 N2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *N2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C4 N2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H51 C4 *C5 H52 0.0000 0.00 180.00 0.00 0.0000 + +!/home/alex/param/general/Cyprus/toppar +!toppar_all22_flavopyridol_apr05.str +!piperidine models only + +RESI PIP1 1.00 ! C6H14N N-methyl piperidinium + !methyl axial to ring + !Note that PIP1 and 2 only differ by the configuration about the N +GROUP +ATOM C1 CG334 0.15 +ATOM H1A HGA3 0.09 +ATOM H1B HGA3 0.09 ! C15--C16 +ATOM H1C HGA3 0.09 ! / \ +ATOM N1 NG3P1 -0.40 ! C14 (+) N1--C1 +ATOM HNA HGP2 0.32 ! \ / +ATOM C12 CG324 0.15 ! C13--C12 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +ATOM C16 CG324 0.15 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C13 CG321 -0.18 +ATOM H13A HGA2 0.09 +ATOM H13B HGA2 0.09 +GROUP +ATOM C14 CG321 -0.18 +ATOM H14A HGA2 0.09 +ATOM H14B HGA2 0.09 +GROUP +ATOM C15 CG321 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +BOND C1 H1A C1 H1B C1 H1C C1 N1 +BOND N1 HNA +BOND N1 C16 N1 C12 C12 H12A C12 H12B +BOND C12 C13 C13 H13A C13 H13B +BOND C13 C14 C14 H14A C14 H14B C14 C15 +BOND C15 H15A C15 H15B C15 C16 C16 H16A +BOND C16 H16B + +IC C16 N1 C12 C13 0.0000 0.00 -60.00 0.00 0.0000 +IC N1 C12 C13 C14 0.0000 0.00 60.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 -60.00 0.00 0.0000 +IC C13 C14 C15 C16 0.0000 0.00 60.00 0.00 0.0000 +IC C12 C16 *N1 C1 0.0000 0.00 -120.00 0.00 0.0000 +IC H1A N1 *C1 H1B 0.0000 0.00 120.00 0.00 0.0000 +IC H1A N1 *C1 H1C 0.0000 0.00 -120.00 0.00 0.0000 +IC H1A C1 N1 C16 0.0000 0.00 180.00 0.00 0.0000 +IC C16 C1 *N1 C12 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C1 *N1 HNA 0.0000 0.00 -120.00 0.00 0.0000 +IC C13 N1 *C12 H12A 0.0000 0.00 120.00 0.00 0.0000 +IC H12A N1 *C12 H12B 0.0000 0.00 120.00 0.00 0.0000 +IC C15 N1 *C16 H16A 0.0000 0.00 120.00 0.00 0.0000 +IC C15 N1 *C16 H16B 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C12 *C13 H13A 0.0000 0.00 120.00 0.00 0.0000 +IC H13A C12 *C13 H13B 0.0000 0.00 120.00 0.00 0.0000 +IC C15 C13 *C14 H14A 0.0000 0.00 -120.00 0.00 0.0000 +IC H14A C13 *C14 H14B 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C16 *C15 H15A 0.0000 0.00 120.00 0.00 0.0000 +IC C14 C16 *C15 H15B 0.0000 0.00 -120.00 0.00 0.0000 + +PATCH FIRST NONE LAST NONE + + +RESI PIP2 1.00 ! C6H14N N-methyl piperidinium + !methyl equitorial to ring +GROUP +ATOM C1 CG334 0.15 +ATOM H1A HGA3 0.09 +ATOM H1B HGA3 0.09 ! C15--C16 +ATOM H1C HGA3 0.09 ! / \ +ATOM N1 NG3P1 -0.40 ! C14 (+) N1--C1 +ATOM HNA HGP2 0.32 ! \ / +ATOM C12 CG324 0.15 ! C13--C12 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +ATOM C16 CG324 0.15 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C13 CG321 -0.18 +ATOM H13A HGA2 0.09 +ATOM H13B HGA2 0.09 +GROUP +ATOM C14 CG321 -0.18 +ATOM H14A HGA2 0.09 +ATOM H14B HGA2 0.09 +GROUP +ATOM C15 CG321 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +BOND C1 H1A C1 H1B C1 H1C C1 N1 +BOND N1 HNA +BOND N1 C16 N1 C12 C12 H12A C12 H12B +BOND C12 C13 C13 H13A C13 H13B +BOND C13 C14 C14 H14A C14 H14B C14 C15 +BOND C15 H15A C15 H15B C15 C16 C16 H16A +BOND C16 H16B + +IC C16 N1 C12 C13 0.0000 0.00 -60.00 0.00 0.0000 +IC N1 C12 C13 C14 0.0000 0.00 60.00 0.00 0.0000 +IC C12 C13 C14 C15 0.0000 0.00 -60.00 0.00 0.0000 +IC C13 C14 C15 C16 0.0000 0.00 60.00 0.00 0.0000 +IC C12 C16 *N1 C1 0.0000 0.00 120.00 0.00 0.0000 +IC H1A N1 *C1 H1B 0.0000 0.00 120.00 0.00 0.0000 +IC H1A N1 *C1 H1C 0.0000 0.00 -120.00 0.00 0.0000 +IC H1A C1 N1 C16 0.0000 0.00 180.00 0.00 0.0000 +IC C16 C1 *N1 C12 0.0000 0.00 -120.00 0.00 0.0000 +IC C12 C1 *N1 HNA 0.0000 0.00 120.00 0.00 0.0000 +IC C13 N1 *C12 H12A 0.0000 0.00 120.00 0.00 0.0000 +IC H12A N1 *C12 H12B 0.0000 0.00 120.00 0.00 0.0000 +IC C15 N1 *C16 H16A 0.0000 0.00 120.00 0.00 0.0000 +IC C15 N1 *C16 H16B 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C12 *C13 H13A 0.0000 0.00 120.00 0.00 0.0000 +IC H13A C12 *C13 H13B 0.0000 0.00 120.00 0.00 0.0000 +IC C15 C13 *C14 H14A 0.0000 0.00 -120.00 0.00 0.0000 +IC H14A C13 *C14 H14B 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C16 *C15 H15A 0.0000 0.00 120.00 0.00 0.0000 +IC C14 C16 *C15 H15B 0.0000 0.00 -120.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI PIP3 1.00 ! C6H14NO 3-hydroxy-N-methyl piperidinium +GROUP +ATOM C1 CG334 0.15 ! group charge should be 1.0 +ATOM H1A HGA3 0.09 +ATOM H1B HGA3 0.09 ! C15--C16 +ATOM H1C HGA3 0.09 ! / \ +ATOM N1 NG3P1 -0.40 ! ----C14 (+) N1--C1 +ATOM HNA HGP2 0.32 ! \ / +ATOM C12 CG324 0.15 ! C13--C12 +ATOM H12A HGA2 0.09 ! / +ATOM H12B HGA2 0.09 ! H-O3 +ATOM C16 CG324 0.15 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C13 CG311 0.14 +ATOM H13 HGA1 0.09 +ATOM O3 OG311 -0.65 +ATOM HO3 HGP1 0.42 +GROUP +ATOM C14 CG321 -0.18 +ATOM H14A HGA2 0.09 +ATOM H14B HGA2 0.09 +GROUP +ATOM C15 CG321 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +BOND C1 H1A C1 H1B C1 H1C C1 N1 +BOND N1 HNA +BOND N1 C16 N1 C12 C12 H12A C12 H12B +BOND C12 C13 C13 H13 C13 O3 O3 HO3 +BOND C13 C14 C14 H14A C14 H14B C14 C15 +BOND C15 H15A C15 H15B C15 C16 C16 H16A +BOND C16 H16B +IC C14 C15 C16 N1 .0000 .00 -60.00 .00 .0000 +IC C15 C16 N1 C12 .0000 .00 60.00 .00 .0000 +IC C16 N1 C12 C13 .0000 .00 -60.00 .00 .0000 +IC N1 C12 C13 C14 .0000 .00 60.00 .00 .0000 +IC C12 C16 *N1 C1 .0000 .00 120.00 .00 .0000 +IC C12 C16 *N1 HNA .0000 .00 -120.00 .00 .0000 +IC C16 N1 C1 H1A .0000 .00 120.00 .00 .0000 +IC H1A N1 *C1 H1B .0000 .00 120.00 .00 .0000 +IC H1A N1 *C1 H1C .0000 .00 -120.00 .00 .0000 +IC C13 N1 *C12 H12A .0000 .00 120.00 .00 .0000 +IC C13 N1 *C12 H12B .0000 .00 -120.00 .00 .0000 +IC C15 N1 *C16 H16A .0000 .00 120.00 .00 .0000 +IC C15 N1 *C16 H16B .0000 .00 -120.00 .00 .0000 +IC C12 C14 *C13 O3 .0000 .00 120.00 .00 .0000 +IC C12 C14 *C13 H13 .0000 .00 -120.00 .00 .0000 +IC C12 C13 O3 HO3 .0000 .00 60.00 .00 .0000 +IC C15 C13 *C14 H14A .0000 .00 120.00 .00 .0000 +IC C15 C13 *C14 H14B .0000 .00 -120.00 .00 .0000 +IC C14 C16 *C15 H15A .0000 .00 120.00 .00 .0000 +IC C14 C16 *C15 H15B .0000 .00 -120.00 .00 .0000 +PATCH FIRST NONE LAST NONE + + +!RESI DUM 0.00 ! DUMMY ATOM +!GROUP +!ATOM DUM DUM 0.00 +!PATCHING FIRST NONE LAST NONE + +!RESI HE 0.00 ! helium +!GROUP +!ATOM HE HE 0.00 +!PATCHING FIRST NONE LAST NONE + +!RESI NE 0.00 ! neon +!GROUP +!ATOM NE NE 0.00 +!PATCHING FIRST NONE LAST NONE + +!adm jr(?), july2006 +RESI ALF4 -1.00 ! AlF4 Aluminum tetraflouride, tetrahedral geometry +GROUP +ATOM AL1 ALG1 1.16 +ATOM F1 FGP1 -0.54 +ATOM F2 FGP1 -0.54 +ATOM F3 FGP1 -0.54 +ATOM F4 FGP1 -0.54 + +BOND AL1 F1 AL1 F2 AL1 F3 AL1 F4 + +IC F2 F1 *AL1 F3 0.0000 0.00 120.00 0.00 0.0000 +IC F2 F1 *AL1 F4 0.0000 0.00 -120.00 0.00 0.0000 + +RESI FLUB 0.00 ! C6H5F fluorobenzene, adm jr. +GROUP ! atom numbering based on difluorotoluene +ATOM C1 CG2R61 -0.10 +ATOM H1 HGR62 0.15 ! H5 H4 +ATOM C2 CG2R61 -0.115 ! \ ___ / +ATOM H2 HGR61 0.115 ! C5---C4 +ATOM C3 CG2R61 -0.115 ! / \ +ATOM H3 HGR61 0.115 ! F6--C6 C3--H3 +ATOM C4 CG2R61 -0.115 ! \\ // +ATOM H4 HGR61 0.115 ! C1---C2 +ATOM C5 CG2R61 -0.10 ! / \ +ATOM H5 HGR62 0.15 ! H1 H2 +ATOM C6 CG2R66 0.11 +ATOM F6 FGR1 -0.21 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 +BOND C6 C1 C6 F6 +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *C6 F6 0.0000 0.00 180.00 0.00 0.0000 + +RESI BROB 0.000 ! C6H5Br bromobenzene +GROUP +ATOM C1 CG2R61 -0.06 +ATOM H1 HGR62 0.15 ! H5 H4 +ATOM C2 CG2R61 -0.115 ! \ ___ / +ATOM H2 HGR61 0.115 ! C5---C4 +ATOM C3 CG2R61 -0.115 ! / \ +ATOM H3 HGR61 0.115 ! BR--C6 C3--H3 +ATOM C4 CG2R61 -0.115 ! \\ // +ATOM H4 HGR61 0.115 ! C1---C2 +ATOM C5 CG2R61 -0.06 ! / \ +ATOM H5 HGR62 0.15 ! H1 H2 +ATOM C6 CG2R61 -0.08 +ATOM BR BRGR1 -0.10 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 +BOND C6 C1 C6 BR +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *C6 BR 0.0000 0.00 180.00 0.00 0.0000 + +RESI CHLB 0.000 ! C6H5Cl compound # : chlorobenzene +GROUP +ATOM C1 CG2R61 -0.10 +ATOM H1 HGR62 0.15 ! H5 H4 +ATOM C2 CG2R61 -0.115 ! \ ___ / +ATOM H2 HGR61 0.115 ! C5---C4 +ATOM C3 CG2R61 -0.115 ! / \ +ATOM H3 HGR61 0.115 ! CL--C6 C3--H3 +ATOM C4 CG2R61 -0.115 ! \\ // +ATOM H4 HGR61 0.115 ! C1---C2 +ATOM C5 CG2R61 -0.10 ! / \ +ATOM H5 HGR62 0.15 ! H1 H2 +ATOM C6 CG2R61 0.03 +ATOM CL CLGR1 -0.13 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 +BOND C6 C1 C6 CL +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *C6 CL 0.0000 0.00 180.00 0.00 0.0000 + +RESI IODB 0.000 ! C6H5I iodobenzene +GROUP +ATOM C1 CG2R61 -0.06 +ATOM H1 HGR62 0.14 ! H5 H4 +ATOM C2 CG2R61 -0.115 ! \ ___ / +ATOM H2 HGR61 0.115 ! C5---C4 +ATOM C3 CG2R61 -0.115 ! / \ +ATOM H3 HGR61 0.115 ! I--C6 C3--H3 +ATOM C4 CG2R61 -0.115 ! \\ // +ATOM H4 HGR61 0.115 ! C1---C2 +ATOM C5 CG2R61 -0.06 ! / \ +ATOM H5 HGR62 0.14 ! H1 H2 +ATOM C6 CG2R61 -0.08 +ATOM I6 IGR1 -0.08 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 +BOND C6 C1 C6 I6 +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *C6 I6 0.0000 0.00 180.00 0.00 0.0000 + +RESI UREA 0.00 ! CH4N2O Urea, adm +GROUP +ATOM N1 NG2S2 -0.69 +ATOM H11 HGP1 0.34 +ATOM H12 HGP1 0.34 +ATOM C2 CG2O6 0.60 +ATOM O2 OG2D1 -0.58 +ATOM N3 NG2S2 -0.69 +ATOM H31 HGP1 0.34 +ATOM H32 HGP1 0.34 + +BOND C2 O2 C2 N1 C2 N3 +BOND N1 H11 N1 H12 +BOND N3 H31 N3 H32 +IMPR C2 N1 N3 O2 + +IC O2 C2 N1 H11 0.0000 0.00 0.00 0.00 0.0000 +IC H11 C2 *N1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC H11 N1 C2 N3 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C2 N3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H31 C2 *N3 H32 0.0000 0.00 180.00 0.00 0.0000 + +RESI PY01 0.000 ! C5H6O 4H-Pyran, maybridge list, adm +GROUP +ATOM O1 OG3R60 -0.32 ! new atom type!! +ATOM C2 CG2D1O -0.04 ! new atom type!! +ATOM H21 HGA4 0.20 ! O1 +ATOM C3 CG2D1 -0.15 ! / \ +ATOM H31 HGA4 0.15 ! H21-C2 C6-H61 +ATOM C4 CG321 -0.18 ! || || +ATOM H41 HGA2 0.09 ! H31-C3 C5-H51 +ATOM H42 HGA2 0.09 ! \ / +ATOM C5 CG2D1 -0.15 ! C4 +ATOM H51 HGA4 0.15 ! / \ +ATOM C6 CG2D1O -0.04 ! H41 H42 +ATOM H61 HGA4 0.20 + +BOND O1 C2 C2 H21 C2 C3 C3 H31 +BOND C3 C4 C4 H41 C4 H42 C4 C5 C5 H51 +BOND C5 C6 C6 H61 C6 O1 + +IC C6 O1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 O1 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC C5 O1 *C6 H61 0.0000 0.00 180.00 0.00 0.0000 + +RESI PY02 0.000 ! C5H6O 2H-Pyran, maybridge list, adm +GROUP ! Note use of conjugated C types +ATOM O1 OG3R60 -0.37 +ATOM C2 CG321 0.00 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 ! H21 O1 +ATOM C3 CG2DC2 -0.15 ! \ / \ +ATOM H31 HGA4 0.15 ! H22-C2 C6-H61 +ATOM C4 CG2DC2 -0.15 ! | || +ATOM H41 HGA4 0.15 ! H31-C3 C5-H51 +ATOM C5 CG2DC1 -0.15 ! \\ / +ATOM H51 HGA4 0.15 ! C4 +ATOM C6 CG2D1O 0.00 ! | +ATOM H61 HGA4 0.19 ! H41 + +BOND O1 C2 C2 H21 C2 H22 C2 C3 C3 H31 +BOND C3 C4 C4 H41 C4 C5 C5 H51 +BOND C5 C6 C6 H61 C6 O1 + +!mp2/6-31g* ring +IC C6 O1 C2 C3 0.0000 0.00 51.00 0.00 0.0000 +IC O1 C2 C3 C4 0.0000 0.00 -42.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 8.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 18.00 0.00 0.0000 +IC C4 C5 C6 O1 0.0000 0.00 -8.00 0.00 0.0000 +IC C5 C6 O1 C2 0.0000 0.00 -27.00 0.00 0.0000 +IC C3 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 O1 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC C5 O1 *C6 H61 0.0000 0.00 180.00 0.00 0.0000 + +RESI NITB 0.000 ! C6H5NO2 nitrobenzene +GROUP +ATOM C1 CG2R61 -0.18 +ATOM H1 HGR61 0.16 ! H5 H4 +ATOM C2 CG2R61 -0.115 ! \ ___ / +ATOM H2 HGR61 0.115 ! O6A C5---C4 +ATOM C3 CG2R61 -0.115 ! \ + / \ +ATOM H3 HGR61 0.115 ! - N6--C6 C3--H3 +ATOM C4 CG2R61 -0.115 ! / \\ // +ATOM H4 HGR61 0.115 ! O6B C1---C2 +ATOM C5 CG2R61 -0.18 ! / \ +ATOM H5 HGR61 0.16 ! H1 H2 +ATOM C6 CG2R61 0.32 +ATOM N6 NG2O1 0.40 +ATOM O6A OG2N1 -0.34 +ATOM O6B OG2N1 -0.34 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 +BOND C6 C1 C6 N6 N6 O6A N6 O6B +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *C6 N6 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C6 N6 O6A 0.0000 0.00 180.00 0.00 0.0000 +IC O6A C6 *N6 O6B 0.0000 0.00 180.00 0.00 0.0000 + +RESI PYRL 0.000 ! C4H5N pyrrole +GROUP ! H2 H1 +ATOM C1 CG2R51 -0.04 ! \ ____ / +ATOM H1 HGR52 0.14 ! C2----C1 +ATOM C2 CG2R51 -0.25 ! | \ +ATOM H2 HGR51 0.15 ! | N5--H5 +ATOM C3 CG2R51 -0.25 ! |____ / +ATOM H3 HGR51 0.15 ! C3----C4 +ATOM C4 CG2R51 -0.04 ! / \ +ATOM H4 HGR52 0.14 ! H3 H4 +ATOM N5 NG2R51 -0.35 +ATOM H5 HGP1 0.35 +BOND C1 H1 C1 C2 C2 H2 C2 C3 C3 H3 +BOND C3 C4 C4 H4 C4 N5 N5 H5 N5 C1 +IC C2 N5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC N5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C1 *N5 H5 0.0000 0.00 180.00 0.00 0.0000 + +RESI FURA 0.00 ! C4H4O furan +GROUP ! H2 H1 +ATOM C1 CG2R51 0.10 ! \ ____ / +ATOM H1 HGR52 0.14 ! C2----C1 +ATOM C2 CG2R51 -0.25 ! | \ +ATOM H2 HGR51 0.15 ! | O5 +ATOM C3 CG2R51 -0.25 ! |____ / +ATOM H3 HGR51 0.15 ! C3----C4 +ATOM C4 CG2R51 0.10 ! / \ +ATOM H4 HGR52 0.14 ! H3 H4 +ATOM O5 OG2R50 -0.28 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 H3 C3 C4 C4 H4 C4 O5 O5 C1 +IC C2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC O5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC O5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 + +RESI THIP 0.000 ! C4H4S thiophene +GROUP +ATOM C1 CG2R51 -0.06 ! H2 H1 +ATOM H1 HGR52 0.18 ! \ ____ / +ATOM C2 CG2R51 -0.24 ! C2----C1 +ATOM H2 HGR51 0.17 ! | \ +ATOM C3 CG2R51 -0.24 ! | S5 +ATOM H3 HGR51 0.17 ! |____ / +ATOM C4 CG2R51 -0.06 ! C3----C4 +ATOM H4 HGR52 0.18 ! / \ +ATOM S5 SG2R50 -0.10 ! H3 H4 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 H3 C3 C4 C4 H4 C4 S5 S5 C1 +IC C2 S5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC S5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC S5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 + +RESI OXAZ 0.000 ! C3H3NO oxazole +GROUP ! H2 H1 +ATOM C1 CG2R51 0.11 ! \ ____ / +ATOM H1 HGR52 0.12 ! C2----C1 +ATOM C2 CG2R51 0.15 ! | \ +ATOM H2 HGR52 0.11 ! | O5 +ATOM N3 NG2R50 -0.61 ! |____ / +ATOM C4 CG2R53 0.22 ! N3----C4 +ATOM H4 HGR52 0.19 ! \ +ATOM O5 OG2R50 -0.29 ! H4 +BOND C1 H1 C1 C2 C2 H2 C2 N3 +BOND N3 C4 C4 H4 C4 O5 O5 C1 +IC C2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC O5 C1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC O5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 + +RESI ISOX 0.000 ! C3H3NO isoxazole +GROUP ! H2 H1 +ATOM C1 CG2R51 0.28 ! \ ____ / +ATOM H1 HGR52 0.13 ! C2----C1 +ATOM C2 CG2R51 -0.43 ! | \ +ATOM H2 HGR51 0.18 ! | O5 +ATOM C3 CG2R52 0.35 ! |____ / +ATOM H3 HGR52 0.11 ! C3----N4 +ATOM N4 NG2R50 -0.45 ! / +ATOM O5 OG2R50 -0.17 ! H3 + +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 N4 C3 H3 N4 O5 O5 C1 +IC C1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC O5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 + +RESI THAZ 0.000 ! C3H3NS thiazole +GROUP ! H2 H1 +ATOM C1 CG2R51 -0.30 ! \ ____ / +ATOM H1 HGR52 0.21 ! C2----C1 +ATOM C2 CG2R51 0.20 ! | \ +ATOM H2 HGR52 0.13 ! | S5 +ATOM N3 NG2R50 -0.61 ! |____ / +ATOM C4 CG2R53 0.22 ! N3----C4 +ATOM H4 HGR52 0.14 ! \ +ATOM S5 SG2R50 0.01 ! H4 +BOND C1 H1 C1 C2 C2 H2 C2 N3 +BOND N3 C4 C4 H4 C4 S5 S5 C1 +IC C1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC S5 C1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 S5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC S5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 + +RESI ISOT 0.000 ! C3H3NS isothiazole +GROUP ! H2 H1 +ATOM C1 CG2R51 -0.04 ! \ ____ / +ATOM H1 HGR52 0.16 ! C2----C1 +ATOM C2 CG2R51 -0.20 ! | \ +ATOM H2 HGR51 0.13 ! | S5 +ATOM C3 CG2R52 0.23 ! |____ / +ATOM H3 HGR52 0.11 ! C3----N4 +ATOM N4 NG2R50 -0.53 ! / +ATOM S5 SG2R50 0.14 ! H3 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 N4 C3 H3 N4 S5 S5 C1 +IC S5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 S5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 + +RESI PYRZ 0.000 ! C3H4N2 pyrazole +GROUP +ATOM C1 CG2R51 -0.03 ! H2 H1 +ATOM H1 HGR52 0.15 ! \ ____ / +ATOM C2 CG2R51 -0.24 ! C2----C1 +ATOM H2 HGR51 0.14 ! | \ +ATOM C3 CG2R52 0.14 ! | N5--H5 +ATOM H3 HGR52 0.13 ! |____ / +ATOM N4 NG2R50 -0.57 ! C3----N4 +ATOM N5 NG2R51 -0.05 ! / +ATOM H5 HGP1 0.33 ! H3 +BOND C1 H1 C1 C2 C2 H2 C2 C3 +BOND C3 H3 C3 N4 N4 N5 N5 H5 N5 C1 +IC C1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC N5 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C1 *N5 H5 0.0000 0.00 180.00 0.00 0.0000 + +RESI OXAD 0.000 ! C2H2N2O oxadiazole123 +GROUP ! H2 H1 +ATOM C1 CG2R51 0.17 ! \ ____ / +ATOM H1 HGR52 0.14 ! C2----C1 +ATOM C2 CG2R51 0.19 ! | \ +ATOM H2 HGR52 0.10 ! | O5 +ATOM N3 NG2R50 -0.32 ! |____ / +ATOM N4 NG2R50 -0.10 ! N3----N4 +ATOM O5 OG2R50 -0.18 +BOND C1 H1 C1 C2 C2 H2 C2 N3 +BOND N3 N4 N4 O5 O5 C1 +IC C1 C2 N3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 N4 O5 0.0000 0.00 0.00 0.00 0.0000 +IC N3 N4 O5 C1 0.0000 0.00 0.00 0.00 0.0000 +IC O5 C1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 + +RESI TRZ3 0.000 ! C2H3N3 triazole123 +GROUP ! H2 H1 +ATOM C1 CG2R51 -0.35 ! \ ____ / +ATOM H1 HGR52 0.20 ! C2----C1 +ATOM C2 CG2R51 0.25 ! | \ +ATOM H2 HGR52 0.11 ! | N5--H5 +ATOM N3 NG2R50 -0.41 ! |____ / +ATOM N4 NG2R50 -0.37 ! N3----N4 +ATOM N5 NG2R51 0.28 +ATOM H5 HGP1 0.29 +BOND C1 H1 C1 C2 C2 H2 C2 N3 +BOND N3 N4 N4 N5 N5 H5 N5 C1 +IC C2 N5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N5 C1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 N3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC N4 C1 *N5 H5 0.0000 0.00 180.00 0.00 0.0000 + +RESI PYRD 0.000 ! C4H4N2 pyridazine +GROUP +ATOM N1 NG2R62 -0.44 +ATOM N2 NG2R62 -0.44 ! H5 H6 +ATOM C3 CG2R61 0.31 ! \ / +ATOM H3 HGR62 0.11 ! C5----C6 +ATOM C4 CG2R61 -0.16 ! / \ +ATOM H4 HGR61 0.18 ! H4--C4 N1 +ATOM C5 CG2R61 -0.16 ! \\ // +ATOM H5 HGR61 0.18 ! C3----N2 +ATOM C6 CG2R61 0.31 ! / +ATOM H6 HGR62 0.11 ! H3 + +BOND N1 N2 N2 C3 C3 C4 C4 C5 C5 C6 C6 N1 +BOND C3 H3 C4 H4 C5 H5 C6 H6 + +IC N1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC N2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 N1 N2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C4 N2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 + + +RESI PYZN 0.000 ! C4H4N2 pyrazine +GROUP +ATOM N1 NG2R60 -0.56 ! H5 H6 +ATOM C2 CG2R61 0.18 ! \ ____ / +ATOM H2 HGR62 0.10 ! C5----C6 +ATOM C3 CG2R61 0.18 ! / \ +ATOM H3 HGR62 0.10 ! N4 N1 +ATOM N4 NG2R60 -0.56 ! \\ // +ATOM C5 CG2R61 0.18 ! C3----C2 +ATOM H5 HGR62 0.10 ! / \ +ATOM C6 CG2R61 0.18 ! H3 H2 +ATOM H6 HGR62 0.10 +BOND C6 H6 C6 C5 C5 H5 C5 N4 N4 C3 +BOND C3 H3 C3 C2 C2 H2 C2 N1 N1 C6 +IC N1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 N4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N1 C6 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C6 N1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 + + +RESI PYRM 0.00 ! C4H4N2 pyrimidine +GROUP +ATOM N1 NG2R62 -0.73 ! H5 H6 +ATOM C2 CG2R64 0.50 ! \ ___ / +ATOM H2 HGR62 0.14 ! C5---C6 +ATOM N3 NG2R62 -0.73 ! / \ +ATOM C4 CG2R61 0.29 ! H4--C4 N1 +ATOM H4 HGR62 0.12 ! \\ // +ATOM C5 CG2R61 -0.115 ! N3---C2 +ATOM H5 HGR61 0.115 ! \ +ATOM C6 CG2R61 0.29 ! H2 +ATOM H6 HGR62 0.12 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 +BOND C2 H2 C4 H4 C5 H5 C6 H6 + +IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 + +RESI TRIA 0.00 ! C3H3N3 1,3,5-triazine +GROUP +ATOM N1 NG2R62 -0.88 ! H6 +ATOM C2 CG2R64 0.78 ! ___ / +ATOM H2 HGR62 0.10 ! N5---C6 +ATOM N3 NG2R62 -0.88 ! / \ +ATOM C4 CG2R64 0.78 ! H4--C4 N1 +ATOM H4 HGR62 0.10 ! \\ // +ATOM N5 NG2R62 -0.88 ! N3---C2 +ATOM C6 CG2R64 0.78 ! \ +ATOM H6 HGR62 0.10 ! H2 + +BOND C6 H6 C6 N5 N5 C4 C4 H4 C4 N3 +BOND N3 C2 C2 H2 C2 N1 N1 C6 + +IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 N5 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C4 N5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC N5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 + +RESI TRIB 0.00 ! C3H3N3 1,2,4-triazine +GROUP +ATOM N1 NG2R62 -0.41 ! H5 H6 +ATOM N2 NG2R62 -0.53 ! \ ___ / +ATOM C3 CG2R64 0.72 ! C5---C6 +ATOM H3 HGR62 0.09 ! / \ +ATOM N4 NG2R62 -0.75 ! N4 N1 +ATOM C5 CG2R61 0.36 ! \\ // +ATOM H5 HGR62 0.09 ! C3---N2 +ATOM C6 CG2R61 0.36 ! / +ATOM H6 HGR62 0.07 ! H3 + + +BOND N1 N2 N2 C3 C3 N4 N4 C5 C5 C6 C6 N1 +BOND C3 H3 C5 H5 C6 H6 + +IC C6 N1 N2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 N2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC N2 C3 N4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC N4 N2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C6 N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 + +RESI THP 0.00 ! C5H10O tetrahydropyran sng +GROUP +ATOM O1 OG3C61 -0.40 +ATOM C2 CG321 0.02 ! O1 +ATOM H21 HGA2 0.09 ! / \ +ATOM H22 HGA2 0.09 ! C6 C2 +ATOM C6 CG321 0.02 ! | | +ATOM H61 HGA2 0.09 ! C5 C3 +ATOM H62 HGA2 0.09 ! \ / +GROUP ! C4 +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +ATOM C5 CG321 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +IC C6 O1 C2 C3 0.0000 0.00 -60.00 0.00 0.0000 +IC O1 C2 C3 C4 0.0000 0.00 60.00 0.00 0.0000 +IC C2 O1 C6 C5 0.0000 0.00 60.00 0.00 0.0000 +IC C3 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 O1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 O1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 O1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 + +BOND O1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 O1 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 +BOND C4 H41 C4 H42 +BOND C5 H51 C5 H52 +BOND C6 H61 C6 H62 + +PATC FIRS NONE LAST NONE + +RESI DIOX 0.00 ! C4H8O2 dioxane14 +GROUP +ATOM O1 OG3C61 -0.40 +ATOM C2 CG321 0.02 +ATOM H21 HGA2 0.09 ! H52 H61 H62 +ATOM H22 HGA2 0.09 ! \ \ / +ATOM C3 CG321 0.02 ! H51--C5---C6 +ATOM H31 HGA2 0.09 ! / \ +ATOM H32 HGA2 0.09 ! O4 O1 +ATOM O4 OG3C61 -0.40 ! \ / +ATOM C5 CG321 0.02 ! H31--C3---C2 +ATOM H51 HGA2 0.09 ! / / \ +ATOM H52 HGA2 0.09 ! H32 H21 H22 +ATOM C6 CG321 0.02 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 + +BOND O1 C2 C2 C3 C3 O4 O4 C5 C5 C6 C6 O1 +BOND C2 H21 C2 H22 C3 H31 C3 H32 +BOND C6 H61 C6 H62 C5 H51 C5 H52 + +IC O1 C2 C3 O4 0.0000 0.00 60.00 0.00 0.0000 +IC C2 C3 O4 C5 0.0000 0.00 -60.00 0.00 0.0000 +IC C3 O4 C5 C6 0.0000 0.00 60.00 0.00 0.0000 +IC O4 C5 C6 O1 0.0000 0.00 -60.00 0.00 0.0000 +IC O1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 O4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 O4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC O4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC O4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 O1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 O1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 + +RESI DIXB 0.00 ! C4H8O2 1,3-dioxane +GROUP +ATOM O1 OG3C61 -0.40 +ATOM C2 CG321 0.22 +ATOM H21 HGA2 0.09 ! H52 H61 H62 +ATOM H22 HGA2 0.09 ! \ \ / +ATOM O3 OG3C61 -0.40 ! H51--C5---C6 +ATOM C4 CG321 0.02 ! / \ +ATOM H41 HGA2 0.09 ! H42-C4 O1 +ATOM H42 HGA2 0.09 ! / \ / +ATOM C5 CG321 -0.18 ! H41 O3---C2 +ATOM H51 HGA2 0.09 ! / \ +ATOM H52 HGA2 0.09 ! H21 H22 +ATOM C6 CG321 0.02 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 + +BOND O1 C2 C2 O3 O3 C4 C4 C5 C5 C6 C6 O1 +BOND C2 H21 C2 H22 C4 H41 C4 H42 +BOND C6 H61 C6 H62 C5 H51 C5 H52 + +IC C6 O1 C2 O3 0.0000 0.00 -60.00 0.00 0.0000 +IC O1 C2 O3 C4 0.0000 0.00 60.00 0.00 0.0000 +IC C2 O3 C4 C5 0.0000 0.00 60.00 0.00 0.0000 +IC O3 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O3 O1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 O3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 O3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 O1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 O1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 + +RESI PIP 1.00 ! C5H12N piperidine +GROUP +ATOM N1 NG3P2 -0.40 +ATOM H11 HGP2 0.32 +ATOM H12 HGP2 0.32 ! C5---C6 H11 +ATOM C2 CG324 0.20 ! / \ / +ATOM H21 HGA2 0.09 ! C4 (+) N1 +ATOM H22 HGA2 0.09 ! \ / \ +ATOM C6 CG324 0.20 ! C3---C2 H12 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 +GROUP +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG321 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 N1 +BOND N1 H11 N1 H12 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 +BOND C4 H41 C4 H42 +BOND C5 H51 C5 H52 +BOND C6 H61 C6 H62 + +IC C6 N1 C2 C3 0.0000 0.00 -60.00 0.00 0.0000 +IC N1 C2 C3 C4 0.0000 0.00 60.00 0.00 0.0000 +IC C2 N1 C6 C5 0.0000 0.00 60.00 0.00 0.0000 +IC C2 C6 *N1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *N1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 N1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 N1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 N1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 + +RESI THPS 0.00 ! C5H10S tetrahydro-thiopyran (thiane) +GROUP +ATOM S1 SG311 -0.24 ! from ethylmethylsulfide (-0.09) +ATOM C2 CG321 -0.06 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG321 -0.18 ! H52 H61 H62 +ATOM H31 HGA2 0.09 ! \ \ / +ATOM H32 HGA2 0.09 ! H51--C5---C6 +ATOM C4 CG321 -0.18 ! H41 / \ +ATOM H41 HGA2 0.09 ! \ / \ +ATOM H42 HGA2 0.09 ! C4 S1 +ATOM C5 CG321 -0.18 ! / \ / +ATOM H51 HGA2 0.09 ! H42 \ / +ATOM H52 HGA2 0.09 ! H31--C3---C2 +ATOM C6 CG321 -0.06 ! / / \ +ATOM H61 HGA2 0.09 ! H32 H21 H22 +ATOM H62 HGA2 0.09 + +BOND S1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 S1 +BOND C2 H21 C2 H22 C3 H31 C3 H32 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND C6 H61 C6 H62 + +IC S1 C2 C3 C4 0.0000 0.00 -60.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 60.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 -60.00 0.00 0.0000 +IC C6 S1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 +IC C3 S1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 S1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C6 C4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 S1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 S1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 + +RESI DITH 0.00 ! C4H8S2 1,4-dithiane +GROUP +ATOM S1 SG311 -0.22 ! from ethylmethylsulfide (-0.09) +ATOM C2 CG321 -0.07 +ATOM H21 HGA2 0.09 ! H52 H61 H62 +ATOM H22 HGA2 0.09 ! \ \ / +ATOM C3 CG321 -0.07 ! H51--C5---C6 +ATOM H31 HGA2 0.09 ! / \ +ATOM H32 HGA2 0.09 ! / \ +ATOM S4 SG311 -0.22 ! S4 S1 +ATOM C5 CG321 -0.07 ! \ / +ATOM H51 HGA2 0.09 ! \ / +ATOM H52 HGA2 0.09 ! H31--C3---C2 +ATOM C6 CG321 -0.07 ! / / \ +ATOM H61 HGA2 0.09 ! H32 H21 H22 +ATOM H62 HGA2 0.09 + +BOND S1 C2 C2 C3 C3 S4 S4 C5 C5 C6 C6 S1 +BOND C2 H21 C2 H22 C3 H31 C3 H32 +BOND C5 H51 C5 H52 +BOND C6 H61 C6 H62 + +IC S1 C2 C3 S4 0.0000 0.00 -60.00 0.00 0.0000 +IC C2 C3 S4 C5 0.0000 0.00 60.00 0.00 0.0000 +IC C3 S4 C5 C6 0.0000 0.00 -60.00 0.00 0.0000 +IC C6 S1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 +IC C3 S1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 S1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC S4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC S4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 S4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C6 S4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 S1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 S1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 + +RESI TRIT 0.00 ! C3H6S3 trithiane135 +GROUP +ATOM S1 SG311 -0.18 +ATOM C2 CG321 0.00 ! H61 H62 +ATOM H21 HGA2 0.09 ! \ / +ATOM H22 HGA2 0.09 ! H41 S5---C6 +ATOM S3 SG311 -0.18 ! \ / \ +ATOM C4 CG321 0.00 ! C4 S1 +ATOM H41 HGA2 0.09 ! / \ / +ATOM H42 HGA2 0.09 ! H42 S3---C2 +ATOM S5 SG311 -0.18 ! / \ +ATOM C6 CG321 0.00 ! H21 H22 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 + +BOND S1 C2 C2 S3 S3 C4 C4 S5 S5 C6 C6 S1 +BOND C2 H21 C2 H22 C4 H41 C4 H42 +BOND C6 H61 C6 H62 + +IC S1 C2 S3 C4 0.0000 0.00 60.00 0.00 0.0000 +IC C2 S3 C4 S5 0.0000 0.00 -60.00 0.00 0.0000 +IC S3 C4 S5 C6 0.0000 0.00 60.00 0.00 0.0000 +IC C6 S1 C2 S3 0.0000 0.00 -60.00 0.00 0.0000 +IC S3 S1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC S3 S1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC S5 S3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC S5 S3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC S5 S1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC S5 S1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MORP 1.00 ! C4H10NO morpholine +ATOM O1 OG3C61 -0.28 +ATOM C2 CG321 -0.04 +ATOM H21 HGA2 0.09 ! H52 H61 H62 +ATOM H22 HGA2 0.09 ! \ \ / +ATOM C3 CG324 0.20 ! H51--C5---C6 +ATOM H31 HGA2 0.09 !H41 / \ +ATOM H32 HGA2 0.09 ! \ / \ +ATOM N4 NG3P2 -0.46 ! N4 (+) O1 +ATOM H41 HGP2 0.35 ! / \ / +ATOM H42 HGP2 0.35 !H42 \ / +ATOM C5 CG324 0.20 ! H31--C3---C2 +ATOM H51 HGA2 0.09 ! / / \ +ATOM H52 HGA2 0.09 ! H32 H21 H22 +ATOM C6 CG321 -0.04 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 + +BOND O1 C2 C2 C3 C3 N4 N4 C5 C5 C6 C6 O1 +BOND C2 H21 C2 H22 C3 H31 C3 H32 +BOND N4 H41 N4 H42 +BOND C5 H51 C5 H52 C6 H61 C6 H62 + +IC O1 C2 C3 N4 0.0000 0.00 60.00 0.00 0.0000 +IC C2 C3 N4 C5 0.0000 0.00 -30.00 0.00 0.0000 +IC C3 N4 C5 C6 0.0000 0.00 -30.00 0.00 0.0000 +IC C6 O1 C2 C3 0.0000 0.00 -30.00 0.00 0.0000 +IC C3 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 O1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC N4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC N4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *N4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *N4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 N4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C6 N4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 O1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 O1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 + +RESI TMOR 1.00 ! C4H10NS thiomorpholine +ATOM S1 SG311 -0.12 +ATOM C2 CG321 -0.12 +ATOM H21 HGA2 0.09 ! H52 H61 H62 +ATOM H22 HGA2 0.09 ! \ \ / +ATOM C3 CG324 0.20 ! H51--C5---C6 +ATOM H31 HGA2 0.09 !H41 / \ +ATOM H32 HGA2 0.09 ! \ / \ +ATOM N4 NG3P2 -0.40 ! N4 (+) S1 +ATOM H41 HGP2 0.32 ! / \ / +ATOM H42 HGP2 0.32 !H42 \ / +ATOM C5 CG324 0.20 ! H31--C3---C2 +ATOM H51 HGA2 0.09 ! / / \ +ATOM H52 HGA2 0.09 ! H32 H21 H22 +ATOM C6 CG321 -0.12 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 + +BOND S1 C2 C2 C3 C3 N4 N4 C5 C5 C6 C6 S1 +BOND C2 H21 C2 H22 C3 H31 C3 H32 +BOND N4 H41 N4 H42 +BOND C5 H51 C5 H52 C6 H61 C6 H62 + +IC S1 C2 C3 N4 0.0000 0.00 60.00 0.00 0.0000 +IC C2 C3 N4 C5 0.0000 0.00 -60.00 0.00 0.0000 +IC C3 N4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C6 S1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 S1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 S1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC N4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC N4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *N4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *N4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 N4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C6 N4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 S1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 S1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MGU1 0.00 ! C2H7N3 deprotonated methyl-guanidinium +GROUP ! Ne deprotonated +ATOM C CG2N1 0.66 ! H11 H12 +ATOM N1 NG321 -0.60 ! \ / +ATOM H11 HGPAM2 0.29 ! N1 +ATOM H12 HGPAM2 0.29 ! | +ATOM N2 NG321 -0.60 ! C H41 +ATOM H21 HGPAM2 0.29 ! / \\ / +ATOM H22 HGPAM2 0.29 ! H21-N2 N3--C4-H42 +ATOM N3 NG2D1 -0.86 ! | \ +ATOM C4 CG331 -0.03 ! H22 H43 !extra charge on C4 to neutralize +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 +BOND C N1 C N2 C N3 N3 C4 +BOND N1 H11 N1 H12 N2 H21 N2 H22 +BOND C4 H41 C4 H42 C4 H43 +IMPR C N1 N2 N3 + +IC N3 C N1 H11 0.0000 0.00 150.00 0.00 0.0000 +IC H11 C *N1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 N3 *C N2 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C N2 H21 0.0000 0.00 150.00 0.00 0.0000 +IC H21 C *N2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C N3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C N3 C4 H41 0.0000 0.00 -170.00 0.00 0.0000 +IC H41 N3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 N3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI MGU2 0.00 ! C2H7N3 deprotonated methyl-guanidinium +GROUP ! NH1-H12 (outer) deprotonated +ATOM C CG2N1 0.59 +ATOM N1 NG2D1 -0.91 ! H11 +ATOM H11 HGP1 0.37 ! \ +ATOM N2 NG321 -0.60 ! N1 +ATOM H21 HGPAM2 0.33 ! || +ATOM H22 HGPAM2 0.33 ! C H41 +ATOM N3 NG311 -0.54 ! / \ / +ATOM H31 HGPAM1 0.36 ! H21-N2 N3--C4-H42 +ATOM C4 CG331 -0.20 ! | | \ !carbon charge to neutralize +ATOM H41 HGA3 0.09 ! H22 H31 H43 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 +BOND C N1 C N2 C N3 N3 C4 +BOND N1 H11 N2 H21 N2 H22 N3 H31 +BOND C4 H41 C4 H42 C4 H43 +IMPR C N1 N3 N2 + +IC N3 C N1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC N1 N3 *C N2 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C N2 H21 0.0000 0.00 150.00 0.00 0.0000 +IC H21 C *N2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C N3 C4 0.0000 0.00 -120.00 0.00 0.0000 +IC C C4 *N3 H31 0.0000 0.00 -120.00 0.00 0.0000 +IC C N3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 N3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 N3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +!end adm jr(?), jul2006 + +!start adm jr(?), dec2006 +RESI HDZ1 0.00 ! C4H8N2O Hydrazone model compound +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 ! C1 H3 +ATOM H12 HGA3 0.09 ! \ | +ATOM H13 HGA3 0.09 ! C2--N3 H5 +GROUP ! // \ / +ATOM C2 CG2O1 0.58 ! O2 N4=C5 +ATOM O2 OG2D1 -0.49 ! \ +ATOM N3 NG2S1 -0.34 ! C6 +ATOM H3 HGP1 0.31 +ATOM N4 NG2D1 -0.31 +ATOM C5 CG2D1 -0.24 +ATOM H5 HGA4 0.24 +ATOM C6 CG331 -0.02 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 O2 C2 N3 N3 H3 +BOND N3 N4 C5 H5 C5 C6 C6 H61 C6 H62 C6 H63 +BOND N4 C5 +IMPR C2 C1 N3 O2 +IMPR C5 C6 N4 H5 + +IC C1 C2 N3 N4 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 C2 N3 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 N3 N4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC H61 C5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 +IC H61 C5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 + + +RESI HDZ2 0.00 ! C16H13N3O2 Hydrazone containing drug-like molecule +GROUP +ATOM HG HGR51 0.14 ! HE3 +ATOM CG CG2R51 -0.17 ! | +ATOM CD2 CG2RC0 0.11 ! HG CE3 +ATOM CD1 CG2R51 -0.15 ! \ / \\ +ATOM HD1 HGR52 0.22 ! CG-----CD2 CZ3-HZ3 +ATOM NE1 NG2R51 -0.51 ! || || | +ATOM HE1 HGP1 0.37 ! CD1 CE2 CH2-HH2 +ATOM CE2 CG2RC0 0.24 ! / \ / \ // +ATOM CE3 CG2R61 -0.25 ! HD1 NE1 CZ2 +ATOM HE3 HGR61 0.17 ! | / +ATOM CZ2 CG2R61 -0.11 ! HE1 / +ATOM CZ3 CG2R61 -0.20 ! / +ATOM HZ3 HGR61 0.14 ! / +ATOM CH2 CG2R61 -0.14 ! / +ATOM HH2 HGR61 0.14 ! ___________/ +GROUP ! \ +ATOM C2 CG2O1 0.58 ! \ H3 +ATOM O2 OG2D1 -0.49 ! \ | +ATOM N3 NG2S1 -0.34 ! C2--N3 H5 +ATOM H3 HGP1 0.31 ! // \ / +ATOM N4 NG2D1 -0.31 ! O2 N4=C5 +ATOM C5 CG2DC1 -0.24 ! \ +ATOM H5 HGA4 0.24 ! ________________\ +! | +!Phenol moiety: P added to atom names to avoid conflicts with indole +! | +ATOM CPG CG2R61 0.25 ! | HPD1 HPE1 +GROUP ! | | | +ATOM CPD1 CG2R61 -0.115 ! | CPD1--CPE1 +ATOM HPD1 HGR61 0.115 ! | // \\ +GROUP ! |--CPG CPZ--OPH +ATOM CPD2 CG2R61 -0.115 ! \ / \ +ATOM HPD2 HGR61 0.115 ! CPD2==CPE2 HPH +GROUP ! | | +ATOM CPE1 CG2R61 -0.115 ! HPD2 HPE2 +ATOM HPE1 HGR61 0.115 +GROUP +ATOM CPE2 CG2R61 -0.115 +ATOM HPE2 HGR61 0.115 +GROUP +ATOM CPZ CG2R61 0.11 +ATOM OPH OG311 -0.53 +ATOM HPH HGP1 0.42 + +!indole section +BOND CG HG CD2 CG NE1 CD1 CZ2 CE2 +BOND CZ3 CH2 CD2 CE3 NE1 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 +BOND CZ3 HZ3 CH2 HH2 +BOND CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3 +BOND CZ2 C2 +BOND C2 O2 C2 N3 N3 H3 N3 N4 C5 H5 +BOND N4 C5 C5 CPG +BOND CPD2 CPG CPE1 CPD1 CPZ CPE2 +BOND CPD1 HPD1 CPD2 HPD2 CPE1 HPE1 +BOND CPE2 HPE2 CPZ OPH OPH HPH +BOND CPD1 CPG CPE2 CPD2 CPZ CPE1 +IMPR C2 CZ2 N3 O2 +IMPR C5 CPG N4 H5 + +IC CG CD1 NE1 CE2 0.0000 0.00 0.00 0.00 0.0000 !dihe from 180.0 +IC CD2 HG *CG CD1 0.0000 0.00 180.00 0.00 0.0000 +IC HG CG CD1 NE1 0.0000 0.00 180.00 0.00 0.0000 +IC NE1 CG *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CD1 *NE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CG *CD2 CE3 0.0000 0.00 180.00 0.00 0.0000 +IC CG CD2 CE3 CZ3 0.0000 0.00 180.00 0.00 0.0000 +IC CZ3 CD2 *CE3 HE3 0.0000 0.00 180.00 0.00 0.0000 +IC CD2 NE1 *CE2 CZ2 0.0000 0.00 180.00 0.00 0.0000 +IC CD2 CE3 CZ3 CH2 0.0000 0.00 0.00 0.00 0.0000 !dihe from 180.0 +IC CH2 CE3 *CZ3 HZ3 0.0000 0.00 180.00 0.00 0.0000 +IC CZ2 CZ3 *CH2 HH2 0.0000 0.00 180.00 0.00 0.0000 +IC CH2 CE2 *CZ2 C2 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CZ2 C2 N3 0.0000 0.00 180.00 0.00 0.0000 +IC N3 CZ2 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC CZ2 C2 N3 N4 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 N3 N4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N4 C5 CPG 0.0000 0.00 180.00 0.00 0.0000 +IC CPG N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C5 CPG CPD1 0.0000 0.00 180.00 0.00 0.0000 +IC CPD1 C5 *CPG CPD2 0.0000 0.00 180.00 0.00 0.0000 +IC C5 CPG CPD1 CPE1 0.0000 0.00 180.00 0.00 0.0000 +IC CPE1 CPG *CPD1 HPD1 0.0000 0.00 180.00 0.00 0.0000 +IC C5 CPG CPD2 CPE2 0.0000 0.00 180.00 0.00 0.0000 +IC CPE2 CPG *CPD2 HPD2 0.0000 0.00 180.00 0.00 0.0000 +IC CPG CPD1 CPE1 CPZ 0.0000 0.00 0.00 0.00 0.0000 !dihe from 180.0 +IC CPZ CPD1 *CPE1 HPE1 0.0000 0.00 180.00 0.00 0.0000 +IC CPZ CPD2 *CPE2 HPE2 0.0000 0.00 180.00 0.00 0.0000 +IC CPE2 CPE1 *CPZ OPH 0.0000 0.00 180.00 0.00 0.0000 +IC CPE1 CPZ OPH HPH 0.0000 0.00 180.00 0.00 0.0000 +!end adm jr(?), dec2006 + +!Continuation of Maybridge list, kevo, dec2006 +RESI INDZ 0.00 ! C8H7N indolizine, kevo +GROUP +ATOM C1 CG2R51 -0.28 ! H5 +ATOM H1 HGR51 0.23 ! | +ATOM C2 CG2R51 -0.23 ! H3 C5 +ATOM H2 HGR51 0.19 ! \ / \\ +ATOM C3 CG2R51 0.07 ! C3----N4 C6-H6 +ATOM H3 HGR52 0.14 ! || | | +ATOM N4 NG2RC0 -0.28 ! C2 C9 C7-H7 +ATOM C5 CG2R61 -0.10 ! / \ // \ // +ATOM H5 HGR62 0.24 ! H2 C1 C8 +ATOM C6 CG2R61 -0.14 ! | | +ATOM H6 HGR61 0.17 ! H1 H8 +ATOM C7 CG2R61 -0.15 +ATOM H7 HGR61 0.18 +ATOM C8 CG2R61 -0.22 +ATOM H8 HGR61 0.24 +ATOM C9 CG2RC0 -0.06 + +BOND C1 C2 C2 C3 C3 N4 N4 C9 C9 C1 +BOND N4 C5 C5 C6 C6 C7 C7 C8 C8 C9 +BOND C1 H1 C2 H2 C3 H3 +BOND C5 H5 C6 H6 C7 H7 C8 H8 + +IC C9 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC C3 N4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C9 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C3 *N4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C6 N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI ISOI 0.00 ! C8H7N isoindole, kevo +GROUP +ATOM HG HGR52 0.15 ! HE3 +ATOM CG CG2R51 -0.16 ! | +ATOM CD2 CG2RC0 0.17 ! HG CE3 +ATOM ND1 NG2R51 -0.29 ! \ _____ / \\ +ATOM HD1 HGP1 0.35 ! CG-----CD2 CZ3-HZ3 +ATOM CE1 CG2R51 -0.16 ! | | | +ATOM HE1 HGR52 0.15 ! ND1 CE2 CH2-HH2 +ATOM CE2 CG2RC0 0.17 ! / \ // \ // +ATOM CE3 CG2R61 -0.36 ! HD1 CE1 CZ2 +ATOM HE3 HGR61 0.23 ! | | +ATOM CZ2 CG2R61 -0.36 ! HE1 HZ2 +ATOM HZ2 HGR61 0.23 +ATOM CZ3 CG2R61 -0.30 +ATOM HZ3 HGR61 0.24 +ATOM CH2 CG2R61 -0.30 +ATOM HH2 HGR61 0.24 + +BOND CD2 CE2 +BOND CE1 ND1 ND1 CG +BOND CD2 CE3 CZ3 CH2 CZ2 CE2 +BOND CE1 HE1 ND1 HD1 CG HG +BOND CE3 HE3 CZ3 HZ3 CH2 HH2 CZ2 HZ2 +DOUBLE CE2 CE1 CG CD2 CE3 CZ3 CH2 CZ2 +DONOR HD1 ND1 + +IC CG ND1 CE1 CE2 0.0000 0.00 0.00 0.00 0.0000 +IC ND1 CG CD2 CE2 0.0000 0.00 0.00 0.00 0.0000 +IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 +IC CE2 CG *CD2 CE3 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CD2 CE3 CZ3 0.0000 0.00 0.00 0.00 0.0000 +IC CD2 CE3 CZ3 CH2 0.0000 0.00 0.00 0.00 0.0000 +IC CE3 CZ3 CH2 CZ2 0.0000 0.00 0.00 0.00 0.0000 +IC CZ3 CD2 *CE3 HE3 0.0000 0.00 180.00 0.00 0.0000 +IC CH2 CE3 *CZ3 HZ3 0.0000 0.00 180.00 0.00 0.0000 +IC CZ2 CZ3 *CH2 HH2 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CH2 *CZ2 HZ2 0.0000 0.00 180.00 0.00 0.0000 +IC ND1 CE2 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC CG CE1 *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC ND1 CD2 *CG HG 0.0000 0.00 180.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI INDA 0.00 ! C7H6N2 1H-indazole, kevo +GROUP +ATOM N1 NG2R51 -0.05 ! H5 +ATOM H1 HGP1 0.28 ! | +ATOM N2 NG2R50 -0.60 ! H3 C5 +ATOM C3 CG2R52 0.28 ! \ / \\ +ATOM H3 HGR52 0.09 ! C3-----C4 C6 -H6 +ATOM C4 CG2RC0 -0.11 ! || || | +ATOM C5 CG2R61 -0.43 ! N2 C9 C7 -H7 +ATOM H5 HGR61 0.30 ! \ / \ // +ATOM C6 CG2R61 -0.38 ! N1 C8 +ATOM H6 HGR61 0.28 ! | | +ATOM C7 CG2R61 -0.26 ! H1 H8 +ATOM H7 HGR61 0.24 +ATOM C8 CG2R61 -0.20 +ATOM H8 HGR61 0.15 +ATOM C9 CG2RC0 0.41 + +BOND C3 H3 C4 C3 N1 N2 +BOND C8 C9 +BOND C6 C7 C4 C5 N1 C9 +BOND N1 H1 C5 H5 C6 H6 +BOND C7 H7 C8 H8 +DOUBLE N2 C3 C9 C4 C7 C8 C6 C5 +DONOR H1 N1 +IC C3 N2 N1 C9 0.0000 0.00 0.00 0.00 0.0000 +IC N1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC N2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C9 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI ZIMI 0.00 ! C7H6N2 benzimidazole, kevo +GROUP +ATOM N1 NG2R51 -0.28 ! H5 +ATOM H1 HGP1 0.31 ! | +ATOM C2 CG2R53 0.24 ! C5 +ATOM H2 HGR52 0.14 ! / \\ +ATOM N3 NG2R50 -0.72 ! N3----C4 C6 -H6 +ATOM C4 CG2RC0 0.45 ! || || | +ATOM C5 CG2R61 -0.35 ! C2 C9 C7 -H7 +ATOM H5 HGR61 0.23 ! / \ / \ // +ATOM C6 CG2R61 -0.19 ! H2 N1 C8 +ATOM H6 HGR61 0.20 ! | | +ATOM C7 CG2R61 -0.34 ! H1 H8 +ATOM H7 HGR61 0.24 +ATOM C8 CG2R61 -0.32 +ATOM H8 HGR61 0.22 +ATOM C9 CG2RC0 0.17 + +BOND N1 H1 C2 H2 +BOND C5 H5 C6 H6 C7 H7 C8 H8 +BOND C9 N1 N1 C2 N3 C4 +BOND C4 C5 C6 C7 C8 C9 +DOUBLE C2 N3 C4 C9 C5 C6 C7 C8 +DONOR H1 N1 +IC N3 C2 N1 C9 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C9 N3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C9 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI 2HPR 0.000 ! C4H5N 2H-pyrrole, kevo +GROUP +ATOM N1 NG2R50 -0.72 ! H5 +ATOM C2 CG3C52 0.45 ! \ ____ +ATOM H21 HGA2 0.09 ! C5----N1 H21 +ATOM H22 HGA2 0.09 ! | \ / +ATOM C3 CG2R51 -0.75 ! | C2 +ATOM H3 HGR51 0.33 ! |____ / \ +ATOM C4 CG2R51 0.05 ! C4----C3 H22 +ATOM H4 HGR51 0.15 ! / \ +ATOM C5 CG2R52 0.20 ! H4 H3 +ATOM H5 HGR52 0.11 + +BOND C2 H21 C2 H22 C3 H3 C4 H4 C5 H5 +BOND N1 C2 C2 C3 C4 C5 +DOUBLE C3 C4 C5 N1 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 N1 0.0000 0.00 0.00 0.00 0.0000 +IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 N1 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 + +RESI 2PRL 0.000 ! C4H7N 2-pyrroline, kevo +GROUP +ATOM N1 NG3C51 -0.60 +ATOM H1 HGP1 0.32 ! H3 H41 H42 +ATOM C2 CG2R51 -0.01 ! \ | / +ATOM H2 HGR52 0.17 ! C3----C4 +ATOM C3 CG2R51 -0.36 ! || | +ATOM H3 HGR51 0.20 ! C2 C5--H51 +ATOM C4 CG3C52 -0.10 ! / \ / \ +ATOM H41 HGA2 0.09 ! H2 N1 H52 +ATOM H42 HGA2 0.09 ! | +ATOM C5 CG3C52 0.02 ! H1 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND N1 H1 C2 H2 C3 H3 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 C2 C3 C4 C4 C5 C5 N1 +DOUBLE C2 C3 +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 + +RESI 2PRZ 0.000 ! C3H6N2 2-pyrazoline, kevo +GROUP +ATOM N1 NG3C51 -0.46 +ATOM H1 HGP1 0.34 ! H3 H41 H42 +ATOM N2 NG2R50 -0.49 ! \ | / +ATOM C3 CG2R52 0.32 ! C3----C4 +ATOM H3 HGR52 0.06 ! || | +ATOM C4 CG3C52 -0.15 ! N2 C5--H51 +ATOM H41 HGA2 0.09 ! \ / \ +ATOM H42 HGA2 0.09 ! N1 H52 +ATOM C5 CG3C52 0.02 ! | +ATOM H51 HGA2 0.09 ! H1 +ATOM H52 HGA2 0.09 +!H[45][12] constrained at +0.09, pre1g + +BOND N1 H1 C3 H3 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 N2 C3 C4 C4 C5 C5 N1 +DOUBLE N2 C3 +IC N1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC N2 C3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 +IC N2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC C4 N2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 + +RESI 2IMI 0.000 ! C3H6N2 2-imidazoline, kevo +GROUP +ATOM N1 NG3C51 -0.68 +ATOM H1 HGP1 0.32 ! H41 H42 +ATOM C2 CG2R53 0.61 ! | / +ATOM H2 HGR52 0.06 ! N3----C4 +ATOM N3 NG2R50 -0.79 ! || | +ATOM C4 CG3C52 0.12 ! C2 C5--H51 +ATOM H41 HGA2 0.09 ! / \ / \ +ATOM H42 HGA2 0.09 ! H2 N1 H52 +ATOM C5 CG3C52 0.00 ! | +ATOM H51 HGA2 0.09 ! H1 +ATOM H52 HGA2 0.09 + +BOND N1 H1 C2 H2 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 C2 N3 C4 C4 C5 C5 N1 +DOUBLE C2 N3 +IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 N3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 +!end continuation of Maybridge list, kevo, dec2006 + +!Continuation of Maybridge list, kevo, may2007 +RESI PRLD 0.000 ! C4H9N pyrrolidine, kevo +GROUP +ATOM N1 NG3C51 -0.86 +ATOM H1 HGP1 0.36 +ATOM C2 CG3C52 0.10 ! H32 H42 +ATOM H21 HGA2 0.09 ! \ / +ATOM H22 HGA2 0.09 ! H31--C3----C4--H41 +ATOM C3 CG3C52 -0.21 ! | | +ATOM H31 HGA2 0.09 ! H21--C2 C5--H51 +ATOM H32 HGA2 0.09 ! / \ / \ +ATOM C4 CG3C52 -0.21 ! H22 N1 H52 +ATOM H41 HGA2 0.09 ! | +ATOM H42 HGA2 0.09 ! H1 +ATOM C5 CG3C52 0.10 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 +BOND N1 H1 C2 H21 C2 H22 C3 H31 C3 H32 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +IC C2 C3 C4 C5 0.0000 0.00 10.00 0.00 0.0000 +IC C3 C4 C5 N1 0.0000 0.00 15.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 + +RESI 3PRL 0.000 ! C4H7N 3-pyrroline, kevo +GROUP +ATOM N1 NG3C51 -0.89 +ATOM H1 HGP1 0.37 ! H3 H4 +ATOM C2 CG3C52 0.17 ! \ ____ / +ATOM H21 HGA2 0.09 ! C3----C4 +ATOM H22 HGA2 0.09 ! | | +ATOM C3 CG2R51 -0.28 ! H21--C2 C5--H52 +ATOM H3 HGR51 0.19 ! / \ / \ +ATOM C4 CG2R51 -0.28 ! H22 N1 H51 +ATOM H4 HGR51 0.19 ! | +ATOM C5 CG3C52 0.17 ! H1 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND N1 H1 C2 H21 C2 H22 +BOND C3 H3 C4 H4 C5 H51 C5 H52 +BOND N1 C2 C2 C3 C4 C5 C5 N1 +DOUBLE C3 C4 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 N1 0.0000 0.00 20.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C3 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 + +RESI PRLP 1.000 ! C4H10N pyrrolidine protonated, kevo +GROUP +ATOM N1 NG3P2 -0.22 +ATOM H11 HGP2 0.34 +ATOM H12 HGP2 0.34 +ATOM C2 CG3C54 -0.35 ! H32 H42 +ATOM H21 HGA2 0.28 ! \ / +ATOM H22 HGA2 0.28 ! H31--C3----C4--H41 +ATOM C3 CG3C52 -0.12 ! | | +ATOM H31 HGA2 0.09 ! H21--C2 C5--H51 +ATOM H32 HGA2 0.09 ! / \ / \ +ATOM C4 CG3C52 -0.12 ! H22 N1(+) H52 +ATOM H41 HGA2 0.09 ! / \ +ATOM H42 HGA2 0.09 ! H11 H12 +ATOM C5 CG3C54 -0.35 +ATOM H51 HGA2 0.28 +ATOM H52 HGA2 0.28 + +BOND N1 H11 N1 H12 C2 H21 C2 H22 C3 H31 +BOND C3 H32 C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 +IC C2 C3 C4 C5 0.0000 0.00 40.00 0.00 0.0000 +IC C3 C4 C5 N1 0.0000 0.00 330.00 0.00 0.0000 +IC C2 C5 *N1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C5 *N1 H12 0.0000 0.00 240.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 240.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C3 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 + +RESI 3PRP 1.000 ! C4H8N 3-pyrroline protonated, kevo +GROUP +ATOM N1 NG3P2 -0.40 +ATOM H11 HGP2 0.39 +ATOM H12 HGP2 0.39 ! H3 H4 +ATOM C2 CG3C54 -0.17 ! \ ____ / +ATOM H21 HGA2 0.28 ! C3----C4 +ATOM H22 HGA2 0.28 ! | | +ATOM C3 CG2R51 -0.33 ! H21--C2 C5--H51 +ATOM H3 HGR51 0.25 ! / \ / \ +ATOM C4 CG2R51 -0.33 ! H22 N1(+) H52 +ATOM H4 HGR51 0.25 ! / \ +ATOM C5 CG3C54 -0.17 ! H11 H12 +ATOM H51 HGA2 0.28 +ATOM H52 HGA2 0.28 + +BOND N1 H11 N1 H12 C2 H21 C2 H22 +BOND C3 H3 C4 H4 C5 H51 C5 H52 +BOND N1 C2 C2 C3 C4 C5 C5 N1 +BOND C3 C4 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 N1 0.0000 0.00 20.00 0.00 0.0000 +IC C5 C2 *N1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C2 *N1 H12 0.0000 0.00 240.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C3 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 + +RESI 2PRP 1.000 ! C4H8N 2-pyrroline protonated, kevo +GROUP +ATOM N1 NG3P2 -0.13 +ATOM H11 HGP2 0.33 +ATOM H12 HGP2 0.33 ! H3 H41 H42 +ATOM C2 CG2R51 -0.18 ! \ | / +ATOM H2 HGR52 0.22 ! C3----C4 +ATOM C3 CG2R51 -0.06 ! || | +ATOM H3 HGR51 0.20 ! C2 C5--H51 +ATOM C4 CG3C52 -0.12 ! / \ / \ +ATOM H41 HGA2 0.09 ! H2 N1(+) H52 +ATOM H42 HGA2 0.09 ! / \ +ATOM C5 CG3C54 -0.33 ! H11 H12 +ATOM H51 HGA2 0.28 +ATOM H52 HGA2 0.28 + +BOND N1 H11 N1 H12 C2 H2 C3 H3 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 C2 C3 C4 C4 C5 C5 N1 +BOND C2 C3 +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 +IC C2 C5 *N1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C5 *N1 H12 0.0000 0.00 240.00 0.00 0.0000 +IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 + +RESI 2IMP 1.000 ! C3H7N2 2-imidazoline protonated, kevo +GROUP +ATOM N1 NG2R52 -0.35 +ATOM H1 HGP2 0.38 +ATOM C2 CG2R53 0.52 ! H3 H41 H42 +ATOM H2 HGR53 0.12 ! \ | / +ATOM N3 NG2R52 -0.35 ! (+) N3----C4 +ATOM H3 HGP2 0.38 ! || | +ATOM C4 CG3C54 -0.41 ! C2 C5--H51 +ATOM H41 HGA2 0.28 ! / \ / \ +ATOM H42 HGA2 0.28 ! H2 N1 H52 +ATOM C5 CG3C54 -0.41 ! | +ATOM H51 HGA2 0.28 ! H1 +ATOM H52 HGA2 0.28 +!H[2-5][12] constrained, pre1g + +BOND N1 H1 C2 H2 N3 H3 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 C2 N3 C4 C4 C5 C5 N1 +DOUBLE C2 N3 +IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 C5 0.0000 0.00 -12.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 N3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 + +RESI 2HPP 1.000 ! C4H6N 2H-pyrrole protonated, kevo +GROUP +ATOM N1 NG2R52 -0.27 +ATOM H1 HGP2 0.39 ! H5 H1 +ATOM C2 CG3C54 -0.19 ! \ ____ / +ATOM H21 HGA2 0.28 ! C5----N1 H21 +ATOM H22 HGA2 0.28 ! | (+) \ / +ATOM C3 CG2R51 -0.08 ! | C2 +ATOM H3 HGR51 0.25 ! |____ / \ +ATOM C4 CG2R51 -0.27 ! C4----C3 H22 +ATOM H4 HGR51 0.25 ! / \ +ATOM C5 CG2R52 0.07 ! H4 H3 +ATOM H5 HGR52 0.29 + +BOND N1 H1 C2 H21 C2 H22 C3 H3 C4 H4 C5 H5 +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 N1 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 N1 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +!End continuation of Maybridge list, kevo, may2007 + +!Bile acids and related compounds, chayan, jul2006 +RESI BAM1 0.00 ! C13H24 Bile Acid Model cmpd 1, cacha (to estimate dihedral rotational surface energy) + +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 ! C21 +ATOM H11B HGA2 0.09 ! | +GROUP ! C12 C18 C20--C22 +ATOM C9 CG321 -0.18 ! / \ | | +ATOM H9A HGA2 0.09 ! C11 C13--C17 +ATOM H9B HGA2 0.09 ! | | | +GROUP ! C9 C14 C16 +ATOM C8 CG321 -0.18 ! \ / \ / +ATOM H8A HGA2 0.09 ! C8 C15 +ATOM H8B HGA2 0.09 +GROUP ! Model Compound +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C18 CG331 -0.27 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG331 -0.27 +ATOM H22A HGA3 0.09 +ATOM H22B HGA3 0.09 +ATOM H22C HGA3 0.09 + + +BOND C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 C9 H9A C9 H9B +BOND C9 C8 C8 H8A C8 H8B +BOND C8 C14 C14 H14 C14 C13 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 C13 C12 +BOND C13 C18 C18 H18A C18 H18B C18 H18C +BOND C17 C20 C20 H20 +BOND C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B C22 H22C + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +IC C12 C11 C9 C8 1.5465 113.07 53.26 111.97 1.5369 +IC C11 C9 C8 C14 1.5370 111.97 -54.31 108.19 1.5301 +IC C9 C8 C14 C15 1.5369 108.19 179.63 117.07 1.5242 +IC C8 C14 C15 C16 1.5301 117.07 -157.35 103.25 1.5463 +IC C14 C15 C16 C17 1.5242 103.25 -1.62 106.76 1.5545 +IC C15 C16 C17 C13 1.5463 106.76 32.90 98.76 1.5707 +IC C16 C17 C13 C12 1.5545 98.76 -165.58 115.64 1.5392 +IC C8 C14 C13 C12 1.5301 113.89 -59.62 108.36 1.5392 +IC C8 C14 C13 C17 1.5301 113.89 -179.99 97.80 1.5707 +IC C14 C13 C12 C11 1.5400 108.36 54.13 111.30 1.5465 +IC C13 C8 *C14 C15 1.5400 113.89 120.29 117.07 1.5242 +IC C17 C14 *C13 C12 1.5707 97.80 120.38 108.36 1.5392 +IC C14 C9 *C8 H8A 1.5301 108.19 121.59 109.97 1.1090 +IC H8A C9 *C8 H8B 1.1090 109.97 118.57 109.82 1.1117 +IC C8 C11 *C9 H9A 1.5369 111.97 -119.77 108.41 1.1138 +IC H9A C11 *C9 H9B 1.1138 108.41 -117.69 109.98 1.1118 +IC C9 C12 *C11 H11A 1.5370 113.07 120.55 109.08 1.1127 +IC H11A C12 *C11 H11B 1.1127 109.08 117.14 109.30 1.1121 +IC C14 C13 C12 H12A 1.5400 108.36 174.66 111.17 1.1064 +IC H12A C13 *C12 H12B 1.1064 111.17 119.56 108.93 1.1115 +IC C13 C8 *C14 H14 1.5400 113.89 -118.75 106.87 1.1175 +IC C16 C14 *C15 H15A 1.5463 103.25 119.82 111.17 1.0999 +IC H15A C14 *C15 H15B 1.0999 111.17 119.44 111.12 1.0993 +IC C17 C15 *C16 H16A 1.5545 106.76 121.20 110.63 1.0991 +IC H16A C15 *C16 H16B 1.0991 110.63 117.46 111.19 1.0988 +IC C13 C16 *C17 H17 1.5707 98.76 -113.04 109.96 1.1005 +IC C12 C14 *C13 C18 1.5392 108.36 121.36 113.50 1.5528 +IC C14 C13 C18 H18A 1.5400 113.50 109.24 111.90 1.1059 +IC H18A C13 *C18 H18B 1.1059 111.90 119.52 110.40 1.1089 +IC H18A C13 *C18 H18C 1.1059 111.90 -120.42 111.60 1.1063 +IC C13 C16 *C17 C20 1.5707 98.76 126.23 112.96 1.5593 +IC C16 C17 C20 C22 1.5545 112.96 61.62 107.68 1.5428 +IC C22 C17 *C20 C21 1.5428 107.68 119.44 112.55 1.5383 +IC C21 C17 *C20 H20 1.5383 112.55 122.44 110.57 1.1109 +IC C17 C20 C21 H21A 1.5593 112.55 76.43 111.01 1.1069 +IC H21A C20 *C21 H21B 1.1069 111.01 -121.83 110.68 1.1100 +IC H21A C20 *C21 H21C 1.1069 111.01 118.41 110.01 1.1108 +IC C17 C20 C22 H22A 1.5593 107.68 177.17 110.13 1.1105 +IC H22A C20 *C22 H22B 1.1105 110.13 119.59 111.27 1.1091 +IC H22A C20 *C22 H22C 1.1105 110.13 -119.58 110.32 1.1103 + + +RESI CA -1.00 ! C24H39O5 Cholic Acid, cacha +GROUP +ATOM C3 CG311 0.14 +ATOM O3 OG311 -0.65 +ATOM H3' HGP1 0.42 +ATOM H3 HGA1 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H4A HGA2 0.09 +ATOM H4B HGA2 0.09 +GROUP +ATOM C5 CG311 -0.09 +ATOM H5 HGA1 0.09 +GROUP +ATOM C6 CG321 -0.18 +ATOM H6A HGA2 0.09 +ATOM H6B HGA2 0.09 ! OE1 +GROUP ! || +ATOM C7 CG311 0.14 ! OH Me21 C22 CD +ATOM O7 OG311 -0.65 ! | \ / \ / \ +ATOM H7' HGP1 0.42 ! C12 Me18 C20 CG OE2(-1) +ATOM H7 HGA1 0.09 ! / \ | / +GROUP ! C11 C13---C17 +ATOM C8 CG311 -0.09 ! Me19 | | | +ATOM H8 HGA1 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C14 CG3RC1 -0.09 ! C2 C10 C8 C15 +ATOM H14 HGA1 0.09 ! | | | +GROUP ! C3 C5 C7 +ATOM C15 CG3C52 -0.18 ! / \ / \ / \ +ATOM H15A HGA2 0.09 ! HO C4 C6 OH +ATOM H15B HGA2 0.09 +GROUP ! Cholic Acid (CA) +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 ! no hydrogen +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG311 0.14 +ATOM H12 HGA1 0.09 +ATOM O12 OG311 -0.65 +ATOM H12' HGP1 0.42 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 ! no hydrogen +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM CD CG2O3 0.52 +ATOM OE1 OG2D2 -0.76 +ATOM OE2 OG2D2 -0.76 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7 C7 O7 O7 H7' +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12 C12 O12 O12 H12' +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 CD CD OE1 CD OE2 +IMPR CD OE2 OE1 C23 + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +!ICs based on CHARMM optimized structure +IC C1 C2 C3 C4 1.5324 111.68 -49.58 111.85 1.5384 +IC C2 C3 C4 C5 1.5336 111.85 43.65 115.86 1.5602 +IC C3 C4 C5 C6 1.5384 115.86 -174.25 108.84 1.5528 +IC C4 C5 C6 C7 1.5602 108.84 86.42 115.04 1.5449 +IC C5 C6 C7 C8 1.5528 115.04 38.94 113.04 1.5297 +IC C7 C8 C9 C10 1.5297 113.41 59.71 109.57 1.5432 +IC C8 C9 C10 C1 1.5223 109.57 178.73 111.89 1.5560 +IC C9 C10 C1 C2 1.5432 111.89 63.50 113.76 1.5324 +IC O3 C3 C4 C5 1.4163 109.08 161.75 115.86 1.5602 +IC C4 C2 *C3 O3 1.5384 111.85 -119.36 106.95 1.4163 +IC C4 C2 *C3 H3 1.5384 111.85 121.41 109.41 1.1143 +IC C9 C5 *C10 C19 1.5432 109.52 -123.19 109.67 1.5560 +IC C2 C3 O3 H3' 1.5336 106.95 64.94 104.68 0.9611 +IC C5 C3 *C4 H4A 1.5602 115.86 122.86 108.65 1.1110 +IC H4A C3 *C4 H4B 1.1110 108.65 115.61 108.72 1.1114 +IC C10 C4 *C5 H5 1.5283 114.75 116.75 105.10 1.1173 +IC C7 C5 *C6 H6A 1.5449 115.04 -124.17 109.40 1.1112 +IC H6A C5 *C6 H6B 1.1112 109.40 -115.79 108.30 1.1112 +IC C2 C10 *C1 H1A 1.5324 113.76 119.42 107.87 1.1135 +IC C2 C10 *C1 H1B 1.5324 113.76 -124.15 110.13 1.1095 +IC C1 C3 *C2 H2A 1.5324 111.68 121.97 110.22 1.1118 +IC H2A C3 *C2 H2B 1.1118 110.22 117.25 108.75 1.1127 +!IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config +!IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config +!IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config +!IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config +!IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config +!IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config +IC C6 C7 C8 C14 1.5449 113.04 -167.24 109.07 1.5517 +IC C14 C7 *C8 C9 1.5517 109.07 119.23 113.41 1.5223 +IC C7 C8 C14 C13 1.5297 109.07 -171.16 112.73 1.5504 +IC C13 C8 *C14 C15 1.5504 112.73 117.19 114.03 1.5268 +IC C8 C14 C15 C16 1.5517 114.03 -155.98 103.48 1.5369 +IC C14 C15 C16 C17 1.5268 103.48 2.71 107.62 1.5513 +IC C17 C14 *C13 C12 1.5748 98.26 120.41 106.82 1.5557 +IC C14 C13 C12 C11 1.5504 106.82 50.62 112.18 1.5515 +!IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config +!IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config +!IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config +!IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config +!IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config +!IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config +!IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config +!IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config +!IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config +!IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config +!IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config +!IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config +!IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config +IC C8 C6 *C7 O7 1.5297 113.04 -126.79 108.12 1.4213 +IC O7 C6 *C7 H7 1.4213 108.12 -113.65 106.95 1.1162 +IC C6 C7 O7 H7' 1.5449 108.12 170.74 104.84 0.9615 +IC C9 C7 *C8 H8 1.5223 113.41 122.31 106.89 1.1063 +IC C10 C8 *C9 H9 1.5432 109.57 -116.33 105.86 1.1163 +IC C9 C12 *C11 H11A 1.5553 117.58 122.21 106.83 1.1096 +IC H11A C12 *C11 H11B 1.1096 106.83 114.26 107.91 1.1115 +IC C14 C13 C12 O12 1.5504 106.82 -74.73 114.67 1.4228 +IC O12 C13 *C12 H12 1.4228 114.67 -118.14 108.61 1.1119 +IC C13 C12 O12 H12' 1.5557 114.67 -49.37 105.00 0.9629 +IC C13 C8 *C14 H14 1.5504 112.73 -119.72 109.55 1.1139 +IC C16 C14 *C15 H15A 1.5369 103.48 119.05 111.22 1.1006 +IC H15A C14 *C15 H15B 1.1006 111.22 119.83 112.45 1.0988 +IC C17 C15 *C16 H16A 1.5513 107.62 120.90 110.48 1.1007 +IC H16A C15 *C16 H16B 1.1007 110.48 117.28 111.71 1.1003 +IC C13 C16 *C17 H17 1.5748 100.22 -113.28 108.29 1.1013 +IC C12 C14 *C13 C18 1.5557 106.82 122.03 113.69 1.5568 +IC C14 C13 C18 H18A 1.5504 113.69 3.50 112.14 1.1055 +IC H18A C13 *C18 H18B 1.1055 112.14 119.59 111.31 1.1063 +IC H18A C13 *C18 H18C 1.1055 112.14 -120.84 110.78 1.1084 +IC C5 C10 C19 H19A 1.5283 109.67 9.75 111.22 1.1077 +IC H19A C10 *C19 H19B 1.1077 111.22 120.95 111.67 1.1070 +IC H19A C10 *C19 H19C 1.1077 111.22 -119.64 110.71 1.1092 +IC C13 C16 *C17 C20 1.5748 100.22 127.99 112.63 1.5616 +IC C16 C17 C20 C22 1.5513 112.63 71.02 108.94 1.5487 +IC C22 C17 *C20 C21 1.5487 108.94 122.52 113.13 1.5408 +IC C21 C17 *C20 H20 1.5408 113.13 121.15 109.02 1.1123 +IC C17 C20 C21 H21A 1.5616 113.13 67.60 111.00 1.1068 +IC H21A C20 *C21 H21B 1.1068 111.00 -122.83 111.01 1.1085 +IC H21A C20 *C21 H21C 1.1068 111.00 118.17 109.90 1.1107 +IC C17 C20 C22 C23 1.5616 108.94 -161.91 113.97 1.5494 +IC C23 C20 *C22 H22A 1.5494 113.97 119.29 109.76 1.1125 +IC H22A C20 *C22 H22B 1.1125 109.76 117.37 110.00 1.1113 +IC C20 C22 C23 CD 1.5487 113.97 176.94 113.05 1.5299 +IC CD C22 *C23 H23A 1.5299 113.05 119.90 111.01 1.1071 +IC CD C22 *C23 H23B 1.5299 113.05 -119.56 110.12 1.1084 +IC C22 C23 CD OE1 1.5494 113.05 -178.02 116.54 1.2584 +IC OE1 C23 *CD OE2 1.2584 116.54 175.48 119.00 1.2572 + + +RESI DCA -1.00 ! C24H39O4 deoxycholic acid(DCA), cacha +GROUP +ATOM C3 CG311 0.14 +ATOM O3 OG311 -0.65 +ATOM H3' HGP1 0.42 +ATOM H3 HGA1 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H4A HGA2 0.09 ! OE1 +ATOM H4B HGA2 0.09 ! || +GROUP ! OH Me21 C22 CD +ATOM C5 CG311 -0.09 ! | \ / \ / \ +ATOM H5 HGA1 0.09 ! C12 Me18 C20 CG OE2(-1) +GROUP ! / \ | / +ATOM C6 CG321 -0.18 ! C11 C13---C17 +ATOM H6A HGA2 0.09 ! Me19 | | | +ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C7 CG321 -0.18 ! C2 C10 C8 C15 +ATOM H7A HGA2 0.09 ! | | | +ATOM H7B HGA2 0.09 ! C3 C5 C7 +GROUP ! / \ / \ / +ATOM C8 CG311 -0.09 ! OH C4 C6 +ATOM H8 HGA1 0.09 +GROUP +ATOM C14 CG3RC1 -0.09 ! Deoxycholic acid (DCA) +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 ! no hydrogen +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG311 0.14 +ATOM H12 HGA1 0.09 +ATOM O12 OG311 -0.65 +ATOM H12' HGP1 0.42 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 ! no hydrogen +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM CD CG2O3 0.52 +ATOM OE1 OG2D2 -0.76 +ATOM OE2 OG2D2 -0.76 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7A C7 H7B +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12 C12 O12 O12 H12' +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 CD CD OE1 CD OE2 +IMPR CD OE2 OE1 C23 + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +!ICs based on CHARMM optimized structure +IC C1 C2 C3 C4 1.5324 111.68 -49.58 111.85 1.5384 +IC C2 C3 C4 C5 1.5336 111.85 43.65 115.86 1.5602 +IC C3 C4 C5 C6 1.5384 115.86 -174.25 108.84 1.5528 +IC C4 C5 C6 C7 1.5602 108.84 86.42 115.04 1.5449 +IC C5 C6 C7 C8 1.5528 115.04 38.94 113.04 1.5297 +IC C7 C8 C9 C10 1.5297 113.41 59.71 109.57 1.5432 +IC C8 C9 C10 C1 1.5223 109.57 178.73 111.89 1.5560 +IC C9 C10 C1 C2 1.5432 111.89 63.50 113.76 1.5324 +IC O3 C3 C4 C5 1.4163 109.08 161.75 115.86 1.5602 +IC C4 C2 *C3 O3 1.5384 111.85 -119.36 106.95 1.4163 +IC C4 C2 *C3 H3 1.5384 111.85 121.41 109.41 1.1143 +IC C9 C5 *C10 C19 1.5432 109.52 -123.19 109.67 1.5560 +IC C2 C3 O3 H3' 1.5336 106.95 64.94 104.68 0.9611 +IC C5 C3 *C4 H4A 1.5602 115.86 122.86 108.65 1.1110 +IC H4A C3 *C4 H4B 1.1110 108.65 115.61 108.72 1.1114 +IC C10 C4 *C5 H5 1.5283 114.75 116.75 105.10 1.1173 +IC C7 C5 *C6 H6A 1.5449 115.04 -124.17 109.40 1.1112 +IC H6A C5 *C6 H6B 1.1112 109.40 -115.79 108.30 1.1112 +IC C2 C10 *C1 H1A 1.5324 113.76 119.42 107.87 1.1135 +IC C2 C10 *C1 H1B 1.5324 113.76 -124.15 110.13 1.1095 +IC C1 C3 *C2 H2A 1.5324 111.68 121.97 110.22 1.1118 +IC H2A C3 *C2 H2B 1.1118 110.22 117.25 108.75 1.1127 +!IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config +!IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config +!IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config +!IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config +!IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config +!IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config +IC C6 C7 C8 C14 1.5449 113.04 -167.24 109.07 1.5517 +IC C14 C7 *C8 C9 1.5517 109.07 119.23 113.41 1.5223 +IC C7 C8 C14 C13 1.5297 109.07 -171.16 112.73 1.5504 +IC C13 C8 *C14 C15 1.5504 112.73 117.19 114.03 1.5268 +IC C8 C14 C15 C16 1.5517 114.03 -155.98 103.48 1.5369 +IC C14 C15 C16 C17 1.5268 103.48 2.71 107.62 1.5513 +IC C17 C14 *C13 C12 1.5748 98.26 120.41 106.82 1.5557 +IC C14 C13 C12 C11 1.5504 106.82 50.62 112.18 1.5515 +!IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config +!IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config +!IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config +!IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config +!IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config +!IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config +!IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config +!IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config +!IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config +!IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config +!IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config +!IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config +!IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config +IC C8 C6 *C7 H7A 1.5383 113.44 -126.79 109.41 1.1119 +IC H7A C6 *C7 H7B 1.1119 109.41 -113.65 109.70 1.1112 +IC C9 C7 *C8 H8 1.5223 113.41 122.31 106.89 1.1063 +IC C10 C8 *C9 H9 1.5432 109.57 -116.33 105.86 1.1163 +IC C9 C12 *C11 H11A 1.5553 117.58 122.21 106.83 1.1096 +IC H11A C12 *C11 H11B 1.1096 106.83 114.26 107.91 1.1115 +IC C14 C13 C12 O12 1.5504 106.82 -74.73 114.67 1.4228 +IC O12 C13 *C12 H12 1.4228 114.67 -118.14 108.61 1.1119 +IC C13 C12 O12 H12' 1.5557 114.67 -49.37 105.00 0.9629 +IC C13 C8 *C14 H14 1.5504 112.73 -119.72 109.55 1.1139 +IC C16 C14 *C15 H15A 1.5369 103.48 119.05 111.22 1.1006 +IC H15A C14 *C15 H15B 1.1006 111.22 119.83 112.45 1.0988 +IC C17 C15 *C16 H16A 1.5513 107.62 120.90 110.48 1.1007 +IC H16A C15 *C16 H16B 1.1007 110.48 117.28 111.71 1.1003 +IC C13 C16 *C17 H17 1.5748 100.22 -113.28 108.29 1.1013 +IC C12 C14 *C13 C18 1.5557 106.82 122.03 113.69 1.5568 +IC C14 C13 C18 H18A 1.5504 113.69 3.50 112.14 1.1055 +IC H18A C13 *C18 H18B 1.1055 112.14 119.59 111.31 1.1063 +IC H18A C13 *C18 H18C 1.1055 112.14 -120.84 110.78 1.1084 +IC C5 C10 C19 H19A 1.5283 109.67 9.75 111.22 1.1077 +IC H19A C10 *C19 H19B 1.1077 111.22 120.95 111.67 1.1070 +IC H19A C10 *C19 H19C 1.1077 111.22 -119.64 110.71 1.1092 +IC C13 C16 *C17 C20 1.5748 100.22 127.99 112.63 1.5616 +IC C16 C17 C20 C22 1.5513 112.63 71.02 108.94 1.5487 +IC C22 C17 *C20 C21 1.5487 108.94 122.52 113.13 1.5408 +IC C21 C17 *C20 H20 1.5408 113.13 121.15 109.02 1.1123 +IC C17 C20 C21 H21A 1.5616 113.13 67.60 111.00 1.1068 +IC H21A C20 *C21 H21B 1.1068 111.00 -122.83 111.01 1.1085 +IC H21A C20 *C21 H21C 1.1068 111.00 118.17 109.90 1.1107 +IC C17 C20 C22 C23 1.5616 108.94 -161.91 113.97 1.5494 +IC C23 C20 *C22 H22A 1.5494 113.97 119.29 109.76 1.1125 +IC H22A C20 *C22 H22B 1.1125 109.76 117.37 110.00 1.1113 +IC C20 C22 C23 CD 1.5487 113.97 176.94 113.05 1.5299 +IC CD C22 *C23 H23A 1.5299 113.05 119.90 111.01 1.1071 +IC CD C22 *C23 H23B 1.5299 113.05 -119.56 110.12 1.1084 +IC C22 C23 CD OE1 1.5494 113.05 -178.02 116.54 1.2584 +IC OE1 C23 *CD OE2 1.2584 116.54 175.48 119.00 1.2572 + + +RESI LCA -1.00 ! C24H39O3 LITHOCHOLIC ACID (LCA), cacha +GROUP +ATOM C3 CG311 0.14 +ATOM O3 OG311 -0.65 +ATOM H3' HGP1 0.42 +ATOM H3 HGA1 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H4A HGA2 0.09 ! OE1 +ATOM H4B HGA2 0.09 ! || +GROUP ! H Me21 C22 CD +ATOM C5 CG311 -0.09 ! | \ / \ / \ +ATOM H5 HGA1 0.09 ! C12 Me18 C20 CG OE2(-1) +GROUP ! / \ | / +ATOM C6 CG321 -0.18 ! C11 C13---C17 +ATOM H6A HGA2 0.09 ! Me19 | | | +ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C7 CG321 -0.18 ! C2 C10 C8 C15 +ATOM H7A HGA2 0.09 ! | | | +ATOM H7B HGA2 0.09 ! C3 C5 C7 +GROUP ! / \ / \ / +ATOM C8 CG311 -0.09 ! OH C4 C6 +ATOM H8 HGA1 0.09 +GROUP ! Lithocholic acid (LCA) +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 ! no hydrogen +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 ! no hydrogen +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM CD CG2O3 0.52 +ATOM OE1 OG2D2 -0.76 +ATOM OE2 OG2D2 -0.76 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7A C7 H7B +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 CD CD OE1 CD OE2 +IMPR CD OE2 OE1 C23 + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +!ICs based on CHARMM optimized structure +IC C1 C2 C3 C4 1.5337 112.03 -49.25 111.84 1.5388 +IC C2 C3 C4 C5 1.5350 111.84 44.83 114.98 1.5580 +IC C3 C4 C5 C6 1.5388 114.98 -175.73 110.26 1.5462 +IC C4 C5 C6 C7 1.5580 110.26 75.60 112.05 1.5329 +IC C5 C6 C7 C8 1.5462 112.05 52.55 111.32 1.5462 +IC C7 C8 C9 C10 1.5462 111.19 57.34 111.05 1.5448 +IC C8 C9 C10 C1 1.5356 111.05 -177.00 112.40 1.5563 +IC C9 C10 C1 C2 1.5448 112.40 64.20 114.05 1.5337 +IC O3 C3 C4 C5 1.4166 109.16 163.09 114.98 1.5580 +IC C4 C2 *C3 O3 1.5388 111.84 -119.52 107.04 1.4166 +IC C4 C2 *C3 H3 1.5388 111.84 121.28 109.34 1.1145 +IC C9 C5 *C10 C19 1.5448 110.02 -122.97 109.85 1.5545 +IC C2 C3 O3 H3' 1.5350 107.04 60.89 105.08 0.9602 +IC C5 C3 *C4 H4A 1.5580 114.98 122.28 108.66 1.1112 +IC H4A C3 *C4 H4B 1.1112 108.66 116.01 108.59 1.1102 +IC C10 C4 *C5 H5 1.5336 114.85 117.05 105.40 1.1171 +IC C7 C5 *C6 H6A 1.5329 112.05 -122.19 109.68 1.1114 +IC H6A C5 *C6 H6B 1.1114 109.68 -117.56 109.38 1.1121 +IC C2 C10 *C1 H1A 1.5337 114.05 119.68 107.55 1.1136 +IC C2 C10 *C1 H1B 1.5337 114.05 -124.22 110.15 1.1090 +IC C1 C3 *C2 H2A 1.5337 112.03 122.06 110.32 1.1113 +IC H2A C3 *C2 H2B 1.1113 110.32 117.22 108.67 1.1129 +!IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config +!IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config +!IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config +!IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config +!IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config +!IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config +IC C6 C7 C8 C14 1.5329 111.32 -170.02 106.39 1.5454 +IC C14 C7 *C8 C9 1.5454 106.39 115.37 111.19 1.5356 +IC C7 C8 C14 C13 1.5462 106.39 -177.38 112.55 1.5432 +IC C13 C8 *C14 C15 1.5432 112.55 118.10 116.48 1.5277 +IC C8 C14 C15 C16 1.5454 116.48 -154.70 103.50 1.5439 +IC C14 C15 C16 C17 1.5277 103.50 -1.82 106.89 1.5535 +IC C17 C14 *C13 C12 1.5722 98.05 120.18 108.13 1.5348 +IC C14 C13 C12 C11 1.5432 108.13 53.76 111.21 1.5444 +!IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config +!IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config +!IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config +!IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config +!IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config +!IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config +!IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config +!IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config +!IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config +!IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config +!IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config +!IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config +!IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config +IC C8 C6 *C7 H7A 1.5462 111.32 -120.76 109.56 1.1112 +IC H7A C6 *C7 H7B 1.1112 109.56 -117.60 109.24 1.1114 +IC C9 C7 *C8 H8 1.5356 111.19 124.30 109.39 1.1045 +IC C10 C8 *C9 H9 1.5448 111.05 -116.65 106.44 1.1137 +IC C9 C12 *C11 H11A 1.5521 113.16 121.96 109.10 1.1097 +IC H11A C12 *C11 H11B 1.1097 109.10 116.39 107.43 1.1100 +IC C14 C13 C12 H12A 1.5432 108.13 -66.12 108.72 1.1120 +IC H12A C13 *C12 H12B 1.1120 108.72 -119.32 111.59 1.1062 +IC C13 C8 *C14 H14 1.5432 112.55 -119.67 108.40 1.1145 +IC C16 C14 *C15 H15A 1.5439 103.50 119.46 111.24 1.0997 +IC H15A C14 *C15 H15B 1.0997 111.24 119.60 111.35 1.0990 +IC C17 C15 *C16 H16A 1.5535 106.89 121.34 110.90 1.0992 +IC H16A C15 *C16 H16B 1.0992 110.90 117.31 111.27 1.0993 +IC C13 C16 *C17 H17 1.5722 98.51 -112.99 110.29 1.1004 +IC C12 C14 *C13 C18 1.5348 108.13 121.73 113.93 1.5529 +IC C14 C13 C18 H18A 1.5432 113.93 -4.01 111.83 1.1058 +IC H18A C13 *C18 H18B 1.1058 111.83 120.17 111.33 1.1067 +IC H18A C13 *C18 H18C 1.1058 111.83 -120.74 110.60 1.1083 +IC C5 C10 C19 H19A 1.5336 109.85 -8.12 111.07 1.1083 +IC H19A C10 *C19 H19B 1.1083 111.07 120.82 111.82 1.1063 +IC H19A C10 *C19 H19C 1.1083 111.07 -119.70 110.58 1.1092 +IC C13 C16 *C17 C20 1.5722 98.51 127.11 111.95 1.5637 +IC C16 C17 C20 C22 1.5535 111.95 70.28 109.13 1.5506 +IC C22 C17 *C20 C21 1.5506 109.13 121.97 112.87 1.5401 +IC C21 C17 *C20 H20 1.5401 112.87 121.21 109.11 1.1116 +IC C17 C20 C21 H21A 1.5637 112.87 73.29 110.62 1.1071 +IC H21A C20 *C21 H21B 1.1071 110.62 -122.03 110.43 1.1097 +IC H21A C20 *C21 H21C 1.1071 110.62 118.43 110.33 1.1098 +IC C17 C20 C22 C23 1.5637 109.13 -161.00 114.04 1.5502 +IC C23 C20 *C22 H22A 1.5502 114.04 119.37 110.02 1.1115 +IC H22A C20 *C22 H22B 1.1115 110.02 117.32 109.74 1.1112 +IC C20 C22 C23 CD 1.5506 114.04 177.56 113.25 1.5303 +IC CD C22 *C23 H23A 1.5303 113.25 119.99 110.96 1.1070 +IC CD C22 *C23 H23B 1.5303 113.25 -119.65 110.01 1.1083 +IC C22 C23 CD OE1 1.5502 113.25 -178.85 116.56 1.2588 +IC OE1 C23 *CD OE2 1.2588 116.56 177.44 119.16 1.2573 + + +RESI CDCA -1.00 ! C24H39O4 CHENODEOXYCHOLIC ACID, cacha +GROUP +ATOM C3 CG311 0.14 +ATOM O3 OG311 -0.65 +ATOM H3' HGP1 0.42 +ATOM H3 HGA1 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H4A HGA2 0.09 ! OE1 +ATOM H4B HGA2 0.09 ! || +GROUP ! H Me21 C22 CD +ATOM C5 CG311 -0.09 ! | \ / \ / \ +ATOM H5 HGA1 0.09 ! C12 Me18 C20 CG OE2(-1) +GROUP ! / \ | / +ATOM C6 CG321 -0.18 ! C11 C13---C17 +ATOM H6A HGA2 0.09 ! Me19 | | | +ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C7 CG311 0.14 ! C2 C10 C8 C15 +ATOM O7 OG311 -0.65 ! | | | +ATOM H7' HGP1 0.42 ! C3 C5 C7 +ATOM H7 HGA1 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM C8 CG311 -0.09 +ATOM H8 HGA1 0.09 ! Chenodeoxycholic acid (CDCA) +GROUP +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 ! no hydrogen +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 ! no hydrogen +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM CD CG2O3 0.52 +ATOM OE1 OG2D2 -0.76 +ATOM OE2 OG2D2 -0.76 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7 C7 O7 O7 H7' +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 CD CD OE1 CD OE2 +IMPR CD OE2 OE1 C23 + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +!ICs based on CHARMM optimized structure +IC C1 C2 C3 C4 1.5325 111.74 -49.21 111.88 1.5385 +IC C2 C3 C4 C5 1.5341 111.88 43.74 115.69 1.5597 +IC C3 C4 C5 C6 1.5385 115.69 -175.10 109.04 1.5520 +IC C4 C5 C6 C7 1.5597 109.04 85.37 114.98 1.5440 +IC C5 C6 C7 C8 1.5520 114.98 38.83 113.15 1.5290 +IC C7 C8 C9 C10 1.5290 114.20 57.90 109.53 1.5437 +IC C8 C9 C10 C1 1.5325 109.53 179.78 112.01 1.5562 +IC C9 C10 C1 C2 1.5437 112.01 63.19 113.83 1.5325 +IC O3 C3 C4 C5 1.4164 109.06 161.96 115.69 1.5597 +IC C4 C2 *C3 O3 1.5385 111.88 -119.42 107.04 1.4164 +IC C4 C2 *C3 H3 1.5385 111.88 121.34 109.37 1.1144 +IC C9 C5 *C10 C19 1.5437 109.64 -123.44 109.56 1.5561 +IC C2 C3 O3 H3' 1.5341 107.04 68.70 104.78 0.9606 +IC C5 C3 *C4 H4A 1.5597 115.69 122.74 108.67 1.1111 +IC H4A C3 *C4 H4B 1.1111 108.67 115.74 108.84 1.1112 +IC C10 C4 *C5 H5 1.5278 114.69 116.72 105.05 1.1175 +IC C7 C5 *C6 H6A 1.5440 114.98 -124.18 109.41 1.1112 +IC H6A C5 *C6 H6B 1.1112 109.41 -115.81 108.31 1.1113 +IC C2 C10 *C1 H1A 1.5325 113.83 119.45 107.75 1.1136 +IC C2 C10 *C1 H1B 1.5325 113.83 -124.31 110.15 1.1092 +IC C1 C3 *C2 H2A 1.5325 111.74 122.10 110.26 1.1113 +IC H2A C3 *C2 H2B 1.1113 110.26 117.21 108.67 1.1128 +!IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config +!IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config +!IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config +!IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config +!IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config +!IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config +IC C6 C7 C8 C14 1.5440 113.15 -166.48 108.55 1.5543 +IC C14 C7 *C8 C9 1.5543 108.55 119.88 114.20 1.5325 +IC C7 C8 C14 C13 1.5290 108.55 -174.00 113.09 1.5423 +IC C13 C8 *C14 C15 1.5423 113.09 118.54 116.41 1.5290 +IC C8 C14 C15 C16 1.5543 116.41 -154.98 103.52 1.5436 +IC C14 C15 C16 C17 1.5290 103.52 -2.21 106.91 1.5527 +IC C17 C14 *C13 C12 1.5726 98.14 119.76 107.63 1.5335 +IC C14 C13 C12 C11 1.5423 107.63 55.01 111.17 1.5432 +!IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config +!IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config +!IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config +!IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config +!IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config +!IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config +!IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config +!IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config +!IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config +!IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config +!IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config +!IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config +!IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config +IC C8 C6 *C7 O7 1.5290 113.15 -126.97 108.08 1.4217 +IC O7 C6 *C7 H7 1.4217 108.08 -113.63 107.20 1.1165 +IC C6 C7 O7 H7' 1.5440 108.08 176.29 104.82 0.9615 +IC C9 C7 *C8 H8 1.5325 114.20 122.49 107.19 1.1068 +IC C10 C8 *C9 H9 1.5437 109.53 -117.14 106.58 1.1136 +IC C9 C12 *C11 H11A 1.5549 114.17 122.57 108.68 1.1092 +IC H11A C12 *C11 H11B 1.1092 108.68 115.77 107.30 1.1109 +IC C14 C13 C12 H12A 1.5423 107.63 -64.93 108.84 1.1122 +IC H12A C13 *C12 H12B 1.1122 108.84 -119.33 111.64 1.1063 +IC C13 C8 *C14 H14 1.5423 113.09 -118.19 108.50 1.1148 +IC C16 C14 *C15 H15A 1.5436 103.52 118.98 111.14 1.1003 +IC H15A C14 *C15 H15B 1.1003 111.14 119.93 112.23 1.0983 +IC C17 C15 *C16 H16A 1.5527 106.91 121.32 110.94 1.0995 +IC H16A C15 *C16 H16B 1.0995 110.94 117.27 111.30 1.0996 +IC C13 C16 *C17 H17 1.5726 98.49 -113.15 110.37 1.1004 +IC C12 C14 *C13 C18 1.5335 107.63 121.99 114.21 1.5526 +IC C14 C13 C18 H18A 1.5423 114.21 -3.87 111.99 1.1055 +IC H18A C13 *C18 H18B 1.1055 111.99 120.12 111.33 1.1067 +IC H18A C13 *C18 H18C 1.1055 111.99 -120.94 110.59 1.1084 +IC C5 C10 C19 H19A 1.5278 109.56 4.64 111.20 1.1078 +IC H19A C10 *C19 H19B 1.1078 111.20 121.08 112.01 1.1062 +IC H19A C10 *C19 H19C 1.1078 111.20 -119.52 110.63 1.1093 +IC C13 C16 *C17 C20 1.5726 98.49 127.01 111.91 1.5638 +IC C16 C17 C20 C22 1.5527 111.91 69.89 109.15 1.5504 +IC C22 C17 *C20 C21 1.5504 109.15 122.01 112.87 1.5400 +IC C21 C17 *C20 H20 1.5400 112.87 121.24 109.18 1.1115 +IC C17 C20 C21 H21A 1.5638 112.87 73.30 110.64 1.1072 +IC H21A C20 *C21 H21B 1.1072 110.64 -122.05 110.45 1.1097 +IC H21A C20 *C21 H21C 1.1072 110.64 118.42 110.32 1.1099 +IC C17 C20 C22 C23 1.5638 109.15 -160.90 114.01 1.5501 +IC C23 C20 *C22 H22A 1.5501 114.01 119.25 110.01 1.1115 +IC H22A C20 *C22 H22B 1.1115 110.01 117.37 109.82 1.1111 +IC C20 C22 C23 CD 1.5504 114.01 177.00 113.21 1.5306 +IC CD C22 *C23 H23A 1.5306 113.21 120.02 110.96 1.1069 +IC CD C22 *C23 H23B 1.5306 113.21 -119.58 110.04 1.1084 +IC C22 C23 CD OE1 1.5501 113.21 -177.88 116.45 1.2588 +IC OE1 C23 *CD OE2 1.2588 116.45 173.57 119.02 1.2574 + + +RESI UDCA -1.00 ! C24H39O4 URSODEOXYCHOLIC ACID (UDCA), cacha +GROUP +ATOM C3 CG311 0.14 +ATOM O3 OG311 -0.65 +ATOM H3' HGP1 0.42 +ATOM H3 HGA1 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H4A HGA2 0.09 ! OE1 +ATOM H4B HGA2 0.09 ! || +GROUP ! H Me21 C22 CD +ATOM C5 CG311 -0.09 ! | \ / \ / \ +ATOM H5 HGA1 0.09 ! C12 Me18 C20 CG OE2(-1) +GROUP ! / \ | / +ATOM C6 CG321 -0.18 ! C11 C13---C17 +ATOM H6A HGA2 0.09 ! Me19 | | | +ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C7 CG311 0.14 ! C2 C10 C8 C15 +ATOM O7 OG311 -0.65 ! | | | +ATOM H7' HGP1 0.42 ! C3 C5 C7 +ATOM H7 HGA1 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH (above the plane of the ring) +ATOM C8 CG311 -0.09 +ATOM H8 HGA1 0.09 ! Ursodeoxycholic acid (UDCA) +GROUP +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 ! no hydrogen +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 ! no hydrogen +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM CD CG2O3 0.52 +ATOM OE1 OG2D2 -0.76 +ATOM OE2 OG2D2 -0.76 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7 C7 O7 O7 H7' +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 CD CD OE1 CD OE2 +IMPR CD OE2 OE1 C23 + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +!ICs based on CHARMM optimized structure +IC C1 C2 C3 C4 1.5325 111.74 -49.21 111.88 1.5385 +IC C2 C3 C4 C5 1.5341 111.88 43.74 115.69 1.5597 +IC C3 C4 C5 C6 1.5385 115.69 -175.10 109.04 1.5520 +IC C4 C5 C6 C7 1.5597 109.04 85.37 114.98 1.5440 +IC C5 C6 C7 C8 1.5520 114.98 38.83 113.15 1.5290 +IC C7 C8 C9 C10 1.5290 114.20 57.90 109.53 1.5437 +IC C8 C9 C10 C1 1.5325 109.53 179.78 112.01 1.5562 +IC C9 C10 C1 C2 1.5437 112.01 63.19 113.83 1.5325 +IC O3 C3 C4 C5 1.4164 109.06 161.96 115.69 1.5597 +IC C4 C2 *C3 O3 1.5385 111.88 -119.42 107.04 1.4164 +IC C4 C2 *C3 H3 1.5385 111.88 121.34 109.37 1.1144 +IC C9 C5 *C10 C19 1.5437 109.64 -123.44 109.56 1.5561 +IC C2 C3 O3 H3' 1.5341 107.04 68.70 104.78 0.9606 +IC C5 C3 *C4 H4A 1.5597 115.69 122.74 108.67 1.1111 +IC H4A C3 *C4 H4B 1.1111 108.67 115.74 108.84 1.1112 +IC C10 C4 *C5 H5 1.5278 114.69 116.72 105.05 1.1175 +IC C7 C5 *C6 H6A 1.5440 114.98 -124.18 109.41 1.1112 +IC H6A C5 *C6 H6B 1.1112 109.41 -115.81 108.31 1.1113 +IC C2 C10 *C1 H1A 1.5325 113.83 119.45 107.75 1.1136 +IC C2 C10 *C1 H1B 1.5325 113.83 -124.31 110.15 1.1092 +IC C1 C3 *C2 H2A 1.5325 111.74 122.10 110.26 1.1113 +IC H2A C3 *C2 H2B 1.1113 110.26 117.21 108.67 1.1128 +!IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config +!IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config +!IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config +!IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config +!IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config +!IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config +IC C6 C7 C8 C14 1.5440 113.15 -166.48 108.55 1.5543 +IC C14 C7 *C8 C9 1.5543 108.55 119.88 114.20 1.5325 +IC C7 C8 C14 C13 1.5290 108.55 -174.00 113.09 1.5423 +IC C13 C8 *C14 C15 1.5423 113.09 118.54 116.41 1.5290 +IC C8 C14 C15 C16 1.5543 116.41 -154.98 103.52 1.5436 +IC C14 C15 C16 C17 1.5290 103.52 -2.21 106.91 1.5527 +IC C17 C14 *C13 C12 1.5726 98.14 119.76 107.63 1.5335 +IC C14 C13 C12 C11 1.5423 107.63 55.01 111.17 1.5432 +!IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config +!IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config +!IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config +!IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config +!IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config +!IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config +!IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config +!IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config +!IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config +!IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config +!IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config +!IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config +!IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config +IC C8 C6 *C7 H7 1.5322 112.88 -121.61 108.52 1.1146 +IC H7 C6 *C7 O7 1.1146 108.52 -118.80 106.42 1.4215 +IC C6 C7 O7 H7' 1.5418 106.42 -178.10 104.63 0.9612 +IC C9 C7 *C8 H8 1.5325 114.20 122.49 107.19 1.1068 +IC C10 C8 *C9 H9 1.5437 109.53 -117.14 106.58 1.1136 +IC C9 C12 *C11 H11A 1.5549 114.17 122.57 108.68 1.1092 +IC H11A C12 *C11 H11B 1.1092 108.68 115.77 107.30 1.1109 +IC C14 C13 C12 H12A 1.5423 107.63 -64.93 108.84 1.1122 +IC H12A C13 *C12 H12B 1.1122 108.84 -119.33 111.64 1.1063 +IC C13 C8 *C14 H14 1.5423 113.09 -118.19 108.50 1.1148 +IC C16 C14 *C15 H15A 1.5436 103.52 118.98 111.14 1.1003 +IC H15A C14 *C15 H15B 1.1003 111.14 119.93 112.23 1.0983 +IC C17 C15 *C16 H16A 1.5527 106.91 121.32 110.94 1.0995 +IC H16A C15 *C16 H16B 1.0995 110.94 117.27 111.30 1.0996 +IC C13 C16 *C17 H17 1.5726 98.49 -113.15 110.37 1.1004 +IC C12 C14 *C13 C18 1.5335 107.63 121.99 114.21 1.5526 +IC C14 C13 C18 H18A 1.5423 114.21 -3.87 111.99 1.1055 +IC H18A C13 *C18 H18B 1.1055 111.99 120.12 111.33 1.1067 +IC H18A C13 *C18 H18C 1.1055 111.99 -120.94 110.59 1.1084 +IC C5 C10 C19 H19A 1.5278 109.56 4.64 111.20 1.1078 +IC H19A C10 *C19 H19B 1.1078 111.20 121.08 112.01 1.1062 +IC H19A C10 *C19 H19C 1.1078 111.20 -119.52 110.63 1.1093 +IC C13 C16 *C17 C20 1.5726 98.49 127.01 111.91 1.5638 +IC C16 C17 C20 C22 1.5527 111.91 69.89 109.15 1.5504 +IC C22 C17 *C20 C21 1.5504 109.15 122.01 112.87 1.5400 +IC C21 C17 *C20 H20 1.5400 112.87 121.24 109.18 1.1115 +IC C17 C20 C21 H21A 1.5638 112.87 73.30 110.64 1.1072 +IC H21A C20 *C21 H21B 1.1072 110.64 -122.05 110.45 1.1097 +IC H21A C20 *C21 H21C 1.1072 110.64 118.42 110.32 1.1099 +IC C17 C20 C22 C23 1.5638 109.15 -160.90 114.01 1.5501 +IC C23 C20 *C22 H22A 1.5501 114.01 119.25 110.01 1.1115 +IC H22A C20 *C22 H22B 1.1115 110.01 117.37 109.82 1.1111 +IC C20 C22 C23 CD 1.5504 114.01 177.00 113.21 1.5306 +IC CD C22 *C23 H23A 1.5306 113.21 120.02 110.96 1.1069 +IC CD C22 *C23 H23B 1.5306 113.21 -119.58 110.04 1.1084 +IC C22 C23 CD OE1 1.5501 113.21 -177.88 116.45 1.2588 +IC OE1 C23 *CD OE2 1.2588 116.45 173.57 119.02 1.2574 + + +PRES GYCO -1.00 ! C3H3NO3 previously PRES GLYC, cacha +! patch combination: +! core residue cholic acid (CA) >> glycocholic acid (GCA) +! core residue deoxycholic acid (DCA) >> glycodeoxycholic acid (GDCA) +! core residue lithocholic acid (LCA) >> glycolithocholic acid (GLCA) +! core residue chenodeoxycholic acid (CDCA) >> glycochenodeoxycholic acid (GCDCA) +! core residue ursodeoxycholic acid (UDCA) >> glycoursodeoxycholic acid (GUDCA) + + ! OEG1 + ! || + ! OE1 CDG--OEG2(-1) + ! || | +DELETE ATOM OE2 ! OH Me21 C22 CD CG +ATOM CD CG2O1 0.51 ! | \ / \ / \ / +ATOM OE1 OG2D1 -0.51 ! C12 Me18 C20 C23 NH +ATOM N NG2S1 -0.47 ! / \ | / +ATOM HN HGP1 0.47 ! C11 C13---C17 +ATOM CG CG321 -0.28 ! Me19 | | | +ATOM HG1 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HG2 HGA2 0.09 ! / \|/ \ / \ / +ATOM CDG CG2O3 0.62 ! C2 C10 C8 C15 +ATOM OEG1 OG2D2 -0.76 ! | | | +ATOM OEG2 OG2D2 -0.76 ! C3 C5 C7 + ! / \ / \ / \ + ! HO C4 C6 OH +BOND CD N N HN +BOND N CG CG HG1 CG HG2 ! Glycocholic acid (GCA) +BOND CG CDG CDG OEG1 CDG OEG2 +IMPR CD C23 N OE1 +IMPR CDG OEG1 OEG2 CG + +IC OE1 C23 *CD N 1.2267 119.93 177.01 116.52 1.3368 +IC C23 CD N CG 1.5039 116.52 -173.26 130.72 1.4497 +IC CG CD *N HN 1.4497 130.72 170.32 124.06 1.0161 +IC CD N CG CDG 1.3368 130.72 168.60 104.28 1.5483 +IC CDG N *CG HG1 1.5483 104.28 117.38 111.67 1.1092 +IC CDG N *CG HG2 1.5483 104.28 -117.58 112.23 1.1082 +IC N CG CDG OEG1 1.4497 104.28 148.60 116.21 1.2549 +IC OEG1 CG *CDG OEG2 1.2549 116.21 -149.85 112.75 1.2749 + +!end bile acid related compounds, chayan, jul2006 + +!bile acid related compounds, chayan, dec2006 +RESI GA -2.00 ! C29H45NO7 GLUTAMIC ACID CDCA AMIDE, cacha +GROUP +ATOM C3 CG311 0.14 +ATOM O3 OG311 -0.65 +ATOM H3' HGP1 0.42 +ATOM H3 HGA1 0.09 +GROUP ! OA2(-0.5) +ATOM C4 CG321 -0.18 ! | +ATOM H4A HGA2 0.09 ! O24 CA--OA1(-0.5) +ATOM H4B HGA2 0.09 ! || | +GROUP ! H Me21 C22 C24 CC1 CC3 OG1(-0.5) +ATOM C5 CG311 -0.09 ! | \ / \ / \ / \ / \ / +ATOM H5 HGA1 0.09 ! C12 Me18 C20 C23 NH CC2 CG +GROUP ! / \ | / \ +ATOM C6 CG321 -0.18 ! C11 C13---C17 OG2(-0.5) +ATOM H6A HGA2 0.09 ! Me19 | | | +ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C7 CG311 0.14 ! C2 C10 C8 C15 +ATOM O7 OG311 -0.65 ! | | | +ATOM H7' HGP1 0.42 ! C3 C5 C7 +ATOM H7 HGA1 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM C8 CG311 -0.09 +ATOM H8 HGA1 0.09 ! Glutamic Acid CDCA Amide (GA) +GROUP +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 ! no hydrogen +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 ! no hydrogen +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM C24 CG2O1 0.51 +ATOM O24 OG2D1 -0.51 +ATOM N NG2S1 -0.47 +ATOM HN HGP1 0.47 +GROUP +ATOM CC1 CG311 -0.19 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O3 0.62 +ATOM OA1 OG2D2 -0.76 +ATOM OA2 OG2D2 -0.76 +GROUP +ATOM CC2 CG321 -0.18 +ATOM HC2A HGA2 0.09 +ATOM HC2B HGA2 0.09 +GROUP +ATOM CC3 CG321 -0.28 +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 +ATOM CG CG2O3 0.62 +ATOM OG1 OG2D2 -0.76 +ATOM OG2 OG2D2 -0.76 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7 C7 O7 O7 H7' +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 C24 C24 O24 +BOND C24 N N HN +BOND N CC1 CC1 HC1 CC1 CA CA OA1 CA OA2 +BOND CC1 CC2 CC2 HC2A CC2 HC2B CC2 CC3 +BOND CC3 HC3A CC3 HC3B CC3 CG CG OG1 CG OG2 +IMPR C24 C23 N O24 +IMPR CA OA2 OA1 CC1 +IMPR CG OG2 OG1 CC3 + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +!ICs based on arbitrary CHARMM optimized structure +IC C1 C2 C3 C4 1.5325 111.83 -48.81 111.97 1.5386 +IC C2 C3 C4 C5 1.5343 111.97 43.31 115.75 1.5595 +IC C3 C4 C5 C6 1.5386 115.75 -175.01 109.03 1.5520 +IC C4 C5 C6 C7 1.5595 109.03 85.21 115.02 1.5438 +IC C5 C6 C7 C8 1.5520 115.02 38.61 113.11 1.5276 +IC C7 C8 C9 C10 1.5276 114.59 57.44 109.36 1.5436 +IC C8 C9 C10 C1 1.5364 109.36 -179.93 112.02 1.5561 +IC C9 C10 C1 C2 1.5436 112.02 62.99 113.75 1.5325 +IC O3 C3 C4 C5 1.4166 108.95 161.43 115.75 1.5595 +IC C4 C2 *C3 O3 1.5386 111.97 -119.29 106.97 1.4166 +IC C4 C2 *C3 H3 1.5386 111.97 121.36 109.36 1.1143 +IC C9 C5 *C10 C19 1.5436 109.73 -123.35 109.59 1.5558 +IC C2 C3 O3 H3' 1.5343 106.97 70.81 104.29 0.9610 +IC C5 C3 *C4 H4A 1.5595 115.75 122.78 108.78 1.1109 +IC H4A C3 *C4 H4B 1.1109 108.78 115.85 108.94 1.1114 +IC C10 C4 *C5 H5 1.5280 114.66 116.76 105.20 1.1172 +IC C7 C5 *C6 H6A 1.5438 115.02 -124.32 109.59 1.1107 +IC H6A C5 *C6 H6B 1.1107 109.59 -115.96 108.35 1.1117 +IC C2 C10 *C1 H1A 1.5325 113.75 119.62 107.69 1.1133 +IC C2 C10 *C1 H1B 1.5325 113.75 -124.21 109.99 1.1093 +IC C1 C3 *C2 H2A 1.5325 111.83 121.96 110.22 1.1114 +IC H2A C3 *C2 H2B 1.1114 110.22 117.27 108.72 1.1125 +!IC C1 C2 C3 C4 1.5383 110.44 -62.22 110.66 1.5367 ! for trans config +!IC C2 C3 C4 C5 1.5311 110.66 -52.17 111.70 1.5156 ! for trans config +!IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09 1.5304 ! for trans config +!IC C10 C4 *C5 C6 1.5304 115.09 -177.32 121.28 1.3432 ! for trans config +!IC C4 C5 C6 C7 1.5156 121.28 75.31 123.88 1.5018 ! for trans config +!IC C5 C6 C7 C8 1.3432 123.88 51.01 112.36 1.5506 ! for trans config +IC C6 C7 C8 C14 1.5438 113.11 -165.92 108.46 1.5523 +IC C14 C7 *C8 C9 1.5523 108.46 119.72 114.59 1.5364 +IC C7 C8 C14 C13 1.5276 108.46 -173.32 111.50 1.5366 +IC C13 C8 *C14 C15 1.5366 111.50 118.16 117.80 1.5346 +IC C8 C14 C15 C16 1.5523 117.80 -150.82 103.90 1.5511 +IC C14 C15 C16 C17 1.5346 103.90 -5.86 105.47 1.5512 +IC C17 C14 *C13 C12 1.5566 98.22 118.19 109.26 1.5283 +IC C14 C13 C12 C11 1.5366 109.26 55.66 110.30 1.5429 +!IC C2 C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans config +!IC C2 C10 *C1 H1B 1.5383 114.55 -120.71 108.29 1.1134 ! for trans config +!IC C1 C3 *C2 H2A 1.5383 110.44 121.16 109.41 1.1119 ! for trans config +!IC H2A C3 *C2 H2B 1.1119 109.41 118.30 109.70 1.1112 ! for trans config +!IC C1 C2 C3 O3 1.1119 109.41 -175.00 109.70 1.1112 ! for trans config +!IC C4 C2 *C3 O3 1.5367 110.66 -120.28 109.14 1.4158 ! for trans config +!IC O3 C2 *C3 H3 1.4158 109.14 -118.92 109.40 1.1155 ! for trans config +!IC C2 C3 O3 H3' 1.5311 109.14 60.00 105.39 0.9593 ! for trans config +!IC C5 C3 *C4 H4A 1.5156 111.70 121.99 109.16 1.1099 ! for trans config +!IC H4A C3 *C4 H4B 1.1099 109.16 115.03 107.34 1.1142 ! for trans config +!IC C10 C4 *C5 H5 1.5000 111.00 -120.00 110.10 1.1110 ! for trans config +!IC C7 C5 *C6 H6A 1.5018 110.10 -120.00 110.10 1.1001 ! for trans config +!IC H6A C5 *C6 H6B 1.1110 110.10 -120.00 110.10 1.1110 ! for trans config +IC C8 C6 *C7 O7 1.5276 113.11 -126.99 108.31 1.4225 +IC O7 C6 *C7 H7 1.4225 108.31 -113.92 107.38 1.1176 +IC C6 C7 O7 H7' 1.5438 108.31 -176.31 103.73 0.9623 +IC C9 C7 *C8 H8 1.5364 114.59 122.91 107.14 1.1079 +IC C10 C8 *C9 H9 1.5436 109.36 -116.93 106.27 1.1129 +IC C9 C12 *C11 H11A 1.5599 114.19 122.19 108.67 1.1091 +IC H11A C12 *C11 H11B 1.1091 108.67 115.84 107.52 1.1100 +IC C14 C13 C12 H12A 1.5366 109.26 -63.53 108.77 1.1119 +IC H12A C13 *C12 H12B 1.1119 108.77 -118.49 110.35 1.1099 +IC C13 C8 *C14 H14 1.5366 111.50 -117.92 108.42 1.1139 +IC C16 C14 *C15 H15A 1.5511 103.90 118.25 111.42 1.1022 +IC H15A C14 *C15 H15B 1.1022 111.42 120.29 112.58 1.0964 +IC C17 C15 *C16 H16A 1.5512 105.47 121.54 108.43 1.1009 +IC H16A C15 *C16 H16B 1.1009 108.43 116.18 112.44 1.0973 +IC C13 C16 *C17 H17 1.5566 98.62 -112.31 108.27 1.1016 +IC C12 C14 *C13 C18 1.5283 109.26 123.58 114.19 1.5536 +IC C14 C13 C18 H18A 1.5366 114.19 4.73 112.02 1.1075 +IC H18A C13 *C18 H18B 1.1075 112.02 118.46 111.31 1.1080 +IC H18A C13 *C18 H18C 1.1075 112.02 -121.96 111.70 1.1059 +IC C5 C10 C19 H19A 1.5280 109.59 4.28 111.26 1.1078 +IC H19A C10 *C19 H19B 1.1078 111.26 120.71 111.90 1.1071 +IC H19A C10 *C19 H19C 1.1078 111.26 -119.86 110.79 1.1088 +IC C13 C16 *C17 C20 1.5566 98.62 124.35 118.99 1.5606 +IC C16 C17 C20 C22 1.5512 118.99 -1.33 112.57 1.5470 +IC C22 C17 *C20 C21 1.5470 112.57 123.04 107.65 1.5439 +IC C21 C17 *C20 H20 1.5439 107.65 117.51 109.34 1.1119 +IC C17 C20 C21 H21A 1.5606 107.65 56.27 110.43 1.1095 +IC H21A C20 *C21 H21B 1.1095 110.43 -120.25 109.86 1.1109 +IC H21A C20 *C21 H21C 1.1095 110.43 120.00 110.54 1.1093 +IC C17 C20 C22 C23 1.5606 112.57 -177.70 114.81 1.5506 +IC C23 C20 *C22 H22A 1.5506 114.81 119.77 108.00 1.1166 +IC H22A C20 *C22 H22B 1.1166 108.00 116.45 108.68 1.1124 +IC C20 C22 C23 C24 1.5470 114.81 166.35 110.40 1.4987 +IC C24 C22 *C23 H23A 1.4987 110.40 121.19 111.13 1.1081 +IC C24 C22 *C23 H23B 1.4987 110.40 -118.13 109.46 1.1111 +IC C22 C23 C24 N 1.5506 110.40 46.22 115.40 1.3366 +IC N C23 *C24 O24 1.3366 115.40 -179.81 120.30 1.2285 +IC C23 C24 N CC1 1.4987 115.40 -163.64 129.84 1.4417 +IC CC1 C24 *N HN 1.4417 129.84 178.15 124.42 1.0052 +IC C24 N CC1 CA 1.3366 129.84 -156.03 104.17 1.5535 +IC CA N *CC1 HC1 1.5535 104.17 116.15 110.25 1.1093 +IC HC1 N *CC1 CC2 1.1093 110.25 122.36 109.79 1.5587 +IC N CC1 CA OA1 1.4417 104.17 160.24 120.14 1.2563 +IC OA1 CC1 *CA OA2 1.2563 120.14 -176.18 115.58 1.2715 +IC N CC1 CC2 CC3 1.4417 109.79 58.95 114.87 1.5576 +IC CC3 CC1 *CC2 HC2A 1.5576 114.87 122.98 109.65 1.1108 +IC HC2A CC1 *CC2 HC2B 1.1108 109.65 116.68 107.14 1.1137 +IC CC1 CC2 CC3 CG 1.5587 114.87 -160.82 114.28 1.5329 +IC CG CC2 *CC3 HC3A 1.5329 114.28 119.62 110.64 1.1056 +IC HC3A CC2 *CC3 HC3B 1.1056 110.64 118.51 109.05 1.1085 +IC CC2 CC3 CG OG1 1.5576 114.28 -112.88 118.59 1.2602 +IC OG1 CC3 *CG OG2 1.2602 118.59 -177.02 117.98 1.2616 + +PRES AMGA 0.00 ! C3H4O2 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Alpha-Methyl Glu Acid CDCA Amide + + ! OA1 + ! || + ! O24 CA--OA2--CH3(M) + ! || | + ! OH Me21 C22 C24 CC1 CC3 OG1(-0.5) +ATOM CC1 CG311 0.17 ! | \ / \ / \ / \ / \ / +ATOM HC1 HGA1 0.09 ! C12 Me18 C20 C23 NH CC2 CG +ATOM CA CG2O2 0.90 ! / \ | / \ +ATOM OA1 OG2D1 -0.63 ! C11 C13---C17 OG2(-0.5) +ATOM OA2 OG302 -0.49 ! Me19 | | | +ATOM CM CG331 -0.31 ! C1 | C9 C14 C16 +ATOM HM1 HGA3 0.09 ! / \|/ \ / \ / +ATOM HM2 HGA3 0.09 ! C2 C10 C8 C15 +ATOM HM3 HGA3 0.09 ! | | | + ! C3 C5 C7 + ! / \ / \ / \ + ! HO C4 C6 OH + + ! Alpha-Methyl Glutamic Acid CDCA Amide + +BOND OA2 CM +BOND CM HM1 CM HM2 CM HM3 +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CM 1.5285 111.09 -178.91 115.08 1.4371 +IC HM1 CM OA2 CA 1.1113 109.28 179.56 115.08 1.3429 +IC HM2 CM OA2 CA 1.1136 110.99 60.48 115.08 1.3429 +IC HM3 CM OA2 CA 1.1135 110.99 -61.17 115.08 1.3429 + + +PRES GMGA 0.00 ! C3H5O2 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Gamma-Methyl Glu Acid CDCA Amide + + ! OA1(-0.5) + ! | + ! O24 CA--OA2(-0.5) + ! || | + ! OH Me21 C22 C24 CC1 CC3 OG1 + ! | \ / \ / \ / \ / \ // +ATOM CC3 CG321 0.08 ! C12 Me18 C20 C23 NH CC2 CG +ATOM HC3A HGA2 0.09 ! / \ | / \ +ATOM HC3B HGA2 0.09 ! C11 C13---C17 OG2--CM3(M) +ATOM CG CG2O2 0.90 ! Me19 | | | +ATOM OG1 OG2D1 -0.63 ! C1 | C9 C14 C16 +ATOM OG2 OG302 -0.49 ! / \|/ \ / \ / +ATOM CM CG331 -0.31 ! C2 C10 C8 C15 +ATOM HM1 HGA3 0.09 ! | | | +ATOM HM2 HGA3 0.09 ! C3 C5 C7 +ATOM HM3 HGA3 0.09 ! / \ / \ / \ + ! HO C4 C6 OH + + ! Gamma-Methyl Glutamic Acid CDCA Amide + +BOND OG2 CM +BOND CM HM1 CM HM2 CM HM3 +DELETE IMPR CG OG2 OG1 CC3 +DELETE IMPR CG OG2 OG1 CC3 +IMPR CG CC3 OG1 OG2 + +IC CC3 CG OG2 CM 1.5001 109.42 178.80 114.93 1.4378 +IC HM1 CM OG2 CG 1.1114 109.43 179.48 114.93 1.3439 +IC HM2 CM OG2 CG 1.1140 110.99 60.32 114.93 1.3439 +IC HM3 CM OG2 CG 1.1136 111.06 -61.13 114.93 1.3439 + + +PRES DMGA 0.00 ! C6H9O4 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Alpha,Gamma-Dimethyl Glu Acid CDCA Amide + +ATOM CC1 CG311 0.17 ! OA1 +ATOM HC1 HGA1 0.09 ! || +ATOM CA CG2O2 0.90 ! O24 CA--OA2--CH3(M) +ATOM OA1 OG2D1 -0.63 ! || | +ATOM OA2 OG302 -0.49 ! OH Me21 C22 C24 CC1 CC3 OG1 +ATOM CM CG331 -0.31 ! | \ / \ / \ / \ / \ // +ATOM HM1 HGA3 0.09 ! C12 Me18 C20 C23 NH CC2 CG +ATOM HM2 HGA3 0.09 ! / \ | / \ +ATOM HM3 HGA3 0.09 ! C11 C13---C17 OG2--CM3(N) +ATOM CC3 CG321 0.08 ! Me19 | | | +ATOM HC3A HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HC3B HGA2 0.09 ! / \|/ \ / \ / +ATOM CG CG2O2 0.90 ! C2 C10 C8 C15 +ATOM OG1 OG2D1 -0.63 ! | | | +ATOM OG2 OG302 -0.49 ! C3 C5 C7 +ATOM CN CG331 -0.31 ! / \ / \ / \ +ATOM HN1 HGA3 0.09 ! HO C4 C6 OH +ATOM HN2 HGA3 0.09 +ATOM HN3 HGA3 0.09 ! Alpha,Gamma-Dimethyl Glutamic Acid CDCA Amide + +BOND OA2 CM +BOND CM HM1 CM HM2 CM HM3 +BOND OG2 CN +BOND CN HN1 CN HN2 CN HN3 +DELETE IMPR CA OA2 OA1 CC1 +DELETE IMPR CG OG2 OG1 CC3 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 OG1 OG2 + +IC CC1 CA OA2 CM 1.5215 109.43 -179.14 114.39 1.4397 +IC HM1 CM OA2 CA 1.1119 109.81 179.92 114.39 1.3481 +IC HM2 CM OA2 CA 1.1147 111.25 60.55 114.39 1.3481 +IC HM3 CM OA2 CA 1.1148 111.21 -60.74 114.39 1.3481 +IC CC3 CG OG2 CN 1.5036 109.18 178.54 114.99 1.4389 +IC HN1 CN OG2 CG 1.1119 109.57 179.75 114.99 1.3378 +IC HN2 CN OG2 CG 1.1144 111.15 60.57 114.99 1.3378 +IC HN3 CN OG2 CG 1.1141 111.21 -60.90 114.99 1.3378 + +PRES AMGT 0.00 ! C9H15O4 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Alpha Methyl, Gamma Tert.Butyl Glu Acid CDCA Amide + +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 ! OA1 +ATOM CA CG2O2 0.90 ! || +ATOM OA1 OG2D1 -0.63 ! O24 CA--OA2--CH3(M) +ATOM OA2 OG302 -0.49 ! || | +ATOM CM CG331 -0.31 ! OH Me21 C22 C24 CC1 CC3 OG1 +ATOM HM1 HGA3 0.09 ! | \ / \ / \ / \ / \ // +ATOM HM2 HGA3 0.09 ! C12 Me18 C20 C23 NH CC2 CG CB1 +ATOM HM3 HGA3 0.09 ! / \ | / \ | +ATOM CC3 CG321 0.08 ! C11 C13---C17 OG2--CT--CB2 +ATOM HC3A HGA2 0.09 ! Me19 | | | | +ATOM HC3B HGA2 0.09 ! C1 | C9 C14 C16 CB3 +ATOM CG CG2O2 0.90 ! / \|/ \ / \ / +ATOM OG1 OG2D1 -0.63 ! C2 C10 C8 C15 +ATOM OG2 OG302 -0.49 ! | | | +ATOM CT CG301 -0.04 ! C3 C5 C7 +ATOM CB1 CG331 -0.27 ! / \ / \ / \ +ATOM HB11 HGA3 0.09 ! HO C4 C6 OH +ATOM HB12 HGA3 0.09 +ATOM HB13 HGA3 0.09 ! Alpha Methyl,Gamma Tert.Butyl Glutamic Acid CDCA Amide +ATOM CB2 CG331 -0.27 +ATOM HB21 HGA3 0.09 +ATOM HB22 HGA3 0.09 +ATOM HB23 HGA3 0.09 +ATOM CB3 CG331 -0.27 +ATOM HB31 HGA3 0.09 +ATOM HB32 HGA3 0.09 +ATOM HB33 HGA3 0.09 + +BOND OA2 CM +BOND CM HM1 CM HM2 CM HM3 +BOND OG2 CT +BOND CT CB1 CB1 HB11 CB1 HB12 CB1 HB13 +BOND CT CB2 CB2 HB21 CB2 HB22 CB2 HB23 +BOND CT CB3 CB3 HB31 CB3 HB32 CB3 HB33 +DELETE IMPR CA OA2 OA1 CC1 +DELETE IMPR CG OG2 OG1 CC3 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 OG1 OG2 + +IC CC1 CA OA2 CM 1.5216 109.43 -179.07 114.39 1.4397 +IC HM1 CM OA2 CA 1.1119 109.81 179.90 114.39 1.3481 +IC HM2 CM OA2 CA 1.1147 111.24 60.54 114.39 1.3481 +IC HM3 CM OA2 CA 1.1147 111.21 -60.74 114.39 1.3481 +IC CC3 CG OG2 CT 1.5056 108.23 179.34 121.50 1.4254 +IC CB1 CT OG2 CG 1.5308 105.14 179.25 121.50 1.3210 +IC CB2 CT OG2 CG 1.5354 111.04 62.01 121.50 1.3210 +IC CB3 CT OG2 CG 1.5354 110.89 -63.42 121.50 1.3210 +IC HB11 CB1 CT OG2 1.1097 110.37 -179.27 105.14 1.4254 +IC HB12 CB1 CT OG2 1.1088 110.29 60.60 105.14 1.4254 +IC HB13 CB1 CT OG2 1.1105 110.19 -59.24 105.14 1.4254 +IC HB21 CB2 CT OG2 1.1098 109.96 171.88 111.04 1.4254 +IC HB22 CB2 CT OG2 1.1099 110.24 52.17 111.04 1.4254 +IC HB23 CB2 CT OG2 1.1092 111.27 -68.59 111.04 1.4254 +IC HB31 CB3 CT OG2 1.1098 109.90 -171.74 110.89 1.4254 +IC HB32 CB3 CT OG2 1.1094 111.09 68.88 110.89 1.4254 +IC HB33 CB3 CT OG2 1.1092 110.31 -51.87 110.89 1.4254 + + + +PRES ATGM 0.00 ! C9H15O4 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Gamma Methyl, Alpha Tert.Butyl Glu Acid CDCA Amide + +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 ! OA1 CB1 CB2 +ATOM OA1 OG2D1 -0.63 ! || \ / +ATOM OA2 OG302 -0.49 ! O24 CA--OA2--CT--CB3 +ATOM CT CG301 -0.04 ! || | +ATOM CB1 CG331 -0.27 ! OH Me21 C22 C24 CC1 CC3 OG1 +ATOM HB11 HGA3 0.09 ! | \ / \ / \ / \ / \ // +ATOM HB12 HGA3 0.09 ! C12 Me18 C20 C23 NH CC2 CG +ATOM HB13 HGA3 0.09 ! / \ | / \ +ATOM CB2 CG331 -0.27 ! C11 C13---C17 OG2--CH3(M) +ATOM HB21 HGA3 0.09 ! Me19 | | | +ATOM HB22 HGA3 0.09 ! C1 | C9 C14 C16 +ATOM HB23 HGA3 0.09 ! / \|/ \ / \ / +ATOM CB3 CG331 -0.27 ! C2 C10 C8 C15 +ATOM HB31 HGA3 0.09 ! | | | +ATOM HB32 HGA3 0.09 ! C3 C5 C7 +ATOM HB33 HGA3 0.09 ! / \ / \ / \ +ATOM CC3 CG321 0.08 ! HO C4 C6 OH +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 ! Gamma Methyl, Alpha Tert.Butyl Glutamic Acid CDCA Amide +ATOM CG CG2O2 0.90 +ATOM OG1 OG2D1 -0.63 +ATOM OG2 OG302 -0.49 +ATOM CM CG331 -0.31 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND OA2 CT +BOND CT CB1 CB1 HB11 CB1 HB12 CB1 HB13 +BOND CT CB2 CB2 HB21 CB2 HB22 CB2 HB23 +BOND CT CB3 CB3 HB31 CB3 HB32 CB3 HB33 +BOND OG2 CM +BOND CM HM1 CM HM2 CM HM3 +DELETE IMPR CA OA2 OA1 CC1 +DELETE IMPR CG OG2 OG1 CC3 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 OG1 OG2 + +IC CC1 CA OA2 CT 1.5243 108.15 -178.31 121.38 1.4251 +IC CB1 CT OA2 CA 1.5313 105.10 179.75 121.38 1.3318 +IC CB2 CT OA2 CA 1.5354 111.03 62.52 121.38 1.3318 +IC CB3 CT OA2 CA 1.5351 111.02 -62.94 121.38 1.3318 +IC HB11 CB1 CT OA2 1.1105 110.10 -179.76 105.10 1.4251 +IC HB12 CB1 CT OA2 1.1099 110.43 60.50 105.10 1.4251 +IC HB13 CB1 CT OA2 1.1100 110.42 -60.01 105.10 1.4251 +IC HB21 CB2 CT OA2 1.1101 109.87 172.54 111.03 1.4251 +IC HB22 CB2 CT OA2 1.1093 110.56 52.80 111.03 1.4251 +IC HB23 CB2 CT OA2 1.1095 111.28 -68.22 111.03 1.4251 +IC HB31 CB3 CT OA2 1.1101 109.93 -172.01 111.02 1.4251 +IC HB32 CB3 CT OA2 1.1095 111.24 68.69 111.02 1.4251 +IC HB33 CB3 CT OA2 1.1095 110.50 -52.18 111.02 1.4251 +IC CC3 CG OG2 CM 1.5032 109.19 178.53 114.98 1.4389 +IC HM1 CM OG2 CG 1.1119 109.57 179.56 114.98 1.3378 +IC HM2 CM OG2 CG 1.1145 111.16 60.39 114.98 1.3378 +IC HM3 CM OG2 CG 1.1141 111.21 -61.08 114.98 1.3378 + +PRES ABGA 0.00 ! C9H8O2 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Alpha-Benzyl Glu Acid CDCA Amide +ATOM CC1 CG311 0.17 ! OA1 CD1--CE1 +ATOM HC1 HGA1 0.09 ! || // \\ +ATOM CA CG2O2 0.90 ! O24 CA--OA2--CB--CZ CP +ATOM OA1 OG2D1 -0.63 ! || | \ __ / +ATOM OA2 OG302 -0.49 ! OH Me21 C22 C24 CM1 CC3 CD2--CE2 +ATOM CB CG321 -0.22 ! | \ / \ / \ / \ / \ +ATOM HB1 HGA2 0.09 ! C12 Me18 C20 C23 NH CC2 CG--OG1(-0.5) +ATOM HB2 HGA2 0.09 ! / \ | / | +ATOM CZ CG2R61 0.00 ! C11 C13---C17 OG2(-0.5) +ATOM CD1 CG2R61 -0.115 ! Me19 | | | +ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 +ATOM CD2 CG2R61 -0.115 ! / \|/ \ / \ / +ATOM HD2 HGR61 0.115 ! C2 C10 C8 C15 +ATOM CE1 CG2R61 -0.115 ! | | | +ATOM HE1 HGR61 0.115 ! C3 C5 C7 +ATOM CE2 CG2R61 -0.115 ! / \ / \ / \ +ATOM HE2 HGR61 0.115 ! HO C4 C6 OH +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 ! Alpha-Benzyl Glutamic Acid CDCA Amide + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5276 110.26 -175.22 115.99 1.4474 +IC HB1 CB OA2 CA 1.1152 110.81 49.30 115.99 1.3364 +IC HB2 CB OA2 CA 1.1140 109.30 -69.99 115.99 1.3364 +IC CZ CB OA2 CA 1.5060 114.53 168.41 115.99 1.3364 +IC CD2 CZ CB OA2 1.4042 119.63 -39.76 114.53 1.4474 +IC CD1 CZ CB OA2 1.4055 120.89 141.67 114.53 1.4474 +IC CD1 CD2 *CZ CB 1.4055 119.47 -178.59 119.63 1.5060 +IC CD2 CZ CB HB1 1.4042 119.63 82.33 105.44 1.1152 +IC CD2 CZ CB HB2 1.4042 119.63 -161.94 108.22 1.1140 +IC CB CZ CD1 CE1 1.5060 120.89 178.93 120.21 1.4022 +IC CB CZ CD2 CE2 1.5060 119.63 -178.66 120.33 1.4001 +IC CZ CD1 CE1 CP 1.4055 120.21 -0.33 119.99 1.4018 +IC CD1 CE1 CP CE2 1.4022 119.99 0.00 119.98 1.4008 +IC CE1 CP CE2 CD2 1.4018 119.98 0.28 120.02 1.4001 +IC CE1 CZ *CD1 HD1 1.4022 120.21 179.92 119.72 1.0791 +IC CE2 CZ *CD2 HD2 1.4001 120.33 -179.34 119.97 1.0825 +IC CP CD1 *CE1 HE1 1.4018 119.99 -179.96 120.00 1.0797 +IC CP CD2 *CE2 HE2 1.4008 120.02 -179.26 119.27 1.0807 +IC CE1 CE2 *CP HP 1.4018 119.98 -179.91 119.82 1.0797 + +PRES GBGA 0.00 ! C9H9O2 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Gamma-Benzyl Glu Acid CDCA Amide +ATOM CC3 CG321 0.08 ! OA1(-0.5) +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2(-0.5) +ATOM CG CG2O2 0.90 ! || | +ATOM OG1 OG2D1 -0.63 ! OH Me21 C22 C24 CC1 CC3 CD1--CE1 +ATOM OG2 OG302 -0.49 ! | \ / \ / \ / \ / \ // \\ +ATOM CB CG321 -0.22 ! C12 Me18 C20 C23 NH CC2 CG--OG2--CB--CZ CP +ATOM HB1 HGA2 0.09 ! / \ | / || \ __ / +ATOM HB2 HGA2 0.09 ! C11 C13---C17 OG1 CD2--CE2 +ATOM CZ CG2R61 0.00 ! Me19 | | | +ATOM CD1 CG2R61 -0.115 ! C1 | C9 C14 C16 +ATOM HD1 HGR61 0.115 ! / \|/ \ / \ / +ATOM CD2 CG2R61 -0.115 ! C2 C10 C8 C15 +ATOM HD2 HGR61 0.115 ! | | | +ATOM CE1 CG2R61 -0.115 ! C3 C5 C7 +ATOM HE1 HGR61 0.115 ! / \ / \ / \ +ATOM CE2 CG2R61 -0.115 ! HO C4 C6 OH +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 ! Gamma-Benzyl Glutamic Acid CDCA Amide +ATOM HP HGR61 0.115 + +BOND OG2 CB +BOND CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CG OG2 OG1 CC3 +IMPR CG CC3 OG1 OG2 + +IC CC3 CG OG2 CB 1.5019 110.25 -178.87 116.50 1.4500 +IC HB1 CB OG2 CG 1.1166 111.80 -40.89 116.50 1.3367 +IC HB2 CB OG2 CG 1.1126 107.85 -156.53 116.50 1.3367 +IC CZ CB OG2 CG 1.5090 115.77 84.56 116.50 1.3367 +IC CD2 CZ CB OG2 1.4043 120.63 -105.67 115.77 1.4500 +IC CD1 CZ CB OG2 1.4036 119.72 73.22 115.77 1.4500 +IC CD1 CD2 *CZ CB 1.4036 119.63 178.88 120.63 1.5090 +IC CD2 CZ CB HB1 1.4043 120.63 21.27 108.88 1.1166 +IC CD2 CZ CB HB2 1.4043 120.63 134.60 106.33 1.1126 +IC CB CZ CD1 CE1 1.5090 119.72 -179.56 120.22 1.4014 +IC CB CZ CD2 CE2 1.5090 120.63 179.55 120.19 1.4015 +IC CZ CD1 CE1 CP 1.4036 120.22 0.20 119.95 1.4016 +IC CD1 CE1 CP CE2 1.4014 119.95 0.28 120.04 1.4017 +IC CE1 CP CE2 CD2 1.4016 120.04 -0.28 119.96 1.4015 +IC CE1 CZ *CD1 HD1 1.4014 120.22 179.19 119.50 1.0802 +IC CE2 CZ *CD2 HD2 1.4015 120.19 -178.97 119.56 1.0802 +IC CP CD1 *CE1 HE1 1.4016 119.95 179.43 119.88 1.0801 +IC CP CD2 *CE2 HE2 1.4017 119.96 -179.44 119.89 1.0800 +IC CE1 CE2 *CP HP 1.4016 120.04 -179.29 120.00 1.0800 + +PRES DBGA 0.00 ! C18H17O4 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Alpha,Gamma-Dibenzyl Glu Acid CDCA Amide + +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 ! OA1 CJ1--CK1 +ATOM CA CG2O2 0.90 ! || // \\ +ATOM OA1 OG2D1 -0.63 ! O24 CA--OA2--CH2(B)--CY CQ +ATOM OA2 OG302 -0.49 ! || | \ __ / +ATOM CB CG321 -0.22 ! OH Me21 C22 C24 CC1 CC3 CJ2--CK2 CD1--CE1 +ATOM HB1 HGA2 0.09 ! | \ / \ / \ / \ / \ // \\ +ATOM HB2 HGA2 0.09 ! C12 Me18 C20 C23 NH CC2 CG--OG2--CH2(N)--CZ CP +ATOM CY CG2R61 0.00 ! / \ | / || \ __ / +ATOM CJ1 CG2R61 -0.115 ! C11 C13---C17 OG1 CD2--CE2 +ATOM HJ1 HGR61 0.115 ! Me19 | | | +ATOM CJ2 CG2R61 -0.115 ! C1 | C9 C14 C16 +ATOM HJ2 HGR61 0.115 ! / \|/ \ / \ / +ATOM CK1 CG2R61 -0.115 ! C2 C10 C8 C15 +ATOM HK1 HGR61 0.115 ! | | | +ATOM CK2 CG2R61 -0.115 ! C3 C5 C7 +ATOM HK2 HGR61 0.115 ! / \ / \ / \ +ATOM CQ CG2R61 -0.115 ! HO C4 C6 OH +ATOM HQ HGR61 0.115 +ATOM CC3 CG321 0.08 ! Alpha,Gamma-Dibenzyl Glutamic Acid CDCA Amide +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 +ATOM CG CG2O2 0.90 +ATOM OG1 OG2D1 -0.63 +ATOM OG2 OG302 -0.49 +ATOM CN CG321 -0.22 +ATOM HN1 HGA2 0.09 +ATOM HN2 HGA2 0.09 +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND OG2 CN +BOND CN HN1 CN HN2 CN CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +DELETE IMPR CG OG2 OG1 CC3 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 OG1 OG2 + +IC CC1 CA OA2 CB 1.5206 108.90 105.00 116.86 1.4507 +IC HB1 CB OA2 CA 1.1132 108.27 147.25 116.86 1.3434 +IC HB2 CB OA2 CA 1.1177 112.85 31.14 116.86 1.3434 +IC CY CB OA2 CA 1.5069 114.70 -93.16 116.86 1.3434 +IC CJ2 CY CB OA2 1.4050 120.48 -91.04 114.70 1.4507 +IC CJ1 CY CB OA2 1.4039 119.88 87.42 114.70 1.4507 +IC CJ1 CJ2 *CY CB 1.4039 119.62 178.47 120.48 1.5069 +IC CJ2 CY CB HB1 1.4050 120.48 29.17 107.16 1.1132 +IC CJ2 CY CB HB2 1.4050 120.48 142.14 108.03 1.1177 +IC CB CY CJ1 CK1 1.5069 119.88 -178.91 120.21 1.4011 +IC CB CY CJ2 CK2 1.5069 120.48 178.97 120.16 1.4016 +IC CY CJ1 CK1 CQ 1.4039 120.21 0.12 119.97 1.4012 +IC CJ1 CK1 CQ CK2 1.4011 119.97 0.13 120.06 1.4013 +IC CK1 CQ CK2 CJ2 1.4012 120.06 -0.07 119.97 1.4016 +IC CK1 CY *CJ1 HJ1 1.4011 120.21 179.67 119.77 1.0809 +IC CK2 CY *CJ2 HJ2 1.4016 120.16 179.94 119.94 1.0795 +IC CQ CJ1 *CK1 HK1 1.4012 119.97 179.94 119.95 1.0807 +IC CQ CJ2 *CK2 HK2 1.4013 119.97 179.97 120.09 1.0805 +IC CK1 CK2 *CQ HQ 1.4012 120.06 -179.96 120.02 1.0806 +IC CC3 CG OG2 CN 1.5035 108.85 -165.00 116.75 1.4498 +IC HN1 CN OG2 CG 1.1127 108.18 -45.00 116.75 1.3348 +IC HN2 CN OG2 CG 1.1172 112.24 75.00 116.75 1.3348 +IC CZ CN OG2 CG 1.5070 115.12 -165.00 116.75 1.3348 +IC CD2 CZ CN OG2 1.4041 120.43 180.00 115.12 1.4498 +IC CD1 CZ CN OG2 1.4041 119.89 0.00 115.12 1.4498 +IC CD1 CD2 *CZ CN 1.4041 119.66 178.41 120.43 1.5070 +IC CD2 CZ CN HB1 1.4041 120.43 -88.94 130.32 7.6318 +IC CD2 CZ CN HB2 1.4041 120.43 -83.96 118.87 8.2110 +IC CN CZ CD1 CE1 1.5070 119.89 -179.11 120.18 1.4013 +IC CN CZ CD2 CE2 1.5070 120.43 179.10 120.17 1.4013 +IC CZ CD1 CE1 CP 1.4041 120.18 0.23 119.96 1.4014 +IC CD1 CE1 CP CE2 1.4013 119.96 0.23 120.06 1.4014 +IC CE1 CP CE2 CD2 1.4014 120.06 -0.23 119.97 1.4013 +IC CE1 CZ *CD1 HD1 1.4013 120.18 179.46 119.82 1.0792 +IC CE2 CZ *CD2 HD2 1.4013 120.17 -179.25 119.77 1.0805 +IC CP CD1 *CE1 HE1 1.4014 119.96 179.64 120.04 1.0805 +IC CP CD2 *CE2 HE2 1.4014 119.97 -179.65 119.97 1.0805 +IC CE1 CE2 *CP HP 1.4014 120.06 -179.54 119.96 1.0805 + +PRES AL 1.00 ! C3H9N cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Alpha Lysine CDCA Amide + + ! OA1(-0.5) + ! | + ! O24 CA--OA2(-0.5) +DELETE ATOM CG ! || | +DELETE ATOM OG1 ! OH Me21 C22 C24 CC1 CC3 CC5 +DELETE ATOM OG2 ! | \ / \ / \ / \ / \ / \ +ATOM CC3 CG321 -0.18 ! C12 Me18 C20 C23 NH CC2 CC4 NH3(+1) +ATOM HC3A HGA2 0.09 ! / \ | / +ATOM HC3B HGA2 0.09 ! C11 C13---C17 +ATOM CC4 CG321 -0.18 ! Me19 | | | +ATOM HC4A HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HC4B HGA2 0.09 ! / \|/ \ / \ / +ATOM CC5 CG324 0.13 ! C2 C10 C8 C15 +ATOM HC5A HGA2 0.09 ! | | | +ATOM HC5B HGA2 0.09 ! C3 C5 C7 +ATOM NL NG3P3 -0.30 ! / \ / \ / \ +ATOM HL1 HGP2 0.33 ! HO C4 C6 OH +ATOM HL2 HGP2 0.33 +ATOM HL3 HGP2 0.33 ! Alpha Lysine CDCA Amide + +BOND CC3 CC4 CC4 HC4A CC4 HC4B +BOND CC4 CC5 CC5 HC5A CC5 HC5B +BOND CC5 NL NL HL1 NL HL2 NL HL3 + +IC CC1 CC2 CC3 CC4 1.5561 114.54 179.98 116.18 1.5479 +IC CC2 CC3 CC4 CC5 1.5463 116.18 -57.56 115.63 1.5430 +IC CC5 CC3 *CC4 HC4A 1.5430 115.63 -123.18 108.29 1.1129 +IC HC4A CC3 *CC4 HC4B 1.1129 108.29 -115.77 107.94 1.1143 +IC CC3 CC4 CC5 NL 1.5479 115.63 -52.00 111.91 1.4822 +IC NL CC4 *CC5 HC5A 1.4822 111.91 119.56 110.77 1.1051 +IC NL CC4 *CC5 HC5B 1.4822 111.91 -121.02 110.60 1.1019 +IC HL1 NL CC5 CC4 1.0369 112.46 -11.49 111.91 1.5430 +IC HL2 NL CC5 CC4 1.0708 105.60 100.09 111.91 1.5430 +IC HL3 NL CC5 CC4 1.0308 115.27 -141.75 111.91 1.5430 + +PRES ALME 1.00 ! C6H13NO2 cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) >> Alpha Lysine Methyl Ester CDCA Amide + +DELETE ATOM CG +DELETE ATOM OG1 +DELETE ATOM OG2 +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 ! OA1 +ATOM CA CG2O2 0.90 ! || +ATOM OA1 OG2D1 -0.63 ! O24 CA--OA2--CH3(M) +ATOM OA2 OG302 -0.49 ! || | +ATOM CM CG331 -0.31 ! OH Me21 C22 C24 CC1 CC3 CC5 +ATOM HM1 HGA3 0.09 ! | \ / \ / \ / \ / \ / \ +ATOM HM2 HGA3 0.09 ! C12 Me18 C20 C23 NH CC2 CC4 NH3(+1) +ATOM HM3 HGA3 0.09 ! / \ | / +ATOM CC3 CG321 -0.18 ! C11 C13---C17 +ATOM HC3A HGA2 0.09 ! Me19 | | | +ATOM HC3B HGA2 0.09 ! C1 | C9 C14 C16 +ATOM CC4 CG321 -0.18 ! / \|/ \ / \ / +ATOM HC4A HGA2 0.09 ! C2 C10 C8 C15 +ATOM HC4B HGA2 0.09 ! | | | +ATOM CC5 CG324 0.13 ! C3 C5 C7 +ATOM HC5A HGA2 0.09 ! / \ / \ / \ +ATOM HC5B HGA2 0.09 ! HO C4 C6 OH +ATOM NL NG3P3 -0.30 +ATOM HL1 HGP2 0.33 ! Alpha Lysine Methyl Ester CDCA Amide +ATOM HL2 HGP2 0.33 +ATOM HL3 HGP2 0.33 + +BOND OA2 CM CM HM1 CM HM2 CM HM3 +BOND CC3 CC4 CC4 HC4A CC4 HC4B +BOND CC4 CC5 CC5 HC5A CC5 HC5B +BOND CC5 NL NL HL1 NL HL2 NL HL3 +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CM 1.5257 109.81 -179.93 115.57 1.4395 +IC HM1 CM OA2 CA 1.1130 109.51 -178.65 115.57 1.3318 +IC HM2 CM OA2 CA 1.1137 111.53 62.15 115.57 1.3318 +IC HM3 CM OA2 CA 1.1147 111.32 -60.00 115.57 1.3318 +IC CC1 CC2 CC3 CC4 1.5577 114.43 -162.39 114.31 1.5433 +IC CC2 CC3 CC4 CC5 1.5429 114.31 -58.57 113.71 1.5434 +IC CC5 CC3 *CC4 HC4A 1.5434 113.71 -122.33 108.53 1.1138 +IC HC4A CC3 *CC4 HC4B 1.1138 108.53 -116.24 108.97 1.1147 +IC CC3 CC4 CC5 NL 1.5433 113.71 -46.10 111.29 1.4903 +IC NL CC4 *CC5 HC5A 1.4903 111.29 119.98 110.79 1.1033 +IC NL CC4 *CC5 HC5B 1.4903 111.29 -120.90 110.69 1.1030 +IC HL1 NL CC5 CC4 1.0382 110.29 -57.73 111.29 1.5434 +IC HL2 NL CC5 CC4 1.0532 109.68 61.17 111.29 1.5434 +IC HL3 NL CC5 CC4 1.0388 111.18 -179.42 111.29 1.5434 + + +!end bile acids, chayan, dec2006 + +!Bile acids and related compounds, chayan, may2007 +RESI BAB1 -1.00 ! C29H47N2O6 Bile Acid Basic moiety 1 (BASE FOR NEW COMPOUNDS), cacha +GROUP +ATOM C3 CG311 0.14 ! OG +ATOM O3 OG311 -0.65 ! || +ATOM H3' HGP1 0.42 ! CG--NT--HT2 +ATOM H3 HGA1 0.09 ! / HT1 +GROUP ! CC3 +ATOM C4 CG321 -0.18 ! \ +ATOM H4A HGA2 0.09 ! O24 CC2 +ATOM H4B HGA2 0.09 ! || / +GROUP ! H Me21 C22 C24 CC1 +ATOM C5 CG311 -0.09 ! | \ / \ / \ / \ +ATOM H5 HGA1 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) +GROUP ! / \ | / | +ATOM C6 CG321 -0.18 ! C11 C13---C17 OA2 (-0.5) +ATOM H6A HGA2 0.09 ! Me19 | | | +ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C7 CG311 0.14 ! C2 C10 C8 C15 +ATOM O7 OG311 -0.65 ! | | | +ATOM H7' HGP1 0.42 ! C3 C5 C7 +ATOM H7 HGA1 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM C8 CG311 -0.09 +ATOM H8 HGA1 0.09 ! BAB1 +GROUP +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM C24 CG2O1 0.51 +ATOM O24 OG2D1 -0.51 +ATOM N NG2S1 -0.47 +ATOM HN HGP1 0.47 +GROUP +ATOM CC1 CG311 -0.19 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O3 0.62 +ATOM OA1 OG2D2 -0.76 +ATOM OA2 OG2D2 -0.76 +GROUP +ATOM CC2 CG321 -0.18 +ATOM HC2A HGA2 0.09 +ATOM HC2B HGA2 0.09 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 +GROUP +ATOM CG CG2O1 0.55 +ATOM OG OG2D1 -0.55 +ATOM NT NG2S2 -0.62 +ATOM HT1 HGP1 0.32 +ATOM HT2 HGP1 0.30 + +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7 C7 O7 O7 H7' +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 C24 C24 O24 +BOND C24 N N HN +BOND N CC1 CC1 HC1 CC1 CC2 CC1 CA CA OA1 CA OA2 +BOND CC2 HC2A CC2 HC2B CC2 CC3 +BOND CC3 HC3A CC3 HC3B CC3 CG +BOND CG OG CG NT NT HT1 NT HT2 +IMPR C24 C23 N O24 +IMPR CA OA2 OA1 CC1 +IMPR CG CC3 NT OG + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +!ICs based on arbitrary CHARMM optimized structure +IC C1 C2 C3 C4 1.5325 111.68 -49.45 111.84 1.5383 +IC C2 C3 C4 C5 1.5339 111.84 43.93 115.68 1.5598 +IC C3 C4 C5 C6 1.5383 115.68 -175.10 109.02 1.5521 +IC C4 C5 C6 C7 1.5598 109.02 85.47 114.98 1.5441 +IC C5 C6 C7 C8 1.5521 114.98 39.04 113.05 1.5290 +IC C7 C8 C9 C10 1.5290 114.08 58.26 109.48 1.5439 +IC C8 C9 C10 C1 1.5323 109.48 179.67 111.99 1.5563 +IC C9 C10 C1 C2 1.5439 111.99 63.33 113.83 1.5325 +IC O3 C3 C4 C5 1.4163 109.09 162.18 115.68 1.5598 +IC C4 C2 *C3 O3 1.5383 111.84 -119.44 107.07 1.4163 +IC C4 C2 *C3 H3 1.5383 111.84 121.33 109.38 1.1144 +IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 +IC C2 C3 O3 H3' 1.5339 107.07 70.05 104.87 0.9608 +IC C5 C3 *C4 H4A 1.5598 115.68 122.75 108.69 1.1111 +IC H4A C3 *C4 H4B 1.1111 108.69 115.73 108.82 1.1113 +IC C10 C4 *C5 H5 1.5279 114.70 116.72 105.03 1.1175 +IC C7 C5 *C6 H6A 1.5441 114.98 -124.16 109.39 1.1113 +IC H6A C5 *C6 H6B 1.1113 109.39 -115.80 108.33 1.1112 +IC C2 C10 *C1 H1A 1.5325 113.83 119.39 107.74 1.1137 +IC C2 C10 *C1 H1B 1.5325 113.83 -124.36 110.18 1.1091 +IC C1 C3 *C2 H2A 1.5325 111.68 122.11 110.21 1.1113 +IC H2A C3 *C2 H2B 1.1113 110.21 117.20 108.66 1.1128 +IC C6 C7 C8 C14 1.5441 113.05 -166.95 108.56 1.5542 +IC C14 C7 *C8 C9 1.5542 108.56 119.93 114.08 1.5323 +IC C7 C8 C14 C13 1.5290 108.56 -174.20 113.13 1.5425 +IC C13 C8 *C14 C15 1.5425 113.13 118.56 116.30 1.5285 +IC C8 C14 C15 C16 1.5542 116.30 -154.74 103.56 1.5435 +IC C14 C15 C16 C17 1.5285 103.56 -2.52 106.91 1.5533 +IC C17 C14 *C13 C12 1.5731 98.18 119.81 107.46 1.5340 +IC C14 C13 C12 C11 1.5425 107.46 55.26 111.18 1.5432 +IC C8 C6 *C7 O7 1.5290 113.05 -126.94 107.98 1.4218 +IC O7 C6 *C7 H7 1.4218 107.98 -113.62 107.19 1.1164 +IC C6 C7 O7 H7' 1.5441 107.98 177.77 105.26 0.9614 +IC C9 C7 *C8 H8 1.5323 114.08 122.47 107.18 1.1067 +IC C10 C8 *C9 H9 1.5439 109.48 -117.10 106.56 1.1138 +IC C9 C12 *C11 H11A 1.5547 114.18 122.66 108.77 1.1090 +IC H11A C12 *C11 H11B 1.1090 108.77 115.79 107.30 1.1111 +IC C14 C13 C12 H12A 1.5425 107.46 175.99 111.88 1.1059 +IC H12A C13 *C12 H12B 1.1059 111.88 119.47 108.82 1.1125 +IC C13 C8 *C14 H14 1.5425 113.13 -118.30 108.46 1.1150 +IC C16 C14 *C15 H15A 1.5435 103.56 119.15 111.17 1.1002 +IC H15A C14 *C15 H15B 1.1002 111.17 119.82 112.08 1.0988 +IC C17 C15 *C16 H16A 1.5533 106.91 121.49 110.78 1.0992 +IC H16A C15 *C16 H16B 1.0992 110.78 117.20 110.97 1.0999 +IC C13 C16 *C17 H17 1.5731 98.41 -112.89 110.39 1.1009 +IC C12 C14 *C13 C18 1.5340 107.46 121.97 114.21 1.5526 +IC C14 C13 C18 H18A 1.5425 114.21 116.84 111.38 1.1064 +IC H18A C13 *C18 H18B 1.1064 111.38 119.04 110.59 1.1085 +IC H18A C13 *C18 H18C 1.1064 111.38 -120.17 111.91 1.1058 +IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 +IC C5 C10 C19 H19A 1.5279 109.53 5.08 111.17 1.1079 +IC H19A C10 *C19 H19B 1.1079 111.17 121.06 112.01 1.1061 +IC H19A C10 *C19 H19C 1.1079 111.17 -119.50 110.64 1.1093 +IC C13 C16 *C17 C20 1.5731 98.41 127.01 111.83 1.5649 +IC C16 C17 C20 C22 1.5533 111.83 71.96 108.75 1.5519 +IC C22 C17 *C20 C21 1.5519 108.75 122.38 112.90 1.5396 +IC C21 C17 *C20 H20 1.5396 112.90 120.78 108.89 1.1119 +IC C17 C20 C21 H21A 1.5649 112.90 71.88 110.45 1.1079 +IC H21A C20 *C21 H21B 1.1079 110.45 -121.55 110.43 1.1103 +IC H21A C20 *C21 H21C 1.1079 110.45 118.45 110.89 1.1089 +IC C17 C20 C22 C23 1.5649 108.75 -163.10 113.67 1.5524 +IC C23 C20 *C22 H22A 1.5524 113.67 119.92 108.15 1.1127 +IC H22A C20 *C22 H22B 1.1127 108.15 116.44 108.31 1.1133 +IC C20 C22 C23 C24 1.5519 113.67 176.63 114.01 1.5029 +IC C24 C22 *C23 H23A 1.5029 114.01 120.77 110.50 1.1097 +IC H23A C22 *C23 H23B 1.1097 110.50 118.82 109.42 1.1112 +IC C22 C23 C24 N 1.5524 114.01 0.05 116.58 1.3364 +IC N C23 *C24 O24 1.3364 116.58 -179.90 119.94 1.2265 +IC C23 C24 N CC1 1.5029 116.58 178.79 130.40 1.4446 +IC CC1 C24 *N HN 1.4446 130.40 -174.70 123.77 1.0138 +IC C24 N CC1 CA 1.3364 130.40 -170.40 102.83 1.5482 +IC CA N *CC1 HC1 1.5482 102.83 114.75 109.50 1.1102 +IC HC1 N *CC1 CC2 1.1102 109.50 123.68 113.47 1.5536 +IC N CC1 CA OA1 1.4446 102.83 178.79 119.90 1.2534 +IC OA1 CC1 *CA OA2 1.2534 119.90 177.56 115.53 1.2691 +IC N CC1 CC2 CC3 1.4446 113.47 60.10 115.05 1.5552 +IC CC3 CC1 *CC2 HC2A 1.5552 115.05 126.07 109.17 1.1118 +IC HC2A CC1 *CC2 HC2B 1.1118 109.17 114.51 106.60 1.1142 +IC CC1 CC2 CC3 CG 1.5536 115.05 107.73 115.32 1.5034 +IC CG CC2 *CC3 HC3A 1.5034 115.32 119.05 108.25 1.1125 +IC HC3A CC2 *CC3 HC3B 1.1125 108.25 117.32 110.47 1.1095 +IC CC2 CC3 CG NT 1.5552 115.32 -46.42 118.71 1.3503 +IC NT CC3 *CG OG 1.3503 118.71 -179.05 119.96 1.2327 +IC CC3 CG NT HT2 1.5034 118.71 -177.78 118.60 0.9905 +IC HT2 CG *NT HT1 0.9905 118.60 177.52 119.35 1.0169 + +PRES G4MP 1.00 ! C7H14N2O (01OH03), cacha +! This compund has 4-methylamine piperidine at gamma-position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 ! OG CG2--CG3 HG41 +ATOM OG OG2D1 -0.51 ! || / \ / +ATOM NT NG2S1 -0.47 ! CG---NT--CGT--CG1 NG4 (+) +ATOM HT1 HGP1 0.47 ! / HT1 \ / \ +GROUP ! CC3 CG6--CG5 HG42 +ATOM CGT CG321 -0.18 ! \ +ATOM HGT1 HGA2 0.09 ! O24 CC2 +ATOM HGT2 HGA2 0.09 ! || / +GROUP ! H Me21 C22 C24 CC1 +ATOM CG1 CG311 -0.09 ! | \ / \ / \ / \ +ATOM HG1 HGA1 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) +GROUP ! / \ | / | +ATOM CG2 CG321 -0.18 ! C11 C13---C17 OA2 (-0.5) +ATOM HG21 HGA2 0.09 ! Me19 | | | +ATOM HG22 HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CG3 CG324 0.20 ! C2 C10 C8 C15 +ATOM HG31 HGA2 0.09 ! | | | +ATOM HG32 HGA2 0.09 ! C3 C5 C7 +ATOM NG4 NG3P2 -0.40 ! / \ / \ / \ +ATOM HG41 HGP2 0.32 ! HO C4 C6 OH +ATOM HG42 HGP2 0.32 +ATOM CG5 CG324 0.20 ! G4MP (01OH03) +ATOM HG51 HGA2 0.09 +ATOM HG52 HGA2 0.09 +GROUP +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 NG4 +BOND NG4 HG41 NG4 HG42 NG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 + +IC OG CG NT CGT 1.2271 121.41 13.20 121.99 1.4538 +IC CG NT CGT HGT1 1.3456 121.99 88.64 107.55 1.1142 +IC HGT1 NT *CGT HGT2 1.1142 107.55 -116.19 111.07 1.1174 +IC HGT1 NT *CGT CG1 1.1142 107.55 121.44 115.04 1.5450 +IC NT CGT CG1 HG1 1.4538 115.04 77.21 107.27 1.1164 +IC HG1 CGT *CG1 CG2 1.1164 107.27 -117.50 111.92 1.5436 +IC HG1 CGT *CG1 CG6 1.1164 107.27 118.24 109.86 1.5466 +IC CGT CG1 CG2 CG3 1.5450 111.92 -173.65 113.31 1.5201 +IC CG3 CG1 *CG2 HG21 1.5201 113.31 123.02 108.94 1.1140 +IC CG3 CG1 *CG2 HG22 1.5201 113.31 -119.66 109.16 1.1145 +IC CG1 CG2 CG3 NG4 1.5436 113.31 55.01 108.23 1.5017 +IC NG4 CG2 *CG3 HG31 1.5017 108.23 116.95 112.61 1.1038 +IC NG4 CG2 *CG3 HG32 1.5017 108.23 -117.23 113.22 1.1028 +IC CG2 CG3 NG4 CG5 1.5201 108.23 -61.48 112.36 1.5048 +IC CG5 CG3 *NG4 HG41 1.5048 112.36 118.67 107.00 1.0106 +IC CG5 CG3 *NG4 HG42 1.5048 112.36 -125.21 110.67 1.0050 +IC CG3 NG4 CG5 CG6 1.5017 112.36 62.10 109.26 1.5264 +IC CG6 NG4 *CG5 HG51 1.5264 109.26 121.78 105.74 1.1029 +IC CG6 NG4 *CG5 HG52 1.5264 109.26 -121.65 105.59 1.1034 +IC CG5 CG1 *CG6 HG61 1.5264 111.91 -121.76 108.69 1.1133 +IC CG5 CG1 *CG6 HG62 1.5264 111.91 121.65 108.91 1.1129 + + +PRES G4MPAB 1.00 ! C16H22N2O3 (010203D), cacha +! This compound has 4-methylamine piperidine at gamma position +! and benzyl at alpha position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 ! OG CG2--CG3 HG41 +ATOM NT NG2S1 -0.47 ! || / \ / +ATOM HT1 HGP1 0.47 ! CG---NT--CGT--CG1 NG4 (+) +GROUP ! / HT1 \ / \ +ATOM CGT CG321 -0.18 ! CC3 CG6--CG5 HG42 +ATOM HGT1 HGA2 0.09 ! \ +ATOM HGT2 HGA2 0.09 ! O24 CC2 +GROUP ! || / +ATOM CG1 CG311 -0.09 ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM HG1 HGA1 0.09 ! | \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CA--OA2--CB--CZ CP +ATOM CG2 CG321 -0.18 ! / \ | / || \ __ / +ATOM HG21 HGA2 0.09 ! C11 C13---C17 OA1 CD2--CE2 +ATOM HG22 HGA2 0.09 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CG3 CG324 0.20 ! / \|/ \ / \ / +ATOM HG31 HGA2 0.09 ! C2 C10 C8 C15 +ATOM HG32 HGA2 0.09 ! | | | +ATOM NG4 NG3P2 -0.40 ! C3 C5 C7 +ATOM HG41 HGP2 0.32 ! / \ / \ / \ +ATOM HG42 HGP2 0.32 ! HO C4 C6 OH +ATOM CG5 CG324 0.20 +ATOM HG51 HGA2 0.09 ! G4MPAB (010203D) +ATOM HG52 HGA2 0.09 +GROUP +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 NG4 +BOND NG4 HG41 NG4 HG42 NG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +BOND OA2 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5235 109.54 -176.41 116.53 1.4472 +IC CA OA2 CB HB1 1.3360 116.53 -64.48 110.30 1.1156 +IC CA OA2 CB CZ 1.3360 116.53 176.13 113.68 1.5063 +IC CA OA2 CB HB2 1.3360 116.53 54.52 110.72 1.1160 +IC OA2 CB CZ CD2 1.4472 113.68 -117.39 121.22 1.4060 +IC OA2 CB CZ CD1 1.4472 113.68 62.45 119.30 1.4048 +IC CD1 CD2 *CZ CB 1.4048 119.48 179.84 121.22 1.5063 +IC CD2 CZ CB HB1 1.4060 121.22 121.02 106.39 1.1156 +IC CD2 CZ CB HB2 1.4060 121.22 5.79 107.87 1.1160 +IC CB CZ CD1 CE1 1.5063 119.30 179.52 120.29 1.4015 +IC CB CZ CD2 CE2 1.5063 121.22 -179.50 120.19 1.4018 +IC CZ CD1 CE1 CP 1.4048 120.29 0.00 119.94 1.4007 +IC CD1 CE1 CP CE2 1.4015 119.94 0.62 120.09 1.4005 +IC CE1 CP CE2 CD2 1.4007 120.09 -0.61 120.00 1.4018 +IC CE1 CZ *CD1 HD1 1.4015 120.29 -179.48 119.81 1.0800 +IC CE2 CZ *CD2 HD2 1.4018 120.19 179.40 120.20 1.0796 +IC CP CD1 *CE1 HE1 1.4007 119.94 -179.57 120.13 1.0809 +IC CP CD2 *CE2 HE2 1.4005 120.00 179.35 120.25 1.0815 +IC CE1 CE2 *CP HP 1.4007 120.09 -179.52 119.77 1.0816 +IC OG CG NT CGT 1.2237 121.80 2.70 123.40 1.4463 +IC CG NT CGT HGT1 1.3437 123.40 165.76 109.15 1.1140 +IC HGT1 NT *CGT HGT2 1.1140 109.15 -116.48 109.48 1.1169 +IC HGT1 NT *CGT CG1 1.1140 109.15 121.76 113.44 1.5425 +IC NT CGT CG1 HG1 1.4463 113.44 57.56 106.98 1.1180 +IC HG1 CGT *CG1 CG2 1.1180 106.98 -118.28 112.49 1.5449 +IC HG1 CGT *CG1 CG6 1.1180 106.98 116.87 111.08 1.5446 +IC CGT CG1 CG2 CG3 1.5425 112.49 179.28 110.63 1.5296 +IC CG3 CG1 *CG2 HG21 1.5296 110.63 122.32 109.32 1.1119 +IC CG3 CG1 *CG2 HG22 1.5296 110.63 -120.00 109.52 1.1129 +IC CG1 CG2 CG3 NG4 1.5449 110.63 55.35 110.03 1.5090 +IC NG4 CG2 *CG3 HG31 1.5090 110.03 117.95 113.07 1.1028 +IC NG4 CG2 *CG3 HG32 1.5090 110.03 -117.03 112.44 1.1041 +IC CG2 CG3 NG4 CG5 1.5296 110.03 -57.44 113.44 1.5087 +IC CG5 CG3 *NG4 HG41 1.5087 113.44 120.02 108.22 1.0087 +IC CG5 CG3 *NG4 HG42 1.5087 113.44 -123.98 110.17 1.0071 +IC CG3 NG4 CG5 CG6 1.5090 113.44 57.59 109.66 1.5282 +IC CG6 NG4 *CG5 HG51 1.5282 109.66 122.28 105.76 1.1029 +IC CG6 NG4 *CG5 HG52 1.5282 109.66 -121.41 105.40 1.1040 +IC CG5 CG1 *CG6 HG61 1.5282 110.78 -122.43 109.37 1.1120 +IC CG5 CG1 *CG6 HG62 1.5282 110.78 120.30 108.99 1.1138 + +PRES G4P 1.00 ! C6H12N2O (01OH02), cacha +! This compound has 4-amine piperidine at gamma position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 ! OG CG2--CG3 HG41 +ATOM OG OG2D1 -0.51 ! || / \ / +ATOM NT NG2S1 -0.47 ! CG--NT--CG1 NG4 +ATOM HT1 HGP1 0.47 ! / HT1 \ / \ +GROUP ! CC3 CG6--CG5 HG42 +ATOM CG1 CG311 -0.09 ! \ +ATOM HG1 HGA1 0.09 ! O24 CC2 +GROUP ! || / +ATOM CG2 CG321 -0.18 ! H Me21 C22 C24 CC1 +ATOM HG21 HGA2 0.09 ! | \ / \ / \ / \ +ATOM HG22 HGA2 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) +GROUP ! / \ | / | +ATOM CG3 CG324 0.20 ! C11 C13---C17 OA2 (-0.5) +ATOM HG31 HGA2 0.09 ! Me19 | | | +ATOM HG32 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM NG4 NG3P2 -0.40 ! / \|/ \ / \ / +ATOM HG41 HGP2 0.32 ! C2 C10 C8 C15 +ATOM HG42 HGP2 0.32 ! | | | +ATOM CG5 CG324 0.20 ! C3 C5 C7 +ATOM HG51 HGA2 0.09 ! / \ / \ / \ +ATOM HG52 HGA2 0.09 ! HO C4 C6 OH +GROUP +ATOM CG6 CG321 -0.18 ! G4P (01OH02) +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 + +BOND NT CG1 CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 NG4 +BOND NG4 HG41 NG4 HG42 NG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 + +IC OG CG NT CG1 1.2252 121.32 5.10 125.38 1.4376 +IC CG NT CG1 HG1 1.3388 125.38 -51.92 107.87 1.1178 +IC HG1 NT *CG1 CG2 1.1178 107.87 -118.28 109.63 1.5451 +IC HG1 NT *CG1 CG6 1.1178 107.87 120.36 111.16 1.5418 +IC NT CG1 CG2 CG3 1.4376 109.63 -92.37 112.88 1.5415 +IC CG3 CG1 *CG2 HG21 1.5415 112.88 121.50 108.63 1.1130 +IC CG3 CG1 *CG2 HG22 1.5415 112.88 -121.67 109.79 1.1112 +IC CG1 CG2 CG3 NG4 1.5451 112.88 27.90 112.58 1.5035 +IC NG4 CG2 *CG3 HG31 1.5035 112.58 118.55 112.20 1.1031 +IC NG4 CG2 *CG3 HG32 1.5035 112.58 -117.34 112.10 1.1033 +IC CG2 CG3 NG4 CG5 1.5415 112.58 -56.71 115.17 1.5102 +IC CG5 CG3 *NG4 HG41 1.5102 115.17 117.55 107.51 1.0298 +IC CG5 CG3 *NG4 HG42 1.5102 115.17 -129.75 113.29 1.0008 +IC CG3 NG4 CG5 CG6 1.5035 115.17 21.27 111.60 1.5345 +IC CG6 NG4 *CG5 HG51 1.5345 111.60 121.58 104.25 1.1051 +IC CG6 NG4 *CG5 HG52 1.5345 111.60 -123.20 105.77 1.1005 +IC CG5 CG1 *CG6 HG61 1.5345 110.88 -120.54 109.69 1.1126 +IC CG5 CG1 *CG6 HG62 1.5345 110.88 122.25 109.27 1.1110 + +PRES G4PAB 1.00 ! C15H20N2O3 (010202D), cacha +! This compound has 4-amine piperidine at gamma position +! and benzyl at alpha position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 ! OG CG2--CG3 HG41 +ATOM NT NG2S1 -0.47 ! || / \ / +ATOM HT1 HGP1 0.47 ! CG--NT--CG1 NG4 (+) +GROUP ! / HT1 \ / \ +ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 HG42 +ATOM HG1 HGA1 0.09 ! \ +GROUP ! O24 CC2 +ATOM CG2 CG321 -0.18 ! || / +ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CA--OA2--CB--CZ CP +ATOM CG3 CG324 0.20 ! / \ | / || \ __ / +ATOM HG31 HGA2 0.09 ! C11 C13---C17 OA1 CD2--CE2 +ATOM HG32 HGA2 0.09 ! Me19 | | | +ATOM NG4 NG3P2 -0.40 ! C1 | C9 C14 C16 +ATOM HG41 HGP2 0.32 ! / \|/ \ / \ / +ATOM HG42 HGP2 0.32 ! C2 C10 C8 C15 +ATOM CG5 CG324 0.20 ! | | | +ATOM HG51 HGA2 0.09 ! C3 C5 C7 +ATOM HG52 HGA2 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 ! G4PAB (010202D) +ATOM HG62 HGA2 0.09 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CG1 CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 NG4 +BOND NG4 HG41 NG4 HG42 NG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +BOND OA2 CB +BOND CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5231 109.59 -176.73 116.72 1.4465 +IC HB1 CB OA2 CA 1.1156 110.71 55.90 116.72 1.3350 +IC HB2 CB OA2 CA 1.1156 110.36 -63.25 116.72 1.3350 +IC CZ CB OA2 CA 1.5059 113.59 177.35 116.72 1.3350 +IC CD2 CZ CB OA2 1.4060 121.17 -112.96 113.59 1.4465 +IC CD1 CZ CB OA2 1.4048 119.33 66.62 113.59 1.4465 +IC CD1 CD2 *CZ CB 1.4048 119.49 179.58 121.17 1.5059 +IC CD2 CZ CB HB1 1.4060 121.17 10.10 107.80 1.1156 +IC CD2 CZ CB HB2 1.4060 121.17 125.42 106.41 1.1156 +IC CB CZ CD1 CE1 1.5059 119.33 179.62 120.28 1.4015 +IC CB CZ CD2 CE2 1.5059 121.17 -179.61 120.18 1.4018 +IC CZ CD1 CE1 CP 1.4048 120.28 0.06 119.94 1.4006 +IC CD1 CE1 CP CE2 1.4015 119.94 0.67 120.09 1.4005 +IC CE1 CP CE2 CD2 1.4006 120.09 -0.65 120.00 1.4018 +IC CE1 CZ *CD1 HD1 1.4015 120.28 -179.55 119.88 1.0800 +IC CE2 CZ *CD2 HD2 1.4018 120.18 179.50 120.27 1.0795 +IC CP CD1 *CE1 HE1 1.4006 119.94 -179.64 120.14 1.0810 +IC CP CD2 *CE2 HE2 1.4005 120.00 179.44 120.29 1.0816 +IC CE1 CE2 *CP HP 1.4006 120.09 -179.41 119.77 1.0817 +IC OG CG NT CG1 1.2229 121.22 -0.98 123.49 1.4328 +IC CG NT CG1 HG1 1.3417 123.49 42.04 108.39 1.1209 +IC HG1 NT *CG1 CG2 1.1209 108.39 -119.14 110.90 1.5409 +IC HG1 NT *CG1 CG6 1.1209 108.39 118.05 110.60 1.5391 +IC NT CG1 CG2 CG3 1.4328 110.90 179.86 110.81 1.5271 +IC CG3 CG1 *CG2 HG21 1.5271 110.81 122.78 109.51 1.1117 +IC CG3 CG1 *CG2 HG22 1.5271 110.81 -120.05 109.07 1.1144 +IC CG1 CG2 CG3 NG4 1.5409 110.81 56.29 109.54 1.5089 +IC NG4 CG2 *CG3 HG31 1.5089 109.54 117.78 113.14 1.1028 +IC NG4 CG2 *CG3 HG32 1.5089 109.54 -116.99 112.54 1.1039 +IC CG2 CG3 NG4 CG5 1.5271 109.54 -57.03 113.50 1.5096 +IC CG5 CG3 *NG4 HG41 1.5096 113.50 120.09 108.06 1.0087 +IC CG5 CG3 *NG4 HG42 1.5096 113.50 -124.10 110.07 1.0071 +IC CG3 NG4 CG5 CG6 1.5089 113.50 56.82 110.03 1.5304 +IC CG6 NG4 *CG5 HG51 1.5304 110.03 122.41 105.69 1.1028 +IC CG6 NG4 *CG5 HG52 1.5304 110.03 -121.42 105.25 1.1040 +IC CG5 CG1 *CG6 HG61 1.5304 110.58 -122.01 109.49 1.1127 +IC CG5 CG1 *CG6 HG62 1.5304 110.58 120.54 109.24 1.1133 + +PRES G3PR 1.00 ! C6H12N2O (01OH04(R)), cacha ! Check IC table +! This compound has 3-amine piperidine at gamma position +! core residue Bile Acid Basic moiety 1 (BAB1) +! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 ! HG31 +ATOM OG OG2D1 -0.51 ! | +ATOM NT NG2S1 -0.47 ! OG CG2--NG3(+1)--HG32 +ATOM HT1 HGP1 0.47 ! || / \ +GROUP ! CG--NT--CG1 CG4 +ATOM CG1 CG311 -0.09 ! / HT1 \ / +ATOM HG1 HGA1 0.09 ! CC3 CG6--CG5 +GROUP ! \ +ATOM CG2 CG324 0.20 ! O24 CC2 +ATOM HG21 HGA2 0.09 ! || / +ATOM HG22 HGA2 0.09 ! H Me21 C22 C24 CC1 +ATOM NG3 NG3P2 -0.40 ! | \ / \ / \ / \ +ATOM HG31 HGP2 0.32 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) +ATOM HG32 HGP2 0.32 ! / \ | / | +ATOM CG4 CG324 0.20 ! C11 C13---C17 OA2 (-0.5) +ATOM HG41 HGA2 0.09 ! Me19 | | | +ATOM HG42 HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CG5 CG321 -0.18 ! C2 C10 C8 C15 +ATOM HG51 HGA2 0.09 ! | | | +ATOM HG52 HGA2 0.09 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CG6 CG321 -0.18 ! HO C4 C6 OH +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 ! G3PR (01OH04(R)) + +BOND NT CG1 +BOND CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG3 +BOND NG3 HG31 NG3 HG32 NG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 + +IC CC3 CG NT CG1 1.5047 118.90 -176.48 124.61 1.4438 +IC CG NT CG1 HG1 1.3378 124.61 -36.75 108.87 1.1179 +IC HG1 NT *CG1 CG2 1.1179 108.87 119.19 110.98 1.5420 ! for R config +IC HG1 NT *CG1 CG6 1.1179 108.87 -118.11 109.81 1.5506 ! for R config +IC NT CG1 CG2 NG3 1.4438 110.98 74.30 110.11 1.5058 ! for R config +IC NG3 CG1 *CG2 HG21 1.5058 110.11 118.33 113.56 1.0998 +IC NG3 CG1 *CG2 HG22 1.5058 110.11 -116.73 111.83 1.1032 +IC CG1 CG2 NG3 CG4 1.5420 110.11 58.73 115.65 1.5046 +IC CG4 CG2 *NG3 HG31 1.5046 115.65 131.36 112.19 1.0010 +IC CG4 CG2 *NG3 HG32 1.5046 115.65 -117.57 105.76 1.0308 +IC CG2 NG3 CG4 CG5 1.5058 115.65 -9.08 111.13 1.5355 +IC CG5 NG3 *CG4 HG41 1.5355 111.13 123.33 105.76 1.1009 +IC CG5 NG3 *CG4 HG42 1.5355 111.13 -121.08 104.21 1.1056 +IC NG3 CG4 CG5 CG6 1.5046 111.13 -47.06 110.56 1.5411 +IC CG6 CG4 *CG5 HG51 1.5411 110.56 122.13 110.68 1.1119 +IC CG6 CG4 *CG5 HG52 1.5411 110.56 -120.28 109.02 1.1129 +IC CG5 CG1 *CG6 HG61 1.5411 113.66 -123.82 109.48 1.1121 +IC CG5 CG1 *CG6 HG62 1.5411 113.66 119.91 108.64 1.1155 + +PRES G3PS 1.00 ! C6H12N2O (01OH04(S)), cacha ! Check IC table +! This compound has 3-amine piperidine at gamma position +! core residue Bile Acid Basic moiety 1 (BAB1) +! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 ! HG31 +ATOM OG OG2D1 -0.51 ! | +ATOM NT NG2S1 -0.47 ! OG CG2--NG3(+1)--HG32 +ATOM HT1 HGP1 0.47 ! || / \ +GROUP ! CG--NT--CG1 CG4 +ATOM CG1 CG311 -0.09 ! / HT1 \ / +ATOM HG1 HGA1 0.09 ! CC3 CG6--CG5 +GROUP ! \ +ATOM CG2 CG324 0.20 ! O24 CC2 +ATOM HG21 HGA2 0.09 ! || / +ATOM HG22 HGA2 0.09 ! H Me21 C22 C24 CC1 +ATOM NG3 NG3P2 -0.40 ! | \ / \ / \ / \ +ATOM HG31 HGP2 0.32 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) +ATOM HG32 HGP2 0.32 ! / \ | / | +ATOM CG4 CG324 0.20 ! C11 C13---C17 OA2 (-0.5) +ATOM HG41 HGA2 0.09 ! Me19 | | | +ATOM HG42 HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CG5 CG321 -0.18 ! C2 C10 C8 C15 +ATOM HG51 HGA2 0.09 ! | | | +ATOM HG52 HGA2 0.09 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CG6 CG321 -0.18 ! HO C4 C6 OH +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 ! G3PS (01OH04(S)) + +BOND NT CG1 +BOND CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG3 +BOND NG3 HG31 NG3 HG32 NG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 + +IC CC3 CG NT CG1 1.5067 118.82 -168.68 125.46 1.4406 +IC CG NT CG1 HG1 1.3336 125.46 -54.62 108.34 1.1153 +IC HG1 NT *CG1 CG2 1.1153 108.34 -120.60 110.10 1.5378 ! for S config +IC HG1 NT *CG1 CG6 1.1153 108.34 119.57 110.63 1.5471 ! for S config +IC NT CG1 CG2 NG3 1.4406 110.10 -175.03 112.25 1.5062 ! for S config +IC NG3 CG1 *CG2 HG21 1.5062 112.25 116.92 111.42 1.1050 +IC NG3 CG1 *CG2 HG22 1.5062 112.25 -120.00 112.62 1.1009 +IC CG1 CG2 NG3 CG4 1.5378 112.25 58.60 112.03 1.5047 +IC CG4 CG2 *NG3 HG31 1.5047 112.03 122.85 109.11 1.0062 +IC CG4 CG2 *NG3 HG32 1.5047 112.03 -120.61 108.23 1.0067 +IC CG2 NG3 CG4 CG5 1.5062 112.03 -59.03 109.25 1.5284 +IC CG5 NG3 *CG4 HG41 1.5284 109.25 120.95 105.28 1.1051 +IC CG5 NG3 *CG4 HG42 1.5284 109.25 -122.37 105.83 1.1021 +IC NG3 CG4 CG5 CG6 1.5047 109.25 57.37 110.27 1.5380 +IC CG6 CG4 *CG5 HG51 1.5380 110.27 120.37 109.44 1.1129 +IC CG6 CG4 *CG5 HG52 1.5380 110.27 -121.28 110.59 1.1129 +IC CG5 CG1 *CG6 HG61 1.5380 112.70 -121.55 108.33 1.1151 +IC CG5 CG1 *CG6 HG62 1.5380 112.70 122.04 109.35 1.1123 + +PRES G3PABR 1.00 ! C15H20N2O3 (010204(R)D), cacha ! check IC table +! This compound has 3-amine piperidine at gamma position +! and benzyl at alpha position +! core residue Bile Acid Basic moiety 1 (BAB1) +! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 ! HG31 +ATOM HT1 HGP1 0.47 ! | +GROUP ! OG CG2--NG3(+1)--HG32 +ATOM CG1 CG311 -0.09 ! || / \ +ATOM HG1 HGA1 0.09 ! CG---NT--CG1 CG4 +GROUP ! / HT1 \ / +ATOM CG2 CG324 0.20 ! CC3 CG6--CG5 +ATOM HG21 HGA2 0.09 ! \ +ATOM HG22 HGA2 0.09 ! O24 CC2 +ATOM NG3 NG3P2 -0.40 ! || / +ATOM HG31 HGP2 0.32 ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM HG32 HGP2 0.32 ! | \ / \ / \ / \ // \\ +ATOM CG4 CG324 0.20 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP +ATOM HG41 HGA2 0.09 ! / \ | / || \ __ / +ATOM HG42 HGA2 0.09 ! C11 C13---C17 OA1 CD2--CE2 +GROUP ! Me19 | | | +ATOM CG5 CG321 -0.18 ! C1 | C9 C14 C16 +ATOM HG51 HGA2 0.09 ! / \|/ \ / \ / +ATOM HG52 HGA2 0.09 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM CG6 CG321 -0.18 ! C3 C5 C7 +ATOM HG61 HGA2 0.09 ! / \ / \ / \ +ATOM HG62 HGA2 0.09 ! HO C4 C6 OH +GROUP +ATOM CC1 CG311 0.17 ! G3PABR (010204(R)D) +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CG1 CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG3 +BOND NG3 HG31 NG3 HG32 NG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +BOND OA2 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5247 109.30 -176.15 116.76 1.4477 +IC HB1 CB OA2 CA 1.1153 110.11 -68.10 116.76 1.3346 +IC HB2 CB OA2 CA 1.1158 110.89 51.00 116.76 1.3346 +IC CZ CB OA2 CA 1.5068 113.78 172.70 116.76 1.3346 +IC CD2 CZ CB OA2 1.4048 119.29 56.49 113.78 1.4477 +IC CD1 CZ CB OA2 1.4063 121.26 -123.70 113.78 1.4477 +IC CD1 CD2 *CZ CB 1.4063 119.45 179.81 119.29 1.5068 +IC CD2 CZ CB HB1 1.4048 119.29 -64.86 106.30 1.1153 +IC CD2 CZ CB HB2 1.4048 119.29 179.89 107.79 1.1158 +IC CB CZ CD1 CE1 1.5068 121.26 -179.38 120.20 1.4018 +IC CB CZ CD2 CE2 1.5068 119.29 179.41 120.31 1.4014 +IC CZ CD1 CE1 CP 1.4063 120.20 0.03 120.00 1.4005 +IC CD1 CE1 CP CE2 1.4018 120.00 -0.52 120.09 1.4006 +IC CE1 CP CE2 CD2 1.4005 120.09 0.55 119.94 1.4014 +IC CE1 CZ *CD1 HD1 1.4018 120.20 179.30 120.24 1.0794 +IC CE2 CZ *CD2 HD2 1.4014 120.31 -179.45 119.81 1.0801 +IC CP CD1 *CE1 HE1 1.4005 120.00 179.28 120.29 1.0816 +IC CP CD2 *CE2 HE2 1.4006 119.94 -179.51 120.12 1.0810 +IC CE1 CE2 *CP HP 1.4005 120.09 179.59 120.13 1.0815 +IC CC3 CG NT CG1 1.5011 116.88 179.73 129.61 1.4554 +IC CG NT CG1 HG1 1.3471 129.61 -155.34 103.59 1.1192 +IC HG1 NT *CG1 CG2 1.1192 103.59 116.28 117.90 1.5488 ! for R config +IC HG1 NT *CG1 CG6 1.1192 103.59 -114.20 112.24 1.5460 ! for R config +IC NT CG1 CG2 NG3 1.4554 117.90 78.28 110.69 1.5102 ! for R config +IC NG3 CG1 *CG2 HG21 1.5102 110.69 116.99 112.30 1.1021 +IC NG3 CG1 *CG2 HG22 1.5102 110.69 -118.04 112.47 1.1014 +IC CG1 CG2 NG3 CG4 1.5488 110.69 56.48 114.54 1.5050 +IC CG4 CG2 *NG3 HG31 1.5050 114.54 128.88 111.74 1.0037 +IC CG4 CG2 *NG3 HG32 1.5050 114.54 -116.54 104.32 1.0232 +IC CG2 NG3 CG4 CG5 1.5102 114.54 -57.39 109.28 1.5325 +IC CG5 NG3 *CG4 HG41 1.5325 109.28 121.77 105.46 1.1028 +IC CG5 NG3 *CG4 HG42 1.5325 109.28 -121.69 105.58 1.1031 +IC NG3 CG4 CG5 CG6 1.5050 109.28 55.18 111.03 1.5405 +IC CG6 CG4 *CG5 HG51 1.5405 111.03 121.20 109.59 1.1130 +IC CG6 CG4 *CG5 HG52 1.5405 111.03 -121.12 109.77 1.1134 +IC CG5 CG1 *CG6 HG61 1.5405 112.67 -120.64 108.98 1.1142 +IC CG5 CG1 *CG6 HG62 1.5405 112.67 122.50 109.46 1.1133 + +PRES G3PABS 1.00 ! C15H20N2O3 (010204(S)D), cacha ! check IC table +! This compound has 3-amine piperidine at gamma position +! and benzyl at alpha position +! core residue Bile Acid Basic moiety 1 (BAB1) +! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 ! HG31 +ATOM HT1 HGP1 0.47 ! | +GROUP ! OG CG2--NG3(+1)--HG32 +ATOM CG1 CG311 -0.09 ! || / \ +ATOM HG1 HGA1 0.09 ! CG---NT--CG1 CG4 +GROUP ! / HT1 \ / +ATOM CG2 CG324 0.20 ! CC3 CG6--CG5 +ATOM HG21 HGA2 0.09 ! \ +ATOM HG22 HGA2 0.09 ! O24 CC2 +ATOM NG3 NG3P2 -0.40 ! || / +ATOM HG31 HGP2 0.32 ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM HG32 HGP2 0.32 ! | \ / \ / \ / \ // \\ +ATOM CG4 CG324 0.20 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP +ATOM HG41 HGA2 0.09 ! / \ | / || \ __ / +ATOM HG42 HGA2 0.09 ! C11 C13---C17 OA1 CD2--CE2 +GROUP ! Me19 | | | +ATOM CG5 CG321 -0.18 ! C1 | C9 C14 C16 +ATOM HG51 HGA2 0.09 ! / \|/ \ / \ / +ATOM HG52 HGA2 0.09 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM CG6 CG321 -0.18 ! C3 C5 C7 +ATOM HG61 HGA2 0.09 ! / \ / \ / \ +ATOM HG62 HGA2 0.09 ! HO C4 C6 OH +GROUP +ATOM CC1 CG311 0.17 ! G3PABS (010204(R)D) +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CG1 CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG3 +BOND NG3 HG31 NG3 HG32 NG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +BOND OA2 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5355 110.33 173.10 116.65 1.4498 +IC HB1 CB OA2 CA 1.1133 107.66 -159.94 116.65 1.3360 +IC HB2 CB OA2 CA 1.1172 110.84 -45.26 116.65 1.3360 +IC CZ CB OA2 CA 1.5124 117.67 81.14 116.65 1.3360 +IC CD2 CZ CB OA2 1.4046 119.99 -124.81 117.67 1.4498 +IC CD1 CZ CB OA2 1.4055 120.38 59.26 117.67 1.4498 +IC CD1 CD2 *CZ CB 1.4055 119.50 -175.97 119.99 1.5124 +IC CD2 CZ CB HB1 1.4046 119.99 115.14 105.50 1.1133 +IC CD2 CZ CB HB2 1.4046 119.99 2.48 109.03 1.1172 +IC CB CZ CD1 CE1 1.5124 120.38 174.84 120.09 1.4034 +IC CB CZ CD2 CE2 1.5124 119.99 -174.60 120.33 1.4000 +IC CZ CD1 CE1 CP 1.4055 120.09 0.17 120.04 1.4001 +IC CD1 CE1 CP CE2 1.4034 120.04 0.53 120.04 1.4004 +IC CE1 CP CE2 CD2 1.4001 120.04 -0.28 119.98 1.4000 +IC CE1 CZ *CD1 HD1 1.4034 120.09 -177.48 119.41 1.0806 +IC CE2 CZ *CD2 HD2 1.4000 120.33 177.84 119.72 1.0808 +IC CP CD1 *CE1 HE1 1.4001 120.04 -177.24 120.45 1.0791 +IC CP CD2 *CE2 HE2 1.4004 119.98 178.76 119.77 1.0812 +IC CE1 CE2 *CP HP 1.4001 120.04 178.32 119.79 1.0802 +IC CC3 CG NT CG1 1.4955 118.65 -174.99 125.29 1.4513 +IC CG NT CG1 HG1 1.3420 125.29 72.25 106.27 1.1180 +IC HG1 NT *CG1 CG2 1.1180 106.27 -120.59 116.06 1.5481 ! for S config +IC HG1 NT *CG1 CG6 1.1180 106.27 116.21 109.65 1.5438 ! for S config +IC NT CG1 CG2 NG3 1.4513 116.06 -178.87 111.82 1.5083 ! for S config +IC NG3 CG1 *CG2 HG21 1.5083 111.82 118.34 112.32 1.1010 +IC NG3 CG1 *CG2 HG22 1.5083 111.82 -117.38 113.04 1.1005 +IC CG1 CG2 NG3 CG4 1.5481 111.82 58.07 113.36 1.5025 +IC CG4 CG2 *NG3 HG31 1.5025 113.36 123.57 108.79 1.0183 +IC CG4 CG2 *NG3 HG32 1.5025 113.36 -121.13 108.70 1.0090 +IC CG2 NG3 CG4 CG5 1.5083 113.36 -55.74 109.81 1.5325 +IC CG5 NG3 *CG4 HG41 1.5325 109.81 121.56 105.19 1.1030 +IC CG5 NG3 *CG4 HG42 1.5325 109.81 -122.34 105.61 1.1031 +IC NG3 CG4 CG5 CG6 1.5025 109.81 53.37 112.00 1.5423 +IC CG6 CG4 *CG5 HG51 1.5423 112.00 121.73 109.45 1.1131 +IC CG6 CG4 *CG5 HG52 1.5423 112.00 -121.07 109.56 1.1110 +IC CG5 CG1 *CG6 HG61 1.5423 112.61 -121.49 109.20 1.1133 +IC CG5 CG1 *CG6 HG62 1.5423 112.61 121.00 109.29 1.1144 + +!end bile acids, chayan, may2007 + +!fatty acid binding protein inhibitors, chayan, may2007 +RESI FBIB -1.00 ! C12H15O3 Fatty acid Binding protein Inhibitor B, cacha +! This is a phenyl derivative having +! dimethyl at 2 and ethyl acetate at 4 position +GROUP +ATOM CG CG2R61 0.00 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 ! (-0.5)OD1 HA1 HB1 CD1--CE1 +ATOM HD1 HGR61 0.115 ! \ | | // \\ +GROUP ! CD--CA--CB--CG CZ--OH +ATOM CD2 CG2R61 -0.115 ! / | | \ __ / \ +ATOM HD2 HGR61 0.115 ! (-0.5)OD2 HA2 HB2 CD2--CE2 HH +GROUP ! | | +ATOM CE1 CG2R61 -0.115 ! HD2 CC--C1(Me) +ATOM HE1 HGR61 0.115 ! | +GROUP ! C2(Me) +ATOM CE2 CG2R61 0.00 +GROUP ! COMPOUND "FBIB" +ATOM CC CG311 -0.09 +ATOM HC HGA1 0.09 +ATOM C1 CG331 -0.27 +ATOM H1A HGA3 0.09 +ATOM H1B HGA3 0.09 +ATOM H1C HGA3 0.09 +ATOM C2 CG331 -0.27 +ATOM H2A HGA3 0.09 +ATOM H2B HGA3 0.09 +ATOM H2C HGA3 0.09 +GROUP +ATOM CZ CG2R61 0.11 +ATOM OH OG311 -0.53 +ATOM HH HGP1 0.42 +GROUP +ATOM CB CG321 -0.18 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CA CG321 -0.28 +ATOM HA1 HGA2 0.09 +ATOM HA2 HGA2 0.09 +ATOM CD CG2O3 0.62 +ATOM OD1 OG2D2 -0.76 +ATOM OD2 OG2D2 -0.76 + +BOND CG CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CZ +BOND CG CD2 CD2 HD2 CD2 CE2 CE2 CC CE2 CZ +BOND CG CB CB HB1 CB HB2 CB CA +BOND CA HA1 CA HA2 CA CD CD OD1 CD OD2 +BOND CC HC CC C1 CC C2 +BOND C1 H1A C1 H1B C1 H1C +BOND C2 H2A C2 H2B C2 H2C +BOND CZ OH OH HH +IMPR CD OD2 OD1 CA + +IC CG CD1 CE1 CZ 1.4003 119.98 -0.26 120.25 1.3984 +IC CD1 CE1 CZ CE2 1.4003 120.25 -0.01 120.56 1.4166 +IC CE1 CZ CE2 CD2 1.3984 120.56 0.13 118.30 1.4085 +IC CD1 CD2 *CG CB 1.4003 119.77 -179.27 119.58 1.5048 +IC CE1 CG *CD1 HD1 1.4003 119.98 -179.56 119.47 1.0801 +IC CE2 CG *CD2 HD2 1.4085 121.14 179.42 118.28 1.0793 +IC CZ CD1 *CE1 HE1 1.3984 120.25 -179.58 119.97 1.0797 +IC CZ CD2 *CE2 CC 1.4166 118.30 179.70 119.43 1.5244 +IC CD2 CE2 CC C1 1.4085 119.43 -61.92 108.96 1.5426 +IC C1 CE2 *CC C2 1.5426 108.96 122.45 109.20 1.5429 +IC C1 CE2 *CC HC 1.5426 108.96 -118.75 112.03 1.1131 +IC CE2 CC C1 H1A 1.5244 108.96 -177.62 110.22 1.1101 +IC H1A CC *C1 H1B 1.1101 110.22 120.09 110.82 1.1111 +IC H1A CC *C1 H1C 1.1101 110.22 -119.54 111.08 1.1110 +IC CE2 CC C2 H2A 1.5244 109.20 177.34 110.11 1.1103 +IC H2A CC *C2 H2B 1.1103 110.11 119.41 111.04 1.1107 +IC H2A CC *C2 H2C 1.1103 110.11 -120.01 110.78 1.1110 +IC CE1 CE2 *CZ OH 1.3984 120.56 179.54 121.85 1.4123 +IC CE1 CZ OH HH 1.3984 117.60 176.63 106.54 0.9574 +IC CD2 CG CB HB1 1.4003 119.58 -159.98 109.56 1.1132 +IC CD2 CG CB HB2 1.4003 119.58 -41.93 108.74 1.1119 +IC CD2 CG CB CA 1.4003 119.58 79.08 109.99 1.5472 +IC CG CB CA HA1 1.5048 109.99 61.87 110.80 1.1089 +IC CG CB CA HA2 1.5048 109.99 -59.13 110.94 1.1090 +IC CG CB CA CD 1.5048 109.99 -179.13 111.18 1.5290 +IC CB CA CD OD1 1.5472 111.18 124.07 117.29 1.2587 +IC OD1 CA *CD OD2 1.2587 117.29 167.13 117.17 1.2586 + +PRES FBIA 0.00 ! CH3 Fatty acid Binding protein Inhibitor A, cacha +! This is a phenyl derivative having +! methyl at 2 and ethyl acetate at 4 position +! patch combination: +! core residue Compound "FBIB" >> Compound "FBIA" + +DELETE ATOM CC ! HD1 HE1 +DELETE ATOM HC ! | | +DELETE ATOM C1 ! (-0.5)OD1 HA1 HB1 CD1--CE1 +DELETE ATOM H1A ! \ | | // \\ +DELETE ATOM H1B ! CD--CA--CB--CG CZ--OH +DELETE ATOM H1C ! / | | \ __ / \ +DELETE ATOM C2 ! (-0.5)OD2 HA2 HB2 CD2--CE2 HH +DELETE ATOM H2A ! | | +DELETE ATOM H2B ! HD2 CM(Me) +DELETE ATOM H2C +GROUP ! COMPOUND "FBIA" +ATOM CM CG331 -0.27 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND CE2 CM CM HM1 CM HM2 CM HM3 + +IC CZ CD2 *CE2 CM 1.4166 118.30 179.70 119.43 1.5244 +IC CD2 CE2 CM HM1 1.4085 119.43 -118.92 108.96 1.1426 +IC HM1 CE2 *CM HM2 1.1426 108.96 122.45 109.20 1.1429 +IC HM1 CE2 *CM HM3 1.1426 108.96 -118.75 112.03 1.1131 + +!PRES FBICR 0.00 ! Fatty acid Binding protein Inhibitor, R-isomer, cacha +PRES FBICS 0.00 ! C2H5 Fatty acid Binding protein Inhibitor, S-isomer, cacha +! This is a phenyl derivative having +! 2-methyl ethyl acetate at 4 position +! core residue "FBIB" >> Compound "FBICR" or Compound "FBICS" +! Orientation of the methyl group on ehtyl acetate dictates R/S configuration +! Specific configuration can be obtained by commenting/uncommenting corresponding IC values +! as described in the IC table +DELETE ATOM CB ! HD1 HE1 +DELETE ATOM HB1 ! | | +DELETE ATOM HB2 ! (-0.5)OD1 HA1 CM CD1--CE1 +DELETE ATOM CC ! \ | | // \\ +DELETE ATOM HC ! CD--CA--CBA--CG CZ--OH +DELETE ATOM C1 ! / | | \ __ / \ +DELETE ATOM H1A ! (-0.5)OD2 HA2 HBA CD2--CE2 HH +DELETE ATOM H1B ! | | +DELETE ATOM H1C ! HD2 HE2 +DELETE ATOM C2 +DELETE ATOM H2A ! COMPOUND "FBICR" OR "FBICS" +DELETE ATOM H2B +DELETE ATOM H2C +GROUP +ATOM HE2 HGR61 0.00 +GROUP +ATOM CBA CG311 -0.09 +ATOM HBA HGA1 0.09 +ATOM CM CG331 -0.27 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND CE2 HE2 +BOND CG CBA CBA HBA CBA CM CM HM1 CM HM2 CM HM3 +BOND CBA CA + +IC CZ CD2 *CE2 HE2 1.4028 119.93 -179.94 119.66 1.0804 +IC CD1 CD2 *CG CBA 1.4029 119.56 179.52 120.59 1.4978 +!IC CD2 CG CBA CM 1.4036 120.59 178.00 110.88 1.1144 ! for r-isomer +!IC CD2 CG CBA HBA 1.4036 120.59 -60.83 109.72 1.5424 ! for r-isomer +IC CD2 CG CBA CM 1.4036 120.59 -60.83 109.72 1.5424 ! for s-isomer +IC CD2 CG CBA HBA 1.4036 120.59 178.00 110.88 1.1144 ! for s-isomer +IC CG CBA CM HM1 1.4978 109.72 65.78 111.17 1.1093 +IC HM1 CBA *CM HM2 1.1093 111.17 120.55 110.04 1.1140 +IC HM1 CBA *CM HM3 1.1093 111.17 -120.83 110.06 1.1096 +!End fatty acid binding protein inhibitors, chayan, may2007 + +RESI 2PDO 0.000 ! C4H7NO 2-pyrrolidinone, kevo +GROUP +ATOM N1 NG2R53 -0.58 +ATOM H1 HGP1 0.36 +ATOM C2 CG2R53 0.30 ! H32 H42 +ATOM O2 OG2D1 -0.49 ! \ / +ATOM C3 CG3C52 -0.01 ! H31--C3----C4--H41 +ATOM H31 HGA2 0.09 ! | | +ATOM H32 HGA2 0.09 ! C2 C5--H51 +ATOM C4 CG3C52 -0.19 ! // \ / \ +ATOM H41 HGA2 0.09 ! O2 N1 H52 +ATOM H42 HGA2 0.09 ! | +ATOM C5 CG3C52 0.07 ! H1 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND N1 H1 C2 O2 C3 H31 C3 H32 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 +IMPR C2 C3 N1 O2 +IC C5 N1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C2 C3 C4 0.0000 0.00 15.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 200.00 0.00 0.0000 +IC C3 N1 *C2 O2 0.0000 0.00 181.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 240.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 + +!Acyclic ethers from top_all27_carb_jul2o.inp +RESI DMEE 0.0000 ! C2H6O Dimethylether, viv 2006 +GROUP +ATOM C1 CG331 -0.10 ! H12 H32 +ATOM H11 HGA3 0.09 ! | | +ATOM H12 HGA3 0.09 ! H11--C1---O2---C3--H31 +ATOM H13 HGA3 0.09 ! | | +ATOM O2 OG301 -0.34 ! H13 H33 +ATOM C3 CG331 -0.10 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND C1 O2 O2 C3 +BOND C1 H11 C1 H12 C1 H13 +BOND C3 H31 C3 H32 C3 H33 +IC C1 O2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H31 O2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 O2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 O2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 + +RESI METE 0.0000 ! C3H8O Methyl ethyl ether, viv 2006 +GROUP +ATOM C1 CG331 -0.27 ! H12 H21 H42 +ATOM H11 HGA3 0.09 ! | | | +ATOM H12 HGA3 0.09 ! H11--C1---C2---O3---C4--H41 +ATOM H13 HGA3 0.09 ! | | | +GROUP ! H13 H22 H43 +ATOM C2 CG321 -0.01 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM O3 OG301 -0.34 +ATOM C4 CG331 -0.10 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 C2 C2 O3 O3 C4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 C4 H43 +IC C4 O3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 O3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 O3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 O3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 O3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 +IC O3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 + +RESI DETE 0.0000 ! C4H10O Diethylether, viv 2006 +GROUP +ATOM C1 CG331 -0.27 ! H11 H21 H41 H51 +ATOM H11 HGA3 0.09 ! | | | | +ATOM H12 HGA3 0.09 ! H13--C1---C2---O3---C4---C5--H53 +ATOM H13 HGA3 0.09 ! | | | | +GROUP ! H12 H22 H42 H52 +ATOM C2 CG321 -0.01 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM O3 OG301 -0.34 +ATOM C4 CG321 -0.01 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 + +BOND C1 C2 C2 O3 O3 C4 C4 C5 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 +BOND C5 H51 C5 H52 C5 H53 +IC C1 C2 O3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 C2 O3 0.0000 0.00 180.00 0.00 0.0000 +IC O3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 O3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 O3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC O3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H51 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 +IC H51 C4 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 + +RESI DME 0.0000 ! C4H10O2 Dimethoxyethane, adm jr. +GROUP +ATOM C1 CG331 -0.10 ! H12 H11 +ATOM H11 HGA3 0.09 ! \ / +ATOM H12 HGA3 0.09 ! H13-C1 H31 H32 H61 H62 +ATOM H13 HGA3 0.09 ! \ \ / \ / +ATOM O2 OG301 -0.34 ! O2--C3 C6-H63 +ATOM C3 CG321 -0.01 ! \ / +ATOM H31 HGA2 0.09 ! H41-C4-O5 +ATOM H32 HGA2 0.09 ! | +GROUP ! H42 +ATOM C4 CG321 -0.01 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +ATOM O5 OG301 -0.34 +ATOM C6 CG331 -0.10 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 +BOND C1 O2 O2 C3 +BOND C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 +BOND C4 O5 O5 C6 +BOND C6 H61 C6 H62 C6 H63 +IC C1 O2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 O2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C4 O2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 O2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 !corrected by kevo +IC O2 C3 C4 O5 0.0000 0.00 180.00 0.00 0.0000 +IC O5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC O5 C3 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 !corrected by kevo +IC C3 C4 O5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 O5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC H61 O5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 +IC H61 O5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MPRE 0.0000 ! C4H10O Methyl Propyl Ether, 9/29/06 viv +GROUP +ATOM C1 CG331 -0.10 ! H11 H31 H41 H51 +ATOM H11 HGA3 0.09 ! | | | | +ATOM H12 HGA3 0.09 ! H11 - C1 - O2 - C3 - C4 - C5 - H53 +ATOM H13 HGA3 0.09 ! | | | | +ATOM O2 OG301 -0.34 ! H12 H32 H42 H52 +ATOM C3 CG321 -0.01 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 C1 O2 +BOND O2 C3 C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 C4 C5 +BOND C5 H51 C5 H52 C5 H53 +IC O2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C3 O2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC O2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC O2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C4 C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC C4 H51 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 +IC C4 H51 *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 O2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MBUE 0.0000 ! C5H12O Methyl Butyl Ether, 9/30/06 viv +GROUP +ATOM C1 CG331 -0.10 ! H11 H31 H41 H51 H6A +ATOM H11 HGA3 0.09 ! | | | | | +ATOM H12 HGA3 0.09 ! H11 - C1 - O2 - C3 - C4 - C5 - C6 - H6C +ATOM H13 HGA3 0.09 ! | | | | | +ATOM O2 OG301 -0.34 ! H12 H32 H42 H52 H6B +ATOM C3 CG321 -0.01 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG321 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +GROUP +ATOM C6 CG331 -0.27 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 C1 O2 +BOND O2 C3 C3 H31 C3 H32 C3 C4 +BOND C4 H41 C4 H42 C4 C5 +BOND C5 H51 C5 H52 C5 C6 +BOND C6 H61 C6 H62 C6 H63 +IC O2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C3 O2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC O2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC O2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC C5 H61 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 +IC C5 H61 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 O2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 O2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 + +RESI EPRE 0.0000 ! C5H12O Ethyl propyl ether, viv 9/30/06 +GROUP +ATOM C1 CG331 -0.27 ! H11 H21 H41 H51 H61 +ATOM H11 HGA3 0.09 ! | | | | | +ATOM H12 HGA3 0.09 ! H13 - C1 - C2 - O3 - C4 - C5 - C6 - H63 +ATOM H13 HGA3 0.09 ! | | | | | +GROUP ! H12 H22 H42 H52 H62 +ATOM C2 CG321 -0.01 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM O3 OG301 -0.34 +ATOM C4 CG321 -0.01 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG321 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +GROUP +ATOM C6 CG331 -0.27 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C1 C2 C2 O3 O3 C4 +BOND C4 C5 C5 C6 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 +BOND C4 H41 C4 H42 +BOND C5 H51 C5 H52 +BOND C6 H61 C6 H62 C6 H63 +IC C2 O3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C4 O3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC O3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 O3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC O3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC O3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC C5 H61 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 +IC C5 H61 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 +IC O3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 + +!<<<<<<<<<<<>>>>>>>>>>> +DECL -C2 +DECL -O1 +DECL +C1 +AUTOGENERATE ANGLE DIHE +DEFAULT FIRST HYD1 LAST HYD2 + +RESI PEGM 0.0000 ! C2H4O Peg monomer for polymer construction, viv Nov 2006 +GROUP +ATOM C1 CG321 -0.01 +ATOM H12 HGA2 0.09 ! H11 H21 +ATOM H11 HGA2 0.09 ! | | +ATOM O1 OG301 -0.34 ! (-C2) - C1 - O1 - C2 - +ATOM C2 CG321 -0.01 ! | | +ATOM H21 HGA2 0.09 ! H12 H22 +ATOM H22 HGA2 0.09 + +BOND C1 H11 C1 H12 C1 O1 +BOND O1 C2 C2 H21 C2 H22 +BOND C1 -C2 +IC -O1 -C2 C1 O1 0.0000 0.00 180.00 0.00 0.0000 +IC -C2 C1 O1 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O1 C2 +C1 0.0000 0.00 180.00 0.00 0.0000 +IC -C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC -C2 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 +C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O1 +C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 + +PRES HYD1 0.1700 ! CH3 Complete terminal methyl group adjacent to OCE +ATOM H13 HGA3 0.09 +ATOM C1 CG331 -0.10 ! H13 - +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 + +BOND H13 C1 +IC C2 O1 C1 H13 0.0000 0.00 180.00 0.00 0.0000 +IC H13 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC H13 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 + +PRES HYD2 0.1700 ! CH3 Complete terminal methyl group adjacent to OCE +ATOM H23 HGA3 0.09 +ATOM C2 CG331 -0.10 ! H23 - +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 + +BOND H23 C2 +IC C1 O1 C2 H23 0.0000 0.00 180.00 0.00 0.0000 +IC O1 H23 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O1 H23 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 + +PRES MET1 0.0000 ! CH3 Append terminal methyl group adjacent to CH2 + ! HE2 +ATOM CE CG331 -0.27 ! | +ATOM HE1 HGA3 0.09 ! HE3 - CE - +ATOM HE2 HGA3 0.09 ! | +ATOM HE3 HGA3 0.09 ! HE1 + +BOND CE C1 CE HE1 CE HE2 CE HE3 +IC C2 O1 C1 CE 0.0000 0.00 180.00 0.00 0.0000 +IC CE O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC CE O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C1 CE HE3 0.0000 0.00 180.00 0.00 0.0000 +IC HE3 C1 *CE HE1 0.0000 0.00 120.00 0.00 0.0000 +IC HE3 C1 *CE HE2 0.0000 0.00 -120.00 0.00 0.0000 + +PRES MET2 0.0000 ! CH3 Append terminal methyl group adjacent to CH2 + ! HA3 +ATOM CA CG331 -0.27 ! | +ATOM HA1 HGA3 0.09 ! HA2 - CA - +ATOM HA2 HGA3 0.09 ! | +ATOM HA3 HGA3 0.09 ! HA1 + +BOND CA C2 CA HA1 CA HA2 CA HA3 +IC C1 O1 C2 CA 0.0000 0.00 180.00 0.00 0.0000 +IC O1 CA *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O1 CA *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 CA HA3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 HA3 *CA HA1 0.0000 0.00 120.00 0.00 0.0000 +IC C2 HA3 *CA HA2 0.0000 0.00 -120.00 0.00 0.0000 + +DEFAULT FIRST NONE LAST NONE +!<<<<<<<<<<<>>>>>>>>>>> +!End acyclic ethers from top_all27_carb_jul2o.inp + +!New compounds from the sugar force field +RESI ACO 0.0000 ! C3H6O Acetone, adm, Oct 08 +GROUP +ATOM O1 OG2D3 -0.48 +ATOM C1 CG2O5 0.40 +ATOM C2 CG331 -0.23 ! O1 +ATOM C3 CG331 -0.23 ! || +ATOM H21 HGA3 0.09 ! C1 +ATOM H22 HGA3 0.09 ! / \ +ATOM H23 HGA3 0.09 ! H21--C2 C3--H31 +ATOM H31 HGA3 0.09 ! / | | \ +ATOM H32 HGA3 0.09 ! H22 H32 H33 H32 +ATOM H33 HGA3 0.09 + +BOND C1 C2 C1 C3 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +DOUBLE O1 C1 +IMPR C1 C2 C3 O1 +ACCE O1 +IC C2 C1 C3 H31 1.5366 110.58 135.22 109.51 1.1328 +IC O1 C1 C3 H31 1.2237 122.95 -42.47 109.51 1.1328 +IC O1 C1 C3 H32 1.2237 122.95 77.28 104.63 1.1325 +IC O1 C1 C3 H33 1.2237 122.95 -161.85 105.76 1.0732 +IC C3 C1 C2 H21 1.5233 110.58 -153.74 111.52 1.1204 +IC O1 C1 C2 H21 1.2237 126.42 23.85 111.52 1.1204 +IC O1 C1 C2 H22 1.2237 126.42 148.26 114.11 1.1296 +IC O1 C1 C2 H23 1.2237 126.42 -90.21 101.67 1.1375 + +RESI IPAA 0.00 ! C5H11NO og isopropyl acetamide, based on NMA +GROUP ! n.b.: CL, HL, CR, HR vdw params != c22 +ATOM CL CG331 -0.27 ! ??? this molecule needs optimization +ATOM HL1 HGA3 0.09 +ATOM HL2 HGA3 0.09 ! H211 H212 H213 +ATOM HL3 HGA3 0.09 ! \ | / +GROUP ! C21 +ATOM C CG2O1 0.51 ! HL1\ O / +ATOM O OG2D1 -0.51 ! HL2-- CL -- C -- N -- CR --HR +ATOM N NG2S1 -0.47 ! HL3/ H \ +ATOM H HGP1 0.31 ! C22 +ATOM CR CG311 0.07 ! / | \ +ATOM HR HGA1 0.09 ! H221 H222 H223 +GROUP +ATOM C21 CG331 -0.27 +ATOM H211 HGA3 0.09 +ATOM H212 HGA3 0.09 +ATOM H213 HGA3 0.09 +GROUP +ATOM C22 CG331 -0.27 +ATOM H221 HGA3 0.09 +ATOM H222 HGA3 0.09 +ATOM H223 HGA3 0.09 +BOND HL1 CL HL2 CL HL3 CL +BOND CL C C N N CR +BOND N H +BOND HR CR C21 CR C22 CR +BOND C21 H211 C21 H212 C21 H213 +BOND C22 H221 C22 H222 C22 H223 +DOUBLE C O +IMPR C CL N O +! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) +IC O C N H 1.2240 124.40 -180.00 118.74 0.9902 +IC H N C CL 0.9902 118.74 0.00 115.46 1.4817 +IC O C N CR 1.2240 124.40 0.00 125.23 1.4315 +IC N C CL HL1 1.3414 115.46 180.00 109.20 1.1119 +IC N C CL HL2 1.3414 115.46 60.56 110.24 1.1102 +IC N C CL HL3 1.3414 115.46 -60.56 110.24 1.1102 +IC C N CR HR 1.3414 125.23 180.00 105.39 1.1185 +IC C N CR C21 1.3414 125.23 64.21 112.40 1.5343 +IC C N CR C22 1.3414 125.23 -64.21 112.40 1.5343 +IC N CR C21 H211 1.4315 112.40 53.31 110.44 1.1098 +IC N CR C21 H212 1.4315 112.40 -66.48 110.16 1.1110 +IC N CR C21 H213 1.4315 112.40 173.88 110.46 1.1098 +IC N CR C22 H221 1.4315 112.40 66.48 110.16 1.1110 +IC N CR C22 H222 1.4315 112.40 -53.31 110.44 1.1098 +IC N CR C22 H223 1.4315 112.40 -173.88 110.46 1.1098 + +RESI AMOP -1.00 ! C4H7O3 alpha-methoxy-propionic acid, og +GROUP +ATOM C1 CG311 -0.02 ! CT1 HM1 HM2 HM3 +ATOM C2 CG2O3 0.62 ! CC \ | / +ATOM H1 HGA1 0.09 ! HA CM +ATOM OM OG301 -0.34 ! ethers | +ATOM CM CG331 -0.10 ! CT3 OM O1 (-) +ATOM HM1 HGA3 0.09 ! HA | / +ATOM HM2 HGA3 0.09 ! HA H1--C1--C2 +ATOM HM3 HGA3 0.09 ! HA | \\ +ATOM O1 OG2D2 -0.76 ! OC | O2 +ATOM O2 OG2D2 -0.76 ! OC H01--C0 +GROUP ! | \ +ATOM C0 CG331 -0.27 ! CT3 H02 H03 +ATOM H01 HGA3 0.09 ! HA +ATOM H02 HGA3 0.09 ! HA +ATOM H03 HGA3 0.09 ! HA +BOND C1 H1 C1 OM C1 C0 +BOND C1 C2 C2 O1 +BOND C0 H01 C0 H02 C0 H03 +BOND OM CM +BOND CM HM1 CM HM2 CM HM3 +DOUBLE C2 O2 +IMPR C2 O2 O1 C1 +IC C2 C1 OM CM 1.5370 107.76 -154.77 111.65 1.4194 +IC OM C2 *C1 C0 1.4224 107.76 123.63 111.13 1.5565 +IC OM C2 *C1 H1 1.4224 107.76 -117.54 106.67 1.1094 +IC C1 OM CM HM1 1.4224 111.65 60.37 109.96 1.1106 +IC HM1 OM *CM HM2 1.1106 109.96 -120.84 110.46 1.1094 +IC HM1 OM *CM HM3 1.1106 109.96 119.38 109.38 1.1097 +IC H1 C1 C2 O1 1.1094 106.67 177.14 118.57 1.2599 +IC O1 C1 *C2 O2 1.2599 118.57 -179.67 117.64 1.2609 +IC H1 C1 C0 H01 1.1094 109.13 -60.43 109.93 1.1106 +IC H01 C1 *C0 H02 1.1106 109.93 -118.90 109.59 1.1115 +IC H01 C1 *C0 H03 1.1106 109.93 120.54 111.13 1.1077 +PATC FIRS NONE LAST NONE +!End new compounds from the sugar force field + +!Special project, og, feb2008 +RESI CUME 0.0000 ! C9H12 Cumene (aka. isopropylbenzene), Olgun Guvench +GROUP +ATOM CA1 CG2R61 -0.115 ! HA1 +ATOM HA1 HGR61 0.115 ! | +GROUP ! CA1 +ATOM CA2 CG2R61 -0.115 ! // \ +ATOM HA2 HGR61 0.115 ! HA6--CA6 CA2--HA2 +GROUP ! | || +ATOM CA3 CG2R61 -0.115 ! | || +ATOM HA3 HGR61 0.115 ! HA5--CA5 CA3--HA3 +GROUP ! \\ / +ATOM CA4 CG2R61 0.0 ! CA4 +GROUP ! | +ATOM CA5 CG2R61 -0.115 ! | +ATOM HA5 HGR61 0.115 ! | +GROUP ! -------C4-------- +ATOM CA6 CG2R61 -0.115 ! | | | +ATOM HA6 HGR61 0.115 ! | H41 | +GROUP ! H52-C5-H51 H31-C3-H32 +ATOM C4 CG311 -0.09 ! | | +ATOM H41 HGA1 0.09 ! H53 H33 +GROUP +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 +BOND CA1 HA1 +BOND CA1 CA2 CA2 HA2 +BOND CA3 HA3 CA3 CA4 +BOND CA5 HA5 CA5 CA6 +BOND CA6 HA6 +DOUBLE CA6 CA1 CA4 CA5 CA2 CA3 +BOND C3 H31 C3 H32 C3 H33 +BOND CA4 C4 +BOND C3 C4 +BOND C4 H41 +BOND C4 C5 +BOND C5 H51 C5 H52 C5 H53 +IC CA6 HA1 *CA1 CA2 1.4195 121.85 177.84 121.53 1.4194 +IC HA1 CA1 CA2 CA3 1.0800 121.53 -178.93 121.60 1.3982 +IC CA3 CA1 *CA2 HA2 1.3982 121.60 -179.91 119.41 1.0825 +IC CA1 CA2 CA3 CA4 1.4194 121.60 0.43 120.92 1.4029 +IC CA4 CA2 *CA3 HA3 1.4029 120.92 179.85 119.25 1.0788 +IC HA1 CA1 CA6 CA5 1.0800 121.85 178.93 121.61 1.3985 +IC CA5 CA1 *CA6 HA6 1.3985 121.61 179.93 119.45 1.0824 +IC CA4 CA6 *CA5 HA5 1.4036 120.87 -179.85 119.09 1.0786 +IC CA5 CA3 *CA4 C4 1.4036 118.40 179.75 120.23 1.5147 +IC CA3 CA4 C4 C3 1.4029 120.23 0.00 109.64 1.5411 +IC C3 CA4 *C4 C5 1.5411 109.64 -124.08 109.66 1.5411 +IC C3 CA4 *C4 H41 1.5411 109.64 117.96 107.55 1.1143 +IC CA4 C4 C3 H31 1.5147 109.64 176.65 110.17 1.1098 +IC H31 C4 *C3 H32 1.1098 110.17 119.90 110.84 1.1103 +IC H31 C4 *C3 H33 1.1098 110.17 -119.93 110.47 1.1115 +IC CA4 C4 C5 H51 1.5147 109.66 -176.66 110.16 1.1098 +IC H51 C4 *C5 H52 1.1098 110.16 119.93 110.47 1.1114 +IC H51 C4 *C5 H53 1.1098 110.16 -119.89 110.84 1.1103 +PATCHING FIRST NONE LAST NONE + +RESI BSAT -1.0000 ! C6H5O3S Benzenesulfonate, Olgun Guvench +GROUP +ATOM S SG3O1 1.35 ! O1 +ATOM O1 OG2P1 -0.65 ! | +ATOM O2 OG2P1 -0.65 ! O2--S--O3 +ATOM O3 OG2P1 -0.65 ! | +ATOM CA1 CG2R61 -0.40 ! CA1 +GROUP ! // \ +ATOM CA2 CG2R61 -0.21 ! HA6--CA6 CA2--HA2 +ATOM HA2 HGR61 0.21 ! | || +GROUP ! | || +ATOM CA3 CG2R61 -0.115 ! HA5--CA5 CA3--HA3 +ATOM HA3 HGR61 0.115 ! \\ / +GROUP ! CA4 +ATOM CA4 CG2R61 -0.115 ! | +ATOM HA4 HGR61 0.115 ! HA4 +GROUP +ATOM CA5 CG2R61 -0.115 +ATOM HA5 HGR61 0.115 +GROUP +ATOM CA6 CG2R61 -0.21 +ATOM HA6 HGR61 0.21 +BOND S O1 S O2 S O3 +BOND S CA1 +BOND CA1 CA2 CA2 HA2 +BOND CA3 HA3 CA3 CA4 +BOND CA4 HA4 +BOND CA5 HA5 CA5 CA6 +BOND CA6 HA6 +DOUBLE CA6 CA1 CA4 CA5 CA2 CA3 +ACCEPTOR O1 S +ACCEPTOR O2 S +ACCEPTOR O3 S +IC O1 CA1 *S O2 1.4520 103.94 119.83 106.18 1.4544 +IC O1 CA1 *S O3 1.4520 103.94 -119.70 105.93 1.4543 +IC O1 S CA1 CA6 1.4520 103.94 -90.93 121.85 1.4195 +IC CA6 S *CA1 CA2 1.4195 121.85 177.84 121.53 1.4194 +IC S CA1 CA2 CA3 1.6322 121.53 -178.93 121.60 1.3982 +IC CA3 CA1 *CA2 HA2 1.3982 121.60 -179.91 119.41 1.0825 +IC CA1 CA2 CA3 CA4 1.4194 121.60 0.43 120.92 1.4029 +IC CA4 CA2 *CA3 HA3 1.4029 120.92 179.85 119.25 1.0788 +IC S CA1 CA6 CA5 1.6322 121.85 178.93 121.61 1.3985 +IC CA5 CA1 *CA6 HA6 1.3985 121.61 179.93 119.45 1.0824 +IC CA4 CA6 *CA5 HA5 1.4036 120.87 -179.85 119.09 1.0786 +IC CA5 CA3 *CA4 HA4 1.4036 118.40 179.75 120.23 1.0800 +PATCHING FIRST NONE LAST NONE +!End special project, og, feb2008 + +!Polli's bile acids, chayan, feb2008 +RESI 2MPA 1.00 ! C8H17N2O 2-Methyl Piperidine Amide +! Made in order to build Polli's compounds (Pablo) +GROUP +ATOM CG1 CG314 0.29 +ATOM HG1 HGA1 0.09 ! HG21 HG22 +ATOM NG2 NG3P2 -0.40 ! \ / +ATOM HG21 HGP2 0.32 ! OG HT (+1)NG2--CG3 +ATOM HG22 HGP2 0.32 ! || | / \ +ATOM CG3 CG324 0.20 ! CG---NT--CGT--CG1 CG4 +ATOM HG31 HGA2 0.09 ! / \ / +ATOM HG32 HGA2 0.09 ! HM1--CM--HM3 CG6--CG5 +GROUP ! | +ATOM CG4 CG321 -0.18 ! HM2 +ATOM HG41 HGA2 0.09 +ATOM HG42 HGA2 0.09 ! 2MPA +GROUP +ATOM CG5 CG321 -0.18 +ATOM HG51 HGA2 0.09 +ATOM HG52 HGA2 0.09 +GROUP +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 +GROUP +ATOM CM CG331 -0.27 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 +ATOM HT HGP1 0.47 +GROUP +ATOM CGT CG321 -0.18 +ATOM HGT1 HGA2 0.09 +ATOM HGT2 HGA2 0.09 + +BOND CM HM1 CM HM2 CM HM3 CM CG +BOND CG OG CG NT NT HT +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 NG2 +BOND NG2 HG21 NG2 HG22 NG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +IMPR CG CM NT OG + +IC CM CG NT CGT 1.4784 116.17 178.50 125.70 1.4627 +IC CG NT CGT HGT1 1.3412 125.70 -174.52 107.65 1.1160 +IC HGT1 NT *CGT HGT2 1.1160 107.65 114.70 109.82 1.1155 +IC HGT1 NT *CGT CG1 1.1160 107.65 -119.46 116.84 1.5494 +IC NT CG CM HM1 1.3412 116.17 -62.83 110.69 1.1111 +IC HM1 CG *CM HM2 1.1111 110.69 -119.06 109.32 1.1131 +IC HM1 CG *CM HM3 1.1111 110.69 121.66 110.83 1.1107 +IC CM NT *CG OG 1.4784 116.17 170.21 122.13 1.2240 +IC OG CG NT HT 1.2240 122.13 175.26 115.36 0.9985 +IC CG NT CGT CG1 1.3412 125.70 66.02 116.84 1.5494 +IC NT CGT CG1 HG1 1.4627 116.84 36.30 109.99 1.1056 +IC HG1 CGT *CG1 NG2 1.1056 109.99 -114.94 109.74 1.5010 +IC HG1 CGT *CG1 CG6 1.1056 109.99 124.49 113.69 1.5350 +IC CGT CG1 NG2 CG3 1.5494 109.74 176.09 115.30 1.5001 +IC CG3 CG1 *NG2 HG21 1.5001 115.30 122.39 107.69 1.0058 +IC CG3 CG1 *NG2 HG22 1.5001 115.30 -125.48 107.03 1.0184 +IC CG1 NG2 CG3 CG4 1.5010 115.30 59.26 108.63 1.5313 +IC CG4 NG2 *CG3 HG31 1.5313 108.63 122.04 105.77 1.1032 +IC CG4 NG2 *CG3 HG32 1.5313 108.63 -121.53 105.49 1.1034 +IC NG2 CG3 CG4 CG5 1.5001 108.63 -54.12 110.88 1.5394 +IC CG5 CG3 *CG4 HG41 1.5394 110.88 120.82 109.89 1.1138 +IC CG5 CG3 *CG4 HG42 1.5394 110.88 -121.31 109.72 1.1134 +IC CG3 CG4 CG5 CG6 1.5313 110.88 54.58 111.72 1.5411 +IC CG6 CG4 *CG5 HG51 1.5411 111.72 121.65 109.56 1.1147 +IC CG6 CG4 *CG5 HG52 1.5411 111.72 -121.21 109.32 1.1144 +IC CG5 CG1 *CG6 HG61 1.5411 110.92 -121.44 110.01 1.1127 +IC CG5 CG1 *CG6 HG62 1.5411 110.92 120.54 109.46 1.1130 + + + +!Pablo's Compounds +RESI BPIP 1.00 ! C12H18N Model compound for N-benzyl piperidine, cacha +GROUP +ATOM CB CG324 0.15 +ATOM HB1 HGA2 0.09 ! C3---C2 CD1--CE1 +ATOM HB2 HGA2 0.09 ! / \ // \\ +ATOM N1 NG3P1 -0.40 ! C4 N1--CB--CZ CP +ATOM H1 HGP2 0.32 ! \ / \ __ / +ATOM C2 CG324 0.15 ! C5---C6 CD2--CE2 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 ! BPIP +ATOM C6 CG324 0.15 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 +GROUP +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +GROUP +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 +GROUP +ATOM C5 CG321 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.090 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND N1 H1 N1 C2 C2 H21 C2 H22 +BOND C2 C3 C3 H31 C3 H32 +BOND C3 C4 C4 H41 C4 H42 +BOND C4 C5 C5 H51 C5 H52 +BOND C5 C6 C6 H61 C6 H62 C6 N1 +BOND N1 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 +BOND CZ CD2 CD2 HD2 CD2 CE2 CE2 HE2 +BOND CE1 CP CP HP CP CE2 + +IC C6 N1 C2 C3 1.5157 110.13 -60.42 110.11 1.5319 +IC N1 C2 C3 C4 1.5157 110.11 57.37 110.44 1.5362 +IC C2 C3 C4 C5 1.5319 110.44 -54.84 111.24 1.5362 +IC C3 C4 C5 C6 1.5362 111.24 54.84 110.44 1.5319 +IC C2 C6 *N1 CB 1.5157 110.13 135.82 116.61 1.5015 +IC HB1 N1 *CB HB2 1.1028 107.08 -120.06 107.08 1.1028 +IC HB1 N1 *CB CZ 1.1028 107.08 119.97 107.59 1.4889 +IC HB1 CB N1 C6 1.1028 107.08 173.55 116.61 1.5157 +IC C6 CB *N1 C2 1.5157 116.61 132.96 116.61 1.5157 +IC C2 CB *N1 H1 1.5157 116.61 113.52 105.15 1.0496 +IC C3 N1 *C2 H21 1.5319 110.11 121.51 105.72 1.1025 +IC H21 N1 *C2 H22 1.1025 105.72 116.75 105.78 1.1018 +IC C5 N1 *C6 H61 1.5319 110.11 121.75 105.78 1.1018 +IC C5 N1 *C6 H62 1.5319 110.11 -121.51 105.72 1.1025 +IC C4 C2 *C3 H31 1.5362 110.44 120.70 109.65 1.1137 +IC H31 C2 *C3 H32 1.1137 109.65 118.12 110.23 1.1131 +IC C5 C3 *C4 H41 1.5362 111.24 -121.82 109.83 1.1145 +IC H41 C3 *C4 H42 1.1145 109.83 -117.39 109.30 1.1147 +IC C4 C6 *C5 H51 1.5362 110.44 121.18 110.23 1.1131 +IC C4 C6 *C5 H52 1.5362 110.44 -120.70 109.65 1.1137 +IC C2 N1 CB CZ 1.5157 116.61 66.48 107.59 1.4889 +IC N1 CB CZ CD2 1.5015 107.59 -92.75 120.51 1.4109 +IC N1 CB CZ CD1 1.5015 107.59 92.75 120.51 1.4109 +IC CD1 CD2 *CZ CB 1.4109 118.75 -174.60 120.51 1.4889 +IC CD2 CZ CB HB1 1.4109 120.51 24.38 111.50 1.1028 +IC CD2 CZ CB HB2 1.4109 120.51 150.12 111.50 1.1028 +IC CB CZ CD1 CE1 1.4889 120.51 177.83 120.52 1.4001 +IC CB CZ CD2 CE2 1.4889 120.51 -177.83 120.52 1.4001 +IC CZ CD1 CE1 CP 1.4109 120.52 -1.31 120.00 1.3993 +IC CD1 CE1 CP CE2 1.4001 120.00 -0.66 120.12 1.3993 +IC CE1 CP CE2 CD2 1.3993 120.12 0.66 120.00 1.4001 +IC CE1 CZ *CD1 HD1 1.4001 120.52 -179.79 120.55 1.0802 +IC CE2 CZ *CD2 HD2 1.4001 120.52 179.79 120.55 1.0802 +IC CP CD1 *CE1 HE1 1.3993 120.00 -179.18 120.30 1.0822 +IC CP CD2 *CE2 HE2 1.3993 120.00 179.18 120.30 1.0822 +IC CE1 CE2 *CP HP 1.3993 120.12 178.89 119.94 1.0821 + + +PRES BPAB 1.00 ! C22H26N2O3 Gamma N-benzyl piperidine, alpha benzyl CDCA amide (010201P), cacha +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP ! OG CG3--CG3 CJ1--CK1 +ATOM CG CG2O1 0.51 ! || / \ // \\ +ATOM OG OG2D1 -0.51 ! CG---NT--CG4 NG1(+1) CY CQ +ATOM NT NG2S1 -0.47 ! / HT1 \ / \ / \ __ / +ATOM HT1 HGP1 0.47 ! CC3 CG5--CG6 CBG CJ2--CK2 +GROUP ! \ +ATOM CG4 CG311 -0.09 ! O24 CC2 +ATOM HG4 HGA1 0.09 ! || / +GROUP ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM CG3 CG321 -0.18 ! | \ / \ / \ / \ // \\ +ATOM HG31 HGA2 0.09 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP +ATOM HG32 HGA2 0.09 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OA1 CD2--CE2 +ATOM CG2 CG324 0.15 ! Me19 | | | +ATOM HG21 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HG22 HGA2 0.09 ! / \|/ \ / \ / +ATOM NG1 NG3P1 -0.40 ! C2 C10 C8 C15 +ATOM HG1 HGP2 0.32 ! | | | +ATOM CBG CG324 0.15 ! C3 C5 C7 +ATOM HBG1 HGA2 0.09 ! / \ / \ / \ +ATOM HBG2 HGA2 0.09 ! HO C4 C6 OH +ATOM CG6 CG324 0.15 +ATOM HG61 HGA2 0.09 ! BPAB (010201P) +ATOM HG62 HGA2 0.09 +GROUP +ATOM CG5 CG321 -0.18 +ATOM HG51 HGA2 0.09 +ATOM HG52 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.090 +GROUP +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +GROUP +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +GROUP +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +GROUP +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +GROUP +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CG4 CG4 HG4 CG4 CG3 +BOND CG3 HG31 CG3 HG32 CG3 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG1 +BOND NG1 HG1 NG1 CBG NG1 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG4 +BOND CBG HBG1 CBG HBG2 CBG CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND OA2 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5234 109.38 -153.04 116.99 1.4484 +IC HB1 CB OA2 CA 1.1167 112.82 -38.66 116.99 1.3347 +IC HB2 CB OA2 CA 1.1142 108.54 -155.51 116.99 1.3347 +IC CZ CB OA2 CA 1.5069 113.23 86.00 116.99 1.3347 +IC CD2 CZ CB OA2 1.4041 120.59 -99.33 113.23 1.4484 +IC CD1 CZ CB OA2 1.4045 119.58 76.21 113.23 1.4484 +IC CD1 CD2 *CZ CB 1.4045 119.68 175.54 120.59 1.5069 +IC CD2 CZ CB HB1 1.4041 120.59 27.27 109.20 1.1167 +IC CD2 CZ CB HB2 1.4041 120.59 141.22 106.86 1.1142 +IC CB CZ CD1 CE1 1.5069 119.58 -176.05 120.14 1.4008 +IC CB CZ CD2 CE2 1.5069 120.59 175.62 120.15 1.4011 +IC CZ CD1 CE1 CP 1.4045 120.14 0.56 119.98 1.4008 +IC CD1 CE1 CP CE2 1.4008 119.98 -0.25 120.07 1.4012 +IC CE1 CP CE2 CD2 1.4008 120.07 -0.13 119.97 1.4011 +IC CE1 CZ *CD1 HD1 1.4008 120.14 179.88 120.03 1.0802 +IC CE2 CZ *CD2 HD2 1.4011 120.15 -179.36 120.10 1.0785 +IC CP CD1 *CE1 HE1 1.4008 119.98 -179.84 120.09 1.0803 +IC CP CD2 *CE2 HE2 1.4012 119.97 179.92 120.22 1.0812 +IC CE1 CE2 *CP HP 1.4008 120.07 179.63 119.91 1.0813 +IC HT1 CG *NT CG4 1.0054 116.40 -172.83 124.61 1.4381 +IC CG NT CG4 CG3 1.3416 124.61 170.00 110.67 1.5378 +IC CG3 NT *CG4 HG4 1.5378 110.67 -117.93 107.34 1.1204 +IC CG3 NT *CG4 CG5 1.5378 110.67 122.73 112.97 1.5408 +IC NT CG4 CG3 CG2 1.4381 110.67 70.05 111.85 1.5352 +IC CG4 CG2 *CG3 HG31 1.5378 111.85 121.71 109.54 1.1122 +IC CG4 CG2 *CG3 HG32 1.5378 111.85 -120.95 109.60 1.1132 +IC CG4 CG3 CG2 NG1 1.5378 111.85 55.34 111.06 1.5202 +IC NG1 CG3 *CG2 HG21 1.5202 111.06 118.37 110.41 1.1001 +IC NG1 CG3 *CG2 HG22 1.5202 111.06 -118.11 113.59 1.1007 +IC CG3 CG2 NG1 CG6 1.5352 111.06 -56.33 110.73 1.5109 +IC CG6 CG2 *NG1 HG1 1.5109 110.73 112.39 104.22 1.0469 +IC CG6 CG2 *NG1 CBG 1.5109 110.73 -129.60 117.47 1.4972 +IC CG2 CG3 CG4 CG5 1.5352 111.85 -54.87 109.15 1.5408 +IC CG5 NG1 *CG6 HG61 1.5266 110.48 121.09 105.90 1.1028 +IC CG5 NG1 *CG6 HG62 1.5266 110.48 -122.70 105.64 1.1023 +IC CG6 CG4 *CG5 HG51 1.5266 111.10 121.26 109.77 1.1128 +IC CG6 CG4 *CG5 HG52 1.5266 111.10 -122.01 109.21 1.1123 +IC CG6 NG1 CBG HBG1 1.5109 111.45 -69.57 107.08 1.1032 +IC HBG1 NG1 *CBG HBG2 1.1032 107.08 121.43 107.67 1.1023 +IC CG2 NG1 CBG CY 1.5202 117.47 -60.45 105.98 1.4862 +IC NG1 CBG CY CJ2 1.4972 105.98 -74.47 120.62 1.4104 +IC NG1 CBG CY CJ1 1.4972 105.98 108.23 120.17 1.4090 +IC CBG CY CJ1 CK1 1.4862 120.17 179.26 120.32 1.4003 +IC CBG CY CJ2 CK2 1.4862 120.62 -179.21 120.29 1.4003 +IC CY CJ1 CK1 CQ 1.4090 120.32 -0.80 120.02 1.3998 +IC CJ1 CK1 CQ CK2 1.4003 120.02 -0.38 120.16 1.3998 +IC CK1 CQ CK2 CJ2 1.3998 120.16 0.42 120.02 1.4003 +IC CK1 CY *CJ1 HJ1 1.4003 120.32 179.90 120.54 1.0806 +IC CK2 CY *CJ2 HJ2 1.4003 120.29 179.62 120.62 1.0803 +IC CQ CJ1 *CK1 HK1 1.3998 120.02 -179.40 120.26 1.0821 +IC CQ CJ2 *CK2 HK2 1.3998 120.02 179.37 120.29 1.0822 +IC CK1 CK2 *CQ HQ 1.3998 120.16 179.20 119.92 1.0821 + + +PRES BPAT 1.00 ! C19H28N2O3 Gamma N-benzyl piperidine, alpha tert.butyl CDCA amide (010101P), cacha +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP ! OG CG3--CG3 CJ1--CK1 +ATOM CG CG2O1 0.51 ! || / \ // \\ +ATOM OG OG2D1 -0.51 ! CG---NT--CG4 NG1(+1) CY CQ +ATOM NT NG2S1 -0.47 ! / HT1 \ / \ / \ __ / +ATOM HT1 HGP1 0.47 ! CC3 CG5--CG6 CBG CJ2--CK2 +GROUP ! \ +ATOM CG4 CG311 -0.09 ! O24 CC2 +ATOM HG4 HGA1 0.09 ! || / +GROUP ! H Me21 C22 C24 CC1 CT1 +ATOM CG3 CG321 -0.18 ! | \ / \ / \ / \ / +ATOM HG31 HGA2 0.09 ! C12 Me18 C20 C23 NH CA---OA2---CT--CT2 +ATOM HG32 HGA2 0.09 ! / \ | / || \ +GROUP ! C11 C13---C17 OA1 CT3 +ATOM CG2 CG324 0.15 ! Me19 | | | +ATOM HG21 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HG22 HGA2 0.09 ! / \|/ \ / \ / +ATOM NG1 NG3P1 -0.40 ! C2 C10 C8 C15 +ATOM HG1 HGP2 0.32 ! | | | +ATOM CBG CG324 0.15 ! C3 C5 C7 +ATOM HBG1 HGA2 0.09 ! / \ / \ / \ +ATOM HBG2 HGA2 0.09 ! HO C4 C6 OH +ATOM CG6 CG324 0.15 +ATOM HG61 HGA2 0.09 ! BPAT (010101P) +ATOM HG62 HGA2 0.09 +GROUP +ATOM CG5 CG321 -0.18 +ATOM HG51 HGA2 0.09 +ATOM HG52 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.090 +GROUP +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +GROUP +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +GROUP +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +GROUP +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +GROUP +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CT CG301 -0.04 +ATOM CT1 CG331 -0.27 +ATOM HT11 HGA3 0.09 +ATOM HT12 HGA3 0.09 +ATOM HT13 HGA3 0.09 +ATOM CT2 CG331 -0.27 +ATOM HT21 HGA3 0.09 +ATOM HT22 HGA3 0.09 +ATOM HT23 HGA3 0.09 +ATOM CT3 CG331 -0.27 +ATOM HT31 HGA3 0.09 +ATOM HT32 HGA3 0.09 +ATOM HT33 HGA3 0.09 + +BOND NT CG4 +BOND CG4 HG4 CG4 CG3 +BOND CG3 HG31 CG3 HG32 CG3 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG1 +BOND NG1 HG1 NG1 CBG NG1 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG4 +BOND CBG HBG1 CBG HBG2 CBG CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND OA2 CT +BOND CT CT1 CT1 HT11 CT1 HT12 CT1 HT13 +BOND CT CT2 CT2 HT21 CT2 HT22 CT2 HT23 +BOND CT CT3 CT3 HT31 CT3 HT32 CT3 HT33 +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CT 1.5234 109.10 -173.96 122.03 1.4239 +IC CT1 CT OA2 CA 1.5352 110.85 62.78 122.03 1.3222 +IC CT2 CT OA2 CA 1.5347 111.07 -62.73 122.03 1.3222 +IC CT3 CT OA2 CA 1.5307 105.00 179.91 122.03 1.3222 +IC HT11 CT1 CT OA2 1.1112 109.61 171.34 110.85 1.4239 +IC HT12 CT1 CT OA2 1.1067 111.59 -69.34 110.85 1.4239 +IC HT13 CT1 CT OA2 1.1101 110.52 52.23 110.85 1.4239 +IC HT21 CT2 CT OA2 1.1108 109.79 -171.93 111.07 1.4239 +IC HT22 CT2 CT OA2 1.1080 111.70 68.38 111.07 1.4239 +IC HT23 CT2 CT OA2 1.1104 110.28 -52.79 111.07 1.4239 +IC HT31 CT3 CT OA2 1.1107 110.25 179.66 105.00 1.4239 +IC HT32 CT3 CT OA2 1.1106 110.46 60.01 105.00 1.4239 +IC HT33 CT3 CT OA2 1.1099 110.69 -60.47 105.00 1.4239 +IC HT1 CG *NT CG4 1.0045 117.45 -173.12 124.06 1.4390 +IC CG NT CG4 CG3 1.3436 124.06 168.56 110.90 1.5381 +IC CG3 NT *CG4 HG4 1.5381 110.90 -117.89 107.42 1.1207 +IC CG3 NT *CG4 CG5 1.5381 110.90 122.85 112.85 1.5408 +IC NT CG4 CG3 CG2 1.4390 110.90 70.34 111.99 1.5350 +IC CG4 CG2 *CG3 HG31 1.5381 111.99 121.82 109.60 1.1121 +IC CG4 CG2 *CG3 HG32 1.5381 111.99 -120.93 109.55 1.1133 +IC CG4 CG3 CG2 NG1 1.5381 111.99 55.21 111.05 1.5200 +IC NG1 CG3 *CG2 HG21 1.5200 111.05 118.37 110.38 1.1001 +IC NG1 CG3 *CG2 HG22 1.5200 111.05 -118.12 113.66 1.1004 +IC CG3 CG2 NG1 CG6 1.5350 111.05 -56.35 110.70 1.5109 +IC CG6 CG2 *NG1 HG1 1.5109 110.70 112.41 104.22 1.0468 +IC CG6 CG2 *NG1 CBG 1.5109 110.70 -129.56 117.44 1.4972 +IC CG2 CG3 CG4 CG5 1.5350 111.99 -54.61 109.17 1.5408 +IC CG5 NG1 *CG6 HG61 1.5267 110.50 121.09 105.89 1.1029 +IC CG5 NG1 *CG6 HG62 1.5267 110.50 -122.70 105.62 1.1023 +IC CG6 CG4 *CG5 HG51 1.5267 111.14 121.28 109.72 1.1128 +IC CG6 CG4 *CG5 HG52 1.5267 111.14 -122.01 109.20 1.1124 +IC CG6 NG1 CBG HBG1 1.5109 111.46 -69.49 107.08 1.1032 +IC HBG1 NG1 *CBG HBG2 1.1032 107.08 121.42 107.67 1.1023 +IC CG2 NG1 CBG CY 1.5200 117.44 -60.42 105.99 1.4862 +IC NG1 CBG CY CJ2 1.4972 105.99 -74.52 120.62 1.4104 +IC NG1 CBG CY CJ1 1.4972 105.99 108.18 120.17 1.4090 +IC CBG CY CJ1 CK1 1.4862 120.17 179.26 120.32 1.4003 +IC CBG CY CJ2 CK2 1.4862 120.62 -179.21 120.29 1.4003 +IC CY CJ1 CK1 CQ 1.4090 120.32 -0.80 120.02 1.3998 +IC CJ1 CK1 CQ CK2 1.4003 120.02 -0.38 120.16 1.3998 +IC CK1 CQ CK2 CJ2 1.3998 120.16 0.42 120.02 1.4003 +IC CK1 CY *CJ1 HJ1 1.4003 120.32 179.88 120.54 1.0806 +IC CK2 CY *CJ2 HJ2 1.4003 120.29 179.63 120.62 1.0803 +IC CQ CJ1 *CK1 HK1 1.3998 120.02 -179.41 120.26 1.0821 +IC CQ CJ2 *CK2 HK2 1.3998 120.02 179.38 120.29 1.0822 +IC CK1 CK2 *CQ HQ 1.3998 120.16 179.21 119.92 1.0821 + + +PRES GBP 1.00 ! C13H18N2O Gamma N-benzyl piperidine CDCA amide (01OH01), cacha +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP ! OG CG3--CG3 CJ1--CK1 +ATOM CG CG2O1 0.51 ! || / \ // \\ +ATOM OG OG2D1 -0.51 ! CG---NT--CG4 NG1(+1) CY CQ +ATOM NT NG2S1 -0.47 ! / HT1 \ / \ / \ __ / +ATOM HT1 HGP1 0.47 ! CC3 CG5--CG6 CBG CJ2--CK2 +GROUP ! \ +ATOM CG4 CG311 -0.09 ! O24 CC2 +ATOM HG4 HGA1 0.09 ! || / +GROUP ! H Me21 C22 C24 CC1 +ATOM CG3 CG321 -0.18 ! | \ / \ / \ / \ +ATOM HG31 HGA2 0.09 ! C12 Me18 C20 C23 NH CA---OA2 +ATOM HG32 HGA2 0.09 ! / \ | / || +GROUP ! C11 C13---C17 OA1 +ATOM CG2 CG324 0.15 ! Me19 | | | +ATOM HG21 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HG22 HGA2 0.09 ! / \|/ \ / \ / +ATOM NG1 NG3P1 -0.40 ! C2 C10 C8 C15 +ATOM HG1 HGP2 0.32 ! | | | +ATOM CBG CG324 0.15 ! C3 C5 C7 +ATOM HBG1 HGA2 0.09 ! / \ / \ / \ +ATOM HBG2 HGA2 0.09 ! HO C4 C6 OH +ATOM CG6 CG324 0.15 +ATOM HG61 HGA2 0.09 ! GBP (01OH01) +ATOM HG62 HGA2 0.09 +GROUP +ATOM CG5 CG321 -0.18 +ATOM HG51 HGA2 0.09 +ATOM HG52 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.090 +GROUP +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +GROUP +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +GROUP +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +GROUP +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +GROUP +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND NT CG4 +BOND CG4 HG4 CG4 CG3 +BOND CG3 HG31 CG3 HG32 CG3 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG1 +BOND NG1 HG1 NG1 CBG NG1 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG4 +BOND CBG HBG1 CBG HBG2 CBG CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY + +IC HT1 CG *NT CG4 1.0266 118.64 -178.12 121.63 1.4492 +IC CG NT CG4 CG3 1.3473 121.63 69.87 112.24 1.5369 +IC CG3 NT *CG4 HG4 1.5369 112.24 -119.04 107.41 1.1206 +IC CG3 NT *CG4 CG5 1.5369 112.24 122.72 113.59 1.5392 +IC NT CG4 CG3 CG2 1.4492 112.24 63.89 110.04 1.5253 +IC CG4 CG2 *CG3 HG31 1.5369 110.04 120.66 109.41 1.1118 +IC CG4 CG2 *CG3 HG32 1.5369 110.04 -121.42 110.77 1.1110 +IC CG4 CG3 CG2 NG1 1.5369 110.04 61.26 111.15 1.5205 +IC NG1 CG3 *CG2 HG21 1.5205 111.15 118.11 110.13 1.0998 +IC NG1 CG3 *CG2 HG22 1.5205 111.15 -118.76 113.26 1.0984 +IC CG3 CG2 NG1 CG6 1.5253 111.15 -51.59 113.22 1.5195 +IC CG6 CG2 *NG1 HG1 1.5195 113.22 114.22 104.34 1.0416 +IC CG6 CG2 *NG1 CBG 1.5195 113.22 -126.12 117.02 1.4977 +IC CG2 CG3 CG4 CG5 1.5253 110.04 -62.01 107.88 1.5392 +IC CG5 NG1 *CG6 HG61 1.5363 113.88 122.63 105.32 1.1016 +IC CG5 NG1 *CG6 HG62 1.5363 113.88 -123.87 104.60 1.0916 +IC CG6 CG4 *CG5 HG51 1.5363 113.37 121.63 109.05 1.1130 +IC CG6 CG4 *CG5 HG52 1.5363 113.37 -121.40 108.53 1.1122 +IC CG6 NG1 CBG HBG1 1.5195 107.66 -53.18 106.80 1.1054 +IC HBG1 NG1 *CBG HBG2 1.1054 106.80 120.32 107.39 1.1012 +IC CG2 NG1 CBG CY 1.5205 117.02 -43.82 108.23 1.4811 +IC NG1 CBG CY CJ2 1.4977 108.23 -74.54 121.06 1.4098 +IC NG1 CBG CY CJ1 1.4977 108.23 108.39 119.67 1.4082 +IC CBG CY CJ1 CK1 1.4811 119.67 177.88 120.36 1.3993 +IC CBG CY CJ2 CK2 1.4811 121.06 -178.43 120.27 1.4006 +IC CY CJ1 CK1 CQ 1.4082 120.36 0.02 120.02 1.4003 +IC CJ1 CK1 CQ CK2 1.3993 120.02 -0.22 120.13 1.4003 +IC CK1 CQ CK2 CJ2 1.4003 120.13 -0.37 120.00 1.4006 +IC CK1 CY *CJ1 HJ1 1.3993 120.36 -179.98 119.89 1.0829 +IC CK2 CY *CJ2 HJ2 1.4006 120.27 179.99 120.44 1.0799 +IC CQ CJ1 *CK1 HK1 1.4003 120.02 179.98 119.90 1.0816 +IC CQ CJ2 *CK2 HK2 1.4003 120.00 179.79 119.85 1.0816 +IC CK1 CK2 *CQ HQ 1.4003 120.13 -179.96 120.17 1.0809 + + +PRES 3MSB 1.00 ! C16H22N2O3 (010206(S)D), cacha +! This compound has 3-methylamine piperidine at gamma position +! and benzyl at alpha position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 +ATOM HT1 HGP1 0.47 ! HG31 HG32 +GROUP ! \ / +ATOM CGT CG321 -0.18 ! OG CG2--NG3 (+1) +ATOM HGT1 HGA2 0.09 ! || / \ +ATOM HGT2 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 +GROUP ! / HT1 \ / +ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 +ATOM HG1 HGA1 0.09 ! \ +GROUP ! O24 CC2 +ATOM CG2 CG324 0.20 ! || / +ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ // \\ +ATOM NG3 NG3P2 -0.40 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP +ATOM HG31 HGP2 0.32 ! / \ | / || \ __ / +ATOM HG32 HGP2 0.32 ! C11 C13---C17 OA1 CD2--CE2 +ATOM CG4 CG324 0.20 ! Me19 | | | +ATOM HG41 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HG42 HGA2 0.09 ! / \|/ \ / \ / +GROUP ! C2 C10 C8 C15 +ATOM CG5 CG321 -0.18 ! | | | +ATOM HG51 HGA2 0.09 ! C3 C5 C7 +ATOM HG52 HGA2 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 ! 3MSB (010206(S)D) +ATOM HG62 HGA2 0.09 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG3 +BOND NG3 HG31 NG3 HG32 NG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +BOND OA2 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5242 109.43 -175.98 116.64 1.4476 +IC CA OA2 CB HB1 1.3349 116.64 -66.79 110.19 1.1154 +IC CA OA2 CB CZ 1.3349 116.64 173.93 113.76 1.5066 +IC CA OA2 CB HB2 1.3349 116.64 52.26 110.81 1.1160 +IC OA2 CB CZ CD2 1.4476 113.76 -121.85 121.23 1.4061 +IC OA2 CB CZ CD1 1.4476 113.76 58.24 119.30 1.4048 +IC CD1 CD2 *CZ CB 1.4048 119.46 -179.91 121.23 1.5066 +IC CD2 CZ CB HB1 1.4061 121.23 116.69 106.33 1.1154 +IC CD2 CZ CB HB2 1.4061 121.23 1.46 107.82 1.1160 +IC CB CZ CD1 CE1 1.5066 119.30 179.43 120.30 1.4015 +IC CB CZ CD2 CE2 1.5066 121.23 -179.39 120.20 1.4017 +IC CZ CD1 CE1 CP 1.4048 120.30 -0.06 119.94 1.4007 +IC CD1 CE1 CP CE2 1.4015 119.94 0.59 120.09 1.4005 +IC CE1 CP CE2 CD2 1.4007 120.09 -0.55 120.00 1.4017 +IC CE1 CZ *CD1 HD1 1.4015 120.30 -179.46 119.80 1.0800 +IC CE2 CZ *CD2 HD2 1.4017 120.20 179.33 120.22 1.0796 +IC CP CD1 *CE1 HE1 1.4007 119.94 -179.52 120.13 1.0809 +IC CP CD2 *CE2 HE2 1.4005 120.00 179.30 120.26 1.0816 +IC CE1 CE2 *CP HP 1.4007 120.09 -179.58 119.77 1.0816 +IC OG CG NT CGT 1.2239 122.72 8.77 127.00 1.4536 +IC CG NT CGT HGT1 1.3478 127.00 -166.41 108.33 1.1149 +IC HGT1 NT *CGT HGT2 1.1149 108.33 -115.07 108.53 1.1163 +IC HGT1 NT *CGT CG1 1.1149 108.33 122.64 117.09 1.5521 +IC NT CGT CG1 HG1 1.4536 117.09 69.36 107.48 1.1153 +IC HG1 CGT *CG1 CG2 1.1153 107.48 -120.14 111.66 1.5358 +IC HG1 CGT *CG1 CG6 1.1153 107.48 117.07 111.60 1.5466 +IC CGT CG1 CG2 NG3 1.5521 111.66 179.38 109.85 1.5116 +IC NG3 CG1 *CG2 HG21 1.5116 109.85 117.59 112.64 1.1015 +IC NG3 CG1 *CG2 HG22 1.5116 109.85 -116.95 113.19 1.1017 +IC CG1 CG2 NG3 CG4 1.5358 109.85 58.38 113.58 1.5084 +IC CG4 CG2 *NG3 HG31 1.5084 113.58 124.95 110.23 1.0062 +IC CG4 CG2 *NG3 HG32 1.5084 113.58 -119.78 107.15 1.0101 +IC CG2 NG3 CG4 CG5 1.5116 113.58 -56.76 109.83 1.5314 +IC CG5 NG3 *CG4 HG41 1.5314 109.83 121.43 105.28 1.1036 +IC CG5 NG3 *CG4 HG42 1.5314 109.83 -122.30 105.71 1.1029 +IC NG3 CG4 CG5 CG6 1.5084 109.83 54.36 110.96 1.5395 +IC CG6 CG4 *CG5 HG51 1.5395 110.96 121.27 109.75 1.1134 +IC CG6 CG4 *CG5 HG52 1.5395 110.96 -120.76 109.94 1.1139 +IC CG5 CG1 *CG6 HG61 1.5395 111.48 -121.73 109.49 1.1129 +IC CG5 CG1 *CG6 HG62 1.5395 111.48 120.99 109.18 1.1142 + + +PRES 3MPS 1.00 ! C7H14N2O (01OH06(S)D), cacha +! This compound has 3-methylamine piperidine at gamma position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 +ATOM HT1 HGP1 0.47 ! HG31 HG32 +GROUP ! \ / +ATOM CGT CG321 -0.18 ! OG CG2--NG3 (+1) +ATOM HGT1 HGA2 0.09 ! || / \ +ATOM HGT2 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 +GROUP ! / HT1 \ / +ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 +ATOM HG1 HGA1 0.09 ! \ +GROUP ! O24 CC2 +ATOM CG2 CG324 0.20 ! || / +ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 +ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ +ATOM NG3 NG3P2 -0.40 ! C12 Me18 C20 C23 NH CA---OA2 +ATOM HG31 HGP2 0.32 ! / \ | / || +ATOM HG32 HGP2 0.32 ! C11 C13---C17 OA1 +ATOM CG4 CG324 0.20 ! Me19 | | | +ATOM HG41 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HG42 HGA2 0.09 ! / \|/ \ / \ / +GROUP ! C2 C10 C8 C15 +ATOM CG5 CG321 -0.18 ! | | | +ATOM HG51 HGA2 0.09 ! C3 C5 C7 +ATOM HG52 HGA2 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 ! 3MPS (01OH06(S)D) +ATOM HG62 HGA2 0.09 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG3 +BOND NG3 HG31 NG3 HG32 NG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 + +IC OG CG NT CGT 1.2256 121.47 0.79 124.59 1.4530 +IC CG NT CGT HGT1 1.3392 124.59 149.80 107.85 1.1137 +IC HGT1 NT *CGT HGT2 1.1137 107.85 -116.73 111.18 1.1160 +IC HGT1 NT *CGT CG1 1.1137 107.85 120.07 112.47 1.5501 +IC NT CGT CG1 HG1 1.4530 112.47 83.79 108.38 1.1140 +IC HG1 CGT *CG1 CG2 1.1140 108.38 -117.58 107.80 1.5302 +IC HG1 CGT *CG1 CG6 1.1140 108.38 121.37 112.80 1.5449 +IC CGT CG1 CG2 NG3 1.5501 107.80 -170.55 116.62 1.5027 +IC NG3 CG1 *CG2 HG21 1.5027 116.62 118.47 110.90 1.1061 +IC NG3 CG1 *CG2 HG22 1.5027 116.62 -118.49 111.67 1.1051 +IC CG1 CG2 NG3 CG4 1.5302 116.62 51.23 112.51 1.4981 +IC CG4 CG2 *NG3 HG31 1.4981 112.51 122.69 105.66 1.0135 +IC CG4 CG2 *NG3 HG32 1.4981 112.51 -123.39 108.44 1.0051 +IC CG2 NG3 CG4 CG5 1.5027 112.51 -54.57 109.73 1.5348 +IC CG5 NG3 *CG4 HG41 1.5348 109.73 121.15 105.11 1.1047 +IC CG5 NG3 *CG4 HG42 1.5348 109.73 -122.63 105.65 1.1024 +IC NG3 CG4 CG5 CG6 1.4981 109.73 58.52 111.11 1.5422 +IC CG6 CG4 *CG5 HG51 1.5422 111.11 120.57 109.36 1.1130 +IC CG6 CG4 *CG5 HG52 1.5422 111.11 -121.30 110.16 1.1129 +IC CG5 CG1 *CG6 HG61 1.5422 112.06 -120.86 108.98 1.1136 +IC CG5 CG1 *CG6 HG62 1.5422 112.06 122.05 109.12 1.1131 + + +PRES 2MRB 1.00 ! C16H22N2O3 (010207(R)D), cacha +! This compound has 2-methylamine piperidine at gamma position +! and benzyl at alpha position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 ! HG21 HG22 +ATOM OG OG2D1 -0.51 ! \ / +ATOM NT NG2S1 -0.47 ! OG (+1)NG2--CG3 +ATOM HT1 HGP1 0.47 ! || / \ +GROUP ! CG---NT--CGT--CG1 CG4 +ATOM CGT CG321 -0.18 ! / HT1 \ / +ATOM HGT1 HGA2 0.09 ! CC3 CG6--CG5 +ATOM HGT2 HGA2 0.09 ! \ +GROUP ! O24 CC2 +ATOM CG1 CG314 0.29 ! || / +ATOM HG1 HGA1 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM NG2 NG3P2 -0.40 ! | \ / \ / \ / \ // \\ +ATOM HG21 HGP2 0.32 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP +ATOM HG22 HGP2 0.32 ! / \ | / || \ __ / +ATOM CG3 CG324 0.20 ! C11 C13---C17 OA1 CD2--CE2 +ATOM HG31 HGA2 0.09 ! Me19 | | | +ATOM HG32 HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CG4 CG321 -0.18 ! C2 C10 C8 C15 +ATOM HG41 HGA2 0.09 ! | | | +ATOM HG42 HGA2 0.09 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CG5 CG321 -0.18 ! HO C4 C6 OH +ATOM HG51 HGA2 0.09 +ATOM HG52 HGA2 0.09 ! 2MRB (010207(R)D) +GROUP +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 NG2 +BOND NG2 HG21 NG2 HG22 NG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +BOND OA2 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5251 109.19 -176.53 116.84 1.4475 +IC CA OA2 CB HB1 1.3348 116.84 -68.03 110.09 1.1153 +IC CA OA2 CB CZ 1.3348 116.84 172.79 113.76 1.5068 +IC CA OA2 CB HB2 1.3348 116.84 51.08 110.88 1.1157 +IC OA2 CB CZ CD2 1.4475 113.76 -124.12 121.29 1.4063 +IC OA2 CB CZ CD1 1.4475 113.76 56.05 119.26 1.4048 +IC CD1 CD2 *CZ CB 1.4048 119.45 -179.83 121.29 1.5068 +IC CD2 CZ CB HB1 1.4063 121.29 114.56 106.29 1.1153 +IC CD2 CZ CB HB2 1.4063 121.29 -0.72 107.81 1.1157 +IC CB CZ CD1 CE1 1.5068 119.26 179.46 120.31 1.4013 +IC CB CZ CD2 CE2 1.5068 121.29 -179.43 120.20 1.4018 +IC CZ CD1 CE1 CP 1.4048 120.31 -0.08 119.94 1.4006 +IC CD1 CE1 CP CE2 1.4013 119.94 0.52 120.09 1.4005 +IC CE1 CP CE2 CD2 1.4006 120.09 -0.49 119.99 1.4018 +IC CE1 CZ *CD1 HD1 1.4013 120.31 -179.47 119.81 1.0801 +IC CE2 CZ *CD2 HD2 1.4018 120.20 179.31 120.24 1.0794 +IC CP CD1 *CE1 HE1 1.4006 119.94 -179.52 120.12 1.0810 +IC CP CD2 *CE2 HE2 1.4005 119.99 179.29 120.29 1.0816 +IC CE1 CE2 *CP HP 1.4006 120.09 -179.60 119.79 1.0814 +IC OG CG NT CGT 1.2258 121.77 -9.07 126.25 1.4608 +IC CG NT CGT HGT1 1.3453 126.25 -63.13 109.68 1.1149 +IC HGT1 NT *CGT HGT2 1.1149 109.68 -114.42 107.29 1.1157 +IC HGT1 NT *CGT CG1 1.1149 109.68 125.80 116.89 1.5520 +IC NT CGT CG1 HG1 1.4608 116.89 35.97 109.62 1.1148 +IC HG1 CGT *CG1 NG2 1.1148 109.62 -115.37 110.19 1.4997 +IC HG1 CGT *CG1 CG6 1.1148 109.62 123.79 114.12 1.5387 +IC CGT CG1 NG2 CG3 1.5520 110.19 177.33 115.54 1.5017 +IC CG3 CG1 *NG2 HG21 1.5017 115.54 122.50 107.57 1.0057 +IC CG3 CG1 *NG2 HG22 1.5017 115.54 -125.48 106.76 1.0184 +IC CG1 NG2 CG3 CG4 1.4997 115.54 58.81 109.20 1.5329 +IC CG4 NG2 *CG3 HG31 1.5329 109.20 122.16 105.67 1.1031 +IC CG4 NG2 *CG3 HG32 1.5329 109.20 -121.59 105.38 1.1034 +IC NG2 CG3 CG4 CG5 1.5017 109.20 -54.65 110.62 1.5388 +IC CG5 CG3 *CG4 HG41 1.5388 110.62 120.78 109.91 1.1136 +IC CG5 CG3 *CG4 HG42 1.5388 110.62 -121.22 109.75 1.1132 +IC CG3 CG4 CG5 CG6 1.5329 110.62 54.76 111.04 1.5388 +IC CG6 CG4 *CG5 HG51 1.5388 111.04 121.50 109.70 1.1146 +IC CG6 CG4 *CG5 HG52 1.5388 111.04 -121.04 109.48 1.1142 +IC CG5 CG1 *CG6 HG61 1.5388 112.23 -121.77 109.64 1.1131 +IC CG5 CG1 *CG6 HG62 1.5388 112.23 120.96 109.15 1.1133 + + +PRES 2MPR 1.00 ! C7H14N2O (01OH07(R)D), cacha +! This compound has 3-methylamine piperidine at gamma position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 ! HG31 HG32 +ATOM HT1 HGP1 0.47 ! \ / +GROUP ! OG (+1) NG2--CG3 +ATOM CGT CG321 -0.18 ! || / \ +ATOM HGT1 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 +ATOM HGT2 HGA2 0.09 ! / HT1 \ / +GROUP ! CC3 CG6--CG5 +ATOM CG1 CG314 0.29 ! \ +ATOM HG1 HGA1 0.09 ! O24 CC2 +ATOM NG2 NG3P2 -0.40 ! || / +ATOM HG21 HGP2 0.32 ! H Me21 C22 C24 CC1 +ATOM HG22 HGP2 0.32 ! | \ / \ / \ / \ +ATOM CG3 CG324 0.20 ! C12 Me18 C20 C23 NH CA---OA2 +ATOM HG31 HGA2 0.09 ! / \ | / || +ATOM HG32 HGA2 0.09 ! C11 C13---C17 OA1 +GROUP ! Me19 | | | +ATOM CG4 CG321 -0.18 ! C1 | C9 C14 C16 +ATOM HG41 HGA2 0.09 ! / \|/ \ / \ / +ATOM HG42 HGA2 0.09 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM CG5 CG321 -0.18 ! C3 C5 C7 +ATOM HG51 HGA2 0.09 ! / \ / \ / \ +ATOM HG52 HGA2 0.09 ! HO C4 C6 OH +GROUP +ATOM CG6 CG321 -0.18 ! 2MPR (01OH07(R)D) +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 NG2 +BOND NG2 HG21 NG2 HG22 NG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 + +IC OG CG NT CGT 1.2249 120.85 2.25 124.27 1.4568 +IC CG NT CGT HGT1 1.3396 124.27 30.47 110.37 1.1163 +IC HGT1 NT *CGT HGT2 1.1163 110.37 -116.64 108.59 1.1139 +IC HGT1 NT *CGT CG1 1.1163 110.37 122.29 114.28 1.5472 +IC NT CGT CG1 HG1 1.4568 114.28 59.06 109.88 1.1157 +IC HG1 CGT *CG1 NG2 1.1157 109.88 -114.17 109.66 1.4973 +IC HG1 CGT *CG1 CG6 1.1157 109.88 124.35 113.41 1.5401 +IC CGT CG1 NG2 CG3 1.5472 109.66 -178.06 116.32 1.5005 +IC CG3 CG1 *NG2 HG21 1.5005 116.32 127.76 109.81 1.0015 +IC CG3 CG1 *NG2 HG22 1.5005 116.32 -119.58 107.88 1.0283 +IC CG1 NG2 CG3 CG4 1.4973 116.32 55.95 110.16 1.5319 +IC CG4 NG2 *CG3 HG31 1.5319 110.16 123.18 105.12 1.1032 +IC CG4 NG2 *CG3 HG32 1.5319 110.16 -121.78 104.60 1.1046 +IC NG2 CG3 CG4 CG5 1.5005 110.16 -54.81 110.24 1.5379 +IC CG5 CG3 *CG4 HG41 1.5379 110.24 120.63 109.71 1.1131 +IC CG5 CG3 *CG4 HG42 1.5379 110.24 -121.15 109.61 1.1124 +IC CG3 CG4 CG5 CG6 1.5319 110.24 56.12 110.68 1.5379 +IC CG6 CG4 *CG5 HG51 1.5379 110.68 121.42 109.84 1.1137 +IC CG6 CG4 *CG5 HG52 1.5379 110.68 -120.66 109.46 1.1142 +IC CG5 CG1 *CG6 HG61 1.5379 112.67 -121.48 109.11 1.1130 +IC CG5 CG1 *CG6 HG62 1.5379 112.67 121.55 108.86 1.1125 + + + +!End of Pablo's compounds +!Start of Rana's and Swan's compounds + +RESI 2AMP 0.00 ! C7H8N2O 2-acetamide pyridine, cacha +! Made in order to build Polli's compounds (Rana & Swan) +GROUP +ATOM NZ NG2R60 -0.600 +GROUP +ATOM CE1 CG2R64 0.600 ! O NZ---CE2 +GROUP ! || // \\ +ATOM CD1 CG2R61 -0.115 ! CM--C--NE--CE1 CD2 +ATOM HD1 HGR61 0.115 ! | \ ___ / +GROUP ! HE CD1---CG +ATOM CE2 CG2R61 0.180 +ATOM HE2 HGR62 0.120 ! 2AMP +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 +GROUP +ATOM NE NG2S1 -0.620 +ATOM HE HGP1 0.320 +ATOM C CG2O1 0.550 +ATOM O OG2D1 -0.550 +ATOM CM CG331 -0.27 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND CG HG CG CD1 CD1 HD1 CD1 CE1 CE1 NZ +BOND NZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CG +BOND CE1 NE NE HE NE C C O +BOND C CM CM HM1 CM HM2 CM HM3 +IMPR C CM NE O +IMPR CE1 CD1 NZ NE + +IC CG CD1 CE1 NZ 1.4062 118.77 0.00 121.31 1.3330 +IC CD1 CE1 NZ CE2 1.4051 121.31 0.00 120.60 1.3284 +IC CE1 NZ CE2 CD2 1.3330 120.60 0.00 122.45 1.4013 +IC CD1 CD2 *CG HG 1.4062 118.83 -180.00 120.71 1.0807 +IC CE1 CG *CD1 HD1 1.4051 118.77 180.00 119.96 1.0752 +IC CE2 CG *CD2 HD2 1.4013 118.04 -180.00 121.24 1.0783 +IC NZ CD1 *CE1 NE 1.3330 121.31 -180.00 127.83 1.3987 +IC NZ CD2 *CE2 HE2 1.3284 122.45 -180.00 122.15 1.0814 +IC CD1 CE1 NE C 1.4051 127.83 0.00 128.89 1.3256 +IC C CE1 *NE HE 1.3256 128.89 180.00 109.18 0.9866 +IC CE1 NE C CM 1.3987 128.89 180.00 115.52 1.4775 +IC CM NE *C O 1.4775 115.52 -180.00 123.87 1.2197 +IC O C CM HM1 1.2197 120.61 119.56 110.14 1.1102 +IC O C CM HM2 1.2197 120.61 0.00 109.25 1.1117 +IC O C CM HM3 1.2197 120.61 -119.56 110.14 1.1102 + +RESI 3AMP 0.00 ! C7H8N2O 3-acetamide pyridine, cacha +! Made in order to build Polli's compounds (Rana & Swan) +! Taken from Acetamide and 4-Amino pyridine +GROUP +ATOM NZ NG2R60 -0.600 +GROUP +ATOM CE1 CG2R61 0.180 +ATOM HE1 HGR62 0.120 ! O CE1--NZ +GROUP ! || // \\ +ATOM CE2 CG2R61 0.180 ! CM--C--ND--CD1 CE2 +ATOM HE2 HGR62 0.120 ! | \ ___ / +GROUP ! HD CG---CD2 +ATOM CD1 CG2R61 0.300 +GROUP ! 3AMP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 +GROUP +ATOM ND NG2S1 -0.620 +ATOM HD HGP1 0.320 +ATOM C CG2O1 0.550 +ATOM O OG2D1 -0.550 +ATOM CM CG331 -0.27 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND CG HG CG CD1 CD1 CE1 CE1 HE1 CE1 NZ +BOND NZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CG +BOND CD1 ND ND HD ND C C O +BOND C CM CM HM1 CM HM2 CM HM3 +IMPR C CM ND O + +IC CG CD1 CE1 NZ 1.4078 116.24 0.00 123.96 1.3381 +IC CD1 CE1 NZ CE2 1.4129 123.96 0.00 118.93 1.3292 +IC CE1 NZ CE2 CD2 1.3381 118.93 0.00 122.82 1.4035 +IC CD1 CD2 *CG HG 1.4078 120.04 -180.00 120.23 1.0783 +IC CE1 CG *CD1 ND 1.4129 116.24 -180.00 116.49 1.4213 +IC CE2 CG *CD2 HD2 1.4035 118.00 180.00 121.42 1.0782 +IC NZ CD1 *CE1 HE1 1.3381 123.96 180.00 121.22 1.0791 +IC NZ CD2 *CE2 HE2 1.3292 122.82 -180.00 122.14 1.0813 +IC CE1 CD1 ND C 1.4129 127.27 0.00 126.90 1.3351 +IC C CD1 *ND HD 1.3351 126.90 -180.00 115.12 0.9890 +IC CD1 ND C CM 1.4213 126.90 -180.00 115.67 1.4776 +IC CM ND *C O 1.4776 115.67 180.00 123.60 1.2198 +IC O C CM HM1 1.2198 120.73 119.43 110.22 1.1101 +IC O C CM HM2 1.2198 120.73 0.00 109.14 1.1120 +IC O C CM HM3 1.2198 120.73 -119.43 110.22 1.1101 + +RESI 2AMF 0.00 ! C8H9NO2 2-acetamide phenol, cacha +! Made in order to build Polli's compounds (Rana & Swan) + +GROUP +ATOM CM CG331 -0.27 ! O CD2--CE2 +ATOM HM1 HGA3 0.09 ! || // \\ +ATOM HM2 HGA3 0.09 ! CM--C--N---CZ CP +ATOM HM3 HGA3 0.09 ! | \ ___ / +GROUP ! H CD1---CE2 +ATOM C CG2O1 0.52 ! | +ATOM O OG2D1 -0.52 ! OH(D) +GROUP +ATOM N NG2S1 -0.47 ! 2AMF +ATOM H HGP1 0.33 +ATOM CZ CG2R61 0.14 +GROUP +ATOM CD1 CG2R61 0.11 +ATOM OD OG311 -0.53 +ATOM HOD HGP1 0.42 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 + +BOND CM HM1 CM HM2 CM HM3 CM C +BOND C O C N N H N CZ +BOND CZ CD1 CD1 OD OD HOD CD1 CE1 CE1 HE1 CE1 CP +BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +IMPR C CM N O + +IC N C CM HM1 1.3407 115.20 180.00 109.20 1.1118 +IC HM1 C *CM HM2 1.1118 109.20 119.48 110.20 1.1102 +IC HM1 C *CM HM3 1.1118 109.20 -119.48 110.20 1.1102 +IC N CM *C O 1.3407 115.20 -180.00 119.94 1.2226 +IC CM C N CZ 1.4807 115.20 -180.00 130.65 1.4232 +IC CZ C *N H 1.4232 130.65 180.00 118.72 0.9928 +IC C N CZ CD1 1.3407 130.65 180.00 115.77 1.4149 +IC CD1 N *CZ CD2 1.4149 115.77 -180.00 125.20 1.4017 +IC N CZ CD1 CE1 1.4232 115.77 -180.00 120.37 1.4002 +IC CE1 CZ *CD1 OD 1.4002 120.37 180.00 120.75 1.4188 +IC CZ CD1 OD HOD 1.4149 120.75 -180.00 107.60 0.9602 +IC CZ CD1 CE1 CP 1.4149 120.37 0.00 120.00 1.4013 +IC CP CD1 *CE1 HE1 1.4013 120.00 180.00 120.56 1.0796 +IC CD1 CE1 CP CE2 1.4002 120.00 0.00 119.97 1.3995 +IC CE2 CE1 *CP HP 1.3995 119.97 180.00 120.14 1.0810 +IC CD2 CP *CE2 HE2 1.4022 120.11 180.00 120.11 1.0811 +IC CE2 CZ *CD2 HD2 1.4022 120.52 180.00 120.79 1.0784 +IC HM1 C *CM HM2 1.1118 109.20 119.48 110.20 1.1102 +IC HM1 C *CM HM3 1.1118 109.20 -119.48 110.20 1.1102 +IC HM1 CM C N 1.1118 109.20 180.00 115.20 1.3407 +IC N CM *C O 1.3407 115.20 -180.00 119.94 1.2226 +IC CM C N CZ 1.4807 115.20 -180.00 130.65 1.4232 +IC CZ C *N H 1.4232 130.65 180.00 118.72 0.9928 +IC C N CZ CD1 1.3407 130.65 180.00 115.77 1.4149 +IC CD1 N *CZ CD2 1.4149 115.77 -180.00 125.20 1.4017 +IC N CZ CD1 CE1 1.4232 115.77 -180.00 120.37 1.4002 +IC CE1 CZ *CD1 OD 1.4002 120.37 180.00 120.75 1.4188 +IC CZ CD1 OD HOD 1.4149 120.75 -180.00 107.60 0.9602 +IC CZ CD1 CE1 CP 1.4149 120.37 0.00 120.00 1.4013 +IC CP CD1 *CE1 HE1 1.4013 120.00 180.00 120.56 1.0796 +IC CD1 CE1 CP CE2 1.4002 120.00 0.00 119.97 1.3995 +IC CE2 CE1 *CP HP 1.3995 119.97 180.00 120.14 1.0810 +IC CD2 CP *CE2 HE2 1.4022 120.11 180.00 120.11 1.0811 +IC CE2 CZ *CD2 HD2 1.4022 120.52 180.00 120.79 1.0784 + + + +PRES 2APP 0.00 ! C16H15N2O3 Alpha-Benzyl Gamma-2-Amino Pyridine GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 ! CJ1--CK1 +ATOM HC3B HGA2 0.09 ! // \\ +GROUP ! OA1 CY CJ +ATOM CG CG2O1 0.52 ! | / \ __ / +ATOM OG OG2D1 -0.52 ! O24 CA--OA2---CB CJ2--CK2 +GROUP ! || | +ATOM NG NG2S1 -0.47 ! OH Me21 C22 C24 CC1 CC3 NG NZ---CE2 +ATOM HG HGP1 0.33 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM CZ CG2R64 0.44 ! C12 Me18 C20 C23 NH CC2 CG CZ CP +GROUP ! / \ | / || \ __ / +ATOM CD1 CG2R61 -0.115 ! C11 C13---C17 OG CD1--CE1 +ATOM HD1 HGR61 0.115 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CE1 CG2R61 -0.115 ! / \|/ \ / \ / +ATOM HE1 HGR61 0.115 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM NZ NG2R60 -0.600 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CE2 CG2R61 0.180 ! HO C4 C6 OH +ATOM HE2 HGR62 0.120 +GROUP ! 2APP +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CG OG CG NG NG HG NG CZ +BOND CZ NZ NZ CE2 CE2 HE2 CE2 CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 NG OG +IMPR CZ CD1 NZ NG + +IC CC1 CA OA2 CB 1.5262 109.01 178.05 116.10 1.4465 +IC HB1 CB OA2 CA 1.1154 110.02 65.56 116.10 1.3439 +IC HB2 CB OA2 CA 1.1163 110.83 -53.21 116.10 1.3439 +IC CY CB OA2 CA 1.5059 113.59 -172.68 116.10 1.3439 +IC CJ2 CY CB OA2 1.4053 121.33 -117.38 113.59 1.4465 +IC CJ1 CY CB OA2 1.4046 119.17 62.26 113.59 1.4465 +IC CJ1 CJ2 *CY CB 1.4046 119.50 179.63 121.33 1.5059 +IC CJ2 CY CB HB1 1.4053 121.33 5.26 108.43 1.1154 +IC CJ2 CY CB HB2 1.4053 121.33 120.54 106.20 1.1163 +IC CB CY CJ1 CK1 1.5059 119.17 180.00 120.30 1.4013 +IC CB CY CJ2 CK2 1.5059 121.33 -179.83 120.18 1.4021 +IC CY CJ1 CK1 CQ 1.4046 120.30 -0.04 119.97 1.4011 +IC CJ1 CK1 CQ CK2 1.4013 119.97 0.26 120.01 1.4014 +IC CK1 CQ CK2 CJ2 1.4011 120.01 -0.08 120.03 1.4021 +IC CK1 CY *CJ1 HJ1 1.4013 120.30 -179.72 119.65 1.0800 +IC CK2 CY *CJ2 HJ2 1.4021 120.18 179.57 120.00 1.0798 +IC CQ CJ1 *CK1 HK1 1.4011 119.97 -179.63 120.04 1.0806 +IC CQ CJ2 *CK2 HK2 1.4014 120.03 179.68 120.00 1.0809 +IC CK1 CK2 *CQ HQ 1.4011 120.01 179.51 120.01 1.0810 +IC CC2 CC3 CG NG 1.5506 112.89 -51.60 116.27 1.3339 +IC NG CC3 *CG OG 1.3339 116.27 -171.32 119.51 1.2231 +IC CG CZ *NG HG 1.3339 129.72 179.61 108.48 0.9872 +IC CC3 CG NG CZ 1.4983 116.27 -177.09 129.72 1.4019 +IC CG NG CZ CD1 1.3339 129.72 -1.35 127.25 1.4046 +IC NG CZ CD1 CE1 1.4019 127.25 -179.67 118.62 1.4059 +IC CZ CD1 CE1 CP 1.4046 118.62 0.11 118.91 1.4033 +IC CD1 CE1 CP CE2 1.4059 118.91 0.05 118.00 1.4015 +IC CE1 CP CE2 NZ 1.4033 118.00 0.00 122.46 1.3291 +IC CZ CE1 *CD1 HD1 1.4046 118.62 -179.85 120.00 1.0758 +IC CD1 CP *CE1 HE1 1.4059 118.91 -179.93 120.66 1.0804 +IC CE1 CE2 *CP HP 1.4033 118.00 -179.93 120.73 1.0781 +IC CP NZ *CE2 HE2 1.4015 122.46 -179.90 115.36 1.0811 + + +PRES 3APP 0.00 ! C16H15N2O3 Alpha-Benzyl Gamma-3-Amino Pyridine GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! CJ1--CK1 +ATOM HC3A HGA2 0.09 ! // \\ +ATOM HC3B HGA2 0.09 ! OA1 CY CJ +GROUP ! | / \ __ / +ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 +ATOM OG OG2D1 -0.52 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OG CD1--CE1 +ATOM CD1 CG2R61 -0.115 ! Me19 | | | +ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CE1 CG2R61 -0.115 ! C2 C10 C8 C15 +ATOM HE1 HGR61 0.115 ! | | | +GROUP ! C3 C5 C7 +ATOM CP CG2R61 0.180 ! / \ / \ / \ +ATOM HP HGR62 0.120 ! HO C4 C6 OH +GROUP +ATOM NZ NG2R60 -0.600 ! 3APP +GROUP +ATOM CD2 CG2R61 0.180 +ATOM HD2 HGR62 0.120 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 CD2 NZ NZ CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 NG OG + +IC CC1 CA OA2 CB 1.5266 108.91 178.06 116.23 1.4463 +IC HC1 CC1 CA OA2 1.1142 106.59 -130.75 108.91 1.3434 +IC HB1 CB OA2 CA 1.1155 110.00 65.28 116.23 1.3434 +IC HB2 CB OA2 CA 1.1162 110.85 -53.55 116.23 1.3434 +IC CY CB OA2 CA 1.5060 113.54 -173.02 116.23 1.3434 +IC CJ2 CY CB OA2 1.4052 121.32 -119.04 113.54 1.4463 +IC CJ1 CY CB OA2 1.4048 119.18 60.58 113.54 1.4463 +IC CJ1 CJ2 *CY CB 1.4048 119.50 179.62 121.32 1.5060 +IC CJ2 CY CB HB1 1.4052 121.32 3.54 108.43 1.1155 +IC CJ2 CY CB HB2 1.4052 121.32 118.88 106.21 1.1162 +IC CB CY CJ1 CK1 1.5060 119.18 -179.91 120.31 1.4013 +IC CB CY CJ2 CK2 1.5060 121.32 -179.85 120.18 1.4020 +IC CY CJ1 CK1 CQ 1.4048 120.31 -0.14 119.96 1.4010 +IC CJ1 CK1 CQ CK2 1.4013 119.96 0.31 120.01 1.4014 +IC CK1 CQ CK2 CJ2 1.4010 120.01 -0.07 120.03 1.4020 +IC CK1 CY *CJ1 HJ1 1.4013 120.31 -179.69 119.67 1.0799 +IC CK2 CY *CJ2 HJ2 1.4020 120.18 179.59 120.02 1.0799 +IC CQ CJ1 *CK1 HK1 1.4010 119.96 -179.53 120.06 1.0806 +IC CQ CJ2 *CK2 HK2 1.4014 120.03 179.71 119.99 1.0809 +IC CK1 CK2 *CQ HQ 1.4010 120.01 179.51 120.00 1.0810 +IC CC2 CC3 CG NG 1.5518 114.60 -1.21 117.28 1.3433 +IC CG CZ *NG HG 1.3433 128.03 179.74 114.63 0.9895 +IC NG CC3 *CG OG 1.3433 117.28 179.83 119.35 1.2229 +IC CC3 CG NG CZ 1.5020 117.28 -180.00 128.03 1.4225 +IC CG NG CZ CD2 1.3433 128.03 0.97 126.45 1.4111 +IC NG CZ CD2 NZ 1.4225 126.45 -179.92 123.66 1.3358 +IC CZ CD2 NZ CP 1.4111 123.66 0.08 119.08 1.3292 +IC CD2 NZ CP CE1 1.3358 119.08 0.01 122.82 1.4031 +IC NZ CP CE1 CD1 1.3292 122.82 -0.03 118.00 1.4059 +IC CZ NZ *CD2 HD2 1.4111 123.66 179.94 114.79 1.0796 +IC CZ CE1 *CD1 HD1 1.4072 119.79 179.97 120.05 1.0788 +IC NZ CE1 *CP HP 1.3292 122.82 -179.97 122.13 1.0811 +IC CP CD1 *CE1 HE1 1.4031 118.00 -179.98 121.40 1.0780 + + +PRES 4APP 0.00 ! C16H15N2O3 Alpha-Benzyl Gamma-4-Amino Pyridine GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! CJ1--CK1 +ATOM HC3A HGA2 0.09 ! // \\ +ATOM HC3B HGA2 0.09 ! OA1 CY CJ +GROUP ! | / \ __ / +ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 +ATOM OG OG2D1 -0.52 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 +ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ NZ +ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OG CD1--CE1 +ATOM CD1 CG2R61 -0.115 ! Me19 | | | +ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CE1 CG2R61 0.180 ! C2 C10 C8 C15 +ATOM HE1 HGR62 0.120 ! | | | +GROUP ! C3 C5 C7 +ATOM NZ NG2R60 -0.600 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM CE2 CG2R61 0.180 +ATOM HE2 HGR62 0.120 ! 4APP +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 NZ +BOND NZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 NG OG + +IC CC1 CA OA2 CB 1.5239 109.11 -178.78 115.31 1.4471 +IC HC1 CC1 CA OA2 1.1142 106.36 -134.92 109.11 1.3428 +IC HB1 CB OA2 CA 1.1164 110.53 59.14 115.31 1.3428 +IC HB2 CB OA2 CA 1.1163 110.59 -59.32 115.31 1.3428 +IC CY CB OA2 CA 1.5039 113.58 179.91 115.31 1.3428 +IC CJ2 CY CB OA2 1.4046 120.24 -90.36 113.58 1.4471 +IC CJ1 CY CB OA2 1.4046 120.15 88.42 113.58 1.4471 +IC CJ1 CJ2 *CY CB 1.4046 119.59 178.79 120.24 1.5039 +IC CJ2 CY CB HB1 1.4046 120.24 32.16 107.39 1.1164 +IC CJ2 CY CB HB2 1.4046 120.24 147.07 107.36 1.1163 +IC CB CY CJ1 CK1 1.5039 120.15 -179.79 120.20 1.4015 +IC CB CY CJ2 CK2 1.5039 120.24 179.88 120.19 1.4014 +IC CY CJ1 CK1 CQ 1.4046 120.20 0.22 119.97 1.4011 +IC CJ1 CK1 CQ CK2 1.4015 119.97 0.48 120.05 1.4013 +IC CK1 CQ CK2 CJ2 1.4011 120.05 -0.39 119.98 1.4014 +IC CK1 CY *CJ1 HJ1 1.4015 120.20 -179.58 119.84 1.0799 +IC CK2 CY *CJ2 HJ2 1.4014 120.19 179.62 119.87 1.0801 +IC CQ CJ1 *CK1 HK1 1.4011 119.97 -179.63 120.04 1.0807 +IC CQ CJ2 *CK2 HK2 1.4013 119.98 179.84 119.99 1.0807 +IC CK1 CK2 *CQ HQ 1.4011 120.05 -179.99 119.97 1.0807 +IC CC2 CC3 CG NG 1.5519 114.52 13.37 116.90 1.3446 +IC CG CZ *NG HG 1.3446 129.26 179.52 114.04 0.9891 +IC NG CC3 *CG OG 1.3446 116.90 179.10 119.13 1.2233 +IC CC3 CG NG CZ 1.5018 116.90 -179.26 129.26 1.4198 +IC CG NG CZ CD1 1.3446 129.26 13.81 125.21 1.4032 +IC NG CZ CD1 CE1 1.4198 125.21 -179.01 118.21 1.4006 +IC CZ CD1 CE1 NZ 1.4032 118.21 0.20 122.53 1.3294 +IC CD1 CE1 NZ CE2 1.4006 122.53 0.20 119.84 1.3282 +IC CE1 NZ CE2 CD2 1.3294 119.84 -0.22 122.41 1.4002 +IC CE1 CZ *CD1 HD1 1.4006 118.21 -179.44 122.09 1.0759 +IC CE2 CZ *CD2 HD2 1.4002 118.32 -179.68 121.19 1.0764 +IC NZ CD1 *CE1 HE1 1.3294 122.53 180.00 122.17 1.0810 +IC NZ CD2 *CE2 HE2 1.3282 122.41 -179.87 122.39 1.0812 + + +PRES 2APD 0.00 ! C7H7N2O Gamma-2-Amino Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CM3 NG NZ---CE2 +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CGP CZ CP +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OGP CD1--CE1 +ATOM CZ CG2R64 0.44 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM NZ NG2R60 -0.600 ! / \|/ \ / \ / +GROUP ! C2 C10 C8 C15 +ATOM CE2 CG2R61 0.180 ! | | | +ATOM HE2 HGR62 0.120 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 -0.115 ! HO C4 C6 OH +ATOM HP HGR61 0.115 +GROUP ! 2APD +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR62 0.115 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ NZ NZ CE2 CE2 HE2 CE2 CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG +IMPR CZ CD1 NZ NG + +IC CC2 CC3 CG NG 1.5492 112.40 -59.01 115.58 1.3349 +IC CG CZ *NG HG 1.3349 129.91 179.75 110.72 0.9908 +IC NG CC3 *CG OG 1.3349 115.58 -178.53 120.70 1.2263 +IC CC3 CG NG CZ 1.4933 115.58 179.53 129.91 1.4027 +IC CG NG CZ CD1 1.3349 129.91 -0.74 126.80 1.4060 +IC NG CZ CD1 CE1 1.4027 126.80 -179.83 118.92 1.4057 +IC CZ CD1 CE1 CP 1.4060 118.92 0.05 118.91 1.4029 +IC CD1 CE1 CP CE2 1.4057 118.91 0.03 117.98 1.4010 +IC CE1 CP CE2 NZ 1.4029 117.98 0.00 122.23 1.3271 +IC CZ CE1 *CD1 HD1 1.4060 118.92 -179.87 119.87 1.0753 +IC CD1 CP *CE1 HE1 1.4057 118.91 -179.95 120.76 1.0796 +IC CE1 CE2 *CP HP 1.4029 117.98 -179.95 120.75 1.0774 +IC CP NZ *CE2 HE2 1.4010 122.23 -179.94 115.28 1.0808 + + +PRES 3APD 0.00 ! C7H7N2O Gamma-3-Amino Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CM3 NG CD2---NZ +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CGP CZ CP +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OGP CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CD2 CG2R61 0.180 ! / \|/ \ / \ / +ATOM HD2 HGR62 0.120 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM NZ NG2R60 -0.600 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 0.180 ! HO C4 C6 OH +ATOM HP HGR62 0.120 +GROUP ! 3APD +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR62 0.115 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 CD2 NZ NZ CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5535 114.91 -48.02 117.54 1.3422 +IC CG CZ *NG HG 1.3422 128.46 -179.57 113.64 1.0156 +IC NG CC3 *CG OG 1.3422 117.54 -179.06 119.46 1.2281 +IC CC3 CG NG CZ 1.5030 117.54 -179.13 128.46 1.4197 +IC CG NG CZ CD2 1.3422 128.46 -3.17 126.55 1.4108 +IC NG CZ CD2 NZ 1.4197 126.55 179.85 124.13 1.3390 +IC CZ CD2 NZ CP 1.4108 124.13 -0.43 118.24 1.3305 +IC CD2 NZ CP CE1 1.3390 118.24 0.10 123.37 1.4034 +IC NZ CP CE1 CD1 1.3305 123.37 0.07 117.85 1.4044 +IC CZ NZ *CD2 HD2 1.4108 124.13 -179.72 114.91 1.0790 +IC CZ CE1 *CD1 HD1 1.4056 119.87 -179.90 120.63 1.0809 +IC NZ CE1 *CP HP 1.3305 123.37 179.97 121.76 1.0804 +IC CP CD1 *CE1 HE1 1.4034 117.85 179.97 121.01 1.0770 + + +PRES 4APD 0.00 ! C7H7N2O Gamma-4-Amino Pyridine GA CDCA Amide (alpha-deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ NZ +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CD1 CG2R61 -0.115 ! / \|/ \ / \ / +ATOM HD1 HGR61 0.115 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM CE1 CG2R61 0.180 ! C3 C5 C7 +ATOM HE1 HGR62 0.120 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM NZ NG2R60 -0.600 +GROUP ! 4APD +ATOM CE2 CG2R61 0.180 +ATOM HE2 HGR62 0.120 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 NZ +BOND NZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5535 114.98 -47.60 117.27 1.3441 +IC CG CZ *NG HG 1.3441 129.78 -179.11 112.90 1.0148 +IC NG CC3 *CG OG 1.3441 117.27 -178.79 119.11 1.2283 +IC CC3 CG NG CZ 1.5032 117.27 -179.47 129.78 1.4177 +IC CG NG CZ CD1 1.3441 129.78 -75.00 125.48 1.4027 +IC NG CZ CD1 CE1 1.4177 125.48 178.96 118.11 1.4012 +IC CZ CD1 CE1 NZ 1.4027 118.11 -0.21 123.10 1.3307 +IC CD1 CE1 NZ CE2 1.4012 123.10 -0.04 118.95 1.3315 +IC CE1 NZ CE2 CD2 1.3307 118.95 -0.04 122.87 1.3990 +IC CE1 CZ *CD1 HD1 1.4012 118.11 179.50 121.85 1.0751 +IC CE2 CZ *CD2 HD2 1.3990 118.37 179.96 120.58 1.0785 +IC NZ CD1 *CE1 HE1 1.3307 123.10 -179.94 121.79 1.0804 +IC NZ CD2 *CE2 HE2 1.3315 122.87 179.77 121.77 1.0804 + +PRES 2AFP 0.00 ! C17H16NO4 Alpha-Benzyl Gamma-2-Amino Phenol GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! CJ1--CK1 +ATOM HC3A HGA2 0.09 ! // \\ +ATOM HC3B HGA2 0.09 ! OA1 CY CJ +GROUP ! | / \ __ / +ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 +ATOM OG OG2D1 -0.52 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 +ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OG CD1--CE1 +ATOM CD1 CG2R61 0.11 ! Me19 | | | | +ATOM OD OG311 -0.53 ! C1 | C9 C14 C16 OH(D) +ATOM HOD HGP1 0.42 ! / \|/ \ / \ / +GROUP ! C2 C10 C8 C15 +ATOM CE1 CG2R61 -0.115 ! | | | +ATOM HE1 HGR61 0.115 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 -0.115 ! HO C4 C6 OH +ATOM HP HGR61 0.115 +GROUP ! 2AFP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 OD OD HOD CD1 CE1 CE1 HE1 CE1 CP +BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 NG OG + +IC CC1 CA OA2 CB 1.5213 109.18 176.21 116.81 1.4508 +IC HC1 CC1 CA OA2 1.1144 106.26 -147.37 109.18 1.3426 +IC HB1 CB OA2 CA 1.1133 108.22 148.39 116.81 1.3426 +IC HB2 CB OA2 CA 1.1175 112.74 32.40 116.81 1.3426 +IC CY CB OA2 CA 1.5072 114.91 -92.05 116.81 1.3426 +IC CJ2 CY CB OA2 1.4049 120.41 -89.66 114.91 1.4508 +IC CJ1 CY CB OA2 1.4040 119.97 89.00 114.91 1.4508 +IC CJ1 CJ2 *CY CB 1.4040 119.61 178.67 120.41 1.5072 +IC CJ2 CY CB HB1 1.4049 120.41 30.54 107.06 1.1133 +IC CJ2 CY CB HB2 1.4049 120.41 143.47 108.08 1.1175 +IC CB CY CJ1 CK1 1.5072 119.97 -179.11 120.21 1.4011 +IC CB CY CJ2 CK2 1.5072 120.41 179.16 120.17 1.4015 +IC CY CJ1 CK1 CQ 1.4040 120.21 0.12 119.97 1.4012 +IC CJ1 CK1 CQ CK2 1.4011 119.97 0.14 120.06 1.4013 +IC CK1 CQ CK2 CJ2 1.4012 120.06 -0.07 119.97 1.4015 +IC CK1 CY *CJ1 HJ1 1.4011 120.21 179.64 119.77 1.0808 +IC CK2 CY *CJ2 HJ2 1.4015 120.17 179.97 119.92 1.0795 +IC CQ CJ1 *CK1 HK1 1.4012 119.97 179.91 119.96 1.0806 +IC CQ CJ2 *CK2 HK2 1.4013 119.97 -179.99 120.08 1.0805 +IC CK1 CK2 *CQ HQ 1.4012 120.06 -179.91 120.01 1.0806 +IC CC2 CC3 CG NG 1.5538 115.11 -15.46 117.38 1.3413 +IC CG CZ *NG HG 1.3413 130.29 178.93 113.17 0.9900 +IC HG NG CG OG 0.9900 116.53 176.72 123.61 1.2237 +IC CC3 CG NG CZ 1.5004 117.38 175.23 130.29 1.4278 +IC CG NG CZ CD1 1.3413 130.29 -22.14 127.51 1.4180 +IC NG CZ CD1 OD 1.4278 127.51 -0.04 124.65 1.4137 +IC CZ CD1 OD HOD 1.4180 124.65 20.40 106.30 0.9750 +IC NG CZ CD1 CE1 1.4278 127.51 -178.75 119.88 1.4002 +IC CZ CD1 CE1 CP 1.4180 119.88 -0.93 120.65 1.3996 +IC CD1 CE1 CP CE2 1.4002 120.65 0.22 119.87 1.3982 +IC CE1 CP CE2 CD2 1.3996 119.87 0.26 119.87 1.3997 +IC CD1 CD2 *CP HP 2.4326 60.10 179.91 150.25 1.0810 +IC CE2 CZ *CD2 HD2 1.3997 120.98 -179.92 119.69 1.0796 +IC CP CD1 *CE1 HE1 1.3996 120.65 -179.71 119.51 1.0809 +IC CP CD2 *CE2 HE2 1.3982 119.87 -179.89 120.17 1.0811 + +PRES 3AFP 0.00 ! C17H16NO4 Alpha-Benzyl Gamma-3-Amino Phenol GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! CJ1--CK1 +ATOM HC3A HGA2 0.09 ! // \\ +ATOM HC3B HGA2 0.09 ! OA1 CY CJ +GROUP ! | / \ __ / +ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 +ATOM OG OG2D1 -0.52 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 +ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OG CD1--CE1 +ATOM CD1 CG2R61 -0.115 ! Me19 | | | | +ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 OH(E) +GROUP ! / \|/ \ / \ / +ATOM CE1 CG2R61 0.11 ! C2 C10 C8 C15 +ATOM OE OG311 -0.53 ! | | | +ATOM HOE HGP1 0.42 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 -0.115 ! HO C4 C6 OH +ATOM HP HGR61 0.115 +GROUP ! 3AFP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 OE OE HOE CE1 CP +BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 NG OG + +IC CC1 CA OA2 CB 1.5213 109.19 176.53 116.82 1.4508 +IC HC1 CC1 CA OA2 1.1144 106.19 -147.97 109.19 1.3424 +IC HB1 CB OA2 CA 1.1133 108.20 148.28 116.82 1.3424 +IC HB2 CB OA2 CA 1.1175 112.72 32.34 116.82 1.3424 +IC CY CB OA2 CA 1.5073 114.94 -92.14 116.82 1.3424 +IC CJ2 CY CB OA2 1.4049 120.41 -89.70 114.94 1.4508 +IC CJ1 CY CB OA2 1.4040 119.97 89.00 114.94 1.4508 +IC CJ1 CJ2 *CY CB 1.4040 119.61 178.70 120.41 1.5073 +IC CJ2 CY CB HB1 1.4049 120.41 30.50 107.07 1.1133 +IC CJ2 CY CB HB2 1.4049 120.41 143.43 108.09 1.1175 +IC CB CY CJ1 CK1 1.5073 119.97 -179.14 120.22 1.4011 +IC CB CY CJ2 CK2 1.5073 120.41 179.20 120.17 1.4015 +IC CY CJ1 CK1 CQ 1.4040 120.22 0.11 119.97 1.4012 +IC CJ1 CK1 CQ CK2 1.4011 119.97 0.14 120.06 1.4013 +IC CK1 CQ CK2 CJ2 1.4012 120.06 -0.08 119.97 1.4015 +IC CK1 CY *CJ1 HJ1 1.4011 120.22 179.64 119.75 1.0808 +IC CK2 CY *CJ2 HJ2 1.4015 120.17 179.98 119.90 1.0795 +IC CQ CJ1 *CK1 HK1 1.4012 119.97 179.91 119.95 1.0806 +IC CQ CJ2 *CK2 HK2 1.4013 119.97 -179.99 120.07 1.0805 +IC CK1 CK2 *CQ HQ 1.4012 120.06 -179.90 120.01 1.0806 +IC CC2 CC3 CG NG 1.5550 116.14 -6.99 117.40 1.3442 +IC CG CZ *NG HG 1.3442 129.55 175.98 113.63 0.9888 +IC HG NG CG OG 0.9888 116.71 177.69 124.09 1.2224 +IC CC3 CG NG CZ 1.5026 117.40 171.67 129.55 1.4221 +IC CG NG CZ CD1 1.3442 129.55 8.58 125.65 1.4019 +IC NG CZ CD1 CE1 1.4221 125.65 -176.91 120.47 1.3983 +IC CZ CD1 CE1 OE 1.4019 120.47 -179.93 119.61 1.4070 +IC CD1 CE1 OE HOE 1.3983 119.61 173.29 107.72 0.9583 +IC CZ CD1 CE1 CP 1.4019 120.47 0.29 120.28 1.3988 +IC CD1 CE1 CP CE2 1.3983 120.28 0.19 119.83 1.4012 +IC CE1 CP CE2 CD2 1.3988 119.83 -0.22 119.70 1.4012 +IC CD1 CD2 *CP HP 2.4258 59.83 -179.40 149.86 1.0795 +IC CE1 CZ *CD1 HD1 1.3983 120.47 -179.99 121.26 1.0774 +IC CE2 CZ *CD2 HD2 1.4012 120.77 -179.35 119.71 1.0794 +IC CP CD2 *CE2 HE2 1.4012 119.70 -179.76 120.15 1.0810 + + +PRES 4AFP 0.00 ! C17H16NO4 Alpha-Benzyl Gamma-4-Amino Phenol GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! CJ1--CK1 +ATOM HC3A HGA2 0.09 ! // \\ +ATOM HC3B HGA2 0.09 ! OA1 CY CJ +GROUP ! | / \ __ / +ATOM CG CG2O1 0.52 ! O24 CA--OA2---CB CJ2--CK2 +ATOM OG OG2D1 -0.52 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 +ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP--OH(P) +ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OG CD1--CE1 +ATOM CD1 CG2R61 -0.115 ! Me19 | | | +ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CE1 CG2R61 -0.115 ! C2 C10 C8 C15 +ATOM HE1 HGR61 0.115 ! | | | +GROUP ! C3 C5 C7 +ATOM CE2 CG2R61 -0.115 ! / \ / \ / \ +ATOM HE2 HGR61 0.115 ! HO C4 C6 OH +GROUP +ATOM CD2 CG2R61 -0.115 ! 4AFP +ATOM HD2 HGR61 0.115 +GROUP +ATOM CP CG2R61 0.11 +ATOM OP OG311 -0.53 +ATOM HOP HGP1 0.42 +GROUP +ATOM CC1 CG311 0.17 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.90 +ATOM OA1 OG2D1 -0.63 +ATOM OA2 OG302 -0.49 +ATOM CB CG321 -0.22 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +BOND CP OP OP HOP +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 NG OG + +IC CC1 CA OA2 CB 1.5236 109.09 -178.41 115.32 1.4470 +IC HC1 CC1 CA OA2 1.1142 106.35 -136.56 109.09 1.3425 +IC HB1 CB OA2 CA 1.1165 110.58 58.38 115.32 1.3425 +IC HB2 CB OA2 CA 1.1162 110.53 -60.09 115.32 1.3425 +IC CY CB OA2 CA 1.5038 113.57 178.93 115.32 1.3425 +IC CJ2 CY CB OA2 1.4045 120.04 -86.50 113.57 1.4470 +IC CJ1 CY CB OA2 1.4046 120.35 92.29 113.57 1.4470 +IC CJ1 CJ2 *CY CB 1.4046 119.60 178.79 120.04 1.5038 +IC CJ2 CY CB HB1 1.4045 120.04 35.94 107.19 1.1165 +IC CJ2 CY CB HB2 1.4045 120.04 150.86 107.55 1.1162 +IC CB CY CJ1 CK1 1.5038 120.35 -179.80 120.19 1.4015 +IC CB CY CJ2 CK2 1.5038 120.04 179.88 120.20 1.4014 +IC CY CJ1 CK1 CQ 1.4046 120.19 0.22 119.97 1.4011 +IC CJ1 CK1 CQ CK2 1.4015 119.97 0.49 120.06 1.4013 +IC CK1 CQ CK2 CJ2 1.4011 120.06 -0.40 119.97 1.4014 +IC CK1 CY *CJ1 HJ1 1.4015 120.19 -179.59 119.87 1.0799 +IC CK2 CY *CJ2 HJ2 1.4014 120.20 179.63 119.84 1.0802 +IC CQ CJ1 *CK1 HK1 1.4011 119.97 -179.64 120.03 1.0807 +IC CQ CJ2 *CK2 HK2 1.4013 119.97 179.84 119.99 1.0807 +IC CK1 CK2 *CQ HQ 1.4011 120.06 -179.97 119.97 1.0807 +IC CC2 CC3 CG NG 1.5522 114.66 9.31 116.85 1.3446 +IC CG CZ *NG HG 1.3446 129.70 -179.80 113.69 0.9886 +IC NG CC3 *CG OG 1.3446 116.85 179.97 118.95 1.2231 +IC CC3 CG NG CZ 1.5020 116.85 178.94 129.70 1.4209 +IC CG NG CZ CD1 1.3446 129.70 -12.00 125.34 1.4023 +IC NG CZ CD1 CE1 1.4209 125.34 179.30 120.44 1.4040 +IC CZ CD1 CE1 CP 1.4023 120.44 -0.30 120.10 1.3974 +IC CD1 CE1 CP OP 1.4040 120.10 -179.94 119.57 1.4076 +IC CE1 CP OP HOP 1.3974 119.57 179.31 107.83 0.9582 +IC CD1 CE1 CP CE2 1.4040 120.10 0.00 120.00 1.3995 +IC CE1 CP CE2 CD2 1.3974 120.00 0.08 119.77 1.4034 +IC CE1 CZ *CD1 HD1 1.4040 120.44 179.44 120.86 1.0783 +IC CE2 CZ *CD2 HD2 1.4034 120.68 179.81 119.68 1.0792 +IC CP CD1 *CE1 HE1 1.3974 120.10 -179.87 120.20 1.0802 +IC CP CD2 *CE2 HE2 1.3995 119.77 179.92 119.80 1.0794 + + +PRES 2AFD 0.00 ! C8H8NO2 Gamma-2-Amino Phenol GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 ! OA1 (-0.5) +GROUP ! | +ATOM CG CG2O1 0.52 ! O24 CA--OA2 (-0.5) +ATOM OG OG2D1 -0.52 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 +ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OG CD1--CE1 +ATOM CD1 CG2R61 0.11 ! Me19 | | | | +ATOM OD OG311 -0.53 ! C1 | C9 C14 C16 OH(D) +ATOM HOD HGP1 0.42 ! / \|/ \ / \ / +GROUP ! C2 C10 C8 C15 +ATOM CE1 CG2R61 -0.115 ! | | | +ATOM HE1 HGR61 0.115 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 -0.115 ! HO C4 C6 OH +ATOM HP HGR61 0.115 +GROUP ! 2AFD +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 OD OD HOD CD1 CE1 CE1 HE1 CE1 CP +BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5527 114.79 -49.84 117.53 1.3436 +IC CG CZ *NG HG 1.3436 131.49 -179.00 112.13 1.0158 +IC HG NG CG OG 1.0158 116.38 178.36 123.50 1.2277 +IC CC3 CG NG CZ 1.5021 117.53 -179.31 131.49 1.4281 +IC CG NG CZ CD1 1.3436 131.49 -17.12 128.16 1.4178 +IC NG CZ CD1 OD 1.4281 128.16 -0.87 124.84 1.4130 +IC CZ CD1 OD HOD 1.4178 124.84 13.21 105.74 0.9771 +IC NG CZ CD1 CE1 1.4281 128.16 -180.00 120.02 1.4012 +IC CZ CD1 CE1 CP 1.4178 120.02 -0.79 120.69 1.3997 +IC CD1 CE1 CP CE2 1.4012 120.69 0.09 119.77 1.3979 +IC CE1 CP CE2 CD2 1.3997 119.77 0.21 119.83 1.3990 +IC CD1 CD2 *CP HP 2.4340 59.99 -179.98 150.22 1.0801 +IC CE2 CZ *CD2 HD2 1.3990 121.28 -179.74 119.14 1.0814 +IC CP CD1 *CE1 HE1 1.3997 120.69 -179.78 119.40 1.0802 +IC CP CD2 *CE2 HE2 1.3979 119.83 -179.85 119.73 1.0805 + + +PRES 3AFD 0.00 ! C8H8NO2 Gamma-3-Amino Phenol GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 ! OA1 (-0.5) +GROUP ! | +ATOM CG CG2O1 0.52 ! O24 CA--OA2 (-0.5) +ATOM OG OG2D1 -0.52 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 +ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OG CD1--CE1 +ATOM CD1 CG2R61 -0.115 ! Me19 | | | | +ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 OH(E) +GROUP ! / \|/ \ / \ / +ATOM CE1 CG2R61 0.11 ! C2 C10 C8 C15 +ATOM OE OG311 -0.53 ! | | | +ATOM HOE HGP1 0.42 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 -0.115 ! HO C4 C6 OH +ATOM HP HGR61 0.115 +GROUP ! 3AFD +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 OE OE HOE CE1 CP +BOND CP HP CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5535 114.97 -47.53 117.22 1.3441 +IC CG CZ *NG HG 1.3441 129.77 -178.97 112.88 1.0143 +IC HG NG CG OG 1.0143 117.35 177.56 123.74 1.2279 +IC CC3 CG NG CZ 1.5033 117.22 -179.94 129.77 1.4190 +IC CG NG CZ CD1 1.3441 129.77 -14.90 125.45 1.4020 +IC NG CZ CD1 CE1 1.4190 125.45 179.05 120.37 1.3993 +IC CZ CD1 CE1 OE 1.4020 120.37 179.48 120.07 1.4087 +IC CD1 CE1 OE HOE 1.3993 120.07 179.46 107.22 0.9566 +IC CZ CD1 CE1 CP 1.4020 120.37 -0.43 120.24 1.4003 +IC CD1 CE1 CP CE2 1.3993 120.24 0.04 119.87 1.4014 +IC CE1 CP CE2 CD2 1.4003 119.87 0.07 119.63 1.4004 +IC CD1 CD2 *CP HP 2.4274 59.83 -179.94 149.75 1.0785 +IC CE1 CZ *CD1 HD1 1.3993 120.37 179.29 120.63 1.0774 +IC CE2 CZ *CD2 HD2 1.4004 120.84 -179.99 119.02 1.0816 +IC CP CD2 *CE2 HE2 1.4014 119.63 179.99 119.74 1.0802 + + +PRES 4AFD 0.00 ! C8H8NO2 Gamma-4-Amino Phenol GA CDCA Amide, cacha +! patch combination: +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 ! OA1 (-0.5) +GROUP ! | +ATOM CG CG2O1 0.52 ! O24 CA--OA2 (-0.5) +ATOM OG OG2D1 -0.52 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2--CE2 +ATOM NG NG2S1 -0.47 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM HG HGP1 0.33 ! C12 Me18 C20 C23 NH CC2 CG CZ CP--OH(P) +ATOM CZ CG2R61 0.14 ! / \ | / || \ __ / +GROUP ! C11 C13---C17 OG CD1--CE1 +ATOM CD1 CG2R61 -0.115 ! Me19 | | | +ATOM HD1 HGR61 0.115 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CE1 CG2R61 -0.115 ! C2 C10 C8 C15 +ATOM HE1 HGR61 0.115 ! | | | +GROUP ! C3 C5 C7 +ATOM CE2 CG2R61 -0.115 ! / \ / \ / \ +ATOM HE2 HGR61 0.115 ! HO C4 C6 OH +GROUP +ATOM CD2 CG2R61 -0.115 ! 4AFP +ATOM HD2 HGR61 0.115 +GROUP +ATOM CP CG2R61 0.11 +ATOM OP OG311 -0.53 +ATOM HOP HGP1 0.42 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +BOND CP OP OP HOP +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5534 114.96 -47.72 117.22 1.3442 +IC CG CZ *NG HG 1.3442 129.81 -179.00 112.85 1.0143 +IC NG CC3 *CG OG 1.3442 117.22 -178.69 119.03 1.2282 +IC CC3 CG NG CZ 1.5032 117.22 -179.68 129.81 1.4190 +IC CG NG CZ CD1 1.3442 129.81 -13.97 125.44 1.4028 +IC NG CZ CD1 CE1 1.4190 125.44 178.96 120.46 1.4048 +IC CZ CD1 CE1 CP 1.4028 120.46 -0.32 120.02 1.3982 +IC CD1 CE1 CP OP 1.4048 120.02 -179.99 120.03 1.4082 +IC CE1 CP OP HOP 1.3982 120.03 -179.80 106.81 0.9579 +IC CD1 CE1 CP CE2 1.4048 120.02 -0.03 120.03 1.3994 +IC CE1 CP CE2 CD2 1.3982 120.03 0.06 119.74 1.4022 +IC CE1 CZ *CD1 HD1 1.4048 120.46 179.35 120.40 1.0778 +IC CE2 CZ *CD2 HD2 1.4022 120.80 179.99 119.04 1.0815 +IC CP CD1 *CE1 HE1 1.3982 120.02 -179.92 120.17 1.0792 +IC CP CD2 *CE2 HE2 1.3994 119.74 179.94 119.33 1.0788 + + +RESI GABD -1.00 ! C35H51N2O6 Gamma amino benzene glutamic acid CDCA amide, cacha +GROUP +ATOM C3 CG311 0.14 ! OG CD1--CE1 +ATOM O3 OG311 -0.65 ! || // \\ +ATOM HO3 HGP1 0.42 ! CG--NG--CZ CP +ATOM H3 HGA1 0.09 ! / HG \ __ / +GROUP ! CC3 CD2--CE2 +ATOM C4 CG321 -0.18 ! \ +ATOM H4A HGA2 0.09 ! O24 CC2 +ATOM H4B HGA2 0.09 ! || / +GROUP ! H Me21 C22 C24 CC1 +ATOM C5 CG311 -0.09 ! | \ / \ / \ / \ +ATOM H5 HGA1 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) +GROUP ! / \ | / | +ATOM C6 CG321 -0.18 ! C11 C13---C17 OA2 (-0.5) +ATOM H6A HGA2 0.09 ! Me19 | | | +ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C7 CG311 0.14 ! C2 C10 C8 C15 +ATOM O7 OG311 -0.65 ! | | | +ATOM HO7 HGP1 0.42 ! C3 C5 C7 +ATOM H7 HGA1 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM C8 CG311 -0.09 +ATOM H8 HGA1 0.09 ! GABD +GROUP +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 +GROUP +ATOM C18 CG331 -0.27 !methyl at c13 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 +GROUP +ATOM C19 CG331 -0.27 !methyl at c10 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM C24 CG2O1 0.51 +ATOM O24 OG2D1 -0.51 +ATOM N NG2S1 -0.47 +ATOM HN HGP1 0.47 +GROUP +ATOM CC1 CG311 -0.19 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O3 0.62 +ATOM OA1 OG2D2 -0.76 +ATOM OA2 OG2D2 -0.76 +GROUP +ATOM CC2 CG321 -0.18 +ATOM HC2A HGA2 0.09 +ATOM HC2B HGA2 0.09 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 +GROUP +ATOM CG CG2O1 0.52 +ATOM OG OG2D1 -0.52 +GROUP +ATOM NG NG2S1 -0.47 +ATOM HG HGP1 0.33 +ATOM CZ CG2R61 0.14 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 + +BOND C3 O3 C3 H3 O3 HO3 +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7 C7 O7 O7 HO7 +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 C24 C24 O24 +BOND C24 N N HN +BOND N CC1 CC1 HC1 CC1 CC2 CC1 CA CA OA1 CA OA2 +BOND CC2 HC2A CC2 HC2B CC2 CC3 +BOND CC3 HC3A CC3 HC3B CC3 CG +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +IMPR C24 C23 N O24 +IMPR CA OA2 OA1 CC1 +IMPR CG CC3 NG OG + +! R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL) +!ICs based on arbitrary CHARMM optimized structure +IC C1 C2 C3 C4 1.5325 111.68 -49.44 111.84 1.5383 +IC C2 C3 C4 C5 1.5339 111.84 43.92 115.68 1.5598 +IC C3 C4 C5 C6 1.5383 115.68 -175.08 109.02 1.5521 +IC C4 C5 C6 C7 1.5598 109.02 85.48 114.98 1.5441 +IC C5 C6 C7 C8 1.5521 114.98 39.05 113.05 1.5291 +IC C7 C8 C9 C10 1.5291 114.07 58.27 109.47 1.5439 +IC C8 C9 C10 C1 1.5323 109.47 179.67 111.99 1.5563 +IC C9 C10 C1 C2 1.5439 111.99 63.32 113.83 1.5325 +IC O3 C3 C4 C5 1.4163 109.09 162.16 115.68 1.5598 +IC C4 C2 *C3 O3 1.5383 111.84 -119.44 107.07 1.4163 +IC C4 C2 *C3 H3 1.5383 111.84 121.33 109.38 1.1144 +IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 +IC C2 C3 O3 HO3 1.5339 107.07 70.15 104.87 0.9608 +IC C5 C3 *C4 H4A 1.5598 115.68 122.76 108.69 1.1111 +IC H4A C3 *C4 H4B 1.1111 108.69 115.73 108.82 1.1113 +IC C10 C4 *C5 H5 1.5279 114.71 116.72 105.03 1.1175 +IC C7 C5 *C6 H6A 1.5441 114.98 -124.16 109.39 1.1113 +IC H6A C5 *C6 H6B 1.1113 109.39 -115.80 108.33 1.1112 +IC C2 C10 *C1 H1A 1.5325 113.83 119.39 107.74 1.1137 +IC C2 C10 *C1 H1B 1.5325 113.83 -124.36 110.18 1.1091 +IC C1 C3 *C2 H2A 1.5325 111.68 122.11 110.21 1.1113 +IC H2A C3 *C2 H2B 1.1113 110.21 117.20 108.66 1.1128 +IC C6 C7 C8 C14 1.5441 113.05 -166.97 108.56 1.5542 +IC C14 C7 *C8 C9 1.5542 108.56 119.93 114.07 1.5323 +IC C7 C8 C14 C13 1.5291 108.56 -174.23 113.13 1.5425 +IC C13 C8 *C14 C15 1.5425 113.13 118.56 116.30 1.5285 +IC C8 C14 C15 C16 1.5542 116.30 -154.74 103.56 1.5435 +IC C14 C15 C16 C17 1.5285 103.56 -2.52 106.91 1.5532 +IC C17 C14 *C13 C12 1.5731 98.17 119.81 107.46 1.5340 +IC C14 C13 C12 C11 1.5425 107.46 55.27 111.17 1.5431 +IC C8 C6 *C7 O7 1.5291 113.05 -126.94 107.98 1.4218 +IC O7 C6 *C7 H7 1.4218 107.98 -113.62 107.19 1.1164 +IC C6 C7 O7 HO7 1.5441 107.98 178.15 105.27 0.9614 +IC C9 C7 *C8 H8 1.5323 114.07 122.48 107.18 1.1067 +IC C10 C8 *C9 H9 1.5439 109.47 -117.09 106.55 1.1138 +IC C9 C12 *C11 H11A 1.5547 114.18 122.66 108.77 1.1090 +IC H11A C12 *C11 H11B 1.1090 108.77 115.79 107.30 1.1111 +IC C14 C13 C12 H12A 1.5425 107.46 175.99 111.87 1.1059 +IC H12A C13 *C12 H12B 1.1059 111.87 119.48 108.83 1.1125 +IC C13 C8 *C14 H14 1.5425 113.13 -118.31 108.46 1.1150 +IC C16 C14 *C15 H15A 1.5435 103.56 119.14 111.17 1.1002 +IC H15A C14 *C15 H15B 1.1002 111.17 119.82 112.08 1.0988 +IC C17 C15 *C16 H16A 1.5532 106.91 121.49 110.78 1.0992 +IC H16A C15 *C16 H16B 1.0992 110.78 117.18 110.97 1.0998 +IC C13 C16 *C17 H17 1.5731 98.41 -112.88 110.39 1.1009 +IC C12 C14 *C13 C18 1.5340 107.46 121.96 114.21 1.5526 +IC C14 C13 C18 H18A 1.5425 114.21 116.77 111.39 1.1064 +IC H18A C13 *C18 H18B 1.1064 111.39 119.05 110.59 1.1085 +IC H18A C13 *C18 H18C 1.1064 111.39 -120.16 111.91 1.1058 +IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 +IC C5 C10 C19 H19A 1.5279 109.53 5.11 111.17 1.1079 +IC H19A C10 *C19 H19B 1.1079 111.17 121.06 112.01 1.1062 +IC H19A C10 *C19 H19C 1.1079 111.17 -119.50 110.64 1.1093 +IC C13 C16 *C17 C20 1.5731 98.41 127.02 111.84 1.5649 +IC C16 C17 C20 C22 1.5532 111.84 71.76 108.71 1.5518 +IC C22 C17 *C20 C21 1.5518 108.71 122.37 112.90 1.5396 +IC C21 C17 *C20 H20 1.5396 112.90 120.80 108.91 1.1119 +IC C17 C20 C21 H21A 1.5649 112.90 71.89 110.45 1.1079 +IC H21A C20 *C21 H21B 1.1079 110.45 -121.56 110.44 1.1103 +IC H21A C20 *C21 H21C 1.1079 110.45 118.40 110.88 1.1089 +IC C17 C20 C22 C23 1.5649 108.71 -163.91 113.72 1.5524 +IC C23 C20 *C22 H22A 1.5524 113.72 119.83 108.17 1.1129 +IC H22A C20 *C22 H22B 1.1129 108.17 116.47 108.28 1.1132 +IC C20 C22 C23 C24 1.5518 113.72 174.68 113.87 1.5026 +IC C24 C22 *C23 H23A 1.5026 113.87 120.96 110.57 1.1095 +IC H23A C22 *C23 H23B 1.1095 110.57 118.91 109.38 1.1114 +IC C22 C23 C24 N 1.5524 113.87 6.38 116.55 1.3359 +IC N C23 *C24 O24 1.3359 116.55 -179.98 120.03 1.2265 +IC C23 C24 N CC1 1.5026 116.55 -179.82 130.34 1.4436 +IC CC1 C24 *N HN 1.4436 130.34 -176.24 124.18 1.0134 +IC C24 N CC1 CA 1.3359 130.34 -166.57 103.53 1.5637 +IC CA N *CC1 HC1 1.5637 103.53 115.21 109.79 1.1100 +IC HC1 N *CC1 CC2 1.1100 109.79 123.30 112.57 1.5529 +IC N CC1 CA OA1 1.4436 103.53 -162.71 117.28 1.2563 +IC OA1 CC1 *CA OA2 1.2563 117.28 152.11 113.14 1.2722 +IC N CC1 CC2 CC3 1.4436 112.57 56.12 114.17 1.5540 +IC CC3 CC1 *CC2 HC2A 1.5540 114.17 126.04 108.53 1.1120 +IC HC2A CC1 *CC2 HC2B 1.1120 108.53 114.46 107.25 1.1137 +IC CC1 CC2 CC3 CG 1.5529 114.17 119.76 114.11 1.4995 +IC CG CC2 *CC3 HC3A 1.4995 114.11 120.83 109.21 1.1109 +IC HC3A CC2 *CC3 HC3B 1.1109 109.21 118.15 110.34 1.1107 +IC CC2 CC3 CG NG 1.5540 114.11 -53.86 116.06 1.3423 +IC NG CC3 *CG OG 1.3423 116.06 -178.54 119.61 1.2286 +IC CC3 CG NG HG 1.4995 116.06 0.87 115.97 1.0167 +IC CC3 CG NG CZ 1.4995 116.06 -179.02 130.53 1.4189 +IC CG NG CZ CD1 1.3423 130.53 -7.10 125.50 1.4022 +IC NG CZ CD1 CE1 1.4189 125.50 179.36 120.55 1.4034 +IC CZ CD1 CE1 CP 1.4022 120.55 -0.19 119.96 1.4008 +IC CD1 CE1 CP CE2 1.4034 119.96 0.01 119.92 1.4004 +IC CE1 CP CE2 CD2 1.4008 119.92 0.02 119.80 1.4007 +IC CE1 CZ *CD1 HD1 1.4034 120.55 179.64 120.41 1.0774 +IC CE2 CZ *CD2 HD2 1.4007 120.81 179.97 119.00 1.0814 +IC CP CD1 *CE1 HE1 1.4008 119.96 -179.93 119.80 1.0798 +IC CP CD2 *CE2 HE2 1.4004 119.80 179.93 119.74 1.0797 +IC CE1 CE2 *CP HP 1.4008 119.92 179.95 119.93 1.0796 + + +PRES 4FBD 0.00 ! C3H2F Gamma 4-Fluoro amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HP +ATOM CE1 CG2R61 -0.100 +ATOM HE1 HGR62 0.150 +ATOM CP CG2R66 0.110 +ATOM FP FGR1 -0.210 +ATOM CE2 CG2R61 -0.100 +ATOM HE2 HGR62 0.150 +BOND CP FP +IC CE1 CE2 *CP FP 1.4008 119.92 179.96 119.93 1.0796 + + +PRES 3FBD 0.00 ! C3H2F Gamma 3-Fluoro amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HE1 +ATOM CD1 CG2R61 -0.100 +ATOM HD1 HGR62 0.150 +ATOM CE1 CG2R66 0.110 +ATOM FE1 FGR1 -0.210 +ATOM CP CG2R61 -0.100 +ATOM HP HGR62 0.150 +BOND CE1 FE1 +IC CP CD1 *CE1 FE1 1.4008 119.96 -179.93 119.80 1.0798 + + +PRES 2FBD 0.14 ! C3HF Gamma 2-Fluoro amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HD1 +ATOM CE1 CG2R61 -0.100 +ATOM HE1 HGR62 0.150 +ATOM CD1 CG2R66 0.110 +ATOM FD1 FGR1 -0.210 +ATOM CZ CG2R61 0.190 +BOND CD1 FD1 +IC CE1 CZ *CD1 FD1 1.3985 122.02 176.60 121.03 1.3368 + + +PRES 4FBP 0.00 ! C12H10FO2 Alpha benzyl, Gamma 4-Fluoro amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HP +GROUP ! OG CD1--CE1 +ATOM CC1 CG311 0.17 ! || // \\ +ATOM HC1 HGA1 0.09 ! CG--NG--CZ CP--FP +ATOM CA CG2O2 0.90 ! / HG \ __ / +ATOM OA1 OG2D1 -0.63 ! CC3 CD2--CE2 +ATOM OA2 OG302 -0.49 ! \ +ATOM CB CG321 -0.22 ! O24 CC2 +ATOM HB1 HGA2 0.09 ! || / +ATOM HB2 HGA2 0.09 ! H Me21 C22 C24 CC1 +GROUP ! | \ / \ / \ / \ __ +ATOM CY CG2R61 0.00 ! C12 Me18 C20 C23 NH CA--OA1 CJ1--CK1 +ATOM CJ1 CG2R61 -0.115 ! / \ | / | // \\ +ATOM HJ1 HGR61 0.115 ! C11 C13---C17 OA2--CB--CY CQ +ATOM CJ2 CG2R61 -0.115 ! Me19 | | | \ __ / +ATOM HJ2 HGR61 0.115 ! C1 | C9 C14 C16 CJ2--CK2 +ATOM CK1 CG2R61 -0.115 ! / \|/ \ / \ / +ATOM HK1 HGR61 0.115 ! C2 C10 C8 C15 +ATOM CK2 CG2R61 -0.115 ! | | | +ATOM HK2 HGR61 0.115 ! C3 C5 C7 +ATOM CQ CG2R61 -0.115 ! / \ / \ / \ +ATOM HQ HGR61 0.115 ! HO C4 C6 OH +GROUP +ATOM CE1 CG2R61 -0.100 ! 4FBP +ATOM HE1 HGR62 0.150 +ATOM CP CG2R66 0.110 +ATOM FP FGR1 -0.210 +ATOM CE2 CG2R61 -0.100 +ATOM HE2 HGR62 0.150 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CP FP +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5349 110.60 -171.93 114.63 1.4514 +IC HB1 CB OA2 CA 1.1146 109.86 61.07 114.63 1.3430 +IC HB2 CB OA2 CA 1.1156 110.43 -57.63 114.63 1.3430 +IC CA OA2 CB CY 1.3430 114.63 -177.12 115.21 1.5061 +IC CJ1 CY CB OA2 1.4037 119.63 48.09 115.21 1.4514 +IC CB CY CJ1 CK1 1.5061 119.63 177.33 120.28 1.4016 +IC CY CJ1 CK1 CQ 1.4037 120.28 0.19 119.99 1.4012 +IC CJ1 CK1 CQ CK2 1.4016 119.99 -0.03 120.04 1.4009 +IC CK1 CQ CK2 CJ2 1.4012 120.04 -0.22 119.92 1.4012 +IC CB CY CJ2 CK2 1.5061 120.87 -177.55 120.33 1.4012 +IC CK1 CY *CJ1 HJ1 1.4016 120.28 -179.34 119.52 1.0802 +IC CK2 CY *CJ2 HJ2 1.4012 120.33 179.00 119.92 1.0789 +IC CQ CJ1 *CK1 HK1 1.4012 119.99 -179.93 119.95 1.0805 +IC CQ CJ2 *CK2 HK2 1.4009 119.92 179.15 120.02 1.0814 +IC CK1 CK2 *CQ HQ 1.4012 120.04 179.61 119.92 1.0812 +IC CE1 CE2 *CP FP 1.3937 122.13 178.58 118.94 1.3320 + +PRES 3FBP 0.00 ! C12H10FO2 Alpha benzyl, Gamma 3-Fluoro amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HE1 +GROUP ! OG CD1--CE1--FE1 +ATOM CC1 CG311 0.17 ! || // \\ +ATOM HC1 HGA1 0.09 ! CG--NG--CZ CP +ATOM CA CG2O2 0.90 ! / HG \ __ / +ATOM OA1 OG2D1 -0.63 ! CC3 CD2--CE2 +ATOM OA2 OG302 -0.49 ! \ +ATOM CB CG321 -0.22 ! O24 CC2 +ATOM HB1 HGA2 0.09 ! || / +ATOM HB2 HGA2 0.09 ! H Me21 C22 C24 CC1 +GROUP ! | \ / \ / \ / \ __ +ATOM CY CG2R61 0.00 ! C12 Me18 C20 C23 NH CA--OA1 CJ1--CK1 +ATOM CJ1 CG2R61 -0.115 ! / \ | / | // \\ +ATOM HJ1 HGR61 0.115 ! C11 C13---C17 OA2--CB--CY CQ +ATOM CJ2 CG2R61 -0.115 ! Me19 | | | \ __ / +ATOM HJ2 HGR61 0.115 ! C1 | C9 C14 C16 CJ2--CK2 +ATOM CK1 CG2R61 -0.115 ! / \|/ \ / \ / +ATOM HK1 HGR61 0.115 ! C2 C10 C8 C15 +ATOM CK2 CG2R61 -0.115 ! | | | +ATOM HK2 HGR61 0.115 ! C3 C5 C7 +ATOM CQ CG2R61 -0.115 ! / \ / \ / \ +ATOM HQ HGR61 0.115 ! HO C4 C6 OH +GROUP +ATOM CD1 CG2R61 -0.100 ! 3FBP +ATOM HD1 HGR62 0.150 +ATOM CE1 CG2R66 0.110 +ATOM FE1 FGR1 -0.210 +ATOM CP CG2R61 -0.100 +ATOM HP HGR62 0.150 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CE1 FE1 +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5310 110.63 -175.15 114.31 1.4534 +IC HB1 CB OA2 CA 1.1151 110.56 55.87 114.31 1.3407 +IC HB2 CB OA2 CA 1.1156 109.57 -63.30 114.31 1.3407 +IC CA OA2 CB CY 1.3407 114.31 175.76 116.12 1.5054 +IC CJ1 CY CB OA2 1.4053 119.56 164.70 116.12 1.4534 +IC CB CY CJ1 CK1 1.5054 119.56 177.79 120.29 1.4017 +IC CY CJ1 CK1 CQ 1.4053 120.29 -0.37 119.95 1.4010 +IC CJ1 CK1 CQ CK2 1.4017 119.95 0.24 119.94 1.4000 +IC CK1 CQ CK2 CJ2 1.4010 119.94 0.14 120.12 1.4002 +IC CB CY CJ2 CK2 1.5054 120.97 -177.38 120.26 1.4002 +IC CK1 CY *CJ1 HJ1 1.4017 120.29 -179.60 119.80 1.0797 +IC CK2 CY *CJ2 HJ2 1.4002 120.26 178.59 119.81 1.0794 +IC CQ CJ1 *CK1 HK1 1.4010 119.95 -179.67 120.07 1.0804 +IC CQ CJ2 *CK2 HK2 1.4000 120.12 178.86 119.82 1.0784 +IC CK1 CK2 *CQ HQ 1.4010 119.94 179.70 119.90 1.0807 +IC CD1 CP *CE1 FE1 1.3934 122.09 178.24 118.96 1.3332 + + +PRES 2FBP 0.14 ! C12H9FO2 Alpha benzyl, Gamma 2-Fluoro amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HD1 +GROUP ! FD1 +ATOM CC1 CG311 0.17 ! | +ATOM HC1 HGA1 0.09 ! OG CD1--CE1 +ATOM CA CG2O2 0.90 ! || // \\ +ATOM OA1 OG2D1 -0.63 ! CG--NG--CZ CP +ATOM OA2 OG302 -0.49 ! / HG \ __ / +ATOM CB CG321 -0.22 ! CC3 CD2--CE2 +ATOM HB1 HGA2 0.09 ! \ +ATOM HB2 HGA2 0.09 ! O24 CC2 +GROUP ! || / +ATOM CY CG2R61 0.00 ! H Me21 C22 C24 CC1 +ATOM CJ1 CG2R61 -0.115 ! | \ / \ / \ / \ __ +ATOM HJ1 HGR61 0.115 ! C12 Me18 C20 C23 NH CA--OA1 CJ1--CK1 +ATOM CJ2 CG2R61 -0.115 ! / \ | / | // \\ +ATOM HJ2 HGR61 0.115 ! C11 C13---C17 OA2--CB--CY CQ +ATOM CK1 CG2R61 -0.115 ! Me19 | | | \ __ / +ATOM HK1 HGR61 0.115 ! C1 | C9 C14 C16 CJ2--CK2 +ATOM CK2 CG2R61 -0.115 ! / \|/ \ / \ / +ATOM HK2 HGR61 0.115 ! C2 C10 C8 C15 +ATOM CQ CG2R61 -0.115 ! | | | +ATOM HQ HGR61 0.115 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CE1 CG2R61 -0.100 ! HO C4 C6 OH +ATOM HE1 HGR62 0.150 +ATOM CD1 CG2R66 0.110 ! 2FBP +ATOM FD1 FGR1 -0.210 +ATOM CZ CG2R61 0.190 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CD1 FD1 +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5324 110.58 -171.81 114.58 1.4510 +IC HB1 CB OA2 CA 1.1152 109.67 65.73 114.58 1.3429 +IC HB2 CB OA2 CA 1.1162 110.77 -52.90 114.58 1.3429 +IC CA OA2 CB CY 1.3429 114.58 -172.25 114.95 1.5055 +IC CJ1 CY CB OA2 1.4051 121.08 -129.13 114.95 1.4510 +IC CB CY CJ1 CK1 1.5055 121.08 -177.36 120.29 1.4015 +IC CY CJ1 CK1 CQ 1.4051 120.29 0.38 119.93 1.4010 +IC CJ1 CK1 CQ CK2 1.4015 119.93 -0.45 120.04 1.4010 +IC CK1 CQ CK2 CJ2 1.4010 120.04 0.10 119.98 1.4014 +IC CB CY CJ2 CK2 1.5055 119.39 177.05 120.28 1.4014 +IC CK1 CY *CJ1 HJ1 1.4015 120.29 179.02 119.81 1.0790 +IC CK2 CY *CJ2 HJ2 1.4014 120.28 -179.17 119.50 1.0802 +IC CQ CJ1 *CK1 HK1 1.4010 119.93 179.08 120.10 1.0810 +IC CQ CJ2 *CK2 HK2 1.4010 119.98 -179.89 119.95 1.0805 +IC CK1 CK2 *CQ HQ 1.4010 120.04 -179.60 120.00 1.0812 +IC CZ CE1 *CD1 FD1 1.4058 122.69 179.26 117.93 1.3368 +!End Polli's bile acids, chayan, feb2008 + +!Shapiro's Fatty acid Binding protein Inhibitors, chayan, feb2008 +!Model compound to optimize aromatic-aliphatic ether +RESI MEOB 0.00 ! C7H8O Methoxybenzene (aka anisole, phenyl-methyl ether), cacha +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 ! CD1--CE1 +ATOM HD1 HGR61 0.115 ! / \ +GROUP ! HG--CG CZ--OZ--CM +ATOM CD2 CG2R61 -0.115 ! \ / +ATOM HD2 HGR61 0.115 ! CD2--CE2 +GROUP ! | | +ATOM CE1 CG2R61 -0.115 ! HD2 HE2 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of +ATOM OZ OG301 -0.39 ! RESI C36 and Igor's ethers should +ATOM CM CG331 -0.10 ! be better than analogy to phenol! +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OZ OZ CM +BOND CM HM1 CM HM2 CM HM3 + +IC CG CD1 CE1 CZ 1.3999 119.78 0.00 121.00 1.3997 +IC CD1 CE1 CZ CE2 1.4007 121.00 0.00 118.94 1.4128 +IC CE1 CZ CE2 CD2 1.3997 118.94 0.00 120.14 1.4039 +IC CD1 CD2 *CG HG 1.3999 119.98 180.00 120.06 1.0805 +IC CE1 CG *CD1 HD1 1.4007 119.78 180.00 120.21 1.0804 +IC CE2 CG *CD2 HD2 1.4039 120.17 -180.00 119.86 1.0805 +IC CZ CD1 *CE1 HE1 1.3997 121.00 -180.00 120.31 1.0797 +IC CZ CD2 *CE2 HE2 1.4128 120.14 -180.00 117.62 1.0763 +IC CE1 CE2 *CZ OZ 1.3997 118.94 -180.00 123.32 1.4094 +IC CE2 CZ OZ CM 1.4128 123.32 0.00 117.32 1.4272 +IC CZ OZ CM HM1 1.4094 117.32 -61.22 110.78 1.1121 +IC HM1 OZ *CM HM2 1.1121 110.78 122.45 110.78 1.1121 +IC HM1 OZ *CM HM3 1.1121 110.78 -118.78 108.75 1.1112 + +RESI ETOB 0.00 ! C8H10O Ethoxybenzene (aka phenetole, phenyl-ethyl ether), cacha +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 ! CD1--CE1 +ATOM HD1 HGR61 0.115 ! / \ +GROUP ! HG--CG CZ--OZ--C1--C2(Me) +ATOM CD2 CG2R61 -0.115 ! \ / +ATOM HD2 HGR61 0.115 ! CD2--CE2 +GROUP ! | | +ATOM CE1 CG2R61 -0.115 ! HD2 HE2 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of +ATOM OZ OG301 -0.39 ! RESI C36 and Igor's ethers should +ATOM C1 CG321 -0.01 ! be better than analogy to phenol! +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG331 -0.27 +ATOM H2A HGA3 0.09 +ATOM H2B HGA3 0.09 +ATOM H2C HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OZ OZ C1 +BOND C1 H1A C1 H1B C1 C2 +BOND C2 H2A C2 H2B C2 H2C + +IC CG CD1 CE1 CZ 1.4001 119.79 0.00 120.95 1.3995 +IC CD1 CE1 CZ CE2 1.4009 120.95 0.00 118.98 1.4120 +IC CE1 CZ CE2 CD2 1.3995 118.98 0.00 120.18 1.4036 +IC CD1 CD2 *CG HG 1.4001 119.98 -180.00 120.05 1.0805 +IC CE1 CG *CD1 HD1 1.4009 119.79 180.00 120.21 1.0804 +IC CE2 CG *CD2 HD2 1.4036 120.12 -180.00 119.88 1.0805 +IC CZ CD1 *CE1 HE1 1.3995 120.95 180.00 120.34 1.0797 +IC CZ CD2 *CE2 HE2 1.4120 120.18 180.00 117.95 1.0763 +IC CE1 CE2 *CZ OZ 1.3995 118.98 -180.00 123.18 1.4086 +IC CE2 CZ OZ C1 1.4120 123.18 0.00 117.39 1.4239 +IC CZ OZ C1 H1A 1.4086 117.39 -60.67 110.26 1.1142 +IC H1A OZ *C1 H1B 1.1142 110.26 121.34 110.26 1.1142 +IC H1A OZ *C1 C2 1.1142 110.26 -119.33 107.48 1.5257 +IC OZ C1 C2 H2A 1.4239 107.48 180.00 110.94 1.1094 +IC H2A C1 *C2 H2B 1.1094 110.94 120.60 109.82 1.1110 +IC H2A C1 *C2 H2C 1.1094 110.94 -120.60 109.82 1.1110 + + +PRES FBID 0.00 ! C3H6O Fatty acid Binding protein Inhibitor D, cacha +! This is a phenyl-methyl ether derivative having +! methyl at 2 and ethyl acetate at 4 position +! patch combination: +! core residue Compound "FBIB" >> Compound "FBID" + +DELETE ATOM CC ! HD1 HE1 +DELETE ATOM HC ! | | +DELETE ATOM C1 ! (-0.5)OD1 HA1 HB1 CD1--CE1 +DELETE ATOM H1A ! \ | | // \\ +DELETE ATOM H1B ! CD--CA--CB--CG CZ--OH +DELETE ATOM H1C ! / | | \ __ / \ +DELETE ATOM C2 ! (-0.5)OD2 HA2 HB2 CD2--CE2 CN(Me) +DELETE ATOM H2A ! | | +DELETE ATOM H2B ! HD2 CM(Me) +DELETE ATOM H2C +DELETE ATOM HH +GROUP +ATOM CM CG331 -0.27 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 +GROUP +ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of +ATOM OH OG301 -0.39 ! RESI C36 and Igor's ethers should +ATOM CN CG331 -0.10 ! be better than analogy to phenol! +ATOM HN1 HGA3 0.09 +ATOM HN2 HGA3 0.09 +ATOM HN3 HGA3 0.09 + +BOND CE2 CM CM HM1 CM HM2 CM HM3 +BOND OH CN CN HN1 CN HN2 CN HN3 + +IC CZ CD2 *CE2 CM 1.4150 119.45 178.47 118.38 1.5035 +IC CD2 CE2 CM HM1 1.4035 118.38 -73.69 108.56 1.1101 +IC HM1 CE2 *CM HM2 1.1101 108.56 120.14 109.17 1.1105 +IC HM1 CE2 *CM HM3 1.1101 108.56 -119.98 109.71 1.1110 +IC CE1 CZ OH CN 1.4096 121.48 33.49 115.06 1.4278 +IC CZ OH CN HN1 1.4137 115.06 -76.12 110.63 1.1113 +IC HN1 OH *CN HN2 1.1113 110.63 122.41 111.24 1.1132 +IC HN1 OH *CN HN3 1.1113 110.63 -118.58 108.69 1.1108 + + +PRES FBIE 0.00 ! C2H4O Fatty acid Binding protein Inhibitor D, cacha +! This is a phenyl-methyl ether derivative having +! ethyl acetate at 4 position +! patch combination: +! core residue Compound "FBIB" >> Compound "FBIE" + +DELETE ATOM CC ! HD1 HE1 +DELETE ATOM HC ! | | +DELETE ATOM C1 ! (-0.5)OD1 HA1 HB1 CD1--CE1 +DELETE ATOM H1A ! \ | | // \\ +DELETE ATOM H1B ! CD--CA--CB--CG CZ--OH +DELETE ATOM H1C ! / | | \ __ / \ +DELETE ATOM C2 ! (-0.5)OD2 HA2 HB2 CD2--CE2 CM(Me) +DELETE ATOM H2A ! | | +DELETE ATOM H2B ! HD2 HE2 +DELETE ATOM H2C +DELETE ATOM HH +GROUP +ATOM HE2 HGR61 0.00 +GROUP +ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of +ATOM OH OG301 -0.39 ! RESI C36 and Igor's ethers should +ATOM CM CG331 -0.10 ! be better than analogy to phenol! +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND CE2 HE2 +BOND OH CM CM HM1 CM HM2 CM HM3 + +IC CZ CD2 *CE2 HE2 1.4159 120.13 -179.81 117.32 1.0785 +IC CE1 CZ OH CM 1.4005 117.83 171.75 116.32 1.4272 +IC CZ OH CM HM1 1.4145 116.32 -56.84 110.84 1.1126 +IC HM1 OH *CM HM2 1.1126 110.84 122.15 110.67 1.1120 +IC HM1 OH *CM HM3 1.1126 110.84 -118.98 108.83 1.1108 + +PRES FBIFR -0.10 ! C7H14 Fatty acid Binding protein Inhibitor, R-isomer, cacha +! This is IBUPROFEN (phenyl derivative having +! 2-methyl ethyl acetate at 4 position) +! core residue "FBIB" >> Compound "FBIFR" +! Orientation of the methyl group on ehtyl acetate dictates R/S configuration +DELETE ATOM CA +DELETE ATOM HA1 +DELETE ATOM HA2 +DELETE ATOM CB +DELETE ATOM HB1 +DELETE ATOM HB2 ! HD1 HE1 +DELETE ATOM CC ! | | +DELETE ATOM HC ! (-0.5)OD1 CMG CD1--CE1 CN1 +DELETE ATOM C1 ! \ | // \\ / +DELETE ATOM H1A ! CD--CBG--CG CZM--CM1--CM2 +DELETE ATOM H1B ! / | \ __ / \ +DELETE ATOM H1C ! (-0.5)OD2 HBG CD2--CE2 CN2 +DELETE ATOM C2 ! | | +DELETE ATOM H2A ! HD2 HE2 +DELETE ATOM H2B +DELETE ATOM H2C ! COMPOUND "FBIFR" OR "FBIFS" +DELETE ATOM CZ +DELETE ATOM OH +DELETE ATOM HH +GROUP +ATOM HE2 HGR61 0.00 +GROUP +ATOM CBG CG311 -0.19 +ATOM HBG HGA1 0.09 +ATOM CMG CG331 -0.27 +ATOM HMG1 HGA3 0.09 +ATOM HMG2 HGA3 0.09 +ATOM HMG3 HGA3 0.09 +GROUP +ATOM CZM CG2R61 0.00 +GROUP +ATOM CM1 CG321 -0.18 +ATOM HM1A HGA2 0.09 +ATOM HM1B HGA2 0.09 +GROUP +ATOM CM2 CG311 -0.09 +ATOM HM2 HGA1 0.09 +GROUP +ATOM CN1 CG331 -0.27 +ATOM HN1A HGA3 0.09 +ATOM HN1B HGA3 0.09 +ATOM HN1C HGA3 0.09 +GROUP +ATOM CN2 CG331 -0.27 +ATOM HN2A HGA3 0.09 +ATOM HN2B HGA3 0.09 +ATOM HN2C HGA3 0.09 + +BOND CE2 HE2 +BOND CG CBG CBG CD CBG HBG CBG CMG CMG HMG1 CMG HMG2 CMG HMG3 +BOND CE1 CZM CE2 CZM CZM CM1 CM1 HM1A CM1 HM1B +BOND CM1 CM2 CM2 HM2 CM2 CN1 CN1 HN1A CN1 HN1B CN1 HN1C +BOND CM2 CN2 CN2 HN2A CN2 HN2B CN2 HN2C +IMPR CD OD1 OD2 CBG + +IC CG CD1 CE1 CZM 1.4074 121.22 0.25 120.04 1.4018 +IC CZM CD2 *CE2 HE2 1.4038 120.33 -179.97 119.65 1.0800 +IC CE2 CD2 CG CBG 1.4008 120.74 178.69 123.82 1.5308 +IC CD2 CG CBG CMG 1.4107 123.82 -15.87 111.99 1.5638 +IC CD2 CG CBG HBG 1.4107 123.82 -132.75 108.39 1.1103 +IC CG CBG CMG HMG1 1.5308 111.99 68.31 110.42 1.1099 +IC HMG1 CBG *CMG HMG2 1.1099 110.42 118.37 109.28 1.1117 +IC HMG1 CBG *CMG HMG3 1.1099 110.42 -121.91 110.96 1.1084 +IC CMG CG *CBG CD 1.5638 111.99 126.26 113.97 1.5510 +IC CG CBG CD OD1 1.5308 113.97 1.93 120.65 1.2585 +IC OD1 CBG *CD OD2 1.2585 120.65 172.14 115.78 1.2623 +IC CE1 CE2 CZM CM1 2.4229 30.26 178.92 120.81 1.5097 +IC CE1 CZM CM1 HM1A 1.4018 119.74 50.63 107.54 1.1109 +IC HM1A CZM *CM1 HM1B 1.1109 107.54 117.28 109.24 1.1111 +IC HM1A CZM *CM1 CM2 1.1109 107.54 -120.94 111.69 1.5467 +IC CZM CM1 CM2 HM2 1.5097 111.69 56.61 108.58 1.1171 +IC HM2 CM1 *CM2 CN1 1.1171 108.58 117.56 110.34 1.5373 +IC HM2 CM1 *CM2 CN2 1.1171 108.58 -119.29 112.25 1.5383 +IC CM1 CM2 CN1 HN1A 1.5467 110.34 61.99 110.14 1.1105 +IC HN1A CM2 *CN1 HN1B 1.1105 110.14 119.99 110.39 1.1102 +IC HN1A CM2 *CN1 HN1C 1.1105 110.14 -119.88 110.33 1.1105 +IC CM1 CM2 CN2 HN2A 1.5467 112.25 60.91 110.56 1.1111 +IC HN2A CM2 *CN2 HN2B 1.1111 110.56 119.90 110.46 1.1099 +IC HN2A CM2 *CN2 HN2C 1.1111 110.56 -119.87 110.24 1.1101 + + +PRES FBIFS -0.10 ! C7H14 Fatty acid Binding protein Inhibitor, S-isomer, cacha +! This is IBUPROFEN (phenyl derivative having +! 2-methyl ethyl acetate at 4 position) +! core residue "FBIB" >> Compound "FBIFS" +! Orientation of the methyl group on ehtyl acetate dictates R/S configuration +DELETE ATOM CA +DELETE ATOM HA1 +DELETE ATOM HA2 +DELETE ATOM CB +DELETE ATOM HB1 +DELETE ATOM HB2 +DELETE ATOM CC ! HD1 HE1 +DELETE ATOM HC ! | | +DELETE ATOM C1 ! (-0.5)OD1 CMG CD1--CE1 CN1 +DELETE ATOM H1A ! \ | // \\ / +DELETE ATOM H1B ! CD--CBG--CG CZM--CM1--CM2 +DELETE ATOM H1C ! / | \ __ / \ +DELETE ATOM C2 ! (-0.5)OD2 HBG CD2--CE2 CN2 +DELETE ATOM H2A ! | | +DELETE ATOM H2B ! HD2 HE2 +DELETE ATOM H2C +DELETE ATOM CZ ! COMPOUND "FBIFR" OR "FBIFS" +DELETE ATOM OH +DELETE ATOM HH +GROUP +ATOM HE2 HGR61 0.00 +GROUP +ATOM CBG CG311 -0.19 +ATOM HBG HGA1 0.09 +ATOM CMG CG331 -0.27 +ATOM HMG1 HGA3 0.09 +ATOM HMG2 HGA3 0.09 +ATOM HMG3 HGA3 0.09 +GROUP +ATOM CZM CG2R61 0.00 +GROUP +ATOM CM1 CG321 -0.18 +ATOM HM1A HGA2 0.09 +ATOM HM1B HGA2 0.09 +GROUP +ATOM CM2 CG311 -0.09 +ATOM HM2 HGA1 0.09 +GROUP +ATOM CN1 CG331 -0.27 +ATOM HN1A HGA3 0.09 +ATOM HN1B HGA3 0.09 +ATOM HN1C HGA3 0.09 +GROUP +ATOM CN2 CG331 -0.27 +ATOM HN2A HGA3 0.09 +ATOM HN2B HGA3 0.09 +ATOM HN2C HGA3 0.09 + +BOND CE2 HE2 +BOND CG CBG CBG HBG CBG CD CBG CMG CMG HMG1 CMG HMG2 CMG HMG3 +BOND CE1 CZM CE2 CZM CZM CM1 CM1 HM1A CM1 HM1B +BOND CM1 CM2 CM2 HM2 CM2 CN1 CN1 HN1A CN1 HN1B CN1 HN1C +BOND CM2 CN2 CN2 HN2A CN2 HN2B CN2 HN2C +IMPR CD OD1 OD2 CBG + +IC CG CD1 CE1 CZM 1.4067 120.82 0.59 120.10 1.4030 +IC CZM CD2 *CE2 HE2 1.4050 120.15 -179.82 119.75 1.0799 +IC CE2 CD2 CG CBG 1.3998 120.76 178.17 119.92 1.5233 +IC CD2 CG CBG CMG 1.4058 119.92 -112.06 107.62 1.5610 ! S-isomer +IC CD2 CG CBG HBG 1.4058 119.92 5.06 110.49 1.1095 ! S-isomer +IC CG CBG CMG HMG1 1.5233 107.62 55.81 110.88 1.1088 +IC HMG1 CBG *CMG HMG2 1.1088 110.88 119.89 109.40 1.1116 +IC HMG1 CBG *CMG HMG3 1.1088 110.88 -121.32 110.59 1.1099 +IC CMG CG *CBG CD 1.5610 107.62 -124.32 115.01 1.5504 +IC CG CBG CD OD1 1.5233 115.01 -1.31 120.84 1.2583 +IC OD1 CBG *CD OD2 1.2583 120.84 -175.49 115.85 1.2621 +IC CE1 CE2 CZM CM1 2.4256 30.23 179.20 120.79 1.5096 +IC CE1 CZM CM1 HM1A 1.4030 119.71 50.70 107.54 1.1109 +IC HM1A CZM *CM1 HM1B 1.1109 107.54 117.31 109.24 1.1110 +IC HM1A CZM *CM1 CM2 1.1109 107.54 -120.92 111.68 1.5467 +IC CZM CM1 CM2 HM2 1.5096 111.68 56.65 108.57 1.1172 +IC HM2 CM1 *CM2 CN1 1.1172 108.57 117.56 110.34 1.5373 +IC HM2 CM1 *CM2 CN2 1.1172 108.57 -119.28 112.26 1.5383 +IC CM1 CM2 CN1 HN1A 1.5467 110.34 62.00 110.14 1.1105 +IC HN1A CM2 *CN1 HN1B 1.1105 110.14 119.98 110.39 1.1103 +IC HN1A CM2 *CN1 HN1C 1.1105 110.14 -119.89 110.33 1.1105 +IC CM1 CM2 CN2 HN2A 1.5467 112.26 60.95 110.56 1.1111 +IC HN2A CM2 *CN2 HN2B 1.1111 110.56 119.89 110.46 1.1099 +IC HN2A CM2 *CN2 HN2C 1.1111 110.56 -119.88 110.25 1.1101 +!End Shapiro's Fatty acid Binding protein Inhibitors, chayan, feb2008 + +!Fundamental functional groups, kevo, feb2008 +RESI ACN 0.000 ! C2H3N acetonitrile, kevo +GROUP +ATOM C1 CG331 -0.17 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM C2 CG1N1 0.36 +ATOM N3 NG1T1 -0.46 + +BOND C1 C2 C2 N3 +BOND C1 H11 C1 H12 C1 H13 +IC N3 C2 C1 H11 0.0000 179.90 0.00 0.00 0.0000 +IC C2 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 H11 *C1 H13 0.0000 0.00 240.00 0.00 0.0000 + +!End fundamental functional groups, kevo, feb2008 + +!Continuation of Maybridge list, kevo, feb2008 +RESI 3HPR 0.000 ! C4H5N 3H-pyrrole, kevo +GROUP +ATOM N1 NG2R50 -0.60 +ATOM C2 CG2R52 0.10 +ATOM H2 HGR52 0.13 ! H31 H4 +ATOM C3 CG3C52 0.05 ! \ / +ATOM H31 HGA2 0.09 ! H32--C3---C4 +ATOM H32 HGA2 0.09 ! | || +ATOM C4 CG2R51 -0.30 ! C2 C5 +ATOM H4 HGR51 0.18 ! / \\ / \ +ATOM C5 CG2R51 0.12 ! H2 N1 H5 +ATOM H5 HGR52 0.14 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 N1 +BOND C2 H2 C3 H31 C3 H32 C4 H4 C5 H5 +IC C3 C4 C5 N1 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 240.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 + +RESI 3HIN 0.000 ! C8H7N 3H-indole, kevo +GROUP +ATOM N1 NG2R50 -0.61 +ATOM C2 CG2R52 0.18 +ATOM H2 HGR52 0.11 +ATOM C3 CG3C52 -0.09 ! H5 +ATOM H31 HGA2 0.09 ! | +ATOM H32 HGA2 0.09 ! H31 C5 +ATOM C4 CG2RC0 0.25 ! \ / \\ +ATOM C5 CG2R61 -0.36 ! H32--C3---C4 C6--H6 +ATOM H5 HGR61 0.20 ! | || | +ATOM C6 CG2R61 -0.22 ! C2 C9 C7--H7 +ATOM H6 HGR61 0.21 ! / \\ / \ // +ATOM C7 CG2R61 -0.21 ! H2 N1 C8 +ATOM H7 HGR61 0.21 ! | +ATOM C8 CG2R61 -0.34 ! H8 +ATOM H8 HGR61 0.26 +ATOM C9 CG2RC0 0.23 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 N1 C4 C9 +BOND C2 H2 C3 H31 C3 H32 +BOND C5 H5 C6 H6 C7 H7 C8 H8 +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 240.00 0.00 0.0000 + +RESI INDI 0.000 ! C8H9N indoline, kevo +GROUP +ATOM N1 NG3C51 -0.68 +ATOM H1 HGP1 0.33 +ATOM C2 CG3C52 0.00 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 ! H5 +ATOM C3 CG3C52 -0.12 ! | +ATOM H31 HGA2 0.09 ! H31 C5 +ATOM H32 HGA2 0.09 ! \ / \\ +ATOM C4 CG2RC0 0.11 ! H32--C3---C4 C6--H6 +ATOM C5 CG2R61 -0.40 ! | || | +ATOM H5 HGR61 0.24 ! H22--C2 C9 C7--H7 +ATOM C6 CG2R61 -0.27 ! / \ / \ // +ATOM H6 HGR61 0.22 ! H21 N1 C8 +ATOM C7 CG2R61 -0.20 ! | | +ATOM H7 HGR61 0.20 ! H1 H8 +ATOM C8 CG2R61 -0.29 +ATOM H8 HGR61 0.21 +ATOM C9 CG2RC0 0.29 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 N1 C4 C9 +BOND N1 H1 C2 H21 C2 H22 C3 H31 C3 H32 +BOND C5 H5 C6 H6 C7 H7 C8 H8 +IC N1 C2 C3 C4 0.0000 0.00 330.00 0.00 0.0000 +IC C2 C3 C4 C9 0.0000 0.00 20.00 0.00 0.0000 +IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C2 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 N1 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 240.00 0.00 0.0000 + +RESI ZFUR 0.000 ! C8H6O benzofuran (there's only 1 benzofuran), kevo +GROUP +ATOM O1 OG2R50 -0.28 +ATOM C2 CG2R51 0.02 +ATOM H2 HGR52 0.18 ! H5 +ATOM C3 CG2R51 -0.40 ! | +ATOM H3 HGR51 0.25 ! H3 C5 +ATOM C4 CG2RC0 0.15 ! \ / \\ +ATOM C5 CG2R61 -0.33 ! C3---C4 C6--H6 +ATOM H5 HGR61 0.24 ! || || | +ATOM C6 CG2R61 -0.28 ! C2 C9 C7--H7 +ATOM H6 HGR61 0.23 ! / \ / \ // +ATOM C7 CG2R61 -0.21 ! H2 O1 C8 +ATOM H7 HGR61 0.22 ! | +ATOM C8 CG2R61 -0.34 ! H8 +ATOM H8 HGR61 0.24 +ATOM C9 CG2RC0 0.31 + +BOND O1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 O1 C4 C9 +BOND C2 H2 C3 H3 +BOND C5 H5 C6 H6 C7 H7 C8 H8 +IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C3 O1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 + +RESI ZTHP 0.000 ! C8H6S benzothiophene (there's only 1 benzothiophene), kevo +GROUP +ATOM S1 SG2R50 -0.16 +ATOM C2 CG2R51 -0.09 +ATOM H2 HGR52 0.18 ! H5 +ATOM C3 CG2R51 -0.28 ! | +ATOM H3 HGR51 0.21 ! H3 C5 +ATOM C4 CG2RC0 0.17 ! \ / \\ +ATOM C5 CG2R61 -0.34 ! C3---C4 C6--H6 +ATOM H5 HGR61 0.24 ! || || | +ATOM C6 CG2R61 -0.29 ! C2 C9 C7--H7 +ATOM H6 HGR61 0.24 ! / \ / \ // +ATOM C7 CG2R61 -0.21 ! H2 S1 C8 +ATOM H7 HGR61 0.21 ! | +ATOM C8 CG2R61 -0.23 ! H8 +ATOM H8 HGR61 0.24 +ATOM C9 CG2RC0 0.11 + +BOND S1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 S1 C4 C9 +BOND C2 H2 C3 H3 +BOND C5 H5 C6 H6 C7 H7 C8 H8 +IC S1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C3 S1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 + +RESI ZTHZ 0.000 ! C7H5NS benzothiazole, kevo +GROUP +ATOM S1 SG2R50 -0.25 +ATOM C2 CG2R53 0.16 +ATOM H2 HGR52 0.18 ! H5 +ATOM N3 NG2R50 -0.69 ! | +ATOM C4 CG2RC0 0.64 ! C5 +ATOM C5 CG2R61 -0.46 ! / \\ +ATOM H5 HGR61 0.26 ! N3---C4 C6--H6 +ATOM C6 CG2R61 -0.29 ! || || | +ATOM H6 HGR61 0.26 ! C2 C9 C7--H7 +ATOM C7 CG2R61 -0.38 ! / \ / \ // +ATOM H7 HGR61 0.26 ! H2 S1 C8 +ATOM C8 CG2R61 -0.24 ! | +ATOM H8 HGR61 0.22 ! H8 +ATOM C9 CG2RC0 0.33 + +BOND S1 C2 C2 N3 N3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 S1 C4 C9 +BOND C2 H2 +BOND C5 H5 C6 H6 C7 H7 C8 H8 +IC S1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C9 N3 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC N3 S1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 + +RESI PUR9 0.00 ! C5H4N4 purine (N9H-tautomer), kevo +GROUP +ATOM C5 CG2RC0 0.30 +ATOM N7 NG2R50 -0.73 +ATOM C8 CG2R53 0.37 ! H6 +ATOM H8 HGR52 0.09 ! | +ATOM N9 NG2R51 -0.19 ! C6 +ATOM H9 HGP1 0.29 ! // \ +ATOM N1 NG2R62 -0.73 ! N1 C5--N7\\ +ATOM C2 CG2R64 0.50 ! | || C8-H8 +ATOM H2 HGR62 0.14 ! C2 C4--N9/ +ATOM N3 NG2R62 -0.77 ! / \\ / \ +ATOM C4 CG2RC0 0.44 ! H2 N3 H9 +ATOM C6 CG2R61 0.09 ! Was: CG2R64. See: PYRM. +ATOM H6 HGR62 0.20 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 +BOND C5 N7 N7 C8 C8 N9 N9 C4 +BOND C2 H2 C6 H6 C8 H8 N9 H9 +IC N7 C8 N9 C4 0.0000 0.00 0.00 0.00 0.0000 +IC N9 C8 N7 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C8 N7 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 N7 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C4 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 + +RESI PUR7 0.00 ! C5H4N4 purine (N7H-tautomer), kevo +GROUP +ATOM C5 CG2RC0 0.23 +ATOM N7 NG2R51 -0.22 +ATOM H7 HGP1 0.26 ! H6 +ATOM C8 CG2R53 0.32 ! | +ATOM H8 HGR52 0.12 ! C6 H7 +ATOM N9 NG2R50 -0.57 ! // \ / +ATOM N1 NG2R62 -0.78 ! N1 C5--N7\ +ATOM C2 CG2R64 0.48 ! | || C8-H8 +ATOM H2 HGR62 0.13 ! C2 C4--N9// +ATOM N3 NG2R62 -0.58 ! / \\ / +ATOM C4 CG2RC0 0.21 ! H2 N3 +ATOM C6 CG2R61 0.31 +ATOM H6 HGR62 0.09 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1 +BOND C5 N7 N7 C8 C8 N9 N9 C4 +BOND C2 H2 C6 H6 C8 H8 N7 H7 +IC N7 C8 N9 C4 0.0000 0.00 0.00 0.00 0.0000 +IC N9 C8 N7 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C8 N7 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 N7 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C8 *N7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC N7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +!End continuation of Maybridge list, kevo, feb2008 + +!Continuation of Maybridge list, kevo and erh, jun2008 +RESI CPDE 0.000 ! C5H6 cyclopentadiene, kevo +ATOM C1 CG3C52 0.10 +ATOM H11 HGA2 0.09 ! H3 H4 +ATOM H12 HGA2 0.09 ! \ / +ATOM C2 CG2R51 -0.36 ! C3----C4 +ATOM H2 HGR51 0.22 ! || || +ATOM C3 CG2R51 -0.22 ! C2 C5 +ATOM H3 HGR51 0.22 ! / \ / \ +ATOM C4 CG2R51 -0.22 ! H2 C1 H5 +ATOM H4 HGR51 0.22 ! /\ +ATOM C5 CG2R51 -0.36 ! H11 H12 +ATOM H5 HGR51 0.22 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C1 C1 H11 C1 H12 +BOND C2 H2 C3 H3 C4 H4 C5 H5 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C2 *C1 H12 0.0000 0.00 240.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C1 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 + +RESI INDE 0.00 ! C9H8 indene, kevo +GROUP +ATOM C1 CG3C52 0.02 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM C2 CG2R51 -0.30 ! H5 +ATOM H2 HGR51 0.22 ! | +ATOM C3 CG2R51 -0.43 ! H3 C5 +ATOM H3 HGR51 0.26 ! \ / \\ +ATOM C4 CG2RC0 0.24 ! C3----C4 C6 -H6 +ATOM C5 CG2R61 -0.33 ! || || | +ATOM H5 HGR61 0.22 ! C2 C9 C7 -H7 +ATOM C6 CG2R61 -0.19 ! / \ / \ // +ATOM H6 HGR61 0.20 ! H2 C1 C8 +ATOM C7 CG2R61 -0.22 ! /\ | +ATOM H7 HGR61 0.21 ! H11 H12 H8 +ATOM C8 CG2R61 -0.36 +ATOM H8 HGR61 0.22 +ATOM C9 CG2RC0 0.06 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C4 C9 C9 C1 +BOND C1 H11 C1 H12 C2 H2 C3 H3 +BOND C5 H5 C6 H6 C7 H7 C8 H8 +IC C9 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C9 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C9 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C1 *C9 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C9 C8 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C9 C2 *C1 H12 0.0000 0.00 240.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 + +RESI CRBZ 0.00 ! C12H9N Carbazole, erh +GROUP +ATOM C1 CG2R61 -0.180 +ATOM H1 HGR61 0.180 +ATOM C2 CG2R61 -0.180 +ATOM H2 HGR61 0.180 +ATOM C3 CG2R61 -0.180 +ATOM H3 HGR61 0.180 +ATOM C4 CG2R61 -0.270 ! H4 H7 +ATOM H4 HGR61 0.270 ! | | +ATOM C5 CG2R67 -0.200 ! C4 C7 +ATOM C6 CG2R67 -0.200 ! // \ / \\ +ATOM C7 CG2R61 -0.270 ! H3--C3 C5----C6 C8--H8 +ATOM H7 HGR61 0.270 ! | || || | +ATOM C8 CG2R61 -0.180 ! H2--C2 C13 C11 C9--H9 +ATOM H8 HGR61 0.180 ! \\ / \ / \ // +ATOM C9 CG2R61 -0.180 ! C1 N12 C10 +ATOM H9 HGR61 0.180 ! | | | +ATOM C10 CG2R61 -0.180 ! H1 H12 H10 +ATOM H10 HGR61 0.180 +ATOM C11 CG2RC0 0.200 +ATOM N12 NG2R51 -0.300 +ATOM H12 HGP1 0.300 +ATOM C13 CG2RC0 0.200 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 +BOND C11 N12 N12 C13 C13 C1 C5 C13 C6 C11 +BOND C1 H1 C2 H2 C3 H3 C4 H4 C7 H7 +BOND C8 H8 C9 H9 C10 H10 N12 H12 +IC C5 C13 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C13 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C13 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C13 N12 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C13 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C5 C6 C11 0.0000 0.00 0.00 0.00 0.0000 +IC N12 C6 *C11 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C11 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C11 C10 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C13 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C13 *N12 H12 0.0000 0.00 180.00 0.00 0.0000 + +RESI FLRN 0.00 ! C13H10 Fluorene, erh +GROUP +ATOM C1 CG2R61 -0.140 +ATOM H1 HGR61 0.140 +ATOM C2 CG2R61 -0.170 +ATOM H2 HGR61 0.170 +ATOM C3 CG2R61 -0.190 +ATOM H3 HGR61 0.190 +ATOM C4 CG2R61 -0.280 ! H4 H7 +ATOM H4 HGR61 0.280 ! | | +ATOM C5 CG2R67 -0.240 ! C4 C7 +ATOM C6 CG2R67 -0.240 ! // \ / \\ +ATOM C7 CG2R61 -0.280 ! H3--C3 C5----C6 C8--H8 +ATOM H7 HGR61 0.280 ! | || || | +ATOM C8 CG2R61 -0.190 ! H2--C2 C13 C11 C9--H9 +ATOM H8 HGR61 0.190 ! \\ / \ / \ // +ATOM C9 CG2R61 -0.170 ! C1 C12 C10 +ATOM H9 HGR61 0.170 ! | / \ | +ATOM C10 CG2R61 -0.140 ! H1 H21 H22 H10 +ATOM H10 HGR61 0.140 +ATOM C11 CG2RC0 0.240 +ATOM C12 CG3C52 -0.180 +ATOM H21 HGA2 0.090 +ATOM H22 HGA2 0.090 +ATOM C13 CG2RC0 0.240 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 +BOND C11 C12 C12 C13 C13 C1 C5 C13 C6 C11 +BOND C1 H1 C2 H2 C3 H3 C4 H4 C7 H7 +BOND C8 H8 C9 H9 C10 H10 C12 H21 C12 H22 +IC C5 C13 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C13 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C13 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C13 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C13 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C5 C6 C11 0.0000 0.00 5.00 0.00 0.0000 ! Deliberate distorsion! +IC C5 C11 *C6 C7 0.0000 0.00 180.00 0.00 0.0000 ! Deviating def to make above work +IC C7 C6 C11 C10 0.0000 0.00 0.00 0.00 0.0000 ! Deviating def to make above work +IC C11 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C11 C10 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C13 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C13 *C12 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C11 C13 *C12 H22 0.0000 0.00 -120.00 0.00 0.0000 + +RESI NAFT 0.00 ! C10H8 Naphtalene, kevo +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H1 HGR61 0.115 +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM C3 CG2R61 -0.115 ! H4 H6 +ATOM H3 HGR61 0.115 ! | | +ATOM C4 CG2R61 -0.115 ! C4 C6 +ATOM H4 HGR61 0.115 ! // \ / \\ +ATOM C5 CG2R61 0.000 ! H3--C3 C5 C7--H7 +ATOM C6 CG2R61 -0.115 ! | || | +ATOM H6 HGR61 0.115 ! H2--C2 C10 C8--H8 +ATOM C7 CG2R61 -0.115 ! \\ / \ // +ATOM H7 HGR61 0.115 ! C1 C9 +ATOM C8 CG2R61 -0.115 ! | | +ATOM H8 HGR61 0.115 ! H1 H9 +ATOM C9 CG2R61 -0.115 +ATOM H9 HGR61 0.115 +ATOM C10 CG2R61 0.000 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 C1 C10 +BOND C1 H1 C2 H2 C3 H3 C4 H4 +BOND C6 H6 C7 H7 C8 H8 C9 H9 +IC C5 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI QINL 0.00 ! C9H7N Quinoline, kevo and erh +GROUP +ATOM N1 NG2R60 -0.640 +ATOM C2 CG2R61 0.160 +ATOM H2 HGR62 0.140 +ATOM C3 CG2R61 -0.115 ! H4 H6 +ATOM H3 HGR61 0.115 ! | | +ATOM C4 CG2R61 -0.115 ! C4 C6 +ATOM H4 HGR61 0.115 ! // \ / \\ +ATOM C5 CG2R61 0.000 ! H3--C3 C5 C7--H7 +ATOM C6 CG2R61 -0.115 ! | || | +ATOM H6 HGR61 0.115 ! H2--C2 C10 C8--H8 +ATOM C7 CG2R61 -0.115 ! \\ / \ // +ATOM H7 HGR61 0.115 ! N1 C9 +ATOM C8 CG2R61 -0.115 ! | +ATOM H8 HGR61 0.115 ! H9 +ATOM C9 CG2R61 -0.115 +ATOM H9 HGR61 0.115 +ATOM C10 CG2R61 0.340 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 N1 C10 +BOND C2 H2 C3 H3 C4 H4 +BOND C6 H6 C7 H7 C8 H8 C9 H9 +IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI IQIN 0.00 ! C9H7N Isoquinoline, erh +GROUP +ATOM C1 CG2R61 0.17 +ATOM H1 HGR62 0.15 +ATOM N2 NG2R60 -0.61 +ATOM C3 CG2R61 0.12 ! H4 H6 +ATOM H3 HGR62 0.14 ! | | +ATOM C4 CG2R61 -0.115 ! C4 C6 +ATOM H4 HGR61 0.115 ! // \ / \\ +ATOM C5 CG2R61 0.05 ! H3--C3 C5 C7--H7 +ATOM C6 CG2R61 -0.115 ! | || | +ATOM H6 HGR61 0.115 ! N2 C10 C8--H8 +ATOM C7 CG2R61 -0.115 ! \\ / \ // +ATOM H7 HGR61 0.115 ! C1 C9 +ATOM C8 CG2R61 -0.115 ! | | +ATOM H8 HGR61 0.115 ! H1 H9 +ATOM C9 CG2R61 -0.115 +ATOM H9 HGR61 0.115 +ATOM C10 CG2R61 -0.02 + +BOND C1 N2 N2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 C1 C10 +BOND C1 H1 C3 H3 C4 H4 +BOND C6 H6 C7 H7 C8 H8 C9 H9 +IC C5 C10 C1 N2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C10 N2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI CINL 0.00 ! C8H6N2 Cinnoline, erh +GROUP +ATOM N1 NG2R62 -0.500 +ATOM N2 NG2R62 -0.450 +ATOM C3 CG2R61 0.350 ! H4 H6 +ATOM H3 HGR62 0.070 ! | | +ATOM C4 CG2R61 -0.160 ! C4 C6 +ATOM H4 HGR61 0.180 ! // \ / \\ +ATOM C5 CG2R61 0.000 ! H3--C3 C5 C7--H7 +ATOM C6 CG2R61 -0.115 ! | || | +ATOM H6 HGR61 0.115 ! N2 C10 C8--H8 +ATOM C7 CG2R61 -0.115 ! \\ / \ // +ATOM H7 HGR61 0.115 ! N1 C9 +ATOM C8 CG2R61 -0.115 ! | +ATOM H8 HGR61 0.115 ! H9 +ATOM C9 CG2R61 -0.160 +ATOM H9 HGR61 0.180 +ATOM C10 CG2R61 0.490 + +BOND N1 N2 N2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 N1 C10 +BOND C3 H3 C4 H4 C6 H6 +BOND C7 H7 C8 H8 C9 H9 +IC C5 C10 N1 N2 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI FTAZ 0.00 ! C8H6N2 Phthalazine, erh +GROUP +ATOM C1 CG2R61 0.340 +ATOM H1 HGR62 0.080 +ATOM N2 NG2R62 -0.490 +ATOM N3 NG2R62 -0.490 ! H4 H6 +ATOM C4 CG2R61 0.340 ! | | +ATOM H4 HGR62 0.080 ! C4 C6 +ATOM C5 CG2R61 0.070 ! // \ / \\ +ATOM C6 CG2R61 -0.115 ! N3 C5 C7--H7 +ATOM H6 HGR61 0.115 ! | || | +ATOM C7 CG2R61 -0.115 ! N2 C10 C8--H8 +ATOM H7 HGR61 0.115 ! \\ / \ // +ATOM C8 CG2R61 -0.115 ! C1 C9 +ATOM H8 HGR61 0.115 ! | | +ATOM C9 CG2R61 -0.115 ! H1 H9 +ATOM H9 HGR61 0.115 +ATOM C10 CG2R61 0.070 + +BOND C1 N2 N2 N3 N3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 C1 C10 +BOND C1 H1 C4 H4 C6 H6 +BOND C7 H7 C8 H8 C9 H9 +IC C5 C10 C1 N2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 N3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C10 N2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI QINZ 0.00 ! C8H6N2 Quinazoline, erh +GROUP +ATOM N1 NG2R62 -0.810 +ATOM C2 CG2R64 0.520 +ATOM H2 HGR62 0.140 +ATOM N3 NG2R62 -0.750 ! H4 H6 +ATOM C4 CG2R61 0.280 ! | | +ATOM H4 HGR62 0.130 ! C4 C6 +ATOM C5 CG2R61 0.020 ! // \ / \\ +ATOM C6 CG2R61 -0.115 ! N3 C5 C7--H7 +ATOM H6 HGR61 0.115 ! | || | +ATOM C7 CG2R61 -0.115 ! H2--C2 C10 C8--H8 +ATOM H7 HGR61 0.115 ! \\ / \ // +ATOM C8 CG2R61 -0.115 ! N1 C9 +ATOM H8 HGR61 0.115 ! | +ATOM C9 CG2R61 -0.115 ! H9 +ATOM H9 HGR61 0.115 +ATOM C10 CG2R61 0.470 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 N1 C10 +BOND C2 H2 C4 H4 C6 H6 +BOND C7 H7 C8 H8 C9 H9 +IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC N1 N3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI QINX 0.00 ! C8H6N2 Quinoxaline, erh +GROUP +ATOM N1 NG2R60 -0.580 +ATOM C2 CG2R61 0.090 +ATOM H2 HGR62 0.160 +ATOM C3 CG2R61 0.090 ! H6 +ATOM H3 HGR62 0.160 ! | +ATOM N4 NG2R60 -0.580 ! N4 C6 +ATOM C5 CG2R61 0.330 ! // \ / \\ +ATOM C6 CG2R61 -0.115 ! H3--C3 C5 C7--H7 +ATOM H6 HGR61 0.115 ! | || | +ATOM C7 CG2R61 -0.115 ! H2--C2 C10 C8--H8 +ATOM H7 HGR61 0.115 ! \\ / \ // +ATOM C8 CG2R61 -0.115 ! N1 C9 +ATOM H8 HGR61 0.115 ! | +ATOM C9 CG2R61 -0.115 ! H9 +ATOM H9 HGR61 0.115 +ATOM C10 CG2R61 0.330 + +BOND N1 C2 C2 C3 C3 N4 N4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 N1 C10 +BOND C2 H2 C3 H3 C6 H6 +BOND C7 H7 C8 H8 C9 H9 +IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C10 C5 N4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 N4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 N4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI 18NFD 0.00 ! C8H6N2 1,8-naphthyridine, erh +GROUP +ATOM N1 NG2R62 -0.660 +ATOM C2 CG2R61 0.330 +ATOM H2 HGR62 0.090 +ATOM C3 CG2R61 -0.115 ! H4 H6 +ATOM H3 HGR61 0.115 ! | | +ATOM C4 CG2R61 -0.115 ! C4 C6 +ATOM H4 HGR61 0.115 ! // \ / \\ +ATOM C5 CG2R61 0.000 ! H3--C3 C5 C7--H7 +ATOM C6 CG2R61 -0.115 ! | || | +ATOM H6 HGR61 0.115 ! H2--C2 C10 C8--H8 +ATOM C7 CG2R61 -0.115 ! \\ / \ // +ATOM H7 HGR61 0.115 ! N1 N9 +ATOM C8 CG2R61 0.330 +ATOM H8 HGR62 0.090 +ATOM N9 NG2R62 -0.660 +ATOM C10 CG2R64 0.480 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 N9 +BOND N9 C10 C5 C10 N1 C10 +BOND C2 H2 C3 H3 C4 H4 +BOND C6 H6 C7 H7 C8 H8 +IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C10 N9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 N9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 + +RESI PTID 0.00 ! C6H4N4 pteridine, erh +GROUP +ATOM N1 NG2R62 -0.710 +ATOM C2 CG2R64 0.500 +ATOM H2 HGR62 0.140 +ATOM N3 NG2R62 -0.700 ! H4 +ATOM C4 CG2R61 0.110 ! | +ATOM H4 HGR62 0.180 ! C4 N6 +ATOM C5 CG2R61 0.450 ! // \ / \\ +ATOM N6 NG2R60 -0.640 ! N3 C5 C7--H7 +ATOM C7 CG2R61 0.185 ! | || | +ATOM H7 HGR62 0.105 ! H2--C2 C10 C8--H8 +ATOM C8 CG2R61 0.320 ! \\ / \ // +ATOM H8 HGR62 0.090 ! N1 N9 +ATOM N9 NG2R62 -0.650 +ATOM C10 CG2R64 0.620 +! Manual init guess (analogy to PYZN, PYRM, PUR9 and PUR7) + +BOND N1 C2 C2 N3 N3 C4 C4 C5 +BOND C5 N6 N6 C7 C7 C8 C8 N9 +BOND N9 C10 C5 C10 N1 C10 +BOND C2 H2 C4 H4 C7 H7 C8 H8 +IC C5 C10 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C5 *C10 N9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 N6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 N6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 N9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC N1 N3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 N9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 + +RESI ANTR 0.00 ! C14H10 Anthracene, kevo and erh +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H1 HGR61 0.115 +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM C3 CG2R61 -0.115 +ATOM H3 HGR61 0.115 +ATOM C4 CG2R61 -0.115 +ATOM H4 HGR61 0.115 ! H4 H6 H8 +ATOM C5 CG2R61 0.000 ! | | | +ATOM C6 CG2R61 -0.115 ! C4 C6 C8 +ATOM H6 HGR61 0.115 ! // \ / \\ / \\ +ATOM C7 CG2R61 0.000 ! H3--C3 C5 C7 C9--H9 +ATOM C8 CG2R61 -0.115 ! | || | | +ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 +ATOM C9 CG2R61 -0.115 ! \\ / \ // \ // +ATOM H9 HGR61 0.115 ! C1 C13 C11 +ATOM C10 CG2R61 -0.115 ! | | | +ATOM H10 HGR61 0.115 ! H1 H13 H11 +ATOM C11 CG2R61 -0.115 +ATOM H11 HGR61 0.115 +ATOM C12 CG2R61 0.000 +ATOM C13 CG2R61 -0.115 +ATOM H13 HGR61 0.115 +ATOM C14 CG2R61 0.000 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 +BOND C11 C12 C12 C13 C13 C14 C14 C1 C5 C14 C7 C12 +BOND C1 H1 C2 H2 C3 H3 C4 H4 C6 H6 +BOND C8 H8 C9 H9 C10 H10 C11 H11 C13 H13 +IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C14 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C14 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C14 C13 C12 0.0000 0.00 0.00 0.00 0.0000 +IC C13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C12 *C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C14 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 + +RESI ACRD 0.00 ! C13H9N Acridine, erh +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H1 HGR61 0.115 +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM C3 CG2R61 -0.115 +ATOM H3 HGR61 0.115 +ATOM C4 CG2R61 -0.115 +ATOM H4 HGR61 0.115 ! H4 H6 H8 +ATOM C5 CG2R61 0.000 ! | | | +ATOM C6 CG2R61 -0.115 ! C4 C6 C8 +ATOM H6 HGR61 0.115 ! // \ / \\ / \\ +ATOM C7 CG2R61 0.000 ! H3--C3 C5 C7 C9--H9 +ATOM C8 CG2R61 -0.115 ! | || | | +ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 +ATOM C9 CG2R61 -0.115 ! \\ / \ // \ // +ATOM H9 HGR61 0.115 ! C1 N13 C11 +ATOM C10 CG2R61 -0.115 ! | | +ATOM H10 HGR61 0.115 ! H1 H11 +ATOM C11 CG2R61 -0.115 +ATOM H11 HGR61 0.115 +ATOM C12 CG2R61 0.345 +ATOM N13 NG2R60 -0.690 +ATOM C14 CG2R61 0.345 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 C11 +BOND C11 C12 C12 N13 N13 C14 C14 C1 C5 C14 C7 C12 +BOND C1 H1 C2 H2 C3 H3 C4 H4 C6 H6 +BOND C8 H8 C9 H9 C10 H10 C11 H11 +IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C14 N13 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C14 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C14 N13 C12 0.0000 0.00 0.00 0.00 0.0000 +IC N13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C12 *C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 + +RESI FENZ 0.00 ! C12H8N2 Phenazine, erh +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H1 HGR61 0.115 +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM C3 CG2R61 -0.115 +ATOM H3 HGR61 0.115 +ATOM C4 CG2R61 -0.115 ! H4 H8 +ATOM H4 HGR61 0.115 ! | | +ATOM C5 CG2R61 0.320 ! C4 N6 C8 +ATOM N6 NG2R60 -0.640 ! // \ / \\ / \\ +ATOM C7 CG2R61 0.320 ! H3--C3 C5 C7 C9--H9 +ATOM C8 CG2R61 -0.115 ! | || | | +ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 +ATOM C9 CG2R61 -0.115 ! \\ / \ // \ // +ATOM H9 HGR61 0.115 ! C1 N13 C11 +ATOM C10 CG2R61 -0.115 ! | | +ATOM H10 HGR61 0.115 ! H1 H11 +ATOM C11 CG2R61 -0.115 +ATOM H11 HGR61 0.115 +ATOM C12 CG2R61 0.320 +ATOM N13 NG2R60 -0.640 +ATOM C14 CG2R61 0.320 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 N6 +BOND N6 C7 C7 C8 C8 C9 C9 C10 C10 C11 +BOND C11 C12 C12 N13 N13 C14 C14 C1 C5 C14 C7 C12 +BOND C1 H1 C2 H2 C3 H3 C4 H4 +BOND C8 H8 C9 H9 C10 H10 C11 H11 +IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C14 N13 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C14 *C5 N6 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C5 N6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C14 N13 C12 0.0000 0.00 0.00 0.00 0.0000 +IC N13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C12 *C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 + +RESI FEOZ 0.00 ! C12H9NO Phenoxazine, erh & kevo +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H1 HGR61 0.115 +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM C3 CG2R61 -0.115 +ATOM H3 HGR61 0.115 +ATOM C4 CG2R61 -0.115 ! H4 H8 +ATOM H4 HGR61 0.115 ! | | +ATOM C5 CG2R61 0.130 ! C4 O6 C8 +ATOM O6 OG3R60 -0.260 ! // \ / \ / \\ +ATOM C7 CG2R61 0.130 ! H3--C3 C5 C7 C9--H9 +ATOM C8 CG2R61 -0.115 ! | || || | +ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 +ATOM C9 CG2R61 -0.115 ! \\ / \ / \ // +ATOM H9 HGR61 0.115 ! C1 N13 C11 +ATOM C10 CG2R61 -0.115 ! | | | +ATOM H10 HGR61 0.115 ! H1 H13 H11 +ATOM C11 CG2R61 -0.115 +ATOM H11 HGR61 0.115 +ATOM C12 CG2R61 0.040 +ATOM N13 NG311 -0.470 +ATOM H13 HGPAM1 0.390 +ATOM C14 CG2R61 0.040 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 O6 +BOND O6 C7 C7 C8 C8 C9 C9 C10 C10 C11 +BOND C11 C12 C12 N13 N13 C14 C14 C1 C5 C14 C7 C12 +BOND C1 H1 C2 H2 C3 H3 C4 H4 +BOND C8 H8 C9 H9 C10 H10 C11 H11 N13 H13 +IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C14 N13 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C14 *C5 O6 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C5 O6 C7 0.0000 0.00 -30.00 0.00 0.0000 +IC C5 C14 N13 C12 0.0000 0.00 30.00 0.00 0.0000 +IC N13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 +IC O6 C12 *C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C14 *N13 H13 0.0000 0.00 120.00 0.00 0.0000 + +RESI FETZ 0.00 ! C12H9NS Phenothiazine, erh +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H1 HGR61 0.115 +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM C3 CG2R61 -0.115 +ATOM H3 HGR61 0.115 +ATOM C4 CG2R61 -0.115 ! H4 H8 +ATOM H4 HGR61 0.115 ! | | +ATOM C5 CG2R61 0.130 ! C4 S6 C8 +ATOM S6 SG311 -0.240 ! // \ / \ / \\ +ATOM C7 CG2R61 0.130 ! H3--C3 C5 C7 C9--H9 +ATOM C8 CG2R61 -0.115 ! | || || | +ATOM H8 HGR61 0.115 ! H2--C2 C14 C12 C10-H10 +ATOM C9 CG2R61 -0.115 ! \\ / \ / \ // +ATOM H9 HGR61 0.115 ! C1 N13 C11 +ATOM C10 CG2R61 -0.115 ! | | | +ATOM H10 HGR61 0.115 ! H1 H13 H11 +ATOM C11 CG2R61 -0.115 +ATOM H11 HGR61 0.115 +ATOM C12 CG2R61 -0.010 +ATOM N13 NG311 -0.360 +ATOM H13 HGPAM1 0.360 +ATOM C14 CG2R61 -0.010 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 S6 +BOND S6 C7 C7 C8 C8 C9 C9 C10 C10 C11 +BOND C11 C12 C12 N13 N13 C14 C14 C1 C5 C14 C7 C12 +BOND C1 H1 C2 H2 C3 H3 C4 H4 +BOND C8 H8 C9 H9 C10 H10 C11 H11 N13 H13 +IC C5 C14 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C14 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C14 N13 0.0000 0.00 180.00 0.00 1.4300 +IC C4 C14 *C5 S6 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C5 S6 C7 0.0000 0.00 -30.00 99.00 0.0000 +IC C5 C14 N13 C12 0.0000 0.00 30.00 114.00 1.4300 +IC N13 C7 *C12 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C12 C7 C8 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C12 C11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C14 *N13 H13 0.0000 0.00 120.00 0.00 0.0000 + +RESI DIOL 0.000 ! C3H6O2 1,3-Dioxolane, erh +GROUP +ATOM O1 OG3C51 -0.40 +ATOM C2 CG3C52 0.16 ! H42 +ATOM H21 HGA2 0.09 ! / +ATOM H22 HGA2 0.09 ! O3----C4--H41 +ATOM O3 OG3C51 -0.40 ! | | +ATOM C4 CG3C52 0.05 ! H21--C2 C5--H51 +ATOM H41 HGA2 0.09 ! / \ / \ +ATOM H42 HGA2 0.09 ! H22 O1 H52 +ATOM C5 CG3C52 0.05 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND O1 C2 C2 O3 O3 C4 +BOND C4 C5 C5 O1 +BOND C2 H21 C2 H22 C4 H41 C4 H42 +BOND C5 H51 C5 H52 +IC C4 C5 O1 C2 0.0000 0.00 30.00 0.00 0.0000 +IC O1 C5 C4 O3 0.0000 0.00 0.00 0.00 0.0000 +IC O1 O3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O1 O3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC O3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC O3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC O1 C4 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 + +RESI IMDP 1.000 ! C3H9N2 Imidazolidine protonated, erh and kevo +GROUP +ATOM N1 NG3C51 -0.89 !>=.89 +ATOM H1 HGP1 0.50 !<=.50 +ATOM C2 CG3C54 0.16 +ATOM H21 HGA2 0.28 ! H32 H42 +ATOM H22 HGA2 0.28 ! \(+) / +ATOM N3 NG3P2 -0.89 ! H31--N3----C4--H41 +ATOM H31 HGP2 0.54 !x | | +ATOM H32 HGP2 0.54 !xH21--C2 C5--H51 +ATOM C4 CG3C54 -0.22 ! / \ / \ +ATOM H41 HGA2 0.28 ! H22 N1 H52 +ATOM H42 HGA2 0.28 ! | +ATOM C5 CG3C52 -0.04 ! H1 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND N1 H1 C2 H21 C2 H22 N3 H31 N3 H32 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 C2 C2 N3 C4 C5 C5 N1 N3 C4 +IC C2 N3 C4 C5 0.0000 0.00 -20.00 0.00 0.0000 +IC N3 C4 C5 N1 0.0000 0.00 40.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *N3 H31 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *N3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC N3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC N3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 N3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC N1 N3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 + +RESI PRZP 1.000 ! C3H9N2 Pyrazolidine protonated, kevo +GROUP +ATOM N1 NG3C51 -0.47 +ATOM H1 HGP1 0.35 +ATOM N2 NG3P2 -0.18 ! H32 H42 +ATOM H21 HGP2 0.37 ! \ / +ATOM H22 HGP2 0.37 ! H31--C3----C4--H41 +ATOM C3 CG3C54 -0.30 ! | | +ATOM H31 HGA2 0.28 ! H21--N2(+) C5--H51 +ATOM H32 HGA2 0.28 ! / \ / \ +ATOM C4 CG3C52 -0.18 ! H22 N1 H52 +ATOM H41 HGA2 0.09 ! | +ATOM H42 HGA2 0.09 ! H1 +ATOM C5 CG3C52 0.12 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND N1 H1 N2 H21 N2 H22 C3 H31 C3 H32 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +BOND N1 N2 N2 C3 C4 C5 C5 N1 C3 C4 +IC N2 C3 C4 C5 0.0000 0.00 -20.00 0.00 0.0000 +IC C3 C4 C5 N1 0.0000 0.00 40.00 0.00 0.0000 +IC N2 C5 *N1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC C4 N2 *C3 H31 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 N2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C3 *N2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C3 *N2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C4 *C5 H51 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C4 *C5 H52 0.0000 0.00 120.00 0.00 0.0000 + +RESI QINU 1.00 ! C7H14N Quinuclidine, kevo +GROUP +ATOM N1 NG3P1 0.13 +ATOM H1 HGP2 0.19 +ATOM C2 CG324 0.03 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C6 CG324 0.03 +ATOM H61 HGA2 0.09 ! C5---C6 +ATOM H62 HGA2 0.09 ! / \ (+) +ATOM C7 CG324 0.03 ! H4--C4--C8-C7--N1--H1 +ATOM H71 HGA2 0.09 ! \ / +ATOM H72 HGA2 0.09 ! C3---C2 +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG311 -0.04 +ATOM H4 HGA1 0.09 +ATOM C5 CG321 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +ATOM C8 CG321 -0.18 +ATOM H81 HGA2 0.09 +ATOM H82 HGA2 0.09 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 N1 N1 C7 C7 C8 C8 C4 +BOND N1 H1 C4 H4 +BOND C2 H21 C2 H22 C3 H31 C3 H32 +BOND C5 H51 C5 H52 C6 H61 C6 H62 +BOND C7 H71 C7 H72 C8 H81 C8 H82 +IC C6 N1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N1 C6 C5 0.0000 0.00 -60.00 0.00 0.0000 +IC C2 C6 *N1 C7 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *N1 H1 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 N1 C7 C8 0.0000 0.00 -60.00 0.00 0.0000 +IC C3 N1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 N1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 N1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 N1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C8 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C8 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 +IC C7 C4 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 +IC C7 C4 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 -120.00 0.00 0.0000 + +RESI NORB 0.00 ! C7H12 Norbornane, kevo +GROUP +ATOM C1 CG3RC1 -0.09 +ATOM H1 HGA1 0.09 +ATOM C2 CG3C52 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG3C52 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 ! C5---C6 +ATOM C4 CG3RC1 -0.09 ! / \ +ATOM H4 HGA1 0.09 ! H4--C4---C7---C1--H1 +ATOM C5 CG3C52 -0.18 ! \ / +ATOM H51 HGA2 0.09 ! C3---C2 +ATOM H52 HGA2 0.09 +ATOM C6 CG3C52 -0.18 +ATOM H61 HGA2 0.09 +ATOM H62 HGA2 0.09 +ATOM C7 CG3C52 -0.18 +ATOM H71 HGA2 0.09 +ATOM H72 HGA2 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C1 C1 C7 C7 C4 +BOND C1 H1 C4 H4 C7 H71 C7 H72 +BOND C2 H21 C2 H22 C3 H31 C3 H32 +BOND C5 H51 C5 H52 C6 H61 C6 H62 +IC C6 C1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C1 C6 C5 0.0000 0.00 -60.00 0.00 0.0000 +IC C2 C6 *C1 C7 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C6 *C1 H1 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C4 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C4 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C1 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 + +RESI ADAM 0.00 ! C10H16 Adamantane, kevo and erh +GROUP +ATOM C1 CG311 -0.09 +ATOM H1 HGA1 0.09 +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG311 -0.09 +ATOM H3 HGA1 0.09 +ATOM C4 CG321 -0.18 +ATOM H41 HGA2 0.09 ! _C1_ +ATOM H42 HGA2 0.09 ! _- \ -_ +ATOM C5 CG311 -0.09 ! C2 \ C8 +ATOM H5 HGA1 0.09 ! | C10 | +ATOM C6 CG321 -0.18 ! | | | +ATOM H61 HGA2 0.09 ! C3_ |_C7 +ATOM H62 HGA2 0.09 ! \ -_ _+ \ +ATOM C7 CG311 -0.09 ! \ C9 | \ +ATOM H7 HGA1 0.09 ! \ C5_ \ +ATOM C8 CG321 -0.18 ! \ / -_ \ +ATOM H81 HGA2 0.09 ! C4 -C6 +ATOM H82 HGA2 0.09 +ATOM C9 CG321 -0.18 +ATOM H91 HGA2 0.09 +ATOM H92 HGA2 0.09 +ATOM C10 CG321 -0.18 +ATOM H101 HGA2 0.09 +ATOM H102 HGA2 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C1 +BOND C3 C9 C9 C7 C5 C10 C10 C1 +BOND C1 H1 C3 H3 C5 H5 C7 H7 +BOND C2 H21 C2 H22 C4 H41 C4 H42 +BOND C6 H61 C6 H62 C8 H81 C8 H82 +BOND C9 H91 C9 H92 C10 H101 C10 H102 +IC C1 C2 C3 C9 0.0000 0.00 -60.00 0.00 0.0000 +IC C3 C2 C1 C8 0.0000 0.00 60.00 0.00 0.0000 +IC C2 C1 C8 C7 0.0000 0.00 -60.00 0.00 0.0000 +IC C2 C9 *C3 C4 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C9 *C3 H3 0.0000 0.00 120.00 0.00 0.0000 +IC C9 C8 *C7 C6 0.0000 0.00 -120.00 0.00 0.0000 +IC C9 C8 *C7 H7 0.0000 0.00 120.00 0.00 0.0000 +IC C8 C2 *C1 C10 0.0000 0.00 -120.00 0.00 0.0000 +IC C8 C2 *C1 H1 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 -60.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C7 C1 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 +IC C7 C1 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C7 *C9 H91 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C7 *C9 H92 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C10 H101 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C1 *C10 H102 0.0000 0.00 -120.00 0.00 0.0000 + +RESI AZUL 0.00 ! C10H8 azulene, kevo +!QM has exteremly low freq for 7-ring. In CHARMM, it's way too rigid, +!despite drastically pulling down all force constants. However, +!The final result is more or less in line with naftalene (NAFT). +GROUP +ATOM C1 CG2R51 -0.30 +ATOM H1 HGR51 0.20 +ATOM C2 CG2R51 -0.17 +ATOM H2 HGR51 0.20 +ATOM C3 CG2R51 -0.30 ! H5 +ATOM H3 HGR51 0.20 ! H3 | H6 +ATOM C4 CG2RC7 0.07 ! | C5-_ / +ATOM C5 CG2R71 -0.24 ! C3-_ // -C6 +ATOM H5 HGR71 0.23 ! // -C4 \\ +ATOM C6 CG2R71 -0.15 ! H2--C2 | C7--H7 +ATOM H6 HGR71 0.18 ! \ _=C10 / +ATOM C7 CG2R71 -0.22 ! C1=- \ _=C8 +ATOM H7 HGR71 0.21 ! | C9=- \ +ATOM C8 CG2R71 -0.15 ! H1 | H8 +ATOM H8 HGR71 0.18 ! H9 +ATOM C9 CG2R71 -0.24 +ATOM H9 HGR71 0.23 +ATOM C10 CG2RC7 0.07 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C10 C1 C4 C10 +BOND C1 H1 C2 H2 C3 H3 C5 H5 +BOND C6 H6 C7 H7 C8 H8 C9 H9 +IC C4 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C10 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C4 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C10 *C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +!End continuation of Maybridge list, kevo and erh, jun2008 + +!Team Sugar, og, jun2008 +RESI AMOL -1.00 ! C4H7O4 alpha-methoxy-lactic acid, og +GROUP +ATOM C1 CG301 0.30 ! CT1 HM1 HM2 HM3 +ATOM C2 CG2O3 0.30 ! CC \ | / +ATOM OH OG311 -0.65 ! OH1 CM +ATOM HO HGP1 0.42 ! H | +ATOM OM OG301 -0.34 ! ethers OM O1 (-) +ATOM CM CG331 -0.10 ! CT3 | / +ATOM HM1 HGA3 0.09 ! HA OH--C1--C2 +ATOM HM2 HGA3 0.09 ! HA / | \\ +ATOM HM3 HGA3 0.09 ! HA HO | O2 +ATOM O1 OG2D2 -0.60 ! OC H01--C0 +ATOM O2 OG2D2 -0.60 ! OC | \ +GROUP ! H02 H03 +ATOM C0 CG331 -0.27 ! CT3 +ATOM H01 HGA3 0.09 ! HA +ATOM H02 HGA3 0.09 ! HA +ATOM H03 HGA3 0.09 ! HA +BOND C1 OH OH HO C1 OM C1 C0 +BOND C1 C2 C2 O1 +BOND C0 H01 C0 H02 C0 H03 +BOND OM CM +BOND CM HM1 CM HM2 CM HM3 +BOND C2 O2 +IMPR C2 O2 O1 C1 +IC C2 C1 OM CM 1.5530 103.90 -179.96 113.60 1.4233 +IC OM C2 *C1 C0 1.4292 103.90 120.03 110.17 1.5625 +IC OM C2 *C1 OH 1.4292 103.90 -122.26 107.58 1.4253 +IC C2 C1 OH HO 1.5530 107.58 -175.04 105.92 0.9600 +IC C1 OM CM HM1 1.4292 113.60 51.98 110.67 1.1100 +IC HM1 OM *CM HM2 1.1100 110.67 -121.80 110.69 1.1095 +IC HM1 OM *CM HM3 1.1100 110.67 119.24 109.06 1.1099 +IC OH C1 C2 O1 1.4253 107.58 116.60 118.67 1.2616 +IC O1 C1 *C2 O2 1.2616 118.67 -179.94 118.34 1.2627 +IC OH C1 C0 H01 1.4253 108.18 -61.82 109.95 1.1112 +IC H01 C1 *C0 H02 1.1112 109.95 -118.40 109.70 1.1104 +IC H01 C1 *C0 H03 1.1112 109.95 120.36 111.60 1.1074 +PATC FIRS NONE LAST NONE +!End team Sugar, og, jun2008 + +!Opioid preparation, kevo, jun2008 +RESI CHXE 0.00 ! C6H10 cyclohexene, kevo +GROUP ! Based on RESI TMCH . +ATOM C1 CG321 -0.18 ! We don't really want to optimize it. +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM C2 CG321 -0.18 ! H11 H12 +ATOM H21 HGA2 0.09 ! \ / +ATOM H22 HGA2 0.09 ! H21 C1 H6 +ATOM C3 CG321 -0.18 ! \ / \ / +ATOM H31 HGA2 0.09 ! H22-C2 C6 +ATOM H32 HGA2 0.09 ! | || +ATOM C4 CG321 -0.18 ! H31-C3 C5 +ATOM H41 HGA2 0.09 ! / \ / \ +ATOM H42 HGA2 0.09 ! H32 C4 H5 +ATOM C5 CG2D1 -0.15 ! / \ +ATOM H5 HGA4 0.15 ! H41 H42 +ATOM C6 CG2D1 -0.15 +ATOM H6 HGA4 0.15 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C6 H6 C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 C5 H5 + +IC C1 C2 C3 C4 0.00 0.00 -63.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 46.0 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 -13.0 0.00 0.00 +IC C6 C2 *C1 H11 0.00 0.00 120.0 0.00 0.00 +IC C6 C2 *C1 H12 0.00 0.00 -120.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 +IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 +IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 +IC C3 C5 *C4 H42 0.00 0.00 -120.0 0.00 0.00 +IC C4 C6 *C5 H5 0.00 0.00 180.0 0.00 0.00 +IC C1 C5 *C6 H6 0.00 0.00 180.0 0.00 0.00 +PATCH FIRST NONE LAST NONE + +RESI 2DHF 0.000 ! C4H6O 2,3-dihydrofuran, kevo +GROUP +ATOM O1 OG3C51 -0.33 +ATOM C2 CG2R51 -0.06 +ATOM H2 HGR52 0.20 ! H3 H41 H42 +ATOM C3 CG2R51 -0.41 ! \ | / +ATOM H3 HGR51 0.24 ! C3----C4 +ATOM C4 CG3C52 -0.08 ! || | +ATOM H41 HGA2 0.09 ! C2 C5--H51 +ATOM H42 HGA2 0.09 ! / \ / \ +ATOM C5 CG3C52 0.08 ! H2 O1 H52 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND O1 C2 C2 C3 C3 C4 C4 C5 C5 O1 +BOND C2 H2 C3 H3 +BOND C4 H41 C4 H42 C5 H51 C5 H52 +IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 20.00 0.00 0.0000 +IC C3 O1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C3 *C4 H42 0.0000 0.00 240.00 0.00 0.0000 +IC O1 C4 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC O1 C4 *C5 H52 0.0000 0.00 240.00 0.00 0.0000 +!End opioid preparation, kevo, jun2008 + +!Compounds for GSK/IBM collaboration, kevo, jun2008 +RESI 9MAD 0.00 ! C6H7N5 9-Methyl-Adenine, kevo for gsk/ibm +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +GROUP +ATOM N9 NG2R51 -0.05 ! H61 H62 +ATOM C5 CG2RC0 0.28 ! \ / +ATOM N7 NG2R50 -0.71 ! N6 +ATOM C8 CG2R53 0.34 ! | +ATOM H8 HGR52 0.12 ! C6 +ATOM N1 NG2R62 -0.74 ! // \ +ATOM C2 CG2R64 0.50 ! N1 C5--N7\\ +ATOM H2 HGR62 0.13 ! | || C8-H8 +ATOM N3 NG2R62 -0.75 ! C2 C4--N9/ +ATOM C4 CG2RC0 0.43 ! / \\ / \ +ATOM C6 CG2R64 0.46 ! H2 N3 C1--H13 +ATOM N6 NG2S3 -0.77 ! / \ +ATOM H61 HGP4 0.38 ! H11 H12 +ATOM H62 HGP4 0.38 + +BOND C1 N9 C1 H11 C1 H12 C1 H13 +BOND N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR C6 C5 N1 N6 +IMPR N6 H62 H61 C6 +IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +IC C4 C8 *N9 C1 0.0 0.0 180.0 0.0 0.0 +IC C4 N9 C1 H11 0.0 0.0 180.0 0.0 0.0 +IC N9 H11 *C1 H12 0.0 0.0 120.0 0.0 0.0 +IC N9 H11 *C1 H13 0.0 0.0 -120.0 0.0 0.0 +IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 + +RESI 1MTH 0.00 ! C6H8N2O2 1-Methyl-Thymine, kevo for gsk/ibm +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +GROUP +ATOM N1 NG2R61 -0.34 ! H51 O4 +ATOM C6 CG2R62 0.17 ! | || +ATOM H6 HGR62 0.17 ! H52-C5M C4 H3 +ATOM C2 CG2R63 0.51 ! | \ / \ / +ATOM O2 OG2D4 -0.41 ! H53 C5 N3 +ATOM N3 NG2R61 -0.46 ! || | +ATOM H3 HGP1 0.36 ! H6-C6 C2 +ATOM C4 CG2R63 0.50 ! \ / \\ +ATOM O4 OG2D4 -0.45 ! N1 O2 +ATOM C5 CG2R62 -0.15 ! | +ATOM C5M CG331 -0.11 ! H11--C1--H13 +ATOM H51 HGA3 0.07 ! | +ATOM H52 HGA3 0.07 ! H12 +ATOM H53 HGA3 0.07 + +BOND C1 N1 C1 H11 C1 H12 C1 H13 +BOND N1 C2 N1 C6 +BOND C2 N3 N3 H3 N3 C4 C4 C5 C6 H6 +BOND C5 C5M C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 +IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +IC C2 C6 *N1 C1 0.0 0.0 180.0 0.0 0.0 +IC C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 +IC N1 H11 *C1 H12 0.0 0.0 120.0 0.0 0.0 +IC N1 H11 *C1 H13 0.0 0.0 -120.0 0.0 0.0 +IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 + +RESI PROH 0.00 ! C3H8O n-propanol, kevo for gsk/ibm +GROUP +ATOM O1 OG311 -0.65 +ATOM HO1 HGP1 0.42 +ATOM C1 CG321 0.05 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND O1 HO1 O1 C1 C1 H11 C1 H12 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 C3 C3 H31 C3 H32 C3 H33 +IC C1 C2 C3 H33 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 O1 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C1 O1 HO1 0.0000 0.00 180.00 0.00 0.0000 +IC O1 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC O1 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 H33 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 H33 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 + +RESI PRSH 0.00 ! C3H8S n-thiopropanol, kevo for gsk/ibm +GROUP +ATOM S1 SG311 -0.23 +ATOM HS1 HGP3 0.16 +ATOM C1 CG321 -0.11 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND S1 HS1 S1 C1 C1 H11 C1 H12 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 C3 C3 H31 C3 H32 C3 H33 +IC C1 C2 C3 H33 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 S1 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C1 S1 HS1 0.0000 0.00 180.00 0.00 0.0000 +IC S1 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC S1 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 H33 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 H33 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 + +RESI 2BOH 0.00 ! C4H10O (S)-2-butanol, kevo for gsk/ibm +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +GROUP +ATOM O2 OG311 -0.65 +ATOM HO2 HGP1 0.42 +ATOM C2 CG311 0.14 +ATOM H2 HGA1 0.09 +GROUP +ATOM C3 CG321 -0.18 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 C2 C1 H11 C1 H12 C1 H13 +BOND O2 HO2 O2 C2 C2 H2 +BOND C2 C3 C3 H31 C3 H32 +BOND C3 C4 C4 H41 C4 H42 C4 H43 +IC C2 C3 C4 H43 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C2 C1 H13 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 O2 0.0000 0.00 -120.00 0.00 0.0000 ! S +IC C1 C3 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 ! S +IC C3 C2 O2 HO2 0.0000 0.00 180.00 0.00 0.0000 +IC H13 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC H13 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 H43 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 H43 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 + +RESI NEOP 0.00 ! C5H12 neopentane, kevo for gsk/ibm +GROUP +ATOM C CG301 0.00 +ATOM C1 CG331 -0.27 +ATOM C2 CG331 -0.27 +ATOM C3 CG331 -0.27 ! H32 +ATOM C4 CG331 -0.27 ! | +ATOM H11 HGA3 0.09 ! H31-C3-H33 +ATOM H12 HGA3 0.09 ! H23 | H41 +ATOM H13 HGA3 0.09 ! | | | +ATOM H21 HGA3 0.09 ! H22-C2------C------C4-H42 +ATOM H22 HGA3 0.09 ! | | | +ATOM H23 HGA3 0.09 ! H21 | H43 +ATOM H31 HGA3 0.09 ! H11-C1-H13 +ATOM H32 HGA3 0.09 ! | +ATOM H33 HGA3 0.09 ! H12 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C C1 C C2 C C3 C C4 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +IC C2 C C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C2 C1 *C C3 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2 C1 *C C4 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C3 C C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C4 C C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C1 C C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI MCPE 0.00 ! C6H12 methylcyclopentane, kevo for gsk/ibm +GROUP +ATOM C1 CG3C52 -0.18 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM C2 CG3C52 -0.18 ! H61 H62 +ATOM H21 HGA2 0.09 ! \ / +ATOM H22 HGA2 0.09 ! H51 C6--H63 +ATOM C3 CG3C52 -0.18 ! \ / +ATOM H31 HGA2 0.09 ! H41 C5 H11 +ATOM H32 HGA2 0.09 ! \ / \ / +ATOM C4 CG3C52 -0.18 ! H42--C4 C1--H12 +ATOM H41 HGA2 0.09 ! | | +ATOM H42 HGA2 0.09 ! H31--C3----C2--H21 +ATOM C5 CG3C51 -0.09 ! | | +ATOM H51 HGA1 0.09 ! H32 H22 +GROUP +ATOM C6 CG331 -0.27 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C1 +BOND C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 +BOND C5 H51 C5 C6 C6 H61 C6 H62 C6 H63 +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 -20.0 0.00 0.0000 ! equatorial +IC C3 C4 C5 C1 0.0000 0.00 40.0 0.00 0.0000 ! equatorial +IC C5 C2 *C1 H11 0.0000 0.00 120.0 0.00 0.0000 +IC C5 C2 *C1 H12 0.0000 0.00 240.0 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.0 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 240.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 240.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 C6 0.0000 0.00 240.0 0.00 0.0000 +IC C4 C5 C6 H63 0.0000 0.00 180.0 0.00 0.0000 +IC C5 H63 *C6 H61 0.0000 0.00 120.0 0.00 0.0000 +IC C5 H63 *C6 H62 0.0000 0.00 240.0 0.00 0.0000 + +RESI DMTF 0.00 ! C6H12O (S,R)-dimethyl-tetrahydrofuran +GROUP +ATOM O4' OG3C51 -0.40 +ATOM C1' CG3C51 0.11 +ATOM C2' CG3C52 -0.18 ! H52 H53 H11 H12 +ATOM C3' CG3C52 -0.18 ! \ / \ / +ATOM C4' CG3C51 0.11 ! H51--C5 O4' C1--H13 +ATOM H11' HGA1 0.09 ! \ / \ / +ATOM H21' HGA2 0.09 ! H42'--C4' C1'--H11' +ATOM H22' HGA2 0.09 ! | | +ATOM H31' HGA2 0.09 ! H31'--C3'----C2'--H21' +ATOM H32' HGA2 0.09 ! / \ +ATOM H42' HGA1 0.09 ! H32' H22' +GROUP +ATOM C5 CG331 -0.27 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5 +BOND C1' H11' C2' H21' C2' H22' C3' H31' C3' H32' +BOND C4' H42' C5 H51 C5 H52 C5 H53 +BOND C1' C1 C1 H11 C1 H12 C1 H13 +IC C4' O4' C1' C2' 0.0000 0.00 -40.00 0.00 0.0000 ! equatorial +IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 ! S +IC C2' O4' *C1' C1 0.0000 0.00 -120.00 0.00 0.0000 ! S +IC O4' C1' C2' C3' 0.0000 0.00 20.00 0.00 0.0000 ! equatorial +IC C3' C1' *C2' H21' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' C1' *C2' H22' 0.0000 0.00 -120.00 0.00 0.0000 +IC C4' C2' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C4' C2' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' O4' *C4' C5 0.0000 0.00 120.00 0.00 0.0000 ! R +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 ! R +IC O4' C4' C5 H51 0.0000 0.00 180.00 0.00 0.0000 +IC H51 C4' *C5 H52 0.0000 0.00 120.00 0.00 0.0000 +IC H51 C4' *C5 H53 0.0000 0.00 -120.00 0.00 0.0000 +IC O4' C1' C1 H13 0.0000 0.00 180.00 0.00 0.0000 +IC C1' H13 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C1' H13 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 + +RESI TOLU 0.00 ! C7H8 toluene, copied from pedro/toppar_aromatics.str for gsk/ibm +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 +ATOM CD1 CG2R61 -0.115 ! HD1 HE1 +ATOM HD1 HGR61 0.115 ! | | +ATOM CD2 CG2R61 -0.115 ! CD1--CE1 H11 +ATOM HD2 HGR61 0.115 ! / \ / +ATOM CE1 CG2R61 -0.115 ! HG--CG CZ--CT--H12 +ATOM HE1 HGR61 0.115 ! \ / \ +ATOM CE2 CG2R61 -0.115 ! CD2--CE2 H13 +ATOM HE2 HGR61 0.115 ! | | +ATOM CZ CG2R61 0.000 ! HD2 HE2 +ATOM CT CG331 -0.270 +ATOM H11 HGA3 0.090 +ATOM H12 HGA3 0.090 +ATOM H13 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ CT +BOND CT H11 CT H12 CT H13 +IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 +IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CD2 *CG HG 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CE2 *CZ CT 1.4000 120.00 180.00 120.00 1.5000 +IC CE1 CZ CT H11 1.4000 120.00 90.00 109.50 1.1100 +IC CZ H11 *CT H12 1.5000 109.50 120.00 109.50 1.1100 +IC CZ H11 *CT H13 1.5000 109.50 -120.00 109.50 1.1100 + +RESI BBEN 0.00 ! C10H14 butylbenzene, kevo for gsk/ibm +GROUP +ATOM CG CG2R61 0.000 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CZ CG2R61 -0.115 +ATOM HZ HGR61 0.115 +GROUP +ATOM C1 CG321 -0.18 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 ! HD1 HE1 +ATOM C2 CG321 -0.18 ! | | +ATOM H21 HGA2 0.09 ! H41 H31 H21 H11 CD1--CE1 +ATOM H22 HGA2 0.09 ! | | | | / \ +ATOM C3 CG321 -0.18 ! H43--C4---C3---C2---C1---CG CZ--HZ +ATOM H31 HGA2 0.09 ! | | | | \ / +ATOM H32 HGA2 0.09 ! H42 H32 H22 H12 CD2--CE2 +ATOM C4 CG331 -0.27 ! | | +ATOM H41 HGA3 0.09 ! HD2 HE2 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG C1 C1 C2 C2 C3 C3 C4 +BOND CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ HZ +BOND C1 H11 C1 H12 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 C4 H43 +IC CG CD1 CE1 CZ 0.0000 0.00 0.00 0.00 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 +IC CD1 CD2 *CG C1 0.0000 0.00 180.00 0.00 0.0000 +IC CD2 CG C1 C2 0.0000 0.00 90.00 0.00 0.0000 +IC CG C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 H43 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CE2 *CZ HZ 0.0000 0.00 180.00 0.00 0.0000 +IC CG C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC CG C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 H43 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 H43 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 + +RESI OXYL 0.00 ! C8H10 o-xylene, kevo for gsk/ibm +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 ! HD1 HE1 +ATOM HD2 HGR61 0.115 ! | | +ATOM CE1 CG2R61 -0.115 ! CD1--CE1 H11 +ATOM HE1 HGR61 0.115 ! / \ / +ATOM CE2 CG2R61 0.000 ! HG--CG CZ--C1--H12 +ATOM CZ CG2R61 0.000 ! \ / \ +ATOM C1 CG331 -0.270 ! CD2--CE2 H13 +ATOM H11 HGA3 0.090 ! | \ +ATOM H12 HGA3 0.090 ! HD2 C2--H21 +ATOM H13 HGA3 0.090 ! | \ +ATOM C2 CG331 -0.270 ! H23 H22 +ATOM H21 HGA3 0.090 +ATOM H22 HGA3 0.090 +ATOM H23 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 C2 CZ C1 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 +IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CD2 *CG HG 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 C2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 +IC CE1 CZ C1 H11 1.4000 120.00 0.00 109.50 1.1100 +IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 +IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 +IC CZ CE2 C2 H21 1.4000 120.00 180.00 109.50 1.1100 +IC CE2 H21 *C2 H22 1.5000 109.50 120.00 109.50 1.1100 +IC CE2 H21 *C2 H23 1.5000 109.50 -120.00 109.50 1.1100 + +RESI MXYL 0.00 ! C8H10 m-xylene, kevo for gsk/ibm +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 0.000 ! HD1 HE1 +ATOM CE1 CG2R61 -0.115 ! | | +ATOM HE1 HGR61 0.115 ! CD1--CE1 H11 +ATOM CE2 CG2R61 -0.115 ! / \ / +ATOM HE2 HGR61 0.115 ! HG--CG CZ--C1--H12 +ATOM CZ CG2R61 0.000 ! \ / \ +ATOM C1 CG331 -0.270 ! CD2--CE2 H13 +ATOM H11 HGA3 0.090 ! / \ +ATOM H12 HGA3 0.090 ! H21--C2 HE2 +ATOM H13 HGA3 0.090 ! / | +ATOM C2 CG331 -0.270 ! H22 H23 +ATOM H21 HGA3 0.090 +ATOM H22 HGA3 0.090 +ATOM H23 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 C2 CE1 HE1 +BOND CE2 HE2 CZ C1 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 +IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CD2 *CG HG 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 C2 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 +IC CE1 CZ C1 H11 1.4000 120.00 90.00 109.50 1.1100 +IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 +IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 +IC CE2 CD2 C2 H21 1.4000 120.00 -90.00 109.50 1.1100 +IC CD2 H21 *C2 H22 1.5000 109.50 120.00 109.50 1.1100 +IC CD2 H21 *C2 H23 1.5000 109.50 -120.00 109.50 1.1100 + +RESI PXYL 0.00 ! C8H10 p-xylene, kevo for gsk/ibm +GROUP +ATOM CG CG2R61 0.000 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 ! HD1 HE1 +ATOM HE1 HGR61 0.115 ! | | +ATOM CE2 CG2R61 -0.115 ! H21 CD1--CE1 H11 +ATOM HE2 HGR61 0.115 ! \ / \ / +ATOM CZ CG2R61 0.000 ! H22--C2--CG CZ--C1--H12 +ATOM C1 CG331 -0.270 ! / \ / \ +ATOM H11 HGA3 0.090 ! H23 CD2--CE2 H13 +ATOM H12 HGA3 0.090 ! | | +ATOM H13 HGA3 0.090 ! HD2 HE2 +ATOM C2 CG331 -0.270 +ATOM H21 HGA3 0.090 +ATOM H22 HGA3 0.090 +ATOM H23 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG C2 CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ C1 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 +IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CD2 *CG C2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 +IC CE1 CZ C1 H11 1.4000 120.00 90.00 109.50 1.1100 +IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 +IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 +IC CD2 CG C2 H21 1.4000 120.00 -90.00 109.50 1.1100 +IC CG H21 *C2 H22 1.5000 109.50 120.00 109.50 1.1100 +IC CG H21 *C2 H23 1.5000 109.50 -120.00 109.50 1.1100 + +RESI PSCU 0.00 ! C9H12 pseudocumene (1,2,4-trimethylbenzene), kevo for gsk/ibm +GROUP +ATOM CG CG2R61 0.000 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 ! HD1 HE1 +ATOM HE1 HGR61 0.115 ! | | +ATOM CE2 CG2R61 0.000 ! H31 CD1--CE1 H11 +ATOM CZ CG2R61 0.000 ! \ / \ / +ATOM C1 CG331 -0.270 ! H32--C3--CG CZ--C1--H12 +ATOM H11 HGA3 0.090 ! / \ / \ +ATOM H12 HGA3 0.090 ! H33 CD2--CE2 H13 +ATOM H13 HGA3 0.090 ! | \ +ATOM C2 CG331 -0.270 ! HD2 C2--H21 +ATOM H21 HGA3 0.090 ! | \ +ATOM H22 HGA3 0.090 ! H23 H22 +ATOM H23 HGA3 0.090 +ATOM C3 CG331 -0.270 +ATOM H31 HGA3 0.090 +ATOM H32 HGA3 0.090 +ATOM H33 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG C3 CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 C2 CZ C1 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 +IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CD2 *CG C3 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 C2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 +IC CE1 CZ C1 H11 1.4000 120.00 0.00 109.50 1.1100 +IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 +IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 +IC CZ CE2 C2 H21 1.4000 120.00 180.00 109.50 1.1100 +IC CE2 H21 *C2 H22 1.5000 109.50 120.00 109.50 1.1100 +IC CE2 H21 *C2 H23 1.5000 109.50 -120.00 109.50 1.1100 +IC CD2 CG C3 H31 1.4000 120.00 90.00 109.50 1.1100 +IC CG H31 *C3 H32 1.5000 109.50 120.00 109.50 1.1100 +IC CG H31 *C3 H33 1.5000 109.50 -120.00 109.50 1.1100 + +RESI PCRO 0.00 ! C7H8O p-cresol, kevo for gsk/ibm +GROUP +ATOM CG CG2R61 0.110 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 ! HD1 HE1 +ATOM HE1 HGR61 0.115 ! | | +ATOM CE2 CG2R61 -0.115 ! CD1--CE1 H11 +ATOM HE2 HGR61 0.115 ! / \ / +ATOM CZ CG2R61 0.000 ! H2--O2--CG CZ--C1--H12 +ATOM C1 CG331 -0.270 ! \ / \ +ATOM H11 HGA3 0.090 ! CD2--CE2 H13 +ATOM H12 HGA3 0.090 ! | | +ATOM H13 HGA3 0.090 ! HD2 HE2 +ATOM O2 OG311 -0.530 +ATOM H2 HGP1 0.420 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG O2 CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ C1 O2 H2 +BOND C1 H11 C1 H12 C1 H13 +IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 +IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CD2 *CG O2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CE2 *CZ C1 1.4000 120.00 180.00 120.00 1.5000 +IC CE1 CZ C1 H11 1.4000 120.00 90.00 109.50 1.1100 +IC CZ H11 *C1 H12 1.5000 109.50 120.00 109.50 1.1100 +IC CZ H11 *C1 H13 1.5000 109.50 -120.00 109.50 1.1100 +IC CD2 CG O2 H2 1.4000 120.00 0.00 109.50 0.9600 + +RESI PNPO 0.000 ! C6H5NO3 p-nitrophenol, kevo for gsk/ibm +GROUP +ATOM C1 CG2R61 -0.18 +ATOM H1 HGR61 0.16 +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 ! H5 H4 +ATOM C3 CG2R61 0.110 ! \ ___ / +ATOM O3 OG311 -0.53 ! O6A C5---C4 +ATOM H3 HGP1 0.42 ! \ + / \ +ATOM C4 CG2R61 -0.115 ! - N6--C6 C3--O3--H3 +ATOM H4 HGR61 0.115 ! / \\ // +ATOM C5 CG2R61 -0.18 ! O6B C1---C2 +ATOM H5 HGR61 0.16 ! / \ +ATOM C6 CG2R61 0.32 ! H1 H2 +ATOM N6 NG2O1 0.40 +ATOM O6A OG2N1 -0.34 +ATOM O6B OG2N1 -0.34 + +BOND C1 H1 C1 C2 C2 H2 C2 C3 C3 O3 +BOND O3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6 +BOND C6 C1 C6 N6 N6 O6A N6 O6B +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 O3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *C6 N6 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C6 N6 O6A 0.0000 0.00 180.00 0.00 0.0000 +IC O6A C6 *N6 O6B 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 O3 H3 0.0000 0.00 0.00 0.00 0.0000 + +RESI PCLT 0.00 ! C7H7Cl p-chlorotoluene, kevo for gsk/ibm +GROUP +ATOM CG CG2R61 0.03 +ATOM CL CLGR1 -0.13 +ATOM CD1 CG2R61 -0.10 ! HD1 HE1 +ATOM HD1 HGR62 0.15 ! | | +ATOM CD2 CG2R61 -0.10 ! CD1--CE1 H11 +ATOM HD2 HGR62 0.15 ! / \ / +ATOM CE1 CG2R61 -0.115 ! CL--CG CZ--CT--H12 +ATOM HE1 HGR61 0.115 ! \ / \ +ATOM CE2 CG2R61 -0.115 ! CD2--CE2 H13 +ATOM HE2 HGR61 0.115 ! | | +ATOM CZ CG2R61 0.000 ! HD2 HE2 +ATOM CT CG331 -0.270 +ATOM H11 HGA3 0.090 +ATOM H12 HGA3 0.090 +ATOM H13 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG CL CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ CT +BOND CT H11 CT H12 CT H13 +IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 +IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CD2 *CG CL 1.4000 120.00 180.00 120.00 1.7400 +IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CE2 *CZ CT 1.4000 120.00 180.00 120.00 1.5000 +IC CE1 CZ CT H11 1.4000 120.00 90.00 109.50 1.1100 +IC CZ H11 *CT H12 1.5000 109.50 120.00 109.50 1.1100 +IC CZ H11 *CT H13 1.5000 109.50 -120.00 109.50 1.1100 + +RESI 34MP 0.00 ! C7H9N 3,4-dimethylpyridine, kevo for gsk/ibm +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 0.000 +ATOM CG CG2R61 0.000 ! H32 H33 +ATOM CD2 CG2R61 -0.115 ! \ / +ATOM CE2 CG2R61 0.180 ! H31--CD3 HE1 +ATOM HE1 HGR62 0.120 ! \ | +ATOM HD2 HGR61 0.115 ! H21 CD1--CE1 +ATOM HE2 HGR62 0.120 ! \ / \ +ATOM C3 CG331 -0.270 ! H22--C2--CG NZ +ATOM H31 HGA3 0.090 ! / \ / +ATOM H32 HGA3 0.090 ! H23 CD2--CE2 +ATOM H33 HGA3 0.090 ! | | +ATOM C2 CG331 -0.270 ! HD2 HE2 +ATOM H21 HGA3 0.090 +ATOM H22 HGA3 0.090 +ATOM H23 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG C2 CD1 C3 CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 + +IC CG CD1 CE1 NZ 0.0000 0.00 0.00 0.00 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 +IC CD1 CD2 *CG C2 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CG *CD1 C3 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC CD2 CG C2 H21 0.0000 0.00 0.00 0.00 0.0000 +IC CG H21 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC CG H21 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +IC CG CD1 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC CD1 H31 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC CD1 H31 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 + +RESI 4MEP 0.00 ! C6H7N 4-methylpyridine, kevo for gsk/ibm +GROUP +ATOM NZ NG2R60 -0.600 +ATOM CE1 CG2R61 0.180 +ATOM CD1 CG2R61 -0.115 +ATOM CG CG2R61 0.000 ! HD1 HE1 +ATOM CD2 CG2R61 -0.115 ! | | +ATOM CE2 CG2R61 0.180 ! H21 CD1--CE1 +ATOM HE1 HGR62 0.120 ! \ / \ +ATOM HD1 HGR61 0.115 ! H22--C2--CG NZ +ATOM HD2 HGR61 0.115 ! / \ / +ATOM HE2 HGR62 0.120 ! H23 CD2--CE2 +ATOM C2 CG331 -0.270 ! | | +ATOM H21 HGA3 0.090 ! HD2 HE2 +ATOM H22 HGA3 0.090 +ATOM H23 HGA3 0.090 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 NZ CE1 NZ CE2 +BOND CG C2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND C2 H21 C2 H22 C2 H23 + +IC CG CD1 CE1 NZ 0.0000 0.00 0.00 0.00 0.0000 +IC CD1 CE1 NZ CE2 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 NZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 +IC CD1 CD2 *CG C2 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC NZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC NZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC CD2 CG C2 H21 0.0000 0.00 90.00 0.00 0.0000 +IC CG H21 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC CG H21 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 + +RESI 23MN 0.00 ! C12H12 2,3-dimethylnaphtalene, kevo for gsk/ibm +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H1 HGR61 0.115 +ATOM C2 CG2R61 0.000 +ATOM C3 CG2R61 0.000 +ATOM C4 CG2R61 -0.115 +ATOM H4 HGR61 0.115 +ATOM C5 CG2R61 0.000 +ATOM C6 CG2R61 -0.115 ! H4 H6 +ATOM H6 HGR61 0.115 ! | | +ATOM C7 CG2R61 -0.115 ! H312 H311 C4 C6 +ATOM H7 HGR61 0.115 ! \ | // \ / \\ +ATOM C8 CG2R61 -0.115 ! H313--C31---C3 C5 C7--H7 +ATOM H8 HGR61 0.115 ! | || | +ATOM C9 CG2R61 -0.115 ! H211--C21---C2 C10 C8--H8 +ATOM H9 HGR61 0.115 ! / | \\ / \ // +ATOM C10 CG2R61 0.000 ! H212 H213 C1 C9 +ATOM C21 CG331 -0.270 ! | | +ATOM H211 HGA3 0.090 ! H1 H9 +ATOM H212 HGA3 0.090 +ATOM H213 HGA3 0.090 +ATOM C31 CG331 -0.270 +ATOM H311 HGA3 0.090 +ATOM H312 HGA3 0.090 +ATOM H313 HGA3 0.090 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 C1 C10 +BOND C1 H1 C2 C21 C3 C31 C4 H4 +BOND C6 H6 C7 H7 C8 H8 C9 H9 +BOND C21 H211 C21 H212 C21 H213 +BOND C31 H311 C31 H312 C31 H313 +IC C5 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 C21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 C31 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C21 H211 0.0000 0.00 0.00 0.00 0.0000 +IC C2 H211 *C21 H212 0.0000 0.00 120.00 0.00 0.0000 +IC C2 H211 *C21 H213 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C31 H311 0.0000 0.00 180.00 0.00 0.0000 +IC C3 H311 *C31 H312 0.0000 0.00 120.00 0.00 0.0000 +IC C3 H311 *C31 H313 0.0000 0.00 -120.00 0.00 0.0000 + +RESI 14MN 0.00 ! C12H12 1,4-dimethylnaphtalene, kevo for gsk/ibm +GROUP +ATOM C1 CG2R61 0.000 +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM C3 CG2R61 -0.115 +ATOM H3 HGR61 0.115 +ATOM C4 CG2R61 0.000 ! H412 H411 +ATOM C5 CG2R61 0.000 ! \ | +ATOM C6 CG2R61 -0.115 ! H413--C41 H6 +ATOM H6 HGR61 0.115 ! | | +ATOM C7 CG2R61 -0.115 ! C4 C6 +ATOM H7 HGR61 0.115 ! // \ / \\ +ATOM C8 CG2R61 -0.115 ! H3--C3 C5 C7--H7 +ATOM H8 HGR61 0.115 ! | || | +ATOM C9 CG2R61 -0.115 ! H2--C2 C10 C8--H8 +ATOM H9 HGR61 0.115 ! \\ / \ // +ATOM C10 CG2R61 0.000 ! C1 C9 +ATOM C11 CG331 -0.270 ! | | +ATOM H111 HGA3 0.090 ! H111--C11 H9 +ATOM H112 HGA3 0.090 ! / | +ATOM H113 HGA3 0.090 ! H112 H113 +ATOM C41 CG331 -0.270 +ATOM H411 HGA3 0.090 +ATOM H412 HGA3 0.090 +ATOM H413 HGA3 0.090 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 +BOND C5 C6 C6 C7 C7 C8 C8 C9 +BOND C9 C10 C5 C10 C1 C10 +BOND C1 C11 C2 H2 C3 H3 C4 C41 +BOND C6 H6 C7 H7 C8 H8 C9 H9 +BOND C11 H111 C11 H112 C11 H113 +BOND C41 H411 C41 H412 C41 H413 +IC C5 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C2 *C1 C11 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 C41 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C1 C11 H111 0.0000 0.00 180.00 0.00 0.0000 +IC C1 H111 *C11 H112 0.0000 0.00 120.00 0.00 0.0000 +IC C1 H111 *C11 H113 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C4 C41 H411 0.0000 0.00 0.00 0.00 0.0000 +IC C4 H411 *C41 H412 0.0000 0.00 120.00 0.00 0.0000 +IC C4 H411 *C41 H413 0.0000 0.00 -120.00 0.00 0.0000 +!End compounds for GSK/IBM collaboration, kevo, jun2008 + +!Drug-like molecules, S. Zhong, jun2008 + +RESI FORA -1.00 ! CHO2 formate, from acetate, sz & kevo +GROUP +ATOM C1 CG2O3 0.52 ! H +ATOM O2 OG2D2 -0.76 ! C +ATOM O3 OG2D2 -0.76 ! / \\ +ATOM H4 HGR52 0.00 ! -O O + +BOND C1 H4 +BOND C1 O2 C1 O3 +IMPR C1 O2 O3 H4 +IC O3 O2 *C1 H4 0.00 0.00 180.0 0.0 0.0 +IC H4 O3 *C1 O2 0.00 0.00 180.0 0.0 0.0 !redundant definition needed to enable seeding. + +RESI PMHA 0.00 ! C25H20ClN3O2 3-(N-(3-chloroPhenyl)carnoMoyl)propionyl +GROUP ! Anthracene-9-carbaldehyde Hydrazone, sz +ATOM C1 CG2R61 0.10 +ATOM C2 CG2R61 -0.14 ! H49 H47 +ATOM H3 HGR62 0.22 ! \ / +ATOM C4 CG2R61 0.10 ! H9 C48--C46 +ATOM CL5 CLGR1 -0.18 ! | // \\ +ATOM C6 CG2R61 -0.16 ! C8 H11 H51-C50 C44-H45 +ATOM H7 HGR62 0.19 ! / \\ / \ / +ATOM C8 CG2R61 -0.12 ! H7--C6 C10 O15 H20 H21 H25 H28 C30--C31 +ATOM H9 HGR61 0.12 ! || | || \ / | | // \\ +ATOM C10 CG2R61 -0.16 ! Cl5-C4 C1 C14 C19 N24 C27--C29 C32-H33 +ATOM H11 HGR61 0.19 ! \ // \ / \ / \ / \ // \ / +ATOM N12 NG2S1 -0.47 ! C2 N12 C16 C22 N26 C35==C34 +ATOM H13 HGP1 0.31 ! | | / \ || / \ +ATOM C14 CG2O1 0.51 ! H3 H13 H17 H18 O23 H37-C36 C42-H43 +ATOM O15 OG2D1 -0.51 ! \\ // +ATOM C16 CG321 -0.18 ! Group 2 C38--C40 +ATOM H17 HGA2 0.09 ! / \ +ATOM H18 HGA2 0.09 ! H39 H41 +ATOM C19 CG321 -0.18 +ATOM H20 HGA2 0.09 +ATOM H21 HGA2 0.09 +ATOM C22 CG2O1 0.58 ! Group 3 +ATOM O23 OG2D1 -0.49 +ATOM N24 NG2S1 -0.34 +ATOM H25 HGP1 0.31 +ATOM N26 NG2D1 -0.31 +ATOM C27 CG2DC1 -0.24 +ATOM H28 HGA4 0.24 +ATOM C29 CG2R61 0.25 +ATOM C30 CG2R61 0.00 ! Group 4 +ATOM C31 CG2R61 0.00 +ATOM C32 CG2R61 -0.115 +ATOM H33 HGR61 0.115 +ATOM C34 CG2R61 0.00 +ATOM C35 CG2R61 0.00 +ATOM C36 CG2R61 -0.115 +ATOM H37 HGR61 0.115 +ATOM C38 CG2R61 -0.115 +ATOM H39 HGR61 0.115 +ATOM C40 CG2R61 -0.115 +ATOM H41 HGR61 0.115 +ATOM C42 CG2R61 -0.115 +ATOM H43 HGR61 0.115 +ATOM C44 CG2R61 -0.115 +ATOM H45 HGR61 0.115 +ATOM C46 CG2R61 -0.115 +ATOM H47 HGR61 0.115 +ATOM C48 CG2R61 -0.115 +ATOM H49 HGR61 0.115 +ATOM C50 CG2R61 -0.115 +ATOM H51 HGR61 0.115 + +BOND C1 C2 C2 H3 C2 C4 C4 CL5 +BOND C4 C6 C6 H7 C6 C8 C8 H9 +BOND C8 C10 C10 H11 C10 C1 C1 N12 +BOND N12 H13 N12 C14 C14 O15 C14 C16 +BOND C16 H17 C16 H18 C16 C19 C19 H20 C19 H21 C19 C22 +BOND C22 O23 C22 N24 N24 H25 N24 N26 N26 C27 C27 H28 +BOND C27 C29 +BOND C29 C30 C30 C31 C31 C32 C32 H33 C32 C34 C34 C35 C35 C29 +BOND C30 C50 C50 H51 C50 C48 C48 H49 C48 C46 +BOND C31 C44 C44 H45 C44 C46 C46 H47 +BOND C34 C42 C42 H43 C42 C40 C40 H41 C40 C38 +BOND C35 C36 C36 H37 C36 C38 C38 H39 +IMPR C14 C16 N12 O15 +IMPR C22 C19 N24 O23 +IMPR C27 C29 N26 H28 +IC C1 C2 C4 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C4 C6 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C6 C8 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C8 C10 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C10 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C1 C2 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C4 *C2 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C4 CL5 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C8 *C6 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C10 *C8 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C1 *C10 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C2 *C1 N12 0.0000 0.00 180.00 0.00 0.0000 +IC C14 N12 C1 C10 0.0000 0.00 90.00 0.00 0.0000 +IC C14 C1 *N12 H13 0.0000 0.00 180.00 0.00 0.0000 +IC O15 C14 N12 H13 0.0000 0.00 180.00 0.00 0.0000 +IC O15 N12 *C14 C16 0.0000 0.00 180.00 0.00 0.0000 +IC C19 C16 C14 O15 0.0000 0.00 0.00 0.00 0.0000 +IC C19 C14 *C16 H17 0.0000 0.00 120.00 0.00 0.0000 +IC C19 C14 *C16 H18 0.0000 0.00 -120.00 0.00 0.0000 +IC C22 C19 C16 C14 0.0000 0.00 180.00 0.00 0.0000 +IC C16 C22 *C19 H20 0.0000 0.00 -120.00 0.00 0.0000 +IC C16 C22 *C19 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O23 C22 C19 C16 0.0000 0.00 0.00 0.00 0.0000 +IC N24 O23 *C22 C19 0.0000 0.00 180.00 0.00 0.0000 +IC N26 C22 *N24 H25 0.0000 0.00 180.00 0.00 0.0000 +IC N26 N24 C22 O23 0.0000 0.00 0.00 0.00 0.0000 +IC C27 N26 N24 C22 0.0000 0.00 180.00 0.00 0.0000 +IC C29 N26 *C27 H28 0.0000 0.00 180.00 0.00 0.0000 +IC C29 C27 N26 N24 0.0000 0.00 180.00 0.00 0.0000 +IC C30 C29 C27 N26 0.0000 0.00 90.00 0.00 0.0000 +IC C31 C30 C29 C27 0.0000 0.00 180.00 0.00 0.0000 +IC C32 C31 C30 C29 0.0000 0.00 0.00 0.00 0.0000 +IC C34 C32 C31 C30 0.0000 0.00 0.00 0.00 0.0000 +IC C31 C34 *C32 H33 0.0000 0.00 180.00 0.00 0.0000 +IC C35 C34 C32 C31 0.0000 0.00 0.00 0.00 0.0000 +IC C31 C29 *C30 C50 0.0000 0.00 180.00 0.00 0.0000 +IC C32 C30 *C31 C44 0.0000 0.00 180.00 0.00 0.0000 +IC C48 C50 C30 C31 0.0000 0.00 0.00 0.00 0.0000 +IC C46 C44 C31 C30 0.0000 0.00 0.00 0.00 0.0000 +IC C48 C30 *C50 H51 0.0000 0.00 180.00 0.00 0.0000 +IC C46 C50 *C48 H49 0.0000 0.00 180.00 0.00 0.0000 +IC C44 C48 *C46 H47 0.0000 0.00 180.00 0.00 0.0000 +IC C31 C46 *C44 H45 0.0000 0.00 180.00 0.00 0.0000 +IC C34 C29 *C35 C36 0.0000 0.00 180.00 0.00 0.0000 +IC C32 C35 *C34 C42 0.0000 0.00 180.00 0.00 0.0000 +IC C38 C36 C35 C34 0.0000 0.00 0.00 0.00 0.0000 +IC C40 C42 C34 C35 0.0000 0.00 0.00 0.00 0.0000 +IC C38 C35 *C36 H37 0.0000 0.00 180.00 0.00 0.0000 +IC C40 C36 *C38 H39 0.0000 0.00 180.00 0.00 0.0000 +IC C42 C38 *C40 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C34 C40 *C42 H43 0.0000 0.00 180.00 0.00 0.0000 +!End drug-like molecules, S. Zhong, jun2008 + +!Hydrazine, E. Darian, jun2008 +RESI HDZN 0.00 ! N2H4 Hydrazine neutral, ed +GROUP +ATOM N1 NG3N1 -0.78 +ATOM H11 HGP1 0.39 ! H11 H21 +ATOM H12 HGP1 0.39 ! \ / +GROUP ! N1--N2 +ATOM N2 NG3N1 -0.78 ! / \ +ATOM H21 HGP1 0.39 ! H12 H22 +ATOM H22 HGP1 0.39 + +BOND N1 H11 N1 H12 N1 N2 N2 H21 N2 H22 +IC H11 N1 N2 H21 0.0000 0.0000 60.0000 0.0000 0.0000 +IC N2 H11 *N1 H12 0.0000 0.0000 130.0000 0.0000 0.0000 +IC H21 N1 *N2 H22 0.0000 0.0000 -120.0000 0.0000 0.0000 +!End hydrazine, E. Darian, jun2008 + +!halogenated ethanes, Nov08, adm +RESI CLET 0.00 ! C2H5Cl chloroethane, adm jr. +GROUP +ATOM C1 CG321 0.07 ! CL11 H12 H13 +ATOM CL11 CLGA1 -0.10 ! \ | / +ATOM H12 HGA2 0.14 ! C1 +ATOM H13 HGA2 0.14 ! | +ATOM C2 CG331 -0.52 ! C2 +ATOM H21 HGA3 0.09 ! / | \ +ATOM H22 HGA3 0.09 ! H21 H22 H23 +ATOM H23 HGA3 0.09 + +BOND C1 CL11 C1 H12 C1 H13 +BOND C1 C2 +BOND C2 H21 C2 H22 C2 H23 +IC CL11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 CL11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 CL11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI DCLE 0.00 ! C2H4Cl2 1,1-dichloroethane, adm jr. +GROUP +ATOM C1 CG311 0.12 ! CL11 CL12 H13 +ATOM CL11 CLGA1 -0.04 ! \ | / +ATOM CL12 CLGA1 -0.04 ! C1 +ATOM H13 HGA1 0.22 ! | +ATOM C2 CG331 -0.53 ! C2 +ATOM H21 HGA3 0.09 ! / | \ +ATOM H22 HGA3 0.09 ! H21 H22 H23 +ATOM H23 HGA3 0.09 + +BOND C1 CL11 C1 CL12 C1 H13 +BOND C1 C2 +BOND C2 H21 C2 H22 C2 H23 +IC CL11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 CL11 *C1 CL12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 CL11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI TCLE 0.00 ! C2H3Cl3 1,1,1-trichloroethane, adm jr. +GROUP +ATOM C1 CG301 -0.24 ! CL11 CL12 CL13 +ATOM CL11 CLGA3 0.14 ! \ | / +ATOM CL12 CLGA3 0.14 ! C1 +ATOM CL13 CLGA3 0.14 ! | +ATOM C2 CG331 -0.45 ! C2 +ATOM H21 HGA3 0.09 ! / | \ +ATOM H22 HGA3 0.09 ! H21 H22 H23 +ATOM H23 HGA3 0.09 + +BOND C1 CL11 C1 CL12 C1 CL13 +BOND C1 C2 +BOND C2 H21 C2 H22 C2 H23 +IC CL11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 CL11 *C1 CL12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 CL11 *C1 CL13 0.0000 0.00 -120.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + + +RESI BRET 0.00 ! C2H5Br bromoethane, adm jr. +GROUP +ATOM C1 CG321 0.07 ! BR11 H12 H13 +ATOM BR11 BRGA1 -0.10 ! \ | / +ATOM H12 HGA2 0.14 ! C1 +ATOM H13 HGA2 0.14 ! | +ATOM C2 CG331 -0.52 ! C2 +ATOM H21 HGA3 0.09 ! / | \ +ATOM H22 HGA3 0.09 ! H21 H22 H23 +ATOM H23 HGA3 0.09 + +BOND C1 BR11 C1 H12 C1 H13 +BOND C1 C2 +BOND C2 H21 C2 H22 C2 H23 +IC BR11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 BR11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 BR11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI DBRE 0.00 ! C2H4Br2 1,1-dibromoethane, adm jr. +GROUP +ATOM C1 CG311 0.10 ! BR11 BR12 H13 +ATOM BR11 BRGA2 -0.04 ! \ | / +ATOM BR12 BRGA2 -0.04 ! C1 +ATOM H13 HGA1 0.22 ! | +ATOM C2 CG331 -0.51 ! C2 +ATOM H21 HGA3 0.09 ! / | \ +ATOM H22 HGA3 0.09 ! H21 H22 H23 +ATOM H23 HGA3 0.09 + +BOND C1 BR11 C1 BR12 C1 H13 +BOND C1 C2 +BOND C2 H21 C2 H22 C2 H23 +IC BR11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 BR11 *C1 BR12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 BR11 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI TBRE 0.00 ! C2H3Br3 1,1,1-tribromoethane, adm jr. +GROUP +ATOM C1 CG301 -0.12 ! BR11 BR12 BR13 +ATOM BR11 BRGA3 -0.01 ! \ | / +ATOM BR12 BRGA3 -0.01 ! C1 +ATOM BR13 BRGA3 -0.01 ! | +ATOM C2 CG331 -0.12 ! C2 +ATOM H21 HGA3 0.09 ! / | \ +ATOM H22 HGA3 0.09 ! H21 H22 H23 +ATOM H23 HGA3 0.09 + +BOND C1 BR11 C1 BR12 C1 BR13 +BOND C1 C2 +BOND C2 H21 C2 H22 C2 H23 +IC BR11 C1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 BR11 *C1 BR12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 BR11 *C1 BR13 0.0000 0.00 -120.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +!New compounds by "team CGenFF", Dec 09 +RESI CYIN 0.000 ! C9H6N2 5-cyanoindole, alr +GROUP +ATOM N1 NG2R51 -0.45 ! H6 +ATOM H1 HGP1 0.37 ! | +ATOM C2 CG2RC0 0.23 ! H8 C6 +ATOM C3 CG2R61 -0.29 ! \ / \\ __ +ATOM H3 HGR61 0.17 ! C8-----C7 C5--C10==N10 +ATOM C4 CG2R61 -0.13 ! || || | +ATOM H4 HGR61 0.16 ! C9 C2 C4 +ATOM C5 CG2R61 -0.08 ! / \ / \ // \ +ATOM C6 CG2R61 -0.28 ! H9 N1 C3 H4 +ATOM H6 HGR61 0.20 ! | | +ATOM C7 CG2RC0 0.26 ! H1 H3 +ATOM C8 CG2R51 -0.40 +ATOM H8 HGR51 0.18 +ATOM C9 CG2R51 -0.02 +ATOM H9 HGR52 0.16 +ATOM C10 CG1N1 0.39 +ATOM N10 NG1T1 -0.47 + +BOND N1 C2 C2 C3 +DOUBLE C3 C4 +BOND C4 C5 +DOUBLE C5 C6 +BOND C6 C7 C7 C8 +DOUBLE C7 C2 C8 C9 +BOND C9 N1 +BOND N1 H1 C3 H3 C4 H4 +BOND C5 C10 +TRIPLE C10 N10 +BOND C6 H6 C8 H8 C9 H9 +IC C8 C9 N1 C2 1.3650 110.50 0.00 112.00 1.3700 +IC C9 C8 C7 C2 1.3650 106.40 0.00 108.00 1.3850 +IC C7 C8 C9 N1 1.4300 106.40 0.00 110.50 1.3700 +IC C2 C8 *C7 C6 1.3850 108.00 180.00 133.50 1.3600 +IC C2 C7 C6 C5 1.3850 110.00 0.00 113.20 1.3750 +IC C7 C6 C5 C4 1.3600 113.20 0.00 120.00 1.3750 +IC C6 C5 C4 C3 1.3750 120.00 0.00 120.00 1.3750 +IC C5 C7 *C6 H6 1.3750 113.20 180.00 122.00 1.0800 +IC C4 C6 *C5 C10 1.3750 120.00 180.00 120.00 1.3750 +IC C4 C5 C10 N10 1.3750 120.00 0.00 120.00 1.2800 +IC C3 C5 *C4 H4 1.3750 120.00 180.00 120.00 1.0800 +IC C2 C4 *C3 H3 1.3600 113.20 180.00 120.00 1.0800 +IC C9 C2 *N1 H1 1.3700 112.00 180.00 126.00 0.9760 +IC C8 N1 *C9 H9 1.3650 110.50 180.00 125.00 1.0800 +IC C9 C7 *C8 H8 1.3650 106.40 180.00 126.40 1.0800 + +RESI PHHZ 0.00 ! C6H8N2 Phenylhydrazine (neutral), ed +GROUP +ATOM CG CG2R61 -0.115 ! HG +ATOM HG HGR61 0.115 ! CG +GROUP ! // \ +ATOM CD1 CG2R61 -0.115 ! HD1--CD1 CD2--HD2 +ATOM HD1 HGR61 0.115 ! | || +GROUP ! | || +ATOM CD2 CG2R61 -0.115 ! HE1--CE1 CE2--HE2 +ATOM HD2 HGR61 0.115 ! \\ / +GROUP ! C6 +ATOM CE1 CG2R61 -0.115 ! | +ATOM HE1 HGR61 0.115 ! N7--H71 +GROUP ! / +ATOM CE2 CG2R61 -0.115 ! N8 +ATOM HE2 HGR61 0.115 ! / \ +GROUP ! H81 H82 +ATOM C6 CG2R61 0.24 +ATOM N7 NG3N1 -0.74 +ATOM H71 HGP1 0.48 +ATOM N8 NG3N1 -0.74 +ATOM H81 HGP1 0.38 +ATOM H82 HGP1 0.38 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 C6 CE1 C6 CE2 +BOND CG HG CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 +BOND C6 N7 N7 H71 N7 N8 N8 H81 N8 H82 +IC CG CD1 CE1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CD1 CG CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CE1 *C6 N7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 C6 N7 N8 0.0000 0.0000 30.0000 0.0000 0.0000 +IC N8 C6 *N7 H71 0.0000 0.0000 130.0000 0.0000 0.0000 +IC C6 N7 N8 H81 0.0000 0.0000 -150.0000 0.0000 0.0000 +IC H81 N7 *N8 H82 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI THF2 0.00 ! C5H10O2 THF-2'OME, delete H22'->OM neutral, ed +GROUP +ATOM O4' OG3C51 -0.40 ! Change C2' and H21' type +ATOM C4' CG3C52 0.02 +ATOM C3' CG3C52 -0.18 ! H41' O4' H11' +ATOM C1' CG3C52 0.02 ! \ / \ / +ATOM H11' HGA2 0.09 ! H42'--C4' C1'--H12' +ATOM H12' HGA2 0.09 ! | | +ATOM H31' HGA2 0.09 ! H31'--C3'--C2'--H21' +ATOM H32' HGA2 0.09 ! / | +ATOM H41' HGA2 0.09 ! H32' OM (changed OM to O2') +ATOM H42' HGA2 0.09 ! | +GROUP ! CM +ATOM C2' CG3C51 0.08 ! / | \ +ATOM H21' HGA1 0.09 ! HM1 HM2 HM3 +ATOM O2' OG301 -0.34 +ATOM CM CG331 -0.10 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' +BOND C1' H11' C1' H12' C3' H31' C3' H32' +BOND C4' H41' C4' H42' +BOND C2' H21' O2' C2' O2' CM +BOND CM HM1 CM HM2 CM HM3 +IC C1' O4' C4' C3' 0.0000 0.00 36.00 0.00 0.0000 +IC C3' O4' *C4' H41' 0.0000 0.00 120.00 0.00 0.0000 +IC C3' O4' *C4' H42' 0.0000 0.00 -120.00 0.00 0.0000 +IC C4' O4' C1' C2' 0.0000 0.00 -19.00 0.00 0.0000 +IC C2' O4' *C1' H11' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' O4' *C1' H12' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' H21' 0.0000 0.00 -120.00 0.00 0.0000 +IC C3' C1' *C2' O2' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' C4' *C3' H31' 0.0000 0.00 120.00 0.00 0.0000 +IC C2' C4' *C3' H32' 0.0000 0.00 -120.00 0.00 0.0000 +IC O2' C2' C1' O4' 0.0000 0.00 105.00 0.00 0.0000 +IC C1' C2' O2' CM 0.0000 0.00 -165.00 0.00 0.0000 +IC C2' O2' CM HM1 0.0000 0.00 55.00 0.00 0.0000 +IC C1' O2' *C2' H21' 0.0000 0.00 -120.00 0.00 0.0000 +IC HM1 O2' *CM HM2 0.0000 0.00 118.00 0.00 0.0000 +IC HM3 O2' *CM HM2 0.0000 0.00 -120.00 0.00 0.0000 + +RESI AMCP 1.00 ! C4H10N Aminomethyl Cyclopropane, jhs +ATOM C1 CG3C31 -0.09 ! C6 +ATOM H2 HGA1 0.09 ! / \ +ATOM C3 CG3C31 -0.18 ! C3__C1 +ATOM H4 HGA2 0.09 ! \ +ATOM H5 HGA2 0.09 ! C9 +ATOM C6 CG3C31 -0.18 ! \ +ATOM H7 HGA2 0.09 ! N12+ +ATOM H8 HGA2 0.09 +ATOM C9 CG324 0.21 +ATOM H10 HGA2 0.05 +ATOM H11 HGA2 0.05 +ATOM N12 NG3P3 -0.30 ! from ethylammonium +ATOM H13 HGP2 0.33 +ATOM H14 HGP2 0.33 +ATOM H15 HGP2 0.33 + +BOND C1 C3 C1 C6 C1 C9 C1 H2 +BOND C3 C6 C3 H4 C3 H5 +BOND C6 H7 C6 H8 +BOND C9 N12 C9 H10 C9 H11 +BOND N12 H13 N12 H14 N12 H15 +IC C3 C9 *C1 C6 0.0000 0.00 -60.00 0.00 0.0000 +IC C3 C9 *C1 H2 0.0000 0.00 150.00 0.00 0.0000 +IC C6 C1 *C3 H4 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C1 *C3 H5 0.0000 0.00 100.00 0.00 0.0000 +IC C3 C1 *C6 H7 0.0000 0.00 100.00 0.00 0.0000 +IC C3 C1 *C6 H8 0.0000 0.00 -100.00 0.00 0.0000 +IC C3 C1 C9 N12 0.0000 0.00 150.00 0.00 0.0000 +IC N12 C1 *C9 H10 0.0000 0.00 120.00 0.00 0.0000 +IC N12 C1 *C9 H11 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C9 N12 H13 0.0000 0.00 -60.00 0.00 0.0000 +IC H13 C9 *N12 H14 0.0000 0.00 -120.00 0.00 0.0000 +IC H13 C9 *N12 H15 0.0000 0.00 120.00 0.00 0.0000 +PATCH FIRST NONE LAST NONE + +RESI BTON 0.00 ! C4H8O Butanone, yapol +GROUP +ATOM O1 OG2D3 -0.48 +ATOM C1 CG2O5 0.40 +ATOM C2 CG331 -0.23 ! O1 H41 H42 +ATOM C3 CG321 -0.14 ! || | / +ATOM H21 HGA3 0.09 ! C1 C4--H43 +ATOM H22 HGA3 0.09 ! / \ / +ATOM H23 HGA3 0.09 ! H21--C2 C3--H31 +ATOM H31 HGA2 0.09 ! / | \ +ATOM H32 HGA2 0.09 ! H22 H23 H32 +GROUP +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 C2 C1 C3 C3 C4 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 +BOND C4 H41 C4 H42 C4 H43 +DOUBLE O1 C1 +IMPR C1 C3 C2 O1 +ACCE O1 +IC C2 C1 C3 H31 1.5366 116.31 56.91 107.51 1.1328 +IC O1 C1 C3 H31 1.2237 122.02 -123.36 107.51 1.1328 +IC O1 C1 C3 H32 1.2237 122.02 124.49 107.48 1.1325 +IC C3 C1 C2 H21 1.5233 110.58 -153.74 111.52 1.1204 +IC O1 C1 C2 H21 1.2237 126.42 23.85 111.52 1.1204 +IC O1 C1 C2 H22 1.2237 126.42 148.26 114.11 1.1296 +IC O1 C1 C2 H23 1.2237 126.42 -90.21 101.67 1.1375 +IC O1 C1 C3 C4 1.2237 122.02 0.50 114.19 1.5261 +IC C2 C1 C3 C4 1.5366 116.31 -179.21 114.19 1.5261 +IC C1 C3 C4 H41 1.5233 114.19 -60.64 111.01 1.0980 +IC C1 C3 C4 H42 1.5233 114.19 178.91 110.72 1.0989 +IC C1 C3 C4 H43 1.5233 114.19 58.43 111.02 1.0980 + +RESI CHON 0.00 ! C6H10O cyclohexanone, yapol +GROUP +ATOM O1 OG2D3 -0.48 +ATOM C1 CG2O5 0.40 +ATOM C6 CG321 -0.14 ! O1 +ATOM C2 CG321 -0.14 ! || +ATOM H6A HGA2 0.09 ! H6A C1 H2A +ATOM H6B HGA2 0.09 ! \ / \ / +ATOM H2A HGA2 0.09 ! H6B--C6 C2--H2B +ATOM H2B HGA2 0.09 ! | | + ! H5A--C5 C3--H3A +GROUP ! / \ / \ +ATOM C3 CG321 -0.18 ! H5B C4 H3B +ATOM H3A HGA2 0.09 ! / \ +ATOM H3B HGA2 0.09 ! H4A H4B +GROUP +ATOM C4 CG321 -0.18 +ATOM H4A HGA2 0.09 +ATOM H4B HGA2 0.09 +GROUP +ATOM C5 CG321 -0.18 +ATOM H5A HGA2 0.09 +ATOM H5B HGA2 0.09 + +BOND C1 C2 +BOND C2 H2A C2 H2B C2 C3 +BOND C3 H3A C3 H3B C3 C4 +BOND C4 H4A C4 H4B C4 C5 +BOND C5 H5A C5 H5B C5 C6 +BOND C6 H6A C6 H6B C6 C1 +DOUBLE O1 C1 +IMPR C1 C2 C6 O1 +ACCE O1 +IC C1 C2 C3 C4 0.0000 0.00 -60.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 60.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 +IC C6 C2 *C1 O1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2A 0.0000 0.00 -120.00 0.00 0.0000 +IC H2A C1 *C2 H2B 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 C2 *C3 H3A 0.0000 0.00 -120.00 0.00 0.0000 +IC H3A C2 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C3 *C4 H4A 0.0000 0.00 -120.00 0.00 0.0000 +IC H4A C3 *C4 H4B 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C4 *C5 H5A 0.0000 0.00 -120.00 0.00 0.0000 +IC H5A C4 *C5 H5B 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C1 *C6 H6A 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C1 *C6 H6B 0.0000 0.00 -120.00 0.00 0.0000 +patc firs none last none + +RESI DMTT 0.000 ! C3H6S3 dimethyl trithiocarbonate, kevo +GROUP +ATOM C1 CG331 -0.09 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM S1 SG311 -0.17 ! H11 S H21 +ATOM C CG2O6 0.22 ! | || | +ATOM S SG2D1 -0.24 ! H12--C1---S1---C---S2---C2--H22 +ATOM S2 SG311 -0.17 ! | | +ATOM C2 CG331 -0.09 ! H13 H23 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 + +BOND C1 S1 S1 C C S2 S2 C2 C S +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 +IMPR C S1 S2 S +IC S1 C S2 C2 0.0000 0.00 185.00 0.00 0.0000 +IC S2 C S1 C1 0.0000 0.00 180.00 0.00 0.0000 +IC S1 S2 *C S 0.0000 0.00 185.00 0.00 0.0000 +IC C S1 C1 H11 0.0000 0.00 185.00 0.00 0.0000 +IC C S1 C1 H12 0.0000 0.00 65.00 0.00 0.0000 +IC C S1 C1 H13 0.0000 0.00 305.00 0.00 0.0000 +IC C S2 C2 H21 0.0000 0.00 185.00 0.00 0.0000 ! introduce +IC C S2 C2 H22 0.0000 0.00 65.00 0.00 0.0000 ! 5deg asymmetry +IC C S2 C2 H23 0.0000 0.00 305.00 0.00 0.0000 ! everywhere. + +PRES 3POMP -0.030 ! C8H8O 3-phenoxymethylpyrrolidine (aka alpha-(3-pyrrolidine)anisole), kevo +DELETE ATOM H31 +GROUP +ATOM C3 CG3C51 -0.12 +ATOM H32 HGA1 0.09 +GROUP +ATOM C31 CG321 -0.01 +ATOM H311 HGA2 0.09 +ATOM H312 HGA2 0.09 +ATOM O32 OG301 -0.39 +ATOM C1B CG2R61 -0.115 ! H5B H4B +ATOM H1B HGR61 0.115 ! \ ___ / +ATOM C2B CG2R61 -0.115 ! C5B---C4B H312 H32 H42 +ATOM H2B HGR61 0.115 ! / \ \ \ / +ATOM C3B CG2R61 0.22 ! H6B--C6B C3B---O32---C31----C3----C4--H41 +ATOM C4B CG2R61 -0.115 ! \\ // / | | +ATOM H4B HGR61 0.115 ! C1B---C2B H311 H21--C2 C5--H51 +ATOM C5B CG2R61 -0.115 ! / \ / \ / \ +ATOM H5B HGR61 0.115 ! H1B H2B H22 N1 H52 +ATOM C6B CG2R61 -0.115 ! | +ATOM H6B HGR61 0.115 ! H1 + +BOND C3 C31 C31 O32 C31 H311 C31 H312 O32 C3B +BOND C1B H1B C1B C2B C2B H2B C2B C3B +BOND C3B C4B C4B H4B C4B C5B C5B H5B C5B C6B +BOND C6B H6B C6B C1B +IC C4 C2 *C3 C31 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C31 O32 0.0000 0.00 60.00 0.00 0.0000 ! folded (-120) is best for PES. 60="Axial" +IC C3 O32 *C31 H311 0.0000 0.00 120.00 0.00 0.0000 +IC C3 O32 *C31 H312 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C31 O32 C3B 0.0000 0.00 180.00 0.00 0.0000 ! folded (0) is best for PES. 180="Pointing away from ring" +IC C31 O32 C3B C2B 0.0000 0.00 0.00 0.00 0.0000 ! folded (90) is best for PES. 0="in-plane" like MEOB (unlike EBEN) +IC O32 C2B *C3B C4B 0.0000 0.00 180.00 0.00 0.0000 +IC C4B C3B C2B C1B 0.0000 0.00 0.00 0.00 0.0000 +IC C2B C3B C4B C5B 0.0000 0.00 0.00 0.00 0.0000 +IC C3B C4B C5B C6B 0.0000 0.00 0.00 0.00 0.0000 +IC C2B C6B *C1B H1B 0.0000 0.00 180.00 0.00 0.0000 +IC C3B C1B *C2B H2B 0.0000 0.00 180.00 0.00 0.0000 +IC C5B C3B *C4B H4B 0.0000 0.00 180.00 0.00 0.0000 +IC C6B C4B *C5B H5B 0.0000 0.00 180.00 0.00 0.0000 +IC C1B C5B *C6B H6B 0.0000 0.00 180.00 0.00 0.0000 + +RESI DMCB 0.00 ! C3H7NO2 dimethyl carbamate, kevo & xxwy +GROUP +ATOM C1 CG331 -0.04 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM N2 NG2S1 -0.38 +ATOM H2 HGP1 0.32 ! H11 O31 H41 +ATOM C3 CG2O6 0.20 ! | || | +ATOM O31 OG2D1 -0.39 ! H12--C1---N2---C3---O32---C4--H42 +ATOM O32 OG302 -0.32 ! | | | +ATOM C4 CG331 0.07 ! H13 H2 H43 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 C1 N2 +BOND N2 H2 N2 C3 +BOND C3 O31 C3 O32 O32 C4 +BOND C4 H41 C4 H42 C4 H43 +IMPR C3 N2 O31 O32 +IC C1 N2 C3 O32 0.0000 0.00 -170.00 0.00 0.0000 +IC C3 N2 C1 H11 0.0000 0.00 -150.00 0.00 0.0000 +IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C3 *N2 H2 0.0000 0.00 158.00 0.00 0.0000 +IC O32 N2 *C3 O31 0.0000 0.00 -180.00 0.00 0.0000 +IC N2 C3 O32 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C3 O32 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 O32 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 O32 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +RESI DECB 0.00 ! C5H11NO2 diethyl carbamate, kevo & xxwy +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM C2 CG321 0.05 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM N3 NG2S1 -0.38 +ATOM H3 HGP1 0.32 ! H11 H21 O41 H51 H61 +ATOM C4 CG2O6 0.20 ! | | || | | +ATOM O41 OG2D1 -0.39 ! H12--C1---C2---N3---C4---O42---C5---C6--H62 +ATOM O42 OG302 -0.32 ! | | | | | +ATOM C5 CG321 0.16 ! H13 H22 H3 H52 H63 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +ATOM C6 CG331 -0.27 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 C1 C2 +BOND C2 H21 C2 H22 C2 N3 N3 H3 N3 C4 +BOND C4 O41 C4 O42 O42 C5 +BOND C5 H51 C5 H52 C5 C6 +BOND C6 H61 C6 H62 C6 H63 +IMPR C4 N3 O41 O42 +IC C1 C2 N3 C4 0.0000 0.00 80.00 0.00 0.0000 +IC N3 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 N3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC H21 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *N3 H3 0.0000 0.00 155.00 0.00 0.0000 +IC C2 N3 C4 O41 0.0000 0.00 0.00 0.00 0.0000 +IC O41 N3 *C4 O42 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C4 O42 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C4 O42 C5 C6 0.0000 0.00 -90.00 0.00 0.0000 +IC C6 O42 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C6 O42 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC O42 C5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC H61 C5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 +IC H61 C5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 + +RESI FORH 0.00 ! CH2O2 formic acid, xxwy +GROUP +ATOM C CG2O2 0.38 ! O2 +ATOM H HGR52 0.11 ! // +ATOM O2 OG2D1 -0.40 ! H--C +ATOM O1 OG311 -0.49 ! \ +ATOM HO1 HGP1 0.40 ! O1-HO1 + +BOND C O1 C H O1 HO1 +DOUBLE C O2 +IMPR C O2 O1 H +DONO BLNK HO1 ! O1 +ACCE O1 +ACCE O2 +IC O2 C O1 HO1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC O1 O2 *C H 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI DMA 0.00 ! C4H9NO Dimethylacetamide, xxwy +GROUP +ATOM C CG2O1 0.43 ! H33 +ATOM O OG2D1 -0.52 ! | +ATOM N NG2S0 -0.35 ! O C3--H32 +ATOM C1 CG331 -0.19 ! \\ / \ +ATOM H11 HGA3 0.09 ! C---N H31 +ATOM H12 HGA3 0.09 ! / \ +ATOM H13 HGA3 0.09 ! H11--C1 C2--H23 +ATOM C2 CG331 -0.09 ! / | / | +ATOM H21 HGA3 0.09 ! H12 H13 H21 H22 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 +ATOM C3 CG331 -0.09 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND H11 C1 H12 C1 H13 C1 +BOND H21 C2 H22 C2 H23 C2 +BOND H31 C3 H32 C3 H33 C3 +BOND C C1 C N N C2 N C3 +DOUBLE C O +IMPR C C1 N O +IC O C N C2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O N *C C1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C C2 *N C3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N C C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C N C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C N C3 H31 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI DMF 0.00 ! C3H7NO Dimethylformamide, xxwy +GROUP +ATOM HA HGR52 0.08 +ATOM C CG2O1 0.43 ! HC3 +ATOM O OG2D1 -0.54 ! | +ATOM N NG2S0 -0.33 ! O CC--HC2 +ATOM CC CG331 -0.09 ! \\ / \ +ATOM HC1 HGA3 0.09 ! C--N HC1 +ATOM HC2 HGA3 0.09 ! / \ +ATOM HC3 HGA3 0.09 ! HA CT--HT3 +ATOM CT CG331 -0.09 ! / | +ATOM HT1 HGA3 0.09 ! HT1 HT2 +ATOM HT2 HGA3 0.09 +ATOM HT3 HGA3 0.09 + +BOND HT1 CT HT2 CT HT3 CT +BOND C HA C N N CC N CT +BOND HC1 CC HC2 CC HC3 CC +DOUBLE C O +IMPR C N O HA +IC O C N CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC O N *C HA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CT *N CC 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C N CC HC1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N HC1 *CC HC2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N HC1 *CC HC3 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C N CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N HT1 *CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N HT1 *CT HT3 0.0000 0.0000 -120.0000 0.0000 0.0000 +!IC O C N CT 1.2287 125.40 -180.0000 120.95 1.4495 +!IC O N *C HA 1.2287 125.40 180.0000 112.84 1.1003 +!IC C CT *N CC 1.3646 120.95 -179.0000 117.80 1.4514 +!IC C N CC HC1 1.3646 121.26 0.0000 110.77 1.1140 +!IC N HC1 *CC HC2 1.4514 110.77 118.6600 110.23 1.1108 +!IC N HC1 *CC HC3 1.4514 110.77 -118.6600 110.23 1.1108 +!IC C N CT HT1 1.3646 120.95 0.0000 110.56 1.1133 +!IC N HT1 *CT HT2 1.4495 110.56 118.5900 110.54 1.1115 +!IC N HT1 *CT HT3 1.4495 110.56 -118.5900 110.54 1.1115 + +RESI HEXD 0.00 ! C6H14O2 1,6-hexanediol, xxwy +GROUP +ATOM H11 HGA2 0.09 ! O1-HO1 +ATOM H12 HGA2 0.09 ! | +ATOM HO1 HGP1 0.42 ! H11-C1-H12 +ATOM C1 CG321 0.05 ! | +ATOM O1 OG311 -0.65 ! | +GROUP ! | +ATOM H21 HGA2 0.09 ! H21-C2-H22 +ATOM H22 HGA2 0.09 ! | +ATOM C2 CG321 -0.18 ! | +GROUP ! | +ATOM H31 HGA2 0.09 ! H31-C3-H32 +ATOM H32 HGA2 0.09 ! | +ATOM C3 CG321 -0.18 ! | +GROUP ! | +ATOM H41 HGA2 0.09 ! H41-C4-H42 +ATOM H42 HGA2 0.09 ! | +ATOM C4 CG321 -0.18 ! | +GROUP ! | +ATOM H51 HGA2 0.09 ! H51-C5-H152 +ATOM H52 HGA2 0.09 ! | +ATOM C5 CG321 -0.18 ! | +GROUP ! | +ATOM H61 HGA2 0.09 ! H61-C6-H62 +ATOM H62 HGA2 0.09 ! | +ATOM HO6 HGP1 0.42 ! O6-HO6 +ATOM C6 CG321 0.05 +ATOM O6 OG311 -0.65 + +BOND H11 C1 H12 C1 O1 C1 C1 C2 +BOND H21 C2 H22 C2 C2 C3 O1 HO1 +BOND H31 C3 H32 C3 C3 C4 +BOND H41 C4 H42 C4 C4 C5 +BOND H51 C5 H52 C5 C5 C6 +BOND H61 C6 H62 C6 C6 O6 O6 HO6 +IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00 +IC C2 C3 C4 C5 0.00 0.00 180.0 0.00 0.00 +IC C3 C4 C5 C6 0.00 0.00 180.0 0.00 0.00 +IC C3 C2 C1 O1 0.00 0.00 180.0 0.00 0.00 +IC C2 C1 O1 HO1 0.00 0.00 180.0 0.00 0.00 +IC O1 C2 *C1 H11 0.00 0.00 120.0 0.00 0.00 +IC O1 C2 *C1 H12 0.00 0.00 240.0 0.00 0.00 +IC C1 C3 *C2 H21 0.00 0.00 120.0 0.00 0.00 +IC C1 C3 *C2 H22 0.00 0.00 240.0 0.00 0.00 +IC C2 C4 *C3 H31 0.00 0.00 120.0 0.00 0.00 +IC C2 C4 *C3 H32 0.00 0.00 240.0 0.00 0.00 +IC C3 C5 *C4 H41 0.00 0.00 120.0 0.00 0.00 +IC C3 C5 *C4 H42 0.00 0.00 240.0 0.00 0.00 +IC C4 C6 *C5 H51 0.00 0.00 120.0 0.00 0.00 +IC C4 C6 *C5 H52 0.00 0.00 240.0 0.00 0.00 +IC C4 C5 C6 O6 0.00 0.00 180.0 0.00 0.00 +IC C5 C6 O6 HO6 0.00 0.00 180.0 0.00 0.00 +IC O6 C5 *C6 H61 0.00 0.00 120.0 0.00 0.00 +IC O6 C5 *C6 H62 0.00 0.00 240.0 0.00 0.00 + +RESI TBOH 0.00 ! C4H10O t-butanol, xxwy +GROUP +ATOM C CG301 0.23 ! H12 H13 H33 H32 +ATOM O OG311 -0.65 ! \ / \ / +ATOM HO HGP1 0.42 ! H11--C1 C3--H31 +GROUP ! \ / +ATOM C1 CG331 -0.27 ! C +ATOM H11 HGA3 0.09 ! / \ +ATOM H12 HGA3 0.09 ! O C2--H23 +ATOM H13 HGA3 0.09 ! | | \ +GROUP ! HO H21 H22 +ATOM C2 CG331 -0.27 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 +GROUP +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND C1 C C2 C C3 C C O O HO +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +DONO HO O +ACCE O +IC C1 C C2 H21 0.0000 0.000 180.0000 0.000 0.0000 +IC C H21 *C2 H22 0.0000 0.000 120.0000 0.000 0.0000 +IC C H21 *C2 H23 0.0000 0.000 -120.0000 0.000 0.0000 +IC C2 C C1 H11 0.0000 0.000 180.0000 0.000 0.0000 +IC C H11 *C1 H12 0.0000 0.000 120.0000 0.000 0.0000 +IC C H11 *C1 H13 0.0000 0.000 -120.0000 0.000 0.0000 +IC C1 C C3 H31 0.0000 0.000 180.0000 0.000 0.0000 +IC C H31 *C3 H32 0.0000 0.000 120.0000 0.000 0.0000 +IC C H31 *C3 H33 0.0000 0.000 -120.0000 0.000 0.0000 +IC C1 C2 *C O 0.0000 0.000 120.0000 0.000 0.0000 +IC C1 C2 *C C3 0.0000 0.000 -120.0000 0.000 0.0000 +IC C3 C O HO 0.0000 0.000 180.0000 0.000 0.0000 + +RESI TMAOP 1.00 ! C3H10NO protonated trimethylammoniumoxide (TMAO) +GROUP ! (aka Hydroxy(trimethyl)Ammonium), xxwy +ATOM N NG3P0 -0.53 +ATOM C1 CG334 -0.35 ! H31 H32 +ATOM C2 CG334 -0.35 ! \ / +ATOM C3 CG334 -0.35 ! H11 C3-H33 +ATOM H11 HGP5 0.25 ! \ | +ATOM H12 HGP5 0.25 ! H12-C1---N---O-HO +ATOM H13 HGP5 0.25 ! / | +ATOM H21 HGP5 0.25 ! H1 C2-H23 +ATOM H22 HGP5 0.25 ! / \ +ATOM H23 HGP5 0.25 ! H21 H22 +ATOM H31 HGP5 0.25 +ATOM H32 HGP5 0.25 +ATOM H33 HGP5 0.25 +ATOM O OG311 -0.17 +ATOM HO HGP1 0.50 + +BOND N C1 N C2 N C3 N O O HO +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +IC C2 N C1 H11 0.00 0.00 180.0 0.0 0.0 +IC N H11 *C1 H12 0.00 0.00 120.0 0.0 0.0 +IC N H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0 +IC C1 N C2 H21 0.00 0.00 180.0 0.0 0.0 +IC N H21 *C2 H22 0.00 0.00 120.0 0.0 0.0 +IC N H21 *C2 H23 0.00 0.00 -120.0 0.0 0.0 +IC C1 N C3 H31 0.00 0.00 180.0 0.0 0.0 +IC N H31 *C3 H32 0.00 0.00 120.0 0.0 0.0 +IC N H31 *C3 H33 0.00 0.00 -120.0 0.0 0.0 +IC C1 C2 *N C3 0.00 0.00 120.0 0.0 0.0 +IC C1 C2 *N O 0.00 0.00 -120.0 0.0 0.0 +IC C3 N O HO 0.00 0.00 180.0 0.0 0.0 + +RESI MRDN 0.000 ! C4H3NOS2 methylidene rhodanine, kevo & xxwy +GROUP +ATOM S1 SG311 -0.14 ! H3 S2 +ATOM C2 CG2R53 0.26 ! \ // +ATOM S2 SG2D1 -0.27 ! N3----C2 +ATOM N3 NG2R53 -0.25 ! | | +ATOM H3 HGP1 0.32 ! C4 S1 +ATOM C4 CG2R53 0.29 ! // \ / +ATOM O4 OG2D1 -0.39 ! O4 C5 +ATOM C5 CG252O 0.10 ! || +ATOM C6 CG2DC3 -0.49 ! C6 +ATOM H61 HGA5 0.24 ! / \ +ATOM H62 HGA5 0.33 ! H61 H62 + +BOND S1 C2 C2 N3 N3 C4 C4 C5 +BOND C5 S1 C2 S2 N3 H3 C4 O4 +BOND C5 C6 C6 H61 C6 H62 +IMPR C2 N3 S2 S1 +IMPR C4 C5 N3 O4 +IC C5 C4 N3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C4 N3 C2 S1 0.0000 0.00 0.00 0.00 0.0000 +IC N3 S1 *C2 S2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N3 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 +IC S1 C4 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 H61 0.0000 0.00 0.00 0.00 0.0000 +IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 + +RESI MEOI 0.000 ! C9H7NO methyleneoxindole, kevo & xxwy +GROUP +ATOM C5 CG2DC3 -0.52 +ATOM H51 HGA5 0.29 +ATOM H52 HGA5 0.24 +ATOM C6 CG25C2 -0.10 ! H51 H52 +ATOM C7 CG2R53 0.67 ! \ / +ATOM O7 OG2D1 -0.57 ! H13 C5 +ATOM N8 NG2R51 -0.45 ! | || +ATOM H8 HGP1 0.32 ! C13 C6 O7 +ATOM C9 CG2RC0 0.25 ! // \ / \ // +ATOM C10 CG2R61 -0.34 ! H12--C12 C14 C7 +ATOM H10 HGR61 0.24 ! | || | +ATOM C11 CG2R61 -0.20 ! H11--C11 C9----N8 +ATOM H11 HGR61 0.22 ! \\ / \ +ATOM C12 CG2R61 -0.23 ! C10 H8 +ATOM H12 HGR61 0.21 ! | +ATOM C13 CG2R61 -0.32 ! H10 +ATOM H13 HGR61 0.28 +ATOM C14 CG2RC0 0.01 + +BOND C6 C7 C7 N8 N8 C9 C9 C10 C10 C11 +BOND C11 C12 C12 C13 C13 C14 C14 C6 C9 C14 +BOND C7 O7 N8 H8 C10 H10 C11 H11 C12 H12 +BOND C13 H13 C6 C5 C5 H51 C5 H52 +IMPR C7 C6 N8 O7 +IC C6 C14 C9 N8 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C9 N8 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C9 *C14 C13 0.0000 0.00 180.00 0.00 0.0000 +IC C14 N8 *C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C14 C13 C12 0.0000 0.00 0.00 0.00 0.0000 +IC N8 C6 *C7 O7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *N8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C10 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C13 C11 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C12 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C14 *C6 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C14 C6 C5 H51 0.0000 0.00 0.00 0.00 0.0000 +IC H51 C6 *C5 H52 0.0000 0.00 180.00 0.00 0.0000 + +RESI BAB2 -1.00 ! C29H47N2O6 Bile Acid Basic moiety 1 (BASE FOR NEW COMPOUNDS), cacha +! Based on Glu-UDCA Amide +GROUP +ATOM C3 CG311 0.14 ! OG +ATOM O3 OG311 -0.65 ! || +ATOM H3' HGP1 0.42 ! CG--NT--HT2 +ATOM H3 HGA1 0.09 ! / HT1 +GROUP ! CC3 +ATOM C4 CG321 -0.18 ! \ +ATOM H4A HGA2 0.09 ! O24 CC2 +ATOM H4B HGA2 0.09 ! || / +GROUP ! H Me21 C22 C24 CC1 +ATOM C5 CG311 -0.09 ! | \ / \ / \ / \ +ATOM H5 HGA1 0.09 ! C12 Me18 C20 C23 NH CA--OA1 (-0.5) +GROUP ! / \ | / | +ATOM C6 CG321 -0.18 ! C11 C13---C17 OA2 (-0.5) +ATOM H6A HGA2 0.09 ! Me19 | | | +ATOM H6B HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM C7 CG311 0.14 ! C2 C10 C8 C15 +ATOM O7 OG311 -0.65 ! | | | +ATOM H7' HGP1 0.42 ! C3 C5 C7 +ATOM H7 HGA1 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM C8 CG311 -0.09 +ATOM H8 HGA1 0.09 ! BAB2 +GROUP +ATOM C14 CG3RC1 -0.09 +ATOM H14 HGA1 0.09 +GROUP +ATOM C15 CG3C52 -0.18 +ATOM H15A HGA2 0.09 +ATOM H15B HGA2 0.09 +GROUP +ATOM C16 CG3C52 -0.18 +ATOM H16A HGA2 0.09 +ATOM H16B HGA2 0.09 +GROUP +ATOM C17 CG3C51 -0.09 +ATOM H17 HGA1 0.09 +GROUP +ATOM C13 CG3RC1 0.00 +GROUP +ATOM C18 CG331 -0.27 +ATOM H18A HGA3 0.09 +ATOM H18B HGA3 0.09 +ATOM H18C HGA3 0.09 +GROUP +ATOM C12 CG321 -0.18 +ATOM H12A HGA2 0.09 +ATOM H12B HGA2 0.09 +GROUP +ATOM C11 CG321 -0.18 +ATOM H11A HGA2 0.09 +ATOM H11B HGA2 0.09 +GROUP +ATOM C9 CG311 -0.09 +ATOM H9 HGA1 0.09 +GROUP +ATOM C10 CG301 0.00 +GROUP +ATOM C19 CG331 -0.27 +ATOM H19A HGA3 0.09 +ATOM H19B HGA3 0.09 +ATOM H19C HGA3 0.09 +GROUP +ATOM C1 CG321 -0.18 +ATOM H1A HGA2 0.09 +ATOM H1B HGA2 0.09 +GROUP +ATOM C2 CG321 -0.18 +ATOM H2A HGA2 0.09 +ATOM H2B HGA2 0.09 +GROUP +ATOM C20 CG311 -0.09 +ATOM H20 HGA1 0.09 +GROUP +ATOM C21 CG331 -0.27 +ATOM H21A HGA3 0.09 +ATOM H21B HGA3 0.09 +ATOM H21C HGA3 0.09 +GROUP +ATOM C22 CG321 -0.18 +ATOM H22A HGA2 0.09 +ATOM H22B HGA2 0.09 +GROUP +ATOM C23 CG321 -0.18 +ATOM H23A HGA2 0.09 +ATOM H23B HGA2 0.09 +GROUP +ATOM C24 CG2O1 0.51 +ATOM O24 OG2D1 -0.51 +ATOM N NG2S1 -0.47 +ATOM HN HGP1 0.47 +GROUP +ATOM CC1 CG311 -0.19 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O3 0.62 +ATOM OA1 OG2D2 -0.76 +ATOM OA2 OG2D2 -0.76 +GROUP +ATOM CC2 CG321 -0.18 +ATOM HC2A HGA2 0.09 +ATOM HC2B HGA2 0.09 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 +GROUP +ATOM CG CG2O1 0.55 +ATOM OG OG2D1 -0.55 +ATOM NT NG2S2 -0.62 +ATOM HT1 HGP1 0.32 +ATOM HT2 HGP1 0.30 +BOND C3 O3 C3 H3 O3 H3' +BOND C3 C4 C4 H4A C4 H4B +BOND C4 C5 C5 H5 +BOND C5 C10 C10 C19 C19 H19A C19 H19B C19 H19C +BOND C10 C1 C1 H1A C1 H1B +BOND C1 C2 C2 H2A C2 H2B +BOND C2 C3 +BOND C5 C6 C6 H6A C6 H6B +BOND C6 C7 C7 H7 C7 O7 O7 H7' +BOND C7 C8 C8 H8 +BOND C8 C9 C9 H9 +BOND C9 C10 +BOND C8 C14 C14 H14 +BOND C14 C13 C13 C18 C18 H18A C18 H18B C18 H18C +BOND C13 C12 C12 H12A C12 H12B +BOND C12 C11 C11 H11A C11 H11B +BOND C11 C9 +BOND C14 C15 C15 H15A C15 H15B +BOND C15 C16 C16 H16A C16 H16B +BOND C16 C17 C17 H17 +BOND C17 C13 +BOND C17 C20 C20 H20 C20 C21 C21 H21A C21 H21B C21 H21C +BOND C20 C22 C22 H22A C22 H22B +BOND C22 C23 C23 H23A C23 H23B +BOND C23 C24 C24 O24 +BOND C24 N N HN +BOND N CC1 CC1 HC1 CC1 CC2 CC1 CA CA OA1 CA OA2 +BOND CC2 HC2A CC2 HC2B CC2 CC3 +BOND CC3 HC3A CC3 HC3B CC3 CG +BOND CG OG CG NT NT HT1 NT HT2 +IMPR C24 C23 N O24 +IMPR CA OA2 OA1 CC1 +IMPR CG CC3 NT OG +IC C1 C2 C3 C4 1.5325 111.68 -49.45 111.84 1.5383 +IC C2 C3 C4 C5 1.5339 111.84 43.93 115.68 1.5598 +IC C3 C4 C5 C6 1.5383 115.68 -175.10 109.02 1.5521 +IC C4 C5 C6 C7 1.5598 109.02 85.47 114.98 1.5441 +IC C5 C6 C7 C8 1.5521 114.98 39.04 113.05 1.5290 +IC C7 C8 C9 C10 1.5290 114.08 58.26 109.48 1.5439 +IC C8 C9 C10 C1 1.5323 109.48 179.67 111.99 1.5563 +IC C9 C10 C1 C2 1.5439 111.99 63.33 113.83 1.5325 +IC O3 C3 C4 C5 1.4163 109.09 162.18 115.68 1.5598 +IC C4 C2 *C3 O3 1.5383 111.84 -119.44 107.07 1.4163 +IC C4 C2 *C3 H3 1.5383 111.84 121.33 109.38 1.1144 +IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 +IC C2 C3 O3 H3' 1.5339 107.07 70.05 104.87 0.9608 +IC C5 C3 *C4 H4A 1.5598 115.68 122.75 108.69 1.1111 +IC H4A C3 *C4 H4B 1.1111 108.69 115.73 108.82 1.1113 +IC C10 C4 *C5 H5 1.5279 114.70 116.72 105.03 1.1175 +IC C7 C5 *C6 H6A 1.5441 114.98 -124.16 109.39 1.1113 +IC H6A C5 *C6 H6B 1.1113 109.39 -115.80 108.33 1.1112 +IC C2 C10 *C1 H1A 1.5325 113.83 119.39 107.74 1.1137 +IC C2 C10 *C1 H1B 1.5325 113.83 -124.36 110.18 1.1091 +IC C1 C3 *C2 H2A 1.5325 111.68 122.11 110.21 1.1113 +IC H2A C3 *C2 H2B 1.1113 110.21 117.20 108.66 1.1128 +IC C6 C7 C8 C14 1.5441 113.05 -166.95 108.56 1.5542 +IC C14 C7 *C8 C9 1.5542 108.56 119.93 114.08 1.5323 +IC C7 C8 C14 C13 1.5290 108.56 -174.20 113.13 1.5425 +IC C13 C8 *C14 C15 1.5425 113.13 118.56 116.30 1.5285 +IC C8 C14 C15 C16 1.5542 116.30 -154.74 103.56 1.5435 +IC C14 C15 C16 C17 1.5285 103.56 -2.52 106.91 1.5533 +IC C17 C14 *C13 C12 1.5731 98.18 119.81 107.46 1.5340 +IC C14 C13 C12 C11 1.5425 107.46 55.26 111.18 1.5432 +IC C8 C6 *C7 O7 1.5290 113.05 119.58 107.98 1.4218 +IC O7 C6 *C7 H7 1.4218 107.98 118.83 107.19 1.1164 +IC C6 C7 O7 H7' 1.5441 107.98 178.44 105.26 0.9614 +IC C9 C7 *C8 H8 1.5323 114.08 122.47 107.18 1.1067 +IC C10 C8 *C9 H9 1.5439 109.48 -117.10 106.56 1.1138 +IC C9 C12 *C11 H11A 1.5547 114.18 122.66 108.77 1.1090 +IC H11A C12 *C11 H11B 1.1090 108.77 115.79 107.30 1.1111 +IC C14 C13 C12 H12A 1.5425 107.46 175.99 111.88 1.1059 +IC H12A C13 *C12 H12B 1.1059 111.88 119.47 108.82 1.1125 +IC C13 C8 *C14 H14 1.5425 113.13 -118.30 108.46 1.1150 +IC C16 C14 *C15 H15A 1.5435 103.56 119.15 111.17 1.1002 +IC H15A C14 *C15 H15B 1.1002 111.17 119.82 112.08 1.0988 +IC C17 C15 *C16 H16A 1.5533 106.91 121.49 110.78 1.0992 +IC H16A C15 *C16 H16B 1.0992 110.78 117.20 110.97 1.0999 +IC C13 C16 *C17 H17 1.5731 98.41 -112.89 110.39 1.1009 +IC C12 C14 *C13 C18 1.5340 107.46 121.97 114.21 1.5526 +IC C14 C13 C18 H18A 1.5425 114.21 116.84 111.38 1.1064 +IC H18A C13 *C18 H18B 1.1064 111.38 119.04 110.59 1.1085 +IC H18A C13 *C18 H18C 1.1064 111.38 -120.17 111.91 1.1058 +IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53 1.5562 +IC C5 C10 C19 H19A 1.5279 109.53 5.08 111.17 1.1079 +IC H19A C10 *C19 H19B 1.1079 111.17 121.06 112.01 1.1061 +IC H19A C10 *C19 H19C 1.1079 111.17 -119.50 110.64 1.1093 +IC C13 C16 *C17 C20 1.5731 98.41 127.01 111.83 1.5649 +IC C16 C17 C20 C22 1.5533 111.83 71.96 108.75 1.5519 +IC C22 C17 *C20 C21 1.5519 108.75 122.38 112.90 1.5396 +IC C21 C17 *C20 H20 1.5396 112.90 120.78 108.89 1.1119 +IC C17 C20 C21 H21A 1.5649 112.90 71.88 110.45 1.1079 +IC H21A C20 *C21 H21B 1.1079 110.45 -121.55 110.43 1.1103 +IC H21A C20 *C21 H21C 1.1079 110.45 118.45 110.89 1.1089 +IC C17 C20 C22 C23 1.5649 108.75 -163.10 113.67 1.5524 +IC C23 C20 *C22 H22A 1.5524 113.67 119.92 108.15 1.1127 +IC H22A C20 *C22 H22B 1.1127 108.15 116.44 108.31 1.1133 +IC C20 C22 C23 C24 1.5519 113.67 176.63 114.01 1.5029 +IC C24 C22 *C23 H23A 1.5029 114.01 120.77 110.50 1.1097 +IC H23A C22 *C23 H23B 1.1097 110.50 118.82 109.42 1.1112 +IC C22 C23 C24 N 1.5524 114.01 0.05 116.58 1.3364 +IC N C23 *C24 O24 1.3364 116.58 -179.90 119.94 1.2265 +IC C23 C24 N CC1 1.5029 116.58 178.79 130.40 1.4446 +IC CC1 C24 *N HN 1.4446 130.40 -174.70 123.77 1.0138 +IC C24 N CC1 CA 1.3364 130.40 -170.40 102.83 1.5482 +IC CA N *CC1 HC1 1.5482 102.83 114.75 109.50 1.1102 +IC HC1 N *CC1 CC2 1.1102 109.50 123.68 113.47 1.5536 +IC N CC1 CA OA1 1.4446 102.83 178.79 119.90 1.2534 +IC OA1 CC1 *CA OA2 1.2534 119.90 177.56 115.53 1.2691 +IC N CC1 CC2 CC3 1.4446 113.47 60.10 115.05 1.5552 +IC CC3 CC1 *CC2 HC2A 1.5552 115.05 126.07 109.17 1.1118 +IC HC2A CC1 *CC2 HC2B 1.1118 109.17 114.51 106.60 1.1142 +IC CC1 CC2 CC3 CG 1.5536 115.05 107.73 115.32 1.5034 +IC CG CC2 *CC3 HC3A 1.5034 115.32 119.05 108.25 1.1125 +IC HC3A CC2 *CC3 HC3B 1.1125 108.25 117.32 110.47 1.1095 +IC CC2 CC3 CG NT 1.5552 115.32 -46.42 118.71 1.3503 +IC NT CC3 *CG OG 1.3503 118.71 -179.05 119.96 1.2327 +IC CC3 CG NT HT2 1.5034 118.71 -177.78 118.60 0.9905 +IC HT2 CG *NT HT1 0.9905 118.60 177.52 119.35 1.0169 + +PRES 3MRB 1.00 ! C16H22N2O3 (010206(R)D), cacha +! This compound has 3-methylamine piperidine at gamma position (R-isomer) +! and benzyl at alpha position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 +ATOM HT1 HGP1 0.47 ! HG31 HG32 +GROUP ! \ / +ATOM CGT CG321 -0.18 ! OG CG2--NG3 (+1) +ATOM HGT1 HGA2 0.09 ! || / \ +ATOM HGT2 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 +GROUP ! / HT1 \ / +ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 +ATOM HG1 HGA1 0.09 ! \ +GROUP ! O24 CC2 +ATOM CG2 CG324 0.20 ! || / +ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ // \\ +ATOM NG3 NG3P2 -0.40 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP +ATOM HG31 HGP2 0.32 ! / \ | / || \ __ / +ATOM HG32 HGP2 0.32 ! C11 C13---C17 OA1 CD2--CE2 +ATOM CG4 CG324 0.20 ! Me19 | | | +ATOM HG41 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HG42 HGA2 0.09 ! / \|/ \ / \ / +GROUP ! C2 C10 C8 C15 +ATOM CG5 CG321 -0.18 ! | | | +ATOM HG51 HGA2 0.09 ! C3 C5 C7 +ATOM HG52 HGA2 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 ! 3MRB (010206(R)D) +ATOM HG62 HGA2 0.09 +GROUP +ATOM CC1 CG311 -0.01 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.63 +ATOM OA1 OG2D1 -0.51 +ATOM OA2 OG302 -0.33 +ATOM CB CG321 -0.05 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG3 +BOND NG3 HG31 NG3 HG32 NG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +BOND OA2 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5303 108.41 178.95 117.49 1.4423 +IC CA OA2 CB HB1 1.3389 117.49 -63.60 110.30 1.1151 +IC CA OA2 CB CZ 1.3389 117.49 175.38 113.51 1.5040 +IC CA OA2 CB HB2 1.3389 117.49 55.90 110.62 1.1128 +IC OA2 CB CZ CD2 1.4423 113.51 -83.20 119.67 1.4050 +IC OA2 CB CZ CD1 1.4423 113.51 96.00 120.74 1.4052 +IC CD1 CD2 *CZ CB 1.4052 119.59 179.22 119.67 1.5040 +IC CD2 CZ CB HB1 1.4050 119.67 154.34 107.75 1.1151 +IC CD2 CZ CB HB2 1.4050 119.67 38.67 106.37 1.1128 +IC CB CZ CD1 CE1 1.5040 120.74 179.42 120.16 1.4019 +IC CB CZ CD2 CE2 1.5040 119.67 -179.26 120.19 1.4014 +IC CZ CD1 CE1 CP 1.4052 120.16 0.10 119.97 1.4007 +IC CD1 CE1 CP CE2 1.4019 119.97 1.03 120.10 1.4008 +IC CE1 CP CE2 CD2 1.4007 120.10 -0.88 119.97 1.4014 +IC CE1 CZ *CD1 HD1 1.4019 120.16 -179.61 120.14 1.0798 +IC CE2 CZ *CD2 HD2 1.4014 120.19 179.65 119.92 1.0808 +IC CP CD1 *CE1 HE1 1.4007 119.97 -179.69 120.14 1.0811 +IC CP CD2 *CE2 HE2 1.4008 119.97 179.52 120.22 1.0812 +IC CE1 CE2 *CP HP 1.4007 120.10 -179.21 119.80 1.0818 +IC OG CG NT CGT 1.2255 122.02 -7.42 126.12 1.4473 +IC CG NT CGT CG1 1.3372 126.12 -120.45 106.50 1.5345 +IC CG1 NT *CGT HGT1 1.5345 106.50 -118.61 109.21 1.1138 +IC CG1 NT *CGT HGT2 1.5345 106.50 121.47 112.52 1.1152 +IC NT CGT CG1 HG1 1.4473 106.50 -49.08 105.00 1.1195 +IC HG1 CGT *CG1 CG2 1.1195 105.00 117.96 109.91 1.5332 +IC HG1 CGT *CG1 CG6 1.1195 105.00 -116.91 117.24 1.5386 +IC CGT CG1 CG2 NG3 1.5345 109.91 -165.05 107.18 1.5040 +IC NG3 CG1 *CG2 HG21 1.5040 107.18 115.15 114.00 1.1022 +IC NG3 CG1 *CG2 HG22 1.5040 107.18 -117.58 113.73 1.0992 +IC CG1 CG2 NG3 CG4 1.5332 107.18 -58.17 114.03 1.5040 +IC CG4 CG2 *NG3 HG31 1.5040 114.03 121.47 103.04 1.0297 +IC CG4 CG2 *NG3 HG32 1.5040 114.03 -128.31 110.60 1.0023 +IC CG2 NG3 CG4 CG5 1.5040 114.03 49.95 112.77 1.5402 +IC CG5 NG3 *CG4 HG41 1.5402 112.77 123.21 105.30 1.1028 +IC CG5 NG3 *CG4 HG42 1.5402 112.77 -121.26 104.50 1.1039 +IC NG3 CG4 CG5 CG6 1.5040 112.77 -47.23 111.99 1.5433 +IC CG6 CG4 *CG5 HG51 1.5433 111.99 119.26 108.44 1.1152 +IC CG6 CG4 *CG5 HG52 1.5433 111.99 -123.11 110.16 1.1110 +IC CG5 CG1 *CG6 HG61 1.5433 108.29 -119.60 109.57 1.1132 +IC CG5 CG1 *CG6 HG62 1.5433 108.29 121.59 110.16 1.1111 + +PRES 3MPR 1.00 ! C7H14N2O (01OH06(R)D), cacha +! This compound has 3-methylamine piperidine at gamma position (R-isomer) +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 +ATOM HT1 HGP1 0.47 ! HG31 HG32 +GROUP ! \ / +ATOM CGT CG321 -0.18 ! OG CG2--NG3 (+1) +ATOM HGT1 HGA2 0.09 ! || / \ +ATOM HGT2 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 +GROUP ! / HT1 \ / +ATOM CG1 CG311 -0.09 ! CC3 CG6--CG5 +ATOM HG1 HGA1 0.09 ! \ +GROUP ! O24 CC2 +ATOM CG2 CG324 0.20 ! || / +ATOM HG21 HGA2 0.09 ! H Me21 C22 C24 CC1 +ATOM HG22 HGA2 0.09 ! | \ / \ / \ / \ +ATOM NG3 NG3P2 -0.40 ! C12 Me18 C20 C23 NH CA---OA2 +ATOM HG31 HGP2 0.32 ! / \ | / || +ATOM HG32 HGP2 0.32 ! C11 C13---C17 OA1 +ATOM CG4 CG324 0.20 ! Me19 | | | +ATOM HG41 HGA2 0.09 ! C1 | C9 C14 C16 +ATOM HG42 HGA2 0.09 ! / \|/ \ / \ / +GROUP ! C2 C10 C8 C15 +ATOM CG5 CG321 -0.18 ! | | | +ATOM HG51 HGA2 0.09 ! C3 C5 C7 +ATOM HG52 HGA2 0.09 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 ! 3MPR (01OH06(R)D) +ATOM HG62 HGA2 0.09 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 CG2 +BOND CG2 HG21 CG2 HG22 CG2 NG3 +BOND NG3 HG31 NG3 HG32 NG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 + +IC OG CG NT CGT 1.2255 122.02 -7.42 126.12 1.4473 +IC CG NT CGT CG1 1.3372 126.12 -120.45 106.50 1.5345 +IC CG1 NT *CGT HGT1 1.5345 106.50 -118.61 109.21 1.1138 +IC CG1 NT *CGT HGT2 1.5345 106.50 121.47 112.52 1.1152 +IC NT CGT CG1 HG1 1.4473 106.50 -49.08 105.00 1.1195 +IC HG1 CGT *CG1 CG2 1.1195 105.00 117.96 109.91 1.5332 +IC HG1 CGT *CG1 CG6 1.1195 105.00 -116.91 117.24 1.5386 +IC CGT CG1 CG2 NG3 1.5345 109.91 -165.05 107.18 1.5040 +IC NG3 CG1 *CG2 HG21 1.5040 107.18 115.15 114.00 1.1022 +IC NG3 CG1 *CG2 HG22 1.5040 107.18 -117.58 113.73 1.0992 +IC CG1 CG2 NG3 CG4 1.5332 107.18 -58.17 114.03 1.5040 +IC CG4 CG2 *NG3 HG31 1.5040 114.03 121.47 103.04 1.0297 +IC CG4 CG2 *NG3 HG32 1.5040 114.03 -128.31 110.60 1.0023 +IC CG2 NG3 CG4 CG5 1.5040 114.03 49.95 112.77 1.5402 +IC CG5 NG3 *CG4 HG41 1.5402 112.77 123.21 105.30 1.1028 +IC CG5 NG3 *CG4 HG42 1.5402 112.77 -121.26 104.50 1.1039 +IC NG3 CG4 CG5 CG6 1.5040 112.77 -47.23 111.99 1.5433 +IC CG6 CG4 *CG5 HG51 1.5433 111.99 119.26 108.44 1.1152 +IC CG6 CG4 *CG5 HG52 1.5433 111.99 -123.11 110.16 1.1110 +IC CG5 CG1 *CG6 HG61 1.5433 108.29 -119.60 109.57 1.1132 +IC CG5 CG1 *CG6 HG62 1.5433 108.29 121.59 110.16 1.1111 + +PRES 2MSB 1.00 ! C16H22N2O3 (010207(S)D), cacha +! This compound has 2-methylamine piperidine at gamma position (S-isomer) +! and benzyl at alpha position +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 ! HG21 HG22 +ATOM OG OG2D1 -0.51 ! \ / +ATOM NT NG2S1 -0.47 ! OG (+1)NG2--CG3 +ATOM HT1 HGP1 0.47 ! || / \ +GROUP ! CG---NT--CGT--CG1 CG4 +ATOM CGT CG321 -0.18 ! / HT1 \ / +ATOM HGT1 HGA2 0.09 ! CC3 CG6--CG5 +ATOM HGT2 HGA2 0.09 ! \ +GROUP ! O24 CC2 +ATOM CG1 CG314 0.29 ! || / +ATOM HG1 HGA1 0.09 ! H Me21 C22 C24 CC1 CD1--CE1 +ATOM NG2 NG3P2 -0.40 ! | \ / \ / \ / \ // \\ +ATOM HG21 HGP2 0.32 ! C12 Me18 C20 C23 NH CA---OA2---CB--CZ CP +ATOM HG22 HGP2 0.32 ! / \ | / || \ __ / +ATOM CG3 CG324 0.20 ! C11 C13---C17 OA1 CD2--CE2 +ATOM HG31 HGA2 0.09 ! Me19 | | | +ATOM HG32 HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CG4 CG321 -0.18 ! C2 C10 C8 C15 +ATOM HG41 HGA2 0.09 ! | | | +ATOM HG42 HGA2 0.09 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CG5 CG321 -0.18 ! HO C4 C6 OH +ATOM HG51 HGA2 0.09 +ATOM HG52 HGA2 0.09 ! 2MSB (010207(S)D) +GROUP +ATOM CG6 CG321 -0.18 +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 +GROUP +ATOM CC1 CG311 -0.01 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.63 +ATOM OA1 OG2D1 -0.51 +ATOM OA2 OG302 -0.33 +ATOM CB CG321 -0.05 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CZ CG2R61 0.00 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 NG2 +BOND NG2 HG21 NG2 HG22 NG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 +BOND OA2 CB CB HB1 CB HB2 CB CZ +BOND CZ CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP CP HP +BOND CP CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 + +IC CC1 CA OA2 CB 1.5236 109.54 -177.42 116.65 1.4465 +IC CA OA2 CB HB1 1.3366 116.65 -64.52 110.23 1.1158 +IC CA OA2 CB CZ 1.3366 116.65 176.07 113.61 1.5060 +IC CA OA2 CB HB2 1.3366 116.65 54.51 110.79 1.1153 +IC OA2 CB CZ CD2 1.4465 113.61 -112.74 121.20 1.4061 +IC OA2 CB CZ CD1 1.4465 113.61 66.81 119.31 1.4047 +IC CD1 CD2 *CZ CB 1.4047 119.49 179.56 121.20 1.5060 +IC CD2 CZ CB HB1 1.4061 121.20 125.73 106.48 1.1158 +IC CD2 CZ CB HB2 1.4061 121.20 10.45 107.83 1.1153 +IC CB CZ CD1 CE1 1.5060 119.31 179.64 120.28 1.4014 +IC CB CZ CD2 CE2 1.5060 121.20 -179.62 120.19 1.4018 +IC CZ CD1 CE1 CP 1.4047 120.28 0.05 119.95 1.4006 +IC CD1 CE1 CP CE2 1.4014 119.95 0.67 120.10 1.4005 +IC CE1 CP CE2 CD2 1.4006 120.10 -0.64 119.99 1.4018 +IC CE1 CZ *CD1 HD1 1.4014 120.28 -179.54 119.86 1.0801 +IC CE2 CZ *CD2 HD2 1.4018 120.19 179.49 120.24 1.0792 +IC CP CD1 *CE1 HE1 1.4006 119.95 -179.62 120.12 1.0810 +IC CP CD2 *CE2 HE2 1.4005 119.99 179.44 120.33 1.0815 +IC CE1 CE2 *CP HP 1.4006 120.10 -179.39 119.77 1.0816 +IC OG CG NT CGT 1.2228 120.84 -7.65 123.20 1.4570 +IC CG NT CGT CG1 1.3449 123.20 96.54 115.15 1.5486 +IC CG1 NT *CGT HGT1 1.5486 115.15 -123.43 109.82 1.1176 +IC CG1 NT *CGT HGT2 1.5486 115.15 121.48 107.78 1.1146 +IC NT CGT CG1 HG1 1.4570 115.15 68.02 110.07 1.1142 +IC HG1 CGT *CG1 NG2 1.1142 110.07 114.89 108.81 1.5039 +IC HG1 CGT *CG1 CG6 1.1142 110.07 -124.38 114.33 1.5405 +IC CGT CG1 NG2 CG3 1.5486 108.81 179.78 115.31 1.5090 +IC CG3 CG1 *NG2 HG21 1.5090 115.31 125.72 109.31 1.0053 +IC CG3 CG1 *NG2 HG22 1.5090 115.31 -120.05 106.24 1.0090 +IC CG1 NG2 CG3 CG4 1.5039 115.31 -57.58 110.01 1.5313 +IC CG4 NG2 *CG3 HG31 1.5313 110.01 121.64 105.32 1.1035 +IC CG4 NG2 *CG3 HG32 1.5313 110.01 -122.17 105.62 1.1031 +IC NG2 CG3 CG4 CG5 1.5090 110.01 55.45 110.22 1.5360 +IC CG5 CG3 *CG4 HG41 1.5360 110.22 121.05 109.87 1.1134 +IC CG5 CG3 *CG4 HG42 1.5360 110.22 -120.70 110.12 1.1138 +IC CG3 CG4 CG5 CG6 1.5313 110.22 -55.61 110.75 1.5369 +IC CG6 CG4 *CG5 HG51 1.5369 110.75 121.23 109.73 1.1140 +IC CG6 CG4 *CG5 HG52 1.5369 110.75 -121.10 109.70 1.1150 +IC CG5 CG1 *CG6 HG61 1.5369 112.98 -121.21 109.26 1.1128 +IC CG5 CG1 *CG6 HG62 1.5369 112.98 122.27 109.31 1.1139 + + +PRES 2MPS 1.00 ! C7H14N2O (01OH07(S)D), cacha +! This compound has 3-methylamine piperidine at gamma position (S-isomer) +! core residue Bile Acid Basic moiety 1 (BAB1) +DELETE ATOM HT2 +GROUP +ATOM CG CG2O1 0.51 +ATOM OG OG2D1 -0.51 +ATOM NT NG2S1 -0.47 ! HG31 HG32 +ATOM HT1 HGP1 0.47 ! \ / +GROUP ! OG (+1) NG2--CG3 +ATOM CGT CG321 -0.18 ! || / \ +ATOM HGT1 HGA2 0.09 ! CG---NT--CGT--CG1 CG4 +ATOM HGT2 HGA2 0.09 ! / HT1 \ / +GROUP ! CC3 CG6--CG5 +ATOM CG1 CG314 0.29 ! \ +ATOM HG1 HGA1 0.09 ! O24 CC2 +ATOM NG2 NG3P2 -0.40 ! || / +ATOM HG21 HGP2 0.32 ! H Me21 C22 C24 CC1 +ATOM HG22 HGP2 0.32 ! | \ / \ / \ / \ +ATOM CG3 CG324 0.20 ! C12 Me18 C20 C23 NH CA---OA2 +ATOM HG31 HGA2 0.09 ! / \ | / || +ATOM HG32 HGA2 0.09 ! C11 C13---C17 OA1 +GROUP ! Me19 | | | +ATOM CG4 CG321 -0.18 ! C1 | C9 C14 C16 +ATOM HG41 HGA2 0.09 ! / \|/ \ / \ / +ATOM HG42 HGA2 0.09 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM CG5 CG321 -0.18 ! C3 C5 C7 +ATOM HG51 HGA2 0.09 ! / \ / \ / \ +ATOM HG52 HGA2 0.09 ! HO C4 C6 OH +GROUP +ATOM CG6 CG321 -0.18 ! 2MPS (01OH07(S)D) +ATOM HG61 HGA2 0.09 +ATOM HG62 HGA2 0.09 + +BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1 +BOND CG1 HG1 CG1 NG2 +BOND NG2 HG21 NG2 HG22 NG2 CG3 +BOND CG3 HG31 CG3 HG32 CG3 CG4 +BOND CG4 HG41 CG4 HG42 CG4 CG5 +BOND CG5 HG51 CG5 HG52 CG5 CG6 +BOND CG6 HG61 CG6 HG62 CG6 CG1 + +IC OG CG NT CGT 1.2255 120.76 -0.11 124.20 1.4535 +IC CG NT CGT CG1 1.3396 124.20 89.00 113.92 1.5472 +IC CG1 NT *CGT HGT1 1.5472 113.92 -122.19 110.38 1.1160 +IC CG1 NT *CGT HGT2 1.5472 113.92 121.49 108.57 1.1134 +IC NT CGT CG1 HG1 1.4535 113.92 -58.25 109.55 1.1156 +IC HG1 CGT *CG1 NG2 1.1156 109.55 114.51 110.44 1.4973 +IC HG1 CGT *CG1 CG6 1.1156 109.55 -123.47 112.81 1.5409 +IC CGT CG1 NG2 CG3 1.5472 110.44 175.74 117.06 1.5009 +IC CG3 CG1 *NG2 HG21 1.5009 117.06 121.42 108.94 1.0280 +IC CG3 CG1 *NG2 HG22 1.5009 117.06 -127.82 109.50 1.0039 +IC CG1 NG2 CG3 CG4 1.4973 117.06 -54.19 110.53 1.5314 +IC CG4 NG2 *CG3 HG31 1.5314 110.53 121.79 104.60 1.1041 +IC CG4 NG2 *CG3 HG32 1.5314 110.53 -123.22 105.06 1.1033 +IC NG2 CG3 CG4 CG5 1.5009 110.53 54.50 110.14 1.5371 +IC CG5 CG3 *CG4 HG41 1.5371 110.14 121.18 109.65 1.1124 +IC CG5 CG3 *CG4 HG42 1.5371 110.14 -120.57 109.68 1.1132 +IC CG3 CG4 CG5 CG6 1.5314 110.14 -56.74 110.53 1.5373 +IC CG6 CG4 *CG5 HG51 1.5373 110.53 120.76 109.61 1.1141 +IC CG6 CG4 *CG5 HG52 1.5373 110.53 -121.25 109.83 1.1138 +IC CG5 CG1 *CG6 HG61 1.5373 112.98 -121.67 108.73 1.1128 +IC CG5 CG1 *CG6 HG62 1.5373 112.98 121.47 109.00 1.1129 + +PRES 3A2MPD 0.00 ! C8H9N2O Gamma-3-Amino-2-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 Me(CM) +GROUP ! || | | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CD2 CG2R61 0.300 ! / \|/ \ / \ / +ATOM CM CG331 -0.270 ! C2 C10 C8 C15 +ATOM HM1 HGA3 0.090 ! | | | +ATOM HM2 HGA3 0.090 ! C3 C5 C7 +ATOM HM3 HGA3 0.090 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM NZ NG2R60 -0.600 +GROUP ! 3A2MPD +ATOM CP CG2R61 0.180 +ATOM HP HGR62 0.120 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR62 0.115 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 CM CM HM1 CM HM2 CM HM3 +BOND CD2 NZ NZ CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5543 115.92 -36.64 118.00 1.3402 +IC CG CZ *NG HG 1.3402 127.24 -172.12 113.52 1.0153 +IC NG CC3 *CG OG 1.3402 118.00 -178.84 119.23 1.2279 +IC CC3 CG NG CZ 1.5047 118.00 -177.11 127.24 1.4173 +IC CG NG CZ CD2 1.3402 127.24 -53.74 126.63 1.4232 +IC NG CZ CD2 NZ 1.4173 126.63 -179.11 121.18 1.3371 +IC CZ CD2 NZ CP 1.4232 121.18 1.08 120.70 1.3284 +IC CD2 NZ CP CE1 1.3371 120.70 0.72 122.63 1.3997 +IC NZ CP CE1 CD1 1.3284 122.63 -1.05 117.83 1.4014 +IC CZ NZ *CD2 CM 1.4232 121.18 -177.19 115.74 1.4939 +IC CZ CD2 CM HM1 1.4232 123.02 84.73 108.13 1.1092 +IC HM1 CD2 *CM HM2 1.1092 108.13 119.79 109.25 1.1096 +IC HM1 CD2 *CM HM3 1.1092 108.13 -120.01 109.21 1.1094 +IC CZ CE1 *CD1 HD1 1.4045 119.82 179.62 121.08 1.0815 +IC NZ CE1 *CP HP 1.3284 122.63 -178.98 122.17 1.0800 +IC CP CD1 *CE1 HE1 1.3997 117.83 179.97 121.02 1.0771 + + +PRES 3A2MPP 0.00 ! C17H17N2O3 Gamma-3-Amino-2-methyl Pyridine GA CDCA Amide (alpha protected), cacha +! core residue Glutamic Acid CDCA Amide (GA) + ! CJ1--CK1 +DELETE ATOM OG1 ! // \\ +DELETE ATOM OG2 ! CY CQ +GROUP ! / \ __ / +ATOM CC3 CG321 -0.18 ! OA2--CB CJ2--CK2 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA1 Me(CM) +GROUP ! || | | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CD2 CG2R61 0.300 ! / \|/ \ / \ / +ATOM CM CG331 -0.270 ! C2 C10 C8 C15 +ATOM HM1 HGA3 0.090 ! | | | +ATOM HM2 HGA3 0.090 ! C3 C5 C7 +ATOM HM3 HGA3 0.090 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM NZ NG2R60 -0.600 +GROUP ! 3A2MPP +ATOM CP CG2R61 0.180 +ATOM HP HGR62 0.120 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR62 0.115 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +GROUP +ATOM CC1 CG311 -0.01 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.63 +ATOM OA1 OG2D1 -0.51 +ATOM OA2 OG302 -0.33 +ATOM CB CG321 -0.05 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 CM CM HM1 CM HM2 CM HM3 +BOND CD2 NZ NZ CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 NG OG + +IC CC1 CA OA2 CB 1.5221 108.68 -175.12 115.77 1.4469 +IC HC1 CC1 CA OA2 1.1139 106.96 -144.03 108.68 1.3393 +IC HB1 CB OA2 CA 1.1164 110.99 52.62 115.77 1.3393 +IC HB2 CB OA2 CA 1.1155 110.08 -66.34 115.77 1.3393 +IC CY CB OA2 CA 1.5032 113.31 171.98 115.77 1.3393 +IC CJ2 CY CB OA2 1.4045 119.10 -63.26 113.31 1.4469 +IC CJ1 CY CB OA2 1.4049 121.26 115.57 113.31 1.4469 +IC CJ1 CJ2 *CY CB 1.4049 119.63 178.85 119.10 1.5032 +IC CJ2 CY CB HB1 1.4045 119.10 58.82 106.19 1.1164 +IC CJ2 CY CB HB2 1.4045 119.10 174.18 108.48 1.1155 +IC CB CY CJ1 CK1 1.5032 121.26 -179.06 120.12 1.4017 +IC CB CY CJ2 CK2 1.5032 119.10 179.04 120.23 1.4010 +IC CY CJ1 CK1 CQ 1.4049 120.12 0.13 120.01 1.4014 +IC CJ1 CK1 CQ CK2 1.4017 120.01 0.02 120.07 1.4012 +IC CK1 CQ CK2 CJ2 1.4014 120.07 -0.07 119.94 1.4010 +IC CK1 CY *CJ1 HJ1 1.4017 120.12 179.89 120.04 1.0798 +IC CK2 CY *CJ2 HJ2 1.4010 120.23 -179.86 119.77 1.0802 +IC CQ CJ1 *CK1 HK1 1.4014 120.01 -179.98 120.02 1.0806 +IC CQ CJ2 *CK2 HK2 1.4012 119.94 179.88 120.03 1.0807 +IC CK1 CK2 *CQ HQ 1.4014 120.07 179.94 119.96 1.0807 +IC CC2 CC3 CG NG 1.5542 114.91 -16.91 117.82 1.3394 +IC CG CZ *NG HG 1.3394 123.27 -179.51 116.62 0.9904 +IC NG CC3 *CG OG 1.3394 117.82 179.62 119.61 1.2236 +IC CC3 CG NG CZ 1.4992 117.82 177.13 123.27 1.4197 +IC CG NG CZ CD2 1.3394 123.27 -69.73 124.04 1.4247 +IC NG CZ CD2 NZ 1.4197 124.04 -176.97 120.97 1.3327 +IC CZ CD2 NZ CP 1.4247 120.97 0.50 121.13 1.3277 +IC CD2 NZ CP CE1 1.3327 121.13 1.14 122.26 1.4005 +IC NZ CP CE1 CD1 1.3277 122.26 -0.91 118.06 1.4035 +IC CZ NZ *CD2 CM 1.4247 120.97 -178.59 116.57 1.4945 +IC CZ CD2 CM HM1 1.4247 122.45 71.53 108.26 1.1096 +IC HM1 CD2 *CM HM2 1.1096 108.26 119.36 109.30 1.1107 +IC HM1 CD2 *CM HM3 1.1096 108.26 -120.51 109.27 1.1089 +IC CZ CE1 *CD1 HD1 1.4037 119.50 -179.00 120.49 1.0791 +IC NZ CE1 *CP HP 1.3277 122.26 -179.11 122.38 1.0810 +IC CP CD1 *CE1 HE1 1.4005 118.06 179.76 121.28 1.0781 + + +PRES 3A4MPD 0.00 ! C8H9N2O Gamma-3-Amino-4-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP ! OA1 +ATOM CC3 CG321 -0.18 ! | +ATOM HC3A HGA2 0.09 ! O24 CA--OA2 +ATOM HC3B HGA2 0.09 ! || | +GROUP ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +ATOM CG CG2O1 0.52 ! | \ / \ / \ / \ / \ / \ // \\ +ATOM OG OG2D1 -0.52 ! C12 Me18 C20 C23 NH CC2 CG CZ CP +GROUP ! / \ | / || \ __ / +ATOM NG NG2S1 -0.47 ! C11 C13---C17 OG CD1--CE1 +ATOM HG HGP1 0.33 ! Me19 | | | | +ATOM CZ CG2R61 0.14 ! C1 | C9 C14 C16 Me(CM) +GROUP ! / \|/ \ / \ / +ATOM CD2 CG2R61 0.180 ! C2 C10 C8 C15 +ATOM HD2 HGR62 0.120 ! | | | +GROUP ! C3 C5 C7 +ATOM NZ NG2R60 -0.600 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM CP CG2R61 0.180 +ATOM HP HGR62 0.120 ! 3A4MPD +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR62 0.115 +GROUP +ATOM CD1 CG2R61 0.000 +ATOM CM CG331 -0.270 +ATOM HM1 HGA3 0.090 +ATOM HM2 HGA3 0.090 +ATOM HM3 HGA3 0.090 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 +BOND CD2 NZ NZ CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 CM +BOND CM HM1 CM HM2 CM HM3 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5525 114.66 -48.60 118.08 1.3462 +IC CG CZ *NG HG 1.3462 126.54 -178.10 115.39 1.0162 +IC NG CC3 *CG OG 1.3462 118.08 -179.48 119.23 1.2283 +IC CC3 CG NG CZ 1.5020 118.08 -178.29 126.54 1.4265 +IC CG NG CZ CD2 1.3462 126.54 26.39 123.95 1.4120 +IC NG CZ CD2 NZ 1.4265 123.95 -179.67 124.64 1.3366 +IC CZ CD2 NZ CP 1.4120 124.64 1.51 118.03 1.3276 +IC CD2 NZ CP CE1 1.3366 118.03 0.27 123.29 1.3997 +IC NZ CP CE1 CD1 1.3276 123.29 -0.52 118.73 1.4069 +IC CZ NZ *CD2 HD2 1.4120 124.64 178.81 114.94 1.0798 +IC NZ CE1 *CP HP 1.3276 123.29 -179.59 121.83 1.0808 +IC CP CD1 *CE1 HE1 1.3997 118.73 -179.92 120.40 1.0767 +IC CZ NZ *CD1 CM 1.4166 60.12 161.97 177.14 1.5012 +IC CZ CD1 CM HM1 1.4166 122.60 -76.39 108.52 1.1122 +IC HM1 CD1 *CM HM2 1.1122 108.52 118.88 109.64 1.1117 +IC HM1 CD1 *CM HM3 1.1122 108.52 -120.43 110.64 1.1100 + + +PRES 3A5MPD 0.00 ! C8H9N2O Gamma-3-Amino-5-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | | +GROUP ! C1 | C9 C14 C16 Me(CM) +ATOM CD2 CG2R61 0.180 ! / \|/ \ / \ / +ATOM HD2 HGR62 0.120 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM NZ NG2R60 -0.600 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 0.180 ! HO C4 C6 OH +ATOM HP HGR62 0.120 +GROUP ! 3A5MPD +ATOM CE1 CG2R61 0.000 +ATOM CM CG331 -0.270 +ATOM HM1 HGA3 0.090 +ATOM HM2 HGA3 0.090 +ATOM HM3 HGA3 0.090 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 CD2 NZ NZ CP CP HP +BOND CP CE1 CE1 CM CM HM1 CM HM2 CM HM3 +BOND CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5534 114.93 -46.79 117.53 1.3423 +IC CG CZ *NG HG 1.3423 128.66 -179.60 113.69 1.0157 +IC NG CC3 *CG OG 1.3423 117.53 -179.09 119.44 1.2280 +IC CC3 CG NG CZ 1.5029 117.53 -179.23 128.66 1.4204 +IC CG NG CZ CD2 1.3423 128.66 -3.33 126.46 1.4112 +IC NG CZ CD2 NZ 1.4204 126.46 -179.70 123.49 1.3393 +IC CZ CD2 NZ CP 1.4112 123.49 -0.17 118.65 1.3332 +IC CD2 NZ CP CE1 1.3393 118.65 -0.04 123.55 1.4122 +IC NZ CP CE1 CD1 1.3332 123.55 0.33 116.91 1.4049 +IC CZ NZ *CD2 HD2 1.4112 123.49 -179.82 117.24 1.0814 +IC CZ CE1 *CD1 HD1 1.4037 120.52 -179.76 120.10 1.0806 +IC NZ CE1 *CP HP 1.3332 123.55 179.99 119.15 1.0821 +IC CP CD1 *CE1 CM 1.4122 116.91 -179.23 120.70 1.5005 +IC CD1 CE1 CM HM1 1.4049 120.70 82.83 108.60 1.1108 +IC HM1 CE1 *CM HM2 1.1108 108.60 120.58 109.86 1.1106 +IC HM1 CE1 *CM HM3 1.1108 108.60 -119.40 109.06 1.1121 + + +PRES 3A6MPD 0.00 ! C8H9N2O Gamma-3-Amino-6-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP--Me(CM) +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CD2 CG2R61 0.180 ! / \|/ \ / \ / +ATOM HD2 HGR62 0.120 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM NZ NG2R60 -0.600 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 0.300 ! HO C4 C6 OH +ATOM CM CG331 -0.270 +ATOM HM1 HGA3 0.090 ! 3A6MPD +ATOM HM2 HGA3 0.090 +ATOM HM3 HGA3 0.090 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR62 0.115 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 +BOND CD2 NZ NZ CP CP CM CM HM1 CM HM2 CM HM3 +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5536 114.92 -47.92 117.56 1.3422 +IC CG CZ *NG HG 1.3422 128.44 -179.56 113.65 1.0157 +IC NG CC3 *CG OG 1.3422 117.56 -179.06 119.47 1.2281 +IC CC3 CG NG CZ 1.5031 117.56 -179.10 128.44 1.4197 +IC CG NG CZ CD2 1.3422 128.44 -3.17 126.56 1.4088 +IC NG CZ CD2 NZ 1.4197 126.56 179.85 123.64 1.3373 +IC CZ CD2 NZ CP 1.4088 123.64 -0.45 119.84 1.3272 +IC CD2 NZ CP CE1 1.3373 119.84 0.10 121.50 1.4077 +IC NZ CP CE1 CD1 1.3272 121.50 0.08 118.83 1.4038 +IC CZ NZ *CD2 HD2 1.4088 123.64 -179.72 115.15 1.0789 +IC CZ CE1 *CD1 HD1 1.4042 119.69 -179.90 120.71 1.0810 +IC CP CD1 *CE1 HE1 1.4077 118.83 179.98 120.81 1.0765 +IC NZ CE1 *CP CM 1.3272 121.50 179.95 121.15 1.4853 +IC CE1 CP CM HM1 1.4077 121.15 120.74 108.01 1.1094 +IC HM1 CD2 *CM HM2 1.1094 97.28 111.25 97.26 1.1094 +IC HM1 CD2 *CM HM3 1.1094 97.28 -124.39 129.99 1.1093 + + +PRES 4A2MPD 0.00 ! C8H9N2O Gamma-4-Amino-2-methyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---CE2 +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ NZ +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | | +GROUP ! C1 | C9 C14 C16 Me(CM) +ATOM CD2 CG2R61 -0.115 ! / \|/ \ / \ / +ATOM HD2 HGR61 0.115 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM CE2 CG2R61 0.180 ! C3 C5 C7 +ATOM HE2 HGR62 0.120 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM NZ NG2R60 -0.600 +GROUP ! 4A2MPD +ATOM CE1 CG2R61 0.300 +ATOM CM CG331 -0.270 +ATOM HM1 HGA3 0.090 +ATOM HM2 HGA3 0.090 +ATOM HM3 HGA3 0.090 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 CD2 CE2 CE2 HE2 CE2 NZ +BOND NZ CE1 CE1 CM CM HM1 CM HM2 CM HM3 +BOND CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5535 114.99 -47.53 117.29 1.3441 +IC CG CZ *NG HG 1.3441 129.75 -179.09 112.92 1.0149 +IC NG CC3 *CG OG 1.3441 117.29 -178.78 119.12 1.2283 +IC CC3 CG NG CZ 1.5032 117.29 -179.46 129.75 1.4176 +IC CG NG CZ CD2 1.3441 129.75 -11.88 125.49 1.4013 +IC NG CZ CD2 CE2 1.4176 125.49 178.88 118.08 1.3986 +IC CZ CD2 CE2 NZ 1.4013 118.08 -0.21 122.51 1.3287 +IC CD2 CE2 NZ CE1 1.3986 122.51 0.05 120.56 1.3285 +IC CE2 NZ CE1 CD1 1.3287 120.56 -0.23 121.12 1.4025 +IC CZ CE2 *CD2 HD2 1.4013 118.08 -179.53 120.08 1.0753 +IC CZ CE1 *CD1 HD1 1.4024 119.20 -179.99 120.55 1.0781 +IC NZ CD2 *CE2 HE2 1.3287 122.51 -179.90 122.11 1.0803 +IC NZ CD1 *CE1 CM 1.3285 121.12 179.43 121.32 1.4855 +IC CD1 CE1 CM HM1 1.4025 121.32 126.89 108.18 1.1092 +IC HM1 CE1 *CM HM2 1.1092 108.18 119.25 108.09 1.1089 +IC HM1 CE1 *CM HM3 1.1092 108.18 -120.30 109.96 1.1104 + + +PRES 4A2MPP 0.00 ! C17H17N2O3 Gamma-4-Amino-2-methyl Pyridine GA CDCA Amide (alpha protected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 ! CJ1--CK1 +GROUP ! // \\ +ATOM CC3 CG321 -0.18 ! OA1 CY CQ +ATOM HC3A HGA2 0.09 ! | / \ __ / +ATOM HC3B HGA2 0.09 ! O24 CA--OA2--CB CJ2--CK2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---CE2 +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ NZ +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | | +GROUP ! C1 | C9 C14 C16 Me(CM) +ATOM CD2 CG2R61 -0.115 ! / \|/ \ / \ / +ATOM HD2 HGR61 0.115 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM CE2 CG2R61 0.180 ! C3 C5 C7 +ATOM HE2 HGR62 0.120 ! / \ / \ / \ +GROUP ! HO C4 C6 OH +ATOM NZ NG2R60 -0.600 +GROUP ! 4A2MPP +ATOM CE1 CG2R61 0.300 +ATOM CM CG331 -0.270 +ATOM HM1 HGA3 0.090 +ATOM HM2 HGA3 0.090 +ATOM HM3 HGA3 0.090 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +GROUP +ATOM CC1 CG311 -0.01 +ATOM HC1 HGA1 0.09 +ATOM CA CG2O2 0.63 +ATOM OA1 OG2D1 -0.51 +ATOM OA2 OG302 -0.33 +ATOM CB CG321 -0.05 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 + +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 CD2 CE2 CE2 HE2 CE2 NZ +BOND NZ CE1 CE1 CM CM HM1 CM HM2 CM HM3 +BOND CE1 CD1 CD1 HD1 CD1 CZ +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CG CC3 NG OG + +IC CC1 CA OA2 CB 1.5239 109.11 -178.78 115.31 1.4471 +IC HC1 CC1 CA OA2 1.1142 106.36 -134.87 109.11 1.3428 +IC HB1 CB OA2 CA 1.1164 110.53 59.15 115.31 1.3428 +IC HB2 CB OA2 CA 1.1163 110.59 -59.31 115.31 1.3428 +IC CY CB OA2 CA 1.5039 113.58 179.93 115.31 1.3428 +IC CJ2 CY CB OA2 1.4046 120.25 -90.46 113.58 1.4471 +IC CJ1 CY CB OA2 1.4046 120.15 88.33 113.58 1.4471 +IC CJ1 CJ2 *CY CB 1.4046 119.59 178.79 120.25 1.5039 +IC CJ2 CY CB HB1 1.4046 120.25 32.06 107.40 1.1164 +IC CJ2 CY CB HB2 1.4046 120.25 146.97 107.35 1.1163 +IC CB CY CJ1 CK1 1.5039 120.15 -179.79 120.20 1.4015 +IC CB CY CJ2 CK2 1.5039 120.25 179.88 120.19 1.4014 +IC CY CJ1 CK1 CQ 1.4046 120.20 0.22 119.97 1.4011 +IC CJ1 CK1 CQ CK2 1.4015 119.97 0.48 120.05 1.4013 +IC CK1 CQ CK2 CJ2 1.4011 120.05 -0.38 119.98 1.4014 +IC CK1 CY *CJ1 HJ1 1.4015 120.20 -179.58 119.84 1.0799 +IC CK2 CY *CJ2 HJ2 1.4014 120.19 179.61 119.87 1.0801 +IC CQ CJ1 *CK1 HK1 1.4011 119.97 -179.63 120.04 1.0807 +IC CQ CJ2 *CK2 HK2 1.4013 119.98 179.84 119.99 1.0807 +IC CK1 CK2 *CQ HQ 1.4011 120.05 -179.99 119.97 1.0807 +IC CC2 CC3 CG NG 1.5519 114.50 13.96 116.90 1.3446 +IC CG CZ *NG HG 1.3446 129.24 179.51 114.07 0.9892 +IC NG CC3 *CG OG 1.3446 116.90 179.09 119.15 1.2233 +IC CC3 CG NG CZ 1.5018 116.90 -179.29 129.24 1.4197 +IC CG NG CZ CD2 1.3446 129.24 13.84 125.26 1.4018 +IC NG CZ CD2 CE2 1.4197 125.26 -179.01 118.17 1.3982 +IC CZ CD2 CE2 NZ 1.4018 118.17 0.19 121.97 1.3275 +IC CD2 CE2 NZ CE1 1.3982 121.97 0.25 121.39 1.3249 +IC CE2 NZ CE1 CD1 1.3275 121.39 -0.27 120.72 1.4039 +IC CZ CE2 *CD2 HD2 1.4018 118.17 179.45 119.73 1.0761 +IC CZ CE1 *CD1 HD1 1.4037 119.12 179.72 120.00 1.0760 +IC NZ CD2 *CE2 HE2 1.3275 121.97 -179.97 122.47 1.0810 +IC NZ CD1 *CE1 CM 1.3249 120.72 -179.86 121.70 1.4852 +IC CD1 CE1 CM HM1 1.4039 121.70 120.68 108.10 1.1099 +IC HM1 CE1 *CM HM2 1.1099 108.10 118.69 108.12 1.1099 +IC HM1 CE1 *CM HM3 1.1099 108.10 -120.64 110.47 1.1094 + + +PRES 3A6BPD 0.00 ! C7H6BrN2O Gamma-3-Amino-6-bromo Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP--BR +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CD2 CG2R61 0.120 ! / \|/ \ / \ / +ATOM HD2 HGR62 0.270 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM NZ NG2R60 -0.600 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 -0.080 ! HO C4 C6 OH +ATOM BR BRGR1 -0.100 +GROUP ! 3A6BPD +ATOM CE1 CG2R61 0.120 +ATOM HE1 HGR62 0.270 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 +BOND CD2 NZ NZ CP CP BR +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5540 115.24 -45.81 117.72 1.3410 +IC CG CZ *NG HG 1.3410 128.42 -179.30 113.55 1.0153 +IC NG CC3 *CG OG 1.3410 117.72 -179.06 119.68 1.2286 +IC CC3 CG NG CZ 1.5034 117.72 -178.25 128.42 1.4176 +IC CG NG CZ CD2 1.3410 128.42 -3.63 126.12 1.4068 +IC NG CZ CD2 NZ 1.4176 126.12 179.74 123.57 1.3372 +IC CZ CD2 NZ CP 1.4068 123.57 -0.57 119.25 1.3290 +IC CD2 NZ CP CE1 1.3372 119.25 0.00 122.25 1.4059 +IC NZ CP CE1 CD1 1.3290 122.25 0.26 118.39 1.4018 +IC CZ NZ *CD2 HD2 1.4068 123.57 -179.82 116.18 1.0787 +IC CZ CE1 *CD1 HD1 1.4032 119.66 -179.83 120.65 1.0797 +IC CP CD1 *CE1 HE1 1.4059 118.39 -179.97 121.47 1.0746 +IC NZ CE1 *CP BR 1.3290 122.25 179.86 118.80 1.9014 + + +PRES 3A5BPD 0.00 ! C7H6BrN2O Gamma-3-Amino-5-bromo Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 ! OA1 +ATOM HC3A HGA2 0.09 ! | +ATOM HC3B HGA2 0.09 ! O24 CA--OA2 +GROUP ! || | +ATOM CG CG2O1 0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +ATOM OG OG2D1 -0.52 ! | \ / \ / \ / \ / \ / \ // \\ +GROUP ! C12 Me18 C20 C23 NH CC2 CG CZ CP +ATOM NG NG2S1 -0.47 ! / \ | / || \ __ / +ATOM HG HGP1 0.33 ! C11 C13---C17 OG CD1--CE1 +ATOM CZ CG2R61 0.14 ! Me19 | | | | +GROUP ! C1 | C9 C14 C16 Br +ATOM CD2 CG2R61 0.180 ! / \|/ \ / \ / +ATOM HD2 HGR62 0.120 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM NZ NG2R60 -0.600 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CP CG2R61 0.120 ! HO C4 C6 OH +ATOM HP HGR62 0.270 +GROUP ! 3A5BPD +ATOM CE1 CG2R61 -0.080 +ATOM BR BRGR1 -0.100 +GROUP +ATOM CD1 CG2R61 -0.060 +ATOM HD1 HGR62 0.150 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 +BOND CD2 NZ NZ CP CP HP +BOND CP CE1 CE1 BR CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5539 114.93 -46.89 117.47 1.3414 +IC CG CZ *NG HG 1.3414 128.73 -179.59 113.40 1.0162 +IC NG CC3 *CG OG 1.3414 117.47 -179.17 119.56 1.2281 +IC CC3 CG NG CZ 1.5032 117.47 -179.42 128.73 1.4192 +IC CG NG CZ CD2 1.3414 128.73 -1.78 126.47 1.4101 +IC NG CZ CD2 NZ 1.4192 126.47 -179.99 124.16 1.3390 +IC CZ CD2 NZ CP 1.4101 124.16 -0.27 118.04 1.3323 +IC CD2 NZ CP CE1 1.3390 118.04 0.09 123.58 1.4040 +IC NZ CP CE1 CD1 1.3323 123.58 0.00 117.68 1.4046 +IC CZ NZ *CD2 HD2 1.4101 124.16 -179.81 114.91 1.0791 +IC CZ CE1 *CD1 HD1 1.4055 119.88 -179.96 120.93 1.0813 +IC CP CD1 *CE1 BR 1.4040 117.68 180.00 121.49 1.9030 +IC NZ CE1 *CP HP 1.3323 123.58 179.98 120.99 1.0802 + + +PRES 3CPD 0.00 ! C9H11N2O Gamma-3-Amide Pyridine Lysine CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM CG +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 +ATOM HC3B HGA2 0.09 +GROUP ! OA1 +ATOM CC4 CG321 -0.18 ! | +ATOM HC4A HGA2 0.09 ! O24 CA--OA2 OC +ATOM HC4B HGA2 0.09 ! || | || +GROUP ! OH Me21 C22 C24 CC1 CC3 CC5 CC CD2---NZ +ATOM CC5 CG321 -0.02 ! | \ / \ / \ / \ / \ / \ / \ // \\ +ATOM HC5A HGA2 0.09 ! C12 Me18 C20 C23 NH CC2 CC4 NG CZ CP +ATOM HC5B HGA2 0.09 ! / \ | / \ __ / +ATOM NG NG2S1 -0.47 ! C11 C13---C17 CD1--CE1 +ATOM HG HGP1 0.31 ! Me19 | | | +GROUP ! C1 | C9 C14 C16 +ATOM CC CG2O1 0.52 ! / \|/ \ / \ / +ATOM OC OG2D1 -0.52 ! C2 C10 C8 C15 +GROUP ! | | | +ATOM CZ CG2R61 0.00 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CD2 CG2R61 0.180 ! HO C4 C6 OH +ATOM HD2 HGR62 0.120 +GROUP ! 3CPD +ATOM NZ NG2R60 -0.600 +GROUP +ATOM CP CG2R61 0.180 +ATOM HP HGR62 0.120 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CC3 CC4 CC4 HC4A CC4 HC4B CC4 CC5 +BOND CC5 HC5A CC5 HC5B CC5 NG NG HG +BOND NG CC CC OC CC CZ +BOND CZ CD2 CD2 HD2 CD2 NZ NZ CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +IMPR CC CZ NG OC + +IC CC1 CC2 CC3 CC4 1.5507 114.34 180.00 115.13 1.5423 +IC CC2 CC3 CC4 HC4A 1.5420 115.13 47.51 110.26 1.1108 +IC HC4A CC3 *CC4 HC4B 1.1108 110.26 116.79 107.05 1.1139 +IC CC2 CC3 CC4 CC5 1.5420 115.13 -77.09 115.20 1.5407 +IC CC3 CC4 CC5 HC5A 1.5423 115.20 -159.28 108.95 1.1153 +IC HC5A NG *CC5 HC5B 1.1153 110.83 -116.80 108.42 1.1148 +IC CC3 CC4 CC5 NG 1.5423 115.20 76.82 113.35 1.4396 +IC CC4 CC5 NG CC 1.5407 113.35 94.14 123.08 1.3465 +IC CC5 CC *NG HG 1.4396 123.08 180.00 123.02 1.0168 +IC CC5 NG CC CZ 1.4396 123.08 -179.48 120.02 1.4949 +IC NG CZ *CC OC 1.3465 120.02 -179.84 119.11 1.2317 +IC NG CC CZ CD2 1.3465 120.02 -0.44 123.04 1.4096 +IC CC CZ CD2 NZ 1.4949 123.04 179.89 122.97 1.3360 +IC CZ CD2 NZ CP 1.4096 122.97 -0.08 119.87 1.3266 +IC CD2 NZ CP CE1 1.3360 119.87 0.09 122.66 1.4001 +IC NZ CP CE1 CD1 1.3266 122.66 -0.04 117.99 1.4032 +IC CZ NZ *CD2 HD2 1.4096 122.97 -179.95 114.38 1.0801 +IC CZ CE1 *CD1 HD1 1.4162 119.80 -179.92 119.66 1.0810 +IC NZ CE1 *CP HP 1.3266 122.66 -179.97 122.30 1.0805 +IC CP CD1 *CE1 HE1 1.4001 117.99 179.95 121.24 1.0773 + +PRES 3A26PD 0.60 ! C4H6 Gamma-3-Amino-2,6-dimethyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! 1st patch Glutamic Acid CDCA Amide (GA); 2nd patch 3APD *** double patch *** +DELETE ATOM HD2 +DELETE ATOM HP +ATOM CD2 CG2R61 0.300 ! CM2 +ATOM CM1 CG331 -0.270 ! | +ATOM HM11 HGA3 0.090 ! NG CD2---NZ +ATOM HM12 HGA3 0.090 ! / \ // \\ +ATOM HM13 HGA3 0.090 ! -----CGP CZ CP--CM2 +ATOM CP CG2R61 0.300 ! || \ __ / +ATOM CM2 CG331 -0.270 ! OGP CD1--CE1 +ATOM HM21 HGA3 0.090 +ATOM HM22 HGA3 0.090 +ATOM HM23 HGA3 0.090 +BOND CD2 CM1 CM1 HM11 CM1 HM12 CM1 HM13 +BOND CP CM2 CM2 HM21 CM2 HM22 CM2 HM23 +IC CZ NZ *CD2 CM1 1.4232 120.79 -176.99 115.58 1.4943 +IC CZ CD2 CM1 HM11 1.4232 123.56 83.84 108.07 1.1092 +IC HM11 CD2 *CM1 HM12 1.1092 108.07 119.91 109.35 1.1096 +IC HM11 CD2 *CM1 HM13 1.1092 108.07 -119.82 109.06 1.1094 +IC NZ CE1 *CP CM2 1.3247 120.93 -179.02 120.29 1.4852 +IC NZ CP CM2 HM21 1.3247 118.78 121.68 108.66 1.1090 +IC HM21 CP *CM2 HM22 1.1090 108.66 120.57 108.58 1.1091 +IC HM21 CP *CM2 HM23 1.1090 108.66 -119.74 108.92 1.1105 + + +PRES 3A46PD 0.00 ! C9H11N2O Gamma-3-Amino-4,6-dimethyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 ! OA1 +ATOM HC3B HGA2 0.09 ! | +GROUP ! O24 CA--OA2 +ATOM CG CG2O1 0.52 ! || | +ATOM OG OG2D1 -0.52 ! OH Me21 C22 C24 CC1 CC3 NG CD2---NZ +GROUP ! | \ / \ / \ / \ / \ / \ // \\ +ATOM NG NG2S1 -0.47 ! C12 Me18 C20 C23 NH CC2 CG CZ CP--CM2 +ATOM HG HGP1 0.33 ! / \ | / || \ __ / +ATOM CZ CG2R61 0.14 ! C11 C13---C17 OG CD1--CE1 +GROUP ! Me19 | | | | +ATOM CD2 CG2R61 0.180 ! C1 | C9 C14 C16 CM1 +ATOM HD2 HGR62 0.120 ! / \|/ \ / \ / +GROUP ! C2 C10 C8 C15 +ATOM NZ NG2R60 -0.600 ! | | | +GROUP ! C3 C5 C7 +ATOM CP CG2R61 0.300 ! / \ / \ / \ +ATOM CM2 CG331 -0.270 ! HO C4 C6 OH +ATOM HM21 HGA3 0.090 +ATOM HM22 HGA3 0.090 +ATOM HM23 HGA3 0.090 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR62 0.115 +GROUP +ATOM CD1 CG2R61 0.000 +ATOM CM1 CG331 -0.270 +ATOM HM11 HGA3 0.090 +ATOM HM12 HGA3 0.090 +ATOM HM13 HGA3 0.090 + +BOND CG OG CG NG NG HG NG CZ +BOND CZ CD2 CD2 HD2 +BOND CD2 NZ NZ CP CP CM2 CM2 HM21 CM2 HM22 CM2 HM23 +BOND CP CE1 CE1 HE1 CE1 CD1 +BOND CD1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 +BOND CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5525 114.68 -48.50 118.09 1.3462 +IC CG CZ *NG HG 1.3462 126.53 -178.06 115.39 1.0163 +IC NG CC3 *CG OG 1.3462 118.09 -179.48 119.24 1.2283 +IC CC3 CG NG CZ 1.5020 118.09 -178.28 126.53 1.4265 +IC CG NG CZ CD2 1.3462 126.53 26.25 123.98 1.4099 +IC NG CZ CD2 NZ 1.4265 123.98 -179.65 124.10 1.3349 +IC CZ CD2 NZ CP 1.4099 124.10 1.50 119.63 1.3248 +IC CD2 NZ CP CE1 1.3349 119.63 0.31 121.47 1.4025 +IC NZ CP CE1 CD1 1.3248 121.47 -0.57 119.67 1.4057 +IC CP CD1 *CE1 HE1 1.4025 119.67 -179.96 120.27 1.0763 +IC CZ NZ *CD2 HD2 1.4099 124.10 178.82 115.20 1.0797 +IC CZ CE1 *CD1 CM1 1.4153 118.74 -179.91 118.59 1.5010 +IC CZ CD1 CM1 HM11 1.4153 122.67 42.43 109.65 1.1117 +IC HM11 CD1 *CM1 HM12 1.1117 109.65 120.69 110.64 1.1101 +IC HM11 CD1 *CM1 HM13 1.1117 109.65 -118.88 108.52 1.1122 +IC NZ CE1 *CP CM2 1.3248 121.47 -179.55 119.98 1.4855 +IC NZ CP CM2 HM21 1.3248 118.55 120.51 108.65 1.1091 +IC HM21 CP *CM2 HM22 1.1091 108.65 120.62 108.66 1.1090 +IC HM21 CP *CM2 HM23 1.1091 108.65 -119.67 108.93 1.1106 + + +PRES 2A46PD 0.30 ! C4H6 Gamma-2-Amino 4,6-dimethyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! double patch +! 1st patch Glutamic Acid CDCA Amide (GA); 2nd patch 2APD +DELETE ATOM HE1 +DELETE ATOM HE2 ! CM2 +ATOM CE1 CG2R61 0.000 ! | +ATOM CM1 CG331 -0.270 ! NG NZ---CE2 +ATOM HM11 HGA3 0.090 ! / \ // \\ +ATOM HM12 HGA3 0.090 ! ----CG CZ CP +ATOM HM13 HGA3 0.090 ! || \ __ / +ATOM CE2 CG2R61 0.300 ! OG CD1--CE1 +ATOM CM2 CG331 -0.270 ! | +ATOM HM21 HGA3 0.090 ! CM1 +ATOM HM22 HGA3 0.090 +ATOM HM23 HGA3 0.090 +BOND CE1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 +BOND CE2 CM2 CM2 HM21 CM2 HM22 CM2 HM23 +IC CD1 CP *CE1 CM1 1.4049 118.22 -179.92 120.32 1.4954 +IC CD1 CE1 CM1 HM11 1.4049 121.46 120.27 108.89 1.1107 +IC HM11 CE1 *CM1 HM12 1.1107 108.89 120.08 108.88 1.1108 +IC HM11 CE1 *CM1 HM13 1.1107 108.89 -119.97 109.96 1.1118 +IC CP NZ *CE2 CM2 1.4031 120.54 -179.86 117.53 1.4848 +IC CP CE2 CM2 HM21 1.4031 121.92 122.41 108.06 1.1100 +IC HM21 CE2 *CM2 HM22 1.1100 108.06 118.55 108.05 1.1099 +IC HM21 CE2 *CM2 HM23 1.1100 108.06 -120.69 110.40 1.1091 + + +PRES 2AEPD 0.00 ! C9H11N2O Gamma-2-Aminoehtyl Pyridine GA CDCA Amide (alpha deprotected), cacha +! core residue Glutamic Acid CDCA Amide (GA) +DELETE ATOM OG1 +DELETE ATOM OG2 +GROUP +ATOM CC3 CG321 -0.18 +ATOM HC3A HGA2 0.09 ! OA1 +ATOM HC3B HGA2 0.09 ! | +GROUP ! O24 CA--OA2 +ATOM CG CG2O1 0.52 ! || | +ATOM OG OG2D1 -0.52 ! OH Me21 C22 C24 CC1 CM3 NG CM2 NZ---CE2 +GROUP ! | \ / \ / \ / \ / \ / \ / \ // \\ +ATOM NG NG2S1 -0.47 ! C12 Me18 C20 C23 NH CC2 CG CM1 CZ CP +ATOM HG HGP1 0.33 ! / \ | / || \ __ / +ATOM CM1 CG321 -0.04 ! C11 C13---C17 OG CD1--CE1 +ATOM HM11 HGA2 0.09 ! Me19 | | | +ATOM HM12 HGA2 0.09 ! C1 | C9 C14 C16 +GROUP ! / \|/ \ / \ / +ATOM CM2 CG321 -0.18 ! C2 C10 C8 C15 +ATOM HM21 HGA2 0.09 ! | | | +ATOM HM22 HGA2 0.09 ! C3 C5 C7 +GROUP ! / \ / \ / \ +ATOM CZ CG2R61 0.300 ! HO C4 C6 OH +GROUP +ATOM NZ NG2R60 -0.600 +GROUP +ATOM CE2 CG2R61 0.180 +ATOM HE2 HGR62 0.120 +GROUP +ATOM CP CG2R61 -0.115 +ATOM HP HGR61 0.115 +GROUP +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 + +BOND CG OG CG NG NG HG NG CM1 +BOND CM1 HM11 CM1 HM12 CM1 CM2 CM2 HM21 CM2 HM22 +BOND CM2 CZ CZ NZ NZ CE2 CE2 HE2 CE2 CP CP HP +BOND CP CE1 CE1 HE1 CE1 CD1 CD1 HD1 CD1 CZ +IMPR CG CC3 NG OG + +IC CC2 CC3 CG NG 1.5538 114.55 -50.29 117.81 1.3379 +IC CG CZ *NG HG 1.3379 146.97 179.36 93.64 1.0168 +IC NG CC3 *CG OG 1.3379 117.81 -179.31 120.32 1.2286 +IC CC3 CG NG CM1 1.5026 117.81 178.60 123.77 1.4341 +IC CG NG CM1 CM2 1.3379 123.77 166.12 110.08 1.5334 +IC NG CM2 *CM1 HM11 1.4341 110.08 121.55 109.20 1.1164 +IC HM11 CM2 *CM1 HM12 1.1164 109.20 118.53 110.55 1.1139 +IC NG CM1 CM2 CZ 1.4341 110.08 170.36 110.71 1.4960 +IC CZ CM1 *CM2 HM21 1.4960 110.71 120.16 110.22 1.1105 +IC HM21 CM1 *CM2 HM22 1.1105 110.22 119.17 110.33 1.1120 +IC CM1 CM2 CZ CD1 1.5334 110.71 -84.87 118.37 1.4085 +IC CM2 CZ CD1 CE1 1.4960 118.37 179.16 118.99 1.4033 +IC CZ CD1 CE1 CP 1.4085 118.99 -0.20 118.79 1.4032 +IC CD1 CE1 CP CE2 1.4033 118.79 -0.01 118.33 1.4035 +IC CE1 CP CE2 NZ 1.4032 118.33 -0.05 121.73 1.3296 +IC CZ CE1 *CD1 HD1 1.4085 118.99 -179.95 121.31 1.0780 +IC CD1 CP *CE1 HE1 1.4033 118.79 179.91 120.78 1.0797 +IC CE1 CE2 *CP HP 1.4032 118.33 179.95 120.52 1.0774 +IC CP NZ *CE2 HE2 1.4035 121.73 179.81 117.68 1.0828 + +PRES 2A3HPD 0.00 ! CHO 2-Amino 3-Hydroxy Pyridine CDCA Amide (alpha deprotected), cacha +! core residue GA and it is the second patch to 2APD (use of double patch) + ! NG NZ---CE2 +DELETE ATOM HD1 ! / \ // \\ +GROUP ! ----CG CZ CP +ATOM CD1 CG2R61 0.110 ! || \ __ / +ATOM OD1 OG311 -0.530 ! OG CD1--CE1 +ATOM HOD1 HGP1 0.420 ! | +BOND CD1 OD1 OD1 HOD1 ! OD1 +IC CZ CE1 *CD1 OD1 1.4299 117.44 -179.97 114.67 1.4209 +IC CZ CD1 OD1 HOD1 1.4299 127.89 0.53 106.95 0.9786 + +PRES 2MBD 0.00 ! C2H3 Gamma 2-methyl amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD + +DELETE ATOM HD1 ! CM--CD1--CE1 +ATOM CD1 CG2R61 0.000 ! // \ +ATOM CM CG331 -0.270 !--CG--NG--CZ CP +ATOM HM1 HGA3 0.090 ! || \ __ // +ATOM HM2 HGA3 0.090 ! OG CD2--CE2 +ATOM HM3 HGA3 0.090 +BOND CD1 CM CM HM1 CM HM2 CM HM3 +IC CZ CE1 *CD1 CM 1.4134 118.69 -178.93 119.09 1.5058 +IC CZ CD1 CM HM1 2.8050 42.16 78.76 114.26 1.1110 +IC HM1 CD1 *CM HM2 1.1110 114.26 112.67 91.29 1.1100 +IC HM1 CD1 *CM HM3 1.1110 114.26 -133.69 120.46 1.1114 + + +PRES 3MBD 0.00 ! C2H3 Gamma 3-methyl amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD + +DELETE ATOM HE1 ! CD1--CE1--CM +ATOM CE1 CG2R61 0.000 ! // \ +ATOM CM CG331 -0.270 !--CG--NG--CZ CP +ATOM HM1 HGA3 0.090 ! || \ __ // +ATOM HM2 HGA3 0.090 ! OG CD2--CE2 +ATOM HM3 HGA3 0.090 +BOND CE1 CM CM HM1 CM HM2 CM HM3 + +IC CD1 CP *CE1 CM 1.4042 119.12 -179.98 121.22 1.4967 +IC CD1 CE1 CM HM1 1.4042 119.66 58.53 108.62 1.1109 +IC HM1 CE1 *CM HM2 1.1109 121.07 108.19 81.88 1.1106 +IC HM1 CE1 *CM HM3 1.1109 121.07 -143.61 119.97 1.1108 + + +PRES 4MBD 0.00 ! C2H3 Gamma 4-methyl amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HP ! CD1--CE1 +ATOM CP CG2R61 0.000 ! // \ +ATOM CM CG331 -0.270 !--CG--NG--CZ CP--CM +ATOM HM1 HGA3 0.090 ! || \ __ // +ATOM HM2 HGA3 0.090 ! OG CD2--CE2 +ATOM HM3 HGA3 0.090 +BOND CP CM CM HM1 CM HM2 CM HM3 +IC CE1 CE2 *CP CM 1.4027 118.99 179.94 120.96 1.4962 +IC CE1 CP CM HM1 1.4027 120.05 60.06 108.73 1.1106 +IC HM1 CP *CM HM2 1.1106 108.73 120.04 109.93 1.1111 +IC HM1 CP *CM HM3 1.1106 108.73 -119.90 108.74 1.1106 + +PRES 2XBD -1.00 ! C2O2 Gamma 2-carboxy phenyl GA CDCA amide, cacha +! To be patched with residue GABD + ! OG CD1--CE1 +DELETE ATOM HD2 ! || // \\ +ATOM CD2 CG2R61 -0.100 ! | CG--NG--CZ CP +ATOM CX CG2O3 0.620 ! |\ / HG \ __ / +ATOM OX1 OG2D2 -0.760 ! CC3 CD2--CE2 +ATOM OX2 OG2D2 -0.760 ! | + ! (-0.5)OX1--CX--OX2(-0.5) +BOND CD2 CX CX OX1 CX OX2 +IMPR CX OX1 OX2 CD2 +IC CZ CE2 *CD2 CX 1.4234 118.49 179.85 118.42 1.5417 +IC CZ CD2 CX OX1 1.4234 123.10 90.24 120.07 1.2614 +IC OX1 CD2 *CX OX2 1.2614 120.07 178.02 118.47 1.2663 + + +PRES 3XBD -1.00 ! C2O2 Gamma 3-carboxy phenyl GA CDCA amide, cacha +! To be patched with residue GABD + ! (-0.5)OX1--CX--OX1(-0.5) +DELETE ATOM HE1 ! | +ATOM CE1 CG2R61 -0.100 ! OG CD1--CE1 +ATOM CX CG2O3 0.620 ! || // \\ +ATOM OX1 OG2D2 -0.760 ! | CG--NG--CZ CP +ATOM OX2 OG2D2 -0.760 ! |\ / HG \ __ / + ! CC3 CD2--CE2 +BOND CE1 CX CX OX1 CX OX2 +IMPR CX OX1 OX2 CE1 +IC CD1 CP *CE1 CX 1.4121 118.22 -175.98 121.14 1.5400 +IC CD1 CE1 CX OX1 1.4121 120.51 3.27 118.27 1.2608 +IC OX1 CE1 *CX OX2 1.2608 118.27 -167.99 118.42 1.2655 + + +PRES 4XBD -1.00 ! C2O2 Gamma 4-carboxy phenyl GA CDCA amide, cacha +! To be patched with residue GABD +DELETE ATOM HP ! OG CD1--CE1 OX1(-0.5) +ATOM CP CG2R61 -0.100 ! || // \\ / +ATOM CX CG2O3 0.620 ! | CG--NG--CZ CP--CX +ATOM OX1 OG2D2 -0.760 ! |\ / HG \ __ / \ +ATOM OX2 OG2D2 -0.760 ! CC3 CD2--CE2 OX2(-0.5) +BOND CP CX CX OX1 CX OX2 +IMPR CX OX1 OX2 CP +IC CE1 CE2 *CP CX 1.4118 118.05 179.99 120.66 1.5407 +IC CE1 CP CX OX1 1.4118 121.29 0.02 118.88 1.2647 +IC OX1 CP *CX OX2 1.2647 118.88 179.99 118.86 1.2643 + +PRES 4XEBD -0.86 ! C9H8O2 Gamma 4-carboxy ethyl phenyl GA CDCA amide, cacha +! To be patched with residue GABD +DELETE ATOM CZ +DELETE ATOM CD1 +DELETE ATOM HD1 +DELETE ATOM CE1 ! OG CJ1--CK1 OX1(-0.5) +DELETE ATOM HE1 ! || // \\ / +DELETE ATOM CD2 ! CG--NG--CM1--CM2--CY CQ--CX +DELETE ATOM HD2 ! / HG \ __ / \ +DELETE ATOM CE2 ! CC3 CJ2--CK2 OX2(-0.5) +DELETE ATOM HE2 +DELETE ATOM CP +DELETE ATOM HP +ATOM CM1 CG321 -0.04 +ATOM HM11 HGA2 0.09 +ATOM HM12 HGA2 0.09 +ATOM CM2 CG321 -0.18 +ATOM HM21 HGA2 0.09 +ATOM HM22 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.000 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CQ CG2R61 -0.100 +ATOM CX CG2O3 0.620 +ATOM OX1 OG2D2 -0.760 +ATOM OX2 OG2D2 -0.760 +BOND NG CM1 CM1 HM11 CM1 HM12 CM1 CM2 +BOND CM2 HM21 CM2 HM22 CM2 CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CQ CX CX OX1 CX OX2 +IMPR CX OX1 OX2 CQ +IC CC3 CG NG CM1 1.4988 116.82 -179.37 123.36 1.4381 +IC CG NG CM1 CM2 1.3386 123.36 -179.46 111.10 1.5340 +IC NG CM2 *CM1 HM11 1.4381 111.10 121.09 109.49 1.1152 +IC HM11 CM2 *CM1 HM12 1.1152 109.49 117.77 109.51 1.1153 +IC NG CM1 CM2 CY 1.4381 111.10 179.82 110.46 1.5095 +IC CM1 CY *CM2 HM21 1.5340 110.46 121.17 109.19 1.1118 +IC HM21 CY *CM2 HM22 1.1118 109.19 117.66 109.24 1.1120 +IC CM1 CM2 CY CJ1 1.5340 110.46 90.37 120.27 1.4016 +IC CM2 CY CJ1 CK1 1.5095 120.27 179.91 120.28 1.4008 +IC CY CJ1 CK1 CQ 1.4016 120.28 0.12 121.07 1.4150 +IC CJ1 CK1 CQ CK2 1.4008 121.07 0.22 117.79 1.4150 +IC CK1 CQ CK2 CJ2 1.4150 117.79 -0.22 121.07 1.4007 +IC CK1 CY *CJ1 HJ1 1.4008 120.28 -179.90 119.73 1.0789 +IC CK2 CY *CJ2 HJ2 1.4007 120.28 179.91 119.73 1.0788 +IC CQ CJ1 *CK1 HK1 1.4150 121.07 -179.94 119.81 1.0809 +IC CQ CJ2 *CK2 HK2 1.4150 121.07 179.95 119.81 1.0809 +IC CK1 CK2 *CQ CX 1.4150 117.79 179.95 121.10 1.5435 +IC CK1 CQ CX OX1 1.4150 121.11 0.13 116.99 1.2633 +IC OX1 CQ *CX OX2 1.2633 116.99 179.67 116.99 1.2633 + +PRES 3XBP -1.00 ! C11H8O4 Alpha benzyl, Gamma 3-carboxy phenyl GA CDCA amide, cacha +! To be patched with residue GABD +DELETE ATOM HE1 ! OG CD1--CE1--CX--OX1(-0.5) +ATOM CE1 CG2R61 -0.100 ! || // \\ \ +ATOM CX CG2O3 0.620 ! CG--NG--CZ CP \ +ATOM OX1 OG2D2 -0.760 ! / HG \ __ / OX2(-0.5) +ATOM OX2 OG2D2 -0.760 ! CC3 CD2--CE2 +GROUP ! \ +ATOM CC1 CG311 -0.01 ! CC2 CJ1--CK1 +ATOM HC1 HGA1 0.09 ! / // \\ +ATOM CA CG2O2 0.63 !-CC1--CA--OA2--CB--CY CQ +ATOM OA1 OG2D1 -0.51 ! | \ __ / +ATOM OA2 OG302 -0.33 ! OA1 CJ2--CK2 +ATOM CB CG321 -0.05 +ATOM HB1 HGA2 0.09 +ATOM HB2 HGA2 0.09 +GROUP +ATOM CY CG2R61 0.00 +ATOM CJ1 CG2R61 -0.115 +ATOM HJ1 HGR61 0.115 +ATOM CJ2 CG2R61 -0.115 +ATOM HJ2 HGR61 0.115 +ATOM CK1 CG2R61 -0.115 +ATOM HK1 HGR61 0.115 +ATOM CK2 CG2R61 -0.115 +ATOM HK2 HGR61 0.115 +ATOM CQ CG2R61 -0.115 +ATOM HQ HGR61 0.115 +BOND OA2 CB +BOND CB HB1 CB HB2 CB CY +BOND CY CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ CQ HQ +BOND CQ CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY +BOND CE1 CX CX OX1 CX OX2 +DELETE IMPR CA OA2 OA1 CC1 +IMPR CA CC1 OA1 OA2 +IMPR CX OX1 OX2 CE1 +IC CC1 CA OA2 CB 1.5612 110.02 -169.48 113.80 1.4482 +IC HC1 CC1 CA OA2 1.1143 105.31 -138.17 110.02 1.3340 +IC HB1 CB OA2 CA 1.1146 109.13 70.79 113.80 1.3340 +IC HB2 CB OA2 CA 1.1139 110.51 -47.32 113.80 1.3340 +IC CY CB OA2 CA 1.5046 115.25 -167.09 113.80 1.3340 +IC CJ2 CY CB OA2 1.4041 119.47 52.44 115.25 1.4482 +IC CJ1 CY CB OA2 1.4047 120.95 -131.01 115.25 1.4482 +IC CJ1 CJ2 *CY CB 1.4047 119.49 176.60 119.47 1.5046 +IC CJ2 CY CB HB1 1.4041 119.47 174.99 108.34 1.1146 +IC CJ2 CY CB HB2 1.4041 119.47 -69.92 105.73 1.1139 +IC CB CY CJ1 CK1 1.5046 120.95 -176.57 120.28 1.4011 +IC CB CY CJ2 CK2 1.5046 119.47 176.36 120.27 1.4016 +IC CY CJ1 CK1 CQ 1.4047 120.28 0.43 119.97 1.4012 +IC CJ1 CK1 CQ CK2 1.4011 119.97 -0.59 120.02 1.4013 +IC CK1 CQ CK2 CJ2 1.4012 120.02 0.33 119.97 1.4016 +IC CK1 CY *CJ1 HJ1 1.4011 120.28 179.19 120.09 1.0813 +IC CK2 CY *CJ2 HJ2 1.4016 120.27 -179.48 119.40 1.0795 +IC CQ CJ1 *CK1 HK1 1.4012 119.97 179.04 119.50 1.0814 +IC CQ CJ2 *CK2 HK2 1.4013 119.97 -179.73 120.01 1.0798 +IC CK1 CK2 *CQ HQ 1.4012 120.02 -179.42 120.05 1.0805 +IC CD1 CP *CE1 CX 1.4130 117.96 -179.80 121.26 1.5397 +IC CD1 CE1 CX OX1 1.4130 120.79 0.27 116.51 1.2620 +IC OX1 CE1 *CX OX2 1.2620 116.51 -179.55 116.84 1.2610 + +PRES 2AMFD 0.00 ! C2H3O Gamma-2-Amino Phenyl methyl ether GA CDCA Amide, cacha +! patch combination: +! core residue GABD +DELETE ATOM HD1 +GROUP +ATOM CD1 CG2R61 0.11 ! OG CD2--CE2 +ATOM OD OG301 -0.54 ! || // \\ +ATOM CM CG331 0.16 ! --CG--NG--CZ CP +ATOM HM1 HGA3 0.09 ! \ __ / +ATOM HM2 HGA3 0.09 ! CM--OD--CD1--CE1 +ATOM HM3 HGA3 0.09 +BOND CD1 OD OD CM CM HM1 CM HM2 CM HM3 +IC NG CZ CD1 OD 1.4205 124.52 -3.45 121.25 1.4058 +IC CZ CD1 OD CM 1.4163 121.25 115.89 111.85 1.4241 +IC CD1 OD CM HM1 1.4058 111.85 -165.29 108.54 1.1105 +IC HM1 OD *CM HM2 1.1105 108.54 118.63 111.53 1.1137 +IC HM1 OD *CM HM3 1.1105 108.54 -119.19 110.77 1.1105 + + +PRES 3AMFD 0.00 ! C2H3O Gamma-3-Amino Phenyl methyl ether GA CDCA Amide, cacha +! patch combination: +! core residue GABD +DELETE ATOM HE1 +GROUP +ATOM CE1 CG2R61 0.11 ! OG CD2--CE2 +ATOM OE OG301 -0.54 ! || // \\ +ATOM CM CG331 0.16 ! --CG--NG--CZ CP +ATOM HM1 HGA3 0.09 ! \ __ / +ATOM HM2 HGA3 0.09 ! CD1--CE1--OE--CM +ATOM HM3 HGA3 0.09 +BOND CE1 OE OE CM CM HM1 CM HM2 CM HM3 +IC CZ CD1 CE1 OE 1.4015 120.67 -179.85 123.17 1.4121 +IC CD1 CE1 OE CM 1.4124 123.17 4.14 116.52 1.4248 +IC CE1 OE CM HM1 1.4121 116.52 -63.56 110.72 1.1124 +IC HM1 OE *CM HM2 1.1124 110.72 122.02 110.86 1.1128 +IC HM1 OE *CM HM3 1.1124 110.72 -118.94 108.92 1.1105 + + +PRES 4AMFD 0.00 ! C2H3O Gamma-4-Amino Phenyl methyl ether GA CDCA Amide, cacha +! patch combination: +! core residue GABD +DELETE ATOM HP +GROUP +ATOM CP CG2R61 0.11 ! OG CD2--CE2 +ATOM OP OG301 -0.54 ! || // \\ +ATOM CM CG331 0.16 ! --CG--NG--CZ CP--OP--CM +ATOM HM1 HGA3 0.09 ! \ __ / +ATOM HM2 HGA3 0.09 ! CD1--CE1 +ATOM HM3 HGA3 0.09 +BOND CP OP OP CM CM HM1 CM HM2 CM HM3 +IC CD1 CE1 CP OP 1.4032 120.95 -179.94 117.95 1.4118 +IC CE1 CP OP CM 1.3994 117.95 179.23 116.73 1.4232 +IC CE1 OP CM HM1 2.4090 147.60 62.27 110.73 1.1123 +IC HM1 OP *CM HM2 1.1123 110.73 118.86 108.79 1.1108 +IC HM1 OP *CM HM3 1.1123 110.73 -122.28 110.75 1.1123 + +PRES 26MD 0.00 ! C4H6 Gamma 2,6-dimethyl amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HD2 +DELETE ATOM HD1 ! CM1--CD1--CE1 +ATOM CD1 CG2R61 0.000 ! // \ +ATOM CM1 CG331 -0.270 !--CG--NG--CZ CP +ATOM HM11 HGA3 0.090 ! || \ __ // +ATOM HM12 HGA3 0.090 ! OG CM2--CD2--CE2 +ATOM HM13 HGA3 0.090 +ATOM CD2 CG2R61 0.000 +ATOM CM2 CG331 -0.270 +ATOM HM21 HGA3 0.090 +ATOM HM22 HGA3 0.090 +ATOM HM23 HGA3 0.090 +BOND CD1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 +BOND CD2 CM2 CM2 HM21 CM2 HM22 CM2 HM23 +IC CZ CE1 *CD1 CM1 1.4107 119.12 -179.77 120.02 1.5047 +IC CZ CD1 CM1 HM11 1.4107 120.86 60.39 108.71 1.1110 +IC HM11 CD1 *CM1 HM12 1.1110 108.71 120.79 110.66 1.1098 +IC HM11 CD1 *CM1 HM13 1.1110 108.71 -118.95 108.53 1.1134 +IC CZ CE2 *CD2 CM2 1.4123 118.93 179.40 119.49 1.5054 +IC CZ CD2 CM2 HM21 1.4123 121.57 52.53 108.64 1.1123 +IC HM21 CD2 *CM2 HM22 1.1123 108.64 120.32 110.67 1.1099 +IC HM21 CD2 *CM2 HM23 1.1123 108.64 -119.01 108.44 1.1111 + +PRES 23MD 0.00 ! C4H6 Gamma 2,3-dimethyl amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HE1 +DELETE ATOM HD1 ! CM1--CD1--CE1--CM2 +ATOM CD1 CG2R61 0.000 ! // \ +ATOM CM1 CG331 -0.270 ! --CG--NG--CZ CP +ATOM HM11 HGA3 0.090 ! || \ __ // +ATOM HM12 HGA3 0.090 ! OG CD2--CE2 +ATOM HM13 HGA3 0.090 +ATOM CE1 CG2R61 0.000 +ATOM CM2 CG331 -0.270 +ATOM HM21 HGA3 0.090 +ATOM HM22 HGA3 0.090 +ATOM HM23 HGA3 0.090 +BOND CD1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 +BOND CE1 CM2 CM2 HM21 CM2 HM22 CM2 HM23 +IC CZ CE1 *CD1 CM1 1.4167 118.80 -179.20 119.49 1.5148 +IC CZ CD1 CM1 HM11 1.4167 121.71 95.98 108.42 1.1105 +IC HM11 CD1 *CM1 HM12 1.1105 108.42 121.46 110.56 1.1094 +IC HM11 CD1 *CM1 HM13 1.1105 108.42 -119.35 109.76 1.1108 +IC CD1 CP *CE1 CM2 1.4202 119.81 -179.88 118.34 1.5043 +IC CD1 CE1 CM2 HM21 1.4202 121.85 48.66 109.10 1.1108 +IC HM21 CE1 *CM2 HM22 1.1108 109.10 119.76 110.41 1.1118 +IC HM21 CE1 *CM2 HM23 1.1108 109.10 -120.08 108.64 1.1104 + +PRES 3CBD 0.00 ! C3H2Cl Gamma 3-Chloro amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HE1 +ATOM CD1 CG2R61 -0.100 ! CD1--CE1--CL +ATOM HD1 HGR62 0.150 ! // \ +ATOM CE1 CG2R61 0.030 ! --CG--NG--CZ CP +ATOM CL CLGR1 -0.130 ! || \ __ // +ATOM CP CG2R61 -0.100 ! OG CD2--CE2 +ATOM HP HGR62 0.150 +BOND CE1 CL +IC CP CD1 *CE1 CL 1.4002 119.96 179.97 120.18 1.7396 + +PRES 4CBD 0.00 ! C3H2Cl Gamma 4-Chloro amino benzene glutamic acid CDCA amide, cacha +!To be patched with residue GABD +DELETE ATOM HP +ATOM CE1 CG2R61 -0.100 ! CD1--CE1 +ATOM HE1 HGR62 0.150 ! // \ +ATOM CP CG2R61 0.030 ! --CG--NG--CZ CP--CL +ATOM CL CLGR1 -0.130 ! || \ __ // +ATOM CE2 CG2R61 -0.100 ! OG CD2--CE2 +ATOM HE2 HGR62 0.150 +BOND CP CL +IC CE1 CE2 *CP CL 1.3996 119.90 -179.82 120.09 1.7397 + +PRES 24MFD 0.00 ! C4H6O2 Gamma-2,4 Dimethoxy amino benzene GA CDCA Amide, cacha +! patch core residue GABD +DELETE ATOM HD1 +DELETE ATOM HP ! OG CD2--CE2 +GROUP ! || // \\ +ATOM CD1 CG2R61 0.11 ! --CG--NG--CZ CP--OP--CN +ATOM OD OG301 -0.54 ! \ __ / +ATOM CM CG331 0.16 ! CM--OD--CD1--CE1 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 +ATOM CP CG2R61 0.11 +ATOM OP OG301 -0.54 +ATOM CN CG331 0.16 +ATOM HN1 HGA3 0.09 +ATOM HN2 HGA3 0.09 +ATOM HN3 HGA3 0.09 +BOND CD1 OD OD CM CM HM1 CM HM2 CM HM3 +BOND CP OP OP CN CN HN1 CN HN2 CN HN3 +IC NG CZ CD1 OD 1.4201 124.87 -5.97 121.19 1.4059 +IC CZ CD1 OD CM 1.4156 121.19 118.27 111.90 1.4248 +IC CD1 OD CM HM1 1.4059 111.90 -164.26 108.54 1.1104 +IC HM1 OD *CM HM2 1.1104 108.54 118.60 111.54 1.1140 +IC HM1 OD *CM HM3 1.1104 108.54 -119.19 110.79 1.1105 +IC CD1 CE1 CP OP 1.4029 121.13 -177.79 118.46 1.4038 +IC CE1 CP OP CN 1.3967 118.46 -146.32 114.18 1.4295 +IC CE1 OP CN HN1 2.4063 137.70 21.69 111.50 1.1134 +IC HN1 OP *CN HN2 1.1134 111.50 119.29 108.75 1.1111 +IC HN1 OP *CN HN3 1.1134 111.50 -122.48 110.76 1.1123 + +PRES 35MFD 0.00 ! C4H6O2 Gamma-3,5 Dimethoxy amino benzene GA CDCA Amide, cacha +! patch core residue GABD +DELETE ATOM HE1 +DELETE ATOM HE2 ! OG CD1--CE1--OE1--CM1 +GROUP ! || // \\ +ATOM CE1 CG2R61 0.11 ! --CG--NG--CZ CP +ATOM OE1 OG301 -0.54 ! \ __ / +ATOM CM1 CG331 0.16 ! CD2--CE2--OE2-CM2 +ATOM HM11 HGA3 0.09 +ATOM HM12 HGA3 0.09 +ATOM HM13 HGA3 0.09 +ATOM CE2 CG2R61 0.11 +ATOM OE2 OG301 -0.54 +ATOM CM2 CG331 0.16 +ATOM HM21 HGA3 0.09 +ATOM HM22 HGA3 0.09 +ATOM HM23 HGA3 0.09 +BOND CE1 OE1 OE1 CM1 CM1 HM11 CM1 HM12 CM1 HM13 +BOND CE2 OE2 OE2 CM2 CM2 HM21 CM2 HM22 CM2 HM23 +IC CZ CD1 CE1 OE1 1.3988 120.42 -179.28 123.08 1.4117 +IC CD1 CE1 OE1 CM1 1.4113 123.08 5.94 116.55 1.4244 +IC CE1 OE1 CM1 HM11 1.4117 116.55 57.38 110.88 1.1128 +IC HM11 OE1 *CM1 HM12 1.1128 110.88 119.03 108.87 1.1105 +IC HM11 OE1 *CM1 HM13 1.1128 110.88 -122.07 110.68 1.1123 +IC CZ CD2 CE2 OE2 1.3995 120.87 -179.50 122.96 1.4111 +IC CD2 CE2 OE2 CM2 1.4067 122.96 3.62 116.04 1.4273 +IC CE2 OE2 CM2 HM21 1.4111 116.04 58.51 111.01 1.1134 +IC HM21 OE2 *CM2 HM22 1.1134 111.01 119.14 109.03 1.1103 +IC HM21 OE2 *CM2 HM23 1.1134 111.01 -121.82 110.85 1.1129 + +!New compounds by "team CGenFF" (mainly xxwy), Jul 10 +RESI STYR 0.00 ! C8H8 styrene, xxwy & oashi +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 ! HD1 HE1 +GROUP ! | | +ATOM CD1 CG2R61 -0.115 ! CD1--CE1 H21 +ATOM HD1 HGR61 0.115 ! / \ / +GROUP ! HG--CG CZ----C1=C2 +ATOM CD2 CG2R61 -0.115 ! \ / / \ +ATOM HD2 HGR61 0.115 ! CD2--CE2 H1 H22 +GROUP ! | | +ATOM CE1 CG2R61 -0.115 ! HD2 HE2 +ATOM HE1 HGR61 0.115 +GROUP +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 +GROUP +ATOM CZ CG2R61 0.0 +GROUP +ATOM C1 CG2DC1 -0.15 +ATOM H1 HGA4 0.15 +GROUP +ATOM C2 CG2DC3 -0.42 +ATOM H21 HGA5 0.21 +ATOM H22 HGA5 0.21 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ C1 +BOND C1 C2 +BOND C1 H1 C2 H21 C2 H22 + +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ C1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CZ C1 C2 0.0000 0.0000 179.0000 0.0000 0.0000 ! Introduce asymmetry +IC C2 CZ *C1 H1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC H21 C1 *C2 H22 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI DMCA 0.000 ! C3H6O3 dimethyl carbonate (CAS: 616-38-6), xxwy +GROUP +ATOM C1 CG331 0.05 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM O1 OG302 -0.24 ! H12 O H22 +ATOM C CG2O6 0.23 ! | || | +ATOM O OG2D1 -0.39 ! H11--C1---O1---C---O2---C2--H21 +ATOM O2 OG302 -0.24 ! | | +ATOM C2 CG331 0.05 ! H13 H23 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 +ATOM H23 HGA3 0.09 + +BOND C1 O1 O1 C C O2 O2 C2 C O +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 +IMPR C O1 O2 O +IC O1 C O2 C2 0.0000 0.00 185.00 0.00 0.0000 +IC O2 C O1 C1 0.0000 0.00 180.00 0.00 0.0000 +IC O1 O2 *C O 0.0000 0.00 185.00 0.00 0.0000 +IC C O1 C1 H11 0.0000 0.00 185.00 0.00 0.0000 +IC H11 O1 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 O1 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C O2 C2 H21 0.0000 0.00 185.00 0.00 0.0000 ! introduce +IC H21 O2 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 ! 5deg asymmetry +IC H21 O2 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 + +RESI DECA 0.000 ! C5H10O3 diethyl carbonate (CAS: 105-58-8), xxwy +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM C2 CG321 0.14 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM O1 OG302 -0.24 ! H12 H21 O H31 H41 +ATOM C CG2O6 0.23 ! | | || | | +ATOM O OG2D1 -0.39 ! H11--C1---C2---O1---C---O2---C3---C4--H42 +ATOM O2 OG302 -0.24 ! | | | | +ATOM C3 CG321 0.14 ! H13 H22 H32 H43 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 C2 C2 O1 O1 C +BOND C O2 O2 C3 C3 C4 C O +BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 +BOND C3 H31 C3 H32 C4 H41 C4 H42 C4 H43 +IMPR C O1 O2 O +IC C1 C2 O1 C 0.0000 0.00 80.00 0.00 0.0000 +IC O1 C2 C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 O1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 O1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 O1 C O2 0.0000 0.00 180.00 0.00 0.0000 +IC O1 C O2 C3 0.0000 0.00 185.00 0.00 0.0000 +IC O1 O2 *C O 0.0000 0.00 180.00 0.00 0.0000 +IC C O2 C3 C4 0.0000 0.00 -80.00 0.00 0.0000 +IC O2 C3 C4 H41 0.0000 0.00 185.00 0.00 0.0000 +IC C4 O2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 O2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +RESI URAC 0.000 ! C4H4N2O2 uracil, xxwy +GROUP +ATOM N1 NG2R61 -0.37 ! O4 +ATOM C6 CG2R62 0.11 ! || +ATOM H6 HGR62 0.18 ! C4 H3 +ATOM C2 CG2R63 0.44 ! / \ / +ATOM O2 OG2D4 -0.45 ! H5-C5 N3 +ATOM N3 NG2R61 -0.53 ! || | +ATOM H3 HGP1 0.38 ! H6-C6 C2 +ATOM C4 CG2R63 0.40 ! \ / \\ +ATOM O4 OG2D4 -0.46 ! N1 O2 +ATOM C5 CG2R62 -0.20 ! | +ATOM H5 HGR62 0.15 ! H1 +ATOM H1 HGP1 0.35 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 C6 N1 +BOND N1 H1 N3 H3 C5 H5 C6 H6 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 +IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C6 *N1 H1 0.0000 0.00 179.00 0.00 0.0000 ! deliberately distorted for test case +IC N1 N3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C5 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 + +RESI 2PYO 0.000 ! C5H5NO 2-Pyridone, xxwy +GROUP +ATOM N1 NG2R61 -0.13 ! H4 +ATOM H1 HGP1 0.28 ! | +ATOM C2 CG2R63 0.16 ! C4 +ATOM O2 OG2D4 -0.48 ! / \\ +ATOM C3 CG2R62 -0.26 ! H5-C5 C3-H3 +ATOM H3 HGR62 0.22 ! || | +ATOM C4 CG2R62 -0.22 ! H6-C6 C2 +ATOM H4 HGR62 0.22 ! \ / \\ +ATOM C5 CG2R62 -0.22 ! N1 O2 +ATOM H5 HGR62 0.15 ! | +ATOM C6 CG2R62 0.15 ! H1 +ATOM H6 HGR62 0.13 + +BOND N1 C2 C2 C3 C4 C5 C6 N1 +BOND N1 H1 C3 H3 C4 H4 C5 H5 C6 H6 +DOUBLE C2 O2 C3 C4 C5 C6 +IMPR C2 C3 N1 O2 +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C6 *N1 H1 0.0000 0.00 179.00 0.00 0.0000 ! deliberately distorted for test case +IC N1 C3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 + +RESI RSRF 0.00 ! C6H10O3 4,6-dioxabicyclo[3.3.0]octan-8-ol; CID9942150, xxwy +GROUP ! IUPAC: (3R,3aS,6aR)-2,3,3a,4,5,6a-hexahydrofuro[2,3-b]furan-3-ol +ATOM C1 CG3RC1 0.07 +ATOM H11 HGA1 0.09 ! H11 +ATOM C2 CG3RC1 0.03 ! H41 O4 | O6 H61 +ATOM H21 HGA1 0.09 ! \ / \ | / \ / +ATOM O4 OG3C51 -0.34 ! H42--C4 C1 C6--H62 +ATOM C4 CG3C52 0.02 ! | | | +ATOM H41 HGA2 0.09 ! H31--C3----C2----C5--H51 +ATOM H42 HGA2 0.09 ! / | \ +ATOM O6 OG3C51 -0.34 ! O3 H21 H52 +ATOM C6 CG3C52 0.02 ! | +ATOM H61 HGA2 0.09 ! H32 +ATOM H62 HGA2 0.09 +ATOM C5 CG3C52 -0.18 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +!GROUP +ATOM C3 CG3C51 0.14 +ATOM H31 HGA1 0.09 +ATOM O3 OG311 -0.65 +ATOM H32 HGP1 0.42 + +BOND C1 O4 C1 C2 C2 C3 C3 C4 C4 O4 C3 O3 +BOND C1 H11 C1 O6 C2 H21 C2 C5 C3 H31 C4 H41 +BOND C4 H42 O3 H32 C5 C6 C6 O6 C5 H51 C5 H52 +BOND C6 H61 C6 H62 +IC C1 O4 C4 C3 0.0 0.0 15.00 0.0 0.0 +IC C3 O4 *C4 H41 0.0 0.0 120.00 0.0 0.0 +IC C3 O4 *C4 H42 0.0 0.0 -120.00 0.0 0.0 +IC C4 O4 C1 C2 0.0 0.0 10.00 0.0 0.0 +IC C2 O4 *C1 H11 0.0 0.0 120.00 0.0 0.0 +IC C2 O4 *C1 O6 0.0 0.0 -120.00 0.0 0.0 +IC C2 C1 O6 C6 0.0 0.0 43.00 0.0 0.0 +IC C1 O6 C6 C5 0.0 0.0 -35.00 0.0 0.0 +IC C5 O6 *C6 H61 0.0 0.0 120.00 0.0 0.0 +IC C5 O6 *C6 H62 0.0 0.0 -120.00 0.0 0.0 +IC C4 C2 *C3 H31 0.0 0.0 120.00 0.0 0.0 +IC C4 C2 *C3 O3 0.0 0.0 -120.00 0.0 0.0 +IC C4 C3 O3 H32 0.0 0.0 -60.00 0.0 0.0 +IC C6 C2 *C5 H51 0.0 0.0 120.00 0.0 0.0 +IC C6 C2 *C5 H52 0.0 0.0 -120.00 0.0 0.0 +IC C3 C5 *C2 H21 0.0 0.0 -120.00 0.0 0.0 + +RESI OXD4 0.000 ! C2H2N2O oxadiazole124, xxwy +GROUP ! H1 +ATOM C1 CG2R53 0.45 ! ____ / +ATOM H1 HGR52 0.17 ! N2----C1 +ATOM N2 NG2R50 -0.64 ! | \ +ATOM C3 CG2R53 0.49 ! | O5 +ATOM H3 HGR52 0.13 ! |____ / +ATOM N4 NG2R50 -0.42 ! C3----N4 +ATOM O5 OG2R50 -0.18 ! / + ! H3 + +BOND C1 H1 C1 N2 N2 C3 C3 H3 +BOND C3 N4 N4 O5 O5 C1 +IC C1 N2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC N2 C3 N4 O5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 N4 O5 C1 0.0000 0.00 0.00 0.00 0.0000 +IC N2 O5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N2 N4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 + +RESI TRZ4 0.00 ! C2H3N3 triazole124 +GROUP ! H1 +ATOM C1 CG2R53 0.23 ! ____ / +ATOM H1 HGR52 0.16 ! N2----C1 +ATOM N2 NG2R50 -0.66 ! | \ +ATOM C3 CG2R53 0.47 ! | N5--H5 +ATOM H3 HGR52 0.11 ! |____ / +ATOM N4 NG2R50 -0.58 ! C3----N4 +ATOM N5 NG2R51 -0.05 ! / +ATOM H5 HGP1 0.32 ! H3 + +BOND C1 H1 C1 N2 N2 C3 C3 H3 +BOND C3 N4 N4 N5 N5 H5 N5 C1 +IC C1 N2 C3 N4 0.0000 0.00 0.00 0.00 0.0000 +IC N2 C3 N4 N5 0.0000 0.00 0.00 0.00 0.0000 +IC N5 C1 N2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC N2 N5 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N4 N2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C1 *N5 H5 0.0000 0.00 180.00 0.00 0.0000 + +RESI HDZ1B 0.00 ! C9H10N2O Hydrazone model compound for comparison with styrene +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +GROUP +ATOM C2 CG2O1 0.58 ! C1 H3 +ATOM O2 OG2D1 -0.49 ! \ | +ATOM N3 NG2S1 -0.34 ! C2--N3 H5 +ATOM H3 HGP1 0.31 ! // \ / +ATOM N4 NG2D1 -0.31 ! O2 N4=C5 +ATOM C5 CG2DC1 -0.24 ! _______________\ +ATOM H5 HGA4 0.24 ! | +ATOM C6G CG2R61 0.25 ! | H6D1 H6E1 +GROUP ! | | | +ATOM C6D1 CG2R61 -0.115 ! | C6D1--C6E1 +ATOM H6D1 HGR61 0.115 ! | // \\ +GROUP ! |--C6G C6Z--H6Z +ATOM C6D2 CG2R61 -0.115 ! \ / +ATOM H6D2 HGR61 0.115 ! C6D2==C6E2 +GROUP ! | | +ATOM C6E1 CG2R61 -0.115 ! H6D2 H6E2 +ATOM H6E1 HGR61 0.115 +GROUP +ATOM C6E2 CG2R61 -0.115 +ATOM H6E2 HGR61 0.115 +GROUP +ATOM C6Z CG2R61 -0.115 +ATOM H6Z HGR61 0.115 + +BOND C1 H11 C1 H12 C1 H13 C1 C2 +BOND C2 O2 C2 N3 N3 H3 N3 N4 C5 H5 +BOND N4 C5 C5 C6G +BOND C6D2 C6G C6E1 C6D1 C6Z C6E2 +BOND C6D1 H6D1 C6D2 H6D2 C6E1 H6E1 +BOND C6E2 H6E2 C6Z H6Z +BOND C6D1 C6G C6E2 C6D2 C6Z C6E1 +IMPR C2 C1 N3 O2 +IMPR C5 C6G N4 H5 + +IC C1 C2 N3 N4 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C1 C2 N3 0.0000 0.00 180.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC N3 C1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 N3 N4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC N3 N4 C5 C6G 0.0000 0.00 180.00 0.00 0.0000 +IC C6G N4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C5 C6G C6D1 0.0000 0.00 179.00 0.00 0.0000 ! Introduce asymmetry +IC C6D1 C5 *C6G C6D2 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6G C6D1 C6E1 0.0000 0.00 180.00 0.00 0.0000 +IC C6E1 C6G *C6D1 H6D1 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6G C6D2 C6E2 0.0000 0.00 180.00 0.00 0.0000 +IC C6E2 C6G *C6D2 H6D2 0.0000 0.00 180.00 0.00 0.0000 +IC C6G C6D1 C6E1 C6Z 0.0000 0.00 0.00 0.00 0.0000 !dihe from 180.0 +IC C6Z C6D1 *C6E1 H6E1 0.0000 0.00 180.00 0.00 0.0000 +IC C6Z C6D2 *C6E2 H6E2 0.0000 0.00 180.00 0.00 0.0000 +IC C6E2 C6E1 *C6Z H6Z 0.0000 0.00 180.00 0.00 0.0000 + +RESI METP -4.00 ! CH3O10P3 Methyl triphosphate, kevo +GROUP +ATOM C1 CG331 -0.17 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM O1 OG303 -0.62 +ATOM P2 PG1 1.50 +ATOM O21 OG2P1 -0.82 +ATOM O22 OG2P1 -0.82 +ATOM O2 OG304 -0.74 +ATOM P3 PG1 1.50 +ATOM O31 OG2P1 -0.82 +ATOM O32 OG2P1 -0.82 +ATOM O3 OG304 -0.86 +ATOM P4 PG2 1.10 +ATOM O41 OG2P1 -0.90 +ATOM O42 OG2P1 -0.90 +ATOM O43 OG2P1 -0.90 + +BOND C1 H11 C1 H12 C1 H13 C1 O1 +BOND O1 P2 P2 O21 P2 O22 P2 O2 +BOND O2 P3 P3 O31 P3 O32 P3 O3 +BOND O3 P4 P4 O41 P4 O42 P4 O43 +IC P3 O3 P4 O43 0.0000 0.00 0.00 0.00 0.0000 +IC P4 O3 P3 O2 0.0000 0.00 180.00 0.00 0.0000 +IC O3 P3 O2 P2 0.0000 0.00 180.00 0.00 0.0000 +IC P3 O2 P2 O1 0.0000 0.00 -90.00 0.00 0.0000 ! from QM +IC O2 P2 O1 C1 0.0000 0.00 180.00 0.00 0.0000 +IC P2 O1 C1 H13 0.0000 0.00 180.00 0.00 0.0000 +IC O1 H13 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC O1 H13 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC O1 O2 *P2 O21 0.0000 0.00 120.00 0.00 0.0000 +IC O1 O2 *P2 O22 0.0000 0.00 -120.00 0.00 0.0000 +IC O2 O3 *P3 O31 0.0000 0.00 120.00 0.00 0.0000 +IC O2 O3 *P3 O32 0.0000 0.00 -120.00 0.00 0.0000 +IC O3 O43 *P4 O41 0.0000 0.00 120.00 0.00 0.0000 +IC O3 O43 *P4 O42 0.0000 0.00 -120.00 0.00 0.0000 + +!New compounds by "team CGenFF", Dec 10 +RESI 4CYT 0.00 ! C8H7N p-cyanotoluene, alr +GROUP +ATOM CG CG2R61 0.10 +ATOM C3N CG1N1 0.36 +ATOM N3C NG1T1 -0.46 +ATOM CD1 CG2R61 -0.115 ! HD1 HE1 +ATOM HD1 HGR61 0.115 ! | | +ATOM CD2 CG2R61 -0.115 ! CD1--CE1 H11 +ATOM HD2 HGR61 0.115 ! __ / \ / +ATOM CE1 CG2R61 -0.115 ! N3C==C3N--CG CZ--CT--H12 +ATOM HE1 HGR61 0.115 ! \ / \ +ATOM CE2 CG2R61 -0.115 ! CD2--CE2 H13 +ATOM HE2 HGR61 0.115 ! | | +ATOM CZ CG2R61 0.00 ! HD2 HE2 +ATOM CT CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 +BOND CE2 CD2 CZ CE1 CZ CE2 +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ CT +BOND CT H11 CT H12 CT H13 +BOND CG C3N +BOND C3N N3C +IC CG CD1 CE1 CZ 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CE1 CZ CE2 1.4000 120.00 0.00 120.00 1.4000 +IC CE1 CZ CE2 CD2 1.4000 120.00 0.00 120.00 1.4000 +IC CD1 CD2 *CG C3N 1.4000 120.00 180.00 120.00 1.2000 +IC N3C C3N CG CD1 1.1200 179.99 0.0000 120.00 1.4000 +IC CE1 CG *CD1 HD1 1.4000 120.00 180.00 120.00 1.0800 +IC CE2 CG *CD2 HD2 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD1 *CE1 HE1 1.4000 120.00 180.00 120.00 1.0800 +IC CZ CD2 *CE2 HE2 1.4000 120.00 180.00 120.00 1.0800 +IC CE1 CE2 *CZ CT 1.4000 120.00 180.00 120.00 1.5000 +IC CE1 CZ CT H11 1.4000 120.00 90.00 109.50 1.1100 +IC CZ H11 *CT H12 1.5000 109.50 120.00 109.50 1.1100 +IC CZ H11 *CT H13 1.5000 109.50 -120.00 109.50 1.1100 + +RESI TMAO 0.00 ! C3H9NO trimethylamine N-oxide, xxwy & ejd +GROUP +ATOM N NG3P0 -0.83 ! H32 +ATOM C1 CG334 -0.35 ! | +ATOM C2 CG334 -0.35 ! H31-C3-H33 +ATOM C3 CG334 -0.35 ! H23 | +ATOM O1 OG312 -0.37 ! | | (+) +ATOM H11 HGP5 0.25 ! H22-C2------N------O1 (-) +ATOM H12 HGP5 0.25 ! | | +ATOM H13 HGP5 0.25 ! H21 | +ATOM H21 HGP5 0.25 ! H11-C1-H13 +ATOM H22 HGP5 0.25 ! | +ATOM H23 HGP5 0.25 ! H12 +ATOM H31 HGP5 0.25 +ATOM H32 HGP5 0.25 +ATOM H33 HGP5 0.25 + +BOND N C1 N C2 N C3 N O1 +BOND C1 H11 C1 H12 C1 H13 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +IC C2 N C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H11 *C1 H13 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C2 C1 *N C3 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C2 C1 *N O1 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC C3 N C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H21 *C2 H23 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC O1 N C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 +!IC C1 N O1 H41 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC N H41 *O1 H42 0.0000 0.0000 120.0000 0.0000 0.0000 +!IC N H41 *O1 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI PHMK 0.000 ! C8H8O phenyl methyl ketone, mcs +GROUP +ATOM C1 CG331 -0.23 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM C2 CG2O5 0.36 ! H8 O2 +ATOM O2 OG2D3 -0.47 ! | || +ATOM C3 CG2R61 0.07 ! H7 C8 C2 H11 +ATOM C4 CG2R61 -0.115 ! \ // \ / \ / +ATOM H4 HGR61 0.115 ! C7 C3 C1-H12 +ATOM C5 CG2R61 -0.115 ! | || \ +ATOM H5 HGR61 0.115 ! H6-C6 C4-H4 H13 +ATOM C6 CG2R61 -0.115 ! \\ / +ATOM H6 HGR61 0.115 ! C5 +ATOM C7 CG2R61 -0.115 ! | +ATOM H7 HGR61 0.115 ! H5 +ATOM C8 CG2R61 -0.115 +ATOM H8 HGR61 0.115 + +BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 O2 +BOND C2 C3 C3 C4 C4 H4 C4 C5 C5 H5 +BOND C5 C6 C6 H6 C6 C7 C7 H7 C7 C8 C8 H8 C8 C3 +IMPR C2 C3 C1 O2 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C2 *C3 C4 0.0000 0.00 -180.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 -180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 -180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 -180.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 -180.00 0.00 0.0000 +IC C7 C3 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 + +RESI PHEK 0.000 ! C9H10O phenyl ethyl ketone, mcs +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM C2 CG321 -0.17 +ATOM H21 HGA2 0.09 +ATOM H22 HGA2 0.09 +ATOM C3 CG2O5 0.34 ! H9 O3 +ATOM O3 OG2D3 -0.47 ! | || +ATOM C4 CG2R61 0.12 ! H8 C9 C3 H21 H11 +ATOM C5 CG2R61 -0.115 ! \ // \ / \ | / +ATOM H5 HGR61 0.115 ! C8 C4 C2-C1-H12 +ATOM C6 CG2R61 -0.115 ! | || | \ +ATOM H6 HGR61 0.115 ! H7-C7 C5-H5 H22 H13 +ATOM C7 CG2R61 -0.115 ! \\ / +ATOM H7 HGR61 0.115 ! C6 +ATOM C8 CG2R61 -0.115 ! | +ATOM H8 HGR61 0.115 ! H6 +ATOM C9 CG2R61 -0.115 +ATOM H9 HGR61 0.115 + +BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 H21 C2 H22 C2 C3 C3 O3 +BOND C3 C4 C4 C5 C5 H5 C5 C6 C6 H6 C6 C7 C7 H7 +BOND C7 C8 C8 H8 C8 C9 C9 H9 C9 C4 +IMPR C3 C4 C2 O3 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 H21 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 O3 0.0000 0.00 -180.00 0.00 0.0000 +IC C2 C3 C4 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C3 *C4 C5 0.0000 0.00 -180.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C6 C7 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C7 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C4 *C9 H9 0.0000 0.00 -180.00 0.00 0.0000 + +RESI BEON 0.00 ! C4H6O butenone (there can be only one), mcs & kevo +GROUP +ATOM C1 CG331 -0.23 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 +ATOM C2 CG2O5 0.38 ! H41 H3 O2 H11 +ATOM O2 OG2D3 -0.46 ! \ | || / +ATOM C3 CG2DC1 -0.11 ! C4 = C3- C2 - C1 -H12 +ATOM H3 HGA4 0.15 ! / \ +ATOM C4 CG2DC3 -0.42 ! H42 H13 +ATOM H41 HGA5 0.21 +ATOM H42 HGA5 0.21 + +BOND C1 H11 C1 H12 C1 H13 C1 C2 +BOND C2 O2 C2 C3 C3 H3 C3 C4 +BOND C4 H41 C4 H42 +IMPR C2 C3 C1 O2 +!IMPR C3 C4 C2 H3 ! Just a test! +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 180.00 0.00 0.0000 + +RESI DMPR 0.00 ! C5H11NO Dimethylpropanamide, mnoon +GROUP +ATOM C CG2O1 0.43 ! H33 +ATOM O OG2D1 -0.52 ! | +ATOM N NG2S0 -0.35 ! O C3--H32 +ATOM C1 CG321 -0.10 ! \\ / \ +ATOM H11 HGA2 0.09 ! C---N H31 +ATOM H12 HGA2 0.09 ! / \ +ATOM C2 CG331 -0.09 ! H11--C1 C2--H23 +ATOM H21 HGA3 0.09 ! / | / | +ATOM H22 HGA3 0.09 ! C4 H12 H21 H22 +ATOM H23 HGA3 0.09 ! /|\ +ATOM C3 CG331 -0.09 ! / | \ +ATOM H31 HGA3 0.09 ! H41 H42 H43 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 +GROUP +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 C4 +BOND C2 H21 C2 H22 C2 H23 +BOND C3 H31 C3 H32 C3 H33 +BOND C C1 C N N C2 N C3 +BOND C4 H41 C4 H42 C4 H43 +DOUBLE C O +IMPR C C1 N O +IC N C C1 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C C4 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C C4 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 N *C O 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C N C3 0.0000 0.00 180.00 0.00 0.0000 +IC C C3 *N C2 0.0000 0.00 180.00 0.00 0.0000 +IC C N C2 H23 0.0000 0.00 0.00 0.00 0.0000 +IC N H23 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC N H23 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C N C3 H33 0.0000 0.00 0.00 0.00 0.0000 +IC N H33 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC N H33 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C C1 C4 H43 0.0000 0.00 180.00 0.00 0.0000 +IC C1 H43 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C1 H43 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 + +RESI DMSO 0.00 ! C2H6OS dimethylsulfoxide (ML Strader, et al.JPC2002_A106_1074), sz +GROUP +ATOM O1 OG2P1 -0.55 +ATOM S2 SG3O3 0.31 ! charges: ML Strader, SE Feller, JPC-A106(6),1074(2002) +ATOM C3 CG331 -0.15 +ATOM H4 HGA3 0.09 ! O1 +ATOM H5 HGA3 0.09 ! || +ATOM H6 HGA3 0.09 ! S2 +ATOM C7 CG331 -0.15 ! / \ +ATOM H8 HGA3 0.09 ! H4--C3 C7--H10 +ATOM H9 HGA3 0.09 ! / | | \ +ATOM H10 HGA3 0.09 ! H5 H6 H8 H9 + +BOND O1 S2 S2 C3 S2 C7 +BOND C3 H4 C3 H5 C3 H6 +BOND C7 H8 C7 H9 C7 H10 +!IMPR S2 C3 C7 O1 ! Just a test! +IC C3 S2 C7 H8 0.0000 0.00 180.00 0.00 0.0000 +IC S2 H8 *C7 H9 0.0000 0.00 120.00 0.00 0.0000 +IC S2 H8 *C7 H10 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C7 *S2 O1 0.0000 0.00 120.00 0.00 0.0000 +IC C7 S2 C3 H4 0.0000 0.00 180.00 0.00 0.0000 +IC S2 H4 *C3 H5 0.0000 0.00 120.00 0.00 0.0000 +IC S2 H4 *C3 H6 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MESO 0.00 ! C3H8OS methylethylsulfoxide, xxwy & mnoon & kevo +GROUP +ATOM O OG2P1 -0.55 +ATOM S SG3O3 0.31 +ATOM C3 CG331 -0.15 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 ! O H11 +ATOM H33 HGA3 0.09 ! || / +ATOM C2 CG321 -0.06 ! S C1--H12 +ATOM H21 HGA2 0.09 ! / \ / \ +ATOM H22 HGA2 0.09 ! H31--C3 C2 H13 +ATOM C1 CG331 -0.27 ! / | | \ +ATOM H11 HGA3 0.09 ! H32 H33 H21 H22 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 + +BOND S C3 S C2 +BOND C3 H31 C3 H32 C3 H33 +BOND C2 H21 C2 H22 C2 C1 +BOND C1 H11 C1 H12 C1 H13 +DOUBLE O S +!IMPR S C2 C3 O ! Just a test! +IC C3 C2 *S O 0.0000 0.00 120.00 0.00 0.0000 +IC C2 S C3 H33 0.0000 0.00 180.00 0.00 0.0000 +IC H33 S *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC H33 S *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 S C2 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 S *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 S *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC S C2 C1 H13 0.0000 0.00 180.00 0.00 0.0000 +IC H13 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC H13 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 + +RESI AMDN 1.00 ! C2H7N2 amidinium cation, sz & pram +GROUP +ATOM C1 CG2N2 0.66 +ATOM C2 CG331 -0.15 ! H3 H4 H5 +ATOM H3 HGA3 0.09 ! \| / +ATOM H4 HGA3 0.09 ! C2 +ATOM H5 HGA3 0.09 ! | +ATOM N6 NG2P1 -0.69 ! +) C1 +ATOM H7 HGP2 0.40 ! // \ +ATOM H8 HGP2 0.40 ! H7-N6 N9-H10 +ATOM N9 NG2P1 -0.69 ! | | +ATOM H10 HGP2 0.40 ! H8 H11 +ATOM H11 HGP2 0.40 + +BOND C1 C2 C2 H3 C2 H4 C2 H5 +BOND C1 N6 N6 H7 N6 H8 +BOND C1 N9 N9 H10 N9 H11 +IMPR C1 N6 N9 C2 +IC N6 C1 C2 H3 0.0000 0.00 90.00 0.00 0.0000 +IC C1 H3 *C2 H4 0.0000 0.00 120.00 0.00 0.0000 +IC C1 H3 *C2 H5 0.0000 0.00 -120.00 0.00 0.0000 +IC N6 C2 *C1 N9 0.0000 0.00 180.00 0.00 0.0000 +IC H7 N6 C1 N9 0.0000 0.00 180.00 0.00 0.0000 +IC H7 C1 *N6 H8 0.0000 0.00 180.00 0.00 0.0000 +IC H10 N9 C1 N6 0.0000 0.00 180.00 0.00 0.0000 +IC H10 C1 *N9 H11 0.0000 0.00 180.00 0.00 0.0000 + +RESI BAMI 1.00 ! C7H9N2 benzamidinium cation, sz & pram +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM C3 CG2R61 -0.115 +ATOM H4 HGR61 0.115 +ATOM C5 CG2R61 -0.115 +ATOM H6 HGR61 0.115 +ATOM C7 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM C9 CG2R61 -0.115 +ATOM H10 HGR61 0.115 +GROUP +ATOM C11 CG2R61 0.19 +ATOM C12 CG2N2 0.73 +ATOM N13 NG2P1 -0.60 +ATOM H14 HGP2 0.32 +ATOM H15 HGP2 0.32 +ATOM N16 NG2P1 -0.60 +ATOM H17 HGP2 0.32 +ATOM H18 HGP2 0.32 + +BOND C1 H2 +BOND C1 C3 C3 H4 C3 C5 C5 H6 +BOND C1 C7 C7 H8 C7 C9 C9 H10 +BOND C11 C5 C11 C12 C11 C9 +BOND C12 N13 N13 H14 N13 H15 C12 N16 N16 H17 N16 H18 +IMPR C12 N13 N16 C11 +IC C1 C3 C5 C11 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C5 C11 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C11 C9 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C11 C9 C7 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C7 C1 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C1 C3 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C3 *C1 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C5 *C3 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C11 *C5 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C7 *C9 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C1 *C7 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C9 *C11 C12 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C11 C12 N13 0.0000 0.00 45.00 0.00 0.0000 +IC N13 C11 *C12 N16 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 N13 H14 0.0000 0.00 0.00 0.00 0.0000 +IC H14 C12 *N13 H15 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C12 N16 H17 0.0000 0.00 0.00 0.00 0.0000 +IC H17 C12 *N16 H18 0.0000 0.00 180.00 0.00 0.0000 + +RESI PNTM 2.00 ! C19H26N4O2 1,5-bis(p-Amidinophenoxy)pentane, Pentamidine, sz & pram +GROUP ! based on PENT, ETOB, PAMI/ARG, +ATOM C1 CG321 -0.18 +ATOM H2 HGA2 0.09 +ATOM H3 HGA2 0.09 ! H11 H5 H2 H8 H32 +ATOM C4 CG321 -0.18 ! \ | | | / +ATOM H5 HGA2 0.09 ! H12-C10-C4--C1--C7--C31-H33 +ATOM H6 HGA2 0.09 ! / | | | \ +ATOM C7 CG321 -0.18 ! O13 H6 H3 H9 O34 +ATOM H8 HGA2 0.09 ! | | +ATOM H9 HGA2 0.09 ! H20-C19==C14 C35==C40-H41 +GROUP ! / \ / \ +ATOM C10 CG321 -0.01 ! H22-C21 C15-H16 H37-C36 C42-H43 +ATOM H11 HGA2 0.09 ! \\ // \\ // +ATOM H12 HGA2 0.09 ! C23--C17-H18 H39-C38--C44 +ATOM O13 OG301 -0.39 ! / \ +ATOM C14 CG2R61 0.22 ! (+) C24 C45 (+) +GROUP ! // \ / \\ +ATOM C15 CG2R61 -0.115 ! H29-N28 N25-H26 H47-N46 N49-H50 +ATOM H16 HGR61 0.115 ! | | | | +ATOM C17 CG2R61 -0.115 ! H30 H27 H48 H51 +ATOM H18 HGR61 0.115 +ATOM C19 CG2R61 -0.115 +ATOM H20 HGR61 0.115 +ATOM C21 CG2R61 -0.115 +ATOM H22 HGR61 0.115 +GROUP ! one positive charge on this group which is from PAMI +ATOM C23 CG2R61 0.19 +ATOM C24 CG2N2 0.73 +ATOM N25 NG2P1 -0.60 +ATOM H26 HGP2 0.32 +ATOM H27 HGP2 0.32 +ATOM N28 NG2P1 -0.60 +ATOM H29 HGP2 0.32 +ATOM H30 HGP2 0.32 +GROUP ! This group is from ETOB +ATOM C31 CG321 -0.01 +ATOM H32 HGA2 0.09 +ATOM H33 HGA2 0.09 +ATOM O34 OG301 -0.39 +ATOM C35 CG2R61 0.22 +GROUP +ATOM C36 CG2R61 -0.115 +ATOM H37 HGR61 0.115 +ATOM C38 CG2R61 -0.115 +ATOM H39 HGR61 0.115 +ATOM C40 CG2R61 -0.115 +ATOM H41 HGR61 0.115 +ATOM C42 CG2R61 -0.115 +ATOM H43 HGR61 0.115 +GROUP ! one positive charge on this group (PAMI) +ATOM C44 CG2R61 0.19 +ATOM C45 CG2N2 0.73 +ATOM N46 NG2P1 -0.60 +ATOM H47 HGP2 0.32 +ATOM H48 HGP2 0.32 +ATOM N49 NG2P1 -0.60 +ATOM H50 HGP2 0.32 +ATOM H51 HGP2 0.32 + +BOND C1 H2 C1 H3 C1 C4 C4 H5 C4 H6 C1 C7 C7 H8 C7 H9 +BOND C4 C10 C10 H11 C10 H12 C10 O13 O13 C14 +BOND C14 C15 C15 H16 C15 C17 C17 H18 +BOND C14 C19 C19 H20 C19 C21 C21 H22 +BOND C17 C23 C21 C23 C23 C24 C24 N25 C24 N28 +BOND N25 H26 N25 H27 N28 H29 N28 H30 +BOND C7 C31 C31 H32 C31 H33 C31 O34 O34 C35 +BOND C35 C36 C36 H37 C36 C38 C38 H39 +BOND C35 C40 C40 H41 C40 C42 C42 H43 +BOND C38 C44 C42 C44 C44 C45 C45 N46 C45 N49 +BOND N46 H47 N46 H48 N49 H50 N49 H51 +IMPR C24 N25 N28 C23 +IMPR C45 N46 N49 C44 +IC C10 C4 C1 C7 0.0000 0.00 180.00 0.00 0.0000 +IC O13 C10 C4 C1 0.0000 0.00 180.00 0.00 0.0000 +IC C14 O13 C10 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C10 O13 C14 C15 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C1 C7 C31 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C7 C31 O34 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C31 O34 C35 0.0000 0.00 180.00 0.00 0.0000 +IC C31 O34 C35 C36 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C7 *C1 H2 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C7 *C1 H3 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C10 *C4 H5 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C10 *C4 H6 0.0000 0.00 -120.00 0.00 0.0000 +IC O13 C4 *C10 H11 0.0000 0.00 120.00 0.00 0.0000 +IC O13 C4 *C10 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C31 C1 *C7 H8 0.0000 0.00 120.00 0.00 0.0000 +IC C31 C1 *C7 H9 0.0000 0.00 -120.00 0.00 0.0000 +IC C7 O34 *C31 H32 0.0000 0.00 120.00 0.00 0.0000 +IC C7 O34 *C31 H33 0.0000 0.00 -120.00 0.00 0.0000 +IC C14 C15 C17 C23 0.0000 0.00 0.00 0.00 0.0000 +IC C15 C17 C23 C21 0.0000 0.00 0.00 0.00 0.0000 +IC C17 C23 C21 C19 0.0000 0.00 0.00 0.00 0.0000 +IC C23 C21 C19 C14 0.0000 0.00 0.00 0.00 0.0000 +IC C21 C19 C14 C15 0.0000 0.00 0.00 0.00 0.0000 +IC C19 C14 C15 C17 0.0000 0.00 0.00 0.00 0.0000 +IC C14 C17 *C15 H16 0.0000 0.00 180.00 0.00 0.0000 +IC C15 C23 *C17 H18 0.0000 0.00 180.00 0.00 0.0000 +IC C17 C21 *C23 C24 0.0000 0.00 180.00 0.00 0.0000 +IC C23 C19 *C21 H22 0.0000 0.00 180.00 0.00 0.0000 +IC C21 C14 *C19 H20 0.0000 0.00 180.00 0.00 0.0000 +IC C19 C15 *C14 O13 0.0000 0.00 180.00 0.00 0.0000 +IC C17 C23 C24 N25 0.0000 0.00 45.00 0.00 0.0000 +IC C23 N25 *C24 N28 0.0000 0.00 180.00 0.00 0.0000 +IC C23 C24 N25 H26 0.0000 0.00 0.00 0.00 0.0000 +IC C24 H26 *N25 H27 0.0000 0.00 180.00 0.00 0.0000 +IC C23 C24 N28 H29 0.0000 0.00 0.00 0.00 0.0000 +IC C24 H29 *N28 H30 0.0000 0.00 180.00 0.00 0.0000 +IC C35 C36 C38 C44 0.0000 0.00 0.00 0.00 0.0000 +IC C36 C38 C44 C42 0.0000 0.00 0.00 0.00 0.0000 +IC C38 C44 C42 C40 0.0000 0.00 0.00 0.00 0.0000 +IC C44 C42 C40 C35 0.0000 0.00 0.00 0.00 0.0000 +IC C42 C40 C35 C36 0.0000 0.00 0.00 0.00 0.0000 +IC C40 C35 C36 C38 0.0000 0.00 0.00 0.00 0.0000 +IC C35 C38 *C36 H37 0.0000 0.00 180.00 0.00 0.0000 +IC C36 C44 *C38 H39 0.0000 0.00 180.00 0.00 0.0000 +IC C38 C42 *C44 C45 0.0000 0.00 180.00 0.00 0.0000 +IC C44 C40 *C42 H43 0.0000 0.00 180.00 0.00 0.0000 +IC C42 C35 *C40 H41 0.0000 0.00 180.00 0.00 0.0000 +IC C40 C36 *C35 O34 0.0000 0.00 180.00 0.00 0.0000 +IC C38 C44 C45 N46 0.0000 0.00 45.00 0.00 0.0000 +IC C44 N46 *C45 N49 0.0000 0.00 180.00 0.00 0.0000 +IC C44 C45 N46 H47 0.0000 0.00 0.00 0.00 0.0000 +IC C45 H47 *N46 H48 0.0000 0.00 180.00 0.00 0.0000 +IC C44 C45 N49 H50 0.0000 0.00 0.00 0.00 0.0000 +IC C45 H50 *N49 H51 0.0000 0.00 180.00 0.00 0.0000 + +RESI MHYO 0.000 ! C4H4N2O2 5-methylenehydantoin, xxwy +GROUP +ATOM N1 NG2R53 -0.18 ! H3 O2 +ATOM C2 CG2R53 0.25 ! \ // +ATOM O2 OG2D1 -0.43 ! N3----C2 +ATOM N3 NG2R53 -0.25 ! | | +ATOM H3 HGP1 0.35 ! C4 N1 +ATOM C4 CG2R53 0.26 ! // \ / \ +ATOM O4 OG2D1 -0.41 ! O4 C5 H1 +ATOM C5 CG252O 0.09 ! || +ATOM C6 CG2DC3 -0.46 ! C6 +ATOM H61 HGA5 0.23 ! / \ +ATOM H62 HGA5 0.24 ! H61 H62 +ATOM H1 HGP1 0.31 + +BOND N1 C2 C2 N3 N3 C4 C4 C5 +BOND C5 N1 C2 O2 N3 H3 C4 O4 +BOND C5 C6 C6 H61 C6 H62 N1 H1 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 O4 +IC C5 C4 N3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C4 N3 C2 N1 0.0000 0.00 0.00 0.00 0.0000 +IC N3 N1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N3 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C4 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 H61 0.0000 0.00 0.00 0.00 0.0000 +IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 + +RESI MOET 0.00 ! C3H6O Methoxyethene, xxwy +GROUP +ATOM C1 CG2D2 -0.53 +ATOM H11 HGA5 0.23 +ATOM H12 HGA5 0.23 ! H41 +ATOM C2 CG2D1O -0.14 ! / +ATOM H21 HGA4 0.21 ! H11 O3---C4--H42 +ATOM O3 OG301 -0.28 ! \ / \ +ATOM C4 CG331 0.01 ! C1==C2 H43 +ATOM H41 HGA3 0.09 ! / \ +ATOM H42 HGA3 0.09 ! H12 H21 +ATOM H43 HGA3 0.09 + +BOND C1 C2 C2 O3 O3 C4 C1 H11 +BOND C1 H12 C2 H21 C4 H41 C4 H42 C4 H43 +IMPR C2 C1 O3 H21 +IC C1 C2 O3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC O3 C2 C1 H11 0.0000 0.00 0.00 0.00 0.0000 +IC C2 H11 *C1 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O3 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC O3 H41 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC O3 H41 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MOBU 0.00 ! C5H8O 1-Methoxy-1,3-butadiene, CAS Num: 10034-09-0, xxwy +GROUP +ATOM C1 CG2D1O -0.14 +ATOM H11 HGA4 0.21 ! H1 +ATOM C2 CG2DC1 -0.30 ! / +ATOM H21 HGA4 0.23 ! H21 O1---C--H2 +ATOM O1 OG301 -0.28 ! \ / \ +ATOM C CG331 0.01 ! H41 C2==C1 H3 +ATOM H1 HGA3 0.09 ! \ / \ +ATOM H2 HGA3 0.09 ! C4==C3 H11 +ATOM H3 HGA3 0.09 ! / \ +ATOM C3 CG2DC2 -0.15 ! H42 H31 +ATOM H31 HGA4 0.15 +ATOM C4 CG2DC3 -0.42 +ATOM H41 HGA5 0.21 +ATOM H42 HGA5 0.21 +BOND C1 C2 C1 O1 O1 C C1 H11 +BOND C2 H21 C H1 C H2 C H3 +BOND C2 C3 C3 C4 C3 H31 C4 H41 C4 H42 +IMPR C1 C2 O1 H11 +IC C2 C1 O1 C 0.0000 0.00 180.00 0.00 0.0000 +IC O1 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C2 O1 *C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C4 H41 0.0000 0.00 0.00 0.00 0.0000 +IC C3 H41 *C4 H42 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O1 C H1 0.0000 0.00 180.00 0.00 0.0000 +IC O1 H1 *C H2 0.0000 0.00 120.00 0.00 0.0000 +IC O1 H1 *C H3 0.0000 0.00 -120.00 0.00 0.0000 + +RESI BSAM 0.00 ! C6H7NO2S Benzenesulfonamide, CAS Num: 98-10-2, xxwy +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 ! HD1 HE1 +ATOM HD2 HGR61 0.115 ! | __ | +ATOM CE2 CG2R61 -0.115 ! CD1--CE1 O11 H21 +ATOM HE2 HGR61 0.115 ! / \ || / +ATOM CZ CG2R61 0.24 ! HG--CG CZ--S1--N2 +ATOM S1 SG3O2 0.61 ! \\ // || \ +ATOM O11 OG2P1 -0.42 ! CD2--CE2 O12 H22 +ATOM O12 OG2P1 -0.42 ! | | +ATOM N2 NG321 -0.77 ! HD2 HE2 +ATOM H21 HGP1 0.38 +ATOM H22 HGP1 0.38 + +BOND CD1 CG CD2 CG CE1 CD1 CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CZ S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 H22 +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ S1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CZ S1 N2 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CZ N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CZ N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CZ S1 N2 H21 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC S1 H21 *N2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 + +RESI MSAM 0.00 ! CH5NO2S Methanesulfonamide, CAS Num: 3144-09-0, xxwy +GROUP +ATOM C3 CG331 -0.07 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 ! H31 O11 H21 +ATOM S1 SG3O2 0.65 ! \ || / +ATOM O11 OG2P1 -0.42 ! H32--C3--S1--N2 +ATOM O12 OG2P1 -0.42 ! / || \ +ATOM N2 NG321 -0.77 ! H33 O12 H22 +ATOM H21 HGP1 0.38 +ATOM H22 HGP1 0.38 + +BOND C3 S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 H22 +BOND C3 H31 C3 H32 C3 H33 +IC C3 S1 N2 H21 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC S1 H21 *N2 H22 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC N2 S1 C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC S1 H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S1 H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 + + +RESI MMSM 0.00 ! C2H7NO2S N-Methylmethanesulfonamide, xxwy +GROUP +ATOM C3 CG331 -0.05 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 ! H31 O11 H21 +ATOM S1 SG3O2 0.60 ! \ || / +ATOM O11 OG2P1 -0.42 ! H32--C3--S1--N2 H41 +ATOM O12 OG2P1 -0.42 ! / || \ / +ATOM N2 NG311 -0.57 ! H33 O12 C4--H42 +ATOM H21 HGP1 0.35 ! \ +ATOM C4 CG331 -0.03 ! H43 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C3 S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C4 +BOND C3 H31 C3 H32 C3 H33 C4 H41 C4 H42 C4 H43 +IC C3 S1 N2 C4 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC S1 C4 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC N2 S1 C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC S1 H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S1 H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC S1 N2 C4 H41 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N2 H41 *C4 H42 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N2 H41 *C4 H43 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI EESM 0.00 ! C4H11NO2S N-Ethylethanesulfonamide, xxwy +GROUP +ATOM C3 CG321 0.04 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM S1 SG3O2 0.60 +ATOM O11 OG2P1 -0.42 +ATOM O12 OG2P1 -0.42 +ATOM N2 NG311 -0.57 +ATOM H21 HGP1 0.35 ! H51 H31 O11 H21 H41 H61 +ATOM C4 CG321 0.06 ! | | || | | | +ATOM H41 HGA2 0.09 ! H52--C5--C3--S1--N2--C4--C6--H62 +ATOM H42 HGA2 0.09 ! | | || | | +ATOM C5 CG331 -0.27 ! H53 H32 O12 H42 H63 +ATOM H51 HGA3 0.09 +ATOM H52 HGA3 0.09 +ATOM H53 HGA3 0.09 +ATOM C6 CG331 -0.27 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C3 S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C4 +BOND C3 H31 C3 H32 C3 C5 C4 H41 C4 H42 C4 C6 +BOND C5 H51 C5 H52 C5 H53 C6 H61 C6 H62 C6 H63 +IC C3 S1 N2 C4 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC S1 C4 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC N2 S1 C3 C5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC S1 C5 *C3 H31 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S1 C5 *C3 H32 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC S1 N2 C4 C6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N2 C6 *C4 H41 0.0000 0.0000 120.0000 0.0000 0.0000 +IC N2 C6 *C4 H42 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC S1 C3 C5 H51 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3 H51 *C5 H52 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 H51 *C5 H53 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC N2 C4 C6 H61 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4 H61 *C6 H62 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C4 H61 *C6 H63 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI MBSM 0.00 ! C7H9NO2S N-Methylbenzenesulfonamide, xxwy +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 ! HD1 HE1 +ATOM HD2 HGR61 0.115 ! | __ | +ATOM CE2 CG2R61 -0.115 ! CD1--CE1 O11 H21 H31 +ATOM HE2 HGR61 0.115 ! / \ || | / +ATOM CZ CG2R61 0.24 ! HG--CG CZ--S1--N2--C3--H32 +ATOM S1 SG3O2 0.58 ! \\ // || \ +ATOM O11 OG2P1 -0.42 ! CD2--CE2 O12 H33 +ATOM O12 OG2P1 -0.42 ! | | +ATOM N2 NG311 -0.57 ! HD2 HE2 +ATOM H21 HGP1 0.35 +ATOM C3 CG331 -0.03 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND CD1 CG CD2 CG CE1 CD1 CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CZ S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C3 +BOND C3 H31 C3 H32 C3 H33 +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ S1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CZ S1 N2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CZ N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CZ N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CZ S1 N2 C3 0.0000 0.0000 -80.0000 0.0000 0.0000 +IC S1 C3 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S1 N2 C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC H31 N2 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC H31 N2 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 + +RESI PMSM 0.00 ! C7H9NO2S N-Phenylmethanesulfonamide, xxwy +GROUP +ATOM C3 CG331 -0.03 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 +ATOM S1 SG3O2 0.42 +ATOM O11 OG2P1 -0.36 +ATOM O12 OG2P1 -0.36 ! H51 H61 +ATOM N2 NG311 -0.48 ! | __ | +ATOM H21 HGP1 0.33 ! H31 O11 H21 C51--C61 +ATOM C4 CG2R61 0.21 ! \ || | / \ +ATOM C51 CG2R61 -0.115 ! H32--C3--S1--N2--C4 C7--H7 +ATOM H51 HGR61 0.115 ! / || \\ // +ATOM C52 CG2R61 -0.115 ! H33 O12 C52--C62 +ATOM H52 HGR61 0.115 ! | | +ATOM C61 CG2R61 -0.115 ! H52 H62 +ATOM H61 HGR61 0.115 +ATOM C62 CG2R61 -0.115 +ATOM H62 HGR61 0.115 +ATOM C7 CG2R61 -0.115 +ATOM H7 HGR61 0.115 + +BOND C3 S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C4 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 C51 C4 C52 C51 C61 C52 C62 C7 C61 C7 C62 +BOND C51 H51 C52 H52 C61 H61 C62 H62 C7 H7 +IC C3 S1 N2 C4 0.0000 0.0000 50.0000 0.0000 0.0000 +IC S1 C4 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C3 N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC N2 S1 C3 H31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC S1 H31 *C3 H32 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S1 H31 *C3 H33 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC S1 N2 C4 C51 0.0000 0.0000 60.0000 0.0000 0.0000 +IC N2 C51 *C4 C52 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C52 C4 C51 C61 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C51 C4 C52 C62 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4 C51 C61 C7 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C4 C61 *C51 H51 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4 C62 *C52 H52 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C51 *C61 H61 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C52 *C62 H62 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C61 C62 *C7 H7 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI PBSM 0.00 ! C12H11NO2S N-Phenylbenzenesulfonamide, CAS Num: 1678-25-7, xxwy +GROUP +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CE1 CG2R61 -0.115 +ATOM HE1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CE2 CG2R61 -0.115 +ATOM HE2 HGR61 0.115 ! HD1 HE1 H41 H51 +ATOM CZ CG2R61 0.23 ! | __ | | __ | +ATOM S1 SG3O2 0.58 ! CD1--CE1 O11 H21 C41--C51 +ATOM O11 OG2P1 -0.40 ! / \ || | / \ +ATOM O12 OG2P1 -0.40 ! HG--CG CZ--S1--N2--C3 C6--H6 +ATOM N2 NG311 -0.57 ! \\ // || \\ // +ATOM H21 HGP1 0.32 ! CD2--CE2 O12 C42--C52 +ATOM C3 CG2R61 0.24 ! | | | | +ATOM C41 CG2R61 -0.115 ! HD2 HE2 H42 H52 +ATOM H41 HGR61 0.115 +ATOM C42 CG2R61 -0.115 +ATOM H42 HGR61 0.115 +ATOM C51 CG2R61 -0.115 +ATOM H51 HGR61 0.115 +ATOM C52 CG2R61 -0.115 +ATOM H52 HGR61 0.115 +ATOM C6 CG2R61 -0.115 +ATOM H6 HGR61 0.115 + +BOND CD1 CG CD2 CG CE1 CD1 CE2 CD2 CZ CE1 CZ CE2 +BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 +BOND CZ S1 S1 N2 S1 O11 S1 O12 N2 H21 N2 C3 +BOND C3 C41 C3 C42 C41 C51 C42 C52 C6 C51 C6 C52 +BOND C41 H41 C42 H42 C51 H51 C52 H52 C6 H6 +IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE1 CE2 *CZ S1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CE2 CZ S1 N2 0.0000 0.0000 90.0000 0.0000 0.0000 +IC CZ N2 *S1 O11 0.0000 0.0000 120.0000 0.0000 0.0000 +IC CZ N2 *S1 O12 0.0000 0.0000 -120.0000 0.0000 0.0000 +IC CZ S1 N2 C3 0.0000 0.0000 50.0000 0.0000 0.0000 +IC S1 C3 *N2 H21 0.0000 0.0000 120.0000 0.0000 0.0000 +IC S1 N2 C3 C41 0.0000 0.0000 -110.0000 0.0000 0.0000 +IC N2 C41 *C3 C42 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C42 C3 C41 C51 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C41 C3 C42 C52 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C3 C41 C51 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C3 C51 *C41 H41 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3 C52 *C42 H42 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C41 *C51 H51 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C42 *C52 H52 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C51 C52 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI MMST 0.00 ! C2H6O3S Methyl methanesulfonate, CAS Num: 66-27-3, xxwy +GROUP +ATOM S1 SG3O2 0.24 +ATOM C2 CG331 0.05 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 ! O3 O4 +ATOM H23 HGA3 0.09 ! \\ // +ATOM O3 OG2P1 -0.32 ! S1 H61 +ATOM O4 OG2P1 -0.32 ! / \ / +ATOM O5 OG303 -0.24 ! H21--C2 O5---C6--H62 +ATOM C6 CG331 0.05 ! / | \ +ATOM H61 HGA3 0.09 ! H22 H23 H63 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND S1 C2 C2 H21 C2 H22 C2 H23 +BOND S1 O3 S1 O4 S1 O5 +BOND O5 C6 C6 H61 C6 H62 C6 H63 +IC C2 O5 *S1 O3 0.0000 0.00 113.00 0.00 0.0000 +IC C2 O5 *S1 O4 0.0000 0.00 -113.00 0.00 0.0000 +IC O5 S1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC H21 S1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 S1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 S1 O5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC S1 O5 C6 H61 0.0000 0.00 180.00 0.00 0.0000 +IC H61 O5 *C6 H62 0.0000 0.00 120.00 0.00 0.0000 +IC H61 O5 *C6 H63 0.0000 0.00 -120.00 0.00 0.0000 + +RESI MSNA -1.00 ! CH3O3S methyl sulfonate, xhe +GROUP +ATOM S SG3O1 0.73 ! O1 +ATOM O1 OG2P1 -0.55 ! | +ATOM O2 OG2P1 -0.55 ! O2---S---O3 +ATOM O3 OG2P1 -0.55 ! | +ATOM C1 CG331 -0.35 ! | +ATOM H11 HGA3 0.09 ! H11-C1-H12 +ATOM H12 HGA3 0.09 ! | +ATOM H13 HGA3 0.09 ! H13 + +BOND S O1 S O2 S O3 +BOND S C1 C1 H11 C1 H12 +BOND C1 H13 +ACCEPTOR O1 S +ACCEPTOR O2 S +ACCEPTOR O3 S +IC H13 C1 S O1 0.0 0.00 180.00 0.0 0.0 +IC C1 O1 *S O2 0.0 0.00 120.00 0.0 0.0 +IC C1 O1 *S O3 0.0 0.00 -120.00 0.0 0.0 +IC S H13 *C1 H11 0.0 0.00 120.00 0.0 0.0 +IC S H13 *C1 H12 0.0 0.00 -120.00 0.0 0.0 + +RESI ESNA -1.00 ! C2H5O3S ethyl sulfonate, xhe +GROUP +ATOM S SG3O1 0.73 ! O1 +ATOM O1 OG2P1 -0.55 ! | +ATOM O2 OG2P1 -0.55 ! O2---S---O3 +ATOM O3 OG2P1 -0.55 ! | +ATOM C1 CG321 -0.26 ! | +ATOM H11 HGA2 0.09 ! H11-C1-H12 +ATOM H12 HGA2 0.09 ! | +GROUP ! | +ATOM C2 CG331 -0.27 ! H21-C2-H22 +ATOM H21 HGA3 0.09 ! | +ATOM H22 HGA3 0.09 ! | +ATOM H23 HGA3 0.09 ! H23 + +BOND S O1 S O2 S O3 +BOND S C1 C1 H11 C1 H12 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 H23 +ACCEPTOR O1 S +ACCEPTOR O2 S +ACCEPTOR O3 S +IC C2 C1 S O1 0.0 0.00 180.00 0.0 0.0 +IC C1 O1 *S O2 0.0 0.00 120.00 0.0 0.0 +IC C1 O1 *S O3 0.0 0.00 -120.00 0.0 0.0 +IC S C2 *C1 H11 0.0 0.00 120.00 0.0 0.0 +IC S C2 *C1 H12 0.0 0.00 -120.00 0.0 0.0 +IC S C1 C2 H23 0.0 0.00 180.00 0.0 0.0 +IC C1 H23 *C2 H21 0.0 0.00 120.00 0.0 0.0 +IC C1 H23 *C2 H22 0.0 0.00 -120.00 0.0 0.0 + +RESI PSNA -1.00 ! C3H7O3S propyl sulfonate, xhe +GROUP +ATOM S SG3O1 0.73 ! O1 +ATOM O1 OG2P1 -0.55 ! | +ATOM O2 OG2P1 -0.55 ! O2---S---O3 +ATOM O3 OG2P1 -0.55 ! | +ATOM C1 CG321 -0.26 ! | +ATOM H11 HGA2 0.09 ! H11-C1-H12 +ATOM H12 HGA2 0.09 ! | +GROUP ! | +ATOM C2 CG321 -0.18 ! H21-C2-H22 +ATOM H21 HGA2 0.09 ! | +ATOM H22 HGA2 0.09 ! | +GROUP ! | +ATOM C3 CG331 -0.27 ! H31-C3-H32 +ATOM H31 HGA3 0.09 ! | +ATOM H32 HGA3 0.09 ! | +ATOM H33 HGA3 0.09 ! H33 + +BOND S O1 S O2 S O3 +BOND S C1 C1 H11 C1 H12 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 C3 C3 H31 C3 H32 +BOND C3 H33 +ACCEPTOR O1 S +ACCEPTOR O2 S +ACCEPTOR O3 S +IC C2 C1 S O1 0.0 0.00 180.00 0.0 0.0 +IC C1 O1 *S O2 0.0 0.00 120.00 0.0 0.0 +IC C1 O1 *S O3 0.0 0.00 -120.00 0.0 0.0 +IC S C2 *C1 H11 0.0 0.00 120.00 0.0 0.0 +IC S C2 *C1 H12 0.0 0.00 -120.00 0.0 0.0 +IC S C1 C2 C3 0.0 0.00 180.00 0.0 0.0 +IC C1 C3 *C2 H21 0.0 0.00 120.00 0.0 0.0 +IC C1 C3 *C2 H22 0.0 0.00 -120.00 0.0 0.0 +IC C1 C2 C3 H31 0.0 0.00 180.00 0.0 0.0 +IC C2 H31 *C3 H32 0.0 0.00 120.00 0.0 0.0 +IC C2 H31 *C3 H33 0.0 0.00 -120.00 0.0 0.0 + +RESI DMSN 0.00 ! C2H6O2S dimethyl sulfone, xhe +GROUP +ATOM S SG3O2 0.14 +ATOM O1 OG2P1 -0.36 ! H31 +ATOM O2 OG2P1 -0.36 ! | +ATOM C3 CG331 0.02 ! H32-C3-H33 +ATOM H31 HGA3 0.09 ! | +ATOM H32 HGA3 0.09 ! O1=S=O2 +ATOM H33 HGA3 0.09 ! | +ATOM C4 CG331 0.02 ! H42-C4-H43 +ATOM H41 HGA3 0.09 ! | +ATOM H42 HGA3 0.09 ! H41 +ATOM H43 HGA3 0.09 + +BOND S O1 S O2 S C3 S C4 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 H43 +ACCEPTOR O1 S +ACCEPTOR O2 S +IC C3 C4 *S O1 0.00 0.0000 120.0 0.00 0.00 +IC C3 C4 *S O2 0.00 0.0000 -120.0 0.00 0.00 +IC C4 S C3 H31 0.00 0.0000 180.000 0.00 0.00 +IC S H31 *C3 H32 0.00 0.0000 120.000 0.00 0.00 +IC S H31 *C3 H33 0.00 0.0000 -120.000 0.00 0.00 +IC C3 S C4 H41 0.00 0.0000 180.000 0.00 0.00 +IC S H41 *C4 H42 0.00 0.0000 120.000 0.00 0.00 +IC S H41 *C4 H43 0.00 0.0000 -120.000 0.00 0.00 + +RESI MESN 0.00 ! C3H8O2S methyl ethyl sulfone, xhe +GROUP +ATOM S SG3O2 0.14 +ATOM O1 OG2P1 -0.36 +ATOM O2 OG2P1 -0.36 ! H31 +ATOM C3 CG331 0.02 ! | +ATOM H31 HGA3 0.09 ! H32-C3-H33 +ATOM H32 HGA3 0.09 ! | +ATOM H33 HGA3 0.09 ! O1=S=O2 +ATOM C4 CG321 0.11 ! | +ATOM H41 HGA2 0.09 ! H42-C4-H43 +ATOM H42 HGA2 0.09 ! | +GROUP ! H51-C5-H52 +ATOM C5 CG331 -0.270 ! | +ATOM H51 HGA3 0.090 ! H53 +ATOM H52 HGA3 0.090 +ATOM H53 HGA3 0.090 + +BOND S O1 S O2 S C3 S C4 +BOND C3 H31 C3 H32 C3 H33 +BOND C4 H41 C4 H42 C4 C5 +BOND C5 H51 C5 H52 C5 H53 +ACCEPTOR O1 S +ACCEPTOR O2 S +IC C3 C4 *S O1 0.00 0.0000 120.0 0.00 0.00 +IC C3 C4 *S O2 0.00 0.0000 -120.0 0.00 0.00 +IC C4 S C3 H31 0.00 0.0000 180.000 0.00 0.00 +IC S H31 *C3 H32 0.00 0.0000 120.000 0.00 0.00 +IC S H31 *C3 H33 0.00 0.0000 -120.000 0.00 0.00 +IC C3 S C4 C5 0.00 0.0000 180.000 0.00 0.00 +IC S C5 *C4 H41 0.00 0.0000 120.000 0.00 0.00 +IC S C5 *C4 H42 0.00 0.0000 -120.000 0.00 0.00 +IC S C4 C5 H51 0.00 0.0000 180.00 0.00 0.00 +IC C4 H51 *C5 H52 0.00 0.0000 120.00 0.00 0.00 +IC C4 H51 *C5 H53 0.00 0.0000 -120.00 0.00 0.00 + +RESI MTDO 0.000 ! C4H3NO2S 5-methylene-2,4-thiazolidinedione, kevo & xxwy & oashi +GROUP +ATOM S1 SG311 -0.15 ! H3 O2 +ATOM C2 CG2R53 0.42 ! \ // +ATOM O2 OG2D1 -0.46 ! N3----C2 +ATOM N3 NG2R53 -0.36 ! | | +ATOM H3 HGP1 0.44 ! C4 S1 +ATOM C4 CG2R53 0.26 ! // \ / +ATOM O4 OG2D1 -0.45 ! O4 C5 +ATOM C5 CG252O 0.22 ! || +ATOM C6 CG2DC3 -0.58 ! C6 +ATOM H61 HGA5 0.33 ! / \ +ATOM H62 HGA5 0.33 ! H61 H62 + +BOND S1 C2 C2 N3 N3 C4 C4 C5 +BOND C5 S1 C2 O2 N3 H3 C4 O4 +BOND C5 C6 C6 H61 C6 H62 +IMPR C2 N3 O2 S1 +IMPR C4 C5 N3 O4 +IC C5 C4 N3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C4 N3 C2 S1 0.0000 0.00 0.00 0.00 0.0000 +IC N3 S1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N3 *C4 O4 0.0000 0.00 180.00 0.00 0.0000 +IC S1 C4 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C6 H61 0.0000 0.00 0.00 0.00 0.0000 +IC H61 C5 *C6 H62 0.0000 0.00 180.00 0.00 0.0000 + +RESI ZDOL 0.000 ! C7H6O2 1,3-benzodioxole, pram & oashi & kevo +GROUP +ATOM C1 CG2RC0 0.03 +ATOM O1 OG3C51 -0.31 +ATOM C2 CG3C52 0.38 ! H7 +ATOM H21 HGA2 0.09 ! | +ATOM H22 HGA2 0.09 ! H6 C7 +ATOM O2 OG3C51 -0.31 ! \ // \ H21 +ATOM C3 CG2RC0 0.03 ! C6 C1--O1\ / +ATOM C4 CG2R61 -0.32 ! | || C2 +ATOM H4 HGR61 0.28 ! C5 C3--O2/ \ +ATOM C5 CG2R61 -0.15 ! / \\ / H22 +ATOM H5 HGR61 0.19 ! H5 C4 +ATOM C6 CG2R61 -0.15 ! | +ATOM H6 HGR61 0.19 ! H4 +ATOM C7 CG2R61 -0.32 +ATOM H7 HGR61 0.28 + +BOND C1 O1 O1 C2 C2 H21 C2 H22 C2 O2 +BOND O2 C3 C3 C1 C3 C4 C4 H4 C4 C5 +BOND C5 H5 C5 C6 C6 H6 C6 C7 C7 H7 +BOND C7 C1 +IC C1 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C7 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C7 C1 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C1 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C7 C1 O1 C2 0.0000 0.00 160.00 0.00 0.0000 ! nonplanar +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C3 *C1 O1 0.0000 0.00 177.50 0.00 0.0000 ! nonplanar +IC C4 C1 *C3 O2 0.0000 0.00 -177.50 0.00 0.0000 ! nonplanar +IC O1 O2 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC O1 O2 *C2 H22 0.0000 0.00 240.00 0.00 0.0000 + +!New compounds by "team CGenFF", Sep 11 +RESI AMET 0.000 ! C2H5N ethenamine (CAS: 593-67-9), pram (parameters tweaked by kevo) +GROUP ! Notes: - tautomer of ethanimine (CAS: 20729-41-3) +ATOM C1 CG2D2 -0.50 ! - both tautomers predited to be basic (ACD) +ATOM H2 HGA5 0.21 ! - probably unstable +ATOM H3 HGA5 0.21 +ATOM C4 CG2D1O -0.13 ! H2 H5 H7 +ATOM H5 HGA4 0.24 ! \ | / +ATOM N6 NG321 -0.81 ! C1==C4--N6 +ATOM H7 HGPAM2 0.39 ! / \ +ATOM H8 HGPAM2 0.39 ! H3 H8 + +BOND C1 H2 C1 H3 C1 C4 +BOND C4 H5 C4 N6 N6 H7 N6 H8 +IMPR C4 C1 N6 H5 +IC C1 C4 N6 H7 0.0000 0.00 180.00 0.00 0.0000 +IC H2 C1 C4 N6 0.0000 0.00 180.00 0.00 0.0000 +IC H2 C4 *C1 H3 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C1 *C4 H5 0.0000 0.00 180.00 0.00 0.0000 +IC H7 C4 *N6 H8 0.0000 0.00 180.00 0.00 0.0000 + +RESI DMOP 0.00 ! C5H12O2 dimethoxypropane, sna +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 ! H52 +ATOM H13 HGA3 0.09 ! | +GROUP ! H51-C5-H53 +ATOM C2 CG301 0.40 ! | +ATOM O4 OG301 -0.38 ! H11 O4 H31 +ATOM C5 CG331 -0.09 ! | | | +ATOM H51 HGA3 0.09 ! H12-C1----C2----C3-H32 +ATOM H52 HGA3 0.09 ! | | | +ATOM H53 HGA3 0.09 ! H13 O6 H33 +ATOM O6 OG301 -0.38 ! | +ATOM C7 CG331 -0.09 ! H71-C7-H73 +ATOM H71 HGA3 0.09 ! | +ATOM H72 HGA3 0.09 ! H72 +ATOM H73 HGA3 0.09 +GROUP +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND C1 C2 C2 C3 C2 O4 O4 C5 C2 O6 O6 C7 +BOND C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 C3 H33 +BOND C5 H51 C5 H52 C5 H53 C7 H71 C7 H72 C7 H73 +IC C1 C2 C3 H31 0.0000 0.00 -177.05 0.00 0.0000 +IC C1 C3 *C2 O4 0.0000 0.00 -119.46 0.00 0.0000 +IC C1 C3 *C2 O6 0.0000 0.00 115.38 0.00 0.0000 +IC C1 C2 O4 C5 0.0000 0.00 -145.11 0.00 0.0000 +IC C1 C2 O6 C7 0.0000 0.00 -162.42 0.00 0.0000 +IC C3 C2 C1 H11 0.0000 0.00 -59.81 0.00 0.0000 +IC C2 O4 C5 H51 0.0000 0.00 -177.01 0.00 0.0000 +IC C2 O6 C7 H71 0.0000 0.00 -178.00 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 +IC H51 O4 *C5 H52 0.0000 0.00 118.35 0.00 0.0000 +IC H51 O4 *C5 H53 0.0000 0.00 -123.77 0.00 0.0000 +IC H71 O6 *C7 H72 0.0000 0.00 118.30 0.00 0.0000 +IC H71 O6 *C7 H73 0.0000 0.00 -118.47 0.00 0.0000 + +RESI DMBU 0.00 ! C6H14O2 dimethoxybutane, sna +GROUP +ATOM C1 CG331 -0.27 +ATOM H11 HGA3 0.09 ! H62 +ATOM H12 HGA3 0.09 ! | +ATOM H13 HGA3 0.09 ! H61-C6-H63 +GROUP ! | +ATOM C6 CG331 -0.06 ! | +ATOM H61 HGA3 0.09 ! | +ATOM H62 HGA3 0.09 ! H11 O5 H31 H41 +ATOM H63 HGA3 0.09 ! | | | | +ATOM O5 OG301 -0.34 ! H12-C1----C2----C3----C4-H42 +ATOM C2 CG301 0.26 ! | | | | +ATOM O7 OG301 -0.34 ! H13 O7 H32 H43 +ATOM C8 CG331 -0.06 ! | +ATOM H81 HGA3 0.09 ! | +ATOM H82 HGA3 0.09 ! | +ATOM H83 HGA3 0.09 ! H81-C8-H83 +GROUP ! | +ATOM C3 CG321 -0.18 ! H82 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C2 O5 O5 C6 C2 O7 +BOND O7 C8 C1 H11 C1 H12 C1 H13 C3 H31 C3 H32 +BOND C4 H41 C4 H42 C4 H43 C6 H61 C6 H62 C6 H63 +BOND C8 H81 C8 H82 C8 H83 +IC C1 C2 C3 C4 0.0000 0.00 178.49 0.00 0.0000 +IC C1 C3 *C2 O5 0.0000 0.00 116.78 0.00 0.0000 +IC C1 C3 *C2 O7 0.0000 0.00 -116.78 0.00 0.0000 +IC C1 C2 O5 C6 0.0000 0.00 60.00 0.00 0.0000 ! minimum used in parametrization. Try -69.33 -69.33 for two other minima. +IC C1 C2 O7 C8 0.0000 0.00 -60.00 0.00 0.0000 ! minimum used in parametrization. Try -54.16 -175.82 for two other minima. +IC C3 C2 C1 H11 0.0000 0.00 -170.79 0.00 0.0000 +IC C2 C3 C4 H41 0.0000 0.00 -179.00 0.00 0.0000 +IC C2 O5 C6 H61 0.0000 0.00 -177.12 0.00 0.0000 +IC C2 O7 C8 H81 0.0000 0.00 -176.20 0.00 0.0000 +IC C1 C2 C3 H31 0.0000 0.00 -61.01 0.00 0.0000 +IC C1 C2 C3 H32 0.0000 0.00 56.69 0.00 0.0000 +IC H11 C2 *C1 H12 0.0000 0.00 -119.96 0.00 0.0000 +IC H11 C2 *C1 H13 0.0000 0.00 118.92 0.00 0.0000 +IC H41 C3 *C4 H42 0.0000 0.00 -119.43 0.00 0.0000 +IC H41 C3 *C4 H43 0.0000 0.00 119.41 0.00 0.0000 +IC H61 O5 *C6 H62 0.0000 0.00 -118.05 0.00 0.0000 +IC H61 O5 *C6 H63 0.0000 0.00 118.28 0.00 0.0000 +IC H81 O7 *C8 H82 0.0000 0.00 -117.74 0.00 0.0000 +IC H81 O7 *C8 H83 0.0000 0.00 118.36 0.00 0.0000 + +!New compounds by "team CGenFF", Aug 13 +RESI NIME 0.00 ! CH3NO2 nitromethane, abar +GROUP +ATOM C1 CG334 0.20 +ATOM H11 HGA3 0.09 ! H11 O21 +ATOM H12 HGA3 0.09 ! \ // +ATOM H13 HGA3 0.09 ! H12--C1-N2 +ATOM N2 NG2O1 0.11 ! / \\ +ATOM O21 OG2N1 -0.29 ! H13 O22 +ATOM O22 OG2N1 -0.29 + +BOND C1 H11 C1 H12 C1 H13 C1 N2 N2 O21 N2 O22 +IMPR N2 O21 O22 C1 +IC O21 N2 C1 H11 0.0000 0.00 -29.00 0.00 0.0000 +IC H11 N2 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N2 *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 O21 *N2 O22 0.0000 0.00 180.00 0.00 0.0000 + +RESI NIPR 0.00 ! C3H7NO2 nitropropane, abar +GROUP +ATOM C1 CG324 0.26 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM N1 NG2O1 0.14 +ATOM O11 OG2N1 -0.29 ! H32 H22 H11 O11 +ATOM O12 OG2N1 -0.29 ! \ | | // +ATOM C2 CG321 -0.18 ! H31--C3--C2--C1--N1 +ATOM H21 HGA2 0.09 ! / | | \\ +ATOM H22 HGA2 0.09 ! H33 H21 H12 O12 +ATOM C3 CG331 -0.27 +ATOM H31 HGA3 0.09 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 N1 C1 C2 N1 O11 N1 O12 +BOND C2 H21 C2 H22 C2 C3 C3 H31 C3 H32 C3 H33 +IMPR N1 O11 O12 C1 +IC C1 C2 C3 H31 0.0000 0.00 180.00 0.00 0.0000 +IC H31 C2 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC H31 C2 *C3 H33 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C2 C1 N1 0.0000 0.00 -180.00 0.00 0.0000 +IC C2 N1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C2 N1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C1 N1 O11 0.0000 0.00 90.00 0.00 0.0000 +IC O11 C1 *N1 O12 0.0000 0.00 180.00 0.00 0.0000 + +RESI CBU 0.00 ! C4H8 cyclobutane, lsk & kevo +GROUP +ATOM C1 CG3C41 -0.18 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +GROUP +ATOM C2 CG3C41 -0.18 ! H12 H22 +ATOM H21 HGA2 0.09 ! | | +ATOM H22 HGA2 0.09 ! H11-C1--C2-H21 +GROUP ! | | +ATOM C3 CG3C41 -0.18 ! H41-C4--C3-H31 +ATOM H31 HGA2 0.09 ! | | +ATOM H32 HGA2 0.09 ! H42 H32 +GROUP +ATOM C4 CG3C41 -0.18 +ATOM H41 HGA2 0.09 +ATOM H42 HGA2 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C1 +BOND C1 H11 C1 H12 +BOND C2 H21 C2 H22 +BOND C3 H31 C3 H32 +BOND C4 H41 C4 H42 +IC C1 C2 C3 C4 0.0000 0.00 25.00 0.00 0.0000 +IC C4 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C3 *C2 H21 0.0000 0.00 120.00 0.00 0.0000 +IC C1 C3 *C2 H22 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C1 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C1 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 + +RESI AZDO 0.00 ! C3H5NO beta-lactam, 2-azetidinone, lsk & kevo +GROUP +ATOM N1 NG2R43 -0.54 +ATOM H1 HGP1 0.36 +GROUP +ATOM C2 CG2R53 0.29 ! H32 H31 +ATOM O2 OG2D1 -0.47 ! \ / +GROUP ! C3 +ATOM C3 CG3C41 -0.01 ! / \ +ATOM H31 HGA2 0.09 ! H41--C4 C2=O2 +ATOM H32 HGA2 0.09 ! / \ / +GROUP ! H42 N1 +ATOM C4 CG3C41 0.01 ! | +ATOM H41 HGA2 0.09 ! H1 +ATOM H42 HGA2 0.09 + +BOND N1 H1 C2 O2 +BOND C3 H31 C3 H32 +BOND C4 H41 C4 H42 +BOND N1 C2 C2 C3 C3 C4 C4 N1 +IMPR C2 C3 N1 O2 +IC N1 C2 C3 C4 0.0000 0.00 15.00 0.00 0.0000 +IC C2 C4 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C3 N1 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C4 C2 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 N1 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 N1 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 + +RESI ZOIC 0.000 ! C7H6O2 neutral benzoic acid, jal +GROUP +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 ! H3 H2 +ATOM C3 CG2R61 -0.115 ! \ ___ / +ATOM H3 HGR61 0.115 ! C3---C2 O7 +ATOM C4 CG2R61 -0.115 ! / \ // +ATOM H4 HGR61 0.115 ! H4--C4 C1--C7 +ATOM C5 CG2R61 -0.115 ! \\ // \ +ATOM H5 HGR61 0.115 ! C5---C6 O8--H8 +ATOM C6 CG2R61 -0.115 ! / \ +ATOM H6 HGR61 0.115 ! H5 H6 +GROUP +ATOM C1 CG2R61 0.080 +ATOM C7 CG2O2 0.460 +ATOM O7 OG2D1 -0.460 +ATOM O8 OG311 -0.510 +ATOM H8 HGP1 0.430 + +BOND C1 C2 C2 H2 C2 C3 C3 H3 C3 C4 C4 H4 +BOND C4 C5 C5 H5 C5 C6 C6 H6 C6 C1 +BOND C1 C7 C7 O7 C7 O8 O8 H8 +IMPR C7 C1 O7 O8 +! Seed can be either C1 C2 C3 (line 1-2) OR C6 C1 C2 (line 2-3) +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C1 C6 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C2 *C1 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C7 O8 0.0000 0.00 45.00 0.00 0.0000 +IC C1 O8 *C7 O7 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C7 O8 H8 0.0000 0.00 180.00 0.00 0.0000 + +RESI MBOA 0.000 ! C8H8O2 methylbenzoate, jal +GROUP +ATOM C2 CG2R61 -0.115 +ATOM H2 HGR61 0.115 ! H3 H2 +ATOM C3 CG2R61 -0.115 ! \ ___ / +ATOM H3 HGR61 0.115 ! C3---C2 O7 +ATOM C4 CG2R61 -0.115 ! / \ // +ATOM H4 HGR61 0.115 ! H4--C4 C1--C7 H81 +ATOM C5 CG2R61 -0.115 ! \\ // \ | +ATOM H5 HGR61 0.115 ! C5---C6 O8--C8--H83 +ATOM C6 CG2R61 -0.115 ! / \ | +ATOM H6 HGR61 0.115 ! H5 H6 H82 +GROUP +ATOM C1 CG2R61 0.080 +ATOM C7 CG2O2 0.460 +ATOM O7 OG2D1 -0.460 +ATOM O8 OG302 -0.310 +ATOM C8 CG331 -0.040 +ATOM H81 HGA3 0.090 +ATOM H82 HGA3 0.090 +ATOM H83 HGA3 0.090 + +BOND C1 C2 C2 H2 C2 C3 C3 H3 C3 C4 C4 H4 +BOND C4 C5 C5 H5 C5 C6 C6 H6 C6 C1 +BOND C1 C7 C7 O7 C7 O8 O8 C8 +BOND C8 H81 C8 H82 C8 H83 +IMPR C7 C1 O7 O8 +! Seed can be either C1 C2 C3 (line 1-2) OR C6 C1 C2 (line 2-3) +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C1 C6 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C2 *C1 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C1 C7 O8 0.0000 0.00 45.00 0.00 0.0000 +IC C1 O8 *C7 O7 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C7 O8 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C7 O8 C8 H83 0.0000 0.00 180.00 0.00 0.0000 +IC O8 H83 *C8 H81 0.0000 0.00 120.00 0.00 0.0000 +IC O8 H83 *C8 H82 0.0000 0.00 -120.00 0.00 0.0000 + +RESI 1EOX 0.00 ! C2H4O 1-ethylene oxide, sc +GROUP +ATOM O1 OG3C31 -0.40 +ATOM C1 CG3C31 0.02 ! H2 H3 +ATOM H1 HGA2 0.09 ! \ / +ATOM H2 HGA2 0.09 ! H1--C1--C2--H4 +ATOM C2 CG3C31 0.02 ! \ / +ATOM H3 HGA2 0.09 ! O1 +ATOM H4 HGA2 0.09 + +BOND C1 H1 C1 H2 C2 H3 C2 H4 +BOND C1 O1 C2 O1 +BOND C1 C2 +IC C1 O1 *C2 H1 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 O1 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 +IC O1 C2 *C1 H3 0.0000 0.00 120.00 0.00 0.0000 +IC O1 C2 *C1 H4 0.0000 0.00 -120.00 0.00 0.0000 + +RESI 1BOX 0.00 ! C4H8O 1-butene oxide, sc +GROUP +ATOM O1 OG3C31 -0.40 +ATOM C1 CG3C31 0.02 +ATOM H11 HGA2 0.09 +ATOM H12 HGA2 0.09 +ATOM C2 CG3C31 0.11 +ATOM H2 HGA1 0.09 +ATOM C3 CG321 -0.18 ! H12 H2 H31 H41 +ATOM H31 HGA2 0.09 ! \ | | | +ATOM H32 HGA2 0.09 ! H11--C1--C2--C3--C4--H42 +ATOM C4 CG331 -0.27 ! \ / | | +ATOM H41 HGA3 0.09 ! O1 H32 H43 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 H11 C1 H12 C2 H2 C3 H31 C3 H32 C4 H41 C4 H42 C4 H43 +BOND C1 O1 C2 O1 +BOND C1 C2 C2 C3 C3 C4 +IC C1 O1 *C2 C3 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 O1 *C2 H2 0.0000 0.00 120.00 0.00 0.0000 +IC O1 C2 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC O1 C2 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC C1 C2 C3 C4 0.0000 0.00 -140.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C3 C4 H43 0.0000 0.00 180.00 0.00 0.0000 +IC C3 H43 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 H43 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 + +RESI PMST 0.00 ! C7H8O3S phenyl methanesulfonate, xxwy +GROUP +ATOM S1 SG3O2 0.24 +ATOM C2 CG331 0.05 +ATOM H21 HGA3 0.09 +ATOM H22 HGA3 0.09 ! O11 O12 HE1 HD1 +ATOM H23 HGA3 0.09 ! \\ // | | +ATOM O11 OG2P1 -0.32 ! S1 CE1--CD1 +ATOM O12 OG2P1 -0.32 ! / \ // \\ +ATOM O3 OG303 -0.24 ! H21--C2 O3---CZ CG--HG +ATOM CZ CG2R61 0.32 ! / | \ __ / +ATOM CE1 CG2R61 -0.115 ! H22 H23 CE2--CD2 +ATOM HE1 HGR61 0.115 ! | | +ATOM CE2 CG2R61 -0.115 ! HE2 HD2 +ATOM HE2 HGR61 0.115 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 + +BOND S1 C2 C2 H21 C2 H22 C2 H23 +BOND S1 O11 S1 O12 S1 O3 +BOND O3 CZ CZ CE1 CZ CE2 CE1 HE1 CE2 HE2 +BOND CE1 CD1 CE2 CD2 CD1 HD1 CD2 HD2 +BOND CD1 CG CD2 CG CG HG +IC C2 O3 *S1 O11 0.0000 0.00 113.00 0.00 0.0000 +IC C2 O3 *S1 O12 0.0000 0.00 -113.00 0.00 0.0000 +IC O3 S1 C2 H21 0.0000 0.00 180.00 0.00 0.0000 +IC H21 S1 *C2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC H21 S1 *C2 H23 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 S1 O3 CZ 0.0000 0.00 180.00 0.00 0.0000 +IC S1 O3 CZ CE1 0.0000 0.00 90.00 0.00 0.0000 +IC O3 CE1 *CZ CE2 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CZ CE1 CD1 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 +IC CZ CE1 CD1 CG 0.0000 0.00 0.00 0.00 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC CG CE1 *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CG CE2 *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.00 180.00 0.00 0.0000 + +RESI MSMT 0.00 ! CH5NO3S methyl sulfamate, xxwy +GROUP +ATOM S1 SG3O2 0.22 +ATOM N2 NG321 -0.46 +ATOM H21 HGP1 0.35 ! O11 O12 +ATOM H22 HGP1 0.35 ! \\ // +ATOM O11 OG2P1 -0.28 ! S1 H41 +ATOM O12 OG2P1 -0.28 ! / \ / +ATOM O3 OG303 -0.24 ! H21--N2 O3---C4--H42 +ATOM C4 CG331 0.07 ! / \ +ATOM H41 HGA3 0.09 ! H22 H43 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND S1 N2 N2 H21 N2 H22 +BOND S1 O11 S1 O12 S1 O3 +BOND O3 C4 C4 H41 C4 H42 C4 H43 +IC N2 O3 *S1 O11 0.0000 0.00 113.00 0.00 0.0000 +IC N2 O3 *S1 O12 0.0000 0.00 -113.00 0.00 0.0000 +IC O3 S1 N2 H21 0.0000 0.00 -60.00 0.00 0.0000 +IC H21 S1 *N2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC N2 S1 O3 C4 0.0000 0.00 180.00 0.00 0.0000 +IC S1 O3 C4 H41 0.0000 0.00 180.00 0.00 0.0000 +IC H41 O3 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC H41 O3 *C4 H43 0.0000 0.00 -120.00 0.00 0.0000 + +RESI PSMT 0.00 ! C6H7NO3S phenyl sulfamate, xxwy +GROUP +ATOM S1 SG3O2 0.22 +ATOM N2 NG321 -0.46 +ATOM H21 HGP1 0.35 ! O11 O12 HE1 HD1 +ATOM H22 HGP1 0.35 ! \\ // | | +ATOM O11 OG2P1 -0.28 ! S1 CE1--CD1 +ATOM O12 OG2P1 -0.28 ! / \ // \\ +ATOM O3 OG303 -0.24 ! H21--N2 O3---CZ CG--HG +ATOM CZ CG2R61 0.34 ! / \ __ / +ATOM CE1 CG2R61 -0.115 ! H22 CE2--CD2 +ATOM HE1 HGR61 0.115 ! | | +ATOM CE2 CG2R61 -0.115 ! HE2 HD2 +ATOM HE2 HGR61 0.115 +ATOM CD1 CG2R61 -0.115 +ATOM HD1 HGR61 0.115 +ATOM CD2 CG2R61 -0.115 +ATOM HD2 HGR61 0.115 +ATOM CG CG2R61 -0.115 +ATOM HG HGR61 0.115 + +BOND S1 N2 N2 H21 N2 H22 +BOND S1 O11 S1 O12 S1 O3 +BOND O3 CZ CZ CE1 CZ CE2 CE1 HE1 CE2 HE2 +BOND CE1 CD1 CE2 CD2 CD1 HD1 CD2 HD2 +BOND CD1 CG CD2 CG CG HG +IC N2 O3 *S1 O11 0.0000 0.00 113.00 0.00 0.0000 +IC N2 O3 *S1 O12 0.0000 0.00 -113.00 0.00 0.0000 +IC O3 S1 N2 H21 0.0000 0.00 -60.00 0.00 0.0000 +IC H21 S1 *N2 H22 0.0000 0.00 120.00 0.00 0.0000 +IC N2 S1 O3 CZ 0.0000 0.00 180.00 0.00 0.0000 +IC S1 O3 CZ CE1 0.0000 0.00 90.00 0.00 0.0000 +IC O3 CE1 *CZ CE2 0.0000 0.00 180.00 0.00 0.0000 +IC CE2 CZ CE1 CD1 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 CZ CE2 CD2 0.0000 0.00 0.00 0.00 0.0000 +IC CZ CE1 CD1 CG 0.0000 0.00 0.00 0.00 0.0000 +IC CZ CD1 *CE1 HE1 0.0000 0.00 180.00 0.00 0.0000 +IC CZ CD2 *CE2 HE2 0.0000 0.00 180.00 0.00 0.0000 +IC CG CE1 *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CG CE2 *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000 +IC CD1 CD2 *CG HG 0.0000 0.00 180.00 0.00 0.0000 + +RESI OBTZ 0.00 ! C7H8N2O2S 1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine model compound for drug hydrochlorothiazide, xxwy +GROUP +ATOM S1 SG3O2 0.33 +ATOM N2 NG311 -0.55 +ATOM H2 HGP1 0.38 ! H6 H4 +ATOM O11 OG2P1 -0.34 ! | | +ATOM O12 OG2P1 -0.34 ! C6 N4 H31 +ATOM C3 CG321 0.29 ! // \ / \ / +ATOM H31 HGA2 0.09 ! H7---C7 C5 C3---H32 +ATOM H32 HGA2 0.09 ! | || | +ATOM N4 NG311 -0.76 ! H8---C8 C10 N2---H2 +ATOM H4 HGPAM1 0.39 ! \\ / \ / +ATOM C5 CG2R61 0.32 ! C9 S1 +ATOM C6 CG2R61 -0.115 ! | // \\ +ATOM H6 HGR61 0.115 ! H9 O11 O12 +ATOM C7 CG2R61 -0.115 +ATOM H7 HGR61 0.115 +ATOM C8 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM C9 CG2R61 -0.115 +ATOM H9 HGR61 0.115 +ATOM C10 CG2R61 0.100 + +BOND S1 N2 N2 C3 C3 N4 N4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 S1 +BOND C5 C10 S1 O11 S1 O12 N2 H2 C3 H31 +BOND C3 H32 N4 H4 C6 H6 C7 H7 C8 H8 C9 H9 +IC C5 C10 S1 N2 0.0000 0.00 -20.00 0.00 0.0000 +IC S1 C10 C5 N4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 N4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC S1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C10 N2 *S1 O11 0.0000 0.00 -120.00 0.00 0.0000 +IC C10 N2 *S1 O12 0.0000 0.00 120.00 0.00 0.0000 +IC S1 C3 *N2 H2 0.0000 0.00 120.00 0.00 0.0000 +IC N2 N4 *C3 H31 0.0000 0.00 -120.00 0.00 0.0000 +IC N2 N4 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *N4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI AOBT 0.00 ! C8H12N2O2S acyclic model compound for OBTZ, xxwy +GROUP +ATOM S1 SG3O2 0.56 +ATOM N2 NG311 -0.60 +ATOM H2 HGP1 0.37 +ATOM O11 OG2P1 -0.43 ! H6 H4 +ATOM O12 OG2P1 -0.43 ! | | +ATOM C3 CG321 0.21 ! C6 N4 H31 +ATOM H31 HGA2 0.09 ! // \ / \ / +ATOM H32 HGA2 0.09 ! H7---C7 C5 C3---H32 +ATOM N4 NG311 -0.56 ! | || | +ATOM H4 HGPAM1 0.37 ! H8---C8 C10 N2--H2 HS1 +ATOM C5 CG2R61 0.05 ! \\ / | \ / +ATOM C6 CG2R61 -0.115 ! C9 H10 S1---CS--HS2 +ATOM H6 HGR61 0.115 ! | // \\ \ +ATOM C7 CG2R61 -0.115 ! H9 O11 O12 HS3 +ATOM H7 HGR61 0.115 +ATOM C8 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM C9 CG2R61 -0.115 +ATOM H9 HGR61 0.115 +ATOM C10 CG2R61 -0.115 +ATOM H10 HGR61 0.115 +ATOM CS CG331 0.010 +ATOM HS1 HGA3 0.090 +ATOM HS2 HGA3 0.090 +ATOM HS3 HGA3 0.090 + +BOND S1 N2 N2 C3 C3 N4 N4 C5 C5 C6 +BOND C6 C7 C7 C8 C8 C9 C9 C10 C10 H10 +BOND C5 C10 S1 O11 S1 O12 N2 H2 C3 H31 +BOND C3 H32 N4 H4 C6 H6 C7 H7 C8 H8 C9 H9 +BOND S1 CS CS HS1 CS HS2 CS HS3 +IC CS S1 N2 C3 0.0000 0.00 -60.00 0.00 0.0000 +IC S1 N2 C3 N4 0.0000 0.00 180.00 0.00 0.0000 +IC N2 C3 N4 C5 0.0000 0.00 60.00 0.00 0.0000 +IC C3 N4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C6 *C5 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C5 C10 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC N2 S1 CS HS1 0.0000 0.00 180.00 0.00 0.0000 +IC HS1 S1 *CS HS2 0.0000 0.00 120.00 0.00 0.0000 +IC HS1 S1 *CS HS3 0.0000 0.00 -120.00 0.00 0.0000 +IC CS N2 *S1 O11 0.0000 0.00 -120.00 0.00 0.0000 +IC CS N2 *S1 O12 0.0000 0.00 120.00 0.00 0.0000 +IC S1 C3 *N2 H2 0.0000 0.00 120.00 0.00 0.0000 +IC N2 N4 *C3 H31 0.0000 0.00 -120.00 0.00 0.0000 +IC N2 N4 *C3 H32 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *N4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C5 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 + +!New compounds by "team CGenFF", Feb 15 +RESI 2BTY 0.000 ! C4H6 2-butyne, kevo & rima +GROUP +ATOM C1 CG331 -0.19 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 +ATOM H13 HGA3 0.09 ! H11 H41 +ATOM C2 CG1T1 -0.08 ! | __ | +GROUP ! H12--C1--C2==C3--C4--H42 +ATOM C3 CG1T1 -0.08 ! | | +ATOM C4 CG331 -0.19 ! H13 H43 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 +BOND C1 H11 C1 H12 C1 H13 +BOND C4 H41 C4 H42 C4 H43 +!!Just a test +!DIHE H11 C2 C3 H41 +!DIHE H11 C2 C3 H42 +!DIHE H11 C2 C3 H43 +!DIHE H12 C2 C3 H41 +!DIHE H12 C2 C3 H42 +!DIHE H12 C2 C3 H43 +!DIHE H13 C2 C3 H41 +!DIHE H13 C2 C3 H42 +!DIHE H13 C2 C3 H43 +IC C1 C2 C3 C4 0.0000 179.90 0.00 179.90 0.0000 +IC C3 C2 C1 H11 0.0000 179.90 0.00 0.00 0.0000 +IC C2 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 H11 *C1 H13 0.0000 0.00 240.00 0.00 0.0000 +IC C2 C3 C4 H41 0.0000 179.90 0.00 0.00 0.0000 +IC C3 H41 *C4 H42 0.0000 0.00 120.00 0.00 0.0000 +IC C3 H41 *C4 H43 0.0000 0.00 240.00 0.00 0.0000 + +RESI PRPY 0.000 ! C3H4 propyne, xxwy, mnoon, rima & kevo +GROUP +ATOM C1 CG331 -0.14 +ATOM H11 HGA3 0.09 ! H11 +ATOM H12 HGA3 0.09 ! | __ +ATOM H13 HGA3 0.09 ! H12--C1--C2==C3--H31 +ATOM C2 CG1T1 -0.01 ! | +ATOM C3 CG1T2 -0.41 ! H13 +ATOM H31 HGPAM1 0.29 + +BOND C1 C2 C2 C3 C3 H31 +BOND C1 H11 C1 H12 C1 H13 +IC C1 C2 C3 H31 0.0000 179.90 0.00 179.90 0.0000 +IC C3 C2 C1 H11 0.0000 179.90 0.00 0.00 0.0000 +IC C2 H11 *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC C2 H11 *C1 H13 0.0000 0.00 240.00 0.00 0.0000 + +RESI CYPE 0.000 ! C5H8 cyclopentene abar & rima +GROUP +ATOM C1 CG2R51 -0.12 +ATOM H1 HGR51 0.12 +ATOM C2 CG2R51 -0.12 ! H2 H31 H32 +ATOM H2 HGR51 0.12 ! \ \ / +ATOM C3 CG3C52 -0.18 ! C2---C3 H41 +ATOM H31 HGA2 0.09 ! || \ / +ATOM H32 HGA2 0.09 ! || C4 +ATOM C4 CG3C52 -0.18 ! || / \ +ATOM H41 HGA2 0.09 ! C1---C5 H42 +ATOM H42 HGA2 0.09 ! / / \ +ATOM C5 CG3C52 -0.18 ! H1 H51 H52 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND C1 C2 C1 C5 C1 H1 C2 C3 C2 H2 +BOND C3 C4 C3 H31 C3 H32 +BOND C4 C5 C4 H41 C4 H42 C5 H51 C5 H52 +IC C1 C2 C3 C4 0.0000 0.00 0.0 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.0 0.00 0.0000 +IC C5 C2 *C1 H1 0.0000 0.00 180.0 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.0 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.0 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.0 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.0 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.0 0.00 0.0000 +IC C4 C1 *C5 H51 0.0000 0.00 120.0 0.00 0.0000 +IC C4 C1 *C5 H52 0.0000 0.00 -120.0 0.00 0.0000 + +RESI 13BPO 0.00 ! C8H8N2 1,3-bipyrrole, lf +GROUP +ATOM N1 NG2R57 -0.35 +ATOM C2 CG2R51 -0.04 +ATOM H2 HGR52 0.14 +ATOM C3 CG2R51 -0.25 +ATOM H3 HGR51 0.15 +ATOM C4 CG2R51 -0.25 ! H4 H5 H9 H10 +ATOM H4 HGR51 0.15 ! \ / \ / +ATOM C5 CG2R51 -0.04 ! C4==C5 C9==C10 +ATOM H5 HGR52 0.14 ! | \ / | +ATOM N6 NG2R51 -0.35 ! | N1--C8 | +ATOM H6 HGP1 0.35 ! | / \ | +ATOM C7 CG2R51 -0.04 ! C3==C2 C7--N6 +ATOM H7 HGR52 0.14 ! / \ / \ +ATOM C8 CG2R57 0.25 ! H3 H2 H7 H6 +ATOM C9 CG2R51 -0.25 +ATOM H9 HGR51 0.15 +ATOM C10 CG2R51 -0.04 +ATOM H10 HGR52 0.14 + +BOND N1 C5 N1 C2 N1 C8 C2 C3 C2 H2 +BOND C3 C4 C3 H3 C4 C5 C4 H4 C5 H5 +BOND N6 C10 N6 C7 N6 H6 C7 C8 C7 H7 +BOND C8 C9 C9 C10 C9 H9 C10 H10 +IC N1 C8 C7 N6 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C7 *C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C2 *N1 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C8 N1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C8 N1 C5 C4 0.0000 0.00 180.00 0.00 0.0000 +IC C8 N6 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C10 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C8 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 + +RESI 11BPO 0.00 ! C8H8N2 1,1-bipyrrole, lf +GROUP +ATOM C2 CG2R51 -0.04 +ATOM H2 HGR52 0.14 +ATOM N1 NG2R57 0.00 +ATOM C5 CG2R51 -0.04 +ATOM H5 HGR52 0.14 +ATOM C4 CG2R51 -0.25 ! H4 H5 H7 H8 +ATOM H4 HGR51 0.15 ! \ / \ / +ATOM C3 CG2R51 -0.25 ! C4==C5 C7==C8 +ATOM H3 HGR51 0.15 ! | \ / | +ATOM C8 CG2R51 -0.25 ! | N1--N6 | +ATOM H8 HGR51 0.15 ! | / \ | +ATOM C7 CG2R51 -0.04 ! C3==C2 C10==C9 +ATOM H7 HGR52 0.14 ! / \ / \ +ATOM N6 NG2R57 0.00 ! H3 H2 H10 H9 +ATOM C10 CG2R51 -0.04 +ATOM H10 HGR52 0.14 +ATOM C9 CG2R51 -0.25 +ATOM H9 HGR51 0.15 + +BOND C2 H2 C2 N1 C2 C3 N1 C5 N1 N6 +BOND C5 H5 C5 C4 C4 H4 C4 C3 C3 H3 +BOND C8 H8 C8 C7 C8 C9 C7 H7 +BOND C7 N6 N6 C10 C10 H10 C10 C9 C9 H9 +IC N1 N6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C7 *N6 C10 0.0000 0.00 180.00 0.00 0.0000 +IC N1 N6 C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C7 N6 N1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC N6 C2 *N1 C5 0.0000 0.00 180.00 0.00 0.0000 +IC N6 N1 C5 C4 0.0000 0.00 180.00 0.00 0.0000 +IC N6 N1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 + +RESI 33BPO 0.00 ! C8H8N2 3,3-bipyrrole, lf +GROUP +ATOM C5 CG2R51 -0.04 +ATOM H5 HGR52 0.14 +ATOM C4 CG2R57 -0.10 +ATOM C3 CG2R51 -0.25 +ATOM H3 HGR51 0.15 +ATOM C2 CG2R51 -0.04 ! H2 H3 H9 H10 +ATOM H2 HGR52 0.14 ! \ / \ / +ATOM N1 NG2R51 -0.35 ! C2==C3 C9==C10 +ATOM H1 HGP1 0.35 ! | \ / | +ATOM C10 CG2R51 -0.04 ! | C4--C8 | +ATOM H10 HGR52 0.14 ! | // \\ | +ATOM C9 CG2R51 -0.25 ! N1--C5 C7--N6 +ATOM H9 HGR51 0.15 ! / \ / \ +ATOM C8 CG2R57 -0.10 ! H1 H5 H7 H6 +ATOM C7 CG2R51 -0.04 +ATOM H7 HGR52 0.14 +ATOM N6 NG2R51 -0.35 +ATOM H6 HGP1 0.35 + +BOND C5 H5 C5 C4 C5 N1 C4 C3 C4 C8 +BOND C3 H3 C3 C2 C2 H2 C2 N1 N1 H1 +BOND C10 H10 C10 C9 C10 N6 C9 H9 +BOND C9 C8 C8 C7 C7 H7 C7 N6 N6 H6 +IC C4 C8 C7 N6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C7 *C8 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C8 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C5 *C4 C3 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C4 C3 C2 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C4 C5 N1 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C5 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C10 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C9 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 + +RESI TRZ2 0.00 ! C2H3N3 2H-1,2,3-triazole, lf +GROUP ! H4 +ATOM C4 CG2R52 0.06 ! \ +ATOM H4 HGR52 0.16 ! C4==N3 +ATOM C5 CG2R52 0.06 ! | \ +ATOM H5 HGR52 0.16 ! | N2--H2 +ATOM N1 NG2R50 -0.55 ! | / +ATOM N2 NG2R51 0.39 ! C5==N1 +ATOM H2 HGP1 0.27 ! / +ATOM N3 NG2R50 -0.55 ! H5 + +BOND C4 H4 C4 C5 C4 N3 C5 H5 +BOND C5 N1 N1 N2 N2 H2 N2 N3 +IC N1 N2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC N2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC N1 N3 *N2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 N1 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 + +RESI 22BPY 0.000 ! C10H8N2 2,2'-bipyridine, kevo +GROUP +ATOM N1 NG2R60 -0.600 +ATOM C2 CG2R67 0.300 ! H5 +ATOM C3 CG2R61 -0.115 ! | +ATOM H3 HGR61 0.115 ! C5 +ATOM C4 CG2R61 -0.115 ! // \ +ATOM H4 HGR61 0.115 ! H6--C6 C4--H4 +ATOM C5 CG2R61 -0.115 ! | || +ATOM H5 HGR61 0.115 ! N1 C3--H3 +ATOM C6 CG2R61 0.180 ! \\ / +ATOM H6 HGR62 0.120 ! C2 +GROUP ! | +ATOM N7 NG2R60 -0.600 ! C8 +ATOM C8 CG2R67 0.300 ! // \ +ATOM C9 CG2R61 -0.115 ! H9--C9 N7 +ATOM H9 HGR61 0.115 ! | || +ATOM C10 CG2R61 -0.115 ! H10-C10 C12-H12 +ATOM H10 HGR61 0.115 ! \\ / +ATOM C11 CG2R61 -0.115 ! C11 +ATOM H11 HGR61 0.115 ! | +ATOM C12 CG2R61 0.180 ! H11 +ATOM H12 HGR62 0.120 + +BOND N1 C2 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C6 N1 C3 H3 C4 H4 C5 H5 C6 H6 +BOND C2 C8 +BOND N7 C8 C8 C9 C9 C10 C10 C11 C11 C12 +BOND C12 N7 C9 H9 C10 H10 C11 H11 C12 H12 +!Special! Use IC SEED C2 C8 N7 for cleaner dipoles for asymmetric conformations! +IC C8 N1 *C2 C3 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C2 N1 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N1 C2 C8 N7 0.0000 0.00 175.00 0.00 0.0000 ! deliberate distortion +IC C2 N7 *C8 C9 0.0000 0.00 180.00 0.00 0.0000 ! use in reverse order as IC SEED +IC N7 C8 C9 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C8 N7 C12 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 N7 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 + +RESI ETRZ 0.000 ! C4H7N3 1-ethyl-1,2,3-triazole, kevo +GROUP +ATOM N1 NG2R51 0.28 +ATOM N2 NG2R50 -0.37 +ATOM N3 NG2R50 -0.41 +ATOM C4 CG2R51 0.25 ! H4 H5 H71 H72 +ATOM H4 HGR52 0.11 ! \ ___ / | / +ATOM C5 CG2R51 -0.35 ! C4---C5 C7--H73 +ATOM H5 HGR52 0.20 ! | \ / +ATOM C6 CG321 0.11 ! | N1---C6 +ATOM H61 HGA2 0.09 ! |___ / | \ +ATOM H62 HGA2 0.09 ! N3---N2 H61 H62 +GROUP +ATOM C7 CG331 -0.27 +ATOM H71 HGA3 0.09 +ATOM H72 HGA3 0.09 +ATOM H73 HGA3 0.09 + +BOND N1 C5 N1 N2 N1 C6 N2 N3 N3 C4 +BOND C4 C5 C4 H4 C5 H5 C6 C7 C6 H61 +BOND C6 H62 C7 H71 C7 H72 C7 H73 +IC N1 N2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC N3 N2 N1 C5 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 N1 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N2 *N1 C6 0.0000 0.00 180.00 0.00 0.0000 +IC N2 N1 C6 C7 0.0000 0.00 90.00 0.00 0.0000 ! rotatable bond +IC N1 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC N1 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC N1 C6 C7 H73 0.0000 0.00 180.00 0.00 0.0000 +IC C6 H73 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 +IC C6 H73 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 + +RESI YTHY 0.00 ! C8H6N2O2 2,4(1H,3H)-quinazolinedione (CAS # 86-96-4), isg +GROUP +ATOM C1 CG2R61 -0.115 +ATOM C2 CG2R61 -0.115 +ATOM C3 CG2R61 -0.115 +ATOM C4 CG2R62 0.340 +ATOM C5 CG2R62 -0.070 ! H6 O8 +ATOM C6 CG2R61 -0.115 ! | || +ATOM H6 HGR61 0.115 ! C6 C8 H9 +ATOM C8 CG2R63 0.510 ! // \ / \ / +ATOM N9 NG2R61 -0.570 ! H1--C1 C5 N9 +ATOM C10 CG2R63 0.450 ! | || | +ATOM N11 NG2R61 -0.490 ! H2--C2 C4 C10 +ATOM H11 HGP1 0.360 ! \\ / \ / \\ +ATOM O10 OG2D4 -0.450 ! C3 N11 O10 +ATOM H9 HGP1 0.390 ! | | +ATOM O8 OG2D4 -0.470 ! H3 H11 +ATOM H3 HGR61 0.115 +ATOM H2 HGR61 0.115 +ATOM H1 HGR61 0.115 + +BOND C1 C2 C1 H1 C2 C3 C2 H2 C3 C4 C3 H3 +BOND C4 C5 C5 C6 C5 C8 C6 C1 C6 H6 C8 N9 +BOND C8 O8 N9 C10 N9 H9 C10 N11 C10 O10 N11 C4 N11 H11 +IMPR C8 C5 N9 O8 +IMPR C10 N9 N11 O10 +IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C4 N11 C10 0.0000 0.00 -1.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N9 *C8 O8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N9 N11 *C10 O10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 + +RESI RIN 0.000 ! C9H6O2 coumarin (CAS # 91-64-5), isg +GROUP +ATOM C7 CG2R61 -0.115 +ATOM C6 CG2R61 -0.115 +ATOM C5 CG2R62 -0.010 +ATOM C10 CG2R62 0.400 ! H6 H4 +ATOM C9 CG2R61 -0.115 ! | | +ATOM C8 CG2R61 -0.115 ! C6 C4 H3 +ATOM H4 HGR62 0.230 ! // \ / \\ / +ATOM H7 HGR61 0.115 ! H7--C7 C5 C3 +ATOM H6 HGR61 0.115 ! | || | +ATOM C4 CG2R62 -0.230 ! H8--C8 C10 C2 +ATOM H9 HGR61 0.115 ! \\ / \ / \\ +ATOM H8 HGR61 0.115 ! C9 O1 O2 +ATOM C3 CG2R62 -0.260 ! | +ATOM H3 HGR62 0.200 ! H9 +ATOM O1 OG3R60 -0.360 +ATOM C2 CG2R63 0.490 +ATOM O2 OG2D4 -0.460 + +BOND C7 C6 C7 C8 C7 H7 C6 C5 C6 H6 C5 C10 C5 C4 +BOND C10 C9 C10 O1 C9 C8 C9 H9 C8 H8 H4 C4 C4 C3 +BOND C3 H3 C3 C2 O1 C2 C2 O2 +IMPR C2 C3 O2 O1 +IC C5 C10 O1 C2 0.0000 0.00 -1.00 0.00 0.0000 +IC O1 C10 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C5 C4 C3 0.0000 0.00 0.00 0.00 0.0000 +IC O1 C5 *C10 C9 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C10 *C5 C6 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C5 C6 C7 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C10 C9 C8 0.0000 0.00 0.00 0.00 0.0000 +IC O1 C3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C7 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C8 *C7 H7 0.0000 0.00 180.00 0.00 0.0000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 + +RESI YTS2 0.00 ! C8H6N2S2 2,4(1H,3H)-quinazolinedithione (CAS # 5993-69-1), isg +GROUP +ATOM C1 CG2R61 -0.115 +ATOM C2 CG2R61 -0.115 +ATOM C3 CG2R61 -0.115 +ATOM C4 CG2R61 0.490 +ATOM C5 CG2R61 0.120 ! H6 S8 +ATOM C6 CG2R61 -0.115 ! | || +ATOM H1 HGR61 0.115 ! C6 C8 H9 +ATOM H2 HGR61 0.115 ! // \ / \ / +ATOM H3 HGR61 0.115 ! H1--C1 C5 N9 +ATOM H6 HGR61 0.115 ! | || | +ATOM C8 CG2R63 0.100 ! H2--C2 C4 C10 +ATOM S8 SG2D1 -0.240 ! \\ / \ / \\ +ATOM N9 NG2R61 -0.600 ! C3 N11 S10 +ATOM H9 HGP1 0.420 ! | | +ATOM C10 CG2R63 0.140 ! H3 H11 +ATOM S10 SG2D1 -0.240 +ATOM N11 NG2R61 -0.600 +ATOM H11 HGP1 0.410 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 H1 C1 H2 C2 +BOND H3 C3 H6 C6 C5 C8 C8 S8 C8 N9 N9 H9 N9 C10 +BOND C10 S10 C10 N11 N11 H11 N11 C4 C6 C1 +IMPR C8 C5 N9 S8 +IMPR C10 N9 N11 S10 +IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N9 *C8 S8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N9 N11 *C10 S10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 + +RESI YT4S 0.00 ! C8H6N2OS 2,3-dihydro-2-thioxo-4(1H)-quinazolinone (CAS # 13906-09-7), isg +GROUP +ATOM C1 CG2R61 -0.115 +ATOM C2 CG2R61 -0.115 +ATOM C3 CG2R61 -0.115 +ATOM C4 CG2R62 0.360 +ATOM C5 CG2R62 -0.050 ! H6 O8 +ATOM C6 CG2R61 -0.115 ! | || +ATOM H1 HGR61 0.115 ! C6 C8 H9 +ATOM H2 HGR61 0.115 ! // \ / \ / +ATOM H3 HGR61 0.115 ! H1--C1 C5 N9 +ATOM H6 HGR61 0.115 ! | || | +ATOM C8 CG2R63 0.500 ! H2--C2 C4 C10 +ATOM O8 OG2D4 -0.460 ! \\ / \ / \\ +ATOM N9 NG2R61 -0.410 ! C3 N11 S10 +ATOM H9 HGP1 0.370 ! | | +ATOM C10 CG2R63 -0.100 ! H3 H11 +ATOM S10 SG2D1 -0.240 +ATOM N11 NG2R61 -0.290 +ATOM H11 HGP1 0.320 + +BOND C1 C2 C1 H1 C1 C6 C2 C3 C2 H2 C3 C4 C3 H3 C4 C5 +BOND C4 N11 C5 C8 C5 C6 C6 H6 N11 H11 N11 C10 C10 S10 C10 N9 +BOND N9 H9 N9 C8 C8 O8 +IMPR C8 C5 N9 O8 +IMPR C10 N11 N9 S10 +IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N9 *C8 O8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N9 N11 *C10 S10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 + +RESI YT2S 0.00 ! C8H6N2OS 3,4-dihydro-4-thioxo-2(1H)-quinazolinone (CAS # 17796-47-3) isg +GROUP +ATOM C1 CG2R61 -0.115 +ATOM C2 CG2R61 -0.115 +ATOM C3 CG2R61 -0.115 +ATOM C4 CG2R62 0.340 +ATOM C5 CG2R62 -0.040 ! H6 S8 +ATOM C6 CG2R61 -0.115 ! | || +ATOM C8 CG2R63 0.110 ! C6 C8 H9 +ATOM S8 SG2D1 -0.280 ! // \ / \ / +ATOM N9 NG2R61 -0.310 ! H1--C1 C5 N9 +ATOM H9 HGP1 0.310 ! | || | +ATOM C10 CG2R63 0.440 ! H2--C2 C4 C10 +ATOM O10 OG2D4 -0.450 ! \\ / \ / \\ +ATOM N11 NG2R61 -0.490 ! C3 N11 O10 +ATOM H11 HGP1 0.370 ! | | +ATOM H1 HGR61 0.115 ! H3 H11 +ATOM H2 HGR61 0.115 +ATOM H3 HGR61 0.115 +ATOM H6 HGR61 0.115 + +BOND C1 C6 C1 H1 C1 C2 C2 H2 C2 C3 C3 H3 C3 C4 +BOND C4 C5 C4 N11 C5 C6 C6 H6 C5 C8 C8 S8 C8 N9 +BOND N9 H9 N9 C10 C10 O10 C10 N11 N11 H11 +IMPR C8 C5 N9 S8 +IMPR C10 N9 N11 O10 +IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N9 *C8 S8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N9 N11 *C10 O10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 + +RESI TC243C 0.00 ! C8H6N2O 4(3H)-quinazolinone (CAS # 491-36-1), isg +GROUP +ATOM H10 HGR62 0.150 +ATOM H3 HGR61 0.115 +ATOM H2 HGR61 0.115 +ATOM H1 HGR61 0.115 ! H6 O8 +ATOM H6 HGR61 0.115 ! | || +ATOM H9 HGP1 0.350 ! C6 C8 H9 +ATOM C10 CG2R64 0.440 ! // \ / \ / +ATOM N11 NG2R62 -0.770 ! H1--C1 C5 N9 +ATOM C4 CG2R62 0.340 ! | || | +ATOM C3 CG2R61 -0.115 ! H2--C2 C4 C10 +ATOM C2 CG2R61 -0.115 ! \\ / \ // \ +ATOM C1 CG2R61 -0.115 ! C3 N11 H10 +ATOM C6 CG2R61 -0.115 ! | +ATOM C5 CG2R62 0.190 ! H3 +ATOM C8 CG2R63 0.090 +ATOM O8 OG2D4 -0.400 +ATOM N9 NG2R61 -0.390 + +BOND C10 H10 C10 N11 C10 N9 N11 C4 C4 C3 C4 C5 C3 H3 +BOND C3 C2 C2 H2 C2 C1 C1 H1 C1 C6 C6 H6 C6 C5 +BOND C5 C8 C8 O8 C8 N9 N9 H9 +IMPR C8 C5 N9 O8 +IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C5 *C4 N11 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C8 N9 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N9 *C8 O8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *N9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC N9 N11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 + +RESI 4PYO 0.00 ! C5H5NO 4(1H)-pyridinone (CAS # 108-96-3), isg +GROUP +ATOM O1 OG2D4 -0.57 +ATOM C1 CG2R63 0.46 +ATOM C21 CG2R62 -0.38 ! H22 H32 +ATOM C31 CG2R62 -0.07 ! | | +ATOM N1 NG2R61 -0.11 ! C22==C32 +ATOM C32 CG2R62 -0.07 ! / \ +ATOM C22 CG2R62 -0.38 ! O1==C1 N1--H1 +ATOM H21 HGR62 0.22 ! \ / +ATOM H22 HGR62 0.22 ! C21==C31 +ATOM H32 HGR62 0.20 ! | | +ATOM H31 HGR62 0.20 ! H21 H31 +ATOM H1 HGP1 0.28 + +BOND O1 C1 C1 C21 C21 H21 C21 C31 C31 H31 C31 N1 N1 H1 +BOND N1 C32 C32 H32 C32 C22 C22 H22 C22 C1 +IMPR C1 C21 C22 O1 +IC C1 C22 C32 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C22 C32 N1 C31 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C32 N1 C31 C21 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C22 C21 *C1 O1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C32 C1 *C22 H22 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C31 C1 *C21 H21 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C22 *C32 H32 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C21 *C31 H31 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C32 C31 *N1 H1 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case + +RESI 1PH4PO 0.00 ! C11H9NO 1-phenyl-4(1H)-pyridinone (CAS # 39076-91-0), isg +GROUP +ATOM O4 OG2D4 -0.570 +ATOM C4 CG2R63 0.460 +ATOM C3 CG2R62 -0.380 +ATOM C2 CG2R62 -0.070 +ATOM N1 NG2R67 -0.110 +ATOM C6 CG2R62 -0.070 +ATOM C5 CG2R62 -0.380 +ATOM H3 HGR62 0.220 ! H5 H6 H8 H9 +ATOM H5 HGR62 0.220 ! | | | | +ATOM H6 HGR62 0.200 ! C5==C6 C8==C9 +ATOM H2 HGR62 0.200 ! / \ / \ +ATOM C7 CG2R67 0.280 ! O4==C4 N1--C7 C10--H10 +ATOM C8 CG2R61 -0.115 ! \ / \\ // +ATOM C9 CG2R61 -0.115 ! C3==C2 C12--C11 +ATOM C10 CG2R61 -0.115 ! | | | | +ATOM C11 CG2R61 -0.115 ! H3 H2 H12 H11 +ATOM C12 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND O4 C4 C4 C3 C4 C5 C3 C2 C3 H3 C5 H5 C2 N1 C2 H2 C5 C6 +BOND C6 H6 C6 N1 N1 C7 C7 C8 C7 C12 C12 C11 C12 H12 C8 C9 C8 H8 +BOND C11 C10 C11 H11 C9 C10 C9 H9 C10 H10 +IMPR C4 C3 C5 O4 +IC C4 C5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C5 C3 *C4 O4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C3 *C2 H2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI 21QU 0.00 ! C9H7NO 2(1H)-quinolinone (CAS # 59-31-4), isg +GROUP +ATOM C1 CG2R61 -0.115 +ATOM C2 CG2R61 -0.115 +ATOM C3 CG2R61 -0.115 +ATOM C4 CG2R62 0.280 +ATOM C5 CG2R62 -0.090 ! H6 H8 +ATOM C6 CG2R61 -0.115 ! | | +ATOM H11 HGP1 0.300 ! C6 C8 H9 +ATOM C8 CG2R62 -0.200 ! // \ / \\ / +ATOM C9 CG2R62 -0.180 ! H1--C1 C5 C9 +ATOM C10 CG2R63 0.240 ! | || | +ATOM N11 NG2R61 -0.260 ! H2--C2 C4 C10 +ATOM H6 HGR61 0.115 ! \\ / \ / \\ +ATOM H1 HGR61 0.115 ! C3 N11 O10 +ATOM H2 HGR61 0.115 ! | | +ATOM H3 HGR61 0.115 ! H3 H11 +ATOM H8 HGR62 0.220 +ATOM H9 HGR62 0.180 +ATOM O10 OG2D4 -0.490 + +BOND O10 C10 N11 C10 N11 H11 N11 C4 C10 C9 H3 C3 H2 C2 C4 C3 +BOND C4 C5 C3 C2 C2 C1 H9 C9 C9 C8 C1 H1 C1 C6 C5 C8 +BOND C5 C6 C8 H8 C6 H6 +IMPR C10 C9 N11 O10 +IC C5 C4 C3 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C5 *C4 N11 0.0000 0.00 179.00 0.00 0.0000 +IC C6 C4 *C5 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C8 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C4 N11 C10 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C5 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 N11 *C10 O10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C4 *N11 H11 0.0000 0.00 180.00 0.00 0.0000 + +RESI 1PH2PO 0.00 ! C11H9NO 1-phenyl-2(1H)-pyridinone (CAS # 13131-02-7), isg +GROUP +ATOM N1 NG2R67 -0.130 +ATOM C2 CG2R63 0.160 +ATOM O2 OG2D4 -0.480 +ATOM C3 CG2R62 -0.260 +ATOM H3 HGR62 0.220 +ATOM C4 CG2R62 -0.220 +ATOM H4 HGR62 0.220 +ATOM C5 CG2R62 -0.220 ! H3 O2 H8 H9 +ATOM H5 HGR62 0.150 ! | || | | +ATOM C6 CG2R62 0.150 ! C3--C2 C8==C9 +ATOM H6 HGR62 0.130 ! // \ / \ +ATOM C7 CG2R67 0.280 ! H4--C4 N1--C7 C10--H10 +ATOM C8 CG2R61 -0.115 ! \ / \\ // +ATOM C9 CG2R61 -0.115 ! C5==C6 C12--C11 +ATOM C10 CG2R61 -0.115 ! | | | | +ATOM C11 CG2R61 -0.115 ! H5 H6 H12 H11 +ATOM C12 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND C2 N1 C2 O2 C2 C3 C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 +BOND C5 C6 C6 H6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 +BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 +IMPR C2 C3 N1 O2 +IC C4 C5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI 3PHURA 0.00 ! C10H8N2O2 3-phenyl-2,4(1H,3H)-pyrimidinedione (CAS # 4260-40-6), isg +GROUP +ATOM N1 NG2R67 -0.530 +ATOM C2 CG2R63 0.400 +ATOM O2 OG2D4 -0.460 +ATOM C3 CG2R62 -0.200 +ATOM H3 HGR62 0.150 +ATOM C4 CG2R62 0.110 +ATOM H4 HGR62 0.180 +ATOM N5 NG2R61 -0.370 ! H3 O2 H8 H9 +ATOM H5 HGP1 0.350 ! | || | | +ATOM C6 CG2R63 0.440 ! C3--C2 C8==C9 +ATOM O6 OG2D4 -0.450 ! // \ / \ +ATOM C7 CG2R67 0.380 ! H4--C4 N1--C7 C10--H10 +ATOM C8 CG2R61 -0.115 ! \ / \\ // +ATOM C9 CG2R61 -0.115 ! N5--C6 C12--C11 +ATOM C10 CG2R61 -0.115 ! | || | | +ATOM C11 CG2R61 -0.115 ! H5 O6 H12 H11 +ATOM C12 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND C2 N1 C2 O2 C2 C3 C3 H3 C3 C4 C4 H4 C4 N5 N5 H5 +BOND N5 C6 C6 O6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 +BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 +IMPR C2 C3 N1 O2 +IMPR C6 N5 N1 O6 +IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *N5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N5 *C6 O6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI URA2S 0.00 ! C4H4N2OS 2,3-dihydro-2-thioxo-4(1H)pyrimidinone (CAS # 141-90-2), isg +GROUP +ATOM C2 CG2R63 -0.04 +ATOM C4 CG2R63 0.52 ! O4 +ATOM C5 CG2R62 -0.24 ! || +ATOM C6 CG2R62 0.08 ! C4 H3 +ATOM H1 HGP1 0.33 ! / \ / +ATOM H3 HGP1 0.37 ! H5--C5 N3 +ATOM H5 HGR62 0.17 ! || | +ATOM H6 HGR62 0.20 ! H6--C6 C2 +ATOM O4 OG2D4 -0.49 ! \ / \\ +ATOM S2 SG2D1 -0.30 ! N1 S2 +ATOM N1 NG2R61 -0.22 ! | +ATOM N3 NG2R61 -0.38 ! H1 + +BOND C2 S2 C2 N1 C2 N3 C4 C5 C4 O4 C4 N3 +BOND C5 C6 C5 H5 C6 H6 C6 N1 H1 N1 H3 N3 +IMPR C2 N1 N3 S2 +IMPR C4 C5 N3 O4 +IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C5 *C4 O4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *N3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C6 *N1 H1 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case + +RESI 3PH2SR 0.00 ! C10H8N2OS 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinone (CAS # 53632-80-7), isg +GROUP +ATOM N1 NG2R67 -0.380 +ATOM C2 CG2R63 0.520 +ATOM O2 OG2D4 -0.490 +ATOM C3 CG2R62 -0.240 +ATOM H3 HGR62 0.170 +ATOM C4 CG2R62 0.080 +ATOM H4 HGR62 0.200 +ATOM N5 NG2R61 -0.220 ! H3 O2 H8 H9 +ATOM H5 HGP1 0.330 ! | || | | +ATOM C6 CG2R63 -0.040 ! C3--C2 C8==C9 +ATOM S6 SG2D1 -0.300 ! // \ / \ +ATOM C7 CG2R67 0.370 ! H4--C4 N1--C7 C10--H10 +ATOM C8 CG2R61 -0.115 ! \ / \\ // +ATOM C9 CG2R61 -0.115 ! N5--C6 C12--C11 +ATOM C10 CG2R61 -0.115 ! | || | | +ATOM C11 CG2R61 -0.115 ! H5 S6 H12 H11 +ATOM C12 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND C2 N1 C2 O2 C2 C3 C3 H3 C3 C4 C4 H4 C4 N5 N5 H5 +BOND N5 C6 C6 S6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 +BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 +IMPR C2 C3 N1 O2 +IMPR C6 N5 N1 S6 +IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *N5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N5 *C6 S6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI URA4S 0.00 ! C4H4N2OS 3,4-dihydro-4-thioxo-2(1H)-pyrimidinone (CAS # 591-28-6), isg +GROUP +ATOM C2 CG2R63 0.41 +ATOM C4 CG2R63 0.11 ! S4 +ATOM C5 CG2R62 -0.31 ! || +ATOM C6 CG2R62 0.04 ! C4 H3 +ATOM H1 HGP1 0.35 ! / \ / +ATOM H3 HGP1 0.34 ! H5--C5 N3 +ATOM H5 HGR62 0.20 ! || | +ATOM H6 HGR62 0.23 ! H6--C6 C2 +ATOM S4 SG2D1 -0.28 ! \ / \\ +ATOM O2 OG2D4 -0.44 ! N1 O2 +ATOM N1 NG2R61 -0.30 ! | +ATOM N3 NG2R61 -0.35 ! H1 + +BOND C2 O2 C2 N1 C2 N3 C4 C5 C4 S4 C4 N3 C5 C6 +BOND C5 H5 C6 H6 C6 N1 H1 N1 H3 N3 +IMPR C2 N1 N3 O2 +IMPR C4 C5 N3 S4 +IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C5 *C4 S4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *N3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C6 *N1 H1 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case + +RESI 3PH4SR 0.00 ! C10H8N2OS 2,3-dihydro-3-phenyl-2-oxo-4(1H)pyrimidinethione, isg +GROUP +ATOM N1 NG2R67 -0.350 +ATOM C2 CG2R63 0.110 +ATOM S2 SG2D1 -0.280 +ATOM C3 CG2R62 -0.310 +ATOM H3 HGR62 0.200 +ATOM C4 CG2R62 0.040 +ATOM H4 HGR62 0.230 +ATOM N5 NG2R61 -0.300 ! H3 S2 H8 H9 +ATOM H5 HGP1 0.350 ! | || | | +ATOM C6 CG2R63 0.410 ! C3--C2 C8==C9 +ATOM O6 OG2D4 -0.440 ! // \ / \ +ATOM C7 CG2R67 0.340 ! H4--C4 N1--C7 C10--H10 +ATOM C8 CG2R61 -0.115 ! \ / \\ // +ATOM C9 CG2R61 -0.115 ! N5--C6 C12--C11 +ATOM C10 CG2R61 -0.115 ! | || | | +ATOM C11 CG2R61 -0.115 ! H5 O6 H12 H11 +ATOM C12 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND C2 N1 C2 S2 C2 C3 C3 H3 C3 C4 C4 H4 C4 N5 N5 H5 +BOND N5 C6 C6 O6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 +BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 +IMPR C2 C3 N1 S2 +IMPR C6 N5 N1 O6 +IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *N5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N5 *C6 O6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI URA24S 0.00 ! C4H4N2S2 2,4(1H,3H)-pyrimidinedithione (CAS # 2001-93-6), isg +GROUP +ATOM N1 NG2R61 -0.12 +ATOM C2 CG2R63 -0.13 ! S4 +ATOM N3 NG2R61 -0.17 ! || +ATOM C4 CG2R63 0.04 ! C4 H3 +ATOM C5 CG2R61 -0.17 ! / \ / +ATOM C6 CG2R61 -0.06 ! H5--C5 N3 +ATOM H1 HGP1 0.33 ! || | +ATOM H3 HGP1 0.32 ! H6--C6 C2 +ATOM H5 HGR62 0.19 ! \ / \\ +ATOM H6 HGR62 0.26 ! N1 S2 +ATOM S4 SG2D1 -0.26 ! | +ATOM S2 SG2D1 -0.23 ! H1 + +BOND N1 H1 N1 C2 N1 C6 C2 S2 C2 N3 N3 H3 N3 C4 +BOND C4 S4 C4 C5 C5 H5 C5 C6 C6 H6 +IMPR C2 N1 N3 S2 +IMPR C4 C5 N3 S4 +IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C5 *C4 S4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *N3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C6 *N1 H1 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case + +RESI 3PH24S 0.00 ! C10H8N2S2 2,3-dihydro-3-phenyl-2-thioxo-4(1H)pyrimidinethione, isg +GROUP +ATOM N1 NG2R67 -0.170 +ATOM C2 CG2R63 0.040 +ATOM S2 SG2D1 -0.260 +ATOM C3 CG2R61 -0.170 +ATOM H3 HGR62 0.190 +ATOM C4 CG2R61 -0.060 +ATOM H4 HGR62 0.260 +ATOM N5 NG2R61 -0.120 ! H3 S2 H8 H9 +ATOM H5 HGP1 0.330 ! | || | | +ATOM C6 CG2R63 -0.130 ! C3--C2 C8==C9 +ATOM S6 SG2D1 -0.230 ! // \ / \ +ATOM C7 CG2R67 0.320 ! H4--C4 N1--C7 C10--H10 +ATOM C8 CG2R61 -0.115 ! \ / \\ // +ATOM C9 CG2R61 -0.115 ! N5--C6 C12--C11 +ATOM C10 CG2R61 -0.115 ! | || | | +ATOM C11 CG2R61 -0.115 ! H5 S6 H12 H11 +ATOM C12 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND C2 N1 C2 S2 C2 C3 C3 H3 C3 C4 C4 H4 C4 N5 N5 H5 +BOND N5 C6 C6 S6 C6 N1 N1 C7 C7 C8 C7 C12 C8 H8 +BOND C8 C9 C9 H9 C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 +IMPR C2 C3 N1 S2 +IMPR C6 N5 N1 S6 +IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *N5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N5 *C6 S6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI 43HPY 0.00 ! C4H4N2O 4(3H)-pyrimidinone (CAS # 4562-27-0), isg +GROUP +ATOM C6 CG2R62 -0.21 +ATOM C5 CG2R62 0.35 ! O1 +ATOM N4 NG2R62 -0.76 ! || +ATOM C3 CG2R64 0.42 ! C1 H2 +ATOM N2 NG2R61 -0.30 ! / \ / +ATOM H2 HGP1 0.33 ! H6--C6 N2 +ATOM C1 CG2R63 0.21 ! || | +ATOM O1 OG2D4 -0.46 ! H5--C5 C3 +ATOM H6 HGR62 0.15 ! \ // \ +ATOM H5 HGR62 0.11 ! N4 H3 +ATOM H3 HGR62 0.16 + +BOND C6 C1 C6 C5 C6 H6 C5 N4 C5 H5 +BOND N4 C3 C3 N2 C3 H3 N2 H2 N2 C1 C1 O1 +IMPR C1 C6 N2 O1 +IC C1 N2 C3 N4 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N2 C3 N4 C5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C3 N4 C5 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N2 C6 *C1 O1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3 C1 *N2 H2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C5 C1 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N4 N2 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N4 C6 *C5 H5 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case + +RESI 43PPY 0.00 ! C10H8N2O 3-phenyl-4(3H)-pyrimidinone (CAS # 52090-51-4), isg +GROUP +ATOM N1 NG2R67 -0.300 +ATOM C2 CG2R63 0.210 +ATOM O2 OG2D4 -0.460 +ATOM C3 CG2R62 -0.210 +ATOM H3 HGR62 0.150 +ATOM C4 CG2R62 0.350 +ATOM H4 HGR62 0.110 ! H3 O2 H8 H9 +ATOM N5 NG2R62 -0.760 ! \ // \ / +ATOM C6 CG2R64 0.420 ! C3--C2 C8--C9 +ATOM H6 HGR62 0.160 ! // \ // \\ +ATOM C7 CG2R67 0.330 ! H4--C4 N1--C7 C10--H10 +ATOM C8 CG2R61 -0.115 ! \ / \ / +ATOM C9 CG2R61 -0.115 ! N5==C6 C12==C11 +ATOM C10 CG2R61 -0.115 ! \ / \ +ATOM C11 CG2R61 -0.115 ! H6 H12 H11 +ATOM C12 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND N1 C7 N1 C2 N1 C6 C2 O2 C2 C3 C3 H3 C3 C4 C4 H4 +BOND C4 N5 N5 C6 C6 H6 C7 C8 C8 H8 C8 C9 C9 H9 +BOND C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 C12 C7 +IMPR C2 C3 N1 O2 +IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C3 *C2 O2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI 43HSPY 0.00 ! C4H4N2S 4(3H)-pyrimidinethione (CAS # 1450-86-8), isg +GROUP +ATOM C6 CG2R61 -0.03 +ATOM C5 CG2R61 0.21 ! S1 +ATOM N4 NG2R62 -0.73 ! || +ATOM C3 CG2R64 0.59 ! C1 H2 +ATOM N2 NG2R61 -0.24 ! / \ / +ATOM H2 HGP1 0.32 ! H6--C6 N2 +ATOM C1 CG2R63 -0.37 ! || | +ATOM S1 SG2D1 -0.21 ! H5--C5 C3 +ATOM H6 HGR62 0.16 ! \ // \ +ATOM H5 HGR62 0.17 ! N4 H3 +ATOM H3 HGR62 0.13 + +BOND C1 S1 C1 N2 C1 C6 N2 H2 N2 C3 +BOND C3 H3 C3 N4 N4 C5 C5 H5 C5 C6 C6 H6 +IMPR C1 C6 N2 S1 +IC C1 N2 C3 N4 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N2 C3 N4 C5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C3 N4 C5 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N2 C6 *C1 S1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3 C1 *N2 H2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C5 C1 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N4 N2 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N4 C6 *C5 H5 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case + +RESI 43HSPP 0.00 ! C10H8N2S 3-phenyl-4(3H)-pyrimidinethione, isg +GROUP +ATOM N1 NG2R67 -0.240 +ATOM C2 CG2R63 -0.370 +ATOM S2 SG2D1 -0.210 +ATOM C3 CG2R61 -0.030 +ATOM H3 HGR62 0.160 +ATOM C4 CG2R61 0.210 +ATOM H4 HGR62 0.170 ! H3 S2 H8 H9 +ATOM N5 NG2R62 -0.730 ! \ // \ / +ATOM C6 CG2R64 0.590 ! C3--C2 C8--C9 +ATOM H6 HGR62 0.130 ! // \ // \\ +ATOM C7 CG2R67 0.320 ! H4--C4 N1--C7 C10--H10 +ATOM C8 CG2R61 -0.115 ! \ / \ / +ATOM C9 CG2R61 -0.115 ! N5==C6 C12==C11 +ATOM C10 CG2R61 -0.115 ! \ / \ +ATOM C11 CG2R61 -0.115 ! H6 H12 H11 +ATOM C12 CG2R61 -0.115 +ATOM H8 HGR61 0.115 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND N1 C7 N1 C2 N1 C6 C2 S2 C2 C3 C3 H3 C3 C4 C4 H4 +BOND C4 N5 N5 C6 C6 H6 C7 C8 C8 H8 C8 C9 C9 H9 +BOND C9 C10 C10 H10 C10 C11 C11 H11 C11 C12 C12 H12 C12 C7 +IMPR C2 C3 N1 S2 +IC C4 N5 C6 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C6 N1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 N1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C2 *N1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 N1 C7 C12 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 N1 *C7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C8 C7 C12 C11 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C7 C12 C11 C10 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C12 C11 C10 C9 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C9 C7 *C8 H8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C10 C8 *C9 H9 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C11 C9 *C10 H10 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C12 C10 *C11 H11 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C7 C11 *C12 H12 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI 4O2SM 0.00 ! C5H6N2OS 2-(methylthio)-4(3H)-pyrimidinone (CAS # 5751-20-2), isg +GROUP +ATOM N1 NG2R62 -0.76 +ATOM C2 CG2R64 0.58 ! O4 +ATOM N3 NG2R61 -0.30 ! || +ATOM C4 CG2R63 0.21 ! C4 H3 +ATOM C5 CG2R62 -0.21 ! / \ / +ATOM C6 CG2R62 0.35 ! H5--C5 N3 +ATOM H3 HGP1 0.33 ! || | +ATOM H5 HGR62 0.15 ! H6--C6 C2 +ATOM H6 HGR62 0.11 ! \ // \ +ATOM O4 OG2D4 -0.46 ! N1 S2 +ATOM S2 SG311 -0.07 ! | +ATOM C7 CG331 -0.20 ! H72--C7--H73 +ATOM H71 HGA3 0.09 ! | +ATOM H72 HGA3 0.09 ! H71 +ATOM H73 HGA3 0.09 + +BOND N1 C2 N1 C6 C2 S2 C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 +BOND C5 H5 C5 C6 C6 H6 S2 C7 C7 H71 C7 H72 C7 H73 +IMPR C4 C5 N3 O4 +IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C5 *C4 O4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 C4 *N3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C4 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N3 *C2 S2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C5 *C6 H6 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case +IC N3 C2 S2 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 S2 C7 H71 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C2 S2 C7 H72 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC C2 S2 C7 H73 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI 2SMPYR 0.00 ! C5H6N2S 2-(methylthio)-pyrimidine (CAS # 823-09-6), isg +GROUP +ATOM N1 NG2R62 -0.730 +ATOM C2 CG2R64 0.640 ! H6 +ATOM N3 NG2R62 -0.730 ! | +ATOM C4 CG2R61 0.290 ! C6 +ATOM C5 CG2R61 -0.115 ! / \\ +ATOM C6 CG2R61 0.290 ! H5--C5 N1 +ATOM H4 HGR62 0.120 ! || | +ATOM H5 HGR61 0.115 ! H4--C4 C2 +ATOM H6 HGR62 0.120 ! \ // \ +ATOM S7 SG311 -0.070 ! N3 S7 +ATOM C8 CG331 -0.200 ! | +ATOM H81 HGA3 0.090 ! H81--C8--H83 +ATOM H82 HGA3 0.090 ! | +ATOM H83 HGA3 0.090 ! H82 + +BOND N1 C2 N1 C6 C2 S7 C2 N3 N3 C4 C4 H4 C4 C5 +BOND C5 H5 C5 C6 C6 H6 S7 C8 C8 H81 C8 H82 C8 H83 +IC C4 N3 C2 N1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C2 N1 C6 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C2 N1 C6 C5 0.0000 0.0000 0.0000 0.0000 0.0000 +IC N3 C5 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4 C6 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 C5 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N1 N3 *C2 S7 0.0000 0.0000 179.0000 0.0000 0.0000 ! deliberately distorted for test case +IC N3 C2 S7 C8 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C2 S7 C8 H81 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C2 S7 C8 H82 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC C2 S7 C8 H83 0.0000 0.0000 180.0000 0.0000 0.0000 + +RESI NZAD 0.00 ! C9H11NO N-benzylacetamide (CAS # 588-46-5), isg +GROUP +ATOM C1 CG2R61 0.000 +ATOM C2 CG2R61 -0.115 +ATOM C3 CG2R61 -0.115 +ATOM C4 CG2R61 -0.115 +ATOM C5 CG2R61 -0.115 +ATOM C6 CG2R61 -0.115 +ATOM H2 HGR61 0.115 +ATOM H3 HGR61 0.115 +ATOM H4 HGR61 0.115 ! H5 H6 O9 H102 +ATOM H5 HGR61 0.115 ! | | \\ | +ATOM H6 HGR61 0.115 ! C5==C6 H71 C9--C10--H103 +GROUP ! / \ | / | +ATOM C7 CG321 -0.020 ! H4--C4 C1--C7--N8 H101 +ATOM H71 HGA2 0.090 ! \\ // | | +ATOM H72 HGA2 0.090 ! C3--C2 H72 H8 +ATOM N8 NG2S1 -0.470 ! | | +ATOM H8 HGP1 0.310 ! H3 H2 +ATOM C9 CG2O1 0.510 +ATOM O9 OG2D1 -0.510 +GROUP +ATOM C10 CG331 -0.270 +ATOM H101 HGA3 0.090 +ATOM H102 HGA3 0.090 +ATOM H103 HGA3 0.090 + +BOND C1 C2 C2 H2 C2 C3 C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 +BOND C5 C6 C6 H6 C6 C1 C1 C7 C7 H71 C7 H72 C7 N8 N8 H8 +BOND N8 C9 C9 O9 C9 C10 C10 H101 C10 H102 C10 H103 +IMPR C9 C10 N8 O9 +IC C4 C5 C6 C1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C5 C6 C1 C2 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 C1 C2 C3 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C6 C2 *C1 C7 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C5 C1 *C6 H6 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C3 C1 *C2 H2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4 C6 *C5 H5 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C4 C2 *C3 H3 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C5 C3 *C4 H4 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C6 C1 C7 N8 0.0000 0.0000 70.0000 0.0000 0.0000 ! Orig 180 +IC C1 N8 *C7 H71 0.0000 0.0000 120.0000 0.0000 0.0000 ! Orig 60 +IC C1 N8 *C7 H72 0.0000 0.0000 -120.0000 0.0000 0.0000 ! Orig -60 +IC C1 C7 N8 C9 0.0000 0.0000 -90.0000 0.0000 0.0000 ! Orig 180 +IC C7 C9 *N8 H8 0.0000 0.0000 -160.0000 0.0000 0.0000 ! Orig 180 +IC C7 N8 C9 C10 0.0000 0.0000 180.0000 0.0000 0.0000 ! Orig 180 +IC N8 C10 *C9 O9 0.0000 0.0000 -180.0000 0.0000 0.0000 ! Orig 180 +IC N8 C9 C10 H101 0.0000 0.0000 -150.0000 0.0000 0.0000 ! Orig 90 +IC H101 C9 *C10 H102 0.0000 0.0000 -120.0000 0.0000 0.0000 ! Orig -30 +IC H101 C9 *C10 H103 0.0000 0.0000 120.0000 0.0000 0.0000 ! Orig 150 + +RESI NMSM -1.00 ! CH4NO3S N-methyl-sulfamate, my & kevo +GROUP +ATOM S1 SG3O1 0.62 +ATOM O11 OG2P1 -0.50 +ATOM O12 OG2P1 -0.50 +ATOM O13 OG2P1 -0.50 ! O11 H21 H31 +ATOM N2 NG2S3 -0.52 ! \\ | / +ATOM H21 HGP1 0.33 ! (-) O12=S1--N2--C3--H32 +ATOM C3 CG331 -0.20 ! // \ +ATOM H31 HGA3 0.09 ! O13 H33 +ATOM H32 HGA3 0.09 +ATOM H33 HGA3 0.09 + +BOND S1 O11 S1 O12 S1 O13 S1 N2 N2 H21 +BOND N2 C3 C3 H31 C3 H32 C3 H33 +IC S1 N2 C3 H31 0.0000 0.00 -60.42 0.00 0.0000 +IC N2 H31 *C3 H32 0.0000 0.00 117.9 0.00 0.0000 +IC N2 H31 *C3 H33 0.0000 0.00 -123.1 0.00 0.0000 +IC H31 C3 N2 H21 0.0000 0.00 -176.0 0.00 0.0000 +IC C3 N2 S1 O11 0.0000 0.00 -51.92 0.00 0.0000 +IC N2 O11 *S1 O12 0.0000 0.00 -112.5 0.00 0.0000 +IC N2 O11 *S1 O13 0.0000 0.00 110.8 0.00 0.0000 + +RESI NESM -1.00 ! C2H6NO3S N-ethyl-sulfamate, my +GROUP +ATOM S1 SG3O1 0.62 +ATOM O11 OG2P1 -0.50 +ATOM O12 OG2P1 -0.50 +ATOM O13 OG2P1 -0.50 +ATOM N2 NG2S3 -0.52 ! O11 H21 H31 H41 +ATOM H21 HGP1 0.33 ! \\ | / / +ATOM C3 CG321 -0.11 ! (-) O12=S1--N2--C3 -- C4 - H42 +ATOM H31 HGA2 0.09 ! // \ \ +ATOM H32 HGA2 0.09 ! O13 H32 H43 +ATOM C4 CG331 -0.27 +ATOM H41 HGA3 0.09 +ATOM H42 HGA3 0.09 +ATOM H43 HGA3 0.09 + +BOND S1 O11 S1 O12 S1 O13 S1 N2 N2 H21 N2 C3 +BOND C3 H31 C3 H32 C3 C4 C4 H41 C4 H42 C4 H43 +IC S1 N2 C3 H31 0.0000 0.00 -60.42 0.00 0.0000 +IC N2 H31 *C3 H32 0.0000 0.00 117.9 0.00 0.0000 +IC N2 H31 *C3 C4 0.0000 0.00 -126.1 0.00 0.0000 +IC H31 C3 N2 H21 0.0000 0.00 -176.0 0.00 0.0000 +IC C3 N2 S1 O11 0.0000 0.00 -51.92 0.00 0.0000 +IC N2 O11 *S1 O12 0.0000 0.00 -112.5 0.00 0.0000 +IC N2 O11 *S1 O13 0.0000 0.00 110.8 0.00 0.0000 +IC N2 C3 C4 H41 0.0000 0.00 -58.51 0.00 0.0000 +IC C3 H41 *C4 H42 0.0000 0.00 122.1 0.00 0.0000 +IC C3 H41 *C4 H43 0.0000 0.00 -120.4 0.00 0.0000 + +RESI MESI 0.000 ! C3H10N2O2S N-methyl,N'-ethylsulfamide, rting +GROUP +ATOM C1 CG331 -0.02 +ATOM N2 NG311 -0.63 +ATOM H2 HGP1 0.37 ! H11 H2 O31 H4 H51 H61 +ATOM H11 HGA3 0.09 ! | | || | | / +ATOM H13 HGA3 0.09 ! H12-C1-N2-S3-N4-C5-C6-H62 +ATOM H12 HGA3 0.09 ! | || | \ +ATOM S3 SG3O2 0.80 ! H13 O32 H52 H63 +ATOM N4 NG311 -0.50 +ATOM H4 HGP1 0.33 +ATOM C5 CG321 0.06 +ATOM C6 CG331 -0.27 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 +ATOM O31 OG2P1 -0.43 +ATOM O32 OG2P1 -0.43 + +BOND C1 N2 C1 H11 C1 H13 C1 H12 N2 H2 +BOND N2 S3 S3 N4 S3 O31 S3 O32 N4 H4 +BOND N4 C5 C5 C6 C5 H51 C5 H52 C6 H61 C6 H62 C6 H63 +IC C1 N2 S3 O32 1.46875 116.231 -165.443 104.674 1.46516 +IC C1 N2 S3 O31 1.46875 116.231 -32.882 113.246 1.46416 +IC C1 N2 S3 N4 1.46875 116.231 77.486 97.671 1.67030 +IC N2 S3 N4 C5 1.66703 97.671 -162.329 116.007 1.47543 +IC N2 S3 N4 H4 1.66703 97.671 69.008 108.612 1.02191 +IC O31 S3 N4 H4 1.46416 105.323 -174.260 108.612 1.02191 +IC O32 S3 N4 H4 1.46516 113.734 -47.774 108.612 1.02191 +IC H51 C5 N4 H4 1.09138 106.498 -178.564 113.090 1.02191 +IC H52 C5 N4 H4 1.09413 105.601 -64.441 113.090 1.02191 +IC H51 C5 C6 H61 1.09138 111.162 -178.617 110.870 1.09423 +IC H51 C5 C6 H62 1.09138 111.162 -58.335 111.115 1.09210 +IC H51 C5 C6 H63 1.09138 111.162 61.785 110.137 1.09428 +IC H52 C5 C6 H61 1.09413 110.839 61.859 110.870 1.09423 +IC H52 C5 C6 H62 1.09413 110.839 -177.859 111.115 1.09210 +IC H52 C5 C6 H63 1.09413 110.839 -57.738 110.137 1.09428 +IC S3 N2 C1 H11 1.66703 116.231 -59.314 108.009 1.08999 +IC S3 N2 C1 H12 1.66703 116.231 61.802 113.066 1.09416 +IC S3 N2 C1 H13 1.66703 116.231 -176.624 107.554 1.09122 +IC H2 N2 C1 H11 1.02043 114.022 175.001 108.009 1.08999 +IC H2 N2 C1 H12 1.02043 114.022 -63.884 113.066 1.09416 +IC H2 N2 C1 H13 1.02043 114.022 57.691 107.554 1.09416 +IC S3 N4 C5 C6 1.67030 116.007 -68.483 114.796 1.52388 +IC S3 N4 C5 H51 1.67030 116.007 54.992 106.498 1.09138 +IC S3 N4 C5 H52 1.67030 116.007 169.115 105.601 1.09413 +IC N4 C5 C6 H61 1.47543 114.796 -57.668 110.870 1.09423 +IC N4 C5 C6 H62 1.47543 114.796 62.614 111.115 1.09210 +IC N4 C5 C6 H63 1.47543 114.796 -177.165 110.137 1.09428 + +RESI NACT -1.000 ! C4H8NO4S N-acetyltaurine, xxwy +GROUP +ATOM S SG3O1 0.73 +ATOM O1 OG2P1 -0.55 +ATOM O2 OG2P1 -0.55 ! O1 +ATOM O3 OG2P1 -0.55 ! | +ATOM C1 CG321 -0.26 ! O2---S---O3 +ATOM H11 HGA2 0.09 ! | +ATOM H12 HGA2 0.09 ! H11-C1-H12 +ATOM C2 CG321 -0.02 ! | +ATOM H21 HGA2 0.09 ! H21-C2-H22 +ATOM H22 HGA2 0.09 ! | +ATOM N NG2S1 -0.47 ! N-H +ATOM H HGP1 0.31 ! | +ATOM C CG2O1 0.51 ! C=O +ATOM O OG2D1 -0.51 ! | +ATOM C3 CG331 -0.27 ! H31-C3-H32 +ATOM H31 HGA3 0.09 ! | +ATOM H32 HGA3 0.09 ! H33 +ATOM H33 HGA3 0.09 + +BOND S O1 S O2 S O3 +BOND S C1 C1 H11 C1 H12 +BOND C1 C2 C2 H21 C2 H22 +BOND C2 N N C N H +BOND C C3 C3 H31 C3 H32 +BOND C3 H33 +DOUBLE C O +IMPR C C3 N O +IC C2 C1 S O1 0.0 0.00 180.00 0.0 0.0 +IC C1 O1 *S O2 0.0 0.00 120.00 0.0 0.0 +IC C1 O1 *S O3 0.0 0.00 -120.00 0.0 0.0 +IC S C2 *C1 H11 0.0 0.00 120.00 0.0 0.0 +IC S C2 *C1 H12 0.0 0.00 -120.00 0.0 0.0 +IC S C1 C2 N 0.0 0.00 180.00 0.0 0.0 +IC C1 N *C2 H21 0.0 0.00 120.00 0.0 0.0 +IC C1 N *C2 H22 0.0 0.00 -120.00 0.0 0.0 +IC C1 C2 N C 0.0 0.00 180.00 0.0 0.0 +IC C C2 *N H 0.0 0.00 180.00 0.0 0.0 +IC C2 N C C3 0.0 0.00 180.00 0.0 0.0 +IC C3 N *C O 0.0 0.00 180.00 0.0 0.0 +IC N C C3 H31 0.0 0.00 180.00 0.0 0.0 +IC C H31 *C3 H32 0.0 0.00 120.00 0.0 0.0 +IC C H31 *C3 H33 0.0 0.00 -120.00 0.0 0.0 + +PRES TAUR -1.00 ! C3H5NO4S taurine patch for bile acid, cacha & kevo +! patch combination: +! core residue cholic acid (CA) >> taurocholic acid (TCA) +! core residue deoxycholic acid (DCA) >> taurodeoxycholic acid (TDCA) +! core residue lithocholic acid (LCA) >> taurolithocholic acid (TLCA) +! core residue chenodeoxycholic acid (CDCA) >> taurochenodeoxycholic acid (TCDCA) +! core residue ursodeoxycholic acid (UDCA) >> tauroursodeoxycholic acid (TUDCA) +DELETE ATOM OE2 +ATOM CD CG2O1 0.51 ! OE1 O1S +ATOM OE1 OG2D1 -0.51 ! || || +ATOM N NG2S1 -0.47 ! OH Me21 C22 CD C1G S--O2S(-1) +ATOM HN HGP1 0.31 ! | \ / \ / \ / \ / \\ +ATOM C1G CG321 -0.02 ! C12 Me18 C20 C23 NH C2G O3S +ATOM H1GA HGA2 0.09 ! / \ | / +ATOM H1GB HGA2 0.09 ! C11 C13---C17 +ATOM C2G CG321 -0.26 ! Me19 | | | +ATOM H2GA HGA2 0.09 ! C1 | C9 C14 C16 +ATOM H2GB HGA2 0.09 ! / \|/ \ / \ / +ATOM S SG3O1 0.73 ! C2 C10 C8 C15 Taurocholic acid (TCA) +ATOM O1S OG2P1 -0.55 ! | | | +ATOM O2S OG2P1 -0.55 ! C3 C5 C7 +ATOM O3S OG2P1 -0.55 ! / \ / \ / \ + ! HO C4 C6 OH +BOND CD N N HN +BOND N C1G C1G H1GA C1G H1GB +BOND C1G C2G C2G H2GA C2G H2GB +BOND C2G S S O1S S O2S S O3S +IMPR CD C23 N OE1 +IC OE1 C23 *CD N 1.2243 119.69 -179.68 116.74 1.3409 +IC C23 CD N C1G 1.5017 116.74 -179.30 126.20 1.4354 +IC C1G CD *N HN 1.4354 126.20 179.36 118.75 0.9870 +IC CD N C1G C2G 1.3409 126.20 178.33 109.02 1.5463 +IC C2G N *C1G H1GA 1.5463 109.02 120.57 110.50 1.1164 +IC H1GA N *C1G H1GB 1.1164 110.50 118.98 110.47 1.1166 +IC N C1G C2G S 1.4354 109.02 -179.35 119.43 1.8188 +IC S C1G *C2G H2GA 1.8188 119.43 121.46 108.45 1.1077 +IC H2GA C1G *C2G H2GB 1.1077 108.45 116.91 108.50 1.1077 +IC C1G C2G S O1S 1.5463 119.43 179.97 107.05 1.5726 +IC O1S C2G *S O2S 1.5726 107.05 118.76 109.79 1.5714 +IC O1S C2G *S O3S 1.5726 107.05 -118.67 109.74 1.5715 + +RESI MICY 0.00 ! C2H3NO methyl isocyanate, xxwy +GROUP +ATOM O OG2D5 -0.43 +ATOM C CG2O7 0.68 ! H11 +ATOM N NG2D1 -0.52 ! | +ATOM C1 CG331 -0.00 ! H12--C1--N==C==O +ATOM H11 HGA3 0.09 ! | +ATOM H12 HGA3 0.09 ! H13 +ATOM H13 HGA3 0.09 + +DOUBLE O C C N +BOND C1 N +BOND C1 H11 C1 H12 C1 H13 +IC O C N C1 0.0000 0.00 180.00 0.00 0.0000 +IC C N C1 H11 0.0000 0.00 180.00 0.00 0.0000 +IC H11 N *C1 H12 0.0000 0.00 120.00 0.00 0.0000 +IC H11 N *C1 H13 0.0000 0.00 -120.00 0.00 0.0000 + +! Added to address gap in coverage - still eligible for future improvement +RESI CO31 -1.00 ! CHO3 bicarbonate, xxwy & kevo +ATOM C CG2O6 0.69 ! H3 O1 +ATOM H3 HGP1 0.43 ! | / +ATOM O1 OG2D2 -0.76 ! O3--C (-) +ATOM O2 OG2D2 -0.76 ! \ +ATOM O3 OG311 -0.60 ! O2 + +BOND C O1 C O2 C O3 O3 H3 +IMPR C O1 O2 O3 +! seed = O1 C O2 +IC O2 O1 *C O3 0.0000 0.00 180.00 0.00 0.0000 +IC O1 C O3 H3 0.0000 0.00 0.00 0.00 0.0000 + +RESI GBL 0.00 ! C4H6O2 Gamma-butyrolactone (aka. oxolan-2-one which provided atom numbering), ctsai +GROUP +ATOM O1 OG3C51 -0.27 +ATOM C2 CG2R53 0.15 +ATOM O2 OG2D1 -0.39 +ATOM C3 CG3C52 0.07 ! H41 H32 +ATOM H31 HGA2 0.09 ! | | +ATOM H32 HGA2 0.09 ! H42--C4--C3--H31 +ATOM C4 CG3C52 -0.19 ! / \ +ATOM H41 HGA2 0.09 ! H51--C5 C2 +ATOM H42 HGA2 0.09 ! / \ / \\ +ATOM C5 CG3C52 0.09 ! H52 O1 O2 +ATOM H51 HGA2 0.09 +ATOM H52 HGA2 0.09 + +BOND O1 C5 O1 C2 C2 C3 C2 O2 C3 C4 +BOND C3 H31 C3 H32 C4 C5 C4 H41 C4 H42 +BOND C5 H51 C5 H52 +IMPR C2 C3 O2 O1 +IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C2 O1 C5 0.0000 0.00 0.00 0.00 0.0000 +IC O1 C3 *C2 O2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 +IC C3 C5 *C4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 O1 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 O1 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 + +RESI B2FO 0.00 ! C4H4O2 5H-furan-2-one, ctsai +GROUP +ATOM O1 OG3C51 -0.31 +ATOM C2 CG2R53 0.29 +ATOM C3 CG2R51 -0.14 ! H3 H4 +ATOM H3 HGR51 0.22 ! | | +ATOM C4 CG2R51 -0.22 ! C3==C4 H51 +ATOM H4 HGR51 0.22 ! / \ / +ATOM C5 CG3C52 0.19 ! O6==C2 C5 +ATOM H51 HGA2 0.09 ! \ / \ +ATOM H52 HGA2 0.09 ! O1 H52 +ATOM O6 OG2D1 -0.43 + +BOND O1 C2 O1 C5 C2 C3 C2 O6 C3 C4 +BOND C3 H3 C4 C5 C4 H4 C5 H51 C5 H52 +IMPR C2 C3 O6 O1 +IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C2 O1 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 O1 *C2 O6 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 120.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 -120.00 0.00 0.0000 +IC C4 O1 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC C4 O1 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 + +RESI A2FO 0.00 ! C4H4O2 3H-furan-2-one, ctsai +GROUP +ATOM O1 OG3C51 -0.23 +ATOM C2 CG2R53 0.30 +ATOM C3 CG3C52 0.06 ! H31 H4 +ATOM H31 HGA2 0.09 ! | / +ATOM H32 HGA2 0.09 ! H32--C3--C4 +ATOM C4 CG2R51 -0.28 ! / \\ +ATOM H4 HGR51 0.21 ! C2 C5 +ATOM C5 CG2R51 -0.05 ! // \ / \ +ATOM H5 HGR52 0.21 ! O6 O1 H5 +ATOM O6 OG2D1 -0.40 + +BOND O1 C2 O1 C5 C2 O6 C2 C3 C3 C4 +BOND C3 H31 C3 H32 C4 C5 C4 H4 C5 H5 +IMPR C2 C3 O6 O1 +IC O1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C2 O1 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 O1 *C2 O6 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 120.00 0.00 0.0000 +IC C4 O1 *C5 H5 0.0000 0.00 -120.00 0.00 0.0000 +IC C2 C4 *C3 H31 0.0000 0.00 120.00 0.00 0.0000 +IC C2 C4 *C3 H32 0.0000 0.00 -120.00 0.00 0.0000 + +! 3.1 additions, Jul 15 +RESI MT2A 0.00 ! C4H10N2S (Z)-N'-ethyl(methylsulfanyl)methanimidamide, fylin +GROUP +ATOM C1 CG331 -0.04 +ATOM H11 HGA3 0.09 +ATOM H12 HGA3 0.09 ! H13 +ATOM H13 HGA3 0.09 ! | +ATOM S2 SG311 -0.29 ! H11- C1 -S2 H41 +ATOM C3 CG2N2 0.56 ! | \ / +ATOM N4 NG321 -0.96 ! H12 C3 - N4 +ATOM H41 HGPAM2 0.43 ! || \ +ATOM H42 HGPAM2 0.43 ! N5 H42 +ATOM N5 NG2D1 -0.60 ! / +ATOM C6 CG321 0.02 ! H61 - C6 - H62 +ATOM H61 HGA2 0.09 ! | +ATOM H62 HGA2 0.09 ! H71 - C7 - H72 +ATOM C7 CG331 -0.27 ! | +ATOM H71 HGA3 0.09 ! H73 +ATOM H72 HGA3 0.09 +ATOM H73 HGA3 0.09 + +BOND C1 H11 C1 H12 C1 H13 C1 S2 S2 C3 +BOND C3 N4 N4 H41 N4 H42 C3 N5 +BOND N5 C6 C6 H61 C6 H62 +BOND C6 C7 C7 H71 C7 H72 C7 H73 +IMPR C3 N5 N4 S2 +IC C1 S2 C3 N5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 S2 C1 H13 0.0000 0.00 150.00 0.00 0.0000 +IC S2 H13 *C1 H11 0.0000 0.00 120.00 0.00 0.0000 +IC S2 H13 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000 +IC S2 N5 *C3 N4 0.0000 0.00 180.00 0.00 0.0000 +IC S2 C3 N4 H41 0.0000 0.00 120.00 0.00 0.0000 +IC S2 C3 N4 H42 0.0000 0.00 -120.00 0.00 0.0000 +IC S2 C3 N5 C6 0.0000 0.00 165.00 0.00 0.0000 +IC C3 N5 C6 C7 0.0000 0.00 155.00 0.00 0.0000 +IC N5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC N5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC N5 C6 C7 H73 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 H73 *C7 H71 0.0000 0.00 55.00 0.00 0.0000 +IC C6 H73 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 + +RESI DH3T 0.00 ! C4H8N2S 5,6-dihydro-4H-1,3-thiazin-2-amine, fylin +GROUP +ATOM S1 SG311 -0.29 +ATOM C2 CG2N2 0.56 +ATOM N3 NG321 -0.96 ! H31 +ATOM H31 HGPAM2 0.43 ! | +ATOM H32 HGPAM2 0.43 ! H71 S1 N3-H32 +ATOM N4 NG2D1 -0.60 ! \ / \ / +ATOM C5 CG321 0.02 ! H72-C7 C2 +ATOM H51 HGA2 0.09 ! | || +ATOM H52 HGA2 0.09 ! H61-C6 N4 +ATOM C6 CG321 -0.18 ! / \ / +ATOM H61 HGA2 0.09 ! H62 C5 +ATOM H62 HGA2 0.09 ! / \ +ATOM C7 CG321 0.05 ! H51 H52 +ATOM H71 HGA2 0.09 +ATOM H72 HGA2 0.09 + +BOND S1 C2 S1 C7 C2 N3 C2 N4 N3 H31 N3 H32 +BOND N4 C5 C5 H51 C5 H52 C5 C6 C6 H61 C6 H62 +BOND C6 C7 C7 H71 C7 H72 +IMPR C2 N4 N3 S1 +IC S1 C2 N4 C5 0.0000 0.00 65.00 0.00 0.0000 +IC C2 N4 C5 C6 0.0000 0.00 -10.00 0.00 0.0000 +IC N4 C2 S1 C7 0.0000 0.00 -30.00 0.00 0.0000 +IC S1 N4 *C2 N3 0.0000 0.00 180.00 0.00 0.0000 +IC S1 C2 N3 H31 0.0000 0.00 0.00 0.00 0.0000 +IC C2 H31 *N3 H32 0.0000 0.00 180.00 0.00 0.0000 +IC N4 C6 *C5 H51 0.0000 0.00 120.00 0.00 0.0000 +IC N4 C6 *C5 H52 0.0000 0.00 -120.00 0.00 0.0000 +IC C5 C7 *C6 H61 0.0000 0.00 120.00 0.00 0.0000 +IC C5 C7 *C6 H62 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 S1 *C7 H71 0.0000 0.00 120.00 0.00 0.0000 +IC C6 S1 *C7 H72 0.0000 0.00 -120.00 0.00 0.0000 + +RESI EEPI 0.00 ! C5H11N (E)-ethylidene(propyl)amine, fylin +GROUP +ATOM C1 CG331 -0.27 +ATOM C2 CG321 -0.18 +ATOM C3 CG321 0.04 +ATOM N4 NG2D1 -0.60 +ATOM C5 CG2D1 0.23 +ATOM C6 CG331 -0.27 +ATOM H11 HGA3 0.09 ! H13 H21 H32 H51 H61 +ATOM H12 HGA3 0.09 ! | | | | | +ATOM H13 HGA3 0.09 ! H12-C1--C2--C3--N4=C5--C6--H63 (trans) +ATOM H21 HGA2 0.09 ! | | | | +ATOM H22 HGA2 0.09 ! H11 H22 H31 H62 +ATOM H31 HGA2 0.09 +ATOM H32 HGA2 0.09 +ATOM H51 HGA4 0.15 +ATOM H61 HGA3 0.09 +ATOM H62 HGA3 0.09 +ATOM H63 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 N4 N4 C5 +BOND C5 C6 C5 H51 C1 H11 C1 H12 +BOND C1 H13 C2 H21 C2 H22 C3 H31 +BOND C3 H32 C6 H61 C6 H62 C6 H63 +IMPR C5 C6 N4 H51 +IC C1 C2 C3 N4 0.0000 0.00 165.00 0.00 0.0000 +IC H11 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC H12 C1 C2 C3 0.0000 0.00 60.00 0.00 0.0000 +IC H13 C1 C2 C3 0.0000 0.00 -60.00 0.00 0.0000 +IC H21 C2 C3 N4 0.0000 0.00 60.00 0.00 0.0000 +IC H22 C2 C3 N4 0.0000 0.00 -60.00 0.00 0.0000 +IC C2 C3 N4 C5 0.0000 0.00 155.00 0.00 0.0000 +IC H31 C3 N4 C5 0.0000 0.00 60.00 0.00 0.0000 +IC H32 C3 N4 C5 0.0000 0.00 -60.00 0.00 0.0000 +IC C3 N4 C5 H51 0.0000 0.00 0.00 0.00 0.0000 +IC C3 N4 C5 C6 0.0000 0.00 170.00 0.00 0.0000 +IC N4 C5 C6 H61 0.0000 0.00 160.00 0.00 0.0000 +IC N4 C5 C6 H62 0.0000 0.00 60.00 0.00 0.0000 +IC N4 C5 C6 H63 0.0000 0.00 -60.00 0.00 0.0000 + +RESI PYRH 1.00 ! C4H5N2 pyrimidin-1-ium, fylin +GROUP +ATOM N1 NG2R62 -0.49 +ATOM C2 CG2R62 0.38 ! H5 H6 +ATOM N3 NG2R61 -0.53 ! \ ___ / +ATOM C4 CG2R62 0.24 ! C5---C6 +ATOM C5 CG2R62 0.08 ! / \ +ATOM C6 CG2R62 0.11 ! H4--C4 N1 +ATOM H3 HGP2 0.46 ! \\ // +ATOM H2 HGR63 0.23 ! N3---C2 +ATOM H4 HGR63 0.19 ! /(+1) \ +ATOM H6 HGR63 0.22 ! H3 H2 +ATOM H5 HGR63 0.11 + +BOND N1 C2 N1 C6 C2 N3 N3 C4 C4 C5 C5 C6 +BOND N3 H3 C2 H2 C4 H4 C6 H6 C5 H5 +IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C6 N1 C2 N3 0.0000 0.00 0.00 0.00 0.0000 +IC N3 N1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C2 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 + +RESI PIUM 1.00 ! C5H6N pyridin-1-ium, fylin +GROUP +ATOM C1 CG2R62 0.15 +ATOM C5 CG2R62 0.15 ! H3 +ATOM H1 HGR63 0.20 ! | +ATOM H5 HGR63 0.20 ! C3 +ATOM C2 CG2R62 -0.09 ! / \\ +ATOM C4 CG2R62 -0.09 ! H4--C4 C2--H2 +ATOM H2 HGR63 0.18 ! || | +ATOM H4 HGR63 0.18 ! H5--C5 C1--H1 +ATOM C3 CG2R62 -0.19 ! \+// +ATOM H3 HGR63 0.25 ! N6 +ATOM N6 NG2R61 -0.35 ! | +ATOM H6 HGP2 0.41 ! H6 + +BOND C1 C2 C1 N6 C1 H1 C2 C3 C2 H2 C3 C4 +BOND C3 H3 C4 C5 C4 H4 C5 N6 C5 H5 N6 H6 + +IC N6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.000 +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.000 +IC C3 C4 C5 N6 0.0000 0.00 0.00 0.00 0.000 +IC C4 C5 N6 C1 0.0000 0.00 0.00 0.00 0.000 +IC N6 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.000 +IC C4 N6 *C5 H5 0.0000 0.00 180.00 0.00 0.000 +IC C5 C1 *N6 H6 0.0000 0.00 180.00 0.00 0.000 + +RESI PYO2B 0.000 ! C11H9NO 4-phenyl-1,2-dihydropyridin-2-one, fylin +GROUP +ATOM C1 CG2R63 0.16 ! H5 H4 H13 H12 +ATOM C2 CG2R62 -0.26 ! \ / \ / +ATOM C3 CG2R67 0.00 ! C5 = C4 C13-C12 +ATOM C4 CG2R62 -0.22 ! / \ // \\ +ATOM C5 CG2R62 0.15 ! H6-N6 C3---C8 C11-H11 +ATOM N6 NG2R61 -0.13 ! \ // \ / +ATOM C9 CG2R61 -0.115 ! C1--C2 C9=C10 +ATOM C10 CG2R61 -0.115 ! // \ / \ +ATOM C11 CG2R61 -0.115 ! O7 H2 H9 H10 +ATOM C12 CG2R61 -0.115 +ATOM C13 CG2R61 -0.115 +ATOM C8 CG2R67 0.00 +ATOM O7 OG2D4 -0.48 +ATOM H2 HGR62 0.22 +ATOM H4 HGR62 0.15 +ATOM H5 HGR62 0.13 +ATOM H6 HGP1 0.28 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 +ATOM H13 HGR61 0.115 + +BOND C1 C2 C1 N6 C2 C3 C3 C4 C4 C5 C5 N6 +BOND C9 C10 C9 C8 C10 C11 C11 C12 C12 C13 C13 C8 +BOND C3 C8 C1 O7 C2 H2 C4 H4 C5 H5 N6 H6 +BOND C9 H9 C10 H10 C11 H11 C12 H12 C13 H13 +IMPR C1 C2 N6 O7 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 N6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 N6 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 N6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C2 *C1 O7 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C8 C9 0.0000 0.00 -40.00 0.00 0.0000 +IC C3 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 0.00 0.00 0.0000 +IC C11 C12 C13 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C13 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C8 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 + +RESI PYO3B 0.000 ! C11H9NO 5-phenyl-1,2-dihydropyridin-2-one, fylin +GROUP +ATOM N1 NG2R61 -0.13 ! H5 H4 H13 H12 +ATOM C2 CG2R62 0.15 ! \ / \ / +ATOM C3 CG2R67 -0.07 ! C5 = C4 C13-C12 +ATOM C4 CG2R62 -0.22 ! / \ // \\ +ATOM C5 CG2R62 -0.26 ! O7=C6 C3---C8 C11-H11 +ATOM C6 CG2R63 0.16 ! \ // \ / +ATOM C9 CG2R61 -0.115 ! N1--C2 C9=C10 +ATOM C10 CG2R61 -0.115 ! // \ / \ +ATOM C11 CG2R61 -0.115 ! H1 H2 H9 H10 +ATOM C12 CG2R61 -0.115 +ATOM C13 CG2R61 -0.115 +ATOM C8 CG2R67 0.00 +ATOM H2 HGR62 0.13 +ATOM H4 HGR62 0.22 +ATOM H5 HGR62 0.22 +ATOM O7 OG2D4 -0.48 +ATOM H9 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 +ATOM H13 HGR61 0.115 +ATOM H1 HGP1 0.28 + +BOND N1 C2 N1 C6 C2 C3 C3 C4 C4 C5 C5 C6 +BOND C9 C10 C9 C8 C10 C11 C11 C12 C12 C13 C13 C8 +BOND C3 C8 C2 H2 C4 H4 C5 H5 C6 O7 C9 H9 +BOND C10 H10 C11 H11 C12 H12 C13 H13 N1 H1 +IMPR C6 C5 N1 O7 + +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 O7 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C2 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C8 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 0.00 0.00 0.0000 +IC C11 C12 C13 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C13 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C8 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 + + +RESI PIUB 1.000 ! C11H10N 4-phenylpyridine, fylin +GROUP ! transfr +ATOM C1 CG2R62 0.15 +ATOM N2 NG2R61 -0.35 ! H1 H6 H12 H11 +ATOM C3 CG2R62 0.15 ! \ / \ / +ATOM C4 CG2R62 -0.09 ! C1--C6 C12-C11 +ATOM C5 CG2R67 0.06 ! // \\ // \\ +ATOM C6 CG2R62 -0.09 ! H2-N2+ C5 ---C7 C10-H10 +ATOM C7 CG2R67 0.00 ! \ / \ / +ATOM C8 CG2R61 -0.115 ! C3=C4 C8=C9 +ATOM C12 CG2R61 -0.115 ! / \ / \ +ATOM C11 CG2R61 -0.115 ! H3 H4 H8 H9 +ATOM C10 CG2R61 -0.115 +ATOM C9 CG2R61 -0.115 +ATOM H2 HGP2 0.41 +ATOM H1 HGR63 0.20 +ATOM H3 HGR63 0.20 +ATOM H4 HGR63 0.18 +ATOM H6 HGR63 0.18 +ATOM H8 HGR61 0.115 +ATOM H12 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H10 HGR61 0.115 +ATOM H9 HGR61 0.115 + +BOND C1 N2 C1 C6 N2 C3 C3 C4 C4 C5 C5 C6 +BOND C5 C7 C12 C11 C11 C10 C10 C9 C8 C9 C8 C7 +BOND C7 C12 N2 H2 C1 H1 C3 H3 C4 H4 C6 H6 +BOND C8 H8 C12 H12 C11 H11 C10 H10 C9 H9 + +IC C1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.000 +IC N2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.000 +IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.000 +IC C5 C6 C1 N2 0.0000 0.00 0.00 0.00 0.000 +IC C6 C1 N2 C3 0.0000 0.00 0.00 0.00 0.000 +IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.000 +IC C4 C6 *C5 C7 0.0000 0.00 180.00 0.00 0.000 +IC C5 C1 *C6 H6 0.0000 0.00 180.00 0.00 0.000 +IC C6 N2 *C1 H1 0.0000 0.00 180.00 0.00 0.000 +IC C1 C3 *N2 H2 0.0000 0.00 180.00 0.00 0.000 +IC C4 C5 C7 C8 0.0000 0.00 0.00 0.00 0.000 +IC C5 C7 C8 C9 0.0000 0.00 180.00 0.00 0.000 +IC C7 C8 C9 C10 0.0000 0.00 0.00 0.00 0.000 +IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.000 +IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.000 +IC C10 C11 C12 C7 0.0000 0.00 0.00 0.00 0.000 +IC C7 C9 *C8 H8 0.0000 0.00 180.00 0.00 0.000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.000 +IC C11 C7 *C12 H12 0.0000 0.00 180.00 0.00 0.000 + + +RESI PYO2F 0.000 ! C11H8FNO 4-(2-fluorophenyl)-1,2-dihydropyridin-2-one, fylin +GROUP ! CHARGE +ATOM C1 CG2R63 0.16 +ATOM C2 CG2R62 -0.26 ! H5 H4 H13 H12 +ATOM C3 CG2R67 0.00 ! \ / \ / +ATOM C4 CG2R62 -0.22 ! C5 = C4 C13-C12 +ATOM C5 CG2R62 0.15 ! / \ // \\ +ATOM N6 NG2R61 -0.13 ! H6-N6 C3---C8 C11-H11 +ATOM O7 OG2D4 -0.48 ! \ // \ / +ATOM C8 CG2R67 0.185 ! C1--C2 C9=C10 +ATOM C9 CG2R66 0.10 ! // \ / \ +ATOM C10 CG2R61 -0.13 ! O7 H2 F9 H10 +ATOM C11 CG2R61 -0.18 +ATOM C12 CG2R61 -0.10 +ATOM C13 CG2R61 -0.18 +ATOM H2 HGR62 0.22 +ATOM H4 HGR62 0.15 +ATOM H5 HGR62 0.13 +ATOM H6 HGP1 0.28 +ATOM F9 FGR1 -0.23 +ATOM H10 HGR62 0.19 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 +ATOM H13 HGR61 0.115 + +BOND C1 C2 C1 N6 C1 O7 C2 C3 C2 H2 C3 C4 +BOND C3 C8 C4 C5 C4 H4 C5 N6 C5 H5 N6 H6 +BOND C8 C9 C8 C13 C9 C10 C9 F9 C10 C11 C10 H10 +BOND C11 C12 C11 H11 C12 C13 C12 H12 C13 H13 +IMPR C1 C2 N6 O7 + +IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 N6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 N6 C1 0.0000 0.00 0.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 N6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 C1 *N6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC N6 C2 *C1 O7 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C8 C9 0.0000 0.00 -40.00 0.00 0.0000 +IC C3 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 0.00 0.00 0.0000 +IC C11 C12 C13 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C10 *C9 F9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C13 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C8 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 + + +RESI PYO3F 0.000 ! C11H8FNO 5-(2-fluorophenyl)-1,2-dihydropyridin-2-one, fylin +GROUP ! CHARGE +ATOM N1 NG2R61 -0.13 +ATOM C2 CG2R62 0.15 ! H5 H4 H13 H12 +ATOM C3 CG2R67 -0.07 ! \ / \ / +ATOM C4 CG2R62 -0.22 ! C5 = C4 C13-C12 +ATOM C5 CG2R62 -0.26 ! / \ // \\ +ATOM C6 CG2R63 0.16 ! O7=C6 C3---C8 C11-H11 +ATOM O7 OG2D4 -0.48 ! \ // \ / +ATOM C8 CG2R67 0.185 ! N1--C2 C9=C10 +ATOM C9 CG2R66 0.10 ! // \ / \ +ATOM C10 CG2R61 -0.13 ! H1 H2 F9 H10 +ATOM C11 CG2R61 -0.18 +ATOM C12 CG2R61 -0.10 +ATOM C13 CG2R61 -0.18 +ATOM H1 HGP1 0.28 +ATOM H2 HGR62 0.13 +ATOM H4 HGR62 0.22 +ATOM H5 HGR62 0.22 +ATOM F9 FGR1 -0.23 +ATOM H10 HGR62 0.19 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 +ATOM H13 HGR61 0.115 + +BOND N1 C2 N1 C6 N1 H1 C2 C3 C2 H2 C3 C4 +BOND C3 C8 C4 C5 C4 H4 C5 C6 C5 H5 C6 O7 +BOND C8 C13 C8 C9 C9 C10 C9 F9 C10 C11 C10 H10 +BOND C11 C12 C11 H11 C12 C13 C12 H12 C13 H13 +IMPR C6 C5 N1 O7 + +IC N1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC N1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 C8 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 O7 0.0000 0.00 180.00 0.00 0.0000 +IC C6 C2 *N1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C3 C8 C9 0.0000 0.00 0.00 0.00 0.0000 +IC C3 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 +IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.0000 +IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.0000 +IC C10 C11 C12 C13 0.0000 0.00 0.00 0.00 0.0000 +IC C11 C12 C13 C8 0.0000 0.00 0.00 0.00 0.0000 +IC C8 C10 *C9 F9 0.0000 0.00 180.00 0.00 0.0000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.0000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.0000 +IC C11 C13 *C12 H12 0.0000 0.00 180.00 0.00 0.0000 +IC C12 C8 *C13 H13 0.0000 0.00 180.00 0.00 0.0000 + +RESI PIUF 1.000 ! C11H9FN 4-(2-fluorophenyl)pyridine, fylin +GROUP ! CHARGE +ATOM C1 CG2R62 0.15 +ATOM N2 NG2R61 -0.35 ! H1 H6 H12 H11 +ATOM C3 CG2R62 0.15 ! \ / \ / +ATOM C4 CG2R62 -0.09 ! C1--C6 C12-C11 +ATOM C5 CG2R67 0.06 ! // \\ // \\ +ATOM C6 CG2R62 -0.09 ! H2-N2+ C5 ---C7 C10-H10 +ATOM C7 CG2R67 0.185 ! \ / \ / +ATOM C8 CG2R66 0.10 ! C3=C4 C8=C9 +ATOM C9 CG2R61 -0.13 ! / \ / \ +ATOM C10 CG2R61 -0.18 ! H3 H4 F8 H9 +ATOM C11 CG2R61 -0.10 +ATOM C12 CG2R61 -0.18 +ATOM H1 HGR63 0.20 +ATOM H2 HGP2 0.41 +ATOM H3 HGR63 0.20 +ATOM H4 HGR63 0.18 +ATOM H6 HGR63 0.18 +ATOM F8 FGR1 -0.23 +ATOM H9 HGR62 0.19 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND C1 N2 C1 C6 C1 H1 N2 C3 N2 H2 C3 C4 +BOND C3 H3 C4 C5 C4 H4 C5 C6 C5 C7 C6 H6 +BOND C7 C12 C7 C8 C8 C9 C8 F8 C9 C10 C9 H9 +BOND C10 C11 C10 H10 C11 C12 C11 H11 C12 H12 + +IC C1 N2 C3 C4 0.0000 0.00 0.00 0.00 0.000 +IC N2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.000 +IC C3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.000 +IC C4 C5 C6 C1 0.0000 0.00 0.00 0.00 0.000 +IC C5 C6 C1 N2 0.0000 0.00 0.00 0.00 0.000 +IC C6 C1 N2 C3 0.0000 0.00 0.00 0.00 0.000 +IC N2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.000 +IC C4 C6 *C5 C7 0.0000 0.00 180.00 0.00 0.000 +IC C5 C1 *C6 H6 0.0000 0.00 180.00 0.00 0.000 +IC C6 N2 *C1 H1 0.0000 0.00 180.00 0.00 0.000 +IC C1 C3 *N2 H2 0.0000 0.00 180.00 0.00 0.000 +IC C4 C5 C7 C8 0.0000 0.00 0.00 0.00 0.000 +IC C5 C7 C8 C9 0.0000 0.00 180.00 0.00 0.000 +IC C7 C8 C9 C10 0.0000 0.00 0.00 0.00 0.000 +IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.000 +IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.000 +IC C10 C11 C12 C7 0.0000 0.00 0.00 0.00 0.000 +IC C7 C9 *C8 F8 0.0000 0.00 180.00 0.00 0.000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.000 +IC C11 C7 *C12 H12 0.0000 0.00 180.00 0.00 0.000 + +RESI PYRF 1.000 ! C10H8FN2 5-(2-fluorophenyl)pyrimidin-2-yl, fylin +GROUP ! CHARGE +ATOM N1 NG2R62 -0.49 +ATOM C2 CG2R62 0.38 ! H6 H12 H11 +ATOM N3 NG2R61 -0.53 ! / \ / +ATOM C4 CG2R62 0.24 ! N1 == C6 C12--C11 +ATOM C5 CG2R67 0.19 ! / \ // \\ +ATOM C6 CG2R62 0.11 ! H2-C2 C5 ---C7 C10-H10 +ATOM C7 CG2R67 0.185 ! \\ // \ / +ATOM C8 CG2R66 0.10 ! (+1)N3--C4 C8=C9 +ATOM C9 CG2R61 -0.13 ! / \ / \ +ATOM C10 CG2R61 -0.18 ! H3 H4 F8 H9 +ATOM C11 CG2R61 -0.10 +ATOM C12 CG2R61 -0.18 +ATOM H2 HGR63 0.23 +ATOM H3 HGP2 0.46 +ATOM H4 HGR63 0.19 +ATOM H6 HGR63 0.22 +ATOM F8 FGR1 -0.23 +ATOM H9 HGR62 0.19 +ATOM H10 HGR61 0.115 +ATOM H11 HGR61 0.115 +ATOM H12 HGR61 0.115 + +BOND N1 C2 N1 C6 C2 N3 C2 H2 N3 C4 N3 H3 +BOND C4 C5 C4 H4 C5 C6 C5 C7 C6 H6 C7 C8 +BOND C7 C12 C8 C9 C8 F8 C9 C10 C9 H9 C10 C11 +BOND C10 H10 C11 C12 C11 H11 C12 H12 + +IC N1 C2 N3 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C2 N3 C4 C5 0.0000 0.00 0.00 0.00 0.0000 +IC N3 C4 C5 C6 0.0000 0.00 0.00 0.00 0.0000 +IC C4 C5 C6 N1 0.0000 0.00 0.00 0.00 0.0000 +IC N1 N3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *N3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC N3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 C7 0.0000 0.00 180.00 0.00 0.0000 +IC C5 N1 *C6 H6 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C5 C7 C8 0.0000 0.00 0.00 0.00 0.000 +IC C5 C7 C8 C9 0.0000 0.00 180.00 0.00 0.000 +IC C7 C8 C9 C10 0.0000 0.00 0.00 0.00 0.000 +IC C8 C9 C10 C11 0.0000 0.00 0.00 0.00 0.000 +IC C9 C10 C11 C12 0.0000 0.00 0.00 0.00 0.000 +IC C10 C11 C12 C7 0.0000 0.00 0.00 0.00 0.000 +IC C7 C9 *C8 F8 0.0000 0.00 180.00 0.00 0.000 +IC C8 C10 *C9 H9 0.0000 0.00 180.00 0.00 0.000 +IC C9 C11 *C10 H10 0.0000 0.00 180.00 0.00 0.000 +IC C10 C12 *C11 H11 0.0000 0.00 180.00 0.00 0.000 +IC C11 C7 *C12 H12 0.0000 0.00 180.00 0.00 0.000 + +RESI BTMC 0.00 ! C7H11N3O N4,N4,-O-trimethylcytosine, yxu +GROUP +ATOM N1 NG2R61 -0.03 +ATOM C2 CG2R63 0.57 +ATOM O2 OG2D4 -0.52 ! H73 H83 +ATOM N3 NG2R62 -0.74 ! \ / +ATOM C4 CG2R64 0.60 ! H72-C7 C8-H82 +ATOM N4 NG301 -0.37 ! / \ / \ +ATOM C5 CG2R62 -0.18 ! H71 N4 H81 +ATOM H5 HGR62 0.03 ! | +ATOM C6 CG2R62 0.11 ! C4 +ATOM H6 HGR62 0.13 ! / \\ +ATOM C7 CG331 -0.07 ! H5-C5 N3 +ATOM H71 HGA3 0.09 ! || | +ATOM H72 HGA3 0.09 ! H6-C6 C2 +ATOM H73 HGA3 0.09 ! \ / \\ +ATOM C8 CG331 -0.07 ! N1 O2 +ATOM H81 HGA3 0.09 ! \ +ATOM H82 HGA3 0.09 ! \ +ATOM H83 HGA3 0.09 ! \ +GROUP +ATOM CM CG331 -0.27 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND CM HM1 CM HM2 CM HM3 +BOND N1 C2 N1 C6 C2 O2 C2 N3 +BOND N3 C4 C4 C5 C4 N4 N4 C7 +BOND N4 C8 C7 H71 C7 H72 C7 H73 +BOND C8 H81 C8 H82 C8 H83 C5 C6 +BOND C5 H5 C6 H6 +BOND CM N1 +IMPR C2 N1 N3 O2 C4 C5 N3 N4 +ACCE O2 C2 +ACCE N3 +IC C2 C6 *N1 CM 1.4228 119.21 179.94 121.44 1.4761 +IC C6 N1 C2 N3 1.3609 119.21 -0.05 119.30 1.3580 +IC N3 N1 *C2 O2 1.3580 119.30 -179.92 118.95 1.2300 +IC N1 C2 N3 C4 1.4228 119.30 0.02 121.89 1.3575 +IC C2 N3 C4 N4 1.3580 121.89 179.99 119.16 1.3747 +IC N4 N3 *C4 C5 1.3747 119.16 -179.98 119.18 1.4365 +IC C6 C4 *C5 H5 1.3659 118.58 179.99 122.05 1.0892 +IC C5 N1 *C6 H6 1.3659 121.84 -179.99 116.76 1.0899 +IC N3 C4 N4 C7 1.3575 119.16 170.00 121.80 1.4600 +IC C7 C4 *N4 C8 1.4600 121.80 -160.00 120.54 1.4628 +IC C4 N4 C7 H71 1.3747 121.80 -179.87 111.57 1.1122 +IC H71 N4 *C7 H72 1.1122 111.57 119.71 111.21 1.1131 +IC H71 N4 *C7 H73 1.1122 111.57 -119.64 111.21 1.1146 +IC C4 N4 C8 H81 1.3747 120.54 -179.93 112.02 1.1111 +IC H81 N4 *C8 H82 1.1111 112.02 120.29 111.11 1.1140 +IC H81 N4 *C8 H83 1.1111 112.02 -120.18 111.05 1.1147 +IC C6 N1 CM HM1 1.3609 121.44 120.78 110.62 1.1145 +IC HM1 N1 *CM HM2 1.1145 110.62 118.50 110.67 1.1148 +IC HM1 N1 *CM HM3 1.1145 110.62 -120.76 112.73 1.1124 + +RESI BM6A 0.00 ! C8H11N5 N6,N6-dimethyladenosine, MA6, DMA, yxu +GROUP +ATOM N9 NG2R51 -0.01 +ATOM C8 CG2R53 0.31 +ATOM H8 HGR52 0.09 +ATOM N7 NG2R50 -0.67 +ATOM C5 CG2RC0 0.41 +ATOM C6 CG2R64 0.52 ! H91 H101 +ATOM N6 NG301 -0.53 ! \ / +ATOM N1 NG2R62 -0.69 ! H92 -C9 C10-H102 +ATOM C2 CG2R64 0.57 ! / \ / \ +ATOM H2 HGR62 0.08 ! H93 N6 H103 +ATOM N3 NG2R62 -0.87 ! | +ATOM C4 CG2RC0 0.43 ! C6 +ATOM C9 CG331 -0.09 ! // \ +ATOM H91 HGA3 0.09 ! N1 C5--N7\\ +ATOM H92 HGA3 0.09 ! | || C8-H8 +ATOM H93 HGA3 0.09 ! C2 C4--N9/ +ATOM C10 CG331 -0.09 ! / \\ / \ +ATOM H101 HGA3 0.09 ! H2 N3 \ +ATOM H102 HGA3 0.09 ! \ +ATOM H103 HGA3 0.09 ! \ +GROUP +ATOM CM CG331 -0.27 +ATOM HM1 HGA3 0.09 +ATOM HM2 HGA3 0.09 +ATOM HM3 HGA3 0.09 + +BOND CM HM1 CM HM2 CM HM3 +BOND N9 C8 N9 C4 C8 N7 C8 H8 +BOND N7 C5 C5 C6 C5 C4 C6 N6 +BOND C6 N1 N6 C10 N6 C9 N1 C2 +BOND C2 N3 C2 H2 N3 C4 C10 H101 +BOND C10 H102 C10 H103 C9 H91 C9 H92 +BOND C9 H93 +BOND CM N9 +IMPR C6 C5 N1 N6 +ACCE N3 +ACCE N7 +ACCE N1 +IC C8 C4 *N9 CM 1.3791 106.12 -179.87 126.32 1.4712 +IC C4 N9 C8 N7 1.3828 106.12 0.04 113.88 1.3241 +IC N7 N9 *C8 H8 1.3241 113.88 -179.96 121.51 1.0919 +IC N9 C8 N7 C5 1.3791 113.88 0.03 103.97 1.4048 +IC C4 N7 *C5 C6 1.4035 110.12 -179.72 133.42 1.4200 +IC N7 C5 C6 N6 1.4048 133.42 0.69 126.34 1.3855 +IC N6 C5 *C6 N1 1.3855 126.34 177.74 117.19 1.3810 +IC C5 C6 N1 C2 1.4200 117.19 1.71 121.05 1.3551 +IC C6 N1 C2 N3 1.3810 121.05 -1.00 124.74 1.3537 +IC N3 N1 *C2 H2 1.3537 124.74 -179.63 117.62 1.0920 +IC C5 C6 N6 C10 1.4200 126.34 166.31 121.38 1.4628 +IC C10 C6 *N6 C9 1.4628 121.38 177.05 122.46 1.4607 +IC C6 N6 C9 H91 1.3855 122.46 -165.22 111.64 1.1121 +IC H91 N6 *C9 H92 1.1121 111.64 119.65 111.59 1.1136 +IC H91 N6 *C9 H93 1.1121 111.64 -120.01 111.04 1.1137 +IC C6 N6 C10 H101 1.3855 121.38 -169.68 111.73 1.1118 +IC H101 N6 *C10 H102 1.1118 111.73 119.69 111.45 1.1139 +IC H101 N6 *C10 H103 1.1118 111.73 -120.15 110.95 1.1142 +IC C4 N9 CM HM1 1.3828 126.32 58.88 110.04 1.1126 +IC HM1 N9 *CM HM2 1.1126 110.04 120.79 112.49 1.1119 +IC HM1 N9 *CM HM3 1.1126 110.04 -118.33 110.07 1.1124 + +RESI DMAN 0.00 ! C8H11N N,N-dimethylaniline, sc & kevo +GROUP +ATOM C1 CG2R61 -0.115 +ATOM H1 HGR61 0.115 +ATOM C2 CG2R61 -0.115 ! H3 +ATOM H2 HGR61 0.115 ! | +ATOM C3 CG2R61 -0.115 ! C3 +ATOM H3 HGR61 0.115 ! / \\ +ATOM C4 CG2R61 -0.115 ! H2--C2 C4--H4 +ATOM H4 HGR61 0.115 ! || | +ATOM C5 CG2R61 -0.115 ! || | +ATOM H5 HGR61 0.115 ! H1--C1 C5--H5 +ATOM C6 CG2R61 0.13 ! \ // +ATOM N1 NG301 -0.49 ! C6 +ATOM C7 CG331 -0.09 ! | +ATOM H71 HGA3 0.09 ! N1 +ATOM H72 HGA3 0.09 ! / \ +ATOM H73 HGA3 0.09 ! H71--C7 C8--H83 +ATOM C8 CG331 -0.09 ! / \ / \ +ATOM H81 HGA3 0.09 ! / \ / \ +ATOM H82 HGA3 0.09 ! H72 H73 H81 H82 +ATOM H83 HGA3 0.09 + +BOND C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1 +BOND C1 H1 C2 H2 C3 H3 C4 H4 C5 H5 +BOND C7 H71 C7 H72 C7 H73 C8 H81 C8 H82 C8 H83 +BOND C6 N1 C7 N1 C8 N1 +IC C6 N1 C7 H71 0.0000 0.00 180.00 0.00 0.0000 +IC N1 H71 *C7 H72 0.0000 0.00 120.00 0.00 0.0000 +IC N1 H71 *C7 H73 0.0000 0.00 -120.00 0.00 0.0000 +IC C6 C7 *N1 C8 0.0000 0.00 -140.00 0.00 0.0000 +IC C6 N1 C8 H81 0.0000 0.00 180.00 0.00 0.0000 +IC N1 H81 *C8 H82 0.0000 0.00 120.00 0.00 0.0000 +IC N1 H81 *C8 H83 0.0000 0.00 -120.00 0.00 0.0000 +IC C7 N1 C6 C1 0.0000 0.00 170.00 0.00 0.0000 +IC N1 C1 *C6 C5 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C6 C5 C4 0.0000 0.00 0.00 0.00 0.0000 +IC C5 C6 C1 C2 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000 +IC C6 C2 *C1 H1 0.0000 0.00 180.00 0.00 0.0000 +IC C1 C3 *C2 H2 0.0000 0.00 180.00 0.00 0.0000 +IC C2 C4 *C3 H3 0.0000 0.00 180.00 0.00 0.0000 +IC C3 C5 *C4 H4 0.0000 0.00 180.00 0.00 0.0000 +IC C4 C6 *C5 H5 0.0000 0.00 180.00 0.00 0.0000 + +END diff --git a/charmm/toppar/top_all36_lipid.rtf b/charmm/toppar/top_all36_lipid.rtf new file mode 100644 index 00000000..77886619 --- /dev/null +++ b/charmm/toppar/top_all36_lipid.rtf @@ -0,0 +1,11768 @@ +* \\\\\\\ CHARMM36 All-Hydrogen Lipid Topology File /////// +* All comments and questions should be submitted to the +* parameter forum at the CHARMM website: www.charmm.org +* +36 1 + +!NOTE: Reordering of atoms in the choline region of the PC lipids as +!requried for the domain decomposition code in CHARMM. This will not +!change the energies/forces, but PSFs generated with the previous +!lipid toppar files may not work. To overcome this a toppar stream +!file, toppar_all36_lipid_orig_pc_atom_order.str, has been created +!which contains the original atom ordering. August 2012 +! + +!references +! +!Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph +!W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor +!Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of +!the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six +!Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843 +! +! PUFA Modifications +!Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving +!the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B. +!2012 ASAP http://dx.doi.org/10.1021/jp304056p + +!Atom nomenclature is based on that of Sundaralingan, M., +!Ann. N.Y. Acad. Sci. USA, 195:324-355, 1972 +!see lipid_convert.tgz for information on nomenclature conversion +!Renaming of atom types by Rick Venable due to switching to the +!nomenclature of Sundaralingan, M., Ann. N.Y. Acad. Sci. USA, +!195:324-355, 1972 +! +!1) toppar_all36_lipid_oldxopc.str +!2) convert_lipid_c27_c36_xopc.str +! +!The above stream files have 1) the old definitions of DOPC +!and POPC, which replace the new definitions when used. The second +!stream file does a RENAME conversion, which allows old coord sets to +!be updated to the new "all36_lipid" convention. + +MASS 136 HL 1.008000 H ! polar H (equivalent to protein H) +MASS 137 HCL 1.008000 H ! charged H for PE (equivalent to protein HC) +MASS 138 HOL 1.008000 H ! Nucleic acid phosphate hydroxyl proton +MASS 139 HAL1 1.008000 H ! alphatic proton +MASS 140 HAL2 1.008000 H ! alphatic proton +MASS 141 HAL3 1.008000 H ! alphatic proton +MASS 142 HEL1 1.008000 H ! for alkene; RHC=CR +MASS 143 HEL2 1.008000 H ! for alkene; H2C=CR. Currently unused. +MASS 144 HBL 1.008000 H ! POPS SER backbone H +MASS 145 CL 12.011000 C ! carbonyl C (acetic acid/methyl acetate) +MASS 146 CTL1 12.011000 C ! sp3 carbon with 1 H (-CH1-) +MASS 147 CTL2 12.011000 C ! carbon of methylene group (-CH2-) +MASS 148 CTL3 12.011000 C ! carbon of methyl group (-CH3) +MASS 149 CTL5 12.011000 C ! carbon of methyl group (-CH3) for tetramethylammonium +MASS 150 CEL1 12.011000 C ! for alkene; RHC=CR +MASS 151 CEL2 12.011000 C ! for alkene; H2C=CR. Currently unused. +MASS 152 CCL 12.011000 C ! for POPS +MASS 153 NTL 14.007000 N ! ammonium nitrogen +MASS 154 NH3L 14.007000 N ! nitrogen phosphatidylethanolamine +MASS 155 OBL 15.999400 O ! acetic acid carboxyl oxygen (e. to protein OB) +MASS 156 OCL 15.999400 O ! acetate oxygen +MASS 157 OSL 15.999400 O ! ester oxygen +MASS 158 O2L 15.999400 O ! Nucleic acid =O in phosphate or sulfate +MASS 159 OHL 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen +MASS 160 OSLP 15.999400 O ! Phosphate oxygen, to avoid conflict with methylacetate type O +MASS 161 PL 30.974000 P ! phosphorus +MASS 162 SL 32.060000 S ! Sulfate sulfur +MASS 163 CRL1 12.011000 C ! sp3 carbon with 1 H on a ring (-CH1-) for sterols +MASS 164 CRL2 12.011000 C ! carbon of methylene group on a ring (-CH2-) for sterols + +DEFA FIRS none LAST none +AUTOGENERATE ANGLES DIHEDRALS + +RESI LPPC 0.00 ! deoxylysophosphatidylcholine +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL2 -0.18 ! HR---C2----HS +ATOM HS HAL2 0.09 ! | +ATOM HR HAL2 0.09 ! | +GROUP ! | +ATOM C3 CTL2 0.08 ! HX---C3---HY +ATOM HX HAL2 0.09 ! | +ATOM HY HAL2 0.09 ! | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL3 -0.27 ! | +ATOM H12X HAL3 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL3 0.09 ! | +ATOM H12Z HAL3 0.09 ! H12Z + ! +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 HR C2 C3 +BOND C3 HX C3 HY C3 O31 + +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 H12Z + +IMPR C31 O31 C32 O32 + +!IC table from IC generated, minimized geometry +IC C13 N C12 C11 1.5007 109.16 60.77 118.01 1.5532 +IC C13 C12 *N C14 1.5007 109.16 118.95 109.93 1.4962 +IC C13 C12 *N C15 1.5007 109.16 -118.66 109.79 1.4970 +IC C12 N C13 H13A 1.5283 109.16 -176.25 113.90 1.0739 +IC H13A N *C13 H13B 1.0739 113.90 -125.02 111.72 1.0902 +IC H13A N *C13 H13C 1.0739 113.90 122.64 109.30 1.0955 +IC C12 N C14 H14A 1.5283 109.93 -59.08 109.81 1.0869 +IC H14A N *C14 H14B 1.0869 109.81 -118.79 110.87 1.0821 +IC H14A N *C14 H14C 1.0869 109.81 119.79 111.30 1.0813 +IC C12 N C15 H15A 1.5283 109.79 177.61 111.54 1.0806 +IC H15A N *C15 H15B 1.0806 111.54 -118.99 108.75 1.0881 +IC H15A N *C15 H15C 1.0806 111.54 122.56 111.42 1.0805 +IC C13 N C12 C11 1.5007 109.16 60.77 118.01 1.5532 +IC C11 N *C12 H12A 1.5532 118.01 -118.57 109.22 1.0958 +IC H12A N *C12 H12B 1.0958 109.22 -116.61 110.32 1.0792 +IC N C12 C11 O12 1.5283 118.01 -64.38 111.82 1.4242 +IC O12 C12 *C11 H11A 1.4242 111.82 -122.02 109.25 1.1168 +IC H11A C12 *C11 H11B 1.1168 109.25 -116.56 110.01 1.1107 +IC C12 C11 O12 P 1.5532 111.82 -63.93 119.44 1.5956 +IC C11 O12 P O11 1.4242 119.44 -108.05 103.40 1.5764 +IC O11 O12 *P O13 1.5764 103.40 -117.37 105.77 1.4773 +IC O11 O12 *P O14 1.5764 103.40 117.10 108.18 1.4806 +IC O12 P O11 C1 1.5956 103.40 -60.59 122.33 1.4218 +IC P O11 C1 C2 1.5764 122.33 128.18 108.48 1.5345 +IC C2 O11 *C1 HA 1.5345 108.48 -121.51 113.56 1.1178 +IC HA O11 *C1 HB 1.1178 113.56 -119.54 108.81 1.1133 +IC O11 C1 C2 C3 1.4218 108.48 -69.15 113.12 1.5322 +IC C3 C1 *C2 HS 1.5322 113.12 -121.29 109.24 1.1115 +IC HS C1 *C2 HR 1.1115 109.24 -117.52 108.27 1.1121 +IC C1 C2 C3 O31 1.5345 113.12 -65.92 107.84 1.4362 +IC O31 C2 *C3 HX 1.4362 107.84 -120.29 109.69 1.1138 +IC HX C2 *C3 HY 1.1138 109.69 -118.31 108.07 1.1170 +IC C2 C3 O31 C31 1.5322 107.84 166.14 114.22 1.3189 +IC C3 O31 C31 C32 1.4362 114.22 -174.70 108.67 1.5288 +IC C32 O31 *C31 O32 1.5288 108.67 -179.80 126.24 1.2203 +IC O31 C31 C32 C33 1.3189 108.67 -167.94 112.47 1.5443 +IC C33 C31 *C32 H2X 1.5443 112.47 -121.71 107.41 1.1092 +IC H2X C31 *C32 H2Y 1.1092 107.41 -116.85 107.91 1.1098 +IC C31 C32 C33 C34 1.5288 112.47 179.46 112.33 1.5340 +IC C34 C32 *C33 H3X 1.5340 112.33 -120.43 109.16 1.1152 +IC H3X C32 *C33 H3Y 1.1152 109.16 -117.67 110.02 1.1133 +IC C32 C33 C34 C35 1.5443 112.33 -176.69 112.31 1.5344 +IC C35 C33 *C34 H4X 1.5344 112.31 -122.05 109.68 1.1126 +IC H4X C33 *C34 H4Y 1.1126 109.68 -117.48 108.87 1.1140 +IC C33 C34 C35 C36 1.5340 112.31 175.27 112.83 1.5344 +IC C36 C34 *C35 H5X 1.5344 112.83 -120.53 108.69 1.1140 +IC H5X C34 *C35 H5Y 1.1140 108.69 -117.22 109.46 1.1123 +IC C34 C35 C36 C37 1.5344 112.83 -177.21 112.46 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.46 -121.92 109.58 1.1126 +IC H6X C35 *C36 H6Y 1.1126 109.58 -117.43 108.81 1.1138 +IC C35 C36 C37 C38 1.5344 112.46 176.32 112.59 1.5343 +IC C38 C36 *C37 H7X 1.5343 112.59 -120.81 108.90 1.1137 +IC H7X C36 *C37 H7Y 1.1137 108.90 -117.41 109.31 1.1128 +IC C36 C37 C38 C39 1.5347 112.59 -178.70 112.72 1.5347 +IC C39 C37 *C38 H8X 1.5347 112.72 -121.68 109.25 1.1130 +IC H8X C37 *C38 H8Y 1.1130 109.25 -117.35 108.93 1.1136 +IC C37 C38 C39 C310 1.5343 112.72 179.00 112.44 1.5346 +IC C310 C38 *C39 H9X 1.5346 112.44 -121.08 109.08 1.1133 +IC H9X C38 *C39 H9Y 1.1133 109.08 -117.47 109.24 1.1129 +IC C38 C39 C310 C311 1.5347 112.44 -179.02 112.83 1.5338 +IC C311 C39 *C310 H10X 1.5338 112.83 -121.47 109.09 1.1131 +IC H10X C39 *C310 H10Y 1.1131 109.09 -117.30 109.04 1.1134 +IC C39 C310 C311 C312 1.5346 112.83 -179.46 113.19 1.5308 +IC C312 C310 *C311 H11X 1.5308 113.19 -121.59 108.75 1.1142 +IC H11X C310 *C311 H11Y 1.1142 108.75 -116.77 108.84 1.1140 +IC C310 C311 C312 H12X 1.5338 113.19 60.40 110.44 1.1113 +IC H12X C311 *C312 H12Y 1.1113 110.44 -119.80 110.43 1.1114 +IC H12X C311 *C312 H12Z 1.1113 110.44 120.09 110.66 1.1113 + +RESI DLPC 0.00 ! 2,3 dilauroyl-D-glycero-1-Phosphatidylcholine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - N(CH3)3 +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL3 -0.27 ! | +ATOM H12R HAL3 0.09 ! H12R---C212--H12S | +ATOM H12S HAL3 0.09 ! | +ATOM H12T HAL3 0.09 ! H12T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL3 -0.27 ! | +ATOM H12X HAL3 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL3 0.09 ! | +ATOM H12Z HAL3 0.09 ! H12Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 H12T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 H12Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 N C12 C11 1.4966 111.24 166.28 118.98 1.5540 +IC C13 C12 *N C14 1.4966 111.24 -121.31 109.70 1.5014 +IC C13 C12 *N C15 1.4966 111.24 120.39 109.59 1.5032 +IC C12 N C13 H13A 1.5282 111.24 -61.73 111.02 1.0824 +IC H13A N *C13 H13B 1.0824 111.02 -119.31 110.03 1.0843 +IC H13A N *C13 H13C 1.0824 111.02 121.33 110.99 1.0825 +IC C12 N C14 H14A 1.5282 109.70 -175.08 112.24 1.0791 +IC H14A N *C14 H14B 1.0791 112.24 -124.93 112.61 1.0781 +IC H14A N *C14 H14C 1.0791 112.24 117.38 109.50 1.0986 +IC C12 N C15 H15A 1.5282 109.59 -61.54 112.73 1.0781 +IC H15A N *C15 H15B 1.0781 112.73 -124.99 112.40 1.0795 +IC H15A N *C15 H15C 1.0781 112.73 117.76 109.79 1.0975 +IC C11 N *C12 H12A 1.5540 118.98 -122.28 108.97 1.0812 +IC H12A N *C12 H12B 1.0812 108.97 -117.10 108.29 1.0835 +IC N C12 C11 O12 1.5282 118.98 60.04 111.29 1.4211 +IC O12 C12 *C11 H11A 1.4211 111.29 -126.93 110.16 1.1157 +IC H11A C12 *C11 H11B 1.1157 110.16 -114.93 108.04 1.1136 +IC C12 C11 O12 P 1.5540 111.29 -112.41 123.03 1.5867 +IC C11 O12 P O11 1.4211 123.03 -112.11 102.86 1.5750 +IC O11 O12 *P O13 1.5750 102.86 -117.06 105.38 1.4772 +IC O11 O12 *P O14 1.5750 102.86 117.53 108.43 1.4796 +IC O12 P O11 C1 1.5867 102.86 -56.61 121.12 1.4309 +IC P O11 C1 C2 1.5750 121.12 -83.15 112.71 1.5564 +IC C2 O11 *C1 HA 1.5564 112.71 -117.95 107.87 1.1127 +IC HA O11 *C1 HB 1.1127 107.87 -117.85 112.30 1.1145 +IC O11 C1 C2 C3 1.4309 112.71 -172.05 111.41 1.5541 +IC C3 C1 *C2 O21 1.5541 111.41 122.05 108.04 1.4389 +IC C3 C1 *C2 HS 1.5541 111.41 -118.42 106.92 1.1167 +IC C1 C2 O21 C21 1.5564 108.04 158.54 115.01 1.3183 +IC C2 O21 C21 C22 1.4389 115.01 -173.62 109.25 1.5301 +IC C22 O21 *C21 O22 1.5301 109.25 -179.40 126.05 1.2181 +IC O21 C21 C22 C23 1.3183 109.25 -117.90 111.70 1.5446 +IC C23 C21 *C22 H2R 1.5446 111.70 -120.98 107.48 1.1089 +IC H2R C21 *C22 H2S 1.1089 107.48 -117.26 108.89 1.1098 +IC C1 C2 C3 O31 1.5564 111.41 -53.99 110.37 1.4448 +IC O31 C2 *C3 HX 1.4448 110.37 -121.24 109.56 1.1120 +IC HX C2 *C3 HY 1.1120 109.56 -116.88 106.08 1.1171 +IC C2 C3 O31 C31 1.5541 110.37 157.10 114.49 1.3276 +IC C3 O31 C31 C32 1.4448 114.49 -179.05 109.34 1.5276 +IC C32 O31 *C31 O32 1.5276 109.34 178.85 125.77 1.2163 +IC O31 C31 C32 C33 1.3276 109.34 -71.25 112.33 1.5453 +IC C33 C31 *C32 H2X 1.5453 112.33 -121.91 107.83 1.1087 +IC H2X C31 *C32 H2Y 1.1087 107.83 -117.09 107.48 1.1098 +IC C21 C22 C23 C24 1.5301 111.70 174.22 112.39 1.5364 +IC C24 C22 *C23 H3R 1.5364 112.39 -120.52 108.74 1.1143 +IC H3R C22 *C23 H3S 1.1143 108.74 -117.72 109.66 1.1144 +IC C22 C23 C24 C25 1.5446 112.39 176.17 113.71 1.5389 +IC C25 C23 *C24 H4R 1.5389 113.71 -121.29 108.85 1.1139 +IC H4R C23 *C24 H4S 1.1139 108.85 -117.02 108.83 1.1137 +IC C23 C24 C25 C26 1.5364 113.71 58.19 113.57 1.5361 +IC C26 C24 *C25 H5R 1.5361 113.57 -121.29 108.91 1.1134 +IC H5R C24 *C25 H5S 1.1134 108.91 -117.11 108.87 1.1132 +IC C24 C25 C26 C27 1.5389 113.57 178.62 113.16 1.5366 +IC C27 C25 *C26 H6R 1.5366 113.16 -122.19 109.43 1.1127 +IC H6R C25 *C26 H6S 1.1127 109.43 -117.10 108.68 1.1096 +IC C25 C26 C27 C28 1.5361 113.16 174.50 113.47 1.5400 +IC C28 C26 *C27 H7R 1.5400 113.47 -122.95 110.10 1.1120 +IC H7R C26 *C27 H7S 1.1120 110.10 -116.75 107.49 1.1142 +IC C26 C27 C28 C29 1.5366 113.47 -95.83 114.71 1.5424 +IC C29 C27 *C28 H8R 1.5424 114.71 -118.57 107.61 1.1152 +IC H8R C27 *C28 H8S 1.1152 107.61 -116.24 109.93 1.1111 +IC C27 C28 C29 C210 1.5400 114.71 63.13 115.93 1.5407 +IC C210 C28 *C29 H9R 1.5407 115.93 -121.53 108.05 1.1138 +IC H9R C28 *C29 H9S 1.1138 108.05 -115.66 108.55 1.1127 +IC C28 C29 C210 C211 1.5424 115.93 62.76 115.20 1.5388 +IC C211 C29 *C21 H10R 6.0255 16.54 100.54 10.30 5.9276 +IC H10R C29 *C21 H10S 5.9276 10.30 -42.25 16.19 7.2059 +IC C29 C210 C211 C212 1.5407 115.20 64.60 114.34 1.5319 +IC C212 C210 *C21 H11R 7.2454 20.82 -38.90 18.34 5.6305 +IC H11R C210 *C21 H11S 5.6305 18.34 64.37 16.79 5.3167 +IC C210 C211 C212 H12R 1.5388 114.34 -64.54 110.77 1.1107 +IC H12R C211 *C21 H12S 7.9945 7.88 89.82 10.46 7.8159 +IC H12R C211 *C21 H12T 7.9945 7.88 40.24 16.78 7.0865 +IC C31 C32 C33 C34 1.5276 112.33 -71.63 112.59 1.5348 +IC C34 C32 *C33 H3X 1.5348 112.59 -119.64 108.68 1.1142 +IC H3X C32 *C33 H3Y 1.1142 108.68 -117.31 110.23 1.1138 +IC C32 C33 C34 C35 1.5453 112.59 178.52 112.65 1.5353 +IC C35 C33 *C34 H4X 1.5353 112.65 -120.91 109.18 1.1129 +IC H4X C33 *C34 H4Y 1.1129 109.18 -117.55 109.26 1.1133 +IC C33 C34 C35 C36 1.5348 112.65 173.82 114.44 1.5403 +IC C36 C34 *C35 H5X 1.5403 114.44 -121.24 108.76 1.1138 +IC H5X C34 *C35 H5Y 1.1138 108.76 -116.91 108.64 1.1138 +IC C34 C35 C36 C37 1.5353 114.44 58.04 114.79 1.5396 +IC C37 C35 *C36 H6X 1.5396 114.79 -123.72 109.93 1.1120 +IC H6X C35 *C36 H6Y 1.1120 109.93 -116.21 107.23 1.1147 +IC C35 C36 C37 C38 1.5403 114.79 -96.72 113.37 1.5384 +IC C38 C36 *C37 H7X 1.5384 113.37 124.26 109.66 1.1114 +IC H7X C36 *C37 H7Y 1.1114 109.66 116.90 108.33 1.1150 +IC C36 C37 C38 C39 1.5396 113.37 -176.98 113.66 1.5393 +IC C39 C37 *C38 H8X 1.5393 113.66 -123.13 110.21 1.1107 +IC H8X C37 *C38 H8Y 1.1107 110.21 -116.72 108.12 1.1141 +IC C37 C38 C39 C310 1.5384 113.66 -67.32 114.98 1.5412 +IC C310 C38 *C39 H9X 1.5412 114.98 121.99 108.65 1.1131 +IC H9X C38 *C39 H9Y 1.1131 108.65 116.07 108.54 1.1129 +IC C38 C39 C310 C311 1.5393 114.98 -59.10 115.15 1.5391 +IC C311 C39 *C31 H10X 4.3520 21.08 -62.16 20.70 5.5478 +IC H10X C39 *C31 H10Y 5.5478 20.70 44.35 19.66 6.4331 +IC C39 C310 C311 C312 1.5412 115.15 -56.76 114.89 1.5327 +IC C312 C310 *C31 H11X 4.8312 27.76 25.46 5.09 3.4146 +IC H11X C310 *C31 H11Y 3.4146 5.09 -91.07 21.38 4.4060 +IC C310 C311 C312 H12X 1.5391 114.89 -57.58 110.52 1.1109 +IC H12X C311 *C31 H12Y 5.8485 18.17 43.95 25.29 5.0871 +IC H12X C311 *C31 H12Z 5.8485 18.17 0.07 29.12 4.3175 + +RESI DLPE 0.00 ! 2,3 dilauroyl-D-glycero-1-Phosphatidylethanolamine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL3 -0.27 ! | +ATOM H12R HAL3 0.09 ! H12R---C212--H12S | +ATOM H12S HAL3 0.09 ! | +ATOM H12T HAL3 0.09 ! H12T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL3 -0.27 ! | +ATOM H12X HAL3 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL3 0.09 ! | +ATOM H12Z HAL3 0.09 ! H12Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 H12T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 H12Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.5081 111.59 -73.10 113.26 1.4276 +IC C11 N *C12 H12A 1.5457 111.59 -120.62 107.97 1.1100 +IC HN1 C12 *N HN2 1.0538 110.27 -125.06 113.96 1.0325 +IC HN1 C12 *N HN3 1.0538 110.27 115.83 105.31 1.0629 +IC HN1 N C12 C11 1.0538 110.27 -58.43 111.59 1.5457 +IC H12A N *C12 H12B 1.1100 107.97 -118.48 107.57 1.1089 +IC O12 C12 *C11 H11A 1.4276 113.26 -118.43 107.57 1.1140 +IC H11A C12 *C11 H11B 1.1140 107.57 -115.51 110.35 1.1121 +IC C12 C11 O12 P 1.5457 113.26 73.21 123.11 1.5821 +IC C11 O12 P O11 1.4276 123.11 34.25 100.92 1.5725 +IC O11 O12 *P O13 1.5725 100.92 118.29 112.02 1.4695 +IC O11 O12 *P O14 1.5725 100.92 -108.59 105.98 1.4820 +IC O12 P O11 C1 1.5821 100.92 93.08 123.05 1.4250 +IC P O11 C1 C2 1.5725 123.05 -158.55 108.93 1.5522 +IC C2 O11 *C1 HA 1.5522 108.93 -118.72 109.36 1.1135 +IC HA O11 *C1 HB 1.1135 109.36 -119.33 112.35 1.1156 +IC O11 C1 C2 C3 1.4250 108.93 -50.37 110.31 1.5644 +IC C3 C1 *C2 O21 1.5644 110.31 122.15 109.56 1.4463 !defines S chirality +IC C3 C1 *C2 HS 1.5644 110.31 -116.40 109.18 1.1165 !defines S chirality +IC C1 C2 O21 C21 1.5522 109.56 79.76 113.36 1.3301 +IC C2 O21 C21 C22 1.4463 113.36 -171.78 109.82 1.5286 +IC C22 O21 *C21 O22 1.5286 109.82 179.59 125.69 1.2157 +IC O21 C21 C22 C23 1.3301 109.82 -96.56 112.64 1.5461 +IC C23 C21 *C22 H2R 1.5461 112.64 -119.55 106.22 1.1113 +IC H2R C21 *C22 H2S 1.1113 106.22 -116.80 109.41 1.1071 +IC C1 C2 C3 O31 1.5522 110.31 153.88 112.56 1.4435 +IC O31 C2 *C3 HX 1.4435 112.56 -125.97 110.32 1.1120 +IC HX C2 *C3 HY 1.1120 110.32 -114.28 106.98 1.1128 +IC C2 C3 O31 C31 1.5644 112.56 -90.79 115.60 1.3262 +IC C3 O31 C31 C32 1.4435 115.60 169.19 109.07 1.5269 +IC C32 O31 *C31 O32 1.5269 109.07 -178.13 126.32 1.2224 +IC O31 C31 C32 C33 1.3262 109.07 105.25 113.97 1.5441 +IC C33 C31 *C32 H2X 1.5441 113.97 -122.05 108.45 1.1103 +IC H2X C31 *C32 H2Y 1.1103 108.45 -116.70 107.29 1.1094 +IC C21 C22 C23 C24 1.5286 112.64 72.21 112.51 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.51 -123.50 110.52 1.1136 +IC H3R C22 *C23 H3S 1.1136 110.52 -117.13 108.24 1.1150 +IC C22 C23 C24 C25 1.5461 112.51 173.89 113.24 1.5353 +IC C25 C23 *C24 H4R 1.5353 113.24 -120.86 108.78 1.1132 +IC H4R C23 *C24 H4S 1.1132 108.78 -117.56 109.21 1.1134 +IC C23 C24 C25 C26 1.5338 113.24 -179.11 112.15 1.5349 +IC C26 C24 *C25 H5R 1.5349 112.15 -121.41 109.36 1.1133 +IC H5R C24 *C25 H5S 1.1133 109.36 -117.59 109.16 1.1133 +IC C24 C25 C26 C27 1.5353 112.15 177.84 113.48 1.5342 +IC C27 C25 *C26 H6R 1.5342 113.48 -121.24 108.98 1.1132 +IC H6R C25 *C26 H6S 1.1132 108.98 -117.52 109.02 1.1130 +IC C25 C26 C27 C28 1.5349 113.48 -179.41 112.03 1.5353 +IC C28 C26 *C27 H7R 1.5353 112.03 -121.20 109.25 1.1132 +IC H7R C26 *C27 H7S 1.1132 109.25 -117.63 109.28 1.1130 +IC C26 C27 C28 C29 1.5342 112.03 -179.77 113.13 1.5342 +IC C29 C27 *C28 H8R 1.5342 113.13 -121.43 109.07 1.1131 +IC H8R C27 *C28 H8S 1.1131 109.07 -117.27 109.04 1.1132 +IC C27 C28 C29 C210 1.5353 113.13 -179.80 112.43 1.5353 +IC C210 C28 *C29 H9R 1.5353 112.43 -121.20 109.12 1.1132 +IC H9R C28 *C29 H9S 1.1132 109.12 -117.50 109.24 1.1131 +IC C28 C29 C210 C211 1.5342 112.43 -179.68 112.77 1.5338 +IC C211 C29 *C210 H10R 1.5338 112.77 -121.35 109.16 1.1131 +IC H10R C29 *C210 H10S 1.1131 109.16 -117.35 109.14 1.1132 +IC C29 C210 C211 C212 1.5353 112.77 -179.85 113.38 1.5309 +IC C212 C210 *C211 H11R 1.5309 113.38 -121.68 108.78 1.1141 +IC H11R C210 *C211 H11S 1.1141 108.78 -116.64 108.78 1.1140 +IC C210 C211 C212 H12R 1.5338 113.38 60.06 110.50 1.1112 +IC H12R C211 *C212 H12S 1.1112 110.50 -119.88 110.53 1.1113 +IC H12R C211 *C212 H12T 1.1112 110.50 120.06 110.61 1.1113 +IC C31 C32 C33 C34 1.5269 113.97 -176.87 110.60 1.5345 +IC C34 C32 *C33 H3X 1.5345 110.60 -121.15 110.42 1.1131 +IC H3X C32 *C33 H3Y 1.1131 110.42 -119.02 109.90 1.1145 +IC C32 C33 C34 C35 1.5441 110.60 178.15 113.68 1.5334 +IC C35 C33 *C34 H4X 1.5334 113.68 -121.01 108.74 1.1141 +IC H4X C33 *C34 H4Y 1.1141 108.74 -116.97 109.36 1.1132 +IC C33 C34 C35 C36 1.5345 113.68 -177.06 111.90 1.5350 +IC C36 C34 *C35 H5X 1.5350 111.90 -121.43 109.53 1.1127 +IC H5X C34 *C35 H5Y 1.1127 109.53 -117.89 109.27 1.1134 +IC C34 C35 C36 C37 1.5334 111.90 179.23 112.99 1.5340 +IC C37 C35 *C36 H6X 1.5340 112.99 -121.08 108.94 1.1138 +IC H6X C35 *C36 H6Y 1.1138 108.94 -117.23 109.34 1.1132 +IC C35 C36 C37 C38 1.5350 112.99 -177.88 112.25 1.5344 +IC C38 C36 *C37 H7X 1.5344 112.25 -121.43 109.33 1.1129 +IC H7X C36 *C37 H7Y 1.1129 109.33 -117.59 109.16 1.1132 +IC C36 C37 C38 C39 1.5340 112.25 179.64 112.89 1.5342 +IC C39 C37 *C38 H8X 1.5342 112.89 -121.23 109.02 1.1134 +IC H8X C37 *C38 H8Y 1.1134 109.02 -117.22 109.17 1.1131 +IC C37 C38 C39 C310 1.5344 112.89 -179.25 112.43 1.5347 +IC C310 C38 *C39 H9X 1.5347 112.43 -121.34 109.21 1.1130 +IC H9X C38 *C39 H9Y 1.1130 109.21 -117.49 109.18 1.1132 +IC C38 C39 C310 C311 1.5342 112.43 -179.94 112.73 1.5336 +IC C311 C39 *C310 H10X 1.5336 112.73 -121.36 109.09 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.09 -117.30 109.12 1.1130 +IC C39 C310 C311 C312 1.5347 112.73 -179.76 113.35 1.5310 +IC C312 C310 *C311 H11X 1.5310 113.35 -121.66 108.73 1.1141 +IC H11X C310 *C311 H11Y 1.1141 108.73 -116.65 108.75 1.1141 +IC C310 C311 C312 H12X 1.5336 113.35 60.17 110.49 1.1114 +IC H12X C311 *C312 H12Y 1.1114 110.49 -119.95 110.51 1.1114 +IC H12X C311 *C312 H12Z 1.1114 110.49 120.02 110.54 1.1114 + +RESI DLPS -1.00 ! 2,3 dilauroyl-D-glycero-1-Phosphatidylserine +! +! R1 - CH2 +! | (-) +! R2 - CH CO2 +! | (-) | (+) +! CH2 - PO4 - CH2 - CH - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL3 -0.27 ! | +ATOM H12R HAL3 0.09 ! H12R---C212--H12S | +ATOM H12S HAL3 0.09 ! | +ATOM H12T HAL3 0.09 ! H12T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL3 -0.27 ! | +ATOM H12X HAL3 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL3 0.09 ! | +ATOM H12Z HAL3 0.09 ! H12Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 H12T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 H12Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 C13 C12 O13B O13A + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.4891 109.93 64.23 111.52 1.4345 +IC N C12 C13 O13B 1.4891 108.78 -175.98 117.97 1.2539 +IC HN1 C12 *N HN2 1.0594 109.33 118.39 102.42 1.0478 +IC HN1 C12 *N HN3 1.0594 109.33 -123.51 111.37 1.0290 +IC HN1 N C12 C11 1.0594 109.33 -16.80 109.93 1.5580 +IC C11 N *C12 C13 1.5580 109.93 -121.84 108.78 1.5424 +IC C13 N *C12 H12A 1.5424 108.78 -117.79 109.18 1.0794 +IC O13B C12 *C13 O13A 1.2539 117.97 178.90 118.13 1.2655 +IC O12 C12 *C11 H11A 1.4345 111.52 -126.26 110.05 1.1169 +IC H11A C12 *C11 H11B 1.1169 110.05 -115.34 107.30 1.1148 +IC C12 C11 O12 P 1.5580 111.52 -99.98 122.21 1.5848 +IC C11 O12 P O11 1.4345 122.21 -55.63 102.29 1.5789 +IC O11 O12 *P O13 1.5789 102.29 -117.49 109.44 1.4730 +IC O11 O12 *P O14 1.5789 102.29 114.26 105.55 1.4828 +IC O12 P O11 C1 1.5848 102.29 -57.27 120.48 1.4322 +IC P O11 C1 C2 1.5789 120.48 -87.79 112.61 1.5559 +IC C2 O11 *C1 HA 1.5559 112.61 -118.54 108.31 1.1125 +IC HA O11 *C1 HB 1.1125 108.31 -117.75 112.02 1.1146 +IC O11 C1 C2 C3 1.4322 112.61 -179.46 111.68 1.5589 +IC C3 C1 *C2 O21 1.5589 111.68 122.72 107.77 1.4403 +IC C3 C1 *C2 HS 1.5589 111.68 -118.15 106.82 1.1170 +IC C1 C2 O21 C21 1.5559 107.77 162.21 115.61 1.3150 +IC C2 O21 C21 C22 1.4403 115.61 -174.15 108.52 1.5308 +IC C22 O21 *C21 O22 1.5308 108.52 -178.93 126.48 1.2177 +IC O21 C21 C22 C23 1.3150 108.52 -161.76 112.30 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.30 -121.50 107.45 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.45 -116.98 108.10 1.1093 +IC C1 C2 C3 O31 1.5559 111.68 -52.51 110.63 1.4450 +IC O31 C2 *C3 HX 1.4450 110.63 -119.21 108.84 1.1107 +IC HX C2 *C3 HY 1.1107 108.84 -115.84 107.52 1.1153 +IC C2 C3 O31 C31 1.5589 110.63 112.86 117.20 1.3272 +IC C3 O31 C31 C32 1.4450 117.20 -168.35 109.07 1.5279 +IC C32 O31 *C31 O32 1.5279 109.07 177.73 126.07 1.2164 +IC O31 C31 C32 C33 1.3272 109.07 -74.25 112.64 1.5444 +IC C33 C31 *C32 H2X 1.5444 112.64 -122.66 108.07 1.1084 +IC H2X C31 *C32 H2Y 1.1084 108.07 -116.55 107.15 1.1113 +IC C21 C22 C23 C24 1.5308 112.30 177.91 112.32 1.5359 +IC C24 C22 *C23 H3R 1.5359 112.32 -121.07 108.67 1.1133 +IC H3R C22 *C23 H3S 1.1133 108.67 -117.41 109.71 1.1143 +IC C22 C23 C24 C25 1.5451 112.32 179.66 113.72 1.5385 +IC C25 C23 *C24 H4R 1.5385 113.72 -121.18 108.53 1.1139 +IC H4R C23 *C24 H4S 1.1139 108.53 -116.88 109.06 1.1131 +IC C23 C24 C25 C26 1.5359 113.72 62.22 113.52 1.5367 +IC C26 C24 *C25 H5R 1.5367 113.52 -121.83 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.13 108.61 1.1135 +IC C24 C25 C26 C27 1.5385 113.52 176.56 112.95 1.5368 +IC C27 C25 *C26 H6R 1.5368 112.95 -121.36 109.02 1.1128 +IC H6R C25 *C26 H6S 1.1128 109.02 -117.16 108.98 1.1100 +IC C25 C26 C27 C28 1.5367 112.95 -179.20 113.93 1.5399 +IC C28 C26 *C27 H7R 1.5399 113.93 -123.64 110.16 1.1113 +IC H7R C26 *C27 H7S 1.1113 110.16 -116.59 107.25 1.1144 +IC C26 C27 C28 C29 1.5368 113.93 -93.70 114.93 1.5420 +IC C29 C27 *C28 H8R 1.5420 114.93 -118.47 107.45 1.1152 +IC H8R C27 *C28 H8S 1.1152 107.45 -115.96 109.97 1.1105 +IC C27 C28 C29 C210 1.5399 114.93 66.39 115.90 1.5399 +IC C210 C28 *C29 H9R 1.5399 115.90 -122.16 108.40 1.1133 +IC H9R C28 *C29 H9S 1.1133 108.40 -115.77 108.31 1.1129 +IC C28 C29 C210 C211 1.5420 115.90 58.41 115.07 1.5388 +IC C211 C29 *C21 H10R 6.3253 16.96 95.07 9.47 6.0286 +IC H10R C29 *C21 H10S 6.0286 9.47 -36.77 15.90 7.3839 +IC C29 C210 C211 C212 1.5399 115.07 62.51 114.55 1.5323 +IC C212 C210 *C21 H11R 7.6123 19.62 -35.47 18.04 5.8989 +IC H11R C210 *C21 H11S 5.8989 18.04 60.92 17.08 5.6654 +IC C210 C211 C212 H12R 1.5388 114.55 -63.16 110.67 1.1109 +IC H12R C211 *C21 H12S 8.3272 6.96 47.64 15.22 7.5216 +IC H12R C211 *C21 H12T 8.3272 6.96 101.62 9.10 8.1865 +IC C31 C32 C33 C34 1.5279 112.64 -75.87 112.70 1.5364 +IC C34 C32 *C33 H3X 1.5364 112.70 -119.26 108.25 1.1151 +IC H3X C32 *C33 H3Y 1.1151 108.25 -116.69 110.11 1.1123 +IC C32 C33 C34 C35 1.5444 112.70 178.13 113.13 1.5382 +IC C35 C33 *C34 H4X 1.5382 113.13 -123.33 110.68 1.1125 +IC H4X C33 *C34 H4Y 1.1125 110.68 -116.62 107.51 1.1143 +IC C33 C34 C35 C36 1.5364 113.13 -99.87 114.17 1.5392 +IC C36 C34 *C35 H5X 1.5392 114.17 -119.78 108.39 1.1145 +IC H5X C34 *C35 H5Y 1.1145 108.39 -116.66 109.33 1.1122 +IC C34 C35 C36 C37 1.5382 114.17 58.34 114.39 1.5358 +IC C37 C35 *C36 H6X 1.5358 114.39 -121.49 108.81 1.1134 +IC H6X C35 *C36 H6Y 1.1134 108.81 -116.81 108.64 1.1131 +IC C35 C36 C37 C38 1.5392 114.39 177.41 112.36 1.5361 +IC C38 C36 *C37 H7X 1.5361 112.36 -121.51 109.38 1.1127 +IC H7X C36 *C37 H7Y 1.1127 109.38 -117.65 108.97 1.1127 +IC C36 C37 C38 C39 1.5358 112.36 -179.01 113.81 1.5389 +IC C39 C37 *C38 H8X 1.5389 113.81 -122.34 109.05 1.1122 +IC H8X C37 *C38 H8Y 1.1122 109.05 -116.63 108.59 1.1131 +IC C37 C38 C39 C310 1.5361 113.81 -60.02 115.00 1.5410 +IC C310 C38 *C39 H9X 1.5410 115.00 121.40 108.49 1.1136 +IC H9X C38 *C39 H9Y 1.1136 108.49 116.27 108.68 1.1127 +IC C38 C39 C310 C311 1.5389 115.00 -56.60 115.12 1.5388 +IC C311 C39 *C31 H10X 5.1057 25.95 -55.74 21.34 5.7488 +IC H10X C39 *C31 H10Y 5.7488 21.34 -12.53 13.96 4.1024 +IC C39 C310 C311 C312 1.5410 115.12 -57.44 114.57 1.5324 +IC C312 C310 *C31 H11X 6.5942 20.77 20.50 25.40 4.6121 +IC H11X C310 *C31 H11Y 4.6121 25.40 -52.28 25.06 4.8387 +IC C310 C311 C312 H12X 1.5388 114.57 -55.45 110.37 1.1106 +IC H12X C311 *C31 H12Y 7.2220 5.07 -173.55 9.39 7.0599 +IC H12X C311 *C31 H12Z 7.2220 5.07 102.38 12.47 6.8714 + +RESI DLPA -1.00 ! 2,3 dilauroyl-D-glycero-1-Phosphatidic acid +! +! R1 - CH2 +! | +! R2 - CH +! | (-) +! CH2 - PO4 - H +! +! Polar Head and glycerol backbone +GROUP ! H12 + ! | +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.82 ! \ / alpha3 +ATOM O14 O2L -0.82 ! P (+) +ATOM O12 OHL -0.68 ! / \ alpha2 +ATOM H12 HOL 0.34 ! (-) O14 O11 +ATOM O11 OSLP -0.62 ! | +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL3 -0.27 ! | +ATOM H12R HAL3 0.09 ! H12R---C212--H12S | +ATOM H12S HAL3 0.09 ! | +ATOM H12T HAL3 0.09 ! H12T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL3 -0.27 ! | +ATOM H12X HAL3 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL3 0.09 ! | +ATOM H12Z HAL3 0.09 ! H12Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 H12T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 H12Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC O11 P O12 H12 1.5807 107.12 179.80 105.25 0.9594 +IC O12 O11 *P O13 1.5648 107.12 112.86 111.62 1.4716 +IC O12 O11 *P O14 1.5648 107.12 -112.61 111.22 1.4723 +IC O12 P O11 C1 1.5648 107.12 177.80 116.98 1.4333 +IC P O11 C1 C2 1.5807 116.98 177.37 111.07 1.5515 +IC C2 O11 *C1 HA 1.5515 111.07 -119.84 110.91 1.1162 +IC HA O11 *C1 HB 1.1162 110.91 -120.43 110.17 1.1153 +IC O11 C1 C2 C3 1.4333 111.07 176.43 111.27 1.5550 +IC C3 C1 *C2 O21 1.5550 111.27 121.76 108.25 1.4404 +IC C3 C1 *C2 HS 1.5550 111.27 -118.60 106.44 1.1164 +IC C1 C2 O21 C21 1.5515 108.25 160.25 115.39 1.3128 +IC C2 O21 C21 C22 1.4404 115.39 -175.42 109.02 1.5311 +IC C22 O21 *C21 O22 1.5311 109.02 -179.90 126.22 1.2211 +IC O21 C21 C22 C23 1.3128 109.02 -146.89 112.22 1.5455 +IC C23 C21 *C22 H2R 1.5455 112.22 -121.45 107.29 1.1089 +IC H2R C21 *C22 H2S 1.1089 107.29 -117.05 108.56 1.1101 +IC C1 C2 C3 O31 1.5515 111.27 -53.46 110.54 1.4449 +IC O31 C2 *C3 HX 1.4449 110.54 -121.38 109.64 1.1117 +IC HX C2 *C3 HY 1.1117 109.64 -117.05 105.80 1.1178 +IC C2 C3 O31 C31 1.5550 110.54 158.35 114.35 1.3256 +IC C3 O31 C31 C32 1.4449 114.35 -176.09 109.65 1.5294 +IC C32 O31 *C31 O32 1.5294 109.65 179.65 125.67 1.2169 +IC O31 C31 C32 C33 1.3256 109.65 -72.37 112.57 1.5466 +IC C33 C31 *C32 H2X 1.5466 112.57 -121.63 107.53 1.1091 +IC H2X C31 *C32 H2Y 1.1091 107.53 -117.09 107.69 1.1107 +IC C21 C22 C23 C24 1.5311 112.22 179.54 112.51 1.5364 +IC C24 C22 *C23 H3R 1.5364 112.51 -121.13 108.49 1.1130 +IC H3R C22 *C23 H3S 1.1130 108.49 -117.39 109.92 1.1139 +IC C22 C23 C24 C25 1.5455 112.51 -179.22 113.65 1.5384 +IC C25 C23 *C24 H4R 1.5384 113.65 -121.46 108.66 1.1134 +IC H4R C23 *C24 H4S 1.1134 108.66 -116.72 109.19 1.1125 +IC C23 C24 C25 C26 1.5364 113.65 62.74 113.39 1.5362 +IC C26 C24 *C25 H5R 1.5362 113.39 -121.74 108.99 1.1124 +IC H5R C24 *C25 H5S 1.1124 108.99 -117.06 108.76 1.1132 +IC C24 C25 C26 C27 1.5384 113.39 177.89 113.04 1.5364 +IC C27 C25 *C26 H6R 1.5364 113.04 -121.64 108.93 1.1132 +IC H6R C25 *C26 H6S 1.1132 108.93 -117.12 108.97 1.1105 +IC C25 C26 C27 C28 1.5362 113.04 178.52 113.41 1.5398 +IC C28 C26 *C27 H7R 1.5398 113.41 -123.32 110.02 1.1121 +IC H7R C26 *C27 H7S 1.1121 110.02 -116.54 107.46 1.1143 +IC C26 C27 C28 C29 1.5364 113.41 -97.04 114.60 1.5421 +IC C29 C27 *C28 H8R 1.5421 114.60 -118.72 107.58 1.1150 +IC H8R C27 *C28 H8S 1.1150 107.58 -116.06 109.94 1.1114 +IC C27 C28 C29 C210 1.5398 114.60 65.36 115.76 1.5407 +IC C210 C28 *C29 H9R 1.5407 115.76 -121.82 108.23 1.1136 +IC H9R C28 *C29 H9S 1.1136 108.23 -115.82 108.37 1.1128 +IC C28 C29 C210 C211 1.5421 115.76 61.40 114.96 1.5394 +IC C211 C29 *C21 H10R 6.2855 16.87 58.09 15.94 7.3741 +IC H10R C29 *C21 H10S 7.3741 15.94 37.59 9.67 6.0245 +IC C29 C210 C211 C212 1.5407 114.96 61.78 114.52 1.5321 +IC C212 C210 *C21 H11R 7.5634 19.79 -35.10 18.02 5.8397 +IC H11R C210 *C21 H11S 5.8397 18.02 61.72 17.11 5.6424 +IC C210 C211 C212 H12R 1.5394 114.52 -64.52 110.83 1.1101 +IC H12R C211 *C21 H12S 8.2634 7.45 100.22 8.93 8.1609 +IC H12R C211 *C21 H12T 8.2634 7.45 47.68 15.45 7.4617 +IC C31 C32 C33 C34 1.5294 112.57 -62.93 112.69 1.5345 +IC C34 C32 *C33 H3X 1.5345 112.69 -120.38 108.62 1.1136 +IC H3X C32 *C33 H3Y 1.1136 108.62 -117.11 109.87 1.1139 +IC C32 C33 C34 C35 1.5466 112.69 -175.81 113.30 1.5377 +IC C35 C33 *C34 H4X 1.5377 113.30 -121.47 108.66 1.1126 +IC H4X C33 *C34 H4Y 1.1126 108.66 -116.84 109.49 1.1131 +IC C33 C34 C35 C36 1.5345 113.30 -171.47 112.34 1.5367 +IC C36 C34 *C35 H5X 1.5367 112.34 -120.86 108.21 1.1127 +IC H5X C34 *C35 H5Y 1.1127 108.21 -117.27 109.95 1.1122 +IC C34 C35 C36 C37 1.5377 112.34 78.14 112.77 1.5375 +IC C37 C35 *C36 H6X 1.5375 112.77 -120.98 108.02 1.1135 +IC H6X C35 *C36 H6Y 1.1135 108.02 -117.38 110.10 1.1132 +IC C35 C36 C37 C38 1.5367 112.77 -156.33 112.62 1.5359 +IC C38 C36 *C37 H7X 1.5359 112.62 -122.93 109.55 1.1121 +IC H7X C36 *C37 H7Y 1.1121 109.55 -116.93 108.87 1.1128 +IC C36 C37 C38 C39 1.5375 112.62 -179.76 114.09 1.5399 +IC C39 C37 *C38 H8X 1.5399 114.09 -121.35 108.41 1.1131 +IC H8X C37 *C38 H8Y 1.1131 108.41 -116.50 109.16 1.1129 +IC C37 C38 C39 C310 1.5359 114.09 -54.04 115.37 1.5428 +IC C310 C38 *C39 H9X 1.5428 115.37 121.48 108.41 1.1134 +IC H9X C38 *C39 H9Y 1.1134 108.41 115.94 108.45 1.1126 +IC C38 C39 C310 C311 1.5399 115.37 -54.53 115.53 1.5405 +IC C311 C39 *C31 H10X 5.4305 19.11 -39.82 17.59 7.1316 +IC H10X C39 *C31 H10Y 7.1316 17.59 -37.40 16.13 5.8102 +IC C39 C310 C311 C312 1.5428 115.53 -59.09 114.74 1.5325 +IC C312 C310 *C31 H11X 6.4402 23.45 -48.72 18.92 5.1916 +IC H11X C310 *C31 H11Y 5.1916 18.92 71.99 14.56 4.5649 +IC C310 C311 C312 H12X 1.5405 114.74 -56.49 110.38 1.1108 +IC H12X C311 *C31 H12Y 7.3427 9.58 63.13 15.60 6.8602 +IC H12X C311 *C31 H12Z 7.3427 9.58 16.97 20.48 6.1636 + +RESI DLPG -1.00 ! 2,3 dilauroyl-D-glycero-1-Phosphatidylglycerol +! +! R1 - CH2 +! | +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH(OH) - CH2OH +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL3 -0.27 ! | +ATOM H12R HAL3 0.09 ! H12R---C212--H12S | +ATOM H12S HAL3 0.09 ! | +ATOM H12T HAL3 0.09 ! H12T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL3 -0.27 ! | +ATOM H12X HAL3 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL3 0.09 ! | +ATOM H12Z HAL3 0.09 ! H12Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 H12T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 H12Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 C12 C11 O12 1.5488 112.66 -35.81 112.39 1.4344 +IC OC3 C13 C12 C11 1.4270 110.57 -42.21 112.66 1.5571 +IC OC3 C12 *C13 H13A 1.4270 110.57 -122.49 109.88 1.1107 +IC OC3 C12 *C13 H13B 1.4270 110.57 118.97 108.79 1.1138 +IC C12 C13 OC3 HO3 1.5488 110.57 57.80 102.36 0.9730 +IC C11 C13 *C12 OC2 1.5571 112.66 -123.12 109.82 1.4244 +IC OC2 C13 *C12 H12A 1.4244 109.82 -117.60 108.41 1.1125 +IC C13 C12 OC2 HO2 1.5488 109.82 76.72 104.26 0.9856 +IC O12 C12 *C11 H11A 1.4344 112.39 -127.09 110.08 1.1160 +IC H11A C12 *C11 H11B 1.1160 110.08 -115.04 106.84 1.1128 +IC C12 C11 O12 P 1.5571 112.39 -88.77 119.48 1.5876 +IC C11 O12 P O11 1.4344 119.48 -61.43 101.30 1.5863 +IC O11 O12 *P O13 1.5863 101.30 -115.24 108.56 1.4777 +IC O11 O12 *P O14 1.5863 101.30 114.96 107.76 1.4796 +IC O12 P O11 C1 1.5876 101.30 -76.29 119.38 1.4327 +IC P O11 C1 C2 1.5863 119.38 -98.06 111.23 1.5544 +IC C2 O11 *C1 HA 1.5544 111.23 -119.43 109.09 1.1120 +IC HA O11 *C1 HB 1.1120 109.09 -117.62 112.27 1.1163 +IC O11 C1 C2 C3 1.4327 111.23 155.08 111.33 1.5580 +IC C3 C1 *C2 O21 1.5580 111.33 121.74 107.47 1.4417 +IC C3 C1 *C2 HS 1.5580 111.33 -118.17 107.50 1.1176 +IC C1 C2 O21 C21 1.5544 107.47 164.23 115.49 1.3176 +IC C2 O21 C21 C22 1.4417 115.49 178.81 109.28 1.5305 +IC C22 O21 *C21 O22 1.5305 109.28 -178.37 126.55 1.2162 +IC O21 C21 C22 C23 1.3176 109.28 -131.34 111.14 1.5453 +IC C23 C21 *C22 H2R 1.5453 111.14 -120.90 107.65 1.1085 +IC H2R C21 *C22 H2S 1.1085 107.65 -117.65 108.99 1.1090 +IC C1 C2 C3 O31 1.5544 111.33 -52.96 111.19 1.4430 +IC O31 C2 *C3 HX 1.4430 111.19 -125.73 110.75 1.1127 +IC HX C2 *C3 HY 1.1127 110.75 -116.02 106.99 1.1115 +IC C2 C3 O31 C31 1.5580 111.19 -84.70 114.67 1.3353 +IC C3 O31 C31 C32 1.4430 114.67 169.86 108.81 1.5299 +IC C32 O31 *C31 O32 1.5299 108.81 177.38 125.35 1.2164 +IC O31 C31 C32 C33 1.3353 108.81 159.05 112.77 1.5460 +IC C33 C31 *C32 H2X 1.5460 112.77 -123.39 109.05 1.1076 +IC H2X C31 *C32 H2Y 1.1076 109.05 -117.03 106.18 1.1130 +IC C21 C22 C23 C24 1.5305 111.14 175.26 112.68 1.5349 +IC C24 C22 *C23 H3R 1.5349 112.68 -120.99 108.81 1.1138 +IC H3R C22 *C23 H3S 1.1138 108.81 -117.44 109.55 1.1145 +IC C22 C23 C24 C25 1.5453 112.68 177.70 113.53 1.5386 +IC C25 C23 *C24 H4R 1.5386 113.53 -121.19 108.71 1.1137 +IC H4R C23 *C24 H4S 1.1137 108.71 -116.99 108.95 1.1129 +IC C23 C24 C25 C26 1.5349 113.53 61.28 113.60 1.5365 +IC C26 C24 *C25 H5R 1.5365 113.60 -121.63 109.02 1.1133 +IC H5R C24 *C25 H5S 1.1133 109.02 -117.12 108.66 1.1129 +IC C24 C25 C26 C27 1.5386 113.60 176.81 112.99 1.5371 +IC C27 C25 *C26 H6R 1.5371 112.99 -121.62 109.15 1.1127 +IC H6R C25 *C26 H6S 1.1127 109.15 -117.04 108.75 1.1098 +IC C25 C26 C27 C28 1.5365 112.99 -179.86 113.84 1.5403 +IC C28 C26 *C27 H7R 1.5403 113.84 -123.53 110.08 1.1118 +IC H7R C26 *C27 H7S 1.1118 110.08 -116.74 107.22 1.1147 +IC C26 C27 C28 C29 1.5371 113.84 -94.53 114.98 1.5423 +IC C29 C27 *C28 H8R 1.5423 114.98 -118.62 107.55 1.1151 +IC H8R C27 *C28 H8S 1.1151 107.55 -115.96 109.87 1.1107 +IC C27 C28 C29 C210 1.5403 114.98 64.14 115.87 1.5403 +IC C210 C28 *C29 H9R 1.5403 115.87 -121.83 108.31 1.1137 +IC H9R C28 *C29 H9S 1.1137 108.31 -115.81 108.37 1.1131 +IC C28 C29 C210 C211 1.5423 115.87 59.81 115.11 1.5388 +IC C211 C29 *C21 H10R 6.1917 16.71 58.06 16.02 7.3189 +IC H10R C29 *C21 H10S 7.3189 16.02 39.64 9.92 6.0006 +IC C29 C210 C211 C212 1.5403 115.11 63.48 114.60 1.5323 +IC C212 C210 *C21 H11R 7.4422 20.21 -37.03 18.08 5.7731 +IC H11R C210 *C21 H11S 5.7731 18.08 62.75 16.88 5.5091 +IC C210 C211 C212 H12R 1.5388 114.60 -63.42 110.71 1.1104 +IC H12R C211 *C21 H12S 8.1749 7.44 94.78 9.78 8.0156 +IC H12R C211 *C21 H12T 8.1749 7.44 43.36 16.00 7.3146 +IC C31 C32 C33 C34 1.5299 112.77 -69.13 113.47 1.5366 +IC C34 C32 *C33 H3X 1.5366 113.47 -120.56 108.49 1.1138 +IC H3X C32 *C33 H3Y 1.1138 108.49 -116.78 109.56 1.1146 +IC C32 C33 C34 C35 1.5460 113.47 179.47 111.91 1.5361 +IC C35 C33 *C34 H4X 1.5361 111.91 -120.27 108.72 1.1128 +IC H4X C33 *C34 H4Y 1.1128 108.72 -117.78 109.88 1.1117 +IC C33 C34 C35 C36 1.5366 111.91 -176.09 114.38 1.5378 +IC C36 C34 *C35 H5X 1.5378 114.38 -122.11 108.55 1.1125 +IC H5X C34 *C35 H5Y 1.1125 108.55 -116.55 108.53 1.1134 +IC C34 C35 C36 C37 1.5361 114.38 64.23 113.71 1.5384 +IC C37 C35 *C36 H6X 1.5384 113.71 -123.26 109.44 1.1114 +IC H6X C35 *C36 H6Y 1.1114 109.44 -116.46 107.95 1.1137 +IC C35 C36 C37 C38 1.5378 113.71 -112.31 113.00 1.5356 +IC C38 C36 *C37 H7X 1.5356 113.00 -120.62 109.15 1.1127 +IC H7X C36 *C37 H7Y 1.1127 109.15 -116.85 109.17 1.1122 +IC C36 C37 C38 C39 1.5384 113.00 179.54 113.61 1.5384 +IC C39 C37 *C38 H8X 1.5384 113.61 -122.94 109.27 1.1115 +IC H8X C37 *C38 H8Y 1.1115 109.27 -116.56 107.99 1.1133 +IC C37 C38 C39 C310 1.5356 113.61 -67.79 114.78 1.5409 +IC C310 C38 *C39 H9X 1.5409 114.78 121.64 108.49 1.1131 +IC H9X C38 *C39 H9Y 1.1131 108.49 116.32 108.77 1.1127 +IC C38 C39 C310 C311 1.5384 114.78 -60.02 115.17 1.5390 +IC C311 C39 *C31 H10X 4.3669 20.38 -77.56 19.42 5.1399 +IC H10X C39 *C31 H10Y 5.1399 19.42 43.15 20.02 6.2479 +IC C39 C310 C311 C312 1.5409 115.17 -54.81 114.62 1.5319 +IC C312 C310 *C31 H11X 5.2048 28.12 29.00 13.18 3.4733 +IC H11X C310 *C31 H11Y 3.4733 13.18 -85.71 21.85 4.2194 +IC C310 C311 C312 H12X 1.5390 114.62 -55.10 110.50 1.1105 +IC H12X C311 *C31 H12Y 6.1611 13.80 52.73 21.20 5.5856 +IC H12X C311 *C31 H12Z 6.1611 13.80 8.73 26.64 4.8649 + +RESI DMPC 0.00 ! 2,3 dimyristoyl-D-glycero-1-Phosphatidylcholine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - N(CH3)3 +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL3 -0.27 ! | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 N C12 C11 1.4955 110.64 57.27 116.86 1.5415 +IC C15 N C12 C11 1.4976 109.72 180.00 116.86 1.5415 +IC C13 C12 *N C14 1.4955 110.64 -119.74 108.01 1.5030 +IC C13 C12 *N C15 1.4955 110.64 122.73 109.72 1.4976 +IC C12 N C13 H13A 1.5224 110.64 -177.67 111.18 1.0813 +IC H13A N *C13 H13B 1.0813 111.18 119.03 109.35 1.0870 +IC H13A N *C13 H13C 1.0813 111.18 -122.04 111.32 1.0813 +IC C12 N C14 H14A 1.5224 108.01 56.08 111.03 1.0952 +IC H14A N *C14 H14B 1.0952 111.03 123.93 113.88 1.0740 +IC H14A N *C14 H14C 1.0952 111.03 -112.36 110.24 1.0938 +IC C12 N C15 H15A 1.5224 109.72 176.74 110.89 1.0821 +IC H15A N *C15 H15B 1.0821 110.89 121.45 111.48 1.0812 +IC H15A N *C15 H15C 1.0821 110.89 -118.76 109.68 1.0875 +IC C11 N *C12 H12A 1.5415 116.86 -126.38 111.91 1.0785 +IC H12A N *C12 H12B 1.0785 111.91 -116.30 108.18 1.0972 +IC N C12 C11 O12 1.5224 116.86 127.42 108.31 1.4234 +IC O12 C12 *C11 H11A 1.4234 108.31 -123.13 113.24 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.24 -118.65 109.16 1.1130 +IC C12 C11 O12 P 1.5415 108.31 -67.88 118.40 1.5875 +IC C11 O12 P O11 1.4234 118.40 -166.94 104.13 1.5782 +IC O11 O12 *P O13 1.5782 104.13 117.91 108.15 1.4793 +IC O11 O12 *P O14 1.5782 104.13 -117.27 106.75 1.4823 +IC O12 P O11 C1 1.5875 104.13 177.32 118.17 1.4318 +IC P O11 C1 C2 1.5782 118.17 167.65 110.87 1.5511 +IC C2 O11 *C1 HA 1.5511 110.87 -119.11 111.42 1.1172 +IC HA O11 *C1 HB 1.1172 111.42 -120.82 110.01 1.1145 +IC O11 C1 C2 C3 1.4318 110.87 177.69 110.63 1.5578 +IC C3 C1 *C2 O21 1.5578 110.63 120.78 108.07 1.4415 !defines S chirality +IC C3 C1 *C2 HS 1.5578 110.63 -118.30 106.69 1.1168 !defines S chirality +IC C1 C2 O21 C21 1.5511 108.07 147.89 115.06 1.3179 +IC C2 O21 C21 C22 1.4415 115.06 179.61 108.77 1.5289 +IC C22 O21 *C21 O22 1.5289 108.77 -179.08 126.52 1.2183 +IC O21 C21 C22 C23 1.3179 108.77 -173.00 112.01 1.5450 +IC C23 C21 *C22 H2R 1.5450 112.01 -121.50 107.73 1.1091 +IC H2R C21 *C22 H2S 1.1091 107.73 -117.24 107.85 1.1091 +IC C1 C2 C3 O31 1.5511 110.63 175.48 112.70 1.4436 +IC O31 C2 *C3 HX 1.4436 112.70 -118.48 106.61 1.1129 +IC HX C2 *C3 HY 1.1129 106.61 -115.12 109.44 1.1145 +IC C2 C3 O31 C31 1.5578 112.70 87.10 115.14 1.3313 +IC C3 O31 C31 C32 1.4436 115.14 -172.45 108.40 1.5287 +IC C32 O31 *C31 O32 1.5287 108.40 -178.98 125.63 1.2169 +IC O31 C31 C32 C33 1.3313 108.40 -169.89 113.40 1.5448 +IC C33 C31 *C32 H2X 1.5448 113.40 -121.09 107.19 1.1104 +IC H2X C31 *C32 H2Y 1.1104 107.19 -116.85 108.01 1.1089 +IC C21 C22 C23 C24 1.5289 112.01 177.45 112.54 1.5336 +IC C24 C22 *C23 H3R 1.5336 112.54 -120.79 109.48 1.1146 +IC H3R C22 *C23 H3S 1.1146 109.48 -117.62 109.70 1.1144 +IC C22 C23 C24 C25 1.5450 112.54 -177.78 112.24 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.24 -121.51 109.37 1.1130 +IC H4R C23 *C24 H4S 1.1130 109.37 -117.64 109.09 1.1133 +IC C23 C24 C25 C26 1.5336 112.24 178.33 112.83 1.5342 +IC C26 C24 *C25 H5R 1.5342 112.83 -121.07 108.90 1.1136 +IC H5R C24 *C25 H5S 1.1136 108.90 -117.22 109.21 1.1132 +IC C24 C25 C26 C27 1.5346 112.83 -177.92 112.39 1.5344 +IC C27 C25 *C26 H6R 1.5344 112.39 -121.57 109.28 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.28 -117.51 109.01 1.1133 +IC C25 C26 C27 C28 1.5342 112.39 178.43 112.74 1.5342 +IC C28 C26 *C27 H7R 1.5342 112.74 -121.06 108.92 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.92 -117.29 109.22 1.1131 +IC C26 C27 C28 C29 1.5344 112.74 -178.17 112.46 1.5345 +IC C29 C27 *C28 H8R 1.5345 112.46 -121.56 109.25 1.1130 +IC H8R C27 *C28 H8S 1.1130 109.25 -117.46 109.01 1.1133 +IC C27 C28 C29 C210 1.5342 112.46 178.92 112.68 1.5343 +IC C210 C28 *C29 H9R 1.5343 112.68 -121.11 108.98 1.1135 +IC H9R C28 *C29 H9S 1.1135 108.98 -117.36 109.19 1.1131 +IC C28 C29 C210 C211 1.5345 112.68 -178.62 112.55 1.5345 +IC C211 C29 *C210 H10R 1.5345 112.55 -121.48 109.19 1.1130 +IC H10R C29 *C210 H10S 1.1130 109.19 -117.42 109.05 1.1132 +IC C29 C210 C211 C212 1.5343 112.55 179.33 112.62 1.5345 +IC C212 C210 *C211 H11R 1.5345 112.62 -121.19 109.03 1.1133 +IC H11R C210 *C211 H11S 1.1133 109.03 -117.37 109.14 1.1131 +IC C210 C211 C212 C213 1.5345 112.62 -179.30 112.67 1.5338 +IC C213 C211 *C212 H12R 1.5338 112.67 -121.40 109.15 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.15 -117.41 109.09 1.1133 +IC C211 C212 C213 C214 1.5345 112.67 179.80 113.26 1.5308 +IC C214 C212 *C213 H13R 1.5308 113.26 -121.66 108.77 1.1142 +IC H13R C212 *C213 H13S 1.1142 108.77 -116.66 108.78 1.1140 +IC C212 C213 C214 H14R 1.5338 113.26 -59.87 110.43 1.1113 +IC H14R C213 *C214 H14S 1.1113 110.43 119.85 110.46 1.1113 +IC H14R C213 *C214 H14T 1.1113 110.43 -120.04 110.62 1.1112 +IC C31 C32 C33 C34 1.5287 113.40 179.64 111.32 1.5341 +IC C34 C32 *C33 H3X 1.5341 111.32 -120.86 109.71 1.1137 +IC H3X C32 *C33 H3Y 1.1137 109.71 -118.09 109.81 1.1143 +IC C32 C33 C34 C35 1.5448 111.32 -176.82 113.37 1.5345 +IC C35 C33 *C34 H4X 1.5345 113.37 -121.80 109.05 1.1135 +IC H4X C33 *C34 H4Y 1.1135 109.05 -117.12 108.83 1.1136 +IC C33 C34 C35 C36 1.5341 113.37 178.26 111.94 1.5348 +IC C36 C34 *C35 H5X 1.5348 111.94 -120.83 109.02 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.02 -117.61 109.44 1.1129 +IC C34 C35 C36 C37 1.5345 111.94 -176.79 113.19 1.5342 +IC C37 C35 *C36 H6X 1.5342 113.19 -121.90 109.15 1.1132 +IC H6X C35 *C36 H6Y 1.1132 109.15 -117.14 108.76 1.1136 +IC C35 C36 C37 C38 1.5348 113.19 177.72 112.13 1.5346 +IC C38 C36 *C37 H7X 1.5346 112.13 -120.80 109.00 1.1133 +IC H7X C36 *C37 H7Y 1.1133 109.00 -117.59 109.40 1.1128 +IC C36 C37 C38 C39 1.5342 112.13 -177.62 112.99 1.5342 +IC C39 C37 *C38 H8X 1.5342 112.99 -121.75 109.20 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.20 -117.24 108.86 1.1136 +IC C37 C38 C39 C310 1.5346 112.99 178.21 112.22 1.5344 +IC C310 C38 *C39 H9X 1.5344 112.22 -120.97 109.07 1.1134 +IC H9X C38 *C39 H9Y 1.1134 109.07 -117.54 109.30 1.1130 +IC C38 C39 C310 C311 1.5342 112.22 -178.81 112.83 1.5339 +IC C311 C39 *C310 H10X 1.5339 112.83 -121.55 109.12 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.12 -117.29 108.97 1.1134 +IC C39 C310 C311 C312 1.5344 112.83 179.12 112.41 1.5346 +IC C312 C310 *C311 H11X 1.5346 112.41 -121.13 109.11 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.11 -117.49 109.19 1.1130 +IC C310 C311 C312 C313 1.5339 112.41 -179.72 112.68 1.5336 +IC C313 C311 *C312 H12X 1.5336 112.68 -121.39 109.14 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.14 -117.34 109.09 1.1133 +IC C311 C312 C313 C314 1.5346 112.68 179.81 113.29 1.5308 +IC C314 C312 *C313 H13X 1.5308 113.29 -121.66 108.73 1.1141 +IC H13X C312 *C313 H13Y 1.1141 108.73 -116.66 108.73 1.1141 +IC C312 C313 C314 H14X 1.5336 113.29 -59.97 110.46 1.1113 +IC H14X C313 *C314 H14Y 1.1113 110.46 119.87 110.46 1.1113 +IC H14X C313 *C314 H14Z 1.1113 110.46 -120.06 110.59 1.1112 + +RESI DMPE 0.00 ! 2,3 dimyristoyl-D-glycero-1-Phosphatidylethanolamine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL3 -0.27 ! | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.5040 110.06 37.96 113.23 1.4300 +IC HN1 C12 *N HN2 1.0519 111.98 111.19 103.26 1.0560 +IC HN1 C12 *N HN3 1.0519 111.98 -130.65 114.42 1.0329 +IC HN1 N C12 C11 1.0519 111.98 -155.31 110.06 1.5445 +IC C11 N *C12 H12A 1.5445 110.06 -123.21 109.15 1.1064 +IC H12A N *C12 H12B 1.1064 109.15 -117.87 107.00 1.1123 +IC O12 C12 *C11 H11A 1.4300 113.23 -119.75 108.62 1.1136 +IC H11A C12 *C11 H11B 1.1136 108.62 -116.18 109.63 1.1165 +IC C12 C11 O12 P 1.5445 113.23 61.76 121.26 1.5856 +IC C11 O12 P O11 1.4300 121.26 -94.85 96.42 1.5947 +IC O11 O12 *P O13 1.5947 96.42 -114.16 111.76 1.4689 +IC O11 O12 *P O14 1.5947 96.42 110.57 109.00 1.4745 +IC O12 P O11 C1 1.5856 96.42 -179.22 118.51 1.4322 +IC P O11 C1 C2 1.5947 118.51 -85.25 112.29 1.5578 +IC C2 O11 *C1 HA 1.5578 112.29 -120.35 108.89 1.1125 +IC HA O11 *C1 HB 1.1125 108.89 -115.99 111.98 1.1175 +IC O11 C1 C2 C3 1.4322 112.29 125.40 111.20 1.5557 +IC C3 C1 *C2 O21 1.5557 111.20 121.39 110.46 1.4365 +IC C3 C1 *C2 HS 1.5557 111.20 -116.63 109.13 1.1159 +IC C1 C2 O21 C21 1.5578 110.46 78.76 117.58 1.3104 +IC C2 O21 C21 C22 1.4365 117.58 -179.78 108.04 1.5269 +IC C22 O21 *C21 O22 1.5269 108.04 -179.13 126.86 1.2225 +IC O21 C21 C22 C23 1.3104 108.04 -175.16 113.24 1.5474 +IC C23 C21 *C22 H2R 1.5474 113.24 -121.79 107.82 1.1099 +IC H2R C21 *C22 H2S 1.1099 107.82 -115.95 107.16 1.1091 +IC C1 C2 C3 O31 1.5578 111.20 -177.26 111.83 1.4452 +IC O31 C2 *C3 HX 1.4452 111.83 -125.83 109.24 1.1147 +IC HX C2 *C3 HY 1.1147 109.24 -115.47 107.06 1.1146 +IC C2 C3 O31 C31 1.5557 111.83 -93.92 116.04 1.3277 +IC C3 O31 C31 C32 1.4452 116.04 178.31 108.50 1.5281 +IC C32 O31 *C31 O32 1.5281 108.50 -179.94 126.25 1.2166 +IC O31 C31 C32 C33 1.3277 108.50 -174.75 112.68 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.68 -121.34 107.66 1.1099 +IC H2X C31 *C32 H2Y 1.1099 107.66 -117.10 108.00 1.1092 +IC C21 C22 C23 C24 1.5269 113.24 179.71 112.17 1.5361 +IC C24 C22 *C23 H3R 1.5361 112.17 -121.83 110.58 1.1131 +IC H3R C22 *C23 H3S 1.1131 110.58 -118.37 108.98 1.1148 +IC C22 C23 C24 C25 1.5474 112.17 -71.53 113.71 1.5370 +IC C25 C23 *C24 H4R 1.5370 113.71 -121.99 109.75 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.75 -116.77 108.11 1.1141 +IC C23 C24 C25 C26 1.5361 113.71 155.45 112.31 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.31 -118.66 109.50 1.1120 +IC H5R C24 *C25 H5S 1.1120 109.50 -117.66 110.20 1.1116 +IC C24 C25 C26 C27 1.5370 112.31 -171.99 112.88 1.5383 +IC C27 C25 *C26 H6R 1.5383 112.88 -124.17 110.65 1.1114 +IC H6R C25 *C26 H6S 1.1114 110.65 -116.41 107.31 1.1136 +IC C25 C26 C27 C28 1.5347 112.88 140.44 113.43 1.5388 +IC C28 C26 *C27 H7R 1.5388 113.43 -121.51 110.20 1.1125 +IC H7R C26 *C27 H7S 1.1125 110.20 -116.85 108.13 1.1132 +IC C26 C27 C28 C29 1.5383 113.43 -93.08 114.39 1.5419 +IC C29 C27 *C28 H8R 1.5419 114.39 -119.27 108.35 1.1146 +IC H8R C27 *C28 H8S 1.1146 108.35 -116.73 109.52 1.1117 +IC C27 C28 C29 C210 1.5388 114.39 58.65 114.60 1.5372 +IC C210 C28 *C29 H9R 1.5372 114.60 -121.68 108.89 1.1133 +IC H9R C28 *C29 H9S 1.1133 108.89 -116.32 108.01 1.1128 +IC C28 C29 C210 C211 1.5419 114.60 177.83 113.74 1.5367 +IC C211 C29 *C21 H10R 6.1073 20.38 -68.62 16.15 6.0147 +IC H10R C29 *C21 H10S 6.0147 16.15 59.74 1.13 5.0119 +IC C29 C210 C211 C212 1.5372 113.74 -74.85 113.36 1.5358 +IC C212 C210 *C21 H11R 7.3364 18.70 14.16 21.30 5.2596 +IC H11R C210 *C21 H11S 5.2596 21.30 38.19 19.65 6.4510 +IC C210 C211 C212 C213 1.5367 113.36 -172.01 113.38 1.5373 +IC C213 C211 *C21 H12R 7.8190 15.93 -74.24 4.24 8.2187 +IC H12R C211 *C21 H12S 8.2187 4.24 12.53 15.55 7.3012 +IC C211 C212 C213 C214 1.5358 113.38 -61.69 114.42 1.5318 +IC C214 C212 *C21 H13R 8.3133 17.59 -54.31 11.66 8.7627 +IC H13R C212 *C21 H13S 8.7627 11.66 7.43 17.15 7.1546 +IC C212 C213 C214 H14R 1.5373 114.42 -56.02 110.43 1.1107 +IC H14R C213 *C21 H14S 9.0675 12.21 -23.37 16.25 7.5699 +IC H14R C213 *C21 H14T 9.0675 12.21 -54.42 12.99 8.9126 +IC C31 C32 C33 C34 1.5281 112.68 -178.50 111.72 1.5332 +IC C34 C32 *C33 H3X 1.5332 111.72 -121.04 109.86 1.1142 +IC H3X C32 *C33 H3Y 1.1142 109.86 -118.18 109.78 1.1144 +IC C32 C33 C34 C35 1.5450 111.72 179.92 112.95 1.5367 +IC C35 C33 *C34 H4X 1.5367 112.95 -121.58 108.52 1.1134 +IC H4X C33 *C34 H4Y 1.1134 108.52 -117.16 108.99 1.1133 +IC C33 C34 C35 C36 1.5332 112.95 172.44 113.60 1.5407 +IC C36 C34 *C35 H5X 1.5407 113.60 -120.33 108.65 1.1138 +IC H5X C34 *C35 H5Y 1.1138 108.65 -116.65 109.08 1.1121 +IC C34 C35 C36 C37 1.5367 113.60 59.31 114.72 1.5390 +IC C37 C35 *C36 H6X 1.5390 114.72 -120.81 108.04 1.1142 +IC H6X C35 *C36 H6Y 1.1142 108.04 -116.56 109.13 1.1130 +IC C35 C36 C37 C38 1.5407 114.72 70.57 113.66 1.5369 +IC C38 C36 *C37 H7X 1.5369 113.66 -123.21 109.08 1.1096 +IC H7X C36 *C37 H7Y 1.1096 109.08 -116.24 108.85 1.1133 +IC C36 C37 C38 C39 1.5390 113.66 -171.01 113.66 1.5398 +IC C39 C37 *C38 H8X 1.5398 113.66 -121.08 108.21 1.1134 +IC H8X C37 *C38 H8Y 1.1134 108.21 -116.24 109.89 1.1099 +IC C37 C38 C39 C310 1.5369 113.66 68.64 114.70 1.5406 +IC C310 C38 *C39 H9X 1.5406 114.70 -122.60 108.99 1.1131 +IC H9X C38 *C39 H9Y 1.1131 108.99 -116.65 108.25 1.1141 +IC C38 C39 C310 C311 1.5398 114.70 59.38 113.58 1.5368 +IC C311 C39 *C31 H10X 6.5292 15.94 77.17 13.71 6.8639 +IC H10X C39 *C31 H10Y 6.8639 13.71 -36.51 15.24 8.2049 +IC C39 C310 C311 C312 1.5406 113.58 174.79 112.92 1.5358 +IC C312 C310 *C31 H11X 6.2399 19.58 -75.35 12.33 5.6792 +IC H11X C310 *C31 H11Y 5.6792 12.33 22.26 16.99 7.2853 +IC C310 C311 C312 C313 1.5368 112.92 177.61 113.44 1.5372 +IC C313 C311 *C31 H12X 5.7740 23.07 62.66 18.90 5.7045 +IC H12X C311 *C31 H12Y 5.7045 18.90 -24.95 17.04 7.2700 +IC C311 C312 C313 C314 1.5358 113.44 63.25 114.44 1.5324 +IC C314 C312 *C31 H13X 6.8987 21.92 -0.94 16.95 4.7878 +IC H13X C312 *C31 H13Y 4.7878 16.95 49.69 20.28 5.8499 +IC C312 C313 C314 H14X 1.5372 114.44 -64.16 110.75 1.1108 +IC H14X C313 *C31 H14Y 7.0643 15.91 53.48 17.15 6.8864 +IC H14X C313 *C31 H14Z 7.0643 15.91 42.84 5.47 7.8630 + +RESI DMPS -1.00 ! 2,3 dimyristoyl-D-glycero-1-Phosphatidylserine +! +! R1 - CH2 +! | (-) +! R2 - CH CO2 +! | (-) | (+) +! CH2 - PO4 - CH2 - CH - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL3 -0.27 ! | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 C13 C12 O13B O13A + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.4858 109.77 -65.50 111.66 1.4336 +IC N C12 C13 O13B 1.4858 108.85 -1.67 118.22 1.2652 +IC HN1 C12 *N HN2 1.0452 111.38 120.72 103.02 1.0477 +IC HN1 C12 *N HN3 1.0452 111.38 -120.26 108.46 1.0568 +IC HN1 N C12 C11 1.0452 111.38 123.18 109.77 1.5593 +IC C11 N *C12 C13 1.5593 109.77 122.62 108.85 1.5432 +IC C13 N *C12 H12A 1.5432 108.85 117.12 108.82 1.0791 +IC O13B C12 *C13 O13A 1.2652 118.22 178.49 117.98 1.2552 +IC O12 C12 *C11 H11A 1.4336 111.66 -118.44 107.33 1.1148 +IC H11A C12 *C11 H11B 1.1148 107.33 -115.33 110.23 1.1162 +IC C12 C11 O12 P 1.5593 111.66 98.49 122.72 1.5825 +IC C11 O12 P O11 1.4336 122.72 -153.54 101.44 1.5841 +IC O11 O12 *P O13 1.5841 101.44 -117.41 110.63 1.4730 +IC O11 O12 *P O14 1.5841 101.44 112.67 106.48 1.4828 +IC O12 P O11 C1 1.5825 101.44 51.40 120.57 1.4299 +IC P O11 C1 C2 1.5841 120.57 94.31 110.59 1.5514 +IC C2 O11 *C1 HA 1.5514 110.59 -124.77 112.69 1.1134 +IC HA O11 *C1 HB 1.1134 112.69 -117.39 108.43 1.1132 +IC O11 C1 C2 C3 1.4299 110.59 56.91 110.13 1.5557 +IC C3 C1 *C2 O21 1.5557 110.13 121.33 110.22 1.4406 +IC C3 C1 *C2 HS 1.5557 110.13 -116.58 109.10 1.1161 +IC C1 C2 O21 C21 1.5514 110.22 74.77 115.03 1.3189 +IC C2 O21 C21 C22 1.4406 115.03 -174.87 109.18 1.5267 +IC C22 O21 *C21 O22 1.5267 109.18 -178.97 126.08 1.2208 +IC O21 C21 C22 C23 1.3189 109.18 147.16 112.13 1.5469 +IC C23 C21 *C22 H2R 1.5469 112.13 -120.96 108.38 1.1106 +IC H2R C21 *C22 H2S 1.1106 108.38 -117.19 107.82 1.1080 +IC C1 C2 C3 O31 1.5514 110.13 177.33 112.10 1.4464 +IC O31 C2 *C3 HX 1.4464 112.10 -126.05 108.82 1.1147 +IC HX C2 *C3 HY 1.1147 108.82 -114.63 106.97 1.1139 +IC C2 C3 O31 C31 1.5557 112.10 -95.35 115.74 1.3256 +IC C3 O31 C31 C32 1.4464 115.74 176.51 108.73 1.5289 +IC C32 O31 *C31 O32 1.5289 108.73 179.39 126.49 1.2173 +IC O31 C31 C32 C33 1.3256 108.73 -164.90 111.78 1.5438 +IC C33 C31 *C32 H2X 1.5438 111.78 -121.18 107.70 1.1089 +IC H2X C31 *C32 H2Y 1.1089 107.70 -117.52 108.21 1.1093 +IC C21 C22 C23 C24 1.5267 112.13 -173.46 112.29 1.5354 +IC C24 C22 *C23 H3R 1.5354 112.29 -123.07 110.79 1.1131 +IC H3R C22 *C23 H3S 1.1131 110.79 -117.84 108.75 1.1160 +IC C22 C23 C24 C25 1.5469 112.29 -73.86 114.15 1.5392 +IC C25 C23 *C24 H4R 1.5392 114.15 -121.75 109.46 1.1137 +IC H4R C23 *C24 H4S 1.1137 109.46 -116.12 108.02 1.1136 +IC C23 C24 C25 C26 1.5354 114.15 138.76 112.43 1.5367 +IC C26 C24 *C25 H5R 1.5367 112.43 -121.50 110.46 1.1121 +IC H5R C24 *C25 H5S 1.1121 110.46 -117.08 108.30 1.1134 +IC C24 C25 C26 C27 1.5392 112.43 -80.69 112.18 1.5362 +IC C27 C25 *C26 H6R 1.5362 112.18 -120.78 109.92 1.1128 +IC H6R C25 *C26 H6S 1.1128 109.92 -117.54 108.59 1.1129 +IC C25 C26 C27 C28 1.5367 112.18 157.36 113.40 1.5360 +IC C28 C26 *C27 H7R 1.5360 113.40 -120.39 108.49 1.1126 +IC H7R C26 *C27 H7S 1.1126 108.49 -116.63 109.16 1.1122 +IC C26 C27 C28 C29 1.5362 113.40 171.72 113.83 1.5403 +IC C29 C27 *C28 H8R 1.5403 113.83 -121.54 109.21 1.1130 +IC H8R C27 *C28 H8S 1.1130 109.21 -116.82 108.47 1.1133 +IC C27 C28 C29 C210 1.5360 113.83 48.81 115.14 1.5405 +IC C210 C28 *C29 H9R 1.5405 115.14 123.12 108.85 1.1124 +IC H9R C28 *C29 H9S 1.1124 108.85 116.31 108.22 1.1140 +IC C28 C29 C210 C211 1.5403 115.14 57.49 115.62 1.5392 +IC C211 C29 *C21 H10R 5.5834 20.76 82.55 12.77 5.2155 +IC H10R C29 *C21 H10S 5.2155 12.77 -29.19 18.29 6.7126 +IC C29 C210 C211 C212 1.5405 115.62 61.83 115.64 1.5400 +IC C212 C210 *C21 H11R 6.9148 21.84 -27.60 20.30 5.0048 +IC H11R C210 *C21 H11S 5.0048 20.30 60.48 20.63 5.1267 +IC C210 C211 C212 C213 1.5392 115.64 68.06 114.54 1.5387 +IC C213 C211 *C21 H12R 7.8860 10.25 -61.74 16.43 6.8022 +IC H12R C211 *C21 H12S 6.8022 16.43 -53.00 8.88 7.5347 +IC C211 C212 C213 C214 1.5400 114.54 -96.54 114.70 1.5325 +IC C214 C212 *C21 H13R 8.9829 11.30 -76.75 10.99 8.4977 +IC H13R C212 *C21 H13S 8.4977 10.99 37.09 16.91 7.4427 +IC C212 C213 C214 H14R 1.5387 114.70 -58.95 110.31 1.1111 +IC H14R C213 *C21 H14S 9.5741 9.14 -78.92 7.58 9.7374 +IC H14R C213 *C21 H14T 9.5741 9.14 -43.73 14.18 8.6761 +IC C31 C32 C33 C34 1.5289 111.78 -179.81 112.76 1.5334 +IC C34 C32 *C33 H3X 1.5334 112.76 -120.90 109.05 1.1126 +IC H3X C32 *C33 H3Y 1.1126 109.05 -117.56 109.79 1.1148 +IC C32 C33 C34 C35 1.5438 112.76 -179.27 112.12 1.5371 +IC C35 C33 *C34 H4X 1.5371 112.12 -121.69 108.46 1.1110 +IC H4X C33 *C34 H4Y 1.1110 108.46 -117.05 109.47 1.1128 +IC C33 C34 C35 C36 1.5334 112.12 -177.32 113.98 1.5395 +IC C36 C34 *C35 H5X 1.5395 113.98 -120.62 108.03 1.1141 +IC H5X C34 *C35 H5Y 1.1141 108.03 -116.11 109.21 1.1116 +IC C34 C35 C36 C37 1.5371 113.98 67.64 114.63 1.5396 +IC C37 C35 *C36 H6X 1.5396 114.63 -121.76 108.19 1.1135 +IC H6X C35 *C36 H6Y 1.1135 108.19 -116.59 108.91 1.1134 +IC C35 C36 C37 C38 1.5395 114.63 69.45 113.46 1.5389 +IC C38 C36 *C37 H7X 1.5389 113.46 -123.20 109.09 1.1099 +IC H7X C36 *C37 H7Y 1.1099 109.09 -116.49 108.73 1.1135 +IC C36 C37 C38 C39 1.5396 113.46 -174.23 114.27 1.5408 +IC C39 C37 *C38 H8X 1.5408 114.27 -120.60 107.53 1.1141 +IC H8X C37 *C38 H8Y 1.1141 107.53 -116.34 110.06 1.1095 +IC C37 C38 C39 C310 1.5389 114.27 77.75 115.25 1.5942 +IC C310 C38 *C39 H9X 1.5942 115.25 -124.52 109.22 1.1126 +IC H9X C38 *C39 H9Y 1.1126 109.22 -114.49 108.25 1.1149 +IC C38 C39 C310 C311 1.5408 115.25 -1.83 128.87 1.5918 +IC C311 C39 *C31 H10X 5.9864 15.43 -44.24 11.75 7.2949 +IC H10X C39 *C31 H10Y 7.2949 11.75 91.51 11.63 7.2571 +IC C39 C310 C311 C312 1.5942 128.87 122.79 114.86 1.5432 +IC C312 C310 *C31 H11X 5.9352 18.57 -131.67 3.88 5.2775 +IC H11X C310 *C31 H11Y 5.2775 3.88 -148.78 13.72 5.9318 +IC C310 C311 C312 C313 1.5918 114.86 -107.36 114.68 1.5403 +IC C313 C311 *C31 H12X 5.3509 25.70 57.62 21.12 5.6041 +IC H12X C311 *C31 H12Y 5.6041 21.12 -28.67 17.17 7.0158 +IC C311 C312 C313 C314 1.5432 114.68 73.28 115.35 1.5320 +IC C314 C312 *C31 H13X 6.3480 24.10 4.58 16.30 4.2989 +IC H13X C312 *C31 H13Y 4.2989 16.30 46.63 21.34 5.5244 +IC C312 C313 C314 H14X 1.5403 115.35 -64.19 110.85 1.1089 +IC H14X C313 *C31 H14Y 6.4590 18.46 50.83 19.65 6.2760 +IC H14X C313 *C31 H14Z 6.4590 18.46 36.61 7.86 7.3589 + +RESI DMPA -1.00 ! 2,3 dimyristoyl-D-glycero-1-Phosphatidic acid +! +! R1 - CH2 +! | +! R2 - CH +! | (-) +! CH2 - PO4 - H +! +! Polar Head and glycerol backbone +GROUP ! H12 + ! | +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.82 ! \ / alpha3 +ATOM O14 O2L -0.82 ! P (+) +ATOM O12 OHL -0.68 ! / \ alpha2 +ATOM H12 HOL 0.34 ! (-) O14 O11 +ATOM O11 OSLP -0.62 ! | +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL3 -0.27 ! | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC O11 P O12 H12 1.5789 105.28 179.39 105.08 0.9601 +IC O12 O11 *P O13 1.5667 105.28 111.83 112.10 1.4709 +IC O12 O11 *P O14 1.5667 105.28 -111.35 111.87 1.4700 +IC O12 P O11 C1 1.5667 105.28 -68.74 121.14 1.4306 +IC P O11 C1 C2 1.5789 121.14 94.60 111.38 1.5535 +IC C2 O11 *C1 HA 1.5535 111.38 -124.61 113.12 1.1163 +IC HA O11 *C1 HB 1.1163 113.12 -117.86 107.52 1.1125 +IC O11 C1 C2 C3 1.4306 111.38 34.79 111.14 1.5566 +IC C3 C1 *C2 O21 1.5566 111.14 119.87 110.44 1.4391 +IC C3 C1 *C2 HS 1.5566 111.14 -117.42 108.74 1.1158 +IC C1 C2 O21 C21 1.5535 110.44 72.92 116.07 1.3132 +IC C2 O21 C21 C22 1.4391 116.07 -176.55 107.94 1.5301 +IC C22 O21 *C21 O22 1.5301 107.94 -177.86 126.98 1.2166 +IC O21 C21 C22 C23 1.3132 107.94 161.44 112.88 1.5461 +IC C23 C21 *C22 H2R 1.5461 112.88 -121.42 107.99 1.1101 +IC H2R C21 *C22 H2S 1.1101 107.99 -116.61 107.35 1.1081 +IC C1 C2 C3 O31 1.5535 111.14 178.34 111.61 1.4464 +IC O31 C2 *C3 HX 1.4464 111.61 -125.67 108.73 1.1145 +IC HX C2 *C3 HY 1.1145 108.73 -115.18 107.65 1.1128 +IC C2 C3 O31 C31 1.5566 111.61 -92.62 116.14 1.3219 +IC C3 O31 C31 C32 1.4464 116.14 172.46 108.16 1.5293 +IC C32 O31 *C31 O32 1.5293 108.16 179.61 127.04 1.2163 +IC O31 C31 C32 C33 1.3219 108.16 -165.86 112.47 1.5442 +IC C33 C31 *C32 H2X 1.5442 112.47 -121.22 107.28 1.1091 +IC H2X C31 *C32 H2Y 1.1091 107.28 -117.11 108.17 1.1093 +IC C21 C22 C23 C24 1.5301 112.88 -179.46 112.01 1.5353 +IC C24 C22 *C23 H3R 1.5353 112.01 -122.58 110.58 1.1132 +IC H3R C22 *C23 H3S 1.1132 110.58 -117.58 108.46 1.1152 +IC C22 C23 C24 C25 1.5461 112.01 -76.56 113.48 1.5387 +IC C25 C23 *C24 H4R 1.5387 113.48 -121.53 109.58 1.1132 +IC H4R C23 *C24 H4S 1.1132 109.58 -116.31 108.08 1.1132 +IC C23 C24 C25 C26 1.5353 113.48 141.29 113.06 1.5362 +IC C26 C24 *C25 H5R 1.5362 113.06 -121.25 110.07 1.1126 +IC H5R C24 *C25 H5S 1.1126 110.07 -116.77 108.36 1.1131 +IC C24 C25 C26 C27 1.5387 113.06 -79.04 112.34 1.5366 +IC C27 C25 *C26 H6R 1.5366 112.34 -120.02 109.21 1.1133 +IC H6R C25 *C26 H6S 1.1133 109.21 -117.63 109.27 1.1124 +IC C25 C26 C27 C28 1.5362 112.34 173.35 112.96 1.5348 +IC C28 C26 *C27 H7R 1.5348 112.96 -121.40 109.06 1.1128 +IC H7R C26 *C27 H7S 1.1128 109.06 -116.95 108.88 1.1129 +IC C26 C27 C28 C29 1.5366 112.96 172.03 113.68 1.5380 +IC C29 C27 *C28 H8R 1.5380 113.68 -121.52 109.14 1.1129 +IC H8R C27 *C28 H8S 1.1129 109.14 -117.01 108.49 1.1135 +IC C27 C28 C29 C210 1.5348 113.68 53.19 113.73 1.5374 +IC C210 C28 *C29 H9R 1.5374 113.73 121.72 108.40 1.1126 +IC H9R C28 *C29 H9S 1.1126 108.40 116.86 109.29 1.1131 +IC C28 C29 C210 C211 1.5380 113.73 168.39 113.38 1.5380 +IC C211 C29 *C21 H10R 7.3620 20.35 -50.22 17.35 6.2941 +IC H10R C29 *C21 H10S 6.2941 17.35 60.06 12.17 5.4122 +IC C29 C210 C211 C212 1.5374 113.38 -102.08 113.97 1.5389 +IC C212 C210 *C21 H11R 8.2919 13.68 44.45 18.11 6.9239 +IC H11R C210 *C21 H11S 6.9239 18.11 31.91 10.90 8.0810 +IC C210 C211 C212 C213 1.5380 113.97 60.74 114.36 1.5347 +IC C213 C211 *C21 H12R 9.1967 12.69 44.64 16.08 7.8088 +IC H12R C211 *C21 H12S 7.8088 16.08 29.26 9.70 9.0362 +IC C211 C212 C213 C214 1.5389 114.36 178.80 113.09 1.5310 +IC C214 C212 *C21 H13R 10.2849 9.96 -37.09 14.45 8.6808 +IC H13R C212 *C21 H13S 8.6808 14.45 -37.48 10.07 9.7760 +IC C212 C213 C214 H14R 1.5347 113.09 179.23 110.64 1.1108 +IC H14R C213 *C21 H14S 10.9911 7.12 79.61 7.64 10.9245 +IC H14R C213 *C21 H14T 10.9911 7.12 38.17 12.33 9.9358 +IC C31 C32 C33 C34 1.5293 112.47 -174.51 111.81 1.5321 +IC C34 C32 *C33 H3X 1.5321 111.81 -121.75 109.76 1.1134 +IC H3X C32 *C33 H3Y 1.1134 109.76 -117.95 109.57 1.1147 +IC C32 C33 C34 C35 1.5442 111.81 -179.26 112.87 1.5358 +IC C35 C33 *C34 H4X 1.5358 112.87 -121.38 108.05 1.1123 +IC H4X C33 *C34 H4Y 1.1123 108.05 -116.78 109.64 1.1132 +IC C33 C34 C35 C36 1.5321 112.87 -168.27 112.56 1.5361 +IC C36 C34 *C35 H5X 1.5361 112.56 -121.53 108.31 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.31 -117.07 109.66 1.1128 +IC C34 C35 C36 C37 1.5358 112.56 78.69 112.29 1.5364 +IC C37 C35 *C36 H6X 1.5364 112.29 -122.01 108.94 1.1127 +IC H6X C35 *C36 H6Y 1.1127 108.94 -117.55 109.44 1.1131 +IC C35 C36 C37 C38 1.5361 112.29 -168.17 113.36 1.5354 +IC C38 C36 *C37 H7X 1.5354 113.36 -122.16 108.81 1.1128 +IC H7X C36 *C37 H7Y 1.1128 108.81 -116.52 109.03 1.1099 +IC C36 C37 C38 C39 1.5364 113.36 -173.54 113.83 1.5407 +IC C39 C37 *C38 H8X 1.5407 113.83 -123.68 109.70 1.1121 +IC H8X C37 *C38 H8Y 1.1121 109.70 -116.58 107.67 1.1145 +IC C37 C38 C39 C310 1.5354 113.83 -73.53 116.32 1.5934 +IC C310 C38 *C39 H9X 1.5934 116.32 -121.02 108.05 1.1150 +IC H9X C38 *C39 H9Y 1.1150 108.05 -114.19 108.91 1.1132 +IC C38 C39 C310 C311 1.5407 116.32 6.13 130.96 1.5905 +IC C311 C39 *C31 H10X 7.5249 17.78 -47.48 9.72 7.8180 +IC H10X C39 *C31 H10Y 7.8180 9.72 70.87 11.62 8.8894 +IC C39 C310 C311 C312 1.5934 130.96 122.16 114.97 1.5461 +IC C312 C310 *C31 H11X 7.0205 15.64 88.13 9.86 6.7847 +IC H11X C310 *C31 H11Y 6.7847 9.86 -34.46 14.77 8.1780 +IC C310 C311 C312 C313 1.5905 114.97 -94.65 115.98 1.5419 +IC C313 C311 *C31 H12X 5.7287 16.69 56.04 16.50 7.0228 +IC H12X C311 *C31 H12Y 7.0228 16.50 -43.96 16.17 7.8860 +IC C311 C312 C313 C314 1.5461 115.98 87.01 115.71 1.5333 +IC C314 C312 *C31 H13X 6.1529 21.53 -59.25 6.65 4.9479 +IC H13X C312 *C31 H13Y 4.9479 6.65 125.45 14.12 5.4998 +IC C312 C313 C314 H14X 1.5419 115.71 -65.51 111.33 1.1087 +IC H14X C313 *C31 H14Y 6.5701 19.02 37.82 22.34 5.4586 +IC H14X C313 *C31 H14Z 6.5701 19.02 49.36 15.67 7.0597 + +RESI DMPG -1.00 ! 2,3 dimyristoyl-D-glycero-1-Phosphatidylglycerol +! +! R1 - CH2 +! | +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH(OH) - CH2OH +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL3 -0.27 ! | +ATOM H14R HAL3 0.09 ! H14R---C214--H14S | +ATOM H14S HAL3 0.09 ! | +ATOM H14T HAL3 0.09 ! H14T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL3 -0.27 ! | +ATOM H14X HAL3 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL3 0.09 ! | +ATOM H14Z HAL3 0.09 ! H14Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 H14T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 H14Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 C12 C11 O12 1.5492 112.61 39.08 112.05 1.4332 +IC OC3 C13 C12 C11 1.4273 110.57 41.85 112.61 1.5531 +IC OC3 C12 *C13 H13A 1.4273 110.57 -119.10 109.19 1.1121 +IC OC3 C12 *C13 H13B 1.4273 110.57 122.38 109.91 1.1106 +IC C12 C13 OC3 HO3 1.5492 110.57 -58.22 102.68 0.9724 +IC C11 C13 *C12 OC2 1.5531 112.61 122.46 110.08 1.4233 +IC OC2 C13 *C12 H12A 1.4233 110.08 118.05 108.42 1.1125 +IC C13 C12 OC2 HO2 1.5492 110.08 -83.06 103.49 0.9780 +IC O12 C12 *C11 H11A 1.4332 112.05 -117.95 107.12 1.1130 +IC H11A C12 *C11 H11B 1.1130 107.12 -114.86 110.00 1.1169 +IC C12 C11 O12 P 1.5531 112.05 98.93 120.46 1.5860 +IC C11 O12 P O11 1.4332 120.46 -62.16 100.61 1.5949 +IC O11 O12 *P O13 1.5949 100.61 -114.96 109.25 1.4761 +IC O11 O12 *P O14 1.5949 100.61 113.98 109.18 1.4764 +IC O12 P O11 C1 1.5860 100.61 -99.43 118.25 1.4319 +IC P O11 C1 C2 1.5949 118.25 -175.15 110.39 1.5502 +IC C2 O11 *C1 HA 1.5502 110.39 -121.33 110.79 1.1139 +IC HA O11 *C1 HB 1.1139 110.79 -120.07 110.82 1.1172 +IC O11 C1 C2 C3 1.4319 110.39 53.51 111.21 1.5541 +IC C3 C1 *C2 O21 1.5541 111.21 119.86 109.38 1.4369 +IC C3 C1 *C2 HS 1.5541 111.21 -117.66 108.61 1.1166 +IC C1 C2 O21 C21 1.5502 109.38 77.93 115.26 1.3167 +IC C2 O21 C21 C22 1.4369 115.26 -172.76 108.18 1.5287 +IC C22 O21 *C21 O22 1.5287 108.18 -179.77 126.45 1.2185 +IC O21 C21 C22 C23 1.3167 108.18 -169.25 113.11 1.5462 +IC C23 C21 *C22 H2R 1.5462 113.11 122.41 107.63 1.1094 +IC H2R C21 *C22 H2S 1.1094 107.63 116.57 107.12 1.1098 +IC C1 C2 C3 O31 1.5502 111.21 -166.56 111.78 1.4442 +IC O31 C2 *C3 HX 1.4442 111.78 -126.14 109.25 1.1143 +IC HX C2 *C3 HY 1.1143 109.25 -115.50 107.44 1.1131 +IC C2 C3 O31 C31 1.5541 111.78 -93.02 117.00 1.3225 +IC C3 O31 C31 C32 1.4442 117.00 178.72 108.12 1.5310 +IC C32 O31 *C31 O32 1.5310 108.12 178.18 126.85 1.2164 +IC O31 C31 C32 C33 1.3225 108.12 -157.23 113.09 1.5449 +IC C33 C31 *C32 H2X 1.5449 113.09 121.71 108.25 1.1099 +IC H2X C31 *C32 H2Y 1.1099 108.25 116.97 107.26 1.1090 +IC C21 C22 C23 C24 1.5287 113.11 -172.18 112.95 1.5374 +IC C24 C22 *C23 H3R 1.5374 112.95 -121.90 109.32 1.1135 +IC H3R C22 *C23 H3S 1.1135 109.32 -117.44 109.53 1.1153 +IC C22 C23 C24 C25 1.5462 112.95 -56.90 113.51 1.5355 +IC C25 C23 *C24 H4R 1.5355 113.51 -121.64 108.81 1.1132 +IC H4R C23 *C24 H4S 1.1132 108.81 -117.03 108.89 1.1135 +IC C23 C24 C25 C26 1.5374 113.51 -177.01 112.98 1.5358 +IC C26 C24 *C25 H5R 1.5358 112.98 -120.25 109.14 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.14 -117.41 109.11 1.1120 +IC C24 C25 C26 C27 1.5355 112.98 -173.30 113.10 1.5381 +IC C27 C25 *C26 H6R 1.5381 113.10 -122.92 109.70 1.1120 +IC H6R C25 *C26 H6S 1.1120 109.70 -117.15 108.04 1.1141 +IC C25 C26 C27 C28 1.5358 113.10 -69.10 114.00 1.5391 +IC C28 C26 *C27 H7R 1.5391 114.00 -121.38 108.86 1.1133 +IC H7R C26 *C27 H7S 1.1133 108.86 -116.07 108.55 1.1131 +IC C26 C27 C28 C29 1.5381 114.00 126.36 113.71 1.5381 +IC C29 C27 *C28 H8R 1.5381 113.71 -122.22 109.96 1.1122 +IC H8R C27 *C28 H8S 1.1122 109.96 -116.63 108.39 1.1134 +IC C27 C28 C29 C210 1.5391 113.71 -71.33 113.21 1.5374 +IC C210 C28 *C29 H9R 1.5374 113.21 123.08 109.33 1.1111 +IC H9R C28 *C29 H9S 1.1111 109.33 116.99 108.53 1.1137 +IC C28 C29 C210 C211 1.5381 113.21 -177.16 113.69 1.5373 +IC C211 C29 *C21 H10R 6.7466 20.34 -53.81 9.34 5.4537 +IC H10R C29 *C21 H10S 5.4537 9.34 114.37 12.24 5.7425 +IC C29 C210 C211 C212 1.5374 113.69 -99.55 114.37 1.5384 +IC C212 C210 *C21 H11R 6.8917 21.93 51.85 19.82 6.3258 +IC H11R C210 *C21 H11S 6.3258 19.82 -8.11 11.82 7.8041 +IC C210 C211 C212 C213 1.5373 114.37 63.27 114.43 1.5340 +IC C213 C211 *C21 H12R 7.8244 18.59 29.82 18.40 5.9629 +IC H12R C211 *C21 H12S 5.9629 18.40 25.12 16.35 7.5133 +IC C211 C212 C213 C214 1.5384 114.43 175.20 112.89 1.5310 +IC C214 C212 *C21 H13R 8.4144 15.48 -51.97 16.84 7.4437 +IC H13R C212 *C21 H13S 7.4437 16.84 -15.01 8.47 8.7319 +IC C212 C213 C214 H14R 1.5340 112.89 179.31 110.77 1.1108 +IC H14R C213 *C21 H14S 9.2035 11.48 22.44 16.11 7.7219 +IC H14R C213 *C21 H14T 9.2035 11.48 55.92 12.67 8.9837 +IC C31 C32 C33 C34 1.5310 113.09 -178.28 111.59 1.5346 +IC C34 C32 *C33 H3X 1.5346 111.59 -120.83 109.33 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.33 -117.99 110.03 1.1144 +IC C32 C33 C34 C35 1.5449 111.59 -174.31 113.11 1.5364 +IC C35 C33 *C34 H4X 1.5364 113.11 -122.25 108.62 1.1122 +IC H4X C33 *C34 H4Y 1.1122 108.62 -116.91 108.87 1.1136 +IC C33 C34 C35 C36 1.5346 113.11 178.97 113.24 1.5389 +IC C36 C34 *C35 H5X 1.5389 113.24 -120.22 107.97 1.1141 +IC H5X C34 *C35 H5Y 1.1141 107.97 -116.72 109.51 1.1114 +IC C34 C35 C36 C37 1.5364 113.24 73.83 113.88 1.5375 +IC C37 C35 *C36 H6X 1.5375 113.88 -121.61 108.15 1.1135 +IC H6X C35 *C36 H6Y 1.1135 108.15 -116.83 109.39 1.1129 +IC C35 C36 C37 C38 1.5389 113.88 76.26 113.19 1.5381 +IC C38 C36 *C37 H7X 1.5381 113.19 -122.91 109.29 1.1105 +IC H7X C36 *C37 H7Y 1.1105 109.29 -116.75 109.13 1.1135 +IC C36 C37 C38 C39 1.5375 113.19 -167.61 113.26 1.5378 +IC C39 C37 *C38 H8X 1.5378 113.26 -121.09 107.81 1.1135 +IC H8X C37 *C38 H8Y 1.1135 107.81 -116.68 110.45 1.1117 +IC C37 C38 C39 C310 1.5381 113.26 100.04 113.52 1.5398 +IC C310 C38 *C39 H9X 1.5398 113.52 -123.52 109.65 1.1119 +IC H9X C38 *C39 H9Y 1.1119 109.65 -117.03 108.47 1.1143 +IC C38 C39 C310 C311 1.5378 113.52 -60.17 114.06 1.5370 +IC C311 C39 *C31 H10X 6.4738 13.56 -53.13 14.93 7.9571 +IC H10X C39 *C31 H10Y 7.9571 14.93 46.49 14.58 8.6271 +IC C39 C310 C311 C312 1.5398 114.06 -176.63 113.77 1.5373 +IC C312 C310 *C31 H11X 6.3576 17.14 168.76 2.60 5.6838 +IC H11X C310 *C31 H11Y 5.6838 2.60 -93.22 14.15 6.5946 +IC C310 C311 C312 C313 1.5370 113.77 -64.55 113.62 1.5352 +IC C313 C311 *C31 H12X 6.4874 22.88 53.04 18.77 5.5392 +IC H12X C311 *C31 H12Y 5.5392 18.77 -5.18 16.79 7.3137 +IC C311 C312 C313 C314 1.5373 113.62 -174.69 113.22 1.5307 +IC C314 C312 *C31 H13X 6.7455 22.28 -48.62 15.57 7.4716 +IC H13X C312 *C31 H13Y 7.4716 15.57 -1.88 19.78 5.7427 +IC C312 C313 C314 H14X 1.5352 113.22 -59.68 110.52 1.1110 +IC H14X C313 *C31 H14Y 7.6334 15.18 -48.36 17.66 7.1324 +IC H14X C313 *C31 H14Z 7.6334 15.18 -10.75 19.60 5.9480 + +RESI DPPC 0.00 ! 2,3 dipalmitoyl-D-glycero-1-Phosphatidylcholine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - N(CH3)3 +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL3 -0.27 ! | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 N C12 C11 1.4954 110.61 57.30 116.86 1.5411 +IC C15 N C12 C11 1.4975 109.67 -179.96 116.86 1.5411 +IC C13 C12 *N C14 1.4954 110.61 -119.72 108.04 1.5030 +IC C13 C12 *N C15 1.4954 110.61 122.74 109.67 1.4975 +IC C12 N C13 H13A 1.5222 110.61 -177.62 111.18 1.0811 +IC H13A N *C13 H13B 1.0811 111.18 119.00 109.33 1.0870 +IC H13A N *C13 H13C 1.0811 111.18 -122.05 111.32 1.0813 +IC C12 N C14 H14A 1.5222 108.04 55.75 111.02 1.0953 +IC H14A N *C14 H14B 1.0953 111.02 123.86 113.88 1.0740 +IC H14A N *C14 H14C 1.0953 111.02 -112.40 110.25 1.0937 +IC C12 N C15 H15A 1.5222 109.67 176.85 110.89 1.0820 +IC H15A N *C15 H15B 1.0820 110.89 121.48 111.48 1.0813 +IC H15A N *C15 H15C 1.0820 110.89 -118.74 109.66 1.0876 +IC C11 N *C12 H12A 1.5411 116.86 -126.39 111.90 1.0787 +IC H12A N *C12 H12B 1.0787 111.90 -116.29 108.17 1.0973 +IC N C12 C11 O12 1.5222 116.86 127.40 108.21 1.4230 +IC O12 C12 *C11 H11A 1.4230 108.21 -123.09 113.27 1.1137 +IC H11A C12 *C11 H11B 1.1137 113.27 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5411 108.21 -68.07 118.42 1.5874 +IC C11 O12 P O11 1.4230 118.42 -166.83 104.01 1.5775 +IC O11 O12 *P O13 1.5775 104.01 117.90 108.15 1.4792 +IC O11 O12 *P O14 1.5775 104.01 -117.24 106.77 1.4822 +IC O12 P O11 C1 1.5874 104.01 178.48 118.38 1.4312 +IC P O11 C1 C2 1.5775 118.38 167.50 110.65 1.5505 +IC C2 O11 *C1 HA 1.5505 110.65 -119.12 111.48 1.1171 +IC HA O11 *C1 HB 1.1171 111.48 -120.88 110.00 1.1145 +IC O11 C1 C2 C3 1.4312 110.65 176.57 110.77 1.5573 +IC C3 C1 *C2 O21 1.5573 110.77 120.75 108.04 1.4418 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.77 -118.27 106.63 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5505 108.04 147.09 115.01 1.3179 +IC C2 O21 C21 C22 1.4418 115.01 179.22 108.80 1.5292 +IC C22 O21 *C21 O22 1.5292 108.80 -178.84 126.50 1.2187 +IC O21 C21 C22 C23 1.3179 108.80 -177.42 111.91 1.5450 +IC C23 C21 *C22 H2R 1.5450 111.91 -121.60 107.88 1.1091 +IC H2R C21 *C22 H2S 1.1091 107.88 -117.29 107.69 1.1091 +IC C1 C2 C3 O31 1.5505 110.77 174.77 112.55 1.4433 +IC O31 C2 *C3 HX 1.4433 112.55 -118.38 106.64 1.1128 +IC HX C2 *C3 HY 1.1128 106.64 -115.20 109.46 1.1144 +IC C2 C3 O31 C31 1.5573 112.55 88.07 115.30 1.3310 +IC C3 O31 C31 C32 1.4433 115.30 -172.19 108.29 1.5287 +IC C32 O31 *C31 O32 1.5287 108.29 -179.12 125.69 1.2167 +IC O31 C31 C32 C33 1.3310 108.29 -167.41 113.60 1.5449 +IC C33 C31 *C32 H2X 1.5449 113.60 -121.15 107.11 1.1105 +IC H2X C31 *C32 H2Y 1.1105 107.11 -116.79 108.04 1.1091 +IC C21 C22 C23 C24 1.5292 111.91 176.40 112.78 1.5339 +IC C24 C22 *C23 H3R 1.5339 112.78 -120.84 109.53 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.53 -117.51 109.55 1.1144 +IC C22 C23 C24 C25 1.5450 112.78 -179.42 112.02 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.02 -121.40 109.42 1.1129 +IC H4R C23 *C24 H4S 1.1129 109.42 -117.70 109.09 1.1132 +IC C23 C24 C25 C26 1.5339 112.02 177.20 113.15 1.5345 +IC C26 C24 *C25 H5R 1.5345 113.15 -121.11 108.85 1.1137 +IC H5R C24 *C25 H5S 1.1137 108.85 -117.08 109.10 1.1133 +IC C24 C25 C26 C27 1.5348 113.15 -179.00 112.16 1.5349 +IC C27 C25 *C26 H6R 1.5349 112.16 -121.50 109.37 1.1128 +IC H6R C25 *C26 H6S 1.1128 109.37 -117.60 108.99 1.1133 +IC C25 C26 C27 C28 1.5345 112.16 177.46 113.03 1.5345 +IC C28 C26 *C27 H7R 1.5345 113.03 -121.07 108.86 1.1136 +IC H7R C26 *C27 H7S 1.1136 108.86 -117.16 109.14 1.1132 +IC C26 C27 C28 C29 1.5349 113.03 -178.73 112.29 1.5348 +IC C29 C27 *C28 H8R 1.5348 112.29 -121.53 109.34 1.1129 +IC H8R C27 *C28 H8S 1.1129 109.34 -117.54 108.99 1.1133 +IC C27 C28 C29 C210 1.5345 112.29 177.77 112.89 1.5345 +IC C210 C28 *C29 H9R 1.5345 112.89 -121.06 108.89 1.1135 +IC H9R C28 *C29 H9S 1.1135 108.89 -117.23 109.16 1.1131 +IC C28 C29 C210 C211 1.5348 112.89 -178.85 112.40 1.5348 +IC C211 C29 *C210 H10R 1.5348 112.40 -121.51 109.29 1.1130 +IC H10R C29 *C210 H10S 1.1130 109.29 -117.49 109.00 1.1133 +IC C29 C210 C211 C212 1.5345 112.40 178.16 112.78 1.5345 +IC C212 C210 *C211 H11R 1.5345 112.78 -121.11 108.96 1.1135 +IC H11R C210 *C211 H11S 1.1135 108.96 -117.30 109.16 1.1131 +IC C210 C211 C212 C213 1.5348 112.78 -179.23 112.49 1.5347 +IC C213 C211 *C212 H12R 1.5347 112.49 -121.45 109.24 1.1130 +IC H12R C211 *C212 H12S 1.1130 109.24 -117.45 109.03 1.1133 +IC C211 C212 C213 C214 1.5345 112.49 178.82 112.71 1.5347 +IC C214 C212 *C213 H13R 1.5347 112.71 -121.19 109.01 1.1133 +IC H13R C212 *C213 H13S 1.1133 109.01 -117.33 109.14 1.1131 +IC C212 C213 C214 C215 1.5347 112.71 -179.59 112.61 1.5341 +IC C215 C213 *C214 H14R 1.5341 112.61 -121.38 109.18 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.18 -117.39 109.09 1.1133 +IC C213 C214 C215 C216 1.5347 112.61 179.60 113.33 1.5309 +IC C216 C214 *C215 H15R 1.5309 113.33 -121.65 108.72 1.1142 +IC H15R C214 *C215 H15S 1.1142 108.72 -116.62 108.76 1.1141 +IC C214 C215 C216 H16R 1.5341 113.33 -59.94 110.45 1.1113 +IC H16R C215 *C216 H16S 1.1113 110.45 119.88 110.47 1.1113 +IC H16R C215 *C216 H16T 1.1113 110.45 -120.04 110.63 1.1112 +IC C31 C32 C33 C34 1.5287 113.60 179.68 111.12 1.5341 +IC C34 C32 *C33 H3X 1.5341 111.12 -120.80 109.72 1.1137 +IC H3X C32 *C33 H3Y 1.1137 109.72 -118.17 109.87 1.1142 +IC C32 C33 C34 C35 1.5449 111.12 -176.44 113.54 1.5344 +IC C35 C33 *C34 H4X 1.5344 113.54 -121.87 109.02 1.1135 +IC H4X C33 *C34 H4Y 1.1135 109.02 -117.04 108.81 1.1137 +IC C33 C34 C35 C36 1.5341 113.54 178.53 111.77 1.5349 +IC C36 C34 *C35 H5X 1.5349 111.77 -120.78 109.03 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.03 -117.69 109.50 1.1128 +IC C34 C35 C36 C37 1.5344 111.77 -176.24 113.37 1.5344 +IC C37 C35 *C36 H6X 1.5344 113.37 -122.00 109.13 1.1132 +IC H6X C35 *C36 H6Y 1.1132 109.13 -117.05 108.69 1.1137 +IC C35 C36 C37 C38 1.5349 113.37 177.81 111.98 1.5349 +IC C38 C36 *C37 H7X 1.5349 111.98 -120.73 108.96 1.1133 +IC H7X C36 *C37 H7Y 1.1133 108.96 -117.64 109.48 1.1127 +IC C36 C37 C38 C39 1.5344 111.98 -176.74 113.17 1.5344 +IC C39 C37 *C38 H8X 1.5344 113.17 -121.93 109.18 1.1131 +IC H8X C37 *C38 H8Y 1.1131 109.18 -117.13 108.74 1.1137 +IC C37 C38 C39 C310 1.5349 113.17 177.75 112.16 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.16 -120.81 108.99 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.99 -117.58 109.40 1.1128 +IC C38 C39 C310 C311 1.5344 112.16 -177.62 113.02 1.5345 +IC C311 C39 *C310 H10X 1.5345 113.02 -121.78 109.17 1.1131 +IC H10X C39 *C310 H10Y 1.1131 109.17 -117.21 108.84 1.1136 +IC C39 C310 C311 C312 1.5348 113.02 178.36 112.30 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.30 -120.94 109.01 1.1133 +IC H11X C310 *C311 H11Y 1.1133 109.01 -117.52 109.31 1.1129 +IC C310 C311 C312 C313 1.5345 112.30 -178.23 112.89 1.5345 +IC C313 C311 *C312 H12X 1.5345 112.89 -121.63 109.15 1.1131 +IC H12X C311 *C312 H12Y 1.1131 109.15 -117.28 108.93 1.1135 +IC C311 C312 C313 C314 1.5348 112.89 178.95 112.43 1.5350 +IC C314 C312 *C313 H13X 1.5350 112.43 -121.07 109.04 1.1133 +IC H13X C312 *C313 H13Y 1.1133 109.04 -117.48 109.23 1.1130 +IC C312 C313 C314 C315 1.5345 112.43 -178.86 112.82 1.5338 +IC C315 C313 *C314 H14X 1.5338 112.82 -121.48 109.14 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.14 -117.32 109.05 1.1133 +IC C313 C314 C315 C316 1.5350 112.82 179.62 113.25 1.5310 +IC C316 C314 *C315 H15X 1.5310 113.25 -121.59 108.75 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.75 -116.70 108.80 1.1140 +IC C314 C315 C316 H16X 1.5338 113.25 -59.74 110.45 1.1114 +IC H16X C315 *C316 H16Y 1.1114 110.45 119.85 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1114 110.45 -120.06 110.62 1.1112 + +RESI DPPE 0.00 ! 2,3 dipalmitoyl-D-glycero-1-Phosphatidylethanolamine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL3 -0.27 ! | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.5057 110.97 -62.47 110.71 1.4270 +IC HN1 C12 *N HN2 1.0638 106.70 113.19 110.24 1.0543 +IC HN1 C12 *N HN3 1.0638 106.70 -120.35 114.80 1.0324 +IC HN1 N C12 C11 1.0638 106.70 3.91 110.97 1.5406 +IC C11 N *C12 H12A 1.5406 110.97 122.22 108.24 1.1075 +IC H12A N *C12 H12B 1.1075 108.24 118.08 107.49 1.1112 +IC O12 C12 *C11 H11A 1.4270 110.71 -118.29 108.33 1.1146 +IC H11A C12 *C11 H11B 1.1146 108.33 -116.10 110.62 1.1176 +IC C12 C11 O12 P 1.5406 110.71 100.57 121.92 1.5871 +IC C11 O12 P O11 1.4270 121.92 -154.88 102.25 1.5814 +IC O11 O12 *P O13 1.5814 102.25 -118.56 109.16 1.4678 +IC O11 O12 *P O14 1.5814 102.25 113.09 104.81 1.4835 +IC O12 P O11 C1 1.5871 102.25 -23.47 121.99 1.4280 +IC P O11 C1 C2 1.5814 121.99 89.21 111.06 1.5474 +IC C2 O11 *C1 HA 1.5474 111.06 -123.17 112.41 1.1160 +IC HA O11 *C1 HB 1.1160 112.41 -117.95 108.85 1.1130 +IC O11 C1 C2 C3 1.4280 111.06 58.02 110.50 1.5580 +IC C3 C1 *C2 O21 1.5580 110.50 122.15 107.35 1.4388 +IC C3 C1 *C2 HS 1.5580 110.50 -117.62 106.68 1.1147 +IC C1 C2 O21 C21 1.5474 107.35 146.88 114.92 1.3210 +IC C2 O21 C21 C22 1.4388 114.92 -171.74 110.19 1.5316 +IC C22 O21 *C21 O22 1.5316 110.19 176.46 125.87 1.2200 +IC O21 C21 C22 C23 1.3210 110.19 -31.58 115.14 1.5479 +IC C23 C21 *C22 H2R 1.5479 115.14 -122.28 107.22 1.1099 +IC H2R C21 *C22 H2S 1.1099 107.22 -116.10 106.69 1.1099 +IC C1 C2 C3 O31 1.5474 110.50 -179.86 113.76 1.4446 +IC O31 C2 *C3 HX 1.4446 113.76 -119.55 106.72 1.1128 +IC HX C2 *C3 HY 1.1128 106.72 -114.85 108.93 1.1152 +IC C2 C3 O31 C31 1.5580 113.76 80.37 115.81 1.3230 +IC C3 O31 C31 C32 1.4446 115.81 177.76 109.41 1.5249 +IC C32 O31 *C31 O32 1.5249 109.41 -178.66 126.04 1.2219 +IC O31 C31 C32 C33 1.3230 109.41 -162.24 111.90 1.5452 +IC C33 C31 *C32 H2X 1.5452 111.90 120.83 108.03 1.1097 +IC H2X C31 *C32 H2Y 1.1097 108.03 117.34 107.97 1.1097 +IC C21 C22 C23 C24 1.5316 115.14 172.56 111.78 1.5351 +IC C24 C22 *C23 H3R 1.5351 111.78 -120.43 110.86 1.1141 +IC H3R C22 *C23 H3S 1.1141 110.86 -118.29 108.87 1.1110 +IC C22 C23 C24 C25 1.5479 111.78 175.20 114.13 1.5388 +IC C25 C23 *C24 H4R 1.5388 114.13 -122.15 109.40 1.1117 +IC H4R C23 *C24 H4S 1.1117 109.40 -116.51 108.51 1.1140 +IC C23 C24 C25 C26 1.5351 114.13 -66.85 114.10 1.5388 +IC C26 C24 *C25 H5R 1.5388 114.10 -119.38 107.26 1.1154 +IC H5R C24 *C25 H5S 1.1154 107.26 -116.50 110.11 1.1114 +IC C24 C25 C26 C27 1.5388 114.10 100.57 113.97 1.5381 +IC C27 C25 *C26 H6R 1.5381 113.97 -124.26 109.29 1.1102 +IC H6R C25 *C26 H6S 1.1102 109.29 -116.46 108.45 1.1145 +IC C25 C26 C27 C28 1.5388 113.97 -177.48 113.00 1.5388 +IC C28 C26 *C27 H7R 1.5388 113.00 -120.02 107.81 1.1143 +IC H7R C26 *C27 H7S 1.1143 107.81 -116.70 110.61 1.1095 +IC C26 C27 C28 C29 1.5381 113.00 73.51 114.48 1.5394 +IC C29 C27 *C28 H8R 1.5394 114.48 121.55 109.10 1.1131 +IC H8R C27 *C28 H8S 1.1131 109.10 116.45 108.17 1.1129 +IC C27 C28 C29 C210 1.5388 114.48 75.29 113.06 1.5373 +IC C210 C28 *C29 H9R 1.5373 113.06 119.46 108.33 1.1143 +IC H9R C28 *C29 H9S 1.1143 108.33 117.04 110.12 1.1106 +IC C28 C29 C210 C211 1.5394 113.06 -179.99 113.53 1.5392 +IC C211 C29 *C21 H10R 5.7263 24.45 -52.33 19.56 6.4218 +IC H10R C29 *C21 H10S 6.4218 19.56 -7.26 16.47 4.6680 +IC C29 C210 C211 C212 1.5373 113.53 107.52 113.66 1.5393 +IC C212 C210 *C21 H11R 4.5647 26.89 25.24 19.43 6.4275 +IC H11R C210 *C21 H11S 6.4275 19.43 -49.66 19.34 6.3953 +IC C210 C211 C212 C213 1.5392 113.66 -67.51 114.71 1.5372 +IC C213 C211 *C21 H12R 3.9020 22.44 -113.11 15.60 4.0036 +IC H12R C211 *C21 H12S 4.0036 15.60 51.31 22.29 5.1729 +IC C211 C212 C213 C214 1.5393 114.71 -73.19 113.34 1.5359 +IC C214 C212 *C21 H13R 5.1258 30.02 -21.12 24.58 3.1078 +IC H13R C212 *C21 H13S 3.1078 24.58 67.39 28.08 3.7253 +IC C212 C213 C214 C215 1.5372 113.34 179.89 113.82 1.5359 +IC C215 C213 *C21 H14R 5.2338 28.21 -55.53 17.24 5.5482 +IC H14R C213 *C21 H14S 5.5482 17.24 78.44 8.05 5.9707 +IC C213 C214 C215 C216 1.5359 113.82 -66.88 113.92 1.5311 +IC C216 C214 *C21 H15R 5.3823 28.19 -53.75 25.03 4.6187 +IC H15R C214 *C21 H15S 4.6187 25.03 9.17 18.56 6.2799 +IC C214 C215 C216 H16R 1.5359 113.92 -178.32 110.68 1.1109 +IC H16R C215 *C21 H16S 5.8584 21.81 48.56 19.67 6.2163 +IC H16R C215 *C21 H16T 5.8584 21.81 34.57 24.54 4.5432 +IC C31 C32 C33 C34 1.5249 111.90 173.88 112.09 1.5326 +IC C34 C32 *C33 H3X 1.5326 112.09 121.48 110.07 1.1135 +IC H3X C32 *C33 H3Y 1.1135 110.07 118.51 109.64 1.1148 +IC C32 C33 C34 C35 1.5452 112.09 -177.02 112.91 1.5371 +IC C35 C33 *C34 H4X 1.5371 112.91 -122.36 108.99 1.1120 +IC H4X C33 *C34 H4Y 1.1120 108.99 -117.01 109.04 1.1140 +IC C33 C34 C35 C36 1.5326 112.91 177.47 112.62 1.5375 +IC C36 C34 *C35 H5X 1.5375 112.62 -119.93 108.27 1.1141 +IC H5X C34 *C35 H5Y 1.1141 108.27 -117.45 110.11 1.1117 +IC C34 C35 C36 C37 1.5371 112.62 73.42 113.16 1.5383 +IC C37 C35 *C36 H6X 1.5383 113.16 -122.28 107.64 1.1110 +IC H6X C35 *C36 H6Y 1.1110 107.64 -116.60 109.48 1.1132 +IC C35 C36 C37 C38 1.5375 113.16 -173.58 114.67 1.5422 +IC C38 C36 *C37 H7X 1.5422 114.67 -121.06 108.09 1.1138 +IC H7X C36 *C37 H7Y 1.1138 108.09 -115.65 109.43 1.1074 +IC C36 C37 C38 C39 1.5383 114.67 60.50 116.34 1.5430 +IC C39 C37 *C38 H8X 1.5430 116.34 -120.51 107.04 1.1150 +IC H8X C37 *C38 H8Y 1.1150 107.04 -115.94 109.39 1.1128 +IC C37 C38 C39 C310 1.5422 116.34 81.64 116.19 1.5424 +IC C310 C38 *C39 H9X 1.5424 116.19 118.69 107.12 1.1159 +IC H9X C38 *C39 H9Y 1.1159 107.12 115.61 110.64 1.1092 +IC C38 C39 C310 C311 1.5430 116.19 -62.61 115.21 1.5371 +IC C311 C39 *C31 H10X 7.2268 16.24 34.33 13.86 8.9713 +IC H10X C39 *C31 H10Y 8.9713 13.86 -48.51 13.27 9.2942 +IC C39 C310 C311 C312 1.5424 115.21 -160.44 113.61 1.5376 +IC C312 C310 *C31 H11X 7.5244 17.04 -67.94 12.19 7.1444 +IC H11X C310 *C31 H11Y 7.1444 12.19 116.65 2.95 6.3634 +IC C310 C311 C312 C313 1.5371 113.61 100.82 114.93 1.5418 +IC C313 C311 *C31 H12X 7.1363 20.81 -28.85 12.13 8.6337 +IC H12X C311 *C31 H12Y 8.6337 12.13 -24.87 17.15 7.2190 +IC C311 C312 C313 C314 1.5376 114.93 -70.22 115.41 1.5381 +IC C314 C312 *C31 H13X 8.0163 18.95 -52.25 16.37 7.5529 +IC H13X C312 *C31 H13Y 7.5529 16.37 30.89 13.81 6.0545 +IC C312 C313 C314 C315 1.5418 115.41 92.50 114.00 1.5357 +IC C315 C313 *C31 H14X 7.5706 19.91 -46.93 13.27 8.3565 +IC H14X C313 *C31 H14Y 8.3565 13.27 57.02 8.44 8.9732 +IC C313 C314 C315 C316 1.5381 114.00 178.22 113.12 1.5307 +IC C316 C314 *C31 H15X 8.7835 16.73 -10.98 13.46 6.6927 +IC H15X C314 *C31 H15Y 6.6927 13.46 54.64 15.58 7.4175 +IC C314 C315 C316 H16X 1.5357 113.12 60.42 110.36 1.1113 +IC H16X C315 *C31 H16Y 9.6613 4.19 -21.95 13.28 8.6928 +IC H16X C315 *C31 H16Z 9.6613 4.19 -77.33 10.61 9.1221 + +RESI DPPS -1.00 ! 2,3 dipalmitoyl-D-glycero-1-Phosphatidylserine +! +! R1 - CH2 +! | (-) +! R2 - CH CO2 +! | (-) | (+) +! CH2 - PO4 - CH2 - CH - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL3 -0.27 ! | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 C13 C12 O13B O13A + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.4892 109.79 -66.07 111.86 1.4332 +IC N C12 C13 O13B 1.4892 108.30 177.11 118.01 1.2553 +IC HN1 C12 *N HN2 1.0293 111.95 119.77 101.90 1.0502 +IC HN1 C12 *N HN3 1.0293 111.95 -122.92 108.25 1.0597 +IC HN1 N C12 C11 1.0293 111.95 127.72 109.79 1.5597 +IC C11 N *C12 C13 1.5597 109.79 122.24 108.30 1.5440 +IC C13 N *C12 H12A 1.5440 108.30 117.18 109.21 1.0794 +IC O13B C12 *C13 O13A 1.2553 118.01 -178.54 118.17 1.2648 +IC O12 C12 *C11 H11A 1.4332 111.86 -118.46 107.28 1.1149 +IC H11A C12 *C11 H11B 1.1149 107.28 -115.37 110.30 1.1160 +IC C12 C11 O12 P 1.5597 111.86 94.99 122.93 1.5835 +IC C11 O12 P O11 1.4332 122.93 -142.74 101.19 1.5825 +IC O11 O12 *P O13 1.5825 101.19 -116.49 110.28 1.4734 +IC O11 O12 *P O14 1.5825 101.19 112.69 106.84 1.4821 +IC O12 P O11 C1 1.5835 101.19 -39.85 119.07 1.4288 +IC P O11 C1 C2 1.5825 119.07 -174.92 110.29 1.5511 +IC C2 O11 *C1 HA 1.5511 110.29 -120.67 110.89 1.1147 +IC HA O11 *C1 HB 1.1147 110.89 -120.35 110.50 1.1166 +IC O11 C1 C2 C3 1.4288 110.29 48.35 111.17 1.5568 +IC C3 C1 *C2 O21 1.5568 111.17 120.41 109.13 1.4417 +IC C3 C1 *C2 HS 1.5568 111.17 -117.26 108.54 1.1162 +IC C1 C2 O21 C21 1.5511 109.13 74.41 113.96 1.3221 +IC C2 O21 C21 C22 1.4417 113.96 -167.99 109.53 1.5272 +IC C22 O21 *C21 O22 1.5272 109.53 -179.65 126.21 1.2174 +IC O21 C21 C22 C23 1.3221 109.53 64.25 112.68 1.5472 +IC C23 C21 *C22 H2R 1.5472 112.68 -121.83 108.11 1.1086 +IC H2R C21 *C22 H2S 1.1086 108.11 -117.26 107.11 1.1097 +IC C1 C2 C3 O31 1.5511 111.17 -177.57 112.74 1.4497 +IC O31 C2 *C3 HX 1.4497 112.74 -119.77 106.93 1.1126 +IC HX C2 *C3 HY 1.1126 106.93 -114.79 109.26 1.1151 +IC C2 C3 O31 C31 1.5568 112.74 84.35 114.46 1.3283 +IC C3 O31 C31 C32 1.4497 114.46 -179.97 109.38 1.5308 +IC C32 O31 *C31 O32 1.5308 109.38 179.93 126.01 1.2155 +IC O31 C31 C32 C33 1.3283 109.38 -170.84 111.34 1.5485 +IC C33 C31 *C32 H2X 1.5485 111.34 121.61 108.40 1.1087 +IC H2X C31 *C32 H2Y 1.1087 108.40 117.43 107.14 1.1088 +IC C21 C22 C23 C24 1.5272 112.68 175.56 111.73 1.5363 +IC C24 C22 *C23 H3R 1.5363 111.73 -120.81 110.11 1.1145 +IC H3R C22 *C23 H3S 1.1145 110.11 -117.48 109.04 1.1116 +IC C22 C23 C24 C25 1.5472 111.73 173.71 114.56 1.5410 +IC C25 C23 *C24 H4R 1.5410 114.56 -123.15 109.70 1.1117 +IC H4R C23 *C24 H4S 1.1117 109.70 -116.25 107.41 1.1147 +IC C23 C24 C25 C26 1.5363 114.56 -101.06 113.88 1.5404 +IC C26 C24 *C25 H5R 1.5404 113.88 -117.91 107.22 1.1152 +IC H5R C24 *C25 H5S 1.1152 107.22 -116.69 110.63 1.1112 +IC C24 C25 C26 C27 1.5410 113.88 78.48 113.78 1.5359 +IC C27 C25 *C26 H6R 1.5359 113.78 -122.82 108.25 1.1113 +IC H6R C25 *C26 H6S 1.1113 108.25 -116.47 109.24 1.1134 +IC C25 C26 C27 C28 1.5404 113.78 -167.71 114.19 1.5391 +IC C28 C26 *C27 H7R 1.5391 114.19 -122.39 108.82 1.1132 +IC H7R C26 *C27 H7S 1.1132 108.82 -116.22 109.45 1.1093 +IC C26 C27 C28 C29 1.5359 114.19 63.84 114.54 1.5407 +IC C29 C27 *C28 H8R 1.5407 114.54 -123.40 109.69 1.1120 +IC H8R C27 *C28 H8S 1.1120 109.69 -116.61 107.71 1.1148 +IC C27 C28 C29 C210 1.5391 114.54 47.95 113.52 1.5387 +IC C210 C28 *C29 H9R 1.5387 113.52 121.39 108.13 1.1124 +IC H9R C28 *C29 H9S 1.1124 108.13 116.73 109.70 1.1119 +IC C28 C29 C210 C211 1.5407 113.52 163.36 114.10 1.5371 +IC C211 C29 *C21 H10R 6.4029 22.05 -57.44 14.61 5.3325 +IC H10R C29 *C21 H10S 5.3325 14.61 103.70 10.12 4.9740 +IC C29 C210 C211 C212 1.5387 114.10 -103.31 113.12 1.5385 +IC C212 C210 *C21 H11R 6.8707 21.06 49.29 21.37 5.9018 +IC H11R C210 *C21 H11S 5.9018 21.37 6.40 12.59 7.3666 +IC C210 C211 C212 C213 1.5371 113.12 64.11 114.92 1.5375 +IC C213 C211 *C21 H12R 7.9157 17.01 58.55 15.73 7.4795 +IC H12R C211 *C21 H12S 7.4795 15.73 -29.21 19.67 6.0830 +IC C211 C212 C213 C214 1.5385 114.92 72.92 113.24 1.5357 +IC C214 C212 *C21 H13R 9.2399 7.09 23.37 16.22 7.6363 +IC H13R C212 *C21 H13S 7.6363 16.22 48.45 12.87 8.2194 +IC C212 C213 C214 C215 1.5375 113.24 179.54 113.61 1.5368 +IC C215 C213 *C21 H14R 10.3725 4.79 -62.68 11.93 9.1709 +IC H14R C213 *C21 H14S 9.1709 11.93 -59.77 8.46 9.6559 +IC C213 C214 C215 C216 1.5357 113.61 -60.55 114.65 1.5327 +IC C216 C214 *C21 H15R 10.8653 11.50 -58.65 11.55 10.1771 +IC H15R C214 *C21 H15S 10.1771 11.55 -14.52 4.14 11.2725 +IC C214 C215 C216 H16R 1.5368 114.65 -175.03 110.26 1.1114 +IC H16R C215 *C21 H16S 11.8086 8.52 8.95 12.18 10.1775 +IC H16R C215 *C21 H16T 11.8086 8.52 49.95 10.86 11.1647 +IC C31 C32 C33 C34 1.5308 111.34 -178.05 114.31 1.5377 +IC C34 C32 *C33 H3X 1.5377 114.31 121.43 109.27 1.1154 +IC H3X C32 *C33 H3Y 1.1154 109.27 116.81 109.17 1.1147 +IC C32 C33 C34 C35 1.5485 114.31 61.00 113.22 1.5352 +IC C35 C33 *C34 H4X 1.5352 113.22 -122.19 109.81 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.81 -117.41 108.08 1.1148 +IC C33 C34 C35 C36 1.5377 113.22 167.33 113.42 1.5371 +IC C36 C34 *C35 H5X 1.5371 113.42 -121.19 109.26 1.1136 +IC H5X C34 *C35 H5Y 1.1136 109.26 -117.18 108.56 1.1100 +IC C34 C35 C36 C37 1.5352 113.42 170.70 113.15 1.5402 +IC C37 C35 *C36 H6X 1.5402 113.15 -122.74 110.16 1.1113 +IC H6X C35 *C36 H6Y 1.1113 110.16 -116.48 107.91 1.1132 +IC C35 C36 C37 C38 1.5371 113.15 -107.42 114.17 1.5413 +IC C38 C36 *C37 H7X 1.5413 114.17 -119.83 108.30 1.1143 +IC H7X C36 *C37 H7Y 1.1143 108.30 -116.34 109.57 1.1116 +IC C36 C37 C38 C39 1.5402 114.17 57.75 115.11 1.5391 +IC C39 C37 *C38 H8X 1.5391 115.11 -120.86 107.77 1.1143 +IC H8X C37 *C38 H8Y 1.1143 107.77 -116.36 109.13 1.1127 +IC C37 C38 C39 C310 1.5413 115.11 66.40 114.23 1.5367 +IC C310 C38 *C39 H9X 1.5367 114.23 120.97 108.85 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.85 116.45 108.65 1.1110 +IC C38 C39 C310 C311 1.5391 114.23 -179.12 113.89 1.5404 +IC C311 C39 *C31 H10X 6.2934 21.31 -47.35 17.01 7.4132 +IC H10X C39 *C31 H10Y 7.4132 17.01 -17.22 15.51 5.7158 +IC C39 C310 C311 C312 1.5367 113.89 58.71 114.22 1.5404 +IC C312 C310 *C31 H11X 5.3241 22.48 -57.41 19.30 6.1883 +IC H11X C310 *C31 H11Y 6.1883 19.30 38.38 16.93 7.3078 +IC C310 C311 C312 C313 1.5404 114.22 -99.82 114.24 1.5395 +IC C313 C311 *C31 H12X 6.2651 23.77 33.63 13.80 4.5403 +IC H12X C311 *C31 H12Y 4.5403 13.80 -82.82 17.81 4.9762 +IC C311 C312 C313 C314 1.5404 114.24 -73.49 113.17 1.5370 +IC C314 C312 *C31 H13X 7.3031 15.08 73.86 14.00 6.9234 +IC H13X C312 *C31 H13Y 6.9234 14.00 -34.30 21.82 5.8233 +IC C312 C313 C314 C315 1.5395 113.17 -176.13 113.94 1.5364 +IC C315 C313 *C31 H14X 8.3780 11.68 -41.53 18.01 6.9121 +IC H14X C313 *C31 H14Y 6.9121 18.01 -38.94 11.56 7.9207 +IC C313 C314 C315 C316 1.5370 113.94 -63.79 114.35 1.5316 +IC C316 C314 *C31 H15X 9.2795 11.54 -49.87 15.35 8.0230 +IC H15X C314 *C31 H15Y 8.0230 15.35 -34.00 8.38 9.1060 +IC C314 C315 C316 H16X 1.5364 114.35 -176.22 110.44 1.1109 +IC H16X C315 *C31 H16Y 10.1379 8.04 22.11 14.30 8.8264 +IC H16X C315 *C31 H16Z 10.1379 8.04 64.08 10.71 9.7633 + +RESI DPPA -1.00 ! 2,3 dipalmitoyl--D-glycero-1-Phosphatidic acid +! +! R1 - CH2 +! | +! R2 - CH +! | (-) +! CH2 - PO4 - H +! +! Polar Head and glycerol backbone +GROUP ! H12 + ! | +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.82 ! \ / alpha3 +ATOM O14 O2L -0.82 ! P (+) +ATOM O12 OHL -0.68 ! / \ alpha2 +ATOM H12 HOL 0.34 ! (-) O14 O11 +ATOM O11 OSLP -0.62 ! | +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL3 -0.27 ! | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC O11 P O12 H12 1.5816 105.94 -176.82 105.36 0.9597 +IC O12 O11 *P O13 1.5645 105.94 112.01 111.41 1.4721 +IC O12 O11 *P O14 1.5645 105.94 -112.18 111.94 1.4702 +IC O12 P O11 C1 1.5645 105.94 -71.73 118.23 1.4314 +IC P O11 C1 C2 1.5816 118.23 -173.42 110.42 1.5524 +IC C2 O11 *C1 HA 1.5524 110.42 -121.50 111.27 1.1146 +IC HA O11 *C1 HB 1.1146 111.27 -120.30 110.09 1.1174 +IC O11 C1 C2 C3 1.4314 110.42 32.62 110.59 1.5581 +IC C3 C1 *C2 O21 1.5581 110.59 120.14 109.54 1.4411 +IC C3 C1 *C2 HS 1.5581 110.59 -117.28 108.89 1.1154 +IC C1 C2 O21 C21 1.5524 109.54 71.21 114.13 1.3179 +IC C2 O21 C21 C22 1.4411 114.13 -165.28 109.22 1.5267 +IC C22 O21 *C21 O22 1.5267 109.22 -179.94 126.59 1.2185 +IC O21 C21 C22 C23 1.3179 109.22 58.08 112.19 1.5464 +IC C23 C21 *C22 H2R 1.5464 112.19 -121.68 108.09 1.1086 +IC H2R C21 *C22 H2S 1.1086 108.09 -117.42 107.19 1.1092 +IC C1 C2 C3 O31 1.5524 110.59 168.87 113.51 1.4480 +IC O31 C2 *C3 HX 1.4480 113.51 -119.34 106.36 1.1130 +IC HX C2 *C3 HY 1.1130 106.36 -114.69 109.13 1.1153 +IC C2 C3 O31 C31 1.5581 113.51 77.85 114.96 1.3223 +IC C3 O31 C31 C32 1.4480 114.96 179.20 108.72 1.5297 +IC C32 O31 *C31 O32 1.5297 108.72 -179.17 126.48 1.2160 +IC O31 C31 C32 C33 1.3223 108.72 -172.45 111.89 1.5463 +IC C33 C31 *C32 H2X 1.5463 111.89 120.98 107.64 1.1092 +IC H2X C31 *C32 H2Y 1.1092 107.64 117.26 107.98 1.1084 +IC C21 C22 C23 C24 1.5267 112.19 175.92 112.10 1.5352 +IC C24 C22 *C23 H3R 1.5352 112.10 -121.22 110.20 1.1144 +IC H3R C22 *C23 H3S 1.1144 110.20 -117.09 109.01 1.1131 +IC C22 C23 C24 C25 1.5464 112.10 169.42 113.73 1.5400 +IC C25 C23 *C24 H4R 1.5400 113.73 -122.22 109.52 1.1125 +IC H4R C23 *C24 H4S 1.1125 109.52 -116.54 107.92 1.1137 +IC C23 C24 C25 C26 1.5352 113.73 -105.46 113.19 1.5398 +IC C26 C24 *C25 H5R 1.5398 113.19 -118.95 107.96 1.1143 +IC H5R C24 *C25 H5S 1.1143 107.96 -116.97 110.17 1.1121 +IC C24 C25 C26 C27 1.5400 113.19 71.19 113.63 1.5373 +IC C27 C25 *C26 H6R 1.5373 113.63 -122.19 107.57 1.1111 +IC H6R C25 *C26 H6S 1.1111 107.57 -116.44 109.54 1.1126 +IC C25 C26 C27 C28 1.5398 113.63 -162.37 114.47 1.5405 +IC C28 C26 *C27 H7R 1.5405 114.47 -122.52 108.53 1.1133 +IC H7R C26 *C27 H7S 1.1133 108.53 -115.83 109.51 1.1083 +IC C26 C27 C28 C29 1.5373 114.47 65.65 114.87 1.5417 +IC C29 C27 *C28 H8R 1.5417 114.87 -122.39 108.61 1.1125 +IC H8R C27 *C28 H8S 1.1125 108.61 -116.27 108.57 1.1124 +IC C27 C28 C29 C210 1.5405 114.87 57.11 115.92 1.5430 +IC C210 C28 *C29 H9R 1.5430 115.92 123.11 109.07 1.1124 +IC H9R C28 *C29 H9S 1.1124 109.07 115.74 108.00 1.1127 +IC C28 C29 C210 C211 1.5417 115.92 78.72 114.95 1.5410 +IC C211 C29 *C21 H10R 6.0413 22.61 59.73 18.34 6.0913 +IC H10R C29 *C21 H10S 6.0913 18.34 -12.50 7.26 4.6601 +IC C29 C210 C211 C212 1.5430 114.95 -116.06 115.09 1.5417 +IC C212 C210 *C21 H11R 5.1474 27.10 40.81 19.33 6.4028 +IC H11R C210 *C21 H11S 6.4028 19.33 -47.54 16.08 7.0023 +IC C210 C211 C212 C213 1.5410 115.09 81.88 115.76 1.5376 +IC C213 C211 *C21 H12R 5.3783 25.57 56.67 21.01 5.7167 +IC H12R C211 *C21 H12S 5.7167 21.01 1.43 11.63 4.1102 +IC C211 C212 C213 C214 1.5417 115.76 62.94 113.89 1.5364 +IC C214 C212 *C21 H13R 6.9012 18.22 21.04 24.57 4.9886 +IC H13R C212 *C21 H13S 4.9886 24.57 -50.12 24.50 5.1220 +IC C212 C213 C214 C215 1.5376 113.89 176.97 112.59 1.5336 +IC C215 C213 *C21 H14R 7.4931 12.95 -117.36 6.07 7.4528 +IC H14R C213 *C21 H14S 7.4528 6.07 -142.25 8.62 7.3321 +IC C213 C214 C215 C216 1.5364 112.59 -179.50 113.24 1.5310 +IC C216 C214 *C21 H15R 9.0163 10.48 19.44 17.53 7.1907 +IC H15R C214 *C21 H15S 7.1907 17.53 -48.83 17.21 7.3148 +IC C214 C215 C216 H16R 1.5336 113.24 -179.96 110.42 1.1113 +IC H16R C215 *C21 H16S 9.5324 5.29 -140.37 6.28 9.4718 +IC H16R C215 *C21 H16T 9.5324 5.29 115.15 7.56 9.3749 +IC C31 C32 C33 C34 1.5297 111.89 175.33 112.45 1.5336 +IC C34 C32 *C33 H3X 1.5336 112.45 122.11 109.85 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.85 117.51 109.20 1.1151 +IC C32 C33 C34 C35 1.5463 112.45 -176.15 112.80 1.5368 +IC C35 C33 *C34 H4X 1.5368 112.80 -122.23 109.26 1.1118 +IC H4X C33 *C34 H4Y 1.1118 109.26 -117.24 108.46 1.1133 +IC C33 C34 C35 C36 1.5336 112.80 172.61 113.83 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.83 -119.92 107.88 1.1145 +IC H5X C34 *C35 H5Y 1.1145 107.88 -116.73 109.60 1.1120 +IC C34 C35 C36 C37 1.5368 113.83 69.29 114.47 1.5406 +IC C37 C35 *C36 H6X 1.5406 114.47 -123.10 108.54 1.1122 +IC H6X C35 *C36 H6Y 1.1122 108.54 -115.84 108.55 1.1136 +IC C35 C36 C37 C38 1.5396 114.47 -126.05 113.77 1.5406 +IC C38 C36 *C37 H7X 1.5406 113.77 -120.41 108.14 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.14 -116.16 109.81 1.1106 +IC C36 C37 C38 C39 1.5406 113.77 69.90 114.03 1.5380 +IC C39 C37 *C38 H8X 1.5380 114.03 -121.39 108.10 1.1134 +IC H8X C37 *C38 H8Y 1.1134 108.10 -116.87 109.43 1.1126 +IC C37 C38 C39 C310 1.5406 114.03 75.43 113.42 1.5362 +IC C310 C38 *C39 H9X 1.5362 113.42 120.82 109.22 1.1130 +IC H9X C38 *C39 H9Y 1.1130 109.22 116.90 109.06 1.1105 +IC C38 C39 C310 C311 1.5380 113.42 -162.61 114.37 1.5390 +IC C311 C39 *C31 H10X 5.8375 21.27 -28.85 16.15 7.6495 +IC H10X C39 *C31 H10Y 7.6495 16.15 -32.50 18.11 6.2888 +IC C39 C310 C311 C312 1.5362 114.37 -60.29 115.32 1.5386 +IC C312 C310 *C31 H11X 6.6466 22.60 -54.13 18.78 6.0145 +IC H11X C310 *C31 H11Y 6.0145 18.78 47.30 11.65 4.7624 +IC C310 C311 C312 C313 1.5390 115.32 92.00 113.74 1.5392 +IC C313 C311 *C31 H12X 6.4082 23.72 -51.80 18.18 6.7026 +IC H12X C311 *C31 H12Y 6.7026 18.18 36.79 9.70 7.7005 +IC C311 C312 C313 C314 1.5386 113.74 172.94 113.77 1.5392 +IC C314 C312 *C31 H13X 7.5107 19.80 50.20 19.05 6.6388 +IC H13X C312 *C31 H13Y 6.6388 19.05 -40.41 16.81 5.4015 +IC C312 C313 C314 C315 1.5392 113.77 96.33 114.54 1.5394 +IC C315 C313 *C31 H14X 8.8064 7.46 -27.12 16.78 7.2510 +IC H14X C313 *C31 H14Y 7.2510 16.78 -49.46 13.25 7.8478 +IC C313 C314 C315 C316 1.5392 114.54 -61.20 115.22 1.5318 +IC C316 C314 *C31 H15X 9.5613 10.75 -63.75 12.84 8.7045 +IC H15X C314 *C31 H15Y 8.7045 12.84 -43.72 4.79 9.5540 +IC C314 C315 C316 H16X 1.5394 115.22 -176.13 110.54 1.1109 +IC H16X C315 *C31 H16Y 10.5468 7.86 6.42 13.91 9.0878 +IC H16X C315 *C31 H16Z 10.5468 7.86 51.47 11.93 9.8230 + +RESI DPPG -1.00 ! 2,3 dipalmitoyl-D-glycero-1-Phosphatidylglycerol +! +! R1 - CH2 +! | +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH(OH) - CH2OH +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL3 -0.27 ! | +ATOM H16R HAL3 0.09 ! H16R---C216--H16S | +ATOM H16S HAL3 0.09 ! | +ATOM H16T HAL3 0.09 ! H16T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 H16T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 C12 C11 O12 1.5516 113.86 177.39 110.94 1.4329 +IC OC3 C13 C12 C11 1.4279 111.62 -65.28 113.86 1.5470 +IC OC3 C12 *C13 H13A 1.4279 111.62 121.64 109.30 1.1114 +IC OC3 C12 *C13 H13B 1.4279 111.62 -120.05 108.33 1.1124 +IC C12 C13 OC3 HO3 1.5516 111.62 -33.25 102.56 0.9680 +IC C11 C13 *C12 OC2 1.5470 113.86 121.19 110.87 1.4235 +IC OC2 C13 *C12 H12A 1.4235 110.87 118.76 108.06 1.1153 +IC C13 C12 OC2 HO2 1.5516 110.87 -162.63 100.60 0.9696 +IC O12 C12 *C11 H11A 1.4329 110.94 -119.23 108.49 1.1130 +IC H11A C12 *C11 H11B 1.1130 108.49 -115.94 109.18 1.1161 +IC C12 C11 O12 P 1.5470 110.94 93.63 120.04 1.5904 +IC C11 O12 P O11 1.4329 120.04 -164.47 101.59 1.5892 +IC O11 O12 *P O13 1.5892 101.59 -114.60 108.45 1.4755 +IC O11 O12 *P O14 1.5892 101.59 115.63 108.70 1.4781 +IC O12 P O11 C1 1.5904 101.59 -27.62 118.80 1.4303 +IC P O11 C1 C2 1.5892 118.80 -158.81 110.93 1.5511 +IC C2 O11 *C1 HA 1.5511 110.93 -121.63 110.24 1.1129 +IC HA O11 *C1 HB 1.1129 110.24 -120.25 111.14 1.1186 +IC O11 C1 C2 C3 1.4303 110.93 40.46 111.05 1.5560 +IC C3 C1 *C2 O21 1.5560 111.05 119.58 109.27 1.4407 +IC C3 C1 *C2 HS 1.5560 111.05 -118.08 109.07 1.1154 +IC C1 C2 O21 C21 1.5511 109.27 68.77 114.61 1.3180 +IC C2 O21 C21 C22 1.4407 114.61 -162.88 109.06 1.5280 +IC C22 O21 *C21 O22 1.5280 109.06 179.13 126.56 1.2166 +IC O21 C21 C22 C23 1.3180 109.06 53.17 112.18 1.5469 +IC C23 C21 *C22 H2R 1.5469 112.18 -121.75 108.04 1.1082 +IC H2R C21 *C22 H2S 1.1082 108.04 -117.37 107.14 1.1094 +IC C1 C2 C3 O31 1.5511 111.05 170.57 112.26 1.4479 +IC O31 C2 *C3 HX 1.4479 112.26 -118.84 106.67 1.1132 +IC HX C2 *C3 HY 1.1132 106.67 -115.02 109.54 1.1151 +IC C2 C3 O31 C31 1.5560 112.26 81.50 114.74 1.3253 +IC C3 O31 C31 C32 1.4479 114.74 -173.33 108.08 1.5332 +IC C32 O31 *C31 O32 1.5332 108.08 179.61 126.15 1.2144 +IC O31 C31 C32 C33 1.3253 108.08 -177.04 113.81 1.5470 +IC C33 C31 *C32 H2X 1.5470 113.81 120.66 106.88 1.1097 +IC H2X C31 *C32 H2Y 1.1097 106.88 116.70 107.98 1.1088 +IC C21 C22 C23 C24 1.5280 112.18 176.06 112.34 1.5342 +IC C24 C22 *C23 H3R 1.5342 112.34 -121.17 110.08 1.1143 +IC H3R C22 *C23 H3S 1.1143 110.08 -117.33 109.19 1.1136 +IC C22 C23 C24 C25 1.5469 112.34 172.23 113.38 1.5396 +IC C25 C23 *C24 H4R 1.5396 113.38 -121.91 109.32 1.1126 +IC H4R C23 *C24 H4S 1.1126 109.32 -116.59 108.35 1.1133 +IC C23 C24 C25 C26 1.5342 113.38 -110.46 113.02 1.5385 +IC C26 C24 *C25 H5R 1.5385 113.02 -119.35 108.07 1.1142 +IC H5R C24 *C25 H5S 1.1142 108.07 -116.98 110.21 1.1123 +IC C24 C25 C26 C27 1.5396 113.02 71.03 113.93 1.5386 +IC C27 C25 *C26 H6R 1.5386 113.93 -122.08 107.49 1.1113 +IC H6R C25 *C26 H6S 1.1113 107.49 -115.96 109.74 1.1126 +IC C25 C26 C27 C28 1.5385 113.93 -147.59 113.65 1.5384 +IC C28 C26 *C27 H7R 1.5384 113.65 -122.39 108.56 1.1131 +IC H7R C26 *C27 H7S 1.1131 108.56 -116.03 110.04 1.1090 +IC C26 C27 C28 C29 1.5386 113.65 71.07 114.17 1.5413 +IC C29 C27 *C28 H8R 1.5413 114.17 -122.30 108.62 1.1126 +IC H8R C27 *C28 H8S 1.1126 108.62 -116.50 108.97 1.1126 +IC C27 C28 C29 C210 1.5384 114.17 63.16 115.43 1.5418 +IC C210 C28 *C29 H9R 1.5418 115.43 121.54 108.37 1.1128 +IC H9R C28 *C29 H9S 1.1128 108.37 116.25 109.17 1.1117 +IC C28 C29 C210 C211 1.5413 115.43 63.77 114.21 1.5383 +IC C211 C29 *C21 H10R 5.7002 24.22 61.29 19.31 5.4148 +IC H10R C29 *C21 H10S 5.4148 19.31 -45.05 6.15 4.1763 +IC C29 C210 C211 C212 1.5418 114.21 -100.84 113.98 1.5369 +IC C212 C210 *C21 H11R 5.2218 28.62 50.44 22.04 5.7557 +IC H11R C210 *C21 H11S 5.7557 22.04 -37.21 14.50 6.7798 +IC C210 C211 C212 C213 1.5383 113.98 -177.16 114.12 1.5399 +IC C213 C211 *C21 H12R 6.2275 24.49 -10.79 18.11 4.1637 +IC H12R C211 *C21 H12S 4.1637 18.11 -40.97 22.34 5.4886 +IC C211 C212 C213 C214 1.5369 114.12 -62.39 113.99 1.5381 +IC C214 C212 *C21 H13R 7.6683 7.46 34.04 19.37 6.2621 +IC H13R C212 *C21 H13S 6.2621 19.37 -51.02 19.78 6.1349 +IC C212 C213 C214 C215 1.5399 113.99 100.10 113.99 1.5357 +IC C215 C213 *C21 H14R 8.5188 9.30 155.53 5.65 8.2786 +IC H14R C213 *C21 H14S 8.2786 5.65 -74.03 12.62 7.7720 +IC C213 C214 C215 C216 1.5381 113.99 -177.56 112.99 1.5303 +IC C216 C214 *C21 H15R 9.9341 7.78 -54.23 13.51 8.6789 +IC H15R C214 *C21 H15S 8.6789 13.51 47.42 15.44 8.1446 +IC C214 C215 C216 H16R 1.5357 112.99 60.73 110.35 1.1114 +IC H16R C215 *C21 H16S 10.0022 9.94 -71.95 4.09 10.5937 +IC H16R C215 *C21 H16T 10.0022 9.94 70.49 6.25 10.4440 +IC C31 C32 C33 C34 1.5332 113.81 -69.76 113.48 1.5379 +IC C34 C32 *C33 H3X 1.5379 113.48 -120.04 107.81 1.1134 +IC H3X C32 *C33 H3Y 1.1134 107.81 -116.77 110.11 1.1132 +IC C32 C33 C34 C35 1.5470 113.48 -174.70 113.05 1.5388 +IC C35 C33 *C34 H4X 1.5388 113.05 -119.75 108.33 1.1150 +IC H4X C33 *C34 H4Y 1.1150 108.33 -117.08 109.89 1.1110 +IC C33 C34 C35 C36 1.5379 113.05 78.95 113.54 1.5371 +IC C36 C34 *C35 H5X 1.5371 113.54 -121.79 108.12 1.1132 +IC H5X C34 *C35 H5Y 1.1132 108.12 -116.65 109.34 1.1131 +IC C34 C35 C36 C37 1.5388 113.54 79.35 112.97 1.5380 +IC C37 C35 *C36 H6X 1.5380 112.97 -122.73 108.56 1.1104 +IC H6X C35 *C36 H6Y 1.1104 108.56 -116.99 109.20 1.1133 +IC C35 C36 C37 C38 1.5371 112.97 -169.78 113.78 1.5391 +IC C38 C36 *C37 H7X 1.5391 113.78 -121.49 108.40 1.1136 +IC H7X C36 *C37 H7Y 1.1136 108.40 -116.03 109.71 1.1109 +IC C36 C37 C38 C39 1.5380 113.78 63.43 114.72 1.5407 +IC C39 C37 *C38 H8X 1.5407 114.72 -122.16 108.70 1.1128 +IC H8X C37 *C38 H8Y 1.1128 108.70 -116.71 108.42 1.1134 +IC C37 C38 C39 C310 1.5391 114.72 57.40 113.74 1.5377 +IC C310 C38 *C39 H9X 1.5377 113.74 121.23 108.61 1.1128 +IC H9X C38 *C39 H9Y 1.1128 108.61 116.24 109.15 1.1087 +IC C38 C39 C310 C311 1.5407 113.74 177.22 114.38 1.5396 +IC C311 C39 *C31 H10X 6.7302 21.15 -51.66 12.25 5.4275 +IC H10X C39 *C31 H10Y 5.4275 12.25 -2.84 17.29 7.1341 +IC C39 C310 C311 C312 1.5377 114.38 98.32 114.24 1.5401 +IC C312 C310 *C31 H11X 5.7098 23.45 8.45 15.08 7.6585 +IC H11X C310 *C31 H11Y 7.6585 15.08 -47.85 17.43 7.1025 +IC C310 C311 C312 C313 1.5396 114.24 -72.50 116.35 1.5390 +IC C313 C311 *C31 H12X 5.6215 22.21 -78.42 9.29 4.7736 +IC H12X C311 *C31 H12Y 4.7736 9.29 19.65 18.78 6.2615 +IC C311 C312 C313 C314 1.5401 116.35 -73.79 114.08 1.5401 +IC C314 C312 *C31 H13X 7.0335 20.16 38.94 22.48 5.4367 +IC H13X C312 *C31 H13Y 5.4367 22.48 -52.01 21.71 4.9428 +IC C312 C313 C314 C315 1.5390 114.08 98.09 114.78 1.5367 +IC C315 C313 *C31 H14X 8.0336 8.09 -74.65 14.63 7.0784 +IC H14X C313 *C31 H14Y 7.0784 14.63 -65.72 8.61 7.5607 +IC C313 C314 C315 C316 1.5401 114.78 70.46 113.76 1.5324 +IC C316 C314 *C31 H15X 7.9760 18.37 14.50 5.89 9.0340 +IC H15X C314 *C31 H15Y 9.0340 5.89 40.94 14.15 8.1542 +IC C314 C315 C316 H16X 1.5367 113.76 178.55 110.62 1.1105 +IC H16X C315 *C31 H16Y 8.9048 13.62 -43.76 15.54 8.1029 +IC H16X C315 *C31 H16Z 8.9048 13.62 0.25 15.11 7.1178 + +RESI DSPC 0.00 ! 2,3 distearoyl-D-glycero-1-Phosphatidylcholine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - N(CH3)3 +! +! Polar Head and glycerol backbone +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C13 CTL5 -0.35 ! H15A-C15-H15C +ATOM H13A HL 0.25 ! | +ATOM H13B HL 0.25 ! H13B | H14A +ATOM H13C HL 0.25 ! | | | +ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) +ATOM H14A HL 0.25 ! | | | +ATOM H14B HL 0.25 ! H13C | H14C +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! | alpha6 +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +ATOM C12 CTL2 -0.10 ! H12A--C12---H12B +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! | +GROUP ! alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S +ATOM H16S HAL2 0.09 ! | | +GROUP ! +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S +ATOM H17S HAL2 0.09 ! | | +GROUP ! +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 N C12 C11 1.4955 110.70 -56.80 116.85 1.5412 +IC C13 C12 *N C14 1.4955 110.70 -122.78 109.57 1.4976 +IC C13 C12 *N C15 1.4955 110.70 119.79 108.07 1.5033 +IC C12 N C13 H13A 1.5226 110.70 58.81 109.31 1.0869 +IC H13A N *C13 H13B 1.0869 109.31 -118.98 111.34 1.0812 +IC H13A N *C13 H13C 1.0869 109.31 118.94 111.15 1.0812 +IC C12 N C14 H14A 1.5226 109.57 61.55 111.51 1.0812 +IC H14A N *C14 H14B 1.0812 111.51 -119.73 109.64 1.0879 +IC H14A N *C14 H14C 1.0812 111.51 121.59 110.93 1.0818 +IC C12 N C15 H15A 1.5226 108.07 -179.78 113.90 1.0739 +IC H15A N *C15 H15B 1.0739 113.90 -123.64 110.27 1.0942 +IC H15A N *C15 H15C 1.0739 113.90 123.94 111.08 1.0953 +IC C11 N *C12 H12A 1.5412 116.85 -117.44 108.15 1.0975 +IC H12A N *C12 H12B 1.0975 108.15 -116.18 111.87 1.0788 +IC N C12 C11 O12 1.5226 116.85 -127.15 108.28 1.4233 +IC O12 C12 *C11 H11A 1.4233 108.28 -118.23 109.14 1.1127 +IC H11A C12 *C11 H11B 1.1127 109.14 -118.67 113.18 1.1138 +IC C12 C11 O12 P 1.5412 108.28 68.39 118.29 1.5879 +IC C11 O12 P O11 1.4233 118.29 167.38 103.42 1.5759 +IC O11 O12 *P O13 1.5759 103.42 -118.26 108.05 1.4788 +IC O11 O12 *P O14 1.5759 103.42 116.47 106.46 1.4811 +IC O12 P O11 C1 1.5879 103.42 52.34 120.65 1.4314 +IC P O11 C1 C2 1.5759 120.65 108.46 110.89 1.5522 +IC C2 O11 *C1 HA 1.5522 110.89 -124.25 114.00 1.1163 +IC HA O11 *C1 HB 1.1163 114.00 -118.44 107.67 1.1130 +IC O11 C1 C2 C3 1.4314 110.89 35.51 110.44 1.5598 +IC C3 C1 *C2 O21 1.5598 110.44 120.20 109.63 1.4412 +IC C3 C1 *C2 HS 1.5598 110.44 -117.26 109.38 1.1161 +IC C1 C2 O21 C21 1.5522 109.63 73.45 114.76 1.3198 +IC C2 O21 C21 C22 1.4412 114.76 -174.95 108.98 1.5271 +IC C22 O21 *C21 O22 1.5271 108.98 -179.21 126.54 1.2165 +IC O21 C21 C22 C23 1.3198 108.98 69.17 112.12 1.5454 +IC C23 C21 *C22 H2R 1.5454 112.12 -120.86 107.49 1.1097 +IC H2R C21 *C22 H2S 1.1097 107.49 -117.26 107.96 1.1085 +IC C1 C2 C3 O31 1.5522 110.44 158.49 113.28 1.4449 +IC O31 C2 *C3 HX 1.4449 113.28 -118.50 106.51 1.1127 +IC HX C2 *C3 HY 1.1127 106.51 -115.10 109.35 1.1145 +IC C2 C3 O31 C31 1.5598 113.28 76.61 115.36 1.3217 +IC C3 O31 C31 C32 1.4449 115.36 -172.28 108.03 1.5292 +IC C32 O31 *C31 O32 1.5292 108.03 178.61 126.37 1.2165 +IC O31 C31 C32 C33 1.3217 108.03 -171.00 113.43 1.5450 +IC C33 C31 *C32 H2X 1.5450 113.43 122.58 108.40 1.1090 +IC H2X C31 *C32 H2Y 1.1090 108.40 116.71 106.78 1.1104 +IC C21 C22 C23 C24 1.5271 112.12 69.99 112.82 1.5359 +IC C24 C22 *C23 H3R 1.5359 112.82 119.77 107.99 1.1130 +IC H3R C22 *C23 H3S 1.1130 107.99 116.99 110.26 1.1137 +IC C22 C23 C24 C25 1.5454 112.82 -176.22 114.43 1.5405 +IC C25 C23 *C24 H4R 1.5405 114.43 -122.37 109.02 1.1132 +IC H4R C23 *C24 H4S 1.1132 109.02 -116.84 108.99 1.1144 +IC C23 C24 C25 C26 1.5359 114.43 -62.74 114.59 1.5386 +IC C26 C24 *C25 H5R 1.5386 114.59 -119.80 107.07 1.1148 +IC H5R C24 *C25 H5S 1.1148 107.07 -116.11 110.00 1.1120 +IC C24 C25 C26 C27 1.5405 114.59 95.68 113.38 1.5385 +IC C27 C25 *C26 H6R 1.5385 113.38 -124.77 109.24 1.1094 +IC H6R C25 *C26 H6S 1.1094 109.24 -116.24 108.54 1.1145 +IC C25 C26 C27 C28 1.5386 113.38 -174.63 114.01 1.5386 +IC C28 C26 *C27 H7R 1.5386 114.01 -120.04 107.07 1.1147 +IC H7R C26 *C27 H7S 1.1147 107.07 -116.29 110.97 1.1103 +IC C26 C27 C28 C29 1.5385 114.01 96.11 114.10 1.5403 +IC C29 C27 *C28 H8R 1.5403 114.10 -125.01 110.20 1.1112 +IC H8R C27 *C28 H8S 1.1112 110.20 -116.63 107.50 1.1156 +IC C27 C28 C29 C210 1.5386 114.10 -70.59 114.34 1.5367 +IC C210 C28 *C29 H9R 1.5367 114.34 123.15 108.85 1.1111 +IC H9R C28 *C29 H9S 1.1111 108.85 116.35 108.32 1.1138 +IC C28 C29 C210 C211 1.5403 114.34 -176.59 113.89 1.5391 +IC C211 C29 *C21 H10R 7.1231 20.94 42.49 14.87 5.5936 +IC H10R C29 *C21 H10S 5.5936 14.87 10.84 17.04 7.3386 +IC C29 C210 C211 C212 1.5367 113.89 -98.43 114.36 1.5411 +IC C212 C210 *C21 H11R 6.2296 22.93 34.20 15.26 7.6660 +IC H11R C210 *C21 H11S 7.6660 15.26 -53.30 13.69 7.9695 +IC C210 C211 C212 C213 1.5391 114.36 67.22 115.66 1.5396 +IC C213 C211 *C21 H12R 5.7976 20.12 51.93 17.64 6.9765 +IC H12R C211 *C21 H12S 6.9765 17.64 28.99 12.82 5.4620 +IC C211 C212 C213 C214 1.5411 115.66 59.27 115.02 1.5394 +IC C214 C212 *C21 H13R 7.1149 21.13 35.81 19.89 5.4204 +IC H13R C212 *C21 H13S 5.4204 19.89 -60.20 19.14 5.1386 +IC C212 C213 C214 C215 1.5396 115.02 55.26 113.95 1.5372 +IC C215 C213 *C21 H14R 8.2302 7.12 -58.84 15.96 7.0385 +IC H14R C213 *C21 H14S 7.0385 15.96 -56.69 10.60 7.5967 +IC C213 C214 C215 C216 1.5394 113.95 168.57 113.50 1.5392 +IC C216 C214 *C21 H15R 9.4760 7.13 34.44 15.27 7.9557 +IC H15R C214 *C21 H15S 7.9557 15.27 48.78 11.46 8.6265 +IC C214 C215 C216 C217 1.5372 113.50 58.84 114.80 1.5388 +IC C217 C215 *C21 H16R 10.1942 10.61 97.74 4.71 10.2620 +IC H16R C215 *C21 H16S 10.2620 4.71 -36.58 12.30 9.3186 +IC C215 C216 C217 C218 1.5392 114.80 58.51 114.57 1.5326 +IC C218 C216 *C21 H17R 10.7326 12.86 60.03 7.85 11.1201 +IC H17R C216 *C21 H17S 11.1201 7.85 -11.50 13.03 9.6379 +IC C216 C217 C218 H18R 1.5388 114.57 176.51 110.53 1.1110 +IC H18R C217 *C21 H18S 11.4218 9.61 -56.04 9.75 11.3848 +IC H18R C217 *C21 H18T 11.4218 9.61 -27.02 12.39 9.9809 +IC C31 C32 C33 C34 1.5292 113.43 -170.28 111.21 1.5332 +IC C34 C32 *C33 H3X 1.5332 111.21 120.10 110.03 1.1147 +IC H3X C32 *C33 H3Y 1.1147 110.03 118.23 109.81 1.1132 +IC C32 C33 C34 C35 1.5450 111.21 -176.05 113.54 1.5351 +IC C35 C33 *C34 H4X 1.5351 113.54 -121.74 108.36 1.1123 +IC H4X C33 *C34 H4Y 1.1123 108.36 -116.85 109.27 1.1133 +IC C33 C34 C35 C36 1.5332 113.54 -173.08 112.41 1.5369 +IC C36 C34 *C35 H5X 1.5369 112.41 -120.59 108.12 1.1137 +IC H5X C34 *C35 H5Y 1.1137 108.12 -117.34 110.07 1.1123 +IC C34 C35 C36 C37 1.5351 112.41 79.92 112.93 1.5377 +IC C37 C35 *C36 H6X 1.5377 112.93 -122.78 108.85 1.1112 +IC H6X C35 *C36 H6Y 1.1112 108.85 -117.00 109.19 1.1136 +IC C35 C36 C37 C38 1.5369 112.93 -171.43 113.51 1.5370 +IC C38 C36 *C37 H7X 1.5370 113.51 123.17 110.47 1.1090 +IC H7X C36 *C37 H7Y 1.1090 110.47 116.35 107.70 1.1141 +IC C36 C37 C38 C39 1.5377 113.51 74.76 115.02 1.5420 +IC C39 C37 *C38 H8X 1.5420 115.02 -122.14 108.20 1.1135 +IC H8X C37 *C38 H8Y 1.1135 108.20 -116.32 108.91 1.1135 +IC C37 C38 C39 C310 1.5370 115.02 72.40 114.50 1.5419 +IC C310 C38 *C39 H9X 1.5419 114.50 118.03 106.48 1.1158 +IC H9X C38 *C39 H9Y 1.1158 106.48 115.69 110.84 1.1079 +IC C38 C39 C310 C311 1.5420 114.50 -99.06 115.90 1.5416 +IC C311 C39 *C31 H10X 6.8537 16.35 -47.51 15.02 8.2809 +IC H10X C39 *C31 H10Y 8.2809 15.02 45.06 13.76 8.9732 +IC C39 C310 C311 C312 1.5419 115.90 -66.87 114.14 1.5385 +IC C312 C310 *C31 H11X 6.9998 17.92 -66.08 14.32 7.0432 +IC H11X C310 *C31 H11Y 7.0432 14.32 9.50 2.06 5.9099 +IC C310 C311 C312 C313 1.5416 114.14 108.65 113.68 1.5372 +IC C313 C311 *C31 H12X 6.1447 21.99 -11.70 13.99 8.0543 +IC H12X C311 *C31 H12Y 8.0543 13.99 -38.85 17.95 7.0221 +IC C311 C312 C313 C314 1.5385 113.68 -177.98 113.55 1.5390 +IC C314 C312 *C31 H13X 6.8448 21.39 56.07 17.96 6.2856 +IC H13X C312 *C31 H13Y 6.2856 17.96 -47.40 9.31 5.0804 +IC C312 C313 C314 C315 1.5372 113.55 98.22 114.39 1.5413 +IC C315 C313 *C31 H14X 7.9680 15.09 -29.43 20.13 6.2085 +IC H14X C313 *C31 H14Y 6.2085 20.13 -34.32 15.21 7.4001 +IC C313 C314 C315 C316 1.5390 114.39 -61.32 115.57 1.5384 +IC C316 C314 *C31 H15X 9.0929 9.58 -86.80 10.31 8.5276 +IC H15X C314 *C31 H15Y 8.5276 10.31 43.88 15.99 7.6401 +IC C314 C315 C316 C317 1.5413 115.57 -64.76 113.97 1.5352 +IC C317 C315 *C31 H16X 9.9401 10.70 -53.64 13.82 8.7951 +IC H16X C315 *C31 H16Y 8.7951 13.82 -34.11 6.99 9.8471 +IC C315 C316 C317 C318 1.5384 113.97 179.24 112.97 1.5312 +IC C318 C316 *C31 H17X 11.1416 8.71 70.01 10.20 10.4005 +IC H17X C316 *C31 H17Y 10.4005 10.20 -40.43 13.37 9.3984 +IC C316 C317 C318 H18X 1.5352 112.97 -179.62 110.67 1.1109 +IC H18X C317 *C31 H18Y 11.8049 6.04 -45.75 10.81 10.8979 +IC H18X C317 *C31 H18Z 11.8049 6.04 -92.16 6.14 11.7909 + +RESI DSPE 0.00 ! 2,3-distearoyl-D-glycero-1-Phosphatidylethanolamine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S +ATOM H16S HAL2 0.09 ! | | +GROUP ! +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S +ATOM H17S HAL2 0.09 ! | | +GROUP ! +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.5054 110.81 -64.44 110.62 1.4250 +IC HN1 C12 *N HN2 1.0639 106.37 113.30 110.46 1.0532 +IC HN1 C12 *N HN3 1.0639 106.37 -119.69 114.82 1.0325 +IC HN1 N C12 C11 1.0639 106.37 7.83 110.81 1.5396 +IC C11 N *C12 H12A 1.5396 110.81 122.06 108.20 1.1072 +IC H12A N *C12 H12B 1.1072 108.20 118.24 107.69 1.1119 +IC O12 C12 *C11 H11A 1.4250 110.62 -117.83 107.89 1.1149 +IC H11A C12 *C11 H11B 1.1149 107.89 -116.49 111.07 1.1174 +IC C12 C11 O12 P 1.5396 110.62 99.60 122.72 1.5835 +IC C11 O12 P O11 1.4250 122.72 -154.10 101.81 1.5812 +IC O11 O12 *P O13 1.5812 101.81 -118.50 109.49 1.4707 +IC O11 O12 *P O14 1.5812 101.81 113.02 104.96 1.4818 +IC O12 P O11 C1 1.5835 101.81 -19.40 121.73 1.4292 +IC P O11 C1 C2 1.5812 121.73 92.19 111.43 1.5499 +IC C2 O11 *C1 HA 1.5499 111.43 -124.00 112.69 1.1159 +IC HA O11 *C1 HB 1.1159 112.69 -117.54 108.40 1.1129 +IC O11 C1 C2 C3 1.4292 111.43 52.07 110.92 1.5571 +IC C3 C1 *C2 O21 1.5571 110.92 120.79 107.73 1.4415 +IC C3 C1 *C2 HS 1.5571 110.92 -116.43 107.80 1.1144 +IC C1 C2 O21 C21 1.5499 107.73 97.93 114.67 1.3257 +IC C2 O21 C21 C22 1.4415 114.67 -161.60 110.82 1.5355 +IC C22 O21 *C21 O22 1.5355 110.82 178.51 125.51 1.2182 +IC O21 C21 C22 C23 1.3257 110.82 2.52 115.63 1.5494 +IC C23 C21 *C22 H2R 1.5494 115.63 -123.54 107.99 1.1083 +IC H2R C21 *C22 H2S 1.1083 107.99 -115.52 106.07 1.1104 +IC C1 C2 C3 O31 1.5499 110.92 -179.89 113.29 1.4461 +IC O31 C2 *C3 HX 1.4461 113.29 -119.86 107.00 1.1130 +IC HX C2 *C3 HY 1.1130 107.00 -115.09 109.03 1.1146 +IC C2 C3 O31 C31 1.5571 113.29 78.32 116.32 1.3191 +IC C3 O31 C31 C32 1.4461 116.32 178.69 109.23 1.5253 +IC C32 O31 *C31 O32 1.5253 109.23 -179.86 126.12 1.2226 +IC O31 C31 C32 C33 1.3191 109.23 -176.72 112.67 1.5444 +IC C33 C31 *C32 H2X 1.5444 112.67 120.67 108.11 1.1095 +IC H2X C31 *C32 H2Y 1.1095 108.11 117.33 108.00 1.1097 +IC C21 C22 C23 C24 1.5355 115.63 167.97 112.07 1.5370 +IC C24 C22 *C23 H3R 1.5370 112.07 -120.30 110.30 1.1144 +IC H3R C22 *C23 H3S 1.1144 110.30 -118.02 109.32 1.1117 +IC C22 C23 C24 C25 1.5494 112.07 172.79 113.43 1.5399 +IC C25 C23 *C24 H4R 1.5399 113.43 -122.81 109.71 1.1124 +IC H4R C23 *C24 H4S 1.1124 109.71 -116.61 108.00 1.1147 +IC C23 C24 C25 C26 1.5370 113.43 -105.08 114.10 1.5399 +IC C26 C24 *C25 H5R 1.5399 114.10 -119.16 108.33 1.1146 +IC H5R C24 *C25 H5S 1.1146 108.33 -116.56 109.85 1.1116 +IC C24 C25 C26 C27 1.5399 114.10 61.38 114.78 1.5373 +IC C27 C25 *C26 H6R 1.5373 114.78 -121.11 107.98 1.1143 +IC H6R C25 *C26 H6S 1.1143 107.98 -116.46 109.04 1.1134 +IC C25 C26 C27 C28 1.5399 114.78 69.30 113.73 1.5377 +IC C28 C26 *C27 H7R 1.5377 113.73 -123.44 109.11 1.1107 +IC H7R C26 *C27 H7S 1.1107 109.11 -116.43 108.46 1.1138 +IC C26 C27 C28 C29 1.5373 113.73 -176.54 113.06 1.5388 +IC C29 C27 *C28 H8R 1.5388 113.06 -120.36 108.08 1.1137 +IC H8R C27 *C28 H8S 1.1137 108.08 -116.82 110.24 1.1102 +IC C27 C28 C29 C210 1.5377 113.06 75.17 113.98 1.5401 +IC C210 C28 *C29 H9R 1.5401 113.98 121.85 109.12 1.1119 +IC H9R C28 *C29 H9S 1.1119 109.12 116.41 108.30 1.1130 +IC C28 C29 C210 C211 1.5388 113.98 74.22 114.07 1.5396 +IC C211 C29 *C21 H10R 4.4594 22.26 106.42 13.19 4.2538 +IC H10R C29 *C21 H10S 4.2538 13.19 -44.65 20.92 5.5377 +IC C29 C210 C211 C212 1.5401 114.07 74.48 114.17 1.5394 +IC C212 C210 *C21 H11R 5.7370 26.71 -43.94 26.06 4.3337 +IC H11R C210 *C21 H11S 4.3337 26.06 58.74 23.68 3.6429 +IC C210 C211 C212 C213 1.5396 114.17 75.53 113.57 1.5391 +IC C213 C211 *C21 H12R 6.2281 20.46 -69.22 4.30 6.6025 +IC H12R C211 *C21 H12S 6.6025 4.30 6.63 19.11 5.8129 +IC C211 C212 C213 C214 1.5394 113.57 -128.33 114.27 1.5368 +IC C214 C212 *C21 H13R 7.6797 14.74 -45.98 19.75 6.3480 +IC H13R C212 *C21 H13S 6.3480 19.75 45.32 22.01 5.6795 +IC C212 C213 C214 C215 1.5391 114.27 72.46 113.01 1.5349 +IC C215 C213 *C21 H14R 7.9882 15.16 80.67 5.40 8.2965 +IC H14R C213 *C21 H14S 8.2965 5.40 -157.79 7.33 8.1934 +IC C213 C214 C215 C216 1.5368 113.01 -179.87 113.02 1.5353 +IC C216 C214 *C21 H15R 9.5153 11.99 27.19 16.25 7.6796 +IC H15R C214 *C21 H15S 7.6796 16.25 -49.60 16.28 7.5984 +IC C214 C215 C216 C217 1.5349 113.02 -170.82 113.33 1.5367 +IC C217 C215 *C21 H16R 10.0979 9.33 -107.29 5.81 9.9636 +IC H16R C215 *C21 H16S 9.9636 5.81 -138.71 5.22 9.9997 +IC C215 C216 C217 C218 1.5353 113.33 -58.20 114.49 1.5322 +IC C218 C216 *C21 H17R 9.8608 15.17 -28.86 7.53 11.2017 +IC H17R C216 *C21 H17S 11.2017 7.53 -24.53 12.65 9.8767 +IC C216 C217 C218 H18R 1.5367 114.49 -55.85 110.42 1.1111 +IC H18R C217 *C21 H18S 10.2135 12.33 -34.25 10.81 8.8234 +IC H18R C217 *C21 H18T 10.2135 12.33 -47.94 11.88 10.5572 +IC C31 C32 C33 C34 1.5253 112.67 -178.48 111.44 1.5322 +IC C34 C32 *C33 H3X 1.5322 111.44 121.03 110.47 1.1134 +IC H3X C32 *C33 H3Y 1.1134 110.47 118.71 109.62 1.1142 +IC C32 C33 C34 C35 1.5444 111.44 -173.46 112.99 1.5348 +IC C35 C33 *C34 H4X 1.5348 112.99 120.79 108.93 1.1139 +IC H4X C33 *C34 H4Y 1.1139 108.93 116.97 109.06 1.1123 +IC C33 C34 C35 C36 1.5322 112.99 178.22 112.64 1.5365 +IC C36 C34 *C35 H5X 1.5365 112.64 -119.93 108.26 1.1143 +IC H5X C34 *C35 H5Y 1.1143 108.26 -117.45 109.95 1.1120 +IC C34 C35 C36 C37 1.5348 112.64 74.92 113.45 1.5375 +IC C37 C35 *C36 H6X 1.5375 113.45 -122.56 108.47 1.1122 +IC H6X C35 *C36 H6Y 1.1122 108.47 -116.76 109.02 1.1136 +IC C35 C36 C37 C38 1.5365 113.45 -177.36 113.46 1.5382 +IC C38 C36 *C37 H7X 1.5382 113.46 -120.61 108.32 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.32 -116.77 110.33 1.1104 +IC C36 C37 C38 C39 1.5375 113.46 64.37 115.50 1.5424 +IC C39 C37 *C38 H8X 1.5424 115.50 -121.64 108.27 1.1140 +IC H8X C37 *C38 H8Y 1.1140 108.27 -116.31 108.66 1.1135 +IC C37 C38 C39 C310 1.5382 115.50 66.64 114.85 1.5410 +IC C310 C38 *C39 H9X 1.5410 114.85 118.23 106.45 1.1160 +IC H9X C38 *C39 H9Y 1.1160 106.45 115.42 110.46 1.1067 +IC C38 C39 C310 C311 1.5424 114.85 -91.56 116.18 1.5425 +IC C311 C39 *C31 H10X 7.0195 15.23 -4.13 13.61 9.1635 +IC H10X C39 *C31 H10Y 9.1635 13.61 -45.02 14.48 8.4446 +IC C39 C310 C311 C312 1.5410 116.18 -85.92 114.95 1.5399 +IC C312 C310 *C31 H11X 7.3490 17.83 -65.53 12.68 6.9645 +IC H11X C310 *C31 H11Y 6.9645 12.68 105.60 3.24 6.1273 +IC C310 C311 C312 C313 1.5425 114.95 88.99 114.30 1.5368 +IC C313 C311 *C31 H12X 7.2426 20.81 -38.79 12.35 8.4338 +IC H12X C311 *C31 H12Y 8.4338 12.35 -14.41 17.84 6.8711 +IC C311 C312 C313 C314 1.5399 114.30 176.73 113.77 1.5393 +IC C314 C312 *C31 H13X 7.9271 18.93 53.51 15.83 7.9221 +IC H13X C312 *C31 H13Y 7.9221 15.83 -17.45 15.76 6.2293 +IC C312 C313 C314 C315 1.5368 113.77 59.84 114.72 1.5395 +IC C315 C313 *C31 H14X 9.3787 10.23 48.91 15.10 8.0559 +IC H14X C313 *C31 H14Y 8.0559 15.10 -46.05 16.94 7.4445 +IC C313 C314 C315 C316 1.5393 114.72 57.27 113.80 1.5367 +IC C316 C314 *C31 H15X 10.2882 6.55 161.84 5.73 9.9046 +IC H15X C314 *C31 H15Y 9.9046 5.73 -75.46 10.14 9.4781 +IC C314 C315 C316 C317 1.5395 113.80 175.39 112.74 1.5342 +IC C317 C315 *C31 H16X 11.7389 5.37 3.80 12.32 10.0232 +IC H16X C315 *C31 H16Y 10.0232 12.32 -49.95 11.40 10.3282 +IC C315 C316 C317 C318 1.5367 112.74 179.25 113.28 1.5311 +IC C318 C316 *C31 H17X 12.7409 3.67 176.00 5.93 12.1219 +IC H17X C316 *C31 H17Y 12.1219 5.93 -75.11 7.81 11.8473 +IC C316 C317 C318 H18X 1.5342 113.28 -179.57 110.58 1.1113 +IC H18X C317 *C31 H18Y 13.7564 3.79 8.27 9.58 12.5526 +IC H18X C317 *C31 H18Z 13.7564 3.79 -43.55 8.87 12.8199 + +RESI DSPS -1.00 ! 2,3-distearoyl-D-glycero-1-Phosphatidylserine +! +! R1 - CH2 +! | (-) +! R2 - CH CO2 +! | (-) | (+) +! CH2 - PO4 - CH2 - CH - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S +ATOM H16S HAL2 0.09 ! | | +GROUP ! +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S +ATOM H17S HAL2 0.09 ! | | +GROUP ! +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 C13 C12 O13B O13A + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.4893 109.83 -66.57 111.42 1.4332 +IC N C12 C13 O13B 1.4893 108.59 176.32 118.00 1.2543 +IC HN1 C12 *N HN2 1.0292 111.80 118.90 102.00 1.0493 +IC HN1 C12 *N HN3 1.0292 111.80 -123.29 108.74 1.0598 +IC HN1 N C12 C11 1.0292 111.80 133.59 109.83 1.5583 +IC C11 N *C12 C13 1.5583 109.83 122.20 108.59 1.5426 +IC C13 N *C12 H12A 1.5426 108.59 117.46 109.23 1.0792 +IC O13B C12 *C13 O13A 1.2543 118.00 -178.62 118.11 1.2654 +IC O12 C12 *C11 H11A 1.4332 111.42 -118.35 107.45 1.1149 +IC H11A C12 *C11 H11B 1.1149 107.45 -115.46 110.35 1.1164 +IC C12 C11 O12 P 1.5583 111.42 98.57 122.48 1.5832 +IC C11 O12 P O11 1.4332 122.48 -156.29 101.34 1.5818 +IC O11 O12 *P O13 1.5818 101.34 -116.69 110.11 1.4732 +IC O11 O12 *P O14 1.5818 101.34 113.46 106.34 1.4824 +IC O12 P O11 C1 1.5832 101.34 -51.08 118.56 1.4295 +IC P O11 C1 C2 1.5818 118.56 177.64 110.16 1.5453 +IC C2 O11 *C1 HA 1.5453 110.16 -119.69 111.62 1.1160 +IC HA O11 *C1 HB 1.1160 111.62 -120.58 110.57 1.1155 +IC O11 C1 C2 C3 1.4295 110.16 55.31 110.66 1.5589 +IC C3 C1 *C2 O21 1.5589 110.66 121.77 106.57 1.4402 +IC C3 C1 *C2 HS 1.5589 110.66 -118.05 107.02 1.1162 +IC C1 C2 O21 C21 1.5453 106.57 150.42 116.02 1.3173 +IC C2 O21 C21 C22 1.4402 116.02 -171.16 109.55 1.5337 +IC C22 O21 *C21 O22 1.5337 109.55 175.84 126.68 1.2162 +IC O21 C21 C22 C23 1.3173 109.55 -40.36 115.70 1.5489 +IC C23 C21 *C22 H2R 1.5489 115.70 -123.33 107.45 1.1085 +IC H2R C21 *C22 H2S 1.1085 107.45 -115.61 106.22 1.1102 +IC C1 C2 C3 O31 1.5453 110.66 -178.43 112.93 1.4451 +IC O31 C2 *C3 HX 1.4451 112.93 -119.96 107.02 1.1122 +IC HX C2 *C3 HY 1.1122 107.02 -114.62 108.91 1.1153 +IC C2 C3 O31 C31 1.5589 112.93 81.92 114.63 1.3321 +IC C3 O31 C31 C32 1.4451 114.63 -172.95 108.55 1.5265 +IC C32 O31 *C31 O32 1.5265 108.55 -179.70 126.10 1.2161 +IC O31 C31 C32 C33 1.3321 108.55 -169.62 113.41 1.5450 +IC C33 C31 *C32 H2X 1.5450 113.41 122.60 108.22 1.1085 +IC H2X C31 *C32 H2Y 1.1085 108.22 116.86 106.89 1.1104 +IC C21 C22 C23 C24 1.5337 115.70 166.19 110.98 1.5367 +IC C24 C22 *C23 H3R 1.5367 110.98 -119.29 110.34 1.1145 +IC H3R C22 *C23 H3S 1.1145 110.34 -118.50 109.68 1.1106 +IC C22 C23 C24 C25 1.5489 110.98 177.85 114.55 1.5398 +IC C25 C23 *C24 H4R 1.5398 114.55 -123.69 109.53 1.1124 +IC H4R C23 *C24 H4S 1.1124 109.53 -115.99 107.45 1.1147 +IC C23 C24 C25 C26 1.5367 114.55 -107.75 113.11 1.5381 +IC C26 C24 *C25 H5R 1.5381 113.11 -118.26 107.52 1.1158 +IC H5R C24 *C25 H5S 1.1158 107.52 -116.99 110.66 1.1120 +IC C24 C25 C26 C27 1.5398 113.11 80.59 113.41 1.5344 +IC C27 C25 *C26 H6R 1.5344 113.41 -122.73 108.41 1.1113 +IC H6R C25 *C26 H6S 1.1113 108.41 -116.47 109.55 1.1128 +IC C25 C26 C27 C28 1.5381 113.41 -158.33 113.82 1.5394 +IC C28 C26 *C27 H7R 1.5394 113.82 -121.96 108.36 1.1132 +IC H7R C26 *C27 H7S 1.1132 108.36 -115.75 109.43 1.1092 +IC C26 C27 C28 C29 1.5344 113.82 69.51 114.89 1.5440 +IC C29 C27 *C28 H8R 1.5440 114.89 -122.86 109.02 1.1120 +IC H8R C27 *C28 H8S 1.1120 109.02 -116.01 108.15 1.1135 +IC C27 C28 C29 C210 1.5394 114.89 51.90 115.07 1.5416 +IC C210 C28 *C29 H9R 1.5416 115.07 121.50 108.12 1.1137 +IC H9R C28 *C29 H9S 1.1137 108.12 116.43 109.21 1.1127 +IC C28 C29 C210 C211 1.5440 115.07 53.04 113.37 1.5397 +IC C211 C29 *C21 H10R 5.7673 21.55 78.11 4.78 4.7086 +IC H10R C29 *C21 H10S 4.7086 4.78 -13.23 18.08 5.9943 +IC C29 C210 C211 C212 1.5416 113.37 178.61 114.23 1.5866 +IC C212 C210 *C21 H11R 5.0588 27.61 -18.10 16.56 6.8518 +IC H11R C210 *C21 H11S 6.8518 16.56 -36.31 21.84 5.7235 +IC C210 C211 C212 C213 1.5397 114.23 122.02 131.52 1.5934 +IC C213 C211 *C21 H12R 4.4877 29.63 3.88 17.69 5.9281 +IC H12R C211 *C21 H12S 5.9281 17.69 31.51 7.88 4.0846 +IC C211 C212 C213 C214 1.5866 131.52 -6.63 117.77 1.5445 +IC C214 C212 *C21 H13R 4.4367 32.02 48.17 24.48 5.3636 +IC H13R C212 *C21 H13S 5.3636 24.48 14.65 22.70 3.6579 +IC C212 C213 C214 C215 1.5934 117.77 65.51 117.48 1.5425 +IC C215 C213 *C21 H14R 5.8678 25.32 39.55 28.10 4.3791 +IC H14R C213 *C21 H14S 4.3791 28.10 -51.21 28.96 3.7604 +IC C213 C214 C215 C216 1.5445 117.48 49.82 115.65 1.5356 +IC C216 C214 *C21 H15R 7.0286 2.73 -121.88 15.53 6.0842 +IC H15R C214 *C21 H15S 6.0842 15.53 -67.80 14.55 6.1747 +IC C214 C215 C216 C217 1.5425 115.65 -176.51 111.52 1.5364 +IC C217 C215 *C21 H16R 8.3727 3.42 25.77 15.99 7.1004 +IC H16R C215 *C21 H16S 7.1004 15.99 -54.64 16.06 7.0896 +IC C215 C216 C217 C218 1.5356 111.52 175.21 114.00 1.5301 +IC C218 C216 *C21 H17R 9.5976 0.83 78.52 11.93 8.4792 +IC H17R C216 *C21 H17S 8.4792 11.93 62.62 11.40 8.5553 +IC C216 C217 C218 H18R 1.5364 114.00 -177.20 110.68 1.1112 +IC H18R C217 *C21 H18S 10.5203 2.48 11.05 11.36 9.6329 +IC H18R C217 *C21 H18T 10.5203 2.48 -46.76 10.76 9.7500 +IC C31 C32 C33 C34 1.5265 113.41 -178.31 110.43 1.5319 +IC C34 C32 *C33 H3X 1.5319 110.43 120.52 109.82 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.82 118.38 109.88 1.1135 +IC C32 C33 C34 C35 1.5450 110.43 -177.75 114.37 1.5349 +IC C35 C33 *C34 H4X 1.5349 114.37 -122.75 108.44 1.1128 +IC H4X C33 *C34 H4Y 1.1128 108.44 -116.39 108.05 1.1123 +IC C33 C34 C35 C36 1.5319 114.37 175.06 112.43 1.5394 +IC C36 C34 *C35 H5X 1.5394 112.43 -119.99 108.22 1.1143 +IC H5X C34 *C35 H5Y 1.1143 108.22 -117.36 109.81 1.1120 +IC C34 C35 C36 C37 1.5349 112.43 70.40 113.76 1.5387 +IC C37 C35 *C36 H6X 1.5387 113.76 -122.04 108.16 1.1115 +IC H6X C35 *C36 H6Y 1.1115 108.16 -116.63 109.20 1.1126 +IC C35 C36 C37 C38 1.5394 113.76 -172.58 113.92 1.5395 +IC C38 C36 *C37 H7X 1.5395 113.92 -121.21 108.03 1.1132 +IC H7X C36 *C37 H7Y 1.1132 108.03 -116.35 110.34 1.1098 +IC C36 C37 C38 C39 1.5387 113.92 66.63 115.49 1.5437 +IC C39 C37 *C38 H8X 1.5437 115.49 -122.24 108.31 1.1133 +IC H8X C37 *C38 H8Y 1.1133 108.31 -116.30 108.32 1.1142 +IC C37 C38 C39 C310 1.5395 115.49 63.09 114.80 1.5430 +IC C310 C38 *C39 H9X 1.5430 114.80 119.20 106.81 1.1149 +IC H9X C38 *C39 H9Y 1.1149 106.81 115.88 110.23 1.1109 +IC C38 C39 C310 C311 1.5437 114.80 -97.22 114.16 1.5393 +IC C311 C39 *C31 H10X 6.6715 14.51 -56.88 14.89 7.9593 +IC H10X C39 *C31 H10Y 7.9593 14.89 44.28 14.35 8.7846 +IC C39 C310 C311 C312 1.5430 114.16 -70.86 113.83 1.5380 +IC C312 C310 *C31 H11X 7.0785 18.66 -65.75 13.00 6.4770 +IC H11X C310 *C31 H11Y 6.4770 13.00 115.10 4.73 5.8493 +IC C310 C311 C312 C313 1.5393 113.83 136.63 112.63 1.5361 +IC C313 C311 *C31 H12X 6.1944 22.54 5.99 13.35 8.0241 +IC H12X C311 *C31 H12Y 8.0241 13.35 -48.85 16.60 7.4442 +IC C311 C312 C313 C314 1.5380 112.63 174.59 114.70 1.5377 +IC C314 C312 *C31 H13X 7.0177 21.15 53.80 17.07 6.1607 +IC H13X C312 *C31 H13Y 6.1607 17.07 -63.18 10.26 5.2003 +IC C312 C313 C314 C315 1.5361 114.70 57.88 114.33 1.5376 +IC C315 C313 *C31 H14X 8.4373 10.18 -6.61 19.01 6.6105 +IC H14X C313 *C31 H14Y 6.6105 19.01 -46.66 16.56 7.2074 +IC C313 C314 C315 C316 1.5377 114.33 -96.95 113.29 1.5381 +IC C316 C314 *C31 H15X 9.5006 4.63 -89.74 11.68 8.5155 +IC H15X C314 *C31 H15Y 8.5155 11.68 -68.78 8.43 8.8490 +IC C314 C315 C316 C317 1.5376 113.29 178.54 113.74 1.5364 +IC C317 C315 *C31 H16X 10.8975 4.54 5.72 12.92 9.3175 +IC H16X C315 *C31 H16Y 9.3175 12.92 51.98 11.50 9.6267 +IC C315 C316 C317 C318 1.5381 113.74 -66.93 114.18 1.5322 +IC C318 C316 *C31 H17X 11.1830 10.86 -72.50 7.43 11.2104 +IC H17X C316 *C31 H17Y 11.2104 7.43 149.41 1.48 11.6438 +IC C316 C317 C318 H18X 1.5364 114.18 -176.65 110.61 1.1110 +IC H18X C317 *C31 H18Y 12.2679 8.45 34.05 11.41 11.0240 +IC H18X C317 *C31 H18Z 12.2679 8.45 -14.05 11.59 10.6507 + +RESI DSPA -1.00 ! 2,3-distearoyl--D-glycero-1-Phosphatidic acid +! +! R1 - CH2 +! | +! R2 - CH +! | (-) +! CH2 - PO4 - H +! +! Polar Head and glycerol backbone +GROUP ! H12 + ! | +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.82 ! \ / alpha3 +ATOM O14 O2L -0.82 ! P (+) +ATOM O12 OHL -0.68 ! / \ alpha2 +ATOM H12 HOL 0.34 ! (-) O14 O11 +ATOM O11 OSLP -0.62 ! | +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S +ATOM H16S HAL2 0.09 ! | | +GROUP ! +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S +ATOM H17S HAL2 0.09 ! | | +GROUP ! +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC O11 P O12 H12 1.5797 106.19 -174.43 105.34 0.9597 +IC O12 O11 *P O13 1.5645 106.19 112.41 111.47 1.4708 +IC O12 O11 *P O14 1.5645 106.19 -112.06 111.74 1.4720 +IC O12 P O11 C1 1.5645 106.19 -73.73 119.29 1.4309 +IC P O11 C1 C2 1.5797 119.29 -163.52 110.54 1.5550 +IC C2 O11 *C1 HA 1.5550 110.54 -121.71 110.85 1.1135 +IC HA O11 *C1 HB 1.1135 110.85 -120.19 110.56 1.1179 +IC O11 C1 C2 C3 1.4309 110.54 30.10 110.38 1.5588 +IC C3 C1 *C2 O21 1.5588 110.38 120.44 109.26 1.4433 +IC C3 C1 *C2 HS 1.5588 110.38 -117.04 108.90 1.1156 +IC C1 C2 O21 C21 1.5550 109.26 70.02 113.24 1.3201 +IC C2 O21 C21 C22 1.4433 113.24 -160.90 109.65 1.5271 +IC C22 O21 *C21 O22 1.5271 109.65 179.14 126.45 1.2176 +IC O21 C21 C22 C23 1.3201 109.65 58.21 112.49 1.5469 +IC C23 C21 *C22 H2R 1.5469 112.49 -122.89 108.71 1.1070 +IC H2R C21 *C22 H2S 1.1070 108.71 -117.07 106.43 1.1101 +IC C1 C2 C3 O31 1.5550 110.38 173.23 114.24 1.4483 +IC O31 C2 *C3 HX 1.4483 114.24 -119.90 106.40 1.1131 +IC HX C2 *C3 HY 1.1131 106.40 -114.40 108.90 1.1153 +IC C2 C3 O31 C31 1.5588 114.24 79.01 114.95 1.3247 +IC C3 O31 C31 C32 1.4483 114.95 171.52 108.44 1.5301 +IC C32 O31 *C31 O32 1.5301 108.44 -177.69 126.56 1.2146 +IC O31 C31 C32 C33 1.3247 108.44 176.71 113.03 1.5469 +IC C33 C31 *C32 H2X 1.5469 113.03 120.38 106.81 1.1102 +IC H2X C31 *C32 H2Y 1.1102 106.81 116.90 108.49 1.1084 +IC C21 C22 C23 C24 1.5271 112.49 164.67 111.95 1.5352 +IC C24 C22 *C23 H3R 1.5352 111.95 122.59 109.31 1.1129 +IC H3R C22 *C23 H3S 1.1129 109.31 117.45 110.08 1.1159 +IC C22 C23 C24 C25 1.5469 111.95 172.97 113.75 1.5391 +IC C25 C23 *C24 H4R 1.5391 113.75 -122.90 109.75 1.1116 +IC H4R C23 *C24 H4S 1.1116 109.75 -116.47 107.71 1.1141 +IC C23 C24 C25 C26 1.5352 113.75 -106.03 113.30 1.5384 +IC C26 C24 *C25 H5R 1.5384 113.30 -119.17 108.03 1.1144 +IC H5R C24 *C25 H5S 1.1144 108.03 -116.83 110.12 1.1126 +IC C24 C25 C26 C27 1.5391 113.30 72.13 113.44 1.5358 +IC C27 C25 *C26 H6R 1.5358 113.44 -122.40 108.19 1.1118 +IC H6R C25 *C26 H6S 1.1118 108.19 -116.74 109.22 1.1131 +IC C25 C26 C27 C28 1.5384 113.44 -170.55 113.87 1.5387 +IC C28 C26 *C27 H7R 1.5387 113.87 122.06 109.68 1.1107 +IC H7R C26 *C27 H7S 1.1107 109.68 116.15 108.48 1.1137 +IC C26 C27 C28 C29 1.5358 113.87 64.07 114.80 1.5443 +IC C29 C27 *C28 H8R 1.5443 114.80 -122.62 109.09 1.1125 +IC H8R C27 *C28 H8S 1.1125 109.09 -116.13 108.08 1.1138 +IC C27 C28 C29 C210 1.5387 114.80 48.45 116.66 1.5478 +IC C210 C28 *C29 H9R 1.5478 116.66 123.25 108.70 1.1122 +IC H9R C28 *C29 H9S 1.1122 108.70 115.69 107.76 1.1136 +IC C28 C29 C210 C211 1.5443 116.66 67.81 115.63 1.5897 +IC C211 C29 *C21 H10R 6.2419 20.94 73.41 9.77 5.3549 +IC H10R C29 *C21 H10S 5.3549 9.77 -15.73 17.13 6.9218 +IC C29 C210 C211 C212 1.5478 115.63 -121.19 128.44 1.5929 +IC C212 C210 *C21 H11R 5.2086 26.76 38.87 16.82 5.9507 +IC H11R C210 *C21 H11S 5.9507 16.82 -76.03 16.59 5.9467 +IC C210 C211 C212 C213 1.5897 128.44 116.88 115.59 1.5460 +IC C213 C211 *C21 H12R 5.6140 25.18 58.38 20.70 5.5387 +IC H12R C211 *C21 H12S 5.5387 20.70 -23.71 8.19 4.1444 +IC C211 C212 C213 C214 1.5929 115.59 59.27 116.27 1.5932 +IC C214 C212 *C21 H13R 7.1806 16.87 12.79 24.10 5.1670 +IC H13R C212 *C21 H13S 5.1670 24.10 -47.73 23.38 5.4912 +IC C212 C213 C214 C215 1.5460 116.27 -11.59 131.59 1.5907 +IC C215 C213 *C21 H14R 8.3796 7.41 96.21 6.34 7.2569 +IC H14R C213 *C21 H14S 7.2569 6.34 -148.46 11.05 6.9654 +IC C213 C214 C215 C216 1.5932 131.59 -120.65 114.14 1.5448 +IC C216 C214 *C21 H15R 9.5243 8.30 -91.04 9.60 8.9278 +IC H15R C214 *C21 H15S 8.9278 9.60 45.04 15.22 8.1472 +IC C214 C215 C216 C217 1.5907 114.14 85.86 115.64 1.5401 +IC C217 C215 *C21 H16R 9.5729 14.90 4.74 3.69 10.4656 +IC H16R C215 *C21 H16S 10.4656 3.69 53.52 10.95 9.7008 +IC C215 C216 C217 C218 1.5448 115.64 65.88 114.51 1.5325 +IC C218 C216 *C21 H17R 9.8439 15.22 49.81 11.06 10.5025 +IC H17R C216 *C21 H17S 10.5025 11.06 -1.62 12.80 8.7371 +IC C216 C217 C218 H18R 1.5401 114.51 176.03 110.41 1.1110 +IC H18R C217 *C21 H18S 10.1477 12.27 -48.04 10.43 10.7485 +IC H18R C217 *C21 H18T 10.1477 12.27 -39.05 13.08 9.0334 +IC C31 C32 C33 C34 1.5301 113.03 167.20 111.36 1.5341 +IC C34 C32 *C33 H3X 1.5341 111.36 121.73 109.34 1.1131 +IC H3X C32 *C33 H3Y 1.1131 109.34 118.01 110.38 1.1147 +IC C32 C33 C34 C35 1.5469 111.36 171.01 114.15 1.5383 +IC C35 C33 *C34 H4X 1.5383 114.15 -121.40 108.37 1.1115 +IC H4X C33 *C34 H4Y 1.1115 108.37 -116.15 108.73 1.1133 +IC C33 C34 C35 C36 1.5341 114.15 -114.73 112.49 1.5380 +IC C36 C34 *C35 H5X 1.5380 112.49 -119.62 108.26 1.1141 +IC H5X C34 *C35 H5Y 1.1141 108.26 -117.23 110.26 1.1120 +IC C34 C35 C36 C37 1.5383 112.49 71.99 113.19 1.5373 +IC C37 C35 *C36 H6X 1.5373 113.19 -121.94 107.90 1.1120 +IC H6X C35 *C36 H6Y 1.1120 107.90 -116.61 109.68 1.1127 +IC C35 C36 C37 C38 1.5380 113.19 -162.68 113.80 1.5396 +IC C38 C36 *C37 H7X 1.5396 113.80 -121.51 108.07 1.1136 +IC H7X C36 *C37 H7Y 1.1136 108.07 -115.90 109.83 1.1105 +IC C36 C37 C38 C39 1.5373 113.80 70.35 114.82 1.5425 +IC C39 C37 *C38 H8X 1.5425 114.82 -122.75 108.79 1.1126 +IC H8X C37 *C38 H8Y 1.1126 108.79 -116.58 108.25 1.1140 +IC C37 C38 C39 C310 1.5396 114.82 60.49 113.57 1.5385 +IC C310 C38 *C39 H9X 1.5385 113.57 120.45 108.34 1.1133 +IC H9X C38 *C39 H9Y 1.1133 108.34 116.82 109.63 1.1110 +IC C38 C39 C310 C311 1.5425 113.57 173.52 114.38 1.5399 +IC C311 C39 *C31 H10X 6.7016 21.46 -57.76 17.39 6.2598 +IC H10X C39 *C31 H10Y 6.2598 17.39 47.74 7.84 5.0407 +IC C39 C310 C311 C312 1.5385 114.38 62.05 115.18 1.5396 +IC C312 C310 *C31 H11X 6.9383 21.80 -51.47 20.06 6.2696 +IC H11X C310 *C31 H11Y 6.2696 20.06 6.02 11.84 7.7484 +IC C310 C311 C312 C313 1.5399 115.18 50.74 113.69 1.5375 +IC C313 C311 *C31 H12X 5.8370 22.37 -32.36 16.30 7.5029 +IC H12X C311 *C31 H12Y 7.5029 16.30 50.67 15.33 7.7267 +IC C311 C312 C313 C314 1.5396 113.69 166.12 114.62 1.5387 +IC C314 C312 *C31 H13X 6.5349 21.89 -32.48 8.99 4.9693 +IC H13X C312 *C31 H13Y 4.9693 8.99 90.03 15.83 5.6291 +IC C312 C313 C314 C315 1.5375 114.62 51.45 115.05 1.5374 +IC C315 C313 *C31 H14X 7.9249 13.01 -10.79 20.99 6.0127 +IC H14X C313 *C31 H14Y 6.0127 20.99 -43.36 17.72 6.8063 +IC C313 C314 C315 C316 1.5387 115.05 59.49 113.96 1.5353 +IC C316 C314 *C31 H15X 8.1062 16.13 -66.55 7.37 8.4746 +IC H15X C314 *C31 H15Y 8.4746 7.37 131.44 5.84 8.5742 +IC C314 C315 C316 C317 1.5374 113.96 176.07 112.07 1.5340 +IC C317 C315 *C31 H16X 9.6136 12.53 -19.17 15.89 7.6174 +IC H16X C315 *C31 H16Y 7.6174 15.89 49.91 15.88 7.8275 +IC C315 C316 C317 C318 1.5353 112.07 -178.55 113.54 1.5302 +IC C318 C316 *C31 H17X 10.1212 10.03 -94.87 6.43 10.0200 +IC H17X C316 *C31 H17Y 10.0200 6.43 -150.77 4.06 10.1726 +IC C316 C317 C318 H18X 1.5340 113.54 -179.77 110.50 1.1113 +IC H18X C317 *C31 H18Y 11.2278 8.12 -19.71 12.88 9.7821 +IC H18X C317 *C31 H18Z 11.2278 8.12 28.91 12.69 9.9307 + +RESI DSPG -1.00 ! 2,3-distearoyl-D-glycero-1-Phosphatidylglycerol +! +! R1 - CH2 +! | +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH(OH) - CH2OH +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S +ATOM H3S HAL2 0.09 ! | | +GROUP ! +ATOM C24 CTL2 -0.18 ! | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | +GROUP ! +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S +ATOM H5S HAL2 0.09 ! | | +GROUP ! +ATOM C26 CTL2 -0.18 ! | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | +GROUP ! +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S +ATOM H7S HAL2 0.09 ! | | +GROUP ! +ATOM C28 CTL2 -0.18 ! | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | +GROUP ! +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R ---C29---H9S +ATOM H9S HAL2 0.09 ! | | +GROUP ! +ATOM C210 CTL2 -0.18 ! | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | +GROUP ! +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S +ATOM H11S HAL2 0.09 ! | | +GROUP ! +ATOM C212 CTL2 -0.18 ! | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | +GROUP ! +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S +ATOM H13S HAL2 0.09 ! | | +GROUP ! +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S +ATOM H14S HAL2 0.09 ! | | +GROUP ! +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S +ATOM H15S HAL2 0.09 ! | | +GROUP ! +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S +ATOM H16S HAL2 0.09 ! | | +GROUP ! +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S +ATOM H17S HAL2 0.09 ! | | +GROUP ! +ATOM C218 CTL3 -0.27 ! | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain #2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain #3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 C12 C11 O12 1.5527 114.46 177.24 109.46 1.4326 +IC OC3 C13 C12 C11 1.4270 111.73 -65.37 114.46 1.5449 +IC OC3 C12 *C13 H13A 1.4270 111.73 121.66 109.71 1.1109 +IC OC3 C12 *C13 H13B 1.4270 111.73 -119.89 108.39 1.1123 +IC C12 C13 OC3 HO3 1.5527 111.73 -30.89 102.85 0.9681 +IC C11 C13 *C12 OC2 1.5449 114.46 121.77 110.89 1.4224 +IC OC2 C13 *C12 H12A 1.4224 110.89 118.35 108.37 1.1141 +IC C13 C12 OC2 HO2 1.5527 110.89 -158.95 100.56 0.9714 +IC O12 C12 *C11 H11A 1.4326 109.46 -120.59 109.31 1.1146 +IC H11A C12 *C11 H11B 1.1146 109.31 -117.47 107.92 1.1167 +IC C12 C11 O12 P 1.5449 109.46 163.97 118.76 1.5886 +IC C11 O12 P O11 1.4326 118.76 156.86 101.13 1.5890 +IC O11 O12 *P O13 1.5890 101.13 -114.16 108.58 1.4783 +IC O11 O12 *P O14 1.5890 101.13 115.79 109.11 1.4764 +IC O12 P O11 C1 1.5886 101.13 -60.17 117.54 1.4310 +IC P O11 C1 C2 1.5890 117.54 176.83 111.12 1.5541 +IC C2 O11 *C1 HA 1.5541 111.12 -121.22 111.69 1.1155 +IC HA O11 *C1 HB 1.1155 111.69 -120.21 109.38 1.1164 +IC O11 C1 C2 C3 1.4310 111.12 34.34 111.18 1.5587 +IC C3 C1 *C2 O21 1.5587 111.18 120.62 108.83 1.4440 +IC C3 C1 *C2 HS 1.5587 111.18 -117.18 108.49 1.1160 +IC C1 C2 O21 C21 1.5541 108.83 70.02 113.21 1.3230 +IC C2 O21 C21 C22 1.4440 113.21 -161.00 109.96 1.5276 +IC C22 O21 *C21 O22 1.5276 109.96 179.03 126.20 1.2172 +IC O21 C21 C22 C23 1.3230 109.96 58.21 112.90 1.5482 +IC C23 C21 *C22 H2R 1.5482 112.90 -122.94 108.49 1.1076 +IC H2R C21 *C22 H2S 1.1076 108.49 -117.04 106.39 1.1108 +IC C1 C2 C3 O31 1.5541 111.18 179.77 113.62 1.4493 +IC O31 C2 *C3 HX 1.4493 113.62 -119.97 106.73 1.1125 +IC HX C2 *C3 HY 1.1125 106.73 -114.77 109.12 1.1154 +IC C2 C3 O31 C31 1.5587 113.62 80.60 114.51 1.3266 +IC C3 O31 C31 C32 1.4493 114.51 174.48 109.12 1.5298 +IC C32 O31 *C31 O32 1.5298 109.12 -178.62 126.32 1.2152 +IC O31 C31 C32 C33 1.3266 109.12 -178.76 111.83 1.5528 +IC C33 C31 *C32 H2X 1.5528 111.83 120.53 107.45 1.1094 +IC H2X C31 *C32 H2Y 1.1094 107.45 117.20 107.94 1.1083 +IC C21 C22 C23 C24 1.5276 112.90 164.78 111.90 1.5369 +IC C24 C22 *C23 H3R 1.5369 111.90 -120.33 110.35 1.1155 +IC H3R C22 *C23 H3S 1.1155 110.35 -117.56 109.07 1.1129 +IC C22 C23 C24 C25 1.5482 111.90 169.91 114.04 1.5408 +IC C25 C23 *C24 H4R 1.5408 114.04 -122.16 109.32 1.1123 +IC H4R C23 *C24 H4S 1.1123 109.32 -116.31 108.21 1.1136 +IC C23 C24 C25 C26 1.5369 114.04 -112.58 113.07 1.5394 +IC C26 C24 *C25 H5R 1.5394 113.07 -119.77 108.32 1.1139 +IC H5R C24 *C25 H5S 1.1139 108.32 -117.09 110.18 1.1120 +IC C24 C25 C26 C27 1.5408 113.07 71.79 113.03 1.5375 +IC C27 C25 *C26 H6R 1.5375 113.03 -122.37 107.70 1.1101 +IC H6R C25 *C26 H6S 1.1101 107.70 -116.14 109.88 1.1125 +IC C25 C26 C27 C28 1.5394 113.03 -146.71 114.97 1.5414 +IC C28 C26 *C27 H7R 1.5414 114.97 -123.08 108.51 1.1127 +IC H7R C26 *C27 H7S 1.1127 108.51 -114.67 108.99 1.1079 +IC C26 C27 C28 C29 1.5375 114.97 64.54 115.43 1.5450 +IC C29 C27 *C28 H8R 1.5450 115.43 -122.27 108.43 1.1126 +IC H8R C27 *C28 H8S 1.1126 108.43 -115.77 108.15 1.1118 +IC C27 C28 C29 C210 1.5414 115.43 57.12 116.34 1.5438 +IC C210 C28 *C29 H9R 1.5438 116.34 124.04 109.60 1.1116 +IC H9R C28 *C29 H9S 1.1116 109.60 115.33 107.40 1.1129 +IC C28 C29 C210 C211 1.5450 116.34 92.22 115.61 1.5403 +IC C211 C29 *C21 H10R 5.8194 23.60 62.38 17.36 5.2844 +IC H10R C29 *C21 H10S 5.2844 17.36 -89.76 5.85 4.3730 +IC C29 C210 C211 C212 1.5438 115.61 -65.13 115.67 1.5370 +IC C212 C210 *C21 H11R 6.3127 23.97 47.46 23.65 5.2335 +IC H11R C210 *C21 H11S 5.2335 23.65 4.21 15.19 6.7920 +IC C210 C211 C212 C213 1.5403 115.67 -57.02 114.10 1.5383 +IC C213 C211 *C21 H12R 5.4602 26.20 34.13 17.02 6.8947 +IC H12R C211 *C21 H12S 6.8947 17.02 -53.67 15.32 7.1404 +IC C211 C212 C213 C214 1.5370 114.10 -170.17 114.14 1.5389 +IC C214 C212 *C21 H13R 6.4689 23.27 23.30 14.36 4.5967 +IC H13R C212 *C21 H13S 4.5967 14.36 -71.97 18.83 5.2276 +IC C212 C213 C214 C215 1.5383 114.14 -44.39 114.15 1.5345 +IC C215 C213 *C21 H14R 7.8518 8.47 10.62 20.04 6.2242 +IC H14R C213 *C21 H14S 6.2242 20.04 48.89 16.88 6.7112 +IC C213 C214 C215 C216 1.5389 114.15 -174.08 112.75 1.5347 +IC C216 C214 *C21 H15R 8.9073 5.78 -75.89 13.30 7.8767 +IC H15R C214 *C21 H15S 7.8767 13.30 -64.58 8.92 8.3139 +IC C214 C215 C216 C217 1.5345 112.75 -164.48 113.10 1.5367 +IC C217 C215 *C21 H16R 10.3283 4.19 33.88 12.99 8.9106 +IC H16R C215 *C21 H16S 8.9106 12.99 -52.55 13.37 8.8213 +IC C215 C216 C217 C218 1.5347 113.10 -57.86 114.48 1.5326 +IC C218 C216 *C21 H17R 10.7276 10.74 -75.19 8.10 10.5809 +IC H17R C216 *C21 H17S 10.5809 8.10 -166.85 1.09 11.0629 +IC C216 C217 C218 H18R 1.5367 114.48 -177.64 110.43 1.1110 +IC H18R C217 *C21 H18S 11.8109 8.33 -11.59 12.22 10.2196 +IC H18R C217 *C21 H18T 11.8109 8.33 35.94 11.83 10.6434 +IC C31 C32 C33 C34 1.5298 111.83 170.63 114.27 1.5918 +IC C34 C32 *C33 H3X 1.5918 114.27 123.49 109.22 1.1134 +IC H3X C32 *C33 H3Y 1.1134 109.22 116.29 107.65 1.1173 +IC C32 C33 C34 C35 1.5528 114.27 116.49 127.65 1.5940 +IC C35 C33 *C34 H4X 1.5940 127.65 -69.94 79.89 1.1249 +IC H4X C33 *C34 H4Y 1.1249 79.89 142.61 81.15 1.1349 +IC C33 C34 C35 C36 1.5918 127.65 -121.62 114.80 1.5445 +IC C36 C34 *C35 H5X 1.5445 114.80 -118.03 107.93 1.1160 +IC H5X C34 *C35 H5Y 1.1160 107.93 -117.35 110.21 1.1110 +IC C34 C35 C36 C37 1.5940 114.80 84.08 114.55 1.5394 +IC C37 C35 *C36 H6X 1.5394 114.55 -122.72 108.07 1.1131 +IC H6X C35 *C36 H6Y 1.1131 108.07 -116.55 109.08 1.1134 +IC C35 C36 C37 C38 1.5445 114.55 -167.23 112.81 1.5386 +IC C38 C36 *C37 H7X 1.5386 112.81 -123.16 110.28 1.1112 +IC H7X C36 *C37 H7Y 1.1112 110.28 -116.30 107.95 1.1075 +IC C36 C37 C38 C39 1.5394 112.81 158.78 114.66 1.5421 +IC C39 C37 *C38 H8X 1.5421 114.66 -121.91 109.39 1.1095 +IC H8X C37 *C38 H8Y 1.1095 109.39 -115.53 108.69 1.1126 +IC C37 C38 C39 C310 1.5386 114.66 -53.13 117.06 1.5456 +IC C310 C38 *C39 H9X 1.5456 117.06 121.00 107.46 1.1144 +IC H9X C38 *C39 H9Y 1.1144 107.46 115.86 108.70 1.1131 +IC C38 C39 C310 C311 1.5421 117.06 -66.60 116.96 1.5427 +IC C311 C39 *C31 H10X 5.8851 20.92 -58.96 17.59 6.5549 +IC H10X C39 *C31 H10Y 6.5549 17.59 -22.07 8.84 5.0878 +IC C39 C310 C311 C312 1.5456 116.96 73.83 115.78 1.5387 +IC C312 C310 *C31 H11X 5.2812 25.72 -29.63 17.56 6.9533 +IC H11X C310 *C31 H11Y 6.9533 17.56 -28.89 20.87 5.5224 +IC C310 C311 C312 C313 1.5427 115.78 156.38 114.20 1.5382 +IC C313 C311 *C31 H12X 5.2586 26.04 50.86 20.93 6.1018 +IC H12X C311 *C31 H12Y 6.1018 20.93 12.33 17.62 4.3754 +IC C311 C312 C313 C314 1.5387 114.20 55.56 115.80 1.5406 +IC C314 C312 *C31 H13X 6.6649 21.48 -8.59 23.86 4.5356 +IC H13X C312 *C31 H13Y 4.5356 23.86 49.87 23.85 5.2123 +IC C312 C313 C314 C315 1.5382 115.80 67.80 115.10 1.5406 +IC C315 C313 *C31 H14X 7.8353 3.11 -88.74 14.50 6.7777 +IC H14X C313 *C31 H14Y 6.7777 14.50 -65.72 12.87 6.9758 +IC C313 C314 C315 C316 1.5406 115.10 -91.14 115.66 1.5398 +IC C316 C314 *C31 H15X 8.6157 13.11 -56.84 15.69 7.6256 +IC H15X C314 *C31 H15Y 7.6256 15.69 -29.61 6.65 8.6426 +IC C314 C315 C316 C317 1.5406 115.66 -64.38 114.07 1.5364 +IC C317 C315 *C31 H16X 9.3815 13.84 -45.58 15.69 8.0762 +IC H16X C315 *C31 H16Y 8.0762 15.69 -20.16 9.55 9.4547 +IC C315 C316 C317 C318 1.5398 114.07 -177.03 113.16 1.5310 +IC C318 C316 *C31 H17X 10.4025 11.11 68.75 10.20 10.0175 +IC H17X C316 *C31 H17Y 10.0175 10.20 -32.28 14.37 8.7694 +IC C316 C317 C318 H18X 1.5364 113.16 -60.30 110.38 1.1114 +IC H18X C317 *C31 H18Y 9.9933 12.42 39.24 7.99 11.0428 +IC H18X C317 *C31 H18Z 9.9933 12.42 -35.35 7.42 11.1187 + + +RESI DOPC 0.00 ! 2,3-dioleoyl-D-glycero-1-phosphatidylcholine +! +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C12 CTL2 -0.10 ! H15A-C15-H15C +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H13B | H14A +ATOM C13 CTL5 -0.35 ! | | | +ATOM H13A HL 0.25 ! H13A-C13----N----C14-H14B (+) +ATOM H13B HL 0.25 ! | | | +ATOM H13C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | +ATOM H14A HL 0.25 ! | +ATOM H14B HL 0.25 ! | alpha6 +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H12A--C12---H12B +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +IC C15 N C12 C11 1.5031 108.03 -62.19 116.82 1.5409 +IC C13 C12 *N C14 1.4955 110.60 122.73 109.67 1.4976 +IC C13 C12 *N C15 1.4955 110.60 -119.76 108.04 1.5032 +IC C13 N C12 C11 1.4955 110.60 57.52 116.83 1.5412 +IC C11 N *C12 H12A 1.5412 116.83 -126.40 111.94 1.0787 +IC H12A N *C12 H12B 1.0787 111.94 -116.29 108.17 1.0974 +IC C14 N C13 H13A 1.4976 110.99 179.50 109.35 1.0869 +IC H13A N *C13 H13B 1.0869 109.35 118.93 111.32 1.0813 +IC H13A N *C13 H13C 1.0869 109.35 -119.04 111.19 1.0811 +IC C13 N C14 H14A 1.4955 110.99 -179.22 109.65 1.0877 +IC H14A N *C14 H14B 1.0877 109.65 118.74 110.91 1.0820 +IC H14A N *C14 H14C 1.0877 109.65 -119.76 111.49 1.0812 +IC C13 N C15 H15A 1.4955 109.44 -64.69 111.04 1.0951 +IC H15A N *C15 H15B 1.0951 111.04 123.93 113.87 1.0740 +IC H15A N *C15 H15C 1.0951 111.04 -112.38 110.25 1.0938 +IC N C12 C11 O12 1.5223 116.83 127.52 108.22 1.4232 +IC O12 C12 *C11 H11A 1.4232 108.22 -123.07 113.25 1.1138 +IC H11A C12 *C11 H11B 1.1138 113.25 -118.71 109.20 1.1129 +IC C12 C11 O12 P 1.5412 108.22 -67.94 118.41 1.5875 +IC C11 O12 P O11 1.4232 118.41 -166.85 104.05 1.5781 +IC O11 O12 *P O13 1.5781 104.05 117.80 108.05 1.4795 +IC O11 O12 *P O14 1.5781 104.05 -117.37 106.82 1.4822 +IC O12 P O11 C1 1.5875 104.05 167.61 118.26 1.4316 +IC P O11 C1 C2 1.5781 118.26 168.12 110.80 1.5508 +IC C2 O11 *C1 HA 1.5508 110.80 -119.17 111.41 1.1170 +IC HA O11 *C1 HB 1.1170 111.41 -120.80 110.01 1.1146 +IC O11 C1 C2 C3 1.4316 110.80 176.77 110.71 1.5573 +IC C3 C1 *C2 O21 1.5573 110.71 120.62 108.02 1.4410 !defines S chirality +IC C3 C1 *C2 HS 1.5573 110.71 -118.37 106.71 1.1170 !defines S chirality +IC C1 C2 O21 C21 1.5508 108.02 147.52 115.15 1.3177 +IC C2 O21 C21 C22 1.4410 115.15 179.16 108.63 1.5289 +IC C22 O21 *C21 O22 1.5289 108.63 -178.85 126.55 1.2187 +IC O21 C21 C22 C23 1.3177 108.63 -177.70 112.21 1.5449 +IC C23 C21 *C22 H2R 1.5449 112.21 -121.72 107.88 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.88 -117.16 107.60 1.1093 +IC C1 C2 C3 O31 1.5508 110.71 176.05 112.62 1.4438 +IC O31 C2 *C3 HX 1.4438 112.62 -118.51 106.65 1.1128 +IC HX C2 *C3 HY 1.1128 106.65 -115.12 109.46 1.1145 +IC C2 C3 O31 C31 1.5573 112.62 87.12 115.04 1.3313 +IC C3 O31 C31 C32 1.4438 115.04 -172.98 108.55 1.5288 +IC C32 O31 *C31 O32 1.5288 108.55 -178.89 125.60 1.2170 +IC O31 C31 C32 C33 1.3313 108.55 -166.73 113.05 1.5447 +IC C33 C31 *C32 H2X 1.5447 113.05 -121.10 107.23 1.1103 +IC H2X C31 *C32 H2Y 1.1103 107.23 -117.00 108.11 1.1090 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 H18R 1.5339 113.30 -59.98 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.84 110.45 1.1114 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 H18X 1.5340 113.30 -59.94 110.46 1.1113 +IC H18X C317 *C318 H18Y 1.1113 110.46 119.86 110.45 1.1113 +IC H18X C317 *C318 H18Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DOPE 0.00 ! 2,3-dioleoyl-D-glycero-1-phosphatidylethanolamine +! +! R1 - CH2 +! | (angles and atom names from Sundaralingam) +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2- - - - - - - +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S +ATOM H2S HAL2 0.09 ! | | +GROUP ! beta4 +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +IC N C12 C11 O12 1.5110 111.97 65.84 112.46 1.4308 +IC HN1 C12 *N HN2 1.0342 114.60 119.70 105.60 1.0654 +IC HN1 C12 *N HN3 1.0342 114.60 -127.78 110.56 1.0397 +IC HN1 N C12 C11 1.0342 114.60 -177.91 111.97 1.5465 +IC C11 N *C12 H12A 1.5465 111.97 -121.58 107.97 1.1086 +IC H12A N *C12 H12B 1.1086 107.97 -118.25 107.67 1.1104 +IC O12 C12 *C11 H11A 1.4308 112.46 -126.31 111.01 1.1167 +IC H11A C12 *C11 H11B 1.1167 111.01 -115.41 107.63 1.1146 +IC C12 C11 O12 P 1.5465 112.46 -80.62 120.62 1.5839 +IC C11 O12 P O11 1.4308 120.62 -156.78 104.60 1.5751 +IC O11 O12 *P O13 1.5751 104.60 -117.47 103.31 1.4823 +IC O11 O12 *P O14 1.5751 104.60 120.67 107.16 1.4736 +IC O12 P O11 C1 1.5839 104.60 -58.82 120.34 1.4318 +IC P O11 C1 C2 1.5751 120.34 -92.48 111.72 1.5536 +IC C2 O11 *C1 HA 1.5536 111.72 -119.08 108.93 1.1133 +IC HA O11 *C1 HB 1.1133 108.93 -117.83 112.18 1.1155 +IC O11 C1 C2 C3 1.4318 111.72 162.49 110.59 1.5553 +IC C3 C1 *C2 O21 1.5553 110.59 120.51 108.20 1.4410 +IC C3 C1 *C2 HS 1.5553 110.59 -117.47 107.37 1.1169 +IC C1 C2 O21 C21 1.5536 108.20 145.45 115.07 1.3229 +IC C2 O21 C21 C22 1.4410 115.07 175.60 109.17 1.5330 +IC C22 O21 *C21 O22 1.5330 109.17 179.92 126.38 1.2173 +IC O21 C21 C22 C23 1.3229 109.17 -134.07 111.55 1.5472 +IC C23 C21 *C22 H2R 1.5472 111.55 -119.81 106.70 1.1095 +IC H2R C21 *C22 H2S 1.1095 106.70 -117.59 109.58 1.1081 +IC C1 C2 C3 O31 1.5536 110.59 178.88 111.62 1.4432 +IC O31 C2 *C3 HX 1.4432 111.62 -121.40 107.66 1.1142 +IC HX C2 *C3 HY 1.1142 107.66 -116.77 107.26 1.1152 +IC C2 C3 O31 C31 1.5553 111.62 174.54 113.52 1.3270 +IC C3 O31 C31 C32 1.4432 113.52 178.76 109.19 1.5276 +IC C32 O31 *C31 O32 1.5276 109.19 -179.68 125.26 1.2176 +IC O31 C31 C32 C33 1.3270 109.19 -153.26 112.50 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.50 120.40 107.84 1.1092 +IC H2X C31 *C32 H2Y 1.1092 107.84 117.16 108.28 1.1081 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 H18R 1.5339 113.30 -59.98 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.84 110.45 1.1114 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 H18X 1.5340 113.30 -59.94 110.46 1.1113 +IC H18X C317 *C318 H18Y 1.1113 110.46 119.86 110.45 1.1113 +IC H18X C317 *C318 H18Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DOPS -1.00 ! 2,3-dioleoyl-D-glycero-1-phosphatidylserine +! +! R1 - CH2 +! | (-) +! R2 - CH CO2 +! | (-) | (+) +! CH2 - PO4 - CH2 - CH - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 C13 C12 O13B O13A + +IC N C12 C11 O12 1.4924 109.59 -36.83 114.43 1.4356 +IC N C12 C13 O13B 1.4924 110.59 -179.72 118.02 1.2545 +IC HN1 C12 *N HN2 1.0346 106.39 118.04 106.67 1.0582 +IC HN1 C12 *N HN3 1.0346 106.39 -118.31 107.13 1.0373 +IC HN1 N C12 C11 1.0346 106.39 -47.71 109.59 1.5667 +IC C11 N *C12 C13 1.5667 109.59 124.17 110.59 1.5415 +IC C13 N *C12 H12A 1.5415 110.59 116.85 107.76 1.0804 +IC O13B C12 *C13 O13A 1.2545 118.02 -178.76 118.14 1.2642 +IC O12 C12 *C11 H11A 1.4356 114.43 -124.67 108.62 1.1152 +IC H11A C12 *C11 H11B 1.1152 108.62 -115.01 108.11 1.1136 +IC C12 C11 O12 P 1.5667 114.43 -57.62 123.15 1.5823 +IC C11 O12 P O11 1.4356 123.15 -33.91 102.25 1.5778 +IC O11 O12 *P O13 1.5778 102.25 113.53 104.91 1.4849 +IC O11 O12 *P O14 1.5778 102.25 -117.35 110.47 1.4716 +IC O12 P O11 C1 1.5823 102.25 153.73 122.12 1.4299 +IC P O11 C1 C2 1.5778 122.12 103.33 112.63 1.5620 +IC C2 O11 *C1 HA 1.5620 112.63 -124.50 113.71 1.1165 +IC HA O11 *C1 HB 1.1165 113.71 -117.26 106.84 1.1126 +IC O11 C1 C2 C3 1.4299 112.63 11.79 111.98 1.5610 +IC C3 C1 *C2 O21 1.5610 111.98 121.40 109.82 1.4435 +IC C3 C1 *C2 HS 1.5610 111.98 -117.10 108.48 1.1163 +IC C1 C2 O21 C21 1.5620 109.82 68.92 114.10 1.3212 +IC C2 O21 C21 C22 1.4435 114.10 -166.83 108.56 1.5296 +IC C22 O21 *C21 O22 1.5296 108.56 178.35 126.33 1.2167 +IC O21 C21 C22 C23 1.3212 108.56 171.14 112.38 1.5479 +IC C23 C21 *C22 H2R 1.5479 112.38 -120.89 106.82 1.1096 +IC H2R C21 *C22 H2S 1.1096 106.82 -116.68 108.48 1.1079 +IC C1 C2 C3 O31 1.5620 111.98 166.06 113.99 1.4460 +IC O31 C2 *C3 HX 1.4460 113.99 -119.10 106.66 1.1129 +IC HX C2 *C3 HY 1.1129 106.66 -115.17 109.32 1.1144 +IC C2 C3 O31 C31 1.5610 113.99 74.23 115.62 1.3230 +IC C3 O31 C31 C32 1.4460 115.62 177.35 110.26 1.5339 +IC C32 O31 *C31 O32 1.5339 110.26 -179.39 126.39 1.2158 +IC O31 C31 C32 C33 1.3230 110.26 15.26 114.53 1.5470 +IC C33 C31 *C32 H2X 1.5470 114.53 121.61 106.59 1.1100 +IC H2X C31 *C32 H2Y 1.1100 106.59 116.04 107.18 1.1088 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 H18R 1.5339 113.30 -59.98 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.84 110.45 1.1114 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 H18X 1.5340 113.30 -59.94 110.46 1.1113 +IC H18X C317 *C318 H18Y 1.1113 110.46 119.86 110.45 1.1113 +IC H18X C317 *C318 H18Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DOPA -1.00 ! 2,3-dioleoyl-D-glycero-1-phosphatidic acid +! +! R1 - CH2 +! | +! R2 - CH +! | (-) +! CH2 - PO4 - H +! +! Polar Head and glycerol backbone +GROUP ! H12 + ! | +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.82 ! \ / alpha3 +ATOM O14 O2L -0.82 ! P (+) +ATOM O12 OHL -0.68 ! / \ alpha2 +ATOM H12 HOL 0.34 ! (-) O14 O11 +ATOM O11 OSLP -0.62 ! | +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +IC O11 P O12 H12 1.5787 106.47 -176.07 105.33 0.9598 +IC O12 O11 *P O13 1.5649 106.47 112.30 110.73 1.4710 +IC O12 O11 *P O14 1.5649 106.47 -112.57 112.05 1.4711 +IC O12 P O11 C1 1.5649 106.47 -66.24 121.23 1.4324 +IC P O11 C1 C2 1.5787 121.23 -118.39 111.55 1.5575 +IC C2 O11 *C1 HA 1.5575 111.55 -120.41 108.18 1.1110 +IC HA O11 *C1 HB 1.1110 108.18 -118.59 113.07 1.1183 +IC O11 C1 C2 C3 1.4324 111.55 53.40 111.33 1.5563 +IC C3 C1 *C2 O21 1.5563 111.33 120.55 109.40 1.4416 +IC C3 C1 *C2 HS 1.5563 111.33 -117.52 108.24 1.1150 +IC C1 C2 O21 C21 1.5575 109.40 69.37 114.94 1.3195 +IC C2 O21 C21 C22 1.4416 114.94 -160.31 109.54 1.5319 +IC C22 O21 *C21 O22 1.5319 109.54 176.37 126.44 1.2150 +IC O21 C21 C22 C23 1.3195 109.54 -119.57 113.41 1.5464 +IC C23 C21 *C22 H2R 1.5464 113.41 -119.29 105.57 1.1109 +IC H2R C21 *C22 H2S 1.1109 105.57 -116.59 109.59 1.1088 +IC C1 C2 C3 O31 1.5575 111.33 -164.59 113.02 1.4460 +IC O31 C2 *C3 HX 1.4460 113.02 -127.61 109.11 1.1151 +IC HX C2 *C3 HY 1.1151 109.11 -114.61 107.22 1.1116 +IC C2 C3 O31 C31 1.5563 113.02 -100.10 116.86 1.3192 +IC C3 O31 C31 C32 1.4460 116.86 -168.86 107.89 1.5336 +IC C32 O31 *C31 O32 1.5336 107.89 177.06 127.12 1.2154 +IC O31 C31 C32 C33 1.3192 107.89 -165.38 112.39 1.5426 +IC C33 C31 *C32 H2X 1.5426 112.39 122.05 108.50 1.1086 +IC H2X C31 *C32 H2Y 1.1086 108.50 117.11 107.05 1.1092 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 H18R 1.5339 113.30 -59.98 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.84 110.45 1.1114 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 H18X 1.5340 113.30 -59.94 110.46 1.1113 +IC H18X C317 *C318 H18Y 1.1113 110.46 119.86 110.45 1.1113 +IC H18X C317 *C318 H18Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI DOPG -1.00 ! 2,3-dioleoyl-D-glycero-1-phosphatidylglycerol +! +! R1 - CH2 +! | +! R2 - CH +! | +! CH2 - PO4 - CH2 - CH(OH) - CH2OH +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CEL1 -0.15 ! | +ATOM H9X HEL1 0.15 ! H9X ---C39 +GROUP ! || +ATOM C310 CEL1 -0.15 ! || +ATOM H10X HEL1 0.15 ! H10X---C310 +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H9R +DOUBLE C29 C210 +BOND C210 H10R C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X +DOUBLE C39 C310 +BOND C310 H10X C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +IC C13 C12 C11 O12 1.5583 113.89 93.01 113.50 1.4295 +IC OC3 C13 C12 C11 1.4375 112.31 69.20 113.89 1.5573 +IC OC3 C12 *C13 H13A 1.4375 112.31 119.90 108.06 1.1118 +IC OC3 C12 *C13 H13B 1.4375 112.31 -123.06 109.89 1.1097 +IC C12 C13 OC3 HO3 1.5583 112.31 -141.84 106.96 0.9777 +IC C11 C13 *C12 OC2 1.5573 113.89 -121.65 107.64 1.4259 +IC OC2 C13 *C12 H12A 1.4259 107.64 -117.84 109.30 1.1131 +IC C13 C12 OC2 HO2 1.5583 107.64 38.09 100.52 0.9671 +IC O12 C12 *C11 H11A 1.4295 113.50 -126.35 109.70 1.1125 +IC H11A C12 *C11 H11B 1.1125 109.70 -115.65 107.71 1.1131 +IC C12 C11 O12 P 1.5573 113.50 -72.69 124.80 1.5783 +IC C11 O12 P O11 1.4295 124.80 -30.02 102.66 1.5825 +IC O11 O12 *P O13 1.5825 102.66 113.88 109.00 1.4783 +IC O11 O12 *P O14 1.5825 102.66 -115.27 109.77 1.4781 +IC O12 P O11 C1 1.5783 102.66 -80.21 120.83 1.4246 +IC P O11 C1 C2 1.5825 120.83 177.68 108.67 1.5488 +IC C2 O11 *C1 HA 1.5488 108.67 -120.91 111.25 1.1145 +IC HA O11 *C1 HB 1.1145 111.25 -120.47 110.06 1.1152 +IC O11 C1 C2 C3 1.4246 108.67 45.70 110.42 1.5580 +IC C3 C1 *C2 O21 1.5580 110.42 120.25 110.13 1.4420 +IC C3 C1 *C2 HS 1.5580 110.42 -116.94 108.10 1.1164 +IC C1 C2 O21 C21 1.5488 110.13 74.82 114.08 1.3218 +IC C2 O21 C21 C22 1.4420 114.08 -171.58 108.87 1.5297 +IC C22 O21 *C21 O22 1.5297 108.87 -179.18 126.27 1.2166 +IC O21 C21 C22 C23 1.3218 108.87 167.60 112.03 1.5460 +IC C23 C21 *C22 H2R 1.5460 112.03 -121.40 108.25 1.1088 +IC H2R C21 *C22 H2S 1.1088 108.25 -117.05 107.34 1.1068 +IC C1 C2 C3 O31 1.5488 110.42 -172.10 112.95 1.4472 +IC O31 C2 *C3 HX 1.4472 112.95 -119.90 106.80 1.1123 +IC HX C2 *C3 HY 1.1123 106.80 -114.66 109.95 1.1147 +IC C2 C3 O31 C31 1.5580 112.95 84.38 114.39 1.3267 +IC C3 O31 C31 C32 1.4472 114.39 176.82 109.50 1.5275 +IC C32 O31 *C31 O32 1.5275 109.50 -179.44 126.11 1.2173 +IC O31 C31 C32 C33 1.3267 109.50 -66.76 112.63 1.5535 +IC C33 C31 *C32 H2X 1.5535 112.63 121.43 107.50 1.1085 +IC H2X C31 *C32 H2Y 1.1085 107.50 116.64 107.32 1.1097 +IC C21 C22 C23 C24 1.5289 112.21 175.76 112.39 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.39 -120.69 109.57 1.1147 +IC H3R C22 *C23 H3S 1.1147 109.57 -117.65 109.64 1.1142 +IC C22 C23 C24 C25 1.5449 112.39 -179.39 112.35 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.35 -121.52 109.41 1.1131 +IC H4R C23 *C24 H4S 1.1131 109.41 -117.57 108.97 1.1134 +IC C23 C24 C25 C26 1.5338 112.35 176.31 112.80 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.80 -121.01 108.95 1.1135 +IC H5R C24 *C25 H5S 1.1135 108.95 -117.24 109.16 1.1132 +IC C24 C25 C26 C27 1.5346 112.80 -179.44 112.48 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.48 -121.49 109.32 1.1129 +IC H6R C25 *C26 H6S 1.1129 109.32 -117.47 108.94 1.1132 +IC C25 C26 C27 C28 1.5344 112.48 176.92 112.46 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.46 -121.38 108.40 1.1139 +IC H7R C26 *C27 H7S 1.1139 108.40 -116.93 108.77 1.1139 +IC C26 C27 C28 C29 1.5356 112.46 -178.53 111.43 1.5097 +IC C29 C27 *C28 H8R 1.5097 111.43 -123.58 107.80 1.1132 +IC H8R C27 *C28 H8S 1.1132 107.80 -115.43 108.37 1.1128 +IC C27 C28 C29 C210 1.5398 111.43 -126.96 126.62 1.3465 +IC C210 C28 *C29 H9R 1.3465 126.62 178.41 114.65 1.1012 +IC C28 C29 C210 C211 1.5097 126.62 -1.69 126.32 1.5088 +IC C211 C29 *C210 H10R 1.5088 126.32 -179.55 118.79 1.1012 +IC C29 C210 C211 C212 1.3465 126.32 93.02 112.15 1.5392 +IC C212 C210 *C211 H11R 1.5392 112.15 -121.30 111.28 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.28 -117.50 110.00 1.1126 +IC C210 C211 C212 C213 1.5088 112.15 -178.81 112.29 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.29 -121.34 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -118.01 109.42 1.1144 +IC C211 C212 C213 C214 1.5392 112.29 179.81 112.68 1.5345 +IC C214 C212 *C213 H13R 1.5345 112.68 -121.26 109.04 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.04 -117.39 109.10 1.1131 +IC C212 C213 C214 C215 1.5354 112.68 179.80 112.59 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.59 -121.29 109.09 1.1132 +IC H14R C213 *C214 H14S 1.1132 109.09 -117.37 109.11 1.1133 +IC C213 C214 C215 C216 1.5345 112.59 -179.58 112.63 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.63 -121.36 109.09 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.09 -117.38 109.07 1.1132 +IC C214 C215 C216 C217 1.5347 112.63 179.65 112.69 1.5339 +IC C217 C215 *C216 H16R 1.5339 112.69 -121.27 109.11 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.11 -117.36 109.14 1.1132 +IC C215 C216 C217 C218 1.5347 112.69 -179.93 113.30 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.30 -121.70 108.75 1.1140 +IC H17R C216 *C217 H17S 1.1140 108.75 -116.65 108.73 1.1141 +IC C216 C217 C218 H18R 1.5339 113.30 -59.98 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.84 110.45 1.1114 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.09 110.62 1.1112 +IC C31 C32 C33 C34 1.5288 113.05 179.24 111.73 1.5343 +IC C34 C32 *C33 H3X 1.5343 111.73 -120.85 109.62 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.62 -117.95 109.78 1.1144 +IC C32 C33 C34 C35 1.5447 111.73 -176.74 112.91 1.5345 +IC C35 C33 *C34 H4X 1.5345 112.91 -121.67 109.15 1.1134 +IC H4X C33 *C34 H4Y 1.1134 109.15 -117.32 108.98 1.1134 +IC C33 C34 C35 C36 1.5343 112.91 178.63 112.42 1.5349 +IC C36 C34 *C35 H5X 1.5349 112.42 -120.99 108.94 1.1133 +IC H5X C34 *C35 H5Y 1.1133 108.94 -117.41 109.31 1.1131 +IC C34 C35 C36 C37 1.5345 112.42 -176.73 112.80 1.5356 +IC C37 C35 *C36 H6X 1.5356 112.80 -121.69 109.16 1.1130 +IC H6X C35 *C36 H6Y 1.1130 109.16 -117.32 108.94 1.1133 +IC C35 C36 C37 C38 1.5349 112.80 178.92 112.27 1.5402 +IC C38 C36 *C37 H7X 1.5402 112.27 -121.37 108.23 1.1139 +IC H7X C36 *C37 H7Y 1.1139 108.23 -117.01 109.05 1.1137 +IC C36 C37 C38 C39 1.5356 112.27 -174.92 111.69 1.5099 +IC C39 C37 *C38 H8X 1.5099 111.69 -124.14 107.77 1.1124 +IC H8X C37 *C38 H8Y 1.1124 107.77 -115.13 108.30 1.1128 +IC C37 C38 C39 C310 1.5402 111.69 -121.39 127.35 1.3470 +IC C310 C38 *C39 H9X 1.3470 127.35 179.11 114.24 1.1012 +IC C38 C39 C310 C311 1.5099 127.35 -0.69 127.25 1.5096 +IC C311 C39 *C310 H10X 1.5096 127.25 179.82 118.43 1.1012 +IC C39 C310 C311 C312 1.3470 127.25 106.03 111.65 1.5393 +IC C312 C310 *C311 H11X 1.5393 111.65 -121.49 112.10 1.1123 +IC H11X C310 *C311 H11Y 1.1123 112.10 -117.95 109.83 1.1127 +IC C310 C311 C312 C313 1.5096 111.65 179.63 112.41 1.5355 +IC C313 C311 *C312 H12X 1.5355 112.41 -121.09 109.75 1.1135 +IC H12X C311 *C312 H12Y 1.1135 109.75 -118.07 109.46 1.1143 +IC C311 C312 C313 C314 1.5393 112.41 -178.89 112.60 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.60 -121.37 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.41 109.08 1.1131 +IC C312 C313 C314 C315 1.5355 112.60 179.88 112.66 1.5347 +IC C315 C313 *C314 H14X 1.5347 112.66 -121.27 109.06 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.06 -117.36 109.14 1.1133 +IC C313 C314 C315 C316 1.5347 112.66 -179.12 112.61 1.5348 +IC C316 C314 *C315 H15X 1.5348 112.61 -121.34 109.09 1.1132 +IC H15X C314 *C315 H15Y 1.1132 109.09 -117.41 109.09 1.1132 +IC C314 C315 C316 C317 1.5347 112.61 179.83 112.71 1.5340 +IC C317 C315 *C316 H16X 1.5340 112.71 -121.28 109.10 1.1132 +IC H16X C315 *C316 H16Y 1.1132 109.10 -117.35 109.13 1.1133 +IC C315 C316 C317 C318 1.5348 112.71 -179.67 113.30 1.5309 +IC C318 C316 *C317 H17X 1.5309 113.30 -121.68 108.77 1.1141 +IC H17X C316 *C317 H17Y 1.1141 108.77 -116.68 108.76 1.1141 +IC C316 C317 C318 H18X 1.5340 113.30 -59.94 110.46 1.1113 +IC H18X C317 *C318 H18Y 1.1113 110.46 119.86 110.45 1.1113 +IC H18X C317 *C318 H18Z 1.1113 110.46 -120.06 110.61 1.1112 + +RESI POPC 0.00 ! 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidylcholine +! +! Palmitoyl - CH2 +! | +! Oleyol - CH +! | (-) (+) +! CH2 - PO4 - CH2 - CH2 - N-(CH3)3 +! +! Polar Head and glycerol backbone +! +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C12 CTL2 -0.10 ! H15A-C15-H15C +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H13B | H14A +ATOM C13 CTL5 -0.35 ! | | | +ATOM H13A HL 0.25 ! H13A-C13----N----C14-H14B (+) +ATOM H13B HL 0.25 ! | | | +ATOM H13C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | +ATOM H14A HL 0.25 ! | +ATOM H14B HL 0.25 ! | alpha6 +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H12A--C12---H12B +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +!IC table from IC generate, minimized geometry +IC C13 N C12 C11 1.4950 110.81 58.46 117.00 1.5420 +IC C13 C12 *N C14 1.4950 110.81 122.75 109.46 1.4979 +IC C13 C12 *N C15 1.4950 110.81 -120.02 108.16 1.5034 +IC C11 N *C12 H12A 1.5420 117.00 -126.73 111.85 1.0787 +IC H12A N *C12 H12B 1.0787 111.85 -115.99 107.93 1.0977 +IC C14 N C13 H13A 1.4979 111.01 179.36 109.41 1.0866 +IC H13A N *C13 H13B 1.0866 109.41 119.11 111.31 1.0813 +IC H13A N *C13 H13C 1.0866 109.41 -119.02 111.10 1.0815 +IC C13 N C14 H14A 1.4950 111.01 -179.09 109.58 1.0882 +IC H14A N *C14 H14B 1.0882 109.58 118.63 110.95 1.0819 +IC H14A N *C14 H14C 1.0882 109.58 -119.72 111.56 1.0811 +IC C13 N C15 H15A 1.4950 109.49 -176.86 110.11 1.0949 +IC H15A N *C15 H15B 1.0949 110.11 112.40 111.19 1.0942 +IC H15A N *C15 H15C 1.0949 110.11 -123.40 113.89 1.0740 +IC N C12 C11 O12 1.5227 117.00 126.96 108.43 1.4243 +IC O12 C12 *C11 H11A 1.4243 108.43 -123.15 113.04 1.1139 +IC H11A C12 *C11 H11B 1.1139 113.04 -118.48 109.10 1.1129 +IC C12 C11 O12 P 1.5420 108.43 -67.66 118.24 1.5905 +IC C11 O12 P O11 1.4243 118.24 -168.65 103.08 1.5759 +IC O11 O12 *P O13 1.5759 103.08 117.52 107.25 1.4784 +IC O11 O12 *P O14 1.5759 103.08 -117.26 106.69 1.4808 +IC O12 P O11 C1 1.5905 103.08 53.06 121.96 1.4290 +IC P O11 C1 C2 1.5759 121.96 -120.83 111.03 1.5486 +IC C2 O11 *C1 HA 1.5486 111.03 -118.56 108.65 1.1130 +IC HA O11 *C1 HB 1.1130 108.65 -119.01 113.55 1.1171 +IC O11 C1 C2 O21 1.4290 111.03 -176.04 106.79 1.4418 +IC O21 C1 *C2 C3 1.4418 106.79 -121.29 111.26 1.5597 !defines S chirality +IC C3 C1 *C2 HS 1.5597 111.26 -118.26 107.07 1.1169 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.79 150.93 115.28 1.3209 +IC C2 O21 C21 C22 1.4418 115.28 176.64 108.60 1.5290 +IC C22 O21 *C21 O22 1.5290 108.60 179.59 126.50 1.2169 +IC O21 C21 C22 C23 1.3209 108.60 -179.01 112.27 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.27 -121.28 107.76 1.1092 +IC H2R C21 *C22 H2S 1.1092 107.76 -117.26 107.89 1.1091 +IC C1 C2 C3 O31 1.5486 111.26 173.79 112.94 1.4459 +IC O31 C2 *C3 HX 1.4459 112.94 126.42 109.02 1.1150 +IC HX C2 *C3 HY 1.1150 109.02 114.46 106.69 1.1125 +IC C2 C3 O31 C31 1.5597 112.94 88.29 114.93 1.3313 +IC C3 O31 C31 C32 1.4459 114.93 -173.14 108.62 1.5287 +IC C32 O31 *C31 O32 1.5287 108.62 -178.86 125.93 1.2161 +IC O31 C31 C32 C33 1.3313 108.62 -179.25 112.61 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.61 -120.75 107.37 1.1102 +IC H2X C31 *C32 H2Y 1.1102 107.37 -117.25 108.05 1.1083 +IC C21 C22 C23 C24 1.5290 112.27 -178.80 112.39 1.5341 +IC C24 C22 *C23 H3R 1.5341 112.39 -121.30 109.66 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.66 -117.71 109.63 1.1148 +IC C22 C23 C24 C25 1.5451 112.39 179.92 112.37 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.37 -121.09 109.19 1.1134 +IC H4R C23 *C24 H4S 1.1134 109.19 -117.63 109.29 1.1131 +IC C23 C24 C25 C26 1.5341 112.37 -179.65 112.86 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.86 -121.43 109.08 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.08 -117.25 109.07 1.1134 +IC C24 C25 C26 C27 1.5348 112.86 -179.97 112.46 1.5357 +IC C27 C25 *C26 H6R 1.5357 112.46 -121.19 109.17 1.1131 +IC H6R C25 *C26 H6S 1.1131 109.17 -117.50 109.15 1.1129 +IC C25 C26 C27 C28 1.5347 112.46 179.27 112.54 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.54 -121.63 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.90 108.70 1.1141 +IC C26 C27 C28 C29 1.5357 112.54 -178.53 111.36 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.36 -123.49 107.78 1.1133 +IC H8R C27 *C28 H8S 1.1133 107.78 -115.41 108.52 1.1127 +IC C27 C28 C29 C210 1.5398 111.36 -121.90 126.64 1.3464 +IC C210 C28 *C29 H91 1.3464 126.64 178.40 114.63 1.1012 +IC C28 C29 C210 C211 1.5099 126.64 -1.49 126.31 1.5089 +IC C211 C29 *C210 H101 1.5089 126.31 -179.72 118.80 1.1013 +IC C29 C210 C211 C212 1.3464 126.31 89.31 112.19 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.19 -121.31 111.20 1.1134 +IC H11R C210 *C211 H11S 1.1134 111.20 -117.51 109.99 1.1127 +IC C210 C211 C212 C213 1.5089 112.19 -179.78 112.31 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.31 -121.28 109.81 1.1134 +IC H12R C211 *C212 H12S 1.1134 109.81 -118.01 109.39 1.1144 +IC C211 C212 C213 C214 1.5394 112.31 179.16 112.70 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.70 -121.26 109.08 1.1132 +IC H13R C212 *C213 H13S 1.1132 109.08 -117.39 109.07 1.1131 +IC C212 C213 C214 C215 1.5354 112.70 179.34 112.55 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.55 -121.30 109.14 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.14 -117.39 109.08 1.1133 +IC C213 C214 C215 C216 1.5346 112.55 179.77 112.71 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.71 -121.31 109.08 1.1132 +IC H15R C214 *C215 H15S 1.1132 109.08 -117.38 109.06 1.1132 +IC C214 C215 C216 C217 1.5347 112.71 179.71 112.62 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.62 -121.30 109.16 1.1132 +IC H16R C215 *C216 H16S 1.1132 109.16 -117.41 109.13 1.1133 +IC C215 C216 C217 C218 1.5347 112.62 179.90 113.34 1.5308 +IC C218 C216 *C217 H17R 1.5308 113.34 -121.66 108.75 1.1141 +IC H17R C216 *C217 H17S 1.1141 108.75 -116.66 108.75 1.1141 +IC C216 C217 C218 H18R 1.5341 113.34 -60.00 110.46 1.1113 +IC H18R C217 *C218 H18S 1.1113 110.46 119.87 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1113 110.46 -120.05 110.61 1.1112 +IC C31 C32 C33 C34 1.5287 112.61 -178.86 112.01 1.5338 +IC C34 C32 *C33 H3X 1.5338 112.01 -121.48 109.83 1.1138 +IC H3X C32 *C33 H3Y 1.1138 109.83 -117.75 109.42 1.1150 +IC C32 C33 C34 C35 1.5449 112.01 179.84 112.77 1.5347 +IC C35 C33 *C34 H4X 1.5347 112.77 -121.17 108.96 1.1136 +IC H4X C33 *C34 H4Y 1.1136 108.96 -117.41 109.17 1.1130 +IC C33 C34 C35 C36 1.5338 112.77 -179.85 112.41 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.41 -121.34 109.12 1.1131 +IC H5X C34 *C35 H5Y 1.1131 109.12 -117.37 109.10 1.1134 +IC C34 C35 C36 C37 1.5347 112.41 -179.32 112.86 1.5347 +IC C37 C35 *C36 H6X 1.5347 112.86 -121.41 109.03 1.1133 +IC H6X C35 *C36 H6Y 1.1133 109.03 -117.30 109.00 1.1132 +IC C35 C36 C37 C38 1.5346 112.86 179.55 112.41 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.41 -121.18 109.06 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.06 -117.42 109.19 1.1132 +IC C36 C37 C38 C39 1.5347 112.41 -178.88 112.84 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.84 -121.50 109.09 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.09 -117.30 108.97 1.1133 +IC C37 C38 C39 C310 1.5347 112.84 179.23 112.47 1.5348 +IC C310 C38 *C39 H9X 1.5348 112.47 -121.14 109.05 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.05 -117.44 109.20 1.1131 +IC C38 C39 C310 C311 1.5346 112.47 -178.98 112.76 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.76 -121.46 109.11 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.11 -117.33 109.01 1.1133 +IC C39 C310 C311 C312 1.5348 112.76 179.33 112.56 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.56 -121.19 109.07 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.07 -117.41 109.15 1.1131 +IC C310 C311 C312 C313 1.5346 112.56 -179.57 112.68 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.68 -121.37 109.11 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.11 -117.37 109.06 1.1132 +IC C311 C312 C313 C314 1.5348 112.68 179.70 112.62 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.62 -121.28 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.40 109.09 1.1132 +IC C312 C313 C314 C315 1.5346 112.62 179.93 112.69 1.5340 +IC C315 C313 *C314 H14X 1.5340 112.69 -121.31 109.12 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.12 -117.38 109.12 1.1132 +IC C313 C314 C315 C316 1.5348 112.69 179.95 113.32 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.32 -121.68 108.76 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.76 -116.66 108.75 1.1141 +IC C314 C315 C316 H16X 1.5340 113.32 -60.01 110.46 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.46 119.87 110.46 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.46 -120.07 110.61 1.1113 + +RESI POPE 0.00 ! 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidylethanolamine +! +! Palmitoyl - CH2 +! | +! Oleyl - CH +! | +! CH2 - PO4 - CH2 - CH2 - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL2 0.13 ! | +ATOM H12A HAL2 0.09 ! H12A--C12---H12B +ATOM H12B HAL2 0.09 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O11 OSLP -0.57 ! / \ alpha2 +ATOM O12 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 C1 O11 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.5078 111.09 68.79 110.33 1.4254 +IC C11 N *C12 H12A 1.5400 111.09 -122.33 108.17 1.1079 +IC H12A N *C12 H12B 1.1079 108.17 -118.40 107.74 1.1112 +IC C11 C12 N HN1 1.5400 111.09 -35.27 106.06 1.0664 +IC HN1 C12 *N HN2 1.0664 106.06 114.05 112.10 1.0358 +IC HN1 C12 *N HN3 1.0664 106.06 -118.21 113.62 1.0353 +IC O12 C12 *C11 H11A 1.4254 110.33 -126.01 111.43 1.1173 +IC H11A C12 *C11 H11B 1.1173 111.43 -116.40 108.25 1.1146 +IC C12 C11 O12 P 1.5400 110.33 -98.67 122.01 1.5838 +IC C11 O12 P O11 1.4254 122.01 175.28 101.96 1.5733 +IC O11 O12 *P O13 1.5733 101.96 118.35 108.16 1.4702 +IC O11 O12 *P O14 1.5733 101.96 -114.83 104.73 1.4823 +IC O12 P O11 C1 1.5838 101.96 61.31 122.26 1.4287 +IC P O11 C1 C2 1.5733 122.26 -120.45 111.00 1.5491 +IC C2 O11 *C1 HA 1.5491 111.00 -118.16 108.31 1.1134 +IC HA O11 *C1 HB 1.1134 108.31 -118.72 113.73 1.1170 +IC O11 C1 C2 O21 1.4287 111.00 -170.08 107.01 1.4406 +IC O21 C1 *C2 C3 1.4406 107.01 -121.48 111.36 1.5593 !defines S chirality +IC C3 C1 *C2 HS 1.5593 111.36 -118.41 106.90 1.1168 !defines S chirality +IC C1 C2 O21 C21 1.5491 107.01 151.66 115.21 1.3219 +IC C2 O21 C21 C22 1.4406 115.21 176.14 108.47 1.5289 +IC C22 O21 *C21 O22 1.5289 108.47 179.75 126.36 1.2176 +IC O21 C21 C22 C23 1.3219 108.47 -177.19 112.65 1.5452 +IC C23 C21 *C22 H2R 1.5452 112.65 -121.46 107.75 1.1093 +IC H2R C21 *C22 H2S 1.1093 107.75 -117.05 107.80 1.1094 +IC C1 C2 C3 O31 1.5491 111.36 174.62 112.78 1.4451 +IC O31 C2 *C3 HX 1.4451 112.78 126.20 108.61 1.1134 +IC HX C2 *C3 HY 1.1134 108.61 114.63 106.76 1.1126 +IC C2 C3 O31 C31 1.5593 112.78 94.47 115.64 1.3298 +IC C3 O31 C31 C32 1.4451 115.64 -170.85 108.57 1.5287 +IC C32 O31 *C31 O32 1.5287 108.57 -178.35 125.82 1.2178 +IC O31 C31 C32 C33 1.3298 108.57 176.09 113.01 1.5453 +IC C33 C31 *C32 H2X 1.5453 113.01 -120.86 107.43 1.1106 +IC H2X C31 *C32 H2Y 1.1106 107.43 -117.02 107.94 1.1084 +IC C21 C22 C23 C24 1.5289 112.65 179.22 112.12 1.5344 +IC C24 C22 *C23 H3R 1.5344 112.12 -120.98 109.71 1.1144 +IC H3R C22 *C23 H3S 1.1144 109.71 -117.88 109.69 1.1144 +IC C22 C23 C24 C25 1.5452 112.12 179.62 112.63 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.63 -121.34 109.27 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.27 -117.46 109.10 1.1131 +IC C23 C24 C25 C26 1.5344 112.63 177.81 112.75 1.5350 +IC C26 C24 *C25 H5R 1.5350 112.75 -121.19 109.09 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.09 -117.33 109.08 1.1133 +IC C24 C25 C26 C27 1.5348 112.75 179.27 112.53 1.5359 +IC C27 C25 *C26 H6R 1.5359 112.53 -121.31 109.26 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.26 -117.44 109.05 1.1132 +IC C25 C26 C27 C28 1.5350 112.53 177.65 112.47 1.5399 +IC C28 C26 *C27 H7R 1.5399 112.47 -121.59 108.56 1.1135 +IC H7R C26 *C27 H7S 1.1135 108.56 -116.88 108.73 1.1139 +IC C26 C27 C28 C29 1.5359 112.47 -179.09 111.48 1.5100 +IC C29 C27 *C28 H8R 1.5100 111.48 -123.55 107.71 1.1131 +IC H8R C27 *C28 H8S 1.1131 107.71 -115.31 108.52 1.1127 +IC C27 C28 C29 C210 1.5399 111.48 -120.51 126.65 1.3465 +IC C210 C28 *C29 H91 1.3465 126.65 178.55 114.65 1.1012 +IC C28 C29 C210 C211 1.5100 126.65 -1.33 126.32 1.5088 +IC C211 C29 *C210 H101 1.5088 126.32 -179.89 118.81 1.1013 +IC C29 C210 C211 C212 1.3465 126.32 90.84 112.10 1.5393 +IC C212 C210 *C211 H11R 1.5393 112.10 -121.27 111.29 1.1133 +IC H11R C210 *C211 H11S 1.1133 111.29 -117.47 110.08 1.1126 +IC C210 C211 C212 C213 1.5088 112.10 -179.38 112.20 1.5348 +IC C213 C211 *C212 H12R 1.5348 112.20 -121.32 109.91 1.1132 +IC H12R C211 *C212 H12S 1.1132 109.91 -118.08 109.39 1.1144 +IC C211 C212 C213 C214 1.5393 112.20 178.10 112.82 1.5344 +IC C214 C212 *C213 H13R 1.5344 112.82 -121.13 108.97 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.97 -117.33 109.12 1.1130 +IC C212 C213 C214 C215 1.5348 112.82 179.61 112.29 1.5344 +IC C215 C213 *C214 H14R 1.5344 112.29 -121.35 109.32 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.32 -117.49 109.04 1.1133 +IC C213 C214 C215 C216 1.5344 112.29 178.10 112.83 1.5343 +IC C216 C214 *C215 H15R 1.5343 112.83 -121.22 109.06 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.06 -117.27 109.05 1.1132 +IC C214 C215 C216 C217 1.5344 112.83 179.20 112.48 1.5338 +IC C217 C215 *C216 H16R 1.5338 112.48 -121.30 109.23 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.23 -117.48 109.17 1.1133 +IC C215 C216 C217 C218 1.5343 112.48 179.30 113.32 1.5307 +IC C218 C216 *C217 H17R 1.5307 113.32 -121.67 108.76 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.76 -116.60 108.71 1.1141 +IC C216 C217 C218 H18R 1.5338 113.32 -60.32 110.45 1.1114 +IC H18R C217 *C218 H18S 1.1114 110.45 119.86 110.49 1.1113 +IC H18R C217 *C218 H18T 1.1114 110.45 -120.04 110.58 1.1112 +IC C31 C32 C33 C34 1.5287 113.01 -179.36 111.84 1.5345 +IC C34 C32 *C33 H3X 1.5345 111.84 -121.48 110.04 1.1135 +IC H3X C32 *C33 H3Y 1.1135 110.04 -117.95 109.39 1.1149 +IC C32 C33 C34 C35 1.5453 111.84 178.35 112.93 1.5350 +IC C35 C33 *C34 H4X 1.5350 112.93 -121.06 108.92 1.1138 +IC H4X C33 *C34 H4Y 1.1138 108.92 -117.32 109.20 1.1130 +IC C33 C34 C35 C36 1.5345 112.93 -179.86 112.46 1.5352 +IC C36 C34 *C35 H5X 1.5352 112.46 -121.45 109.25 1.1129 +IC H5X C34 *C35 H5Y 1.1129 109.25 -117.43 109.01 1.1134 +IC C34 C35 C36 C37 1.5350 112.46 179.21 112.88 1.5352 +IC C37 C35 *C36 H6X 1.5352 112.88 -121.25 109.00 1.1134 +IC H6X C35 *C36 H6Y 1.1134 109.00 -117.27 109.08 1.1131 +IC C35 C36 C37 C38 1.5352 112.88 179.79 112.50 1.5352 +IC C38 C36 *C37 H7X 1.5352 112.50 -121.35 109.17 1.1130 +IC H7X C36 *C37 H7Y 1.1130 109.17 -117.42 109.08 1.1132 +IC C36 C37 C38 C39 1.5352 112.50 179.41 112.91 1.5352 +IC C39 C37 *C38 H8X 1.5352 112.91 -121.30 109.04 1.1133 +IC H8X C37 *C38 H8Y 1.1133 109.04 -117.27 109.05 1.1132 +IC C37 C38 C39 C310 1.5352 112.91 179.74 112.46 1.5353 +IC C310 C38 *C39 H9X 1.5353 112.46 -121.33 109.17 1.1131 +IC H9X C38 *C39 H9Y 1.1131 109.17 -117.42 109.10 1.1132 +IC C38 C39 C310 C311 1.5352 112.46 179.50 112.91 1.5350 +IC C311 C39 *C310 H10X 1.5350 112.91 -121.32 109.05 1.1133 +IC H10X C39 *C310 H10Y 1.1133 109.05 -117.29 109.05 1.1132 +IC C39 C310 C311 C312 1.5353 112.91 179.80 112.52 1.5354 +IC C312 C310 *C311 H11X 1.5354 112.52 -121.32 109.16 1.1131 +IC H11X C310 *C311 H11Y 1.1131 109.16 -117.41 109.11 1.1132 +IC C310 C311 C312 C313 1.5350 112.52 179.66 112.78 1.5349 +IC C313 C311 *C312 H12X 1.5349 112.78 -121.30 109.08 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.08 -117.35 109.09 1.1132 +IC C311 C312 C313 C314 1.5354 112.78 179.95 112.66 1.5353 +IC C314 C312 *C313 H13X 1.5353 112.66 -121.33 109.10 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.10 -117.38 109.07 1.1132 +IC C312 C313 C314 C315 1.5349 112.66 179.95 112.69 1.5341 +IC C315 C313 *C314 H14X 1.5341 112.69 -121.30 109.17 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.17 -117.38 109.15 1.1132 +IC C313 C314 C315 C316 1.5353 112.69 179.98 113.37 1.5312 +IC C316 C314 *C315 H15X 1.5312 113.37 -121.71 108.74 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.74 -116.61 108.74 1.1141 +IC C314 C315 C316 H16X 1.5341 113.37 -59.94 110.51 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.51 119.91 110.52 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.51 -120.06 110.58 1.1112 + +RESI POPS -1.00 ! 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidylserine +! +! Palmitoyl - CH2 +! | (-) +! Oleoyl - CH CO2 +! | (-) | (+) +! CH2 - PO4 - CH2 - CH - NH3 +! +! Polar Head and glycerol backbone +GROUP ! +ATOM N NH3L -0.30 ! HN2 +ATOM HN1 HCL 0.33 ! | +ATOM HN2 HCL 0.33 ! | +ATOM HN3 HCL 0.33 ! | +ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3 +ATOM H12A HBL 0.10 ! | +GROUP ! | O13A (-) +ATOM C13 CCL 0.34 ! | || +ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B +ATOM O13B OCL -0.67 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND N HN1 N HN2 N HN3 N C12 +BOND O13B C13 C13 C12 +DOUBLE C13 O13A +BOND C12 H12A C12 C11 C1 O11 +BOND C11 H11A C11 H11B C11 O12 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 C13 C12 O13B O13A + +!IC table from IC generate, minimized geometry +IC N C12 C11 O12 1.4892 110.33 60.56 112.04 1.4390 +IC N C12 C13 O13B 1.4892 109.53 -177.41 117.87 1.2553 +IC C11 N *C12 C13 1.5611 110.33 -123.90 109.53 1.5407 +IC C13 N *C12 H12A 1.5407 109.53 -116.02 108.38 1.0781 +IC HN1 N C12 C11 1.0454 110.41 -117.56 110.33 1.5611 +IC HN1 C12 *N HN2 1.0454 110.41 121.15 108.26 1.0580 +IC HN1 C12 *N HN3 1.0454 110.41 -120.80 103.02 1.0474 +IC O13B C12 *C13 O13A 1.2553 117.87 177.95 118.17 1.2648 +IC O12 C12 *C11 H11A 1.4390 112.04 -126.32 109.67 1.1172 +IC H11A C12 *C11 H11B 1.1172 109.67 -114.74 107.27 1.1147 +IC C12 C11 O12 P 1.5611 112.04 -98.86 120.96 1.5875 +IC C11 O12 P O11 1.4390 120.96 147.32 102.15 1.5764 +IC O11 O12 *P O13 1.5764 102.15 117.22 109.94 1.4724 +IC O11 O12 *P O14 1.5764 102.15 -112.56 106.22 1.4823 +IC O12 P O11 C1 1.5875 102.15 37.44 124.60 1.4242 +IC P O11 C1 C2 1.5764 124.60 -116.16 109.98 1.5498 +IC C2 O11 *C1 HA 1.5498 109.98 -117.32 107.50 1.1131 +IC HA O11 *C1 HB 1.1131 107.50 -118.29 113.74 1.1147 +IC O11 C1 C2 O21 1.4242 109.98 -146.90 108.63 1.4417 +IC O21 C1 *C2 C3 1.4417 108.63 -122.13 111.53 1.5568 !defines S chirality +IC C3 C1 *C2 HS 1.5568 111.53 -118.09 105.71 1.1179 !defines S chirality +IC C1 C2 O21 C21 1.5498 108.63 151.73 114.74 1.3222 +IC C2 O21 C21 C22 1.4417 114.74 173.79 108.64 1.5288 +IC C22 O21 *C21 O22 1.5288 108.64 -179.69 126.47 1.2177 +IC O21 C21 C22 C23 1.3222 108.64 178.90 112.26 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.26 -121.78 108.06 1.1089 +IC H2R C21 *C22 H2S 1.1089 108.06 -117.20 107.52 1.1095 +IC C1 C2 C3 O31 1.5498 111.53 -171.28 112.79 1.4438 +IC O31 C2 *C3 HX 1.4438 112.79 125.24 109.10 1.1078 +IC HX C2 *C3 HY 1.1078 109.10 114.68 107.27 1.1126 +IC C2 C3 O31 C31 1.5568 112.79 83.27 115.09 1.3297 +IC C3 O31 C31 C32 1.4438 115.09 -171.75 108.79 1.5271 +IC C32 O31 *C31 O32 1.5271 108.79 -178.65 125.65 1.2211 +IC O31 C31 C32 C33 1.3297 108.79 161.87 112.85 1.5450 +IC C33 C31 *C32 H2X 1.5450 112.85 -120.68 107.68 1.1109 +IC H2X C31 *C32 H2Y 1.1109 107.68 -117.29 107.91 1.1085 +IC C21 C22 C23 C24 1.5288 112.26 175.83 112.36 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.36 -120.78 109.67 1.1148 +IC H3R C22 *C23 H3S 1.1148 109.67 -117.71 109.57 1.1142 +IC C22 C23 C24 C25 1.5451 112.36 178.77 112.41 1.5346 +IC C25 C23 *C24 H4R 1.5346 112.41 -121.33 109.33 1.1132 +IC H4R C23 *C24 H4S 1.1132 109.33 -117.52 109.03 1.1133 +IC C23 C24 C25 C26 1.5338 112.41 176.76 112.74 1.5344 +IC C26 C24 *C25 H5R 1.5344 112.74 -121.22 109.09 1.1134 +IC H5R C24 *C25 H5S 1.1134 109.09 -117.24 108.99 1.1133 +IC C24 C25 C26 C27 1.5346 112.74 177.93 112.55 1.5355 +IC C27 C25 *C26 H6R 1.5355 112.55 -121.24 109.21 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.21 -117.45 108.99 1.1131 +IC C25 C26 C27 C28 1.5344 112.55 177.53 112.38 1.5395 +IC C28 C26 *C27 H7R 1.5395 112.38 -121.60 108.62 1.1136 +IC H7R C26 *C27 H7S 1.1136 108.62 -116.96 108.55 1.1141 +IC C26 C27 C28 C29 1.5355 112.38 179.04 111.48 1.5099 +IC C29 C27 *C28 H8R 1.5099 111.48 -123.40 107.63 1.1134 +IC H8R C27 *C28 H8S 1.1134 107.63 -115.31 108.46 1.1127 +IC C27 C28 C29 C210 1.5395 111.48 -124.52 126.42 1.3464 +IC C210 C28 *C29 H91 1.3464 126.42 178.24 114.73 1.1013 +IC C28 C29 C210 C211 1.5099 126.42 -1.71 126.08 1.5090 +IC C211 C29 *C210 H101 1.5090 126.08 -179.55 118.87 1.1011 +IC C29 C210 C211 C212 1.3464 126.08 89.09 112.29 1.5394 +IC C212 C210 *C211 H11R 1.5394 112.29 -121.07 111.01 1.1135 +IC H11R C210 *C211 H11S 1.1135 111.01 -117.45 110.16 1.1125 +IC C210 C211 C212 C213 1.5090 112.29 -176.91 112.28 1.5354 +IC C213 C211 *C212 H12R 1.5354 112.28 -121.60 109.80 1.1130 +IC H12R C211 *C212 H12S 1.1130 109.80 -117.99 109.42 1.1146 +IC C211 C212 C213 C214 1.5394 112.28 179.36 112.72 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.72 -121.06 108.92 1.1134 +IC H13R C212 *C213 H13S 1.1134 108.92 -117.38 109.19 1.1129 +IC C212 C213 C214 C215 1.5354 112.72 -178.89 112.54 1.5347 +IC C215 C213 *C214 H14R 1.5347 112.54 -121.45 109.16 1.1130 +IC H14R C213 *C214 H14S 1.1130 109.16 -117.40 109.07 1.1135 +IC C213 C214 C215 C216 1.5346 112.54 -180.00 112.69 1.5347 +IC C216 C214 *C215 H15R 1.5347 112.69 -121.21 109.00 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.00 -117.38 109.14 1.1130 +IC C214 C215 C216 C217 1.5347 112.69 -179.46 112.66 1.5341 +IC C217 C215 *C216 H16R 1.5341 112.66 -121.40 109.16 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.16 -117.37 109.09 1.1134 +IC C215 C216 C217 C218 1.5347 112.66 -179.98 113.32 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.32 -121.60 108.70 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.70 -116.66 108.79 1.1140 +IC C216 C217 C218 H18R 1.5341 113.32 -59.82 110.42 1.1115 +IC H18R C217 *C218 H18S 1.1115 110.42 119.85 110.47 1.1113 +IC H18R C217 *C218 H18T 1.1115 110.42 -120.03 110.61 1.1112 +IC C31 C32 C33 C34 1.5271 112.85 -177.68 111.59 1.5339 +IC C34 C32 *C33 H3X 1.5339 111.59 -121.61 110.20 1.1136 +IC H3X C32 *C33 H3Y 1.1136 110.20 -118.17 109.28 1.1150 +IC C32 C33 C34 C35 1.5450 111.59 176.03 113.15 1.5347 +IC C35 C33 *C34 H4X 1.5347 113.15 -120.89 108.78 1.1139 +IC H4X C33 *C34 H4Y 1.1139 108.78 -117.26 109.17 1.1131 +IC C33 C34 C35 C36 1.5339 113.15 -179.37 112.00 1.5345 +IC C36 C34 *C35 H5X 1.5345 112.00 -121.50 109.37 1.1129 +IC H5X C34 *C35 H5Y 1.1129 109.37 -117.56 109.01 1.1134 +IC C34 C35 C36 C37 1.5347 112.00 177.84 113.27 1.5346 +IC C37 C35 *C36 H6X 1.5346 113.27 -121.22 108.84 1.1135 +IC H6X C35 *C36 H6Y 1.1135 108.84 -117.10 108.96 1.1132 +IC C35 C36 C37 C38 1.5345 113.27 -179.66 111.94 1.5346 +IC C38 C36 *C37 H7X 1.5346 111.94 -121.33 109.26 1.1130 +IC H7X C36 *C37 H7Y 1.1130 109.26 -117.59 109.12 1.1132 +IC C36 C37 C38 C39 1.5346 111.94 179.12 113.27 1.5344 +IC C39 C37 *C38 H8X 1.5344 113.27 -121.37 108.89 1.1134 +IC H8X C37 *C38 H8Y 1.1134 108.89 -117.09 108.92 1.1134 +IC C37 C38 C39 C310 1.5346 113.27 -179.84 111.99 1.5347 +IC C310 C38 *C39 H9X 1.5347 111.99 -121.24 109.21 1.1130 +IC H9X C38 *C39 H9Y 1.1130 109.21 -117.59 109.19 1.1131 +IC C38 C39 C310 C311 1.5344 111.99 179.85 113.15 1.5343 +IC C311 C39 *C310 H10X 1.5343 113.15 -121.44 108.93 1.1134 +IC H10X C39 *C310 H10Y 1.1134 108.93 -117.13 108.92 1.1134 +IC C39 C310 C311 C312 1.5347 113.15 -179.98 112.17 1.5348 +IC C312 C310 *C311 H11X 1.5348 112.17 -121.21 109.15 1.1131 +IC H11X C310 *C311 H11Y 1.1131 109.15 -117.55 109.19 1.1131 +IC C310 C311 C312 C313 1.5343 112.17 -179.66 112.96 1.5343 +IC C313 C311 *C312 H12X 1.5343 112.96 -121.42 109.01 1.1133 +IC H12X C311 *C312 H12Y 1.1133 109.01 -117.23 109.00 1.1133 +IC C311 C312 C313 C314 1.5348 112.96 -179.93 112.38 1.5349 +IC C314 C312 *C313 H13X 1.5349 112.38 -121.24 109.09 1.1131 +IC H13X C312 *C313 H13Y 1.1131 109.09 -117.47 109.14 1.1131 +IC C312 C313 C314 C315 1.5343 112.38 -179.68 112.83 1.5337 +IC C315 C313 *C314 H14X 1.5337 112.83 -121.38 109.07 1.1133 +IC H14X C313 *C314 H14Y 1.1133 109.07 -117.29 109.07 1.1133 +IC C313 C314 C315 C316 1.5349 112.83 -179.98 113.22 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.22 -121.63 108.75 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.75 -116.70 108.78 1.1141 +IC C314 C315 C316 H16X 1.5337 113.22 -59.85 110.43 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.43 119.83 110.44 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.43 -120.08 110.63 1.1111 + +RESI POPA -1.00 ! 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidic acid +! +! Palmitoyl - CH2 +! | +! Oleyl - CH +! | (-) +! CH2 - PO4 - H +! +! Polar Head and glycerol backbone +GROUP ! H12 + ! | +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.82 ! \ / alpha3 +ATOM O14 O2L -0.82 ! P (+) +ATOM O12 OHL -0.68 ! / \ alpha2 +ATOM H12 HOL 0.34 ! (-) O14 O11 +ATOM O11 OSLP -0.62 ! | +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND O12 P P O11 P O13 P O14 +BOND O12 H12 O11 C1 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC H12 O12 P O11 0.9603 104.90 175.02 104.77 1.5790 +IC O12 O11 *P O13 1.5667 104.77 111.35 112.54 1.4699 +IC O12 O11 *P O14 1.5667 104.77 -111.29 111.81 1.4718 +IC O12 P O11 C1 1.5667 104.77 74.19 120.92 1.4311 +IC P O11 C1 C2 1.5790 120.92 -130.06 110.78 1.5478 +IC C2 O11 *C1 HA 1.5478 110.78 -120.11 109.49 1.1119 +IC HA O11 *C1 HB 1.1119 109.49 -119.44 112.98 1.1188 +IC O11 C1 C2 O21 1.4311 110.78 170.72 106.82 1.4423 +IC O21 C1 *C2 C3 1.4423 106.82 -120.90 110.73 1.5605 !defines S chirality +IC C3 C1 *C2 HS 1.5605 110.73 -118.02 107.55 1.1160 !defines S chirality +IC C1 C2 O21 C21 1.5478 106.82 152.06 115.88 1.3149 +IC C2 O21 C21 C22 1.4423 115.88 174.71 108.37 1.5300 +IC C22 O21 *C21 O22 1.5300 108.37 179.81 126.94 1.2175 +IC O21 C21 C22 C23 1.3149 108.37 -178.59 112.34 1.5450 +IC C23 C21 *C22 H2R 1.5450 112.34 -121.58 107.75 1.1090 +IC H2R C21 *C22 H2S 1.1090 107.75 -117.05 107.65 1.1093 +IC C1 C2 C3 O31 1.5478 110.73 171.60 113.11 1.4470 +IC O31 C2 *C3 HX 1.4470 113.11 126.56 109.07 1.1156 +IC HX C2 *C3 HY 1.1156 109.07 114.23 106.54 1.1130 +IC C2 C3 O31 C31 1.5605 113.11 86.70 115.13 1.3282 +IC C3 O31 C31 C32 1.4470 115.13 -175.02 108.29 1.5304 +IC C32 O31 *C31 O32 1.5304 108.29 -179.30 126.46 1.2152 +IC O31 C31 C32 C33 1.3282 108.29 178.67 112.57 1.5449 +IC C33 C31 *C32 H2X 1.5449 112.57 -120.87 107.35 1.1099 +IC H2X C31 *C32 H2Y 1.1099 107.35 -117.25 107.83 1.1084 +IC C21 C22 C23 C24 1.5300 112.34 179.69 112.29 1.5338 +IC C24 C22 *C23 H3R 1.5338 112.29 -121.16 109.58 1.1143 +IC H3R C22 *C23 H3S 1.1143 109.58 -117.64 109.55 1.1144 +IC C22 C23 C24 C25 1.5450 112.29 179.90 112.52 1.5347 +IC C25 C23 *C24 H4R 1.5347 112.52 -121.27 109.11 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.11 -117.44 109.11 1.1133 +IC C23 C24 C25 C26 1.5338 112.52 179.93 112.62 1.5345 +IC C26 C24 *C25 H5R 1.5345 112.62 -121.39 109.04 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.04 -117.27 109.05 1.1133 +IC C24 C25 C26 C27 1.5347 112.62 -179.86 112.65 1.5355 +IC C27 C25 *C26 H6R 1.5355 112.65 -121.31 109.06 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.06 -117.35 109.04 1.1131 +IC C25 C26 C27 C28 1.5345 112.65 179.79 112.33 1.5397 +IC C28 C26 *C27 H7R 1.5397 112.33 -121.64 108.44 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.44 -116.96 108.77 1.1140 +IC C26 C27 C28 C29 1.5355 112.33 -177.65 111.53 1.5098 +IC C29 C27 *C28 H8R 1.5098 111.53 -123.76 107.67 1.1128 +IC H8R C27 *C28 H8S 1.1128 107.67 -115.16 108.45 1.1128 +IC C27 C28 C29 C210 1.5397 111.53 -118.93 126.95 1.3468 +IC C210 C28 *C29 H91 1.3468 126.95 178.64 114.42 1.1012 +IC C28 C29 C210 C211 1.5098 126.95 -1.06 126.70 1.5093 +IC C211 C29 *C210 H101 1.5093 126.70 179.97 118.62 1.1011 +IC C29 C210 C211 C212 1.3468 126.70 96.43 111.97 1.5393 +IC C212 C210 *C211 H11R 1.5393 111.97 -121.33 111.63 1.1129 +IC H11R C210 *C211 H11S 1.1129 111.63 -117.66 109.97 1.1125 +IC C210 C211 C212 C213 1.5093 111.97 -179.20 112.31 1.5355 +IC C213 C211 *C212 H12R 1.5355 112.31 -121.28 109.77 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.77 -118.03 109.44 1.1145 +IC C211 C212 C213 C214 1.5393 112.31 -179.38 112.67 1.5346 +IC C214 C212 *C213 H13R 1.5346 112.67 -121.30 109.02 1.1133 +IC H13R C212 *C213 H13S 1.1133 109.02 -117.38 109.09 1.1129 +IC C212 C213 C214 C215 1.5355 112.67 179.76 112.66 1.5349 +IC C215 C213 *C214 H14R 1.5349 112.66 -121.34 109.11 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.11 -117.34 109.05 1.1134 +IC C213 C214 C215 C216 1.5346 112.66 -179.43 112.59 1.5348 +IC C216 C214 *C215 H15R 1.5348 112.59 -121.30 109.06 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.06 -117.41 109.12 1.1130 +IC C214 C215 C216 C217 1.5349 112.59 -179.92 112.76 1.5340 +IC C217 C215 *C216 H16R 1.5340 112.76 -121.38 109.12 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.12 -117.32 109.09 1.1134 +IC C215 C216 C217 C218 1.5348 112.76 -179.79 113.22 1.5309 +IC C218 C216 *C217 H17R 1.5309 113.22 -121.60 108.73 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.73 -116.70 108.81 1.1140 +IC C216 C217 C218 H18R 1.5340 113.22 -59.81 110.41 1.1115 +IC H18R C217 *C218 H18S 1.1115 110.41 119.81 110.47 1.1113 +IC H18R C217 *C218 H18T 1.1115 110.41 -120.04 110.64 1.1111 +IC C31 C32 C33 C34 1.5304 112.57 -179.65 112.12 1.5339 +IC C34 C32 *C33 H3X 1.5339 112.12 -121.49 109.73 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.73 -117.57 109.29 1.1149 +IC C32 C33 C34 C35 1.5449 112.12 179.11 112.65 1.5346 +IC C35 C33 *C34 H4X 1.5346 112.65 -121.15 108.95 1.1134 +IC H4X C33 *C34 H4Y 1.1134 108.95 -117.42 109.10 1.1130 +IC C33 C34 C35 C36 1.5339 112.65 179.84 112.55 1.5345 +IC C36 C34 *C35 H5X 1.5345 112.55 -121.46 109.09 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.09 -117.21 108.95 1.1134 +IC C34 C35 C36 C37 1.5346 112.55 179.40 112.70 1.5345 +IC C37 C35 *C36 H6X 1.5345 112.70 -121.28 108.98 1.1132 +IC H6X C35 *C36 H6Y 1.1132 108.98 -117.31 109.01 1.1131 +IC C35 C36 C37 C38 1.5345 112.70 179.82 112.55 1.5346 +IC C38 C36 *C37 H7X 1.5346 112.55 -121.38 109.08 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.08 -117.30 109.01 1.1133 +IC C36 C37 C38 C39 1.5345 112.55 179.54 112.66 1.5345 +IC C39 C37 *C38 H8X 1.5345 112.66 -121.30 109.03 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.03 -117.33 109.03 1.1132 +IC C37 C38 C39 C310 1.5346 112.66 179.81 112.56 1.5345 +IC C310 C38 *C39 H9X 1.5345 112.56 -121.34 109.08 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.08 -117.34 109.04 1.1133 +IC C38 C39 C310 C311 1.5345 112.56 179.67 112.65 1.5345 +IC C311 C39 *C310 H10X 1.5345 112.65 -121.31 109.06 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.06 -117.34 109.05 1.1132 +IC C39 C310 C311 C312 1.5345 112.65 179.83 112.56 1.5345 +IC C312 C310 *C311 H11X 1.5345 112.56 -121.33 109.09 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.09 -117.36 109.07 1.1132 +IC C310 C311 C312 C313 1.5345 112.56 179.76 112.66 1.5345 +IC C313 C311 *C312 H12X 1.5345 112.66 -121.31 109.07 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.07 -117.35 109.06 1.1132 +IC C311 C312 C313 C314 1.5345 112.66 179.88 112.58 1.5347 +IC C314 C312 *C313 H13X 1.5347 112.58 -121.32 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.37 109.07 1.1132 +IC C312 C313 C314 C315 1.5345 112.58 179.85 112.70 1.5339 +IC C315 C313 *C314 H14X 1.5339 112.70 -121.32 109.10 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.10 -117.34 109.09 1.1132 +IC C313 C314 C315 C316 1.5347 112.70 179.95 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.74 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.74 -116.64 108.74 1.1141 +IC C314 C315 C316 H16X 1.5339 113.30 -59.96 110.44 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.44 119.85 110.44 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.44 -120.07 110.60 1.1112 + +RESI POPG -1.00 ! 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidylglycerol +! +! Palmitoyl - CH2 +! | +! Oleoyl- CH +! | +! CH2 - PO4 - CH2 - CH(OH) - CH2OH +! +! Polar Head and glycerol backbone +GROUP ! +ATOM C13 CTL2 0.05 ! +ATOM H13A HAL2 0.09 ! H13A +ATOM H13B HAL2 0.09 ! | +ATOM OC3 OHL -0.65 ! | +ATOM HO3 HOL 0.42 ! H13B--C13---OC3--HO3 +GROUP ! | +ATOM C12 CTL1 0.14 ! | +ATOM H12A HAL1 0.09 ! | +ATOM OC2 OHL -0.65 ! H12A--C12---OC2--HO2 +ATOM HO2 HOL 0.42 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL3 -0.27 ! | +ATOM H16X HAL3 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL3 0.09 ! | +ATOM H16Z HAL3 0.09 ! H16Z + +! Polar Head +BOND HO3 OC3 OC3 C13 C13 H13A C13 H13B C13 C12 +BOND HO2 OC2 OC2 C12 C12 H12A C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 H16Z + +IMPR C21 O21 C22 O22 C31 O31 C32 O32 + +!IC table from IC generate, minimized geometry +IC C13 C12 C11 O12 1.5527 112.85 -172.43 115.75 1.4326 +IC OC3 C13 C12 C11 1.4270 111.28 66.71 112.85 1.5633 +IC C11 C13 *C12 OC2 1.5633 112.85 -123.90 110.15 1.4283 +IC OC3 C12 *C13 H13A 1.4270 111.28 119.84 108.43 1.1124 +IC OC3 C12 *C13 H13B 1.4270 111.28 -121.62 109.64 1.1108 +IC C12 C13 OC3 HO3 1.5527 111.28 31.95 102.00 0.9699 +IC OC2 C13 *C12 H12A 1.4283 110.15 -117.28 107.28 1.1148 +IC C13 C12 OC2 HO2 1.5527 110.15 -171.78 103.00 0.9822 +IC O12 C12 *C11 H11A 1.4326 115.75 -123.85 108.44 1.1130 +IC H11A C12 *C11 H11B 1.1130 108.44 -115.56 107.30 1.1122 +IC C12 C11 O12 P 1.5633 115.75 -47.69 121.24 1.5793 +IC C11 O12 P O11 1.4326 121.24 -163.05 101.81 1.5842 +IC O11 O12 *P O13 1.5842 101.81 115.87 108.46 1.4772 +IC O11 O12 *P O14 1.5842 101.81 -115.89 106.55 1.4794 +IC O12 P O11 C1 1.5793 101.81 52.06 120.97 1.4307 +IC P O11 C1 C2 1.5842 120.97 -123.35 111.16 1.5486 +IC C2 O11 *C1 HA 1.5486 111.16 -119.56 109.11 1.1121 +IC HA O11 *C1 HB 1.1121 109.11 -119.08 113.21 1.1182 +IC O11 C1 C2 O21 1.4307 111.16 174.21 106.66 1.4420 +IC O21 C1 *C2 C3 1.4420 106.66 -120.98 111.16 1.5605 !defines S chirality +IC C3 C1 *C2 HS 1.5605 111.16 -118.20 107.43 1.1163 !defines S chirality +IC C1 C2 O21 C21 1.5486 106.66 151.72 115.89 1.3162 +IC C2 O21 C21 C22 1.4420 115.89 174.64 108.39 1.5300 +IC C22 O21 *C21 O22 1.5300 108.39 179.62 126.87 1.2174 +IC O21 C21 C22 C23 1.3162 108.39 -178.91 112.40 1.5451 +IC C23 C21 *C22 H2R 1.5451 112.40 -121.55 107.75 1.1090 +IC H2R C21 *C22 H2S 1.1090 107.75 -117.07 107.65 1.1094 +IC C1 C2 C3 O31 1.5486 111.16 173.26 113.08 1.4465 +IC O31 C2 *C3 HX 1.4465 113.08 126.36 109.19 1.1155 +IC HX C2 *C3 HY 1.1155 109.19 114.42 106.70 1.1130 +IC C2 C3 O31 C31 1.5605 113.08 85.33 114.98 1.3287 +IC C3 O31 C31 C32 1.4465 114.98 -175.76 108.36 1.5299 +IC C32 O31 *C31 O32 1.5299 108.36 -179.46 126.35 1.2156 +IC O31 C31 C32 C33 1.3287 108.36 179.34 112.58 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.58 -120.90 107.34 1.1099 +IC H2X C31 *C32 H2Y 1.1099 107.34 -117.24 107.84 1.1085 +IC C21 C22 C23 C24 1.5300 112.40 179.84 112.28 1.5340 +IC C24 C22 *C23 H3R 1.5340 112.28 -121.15 109.56 1.1144 +IC H3R C22 *C23 H3S 1.1144 109.56 -117.66 109.59 1.1144 +IC C22 C23 C24 C25 1.5451 112.28 -179.93 112.52 1.5348 +IC C25 C23 *C24 H4R 1.5348 112.52 -121.28 109.14 1.1133 +IC H4R C23 *C24 H4S 1.1133 109.14 -117.44 109.11 1.1133 +IC C23 C24 C25 C26 1.5340 112.52 179.89 112.69 1.5347 +IC C26 C24 *C25 H5R 1.5347 112.69 -121.36 109.01 1.1132 +IC H5R C24 *C25 H5S 1.1132 109.01 -117.25 109.07 1.1133 +IC C24 C25 C26 C27 1.5348 112.69 -179.62 112.61 1.5356 +IC C27 C25 *C26 H6R 1.5356 112.61 -121.31 109.08 1.1132 +IC H6R C25 *C26 H6S 1.1132 109.08 -117.38 109.05 1.1131 +IC C25 C26 C27 C28 1.5347 112.61 179.89 112.39 1.5398 +IC C28 C26 *C27 H7R 1.5398 112.39 -121.64 108.41 1.1137 +IC H7R C26 *C27 H7S 1.1137 108.41 -116.93 108.78 1.1140 +IC C26 C27 C28 C29 1.5356 112.39 -177.47 111.53 1.5098 +IC C29 C27 *C28 H8R 1.5098 111.53 -123.70 107.68 1.1128 +IC H8R C27 *C28 H8S 1.1128 107.68 -115.21 108.48 1.1128 +IC C27 C28 C29 C210 1.5398 111.53 -118.23 126.87 1.3467 +IC C210 C28 *C29 H91 1.3467 126.87 178.64 114.46 1.1012 +IC C28 C29 C210 C211 1.5098 126.87 -1.03 126.59 1.5093 +IC C211 C29 *C210 H101 1.5093 126.59 179.83 118.67 1.1011 +IC C29 C210 C211 C212 1.3467 126.59 93.85 111.91 1.5393 +IC C212 C210 *C211 H11R 1.5393 111.91 -121.29 111.52 1.1130 +IC H11R C210 *C211 H11S 1.1130 111.52 -117.67 110.00 1.1125 +IC C210 C211 C212 C213 1.5093 111.91 -179.44 112.42 1.5355 +IC C213 C211 *C212 H12R 1.5355 112.42 -121.31 109.78 1.1133 +IC H12R C211 *C212 H12S 1.1133 109.78 -117.99 109.39 1.1145 +IC C211 C212 C213 C214 1.5393 112.42 -179.85 112.61 1.5347 +IC C214 C212 *C213 H13R 1.5347 112.61 -121.24 109.06 1.1133 +IC H13R C212 *C213 H13S 1.1133 109.06 -117.42 109.11 1.1129 +IC C212 C213 C214 C215 1.5355 112.61 179.58 112.66 1.5348 +IC C215 C213 *C214 H14R 1.5348 112.66 -121.34 109.11 1.1131 +IC H14R C213 *C214 H14S 1.1131 109.11 -117.35 109.06 1.1134 +IC C213 C214 C215 C216 1.5347 112.66 -179.86 112.61 1.5349 +IC C216 C214 *C215 H15R 1.5349 112.61 -121.26 109.07 1.1133 +IC H15R C214 *C215 H15S 1.1133 109.07 -117.41 109.12 1.1130 +IC C214 C215 C216 C217 1.5348 112.61 179.90 112.71 1.5340 +IC C217 C215 *C216 H16R 1.5340 112.71 -121.38 109.14 1.1131 +IC H16R C215 *C216 H16S 1.1131 109.14 -117.33 109.09 1.1134 +IC C215 C216 C217 C218 1.5349 112.71 180.00 113.31 1.5310 +IC C218 C216 *C217 H17R 1.5310 113.31 -121.61 108.71 1.1142 +IC H17R C216 *C217 H17S 1.1142 108.71 -116.68 108.78 1.1140 +IC C216 C217 C218 H18R 1.5340 113.31 -59.87 110.43 1.1115 +IC H18R C217 *C218 H18S 1.1115 110.43 119.84 110.48 1.1112 +IC H18R C217 *C218 H18T 1.1115 110.43 -120.02 110.62 1.1112 +IC C31 C32 C33 C34 1.5299 112.58 -179.46 112.10 1.5339 +IC C34 C32 *C33 H3X 1.5339 112.10 -121.48 109.72 1.1140 +IC H3X C32 *C33 H3Y 1.1140 109.72 -117.58 109.31 1.1149 +IC C32 C33 C34 C35 1.5448 112.10 179.21 112.66 1.5346 +IC C35 C33 *C34 H4X 1.5346 112.66 -121.16 108.94 1.1134 +IC H4X C33 *C34 H4Y 1.1134 108.94 -117.41 109.10 1.1130 +IC C33 C34 C35 C36 1.5339 112.66 -179.91 112.56 1.5346 +IC C36 C34 *C35 H5X 1.5346 112.56 -121.46 109.07 1.1132 +IC H5X C34 *C35 H5Y 1.1132 109.07 -117.21 108.96 1.1134 +IC C34 C35 C36 C37 1.5346 112.56 179.56 112.70 1.5346 +IC C37 C35 *C36 H6X 1.5346 112.70 -121.29 108.98 1.1132 +IC H6X C35 *C36 H6Y 1.1132 108.98 -117.32 109.02 1.1131 +IC C35 C36 C37 C38 1.5346 112.70 179.89 112.56 1.5347 +IC C38 C36 *C37 H7X 1.5347 112.56 -121.38 109.07 1.1132 +IC H7X C36 *C37 H7Y 1.1132 109.07 -117.30 109.01 1.1133 +IC C36 C37 C38 C39 1.5346 112.56 179.63 112.69 1.5346 +IC C39 C37 *C38 H8X 1.5346 112.69 -121.30 109.02 1.1132 +IC H8X C37 *C38 H8Y 1.1132 109.02 -117.33 109.03 1.1132 +IC C37 C38 C39 C310 1.5347 112.69 179.94 112.58 1.5346 +IC C310 C38 *C39 H9X 1.5346 112.58 -121.36 109.09 1.1132 +IC H9X C38 *C39 H9Y 1.1132 109.09 -117.34 109.04 1.1132 +IC C38 C39 C310 C311 1.5346 112.58 179.62 112.67 1.5346 +IC C311 C39 *C310 H10X 1.5346 112.67 -121.29 109.04 1.1132 +IC H10X C39 *C310 H10Y 1.1132 109.04 -117.34 109.06 1.1132 +IC C39 C310 C311 C312 1.5346 112.67 -179.93 112.59 1.5346 +IC C312 C310 *C311 H11X 1.5346 112.59 -121.36 109.10 1.1132 +IC H11X C310 *C311 H11Y 1.1132 109.10 -117.36 109.05 1.1132 +IC C310 C311 C312 C313 1.5346 112.59 179.64 112.65 1.5346 +IC C313 C311 *C312 H12X 1.5346 112.65 -121.28 109.06 1.1132 +IC H12X C311 *C312 H12Y 1.1132 109.06 -117.36 109.08 1.1132 +IC C311 C312 C313 C314 1.5346 112.65 -179.95 112.60 1.5348 +IC C314 C312 *C313 H13X 1.5348 112.60 -121.34 109.09 1.1132 +IC H13X C312 *C313 H13Y 1.1132 109.09 -117.37 109.06 1.1132 +IC C312 C313 C314 C315 1.5346 112.60 179.75 112.70 1.5339 +IC C315 C313 *C314 H14X 1.5339 112.70 -121.31 109.09 1.1132 +IC H14X C313 *C314 H14Y 1.1132 109.09 -117.35 109.10 1.1132 +IC C313 C314 C315 C316 1.5348 112.70 179.98 113.30 1.5309 +IC C316 C314 *C315 H15X 1.5309 113.30 -121.68 108.75 1.1141 +IC H15X C314 *C315 H15Y 1.1141 108.75 -116.64 108.73 1.1141 +IC C314 C315 C316 H16X 1.5339 113.30 -59.99 110.44 1.1113 +IC H16X C315 *C316 H16Y 1.1113 110.44 119.85 110.44 1.1113 +IC H16X C315 *C316 H16Z 1.1113 110.44 -120.07 110.60 1.1112 + +RESI SAPC 0.00 ! 3-stearoyl-2-arachidonyl-D-glycero-1-phosphatidylcholine +! +! Stearoyl - CH2 +! | +! Arachidonyl - CH +! | (-) (+) +! CH2 - PO4 - CH2 - CH2 - N-(CH3)3 +! Polar Head and glycerol backbone +! +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C12 CTL2 -0.10 ! H15A-C15-H15C +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H13B | H14A +ATOM C13 CTL5 -0.35 ! | | | +ATOM H13A HL 0.25 ! H13A-C13----N----C14-H14B (+) +ATOM H13B HL 0.25 ! | | | +ATOM H13C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | +ATOM H14A HL 0.25 ! | +ATOM H14B HL 0.25 ! | alpha6 +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H12A--C12---H12B +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CEL1 -0.15 ! | | +ATOM H5R HEL1 0.15 ! H5R ---C25 | +GROUP ! |! (CIS) | +ATOM C26 CEL1 -0.15 ! |! | +ATOM H6R HEL1 0.15 ! H6R ---C26 | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CEL1 -0.15 ! | | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! |! (CIS) | +ATOM C29 CEL1 -0.15 ! |! | +ATOM H9R HEL1 0.15 ! H9R ---C29 | +GROUP ! | | +ATOM C210 CTL2 -0.18 ! | | +ATOM H10R HAL2 0.09 ! H10R---C210--H10S | +ATOM H10S HAL2 0.09 ! | | +GROUP ! | | +ATOM C211 CEL1 -0.15 ! | | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! |! (CIS) | +ATOM C212 CEL1 -0.15 ! |! | +ATOM H12R HEL1 0.15 ! H12R---C212 | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CEL1 -0.15 ! | | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! |! (CIS) | +ATOM C215 CEL1 -0.15 ! |! | +ATOM H15R HEL1 0.15 ! H15R---C215 | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL2 -0.27 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CTL2 -0.18 ! | | +ATOM H19R HAL2 0.09 ! H19R---C219--H19S | +ATOM H19S HAL2 0.09 ! | | +GROUP ! | | +ATOM C220 CTL3 -0.18 ! | | +ATOM H20R HAL3 0.09 ! H20R---C220--H20S | +ATOM H20S HAL3 0.09 ! | | +ATOM H20T HAL3 0.09 ! H20T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R +DOUBLE C25 C26 +BOND C26 H6R C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R +DOUBLE C28 C29 +BOND C29 H9R C29 C210 +BOND C210 H10R C210 H10S C210 C211 +BOND C211 H11R +DOUBLE C211 C212 +BOND C212 H12R C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R +DOUBLE C214 C215 +BOND C215 H15R C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R C219 H19S C219 C220 +BOND C220 H20R C220 H20S C220 H20T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +!IC table from IC generate, geometry is guessed +IC C13 N C12 C11 1.4894 108.75 169.53 117.05 1.5301 +IC C13 C12 *N C14 1.4894 108.75 116.38 106.66 1.5005 +IC C13 C12 *N C15 1.4894 108.75 -122.91 111.69 1.4923 +IC C11 N *C12 H12A 1.5301 117.05 -126.36 111.92 1.0785 +IC H12A N *C12 H12B 1.0785 111.92 -115.08 107.27 1.0941 +IC C14 N C13 H13A 1.5005 108.12 58.37 111.66 1.0796 +IC H13A N *C13 H13B 1.0796 111.66 122.61 111.57 1.0840 +IC H13A N *C13 H13C 1.0796 111.66 -119.50 108.70 1.0918 +IC C13 N C14 H14A 1.4894 108.12 166.58 110.73 1.0972 +IC H14A N *C14 H14B 1.0972 110.73 123.94 113.75 1.0745 +IC H14A N *C14 H14C 1.0972 110.73 -112.48 110.16 1.0903 +IC C13 N C15 H15A 1.4894 111.05 59.17 110.92 1.0811 +IC H15A N *C15 H15B 1.0811 110.92 119.25 109.28 1.0863 +IC H15A N *C15 H15C 1.0811 110.92 -121.78 110.77 1.0814 +IC N C12 C11 O12 1.5138 117.05 141.06 105.81 1.4195 +IC O12 C12 *C11 H11A 1.4195 105.81 -123.27 113.13 1.1166 +IC H11A C12 *C11 H11B 1.1166 113.13 -119.01 109.98 1.1100 +IC C12 C11 O12 P 1.5301 105.81 -96.66 119.22 1.5958 +IC C11 O12 P O11 1.4195 119.22 146.34 101.18 1.5867 +IC O11 O12 *P O13 1.5867 101.18 -114.47 107.73 1.4832 +IC O11 O12 *P O14 1.5867 101.18 116.82 109.30 1.4741 +IC O12 P O11 C1 1.5958 101.18 -87.51 122.31 1.4271 +IC P O11 C1 C2 1.5867 122.31 99.45 111.45 1.5517 +IC C2 O11 *C1 HA 1.5517 111.45 117.99 107.86 1.1119 +IC HA O11 *C1 HB 1.1119 107.86 116.85 112.59 1.1137 +IC O11 C1 C2 O21 1.4271 111.45 -175.58 109.40 1.4420 +IC O21 C1 *C2 C3 1.4420 109.40 -121.10 110.56 1.5561 +IC C3 C1 *C2 HS 1.5561 110.56 -116.88 109.10 1.1148 +IC C1 C2 O21 C21 1.5517 109.40 75.31 115.18 1.3240 +IC C2 O21 C21 C22 1.4420 115.18 -167.64 109.38 1.5349 +IC C22 O21 *C21 O22 1.5349 109.38 177.97 125.87 1.2208 +IC O21 C21 C22 C23 1.3240 109.38 -106.88 114.46 1.5510 +IC C23 C21 *C22 H2R 1.5510 114.46 120.85 107.59 1.1114 +IC H2R C21 *C22 H2S 1.1114 107.59 115.88 108.08 1.1076 +IC C1 C2 C3 O31 1.5517 110.56 -174.46 111.33 1.4462 +IC O31 C2 *C3 HX 1.4462 111.33 -122.32 107.11 1.1154 +IC HX C2 *C3 HY 1.1154 107.11 -116.45 107.97 1.1151 +IC C2 C3 O31 C31 1.5561 111.33 -170.38 113.09 1.3331 +IC C3 O31 C31 C32 1.4462 113.09 -178.75 108.33 1.5405 +IC C32 O31 *C31 O32 1.5405 108.33 -179.57 125.60 1.2151 +IC O31 C31 C32 C33 1.3331 108.33 -179.15 116.85 1.6060 +IC C33 C31 *C32 H2X 1.6060 116.85 -121.70 105.08 1.1113 +IC H2X C31 *C32 H2Y 1.1113 105.08 -115.26 107.43 1.1071 +IC C21 C22 C23 C24 1.5329 113.78 180.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 !cis db +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 180.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 180.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 !cis db +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 180.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 180.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 !cis db +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 180.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 180.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 !cis db +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SDPC 0.00 ! 3-stearoyl-2-docosahexaenoyl-D-glycero-1-phosphatidylcholine +! +! Stearoyl - CH2 +! | +! Docosahexaenoyl - CH +! | (-) (+) +! CH2 - PO4 - CH2 - CH2 - N-(CH3)3 +! +! Polar Head and glycerol backbone +! +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C12 CTL2 -0.10 ! H15A-C15-H15C +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H13B | H14A +ATOM C13 CTL5 -0.35 ! | | | +ATOM H13A HL 0.25 ! H13A-C13----N----C14-H14B (+) +ATOM H13B HL 0.25 ! | | | +ATOM H13C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | +ATOM H14A HL 0.25 ! | +ATOM H14B HL 0.25 ! | alpha6 +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H12A--C12---H12B +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CEL1 -0.15 ! | | +ATOM H4R HEL1 0.15 ! H4R ---C24 | +GROUP ! |! (CIS) | +ATOM C25 CEL1 -0.15 ! |! | +ATOM H5R HEL1 0.15 ! H4R ---C25 | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CEL1 -0.15 ! | | +ATOM H7R HEL1 0.15 ! H7R ---C27 | +GROUP ! |! (CIS) | +ATOM C28 CEL1 -0.15 ! |! | +ATOM H8R HEL1 0.15 ! H8R ---C28 | +GROUP ! | | +ATOM C29 CTL2 -0.18 ! | | +ATOM H9R HAL2 0.09 ! H9R----C29---H9S | +ATOM H9S HAL2 0.09 ! | | +GROUP ! | | +ATOM C210 CEL1 -0.15 ! | | +ATOM H10R HEL1 0.15 ! H10R---C210 | +GROUP ! |! (CIS) | +ATOM C211 CEL1 -0.15 ! |! | +ATOM H11R HEL1 0.15 ! H11R---C211 | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CEL1 -0.15 ! | | +ATOM H13R HEL1 0.15 ! H13R---C213 | +GROUP ! |! (CIS) | +ATOM C214 CEL1 -0.15 ! |! | +ATOM H14R HEL1 0.15 ! H14R---C214 | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CEL1 -0.15 ! | | +ATOM H16R HEL1 0.15 ! H16R---C216 | +GROUP ! |! (CIS) | +ATOM C217 CEL1 -0.15 ! |! | +ATOM H17R HEL1 0.15 ! H17R---C217 | +GROUP ! | | +ATOM C218 CTL2 -0.18 ! | | +ATOM H18R HAL2 0.09 ! H18R---C218--H18S | +ATOM H18S HAL2 0.09 ! | | +GROUP ! | | +ATOM C219 CEL1 -0.15 ! | | +ATOM H19R HEL1 0.15 ! H19R---C219 | +GROUP ! |! (CIS) | +ATOM C220 CEL1 -0.15 ! |! | +ATOM H20R HEL1 0.15 ! H20R---C220 | +GROUP ! | | +ATOM C221 CTL2 -0.18 ! | | +ATOM H21R HAL2 0.09 ! H21R---C221--H21S | +ATOM H21S HAL2 0.09 ! | | +GROUP ! | | +ATOM C222 CTL3 -0.27 ! | | +ATOM H22R HAL3 0.09 ! H22R---C222--H22S | +ATOM H22S HAL3 0.09 ! | | +ATOM H22T HAL3 0.09 ! H22T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R +DOUBLE C24 C25 +BOND C25 H5R C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R +DOUBLE C27 C28 +BOND C28 H8R C28 C29 +BOND C29 H9R C29 H9S C29 C210 +BOND C210 H10R +DOUBLE C210 C211 +BOND C211 H11R C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R +DOUBLE C213 C214 +BOND C214 H14R C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R +DOUBLE C216 C217 +BOND C217 H17R C217 C218 +BOND C218 H18R C218 H18S C218 C219 +BOND C219 H19R +DOUBLE C219 C220 +BOND C220 H20R C220 C221 +BOND C221 H21R C221 H21S C221 C222 +BOND C222 H22R C222 H22S C222 H22T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +!IC table from IC generate, geometry is guessed +IC C13 N C12 C11 1.5025 109.38 -75.54 119.27 1.5529 +IC C13 C12 *N C14 1.5025 109.38 118.57 109.88 1.5014 +IC C13 C12 *N C15 1.5025 109.38 -120.06 111.03 1.4969 +IC C11 N *C12 H12A 1.5529 119.27 -122.46 108.90 1.0813 +IC C11 N *C12 H12B 1.5529 119.27 122.46 108.90 1.0813 +IC C14 N C13 H13A 1.5014 108.14 54.63 112.42 1.0793 +IC H13A N *C13 H13B 1.0793 112.42 124.95 112.66 1.0787 +IC H13A N *C13 H13C 1.0793 112.42 -117.33 109.87 1.0973 +IC C13 N C14 H14A 1.5025 108.14 179.71 112.53 1.0782 +IC H14A N *C14 H14B 1.0782 112.53 -117.73 109.58 1.0984 +IC H14A N *C14 H14C 1.0782 112.53 124.81 112.18 1.0792 +IC C13 N C15 H15A 1.5025 108.78 58.26 110.07 1.0842 +IC H15A N *C15 H15B 1.0842 110.07 119.38 111.02 1.0824 +IC H15A N *C15 H15C 1.0842 110.07 -119.39 110.90 1.0828 +IC N C12 C11 O12 1.5261 119.27 61.50 111.44 1.4207 +IC O12 C12 *C11 H11A 1.4207 111.44 -127.11 110.31 1.1153 +IC O12 C12 *C11 H11B 1.5529 119.27 122.46 108.90 1.0813 +IC C12 C11 O12 P 1.5529 111.44 -110.28 123.53 1.5856 +IC C11 O12 P O11 1.4207 123.53 -117.07 102.54 1.5781 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5347 115.21 180.00 110.44 1.5096 +IC C24 C22 *C23 H3R 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C22 *C23 H3S 1.5192 121.35 123.34 106.97 1.1128 +IC C22 C23 C24 C25 1.5530 110.44 180.00 127.08 1.3487 +IC C25 C23 *C24 H4R 1.3487 127.08 180.00 114.44 1.1010 +IC C23 C24 C25 C26 1.5096 127.08 0.00 127.17 1.5116 !cis db +IC C26 C24 *C25 H5R 1.5116 127.17 179.68 118.27 1.1015 +IC C24 C25 C26 C27 1.3487 127.17 180.00 111.97 1.5099 +IC C27 C25 *C26 H6R 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C25 *C26 H6S 1.5192 121.35 123.34 106.97 1.1128 +IC C25 C26 C27 C28 1.5116 111.97 180.00 126.68 1.3492 +IC C28 C26 *C27 H7R 1.3492 126.68 178.47 114.82 1.1014 +IC C26 C27 C28 C29 1.5099 126.68 0.00 126.94 1.5099 !cis db +IC C29 C27 *C28 H8R 1.5099 126.94 -177.42 118.69 1.1018 +IC C27 C28 C29 C210 1.3492 126.94 180.00 111.95 1.5084 +IC C210 C28 *C29 H9R 1.5396 113.52 -123.43 110.53 1.1101 +IC C210 C28 *C29 H9S 1.5192 121.35 123.34 106.97 1.1128 +IC C28 C29 C210 C211 1.5099 111.95 180.00 126.47 1.3485 +IC C211 C29 *C210 H10R 1.3453 125.97 -176.85 115.39 1.1011 +IC C29 C210 C211 C212 1.5084 126.47 0.00 127.07 1.5122 !cis db +IC C212 C210 *C211 H11R 1.5097 125.28 178.19 119.65 1.1004 +IC C210 C211 C212 C213 1.3485 127.07 180.00 112.04 1.5115 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5192 121.35 123.34 106.97 1.1128 +IC C211 C212 C213 C214 1.5122 112.04 180.00 126.62 1.3479 +IC C214 C212 *C213 H13R 1.3453 125.97 -176.85 115.39 1.1011 +IC C212 C213 C214 C215 1.5115 126.62 0.00 127.02 1.5107 !cis db +IC C215 C213 *C214 H14R 1.5097 125.28 178.19 119.65 1.1004 +IC C213 C214 C215 C216 1.3479 127.02 180.00 112.92 1.5093 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5192 121.35 123.34 106.97 1.1128 +IC C214 C215 C216 C217 1.5107 112.92 180.00 124.28 1.3467 +IC C217 C215 *C216 H16R 1.3453 125.97 -176.85 115.39 1.1011 +IC C215 C216 C217 C218 1.5093 124.28 0.00 126.43 1.5125 !cis db +IC C218 C216 *C217 H17R 1.5097 125.28 178.19 119.65 1.1004 +IC C216 C217 C218 C219 1.3467 126.43 180.00 116.29 1.5121 +IC C219 C217 *C218 H18R 1.5396 113.52 -123.43 110.53 1.1101 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5125 116.29 180.00 124.57 1.3458 +IC C220 C218 *C219 H19R 1.3453 125.97 -176.85 115.39 1.1011 +IC C218 C219 C220 C221 1.5121 124.57 0.00 126.91 1.5106 !cis db +IC C221 C219 *C220 H20R 1.5097 125.28 178.19 119.65 1.1004 +IC C219 C220 C221 C222 1.3458 126.91 0.74 115.89 1.5382 +IC C222 C220 *C221 H21R 1.5396 113.52 -123.43 110.53 1.1101 +IC C222 C220 *C221 H21S 1.5192 121.35 123.34 106.97 1.1128 +IC C220 C221 C222 H22R 1.5106 115.89 -60.86 110.71 1.1115 +IC H22R C221 *C222 H22S 1.5396 113.52 -123.43 110.53 1.1101 +IC H22R C221 *C222 H22T 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 123.34 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 123.34 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI SOPC 0.00 ! 3-stearoyl-2-oleoyl-D-glycero-1-phosphatidylcholine +! +! Stearoyl - CH2 +! | +! Oleoyl - CH +! | (-) (+) +! CH2 - PO4 - CH2 - CH2 - N-(CH3)3 +! +! Polar Head and glycerol backbone +! +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C12 CTL2 -0.10 ! H15A-C15-H15C +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H13B | H14A +ATOM C13 CTL5 -0.35 ! | | | +ATOM H13A HL 0.25 ! H13A-C13----N----C14-H14B (+) +ATOM H13B HL 0.25 ! | | | +ATOM H13C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | +ATOM H14A HL 0.25 ! | +ATOM H14B HL 0.25 ! | alpha6 +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H12A--C12---H12B +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | | +ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | +ATOM H3S HAL2 0.09 ! | | +GROUP ! | | +ATOM C24 CTL2 -0.18 ! | | +ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | +ATOM H4S HAL2 0.09 ! | | +GROUP ! | | +ATOM C25 CTL2 -0.18 ! | | +ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | +ATOM H5S HAL2 0.09 ! | | +GROUP ! | | +ATOM C26 CTL2 -0.18 ! | | +ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | +ATOM H6S HAL2 0.09 ! | | +GROUP ! | | +ATOM C27 CTL2 -0.18 ! | | +ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | +ATOM H7S HAL2 0.09 ! | | +GROUP ! | | +ATOM C28 CTL2 -0.18 ! | | +ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | +ATOM H8S HAL2 0.09 ! | | +GROUP ! | | +ATOM C29 CEL1 -0.15 ! | | +ATOM H91 HEL1 0.15 ! H91 ---C29 | +GROUP ! || (CIS) | +ATOM C210 CEL1 -0.15 ! || | +ATOM H101 HEL1 0.15 ! H101---C210 | +GROUP ! | | +ATOM C211 CTL2 -0.18 ! | | +ATOM H11R HAL2 0.09 ! H11R---C211--H11S | +ATOM H11S HAL2 0.09 ! | | +GROUP ! | | +ATOM C212 CTL2 -0.18 ! | | +ATOM H12R HAL2 0.09 ! H12R---C212--H12S | +ATOM H12S HAL2 0.09 ! | | +GROUP ! | | +ATOM C213 CTL2 -0.18 ! | | +ATOM H13R HAL2 0.09 ! H13R---C213--H13S | +ATOM H13S HAL2 0.09 ! | | +GROUP ! | | +ATOM C214 CTL2 -0.18 ! | | +ATOM H14R HAL2 0.09 ! H14R---C214--H14S | +ATOM H14S HAL2 0.09 ! | | +GROUP ! | | +ATOM C215 CTL2 -0.18 ! | | +ATOM H15R HAL2 0.09 ! H15R---C215--H15S | +ATOM H15S HAL2 0.09 ! | | +GROUP ! | | +ATOM C216 CTL2 -0.18 ! | | +ATOM H16R HAL2 0.09 ! H16R---C216--H16S | +ATOM H16S HAL2 0.09 ! | | +GROUP ! | | +ATOM C217 CTL2 -0.18 ! | | +ATOM H17R HAL2 0.09 ! H17R---C217--H17S | +ATOM H17S HAL2 0.09 ! | | +GROUP ! | | +ATOM C218 CTL3 -0.27 ! | | +ATOM H18R HAL3 0.09 ! H18R---C218--H18S | +ATOM H18S HAL3 0.09 ! | | +ATOM H18T HAL3 0.09 ! H18T | +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CTL2 -0.18 ! | +ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y +ATOM H5Y HAL2 0.09 ! | +GROUP ! | +ATOM C36 CTL2 -0.18 ! | +ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y +ATOM H6Y HAL2 0.09 ! | +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CTL2 -0.18 ! | +ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y +ATOM H8Y HAL2 0.09 ! | +GROUP ! | +ATOM C39 CTL2 -0.18 ! | +ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y +ATOM H9Y HAL2 0.09 ! | +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! H10X---C310--H10Y +ATOM H10Y HAL2 0.09 ! | +GROUP ! | +ATOM C311 CTL2 -0.18 ! | +ATOM H11X HAL2 0.09 ! H11X---C311--H11Y +ATOM H11Y HAL2 0.09 ! | +GROUP ! | +ATOM C312 CTL2 -0.18 ! | +ATOM H12X HAL2 0.09 ! H12X---C312--H12Y +ATOM H12Y HAL2 0.09 ! | +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313--H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CTL2 -0.18 ! | +ATOM H14X HAL2 0.09 ! H14X---C314--H14Y +ATOM H14Y HAL2 0.09 ! | +GROUP ! | +ATOM C315 CTL2 -0.18 ! | +ATOM H15X HAL2 0.09 ! H15X---C315--H15Y +ATOM H15Y HAL2 0.09 ! | +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316--H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL3 -0.27 ! | +ATOM H18X HAL3 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL3 0.09 ! | +ATOM H18Z HAL3 0.09 ! H18Z + +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND O21 C21 +BOND C21 C22 +DOUBLE C21 O22 +BOND C22 H2R C22 H2S C22 C23 +BOND C23 H3R C23 H3S C23 C24 +BOND C24 H4R C24 H4S C24 C25 +BOND C25 H5R C25 H5S C25 C26 +BOND C26 H6R C26 H6S C26 C27 +BOND C27 H7R C27 H7S C27 C28 +BOND C28 H8R C28 H8S C28 C29 +BOND C29 H91 +DOUBLE C29 C210 +BOND C210 H101 C210 C211 +BOND C211 H11R C211 H11S C211 C212 +BOND C212 H12R C212 H12S C212 C213 +BOND C213 H13R C213 H13S C213 C214 +BOND C214 H14R C214 H14S C214 C215 +BOND C215 H15R C215 H15S C215 C216 +BOND C216 H16R C216 H16S C216 C217 +BOND C217 H17R C217 H17S C217 C218 +BOND C218 H18R C218 H18S C218 H18T +! Chain From C3 +BOND O31 C31 +BOND C31 C32 +DOUBLE C31 O32 +BOND C32 H2X C32 H2Y C32 C33 +BOND C33 H3X C33 H3Y C33 C34 +BOND C34 H4X C34 H4Y C34 C35 +BOND C35 H5X C35 H5Y C35 C36 +BOND C36 H6X C36 H6Y C36 C37 +BOND C37 H7X C37 H7Y C37 C38 +BOND C38 H8X C38 H8Y C38 C39 +BOND C39 H9X C39 H9Y C39 C310 +BOND C310 H10X C310 H10Y C310 C311 +BOND C311 H11X C311 H11Y C311 C312 +BOND C312 H12X C312 H12Y C312 C313 +BOND C313 H13X C313 H13Y C313 C314 +BOND C314 H14X C314 H14Y C314 C315 +BOND C315 H15X C315 H15Y C315 C316 +BOND C316 H16X C316 H16Y C316 C317 +BOND C317 H17X C317 H17Y C317 C318 +BOND C318 H18X C318 H18Y C318 H18Z +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +!IC table from IC generate, geometry is guessed +IC C13 N C12 C11 1.5025 109.38 -75.54 119.27 1.5529 +IC C13 C12 *N C14 1.5025 109.38 118.57 109.88 1.5014 +IC C13 C12 *N C15 1.5025 109.38 -120.06 111.03 1.4969 +IC C11 N *C12 H12A 1.5529 119.27 -122.46 108.90 1.0813 +IC C11 N *C12 H12B 1.5529 119.27 122.46 108.90 1.0813 +IC C14 N C13 H13A 1.5014 108.14 54.63 112.42 1.0793 +IC H13A N *C13 H13B 1.0793 112.42 124.95 112.66 1.0787 +IC H13A N *C13 H13C 1.0793 112.42 -117.33 109.87 1.0973 +IC C13 N C14 H14A 1.5025 108.14 179.71 112.53 1.0782 +IC H14A N *C14 H14B 1.0782 112.53 -117.73 109.58 1.0984 +IC H14A N *C14 H14C 1.0782 112.53 124.81 112.18 1.0792 +IC C13 N C15 H15A 1.5025 108.78 58.26 110.07 1.0842 +IC H15A N *C15 H15B 1.0842 110.07 119.38 111.02 1.0824 +IC H15A N *C15 H15C 1.0842 110.07 -119.39 110.90 1.0828 +IC N C12 C11 O12 1.5261 119.27 61.50 111.44 1.4207 +IC O12 C12 *C11 H11A 1.4207 111.44 -127.11 110.31 1.1153 +IC O12 C12 *C11 H11B 1.5529 119.27 122.46 108.90 1.0813 +IC C12 C11 O12 P 1.5529 111.44 -110.28 123.53 1.5856 +IC C11 O12 P O11 1.4207 123.53 -117.07 102.54 1.5781 +IC O11 O12 *P O13 1.5781 102.54 -116.75 105.99 1.4757 +IC O11 O12 *P O14 1.5781 102.54 117.14 108.09 1.4794 +IC O12 P O11 C1 1.5856 102.54 47.49 122.31 1.4299 +IC P O11 C1 C2 1.5781 122.31 -121.63 111.37 1.5551 +IC C2 O11 *C1 HA 1.5551 111.37 -121.22 112.98 1.1162 +IC C2 O11 *C1 HB 1.5529 119.27 122.46 108.90 1.0813 +IC O11 C1 C2 O21 1.4299 111.37 167.62 109.06 1.4416 +IC O21 C1 *C2 C3 1.4416 109.06 -120.10 112.09 1.5542 +IC C3 C1 *C2 HS 1.5542 112.09 -117.49 108.37 1.1164 +IC C1 C2 O21 C21 1.5551 109.06 75.28 114.44 1.3230 +IC C2 O21 C21 C22 1.4416 114.44 -169.77 110.64 1.5347 +IC C22 O21 *C21 O22 1.5347 110.64 178.85 126.03 1.2164 +IC O21 C21 C22 C23 1.3230 110.64 8.34 115.21 1.5530 +IC C23 C21 *C22 H2R 1.5530 115.21 -122.63 106.55 1.1097 +IC C23 C21 *C22 H2S 1.5529 119.27 122.46 108.90 1.0813 +IC C1 C2 C3 O31 1.5551 112.09 -164.18 111.18 1.4463 +IC O31 C2 *C3 HX 1.4463 111.18 -123.28 107.24 1.1146 +IC O31 C2 *C3 HY 1.5529 119.27 122.46 108.90 1.0813 +IC C2 C3 O31 C31 1.5542 111.18 -171.35 113.07 1.3278 +IC C3 O31 C31 C32 1.4463 113.07 -168.42 109.99 1.5299 +IC C32 O31 *C31 O32 1.5299 109.99 176.32 125.54 1.2191 +IC O31 C31 C32 C33 1.3278 109.99 -122.12 112.51 1.5448 +IC C33 C31 *C32 H2X 1.5448 112.51 -119.13 105.91 1.1108 +IC C33 C31 *C32 H2Y 1.5192 121.35 123.34 106.97 1.1128 +IC C21 C22 C23 C24 1.5285 113.04 -70.28 113.21 1.5360 +IC C24 C22 *C23 H3R 1.5360 113.21 -119.83 108.42 1.1148 +IC C24 C22 *C23 H3S 1.5396 113.52 -123.43 110.53 1.1101 +IC C22 C23 C24 C25 1.5450 113.21 -172.34 113.68 1.5399 +IC C25 C23 *C24 H4R 1.5399 113.68 120.91 108.91 1.1136 +IC C25 C23 *C24 H4S 1.5396 113.52 -123.43 110.53 1.1101 +IC C23 C24 C25 C26 1.5360 113.68 -56.95 113.57 1.5353 +IC C26 C24 *C25 H5R 1.5353 113.57 121.41 108.70 1.1129 +IC C26 C24 *C25 H5S 1.5396 113.52 -123.43 110.53 1.1101 +IC C24 C25 C26 C27 1.5399 113.57 -173.39 113.79 1.5375 +IC C27 C25 *C26 H6R 1.5375 113.79 122.09 109.21 1.1127 +IC C27 C25 *C26 H6S 1.5396 113.52 -123.43 110.53 1.1101 +IC C25 C26 C27 C28 1.5353 113.79 177.45 113.35 1.5458 +IC C28 C26 *C27 H7R 1.5458 113.35 119.87 108.07 1.1139 +IC C28 C26 *C27 H7S 1.5396 113.52 -123.43 110.53 1.1101 +IC C26 C27 C28 C29 1.5375 113.35 67.78 114.46 1.5115 +IC C29 C27 *C28 H8R 1.5115 114.46 121.34 107.89 1.1131 +IC C29 C27 *C28 H8S 1.5396 113.52 -123.43 110.53 1.1101 +IC C27 C28 C29 C210 1.5458 114.46 180.00 126.91 1.3502 +IC C210 C28 *C29 H91 1.3502 126.91 -178.81 114.69 1.1010 +IC C28 C29 C210 C211 1.5115 126.91 0.00 126.69 1.5092 !cis db +IC C211 C29 *C210 H101 1.5099 126.94 -177.42 118.69 1.1018 +IC C29 C210 C211 C212 1.3502 126.69 180.00 111.86 1.5417 +IC C212 C210 *C211 H11R 1.5396 113.52 -123.43 110.53 1.1101 +IC C212 C210 *C211 H11S 1.5097 125.28 121.00 119.65 1.1004 +IC C210 C211 C212 C213 1.5092 111.86 180.00 113.99 1.5334 +IC C213 C211 *C212 H12R 1.5396 113.52 -123.43 110.53 1.1101 +IC C213 C211 *C212 H12S 1.5097 125.28 121.00 119.65 1.1004 +IC C211 C212 C213 C214 1.5417 113.99 180.00 111.46 1.5365 +IC C214 C212 *C213 H13R 1.5396 113.52 -123.43 110.53 1.1101 +IC C214 C212 *C213 H13S 1.5097 125.28 121.00 119.65 1.1004 +IC C212 C213 C214 C215 1.5334 111.46 180.00 114.22 1.5376 +IC C215 C213 *C214 H14R 1.5396 113.52 -123.43 110.53 1.1101 +IC C215 C213 *C214 H14S 1.5097 125.28 121.00 119.65 1.1004 +IC C213 C214 C215 C216 1.5365 114.22 180.00 114.97 1.5385 +IC C216 C214 *C215 H15R 1.5396 113.52 -123.43 110.53 1.1101 +IC C216 C214 *C215 H15S 1.5097 125.28 121.00 119.65 1.1004 +IC C214 C215 C216 C217 1.5376 114.97 180.00 113.95 1.5347 +IC C217 C215 *C216 H16R 1.5396 113.52 -123.43 110.53 1.1101 +IC C217 C215 *C216 H16S 1.5097 125.28 121.00 119.65 1.1004 +IC C215 C216 C217 C218 1.5385 113.95 180.00 113.05 1.5311 +IC C218 C216 *C217 H17R 1.5396 113.52 -123.43 110.53 1.1101 +IC C218 C216 *C217 H17S 1.5097 125.28 121.00 119.65 1.1004 +IC C216 C217 C218 H18R 1.5347 113.05 180.00 110.58 1.1110 +IC H18R C217 *C218 H18S 1.5396 113.52 -123.43 110.53 1.1101 +IC H18R C217 *C218 H18T 1.5097 125.28 121.00 119.65 1.1004 +IC C31 C32 C33 C34 1.5405 116.85 180.00 126.13 1.5951 +IC C34 C32 *C33 H3X 1.5410 113.36 -119.96 111.74 1.1148 +IC C34 C32 *C33 H3Y 1.5192 121.35 121.00 106.97 1.1128 +IC C32 C33 C34 C35 1.6060 126.13 180.00 113.36 1.5410 +IC C35 C33 *C34 H4X 1.5396 113.52 -123.43 110.53 1.1101 +IC C35 C33 *C34 H4Y 1.5192 121.35 121.00 106.97 1.1128 +IC C33 C34 C35 C36 1.5951 113.36 180.00 113.52 1.5396 +IC C36 C34 *C35 H5X 1.5396 113.52 -123.43 110.53 1.1101 +IC C36 C34 *C35 H5Y 1.5192 121.35 123.34 106.97 1.1128 +IC C34 C35 C36 C37 1.5410 113.52 180.00 114.47 1.5397 +IC C37 C35 *C36 H6X 1.5396 113.52 -123.43 110.53 1.1101 +IC C37 C35 *C36 H6Y 1.5192 121.35 123.34 106.97 1.1128 +IC C35 C36 C37 C38 1.5396 114.47 180.00 113.41 1.5386 +IC C38 C36 *C37 H7X 1.5396 113.52 -123.43 110.53 1.1101 +IC C38 C36 *C37 H7Y 1.5192 121.35 123.34 106.97 1.1128 +IC C36 C37 C38 C39 1.5397 113.41 180.00 113.71 1.5382 +IC C39 C37 *C38 H8X 1.5396 113.52 -123.43 110.53 1.1101 +IC C39 C37 *C38 H8Y 1.5192 121.35 123.34 106.97 1.1128 +IC C37 C38 C39 C310 1.5386 113.71 180.00 113.75 1.5392 +IC C310 C38 *C39 H9X 1.5396 113.52 -123.43 110.53 1.1101 +IC C310 C38 *C39 H9Y 1.5192 121.35 123.34 106.97 1.1128 +IC C38 C39 C310 C311 1.5382 113.75 180.00 114.19 1.5353 +IC C311 C39 *C310 H10X 1.5396 113.52 -123.43 110.53 1.1101 +IC C311 C39 *C310 H10Y 1.5192 121.35 123.34 106.97 1.1128 +IC C39 C310 C311 C312 1.5392 114.19 180.00 112.28 1.5347 +IC C312 C310 *C311 H11X 1.5396 113.52 -123.43 110.53 1.1101 +IC C312 C310 *C311 H11Y 1.5192 121.35 123.34 106.97 1.1128 +IC C310 C311 C312 C313 1.5353 112.28 180.00 113.98 1.5367 +IC C313 C311 *C312 H12X 1.5396 113.52 -123.43 110.53 1.1101 +IC C313 C311 *C312 H12Y 1.5192 121.35 123.34 106.97 1.1128 +IC C311 C312 C313 C314 1.5347 113.98 180.00 113.72 1.5377 +IC C314 C312 *C313 H13X 1.5396 113.52 -123.43 110.53 1.1101 +IC C314 C312 *C313 H13Y 1.5192 121.35 123.34 106.97 1.1128 +IC C312 C313 C314 C315 1.5367 113.72 180.00 113.85 1.5357 +IC C315 C313 *C314 H14X 1.5396 113.52 -123.43 110.53 1.1101 +IC C315 C313 *C314 H14Y 1.5192 121.35 123.34 106.97 1.1128 +IC C313 C314 C315 C316 1.5377 113.85 180.00 111.81 1.5374 +IC C316 C314 *C315 H15X 1.5396 113.52 -123.43 110.53 1.1101 +IC C316 C314 *C315 H15Y 1.5192 121.35 123.34 106.97 1.1128 +IC C314 C315 C316 C317 1.5357 111.81 180.00 114.29 1.5985 +IC C317 C315 *C316 H16X 1.5396 113.52 -123.43 110.53 1.1101 +IC C317 C315 *C316 H16Y 1.5192 121.35 123.34 106.97 1.1128 +IC C315 C316 C317 C318 1.5374 114.29 180.00 130.92 1.5745 +IC C318 C316 *C317 H17X 1.5396 113.52 -123.43 110.53 1.1101 +IC C318 C316 *C317 H17Y 1.5192 121.35 123.34 106.97 1.1128 +IC C316 C317 C318 H18X 1.5985 130.92 180.00 110.90 1.1113 +IC H18X C317 *C318 H18Y 1.5396 113.52 -123.43 110.53 1.1101 +IC H18X C317 *C318 H18Z 1.5192 121.35 123.34 106.97 1.1128 + +RESI DAPC 0.00 ! 2,3-diarachidonyl-D-glycero-1-phosphatidylcholine (20:4 20:4 PC) +! +! R1 - CH2 +! | +! R2 - CH +! | (-) (+) +! CH2 - PO4 - CH2 - CH2 - N-(CH3)3 +! +! Polar Head and glycerol backbone +! +GROUP ! H15B +ATOM N NTL -0.60 ! | +ATOM C12 CTL2 -0.10 ! H15A-C15-H15C +ATOM H12A HL 0.25 ! | +ATOM H12B HL 0.25 ! H13B | H14A +ATOM C13 CTL5 -0.35 ! | | | +ATOM H13A HL 0.25 ! H13A-C13----N----C14-H14B (+) +ATOM H13B HL 0.25 ! | | | +ATOM H13C HL 0.25 ! H13C | H14C +ATOM C14 CTL5 -0.35 ! | +ATOM H14A HL 0.25 ! | +ATOM H14B HL 0.25 ! | alpha6 +ATOM H14C HL 0.25 ! | +ATOM C15 CTL5 -0.35 ! | +ATOM H15A HL 0.25 ! H12A--C12---H12B +ATOM H15B HL 0.25 ! | +ATOM H15C HL 0.25 ! | +GROUP ! | alpha5 +ATOM C11 CTL2 -0.08 ! | +ATOM H11A HAL2 0.09 ! H11A--C11---H11B +ATOM H11B HAL2 0.09 ! | alpha4 +ATOM P PL 1.50 ! (-) O13 O12 +ATOM O13 O2L -0.78 ! \ / alpha3 +ATOM O14 O2L -0.78 ! P (+) +ATOM O12 OSLP -0.57 ! / \ alpha2 +ATOM O11 OSLP -0.57 ! (-) O14 O11 +ATOM C1 CTL2 -0.08 ! | alpha1 +ATOM HA HAL2 0.09 ! HA---C1---HB +ATOM HB HAL2 0.09 ! | theta1 +GROUP ! | +ATOM C2 CTL1 0.17 ! HS---C2-------------- +ATOM HS HAL1 0.09 ! | beta1 | +ATOM O21 OSL -0.49 ! O22 O21 theta3 +ATOM C21 CL 0.90 ! \\ / beta2 | +ATOM O22 OBL -0.63 ! C21 | +ATOM C22 CTL2 -0.22 ! | beta3 | +ATOM H2R HAL2 0.09 ! H2R---C22---H2S | +ATOM H2S HAL2 0.09 ! | | +GROUP ! | beta4 | +ATOM C3 CTL2 0.08 ! | | +ATOM HX HAL2 0.09 ! | HX---C3---HY +ATOM HY HAL2 0.09 ! | | gamma1 +ATOM O31 OSL -0.49 ! | O32 O31 +ATOM C31 CL 0.90 ! | \\ / gamma2 +ATOM O32 OBL -0.63 ! | C31 +ATOM C32 CTL2 -0.22 ! | | gamma3 +ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y +ATOM H2Y HAL2 0.09 ! | | +GROUP ! | | gamma4 +ATOM C23 CTL2 -0.18 ! | ! +ATOM H3R HAL2 0.09 ! H3R---C23---H3S ! +ATOM H3S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C24 CTL2 -0.18 ! | ! +ATOM H4R HAL2 0.09 ! H4R---C24---H4S ! +ATOM H4S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C25 CEL1 -0.15 ! | ! +ATOM H5R HEL1 0.15 ! H5R---C25 ! +GROUP ! || ! +ATOM C26 CEL1 -0.15 ! || ! +ATOM H6R HEL1 0.15 ! H6R---C26 ! +GROUP ! | ! +ATOM C27 CTL2 -0.18 ! | ! +ATOM H7R HAL2 0.09 ! H7R---C27--H7S ! +ATOM H7S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C28 CEL1 -0.15 ! | ! +ATOM H8R HEL1 0.15 ! H8R---C28 ! +GROUP ! || ! +ATOM C29 CEL1 -0.15 ! || ! +ATOM H9R HEL1 0.15 ! H9R---C29 ! +GROUP ! | ! +ATOM C210 CTL2 -0.18 ! | ! +ATOM H10R HAL2 0.09 ! | ! +ATOM H10S HAL2 0.09 ! H10R---C210--H10S ! +GROUP ! | ! +ATOM C211 CEL1 -0.15 ! | ! +ATOM H11R HEL1 0.15 ! H11R---C211 ! +GROUP ! || ! +ATOM C212 CEL1 -0.15 ! || ! +ATOM H12R HEL1 0.15 ! H12R---C212 ! +GROUP ! | ! +ATOM C213 CTL2 -0.18 ! | ! +ATOM H13R HAL2 0.09 ! H13R---C213---H13S ! +ATOM H13S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C214 CEL1 -0.15 ! | ! +ATOM H14R HEL1 0.15 ! H14R---C214 ! +GROUP ! || ! +ATOM C215 CEL1 -0.15 ! || ! +ATOM H15R HEL1 0.15 ! H15R---C215 ! +GROUP ! | ! +ATOM C216 CTL2 -0.18 ! | ! +ATOM H16R HAL2 0.09 ! H16R---C216--H16S ! +ATOM H16S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C217 CTL2 -0.18 ! | ! +ATOM H17R HAL2 0.09 ! H17R---C217--H17S ! +ATOM H17S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C218 CTL2 -0.18 ! | ! +ATOM H18R HAL2 0.09 ! H18R---C218--H18S ! +ATOM H18S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C219 CTL2 -0.18 ! | ! +ATOM H19R HAL2 0.09 ! H19R---C219--H19S ! +ATOM H19S HAL2 0.09 ! | ! +GROUP ! | ! +ATOM C220 CTL3 -0.27 ! | ! +ATOM H20R HAL3 0.09 ! H20R---C220--H20S ! +ATOM H20S HAL3 0.09 ! | ! +ATOM H20T HAL3 0.09 ! H20T ! +GROUP ! | +ATOM C33 CTL2 -0.18 ! | +ATOM H3X HAL2 0.09 ! H3X---C33---H3Y +ATOM H3Y HAL2 0.09 ! | +GROUP ! | +ATOM C34 CTL2 -0.18 ! | +ATOM H4X HAL2 0.09 ! H4X---C34---H4Y +ATOM H4Y HAL2 0.09 ! | +GROUP ! | +ATOM C35 CEL1 -0.15 ! | +ATOM H5X HEL1 0.15 ! H5X---C35 +GROUP ! || +ATOM C36 CEL1 -0.15 ! || +ATOM H6X HEL1 0.15 ! H6X---C36 +GROUP ! | +ATOM C37 CTL2 -0.18 ! | +ATOM H7X HAL2 0.09 ! H7X---C37---H7Y +ATOM H7Y HAL2 0.09 ! | +GROUP ! | +ATOM C38 CEL1 -0.15 ! | +ATOM H8X HEL1 0.15 ! H8X---C38 +GROUP ! || +ATOM C39 CEL1 -0.15 ! || +ATOM H9X HEL1 0.15 ! H9X---C39 +GROUP ! | +ATOM C310 CTL2 -0.18 ! | +ATOM H10X HAL2 0.09 ! | +ATOM H10Y HAL2 0.09 ! H10X---C310--H10Y +GROUP ! | +ATOM C311 CEL1 -0.15 ! | +ATOM H11X HEL1 0.15 ! H11X---C311 +GROUP ! || +ATOM C312 CEL1 -0.15 ! || +ATOM H12X HEL1 0.15 ! H12X---C312 +GROUP ! | +ATOM C313 CTL2 -0.18 ! | +ATOM H13X HAL2 0.09 ! H13X---C313---H13Y +ATOM H13Y HAL2 0.09 ! | +GROUP ! | +ATOM C314 CEL1 -0.15 ! | +ATOM H14X HEL1 0.15 ! H14X---C314 +GROUP ! || +ATOM C315 CEL1 -0.15 ! || +ATOM H15X HEL1 0.15 ! H15X---C315 +GROUP ! | +ATOM C316 CTL2 -0.18 ! | +ATOM H16X HAL2 0.09 ! H16X---C316---H16Y +ATOM H16Y HAL2 0.09 ! | +GROUP ! | +ATOM C317 CTL2 -0.18 ! | +ATOM H17X HAL2 0.09 ! H17X---C317--H17Y +ATOM H17Y HAL2 0.09 ! | +GROUP ! | +ATOM C318 CTL2 -0.18 ! | +ATOM H18X HAL2 0.09 ! H18X---C318--H18Y +ATOM H18Y HAL2 0.09 ! | +GROUP ! | +ATOM C319 CTL2 -0.18 ! | +ATOM H19X HAL2 0.09 ! H19X---C319--H19Y +ATOM H19Y HAL2 0.09 ! | +GROUP ! | +ATOM C320 CTL3 -0.27 ! | +ATOM H20X HAL3 0.09 ! H20X---C320--H20Y +ATOM H20Y HAL3 0.09 ! | +ATOM H20Z HAL3 0.09 ! H20Z +! Polar Head +BOND N C13 N C14 N C15 +BOND C13 H13A C13 H13B C13 H13C +BOND C14 H14A C14 H14B C14 H14C +BOND C15 H15A C15 H15B C15 H15C +BOND N C12 +BOND C12 H12A C12 H12B C12 C11 +BOND C11 H11A C11 H11B C11 O12 O11 C1 +BOND O12 P P O11 P O13 P O14 +! Glycerol Backbone +BOND C1 HA C1 HB C1 C2 +BOND C2 HS C2 C3 C2 O21 +BOND C3 HX C3 HY C3 O31 +! Chain from C2 +BOND C21 O21 C21 C22 +DOUBLE C21 O22 +BOND C22 C23 C22 H2R C22 H2S +BOND C23 C24 C23 H3R C23 H3S +BOND C24 C25 C24 H4R C24 H4S +DOUBLE C25 C26 +BOND C25 H5R +BOND C26 C27 C26 H6R +BOND C27 C28 C27 H7R C27 H7S +DOUBLE C28 C29 +BOND C28 H8R +BOND C29 C210 C29 H9R +BOND C210 C211 C210 H10R C210 H10S +DOUBLE C211 C212 +BOND C211 H11R +BOND C212 C213 C212 H12R +BOND C213 C214 C213 H13R C213 H13S +DOUBLE C214 C215 +BOND C214 H14R +BOND C215 C216 C215 H15R +BOND C216 C217 C216 H16R C216 H16S +BOND C217 C218 C217 H17R C217 H17S +BOND C218 C219 C218 H18R C218 H18S +BOND C219 C220 C219 H19R C219 H19S +BOND C220 H20T C220 H20R C220 H20S +! Chain From C3 +BOND C31 O31 C31 C32 +DOUBLE C31 O32 +BOND C32 C33 C32 H2X C32 H2Y +BOND C33 C34 C33 H3X C33 H3Y +BOND C34 C35 C34 H4X C34 H4Y +DOUBLE C35 C36 +BOND C35 H5X +BOND C36 C37 C36 H6X +BOND C37 C38 C37 H7X C37 H7Y +DOUBLE C38 C39 +BOND C38 H8X +BOND C39 C310 C39 H9X +BOND C310 C311 C310 H10X C310 H10Y +DOUBLE C311 C312 +BOND C311 H11X +BOND C312 C313 C312 H12X +BOND C313 C314 C313 H13X C313 H13Y +DOUBLE C314 C315 +BOND C314 H14X +BOND C315 C316 C315 H15X +BOND C316 C317 C316 H16X C316 H16Y +BOND C317 C318 C317 H17X C317 H17Y +BOND C318 C319 C318 H18X C318 H18Y +BOND C319 C320 C319 H19X C319 H19Y +BOND C320 H20Z C320 H20X C320 H20Y +IMPR C21 O21 C22 O22 C31 O31 C32 O32 +!IC table from IC generate, geometry is guessed +IC C13 N C12 C11 1.5005 109.34 -51.82 118.22 1.5547 +IC C13 C12 *N C14 1.5005 109.34 -118.51 109.64 1.4974 +IC C13 C12 *N C15 1.5005 109.34 119.15 110.24 1.4962 +IC C11 N *C12 H12A 1.5547 118.22 -125.67 110.33 1.0793 +IC H12A N *C12 H12B 1.0793 110.33 -115.76 109.23 1.0957 +IC C14 N C13 H13A 1.4974 108.23 61.00 111.38 1.0960 +IC H13A N *C13 H13B 1.0960 111.38 -124.27 114.13 1.0734 +IC H13A N *C13 H13C 1.0960 111.38 111.83 109.59 1.0927 +IC C13 N C14 H14A 1.5005 108.23 -179.66 111.63 1.0810 +IC H14A N *C14 H14B 1.0810 111.63 -121.80 110.90 1.0819 +IC H14A N *C14 H14C 1.0810 111.63 119.75 109.60 1.0881 +IC C13 N C15 H15A 1.5005 108.46 -179.84 111.45 1.0808 +IC H15A N *C15 H15B 1.0808 111.45 -119.41 109.20 1.0866 +IC H15A N *C15 H15C 1.0808 111.45 121.80 110.97 1.0815 +IC N C12 C11 O12 1.5273 118.22 69.62 111.90 1.4262 +IC O12 C12 *C11 H11A 1.4262 111.90 -121.72 110.21 1.1107 +IC H11A C12 *C11 H11B 1.1107 110.21 -116.97 108.97 1.1164 +IC C12 C11 O12 P 1.5547 111.90 56.58 119.25 1.5954 +IC C11 O12 P O11 1.4262 119.25 125.38 103.46 1.5769 +IC O11 O12 *P O13 1.5769 103.46 -117.59 108.11 1.4797 +IC O11 O12 *P O14 1.5769 103.46 116.77 106.20 1.4775 +IC O12 P O11 C1 1.5954 103.46 33.43 121.47 1.4291 +IC P O11 C1 C2 1.5769 121.47 146.27 110.07 1.5526 +IC C2 O11 *C1 HA 1.5526 110.07 -121.29 113.08 1.1166 +IC HA O11 *C1 HB 1.1166 113.08 -120.24 108.73 1.1132 +IC O11 C1 C2 C3 1.4291 110.07 37.91 111.11 1.5544 +IC C3 C1 *C2 O21 1.5544 111.11 119.78 110.70 1.4395 +IC C3 C1 *C2 HS 1.5544 111.11 -117.46 108.81 1.1157 +IC C1 C2 O21 C21 1.5526 110.70 72.82 115.87 1.3174 +IC C2 O21 C21 C22 1.4395 115.87 179.18 109.41 1.5329 +IC C22 O21 *C21 O22 1.5329 109.41 -178.52 126.45 1.2180 +IC O21 C21 C22 C23 1.3174 109.41 180.00 113.78 1.5483 +IC C23 C21 *C22 H2R 1.5483 113.78 -121.17 107.02 1.1096 +IC C23 C21 *C22 H2S 1.5483 113.78 122.25 107.54 1.1088 +IC C1 C2 C3 O31 1.5526 111.11 179.84 110.78 1.4471 +IC O31 C2 *C3 HX 1.4471 110.78 -122.23 106.07 1.1170 +IC HX C2 *C3 HY 1.1170 106.07 -116.50 109.11 1.1127 +IC C2 C3 O31 C31 1.5544 110.78 -158.57 113.91 1.3265 +IC C3 O31 C31 C32 1.4471 113.91 178.20 108.97 1.5287 +IC C32 O31 *C31 O32 1.5287 108.97 178.94 125.84 1.2167 +IC O31 C31 C32 C33 1.3265 108.97 180.00 111.97 1.5453 +IC C33 C31 *C32 H2X 1.5453 111.97 -120.94 107.50 1.1090 +IC C33 C31 *C32 H2Y 1.5453 111.97 121.71 108.29 1.1085 +IC C21 C22 C23 C24 1.5329 113.78 180.00 112.27 1.5435 +IC C24 C22 *C23 H3R 1.5435 112.27 -122.24 109.63 1.1133 +IC C24 C22 *C23 H3S 1.5435 112.27 120.06 108.89 1.1154 +IC C22 C23 C24 C25 1.5483 112.27 180.00 115.67 1.5107 +IC C25 C23 *C24 H4R 1.5107 115.67 -121.06 107.11 1.1144 +IC C25 C23 *C24 H4S 1.5107 115.67 124.06 108.43 1.1128 +IC C23 C24 C25 C26 1.5435 115.67 180.00 125.97 1.3453 +IC C26 C24 *C25 H5R 1.3453 125.97 -176.85 115.39 1.1011 +IC C24 C25 C26 C27 1.5107 125.97 0.00 125.28 1.5097 !cis db +IC C27 C25 *C26 H6R 1.5097 125.28 178.19 119.65 1.1004 +IC C25 C26 C27 C28 1.3453 125.28 180.00 121.35 1.5192 +IC C28 C26 *C27 H7R 1.5192 121.35 -124.15 108.68 1.1135 +IC C28 C26 *C27 H7S 1.5192 121.35 123.34 106.97 1.1121 +IC C26 C27 C28 C29 1.5097 121.35 180.00 132.80 1.3549 +IC C29 C27 *C28 H8R 1.3549 132.80 -178.43 111.35 1.1010 +IC C27 C28 C29 C210 1.5192 132.80 0.00 130.38 1.5115 !cis db +IC C210 C28 *C29 H9R 1.5115 130.38 178.53 117.07 1.1014 +IC C28 C29 C210 C211 1.3549 130.38 180.00 111.80 1.5083 +IC C211 C29 *C210 H10R 1.5192 121.35 -124.15 108.68 1.1135 +IC C211 C29 *C210 H10S 1.5192 121.35 123.34 106.97 1.1128 +IC C29 C210 C211 C212 1.5115 111.80 180.00 124.32 1.3436 +IC C212 C210 *C211 H11R 1.3453 125.97 -176.85 115.39 1.1011 +IC C210 C211 C212 C213 1.5083 124.32 0.00 125.45 1.5067 !cis db +IC C213 C211 *C212 H12R 1.5097 125.28 178.19 119.65 1.1004 +IC C211 C212 C213 C214 1.3436 125.45 180.00 111.57 1.5090 +IC C214 C212 *C213 H13R 1.5192 121.35 -124.15 108.68 1.1135 +IC C214 C212 *C213 H13S 1.5192 121.35 123.34 106.97 1.1128 +IC C212 C213 C214 C215 1.5067 111.57 180.00 126.10 1.3471 +IC C215 C213 *C214 H14R 1.3453 125.97 -176.85 115.39 1.1011 +IC C213 C214 C215 C216 1.5090 126.10 0.00 125.86 1.5091 !cis db +IC C216 C214 *C215 H15R 1.5097 125.28 178.19 119.65 1.1004 +IC C214 C215 C216 C217 1.3471 125.86 180.00 113.25 1.5428 +IC C217 C215 *C216 H16R 1.5192 121.35 -124.15 108.68 1.1135 +IC C217 C215 *C216 H16S 1.5192 121.35 123.34 106.97 1.1128 +IC C215 C216 C217 C218 1.5091 113.25 180.00 115.19 1.5395 +IC C218 C216 *C217 H17R 1.5192 121.35 -124.15 108.68 1.1135 +IC C218 C216 *C217 H17S 1.5192 121.35 123.34 106.97 1.1128 +IC C216 C217 C218 C219 1.5428 115.19 180.00 113.95 1.5345 +IC C219 C217 *C218 H18R 1.5192 121.35 -124.15 108.68 1.1135 +IC C219 C217 *C218 H18S 1.5192 121.35 123.34 106.97 1.1128 +IC C217 C218 C219 C220 1.5395 113.95 180.00 112.95 1.5309 +IC C220 C218 *C219 H19R 1.5192 121.35 -124.15 108.68 1.1135 +IC C220 C218 *C219 H19S 1.5192 121.35 123.34 106.97 1.1128 +IC C218 C219 C220 H20T 1.5345 112.95 180.00 110.39 1.1115 +IC H20T C219 *C220 H20R 1.5192 121.35 -124.15 108.68 1.1135 +IC H20T C219 *C220 H20S 1.5192 121.35 123.34 106.97 1.1128 +IC C31 C32 C33 C34 1.5287 111.97 180.00 112.58 1.5385 +IC C34 C32 *C33 H3X 1.5385 112.58 -122.10 109.10 1.1140 +IC C34 C32 *C33 H3Y 1.5385 112.58 121.05 109.26 1.1142 +IC C32 C33 C34 C35 1.5453 112.58 180.00 110.80 1.5074 +IC C35 C33 *C34 H4X 1.5074 110.80 -121.89 108.15 1.1141 +IC C35 C33 *C34 H4Y 1.5074 110.80 121.81 109.29 1.1125 +IC C33 C34 C35 C36 1.5385 110.80 180.00 124.10 1.3433 +IC C36 C34 *C35 H5X 1.3433 124.10 174.75 116.37 1.1008 +IC C34 C35 C36 C37 1.5074 124.10 0.00 125.00 1.5143 !cis db +IC C37 C35 *C36 H6X 1.5143 125.00 -174.44 119.05 1.1017 +IC C35 C36 C37 C38 1.3433 125.00 180.00 117.59 1.5177 +IC C38 C36 *C37 H7X 1.5177 117.59 -122.41 107.65 1.1123 +IC C38 C36 *C37 H7Y 1.5177 117.59 123.72 109.79 1.1133 +IC C36 C37 C38 C39 1.5143 117.59 180.00 126.89 1.3482 +IC C39 C37 *C38 H8X 1.3482 126.89 179.60 114.90 1.1010 +IC C37 C38 C39 C310 1.5177 126.89 0.00 126.25 1.5108 !cis db +IC C310 C38 *C39 H9X 1.5108 126.25 -179.63 118.76 1.1018 +IC C38 C39 C310 C311 1.3482 126.25 180.00 114.73 1.5131 +IC C311 C39 *C310 H10X 1.5177 117.59 -122.41 107.65 1.1123 +IC C311 C39 *C310 H10Y 1.5177 117.59 123.72 109.79 1.1133 +IC C39 C310 C311 C312 1.5108 114.73 180.00 127.49 1.3509 +IC C312 C310 *C311 H11X 1.3482 126.89 179.60 114.90 1.1010 +IC C310 C311 C312 C313 1.5131 127.49 0.00 126.92 1.5159 !cis db +IC C313 C311 *C312 H12X 1.5108 126.25 -179.63 118.76 1.1018 +IC C311 C312 C313 C314 1.3509 126.92 180.00 118.29 1.5170 +IC C314 C312 *C313 H13X 1.5177 117.59 -122.41 107.65 1.1123 +IC C314 C312 *C313 H13Y 1.5177 117.59 123.72 109.79 1.1133 +IC C312 C313 C314 C315 1.5159 118.29 180.00 127.41 1.3481 +IC C315 C313 *C314 H14X 1.3509 126.92 180.00 118.29 1.5170 +IC C313 C314 C315 C316 1.5170 127.41 0.00 125.25 1.5075 !cis db +IC C316 C314 *C315 H15X 1.5108 126.25 -179.63 118.76 1.1018 +IC C314 C315 C316 C317 1.3481 125.25 180.00 113.42 1.5450 +IC C317 C315 *C316 H16X 1.5177 117.59 -122.41 107.65 1.1123 +IC C317 C315 *C316 H16Y 1.5177 117.59 123.72 109.79 1.1133 +IC C315 C316 C317 C318 1.5075 113.42 180.00 116.08 1.5437 +IC C318 C316 *C317 H17X 1.5177 117.59 -122.41 107.65 1.1123 +IC C318 C316 *C317 H17Y 1.5177 117.59 123.72 109.79 1.1133 +IC C316 C317 C318 C319 1.5450 116.08 180.00 116.10 1.6007 +IC C319 C317 *C318 H18X 1.5177 117.59 -122.41 107.65 1.1123 +IC C319 C317 *C318 H18Y 1.5177 117.59 123.72 109.79 1.1133 +IC C317 C318 C319 C320 1.5437 116.10 180.00 132.00 1.5738 +IC C320 C318 *C319 H19X 1.5177 117.59 -122.41 107.65 1.1123 +IC C320 C318 *C319 H19Y 1.5177 117.59 123.72 109.79 1.1133 +IC C318 C319 C320 H20Z 1.6007 132.00 -119.54 110.70 1.1112 +IC H20Z C319 *C320 H20X 1.5177 117.59 -122.41 107.65 1.1123 +IC H20Z C319 *C320 H20Y 1.5177 117.59 123.72 109.79 1.1133 + +END diff --git a/charmm/toppar/top_all36_na.rtf b/charmm/toppar/top_all36_na.rtf new file mode 100644 index 00000000..3881e170 --- /dev/null +++ b/charmm/toppar/top_all36_na.rtf @@ -0,0 +1,857 @@ +* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File //// +* Alexander D. MacKerell Jr. and coworkers +* April 2011 +* All comments to the CHARMM web site: www.charmm.org +* parameter set discussion forum +* +36 1 + +!2010/2011 additions +! ejd, 2010 RNA update +! adm, 2011 DNA update +! For DNA update, new atom type required for P of DNA. This required +! replication of a number of parameters and the creation of new +! patches, DEOX and DEO5, to convert RNA to DNA, such that previous +! CHARMM scripts to generate DNA will no longer work. Note that the +! atom type change to P3 ONLY applies to the phosphodester linkage in +! DNA and NOT to terminal phosphates, DMP etc. +! + +!example of new generate/patch combination to generate DNA +! +!read sequence card +!* 1bna, strand 1 +!* +!3 +!cyt gua cyt +! +!generate a first 5ter last 3ter setup warn +! +!patch deo5 a 1 setup warn !special patch for 5-terminal deoxy residue +!patch deox a 2 setup warn !new patch to convert RNA to DNA +!patch deox a 3 setup warn !no special patch required for 3-terminal deoxy residue +! +!autogenerate angles dihedrals !Use of AUTOGENERATE is essential + +! +!references +! +!NUCLEIC ACIDS +! +!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D., +!“Impact of 2’-hydroxyl sampling on the conformational properties of +!RNA: Update of the CHARMM all-atom additive force field for RNA,” +!JCC, 32: 1929-1943, 2011, PMC3082605 +! +!Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. +!and MacKerell Jr., A.D. “Optimization of the CHARMM additive force +!field for DNA: Improved treatment of the BI/BII conformational +!equilibrium,” JCTC, 8:348–362, 2012, PMC3285246 +! + +!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for +!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and +!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104. +! +!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for +!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA +!and RNA in Solution. JCC, 2000, 21: 105-120. +! + + +MASS 91 HN1 1.008000 H ! Nucleic acid amine proton +MASS 92 HN2 1.008000 H ! Nucleic acid ring nitrogen proton +MASS 93 HN3 1.008000 H ! Nucleic acid aromatic carbon proton +MASS 94 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton +MASS 95 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton +MASS 96 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton +MASS 97 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) +MASS 98 HN8 1.008000 H ! Bound to CN8 in nucleic acids/model compounds +MASS 99 HN9 1.008000 H ! Bound to CN9 in nucleic acids/model compounds +MASS 100 CN1 12.011000 C ! Nucleic acid carbonyl carbon +MASS 101 CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2) +MASS 102 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide +MASS 103 CN3 12.011000 C ! Nucleic acid aromatic carbon +MASS 104 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5 +MASS 105 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 +MASS 106 CN5 12.011000 C ! Nucleic acid purine C4 and C5 +MASS 107 CN5G 12.011000 C ! Nucleic acid guanine C5 +MASS 108 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) +MASS 109 CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1' +MASS 110 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) +MASS 111 CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) +MASS 112 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) +MASS 113 NN1 14.007000 N ! Nucleic acid amide nitrogen +MASS 114 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen +MASS 115 NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE +MASS 116 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 +MASS 117 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 +MASS 118 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen +MASS 119 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 +MASS 120 NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3 +MASS 121 NN4 14.007000 N ! Nucleic acid purine N7 +MASS 122 NN6 14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3) +MASS 123 ON1 15.999400 O ! Nucleic acid carbonyl oxygen +MASS 124 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 +MASS 125 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen +MASS 126 ON3 15.999400 O ! Nucleic acid =O in phosphate +MASS 127 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen +MASS 128 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen +MASS 129 ON6 15.999400 O ! Nucleic acid deoxyribose ring oxygen +MASS 130 ON6B 15.999400 O ! Nucleic acid ribose ring oxygen +MASS 131 P 30.974000 P ! phosphorus +MASS 132 P2 30.974000 P ! phosphorus, adm, 2011 DNA update + +DECL +P +DECL +O1P +DECL +O2P +DECL +O5' +DECL -O3' + +DEFA FIRS none LAST none +AUTOGENERATE ANGLES DIHEDRALS PATCH + +RESI GUA -1.00 ! O6 +ATOM P P 1.50 ! || +ATOM O1P ON3 -0.78 ! C6 +ATOM O2P ON3 -0.78 ! / \ +ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\ +ATOM C5' CN8B -0.08 ! | || C8-H8 +ATOM H5' HN8 0.09 ! C2 C4--N9/ +ATOM H5'' HN8 0.09 ! / \\ / \ +GROUP ! H21-N2 N3 \ +ATOM C4' CN7 0.16 ! | \ +ATOM H4' HN7 0.09 ! H22 \ +ATOM O4' ON6B -0.50 ! \ +ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ +ATOM H1' HN7 0.09 ! | | \ / \ \ +GROUP ! -P-O5'-C5'---C4' C1' +ATOM N9 NN2B -0.02 ! | | \ / \ +ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1' +ATOM N2 NN1 -0.68 ! / \ / \ +ATOM H21 HN1 0.32 ! O3' H3' O2' H2'' +ATOM H22 HN1 0.35 ! | | +ATOM N3 NN3G -0.74 ! H2' +ATOM C2 CN2 0.75 +ATOM N1 NN2G -0.34 +ATOM H1 HN2 0.26 +ATOM C6 CN1 0.54 +ATOM O6 ON1 -0.51 +ATOM C5 CN5G 0.00 +ATOM N7 NN4 -0.60 +ATOM C8 CN4 0.25 +ATOM H8 HN3 0.16 +GROUP +ATOM C2' CN7B 0.14 +ATOM H2'' HN7 0.09 +ATOM O2' ON5 -0.66 +ATOM H2' HN5 0.43 +GROUP +ATOM C3' CN7 0.01 +ATOM H3' HN7 0.09 +ATOM O3' ON2 -0.57 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N2 C2 N1 N2 H21 +BOND N2 H22 N1 H1 N1 C6 C6 C5 +BOND C5 N7 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 +DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 +IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 +DONO H21 N2 +DONO H22 N2 +DONO H1 N1 +DONO H2' O2' +ACCE O6 C6 +ACCE N3 +ACCE N7 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +! Chi and sugar-phosphate backbone in B-DNA like conformation +BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck +BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 +BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 +BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 +BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 +BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 +BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 +BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 +BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 +BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 +BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 +BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 +BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 +BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + + +RESI ADE -1.00 ! H61 H62! +ATOM P P 1.50 ! \ / +ATOM O1P ON3 -0.78 ! N6 +ATOM O2P ON3 -0.78 ! | +ATOM O5' ON2 -0.57 ! C6 +ATOM C5' CN8B -0.08 ! // \ +ATOM H5' HN8 0.09 ! N1 C5--N7\\ +ATOM H5'' HN8 0.09 ! | || C8-H8 +GROUP ! C2 C4--N9/ +ATOM C4' CN7 0.16 ! / \\ / \ +ATOM H4' HN7 0.09 ! H2 N3 \ +ATOM O4' ON6B -0.50 ! \ +ATOM C1' CN7B 0.16 ! \ +ATOM H1' HN7 0.09 ! \ +GROUP ! O1P H5' H4' O4' \ +ATOM N9 NN2 -0.05 ! | | \ / \ \ +ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1' +ATOM N7 NN4 -0.71 ! | | \ / \ +ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1' +ATOM H8 HN3 0.12 ! / \ / \ +ATOM N1 NN3A -0.74 ! O3' H3' O2' H2'' +ATOM C2 CN4 0.50 ! | | +ATOM H2 HN3 0.13 ! H2' +ATOM N3 NN3A -0.75 +ATOM C4 CN5 0.43 +ATOM C6 CN2 0.46 +ATOM N6 NN1 -0.77 +ATOM H61 HN1 0.38 +ATOM H62 HN1 0.38 +GROUP +ATOM C2' CN7B 0.14 +ATOM H2'' HN7 0.09 +ATOM O2' ON5 -0.66 +ATOM H2' HN5 0.43 +GROUP +ATOM C3' CN7 0.01 +ATOM H3' HN7 0.09 +ATOM O3' ON2 -0.57 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 +BOND C2 N1 C6 N6 +BOND N6 H61 N6 H62 C6 C5 C5 N7 +BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C8 H8 C2 H2 +DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 +IMPR N6 C6 H61 H62 C6 N1 C5 N6 +DONO H61 N6 +DONO H62 N6 +DONO H2' O2' +ACCE N3 +ACCE N7 +ACCE N1 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck +BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 +BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi +BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 +BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 +BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 +BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 +BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 +BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 +BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 +BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 +BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 +BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 +BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 +BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 +BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 +BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 +BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 +BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +RESI CYT -1.00 +ATOM P P 1.50 ! +ATOM O1P ON3 -0.78 ! H42 H41 +ATOM O2P ON3 -0.78 ! \ / +ATOM O5' ON2 -0.57 ! N4 +ATOM C5' CN8B -0.08 ! | +ATOM H5' HN8 0.09 ! C4 +ATOM H5'' HN8 0.09 ! / \\ +GROUP ! H5-C5 N3 +ATOM C4' CN7 0.16 ! || | +ATOM H4' HN7 0.09 ! H6-C6 C2 +ATOM O4' ON6B -0.50 ! \ / \\ +ATOM C1' CN7B 0.16 ! N1 O2 +ATOM H1' HN7 0.09 ! \ +GROUP ! \ +ATOM N1 NN2 -0.13 ! \ +ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \ +ATOM H6 HN3 0.17 ! | | \ / \ \ +ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1' +ATOM H5 HN3 0.07 ! | | \ / \ +ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1' +ATOM O2 ON1C -0.49 ! / \ / \ +ATOM N3 NN3 -0.66 ! O3' H3' O2' H2'' +ATOM C4 CN2 0.65 ! | | +ATOM N4 NN1 -0.75 ! H2' +ATOM H41 HN1 0.37 +ATOM H42 HN1 0.33 +GROUP +ATOM C2' CN7B 0.14 +ATOM H2'' HN7 0.09 +ATOM O2' ON5 -0.66 +ATOM H2' HN5 0.43 +GROUP +ATOM C3' CN7 0.01 +ATOM H3' HN7 0.09 +ATOM O3' ON2 -0.57 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 +BOND C2 N3 C4 N4 N4 H41 N4 H42 +BOND C4 C5 C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 +DOUBLE C2 O2 C5 C6 N3 C4 +IMPR C2 N1 N3 O2 C4 N3 C5 N4 +IMPR N4 C4 H41 H42 +DONO H42 N4 +DONO H2' O2' +DONO H41 N4 +ACCE O2 C2 +ACCE N3 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma +BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta +BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon +BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta +BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 +BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 +BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 +BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 +BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 +BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 +BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 +BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 +BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 +BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +RESI THY -1.00 ! H51 O4 +ATOM P P 1.50 ! | || +ATOM O1P ON3 -0.78 ! H52-C5M C4 H3 +ATOM O2P ON3 -0.78 ! | \ / \ / +ATOM O5' ON2 -0.57 ! H53 C5 N3 +ATOM C5' CN8B -0.08 ! || | +ATOM H5' HN8 0.09 ! H6-C6 C2 +ATOM H5'' HN8 0.09 ! \ / \\ +GROUP ! N1 O2 +ATOM C4' CN7 0.16 ! \ +ATOM H4' HN7 0.09 ! \ +ATOM O4' ON6B -0.50 ! \ +ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ +ATOM H1' HN7 0.09 ! | | \ / \ \ +GROUP ! -P-O5'-C5'---C4' C1' +ATOM N1 NN2B -0.34 ! | | \ / \ +ATOM C6 CN3 0.17 ! O2P H5'' C3'--C2' H1' +ATOM H6 HN3 0.17 ! / \ / \ +ATOM C2 CN1T 0.51 ! O3' H3' O2' H2'' +ATOM O2 ON1 -0.41 ! | | +ATOM N3 NN2U -0.46 ! H2' +ATOM H3 HN2 0.36 ! +ATOM C4 CN1 0.50 ! +ATOM O4 ON1 -0.45 ! +ATOM C5 CN3T -0.15 +ATOM C5M CN9 -0.11 +ATOM H51 HN9 0.07 +ATOM H52 HN9 0.07 +ATOM H53 HN9 0.07 +GROUP +ATOM C2' CN7B 0.14 +ATOM H2'' HN7 0.09 +ATOM O2' ON5 -0.66 +ATOM H2' HN5 0.43 +GROUP +ATOM C3' CN7 0.01 +ATOM H3' HN7 0.09 +ATOM O3' ON2 -0.57 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 +BOND C2 N3 N3 H3 N3 C4 C4 C5 +BOND C5 C5M C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M +DONO H3 N3 +DONO H2' O2' +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' + +BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha +BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta +BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 +BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 +BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 +BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 +BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 +BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 +BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi +BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 +BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 +BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 +BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 +BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 +BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 +BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 +BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 +BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 +BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 +BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 + +RESI URA -1.00 ! O4 +ATOM P P 1.50 ! || +ATOM O1P ON3 -0.78 ! C4 H3 +ATOM O2P ON3 -0.78 ! / \ / +ATOM O5' ON2 -0.57 ! H5-C5 N3 +ATOM C5' CN8B -0.08 ! || | +ATOM H5' HN8 0.09 ! H6-C6 C2 +ATOM H5'' HN8 0.09 ! \ / \\ +GROUP ! N1 O2 +ATOM C4' CN7 0.16 ! \ +ATOM H4' HN7 0.09 ! \ +ATOM O4' ON6B -0.50 ! \ +ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ +ATOM H1' HN7 0.09 ! | | \ / \ \ +GROUP ! -P-O5'-C5'---C4' C1' +ATOM N1 NN2B -0.34 ! | | \ / \ +ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1' +ATOM H6 HN3 0.14 ! / \ / \ +ATOM C2 CN1T 0.55 ! O3' H3' O2' H2'' +ATOM O2 ON1 -0.45 ! | | +ATOM N3 NN2U -0.46 ! H2' +ATOM H3 HN2 0.36 ! +ATOM C4 CN1 0.53 ! +ATOM O4 ON1 -0.48 ! +ATOM C5 CN3 -0.15 ! +ATOM H5 HN3 0.10 ! +GROUP +ATOM C2' CN7B 0.14 +ATOM H2'' HN7 0.09 +ATOM O2' ON5 -0.66 +ATOM H2' HN5 0.43 +GROUP +ATOM C3' CN7 0.01 +ATOM H3' HN7 0.09 +ATOM O3' ON2 -0.57 +BOND P O1P P O2P P O5' +BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' +BOND C1' N1 C1' C2' N1 C2 N1 C6 +BOND C2 N3 N3 H3 N3 C4 C4 C5 +BOND C2' C3' C3' O3' O3' +P +BOND C2' O2' O2' H2' +BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' +BOND C5' H5'' C5 H5 C6 H6 +DOUBLE C2 O2 C4 O4 C5 C6 +IMPR C2 N1 N3 O2 C4 N3 C5 O4 +DONO H3 N3 +DONO H2' O2' +ACCE O2 C2 +ACCE O4 C4 +ACCE O1P P +ACCE O2P P +ACCE O2' +ACCE O3' +ACCE O4' +ACCE O5' +BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 +BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 +BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 +BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 +BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 +BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 +BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 +BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 +BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 +BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 +BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 +BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 +BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 +BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 +BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 +BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 +BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 +BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 +BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 +BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 +BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 +BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 +BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 +BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 +BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 +BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 +BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 +BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 +BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 + +! NOTE the option to regenerate all angles and dihedrals allows +! the explicit inclusion of the THET and DIHE terms to be omitted +! even if the PRES is used in a PATCH statement. It is important to +! inspect the patches prior to use to determine if they should be used +! in a GENErate or PATCh statement and/or if the AUTOgeneration of +! angles and dihedrals is required. +! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the +! documentation + +PRES DEO5 0.00 ! Patch to make the 5-terminal nucleotide into DEOXYribose +DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS + +GROUP ! To correct O4' atom type in DNA (NF) +ATOM C4' CN7 0.16 ! +ATOM H4' HN7 0.09 ! +ATOM O4' ON6 -0.50 ! +ATOM C1' CN7B 0.16 ! +ATOM H1' HN7 0.09 ! +GROUP +ATOM C2' CN8 -0.18 +ATOM H2' HN8 0.09 +ATOM H2'' HN8 0.09 + +BOND C2' H2' +BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +PRES DEOX 1.50 ! Patch to make non 5-terminal DEOXyribose nucleotides +DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS + +ATOM P P2 1.50 ! switch type P to type P2 as required to apply + ! 2011 DNA update to zeta in DNA only +GROUP ! To correct O4' atom type in DNA (NF) +ATOM C4' CN7 0.16 ! +ATOM H4' HN7 0.09 ! +ATOM O4' ON6 -0.50 ! +ATOM C1' CN7B 0.16 ! +ATOM H1' HN7 0.09 ! +GROUP +ATOM C2' CN8 -0.18 +ATOM H2' HN8 0.09 +ATOM H2'' HN8 0.09 + +BOND C2' H2' +BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 + +PRES 5TER 0.00 ! 5'-terminal HYDROXYL patch, from MeOH + ! use in generate statement +GROUP +ATOM H5T HN5 0.43 +ATOM O5' ON5 -0.66 +ATOM C5' CN8B 0.05 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +! +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P +! +BOND H5T O5' +DONO H5T O5' +BILD H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 + +PRES 5MET 0.00 ! 5'-ribose METHYL patch + ! use in generate statement, doesn't work with DEOx patches +GROUP +ATOM C5' CN9 -0.27 +ATOM H5' HN9 0.09 +ATOM H5'' HN9 0.09 +ATOM H53' HN9 0.09 ! Can't use ''' and avoid conflict with THY +! +DELETE ATOM O5' +DELETE ATOM P +DELETE ATOM O1P +DELETE ATOM O2P +! +BOND C5' H53' +IC C3' C4' C5' H53' 0.0000 0.00 180.00 0.00 0.0000 +IC H53' C4' *C5' H5' 0.0000 0.00 120.00 0.00 0.0000 +IC H53' C4' *C5' H5'' 0.0000 0.00 -120.00 0.00 0.0000 + +PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch + ! use in generate statement +GROUP +ATOM C5' CN8B -0.08 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +ATOM P P 1.50 +ATOM O1P ON3 -0.82 +ATOM O2P ON3 -0.82 +ATOM O5' ON2 -0.62 +ATOM O5T ON4 -0.68 +ATOM H5T HN4 0.34 +BOND O5T P H5T O5T +DONO H5T O5T +! Built in B-DNA-like conformation (NF) +BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 +BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 +BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 +BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 +BILD H5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 + +PRES 5POM -1.00 ! 5'terminal Methyl-Phosphate patch + ! use in generate statement +GROUP +ATOM C5' CN8B -0.08 +ATOM H5' HN8 0.09 +ATOM H5'' HN8 0.09 +ATOM P P 1.50 +ATOM O1P ON3 -0.78 +ATOM O2P ON3 -0.78 +ATOM O5' ON2 -0.57 +ATOM O5T ON2 -0.57 +ATOM C5T CN9 -0.17 +ATOM H5T1 HN9 0.09 +ATOM H5T2 HN9 0.09 +ATOM H5T3 HN9 0.09 + +BOND O5T P O5T C5T C5T H5T1 C5T H5T2 +BOND C5T H5T3 +!DONO H5T O5T +! Built in B-DNA-like conformation (NF) +BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 +BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 +BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 +BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 +BILD C5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 +BILD H5T1 C5T O5T P 0.0000 000.00 180.20 000.00 0.0000 +BILD H5T2 C5T O5T P 0.0000 000.00 60.00 000.00 0.0000 +BILD H5T3 C5T O5T P 0.0000 000.00 -60.00 000.00 0.0000 + +PRES 3TER 0.00 ! 3'terminal HYDROXYL patch, from MeOH + ! use in generate statement +GROUP +ATOM C3' CN7 0.14 +ATOM H3' HN7 0.09 +ATOM O3' ON5 -0.66 +ATOM H3T HN5 0.43 +BOND O3' H3T +DONO H3T O3' +BILD H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 + +PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch + ! use in generate statement +GROUP +ATOM C3' CN7 0.01 +ATOM H3' HN7 0.09 +ATOM P3 P 1.50 +ATOM O1P3 ON3 -0.82 +ATOM O2P3 ON3 -0.82 +ATOM O3' ON2 -0.62 +ATOM O3T ON4 -0.68 +ATOM H3T HN4 0.34 +BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T H3T +DONO H3T O3T +ACCE O3T +ACCE O1P3 +ACCE O2P3 +! Build in B-DNA-like conformation (NF) +BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 +BILD C3' O3' P3 O3T 0.0000 000.00 -95.20 000.00 0.0000 +BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 +BILD H3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 + +PRES 3POM -1.00 ! 3'terminal Methyl Phosphate patch + ! use in generate statement +! To build model compound with OPO3-CH3 at the 3' end (nicolas) +GROUP +ATOM C3' CN7 0.01 +ATOM H3' HN7 0.09 +ATOM P3 P 1.50 +ATOM O1P3 ON3 -0.78 +ATOM O2P3 ON3 -0.78 +ATOM O3' ON2 -0.57 +ATOM O3T ON2 -0.57 +ATOM C3T CN9 -0.17 +ATOM H3T1 HN9 0.09 +ATOM H3T2 HN9 0.09 +ATOM H3T3 HN9 0.09 + +BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T C3T +BOND C3T H3T1 C3T H3T2 C3T H3T3 +ACCE O3' +ACCE O5' +ACCE O1P3 +ACCE O2P3 +BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 +BILD C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000 +BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 +BILD C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 +BILD H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000 +BILD H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000 +BILD H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000 + +PRES 3PO3 -2.00 ! 3'terminal PHOSPHATE patch + ! use in generate statement + ! Added by Nicolas, to be consistent with model componds +GROUP +ATOM C3' CN7 -0.09 +ATOM H3' HN7 0.09 +ATOM P3 P 1.10 +ATOM O3' ON2 -0.40 +ATOM O1P3 ON3 -0.90 +ATOM O2P3 ON3 -0.90 +ATOM O3P3 ON3 -0.90 +BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3P3 +ACCE O1P3 +ACCE O2P3 +ACCE O3P3 +BILD C4' C3' O3' P3 0.0000 000.00 180.00 000.00 0.0000 +BILD C3' O3' P3 O3P3 0.0000 000.00 -39.52 000.00 0.0000 +BILD O3P3 O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 +BILD O3P3 O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 +BILD O3' P3 O3P3 O3T 0.0000 000.00 180.00 000.00 0.0000 +BILD P3 O3P3 O3T H3T 0.0000 000.00 180.00 000.00 0.0000 + +PRES DELB 0.00 ! patch to delete all possible base atoms + ! of Cyt,Gua,Ade,Thy and Ura + ! +!note: error messages will be obtained due to atoms not present in +!residue being "deleted" by this patch +!cyt section +DELE ATOM N1 +DELE ATOM C6 +DELE ATOM H6 +DELE ATOM C2 +DELE ATOM O2 +DELE ATOM N3 +DELE ATOM C4 +DELE ATOM N4 +DELE ATOM H41 +DELE ATOM H42 +DELE ATOM C5 +DELE ATOM H5 +!gua section +DELE ATOM N9 +DELE ATOM H1 +DELE ATOM N2 +DELE ATOM H21 +DELE ATOM H22 +DELE ATOM O6 +DELE ATOM N7 +DELE ATOM C8 +DELE ATOM H8 +!ade section +DELE ATOM H2 +DELE ATOM N6 +DELE ATOM H61 +DELE ATOM H62 +!thy/ura section +DELE ATOM H3 +DELE ATOM O4 +DELE ATOM C5M +DELE ATOM H51 +DELE ATOM H52 +DELE ATOM H53 + +PRES CY35 0.0 ! patch to make a cyclic 3'-5' nucleotide + ! use AUTOGEN ANGLE DIHE after this patch +BOND O3' P ! but before water-generation + +PRES LKNA 0.0 ! Patch to join to nucleic acid segments (eg for IMAGES) + ! eg: patch sega 10 segb 1 + ! sega should have std 3' (gene sega ... last none) + ! segb should have std 5' (gene segb ... first none) + ! USE AUTOgen ANGL DIHE after this patch, + ! but before water-generation +BOND 1O3' 2P +IC 1O3' 2P 2O5' 2C5' 1.6001 101.45 -39.25 119.00 1.4401 +IC 1O3' 2O5' *2P 2O1P 1.6001 101.45 -115.82 109.74 1.4802 +IC 1O3' 2O5' *2P 2O2P 1.6001 101.45 115.90 109.80 1.4801 +IC 1C4' 1C3' 1O3' 2P 1.5284 111.92 159.13 119.05 1.6001 +IC 1C3' 1O3' 2P 2O5' 1.4212 119.05 -98.86 101.45 1.5996 + +end + diff --git a/charmm/toppar/top_all36_prot.rtf b/charmm/toppar/top_all36_prot.rtf new file mode 100644 index 00000000..ca82bc02 --- /dev/null +++ b/charmm/toppar/top_all36_prot.rtf @@ -0,0 +1,1777 @@ +*>>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<< +*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< +*>>>>>>>>>>>>>>>>>>>>>>>>>> May 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<< +* All comments to the CHARMM web site: www.charmm.org +* parameter set discussion forum +* +36 1 + +!references +! +!Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P. +!Mittal, J., Feig, M. and MacKerell, A.D., Jr. "Optimization of the +!additive CHARMM all-atom protein force field targeting improved +!sampling of the backbone phi, psi and sidechain chi1 and chi2 +!dihedral angles," JCTC, 8: 3257-3273, 2013, PMC3549273 + +!MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved +!treatment of the protein backbone in empirical force fields," Journal +!of the American Chemical Society, 126: 698-699, 2004 +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. +! + +MASS 31 H 1.00800 ! polar H +MASS 32 HC 1.00800 ! N-ter H +MASS 33 HA 1.00800 ! nonpolar H +MASS 34 HP 1.00800 ! aromatic H +MASS 35 HB1 1.00800 ! backbone H +MASS 36 HB2 1.00800 ! aliphatic backbone H, to CT2 +MASS 37 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS 38 HR2 1.00800 ! (+) his HE1 +MASS 39 HR3 1.00800 ! neutral his HG, HD2 +MASS 40 HS 1.00800 ! thiol hydrogen +MASS 41 HE1 1.00800 ! for alkene; RHC=CR +MASS 42 HE2 1.00800 ! for alkene; H2C=CR +MASS 43 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS 44 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS 45 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS 46 C 12.01100 ! carbonyl C, peptide backbone +MASS 47 CA 12.01100 ! aromatic C +MASS 48 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens +MASS 49 CT1 12.01100 ! aliphatic sp3 C for CH +MASS 50 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS 51 CT2A 12.01100 ! from CT2 (asp, glu, hsp chi1/chi2 fitting) +MASS 52 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS 53 CPH1 12.01100 ! his CG and CD2 carbons +MASS 54 CPH2 12.01100 ! his CE1 carbon +MASS 55 CPT 12.01100 ! trp C between rings +MASS 56 CY 12.01100 ! TRP C in pyrrole ring +MASS 57 CP1 12.01100 ! tetrahedral C (proline CA) +MASS 58 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS 59 CP3 12.01100 ! tetrahedral C (proline CD) +MASS 60 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS 61 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS 62 CS 12.01100 ! thiolate carbon +MASS 63 CE1 12.01100 ! for alkene; RHC=CR +MASS 64 CE2 12.01100 ! for alkene; H2C=CR +MASS 65 CAI 12.01100 ! aromatic C next to CPT in trp +MASS 66 N 14.00700 ! proline N +MASS 67 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS 68 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS 69 NR3 14.00700 ! charged his ring nitrogen +MASS 70 NH1 14.00700 ! peptide nitrogen +MASS 71 NH2 14.00700 ! amide nitrogen +MASS 72 NH3 14.00700 ! ammonium nitrogen +MASS 73 NC2 14.00700 ! guanidinium nitrogen +MASS 74 NY 14.00700 ! TRP N in pyrrole ring +MASS 75 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS 76 O 15.99900 ! carbonyl oxygen +MASS 77 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS 78 OC 15.99900 ! carboxylate oxygen +MASS 79 OH1 15.99900 ! hydroxyl oxygen +MASS 80 OS 15.99940 ! ester oxygen +MASS 81 S 32.06000 ! sulphur +MASS 82 SM 32.06000 ! sulfur C-S-S-C type +MASS 83 SS 32.06000 ! thiolate sulfur + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA +DEFA FIRS NTER LAST CTER +AUTO ANGLES DIHE + +RESI ALA 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | / +GROUP ! HA-CA--CB-HB2 +ATOM CB CT3 -0.27 ! | \ +ATOM HB1 HA3 0.09 ! | HB3 +ATOM HB2 HA3 0.09 ! O=C +ATOM HB3 HA3 0.09 ! | +GROUP ! +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA N HN N CA +BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +RESI ARG 1.00 +GROUP +ATOM N NH1 -0.47 ! | HH11 +ATOM HN H 0.31 ! HN-N | +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12 +ATOM HA HB1 0.09 ! | | | | | //(+) +GROUP ! HA-CA--CB--CG--CD--NE--CZ +ATOM CB CT2 -0.18 ! | | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 NH2-HH22 +ATOM HB2 HA2 0.09 ! O=C | +GROUP ! | HH21 +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CT2 0.20 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +ATOM NE NC2 -0.70 +ATOM HE HC 0.44 +ATOM CZ C 0.64 +ATOM NH1 NC2 -0.80 +ATOM HH11 HC 0.46 +ATOM HH12 HC 0.46 +ATOM NH2 NC2 -0.80 +ATOM HH21 HC 0.46 +ATOM HH22 HC 0.46 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG NE CD CZ NE +BOND NH2 CZ N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 +BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 +DOUBLE O C CZ NH1 +IMPR N -C CA HN C CA +N O +IMPR CZ NH1 NH2 NE +IMPR NH1 HH11 HH12 CZ +IMPR NH2 HH21 HH22 CZ +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +RESI ASN 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1) +ATOM HA HB1 0.09 ! | | || / +GROUP ! HA-CA--CB--CG--ND2 +ATOM CB CT2 -0.18 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 HD22 (trans to OD1) +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CC 0.55 +ATOM OD1 O -0.55 +GROUP +ATOM ND2 NH2 -0.62 +ATOM HD21 H 0.32 +ATOM HD22 H 0.30 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 +DOUBLE C O CG OD1 +IMPR N -C CA HN C CA +N O +IMPR CG ND2 CB OD1 CG CB ND2 OD1 +IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +RESI ASP -1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 OD1 +ATOM HA HB1 0.09 ! | | // +GROUP ! HA-CA--CB--CG +ATOM CB CT2A -0.28 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 OD2(-) +ATOM HB2 HA2 0.09 ! O=C +ATOM CG CC 0.62 ! | +ATOM OD1 OC -0.76 +ATOM OD2 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB OD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 +DOUBLE O C CG OD1 +IMPR N -C CA HN C CA +N O +IMPR CG CB OD2 OD1 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +RESI CYS 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | | +GROUP ! HA-CA--CB--SG +ATOM CB CT2 -0.11 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG1 +ATOM HB2 HA2 0.09 ! O=C +ATOM SG S -0.23 ! | +ATOM HG1 HS 0.16 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA SG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 SG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 SG +ACCEPTOR O C +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +RESI GLN 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1) +ATOM HA HB1 0.09 ! | | | || / +GROUP ! HA-CA--CB--CG--CD--NE2 +ATOM CB CT2 -0.18 ! | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 HE22 (trans to OE1) +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CC 0.55 +ATOM OE1 O -0.55 +GROUP +ATOM NE2 NH2 -0.62 +ATOM HE21 H 0.32 +ATOM HE22 H 0.30 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG NE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 NE2 HE21 NE2 HE22 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD NE2 CG OE1 CD CG NE2 OE1 +IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +RESI GLU -1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 OE1 +ATOM HA HB1 0.09 ! | | | // +GROUP ! HA-CA--CB--CG--CD +ATOM CB CT2A -0.18 ! | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 OE2(-) +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.28 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +ATOM CD CC 0.62 +ATOM OE1 OC -0.76 +ATOM OE2 OC -0.76 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG OE2 CD +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 +DOUBLE O C CD OE1 +IMPR N -C CA HN C CA +N O +IMPR CD CG OE2 OE1 +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI GLY 0.00 +!GROUP +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! N-H +ATOM CA CT2 -0.02 ! | +ATOM HA1 HB2 0.09 ! | +ATOM HA2 HB2 0.09 ! HA1-CA-HA2 +GROUP ! | +ATOM C C 0.51 ! | +ATOM O O -0.51 ! C=O + ! | +BOND N HN N CA C CA +BOND C +N CA HA1 CA HA2 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 +PATCHING FIRS GLYP + +RESI HSD 0.00 ! neutral HIS, proton on ND1 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB1 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2 -0.09 ! | | \\ || +ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA2 0.09 ! O=C | +ATOM ND1 NR1 -0.36 ! | HD2 +ATOM HD1 H 0.32 +ATOM CG CPH1 -0.05 +GROUP +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +ATOM NE2 NR2 -0.70 +ATOM CD2 CPH1 0.22 +ATOM HD2 HR3 0.10 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CG CD2 CE1 NE2 +IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +RESI HSE 0.00 ! neutral His, proton on NE2 +GROUP +ATOM N NH1 -0.47 ! | HE1 +ATOM HN H 0.31 ! HN-N __ / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB1 0.09 ! | | / | +GROUP ! HA-CA--CB--CG | +ATOM CB CT2 -0.08 ! | | \\ | +ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2 +ATOM HB2 HA2 0.09 ! O=C | \ +ATOM ND1 NR2 -0.70 ! | HD2 HE2 +ATOM CG CPH1 0.22 +ATOM CE1 CPH2 0.25 +ATOM HE1 HR1 0.13 +GROUP +ATOM NE2 NR1 -0.36 +ATOM HE2 H 0.32 +ATOM CD2 CPH1 -0.05 +ATOM HD2 HR3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG +BOND NE2 CD2 N HN N CA +BOND C CA C +N NE2 CE1 CA HA CB HB1 +BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG CE1 ND1 +IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +RESI HSP 1.00 ! Protonated His +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 ND1--CE1 +ATOM HA HB1 0.09 ! | | / || +GROUP ! HA-CA--CB--CG || +ATOM CB CT2A -0.05 ! | | \\ || +ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2(+) +ATOM HB2 HA2 0.09 ! O=C | \ +ATOM CD2 CPH1 0.19 ! | HD2 HE2 +ATOM HD2 HR1 0.13 +ATOM CG CPH1 0.19 +GROUP +ATOM NE2 NR3 -0.51 +ATOM HE2 H 0.44 +ATOM ND1 NR3 -0.51 +ATOM HD1 H 0.44 +ATOM CE1 CPH2 0.32 +ATOM HE1 HR2 0.18 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB ND1 CG CE1 ND1 +BOND NE2 CD2 N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 +DOUBLE O C CD2 CG NE2 CE1 +IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +RESI ILE 0.00 +GROUP +ATOM N NH1 -0.47 ! | HG21 HG22 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | CG2--HG23 +ATOM HA HB1 0.09 ! | / +GROUP ! HA-CA--CB-HB HD1 +ATOM CB CT1 -0.09 ! | \ / +ATOM HB HA1 0.09 ! | CG1--CD--HD2 +GROUP ! O=C / \ \ +ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3 +ATOM HG21 HA3 0.09 +ATOM HG22 HA3 0.09 +ATOM HG23 HA3 0.09 +GROUP +ATOM CG1 CT2 -0.18 +ATOM HG11 HA2 0.09 +ATOM HG12 HA2 0.09 +GROUP +ATOM CD CT3 -0.27 +ATOM HD1 HA3 0.09 +ATOM HD2 HA3 0.09 +ATOM HD3 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG1 CB CG2 CB CD CG1 +BOND N HN N CA C CA C +N +BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 +BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 + +RESI LEU 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD11 HD12 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | HB1 CD1--HD13 +ATOM HA HB1 0.09 ! | | / +GROUP ! HA-CA--CB--CG-HG +ATOM CB CT2 -0.18 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 CD2--HD23 +ATOM HB2 HA2 0.09 ! O=C | \ +GROUP ! | HD21 HD22 +ATOM CG CT1 -0.09 +ATOM HG HA1 0.09 +GROUP +ATOM CD1 CT3 -0.27 +ATOM HD11 HA3 0.09 +ATOM HD12 HA3 0.09 +ATOM HD13 HA3 0.09 +GROUP +ATOM CD2 CT3 -0.27 +ATOM HD21 HA3 0.09 +ATOM HD22 HA3 0.09 +ATOM HD23 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD1 CG CD2 CG +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 +BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +RESI LYS 1.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 +ATOM HA HB1 0.09 ! | | | | | / +GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 +ATOM CB CT2 -0.18 ! | | | | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 HE2 HZ3 +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM CD CT2 -0.18 +ATOM HD1 HA2 0.09 +ATOM HD2 HA2 0.09 +GROUP +ATOM CE CT2 0.21 +ATOM HE1 HA2 0.05 +ATOM HE2 HA2 0.05 +ATOM NZ NH3 -0.30 +ATOM HZ1 HC 0.33 +ATOM HZ2 HC 0.33 +ATOM HZ3 HC 0.33 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD CG CE CD NZ CE +BOND N HN N CA C CA +BOND C +N CA HA CB HB1 CB HB2 CG HG1 +BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 +DOUBLE O C +BOND NZ HZ1 NZ HZ2 NZ HZ3 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI MET 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 HG1 HE1 +ATOM HA HB1 0.09 ! | | | | +GROUP ! HA-CA--CB--CG--SD--CE--HE3 +ATOM CB CT2 -0.18 ! | | | | +ATOM HB1 HA2 0.09 ! | HB2 HG2 HE2 +ATOM HB2 HA2 0.09 ! O=C +GROUP ! | +ATOM CG CT2 -0.14 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +ATOM SD S -0.09 +ATOM CE CT3 -0.22 +ATOM HE1 HA3 0.09 +ATOM HE2 HA3 0.09 +ATOM HE3 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB SD CG CE SD +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 +BOND CE HE1 CE HE2 CE HE3 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +RESI PHE 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | | +ATOM CA CT1 0.07 ! | HB1 CD1--CE1 +ATOM HA HB1 0.09 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--HZ +ATOM CB CT2 -0.18 ! | | \ __ / +ATOM HB1 HA2 0.09 ! | HB2 CD2--CE2 +ATOM HB2 HA2 0.09 ! O=C | | +GROUP ! | HD2 HE2 +ATOM CG CA 0.00 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA -0.115 +ATOM HZ HP 0.115 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 N HN +BOND N CA C CA C +N CA HA +BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 +DOUBLE O C CD1 CG CZ CE1 CE2 CD2 +BOND CE2 HE2 CZ HZ +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +RESI PRO 0.00 +GROUP ! HD1 HD2 +ATOM N N -0.29 ! | \ / +ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02 +ATOM HD1 HA2 0.09 ! | \ / +ATOM HD2 HA2 0.09 ! | CG +ATOM CA CP1 0.02 ! | / \ +ATOM HA HB1 0.09 ! HA-CA--CB HG2 +GROUP ! | / \ +ATOM CB CP2 -0.18 ! | HB1 HB2 +ATOM HB1 HA2 0.09 ! O=C +ATOM HB2 HA2 0.09 ! | +GROUP +ATOM CG CP2 -0.18 +ATOM HG1 HA2 0.09 +ATOM HG2 HA2 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND C CA C +N +BOND N CA CA CB CB CG CG CD N CD +BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB +DOUBLE O C +IMPR N -C CA CD +IMPR C CA +N O +CMAP -C N CA C N CA C +N +ACCEPTOR O C +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC CA CG *CB HB1 1.4585 102.5600 120.0000 109.0200 1.1131 +IC CA CG *CB HB2 1.4585 102.5600 -120.0000 109.0200 1.1131 +IC CB CD *CG HG1 1.5399 104.3900 120.0000 112.9500 1.1077 +IC CB CD *CG HG2 1.5399 104.3900 -120.0000 109.2200 1.1143 +IC N CG *CD HD1 1.5322 103.2100 120.0000 110.0300 1.1137 +IC N CG *CD HD2 1.5322 103.2100 -120.0000 110.0000 1.1144 +PATCHING FIRS PROP + +RESI SER 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | | +GROUP ! HA-CA--CB--OG +ATOM CB CT2 0.05 ! | | \ +ATOM HB1 HA2 0.09 ! | HB2 HG1 +ATOM HB2 HA2 0.09 ! O=C +ATOM OG OH1 -0.66 ! | +ATOM HG1 H 0.43 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA OG CB N HN N CA +BOND C CA C +N CA HA CB HB1 +BOND CB HB2 OG HG1 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +RESI THR 0.00 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | OG1--HG1 +ATOM HA HB1 0.09 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 0.14 ! | \ +ATOM HB HA1 0.09 ! | CG2--HG21 +ATOM OG1 OH1 -0.66 ! O=C / \ +ATOM HG1 H 0.43 ! | HG21 HG22 +GROUP +ATOM CG2 CT3 -0.27 +ATOM HG21 HA3 0.09 +ATOM HG22 HA3 0.09 +ATOM HG23 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA OG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +RESI TRP 0.00 +GROUP +ATOM N NH1 -0.47 ! | HE3 +ATOM HN H 0.31 ! HN-N | +ATOM CA CT1 0.07 ! | HB1 CE3 +ATOM HA HB1 0.09 ! | | / \\ +GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 +ATOM CB CT2 -0.18 ! | | || || | +ATOM HB1 HA2 0.09 ! | HB2 CD1 CE2 CH2-HH2 +ATOM HB2 HA2 0.09 ! O=C / \ / \ // +GROUP ! | HD1 NE1 CZ2 +ATOM CG CY -0.03 ! | | +ATOM CD1 CA -0.15 ! HE1 HZ2 +ATOM HD1 HP 0.22 +ATOM NE1 NY -0.51 +ATOM HE1 H 0.37 +ATOM CE2 CPT 0.24 +ATOM CD2 CPT 0.11 +ATOM CE3 CAI -0.25 +ATOM HE3 HP 0.17 +ATOM CZ3 CA -0.20 +ATOM HZ3 HP 0.14 +ATOM CZ2 CAI -0.27 +ATOM HZ2 HP 0.16 +ATOM CH2 CA -0.14 +ATOM HH2 HP 0.14 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG NE1 CD1 +BOND CZ2 CE2 +BOND N HN N CA C CA C +N +BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 +BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 +BOND CZ3 HZ3 CH2 HH2 +DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI TYR 0.00 +GROUP +ATOM N NH1 -0.47 ! | HD1 HE1 +ATOM HN H 0.31 ! HN-N | | +ATOM CA CT1 0.07 ! | HB1 CD1--CE1 +ATOM HA HB1 0.09 ! | | // \\ +GROUP ! HA-CA--CB--CG CZ--OH +ATOM CB CT2 -0.18 ! | | \ __ / \ +ATOM HB1 HA2 0.09 ! | HB2 CD2--CE2 HH +ATOM HB2 HA2 0.09 ! O=C | | +GROUP ! | HD2 HE2 +ATOM CG CA 0.00 +GROUP +ATOM CD1 CA -0.115 +ATOM HD1 HP 0.115 +GROUP +ATOM CE1 CA -0.115 +ATOM HE1 HP 0.115 +GROUP +ATOM CZ CA 0.11 +ATOM OH OH1 -0.54 +ATOM HH H 0.43 +GROUP +ATOM CD2 CA -0.115 +ATOM HD2 HP 0.115 +GROUP +ATOM CE2 CA -0.115 +ATOM HE2 HP 0.115 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG CB CD2 CG CE1 CD1 +BOND CZ CE2 OH CZ +BOND N HN N CA C CA C +N +BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 +BOND CE1 HE1 CE2 HE2 OH HH +DOUBLE O C CD1 CG CE1 CZ CE2 CD2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +DONOR HH OH +ACCEPTOR OH +ACCEPTOR O C +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +RESI VAL 0.00 +GROUP +ATOM N NH1 -0.47 ! | HG11 HG12 +ATOM HN H 0.31 ! HN-N | / +ATOM CA CT1 0.07 ! | CG1--HG13 +ATOM HA HB1 0.09 ! | / +GROUP ! HA-CA--CB-HB +ATOM CB CT1 -0.09 ! | \ +ATOM HB HA1 0.09 ! | CG2--HG21 +GROUP ! O=C / \ +ATOM CG1 CT3 -0.27 ! | HG21 HG22 +ATOM HG11 HA3 0.09 +ATOM HG12 HA3 0.09 +ATOM HG13 HA3 0.09 +GROUP +ATOM CG2 CT3 -0.27 +ATOM HG21 HA3 0.09 +ATOM HG22 HA3 0.09 +ATOM HG23 HA3 0.09 +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA CG1 CB CG2 CB N HN +BOND N CA C CA C +N CA HA +BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 +BOND CG2 HG22 CG2 HG23 +DOUBLE O C +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +RESI ALAD 0.00 ! Alanine dipeptide +GROUP +ATOM CL CT3 -0.27 +ATOM HL1 HA3 0.09 +ATOM HL2 HA3 0.09 +ATOM HL3 HA3 0.09 +GROUP +ATOM CLP C 0.51 +ATOM OL O -0.51 +GROUP +ATOM NL NH1 -0.47 +ATOM HL H 0.31 +ATOM CA CT1 0.07 +ATOM HA HB1 0.09 +GROUP +ATOM CB CT3 -0.27 ! HL1 OL OR HR1 +ATOM HB1 HA3 0.09 ! \ || HL HA || HR / +ATOM HB2 HA3 0.09 ! \ || | | || | / +ATOM HB3 HA3 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 +GROUP ! / | \ +ATOM CRP C 0.51 ! / HB1--CB--HB3 \ +ATOM OR O -0.51 ! HL3 | HR3 +GROUP ! HB2 +ATOM NR NH1 -0.47 +ATOM HR H 0.31 +ATOM CR CT3 -0.11 +ATOM HR1 HA3 0.09 +ATOM HR2 HA3 0.09 +ATOM HR3 HA3 0.09 + +BOND CL CLP CLP NL NL CA +BOND CA CRP CRP NR NR CR +DOUBLE CLP OL CRP OR +BOND NL HL NR HR +BOND CA HA CA CB +BOND CL HL1 CL HL2 CL HL3 +BOND CB HB1 CB HB2 CB HB3 +BOND CR HR1 CR HR2 CR HR3 +IMPR CLP CL NL OL NL CLP CA HL +IMPR CRP CA NR OR NR CRP CR HR + +CMAP CLP NL CA CRP NL CA CRP NR + +ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0 +ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic nl ca crp or 0.0 0.0 0.0 0.0 0.0 +ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left +ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0 +ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0 +ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right +ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0 +ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0 +ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0 +ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0 +ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0 +ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0 +ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0 +ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0 +ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0 +ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0 +ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0 +ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0 +ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 +ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 +ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0 +ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0 +ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0 +ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0 +patch first none last none + +PRES NTER 1.00 ! standard N-terminus +GROUP ! use in generate statement +ATOM N NH3 -0.30 ! +ATOM HT1 HC 0.33 ! HT1 +ATOM HT2 HC 0.33 ! (+)/ +ATOM HT3 HC 0.33 ! --CA--N--HT2 +ATOM CA CT1 0.21 ! | \ +ATOM HA HB1 0.10 ! HA HT3 +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES GLYP 1.00 ! Glycine N-terminus +GROUP ! use in generate statement +ATOM N NH3 -0.30 ! +ATOM HT1 HC 0.33 ! HA1 HT1 +ATOM HT2 HC 0.33 ! | (+)/ +ATOM HT3 HC 0.33 ! --CA--N--HT2 +ATOM CA CT2 0.13 ! | \ +ATOM HA1 HB2 0.09 ! HA2 HT3 +ATOM HA2 HB2 0.09 ! +DELETE ATOM HN +BOND HT1 N HT2 N HT3 N +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES PROP 1.00 ! Proline N-Terminal +GROUP ! use in generate statement +ATOM N NP -0.07 ! HA +ATOM HN1 HC 0.24 ! | +ATOM HN2 HC 0.24 ! -CA HN1 +ATOM CD CP3 0.16 ! / \ / +ATOM HD1 HA2 0.09 ! N(+) +ATOM HD2 HA2 0.09 ! / \ +ATOM CA CP1 0.16 ! -CD HN2 +ATOM HA HB1 0.09 ! | \ +BOND HN1 N HN2 N ! HD1 HD2 +DONOR HN1 N +DONOR HN2 N +IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES ACE 0.00 ! acetylated N-terminus + ! do NOT use to create dipeptides, see ACED +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA3 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA3 0.09 ! \ | / +ATOM HY3 HA3 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA HN +CMAP CY N CA C N CA C +N +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACED 0.00 ! acetylated N-terminus (to create dipeptide) +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA3 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA3 0.09 ! \ | / +ATOM HY3 HA3 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA HN +CMAP CY N CA C N CA C NT +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACP 0.00 ! acetylated N-terminus for proline + ! do NOT use to create dipeptide, see ACPD +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA3 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA3 0.09 ! \ | / +ATOM HY3 HA3 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA CD +CMAP CY N CA C N CA C +N +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACPD 0.00 ! acetylated N-terminus for proline (to create dipeptide) +GROUP ! use in generate statement +ATOM CAY CT3 -0.27 ! +ATOM HY1 HA3 0.09 ! HY1 HY2 HY3 +ATOM HY2 HA3 0.09 ! \ | / +ATOM HY3 HA3 0.09 ! CAY +GROUP ! | +ATOM CY C 0.51 ! CY=OY +ATOM OY O -0.51 ! | + ! +BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 +DOUBLE OY CY +IMPR CY CAY N OY +IMPR N CY CA CD +CMAP CY N CA C N CA C NT +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES NNEU 0.00 ! neutral N-terminus; charges from LSN +GROUP ! use in generate statement +ATOM N NH2 -0.96 ! +ATOM HT1 H 0.34 ! HT1 +ATOM HT2 H 0.34 ! / + ! --CA--N--HT2 +ATOM CA CT1 0.19 ! | ! change to CT2 for neutral N terminal glycine +ATOM HA HB1 0.09 ! HA ! change to HA1 and HB2 and add HA2 atom for N terminal glycine +DELETE ATOM HN +BOND HT1 N HT2 N +DONOR HT1 N +DONOR HT2 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES NGNE 0.00 ! neutral N-terminal glycine; charges from LSN +GROUP ! use in generate statement +ATOM N NH2 -0.96 ! +ATOM HT1 H 0.34 ! HA1 HT1 +ATOM HT2 H 0.34 ! | / + ! --CA--N--HT2 +ATOM CA CT2 0.10 ! | ! change to CT2 for neutral N terminal glycine +ATOM HA1 HB2 0.09 ! HA2 ! change to HA1 and HB2 and add HA2 atom for N terminal glycine +ATOM HA2 HB2 0.09 ! HA2 ! change to HA1 and HB2 and add HA2 atom for N terminal glycine +DELETE ATOM HN +BOND HT1 N HT2 N +DONOR HT1 N +DONOR HT2 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CTER -1.00 ! standard C-terminus +GROUP ! use in generate statement +ATOM C CC 0.34 ! OT2(-) +ATOM OT1 OC -0.67 ! / +ATOM OT2 OC -0.67 ! -C +DELETE ATOM O ! \\ +BOND C OT2 ! OT1 +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CNEU 0.00 ! protonated (neutral) C-terminu, charges from ASPP +GROUP ! use in generate statement; C reduced to balance charges +ATOM C CD 0.72 ! OT2-HT2 +ATOM OT1 OB -0.55 ! / +ATOM OT2 OH1 -0.61 ! -C +ATOM HT2 H 0.44 ! \\ +DELETE ATOM O ! OT1 +BOND C OT2 OT2 HT2 +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CTP 0.00 ! protonated C-terminus +GROUP ! use in generate statement +ATOM C CD 0.72 ! OT2--HT2 +ATOM OT1 OB -0.55 ! / +ATOM OT2 OH1 -0.61 ! -C +ATOM HT2 H 0.44 ! \\ +DELETE ATOM O ! OT1 +BOND C OT2 OT2 HT2 ! +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT1 0.00 ! methylated C-terminus from methyl acetate +GROUP ! use in generate statement +ATOM N NH1 -0.47 ! don't use with Gly or Pro +ATOM HN H 0.31 ! OT1 +ATOM CA CT1 0.17 ! | // +ATOM HA HB1 0.09 ! -N--CA--C HT1 +ATOM C CD 0.63 ! | | \ / +ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2 +ATOM OT2 OS -0.34 ! \ +ATOM CT CT3 -0.14 ! HT3 +ATOM HT1 HA3 0.09 ! +ATOM HT2 HA3 0.09 ! +ATOM HT3 HA3 0.09 ! +DELETE ATOM O +BOND C OT2 OT2 CT +BOND CT HT1 CT HT2 CT HT3 +DOUBLE C OT1 +IMPR C CA OT2 OT1 +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 + +PRES CT2 0.00 ! amidated C-terminus +GROUP ! use in generate statement +ATOM C CC 0.55 ! +ATOM O O -0.55 ! | +GROUP ! O=C +ATOM NT NH2 -0.62 ! | +ATOM HT1 H 0.32 ! NT +ATOM HT2 H 0.30 ! / \ +BOND C NT ! HT1 HT2 (HT1 is cis to O) +BOND NT HT1 NT HT2 ! +IMPR C NT CA O C CA NT O +IMPR NT C HT1 HT2 NT C HT2 HT1 +DONOR HT1 NT +DONOR HT2 NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT3 0.00 ! N-Methylamide C-terminus +GROUP ! use in generate statement +ATOM C C 0.51 ! +ATOM O O -0.51 ! | +GROUP ! C=O +ATOM NT NH1 -0.47 ! | +ATOM HNT H 0.31 ! NT-HNT +ATOM CAT CT3 -0.11 ! | +ATOM HT1 HA3 0.09 ! HT1-CAT-HT3 +ATOM HT2 HA3 0.09 ! | +ATOM HT3 HA3 0.09 ! HT2 + ! +BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 +IMPR NT C CAT HNT C CA NT O +CMAP -C N CA C N CA C NT +!CMAP CY N CA C N CA C NT +DONOR HNT NT +IC N CA C NT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 + ! via acetic acid, use in a patch statement and + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM CB CT2 -0.21 ! +ATOM HB1 HA2 0.09 ! HB1 OD1 +ATOM HB2 HA2 0.09 ! | // +ATOM CG CD 0.75 ! -CB--CG +ATOM OD1 OB -0.55 ! | \ +ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2 +ATOM HD2 H 0.44 ! +BOND OD2 HD2 +DONOR HD2 OD2 +IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 + ! via acetic acid, use in a patch statement and + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM CG CT2 -0.21 ! +ATOM HG1 HA2 0.09 ! HG1 OE1 +ATOM HG2 HA2 0.09 ! | // +ATOM CD CD 0.75 ! -CG--CD +ATOM OE1 OB -0.55 ! | \ +ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2 +ATOM HE2 H 0.44 ! +BOND OE2 HE2 +DONOR HE2 OE2 +IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES LSN 0.00 ! patch for neutral lysine based on methylamine + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +!delete atom and reassign charges +DELETE ATOM HZ3 +GROUP +ATOM CE CT2 0.13 +ATOM HE1 HA2 0.075 +ATOM HE2 HA2 0.075 +ATOM NZ NH2 -0.96 +ATOM HZ1 HC 0.34 +ATOM HZ2 HC 0.34 + +RESI CYM -1.00 ! Anionic Cysteine + ! Thiolate form based on RESI MES1 & ES1 (adm jr.) + ! in toppar_*_prot_model.str +! Foloppe, N., J. Sagemark, K. Nordstrand, K.D. Berndt, and L. Nilsson +! (2001). J. Mol. Biol. 310:449-470. +! Ported to CHARMM36 by kevo and beta hydrogens changed +! from HA to HA2 based on other AA and RESI ES1 +GROUP +ATOM N NH1 -0.47 ! | +ATOM HN H 0.31 ! HN-N +ATOM CA CT1 0.07 ! | HB1 +ATOM HA HB1 0.09 ! | | - +GROUP ! HA-CA--CB--SG (thiolate) +ATOM CB CS -0.38 ! | | +ATOM HB1 HA2 0.09 ! | HB2 +ATOM HB2 HA2 0.09 ! O=C +ATOM SG SS -0.80 ! | +GROUP +ATOM C C 0.51 +ATOM O O -0.51 +BOND CB CA SG CB N HN N CA +BOND O C C CA C +N CA HA CB HB1 CB HB2 +IMPR N -C CA HN C CA +N O +CMAP -C N CA C N CA C +N +DONOR HN N +ACCEPTOR O C +! IC table copied by kevo from RESI CYS +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 + +PRES CYSD -1.00 ! patch to deprotonate cysteine by kevo +DELETE ATOM HG1 ! from RESI ES1 in toppar_*_prot_model.str +ATOM CB CS -0.38 +ATOM HB1 HA2 0.09 +ATOM HB2 HA2 0.09 +ATOM SG SS -0.80 +! Doesn't require AUTOgenerate. + +PRES SERD -1.00 ! patch to deprotonate serine by kevo +DELETE ATOM HG1 ! from RESI ETO in toppar_*_prot_model.str +ATOM CB CT2 -0.30 +ATOM HB1 HA2 0.11 +ATOM HB2 HA2 0.11 +ATOM OG OC -0.92 +! That's all, folks! Doesn't even need AUTOgenerate. + +PRES LINK 0.00 ! linkage for IMAGES or for joining segments + ! 1 refers to previous (N terminal) + ! 2 refers to next (C terminal) + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +!the need for the explicit specification of angles and dihedrals in +!patches linking images has not been tested +!ANGLE 1C 2N 2CA 1CA 1C 2N +!ANGLE 1O 1C 2N 1C 2N 2HN +!DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB +!DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N +!DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA +!DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM 1CB CT2 -0.10 ! +ATOM 1SG SM -0.08 ! 2SG--2CB-- +GROUP ! / +ATOM 2SG SM -0.08 ! -1CB--1SG +ATOM 2CB CT2 -0.10 ! +DELETE ATOM 1HG1 +DELETE ATOM 2HG1 +BOND 1SG 2SG +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +GROUP +ATOM CE1 CPH2 0.25 ! HE1 +ATOM HE1 HR1 0.13 ! / +ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1 +ATOM CG CPH1 0.22 ! | / | +ATOM CB CT2 -0.08 ! -CB--CG | +ATOM HB1 HA2 0.09 ! | \ | +ATOM HB2 HA2 0.09 ! HB2 CD2--NE2 +GROUP ! | \ +ATOM NE2 NR1 -0.36 ! HD2 HE2 +ATOM HE2 H 0.32 +ATOM CD2 CPH1 -0.05 +ATOM HD2 HR3 0.09 +DELETE ATOM HD1 +DELETE ACCE NE2 +BOND NE2 HE2 +IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 +DONOR HE2 NE2 +ACCEPTOR ND1 +IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 + +! patches for cyclic peptides +PRES LIG1 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus + ! use in a patch statement, perform initial + ! generation using first NONE last NONE + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG2 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES LIG3 0.00000 ! linkage for cyclic peptide + ! 1 refers to the C terminus which is a glycine + ! 2 refers to the N terminus which is a glycine + ! use in a patch statement, perform initial + ! generation using first NONE last NONE + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 1C 2N +IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +END + diff --git a/charmm/toppar/toph19.inp b/charmm/toppar/toph19.inp new file mode 100644 index 00000000..10acac0a --- /dev/null +++ b/charmm/toppar/toph19.inp @@ -0,0 +1,1319 @@ +* TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 +* + 20 1 ! Version number + +!references +!Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D. +!Thesis, Department of Chemistry, Harvard University, Cambridge, MA, +!USA, 1985 +! +!and +! +!Neria, E., Fischer, S., and Karplus, M. Simulation of Activation Free +!Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105: +!1902-21. + +MASS 1 H 1.00800 ! hydrogen which can h-bond to neutral atom +MASS 2 HC 1.00800 ! - " - charged atom +MASS 3 HA 1.00800 ! aliphatic hydrogen +MASS 4 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 5 LP 0.0 ! ST2 LONE PAIR +MASS 10 CT 12.01100 ! aliphatic carbon +MASS 11 C 12.01100 ! carbonyl carbon +MASS 12 CH1E 13.01900 ! extended atom carbon w/ one hydrogen +MASS 13 CH2E 14.02700 ! - " - two +MASS 14 CH3E 15.03500 ! - " - three +MASS 15 CR1E 13.01900 ! - " - in aromatic ring w/ one H +MASS 16 CM 12.01100 ! carbon in carbonmonoxide +MASS 31 N 14.00670 ! peptide nitrogen with no hydrogens attached +MASS 32 NR 14.00670 ! nitrogen in aromatic ring with no hydrogens +MASS 33 NP 14.00670 ! pyrole nitrogen +!MASS 34 NH1E 15.01470 ! extended atom peptide nitrogen with one hydrogen +!MASS 35 NH2E 16.02270 ! - " - two -"- +!MASS 36 NH3E 17.03070 ! - " - three -"- +!MASS 37 NC2E 16.02270 ! extended atom charged guanidinium nitrogen w/ 2 H +MASS 38 NH1 14.00670 ! peptide nitrogen bound to one hydrogen +MASS 39 NH2 14.00670 ! - " - two -"- +MASS 40 NH3 14.00670 ! nitrogen bound to three hydrogens +MASS 41 NC2 14.00670 ! charged guanidinuim nitrogen bound to two hydrogens +MASS 51 O 15.99940 ! carbonyl oxygen +MASS 52 OC 15.99940 ! carboxy oxygen +!MASS 53 OH1E 17.00740 ! extended atom hydroxy oxygen +!MASS 54 OH2E 18.01540 ! extended atom water +MASS 55 OH1 15.99940 ! hydroxy oxygen +MASS 56 OH2 15.99940 ! ST2 water oxygen +MASS 57 OM 15.99940 ! oxygen in carbonmonoxide +MASS 58 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 59 OS 15.99940 ! ester oxygen +MASS 81 S 32.06000 ! sulphur +MASS 82 SH1E 33.06800 ! extended atom sulphur with one hydrogen +MASS 91 FE 55.84700 ! iron + +DECL -C +DECL -O +DECL +N +DECL +H +DECL +CA + +AUTOGENERATE ANGLES +DEFA FIRS NTER LAST CTER + +RESI ALA 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH3E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB +DIHE -C N CA C N CA C +N CA C +N +CA +IMPH N -C CA H C CA +N O CA N C CB +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 + +RESI ARG 1.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +ATOM CG CH2E 0.00 +GROU +ATOM CD CH2E 0.10 +ATOM NE NH1 -0.40 +ATOM HE H 0.30 +ATOM CZ C 0.50 +GROU +ATOM NH1 NC2 -0.45 +ATOM HH11 HC 0.35 +ATOM HH12 HC 0.35 +GROU +ATOM NH2 NC2 -0.45 +ATOM HH21 HC 0.35 +ATOM HH22 HC 0.35 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG CD CD NE NE HE +BOND NE CZ CZ NH1 CZ NH2 NH1 HH11 NH1 HH12 +BOND NH2 HH21 NH2 HH22 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD CB CG CD NE +DIHE CG CD NE CZ CD NE CZ NH1 NE CZ NH1 HH11 +DIHE NE CZ NH2 HH21 NE CZ NH1 HH12 NE CZ NH2 HH22 +IMPH N -C CA H C CA +N O CA N C CB +IMPH NE CD CZ HE CZ NH1 NH2 NE +DONO H N +DONO HE NE +DONO HH11 NH1 +DONO HH12 NH1 +DONO HH21 NH2 +DONO HH22 NH2 +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 +IC CB CG CD NE 0.0000 0.00 180.00 0.00 0.0000 +IC CG CD NE CZ 0.0000 0.00 180.00 0.00 0.0000 +IC CD NE CZ NH1 0.0000 0.00 180.00 0.00 0.0000 +IC NH1 NE *CZ NH2 0.0000 0.00 180.00 0.00 0.0000 +IC CD CZ *NE HE 0.0000 0.00 180.00 0.00 0.0000 +IC NE CZ NH1 HH11 0.0000 0.00 180.00 0.00 0.0000 +IC HH11 CZ *NH1 HH12 0.0000 0.00 180.00 0.00 0.0000 +IC NE CZ NH2 HH21 0.0000 0.00 180.00 0.00 0.0000 +IC HH21 CZ *NH2 HH22 0.0000 0.00 180.00 0.00 0.0000 + +RESI ASN 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +GROU +ATOM CG C 0.55 +ATOM OD1 O -0.55 +GROU +ATOM ND2 NH2 -0.60 +ATOM HD21 H 0.30 +ATOM HD22 H 0.30 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG OD1 CG ND2 ND2 HD21 +BOND ND2 HD22 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG OD1 CB CG ND2 HD21 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG OD1 ND2 CB ND2 HD21 HD22 CG +DONO H N +DONO HD21 ND2 +DONO HD22 ND2 +ACCE OD1 CG +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG OD1 0.0000 0.00 180.00 0.00 0.0000 +IC OD1 CB *CG ND2 0.0000 0.00 180.00 0.00 0.0000 +IC OD1 CG ND2 HD21 0.0000 0.00 180.00 0.00 0.0000 +IC HD21 CG *ND2 HD22 0.0000 0.00 180.00 0.00 0.0000 + +RESI ASP -1.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E -0.16 +ATOM CG C 0.36 +ATOM OD1 OC -0.60 +ATOM OD2 OC -0.60 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG OD1 CG OD2 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG OD1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG OD1 OD2 CB +DONO H N +ACCE OD1 CG +ACCE OD2 CG +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG OD1 0.0000 0.00 180.00 0.00 0.0000 +IC OD1 CB *CG OD2 0.0000 0.00 180.00 0.00 0.0000 + +RESI CYS 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.19 +ATOM SG SH1E -0.19 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB SG +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB SG +IMPH N -C CA H C CA +N O CA N C CB +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB SG 0.0000 0.00 180.00 0.00 0.0000 + +RESI GLN 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +ATOM CG CH2E 0.00 +GROU +ATOM CD C 0.55 +ATOM OE1 O -0.55 +GROU +ATOM NE2 NH2 -0.60 +ATOM HE21 H 0.30 +ATOM HE22 H 0.30 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG CD CD OE1 CD NE2 +BOND NE2 HE21 NE2 HE22 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD CB CG CD OE1 +DIHE CG CD NE2 HE21 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CD OE1 NE2 CG NE2 HE21 HE22 CD +DONO H N +DONO HE21 NE2 +DONO HE22 NE2 +ACCE OE1 CD +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 +IC CB CG CD OE1 0.0000 0.00 180.00 0.00 0.0000 +IC OE1 CG *CD NE2 0.0000 0.00 180.00 0.00 0.0000 +IC OE1 CD NE2 HE21 0.0000 0.00 180.00 0.00 0.0000 +IC HE21 CD *NE2 HE22 0.0000 0.00 180.00 0.00 0.0000 + +RESI GLU -1.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +GROU +ATOM CG CH2E -0.16 +ATOM CD C 0.36 +ATOM OE1 OC -0.60 +ATOM OE2 OC -0.60 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG CD CD OE1 CD OE2 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD CB CG CD OE1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CD OE1 OE2 CG +DONO H N +ACCE OE1 CD +ACCE OE2 CD +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 +IC CB CG CD OE1 0.0000 0.00 180.00 0.00 0.0000 +IC OE1 CG *CD OE2 0.0000 0.00 180.00 0.00 0.0000 + +RESI GLY 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH2E 0.10 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +DIHE -C N CA C N CA C +N CA C +N +CA +IMPH N -C CA H C CA +N O +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +PATC FIRS GLYP + +RESI HIS 0.00000 ! Rings charges from Del Bene and Cohen +GROU ! JACS 100:5285 (1978) Imidazole sto-3g calc. +ATOM N NH1 -0.35 ! Note that this residue has non-neutral groups. +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +GROUP +ATOM CG C 0.10 +ATOM ND1 NH1 -0.40 +ATOM HD1 H 0.30 +GROU +ATOM CD2 CR1E 0.10 +ATOM NE2 NR -0.40 +ATOM CE1 CR1E 0.30 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG ND1 CG CD2 ND1 HD1 +BOND ND1 CE1 CD2 NE2 CE1 NE2 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG ND1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG ND1 CD2 CB ND1 CG CE1 HD1 CG ND1 CE1 NE2 +IMPH ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 +IMPH CD2 CG ND1 CE1 +DONO H N +DONO HD1 ND1 +ACCE NE2 +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD2 0.0000 0.00 90.00 0.00 0.0000 +IC CD2 CB *CG ND1 0.0000 0.00 180.00 0.00 0.0000 +IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 +IC ND1 CG CD2 NE2 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 + +RESI HSD 0.00000 ! see HIS above. +GROUP +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +GROUP +ATOM CG C 0.10 +ATOM ND1 NR -0.40 +ATOM CE1 CR1E 0.30 +GROU +ATOM CD2 CR1E 0.10 +ATOM NE2 NH1 -0.40 +ATOM HE2 H 0.30 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG ND1 CG CD2 ND1 CE1 +BOND CD2 NE2 CE1 NE2 NE2 HE2 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG ND1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG ND1 CD2 CB NE2 CE1 CD2 HE2 CG ND1 CE1 NE2 +IMPH ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 +IMPH CD2 CG ND1 CE1 +DONO H N +DONO HE2 NE2 +ACCE ND1 +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD2 0.0000 0.00 90.00 0.00 0.0000 +IC CD2 CB *CG ND1 0.0000 0.00 180.00 0.00 0.0000 +IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 +IC ND1 CG CD2 NE2 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 CD2 *NE2 HE2 0.0000 0.00 180.00 0.00 0.0000 + +RESI HSC 1.00000 ! Doubly protonated histidine. Ring charges +GROU +ATOM N NH1 -0.35 ! Hayes and Kollman jacs 98:3335 (1976). +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.10 +ATOM CG C 0.15 +ATOM CD2 CR1E 0.20 +GROU +ATOM ND1 NH1 -0.30 +ATOM HD1 H 0.35 +GROU +ATOM CE1 CR1E 0.45 +GROU +ATOM NE2 NH1 -0.30 +ATOM HE2 H 0.35 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG ND1 CG CD2 ND1 HD1 +BOND ND1 CE1 CD2 NE2 CE1 NE2 NE2 HE2 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG ND1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG ND1 CD2 CB ND1 CG CE1 HD1 CG ND1 CE1 NE2 +IMPH ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 +IMPH CD2 CG ND1 CE1 NE2 CD2 CE1 HE2 +DONO H N +DONO HD1 ND1 +DONO HE2 NE2 +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD2 0.0000 0.00 90.00 0.00 0.0000 +IC CD2 CB *CG ND1 0.0000 0.00 180.00 0.00 0.0000 +IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 +IC ND1 CG CD2 NE2 0.0000 0.00 0.00 0.00 0.0000 +IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 +IC CE1 CD2 *NE2 HE2 0.0000 0.00 180.00 0.00 0.0000 + +RESI ILE 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH1E 0.00 +ATOM CG2 CH3E 0.00 +GROU +ATOM CG1 CH2E 0.00 +ATOM CD CH3E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG1 CB CG2 CG1 CD +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG1 CA CB CG1 CD +IMPH N -C CA H C CA +N O CA N C CB +IMPH CB CG1 CG2 CA +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG1 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG1 CD 0.0000 0.00 180.00 0.00 0.0000 +IC CG1 CA *CB CG2 0.0000 0.00 -120.00 0.00 0.0000 + +RESI LEU 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +ATOM CG CH1E 0.00 +ATOM CD1 CH3E 0.00 +ATOM CD2 CH3E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG CD1 CG CD2 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD2 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG CD2 CD1 CB +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD1 0.0000 0.00 180.00 0.00 0.0000 +IC CD1 CB *CG CD2 0.0000 0.00 120.00 0.00 0.0000 + +RESI LYS 1.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +ATOM CG CH2E 0.00 +ATOM CD CH2E 0.00 +GROU +ATOM CE CH2E 0.25 +ATOM NZ NH3 -0.30 +ATOM HZ1 HC 0.35 +ATOM HZ2 HC 0.35 +ATOM HZ3 HC 0.35 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG CD CD CE CE NZ +BOND NZ HZ1 NZ HZ2 NZ HZ3 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD CB CG CD CE +DIHE CG CD CE NZ CD CE NZ HZ1 CD CE NZ HZ2 +DIHE CD CE NZ HZ3 +IMPH N -C CA H C CA +N O CA N C CB +DONO H N +DONO HZ1 NZ +DONO HZ2 NZ +DONO HZ3 NZ +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 +IC CB CG CD CE 0.0000 0.00 180.00 0.00 0.0000 +IC CG CD CE NZ 0.0000 0.00 180.00 0.00 0.0000 +IC CD CE NZ HZ1 0.0000 0.00 180.00 0.00 0.0000 +IC HZ1 CE *NZ HZ2 0.0000 0.00 120.00 0.00 0.0000 +IC HZ2 CE *NZ HZ3 0.0000 0.00 120.00 0.00 0.0000 + +RESI MET 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +GROU +ATOM CG CH2E 0.06 +ATOM SD S -0.12 +ATOM CE CH3E 0.06 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG SD SD CE +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG SD CB CG SD CE +IMPH N -C CA H C CA +N O CA N C CB +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG SD 0.0000 0.00 180.00 0.00 0.0000 +IC CB CG SD CE 0.0000 0.00 180.00 0.00 0.0000 + +! Penicillamine +RESI PEN 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CT 0.19 +ATOM CG1 CH3E 0.0 +ATOM CG2 CH3E 0.0 +ATOM SG SH1E -0.19 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB SG CB CG1 CB CG2 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB SG +IMPH N -C CA H C CA +N O CA N C CB +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB SG 0.0000 0.00 180.00 0.00 0.0000 +IC SG CA *CB CG1 0.0000 0.00 120.00 0.00 0.0000 +IC SG CA *CB CG2 0.0000 0.00 -120.00 0.00 0.0000 + +RESI PHE 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +ATOM CG C 0.00 CZ +ATOM CD1 CR1E 0.00 CE2 +ATOM CD2 CR1E 0.00 CE1 +GROU +ATOM CE1 CR1E 0.00 +ATOM CE2 CR1E 0.00 +ATOM CZ CR1E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG CD1 CG CD2 CD1 CE1 +BOND CD2 CE2 CE1 CZ CE2 CZ +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG CD1 CE1 CZ CD1 CE1 CZ CE2 CE1 CZ CE2 CD2 +IMPH CZ CE2 CD2 CG CE2 CD2 CG CD1 CD2 CG CD1 CE1 +IMPH CG CD1 CD2 CB +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD1 0.0000 0.00 90.00 0.00 0.0000 +IC CD1 CB *CG CD2 0.0000 120.00 180.00 120.00 0.0000 +IC CD1 CG CD2 CE2 0.0000 120.00 0.00 120.00 0.0000 +IC CD2 CG CD1 CE1 0.0000 120.00 0.00 120.00 0.0000 +IC CG CD1 CE1 CZ 0.0000 120.00 0.00 120.00 0.0000 + +RESI PRO 0.00000 +GROU +ATOM N N -0.20 +ATOM CD CH2E 0.10 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +ATOM CG CH2E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N CD +BOND CA CB CB CG CG CD +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD CB CG CD N +DIHE CG CD N CA +IMPH N CA CD -C C CA +N O CA N C CB +ACCE O C +IC -C CA *N CD 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 -60.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC C N *CA CB 0.0000 0.00 -120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 0.00 108.00 0.0000 +PATC FIRS PROP + +RESI SER 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.25 +ATOM OG OH1 -0.65 +ATOM HG H 0.40 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB OG OG HG +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB OG CA CB OG HG +IMPH N -C CA H C CA +N O CA N C CB +DONO H N +DONO HG OG +ACCE OG +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB OG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB OG HG 0.0000 0.00 180.00 0.00 0.0000 + +RESI THR 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH1E 0.25 +ATOM OG1 OH1 -0.65 +ATOM HG1 H 0.40 +GROU +ATOM CG2 CH3E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB OG1 CB CG2 OG1 HG1 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB OG1 CA CB OG1 HG1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CB OG1 CG2 CA +DONO H N +DONO HG1 OG1 +ACCE OG1 +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB OG1 0.0000 0.00 180.00 0.00 0.0000 +IC OG1 CA *CB CG2 0.0000 0.00 -120.00 0.00 0.0000 +IC CA CB OG1 HG1 0.0000 0.00 180.00 0.00 0.0000 + +RESI TRP 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +GROU +ATOM CG C -0.03 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 +ATOM CD2 C 0.10 NE1 CE2 CE3 CZ2 CZ3 CH2 +ATOM CE2 C -0.04 CE3 CZ2 CZ3 CH2 +ATOM CE3 CR1E -0.03 CZ2 CZ3 CH2 +GROU +ATOM CD1 CR1E 0.06 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 +ATOM NE1 NH1 -0.36 CE2 CE3 CZ2 CZ3 CH2 +ATOM HE1 H 0.30 +GROU +ATOM CZ2 CR1E 0.00 CZ3 CH2 +ATOM CZ3 CR1E 0.00 CH2 +ATOM CH2 CR1E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG CD1 CG CD2 CD1 NE1 +BOND CD2 CE2 NE1 HE1 NE1 CE2 CD2 CE3 CE2 CZ2 +BOND CE3 CZ3 CZ2 CH2 CZ3 CH2 +! The ring angles are only assigned for the five and six member rings. +! The angles CG CD2 CE3 and NE1 CE2 CZ2 are left out to avoid conflicts +! with the histidine angle parameters and to preserve symmetry. +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD1 +! The following dihedrals span the rings and keep them parallel. +DIHE CD1 CE2 CD2 CZ3 CD1 CD2 CE2 CH2 +DIHE CZ2 CE2 CD2 CG CE3 CD2 CE2 NE1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG CD1 CD2 CB NE1 CD1 CE2 HE1 CD2 CE2 CZ2 CH2 +IMPH CE2 CZ2 CH2 CZ3 CZ2 CH2 CZ3 CE3 CH2 CZ3 CE3 CD2 +IMPH CZ3 CE3 CD2 CE2 CE3 CD2 CE2 CZ2 CG CD1 NE1 CE2 +IMPH CD1 NE1 CE2 CD2 NE1 CE2 CD2 CG CE2 CD2 CG CD1 +IMPH CD2 CG CD1 NE1 +! These impropers are skipped IMPH CD2 CG CE3 CE2 CE2 CZ2 NE1 CD2 +! because the rings are kept flat by the proper dihedrals noted above. +DONO H N +DONO HE1 NE1 +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD2 0.0000 0.00 90.00 127.45 1.3673 +IC CD2 CB *CG CD1 1.3673 127.45 180.00 121.78 1.3815 +IC CD1 CG CD2 CE2 1.3815 110.77 0.00 102.51 1.3551 +IC CD2 CG CD1 NE1 1.3673 110.77 0.00 106.30 1.3203 +IC CE2 CD1 *NE1 HE1 1.3374 108.05 180.00 125.46 0.9802 +IC CE2 CG *CD2 CE3 1.3551 102.51 180.00 134.73 1.3728 +IC CE2 CD2 CE3 CZ3 1.3551 122.76 0.00 115.22 1.3882 +IC CE3 CD2 CE2 CZ2 1.3728 122.76 0.00 123.56 1.3712 +IC CD2 CE2 CZ2 CH2 1.3551 123.56 0.00 114.96 1.3877 + +RESI TYR 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH2E 0.00 +ATOM CG C 0.00 CZ +GROU +ATOM CD1 CR1E 0.00 CE2 +ATOM CE1 CR1E 0.00 CD2 +GROU +ATOM CD2 CR1E 0.00 +ATOM CE2 CR1E 0.00 +GROU +ATOM CZ C 0.25 +ATOM OH OH1 -0.65 +ATOM HH H 0.40 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG CG CD1 CG CD2 CD1 CE1 +BOND CD2 CE2 CE1 CZ CE2 CZ CZ OH OH HH +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG CA CB CG CD1 CE2 CZ OH HH +IMPH N -C CA H C CA +N O CA N C CB +IMPH CG CD1 CD2 CB CZ CE1 CE2 OH CG CD1 CE1 CZ +IMPH CD1 CE1 CZ CE2 CE1 CZ CE2 CD2 CZ CE2 CD2 CG +IMPH CE2 CD2 CG CD1 CD2 CG CD1 CE1 +DONO H N +DONO HH OH +ACCE OH +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 +IC CA CB CG CD1 0.0000 0.00 90.00 0.00 0.0000 +IC CD1 CB *CG CD2 0.0000 120.00 180.00 120.00 0.0000 +IC CD2 CG CD1 CE1 0.0000 120.00 0.00 120.00 0.0000 +IC CD1 CG CD2 CE2 0.0000 120.00 0.00 120.00 0.0000 +IC CG CD1 CE1 CZ 0.0000 120.00 0.00 120.00 0.0000 +IC CE2 CE1 *CZ OH 0.0000 120.00 180.00 120.00 0.0000 +IC CE1 CZ OH HH 0.0000 120.00 180.00 0.00 0.0000 + +RESI VAL 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH1E 0.10 +GROU +ATOM CB CH1E 0.00 +ATOM CG1 CH3E 0.00 +ATOM CG2 CH3E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND N CA CA C C +N C O N H +BOND CA CB CB CG1 CB CG2 +DIHE -C N CA C N CA C +N CA C +N +CA +DIHE N CA CB CG1 +IMPH N -C CA H C CA +N O CA N C CB +IMPH CB CG2 CG1 CA +DONO H N +ACCE O C +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 +IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 +IC N CA CB CG1 0.0000 0.00 180.00 0.00 0.0000 +IC CG1 CA *CB CG2 0.0000 0.00 120.00 0.00 0.0000 + + +RESI HEME -2.00000 +GROU +ATOM FE FE 0.24 +ATOM NA NP -0.18 +ATOM NB NP -0.18 +ATOM NC NP -0.18 +ATOM ND NP -0.18 +GROU +ATOM C1A C 0.03 +ATOM CHA CR1E 0.04 +ATOM C4D C 0.02 +GROU +ATOM C1B C 0.03 +ATOM CHB CR1E 0.04 +ATOM C4A C 0.02 +GROU +ATOM C1C C 0.03 +ATOM CHC CR1E 0.04 +ATOM C4B C 0.02 +GROU +ATOM C1D C 0.03 +ATOM CHD CR1E 0.04 +ATOM C4C C 0.02 +GROU +ATOM C2A C -0.02 +ATOM CAA CH2E 0.04 +GROU +ATOM C3A C 0.02 +ATOM CMA CH3E -0.04 +GROU +ATOM CBA CH2E -0.10 +ATOM CGA C 0.30 +ATOM O1A OC -0.50 +ATOM O2A OC -0.50 +GROU +ATOM C2B C 0.02 +ATOM CMB CH3E -0.04 +GROU +ATOM C3B C -0.05 +ATOM CAB CR1E 0.03 +ATOM CBB CH2E -0.10 +GROU +ATOM C2C C 0.02 +ATOM CMC CH3E -0.04 +GROU +ATOM C3C C -0.05 +ATOM CAC CR1E 0.03 +ATOM CBC CH2E -0.10 +GROU +ATOM C2D C 0.02 +ATOM CMD CH3E -0.04 +GROU +ATOM C3D C -0.02 +ATOM CAD CH2E 0.04 +GROU +ATOM CBD CH2E -0.10 +ATOM CGD C 0.30 +ATOM O1D OC -0.50 +ATOM O2D OC -0.50 +BOND FE NA FE NB FE NC FE ND NA C1A +BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA +BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA +BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B +BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB +BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C +BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC +BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D +BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD +BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A +DIHE NA C4A CHB C1B C4A CHB C1B NB NB C4B CHC C1C +DIHE C4B CHC C1C NC NC C4C CHD C1D C4C CHD C1D ND +DIHE ND C4D CHA C1A C4D CHA C1A NA C1A C2A CAA CBA +DIHE C2A CAA CBA CGA CAA CBA CGA O1A C2B C3B CAB CBB +DIHE C2C C3C CAC CBC C2D C3D CAD CBD C3D CAD CBD CGD +DIHE CAD CBD CGD O1D +IMPH FE C1A C4A NA FE C1B C4B NB FE C1C C4C NC +IMPH FE C1D C4D ND CHA NA C2A C1A CHB NA C3A C4A +IMPH CHB NB C2B C1B CHC NB C3B C4B CHC NC C2C C1C +IMPH CHD NC C3C C4C CHD ND C2D C1D CHA ND C3D C4D +IMPH C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB +IMPH C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC +IMPH C2D C1D C3D CMD C3D C2D C4D CAD CBA O1A O2A CGA +IMPH CBD O1D O2D CGD +ACCE NA +ACCE O1A CGA +ACCE O2A CGA +ACCE NB +ACCE NC +ACCE ND +ACCE O1D CGD +ACCE O2D CGD +PATC FIRS NONE LAST NONE + +RESI ACE 0.00000 ! Acetyl blocking group with standard naming. +GROU +ATOM CH3 CH3E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND CH3 C C +N C O +DIHE CH3 C +N +CA +IMPH C CH3 +N O +ACCE O C +IC +N CH3 *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CH3 C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +! +! formamide. Charges according to Reiher (from States?) +RESI FORM 0.00000 +GROU +ATOM HA HA 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +GROU +ATOM N NH2 -0.60 +ATOM H1 H 0.30 +ATOM H2 H 0.30 +BOND HA C C N C O +BOND N H2 N H1 +DIHE HA C N H2 +IMPH C HA N O +IMPH N C H2 H1 +ACCE O C +DONO H1 N +IC N HA *C O 0.0000 0.00 180.00 0.00 0.0000 +IC HA C N H2 0.0000 0.00 180.00 0.00 0.0000 +IC C H2 *N H1 0.0000 0.00 180.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI AMN 0.00000 +GROU +ATOM CL CH3E 0.00 +GROU +ATOM C C 0.55 +ATOM O O -0.55 +BOND CL C C +N C O +DIHE CL C +N +CA +IMPH C CL +N O +ACCE O C +IC +N CL *C O 0.0000 0.00 180.00 0.00 0.0000 +IC CL C +N +CA 0.0000 0.00 180.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI CBX 0.00000 +GROU +ATOM N NH1 -0.35 +ATOM H H 0.25 +ATOM CA CH3E 0.10 +BOND N CA N H +IMPH N -C CA H +DONO H N +IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +PRES NTER 1.00000 +GROU +ATOM HT1 HC 0.35 +ATOM HT2 HC 0.35 +ATOM N NH3 -0.30 +ATOM HT3 HC 0.35 +DELETE ATOM H +ATOM CA CH1E 0.25 +BOND HT1 N HT2 N HT3 N +DIHE HT2 N CA C HT1 N CA C HT3 N CA C +DONO HT1 N +DONO HT2 N +DONO HT3 N +IC HT1 N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC HT2 CA *N HT1 0.0000 0.00 120.00 0.00 0.0000 +IC HT3 CA *N HT2 0.0000 0.00 120.00 0.00 0.0000 + +PRES GLYP 1.00000 +GROUP +ATOM HT1 HC 0.35 +ATOM HT2 HC 0.35 +ATOM N NH3 -0.30 +ATOM HT3 HC 0.35 +DELETE ATOM H +ATOM CA CH2E 0.25 +BOND HT1 N HT2 N HT3 N +DIHE HT2 N CA C HT1 N CA C HT3 N CA C +DONO HT1 N +DONO HT2 N +DONO HT3 N +IC HT1 N CA C 0.0000 0.00 180.00 0.00 0.0000 +IC HT2 CA *N HT1 0.0000 0.00 120.00 0.00 0.0000 +IC HT3 CA *N HT2 0.0000 0.00 120.00 0.00 0.0000 + +PRES PROP 1.00000 +GROUP +ATOM HT1 HC 0.35 +ATOM HT2 HC 0.35 +ATOM N NH3 -0.20 +ATOM CD CH2E 0.25 +ATOM CA CH1E 0.25 +BOND HT1 N HT2 N +DIHE HT2 N CA C HT1 N CA C +DONO HT1 N +DONO HT2 N +IC HT1 CA *N CD 0.0000 0.00 120.00 0.00 0.0000 +IC HT2 CA *N HT1 0.0000 0.00 120.00 0.00 0.0000 + +PRES CTER -1.00000 +GROU +ATOM C C 0.14 +ATOM OT1 OC -0.57 +ATOM OT2 OC -0.57 +DELETE ATOM O +BOND C OT1 C OT2 +DIHE N CA C OT2 +IMPH C CA OT2 OT1 +ACCE OT1 C +ACCE OT2 C +IC N CA C OT2 0.0 0.0 180.0 0.0 0.0 +IC OT2 CA *C OT1 0.0 0.0 180.0 0.0 0.0 + +PRES LINK 0.0 ! linkage for IMAGES or for joining segments +! 1 refers to previous (N terminal), 2 refers to next (C terminal) +BOND 1C 2N +THET 1C 2N 2CA 1CA 1C 2N +THET 1O 1C 2N 1C 2N 2H +DIHE 1C 2N 2CA 2C 1N 1CA 1C 2N 1CA 1C 2N 2CA +IMPH 2N 1C 2CA 2H 1C 1CA 2N 1O +IC 1N 1CA 1C 2N 0.0000 0.00 180.00 0.00 0.0000 +IC 2N 1CA *1C 1O 0.0000 0.00 180.00 0.00 0.0000 +IC 1CA 1C 2N 2CA 0.0000 0.00 180.00 0.00 0.0000 +IC 1C 2N 2CA 2C 0.0000 0.00 180.00 0.00 0.0000 +IC 1C 2CA *2N 2H 0.0000 0.00 180.00 0.00 0.0000 + +RESI O2 0.00000 +GROUP +ATOM O1 OM 0.021 +ATOM O2 OM -0.021 +BOND O1 O2 +PATC FIRS NONE LAST NONE + +RESI CO2P 0.00000 +GROUP +ATOM C CM 0.021 +ATOM O OM -0.021 +BOND C O +PATC FIRS NONE LAST NONE + +RESI CO 0.00000 +GROUP +ATOM C CM 0.021 +ATOM O OM -0.021 +BOND C O +PATC FIRS NONE LAST NONE + +RESI ETH 0.00000 +GROU +ATOM C2 CH3E 0.00 +GROU +ATOM C1 CH2E 0.25 +ATOM O OH1 -0.65 +ATOM H H 0.40 +BOND C2 C1 C1 O O H +DIHE C2 C1 O H +DONO H O +ACCE O +IC C2 C1 O H 0.0000 0.00 180.00 0.00 0.0000 +IC C1 O H BLNK 0.0000 0.00 0.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +RESI ST2 .000 ! NOW INCLUDES THE LONE PAIRS GIVING 5 ATOMS FOR ST2 +GROUP +ATOM OX2 OH2 .00 +ATOM HX1 H .24 +ATOM HX2 H .24 +ATOM LX1 LP -.24 +ATOM LX2 LP -.24 +BOND OX2 HX1 OX2 HX2 +BOND OX2 LX1 OX2 LX2 +! NOTE: NO DONORS OR ACCEPTORS FOR ST2 +PATC FIRS NONE LAST NONE + +RESI TIP3 .000 ! TIPS3P WATER MODEL +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +ANGLE H1 OH2 H2 +ACCE OH2 +PATC FIRS NONE LAST NONE + +RESI OH2 .000 ! TIPS3P WATER MODEL +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE +ANGLE H1 OH2 H2 +ACCE OH2 +PATC FIRS NONE LAST NONE + +RESI SO4 -2.0 +GROUP +ATOM S S 0.0 +ATOM O1 OC -0.5 +ATOM O2 OC -0.5 +ATOM O3 OC -0.5 +ATOM O4 OC -0.5 +BOND S O1 S O2 S O3 S O4 +ACCE O1 S +ACCE O2 S +ACCE O3 S +ACCE O4 S +PATC FIRS NONE LAST NONE + +RESI COH 0.00000 +GROU +ATOM C CH3E 0.25 +ATOM O OH1 -0.65 +ATOM H H 0.40 +BOND C O O H +DONO H O +ACCE O +IC C O H BLNK 0.0000 0.00 0.00 0.00 0.0000 +PATC FIRS NONE LAST NONE + +PRES DISU 0.000 ! PATCH FOR DISULFIDES. Patch must be 1-CYS and 2-CYS. +GROUP +ATOM 1CB CH2E 0.19 +ATOM 1SG S -0.19 +GROUP +ATOM 2SG S -0.19 +ATOM 2CB CH2E 0.19 +BOND 1SG 2SG +ANGLE 1CB 1SG 2SG 1SG 2SG 2CB +DIHE 1CA 1CB 1SG 2SG 1CB 1SG 2SG 2CB 1SG 2SG 2CB 2CA +IC 1CA 1CB 1SG 2SG 0.0 0.0 180.0 0.0 0.0 +IC 1CB 1SG 2SG 2CB 0.0 0.0 180.0 0.0 0.0 +IC 1SG 2SG 2CB 2CA 0.0 0.0 180.0 0.0 0.0 + +PRES FHEM 0.0 ! FIX UP THE HEME BY DELETING UNWANTED ANGLES +DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND + +PRES PHEM 0.0 ! Patch for HEME. Patch residues must be 1-HIS, and 2-HEME. +BOND 1NE2 2FE +ANGL 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB +ANGL 1NE2 2FE 2NC 1NE2 2FE 2ND +DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND +DIHE 1CD2 1NE2 2FE 2NA + +PRES PLO2 0.0 ! Patch residue for Heme ligand. Residues must be +! 1-O2 , 2-HEME , and 3-HIS +! O1 of the oxygen is bonded to the iron. +BOND 1O1 2FE +!ANGL 1O1 2FE 3NE2 +ANGL 1O2 1O1 2FE 1O1 2FE 2NA 1O1 2FE 2NB +ANGL 1O1 2FE 2NC 1O1 2FE 2ND +DIHE 1O2 1O1 2FE 2NA + +PRES PLIG 0.0 ! Patch residue for Heme ligand. Residues must be, +! 1-CO , 2-HEME , and 3-HIS +BOND 1C 2FE +!ANGL 1C 2FE 3NE2 +ANGL 1O 1C 2FE 1C 2FE 2NA 1C 2FE 2NB +ANGL 1C 2FE 2NC 1C 2FE 2ND +DIHE 1O 1C 2FE 2NA + +PRES LTOD 0.0 +DELE IMPR 1CA 1N 1C 1CB +IMPR 1CA 1C 1N 1CB + +PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 +! +! +! ND1--CE1 +! / | +! -CB--CG | +! \ | +! CD2--NE2 +! \ +! HE2 +GROUP +ATOM CG C 0.10 +ATOM ND1 NR -0.40 +ATOM CE1 CR1E 0.30 +GROU +ATOM CD2 CR1E 0.10 +ATOM NE2 NH1 -0.40 +ATOM HE2 H 0.30 +DELETE ATOM HD1 +DELETE ACCE NE2 +BOND NE2 HE2 +ANGLE CE1 NE2 HE2 CD2 NE2 HE2 +IMPR NE2 CE1 CD2 HE2 +DONOR HE2 NE2 +ACCEPTOR ND1 +IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 + + +END diff --git a/charmm/toppar/toppar_all.history b/charmm/toppar/toppar_all.history new file mode 100755 index 00000000..ba1ac3dd --- /dev/null +++ b/charmm/toppar/toppar_all.history @@ -0,0 +1,872 @@ + +Recent advances in the development of empirical force field parameters +have led to frequent updates of the all-hydrogen (all22) parameter +sets supplied with charmm. Currently, the all-hydrogen parameters are +updated with the release of every version of charmm. In order to +allow the user to remain current with the evolution of the parameters +and to obtain parameters from previously released versions of charmm +the following procedure in being instituted as of January 1994, +coinciding with the release of charmm versions c23f3 and c24a1. This +system will also allow users in publicatons to specify the version of +charmm from which the parameters were obtained. Other users will then +be able to readily obtain the particular version of the parameters and +reproduce the published work if so desired. + +1) The toppar directory will contain only the parameters released with +the current version of charmm. Note that the all22 topology and +parameter filenames will not change with new versions of charmm as of +the c22g5_c23f2 release. Information on dates and parameter +development associated version numbers will be placed in the +individual file headers. Parameter development version numbers will +be maintained separately from the charmm version number to accomodate +the lack of change in a particular file between different versions of +charmm. Topology and parameter files that are coupled will have the +same version numbers. In this system the charmm parameters will be +updated only when a new version of charmm is released. The interested +user can get information on intermediate developments in the +parameters by contacting the parameter discussion forum at +www.charmm.org. + +2) A history of changes to the parameters, see below, will be included +with the toppar directory in the file toppar_all.history. This will +contain general information on changes between consecutive versions of +the parameters. The user may "diff" files of interest to obtain the +exact changes made. + +3) A toppar_history directory tree will be incorporated into the +support directory. Subdirectories will be named based on the +different versions of charmm. Some subdirectory names will contain +more than one charmm version descriptor. This will occur only when +those versions have been released simultaneously, such that the +parameters are identical. Once a toppar_history subdirectory has +been created it will never be altered. + +4) current subdirectories in toppar_history + + toppar/toppar_history/c22g2_g3_g4_c23a1_a2_f1 + => from versions c22g2, c22g3, c22g4, c23a1, c23a2 and c23f1 + toppar/toppar_history/c22g5_c23a2_f2 + => from versions c22g5 and c23f2 + toppar/toppar_history/c23f3_f4_f5_c24a1_a2_a3 + => from versions c23f3, c23f4, c23f5, c24a1, c24a2 and c24a3 + toppar/toppar_history/c24b1 + => from version c24b1 + toppar/toppar_history/c24b2_g1_g2_c25a0_a1_a2_a3 + => from versions c24b2, c24g1, c24g2, c25a0, c25a1, c25a2 and c25a3 + toppar/toppar_history/c25b1_b2_c26a1_a2 + => from versions c25b1, c25b2, c26a1 and c26a2 + toppar/toppar_history/c26b1_b2_c27a1_a2 + => from versions c26b1, c26b2, c27a1, and c27a2 + toppar/toppar_history/c28a1_to_c31a2 + => versions c28a1 through c31a2 + toppar/toppar_history/c31b1 + => version c31b1 + +5) Extended atom parameter sets for proteins and nucleic acids +(toph19.inp, param19.inp, toprna10r_22.inp and pardna10_22.inp) are +included in the toppar directory. These parameters are stable, have +been used in a wide variety of systems and are of use in both vacuum +(with r dielectric) and in condensed phase simulations. + +6) Parameter set for analysis of hydrogen bonds (par_hbond.inp) added +in July 1997 and all hbond parameters removed from the all-hydrogen +parameter files. Note that the parameters in par_hbond.inp are for +analysis only. Using them for energy, minimization and dynamics +calculations with give INCORRECT results. + +7) Parameters for ACE continuum solvatiom model included +(acepar19.inp, acepar22_prot.inp, acepar27_na.inp). These files are +to be used with the appropriate topology and parameter files and are +maintained by Michael Schaefer. + +8) Topology and parameters for the Charge Equilibration (CHEQ) +electronic polarizable model included (top_all27_prot_na.rtf, +par_all30_cheq_prot.inp). These should be considered a preliminary +polarizable force field for proteins. Additional refinement in +progress. + +9) A polarizable model based on a classical Drude oscillator is in +progress. A drude subdirectory has been created that contains the +toppar files along with example inputs. See the 00readme file for +details. Note that the Drude model is developmental and significant +additions and changes in the format are expected. However, the +parameters included in this subdirectory are published and not +anticipated to change in the near future. + +10) Parameters for silicate surfaces have been added to CHARMM. These +have been placed in the subdirectory, silicates, which contains code +and examples to generate silicate surfaces. + +11) Parmaters for ethers added to CHARMM. See top_all34_ethers.rtf and +par_all34_ethers.prm + +12) non_charmm: Contains toppar files for AMBER, Bristol-Myers Squibb +(BMS) and OPLS force fields along with a stream file for the SPC and +SPC/E water models. These files have been tested to the extent that +they may be considered reliable representations of the original force +fields, though potentially not exact representations. These files are +NOT maintained and, thus, use at your own risk. See the 00readme +files and note that AMBER requires a special version of CHARMM as +described in the 00readme file. + +13) subdirectory tamdfff: An internal coordinate force field (ICFF) +that was built based on the CHARMM 22 protein force field. +Specifically, it provides a backbone covalent geometry suitable for +torsion angle molecular dynamics (TAMD) and the necessary CMAP +cross-term corrections to suppress distortions of the potential energy +surface due to rigid covalent geometry. Additional details can be +found in tamd.doc. + +14) subdirectory rush: A simple implicit-solvent protein force-field +that adds terms to the bonded portion (bond + angle + dihe + impr + +urey) of the all-atom CHARMM22 force field to account for +volume-exclusion (_R_epulsion), the hydrophobic effect (_U_nburied +_S_urface), and intra-molecular and protein-solvent hydrogen-bonding +(_H_ydrogen-bonding) (hence _R_ _U_ _S_ _H_). Usage instructions are +in doc/rush.doc + +15) subdirectory gbsw: Optimized protein backbone parameters +(par_all22_prot_gbsw.inp) and atomic input radii (radius_gbsw.str) for +a balanced GBSW implicit solvent force field. The backbone phi/psi +cross-term (CMAP) and the atomic input radii have been re-optimized +specifically to balance the solvation and intramolecular interactions +and to capture experimental conformational equilibria of both helical +peptides and beta-hairpins. Additional information can be found in +gbsw.doc. + +questions to www.charmm.org, Parameter Discussion Forum + +Alexander D. MacKerell Jr. +School of Pharmacy +University of Maryland, Baltimore +20 Penn Street +Baltimore, MD 21201 + +Summary of c22g2 to c22g3 topology and parameter file changes + + No changes + +Summary of c22g3 to c22g4 topology and parameter file changes + + No changes + +Summary of c22g4/c23a1/c23a2/c23f1 to c22g5/c23f2 topology and +parameter file changes + +CVS information + +Revision 1.1: c22g4, c23a1, c23a2 and c23f1 (all identical) +Revision 1.2: c22g5 and c23f2 (all identical) + +Changes annotated with * will have an effect on +calculated energies and forces of the related compounds + +lipids: + + 1) addition of sulfate parameters including residues for + methylsulfate and dodecylsulfate + +* 2) update of ethylacetate and methylpropionate dihedrals + +* 3) update of choline dihedrals + + 4) format correction to acetic acid improper + + 5) significant figures on TIP3P HT and OT Rmin changed + to be compatible with the protein and nucleic acid + parameters + + 6) chloride anion mass corrected from 34.00 to 35.45 + (kinetic energies will be affected). + +nucleic acids: + + 1) angle parameter for 2' ester added + + 2) significant figures on TIP3P HT and OT Rmin changed + to be compatible with the protein and nucleic acid + parameters + +* 3) correction of ribose C2' and C3' hydroxyl charges + + 4) miscellaneous multiple dihedral specifications in topology + removed + + 5) patch PLWA removed due to in being incorrect + + +proteins (also the top_all22_model*.inp file): + +* 1) update of proline parameters + + 2) methyl/ethylthiolate parameters added + +* 3) thiol hydrogen atom type corrected to HS + + 4) missing methylamine parameters added + + 5) missing parameters for lactams added + +* 6) backbone dihedrals parameters updated based on new carbonyl C VDW + parameters + +* 7) alcohol dihedrals updated + +* 8) backbone carbonyl C VDW updated + +* 9) proline nitrgen VDW 1,4 term added + + 10) patches LIG1, LIG2 and LIG3 for cyclic peptides added + + +toph19.inp: + + 1) residue CO2P, 2 point carbon monoxide added + + 2) patch HS2 to move His proton from ND1 to NE2 added + +Summary of c22g5/c23f2 to c23f3/c24a1 topology and +parameter files changes. + +lipids: no changes + +nucleic acids: + + 1) parameters added for 5-methylcytosine, including patches + PRES 5MC1 to create 5-methylcytosine base only and + PRES 5MC2 to change CYT to 5-methylcytosine in DNA/RNA + +proteins: no changes + +Summary of c23f3/c24a1 to c24b1 topology and parameter +file changes. See directory toppar_history/c23f3_f4_f5_c24a1_a2_a3 +for topology and parameter files included with the c23f3 to c23f5 +and c24a1 to c24a3 releases. + +lipids: + + 1) ordering of multiple dihedrals corrected to + comply with changes in the dihedral angle + energy routines + + 2) OSL CL CTL2 CTLX 0.00 6 180.00 ! methyl acetate + dihedrals deleted. + + 3) previously commented out dihedrals removed + +proteins: + + topology file + + 1) RESI dum: dummy atom added + + 2) patches added for phosphotyrosine and model + compounds. see topology file for details. + PRES TP1 (anionic) + PRES TP1A (model compound) + PRES TP2 (dianionic) + PRES TP2A (model compound) + + model compound topology file + + 1) RESI DUM: dummy atom added + + 2) RESI OCOH: octanol added + + parameter file + + 1) dihedrals for zwitterionic glycine and acetylated gly n-terminus + added + + 2) alcohol parameters added for extended chain compounds such + as octanol. + + 3) nonbond dummy atom parameter added + +nucleic acids: + + topology + + 1) PRES INO1: patch to convert guanine base to inosine + + 2) RESI NIC: oxidized nicotinamide + + 3) RESI NICH: reduced nicotinamide + + 4) RESI PPI1: Inorganic phosphate + + 5) RESI ADP: adenosine diphosphate + + 6) RESI ATP: adenosine triphosphate + + 7) PRES 5DP: patch to create 5' diphosphate on nucleotides + + 8) RESI NAD: oxidized nicotinamide adenine dinucleotide + + 9) RESI NADH: reduced nicotinamide adenine dinucleotide + + 10) PRES 5MC1/5MC2: atom type CN3B changed to CN3D to + avoid conflict with NAD + + 11) Correction to NBFIX for SOD and MG: ON1C atom types added + + parameter file + + 1) previously commented parameters removed + + 2) parameters added for inosine + + 3) parameters added for + A) NAD+/NADH + B) Pyrophosphate + these will allow for calculations on NAD+/NADH and triphosphates + of all the nucleotides + + 4) subset of parameters converted from CN3B atom type to + CN3D (avoid 5MC/NAD conflict) + +Summary of c24b1 to c24b2 topology and parameter file changes + +To all sets: + +vdW parameter wildcards are included but commented out. These can be +used to minimize memory requirements. Note that the ordering of the +wildcards is essential to produce the correct results. The use of +wildcards in the combined files has not been tested. + +proteins: + + 1) top_all22_model_b4c.inp renamed to top_all22_model_b5c.inp to be in + sync with the protein files (par_all22_prot_b5c.inp, + top_all22_prot_b5c.inp). + + 2) alkene parameters added + + Additions to the model topology file + > Resi ETHE 0.00 ! ethylene, yin/adm jr. + > Resi PRPE 0.00 ! propene, yin/adm jr. + > Resi BTE1 0.00 ! 1-Butene, yin/adm jr. + > Resi BTE2 0.00 ! 2-Butene, yin/adm jr. + + 3) Helium and Neon parameters added + + Additions to the model topology file + > RESI HE1 0.00 ! helium + > RESI NE1 0.00 ! neon + + 4) atom ordering in MASS list altered. + +sugars + + 1) John Brady's all-hydrogen sugar parameters added. + par_all22_sugar_1a.inp + top_all22_sugar_1a.inp + +nucleic acids + +* 1) NAD+/NADH/PPI parameters corrected. + + 2) atom ordering in MASS list altered. + +lipids + + 1) Alkene parameters added (they are identical to those added + to the proteins) + + Additions to the topology + > Resi ETHE 0.00 ! ethylene, yin/adm jr. + > Resi PRPE 0.00 ! propene, yin/adm jr. + > Resi BTE1 0.00 ! 1-Butene, yin/adm jr. + > Resi BTE2 0.00 ! 2-Butene, yin/adm jr. + + 2) Potassium parameters added + + 3) Dummy residue added + > RESI DUM 0.00 ! DUMMY ATOM + + 4) atom ordering in MASS list altered in topology file. + + +Summary of c24b2_g1_g2_c25a0_a1_a2_a3 to c25b1/c26a1 topology and +parameter file changes. July 1997 + +Changes annotated with * will have an effect on +calculated energies and forces of the related compounds. + +All the all-hydrogen topology files have been modified for use with +MMFF. This includes addition of atomic type to MASS list, +specification of DOUBLE and TRIPLE bonds where appropriate and +addition of the TP3M MMFF water model. No changes required in the +parameter files. Note that these changes allow the CHARMM +all-hydrogen topology/parameter files to be used with the MMFF +facilities. Note that the CHARMM all-hydrogen parameters are NOT +designed to be compatible with the MMFF parameters. Use CHARMM with +MMFF parameters at your own risk. + +The hbond parameters in all-hydrogen parameter files have been removed +simplied and a new parameter file, par_hbond.inp, added. This may be +used for hbond analysis. Note that the parameters in par_hbond.inp +are for analysis only. Using them for energy, minimization and +dynamics calculations with give INCORRECT results. + +Cutnb has been increased to 14.0 A in the all-hydrogen parameter files +to produce 2 A buffer region (ctonb is 12.0 A) optimal for heuristic +list updating. + +proteins (also the top_all22_model.inp file): + + 1) dihedral parameters for neutral glycine and glycine dipeptide added + +nucleic acids: + + 1) PRES 3MET, 3'terminal Methyl patch added + + 2) PRES NOBA, patch to delete all base atoms added. + + 3) RESI NDPH, residue for reduced NADPH added. No NADP+ yet available. + +lipids: + + 1) additional parameters for double bonds added. + + 2) 2-hexene added. + + *3) Additional NBFIXes associated with sodium (SOD), potassium (K) and + magnesium (MG) added to make them consistent with nucleic acids (for + Mg) and Benoit Roux's thesis (for SOD and K). Changes also made in + the combined protein_lipid files. Energetics involving these ions + will be effected by these additions. + +Summary of c25b1/c26a1 to c26b1 topology and parameter file changes. +September 1998 + +Changes in the all topology and parameter files involved only bugfixes +and minor additions or corrections, as outlined below. + +Changes annotated with * will have an effect on +calculated energies and forces of the related compounds. + +1) Appropriate references added to initial portions of all files. + +2) Detailed description of the form and variables of each of the +energy terms added in all files. + +proteins: + + no changes + +nucleic acids: + + 1) minor corrections to NAD etc. IC tables + + 2) RESI NADP, residue for oxidized NADP+ added. + +lipids: + + *1) Correction to alkene parameters. Includes additional refinement to + improve agreement with a.i. for -C=C- surface. See alkene reference. + + 2) Commented parameters associated with ions removed. + +par_hbond.inp + + 1) Hbond parameters corrected to cover all (hopefully) possibilities. + +toph19.inp + + 1) Version number changed to 22 to maintain compatibility + +Addition of new lipid and nucleic acid topology and parameter (all27) +files to c27a1. These parameters will only be included in the +developmental version of Charmm27 to allow for testing. + +CHARMM27 force field + +nucleic acids: + + 1) The all27 nucleic acid parameters represent a complete overhall +of the Charmm22 nucleic acid parameters. This was performed to +correct problems with the equilibrium between the A and B forms of DNA +as well as take advantage of an extensive amount of new experimental +and ab initio data on nucleic acid model compounds. Manuscript +preparation is in progress with submission expected by the end of +1998. + + 2) Alternate nucleic acid bases (5-methylcytosine, inosine) and +other compounds (ATP, NAD etc.) are effected by the changes such that +published data on these compounds cannot be exactly reproduced using +the all27 parameter set. Tests and parameter reoptimization by adm +jr. have been performed in order to insure consistency with published +works. + +lipids: + + 1) New alkane LJ and dihedral parameters. The LJ parameters have +been optimized to more accurately reproduce experimental condensed +phase properties (Yin and MacKerell) and the dihedral parameters have +been optimized to lower the butane CCCC gauche energy to 0.63 +kcal/mole. + + 2) New phosphate charges and dihedral parameters to better reproduce +interactions of DMP with water and DMP conformational energetics. + +proteins: + + 1) No all27 protein parameter set is available as of Sept. 98. +Based on the changes in the nucleic acid and lipid files it is +expected that the protein all22 parameters will be compatible with the +all27 nucleic acid and lipid parameters, however, no explicit tests +have been performed to date. The statement that compatibility can be +expected is based on the maintainence of the all22 parameter +optimization philosophy during the optimization of the all 27 +parameters. Please contact adm jr. for more details. + + +Summary of c26b2/c27a2 to c27b1/c28a1 topology and parameter file changes. +August 1999 + +proteins: + + 1) change alkene atom types HA1 and HE2 to HE1 and HE2 + + 2) reording of selected residues to optimize BYCC list generation HSD, +HSE, HSP, TYR, PHE, TRP, PRO, Pres PROP + + 3) atom types CT1n, CT2n, CT3n added to top_all22_model to facilitate +addition of new aliphatic carbon parameters (not supported in the +parameter set as of 8/99) + + 4) neutral glycine added to top_all22_model + +lipids: + + 1) RESI POPC and RESI POPE added + + 2) Modular DPPC based on RESI PALM, PCGL and PRES EST1, EST2 added + + 3) Atom type OCL (carboxylate) and associated parameters added from +protein set as required for RESI PALM + + 4) improper atoms reordered + + 5) buta and mp_1 atoms reordered and resi CL renamed to CLA +to be consistent with protein and nucleic acid topologies + + 6) Calcium and Cesium parameters removed to avoid overlap +with nucleic acid and proteins sets + + 7) Potassium atom type and residue name changed from K to POT + +nucleic acids: + + 1) reording of selected residues to optimize BYCC list generation +GUA, ADE, CYT + + 2) improper atoms reordered and certain associated parameters altered +as required to maintain energies and forces. + +Summary of c27b? to c31a2 topology and parameter file changes. +July 2004 + +Reorganization of topology and parameter files was undertaken. This +was performed to minimize the size of the parent topology and +parameter files (e.g. top_all22_prot.inp and par_all22_prot.inp) by +including only biomolecular subunits (e.g. the amino acids), the +relevant patches, water and ions. The remaining molecules have been +moved to toppar stream files in the toppar/stream directory. + +A significant change/correction was the removal of all ANGLe and +DIHEdral specifications in the topology files for the patches, except +in cases where special terms are required (eg. heme related patches). +For all of these special cases it is necessary to call AUTOgenerate +ANGLes DIHEdrals following implementation of all patches. + +See doc/rtop.doc and parmfile.doc for details. + +proteins: + + all27 model, including model compounds + + 1) Model compounds to toppar_all22_prot_model.str + + 2) Heme and related residues/patches to toppar_all22_prot_heme.str + + 3) CO2 parameters added (toppar_all22_prot_heme.str) + +* 4) Heme vinyl converted to new alkene parameters + + 5) Pyridines added (toppar_all22_prot_pyridines.str) + + 6) Aldehydes added (toppar_all22_prot_aldehydes.str) + + 7) Fluoroalkanes added (toppar_all22_prot_fluoro_alkanes.str) + + 8) Extension to include C27 alkane parameters (not tested) +(toppar_all22_prot_aliphatic_c27.str) + +* 9) Addition of cross-term dihedral grid correction map (CMAP) to +all27 protein model for treatment of phi, psi backbone of +alanine-based (all residues except glycine and proline), glycine and +proline residues. This required addition of patches ACED and ACPD for +creation of dipeptides in combination with CT3. + + ACE continuum model solvation parameters added: (acepar19.inp, +acepar22_prot.inp, acepar27_na.inp) + + Charge Equilibration Model (CHEQ) preliminary protein force field +parameters added (top_all30_cheq_prot.inp, par_all30_cheq_prot.inp) + +lipids: + + 1) Model compounds to toppar_all27_lipid_model.str + + 2) polyunsaturated parameters added (RESIs DIPE, DIHE, OLEO (to +create DOPC), DHA, STEA) + +* 3) alkene parameters corrected + + 4) hexane rtf repaired + + 5) cholesterol toppar information added to +toppar_all27_lipid_cholesterol.str (RESI CHL1, CHNS, CHM1) + +* 6) correction of ester parameters based on methyl butyrate QM data +(RESI MBUT, feller/adm jr.) + + 7) Tetraethyl ammonium added (RESI TEA, roux) + + 8) POPC ICs corrected + + 9) Glycerol head group model compunds added (RESI GLYC, GLYP) + +nucleic acids: + + 1) Model compounds to toppar_all27_na_model.str + + 2) PPI2 added (dianonic pyrophosphate) + + 3) 5MET ICs added + + 4) NAD, ATP, PPI and related compounds to +toppar_all27_na_nad_ppi.str and correction to ADP made. + + 5) Base modifications to toppar_all27_na_base_modifications.str + + 6) Backbone modifications to toppar_all27_na_bkb_modifications.str + + 7) Carbocyclic (bicyclo, constrained) sugars added +(toppar_all27_na_carbocyclic.str) + +other: + + 1) Optimized neutral amines added (toppar_amines.str) + + 2) Miscellaneous patches that require both nucleic acid and protein +topology and parameter information (toppar_prot_na_all.str). + Phosphorylated tyrosine, serine, and threonine + S-adenosy-homocysteine (SAH) + + 3) Standalone stream file for water and ions (toppar_water_ions.str) + + 4) Stream file for dummy atom, helium and neon +(toppar_dum_nobel_gases.str) + + 5) Hydrogen bond analysis parameters moved to toppar_hbond.str + +External force fields supported by CHARMM: see directory toppar/non_charmm + + 1) Bristol-Myers Squibb (BMS) nucleic acid force field +(top_bms_dec03.rtf, par_bms_dec03.prm) + + 2) AMBER force fields (note that AMBER keyword needed in pref.dat) + i) Cornell et all force fields (top_amber_cornell.inp, + par_amber_cornell.inp) + ii) 1998 update of Cornell et al., DNA force field + (top_amber_cornell.inp, par_amber_98.inp) + + 3) OPLS-AA force field (use "NONBond GEOMetric" command to invoke +proper combining rules for OPLS, top_opls_aa.inp, par_opls_aa.inp, +par_opls_ligand.inp) + + +Summary of changes in version c32 + +Polarizable force field: see directory toppar/drude + + 1) Model based on classical Drude oscillator added. Model under +developement; see 00readme for details. + +External force fields supported by charmm: see directory toppar/non_charmm + + 1) toppar_water_misc.str contains SPC and SPC/E water models + +Silicate surfaces (Quartz, Kaolinite): toppar/silicates + + 1) Force field for silicate surfaces added. Additive model +developed to be consistent with the CHARMM22 and 27 force fields. +Code for generation of extended surfaces included. + +Lipids: + +* 1) Missing improper added to EST1 and EST2 patches + +Proteins: + + 1) Retinol and related compound parameters added in +stream/toppar_all22_prot_retinol.str. additional atoms types added to +parent protein topology and parameter files to accomidate new +compounds. + +* 2) Correction to toppar_amines.str internal terms + +Nucleic acids: + + 1) Peptide nucleic acid parameters from L. Nilsson and coworkers +added to toppar_all27_na_bkb_modifications.str + + 2) Corrections to ACCE O1P2 bugs. + +Summary of changes in version c33 + +* 1) CMAP term for protonated histidine (RESI HSP) was omitted from +the topology files containing proteins. This was corrected in the +c33b1 release. + + 2) Special parameters for gbsw model added. See gbsw subdirectory +and parmfile.doc for details. + +Summary of changes in version c34 + + 1) Ether parameters added. See top_all34_ethers.rtf and +par_all34_ethers.prm + + 2) Drude command revised and toppar format updated and additional +residues/parameters added. See drude.tar.gz + + 3) rush parameters for protein folding added. See rush subdirectory +and parmfile.doc for details. + + 4) tamdfff parameters added for internal coordinate dynamics. See +tamdfff subdirectory and parmfile.doc for details. + +Summary of changes in version C35 + + 1) New carbohydrate force field parameters added. This includes an +extensive set of monosaccharides, acyclic analogs and glycosyl +linkages. The parameters are designed to be compatible with the +CHARMM22 and 27 additive force fields. + + 2) Lipids: Minor corrections to several residues used for generation +of lipids. Myristic acid added to allow for creation of DMPC. New +model compounds added to toppar_all27_lipid_model.str. + + 3) Proteins: Neutral N- and C-terminal patches added: NNEU and CNEU. + + 4) Proteins: Topology and parameter files WITHOUT CMAP no longer the +default and not included in the toppar directory. Note that the +original CHARMM22 model may be reproduced by including the SKIPE CMAP +command in the charmm input script. + + 5) Lipids: New generation lipid topology and parameter files, +top_all32_lipid.rtf and par_all32_lipid.prm added. These include +update of the lipid order parameters that yield improvements in the +lipid order parameters. + + 6) Ethers: Modification of selected ether dihedral performed to yield +top_all35_ethers.rtf and par_all35_ethers.prm + +Summary of changes in version C36 + + 1) Lipids: New generation lipid topology and parameter files, +top_all36_lipid.rtf and par_all36_lipid.prm added. These include +additional optimization of the dihedral parameters and adjustments of +the nonbond parameters for the ester moieties in the esterified +glycerol linker region. Note that as of January 2010, the lipids that +contain inositol are NOT based on the all36* carbohydrates parameters +and have not been validated. + + 2) Carbohydrates: Ongoing extensions of the carbohydrate parameters +to include furanoses, non-hydroxyl substituents and so on. This is +the *all36* set. + + 3) CHARMM General FF (CGenFF): Initial release of CGenFF. + + 4) Revised additive protein FF completed; top_all36_prot.rtf and +par_all36_prot.prm. Initial release to developers with inclusion +in CHARMM distribution version in C37 + + 5) Revised additive nucleic acid FF completed; top_all36_na.rtf and +par_all36_na.prm. Initial release to developers with inclusion +in CHARMM distribution version in C37. + + 6) Toppar files formats changed to allow individual toppar files +to be combined without creation of explicit combined files. Changes +are described in 00toppar_file_format.txt + +Summary of changes in version C37 + + 1) Full "C36" release of additive force field including most recent + protein, nucleic acid, lipid, carbohydrate and CGenFF parameters. + + 2) Revised additive protein FF completed; top_all36_prot.rtf and +par_all36_prot.prm included in distribution version. + + 3) Revised additive nucleic FF completed; top_all36_na.rtf and +par_all36_na.prm included in distribution version. + + 4) Modification to C36 lipids + i) PUFA based alkene parameters modified (will change energies) + ii) New cholesterol parameters (toppar_all36_lipid_cholesterol.str, will change energies) + iii) Additional bacterial lipids added (toppar_all36_lipid_bacterial.str) + +Summary of changes in version C38 + + 1) Parameter bugfixes, including conversion of nonbond truncation default to + fshift, vfswitch in select toppar file + + 2) Stream file for reactive RNA added (toppar_all36_na_reactive_rna.str) + + 3) Stream file for neutral arginine added (toppar_all36_prot_arg0.str) + + 4) polarizable SWM6 water parameters and test cases added to the drude directory + + 5) Update of Drude documentation + + 6) Sodium NBFIX parameters added to toppar_water_ions.str (Sep. 2013) + + 7) Ceramide/sphingomyelin stream file (Sep. 2013) + + 8) Cholesterol atom reordering for Domdec (Dec. 2013) + + 9) Update of carbohydrate patches and 1,6 glycosidic linkage parameters (Dec. 2013) + + 10) Correction of CTD1 LJ parameters and Proline D CMAP in toppar_all36_prot_d_aminoacids.str + +Summary of changes in version C39/40 + + 1) Minor bug fixes + + 2) CHARMM36 FFs in Gromacs format ( http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs ) + + 3) Addition of various water models in non_charmm subdirectory + + 4) stream files moved to subdirectories ( toppar/stream/*/*.str ) + + 5) Addition of a collection of lipids, glycolipids and lipid-modified amino acids in the stream/lipid subdirectory + + 6) Addition of glycoprotein linkages in stream/prot subdirectory + + 7) Release of polarizable classical Drude-2013 oscililator model for proteins, DNA, + DPPC lipids and carbohydrates (polyols and hexapyranoses). + + 8) Patches for ionized cysteine and serine added to protein parent files + + 9) Addition of posttranslation patches in stream/prot subdirectory in toppar_all36_prot_modify_res.str + + 10) Extensive set of ions (coverage of periodic table) in misc/toppar_ions_won.str + + 11) New AAM version of the OPLS protein FF in non_charmm directory: top_opls_aam.inp and par_opls_aam.inp + + 12) Amber parm14sb_all.rtf and .prm added to non_charmm directory: includes proteins and nucleic acids + + diff --git a/charmm/toppar/toppar_water_ions.str b/charmm/toppar/toppar_water_ions.str new file mode 100644 index 00000000..762c8f73 --- /dev/null +++ b/charmm/toppar/toppar_water_ions.str @@ -0,0 +1,330 @@ +* Toplogy and parameter information for water and ions. +* + +!Testcase +!test_water_ions.inp + +! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, +! which will only apply if the main files containing carboxylate atom types +! have been read in first! + +!references +! +!TIP3P water model +! +!W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; +!M.L. Klein; "Comparison of simple potential functions for +!simulating liquid water", J. Chem. Phys. 79 926-935 (1983). +! +!IONS +! +!Ions from Roux and coworkers +! +!Beglov, D. and Roux, B., Finite Representation of an Infinite +!Bulk System: Solvent Boundary Potential for Computer Simulations, +!Journal of Chemical Physics, 1994, 100: 9050-9063 +! +!ZINC +! +!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and +!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: +!Structure, Function, and Genetics 23:12-31 (1995) + +!test "append" to determine if previous toppar files have been read and +!add append to "read rtf card" if true +set nat ?NATC +set app +!We're exploiting what is arguably a bug in the parser. On the left hand side, +!the quotes have priority, so NAT is correctly substituted. On the right hand +!side, the ? has priority and NATC" (sic) is not a valid substitution... +if "@NAT" ne "?NATC" if @nat ne 0 set app append + +read rtf card @app +* Topology for water and ions +* +31 1 + +MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 H ! hydroxide hydrogen +MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 O ! hydroxide oxygen +MASS 5 LIT 6.94100 LI ! Lithium ion +MASS 6 SOD 22.98977 NA ! Sodium Ion +MASS 7 MG 24.30500 MG ! Magnesium Ion +MASS 8 POT 39.09830 K ! Potassium Ion +MASS 9 CAL 40.08000 CA ! Calcium Ion +MASS 10 RUB 85.46780 RB ! Rubidium Ion +MASS 11 CES 132.90545 CS ! Cesium Ion +MASS 12 BAR 137.32700 BA ! Barium Ion +MASS 13 ZN 65.37000 ZN ! zinc (II) cation +MASS 14 CAD 112.41100 CD ! cadmium (II) cation +MASS 15 CLA 35.45000 CL ! Chloride Ion + +default first none last none + +RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral +GROUP +ATOM OH2 OT -0.834 +ATOM H1 HT 0.417 +ATOM H2 HT 0.417 +BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake +ANGLE H1 OH2 H2 ! required +DONOR H1 OH2 +DONOR H2 OH2 +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p +GROUP +ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup +ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup +ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup +BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p +ANGLE H1 OH2 H2 ! required +DONOR H1 OH2 +DONOR H2 OH2 +ACCEPTOR OH2 +PATCHING FIRS NONE LAST NONE + +RESI OH -1.00 ! hydroxide ion by adm.jr. +GROUP +ATOM O1 OX -1.32 +ATOM H1 HX 0.32 +BOND O1 H1 +DONOR H1 O1 +ACCEPTOR O1 + +! Ion parameters from Benoit Roux and Coworkers +! As of 8/10 new NBFIX terms required +! +RESI LIT 1.00 ! Lithium Ion +GROUP +ATOM LIT LIT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.00 ! Sodium Ion +GROUP +ATOM SOD SOD 1.00 +PATCHING FIRST NONE LAST NONE + +RESI MG 2.00 ! Magnesium Ion +GROUP +ATOM MG MG 2.00 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.00 ! Potassium Ion +GROUP +ATOM POT POT 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CAL 2.00 ! Calcium Ion +GROUP +ATOM CAL CAL 2.00 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.00 ! Rubidium Ion +GROUP +ATOM RUB RUB 1.00 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.00 ! Cesium Ion +GROUP +ATOM CES CES 1.00 +PATCHING FIRST NONE LAST NONE + +RESI BAR 2.00 ! Barium Ion +GROUP +ATOM BAR BAR 2.00 +PATCHING FIRST NONE LAST NONE + +RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote +GROUP +ATOM ZN ZN 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CD2 2.00 ! Cadmium (II) cation +GROUP +ATOM CD CAD 2.00 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.00 ! Chloride Ion +GROUP +ATOM CLA CLA -1.00 +PATCHING FIRST NONE LAST NONE + +END + +read para card flex @app +* Parameters for water and ions +* + +ATOMS +MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS 2 HX 1.00800 ! hydroxide hydrogen +MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS 4 OX 15.99940 ! hydroxide oxygen +MASS 5 LIT 6.94100 ! Lithium ion +MASS 6 SOD 22.98977 ! Sodium Ion +MASS 7 MG 24.30500 ! Magnesium Ion +MASS 8 POT 39.09830 ! Potassium Ion +MASS 9 CAL 40.08000 ! Calcium Ion +MASS 10 RUB 85.46780 ! Rubidium Ion +MASS 11 CES 132.90545 ! Cesium Ion +MASS 12 BAR 137.32700 ! Barium Ion +MASS 13 ZN 65.37000 ! zinc (II) cation +MASS 14 CAD 112.41100 ! cadmium (II) cation +MASS 15 CLA 35.45000 ! Chloride Ion + +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) +HT OT 450.0 0.9572 ! from TIPS3P geometry +OX HX 545.0 0.9700 ! hydroxide ion + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + + +! +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + +!TIP3P LJ parameters +HT 0.0 -0.046 0.2245 +OT 0.0 -0.1521 1.7682 + +!for hydroxide +OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 + +!ions +LIT 0.0 -0.00233 1.2975 ! Lithium + ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) +SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium + ! ddG of -18.6 kcal/mol with K+ from S. Noskov +MG 0.0 -0.0150 1.18500 ! Magnesium + ! B. Roux dA = -441.65 +POT 0.0 -0.0870 1.76375 ! Potassium + ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol +CAL 0.0 -0.120 1.367 ! Calcium + ! S. Marchand and B. Roux, dA = -384.8 kcal/mol +RUB 0.0000 -0.15 1.90 ! Rubidium + ! delta A with respect to POT is +6.0 kcal/mol in bulk water +CES 0.0 -0.1900 2.100 ! Cesium + ! delta A with respect to POT is +12.0 kcal/mol +BAR 0.0 -0.150 1.890 ! Barium + ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol +ZN 0.000000 -0.250000 1.090000 ! Zinc + ! RHS March 18, 1990 +CAD 0.000000 -0.120000 1.357000 ! Cadmium + ! S. Marchand and B. Roux, from delta delta G +CLA 0.0 -0.150 2.27 ! Chloride + ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol + +NBFIX +! Emin Rmin +! (kcal/mol) (A) +SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 +END + +! The following section contains NBFixes for sodium interacting with +! carboxylate oxygens of various CHARMM force fields. It will generate +! level -1 warnings whenever any of these force fields have not been +! read prior to the current stream file. Since we don't want to force +! the user to always read all the force fields, we're suppressing the +! warnings. The only side effect is that you will have "most severe +! warning was at level 0" at the end of your output. Also note that +! the user is responsible for reading the current file last if they +! want the NBFixes to apply. A more elegant solution would require new +! features to be added to CHARMM. +! parallel fix, to avoid duplicated messages in the log +set para +if ?NUMNODE gt 1 set para node 0 + +set wrn ?WRNLEV +! Some versions of CHARMM don't seem to initialize wrnlev... +if "@WRN" eq "?WRNLEV" set wrn 5 +set bom ?bomlev +WRNLEV -1 @PARA +BOMLEV -1 @PARA +read para card flex append +* NBFix between carboxylate and sodium +* + +! These NBFixes will only apply if the main files have been read in first!!! +NBFIX + +!new SOD NBFIX values +! Simulations of Anionic Lipid Membranes: Development of Interaction-Specific +! Ion Parameters and Validation using NMR Data. +! Venable, R.M.; Luo, Y,; Gawrisch, K.; Roux, B.; Pastor, R.W. +! J. Phys. Chem. B 2013, 117 (35), pp 10183–10192. DOI: 10.1021/jp401512z +! +! prot +SOD OC -0.07502 3.23 ! osmotic P; carboxylate =O +SOD OS -0.07502 3.13 ! POPC optim.; ester =O +!! NA +!SOD ON3 -0.07502 3.16 ! POPC optim.; phosphate =O UNVALIDATED +!! lipid +SOD OCL -0.07502 3.23 ! osmotic P; carboxylate =O +SOD OBL -0.07502 3.13 ! POPC optim.; ester =O +SOD O2L -0.07502 3.16 ! POPC optim.; phosphate =O +!! carb +SOD OC2D2 -0.07502 3.23 ! osmotic P; carboxylate =O +SOD OC2DP -0.07502 3.16 ! POPC optim.; phosphate =O +!! CGenFF +SOD OG2D2 -0.07502 3.23 ! osmotic P; carboxylate =O +! OG2D1 in CGenFF shared between esters, amides, aldehydes,... +!SOD OG2D1 -0.07502 3.13 ! POPC optim.; ester =O +SOD OG2P1 -0.07502 3.16 ! POPC optim.; phosphate =O + +END +BOMLEV @bom @PARA +WRNLEV @wrn @PARA + +return + From 113d824fb4bd6ebd3fabb4ac85d5afa08a912fbc Mon Sep 17 00:00:00 2001 From: ChayaSt Date: Thu, 2 Mar 2017 12:13:38 -0500 Subject: [PATCH 2/2] converted some lipids --- charmm/charmm36_lipid.yaml | 49 + charmm/ffxml/charmm36_lipid.xml | 25208 ++++++++++++++++++++++++++++++ 2 files changed, 25257 insertions(+) create mode 100644 charmm/charmm36_lipid.yaml create mode 100644 charmm/ffxml/charmm36_lipid.xml diff --git a/charmm/charmm36_lipid.yaml b/charmm/charmm36_lipid.yaml new file mode 100644 index 00000000..851be6de --- /dev/null +++ b/charmm/charmm36_lipid.yaml @@ -0,0 +1,49 @@ +# for CharMM36 --> OpenMM ffxml conversion +# Author: Chaya D. Stern, choderalab +# The include files structure is based on the file structure of unzipped toppar_c36_aug15.tgz +# excluded files include files that need to be excluded from the conversion because of duplicate parameters with different +# values. 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